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	A	T	G	C	Cg	cG	tCw	wGa	tCa	tGa	tCt	aGa	tC	Ga	tCh	dGa	cC	Gg	wrC	Gyw	Cc	gG	wA	Tw	tC_mutation	tC_mutation_to_G	tC_mutation_to_T	APOBEC_mutation	APOBEC_mutation_to_G	APOBEC_mutation_to_T	"CONTEXT(+/-20)"	a_counts	t_counts	g_counts	c_counts	cg_counts	tcw_counts	wga_counts	tca_counts	tga_counts	tct_counts	aga_counts	tc_counts	ga_counts	tch_counts	dga_counts	cc_counts	gg_counts	wrc_counts	gyw_counts	cc_counts	gg_counts	wa_counts	tw_counts	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_CancerGermlineMut	i_CGC_CancerMolecularGenetics	i_CGC_CancerSomaticMut	i_CGC_CancerSyndrome	i_CGC_Chr	i_CGC_ChrBand	i_CGC_GeneID	i_CGC_Name	i_CGC_OtherGermlineMut	i_CGC_TissueType	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_AccessionNumbers	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_EnzymeIDs	i_HGNC_Genefamilydescription	i_HGNC_HGNCID	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_NameSynonyms	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_PrimaryIDs	i_HGNC_PubmedIDs	i_HGNC_RecordType	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_SecondaryIDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGAIDs	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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos1coor	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	newbase	end	tum_allele1	tum_allele2	start	effect_idx	newbase_idx	pat_idx	is_coding	is_flank	is_indel	is_ins	is_del	is_missense	is_nonsense	is_splice	is_silent	gene_idx	context_and_effect	context65	categ_idx	trackpos	categ	gene	chr	pos	type	classification	ref_allele	patient	DistBetween_Mutations	Distance_to_LT_end	Distance_to_RT_end	Strain_Mutation_ID	Dataset_Mutation_ID	Complex_ID	Complex_Size	StrainCluster_ID	Dataset_Cluster_ID	Distance_Between_Clusters	Cluster_Size_Mutations	Cluster_Size_Complexes	Cluster_Length	Cluster_Coordination	Content_of_non_coordinated_cluster	Cluster_Pvalue
WDR64	128025	hgsc.bcm.edu	37	chr1	241875146	241875146	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaagaggagccaacactttTtgctactgtgttaaggcaaa	13	10	9	9	0	0	1	0	0	0	1	0	2	0	2	2	2	4	3	2	2	5	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr1:241875146T>C	ENST00000366552.2	+	8	1194	c.987T>C	c.(985-987)ttT>ttC	p.F329F	WDR64_ENST00000437684.2_Silent_p.F329F	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	329										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			CCAACACTTTTTGCTACTGTG	0.393																																					p.F329F		.											.	WDR64-91	0			c.T987C						.						119	111	114					1																	241875146		2203	4300	6503	SO:0001819	synonymous_variant	128025	exon8			CACTTTTTGCTAC	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"WD repeat domain containing"	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.987T>C	1.37:g.241875146T>C		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_144625	0	0	0	0	0	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	37																																																																																				.		0.393	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		C	241875146	T	C	241875146	2	2	1	1	0	0	0	0	0	0	0	1	17348	1838	64	3		3	WDR64	1	241875146	Silent	SNP	T	TCGA-A4-7286-01A-11D-2136-08		241875146	7375475	1	1											
NCOA1	8648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	24991159	24991159	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaggcggggacccttacCtgaaccagcctggtccactg	7	8	13	13	1	0	1	0	1	0	0	1	2	1	2	5	5	3	1	5	5	3	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:24991159C>T	ENST00000406961.1	+	23	4877	c.4225C>T	c.(4225-4227)Ctg>Ttg	p.L1409L	NCOA1_ENST00000395856.3_Silent_p.L1408L|NCOA1_ENST00000407230.1_3'UTR|NCOA1_ENST00000405141.1_3'UTR|NCOA1_ENST00000348332.3_Silent_p.L1409L|NCOA1_ENST00000288599.5_3'UTR|NCOA1_ENST00000538539.1_3'UTR			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1409					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGACCCTTACCTGAACCAGCC	0.532			T	PAX3	alveolar rhadomyosarcoma																																p.L1409L		.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1-228	0			c.C4225T						.						89	90	90					2																	24991159		2203	4300	6503	SO:0001819	synonymous_variant	8648	exon21			CCTTACCTGAACC	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.4225C>T	2.37:g.24991159C>T		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	141	27	NM_003743	0	0	2	2	0	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	37	CCDS1712.1																																																																																			.		0.532	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		T	24991159	C	T	24991159	2	4	1	1	0	0	0	0	0	0	0	1	10254	680	24	2		2	NCOA1	2	24991159	Silent	SNP	C	TCGA-A4-7286-01A-11D-2136-08		24991159	218208214	2	2											
CCDC75	253635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37319335	37319336	+	Missense_Mutation	DNP	AA	AA	CT																															cttaaaaataagcaagatgaAatgaagctagaaggagatct																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:37319335_37319336AA>CT	ENST00000608836.1	+	6	610_611	c.465_466AA>CT	c.(463-468)gaAAtg>gaCTtg	p.155_156EM>DL	GPATCH11_ENST00000409774.1_Missense_Mutation_p.181_182EM>DL|GPATCH11_ENST00000281932.5_Missense_Mutation_p.52_53EM>DL	NM_174931.2	NP_777591.3	Q8N954	GPT11_HUMAN	G patch domain containing 11	155							nucleic acid binding (GO:0003676)										AGCAAGATGAAATGAAGCTAGA	0.361																																					p.EM155DL		.											.	.	0			c.A466T						.																																			SO:0001583	missense	253635	exon6			GATGAAATGAAGC	AK095667	CCDS1785.2, CCDS62891.1, CCDS1785.3	2p22.2	2013-11-05	2013-01-28	2013-01-28	ENSG00000152133	ENSG00000152133		"G patch domain containing"	26768	protein-coding gene	gene with protein product	"centromere protein Y"		"coiled-coil domain containing 75"	CCDC75			Standard	NM_001278505		Approved	FLJ38348, CENPY, CENP-Y	uc010ezz.3	Q8N954	OTTHUMG00000128469	Exception_encountered	2.37:g.37319335_37319336delinsCT	ENSP00000476383:p.E155_M156delinsDL	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	28	9		0	0	0	0	0	A8K0D9|B7Z2G4|B8ZZ44	Missense_Mutation	DNP	ENST00000608836.1	37	CCDS1785.2																																																																																			.		0.361	GPATCH11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_174931		CT	37319336	AA	CT	37319335	3	2	1	1	0	0	0	0	1	0	0	0	2855	11	1	5	483	5	CCDC75	2	37319335	Missense_Mutation	DNP	AA	TCGA-A4-7286-01A-11D-2136-08	12328176	37319335	205880038	3	3											
RTKN	6242	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74657398	74657398	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagagcacattgctctgaaAggagatgtctgtgagggtcc	11	9	13	8	0	2	4	0	2	2	2	3	5	3	4	1	2	2	2	1	2	2	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:74657398A>G	ENST00000233330.6	-	5	693	c.376T>C	c.(376-378)Ttt>Ctt	p.F126L	RTKN_ENST00000305557.5_Missense_Mutation_p.F163L|RTKN_ENST00000484453.1_5'Flank|RTKN_ENST00000272430.5_Missense_Mutation_p.F176L	NM_001015056.1	NP_001015056.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						TTGCTCTGAAAGGAGATGTCT	0.562																																					p.F176L		.											.	RTKN-91	0			c.T526C						.						101	89	93					2																	74657398		2203	4300	6503	SO:0001583	missense	6242	exon5			TCTGAAAGGAGAT	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.376T>C	2.37:g.74657398A>G	ENSP00000233330:p.Phe126Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	44	8	NM_001015055	0	0	14	20	6		Missense_Mutation	SNP	ENST00000233330.6	37	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.037389	0.93630	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.53857	0.6;0.6;0.6	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	M	0.81112	2.525	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.74494	-0.3647	10	0.48119	T	0.1	.	12.7658	0.57391	1.0:0.0:0.0:0.0	.	176;163	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	L	163;176;126	ENSP00000305298:F163L;ENSP00000272430:F176L;ENSP00000233330:F126L	ENSP00000233330:F126L	F	-	1	0	RTKN	74510906	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.671000	0.91174	2.111000	0.64477	0.460000	0.39030	TTT	.		0.562	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		G	74657398	A	G	74657398	3	3	1	1	0	0	0	0	1	0	0	0	13754	72	3	3	1197	3	RTKN	2	74657398	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	37338063	74657398	168541975	4	4											
SPOPL	339745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	139308572	139308572	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaaagtgaagttcgagcAaaattcaaattttcccttct	14	12	5	10	1	2	1	1	1	1	0	4	2	3	1	2	0	1	2	2	0	6	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:139308572A>G	ENST00000280098.4	+	4	679	c.300A>G	c.(298-300)gcA>gcG	p.A100A		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	100	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(2)|cervix(2)|endometrium(2)|large_intestine(2)|lung(11)|skin(2)	21				BRCA - Breast invasive adenocarcinoma(221;0.0296)		AAGTTCGAGCAAAATTCAAAT	0.368																																					p.A100A		.											.	SPOPL-92	0			c.A300G						.						69	73	72					2																	139308572		2203	4299	6502	SO:0001819	synonymous_variant	339745	exon4			TCGAGCAAAATTC		CCDS33298.1	2q22.1	2013-01-09			ENSG00000144228	ENSG00000144228		"BTB/POZ domain containing"	27934	protein-coding gene	gene with protein product	"HIB homolog 2", "roadkill homolog 2"						Standard	NM_001001664		Approved	BTBD33	uc002tvh.3	Q6IQ16	OTTHUMG00000153635	ENST00000280098.4:c.300A>G	2.37:g.139308572A>G		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	119	32	NM_001001664	0	0	1	1	0		Silent	SNP	ENST00000280098.4	37	CCDS33298.1																																																																																			.		0.368	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1			G	139308572	A	G	139308572	2	3	1	1	0	0	0	0	0	0	0	1	15117	117	5	3		3	SPOPL	2	139308572	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08	64651174	139308572	103890801	5	5											
KYNU	8942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	143718222	143718222	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	accttaagaatagaggatatCcttgaagtaattgagaagga	17	10	10	4	0	0	4	0	2	0	3	1	7	1	6	2	2	0	1	2	2	7	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:143718222C>G	ENST00000264170.4	+	8	870	c.612C>G	c.(610-612)atC>atG	p.I204M	KYNU_ENST00000375773.2_Missense_Mutation_p.I204M|KYNU_ENST00000409512.1_Missense_Mutation_p.I204M	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		TAGAGGATATCCTTGAAGTAA	0.368																																					p.I204M		.											.	KYNU-92	0			c.C612G						.						105	106	106					2																	143718222		2203	4300	6503	SO:0001583	missense	8942	exon9			GGATATCCTTGAA	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.612C>G	2.37:g.143718222C>G	ENSP00000264170:p.Ile204Met	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	93	15	NM_001199241	0	0	3	3	0		Missense_Mutation	SNP	ENST00000264170.4	37	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.960574	0.53400	.	.	ENSG00000115919	ENST00000264170;ENST00000375773;ENST00000409512	T;T;T	0.58797	0.31;0.31;0.31	5.35	-0.683	0.11335	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	T	0.76176	0.3951	M	0.93898	3.47	0.80722	D	1	D;D	0.76494	0.975;0.999	D;D	0.85130	0.927;0.997	T	0.72567	-0.4254	10	0.72032	D	0.01	.	6.1677	0.20400	0.123:0.4133:0.0:0.4637	.	204;204	Q16719;Q9BVW3	KYNU_HUMAN;.	M	204	ENSP00000264170:I204M;ENSP00000364928:I204M;ENSP00000386731:I204M	ENSP00000264170:I204M	I	+	3	3	KYNU	143434692	0.998000	0.40836	0.989000	0.46669	0.991000	0.79684	0.528000	0.23002	-0.374000	0.07967	-0.147000	0.13772	ATC	.		0.368	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998		G	143718222	C	G	143718222	3	3	1	1	0	0	0	0	1	0	0	0	8608	845	30	4	638	4	KYNU	2	143718222	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	4409650	143718222	99481151	6	6											
LY75	4065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160665004	160665004	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccaaactctcatggtaatgTtattattttccctcatcagt	10	16	5	10	0	3	0	3	0	1	0	5	0	4	0	2	1	1	2	2	1	4	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:160665004T>C	ENST00000263636.4	-	33	4805	c.4778A>G	c.(4777-4779)aAc>aGc	p.N1593S	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.N1593S|LY75_ENST00000553424.1_Missense_Mutation_p.N1593S|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.N1593S|LY75_ENST00000554112.1_Missense_Mutation_p.N1593S	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1593	C-type lectin 10. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		CATGGTAATGTTATTATTTTC	0.338																																					p.N1593S		.											.	LY75-90	0			c.A4778G						.						224	217	219					2																	160665004		2202	4299	6501	SO:0001583	missense	4065	exon33			GTAATGTTATTAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"CD molecules", "C-type lectin domain containing"	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4778A>G	2.37:g.160665004T>C	ENSP00000263636:p.Asn1593Ser	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	82	21	NM_002349	0	0	2	4	2	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	10.94	1.491766	0.26774	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.06849	3.25;3.25;3.25;3.25;3.25	5.55	5.55	0.83447	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.242632	0.21380	U	0.075495	T	0.09818	0.0241	L	0.33710	1.025	0.26761	N	0.969999	B;P;D	0.53619	0.082;0.912;0.961	B;P;P	0.52066	0.087;0.574;0.689	T	0.09422	-1.0675	10	0.08381	T	0.77	-17.923	9.2003	0.37254	0.2708:0.0:0.0:0.7292	.	1593;1593;1593	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	S	1593	ENSP00000451511:N1593S;ENSP00000451446:N1593S;ENSP00000263636:N1593S;ENSP00000423463:N1593S;ENSP00000421035:N1593S	ENSP00000423463:N1593S	N	-	2	0	LY75;LY75-CD302	160373250	0.999000	0.42202	0.998000	0.56505	0.984000	0.73092	2.859000	0.48364	2.105000	0.64084	0.402000	0.26972	AAC	.		0.338	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160665004	T	C	160665004	3	2	1	1	0	0	0	0	1	0	0	0	9124	1725	60	3	402	3	LY75	2	160665004	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	16946782	160665004	82534369	7	7											
ABCA12	26154	broad.mit.edu;bcgsc.ca	37	chr2	215821466	215821466	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatttgaaaatcgcaatgaTaccaattgaaaacgctacag	18	10	6	7	2	0	3	0	3	0	0	1	3	0	3	1	0	3	2	1	0	9	5	rs368283339		TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:215821466T>C	ENST00000272895.7	-	42	6373	c.6154A>G	c.(6154-6156)Atc>Gtc	p.I2052V	AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.I1734V	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2052					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ATCGCAATGATACCAATTGAA	0.348																																					p.I2052V	Ovarian(66;664 1488 5121 34295)												.	ABCA12-99	0			c.A6154G						.	T	VAL/ILE,VAL/ILE	0,4406		0,0,2203	108	107	107		5200,6154	3.9	1	2		107	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ABCA12	NM_015657.3,NM_173076.2	29,29	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign,benign	1734/2278,2052/2596	215821466	1,13005	2203	4300	6503	SO:0001583	missense	26154	exon42			CAATGATACCAAT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6154A>G	2.37:g.215821466T>C	ENSP00000272895:p.Ile2052Val	Somatic	116	1		WXS	Illumina HiSeq	Phase_I	125	5	NM_173076	0	0	3	3	0	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	0.080	-1.185337	0.01620	0.0	1.16E-4	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.88201	-2.35;-2.35	5.69	3.88	0.44766	.	0.106321	0.41500	N	0.000861	T	0.70824	0.3268	N	0.04148	-0.265	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.60772	-0.7197	10	0.06625	T	0.88	.	8.1764	0.31285	0.0:0.6864:0.0:0.3136	.	2052;1734	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	V	2052;1734	ENSP00000272895:I2052V;ENSP00000374312:I1734V	ENSP00000272895:I2052V	I	-	1	0	ABCA12	215529711	0.996000	0.38824	1.000000	0.80357	0.872000	0.50106	1.295000	0.33377	0.743000	0.32719	-0.242000	0.12053	ATC	.		0.348	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215821466	T	C	215821466	3	2	1	1	0	0	0	0	1	0	0	0	30	1406	49	3	1681	3	ABCA12	2	215821466	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	55156462	215821466	27377907	8	8											
DLEC1	9940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	38159473	38159473	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaggaggagacagcctcAgcggacaagcagctggtgct	10	6	16	9	1	1	2	1	1	0	1	1	5	1	4	1	4	5	3	1	4	1	0	rs201702862		TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr3:38159473A>G	ENST00000308059.6	+	33	4683	c.4662A>G	c.(4660-4662)tcA>tcG	p.S1554S	DLEC1_ENST00000346219.3_Silent_p.S1554S|DLEC1_ENST00000452631.2_Silent_p.S1557S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		AGACAGCCTCAGCGGACAAGC	0.612											OREG0015476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1	0.000199681	0	0	5008	,	,		20227	0.001		0	False		,,,				2504	0				p.S1554S		.											.	DLEC1-161	0			c.A4662G						.						38	47	44					3																	38159473		2188	4287	6475	SO:0001819	synonymous_variant	9940	exon33			AGCCTCAGCGGAC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.4662A>G	3.37:g.38159473A>G		Somatic	32	0	876	WXS	Illumina HiSeq	Phase_I	23	5	NM_007337	0	0	0	0	0		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			A|0.999;G|0.000		0.612	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		G	38159473	A	G	38159473	2	3	1	1	0	0	0	0	0	0	0	1	4563	175	7	3		3	DLEC1	3	38159473	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08		38159473	159862957	9	9											
RGS12	6002	hgsc.bcm.edu;broad.mit.edu	37	chr4	3441324	3441324	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcaggccagtggtgggccTcctacatcagacctccctgg	6	8	12	15	1	1	1	1	0	0	1	4	1	3	1	5	4	1	1	5	4	1	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr4:3441324T>C	ENST00000344733.5	+	18	5161	c.4257T>C	c.(4255-4257)ccT>ccC	p.P1419P	RGS12_ENST00000338806.4_Silent_p.P771P|HGFAC_ENST00000382774.3_5'Flank|HGFAC_ENST00000511533.1_5'Flank	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	1419					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTGGTGGGCCTCCTACATCAG	0.677																																					p.P1419P		.											.	RGS12-226	0			c.T4257C						.						29	28	28					4																	3441324		2201	4296	6497	SO:0001819	synonymous_variant	6002	exon18			TGGGCCTCCTACA	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"Regulators of G-protein signaling"	9994	protein-coding gene	gene with protein product		602512	"regulator of G-protein signalling 12"			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.4257T>C	4.37:g.3441324T>C		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	39	8	NM_198229	0	0	3	3	0	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Silent	SNP	ENST00000344733.5	37	CCDS3366.1																																																																																			.		0.677	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		C	3441324	T	C	3441324	2	2	1	1	0	0	0	0	0	0	0	1	13327	1538	54	3		3	RGS12	4	3441324	Silent	SNP	T	TCGA-A4-7286-01A-11D-2136-08		3441324	187712952	10	10											
CCNG2	901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	78082688	78082688	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgaaagcttgcaactgcCgactcatcttttcaaaagca	13	10	7	11	1	3	1	2	1	1	0	3	2	3	1	1	0	6	4	1	0	4	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr4:78082688C>T	ENST00000316355.5	+	5	939	c.583C>T	c.(583-585)Cga>Tga	p.R195*	CCNG2_ENST00000354403.5_Nonsense_Mutation_p.R195*|CCNG2_ENST00000502280.1_Nonsense_Mutation_p.R195*|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000395640.1_Nonsense_Mutation_p.R195*|CCNG2_ENST00000509972.1_Nonsense_Mutation_p.R195*	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	195					cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						TTGCAACTGCCGACTCATCTT	0.294																																					p.R195X		.											.	CCNG2-416	0			c.C583T						.						52	59	57					4																	78082688		2202	4300	6502	SO:0001587	stop_gained	901	exon5			AACTGCCGACTCA	BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.583C>T	4.37:g.78082688C>T	ENSP00000315743:p.Arg195*	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	57	9	NM_004354	0	0	10	10	0	B4DF25|Q6FGA7|Q6FGC6	Nonsense_Mutation	SNP	ENST00000316355.5	37	CCDS3581.1	.	.	.	.	.	.	.	.	.	.	C	38	6.688916	0.97764	.	.	ENSG00000138764	ENST00000316355;ENST00000354403;ENST00000502280;ENST00000395640;ENST00000509972	.	.	.	5.52	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.4327	15.8563	0.78979	0.1366:0.8634:0.0:0.0	.	.	.	.	X	195	.	ENSP00000315743:R195X	R	+	1	2	CCNG2	78301712	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.923000	0.48868	1.331000	0.45412	-0.152000	0.13540	CGA	.		0.294	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252404.3	NM_004354		T	78082688	C	T	78082688	4	4	1	1	0	0	0	0	0	1	0	0	2930	644	23	1	597	1	CCNG2	4	78082688	Nonsense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	74641364	78082688	113071588	11	11											
SYNPO2	171024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	119952706	119952706	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacctcctcctgtggcctatAatcctatccactcgccgtct	6	12	5	18	2	1	0	0	0	1	0	6	0	5	0	7	1	0	0	7	1	3	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr4:119952706A>T	ENST00000429713.2	+	4	2958	c.2776A>T	c.(2776-2778)Aat>Tat	p.N926Y	SYNPO2_ENST00000434046.2_Missense_Mutation_p.N926Y|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.N926Y	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	926						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TGTGGCCTATAATCCTATCCA	0.572																																					p.N926Y		.											.	SYNPO2-92	0			c.A2776T						.						87	82	84					4																	119952706		2203	4300	6503	SO:0001583	missense	171024	exon4			GCCTATAATCCTA	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2776A>T	4.37:g.119952706A>T	ENSP00000395143:p.Asn926Tyr	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	108	30	NM_001128934	0	0	0	0	0	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.3|20.3	3.960913|3.960913	0.74016|0.74016	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.15017|.	2.46;2.58;2.46|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.77239|.	0.4101|.	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.997|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.997;0.991|.	T|.	0.78874|.	-0.2032|.	9|.	.|.	.|.	.|.	-24.3416|-24.3416	15.8861|15.8861	0.79251|0.79251	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	926;926;926;926|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	Y|L	926|877	ENSP00000306015:N926Y;ENSP00000395143:N926Y;ENSP00000390965:N926Y|.	.|.	N|X	+|+	1|2	0|2	SYNPO2|SYNPO2	120172154|120172154	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	9.339000|9.339000	0.96797|0.96797	2.156000|2.156000	0.67533|0.67533	0.533000|0.533000	0.62120|0.62120	AAT|TAA	.		0.572	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			T	119952706	A	T	119952706	3	4	1	1	0	0	0	0	1	0	0	0	15489	362	13	5	2790	5	SYNPO2	4	119952706	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	41870018	119952706	71201570	12	12											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811126	140811126	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgttgCtgttgctgtttctgctgcat	1	18	12	10	0	1	0	0	0	1	0	1	0	1	0	0	0	9	12	0	0	0	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr4:140811126C>T	ENST00000509479.2	-	2	2320	c.1464G>A	c.(1462-1464)caG>caA	p.Q488Q	MAML3_ENST00000327122.5_Silent_p.Q332Q|MAML3_ENST00000398940.1_Silent_p.Q27Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgttgctgttgctgtt	0.547																																					p.Q488Q		.											.	MAML3-455	0			c.G1464A						.						17	20	19					4																	140811126		2194	4294	6488	SO:0001819	synonymous_variant	55534	exon2			CTGTTGCTGTTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1464G>A	4.37:g.140811126C>T		Somatic	34	1		WXS	Illumina HiSeq	Phase_I	28	2	NM_018717	0	0	0	0	0		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.		0.547	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811126	C	T	140811126	2	4	1	1	0	0	0	0	0	0	0	1	9232	796	28	2		2	MAML3	4	140811126	Silent	SNP	C	TCGA-A4-7286-01A-11D-2136-08	20858420	140811126	50343150	13	13											
FTMT	94033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	121188229	121188229	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaggtgacccccatttgtgcGatttcctggaaacctactac	10	11	8	12	1	0	1	0	1	0	0	1	3	1	2	4	2	4	0	4	2	4	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr5:121188229G>A	ENST00000321339.1	+	1	580	c.571G>A	c.(571-573)Gat>Aat	p.D191N		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	191	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CCATTTGTGCGATTTCCTGGA	0.507																																					p.D191N		.											.	FTMT-91	0			c.G571A						.						133	130	131					5																	121188229		2203	4300	6503	SO:0001583	missense	94033	exon1			TTGTGCGATTTCC	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.571G>A	5.37:g.121188229G>A	ENSP00000313691:p.Asp191Asn	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	217	55	NM_177478	0	0	0	0	0		Missense_Mutation	SNP	ENST00000321339.1	37	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316794	0.81469	.	.	ENSG00000181867	ENST00000321339	T	0.70516	-0.49	3.39	3.39	0.38822	Ferritin/ribonucleotide reductase-like (1);Ferritin, conserved site (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.000000	0.85682	D	0.000000	T	0.78253	0.4254	M	0.67700	2.07	0.58432	D	0.999999	P	0.52577	0.954	P	0.57548	0.823	T	0.81355	-0.0970	10	0.72032	D	0.01	.	13.0805	0.59112	0.0:0.0:1.0:0.0	.	191	Q8N4E7	FTMT_HUMAN	N	191	ENSP00000313691:D191N	ENSP00000313691:D191N	D	+	1	0	FTMT	121216128	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.967000	0.93402	2.185000	0.69588	0.609000	0.83330	GAT	.		0.507	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121188229	G	A	121188229	3	1	1	1	0	0	0	0	1	0	0	0	6104	1058	37	1	573	1	FTMT	5	121188229	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		121188229	59727031	14	14											
TRIM52	84851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	180687083	180687083	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctcggcacaccacacagatGgcctctttgtccacctcaca	9	9	6	17	1	3	1	1	0	2	1	5	1	4	1	4	2	0	1	4	2	0	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr5:180687083G>T	ENST00000327767.4	-	1	1036	c.732C>A	c.(730-732)gcC>gcA	p.A244A	TRIM52_ENST00000514805.1_5'UTR|CTC-338M12.4_ENST00000511331.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA|CTC-338M12.4_ENST00000506340.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|TRIM52-AS1_ENST00000507434.1_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	244					positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CCACACAGATGGCCTCTTTGT	0.537																																					p.A244A		.											.	TRIM52-90	0			c.C732A						.						135	129	131					5																	180687083		2203	4300	6503	SO:0001819	synonymous_variant	84851	exon1			ACAGATGGCCTCT		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19024	protein-coding gene	gene with protein product			"tripartite motif-containing 52"				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.732C>A	5.37:g.180687083G>T		Somatic	257	0		WXS	Illumina HiSeq	Phase_I	155	39	NM_032765	0	0	1	2	1		Silent	SNP	ENST00000327767.4	37	CCDS4467.1																																																																																			.		0.537	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765		T	180687083	G	T	180687083	2	4	1	1	0	0	0	0	0	0	0	1	16560	1335	47	4		4	TRIM52	5	180687083	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	59498854	180687083	228177	15	15											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725794	15725794	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgctgctgctgatggtgGtgatggtggtggtggtggtg	2	14	21	4	0	0	2	0	2	0	0	0	2	0	2	0	7	4	4	0	7	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:15725794G>C	ENST00000262041.5	-	1	643	c.234C>G	c.(232-234)caC>caG	p.H78Q	AC005550.4_ENST00000442176.1_lincRNA|AC005550.5_ENST00000438923.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	78	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		gctgatggtggtgatggtggt	0.622																																					p.H78Q	Esophageal Squamous(140;197 1769 16409 18257 29929)	.											.	MEOX2-515	0			c.C234G						.						21	22	22					7																	15725794		2203	4300	6503	SO:0001583	missense	4223	exon1			ATGGTGGTGATGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.234C>G	7.37:g.15725794G>C	ENSP00000262041:p.His78Gln	Somatic	16	2		WXS	Illumina HiSeq	Phase_I	13	3	NM_005924	0	0	0	0	0	B2R8I7|O75263|Q9UPL6	Missense_Mutation	SNP	ENST00000262041.5	37	CCDS34605.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.261308	0.23051	.	.	ENSG00000106511	ENST00000262041	D	0.90133	-2.62	5.33	-0.657	0.11432	.	0.000000	0.64402	D	0.000002	T	0.81856	0.4911	L	0.44542	1.39	0.38139	D	0.938398	B	0.09022	0.002	B	0.04013	0.001	T	0.68911	-0.5284	10	0.02654	T	1	-15.7329	11.015	0.47682	0.5519:0.0:0.4481:0.0	.	78	P50222	MEOX2_HUMAN	Q	78	ENSP00000262041:H78Q	ENSP00000262041:H78Q	H	-	3	2	MEOX2	15692319	0.956000	0.32656	0.998000	0.56505	0.962000	0.63368	0.018000	0.13422	-0.067000	0.12976	0.655000	0.94253	CAC	.		0.622	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		C	15725794	G	C	15725794	3	2	1	1	0	0	0	0	1	0	0	0	9499	1252	44	4	692	4	MEOX2	7	15725794	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		15725794	143412869	16	16			1	1		2	2	16	G		2.713427e-05
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725809	15725809	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggtggtgatggtggtggtgGtggtggtggtggtggtgccc	1	13	24	3	0	0	1	0	1	0	0	0	1	0	1	1	11	1	0	1	11	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:15725809G>A	ENST00000262041.5	-	1	628	c.219C>T	c.(217-219)caC>caT	p.H73H	AC005550.4_ENST00000442176.1_lincRNA|AC005550.5_ENST00000438923.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	73	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtggtggtggtggtggt	0.597																																					p.H73H	Esophageal Squamous(140;197 1769 16409 18257 29929)	.											.	MEOX2-515	0			c.C219T						.						22	23	23					7																	15725809		2203	4299	6502	SO:0001819	synonymous_variant	4223	exon1			GTGGTGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.219C>T	7.37:g.15725809G>A		Somatic	16	2		WXS	Illumina HiSeq	Phase_I	17	8	NM_005924	0	0	0	0	0	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	37	CCDS34605.1																																																																																			.		0.597	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725809	G	A	15725809	2	1	1	1	0	0	0	0	0	0	0	1	9499	1252	44	2		2	MEOX2	7	15725809	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	15	15725809	143412854	17	17			1	1		2	2	16	G		2.713427e-05
FKBP9	11328	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	33014881	33014881	+	Frame_Shift_Del	DEL	C	C	-																															agaccaggttcagattcacaCctatttcaagcccccgagtt																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:33014881delC	ENST00000242209.4	+	3	624	c.455delC	c.(454-456)accfs	p.T152fs	FKBP9_ENST00000538443.1_Frame_Shift_Del_p.T14fs|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Frame_Shift_Del_p.T205fs	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	152					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			CAGATTCACACCTATTTCAAG	0.468																																					p.T152fs		.											.	FKBP9-651	0			c.455delC						.						114	103	107					7																	33014881		2203	4300	6503	SO:0001589	frameshift_variant	11328	exon3			.	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"EF-hand domain containing"	3725	protein-coding gene	gene with protein product			"FK506-binding protein 9 (63 kD)"			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.455delC	7.37:g.33014881delC	ENSP00000242209:p.Thr152fs	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	95	17	NM_007270	0	0	0	0	0	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Frame_Shift_Del	DEL	ENST00000242209.4	37	CCDS5439.1																																																																																			.		0.468	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		-	33014881	C	-	33014881	7	5	1	1	0	1	0	1	0	0	0	0	5934	507	18	0	465	0	FKBP9	7	33014881	Frame_Shift_Del	DEL	C	TCGA-A4-7286-01A-11D-2136-08	17289072	33014881	126123782	18	18											
DDX56	54606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44607797	44607797	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgccgcagcagctggaggTccctagggttgtcttcaaag	8	9	13	11	1	2	0	1	0	1	0	3	1	3	1	2	3	3	4	2	3	2	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:44607797T>G	ENST00000258772.5	-	12	1515	c.1409A>C	c.(1408-1410)gAc>gCc	p.D470A	DDX56_ENST00000431640.1_Missense_Mutation_p.D430A|DDX56_ENST00000485367.1_5'UTR	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	470					ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						CAGCTGGAGGTCCCTAGGGTT	0.567																																					p.D470A		.											.	DDX56-227	0			c.A1409C						.						80	76	77					7																	44607797		2203	4300	6503	SO:0001583	missense	54606	exon12			TGGAGGTCCCTAG	AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"DEAD-boxes"	18193	protein-coding gene	gene with protein product	"nucleolar helicase of 61 kDa"	608023	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.1409A>C	7.37:g.44607797T>G	ENSP00000258772:p.Asp470Ala	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	53	9	NM_019082	0	0	19	32	13	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	37	CCDS5492.1	.	.	.	.	.	.	.	.	.	.	.	27.7	4.856346	0.91355	.	.	ENSG00000136271	ENST00000258772;ENST00000431640;ENST00000448192	T;T	0.07908	3.19;3.15	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.34658	0.0905	M	0.88570	2.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.26608	-1.0098	10	0.62326	D	0.03	-35.5767	13.7285	0.62771	0.0:0.0:0.0:1.0	.	430;470	C9JV95;Q9NY93	.;DDX56_HUMAN	A	470;430;75	ENSP00000258772:D470A;ENSP00000393488:D430A	ENSP00000258772:D470A	D	-	2	0	DDX56	44574322	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	6.924000	0.75823	2.137000	0.66172	0.533000	0.62120	GAC	.		0.567	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082		G	44607797	T	G	44607797	3	3	1	1	0	0	0	0	1	0	0	0	4380	1667	58	5	246	5	DDX56	7	44607797	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	11592916	44607797	114530866	19	19											
RELN	5649	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	103234873	103234873	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagtcctcccctgagaacacGggctgccaccagcggaacct	9	6	10	16	2	0	1	0	1	0	1	2	3	2	2	6	2	4	1	6	2	3	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:103234873G>C	ENST00000428762.1	-	26	3765	c.3606C>G	c.(3604-3606)ccC>ccG	p.P1202P	RELN_ENST00000343529.5_Silent_p.P1202P|RELN_ENST00000424685.2_Silent_p.P1202P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1202					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CTGAGAACACGGGCTGCCACC	0.488																																					p.P1202P	NSCLC(146;835 1944 15585 22231 52158)	.											.	RELN-574	0			c.C3606G						.						182	181	181					7																	103234873		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon26			GAACACGGGCTGC		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.3606C>G	7.37:g.103234873G>C		Somatic	334	0		WXS	Illumina HiSeq	Phase_I	341	22	NM_173054	0	0	1	1	0	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			.		0.488	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103234873	G	C	103234873	2	2	1	1	0	0	0	0	0	0	0	1	13252	1103	39	4		4	RELN	7	103234873	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	58627076	103234873	55903790	20	20											
CFTR	1080	hgsc.bcm.edu	37	chr7	117174330	117174330	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttccatttttcttttagActttaaagctgtcaagccgt	9	18	5	9	1	2	1	1	0	1	1	3	1	3	1	2	0	2	1	2	0	4	7	rs200885306		TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:117174330A>G	ENST00000003084.6	+	5	622	c.490A>G	c.(490-492)Act>Gct	p.T164A	CFTR_ENST00000454343.1_Splice_Site_p.T164A	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	164	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TTTCTTTTAGACTTTAAAGCT	0.264									Cystic Fibrosis																												p.T164A		.											.	CFTR-518	0			c.A490G						.	A	ALA/THR	0,4404		0,0,2202	53	51	52		490	5.5	1	7		52	2,8594	2.2+/-6.3	0,2,4296	yes	missense-near-splice	CFTR	NM_000492.3	58	0,2,6498	GG,GA,AA		0.0233,0.0,0.0154	benign	164/1481	117174330	2,12998	2202	4298	6500	SO:0001630	splice_region_variant	1080	exon5	Familial Cancer Database	CF	TTTTAGACTTTAA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.490-1A>G	7.37:g.117174330A>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_000492	0	0	0	0	0	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.462862	0.26248	0.0	2.33E-4	ENSG00000001626	ENST00000003084;ENST00000454343	D;D	0.91237	-2.81;-2.81	5.5	5.5	0.81552	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.044119	0.85682	D	0.000000	D	0.84768	0.5545	N	0.11724	0.165	0.58432	D	0.999999	B	0.18968	0.032	B	0.35859	0.212	T	0.79509	-0.1774	9	.	.	.	-21.6143	15.9153	0.79512	1.0:0.0:0.0:0.0	.	164	P13569	CFTR_HUMAN	A	164	ENSP00000003084:T164A;ENSP00000403677:T164A	.	T	+	1	0	CFTR	116961566	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.628000	0.90979	2.213000	0.71641	0.477000	0.44152	ACT	.		0.264	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	Missense_Mutation	G	117174330	A	G	117174330	5	3	1	1	0	0	0	0	0	0	1	0	3300	289	10	3	508	3	CFTR	7	117174330	Splice_Site	SNP	A	TCGA-A4-7286-01A-11D-2136-08	13939457	117174330	41964333	21	21											
C7orf58	79974	hgsc.bcm.edu	37	chr7	120655879	120655879	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaaggctcaatgctggccTagggccggggctactagaac	11	6	14	10	1	1	2	1	0	0	2	1	2	1	2	2	5	3	3	2	5	6	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:120655879T>C	ENST00000310396.5	+	3	877	c.410T>C	c.(409-411)cTa>cCa	p.L137P	CPED1_ENST00000450913.2_Missense_Mutation_p.L137P|CPED1_ENST00000495036.1_3'UTR|CPED1_ENST00000340646.5_Missense_Mutation_p.L137P	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	137						endoplasmic reticulum (GO:0005783)											AATGCTGGCCTAGGGCCGGGG	0.448																																					p.L137P		.											.	.	0			c.T410C						.						60	48	52					7																	120655879		2203	4300	6503	SO:0001583	missense	79974	exon2			CTGGCCTAGGGCC		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.410T>C	7.37:g.120655879T>C	ENSP00000309772:p.Leu137Pro	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_001105533	0	0	0	0	0	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	T	3.706	-0.060530	0.07317	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000340646	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.84	-3.37	0.04898	.	1.302160	0.04994	N	0.467807	T	0.26340	0.0643	N	0.20401	0.57	0.19775	N	0.999959	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.003	T	0.25152	-1.0140	10	0.48119	T	0.1	.	6.7639	0.23556	0.0:0.3864:0.1286:0.485	.	137;137	A4D0V7-2;A4D0V7	.;CG058_HUMAN	P	137	ENSP00000309772:L137P;ENSP00000398082:L137P;ENSP00000406122:L137P;ENSP00000345235:L137P	ENSP00000309772:L137P	L	+	2	0	C7orf58	120443115	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.173000	0.09854	-0.867000	0.04063	0.482000	0.46254	CTA	.		0.448	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		C	120655879	T	C	120655879	3	2	1	1	0	0	0	0	1	0	0	0	2411	1522	53	3	416	3	C7orf58	7	120655879	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	3481549	120655879	38482784	22	22											
PRSS55	203074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	10388999	10388999	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	catctgcctccccacgcagcCcggccctgccacatggcgcg	5	5	10	21	4	1	0	0	0	1	0	2	0	2	0	6	2	3	1	6	2	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr8:10388999C>G	ENST00000328655.3	+	3	582	c.542C>G	c.(541-543)cCc>cGc	p.P181R	PRSS55_ENST00000522210.1_Missense_Mutation_p.P181R|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	181	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						CCCACGCAGCCCGGCCCTGCC	0.587																																					p.P181R		.											.	PRSS55-91	0			c.C542G						.						70	64	66					8																	10388999		2203	4300	6503	SO:0001583	missense	203074	exon3			CGCAGCCCGGCCC	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.542C>G	8.37:g.10388999C>G	ENSP00000333003:p.Pro181Arg	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	102	11	NM_001197020	0	0	0	0	0	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	C	5.554	0.287080	0.10513	.	.	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.88509	-2.39;-2.39	4.79	-3.88	0.04205	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.401620	0.05168	N	0.499078	T	0.71256	0.3318	N	0.11427	0.14	0.09310	N	1	B	0.31256	0.316	B	0.28553	0.091	T	0.62210	-0.6902	10	0.16896	T	0.51	.	1.6522	0.02774	0.3222:0.3223:0.2083:0.1472	.	181	Q6UWB4	PRS55_HUMAN	R	181	ENSP00000333003:P181R;ENSP00000430459:P181R	ENSP00000333003:P181R	P	+	2	0	PRSS55	10426409	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.518000	0.06267	-0.898000	0.03906	-2.547000	0.00178	CCC	.		0.587	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		G	10388999	C	G	10388999	3	3	1	1	0	0	0	0	1	0	0	0	12663	623	22	4	552	4	PRSS55	8	10388999	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		10388999	135975023	23	23											
TRHR	7201	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr8	110131438	110131438	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacagtgccatcaacccGgtgatttacaatctcatgtc	11	11	6	13	1	3	1	3	1	1	0	5	1	3	1	2	1	4	0	2	1	4	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr8:110131438G>A	ENST00000518632.1	+	3	1302	c.951G>A	c.(949-951)ccG>ccA	p.P317P	TRHR_ENST00000311762.2_Silent_p.P317P			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	317					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			CCATCAACCCGGTGATTTACA	0.438																																					p.P317P		.											.	TRHR-620	0			c.G951A						.						214	212	213					8																	110131438		2203	4299	6502	SO:0001819	synonymous_variant	7201	exon2			CAACCCGGTGATT		CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.951G>A	8.37:g.110131438G>A		Somatic	250	2		WXS	Illumina HiSeq	Phase_I	333	67	NM_003301	0	0	0	0	0	Q2M339	Silent	SNP	ENST00000518632.1	37	CCDS6311.1																																																																																			.		0.438	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1			A	110131438	G	A	110131438	2	1	1	1	0	0	0	0	0	0	0	1	16513	1103	39	1		1	TRHR	8	110131438	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	99742439	110131438	36232584	24	24											
COL22A1	169044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	139790649	139790649	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccaggtggtccttggggccCctgcagaagagcatttacag	8	9	13	11	0	0	2	0	0	0	2	2	2	2	2	4	4	3	2	4	4	2	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr8:139790649C>T	ENST00000303045.6	-	15	2151	c.1705G>A	c.(1705-1707)Ggg>Agg	p.G569R	COL22A1_ENST00000435777.1_Splice_Site_p.G569R	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	569	Collagen-like 3.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CCTTGGGGCCCCTGCAGAAGA	0.572										HNSCC(7;0.00092)																											p.G569R		.											.	COL22A1-103	0			c.G1705A						.						41	46	44					8																	139790649		2203	4300	6503	SO:0001630	splice_region_variant	169044	exon15			GGGGCCCCTGCAG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1705-1G>A	8.37:g.139790649C>T		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	59	21	NM_152888	0	0	0	0	0	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	5.522	0.281168	0.10458	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000522546	D;D;D	0.99488	-5.77;-3.26;-6.0	4.97	3.15	0.36227	.	0.000000	0.48286	U	0.000185	D	0.99127	0.9699	H	0.96633	3.855	0.44966	D	0.997988	B	0.20052	0.041	B	0.26202	0.067	D	0.99679	1.0998	10	0.72032	D	0.01	.	6.7777	0.23628	0.0:0.7264:0.1791:0.0945	.	569	Q8NFW1	COMA1_HUMAN	R	569;569;19	ENSP00000303153:G569R;ENSP00000387655:G569R;ENSP00000428244:G19R	ENSP00000303153:G569R	G	-	1	0	COL22A1	139859831	1.000000	0.71417	0.962000	0.40283	0.102000	0.19082	3.260000	0.51523	0.791000	0.33826	-0.176000	0.13171	GGG	.		0.572	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Missense_Mutation	T	139790649	C	T	139790649	5	4	1	1	0	0	0	0	0	0	1	0	3687	637	22	2	3379	2	COL22A1	8	139790649	Splice_Site	SNP	C	TCGA-A4-7286-01A-11D-2136-08	29659211	139790649	6573373	25	25											
UHRF2	115426	hgsc.bcm.edu	37	chr9	6493920	6493920	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcagctgatcaaacattaaCaaacatgaacaggtactact	17	10	5	9	0	2	2	2	2	0	0	2	2	2	2	0	1	7	2	0	1	6	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr9:6493920C>G	ENST00000276893.5	+	10	1760	c.1592C>G	c.(1591-1593)aCa>aGa	p.T531R	UHRF2_ENST00000485617.2_3'UTR	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	531	Methyl-CpG binding and interaction with HDAC1.|YDG. {ECO:0000255|PROSITE- ProRule:PRU00358}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		CAAACATTAACAAACATGAAC	0.373																																					p.T531R		.											.	UHRF2-721	0			c.C1592G						.						71	63	66					9																	6493920		2203	4300	6503	SO:0001583	missense	115426	exon10			CATTAACAAACAT	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	12557	protein-coding gene	gene with protein product	"Np95-like ring finger protein"	615211	"ubiquitin-like with PHD and ring finger domains 2"			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.1592C>G	9.37:g.6493920C>G	ENSP00000276893:p.Thr531Arg	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_152896	0	0	0	0	0	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.683378	0.88542	.	.	ENSG00000147854	ENST00000276893	D	0.86366	-2.11	5.27	5.27	0.74061	SRA-YDG (4);	0.000000	0.85682	D	0.000000	D	0.94082	0.8103	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.993;0.997	D	0.94545	0.7748	10	0.66056	D	0.02	-10.3302	18.8971	0.92427	0.0:1.0:0.0:0.0	.	308;531	B3KV82;Q96PU4	.;UHRF2_HUMAN	R	531	ENSP00000276893:T531R	ENSP00000276893:T531R	T	+	2	0	UHRF2	6483920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.704000	0.84595	2.475000	0.83589	0.591000	0.81541	ACA	.		0.373	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		G	6493920	C	G	6493920	3	3	1	1	0	0	0	0	1	0	0	0	17003	478	17	4	1630	4	UHRF2	9	6493920	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		6493920	134719511	26	26											
ANKS6	203286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	101533259	101533259	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaatgaggcgagtggttgaAgtttccagaattggcagaag	12	10	15	4	1	0	5	0	3	0	2	1	6	1	5	1	3	0	3	1	3	4	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr9:101533259A>T	ENST00000353234.4	-	10	1938	c.1891T>A	c.(1891-1893)Ttc>Atc	p.F631I	ANKS6_ENST00000540940.1_Missense_Mutation_p.F436I|ANKS6_ENST00000375018.1_Missense_Mutation_p.F631I|ANKS6_ENST00000375019.2_Missense_Mutation_p.F330I			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	631	Ser-rich.					cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				GAGTGGTTGAAGTTTCCAGAA	0.582																																					p.F631I		.											.	ANKS6-92	0			c.T1891A						.						51	57	55					9																	101533259		1872	4107	5979	SO:0001583	missense	203286	exon10			GGTTGAAGTTTCC	AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26724	protein-coding gene	gene with protein product		615370	"sterile alpha motif domain containing 6", "ankyrin repeat domain 14"	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.1891T>A	9.37:g.101533259A>T	ENSP00000297837:p.Phe631Ile	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	56	13	NM_173551	0	0	0	1	1	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	37	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.990515|3.990515	0.74589|0.74589	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940|ENST00000444472	T;T;T;T|.	0.70045|.	1.72;-0.45;-0.45;1.97|.	5.76|5.76	4.61|4.61	0.57282|0.57282	.|.	0.212682|.	0.51477|.	D|.	0.000093|.	T|T	0.62380|0.62380	0.2423|0.2423	L|L	0.56769|0.56769	1.78|1.78	0.43617|0.43617	D|D	0.995998|0.995998	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.83275|.	0.996;0.991|.	T|T	0.59215|0.59215	-0.7496|-0.7496	10|5	0.36615|.	T|.	0.2|.	-12.8842|-12.8842	11.2813|11.2813	0.49197|0.49197	0.8468:0.1532:0.0:0.0|0.8468:0.1532:0.0:0.0	.|.	631;631|.	Q68DC2-4;Q68DC2|.	.;ANKS6_HUMAN|.	I|H	330;631;631;436|99	ENSP00000364159:F330I;ENSP00000364158:F631I;ENSP00000297837:F631I;ENSP00000442189:F436I|.	ENSP00000297837:F631I|.	F|L	-|-	1|2	0|0	ANKS6|ANKS6	100573080|100573080	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.549000|0.549000	0.35272|0.35272	5.521000|5.521000	0.67086|0.67086	0.994000|0.994000	0.38892|0.38892	-0.648000|-0.648000	0.03929|0.03929	TTC|CTT	.		0.582	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		T	101533259	A	T	101533259	3	4	1	1	0	0	0	0	1	0	0	0	692	72	3	5	748	5	ANKS6	9	101533259	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	95039339	101533259	39680172	27	27											
ALG2	85365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	101980774	101980774	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcttcctttcgtatctgttGatggagagcagcaggaattt	8	16	10	7	1	2	2	0	1	2	1	4	4	3	3	1	2	2	4	1	2	2	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr9:101980774G>A	ENST00000476832.1	-	2	754	c.693C>T	c.(691-693)atC>atT	p.I231I	ALG2_ENST00000319033.6_Silent_p.I138I	NM_033087.3	NP_149078.1	O75340	PDCD6_HUMAN	ALG2, alpha-1,3/1,6-mannosyltransferase	0					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|prostate(2)	22		Acute lymphoblastic leukemia(62;0.0559)				CGTATCTGTTGATGGAGAGCA	0.463																																					p.I231I		.											.	ALG2-92	0			c.C693T						.						124	124	124					9																	101980774		2203	4300	6503	SO:0001819	synonymous_variant	85365	exon2			TCTGTTGATGGAG	AK027417	CCDS6739.1	9q31.1	2013-02-22	2013-02-22		ENSG00000119523	ENSG00000119523	2.4.1.132, 2.4.1.257	"Glycosyltransferase group 1 domain containing"	23159	protein-coding gene	gene with protein product		607905	"asparagine-linked glycosylation 2 homolog (yeast, alpha-1,3-mannosyltransferase)", "asparagine-linked glycosylation 2, alpha-1,3-mannosyltransferase homolog (S. cerevisiae)"			12684507	Standard	NR_024532		Approved	CDGIi, FLJ14511, hALPG2, NET38	uc004azf.3	Q9H553	OTTHUMG00000020355	ENST00000476832.1:c.693C>T	9.37:g.101980774G>A		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	98	25	NM_033087	0	0	5	5	0	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Silent	SNP	ENST00000476832.1	37	CCDS6739.1																																																																																			.		0.463	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087		A	101980774	G	A	101980774	2	1	1	1	0	0	0	0	0	0	0	1	519	1280	45	2		2	ALG2	9	101980774	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	447515	101980774	39232657	28	28											
PCDH15	65217	broad.mit.edu;bcgsc.ca	37	chr10	55617003	55617003	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaacaatgacttgcatatcCagctgattgaccacggagac	14	8	9	10	1	0	4	0	3	0	1	1	6	1	4	2	1	3	2	2	1	3	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr10:55617003C>A	ENST00000320301.6	-	28	4132	c.3738G>T	c.(3736-3738)ctG>ctT	p.L1246L	PCDH15_ENST00000395433.1_Silent_p.L1224L|PCDH15_ENST00000414778.1_Silent_p.L1251L|PCDH15_ENST00000395438.1_Silent_p.L1246L|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Silent_p.L1253L|PCDH15_ENST00000395430.1_Silent_p.L1246L|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000373965.2_Silent_p.L1253L|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000437009.1_Silent_p.L1175L|PCDH15_ENST00000361849.3_Silent_p.L1246L|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Silent_p.L1209L|PCDH15_ENST00000409834.1_Silent_p.L857L|PCDH15_ENST00000373957.3_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1246	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.L1251L(2)|p.L1246L(2)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CTTGCATATCCAGCTGATTGA	0.333										HNSCC(58;0.16)																											p.L1251L													.	PCDH15-193	4	Substitution - coding silent(4)	lung(4)	c.G3753T						.						76	76	76					10																	55617003		2203	4299	6502	SO:0001819	synonymous_variant	65217	exon29			CATATCCAGCTGA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3738G>T	10.37:g.55617003C>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	128	6	NM_001142763	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.		0.333	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55617003	C	A	55617003	2	1	1	1	0	0	0	0	0	0	0	1	11537	581	21	4		4	PCDH15	10	55617003	Silent	SNP	C	TCGA-A4-7286-01A-11D-2136-08		55617003	79917744	29	29											
DOCK1	1793	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	129245700	129245700	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggcggacgtggccgatgTcccaccccctctgcctctca	4	7	13	17	3	2	0	1	0	2	0	4	2	3	1	5	4	1	0	5	4	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr10:129245700T>A	ENST00000280333.6	+	51	5502	c.5393T>A	c.(5392-5394)gTc>gAc	p.V1798D		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1798	Interaction with NCK2 second and third SH3 domain (minor).				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GTGGCCGATGTCCCACCCCCT	0.592																																					p.V1798D													.	DOCK1-698	0			c.T5393A						.						39	44	42					10																	129245700		1998	4174	6172	SO:0001583	missense	1793	exon51			CCGATGTCCCACC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5393T>A	10.37:g.129245700T>A	ENSP00000280333:p.Val1798Asp	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	20	4	NM_001380	0	0	6	9	3	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	T	14.26	2.480917	0.44044	.	.	ENSG00000150760	ENST00000280333	T	0.03982	3.74	5.22	4.09	0.47781	.	1.233990	0.05657	N	0.586186	T	0.05686	0.0149	L	0.40543	1.245	0.51233	D	0.999914	B;B	0.23058	0.079;0.079	B;B	0.25884	0.064;0.064	T	0.40117	-0.9580	10	0.12103	T	0.63	.	8.0983	0.30842	0.0:0.1519:0.0:0.8481	.	1798;1798	B2RUU3;Q14185	.;DOCK1_HUMAN	D	1798	ENSP00000280333:V1798D	ENSP00000280333:V1798D	V	+	2	0	DOCK1	129135690	0.696000	0.27757	0.918000	0.36340	0.711000	0.40976	2.404000	0.44539	2.099000	0.63709	0.533000	0.62120	GTC	.		0.592	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	129245700	T	A	129245700	3	1	1	1	0	0	0	0	1	0	0	0	4695	1667	58	5	5595	5	DOCK1	10	129245700	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	73628697	129245700	6289047	30	30											
CCKBR	887	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	6281226	6281226	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgggggcttccctgtgccGcccgggggcgcctctcctca	1	7	15	18	4	2	0	1	0	1	0	4	0	3	0	6	4	1	1	6	4	0	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr11:6281226G>C	ENST00000334619.2	+	1	261	c.68G>C	c.(67-69)cGc>cCc	p.R23P	CCKBR_ENST00000531712.1_Missense_Mutation_p.R23P|CCKBR_ENST00000525462.1_Missense_Mutation_p.R23P|CCKBR_ENST00000532715.1_Missense_Mutation_p.R23P|CCKBR_ENST00000525014.1_Missense_Mutation_p.R23P	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	23					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	TCCCTGTGCCGCCCGGGGGCG	0.716																																					p.R23P		.											.	CCKBR-574	0			c.G68C						.						9	13	12					11																	6281226		2165	4246	6411	SO:0001583	missense	887	exon1			TGTGCCGCCCGGG	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.68G>C	11.37:g.6281226G>C	ENSP00000335544:p.Arg23Pro	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	26	7	NM_176875	0	0	0	0	0	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	g	8.885	0.952549	0.18431	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525014;ENST00000525462;ENST00000531712	T;T;T;T;T	0.77098	0.34;-1.07;-0.06;0.35;0.15	2.75	2.75	0.32379	.	0.513554	0.16331	U	0.219138	T	0.78027	0.4219	L	0.47716	1.5	0.31075	N	0.712597	D;B	0.61080	0.989;0.337	P;B	0.56865	0.808;0.11	T	0.74156	-0.3756	10	0.31617	T	0.26	.	9.2026	0.37268	0.0:0.0:1.0:0.0	.	23;23	P32239-2;P32239	.;GASR_HUMAN	P	23	ENSP00000335544:R23P;ENSP00000432079:R23P;ENSP00000437001:R23P;ENSP00000435534:R23P;ENSP00000435675:R23P	ENSP00000335544:R23P	R	+	2	0	CCKBR	6237802	1.000000	0.71417	0.996000	0.52242	0.042000	0.13812	1.757000	0.38400	1.859000	0.53934	0.580000	0.79431	CGC	.		0.716	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		C	6281226	G	C	6281226	3	2	1	1	0	0	0	0	1	0	0	0	2887	1087	38	4	70	4	CCKBR	11	6281226	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		6281226	128725290	31	31											
SLC17A6	57084	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	22363111	22363112	+	Frame_Shift_Del	DEL	GA	GA	-																															aagacaccggggagacaatcGagctgacggaggatgggaag																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr11:22363111_22363112delGA	ENST00000263160.3	+	2	561_562	c.124_125delGA	c.(124-126)gagfs	p.E42fs		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	42					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						GGAGACAATCGAGCTGACGGAG	0.649																																					p.42_42del		.											.	SLC17A6-580	0			c.124_125del						.																																			SO:0001589	frameshift_variant	57084	exon2			.	AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"Solute carriers"	16703	protein-coding gene	gene with protein product	"vesicular glutamate transporter 2", "differentiation-associated Na-dependent inorganic phosphate cotransporter"	607563	"solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.124_125delGA	11.37:g.22363111_22363112delGA	ENSP00000263160:p.Glu42fs	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	112	17	NM_020346	0	0	0	0	0	A6NKS2	Frame_Shift_Del	DEL	ENST00000263160.3	37	CCDS7856.1																																																																																			.		0.649	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		-	22363112	GA	-	22363111	7	5	1	1	0	1	0	1	0	0	0	0	14453	1059	37	0	130	0	SLC17A6	11	22363111	Frame_Shift_Del	DEL	GA	TCGA-A4-7286-01A-11D-2136-08	16081885	22363111	112643405	32	32											
LRP4	4038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46920187	46920187	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcattgatgcacaggccacTgtcacacatgaactccccag	11	8	8	14	0	1	2	1	2	0	0	2	2	2	2	3	1	3	2	3	1	1	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr11:46920187T>A	ENST00000378623.1	-	7	960	c.718A>T	c.(718-720)Agt>Tgt	p.S240C		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	240	LDL-receptor class A 6. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CACAGGCCACTGTCACACATG	0.567																																					p.S240C		.											.	LRP4-94	0			c.A718T						.						160	153	156					11																	46920187		2201	4299	6500	SO:0001583	missense	4038	exon7			GGCCACTGTCACA	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.718A>T	11.37:g.46920187T>A	ENSP00000367888:p.Ser240Cys	Somatic	325	1		WXS	Illumina HiSeq	Phase_I	294	67	NM_002334	0	0	0	0	0	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	32	5.116456	0.94385	.	.	ENSG00000134569	ENST00000378623	D	0.95918	-3.85	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.98632	0.9542	H	0.97940	4.11	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.976	D	0.99694	1.1002	10	0.72032	D	0.01	.	15.3761	0.74607	0.0:0.0:0.0:1.0	.	285;240	C9JRN7;O75096	.;LRP4_HUMAN	C	240	ENSP00000367888:S240C	ENSP00000367888:S240C	S	-	1	0	LRP4	46876763	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.040000	0.89188	2.047000	0.60756	0.459000	0.35465	AGT	.		0.567	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		A	46920187	T	A	46920187	3	1	1	1	0	0	0	0	1	0	0	0	8984	1580	55	5	5127	5	LRP4	11	46920187	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	24557076	46920187	88086329	33	33											
EPS8	2059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	15784493	15784493	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgacacaggaacaggtgCtggagtggaagggggaaggg	11	6	19	5	0	0	1	0	1	0	0	0	5	0	5	0	7	2	1	0	7	3	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:15784493C>A	ENST00000281172.5	-	18	2363	c.1927G>T	c.(1927-1929)Gca>Tca	p.A643S	EPS8_ENST00000542903.1_Missense_Mutation_p.A383S|EPS8_ENST00000540613.1_Missense_Mutation_p.A383S|EPS8_ENST00000543612.1_Missense_Mutation_p.A643S|EPS8_ENST00000543523.1_Missense_Mutation_p.A643S	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	643	Pro-rich.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		GGAACAGGTGCTGGAGTGGAA	0.547																																					p.A643S		.											.	EPS8-94	0			c.G1927T						.						152	128	136					12																	15784493		2203	4300	6503	SO:0001583	missense	2059	exon18			CAGGTGCTGGAGT	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.1927G>T	12.37:g.15784493C>A	ENSP00000281172:p.Ala643Ser	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	173	28	NM_004447	0	0	21	28	7	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	37	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064340	0.55432	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000540613;ENST00000542903;ENST00000543223	T;T;T;T;T	0.08546	3.21;3.21;3.21;3.08;3.08	5.75	5.75	0.90469	.	0.131007	0.51477	D	0.000098	T	0.19846	0.0477	L	0.38531	1.155	0.44104	D	0.996874	D	0.63880	0.993	D	0.72625	0.978	T	0.02654	-1.1128	10	0.20519	T	0.43	-4.529	18.1274	0.89590	0.0:1.0:0.0:0.0	.	643	Q12929	EPS8_HUMAN	S	643;643;643;383;383;643	ENSP00000441867:A643S;ENSP00000281172:A643S;ENSP00000442388:A643S;ENSP00000441888:A383S;ENSP00000437806:A383S	ENSP00000281172:A643S	A	-	1	0	EPS8	15675760	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	2.997000	0.49457	2.714000	0.92807	0.650000	0.86243	GCA	.		0.547	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			A	15784493	C	A	15784493	3	1	1	1	0	0	0	0	1	0	0	0	5207	797	28	4	557	4	EPS8	12	15784493	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		15784493	118067402	34	34											
SFRS2IP	9169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46320210	46320210	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccaccgattttcattctGatctttataggcaaaactac	11	15	5	10	1	3	1	1	1	2	0	3	2	3	1	2	1	3	1	2	1	5	8			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:46320210G>T	ENST00000369367.3	-	11	3507	c.3274C>A	c.(3274-3276)Cag>Aag	p.Q1092K	SCAF11_ENST00000465950.1_Missense_Mutation_p.Q777K|SCAF11_ENST00000419565.2_Missense_Mutation_p.Q1092K|SCAF11_ENST00000549162.1_Missense_Mutation_p.Q900K|SCAF11_ENST00000550629.1_5'Flank	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1092					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TTTTCATTCTGATCTTTATAG	0.433																																					p.Q1092K		.											.	SCAF11-93	0			c.C3274A						.						68	73	71					12																	46320210		2203	4300	6503	SO:0001583	missense	9169	exon11			CATTCTGATCTTT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.3274C>A	12.37:g.46320210G>T	ENSP00000358374:p.Gln1092Lys	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	145	23	NM_004719	0	0	2	2	0	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546855	0.65198	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.85	5.85	0.93711	.	0.089021	0.49916	D	0.000137	T	0.64294	0.2585	M	0.62723	1.935	0.28696	N	0.904354	D;D	0.71674	0.998;0.988	D;P	0.65684	0.937;0.788	T	0.58578	-0.7612	10	0.12766	T	0.61	-12.0691	20.1563	0.98114	0.0:0.0:1.0:0.0	.	900;1092	F8VXG7;Q99590	.;SCAFB_HUMAN	K	777;1092;900;1092	ENSP00000449812:Q777K;ENSP00000358374:Q1092K;ENSP00000448864:Q900K;ENSP00000413036:Q1092K	ENSP00000358374:Q1092K	Q	-	1	0	SCAF11	44606477	1.000000	0.71417	0.980000	0.43619	0.815000	0.46073	5.535000	0.67173	2.775000	0.95449	0.655000	0.94253	CAG	.		0.433	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		T	46320210	G	T	46320210	3	4	1	1	0	0	0	0	1	0	0	0	14209	1299	45	4	1137	4	SFRS2IP	12	46320210	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08	30535717	46320210	87531685	35	35											
INHBC	3626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57828750	57828750	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggcggtcagtgtccAgcatgtggggggcccacctt	6	8	16	11	1	1	1	1	0	0	1	2	1	2	1	3	5	2	2	3	5	0	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:57828750A>C	ENST00000309668.2	+	1	208	c.81A>C	c.(79-81)ccA>ccC	p.P27P	RP11-756H6.1_ENST00000547552.1_lincRNA	NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	27					growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)			breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						GTCAGTGTCCAGCATGTGGGG	0.607																																					p.P27P		.											.	INHBC-514	0			c.A81C						.						41	41	41					12																	57828750		2203	4300	6503	SO:0001819	synonymous_variant	3626	exon1			GTGTCCAGCATGT		CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.81A>C	12.37:g.57828750A>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	97	15	NM_005538	0	0	1	1	0	A1L3Y2	Silent	SNP	ENST00000309668.2	37	CCDS8938.1																																																																																			.		0.607	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538		C	57828750	A	C	57828750	2	2	1	1	0	0	0	0	0	0	0	1	7764	175	7	5		5	INHBC	12	57828750	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08	11508540	57828750	76023145	36	36											
ALDH1L2	160428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	105428135	105428135	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgaacaaccgcccagcagcAatacagttctctcctttgtt	11	10	6	14	2	1	0	0	0	1	0	3	1	2	0	3	0	5	4	3	0	4	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:105428135A>C	ENST00000258494.9	-	19	2327	c.2187T>G	c.(2185-2187)atT>atG	p.I729M	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	729	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						GCCCAGCAGCAATACAGTTCT	0.418																																					p.I729M		.											.	ALDH1L2-91	0			c.T2187G						.						107	90	96					12																	105428135		2203	4300	6503	SO:0001583	missense	160428	exon19			AGCAGCAATACAG	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2187T>G	12.37:g.105428135A>C	ENSP00000258494:p.Ile729Met	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	91	18	NM_001034173	0	0	0	0	0	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	37	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699315	0.68501	.	.	ENSG00000136010	ENST00000258494	T	0.76839	-1.05	5.46	-0.924	0.10462	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);Aldehyde dehydrogenase, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.76442	0.3988	N	0.20574	0.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75227	-0.3392	10	0.87932	D	0	.	11.4475	0.50131	0.6024:0.0:0.3976:0.0	.	729	Q3SY69	AL1L2_HUMAN	M	729	ENSP00000258494:I729M	ENSP00000258494:I729M	I	-	3	3	ALDH1L2	103952265	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	1.140000	0.31516	-0.085000	0.12573	-0.388000	0.06559	ATT	.		0.418	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		C	105428135	A	C	105428135	3	2	1	1	0	0	0	0	1	0	0	0	495	126	5	5	604	5	ALDH1L2	12	105428135	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	47599385	105428135	28423760	37	37											
MORN3	283385	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	122107353	122107353	+	Frame_Shift_Del	DEL	G	G	-																															ccggtcccaccccttccacaGggactccgacttttttgggc																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:122107353delG	ENST00000355329.3	-	1	207	c.37delC	c.(37-39)ctgfs	p.L13fs		NM_173855.4	NP_776254.3	Q6PF18	MORN3_HUMAN	MORN repeat containing 3	13						nucleus (GO:0005634)				breast(2)|large_intestine(1)|lung(4)|skin(1)|stomach(1)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)		CCCTTCCACAGGGACTCCGAC	0.602																																					p.L13fs		.											.	MORN3-90	0			c.37delC						.						126	115	119					12																	122107353		2203	4300	6503	SO:0001589	frameshift_variant	283385	exon1			.	BC057760	CCDS31917.1	12q24.31	2006-01-17			ENSG00000139714	ENSG00000139714			29807	protein-coding gene	gene with protein product							Standard	NM_173855		Approved		uc001uax.3	Q6PF18	OTTHUMG00000169075	ENST00000355329.3:c.37delC	12.37:g.122107353delG	ENSP00000347486:p.Leu13fs	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	236	42	NM_173855	0	0	0	0	0	Q86YQ9	Frame_Shift_Del	DEL	ENST00000355329.3	37	CCDS31917.1																																																																																			.		0.602	MORN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402154.1	NM_173855		-	122107353	G	-	122107353	7	5	1	1	0	1	0	1	0	0	0	0	9734	991	35	0	705	0	MORN3	12	122107353	Frame_Shift_Del	DEL	G	TCGA-A4-7286-01A-11D-2136-08	16679218	122107353	11744542	38	38											
RNF6	6049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	26788332	26788332	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgccacccctactgtcacTgtttcgagtatgaggctggg	6	11	11	13	1	1	1	1	1	0	0	2	2	1	1	4	2	2	3	4	2	2	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr13:26788332T>A	ENST00000381588.4	-	5	2439	c.1687A>T	c.(1687-1689)Agt>Tgt	p.S563C	RNF6_ENST00000381570.3_Missense_Mutation_p.S563C|RNF6_ENST00000399762.2_Missense_Mutation_p.S207C|RNF6_ENST00000346166.3_Missense_Mutation_p.S563C|RNF6_ENST00000468480.1_Intron	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	563					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		CTACTGTCACTGTTTCGAGTA	0.483																																					p.S563C		.											.	RNF6-228	0			c.A1687T						.						152	148	149					13																	26788332		2203	4300	6503	SO:0001583	missense	6049	exon5			TGTCACTGTTTCG	AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1687A>T	13.37:g.26788332T>A	ENSP00000371000:p.Ser563Cys	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	185	50	NM_183043	0	0	5	7	2	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Missense_Mutation	SNP	ENST00000381588.4	37	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	T	5.021	0.189542	0.09547	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570;ENST00000399762	T;T;T;T	0.15834	2.97;2.97;2.97;2.39	4.87	0.818	0.18778	.	0.588235	0.19777	N	0.106316	T	0.18215	0.0437	L	0.43152	1.355	0.09310	N	1	D;P	0.56287	0.975;0.948	P;B	0.49047	0.599;0.41	T	0.08371	-1.0725	10	0.59425	D	0.04	-0.6579	8.2879	0.31939	0.0:0.069:0.3791:0.552	.	207;563	B4DDP0;Q9Y252	.;RNF6_HUMAN	C	563;563;563;207	ENSP00000342121:S563C;ENSP00000371000:S563C;ENSP00000370982:S563C;ENSP00000382665:S207C	ENSP00000342121:S563C	S	-	1	0	RNF6	25686332	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.774000	0.26675	0.069000	0.16605	0.460000	0.39030	AGT	.		0.483	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		A	26788332	T	A	26788332	3	1	1	1	0	0	0	0	1	0	0	0	13530	1580	55	5	374	5	RNF6	13	26788332	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08		26788332	88381546	39	39											
TEP1	7011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20857434	20857434	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acagcctgagagtgtcacatCattgggattcaaatctgttg	11	12	10	8	0	4	1	3	1	1	1	4	3	4	2	1	1	1	1	1	1	1	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr14:20857434C>T	ENST00000262715.5	-	17	2528	c.2488G>A	c.(2488-2490)Gat>Aat	p.D830N	TEP1_ENST00000556935.1_Missense_Mutation_p.D722N	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	830					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGTGTCACATCATTGGGATTC	0.418																																					p.D830N		.											.	TEP1-95	0			c.G2488A						.						170	144	153					14																	20857434		2203	4300	6503	SO:0001583	missense	7011	exon17			TCACATCATTGGG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.2488G>A	14.37:g.20857434C>T	ENSP00000262715:p.Asp830Asn	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	77	17	NM_007110	0	0	0	0	0	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.675408	0.47781	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.51817	0.7;0.69	5.14	5.14	0.70334	.	0.398706	0.30219	N	0.010131	T	0.55481	0.1923	L	0.41824	1.3	0.80722	D	1	D;B;D	0.57257	0.979;0.005;0.964	P;B;P	0.59703	0.862;0.01;0.732	T	0.55483	-0.8134	10	0.51188	T	0.08	-3.8703	14.0724	0.64868	0.0:1.0:0.0:0.0	.	722;180;830	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	N	830;830;722	ENSP00000262715:D830N;ENSP00000452574:D722N	ENSP00000262715:D830N	D	-	1	0	TEP1	19927274	0.981000	0.34729	0.998000	0.56505	0.734000	0.41952	0.854000	0.27791	2.392000	0.81423	0.561000	0.74099	GAT	.		0.418	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20857434	C	T	20857434	3	4	1	1	0	0	0	0	1	0	0	0	15791	826	29	2	5551	2	TEP1	14	20857434	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		20857434	86492106	40	40											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64520135	64520135	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttacatgttttaaatcagatAaaatctcaattacagcagcc	16	13	4	8	0	2	1	2	0	1	1	3	1	2	1	1	0	4	2	1	0	7	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr14:64520135A>G	ENST00000344113.4	+	48	9716	c.9504A>G	c.(9502-9504)atA>atG	p.I3168M	SYNE2_ENST00000358025.3_Missense_Mutation_p.I3168M|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.I3201M	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3168					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TAAATCAGATAAAATCTCAAT	0.318																																					p.I3168M		.											.	SYNE2-164	0			c.A9504G						.						42	42	42					14																	64520135		1807	4067	5874	SO:0001583	missense	23224	exon48			TCAGATAAAATCT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9504A>G	14.37:g.64520135A>G	ENSP00000341781:p.Ile3168Met	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_182914	0	0	1	1	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131028	0.37630	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.59906	0.61;0.61;0.23	5.39	2.83	0.33086	.	0.202730	0.35040	N	0.003495	T	0.51432	0.1674	L	0.29908	0.895	0.80722	D	1	P;D	0.54047	0.94;0.964	P;P	0.55545	0.605;0.778	T	0.47169	-0.9138	10	0.38643	T	0.18	.	4.6279	0.12488	0.5373:0.1327:0.0:0.33	.	3168;3168	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	M	3168;3168;3201;3201	ENSP00000350719:I3168M;ENSP00000341781:I3168M;ENSP00000452570:I3201M	ENSP00000261678:I3201M	I	+	3	3	SYNE2	63589888	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	0.494000	0.22467	0.850000	0.35239	0.379000	0.24179	ATA	.		0.318	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64520135	A	G	64520135	3	3	1	1	0	0	0	0	1	0	0	0	15478	352	13	3	9690	3	SYNE2	14	64520135	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	43662701	64520135	42829405	41	41											
ATP10A	57194	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	25959389	25959389	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcaaacctcaccctcacCtgcaagagaaatggtcagaa	15	6	7	13	0	4	2	4	0	0	2	4	3	4	2	3	1	3	2	3	1	4	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr15:25959389C>G	ENST00000356865.6	-	10	1888		c.e10-1			NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TCACCCTCACCTGCAAGAGAA	0.582																																					.		.											.	ATP10A-139	0			c.1777-1G>C						.						26	30	29					15																	25959389		2188	4268	6456	SO:0001630	splice_region_variant	57194	exon11			CCTCACCTGCAAG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1777-1G>C	15.37:g.25959389C>G		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	43	5	NM_024490	0	0	0	0	0	Q4G0S9|Q969I4	Splice_Site	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.018554	0.75275	.	.	ENSG00000206190	ENST00000356865	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6469	0.88151	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP10A	23510482	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	6.761000	0.74945	2.412000	0.81896	0.655000	0.94253	.	.		0.582	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	Intron	G	25959389	C	G	25959389	5	3	1	1	0	0	0	0	0	0	1	0	1117	695	24	4	2771	4	ATP10A	15	25959389	Splice_Site	SNP	C	TCGA-A4-7286-01A-11D-2136-08		25959389	76572003	42	42											
ALDH3A2	224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	19575183	19575183	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaaggtggattggggaaaaTtttttctcttgaaacggttc	11	14	11	5	1	1	1	0	1	1	0	3	3	1	3	0	5	1	1	0	5	4	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:19575183T>A	ENST00000176643.6	+	9	1803	c.1357T>A	c.(1357-1359)Ttt>Att	p.F453I	ALDH3A2_ENST00000579855.1_Missense_Mutation_p.F453I|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.F453I|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.F453I|ALDH3A2_ENST00000571163.1_Intron|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.F453I			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	453					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					TTGGGGAAAATTTTTTCTCTT	0.423																																					p.F453I		.											.	ALDH3A2-228	0			c.T1357A						.						129	143	138					17																	19575183		2203	4300	6503	SO:0001583	missense	224	exon9			GGAAAATTTTTTC	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"Aldehyde dehydrogenases"	403	protein-coding gene	gene with protein product	"fatty aldehyde dehydrogenase"	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.1357T>A	17.37:g.19575183T>A	ENSP00000176643:p.Phe453Ile	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	298	65	NM_001031806	0	0	9	14	5	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.144131	0.37825	.	.	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	T;T;T	0.80909	-1.42;-1.42;-1.43	6.07	3.72	0.42706	.	0.133335	0.64402	D	0.000001	T	0.66703	0.2816	N	0.24115	0.695	0.22656	N	0.998887	B;P	0.37061	0.444;0.58	B;B	0.39068	0.133;0.289	T	0.55237	-0.8172	10	0.22706	T	0.39	-18.8603	8.3131	0.32084	0.0:0.0691:0.1325:0.7984	.	453;453	P51648;P51648-2	AL3A2_HUMAN;.	I	453	ENSP00000176643:F453I;ENSP00000378942:F453I;ENSP00000345774:F453I	ENSP00000176643:F453I	F	+	1	0	ALDH3A2	19515775	0.922000	0.31269	0.032000	0.17829	0.671000	0.39405	1.408000	0.34668	1.093000	0.41377	0.533000	0.62120	TTT	.		0.423	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			A	19575183	T	A	19575183	3	1	1	1	0	0	0	0	1	0	0	0	498	1493	52	5	1391	5	ALDH3A2	17	19575183	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08		19575183	61620027	43	43											
PROCA1	83871	hgsc.bcm.edu;bcgsc.ca	37	chr17	27038593	27038593	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgcccctcttaccgcggCatctgctctcatcccacgag	5	8	7	21	4	3	0	1	0	3	0	5	1	4	0	6	1	2	2	6	1	1	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:27038593C>T	ENST00000395245.3	-	0	1736				PROCA1_ENST00000439862.3_5'Flank|PROCA1_ENST00000301039.2_Missense_Mutation_p.C29Y|PROCA1_ENST00000581289.1_Missense_Mutation_p.C29Y|PROCA1_ENST00000579650.1_5'Flank	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family						antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CTTACCGCGGCATCTGCTCTC	0.682																																					p.C29Y	Pancreas(175;216 2049 29940 32498 41589)	.											.	PROCA1-91	0			c.G86A						.						78	68	72					17																	27038593		2203	4300	6503	SO:0001628	intergenic_variant	147011	exon1			CCGCGGCATCTGC	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"RAB, member RAS oncogene"	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680		17.37:g.27038593C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	86	13	NM_152465	0	0	0	0	0	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	37	CCDS11240.1	.	.	.	.	.	.	.	.	.	.	C	8.048	0.765458	0.15914	.	.	ENSG00000167525	ENST00000301039	T	0.29917	1.55	2.0	2.0	0.26442	.	0.967617	0.08473	U	0.940674	T	0.16642	0.0400	N	0.08118	0	0.27121	N	0.962131	B	0.11235	0.004	B	0.14023	0.01	T	0.16748	-1.0392	10	0.56958	D	0.05	.	7.523	0.27639	0.0:1.0:0.0:0.0	.	29	Q8NCQ7-2	.	Y	29	ENSP00000301039:C29Y	ENSP00000301039:C29Y	C	-	2	0	PROCA1	24062720	0.026000	0.19158	0.014000	0.15608	0.004000	0.04260	0.601000	0.24119	1.414000	0.47017	0.514000	0.50259	TGC	.		0.682	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934		T	27038593	C	T	27038593	1	4	1	0	1	0	0	0	0	0	0	0	12575	710	25	2		2	PROCA1	17	27038593	IGR	SNP	C	TCGA-A4-7286-01A-11D-2136-08	7463410	27038593	54156617	44	44											
ENGASE	64772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	77079593	77079593	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgactggagcgttatctgcCcacacatagcatctgctcct	8	10	8	15	2	2	0	0	0	2	0	3	2	3	1	3	1	4	3	3	1	2	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:77079593C>G	ENST00000579016.1	+	9	1172	c.1172C>G	c.(1171-1173)cCc>cGc	p.P391R	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	391						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CGTTATCTGCCCACACATAGC	0.617																																					p.P391R		.											.	ENGASE-91	0			c.C1172G						.						111	118	116					17																	77079593		2136	4241	6377	SO:0001583	missense	64772	exon9			ATCTGCCCACACA	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1172C>G	17.37:g.77079593C>G	ENSP00000462333:p.Pro391Arg	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	78	11	NM_001042573	0	0	4	5	1	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987187	0.35036	.	.	ENSG00000167280	ENST00000545583	.	.	.	5.47	5.47	0.80525	Glycoside hydrolase, family 85 (1);	0.309415	0.36778	N	0.002406	T	0.61173	0.2326	M	0.69823	2.125	0.80722	D	1	P	0.45240	0.854	P	0.46144	0.505	T	0.59685	-0.7408	9	0.28530	T	0.3	-4.1388	12.6473	0.56742	0.0:0.9243:0.0:0.0757	.	391	Q8NFI3	ENASE_HUMAN	R	391	.	ENSP00000438577:P391R	P	+	2	0	ENGASE	74591188	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	2.094000	0.41719	2.563000	0.86464	0.561000	0.74099	CCC	.		0.617	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		G	77079593	C	G	77079593	3	3	1	1	0	0	0	0	1	0	0	0	5131	623	22	4	1206	4	ENGASE	17	77079593	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	50041000	77079593	4115617	45	45											
AATK	9625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79094952	79094952	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgctcgcggctgccctccAgaggggccagtggccgacgg	5	4	17	15	5	0	1	0	0	0	1	2	2	1	1	4	5	2	2	4	5	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:79094952A>T	ENST00000326724.4	-	11	2808	c.2784T>A	c.(2782-2784)tcT>tcA	p.S928S	AATK_ENST00000417379.1_Silent_p.S825S	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	928					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCTGCCCTCCAGAGGGGCCAG	0.647																																					p.S928S		.											.	AATK-933	0			c.T2784A						.						10	12	11					17																	79094952		1972	4143	6115	SO:0001819	synonymous_variant	9625	exon11			CCCTCCAGAGGGG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.2784T>A	17.37:g.79094952A>T		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	27	7	NM_001080395	0	0	0	0	0	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	A	0.866	-0.733743	0.03111	.	.	ENSG00000181409	ENST00000417379	.	.	.	3.95	-2.58	0.06228	.	.	.	.	.	T	0.43188	0.1236	.	.	.	0.37603	D	0.920626	.	.	.	.	.	.	T	0.43048	-0.9415	4	.	.	.	.	5.1955	0.15233	0.3603:0.1879:0.4518:0.0	.	.	.	.	Q	881	.	.	L	-	2	0	AATK	76709547	0.166000	0.22962	0.006000	0.13384	0.142000	0.21351	0.558000	0.23469	-0.121000	0.11787	-0.464000	0.05259	CTG	.		0.647	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79094952	A	T	79094952	2	4	1	1	0	0	0	0	0	0	0	1	26	175	7	5		5	AATK	17	79094952	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08	2015359	79094952	2100258	46	46											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22154841	22154841	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcacatttgtagggttTctctccagtatgaattacct	8	18	6	9	0	3	1	1	1	2	0	5	1	4	1	2	1	1	3	2	1	4	7			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr19:22154841T>C	ENST00000397126.4	-	4	3143	c.2995A>G	c.(2995-2997)Aaa>Gaa	p.K999E	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	999					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTGTAGGGTTTCTCTCCAGTA	0.358																																					p.K999E		.											.	ZNF208-7	0			c.A2995G						.						59	65	63					19																	22154841		2095	4240	6335	SO:0001583	missense	7757	exon4			AGGGTTTCTCTCC	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2995A>G	19.37:g.22154841T>C	ENSP00000380315:p.Lys999Glu	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_007153	0	2	52	54	0		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.228557	0.39399	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.27104	1.69	2.58	2.58	0.30949	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.44414	0.1292	.	.	.	0.26358	N	0.977095	P	0.51791	0.948	D	0.64237	0.923	T	0.18335	-1.0340	8	0.87932	D	0	.	9.4923	0.38967	0.0:0.0:0.0:1.0	.	871	O43345	ZN208_HUMAN	E	999;871	ENSP00000380315:K999E	ENSP00000380315:K999E	K	-	1	0	ZNF208	21946681	0.119000	0.22226	0.028000	0.17463	0.366000	0.29705	2.087000	0.41653	0.848000	0.35191	0.240000	0.17902	AAA	.		0.358	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22154841	T	C	22154841	3	2	1	1	0	0	0	0	1	0	0	0	17798	1792	62	3	851	3	ZNF208	19	22154841	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08		22154841	36974142	47	47											
FCGRT	2217	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	50017180	50017180	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccttaccgcggtgtccTcgcctgccccggggactcct	4	8	10	19	4	0	0	0	0	0	0	3	1	2	1	8	3	2	0	8	3	1	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr19:50017180T>C	ENST00000221466.5	+	3	601	c.115T>C	c.(115-117)Tcg>Ccg	p.S39P	FCGRT_ENST00000596975.1_Missense_Mutation_p.S39P|FCGRT_ENST00000426395.3_Missense_Mutation_p.S39P|FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000599988.1_Intron	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	39	Alpha-1.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		CGCGGTGTCCTCGCCTGCCCC	0.657																																					p.S39P		.											.	FCGRT-91	0			c.T115C						.						128	127	127					19																	50017180		2203	4300	6503	SO:0001583	missense	2217	exon3			GTGTCCTCGCCTG	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"Immunoglobulin superfamily / C1-set domain containing"	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.115T>C	19.37:g.50017180T>C	ENSP00000221466:p.Ser39Pro	Somatic	286	2		WXS	Illumina HiSeq	Phase_I	231	64	NM_001136019	0	0	37	58	21	Q5HYM5|Q9HBV7|Q9NZ19	Missense_Mutation	SNP	ENST00000221466.5	37	CCDS12770.1	.	.	.	.	.	.	.	.	.	.	T	9.571	1.121014	0.20877	.	.	ENSG00000104870	ENST00000221466;ENST00000426395;ENST00000415900;ENST00000452439	T;T	0.00730	5.77;5.77	4.6	-9.19	0.00685	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	3.212320	0.01032	N	0.004150	T	0.00875	0.0029	L	0.42686	1.345	0.09310	N	1	P	0.36249	0.545	B	0.34652	0.187	T	0.06356	-1.0831	10	0.87932	D	0	.	5.6115	0.17408	0.2613:0.1951:0.46:0.0836	.	39	P55899	FCGRN_HUMAN	P	39	ENSP00000221466:S39P;ENSP00000410798:S39P	ENSP00000221466:S39P	S	+	1	0	FCGRT	54708992	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-4.455000	0.00231	-5.243000	0.00018	-1.310000	0.01310	TCG	.		0.657	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			C	50017180	T	C	50017180	3	2	1	1	0	0	0	0	1	0	0	0	5805	1551	54	3	121	3	FCGRT	19	50017180	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	27862339	50017180	9111803	48	48											
PCSK2	5126	hgsc.bcm.edu	37	chr20	17462695	17462695	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgtggagagaagcctgaaaAgcatccttaacaagaactag	16	6	10	9	1	0	3	0	1	0	2	1	5	1	4	3	1	4	1	3	1	7	2	rs375179104		TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:17462695A>G	ENST00000262545.2	+	12	2212	c.1897A>G	c.(1897-1899)Agc>Ggc	p.S633G	PCSK2_ENST00000536609.1_Missense_Mutation_p.S598G|PCSK2_ENST00000459871.1_3'UTR|PCSK2_ENST00000377899.1_Missense_Mutation_p.S614G	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	633					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	AAGCCTGAAAAGCATCCTTAA	0.587																																					p.S633G		.											.	PCSK2-157	0			c.A1897G						.	A	GLY/SER,GLY/SER,GLY/SER	0,4370		0,0,2185	32	28	29		1840,1792,1897	4.7	1	20		29	1,8553		0,1,4276	no	missense,missense,missense	PCSK2	NM_001201528.1,NM_001201529.1,NM_002594.3	56,56,56	0,1,6461	GG,GA,AA		0.0117,0.0,0.0077	benign,benign,benign	614/620,598/604,633/639	17462695	1,12923	2185	4277	6462	SO:0001583	missense	5126	exon12			CTGAAAAGCATCC	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1897A>G	20.37:g.17462695A>G	ENSP00000262545:p.Ser633Gly	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_002594	0	0	0	0	0	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	37	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017933	0.54576	0.0	1.17E-4	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	T;T;T	0.72167	-0.44;-0.45;-0.63	5.77	4.67	0.58626	.	0.035091	0.85682	N	0.000000	T	0.71693	0.3370	N	0.22421	0.69	0.58432	D	0.999999	B;B;P	0.52842	0.0;0.005;0.956	B;B;D	0.65010	0.0;0.007;0.931	T	0.73471	-0.3972	10	0.66056	D	0.02	-33.2862	10.6214	0.45483	0.9241:0.0:0.0759:0.0	.	598;614;633	B4DFQ3;B1ANH9;P16519	.;.;NEC2_HUMAN	G	614;633;598	ENSP00000367131:S614G;ENSP00000262545:S633G;ENSP00000437458:S598G	ENSP00000262545:S633G	S	+	1	0	PCSK2	17410695	1.000000	0.71417	0.976000	0.42696	0.275000	0.26752	7.124000	0.77185	1.005000	0.39183	0.377000	0.23210	AGC	.		0.587	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		G	17462695	A	G	17462695	3	3	1	1	0	0	0	0	1	0	0	0	11627	72	3	3	1943	3	PCSK2	20	17462695	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08		17462695	45562825	49	49											
CSRP2BP	57325	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	18142850	18142850	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tttcagaagcagatctgattCcagatgtgatgcccccacaa	12	10	8	11	0	2	5	1	2	1	3	3	5	3	5	3	0	2	1	3	0	2	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:18142850C>G	ENST00000435364.3	+	5	1410	c.1069C>G	c.(1069-1071)Cca>Gca	p.P357A	CSRP2BP_ENST00000489634.2_Missense_Mutation_p.P229A|CSRP2BP_ENST00000377681.3_Missense_Mutation_p.P356A	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	357					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						AGATCTGATTCCAGATGTGAT	0.458																																					p.P357A		.											.	CSRP2BP-525	0			c.C1069G						.						216	229	224					20																	18142850		2203	4300	6503	SO:0001583	missense	57325	exon5			CTGATTCCAGATG	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"cysteine rich protein 2 binding protein", "ATAC component 2 homolog (Drosophila)"					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1069C>G	20.37:g.18142850C>G	ENSP00000392318:p.Pro357Ala	Somatic	596	0		WXS	Illumina HiSeq	Phase_I	629	129	NM_020536	0	0	0	0	0	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555785	0.86231	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.43294	0.95;0.95;0.95;0.99	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.55955	0.1953	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.994	T	0.57004	-0.7885	10	0.72032	D	0.01	-20.8382	20.5666	0.99351	0.0:1.0:0.0:0.0	.	229;357	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	A	357;356;357;229	ENSP00000278816:P357A;ENSP00000366909:P356A;ENSP00000392318:P357A;ENSP00000425909:P229A	ENSP00000278816:P357A	P	+	1	0	CSRP2BP	18090850	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	7.364000	0.79526	2.854000	0.98071	0.655000	0.94253	CCA	.		0.458	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		G	18142850	C	G	18142850	3	3	1	1	0	0	0	0	1	0	0	0	3974	855	30	4	1087	4	CSRP2BP	20	18142850	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	680155	18142850	44882670	50	50											
HM13	81502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	30137040	30137040	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaacaacctttttggcctgGccttctcccttaatggagta	8	13	7	13	0	1	0	0	0	1	0	2	1	1	1	5	3	2	1	5	3	4	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:30137040G>A	ENST00000340852.5	+	6	695	c.571G>A	c.(571-573)Gcc>Acc	p.A191T	HM13_ENST00000335574.5_Missense_Mutation_p.A191T|HM13_ENST00000398174.3_Missense_Mutation_p.A191T|HM13_ENST00000376127.3_Intron|HM13_ENST00000492709.1_3'UTR	NM_030789.2	NP_110416.1	Q8TCT9	HM13_HUMAN	histocompatibility (minor) 13	191					membrane protein proteolysis (GO:0033619)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			TTTTGGCCTGGCCTTCTCCCT	0.567																																					p.A191T		.											.	HM13-153	0			c.G571A						.						216	199	205					20																	30137040		2203	4300	6503	SO:0001583	missense	81502	exon6			GGCCTGGCCTTCT	AL110115	CCDS13182.1, CCDS13183.1, CCDS42861.1	20q11.21	2012-02-21			ENSG00000101294	ENSG00000101294			16435	protein-coding gene	gene with protein product	"signal peptide peptidase beta", "presenilin-like protein 3", "intramembrane protease", "signal peptide peptidase like 1"	607106				12077416, 14704149	Standard	NM_030789		Approved	H13, dJ324O17.1, SPP, PSL3, IMP1, IMPAS, PSENL3, SPPL1	uc002wwc.3	Q8TCT9	OTTHUMG00000032175	ENST00000340852.5:c.571G>A	20.37:g.30137040G>A	ENSP00000343032:p.Ala191Thr	Somatic	326	0		WXS	Illumina HiSeq	Phase_I	349	63	NM_178581	0	0	68	90	22	B2RAY5|E1P5L3|Q15K36|Q540H8|Q5JWP2|Q5JWP3|Q5JWP4|Q5JWP5|Q7Z4F2|Q86Y35|Q95H87|Q9H110|Q9H111	Missense_Mutation	SNP	ENST00000340852.5	37	CCDS13182.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.315948	0.81469	.	.	ENSG00000101294	ENST00000335574;ENST00000340852;ENST00000398174	T;T;T	0.21361	2.01;2.01;2.01	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.42359	0.1199	M	0.73962	2.25	0.80722	D	1	P;P;B	0.43519	0.809;0.802;0.338	P;P;B	0.54210	0.745;0.607;0.281	T	0.21314	-1.0249	10	0.48119	T	0.1	-2.7651	17.5166	0.87776	0.0:0.0:1.0:0.0	.	191;191;191	Q8TCT9;Q8TCT9-4;Q8TCT9-2	HM13_HUMAN;.;.	T	191	ENSP00000335294:A191T;ENSP00000343032:A191T;ENSP00000381237:A191T	ENSP00000335294:A191T	A	+	1	0	HM13	29600701	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.992000	0.93519	2.604000	0.88044	0.650000	0.86243	GCC	.		0.567	HM13-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078527.2	NM_178580		A	30137040	G	A	30137040	3	1	1	1	0	0	0	0	1	0	0	0	7238	1203	42	2	660	2	HM13	20	30137040	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08	11994190	30137040	32888480	51	51											
CHD6	84181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	40080522	40080522	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaggtgtgatcagttccCaaatgaaactcttgatcttc	10	14	9	8	0	3	3	1	3	2	0	5	3	4	3	1	2	1	2	1	2	3	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:40080522C>G	ENST00000373233.3	-	22	3644	c.3467G>C	c.(3466-3468)tGg>tCg	p.W1156S	CHD6_ENST00000309279.7_Missense_Mutation_p.W639S	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1156					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GATCAGTTCCCAAATGAAACT	0.522																																					p.W1156S		.											.	CHD6-238	0			c.G3467C						.						259	206	224					20																	40080522		2203	4300	6503	SO:0001583	missense	84181	exon22			AGTTCCCAAATGA	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3467G>C	20.37:g.40080522C>G	ENSP00000362330:p.Trp1156Ser	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	279	45	NM_032221	0	0	2	3	1	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.899700|4.899700	0.91962|0.91962	.|.	.|.	ENSG00000124177|ENSG00000124177	ENST00000440697|ENST00000373233;ENST00000309279	.|D;D	.|0.98060	.|-4.69;-4.69	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.000000	.|0.56097	.|D	.|0.000033	D|D	0.98801|0.98801	0.9596|0.9596	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|D	.|0.72982	.|0.979	D|D	0.99651|0.99651	1.0991|1.0991	5|10	.|0.87932	.|D	.|0	-10.1751|-10.1751	20.0435|20.0435	0.97601|0.97601	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1156	.|Q8TD26	.|CHD6_HUMAN	R|S	342|1156;639	.|ENSP00000362330:W1156S;ENSP00000308684:W639S	.|ENSP00000308684:W639S	G|W	-|-	1|2	0|0	CHD6|CHD6	39513936|39513936	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.776000|7.776000	0.85560|0.85560	2.731000|2.731000	0.93534|0.93534	0.650000|0.650000	0.86243|0.86243	GGG|TGG	.		0.522	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			G	40080522	C	G	40080522	3	3	1	1	0	0	0	0	1	0	0	0	3335	595	21	4	4744	4	CHD6	20	40080522	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	9943482	40080522	22944998	52	52											
PARD6B	84612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49367023	49367023	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggaacaatcataacattaTgaaaccgtggtttgaatgtt	15	13	8	5	1	1	2	1	2	0	0	1	3	1	3	1	2	3	2	1	2	6	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:49367023T>C	ENST00000371610.2	+	3	1360	c.1117T>C	c.(1117-1119)Tga>Cga	p.*373R	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	0					axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						CATAACATTATGAAACCGTGG	0.398																																					p.X373R		.											.	PARD6B-91	0			c.T1117C						.						35	34	34					20																	49367023		2202	4298	6500	SO:0001578	stop_lost	84612	exon3			ACATTATGAAACC	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"par-6 (partitioning defective 6, C.elegans) homolog beta", "par-6 partitioning defective 6 homolog beta (C. elegans)"			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.1117T>C	20.37:g.49367023T>C	ENSP00000360672:p.*373Argext*13	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	62	11	NM_032521	0	0	2	3	1	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	37	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695570	0.30052	.	.	ENSG00000124171	ENST00000371610	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5383	0.76021	0.0:0.0:0.0:1.0	.	.	.	.	R	373	.	.	X	+	1	0	PARD6B	48800430	1.000000	0.71417	0.503000	0.27626	0.446000	0.32137	6.377000	0.73145	2.073000	0.62155	0.482000	0.46254	TGA	.		0.398	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		C	49367023	T	C	49367023	4	2	1	1	0	0	0	0	0	0	0	0	11472	1477	51	3	1127	3	PARD6B	20	49367023	Nonstop_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	9286501	49367023	13658497	53	53											
PRPF6	57473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62648174	62648174	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggaggaagatcggaagcaTacctggatggaggatgctga	13	6	17	5	1	0	2	0	1	0	1	1	9	0	8	1	6	3	2	1	6	3	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:62648174T>C	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.H541H			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					ATCGGAAGCATACCTGGATGG	0.552																																					p.H541H		.											.	PRPF6-70	0			c.T1623C						.						183	150	161					20																	62648174		2203	4300	6503	SO:0001627	intron_variant	24148	exon12			GAAGCATACCTGG	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.4+31883A>G	20.37:g.62648174T>C		Somatic	80	2		WXS	Illumina HiSeq	Phase_I	77	13	NM_012469	0	0	21	30	9	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			.		0.552	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62648174	T	C	62648174	1	2	1	0	1	0	0	0	0	0	0	0	12603	1403	49	3		3	PRPF6	20	62648174	Intron	SNP	T	TCGA-A4-7286-01A-11D-2136-08	13281151	62648174	377346	54	54											
EDA	1896	hgsc.bcm.edu	37	chrX	69243092	69243092	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agttaaaaacaagaaaaaggGtaagttcctgactttataaa	20	10	7	4	0	0	2	0	1	0	1	1	2	1	2	1	1	1	3	1	1	10	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chrX:69243092G>C	ENST00000374552.4	+	3	768		c.e3+1		EDA_ENST00000374553.2_Splice_Site|MIR676_ENST00000390702.2_RNA|EDA_ENST00000524573.1_Splice_Site	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A						cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						AAGAAAAAGGGTAAGTTCCTG	0.264																																					.		.											.	EDA-195	0			c.526+1G>C						.						38	35	36					X																	69243092		2196	4292	6488	SO:0001630	splice_region_variant	1896	exon3			AAAAGGGTAAGTT	U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"Tumor necrosis factor (ligand) superfamily"	3157	protein-coding gene	gene with protein product		300451	"ectodermal dysplasia 1, anhidrotic", "oligodontia 1"	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.526+1G>C	X.37:g.69243092G>C		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	19	2	NM_001399	0	0	0	0	0	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Splice_Site	SNP	ENST00000374552.4	37	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.381525	0.42207	.	.	ENSG00000158813	ENST00000374552;ENST00000374553;ENST00000524573;ENST00000503592	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7627	0.62977	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EDA	69159817	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	4.821000	0.62679	2.348000	0.79779	0.513000	0.50165	.	.		0.264	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399	Intron	C	69243092	G	C	69243092	5	2	1	1	0	0	0	0	0	0	1	0	4914	1275	44	4	673	4	EDA	23	69243092	Splice_Site	SNP	G	TCGA-A4-7286-01A-11D-2136-08		69243092	86027468	55	55											
BHLHB9	80823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	102004858	102004858	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggattaagccatttgcttGtccttgcaaaatggaatgct	10	14	10	7	0	0	0	0	0	0	0	1	2	1	2	2	2	4	3	2	2	4	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chrX:102004858G>C	ENST00000372735.1	+	4	1520	c.935G>C	c.(934-936)tGt>tCt	p.C312S	BHLHB9_ENST00000447531.1_Missense_Mutation_p.C312S|BHLHB9_ENST00000448867.1_Missense_Mutation_p.C312S|BHLHB9_ENST00000457056.1_Missense_Mutation_p.C312S|BHLHB9_ENST00000361229.4_Missense_Mutation_p.C312S			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	312					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCATTTGCTTGTCCTTGCAAA	0.398																																					p.C312S		.											.	BHLHB9-132	0			c.G935C						.						93	85	88					X																	102004858		2203	4300	6503	SO:0001583	missense	80823	exon2			TTGCTTGTCCTTG	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"Basic helix-loop-helix proteins", "Armadillo repeat containing"	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.935G>C	X.37:g.102004858G>C	ENSP00000361820:p.Cys312Ser	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_001142530	0	0	1	1	0	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084883	0.55861	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	4.68	4.68	0.58851	Armadillo-type fold (1);	0.000000	0.51477	D	0.000090	T	0.47857	0.1468	L	0.52905	1.665	0.33452	D	0.583863	D	0.89917	1.0	D	0.91635	0.999	T	0.57118	-0.7866	9	.	.	.	-17.5444	11.7841	0.52032	0.0:0.0:1.0:0.0	.	312	Q6PI77	BHLH9_HUMAN	S	312	ENSP00000403226:C312S;ENSP00000354675:C312S;ENSP00000405893:C312S;ENSP00000391722:C312S;ENSP00000361820:C312S	.	C	+	2	0	BHLHB9	101891514	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.642000	0.54367	2.557000	0.86248	0.594000	0.82650	TGT	.		0.398	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		C	102004858	G	C	102004858	3	2	1	1	0	0	0	0	1	0	0	0	1421	1377	48	4	937	4	BHLHB9	23	102004858	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08	32761766	102004858	53265702	56	56											
PLA2G2D	26279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	20440719	20440719	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctccttgtcacaggcaCacagctgctgctcacaccag	9	7	7	18	0	2	0	2	0	0	0	3	0	3	0	4	1	3	4	4	1	0	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:20440719C>T	ENST00000375105.3	-	4	384	c.326G>A	c.(325-327)tGt>tAt	p.C109Y		NM_012400.2	NP_036532.1	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID	109					glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTCACAGGCACACAGCTGCTG	0.597										Multiple Myeloma(11;0.12)																											p.C109Y	Melanoma(60;742 1548 31762 39240)	.											.	PLA2G2D-90	0			c.G326A						.						63	60	61					1																	20440719		2203	4300	6503	SO:0001583	missense	26279	exon4			CAGGCACACAGCT	AF112982	CCDS203.1, CCDS72721.1	1p36.12	2008-09-19			ENSG00000117215	ENSG00000117215	3.1.1.4		9033	protein-coding gene	gene with protein product		605630				10455175	Standard	NM_012400		Approved	sPLA2S	uc001bcz.4	Q9UNK4	OTTHUMG00000002701	ENST00000375105.3:c.326G>A	1.37:g.20440719C>T	ENSP00000364246:p.Cys109Tyr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	61	15	NM_012400	0	0	2	2	0	A8K2Z1|B1AEL9|Q9UK01	Missense_Mutation	SNP	ENST00000375105.3	37	CCDS203.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.873650	0.72180	.	.	ENSG00000117215	ENST00000375105	D	0.86097	-2.07	5.2	5.2	0.72013	Phospholipase A2 (3);	0.000000	0.53938	D	0.000050	D	0.94443	0.8212	H	0.95365	3.66	0.47949	D	0.999553	D	0.89917	1.0	D	0.97110	1.0	D	0.95704	0.8752	10	0.87932	D	0	-24.7657	14.2445	0.65978	0.0:1.0:0.0:0.0	.	109	Q9UNK4	PA2GD_HUMAN	Y	109	ENSP00000364246:C109Y	ENSP00000364246:C109Y	C	-	2	0	PLA2G2D	20313306	0.996000	0.38824	0.998000	0.56505	0.910000	0.53928	4.132000	0.57977	2.443000	0.82685	0.462000	0.41574	TGT	.		0.597	PLA2G2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007683.1			T	20440719	C	T	20440719	3	4	2	1	0	0	0	0	1	0	0	0	12023	478	17	2	115	2	PLA2G2D	1	20440719	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		20440719	228809902	1	57											
AGL	178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	100327977	100327977	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acttagggttgcaaaagaatCaggtaatgtcagcttgcttt	12	13	10	6	0	2	1	2	0	0	1	2	1	2	1	0	2	3	5	0	2	5	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:100327977C>G	ENST00000294724.4	+	4	936	c.458C>G	c.(457-459)tCa>tGa	p.S153*	AGL_ENST00000370161.2_Nonsense_Mutation_p.S137*|AGL_ENST00000361302.3_Nonsense_Mutation_p.S137*|AGL_ENST00000370163.3_Nonsense_Mutation_p.S153*|AGL_ENST00000361915.3_Nonsense_Mutation_p.S153*|AGL_ENST00000370165.3_Nonsense_Mutation_p.S153*|AGL_ENST00000361522.4_Nonsense_Mutation_p.S136*	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	153					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		GCAAAAGAATCAGGTAATGTC	0.338																																					p.S153X		.											.	AGL-92	0			c.C458G						.						159	150	153					1																	100327977		2203	4300	6503	SO:0001587	stop_gained	178	exon4			AAGAATCAGGTAA	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.458C>G	1.37:g.100327977C>G	ENSP00000294724:p.Ser153*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	102	23	NM_000644	0	0	0	0	0	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Nonsense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	C	39	7.619744	0.98393	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	.	.	.	5.53	5.53	0.82687	.	0.435109	0.23914	N	0.043307	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	19.4571	0.94897	0.0:1.0:0.0:0.0	.	.	.	.	X	153;153;153;153;137;137;136	.	ENSP00000294724:S153X	S	+	2	0	AGL	100100565	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	7.764000	0.85297	2.599000	0.87857	0.655000	0.94253	TCA	.		0.338	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100327977	C	G	100327977	4	3	2	1	0	0	0	0	0	1	0	0	384	838	29	4	537	4	AGL	1	100327977	Nonsense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	79887258	100327977	148922644	2	58											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150415711	150415711	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtttaattccaacagcatcTacaaatccaaaagctgctct	14	12	4	11	0	2	0	0	0	2	0	4	0	4	0	2	0	5	4	2	0	6	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:150415711T>C	ENST00000369068.4	+	5	523	c.519T>C	c.(517-519)tcT>tcC	p.S173S	RPRD2_ENST00000401000.4_Silent_p.S147S|RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000539519.1_Silent_p.S147S	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	173						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CAACAGCATCTACAAATCCAA	0.308																																					p.S173S		.											.	RPRD2-23	0			c.T519C						.						77	67	70					1																	150415711		1804	4072	5876	SO:0001819	synonymous_variant	23248	exon5			AGCATCTACAAAT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.519T>C	1.37:g.150415711T>C		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	9	2	NM_015203	0	0	2	2	0	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Silent	SNP	ENST00000369068.4	37	CCDS44216.1																																																																																			.		0.308	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150415711	T	C	150415711	2	2	2	1	0	0	0	0	0	0	0	1	13649	1509	53	3		3	RPRD2	1	150415711	Silent	SNP	T	TCGA-A4-7287-01A-11D-2136-08	50087734	150415711	98834910	3	59											
NTRK1	4914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156843561	156843561	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatgagaccagcttcatcttCactgagttcctggagccggc	9	10	10	12	1	3	2	2	2	1	1	4	4	4	3	3	2	2	2	3	2	1	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:156843561C>T	ENST00000524377.1	+	8	1028	c.987C>T	c.(985-987)ttC>ttT	p.F329F	NTRK1_ENST00000392302.2_Silent_p.F299F|NTRK1_ENST00000368196.3_Silent_p.F329F|NTRK1_ENST00000358660.3_Silent_p.F329F	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	329	Ig-like C2-type 2.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GCTTCATCTTCACTGAGTTCC	0.617			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.F329F		.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1-1393	0			c.C987T						.						44	36	39					1																	156843561		2203	4299	6502	SO:0001819	synonymous_variant	4914	exon8			CATCTTCACTGAG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.987C>T	1.37:g.156843561C>T		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	25	8	NM_001012331	0	0	0	0	0	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	37	CCDS1161.1																																																																																			.		0.617	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156843561	C	T	156843561	2	4	2	1	0	0	0	0	0	0	0	1	10732	825	29	2		2	NTRK1	1	156843561	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08	6427850	156843561	92407060	4	60											
GORAB	92344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	170501324	170501324	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgttggcagtcgcggctgCgagatttgggcacttttggg	5	12	17	7	3	0	1	0	0	0	1	1	2	0	1	0	4	1	4	0	4	0	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:170501324C>T	ENST00000367763.3	+	1	55	c.35C>T	c.(34-36)gCg>gTg	p.A12V	GORAB_ENST00000367762.1_Missense_Mutation_p.A12V|RP11-576I22.2_ENST00000421020.1_RNA|RP11-576I22.2_ENST00000456083.1_RNA	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	12						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						GTCGCGGCTGCGAGATTTGGG	0.622																																					p.A12V		.											.	GORAB-90	0			c.C35T						.						51	62	58					1																	170501324		2203	4300	6503	SO:0001583	missense	92344	exon1			CGGCTGCGAGATT	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"gerodermia osteodysplastica"	607983	"SCY1-like 1 binding protein 1"	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.35C>T	1.37:g.170501324C>T	ENSP00000356737:p.Ala12Val	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	95	16	NM_152281	0	0	0	1	1	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	37	CCDS1289.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.836253	0.32421	.	.	ENSG00000120370	ENST00000367763;ENST00000367762	T;T	0.79247	-0.28;-1.25	5.24	-10.5	0.00291	.	3.953700	0.00937	N	0.002796	T	0.28167	0.0695	N	0.08118	0	0.09310	N	1	B;B	0.17268	0.021;0.021	B;B	0.14023	0.005;0.01	T	0.36986	-0.9725	10	0.37606	T	0.19	.	7.2128	0.25943	0.1379:0.6439:0.1383:0.0799	.	12;12	Q5T7V8-2;Q5T7V8	.;GORAB_HUMAN	V	12	ENSP00000356737:A12V;ENSP00000356736:A12V	ENSP00000356736:A12V	A	+	2	0	GORAB	168767948	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.322000	0.00253	-3.663000	0.00124	-1.000000	0.02509	GCG	.		0.622	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281		T	170501324	C	T	170501324	3	4	2	1	0	0	0	0	1	0	0	0	6594	768	27	1	37	1	GORAB	1	170501324	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	13657763	170501324	78749297	5	61											
RGS21	431704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	192321246	192321246	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaatgttgagttctggcttgCctgtgaagactttaagaaaa	13	13	10	5	0	1	4	0	2	1	2	1	4	1	4	1	1	1	3	1	1	5	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:192321246C>A	ENST00000417209.2	+	4	332	c.158C>A	c.(157-159)gCc>gAc	p.A53D		NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	53	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						TTCTGGCTTGCCTGTGAAGAC	0.328																																					p.A53D		.											.	RGS21-92	0			c.C158A						.						68	66	66					1																	192321246		1836	4106	5942	SO:0001583	missense	431704	exon4			GGCTTGCCTGTGA	AY643711	CCDS41448.1	1q31.2	2013-09-24	2007-08-14		ENSG00000253148	ENSG00000253148		"Regulators of G-protein signaling"	26839	protein-coding gene	gene with protein product		612407	"regulator of G-protein signalling 21"			15066150	Standard	NM_001039152		Approved		uc001gsh.3	Q2M5E4	OTTHUMG00000035594	ENST00000417209.2:c.158C>A	1.37:g.192321246C>A	ENSP00000428343:p.Ala53Asp	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	51	11	NM_001039152	0	0	0	0	0		Missense_Mutation	SNP	ENST00000417209.2	37	CCDS41448.1	.	.	.	.	.	.	.	.	.	.	C	32	5.159165	0.94686	.	.	ENSG00000253148	ENST00000417209	T	0.02015	4.5	5.77	5.77	0.91146	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.33691	U	0.004656	T	0.14313	0.0346	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00016	-1.2383	10	0.87932	D	0	.	18.5418	0.91031	0.0:1.0:0.0:0.0	.	53	Q2M5E4	RGS21_HUMAN	D	53	ENSP00000428343:A53D	ENSP00000428343:A53D	A	+	2	0	RGS21	190587869	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.747000	0.85070	2.733000	0.93635	0.557000	0.71058	GCC	.		0.328	RGS21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086387.2			A	192321246	C	A	192321246	3	1	2	1	0	0	0	0	1	0	0	0	13336	739	26	4	168	4	RGS21	1	192321246	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	21819922	192321246	56929375	6	62											
CDC73	79577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	193099338	193099338	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtggttagaagacctgatcGaaaagatctacttggatatc	13	12	10	6	1	1	4	0	1	1	3	3	6	1	5	1	2	1	1	1	2	6	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:193099338G>A	ENST00000367435.3	+	3	456	c.272G>A	c.(271-273)cGa>cAa	p.R91Q		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	91			R -> P (found in a patient with isolated hyperparathyroidism and parathyroid adenomas). {ECO:0000269|PubMed:17639062}.		cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.R91Q(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						AGACCTGATCGAAAAGATCTA	0.294																																					p.R91Q		.											.	CDC73-1009	1	Substitution - Missense(1)	large_intestine(1)	c.G272A	GRCh37	CM072926	CDC73	M		.						140	144	143					1																	193099338		2203	4300	6503	SO:0001583	missense	79577	exon3			CTGATCGAAAAGA	AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.272G>A	1.37:g.193099338G>A	ENSP00000356405:p.Arg91Gln	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	61	7	NM_024529	0	0	22	26	4	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	37	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351125	0.95830	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	D	0.91407	-2.84	5.62	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.95648	0.8585	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96226	0.9164	10	0.87932	D	0	-10.3544	14.535	0.67953	0.0704:0.0:0.9296:0.0	.	91	Q6P1J9	CDC73_HUMAN	Q	91	ENSP00000356405:R91Q	ENSP00000356405:R91Q	R	+	2	0	CDC73	191365961	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.743000	0.98849	1.377000	0.46286	0.561000	0.74099	CGA	.		0.294	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		A	193099338	G	A	193099338	3	1	2	1	0	0	0	0	1	0	0	0	3091	1058	37	1	282	1	CDC73	1	193099338	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	778092	193099338	56151283	7	63											
SNRPE	6635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	203832834	203832835	+	Missense_Mutation	DNP	GG	GG	AA																															ctatgagcaagtgaatatgcGgatagaaggctgtatcattg																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:203832834_203832835GG>AA	ENST00000414487.2	+	3	170_171	c.125_126GG>AA	c.(124-126)cGG>cAA	p.R42Q	SNRPE_ENST00000367208.1_Missense_Mutation_p.R2Q|SNRPE_ENST00000483099.1_3'UTR	NM_003094.2	NP_003085.1	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E	42					gene expression (GO:0010467)|hair cycle (GO:0042633)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	RNA binding (GO:0003723)			breast(1)|large_intestine(2)|lung(1)|skin(1)	5	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GTGAATATGCGGATAGAAGGCT	0.426																																					p.R42Q	Ovarian(83;324 1318 17952 32395 39614)	.											.	SNRPE	0			c.G126A						.																																			SO:0001583	missense	6635	exon3			TATGCGGATAGAA	M37716	CCDS30979.1	1q32	2011-10-11			ENSG00000182004	ENSG00000182004			11161	protein-coding gene	gene with protein product		128260				1835977, 2143747	Standard	NM_003094		Approved	Sm-E	uc001hai.3	P62304	OTTHUMG00000035985	Exception_encountered	1.37:g.203832834_203832835delinsAA	ENSP00000400591:p.Arg42Gln	Somatic	239	1		WXS	Illumina HiSeq	Phase_I	247	87		0	0	0	0	0	B2R5B9|P08578|Q15498|Q5BKT2	Missense_Mutation	DNP	ENST00000414487.2	37	CCDS30979.1																																																																																			.		0.426	SNRPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087703.1	NM_003094		AA	203832835	GG	AA	203832834	3	1	2	1	0	0	0	0	1	0	0	0	14899	1116	39	1	135	1	SNRPE	1	203832834	Missense_Mutation	DNP	GG	TCGA-A4-7287-01A-11D-2136-08	10733496	203832834	45417787	8	64											
LBR	3930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	225599084	225599084	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaaaagtatttgagatcAaaagtaccaattcgagggtt	16	11	8	6	1	2	1	2	1	0	1	3	3	2	1	1	1	1	3	1	1	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:225599084A>T	ENST00000338179.2	-	9	1268	c.1143T>A	c.(1141-1143)ttT>ttA	p.F381L	LBR_ENST00000272163.4_Missense_Mutation_p.F381L|AC092811.1_ENST00000366845.2_5'Flank	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	381					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		ATTTGAGATCAAAAGTACCAA	0.373																																					p.F381L		.											.	LBR-228	0			c.T1143A						.						122	130	127					1																	225599084		2203	4300	6503	SO:0001583	missense	3930	exon9			GAGATCAAAAGTA	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1143T>A	1.37:g.225599084A>T	ENSP00000339883:p.Phe381Leu	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	153	28	NM_194442	0	1	45	74	28	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	37	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040696	0.55003	.	.	ENSG00000143815	ENST00000272163;ENST00000338179;ENST00000424022	D;D;D	0.96885	-4.16;-4.16;-4.16	6.16	2.64	0.31445	.	0.045876	0.85682	D	0.000000	D	0.93135	0.7814	L	0.33710	1.025	0.48288	D	0.99962	P	0.39782	0.688	P	0.46685	0.524	D	0.87185	0.2230	10	0.13853	T	0.58	-33.8453	9.3222	0.37971	0.796:0.0:0.204:0.0	.	381	Q14739	LBR_HUMAN	L	381;381;12	ENSP00000272163:F381L;ENSP00000339883:F381L;ENSP00000397817:F12L	ENSP00000272163:F381L	F	-	3	2	LBR	223665707	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.577000	0.53885	0.212000	0.20703	0.528000	0.53228	TTT	.		0.373	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		T	225599084	A	T	225599084	3	4	2	1	0	0	0	0	1	0	0	0	8673	127	5	5	728	5	LBR	1	225599084	Missense_Mutation	SNP	A	TCGA-A4-7287-01A-11D-2136-08	21766250	225599084	23651537	9	65											
CCDC85A	114800	broad.mit.edu	37	chr2	56420491	56420491	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaagtggaggcagcggcGgaggcagcagggagggcacc	10	1	22	8	2	0	0	0	0	0	0	0	5	0	4	1	8	2	4	1	8	1	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr2:56420491G>A	ENST00000407595.2	+	2	1658	c.1156G>A	c.(1156-1158)Gga>Aga	p.G386R	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	386										breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGGCAGCGGCGGAGGCAGCAG	0.627																																					p.G386R													.	CCDC85A-73	0			c.G1156A						.						24	30	28					2																	56420491		2195	4299	6494	SO:0001583	missense	114800	exon2			AGCGGCGGAGGCA	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.1156G>A	2.37:g.56420491G>A	ENSP00000384040:p.Gly386Arg	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	13	3	NM_001080433	0	0	0	0	0		Missense_Mutation	SNP	ENST00000407595.2	37	CCDS46290.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.836447	0.32421	.	.	ENSG00000055813	ENST00000407595	.	.	.	5.02	3.23	0.37069	.	0.151903	0.64402	D	0.000013	T	0.42921	0.1224	L	0.47716	1.5	0.54753	D	0.999988	D	0.56035	0.974	B	0.42798	0.398	T	0.21552	-1.0242	9	0.15952	T	0.53	-16.1309	11.2343	0.48931	0.1496:0.0:0.8504:0.0	.	386	Q96PX6	CC85A_HUMAN	R	386	.	ENSP00000384040:G386R	G	+	1	0	CCDC85A	56273995	0.077000	0.21312	0.094000	0.20943	0.180000	0.23129	0.649000	0.24843	0.531000	0.28639	0.484000	0.47621	GGA	.		0.627	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1			A	56420491	G	A	56420491	3	1	2	1	0	0	0	0	1	0	0	0	2865	1117	39	1	1162	1	CCDC85A	2	56420491	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		56420491	186778882	10	66											
TMEM150A	129303	ucsc.edu	37	chr2	85828227	85828227	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagggcaggactcgttgtaGgacctggcaggcaggacagg	9	5	19	8	1	0	0	0	0	0	0	1	4	0	4	1	8	0	5	1	8	1	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr2:85828227G>T	ENST00000409668.1	-	3	584	c.117C>A	c.(115-117)tcC>tcA	p.S39S	TMEM150A_ENST00000306353.3_Missense_Mutation_p.P9H|TMEM150A_ENST00000334462.5_Silent_p.S39S			Q86TG1	T150A_HUMAN	transmembrane protein 150A	39					catabolic process (GO:0009056)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|lung(1)|skin(1)	7						ACTCGTTGTAGGACCTGGCAG	0.627																																					p.S39S													.	TMEM150A-90	0			c.C117A						.						47	40	42					2																	85828227		2203	4300	6503	SO:0001819	synonymous_variant	129303	exon4			GTTGTAGGACCTG	AK098152	CCDS33233.1	2p11.2	2009-06-12	2009-06-12	2009-06-12	ENSG00000168890	ENSG00000168890			24677	protein-coding gene	gene with protein product			"transmembrane protein 150"	TMEM150		10858565	Standard	NM_001031738		Approved	TM6P1, FLJ90024	uc002spy.2	Q86TG1	OTTHUMG00000130168	ENST00000409668.1:c.117C>A	2.37:g.85828227G>T		Somatic	54	0		WXS	Illumina HiSeq		36	4	NM_001031738	0	0	1	1	0	A8K764|B7WPQ9|D6W5L2|Q8N2R6	Silent	SNP	ENST00000409668.1	37	CCDS33233.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151229	0.57151	.	.	ENSG00000168890	ENST00000306353;ENST00000425160	T	0.50001	0.76	5.06	4.19	0.49359	.	.	.	.	.	T	0.39306	0.1073	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.30001	-0.9993	8	0.87932	D	0	-8.475	9.5166	0.39109	0.0975:0.0:0.9025:0.0	.	9	Q86TG1-2	.	H	9	ENSP00000302715:P9H	ENSP00000302715:P9H	P	-	2	0	TMEM150A	85681738	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.690000	0.25451	1.122000	0.41944	0.655000	0.94253	CCT	.		0.627	TMEM150A-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329474.1	NM_153342		T	85828227	G	T	85828227	2	4	2	1	0	0	0	0	0	0	0	1	16099	987	35	4		4	TMEM150A	2	85828227	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	29407736	85828227	157371146	11	67											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38149133	38149133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtacctacagagcagccagGtggaggttagaaatctctac	12	9	11	9	0	1	2	0	0	1	2	2	3	1	3	2	3	5	3	2	3	5	4	rs141938666	byFrequency	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:38149133G>A	ENST00000308059.6	+	20	2944	c.2923G>A	c.(2923-2925)Gtg>Atg	p.V975M	DLEC1_ENST00000452631.2_Missense_Mutation_p.V975M|DLEC1_ENST00000346219.3_Missense_Mutation_p.V975M					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGCAGCCAGGTGGAGGTTAG	0.507													G|||	9	0.00179712	0	0	5008	,	,		18744	0.0089		0	False		,,,				2504	0				p.V975M		.											.	DLEC1-161	0			c.G2923A						.						80	81	81					3																	38149133		1959	4147	6106	SO:0001583	missense	9940	exon20			AGCCAGGTGGAGG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.2923G>A	3.37:g.38149133G>A	ENSP00000308597:p.Val975Met	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	39	10	NM_007337	0	0	0	0	0		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	6	0.0027472527472527475	0	0.0	0	0.0	6	0.01048951048951049	0	0.0	G	13.63	2.294945	0.40594	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.07800	3.16;3.16;3.39	5.05	-0.716	0.11212	.	0.181665	0.37136	N	0.002225	T	0.08758	0.0217	L	0.51422	1.61	0.21950	N	0.999458	P;B;D;P	0.54964	0.935;0.205;0.969;0.935	B;B;P;B	0.52066	0.424;0.078;0.689;0.424	T	0.08249	-1.0731	10	0.56958	D	0.05	-8.7464	10.246	0.43341	0.0:0.5584:0.2143:0.2274	.	975;975;975;975	F8W6T4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	M	975	ENSP00000308597:V975M;ENSP00000315914:V975M;ENSP00000410427:V975M	ENSP00000308597:V975M	V	+	1	0	DLEC1	38124137	0.092000	0.21681	0.469000	0.27204	0.960000	0.62799	0.026000	0.13599	-0.125000	0.11703	0.561000	0.74099	GTG	G|0.997;A|0.003		0.507	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38149133	G	A	38149133	3	1	2	1	0	0	0	0	1	0	0	0	4563	1261	44	2	3001	2	DLEC1	3	38149133	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		38149133	159873297	12	68											
HYAL1	3373	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	50340364	50340364	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaggtcaggaagagggcgcaGatgggaagcaggtgggctgc	11	4	20	6	1	1	2	1	0	0	2	1	4	1	4	0	6	2	3	0	6	3	0	rs370239620		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:50340364G>C	ENST00000266031.4	-	1	639	c.24C>G	c.(22-24)atC>atG	p.I8M	HYAL1_ENST00000447605.2_Intron|HYAL1_ENST00000395144.2_Missense_Mutation_p.I8M|HYAL1_ENST00000395143.2_Missense_Mutation_p.I8M|HYAL1_ENST00000457214.2_Intron|HYAL1_ENST00000320295.8_Missense_Mutation_p.I8M			Q12794	HYAL1_HUMAN	hyaluronoglucosaminidase 1	8					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to pH (GO:0071467)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal joint morphogenesis (GO:0060272)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|negative regulation of cell growth (GO:0030308)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of growth (GO:0045927)|positive regulation of hyaluranon cable assembly (GO:1900106)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|hyaluranon cable (GO:0036117)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	hyaluronan synthase activity (GO:0050501)|hyalurononglucosaminidase activity (GO:0004415)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AGAGGGCGCAGATGGGAAGCA	0.607																																					p.I8M		.											.	HYAL1-278	0			c.C24G						.						35	38	37					3																	50340364		2203	4300	6503	SO:0001583	missense	3373	exon2			GGCGCAGATGGGA	U90094	CCDS2816.1, CCDS2817.1, CCDS46832.1, CCDS46833.1	3p21.31	2014-07-17			ENSG00000114378	ENSG00000114378	3.2.1.35		5320	protein-coding gene	gene with protein product		607071				9223416, 9409739	Standard	NM_153281		Approved	LUCA1, HYAL-1, FUS2, NAT6	uc003czp.4	Q12794	OTTHUMG00000156941	ENST00000266031.4:c.24C>G	3.37:g.50340364G>C	ENSP00000266031:p.Ile8Met	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	46	6	NM_033159	0	0	3	3	0	Q6FH23|Q6PIZ6|Q7KYU2|Q7LE34|Q8NFK5|Q8NFK6|Q8NFK7|Q8NFK8|Q8NFK9|Q93013|Q9UKD5|Q9UNI8	Missense_Mutation	SNP	ENST00000266031.4	37	CCDS2816.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780578	0.49891	.	.	ENSG00000114378	ENST00000395144;ENST00000266031;ENST00000320295;ENST00000395143;ENST00000418723;ENST00000452672	T;T;T;T;T;T	0.48522	2.16;2.16;2.16;1.83;0.81;0.81	5.3	1.26	0.21427	.	3.721710	0.00447	N	0.000080	T	0.49236	0.1545	L	0.50333	1.59	0.24266	N	0.99527	P;P;P	0.37636	0.603;0.603;0.468	B;B;B	0.42386	0.386;0.295;0.293	T	0.34179	-0.9839	10	0.46703	T	0.11	-3.0796	6.6937	0.23187	0.2193:0.0:0.6565:0.1242	.	8;8;8	Q12794-7;Q12794-2;Q12794	.;.;HYAL1_HUMAN	M	8	ENSP00000378576:I8M;ENSP00000266031:I8M;ENSP00000346068:I8M;ENSP00000378575:I8M;ENSP00000394526:I8M;ENSP00000391666:I8M	ENSP00000266031:I8M	I	-	3	3	HYAL1	50315368	0.761000	0.28439	0.005000	0.12908	0.266000	0.26442	1.468000	0.35332	0.324000	0.23333	0.655000	0.94253	ATC	.		0.607	HYAL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346703.1			C	50340364	G	C	50340364	3	2	2	1	0	0	0	0	1	0	0	0	7484	932	33	4	1295	4	HYAL1	3	50340364	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	12191231	50340364	147682066	13	69											
SERPINI2	5276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	167170764	167170764	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagccaccactaaatatctcGgttatgttcaaagaatacaa	16	10	5	10	1	2	1	1	0	1	1	3	1	2	1	2	1	2	2	2	1	8	5	rs140665807	byFrequency	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:167170764G>A	ENST00000476257.1	-	7	1222	c.924C>T	c.(922-924)acC>acT	p.T308T	SERPINI2_ENST00000471111.1_Silent_p.T308T|SERPINI2_ENST00000264677.4_Silent_p.T308T|SERPINI2_ENST00000461846.1_Silent_p.T308T			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	308					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						TAAATATCTCGGTTATGTTCA	0.279													G|||	3	0.000599042	0.0015	0	5008	,	,		16433	0		0.001	False		,,,				2504	0				p.T318T		.											.	SERPINI2-228	0			c.C954T						.	G		4,4402	8.1+/-20.4	0,4,2199	65	63	64		924	-7.4	0.8	3	dbSNP_134	64	1,8595	1.2+/-3.3	0,1,4297	yes	coding-synonymous	SERPINI2	NM_006217.3		0,5,6496	AA,AG,GG		0.0116,0.0908,0.0385		308/406	167170764	5,12997	2203	4298	6501	SO:0001819	synonymous_variant	5276	exon7			TATCTCGGTTATG	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"Serine (or cysteine) peptidase inhibitors"	8945	protein-coding gene	gene with protein product		605587	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2", "serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.924C>T	3.37:g.167170764G>A		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	48	17	NM_001012303	0	0	0	0	0		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			G|1.000;A|0.000		0.279	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		A	167170764	G	A	167170764	2	1	2	1	0	0	0	0	0	0	0	1	14151	1103	39	1		1	SERPINI2	3	167170764	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	116830400	167170764	30851666	14	70											
DCK	1633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	71892401	71892401	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaccaacttcgattatcttCaagaggtgcctatcttaaca	13	12	6	10	1	3	1	1	0	2	1	4	3	3	1	2	1	4	0	2	1	6	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:71892401C>A	ENST00000286648.5	+	6	1082	c.685C>A	c.(685-687)Caa>Aaa	p.Q229K	DCK_ENST00000504952.1_Missense_Mutation_p.Q229K|DCK_ENST00000504730.1_Nonsense_Mutation_p.S190*	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	229					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	CGATTATCTTCAAGAGGTGCC	0.284																																					p.Q229K		.											.	DCK-116	0			c.C685A						.						43	45	44					4																	71892401		2202	4288	6490	SO:0001583	missense	1633	exon6			TATCTTCAAGAGG	M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.685C>A	4.37:g.71892401C>A	ENSP00000286648:p.Gln229Lys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	39	13	NM_000788	0	0	16	23	7	B2R8V6|Q5TZY7|Q6FI11	Missense_Mutation	SNP	ENST00000286648.5	37	CCDS3548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.0|27.0	4.787431|4.787431	0.90367|0.90367	.|.	.|.	ENSG00000156136|ENSG00000156136	ENST00000286648;ENST00000504952|ENST00000504730	D;D|.	0.97870|.	-4.58;-4.58|.	5.78|5.78	4.92|4.92	0.64577|0.64577	.|.	0.274194|.	0.41194|.	D|.	0.000924|.	T|.	0.49864|.	0.1582|.	N|N	0.16233|0.16233	0.39|0.39	0.45272|0.45272	D|D	0.998276|0.998276	B|.	0.09022|.	0.002|.	B|.	0.09377|.	0.004|.	T|.	0.44483|.	-0.9325|.	10|.	0.05351|.	T|.	0.99|.	.|.	16.6255|16.6255	0.84969|0.84969	0.0:0.8699:0.1301:0.0|0.0:0.8699:0.1301:0.0	.|.	229|.	P27707|.	DCK_HUMAN|.	K|X	229|190	ENSP00000286648:Q229K;ENSP00000421508:Q229K|.	ENSP00000286648:Q229K|.	Q|S	+|+	1|2	0|0	DCK|DCK	72111265|72111265	0.983000|0.983000	0.35010|0.35010	0.987000|0.987000	0.45799|0.45799	0.467000|0.467000	0.32768|0.32768	3.040000|3.040000	0.49799|0.49799	1.391000|1.391000	0.46566|0.46566	0.591000|0.591000	0.81541|0.81541	CAA|TCA	.		0.284	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2			A	71892401	C	A	71892401	3	1	2	1	0	0	0	0	1	0	0	0	4296	827	29	4	707	4	DCK	4	71892401	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		71892401	119261875	15	71											
PDE5A	8654	hgsc.bcm.edu	37	chr4	120486567	120486567	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaaataagcagcaaagtccTaaaaaacagataatagacaa	23	5	5	8	0	0	2	0	0	0	2	1	2	1	2	2	0	3	2	2	0	9	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:120486567T>C	ENST00000354960.3	-	5	1223		c.e5-2		PDE5A_ENST00000394439.1_Splice_Site|PDE5A_ENST00000264805.5_Splice_Site	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific						blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	AGCAAAGTCCTAAAAAACAGA	0.353																																					.		.											.	PDE5A-90	0			c.778-2A>G						.						77	69	72					4																	120486567		2203	4299	6502	SO:0001630	splice_region_variant	8654	exon6			AAGTCCTAAAAAA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.904-2A>G	4.37:g.120486567T>C		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_033430	0	0	0	0	0	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Splice_Site	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.083965	0.76642	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.68	0.77360	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDE5A	120706015	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.346000	0.79347	2.241000	0.73720	0.482000	0.46254	.	.		0.353	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	Intron	C	120486567	T	C	120486567	5	2	2	1	0	0	0	0	0	0	1	0	11670	1536	53	3	1793	3	PDE5A	4	120486567	Splice_Site	SNP	T	TCGA-A4-7287-01A-11D-2136-08	48594166	120486567	70667709	16	72											
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	126371574	126371574	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttcttcaggaaatgaagaaGgcatttttgcaatcaattct	13	15	7	6	0	4	2	2	1	2	1	4	3	4	3	0	2	1	2	0	2	5	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:126371574G>A	ENST00000394329.3	+	9	9416	c.9403G>A	c.(9403-9405)Ggc>Agc	p.G3135S	FAT4_ENST00000335110.5_Missense_Mutation_p.G1433S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3135	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AAATGAAGAAGGCATTTTTGC	0.388																																					p.G3135S		.											.	FAT4-108	0			c.G9403A						.						67	68	68					4																	126371574		2203	4300	6503	SO:0001583	missense	79633	exon9			GAAGAAGGCATTT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9403G>A	4.37:g.126371574G>A	ENSP00000377862:p.Gly3135Ser	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	37	15	NM_024582	0	0	0	0	0	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464553	0.43736	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.61859	0.07;0.07	5.63	4.79	0.61399	Cadherin (4);Cadherin-like (1);	0.000000	0.35067	U	0.003472	T	0.60650	0.2285	N	0.25647	0.755	0.80722	D	1	P;D;D	0.89917	0.839;1.0;1.0	B;D;D	0.97110	0.287;0.997;1.0	T	0.54951	-0.8216	10	0.08599	T	0.76	.	14.512	0.67794	0.0698:0.0:0.9302:0.0	.	1433;3135;3135	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	S	3135;1433	ENSP00000377862:G3135S;ENSP00000335169:G1433S	ENSP00000335169:G1433S	G	+	1	0	FAT4	126591024	1.000000	0.71417	0.835000	0.33067	0.669000	0.39330	7.835000	0.86780	1.389000	0.46526	0.655000	0.94253	GGC	.		0.388	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126371574	G	A	126371574	3	1	2	1	0	0	0	0	1	0	0	0	5711	1000	35	2	9437	2	FAT4	4	126371574	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	5885007	126371574	64782702	17	73											
PCDHA6	56142	broad.mit.edu;bcgsc.ca	37	chr5	140209735	140209735	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgggcgtcggtgggcgccGcgggcccagaggcggcgctg	3	3	21	14	8	0	1	0	0	0	1	1	1	0	1	2	6	0	1	2	6	0	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr5:140209735G>A	ENST00000529310.1	+	1	2173	c.2059G>A	c.(2059-2061)Gcg>Acg	p.A687T	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	687					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGGCGCCGCGGGCCCAGA	0.672																																					p.A687T													.	PCDHA6-92	0			c.G2059A						.						40	46	44					5																	140209735		2197	4279	6476	SO:0001583	missense	56142	exon1			GGCGCCGCGGGCC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"Cadherins / Protocadherins : Clustered"	8672	other	complex locus constituent	"KIAA0345-like 8"	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.2059G>A	5.37:g.140209735G>A	ENSP00000433378:p.Ala687Thr	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	83	6	NM_018909	0	0	0	0	0	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	G	4.857	0.159299	0.09236	.	.	ENSG00000081842	ENST00000529310	T	0.51574	0.7	3.98	-1.4	0.08968	.	0.873151	0.09225	N	0.831374	T	0.26484	0.0647	N	0.25890	0.77	0.09310	N	0.999999	B;B	0.10296	0.001;0.003	B;B	0.06405	0.002;0.002	T	0.18840	-1.0324	10	0.26408	T	0.33	.	0.96	0.01393	0.3808:0.1123:0.279:0.2279	.	687;687	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	T	687	ENSP00000433378:A687T	ENSP00000433378:A687T	A	+	1	0	PCDHA6	140189919	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.411000	0.01040	-0.449000	0.07117	-0.683000	0.03753	GCG	.		0.672	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140209735	G	A	140209735	3	1	2	1	0	0	0	0	1	0	0	0	11554	1087	38	1	2061	1	PCDHA6	5	140209735	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		140209735	40705525	18	74											
HIST1H4C	8364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	26104205	26104205	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcaaaggcggaaaaggCttggggaagggtggtgctaa	11	5	19	6	3	0	0	0	0	0	0	0	2	0	2	0	8	1	3	0	8	5	2	rs139978722	byFrequency	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:26104205C>G	ENST00000377803.2	+	1	102	c.30C>G	c.(28-30)ggC>ggG	p.G10G		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	10					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						GCGGAAAAGGCTTGGGGAAGG	0.532																																					p.G10G		.											.	HIST1H4C-68	0			c.C30G						.						57	58	58					6																	26104205		2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			AAAAGGCTTGGGG	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"Histones / Replication-dependent"	4787	protein-coding gene	gene with protein product		602827	"H4 histone family, member G", "histone 1, H4c"	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.30C>G	6.37:g.26104205C>G		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	88	21	NM_003542	0	0	1	1	0	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	37	CCDS4583.1																																																																																			C|0.999;T|0.001		0.532	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		G	26104205	C	G	26104205	2	3	2	1	0	0	0	0	0	0	0	1	7188	784	28	4		4	HIST1H4C	6	26104205	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08		26104205	145010862	19	75											
ZNF192	7745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	28116192	28116192	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttttcaggctctaatggctGaagaatcaagaaagccttca	13	11	8	9	0	4	3	3	1	1	2	4	3	4	3	1	2	1	2	1	2	5	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:28116192G>A	ENST00000330236.6	+	2	191	c.7G>A	c.(7-9)Gaa>Aaa	p.E3K	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.E3K	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	3					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)										TCTAATGGCTGAAGAATCAAG	0.473																																					p.E3K		.											.	.	0			c.G7A						.						50	48	49					6																	28116192		2203	4300	6503	SO:0001583	missense	7745	exon2			ATGGCTGAAGAAT		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.7G>A	6.37:g.28116192G>A	ENSP00000332750:p.Glu3Lys	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	35	12	NM_006298	0	0	1	2	1	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	37	CCDS4645.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.614734	0.46631	.	.	ENSG00000198315	ENST00000330236;ENST00000457389;ENST00000536028	T;T;T	0.05580	3.42;3.42;3.99	5.2	-0.593	0.11667	.	1.155400	0.06424	N	0.722860	T	0.01189	0.0039	N	0.19112	0.55	0.22827	N	0.998682	B	0.02656	0.0	B	0.01281	0.0	T	0.48592	-0.9022	10	0.42905	T	0.14	.	3.6279	0.08120	0.2558:0.0:0.4473:0.2969	.	3	Q15776	ZN192_HUMAN	K	3	ENSP00000332750:E3K;ENSP00000402948:E3K;ENSP00000439117:E3K	ENSP00000332750:E3K	E	+	1	0	ZNF192	28224171	0.141000	0.22595	0.921000	0.36526	0.930000	0.56654	0.165000	0.16564	-0.225000	0.09913	0.563000	0.77884	GAA	.		0.473	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			A	28116192	G	A	28116192	3	1	2	1	0	0	0	0	1	0	0	0	17788	1291	45	2	9	2	ZNF192	6	28116192	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	2011987	28116192	142998875	20	76											
CFB	629	bcgsc.ca	37	chr6	31919751	31919751	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	actttcacatcaacctctttCaagtgctgccctggctgaag	9	12	7	13	0	4	1	3	1	1	0	4	1	4	1	2	1	3	2	2	1	3	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:31919751C>G	ENST00000425368.2	+	18	2752	c.2239C>G	c.(2239-2241)Caa>Gaa	p.Q747E	CFB_ENST00000477310.1_Missense_Mutation_p.Q1098E|CFB_ENST00000456570.1_Missense_Mutation_p.Q1249E|CFB_ENST00000556679.1_Missense_Mutation_p.Q1249E	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	747	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						CAACCTCTTTCAAGTGCTGCC	0.502																																					p.Q747E													.	CFB-91	0			c.C2239G						.						268	291	283					6																	31919751		1510	2709	4219	SO:0001583	missense	629	exon18			CTCTTTCAAGTGC	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"Complement system"	1037	protein-coding gene	gene with protein product		138470	"B-factor, properdin"	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.2239C>G	6.37:g.31919751C>G	ENSP00000416561:p.Gln747Glu	Somatic	419	0		WXS	Illumina HiSeq	Phase_1	319	7	NM_001710	0	0	19	19	0	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.65|13.65	2.299415|2.299415	0.40694|0.40694	.|.	.|.	ENSG00000243649|ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000483004|ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310	T|T;T;T;T	0.28666|0.28666	1.6|1.6;1.6;1.6;1.6	5.54|5.54	4.67|4.67	0.58626|0.58626	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	.|0.361824	.|0.24091	.|N	.|0.041637	T|T	0.06142|0.06142	0.0159|0.0159	N|N	0.04335|0.04335	-0.225|-0.225	0.34044|0.34044	D|D	0.655353|0.655353	.|B;B	.|0.30741	.|0.293;0.062	.|B;B	.|0.27076	.|0.076;0.017	T|T	0.09335|0.09335	-1.0679|-1.0679	7|10	0.72032|0.66056	D|D	0.01|0.02	-2.5092|-2.5092	8.9919|8.9919	0.36028|0.36028	0.1615:0.6642:0.1742:0.0|0.1615:0.6642:0.1742:0.0	.|.	.|1249;747	.|B4E1Z4;P00751	.|.;CFAB_HUMAN	L|E	287|1249;747;1249;1098	ENSP00000419887:F287L|ENSP00000451848:Q1249E;ENSP00000416561:Q747E;ENSP00000410815:Q1249E;ENSP00000418996:Q1098E	ENSP00000419887:F287L|ENSP00000416561:Q747E	F|Q	+|+	3|1	2|0	CFB|CFB;XXbac-BPG116M5.17	32027730|32027730	0.962000|0.962000	0.33011|0.33011	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.751000|0.751000	0.26348|0.26348	1.563000|1.563000	0.49615|0.49615	0.655000|0.655000	0.94253|0.94253	TTC|CAA	.		0.502	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		G	31919751	C	G	31919751	3	3	2	1	0	0	0	0	1	0	0	0	3284	827	29	4	2309	4	CFB	6	31919751	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	3803559	31919751	139195316	21	77											
TFEB	7942	ucsc.edu	37	chr6	41658862	41658862	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctgctgcatgtaatgcatGacagcctgttgctgcatgcg	7	12	12	10	1	0	1	0	1	0	0	0	1	0	1	1	0	8	8	1	0	1	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:41658862G>A	ENST00000230323.4	-	3	391	c.90C>T	c.(88-90)gtC>gtT	p.V30V	TFEB_ENST00000420312.1_Silent_p.V30V|TFEB_ENST00000373033.1_Silent_p.V30V|TFEB_ENST00000358871.2_Silent_p.V44V|TFEB_ENST00000403298.4_Silent_p.V30V|TFEB_ENST00000394283.1_Silent_p.V30V	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	30	Gln-rich.				autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TGTAATGCATGACAGCCTGTT	0.657			T	ALPHA	renal (childhood epithelioid)						OREG0004069	type=REGULATORY REGION|Gene=TFEB|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V44V				Dom	yes		6	6p21	7942	transcription factor EB		"E,M"	.	TFEB-659	0			c.C132T						.						18	15	16					6																	41658862		2195	4291	6486	SO:0001819	synonymous_variant	7942	exon2			ATGCATGACAGCC	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"Basic helix-loop-helix proteins"	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.90C>T	6.37:g.41658862G>A		Somatic	16	0	902	WXS	Illumina HiSeq		11	2	NM_001167827	0	0	8	8	0	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																			.		0.657	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3			A	41658862	G	A	41658862	2	1	2	1	0	0	0	0	0	0	0	1	15833	1277	45	2		2	TFEB	6	41658862	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	9739111	41658862	129456205	22	78											
CRISP3	10321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	49696475	49696475	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtttgaacaattgcaggaggCcttgcaactgtccctgacca	10	10	10	11	0	0	2	0	2	0	0	1	3	1	3	3	2	4	3	3	2	3	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:49696475C>T	ENST00000393666.1	-	7	712	c.706G>A	c.(706-708)Gcc>Acc	p.A236T	CRISP3_ENST00000423399.2_Missense_Mutation_p.A146T|CRISP3_ENST00000371159.4_Missense_Mutation_p.A267T|CRISP3_ENST00000263045.4_Missense_Mutation_p.A249T|CRISP3_ENST00000433368.2_Missense_Mutation_p.A259T			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	236	ShKT. {ECO:0000255|PROSITE- ProRule:PRU01005}.				defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			TTGCAGGAGGCCTTGCAACTG	0.403																																					p.A259T		.											.	CRISP3-92	0			c.G775A						.						188	169	175					6																	49696475		2203	4300	6503	SO:0001583	missense	10321	exon8			AGGAGGCCTTGCA	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.706G>A	6.37:g.49696475C>T	ENSP00000377274:p.Ala236Thr	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	120	38	NM_001190986	0	0	17	41	24	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		.	.	.	.	.	.	.	.	.	.	C	17.52	3.410104	0.62399	.	.	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159	T;T;T;T;T	0.16073	2.88;2.87;2.9;2.37;2.87	4.55	4.55	0.56014	Cysteine-rich secretory protein (1);	0.089556	0.44285	U	0.000474	T	0.21921	0.0528	M	0.83483	2.645	0.30644	N	0.756123	D	0.60575	0.988	P	0.50590	0.645	T	0.06180	-1.0841	10	0.72032	D	0.01	.	13.1387	0.59423	0.0:1.0:0.0:0.0	.	236	P54108	CRIS3_HUMAN	T	249;259;236;146;267	ENSP00000263045:A249T;ENSP00000389026:A259T;ENSP00000377274:A236T;ENSP00000410469:A146T;ENSP00000360201:A267T	ENSP00000263045:A249T	A	-	1	0	CRISP3	49804434	0.287000	0.24315	0.827000	0.32855	0.121000	0.20230	1.129000	0.31381	2.236000	0.73375	0.609000	0.83330	GCC	.		0.403	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061		T	49696475	C	T	49696475	3	4	2	1	0	0	0	0	1	0	0	0	3887	739	26	2	35	2	CRISP3	6	49696475	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	8037613	49696475	121418592	23	79											
COL9A1	1297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	70990561	70990561	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggagctcctggctttcccGgttcacctgcaggaccctga	5	10	11	15	1	1	1	1	1	0	0	3	3	3	3	4	4	2	4	4	4	0	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:70990561G>A	ENST00000357250.6	-	10	1087	c.929C>T	c.(928-930)cCg>cTg	p.P310L	COL9A1_ENST00000370499.4_Missense_Mutation_p.P67L|COL9A1_ENST00000320755.7_Missense_Mutation_p.P67L|COL9A1_ENST00000370496.3_Missense_Mutation_p.P310L|COL9A1_ENST00000489611.1_5'Flank	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	310	Collagen-like 1.|Triple-helical region (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						TGGCTTTCCCGGTTCACCTGC	0.627																																					p.P310L		.											.	COL9A1-94	0			c.C929T						.						18	19	19					6																	70990561		2203	4300	6503	SO:0001583	missense	1297	exon10			TTTCCCGGTTCAC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.929C>T	6.37:g.70990561G>A	ENSP00000349790:p.Pro310Leu	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	28	9	NM_001851	0	0	0	0	0	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.410959	0.25465	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499;ENST00000370496	D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.28	5.6	4.72	0.59763	.	0.325795	0.37012	N	0.002296	D	0.90435	0.7005	M	0.84846	2.72	0.46981	D	0.999279	P;P	0.44429	0.835;0.516	B;B	0.38327	0.271;0.135	D	0.89481	0.3750	10	0.30854	T	0.27	.	15.4859	0.75569	0.0:0.139:0.861:0.0	.	310;67	P20849;P20849-2	CO9A1_HUMAN;.	L	310;67;67;310	ENSP00000349790:P310L;ENSP00000315252:P67L;ENSP00000359530:P67L;ENSP00000359527:P310L	ENSP00000315252:P67L	P	-	2	0	COL9A1	71047282	0.999000	0.42202	0.747000	0.31113	0.002000	0.02628	4.673000	0.61604	1.347000	0.45714	0.563000	0.77884	CCG	.		0.627	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	70990561	G	A	70990561	3	1	2	1	0	0	0	0	1	0	0	0	3713	1116	39	1	1952	1	COL9A1	6	70990561	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	21294086	70990561	100124506	24	80											
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76660465	76660465	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acaggagtggtatcctccaaGaaatgatctgggacagaaac	15	7	11	8	0	1	3	0	1	1	2	3	5	3	5	2	3	1	1	2	3	4	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660465G>C	ENST00000369950.3	-	13	1827	c.1638C>G	c.(1636-1638)ttC>ttG	p.F546L	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TATCCTCCAAGAAATGATCTG	0.483																																					p.F546L	Pancreas(37;839 1141 2599 26037)	.											.	IMPG1-93	0			c.C1638G						.						93	79	84					6																	76660465		2203	4300	6503	SO:0001583	missense	3617	exon13			CTCCAAGAAATGA	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1638C>G	6.37:g.76660465G>C	ENSP00000358966:p.Phe546Leu	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	63	15	NM_001563	0	0	0	0	0		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	9.188	1.025421	0.19512	.	.	ENSG00000112706	ENST00000369950	T	0.19532	2.14	5.67	0.817	0.18773	.	0.942898	0.08930	N	0.873167	T	0.08223	0.0205	M	0.73598	2.24	0.09310	N	1	B	0.26258	0.145	B	0.20955	0.032	T	0.42292	-0.9460	10	0.15066	T	0.55	.	8.972	0.35912	0.39:0.0:0.61:0.0	.	546	Q17R60	IMPG1_HUMAN	L	546	ENSP00000358966:F546L	ENSP00000358966:F546L	F	-	3	2	IMPG1	76717185	0.000000	0.05858	0.026000	0.17262	0.005000	0.04900	-0.651000	0.05372	0.055000	0.16094	-0.142000	0.14014	TTC	.		0.483	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		C	76660465	G	C	76660465	3	2	2	1	0	0	0	0	1	0	0	0	7749	933	33	4	775	4	IMPG1	6	76660465	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	5669904	76660465	94454602	25	81			1	2		4	3	172	N	G	6.211013e-08
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76660529	76660529	+	Missense_Mutation	SNP	G	G	A																															cagatggggcaggagtgtcaGacagatccatttcatctagg																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660529G>A	ENST00000369950.3	-	13	1763	c.1574C>T	c.(1573-1575)tCt>tTt	p.S525F	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				AGGAGTGTCAGACAGATCCAT	0.488																																					p.S525F	Pancreas(37;839 1141 2599 26037)	.											.	IMPG1-93	0			c.C1574T						.						97	80	86					6																	76660529		2203	4300	6503	SO:0001583	missense	3617	exon13			GTGTCAGACAGAT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1574C>T	6.37:g.76660529G>A	ENSP00000358966:p.Ser525Phe	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	40	9	NM_001563	0	0	0	0	0		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.206277	0.39003	.	.	ENSG00000112706	ENST00000369950	T	0.21031	2.03	4.94	2.19	0.27852	.	1.695600	0.02971	N	0.144359	T	0.07954	0.0199	L	0.38175	1.15	0.09310	N	0.999999	P	0.46706	0.883	B	0.44044	0.439	T	0.13361	-1.0512	10	0.39692	T	0.17	.	4.5254	0.11980	0.435:0.0:0.4185:0.1465	.	525	Q17R60	IMPG1_HUMAN	F	525	ENSP00000358966:S525F	ENSP00000358966:S525F	S	-	2	0	IMPG1	76717249	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.632000	0.24583	0.339000	0.23719	0.650000	0.86243	TCT	.		0.488	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76660529	G	A	76660529	3	1	2	1	0	0	0	0	1	0	0	0	7749	942	33	2	839	2	IMPG1	6	76660529	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	64	76660529	94454538	26	82	1	2	1	2		4	3	172	N	G	6.211013e-08
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76660533	76660533	+	Silent	SNP	G	G	A																															tggggcaggagtgtcagacaGatccatttcatctaggtgtc																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660533G>A	ENST00000369950.3	-	13	1759	c.1570C>T	c.(1570-1572)Ctg>Ttg	p.L524L	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GTGTCAGACAGATCCATTTCA	0.493																																					p.L524L	Pancreas(37;839 1141 2599 26037)	.											.	IMPG1-93	0			c.C1570T						.						99	82	88					6																	76660533		2203	4300	6503	SO:0001819	synonymous_variant	3617	exon13			CAGACAGATCCAT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1570C>T	6.37:g.76660533G>A		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	39	10	NM_001563	0	0	0	0	0		Silent	SNP	ENST00000369950.3	37	CCDS4985.1																																																																																			.		0.493	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76660533	G	A	76660533	2	1	2	1	0	0	0	0	0	0	0	1	7749	933	33	2		2	IMPG1	6	76660533	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	4	76660533	94454534	27	83	1	2	1	2		4	3	172	N	G	6.211013e-08
IMPG1	3617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76660636	76660636	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attcccagagccagttggctGattgcagaataatcactggt	11	11	10	9	0	1	3	1	1	0	2	2	3	2	3	2	2	2	3	2	2	2	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660636G>A	ENST00000369950.3	-	13	1656	c.1467C>T	c.(1465-1467)atC>atT	p.I489I	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				CCAGTTGGCTGATTGCAGAAT	0.498																																					p.I489I	Pancreas(37;839 1141 2599 26037)	.											.	IMPG1-93	0			c.C1467T						.						159	151	153					6																	76660636		2203	4300	6503	SO:0001819	synonymous_variant	3617	exon13			TTGGCTGATTGCA	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.1467C>T	6.37:g.76660636G>A		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	78	20	NM_001563	0	0	0	0	0		Silent	SNP	ENST00000369950.3	37	CCDS4985.1																																																																																			.		0.498	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76660636	G	A	76660636	2	1	2	1	0	0	0	0	0	0	0	1	7749	1280	45	2		2	IMPG1	6	76660636	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	103	76660636	94454431	28	84			1	2		4	3	172	N	G	6.211013e-08
LAMA4	3910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	112454683	112454683	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctaggggaaggtgtgctctGagggccctggaaaagaaagt	11	8	16	6	0	2	2	0	1	2	1	2	4	2	4	1	5	1	1	1	5	5	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:112454683G>C	ENST00000230538.7	-	27	3961	c.3564C>G	c.(3562-3564)ctC>ctG	p.L1188L	LAMA4_ENST00000522006.1_Silent_p.L1181L|LAMA4_ENST00000389463.4_Silent_p.L1181L|LAMA4_ENST00000424408.2_Silent_p.L1181L	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1188	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GGTGTGCTCTGAGGGCCCTGG	0.438																																					p.L1188L		.											.	LAMA4-140	0			c.C3564G						.						101	96	97					6																	112454683		2203	4300	6503	SO:0001819	synonymous_variant	3910	exon27			TGCTCTGAGGGCC		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.3564C>G	6.37:g.112454683G>C		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	119	29	NM_001105206	0	0	0	0	0	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			.		0.438	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		C	112454683	G	C	112454683	2	2	2	1	0	0	0	0	0	0	0	1	8629	1277	45	4		4	LAMA4	6	112454683	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	35794047	112454683	58660384	29	85											
MSRA	4482	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	9912062	9912062	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cggagggcttgccagctcctCctcctccacagcctctttcc	4	10	8	19	1	1	0	0	0	1	0	6	1	6	1	7	2	3	2	7	2	0	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:9912062C>T	ENST00000317173.4	+	1	285	c.36C>T	c.(34-36)ctC>ctT	p.L12L	MSRA_ENST00000441698.2_Silent_p.L12L|RP11-1E4.1_ENST00000562143.1_RNA|MSRA_ENST00000518255.1_Silent_p.L12L	NM_012331.3	NP_036463.1	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A	12				Missing (in Ref. 6; AAG09689). {ECO:0000305}.	cellular protein modification process (GO:0006464)|methionine metabolic process (GO:0006555)|protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptide-methionine (S)-S-oxide reductase activity (GO:0008113)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(4)	8		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	GCCAGCTCCTCCTCCTCCACA	0.716																																					p.L12L	NSCLC(88;1378 1469 30580 49103 52286)	.											.	MSRA-90	0			c.C36T						.						36	35	36					8																	9912062		2203	4300	6503	SO:0001819	synonymous_variant	4482	exon1			GCTCCTCCTCCTC	BC054033	CCDS5975.1, CCDS47798.1, CCDS47799.1, CCDS56522.1	8p23.1	2009-07-10			ENSG00000175806	ENSG00000175806	1.8.4.11		7377	protein-coding gene	gene with protein product		601250				10452521	Standard	NM_012331		Approved		uc003wsx.3	Q9UJ68	OTTHUMG00000090517	ENST00000317173.4:c.36C>T	8.37:g.9912062C>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	43	16	NM_012331	0	0	8	8	0	E9PAS8|Q52TC4|Q549N4|Q66MI7	Silent	SNP	ENST00000317173.4	37	CCDS5975.1																																																																																			.		0.716	MSRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207005.1	NM_012331		T	9912062	C	T	9912062	2	4	2	1	0	0	0	0	0	0	0	1	9912	842	30	2		2	MSRA	8	9912062	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08		9912062	136451960	30	86			2	3		2	2	42	C		8.475985e-05
MSRA	4482	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	9912103	9912103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgtcccgaggatgggcaactCggcctcgaacatcgtcagcc	8	6	12	15	5	1	0	1	0	0	0	5	3	2	1	3	3	3	1	3	3	2	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:9912103C>T	ENST00000317173.4	+	1	326	c.77C>T	c.(76-78)tCg>tTg	p.S26L	MSRA_ENST00000441698.2_Missense_Mutation_p.S26L|RP11-1E4.1_ENST00000562143.1_RNA|MSRA_ENST00000518255.1_Missense_Mutation_p.S26L	NM_012331.3	NP_036463.1	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A	26					cellular protein modification process (GO:0006464)|methionine metabolic process (GO:0006555)|protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptide-methionine (S)-S-oxide reductase activity (GO:0008113)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(4)	8		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	ATGGGCAACTCGGCCTCGAAC	0.697																																					p.S26L	NSCLC(88;1378 1469 30580 49103 52286)	.											.	MSRA-90	0			c.C77T						.						38	37	37					8																	9912103		2203	4300	6503	SO:0001583	missense	4482	exon1			GCAACTCGGCCTC	BC054033	CCDS5975.1, CCDS47798.1, CCDS47799.1, CCDS56522.1	8p23.1	2009-07-10			ENSG00000175806	ENSG00000175806	1.8.4.11		7377	protein-coding gene	gene with protein product		601250				10452521	Standard	NM_012331		Approved		uc003wsx.3	Q9UJ68	OTTHUMG00000090517	ENST00000317173.4:c.77C>T	8.37:g.9912103C>T	ENSP00000313921:p.Ser26Leu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	51	15	NM_012331	0	0	9	10	1	E9PAS8|Q52TC4|Q549N4|Q66MI7	Missense_Mutation	SNP	ENST00000317173.4	37	CCDS5975.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622922	0.28889	.	.	ENSG00000175806	ENST00000317173;ENST00000441698;ENST00000518255	.	.	.	4.84	3.94	0.45596	.	0.300238	0.32015	N	0.006711	T	0.34629	0.0904	L	0.42245	1.32	0.34862	D	0.74275	D;B	0.53885	0.963;0.249	B;B	0.37601	0.254;0.036	T	0.50039	-0.8874	8	.	.	.	0.3672	10.6214	0.45483	0.1922:0.8078:0.0:0.0	.	26;26	Q9UJ68-4;Q9UJ68	.;MSRA_HUMAN	L	26	.	.	S	+	2	0	MSRA	9949513	0.147000	0.22687	0.178000	0.23040	0.019000	0.09904	1.820000	0.39032	1.113000	0.41760	0.313000	0.20887	TCG	.		0.697	MSRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207005.1	NM_012331		T	9912103	C	T	9912103	3	4	2	1	0	0	0	0	1	0	0	0	9912	893	31	1	79	1	MSRA	8	9912103	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	41	9912103	136451919	31	87			2	3		2	2	42	C		8.475985e-05
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	37730588	37730589	+	Frame_Shift_Ins	INS	-	-	G																															gcaccatgtcccaattcagaINSggggacagatgcctggccag																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:37730588_37730589insG	ENST00000330843.4	-	4	1743_1744	c.1731_1732insC	c.(1729-1734)ccctctfs	p.S578fs	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)	578	Ser-rich.				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)			CCCAATTCAGAGGGGACAGATG	0.559																																					p.S578fs		.											.	RAB11FIP1-92	0			c.1732_1733insC						.																																			SO:0001589	frameshift_variant	80223	exon4			.	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.1732dupC	8.37:g.37730592_37730592dupG	ENSP00000331342:p.Ser578fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	77	26	NM_001002814	0	0	0	0	0	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Frame_Shift_Ins	INS	ENST00000330843.4	37	CCDS34882.1																																																																																			.		0.559	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		G	37730589	-	G	37730588	7	5	2	1	0	1	1	0	0	0	0	0	12925	304	11	0	2131	0	RAB11FIP1	8	37730588	Frame_Shift_Ins	INS	-	TCGA-A4-7287-01A-11D-2136-08	27818485	37730588	108633434	32	88											
ZNF189	7743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	104170234	104170234	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttttgaacagagataaggatGaggagccaactgtaaaacaa	18	8	10	5	0	0	3	0	2	0	1	0	6	0	5	1	2	4	1	1	2	6	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:104170234G>C	ENST00000339664.2	+	3	313	c.184G>C	c.(184-186)Gag>Cag	p.E62Q	ZNF189_ENST00000259395.4_Missense_Mutation_p.E20Q|ZNF189_ENST00000374861.3_Missense_Mutation_p.E48Q	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	62	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				AGATAAGGATGAGGAGCCAAC	0.368																																					p.E62Q		.											.	ZNF189-229	0			c.G184C						.						58	60	60					9																	104170234		2202	4300	6502	SO:0001583	missense	7743	exon3			AAGGATGAGGAGC	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"Zinc fingers, C2H2-type", "-"	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.184G>C	9.37:g.104170234G>C	ENSP00000342019:p.Glu62Gln	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_003452	0	0	2	3	1	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	G	5.540	0.284544	0.10513	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.05580	5.66;5.66;3.42	4.79	4.79	0.61399	Krueppel-associated box (3);	0.000000	0.49916	D	0.000140	T	0.03220	0.0094	N	0.16201	0.385	0.34306	D	0.684889	B;B;B	0.33073	0.396;0.396;0.006	B;B;B	0.26864	0.074;0.074;0.011	T	0.43261	-0.9402	10	0.14252	T	0.57	.	9.2106	0.37316	0.0942:0.0:0.9058:0.0	.	47;48;62	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	Q	48;62;20	ENSP00000363995:E48Q;ENSP00000342019:E62Q;ENSP00000259395:E20Q	ENSP00000259395:E20Q	E	+	1	0	ZNF189	103210055	0.191000	0.23288	1.000000	0.80357	0.895000	0.52256	0.622000	0.24433	2.941000	0.99782	0.655000	0.94253	GAG	.		0.368	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		C	104170234	G	C	104170234	3	2	2	1	0	0	0	0	1	0	0	0	17786	1291	45	4	194	4	ZNF189	9	104170234	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		104170234	37043197	33	89											
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114148697	114148697	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catattgcttgtaaggttctTaaccaaatcttgaagaattt	13	16	6	6	0	2	2	0	1	2	1	2	2	2	2	1	1	2	3	1	1	6	8			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:114148697T>C	ENST00000338205.5	-	31	3706	c.3487A>G	c.(3487-3489)Aag>Gag	p.K1163E	KIAA0368_ENST00000374378.3_5'UTR|KIAA0368_ENST00000259335.4_Missense_Mutation_p.K1341E			Q5VYK3	ECM29_HUMAN	KIAA0368	1169					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GTAAGGTTCTTAACCAAATCT	0.284																																					p.K1341E		.											.	KIAA0368-68	0			c.A4021G						.						53	50	51					9																	114148697		1805	4075	5880	SO:0001583	missense	23392	exon33			GGTTCTTAACCAA	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.3487A>G	9.37:g.114148697T>C	ENSP00000339889:p.Lys1163Glu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_001080398	0	0	13	13	0	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	T	7.860	0.725839	0.15439	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.65732	-0.17	6.02	6.02	0.97574	.	0.222920	0.47093	D	0.000258	T	0.47544	0.1451	N	0.20401	0.57	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.42396	-0.9454	10	0.13108	T	0.6	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	638	B3KXF2	.	E	1163;1341;638	ENSP00000259335:K1341E	ENSP00000259335:K1341E	K	-	1	0	KIAA0368	113188518	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.127000	0.50484	2.299000	0.77371	0.528000	0.53228	AAG	.		0.284	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		C	114148697	T	C	114148697	3	2	2	1	0	0	0	0	1	0	0	0	8192	1763	61	3	2108	3	KIAA0368	9	114148697	Missense_Mutation	SNP	T	TCGA-A4-7287-01A-11D-2136-08	9978463	114148697	27064734	34	90											
TSC1	7248	broad.mit.edu;bcgsc.ca	37	chr9	135796822	135796826	+	Splice_Site	DEL	GGCTA	GGCTA	-																															ttcgcacatgctccatcattGgctagaagagttgggttgac																								rs118203425|rs118203423		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GGCTA	GGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:135796822_135796826delGGCTA	ENST00000298552.3	-	8	885_886	c.664_665delTAGCC	c.(664-666)tag>g	p.*222fs	TSC1_ENST00000403810.1_Splice_Site_p.*222fs|TSC1_ENST00000475903.1_5'Flank|TSC1_ENST00000440111.2_Splice_Site_p.*222fs|TSC1_ENST00000545250.1_Splice_Site_p.*171fs	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	222					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CTCCATCATTGGCTAGAAGAGTTGG	0.376			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.222_222del			yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1-1906	1	Unknown(1)	bone(1)	c.664_665del						.																																			SO:0001630	splice_region_variant	7248	exon8	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ATCATTGGCTAGA	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.664-1TAGCC>-	9.37:g.135796822_135796826delGGCTA		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	31	8	NM_000368	0	0	0	0	0	B7Z897|Q5VVN5	Frame_Shift_Del	DEL	ENST00000298552.3	37	CCDS6956.1																																																																																			.		0.376	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		Frame_Shift_Del	-	135796826	GGCTA	-	135796822	8	5	2	1	0	1	0	1	0	0	1	0	16638	1362	47	0	2893	0	TSC1	9	135796822	Splice_Site	DEL	GGCTA	TCGA-A4-7287-01A-11D-2136-08	21648125	135796822	5416609	35	91											
ITGB1	3688	hgsc.bcm.edu	37	chr10	33212557	33212557	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attattttccaggtgacattGtccatcatttggtaaaacaa	13	15	6	7	0	1	1	1	1	0	0	3	1	3	1	2	2	1	1	2	2	4	6			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr10:33212557G>C	ENST00000396033.2	-	7	1033	c.898C>G	c.(898-900)Caa>Gaa	p.Q300E	ITGB1_ENST00000302278.3_Missense_Mutation_p.Q300E|ITGB1_ENST00000374956.4_Missense_Mutation_p.Q300E|ITGB1_ENST00000423113.1_Missense_Mutation_p.Q300E|ITGB1_ENST00000484088.1_5'Flank	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	300	VWFA.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	AGGTGACATTGTCCATCATTT	0.398																																					p.Q300E		.											.	ITGB1-1084	0			c.C898G						.						86	74	78					10																	33212557		2203	4300	6503	SO:0001583	missense	3688	exon7			GACATTGTCCATC	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.898C>G	10.37:g.33212557G>C	ENSP00000379350:p.Gln300Glu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_002211	0	0	136	136	0	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Missense_Mutation	SNP	ENST00000396033.2	37	CCDS7174.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.086740	0.36855	.	.	ENSG00000150093	ENST00000396033;ENST00000423113;ENST00000302278;ENST00000374956	D;D;D;D	0.92397	-3.03;-3.03;-3.03;-3.03	5.57	5.57	0.84162	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.244954	0.42548	D	0.000686	D	0.82490	0.5048	N	0.08118	0	0.23727	N	0.997003	B;B;B;B;B	0.25312	0.0;0.0;0.0;0.123;0.001	B;B;B;B;B	0.26969	0.001;0.001;0.001;0.075;0.001	T	0.67185	-0.5734	10	0.15952	T	0.53	.	13.5534	0.61745	0.0:0.0:0.7397:0.2603	.	300;300;300;300;300	P05556-2;P05556;P05556-5;P05556-3;P05556-4	.;ITB1_HUMAN;.;.;.	E	300	ENSP00000379350:Q300E;ENSP00000388694:Q300E;ENSP00000303351:Q300E;ENSP00000364094:Q300E	ENSP00000303351:Q300E	Q	-	1	0	ITGB1	33252563	0.937000	0.31787	0.968000	0.41197	0.781000	0.44180	3.946000	0.56644	2.641000	0.89580	0.655000	0.94253	CAA	.		0.398	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		C	33212557	G	C	33212557	3	2	2	1	0	0	0	0	1	0	0	0	7911	1386	48	4	1776	4	ITGB1	10	33212557	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		33212557	102322190	36	92											
EXOC6	54536	hgsc.bcm.edu	37	chr10	94700514	94700514	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttccagtgaaccgactttttGaccttttatttgaaataaga	12	16	6	7	1	0	4	0	3	0	1	1	5	1	4	3	0	1	0	3	0	4	7			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr10:94700514G>C	ENST00000260762.6	+	13	1257	c.1243G>C	c.(1243-1245)Gac>Cac	p.D415H	EXOC6_ENST00000371547.4_Missense_Mutation_p.D431H|EXOC6_ENST00000371552.4_Missense_Mutation_p.D410H|EXOC6_ENST00000443748.2_Missense_Mutation_p.D312H	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	415					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				CCGACTTTTTGACCTTTTATT	0.303																																					p.D415H		.											.	EXOC6-91	0			c.G1243C						.						79	80	80					10																	94700514		2203	4299	6502	SO:0001583	missense	54536	exon13			CTTTTTGACCTTT	BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"SEC15-like 1 (S. cerevisiae)"	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.1243G>C	10.37:g.94700514G>C	ENSP00000260762:p.Asp415His	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	48	3	NM_019053	0	0	6	6	0	E9PHI3|Q5VXH8|Q9NZ24	Missense_Mutation	SNP	ENST00000260762.6	37	CCDS7424.2	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795381	0.90453	.	.	ENSG00000138190	ENST00000371547;ENST00000371552;ENST00000443748;ENST00000260762	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	6.07	6.07	0.98685	.	0.101356	0.64402	D	0.000001	T	0.63379	0.2506	M	0.85542	2.76	0.80722	D	1	D;D;D;D;D	0.89917	0.994;1.0;0.994;0.994;0.994	P;D;P;P;P	0.72075	0.873;0.976;0.873;0.873;0.873	T	0.66052	-0.6019	10	0.87932	D	0	-12.8758	20.6593	0.99626	0.0:0.0:1.0:0.0	.	431;312;407;415;410	F2Z2Q3;E7EW84;B4DEZ1;Q8TAG9;E9PHI3	.;.;.;EXOC6_HUMAN;.	H	431;410;312;415	ENSP00000360602:D431H;ENSP00000360607:D410H;ENSP00000396206:D312H;ENSP00000260762:D415H	ENSP00000260762:D415H	D	+	1	0	EXOC6	94690494	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.837000	0.99465	2.885000	0.99019	0.655000	0.94253	GAC	.		0.303	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053		C	94700514	G	C	94700514	3	2	2	1	0	0	0	0	1	0	0	0	5321	1290	45	4	1383	4	EXOC6	10	94700514	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	61487957	94700514	40834233	37	93											
OR10Q1	219960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57996225	57996225	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgtgttgccacagaggatCatcaagtagaggaggaggaa	13	7	15	6	0	2	2	2	0	0	2	2	6	2	6	1	4	1	3	1	4	3	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr11:57996225C>T	ENST00000316770.2	-	1	165	c.123G>A	c.(121-123)atG>atA	p.M41I		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	41						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)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CACAGAGGATCATCAAGTAGA	0.527																																					p.M41I		.											.	OR10Q1-70	0			c.G123A						.						114	122	119					11																	57996225		2200	4294	6494	SO:0001583	missense	219960	exon1			GAGGATCATCAAG	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"GPCR / Class A : Olfactory receptors"	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.123G>A	11.37:g.57996225C>T	ENSP00000314324:p.Met41Ile	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	106	28	NM_001004471	0	0	0	0	0	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	.	.	.	.	.	.	.	.	.	.	C	8.116	0.779975	0.16120	.	.	ENSG00000180475	ENST00000316770	T	0.00392	7.58	5.28	2.25	0.28309	.	0.123417	0.36555	N	0.002525	T	0.00178	0.0005	N	0.13168	0.305	0.09310	N	1	B	0.34181	0.44	B	0.30646	0.118	T	0.31558	-0.9939	10	0.10377	T	0.69	.	11.4267	0.50015	0.136:0.3334:0.5306:0.0	.	41	Q8NGQ4	O10Q1_HUMAN	I	41	ENSP00000314324:M41I	ENSP00000314324:M41I	M	-	3	0	OR10Q1	57752801	0.000000	0.05858	0.013000	0.15412	0.626000	0.37791	-0.168000	0.09925	0.305000	0.22832	0.650000	0.86243	ATG	.		0.527	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471		T	57996225	C	T	57996225	3	4	2	1	0	0	0	0	1	0	0	0	10942	826	29	2	840	2	OR10Q1	11	57996225	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		57996225	77010291	38	94											
PDGFD	80310	hgsc.bcm.edu	37	chr11	103797648	103797648	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaatgacatacctcatgatActttttcacggttttccctg	10	15	6	10	1	2	3	2	2	0	1	3	3	3	3	2	1	2	1	2	1	3	6			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr11:103797648A>T	ENST00000393158.2	-	6	1158	c.979T>A	c.(979-981)Tat>Aat	p.Y327N	PDGFD_ENST00000302251.5_Missense_Mutation_p.Y321N			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	327					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		ACCTCATGATACTTTTTCACG	0.458																																					p.Y327N		.											.	PDGFD-723	0			c.T979A						.						84	68	73					11																	103797648		2202	4299	6501	SO:0001583	missense	80310	exon6			CATGATACTTTTT	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"spinal cord derived growth factor B"	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.979T>A	11.37:g.103797648A>T	ENSP00000376865:p.Tyr327Asn	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	17	2	NM_025208	0	0	0	0	0	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	37	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.393299	0.83011	.	.	ENSG00000170962	ENST00000393158;ENST00000302251	T;T	0.29142	1.58;1.58	5.88	5.88	0.94601	Platelet-derived growth factor (PDGF) (3);	0.201547	0.45361	D	0.000370	T	0.50871	0.1641	M	0.66939	2.045	0.46113	D	0.998875	D;D	0.57257	0.979;0.974	P;P	0.58331	0.837;0.748	T	0.53528	-0.8426	10	0.87932	D	0	-24.9983	16.2879	0.82732	1.0:0.0:0.0:0.0	.	327;321	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	N	327;321	ENSP00000376865:Y327N;ENSP00000302193:Y321N	ENSP00000302193:Y321N	Y	-	1	0	PDGFD	103302858	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.025000	0.76449	2.242000	0.73789	0.533000	0.62120	TAT	.		0.458	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208		T	103797648	A	T	103797648	3	4	2	1	0	0	0	0	1	0	0	0	11686	391	14	5	141	5	PDGFD	11	103797648	Missense_Mutation	SNP	A	TCGA-A4-7287-01A-11D-2136-08	45801423	103797648	31208868	39	95											
PFDN5	5204	hgsc.bcm.edu	37	chr12	53689653	53689653	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcttgtccacgtccattgctCagctcaaagtggtacagacc	9	11	8	13	1	3	1	2	0	1	1	5	1	5	1	3	1	3	3	3	1	2	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:53689653C>G	ENST00000551018.1	+	2	380	c.103C>G	c.(103-105)Cag>Gag	p.Q35E	PFDN5_ENST00000334478.4_Missense_Mutation_p.Q35E|PFDN5_ENST00000351500.3_Intron|PFDN5_ENST00000550846.1_Intron|RP11-680A11.5_ENST00000550263.1_RNA	NM_002624.3	NP_002615.2	Q99471	PFD5_HUMAN	prefoldin subunit 5	35					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	transcription corepressor activity (GO:0003714)			kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)	8						GTCCATTGCTCAGCTCAAAGT	0.572																																					p.Q35E		.											.	PFDN5-227	0			c.C103G						.						103	86	92					12																	53689653		2203	4300	6503	SO:0001583	missense	5204	exon2			ATTGCTCAGCTCA	D89667	CCDS8853.1, CCDS8854.1	12q13.13	2008-05-14	2006-02-24						8869	protein-coding gene	gene with protein product		604899	"prefoldin 5"			9630229, 9792694	Standard	NM_002624		Approved	PFD5, MM-1	uc001scl.3	Q99471	OTTHUMG00000169675	ENST00000551018.1:c.103C>G	12.37:g.53689653C>G	ENSP00000447942:p.Gln35Glu	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_002624	0	0	571	571	0	A8K9A8|Q54AA8|Q9C083|Q9C084	Missense_Mutation	SNP	ENST00000551018.1	37	CCDS8853.1	.	.	.	.	.	.	.	.	.	.	C	33	5.198192	0.94997	.	.	ENSG00000123349	ENST00000551018;ENST00000334478	T;T	0.42513	0.97;0.97	5.73	5.73	0.89815	Prefoldin (1);Prefoldin subunit (1);	0.000000	0.85682	D	0.000000	T	0.57858	0.2082	M	0.72576	2.205	0.80722	D	1	P	0.48162	0.906	P	0.52343	0.696	T	0.59273	-0.7485	10	0.66056	D	0.02	.	17.7778	0.88515	0.0:1.0:0.0:0.0	.	35	Q99471	PFD5_HUMAN	E	35	ENSP00000447942:Q35E;ENSP00000334188:Q35E	ENSP00000243040:Q35E	Q	+	1	0	PFDN5	51975920	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.970000	0.76099	2.882000	0.98803	0.655000	0.94253	CAG	.		0.572	PFDN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405368.2			G	53689653	C	G	53689653	3	3	2	1	0	0	0	0	1	0	0	0	11784	827	29	4	109	4	PFDN5	12	53689653	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		53689653	80162242	40	96											
ZNF385A	25946	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54764720	54764720	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttagacccacctgtttcagTtggacctccgagttgacctt	7	13	8	13	1	1	2	1	1	0	1	2	4	2	3	5	1	0	3	5	1	1	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:54764720T>C	ENST00000338010.5	-	6	878	c.825A>G	c.(823-825)caA>caG	p.Q275Q	ZNF385A_ENST00000551109.1_Silent_p.Q255Q|ZNF385A_ENST00000551771.1_Silent_p.Q174Q|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA|ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000352268.6_Silent_p.Q194Q|ZNF385A_ENST00000394313.2_Silent_p.Q255Q|ZNF385A_ENST00000546970.1_Silent_p.Q255Q	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	275	Necessary for binding to ITPR1, CEBPA and p53/TP53 mRNAs. {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						CCTGTTTCAGTTGGACCTCCG	0.597											OREG0021894	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q275Q		.											.	ZNF385A-23	0			c.A825G						.						89	96	94					12																	54764720		2203	4300	6503	SO:0001819	synonymous_variant	25946	exon6			TTTCAGTTGGACC	AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"zinc finger protein 385"	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.825A>G	12.37:g.54764720T>C		Somatic	217	0	1002	WXS	Illumina HiSeq	Phase_I	122	34	NM_001130967	0	0	1	2	1	B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Silent	SNP	ENST00000338010.5	37	CCDS44911.1																																																																																			.		0.597	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1	NM_015481		C	54764720	T	C	54764720	2	2	2	1	0	0	0	0	0	0	0	1	17908	1722	60	3		3	ZNF385A	12	54764720	Silent	SNP	T	TCGA-A4-7287-01A-11D-2136-08	1075067	54764720	79087175	41	97											
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76424937	76424937	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgctgctgTtgctgctgctgctgctggtg	0	15	15	11	0	0	0	0	0	0	0	0	0	0	0	0	1	11	12	0	1	0	1	rs111754051|rs398020175|rs71716769|rs57875368|rs76176478	byFrequency	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:76424937T>C	ENST00000266671.5	-	1	2775	c.585A>G	c.(583-585)caA>caG	p.Q195Q	RP11-290L1.3_ENST00000552367.1_RNA|RP11-290L1.2_ENST00000547721.1_RNA|PHLDA1_ENST00000602540.1_Silent_p.Q54Q			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	195	PH.|Poly-Gln.				apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				gctgctgctgttgctgctgct	0.652																																					p.Q195Q		.											.	PHLDA1-90	0			c.A585G						.																																			SO:0001819	synonymous_variant	22822	exon1			CTGCTGTTGCTGC	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.585A>G	12.37:g.76424937T>C		Somatic	51	1		WXS	Illumina HiSeq	Phase_I	33	3	NM_007350	1	6	91	8204	8106	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Silent	SNP	ENST00000266671.5	37	CCDS31861.1																																																																																			.		0.652	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		C	76424937	T	C	76424937	2	2	2	1	0	0	0	0	0	0	0	1	11874	1722	60	3		3	PHLDA1	12	76424937	Silent	SNP	T	TCGA-A4-7287-01A-11D-2136-08	21660217	76424937	57426958	42	98											
C12orf74	338809	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	93100691	93100691	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gccaggaagcccaaaggattCttcacacttgctgtcaccct	10	9	8	14	0	3	0	2	0	1	0	3	2	3	2	3	2	2	1	3	2	2	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:93100691C>G	ENST00000397833.3	+	2	735	c.284C>G	c.(283-285)tCt>tGt	p.S95C	C12orf74_ENST00000544406.2_Missense_Mutation_p.S95C	NM_001037671.3|NM_001178097.2	NP_001032760.1|NP_001171568.1	Q32Q52	CL074_HUMAN	chromosome 12 open reading frame 74	95										kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	10						CCAAAGGATTCTTCACACTTG	0.582																																					p.S95C		.											.	C12orf74-90	0			c.C284G						.						55	59	58					12																	93100691		1914	4126	6040	SO:0001583	missense	338809	exon2			AGGATTCTTCACA	BC043363	CCDS41819.1, CCDS53818.1	12q22	2012-08-16			ENSG00000214215	ENSG00000214215			27887	protein-coding gene	gene with protein product						12477932	Standard	NM_001037671		Approved		uc001tch.2	Q32Q52	OTTHUMG00000170105	ENST00000397833.3:c.284C>G	12.37:g.93100691C>G	ENSP00000380933:p.Ser95Cys	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	87	23	NM_001037671	0	0	0	0	0	F5H4P0	Missense_Mutation	SNP	ENST00000397833.3	37	CCDS41819.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525193	0.27299	.	.	ENSG00000214215	ENST00000397833;ENST00000544406	.	.	.	4.98	0.507	0.16967	.	.	.	.	.	T	0.24314	0.0589	N	0.24115	0.695	0.09310	N	1	B;B	0.20261	0.043;0.043	B;B	0.21546	0.035;0.035	T	0.20940	-1.0260	8	0.37606	T	0.19	.	3.0572	0.06188	0.175:0.401:0.327:0.097	.	95;95	F5H4P0;Q32Q52	.;CL074_HUMAN	C	95	.	ENSP00000380933:S95C	S	+	2	0	C12orf74	91624822	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.457000	0.06745	0.212000	0.20703	0.462000	0.41574	TCT	.		0.582	C12orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407285.1	NM_001037671		G	93100691	C	G	93100691	3	3	2	1	0	0	0	0	1	0	0	0	1718	913	32	4	286	4	C12orf74	12	93100691	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	16675754	93100691	40751204	43	99											
HS3ST6	64711	hgsc.bcm.edu	37	chr16	1962102	1962102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccacgatcagcttcgtgTccggggacatggcgtggatg	7	8	14	12	4	1	0	1	0	0	0	3	3	2	2	3	4	1	1	3	4	0	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr16:1962102T>C	ENST00000293937.3	-	2	517	c.518A>G	c.(517-519)gAc>gGc	p.D173G	HS3ST6_ENST00000443547.1_Missense_Mutation_p.D142G|HS3ST6_ENST00000454677.2_Missense_Mutation_p.D190G			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	173					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						CAGCTTCGTGTCCGGGGACAT	0.682																																					p.D142G		.											.	.	0			c.A425G						.						20	23	22					16																	1962102		2196	4299	6495	SO:0001583	missense	64711	exon2			TTCGTGTCCGGGG			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"Sulfotransferases, membrane-bound"	14178	protein-coding gene	gene with protein product			"heparan sulfate (glucosamine) 3-O-sulfotransferase 5"	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.518A>G	16.37:g.1962102T>C	ENSP00000293937:p.Asp173Gly	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	18	3	NM_001009606	0	0	2	2	0	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37		.	.	.	.	.	.	.	.	.	.	t	9.096	1.002873	0.19121	.	.	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	T;T	0.57595	0.39;0.39	4.83	2.5	0.30297	Sulfotransferase domain (1);	0.401910	0.29126	N	0.013071	T	0.43033	0.1229	L	0.42632	1.34	0.31735	N	0.636552	B	0.02656	0.0	B	0.10450	0.005	T	0.44128	-0.9348	10	0.42905	T	0.14	.	10.9406	0.47270	0.0:0.0:0.3168:0.6832	.	173	Q96QI5	HS3S6_HUMAN	G	173;142;212	ENSP00000293937:D173G;ENSP00000390354:D142G	ENSP00000293937:D173G	D	-	2	0	HS3ST6	1902103	1.000000	0.71417	0.850000	0.33497	0.970000	0.65996	2.195000	0.42677	0.207000	0.20607	0.409000	0.27619	GAC	.		0.682	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606		C	1962102	T	C	1962102	3	2	2	1	0	0	0	0	1	0	0	0	7390	1667	58	3	514	3	HS3ST6	16	1962102	Missense_Mutation	SNP	T	TCGA-A4-7287-01A-11D-2136-08		1962102	88392651	44	100											
KCNJ12	3768	broad.mit.edu;bcgsc.ca	37	chr17	21319100	21319100	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccatcggctacgggctgcGctgtgtgacggaggagtgcc	6	7	16	12	4	0	1	0	1	0	0	1	3	0	3	2	4	3	3	2	4	1	1	rs534524767	byFrequency	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:21319100G>A	ENST00000583088.1	+	3	1341	c.446G>A	c.(445-447)cGc>cAc	p.R149H	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R149H	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	149					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TACGGGCTGCGCTGTGTGACG	0.642										Prostate(3;0.18)			.|||	5	0.000998403	0	0	5008	,	,		35116	0		0	False		,,,				2504	0.0051				p.R149H													.	.	0			c.G446A						.						55	53	54					17																	21319100		2203	4300	6503	SO:0001583	missense	100134444	exon3			GGCTGCGCTGTGT	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.446G>A	17.37:g.21319100G>A	ENSP00000463778:p.Arg149His	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	68	5	NM_001194958	0	0	0	0	0	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.998856	0.93227	.	.	ENSG00000184185	ENST00000331718	D	0.97016	-4.21	5.32	5.32	0.75619	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98735	0.9575	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99663	1.0994	10	0.87932	D	0	.	18.9979	0.92821	0.0:0.0:1.0:0.0	.	149	Q14500	IRK12_HUMAN	H	149	ENSP00000328150:R149H	ENSP00000328150:R149H	R	+	2	0	KCNJ12	21259693	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.690000	0.98676	2.496000	0.84212	0.655000	0.94253	CGC	.		0.642	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319100	G	A	21319100	3	1	2	1	0	0	0	0	1	0	0	0	8067	1087	38	1	448	1	KCNJ12	17	21319100	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		21319100	59876110	45	101											
SUZ12	23512	hgsc.bcm.edu	37	chr17	30323881	30323881	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaaactctggaatctccAtgtcatgaagcatgggtagg	12	10	12	7	0	3	2	1	2	2	0	4	4	3	3	1	3	2	2	1	3	4	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:30323881A>G	ENST00000322652.5	+	15	2088	c.1859A>G	c.(1858-1860)cAt>cGt	p.H620R	SUZ12_ENST00000580398.1_Missense_Mutation_p.H597R	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	620	VEFS-box.				histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				TGGAATCTCCATGTCATGAAG	0.308			T	JAZF1	endometrial stromal tumours																																p.H620R		.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12-658	0			c.A1859G						.						49	51	50					17																	30323881		2202	4295	6497	SO:0001583	missense	23512	exon15			ATCTCCATGTCAT	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"Zinc fingers, C2H2-type"	17101	protein-coding gene	gene with protein product		606245	"suppressor of zeste 12 homolog (Drosophila)"			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1859A>G	17.37:g.30323881A>G	ENSP00000316578:p.His620Arg	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	37	3	NM_015355	0	0	16	16	0	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	37	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	a	14.14	2.447028	0.43429	.	.	ENSG00000178691	ENST00000322652	T	0.54071	0.59	5.67	5.67	0.87782	Polycomb protein, VEFS-Box (1);	0.105878	0.64402	D	0.000002	T	0.72637	0.3485	M	0.76574	2.34	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.994	T	0.76124	-0.3074	10	0.72032	D	0.01	-1.1555	15.9473	0.79803	1.0:0.0:0.0:0.0	.	620;620	A8K1U9;Q15022	.;SUZ12_HUMAN	R	620	ENSP00000316578:H620R	ENSP00000316578:H620R	H	+	2	0	SUZ12	27347994	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.942000	0.92970	2.164000	0.68074	0.456000	0.33151	CAT	.		0.308	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355		G	30323881	A	G	30323881	3	3	2	1	0	0	0	0	1	0	0	0	15448	217	8	3	1917	3	SUZ12	17	30323881	Missense_Mutation	SNP	A	TCGA-A4-7287-01A-11D-2136-08	9004781	30323881	50871329	46	102											
COASY	80347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40717244	40717244	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctctgttcccctccccaGaagcagctgaagatactcac	9	8	7	17	0	2	3	1	1	1	2	4	3	4	3	5	0	3	3	5	0	3	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:40717244G>T	ENST00000393818.2	+	6	1758		c.e6-1		COASY_ENST00000449624.1_Splice_Site|MLX_ENST00000346833.4_5'Flank|MLX_ENST00000435881.2_5'Flank|MLX_ENST00000246912.4_5'Flank|COASY_ENST00000420359.1_Splice_Site|COASY_ENST00000421097.2_Splice_Site|COASY_ENST00000590958.1_Splice_Site	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase						cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCCCTCCCCAGAAGCAGCTGA	0.562																																					.		.											.	COASY-115	0			c.1303-1G>T						.						135	138	137					17																	40717244		2203	4300	6503	SO:0001630	splice_region_variant	80347	exon7			TCCCCAGAAGCAG	AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"Coenzyme A synthase"			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.1303-1G>T	17.37:g.40717244G>T		Somatic	307	0		WXS	Illumina HiSeq	Phase_I	219	45	NM_001042529	0	0	0	2	2	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Splice_Site	SNP	ENST00000393818.2	37	CCDS11429.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.197183	0.79015	.	.	ENSG00000068120	ENST00000421097;ENST00000449624;ENST00000420359;ENST00000393818	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7387	0.85454	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COASY	37970770	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.174000	0.89682	2.649000	0.89929	0.556000	0.70494	.	.		0.562	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233	Intron	T	40717244	G	T	40717244	5	4	2	1	0	0	0	0	0	0	1	0	3658	956	33	4	1415	4	COASY	17	40717244	Splice_Site	SNP	G	TCGA-A4-7287-01A-11D-2136-08	10393363	40717244	40477966	47	103											
AOC2	314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40997487	40997487	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagtctggccggttggaaGtggttagagtccctctacct	7	13	12	9	1	2	1	0	0	2	1	3	2	3	2	3	4	1	2	3	4	4	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:40997487G>C	ENST00000253799.3	+	1	871	c.844G>C	c.(844-846)Gtg>Ctg	p.V282L	AOC2_ENST00000452774.2_Missense_Mutation_p.V282L	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	282					amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CCGGTTGGAAGTGGTTAGAGT	0.572																																					p.V282L		.											.	AOC2-92	0			c.G844C						.						85	85	85					17																	40997487		2203	4300	6503	SO:0001583	missense	314	exon1			TTGGAAGTGGTTA	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.844G>C	17.37:g.40997487G>C	ENSP00000253799:p.Val282Leu	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	102	23	NM_009590	0	0	0	0	0	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902404	0.33628	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.22945	1.93;1.93	5.75	5.75	0.90469	Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	0.267133	0.37219	N	0.002188	T	0.18087	0.0434	N	0.08118	0	0.19945	N	0.99994	P;P	0.50617	0.533;0.937	B;P	0.49561	0.069;0.615	T	0.16424	-1.0403	10	0.10902	T	0.67	-33.3282	14.1397	0.65311	0.0717:0.0:0.9283:0.0	.	282;282	O75106;O75106-2	AOC2_HUMAN;.	L	282	ENSP00000253799:V282L;ENSP00000406134:V282L	ENSP00000253799:V282L	V	+	1	0	AOC2	38251013	0.986000	0.35501	0.707000	0.30419	0.755000	0.42902	2.284000	0.43478	2.720000	0.93068	0.561000	0.74099	GTG	.		0.572	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158		C	40997487	G	C	40997487	3	2	2	1	0	0	0	0	1	0	0	0	727	1029	36	4	846	4	AOC2	17	40997487	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	280243	40997487	40197723	48	104											
MAPT	4137	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	44101444	44101444	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccacggcatctcagcaatgtCtcctccaccggcagcatcga	9	7	8	17	3	2	0	1	0	2	0	6	1	3	0	4	2	2	4	4	2	1	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:44101444C>G	ENST00000571987.1	+	13	2184	c.2184C>G	c.(2182-2184)gtC>gtG	p.V728V	MAPT_ENST00000262410.5_Silent_p.V728V|MAPT_ENST00000347967.5_Silent_p.V286V|MAPT_ENST00000334239.8_Silent_p.V322V|MAPT_ENST00000351559.5_Silent_p.V411V|MAPT_ENST00000431008.3_Silent_p.V380V|MAPT_ENST00000344290.5_Silent_p.V746V|MAPT_ENST00000574436.1_Silent_p.V411V|MAPT_ENST00000446361.3_Silent_p.V353V|MAPT_ENST00000535772.1_Silent_p.V380V|MAPT_ENST00000576518.1_Silent_p.V311V|MAPT_ENST00000415613.2_Silent_p.V746V|MAPT_ENST00000420682.2_Silent_p.V382V|MAPT_ENST00000340799.5_Silent_p.V382V			P10636	TAU_HUMAN	microtubule-associated protein tau	728					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TCAGCAATGTCTCCTCCACCG	0.622																																					p.V746V		.											.	MAPT-91	0			c.C2238G						.						124	105	112					17																	44101444		2203	4300	6503	SO:0001819	synonymous_variant	4137	exon15			CAATGTCTCCTCC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.2184C>G	17.37:g.44101444C>G		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	155	10	NM_001123066	0	0	0	0	0	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			.		0.622	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		G	44101444	C	G	44101444	2	3	2	1	0	0	0	0	0	0	0	1	9322	900	32	4		4	MAPT	17	44101444	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08	3103957	44101444	37093766	49	105											
TYMS	7298	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	662242	662242	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcctgggattctccaccAgagaagaaggggacttgggc	11	6	14	10	0	1	2	0	0	1	2	2	5	1	4	3	4	1	0	3	4	2	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:662242A>G	ENST00000323274.10	+	3	515	c.376A>G	c.(376-378)Aga>Gga	p.R126G	TYMS_ENST00000323224.7_Missense_Mutation_p.R126G|TYMS_ENST00000323250.5_Intron	NM_001071.2	NP_001062.1	P04818	TYSY_HUMAN	thymidylate synthetase	126					aging (GO:0007568)|cartilage development (GO:0051216)|circadian rhythm (GO:0007623)|deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|developmental growth (GO:0048589)|dTMP biosynthetic process (GO:0006231)|dTTP biosynthetic process (GO:0006235)|dUMP metabolic process (GO:0046078)|G1/S transition of mitotic cell cycle (GO:0000082)|immortalization of host cell by virus (GO:0019088)|intestinal epithelial cell maturation (GO:0060574)|mitotic cell cycle (GO:0000278)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|organ regeneration (GO:0031100)|polysaccharide metabolic process (GO:0005976)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to organophosphorus (GO:0046683)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|response to vitamin A (GO:0033189)|small molecule metabolic process (GO:0044281)|tetrahydrofolate metabolic process (GO:0046653)|uracil metabolic process (GO:0019860)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cofactor binding (GO:0048037)|drug binding (GO:0008144)|folic acid binding (GO:0005542)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|thymidylate synthase activity (GO:0004799)			endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(2)	8					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Methotrexate(DB00563)|Pemetrexed(DB00642)|Pralatrexate(DB06813)|Raltitrexed(DB00293)|Trifluridine(DB00432)|Trimethoprim(DB00440)	ATTCTCCACCAGAGAAGAAGG	0.498																																					p.R126G		.											.	TYMS-227	0			c.A376G						.						249	271	264					18																	662242		2203	4300	6503	SO:0001583	missense	7298	exon3			TCCACCAGAGAAG	X02308	CCDS11821.1	18p11.31-p11.21	2014-09-17			ENSG00000176890	ENSG00000176890	2.1.1.45		12441	protein-coding gene	gene with protein product		188350		TS			Standard	NM_001071		Approved	Tsase, TMS, HsT422	uc010dka.1	P04818	OTTHUMG00000131473	ENST00000323274.10:c.376A>G	18.37:g.662242A>G	ENSP00000315644:p.Arg126Gly	Somatic	528	1		WXS	Illumina HiSeq	Phase_I	416	65	NM_001071	0	0	45	56	11	Q8WYK3|Q8WYK4	Missense_Mutation	SNP	ENST00000323274.10	37	CCDS11821.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.893809	0.33442	.	.	ENSG00000176890	ENST00000323274;ENST00000323224	.	.	.	5.7	2.02	0.26589	Thymidylate synthase/dCMP hydroxymethylase domain (2);	0.000000	0.85682	D	0.000000	D	0.84334	0.5449	H	0.94222	3.51	0.80722	D	1	B;B	0.32051	0.325;0.354	B;P	0.46629	0.198;0.522	D	0.85170	0.0997	9	0.87932	D	0	-23.4672	14.3261	0.66521	0.5015:0.4985:0.0:0.0	.	126;126	Q8WYK3;P04818	.;TYSY_HUMAN	G	126	.	ENSP00000314727:R126G	R	+	1	2	TYMS	652242	0.843000	0.29541	0.251000	0.24312	0.407000	0.30961	1.774000	0.38573	0.089000	0.17243	0.460000	0.39030	AGA	.		0.498	TYMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254316.1	NM_001071		G	662242	A	G	662242	3	3	2	1	0	0	0	0	1	0	0	0	16845	180	7	3	386	3	TYMS	18	662242	Missense_Mutation	SNP	A	TCGA-A4-7287-01A-11D-2136-08		662242	77415006	50	106											
NDC80	10403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2616466	2616466	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggagcagattgctaaagttGatagagaatatgaagaatgc	17	9	12	3	0	0	5	0	2	0	3	0	7	0	6	0	1	3	3	0	1	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:2616466G>C	ENST00000261597.4	+	17	2004	c.1822G>C	c.(1822-1824)Gat>Cat	p.D608H		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	608	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						TGCTAAAGTTGATAGAGAATA	0.269																																					p.D608H		.											.	NDC80-91	0			c.G1822C						.						44	47	46					18																	2616466		2200	4284	6484	SO:0001583	missense	10403	exon17			AAAGTTGATAGAG	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1822G>C	18.37:g.2616466G>C	ENSP00000261597:p.Asp608His	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	60	17	NM_006101	0	0	35	35	0	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	8.778	0.927542	0.18056	.	.	ENSG00000080986	ENST00000261597	T	0.51325	0.71	5.32	3.48	0.39840	.	0.281499	0.39834	N	0.001252	T	0.43942	0.1270	M	0.62723	1.935	0.38915	D	0.957602	P	0.39216	0.664	B	0.38655	0.278	T	0.42498	-0.9448	10	0.46703	T	0.11	-22.92	9.4287	0.38597	0.0766:0.0:0.7799:0.1435	.	608	O14777	NDC80_HUMAN	H	608	ENSP00000261597:D608H	ENSP00000261597:D608H	D	+	1	0	NDC80	2606466	0.973000	0.33851	0.655000	0.29622	0.368000	0.29767	1.715000	0.37971	0.699000	0.31761	-0.266000	0.10368	GAT	.		0.269	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		C	2616466	G	C	2616466	3	2	2	1	0	0	0	0	1	0	0	0	10268	1290	45	4	1884	4	NDC80	18	2616466	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	1954224	2616466	75460782	51	107											
NDC80	10403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2616517	2616517	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atctctcggaaaatattaaaGagattagagataagtatgag	18	11	9	3	1	1	3	0	1	1	2	3	6	1	4	0	1	0	1	0	1	8	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:2616517G>C	ENST00000261597.4	+	17	2055	c.1873G>C	c.(1873-1875)Gag>Cag	p.E625Q		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	625	Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						AAATATTAAAGAGATTAGAGA	0.299																																					p.E625Q		.											.	NDC80-91	0			c.G1873C						.						40	43	42					18																	2616517		2199	4282	6481	SO:0001583	missense	10403	exon17			ATTAAAGAGATTA	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1873G>C	18.37:g.2616517G>C	ENSP00000261597:p.Glu625Gln	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_006101	0	0	32	43	11	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	7.891	0.732376	0.15507	.	.	ENSG00000080986	ENST00000261597	T	0.49432	0.78	5.47	4.59	0.56863	.	0.333418	0.34245	N	0.004123	T	0.34948	0.0915	L	0.47716	1.5	0.28039	N	0.933831	P	0.39216	0.664	B	0.34242	0.178	T	0.18871	-1.0323	10	0.15066	T	0.55	-4.8199	10.1561	0.42823	0.0768:0.137:0.7862:0.0	.	625	O14777	NDC80_HUMAN	Q	625	ENSP00000261597:E625Q	ENSP00000261597:E625Q	E	+	1	0	NDC80	2606517	1.000000	0.71417	0.991000	0.47740	0.167000	0.22549	2.210000	0.42816	1.407000	0.46875	0.555000	0.69702	GAG	.		0.299	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		C	2616517	G	C	2616517	3	2	2	1	0	0	0	0	1	0	0	0	10268	943	33	4	1935	4	NDC80	18	2616517	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	51	2616517	75460731	52	108											
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4544313	4544313	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggaccctgcgccctgcgcTcgcccaggcggctgacgctc	3	5	14	19	6	0	1	0	1	0	0	2	2	0	2	3	3	2	3	3	3	0	0	rs564925636		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:4544313T>C	ENST00000586582.1	-	17	2277	c.1967A>G	c.(1966-1968)gAg>gGg	p.E656G	RN7SL121P_ENST00000584223.1_RNA|SEMA6B_ENST00000586965.1_Intron|SEMA6B_ENST00000301293.3_Missense_Mutation_p.E656G	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	656					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		cgccctgcgctcgcccAGGCG	0.796													T|||	1	0.000199681	0	0	5008	,	,		4939	0		0.001	False		,,,				2504	0				p.E656G		.											.	SEMA6B-91	0			c.A1967G						.																																			SO:0001583	missense	10501	exon17			CTGCGCTCGCCCA	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"Semaphorins"	10739	protein-coding gene	gene with protein product	"Sema VIb", "semaphorin Z", "semaphorin VIB"	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.1967A>G	19.37:g.4544313T>C	ENSP00000467290:p.Glu656Gly	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_032108	0	0	0	0	0	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	.	6.330	0.429030	0.11987	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.18657	2.2	3.38	3.38	0.38709	.	1.330970	0.05416	N	0.543405	T	0.28863	0.0716	N	0.12182	0.205	0.34419	D	0.697296	D	0.71674	0.998	D	0.70227	0.968	T	0.25676	-1.0125	10	0.87932	D	0	.	8.1934	0.31381	0.0:0.0:0.0:1.0	.	656	Q9H3T3	SEM6B_HUMAN	G	656	ENSP00000301293:E656G	ENSP00000301292:E656G	E	-	2	0	SEMA6B	4495313	0.982000	0.34865	0.987000	0.45799	0.244000	0.25665	0.903000	0.28475	1.166000	0.42689	0.397000	0.26171	GAG	.		0.796	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		C	4544313	T	C	4544313	3	2	2	1	0	0	0	0	1	0	0	0	14072	1551	54	3	703	3	SEMA6B	19	4544313	Missense_Mutation	SNP	T	TCGA-A4-7287-01A-11D-2136-08		4544313	54584670	53	109											
FBXW9	84261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12800616	12800616	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttgcggttggcgaagacgtGcagcaggccctggttgtcac	6	9	16	10	3	1	1	1	0	0	1	1	2	1	1	1	4	3	5	1	4	1	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:12800616G>A	ENST00000380339.3	-	7	1231	c.1195C>T	c.(1195-1197)Cac>Tac	p.H399Y	CTD-2659N19.2_ENST00000585742.1_RNA|FBXW9_ENST00000587955.1_Missense_Mutation_p.H389Y|FBXW9_ENST00000544494.1_Missense_Mutation_p.H107Y|CTD-2192J16.26_ENST00000593554.1_lincRNA|FBXW9_ENST00000393261.3_Missense_Mutation_p.H369Y			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	399					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GCGAAGACGTGCAGCAGGCCC	0.647																																					p.H369Y		.											.	FBXW9-227	0			c.C1105T						.						63	62	62					19																	12800616		2203	4300	6503	SO:0001583	missense	84261	exon7			AGACGTGCAGCAG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.1195C>T	19.37:g.12800616G>A	ENSP00000369696:p.His399Tyr	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	98	22	NM_032301	0	0	11	24	13	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		.	.	.	.	.	.	.	.	.	.	G	11.70	1.716443	0.30413	.	.	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	T;T;T	0.75367	-0.93;-0.93;-0.93	4.62	3.5	0.40072	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.191473	0.45361	N	0.000365	T	0.48390	0.1497	N	0.11106	0.095	0.42212	D	0.991813	B;B;B	0.28880	0.226;0.011;0.002	B;B;B	0.22386	0.039;0.023;0.006	T	0.51356	-0.8716	10	0.51188	T	0.08	-14.7405	3.666	0.08255	0.3848:0.0:0.6152:0.0	.	389;399;369	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	Y	107;369;399	ENSP00000442714:H107Y;ENSP00000376945:H369Y;ENSP00000369696:H399Y	ENSP00000369696:H399Y	H	-	1	0	FBXW9	12661616	1.000000	0.71417	1.000000	0.80357	0.522000	0.34438	3.310000	0.51911	2.129000	0.65627	0.484000	0.47621	CAC	.		0.647	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		A	12800616	G	A	12800616	3	1	2	1	0	0	0	0	1	0	0	0	5790	1319	46	2	287	2	FBXW9	19	12800616	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	8256303	12800616	46328367	54	110											
KLHL26	55295	broad.mit.edu	37	chr19	18778682	18778682	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcgaggagttcctgaaggcgGccatgagcgtggagacctgc	8	6	17	10	3	0	3	0	2	0	1	1	6	1	4	3	4	2	1	3	4	1	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:18778682G>A	ENST00000300976.4	+	3	565	c.475G>A	c.(475-477)Gcc>Acc	p.A159T	KLHL26_ENST00000599006.1_Intron|KLHL26_ENST00000596843.1_3'UTR	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	159										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CCTGAAGGCGGCCATGAGCGT	0.647																																					p.A159T													.	KLHL26-91	0			c.G475A						.						83	66	72					19																	18778682		2203	4299	6502	SO:0001583	missense	55295	exon3			AAGGCGGCCATGA		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"Kelch-like", "BTB/POZ domain containing"	25623	protein-coding gene	gene with protein product			"kelch-like 26 (Drosophila)"				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.475G>A	19.37:g.18778682G>A	ENSP00000300976:p.Ala159Thr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	48	3	NM_018316	0	0	9	9	0	Q8TAP0|Q9NUX3	Missense_Mutation	SNP	ENST00000300976.4	37	CCDS12384.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793922	0.70452	.	.	ENSG00000167487	ENST00000300976	T	0.75260	-0.92	5.04	5.04	0.67666	BTB/POZ-like (1);BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	N	0.25485	0.75	0.80722	D	1	P	0.41188	0.741	B	0.42462	0.388	T	0.65331	-0.6194	9	.	.	.	.	17.3648	0.87360	0.0:0.0:1.0:0.0	.	159	Q53HC5	KLH26_HUMAN	T	159	ENSP00000300976:A159T	.	A	+	1	0	KLHL26	18639682	1.000000	0.71417	0.961000	0.40146	0.650000	0.38633	9.323000	0.96364	2.341000	0.79615	0.591000	0.81541	GCC	.		0.647	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		A	18778682	G	A	18778682	3	1	2	1	0	0	0	0	1	0	0	0	8402	1203	42	2	485	2	KLHL26	19	18778682	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	5978066	18778682	40350301	55	111											
LYPD3	27076	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	43967294	43967300	+	Frame_Shift_Del	DEL	GTTGCCG	GTTGCCG	-																															tcacctgccgtcaaggtgacGttgccgtcgaagcagccctt																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GTTGCCG	GTTGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:43967294_43967300delGTTGCCG	ENST00000244333.3	-	4	610_616	c.522_528delCGGCAAC	c.(520-528)gacggcaacfs	p.DGN174fs		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	174	UPAR/Ly6 2.				cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				TCAAGGTGACGTTGCCGTCGAAGCAGC	0.647																																					p.174_176del		.											.	LYPD3-91	0			c.522_528del						.																																			SO:0001589	frameshift_variant	27076	exon4			.	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.522_528delCGGCAAC	19.37:g.43967294_43967300delGTTGCCG	ENSP00000244333:p.Asp174fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	98	20	NM_014400	0	0	0	0	0	Q9UJ74	Frame_Shift_Del	DEL	ENST00000244333.3	37	CCDS12620.1																																																																																			.		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		-	43967300	GTTGCCG	-	43967294	7	5	2	1	0	1	0	1	0	0	0	0	9136	1136	40	0	520	0	LYPD3	19	43967294	Frame_Shift_Del	DEL	GTTGCCG	TCGA-A4-7287-01A-11D-2136-08	25188612	43967294	15161689	56	112											
SIRPG	55423	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	1615980	1615980	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcaaggcgtttgctgacCgccagctgcccatcatgctt	7	9	12	13	2	1	1	1	1	0	0	1	1	1	1	3	2	4	5	3	2	1	2	rs147655438		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:1615980C>A	ENST00000303415.3	-	4	1078	c.1014G>T	c.(1012-1014)gcG>gcT	p.A338A	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000381583.2_Intron|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000381580.1_Silent_p.A305A|SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000216927.4_Intron	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	338	Ig-like C1-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GTTTGCTGACCGCCAGCTGCC	0.502																																					p.A338A		.											.	SIRPG-23	0			c.G1014T						.						116	94	101					20																	1615980		2203	4300	6503	SO:0001819	synonymous_variant	55423	exon4			GCTGACCGCCAGC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1014G>T	20.37:g.1615980C>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	90	24	NM_018556	0	0	2	2	0	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			C|1.000;T|0.000		0.502	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1615980	C	A	1615980	2	1	2	1	0	0	0	0	0	0	0	1	14368	639	23	4		4	SIRPG	20	1615980	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08		1615980	61409540	57	113											
PRIC285	85441	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62203482	62203482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttgggcagagctcgaacttgGagagtcccgggggtggggaa	8	7	19	7	2	0	2	0	0	0	2	2	5	1	3	1	6	2	2	1	6	2	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:62203482G>A	ENST00000467148.1	-	1	326	c.257C>T	c.(256-258)tCc>tTc	p.S86F	HELZ2_ENST00000479540.1_5'UTR	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	86					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CTCGAACTTGGAGAGTCCCGG	0.627																																					p.S86F													.	.	0			c.C257T						.						25	26	25					20																	62203482		2185	4295	6480	SO:0001583	missense	85441	exon2			AACTTGGAGAGTC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.257C>T	20.37:g.62203482G>A	ENSP00000417401:p.Ser86Phe	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_001037335	0	0	4	4	0	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	9.215	1.031799	0.19590	.	.	ENSG00000130589	ENST00000467148	T	0.02944	4.1	4.12	1.89	0.25635	.	1.072950	0.07266	N	0.868321	T	0.10337	0.0253	M	0.63428	1.95	0.09310	N	1	D;B	0.71674	0.998;0.407	D;B	0.65443	0.935;0.054	T	0.27739	-1.0065	10	0.66056	D	0.02	-28.6382	5.3566	0.16065	0.0925:0.2127:0.5726:0.1222	.	86;86	Q4VXQ0;Q9BYK8	.;PR285_HUMAN	F	86	ENSP00000417401:S86F	ENSP00000417401:S86F	S	-	2	0	RP4-697K14.7	61673926	0.002000	0.14202	0.140000	0.22221	0.123000	0.20343	0.808000	0.27154	0.728000	0.32382	-0.152000	0.13540	TCC	.		0.627	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62203482	G	A	62203482	3	1	2	1	0	0	0	0	1	0	0	0	12514	1174	41	2	7791	2	PRIC285	20	62203482	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	60587502	62203482	822038	58	114											
PRPF6	57473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	62642850	62642850	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gagatcaaccgtgagcagtgGatccaggtgggccgcaggcg	9	5	17	10	3	1	2	1	1	0	1	2	4	2	3	3	4	2	2	3	4	1	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:62642850G>C	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Missense_Mutation_p.W506C			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GTGAGCAGTGGATCCAGGTGG	0.602																																					p.W506C		.											.	PRPF6-70	0			c.G1518C						.						44	38	40					20																	62642850		2203	4300	6503	SO:0001627	intron_variant	24148	exon11			GCAGTGGATCCAG	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.4+37207C>G	20.37:g.62642850G>C		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	24	3	NM_012469	0	0	0	0	0	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	37	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870612	0.72065	.	.	ENSG00000101161	ENST00000266079;ENST00000535781	T;T	0.50277	0.75;0.75	5.13	4.18	0.49190	.	0.000000	0.85682	D	0.000000	T	0.78194	0.4245	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.988	D;P	0.83275	0.996;0.886	D	0.85224	0.1028	10	0.87932	D	0	.	13.52	0.61561	0.0755:0.0:0.9245:0.0	.	506;506	O94906-2;O94906	.;PRP6_HUMAN	C	506	ENSP00000266079:W506C;ENSP00000446216:W506C	ENSP00000266079:W506C	W	+	3	0	PRPF6	62113294	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	9.220000	0.95180	1.154000	0.42482	0.609000	0.83330	TGG	.		0.602	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62642850	G	C	62642850	1	2	2	0	1	0	0	0	0	0	0	0	12603	1183	41	4		4	PRPF6	20	62642850	Intron	SNP	G	TCGA-A4-7287-01A-11D-2136-08	439368	62642850	382670	59	115											
FTCD	10841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47571511	47571511	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcccgcaggttgagcgcGatgcggtgggcttgctcctt	3	11	15	12	4	0	1	0	1	0	0	2	2	2	1	2	3	4	5	2	3	0	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr21:47571511G>T	ENST00000291670.5	-	5	640	c.597C>A	c.(595-597)atC>atA	p.I199I	FTCD_ENST00000397748.1_Silent_p.I199I|FTCD_ENST00000397743.1_Silent_p.I199I|FTCD_ENST00000359679.2_Silent_p.I199I|FTCD_ENST00000498355.2_5'UTR|FTCD-AS1_ENST00000446649.1_RNA|FTCD_ENST00000355384.2_Silent_p.I199I|FTCD_ENST00000397746.3_Silent_p.I199I	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	199	Formiminotransferase C-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	GGTTGAGCGCGATGCGGTGGG	0.647																																					p.I199I		.											.	FTCD-92	0			c.C597A						.						67	71	69					21																	47571511		2203	4300	6503	SO:0001819	synonymous_variant	10841	exon5			GAGCGCGATGCGG	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"formiminotransferase cyclodeaminase"			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.597C>A	21.37:g.47571511G>T		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	97	27	NM_206965	0	0	0	0	0	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Silent	SNP	ENST00000291670.5	37	CCDS13731.1																																																																																			.		0.647	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657		T	47571511	G	T	47571511	2	4	2	1	0	0	0	0	0	0	0	1	6100	1048	37	4		4	FTCD	21	47571511	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08		47571511	558384	60	116											
DGCR2	9993	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	19028613	19028613	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtccgggtggatggaggcctCgtagggcggcggagggtcgt	4	7	22	8	5	0	0	0	0	0	0	3	3	1	3	2	8	0	1	2	8	1	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr22:19028613C>T	ENST00000263196.7	-	9	1601	c.1354G>A	c.(1354-1356)Gag>Aag	p.E452K	DGCR2_ENST00000537045.1_Missense_Mutation_p.E411K|DGCR2_ENST00000545799.1_3'UTR	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	452					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					ATGGAGGCCTCGTAGGGCGGC	0.632																																					p.E452K													.	DGCR2-90	0			c.G1354A						.						68	59	62					22																	19028613		2203	4300	6503	SO:0001583	missense	9993	exon9			AGGCCTCGTAGGG	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"integral membrane protein DGCR2"	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1354G>A	22.37:g.19028613C>T	ENSP00000263196:p.Glu452Lys	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	46	7	NM_005137	0	0	26	39	13	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	.	.	.	.	.	.	.	.	.	.	C	34	5.312202	0.95655	.	.	ENSG00000070413	ENST00000537045;ENST00000263196	T;D	0.97994	0.46;-4.65	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.98620	0.9538	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.994	D	0.99449	1.0940	10	0.72032	D	0.01	.	20.0384	0.97572	0.0:1.0:0.0:0.0	.	408;452	B7Z3T5;P98153	.;IDD_HUMAN	K	411;452	ENSP00000440062:E411K;ENSP00000263196:E452K	ENSP00000263196:E452K	E	-	1	0	DGCR2	17408613	1.000000	0.71417	0.999000	0.59377	0.449000	0.32228	7.722000	0.84778	2.837000	0.97791	0.655000	0.94253	GAG	.		0.632	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137		T	19028613	C	T	19028613	3	4	2	1	0	0	0	0	1	0	0	0	4472	893	31	1	306	1	DGCR2	22	19028613	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		19028613	32275953	61	117											
CXorf21	80231	bcgsc.ca	37	chrX	30578342	30578342	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cttgtgtttcatccacagagGaataggaaagggtagcaaca	14	9	11	7	0	1	1	1	0	0	1	2	3	2	3	1	3	2	3	1	3	5	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:30578342G>T	ENST00000378962.3	-	3	453	c.131C>A	c.(130-132)tCc>tAc	p.S44Y		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	44										kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						ATCCACAGAGGAATAGGAAAG	0.453																																					p.S44Y													.	CXorf21-131	0			c.C131A						.						148	128	135					X																	30578342		2202	4300	6502	SO:0001583	missense	80231	exon3			ACAGAGGAATAGG	BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.131C>A	X.37:g.30578342G>T	ENSP00000368245:p.Ser44Tyr	Somatic	282	0		WXS	Illumina HiSeq	Phase_1	210	8	NM_025159	0	0	0	0	0		Missense_Mutation	SNP	ENST00000378962.3	37	CCDS14224.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.891588	0.52014	.	.	ENSG00000120280	ENST00000378962	.	.	.	5.25	4.38	0.52667	.	0.090773	0.47852	D	0.000207	T	0.62660	0.2446	L	0.56769	1.78	0.35472	D	0.797434	D	0.60575	0.988	P	0.59761	0.863	T	0.72792	-0.4186	9	0.66056	D	0.02	-3.4973	10.5321	0.44983	0.0:0.1493:0.7064:0.1444	.	44	Q9HAI6	CX021_HUMAN	Y	44	.	ENSP00000368245:S44Y	S	-	2	0	CXorf21	30488263	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	3.164000	0.50770	1.179000	0.42884	0.544000	0.68410	TCC	.		0.453	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	NM_025159		T	30578342	G	T	30578342	3	4	2	1	0	0	0	0	1	0	0	0	4107	1174	41	4	778	4	CXorf21	23	30578342	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		30578342	124692218	62	118											
MSN	4478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	64936758	64936758	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccaccgggaagcagctatttGaccaggtaaggcggagactc	11	6	13	11	2	0	2	0	1	0	1	1	4	0	3	3	4	2	3	3	4	3	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:64936758G>C	ENST00000360270.5	+	2	263	c.91G>C	c.(91-93)Gac>Cac	p.D31H		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	31	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)		MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						GCAGCTATTTGACCAGGTAAG	0.507			T	ALK	ALCL																																p.D31H		.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN-1086	0			c.G91C						.						132	99	111					X																	64936758		2203	4300	6503	SO:0001583	missense	4478	exon2			CTATTTGACCAGG	M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.91G>C	X.37:g.64936758G>C	ENSP00000353408:p.Asp31His	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	77	13	NM_002444	0	0	0	0	0		Missense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	g	17.67	3.446489	0.63178	.	.	ENSG00000147065	ENST00000360270	T	0.80304	-1.36	5.73	5.73	0.89815	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.90892	0.7138	H	0.98155	4.16	0.80722	D	1	P	0.43542	0.81	P	0.47891	0.56	D	0.93688	0.7004	10	0.87932	D	0	.	16.1334	0.81461	0.0:0.0:1.0:0.0	.	31	P26038	MOES_HUMAN	H	31	ENSP00000353408:D31H	ENSP00000353408:D31H	D	+	1	0	MSN	64853483	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.899000	0.92544	2.412000	0.81896	0.597000	0.82753	GAC	.		0.507	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		C	64936758	G	C	64936758	3	2	2	1	0	0	0	0	1	0	0	0	9910	1290	45	4	97	4	MSN	23	64936758	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	34358416	64936758	90333802	63	119											
OGT	8473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70782731	70782731	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ataccctgggacgagtggtgCgcttttcatggattatatta	9	14	11	7	2	1	0	1	0	0	0	1	3	1	2	1	3	2	1	1	3	4	6			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:70782731C>T	ENST00000373719.3	+	16	2229	c.2012C>T	c.(2011-2013)gCg>gTg	p.A671V	OGT_ENST00000373701.3_Missense_Mutation_p.A661V	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	671					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					ACGAGTGGTGCGCTTTTCATG	0.393																																					p.A671V		.											.	OGT-113	0			c.C2012T						.						129	115	120					X																	70782731		2203	4300	6503	SO:0001583	missense	8473	exon16			GTGGTGCGCTTTT	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"Tetratricopeptide (TTC) repeat domain containing"	8127	protein-coding gene	gene with protein product	"UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"	300255	"O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.2012C>T	X.37:g.70782731C>T	ENSP00000362824:p.Ala671Val	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	132	31	NM_181672	0	1	12	13	0	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	37	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612830	0.87258	.	.	ENSG00000147162	ENST00000373719;ENST00000373701	T;T	0.18338	2.22;2.22	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.42063	0.1186	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.99;0.989	T	0.15435	-1.0437	10	0.23302	T	0.38	.	17.876	0.88825	0.0:1.0:0.0:0.0	.	545;661;671	Q548W1;O15294-3;O15294	.;.;OGT1_HUMAN	V	671;661	ENSP00000362824:A671V;ENSP00000362805:A661V	ENSP00000362805:A661V	A	+	2	0	OGT	70699456	1.000000	0.71417	0.922000	0.36590	0.793000	0.44817	7.626000	0.83164	2.410000	0.81850	0.594000	0.82650	GCG	.		0.393	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		T	70782731	C	T	70782731	3	4	2	1	0	0	0	0	1	0	0	0	10873	768	27	1	2074	1	OGT	23	70782731	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	5845973	70782731	84487829	64	120											
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123197834	123197834	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaacagagtagatatttCaagaagtcaactgatagatg	16	11	8	6	0	3	5	3	1	0	4	3	5	3	5	0	0	2	1	0	0	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:123197834C>A	ENST00000371160.1	+	20	2248	c.1958C>A	c.(1957-1959)tCa>tAa	p.S653*	STAG2_ENST00000371157.3_Nonsense_Mutation_p.S653*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.S653*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.S653*|STAG2_ENST00000371145.3_Nonsense_Mutation_p.S653*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.S584*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	653					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GTAGATATTTCAAGAAGTCAA	0.333																																					p.S653X		.											.	STAG2-134	0			c.C1958A						.						64	56	59					X																	123197834		2203	4300	6503	SO:0001587	stop_gained	10735	exon20			ATATTTCAAGAAG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1958C>A	X.37:g.123197834C>A	ENSP00000360202:p.Ser653*	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	61	15	NM_001042749	0	0	4	4	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	40	8.002701	0.98605	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.28	5.28	0.74379	.	0.124104	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-19.1078	18.0751	0.89424	0.0:1.0:0.0:0.0	.	.	.	.	X	653;584;653;653;653;653	.	ENSP00000218089:S653X	S	+	2	0	STAG2	123025515	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.759000	0.85235	2.203000	0.70933	0.600000	0.82982	TCA	.		0.333	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123197834	C	A	123197834	4	1	2	1	0	0	0	0	0	1	0	0	15275	838	29	4	2028	4	STAG2	23	123197834	Nonsense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	52415103	123197834	32072726	65	121											
DDI2	84301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15957021	15957021	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgctgaaggaacgcaatcCacccctggcagaagctctgc	10	7	10	14	1	1	2	0	1	1	1	2	3	2	3	3	2	4	4	3	2	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:15957021C>T	ENST00000480945.1	+	3	641	c.470C>T	c.(469-471)cCa>cTa	p.P157L		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	157							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAACGCAATCCACCCCTGGCA	0.502																																					p.P157L		.											.	DDI2-44	0			c.C470T						.						90	85	86					1																	15957021		2203	4300	6503	SO:0001583	missense	84301	exon3			GCAATCCACCCCT		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.470C>T	1.37:g.15957021C>T	ENSP00000417748:p.Pro157Leu	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	92	33	NM_032341	0	0	3	5	2	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	37	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	C	31	5.082015	0.94050	.	.	ENSG00000197312	ENST00000480945	T	0.43294	0.95	5.67	5.67	0.87782	.	0.000000	0.85682	U	0.000000	T	0.73674	0.3617	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79492	-0.1781	10	0.87932	D	0	-24.5775	19.3867	0.94560	0.0:1.0:0.0:0.0	.	157	Q5TDH0	DDI2_HUMAN	L	157	ENSP00000417748:P157L	ENSP00000449475:P42L	P	+	2	0	DDI2	15829608	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	7.323000	0.79105	2.684000	0.91462	0.650000	0.86243	CCA	.		0.502	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		T	15957021	C	T	15957021	3	4	3	1	0	0	0	0	1	0	0	0	4335	594	21	2	480	2	DDI2	1	15957021	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		15957021	233293600	1	122											
GALE	11313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24124297	24124297	+	IGR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	catcaaggggcaggtactggGggttcccgtacacagtggct	8	8	15	10	1	1	0	1	0	0	0	2	0	2	0	1	6	2	5	1	6	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:24124297G>T	ENST00000374514.3	+	0	1810				GALE_ENST00000374497.3_Missense_Mutation_p.P139H|GALE_ENST00000470383.1_5'Flank	NM_007260.2	NP_009191.1	O95372	LYPA2_HUMAN	lysophospholipase II						fatty acid metabolic process (GO:0006631)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		CAGGTACTGGGGGTTCCCGTA	0.587																																					p.P139H		.											.	GALE-90	0			c.C416A						.																																			SO:0001628	intergenic_variant	2582	exon6			TACTGGGGGTTCC	AF098668	CCDS241.1	1p36.11	2008-08-08			ENSG00000011009	ENSG00000011009	3.1.1.5		6738	protein-coding gene	gene with protein product							Standard	NM_007260		Approved	APT-2	uc001bht.3	O95372	OTTHUMG00000002961		1.37:g.24124297G>T		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	57	29	NM_000403	0	0	78	168	90	Q7Z4Z2	Missense_Mutation	SNP	ENST00000374514.3	37	CCDS241.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199561	0.58126	.	.	ENSG00000117308	ENST00000374498;ENST00000374497;ENST00000429356;ENST00000418277;ENST00000425913;ENST00000445705	D;D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2;-3.2	4.72	3.81	0.43845	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97349	0.9133	H	0.94183	3.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97877	1.0289	10	0.87932	D	0	-12.5969	12.5955	0.56468	0.0812:0.0:0.9188:0.0	.	65;75;139;139	B3KQ39;E9PH43;Q38G75;Q14376	.;.;.;GALE_HUMAN	H	75;139;75;75;139;139	ENSP00000363621:P139H;ENSP00000398585:P75H;ENSP00000414719:P75H;ENSP00000393359:P139H;ENSP00000398257:P139H	ENSP00000363621:P139H	P	-	2	0	GALE	23996884	1.000000	0.71417	1.000000	0.80357	0.406000	0.30931	9.191000	0.94940	1.224000	0.43551	-0.136000	0.14681	CCC	G|1.000;C|0.000		0.587	LYPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008245.1			T	24124297	G	T	24124297	1	4	3	0	1	0	0	0	0	0	0	0	6222	1232	43	4		4	GALE	1	24124297	IGR	SNP	G	TCGA-A4-7288-01A-11D-2136-08	8167276	24124297	225126324	2	123											
NUDC	10726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27250638	27250638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactttttcattggaggagAagaagggatggcagagaagg	14	8	16	3	0	1	4	1	0	0	4	1	8	1	6	0	5	0	1	0	5	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:27250638A>G	ENST00000321265.5	+	2	263	c.140A>G	c.(139-141)gAa>gGa	p.E47G		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	47					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		ATTGGAGGAGAAGAAGGGATG	0.458																																					p.E47G		.											.	NUDC-91	0			c.A140G						.						90	87	88					1																	27250638		2203	4300	6503	SO:0001583	missense	10726	exon2			GAGGAGAAGAAGG		CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"nuclear distribution gene C homolog (A. nidulans)", "nuclear distribution C homolog (A. nidulans)"				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.140A>G	1.37:g.27250638A>G	ENSP00000319664:p.Glu47Gly	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	74	31	NM_006600	0	0	133	278	145	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	37	CCDS292.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.191460	0.38707	.	.	ENSG00000090273	ENST00000435827;ENST00000321265	D	0.81908	-1.55	5.49	5.49	0.81192	.	0.143063	0.64402	D	0.000008	T	0.70798	0.3265	N	0.16790	0.44	0.54753	D	0.999987	B	0.06786	0.001	B	0.13407	0.009	T	0.65475	-0.6159	10	0.18710	T	0.47	-0.1195	14.4801	0.67576	1.0:0.0:0.0:0.0	.	47	Q9Y266	NUDC_HUMAN	G	51;47	ENSP00000319664:E47G	ENSP00000319664:E47G	E	+	2	0	NUDC	27123225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.005000	0.88553	2.222000	0.72286	0.533000	0.62120	GAA	.		0.458	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			G	27250638	A	G	27250638	3	3	3	1	0	0	0	0	1	0	0	0	10747	246	9	3	146	3	NUDC	1	27250638	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	3126341	27250638	221999983	3	124											
DOCK7	85440	hgsc.bcm.edu;bcgsc.ca	37	chr1	63119666	63119666	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctccttacctttcttcaggTacagctgaaacaagagttct	10	14	6	11	0	4	2	1	1	3	1	5	2	4	2	2	1	4	3	2	1	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:63119666T>C	ENST00000340370.5	-	3	326	c.309A>G	c.(307-309)gtA>gtG	p.V103V	DOCK7_ENST00000404627.2_Silent_p.V103V|DOCK7_ENST00000251157.5_Silent_p.V103V	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	103					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TTTCTTCAGGTACAGCTGAAA	0.388																																					p.V103V		.											.	DOCK7-92	0			c.A309G						.						56	57	57					1																	63119666		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon3			TTCAGGTACAGCT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.309A>G	1.37:g.63119666T>C		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_001272002	0	0	0	0	0	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1																																																																																			.		0.388	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		C	63119666	T	C	63119666	2	2	3	1	0	0	0	0	0	0	0	1	4703	1625	57	3		3	DOCK7	1	63119666	Silent	SNP	T	TCGA-A4-7288-01A-11D-2136-08	35869028	63119666	186130955	4	125											
CTH	1491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	70877247	70877247	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtccaccacgttcaagcaagGggcgcctggccagcactcgg	8	5	13	15	3	1	0	1	0	0	0	3	0	2	0	4	4	2	3	4	4	2	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:70877247G>C	ENST00000370938.3	+	1	293	c.149G>C	c.(148-150)gGg>gCg	p.G50A	CTH_ENST00000464926.1_3'UTR|CTH_ENST00000346806.2_Missense_Mutation_p.G50A|CTH_ENST00000411986.2_Missense_Mutation_p.G50A	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TTCAAGCAAGGGGCGCCTGGC	0.572																																					p.G50A		.											.	CTH-91	0			c.G149C						.						51	50	50					1																	70877247		2203	4300	6503	SO:0001583	missense	1491	exon1			AGCAAGGGGCGCC	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.149G>C	1.37:g.70877247G>C	ENSP00000359976:p.Gly50Ala	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	83	29	NM_001190463	0	0	18	35	17	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000370938.3	37	CCDS650.1	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.375323	0.01214	.	.	ENSG00000116761	ENST00000411986;ENST00000370938;ENST00000346806	D;D;D	0.83673	-1.75;-1.55;-1.75	5.18	-8.32	0.00996	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	1.452490	0.03681	N	0.245551	T	0.29882	0.0747	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.14023	0.01;0.002;0.001	T	0.35822	-0.9773	10	0.20519	T	0.43	-5.4518	1.6154	0.02702	0.3741:0.2347:0.2428:0.1485	.	50;50;50	E9PDV0;P32929-2;P32929	.;.;CGL_HUMAN	A	50	ENSP00000413407:G50A;ENSP00000359976:G50A;ENSP00000311554:G50A	ENSP00000311554:G50A	G	+	2	0	CTH	70649835	0.000000	0.05858	0.000000	0.03702	0.237000	0.25408	-0.581000	0.05820	-1.909000	0.01085	-2.768000	0.00120	GGG	.		0.572	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		C	70877247	G	C	70877247	3	2	3	1	0	0	0	0	1	0	0	0	4015	1232	43	4	151	4	CTH	1	70877247	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	7757581	70877247	178373374	5	126											
DNTTIP2	30836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94337674	94337674	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcatttttcttgtaaaatCttttcgggtccatgctggct	7	19	7	8	1	3	0	1	0	2	0	5	0	4	0	1	2	1	3	1	2	3	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:94337674C>A	ENST00000436063.2	-	5	2078	c.2021G>T	c.(2020-2022)aGa>aTa	p.R674I		NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	674					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CTTGTAAAATCTTTTCGGGTC	0.408																																					p.R674I		.											.	.	0			c.G2021T						.						265	258	260					1																	94337674		1860	4107	5967	SO:0001583	missense	30836	exon5			TAAAATCTTTTCG	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.2021G>T	1.37:g.94337674C>A	ENSP00000411010:p.Arg674Ile	Somatic	338	1		WXS	Illumina HiSeq	Phase_I	302	135	NM_014597	0	0	12	21	9	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550698	0.86127	.	.	ENSG00000067334	ENST00000436063	T	0.51817	0.69	6.02	5.1	0.69264	Fcf2 pre-rRNA processing (1);	0.159613	0.50627	D	0.000114	T	0.66607	0.2806	M	0.91920	3.255	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.75502	-0.3295	10	0.87932	D	0	.	11.1086	0.48218	0.0:0.7959:0.1307:0.0734	.	674	Q5QJE6	TDIF2_HUMAN	I	674	ENSP00000411010:R674I	ENSP00000411010:R674I	R	-	2	0	DNTTIP2	94110262	1.000000	0.71417	0.974000	0.42286	0.972000	0.66771	4.733000	0.62036	1.539000	0.49286	0.650000	0.86243	AGA	.		0.408	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		A	94337674	C	A	94337674	3	1	3	1	0	0	0	0	1	0	0	0	4693	913	32	4	261	4	DNTTIP2	1	94337674	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	23460427	94337674	154912947	6	127											
SETDB1	9869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150936790	150936790	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgggcagtgtggaaggcaagGagctactctgttgctgtggg	7	10	18	6	0	1	0	0	0	1	0	1	2	1	2	0	5	3	5	0	5	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:150936790G>A	ENST00000271640.5	+	22	4016	c.3826G>A	c.(3826-3828)Gag>Aag	p.E1276K	CERS2_ENST00000561294.1_3'UTR|RP11-316M1.12_ENST00000561111.1_RNA|CERS2_ENST00000345896.4_5'Flank|RP11-316M1.12_ENST00000560481.1_RNA|SETDB1_ENST00000368969.4_Missense_Mutation_p.E1275K	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	1276	Post-SET. {ECO:0000255|PROSITE- ProRule:PRU00155}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGAAGGCAAGGAGCTACTCTG	0.507																																					p.E1276K		.											.	SETDB1-228	0			c.G3826A						.						183	141	155					1																	150936790		2203	4300	6503	SO:0001583	missense	9869	exon22			GGCAAGGAGCTAC	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.3826G>A	1.37:g.150936790G>A	ENSP00000271640:p.Glu1276Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	63	16	NM_001145415	0	0	11	22	11	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Missense_Mutation	SNP	ENST00000271640.5	37	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	G	8.523	0.869314	0.17322	.	.	ENSG00000143379	ENST00000271640;ENST00000368969	D;D	0.87029	-2.2;-2.2	4.81	4.81	0.61882	Post-SET domain (2);	0.167783	0.50627	D	0.000103	T	0.51483	0.1677	N	0.04090	-0.28	0.80722	D	1	B;B	0.19445	0.036;0.02	B;B	0.17979	0.02;0.007	T	0.55373	-0.8151	10	0.02654	T	1	.	11.2196	0.48846	0.0851:0.0:0.9149:0.0	.	1275;1276	Q15047-3;Q15047	.;SETB1_HUMAN	K	1276;1275	ENSP00000271640:E1276K;ENSP00000357965:E1275K	ENSP00000271640:E1276K	E	+	1	0	SETDB1	149203414	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.694000	0.84235	2.493000	0.84123	0.462000	0.41574	GAG	.		0.507	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			A	150936790	G	A	150936790	3	1	3	1	0	0	0	0	1	0	0	0	14170	1175	41	2	3908	2	SETDB1	1	150936790	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	56599116	150936790	98313831	7	128											
SLC27A3	11000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153752431	153752431	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggtgcctacctgcccctcAcaactgcccggtacagcgcc	7	7	9	18	2	1	0	1	0	0	0	1	0	1	0	6	2	7	1	6	2	4	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:153752431A>T	ENST00000368661.3	+	10	2211	c.2146A>T	c.(2146-2148)Aca>Tca	p.T716S	SLC27A3_ENST00000271857.2_Missense_Mutation_p.T797S|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	716					fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCTGCCCCTCACAACTGCCCG	0.597																																					p.T716S		.											.	SLC27A3-91	0			c.A2146T						.						79	59	66					1																	153752431		2203	4300	6503	SO:0001583	missense	11000	exon10			CCCCTCACAACTG	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"Acyl-CoA synthetase family", "Solute carriers"	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.2146A>T	1.37:g.153752431A>T	ENSP00000357650:p.Thr716Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	40	18	NM_024330	0	0	15	36	21	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	37	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.033819	0.75504	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.58797	0.31;0.33	4.36	4.36	0.52297	.	0.131608	0.49916	D	0.000131	T	0.47710	0.1460	L	0.49513	1.565	0.35861	D	0.827484	P	0.47545	0.897	P	0.51945	0.685	T	0.49331	-0.8951	10	0.33940	T	0.23	-10.5075	10.175	0.42933	1.0:0.0:0.0:0.0	.	716	Q5K4L6	S27A3_HUMAN	S	797;716	ENSP00000271857:T797S;ENSP00000357650:T716S	ENSP00000271857:T797S	T	+	1	0	SLC27A3	152019055	1.000000	0.71417	0.999000	0.59377	0.431000	0.31685	6.078000	0.71282	1.976000	0.57569	0.477000	0.44152	ACA	.		0.597	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		T	153752431	A	T	153752431	3	4	3	1	0	0	0	0	1	0	0	0	14559	159	6	5	2184	5	SLC27A3	1	153752431	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	2815641	153752431	95498190	8	129											
DDX59	83479	hgsc.bcm.edu;broad.mit.edu	37	chr1	200635600	200635600	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttttggaaaatgacttaacgGgctcttcagaaggatggctg	11	12	12	6	1	2	2	1	1	1	1	2	4	2	4	0	4	1	2	0	4	4	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:200635600G>C	ENST00000331314.6	-	2	482	c.269C>G	c.(268-270)cCc>cGc	p.P90R	DDX59_ENST00000367348.3_Missense_Mutation_p.P90R|DDX59_ENST00000447706.2_Missense_Mutation_p.P90R	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	90						cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						TGACTTAACGGGCTCTTCAGA	0.522																																					p.P90R		.											.	DDX59-155	0			c.C269G						.						76	73	74					1																	200635600		2203	4300	6503	SO:0001583	missense	83479	exon2			TTAACGGGCTCTT	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"Zinc fingers, HIT-type", "DEAD-boxes"	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.269C>G	1.37:g.200635600G>C	ENSP00000330460:p.Pro90Arg	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_001031725	0	0	13	13	0	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	37	CCDS30964.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702280	0.68501	.	.	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314;ENST00000436897	T;T;T;T	0.50001	1.42;1.44;1.8;0.76	5.33	5.33	0.75918	.	0.052721	0.85682	D	0.000000	T	0.47691	0.1459	M	0.61703	1.905	0.80722	D	1	P;P	0.38473	0.633;0.633	B;B	0.33750	0.169;0.169	T	0.52351	-0.8587	10	0.48119	T	0.1	-19.137	19.0716	0.93140	0.0:0.0:1.0:0.0	.	90;90	B7Z5N6;Q5T1V6	.;DDX59_HUMAN	R	90	ENSP00000394367:P90R;ENSP00000356317:P90R;ENSP00000330460:P90R;ENSP00000391312:P90R	ENSP00000330460:P90R	P	-	2	0	DDX59	198902223	1.000000	0.71417	0.988000	0.46212	0.825000	0.46686	9.440000	0.97547	2.505000	0.84491	0.550000	0.68814	CCC	.		0.522	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4		C	200635600	G	C	200635600	3	2	3	1	0	0	0	0	1	0	0	0	4382	1232	43	4	1618	4	DDX59	1	200635600	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	46883169	200635600	48615021	9	130											
BTG2	7832	broad.mit.edu	37	chr1	203274779	203274779	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctcccggagatcgccgcCgccgtgggcttcctctccag	4	8	12	17	5	1	1	0	0	1	1	5	2	3	1	6	2	1	2	6	2	0	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:203274779C>T	ENST00000290551.4	+	1	116	c.45C>T	c.(43-45)gcC>gcT	p.A15A	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	15					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			AGATCGCCGCCGCCGTGGGCT	0.682																																					p.A15A													.	BTG2-651	0			c.C45T						.						18	16	17					1																	203274779		2185	4271	6456	SO:0001819	synonymous_variant	7832	exon1			CGCCGCCGCCGTG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.45C>T	1.37:g.203274779C>T		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	12	3	NM_006763	0	0	78	151	73	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.		0.682	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		T	203274779	C	T	203274779	2	4	3	1	0	0	0	0	0	0	0	1	1557	639	23	1		1	BTG2	1	203274779	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	2639179	203274779	45975842	10	131											
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	109383218	109383218	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcaaactaagaatgctgAtgcgaagagaacaagtacta	18	7	10	6	1	0	3	0	1	0	2	0	5	0	3	0	1	5	3	0	1	8	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:109383218A>C	ENST00000283195.6	+	20	6349	c.6223A>C	c.(6223-6225)Atg>Ctg	p.M2075L		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2075	RanBD1 2. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AAGAATGCTGATGCGAAGAGA	0.408																																					p.M2075L		.											.	RANBP2-675	0			c.A6223C						.						190	209	202					2																	109383218		2202	4285	6487	SO:0001583	missense	5903	exon20			ATGCTGATGCGAA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.6223A>C	2.37:g.109383218A>C	ENSP00000283195:p.Met2075Leu	Somatic	697	0		WXS	Illumina HiSeq	Phase_I	566	257	NM_006267	0	0	43	61	18	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.065716	0.76187	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.50548	0.74	5.65	5.65	0.86999	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.69269	0.3092	M	0.73962	2.25	0.42261	D	0.992016	D	0.76494	0.999	D	0.83275	0.996	T	0.73603	-0.3930	9	0.72032	D	0.01	-23.7784	15.8694	0.79101	1.0:0.0:0.0:0.0	.	2075	P49792	RBP2_HUMAN	L	1099;2075	ENSP00000283195:M2075L	ENSP00000283195:M2075L	M	+	1	0	RANBP2	108749650	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.143000	0.66587	0.455000	0.32223	ATG	.		0.408	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109383218	A	C	109383218	3	2	3	1	0	0	0	0	1	0	0	0	13060	333	12	5	6301	5	RANBP2	2	109383218	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08		109383218	133816155	11	132											
RIF1	55183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152319615	152319615	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatctagtacagaaaattCtttcgttgtcagcagtagtt	11	15	8	7	1	3	1	1	0	2	1	4	1	3	1	0	0	3	6	0	0	5	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:152319615C>A	ENST00000243326.5	+	29	4064	c.3581C>A	c.(3580-3582)tCt>tAt	p.S1194Y	RIF1_ENST00000453091.2_Missense_Mutation_p.S1194Y|RIF1_ENST00000428287.2_Missense_Mutation_p.S1194Y|RIF1_ENST00000444746.2_Missense_Mutation_p.S1194Y|RIF1_ENST00000430328.2_Missense_Mutation_p.S1194Y			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ACAGAAAATTCTTTCGTTGTC	0.368																																					p.S1194Y		.											.	RIF1-300	0			c.C3581A						.						97	95	96					2																	152319615		2203	4300	6503	SO:0001583	missense	55183	exon30			AAAATTCTTTCGT	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3581C>A	2.37:g.152319615C>A	ENSP00000243326:p.Ser1194Tyr	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	108	23	NM_018151	0	0	4	4	0	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	C	5.213	0.224840	0.09916	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.11712	2.76;2.75;2.75;2.76;2.75	5.06	4.17	0.49024	.	0.650132	0.14971	N	0.287787	T	0.10078	0.0247	N	0.19112	0.55	0.43234	D	0.995138	P;P	0.51351	0.94;0.944	B;P	0.44811	0.332;0.461	T	0.16070	-1.0415	10	0.62326	D	0.03	-4.9829	13.5366	0.61650	0.0:0.9222:0.0:0.0778	.	1194;1194	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	Y	1194	ENSP00000390181:S1194Y;ENSP00000414615:S1194Y;ENSP00000415691:S1194Y;ENSP00000243326:S1194Y;ENSP00000416123:S1194Y	ENSP00000243326:S1194Y	S	+	2	0	RIF1	152027861	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	0.710000	0.25748	2.339000	0.79563	0.563000	0.77884	TCT	.		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			A	152319615	C	A	152319615	3	1	3	1	0	0	0	0	1	0	0	0	13391	913	32	4	3695	4	RIF1	2	152319615	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	42936397	152319615	90879758	12	133											
ZNF804A	91752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	185802128	185802128	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagaatccatatccttaagtGacaatgaagaaatgtgtaaa	18	10	7	6	0	0	4	0	2	0	2	2	4	2	4	2	0	0	1	2	0	8	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:185802128G>C	ENST00000302277.6	+	4	2599	c.2005G>C	c.(2005-2007)Gac>Cac	p.D669H		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	669							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						ATCCTTAAGTGACAATGAAGA	0.323																																					p.D669H		.											.	ZNF804A-163	0			c.G2005C						.						83	86	85					2																	185802128		2203	4297	6500	SO:0001583	missense	91752	exon4			TTAAGTGACAATG	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2005G>C	2.37:g.185802128G>C	ENSP00000303252:p.Asp669His	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	112	44	NM_194250	0	0	0	0	0	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829378	0.50845	.	.	ENSG00000170396	ENST00000302277	T	0.05996	3.36	5.54	4.47	0.54385	.	0.381496	0.22235	N	0.062766	T	0.03608	0.0103	N	0.08118	0	0.09310	N	1	B	0.33448	0.412	B	0.31191	0.125	T	0.41680	-0.9495	10	0.46703	T	0.11	-15.3768	10.7923	0.46440	0.0812:0.0:0.7837:0.1351	.	669	Q7Z570	Z804A_HUMAN	H	669	ENSP00000303252:D669H	ENSP00000303252:D669H	D	+	1	0	ZNF804A	185510373	0.943000	0.32029	0.885000	0.34714	0.589000	0.36550	1.746000	0.38288	2.609000	0.88269	0.655000	0.94253	GAC	.		0.323	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185802128	G	C	185802128	3	2	3	1	0	0	0	0	1	0	0	0	18202	1290	45	4	2019	4	ZNF804A	2	185802128	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	33482513	185802128	57397245	13	134											
ANKRD44	91526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198001337	198001337	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacttctggaagcaacagcCcggtgcagtggagtcagcca	10	7	12	12	1	3	0	2	0	1	0	3	2	3	2	2	3	5	2	2	3	2	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:198001337C>A	ENST00000328737.2	-	4	241	c.165G>T	c.(163-165)cgG>cgT	p.R55R	ANKRD44_ENST00000337207.5_Silent_p.R55R|ANKRD44_ENST00000409919.1_Silent_p.R80R|ANKRD44_ENST00000409153.1_Silent_p.R80R|ANKRD44_ENST00000539527.1_Silent_p.R8R|ANKRD44_ENST00000282272.8_Silent_p.R72R|ANKRD44_ENST00000450567.1_Silent_p.R55R			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	80										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AAGCAACAGCCCGGTGCAGTG	0.443																																					p.R80R		.											.	ANKRD44-230	0			c.G240T						.						86	86	86					2																	198001337		2203	4300	6503	SO:0001819	synonymous_variant	91526	exon4			AACAGCCCGGTGC	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.165G>T	2.37:g.198001337C>A		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	67	30	NM_153697	0	0	0	1	1	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																				.		0.443	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		A	198001337	C	A	198001337	2	1	3	1	0	0	0	0	0	0	0	1	672	610	22	4		4	ANKRD44	2	198001337	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	12199209	198001337	45198036	14	135											
RBM44	375316	hgsc.bcm.edu	37	chr2	238726834	238726834	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcagagataatcaggcaatAgaagataatacgtccctaaa	18	8	8	7	1	2	3	2	0	0	3	3	4	3	3	1	1	1	1	1	1	8	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:238726834A>G	ENST00000409864.1	+	3	1529	c.1275A>G	c.(1273-1275)atA>atG	p.I425M	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.I425M			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	424						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		ATCAGGCAATAGAAGATAATA	0.388																																					p.I425M		.											.	RBM44-26	0			c.A1275G						.						48	45	46					2																	238726834		1910	4121	6031	SO:0001583	missense	375316	exon3			GGCAATAGAAGAT	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1275A>G	2.37:g.238726834A>G	ENSP00000386727:p.Ile425Met	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_001080504	0	0	0	0	0	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	A	5.735	0.320040	0.10845	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.23950	1.88;1.88	5.86	-9.86	0.00473	.	2.411480	0.01194	N	0.007402	T	0.14657	0.0354	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.17228	-1.0376	10	0.40728	T	0.16	6.4429	4.7765	0.13182	0.1714:0.1865:0.497:0.1451	.	424	Q6ZP01	RBM44_HUMAN	M	425	ENSP00000321179:I425M;ENSP00000386727:I425M	ENSP00000321179:I425M	I	+	3	3	RBM44	238391573	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.866000	0.04245	-1.235000	0.02545	0.482000	0.46254	ATA	.		0.388	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		G	238726834	A	G	238726834	3	3	3	1	0	0	0	0	1	0	0	0	13170	410	15	3	1281	3	RBM44	2	238726834	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	40725497	238726834	4472539	15	136											
DCP1A	55802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	53376261	53376261	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagattgtgcatatttagtcGattcacaatggtaaaaccat	14	14	7	6	1	1	1	1	0	0	1	2	2	1	1	1	1	2	2	1	1	6	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:53376261G>T	ENST00000607628.1	-	3	323	c.214C>A	c.(214-216)Cga>Aga	p.R72R	DCP1A_ENST00000606822.1_Silent_p.R72R|DCP1A_ENST00000480258.1_5'UTR|DCP1A_ENST00000294241.6_Silent_p.R72R	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	72					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		ATATTTAGTCGATTCACAATG	0.318																																					p.R72R		.											.	DCP1A-90	0			c.C214A						.						55	54	55					3																	53376261		1826	4080	5906	SO:0001819	synonymous_variant	55802	exon3			TTAGTCGATTCAC	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"DCP1 decapping enzyme homolog A (S. cerevisiae)"				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.214C>A	3.37:g.53376261G>T		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	17	11	NM_018403	0	0	5	9	4	B4DHN9|U3KQM8	Silent	SNP	ENST00000607628.1	37																																																																																				.		0.318	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403		T	53376261	G	T	53376261	2	4	3	1	0	0	0	0	0	0	0	1	4304	1066	37	4		4	DCP1A	3	53376261	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08		53376261	144646169	16	137											
MORC1	27136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	108703606	108703606	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcttttcattgctagaaCatcattgcacagctcctgtt	8	16	6	11	0	3	1	2	0	1	1	4	1	4	1	1	0	4	5	1	0	2	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:108703606C>T	ENST00000483760.1	-	22	2261	c.2218G>A	c.(2218-2220)Gtt>Att	p.V740I	MORC1_ENST00000232603.5_Missense_Mutation_p.V761I					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						ATTGCTAGAACATCATTGCAC	0.363																																					p.V761I		.											.	MORC1-98	0			c.G2281A						.						105	94	98					3																	108703606		2203	4299	6502	SO:0001583	missense	27136	exon23			CTAGAACATCATT	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2218G>A	3.37:g.108703606C>T	ENSP00000417282:p.Val740Ile	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_014429	0	0	0	0	0		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	C	1.485	-0.556108	0.03967	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05580	3.44;3.42	5.49	-3.41	0.04839	.	1.888090	0.02334	N	0.074205	T	0.04092	0.0114	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.41378	-0.9512	10	0.25751	T	0.34	3.2721	11.5425	0.50675	0.0:0.5909:0.0:0.4091	.	740;761	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	761;740	ENSP00000232603:V761I;ENSP00000417282:V740I	ENSP00000232603:V761I	V	-	1	0	MORC1	110186296	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.274000	0.02820	-0.729000	0.04875	0.655000	0.94253	GTT	.		0.363	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108703606	C	T	108703606	3	4	3	1	0	0	0	0	1	0	0	0	9726	478	17	2	697	2	MORC1	3	108703606	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	55327345	108703606	89318824	17	138											
PLOD2	5352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	145803003	145803003	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttggatttgtcaaaacAacatctgcatccacactaaa	14	11	5	11	0	2	0	1	0	1	0	4	1	4	1	2	1	3	1	2	1	5	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:145803003A>T	ENST00000360060.3	-	11	1362	c.1185T>A	c.(1183-1185)gtT>gtA	p.V395V	RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Silent_p.V395V|PLOD2_ENST00000461497.1_Silent_p.V55V|PLOD2_ENST00000494950.1_Silent_p.V340V	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	395					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TTGTCAAAACAACATCTGCAT	0.284																																					p.V395V		.											.	PLOD2-92	0			c.T1185A						.						70	70	70					3																	145803003		2203	4297	6500	SO:0001819	synonymous_variant	5352	exon11			CAAAACAACATCT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1185T>A	3.37:g.145803003A>T		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	54	21	NM_182943	0	0	29	48	19	B3KWS3|Q59ED2|Q8N170	Silent	SNP	ENST00000360060.3	37	CCDS3131.1																																																																																			.		0.284	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145803003	A	T	145803003	2	4	3	1	0	0	0	0	0	0	0	1	12128	117	5	5		5	PLOD2	3	145803003	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	37099397	145803003	52219427	18	139											
TBL1XR1	79718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	176767825	176767825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccttgttgcttggaacaTcttgccctccttctcgtata	6	16	6	13	1	2	0	0	0	2	0	5	1	4	1	3	1	3	3	3	1	3	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:176767825T>C	ENST00000430069.1	-	7	921	c.662A>G	c.(661-663)gAt>gGt	p.D221G	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.D221G|TBL1XR1-AS1_ENST00000454723.2_RNA			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	221					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			GCTTGGAACATCTTGCCCTCC	0.413																																					p.D221G		.											.	TBL1XR1-187	0			c.A662G						.						167	157	160					3																	176767825		2000	4151	6151	SO:0001583	missense	79718	exon7			GGAACATCTTGCC	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"WD repeat domain containing"	29529	protein-coding gene	gene with protein product		608628	"transducin (beta)-like 1X-linked receptor 1"			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.662A>G	3.37:g.176767825T>C	ENSP00000405574:p.Asp221Gly	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	50	27	NM_024665	0	0	14	29	15	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	37	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.486855	0.63962	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	T;T	0.54279	0.58;0.58	5.23	5.23	0.72850	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	L	0.39514	1.22	0.80722	D	1	B	0.28933	0.228	B	0.29077	0.098	T	0.32508	-0.9904	10	0.23302	T	0.38	-8.7332	14.6231	0.68599	0.0:0.0:0.0:1.0	.	221	Q9BZK7	TBL1R_HUMAN	G	221;221;83	ENSP00000405574:D221G;ENSP00000413251:D221G	ENSP00000405574:D221G	D	-	2	0	TBL1XR1	178250519	1.000000	0.71417	0.971000	0.41717	0.936000	0.57629	8.031000	0.88826	2.100000	0.63781	0.533000	0.62120	GAT	.		0.413	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		C	176767825	T	C	176767825	3	2	3	1	0	0	0	0	1	0	0	0	15672	1435	50	3	922	3	TBL1XR1	3	176767825	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	30964822	176767825	21254605	19	140											
MAP3K13	9175	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	185191375	185191375	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccctctgctgagccagtgggGaggagccctgacctttccaa	7	8	12	14	0	1	2	0	2	1	0	2	4	2	4	5	3	3	1	5	3	1	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:185191375G>A	ENST00000265026.3	+	11	2590	c.2256G>A	c.(2254-2256)ggG>ggA	p.G752G	MAP3K13_ENST00000535426.1_Silent_p.G608G|MAP3K13_ENST00000443863.1_Silent_p.G608G|MAP3K13_ENST00000446828.1_Silent_p.G545G|MAP3K13_ENST00000424227.1_Silent_p.G752G	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			AGCCAGTGGGGAGGAGCCCTG	0.542																																					p.G752G		.											.	MAP3K13-548	0			c.G2256A						.						97	100	99					3																	185191375		2203	4300	6503	SO:0001819	synonymous_variant	9175	exon11			AGTGGGGAGGAGC	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.2256G>A	3.37:g.185191375G>A		Somatic	219	0		WXS	Illumina HiSeq	Phase_I	185	10	NM_004721	0	0	8	8	0		Silent	SNP	ENST00000265026.3	37	CCDS3270.1																																																																																			.		0.542	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		A	185191375	G	A	185191375	2	1	3	1	0	0	0	0	0	0	0	1	9272	1161	41	2		2	MAP3K13	3	185191375	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08	8423550	185191375	12831055	20	141											
AHSG	197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186335047	186335047	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgctgaacgacaccagggtgGtgcacgccgcgaaagctgcc	9	4	14	14	5	0	1	0	1	0	0	0	3	0	1	3	2	4	3	3	2	2	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:186335047G>A	ENST00000273784.5	+	4	560	c.484G>A	c.(484-486)Gtg>Atg	p.V162M	AHSG_ENST00000411641.2_Missense_Mutation_p.V161M	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	161	Cystatin fetuin-A-type 2. {ECO:0000255|PROSITE-ProRule:PRU00861}.			PLLAPLNDTRVVHAAKAALAAFNAQNNGSNFQL -> MVGW QEGANHKNGAGRSQKQEMAEKMVPEVASG (in Ref. 12; AAF69649). {ECO:0000305}.	acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CACCAGGGTGGTGCACGCCGC	0.612											OREG0015968	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V161M		.											.	AHSG-90	0			c.G481A						.						71	68	69					3																	186335047		2203	4300	6503	SO:0001583	missense	197	exon4			AGGGTGGTGCACG	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.484G>A	3.37:g.186335047G>A	ENSP00000273784:p.Val162Met	Somatic	164	0	2006	WXS	Illumina HiSeq	Phase_I	120	63	NM_001622	0	0	0	0	0	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		.	.	.	.	.	.	.	.	.	.	g	16.33	3.091941	0.55968	.	.	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.27720	1.65;1.65	5.61	2.7	0.31948	Proteinase inhibitor I25, cystatin (2);	0.536617	0.18379	N	0.143005	T	0.51398	0.1672	M	0.82323	2.585	0.30380	N	0.782048	D;D;D;D	0.76494	0.999;0.999;0.974;0.997	D;D;P;D	0.79108	0.983;0.992;0.842;0.985	T	0.52653	-0.8547	10	0.87932	D	0	-14.4644	4.9244	0.13885	0.1851:0.1755:0.6394:0.0	.	227;161;162;161	F5H0Q5;P02765;C9JV77;B7Z556	.;FETUA_HUMAN;.;.	M	161;227;162	ENSP00000393887:V161M;ENSP00000273784:V162M	ENSP00000273784:V162M	V	+	1	0	AHSG	187817741	0.998000	0.40836	1.000000	0.80357	0.460000	0.32559	0.737000	0.26144	1.513000	0.48852	0.561000	0.74099	GTG	.		0.612	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622		A	186335047	G	A	186335047	3	1	3	1	0	0	0	0	1	0	0	0	420	1261	44	2	495	2	AHSG	3	186335047	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	1143672	186335047	11687383	21	142											
WHSC2	7469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1985129	1985129	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catctcaaacactgtgtccaCcagcatggttgtgctaccct	9	11	7	14	0	1	0	1	0	1	0	3	0	2	0	3	1	4	3	3	1	2	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:1985129C>T	ENST00000411638.2	-	11	1519	c.1504G>A	c.(1504-1506)Gtg>Atg	p.V502M	NELFA_ENST00000542778.1_Missense_Mutation_p.V367M|NELFA_ENST00000382882.3_Missense_Mutation_p.V513M|MIR943_ENST00000401286.1_RNA	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	502					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)										ACTGTGTCCACCAGCATGGTT	0.592																																					p.V513M		.											.	.	0			c.G1537A						.						223	192	203					4																	1985129		2203	4300	6503	SO:0001583	missense	7469	exon11			TGTCCACCAGCAT	AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"Wolf-Hirschhorn syndrome candidate 2"	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.1504G>A	4.37:g.1985129C>T	ENSP00000399165:p.Val502Met	Somatic	255	0		WXS	Illumina HiSeq	Phase_I	180	81	NM_005663	0	0	17	37	20	A2A2T1|O95392	Missense_Mutation	SNP	ENST00000411638.2	37		.	.	.	.	.	.	.	.	.	.	C	31	5.095651	0.94197	.	.	ENSG00000185049	ENST00000382882;ENST00000416258;ENST00000542778;ENST00000411638	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.74696	0.3750	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78193	-0.2299	10	0.87932	D	0	-33.4962	18.8462	0.92208	0.0:1.0:0.0:0.0	.	502	Q9H3P2	NELFA_HUMAN	M	513;506;367;502	ENSP00000372335:V513M;ENSP00000387647:V506M;ENSP00000445757:V367M;ENSP00000399165:V502M	ENSP00000372335:V513M	V	-	1	0	WHSC2	1954927	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.720000	0.84759	2.466000	0.83321	0.462000	0.41574	GTG	.		0.592	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663		T	1985129	C	T	1985129	3	4	3	1	0	0	0	0	1	0	0	0	17397	507	18	2	86	2	WHSC2	4	1985129	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1985129	189169147	22	143											
COMMD8	54951	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	47462160	47462160	+	Splice_Site	DEL	C	C	-																															agaaatgtgcagagaagttaCctcttcatcaggtaagtttt																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:47462160delC	ENST00000381571.4	-	2	290		c.e2+1			NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8											large_intestine(2)|lung(5)|prostate(1)	8						AGAGAAGTTACCTCTTCATCA	0.338																																					.		.											.	COMMD8-90	0			c.222+1G>-						.						93	97	96					4																	47462160		2203	4300	6503	SO:0001630	splice_region_variant	54951	exon3			.	AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.222+1G>-	4.37:g.47462160delC		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	72	33	NM_017845	0	0	0	0	0	Q8WUR4|Q9HC15	Splice_Site	DEL	ENST00000381571.4	37	CCDS3475.1																																																																																			.		0.338	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845	Intron	-	47462160	C	-	47462160	8	5	3	1	0	1	0	1	0	0	1	0	3728	521	18	0	344	0	COMMD8	4	47462160	Splice_Site	DEL	C	TCGA-A4-7288-01A-11D-2136-08	45477031	47462160	143692116	23	144	2	3									
COMMD8	54951	hgsc.bcm.edu	37	chr4	47462161	47462163	+	Splice_Site	DEL	CTC	CTC	-																															gaaatgtgcagagaagttacCtcttcatcaggtaagttttt																								rs550666373		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:47462161_47462163delCTC	ENST00000381571.4	-	2	287_289	c.220_222delGAG	c.(220-222)gagdel	p.E74del		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	74										large_intestine(2)|lung(5)|prostate(1)	8						GAGAAGTTACCTCTTCATCAGGT	0.335																																					p.74_74del		.											.	COMMD8-90	0			c.220_222del						.																																			SO:0001630	splice_region_variant	54951	exon2			.	AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.222+1GAG>-	4.37:g.47462161_47462163delCTC		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	77	21	NM_017845	0	0	0	0	0	Q8WUR4|Q9HC15	In_Frame_Del	DEL	ENST00000381571.4	37	CCDS3475.1																																																																																			.		0.335	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845	In_Frame_Del	-	47462163	CTC	-	47462161	8	5	3	1	0	1	0	1	0	0	1	0	3728	695	24	0	345	0	COMMD8	4	47462161	Splice_Site	DEL	CTC	TCGA-A4-7288-01A-11D-2136-08	1	47462161	143692115	24	145	2	3									
COMMD8	54951	hgsc.bcm.edu;bcgsc.ca	37	chr4	47462163	47462163	+	Missense_Mutation	SNP	C	C	T																															aatgtgcagagaagttacctCttcatcaggtaagtttttac																								rs550666373		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:47462163C>T	ENST00000381571.4	-	2	287	c.220G>A	c.(220-222)Gag>Aag	p.E74K		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	74										large_intestine(2)|lung(5)|prostate(1)	8						GAAGTTACCTCTTCATCAGGT	0.338													C|||	1	0.000199681	0	0	5008	,	,		16976	0		0	False		,,,				2504	0.001				p.E74K		.											.	COMMD8-90	0			c.G220A						.						94	98	97					4																	47462163		2203	4300	6503	SO:0001583	missense	54951	exon2			TTACCTCTTCATC	AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.220G>A	4.37:g.47462163C>T	ENSP00000370984:p.Glu74Lys	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	76	36	NM_017845	0	0	0	0	0	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	37	CCDS3475.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835702	0.50951	.	.	ENSG00000169019	ENST00000381571	T	0.10382	2.88	5.48	4.45	0.53987	.	0.093678	0.64402	D	0.000001	T	0.12475	0.0303	L	0.54908	1.71	0.53688	D	0.999977	B	0.21688	0.059	B	0.21917	0.037	T	0.05305	-1.0893	10	0.26408	T	0.33	-13.9433	14.0881	0.64971	0.0:0.9117:0.0:0.0883	.	74	Q9NX08	COMD8_HUMAN	K	74	ENSP00000370984:E74K	ENSP00000370984:E74K	E	-	1	0	COMMD8	47156920	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.167000	0.50793	2.574000	0.86865	0.591000	0.81541	GAG	.		0.338	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845		T	47462163	C	T	47462163	3	4	3	1	0	0	0	0	1	0	0	0	3728	922	32	2	347	2	COMMD8	4	47462163	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	2	47462163	143692113	25	146	2	3									
CEP135	9662	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	56847415	56847423	+	In_Frame_Del	DEL	TAAGAAAGG	TAAGAAAGG	-																															tcaggaagaattatctgcccTaagaaaggaatccacccaaa																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	TAAGAAAGG	TAAGAAAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:56847415_56847423delTAAGAAAGG	ENST00000257287.4	+	13	1773_1781	c.1649_1657delTAAGAAAGG	c.(1648-1659)ctaagaaaggaa>caa	p.550_553LRKE>Q		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	550					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TTATCTGCCCTAAGAAAGGAATCCACCCA	0.321																																					p.550_553del		.											.	CEP135-94	0			c.1649_1657del						.																																			SO:0001651	inframe_deletion	9662	exon13			.	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1649_1657delTAAGAAAGG	4.37:g.56847415_56847423delTAAGAAAGG	ENSP00000257287:p.Leu550_Glu553delinsGln	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	56	19	NM_025009	0	0	0	0	0	B2RMY0|O75130|Q58F25|Q9H8H7	In_Frame_Del	DEL	ENST00000257287.4	37	CCDS33986.1																																																																																			.		0.321	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		-	56847423	TAAGAAAGG	-	56847415	7	5	3	1	0	1	0	1	0	0	0	0	3253	1522	53	0	1695	0	CEP135	4	56847415	In_Frame_Del	DEL	TAAGAAAGG	TCGA-A4-7288-01A-11D-2136-08	9385252	56847415	134306861	26	147											
AASDH	132949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57204741	57204741	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacactttcccatcagtagAtgctgctgccagcaacattt	10	11	6	14	0	1	1	1	0	0	1	2	1	2	1	3	0	5	4	3	0	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:57204741A>G	ENST00000205214.6	-	15	3304	c.3124T>C	c.(3124-3126)Tct>Cct	p.S1042P	AASDH_ENST00000451613.1_3'UTR|AASDH_ENST00000513376.1_Missense_Mutation_p.S942P|AASDH_ENST00000434343.2_Missense_Mutation_p.S557P	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1042					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CCATCAGTAGATGCTGCTGCC	0.443																																					p.S1042P		.											.	AASDH-94	0			c.T3124C						.						83	78	80					4																	57204741		2203	4300	6503	SO:0001583	missense	132949	exon15			CAGTAGATGCTGC	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.3124T>C	4.37:g.57204741A>G	ENSP00000205214:p.Ser1042Pro	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	66	29	NM_181806	0	0	7	8	1	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	A	31	5.102080	0.94245	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.58797	0.31;0.31;0.31	6.04	6.04	0.98038	Quinonprotein alcohol dehydrogenase-like (2);	0.000000	0.85682	D	0.000000	T	0.81592	0.4855	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85713	0.1320	10	0.87932	D	0	-12.0294	16.6275	0.84975	1.0:0.0:0.0:0.0	.	1042	Q4L235	ACSF4_HUMAN	P	1042;942;557	ENSP00000205214:S1042P;ENSP00000423760:S942P;ENSP00000392158:S557P	ENSP00000205214:S1042P	S	-	1	0	AASDH	56899498	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.532000	0.81985	2.330000	0.79161	0.529000	0.55759	TCT	.		0.443	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		G	57204741	A	G	57204741	3	3	3	1	0	0	0	0	1	0	0	0	22	333	12	3	176	3	AASDH	4	57204741	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	357326	57204741	133949535	27	148											
RG9MTD2	93587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100470297	100470297	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgattttccttatcctgcTtttcttcatgtggtgaatct	5	21	7	8	0	3	2	1	2	2	0	5	2	5	2	2	1	1	1	2	1	2	6			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:100470297T>C	ENST00000273962.3	-	8	1280	c.968A>G	c.(967-969)aAg>aGg	p.K323R	TRMT10A_ENST00000394877.3_Missense_Mutation_p.K323R|TRMT10A_ENST00000394876.2_Missense_Mutation_p.K323R	NM_152292.4	NP_689505.1	Q8TBZ6	TM10A_HUMAN	tRNA methyltransferase 10 homolog A (S. cerevisiae)	323					magnesium ion homeostasis (GO:0010960)	extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										CTTATCCTGCTTTTCTTCATG	0.408																																					p.K323R		.											.	.	0			c.A968G						.						229	204	212					4																	100470297		2203	4300	6503	SO:0001583	missense	93587	exon8			TCCTGCTTTTCTT	BC028373	CCDS3650.1	4q23	2012-06-28	2012-06-28	2012-06-28	ENSG00000145331	ENSG00000145331			28403	protein-coding gene	gene with protein product			"RNA (guanine-9-) methyltransferase domain containing 2"	RG9MTD2		12477932	Standard	NM_152292		Approved	MGC27034, TRM10	uc003hva.4	Q8TBZ6	OTTHUMG00000131025	ENST00000273962.3:c.968A>G	4.37:g.100470297T>C	ENSP00000273962:p.Lys323Arg	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	154	83	NM_001134666	0	0	1	1	0	B2R8X7|Q9Y2T9	Missense_Mutation	SNP	ENST00000273962.3	37	CCDS3650.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.557204	0.27827	.	.	ENSG00000145331	ENST00000394877;ENST00000273962;ENST00000394876	T;T;T	0.18338	2.22;2.22;2.22	5.77	3.27	0.37495	.	2.001830	0.01754	N	0.030106	T	0.11024	0.0269	N	0.14661	0.345	0.09310	N	1	B	0.28713	0.22	B	0.21708	0.036	T	0.25779	-1.0122	10	0.16896	T	0.51	-3.9397	7.5405	0.27735	0.0:0.0782:0.1452:0.7766	.	323	Q8TBZ6	RG9D2_HUMAN	R	323	ENSP00000378343:K323R;ENSP00000273962:K323R;ENSP00000378342:K323R	ENSP00000273962:K323R	K	-	2	0	RG9MTD2	100689320	0.014000	0.17966	0.146000	0.22360	0.546000	0.35178	1.895000	0.39778	1.082000	0.41137	0.533000	0.62120	AAG	.		0.408	TRMT10A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253668.1	NM_152292		C	100470297	T	C	100470297	3	2	3	1	0	0	0	0	1	0	0	0	13304	1609	56	3	55	3	RG9MTD2	4	100470297	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	43265556	100470297	90683979	28	149											
TET2	54790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	106156045	106156045	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatgctaaatacctgttccTttcagaaaccagaacaacta	16	10	4	11	0	1	2	1	0	0	2	2	2	2	2	3	0	5	2	3	0	8	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:106156045T>A	ENST00000540549.1	+	3	1806	c.946T>A	c.(946-948)Ttt>Att	p.F316I	TET2_ENST00000513237.1_Missense_Mutation_p.F337I|TET2_ENST00000394764.1_Missense_Mutation_p.F316I|TET2_ENST00000413648.2_Missense_Mutation_p.F316I|TET2_ENST00000545826.1_Missense_Mutation_p.F316I|TET2_ENST00000305737.2_Missense_Mutation_p.F316I|TET2_ENST00000380013.4_Missense_Mutation_p.F316I			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	316					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TACCTGTTCCTTTCAGAAACC	0.453			"Mis N, F"		MDS																																p.F316I		.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2-4618	0			c.T946A						.						85	82	83					4																	106156045		2203	4300	6503	SO:0001583	missense	54790	exon3			TGTTCCTTTCAGA	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.946T>A	4.37:g.106156045T>A	ENSP00000442788:p.Phe316Ile	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	60	36	NM_001127208	0	0	3	4	1	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030078	0.35797	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110	T;T;T;T;T;T;T	0.04970	3.53;4.27;3.52;4.26;4.27;3.53;3.55	4.98	-0.249	0.13011	.	2.314700	0.02876	U	0.132326	T	0.06005	0.0156	L	0.29908	0.895	0.24527	N	0.994132	B;B;B	0.11235	0.002;0.002;0.004	B;B;B	0.12156	0.002;0.002;0.007	T	0.41538	-0.9503	10	0.66056	D	0.02	.	4.0271	0.09692	0.2106:0.5083:0.0:0.2811	.	337;316;316	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	I	316;316;316;337;316;316;316;316	ENSP00000306705:F316I;ENSP00000442788:F316I;ENSP00000442867:F316I;ENSP00000425443:F337I;ENSP00000369351:F316I;ENSP00000378245:F316I;ENSP00000391448:F316I	ENSP00000265149:F316I	F	+	1	0	TET2	106375494	0.211000	0.23529	0.867000	0.34043	0.171000	0.22731	0.357000	0.20199	-0.016000	0.14127	0.533000	0.62120	TTT	.		0.453	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106156045	T	A	106156045	3	1	3	1	0	0	0	0	1	0	0	0	15802	1609	56	5	948	5	TET2	4	106156045	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	5685748	106156045	84998231	29	150											
LARP1B	55132	hgsc.bcm.edu	37	chr4	128999004	128999004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagaaaagaaaaagaagagaAggttgaaaagagaagtaaca	25	4	11	1	0	0	6	0	1	0	5	0	8	0	6	0	1	1	2	0	1	11	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:128999004A>G	ENST00000326639.6	+	4	315	c.104A>G	c.(103-105)aAg>aGg	p.K35R	LARP1B_ENST00000512292.1_Missense_Mutation_p.K35R|LARP1B_ENST00000441387.1_Missense_Mutation_p.K35R|LARP1B_ENST00000394288.3_Missense_Mutation_p.K35R|LARP1B_ENST00000432347.2_Missense_Mutation_p.K35R|LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000427266.1_Missense_Mutation_p.K35R|LARP1B_ENST00000264584.5_Missense_Mutation_p.K35R	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	35						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						AAAGAAGAGAAGGTTGAAAAG	0.368																																					p.K35R		.											.	LARP1B-68	0			c.A104G						.						69	72	71					4																	128999004		2203	4300	6503	SO:0001583	missense	55132	exon4			AAGAGAAGGTTGA		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.104A>G	4.37:g.128999004A>G	ENSP00000321997:p.Lys35Arg	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_032239	0	0	28	28	0	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.875510	0.72180	.	.	ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266	T;T;T;T;T;T;T;T	0.49139	1.81;1.38;1.3;0.81;0.79;1.74;1.81;1.37	3.95	3.95	0.45737	.	0.569681	0.18331	N	0.144487	T	0.48484	0.1502	L	0.31752	0.955	0.80722	D	1	D;P;P;P	0.58620	0.983;0.859;0.859;0.859	P;B;B;B	0.55923	0.787;0.274;0.274;0.274	T	0.37753	-0.9692	10	0.32370	T	0.25	.	12.9379	0.58325	1.0:0.0:0.0:0.0	.	35;35;35;35	Q659C4;G3XAJ5;Q659C4-3;G3V0E9	LAR1B_HUMAN;.;.;.	R	35	ENSP00000321997:K35R;ENSP00000422850:K35R;ENSP00000427281:K35R;ENSP00000377829:K35R;ENSP00000390395:K35R;ENSP00000264584:K35R;ENSP00000396521:K35R;ENSP00000403586:K35R	ENSP00000264584:K35R	K	+	2	0	LARP1B	129218454	0.995000	0.38212	0.998000	0.56505	0.979000	0.70002	3.314000	0.51943	1.791000	0.52520	0.386000	0.25728	AAG	.		0.368	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		G	128999004	A	G	128999004	3	3	3	1	0	0	0	0	1	0	0	0	8650	72	3	3	110	3	LARP1B	4	128999004	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	22842959	128999004	62155272	30	151											
SLC12A7	10723	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	1064225	1064225	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggcgcagcaggaagggcagCagcatgagcatgccgccgtc	9	4	16	12	3	0	1	0	1	0	0	1	2	0	2	2	3	5	6	2	3	1	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr5:1064225C>G	ENST00000264930.5	-	19	2623	c.2580G>C	c.(2578-2580)ctG>ctC	p.L860L	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	860					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GGAAGGGCAGCAGCATGAGCA	0.697																																					p.L860L		.											.	SLC12A7-138	0			c.G2580C						.						43	38	39					5																	1064225		2200	4296	6496	SO:0001819	synonymous_variant	10723	exon19			GGGCAGCAGCATG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2580G>C	5.37:g.1064225C>G		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	40	19	NM_006598	0	0	72	147	75	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	C	7.240	0.601120	0.13939	.	.	ENSG00000113504	ENST00000513223	.	.	.	4.26	3.35	0.38373	.	.	.	.	.	T	0.54415	0.1857	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47761	-0.9092	4	.	.	.	.	5.8497	0.18685	0.2009:0.696:0.0:0.1031	.	.	.	.	P	218	.	.	A	-	1	0	SLC12A7	1117225	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	1.547000	0.36190	0.716000	0.32124	0.313000	0.20887	GCT	.		0.697	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		G	1064225	C	G	1064225	2	3	3	1	0	0	0	0	0	0	0	1	14420	697	25	4		4	SLC12A7	5	1064225	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1064225	179851035	31	152											
TNPO1	3842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	72192301	72192301	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctagctgatttcatgccaatAttgggaaccaacctaaatcc	13	11	6	11	0	1	1	1	1	0	0	2	2	2	2	4	1	4	1	4	1	7	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr5:72192301A>G	ENST00000337273.5	+	19	2586	c.2160A>G	c.(2158-2160)atA>atG	p.I720M	TNPO1_ENST00000506351.2_Missense_Mutation_p.I712M|TNPO1_ENST00000454282.1_Missense_Mutation_p.I670M|TNPO1_ENST00000523768.1_Missense_Mutation_p.I670M	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	720					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		TCATGCCAATATTGGGAACCA	0.338																																					p.I720M		.											.	TNPO1-228	0			c.A2160G						.						62	61	62					5																	72192301		2203	4300	6503	SO:0001583	missense	3842	exon19			GCCAATATTGGGA	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.2160A>G	5.37:g.72192301A>G	ENSP00000336712:p.Ile720Met	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	60	22	NM_002270	0	0	47	86	39	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.971943	0.34754	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351;ENST00000519220	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.66	1.57	0.23409	Armadillo-like helical (1);Armadillo-type fold (1);	0.084050	0.85682	D	0.000000	T	0.40145	0.1105	M	0.84773	2.715	0.80722	D	1	B;B	0.21225	0.053;0.011	B;B	0.28232	0.087;0.029	T	0.29058	-1.0024	10	0.52906	T	0.07	-14.1628	6.2257	0.20706	0.3859:0.1164:0.0:0.4977	.	670;720	Q92973-3;Q92973	.;TNPO1_HUMAN	M	720;670;670;712;231	ENSP00000336712:I720M;ENSP00000398524:I670M;ENSP00000428899:I670M;ENSP00000425118:I712M	ENSP00000336712:I720M	I	+	3	3	TNPO1	72228057	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.854000	0.27791	0.371000	0.24564	-0.316000	0.08728	ATA	.		0.338	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		G	72192301	A	G	72192301	3	3	3	1	0	0	0	0	1	0	0	0	16367	439	16	3	2234	3	TNPO1	5	72192301	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	71128076	72192301	108722959	32	153											
TCERG1	10915	hgsc.bcm.edu	37	chr5	145838583	145838583	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggcccaggcgcaggctcAggcccaggcgcaggctcagg	7	3	16	15	2	3	0	3	0	0	0	3	0	3	0	2	7	0	4	2	7	0	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr5:145838583A>G	ENST00000296702.5	+	4	613	c.575A>G	c.(574-576)cAg>cGg	p.Q192R	TCERG1_ENST00000394421.2_Missense_Mutation_p.Q192R	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	192	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			gcgcaggctcaggcccaggcg	0.657																																					p.Q192R		.											.	TCERG1-92	0			c.A575G						.						39	39	39					5																	145838583		2202	4300	6502	SO:0001583	missense	10915	exon4			AGGCTCAGGCCCA	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.575A>G	5.37:g.145838583A>G	ENSP00000296702:p.Gln192Arg	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_006706	0	0	9	9	0	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	A	9.852	1.193875	0.22037	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.35421	1.31;1.31	3.67	3.67	0.42095	.	0.273564	0.34777	N	0.003698	T	0.20659	0.0497	L	0.38175	1.15	0.21897	N	0.999481	P;P;B	0.38110	0.618;0.58;0.444	B;B;B	0.24394	0.043;0.053;0.024	T	0.13176	-1.0519	10	0.28530	T	0.3	-3.8538	8.8675	0.35296	1.0:0.0:0.0:0.0	.	192;192;192	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	R	192	ENSP00000296702:Q192R;ENSP00000377943:Q192R	ENSP00000296702:Q192R	Q	+	2	0	TCERG1	145818776	0.971000	0.33674	0.987000	0.45799	0.570000	0.35934	0.988000	0.29616	1.665000	0.50811	0.260000	0.18958	CAG	.		0.657	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		G	145838583	A	G	145838583	3	3	3	1	0	0	0	0	1	0	0	0	15717	188	7	3	589	3	TCERG1	5	145838583	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	73646282	145838583	35076677	33	154											
SCGN	10590	hgsc.bcm.edu;broad.mit.edu	37	chr6	25701512	25701512	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacgtgaacaaggatggaaaAattcagaagtctgagctggc	15	7	13	6	1	2	3	1	2	1	1	2	6	2	5	0	3	2	1	0	3	5	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr6:25701512A>T	ENST00000377961.2	+	11	948	c.780A>T	c.(778-780)aaA>aaT	p.K260N	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	260	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						AGGATGGAAAAATTCAGAAGT	0.483																																					p.K260N		.											.	SCGN-93	0			c.A780T						.						137	122	127					6																	25701512		2203	4300	6503	SO:0001583	missense	10590	exon11			TGGAAAAATTCAG	BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"EF-hand domain containing"	16941	protein-coding gene	gene with protein product	"calbindin-like"	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.780A>T	6.37:g.25701512A>T	ENSP00000367197:p.Lys260Asn	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	106	9	NM_006998	0	0	11	13	2	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Missense_Mutation	SNP	ENST00000377961.2	37	CCDS4561.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.222783	0.79464	.	.	ENSG00000079689	ENST00000377961	T	0.56103	0.48	5.43	1.84	0.25277	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.58821	0.2149	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62248	-0.6894	10	0.87932	D	0	.	7.8814	0.29624	0.7455:0.0:0.2545:0.0	.	260	O76038	SEGN_HUMAN	N	260	ENSP00000367197:K260N	ENSP00000367197:K260N	K	+	3	2	SCGN	25809491	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.257000	0.32932	0.372000	0.24591	0.533000	0.62120	AAA	.		0.483	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			T	25701512	A	T	25701512	3	4	3	1	0	0	0	0	1	0	0	0	13935	11	1	5	822	5	SCGN	6	25701512	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08		25701512	145413555	34	155											
TRAF3IP2	10758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	111912700	111912700	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggctgggaatcatatcccGtgtctatggttggcagatcc	7	11	14	9	1	2	1	1	0	1	1	4	2	4	2	2	5	0	3	2	5	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr6:111912700G>T	ENST00000340026.6	-	3	1211	c.617C>A	c.(616-618)aCg>aAg	p.T206K	TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.T197K|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.T197K|TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000392556.4_5'UTR			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	206	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		ATCATATCCCGTGTCTATGGT	0.627																																					p.T197K		.											.	TRAF3IP2-228	0			c.C590A						.						61	62	62					6																	111912700		2203	4300	6503	SO:0001583	missense	10758	exon2			TATCCCGTGTCTA	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.617C>A	6.37:g.111912700G>T	ENSP00000345984:p.Thr206Lys	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	107	12	NM_147686	0	0	15	16	1	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		.	.	.	.	.	.	.	.	.	.	G	18.22	3.576782	0.65878	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.37584	1.2;1.2;1.19	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.49201	0.1543	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.97;0.987;0.97	T	0.52011	-0.8632	10	0.87932	D	0	-10.0022	12.3995	0.55404	0.0771:0.0:0.9229:0.0	.	206;197;197	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	K	206;197;206;197	ENSP00000357750:T197K;ENSP00000345984:T206K;ENSP00000352889:T197K	ENSP00000345984:T206K	T	-	2	0	TRAF3IP2	112019393	1.000000	0.71417	0.988000	0.46212	0.642000	0.38348	3.685000	0.54678	2.702000	0.92279	0.555000	0.69702	ACG	.		0.627	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			T	111912700	G	T	111912700	3	4	3	1	0	0	0	0	1	0	0	0	16474	1145	40	4	1139	4	TRAF3IP2	6	111912700	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	86211188	111912700	59202367	35	156											
POM121	9883	hgsc.bcm.edu;broad.mit.edu	37	chr7	72416770	72416770	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcagcacacccgcaaaaaGtagcctttgtcccctgtccc	10	7	8	16	1	0	0	0	0	0	0	2	0	2	0	5	1	2	4	5	1	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr7:72416770G>A	ENST00000434423.2	+	13	3747	c.3747G>A	c.(3745-3747)aaG>aaA	p.K1249K	NSUN5P2_ENST00000388955.4_RNA|POM121_ENST00000446813.1_Intron|POM121_ENST00000257622.4_Silent_p.K984K|POM121_ENST00000395270.1_Intron|POM121_ENST00000358357.3_Silent_p.K984K			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1249	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CCCGCAAAAAGTAGCCTTTGT	0.592																																					p.K984K		.											.	POM121-226	0			c.G2952A						.						27	28	28					7																	72416770		2203	4295	6498	SO:0001819	synonymous_variant	9883	exon13			CAAAAAGTAGCCT	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"-"	19702	protein-coding gene	gene with protein product		615753	"POM121 membrane glycoprotein (rat)", "POM121 membrane glycoprotein"			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3747G>A	7.37:g.72416770G>A		Somatic	106	1		WXS	Illumina HiSeq	Phase_I	108	26	NM_172020	0	0	117	142	25	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000434423.2	37																																																																																				.		0.592	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			A	72416770	G	A	72416770	2	1	3	1	0	0	0	0	0	0	0	1	12265	1020	36	2		2	POM121	7	72416770	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08		72416770	86721893	36	157											
PCLO	27445	bcgsc.ca	37	chr7	82784463	82784463	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggctgttgagatgggggCtttgctgagccaggctgttg	5	11	17	8	0	0	2	0	2	0	1	0	3	0	2	2	4	2	6	2	4	0	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr7:82784463C>T	ENST00000333891.9	-	2	1831	c.1494G>A	c.(1492-1494)aaG>aaA	p.K498K	PCLO_ENST00000423517.2_Silent_p.K498K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GAGATGGGGGCTTTGCTGAGC	0.607																																					p.K498K													.	PCLO-29	0			c.G1494A						.						97	106	103					7																	82784463		1950	4134	6084	SO:0001819	synonymous_variant	27445	exon2			TGGGGGCTTTGCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1494G>A	7.37:g.82784463C>T		Somatic	290	9		WXS	Illumina HiSeq	Phase_1	357	108	NM_014510	0	0	8	12	4		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			.		0.607	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82784463	C	T	82784463	2	4	3	1	0	0	0	0	0	0	0	1	11609	796	28	2		2	PCLO	7	82784463	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	10367693	82784463	76354200	37	158											
PDIA4	9601	broad.mit.edu	37	chr7	148702375	148702375	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agccccaggtccttcacctcCccagcatagtcctcttcgtc	6	10	6	19	1	2	0	1	0	1	0	7	0	5	0	7	1	2	1	7	1	1	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr7:148702375C>T	ENST00000286091.4	-	9	1612	c.1380G>A	c.(1378-1380)ggG>ggA	p.G460G		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	460					cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			CCTTCACCTCCCCAGCATAGT	0.572											OREG0018420	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G460G													.	PDIA4-524	0			c.G1380A						.						196	163	174					7																	148702375		2203	4300	6503	SO:0001819	synonymous_variant	9601	exon9			CACCTCCCCAGCA	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"Protein disulfide isomerases"	30167	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 4"			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1380G>A	7.37:g.148702375C>T		Somatic	289	0	1719	WXS	Illumina HiSeq	Phase_I	299	9	NM_004911	0	0	311	322	11	A8K4K6|Q549T6	Silent	SNP	ENST00000286091.4	37	CCDS5893.1																																																																																			.		0.572	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		T	148702375	C	T	148702375	2	4	3	1	0	0	0	0	0	0	0	1	11696	610	22	2		2	PDIA4	7	148702375	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	65917912	148702375	10436288	38	159											
ZDHHC2	51201	broad.mit.edu	37	chr8	17043867	17043867	+	Frame_Shift_Del	DEL	T	T	-																															cctgatggcctatcatctacTttttgcaatgtttgtctggt																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:17043867delT	ENST00000262096.8	+	3	880	c.185delT	c.(184-186)cttfs	p.L62fs		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	62					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TATCATCTACTTTTTGCAATG	0.284																																					p.L62fs													.	.	0			c.185delT						.						125	110	114					8																	17043867		1830	4082	5912	SO:0001589	frameshift_variant	51201	exon3			ATCTACTTTTTGC	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"Zinc fingers, DHHC-type"	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.185delT	8.37:g.17043867delT	ENSP00000262096:p.Leu62fs	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_016353	0	0	0	0	0	D3DSP5	Frame_Shift_Del	DEL	ENST00000262096.8	37	CCDS47810.1																																																																																			.		0.284	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		-	17043867	T	-	17043867	7	5	3	1	0	1	0	1	0	0	0	0	17642	1609	56	0	195	0	ZDHHC2	8	17043867	Frame_Shift_Del	DEL	T	TCGA-A4-7288-01A-11D-2136-08		17043867	129320155	39	160											
LPL	4023	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	19816813	19816813	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatttttctgggactgagaGtgaaacccataccaatcagg	12	11	9	9	0	3	2	2	2	1	1	3	4	3	3	2	2	2	0	2	2	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:19816813G>C	ENST00000311322.8	+	7	1531	c.1061G>C	c.(1060-1062)aGt>aCt	p.S354T		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	354	Heparin-binding. {ECO:0000250}.|PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	GGGACTGAGAGTGAAACCCAT	0.453																																					p.S354T		.											.	LPL-92	0			c.G1061C						.						111	99	103					8																	19816813		2203	4300	6503	SO:0001583	missense	4023	exon7			CTGAGAGTGAAAC		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.1061G>C	8.37:g.19816813G>C	ENSP00000309757:p.Ser354Thr	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	61	26	NM_000237	0	0	10	14	4	B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	37	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	G	0.380	-0.928995	0.02359	.	.	ENSG00000175445	ENST00000311322;ENST00000535763	T	0.62364	0.03	5.93	0.818	0.18778	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	6.232250	0.00166	N	0.000000	T	0.45776	0.1359	N	0.19112	0.55	0.21675	N	0.999596	B	0.02656	0.0	B	0.08055	0.003	T	0.13980	-1.0489	8	.	.	.	-1.2704	4.6754	0.12710	0.3185:0.2811:0.4004:0.0	.	354	P06858	LIPL_HUMAN	T	354;340	ENSP00000309757:S354T	.	S	+	2	0	LPL	19861093	0.007000	0.16637	0.000000	0.03702	0.149000	0.21700	0.725000	0.25970	-0.125000	0.11703	0.643000	0.83706	AGT	.		0.453	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			C	19816813	G	C	19816813	3	2	3	1	0	0	0	0	1	0	0	0	8946	1029	36	4	1087	4	LPL	8	19816813	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	2772946	19816813	126547209	40	161											
PLEKHA2	59339	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	38810172	38810172	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcggaagagctggaaacgtCgcttctttgcacttgatgac	10	10	12	9	3	1	3	0	2	1	1	2	5	1	5	0	2	4	3	0	2	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:38810172C>A	ENST00000521746.1	+	8	886	c.652C>A	c.(652-654)Cgc>Agc	p.R218S	PLEKHA2_ENST00000388745.4_3'UTR|PLEKHA2_ENST00000420274.1_Missense_Mutation_p.R218S			Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2	218	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell-matrix adhesion (GO:0001954)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	13		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			CTGGAAACGTCGCTTCTTTGC	0.468																																					p.R218S													.	.	0			c.C652A						.						98	88	91					8																	38810172		1970	4153	6123	SO:0001583	missense	59339	exon8			AAACGTCGCTTCT	AF286164	CCDS75732.1	8p11.21	2013-01-10	2002-01-14			ENSG00000169499		"Pleckstrin homology (PH) domain containing"	14336	protein-coding gene	gene with protein product	"tandem PH Domain containing protein-2"	607773	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2"			11001876	Standard	NM_021623		Approved	TAPP2	uc003xmi.4	Q9HB19		ENST00000521746.1:c.652C>A	8.37:g.38810172C>A	ENSP00000430938:p.Arg218Ser	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	37	8	NM_021623	0	0	23	42	19		Missense_Mutation	SNP	ENST00000521746.1	37		.	.	.	.	.	.	.	.	.	.	C	23.7	4.450211	0.84101	.	.	ENSG00000169499	ENST00000521746;ENST00000420274;ENST00000535929	T;T	0.26067	1.76;1.76	5.94	5.07	0.68467	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.66781	0.2824	H	0.98629	4.285	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.79455	-0.1796	10	0.87932	D	0	.	12.5681	0.56320	0.0:0.9221:0.0:0.0779	.	218;218	Q9HB19;A8K727	PKHA2_HUMAN;.	S	218;218;168	ENSP00000430938:R218S;ENSP00000393860:R218S	ENSP00000393860:R218S	R	+	1	0	PLEKHA2	38929329	0.995000	0.38212	0.997000	0.53966	0.995000	0.86356	3.595000	0.54016	1.522000	0.49001	0.650000	0.86243	CGC	.		0.468	PLEKHA2-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000377068.1	NM_021623		A	38810172	C	A	38810172	3	1	3	1	0	0	0	0	1	0	0	0	12082	884	31	4	678	4	PLEKHA2	8	38810172	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	18993359	38810172	107553850	41	162											
RP1	6101	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	55540098	55540099	+	Frame_Shift_Ins	INS	-	-	T																															tccacggtcaacattcagagINStgttcctaagtgcagtgaaa																								rs139588212|rs145115379		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:55540098_55540099insT	ENST00000220676.1	+	4	3804_3805	c.3656_3657insT	c.(3655-3660)agtgttfs	p.V1220fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1220					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AACATTCAGAGTGTTCCTAAGT	0.446																																					p.S1219fs	Colon(91;1014 1389 7634 14542 40420)	.											.	RP1-102	0			c.3656_3657insT						.																																			SO:0001589	frameshift_variant	6101	exon4			.	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3657dupT	8.37:g.55540099_55540099dupT	ENSP00000220676:p.Val1220fs	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	123	58	NM_006269	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000220676.1	37	CCDS6160.1																																																																																			.		0.446	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55540099	-	T	55540098	7	5	3	1	0	1	1	0	0	0	0	0	13564	1029	36	0	3666	0	RP1	8	55540098	Frame_Shift_Ins	INS	-	TCGA-A4-7288-01A-11D-2136-08	16729926	55540098	90823924	42	163											
NBN	4683	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	90960111	90960111	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcacgtttcttcccaatttCattttcttgctaaagaaata	11	18	3	9	1	4	1	2	0	2	1	5	1	5	1	1	0	1	2	1	0	5	9			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:90960111C>T	ENST00000265433.3	-	12	2009	c.1855G>A	c.(1855-1857)Gaa>Aaa	p.E619K	NBN_ENST00000409330.1_Missense_Mutation_p.E537K	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	619					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTCCCAATTTCATTTTCTTGC	0.299								Homologous recombination																													p.E619K													.	NBN-1395	0			c.G1855A						.						63	57	59					8																	90960111		2197	4291	6488	SO:0001583	missense	4683	exon12			CAATTTCATTTTC	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1855G>A	8.37:g.90960111C>T	ENSP00000265433:p.Glu619Lys	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_002485	0	0	0	0	0	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.628275	0.46944	.	.	ENSG00000104320	ENST00000265433;ENST00000409330	T;T	0.59906	2.08;0.23	5.12	5.12	0.69794	.	0.604049	0.16593	N	0.207679	T	0.46229	0.1382	L	0.29908	0.895	0.48830	D	0.999714	P;B	0.35208	0.49;0.142	B;B	0.28011	0.085;0.037	T	0.53301	-0.8458	10	0.87932	D	0	-19.514	16.0643	0.80861	0.0:1.0:0.0:0.0	.	619;619	A6H8Y5;O60934	.;NBN_HUMAN	K	619;537	ENSP00000265433:E619K;ENSP00000386924:E537K	ENSP00000265433:E619K	E	-	1	0	NBN	91029287	1.000000	0.71417	0.980000	0.43619	0.504000	0.33889	1.462000	0.35266	2.375000	0.81037	0.591000	0.81541	GAA	.		0.299	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		T	90960111	C	T	90960111	3	4	3	1	0	0	0	0	1	0	0	0	10216	835	29	2	429	2	NBN	8	90960111	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	35420013	90960111	55403911	43	164											
TTC35	9694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	109462083	109462083	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaatgagaaaatggagagaAgaaaactcaagaaatagtga	24	5	10	2	0	1	5	1	2	0	4	1	8	1	6	0	1	1	0	0	1	10	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:109462083A>G	ENST00000220853.3	+	2	107	c.72A>G	c.(70-72)gaA>gaG	p.E24E		NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	24						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											AATGGAGAGAAGAAAACTCAA	0.318																																					p.E24E		.											.	.	0			c.A72G						.						97	112	107					8																	109462083		2203	4298	6501	SO:0001819	synonymous_variant	9694	exon2			GAGAGAAGAAAAC	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.72A>G	8.37:g.109462083A>G		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	82	36	NM_014673	0	0	18	31	13	Q8WUE1	Silent	SNP	ENST00000220853.3	37	CCDS6309.1																																																																																			.		0.318	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		G	109462083	A	G	109462083	2	3	3	1	0	0	0	0	0	0	0	1	16736	69	3	3		3	TTC35	8	109462083	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	18501972	109462083	36901939	44	165											
AQP7	364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	33385805	33385805	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctgttcctggcagtgctggGttgttctcctggtccgtgat	2	16	13	10	1	2	1	0	1	2	0	5	1	4	1	3	3	1	5	3	3	0	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr9:33385805G>T	ENST00000537089.1	-	6	627	c.309C>A	c.(307-309)aaC>aaA	p.N103K	AQP7_ENST00000377425.4_Missense_Mutation_p.N138K|AQP7_ENST00000539936.1_Missense_Mutation_p.N195K|AQP7_ENST00000541274.1_Missense_Mutation_p.P64T			O14520	AQP7_HUMAN	aquaporin 7	195					excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		GCAGTGCTGGGTTGTTCTCCT	0.617																																					p.N195K		.											.	AQP7-90	0			c.C585A						.						121	106	111					9																	33385805		2203	4300	6503	SO:0001583	missense	364	exon7			TGCTGGGTTGTTC	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"Ion channels / Aquaporins"	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.309C>A	9.37:g.33385805G>T	ENSP00000441619:p.Asn103Lys	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	130	39	NM_001170	0	0	38	64	26	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	0.022|0.022	-1.416408|-1.416408	0.01136|0.01136	.|.	.|.	ENSG00000165269|ENSG00000165269	ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503|ENST00000541274	D;D;D;D;D;D;D;D;D|T	0.84660|0.48836	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88|0.8	4.77|4.77	0.809|0.809	0.18725|0.18725	Aquaporin-like (2);|.	0.423208|.	0.29383|.	N|.	0.012320|.	T|T	0.37758|0.37758	0.1015|0.1015	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	B;B;B;B|B	0.25007|0.27286	0.022;0.049;0.022;0.116|0.174	B;B;B;B|B	0.25987|0.26310	0.038;0.063;0.038;0.065|0.068	T|T	0.24584|0.24584	-1.0156|-1.0156	10|9	0.16896|0.38643	T|T	0.51|0.18	-15.7477|-15.7477	7.845|7.845	0.29421|0.29421	0.3724:0.0:0.6276:0.0|0.3724:0.0:0.6276:0.0	.|.	194;195;138;195|64	Q5T5M0;B7Z4U2;Q6P5T0;O14520|B7Z7F6	.;.;.;AQP7_HUMAN|.	K|T	103;194;63;195;138;103;194;195;131|64	ENSP00000441619:N103K;ENSP00000368821:N194K;ENSP00000412868:N63K;ENSP00000297988:N195K;ENSP00000396111:N138K;ENSP00000410138:N103K;ENSP00000368820:N194K;ENSP00000439534:N195K;ENSP00000368817:N131K|ENSP00000438860:P64T	ENSP00000297988:N195K|ENSP00000438860:P64T	N|P	-|-	3|1	2|0	AQP7|AQP7	33375805|33375805	0.000000|0.000000	0.05858|0.05858	0.060000|0.060000	0.19600|0.19600	0.083000|0.083000	0.17756|0.17756	-0.334000|-0.334000	0.07883|0.07883	-0.018000|-0.018000	0.14079|0.14079	0.454000|0.454000	0.30748|0.30748	AAC|CCC	.		0.617	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170		T	33385805	G	T	33385805	3	4	3	1	0	0	0	0	1	0	0	0	831	1252	44	4	451	4	AQP7	9	33385805	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		33385805	107827626	45	166											
C10orf71	118461	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	50530974	50530974	+	Frame_Shift_Del	DEL	G	G	-																															gtccagaggagactggaggtGccagtttccggcctaaggag																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr10:50530974delG	ENST00000374144.3	+	3	672	c.384delG	c.(382-384)gtgfs	p.V128fs	C10orf71_ENST00000323868.4_Frame_Shift_Del_p.V128fs			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	128										endometrium(1)	1						GACTGGAGGTGCCAGTTTCCG	0.547																																					p.V128fs		.											.	C10orf71-90	0			c.384delG						.						81	95	91					10																	50530974		1948	4145	6093	SO:0001589	frameshift_variant	118461	exon3			.	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.384delG	10.37:g.50530974delG	ENSP00000363259:p.Val128fs	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	122	44	NM_001135196	0	0	0	0	0	A0AVL8	Frame_Shift_Del	DEL	ENST00000374144.3	37	CCDS44387.1																																																																																			.		0.547	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		-	50530974	G	-	50530974	7	5	3	1	0	1	0	1	0	0	0	0	1618	1306	46	0	386	0	C10orf71	10	50530974	Frame_Shift_Del	DEL	G	TCGA-A4-7288-01A-11D-2136-08		50530974	85003773	46	167											
SIGIRR	59307	broad.mit.edu;bcgsc.ca	37	chr11	406878	406878	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagagcagcaaggtcaccaGgtggcggtgctggcgcagca	9	4	16	12	2	1	1	1	0	0	1	1	1	1	1	2	5	4	5	2	5	1	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:406878G>T	ENST00000431843.2	-	8	1150	c.844C>A	c.(844-846)Ctg>Atg	p.L282M	SIGIRR_ENST00000332725.3_Missense_Mutation_p.L282M|SIGIRR_ENST00000397632.3_Missense_Mutation_p.L282M|SIGIRR_ENST00000529486.1_5'Flank|SIGIRR_ENST00000531205.1_Missense_Mutation_p.L282M|SIGIRR_ENST00000382520.2_Missense_Mutation_p.L282M	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	282	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGGTCACCAGGTGGCGGTGC	0.736																																					p.L282M													.	SIGIRR-90	0			c.C844A						.						5	7	7					11																	406878		2006	4048	6054	SO:0001583	missense	59307	exon8			TCACCAGGTGGCG		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30575	protein-coding gene	gene with protein product	"single immunoglobulin domain IL1R1 related"	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.844C>A	11.37:g.406878G>T	ENSP00000403104:p.Leu282Met	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	11	5	NM_001135053	0	0	70	152	82	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	37	CCDS31325.1	.	.	.	.	.	.	.	.	.	.	g	23.5	4.425513	0.83667	.	.	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520;ENST00000528209	T;T;T;T;T;T	0.23950	2.97;2.97;2.97;2.97;2.97;1.88	3.42	3.42	0.39159	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.588123	0.16847	N	0.197084	T	0.23572	0.0570	N	0.17474	0.49	0.27755	N	0.944016	D;P	0.63046	0.992;0.927	P;P	0.57204	0.815;0.69	T	0.03483	-1.1032	10	0.33940	T	0.23	.	6.5078	0.22204	0.0:0.2504:0.451:0.2985	.	282;282	C9JFX4;Q6IA17	.;SIGIR_HUMAN	M	282;282;282;282;282;178	ENSP00000403104:L282M;ENSP00000380756:L282M;ENSP00000333656:L282M;ENSP00000433022:L282M;ENSP00000371960:L282M;ENSP00000435135:L178M	ENSP00000333656:L282M	L	-	1	2	SIGIRR	396878	0.015000	0.18098	1.000000	0.80357	0.983000	0.72400	0.396000	0.20867	1.638000	0.50547	0.484000	0.47621	CTG	.		0.736	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805		T	406878	G	T	406878	3	4	3	1	0	0	0	0	1	0	0	0	14336	991	35	4	400	4	SIGIRR	11	406878	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		406878	134599638	47	168											
MUC2	4583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1075662	1075662	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctcagagggcagaaccCgaaaccacggccacaacgtc	12	3	9	17	3	1	2	1	0	0	2	3	3	2	2	4	2	3	1	4	2	3	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:1075662C>G	ENST00000441003.2	+	2	115	c.88C>G	c.(88-90)Cga>Gga	p.R30G	MUC2_ENST00000359061.5_Missense_Mutation_p.R30G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	30					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GGGCAGAACCCGAAACCACGG	0.632																																					p.R30G		.											.	MUC2-90	0			c.C88G						.						30	35	33					11																	1075662		2128	4223	6351	SO:0001583	missense	4583	exon2			AGAACCCGAAACC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.88C>G	11.37:g.1075662C>G	ENSP00000415183:p.Arg30Gly	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	38	11	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	8.980	0.975205	0.18736	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12672	2.69;2.66	3.78	2.81	0.32909	.	0.537890	0.13893	U	0.355461	T	0.10637	0.0260	L	0.27053	0.805	0.09310	N	1	P	0.40398	0.716	P	0.44477	0.451	T	0.15694	-1.0428	10	0.08837	T	0.75	.	8.7802	0.34787	0.1808:0.6671:0.1521:0.0	.	30	E7EUV1	.	G	30	ENSP00000415183:R30G;ENSP00000351956:R30G	ENSP00000351956:R30G	R	+	1	2	MUC2	1065662	0.009000	0.17119	0.001000	0.08648	0.150000	0.21749	2.439000	0.44846	0.525000	0.28522	0.491000	0.48974	CGA	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1075662	C	G	1075662	3	3	3	1	0	0	0	0	1	0	0	0	10000	644	23	4	94	4	MUC2	11	1075662	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	668784	1075662	133930854	48	169											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1268402	1268402	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacacctgcagccaccagcaGcacagtgactccctcctctg	9	6	7	19	0	1	1	0	1	1	0	3	1	3	1	5	0	4	3	5	0	0	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:1268402G>A	ENST00000529681.1	+	31	10350	c.10292G>A	c.(10291-10293)aGc>aAc	p.S3431N	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3434N	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3431	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.S3410N(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		gccaccagcagcacAGTGACT	0.682																																					p.S3431N		.											.	.	1	Substitution - Missense(1)	prostate(1)	c.G10292A						.						41	76	64					11																	1268402		2093	4144	6237	SO:0001583	missense	727897	exon31			CCAGCAGCACAGT	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.10292G>A	11.37:g.1268402G>A	ENSP00000436812:p.Ser3431Asn	Somatic	16	2		WXS	Illumina HiSeq	Phase_I	19	4	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	3.121	-0.180464	0.06380	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637	T;T	0.20598	2.06;2.24	2.38	-2.65	0.06095	.	.	.	.	.	T	0.11965	0.0291	L	0.29908	0.895	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.31888	-0.9927	9	0.87932	D	0	.	2.2793	0.04110	0.1745:0.3567:0.3457:0.1231	.	3434	E9PBJ0	.	N	3431;3434;3403	ENSP00000436812:S3431N;ENSP00000415793:S3434N	ENSP00000343037:S3403N	S	+	2	0	MUC5B	1224978	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.426000	0.02443	-0.630000	0.05567	-0.714000	0.03626	AGC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1268402	G	A	1268402	3	1	3	1	0	0	0	0	1	0	0	0	10004	971	34	2	10423	2	MUC5B	11	1268402	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	192740	1268402	133738114	49	170											
SLC5A12	159963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	26725402	26725402	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattgtggaatcccccagcAtgagttgatccttgaatgag	11	11	10	9	0	0	4	0	4	0	0	2	5	2	5	3	1	1	2	3	1	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:26725402A>G	ENST00000396005.3	-	5	927	c.618T>C	c.(616-618)caT>caC	p.H206H	SLC5A12_ENST00000280467.6_Silent_p.H206H	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	206					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						ATCCCCCAGCATGAGTTGATC	0.388																																					p.H206H		.											.	SLC5A12-92	0			c.T618C						.						233	218	223					11																	26725402		2203	4299	6502	SO:0001819	synonymous_variant	159963	exon5			CCCAGCATGAGTT	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.618T>C	11.37:g.26725402A>G		Somatic	287	0		WXS	Illumina HiSeq	Phase_I	225	91	NM_178498	0	0	3	4	1	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			.		0.388	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26725402	A	G	26725402	2	3	3	1	0	0	0	0	0	0	0	1	14696	214	8	3		3	SLC5A12	11	26725402	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	25457000	26725402	108281114	50	171											
TCP11L1	55346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	33083137	33083137	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggaccttatgactcagaaGtataaacacgccctgccagt	13	8	9	11	1	1	2	1	1	0	1	1	4	1	3	3	1	2	1	3	1	5	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:33083137G>C	ENST00000334274.4	+	7	1237	c.837G>C	c.(835-837)aaG>aaC	p.K279N	TCP11L1_ENST00000324357.9_Missense_Mutation_p.K58N|TCP11L1_ENST00000432887.1_Missense_Mutation_p.K279N|TCP11L1_ENST00000531632.2_Missense_Mutation_p.K279N	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	279						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						TGACTCAGAAGTATAAACACG	0.527																																					p.K279N		.											.	TCP11L1-90	0			c.G837C						.						57	57	57					11																	33083137		2202	4298	6500	SO:0001583	missense	55346	exon7			TCAGAAGTATAAA	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.837G>C	11.37:g.33083137G>C	ENSP00000335595:p.Lys279Asn	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	55	22	NM_001145541	0	0	7	20	13	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	37	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.764820	0.31228	.	.	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887;ENST00000324357	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	5.01	5.01	0.66863	.	0.702810	0.14718	N	0.302495	T	0.08582	0.0213	L	0.29908	0.895	0.09310	N	1	B	0.25007	0.116	B	0.22152	0.038	T	0.27331	-1.0077	10	0.21540	T	0.41	-10.0501	10.8411	0.46715	0.0965:0.0:0.9035:0.0	.	279	Q9NUJ3	T11L1_HUMAN	N	279;279;279;58	ENSP00000335595:K279N;ENSP00000433067:K279N;ENSP00000395070:K279N;ENSP00000316279:K58N	ENSP00000316279:K58N	K	+	3	2	TCP11L1	33039713	0.874000	0.30092	0.537000	0.28052	0.762000	0.43233	1.682000	0.37628	2.320000	0.78422	0.555000	0.69702	AAG	.		0.527	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		C	33083137	G	C	33083137	3	2	3	1	0	0	0	0	1	0	0	0	15746	1020	36	4	859	4	TCP11L1	11	33083137	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	6357735	33083137	101923379	51	172											
NDUFS3	4722	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47605943	47605943	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagttccgcaaatttgacctGaacagcccctgggaggcttt	9	10	11	11	1	0	2	0	2	0	0	1	4	1	3	4	2	2	3	4	2	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:47605943G>A	ENST00000263774.4	+	7	787	c.705G>A	c.(703-705)ctG>ctA	p.L235L	NDUFS3_ENST00000533507.1_3'UTR|FAM180B_ENST00000356737.2_5'Flank|FAM180B_ENST00000538490.1_5'Flank	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	235					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	AATTTGACCTGAACAGCCCCT	0.557																																					p.L235L	Pancreas(15;551 601 22438 23457 52512)	.											.	NDUFS3-90	0			c.G705A						.						137	141	140					11																	47605943		2201	4298	6499	SO:0001819	synonymous_variant	4722	exon7			TGACCTGAACAGC	AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7710	protein-coding gene	gene with protein product	"complex I 30kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"	603846	"NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.705G>A	11.37:g.47605943G>A		Somatic	305	0		WXS	Illumina HiSeq	Phase_I	205	85	NM_004551	0	0	71	117	46	B2R9J1|B4DFM8|Q9UNQ8	Silent	SNP	ENST00000263774.4	37	CCDS7941.1																																																																																			.		0.557	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551		A	47605943	G	A	47605943	2	1	3	1	0	0	0	0	0	0	0	1	10319	1277	45	2		2	NDUFS3	11	47605943	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08	14522806	47605943	87400573	52	173											
ATL3	25923	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	63403801	63403802	+	Frame_Shift_Ins	INS	-	-	A																															tgctctttgaattcaccagcINSaatatctgttcacaggacga																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:63403801_63403802insA	ENST00000398868.3	-	9	1131_1132	c.855_856insT	c.(853-858)attgctfs	p.A286fs	ATL3_ENST00000538786.1_Frame_Shift_Ins_p.A268fs|ATL3_ENST00000332645.4_Frame_Shift_Ins_p.A313fs|RP11-697H9.2_ENST00000540307.1_RNA	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3	286	GB1/RHD3-type G.				endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						AATTCACCAGCAATATCTGTTC	0.416											OREG0021036	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A286fs		.											.	ATL3-69	0			c.856_857insT						.																																			SO:0001589	frameshift_variant	25923	exon9			.		CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.856dupT	11.37:g.63403803_63403803dupA	ENSP00000381844:p.Ala286fs	Somatic	135	0	1068	WXS	Illumina HiSeq	Phase_I	110	44	NM_015459	0	0	0	0	0	Q8N7W5|Q9H8Q5|Q9UFL1	Frame_Shift_Ins	INS	ENST00000398868.3	37	CCDS41663.1																																																																																			.		0.416	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459		A	63403802	-	A	63403801	7	5	3	1	0	1	1	0	0	0	0	0	1109	710	25	0	789	0	ATL3	11	63403801	Frame_Shift_Ins	INS	-	TCGA-A4-7288-01A-11D-2136-08	15797858	63403801	71602715	53	174											
CCDC67	159989	hgsc.bcm.edu	37	chr11	93122277	93122277	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagatcaaccaaatcatgaaAaagaattgaacaaggtatga	22	7	7	5	0	2	5	2	3	0	2	2	5	2	5	1	1	2	1	1	1	9	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:93122277A>G	ENST00000298050.3	+	9	1127	c.1027A>G	c.(1027-1029)Aaa>Gaa	p.K343E	CCDC67_ENST00000525646.1_Missense_Mutation_p.K85E	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	343					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				AAATCATGAAAAAGAATTGAA	0.313																																					p.K343E		.											.	CCDC67-91	0			c.A1027G						.						39	36	37					11																	93122277		1813	4080	5893	SO:0001583	missense	159989	exon9			CATGAAAAAGAAT	AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325			26344	protein-coding gene	gene with protein product						24240477	Standard	NM_181645		Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000298050.3:c.1027A>G	11.37:g.93122277A>G	ENSP00000298050:p.Lys343Glu	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	20	2	NM_181645	0	0	0	0	0	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217670	0.39201	.	.	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646	T;T;T	0.22336	1.96;1.96;1.96	5.8	5.8	0.92144	.	0.274240	0.36234	N	0.002711	T	0.14227	0.0344	L	0.48362	1.52	0.29128	N	0.87982	B;B;P	0.39181	0.347;0.183;0.663	B;B;B	0.33196	0.146;0.12;0.159	T	0.10200	-1.0640	10	0.07990	T	0.79	.	8.6983	0.34310	0.9155:0.0:0.0845:0.0	.	343;343;335	Q05D60;E9PJR5;Q6ZRU6	CCD67_HUMAN;.;.	E	343;343;85	ENSP00000432111:K343E;ENSP00000298050:K343E;ENSP00000435079:K85E	ENSP00000298050:K343E	K	+	1	0	CCDC67	92761925	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	2.183000	0.42565	2.219000	0.72066	0.533000	0.62120	AAA	.		0.313	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		G	93122277	A	G	93122277	3	3	3	1	0	0	0	0	1	0	0	0	2845	15	1	3	1057	3	CCDC67	11	93122277	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	29718476	93122277	41884239	54	175											
CNTN5	53942	hgsc.bcm.edu	37	chr11	99690467	99690467	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttattcccccatcaatctttAtcattcctcagatgccttca	9	16	2	14	0	5	1	4	0	1	1	7	1	7	1	4	0	1	0	4	0	3	6	rs202073412		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:99690467A>C	ENST00000524871.1	+	4	538	c.248A>C	c.(247-249)tAt>tCt	p.Y83S	CNTN5_ENST00000527185.1_Missense_Mutation_p.Y83S|CNTN5_ENST00000528682.1_Missense_Mutation_p.Y83S|CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000279463.3_Missense_Mutation_p.Y83S	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	83					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ATCAATCTTTATCATTCCTCA	0.428																																					p.Y83S		.											.	CNTN5-366	0			c.A248C						.						48	47	47					11																	99690467		1873	4084	5957	SO:0001583	missense	53942	exon3			ATCTTTATCATTC	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.248A>C	11.37:g.99690467A>C	ENSP00000435637:p.Tyr83Ser	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_001243270	0	0	0	0	0	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.952057	0.53293	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	T;T;T;T	0.54675	0.56;0.64;0.64;0.64	5.06	5.06	0.68205	.	0.382752	0.24559	N	0.037483	T	0.58595	0.2133	N	0.19112	0.55	0.44061	D	0.996801	D;D	0.71674	0.998;0.998	D;D	0.76071	0.987;0.987	T	0.64145	-0.6476	10	0.72032	D	0.01	.	14.699	0.69142	1.0:0.0:0.0:0.0	.	83;83	E9PKE8;O94779	.;CNTN5_HUMAN	S	83	ENSP00000433575:Y83S;ENSP00000436185:Y83S;ENSP00000435637:Y83S;ENSP00000279463:Y83S	ENSP00000279463:Y83S	Y	+	2	0	CNTN5	99195677	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	6.120000	0.71596	2.208000	0.71279	0.528000	0.53228	TAT	.		0.428	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		C	99690467	A	C	99690467	3	2	3	1	0	0	0	0	1	0	0	0	3650	449	16	5	254	5	CNTN5	11	99690467	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	6568190	99690467	35316049	55	176											
ATP5L	10632	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118272388	118272388	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattccagaaccatggcccAatttgtccgtaaccttgtgg	9	11	8	13	1	0	1	0	0	0	1	2	1	2	1	6	2	2	1	6	2	3	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:118272388A>G	ENST00000300688.3	+	1	520	c.8A>G	c.(7-9)cAa>cGa	p.Q3R	ATP5L_ENST00000524422.1_Missense_Mutation_p.Q3R|ATP5L_ENST00000529770.1_3'UTR|RP11-770J1.5_ENST00000534438.1_5'UTR|RP11-770J1.5_ENST00000531742.1_5'Flank	NM_006476.4	NP_006467.4	O75964	ATP5L_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G	3					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)	7	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)		ACCATGGCCCAATTTGTCCGT	0.667																																					p.Q3R		.											.	ATP5L-90	0			c.A8G						.						45	40	42					11																	118272388		2200	4296	6496	SO:0001583	missense	10632	exon1			TGGCCCAATTTGT	AF092124	CCDS8397.1	11q23.3	2012-10-12	2010-06-11		ENSG00000167283	ENSG00000167283		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	14247	protein-coding gene	gene with protein product			"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G"			11230166, 11042152	Standard	NR_033759		Approved	ATP5JG	uc001psx.3	O75964		ENST00000300688.3:c.8A>G	11.37:g.118272388A>G	ENSP00000300688:p.Gln3Arg	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	49	20	NM_006476	0	0	264	526	262	A8K0K3|Q96BV6|Q9UBZ7	Missense_Mutation	SNP	ENST00000300688.3	37	CCDS8397.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.880213	0.51801	.	.	ENSG00000167283	ENST00000300688;ENST00000524422	.	.	.	6.17	5.05	0.67936	.	0.166760	0.56097	D	0.000039	T	0.56804	0.2010	L	0.61387	1.9	0.39789	D	0.972403	B	0.06786	0.001	B	0.09377	0.004	T	0.54403	-0.8299	9	0.36615	T	0.2	-2.3772	9.3868	0.38347	0.9198:0.0:0.0802:0.0	.	3	O75964	ATP5L_HUMAN	R	3	.	ENSP00000300688:Q3R	Q	+	2	0	ATP5L	117777598	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	3.233000	0.51311	1.142000	0.42291	0.533000	0.62120	CAA	.		0.667	ATP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389220.1	NM_006476		G	118272388	A	G	118272388	3	3	3	1	0	0	0	0	1	0	0	0	1161	130	5	3	10	3	ATP5L	11	118272388	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	18581921	118272388	16734128	56	177											
TMEM45B	120224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	129724698	129724698	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactggttatggctgtggcAgtattcatggaaggtaattt	10	14	13	4	0	1	1	1	0	0	1	1	2	1	2	0	5	0	5	0	5	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:129724698A>G	ENST00000524567.1	+	3	653	c.372A>G	c.(370-372)gcA>gcG	p.A124A	TMEM45B_ENST00000281441.3_Silent_p.A124A			Q96B21	TM45B_HUMAN	transmembrane protein 45B	124						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		TGGCTGTGGCAGTATTCATGG	0.453																																					p.A124A		.											.	TMEM45B-90	0			c.A372G						.						138	125	129					11																	129724698		2201	4297	6498	SO:0001819	synonymous_variant	120224	exon3			TGTGGCAGTATTC	AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.372A>G	11.37:g.129724698A>G		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	103	39	NM_138788	0	0	0	0	0	A8K2L8	Silent	SNP	ENST00000524567.1	37	CCDS8482.1																																																																																			.		0.453	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788		G	129724698	A	G	129724698	2	3	3	1	0	0	0	0	0	0	0	1	16202	175	7	3		3	TMEM45B	11	129724698	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	11452310	129724698	5281818	57	178											
IFFO1	25900	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6649694	6649694	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcgcgatcggagtcctcAgcctcgcttggcggcggcgg	5	7	15	14	7	1	0	1	0	0	0	5	2	2	1	2	5	1	1	2	5	0	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:6649694A>G	ENST00000396840.2	-	9	1676	c.1635T>C	c.(1633-1635)gcT>gcC	p.A545A	IFFO1_ENST00000356896.4_Silent_p.A549A|IFFO1_ENST00000336604.4_Silent_p.A548A|RP5-940J5.9_ENST00000602946.1_RNA|RP5-940J5.8_ENST00000499202.2_RNA|IFFO1_ENST00000436152.2_Silent_p.A242A|IFFO1_ENST00000465801.1_Silent_p.A241A			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	545						intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						CGGAGTCCTCAGCCTCGCTTG	0.617																																					p.A557A		.											.	IFFO1-68	0			c.T1671C						.						53	54	54					12																	6649694		2203	4300	6503	SO:0001819	synonymous_variant	25900	exon10			GTCCTCAGCCTCG	AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"Intermediate filament family orphans"	24970	protein-coding gene	gene with protein product		610495	"intermediate filament family orphan"	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.1635T>C	12.37:g.6649694A>G		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	89	83	NM_001193457	0	0	2	8	6	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Silent	SNP	ENST00000396840.2	37		.	.	.	.	.	.	.	.	.	.	A	12.53	1.964511	0.34659	.	.	ENSG00000010295	ENST00000416019;ENST00000423501	.	.	.	4.84	1.14	0.20703	.	.	.	.	.	T	0.30727	0.0774	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.07966	-1.0745	6	.	.	.	0.8566	4.8721	0.13639	0.4992:0.2689:0.2318:0.0	.	240	Q6P593	.	P	279;185	.	.	L	-	2	0	IFFO1	6519955	0.938000	0.31826	1.000000	0.80357	0.982000	0.71751	-0.065000	0.11617	0.887000	0.36136	0.459000	0.35465	CTG	.		0.617	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000280428.1	NM_080730		G	6649694	A	G	6649694	2	3	3	1	0	0	0	0	0	0	0	1	7531	175	7	3		3	IFFO1	12	6649694	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08		6649694	127202201	58	179											
ARID2	196528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46285793	46285793	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcctcttcctcaaaaaGgataagcactgttcaaagga	13	11	7	10	0	3	0	2	0	1	0	5	2	5	2	2	2	2	3	2	2	4	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:46285793G>A	ENST00000334344.6	+	18	5233		c.e18-1		ARID2_ENST00000457135.1_Splice_Site|ARID2_ENST00000422737.1_Splice_Site|ARID2_ENST00000479608.1_Splice_Site|ARID2_ENST00000444670.1_Splice_Site	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCCTCAAAAAGGATAAGCACT	0.388			"N, S, F"		hepatocellular carcinoma																																.		.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2-100	0			c.5062-1G>A						.						117	109	112					12																	46285793		2203	4300	6503	SO:0001630	splice_region_variant	196528	exon18			CAAAAAGGATAAG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.5062-1G>A	12.37:g.46285793G>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	59	54	NM_152641	0	0	0	0	0	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Splice_Site	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730640	0.48939	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6022	0.91253	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARID2	44572060	1.000000	0.71417	1.000000	0.80357	0.654000	0.38779	9.070000	0.93974	2.690000	0.91761	0.655000	0.94253	.	.		0.388	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Intron	A	46285793	G	A	46285793	5	1	3	1	0	0	0	0	0	0	1	0	915	1014	35	2	5131	2	ARID2	12	46285793	Splice_Site	SNP	G	TCGA-A4-7288-01A-11D-2136-08	39636099	46285793	87566102	59	180											
ESPL1	9700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53685605	53685605	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacgtctacagggcctgacAgtaccaagcaatagccacct	12	6	10	13	1	1	1	0	1	1	0	1	2	1	2	4	2	4	2	4	2	5	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:53685605A>G	ENST00000257934.4	+	26	5743	c.5652A>G	c.(5650-5652)acA>acG	p.T1884T	ESPL1_ENST00000552462.1_Silent_p.T1884T	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1884					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						AGGGCCTGACAGTACCAAGCA	0.587																																					p.T1884T	Colon(53;1069 1201 2587 5382)	.											.	ESPL1-228	0			c.A5652G						.						130	115	120					12																	53685605		2203	4300	6503	SO:0001819	synonymous_variant	9700	exon26			CCTGACAGTACCA	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5652A>G	12.37:g.53685605A>G		Somatic	189	0		WXS	Illumina HiSeq	Phase_I	140	126	NM_012291	0	0	0	8	8		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			.		0.587	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		G	53685605	A	G	53685605	2	3	3	1	0	0	0	0	0	0	0	1	5266	175	7	3		3	ESPL1	12	53685605	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	7399812	53685605	80166290	60	181											
LHX5	64211	hgsc.bcm.edu	37	chr12	113909129	113909129	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagagcggcgcggcctcttAcctgaaaaagtcatttttgc	9	10	11	11	3	2	2	1	1	1	1	2	2	2	2	2	2	3	1	2	2	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:113909129A>G	ENST00000261731.3	-	1	747		c.e1+1		RP11-82C23.2_ENST00000551357.2_RNA|LHX5_ENST00000557836.1_5'Flank	NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5						cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						GCGGCCTCTTACCTGAAAAAG	0.627																																					.		.											.	LHX5-90	0			c.173+2T>C						.						33	32	32					12																	113909129		2203	4300	6503	SO:0001630	splice_region_variant	64211	exon2			CCTCTTACCTGAA	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"Homeoboxes / LIM class"	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.173+1T>C	12.37:g.113909129A>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_022363	0	0	0	0	0	Q32MA4	Splice_Site	SNP	ENST00000261731.3	37	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.067179	0.55539	.	.	ENSG00000089116	ENST00000261731	.	.	.	4.03	2.86	0.33363	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7917	0.40710	0.846:0.0:0.0:0.154	.	.	.	.	.	-1	.	.	.	-	.	.	LHX5	112393512	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.139000	0.94554	0.585000	0.29608	-0.516000	0.04426	.	.		0.627	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363	Intron	G	113909129	A	G	113909129	5	3	3	1	0	0	0	0	0	0	1	0	8796	405	14	3	1053	3	LHX5	12	113909129	Splice_Site	SNP	A	TCGA-A4-7288-01A-11D-2136-08	60223524	113909129	19942766	61	182											
ALG5	29880	broad.mit.edu	37	chr13	37539814	37539814	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctttgacacaaaggaacCacaccagaaagtggaaccca	16	6	7	12	0	0	2	0	1	0	1	1	4	1	4	4	2	2	0	4	2	4	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr13:37539814C>T	ENST00000239891.3	-	8	737	c.671G>A	c.(670-672)tGg>tAg	p.W224*	ALG5_ENST00000413537.2_3'UTR|ALG5_ENST00000443765.1_Nonsense_Mutation_p.W194*	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	224					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		ACAAAGGAACCACACCAGAAA	0.408																																					p.W224X													.	ALG5-90	0			c.G671A						.						109	106	107					13																	37539814		2203	4300	6503	SO:0001587	stop_gained	29880	exon8			AGGAACCACACCA	AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"Glycosyltransferase family 2 domain containing"	20266	protein-coding gene	gene with protein product		604565	"asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)", "asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.671G>A	13.37:g.37539814C>T	ENSP00000239891:p.Trp224*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	83	4	NM_013338	0	0	63	63	0	B4DR37|Q5TBA6	Nonsense_Mutation	SNP	ENST00000239891.3	37	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	C	37	6.551986	0.97658	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	20.093	0.97828	0.0:1.0:0.0:0.0	.	.	.	.	X	194;224	.	ENSP00000239891:W224X	W	-	2	0	ALG5	36437814	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.794000	0.85869	2.756000	0.94617	0.561000	0.74099	TGG	.		0.408	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338		T	37539814	C	T	37539814	4	4	3	1	0	0	0	0	0	1	0	0	521	595	21	2	315	2	ALG5	13	37539814	Nonsense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		37539814	77630064	62	183											
HNRNPC	3183	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	21679712	21679713	+	Frame_Shift_Del	DEL	AT	AT	-																															tgctcctcttctgacttatcAttcttcatctctactgcgga																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:21679712_21679713delAT	ENST00000320084.7	-	7	928_929	c.689_690delAT	c.(688-690)aatfs	p.N230fs	HNRNPC_ENST00000556513.1_Intron|HNRNPC_ENST00000336053.6_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000555309.1_Frame_Shift_Del_p.N229fs|HNRNPC_ENST00000557201.1_Frame_Shift_Del_p.N230fs|HNRNPC_ENST00000556142.1_Intron|HNRNPC_ENST00000556628.1_Frame_Shift_Del_p.N150fs|HNRNPC_ENST00000554969.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000553300.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000449098.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000553753.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000555883.1_Frame_Shift_Del_p.N174fs|HNRNPC_ENST00000430246.2_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000555914.1_Frame_Shift_Del_p.N216fs|HNRNPC_ENST00000556897.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000554455.1_Frame_Shift_Del_p.N230fs|HNRNPC_ENST00000420743.2_Frame_Shift_Del_p.N230fs	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	230	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		CTGACTTATCATTCTTCATCTC	0.505																																					p.230_230del	NSCLC(108;607 2244 12726 38757)	.											.	HNRNPC-90	0			c.689_690del						.																																			SO:0001589	frameshift_variant	3183	exon8			.		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.689_690delAT	14.37:g.21679712_21679713delAT	ENSP00000319690:p.Asn230fs	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	31	16	NM_031314	0	0	0	0	0	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Frame_Shift_Del	DEL	ENST00000320084.7	37	CCDS41915.1																																																																																			.		0.505	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			-	21679713	AT	-	21679712	7	5	3	1	0	1	0	1	0	0	0	0	7283	214	8	0	238	0	HNRNPC	14	21679712	Frame_Shift_Del	DEL	AT	TCGA-A4-7288-01A-11D-2136-08		21679712	85669828	63	184											
RAB2B	84932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21931921	21931921	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacatccctgcgggactctAggtcactgcaagagattaat	11	10	9	11	1	3	1	2	0	1	1	4	3	4	2	1	2	2	1	1	2	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:21931921A>G	ENST00000397762.1	-	6	468	c.368T>C	c.(367-369)cTa>cCa	p.L123P	RAB2B_ENST00000461909.1_5'UTR	NM_001163380.1|NM_032846.3	NP_001156852.1|NP_116235.2	Q8WUD1	RAB2B_HUMAN	RAB2B, member RAS oncogene family	123					positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6	all_cancers(95;0.000858)		Epithelial(56;1.53e-06)|all cancers(55;1.44e-05)	GBM - Glioblastoma multiforme(265;0.00391)		GCGGGACTCTAGGTCACTGCA	0.408																																					p.L123P	Melanoma(131;1007 1750 28652 34486 42672)	.											.	RAB2B-228	0			c.T368C						.						86	80	82					14																	21931921		2203	4300	6503	SO:0001583	missense	84932	exon6			GACTCTAGGTCAC	AK027730	CCDS9570.1	14q11.1	2006-12-18			ENSG00000129472	ENSG00000129472		"RAB, member RAS oncogene"	20246	protein-coding gene	gene with protein product		607466				12376746	Standard	NM_032846		Approved	FLJ14824	uc010tlt.2	Q8WUD1	OTTHUMG00000029693	ENST00000397762.1:c.368T>C	14.37:g.21931921A>G	ENSP00000380869:p.Leu123Pro	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	85	37	NM_032846	0	0	0	0	0	B2RD03|D3DS24|Q6NZ33	Missense_Mutation	SNP	ENST00000397762.1	37	CCDS9570.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.416717	0.83449	.	.	ENSG00000129472	ENST00000397762;ENST00000304034	D	0.85013	-1.93	5.62	5.62	0.85841	Small GTP-binding protein domain (1);	0.000000	0.52532	D	0.000080	D	0.96137	0.8741	H	0.99712	4.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.99;0.998	D	0.97978	1.0347	10	0.87932	D	0	.	14.8111	0.69996	1.0:0.0:0.0:0.0	.	123;77;58	Q8WUD1;B4DUD4;Q6NZ33	RAB2B_HUMAN;.;.	P	123	ENSP00000380869:L123P	ENSP00000302005:L123P	L	-	2	0	RAB2B	21001761	1.000000	0.71417	0.984000	0.44739	0.958000	0.62258	6.854000	0.75440	2.145000	0.66743	0.533000	0.62120	CTA	.		0.408	RAB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074053.4			G	21931921	A	G	21931921	3	3	3	1	0	0	0	0	1	0	0	0	12950	420	15	3	294	3	RAB2B	14	21931921	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	252209	21931921	85417619	64	185											
PCK2	5106	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24568928	24568928	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggatgaggtttgacagtgaAggtgagggactctcagatca	11	10	15	5	0	2	5	2	4	1	1	3	7	2	7	0	4	0	1	0	4	1	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:24568928A>C	ENST00000216780.4	+	6	1282	c.1014A>C	c.(1012-1014)gaA>gaC	p.E338D	NRL_ENST00000561028.1_Intron|PCK2_ENST00000561286.1_Splice_Site_p.E204D|PCK2_ENST00000545054.2_Splice_Site_p.E204D|PCK2_ENST00000559250.1_Splice_Site_p.E350D|PCK2_ENST00000558096.1_Splice_Site_p.E204D|PCK2_ENST00000396973.4_Splice_Site_p.E338D	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	338					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		TTGACAGTGAAGGTGAGGGAC	0.517																																					p.E338D		.											.	PCK2-227	0			c.A1014C						.						209	179	189					14																	24568928		2203	4300	6503	SO:0001630	splice_region_variant	5106	exon6			CAGTGAAGGTGAG	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.1015+1A>C	14.37:g.24568928A>C		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	118	29	NM_001018073	0	0	0	1	1	O43253|Q86U01|Q9BV62	Missense_Mutation	SNP	ENST00000216780.4	37	CCDS9609.1	.	.	.	.	.	.	.	.	.	.	A	8.481	0.859731	0.17178	.	.	ENSG00000100889	ENST00000216780;ENST00000396973;ENST00000545054	T;T;T	0.06849	3.25;3.25;3.25	5.5	-8.34	0.00988	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.280145	0.45606	N	0.000341	T	0.01695	0.0054	N	0.02120	-0.675	0.43088	D	0.99475	B;B;B;B	0.09022	0.001;0.0;0.002;0.0	B;B;B;B	0.15052	0.012;0.012;0.007;0.006	T	0.43245	-0.9403	10	0.02654	T	1	-4.464	9.0824	0.36561	0.2559:0.5071:0.0:0.237	.	204;338;338;338	B4DW73;Q16822;Q16822-2;Q6IB91	.;PCKGM_HUMAN;.;.	D	338;338;204	ENSP00000216780:E338D;ENSP00000380171:E338D;ENSP00000441826:E204D	ENSP00000216780:E338D	E	+	3	2	PCK2	23638768	0.996000	0.38824	0.953000	0.39169	0.948000	0.59901	0.536000	0.23129	-0.926000	0.03770	0.459000	0.35465	GAA	.		0.517	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073	Missense_Mutation	C	24568928	A	C	24568928	5	2	3	1	0	0	0	0	0	0	1	0	11608	86	3	5	1036	5	PCK2	14	24568928	Splice_Site	SNP	A	TCGA-A4-7288-01A-11D-2136-08	2637007	24568928	82780612	65	186											
C14orf183	196913	hgsc.bcm.edu	37	chr14	50550535	50550535	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggtgccgtgggcggcaccCaccaggcatgaggtccacca	7	4	14	16	3	0	1	0	1	0	0	1	1	1	1	6	5	1	2	6	5	0	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:50550535C>G	ENST00000305273.1	-	5	808	c.809G>C	c.(808-810)tGg>tCg	p.W270S	RP11-58E21.7_ENST00000556019.2_lincRNA|RP11-58E21.5_ENST00000603228.1_lincRNA	NM_001014830.1	NP_001014830.1	Q8WXQ3	CN183_HUMAN	chromosome 14 open reading frame 183	270										endometrium(2)|large_intestine(2)|lung(3)	7						GGGCGGCACCCACCAGGCATG	0.657																																					p.W270S		.											.	C14orf183-90	0			c.G809C						.						33	39	37					14																	50550535		2019	4173	6192	SO:0001583	missense	196913	exon5			GGCACCCACCAGG	AF390030	CCDS45101.1	14q21.3	2012-09-26			ENSG00000168260	ENSG00000168260			27285	protein-coding gene	gene with protein product							Standard	NM_001014830		Approved		uc010tqk.2	Q8WXQ3	OTTHUMG00000170858	ENST00000305273.1:c.809G>C	14.37:g.50550535C>G	ENSP00000303234:p.Trp270Ser	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_001014830	0	0	0	0	0		Missense_Mutation	SNP	ENST00000305273.1	37	CCDS45101.1	.	.	.	.	.	.	.	.	.	.	C	8.551	0.875519	0.17395	.	.	ENSG00000168260	ENST00000305273	.	.	.	3.82	1.99	0.26369	.	.	.	.	.	T	0.31544	0.0800	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	P	0.61003	0.882	T	0.10730	-1.0617	8	0.87932	D	0	.	6.3715	0.21483	0.0:0.7729:0.0:0.2271	.	270	Q8WXQ3	CN183_HUMAN	S	270	.	ENSP00000303234:W270S	W	-	2	0	C14orf183	49620285	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.002000	0.03686	0.588000	0.29660	0.460000	0.39030	TGG	.		0.657	C14orf183-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000410705.1	NM_001014830		G	50550535	C	G	50550535	3	3	3	1	0	0	0	0	1	0	0	0	1770	595	21	4	168	4	C14orf183	14	50550535	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	25981607	50550535	56799005	66	187											
NID2	22795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	52494036	52494036	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaggtatgactgccatcctCacaggggttggcaggtgggg	8	8	16	9	0	1	1	1	1	0	0	2	1	2	1	2	7	1	3	2	7	1	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:52494036C>T	ENST00000216286.5	-	12	2556	c.2557G>A	c.(2557-2559)Gag>Aag	p.E853K	NID2_ENST00000541773.1_Intron	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	853	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					CTGCCATCCTCACAGGGGTTG	0.572																																					p.E853K		.											.	NID2-158	0			c.G2557A						.						37	36	36					14																	52494036		2203	4300	6503	SO:0001583	missense	22795	exon12			CATCCTCACAGGG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2557G>A	14.37:g.52494036C>T	ENSP00000216286:p.Glu853Lys	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	37	15	NM_007361	0	0	8	12	4	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.692957	0.48202	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000395707	D	0.87334	-2.24	5.76	4.86	0.63082	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.479683	0.23171	N	0.051140	T	0.81894	0.4919	L	0.42008	1.315	0.80722	D	1	B;P;B	0.35411	0.04;0.5;0.417	B;B;B	0.35278	0.017;0.09;0.199	T	0.77705	-0.2488	10	0.11182	T	0.66	.	15.3665	0.74526	0.0:0.8547:0.1453:0.0	.	447;855;853	E7EPP3;Q5CZI2;Q14112	.;.;NID2_HUMAN	K	853;447;855	ENSP00000216286:E853K	ENSP00000216286:E853K	E	-	1	0	NID2	51563786	0.975000	0.34042	0.998000	0.56505	0.694000	0.40290	1.623000	0.37008	1.397000	0.46682	0.563000	0.77884	GAG	.		0.572	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52494036	C	T	52494036	3	4	3	1	0	0	0	0	1	0	0	0	10441	835	29	2	1614	2	NID2	14	52494036	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	1943501	52494036	54855504	67	188											
PPM1A	5494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	60750192	60750192	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgattttgtaagatccagActtgaagtcactgatgacct	11	14	9	7	0	1	6	1	4	0	2	2	6	2	6	2	0	0	1	2	0	2	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:60750192A>T	ENST00000395076.4	+	2	1201	c.771A>T	c.(769-771)agA>agT	p.R257S	PPM1A_ENST00000325658.3_Missense_Mutation_p.R257S|PPM1A_ENST00000529574.1_Missense_Mutation_p.R257S|PPM1A_ENST00000325642.3_Missense_Mutation_p.R330S	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	257					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		TAAGATCCAGACTTGAAGTCA	0.348																																					p.R330S		.											.	PPM1A-227	0			c.A990T						.						153	150	151					14																	60750192		2203	4300	6503	SO:0001583	missense	5494	exon2			ATCCAGACTTGAA	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.771A>T	14.37:g.60750192A>T	ENSP00000378514:p.Arg257Ser	Somatic	329	1		WXS	Illumina HiSeq	Phase_I	232	94	NM_177952	0	1	33	74	40	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.391550	0.62066	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076;ENST00000325658	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.69	0.8	0.18672	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.37732	0.1014	M	0.80982	2.52	0.80722	D	1	D;D;D	0.71674	0.985;0.998;0.985	D;D;D	0.70716	0.909;0.97;0.909	T	0.14090	-1.0485	10	0.66056	D	0.02	-4.9401	9.4876	0.38940	0.6003:0.0:0.3997:0.0	.	257;257;257	P35813;P35813-2;B2R8E4	PPM1A_HUMAN;.;.	S	330;257;257;257	ENSP00000327255:R330S;ENSP00000432966:R257S;ENSP00000378514:R257S;ENSP00000314850:R257S	ENSP00000327255:R330S	R	+	3	2	PPM1A	59819945	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.406000	0.21032	0.109000	0.17891	0.477000	0.44152	AGA	.		0.348	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003		T	60750192	A	T	60750192	3	4	3	1	0	0	0	0	1	0	0	0	12364	272	10	5	996	5	PPM1A	14	60750192	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	8256156	60750192	46599348	68	189											
EML5	161436	hgsc.bcm.edu	37	chr14	89178771	89178771	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaggcctgaaacacatgTccatgaagcccaatgaacac	15	7	7	12	0	1	3	1	3	0	0	2	3	2	3	3	1	3	0	3	1	5	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:89178771T>C	ENST00000380664.5	-	10	1500	c.1501A>G	c.(1501-1503)Aca>Gca	p.T501A	EML5_ENST00000554922.1_Missense_Mutation_p.T501A|EML5_ENST00000352093.5_Missense_Mutation_p.T501A			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	501						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GAAACACATGTCCATGAAGCC	0.323																																					p.T501A		.											.	EML5-93	0			c.A1501G						.						70	66	67					14																	89178771		1828	4088	5916	SO:0001583	missense	161436	exon10			CACATGTCCATGA	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.1501A>G	14.37:g.89178771T>C	ENSP00000370039:p.Thr501Ala	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_183387	0	0	1	1	0	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561037	0.86335	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.58506	0.55;0.33;0.59	4.7	4.7	0.59300	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73418	0.3584	H	0.94264	3.515	0.53005	D	0.999961	P	0.45768	0.866	P	0.46585	0.521	T	0.82368	-0.0492	10	0.72032	D	0.01	-17.053	14.3397	0.66617	0.0:0.0:0.0:1.0	.	501	Q05BV3	EMAL5_HUMAN	A	501	ENSP00000451998:T501A;ENSP00000298315:T501A;ENSP00000370039:T501A	ENSP00000298315:T501A	T	-	1	0	EML5	88248524	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.525000	0.81892	1.954000	0.56735	0.528000	0.53228	ACA	.		0.323	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			C	89178771	T	C	89178771	3	2	3	1	0	0	0	0	1	0	0	0	5113	1667	58	3	4568	3	EML5	14	89178771	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	28428579	89178771	18170769	69	190											
UBR1	197131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43299483	43299483	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtcactgactgctggggtgCtaccaaaagaaatgatcaga	14	8	11	8	0	2	4	2	2	0	2	2	4	2	4	1	2	3	2	1	2	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr15:43299483C>A	ENST00000290650.4	-	30	3288		c.e30-1		UBR1_ENST00000382177.2_Splice_Site|UBR1_ENST00000568782.1_Splice_Site	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1						cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TGCTGGGGTGCTACCAAAAGA	0.403																																					.		.											.	UBR1-91	0			c.3210-1G>T						.						48	44	45					15																	43299483		2203	4299	6502	SO:0001630	splice_region_variant	197131	exon31			GGGGTGCTACCAA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3210-1G>T	15.37:g.43299483C>A		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	19	8	NM_174916	0	0	0	0	0	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Splice_Site	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550046	0.65311	.	.	ENSG00000159459	ENST00000290650	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1988	0.89831	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBR1	41086775	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.935000	0.56560	2.534000	0.85438	0.655000	0.94253	.	.		0.403	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	Intron	A	43299483	C	A	43299483	5	1	3	1	0	0	0	0	0	0	1	0	16934	811	28	4	2112	4	UBR1	15	43299483	Splice_Site	SNP	C	TCGA-A4-7288-01A-11D-2136-08		43299483	59231909	70	191											
PARP6	56965	broad.mit.edu;bcgsc.ca	37	chr15	72556908	72556908	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcttactttttcaactgaAgacccagcccaaatccttcc	10	13	4	14	0	2	2	1	1	1	1	4	2	4	2	4	0	3	1	4	0	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr15:72556908A>G	ENST00000569795.1	-	8	1070	c.383T>C	c.(382-384)cTt>cCt	p.L128P	PARP6_ENST00000260376.7_Missense_Mutation_p.L128P|PARP6_ENST00000287196.9_Missense_Mutation_p.L128P|PARP6_ENST00000413097.2_5'UTR			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	128							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						TTTCAACTGAAGACCCAGCCC	0.428																																					p.L128P													.	PARP6-522	0			c.T383C						.						122	115	117					15																	72556908		1851	4081	5932	SO:0001583	missense	56965	exon7			AACTGAAGACCCA	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.383T>C	15.37:g.72556908A>G	ENSP00000456348:p.Leu128Pro	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	109	5	NM_020214	0	0	0	0	0	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	37	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	A	22.2	4.259245	0.80246	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000336471	.	.	.	5.5	5.5	0.81552	.	0.061156	0.64402	D	0.000002	T	0.40272	0.1110	N	0.14661	0.345	0.80722	D	1	P;P	0.47409	0.694;0.895	B;B	0.44278	0.346;0.445	T	0.30416	-0.9979	9	0.32370	T	0.25	-0.6581	14.7832	0.69781	1.0:0.0:0.0:0.0	.	128;128	Q0VDG0;Q2NL67	.;PARP6_HUMAN	P	128	.	ENSP00000260376:L128P	L	-	2	0	PARP6	70343962	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.265000	0.95647	2.087000	0.62958	0.460000	0.39030	CTT	.		0.428	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		G	72556908	A	G	72556908	3	3	3	1	0	0	0	0	1	0	0	0	11490	72	3	3	1577	3	PARP6	15	72556908	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	29257425	72556908	29974484	71	192											
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90634783	90634783	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacttcaggagggggcactAccttctccttgatgaactgc	8	10	10	13	0	2	2	1	2	1	0	3	3	2	3	3	3	3	1	3	3	2	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr15:90634783A>G	ENST00000330062.3	-	2	321		c.e2+1		IDH2_ENST00000540499.2_Splice_Site|IDH2_ENST00000559482.1_Splice_Site|IDH2_ENST00000539790.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial						2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			AGGGGGCACTACCTTCTCCTT	0.577			M		GBM																																.		.		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	.	IDH2-15118	0			c.207+2T>C						.						169	135	146					15																	90634783		2200	4298	6498	SO:0001630	splice_region_variant	3418	exon3			GGCACTACCTTCT		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.207+1T>C	15.37:g.90634783A>G		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	95	12	NM_002168	0	0	0	7	7	B2R6L6|B4DFL2|Q96GT3	Splice_Site	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066137	0.55539	.	.	ENSG00000182054	ENST00000330062;ENST00000540499	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0239	0.58804	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IDH2	88435787	1.000000	0.71417	0.925000	0.36789	0.501000	0.33797	9.290000	0.96065	1.965000	0.57142	0.459000	0.35465	.	.		0.577	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1		Intron	G	90634783	A	G	90634783	5	3	3	1	0	0	0	0	0	0	1	0	7516	405	14	3	1189	3	IDH2	15	90634783	Splice_Site	SNP	A	TCGA-A4-7288-01A-11D-2136-08	18077875	90634783	11896609	72	193											
RAB40C	57799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	677608	677608	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaactgctcgcggagtaacTgcaagatctcctagcgggga	11	7	13	10	3	1	2	0	0	1	2	3	4	1	4	1	3	5	3	1	3	4	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:677608T>C	ENST00000248139.3	+	6	1035	c.832T>C	c.(832-834)Tgc>Cgc	p.C278R	RAB40C_ENST00000538492.1_Missense_Mutation_p.C278R|RAB40C_ENST00000535977.1_Missense_Mutation_p.C278R|RAB40C_ENST00000539661.1_Missense_Mutation_p.C278R	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	278					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				GCGGAGTAACTGCAAGATCTC	0.697																																					p.C278R	Melanoma(123;1631 1690 28262 44104 44957)	.											.	RAB40C-227	0			c.T832C						.						47	51	49					16																	677608		2201	4300	6501	SO:0001583	missense	57799	exon6			AGTAACTGCAAGA	Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"RAB, member RAS oncogene"	18285	protein-coding gene	gene with protein product			"RAS-like, family 8, member C"	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.832T>C	16.37:g.677608T>C	ENSP00000248139:p.Cys278Arg	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	104	59	NM_021168	0	0	14	35	21	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Missense_Mutation	SNP	ENST00000248139.3	37	CCDS10413.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.889349	0.72524	.	.	ENSG00000197562	ENST00000535977;ENST00000539661;ENST00000538492;ENST00000248139	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.81725	0.4883	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.87578	0.998;0.814	D	0.83701	0.0182	10	0.87932	D	0	.	13.6194	0.62128	0.0:0.0:0.0:1.0	.	278;259	Q96S21;Q5PXE8	RB40C_HUMAN;.	R	278	ENSP00000438492:C278R;ENSP00000445050:C278R;ENSP00000438382:C278R;ENSP00000248139:C278R	ENSP00000248139:C278R	C	+	1	0	RAB40C	617609	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.918000	0.87506	1.808000	0.52836	0.459000	0.35465	TGC	.		0.697	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168		C	677608	T	C	677608	3	2	3	1	0	0	0	0	1	0	0	0	12974	1580	55	3	854	3	RAB40C	16	677608	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08		677608	89677145	73	194											
HS3ST2	9956	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	22926750	22926750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaatcgagcctcctgcctcGatgcttgggcaaatcaaaag	12	8	10	11	2	1	1	1	0	0	1	4	3	2	1	3	1	3	2	3	1	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:22926750G>A	ENST00000261374.3	+	2	1405	c.971G>A	c.(970-972)cGa>cAa	p.R324Q		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	324					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		CTCCTGCCTCGATGCTTGGGC	0.403																																					p.R324Q		.											.	HS3ST2-516	0			c.G971A						.						135	148	143					16																	22926750		2197	4300	6497	SO:0001583	missense	9956	exon2			TGCCTCGATGCTT	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"Sulfotransferases, membrane-bound"	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.971G>A	16.37:g.22926750G>A	ENSP00000261374:p.Arg324Gln	Somatic	264	0		WXS	Illumina HiSeq	Phase_I	328	17	NM_006043	0	0	2	2	0	Q52LZ1	Missense_Mutation	SNP	ENST00000261374.3	37	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382090	0.82792	.	.	ENSG00000122254	ENST00000261374	D	0.83755	-1.76	5.11	5.11	0.69529	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.89860	0.6837	M	0.79805	2.47	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.89491	0.3757	10	0.44086	T	0.13	.	11.0723	0.48010	0.0843:0.0:0.9157:0.0	.	324	Q9Y278	HS3S2_HUMAN	Q	324	ENSP00000261374:R324Q	ENSP00000261374:R324Q	R	+	2	0	HS3ST2	22834251	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.872000	0.75536	2.375000	0.81037	0.561000	0.74099	CGA	.		0.403	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		A	22926750	G	A	22926750	3	1	3	1	0	0	0	0	1	0	0	0	7385	1058	37	1	977	1	HS3ST2	16	22926750	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	22249142	22926750	67428003	74	195											
PRSS8	5652	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31144179	31144179	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtagctggggtgggggAtgatgtccttcagggtgctg	5	10	21	5	0	1	1	1	1	0	0	2	3	2	3	1	7	2	3	1	7	1	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:31144179A>G	ENST00000317508.6	-	4	625	c.362T>C	c.(361-363)aTc>aCc	p.I121T	PRSS8_ENST00000568261.1_Missense_Mutation_p.I67T|RP11-388M20.2_ENST00000563605.1_RNA	NM_002773.3	NP_002764.1	Q16651	PRSS8_HUMAN	protease, serine, 8	121	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				positive regulation of sodium ion transport (GO:0010765)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	8						GGGGTGGGGGATGATGTCCTT	0.622																																					p.I121T		.											.	.	0			c.T362C						.						127	144	138					16																	31144179		2166	4255	6421	SO:0001583	missense	5652	exon4			TGGGGGATGATGT	U33446	CCDS45469.1	16p11.2	2010-05-07	2007-02-21			ENSG00000052344		"Serine peptidases / Serine peptidases"	9491	protein-coding gene	gene with protein product	"prostasin"	600823				8838796, 7768952	Standard	NM_002773		Approved		uc002ebc.4	Q16651		ENST00000317508.6:c.362T>C	16.37:g.31144179A>G	ENSP00000319730:p.Ile121Thr	Somatic	248	1		WXS	Illumina HiSeq	Phase_I	344	94	NM_002773	0	0	10	12	2	B4DWP2|Q9UCA3	Missense_Mutation	SNP	ENST00000317508.6	37	CCDS45469.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.686219	0.29962	.	.	ENSG00000052344	ENST00000317508	D	0.90069	-2.61	5.45	4.29	0.51040	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.334685	0.25897	N	0.027586	D	0.83473	0.5262	L	0.49350	1.555	0.09310	N	1	B;B	0.27416	0.178;0.178	B;B	0.28638	0.092;0.056	T	0.75127	-0.3427	10	0.56958	D	0.05	.	5.2809	0.15674	0.7586:0.0:0.0836:0.1578	.	67;121	B4DWP2;Q16651	.;PRSS8_HUMAN	T	121	ENSP00000319730:I121T	ENSP00000319730:I121T	I	-	2	0	PRSS8	31051680	0.998000	0.40836	0.255000	0.24374	0.002000	0.02628	2.349000	0.44054	2.066000	0.61787	0.459000	0.35465	ATC	.		0.622	PRSS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433536.1	NM_002773		G	31144179	A	G	31144179	3	3	3	1	0	0	0	0	1	0	0	0	12664	333	12	3	681	3	PRSS8	16	31144179	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	8217429	31144179	59210574	75	196											
ABCC11	85320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	48249161	48249161	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtacattttaatcagcttaAtgcaagtgagaacttcactg	13	14	7	7	0	2	1	2	1	0	1	2	2	2	1	0	0	4	3	0	0	5	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:48249161A>G	ENST00000394747.1	-	7	1395	c.1046T>C	c.(1045-1047)aTt>aCt	p.I349T	ABCC11_ENST00000353782.5_Missense_Mutation_p.I349T|ABCC11_ENST00000356608.2_Missense_Mutation_p.I349T|ABCC11_ENST00000394748.1_Missense_Mutation_p.I349T|ABCC11_ENST00000537808.1_Missense_Mutation_p.I349T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	349	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	AATCAGCTTAATGCAAGTGAG	0.453																																					p.I349T		.											.	ABCC11-95	0			c.T1046C						.						148	144	145					16																	48249161		2201	4300	6501	SO:0001583	missense	85320	exon7			AGCTTAATGCAAG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1046T>C	16.37:g.48249161A>G	ENSP00000378230:p.Ile349Thr	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	139	42	NM_033151	0	0	0	0	0	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099866	0.76983	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11	5.23	5.23	0.72850	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.125360	0.53938	D	0.000060	D	0.95642	0.8583	M	0.80982	2.52	0.48632	D	0.999682	D;D	0.62365	0.979;0.991	P;D	0.72625	0.801;0.978	D	0.96028	0.9014	10	0.87932	D	0	-4.6607	12.6309	0.56657	1.0:0.0:0.0:0.0	.	349;349	Q96J66-2;Q96J66	.;ABCCB_HUMAN	T	349	ENSP00000311326:I349T;ENSP00000349017:I349T;ENSP00000378231:I349T;ENSP00000378230:I349T;ENSP00000438530:I349T	ENSP00000311326:I349T	I	-	2	0	ABCC11	46806662	1.000000	0.71417	0.599000	0.28851	0.926000	0.56050	6.131000	0.71670	1.978000	0.57642	0.528000	0.53228	ATT	.		0.453	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		G	48249161	A	G	48249161	3	3	3	1	0	0	0	0	1	0	0	0	51	101	4	3	3194	3	ABCC11	16	48249161	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	17104982	48249161	42105592	76	197											
INPP5K	51763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	1400005	1400005	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggctgctggggaagtccgaGgttgaagagtagctgaccat	9	8	17	7	1	0	3	0	2	0	1	1	5	1	4	2	4	2	5	2	4	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:1400005G>C	ENST00000421807.2	-	9	1444	c.1056C>G	c.(1054-1056)acC>acG	p.T352T	INPP5K_ENST00000320345.6_Silent_p.T276T|INPP5K_ENST00000542125.1_Silent_p.T256T|INPP5K_ENST00000406424.4_Silent_p.T276T|INPP5K_ENST00000397335.3_Silent_p.T260T	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	352	Required for ruffle localization.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						GGAAGTCCGAGGTTGAAGAGT	0.567																																					p.T352T		.											.	INPP5K-68	0			c.C1056G						.						141	113	123					17																	1400005		2203	4300	6503	SO:0001819	synonymous_variant	51763	exon9			GTCCGAGGTTGAA		CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.1056C>G	17.37:g.1400005G>C		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	124	68	NM_016532	0	0	23	55	32	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	37	CCDS11004.1																																																																																			.		0.567	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			C	1400005	G	C	1400005	2	2	3	1	0	0	0	0	0	0	0	1	7781	987	35	4		4	INPP5K	17	1400005	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08		1400005	79795205	77	198											
ACLY	47	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40048661	40048661	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaagacagggatcaggatCtctttgtgcccccagtaaaa	12	10	10	9	0	2	2	1	1	1	1	3	4	2	4	2	2	1	1	2	2	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:40048661C>A	ENST00000352035.2	-	16	1771	c.1641G>T	c.(1639-1641)gaG>gaT	p.E547D	ACLY_ENST00000590151.1_Missense_Mutation_p.E547D|ACLY_ENST00000537919.1_Missense_Mutation_p.E276D|ACLY_ENST00000393896.2_Missense_Mutation_p.E537D|ACLY_ENST00000353196.1_Missense_Mutation_p.E537D	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	547					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				GGATCAGGATCTCTTTGTGCC	0.493																																					p.E547D	Colon(64;807 1396 15971 30971)	.											.	ACLY-228	0			c.G1641T						.						128	113	118					17																	40048661		2203	4300	6503	SO:0001583	missense	47	exon16			CAGGATCTCTTTG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.1641G>T	17.37:g.40048661C>A	ENSP00000253792:p.Glu547Asp	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	180	68	NM_001096	0	0	129	201	72	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	37	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.447728	0.84101	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	D;D;D;D	0.89939	-1.61;-1.62;-2.59;-1.62	5.49	4.52	0.55395	CoA-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95373	0.8498	H	0.95328	3.655	0.80722	D	1	P;D;D;D;P	0.57899	0.92;0.981;0.981;0.973;0.92	D;P;P;D;D	0.66084	0.922;0.805;0.805;0.941;0.922	D	0.95675	0.8727	10	0.72032	D	0.01	.	10.7053	0.45952	0.0:0.8307:0.0:0.1693	.	276;591;601;537;547	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	D	547;601;537;276;537	ENSP00000253792:E547D;ENSP00000345398:E537D;ENSP00000445349:E276D;ENSP00000377474:E537D	ENSP00000253792:E547D	E	-	3	2	ACLY	37302187	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.474000	0.35398	1.430000	0.47334	0.561000	0.74099	GAG	.		0.493	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		A	40048661	C	A	40048661	3	1	3	1	0	0	0	0	1	0	0	0	143	912	32	4	1720	4	ACLY	17	40048661	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	38648656	40048661	41146549	78	199											
HDAC5	10014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42158172	42158172	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaagaagttcccgttgtCatagcgatgcagagagatgt	12	10	13	6	2	1	3	1	0	0	3	2	6	2	4	1	1	2	3	1	1	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:42158172C>A	ENST00000393622.2	-	21	3017	c.2686G>T	c.(2686-2688)Gac>Tac	p.D896Y	HDAC5_ENST00000336057.5_Missense_Mutation_p.D811Y|HDAC5_ENST00000586802.1_Missense_Mutation_p.D896Y|HDAC5_ENST00000225983.6_Missense_Mutation_p.D897Y	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	896	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TTCCCGTTGTCATAGCGATGC	0.562																																					p.D897Y		.											.	HDAC5-227	0			c.G2689T						.						117	103	108					17																	42158172		2203	4300	6503	SO:0001583	missense	10014	exon21			CGTTGTCATAGCG	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2686G>T	17.37:g.42158172C>A	ENSP00000377244:p.Asp896Tyr	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	119	44	NM_001015053	0	0	63	88	25	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	37	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376869	0.82682	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.55234	0.53;0.53;0.64	4.63	4.63	0.57726	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	T	0.80138	0.4568	H	0.94886	3.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.989;1.0	D	0.86300	0.1679	10	0.87932	D	0	-22.7715	16.4039	0.83651	0.0:1.0:0.0:0.0	.	811;897;896	Q9UQL6-2;Q9UQL6-3;Q9UQL6	.;.;HDAC5_HUMAN	Y	897;896;811	ENSP00000225983:D897Y;ENSP00000377244:D896Y;ENSP00000337290:D811Y	ENSP00000225983:D897Y	D	-	1	0	HDAC5	39513698	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.630000	0.83225	2.411000	0.81874	0.563000	0.77884	GAC	.		0.562	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		A	42158172	C	A	42158172	3	1	3	1	0	0	0	0	1	0	0	0	7031	826	29	4	710	4	HDAC5	17	42158172	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	2109511	42158172	39037038	79	200											
IMP5	162540	broad.mit.edu;bcgsc.ca	37	chr17	43922606	43922611	+	In_Frame_Del	DEL	GGCCAA	GGCCAA	-																															cgaaaggctggctggctcagGgccaaggtgcccacgggctg																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	GGCCAA	GGCCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:43922606_43922611delGGCCAA	ENST00000329196.5	+	1	351_356	c.334_339delGGCCAA	c.(334-339)ggccaadel	p.GQ112del	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	112	PA.					endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										GCTGGCTCAGGGCCAAGGTGCCCACG	0.68																																					p.112_113del													.	.	0			c.334_339del						.																																			SO:0001651	inframe_deletion	162540	exon1			GCTCAGGGCCAAG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"intramembrane protease 5"	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.334_339delGGCCAA	17.37:g.43922606_43922611delGGCCAA	ENSP00000332488:p.Gly112_Gln113del	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	94	10	NM_175882	0	0	0	0	0	Q8TC67|Q8WVZ6	In_Frame_Del	DEL	ENST00000329196.5	37	CCDS32673.1																																																																																			.		0.68	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882		-	43922611	GGCCAA	-	43922606	7	5	3	1	0	1	0	1	0	0	0	0	7742	1232	43	0	336	0	IMP5	17	43922606	In_Frame_Del	DEL	GGCCAA	TCGA-A4-7288-01A-11D-2136-08	1764434	43922606	37272604	80	201											
AFG3L2	10939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	12358734	12358734	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaaattcacaaattccaTgatctctagcttggcctcct	12	12	5	12	0	2	2	1	1	1	1	5	2	4	2	3	1	1	1	3	1	4	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr18:12358734T>C	ENST00000269143.3	-	8	1192	c.961A>G	c.(961-963)Atg>Gtg	p.M321V		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	321					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	ACAAATTCCATGATCTCTAGC	0.383																																					p.M321V		.											.	AFG3L2-90	0			c.A961G						.						86	78	80					18																	12358734		2203	4300	6503	SO:0001583	missense	10939	exon8			ATTCCATGATCTC	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.961A>G	18.37:g.12358734T>C	ENSP00000269143:p.Met321Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	67	27	NM_006796	0	0	99	183	84	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	37	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.163727	0.78226	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	T	0.39787	1.06	5.76	5.76	0.90799	Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	L	0.42744	1.35	0.80722	D	1	P	0.45986	0.87	P	0.47251	0.542	T	0.45469	-0.9259	10	0.66056	D	0.02	.	16.0735	0.80951	0.0:0.0:0.0:1.0	.	321	Q9Y4W6	AFG32_HUMAN	V	321;336	ENSP00000269143:M321V	ENSP00000269143:M321V	M	-	1	0	AFG3L2	12348734	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.912000	0.69948	2.195000	0.70347	0.533000	0.62120	ATG	.		0.383	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		C	12358734	T	C	12358734	3	2	3	1	0	0	0	0	1	0	0	0	360	1464	51	3	1472	3	AFG3L2	18	12358734	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08		12358734	65718514	81	202											
APC2	10297	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	1468067	1468067	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagctccctcagcgagccCgagccctcggagccgccggc	5	3	13	20	5	1	0	1	0	0	0	3	3	2	1	6	2	5	1	6	2	0	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:1468067C>T	ENST00000535453.1	+	14	6480	c.4767C>T	c.(4765-4767)ccC>ccT	p.P1589P	APC2_ENST00000238483.4_Silent_p.P1315P|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_Silent_p.P1589P			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCAGCGAGCCCGAGCCCTCGG	0.766																																					p.P1589P		.											.	APC2-290	0			c.C4767T						.						4	4	4					19																	1468067		1704	3627	5331	SO:0001819	synonymous_variant	10297	exon15			CGAGCCCGAGCCC		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.4767C>T	19.37:g.1468067C>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	20	9	NM_005883	0	0	0	0	0	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			.		0.766	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		T	1468067	C	T	1468067	2	4	3	1	0	0	0	0	0	0	0	1	764	639	23	1		1	APC2	19	1468067	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1468067	57660916	82	203											
NACC1	112939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13249116	13249116	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcctacaccaccttcatcAgtgaaacgggcaagatcgag	13	6	9	13	3	2	2	2	1	0	1	3	3	2	2	3	1	2	1	3	1	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:13249116A>G	ENST00000292431.4	+	6	1606	c.1480A>G	c.(1480-1482)Agt>Ggt	p.S494G	CTC-250I14.3_ENST00000591825.1_RNA	NM_052876.3	NP_443108.1	Q96RE7	NACC1_HUMAN	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	494					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear body (GO:0016604)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(3)|skin(1)	9						CACCTTCATCAGTGAAACGGG	0.642																																					p.S494G		.											.	NACC1-90	0			c.A1480G						.						176	135	149					19																	13249116		2203	4300	6503	SO:0001583	missense	112939	exon6			TTCATCAGTGAAA	AF395817	CCDS12294.1	19p13.13	2013-01-09	2008-10-03	2008-10-03		ENSG00000160877		"BEN domain containing", "BTB/POZ domain containing"	20967	protein-coding gene	gene with protein product	"nucleus accumbens associated 1", "BEN domain containing 8"	610672	"BTB (POZ) domain containing 14B"	BTBD14B		12477932	Standard	NM_052876		Approved	NAC1, NAC-1, BEND8, BTBD30	uc002mwm.4	Q96RE7		ENST00000292431.4:c.1480A>G	19.37:g.13249116A>G	ENSP00000292431:p.Ser494Gly	Somatic	193	1		WXS	Illumina HiSeq	Phase_I	161	62	NM_052876	0	0	26	54	28		Missense_Mutation	SNP	ENST00000292431.4	37	CCDS12294.1	.	.	.	.	.	.	.	.	.	.	A	6.336	0.430017	0.11987	.	.	ENSG00000160877	ENST00000292431	T	0.55413	0.52	4.94	3.92	0.45320	.	0.229179	0.43919	D	0.000509	T	0.29817	0.0745	N	0.19112	0.55	0.29280	N	0.870099	B	0.02656	0.0	B	0.01281	0.0	T	0.27571	-1.0070	10	0.02654	T	1	.	8.6147	0.33824	0.9068:0.0:0.0932:0.0	.	494	Q96RE7	NACC1_HUMAN	G	494	ENSP00000292431:S494G	ENSP00000292431:S494G	S	+	1	0	NACC1	13110116	0.945000	0.32115	1.000000	0.80357	0.983000	0.72400	0.957000	0.29215	0.755000	0.32990	0.454000	0.30748	AGT	.		0.642	NACC1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452879.1	NM_052876		G	13249116	A	G	13249116	3	3	3	1	0	0	0	0	1	0	0	0	10160	188	7	3	1498	3	NACC1	19	13249116	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	11781049	13249116	45879867	83	204											
SF4	57794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19420931	19420931	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggtctgtgccttctgcaaCttcagaaactgctgcaagaa	10	11	9	11	0	3	2	1	0	2	2	3	2	3	2	1	1	6	3	1	1	4	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:19420931C>T	ENST00000247001.5	-	3	632	c.285G>A	c.(283-285)aaG>aaA	p.K95K	SUGP1_ENST00000585763.1_5'UTR|SUGP1_ENST00000334782.5_Silent_p.K95K	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	95					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						CCTTCTGCAACTTCAGAAACT	0.512																																					p.K95K		.											.	SUGP1-91	0			c.G285A						.						149	120	130					19																	19420931		2203	4300	6503	SO:0001819	synonymous_variant	57794	exon3			CTGCAACTTCAGA	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"G patch domain containing"	18643	protein-coding gene	gene with protein product		607992	"splicing factor 4"	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.285G>A	19.37:g.19420931C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	84	36	NM_172231	0	0	18	30	12	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Silent	SNP	ENST00000247001.5	37	CCDS12399.1																																																																																			.		0.512	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		T	19420931	C	T	19420931	2	4	3	1	0	0	0	0	0	0	0	1	14187	564	20	2		2	SF4	19	19420931	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	6171815	19420931	39708052	84	205											
PRR12	57479	hgsc.bcm.edu	37	chr19	50119185	50119185	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgagaagccctccctcctgCggcctgttgagaaggaaaag	10	6	12	13	2	0	2	0	1	0	2	2	5	2	3	5	2	2	1	5	2	4	1	rs200319638	byFrequency	TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:50119185C>G	ENST00000418929.2	+	9	5218	c.5206C>G	c.(5206-5208)Cgg>Ggg	p.R1736G		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	915							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)		CTCCCTCCTGCGGCCTGTTga	0.652																																					p.R1736G		.											.	PRR12-70	0			c.C5206G						.						18	23	22					19																	50119185		1962	4072	6034	SO:0001583	missense	57479	exon9			CTCCTGCGGCCTG	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.5206C>G	19.37:g.50119185C>G	ENSP00000394510:p.Arg1736Gly	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	7	5	NM_020719	0	0	13	26	13	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	5.800	0.331856	0.10956	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	4.9	2.71	0.32032	.	0.215814	0.23676	N	0.045663	T	0.31071	0.0785	L	0.40543	1.245	0.09310	N	1	B	0.26483	0.15	B	0.25884	0.064	T	0.18461	-1.0336	9	0.46703	T	0.11	-19.9557	9.1228	0.36797	0.2505:0.616:0.1334:0.0	.	1736	Q9ULL5-3	.	G	1736;916;916	.	ENSP00000246798:R916G	R	+	1	2	PRR12	54810997	0.045000	0.20229	0.090000	0.20809	0.041000	0.13682	0.816000	0.27267	2.554000	0.86153	0.561000	0.74099	CGG	C|0.999;G|0.001		0.652	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		G	50119185	C	G	50119185	3	3	3	1	0	0	0	0	1	0	0	0	12613	759	27	4	5240	4	PRR12	19	50119185	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	30698254	50119185	9009798	85	206											
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643807	53643807	+	Silent	SNP	A	A	G																															taaggtttctctccagtatgAattccccgatgtcttgcaag																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53643807A>G	ENST00000334197.7	-	5	2342	c.2274T>C	c.(2272-2274)atT>atC	p.I758I	ZNF347_ENST00000601469.2_Silent_p.I759I|ZNF347_ENST00000452676.2_Silent_p.I759I|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	758					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CTCCAGTATGAATTCCCCGAT	0.423																																					p.I759I	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.T2277C						.						157	152	154					19																	53643807		2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			AGTATGAATTCCC	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2274T>C	19.37:g.53643807A>G		Somatic	226	0		WXS	Illumina HiSeq	Phase_I	265	24	NM_001172675	0	0	1	1	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	37	CCDS33097.1																																																																																			.		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		G	53643807	A	G	53643807	2	3	3	1	0	0	0	0	0	0	0	1	17893	242	9	3		3	ZNF347	19	53643807	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	3524622	53643807	5485176	86	207	3	3	1	4		5	3	310	N	G_C_A	4.384839e-07
ZNF347	84671	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	53643811	53643811	+	Missense_Mutation	SNP	C	C	G																															gtttctctccagtatgaattCcccgatgtcttgcaaggtgt																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53643811C>G	ENST00000334197.7	-	5	2338	c.2270G>C	c.(2269-2271)gGa>gCa	p.G757A	ZNF347_ENST00000601469.2_Missense_Mutation_p.G758A|ZNF347_ENST00000452676.2_Missense_Mutation_p.G758A|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	757					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		AGTATGAATTCCCCGATGTCT	0.423																																					p.G758A	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.G2273C						.						159	153	155					19																	53643811		2203	4300	6503	SO:0001583	missense	84671	exon5			TGAATTCCCCGAT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2270G>C	19.37:g.53643811C>G	ENSP00000334146:p.Gly757Ala	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	267	28	NM_001172675	0	0	3	3	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	5.602	0.295791	0.10622	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.16897	2.31;2.31	3.15	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09862	0.0242	N	0.04063	-0.285	0.23739	N	0.996976	B;B	0.27068	0.167;0.0	B;B	0.32864	0.154;0.0	T	0.36138	-0.9760	9	0.72032	D	0.01	.	10.7968	0.46466	0.0:0.6301:0.3699:0.0	.	758;757	G5E9N4;Q96SE7	.;ZN347_HUMAN	A	757;758	ENSP00000334146:G757A;ENSP00000405218:G758A	ENSP00000334146:G757A	G	-	2	0	ZNF347	58335623	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-3.284000	0.00527	0.642000	0.30620	0.650000	0.86243	GGA	.		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		G	53643811	C	G	53643811	3	3	3	1	0	0	0	0	1	0	0	0	17893	855	30	4	253	4	ZNF347	19	53643811	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	4	53643811	5485172	87	208	3	3	1	4		5	3	310	N	G_C_A	4.384839e-07
ZNF347	84671	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	53643814	53643814	+	Missense_Mutation	SNP	C	C	T																															tctctccagtatgaattcccCgatgtcttgcaaggtgtgaa																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53643814C>T	ENST00000334197.7	-	5	2335	c.2267G>A	c.(2266-2268)cGg>cAg	p.R756Q	ZNF347_ENST00000601469.2_Missense_Mutation_p.R757Q|ZNF347_ENST00000452676.2_Missense_Mutation_p.R757Q|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	756					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		ATGAATTCCCCGATGTCTTGC	0.423																																					p.R757Q	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.G2270A						.						159	153	156					19																	53643814		2203	4300	6503	SO:0001583	missense	84671	exon5			ATTCCCCGATGTC	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2267G>A	19.37:g.53643814C>T	ENSP00000334146:p.Arg756Gln	Somatic	229	1		WXS	Illumina HiSeq	Phase_I	265	30	NM_001172675	0	0	8	8	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.421117	0.01126	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.07444	3.19;3.19	3.16	-5.44	0.02624	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03178	0.0093	N	0.26162	0.8	0.09310	N	1	B;B	0.22146	0.065;0.002	B;B	0.12837	0.008;0.001	T	0.46638	-0.9177	9	0.02654	T	1	.	1.0194	0.01514	0.2009:0.2758:0.1158:0.4075	.	757;756	G5E9N4;Q96SE7	.;ZN347_HUMAN	Q	756;757	ENSP00000334146:R756Q;ENSP00000405218:R757Q	ENSP00000334146:R756Q	R	-	2	0	ZNF347	58335626	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.642000	0.02006	-1.289000	0.02375	-2.433000	0.00214	CGG	.		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53643814	C	T	53643814	3	4	3	1	0	0	0	0	1	0	0	0	17893	652	23	1	256	1	ZNF347	19	53643814	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	3	53643814	5485169	88	209	3	3	1	4		5	3	310	N	G_C_A	4.384839e-07
ZNF347	84671	hgsc.bcm.edu	37	chr19	53644104	53644104	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattctgagtgaagaccttGccacactcattacatttgta	12	13	7	9	0	2	3	1	2	1	1	2	4	2	3	2	0	2	1	2	0	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53644104G>C	ENST00000334197.7	-	5	2045	c.1977C>G	c.(1975-1977)ggC>ggG	p.G659G	ZNF347_ENST00000601469.2_Silent_p.G660G|ZNF347_ENST00000452676.2_Silent_p.G660G|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	659					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		TGAAGACCTTGCCACACTCAT	0.403																																					p.G660G	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.C1980G						.						175	157	163					19																	53644104		2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			GACCTTGCCACAC	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1977C>G	19.37:g.53644104G>C		Somatic	195	2		WXS	Illumina HiSeq	Phase_I	174	19	NM_001172675	0	0	6	6	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	37	CCDS33097.1																																																																																			.		0.403	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		C	53644104	G	C	53644104	2	2	3	1	0	0	0	0	0	0	0	1	17893	1306	46	4		4	ZNF347	19	53644104	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08	290	53644104	5484879	89	210			1	4		5	3	310	N	G_C_A	4.384839e-07
ZNF347	84671	hgsc.bcm.edu	37	chr19	53644116	53644116	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaccttgccacactcattAcatttgtaaggtttttcacc	11	14	5	11	0	2	1	2	0	0	1	2	1	2	1	3	1	2	2	3	1	3	6			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53644116A>G	ENST00000334197.7	-	5	2033	c.1965T>C	c.(1963-1965)tgT>tgC	p.C655C	ZNF347_ENST00000601469.2_Silent_p.C656C|ZNF347_ENST00000452676.2_Silent_p.C656C|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	655					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CACACTCATTACATTTGTAAG	0.403																																					p.C656C	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.T1968C						.						173	157	162					19																	53644116		2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			CTCATTACATTTG	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1965T>C	19.37:g.53644116A>G		Somatic	191	2		WXS	Illumina HiSeq	Phase_I	174	13	NM_001172675	0	0	13	13	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	37	CCDS33097.1																																																																																			.		0.403	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		G	53644116	A	G	53644116	2	3	3	1	0	0	0	0	0	0	0	1	17893	389	14	3		3	ZNF347	19	53644116	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	12	53644116	5484867	90	211			1	4		5	3	310	N	G_C_A	4.384839e-07
RBBP9	10741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	18471080	18471080	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccccaagtctgatgtgtacGcagacactaatacaatagca	14	8	7	12	1	1	2	0	1	1	1	1	2	1	2	2	0	3	3	2	0	6	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:18471080G>A	ENST00000337227.4	-	4	368	c.293C>T	c.(292-294)gCg>gTg	p.A98V	RBBP9_ENST00000493184.1_Intron	NM_006606.2	NP_006597.2	O75884	RBBP9_HUMAN	retinoblastoma binding protein 9	98					regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|prostate(1)	9						TGATGTGTACGCAGACACTAA	0.408																																					p.A98V		.											.	RBBP9-227	0			c.C293T						.						158	140	146					20																	18471080		2203	4300	6503	SO:0001583	missense	10741	exon4			GTGTACGCAGACA	AF039564	CCDS13136.1	20p11.2	2008-08-01	2001-11-28		ENSG00000089050	ENSG00000089050			9892	protein-coding gene	gene with protein product		602908	"retinoblastoma-binding protein 9"			9697699, 10449909	Standard	NM_006606		Approved	Bog	uc002wqy.3	O75884	OTTHUMG00000031972	ENST00000337227.4:c.293C>T	20.37:g.18471080G>A	ENSP00000336866:p.Ala98Val	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	111	39	NM_006606	0	0	27	54	27	D3DW31|Q5JPH9|Q9H1D8	Missense_Mutation	SNP	ENST00000337227.4	37	CCDS13136.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350862	0.82132	.	.	ENSG00000089050	ENST00000337227;ENST00000339848	.	.	.	5.26	4.32	0.51571	.	0.000000	0.64402	D	0.000001	T	0.76615	0.4012	M	0.79614	2.46	0.45676	D	0.998592	D	0.89917	1.0	D	0.72625	0.978	T	0.77032	-0.2738	9	0.41790	T	0.15	-9.6629	11.6719	0.51406	0.0851:0.0:0.9149:0.0	.	98	O75884	RBBP9_HUMAN	V	98	.	ENSP00000336866:A98V	A	-	2	0	RBBP9	18419080	1.000000	0.71417	0.983000	0.44433	0.986000	0.74619	6.413000	0.73308	1.455000	0.47813	0.655000	0.94253	GCG	.		0.408	RBBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078175.1	NM_006606		A	18471080	G	A	18471080	3	1	3	1	0	0	0	0	1	0	0	0	13138	1087	38	1	275	1	RBBP9	20	18471080	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		18471080	44554440	91	212											
ENTPD6	955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	25201971	25201971	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtttcagggcagaaagcaggTacggggagggttgctgcctg	8	8	18	7	1	1	1	1	0	0	1	1	2	1	2	1	5	4	6	1	5	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:25201971T>A	ENST00000376652.4	+	11	1208		c.e11+2		ENTPD6_ENST00000360031.2_Splice_Site|ENTPD6_ENST00000354989.5_Splice_Site|ENTPD6_ENST00000433259.2_Intron			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)						response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGAAAGCAGGTACGGGGAGGG	0.582																																					.		.											.	ENTPD6-90	0			c.1045+2T>A						.						87	75	79					20																	25201971		2203	4300	6503	SO:0001630	splice_region_variant	955	exon11			AGCAGGTACGGGG	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.1045+2T>A	20.37:g.25201971T>A		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	41	21	NM_001247	0	0	0	0	0	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Splice_Site	SNP	ENST00000376652.4	37	CCDS13170.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.531860	0.27387	.	.	ENSG00000197586	ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000433417;ENST00000376666	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8578	0.57894	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ENTPD6	25149971	1.000000	0.71417	0.919000	0.36401	0.014000	0.08584	6.084000	0.71335	2.124000	0.65301	0.459000	0.35465	.	.		0.582	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		Intron	A	25201971	T	A	25201971	5	1	3	1	0	0	0	0	0	0	1	0	5156	1652	57	5	1092	5	ENTPD6	20	25201971	Splice_Site	SNP	T	TCGA-A4-7288-01A-11D-2136-08	6730891	25201971	37823549	92	213											
SGK2	10110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42208647	42208647	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgtattcttcagccccatAaactgggatgacctgtacca	11	11	7	12	0	2	1	1	1	1	0	2	2	2	2	4	1	3	2	4	1	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:42208647A>G	ENST00000341458.4	+	11	1284	c.1065A>G	c.(1063-1065)atA>atG	p.I355M	SGK2_ENST00000373092.3_Missense_Mutation_p.I295M|SGK2_ENST00000423407.3_Missense_Mutation_p.I295M|SGK2_ENST00000373100.1_Missense_Mutation_p.I295M|SGK2_ENST00000373077.1_Missense_Mutation_p.I294M|SGK2_ENST00000426287.1_Missense_Mutation_p.I321M	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	355	AGC-kinase C-terminal.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCAGCCCCATAAACTGGGATG	0.502																																					p.I355M		.											.	SGK2-990	0			c.A1065G						.						133	118	123					20																	42208647		2203	4300	6503	SO:0001583	missense	10110	exon11			CCCCATAAACTGG	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.1065A>G	20.37:g.42208647A>G	ENSP00000340608:p.Ile355Met	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	107	51	NM_016276	0	0	22	37	15	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.178740	0.57692	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55	4.62	2.2	0.27929	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.68751	0.3035	M	0.82823	2.61	0.52501	D	0.999953	D;D;D	0.89917	0.998;0.995;1.0	D;D;D	0.77557	0.986;0.972;0.99	T	0.66524	-0.5902	10	0.87932	D	0	.	6.32	0.21213	0.5364:0.3128:0.0:0.1508	.	321;355;295	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	M	295;295;294;295;355;321	ENSP00000362192:I295M;ENSP00000362184:I295M;ENSP00000362168:I294M;ENSP00000392795:I295M;ENSP00000340608:I355M;ENSP00000412214:I321M	ENSP00000340608:I355M	I	+	3	3	SGK2	41642061	0.996000	0.38824	1.000000	0.80357	0.967000	0.64934	0.539000	0.23175	0.183000	0.20059	0.460000	0.39030	ATA	.		0.502	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			G	42208647	A	G	42208647	3	3	3	1	0	0	0	0	1	0	0	0	14241	352	13	3	1107	3	SGK2	20	42208647	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	17006676	42208647	20816873	93	214											
CDH22	64405	broad.mit.edu	37	chr20	44806642	44806642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgccggggctgagggaggCggccatgacaaaggccgtgg	7	3	21	10	4	0	2	0	2	0	0	0	3	0	3	3	8	0	1	3	8	1	0	rs144477780		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:44806642C>T	ENST00000372262.3	-	10	2258	c.1858G>A	c.(1858-1860)Gcc>Acc	p.A620T	CDH22_ENST00000537909.1_Missense_Mutation_p.A620T	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	620					brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CTGAGGGAGGCGGCCATGACA	0.652																																					p.A620T													.	CDH22-95	0			c.G1858A						.	C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	80	63	69		1858	-0.1	0.2	20	dbSNP_134	69	0,8600		0,0,4300	no	missense	CDH22	NM_021248.1	58	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	620/829	44806642	2,13004	2203	4300	6503	SO:0001583	missense	64405	exon11			GGGAGGCGGCCAT	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"Cadherins / Major cadherins"	13251	protein-coding gene	gene with protein product		609920	"cadherin-like 22"	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1858G>A	20.37:g.44806642C>T	ENSP00000361336:p.Ala620Thr	Somatic	43	1		WXS	Illumina HiSeq	Phase_I	40	5	NM_021248	0	0	0	0	0	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062247	0.36373	4.54E-4	0.0	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.37411	1.2;1.2	4.43	-0.0867	0.13680	.	0.131614	0.50627	N	0.000117	T	0.27169	0.0666	L	0.46157	1.445	0.38025	D	0.934971	B	0.11235	0.004	B	0.06405	0.002	T	0.08146	-1.0736	10	0.45353	T	0.12	.	8.4704	0.32982	0.0:0.6374:0.0:0.3626	.	620	Q9UJ99	CAD22_HUMAN	T	620	ENSP00000361336:A620T;ENSP00000437790:A620T	ENSP00000361336:A620T	A	-	1	0	CDH22	44240049	0.777000	0.28628	0.185000	0.23176	0.990000	0.78478	1.573000	0.36472	-0.138000	0.11434	-0.302000	0.09304	GCC	C|1.000;T|0.000		0.652	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		T	44806642	C	T	44806642	3	4	3	1	0	0	0	0	1	0	0	0	3113	768	27	1	636	1	CDH22	20	44806642	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	2597995	44806642	18218878	94	215											
LIMK2	3985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	31655910	31655910	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggtggtgctggcacccaTgtttgagagactctccacag	8	10	13	10	0	1	3	0	2	1	1	2	4	1	3	2	3	1	3	2	3	0	1	rs377628882		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:31655910T>C	ENST00000331728.4	+	5	512	c.398T>C	c.(397-399)aTg>aCg	p.M133T	LIMK2_ENST00000406516.1_Missense_Mutation_p.M55T|LIMK2_ENST00000444929.2_Intron|LIMK2_ENST00000340552.4_Missense_Mutation_p.M112T|LIMK2_ENST00000333611.4_Missense_Mutation_p.M112T	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	133					phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						CTGGCACCCATGTTTGAGAGA	0.602																																					p.M133T		.											.	LIMK2-548	0			c.T398C						.	T	THR/MET,THR/MET,THR/MET	1,4405	2.1+/-5.4	0,1,2202	55	50	52		335,398,335	5.6	1	22		52	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LIMK2	NM_001031801.1,NM_005569.3,NM_016733.2	81,81,81	0,2,6501	CC,CT,TT		0.0116,0.0227,0.0154	benign,benign,benign	112/687,133/639,112/618	31655910	2,13004	2203	4300	6503	SO:0001583	missense	3985	exon5			CACCCATGTTTGA	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.398T>C	22.37:g.31655910T>C	ENSP00000332687:p.Met133Thr	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	38	32	NM_005569	0	0	4	5	1	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Missense_Mutation	SNP	ENST00000331728.4	37	CCDS13891.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234384	0.39498	2.27E-4	1.16E-4	ENSG00000182541	ENST00000406516;ENST00000331728;ENST00000436394;ENST00000333611;ENST00000340552	T;T;T;T	0.73575	-0.76;-0.59;-0.64;-0.71	5.63	5.63	0.86233	.	0.039543	0.85682	D	0.000000	T	0.61862	0.2381	L	0.36672	1.1	0.80722	D	1	B;B;B;P	0.35328	0.01;0.017;0.002;0.495	B;B;B;B	0.33750	0.018;0.008;0.004;0.169	T	0.59397	-0.7462	10	0.20519	T	0.43	-31.4981	10.2918	0.43601	0.1471:0.0:0.0:0.8529	.	165;112;133;55	F5GY29;Q7L3H5;P53671;B5MC51	.;.;LIMK2_HUMAN;.	T	55;133;165;112;112	ENSP00000384602:M55T;ENSP00000332687:M133T;ENSP00000330470:M112T;ENSP00000339916:M112T	ENSP00000332687:M133T	M	+	2	0	LIMK2	29985910	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.829000	0.69316	2.144000	0.66660	0.459000	0.35465	ATG	.		0.602	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733		C	31655910	T	C	31655910	3	2	3	1	0	0	0	0	1	0	0	0	8824	1464	51	3	473	3	LIMK2	22	31655910	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08		31655910	19648656	95	216											
BAIAP2L2	80115	hgsc.bcm.edu	37	chr22	38482355	38482355	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttggcacccggcttggggtgCgggagcgggactggccatcc	4	7	18	12	3	0	0	0	0	0	0	1	2	1	2	3	7	2	2	3	7	0	2	rs371997714|rs113792005|rs66500630	byFrequency	TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:38482355C>G	ENST00000381669.3	-	12	1505	c.1361G>C	c.(1360-1362)cGc>cCc	p.R454P	SLC16A8_ENST00000469516.1_5'Flank	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	454					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					GCTTGGGGTGCGGGAGCGGGA	0.697																																					p.R454P		.											.	BAIAP2L2-91	0			c.G1361C						.						17	19	18					22																	38482355		2066	3890	5956	SO:0001583	missense	80115	exon12			GGGGTGCGGGAGC	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1361G>C	22.37:g.38482355C>G	ENSP00000371085:p.Arg454Pro	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_025045	0	0	0	0	0	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.52|15.52	2.857588|2.857588	0.51376|0.51376	.|.	.|.	ENSG00000128298|ENSG00000128298	ENST00000402500|ENST00000381669;ENST00000428572	.|T	.|0.49139	.|0.79	4.42|4.42	2.26|2.26	0.28386|0.28386	.|.	.|1.035940	.|0.07692	.|U	.|0.938938	.|T	.|0.36026	.|0.0952	L|L	0.38531|0.38531	1.155|1.155	0.19300|0.19300	N|N	0.999976|0.999976	.|P	.|0.43578	.|0.811	.|B	.|0.36719	.|0.231	.|T	.|0.18650	.|-1.0330	.|10	.|0.42905	.|T	.|0.14	.|-8.7443	8.9998|8.9998	0.36074|0.36074	0.0:0.8207:0.0:0.1793|0.0:0.8207:0.0:0.1793	.|.	.|454	.|Q6UXY1	.|BI2L2_HUMAN	.|P	-1|454;145	.|ENSP00000410074:R145P	.|ENSP00000371085:R454P	.|R	-|-	.|2	.|0	BAIAP2L2|BAIAP2L2	36812301|36812301	0.028000|0.028000	0.19301|0.19301	0.834000|0.834000	0.33040|0.33040	0.620000|0.620000	0.37586|0.37586	0.644000|0.644000	0.24766|0.24766	0.846000|0.846000	0.35142|0.35142	0.462000|0.462000	0.41574|0.41574	.|CGC	.		0.697	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		G	38482355	C	G	38482355	3	3	3	1	0	0	0	0	1	0	0	0	1304	768	27	4	240	4	BAIAP2L2	22	38482355	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	6826445	38482355	12822211	96	217											
PLA2G6	8398	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	38536176	38536176	+	Splice_Site	DEL	G	G	-																															cactgcgttccttccaaggaGctgatgaaagaggaagggaa																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:38536176delG	ENST00000332509.3	-	5	793	c.610delC	c.(610-612)ctc>tc	p.L205fs	PLA2G6_ENST00000335539.3_Splice_Site_p.L205fs|PLA2G6_ENST00000402064.1_Splice_Site_p.L205fs|PLA2G6_ENST00000436218.1_Splice_Site_p.S143fs	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	205					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	CTTCCAAGGAGCTGATGAAAG	0.567																																					p.L204fs		.											.	PLA2G6-91	0			c.610delC						.						45	43	44					22																	38536176		2203	4300	6503	SO:0001630	splice_region_variant	8398	exon5			.	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.610-1C>-	22.37:g.38536176delG		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	37	30	NM_003560	0	0	0	0	0	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Frame_Shift_Del	DEL	ENST00000332509.3	37	CCDS13967.1																																																																																			.		0.567	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426	Frame_Shift_Del	-	38536176	G	-	38536176	8	5	3	1	0	1	0	1	0	0	1	0	12034	985	34	0	1862	0	PLA2G6	22	38536176	Splice_Site	DEL	G	TCGA-A4-7288-01A-11D-2136-08	53821	38536176	12768390	97	218											
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47507402	47507402	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggttattttttctcttttAgtctgaaccggacggctttt	5	21	8	7	2	2	1	0	1	2	0	3	2	2	2	1	3	1	2	1	3	3	9			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:47507402A>G	ENST00000337137.4	+	12	1495		c.e12-1		TBC1D22A_ENST00000355704.3_Splice_Site|TBC1D22A_ENST00000406733.1_Splice_Site|TBC1D22A_ENST00000407381.3_Splice_Site	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A								protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TTTCTCTTTTAGTCTGAACCG	0.418																																					.		.											.	TBC1D22A-91	0			c.1330-2A>G						.						127	122	124					22																	47507402		2203	4300	6503	SO:0001630	splice_region_variant	25771	exon12			TCTTTTAGTCTGA	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.1330-1A>G	22.37:g.47507402A>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_014346	0	0	0	0	0	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Splice_Site	SNP	ENST00000337137.4	37	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.226570	0.79576	.	.	ENSG00000054611	ENST00000337137;ENST00000407381;ENST00000355704;ENST00000406733	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1925	0.59719	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TBC1D22A	45886066	1.000000	0.71417	0.990000	0.47175	0.829000	0.46940	7.909000	0.87444	1.993000	0.58246	0.533000	0.62120	.	.		0.418	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346	Intron	G	47507402	A	G	47507402	5	3	3	1	0	0	0	0	0	0	1	0	15643	434	15	3	1374	3	TBC1D22A	22	47507402	Splice_Site	SNP	A	TCGA-A4-7288-01A-11D-2136-08	8971226	47507402	3797164	98	219											
CHD5	26038	ucsc.edu	37	chr1	6211114	6211114	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcttcttgcgcctcctCttgctcttcttgcccagggc	1	16	7	17	1	6	0	0	0	6	0	7	0	7	0	3	1	3	1	3	1	0	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:6211114C>A	ENST00000262450.3	-	7	1071	c.972G>T	c.(970-972)aaG>aaT	p.K324N	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGCGCCTCCTCTTGCTCTTCT	0.592																																					p.K324N													.	CHD5-719	0			c.G972T						.						99	92	94					1																	6211114		2203	4300	6503	SO:0001583	missense	26038	exon7			CCTCCTCTTGCTC	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.972G>T	1.37:g.6211114C>A	ENSP00000262450:p.Lys324Asn	Somatic	64	0		WXS	Illumina HiSeq		40	4	NM_015557	0	0	0	0	0	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	c	12.21	1.870305	0.33069	.	.	ENSG00000116254	ENST00000262450	D	0.85411	-1.98	4.0	4.0	0.46444	Zinc finger, FYVE/PHD-type (1);	0.378995	0.23849	U	0.043961	T	0.76133	0.3945	L	0.41824	1.3	0.80722	D	1	B	0.33694	0.421	B	0.29862	0.108	T	0.73310	-0.4023	10	0.29301	T	0.29	-23.3491	9.9406	0.41578	0.0:0.9028:0.0:0.0972	.	324	Q8TDI0	CHD5_HUMAN	N	324	ENSP00000262450:K324N	ENSP00000262450:K324N	K	-	3	2	CHD5	6133701	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	1.776000	0.38594	1.974000	0.57490	0.457000	0.33378	AAG	.		0.592	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6211114	C	A	6211114	3	1	4	1	0	0	0	0	1	0	0	0	3334	912	32	4	5032	4	CHD5	1	6211114	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		6211114	243039507	1	220											
CLCA2	9635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	86890015	86890015	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taagttcagaactcccattcCtgggagctggagtacagctt	10	11	10	10	0	1	1	1	0	0	1	3	3	3	3	2	2	4	4	2	2	3	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:86890015C>T	ENST00000370565.4	+	1	247	c.85C>T	c.(85-87)Ctg>Ttg	p.L29L		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	29					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		ACTCCCATTCCTGGGAGCTGG	0.443																																					p.L29L	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	.											.	CLCA2-155	0			c.C85T						.						113	103	106					1																	86890015		2203	4300	6503	SO:0001819	synonymous_variant	9635	exon1			CCATTCCTGGGAG		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"chloride channel, calcium activated, family member 2", "chloride channel regulator 2"				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.85C>T	1.37:g.86890015C>T		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	55	35	NM_006536	0	0	0	0	0	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			.		0.443	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86890015	C	T	86890015	2	4	4	1	0	0	0	0	0	0	0	1	3464	680	24	2		2	CLCA2	1	86890015	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08	80678901	86890015	162360606	2	221											
ADAR	103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154574741	154574741	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcctggaaatgtgaggaaAggcaatcaacacctctctgt	12	10	10	9	0	2	1	1	1	1	0	4	3	3	3	2	3	1	2	2	3	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:154574741A>G	ENST00000368474.4	-	2	576	c.377T>C	c.(376-378)cTt>cCt	p.L126P	ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000292205.5_Missense_Mutation_p.L169P|ADAR_ENST00000471068.1_5'UTR	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	126					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		ATGTGAGGAAAGGCAATCAAC	0.537																																					p.L126P		.											.	ADAR-157	0			c.T377C						.						63	65	64					1																	154574741		2203	4300	6503	SO:0001583	missense	103	exon2			GAGGAAAGGCAAT	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.377T>C	1.37:g.154574741A>G	ENSP00000357459:p.Leu126Pro	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	41	24	NM_001111	0	0	5	24	19	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559114	0.45590	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.79749	-1.3;-1.3;-1.3	4.47	4.47	0.54385	.	0.972834	0.08506	N	0.935700	D	0.86167	0.5868	M	0.63843	1.955	0.54753	D	0.999983	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.991;0.991;0.997	T	0.82985	-0.0185	10	0.87932	D	0	-16.02	13.8697	0.63610	1.0:0.0:0.0:0.0	.	126;126;126	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	P	169;126;121	ENSP00000292205:L169P;ENSP00000357459:L126P;ENSP00000431794:L121P	ENSP00000292205:L169P	L	-	2	0	ADAR	152841365	0.992000	0.36948	0.866000	0.34008	0.393000	0.30537	5.187000	0.65087	1.992000	0.58205	0.402000	0.26972	CTT	.		0.537	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		G	154574741	A	G	154574741	3	3	4	1	0	0	0	0	1	0	0	0	281	72	3	3	3359	3	ADAR	1	154574741	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	67684726	154574741	94675880	3	222											
HDGF	3068	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	156715103	156715104	+	Frame_Shift_Ins	INS	-	-	A																															ctcacgtctcgtgggtcccgINSaaaaaaaagacttggtattt																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:156715103_156715104insA	ENST00000357325.5	-	2	463_464	c.149_150insT	c.(148-150)ttcfs	p.F50fs	HDGF_ENST00000368206.5_Frame_Shift_Ins_p.F66fs|HDGF_ENST00000537739.1_Frame_Shift_Ins_p.F50fs|HDGF_ENST00000368209.5_Frame_Shift_Ins_p.F43fs|HDGF_ENST00000416666.2_Frame_Shift_Ins_p.F18fs|HDGF_ENST00000465180.1_5'UTR	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	50	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		CGTGGGTCCCGAAAAAAAAGAC	0.564																																					p.F66fs		.											.	HDGF-226	0			c.198_199insT						.																																			SO:0001589	frameshift_variant	3068	exon2			.	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"high-mobility group protein 1-like"	600339	"hepatoma-derived growth factor (high-mobility group protein 1-like)"			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.150dupT	1.37:g.156715111_156715111dupA	ENSP00000349878:p.Phe50fs	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	21	13	NM_001126050	0	0	0	0	0	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Frame_Shift_Ins	INS	ENST00000357325.5	37	CCDS1156.1																																																																																			.		0.564	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494		A	156715104	-	A	156715103	7	5	4	1	0	1	1	0	0	0	0	0	7039	1049	37	0	592	0	HDGF	1	156715103	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	2140362	156715103	92535518	4	223											
CCT7	10574	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	73471795	73471796	+	Nonsense_Mutation	DNP	GC	GC	TT																															atgatgctcgatgatttgctGcagcttaaaatgattggaat																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:73471795_73471796GC>TT	ENST00000258091.5	+	6	711_712	c.570_571GC>TT	c.(568-573)ctGCag>ctTTag	p.Q191*	CCT7_ENST00000398422.2_Intron|CCT7_ENST00000537131.1_Nonsense_Mutation_p.Q91*|CCT7_ENST00000540468.1_Nonsense_Mutation_p.Q104*|CCT7_ENST00000538797.1_Nonsense_Mutation_p.Q63*|CCT7_ENST00000539919.1_Nonsense_Mutation_p.Q147*|CCT7_ENST00000473786.1_3'UTR	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	191					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						ATGATTTGCTGCAGCTTAAAAT	0.495																																					p.Q191*													.	CCT7-90	0			c.C571T						.																																			SO:0001587	stop_gained	10574	exon6			TTGCTGCAGCTTA	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	Exception_encountered	2.37:g.73471795_73471796delinsTT	ENSP00000258091:p.Gln191*	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	35	11	NM_006429	0	0	0	0	0	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Nonsense_Mutation	DNP	ENST00000258091.5	37	CCDS46336.1																																																																																			.		0.495	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			TT	73471796	GC	TT	73471795	4	4	4	1	0	0	0	0	0	1	0	0	2965	1306	46	4	592	4	CCT7	2	73471795	Nonsense_Mutation	DNP	GC	TCGA-A4-7583-01A-11D-2136-08		73471795	169727578	5	224											
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101706726	101706726	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtaactcaccacatgctatGggagaataaacctgggagcc	14	7	10	10	0	1	1	1	0	0	1	1	3	1	2	3	2	4	2	3	2	5	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:101706726G>C	ENST00000376840.4	-	2	227	c.228C>G	c.(226-228)ccC>ccG	p.P76P	TBC1D8_ENST00000409318.1_Silent_p.P76P			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	76					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CACATGCTATGGGAGAATAAA	0.502																																					p.P76P		.											.	TBC1D8-25	0			c.C228G						.						53	53	53					2																	101706726		1892	4112	6004	SO:0001819	synonymous_variant	11138	exon2			TGCTATGGGAGAA	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.228C>G	2.37:g.101706726G>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	44	3	NM_001102426	0	0	1	1	0	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	37	CCDS46375.1																																																																																			.		0.502	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		C	101706726	G	C	101706726	2	2	4	1	0	0	0	0	0	0	0	1	15657	1335	47	4		4	TBC1D8	2	101706726	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08	28234931	101706726	141492647	6	225											
GORASP2	26003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	171806790	171806790	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataattggagcagatacagTcatgaatgaggtaattcgtg	14	12	11	4	1	1	3	1	2	0	1	2	4	1	4	0	2	2	2	0	2	5	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:171806790T>C	ENST00000234160.4	+	4	1240	c.425T>C	c.(424-426)gTc>gCc	p.V142A	GORASP2_ENST00000493692.1_3'UTR|GORASP2_ENST00000452526.2_Missense_Mutation_p.V154A	NM_001201428.1|NM_015530.4	NP_001188357.1|NP_056345.3	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2, 55kDa	142					mitotic cell cycle (GO:0000278)|organelle organization (GO:0006996)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14						GCAGATACAGTCATGAATGAG	0.368																																					p.V142A		.											.	GORASP2-135	0			c.T425C						.						72	73	73					2																	171806790		2203	4300	6503	SO:0001583	missense	26003	exon4			ATACAGTCATGAA		CCDS33325.1	2q31.1	2012-09-20	2002-08-29		ENSG00000115806	ENSG00000115806			17500	protein-coding gene	gene with protein product		608693	"golgi reassembly stacking protein 2, 55 kDa"			10487747	Standard	NM_015530		Approved	GRASP55, GRS2, GOLPH6	uc002ugj.3	Q9H8Y8	OTTHUMG00000154072	ENST00000234160.4:c.425T>C	2.37:g.171806790T>C	ENSP00000234160:p.Val142Ala	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	76	32	NM_015530	0	0	0	0	0	B4DKT0|Q53TE3|Q96I74|Q96K84|Q9H946|Q9UFW4	Missense_Mutation	SNP	ENST00000234160.4	37	CCDS33325.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.583219	0.65992	.	.	ENSG00000115806	ENST00000234160;ENST00000452526	T;T	0.31247	1.5;1.5	5.95	5.95	0.96441	PDZ/DHR/GLGF (1);	0.116778	0.64402	D	0.000018	T	0.44201	0.1282	M	0.73753	2.245	0.58432	D	0.999992	B;B;B	0.23591	0.045;0.088;0.035	B;B;B	0.36845	0.107;0.168;0.234	T	0.35201	-0.9798	10	0.45353	T	0.12	-6.4014	16.4069	0.83677	0.0:0.0:0.0:1.0	.	98;154;142	B4DNR1;B4DKT0;Q9H8Y8	.;.;GORS2_HUMAN	A	142;154	ENSP00000234160:V142A;ENSP00000410208:V154A	ENSP00000234160:V142A	V	+	2	0	GORASP2	171515036	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	4.174000	0.58256	2.272000	0.75746	0.460000	0.39030	GTC	.		0.368	GORASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333719.2			C	171806790	T	C	171806790	3	2	4	1	0	0	0	0	1	0	0	0	6596	1667	58	3	439	3	GORASP2	2	171806790	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	70100064	171806790	71392583	7	226											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	179411556	179411556	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacaaccttgctgcctccAtcatacgctggggcagacca	9	7	8	17	1	1	1	1	0	0	1	2	1	2	1	5	2	4	3	5	2	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:179411556A>G	ENST00000591111.1	-	291	89900	c.89676T>C	c.(89674-89676)gaT>gaC	p.D29892D	TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Silent_p.D28965D|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Silent_p.D31533D|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.D22593D|TTN_ENST00000460472.2_Silent_p.D22468D|TTN-AS1_ENST00000419746.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Silent_p.D22660D|TTN-AS1_ENST00000591332.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29892	Fibronectin type-III 118. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCTGCCTCCATCATACGCTG	0.498																																					p.D31533D		.											.	TTN-636	0			c.T94599C						.						60	61	61					2																	179411556		2069	4216	6285	SO:0001819	synonymous_variant	7273	exon341			GCCTCCATCATAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.89676T>C	2.37:g.179411556A>G		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	44	22	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179411556	A	G	179411556	2	3	4	1	0	0	0	0	0	0	0	1	16768	214	8	3		3	TTN	2	179411556	Silent	SNP	A	TCGA-A4-7583-01A-11D-2136-08	7604766	179411556	63787817	8	227											
SF3B1	23451	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	198269882	198269882	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgctcttctggactaagtGttgattcatcaacatcaacc	10	15	6	10	0	5	1	3	1	2	0	5	2	5	2	1	1	3	2	1	1	3	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:198269882G>C	ENST00000335508.6	-	11	1548	c.1457C>G	c.(1456-1458)aCa>aGa	p.T486R	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	486	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TGGACTAAGTGTTGATTCATC	0.289			Mis		myelodysplastic syndrome																																p.T486R		.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.C1457G						.						51	54	53					2																	198269882		2201	4295	6496	SO:0001583	missense	23451	exon11			CTAAGTGTTGATT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1457C>G	2.37:g.198269882G>C	ENSP00000335321:p.Thr486Arg	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	42	4	NM_012433	0	0	108	108	0	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931911	0.52866	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	L	0.27053	0.805	0.80722	D	1	B	0.23806	0.091	B	0.23275	0.045	T	0.44817	-0.9303	9	0.35671	T	0.21	.	19.9254	0.97100	0.0:0.0:1.0:0.0	.	486	O75533	SF3B1_HUMAN	R	486	.	ENSP00000335321:T486R	T	-	2	0	SF3B1	197978127	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.721000	0.98766	2.710000	0.92621	0.655000	0.94253	ACA	.		0.289	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198269882	G	C	198269882	3	2	4	1	0	0	0	0	1	0	0	0	14181	1377	48	4	2517	4	SF3B1	2	198269882	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	18858326	198269882	44929491	9	228											
SATB2	23314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	200193570	200193570	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcatggccctcaggtttaCtagaagagactgagaggctg	10	9	13	9	0	1	3	1	1	0	3	1	5	1	3	1	3	2	3	1	3	3	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:200193570C>A	ENST00000417098.1	-	8	2053	c.1237G>T	c.(1237-1239)Gta>Tta	p.V413L	RP11-486F17.1_ENST00000489557.2_RNA|SATB2_ENST00000260926.5_Missense_Mutation_p.V413L|SATB2_ENST00000428695.1_Missense_Mutation_p.V295L|SATB2_ENST00000457245.1_Missense_Mutation_p.V413L|SATB2_ENST00000443023.1_Missense_Mutation_p.V354L	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	413					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CTCAGGTTTACTAGAAGAGAC	0.488																																					p.V413L	Colon(30;262 767 11040 24421 36230)	.											.	SATB2-91	0			c.G1237T						.						93	87	89					2																	200193570		2203	4300	6503	SO:0001583	missense	23314	exon9			GGTTTACTAGAAG	AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1237G>T	2.37:g.200193570C>A	ENSP00000401112:p.Val413Leu	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	46	11	NM_015265	0	0	8	16	8	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	31	5.081487	0.94050	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.54675	0.58;0.59;0.58;0.56;0.58	4.98	4.98	0.66077	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.71273	0.3320	M	0.63428	1.95	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.87578	0.992;0.998	T	0.73030	-0.4111	10	0.66056	D	0.02	-10.9637	18.8143	0.92071	0.0:1.0:0.0:0.0	.	295;413	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	L	413;354;413;295;413	ENSP00000401112:V413L;ENSP00000388764:V354L;ENSP00000260926:V413L;ENSP00000388581:V295L;ENSP00000405420:V413L	ENSP00000260926:V413L	V	-	1	0	SATB2	199901815	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	7.609000	0.82925	2.747000	0.94245	0.650000	0.86243	GTA	.		0.488	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		A	200193570	C	A	200193570	3	1	4	1	0	0	0	0	1	0	0	0	13886	565	20	4	980	4	SATB2	2	200193570	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	1923688	200193570	43005803	10	229											
NOP58	51602	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	203155146	203155146	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaggaaaaattatttcagaTaatttaacatactgcaagtg	17	14	6	4	0	1	1	1	0	0	1	1	2	1	2	0	1	3	1	0	1	8	7			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:203155146T>C	ENST00000264279.5	+	7	826	c.600T>C	c.(598-600)gaT>gaC	p.D200D	SNORD11_ENST00000459124.1_RNA|SNORD11B_ENST00000607707.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	200					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						TTATTTCAGATAATTTAACAT	0.323																																					p.D200D		.											.	NOP58-90	0			c.T600C						.						92	98	96					2																	203155146		2203	4299	6502	SO:0001819	synonymous_variant	51602	exon7			TTCAGATAATTTA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"NOP58 ribonucleoprotein homolog (yeast)"			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.600T>C	2.37:g.203155146T>C		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	76	31	NM_015934	0	0	10	24	14	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			.		0.323	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934		C	203155146	T	C	203155146	2	2	4	1	0	0	0	0	0	0	0	1	10566	1403	49	3		3	NOP58	2	203155146	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08	2961576	203155146	40044227	11	230											
GALNTL2	117248	hgsc.bcm.edu	37	chr3	16217029	16217029	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgcctcatcaagcagccaaGgaggcaggataaggaagccc	13	3	12	13	1	2	0	2	0	0	0	2	3	2	3	4	4	3	2	4	4	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:16217029G>C	ENST00000339732.5	+	1	874	c.371G>C	c.(370-372)aGg>aCg	p.R124T	GALNT15_ENST00000437509.1_Missense_Mutation_p.R124T|GALNT15_ENST00000470031.1_3'UTR	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	124					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										AAGCAGCCAAGGAGGCAGGAT	0.632																																					p.R124T		.											.	.	0			c.G371C						.						27	26	27					3																	16217029		2203	4300	6503	SO:0001583	missense	117248	exon1			AGCCAAGGAGGCA	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"Glycosyltransferase family 2 domain containing"	21531	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 15"	615131	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.371G>C	3.37:g.16217029G>C	ENSP00000344260:p.Arg124Thr	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_054110	0	0	4	4	0	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	.	.	.	.	.	.	.	.	.	.	G	9.292	1.050880	0.19827	.	.	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.57436	0.63;0.4	4.14	1.3	0.21679	.	3.749960	0.01401	U	0.013600	T	0.40498	0.1119	L	0.29908	0.895	0.22562	N	0.998987	B	0.32245	0.361	B	0.30646	0.118	T	0.17471	-1.0368	10	0.14252	T	0.57	.	8.0521	0.30583	0.2627:0.0:0.7373:0.0	.	124	Q8N3T1	GLTL2_HUMAN	T	124	ENSP00000344260:R124T;ENSP00000395873:R124T	ENSP00000344260:R124T	R	+	2	0	GALNTL2	16192033	0.828000	0.29307	0.047000	0.18901	0.887000	0.51463	0.959000	0.29240	0.049000	0.15920	0.442000	0.29010	AGG	.		0.632	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110		C	16217029	G	C	16217029	3	2	4	1	0	0	0	0	1	0	0	0	6242	1000	35	4	373	4	GALNTL2	3	16217029	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		16217029	181805401	12	231											
DALRD3	55152	broad.mit.edu	37	chr3	49055671	49055671	+	Frame_Shift_Del	DEL	G	G	-																															agttggagagacagacccgcGggggtcggcgcgcagcgcag																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:49055671delG	ENST00000341949.4	-	2	252	c.246delC	c.(244-246)cccfs	p.P82fs	DALRD3_ENST00000440857.1_5'UTR|NDUFAF3_ENST00000395458.2_5'Flank|DALRD3_ENST00000496568.1_5'UTR|NDUFAF3_ENST00000326912.4_5'Flank|MIR191_ENST00000384873.1_RNA|DALRD3_ENST00000395462.4_5'UTR|NDUFAF3_ENST00000326925.6_5'Flank|MIR425_ENST00000362162.1_RNA|DALRD3_ENST00000441576.2_Frame_Shift_Del_p.P82fs|DALRD3_ENST00000313778.5_5'UTR	NM_001009996.1	NP_001009996.1	Q5D0E6	DALD3_HUMAN	DALR anticodon binding domain containing 3	82					arginyl-tRNA aminoacylation (GO:0006420)		arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)			breast(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ACAGACCCGCGGGGGTCGGCG	0.741																																					p.P82fs													.	DALRD3-90	0			c.246delC						.						3	4	4					3																	49055671		1719	3615	5334	SO:0001589	frameshift_variant	55152	exon2			ACCCGCGGGGGTC	BC014099	CCDS2783.1, CCDS33754.1, CCDS63632.1	3p21.31	2005-01-10			ENSG00000178149	ENSG00000178149			25536	protein-coding gene	gene with protein product						12477932	Standard	NM_001009996		Approved	FLJ10496	uc003cvk.2	Q5D0E6	OTTHUMG00000156748	ENST00000341949.4:c.246delC	3.37:g.49055671delG	ENSP00000344989:p.Pro82fs	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001009996	0	0	0	0	0	Q7Z5S7|Q86WY1|Q8N105|Q8NA89|Q9NVU8	Frame_Shift_Del	DEL	ENST00000341949.4	37	CCDS33754.1																																																																																			.		0.741	DALRD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345581.1	NM_018114		-	49055671	G	-	49055671	7	5	4	1	0	1	0	1	0	0	0	0	4235	1103	39	0	1429	0	DALRD3	3	49055671	Frame_Shift_Del	DEL	G	TCGA-A4-7583-01A-11D-2136-08	32838642	49055671	148966759	13	232											
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52588791	52588791	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acctggcggaagatggtgggGtggaggccccccagggtgaa	8	5	19	9	1	0	2	0	1	0	1	0	4	0	4	4	8	0	0	4	8	2	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:52588791G>T	ENST00000296302.7	-	27	4559	c.4558C>A	c.(4558-4560)Ccc>Acc	p.P1520T	PBRM1_ENST00000409057.1_Missense_Mutation_p.P1465T|PBRM1_ENST00000409114.3_Intron|PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000410007.1_Missense_Mutation_p.P1440T|PBRM1_ENST00000356770.4_Missense_Mutation_p.P1433T|PBRM1_ENST00000394830.3_Missense_Mutation_p.P1413T|PBRM1_ENST00000337303.4_Intron|SMIM4_ENST00000476842.1_Intron|RNU6-856P_ENST00000516959.1_RNA			Q86U86	PB1_HUMAN	polybromo 1	1520	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGATGGTGGGGTGGAGGCCCC	0.582			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.P1413T		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.C4237A						.						46	46	46					3																	52588791		2203	4300	6503	SO:0001583	missense	55193	exon27			GGTGGGGTGGAGG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4558C>A	3.37:g.52588791G>T	ENSP00000296302:p.Pro1520Thr	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	39	19	NM_018313	0	0	2	6	4	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	15.23	2.771379	0.49680	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000409057;ENST00000410007	T;T;T;T;T	0.34859	1.35;1.34;1.39;1.35;1.35	5.75	5.75	0.90469	.	0.192124	0.47455	D	0.000227	T	0.21761	0.0524	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.32829	0.386;0.386;0.386;0.267;0.386	B;B;B;B;B	0.31101	0.124;0.124;0.124;0.058;0.086	T	0.08411	-1.0723	10	0.22706	T	0.39	-8.6684	18.1254	0.89584	0.0:0.0:1.0:0.0	.	1440;1413;1465;1520;1433	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86;Q86U86-3	.;.;.;PB1_HUMAN;.	T	1433;1413;1520;1465;1440	ENSP00000349213:P1433T;ENSP00000378307:P1413T;ENSP00000296302:P1520T;ENSP00000386593:P1465T;ENSP00000386529:P1440T	ENSP00000296302:P1520T	P	-	1	0	PBRM1	52563831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.959000	0.63666	2.696000	0.92011	0.655000	0.94253	CCC	.		0.582	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52588791	G	T	52588791	3	4	4	1	0	0	0	0	1	0	0	0	11517	1261	44	4	527	4	PBRM1	3	52588791	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	3533120	52588791	145433639	14	233											
IL17RB	55540	hgsc.bcm.edu	37	chr3	53891719	53891719	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaaggtgctacggtgcaggTaaagttcagtgagctgctct	9	11	14	7	1	2	2	1	2	1	0	2	2	2	2	0	3	5	6	0	3	4	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:53891719T>C	ENST00000288167.3	+	8	756		c.e8+2		RP11-884K10.7_ENST00000607783.1_RNA	NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B						cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		ACGGTGCAGGTAAAGTTCAGT	0.468																																					.		.											.	IL17RB-229	0			c.747+2T>C						.						134	114	121					3																	53891719		2203	4300	6503	SO:0001630	splice_region_variant	55540	exon8			TGCAGGTAAAGTT	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"Interleukins and interleukin receptors"	18015	protein-coding gene	gene with protein product		605458	"interleukin 17B receptor"	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.747+2T>C	3.37:g.53891719T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_018725	0	0	215	215	0	Q9BPZ0|Q9NRL4|Q9NRM5	Splice_Site	SNP	ENST00000288167.3	37	CCDS2874.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.775436	0.31411	.	.	ENSG00000056736	ENST00000288167;ENST00000494338	.	.	.	4.76	3.61	0.41365	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4365	0.27158	0.0:0.1013:0.0:0.8987	.	.	.	.	.	-1	.	.	.	+	.	.	IL17RB	53866759	1.000000	0.71417	0.981000	0.43875	0.380000	0.30137	3.510000	0.53393	0.940000	0.37473	0.533000	0.62120	.	.		0.468	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234	Intron	C	53891719	T	C	53891719	5	2	4	1	0	0	0	0	0	0	1	0	7661	1652	57	3	779	3	IL17RB	3	53891719	Splice_Site	SNP	T	TCGA-A4-7583-01A-11D-2136-08	1302928	53891719	144130711	15	234											
ADCY5	111	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	123010068	123010068	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagttggcgatggaggcgaaCatgaccgccacacactcaca	13	5	11	12	3	1	1	1	1	0	0	1	4	1	2	2	3	1	1	2	3	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:123010068C>T	ENST00000462833.1	-	18	4431	c.3219G>A	c.(3217-3219)atG>atA	p.M1073I	ADCY5_ENST00000491190.1_Missense_Mutation_p.M731I|ADCY5_ENST00000309879.5_Missense_Mutation_p.M723I	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	1073	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		TGGAGGCGAACATGACCGCCA	0.582																																					p.M1073I													.	ADCY5-94	0			c.G3219A						.						103	82	89					3																	123010068		2203	4300	6503	SO:0001583	missense	111	exon18			GGCGAACATGACC	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.3219G>A	3.37:g.123010068C>T	ENSP00000419361:p.Met1073Ile	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	74	24	NM_183357	0	0	0	0	0	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.315002	0.81358	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879	T;T;T	0.30182	1.54;1.54;1.54	4.53	4.53	0.55603	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	T	0.45994	0.1370	L	0.46670	1.46	0.58432	D	0.999998	D;D	0.57899	0.959;0.981	P;P	0.61070	0.86;0.883	T	0.34354	-0.9832	10	0.41790	T	0.15	.	17.4829	0.87679	0.0:1.0:0.0:0.0	.	1073;731	O95622;B3KWA8	ADCY5_HUMAN;.	I	1073;731;723	ENSP00000419361:M1073I;ENSP00000418537:M731I;ENSP00000308685:M723I	ENSP00000308685:M723I	M	-	3	0	ADCY5	124492758	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.758000	0.68776	2.362000	0.80069	0.563000	0.77884	ATG	.		0.582	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		T	123010068	C	T	123010068	3	4	4	1	0	0	0	0	1	0	0	0	297	478	17	2	582	2	ADCY5	3	123010068	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	69118349	123010068	75012362	16	235											
CLDN18	51208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	137742626	137742626	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaggactctgccaaagccaAcatgacactgacctccggga	12	5	11	13	1	1	2	0	2	1	0	2	5	2	5	4	3	3	0	4	3	2	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:137742626A>T	ENST00000183605.5	+	2	573	c.347A>T	c.(346-348)aAc>aTc	p.N116I	CLDN18_ENST00000343735.4_Missense_Mutation_p.N116I	NM_016369.3	NP_057453.1	P56856	CLD18_HUMAN	claudin 18	116					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	6						GCCAAAGCCAACATGACACTG	0.502																																					p.N116I		.											.	CLDN18-92	0			c.A347T						.						105	85	92					3																	137742626		2203	4300	6503	SO:0001583	missense	51208	exon2			AAGCCAACATGAC	AF221069, AY102073	CCDS3095.1, CCDS33862.1	3q	2008-08-27			ENSG00000066405	ENSG00000066405		"Claudins"	2039	protein-coding gene	gene with protein product		609210	"surfactant associated protein J"	SFTPJ			Standard	NM_001002026		Approved		uc003ero.1	P56856	OTTHUMG00000159762	ENST00000183605.5:c.347A>T	3.37:g.137742626A>T	ENSP00000183605:p.Asn116Ile	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	68	22	NM_016369	0	0	0	0	0	A5PL21|Q96PH4	Missense_Mutation	SNP	ENST00000183605.5	37	CCDS3095.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.774666	0.49786	.	.	ENSG00000066405	ENST00000343735;ENST00000183605;ENST00000536138	D;D	0.85773	-1.98;-2.03	5.43	4.25	0.50352	.	0.400442	0.26013	N	0.026870	T	0.79684	0.4488	L	0.31065	0.9	0.36035	D	0.839645	P;P	0.38250	0.487;0.624	B;B	0.41332	0.285;0.354	T	0.81972	-0.0688	10	0.48119	T	0.1	.	12.5759	0.56363	0.861:0.139:0.0:0.0	.	116;116	P56856;P56856-2	CLD18_HUMAN;.	I	116;116;105	ENSP00000340939:N116I;ENSP00000183605:N116I	ENSP00000183605:N116I	N	+	2	0	CLDN18	139225316	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.836000	0.55813	0.878000	0.35920	0.528000	0.53228	AAC	.		0.502	CLDN18-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357199.2	NM_001002026		T	137742626	A	T	137742626	3	4	4	1	0	0	0	0	1	0	0	0	3485	43	2	5	577	5	CLDN18	3	137742626	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	14732558	137742626	60279804	17	236											
TMEM41A	90407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	185209397	185209397	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcagatgtttctgactaaaTtttttaatgagggttccagg	10	16	10	5	0	1	3	0	2	1	1	2	3	2	3	1	2	1	3	1	2	3	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:185209397T>A	ENST00000421852.1	-	5	818	c.723A>T	c.(721-723)aaA>aaT	p.K241N	TMEM41A_ENST00000296254.3_3'UTR|TMEM41A_ENST00000475480.1_Intron	NM_080652.3	NP_542383.1	Q96HV5	TM41A_HUMAN	transmembrane protein 41A	241						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|skin(1)	4	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			TCTGACTAAATTTTTTAATGA	0.408																																					p.K241N		.											.	TMEM41A-90	0			c.A723T						.						115	114	115					3																	185209397		2203	4300	6503	SO:0001583	missense	90407	exon5			ACTAAATTTTTTA	BC019884	CCDS3271.1	3q27.2	2006-04-12			ENSG00000163900	ENSG00000163900			30544	protein-coding gene	gene with protein product						12975309	Standard	NM_080652		Approved	MGC15397	uc003fpj.2	Q96HV5	OTTHUMG00000156660	ENST00000421852.1:c.723A>T	3.37:g.185209397T>A	ENSP00000406885:p.Lys241Asn	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	95	41	NM_080652	0	0	11	19	8	A8K4B3|D3DNU2|Q6ZMJ0	Missense_Mutation	SNP	ENST00000421852.1	37	CCDS3271.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.427515	0.43122	.	.	ENSG00000163900	ENST00000421852	.	.	.	6.08	-4.0	0.04057	.	0.341077	0.31772	N	0.007083	T	0.54078	0.1836	M	0.76574	2.34	0.80722	D	1	B	0.14805	0.011	B	0.17433	0.018	T	0.42916	-0.9423	9	0.29301	T	0.29	-18.9262	10.7523	0.46216	0.0:0.4413:0.0938:0.4649	.	241	Q96HV5	TM41A_HUMAN	N	241	.	ENSP00000406885:K241N	K	-	3	2	TMEM41A	186692091	0.000000	0.05858	0.846000	0.33378	0.988000	0.76386	-1.837000	0.01689	-0.284000	0.09102	0.533000	0.62120	AAA	.		0.408	TMEM41A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345174.1	NM_080652		A	185209397	T	A	185209397	3	1	4	1	0	0	0	0	1	0	0	0	16196	1490	52	5	75	5	TMEM41A	3	185209397	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	47466771	185209397	12813033	18	237											
NOP14	8602	ucsc.edu	37	chr4	2945921	2945921	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcagcacacgaacaggccCttcaccacgtcctggaggga	11	4	12	14	2	1	0	1	0	0	0	2	3	2	2	3	4	2	2	3	4	1	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:2945921C>A	ENST00000314262.6	-	13	1818	c.1770G>T	c.(1768-1770)aaG>aaT	p.K590N	NOP14-AS1_ENST00000507702.1_RNA|NOP14-AS1_ENST00000503709.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|NOP14_ENST00000507120.1_5'Flank|NOP14_ENST00000398071.4_Missense_Mutation_p.K590N|NOP14_ENST00000502735.1_Missense_Mutation_p.K590N|NOP14-AS1_ENST00000512712.2_RNA|NOP14_ENST00000416614.2_Missense_Mutation_p.K590N|NOP14-AS1_ENST00000515194.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	590					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						CGAACAGGCCCTTCACCACGT	0.522																																					p.K590N													.	NOP14-91	0			c.G1770T						.						78	71	74					4																	2945921		2203	4300	6503	SO:0001583	missense	8602	exon13			CAGGCCCTTCACC	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"NOP14 homolog (S. cerevisiae)"	611526	"chromosome 4 open reading frame 9", "nucleolar protein 14", "nucleolar protein 14 homolog (yeast)", "NOP14 nucleolar protein homolog (yeast)"	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.1770G>T	4.37:g.2945921C>A	ENSP00000315674:p.Lys590Asn	Somatic	79	0		WXS	Illumina HiSeq		46	5	NM_003703	0	0	8	8	0	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.164355	0.57476	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.47	1.29	0.21616	.	0.216546	0.38381	N	0.001709	T	0.49440	0.1557	M	0.81942	2.565	0.51012	D	0.999909	D;D;D	0.71674	0.998;0.994;0.997	D;P;D	0.70016	0.96;0.871;0.967	T	0.45833	-0.9234	10	0.87932	D	0	-41.0339	6.0194	0.19620	0.1282:0.4985:0.0:0.3733	.	383;590;590	Q96GC8;E9PFK5;P78316	.;.;NOP14_HUMAN	N	590;590;590;590;489	ENSP00000405068:K590N;ENSP00000315674:K590N;ENSP00000427415:K590N;ENSP00000381146:K590N	ENSP00000315674:K590N	K	-	3	2	NOP14	2915719	0.227000	0.23707	0.987000	0.45799	0.892000	0.51952	-0.491000	0.06474	0.296000	0.22592	-0.258000	0.10820	AAG	.		0.522	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		A	2945921	C	A	2945921	3	1	4	1	0	0	0	0	1	0	0	0	10562	680	24	4	827	4	NOP14	4	2945921	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		2945921	188208355	19	238											
PROM1	8842	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	15989284	15989287	+	Splice_Site	DEL	ACCA	ACCA	-																															agaaaacaaagtaaacccttAccaacaatccattccctgtg																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	ACCA	ACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:15989284_15989287delACCA	ENST00000510224.1	-	20	2377_2379	c.2129_2131delTGGT	c.(2128-2133)ttggta>tta	p.V711fs	PROM1_ENST00000508167.1_Splice_Site_p.V702fs|PROM1_ENST00000505450.1_Splice_Site_p.V702fs|PROM1_ENST00000543373.1_Splice_Site_p.V702fs|PROM1_ENST00000447510.2_Splice_Site_p.V711fs|PROM1_ENST00000539194.1_Splice_Site_p.V711fs|PROM1_ENST00000540805.1_Splice_Site_p.V711fs			O43490	PROM1_HUMAN	prominin 1	711					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						GTAAACCCTTACCAACAATCCATT	0.343																																					p.710_710del		.											.	PROM1-207	0			c.2129_2130del						.																																			SO:0001630	splice_region_variant	8842	exon19			.	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.2130+1TGGT>-	4.37:g.15989284_15989287delACCA		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	233	69	NM_006017	0	0	0	0	0	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Frame_Shift_Del	DEL	ENST00000510224.1	37	CCDS47029.1																																																																																			.		0.343	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	Frame_Shift_Del	-	15989287	ACCA	-	15989284	8	5	4	1	0	1	0	1	0	0	1	0	12584	405	14	0	497	0	PROM1	4	15989284	Splice_Site	DEL	ACCA	TCGA-A4-7583-01A-11D-2136-08	13043363	15989284	175164992	20	239											
ATP10D	57205	broad.mit.edu	37	chr4	47538506	47538506	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcattttttcaatgttccCgagcctgatggacatatcat	10	15	7	9	1	2	1	2	1	0	0	3	3	3	2	2	1	2	2	2	1	2	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:47538506C>A	ENST00000273859.3	+	8	1337	c.1068C>A	c.(1066-1068)ccC>ccA	p.P356P	ATP10D_ENST00000504445.1_Silent_p.P356P	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	356					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.P356P(1)		NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TCAATGTTCCCGAGCCTGATG	0.358																																					p.P356P													.	ATP10D-93	1	Substitution - coding silent(1)	kidney(1)	c.C1068A						.						262	259	260					4																	47538506		2203	4300	6503	SO:0001819	synonymous_variant	57205	exon8			TGTTCCCGAGCCT	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.1068C>A	4.37:g.47538506C>A		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	284	9	NM_020453	0	0	17	17	0	A2RRC8|D6REN2|Q8NC70|Q96SR3	Silent	SNP	ENST00000273859.3	37	CCDS3476.1																																																																																			.		0.358	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		A	47538506	C	A	47538506	2	1	4	1	0	0	0	0	0	0	0	1	1119	639	23	4		4	ATP10D	4	47538506	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08	31549222	47538506	143615770	21	240											
SLC10A6	345274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	87749228	87749228	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagatgaaactgatggtcaGaagggtgatgtctgaattcc	14	10	12	5	0	2	6	1	4	1	2	3	6	3	6	1	2	1	0	1	2	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:87749228G>C	ENST00000273905.6	-	4	826	c.679C>G	c.(679-681)Ctg>Gtg	p.L227V	SLC10A6_ENST00000505535.1_Intron	NM_197965.2	NP_932069.1	Q3KNW5	SOAT_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 6	227					sodium-dependent organic anion transport (GO:0043251)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)|sodium-dependent organic anion transmembrane transporter activity (GO:0043250)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	9		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)		CTGATGGTCAGAAGGGTGATG	0.498																																					p.L227V		.											.	SLC10A6-22	0			c.C679G						.						89	81	84					4																	87749228		2203	4300	6503	SO:0001583	missense	345274	exon4			TGGTCAGAAGGGT	AJ583502	CCDS3614.1	4q22.1	2013-07-18	2013-07-18		ENSG00000145283	ENSG00000145283		"Solute carriers"	30603	protein-coding gene	gene with protein product		613366				15020217, 17491011	Standard	NM_197965		Approved	SOAT	uc003hqd.2	Q3KNW5	OTTHUMG00000130596	ENST00000273905.6:c.679C>G	4.37:g.87749228G>C	ENSP00000273905:p.Leu227Val	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	45	16	NM_197965	0	0	0	0	0	Q70EX7	Missense_Mutation	SNP	ENST00000273905.6	37	CCDS3614.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.010693	0.35511	.	.	ENSG00000145283	ENST00000273905	T	0.78816	-1.21	5.28	3.48	0.39840	.	0.167902	0.30320	N	0.009895	T	0.67477	0.2897	L	0.54323	1.7	0.28830	N	0.897216	P	0.42357	0.777	B	0.39339	0.297	T	0.66118	-0.6003	10	0.49607	T	0.09	-15.0839	4.1624	0.10291	0.1683:0.0:0.6333:0.1984	.	227	Q3KNW5	SOAT_HUMAN	V	227	ENSP00000273905:L227V	ENSP00000273905:L227V	L	-	1	2	SLC10A6	87968252	0.998000	0.40836	0.998000	0.56505	0.705000	0.40729	1.536000	0.36072	2.736000	0.93811	0.655000	0.94253	CTG	.		0.498	SLC10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253043.2	NM_197965		C	87749228	G	C	87749228	3	2	4	1	0	0	0	0	1	0	0	0	14410	933	33	4	466	4	SLC10A6	4	87749228	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	40210722	87749228	103405048	22	241											
CAMK2D	817	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	114434488	114434488	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcccaatgcatgtacctgaGaaattccttgtagccagcat	11	12	7	11	0	0	1	0	1	0	1	2	2	2	1	4	0	4	4	4	0	4	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:114434488G>A	ENST00000342666.5	-	12	941	c.942C>T	c.(940-942)ttC>ttT	p.F314F	CAMK2D_ENST00000394526.2_Silent_p.F314F|CAMK2D_ENST00000418639.2_Silent_p.F314F|CAMK2D_ENST00000379773.2_Silent_p.F314F|CAMK2D_ENST00000515496.1_Silent_p.F314F|CAMK2D_ENST00000505990.1_Silent_p.F314F|CAMK2D_ENST00000394522.3_Silent_p.F314F|CAMK2D_ENST00000429180.1_Silent_p.F314F|CAMK2D_ENST00000511664.1_Silent_p.F314F|CAMK2D_ENST00000514328.1_Silent_p.F314F|CAMK2D_ENST00000296402.5_Silent_p.F314F|CAMK2D_ENST00000394524.3_Silent_p.F314F|CAMK2D_ENST00000508738.1_Silent_p.F314F|CAMK2D_ENST00000454265.2_Silent_p.F314F			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	314					calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		ATGTACCTGAGAAATTCCTTG	0.358																																					p.F314F		.											.	CAMK2D-334	0			c.C942T						.						94	93	93					4																	114434488		2203	4300	6503	SO:0001819	synonymous_variant	817	exon12			ACCTGAGAAATTC	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.942C>T	4.37:g.114434488G>A		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	113	42	NM_172128	0	0	1	2	1	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	37	CCDS3703.1	.	.	.	.	.	.	.	.	.	.	G	7.680	0.688715	0.14973	.	.	ENSG00000145349	ENST00000513132	.	.	.	5.36	-2.88	0.05682	.	.	.	.	.	T	0.51839	0.1698	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48031	-0.9070	4	.	.	.	.	8.2973	0.31993	0.2489:0.0:0.6045:0.1466	.	.	.	.	F	18	.	.	L	-	1	0	CAMK2D	114653937	1.000000	0.71417	0.988000	0.46212	0.671000	0.39405	2.348000	0.44045	-0.497000	0.06641	-1.284000	0.01376	CTC	.		0.358	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2			A	114434488	G	A	114434488	2	1	4	1	0	0	0	0	0	0	0	1	2607	933	33	2		2	CAMK2D	4	114434488	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08	26685260	114434488	76719788	23	242											
TLR3	7098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187004092	187004092	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tactcaacctaaccaagaatAaaatctcaaaaatagagagt	21	8	4	8	0	2	2	2	0	1	2	3	3	2	2	2	0	3	0	2	0	10	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:187004092A>C	ENST00000296795.3	+	4	1356	c.1252A>C	c.(1252-1254)Aaa>Caa	p.K418Q	TLR3_ENST00000504367.1_Missense_Mutation_p.K141Q	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	418					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		AACCAAGAATAAAATCTCAAA	0.403																																					p.K418Q		.											.	TLR3-524	0			c.A1252C						.						60	56	57					4																	187004092		2203	4299	6502	SO:0001583	missense	7098	exon4			AAGAATAAAATCT	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"CD molecules"	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1252A>C	4.37:g.187004092A>C	ENSP00000296795:p.Lys418Gln	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	79	26	NM_003265	0	0	11	21	10	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822070	0.32237	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	T;T	0.59083	0.29;0.29	5.78	4.59	0.56863	.	0.253731	0.46145	D	0.000313	T	0.42539	0.1207	L	0.31207	0.915	0.25382	N	0.988604	B	0.24823	0.112	B	0.29176	0.099	T	0.31998	-0.9923	10	0.37606	T	0.19	.	5.6089	0.17394	0.7025:0.1541:0.1434:0.0	.	418	O15455	TLR3_HUMAN	Q	418;418;141	ENSP00000296795:K418Q;ENSP00000423684:K141Q	ENSP00000296795:K418Q	K	+	1	0	TLR3	187241086	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.225000	0.58600	0.999000	0.39023	0.455000	0.32223	AAA	.		0.403	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			C	187004092	A	C	187004092	3	2	4	1	0	0	0	0	1	0	0	0	15984	363	13	5	1262	5	TLR3	4	187004092	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	72569604	187004092	4150184	24	243											
ZFR	51663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	32403408	32403408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaggagaggcagtcggctttGaagcagatacagctgttgaa	13	8	14	6	1	0	4	0	2	0	2	1	5	0	4	0	3	3	5	0	3	4	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:32403408G>A	ENST00000265069.8	-	8	1421	c.1319C>T	c.(1318-1320)tCa>tTa	p.S440L		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	440					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		AGTCGGCTTTGAAGCAGATAC	0.418																																					p.S440L		.											.	ZFR-90	0			c.C1319T						.						188	171	177					5																	32403408		2203	4300	6503	SO:0001583	missense	51663	exon8			GGCTTTGAAGCAG	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1319C>T	5.37:g.32403408G>A	ENSP00000265069:p.Ser440Leu	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	160	70	NM_016107	0	0	21	41	20	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934133	0.73442	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.05925	3.37	5.95	5.95	0.96441	.	0.316034	0.39210	N	0.001439	T	0.09555	0.0235	L	0.43152	1.355	0.58432	D	0.999997	B	0.26935	0.164	B	0.21917	0.037	T	0.08207	-1.0733	10	0.72032	D	0.01	.	20.3719	0.98893	0.0:0.0:1.0:0.0	.	440	Q96KR1	ZFR_HUMAN	L	440;418	ENSP00000265069:S440L	ENSP00000265069:S440L	S	-	2	0	ZFR	32439165	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.494000	0.81503	2.826000	0.97356	0.491000	0.48974	TCA	.		0.418	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			A	32403408	G	A	32403408	3	1	4	1	0	0	0	0	1	0	0	0	17691	1294	45	2	1957	2	ZFR	5	32403408	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		32403408	148511852	25	244											
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	67576767	67576767	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttacagctctgataatacTgaaaacctcataaaagttat	16	13	4	8	0	3	2	1	2	2	0	3	2	3	2	1	0	4	2	1	0	8	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:67576767T>G	ENST00000521381.1	+	7	1465	c.849T>G	c.(847-849)acT>acG	p.T283T	PIK3R1_ENST00000521657.1_Silent_p.T283T|PIK3R1_ENST00000396611.1_Silent_p.T283T|PIK3R1_ENST00000274335.5_Silent_p.T283T	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	283	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CTGATAATACTGAAAACCTCA	0.328			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.T283T		.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1-4332	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.T849G						.						53	58	57					5																	67576767		2203	4299	6502	SO:0001819	synonymous_variant	5295	exon7			TAATACTGAAAAC	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.849T>G	5.37:g.67576767T>G		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	61	18	NM_181523	0	0	4	5	1	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	37	CCDS3993.1																																																																																			.		0.328	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67576767	T	G	67576767	2	3	4	1	0	0	0	0	0	0	0	1	11944	1567	55	5		5	PIK3R1	5	67576767	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08	35173359	67576767	113338493	26	245											
PAPD4	167153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	78975410	78975410	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcttatagctggaataGtcaaatgatttcagttcgtg	10	17	8	6	1	4	1	2	1	2	0	5	2	4	2	0	1	1	2	0	1	5	7			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:78975410G>C	ENST00000296783.3	+	14	1516	c.1217G>C	c.(1216-1218)aGt>aCt	p.S406T	PAPD4_ENST00000423041.2_Missense_Mutation_p.S402T|PAPD4_ENST00000428308.2_Missense_Mutation_p.S406T|PAPD4_ENST00000504233.1_Missense_Mutation_p.S363T|PAPD4_ENST00000453514.1_Missense_Mutation_p.S406T			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	406	PAP-associated.				hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)			biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		AGCTGGAATAGTCAAATGATT	0.323																																					p.S406T		.											.	PAPD4-69	0			c.G1217C						.						106	99	102					5																	78975410		2203	4300	6503	SO:0001583	missense	167153	exon14			GGAATAGTCAAAT	AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"TUTase2"	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.1217G>C	5.37:g.78975410G>C	ENSP00000296783:p.Ser406Thr	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	73	33	NM_173797	0	0	0	0	0	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	37	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.653395	0.29425	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	6.06	4.2	0.49525	PAP/25A-associated (1);	0.512215	0.23215	N	0.050628	T	0.50701	0.1631	N	0.08118	0	0.22982	N	0.998471	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.33954	-0.9848	10	0.30854	T	0.27	-6.8279	7.1177	0.25427	0.1866:0.1805:0.6329:0.0	.	406;402;363	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	T	406;402;363;406;406	ENSP00000397563:S406T;ENSP00000393412:S402T;ENSP00000421966:S363T;ENSP00000396861:S406T;ENSP00000296783:S406T	ENSP00000296783:S406T	S	+	2	0	PAPD4	79011166	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.626000	0.37039	1.428000	0.47296	0.655000	0.94253	AGT	.		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		C	78975410	G	C	78975410	3	2	4	1	0	0	0	0	1	0	0	0	11450	1029	36	4	1263	4	PAPD4	5	78975410	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	11398643	78975410	101939850	27	246											
SLIT3	6586	hgsc.bcm.edu	37	chr5	168112858	168112858	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacgatgcactgggccccgTtctggcactcgtactggtcg	5	9	12	15	4	1	0	0	0	1	0	3	1	1	0	3	3	2	4	3	3	1	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:168112858T>C	ENST00000519560.1	-	31	3808	c.3389A>G	c.(3388-3390)aAc>aGc	p.N1130S	SLIT3_ENST00000332966.8_Missense_Mutation_p.N1137S|SLIT3_ENST00000404867.3_Missense_Mutation_p.N1130S	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1130	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGGGCCCCGTTCTGGCACTC	0.637																																					p.N1137S	Ovarian(29;311 847 10864 17279 24903)	.											.	SLIT3-95	0			c.A3410G						.						39	36	37					5																	168112858		2203	4300	6503	SO:0001583	missense	6586	exon31			GCCCCGTTCTGGC	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3389A>G	5.37:g.168112858T>C	ENSP00000430333:p.Asn1130Ser	Somatic	28	1		WXS	Illumina HiSeq	Phase_I	28	2	NM_001271946	0	0	5	5	0	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373998	0.82573	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.94828	-3.53;-3.53;-3.53	4.76	4.76	0.60689	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97895	0.9308	H	0.94886	3.595	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.99026	1.0819	10	0.72032	D	0.01	.	14.5675	0.68188	0.0:0.0:0.0:1.0	.	1130	O75094	SLIT3_HUMAN	S	1130;1137;1130	ENSP00000430333:N1130S;ENSP00000332164:N1137S;ENSP00000384890:N1130S	ENSP00000332164:N1137S	N	-	2	0	SLIT3	168045436	1.000000	0.71417	0.977000	0.42913	0.821000	0.46438	7.993000	0.88291	1.904000	0.55121	0.459000	0.35465	AAC	.		0.637	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		C	168112858	T	C	168112858	3	2	4	1	0	0	0	0	1	0	0	0	14773	1725	60	3	1206	3	SLIT3	5	168112858	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	89137448	168112858	12802402	28	247											
RDBP	7936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31922209	31922209	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggctcgccgttcagggaaTgaatccgaccctttgggagc	7	8	15	11	3	1	1	1	1	0	0	3	4	2	3	3	4	1	2	3	4	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr6:31922209T>C	ENST00000375429.3	-	8	979	c.753A>G	c.(751-753)tcA>tcG	p.S251S	MIR1236_ENST00000408340.1_RNA|NELFE_ENST00000375425.5_Silent_p.S258S|NELFE_ENST00000444811.2_Silent_p.S221S	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	251					gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										GTTCAGGGAATGAATCCGACC	0.483																																					p.S251S		.											.	.	0			c.A753G						.						96	90	92					6																	31922209		2203	4300	6503	SO:0001819	synonymous_variant	7936	exon8			AGGGAATGAATCC	M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"RNA binding motif (RRM) containing"	13974	protein-coding gene	gene with protein product		154040	"RD RNA-binding protein", "RD RNA binding protein"	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.753A>G	6.37:g.31922209T>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	88	30	NM_002904	0	0	1	1	0	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Silent	SNP	ENST00000375429.3	37	CCDS4730.1																																																																																			.		0.483	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4			C	31922209	T	C	31922209	2	2	4	1	0	0	0	0	0	0	0	1	13220	1451	51	3		3	RDBP	6	31922209	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08		31922209	139192858	29	248											
EYS	346007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	66204808	66204808	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgctgtttcactgtcacatTtagtcgaagtcccagtggac	8	13	9	11	1	2	0	2	0	0	0	4	2	3	1	1	1	1	2	1	1	2	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr6:66204808T>G	ENST00000370621.3	-	4	1022	c.496A>C	c.(496-498)Aat>Cat	p.N166H	EYS_ENST00000370618.3_Missense_Mutation_p.N166H|EYS_ENST00000342421.5_Missense_Mutation_p.N166H|EYS_ENST00000503581.1_Missense_Mutation_p.N166H|EYS_ENST00000393380.2_Missense_Mutation_p.N166H|EYS_ENST00000370616.2_Missense_Mutation_p.N166H			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	166					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ACTGTCACATTTAGTCGAAGT	0.423																																					p.N166H		.											.	EYS-660	0			c.A496C						.						72	64	66					6																	66204808		2203	4300	6503	SO:0001583	missense	346007	exon4			TCACATTTAGTCG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.496A>C	6.37:g.66204808T>G	ENSP00000359655:p.Asn166His	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	97	32	NM_001142801	0	0	0	0	0	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	T	16.65	3.181420	0.57800	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36;-2.36	4.54	3.34	0.38264	.	.	.	.	.	T	0.69824	0.3154	N	0.08118	0	0.21020	N	0.99981	P;P;P	0.49862	0.844;0.929;0.884	B;P;P	0.48030	0.383;0.564;0.51	T	0.64588	-0.6372	9	0.45353	T	0.12	.	9.2337	0.37453	0.0:0.0:0.1827:0.8173	.	166;166;166	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	H	166	ENSP00000424243:N166H;ENSP00000359655:N166H;ENSP00000359650:N166H;ENSP00000377042:N166H;ENSP00000341818:N166H;ENSP00000359652:N166H	ENSP00000341818:N166H	N	-	1	0	EYS	66261529	0.997000	0.39634	0.962000	0.40283	0.996000	0.88848	2.828000	0.48120	0.667000	0.31107	0.482000	0.46254	AAT	.		0.423	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	66204808	T	G	66204808	3	3	4	1	0	0	0	0	1	0	0	0	5345	1841	64	5	9060	5	EYS	6	66204808	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	34282599	66204808	104910259	30	249											
SLC22A16	85413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	110746234	110746234	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagccgtttcccaagggtttCtggaagctttagtgttaaca	9	14	10	8	1	1	0	0	0	1	0	2	1	2	1	2	2	3	4	2	2	5	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr6:110746234C>A	ENST00000368919.3	-	8	1642	c.1576G>T	c.(1576-1578)Gaa>Taa	p.E526*	SLC22A16_ENST00000330550.4_Nonsense_Mutation_p.E492*	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	526					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	CCAAGGGTTTCTGGAAGCTTT	0.408																																					p.E526X		.											.	SLC22A16-91	0			c.G1576T						.						90	89	90					6																	110746234		2203	4300	6503	SO:0001587	stop_gained	85413	exon8			GGGTTTCTGGAAG		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1576G>T	6.37:g.110746234C>A	ENSP00000357915:p.Glu526*	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	135	48	NM_033125	0	0	0	0	0	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Nonsense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	C	38	7.112271	0.98070	.	.	ENSG00000004809	ENST00000368919;ENST00000330550	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.8326	0.78769	0.0:1.0:0.0:0.0	.	.	.	.	X	526;492	.	ENSP00000328583:E492X	E	-	1	0	SLC22A16	110852927	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.424000	0.66464	2.546000	0.85860	0.591000	0.81541	GAA	.		0.408	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		A	110746234	C	A	110746234	4	1	4	1	0	0	0	0	0	1	0	0	14479	922	32	4	161	4	SLC22A16	6	110746234	Nonsense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	44541426	110746234	60368833	31	250											
ETV1	2115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	13971323	13971323	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggacgtccttcccttggcatCgtcggcaaaggaggaaagga	10	7	14	10	3	0	0	0	0	0	0	4	4	2	4	2	6	0	2	2	6	2	2	rs531769320	byFrequency	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr7:13971323C>G	ENST00000430479.1	-	9	1273	c.606G>C	c.(604-606)acG>acC	p.T202T	ETV1_ENST00000420159.2_Silent_p.T144T|ETV1_ENST00000405358.4_Silent_p.T216T|ETV1_ENST00000399357.3_Silent_p.T99T|ETV1_ENST00000242066.5_Silent_p.T184T|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000403527.1_Silent_p.T162T|ETV1_ENST00000403685.1_Silent_p.T184T|ETV1_ENST00000405218.2_Silent_p.T202T|ETV1_ENST00000405192.2_Silent_p.T202T|ETV1_ENST00000343495.5_Silent_p.T184T	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	202					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						CCCTTGGCATCGTCGGCAAAG	0.502			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																p.T202T		.		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	.	ETV1-659	0			c.G606C						.						116	112	113					7																	13971323		2010	4169	6179	SO:0001819	synonymous_variant	2115	exon9			TGGCATCGTCGGC		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"ets variant gene 1"			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.606G>C	7.37:g.13971323C>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	45	17	NM_004956	0	0	1	2	1	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Silent	SNP	ENST00000430479.1	37	CCDS55088.1																																																																																			.		0.502	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		G	13971323	C	G	13971323	2	3	4	1	0	0	0	0	0	0	0	1	5290	871	31	4		4	ETV1	7	13971323	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08		13971323	145167340	32	251											
SUN3	256979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48035693	48035693	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccatgccagtacaattttgCtttattatttttataacttt	10	20	3	8	0	0	0	0	0	0	0	0	0	0	0	2	0	4	2	2	0	6	11			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr7:48035693C>T	ENST00000297325.4	-	7	787	c.628G>A	c.(628-630)Gca>Aca	p.A210T	SUN3_ENST00000395572.2_Missense_Mutation_p.A210T|SUN3_ENST00000453192.2_Missense_Mutation_p.A198T|SUN3_ENST00000412142.1_Missense_Mutation_p.A110T|SUN3_ENST00000473723.1_5'UTR	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	210	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.					integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)				central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TACAATTTTGCTTTATTATTT	0.299																																					p.A210T		.											.	SUN3-514	0			c.G628A						.						82	87	85					7																	48035693		2203	4288	6491	SO:0001583	missense	256979	exon8			ATTTTGCTTTATT	AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"Sad1 and UNC84 domain containing 1"	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.628G>A	7.37:g.48035693C>T	ENSP00000297325:p.Ala210Thr	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	126	40	NM_152782	0	0	0	0	0	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	37	CCDS34636.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484372	0.44147	.	.	ENSG00000164744	ENST00000297325;ENST00000412371;ENST00000412142;ENST00000395572;ENST00000453192;ENST00000438771	T;T;T;T;T;T	0.46063	1.83;0.88;1.84;1.83;2.42;1.84	5.25	4.37	0.52481	Sad1/UNC-like, C-terminal (1);	0.236128	0.42548	N	0.000694	T	0.35537	0.0935	L	0.49350	1.555	0.34170	D	0.669671	B;B;B	0.31503	0.047;0.326;0.192	B;B;B	0.28465	0.019;0.09;0.065	T	0.52873	-0.8517	10	0.87932	D	0	.	9.6842	0.40089	0.0:0.9039:0.0:0.0961	.	198;110;210	E7EWC8;Q8TAQ9-2;Q8TAQ9	.;.;SUN3_HUMAN	T	210;32;110;210;198;110	ENSP00000297325:A210T;ENSP00000406887:A32T;ENSP00000410204:A110T;ENSP00000378939:A210T;ENSP00000387525:A198T;ENSP00000409077:A110T	ENSP00000297325:A210T	A	-	1	0	SUN3	48002218	0.937000	0.31787	0.973000	0.42090	0.803000	0.45373	1.417000	0.34770	1.244000	0.43870	0.650000	0.86243	GCA	.		0.299	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782		T	48035693	C	T	48035693	3	4	4	1	0	0	0	0	1	0	0	0	15425	797	28	2	461	2	SUN3	7	48035693	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	34064370	48035693	111102970	33	252											
PEX1	5189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92151473	92151473	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgttaatttcagccacAttttcaccttgatcactaaa	11	16	4	10	0	4	1	3	1	1	0	4	1	4	1	2	0	1	1	2	0	3	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr7:92151473A>G	ENST00000248633.4	-	2	311	c.216T>C	c.(214-216)aaT>aaC	p.N72N	PEX1_ENST00000428214.1_Silent_p.N72N|PEX1_ENST00000438045.1_Silent_p.N72N	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	72					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTTCAGCCACATTTTCACCTT	0.408																																					p.N72N		.											.	PEX1-91	0			c.T216C						.						130	121	124					7																	92151473		2203	4300	6503	SO:0001819	synonymous_variant	5189	exon2			AGCCACATTTTCA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.216T>C	7.37:g.92151473A>G		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	130	55	NM_000466	0	0	3	9	6	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																			.		0.408	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		G	92151473	A	G	92151473	2	3	4	1	0	0	0	0	0	0	0	1	11761	214	8	3		3	PEX1	7	92151473	Silent	SNP	A	TCGA-A4-7583-01A-11D-2136-08	44115780	92151473	66987190	34	253											
TUSC3	7991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	15508312	15508312	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actatgatgaggggacagacGtttttcagcaggtaaagagt	13	10	13	5	1	1	4	1	2	0	2	1	5	1	5	0	3	1	3	0	3	3	4	rs371225890		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:15508312G>A	ENST00000503731.1	+	3	563	c.415G>A	c.(415-417)Gtt>Att	p.V139I	TUSC3_ENST00000382020.4_Missense_Mutation_p.V139I|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000506802.1_Missense_Mutation_p.V139I|TUSC3_ENST00000509380.1_Missense_Mutation_p.V139I	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	139	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GGGGACAGACGTTTTTCAGCA	0.343																																					p.V139I		.											.	TUSC3-516	0			c.G415A						.	G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	239	237	238		415,415	3.7	1	8		238	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	TUSC3	NM_006765.3,NM_178234.2	29,29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	139/349,139/348	15508312	2,13004	2203	4300	6503	SO:0001583	missense	7991	exon3			ACAGACGTTTTTC	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.415G>A	8.37:g.15508312G>A	ENSP00000424544:p.Val139Ile	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	222	96	NM_178234	0	0	0	0	0	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	37	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809796	0.70797	0.0	2.33E-4	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.47	3.67	0.42095	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.162707	0.53938	N	0.000046	T	0.55893	0.1949	M	0.66297	2.02	0.44323	D	0.997205	D;D;D;D;D;B	0.65815	0.971;0.995;0.981;0.977;0.995;0.004	P;P;D;P;P;B	0.65010	0.838;0.771;0.931;0.613;0.784;0.007	T	0.51411	-0.8709	10	0.27082	T	0.32	-11.5841	10.6624	0.45710	0.0719:0.1325:0.7956:0.0	.	139;139;139;139;139;139	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	I	139	ENSP00000371450:V139I;ENSP00000425777:V139I;ENSP00000423426:V139I;ENSP00000424544:V139I	ENSP00000221167:V139I	V	+	1	0	TUSC3	15552683	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	7.654000	0.83653	0.780000	0.33566	0.563000	0.77884	GTT	.		0.343	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		A	15508312	G	A	15508312	3	1	4	1	0	0	0	0	1	0	0	0	16811	1145	40	1	425	1	TUSC3	8	15508312	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		15508312	130855710	35	254											
PSD3	23362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	18430149	18430149	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagctgccacacaattgatTttgtttatccacccttgcat	10	14	5	12	0	0	1	0	1	0	0	1	1	1	1	3	0	3	3	3	0	2	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:18430149T>A	ENST00000327040.8	-	14	2775	c.2673A>T	c.(2671-2673)aaA>aaT	p.K891N	PSD3_ENST00000428502.2_Missense_Mutation_p.K220N|PSD3_ENST00000440756.2_Missense_Mutation_p.K893N|PSD3_ENST00000523619.1_Missense_Mutation_p.K826N|PSD3_ENST00000286485.8_Missense_Mutation_p.K357N	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	892	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CACAATTGATTTTGTTTATCC	0.433																																					p.K891N		.											.	PSD3-93	0			c.A2673T						.						167	173	171					8																	18430149		2203	4300	6503	SO:0001583	missense	23362	exon14			ATTGATTTTGTTT	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.2673A>T	8.37:g.18430149T>A	ENSP00000324127:p.Lys891Asn	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	225	73	NM_015310	0	0	2	3	1	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.516949	0.64634	.	.	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000286485;ENST00000428502;ENST00000523619	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	5.71	2.04	0.26737	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.683311	0.11566	U	0.551222	T	0.74711	0.3752	L	0.48174	1.505	0.39428	D	0.967023	B;B;B;P	0.37688	0.423;0.423;0.048;0.605	P;P;B;B	0.45946	0.498;0.498;0.061;0.388	T	0.69647	-0.5089	10	0.72032	D	0.01	.	4.8511	0.13537	0.0:0.2364:0.1485:0.615	.	891;892;357;220	E9KL50;Q9NYI0;Q9NYI0-3;B4DKF8	.;PSD3_HUMAN;.;.	N	891;893;357;220;826	ENSP00000324127:K891N;ENSP00000401704:K893N;ENSP00000286485:K357N;ENSP00000393228:K220N;ENSP00000430640:K826N	ENSP00000286485:K357N	K	-	3	2	PSD3	18474429	0.972000	0.33761	0.998000	0.56505	0.918000	0.54935	0.105000	0.15333	0.177000	0.19895	-0.297000	0.09499	AAA	.		0.433	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		A	18430149	T	A	18430149	3	1	4	1	0	0	0	0	1	0	0	0	12677	1838	64	5	482	5	PSD3	8	18430149	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	2921837	18430149	127933873	36	255											
TRIM35	23087	broad.mit.edu;bcgsc.ca	37	chr8	27168425	27168425	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgtcctcgaggcagaagaGgctgagctgtccgcggtgca	7	8	15	11	3	0	3	0	1	0	2	3	4	2	3	2	3	2	4	2	3	1	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:27168425G>T	ENST00000305364.4	-	1	411	c.328C>A	c.(328-330)Ctc>Atc	p.L110I	PTK2B_ENST00000544172.1_5'Flank|TRIM35_ENST00000521253.1_Missense_Mutation_p.L110I|PTK2B_ENST00000338238.4_5'Flank|PTK2B_ENST00000397501.1_5'Flank	NM_171982.3	NP_741983.2	Q9UPQ4	TRI35_HUMAN	tripartite motif containing 35	110					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	14		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)		AGGCAGAAGAGGCTGAGCTGT	0.697																																					p.L110I													.	TRIM35-226	0			c.C328A						.						22	22	22					8																	27168425		2199	4295	6494	SO:0001583	missense	23087	exon1			AGAAGAGGCTGAG	AB029021	CCDS6056.2	8p21.2	2013-01-09	2011-01-25		ENSG00000104228	ENSG00000104228		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16285	protein-coding gene	gene with protein product			"tripartite motif-containing 35"			11331580, 14662771, 12692137	Standard	XM_005273451		Approved	KIAA1098, MAIR, HLS5	uc003xfl.1	Q9UPQ4	OTTHUMG00000102047	ENST00000305364.4:c.328C>A	8.37:g.27168425G>T	ENSP00000301924:p.Leu110Ile	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	24	9	NM_171982	0	0	5	9	4	Q86XQ0|Q8WVA4	Missense_Mutation	SNP	ENST00000305364.4	37	CCDS6056.2	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192407	0.58017	.	.	ENSG00000104228	ENST00000305364;ENST00000380544;ENST00000521253	T;T	0.49720	0.77;0.77	5.5	-1.23	0.09465	Zinc finger, B-box (3);	0.346454	0.25004	N	0.033883	T	0.40932	0.1137	M	0.75777	2.31	0.23095	N	0.998305	P;B	0.43578	0.811;0.338	B;B	0.42386	0.386;0.205	T	0.35475	-0.9787	10	0.54805	T	0.06	.	1.9426	0.03350	0.1458:0.2389:0.3708:0.2446	.	110;110	E5RGB3;Q9UPQ4	.;TRI35_HUMAN	I	110	ENSP00000301924:L110I;ENSP00000428770:L110I	ENSP00000301924:L110I	L	-	1	0	TRIM35	27224342	0.052000	0.20516	0.066000	0.19879	0.473000	0.32948	0.313000	0.19415	-0.221000	0.09973	0.462000	0.41574	CTC	.		0.697	TRIM35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219848.2	NM_171982		T	27168425	G	T	27168425	3	4	4	1	0	0	0	0	1	0	0	0	16542	1000	35	4	1177	4	TRIM35	8	27168425	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	8738276	27168425	119195597	37	256											
ZNF395	55893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	28206721	28206721	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggctgctggggctcgcTgaagcttagcgaccggctcc	4	9	15	13	3	0	1	0	1	0	0	2	2	1	1	2	4	4	7	2	4	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:28206721T>C	ENST00000344423.5	-	9	1482	c.1351A>G	c.(1351-1353)Agc>Ggc	p.S451G	ZNF395_ENST00000523095.1_Missense_Mutation_p.S451G|ZNF395_ENST00000523202.1_Missense_Mutation_p.S451G	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		TGGGGCTCGCTGAAGCTTAGC	0.617																																					p.S451G		.											.	ZNF395-90	0			c.A1351G						.						75	79	78					8																	28206721		2203	4300	6503	SO:0001583	missense	55893	exon9			GCTCGCTGAAGCT	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1351A>G	8.37:g.28206721T>C	ENSP00000340494:p.Ser451Gly	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	70	22	NM_018660	0	0	36	53	17	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	37	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.544128	0.27563	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.46063	0.88;0.88;0.88	5.5	4.27	0.50696	.	0.318422	0.40908	D	0.001000	T	0.19046	0.0457	N	0.05487	-0.04	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.09335	-1.0679	10	0.09338	T	0.73	-15.6215	8.8687	0.35303	0.0:0.0:0.189:0.811	.	451	Q9H8N7	ZN395_HUMAN	G	451	ENSP00000340494:S451G;ENSP00000429640:S451G;ENSP00000428452:S451G	ENSP00000340494:S451G	S	-	1	0	ZNF395	28262640	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.178000	0.50879	2.099000	0.63709	0.459000	0.35465	AGC	.		0.617	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			C	28206721	T	C	28206721	3	2	4	1	0	0	0	0	1	0	0	0	17913	1580	55	3	198	3	ZNF395	8	28206721	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	1038296	28206721	118157301	38	257											
DGAT1	8694	hgsc.bcm.edu	37	chr8	145542536	145542536	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgggccagctatagggatccTtcaggaacagagaaaccacc	13	5	11	12	1	1	1	1	0	0	1	2	4	2	3	4	3	3	1	4	3	4	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:145542536T>G	ENST00000332324.4	-	4	650	c.377A>C	c.(376-378)aAg>aCg	p.K126T	DGAT1_ENST00000527438.1_5'Flank|DGAT1_ENST00000531896.1_Missense_Mutation_p.K126T	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	126					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			ATAGGGATCCTTCAGGAACAG	0.647																																					p.K126T		.											.	.	0			c.A377C						.						29	32	31					8																	145542536		2202	4300	6502	SO:0001583	missense	8694	exon4			GGATCCTTCAGGA	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"diacylglycerol O-acyltransferase homolog 1 (mouse)"			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.377A>C	8.37:g.145542536T>G	ENSP00000332258:p.Lys126Thr	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_012079	0	0	36	36	0	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	37	CCDS6420.1	.	.	.	.	.	.	.	.	.	.	T	14.95	2.689514	0.48097	.	.	ENSG00000185000	ENST00000332324;ENST00000526479;ENST00000531896	T;T	0.34472	1.36;1.36	5.32	5.32	0.75619	.	0.051216	0.85682	D	0.000000	T	0.46927	0.1418	L	0.50333	1.59	0.53005	D	0.999964	D;B	0.53885	0.963;0.126	P;B	0.56434	0.798;0.035	T	0.33777	-0.9855	10	0.34782	T	0.22	-12.7583	13.226	0.59914	0.0:0.0:0.0:1.0	.	126;126	E9PS80;O75907	.;DGAT1_HUMAN	T	126	ENSP00000332258:K126T;ENSP00000432795:K126T	ENSP00000332258:K126T	K	-	2	0	DGAT1	145513344	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.881000	0.56152	2.025000	0.59659	0.454000	0.30748	AAG	.		0.647	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079		G	145542536	T	G	145542536	3	3	4	1	0	0	0	0	1	0	0	0	4468	1609	56	5	1145	5	DGAT1	8	145542536	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	117335815	145542536	821486	39	258											
ARID3C	138715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	34622092	34622092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgccagattaagaggccCatccagccgctcttctgtcc	7	9	9	16	1	2	2	0	0	2	2	4	2	4	2	6	1	2	1	6	1	1	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:34622092C>T	ENST00000378909.2	-	6	1155	c.1063G>A	c.(1063-1065)Ggg>Agg	p.G355R	DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000378913.2_5'Flank|DCTN3_ENST00000477738.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	355	Pro-rich.|REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		TTAAGAGGCCCATCCAGCCGC	0.517																																					p.G355R		.											.	ARID3C-91	0			c.G1063A						.						91	84	87					9																	34622092		2203	4300	6503	SO:0001583	missense	138715	exon6			GAGGCCCATCCAG		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.1063G>A	9.37:g.34622092C>T	ENSP00000368189:p.Gly355Arg	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	130	44	NM_001017363	0	0	0	0	0		Missense_Mutation	SNP	ENST00000378909.2	37	CCDS35006.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.335039	0.41398	.	.	ENSG00000205143	ENST00000378909	T	0.41065	1.01	5.03	5.03	0.67393	REKLES domain (1);	0.000000	0.47093	D	0.000254	T	0.35856	0.0946	L	0.51422	1.61	0.29866	N	0.827257	P	0.39831	0.69	B	0.35727	0.209	T	0.32481	-0.9905	10	0.17369	T	0.5	-15.5988	15.9067	0.79436	0.0:1.0:0.0:0.0	.	355	A6NKF2	ARI3C_HUMAN	R	355	ENSP00000368189:G355R	ENSP00000368189:G355R	G	-	1	0	ARID3C	34612092	0.960000	0.32886	1.000000	0.80357	0.988000	0.76386	1.491000	0.35583	2.612000	0.88384	0.549000	0.68633	GGG	.		0.517	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		T	34622092	C	T	34622092	3	4	4	1	0	0	0	0	1	0	0	0	918	594	21	2	182	2	ARID3C	9	34622092	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		34622092	106591339	40	259											
RUSC2	9853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35547391	35547391	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaccctctacaacaagatGcatggcaccccccgtgccaa	12	5	7	17	1	1	1	0	0	1	1	1	1	1	1	5	1	5	3	5	1	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:35547391G>C	ENST00000455600.1	+	2	1442	c.873G>C	c.(871-873)atG>atC	p.M291I		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	291						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			ACAACAAGATGCATGGCACCC	0.582																																					p.M291I		.											.	RUSC2-91	0			c.G873C						.						79	70	73					9																	35547391		2203	4300	6503	SO:0001583	missense	9853	exon2			CAAGATGCATGGC	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.873G>C	9.37:g.35547391G>C	ENSP00000393922:p.Met291Ile	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	93	31	NM_014806	0	0	5	14	9	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	37	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339018	0.41398	.	.	ENSG00000198853	ENST00000361226;ENST00000455600;ENST00000543478	T;T	0.28069	1.63;1.63	5.61	5.61	0.85477	.	0.089636	0.85682	D	0.000000	T	0.28167	0.0695	L	0.29908	0.895	0.42729	D	0.993703	B	0.24258	0.1	B	0.24541	0.054	T	0.05338	-1.0891	10	0.62326	D	0.03	-8.6538	18.6114	0.91286	0.0:0.0:1.0:0.0	.	291	Q8N2Y8	RUSC2_HUMAN	I	291	ENSP00000355177:M291I;ENSP00000393922:M291I	ENSP00000355177:M291I	M	+	3	0	RUSC2	35537391	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.341000	0.79300	2.649000	0.89929	0.561000	0.74099	ATG	.		0.582	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		C	35547391	G	C	35547391	3	2	4	1	0	0	0	0	1	0	0	0	13783	1319	46	4	875	4	RUSC2	9	35547391	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	925299	35547391	105666040	41	260											
NANS	54187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	100840514	100840514	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgggatgcagtcaatggAcaccatgaagcaagtttatc	13	9	11	8	0	1	1	1	1	0	0	2	3	1	3	1	2	2	3	1	2	4	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:100840514A>G	ENST00000210444.5	+	4	558	c.488A>G	c.(487-489)gAc>gGc	p.D163G	NANS_ENST00000461452.1_3'UTR|TRIM14_ENST00000375098.3_Intron|TRIM14_ENST00000478530.1_5'Flank	NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	163					lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				CAGTCAATGGACACCATGAAG	0.522																																					p.D163G		.											.	NANS-91	0			c.A488G						.						229	181	197					9																	100840514		2203	4300	6503	SO:0001583	missense	54187	exon4			CAATGGACACCAT	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"sialic acid synthase"	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.488A>G	9.37:g.100840514A>G	ENSP00000210444:p.Asp163Gly	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	127	47	NM_018946	0	0	52	63	11	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Missense_Mutation	SNP	ENST00000210444.5	37	CCDS6733.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.487927	0.26686	.	.	ENSG00000095380	ENST00000210444;ENST00000415280	T;T	0.42900	0.96;0.96	5.32	1.49	0.22878	Aldolase-type TIM barrel (1);N-acetylneuraminic acid synthase, N-terminal (1);	0.346769	0.36167	N	0.002757	T	0.16896	0.0406	N	0.02103	-0.685	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.05370	-1.0889	10	0.24483	T	0.36	-13.5844	11.9513	0.52956	0.5778:0.4222:0.0:0.0	.	163	Q9NR45	SIAS_HUMAN	G	163;22	ENSP00000210444:D163G;ENSP00000404107:D22G	ENSP00000210444:D163G	D	+	2	0	NANS	99880335	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	2.784000	0.47774	0.070000	0.16634	-1.293000	0.01348	GAC	.		0.522	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946		G	100840514	A	G	100840514	3	3	4	1	0	0	0	0	1	0	0	0	10180	275	10	3	502	3	NANS	9	100840514	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	65293123	100840514	40372917	42	261											
DOLK	22845	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	131708944	131708945	+	Frame_Shift_Ins	INS	-	-	G																															cctgactttccaccagtgtcINSagagagcgcttgatgagctg																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:131708944_131708945insG	ENST00000372586.3	-	1	953_954	c.638_639insC	c.(637-639)ctgfs	p.L213fs	NUP188_ENST00000372577.2_5'Flank|RP11-101E3.5_ENST00000482796.1_Intron	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	213					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|dolichyl monophosphate biosynthetic process (GO:0043048)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichol kinase activity (GO:0004168)			breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						CCACCAGTGTCAGAGAGCGCTT	0.55																																					p.L213fs		.											.	DOLK-90	0			c.639_640insC						.																																			SO:0001589	frameshift_variant	22845	exon1			.	AB029017	CCDS6915.1	9q34.13	2014-09-17	2007-02-09	2007-02-09	ENSG00000175283	ENSG00000175283			23406	protein-coding gene	gene with protein product	"dolichol kinase 1"	610746	"transmembrane protein 15"	TMEM15		12975309, 16923818	Standard	NM_014908		Approved	KIAA1094, DK1	uc004bwr.3	Q9UPQ8	OTTHUMG00000020765	ENST00000372586.3:c.638_639insC	9.37:g.131708944_131708945insG	ENSP00000361667:p.Leu213fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	105	36	NM_014908	0	0	0	0	0	Q5SRE6	Frame_Shift_Ins	INS	ENST00000372586.3	37	CCDS6915.1																																																																																			.		0.55	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908		G	131708945	-	G	131708944	7	5	4	1	0	1	1	0	0	0	0	0	4714	813	29	0	981	0	DOLK	9	131708944	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	30868430	131708944	9504487	43	262											
THNSL1	79896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	25312238	25312238	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttaaaacggataaacatgCacagcgatttctttcaagaa	16	11	7	7	2	2	1	1	0	1	1	2	3	2	2	0	1	4	2	0	1	6	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr10:25312238C>T	ENST00000524413.1	+	3	433	c.86C>T	c.(85-87)gCa>gTa	p.A29V	THNSL1_ENST00000376356.4_Missense_Mutation_p.A29V			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	29						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	GATAAACATGCACAGCGATTT	0.363																																					p.A29V		.											.	THNSL1-91	0			c.C86T						.						97	99	98					10																	25312238		2203	4300	6503	SO:0001583	missense	79896	exon3			AACATGCACAGCG	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"threonine synthase-like 1 (bacterial)"			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.86C>T	10.37:g.25312238C>T	ENSP00000434887:p.Ala29Val	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	118	48	NM_024838	0	0	1	2	1	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	C	1.381	-0.583490	0.03827	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	T;T	0.07444	3.19;3.19	5.87	1.3	0.21679	.	1.328470	0.05152	N	0.496208	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37596	-0.9699	10	0.02654	T	1	-32.9386	0.8315	0.01132	0.1692:0.23:0.1664:0.4344	.	29	Q8IYQ7	THNS1_HUMAN	V	29	ENSP00000434887:A29V;ENSP00000365534:A29V	ENSP00000365534:A29V	A	+	2	0	THNSL1	25352244	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.012000	0.13287	-0.006000	0.14370	0.557000	0.71058	GCA	.		0.363	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		T	25312238	C	T	25312238	3	4	4	1	0	0	0	0	1	0	0	0	15894	710	25	2	88	2	THNSL1	10	25312238	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		25312238	110222509	44	263											
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411515	51411515	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacccaagagtttttctataGcatttctcatctctgaattt	10	18	4	9	0	3	2	1	1	3	1	5	2	3	2	1	0	2	2	1	0	5	7	rs370100509		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr11:51411515G>A	ENST00000319760.6	-	1	933	c.881C>T	c.(880-882)gCt>gTt	p.A294V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				TTTTTCTATAGCATTTCTCAT	0.358													.|||	1	0.000199681	8e-04	0	5008	,	,		18032	0		0	False		,,,				2504	0				p.A294V		.											.	OR4A5-92	0			c.C881T						.	G	VAL/ALA	1,4395		0,1,2197	27	29	28		881	1.2	0	11		28	0,8588		0,0,4294	no	missense	OR4A5	NM_001005272.3	64	0,1,6491	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	294/316	51411515	1,12983	2198	4294	6492	SO:0001583	missense	81318	exon1			TCTATAGCATTTC	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"GPCR / Class A : Olfactory receptors"	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.881C>T	11.37:g.51411515G>A	ENSP00000367664:p.Ala294Val	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	38	16	NM_001005272	0	0	0	0	0	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	8.667	0.901998	0.17760	2.27E-4	0.0	ENSG00000221840	ENST00000319760	T	0.44881	0.91	2.2	1.19	0.21007	.	0.000000	0.47093	D	0.000248	T	0.43233	0.1238	L	0.58583	1.82	0.09310	N	1	D	0.54397	0.966	P	0.49597	0.616	T	0.32268	-0.9913	10	0.62326	D	0.03	.	8.3068	0.32047	0.0:0.2632:0.7367:0.0	.	294	Q8NH83	OR4A5_HUMAN	V	294	ENSP00000367664:A294V	ENSP00000367664:A294V	A	-	2	0	OR4A5	51268091	0.001000	0.12720	0.032000	0.17829	0.332000	0.28634	0.866000	0.27954	0.438000	0.26450	0.162000	0.16502	GCT	.		0.358	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51411515	G	A	51411515	3	1	4	1	0	0	0	0	1	0	0	0	11069	971	34	2	70	2	OR4A5	11	51411515	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		51411515	83595001	45	264											
MYO7A	4647	broad.mit.edu	37	chr11	76888670	76888670	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcctccttcagaaagtcAtccggggattcaaagacagg	12	9	9	11	1	4	2	4	0	0	2	7	3	7	3	3	3	0	0	3	3	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr11:76888670A>T	ENST00000409709.3	+	19	2535	c.2263A>T	c.(2263-2265)Atc>Ttc	p.I755F	MYO7A_ENST00000409893.1_Missense_Mutation_p.I755F|MYO7A_ENST00000409619.2_Missense_Mutation_p.I744F|MYO7A_ENST00000458637.2_Missense_Mutation_p.I755F	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	755	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TCAGAAAGTCATCCGGGGATT	0.582																																					p.I755F													.	MYO7A-138	0			c.A2263T						.						89	95	93					11																	76888670		2112	4222	6334	SO:0001583	missense	4647	exon19			AAAGTCATCCGGG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.2263A>T	11.37:g.76888670A>T	ENSP00000386331:p.Ile755Phe	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	11	3	NM_001127179	0	0	1	2	1	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	A	17.00	3.277306	0.59758	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56	5.03	5.03	0.67393	.	0.072532	0.56097	D	0.000033	T	0.51109	0.1655	N	0.16656	0.425	0.49915	D	0.999833	B;B;B	0.31485	0.012;0.002;0.325	B;B;B	0.34301	0.025;0.014;0.179	T	0.49890	-0.8891	10	0.30078	T	0.28	.	5.4705	0.16668	0.7727:0.0:0.2273:0.0	.	755;755;755	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	F	755;755;755;744;754;754;631;754	ENSP00000386331:I755F;ENSP00000386689:I755F;ENSP00000392185:I755F;ENSP00000386635:I744F	ENSP00000345075:I631F	I	+	1	0	MYO7A	76566318	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.048000	0.64238	1.910000	0.55303	0.443000	0.29094	ATC	.		0.582	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76888670	A	T	76888670	3	4	4	1	0	0	0	0	1	0	0	0	10107	217	8	5	2333	5	MYO7A	11	76888670	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	25477155	76888670	58117846	46	265											
CCDC84	338657	broad.mit.edu;ucsc.edu	37	chr11	118869166	118869166	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcccgcaaggccatccgCgccgctcaggtggagcgcta	6	4	15	16	6	1	0	1	0	0	0	2	1	2	1	4	4	1	3	4	4	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr11:118869166C>T	ENST00000334418.1	+	2	203	c.147C>T	c.(145-147)cgC>cgT	p.R49R	RP11-110I1.12_ENST00000526453.1_lincRNA	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	49										breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		AGGCCATCCGCGCCGCTCAGG	0.662																																					p.R49R													.	CCDC84-91	0			c.C147T						.						22	23	23					11																	118869166		2199	4295	6494	SO:0001819	synonymous_variant	338657	exon2			CATCCGCGCCGCT	AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166			30460	protein-coding gene	gene with protein product							Standard	NM_198489		Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.147C>T	11.37:g.118869166C>T		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	22	5	NM_198489	0	0	2	7	5		Silent	SNP	ENST00000334418.1	37	CCDS8405.1																																																																																			.		0.662	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389315.1	NM_198489		T	118869166	C	T	118869166	2	4	4	1	0	0	0	0	0	0	0	1	2864	755	27	1		1	CCDC84	11	118869166	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08	41980496	118869166	16137350	47	266											
TULP3	7289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	3048537	3048537	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtgttcacactggattacaActacccactttgtgcagtac	10	12	7	12	1	1	0	1	0	0	0	1	1	1	1	1	1	5	3	1	1	4	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr12:3048537A>C	ENST00000448120.2	+	11	1307	c.1256A>C	c.(1255-1257)aAc>aCc	p.N419T	TULP3_ENST00000397132.2_Missense_Mutation_p.N419T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	419					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CTGGATTACAACTACCCACTT	0.443																																					p.N419T		.											.	TULP3-226	0			c.A1256C						.						313	257	276					12																	3048537		2203	4300	6503	SO:0001583	missense	7289	exon11			ATTACAACTACCC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"Intraflagellar transport homologs"	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1256A>C	12.37:g.3048537A>C	ENSP00000410051:p.Asn419Thr	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	165	48	NM_003324	0	0	32	61	29	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.02|12.02	1.811439|1.811439	0.32053|0.32053	.|.	.|.	ENSG00000078246|ENSG00000078246	ENST00000228245;ENST00000542730;ENST00000448120;ENST00000397132|ENST00000541678;ENST00000538704	D;D|.	0.85088|.	-1.94;-1.94|.	5.64|5.64	1.97|1.97	0.26223|0.26223	Tubby, C-terminal (3);|.	0.134805|.	0.64402|.	D|.	0.000003|.	T|T	0.52661|0.52661	0.1748|0.1748	L|L	0.42487|0.42487	1.325|1.325	0.47214|0.47214	D|D	0.999359|0.999359	B;B;B|.	0.34161|.	0.051;0.078;0.439|.	B;B;B|.	0.40982|.	0.14;0.345;0.332|.	T|T	0.36138|0.36138	-0.9760|-0.9760	9|5	.|.	.|.	.|.	1.337|1.337	8.4366|8.4366	0.32791|0.32791	0.7077:0.0:0.2923:0.0|0.7077:0.0:0.2923:0.0	.|.	243;419;419|.	B7Z1E7;O75386;F8WBZ9|.	.;TULP3_HUMAN;.|.	T|H	419;243;419;419|95;84	ENSP00000410051:N419T;ENSP00000380321:N419T|.	.|.	N|Q	+|+	2|3	0|2	TULP3|TULP3	2918798|2918798	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.640000|0.640000	0.38277|0.38277	1.203000|1.203000	0.32284|0.32284	0.089000|0.089000	0.17243|0.17243	-0.589000|-0.589000	0.04120|0.04120	AAC|CAA	.		0.443	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		C	3048537	A	C	3048537	3	2	4	1	0	0	0	0	1	0	0	0	16808	43	2	5	1298	5	TULP3	12	3048537	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08		3048537	130803358	48	267											
ACAD10	80724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112183962	112183962	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgataggagaaagccaaagcTgaaggactttggaacctttt	14	10	11	6	0	0	3	0	2	0	1	0	6	0	5	2	3	3	1	2	3	5	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr12:112183962T>C	ENST00000313698.4	+	14	2285	c.2130T>C	c.(2128-2130)gcT>gcC	p.A710A	ACAD10_ENST00000392636.2_Silent_p.A312A|ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000455480.2_Silent_p.A741A	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	710						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						AAGCCAAAGCTGAAGGACTTT	0.433																																					p.A741A		.											.	ACAD10-92	0			c.T2223C						.						88	88	88					12																	112183962		2203	4300	6503	SO:0001819	synonymous_variant	80724	exon15			CAAAGCTGAAGGA	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"acyl-Coenzyme A dehydrogenase family, member 10"			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.2130T>C	12.37:g.112183962T>C		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	101	34	NM_001136538	0	0	8	27	19	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Silent	SNP	ENST00000313698.4	37	CCDS31903.1																																																																																			.		0.433	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		C	112183962	T	C	112183962	2	2	4	1	0	0	0	0	0	0	0	1	108	1567	55	3		3	ACAD10	12	112183962	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08	109135425	112183962	21667933	49	268											
GAS6	2621	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	114523928	114523928	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaggtccagcagcctccggTtgacctccagtgtcatgcag	7	8	11	15	1	1	1	1	1	0	0	4	1	4	1	6	2	3	3	6	2	0	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr13:114523928T>C	ENST00000327773.6	-	15	2092	c.1946A>G	c.(1945-1947)aAc>aGc	p.N649S	GAS6_ENST00000357389.3_Missense_Mutation_p.N692S|GAS6_ENST00000450766.1_Missense_Mutation_p.N376S|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000418959.3_Missense_Mutation_p.N350S|GAS6_ENST00000355761.4_Missense_Mutation_p.N595S	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	692	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|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 tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				CAGCCTCCGGTTGACCTCCAG	0.662																																					p.N649S		.											.	GAS6-650	0			c.A1946G						.						51	45	47					13																	114523928		2202	4299	6501	SO:0001583	missense	2621	exon15			CTCCGGTTGACCT		CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"AXL stimulatory factor"	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.1946A>G	13.37:g.114523928T>C	ENSP00000331831:p.Asn649Ser	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	52	23	NM_000820	0	0	22	39	17	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Missense_Mutation	SNP	ENST00000327773.6	37	CCDS45072.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901729	0.33535	.	.	ENSG00000183087	ENST00000357389;ENST00000355761;ENST00000450766;ENST00000418959;ENST00000327773	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	4.72	3.54	0.40534	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.79924	0.4530	M	0.83223	2.63	0.44547	D	0.997504	P;B;B	0.41214	0.742;0.015;0.1	B;B;B	0.32864	0.154;0.026;0.01	T	0.78204	-0.2295	9	0.62326	D	0.03	-27.6441	8.071	0.30689	0.0:0.1832:0.0:0.8168	.	692;376;649	Q14393;B3KVL4;Q14393-2	GAS6_HUMAN;.;.	S	692;595;376;350;649	ENSP00000349962:N692S;ENSP00000348003:N595S;ENSP00000416498:N376S;ENSP00000400117:N350S;ENSP00000331831:N649S	ENSP00000331831:N649S	N	-	2	0	GAS6	113590015	0.993000	0.37304	0.858000	0.33744	0.120000	0.20174	2.505000	0.45424	0.664000	0.31047	0.379000	0.24179	AAC	.		0.662	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820		C	114523928	T	C	114523928	3	2	4	1	0	0	0	0	1	0	0	0	6269	1725	60	3	94	3	GAS6	13	114523928	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08		114523928	645950	50	269											
RBM23	55147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23374814	23374814	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagtgttcattatcaacccaCctgactgggctcttctctct	7	14	6	14	0	5	1	2	1	3	0	6	1	5	1	2	1	1	2	2	1	2	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr14:23374814C>G	ENST00000359890.3	-	6	651		c.e6+1		RBM23_ENST00000555209.1_Intron|RBM23_ENST00000556984.1_5'Flank|RBM23_ENST00000346528.5_Intron|RBM23_ENST00000399922.2_Splice_Site|RBM23_ENST00000542016.2_Splice_Site	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23						mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		TATCAACCCACCTGACTGGGC	0.378																																					.		.											.	RBM23-91	0			c.407+1G>C						.						90	80	83					14																	23374814		1844	4103	5947	SO:0001630	splice_region_variant	55147	exon6			AACCCACCTGACT	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"RNA binding motif (RRM) containing"	20155	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen recep- tors beta"		"RNA-binding region (RNP1, RRM) containing 4"	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.455+1G>C	14.37:g.23374814C>G		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	40	26	NM_018107	0	0	0	2	2	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Splice_Site	SNP	ENST00000359890.3	37	CCDS41921.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065110	0.55432	.	.	ENSG00000100461	ENST00000359890;ENST00000338980;ENST00000399922	.	.	.	4.88	3.99	0.46301	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2615	0.54652	0.0:0.9161:0.0:0.0839	.	.	.	.	.	-1	.	.	.	-	.	.	RBM23	22444654	1.000000	0.71417	0.998000	0.56505	0.851000	0.48451	3.163000	0.50763	1.422000	0.47177	0.655000	0.94253	.	.		0.378	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		Intron	G	23374814	C	G	23374814	5	3	4	1	0	0	0	0	0	0	1	0	13155	521	18	4	899	4	RBM23	14	23374814	Splice_Site	SNP	C	TCGA-A4-7583-01A-11D-2136-08		23374814	83974726	51	270											
MYEF2	50804	ucsc.edu	37	chr15	48446066	48446066	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gctgtccacccggaccaagtCccatcccaatgcctccaaga	10	6	7	18	1	0	1	0	0	0	1	4	2	4	2	7	1	1	1	7	1	3	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr15:48446066C>T	ENST00000324324.7	-	10	1289	c.1010G>A	c.(1009-1011)gGa>gAa	p.G337E	MYEF2_ENST00000267836.6_Missense_Mutation_p.G337E	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	337	Gly-rich.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		CGGACCAAGTCCCATCCCAAT	0.388																																					p.G337E													.	MYEF2-523	0			c.G1010A						.						71	66	67					15																	48446066		2198	4297	6495	SO:0001583	missense	50804	exon10			CCAAGTCCCATCC	AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"RNA binding motif (RRM) containing"	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.1010G>A	15.37:g.48446066C>T	ENSP00000316950:p.Gly337Glu	Somatic	20	0		WXS	Illumina HiSeq		35	4	NM_016132	0	0	11	11	0	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Missense_Mutation	SNP	ENST00000324324.7	37	CCDS32230.1	.	.	.	.	.	.	.	.	.	.	C	33	5.289700	0.95546	.	.	ENSG00000104177	ENST00000324324;ENST00000267836	T;T	0.28895	2.15;1.59	5.97	5.97	0.96955	.	0.093530	0.64402	D	0.000001	T	0.57975	0.2090	M	0.67700	2.07	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.97110	1.0;0.881	T	0.56866	-0.7908	10	0.87932	D	0	-11.7251	20.4324	0.99085	0.0:1.0:0.0:0.0	.	337;337	Q9P2K5-2;Q9P2K5	.;MYEF2_HUMAN	E	337	ENSP00000316950:G337E;ENSP00000267836:G337E	ENSP00000267836:G337E	G	-	2	0	MYEF2	46233358	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.395000	0.79876	2.833000	0.97629	0.585000	0.79938	GGA	.		0.388	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132		T	48446066	C	T	48446066	3	4	4	1	0	0	0	0	1	0	0	0	10049	855	30	2	824	2	MYEF2	15	48446066	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		48446066	54085326	52	271											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	18840922	18840922	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagggcttggttgggtaGccctatcaagagctgcctca	7	10	13	11	1	2	1	2	0	0	1	3	2	3	1	3	3	3	4	3	3	3	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr16:18840922G>T	ENST00000446231.2	-	54	9701	c.9289C>A	c.(9289-9291)Cta>Ata	p.L3097I	SMG1_ENST00000389467.3_Missense_Mutation_p.L3097I			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3097					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGGTTGGGTAGCCCTATCAAG	0.468																																					p.L3097I		.											.	SMG1-1160	0			c.C9289A						.						58	57	57					16																	18840922		1905	4128	6033	SO:0001583	missense	23049	exon54			TGGGTAGCCCTAT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9289C>A	16.37:g.18840922G>T	ENSP00000402515:p.Leu3097Ile	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	70	40	NM_015092	0	0	11	32	21	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.510741	0.44660	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01005	5.45;5.45	6.07	5.11	0.69529	.	0.000000	0.53938	D	0.000041	T	0.00875	0.0029	N	0.12182	0.205	0.41248	D	0.986699	B	0.13145	0.007	B	0.15484	0.013	T	0.67565	-0.5638	10	0.20519	T	0.43	.	16.7418	0.85461	0.0:0.0:0.8697:0.1303	.	3097	Q96Q15	SMG1_HUMAN	I	3097	ENSP00000402515:L3097I;ENSP00000374118:L3097I	ENSP00000374118:L3097I	L	-	1	2	SMG1	18748423	1.000000	0.71417	0.831000	0.32960	0.967000	0.64934	6.417000	0.73337	1.558000	0.49541	0.585000	0.79938	CTA	.		0.468	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18840922	G	T	18840922	3	4	4	1	0	0	0	0	1	0	0	0	14827	962	34	4	1736	4	SMG1	16	18840922	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		18840922	71513831	53	272											
FTSJD1	55783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	71317552	71317552	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttgataatttcttctctctCtctttgaataatgaaatgca	11	18	5	7	0	4	3	0	3	4	0	6	3	4	3	0	0	1	2	0	0	4	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr16:71317552C>T	ENST00000338099.5	-	3	2608	c.2272G>A	c.(2272-2274)Gag>Aag	p.E758K	CMTR2_ENST00000434935.2_Missense_Mutation_p.E758K			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	758					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TCTTCTCTCTCTCTTTGAATA	0.373																																					p.E758K		.											.	FTSJD1-91	0			c.G2272A						.						38	42	41					16																	71317552		2198	4300	6498	SO:0001583	missense	55783	exon3			CTCTCTCTCTTTG	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"adrift homolog (Drosophila)"		"FtsJ methyltransferase domain containing 1"	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.2272G>A	16.37:g.71317552C>T	ENSP00000337512:p.Glu758Lys	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	67	17	NM_018348	0	0	16	23	7	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507361	0.44558	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.15603	2.41;2.41	5.8	4.8	0.61643	.	0.225081	0.35677	N	0.003053	T	0.09555	0.0235	N	0.17082	0.46	0.32079	N	0.593443	B	0.21071	0.051	B	0.17979	0.02	T	0.07214	-1.0784	10	0.27785	T	0.31	-35.113	7.8477	0.29435	0.0:0.6486:0.2684:0.083	.	758	Q8IYT2	FTSJ1_HUMAN	K	758	ENSP00000337512:E758K;ENSP00000411148:E758K	ENSP00000337512:E758K	E	-	1	0	FTSJD1	69875053	0.991000	0.36638	1.000000	0.80357	0.802000	0.45316	1.495000	0.35627	2.741000	0.93983	0.585000	0.79938	GAG	.		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		T	71317552	C	T	71317552	3	4	4	1	0	0	0	0	1	0	0	0	6109	922	32	2	44	2	FTSJD1	16	71317552	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	52476630	71317552	19037201	54	273											
PLCG2	5336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81990321	81990321	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagcgaagaggaactttacTcctcctgtcgccagctgagg	10	8	12	11	2	0	3	0	1	0	2	3	5	2	4	3	2	4	1	3	2	3	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr16:81990321T>G	ENST00000359376.3	+	32	3806	c.3592T>G	c.(3592-3594)Tcc>Gcc	p.S1198A		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1198					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GGAACTTTACTCCTCCTGTCG	0.527																																					p.S1198A		.											.	PLCG2-892	0			c.T3592G						.						59	61	61					16																	81990321		1979	4160	6139	SO:0001583	missense	5336	exon32			CTTTACTCCTCCT		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3592T>G	16.37:g.81990321T>G	ENSP00000352336:p.Ser1198Ala	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	77	28	NM_002661	0	0	6	6	0	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	T	9.506	1.104525	0.20632	.	.	ENSG00000197943	ENST00000359376	T	0.65732	-0.17	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.53658	0.1810	L	0.52573	1.65	0.45205	D	0.998216	B	0.16166	0.016	B	0.12156	0.007	T	0.50224	-0.8853	10	0.10111	T	0.7	.	13.9529	0.64129	0.0:0.0:0.0:1.0	.	1198	P16885	PLCG2_HUMAN	A	1198	ENSP00000352336:S1198A	ENSP00000352336:S1198A	S	+	1	0	PLCG2	80547822	0.988000	0.35896	0.980000	0.43619	0.866000	0.49608	2.961000	0.49168	2.106000	0.64143	0.454000	0.30748	TCC	.		0.527	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			G	81990321	T	G	81990321	3	3	4	1	0	0	0	0	1	0	0	0	12062	1551	54	5	3714	5	PLCG2	16	81990321	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	10672769	81990321	8364432	55	274											
ZNHIT3	9326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34849806	34849806	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgattttctcaatagtgAtgaggaagaagacagagttt	14	12	11	4	0	1	6	1	3	1	3	2	7	1	7	0	1	1	2	0	1	4	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:34849806A>G	ENST00000225410.4	+	4	307	c.242A>G	c.(241-243)gAt>gGt	p.D81G	ZNHIT3_ENST00000592616.1_Missense_Mutation_p.D81G|ZNHIT3_ENST00000588253.1_5'UTR|ZNHIT3_ENST00000590858.1_Intron|ZNHIT3_ENST00000490126.2_5'UTR|RNA5SP439_ENST00000517103.1_RNA	NM_004773.2	NP_004764.1	Q15649	ZNHI3_HUMAN	zinc finger, HIT-type containing 3	81					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			lung(1)|pancreas(1)|prostate(1)	3		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0188)		CTCAATAGTGATGAGGAAGAA	0.373																																					p.D81G	Pancreas(89;112 2361 26810)	.											.	ZNHIT3-90	0			c.A242G						.						152	148	149					17																	34849806		2203	4300	6503	SO:0001583	missense	9326	exon4			ATAGTGATGAGGA	L40410	CCDS11312.1, CCDS62156.1	17q21.1	2014-04-10	2010-09-15	2005-09-08	ENSG00000108278	ENSG00000273611		"Zinc fingers, HIT-type"	12309	protein-coding gene	gene with protein product		604500	"thyroid hormone receptor interactor 3", "zinc finger, HIT type 3"	TRIP3		7776974	Standard	NM_004773		Approved		uc002hms.1	Q15649	OTTHUMG00000188436	ENST00000225410.4:c.242A>G	17.37:g.34849806A>G	ENSP00000225410:p.Asp81Gly	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	162	65	NM_004773	0	0	39	59	20	A8K493|K7EQP1|Q8WVJ3	Missense_Mutation	SNP	ENST00000225410.4	37	CCDS11312.1	.	.	.	.	.	.	.	.	.	.	A	11.65	1.700781	0.30142	.	.	ENSG00000108278	ENST00000225410	.	.	.	6.02	4.94	0.65067	.	0.084595	0.85682	D	0.000000	T	0.69584	0.3127	M	0.72353	2.195	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.68387	-0.5422	9	0.37606	T	0.19	-14.422	9.5969	0.39580	0.8443:0.0:0.0:0.1557	.	81	Q15649	ZNHI3_HUMAN	G	81	.	ENSP00000225410:D81G	D	+	2	0	ZNHIT3	31923919	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	5.963000	0.70372	1.084000	0.41184	-0.327000	0.08410	GAT	.		0.373	ZNHIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256697.1	NM_004773		G	34849806	A	G	34849806	3	3	4	1	0	0	0	0	1	0	0	0	18240	333	12	3	256	3	ZNHIT3	17	34849806	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08		34849806	46345404	56	275											
DLX3	1747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48072053	48072053	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcacctgggtcctgggctgGcagcggctgctcccgatacg	4	8	14	15	3	1	0	1	0	0	0	3	1	3	0	3	4	3	4	3	4	1	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:48072053G>C	ENST00000434704.2	-	1	535	c.310C>G	c.(310-312)Cca>Gca	p.P104A	DLX3_ENST00000512495.2_5'Flank|RP11-1094H24.3_ENST00000511867.1_lincRNA	NM_005220.2	NP_005211.1	O60479	DLX3_HUMAN	distal-less homeobox 3	104					blood vessel development (GO:0001568)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|placenta development (GO:0001890)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						TCCTGGGCTGGCAGCGGCTGC	0.622																																					p.P104A		.											.	DLX3-90	0			c.C310G						.						22	28	26					17																	48072053		2195	4295	6490	SO:0001583	missense	1747	exon1			GGGCTGGCAGCGG		CCDS11556.1	17q21.33	2011-06-20	2005-12-22			ENSG00000064195		"Homeoboxes / ANTP class : NKL subclass"	2916	protein-coding gene	gene with protein product		600525	"distal-less homeo box 3"			7613049	Standard	NM_005220		Approved		uc002ipy.3	O60479		ENST00000434704.2:c.310C>G	17.37:g.48072053G>C	ENSP00000389870:p.Pro104Ala	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	51	25	NM_005220	0	0	0	0	0	B3KQL6	Missense_Mutation	SNP	ENST00000434704.2	37	CCDS11556.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222006	0.39300	.	.	ENSG00000064195	ENST00000434704	D	0.91945	-2.94	5.01	5.01	0.66863	Homeodomain-like (1);	0.078892	0.53938	D	0.000057	D	0.86029	0.5835	N	0.21240	0.645	0.80722	D	1	B	0.11235	0.004	B	0.24006	0.05	T	0.80538	-0.1338	10	0.24483	T	0.36	-29.5674	13.6755	0.62451	0.0:0.0:1.0:0.0	.	104	O60479	DLX3_HUMAN	A	104	ENSP00000389870:P104A	ENSP00000389870:P104A	P	-	1	0	DLX3	45427052	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	4.079000	0.57613	2.617000	0.88574	0.491000	0.48974	CCA	.		0.622	DLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366307.1			C	48072053	G	C	48072053	3	2	4	1	0	0	0	0	1	0	0	0	4583	1203	42	4	565	4	DLX3	17	48072053	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	13222247	48072053	33123157	57	276											
TBCD	6904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80885835	80885835	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctgacacttctgctggctcgGagccagcctgagctgatcga	7	9	12	13	2	1	3	0	3	1	0	3	5	1	4	2	2	4	3	2	2	0	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:80885835G>C	ENST00000355528.4	+	30	2794	c.2664G>C	c.(2662-2664)cgG>cgC	p.R888R	TBCD_ENST00000539345.2_Silent_p.R888R	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	888					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			TGCTGGCTCGGAGCCAGCCTG	0.642																																					p.R888R		.											.	TBCD-22	0			c.G2664C						.						57	60	59					17																	80885835		2056	4211	6267	SO:0001819	synonymous_variant	6904	exon30			GGCTCGGAGCCAG	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.2664G>C	17.37:g.80885835G>C		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	97	33	NM_005993	0	0	48	79	31	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																			.		0.642	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		C	80885835	G	C	80885835	2	2	4	1	0	0	0	0	0	0	0	1	15665	1161	41	4		4	TBCD	17	80885835	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08	32813782	80885835	309375	58	277											
NPC1	4864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	21128030	21128030	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattatagtaattattgacaGggaaggtaatcacaagggca	16	10	10	5	0	1	1	1	1	0	0	1	2	1	2	0	3	0	3	0	3	7	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr18:21128030G>T	ENST00000269228.5	-	11	2251	c.1697C>A	c.(1696-1698)cCt>cAt	p.P566H	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Intron	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	566					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ATTATTGACAGGGAAGGTAAT	0.423																																					p.P566H		.											.	NPC1-92	0			c.C1697A						.						153	147	149					18																	21128030		2203	4300	6503	SO:0001583	missense	4864	exon11			TTGACAGGGAAGG	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1697C>A	18.37:g.21128030G>T	ENSP00000269228:p.Pro566His	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	184	72	NM_000271	0	0	2	9	7	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682504	0.88542	.	.	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.93811	-3.29	5.72	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.95906	0.8667	M	0.81942	2.565	0.80722	D	1	D	0.63880	0.993	P	0.58928	0.848	D	0.96104	0.9071	10	0.66056	D	0.02	-8.8197	14.813	0.70010	0.0692:0.0:0.9308:0.0	.	566	O15118	NPC1_HUMAN	H	566;411	ENSP00000269228:P566H	ENSP00000269228:P566H	P	-	2	0	NPC1	19382028	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.865000	0.87049	1.417000	0.47077	0.563000	0.77884	CCT	.		0.423	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		T	21128030	G	T	21128030	3	4	4	1	0	0	0	0	1	0	0	0	10596	1000	35	4	2199	4	NPC1	18	21128030	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		21128030	56949218	59	278											
RNF165	494470	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	44013351	44013353	+	In_Frame_Del	DEL	CCC	CCC	-																															gtcgctgaccccgctgcccaCcctgcagttccaggacgtca																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr18:44013351_44013353delCCC	ENST00000269439.7	+	2	311_313	c.260_262delCCC	c.(259-264)accctg>atg	p.87_88TL>M	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	87							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		CCGCTGCCCACCCTGCAGTTCCA	0.7																																					p.87_88del		.											.	RNF165-90	0			c.260_262del						.																																			SO:0001651	inframe_deletion	494470	exon2			.	BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"RING-type (C3HC4) zinc fingers"	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.260_262delCCC	18.37:g.44013351_44013353delCCC	ENSP00000269439:p.Thr87_Leu88delinsMet	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	49	15	NM_152470	0	0	0	0	0	B3KVD1	In_Frame_Del	DEL	ENST00000269439.7	37	CCDS32823.1																																																																																			.		0.7	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470		-	44013353	CCC	-	44013351	7	5	4	1	0	1	0	1	0	0	0	0	13488	507	18	0	266	0	RNF165	18	44013351	In_Frame_Del	DEL	CCC	TCGA-A4-7583-01A-11D-2136-08	22885321	44013351	34063897	60	279	4	2									
RNF165	494470	hgsc.bcm.edu;bcgsc.ca	37	chr18	44013357	44013357	+	Missense_Mutation	SNP	A	A	G																															gaccccgctgcccaccctgcAgttccaggacgtcacaggtc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr18:44013357A>G	ENST00000269439.7	+	2	317	c.266A>G	c.(265-267)cAg>cGg	p.Q89R	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	89							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		CCCACCCTGCAGTTCCAGGAC	0.697																																					p.Q89R		.											.	RNF165-90	0			c.A266G						.						35	34	34					18																	44013357		2203	4300	6503	SO:0001583	missense	494470	exon2			CCCTGCAGTTCCA	BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"RING-type (C3HC4) zinc fingers"	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.266A>G	18.37:g.44013357A>G	ENSP00000269439:p.Gln89Arg	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	58	16	NM_152470	0	0	0	0	0	B3KVD1	Missense_Mutation	SNP	ENST00000269439.7	37	CCDS32823.1	.	.	.	.	.	.	.	.	.	.	A	9.420	1.082835	0.20309	.	.	ENSG00000141622	ENST00000269439	T	0.18657	2.2	5.48	4.27	0.50696	.	0.146503	0.47093	D	0.000241	T	0.18676	0.0448	L	0.47716	1.5	0.80722	D	1	B	0.26445	0.149	B	0.28784	0.094	T	0.03717	-1.1010	10	0.12766	T	0.61	-5.9439	13.0518	0.58958	0.8124:0.1876:0.0:0.0	.	89	Q6ZSG1	RN165_HUMAN	R	89	ENSP00000269439:Q89R	ENSP00000269439:Q89R	Q	+	2	0	RNF165	42267355	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.579000	0.46059	2.086000	0.62901	0.455000	0.32223	CAG	.		0.697	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470		G	44013357	A	G	44013357	3	3	4	1	0	0	0	0	1	0	0	0	13488	188	7	3	272	3	RNF165	18	44013357	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	6	44013357	34063891	61	280	4	2									
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1005500	1005500	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggccaacctggctgccgTcatggtcggggacaagacct	8	6	13	14	3	1	1	1	0	0	1	2	2	1	2	4	5	2	1	4	5	2	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:1005500T>C	ENST00000234389.3	+	3	2019	c.2000T>C	c.(1999-2001)gTc>gCc	p.V667A	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	667					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTGGCTGCCGTCATGGTCGGG	0.687																																					p.V667A		.											.	GRIN3B-90	0			c.T2000C						.						39	39	39					19																	1005500		2203	4300	6503	SO:0001583	missense	116444	exon3			CTGCCGTCATGGT		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.2000T>C	19.37:g.1005500T>C	ENSP00000234389:p.Val667Ala	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_138690	0	0	62	62	0	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	.	.	.	.	.	.	.	.	.	.	T	17.64	3.439672	0.63067	.	.	ENSG00000116032	ENST00000234389	T	0.54675	0.56	4.36	4.36	0.52297	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.70448	0.3225	M	0.73962	2.25	0.43613	D	0.995987	D	0.89917	1.0	D	0.87578	0.998	T	0.74156	-0.3756	10	0.66056	D	0.02	.	12.4232	0.55532	0.0:0.0:0.0:1.0	.	667	O60391	NMD3B_HUMAN	A	667	ENSP00000234389:V667A	ENSP00000234389:V667A	V	+	2	0	GRIN3B	956500	1.000000	0.71417	1.000000	0.80357	0.475000	0.33008	6.137000	0.71710	1.635000	0.50512	0.254000	0.18369	GTC	.		0.687	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			C	1005500	T	C	1005500	3	2	4	1	0	0	0	0	1	0	0	0	6805	1667	58	3	2010	3	GRIN3B	19	1005500	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08		1005500	58123483	62	281											
GPX4	22904	ucsc.edu;bcgsc.ca	37	chr19	1106396	1106396	+	IGR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttggacaccgtctctccaCagttcctcatcgacaagaac	10	10	7	14	2	2	1	1	0	1	1	6	3	4	2	3	1	1	2	3	1	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:1106396C>G	ENST00000361757.3	-	0	4922				GPX4_ENST00000354171.8_Intron|GPX4_ENST00000589115.1_Intron	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)						bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTCTCTCCACAGTTCCTCAT	0.662																																					.													.	GPX4-90	0			.						.						54	62	60					19																	1106396		2043	4188	6231	SO:0001628	intergenic_variant	2879	.			TCTCCACAGTTCC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9			19.37:g.1106396C>G		Somatic	116	0		WXS	Illumina HiSeq		52	7	.	0	0	7	106	99	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			.		0.662	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		G	1106396	C	G	1106396	1	3	4	0	1	0	0	0	0	0	0	0	6763	478	17	4		4	GPX4	19	1106396	IGR	SNP	C	TCGA-A4-7583-01A-11D-2136-08	100896	1106396	58022587	63	282											
LDLR	3949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11216253	11216253	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggccccgactgcaaggAcaaatctgacgaggaaaact	13	6	12	10	2	1	1	0	1	1	0	1	5	1	3	2	4	2	1	2	4	4	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:11216253A>C	ENST00000558518.1	+	4	858	c.671A>C	c.(670-672)gAc>gCc	p.D224A	LDLR_ENST00000558013.1_Missense_Mutation_p.D224A|LDLR_ENST00000455727.2_Intron|LDLR_ENST00000545707.1_Intron|LDLR_ENST00000535915.1_Missense_Mutation_p.D183A|LDLR_ENST00000557933.1_Missense_Mutation_p.D224A	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	224	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.		D -> G (in Italy-2).|D -> N (in Portugal).|D -> V (in FH; Cologne patient). {ECO:0000269|PubMed:7649546}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	GACTGCAAGGACAAATCTGAC	0.647																																					p.D224A	GBM(18;201 575 7820 21545)	.											.	LDLR-94	1	Unknown(1)	lung(1)	c.A671C	GRCh37	CM920421|CM950756|CM994425	LDLR	M		.						31	36	34					19																	11216253		2202	4299	6501	SO:0001583	missense	3949	exon4			GCAAGGACAAATC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.671A>C	19.37:g.11216253A>C	ENSP00000454071:p.Asp224Ala	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	66	28	NM_001195798	0	0	0	0	0	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301164	0.81136	.	.	ENSG00000130164	ENST00000252444;ENST00000535915	D;D	0.99220	-5.58;-4.44	5.6	5.6	0.85130	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000010	D	0.99677	0.9879	H	0.98407	4.225	0.80722	D	1	P;D;D;D	0.71674	0.917;0.998;0.996;0.998	D;D;D;D	0.83275	0.92;0.996;0.99;0.99	D	0.97323	0.9945	10	0.87932	D	0	.	14.7566	0.69569	1.0:0.0:0.0:0.0	.	103;183;236;224	B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;LDLR_HUMAN	A	224;183	ENSP00000252444:D224A;ENSP00000440520:D183A	ENSP00000252444:D224A	D	+	2	0	LDLR	11077253	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	9.228000	0.95250	2.139000	0.66308	0.482000	0.46254	GAC	.		0.647	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			C	11216253	A	C	11216253	3	2	4	1	0	0	0	0	1	0	0	0	8725	275	10	5	685	5	LDLR	19	11216253	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	10109857	11216253	47912730	64	283											
AP1M1	8907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	16339616	16339616	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagcggcggtcaacagccaaCaacgtggagatccacattcc	13	5	10	13	3	1	1	1	0	0	1	3	2	3	1	3	3	5	0	3	3	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:16339616C>G	ENST00000291439.3	+	9	1373	c.924C>G	c.(922-924)aaC>aaG	p.N308K	AP1M1_ENST00000541844.1_Missense_Mutation_p.N236K|AP1M1_ENST00000444449.2_Missense_Mutation_p.N320K|AP1M1_ENST00000590756.1_Missense_Mutation_p.N236K|AP1M1_ENST00000429941.2_Intron	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	308	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						CAACAGCCAACAACGTGGAGA	0.617																																					p.N320K		.											.	AP1M1-156	0			c.C960G						.						173	116	135					19																	16339616		2203	4300	6503	SO:0001583	missense	8907	exon10			AGCCAACAACGTG		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.924C>G	19.37:g.16339616C>G	ENSP00000291439:p.Asn308Lys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	56	19	NM_001130524	0	0	76	135	59	Q4TTY5	Missense_Mutation	SNP	ENST00000291439.3	37	CCDS12342.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.429106	0.83667	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844	T;T;T	0.18502	2.21;2.21;2.21	3.64	3.64	0.41730	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.40347	0.1113	M	0.70787	2.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.39901	-0.9591	10	0.62326	D	0.03	-49.532	14.4911	0.67651	0.0:1.0:0.0:0.0	.	320;308	Q4TTY5;Q9BXS5	.;AP1M1_HUMAN	K	320;308;236	ENSP00000388996:N320K;ENSP00000291439:N308K;ENSP00000445682:N236K	ENSP00000291439:N308K	N	+	3	2	AP1M1	16200616	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.764000	0.55264	1.871000	0.54225	0.561000	0.74099	AAC	.		0.617	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		G	16339616	C	G	16339616	3	3	4	1	0	0	0	0	1	0	0	0	734	477	17	4	998	4	AP1M1	19	16339616	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	5123363	16339616	42789367	65	284											
MAST3	23031	broad.mit.edu;bcgsc.ca	37	chr19	18254602	18254603	+	Frame_Shift_Ins	INS	-	-	CT																															tggacatcctctggatcctcINSctgtcagtcatcttcgtccc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:18254602_18254603insCT	ENST00000262811.6	+	21	2282_2283	c.2282_2283insCT	c.(2281-2286)tcctgtfs	p.C762fs	AC007192.6_ENST00000600364.2_RNA	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	762							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						TCTGGATCCTCCTGTCAGTCAT	0.599																																					p.S761fs													.	MAST3-502	0			c.2282_2283insCT						.																																			SO:0001589	frameshift_variant	23031	exon21			GATCCTCCTGTCA	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.2283_2284dupCT	19.37:g.18254603_18254604dupCT	ENSP00000262811:p.Cys762fs	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	23	9	NM_015016	0	0	0	0	0	Q7LDZ8|Q9UPI0	Frame_Shift_Ins	INS	ENST00000262811.6	37	CCDS46014.1																																																																																			.		0.599	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		CT	18254603	-	CT	18254602	7	5	4	1	0	1	1	0	0	0	0	0	9351	855	30	0	2364	0	MAST3	19	18254602	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	1914986	18254602	40874381	66	285											
ZNF99	7652	broad.mit.edu	37	chr19	22941129	22941129	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttccagtatgaattatctTatgttttctaagggctgaga	10	17	8	6	0	2	2	0	2	2	1	3	3	3	2	1	1	0	3	1	1	5	7			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:22941129T>G	ENST00000596209.1	-	4	1672	c.1582A>C	c.(1582-1584)Aag>Cag	p.K528Q	ZNF99_ENST00000397104.3_Missense_Mutation_p.K437Q	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	528					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TGAATTATCTTATGTTTTCTA	0.333																																					p.K528Q													.	ZNF99-24	0			c.A1582C						.																																			SO:0001583	missense	7652	exon4			TTATCTTATGTTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1582A>C	19.37:g.22941129T>G	ENSP00000472969:p.Lys528Gln	Somatic	48	1		WXS	Illumina HiSeq	Phase_I	77	3	NM_001080409	0	0	0	0	0	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	0.033	-1.323055	0.01320	.	.	ENSG00000213973	ENST00000397104	T	0.18016	2.24	1.29	-1.59	0.08453	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15262	0.0368	N	0.20610	0.595	0.09310	N	1	D	0.56035	0.974	P	0.62184	0.899	T	0.07195	-1.0785	9	0.02654	T	1	.	7.2218	0.25992	0.0:0.0:0.6996:0.3004	.	437	A8MXY4	ZNF99_HUMAN	Q	437	ENSP00000380293:K437Q	ENSP00000380293:K437Q	K	-	1	0	ZNF99	22732969	0.000000	0.05858	0.001000	0.08648	0.045000	0.14185	-1.164000	0.03135	-0.293000	0.08986	0.329000	0.21502	AAG	.		0.333	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		G	22941129	T	G	22941129	3	3	4	1	0	0	0	0	1	0	0	0	18236	1763	61	5	1815	5	ZNF99	19	22941129	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	4686527	22941129	36187854	67	286			1	5		2	2	26	N	T_C	6.864184e-05
ZNF99	7652	hgsc.bcm.edu;broad.mit.edu	37	chr19	22941154	22941154	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctaagggctgagaaatgCttaaaagctttgccacattc	12	13	8	8	0	1	1	0	1	1	1	2	2	1	1	1	1	3	3	1	1	4	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:22941154C>G	ENST00000596209.1	-	4	1647	c.1557G>C	c.(1555-1557)aaG>aaC	p.K519N	ZNF99_ENST00000397104.3_Missense_Mutation_p.K428N	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	519					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CTGAGAAATGCTTAAAAGCTT	0.353																																					p.K519N		.											.	ZNF99-24	0			c.G1557C						.						36	37	37					19																	22941154		2012	4190	6202	SO:0001583	missense	7652	exon4			GAAATGCTTAAAA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1557G>C	19.37:g.22941154C>G	ENSP00000472969:p.Lys519Asn	Somatic	44	1		WXS	Illumina HiSeq	Phase_I	63	4	NM_001080409	0	0	0	0	0	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	0.006	-2.118307	0.00349	.	.	ENSG00000213973	ENST00000397104	T	0.07567	3.18	1.16	-2.32	0.06745	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04634	0.0126	L	0.33753	1.03	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46721	-0.9171	9	0.14252	T	0.57	.	1.8516	0.03170	0.1596:0.3714:0.3123:0.1568	.	428	A8MXY4	ZNF99_HUMAN	N	428	ENSP00000380293:K428N	ENSP00000380293:K428N	K	-	3	2	ZNF99	22732994	0.000000	0.05858	0.002000	0.10522	0.184000	0.23303	-7.212000	0.00041	-1.397000	0.02068	-1.031000	0.02408	AAG	.		0.353	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		G	22941154	C	G	22941154	3	3	4	1	0	0	0	0	1	0	0	0	18236	796	28	4	1840	4	ZNF99	19	22941154	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	25	22941154	36187829	68	287			1	5		2	2	26	N	T_C	6.864184e-05
SAMD4B	55095	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	39868382	39868391	+	Frame_Shift_Del	DEL	TCCCACTGAT	TCCCACTGAT	-																															ccacctccaccagctccagcTcccactgatggcagtgagcc																								rs149585231		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	TCCCACTGAT	TCCCACTGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:39868382_39868391delTCCCACTGAT	ENST00000314471.6	+	10	2397_2406	c.1362_1371delTCCCACTGAT	c.(1360-1371)gctcccactgatfs	p.APTD454fs	SAMD4B_ENST00000596368.1_Intron|SAMD4B_ENST00000598913.1_Frame_Shift_Del_p.APTD454fs	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	454					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CAGCTCCAGCTCCCACTGATGGCAGTGAGC	0.648																																					p.454_457del		.											.	SAMD4B-90	0			c.1362_1371del						.																																			SO:0001589	frameshift_variant	55095	exon10			.		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"Sterile alpha motif (SAM) domain containing"	25492	protein-coding gene	gene with protein product	"smaug homolog B (Drosophila)"					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.1362_1371delTCCCACTGAT	19.37:g.39868382_39868391delTCCCACTGAT	ENSP00000317224:p.Ala454fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	61	10	NM_018028	0	0	0	0	0	A5Z0M6|Q6P194	Frame_Shift_Del	DEL	ENST00000314471.6	37	CCDS33020.1																																																																																			.		0.648	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		-	39868391	TCCCACTGAT	-	39868382	7	5	4	1	0	1	0	1	0	0	0	0	13854	1538	54	0	1384	0	SAMD4B	19	39868382	Frame_Shift_Del	DEL	TCCCACTGAT	TCGA-A4-7583-01A-11D-2136-08	16927228	39868382	19260601	69	288											
IRF2BP1	26145	ucsc.edu	37	chr19	46388582	46388582	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccaagcaaggcccttcGcgccccctcagccacggcct	7	4	11	19	3	1	0	1	0	0	0	2	1	1	1	6	3	3	1	6	3	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:46388582G>A	ENST00000302165.3	-	1	794	c.451C>T	c.(451-453)Cga>Tga	p.R151*		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		AAGGCCCTTCGCGCCCCCTCA	0.721																																					p.R151X													.	IRF2BP1-90	0			c.C451T						.						16	17	16					19																	46388582		2190	4269	6459	SO:0001587	stop_gained	26145	exon1			CCCTTCGCGCCCC	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.451C>T	19.37:g.46388582G>A	ENSP00000307265:p.Arg151*	Somatic	36	0		WXS	Illumina HiSeq		23	4	NM_015649	0	0	15	15	0	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Nonsense_Mutation	SNP	ENST00000302165.3	37	CCDS12678.1	.	.	.	.	.	.	.	.	.	.	G	38	6.745799	0.97809	.	.	ENSG00000170604	ENST00000302165	.	.	.	4.47	4.47	0.54385	.	0.096786	0.39544	U	0.001322	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.6658	0.68907	0.0:0.0:1.0:0.0	.	.	.	.	X	151	.	ENSP00000307265:R151X	R	-	1	2	IRF2BP1	51080422	0.088000	0.21588	0.928000	0.36995	0.960000	0.62799	1.596000	0.36718	2.306000	0.77630	0.462000	0.41574	CGA	.		0.721	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		A	46388582	G	A	46388582	4	1	4	1	0	0	0	0	0	1	0	0	7850	1095	38	1	1307	1	IRF2BP1	19	46388582	Nonsense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	6520200	46388582	12740401	70	289											
NOVA2	4858	broad.mit.edu;bcgsc.ca	37	chr19	46443735	46443735	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagttggtgttgtagccgtAacttgccagcgtgttaagcg	7	12	15	7	3	0	0	0	0	0	0	0	1	0	1	2	2	5	5	2	2	3	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:46443735A>G	ENST00000263257.5	-	4	1059	c.865T>C	c.(865-867)Tac>Cac	p.Y289H		NM_002516.2	NP_002507.1	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	289	Ala-rich.				regulation of RNA metabolic process (GO:0051252)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(5)|lung(13)	21		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)		TTGTAGCCGTAACTTGCCAGC	0.731																																					p.Y289H													.	NOVA2-226	0			c.T865C						.						15	11	13					19																	46443735		2152	4236	6388	SO:0001583	missense	4858	exon4			AGCCGTAACTTGC	U70477	CCDS12679.1	19q13.3	2008-07-17				ENSG00000104967			7887	protein-coding gene	gene with protein product	"neuro-oncological ventral antigen 3"	601991		NOVA3		9344654, 10368286	Standard	NM_002516		Approved	ANOVA	uc002pdv.2	Q9UNW9		ENST00000263257.5:c.865T>C	19.37:g.46443735A>G	ENSP00000263257:p.Tyr289His	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	24	4	NM_002516	0	0	0	0	0	O43267|Q9UEA1	Missense_Mutation	SNP	ENST00000263257.5	37	CCDS12679.1	.	.	.	.	.	.	.	.	.	.	A	14.47	2.545341	0.45280	.	.	ENSG00000104967	ENST00000263257	T	0.47177	0.85	3.3	3.3	0.37823	.	0.000000	0.64402	D	0.000001	T	0.58652	0.2137	M	0.73217	2.22	0.46317	D	0.998985	D	0.65815	0.995	P	0.57911	0.829	T	0.60840	-0.7183	10	0.51188	T	0.08	-6.8358	9.7035	0.40200	1.0:0.0:0.0:0.0	.	289	Q9UNW9	NOVA2_HUMAN	H	289	ENSP00000263257:Y289H	ENSP00000263257:Y289H	Y	-	1	0	NOVA2	51135575	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	8.193000	0.89719	1.399000	0.46721	0.392000	0.25879	TAC	.		0.731	NOVA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437210.2	NM_002516		G	46443735	A	G	46443735	3	3	4	1	0	0	0	0	1	0	0	0	10581	362	13	3	617	3	NOVA2	19	46443735	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	55153	46443735	12685248	71	290											
UBOX5	22888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	3102965	3102965	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctccttgtctgggacagatGgctcagctgggcccagggtc	5	9	14	13	0	2	1	1	0	1	1	4	2	3	2	3	4	1	2	3	4	0	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:3102965G>A	ENST00000217173.2	-	3	791	c.320C>T	c.(319-321)cCa>cTa	p.P107L	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.P107L	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						TGGGACAGATGGCTCAGCTGG	0.567																																					p.P107L		.											.	UBOX5-227	0			c.C320T						.						59	59	59					20																	3102965		2203	4300	6503	SO:0001583	missense	22888	exon3			ACAGATGGCTCAG	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.320C>T	20.37:g.3102965G>A	ENSP00000217173:p.Pro107Leu	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	73	23	NM_014948	0	0	6	8	2		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	G	9.568	1.120384	0.20877	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.29397	1.57;1.57	4.8	2.74	0.32292	.	0.705996	0.12704	U	0.446080	T	0.22859	0.0552	L	0.44542	1.39	0.29757	N	0.835874	B;B;B	0.13145	0.004;0.003;0.007	B;B;B	0.08055	0.003;0.002;0.003	T	0.13176	-1.0519	10	0.38643	T	0.18	-0.4251	5.1325	0.14917	0.1731:0.0:0.5509:0.276	.	107;107;107	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	L	107	ENSP00000217173:P107L;ENSP00000311726:P107L	ENSP00000217173:P107L	P	-	2	0	UBOX5	3050965	0.241000	0.23857	0.305000	0.25099	0.964000	0.63967	0.662000	0.25038	1.232000	0.43678	0.563000	0.77884	CCA	.		0.567	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3102965	G	A	3102965	3	1	4	1	0	0	0	0	1	0	0	0	16927	1348	47	2	1317	2	UBOX5	20	3102965	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		3102965	59922555	72	291											
HAO1	54363	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	7886831	7886832	+	In_Frame_Ins	INS	-	-	TTT																															ccctttgcaacaattggcaaINStgatgtcagtcttctcagcc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:7886831_7886832insTTT	ENST00000378789.3	-	4	741_742	c.690_691insAAA	c.(688-693)tcattg>tcaAAAttg	p.230_231SL>SKL		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	230	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ACAATTGGCAATGATGTCAGTC	0.386																																					p.L231delinsKL		.											.	HAO1-93	0			c.691_692insAAA						.																																			SO:0001652	inframe_insertion	54363	exon4			.	AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.690_691insAAA	20.37:g.7886831_7886832insTTT	ENSP00000368066:p.Ser230_Leu231insLys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	183	51	NM_017545	0	0	0	0	0	Q14CQ0|Q9UPZ0|Q9Y3I7	In_Frame_Ins	INS	ENST00000378789.3	37	CCDS13100.1																																																																																			.		0.386	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			TTT	7886832	-	TTT	7886831	7	5	4	1	0	1	1	0	0	0	0	0	6972	98	4	0	441	0	HAO1	20	7886831	In_Frame_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	4783866	7886831	55138689	73	292											
BPIL1	80341	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	31604905	31604906	+	Frame_Shift_Ins	INS	-	-	T																															tgtccacctgggcaccttaaINSttggtaagatctgggagcca																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:31604905_31604906insT	ENST00000170150.3	+	7	769_770	c.574_575insT	c.(574-576)attfs	p.I192fs		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	192						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										GGGCACCTTAATTGGTAAGATC	0.619																																					p.I192fs		.											.	.	0			c.574_575insT						.																																			SO:0001589	frameshift_variant	80341	exon7			.	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"BPI fold containing"	16177	protein-coding gene	gene with protein product		614108	"bactericidal/permeability-increasing protein-like 1"	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.576dupT	20.37:g.31604907_31604907dupT	ENSP00000170150:p.Ile192fs	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	111	35	NM_025227	0	0	0	0	0	Q6UWN3|Q6ZME0|Q8NFQ7	Frame_Shift_Ins	INS	ENST00000170150.3	37	CCDS13210.1																																																																																			.		0.619	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		T	31604906	-	T	31604905	7	5	4	1	0	1	1	0	0	0	0	0	1494	101	4	0	596	0	BPIL1	20	31604905	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	23718074	31604905	31420615	74	293											
NFATC2	4773	ucsc.edu	37	chr20	50049132	50049132	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggggatgagagccccgtgcGgaactgctggcagggagcca	9	4	18	10	2	0	1	0	1	0	1	0	5	0	4	3	5	5	2	3	5	1	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:50049132G>A	ENST00000396009.3	-	9	2413	c.2194C>T	c.(2194-2196)Cgc>Tgc	p.R732C	NFATC2_ENST00000609507.1_Missense_Mutation_p.R513C|NFATC2_ENST00000610033.1_Missense_Mutation_p.R513C|NFATC2_ENST00000371564.3_Missense_Mutation_p.R732C|NFATC2_ENST00000414705.1_Missense_Mutation_p.R712C|NFATC2_ENST00000609943.1_Missense_Mutation_p.R712C	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	732					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					AGCCCCGTGCGGAACTGCTGG	0.682																																					p.R732C													.	NFATC2-92	0			c.C2194T						.						23	28	26					20																	50049132		2203	4299	6502	SO:0001583	missense	4773	exon9			CCGTGCGGAACTG	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2194C>T	20.37:g.50049132G>A	ENSP00000379330:p.Arg732Cys	Somatic	57	0		WXS	Illumina HiSeq		35	4	NM_012340	0	0	2	2	0	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.443944	0.63067	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.15487	2.42;2.42;2.43	5.45	5.45	0.79879	.	0.112084	0.64402	D	0.000013	T	0.38026	0.1025	L	0.48642	1.525	0.51233	D	0.999917	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	P;D;D;P	0.79784	0.891;0.993;0.95;0.899	T	0.05649	-1.0872	10	0.62326	D	0.03	-25.2951	19.296	0.94122	0.0:0.0:1.0:0.0	.	712;712;732;732	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	C	732;732;712	ENSP00000360619:R732C;ENSP00000379330:R732C;ENSP00000396471:R712C	ENSP00000360619:R732C	R	-	1	0	NFATC2	49482539	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	5.521000	0.67086	2.563000	0.86464	0.650000	0.86243	CGC	.		0.682	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		A	50049132	G	A	50049132	3	1	4	1	0	0	0	0	1	0	0	0	10388	1116	39	1	639	1	NFATC2	20	50049132	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	18444227	50049132	12976388	75	294											
BCAS1	8537	bcgsc.ca	37	chr20	52645037	52645037	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttggctgtcacctggcaccTtttcctgtcccttgtccagc	3	14	9	15	0	1	0	1	0	0	0	4	0	4	0	5	2	1	3	5	2	0	4	rs143209009		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:52645037T>C	ENST00000395961.3	-	4	783	c.617A>G	c.(616-618)aAg>aGg	p.K206R	BCAS1_ENST00000411563.1_Missense_Mutation_p.K109R|BCAS1_ENST00000371440.3_Missense_Mutation_p.K206R|BCAS1_ENST00000371435.2_Missense_Mutation_p.K206R	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	206						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			ACCTGGCACCTTTTCCTGTCC	0.552																																					p.K206R													.	BCAS1-652	0			c.A617G						.	T	ARG/LYS	0,4406		0,0,2203	227	209	215		617	2.8	0	20	dbSNP_134	215	1,8599		0,1,4299	no	missense	BCAS1	NM_003657.2	26	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	206/585	52645037	1,13005	2203	4300	6503	SO:0001583	missense	8537	exon4			GGCACCTTTTCCT	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.617A>G	20.37:g.52645037T>C	ENSP00000379290:p.Lys206Arg	Somatic	239	0		WXS	Illumina HiSeq	Phase_1	231	6	NM_003657	0	0	0	0	0	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.562939	0.27915	0.0	1.16E-4	ENSG00000064787	ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000411563	T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4	5.11	2.78	0.32641	.	0.711180	0.13859	N	0.357813	T	0.10121	0.0248	L	0.47716	1.5	0.09310	N	1	D;B;B;B;B;B	0.58268	0.982;0.386;0.386;0.119;0.342;0.342	P;B;B;B;B;B	0.52758	0.708;0.178;0.178;0.079;0.131;0.131	T	0.22347	-1.0219	10	0.37606	T	0.19	-1.5339	5.4467	0.16539	0.0:0.0934:0.1763:0.7303	.	109;206;206;206;206;206	B4E2C4;B2RCQ5;O75363-2;G3XAF7;A0AVG7;O75363	.;.;.;.;.;BCAS1_HUMAN	R	68;206;84;206;206;109	ENSP00000396361:K68R;ENSP00000360495:K206R;ENSP00000379290:K206R;ENSP00000360490:K206R;ENSP00000397442:K109R	ENSP00000360490:K206R	K	-	2	0	BCAS1	52078444	0.004000	0.15560	0.015000	0.15790	0.008000	0.06430	1.170000	0.31883	0.344000	0.23847	0.460000	0.39030	AAG	T|1.000;C|0.000		0.552	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		C	52645037	T	C	52645037	3	2	4	1	0	0	0	0	1	0	0	0	1351	1609	56	3	1173	3	BCAS1	20	52645037	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	2595905	52645037	10380483	76	295											
TAF4	6874	hgsc.bcm.edu	37	chr20	60585136	60585136	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtggtggtcgcccctggtAccgtgcgctgaggagtcccc	5	8	15	13	3	0	1	0	1	0	0	2	2	1	2	5	4	2	2	5	4	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:60585136A>G	ENST00000252996.4	-	4	1726	c.1727T>C	c.(1726-1728)gTa>gCa	p.V576A	TAF4_ENST00000609045.1_5'UTR	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	576					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CGCCCCTGGTACCGTGCGCTG	0.617																																					p.V576A		.											.	TAF4-93	0			c.T1727C						.						97	77	84					20																	60585136		2203	4300	6503	SO:0001583	missense	6874	exon4			CCTGGTACCGTGC	Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1727T>C	20.37:g.60585136A>G	ENSP00000252996:p.Val576Ala	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	49	3	NM_003185	1	0	11	12	0	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	.	.	.	.	.	.	.	.	.	.	A	8.390	0.839537	0.16891	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.23348	1.92;1.91	4.8	3.65	0.41850	.	0.449437	0.23513	N	0.047377	T	0.15782	0.0380	L	0.44542	1.39	0.43471	D	0.995686	P	0.34699	0.464	B	0.28709	0.093	T	0.03739	-1.1008	10	0.02654	T	1	-10.3553	10.7964	0.46464	0.8585:0.0:0.0:0.1414	.	576	O00268	TAF4_HUMAN	A	576;440	ENSP00000252996:V576A;ENSP00000399091:V440A	ENSP00000252996:V576A	V	-	2	0	TAF4	60018531	1.000000	0.71417	0.628000	0.29241	0.112000	0.19704	6.400000	0.73252	1.805000	0.52779	0.260000	0.18958	GTA	.		0.617	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		G	60585136	A	G	60585136	3	3	4	1	0	0	0	0	1	0	0	0	15558	391	14	3	1578	3	TAF4	20	60585136	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	7940099	60585136	2440384	77	296											
SETD4	54093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	37418117	37418117	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaactcctgcacgtgggcTctctgctcttcagcctttgc	6	12	9	14	1	3	1	1	0	2	1	5	1	4	1	2	1	5	3	2	1	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr21:37418117T>C	ENST00000399215.1	-	5	1861	c.489A>G	c.(487-489)agA>agG	p.R163R	SETD4_ENST00000399212.1_Silent_p.R139R|SETD4_ENST00000399201.1_Silent_p.R139R|SETD4_ENST00000332131.4_Silent_p.R163R|SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000399205.1_Silent_p.R139R|SETD4_ENST00000399208.2_Silent_p.R163R|SETD4_ENST00000399207.1_Silent_p.R163R			Q9NVD3	SETD4_HUMAN	SET domain containing 4	163	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GCACGTGGGCTCTCTGCTCTT	0.502																																					p.R163R		.											.	SETD4-154	0			c.A489G						.						99	112	107					21																	37418117		2203	4300	6503	SO:0001819	synonymous_variant	54093	exon6			GTGGGCTCTCTGC	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.489A>G	21.37:g.37418117T>C		Somatic	200	0		WXS	Illumina HiSeq	Phase_I	204	90	NM_001007259	0	0	14	24	10	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Silent	SNP	ENST00000399215.1	37	CCDS13640.1																																																																																			.		0.502	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		C	37418117	T	C	37418117	2	2	4	1	0	0	0	0	0	0	0	1	14165	1548	54	3		3	SETD4	21	37418117	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08		37418117	10711778	78	297											
SIK1	150094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	44841223	44841223	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggacagaggctctcctgacTtgtagaaattcccaaatcca	12	10	8	11	0	1	3	0	1	1	2	4	4	3	4	3	2	0	2	3	2	3	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr21:44841223T>C	ENST00000270162.6	-	6	656	c.524A>G	c.(523-525)aAg>aGg	p.K175R		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CTCTCCTGACTTGTAGAAATT	0.567																																					p.K175R		.											.	SIK1-346	0			c.A524G						.						51	61	58					21																	44841223		2203	4299	6502	SO:0001583	missense	150094	exon6			CCTGACTTGTAGA	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"myocardial SNF1-like kinase"	605705	"SNF1-like kinase"	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.524A>G	21.37:g.44841223T>C	ENSP00000270162:p.Lys175Arg	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	119	46	NM_173354	0	0	4	4	0	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379901	0.61845	.	.	ENSG00000142178	ENST00000270162	T	0.66280	-0.2	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.208643	0.49916	D	0.000136	T	0.45677	0.1354	N	0.12182	0.205	0.45150	D	0.998166	B	0.24721	0.11	B	0.25759	0.063	T	0.40664	-0.9551	10	0.37606	T	0.19	.	14.8612	0.70382	0.0:0.0:0.0:1.0	.	175	P57059	SIK1_HUMAN	R	175	ENSP00000270162:K175R	ENSP00000270162:K175R	K	-	2	0	SIK1	43665651	1.000000	0.71417	0.886000	0.34754	0.944000	0.59088	5.865000	0.69583	1.909000	0.55274	0.459000	0.35465	AAG	.		0.567	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		C	44841223	T	C	44841223	3	2	4	1	0	0	0	0	1	0	0	0	14349	1609	56	3	1863	3	SIK1	21	44841223	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	7423106	44841223	3288672	79	298											
COL18A1	80781	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	46911142	46911143	+	Missense_Mutation	DNP	GA	GA	AT																															gtggcctcctcttccagggaGatccagggaaggacggagtc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr21:46911142_46911143GA>AT	ENST00000359759.4	+	21	3337_3338	c.3316_3317GA>AT	c.(3316-3318)GAt>ATt	p.D1106I	COL18A1_ENST00000400337.2_Missense_Mutation_p.D691I|COL18A1_ENST00000355480.5_Missense_Mutation_p.D871I			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1106	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTTCCAGGGAGATCCAGGGAAG	0.698																																					p.D1106I		.											.	COL18A1	0			c.A2612T						.																																			SO:0001583	missense	80781	exon21			AGGGAGATCCAGG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	Exception_encountered	21.37:g.46911142_46911143delinsAT	ENSP00000352798:p.Asp1106Ile	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	51	18		0	0	0	0	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	DNP	ENST00000359759.4	37																																																																																				.		0.698	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			AT	46911143	GA	AT	46911142	3	1	4	1	0	0	0	0	1	0	0	0	3681	942	33	2	3512	2	COL18A1	21	46911142	Missense_Mutation	DNP	GA	TCGA-A4-7583-01A-11D-2136-08	2069919	46911142	1218753	80	299											
PHF21B	112885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	45312440	45312440	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggccttctggaatgttgggGgctgcttgggtggccggtcc	2	12	18	9	1	1	0	0	0	1	0	2	1	2	1	3	7	1	3	3	7	1	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr22:45312440G>T	ENST00000313237.5	-	4	434	c.284C>A	c.(283-285)cCc>cAc	p.P95H	PHF21B_ENST00000403565.1_5'UTR|PHF21B_ENST00000404079.2_Missense_Mutation_p.P83H|PHF21B_ENST00000396103.3_Missense_Mutation_p.P95H|PHF21B_ENST00000447824.3_Missense_Mutation_p.P83H	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	95							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		GAATGTTGGGGGCTGCTTGGG	0.647																																					p.P95H		.											.	PHF21B-93	0			c.C284A						.						43	48	46					22																	45312440		2202	4300	6502	SO:0001583	missense	112885	exon4			GTTGGGGGCTGCT	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"Zinc fingers, PHD-type"	25161	protein-coding gene	gene with protein product			"PHD finger protein 4"	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.284C>A	22.37:g.45312440G>T	ENSP00000324403:p.Pro95His	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	85	30	NM_138415	0	0	0	0	0	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	37	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671013	0.88348	.	.	ENSG00000056487	ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000420689	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.06	5.06	0.68205	.	0.076937	0.51477	D	0.000089	T	0.47619	0.1455	L	0.54323	1.7	0.47065	D	0.999309	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;P	0.68621	0.919;0.959;0.943;0.885	T	0.48636	-0.9018	10	0.87932	D	0	0.0639	18.4696	0.90767	0.0:0.0:1.0:0.0	.	83;95;83;95	B7Z657;Q96EK2-3;B7Z4F8;Q96EK2	.;.;.;PF21B_HUMAN	H	95;95;83;83;83	ENSP00000324403:P95H;ENSP00000379410:P95H;ENSP00000385105:P83H;ENSP00000388619:P83H;ENSP00000401294:P83H	ENSP00000324403:P95H	P	-	2	0	PHF21B	43691104	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.530000	0.90606	2.346000	0.79739	0.655000	0.94253	CCC	.		0.647	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415		T	45312440	G	T	45312440	3	4	4	1	0	0	0	0	1	0	0	0	11860	1232	43	4	1351	4	PHF21B	22	45312440	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		45312440	5992126	81	300											
GAGE2A	729408	broad.mit.edu	37	chrX	49208295	49208296	+	In_Frame_Ins	INS	-	-	TAT																															gttggcgaggaagatcgaccINStatcggcctagaccaagacg																								rs372553636		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:49208295_49208296insTAT	ENST00000404720.2	+	2	96_97	c.24_25insTAT	c.(25-27)tat>TATtat	p.9_9Y>YY		NM_001098407.1|NM_012196.1	NP_001091877.1|NP_036328.1	Q9UEU5	GGE2D_HUMAN	G antigen 2D	9					cellular defense response (GO:0006968)												GAAGATCGACCTATCGGCCTAG	0.465														477	0.126358	0.031	0.098	3775	,	,		26951	0.0972		0.1441	False		,,,				2504	0.1278				p.T8delinsTY													.	.	0			c.24_25insTAT						.			10,505,1500		1,1,3,4,46,330,82,490,187						-1.1	0			8	27,1244,2482		1,3,16,6,128,539,446,675,577	no	codingComplex	GAGE2D	NM_001098407.1		2,4,19,10,174,869,528,1165,764	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.8662,25.5583,30.9639				37,1749,3982				SO:0001652	inframe_insertion	729447	exon2			ATCGACCTATCGG			Xp11.23	2012-10-02			ENSG00000240257				31959	protein-coding gene	gene with protein product		300735					Standard	NM_001098407		Approved	GAGE8		Q9UEU5	OTTHUMG00000067393	ENST00000404720.2:c.25_27dupTAT	X.37:g.49208296_49208298dupTAT	ENSP00000386110:p.Tyr9dup	Somatic	601	0		WXS	Illumina HiSeq	Phase_I	542	2	NM_001127212	0	0	0	0	0	A6NG46|A6NNR8|B7ZL76|Q4V325	In_Frame_Ins	INS	ENST00000404720.2	37	CCDS43941.1																																																																																			.		0.465	GAGE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144212.1	NM_001098407		TAT	49208296	-	TAT	49208295	7	5	4	1	0	1	1	0	0	0	0	0	6209	668	24	0	236	0	GAGE2A	23	49208295	In_Frame_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08		49208295	106062265	82	301											
KLHL4	56062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	86773063	86773063	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggcaggttgaagagccactCtcgggacagaaacggactga	12	5	15	9	2	1	4	0	2	1	2	2	6	1	6	1	4	2	2	1	4	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:86773063C>G	ENST00000373119.4	+	1	312	c.167C>G	c.(166-168)tCt>tGt	p.S56C	KLHL4_ENST00000373114.4_Missense_Mutation_p.S56C	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	56						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						AAGAGCCACTCTCGGGACAGA	0.547																																					p.S56C		.											.	KLHL4-133	0			c.C167G						.						77	65	69					X																	86773063		2203	4300	6503	SO:0001583	missense	56062	exon1			GCCACTCTCGGGA	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.167C>G	X.37:g.86773063C>G	ENSP00000362211:p.Ser56Cys	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	31	26	NM_019117	0	0	0	1	1	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752200	0.69533	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.76448	-1.02;-0.99	5.05	5.05	0.67936	.	2.035340	0.02405	N	0.081043	D	0.85894	0.5803	L	0.57536	1.79	0.58432	D	0.999993	B;P	0.42973	0.384;0.796	B;P	0.51415	0.345;0.669	T	0.71341	-0.4622	10	0.72032	D	0.01	.	16.3817	0.83467	0.0:1.0:0.0:0.0	.	56;56	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	C	56	ENSP00000362211:S56C;ENSP00000362206:S56C	ENSP00000362206:S56C	S	+	2	0	KLHL4	86659719	1.000000	0.71417	0.968000	0.41197	0.845000	0.48019	6.820000	0.75267	2.327000	0.79052	0.513000	0.50165	TCT	.		0.547	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			G	86773063	C	G	86773063	3	3	4	1	0	0	0	0	1	0	0	0	8412	913	32	4	169	4	KLHL4	23	86773063	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	37564768	86773063	68497497	83	302											
NRK	203447	broad.mit.edu	37	chrX	105167297	105167297	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgctgatactgatggtgAtgatgatgatgagtctaatg	11	13	13	4	0	1	7	0	7	1	0	1	7	1	7	0	1	2	1	0	1	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:105167297A>G	ENST00000243300.9	+	18	3101	c.2798A>G	c.(2797-2799)gAt>gGt	p.D933G	NRK_ENST00000428173.2_Missense_Mutation_p.D934G	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	933	Asp-rich.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						actgatggtgatgatgatgat	0.418										HNSCC(51;0.14)																											p.D933G													.	NRK-630	0			c.A2798G						.						60	54	56					X																	105167297		2077	4184	6261	SO:0001583	missense	203447	exon18			ATGGTGATGATGA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2798A>G	X.37:g.105167297A>G	ENSP00000434830:p.Asp933Gly	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_198465	0	0	0	0	0	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	a	1.372	-0.585913	0.03827	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.77098	-1.06;-1.07	2.99	2.99	0.34606	.	0.956289	0.08542	N	0.930446	T	0.59998	0.2235	N	0.19112	0.55	0.30768	N	0.743377	P;B	0.39282	0.666;0.312	B;B	0.39068	0.289;0.063	T	0.55471	-0.8136	10	0.06757	T	0.87	.	6.8474	0.23996	1.0:0.0:0.0:0.0	.	601;933	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	G	933;934	ENSP00000434830:D933G;ENSP00000438378:D934G	ENSP00000434830:D933G	D	+	2	0	NRK	105053953	0.997000	0.39634	0.399000	0.26333	0.010000	0.07245	0.334000	0.19787	1.420000	0.47138	0.483000	0.47432	GAT	.		0.418	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		G	105167297	A	G	105167297	3	3	4	1	0	0	0	0	1	0	0	0	10681	333	12	3	2868	3	NRK	23	105167297	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	18394234	105167297	50103263	84	303											
GLUD2	2747	ucsc.edu	37	chrX	120182120	120182120	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaatcccaagaactatacCgaaaatgaattggaaaagat	20	8	6	7	1	1	3	1	1	0	2	2	5	2	4	2	1	2	0	2	1	10	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:120182120C>T	ENST00000328078.1	+	1	659	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	194					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						AGAACTATACCGAAAATGAAT	0.453																																					p.T194T													.	GLUD2-131	0			c.C582T						.						123	96	105					X																	120182120		2203	4300	6503	SO:0001819	synonymous_variant	2747	exon1			CTATACCGAAAAT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.582C>T	X.37:g.120182120C>T		Somatic	72	0		WXS	Illumina HiSeq		81	1	NM_012084	0	0	5	5	0	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																			.		0.453	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		T	120182120	C	T	120182120	2	4	4	1	0	0	0	0	0	0	0	1	6497	639	23	1		1	GLUD2	23	120182120	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08	15014823	120182120	35088440	85	304											
CDR1	1038	hgsc.bcm.edu	37	chrX	139866440	139866440	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtgtcttccaacaaaggtAcgtcttccaacaaaggtacg	12	11	8	10	2	2	0	0	0	2	0	4	0	4	0	2	2	4	2	2	2	6	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:139866440A>G	ENST00000370532.2	-	1	283	c.92T>C	c.(91-93)gTa>gCa	p.V31A		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	31	23 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CAACAAAGGTACGTCTTCCAA	0.448																																					p.V31A		.											.	CDR1-130	0			c.T92C						.						171	162	165					X																	139866440		2203	4300	6503	SO:0001583	missense	1038	exon1			AAAGGTACGTCTT		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.92T>C	X.37:g.139866440A>G	ENSP00000359563:p.Val31Ala	Somatic	46	2		WXS	Illumina HiSeq	Phase_I	93	6	NM_004065	0	0	1	1	0	Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	CCDS14670.1	.	.	.	.	.	.	.	.	.	.	A	2.772	-0.255469	0.05829	.	.	ENSG00000184258	ENST00000370532	T	0.35048	1.33	1.84	-0.941	0.10402	.	.	.	.	.	T	0.15912	0.0383	N	0.19112	0.55	0.09310	N	1	P	0.35481	0.504	B	0.29598	0.104	T	0.14420	-1.0473	8	.	.	.	.	2.5052	0.04643	0.6001:0.0:0.1643:0.2356	.	31	P51861	CDR1_HUMAN	A	31	ENSP00000359563:V31A	.	V	-	2	0	CDR1	139694106	0.000000	0.05858	0.011000	0.14972	0.002000	0.02628	-0.414000	0.07114	-0.339000	0.08401	-1.671000	0.00744	GTA	.		0.448	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		G	139866440	A	G	139866440	3	3	4	1	0	0	0	0	1	0	0	0	3177	391	14	3	700	3	CDR1	23	139866440	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	19684320	139866440	15404120	86	305											
CPSF3L	54973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1248497	1248497	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcacgcagtagccgggcAtgatgacctgggggcaggca	8	5	16	12	2	0	2	0	2	0	0	0	2	0	2	3	4	2	6	3	4	1	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:1248497A>G	ENST00000435064.1	-	11	1131	c.1049T>C	c.(1048-1050)aTg>aCg	p.M350T	CPSF3L_ENST00000450926.2_Missense_Mutation_p.M328T|CPSF3L_ENST00000545578.1_Missense_Mutation_p.M321T|CPSF3L_ENST00000421495.2_Missense_Mutation_p.M92T|CPSF3L_ENST00000462432.1_5'UTR|CPSF3L_ENST00000419704.1_Missense_Mutation_p.M249T|CPSF3L_ENST00000411962.1_Missense_Mutation_p.M252T|CPSF3L_ENST00000540437.1_Missense_Mutation_p.M356T	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	350					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GTAGCCGGGCATGATGACCTG	0.677																																					p.M356T		.											.	CPSF3L-90	0			c.T1067C						.						22	21	21					1																	1248497		2196	4288	6484	SO:0001583	missense	54973	exon13			CCGGGCATGATGA	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"integrator complex subunit 11"	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.1049T>C	1.37:g.1248497A>G	ENSP00000413493:p.Met350Thr	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	31	12	NM_001256456	0	0	4	7	3	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Missense_Mutation	SNP	ENST00000435064.1	37	CCDS21.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295485	0.60086	.	.	ENSG00000127054	ENST00000435064;ENST00000411962;ENST00000294579;ENST00000419704;ENST00000540437;ENST00000450926;ENST00000545578	T;T;T;T;T	0.46451	0.95;0.95;0.95;0.95;0.87	5.48	5.48	0.80851	Beta-Casp domain (1);	0.000000	0.85682	D	0.000000	T	0.62085	0.2399	M	0.78049	2.395	0.80722	D	1	P;P;P;P;P;P	0.51933	0.696;0.741;0.949;0.936;0.837;0.741	P;P;P;P;P;P	0.57960	0.535;0.665;0.83;0.738;0.617;0.665	T	0.67632	-0.5621	10	0.87932	D	0	-54.7181	15.5355	0.75998	1.0:0.0:0.0:0.0	.	328;321;252;249;356;350	Q5TA45-3;B4DM87;C9IYS7;Q5TA45-2;G3V1S5;Q5TA45	.;.;.;.;.;INT11_HUMAN	T	350;252;243;249;356;328;321	ENSP00000413493:M350T;ENSP00000404886:M249T;ENSP00000445001:M356T;ENSP00000392848:M328T;ENSP00000444672:M321T	ENSP00000294579:M243T	M	-	2	0	CPSF3L	1238360	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.568000	0.90741	2.077000	0.62373	0.460000	0.39030	ATG	.		0.677	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871		G	1248497	A	G	1248497	3	3	5	1	0	0	0	0	1	0	0	0	3833	217	8	3	781	3	CPSF3L	1	1248497	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08		1248497	248002124	1	306											
PLCH2	9651	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	2430213	2430213	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgtggaggtggagatcAttgggctccctgtggactgc	5	12	15	9	0	1	1	1	0	0	1	2	4	2	3	2	5	1	1	2	5	0	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:2430213A>G	ENST00000419816.2	+	18	2654	c.2380A>G	c.(2380-2382)Att>Gtt	p.I794V	PLCH2_ENST00000378486.3_Missense_Mutation_p.I794V|PLCH2_ENST00000378488.3_Missense_Mutation_p.I758V|PLCH2_ENST00000288766.5_Missense_Mutation_p.I82V|PLCH2_ENST00000449969.1_Missense_Mutation_p.I767V			O75038	PLCH2_HUMAN	phospholipase C, eta 2	794	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		GGTGGAGATCATTGGGCTCCC	0.657																																					p.I794V		.											.	PLCH2-229	0			c.A2380G						.						28	32	31					1																	2430213		2068	4190	6258	SO:0001583	missense	9651	exon18			GAGATCATTGGGC	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.2380A>G	1.37:g.2430213A>G	ENSP00000389803:p.Ile794Val	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	31	14	NM_014638	0	0	0	0	0	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	37		.	.	.	.	.	.	.	.	.	.	A	21.1	4.104041	0.76983	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488;ENST00000288766;ENST00000378483;ENST00000343889;ENST00000278878	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.93	4.93	0.64822	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.25005	0.0607	L	0.28400	0.85	0.48632	D	0.999685	P;P;D;P	0.69078	0.938;0.938;0.997;0.938	P;P;D;P	0.77557	0.679;0.842;0.99;0.842	T	0.01661	-1.1301	10	0.52906	T	0.07	.	13.39	0.60818	1.0:0.0:0.0:0.0	.	641;546;767;794	B9DI81;B9DI82;O75038-2;O75038	.;.;.;PLCH2_HUMAN	V	767;794;758;82;80;641;546	ENSP00000397289:I767V;ENSP00000367747:I794V;ENSP00000367749:I758V;ENSP00000288766:I82V	ENSP00000278878:I546V	I	+	1	0	PLCH2	2420073	1.000000	0.71417	0.993000	0.49108	0.499000	0.33736	5.860000	0.69546	1.845000	0.53610	0.459000	0.35465	ATT	.		0.657	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		G	2430213	A	G	2430213	3	3	5	1	0	0	0	0	1	0	0	0	12064	217	8	3	2450	3	PLCH2	1	2430213	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	1181716	2430213	246820408	2	307											
KIAA1522	57648	broad.mit.edu	37	chr1	33237860	33237860	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctcccccacctgtggcccGcaagccgtctgtgggagtcc	4	7	13	17	2	1	0	0	0	1	0	3	1	3	1	6	3	1	2	6	3	1	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:33237860G>A	ENST00000373480.1	+	6	3006	c.2903G>A	c.(2902-2904)cGc>cAc	p.R968H	KIAA1522_ENST00000401073.2_Missense_Mutation_p.R1027H|KIAA1522_ENST00000294521.3_Intron|YARS_ENST00000469100.1_5'Flank|KIAA1522_ENST00000373481.3_Missense_Mutation_p.R979H	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	968	Pro-rich.									breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CCTGTGGCCCGCAAGCCGTCT	0.662																																					p.R1027H													.	KIAA1522-90	0			c.G3080A						.						30	36	34					1																	33237860		1900	4100	6000	SO:0001583	missense	57648	exon6			TGGCCCGCAAGCC	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.2903G>A	1.37:g.33237860G>A	ENSP00000362579:p.Arg968His	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	78	5	NM_020888	0	0	57	57	0	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043295	0.75732	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.16597	2.33;2.34;2.35	5.05	4.14	0.48551	.	0.086750	0.45867	D	0.000333	T	0.20941	0.0504	M	0.61703	1.905	0.30845	N	0.73524	D;D;D	0.57257	0.979;0.979;0.979	P;P;P	0.46049	0.502;0.502;0.502	T	0.16541	-1.0399	10	0.46703	T	0.11	-11.6125	8.9717	0.35910	0.2107:0.0:0.7892:0.0	.	979;968;1027	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	H	1027;979;968	ENSP00000383851:R1027H;ENSP00000362580:R979H;ENSP00000362579:R968H	ENSP00000362579:R968H	R	+	2	0	KIAA1522	33010447	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.416000	0.52707	1.503000	0.48686	0.650000	0.86243	CGC	.		0.662	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33237860	G	A	33237860	3	1	5	1	0	0	0	0	1	0	0	0	8259	1087	38	1	3102	1	KIAA1522	1	33237860	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	30807647	33237860	216012761	3	308											
HMGB4	127540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	34329977	34329977	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgaaaaggccaaatatgaagCcctggccaaactcgacaaag	17	5	9	10	1	0	2	0	2	0	0	1	3	0	2	3	2	2	0	3	2	7	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:34329977C>T	ENST00000522796.1	+	4	2090	c.185C>T	c.(184-186)gCc>gTc	p.A62V	HMGB4_ENST00000519684.1_Missense_Mutation_p.A62V|HMGB4_ENST00000425537.1_3'UTR|CSMD2_ENST00000373381.4_Intron			Q8WW32	HMGB4_HUMAN	high mobility group box 4	62						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAATATGAAGCCCTGGCCAAA	0.463																																					p.A62V		.											.	HMGB4-90	0			c.C185T						.						120	135	130					1																	34329977		2203	4300	6503	SO:0001583	missense	127540	exon2			ATGAAGCCCTGGC		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.185C>T	1.37:g.34329977C>T	ENSP00000430919:p.Ala62Val	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	133	55	NM_145205	0	0	0	0	0	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	37	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542128	0.65198	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	T;T	0.14144	2.53;2.53	5.58	0.467	0.16721	.	0.232725	0.37053	N	0.002268	T	0.18002	0.0432	M	0.68317	2.08	0.31177	N	0.702474	P	0.40931	0.733	P	0.46758	0.526	T	0.09662	-1.0664	10	0.87932	D	0	.	4.817	0.13372	0.4359:0.4072:0.0:0.1569	.	62	B2R4X7	.	V	62	ENSP00000429214:A62V;ENSP00000430919:A62V	ENSP00000429214:A62V	A	+	2	0	HMGB4	34102564	0.991000	0.36638	0.082000	0.20525	0.854000	0.48673	2.434000	0.44802	-0.049000	0.13379	-0.192000	0.12808	GCC	.		0.463	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		T	34329977	C	T	34329977	3	4	5	1	0	0	0	0	1	0	0	0	7249	739	26	2	187	2	HMGB4	1	34329977	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	1092117	34329977	214920644	4	309											
SFPQ	6421	broad.mit.edu	37	chr1	35658464	35658464	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgctgttggtgtggaggcgGtggcgggatcggaggcttag	4	10	21	6	3	0	0	0	0	0	0	1	3	0	3	0	8	1	3	0	8	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:35658464G>T	ENST00000357214.5	-	1	285	c.187C>A	c.(187-189)Ccg>Acg	p.P63T		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	63	Gln/Glu/Pro-rich.|Poly-Pro.				alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TGTGGAGGCGGTGGCGGGATC	0.711			T	TFE3	papillary renal cell																																p.P63T				Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ-231	0			c.C187A						.						12	14	13					1																	35658464		2026	4094	6120	SO:0001583	missense	6421	exon1			GAGGCGGTGGCGG	X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"RNA binding motif (RRM) containing"	10774	protein-coding gene	gene with protein product	"polypyrimidine tract binding protein associated", "protein phosphatase 1, regulatory subunit 140"	605199	"splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.187C>A	1.37:g.35658464G>T	ENSP00000349748:p.Pro63Thr	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	16	4	NM_005066	0	0	7	24	17	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	37	CCDS388.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.394973	0.25205	.	.	ENSG00000116560	ENST00000357214	T	0.24151	1.87	3.54	1.62	0.23740	.	0.430740	0.23744	N	0.044992	T	0.11452	0.0279	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.19877	-1.0292	10	0.66056	D	0.02	-0.0031	1.1679	0.01819	0.201:0.1743:0.4468:0.1779	.	63	P23246	SFPQ_HUMAN	T	63	ENSP00000349748:P63T	ENSP00000349748:P63T	P	-	1	0	SFPQ	35431051	0.922000	0.31269	0.465000	0.27155	0.454000	0.32378	2.084000	0.41625	0.207000	0.20607	0.485000	0.47835	CCG	.		0.711	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		T	35658464	G	T	35658464	3	4	5	1	0	0	0	0	1	0	0	0	14192	1261	44	4	1976	4	SFPQ	1	35658464	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	1328487	35658464	213592157	5	310											
SSBP3	23648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	54870254	54870254	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcacacaaacttaccaccaCcacgagtgcaaaaacccagg	17	4	5	15	1	1	0	1	0	0	0	1	1	1	0	4	1	4	1	4	1	4	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:54870254C>T	ENST00000371320.3	-	3	596	c.186G>A	c.(184-186)tgG>tgA	p.W62*	SSBP3_ENST00000371319.3_Nonsense_Mutation_p.W62*|SSBP3_ENST00000357475.4_Nonsense_Mutation_p.W62*|SSBP3_ENST00000417664.2_De_novo_Start_OutOfFrame	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	62					head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						CTTACCACCACCACGAGTGCA	0.507																																					p.W62X		.											.	SSBP3-90	0			c.G186A						.						88	76	80					1																	54870254		2203	4300	6503	SO:0001587	stop_gained	23648	exon3			CCACCACCACGAG		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"single-stranded DNA-binding protein 3"			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.186G>A	1.37:g.54870254C>T	ENSP00000360371:p.Trp62*	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	68	19	NM_001009955	0	0	0	0	0	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Nonsense_Mutation	SNP	ENST00000371320.3	37	CCDS591.1	.	.	.	.	.	.	.	.	.	.	C	43	10.209365	0.99360	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	5.03	5.03	0.67393	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2803	18.3392	0.90299	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000350067:W62X	W	-	3	0	SSBP3	54642842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.556000	0.82233	2.502000	0.84385	0.561000	0.74099	TGG	.		0.507	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		T	54870254	C	T	54870254	4	4	5	1	0	0	0	0	0	1	0	0	15213	508	18	2	1044	2	SSBP3	1	54870254	Nonsense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	19211790	54870254	194380367	6	311											
LIX1L	128077	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	145497429	145497430	+	Frame_Shift_Ins	INS	-	-	T																															tgacaacccaaatacagggaINSttggtgccttccgattcatg																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:145497429_145497430insT	ENST00000369308.3	+	4	708_709	c.634_635insT	c.(634-636)attfs	p.I212fs	RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	212										large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAATACAGGGATTGGTGCCTTC	0.45																																					p.I212fs		.											.	LIX1L-91	0			c.634_635insT						.																																			SO:0001589	frameshift_variant	128077	exon4			.	AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"Lix1 homolog (mouse) like", "Lix1 homolog (chicken)-like"			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.636dupT	1.37:g.145497431_145497431dupT	ENSP00000358314:p.Ile212fs	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	44	15	NM_153713	0	0	0	0	0	Q6AI36	Frame_Shift_Ins	INS	ENST00000369308.3	37	CCDS915.1																																																																																			.		0.45	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713		T	145497430	-	T	145497429	7	5	5	1	0	1	1	0	0	0	0	0	8855	333	12	0	648	0	LIX1L	1	145497429	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	90627175	145497429	103753192	7	312											
SLC9A11	284525	ucsc.edu	37	chr1	173490537	173490537	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaggcaagtttggctcttTcctgagtgggaaaaaaaaaa	16	9	10	6	0	1	1	0	1	1	0	2	2	2	2	1	3	1	3	1	3	7	2	rs377309633		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:173490537T>C	ENST00000367714.3	-	22	3064	c.2642A>G	c.(2641-2643)gAa>gGa	p.E881G	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	881					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TTTGGCTCTTTCCTGAGTGGG	0.313																																					p.E881G													.	.	0			c.A2642G						.	T	GLY/GLU	2,4404	2.1+/-5.4	0,2,2201	54	54	54		2642	5.2	1	1		54	0,8598		0,0,4299	no	missense-near-splice	SLC9A11	NM_178527.3	98	0,2,6500	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging	881/1125	173490537	2,13002	2203	4299	6502	SO:0001630	splice_region_variant	284525	exon22			GCTCTTTCCTGAG	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.2641-1A>G	1.37:g.173490537T>C		Somatic	48	0		WXS	Illumina HiSeq		39	4	NM_178527	0	0	0	0	0	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.838389	0.51057	4.54E-4	0.0	ENSG00000162753	ENST00000367714	T	0.43688	0.94	5.18	5.18	0.71444	Cyclic nucleotide-binding-like (1);Cyclic nucleotide-binding domain (1);	0.217466	0.31909	N	0.006861	T	0.47673	0.1458	M	0.68952	2.095	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.53479	-0.8433	10	0.59425	D	0.04	-12.5633	11.4178	0.49962	0.0:0.0:0.0:1.0	.	881	Q5TAH2	S9A11_HUMAN	G	881	ENSP00000356687:E881G	ENSP00000356687:E881G	E	-	2	0	SLC9A11	171757160	1.000000	0.71417	0.991000	0.47740	0.100000	0.18952	4.140000	0.58031	1.966000	0.57179	0.482000	0.46254	GAA	.		0.313	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	Missense_Mutation	C	173490537	T	C	173490537	5	2	5	1	0	0	0	0	0	0	1	0	14743	1797	62	3	760	3	SLC9A11	1	173490537	Splice_Site	SNP	T	TCGA-A4-7584-01A-11D-2136-08	27993108	173490537	75760084	8	313											
GLT25D2	23127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	183944269	183944269	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttttccctcgcagttcgaaGggctgcctgtcgtagtttca	5	15	10	11	3	1	0	1	0	0	0	5	1	2	0	2	1	1	5	2	1	2	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:183944269G>C	ENST00000361927.4	-	3	825	c.454C>G	c.(454-456)Ctt>Gtt	p.L152V	COLGALT2_ENST00000546159.1_Missense_Mutation_p.L152V	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	152					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										GCAGTTCGAAGGGCTGCCTGT	0.438																																					p.L152V		.											.	.	0			c.C454G						.						119	113	115					1																	183944269		2203	4300	6503	SO:0001583	missense	23127	exon3			TTCGAAGGGCTGC	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.454C>G	1.37:g.183944269G>C	ENSP00000354960:p.Leu152Val	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	99	35	NM_015101	0	0	0	0	0	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	37	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519102	0.85495	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.62364	0.03;0.03	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.80889	0.4710	M	0.89840	3.065	0.80722	D	1	D;D	0.67145	0.993;0.996	P;D	0.67725	0.873;0.953	D	0.84426	0.0574	10	0.87932	D	0	.	12.479	0.55831	0.0768:0.0:0.9232:0.0	.	152;152	F5H3T5;Q8IYK4	.;GT252_HUMAN	V	152	ENSP00000439112:L152V;ENSP00000354960:L152V	ENSP00000354960:L152V	L	-	1	0	GLT25D2	182210892	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.705000	0.84606	2.583000	0.87209	0.650000	0.86243	CTT	.		0.438	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		C	183944269	G	C	183944269	3	2	5	1	0	0	0	0	1	0	0	0	6487	1000	35	4	1466	4	GLT25D2	1	183944269	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	10453732	183944269	65306352	9	314											
HMCN1	83872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	186083139	186083139	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacataaaggggggcccccaGagccttgtaattcttttaaa	13	10	9	9	0	1	1	0	0	1	1	1	1	1	1	3	3	2	1	3	3	6	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:186083139G>A	ENST00000271588.4	+	73	11389	c.11160G>A	c.(11158-11160)caG>caA	p.Q3720Q	HMCN1_ENST00000367492.2_Silent_p.Q3720Q	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3720	Ig-like C2-type 36.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GGGGCCCCCAGAGCCTTGTAA	0.423																																					p.Q3720Q		.											.	HMCN1-113	0			c.G11160A						.						114	133	127					1																	186083139		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon73			CCCCCAGAGCCTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11160G>A	1.37:g.186083139G>A		Somatic	278	0		WXS	Illumina HiSeq	Phase_I	208	69	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186083139	G	A	186083139	2	1	5	1	0	0	0	0	0	0	0	1	7241	933	33	2		2	HMCN1	1	186083139	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	2138870	186083139	63167482	10	315											
PROM2	150696	hgsc.bcm.edu	37	chr2	95952306	95952306	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggagaaggtcgtcccccAgcagagccttgtggtcagtt	8	8	13	12	1	1	2	1	0	0	2	3	3	2	2	4	3	2	2	4	3	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:95952306A>G	ENST00000317620.9	+	17	2160	c.2027A>G	c.(2026-2028)cAg>cGg	p.Q676R	PROM2_ENST00000403131.2_Missense_Mutation_p.Q676R|PROM2_ENST00000317668.4_Missense_Mutation_p.Q676R|PROM2_ENST00000542147.1_Missense_Mutation_p.Q627R	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	676					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						GTCGTCCCCCAGCAGAGCCTT	0.602																																					p.Q676R		.											.	PROM2-91	0			c.A2027G						.						47	47	47					2																	95952306		2203	4300	6503	SO:0001583	missense	150696	exon17			TCCCCCAGCAGAG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.2027A>G	2.37:g.95952306A>G	ENSP00000318270:p.Gln676Arg	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_001165977	0	0	0	0	0	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429550	0.43122	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.66	2.13	0.27403	.	0.420605	0.22357	N	0.061138	T	0.55194	0.1905	M	0.74881	2.28	0.28303	N	0.923033	D	0.69078	0.997	D	0.68192	0.956	T	0.48456	-0.9034	10	0.72032	D	0.01	-21.7999	3.8144	0.08809	0.7096:0.0:0.1034:0.187	.	676	Q8N271	PROM2_HUMAN	R	676;676;676;627	ENSP00000385716:Q676R;ENSP00000318520:Q676R;ENSP00000318270:Q676R;ENSP00000442542:Q627R	ENSP00000318270:Q676R	Q	+	2	0	PROM2	95316033	0.996000	0.38824	0.862000	0.33874	0.470000	0.32858	1.552000	0.36244	0.827000	0.34685	0.368000	0.22195	CAG	.		0.602	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		G	95952306	A	G	95952306	3	3	5	1	0	0	0	0	1	0	0	0	12585	188	7	3	2093	3	PROM2	2	95952306	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08		95952306	147247067	11	316											
GCC2	9648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109109239	109109239	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcttaagaatgaaccgacCacaagaagtatgtatgtaca	17	8	8	8	1	0	3	0	1	0	2	0	4	0	3	2	0	3	4	2	0	8	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:109109239C>T	ENST00000309863.6	+	19	5154	c.4440C>T	c.(4438-4440)acC>acT	p.T1480T		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1480					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						ATGAACCGACCACAAGAAGTA	0.373																																					p.T1480T		.											.	GCC2-91	0			c.C4440T						.						85	85	85					2																	109109239		2203	4300	6503	SO:0001819	synonymous_variant	9648	exon19			ACCGACCACAAGA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.4440C>T	2.37:g.109109239C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	45	21	NM_181453	0	0	0	0	0	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	37	CCDS33268.1																																																																																			.		0.373	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		T	109109239	C	T	109109239	2	4	5	1	0	0	0	0	0	0	0	1	6306	581	21	2		2	GCC2	2	109109239	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	13156933	109109239	134090134	12	317											
TTN	7273	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	179611391	179611391	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctctcccccttctcctttttGaatgttagaaatttccagtg	7	17	5	12	0	2	2	0	1	2	1	5	2	3	2	4	0	0	1	4	0	3	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:179611391G>C	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.Q5246E|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCCTTTTTGAATGTTAGAA	0.388																																					p.Q5246E		.											.	TTN-636	0			c.C15736G						.						136	129	131					2																	179611391		2203	4300	6503	SO:0001627	intron_variant	7273	exon46			CTTTTTGAATGTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-4743C>G	2.37:g.179611391G>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	92	40	NM_133379	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	3.110	-0.182790	0.06340	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.65916	-0.18	5.95	5.95	0.96441	.	.	.	.	.	T	0.48352	0.1495	L	0.49778	1.585	0.80722	D	1	P	0.39282	0.666	B	0.28916	0.096	T	0.53063	-0.8491	9	0.02654	T	1	.	15.7227	0.77724	0.0:0.0:0.802:0.198	.	5246	Q8WZ42-6	.	E	5246;527	ENSP00000354117:Q5246E	ENSP00000304714:Q527E	Q	-	1	0	TTN	179319636	0.997000	0.39634	0.984000	0.44739	0.974000	0.67602	2.850000	0.48294	2.825000	0.97269	0.655000	0.94253	CAA	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179611391	G	C	179611391	1	2	5	0	1	0	0	0	0	0	0	0	16768	1299	45	4		4	TTN	2	179611391	Intron	SNP	G	TCGA-A4-7584-01A-11D-2136-08	70502152	179611391	63587982	13	318											
GPR1	2825	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	207040930	207040930	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agctgtttccaggagacacaGattcttggtttctgagttcc	8	14	10	9	0	2	3	0	1	2	2	4	4	4	3	2	2	1	4	2	2	0	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:207040930G>A	ENST00000407325.2	-	3	1404	c.1042C>T	c.(1042-1044)Ctg>Ttg	p.L348L	GPR1_ENST00000437420.1_Silent_p.L348L	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	348					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		AGGAGACACAGATTCTTGGTT	0.428																																					p.L348L		.											.	GPR1-90	0			c.C1042T						.						64	61	62					2																	207040930		2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			GACACAGATTCTT		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.1042C>T	2.37:g.207040930G>A		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	46	17	NM_001098199	0	0	0	0	0	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	37	CCDS2368.1																																																																																			.		0.428	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		A	207040930	G	A	207040930	2	1	5	1	0	0	0	0	0	0	0	1	6641	933	33	2		2	GPR1	2	207040930	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	27429539	207040930	36158443	14	319											
RBM44	375316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238722326	238722326	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggaggcaacctccaaaaagGtaagggtctagtccacttac	13	8	10	10	0	1	0	0	0	1	0	3	1	3	1	3	4	2	2	3	4	6	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:238722326G>T	ENST00000444524.2	+	2	201		c.e2+1		RBM44_ENST00000316997.4_Splice_Site|RBM44_ENST00000409864.1_Splice_Site			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44							cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		CTCCAAAAAGGTAAGGGTCTA	0.448																																					.		.											.	RBM44-26	0			c.76+1G>T						.						55	57	57					2																	238722326		1917	4134	6051	SO:0001630	splice_region_variant	375316	exon2			AAAAAGGTAAGGG	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"RNA binding motif (RRM) containing"	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000444524.2:c.201+1G>T	2.37:g.238722326G>T		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	31	16	NM_001080504	0	0	0	0	0	A0AUW3	Splice_Site	SNP	ENST00000444524.2	37		.	.	.	.	.	.	.	.	.	.	G	10.22	1.289839	0.23478	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	.	.	.	4.25	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4628	0.55741	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM44	238387065	1.000000	0.71417	0.956000	0.39512	0.166000	0.22503	3.694000	0.54742	2.660000	0.90430	0.655000	0.94253	.	.		0.448	RBM44-003	PUTATIVE	basic|exp_conf	processed_transcript	protein_coding	OTTHUMT00000400909.1	NM_001080504	Intron	T	238722326	G	T	238722326	5	4	5	1	0	0	0	0	0	0	1	0	13170	1275	44	4	79	4	RBM44	2	238722326	Splice_Site	SNP	G	TCGA-A4-7584-01A-11D-2136-08	31681396	238722326	4477047	15	320											
GORASP1	64689	hgsc.bcm.edu	37	chr3	39148980	39148980	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaactcaccccgtggaggTggaagccctcggcgccgcct	6	5	14	16	4	1	0	1	0	0	0	2	2	1	2	5	5	2	1	5	5	2	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:39148980T>C	ENST00000319283.3	-	1	874	c.53A>G	c.(52-54)cAc>cGc	p.H18R	TTC21A_ENST00000431162.2_5'Flank|GORASP1_ENST00000479927.1_Missense_Mutation_p.H18R|TTC21A_ENST00000301819.6_5'Flank|GORASP1_ENST00000422110.2_Missense_Mutation_p.H18R|TTC21A_ENST00000440121.1_5'Flank	NM_031899.2	NP_114105.1	Q9BQQ3	GORS1_HUMAN	golgi reassembly stacking protein 1, 65kDa	18	PDZ.				Golgi organization (GO:0007030)|mitotic cell cycle (GO:0000278)|negative regulation of dendrite morphogenesis (GO:0050774)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(1)|ovary(3)|urinary_tract(1)	14				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CCCGTGGAGGTGGAAGCCCTC	0.786																																					p.H18R		.											.	GORASP1-92	0			c.A53G						.						2	2	2					3																	39148980		1235	2829	4064	SO:0001583	missense	64689	exon1			TGGAGGTGGAAGC	AJ409349	CCDS2681.1, CCDS63596.1, CCDS63597.1	3p22-p21.33	2008-04-23	2002-08-29	2002-05-24	ENSG00000114745	ENSG00000114745			16769	protein-coding gene	gene with protein product		606867	"golgi phosphoprotein 5"	GOLPH5			Standard	NM_001278789		Approved	GRASP65, P65, FLJ23443	uc003ciw.1	Q9BQQ3	OTTHUMG00000131292	ENST00000319283.3:c.53A>G	3.37:g.39148980T>C	ENSP00000313869:p.His18Arg	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	11	3	NM_031899	0	0	0	0	0	B3KWC8|Q3SYG7|Q8N272|Q96H42	Missense_Mutation	SNP	ENST00000319283.3	37	CCDS2681.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.789611	0.50102	.	.	ENSG00000114745	ENST00000319283;ENST00000422110;ENST00000479927;ENST00000427459;ENST00000411813;ENST00000441081	T;T;T;T	0.50813	1.62;0.74;0.73;1.62	4.39	1.84	0.25277	PDZ/DHR/GLGF (1);	0.106695	0.64402	U	0.000006	T	0.52354	0.1729	L	0.58669	1.825	0.24833	N	0.992513	D;P;B	0.56035	0.974;0.688;0.024	P;B;B	0.56700	0.804;0.408;0.035	T	0.42616	-0.9441	10	0.87932	D	0	-8.72	6.2398	0.20785	0.1409:0.0812:0.0:0.7779	.	18;18;18	B4E1H8;B3KPY8;Q9BQQ3	.;.;GORS1_HUMAN	R	18	ENSP00000313869:H18R;ENSP00000395709:H18R;ENSP00000419123:H18R;ENSP00000398673:H18R	ENSP00000313869:H18R	H	-	2	0	GORASP1	39123984	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	2.916000	0.48813	0.518000	0.28383	0.397000	0.26171	CAC	.		0.786	GORASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254060.1			C	39148980	T	C	39148980	3	2	5	1	0	0	0	0	1	0	0	0	6595	1696	59	3	1305	3	GORASP1	3	39148980	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08		39148980	158873450	16	321											
RAD54L2	23132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	51697207	51697207	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	attctcacagccactcctgtCcgagccgaggatgtttgcgc	7	10	10	14	3	1	0	1	0	1	0	4	3	3	1	4	1	3	1	4	1	0	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:51697207C>G	ENST00000409535.2	+	22	4300	c.4175C>G	c.(4174-4176)tCc>tGc	p.S1392C	RAD54L2_ENST00000296477.3_Missense_Mutation_p.S1086C	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1392						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		CCACTCCTGTCCGAGCCGAGG	0.567																																					p.S1392C		.											.	RAD54L2-93	0			c.C4175G						.						153	132	139					3																	51697207		2203	4300	6503	SO:0001583	missense	23132	exon22			TCCTGTCCGAGCC	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.4175C>G	3.37:g.51697207C>G	ENSP00000386520:p.Ser1392Cys	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	123	48	NM_015106	0	0	3	4	1	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	37	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	C	17.44	3.390512	0.62066	.	.	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.94092	-3.24;-3.35	5.56	5.56	0.83823	.	0.324591	0.28927	N	0.013698	D	0.85643	0.5744	N	0.08118	0	0.80722	D	1	P;P	0.46327	0.661;0.876	B;B	0.36289	0.221;0.221	D	0.88801	0.3285	10	0.72032	D	0.01	-4.0774	18.5281	0.90980	0.0:1.0:0.0:0.0	.	1392;981	Q9Y4B4;B3KV54	ARIP4_HUMAN;.	C	1392;1086	ENSP00000386520:S1392C;ENSP00000296477:S1086C	ENSP00000296477:S1086C	S	+	2	0	RAD54L2	51672247	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.158000	0.58150	2.609000	0.88269	0.655000	0.94253	TCC	.		0.567	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		G	51697207	C	G	51697207	3	3	5	1	0	0	0	0	1	0	0	0	13026	855	30	4	4257	4	RAD54L2	3	51697207	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	12548227	51697207	146325223	17	322											
MITF	4286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	69928532	69928532	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgccgatggaagtccttAaggtacgtgagtgttgctct	8	12	14	7	2	1	1	0	1	1	0	2	3	2	2	2	3	3	3	2	3	3	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:69928532A>T	ENST00000448226.2	+	2	479	c.352A>T	c.(352-354)Aag>Tag	p.K118*	MITF_ENST00000394355.2_Nonsense_Mutation_p.K93*|MITF_ENST00000328528.6_Nonsense_Mutation_p.K117*|MITF_ENST00000472437.1_Nonsense_Mutation_p.K66*|MITF_ENST00000352241.4_Nonsense_Mutation_p.K118*|MITF_ENST00000314589.5_Nonsense_Mutation_p.K102*			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	118					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GGAAGTCCTTAAGGTACGTGA	0.478			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.K118X	Melanoma(29;269 969 31479 41502 42961)	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF-524	0			c.A352T						.						53	59	57					3																	69928532		2104	4227	6331	SO:0001587	stop_gained	4286	exon2			GTCCTTAAGGTAC		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.352A>T	3.37:g.69928532A>T	ENSP00000391803:p.Lys118*	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	35	19	NM_198159	0	0	0	0	0	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Nonsense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	A	33	5.248140	0.95305	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000429090;ENST00000433517;ENST00000472437;ENST00000457080;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355	.	.	.	6.02	6.02	0.97574	.	0.088619	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	.	.	.	X	118;118;66;66;66;117;117;102;102;93	.	.	K	+	1	0	MITF	70011222	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.923000	0.92808	2.311000	0.77944	0.533000	0.62120	AAG	.		0.478	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69928532	A	T	69928532	4	4	5	1	0	0	0	0	0	1	0	0	9621	363	13	5	523	5	MITF	3	69928532	Nonsense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	18231325	69928532	128093898	18	323											
FAM55C	91775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101520832	101520832	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagagtgctttcttccagAggtatgtactgctttttctt	7	17	9	8	0	2	2	0	0	2	2	3	3	3	2	1	1	3	4	1	1	2	7			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:101520832A>T	ENST00000491511.2	+	5	1803	c.847A>T	c.(847-849)Agt>Tgt	p.S283C	NXPE3_ENST00000273347.5_Splice_Site_p.S283C|NXPE3_ENST00000477909.1_Splice_Site_p.S283C|NXPE3_ENST00000422132.1_Splice_Site_p.S283C	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	283						extracellular region (GO:0005576)											TTTCTTCCAGAGGTATGTACT	0.443																																					p.S283C		.											.	.	0			c.A847T						.						92	98	96					3																	101520832		2177	4287	6464	SO:0001630	splice_region_variant	91775	exon5			TTCCAGAGGTATG	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"family with sequence similarity 55, member C"	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.848+1A>T	3.37:g.101520832A>T		Somatic	233	0		WXS	Illumina HiSeq	Phase_I	174	65	NM_145037	0	0	1	2	1	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	37	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677582	0.88445	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	5.8	5.8	0.92144	.	0.197973	0.64402	D	0.000006	T	0.37461	0.1004	M	0.69823	2.125	0.58432	D	0.999999	D	0.76494	0.999	D	0.71656	0.974	T	0.10941	-1.0608	10	0.66056	D	0.02	-3.0682	16.1475	0.81580	1.0:0.0:0.0:0.0	.	283	Q969Y0	FA55C_HUMAN	C	283	ENSP00000273347:S283C;ENSP00000417485:S283C;ENSP00000418369:S283C;ENSP00000396421:S283C	ENSP00000273347:S283C	S	+	1	0	FAM55C	103003522	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.300000	0.96151	2.213000	0.71641	0.528000	0.53228	AGT	.		0.443	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	Missense_Mutation	T	101520832	A	T	101520832	5	4	5	1	0	0	0	0	0	0	1	0	5605	318	11	5	853	5	FAM55C	3	101520832	Splice_Site	SNP	A	TCGA-A4-7584-01A-11D-2136-08	31592300	101520832	96501598	19	324											
AP2M1	1173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183898969	183898969	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggatgaatgacaagattgTtattgaaaagcagggcaaag	16	9	13	3	0	0	4	0	3	0	1	0	5	0	5	0	2	1	3	0	2	6	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:183898969T>C	ENST00000292807.5	+	7	810	c.662T>C	c.(661-663)gTt>gCt	p.V221A	AP2M1_ENST00000439647.1_Missense_Mutation_p.V219A|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Missense_Mutation_p.V219A|AP2M1_ENST00000411763.2_Missense_Mutation_p.V246A|AP2M1_ENST00000461733.1_3'UTR	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	221	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACAAGATTGTTATTGAAAAG	0.562																																					p.V219A		.											.	AP2M1-90	0			c.T656C						.						145	153	151					3																	183898969		2060	4205	6265	SO:0001583	missense	1173	exon6			AGATTGTTATTGA	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, medium 1", "plasma membrane adaptor AP-2 50kDA protein", "clathrin coat adaptor protein AP50", "clathrin adaptor complex AP2, mu subunit", "HA2 50 kDA subunit", "clathrin assembly protein complex 2 medium chain", "AP-2 mu 2 chain"	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.662T>C	3.37:g.183898969T>C	ENSP00000292807:p.Val221Ala	Somatic	257	0		WXS	Illumina HiSeq	Phase_I	197	87	NM_001025205	0	1	121	243	121	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	37	CCDS43177.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963122	0.53507	.	.	ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000439647	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	6.07	4.91	0.64330	Clathrin adaptor, mu subunit, C-terminal (3);	0.164876	0.53938	D	0.000053	T	0.33059	0.0850	M	0.67569	2.06	0.58432	D	0.999999	B;B;B;B	0.26602	0.003;0.076;0.154;0.127	B;B;B;B	0.41174	0.039;0.349;0.198;0.125	T	0.09122	-1.0689	10	0.46703	T	0.11	.	12.1758	0.54184	0.0:0.0663:0.0:0.9337	.	111;91;221;219	B7Z4N2;B4DTI4;Q96CW1;Q96CW1-2	.;.;AP2M1_HUMAN;.	A	219;246;221;161;206;219	ENSP00000371894:V219A;ENSP00000403362:V246A;ENSP00000292807:V221A;ENSP00000409081:V219A	ENSP00000292807:V221A	V	+	2	0	AP2M1	185381663	1.000000	0.71417	0.993000	0.49108	0.920000	0.55202	7.375000	0.79646	1.119000	0.41883	-0.256000	0.11100	GTT	.		0.562	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068		C	183898969	T	C	183898969	3	2	5	1	0	0	0	0	1	0	0	0	742	1725	60	3	681	3	AP2M1	3	183898969	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	82378137	183898969	14123461	20	325											
FIP1L1	81608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	54266007	54266007	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actgggcttccaccgagcagGttagttacatagttataact	11	12	9	9	1	0	0	0	0	0	0	1	1	1	0	2	2	3	5	2	2	5	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr4:54266007G>C	ENST00000337488.6	+	10	1009		c.e10+1		FIP1L1_ENST00000358575.5_Splice_Site|FIP1L1_ENST00000306932.6_Splice_Site|FIP1L1_ENST00000507922.1_Splice_Site|FIP1L1_ENST00000507166.1_Splice_Site	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1						mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CACCGAGCAGGTTAGTTACAT	0.363			T	PDGFRA	idiopathic hypereosinophilic syndrome																																.		.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1-1083	0			c.701+1G>C						.						132	128	129					4																	54266007		2203	4300	6503	SO:0001630	splice_region_variant	81608	exon8			GAGCAGGTTAGTT	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.815+1G>C	4.37:g.54266007G>C		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	76	31	NM_001134938	0	0	0	7	7	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Splice_Site	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.122802	0.56613	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5077	0.95125	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FIP1L1	53960764	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	7.864000	0.87037	2.683000	0.91414	0.655000	0.94253	.	.		0.363	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	Intron	C	54266007	G	C	54266007	5	2	5	1	0	0	0	0	0	0	1	0	5915	1275	44	4	854	4	FIP1L1	4	54266007	Splice_Site	SNP	G	TCGA-A4-7584-01A-11D-2136-08		54266007	136888269	21	326											
PLRG1	5356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	155465648	155465648	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttttggcattgtaggggcTtttttagccatcagtgcaga	7	15	13	6	0	1	1	1	0	0	1	1	1	1	1	1	4	2	5	1	4	2	7			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr4:155465648T>C	ENST00000499023.2	-	7	669	c.543A>G	c.(541-543)aaA>aaG	p.K181K	PLRG1_ENST00000393905.2_Silent_p.K181K|RNU6-1285P_ENST00000363480.1_RNA|PLRG1_ENST00000302078.5_Silent_p.K172K	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	181					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTGTAGGGGCTTTTTTAGCCA	0.408																																					p.K181K		.											.	PLRG1-90	0			c.A543G						.						139	140	139					4																	155465648		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon7			AGGGGCTTTTTTA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.543A>G	4.37:g.155465648T>C		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	66	25	NM_002669	0	0	15	34	19	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			.		0.408	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		C	155465648	T	C	155465648	2	2	5	1	0	0	0	0	0	0	0	1	12132	1606	56	3		3	PLRG1	4	155465648	Silent	SNP	T	TCGA-A4-7584-01A-11D-2136-08	101199641	155465648	35688628	22	327											
PCSK1	5122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	95761622	95761622	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttctttttcatactgttgttCagcccatatcacctacaagg	9	16	5	11	0	4	0	3	0	1	0	4	0	4	0	2	1	3	2	2	1	4	8			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr5:95761622C>G	ENST00000311106.3	-	3	535	c.298G>C	c.(298-300)Gaa>Caa	p.E100Q	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.E53Q	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	100					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TACTGTTGTTCAGCCCATATC	0.383																																					p.E100Q		.											.	PCSK1-92	0			c.G298C						.						141	129	133					5																	95761622		2203	4300	6503	SO:0001583	missense	5122	exon3			GTTGTTCAGCCCA		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.298G>C	5.37:g.95761622C>G	ENSP00000308024:p.Glu100Gln	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	40	16	NM_000439	0	0	0	0	0	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305017	0.81247	.	.	ENSG00000175426	ENST00000311106;ENST00000508626;ENST00000509190	T;T;T	0.33216	1.42;1.42;2.19	5.63	5.63	0.86233	Proteinase inhibitor, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.35740	0.0942	L	0.39633	1.23	0.58432	D	0.999997	D	0.53312	0.959	P	0.49887	0.625	T	0.01613	-1.1312	10	0.15066	T	0.55	-30.1455	19.6351	0.95728	0.0:1.0:0.0:0.0	.	100	P29120	NEC1_HUMAN	Q	100;53;100	ENSP00000308024:E100Q;ENSP00000421600:E53Q;ENSP00000427294:E100Q	ENSP00000308024:E100Q	E	-	1	0	PCSK1	95787378	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.393000	0.79851	2.805000	0.96524	0.655000	0.94253	GAA	.		0.383	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		G	95761622	C	G	95761622	3	3	5	1	0	0	0	0	1	0	0	0	11626	835	29	4	2011	4	PCSK1	5	95761622	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		95761622	85153638	23	328											
FAM71B	153745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156590018	156590018	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	attccagacttcagcactggGctgggaaactttctggcttc	8	12	10	11	0	2	1	1	0	1	1	4	2	3	2	1	3	2	3	1	3	1	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr5:156590018G>C	ENST00000302938.4	-	2	1353	c.1258C>G	c.(1258-1260)Ccc>Gcc	p.P420A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	420						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCAGCACTGGGCTGGGAAACT	0.488																																					p.P420A		.											.	FAM71B-96	0			c.C1258G						.						102	103	102					5																	156590018		2203	4300	6503	SO:0001583	missense	153745	exon2			CACTGGGCTGGGA		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1258C>G	5.37:g.156590018G>C	ENSP00000305596:p.Pro420Ala	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	113	54	NM_130899	0	0	0	0	0	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.631608	0.00813	.	.	ENSG00000170613	ENST00000302938	T	0.17528	2.27	4.4	-1.91	0.07641	.	0.847983	0.09952	N	0.734546	T	0.10035	0.0246	L	0.48877	1.53	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.42849	-0.9427	10	0.07482	T	0.82	-0.6432	2.0469	0.03562	0.1:0.2599:0.2424:0.3977	.	420	Q8TC56	FA71B_HUMAN	A	420	ENSP00000305596:P420A	ENSP00000305596:P420A	P	-	1	0	FAM71B	156522596	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.057000	0.11768	-0.177000	0.10690	-0.291000	0.09656	CCC	.		0.488	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		C	156590018	G	C	156590018	3	2	5	1	0	0	0	0	1	0	0	0	5627	1203	42	4	563	4	FAM71B	5	156590018	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	60828396	156590018	24325242	24	329											
C6orf136	221545	broad.mit.edu	37	chr6	30615105	30615105	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggaggagaagagggagggAggagagggggcggggagaga	12	0	27	2	2	0	4	0	0	0	4	0	11	0	8	0	9	0	0	0	9	1	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:30615105A>G	ENST00000376473.5	+	1	231				C6orf136_ENST00000528347.2_5'Flank|C6orf136_ENST00000293604.6_Missense_Mutation_p.R33G|C6orf136_ENST00000376471.4_Intron|AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000493705.1_Intron	NM_001109938.2	NP_001103408.1	Q5SQH8	CF136_HUMAN	chromosome 6 open reading frame 136							mitochondrion (GO:0005739)				endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						AGAGGGAGGGAGGAGAGGGGG	0.736																																					p.R33G													.	C6orf136-90	0			c.A97G						.						11	13	13					6																	30615105		1739	3893	5632	SO:0001627	intron_variant	221545	exon1			GGAGGGAGGAGAG	BC016167	CCDS4684.1, CCDS43443.1, CCDS4684.2, CCDS54979.1	6p21.32	2012-02-06			ENSG00000204564	ENSG00000204564			21301	protein-coding gene	gene with protein product							Standard	NM_001109938		Approved	Em:AB023049.8	uc003nqx.4	Q5SQH8	OTTHUMG00000031221	ENST00000376473.5:c.72+25A>G	6.37:g.30615105A>G		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	33	8	NM_001161376	0	0	0	0	0	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Missense_Mutation	SNP	ENST00000376473.5	37	CCDS43443.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.959015	0.74016	.	.	ENSG00000204564	ENST00000293604	.	.	.	5.16	-1.74	0.08056	.	.	.	.	.	T	0.04679	0.0127	N	0.08118	0	0.19300	N	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.42849	-0.9427	7	.	.	.	.	5.8169	0.18497	0.4504:0.1339:0.4157:0.0	.	33	F8VX15	.	G	33	.	.	R	+	1	2	C6orf136	30723084	0.004000	0.15560	0.000000	0.03702	0.005000	0.04900	-0.181000	0.09740	-0.148000	0.11234	-0.408000	0.06270	AGG	.		0.736	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029		G	30615105	A	G	30615105	1	3	5	0	1	0	0	0	0	0	0	0	2337	295	11	3		3	C6orf136	6	30615105	Intron	SNP	A	TCGA-A4-7584-01A-11D-2136-08		30615105	140499962	25	330											
BAK1	578	hgsc.bcm.edu;broad.mit.edu	37	chr6	33543199	33543199	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgatgatggcgagctgccGtcccacctgccccatggtgc	5	7	12	17	3	0	1	0	1	0	0	1	3	1	1	6	2	4	1	6	2	0	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:33543199G>A	ENST00000374467.3	-	4	474	c.226C>T	c.(226-228)Cgg>Tgg	p.R76W	BAK1_ENST00000360661.5_Missense_Mutation_p.R76W|BAK1_ENST00000442998.2_Missense_Mutation_p.R76W	NM_001188.3	NP_001179.1	Q16611	BAK_HUMAN	BCL2-antagonist/killer 1	76					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell negative selection (GO:0002352)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast apoptotic process (GO:0044346)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|limb morphogenesis (GO:0035108)|mitochondrial fusion (GO:0008053)|myeloid cell homeostasis (GO:0002262)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of gene expression (GO:0010629)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|post-embryonic camera-type eye morphogenesis (GO:0048597)|regulation of cell cycle (GO:0051726)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to fungus (GO:0009620)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to mycotoxin (GO:0010046)|response to organic cyclic compound (GO:0014070)|response to UV-C (GO:0010225)|thymocyte apoptotic process (GO:0070242)|vagina development (GO:0060068)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|pore complex (GO:0046930)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4						GCGAGCTGCCGTCCCACCTGC	0.617																																					p.R76W		.											.	BAK1-638	0			c.C226T						.						106	81	89					6																	33543199		2203	4300	6503	SO:0001583	missense	578	exon4			GCTGCCGTCCCAC	U23765	CCDS4781.1	6p21.31	2014-03-07			ENSG00000030110	ENSG00000030110			949	protein-coding gene	gene with protein product		600516		CDN1		7715730, 7715731	Standard	NM_001188		Approved	BCL2L7, BAK	uc003oes.3	Q16611	OTTHUMG00000014530	ENST00000374467.3:c.226C>T	6.37:g.33543199G>A	ENSP00000363591:p.Arg76Trp	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	88	5	NM_001188	0	0	14	14	0	C0H5Y7|Q6I9T6|Q92533	Missense_Mutation	SNP	ENST00000374467.3	37	CCDS4781.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.079097	0.55753	.	.	ENSG00000030110	ENST00000374460;ENST00000374467;ENST00000442998;ENST00000360661	T;T;T	0.04654	3.58;3.58;3.58	4.41	2.63	0.31362	Apoptosis regulator, Bcl-2, BH3 motif, conserved site (1);	0.110712	0.39341	N	0.001388	T	0.06690	0.0171	M	0.64997	1.995	0.33612	D	0.603652	D;D	0.89917	1.0;1.0	D;D	0.81914	0.984;0.995	T	0.09640	-1.0665	10	0.87932	D	0	-19.7966	3.741	0.08530	0.2039:0.0:0.6032:0.1929	.	76;76	B4E0L2;Q16611	.;BAK_HUMAN	W	56;76;76;76	ENSP00000363591:R76W;ENSP00000391258:R76W;ENSP00000353878:R76W	ENSP00000353878:R76W	R	-	1	2	BAK1	33651177	0.936000	0.31750	0.523000	0.27875	0.957000	0.61999	1.834000	0.39171	0.517000	0.28361	0.543000	0.68304	CGG	.		0.617	BAK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040202.1	NM_001188		A	33543199	G	A	33543199	3	1	5	1	0	0	0	0	1	0	0	0	1306	1144	40	1	421	1	BAK1	6	33543199	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	2928094	33543199	137571868	26	331											
BAI3	577	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	69666026	69666027	+	Frame_Shift_Ins	INS	-	-	A																															agctgcccatggaggctccgINSaatgcagagggccatgggca																								rs141698131		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:69666026_69666027insA	ENST00000370598.1	+	7	2127_2128	c.1306_1307insA	c.(1306-1308)gaafs	p.E436fs		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	436	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TGGAGGCTCCGAATGCAGAGGG	0.554																																					p.E436fs		.											.	BAI3-1148	0			c.1306_1307insA						.																																			SO:0001589	frameshift_variant	577	exon7			.	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1308dupA	6.37:g.69666028_69666028dupA	ENSP00000359630:p.Glu436fs	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	53	22	NM_001704	0	0	0	0	0	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Frame_Shift_Ins	INS	ENST00000370598.1	37	CCDS4968.1																																																																																			.		0.554	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	69666027	-	A	69666026	7	5	5	1	0	1	1	0	0	0	0	0	1301	1059	37	0	1324	0	BAI3	6	69666026	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	36122827	69666026	101449041	27	332											
DDO	8528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	110734538	110734538	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttccggctgccacatcactgGtggtatctggagtaaacttg	8	12	11	10	1	2	0	1	0	1	0	3	1	3	1	2	4	2	3	2	4	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:110734538G>A	ENST00000368924.3	-	2	227	c.212C>T	c.(211-213)aCc>aTc	p.T71I	DDO_ENST00000368923.3_Missense_Mutation_p.T71I	NM_003649.2	NP_003640.2	Q99489	OXDD_HUMAN	D-aspartate oxidase	43					aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|D-amino acid catabolic process (GO:0019478)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insemination (GO:0007320)|oxidation-reduction process (GO:0055114)	peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-aspartate oxidase activity (GO:0008445)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|pancreas(1)|skin(3)	24		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		CACATCACTGGTGGTATCTGG	0.493																																					p.T71I		.											.	DDO-155	0			c.C212T						.						133	116	122					6																	110734538		2203	4300	6503	SO:0001583	missense	8528	exon2			TCACTGGTGGTAT	D89858	CCDS5082.1, CCDS5083.1	6q22.1	2008-02-05			ENSG00000203797	ENSG00000203797	1.4.3.1		2727	protein-coding gene	gene with protein product		124450				9163533	Standard	NM_003649		Approved		uc003puc.3	Q99489	OTTHUMG00000015360	ENST00000368924.3:c.212C>T	6.37:g.110734538G>A	ENSP00000357920:p.Thr71Ile	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	125	53	NM_004032	0	0	12	16	4	A8KAG4|Q5JXM4|Q5JXM5|Q5JXM6|Q8N552	Missense_Mutation	SNP	ENST00000368924.3	37	CCDS5082.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287509	0.80803	.	.	ENSG00000203797	ENST00000368924;ENST00000368923;ENST00000368925	D;D;D	0.83250	-1.7;-1.7;-1.7	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.94221	0.8145	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95581	0.8646	10	0.72032	D	0.01	-21.4422	19.187	0.93648	0.0:0.0:1.0:0.0	.	71;71	Q99489-4;Q99489-3	.;.	I	71;71;43	ENSP00000357920:T71I;ENSP00000357919:T71I;ENSP00000357921:T43I	ENSP00000357919:T71I	T	-	2	0	DDO	110841231	1.000000	0.71417	0.997000	0.53966	0.546000	0.35178	7.120000	0.77153	2.614000	0.88457	0.655000	0.94253	ACC	.		0.493	DDO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041796.1			A	110734538	G	A	110734538	3	1	5	1	0	0	0	0	1	0	0	0	4340	1261	44	2	913	2	DDO	6	110734538	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	41068512	110734538	60380529	28	333											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152631610	152631610	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttgcctgggcttgctccaagGcagcttgtaactttttcaac	7	14	9	11	0	1	0	1	0	0	0	2	0	2	0	2	2	5	5	2	2	3	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:152631610G>A	ENST00000367255.5	-	89	17541	c.16940C>T	c.(16939-16941)gCc>gTc	p.A5647V	SYNE1_ENST00000423061.1_Missense_Mutation_p.A5576V|SYNE1_ENST00000341594.5_Missense_Mutation_p.A5259V|SYNE1_ENST00000356820.4_Missense_Mutation_p.A171V|SYNE1_ENST00000448038.1_Missense_Mutation_p.A5576V|SYNE1_ENST00000265368.4_Missense_Mutation_p.A5647V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5647					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.A5647V(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGCTCCAAGGCAGCTTGTAA	0.433										HNSCC(10;0.0054)																											p.A5647V		.											.	SYNE1-607	2	Substitution - Missense(2)	large_intestine(2)	c.C16940T						.						104	103	103					6																	152631610		2203	4300	6503	SO:0001583	missense	23345	exon89			TCCAAGGCAGCTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16940C>T	6.37:g.152631610G>A	ENSP00000356224:p.Ala5647Val	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	50	19	NM_182961	0	0	2	4	2	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327610	0.81690	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50548	1.38;1.38;1.38;1.38;0.74;1.38	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000009	T	0.64136	0.2571	M	0.72118	2.19	0.53688	D	0.99997	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.961;0.961;0.983	T	0.57963	-0.7720	10	0.39692	T	0.17	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	5647;5647;5576	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	V	5647;5576;5647;5576;5259;171	ENSP00000356224:A5647V;ENSP00000396024:A5576V;ENSP00000265368:A5647V;ENSP00000390975:A5576V;ENSP00000341887:A5259V;ENSP00000349276:A171V	ENSP00000265368:A5647V	A	-	2	0	SYNE1	152673303	1.000000	0.71417	0.811000	0.32455	0.720000	0.41350	7.876000	0.87215	2.882000	0.98803	0.655000	0.94253	GCC	.		0.433	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152631610	G	A	152631610	3	1	5	1	0	0	0	0	1	0	0	0	15477	1203	42	2	9758	2	SYNE1	6	152631610	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	41897072	152631610	18483457	29	334											
CYP2W1	54905	hgsc.bcm.edu	37	chr7	1024913	1024913	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgtgtttgtgtccctgctggGtctcatcgatgaggtcatgg	4	14	14	9	2	2	1	2	1	1	0	5	2	3	1	1	3	1	2	1	3	0	1	rs143596553		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:1024913G>C	ENST00000308919.7	+	4	612	c.599G>C	c.(598-600)gGt>gCt	p.G200A	CYP2W1_ENST00000340150.6_Missense_Mutation_p.G144A	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	200					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		TCCCTGCTGGGTCTCATCGAT	0.647																																					p.G200A		.											.	CYP2W1-90	0			c.G599C						.	G	ALA/GLY	2,4272		0,2,2135	52	37	42		599	3.2	0.5	7	dbSNP_134	42	0,8454		0,0,4227	no	missense	CYP2W1	NM_017781.2	60	0,2,6362	CC,CG,GG		0.0,0.0468,0.0157	benign	200/491	1024913	2,12726	2137	4227	6364	SO:0001583	missense	54905	exon4			TGCTGGGTCTCAT	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"Cytochrome P450s"	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.599G>C	7.37:g.1024913G>C	ENSP00000310149:p.Gly200Ala	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	6	3	NM_017781	0	0	1	3	2		Missense_Mutation	SNP	ENST00000308919.7	37	CCDS5319.2	.	.	.	.	.	.	.	.	.	.	G	5.838	0.338852	0.11069	4.68E-4	0.0	ENSG00000073067	ENST00000308919;ENST00000340150	T;T	0.66638	-0.22;-0.22	5.06	3.25	0.37280	.	0.776457	0.12956	N	0.425435	T	0.53965	0.1829	L	0.33485	1.01	0.09310	N	1	B;B	0.22800	0.03;0.075	B;B	0.29524	0.038;0.103	T	0.42310	-0.9459	10	0.23302	T	0.38	.	8.1739	0.31270	0.25:0.0:0.75:0.0	.	144;200	A6NJ10;Q8TAV3	.;CP2W1_HUMAN	A	200;144	ENSP00000310149:G200A;ENSP00000344178:G144A	ENSP00000310149:G200A	G	+	2	0	CYP2W1	991439	0.008000	0.16893	0.502000	0.27614	0.938000	0.57974	1.741000	0.38238	0.536000	0.28733	0.491000	0.48974	GGT	G|1.000;C|0.000		0.647	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781		C	1024913	G	C	1024913	3	2	5	1	0	0	0	0	1	0	0	0	4182	1261	44	4	613	4	CYP2W1	7	1024913	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		1024913	158113750	30	335											
ACTB	60	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5568977	5568977	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaggatgcctctcttgcTctgggcctcgtcgcccacat	4	11	12	14	2	2	1	0	1	2	0	5	2	2	2	3	3	2	1	3	3	0	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:5568977T>C	ENST00000331789.5	-	3	369	c.178A>G	c.(178-180)Agc>Ggc	p.S60G	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	60					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		CCTCTCTTGCTCTGGGCCTCG	0.587																																					p.S60G		.											.	ACTB-226	0			c.A178G						.						71	73	73					7																	5568977		2203	4298	6501	SO:0001583	missense	60	exon3			TCTTGCTCTGGGC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.178A>G	7.37:g.5568977T>C	ENSP00000349960:p.Ser60Gly	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	178	97	NM_001101	0	0	725	2053	1328	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870663	0.51695	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72	4.91	4.91	0.64330	Actin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.92704	0.7681	M	0.81497	2.545	0.45594	D	0.998536	P	0.35033	0.481	P	0.45195	0.473	D	0.93247	0.6631	10	0.87932	D	0	.	12.5141	0.56021	0.0:0.0:0.0:1.0	.	60	P60709	ACTB_HUMAN	G	60;60;60;60;63;60	ENSP00000349960:S60G;ENSP00000407473:S60G;ENSP00000393951:S60G;ENSP00000399487:S63G;ENSP00000401032:S60G	ENSP00000349960:S60G	S	-	1	0	ACTB	5535503	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.816000	0.86201	1.837000	0.53436	0.460000	0.39030	AGC	.		0.587	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		C	5568977	T	C	5568977	3	2	5	1	0	0	0	0	1	0	0	0	193	1551	54	3	965	3	ACTB	7	5568977	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	4544064	5568977	153569686	31	336											
ANKMY2	57037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	16650259	16650260	+	Missense_Mutation	DNP	TC	TC	CT																															acagcttatgtaatgcatctTcatagccaatacttcattca																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:16650259_16650260TC>CT	ENST00000306999.2	-	6	903_904	c.660_661GA>AG	c.(658-663)atGAag>atAGag	p.220_221MK>IE		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	220						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TAATGCATCTTCATAGCCAATA	0.351																																					p.MK220IE		.											.	ANKMY2	0			c.G660A						.																																			SO:0001583	missense	57037	exon6			CATCTTCATAGCC	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.660_661delinsCT	7.37:g.16650259_16650260delinsCT	ENSP00000303570:p.M220_K221delinsIE	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	73	34		0	0	0	0	0	A4D124|Q659G1|Q96BL3	Missense_Mutation	DNP	ENST00000306999.2	37	CCDS5361.1																																																																																			.		0.351	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		CT	16650260	TC	CT	16650259	3	2	5	1	0	0	0	0	1	0	0	0	635	1792	62	3	684	3	ANKMY2	7	16650259	Missense_Mutation	DNP	TC	TCGA-A4-7584-01A-11D-2136-08	11081282	16650259	142488404	32	337											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	82584714	82584714	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcagaacaagaagatctaTggagctcctccatttctgca	13	11	7	10	0	3	3	1	0	2	3	5	4	5	4	2	1	3	2	2	1	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:82584714T>A	ENST00000333891.9	-	5	5892	c.5555A>T	c.(5554-5556)cAt>cTt	p.H1852L	PCLO_ENST00000423517.2_Missense_Mutation_p.H1852L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGAAGATCTATGGAGCTCCTC	0.408																																					p.H1852L		.											.	PCLO-29	0			c.A5555T						.						178	163	168					7																	82584714		1858	4097	5955	SO:0001583	missense	27445	exon5			GATCTATGGAGCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5555A>T	7.37:g.82584714T>A	ENSP00000334319:p.His1852Leu	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	202	67	NM_014510	0	0	1	1	0		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.390651	0.25118	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19938	2.11;2.12	5.57	5.57	0.84162	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.80722	D	1	P;P	0.41848	0.763;0.763	B;B	0.39185	0.293;0.293	T	0.02860	-1.1101	9	0.87932	D	0	.	15.7247	0.77747	0.0:0.0:0.0:1.0	.	1852;1852	Q9Y6V0-5;Q9Y6V0-6	.;.	L	1783;1852;1852	ENSP00000334319:H1852L;ENSP00000388393:H1852L	ENSP00000334319:H1852L	H	-	2	0	PCLO	82422650	0.995000	0.38212	0.924000	0.36721	0.989000	0.77384	2.626000	0.46460	2.116000	0.64780	0.533000	0.62120	CAT	.		0.408	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82584714	T	A	82584714	3	1	5	1	0	0	0	0	1	0	0	0	11609	1464	51	5	9974	5	PCLO	7	82584714	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	65934455	82584714	76553949	33	338											
WDR91	29062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	134871027	134871027	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggggctcggtggccacctAggctcaagcagctctccaga	8	6	13	14	1	2	1	1	0	1	1	4	1	2	1	3	5	2	4	3	5	2	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:134871027A>T	ENST00000354475.4	-	15	2151	c.2120T>A	c.(2119-2121)cTa>cAa	p.L707Q	WDR91_ENST00000423565.1_Missense_Mutation_p.L672Q|WDR91_ENST00000344400.5_3'UTR	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	707										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GTGGCCACCTAGGCTCAAGCA	0.587																																					p.L707Q		.											.	WDR91-137	0			c.T2120A						.						73	60	65					7																	134871027		2203	4300	6503	SO:0001583	missense	29062	exon15			CCACCTAGGCTCA	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.2120T>A	7.37:g.134871027A>T	ENSP00000346466:p.Leu707Gln	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	69	36	NM_014149	0	0	59	159	100	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	A	31	5.060981	0.93846	.	.	ENSG00000105875	ENST00000354475;ENST00000423565	T;T	0.68479	-0.33;-0.33	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82174	-0.0588	10	0.87932	D	0	-16.5822	15.6802	0.77360	1.0:0.0:0.0:0.0	.	707	A4D1P6	WDR91_HUMAN	Q	707;672	ENSP00000346466:L707Q;ENSP00000392555:L672Q	ENSP00000346466:L707Q	L	-	2	0	WDR91	134521567	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.103000	0.63969	0.533000	0.62120	CTA	.		0.587	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		T	134871027	A	T	134871027	3	4	5	1	0	0	0	0	1	0	0	0	17371	420	15	5	127	5	WDR91	7	134871027	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	52286313	134871027	24267636	34	339											
FAM164A	51101	hgsc.bcm.edu	37	chr8	79578395	79578395	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtggcgcgatggagggactGgaaggtgaggcgatgaaggg	9	5	23	4	3	0	2	0	2	0	0	0	7	0	5	0	8	0	0	0	8	2	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr8:79578395G>C	ENST00000263849.4	+	1	114	c.12G>C	c.(10-12)ctG>ctC	p.L4L	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	4							metal ion binding (GO:0046872)										TGGAGGGACTGGAAGGTGAGG	0.672																																					p.L4L		.											.	.	0			c.G12C						.						112	84	93					8																	79578395		2187	4279	6466	SO:0001819	synonymous_variant	51101	exon1			GGGACTGGAAGGT		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"Zinc fingers, C2HC-type containing"	24277	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 70", "family with sequence similarity 164, member A"	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.12G>C	8.37:g.79578395G>C		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	10	6	NM_016010	0	0	0	0	0	Q9Y372	Silent	SNP	ENST00000263849.4	37	CCDS6223.1																																																																																			.		0.672	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		C	79578395	G	C	79578395	2	2	5	1	0	0	0	0	0	0	0	1	5494	1335	47	4		4	FAM164A	8	79578395	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08		79578395	66785627	35	340											
EFR3A	23167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	132968018	132968018	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcgttcctttttagtcgCataggccctccttcttctcc	3	18	5	15	2	3	0	0	0	3	0	8	0	5	0	4	1	0	2	4	1	2	8			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr8:132968018C>T	ENST00000254624.5	+	7	867	c.642C>T	c.(640-642)cgC>cgT	p.R214R	EFR3A_ENST00000334503.4_Silent_p.R214R|EFR3A_ENST00000519656.1_Silent_p.R178R	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	214						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTTTTAGTCGCATAGGCCCTC	0.358																																					p.R214R		.											.	EFR3A-139	0			c.C642T						.						108	111	110					8																	132968018		2203	4300	6503	SO:0001819	synonymous_variant	23167	exon7			TAGTCGCATAGGC	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.642C>T	8.37:g.132968018C>T		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	86	26	NM_015137	0	0	0	0	0	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																			.		0.358	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		T	132968018	C	T	132968018	2	4	5	1	0	0	0	0	0	0	0	1	4969	697	25	2		2	EFR3A	8	132968018	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	53389623	132968018	13396004	36	341											
USP20	10868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	132623219	132623219	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggtctttaacacaggacTccccgccaccctcccaccct	7	9	6	19	1	1	0	0	0	1	0	3	1	3	1	6	2	1	0	6	2	1	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr9:132623219T>C	ENST00000315480.4	+	7	492	c.334T>C	c.(334-336)Tcc>Ccc	p.S112P	USP20_ENST00000358355.1_Missense_Mutation_p.S112P|USP20_ENST00000372429.3_Missense_Mutation_p.S112P			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	112					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				AACACAGGACTCCCCGCCACC	0.567																																					p.S112P		.											.	USP20-658	0			c.T334C						.						146	150	149					9																	132623219		1918	4121	6039	SO:0001583	missense	10868	exon7			CAGGACTCCCCGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.334T>C	9.37:g.132623219T>C	ENSP00000313811:p.Ser112Pro	Somatic	394	1		WXS	Illumina HiSeq	Phase_I	219	72	NM_001008563	0	0	0	0	0	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.787014	0.31593	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.20463	2.07;2.07;2.07	5.66	1.8	0.24995	.	0.866856	0.10550	N	0.661611	T	0.16342	0.0393	L	0.46157	1.445	0.38108	D	0.937486	B	0.02656	0.0	B	0.04013	0.001	T	0.10337	-1.0634	10	0.30078	T	0.28	.	4.2306	0.10601	0.1241:0.0686:0.1298:0.6776	.	112	Q9Y2K6	UBP20_HUMAN	P	112	ENSP00000361506:S112P;ENSP00000313811:S112P;ENSP00000351122:S112P	ENSP00000313811:S112P	S	+	1	0	USP20	131663040	0.020000	0.18652	0.710000	0.30468	0.947000	0.59692	1.028000	0.30128	0.407000	0.25591	0.459000	0.35465	TCC	.		0.567	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			C	132623219	T	C	132623219	3	2	5	1	0	0	0	0	1	0	0	0	17085	1551	54	3	352	3	USP20	9	132623219	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08		132623219	8590212	37	342											
AKR1C3	8644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	5139704	5139704	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaaagctcaattggactatGttgacctctatcttattcat	12	15	6	8	0	4	2	2	1	2	1	4	3	4	3	1	1	1	2	1	1	5	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr10:5139704G>C	ENST00000380554.3	+	3	983	c.331G>C	c.(331-333)Gtt>Ctt	p.V111L	AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.V88L|AKR1C3_ENST00000439082.2_5'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	111					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	ATTGGACTATGTTGACCTCTA	0.403																																					p.V111L		.											.	AKR1C3-515	0			c.G331C						.						146	138	141					10																	5139704		2203	4300	6503	SO:0001583	missense	8644	exon3			GACTATGTTGACC	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.331G>C	10.37:g.5139704G>C	ENSP00000369927:p.Val111Leu	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	89	40	NM_001253908	0	0	31	80	49	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.596157	0.00857	.	.	ENSG00000196139	ENST00000380554	T	0.47528	0.84	1.62	0.671	0.17929	NADP-dependent oxidoreductase domain (3);	0.237158	0.29558	N	0.011809	T	0.23410	0.0566	N	0.17564	0.495	0.80722	D	1	B;B;B	0.23249	0.082;0.005;0.005	B;B;B	0.30251	0.113;0.046;0.046	T	0.06972	-1.0797	10	0.07325	T	0.83	.	4.0982	0.10002	0.3926:0.0:0.6074:0.0	.	111;111;111	B4DKT3;P42330;Q2XPP3	.;AK1C3_HUMAN;.	L	111	ENSP00000369927:V111L	ENSP00000369927:V111L	V	+	1	0	AKR1C3	5129704	1.000000	0.71417	0.072000	0.20136	0.187000	0.23431	2.141000	0.42168	0.234000	0.21139	0.305000	0.20034	GTT	.		0.403	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		C	5139704	G	C	5139704	3	2	5	1	0	0	0	0	1	0	0	0	471	1377	48	4	341	4	AKR1C3	10	5139704	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		5139704	130395043	38	343											
TACR2	6865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	71175766	71175766	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggttctggaagtagcagAaggcacggccaaagtaccag	14	5	14	8	1	1	2	0	0	1	2	1	3	1	3	2	4	2	5	2	4	5	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr10:71175766A>T	ENST00000373306.4	-	1	857	c.314T>A	c.(313-315)tTc>tAc	p.F105Y		NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	105					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						GAAGTAGCAGAAGGCACGGCC	0.552																																					p.F105Y		.											.	TACR2-522	0			c.T314A						.						92	81	85					10																	71175766		2203	4300	6503	SO:0001583	missense	6865	exon1			TAGCAGAAGGCAC		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"GPCR / Class A : Tachykinin receptors"	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.314T>A	10.37:g.71175766A>T	ENSP00000362403:p.Phe105Tyr	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	43	19	NM_001057	0	0	0	0	0	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	37	CCDS7293.1	.	.	.	.	.	.	.	.	.	.	A	7.919	0.738168	0.15574	.	.	ENSG00000075073	ENST00000373306	T	0.38240	1.15	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.063724	0.64402	D	0.000003	T	0.11922	0.0290	N	0.01493	-0.835	0.42246	D	0.99195	B	0.22146	0.065	B	0.20577	0.03	T	0.20140	-1.0284	10	0.02654	T	1	.	10.5582	0.45129	0.8559:0.0:0.0:0.1441	.	105	P21452	NK2R_HUMAN	Y	105	ENSP00000362403:F105Y	ENSP00000362403:F105Y	F	-	2	0	TACR2	70845772	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.205000	0.51090	2.093000	0.63338	0.460000	0.39030	TTC	.		0.552	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1			T	71175766	A	T	71175766	3	4	5	1	0	0	0	0	1	0	0	0	15538	246	9	5	902	5	TACR2	10	71175766	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	66036062	71175766	64358981	39	344											
MRPL17	63875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6703594	6703594	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agtttgatctttgtaccgagGggccagtacttgaaacagct	10	12	11	8	1	1	2	0	2	1	0	1	3	1	2	2	2	4	4	2	2	3	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:6703594G>A	ENST00000288937.6	-	3	387	c.283C>T	c.(283-285)Cct>Tct	p.P95S	MRPL17_ENST00000532676.1_5'UTR	NM_022061.3	NP_071344.1	Q9NRX2	RM17_HUMAN	mitochondrial ribosomal protein L17	95					translation (GO:0006412)	mitochondrial inner membrane (GO:0005743)|ribosome (GO:0005840)	protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			lung(4)	4		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTGTACCGAGGGGCCAGTACT	0.473																																					p.P95S		.											.	MRPL17-90	0			c.C283T						.						115	114	114					11																	6703594		2201	4296	6497	SO:0001583	missense	63875	exon3			ACCGAGGGGCCAG	AB051620	CCDS31412.1	11p15.5-p15.4	2012-09-13				ENSG00000158042		"Mitochondrial ribosomal proteins / large subunits"	14053	protein-coding gene	gene with protein product		611830					Standard	NM_022061		Approved	RPML26, MRP-L26	uc001men.2	Q9NRX2		ENST00000288937.6:c.283C>T	11.37:g.6703594G>A	ENSP00000288937:p.Pro95Ser	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	141	48	NM_022061	0	0	42	73	31	D3DQU3|Q6IAH8|Q96Q53|Q9C066	Missense_Mutation	SNP	ENST00000288937.6	37	CCDS31412.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970737	0.74246	.	.	ENSG00000158042	ENST00000288937;ENST00000532203	.	.	.	5.73	5.73	0.89815	.	0.051442	0.85682	D	0.000000	D	0.83275	0.5219	M	0.85041	2.73	0.58432	D	0.999999	P	0.52061	0.95	D	0.65010	0.931	D	0.85197	0.1013	9	0.72032	D	0.01	-5.0434	17.4724	0.87649	0.0:0.0:1.0:0.0	.	95	Q9NRX2	RM17_HUMAN	S	95;72	.	ENSP00000288937:P95S	P	-	1	0	MRPL17	6660170	1.000000	0.71417	0.999000	0.59377	0.565000	0.35776	6.015000	0.70791	2.720000	0.93068	0.555000	0.69702	CCT	.		0.473	MRPL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384544.1	NM_022061		A	6703594	G	A	6703594	3	1	5	1	0	0	0	0	1	0	0	0	9807	1232	43	2	248	2	MRPL17	11	6703594	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		6703594	128302922	40	345											
DYNC2H1	79659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102987369	102987369	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggagactactcaggatgttgTagatgatgtgtggagacaaa	13	10	14	4	0	1	4	1	1	0	3	1	7	1	5	0	3	1	2	0	3	3	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:102987369T>C	ENST00000375735.2	+	5	836	c.692T>C	c.(691-693)gTa>gCa	p.V231A	DYNC2H1_ENST00000334267.7_Missense_Mutation_p.V231A|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.V231A	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	231	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CAGGATGTTGTAGATGATGTG	0.343																																					p.V231A		.											.	DYNC2H1-68	0			c.T692C						.						187	184	185					11																	102987369		1897	4123	6020	SO:0001583	missense	79659	exon5			ATGTTGTAGATGA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.692T>C	11.37:g.102987369T>C	ENSP00000364887:p.Val231Ala	Somatic	180	1		WXS	Illumina HiSeq	Phase_I	127	56	NM_001377	0	0	2	2	0	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.845053	0.51164	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.59224	0.28;0.28;0.28	5.55	5.55	0.83447	Dynein heavy chain, domain-1 (1);	.	.	.	.	T	0.66886	0.2835	L	0.50919	1.6	0.44899	D	0.99791	D;B;P	0.63880	0.993;0.056;0.481	P;B;B	0.57720	0.826;0.088;0.217	T	0.67237	-0.5721	9	0.45353	T	0.12	.	15.7067	0.77588	0.0:0.0:0.0:1.0	.	231;231;231	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	A	231	ENSP00000364887:V231A;ENSP00000334021:V231A;ENSP00000381167:V231A	ENSP00000334021:V231A	V	+	2	0	DYNC2H1	102492579	1.000000	0.71417	0.996000	0.52242	0.934000	0.57294	7.698000	0.84413	2.104000	0.64026	0.528000	0.53228	GTA	.		0.343	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	102987369	T	C	102987369	3	2	5	1	0	0	0	0	1	0	0	0	4857	1638	57	3	710	3	DYNC2H1	11	102987369	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	96283775	102987369	32019147	41	346											
FDXACB1	91893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	111749725	111749725	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattctcccaggccagtggAtcccgagccaactcggccgg	8	6	12	15	3	1	1	0	0	1	1	4	3	2	2	5	4	2	0	5	4	1	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:111749725A>G	ENST00000260257.4	-	1	179	c.132T>C	c.(130-132)gaT>gaC	p.D44D	ALG9_ENST00000524880.1_Silent_p.D44D|C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000527377.1_5'Flank|C11orf1_ENST00000529270.1_5'Flank|FDXACB1_ENST00000542429.1_5'UTR|C11orf1_ENST00000260276.3_5'Flank|C11orf1_ENST00000528125.1_5'UTR	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	44					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						AGGCCAGTGGATCCCGAGCCA	0.667											OREG0021330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D44D		.											.	FDXACB1-22	0			c.T132C						.						16	22	20					11																	111749725		1936	4151	6087	SO:0001819	synonymous_variant	91893	exon1			CAGTGGATCCCGA		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.132T>C	11.37:g.111749725A>G		Somatic	28	0	1437	WXS	Illumina HiSeq	Phase_I	25	11	NM_138378	0	0	2	3	1	A0PJW7|B4DUU2	Silent	SNP	ENST00000260257.4	37	CCDS44729.1																																																																																			.		0.667	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		G	111749725	A	G	111749725	2	3	5	1	0	0	0	0	0	0	0	1	5825	330	12	3		3	FDXACB1	11	111749725	Silent	SNP	A	TCGA-A4-7584-01A-11D-2136-08	8762356	111749725	23256791	42	347											
MANSC1	54682	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	12483592	12483592	+	Frame_Shift_Del	DEL	T	T	-																															tagctgggagcgcactcacaTtttcaggcagcagatgagct																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:12483592delT	ENST00000535902.1	-	4	1228	c.665delA	c.(664-666)aatfs	p.N222fs	MANSC1_ENST00000396349.3_Frame_Shift_Del_p.N188fs|MANSC1_ENST00000545735.1_Frame_Shift_Del_p.N141fs			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	222						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		CGCACTCACATTTTCAGGCAG	0.502																																					p.N222fs		.											.	MANSC1-90	0			c.665delA						.						101	106	104					12																	12483592		2203	4300	6503	SO:0001589	frameshift_variant	54682	exon4			.	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.665delA	12.37:g.12483592delT	ENSP00000438205:p.Asn222fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	109	37	NM_018050	0	0	0	0	0	Q8NEC1|Q9NW60	Frame_Shift_Del	DEL	ENST00000535902.1	37	CCDS8648.1																																																																																			.		0.502	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050		-	12483592	T	-	12483592	7	5	5	1	0	1	0	1	0	0	0	0	9249	1493	52	0	634	0	MANSC1	12	12483592	Frame_Shift_Del	DEL	T	TCGA-A4-7584-01A-11D-2136-08		12483592	121368303	43	348											
GUCY2C	2984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	14772233	14772233	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgattcccacaactccagcAgcacagggacctgaaatgaa	14	7	8	12	0	0	3	0	3	0	0	2	4	2	4	3	1	3	2	3	1	3	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:14772233A>C	ENST00000261170.3	-	24	2923	c.2787T>G	c.(2785-2787)gcT>gcG	p.A929A	RP11-695J4.2_ENST00000542401.1_RNA|RP11-695J4.2_ENST00000545424.1_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	929	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CAACTCCAGCAGCACAGGGAC	0.483																																					p.A929A		.											.	GUCY2C-338	0			c.T2787G						.						95	93	93					12																	14772233		2203	4300	6503	SO:0001819	synonymous_variant	2984	exon24			TCCAGCAGCACAG		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.2787T>G	12.37:g.14772233A>C		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	91	29	NM_004963	0	0	6	16	10	B2RMY6	Silent	SNP	ENST00000261170.3	37	CCDS8664.1																																																																																			.		0.483	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			C	14772233	A	C	14772233	2	2	5	1	0	0	0	0	0	0	0	1	6917	175	7	5		5	GUCY2C	12	14772233	Silent	SNP	A	TCGA-A4-7584-01A-11D-2136-08	2288641	14772233	119079662	44	349											
CNTN1	1272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	41316146	41316146	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttatcaacaaccctgacaaaCagaaagatgctggaatatac	18	8	6	9	0	1	3	1	1	0	2	1	4	1	4	1	1	5	1	1	1	8	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:41316146C>T	ENST00000551295.2	+	5	433	c.316C>T	c.(316-318)Cag>Tag	p.Q106*	CNTN1_ENST00000348761.2_Nonsense_Mutation_p.Q95*|CNTN1_ENST00000547702.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000547849.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000347616.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000360099.3_Nonsense_Mutation_p.Q106*	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	106	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				CCCTGACAAACAGAAAGATGC	0.398																																					p.Q106X		.											.	CNTN1-1149	0			c.C316T						.						138	123	128					12																	41316146		2203	4300	6503	SO:0001587	stop_gained	1272	exon5			GACAAACAGAAAG	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.316C>T	12.37:g.41316146C>T	ENSP00000447006:p.Gln106*	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	84	38	NM_001256063	0	0	0	0	0	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Nonsense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063249	0.76187	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	.	.	.	5.65	4.74	0.60224	.	0.687302	0.15218	N	0.274073	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	7.1246	0.25465	0.0:0.7637:0.0:0.2363	.	.	.	.	X	106;106;106;106;106;95	.	ENSP00000325660:Q106X	Q	+	1	0	CNTN1	39602413	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.250000	0.32850	2.833000	0.97629	0.585000	0.79938	CAG	.		0.398	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		T	41316146	C	T	41316146	4	4	5	1	0	0	0	0	0	1	0	0	3646	479	17	2	330	2	CNTN1	12	41316146	Nonsense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	26543913	41316146	92535749	45	350											
KIF5A	3798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57975209	57975209	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttattgcagccaaacccgtcCggcctggccactacccagca	9	7	8	17	2	0	0	0	0	0	0	1	0	1	0	6	2	5	2	6	2	3	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:57975209C>T	ENST00000455537.2	+	25	3041	c.2767C>T	c.(2767-2769)Cgg>Tgg	p.R923W	KIF5A_ENST00000286452.5_Missense_Mutation_p.R834W	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	923	Globular.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAAACCCGTCCGGCCTGGCCA	0.547																																					p.R923W		.											.	KIF5A-517	0			c.C2767T						.						74	75	75					12																	57975209		2203	4300	6503	SO:0001583	missense	3798	exon25			CCCGTCCGGCCTG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2767C>T	12.37:g.57975209C>T	ENSP00000408979:p.Arg923Trp	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	125	50	NM_004984	0	0	0	0	0	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159251	0.78226	.	.	ENSG00000155980	ENST00000455537;ENST00000286452;ENST00000547989	T;T	0.81078	-1.38;-1.45	4.52	3.59	0.41128	.	0.201593	0.32343	N	0.006224	D	0.86715	0.5999	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71184	0.972;0.972	D	0.87757	0.2596	10	0.87932	D	0	.	12.7339	0.57212	0.1717:0.8283:0.0:0.0	.	834;923	B7Z2M7;Q12840	.;KIF5A_HUMAN	W	923;834;17	ENSP00000408979:R923W;ENSP00000286452:R834W	ENSP00000286452:R834W	R	+	1	2	KIF5A	56261476	1.000000	0.71417	0.989000	0.46669	0.881000	0.50899	5.716000	0.68437	1.212000	0.43366	0.561000	0.74099	CGG	.		0.547	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57975209	C	T	57975209	3	4	5	1	0	0	0	0	1	0	0	0	8326	643	23	1	2865	1	KIF5A	12	57975209	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	16659063	57975209	75876686	46	351											
NAV3	89795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	78604234	78604234	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactcgagcacacaaagctgCgacagcgaaagcaccagcca	15	3	9	14	3	0	0	0	0	0	0	1	3	0	0	2	0	7	3	2	0	3	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:78604234C>T	ENST00000397909.2	+	40	7268	c.7095C>T	c.(7093-7095)tgC>tgT	p.C2365C	NAV3_ENST00000228327.6_Silent_p.C2343C|NAV3_ENST00000541270.1_Silent_p.C195C|NAV3_ENST00000266692.7_Silent_p.C2166C|NAV3_ENST00000536525.2_Silent_p.C2343C			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2365						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CACAAAGCTGCGACAGCGAAA	0.403										HNSCC(70;0.22)																											p.C2343C		.											.	NAV3-279	0			c.C7029T						.						55	58	57					12																	78604234		1952	4172	6124	SO:0001819	synonymous_variant	89795	exon39			AAGCTGCGACAGC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.7095C>T	12.37:g.78604234C>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	71	26	NM_014903	0	0	0	0	0	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	C	0.069	-1.207030	0.01568	.	.	ENSG00000067798	ENST00000552895;ENST00000551162	.	.	.	5.35	-7.82	0.01205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.2288	19.8674	0.96824	0.0:0.1434:0.0:0.8566	.	.	.	.	X	1238;233	.	.	R	+	1	2	NAV3	77128365	0.348000	0.24861	0.594000	0.28785	0.129000	0.20672	-0.324000	0.07986	-1.610000	0.01583	-2.173000	0.00322	CGA	.		0.403	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78604234	C	T	78604234	2	4	5	1	0	0	0	0	0	0	0	1	10210	776	27	1		1	NAV3	12	78604234	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	20629025	78604234	55247661	47	352											
KIAA1033	23325	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	105527569	105527569	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gatgtacagtcttactacgtCtttgtgagctcatggatgat	9	15	10	7	1	3	2	1	2	2	0	3	4	3	3	0	1	4	2	0	1	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:105527569C>G	ENST00000332180.5	+	14	1308	c.1221C>G	c.(1219-1221)gtC>gtG	p.V407V		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						CTTACTACGTCTTTGTGAGCT	0.323																																					p.V407V		.											.	KIAA1033-91	0			c.C1221G						.						177	171	173					12																	105527569		1859	4091	5950	SO:0001819	synonymous_variant	23325	exon14			CTACGTCTTTGTG	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.1221C>G	12.37:g.105527569C>G		Somatic	139	1		WXS	Illumina HiSeq	Phase_I	119	29	NM_015275	0	0	9	16	7		Silent	SNP	ENST00000332180.5	37	CCDS41826.1																																																																																			.		0.323	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		G	105527569	C	G	105527569	2	3	5	1	0	0	0	0	0	0	0	1	8227	900	32	4		4	KIAA1033	12	105527569	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	26923335	105527569	28324326	48	353											
ABCB9	23457	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	123429030	123429030	+	Frame_Shift_Del	DEL	A	A	-																															gatgacaaggtggcccccgtAgtagaggatgctgacctgga																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:123429030delA	ENST00000542678.1	-	7	4126	c.1288delT	c.(1288-1290)tacfs	p.Y430fs	ABCB9_ENST00000540285.1_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000392439.3_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000344275.7_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000442028.2_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000346530.5_Intron|ABCB9_ENST00000280560.8_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000442833.2_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000541983.1_5'UTR			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	430	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		TGGCCCCCGTAGTAGAGGATG	0.592																																					p.Y430fs	Ovarian(49;786 1333 9175 38236)	.											.	ABCB9-90	0			c.1288delT						.						139	120	127					12																	123429030		2203	4300	6503	SO:0001589	frameshift_variant	23457	exon7			.	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.1288delT	12.37:g.123429030delA	ENSP00000440288:p.Tyr430fs	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	180	58	NM_019625	0	0	0	0	0	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	37	CCDS9241.1																																																																																			.		0.592	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		-	123429030	A	-	123429030	7	5	5	1	0	1	0	1	0	0	0	0	48	420	15	0	1036	0	ABCB9	12	123429030	Frame_Shift_Del	DEL	A	TCGA-A4-7584-01A-11D-2136-08	17901461	123429030	10422865	49	354											
KCTD4	386618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	45768535	45768535	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actataccttcaaggaaagtGtctgggtacttggtcagtgt	10	13	11	7	0	3	0	2	0	1	0	3	1	3	1	1	3	2	1	1	3	5	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr13:45768535G>A	ENST00000379108.1	-	1	317	c.168C>T	c.(166-168)gaC>gaT	p.D56D	KCTD4_ENST00000405872.1_Silent_p.D56D|GTF2F2_ENST00000340473.6_Intron			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	56	BTB.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		CAAGGAAAGTGTCTGGGTACT	0.413																																					p.D56D		.											.	KCTD4-90	0			c.C168T						.						266	265	265					13																	45768535		2203	4300	6503	SO:0001819	synonymous_variant	386618	exon2			GAAAGTGTCTGGG	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.168C>T	13.37:g.45768535G>A		Somatic	288	0		WXS	Illumina HiSeq	Phase_I	182	55	NM_198404	0	0	0	0	0	Q5W0P9	Silent	SNP	ENST00000379108.1	37	CCDS9396.1																																																																																			.		0.413	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			A	45768535	G	A	45768535	2	1	5	1	0	0	0	0	0	0	0	1	8132	1368	48	2		2	KCTD4	13	45768535	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08		45768535	69401343	50	355											
SDCCAG1	9147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	50256253	50256253	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcacggtcttcttcatcCtggtctttgtatttttcttt	4	22	6	9	1	6	0	2	0	4	0	7	0	7	0	1	2	0	2	1	2	1	8			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr14:50256253C>T	ENST00000298310.5	-	27	3107	c.2658G>A	c.(2656-2658)caG>caA	p.Q886Q	NEMF_ENST00000545773.1_Silent_p.Q844Q|NEMF_ENST00000382135.2_Silent_p.Q86Q|NEMF_ENST00000546046.1_Silent_p.Q865Q|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	886					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						CTTCTTCATCCTGGTCTTTGT	0.328																																					p.Q886Q		.											.	NEMF-90	0			c.G2658A						.						130	123	125					14																	50256253		2203	4300	6503	SO:0001819	synonymous_variant	9147	exon27			TTCATCCTGGTCT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2658G>A	14.37:g.50256253C>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	63	17	NM_004713	0	0	6	13	7	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Silent	SNP	ENST00000298310.5	37	CCDS9694.1																																																																																			.		0.328	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		T	50256253	C	T	50256253	2	4	5	1	0	0	0	0	0	0	0	1	13989	680	24	2		2	SDCCAG1	14	50256253	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08		50256253	57093287	51	356											
VRK1	7443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	97321567	97321567	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggaaatttataggtgtacTtggtagattatggccttgct	9	17	11	4	0	0	1	0	0	0	1	0	2	0	2	1	4	2	3	1	4	6	9			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr14:97321567T>A	ENST00000216639.3	+	8	732	c.583T>A	c.(583-585)Ttg>Atg	p.L195M		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		ATAGGTGTACTTGGTAGATTA	0.388																																					p.L195M		.											.	VRK1-358	0			c.T583A						.						199	195	196					14																	97321567		2203	4300	6503	SO:0001583	missense	7443	exon8			GTGTACTTGGTAG	AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.583T>A	14.37:g.97321567T>A	ENSP00000216639:p.Leu195Met	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	105	46	NM_003384	0	0	0	0	0	Q3SYL2	Missense_Mutation	SNP	ENST00000216639.3	37	CCDS9947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.34|19.34	3.808500|3.808500	0.70797|0.70797	.|.	.|.	ENSG00000100749|ENSG00000100749	ENST00000557222|ENST00000216639	.|T	.|0.72835	.|-0.69	5.95|5.95	1.04|1.04	0.20106|0.20106	.|Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.81024|0.81024	0.4737|0.4737	M|M	0.76938|0.76938	2.355|2.355	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.78823|0.78823	-0.2052|-0.2052	6|10	.|0.66056	.|D	.|0.02	-11.377|-11.377	9.4931|9.4931	0.38971|0.38971	0.0:0.2599:0.0:0.7401|0.0:0.2599:0.0:0.7401	.|.	.|195	.|Q99986	.|VRK1_HUMAN	H|M	51|195	.|ENSP00000216639:L195M	.|ENSP00000216639:L195M	L|L	+|+	2|1	0|2	VRK1|VRK1	96391320|96391320	0.992000|0.992000	0.36948|0.36948	0.995000|0.995000	0.50966|0.50966	0.985000|0.985000	0.73830|0.73830	0.976000|0.976000	0.29462|0.29462	-0.050000|-0.050000	0.13356|0.13356	0.533000|0.533000	0.62120|0.62120	CTT|TTG	.		0.388	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384		A	97321567	T	A	97321567	3	1	5	1	0	0	0	0	1	0	0	0	17252	1606	56	5	609	5	VRK1	14	97321567	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	47065314	97321567	10027973	52	357											
FAM82A2	55177	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	41037304	41037305	+	Frame_Shift_Ins	INS	-	-	GCACT																															aggaacctccagcctccaggINSgcactggaggcacctgaagc																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:41037304_41037305insGCACT	ENST00000260385.6	-	4	1744_1745	c.677_678insAGTGC	c.(676-678)gccfs	p.-226fs	RMDN3_ENST00000338376.3_Frame_Shift_Ins_p.-226fs|RMDN3_ENST00000558560.1_Intron			Q96TC7	RMD3_HUMAN	regulator of microtubule dynamics 3						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)	integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CAGCCTCCAGGGCACTGGAGGC	0.599																																					p.A226fs		.											.	.	0			c.678_679insAGTGC						.																																			SO:0001589	frameshift_variant	55177	exon5			.	AK001441	CCDS10063.1	15q15.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000137824	ENSG00000137824			25550	protein-coding gene	gene with protein product		611873	"family with sequence similarity 82, member A2"	FAM82C, FAM82A2		12975309	Standard	XM_005254531		Approved	FLJ10579, PTPIP51, RMD3	uc001zmp.1	Q96TC7	OTTHUMG00000130066	ENST00000260385.6:c.673_677dupAGTGC	15.37:g.41037305_41037309dupGCACT	ENSP00000260385:p.Ala226fs	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	61	16	NM_018145	0	0	0	0	0	A9UMZ9|B3KRR3|Q6ZWE9|Q96H23|Q96SD6|Q9H6G1|Q9NVQ6	Frame_Shift_Ins	INS	ENST00000260385.6	37	CCDS10063.1																																																																																			.		0.599	RMDN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252357.1	NM_018145		GCACT	41037305	-	GCACT	41037304	7	5	5	1	0	1	1	0	0	0	0	0	5650	1219	43	0	770	0	FAM82A2	15	41037304	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08		41037304	61494088	53	358											
DUOX1	53905	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	45453182	45453182	+	Frame_Shift_Del	DEL	C	C	-																															tggtgaaggcggagctgctgCcctcaggtaccagcctggca																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:45453182delC	ENST00000321429.4	+	30	4257	c.3850delC	c.(3850-3852)cccfs	p.P1284fs	DUOX1_ENST00000561166.1_Frame_Shift_Del_p.P930fs|DUOX1_ENST00000389037.3_Frame_Shift_Del_p.P1284fs|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1284	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GGAGCTGCTGCCCTCAGGTAC	0.617																																					p.P1284fs		.											.	DUOX1-142	0			c.3850delC						.						81	65	71					15																	45453182		2198	4298	6496	SO:0001589	frameshift_variant	53905	exon30			.	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3850delC	15.37:g.45453182delC	ENSP00000317997:p.Pro1284fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	61	22	NM_017434	0	0	0	0	0	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Frame_Shift_Del	DEL	ENST00000321429.4	37	CCDS32221.1																																																																																			.		0.617	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		-	45453182	C	-	45453182	7	5	5	1	0	1	0	1	0	0	0	0	4811	739	26	0	3960	0	DUOX1	15	45453182	Frame_Shift_Del	DEL	C	TCGA-A4-7584-01A-11D-2136-08	4415878	45453182	57078210	54	359											
DUOX1	53905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	45456067	45456068	+	Missense_Mutation	DNP	GT	GT	TA																															ctccatcacccactttggccGtcccccctttgagcccttct																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:45456067_45456068GT>TA	ENST00000321429.4	+	34	4891_4892	c.4484_4485GT>TA	c.(4483-4485)cGT>cTA	p.R1495L	DUOX1_ENST00000561166.1_Missense_Mutation_p.R1141L|DUOX1_ENST00000389037.3_Missense_Mutation_p.R1495L|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1495					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CACTTTGGCCGTCCCCCCTTTG	0.55																																					p.R1495L		.											.	DUOX1	0			c.T4485A						.																																			SO:0001583	missense	53905	exon34			TGGCCGTCCCCCC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		Exception_encountered	15.37:g.45456067_45456068delinsTA	ENSP00000317997:p.Arg1495Leu	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	134	58		0	0	0	0	0	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	DNP	ENST00000321429.4	37	CCDS32221.1																																																																																			.		0.55	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		TA	45456068	GT	TA	45456067	3	4	5	1	0	0	0	0	1	0	0	0	4811	1145	40	4	4610	4	DUOX1	15	45456067	Missense_Mutation	DNP	GT	TCGA-A4-7584-01A-11D-2136-08	2885	45456067	57075325	55	360											
ZNF609	23060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64791991	64791991	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaagaggtgcaggggcgcTcaggagatggtgccaatgct	11	6	17	7	1	1	3	1	0	0	3	1	4	1	3	1	5	3	3	1	5	2	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:64791991T>C	ENST00000326648.3	+	1	501	c.373T>C	c.(373-375)Tca>Cca	p.S125P	ZNF609_ENST00000416172.1_Missense_Mutation_p.S125P	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	125						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCAGGGGCGCTCAGGAGATGG	0.567																																					p.S125P		.											.	ZNF609-92	0			c.T373C						.						44	48	46					15																	64791991		2203	4300	6503	SO:0001583	missense	23060	exon1			GGGCGCTCAGGAG	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.373T>C	15.37:g.64791991T>C	ENSP00000316527:p.Ser125Pro	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	62	18	NM_015042	0	0	4	7	3	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	37	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	.	5.590	0.293619	0.10567	.	.	ENSG00000180357	ENST00000416172;ENST00000326648	T	0.42513	0.97	5.5	3.1	0.35709	.	0.722344	0.13093	N	0.414351	T	0.24699	0.0599	N	0.16368	0.405	0.40301	D	0.97861	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.05241	-1.0897	10	0.21540	T	0.41	-18.1137	8.0215	0.30412	0.0:0.0671:0.2567:0.6762	.	125;125	E7ERY8;O15014	.;ZN609_HUMAN	P	125	ENSP00000316527:S125P	ENSP00000316527:S125P	S	+	1	0	ZNF609	62579044	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	1.673000	0.37534	0.419000	0.25927	-0.322000	0.08575	TCA	.		0.567	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		C	64791991	T	C	64791991	3	2	5	1	0	0	0	0	1	0	0	0	18067	1551	54	3	375	3	ZNF609	15	64791991	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	19335924	64791991	37739401	56	361											
CLCN7	1186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1505793	1505793	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctccaagctgaacaggaccCcacctggaaggcaggcggcc	10	3	12	16	1	0	1	0	1	0	0	1	3	1	3	6	5	2	2	6	5	3	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:1505793C>T	ENST00000382745.4	-	11	1525	c.920G>A	c.(919-921)gGg>gAg	p.G307E	CLCN7_ENST00000262318.8_Missense_Mutation_p.G283E|CLCN7_ENST00000448525.1_Missense_Mutation_p.G283E	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	307					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GAACAGGACCCCACCTGGAAG	0.642																																					p.G307E		.											.	CLCN7-92	0			c.G920A						.						89	74	79					16																	1505793		2199	4300	6499	SO:0001583	missense	1186	exon11			AGGACCCCACCTG	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ion channels / Chloride channels : Voltage-sensitive"	2025	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 63"	602727	"chloride channel 7"			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.920G>A	16.37:g.1505793C>T	ENSP00000372193:p.Gly307Glu	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	73	43	NM_001287	0	0	0	0	0	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	37	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.854384	0.71719	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.98701	-5.08;-5.08	5.13	5.13	0.70059	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97845	1.0271	10	0.87932	D	0	-37.9855	17.1357	0.86739	0.0:1.0:0.0:0.0	.	283;307	E9PDB9;P51798	.;CLCN7_HUMAN	E	283;260;307;249	ENSP00000410907:G283E;ENSP00000372193:G307E	ENSP00000262318:G260E	G	-	2	0	CLCN7	1445794	1.000000	0.71417	0.996000	0.52242	0.531000	0.34715	7.468000	0.80943	2.387000	0.81309	0.313000	0.20887	GGG	.		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1505793	C	T	1505793	3	4	5	1	0	0	0	0	1	0	0	0	3474	623	22	2	1557	2	CLCN7	16	1505793	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		1505793	88848960	57	362											
TEKT5	146279	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	10721483	10721483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtgcaggggaaggtcttaCgcatgcccatgcacttctcc	7	9	13	12	1	2	0	0	0	2	0	3	1	2	1	2	4	4	3	2	4	2	2	rs200414450	byFrequency	TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:10721483C>T	ENST00000283025.2	-	7	1486	c.1415G>A	c.(1414-1416)cGt>cAt	p.R472H	TEKT5_ENST00000574923.1_5'UTR	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	472						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						GAAGGTCTTACGCATGCCCAT	0.617													C|||	2	0.000399361	0	0	5008	,	,		16561	0.002		0	False		,,,				2504	0				p.R472H		.											.	TEKT5-92	0			c.G1415A						.						70	65	67					16																	10721483		2197	4300	6497	SO:0001583	missense	146279	exon7			GTCTTACGCATGC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.1415G>A	16.37:g.10721483C>T	ENSP00000283025:p.Arg472His	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	128	11	NM_144674	0	0	0	0	0	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	29.9	5.045589	0.93685	.	.	ENSG00000153060	ENST00000283025	T	0.06218	3.33	4.99	4.99	0.66335	.	0.000000	0.56097	D	0.000032	T	0.31734	0.0806	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.26155	-1.0111	10	0.87932	D	0	-21.4482	15.0558	0.71912	0.0:1.0:0.0:0.0	.	472	Q96M29	TEKT5_HUMAN	H	472	ENSP00000283025:R472H	ENSP00000283025:R472H	R	-	2	0	TEKT5	10628984	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	7.211000	0.77933	2.329000	0.79093	0.505000	0.49811	CGT	C|0.999;T|0.000		0.617	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		T	10721483	C	T	10721483	3	4	5	1	0	0	0	0	1	0	0	0	15788	536	19	1	46	1	TEKT5	16	10721483	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	9215690	10721483	79633270	58	363											
EEF2K	29904	ucsc.edu	37	chr16	22295229	22295229	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggacttgtatacccaggcagCagaggcagcgatggaagcca	12	5	14	10	1	0	1	0	0	0	1	0	4	0	3	2	4	4	4	2	4	3	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:22295229C>T	ENST00000263026.5	+	18	2564	c.2090C>T	c.(2089-2091)gCa>gTa	p.A697V	RP11-141O15.1_ENST00000568125.1_RNA	NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	697					insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		ACCCAGGCAGCAGAGGCAGCG	0.562																																					p.A697V	NSCLC(195;1411 2157 20319 27471 51856)												.	EEF2K-856	0			c.C2090T						.						30	25	26					16																	22295229		2193	4294	6487	SO:0001583	missense	29904	exon18			AGGCAGCAGAGGC	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.2090C>T	16.37:g.22295229C>T	ENSP00000263026:p.Ala697Val	Somatic	33	0		WXS	Illumina HiSeq		10	2	NM_013302	0	0	6	7	1	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	C	35	5.595420	0.96602	.	.	ENSG00000103319	ENST00000263026	T	0.58506	0.33	5.71	5.71	0.89125	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.76421	0.3985	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77531	-0.2553	10	0.87932	D	0	-7.1515	19.8575	0.96767	0.0:1.0:0.0:0.0	.	697	O00418	EF2K_HUMAN	V	697	ENSP00000263026:A697V	ENSP00000263026:A697V	A	+	2	0	EEF2K	22202730	1.000000	0.71417	0.734000	0.30879	0.993000	0.82548	7.416000	0.80143	2.698000	0.92095	0.561000	0.74099	GCA	.		0.562	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		T	22295229	C	T	22295229	3	4	5	1	0	0	0	0	1	0	0	0	4941	710	25	2	2156	2	EEF2K	16	22295229	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	11573746	22295229	68059524	59	364											
CIAPIN1	57019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57463170	57463170	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtaggggcagctggcacagCggaaggcatcgcccaggtag	9	4	18	10	2	0	0	0	0	0	0	1	1	0	1	1	7	2	6	1	7	3	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:57463170C>T	ENST00000569979.1	-	6	699	c.653G>A	c.(652-654)cGc>cAc	p.R218H	CIAPIN1_ENST00000568940.1_Silent_p.P245P|CIAPIN1_ENST00000394391.4_Missense_Mutation_p.R284H|CIAPIN1_ENST00000565961.1_Silent_p.P218P|CIAPIN1_ENST00000569370.1_Silent_p.P245P|CIAPIN1_ENST00000569246.1_5'Flank|CIAPIN1_ENST00000567518.1_Missense_Mutation_p.R271H					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						GCTGGCACAGCGGAAGGCATC	0.532																																					p.R284H		.											.	CIAPIN1-90	0			c.G851A						.						56	57	57					16																	57463170		2015	4178	6193	SO:0001583	missense	57019	exon9			GCACAGCGGAAGG	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.653G>A	16.37:g.57463170C>T	ENSP00000458000:p.Arg218His	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	73	38	NM_020313	1	0	49	121	71		Missense_Mutation	SNP	ENST00000569979.1	37		.	.	.	.	.	.	.	.	.	.	C	34	5.381122	0.95945	.	.	ENSG00000005194	ENST00000394391	T	0.68181	-0.31	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.87184	0.6114	H	0.95539	3.685	0.53688	D	0.99997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91214	0.5001	10	0.72032	D	0.01	-16.045	17.0668	0.86561	0.0:1.0:0.0:0.0	.	271;284	Q6FI81-3;Q6FI81	.;CPIN1_HUMAN	H	284	ENSP00000377914:R284H	ENSP00000377914:R284H	R	-	2	0	CIAPIN1	56020671	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.141000	0.77330	2.347000	0.79759	0.561000	0.74099	CGC	.		0.532	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313		T	57463170	C	T	57463170	3	4	5	1	0	0	0	0	1	0	0	0	3425	768	27	1	91	1	CIAPIN1	16	57463170	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	35167941	57463170	32891583	60	365											
DNAH2	146754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7727461	7727461	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctggaggattcaaccccacGatccccactcgtgttcatcc	8	9	8	16	2	2	0	2	0	0	0	5	3	4	2	5	2	1	2	5	2	1	2	rs368019673		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:7727461G>A	ENST00000572933.1	+	76	12961	c.11501G>A	c.(11500-11502)cGa>cAa	p.R3834Q	DNAH2_ENST00000389173.2_Missense_Mutation_p.R3834Q			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3834	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TCAACCCCACGATCCCCACTC	0.597																																					p.R3834Q		.											.	DNAH2-102	0			c.G11501A						.	G	GLN/ARG	0,4406		0,0,2203	103	87	93		11501	4.1	0.2	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH2	NM_020877.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	3834/4428	7727461	1,13005	2203	4300	6503	SO:0001583	missense	146754	exon75			CCCCACGATCCCC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.11501G>A	17.37:g.7727461G>A	ENSP00000458355:p.Arg3834Gln	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	205	26	NM_020877	0	0	0	0	0	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.690038	0.29962	0.0	1.16E-4	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.08193	3.12	5.03	4.06	0.47325	Dynein heavy chain (1);	0.102365	0.48286	D	0.000190	T	0.04227	0.0117	N	0.25201	0.72	0.44985	D	0.998	B;B	0.32829	0.227;0.386	B;B	0.22753	0.024;0.041	T	0.42396	-0.9454	10	0.10111	T	0.7	.	8.878	0.35356	0.1665:0.0:0.8335:0.0	.	3795;3834	Q9P225-2;Q9P225	.;DYH2_HUMAN	Q	3795;3834	ENSP00000373825:R3834Q	ENSP00000353818:R3795Q	R	+	2	0	DNAH2	7668186	0.186000	0.23225	0.167000	0.22817	0.981000	0.71138	2.589000	0.46145	2.350000	0.79820	0.511000	0.50034	CGA	.		0.597	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7727461	G	A	7727461	3	1	5	1	0	0	0	0	1	0	0	0	4613	1058	37	1	11799	1	DNAH2	17	7727461	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		7727461	73467749	61	366											
EFCAB5	374786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	28407885	28407885	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gattataatggttcattcctGgctctgcctcttcaagatgc	8	15	8	10	0	4	1	2	0	2	1	5	2	5	1	2	2	2	2	2	2	3	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:28407885G>C	ENST00000394835.3	+	17	3504	c.3312G>C	c.(3310-3312)ctG>ctC	p.L1104L	EFCAB5_ENST00000320856.5_Silent_p.L980L|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1104							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GTTCATTCCTGGCTCTGCCTC	0.438																																					p.L1104L		.											.	EFCAB5-70	0			c.G3312C						.						91	88	89					17																	28407885		1881	4112	5993	SO:0001819	synonymous_variant	374786	exon17			ATTCCTGGCTCTG	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3312G>C	17.37:g.28407885G>C		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	63	24	NM_198529	0	0	0	0	0	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			.		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		C	28407885	G	C	28407885	2	2	5	1	0	0	0	0	0	0	0	1	4949	1335	47	4		4	EFCAB5	17	28407885	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	20680424	28407885	52787325	62	367											
KRT32	3882	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	39622089	39622090	+	Frame_Shift_Ins	INS	-	-	C																															ctcaacctgggcctccaggtINScagccttgcacagagtgaga																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:39622089_39622090insC	ENST00000225899.3	-	3	746_747	c.643_644insG	c.(643-645)gacfs	p.D215fs	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	215	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GGCCTCCAGGTCAGCCTTGCAC	0.604																																					p.D215fs		.											.	KRT32-90	0			c.644_645insG						.																																			SO:0001589	frameshift_variant	3882	exon3			.	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"-", "Intermediate filaments type I, keratins (acidic)"	6449	protein-coding gene	gene with protein product	"hard keratin type I"	602760	"keratin, hair, acidic, 2"	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.644dupG	17.37:g.39622090_39622090dupC	ENSP00000225899:p.Asp215fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	146	85	NM_002278	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000225899.3	37	CCDS11393.1																																																																																			.		0.604	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		C	39622090	-	C	39622089	7	5	5	1	0	1	1	0	0	0	0	0	8489	1667	58	0	722	0	KRT32	17	39622089	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	11214204	39622089	41573121	63	368											
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65214853	65214853	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtgcttgagggccattTcatagtcctgcctcttaagt	7	14	10	10	0	2	1	1	1	1	0	3	1	3	1	3	1	3	2	3	1	2	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:65214853T>G	ENST00000358691.5	-	4	234	c.68A>C	c.(67-69)gAa>gCa	p.E23A	HELZ_ENST00000580168.1_Missense_Mutation_p.E23A|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	23						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GAGGGCCATTTCATAGTCCTG	0.473																																					p.E23A		.											.	HELZ-92	0			c.A68C						.						127	119	121					17																	65214853		1892	4130	6022	SO:0001583	missense	9931	exon4			GCCATTTCATAGT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.68A>C	17.37:g.65214853T>G	ENSP00000351524:p.Glu23Ala	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	142	34	NM_014877	0	0	5	5	0	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	t	15.08	2.728346	0.48833	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.75589	-0.95;-0.95	5.27	5.27	0.74061	.	0.046820	0.85682	D	0.000000	T	0.70692	0.3253	L	0.29908	0.895	0.58432	D	0.999999	B;P;B	0.48503	0.247;0.911;0.247	B;P;B	0.47941	0.078;0.562;0.078	T	0.75019	-0.3465	10	0.66056	D	0.02	-4.8435	15.1782	0.72931	0.0:0.0:0.0:1.0	.	23;23;23	B7ZLW2;F8WBX6;P42694	.;.;HELZ_HUMAN	A	23	ENSP00000351524:E23A;ENSP00000411144:E23A	ENSP00000351524:E23A	E	-	2	0	HELZ	62645315	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.414000	0.80117	1.980000	0.57719	0.455000	0.32223	GAA	.		0.473	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65214853	T	G	65214853	3	3	5	1	0	0	0	0	1	0	0	0	7070	1783	62	5	5880	5	HELZ	17	65214853	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	25592764	65214853	15980357	64	369											
COG1	9382	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	71199203	71199203	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggctcagttctggccacagCcaccagctgggatgagctag	8	8	13	12	0	2	1	1	1	1	0	2	2	2	2	3	3	3	4	3	3	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:71199203C>A	ENST00000299886.4	+	8	2218	c.2138C>A	c.(2137-2139)gCc>gAc	p.A713D		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	713					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			CTGGCCACAGCCACCAGCTGG	0.512																																					p.A713D		.											.	COG1-91	0			c.C2138A						.						80	74	76					17																	71199203		2203	4300	6503	SO:0001583	missense	9382	exon8			CCACAGCCACCAG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2138C>A	17.37:g.71199203C>A	ENSP00000299886:p.Ala713Asp	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	87	58	NM_018714	0	0	8	39	31	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.632096	0.67015	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.25414	1.8;1.81	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	M	0.75447	2.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.37572	-0.9700	10	0.35671	T	0.21	-30.898	20.8794	0.99867	0.0:1.0:0.0:0.0	.	713;713;713	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	D	713	ENSP00000400111:A713D;ENSP00000299886:A713D	ENSP00000299886:A713D	A	+	2	0	COG1	68710798	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.941000	0.99782	0.655000	0.94253	GCC	.		0.512	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			A	71199203	C	A	71199203	3	1	5	1	0	0	0	0	1	0	0	0	3663	739	26	4	2168	4	COG1	17	71199203	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	5984350	71199203	9996007	65	370											
FDXR	2232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72861043	72861043	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccagggctgccttcgtgAtgtccgttctctggcacaaa	7	10	10	14	2	1	1	0	1	1	0	4	1	2	1	3	2	1	3	3	2	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:72861043A>C	ENST00000293195.5	-	7	698	c.620T>G	c.(619-621)aTc>aGc	p.I207S	FDXR_ENST00000581530.1_Missense_Mutation_p.I213S|FDXR_ENST00000442102.2_Missense_Mutation_p.I250S|FDXR_ENST00000420580.2_Missense_Mutation_p.I167S|FDXR_ENST00000583917.1_Missense_Mutation_p.I208S|FDXR_ENST00000455107.2_Missense_Mutation_p.I163S|FDXR_ENST00000544854.1_Missense_Mutation_p.I155S|FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000582944.1_Missense_Mutation_p.I199S|FDXR_ENST00000413947.2_Missense_Mutation_p.I238S	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	207					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	TGCCTTCGTGATGTCCGTTCT	0.592											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I250S		.											.	FDXR-226	0			c.T749G						.						96	80	86					17																	72861043		2203	4300	6503	SO:0001583	missense	2232	exon7			TTCGTGATGTCCG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.620T>G	17.37:g.72861043A>C	ENSP00000293195:p.Ile207Ser	Somatic	80	0	1140	WXS	Illumina HiSeq	Phase_I	102	54	NM_001258012	0	0	0	1	1	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	37	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	a	15.15	2.747032	0.49257	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89931	0.6858	H	0.94345	3.525	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.992;0.983;0.984;1.0;0.996;0.984;0.978;1.0;0.978;0.996	D	0.92675	0.6153	10	0.87932	D	0	-11.7911	15.4798	0.75517	1.0:0.0:0.0:0.0	.	167;250;238;205;155;238;207;199;207;213	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;B4DDI7;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;.;ADRO_HUMAN;.	S	167;155;213;163;250;238	ENSP00000414172:I167S;ENSP00000445432:I155S;ENSP00000390875:I163S;ENSP00000416515:I250S;ENSP00000408595:I238S	ENSP00000293195:I213S	I	-	2	0	FDXR	70372638	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.738000	0.68613	2.145000	0.66743	0.454000	0.30748	ATC	.		0.592	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		C	72861043	A	C	72861043	3	2	5	1	0	0	0	0	1	0	0	0	5826	333	12	5	879	5	FDXR	17	72861043	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	1661840	72861043	8334167	66	371											
ITGB4	3691	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	73752854	73752855	+	In_Frame_Ins	INS	-	-	GCTGCA																															actgccctgagcccagactcINSgctgcagctgagctgggagc																								rs370378040		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:73752854_73752855insGCTGCA	ENST00000200181.3	+	37	5154_5155	c.4967_4968insGCTGCA	c.(4966-4971)tcgctg>tcGCTGCAgctg	p.1659_1660insQL	ITGB4_ENST00000579662.1_In_Frame_Ins_p.1589_1590insQL|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000339591.3_In_Frame_Ins_p.1642_1643insQL|ITGB4_ENST00000450894.3_In_Frame_Ins_p.1589_1590insQL|ITGB4_ENST00000449880.2_In_Frame_Ins_p.1642_1643insQL	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1659	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGCCCAGACTCGCTGCAGCTGA	0.658																																					p.S1656delinsSLQ		.											.	ITGB4-227	0			c.4967_4968insGCTGCA						.																																			SO:0001652	inframe_insertion	3691	exon37			.		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4968_4973dupGCTGCA	17.37:g.73752855_73752860dupGCTGCA	ENSP00000200181:p.Gln1658_Leu1659dup	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	143	43	NM_000213	0	0	0	0	0	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	In_Frame_Ins	INS	ENST00000200181.3	37	CCDS11727.1																																																																																			.		0.658	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			GCTGCA	73752855	-	GCTGCA	73752854	7	5	5	1	0	1	1	0	0	0	0	0	7918	893	31	0	5272	0	ITGB4	17	73752854	In_Frame_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	891811	73752854	7442356	67	372											
EMILIN2	84034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2913257	2913257	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcatacctgcgggggcccggGggcattccacctcatcgtgc	5	7	14	15	3	1	0	1	0	0	0	3	0	2	0	4	4	3	2	4	4	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:2913257G>T	ENST00000254528.3	+	8	3176	c.3017G>T	c.(3016-3018)gGg>gTg	p.G1006V	EMILIN2_ENST00000308080.5_3'UTR	NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	1006	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGGGGCCCGGGGGCATTCCAC	0.607																																					p.G1006V		.											.	EMILIN2-93	0			c.G3017T						.						41	43	43					18																	2913257		2203	4300	6503	SO:0001583	missense	84034	exon8			GCCCGGGGGCATT	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.3017G>T	18.37:g.2913257G>T	ENSP00000254528:p.Gly1006Val	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	49	13	NM_032048	0	0	2	4	2	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	37	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989478	0.53934	.	.	ENSG00000132205	ENST00000254528;ENST00000308080	T	0.74842	-0.88	5.61	5.61	0.85477	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79771	-0.1663	10	0.33940	T	0.23	-34.4219	20.0086	0.97443	0.0:0.0:1.0:0.0	.	1006	Q9BXX0	EMIL2_HUMAN	V	1006;283	ENSP00000254528:G1006V	ENSP00000254528:G1006V	G	+	2	0	EMILIN2	2903257	1.000000	0.71417	0.301000	0.25044	0.022000	0.10575	5.618000	0.67722	2.808000	0.96608	0.655000	0.94253	GGG	.		0.607	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2913257	G	T	2913257	3	4	5	1	0	0	0	0	1	0	0	0	5107	1232	43	4	3047	4	EMILIN2	18	2913257	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		2913257	75163991	68	373											
SS18	6760	broad.mit.edu	37	chr18	23670482	23670483	+	Missense_Mutation	DNP	GA	GA	AG																															caccttctgaatcgcagcggGagtgatctcccccttgcctc																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:23670482_23670483GA>AG	ENST00000415083.2	-	1	106_107	c.51_52TC>CT	c.(49-54)acTCcc>acCTcc	p.P18S	SS18_ENST00000542743.1_5'UTR|SS18_ENST00000542420.2_Intron|SS18_ENST00000539849.1_5'UTR|SS18_ENST00000269137.7_Missense_Mutation_p.P18S|SS18_ENST00000585241.1_5'UTR|SS18_ENST00000545952.1_5'UTR	NM_001007559.1|NM_005637.2	NP_001007560.1|NP_005628.2	Q15532	SSXT_HUMAN	synovial sarcoma translocation, chromosome 18	18	Transcriptional activation.				cell morphogenesis (GO:0000902)|ephrin receptor signaling pathway (GO:0048013)|intracellular signal transduction (GO:0035556)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)		SS18/SSX2(706)|SS18/SSX1(1169)|SS18/SSX4(12)	endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(1)	19	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)					ATCGCAGCGGGAGTGATCTCCC	0.683			T	"SSX1,  SSX2"	synovial sarcoma																																p.P21S				Dom	yes		18	18q11.2	6760	"synovial sarcoma translocation, chromosome 18"		M	.	SS18-1968	0			c.T51C						.																																			SO:0001583	missense	6760	exon1			AGCGGGAGTGATC	X79201	CCDS32807.1, CCDS54183.1	18q11.2	2008-07-28				ENSG00000141380			11340	protein-coding gene	gene with protein product		600192		SSXT		8152806, 7951320, 16484776	Standard	XM_005258334		Approved	SYT	uc002kvm.3	Q15532		ENST00000415083.2:c.51_52delinsAG	18.37:g.23670482_23670483delinsAG	ENSP00000414516:p.Pro18Ser	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	10	4	NM_001007559	0	0	0	0	0	B0YJ95|Q16404|Q4VAX1|Q9BXC6	Missense_Mutation	DNP	ENST00000415083.2	37	CCDS32807.1																																																																																			.		0.683	SS18-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446226.1			AG	23670483	GA	AG	23670482	3	1	5	1	0	0	0	0	1	0	0	0	15207	1174	41	2	1248	2	SS18	18	23670482	Missense_Mutation	DNP	GA	TCGA-A4-7584-01A-11D-2136-08	20757225	23670482	54406766	69	374											
C18orf34	374864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	30926327	30926327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaatgagacgaatggccTctgagagcaatgtttccatt	11	14	9	7	1	1	2	0	2	1	2	2	5	2	2	2	1	1	2	2	1	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:30926327T>C	ENST00000383096.3	-	9	688	c.506A>G	c.(505-507)gAg>gGg	p.E169G	CCDC178_ENST00000583930.1_Missense_Mutation_p.E169G|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000402325.1_Missense_Mutation_p.E169G|CCDC178_ENST00000579947.1_Missense_Mutation_p.E169G|CCDC178_ENST00000403303.1_Missense_Mutation_p.E169G|CCDC178_ENST00000300227.8_Missense_Mutation_p.E169G|CCDC178_ENST00000406524.2_Missense_Mutation_p.E169G			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	169																	ACGAATGGCCTCTGAGAGCAA	0.343																																					p.E169G		.											.	.	0			c.A506G						.						93	88	90					18																	30926327		2203	4300	6503	SO:0001583	missense	374864	exon8			ATGGCCTCTGAGA	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.506A>G	18.37:g.30926327T>C	ENSP00000372576:p.Glu169Gly	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_001105528	0	0	0	0	0	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	9.274	1.046438	0.19748	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.57107	1.82;1.82;1.83;1.82;1.83;0.42	5.59	4.36	0.52297	.	.	.	.	.	T	0.65133	0.2662	L	0.54323	1.7	0.31006	N	0.719736	D;D;D;D	0.89917	1.0;0.996;0.996;0.996	D;D;D;D	0.74674	0.984;0.944;0.944;0.944	T	0.65520	-0.6148	9	0.59425	D	0.04	-20.3796	10.1932	0.43039	0.0:0.0:0.1668:0.8332	.	169;169;169;169	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	G	169	ENSP00000385591:E169G;ENSP00000372576:E169G;ENSP00000300227:E169G;ENSP00000385867:E169G;ENSP00000385234:E169G;ENSP00000382130:E169G	ENSP00000300227:E169G	E	-	2	0	C18orf34	29180325	1.000000	0.71417	0.996000	0.52242	0.418000	0.31294	3.210000	0.51129	2.129000	0.65627	0.455000	0.32223	GAG	.		0.343	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		C	30926327	T	C	30926327	3	2	5	1	0	0	0	0	1	0	0	0	1908	1551	54	3	2157	3	C18orf34	18	30926327	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	7255845	30926327	47150921	70	375											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9059472	9059472	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgttctgctagaagagatgGcttctgtcctggagacctca	9	12	11	9	0	3	3	1	0	2	3	4	5	4	3	2	2	1	3	2	2	2	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:9059472G>T	ENST00000397910.4	-	3	28177	c.27974C>A	c.(27973-27975)gCc>gAc	p.A9325D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9327	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGAAGAGATGGCTTCTGTCCT	0.507																																					p.A9325D		.											.	MUC16-566	0			c.C27974A						.						162	157	158					19																	9059472		1993	4179	6172	SO:0001583	missense	94025	exon3			GAGATGGCTTCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27974C>A	19.37:g.9059472G>T	ENSP00000381008:p.Ala9325Asp	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	143	69	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.093	0.202874	0.09704	.	.	ENSG00000181143	ENST00000397910	T	0.02812	4.15	2.43	-4.86	0.03132	.	.	.	.	.	T	0.02727	0.0082	N	0.19112	0.55	.	.	.	P	0.52316	0.952	P	0.50049	0.629	T	0.26677	-1.0096	8	0.87932	D	0	.	4.6628	0.12650	0.5463:0.176:0.2777:0.0	.	9325	B5ME49	.	D	9325	ENSP00000381008:A9325D	ENSP00000381008:A9325D	A	-	2	0	MUC16	8920472	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.962000	0.01514	-1.169000	0.02772	-0.382000	0.06688	GCC	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9059472	G	T	9059472	3	4	5	1	0	0	0	0	1	0	0	0	9998	1203	42	4	15877	4	MUC16	19	9059472	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		9059472	50069511	71	376											
ZNF317	57693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9271676	9271676	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atacgggtgcgatctctgcgGgaaagctttcagcgcgagtt	8	10	14	9	5	2	0	1	0	1	0	3	3	2	1	0	2	5	2	0	2	2	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:9271676G>A	ENST00000247956.6	+	7	1660	c.1355G>A	c.(1354-1356)gGg>gAg	p.G452E	ZNF317_ENST00000360385.3_Missense_Mutation_p.G420E	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	452					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)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GATCTCTGCGGGAAAGCTTTC	0.547																																					p.G452E		.											.	ZNF317-90	0			c.G1355A						.						62	59	60					19																	9271676		2203	4300	6503	SO:0001583	missense	57693	exon7			TCTGCGGGAAAGC	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.1355G>A	19.37:g.9271676G>A	ENSP00000247956:p.Gly452Glu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	58	20	NM_020933	0	0	3	6	3	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	37	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.795593	0.70452	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.07114	3.22;3.22	3.04	3.04	0.35103	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43260	D	0.000600	T	0.22627	0.0546	L	0.59436	1.845	0.47009	D	0.999286	D;D	0.89917	1.0;0.994	D;D	0.83275	0.996;0.924	T	0.01013	-1.1481	10	0.59425	D	0.04	-30.6663	12.2796	0.54757	0.0:0.0:1.0:0.0	.	420;452	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	E	452;420	ENSP00000247956:G452E;ENSP00000353554:G420E	ENSP00000247956:G452E	G	+	2	0	ZNF317	9132676	0.999000	0.42202	0.881000	0.34555	0.542000	0.35054	3.149000	0.50655	2.031000	0.59945	0.491000	0.48974	GGG	.		0.547	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		A	9271676	G	A	9271676	3	1	5	1	0	0	0	0	1	0	0	0	17867	1232	43	2	1377	2	ZNF317	19	9271676	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	212204	9271676	49857307	72	377											
C19orf57	79173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13996869	13996869	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgttccccgaaggaaagagCtggaaagagagcacaaggtg	14	6	14	7	1	0	2	0	0	0	2	1	6	1	4	2	3	2	3	2	3	4	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:13996869C>G	ENST00000586783.1	-	6	1668		c.e6-1		C19orf57_ENST00000346736.2_Splice_Site|C19orf57_ENST00000591586.1_Splice_Site|C19orf57_ENST00000454313.1_Splice_Site			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57						multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			AAGGAAAGAGCTGGAAAGAGA	0.632																																					.		.											.	C19orf57-93	0			c.1669-1G>C						.						33	34	34					19																	13996869		2203	4300	6503	SO:0001630	splice_region_variant	79173	exon8			AAAGAGCTGGAAA	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.1669-1G>C	19.37:g.13996869C>G		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	58	21	NM_024323	0	0	0	0	0	Q13411|Q8N825|Q96D63|Q9BU49	Splice_Site	SNP	ENST00000586783.1	37		.	.	.	.	.	.	.	.	.	.	C	9.061	0.994432	0.19043	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.45762	D	0.998659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7555	0.40500	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C19orf57	13857869	0.176000	0.23096	0.016000	0.15963	0.050000	0.14768	2.605000	0.46283	2.000000	0.58554	0.563000	0.77884	.	.		0.632	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	Intron	G	13996869	C	G	13996869	5	3	5	1	0	0	0	0	0	0	1	0	1945	811	28	4	253	4	C19orf57	19	13996869	Splice_Site	SNP	C	TCGA-A4-7584-01A-11D-2136-08	4725193	13996869	45132114	73	378											
CD22	933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35828752	35828752	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgcgaggtcagcagcagcaaCccggagtacacgacggtatc	11	5	13	12	4	1	0	1	0	0	0	2	3	1	1	1	3	6	5	1	3	3	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:35828752C>T	ENST00000085219.5	+	5	879	c.813C>T	c.(811-813)aaC>aaT	p.N271N	CD22_ENST00000594250.1_Intron|CD22_ENST00000536635.2_Silent_p.N271N|CD22_ENST00000544992.2_Silent_p.N271N|CD22_ENST00000270311.6_Silent_p.N151N|CD22_ENST00000419549.2_Silent_p.N99N|CD22_ENST00000341773.6_Intron	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	271	Ig-like C2-type 2.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GCAGCAGCAACCCGGAGTACA	0.567																																					p.N271N	Ovarian(42;1009 1133 23674 26041)	.											.	CD22-526	0			c.C813T						.						90	75	80					19																	35828752		2203	4300	6503	SO:0001819	synonymous_variant	933	exon5			CAGCAACCCGGAG	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1643	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 2"	107266	"CD22 antigen"			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.813C>T	19.37:g.35828752C>T		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	77	32	NM_001185100	0	0	1	1	0	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			.		0.567	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		T	35828752	C	T	35828752	2	4	5	1	0	0	0	0	0	0	0	1	2991	506	18	2		2	CD22	19	35828752	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	21831883	35828752	23300231	74	379											
EXOC3L2	90332	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	45720794	45720794	+	Frame_Shift_Del	DEL	G	G	-																															cccgacactgaccagccgccGgaacagcctctgcagttgcg																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:45720794delG	ENST00000252482.3	-	7	838	c.811delC	c.(811-813)cggfs	p.R272fs	EXOC3L2_ENST00000413988.1_Frame_Shift_Del_p.R272fs			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	272					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		ACCAGCCGCCGGAACAGCCTC	0.701																																					p.R271fs		.											.	EXOC3L2-91	0			c.811delC						.						9	12	11					19																	45720794		2147	4221	6368	SO:0001589	frameshift_variant	90332	exon8			.	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.811delC	19.37:g.45720794delG	ENSP00000252482:p.Arg272fs	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	19	10	NM_138568	0	0	0	0	0	Q8N9W2|Q96GV2	Frame_Shift_Del	DEL	ENST00000252482.3	37	CCDS12657.1																																																																																			.		0.701	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		-	45720794	G	-	45720794	7	5	5	1	0	1	0	1	0	0	0	0	5318	1115	39	0	430	0	EXOC3L2	19	45720794	Frame_Shift_Del	DEL	G	TCGA-A4-7584-01A-11D-2136-08	9892042	45720794	13408189	75	380											
SCAF1	58506	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	50161552	50161552	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgctaccgctacttccgcAagcacggtcgcaagccaggg	9	5	12	15	5	0	0	0	0	0	0	2	0	1	0	3	2	5	5	3	2	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:50161552A>C	ENST00000360565.3	+	11	3959	c.3835A>C	c.(3835-3837)Aag>Cag	p.K1279Q	IRF3_ENST00000599680.1_5'Flank	NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1279	Necessary for interaction with the CTD domain of POLR2A.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CTACTTCCGCAAGCACGGTCG	0.701																																					p.K1279Q		.											.	SCAF1-68	0			c.A3835C						.						20	18	19					19																	50161552		2196	4296	6492	SO:0001583	missense	58506	exon11			TTCCGCAAGCACG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3835A>C	19.37:g.50161552A>C	ENSP00000353769:p.Lys1279Gln	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	20	10	NM_021228	0	0	18	34	16	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749503	0.69533	.	.	ENSG00000126461	ENST00000360565	T	0.50548	0.74	4.94	4.94	0.65067	.	0.000000	0.41001	D	0.000978	T	0.62575	0.2439	L	0.52905	1.665	0.45076	D	0.998095	D	0.76494	0.999	D	0.71656	0.974	T	0.65800	-0.6080	10	0.72032	D	0.01	-23.9463	13.702	0.62616	1.0:0.0:0.0:0.0	.	1279	Q9H7N4	SFR19_HUMAN	Q	1279	ENSP00000353769:K1279Q	ENSP00000353769:K1279Q	K	+	1	0	SCAF1	54853364	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.499000	0.90494	2.064000	0.61679	0.533000	0.62120	AAG	.		0.701	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		C	50161552	A	C	50161552	3	2	5	1	0	0	0	0	1	0	0	0	13900	131	5	5	3873	5	SCAF1	19	50161552	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	4440758	50161552	8967431	76	381											
LILRB1	10859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55144006	55144006	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgtggctctgatgctggCtacaacagatttgttctgta	8	14	11	8	0	2	2	0	1	2	1	2	2	2	2	0	2	3	5	0	2	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:55144006C>A	ENST00000396331.1	+	7	1110	c.753C>A	c.(751-753)ggC>ggA	p.G251G	LILRB1_ENST00000396332.4_Silent_p.G251G|LILRB1_ENST00000396317.1_Silent_p.G251G|LILRB1_ENST00000324602.7_Silent_p.G251G|LILRB1_ENST00000434867.2_Silent_p.G251G|LILRB1_ENST00000418536.2_Silent_p.G251G|LILRB1_ENST00000448689.1_Silent_p.G251G|LILRB1_ENST00000396315.1_Silent_p.G251G|LILRB1_ENST00000396327.3_Silent_p.G251G|LILRB1_ENST00000396321.2_Silent_p.G251G|LILRB1_ENST00000427581.2_Silent_p.G287G	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	251	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CTGATGCTGGCTACAACAGAT	0.572										HNSCC(37;0.09)																											p.G251G		.											.	LILRB1-137	0			c.C753A						.						100	105	103					19																	55144006		2203	4300	6503	SO:0001819	synonymous_variant	10859	exon6			TGCTGGCTACAAC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.753C>A	19.37:g.55144006C>A		Somatic	173	0		WXS	Illumina HiSeq	Phase_I	110	44	NM_001081637	0	0	2	2	0	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.		0.572	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			A	55144006	C	A	55144006	2	1	5	1	0	0	0	0	0	0	0	1	8812	784	28	4		4	LILRB1	19	55144006	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	4982454	55144006	3984977	77	382											
ZNF543	125919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57839968	57839968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaaagctttttgcgagagtGcagacctcattcaacactac	13	10	8	10	1	2	2	2	0	0	2	2	4	2	2	1	0	5	2	1	0	4	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:57839968G>A	ENST00000321545.4	+	4	1483	c.1138G>A	c.(1138-1140)Gca>Aca	p.A380T		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	380					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)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTGCGAGAGTGCAGACCTCAT	0.512																																					p.A380T		.											.	ZNF543-92	0			c.G1138A						.						84	73	76					19																	57839968		2203	4300	6503	SO:0001583	missense	125919	exon4			GAGAGTGCAGACC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1138G>A	19.37:g.57839968G>A	ENSP00000322545:p.Ala380Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	83	35	NM_213598	0	0	0	1	1	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	G	2.550	-0.304214	0.05495	.	.	ENSG00000178229	ENST00000321545	T	0.15139	2.45	3.14	-2.57	0.06248	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10337	0.0253	N	0.25825	0.765	0.09310	N	1	B	0.21071	0.051	B	0.14023	0.01	T	0.32188	-0.9916	9	0.42905	T	0.14	.	7.5755	0.27933	0.138:0.0:0.7015:0.1605	.	380	Q08ER8	ZN543_HUMAN	T	380	ENSP00000322545:A380T	ENSP00000322545:A380T	A	+	1	0	ZNF543	62531780	0.000000	0.05858	0.000000	0.03702	0.661000	0.39034	-1.477000	0.02331	-0.214000	0.10078	0.561000	0.74099	GCA	.		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		A	57839968	G	A	57839968	3	1	5	1	0	0	0	0	1	0	0	0	18008	1319	46	2	1152	2	ZNF543	19	57839968	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	2695962	57839968	1289015	78	383											
GDF5	8200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34021936	34021936	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcccctcgcagtggaaaGcctcgtactcaaggggtgcg	9	6	13	13	3	1	0	1	0	0	0	3	1	1	1	3	3	4	2	3	3	3	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:34021936G>T	ENST00000374372.1	-	4	1780	c.1277C>A	c.(1276-1278)gCt>gAt	p.A426D	GDF5OS_ENST00000374375.1_5'UTR|GDF5_ENST00000374369.3_Missense_Mutation_p.A426D			P43026	GDF5_HUMAN	growth differentiation factor 5	426					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			GCAGTGGAAAGCCTCGTACTC	0.582																																					p.A426D		.											.	GDF5-226	0			c.C1277A						.						133	115	121					20																	34021936		2203	4300	6503	SO:0001583	missense	8200	exon2			TGGAAAGCCTCGT	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.1277C>A	20.37:g.34021936G>T	ENSP00000363492:p.Ala426Asp	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	72	27	NM_000557	0	0	3	3	0	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.369453	0.82463	.	.	ENSG00000125965	ENST00000374369;ENST00000374372	D;D	0.86769	-2.17;-2.17	4.4	4.4	0.53042	Transforming growth factor beta, conserved site (1);Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.95981	0.8691	H	0.97587	4.035	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97808	1.0249	10	0.87932	D	0	.	17.1668	0.86818	0.0:0.0:1.0:0.0	.	426;426	F1T0J1;P43026	.;GDF5_HUMAN	D	426	ENSP00000363489:A426D;ENSP00000363492:A426D	ENSP00000363489:A426D	A	-	2	0	GDF5	33485350	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.657000	0.98554	2.266000	0.75297	0.462000	0.41574	GCT	.		0.582	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			T	34021936	G	T	34021936	3	4	5	1	0	0	0	0	1	0	0	0	6336	971	34	4	232	4	GDF5	20	34021936	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		34021936	29003584	79	384											
ZNF335	63925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44578919	44578919	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atggtctgggttggggtctgGgtaggggcccgggctgtagg	3	10	22	6	1	2	0	0	0	2	0	2	0	2	0	1	9	0	4	1	9	2	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:44578919G>C	ENST00000322927.2	-	22	3526	c.3426C>G	c.(3424-3426)acC>acG	p.T1142T	ZNF335_ENST00000426788.1_Silent_p.T987T	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1142					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TTGGGGTCTGGGTAGGGGCCC	0.612																																					p.T1142T		.											.	ZNF335-94	0			c.C3426G						.						90	93	92					20																	44578919		2203	4300	6503	SO:0001819	synonymous_variant	63925	exon22			GGTCTGGGTAGGG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3426C>G	20.37:g.44578919G>C		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	97	30	NM_022095	0	0	8	13	5	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			.		0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		C	44578919	G	C	44578919	2	2	5	1	0	0	0	0	0	0	0	1	17884	1219	43	4		4	ZNF335	20	44578919	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	10556983	44578919	18446601	80	385											
PARD6B	84612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49366295	49366295	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccatagaaaaaagccacAtatagtcattagtatgcccc	17	8	5	11	0	1	1	1	0	0	1	1	1	1	1	4	0	3	1	4	0	9	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:49366295A>G	ENST00000371610.2	+	3	632	c.389A>G	c.(388-390)cAt>cGt	p.H130R	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	130	Interaction with PARD3 and CDC42. {ECO:0000250}.				axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.H130R(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						AAAAAGCCACATATAGTCATT	0.403																																					p.H130R		.											.	PARD6B-91	1	Substitution - Missense(1)	kidney(1)	c.A389G						.						76	74	75					20																	49366295		2203	4300	6503	SO:0001583	missense	84612	exon3			AGCCACATATAGT	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"par-6 (partitioning defective 6, C.elegans) homolog beta", "par-6 partitioning defective 6 homolog beta (C. elegans)"			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.389A>G	20.37:g.49366295A>G	ENSP00000360672:p.His130Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	48	16	NM_032521	0	0	5	15	10	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	37	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597328	0.28445	.	.	ENSG00000124171	ENST00000371610	T	0.41400	1.0	5.6	5.6	0.85130	.	0.151580	0.64402	D	0.000014	T	0.36991	0.0987	L	0.43152	1.355	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.11421	-1.0588	10	0.25106	T	0.35	-32.4385	15.7847	0.78294	1.0:0.0:0.0:0.0	.	130	Q9BYG5	PAR6B_HUMAN	R	130	ENSP00000360672:H130R	ENSP00000360672:H130R	H	+	2	0	PARD6B	48799702	0.992000	0.36948	0.650000	0.29550	0.857000	0.48899	3.467000	0.53078	2.135000	0.66039	0.533000	0.62120	CAT	.		0.403	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		G	49366295	A	G	49366295	3	3	5	1	0	0	0	0	1	0	0	0	11472	217	8	3	399	3	PARD6B	20	49366295	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	4787376	49366295	13659225	81	386											
BAGE	85319	hgsc.bcm.edu	37	chr21	11097541	11097541	+	RNA	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgggcaacaagaacgaaaCtcacagagctgtgccatctt	13	7	9	12	1	2	2	1	0	1	2	2	3	2	2	2	1	5	2	2	1	4	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr21:11097541C>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aagaacgaaactcACAGAGCT	0.562																																					.		.											.	.	0			c.119+2G>T						.						29	40	36					21																	11097541		1319	2455	3774			574	exon3			ACGAAACTCACAG	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11097541C>A		Somatic	37	1		WXS	Illumina HiSeq	Phase_I	31	3	NM_001187	0	0	0	0	0	A8K925|Q08ER0	Splice_Site	SNP	ENST00000470054.1	37																																																																																				.		0.562	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		A	11097541	C	A	11097541	1	1	5	0	1	0	0	0	0	0	0	0	1292	579	20	4		4	BAGE	21	11097541	RNA	SNP	C	TCGA-A4-7584-01A-11D-2136-08		11097541	37032354	82	387											
GAL3ST1	9514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30951203	30951203	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtccgcatgcgctcgttggCatggcgcagggcggccacct	4	7	16	14	5	0	0	0	0	0	0	2	0	1	0	3	5	1	5	3	5	0	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr22:30951203C>G	ENST00000402321.1	-	3	1326	c.1009G>C	c.(1009-1011)Gcc>Ccc	p.A337P	GAL3ST1_ENST00000406955.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000338911.5_Missense_Mutation_p.A337P|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.A337P			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	337					galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						CGCTCGTTGGCATGGCGCAGG	0.721																																					p.A337P		.											.	GAL3ST1-90	0			c.G1009C						.						20	22	21					22																	30951203		2199	4288	6487	SO:0001583	missense	9514	exon4			CGTTGGCATGGCG	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"Sulfotransferases, membrane-bound"	24240	protein-coding gene	gene with protein product	"cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.1009G>C	22.37:g.30951203C>G	ENSP00000385735:p.Ala337Pro	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	25	13	NM_004861	0	0	5	13	8	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017684	0.75161	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111	T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.55	5.55	0.83447	.	0.225320	0.47455	D	0.000227	T	0.24547	0.0595	L	0.55990	1.75	0.80722	D	1	P	0.43938	0.822	P	0.48425	0.577	T	0.00557	-1.1672	10	0.30854	T	0.27	-13.5376	12.4548	0.55697	0.0:0.9221:0.0:0.0779	.	337	Q99999	G3ST1_HUMAN	P	337	ENSP00000385825:A337P;ENSP00000385735:A337P;ENSP00000384122:A337P;ENSP00000384388:A337P;ENSP00000343234:A337P;ENSP00000385207:A337P;ENSP00000402587:A337P	ENSP00000343234:A337P	A	-	1	0	GAL3ST1	29281203	0.970000	0.33590	0.958000	0.39756	0.894000	0.52154	2.095000	0.41729	2.615000	0.88500	0.561000	0.74099	GCC	.		0.721	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861		G	30951203	C	G	30951203	3	3	5	1	0	0	0	0	1	0	0	0	6217	710	25	4	266	4	GAL3ST1	22	30951203	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		30951203	20353363	83	388											
CARD10	29775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37914027	37914027	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcctggcccgtgagcagcgtGaagtgttcggggtagtagaa	8	9	16	8	3	0	3	0	2	0	1	2	3	1	3	2	3	2	4	2	3	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr22:37914027G>C	ENST00000403299.1	-	3	540	c.324C>G	c.(322-324)ttC>ttG	p.F108L	CARD10_ENST00000251973.5_Missense_Mutation_p.F108L			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	108	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					TGAGCAGCGTGAAGTGTTCGG	0.622																																					p.F108L		.											.	CARD10-662	0			c.C324G						.						94	80	85					22																	37914027		2203	4300	6503	SO:0001583	missense	29775	exon2			CAGCGTGAAGTGT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.324C>G	22.37:g.37914027G>C	ENSP00000384570:p.Phe108Leu	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	60	13	NM_014550	0	0	14	32	18	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694688	0.88830	.	.	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.20069	2.1;2.1	4.67	3.64	0.41730	DEATH-like (2);Caspase Recruitment (2);	0.151059	0.46442	D	0.000290	T	0.20007	0.0481	L	0.47716	1.5	0.46774	D	0.99919	P	0.40000	0.698	B	0.38683	0.279	T	0.02713	-1.1120	10	0.66056	D	0.02	-23.0196	11.2943	0.49269	0.0863:0.0:0.9137:0.0	.	108	Q9BWT7	CAR10_HUMAN	L	108	ENSP00000384570:F108L;ENSP00000251973:F108L	ENSP00000251973:F108L	F	-	3	2	CARD10	36243973	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.159000	0.58157	1.061000	0.40601	0.462000	0.41574	TTC	.		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		C	37914027	G	C	37914027	3	2	5	1	0	0	0	0	1	0	0	0	2650	1281	45	4	2850	4	CARD10	22	37914027	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	6962824	37914027	13390539	84	389											
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	44870257	44870257	+	Frame_Shift_Del	DEL	T	T	-																															tctacttccattataatgcaTttcagtggtaagttgacata																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chrX:44870257delT	ENST00000377967.4	+	5	477	c.436delT	c.(436-438)tttfs	p.F146fs	KDM6A_ENST00000382899.4_Frame_Shift_Del_p.F146fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.F146fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.F146fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	146	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0(12)|p.0?(6)|p.?(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TTATAATGCATTTCAGTGGTA	0.323			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.F146fs	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	19	No detectable mRNA/protein(12)|Whole gene deletion(6)|Unknown(1)	haematopoietic_and_lymphoid_tissue(11)|oesophagus(4)|breast(2)|pancreas(2)	c.436delT						.						117	99	105					X																	44870257		2203	4297	6500	SO:0001589	frameshift_variant	7403	exon5			.	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.436delT	X.37:g.44870257delT	ENSP00000367203:p.Phe146fs	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	20	13	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																			.		0.323	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44870257	T	-	44870257	7	5	5	1	0	1	0	1	0	0	0	0	8158	1493	52	0	454	0	KDM6A	23	44870257	Frame_Shift_Del	DEL	T	TCGA-A4-7584-01A-11D-2136-08		44870257	110400303	85	390											
MPP1	4354	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	154033610	154033610	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcggagagcgccgtgtgcatGctgcccccactctcgccctc	4	8	11	18	4	1	1	0	0	1	1	4	2	1	1	4	1	4	2	4	1	0	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chrX:154033610G>T	ENST00000369534.3	-	1	186	c.39C>A	c.(37-39)agC>agA	p.S13R	MPP1_ENST00000393531.1_Missense_Mutation_p.S13R|MPP1_ENST00000413259.3_5'UTR	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	13					nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCGTGTGCATGCTGCCCCCAC	0.667																																					p.S13R													.	MPP1-132	0			c.C39A						.						37	29	32					X																	154033610		2202	4299	6501	SO:0001583	missense	4354	exon1			GTGCATGCTGCCC		CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.39C>A	X.37:g.154033610G>T	ENSP00000358547:p.Ser13Arg	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	7	7	NM_001166461	0	0	1	9	8	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Missense_Mutation	SNP	ENST00000369534.3	37	CCDS14762.1	.	.	.	.	.	.	.	.	.	.	g	8.864	0.947541	0.18356	.	.	ENSG00000130830	ENST00000369534;ENST00000393531;ENST00000453245;ENST00000428488;ENST00000369531	T;T;T;T	0.46451	2.2;2.01;0.87;1.64	4.63	2.84	0.33178	.	0.214261	0.47852	D	0.000209	T	0.39809	0.1092	M	0.63843	1.955	0.80722	D	1	P;D;P;B	0.54964	0.624;0.969;0.785;0.437	B;P;B;B	0.45506	0.206;0.483;0.35;0.134	T	0.31475	-0.9942	10	0.87932	D	0	.	5.8086	0.18454	0.2474:0.0:0.7526:0.0	.	13;13;13;13	B4E325;C9J9J4;G3XAI1;Q00013	.;.;.;EM55_HUMAN	R	13	ENSP00000358547:S13R;ENSP00000377165:S13R;ENSP00000410888:S13R;ENSP00000358544:S13R	ENSP00000358544:S13R	S	-	3	2	MPP1	153686804	1.000000	0.71417	0.998000	0.56505	0.210000	0.24377	2.055000	0.41345	0.761000	0.33130	0.529000	0.55759	AGC	.		0.667	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		T	154033610	G	T	154033610	3	4	5	1	0	0	0	0	1	0	0	0	9758	1310	46	4	1425	4	MPP1	23	154033610	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	109163353	154033610	1236950	86	391											
SKI	6497	hgsc.bcm.edu	37	chr1	2160390	2160390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgcggccgcggtgccggCgccggtgcccgcagccaccg	2	2	19	18	9	0	0	0	0	0	0	0	0	0	0	6	5	3	1	6	5	0	0	rs28384811	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:2160390C>G	ENST00000378536.4	+	1	257	c.185C>G	c.(184-186)gCg>gGg	p.A62G		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	62					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		gcggtgccggcgccggTGCCC	0.776													C|||	229	0.0457268	0.0234	0.0576	5008	,	,		4535	0.0079		0.0706	False		,,,				2504	0.0808				p.A62G	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.C185G						.						1	1	1					1																	2160390		788	1840	2628	SO:0001583	missense	6497	exon1			TGCCGGCGCCGGT	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.185C>G	1.37:g.2160390C>G	ENSP00000367797:p.Ala62Gly	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	5	4	NM_003036	0	0	0	0	0	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	37	CCDS39.1	102	0.046703296703296704	20	0.04065040650406504	28	0.07734806629834254	3	0.005244755244755245	51	0.06728232189973615	C	9.688	1.151208	0.21371	.	.	ENSG00000157933	ENST00000378536	D	0.95821	-3.82	2.3	2.3	0.28687	.	.	.	.	.	T	0.47857	0.1468	N	0.08118	0	0.45733	P	0.001363000000000003	D	0.57899	0.981	P	0.58520	0.84	T	0.76271	-0.3020	8	0.20519	T	0.43	-11.9718	7.7374	0.28823	0.0:1.0:0.0:0.0	rs28384811	62	P12755	SKI_HUMAN	G	62	ENSP00000367797:A62G	ENSP00000367797:A62G	A	+	2	0	SKI	2150250	0.994000	0.37717	0.998000	0.56505	0.971000	0.66376	0.878000	0.28126	1.104000	0.41587	0.185000	0.17295	GCG	C|0.953;G|0.047		0.776	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		G	2160390	C	G	2160390	3	3	6	1	0	0	0	0	1	0	0	0	14389	768	27	4	187	4	SKI	1	2160390	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		2160390	247090231	1	392											
BAI2	576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	32207416	32207416	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtacctggacacctcttctCactacaaggcttcacctcct	9	11	5	16	0	3	0	2	0	2	0	5	1	4	1	4	2	2	2	4	2	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:32207416C>A	ENST00000373658.3	-	9	1911	c.1570G>T	c.(1570-1572)Gag>Tag	p.E524*	BAI2_ENST00000398556.3_Nonsense_Mutation_p.E472*|BAI2_ENST00000398547.1_Nonsense_Mutation_p.E457*|BAI2_ENST00000398538.1_Nonsense_Mutation_p.E512*|BAI2_ENST00000440175.2_Nonsense_Mutation_p.E166*|BAI2_ENST00000398542.1_Nonsense_Mutation_p.E457*|BAI2_ENST00000527361.1_Nonsense_Mutation_p.E524*|BAI2_ENST00000257070.4_Nonsense_Mutation_p.E524*|BAI2_ENST00000373655.2_Nonsense_Mutation_p.E524*	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	524	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		CACCTCTTCTCACTACAAGGC	0.652																																					p.E524X		.											.	BAI2-526	0			c.G1570T						.						95	100	98					1																	32207416		2203	4299	6502	SO:0001587	stop_gained	576	exon9			TCTTCTCACTACA	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1570G>T	1.37:g.32207416C>A	ENSP00000362762:p.Glu524*	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	110	17	NM_001703	0	0	0	0	0	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Nonsense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	36	5.737223	0.96865	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125;ENST00000533175	.	.	.	4.95	4.95	0.65309	.	0.000000	0.39985	N	0.001213	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	17.3262	0.87248	0.0:1.0:0.0:0.0	.	.	.	.	X	472;457;524;524;457;524;524;166;512;462;503	.	ENSP00000257070:E524X	E	-	1	0	BAI2	31980003	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	5.765000	0.68834	2.457000	0.83068	0.561000	0.74099	GAG	.		0.652	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32207416	C	A	32207416	4	1	6	1	0	0	0	0	0	1	0	0	1300	835	29	4	3287	4	BAI2	1	32207416	Nonsense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	30047026	32207416	217043205	2	393											
TOE1	114034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45808095	45808095	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcagtacggaccctattcCtggagctaatccgagcccgc	9	8	10	14	3	1	0	1	0	0	0	3	3	3	2	4	2	3	2	4	2	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:45808095C>G	ENST00000372090.5	+	6	1115	c.532C>G	c.(532-534)Ctg>Gtg	p.L178V	MUTYH_ENST00000372110.3_5'Flank|MUTYH_ENST00000529984.1_5'Flank|MUTYH_ENST00000528013.2_5'Flank|MUTYH_ENST00000355498.2_5'Flank|MUTYH_ENST00000450313.1_5'Flank|MUTYH_ENST00000488731.2_5'Flank|MUTYH_ENST00000531105.1_5'Flank|MUTYH_ENST00000372098.3_5'Flank|TOE1_ENST00000539779.1_Missense_Mutation_p.L98V|MUTYH_ENST00000354383.6_5'Flank|MUTYH_ENST00000528332.2_5'Flank|MUTYH_ENST00000372104.1_5'Flank|MUTYH_ENST00000448481.1_5'Flank|MUTYH_ENST00000456914.2_5'Flank|MUTYH_ENST00000372100.5_5'Flank|MUTYH_ENST00000372115.3_5'Flank|TOE1_ENST00000495703.1_3'UTR|TESK2_ENST00000486676.1_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	178						nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					GACCCTATTCCTGGAGCTAAT	0.552																																					p.L178V		.											.	TOE1-90	0			c.C532G						.						97	100	99					1																	45808095		2203	4300	6503	SO:0001583	missense	114034	exon6			CTATTCCTGGAGC		CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.532C>G	1.37:g.45808095C>G	ENSP00000361162:p.Leu178Val	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	168	29	NM_025077	0	0	9	11	2	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Missense_Mutation	SNP	ENST00000372090.5	37	CCDS521.1	.	.	.	.	.	.	.	.	.	.	C	9.622	1.133977	0.21123	.	.	ENSG00000132773	ENST00000372090;ENST00000539779	T;T	0.23552	1.9;1.9	5.79	4.88	0.63580	Ribonuclease H-like (1);	0.129811	0.53938	D	0.000050	T	0.24661	0.0598	L	0.36672	1.1	0.41103	D	0.985687	B;P;P	0.40398	0.164;0.716;0.716	B;B;B	0.42245	0.077;0.381;0.194	T	0.02358	-1.1171	10	0.27785	T	0.31	-8.8608	14.7036	0.69171	0.0:0.9309:0.0:0.0691	.	184;98;178	B4DP23;B4DEM6;Q96GM8	.;.;TOE1_HUMAN	V	178;98	ENSP00000361162:L178V;ENSP00000438900:L98V	ENSP00000361162:L178V	L	+	1	2	TOE1	45580682	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	2.049000	0.41288	1.455000	0.47813	0.655000	0.94253	CTG	.		0.552	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077		G	45808095	C	G	45808095	3	3	6	1	0	0	0	0	1	0	0	0	16381	680	24	4	554	4	TOE1	1	45808095	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	13600679	45808095	203442526	3	394											
CCDC17	149483	broad.mit.edu	37	chr1	46086774	46086774	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccaaagatactgatgatGagggtggtagtctgtagaat	14	10	13	4	0	1	6	0	3	1	3	1	6	1	6	1	2	1	2	1	2	5	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:46086774G>T	ENST00000528266.1	-	11	1547	c.1400C>A	c.(1399-1401)tCa>tAa	p.S467*	CCDC17_ENST00000343901.2_Nonsense_Mutation_p.S435*|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000421127.2_Nonsense_Mutation_p.S458*|CCDC17_ENST00000464739.1_5'UTR			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	467										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TACTGATGATGAGGGTGGTAG	0.522																																					p.S467X													.	CCDC17-23	0			c.C1400A						.						34	35	35					1																	46086774		2203	4300	6503	SO:0001587	stop_gained	149483	exon11			GATGATGAGGGTG		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1400C>A	1.37:g.46086774G>T	ENSP00000432172:p.Ser467*	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	38	5	NM_001114938	0	0	0	0	0	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Nonsense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	.	.	.	.	.	.	.	.	.	.	G	31	5.058885	0.93846	.	.	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	.	.	.	5.19	5.19	0.71726	.	0.178624	0.39407	N	0.001373	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.5395	17.638	0.88128	0.0:0.0:1.0:0.0	.	.	.	.	X	458;435;467	.	ENSP00000341451:S435X	S	-	2	0	CCDC17	45859361	1.000000	0.71417	1.000000	0.80357	0.673000	0.39480	6.283000	0.72646	2.686000	0.91538	0.591000	0.81541	TCA	.		0.522	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		T	46086774	G	T	46086774	4	4	6	1	0	0	0	0	0	1	0	0	2799	1294	45	4	480	4	CCDC17	1	46086774	Nonsense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	278679	46086774	203163847	4	395											
LPHN2	23266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	82456455	82456455	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcagcggactcactcccttCtgtaccaaccccagaagaaa	12	7	6	16	1	3	2	2	0	1	2	4	3	4	3	4	1	3	1	4	1	4	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:82456455C>G	ENST00000370728.1	+	25	4651	c.4006C>G	c.(4006-4008)Ctg>Gtg	p.L1336V	LPHN2_ENST00000394879.1_Missense_Mutation_p.L1338V|LPHN2_ENST00000370721.1_Missense_Mutation_p.L1261V|LPHN2_ENST00000370725.1_Missense_Mutation_p.L1351V|LPHN2_ENST00000335786.5_Missense_Mutation_p.L1293V|LPHN2_ENST00000469377.2_3'UTR|LPHN2_ENST00000370723.1_Missense_Mutation_p.L1338V|LPHN2_ENST00000319517.6_Missense_Mutation_p.L1280V|LPHN2_ENST00000370730.1_Missense_Mutation_p.L1293V|LPHN2_ENST00000370717.2_Missense_Mutation_p.L1351V|LPHN2_ENST00000359929.3_Missense_Mutation_p.L1280V|LPHN2_ENST00000370727.1_Missense_Mutation_p.L1308V|LPHN2_ENST00000271029.4_Missense_Mutation_p.L1308V|LPHN2_ENST00000370713.1_3'UTR|LPHN2_ENST00000370715.1_3'UTR			O95490	LPHN2_HUMAN	latrophilin 2	1336					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		TCACTCCCTTCTGTACCAACC	0.527																																					p.L1280V		.											.	LPHN2-525	0			c.C3838G						.						84	87	86					1																	82456455		2203	4300	6503	SO:0001583	missense	23266	exon20			TCCCTTCTGTACC	AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"-", "GPCR / Class B : Orphans"	18582	protein-coding gene	gene with protein product		607018	"latrophilin 1"	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.4006C>G	1.37:g.82456455C>G	ENSP00000359763:p.Leu1336Val	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	165	44	NM_012302	0	0	34	73	39	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.57|13.57|13.57	2.275917|2.275917|2.275917	0.40294|0.40294|0.40294	.|.|.	.|.|.	ENSG00000117114|ENSG00000117114|ENSG00000117114	ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000402328	.|T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.72835|.	.|-0.52;-0.53;-0.69;-0.63;-0.47;-0.43;-0.63;-0.63;-0.47;-0.43;-0.63;-0.69|.	5.67|5.67|5.67	5.67|5.67|5.67	0.87782|0.87782|0.87782	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000011|.	T|T|T	0.68375|0.68375|0.68375	0.2994|0.2994|0.2994	M|M|M	0.62723|0.62723|0.62723	1.935|1.935|1.935	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P;D|.	.|0.69078|.	.|0.663;0.997|.	.|B;D|.	.|0.76071|.	.|0.395;0.987|.	T|T|T	0.64841|0.64841|0.64841	-0.6312|-0.6312|-0.6312	5|10|5	.|0.59425|.	.|D|.	.|0.04|.	.|.|.	19.773|19.773|19.773	0.96379|0.96379|0.96379	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|1280;260|.	.|O95490-2;B3KVU1|.	.|.;.|.	L|V|C	1227|1261;1336;1293;1308;1351;1338;1280;1280;1351;1338;1308;1293|347	.|ENSP00000359756:L1261V;ENSP00000359763:L1336V;ENSP00000359765:L1293V;ENSP00000359762:L1308V;ENSP00000359760:L1351V;ENSP00000359758:L1338V;ENSP00000353006:L1280V;ENSP00000322270:L1280V;ENSP00000359752:L1351V;ENSP00000378344:L1338V;ENSP00000271029:L1308V;ENSP00000337306:L1293V|.	.|ENSP00000271029:L1308V|.	F|L|S	+|+|+	3|1|2	2|2|0	LPHN2|LPHN2|LPHN2	82229043|82229043|82229043	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.988000|0.988000|0.988000	0.76386|0.76386|0.76386	5.773000|5.773000|5.773000	0.68898|0.68898|0.68898	2.677000|2.677000|2.677000	0.91161|0.91161|0.91161	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTG|TCT	.		0.527	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		G	82456455	C	G	82456455	3	3	6	1	0	0	0	0	1	0	0	0	8941	912	32	4	3912	4	LPHN2	1	82456455	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	36369681	82456455	166794166	5	396											
C1orf51	148523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150259000	150259000	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacctggatccacaccacTccaatttgcaacccccctct	9	9	3	20	0	2	0	1	0	1	0	4	1	4	1	7	1	2	1	7	1	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:150259000T>A	ENST00000290363.5	+	5	1241	c.792T>A	c.(790-792)acT>acA	p.T264T	C1orf51_ENST00000369094.1_Silent_p.T176T|C1orf51_ENST00000369095.1_Silent_p.T264T	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		264					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCCACACCACTCCAATTTGCA	0.522																																					p.T264T		.											.	C1orf51-90	0			c.T792A						.						243	190	208					1																	150259000		2203	4300	6503	SO:0001819	synonymous_variant	148523	exon5			CACCACTCCAATT																												ENST00000290363.5:c.792T>A	1.37:g.150259000T>A		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	183	35	NM_144697	0	0	15	20	5	B2RD43|D3DV01|Q8N795|Q96MG6	Silent	SNP	ENST00000290363.5	37	CCDS949.1																																																																																			.		0.522	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			A	150259000	T	A	150259000	2	1	6	1	0	0	0	0	0	0	0	1	2049	1538	54	5		5	C1orf51	1	150259000	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08	67802545	150259000	98991621	6	397											
CRTC2	200186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153924520	153924520	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catcatagcctgggcccaggCccatgcccctgctgatgccc	6	7	10	18	0	1	1	1	1	0	0	1	1	1	1	6	2	4	1	6	2	1	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:153924520C>A	ENST00000368633.1	-	10	1098	c.971G>T	c.(970-972)gGc>gTc	p.G324V	CRTC2_ENST00000368630.3_Intron|CRTC2_ENST00000476883.1_5'Flank	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	324				MGL -> HGP (in Ref. 1; AAQ98857). {ECO:0000305}.	gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGGCCCAGGCCCATGCCCCT	0.607																																					p.G324V		.											.	CRTC2-228	0			c.G971T						.						58	57	57					1																	153924520		2203	4300	6503	SO:0001583	missense	200186	exon10			CCCAGGCCCATGC	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.971G>T	1.37:g.153924520C>A	ENSP00000357622:p.Gly324Val	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	108	14	NM_181715	0	0	15	25	10	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	c	6.593	0.477845	0.12521	.	.	ENSG00000160741	ENST00000368633	T	0.12774	2.65	4.84	3.92	0.45320	.	0.625789	0.15810	N	0.243526	T	0.05502	0.0145	L	0.36672	1.1	0.48830	D	0.999715	B	0.23249	0.082	B	0.21708	0.036	T	0.09185	-1.0686	10	0.66056	D	0.02	-3.8662	11.1372	0.48381	0.0:0.813:0.187:0.0	.	324	Q53ET0	CRTC2_HUMAN	V	324	ENSP00000357622:G324V	ENSP00000357622:G324V	G	-	2	0	CRTC2	152191144	0.420000	0.25457	0.997000	0.53966	0.095000	0.18619	0.767000	0.26575	1.028000	0.39785	0.450000	0.29827	GGC	.		0.607	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153924520	C	A	153924520	3	1	6	1	0	0	0	0	1	0	0	0	3906	739	26	4	1130	4	CRTC2	1	153924520	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	3665520	153924520	95326101	7	398											
C1orf111	284680	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	162344114	162344114	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtgccacctggaagccatTaggatgtcctgggatgtgat	8	10	15	8	0	0	1	0	1	0	0	1	4	1	4	4	4	2	0	4	4	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:162344114T>C	ENST00000367935.5	-	3	589	c.510A>G	c.(508-510)ctA>ctG	p.L170L	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	170										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			TGGAAGCCATTAGGATGTCCT	0.567																																					p.L170L		.											.	C1orf111-69	0			c.A510G						.						204	196	198					1																	162344114		2203	4300	6503	SO:0001819	synonymous_variant	284680	exon3			AGCCATTAGGATG	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.510A>G	1.37:g.162344114T>C		Somatic	339	1		WXS	Illumina HiSeq	Phase_I	317	53	NM_182581	0	0	0	0	0	Q6X961|Q8NEC3	Silent	SNP	ENST00000367935.5	37	CCDS1238.1																																																																																			.		0.567	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581		C	162344114	T	C	162344114	2	2	6	1	0	0	0	0	0	0	0	1	1990	1741	61	3		3	C1orf111	1	162344114	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08	8419594	162344114	86906507	8	399											
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185278246	185278246	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cactattaaagatttcaaatAaatagggactgcagcaagct	17	10	7	7	0	1	1	1	0	0	1	1	2	1	2	0	1	3	3	0	1	8	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:185278246A>G	ENST00000367498.3	-	4	792	c.170T>C	c.(169-171)tTa>tCa	p.L57S	IVNS1ABP_ENST00000392007.3_5'UTR|IVNS1ABP_ENST00000367497.1_Missense_Mutation_p.L57S|IVNS1ABP_ENST00000459929.1_5'UTR	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	57	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)				breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						GATTTCAAATAAATAGGGACT	0.348																																					p.L57S		.											.	IVNS1ABP-94	0			c.T170C						.						40	41	40					1																	185278246		2203	4300	6503	SO:0001583	missense	10625	exon4			TCAAATAAATAGG	AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.170T>C	1.37:g.185278246A>G	ENSP00000356468:p.Leu57Ser	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_006469	0	0	45	45	0	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Missense_Mutation	SNP	ENST00000367498.3	37	CCDS1368.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.621805	0.87460	.	.	ENSG00000116679	ENST00000367498;ENST00000367497	T;T	0.73152	-0.72;1.8	5.67	5.67	0.87782	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.87430	0.6175	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90273	0.4309	10	0.87932	D	0	.	15.916	0.79517	1.0:0.0:0.0:0.0	.	57	Q9Y6Y0	NS1BP_HUMAN	S	57	ENSP00000356468:L57S;ENSP00000356467:L57S	ENSP00000356467:L57S	L	-	2	0	IVNS1ABP	183544869	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.210000	0.95106	2.164000	0.68074	0.482000	0.46254	TTA	.		0.348	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		G	185278246	A	G	185278246	3	3	6	1	0	0	0	0	1	0	0	0	7951	372	13	3	1806	3	IVNS1ABP	1	185278246	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	22934132	185278246	63972375	9	400											
FAM5C	339479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	190067269	190067269	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgagtctatgacgaagcAagcaagagaaaagatctaga	17	7	11	6	1	2	5	0	2	2	3	2	7	2	5	0	0	2	3	0	0	7	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:190067269A>T	ENST00000367462.3	-	8	2411	c.2180T>A	c.(2179-2181)tTg>tAg	p.L727*	BRINP3_ENST00000534846.1_Nonsense_Mutation_p.L625*	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	727					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											ATGACGAAGCAAGCAAGAGAA	0.463																																					p.L727X		.											.	FAM5C-228	0			c.T2180A						.						115	111	112					1																	190067269		2203	4300	6503	SO:0001587	stop_gained	339479	exon8			CGAAGCAAGCAAG	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.2180T>A	1.37:g.190067269A>T	ENSP00000356432:p.Leu727*	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	129	14	NM_199051	0	0	0	0	0	B3KVP1|B7Z260|O95726|Q2M330	Nonsense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	37	6.250241	0.97412	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	.	.	.	5.72	4.6	0.57074	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7499	0.40470	0.9186:0.0:0.0814:0.0	.	.	.	.	X	727;625	.	ENSP00000356432:L727X	L	-	2	0	FAM5C	188333892	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.237000	0.95368	1.005000	0.39183	0.528000	0.53228	TTG	.		0.463	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190067269	A	T	190067269	4	4	6	1	0	0	0	0	0	1	0	0	5613	131	5	5	124	5	FAM5C	1	190067269	Nonsense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	4789023	190067269	59183352	10	401											
PTPRC	5788	hgsc.bcm.edu;broad.mit.edu	37	chr1	198704382	198704382	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaattgaacattgtaaatGtgagtttgctttttacataa	15	16	7	3	0	0	3	0	2	0	1	0	3	0	3	0	0	3	3	0	0	6	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:198704382G>A	ENST00000367376.2	+	23	2568		c.e23+1		PTPRC_ENST00000352140.3_Splice_Site|PTPRC_ENST00000594404.1_Splice_Site|PTPRC_ENST00000442510.2_Splice_Site|PTPRC_ENST00000348564.6_Splice_Site	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C						axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CATTGTAAATGTGAGTTTGCT	0.274																																					.		.											.	PTPRC-295	0			c.1920+1G>A						.						69	64	66					1																	198704382		2203	4299	6502	SO:0001630	splice_region_variant	5788	exon20			GTAAATGTGAGTT	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2397+1G>A	1.37:g.198704382G>A		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	35	4	NM_080921	0	0	0	0	0	A8K7W6|Q16614|Q9H0Y6	Splice_Site	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	12.65	2.000478	0.35320	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000535566;ENST00000442510;ENST00000348564	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8748	0.92331	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRC	196971005	1.000000	0.71417	0.950000	0.38849	0.039000	0.13416	9.366000	0.97143	2.523000	0.85059	0.655000	0.94253	.	.		0.274	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			Intron	A	198704382	G	A	198704382	5	1	6	1	0	0	0	0	0	0	1	0	12829	1391	48	2	2495	2	PTPRC	1	198704382	Splice_Site	SNP	G	TCGA-A4-7585-01A-11D-2136-08	8637113	198704382	50546239	11	402											
URB2	9816	broad.mit.edu	37	chr1	229771589	229771589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acccataccggcctggttccGctgtctgaagactttgatat	8	12	9	12	2	1	3	0	2	1	1	2	3	2	3	4	2	1	2	4	2	3	4	rs139241970		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:229771589G>A	ENST00000258243.2	+	4	1365	c.1229G>A	c.(1228-1230)cGc>cAc	p.R410H		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	410						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						GCCTGGTTCCGCTGTCTGAAG	0.527																																					p.R410H													.	URB2-174	0			c.G1229A						.	G	HIS/ARG	0,4406		0,0,2203	64	67	66		1229	5.5	1	1	dbSNP_134	66	1,8599	1.2+/-3.3	0,1,4299	no	missense	URB2	NM_014777.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	410/1525	229771589	1,13005	2203	4300	6503	SO:0001583	missense	9816	exon4			GGTTCCGCTGTCT	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.1229G>A	1.37:g.229771589G>A	ENSP00000258243:p.Arg410His	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	98	4	NM_014777	0	0	2	2	0	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.630889	0.67015	0.0	1.16E-4	ENSG00000135763	ENST00000258243	T	0.35236	1.32	5.5	5.5	0.81552	.	0.050790	0.85682	D	0.000000	T	0.55049	0.1896	M	0.68952	2.095	0.58432	D	0.999999	D	0.76494	0.999	P	0.56788	0.806	T	0.51309	-0.8722	9	.	.	.	-23.8334	19.7863	0.96440	0.0:0.0:1.0:0.0	.	410	Q14146	URB2_HUMAN	H	410	ENSP00000258243:R410H	.	R	+	2	0	URB2	227838212	1.000000	0.71417	1.000000	0.80357	0.436000	0.31835	7.325000	0.79124	2.765000	0.95021	0.650000	0.86243	CGC	G|1.000;A|0.000		0.527	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229771589	G	A	229771589	3	1	6	1	0	0	0	0	1	0	0	0	17058	1087	38	1	1239	1	URB2	1	229771589	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	31067207	229771589	19479032	12	403											
TAF1B	9014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	10016047	10016047	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttgaatactcacaacgaaagGagaagggaatcgtgaagatg	17	7	12	5	2	1	4	1	2	0	2	2	7	1	5	0	2	2	0	0	2	7	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:10016047G>C	ENST00000263663.5	+	7	795	c.607G>C	c.(607-609)Gag>Cag	p.E203Q	TAF1B_ENST00000396242.3_Intron	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	203	N-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ACAACGAAAGGAGAAGGGAAT	0.408																																					p.E203Q		.											.	TAF1B-92	0			c.G607C						.						223	193	203					2																	10016047		2203	4300	6503	SO:0001583	missense	9014	exon7			CGAAAGGAGAAGG	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.607G>C	2.37:g.10016047G>C	ENSP00000263663:p.Glu203Gln	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	200	40	NM_005680	0	0	19	36	17	B4DI42|F8WD72|Q15574|Q8WVC3	Missense_Mutation	SNP	ENST00000263663.5	37	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	G	9.995	1.231767	0.22626	.	.	ENSG00000115750	ENST00000263663	T	0.01902	4.57	5.82	4.0	0.46444	.	0.254066	0.44285	D	0.000476	T	0.02807	0.0084	L	0.41236	1.265	0.80722	D	1	B;P	0.52316	0.172;0.952	B;P	0.46659	0.025;0.523	T	0.60419	-0.7267	9	.	.	.	-14.0229	5.6394	0.17554	0.1472:0.178:0.6747:0.0	.	203;203	Q53T94;Q53T94-2	TAF1B_HUMAN;.	Q	203	ENSP00000263663:E203Q	.	E	+	1	0	TAF1B	9933498	1.000000	0.71417	0.994000	0.49952	0.941000	0.58515	1.150000	0.31639	1.442000	0.47568	0.655000	0.94253	GAG	.		0.408	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		C	10016047	G	C	10016047	3	2	6	1	0	0	0	0	1	0	0	0	15552	1175	41	4	633	4	TAF1B	2	10016047	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08		10016047	233183326	13	404											
CAD	790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27460276	27460276	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgtccatgtgcacctgcggGaaccaggtgggacacataag	11	7	13	10	1	0	0	0	0	0	0	1	2	1	2	3	3	3	1	3	3	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:27460276G>A	ENST00000403525.1	+	27	4381	c.4237G>A	c.(4237-4239)Gaa>Aaa	p.E1413K	CAD_ENST00000264705.4_Missense_Mutation_p.E1476K			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACCTGCGGGAACCAGGTGG	0.552																																					p.E1476K		.											.	CAD-295	0			c.G4426A						.						87	84	85					2																	27460276		2203	4300	6503	SO:0001583	missense	790	exon28			CTGCGGGAACCAG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.4237G>A	2.37:g.27460276G>A	ENSP00000384510:p.Glu1413Lys	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	120	20	NM_004341	0	0	11	19	8	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	28.5	4.927886	0.92389	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	T;T	0.46063	0.88;0.88	4.91	4.01	0.46588	Dihydroorotase, conserved site (1);Amidohydrolase 1 (1);	0.167071	0.52532	D	0.000062	T	0.73249	0.3563	H	0.98111	4.15	0.80722	D	1	P;D	0.65815	0.941;0.995	P;P	0.62885	0.66;0.908	T	0.80306	-0.1438	10	0.33141	T	0.24	-0.4186	13.2019	0.59774	0.0:0.0:0.8392:0.1608	.	1413;1476	F8VPD4;P27708	.;PYR1_HUMAN	K	1476;1413	ENSP00000264705:E1476K;ENSP00000384510:E1413K	ENSP00000264705:E1476K	E	+	1	0	CAD	27313780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.360000	0.97119	1.030000	0.39839	0.561000	0.74099	GAA	.		0.552	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27460276	G	A	27460276	3	1	6	1	0	0	0	0	1	0	0	0	2571	1175	41	2	4536	2	CAD	2	27460276	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	17444229	27460276	215739097	14	405											
TSGA10	80705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	99720473	99720473	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtctgccaagttcactttCggtatccattgcctttcttg	5	18	7	11	1	3	0	1	0	2	0	5	0	4	0	3	1	2	2	3	1	2	7	rs545440386	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:99720473C>A	ENST00000393483.3	-	10	1412	c.568G>T	c.(568-570)Gaa>Taa	p.E190*	TSGA10_ENST00000355053.4_Nonsense_Mutation_p.E190*|TSGA10_ENST00000478090.1_5'UTR|TSGA10_ENST00000539964.1_Nonsense_Mutation_p.E190*|TSGA10_ENST00000410001.1_Nonsense_Mutation_p.E190*|TSGA10_ENST00000542655.1_Nonsense_Mutation_p.E190*	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	190					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						AGTTCACTTTCGGTATCCATT	0.348																																					p.E190X		.											.	TSGA10-91	0			c.G568T						.						240	212	222					2																	99720473		2202	4299	6501	SO:0001587	stop_gained	80705	exon9			CACTTTCGGTATC	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.568G>T	2.37:g.99720473C>A	ENSP00000377123:p.Glu190*	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	113	12	NM_182911	0	0	1	2	1	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Nonsense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	42	9.602630	0.99217	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	.	.	.	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-16.4617	16.7002	0.85348	0.0:1.0:0.0:0.0	.	.	.	.	X	190	.	ENSP00000347161:E190X	E	-	1	0	TSGA10	99086905	0.986000	0.35501	0.969000	0.41365	0.988000	0.76386	2.774000	0.47694	2.801000	0.96364	0.650000	0.86243	GAA	.		0.348	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		A	99720473	C	A	99720473	4	1	6	1	0	0	0	0	0	1	0	0	16650	893	31	4	1576	4	TSGA10	2	99720473	Nonsense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	72260197	99720473	143478900	15	406											
LCT	3938	broad.mit.edu;bcgsc.ca	37	chr2	136566494	136566494	+	Frame_Shift_Del	DEL	T	T	-																															tgcagcattcggtcagcggcTtccacatctctggggacccc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:136566494delT	ENST00000264162.2	-	8	3433	c.3423delA	c.(3421-3423)gaafs	p.E1141fs	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1141	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GGTCAGCGGCTTCCACATCTC	0.552																																					p.E1141fs													.	LCT-101	0			c.3423delA						.						71	75	74					2																	136566494		2203	4300	6503	SO:0001589	frameshift_variant	3938	exon8			AGCGGCTTCCACA	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.3423delA	2.37:g.136566494delT	ENSP00000264162:p.Glu1141fs	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	156	21	NM_002299	0	0	0	0	0	Q4ZG58	Frame_Shift_Del	DEL	ENST00000264162.2	37	CCDS2178.1																																																																																			.		0.552	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		-	136566494	T	-	136566494	7	5	6	1	0	1	0	1	0	0	0	0	8714	1606	56	0	2400	0	LCT	2	136566494	Frame_Shift_Del	DEL	T	TCGA-A4-7585-01A-11D-2136-08	36846021	136566494	106632879	16	407											
DARS	1615	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	136736937	136736937	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccgaaccaaaactcgatCtgtaataacagtaaacgatt	18	8	5	10	3	1	0	0	0	1	0	2	3	1	0	2	0	5	2	2	0	8	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:136736937C>A	ENST00000264161.4	-	3	340		c.e3-1		DARS_ENST00000463008.1_Splice_Site|DARS_ENST00000537273.1_Splice_Site	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	AAAACTCGATCTGTAATAACA	0.318																																					.		.											.	DARS-91	0			c.125-1G>T						.						105	108	107					2																	136736937		2203	4300	6503	SO:0001630	splice_region_variant	1615	exon4			CTCGATCTGTAAT	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.125-1G>T	2.37:g.136736937C>A		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	124	25	NM_001349	0	0	0	0	0	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Splice_Site	SNP	ENST00000264161.4	37	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	C	11.16	1.558088	0.27827	.	.	ENSG00000115866	ENST00000264161;ENST00000441323;ENST00000456565;ENST00000449218	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3312	0.83015	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DARS	136453407	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	5.328000	0.65887	2.655000	0.90218	0.462000	0.41574	.	.		0.318	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349	Intron	A	136736937	C	A	136736937	5	1	6	1	0	0	0	0	0	0	1	0	4247	927	32	4	1437	4	DARS	2	136736937	Splice_Site	SNP	C	TCGA-A4-7585-01A-11D-2136-08	170443	136736937	106462436	17	408											
THSD7B	80731	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	138169186	138169186	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgttggaacagggaaaagCagaaagaaggagaaatgcca	18	5	13	5	0	0	3	0	0	0	3	0	6	0	5	1	3	3	2	1	3	6	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:138169186C>A	ENST00000409968.1	+	14	2881	c.2703C>A	c.(2701-2703)agC>agA	p.S901R	THSD7B_ENST00000272643.3_Missense_Mutation_p.S901R|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Missense_Mutation_p.S870R			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	901	TSP type-1 11. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CAGGGAAAAGCAGAAAGAAGG	0.353																																					.													.	THSD7B-75	0			.						.						120	111	114					2																	138169186		1860	4090	5950	SO:0001583	missense	80731	.			GAAAAGCAGAAAG			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2703C>A	2.37:g.138169186C>A	ENSP00000387145:p.Ser901Arg	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	108	15	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	18.21	3.573910	0.65765	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.61040	0.14;0.14;0.14	5.84	4.96	0.65561	.	0.078462	0.85682	D	0.000000	T	0.72070	0.3415	M	0.72353	2.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.69540	-0.5118	10	0.13853	T	0.58	.	14.675	0.68972	0.0:0.9306:0.0:0.0694	.	901;870	Q9C0I4;C9JKN6	THS7B_HUMAN;.	R	901;901;870	ENSP00000387145:S901R;ENSP00000272643:S901R;ENSP00000413841:S870R	ENSP00000272643:S901R	S	+	3	2	THSD7B	137885656	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	2.127000	0.42035	1.467000	0.48044	0.557000	0.71058	AGC	.		0.353	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		A	138169186	C	A	138169186	3	1	6	1	0	0	0	0	1	0	0	0	15912	709	25	4	2660	4	THSD7B	2	138169186	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	1432249	138169186	105030187	18	409											
KIF5C	3800	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	149835496	149835496	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaagcaacagatgttggatCaggatgaggtaaagaatgca	16	8	13	4	0	1	4	1	2	0	2	1	6	1	6	0	3	3	4	0	3	5	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:149835496C>T	ENST00000435030.1	+	13	1722	c.1354C>T	c.(1354-1356)Cag>Tag	p.Q452*	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Nonsense_Mutation_p.Q357*|KIF5C_ENST00000397413.1_Nonsense_Mutation_p.Q220*			O60282	KIF5C_HUMAN	kinesin family member 5C	452					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		GATGTTGGATCAGGATGAGGT	0.353																																					p.Q452X		.											.	KIF5C-69	0			c.C1354T						.						78	78	78					2																	149835496		1852	4105	5957	SO:0001587	stop_gained	3800	exon13			TTGGATCAGGATG	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.1354C>T	2.37:g.149835496C>T	ENSP00000393379:p.Gln452*	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	61	17	NM_004522	0	0	0	0	0	O95079|Q2YDC5	Nonsense_Mutation	SNP	ENST00000435030.1	37		.	.	.	.	.	.	.	.	.	.	C	39	7.391751	0.98255	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	.	.	.	X	452;357;355;220	.	ENSP00000334176:Q355X	Q	+	1	0	KIF5C	149543742	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.627000	0.83176	2.941000	0.99782	0.655000	0.94253	CAG	.		0.353	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		T	149835496	C	T	149835496	4	4	6	1	0	0	0	0	0	1	0	0	8328	827	29	2	1326	2	KIF5C	2	149835496	Nonsense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	11666310	149835496	93363877	19	410											
TTN	7273	bcgsc.ca	37	chr2	179449124	179449124	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaggccagcacaaggataTtcagttgaccggacaagagt	15	6	11	9	1	1	2	1	1	0	1	1	4	1	4	2	3	1	2	2	3	4	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:179449124T>C	ENST00000591111.1	-	261	60455	c.60231A>G	c.(60229-60231)gaA>gaG	p.E20077E	TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000460472.2_Silent_p.E12653E|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.E12845E|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.E21718E|TTN_ENST00000342992.6_Silent_p.E19150E|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.E12778E			Q8WZ42	TITIN_HUMAN	titin	20077	Fibronectin type-III 45. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACAAGGATATTCAGTTGACC	0.458																																					p.E21718E													.	TTN-636	0			c.A65154G						.						109	108	108					2																	179449124		1933	4142	6075	SO:0001819	synonymous_variant	7273	exon311			AGGATATTCAGTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.60231A>G	2.37:g.179449124T>C		Somatic	113	0		WXS	Illumina HiSeq	Phase_1	143	5	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179449124	T	C	179449124	2	2	6	1	0	0	0	0	0	0	0	1	16768	1490	52	3		3	TTN	2	179449124	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08	29613628	179449124	63750249	20	411											
SESTD1	91404	bcgsc.ca	37	chr2	180041254	180041254	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcacggtaaatcctctagccTtacacttctcactgaaacaa	13	11	4	13	1	3	1	2	1	2	0	5	1	4	1	2	1	3	1	2	1	6	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:180041254T>G	ENST00000428443.3	-	4	492	c.176A>C	c.(175-177)aAg>aCg	p.K59T	SESTD1_ENST00000486468.1_5'UTR	NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	59	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			TCCTCTAGCCTTACACTTCTC	0.338																																					p.K59T													.	SESTD1-228	0			c.A176C						.						135	115	122					2																	180041254		2203	4300	6503	SO:0001583	missense	91404	exon4			CTAGCCTTACACT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.176A>C	2.37:g.180041254T>G	ENSP00000415332:p.Lys59Thr	Somatic	47	0		WXS	Illumina HiSeq	Phase_1	68	4	NM_178123	0	0	0	0	0	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.989102	0.74589	.	.	ENSG00000187231	ENST00000428443;ENST00000440010;ENST00000435047	T;T;T	0.66099	-0.19;-0.19;-0.19	5.6	5.6	0.85130	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65719	0.2718	N	0.17345	0.48	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.65598	-0.6129	9	.	.	.	-20.2904	15.7878	0.78322	0.0:0.0:0.0:1.0	.	59	Q86VW0	SESD1_HUMAN	T	59	ENSP00000415332:K59T;ENSP00000416164:K59T;ENSP00000410286:K59T	.	K	-	2	0	SESTD1	179749499	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	8.015000	0.88690	2.132000	0.65825	0.377000	0.23210	AAG	.		0.338	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		G	180041254	T	G	180041254	3	3	6	1	0	0	0	0	1	0	0	0	14159	1609	56	5	1974	5	SESTD1	2	180041254	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	592130	180041254	63158119	21	412											
USP37	57695	hgsc.bcm.edu;bcgsc.ca	37	chr2	219328058	219328058	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaactcggtagctcttttgAggtcatcatcttctttctgt	6	19	7	9	1	6	1	2	1	4	0	7	1	6	1	0	2	2	2	0	2	2	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:219328058A>G	ENST00000258399.3	-	22	2910	c.2498T>C	c.(2497-2499)cTc>cCc	p.L833P	USP37_ENST00000418019.1_Missense_Mutation_p.L833P|USP37_ENST00000415516.1_Missense_Mutation_p.L739P|USP37_ENST00000454775.1_Missense_Mutation_p.L833P	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	833	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		AGCTCTTTTGAGGTCATCATC	0.318																																					p.L833P		.											.	USP37-661	0			c.T2498C						.						107	106	106					2																	219328058		2203	4300	6503	SO:0001583	missense	57695	exon22			CTTTTGAGGTCAT	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.2498T>C	2.37:g.219328058A>G	ENSP00000258399:p.Leu833Pro	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	87	5	NM_020935	0	0	0	0	0	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Missense_Mutation	SNP	ENST00000258399.3	37	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.154173	0.57259	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	T;T;T;T	0.55588	0.55;0.55;0.51;0.55	4.77	4.77	0.60923	Ubiquitin interacting motif (3);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.127314	0.53938	D	0.000041	T	0.65678	0.2714	L	0.59436	1.845	0.80722	D	1	D;D	0.62365	0.989;0.991	P;P	0.61658	0.892;0.881	T	0.68401	-0.5418	10	0.56958	D	0.05	-2.9498	14.7551	0.69557	1.0:0.0:0.0:0.0	.	739;833	Q86T82-2;Q86T82	.;UBP37_HUMAN	P	833;833;739;833	ENSP00000258399:L833P;ENSP00000393662:L833P;ENSP00000400902:L739P;ENSP00000396585:L833P	ENSP00000258399:L833P	L	-	2	0	USP37	219036302	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.305000	0.89960	2.127000	0.65507	0.477000	0.44152	CTC	.		0.318	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		G	219328058	A	G	219328058	3	3	6	1	0	0	0	0	1	0	0	0	17101	304	11	3	461	3	USP37	2	219328058	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	39286804	219328058	23871315	22	413											
PTPRN	5798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220161767	220161767	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccccctgcgcggtggcacAggtgtttggctctgcttggt	2	12	14	13	2	1	0	0	0	1	0	2	0	2	0	2	5	2	4	2	5	0	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:220161767A>C	ENST00000295718.2	-	15	2416	c.2176T>G	c.(2176-2178)Tgt>Ggt	p.C726G	PTPRN_ENST00000423636.2_Missense_Mutation_p.C636G|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.C697G|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000497977.1_5'Flank	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	726	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCGGTGGCACAGGTGTTTGGC	0.637																																					p.C726G		.											.	PTPRN-229	0			c.T2176G						.						95	99	98					2																	220161767		2203	4300	6503	SO:0001583	missense	5798	exon15			TGGCACAGGTGTT		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2176T>G	2.37:g.220161767A>C	ENSP00000295718:p.Cys726Gly	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	75	21	NM_002846	0	0	0	0	0	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.872163	0.33069	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.14516	2.5;2.5;2.5	4.31	4.31	0.51392	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.250911	0.35179	N	0.003398	T	0.24044	0.0582	M	0.67397	2.05	0.39123	D	0.961697	D;B	0.60160	0.987;0.081	P;B	0.51385	0.668;0.078	T	0.06409	-1.0828	10	0.33940	T	0.23	.	13.3146	0.60399	1.0:0.0:0.0:0.0	.	697;726	Q6NSL1;Q16849	.;PTPRN_HUMAN	G	697;726;697;636	ENSP00000386638:C697G;ENSP00000295718:C726G;ENSP00000444244:C636G	ENSP00000295718:C726G	C	-	1	0	PTPRN	219870011	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.355000	0.52262	1.806000	0.52798	0.379000	0.24179	TGT	.		0.637	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			C	220161767	A	C	220161767	3	2	6	1	0	0	0	0	1	0	0	0	12839	188	7	5	799	5	PTPRN	2	220161767	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	833709	220161767	23037606	23	414											
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238275884	238275884	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaaactgtccctcctgaagTtgatggaaccatccaacagg	12	8	10	11	0	0	2	0	2	0	0	3	4	3	4	4	3	3	1	4	3	4	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:238275884T>C	ENST00000295550.4	-	11	5398	c.4946A>G	c.(4945-4947)aAc>aGc	p.N1649S	COL6A3_ENST00000347401.3_Missense_Mutation_p.N1448S|COL6A3_ENST00000472056.1_Missense_Mutation_p.N1042S|COL6A3_ENST00000353578.4_Missense_Mutation_p.N1443S|COL6A3_ENST00000409809.1_Missense_Mutation_p.N1443S|COL6A3_ENST00000346358.4_Missense_Mutation_p.N1449S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1649	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCTCCTGAAGTTGATGGAACC	0.438																																					p.N1649S		.											.	COL6A3-526	0			c.A4946G						.						73	64	67					2																	238275884		2203	4300	6503	SO:0001583	missense	1293	exon11			CTGAAGTTGATGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4946A>G	2.37:g.238275884T>C	ENSP00000295550:p.Asn1649Ser	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	52	9	NM_004369	0	0	10	10	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.285417	0.40394	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.5	5.5	0.81552	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000018	T	0.65217	0.2670	N	0.05031	-0.125	0.46654	D	0.999143	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.87578	0.998;0.998;0.953	T	0.62469	-0.6848	10	0.02654	T	1	.	15.5966	0.76587	0.0:0.0:0.0:1.0	.	1042;1443;1649	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	S	1649;1448;1443;1042;1443;1449	ENSP00000295550:N1649S;ENSP00000315609:N1448S;ENSP00000315873:N1443S;ENSP00000418285:N1042S;ENSP00000386844:N1443S;ENSP00000295546:N1449S	ENSP00000295550:N1649S	N	-	2	0	COL6A3	237940623	1.000000	0.71417	0.994000	0.49952	0.786000	0.44442	4.105000	0.57797	2.080000	0.62538	0.533000	0.62120	AAC	.		0.438	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		C	238275884	T	C	238275884	3	2	6	1	0	0	0	0	1	0	0	0	3707	1725	60	3	4723	3	COL6A3	2	238275884	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	18114117	238275884	4923489	24	415											
SETD5	55209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9512542	9512542	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagacctctctcgtggatccTtgtcacctggtggtgaaagg	8	11	12	10	1	2	2	1	1	1	1	5	3	3	3	3	4	0	0	3	4	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:9512542T>C	ENST00000406341.1	+	18	3314	c.3124T>C	c.(3124-3126)Ttg>Ctg	p.L1042L	SETD5_ENST00000302463.6_Silent_p.L944L|SETD5_ENST00000402466.1_Silent_p.L944L|SETD5_ENST00000407969.1_Silent_p.L1061L|SETD5_ENST00000402198.1_Silent_p.L1042L			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1042										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		TCGTGGATCCTTGTCACCTGG	0.478																																					p.L1042L		.											.	SETD5-70	0			c.T3124C						.						24	23	23					3																	9512542		1861	4094	5955	SO:0001819	synonymous_variant	55209	exon19			GGATCCTTGTCAC	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.3124T>C	3.37:g.9512542T>C		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	25	4	NM_001080517	0	0	4	7	3	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Silent	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	T	8.531	0.871085	0.17322	.	.	ENSG00000168137	ENST00000399686;ENST00000421188	.	.	.	5.51	-0.229	0.13094	.	0.261170	0.47093	D	0.000242	T	0.54367	0.1854	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45673	-0.9245	5	.	.	.	-3.3658	8.5026	0.33168	0.5133:0.3613:0.0:0.1253	.	.	.	.	P	709;372	.	.	L	+	2	0	SETD5	9487542	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	1.768000	0.38511	0.028000	0.15324	-0.649000	0.03915	CTT	.		0.478	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		C	9512542	T	C	9512542	2	2	6	1	0	0	0	0	0	0	0	1	14166	1606	56	3		3	SETD5	3	9512542	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08		9512542	188509888	25	416											
CAPN7	23473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	15262464	15262464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcacaaggacagagatacaCagcagaagaaatagaagtac	20	4	10	7	0	0	4	0	0	0	4	0	6	0	5	0	1	4	3	0	1	7	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:15262464C>T	ENST00000253693.2	+	5	867	c.614C>T	c.(613-615)aCa>aTa	p.T205I		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	205					positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CAGAGATACACAGCAGAAGAA	0.363																																					p.T205I		.											.	CAPN7-91	0			c.C614T						.						59	59	59					3																	15262464		2203	4300	6503	SO:0001583	missense	23473	exon5			GATACACAGCAGA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.614C>T	3.37:g.15262464C>T	ENSP00000253693:p.Thr205Ile	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	65	16	NM_014296	0	0	7	12	5		Missense_Mutation	SNP	ENST00000253693.2	37	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640356	0.87859	.	.	ENSG00000131375	ENST00000253693	T	0.43294	0.95	5.79	4.92	0.64577	.	0.109635	0.64402	D	0.000008	T	0.59959	0.2232	M	0.81802	2.56	0.58432	D	0.999998	D	0.62365	0.991	P	0.56823	0.807	T	0.65092	-0.6252	10	0.54805	T	0.06	-9.0239	12.9819	0.58568	0.0:0.9247:0.0:0.0753	.	205	Q9Y6W3	CAN7_HUMAN	I	205	ENSP00000253693:T205I	ENSP00000253693:T205I	T	+	2	0	CAPN7	15237468	1.000000	0.71417	0.555000	0.28281	0.997000	0.91878	7.223000	0.78033	1.465000	0.48006	0.555000	0.69702	ACA	.		0.363	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		T	15262464	C	T	15262464	3	4	6	1	0	0	0	0	1	0	0	0	2637	478	17	2	632	2	CAPN7	3	15262464	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	5749922	15262464	182759966	26	417											
EXOSC7	23016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	45048921	45048921	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcctttgcagattggctatCggcatgtggtggatgctact	6	14	13	8	1	0	1	0	0	0	1	1	2	0	2	1	4	4	4	1	4	2	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:45048921C>T	ENST00000265564.7	+	7	673	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	CLEC3B_ENST00000490386.1_Intron|EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	209					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		GATTGGCTATCGGCATGTGGT	0.612																																					p.R209W		.											.	EXOSC7-90	0			c.C625T						.						62	53	56					3																	45048921		2203	4300	6503	SO:0001583	missense	23016	exon7			GGCTATCGGCATG	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.625C>T	3.37:g.45048921C>T	ENSP00000265564:p.Arg209Trp	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	31	10	NM_015004	0	0	0	0	0	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	37	CCDS2725.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.879280	0.72294	.	.	ENSG00000075914	ENST00000265564	T	0.44482	0.92	5.77	4.82	0.62117	Exoribonuclease, phosphorolytic domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.66716	0.946;0.946	T	0.62525	-0.6836	10	0.38643	T	0.18	-14.1235	13.4903	0.61390	0.2342:0.7658:0.0:0.0	.	209;209	B2RDZ9;Q15024	.;EXOS7_HUMAN	W	209	ENSP00000265564:R209W	ENSP00000265564:R209W	R	+	1	2	EXOSC7	45023925	0.964000	0.33143	0.994000	0.49952	0.991000	0.79684	2.331000	0.43894	2.723000	0.93209	0.655000	0.94253	CGG	.		0.612	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		T	45048921	C	T	45048921	3	4	6	1	0	0	0	0	1	0	0	0	5332	875	31	1	651	1	EXOSC7	3	45048921	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	29786457	45048921	152973509	27	418											
TREX1	11277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48508760	48508760	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggcccatgtatggggtcAcagcctctgctaggaccaag	9	8	12	12	0	3	0	2	0	1	0	3	1	3	1	3	4	2	2	3	4	3	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:48508760A>T	ENST00000422277.2	+	1	1532	c.871A>T	c.(871-873)Aca>Tca	p.T291S	SHISA5_ENST00000465449.1_5'Flank|TREX1_ENST00000444177.1_Missense_Mutation_p.T226S|TREX1_ENST00000436480.2_Missense_Mutation_p.T236S|TREX1_ENST00000433541.1_Missense_Mutation_p.T97S|TREX1_ENST00000456089.1_Missense_Mutation_p.T97S|TREX1_ENST00000492235.1_3'UTR|TREX1_ENST00000296443.9_Missense_Mutation_p.T236S	NM_016381.4	NP_057465.1	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1	291	Necessary for endoplasmic reticulum localization. {ECO:0000250}.				cell death (GO:0008219)|cellular response to interferon-beta (GO:0035458)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|innate immune response (GO:0045087)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	endoplasmic reticulum membrane (GO:0005789)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|3'-5'-exodeoxyribonuclease activity (GO:0008296)|adenyl deoxyribonucleotide binding (GO:0032558)|double-stranded DNA binding (GO:0003690)|exodeoxyribonuclease III activity (GO:0008853)|metal ion binding (GO:0046872)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein homodimerization activity (GO:0042803)|single-stranded DNA binding (GO:0003697)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|skin(3)	9				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GTATGGGGTCACAGCCTCTGC	0.617																																					p.T291S		.											.	TREX1-227	0			c.A871T	GRCh37	CI075712	TREX1	I		.						97	83	88					3																	48508760		2203	4300	6503	SO:0001583	missense	11277	exon1			GGGGTCACAGCCT	AF151105	CCDS2769.1, CCDS59451.1	3p21.31	2014-09-17			ENSG00000213689	ENSG00000213689			12269	protein-coding gene	gene with protein product		606609	"Aicardi-Goutieres syndrome 1"	AGS1		10391904, 10393201, 16845398	Standard	NM_033629		Approved	DRN3	uc010hka.4	Q9NSU2	OTTHUMG00000156205	ENST00000422277.2:c.871A>T	3.37:g.48508760A>T	ENSP00000390478:p.Thr291Ser	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	93	12	NM_016381	0	0	24	45	21	B2RCN9|Q8TEU2|Q9BPW1|Q9Y4X2	Missense_Mutation	SNP	ENST00000422277.2	37	CCDS43086.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.752702	0.69533	.	.	ENSG00000213689	ENST00000296443;ENST00000433541;ENST00000436480;ENST00000422277;ENST00000444177;ENST00000456089	T;T;T;T;T;T	0.47528	1.49;0.84;1.49;1.44;1.49;0.84	5.1	-6.21	0.02065	.	.	.	.	.	T	0.32010	0.0815	L	0.54323	1.7	0.09310	N	1	B	0.24426	0.103	B	0.19391	0.025	T	0.34304	-0.9834	9	0.10902	T	0.67	.	6.7824	0.23654	0.2855:0.3313:0.3832:0.0	.	291	Q9NSU2	TREX1_HUMAN	S	236;97;236;291;226;97	ENSP00000296443:T236S;ENSP00000412404:T97S;ENSP00000392569:T236S;ENSP00000390478:T291S;ENSP00000415972:T226S;ENSP00000411331:T97S	ENSP00000296443:T236S	T	+	1	0	TREX1	48483764	0.000000	0.05858	0.000000	0.03702	0.852000	0.48524	-0.417000	0.07088	-1.057000	0.03201	0.459000	0.35465	ACA	.		0.617	TREX1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_016381		T	48508760	A	T	48508760	3	4	6	1	0	0	0	0	1	0	0	0	16509	159	6	5	873	5	TREX1	3	48508760	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	3459839	48508760	149513670	28	419											
VPS8	23355	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	184700420	184700420	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtccagttcagccattcctCatctacactctgaaggtaag	10	12	7	12	0	4	1	2	1	2	0	6	1	6	1	3	1	2	2	3	1	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:184700420C>T	ENST00000437079.3	+	41	3658	c.3487C>T	c.(3487-3489)Cat>Tat	p.H1163Y	VPS8_ENST00000436792.2_Missense_Mutation_p.H1161Y|VPS8_ENST00000446204.2_Missense_Mutation_p.H1071Y|VPS8_ENST00000287546.4_Missense_Mutation_p.H1163Y	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1163							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			AGCCATTCCTCATCTACACTC	0.393																																					p.H1163Y		.											.	VPS8-91	0			c.C3487T						.						81	71	75					3																	184700420		1894	4126	6020	SO:0001583	missense	23355	exon40			ATTCCTCATCTAC	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3487C>T	3.37:g.184700420C>T	ENSP00000397879:p.His1163Tyr	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	71	13	NM_001009921	0	0	3	11	8	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	C	0.295	-0.977536	0.02197	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	6.05	6.05	0.98169	.	0.769709	0.13007	N	0.421217	T	0.17789	0.0427	L	0.38175	1.15	0.24222	N	0.995432	B;B;B	0.13145	0.0;0.007;0.0	B;B;B	0.19391	0.0;0.025;0.001	T	0.09684	-1.0663	10	0.62326	D	0.03	-11.998	13.6828	0.62496	0.0:0.8456:0.1544:0.0	.	1163;1071;1161	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	Y	1163;1163;1161;1071	ENSP00000287546:H1163Y;ENSP00000397879:H1163Y;ENSP00000404704:H1161Y;ENSP00000405483:H1071Y	ENSP00000287546:H1163Y	H	+	1	0	VPS8	186183114	0.126000	0.22350	0.812000	0.32479	0.520000	0.34377	1.477000	0.35431	2.878000	0.98634	0.650000	0.86243	CAT	.		0.393	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		T	184700420	C	T	184700420	3	4	6	1	0	0	0	0	1	0	0	0	17251	826	29	2	3641	2	VPS8	3	184700420	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	136191660	184700420	13322010	29	420											
IDUA	3425	hgsc.bcm.edu	37	chr4	980971	980971	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccccgcacctggtgcaTgtggacgcggcccgcgcgct	4	5	16	16	6	0	0	0	0	0	0	0	2	0	1	4	4	1	3	4	4	0	0	rs10794537	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:980971T>G	ENST00000247933.4	+	1	187	c.99T>G	c.(97-99)caT>caG	p.H33Q	IDUA_ENST00000453894.1_Missense_Mutation_p.H33Q|SLC26A1_ENST00000398520.2_Intron	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	33			H -> Q (in dbSNP:rs10794537). {ECO:0000269|PubMed:1362562, ECO:0000269|PubMed:1505961, ECO:0000269|PubMed:1946389, ECO:0000269|PubMed:21394825}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			ACCTGGTGCATGTGGACGCGG	0.801													G|||	4467	0.891973	0.9826	0.8386	5008	,	,		8604	0.8472		0.8042	False		,,,				2504	0.9438				p.H33Q		.											.	IDUA-91	0			c.T99G						.						1	1	1					4																	980971		552	1375	1927	SO:0001583	missense	3425	exon1			GGTGCATGTGGAC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.99T>G	4.37:g.980971T>G	ENSP00000247933:p.His33Gln	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_000203	0	0	0	5	5	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	1801|1801	0.8246336996336996|0.8246336996336996	464|464	0.943089430894309|0.943089430894309	294|294	0.8121546961325967|0.8121546961325967	448|448	0.7832167832167832|0.7832167832167832	595|595	0.7849604221635884|0.7849604221635884	G|G	3.726|3.726	-0.056533|-0.056533	0.07362|0.07362	.|.	.|.	ENSG00000127415|ENSG00000127415	ENST00000504568|ENST00000247933;ENST00000453894;ENST00000502910	.|D;D;D	.|0.93247	.|-3.18;-3.19;-3.03	3.62|3.62	-0.897|-0.897	0.10553|0.10553	.|.	.|0.728933	.|0.12190	.|N	.|0.491278	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.36817|0.36817	-0.9732|-0.9732	4|9	.|0.10111	.|T	.|0.7	.|.	1.2904|1.2904	0.02059|0.02059	0.1461:0.2669:0.3485:0.2385|0.1461:0.2669:0.3485:0.2385	rs10794537|rs10794537	.|33;33	.|B3KWK6;P35475	.|.;IDUA_HUMAN	G|Q	33|33	.|ENSP00000247933:H33Q;ENSP00000396458:H33Q;ENSP00000422952:H33Q	.|ENSP00000247933:H33Q	C|H	+|+	1|3	0|2	IDUA|IDUA	970971|970971	0.000000|0.000000	0.05858|0.05858	0.992000|0.992000	0.48379|0.48379	0.012000|0.012000	0.07955|0.07955	-2.547000|-2.547000	0.00931|0.00931	-0.253000|-0.253000	0.09514|0.09514	-1.482000|-1.482000	0.00985|0.00985	TGT|CAT	T|0.175;G|0.825		0.801	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203		G	980971	T	G	980971	3	3	6	1	0	0	0	0	1	0	0	0	7525	1461	51	5	101	5	IDUA	4	980971	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08		980971	190173305	30	421											
ABCG2	9429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	89042889	89042889	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtgataagctccattcctAtactagtcctttttctttct	8	18	4	11	0	2	1	0	1	2	0	5	1	5	1	3	0	2	1	3	0	4	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:89042889A>C	ENST00000237612.3	-	6	1132	c.587T>G	c.(586-588)aTa>aGa	p.I196R	ABCG2_ENST00000515655.1_Missense_Mutation_p.I196R	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	196	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CTCCATTCCTATACTAGTCCT	0.398																																					p.I196R		.											.	ABCG2-90	0			c.T587G						.						154	147	149					4																	89042889		2203	4300	6503	SO:0001583	missense	9429	exon6			ATTCCTATACTAG	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.587T>G	4.37:g.89042889A>C	ENSP00000237612:p.Ile196Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	75	13	NM_004827	0	0	4	4	0	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.478150	0.84747	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	D;D	0.96168	-3.93;-3.93	5.55	5.55	0.83447	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98601	0.9532	H	0.97240	3.965	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.99755	1.1019	10	0.87932	D	0	-42.7755	15.3809	0.74654	1.0:0.0:0.0:0.0	.	196;196;196	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	R	196	ENSP00000426917:I196R;ENSP00000237612:I196R	ENSP00000237612:I196R	I	-	2	0	ABCG2	89261913	1.000000	0.71417	0.984000	0.44739	0.893000	0.52053	8.948000	0.93006	2.117000	0.64856	0.533000	0.62120	ATA	.		0.398	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		C	89042889	A	C	89042889	3	2	6	1	0	0	0	0	1	0	0	0	69	449	16	5	1424	5	ABCG2	4	89042889	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	88061918	89042889	102111387	31	422											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123156097	123156097	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattttcaagcacaagtgcaGagtctgatatgtattatgga	13	13	9	6	0	2	2	1	1	1	1	2	3	2	3	0	1	2	3	0	1	5	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:123156097G>T	ENST00000264501.4	+	27	3866	c.3493G>T	c.(3493-3495)Gag>Tag	p.E1165*	KIAA1109_ENST00000455637.1_Nonsense_Mutation_p.E1165*|KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000388738.3_Nonsense_Mutation_p.E1165*			Q2LD37	K1109_HUMAN	KIAA1109	1165					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CACAAGTGCAGAGTCTGATAT	0.393																																					p.E1165X		.											.	KIAA1109-80	0			c.G3493T						.						109	106	107					4																	123156097		1863	4108	5971	SO:0001587	stop_gained	84162	exon25			AGTGCAGAGTCTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.3493G>T	4.37:g.123156097G>T	ENSP00000264501:p.Glu1165*	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	107	25	NM_015312	0	0	4	5	1	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Nonsense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.713265|7.713265	0.98447|0.98447	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	.|.	.|.	.|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.138537|.	0.28067|.	U|.	0.016735|.	.|T	.|0.74612	.|0.3739	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73956	.|-0.3819	.|3	0.14656|.	T|.	0.56|.	.|.	18.61|18.61	0.91281|0.91281	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	1165|996	.|.	ENSP00000264501:E1165X|.	E|R	+|+	1|2	0|0	KIAA1109|KIAA1109	123375547|123375547	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.981000|0.981000	0.71138|0.71138	9.147000|9.147000	0.94646|0.94646	2.391000|2.391000	0.81399|0.81399	0.563000|0.563000	0.77884|0.77884	GAG|AGA	.		0.393	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123156097	G	T	123156097	4	4	6	1	0	0	0	0	0	1	0	0	8229	943	33	4	3591	4	KIAA1109	4	123156097	Nonsense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	34113208	123156097	67998179	32	423											
PCDH18	54510	broad.mit.edu;bcgsc.ca	37	chr4	138452043	138452043	+	Frame_Shift_Del	DEL	A	A	-																															agtttaaagtgaccatgtccAtgaagcttacaaactatttc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:138452043delA	ENST00000344876.4	-	1	1586	c.1200delT	c.(1198-1200)catfs	p.H400fs	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000507846.1_Frame_Shift_Del_p.H180fs|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Frame_Shift_Del_p.H400fs	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GACCATGTCCATGAAGCTTAC	0.348																																					p.H400fs													.	PCDH18-185	0			c.1200delT						.						100	106	104					4																	138452043		2203	4300	6503	SO:0001589	frameshift_variant	54510	exon1			ATGTCCATGAAGC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1200delT	4.37:g.138452043delA	ENSP00000355082:p.His400fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	87	13	NM_019035	0	0	0	0	0	A8K7K3|B7ZKT1|Q52LS2	Frame_Shift_Del	DEL	ENST00000344876.4	37	CCDS34064.1																																																																																			.		0.348	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		-	138452043	A	-	138452043	7	5	6	1	0	1	0	1	0	0	0	0	11539	214	8	0	2223	0	PCDH18	4	138452043	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08	15295946	138452043	52702233	33	424											
FASTKD3	79072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7867621	7867621	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcaacaggctactttgAggatccacatgcaacagaat	14	9	8	10	0	1	2	1	1	0	1	2	3	2	3	1	2	5	3	1	2	4	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:7867621A>G	ENST00000264669.5	-	2	712	c.576T>C	c.(574-576)ccT>ccC	p.P192P	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	192					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGCTACTTTGAGGATCCACAT	0.443																																					p.P192P		.											.	FASTKD3-156	0			c.T576C						.						90	90	90					5																	7867621		2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			ACTTTGAGGATCC	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.576T>C	5.37:g.7867621A>G		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	180	23	NM_024091	0	0	13	18	5	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			.		0.443	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867621	A	G	7867621	2	3	6	1	0	0	0	0	0	0	0	1	5706	291	11	3		3	FASTKD3	5	7867621	Silent	SNP	A	TCGA-A4-7585-01A-11D-2136-08		7867621	173047639	34	425											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64537954	64537954	+	IGR	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtatagggtttccagttaTaatactttcctcggaaaggc	11	13	9	8	1	0	0	0	0	0	0	3	1	2	1	2	3	1	3	2	3	6	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:64537954T>G								ADAMTS6 (43362 upstream) : ADAMTS6 (55080 downstream)																							TTTCCAGTTATAATACTTTCC	0.358																																					p.Y637S		.											.	ADAMTS6-226	0			c.A1910C						.						97	101	100					5																	64537954		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon15			CAGTTATAATACT																													5.37:g.64537954T>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_197941	0	0	0	0	0		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	T	16.74	3.205533	0.58234	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680	T;T	0.06608	3.28;7.39	5.62	5.62	0.85841	.	0.054793	0.85682	D	0.000000	T	0.12305	0.0299	M	0.71871	2.18	0.80722	D	1	B;B	0.22346	0.068;0.008	B;B	0.24848	0.056;0.034	T	0.01349	-1.1378	10	0.72032	D	0.01	.	15.8202	0.78633	0.0:0.0:0.0:1.0	.	637;637	D6R9L6;Q9UKP5	.;ATS6_HUMAN	S	637;587;637	ENSP00000370443:Y637S;ENSP00000423551:Y637S	ENSP00000261306:Y587S	Y	-	2	0	ADAMTS6	64573710	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.581000	0.82535	2.139000	0.66308	0.460000	0.39030	TAT	.	0	0.358									G	64537954	T	G	64537954	1	3	6	0	1	0	0	0	0	0	0	0	270	1406	49	5		5	ADAMTS6	5	64537954	IGR	SNP	T	TCGA-A4-7585-01A-11D-2136-08	56670333	64537954	116377306	35	426											
SPATA9	83890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	94994451	94994451	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcttctccggcaatgacCtataaggttttgctttgatt	7	16	9	9	1	1	2	0	2	1	0	2	2	1	2	2	3	1	4	2	3	3	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:94994451C>G	ENST00000274432.8	-	5	782	c.641G>C	c.(640-642)aGg>aCg	p.R214T	SPATA9_ENST00000477047.2_Intron|RFESD_ENST00000508206.1_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	214					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		CGGCAATGACCTATAAGGTTT	0.403																																					p.R214T		.											.	SPATA9-90	0			c.G641C						.						102	98	99					5																	94994451		2203	4299	6502	SO:0001583	missense	83890	exon5			AATGACCTATAAG	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.641G>C	5.37:g.94994451C>G	ENSP00000274432:p.Arg214Thr	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	62	10	NM_031952	0	0	0	0	0	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	37	CCDS4076.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.491277	0.26774	.	.	ENSG00000145757	ENST00000274432	T	0.31510	1.49	5.37	5.37	0.77165	.	0.173364	0.39985	N	0.001210	T	0.31857	0.0810	L	0.27053	0.805	0.80722	D	1	P	0.51351	0.944	P	0.49999	0.628	T	0.02214	-1.1194	10	0.54805	T	0.06	-9.9082	14.4904	0.67647	0.0:1.0:0.0:0.0	.	214	Q9BWV2	SPAT9_HUMAN	T	214	ENSP00000274432:R214T	ENSP00000274432:R214T	R	-	2	0	SPATA9	95020207	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	2.187000	0.42602	2.808000	0.96608	0.650000	0.86243	AGG	.		0.403	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		G	94994451	C	G	94994451	3	3	6	1	0	0	0	0	1	0	0	0	15048	681	24	4	127	4	SPATA9	5	94994451	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	30456497	94994451	85920809	36	427											
SEC24A	10802	broad.mit.edu;bcgsc.ca	37	chr5	133997149	133997160	+	In_Frame_Del	DEL	CTCACAAACAAA	CTCACAAACAAA	-																															tataactatccatccacagcCtcacaaacaaaccattgtcc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	CTCACAAACAAA	CTCACAAACAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:133997149_133997160delCTCACAAACAAA	ENST00000398844.2	+	2	726_737	c.438_449delCTCACAAACAAA	c.(436-450)gcctcacaaacaaac>gcc	p.SQTN147del	SEC24A_ENST00000322887.4_In_Frame_Del_p.SQTN147del	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	147	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CATCCACAGCCTCACAAACAAACCATTGTCCT	0.415																																					p.146_150del													.	SEC24A-68	0			c.438_449del						.																																			SO:0001651	inframe_deletion	10802	exon2			CACAGCCTCACAA	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.438_449delCTCACAAACAAA	5.37:g.133997149_133997160delCTCACAAACAAA	ENSP00000381823:p.Ser147_Asn150del	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	101	12	NM_001252231	0	0	0	0	0	A8MVW3|Q8WUV2|Q96GP7	In_Frame_Del	DEL	ENST00000398844.2	37	CCDS43363.1																																																																																			.		0.415	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			-	133997160	CTCACAAACAAA	-	133997149	7	5	6	1	0	1	0	1	0	0	0	0	14026	668	24	0	444	0	SEC24A	5	133997149	In_Frame_Del	DEL	CTCACAAACAAA	TCGA-A4-7585-01A-11D-2136-08	39002698	133997149	46918111	37	428											
SLC36A2	153201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	150701645	150701645	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggcgaatggacagatccAgaggcagtgcccagcgtgtt	10	6	15	10	3	0	2	0	0	0	2	1	5	1	3	2	3	2	2	2	3	1	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:150701645A>T	ENST00000335244.4	-	9	1271	c.1142T>A	c.(1141-1143)cTg>cAg	p.L381Q	SLC36A2_ENST00000450886.1_Missense_Mutation_p.L105Q|SLC36A2_ENST00000521967.1_Missense_Mutation_p.L381Q	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	381					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GGACAGATCCAGAGGCAGTGC	0.542																																					p.L381Q		.											.	SLC36A2-91	0			c.T1142A						.						138	127	131					5																	150701645		2203	4300	6503	SO:0001583	missense	153201	exon9			AGATCCAGAGGCA	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.1142T>A	5.37:g.150701645A>T	ENSP00000334223:p.Leu381Gln	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	147	31	NM_181776	0	0	0	1	1	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.366710	0.41902	.	.	ENSG00000186335	ENST00000335244;ENST00000450886;ENST00000521967	T;T;T	0.11495	4.19;4.19;2.77	4.76	2.4	0.29515	.	0.920881	0.09207	N	0.833849	T	0.18383	0.0441	L	0.57536	1.79	0.31863	N	0.620713	P;B	0.45531	0.86;0.132	P;B	0.50314	0.637;0.158	T	0.16897	-1.0387	10	0.28530	T	0.3	-0.0361	8.697	0.34303	0.8453:0.0:0.1547:0.0	.	381;381	E5RJJ5;Q495M3	.;S36A2_HUMAN	Q	381;105;381	ENSP00000334223:L381Q;ENSP00000399479:L105Q;ENSP00000430535:L381Q	ENSP00000334223:L381Q	L	-	2	0	SLC36A2	150681838	0.997000	0.39634	0.549000	0.28204	0.633000	0.38033	4.784000	0.62411	0.426000	0.26116	0.460000	0.39030	CTG	.		0.542	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			T	150701645	A	T	150701645	3	4	6	1	0	0	0	0	1	0	0	0	14626	188	7	5	317	5	SLC36A2	5	150701645	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	16704496	150701645	30213615	38	429											
DOCK2	1794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	169463529	169463529	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctacctagaatttctacaAagataacaacagggaggaga	17	7	8	9	0	1	3	0	0	1	3	1	5	1	4	2	2	4	0	2	2	7	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:169463529A>G	ENST00000256935.8	+	36	3715	c.3635A>G	c.(3634-3636)aAa>aGa	p.K1212R	DOCK2_ENST00000520908.1_Missense_Mutation_p.K704R|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Missense_Mutation_p.K273R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1212	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATTTCTACAAAGATAACAAC	0.423																																					p.K1212R		.											.	DOCK2-97	0			c.A3635G						.						135	132	133					5																	169463529		2203	4300	6503	SO:0001583	missense	1794	exon36			TCTACAAAGATAA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3635A>G	5.37:g.169463529A>G	ENSP00000256935:p.Lys1212Arg	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	85	23	NM_004946	0	0	0	0	0	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914002	0.72983	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.55930	0.49;0.49;0.49	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.53174	0.1780	M	0.69463	2.115	0.41312	D	0.987117	P;P	0.46859	0.885;0.468	B;B	0.41299	0.353;0.074	T	0.57510	-0.7799	10	0.38643	T	0.18	.	15.5299	0.75952	1.0:0.0:0.0:0.0	.	704;1212	E7ERW7;Q92608	.;DOCK2_HUMAN	R	1212;704;273	ENSP00000256935:K1212R;ENSP00000429283:K704R;ENSP00000438827:K273R	ENSP00000256935:K1212R	K	+	2	0	DOCK2	169396107	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.358000	0.90090	2.147000	0.66899	0.533000	0.62120	AAA	.		0.423	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169463529	A	G	169463529	3	3	6	1	0	0	0	0	1	0	0	0	4698	14	1	3	3777	3	DOCK2	5	169463529	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	18761884	169463529	11451731	39	430											
NSD1	64324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176696648	176696648	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcgagctgttccttccaaCattgataagatgagacatga	12	11	8	10	1	0	4	0	3	0	2	3	6	2	4	3	0	2	2	3	0	2	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:176696648C>T	ENST00000439151.2	+	16	5394	c.5349C>T	c.(5347-5349)aaC>aaT	p.N1783N	NSD1_ENST00000347982.4_Silent_p.N1514N|NSD1_ENST00000361032.4_Silent_p.N1680N|NSD1_ENST00000354179.4_Silent_p.N1514N	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1783	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TTCCTTCCAACATTGATAAGA	0.488			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.N1783N		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.C5349T	GRCh37	CD052485	NSD1	D		.						107	101	103					5																	176696648		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon16	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTCCAACATTGAT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.5349C>T	5.37:g.176696648C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	89	14	NM_022455	0	0	3	6	3	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			.		0.488	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176696648	C	T	176696648	2	4	6	1	0	0	0	0	0	0	0	1	10695	477	17	2		2	NSD1	5	176696648	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	7233119	176696648	4218612	40	431											
FAM50B	26240	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	3850443	3850443	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgatgaccaggccgacgCggccgaggccaggcgcgccg	6	2	16	17	8	0	1	0	1	0	0	1	4	0	1	6	4	0	0	6	4	0	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:3850443C>T	ENST00000380274.1	+	1	824	c.398C>T	c.(397-399)gCg>gTg	p.A133V	FAM50B_ENST00000380272.3_Missense_Mutation_p.A133V			Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	133						nucleus (GO:0005634)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(3)|urinary_tract(3)	17	Ovarian(93;0.0925)	all_hematologic(90;0.108)				CAGGCCGACGCGGCCGAGGCC	0.687																																					p.A133V													.	FAM50B-91	0			c.C398T						.						21	28	26					6																	3850443		2200	4297	6497	SO:0001583	missense	26240	exon2			CCGACGCGGCCGA	Y18504	CCDS4487.1	6p25.2	2008-05-15			ENSG00000145945	ENSG00000145945			18789	protein-coding gene	gene with protein product		614686				10534398	Standard	NM_012135		Approved	D6S2654E, X5L	uc003mvu.3	Q9Y247	OTTHUMG00000014147	ENST00000380274.1:c.398C>T	6.37:g.3850443C>T	ENSP00000369627:p.Ala133Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	41	7	NM_012135	0	0	24	24	0	Q5T2L6	Missense_Mutation	SNP	ENST00000380274.1	37	CCDS4487.1	.	.	.	.	.	.	.	.	.	.	C	9.550	1.115671	0.20795	.	.	ENSG00000145945	ENST00000380274;ENST00000380272	.	.	.	3.79	-6.51	0.01878	.	2.245500	0.02440	N	0.084415	T	0.04907	0.0132	N	0.12746	0.255	0.09310	N	1	B	0.11235	0.004	B	0.13407	0.009	T	0.11299	-1.0593	9	0.31617	T	0.26	-0.103	1.0834	0.01647	0.2398:0.1759:0.124:0.4603	.	133	Q9Y247	FA50B_HUMAN	V	133	.	ENSP00000369625:A133V	A	+	2	0	FAM50B	3795442	0.000000	0.05858	0.000000	0.03702	0.485000	0.33311	-2.786000	0.00770	-1.203000	0.02652	0.485000	0.47835	GCG	.		0.687	FAM50B-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039693.1	NM_012135		T	3850443	C	T	3850443	3	4	6	1	0	0	0	0	1	0	0	0	5597	768	27	1	400	1	FAM50B	6	3850443	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		3850443	167264624	41	432											
SLC35B3	51000	hgsc.bcm.edu	37	chr6	8413926	8413926	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaactaacaaaccagaccaTacatacctaagagaaagaaa	23	4	4	10	0	0	3	0	0	0	3	0	4	0	3	3	0	5	0	3	0	8	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:8413926T>C	ENST00000379660.4	-	11	1511	c.1062A>G	c.(1060-1062)gtA>gtG	p.V354V		NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	354					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					AACCAGACCATACATACCTAA	0.249																																					p.V354V	Melanoma(83;700 1353 9357 11478 30548)	.											.	SLC35B3-90	0			c.A1062G						.						33	29	31					6																	8413926		2202	4294	6496	SO:0001819	synonymous_variant	51000	exon11			AGACCATACATAC	AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"Solute carriers"	21601	protein-coding gene	gene with protein product	"3' phosphoadenosine 5' phosphosulfate transporter 2"	610845	"chromosome 6 open reading frame 196", "solute carrier family 35, member B3"	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.1062A>G	6.37:g.8413926T>C		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_001142540	0	0	0	0	0	A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Silent	SNP	ENST00000379660.4	37	CCDS4508.1																																																																																			.		0.249	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1	NM_015948		C	8413926	T	C	8413926	2	2	6	1	0	0	0	0	0	0	0	1	14609	1393	49	3		3	SLC35B3	6	8413926	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08	4563483	8413926	162701141	42	433											
ATXN1	6310	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	16327407	16327407	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggaccatcacagaggcccGgacccccgaaggatcacgac	12	2	11	16	3	2	1	2	0	0	1	2	6	2	4	4	4	0	0	4	4	1	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:16327407G>A	ENST00000244769.4	-	8	2071	c.1135C>T	c.(1135-1137)Cgg>Tgg	p.R379W	ATXN1_ENST00000436367.1_Missense_Mutation_p.R379W	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	379					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				ACAGAGGCCCGGACCCCCGAA	0.637																																					p.R379W		.											.	ATXN1-93	0			c.C1135T						.						116	131	126					6																	16327407		2203	4300	6503	SO:0001583	missense	6310	exon7			AGGCCCGGACCCC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1135C>T	6.37:g.16327407G>A	ENSP00000244769:p.Arg379Trp	Somatic	244	2		WXS	Illumina HiSeq	Phase_I	239	56	NM_001128164	0	0	4	6	2	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.196388	0.58126	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	D;D	0.81908	-1.55;-1.55	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	D	0.84999	0.5597	L	0.36672	1.1	0.58432	D	0.999996	D	0.89917	1.0	D	0.79784	0.993	D	0.87603	0.2498	10	0.87932	D	0	-24.3006	17.7777	0.88514	0.0:0.0:1.0:0.0	.	379	P54253	ATX1_HUMAN	W	379	ENSP00000244769:R379W;ENSP00000416360:R379W	ENSP00000244769:R379W	R	-	1	2	ATXN1	16435386	1.000000	0.71417	0.999000	0.59377	0.646000	0.38490	3.159000	0.50731	2.184000	0.69523	0.561000	0.74099	CGG	.		0.637	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327407	G	A	16327407	3	1	6	1	0	0	0	0	1	0	0	0	1210	1115	39	1	1320	1	ATXN1	6	16327407	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	7913481	16327407	154787660	43	434											
CLPS	1208	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	35765001	35765001	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggttgataatgatccccCgggggccaggagctgcatag	9	7	14	11	1	0	2	0	2	0	0	1	3	1	3	4	4	2	3	4	4	2	3	rs140966197	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:35765001C>G	ENST00000259938.2	-	1	87	c.65G>C	c.(64-66)cGg>cCg	p.R22P		NM_001832.3	NP_001823.1	P04118	COL_HUMAN	colipase, pancreatic	22					lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme activator activity (GO:0008047)			large_intestine(2)|lung(2)|prostate(1)	5						AATGATCCCCCGGGGGCCAGG	0.587																																					p.R22P	Melanoma(167;2962 3494 37796)	.											.	CLPS-90	0			c.G65C						.						84	81	82					6																	35765001		2203	4300	6503	SO:0001583	missense	1208	exon1			ATCCCCCGGGGGC		CCDS4811.1, CCDS75437.1, CCDS75438.1	6p21.31	2012-02-06			ENSG00000137392	ENSG00000137392			2085	protein-coding gene	gene with protein product		120105				2045105	Standard	NM_001832		Approved		uc003ole.2	P04118	OTTHUMG00000014578	ENST00000259938.2:c.65G>C	6.37:g.35765001C>G	ENSP00000259938:p.Arg22Pro	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	153	13	NM_001252598	0	0	0	0	0	Q5T9G7|Q5U809	Missense_Mutation	SNP	ENST00000259938.2	37	CCDS4811.1	.	.	.	.	.	.	.	.	.	.	C	9.579	1.123120	0.20959	.	.	ENSG00000137392	ENST00000259938;ENST00000541088	T	0.36878	1.23	4.74	4.74	0.60224	Colipase, N-terminal (1);	0.240709	0.29486	N	0.012016	T	0.52468	0.1736	M	0.73962	2.25	0.42641	D	0.993411	D;B	0.89917	1.0;0.22	D;B	0.85130	0.997;0.117	T	0.56763	-0.7925	10	0.66056	D	0.02	-16.1424	14.5722	0.68218	0.0:1.0:0.0:0.0	.	22;22	G3V1M8;P04118	.;COL_HUMAN	P	22	ENSP00000259938:R22P	ENSP00000259938:R22P	R	-	2	0	CLPS	35872979	0.958000	0.32768	0.993000	0.49108	0.025000	0.11179	3.128000	0.50492	2.462000	0.83206	0.655000	0.94253	CGG	C|0.999;T|0.001		0.587	CLPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040312.1	NM_001832		G	35765001	C	G	35765001	3	3	6	1	0	0	0	0	1	0	0	0	3559	652	23	4	285	4	CLPS	6	35765001	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	19437594	35765001	135350066	44	435											
KIAA0240	23506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42796705	42796705	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtcagattagtggttctggtCaaatacagttaattgggtca	11	14	11	5	0	4	1	3	0	1	1	4	1	4	1	0	3	1	2	0	3	4	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:42796705C>G	ENST00000314073.5	+	6	810	c.634C>G	c.(634-636)Caa>Gaa	p.Q212E	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.Q212E			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	212								p.Q212*(1)									TGGTTCTGGTCAAATACAGTT	0.418																																					p.Q212E		.											.	.	1	Substitution - Nonsense(1)	lung(1)	c.C634G						.						149	143	145					6																	42796705		2203	4300	6503	SO:0001583	missense	23506	exon5			TCTGGTCAAATAC	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"KIAA0240"	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.634C>G	6.37:g.42796705C>G	ENSP00000313933:p.Gln212Glu	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	221	35	NM_015349	0	0	2	5	3	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	37	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.510409	0.64522	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.35973	1.28;1.28	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000005	T	0.50599	0.1625	M	0.61703	1.905	0.58432	D	0.999998	P;D;D	0.61697	0.954;0.99;0.99	D;P;P	0.67900	0.954;0.848;0.848	T	0.36768	-0.9734	10	0.40728	T	0.16	-10.2526	19.7507	0.96267	0.0:1.0:0.0:0.0	.	212;212;212	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	E	212	ENSP00000313933:Q212E;ENSP00000377723:Q212E	ENSP00000313933:Q212E	Q	+	1	0	KIAA0240	42904683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.946000	0.75953	2.722000	0.93159	0.655000	0.94253	CAA	.		0.418	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		G	42796705	C	G	42796705	3	3	6	1	0	0	0	0	1	0	0	0	8185	827	29	4	648	4	KIAA0240	6	42796705	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	7031704	42796705	128318362	45	436											
MRPL2	51069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43023646	43023646	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccatacctgcagctcggAtatattgggcaccccggcct	7	9	9	16	2	0	0	0	0	0	0	2	1	1	1	6	3	3	3	6	3	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:43023646A>C	ENST00000388752.3	-	5	1044	c.620T>G	c.(619-621)aTc>aGc	p.I207S	MRPL2_ENST00000230413.5_Missense_Mutation_p.I207S|CUL7_ENST00000535468.1_5'Flank|CUL7_ENST00000265348.3_5'Flank|MRPL2_ENST00000489623.1_Intron	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	207					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		TGCAGCTCGGATATATTGGGC	0.567																																					p.I207S		.											.	MRPL2-90	0			c.T620G						.						44	39	40					6																	43023646		2203	4300	6503	SO:0001583	missense	51069	exon5			GCTCGGATATATT	AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"Mitochondrial ribosomal proteins / large subunits"	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.620T>G	6.37:g.43023646A>C	ENSP00000373404:p.Ile207Ser	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	41	10	NM_015950	0	0	1	1	0	B2RC56|Q8WUL1|Q96Q56|Q9Y311	Missense_Mutation	SNP	ENST00000388752.3	37	CCDS34454.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.589723	0.86851	.	.	ENSG00000112651	ENST00000388752;ENST00000230413	T;T	0.44482	0.92;0.92	5.94	5.94	0.96194	Translation protein SH3-like (1);Translation protein SH3-like, subgroup (1);Ribosomal protein L2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.47135	0.1429	L	0.49571	1.57	0.80722	D	1	D	0.63880	0.993	D	0.67382	0.951	T	0.37197	-0.9716	10	0.33141	T	0.24	-18.6054	14.9662	0.71196	1.0:0.0:0.0:0.0	.	207	Q5T653	RM02_HUMAN	S	207	ENSP00000373404:I207S;ENSP00000230413:I207S	ENSP00000230413:I207S	I	-	2	0	MRPL2	43131624	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.952000	0.93031	2.272000	0.75746	0.460000	0.39030	ATC	.		0.567	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2			C	43023646	A	C	43023646	3	2	6	1	0	0	0	0	1	0	0	0	9810	333	12	5	309	5	MRPL2	6	43023646	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	226941	43023646	128091421	46	437											
SENP6	26054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76412443	76412443	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcctcattaccatgaaaatGctgtcatacagaaatgttca	15	12	5	9	0	3	2	3	1	0	1	4	2	4	2	2	0	3	2	2	0	5	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:76412443G>A	ENST00000447266.2	+	19	2849	c.2371G>A	c.(2371-2373)Gct>Act	p.A791T	SENP6_ENST00000370010.2_Missense_Mutation_p.A784T|SENP6_ENST00000541192.1_Intron|SENP6_ENST00000370014.3_Missense_Mutation_p.A791T	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	791	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				CCATGAAAATGCTGTCATACA	0.383																																					p.A791T		.											.	SENP6-660	0			c.G2371A						.						59	55	56					6																	76412443		1832	4093	5925	SO:0001583	missense	26054	exon19			GAAAATGCTGTCA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"SUMO1/sentrin specific protease 6"				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.2371G>A	6.37:g.76412443G>A	ENSP00000402527:p.Ala791Thr	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	62	11	NM_015571	0	0	14	21	7	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.545641	0.27652	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000447266	T;T;T	0.12255	2.7;2.7;2.7	5.74	3.51	0.40186	.	0.723156	0.13837	N	0.359285	T	0.02494	0.0076	L	0.33485	1.01	0.24879	N	0.992236	B;B	0.06786	0.001;0.001	B;B	0.11329	0.004;0.006	T	0.41698	-0.9494	10	0.25751	T	0.34	-0.6313	0.5061	0.00588	0.197:0.1755:0.2906:0.3369	.	784;791	Q9GZR1-2;Q9GZR1	.;SENP6_HUMAN	T	784;791;791	ENSP00000359027:A784T;ENSP00000359031:A791T;ENSP00000402527:A791T	ENSP00000359027:A784T	A	+	1	0	SENP6	76469163	0.954000	0.32549	0.998000	0.56505	0.939000	0.58152	0.671000	0.25172	1.214000	0.43395	0.579000	0.79373	GCT	.		0.383	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		A	76412443	G	A	76412443	3	1	6	1	0	0	0	0	1	0	0	0	14082	1319	46	2	2445	2	SENP6	6	76412443	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	33388797	76412443	94702624	47	438											
SHPRH	257218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	146234630	146234630	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ttacctgttttcctagctgtCgagcacagattgggcaaggt	8	13	11	9	1	0	1	0	0	0	1	2	2	1	1	2	2	3	4	2	2	3	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:146234630C>G	ENST00000367505.2	-	24	4574	c.4310G>C	c.(4309-4311)cGa>cCa	p.R1437P	SHPRH_ENST00000367503.3_Missense_Mutation_p.R1441P|SHPRH_ENST00000275233.7_Missense_Mutation_p.R1437P|SHPRH_ENST00000438092.2_Missense_Mutation_p.R1441P			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1437					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TCCTAGCTGTCGAGCACAGAT	0.308																																					p.R1441P		.											.	SHPRH-92	0			c.G4322C						.						123	123	123					6																	146234630		1803	4069	5872	SO:0001583	missense	257218	exon24			AGCTGTCGAGCAC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.4310G>C	6.37:g.146234630C>G	ENSP00000356475:p.Arg1437Pro	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	95	18	NM_173082	0	0	0	0	0	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415831	0.83449	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89	5.52	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.088147	0.47455	D	0.000232	D	0.88514	0.6457	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89205	0.3560	10	0.51188	T	0.08	-9.0526	14.3892	0.66965	0.0:0.9287:0.0:0.0713	.	1437;1441	Q149N8;Q149N8-4	SHPRH_HUMAN;.	P	1437;1441;1441;1437	ENSP00000356475:R1437P;ENSP00000356473:R1441P;ENSP00000412797:R1441P;ENSP00000275233:R1437P	ENSP00000275233:R1437P	R	-	2	0	SHPRH	146276323	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.749000	0.62155	1.469000	0.48083	0.591000	0.81541	CGA	.		0.308	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		G	146234630	C	G	146234630	3	3	6	1	0	0	0	0	1	0	0	0	14323	884	31	4	786	4	SHPRH	6	146234630	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	69822187	146234630	24880437	48	439											
LPA	4018	broad.mit.edu;bcgsc.ca	37	chr6	161027563	161027563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaatagttggaggcgcgaCggcagtcccttctgcgtctg	6	10	15	10	4	2	0	0	0	2	0	3	2	3	1	1	4	1	3	1	4	2	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:161027563C>T	ENST00000316300.5	-	17	2775	c.2731G>A	c.(2731-2733)Gtc>Atc	p.V911I	LPA_ENST00000447678.1_Missense_Mutation_p.V911I			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3419	Kringle 8. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGAGGCGCGACGGCAGTCCCT	0.547																																					p.V911I													.	LPA-74	0			c.G2731A						.						105	110	108					6																	161027563		2068	4257	6325	SO:0001583	missense	4018	exon18			GCGCGACGGCAGT	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2731G>A	6.37:g.161027563C>T	ENSP00000321334:p.Val911Ile	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	194	8	NM_005577	0	0	0	0	0	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	c	11.74	1.727367	0.30593	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.62232	0.04;0.04	2.18	-2.62	0.06152	Kringle (1);Kringle-like fold (1);	.	.	.	.	T	0.21267	0.0512	L	0.38838	1.175	0.09310	N	1	P	0.50943	0.94	P	0.48089	0.566	T	0.26985	-1.0087	9	0.02654	T	1	.	0.3677	0.00374	0.2413:0.3112:0.2389:0.2086	.	3419	P08519	APOA_HUMAN	I	911	ENSP00000321334:V911I;ENSP00000395608:V911I	ENSP00000321334:V911I	V	-	1	0	LPA	160947553	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-2.331000	0.01110	-0.260000	0.09418	0.184000	0.17185	GTC	.		0.547	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161027563	C	T	161027563	3	4	6	1	0	0	0	0	1	0	0	0	8928	536	19	1	3483	1	LPA	6	161027563	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	14792933	161027563	10087504	49	440											
FAM188B	84182	hgsc.bcm.edu	37	chr7	30893077	30893077	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaacaaagcattcatcaggTatgaagcatgccttactcct	13	11	6	11	0	3	1	3	1	0	0	4	1	4	1	2	1	5	3	2	1	5	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:30893077T>C	ENST00000265299.6	+	12	1754		c.e12+2		AQP1_ENST00000509504.1_Splice_Site|AQP1_ENST00000434909.2_Splice_Site|INMT-FAM188B_ENST00000458257.1_Splice_Site	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B											endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATTCATCAGGTATGAAGCATG	0.483																																					.		.											.	FAM188B-90	0			c.1677+2T>C						.						107	105	106					7																	30893077		2030	4197	6227	SO:0001630	splice_region_variant	84182	exon12			ATCAGGTATGAAG	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 67"	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1677+2T>C	7.37:g.30893077T>C		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_032222	0	0	0	0	0	Q71AZ7|Q9H6D2	Splice_Site	SNP	ENST00000265299.6	37	CCDS43565.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.589907	0.28357	.	.	ENSG00000106125;ENSG00000250424	ENST00000265299;ENST00000509504	.	.	.	4.78	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8923	0.47002	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RP5-877J2.1;FAM188B	30859602	1.000000	0.71417	0.993000	0.49108	0.349000	0.29174	4.176000	0.58269	2.148000	0.66965	0.459000	0.35465	.	.		0.483	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	Intron	C	30893077	T	C	30893077	5	2	6	1	0	0	0	0	0	0	1	0	5531	1652	57	3	1725	3	FAM188B	7	30893077	Splice_Site	SNP	T	TCGA-A4-7585-01A-11D-2136-08		30893077	128245586	50	441											
KIAA0895	23366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	36396613	36396613	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtaggtatagtcagatttGaagaatctcagtttttcttt	10	19	8	4	0	3	3	2	1	2	2	4	3	3	3	0	1	0	3	0	1	5	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:36396613G>A	ENST00000297063.6	-	3	815	c.765C>T	c.(763-765)ttC>ttT	p.F255F	KIAA0895_ENST00000338533.5_Silent_p.F242F|KIAA0895_ENST00000317020.6_Silent_p.F204F|KIAA0895_ENST00000415803.2_Silent_p.F242F|KIAA0895_ENST00000436884.1_Silent_p.F104F|KIAA0895_ENST00000453212.1_Intron|KIAA0895_ENST00000480192.1_Intron|KIAA0895_ENST00000440378.1_Silent_p.F204F	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	255										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGTCAGATTTGAAGAATCTCA	0.393																																					p.F255F		.											.	KIAA0895-90	0			c.C765T						.						103	95	97					7																	36396613		1840	4095	5935	SO:0001819	synonymous_variant	23366	exon3			AGATTTGAAGAAT	BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.765C>T	7.37:g.36396613G>A		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	79	11	NM_001100425	0	0	2	2	0	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Silent	SNP	ENST00000297063.6	37	CCDS43570.1																																																																																			.		0.393	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		A	36396613	G	A	36396613	2	1	6	1	0	0	0	0	0	0	0	1	8218	1281	45	2		2	KIAA0895	7	36396613	Silent	SNP	G	TCGA-A4-7585-01A-11D-2136-08	5503536	36396613	122742050	51	442											
VPS41	27072	broad.mit.edu;bcgsc.ca	37	chr7	38783049	38783049	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcttcccacagctctccaTcatcttgctccttggcaaat	9	13	4	15	0	4	0	1	0	3	0	7	0	6	0	3	1	2	3	3	1	2	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:38783049T>A	ENST00000310301.4	-	24	2129	c.2075A>T	c.(2074-2076)gAt>gTt	p.D692V	VPS41_ENST00000395969.2_Missense_Mutation_p.D667V	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	692					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CAGCTCTCCATCATCTTGCTC	0.398																																					p.D692V													.	VPS41-93	0			c.A2075T						.						156	144	148					7																	38783049		2203	4300	6503	SO:0001583	missense	27072	exon24			TCTCCATCATCTT	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"vacuolar protein sorting 41 (yeast homolog)", "vacuolar protein sorting 41 (yeast)"			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.2075A>T	7.37:g.38783049T>A	ENSP00000309457:p.Asp692Val	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	105	6	NM_014396	0	0	40	45	5	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644627	0.87859	.	.	ENSG00000006715	ENST00000310301;ENST00000395969;ENST00000439468	T;T;T	0.24151	1.87;1.87;1.87	5.74	5.74	0.90152	Tetratricopeptide-like helical (1);	0.085770	0.85682	D	0.000000	T	0.59280	0.2182	M	0.91300	3.195	0.80722	D	1	D;D;D	0.61080	0.989;0.989;0.989	D;D;D	0.65573	0.936;0.936;0.936	T	0.69312	-0.5178	10	0.87932	D	0	-31.1895	16.3533	0.83225	0.0:0.0:0.0:1.0	.	692;667;692	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	V	692;667;33	ENSP00000309457:D692V;ENSP00000379297:D667V;ENSP00000395410:D33V	ENSP00000309457:D692V	D	-	2	0	VPS41	38749574	1.000000	0.71417	0.962000	0.40283	0.959000	0.62525	8.040000	0.89188	2.330000	0.79161	0.528000	0.53228	GAT	.		0.398	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			A	38783049	T	A	38783049	3	1	6	1	0	0	0	0	1	0	0	0	17243	1435	50	5	513	5	VPS41	7	38783049	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	2386436	38783049	120355614	52	443											
URGCP	55665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	43918082	43918082	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggccacaggttctgggaaaAtgtccaagtcctcccttccg	9	9	10	13	1	1	0	0	0	1	0	5	1	5	1	5	3	0	1	5	3	3	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:43918082A>C	ENST00000453200.1	-	6	1473	c.980T>G	c.(979-981)aTt>aGt	p.I327S	URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000223341.7_Missense_Mutation_p.I284S|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000402306.3_Missense_Mutation_p.I318S|URGCP_ENST00000447717.3_Missense_Mutation_p.I284S|URGCP_ENST00000443736.1_Missense_Mutation_p.I284S|URGCP_ENST00000336086.6_Missense_Mutation_p.I284S			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	327					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TTCTGGGAAAATGTCCAAGTC	0.512																																					p.I327S		.											.	URGCP-94	0			c.T980G						.						69	70	70					7																	43918082		1897	4129	6026	SO:0001583	missense	55665	exon6			GGGAAAATGTCCA		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.980T>G	7.37:g.43918082A>C	ENSP00000396918:p.Ile327Ser	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	109	24	NM_001077663	0	0	9	18	9	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.526247	0.27299	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.66	5.66	0.87406	.	0.567596	0.17461	N	0.173449	T	0.10981	0.0268	L	0.47716	1.5	0.09310	N	1	B;B	0.30973	0.302;0.302	B;B	0.29942	0.109;0.109	T	0.20207	-1.0282	10	0.49607	T	0.09	-6.1339	8.3974	0.32566	0.913:0.0:0.087:0.0	.	318;327	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	S	284;284;318;284;327;284	ENSP00000223341:I284S;ENSP00000336872:I284S;ENSP00000384955:I318S;ENSP00000392136:I284S;ENSP00000396918:I327S;ENSP00000402803:I284S	ENSP00000223341:I284S	I	-	2	0	URGCP	43884607	0.050000	0.20438	0.044000	0.18714	0.845000	0.48019	3.327000	0.52045	2.158000	0.67659	0.482000	0.46254	ATT	.		0.512	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		C	43918082	A	C	43918082	3	2	6	1	0	0	0	0	1	0	0	0	17059	101	4	5	1819	5	URGCP	7	43918082	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	5135033	43918082	115220581	53	444											
ABCA13	154664	broad.mit.edu	37	chr7	48315672	48315672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttcaggaatatgcaaatgagGattactccagaatgatagaa	17	10	9	5	0	1	4	1	2	0	2	2	6	2	6	1	2	2	1	1	2	7	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:48315672G>A	ENST00000435803.1	+	17	6433	c.6409G>A	c.(6409-6411)Gat>Aat	p.D2137N		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2137					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGCAAATGAGGATTACTCCAG	0.358																																					p.D2137N													.	ABCA13-521	0			c.G6409A						.						37	33	34					7																	48315672		1821	4077	5898	SO:0001583	missense	154664	exon17			AATGAGGATTACT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.6409G>A	7.37:g.48315672G>A	ENSP00000411096:p.Asp2137Asn	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	19	3	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	9.310	1.055426	0.19907	.	.	ENSG00000179869	ENST00000435803	T	0.16073	2.37	4.99	4.02	0.46733	.	0.540328	0.16662	N	0.204754	T	0.11836	0.0288	L	0.39633	1.23	0.22779	N	0.998743	B	0.14012	0.009	B	0.12837	0.008	T	0.25745	-1.0123	9	.	.	.	.	3.275	0.06896	0.4059:0.0:0.5941:0.0	.	2137	Q86UQ4	ABCAD_HUMAN	N	2137	ENSP00000411096:D2137N	.	D	+	1	0	ABCA13	48286218	0.424000	0.25490	0.002000	0.10522	0.442000	0.32017	2.187000	0.42602	1.133000	0.42147	0.484000	0.47621	GAT	.		0.358	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48315672	G	A	48315672	3	1	6	1	0	0	0	0	1	0	0	0	31	1174	41	2	6304	2	ABCA13	7	48315672	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	4397590	48315672	110822991	54	445											
ABCA13	154664	broad.mit.edu;bcgsc.ca	37	chr7	48317816	48317817	+	Frame_Shift_Ins	INS	-	-	T																															atatatcacctaatgaaaagINSttcatttatattagacaatg																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:48317816_48317817insT	ENST00000435803.1	+	18	7049_7050	c.7025_7026insT	c.(7024-7029)agttcafs	p.S2343fs		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2343					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTAATGAAAAGTTCATTTATAT	0.307																																					p.S2342fs													.	ABCA13-521	0			c.7025_7026insT						.																																			SO:0001589	frameshift_variant	154664	exon18			TGAAAAGTTCATT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7027dupT	7.37:g.48317818_48317818dupT	ENSP00000411096:p.Ser2343fs	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	22	8	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Frame_Shift_Ins	INS	ENST00000435803.1	37	CCDS47584.1																																																																																			.		0.307	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48317817	-	T	48317816	7	5	6	1	0	1	1	0	0	0	0	0	31	1029	36	0	6924	0	ABCA13	7	48317816	Frame_Shift_Ins	INS	-	TCGA-A4-7585-01A-11D-2136-08	2144	48317816	110820847	55	446											
LIMK1	3984	bcgsc.ca	37	chr7	73535525	73535525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctccgcatgcacctggccgGccacctgccactgggcccac	5	5	10	21	2	0	0	0	0	0	0	1	0	1	0	8	3	2	2	8	3	0	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:73535525G>A	ENST00000336180.2	+	16	1889	c.1838G>A	c.(1837-1839)gGc>gAc	p.G613D	LIMK1_ENST00000538333.3_Missense_Mutation_p.G579D|LIMK1_ENST00000418310.1_Missense_Mutation_p.G643D	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	613					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CACCTGGCCGGCCACCTGCCA	0.682																																					p.G613D													.	LIMK1-523	0			c.G1838A						.						35	35	35					7																	73535525		2203	4300	6503	SO:0001583	missense	3984	exon16			TGGCCGGCCACCT	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1838G>A	7.37:g.73535525G>A	ENSP00000336740:p.Gly613Asp	Somatic	71	0		WXS	Illumina HiSeq	Phase_1	67	6	NM_002314	1	0	22	23	0	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	G	9.624	1.134668	0.21123	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000538333	T;T;T	0.61742	0.08;0.08;0.08	4.3	3.26	0.37387	Protein kinase-like domain (1);	0.454681	0.24124	N	0.041339	T	0.30823	0.0777	N	0.08118	0	0.39433	D	0.96711	B;B	0.19445	0.002;0.036	B;B	0.18871	0.014;0.023	T	0.14559	-1.0468	10	0.12103	T	0.63	-22.7694	8.7333	0.34512	0.0:0.0:0.6149:0.3851	.	579;613	B7Z6I8;P53667	.;LIMK1_HUMAN	D	643;613;613;579	ENSP00000409717:G643D;ENSP00000336740:G613D;ENSP00000444452:G579D	ENSP00000336740:G613D	G	+	2	0	LIMK1	73173461	1.000000	0.71417	0.996000	0.52242	0.909000	0.53808	3.499000	0.53310	2.157000	0.67596	0.456000	0.33151	GGC	.		0.682	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		A	73535525	G	A	73535525	3	1	6	1	0	0	0	0	1	0	0	0	8823	1203	42	2	1900	2	LIMK1	7	73535525	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	25217709	73535525	85603138	56	447											
RELN	5649	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	103629656	103629656	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcacctcgccctgctcccCatccccttccagctccccgt	4	8	6	23	2	0	0	0	0	0	0	5	1	4	0	9	0	3	3	9	0	0	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:103629656C>T	ENST00000428762.1	-	1	307	c.148G>A	c.(148-150)Ggg>Agg	p.G50R	RELN_ENST00000424685.2_Missense_Mutation_p.G50R|RELN_ENST00000343529.5_Missense_Mutation_p.G50R	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	50	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCCTGCTCCCCATCCCCTTCC	0.642																																					p.G50R	NSCLC(146;835 1944 15585 22231 52158)	.											.	RELN-574	0			c.G148A						.						52	53	53					7																	103629656		2203	4300	6503	SO:0001583	missense	5649	exon1			GCTCCCCATCCCC		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.148G>A	7.37:g.103629656C>T	ENSP00000392423:p.Gly50Arg	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	112	20	NM_173054	0	0	0	0	0	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301758	0.81136	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21361	2.01;2.01;2.01	4.63	4.63	0.57726	Reeler domain (1);	0.000000	0.64402	U	0.000010	T	0.32645	0.0836	N	0.19112	0.55	0.58432	D	0.999997	D;D	0.89917	0.999;1.0	D;D	0.75484	0.976;0.986	T	0.19095	-1.0316	10	0.52906	T	0.07	.	17.6802	0.88240	0.0:1.0:0.0:0.0	.	50;50	P78509-2;P78509	.;RELN_HUMAN	R	50	ENSP00000392423:G50R;ENSP00000345694:G50R;ENSP00000388446:G50R	ENSP00000345694:G50R	G	-	1	0	RELN	103416892	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.718000	0.74713	2.386000	0.81285	0.563000	0.77884	GGG	.		0.642	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103629656	C	T	103629656	3	4	6	1	0	0	0	0	1	0	0	0	13252	594	21	2	10494	2	RELN	7	103629656	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	30094131	103629656	55509007	57	448											
CNOT4	4850	hgsc.bcm.edu;bcgsc.ca	37	chr7	135080545	135080545	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgccccttcaaaaggggAccgtgcactgtgattggatg	9	10	12	10	1	1	1	1	1	0	0	1	3	1	3	3	3	3	1	3	3	3	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:135080545A>G	ENST00000315544.5	-	9	1249	c.970T>C	c.(970-972)Tcc>Ccc	p.S324P	CNOT4_ENST00000428680.2_Missense_Mutation_p.S321P|CNOT4_ENST00000356162.4_Missense_Mutation_p.S324P|CNOT4_ENST00000361528.4_Missense_Mutation_p.S321P|CNOT4_ENST00000541284.1_Missense_Mutation_p.S324P|CNOT4_ENST00000414802.1_Missense_Mutation_p.S324P|CNOT4_ENST00000451834.1_Missense_Mutation_p.S321P|CNOT4_ENST00000423368.2_Missense_Mutation_p.S324P	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	324					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						TCAAAAGGGGACCGTGCACTG	0.478																																					p.S324P	Ovarian(51;766 1130 5502 35047 50875)	.											.	CNOT4-90	0			c.T970C						.						165	162	163					7																	135080545		1957	4148	6105	SO:0001583	missense	4850	exon9			AAGGGGACCGTGC	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"RNA binding motif (RRM) containing"	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.970T>C	7.37:g.135080545A>G	ENSP00000326731:p.Ser324Pro	Somatic	57	1		WXS	Illumina HiSeq	Phase_I	58	4	NM_001190850	0	0	27	27	0	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.751375	0.69533	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	T;T;T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.68915	0.3053	L	0.29908	0.895	0.80722	D	1	B;B;D;B;D;B	0.61080	0.024;0.089;0.989;0.022;0.981;0.009	B;B;P;B;D;B	0.68621	0.01;0.023;0.734;0.013;0.959;0.014	T	0.69331	-0.5173	10	0.44086	T	0.13	-13.0859	15.5751	0.76373	1.0:0.0:0.0:0.0	.	321;324;324;321;324;321	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	P	324;321;324;324;321;324;324;321;324	ENSP00000445508:S324P;ENSP00000388491:S321P;ENSP00000406777:S324P;ENSP00000354673:S321P;ENSP00000416532:S324P;ENSP00000348485:S324P;ENSP00000399108:S321P;ENSP00000326731:S324P	ENSP00000262563:S324P	S	-	1	0	CNOT4	134731085	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.940000	0.92958	2.276000	0.75962	0.455000	0.32223	TCC	.		0.478	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		G	135080545	A	G	135080545	3	3	6	1	0	0	0	0	1	0	0	0	3627	275	10	3	1075	3	CNOT4	7	135080545	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	31450889	135080545	24058118	58	449											
KIAA1549	57670	broad.mit.edu;ucsc.edu	37	chr7	138602635	138602635	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtctctgacggcaagcgaCggtgtgtttttgtttgctat	5	15	14	7	3	1	1	0	1	1	0	2	2	1	1	0	3	2	4	0	3	2	4	rs570277151		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:138602635C>T	ENST00000422774.1	-	2	1785	c.1737G>A	c.(1735-1737)ccG>ccA	p.P579P	KIAA1549_ENST00000242365.4_Silent_p.P529P|KIAA1549_ENST00000440172.1_Silent_p.P579P			Q9HCM3	K1549_HUMAN	KIAA1549	579	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CGGCAAGCGACGGTGTGTTTT	0.478			O	BRAF	pilocytic astrocytoma								C|||	1	0.000199681	0	0	5008	,	,		21163	0.001		0	False		,,,				2504	0				p.P579P	NSCLC(119;1534 1718 44213 46230 50068)			Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549-369	0			c.G1737A						.						65	67	66					7																	138602635		2005	4172	6177	SO:0001819	synonymous_variant	57670	exon2			AAGCGACGGTGTG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1737G>A	7.37:g.138602635C>T		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	17	4	NM_020910	0	0	12	15	3	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																			.		0.478	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138602635	C	T	138602635	2	4	6	1	0	0	0	0	0	0	0	1	8265	523	19	1		1	KIAA1549	7	138602635	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	3522090	138602635	20536028	59	450											
POLB	5423	broad.mit.edu;bcgsc.ca	37	chr8	42213041	42213041	+	Frame_Shift_Del	DEL	A	A	-																															atcttctatacagatctcagAaaaaatgaagataaattgaa																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr8:42213041delA	ENST00000265421.4	+	7	548	c.378delA	c.(376-378)agafs	p.R126fs	POLB_ENST00000538005.1_5'UTR	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	126					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	CAGATCTCAGAAAAAATGAAG	0.303								DNA polymerases (catalytic subunits)																													p.R126fs													.	POLB-1084	0			c.378delA						.						65	69	67					8																	42213041		2203	4298	6501	SO:0001589	frameshift_variant	5423	exon7			TCTCAGAAAAAAT		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.378delA	8.37:g.42213041delA	ENSP00000265421:p.Arg126fs	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	81	9	NM_002690	0	0	0	0	0	B2RC78|Q3KP48|Q6FI34	Frame_Shift_Del	DEL	ENST00000265421.4	37	CCDS6129.1																																																																																			.		0.303	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		-	42213041	A	-	42213041	7	5	6	1	0	1	0	1	0	0	0	0	12215	243	9	0	404	0	POLB	8	42213041	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08		42213041	104150981	60	451											
CHD7	55636	hgsc.bcm.edu	37	chr8	61761115	61761115	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtactacctaagacaagAagtgataggagaccaggcgg	14	6	13	8	1	0	4	0	1	0	3	0	5	0	4	2	3	2	2	2	3	6	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr8:61761115A>C	ENST00000423902.2	+	24	5731	c.5252A>C	c.(5251-5253)gAa>gCa	p.E1751A	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1751					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTAAGACAAGAAGTGATAGGA	0.493																																					p.E1751A		.											.	CHD7-141	0			c.A5252C						.						122	118	119					8																	61761115		1976	4186	6162	SO:0001583	missense	55636	exon24			GACAAGAAGTGAT	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.5252A>C	8.37:g.61761115A>C	ENSP00000392028:p.Glu1751Ala	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_017780	0	0	5	5	0	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.353000	0.61293	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.91180	-2.8	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.92694	0.7678	M	0.88241	2.94	0.80722	D	1	B	0.33826	0.427	B	0.37780	0.258	D	0.93440	0.6793	10	0.87932	D	0	-19.9182	15.2072	0.73190	1.0:0.0:0.0:0.0	.	1751	Q9P2D1	CHD7_HUMAN	A	1751	ENSP00000392028:E1751A	ENSP00000307304:E1751A	E	+	2	0	CHD7	61923669	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.059000	0.61396	0.528000	0.53228	GAA	.		0.493	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		C	61761115	A	C	61761115	3	2	6	1	0	0	0	0	1	0	0	0	3336	246	9	5	5342	5	CHD7	8	61761115	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	19548074	61761115	84602907	61	452											
TRPA1	8989	hgsc.bcm.edu	37	chr8	72950286	72950286	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaaacactaaaatcatacAagtttttattagatatgaat	20	14	3	4	0	1	2	1	1	0	1	1	2	1	2	0	0	2	1	0	0	11	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr8:72950286A>C	ENST00000262209.4	-	20	2524	c.2317T>G	c.(2317-2319)Tgt>Ggt	p.C773G	RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000537896.1_Intron|TRPA1_ENST00000519720.1_5'UTR|RP11-383H13.1_ENST00000457356.4_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	773					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	AAAATCATACAAGTTTTTATT	0.264																																					p.C773G		.											.	TRPA1-230	0			c.T2317G						.						22	23	23					8																	72950286		2188	4261	6449	SO:0001583	missense	8989	exon20			TCATACAAGTTTT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2317T>G	8.37:g.72950286A>C	ENSP00000262209:p.Cys773Gly	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_007332	0	0	0	0	0	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.686665	0.68157	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.79940	-1.32;-1.32	5.58	5.58	0.84498	.	0.042497	0.85682	D	0.000000	D	0.88187	0.6369	M	0.84433	2.695	0.58432	D	0.999993	D	0.55605	0.972	P	0.54590	0.756	D	0.90030	0.4134	10	0.66056	D	0.02	-16.7662	15.4216	0.75015	1.0:0.0:0.0:0.0	.	773	O75762	TRPA1_HUMAN	G	625;773	ENSP00000428151:C625G;ENSP00000262209:C773G	ENSP00000262209:C773G	C	-	1	0	TRPA1	73112840	1.000000	0.71417	0.994000	0.49952	0.924000	0.55760	6.764000	0.74960	2.120000	0.65058	0.533000	0.62120	TGT	.		0.264	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		C	72950286	A	C	72950286	3	2	6	1	0	0	0	0	1	0	0	0	16610	130	5	5	1074	5	TRPA1	8	72950286	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	11189171	72950286	73413736	62	453											
HAS2	3037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	122641473	122641473	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagtaattatccgtttggatAaactggtagccaacaatata	15	13	7	6	1	0	0	0	0	0	0	1	1	1	1	2	2	3	3	2	2	10	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr8:122641473A>T	ENST00000303924.4	-	2	645	c.108T>A	c.(106-108)ttT>ttA	p.F36L		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	36					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)		HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			CCGTTTGGATAAACTGGTAGC	0.423																																					p.F36L		.											.	HAS2-236	0			c.T108A						.						88	85	86					8																	122641473		2203	4300	6503	SO:0001583	missense	3037	exon2			TTGGATAAACTGG	U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.108T>A	8.37:g.122641473A>T	ENSP00000306991:p.Phe36Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	90	16	NM_005328	0	0	1	1	0	Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	37	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	A	8.872	0.949410	0.18356	.	.	ENSG00000170961	ENST00000303924;ENST00000443194	T	0.37584	1.19	6.17	3.85	0.44370	.	0.042814	0.85682	D	0.000000	T	0.22166	0.0534	L	0.28192	0.835	0.53688	D	0.999978	B	0.09022	0.002	B	0.06405	0.002	T	0.05178	-1.0901	10	0.12430	T	0.62	-24.2374	9.8975	0.41327	0.809:0.0:0.191:0.0	.	36	Q92819	HAS2_HUMAN	L	36	ENSP00000306991:F36L	ENSP00000306991:F36L	F	-	3	2	HAS2	122710654	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.132000	0.31418	1.161000	0.42604	-0.250000	0.11733	TTT	.		0.423	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		T	122641473	A	T	122641473	3	4	6	1	0	0	0	0	1	0	0	0	6983	359	13	5	1562	5	HAS2	8	122641473	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	49691187	122641473	23722549	63	454											
ZBTB43	23099	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	129595385	129595385	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatacctgcccagcaactcGtccacagagcatgaccgcct	11	6	8	16	2	0	2	0	1	0	1	2	3	1	2	5	0	5	2	5	0	3	1	rs34266321		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr9:129595385G>T	ENST00000373464.4	+	3	861	c.597G>T	c.(595-597)tcG>tcT	p.S199S	ZBTB43_ENST00000449886.1_Silent_p.S199S|ZBTB43_ENST00000373457.1_Silent_p.S199S	NM_014007.3	NP_054726.1	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	199					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CCAGCAACTCGTCCACAGAGC	0.587																																					p.S199S													.	ZBTB43-91	0			c.G597T						.						40	41	41					9																	129595385		2203	4300	6503	SO:0001819	synonymous_variant	23099	exon2			CAACTCGTCCACA	AF049907	CCDS6867.1	9q33.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000169155	ENSG00000169155		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	17908	protein-coding gene	gene with protein product			"zinc finger protein 297B"	ZNF297B			Standard	NM_014007		Approved	KIAA0414, ZNF-X, FLJ22470, ZBTB22B	uc010mxf.3	O43298	OTTHUMG00000020693	ENST00000373464.4:c.597G>T	9.37:g.129595385G>T		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	59	6	NM_001135776	0	0	3	8	5	Q5JU96	Silent	SNP	ENST00000373464.4	37	CCDS6867.1																																																																																			G|0.999;A|0.001		0.587	ZBTB43-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054124.1	NM_001135776		T	129595385	G	T	129595385	2	4	6	1	0	0	0	0	0	0	0	1	17576	1132	40	4		4	ZBTB43	9	129595385	Silent	SNP	G	TCGA-A4-7585-01A-11D-2136-08		129595385	11618046	64	455											
COL5A1	1289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	137734002	137734002	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atctgtctccctcttccccaGaccaagaaaggctaccagaa	12	8	6	15	0	3	3	0	0	3	3	5	3	4	3	5	1	1	1	5	1	4	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr9:137734002G>C	ENST00000371817.3	+	66	5784		c.e66-1			NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1						axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CTCTTCCCCAGACCAAGAAAG	0.547																																					.		.											.	COL5A1-524	0			c.5371-1G>C						.						89	81	83					9																	137734002		2203	4300	6503	SO:0001630	splice_region_variant	1289	exon66			TCCCCAGACCAAG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.5371-1G>C	9.37:g.137734002G>C		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	100	12	NM_000093	0	0	0	0	0	Q15094|Q5SUX4	Splice_Site	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.985830	0.74589	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3629	0.87356	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL5A1	136873823	1.000000	0.71417	0.075000	0.20258	0.907000	0.53573	9.541000	0.98083	2.174000	0.68829	0.563000	0.77884	.	.		0.547	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Intron	C	137734002	G	C	137734002	5	2	6	1	0	0	0	0	0	0	1	0	3702	956	33	4	5632	4	COL5A1	9	137734002	Splice_Site	SNP	G	TCGA-A4-7585-01A-11D-2136-08	8138617	137734002	3479429	65	456											
PPRC1	23082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	103898442	103898442	+	Frame_Shift_Del	DEL	A	A	-																															ctctgacggagatcttggacAatgcagattctgagaacctt																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr10:103898442delA	ENST00000278070.2	+	3	448	c.409delA	c.(409-411)aatfs	p.N137fs	PPRC1_ENST00000413464.2_Frame_Shift_Del_p.N137fs|PPRC1_ENST00000370012.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	137					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		GATCTTGGACAATGCAGATTC	0.532																																					p.N137fs		.											.	PPRC1-227	0			c.409delA						.						120	108	112					10																	103898442		2203	4300	6503	SO:0001589	frameshift_variant	23082	exon3			.	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.409delA	10.37:g.103898442delA	ENSP00000278070:p.Asn137fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	90	15	NM_015062	0	0	0	0	0	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Frame_Shift_Del	DEL	ENST00000278070.2	37	CCDS7529.1																																																																																			.		0.532	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		-	103898442	A	-	103898442	7	5	6	1	0	1	0	1	0	0	0	0	12439	130	5	0	419	0	PPRC1	10	103898442	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08		103898442	31636305	66	457											
HTRA1	5654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	124273843	124273843	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtaatgaagatatcatgAtcacagtgattcccgaagaa	15	9	11	6	1	2	5	2	3	0	2	3	6	3	5	1	2	0	1	1	2	5	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr10:124273843A>T	ENST00000368984.3	+	9	1539	c.1411A>T	c.(1411-1413)Atc>Ttc	p.I471F		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	471					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				AGATATCATGATCACAGTGAT	0.507																																					p.I471F		.											.	HTRA1-90	0			c.A1411T						.						155	138	144					10																	124273843		2203	4300	6503	SO:0001583	missense	5654	exon9			ATCATGATCACAG	AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"Serine peptidases / Serine peptidases"	9476	protein-coding gene	gene with protein product		602194	"protease, serine, 11 (IGF binding)"	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.1411A>T	10.37:g.124273843A>T	ENSP00000357980:p.Ile471Phe	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	99	20	NM_002775	0	0	161	238	77	D3DRE4|Q9UNS5	Missense_Mutation	SNP	ENST00000368984.3	37	CCDS7630.1	.	.	.	.	.	.	.	.	.	.	A	1.382	-0.583027	0.03827	.	.	ENSG00000166033	ENST00000368984;ENST00000435263;ENST00000420892	D;D	0.82893	-1.66;-1.66	5.48	1.75	0.24633	PDZ/DHR/GLGF (1);	0.119403	0.56097	D	0.000029	T	0.67636	0.2914	L	0.31371	0.925	0.51767	D	0.999938	B	0.06786	0.001	B	0.06405	0.002	T	0.51601	-0.8685	10	0.28530	T	0.3	-8.1432	3.9311	0.09285	0.4669:0.3415:0.0687:0.1228	.	471	Q92743	HTRA1_HUMAN	F	471;438;212	ENSP00000357980:I471F;ENSP00000412676:I212F	ENSP00000357980:I471F	I	+	1	0	HTRA1	124263833	0.991000	0.36638	0.304000	0.25085	0.093000	0.18481	0.396000	0.20867	0.043000	0.15746	-0.313000	0.08912	ATC	.		0.507	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775		T	124273843	A	T	124273843	3	4	6	1	0	0	0	0	1	0	0	0	7474	333	12	5	1445	5	HTRA1	10	124273843	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	20375401	124273843	11260904	67	458											
FAR1	84188	hgsc.bcm.edu	37	chr11	13743391	13743391	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgttaatgaatcaactaaaCcctgaagataaaaaggcaag	20	8	7	6	0	1	3	1	2	0	1	1	3	1	3	1	1	2	2	1	1	10	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr11:13743391C>G	ENST00000354817.3	+	10	1386	c.1242C>G	c.(1240-1242)aaC>aaG	p.N414K	FAR1_ENST00000532502.1_Missense_Mutation_p.N38K	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	414					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						ATCAACTAAACCCTGAAGATA	0.303																																					p.N414K		.											.	FAR1-92	0			c.C1242G						.						68	67	68					11																	13743391		2200	4291	6491	SO:0001583	missense	84188	exon10			ACTAAACCCTGAA	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	26222	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 1"		"male sterility domain containing 2"	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.1242C>G	11.37:g.13743391C>G	ENSP00000346874:p.Asn414Lys	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_032228	0	0	11	11	0	D3DQW8|Q5CZA3	Missense_Mutation	SNP	ENST00000354817.3	37	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333187	0.41297	.	.	ENSG00000197601	ENST00000354817;ENST00000532502	T	0.22539	1.95	5.5	1.55	0.23275	.	0.086625	0.85682	D	0.000000	T	0.19005	0.0456	L	0.43923	1.385	0.32231	N	0.573949	B	0.26318	0.146	B	0.32928	0.155	T	0.14337	-1.0476	10	0.66056	D	0.02	-7.2202	9.0175	0.36179	0.0:0.5608:0.0:0.4392	.	414	Q8WVX9	FACR1_HUMAN	K	414;38	ENSP00000346874:N414K	ENSP00000346874:N414K	N	+	3	2	FAR1	13699967	0.983000	0.35010	0.998000	0.56505	0.984000	0.73092	0.318000	0.19504	0.098000	0.17522	0.650000	0.86243	AAC	.		0.303	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228		G	13743391	C	G	13743391	3	3	6	1	0	0	0	0	1	0	0	0	5693	506	18	4	1276	4	FAR1	11	13743391	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		13743391	121263125	68	459											
ARAP1	116985	broad.mit.edu	37	chr11	72399555	72399555	+	Frame_Shift_Del	DEL	T	T	-																															gtagactttgagactcttaaTaggccactccttctcaggcc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr11:72399555delT	ENST00000393609.3	-	31	4217	c.4015delA	c.(4015-4017)attfs	p.I1339fs	ARAP1_ENST00000426523.1_Frame_Shift_Del_p.I1083fs|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000393605.3_Frame_Shift_Del_p.I1099fs|ARAP1_ENST00000359373.5_Frame_Shift_Del_p.I1328fs|ARAP1-AS1_ENST00000542022.1_RNA|ARAP1_ENST00000455638.2_Frame_Shift_Del_p.I1328fs|ARAP1_ENST00000334211.8_Frame_Shift_Del_p.I1094fs|ARAP1_ENST00000429686.1_Frame_Shift_Del_p.I1022fs	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1339	PH 4. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						AGACTCTTAATAGGCCACTCC	0.577																																					p.I1339fs	Ovarian(102;1198 1520 13195 17913 37529)												.	ARAP1-91	0			c.4015delA						.						74	61	65					11																	72399555		2200	4293	6493	SO:0001589	frameshift_variant	116985	exon31			TCTTAATAGGCCA	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.4015delA	11.37:g.72399555delT	ENSP00000377233:p.Ile1339fs	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	28	8	NM_001040118	0	0	0	0	0	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	37	CCDS41687.1																																																																																			.		0.577	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		-	72399555	T	-	72399555	7	5	6	1	0	1	0	1	0	0	0	0	838	1406	49	0	357	0	ARAP1	11	72399555	Frame_Shift_Del	DEL	T	TCGA-A4-7585-01A-11D-2136-08	58656164	72399555	62606961	69	460											
TECTA	7007	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	120980039	120980039	+	Frame_Shift_Del	DEL	A	A	-																															tgggcagatgtgcacaatggAattcgaggcgagatctatta																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr11:120980039delA	ENST00000392793.1	+	4	589	c.318delA	c.(316-318)ggafs	p.G106fs	TECTA_ENST00000264037.2_Frame_Shift_Del_p.G106fs			O75443	TECTA_HUMAN	tectorin alpha	106	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGCACAATGGAATTCGAGGCG	0.498																																					p.G106fs		.											.	TECTA-225	0			c.318delA						.						105	97	100					11																	120980039		2203	4299	6502	SO:0001589	frameshift_variant	7007	exon3			.	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.318delA	11.37:g.120980039delA	ENSP00000376543:p.Gly106fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	76	19	NM_005422	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000392793.1	37	CCDS8434.1																																																																																			.		0.498	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		-	120980039	A	-	120980039	7	5	6	1	0	1	0	1	0	0	0	0	15779	233	9	0	328	0	TECTA	11	120980039	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08	48580484	120980039	14026477	70	461											
CNTN1	1272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	41327590	41327590	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgttcttaagatcttcAatattcagctagaagatgaa	13	13	9	6	0	4	4	2	1	2	3	4	4	4	4	0	1	1	3	0	1	6	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:41327590A>C	ENST00000551295.2	+	9	1012	c.895A>C	c.(895-897)Aat>Cat	p.N299H	CNTN1_ENST00000547849.1_Missense_Mutation_p.N299H|CNTN1_ENST00000360099.3_Missense_Mutation_p.N299H|CNTN1_ENST00000348761.2_Missense_Mutation_p.N288H|CNTN1_ENST00000547702.1_Missense_Mutation_p.N299H|CNTN1_ENST00000347616.1_Missense_Mutation_p.N299H	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	299	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TAAGATCTTCAATATTCAGCT	0.408																																					p.N299H		.											.	CNTN1-1149	0			c.A895C						.						85	87	87					12																	41327590		2203	4299	6502	SO:0001583	missense	1272	exon9			ATCTTCAATATTC	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.895A>C	12.37:g.41327590A>C	ENSP00000447006:p.Asn299His	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	76	14	NM_001256063	0	0	1	1	0	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293171	0.80914	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	5.24	5.24	0.73138	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	L	0.56124	1.755	0.54753	D	0.999986	D;D;D	0.89917	1.0;0.997;0.998	D;D;D	0.75484	0.986;0.968;0.981	T	0.54309	-0.8313	10	0.46703	T	0.11	.	15.4433	0.75204	1.0:0.0:0.0:0.0	.	299;288;299	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	H	299;299;299;299;299;288	ENSP00000448004:N299H;ENSP00000447006:N299H;ENSP00000448653:N299H;ENSP00000325660:N299H;ENSP00000353213:N299H;ENSP00000261160:N288H	ENSP00000325660:N299H	N	+	1	0	CNTN1	39613857	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.730000	0.91510	2.130000	0.65690	0.528000	0.53228	AAT	.		0.408	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		C	41327590	A	C	41327590	3	2	6	1	0	0	0	0	1	0	0	0	3646	130	5	5	925	5	CNTN1	12	41327590	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		41327590	92524305	71	462											
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41582619	41582619	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgcgggggctgcgcttcggGgctgggcggtggtgaggtgc	1	7	23	10	5	0	1	0	1	0	0	1	1	0	1	1	8	2	3	1	8	0	1	rs74955204	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:41582619G>A	ENST00000402685.2	+	1	370	c.362G>A	c.(361-363)gGg>gAg	p.G121E		NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	121	Gly-rich.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TGCGCTTCGGGGCTGGGCGGT	0.821													G|||	168	0.0335463	8e-04	0.0461	5008	,	,		2271	0.0635		0.0239	False		,,,				2504	0.0481				p.G121E		.											.	PDZRN4-296	0			c.G362A						.						2	1	1					12																	41582619		600	1482	2082	SO:0001583	missense	29951	exon1			CTTCGGGGCTGGG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.362G>A	12.37:g.41582619G>A	ENSP00000384197:p.Gly121Glu	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	9	4	NM_001164595	0	0	0	0	0	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	109	0.04990842490842491	10	0.02032520325203252	12	0.03314917127071823	65	0.11363636363636363	22	0.029023746701846966	G	5.875	0.345515	0.11126	.	.	ENSG00000165966	ENST00000402685	T	0.71461	-0.57	1.11	-0.936	0.10419	.	.	.	.	.	T	0.02848	0.0085	L	0.47190	1.495	0.80722	D	1	.	.	.	.	.	.	T	0.12785	-1.0534	7	0.48119	T	0.1	.	6.1922	0.20530	0.3279:0.0:0.6721:0.0	.	.	.	.	E	121	ENSP00000384197:G121E	ENSP00000384197:G121E	G	+	2	0	PDZRN4	39868886	0.991000	0.36638	0.010000	0.14722	0.064000	0.16182	0.261000	0.18442	-0.372000	0.07992	-0.350000	0.07774	GGG	G|0.950;A|0.050		0.821	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41582619	G	A	41582619	3	1	6	1	0	0	0	0	1	0	0	0	11736	1232	43	2	364	2	PDZRN4	12	41582619	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	255029	41582619	92269276	72	463											
PLEKHA9	51054	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	45567881	45567881	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttccaatgaattatgaattgGtataataggatgtttcatct	13	17	7	4	0	2	2	1	2	1	0	3	3	3	3	1	2	0	2	1	2	7	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:45567881G>T	ENST00000256692.5	-	0	804					NR_037144.1		O95397	PKHA9_HUMAN	pleckstrin homology domain containing, family A member 8 pseudogene 1							cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TTATGAATTGGTATAATAGGA	0.413																																					.													.	PLEKHA8P1-226	0			.						.						133	123	127					12																	45567881		2203	4300	6503			51054	.			GAATTGGTATAAT	AF103731		12q12	2010-11-24	2010-11-24	2010-11-24	ENSG00000134297	ENSG00000134297			30222	pseudogene	pseudogene	"putative glycolipid transfer protein"		"pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 9"	PLEKHA9		12477932	Standard	NR_037144		Approved	FLJ14156	uc001rom.2	O95397			12.37:g.45567881G>T		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	90	21	.	0	0	3	4	1		RNA	SNP	ENST00000256692.5	37																																																																																				.		0.413	PLEKHA8P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000404814.1	NR_037144		T	45567881	G	T	45567881	1	4	6	0	1	0	0	0	0	0	0	0	12089	1261	44	4		4	PLEKHA9	12	45567881	RNA	SNP	G	TCGA-A4-7585-01A-11D-2136-08	3985262	45567881	88284014	73	464											
KRT77	374454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53097170	53097170	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggtactataaacccGcctgctcattgaactaaacg	13	9	8	11	2	1	2	1	1	0	1	1	2	1	2	2	1	6	3	2	1	7	5	rs375217197		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:53097170G>T	ENST00000341809.3	-	1	77	c.49C>A	c.(49-51)Cgg>Agg	p.R17R	KRT77_ENST00000537195.1_5'UTR	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	17	Head.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CTATAAACCCGCCTGCTCATT	0.542																																					p.R17R		.											.	KRT77-187	0			c.C49A						.						64	70	68					12																	53097170		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon1			AAACCCGCCTGCT	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"-", "Intermediate filaments type II, keratins (basic)"	20411	protein-coding gene	gene with protein product		611158	"keratin 1B"	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.49C>A	12.37:g.53097170G>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_175078	0	0	0	0	0	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																			.		0.542	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		T	53097170	G	T	53097170	2	4	6	1	0	0	0	0	0	0	0	1	8511	1086	38	4		4	KRT77	12	53097170	Silent	SNP	G	TCGA-A4-7585-01A-11D-2136-08	7529289	53097170	80754725	74	465											
STAT6	6778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57499083	57499083	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctggaacttggtctgagtCttcagtacctgggggggctg	5	11	16	9	0	3	1	1	1	2	0	3	2	3	2	2	5	2	2	2	5	2	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:57499083C>A	ENST00000300134.3	-	9	1177	c.852G>T	c.(850-852)aaG>aaT	p.K284N	STAT6_ENST00000537215.2_Missense_Mutation_p.K174N|STAT6_ENST00000543873.2_Missense_Mutation_p.K284N|STAT6_ENST00000454075.3_Missense_Mutation_p.K284N|STAT6_ENST00000556155.1_Missense_Mutation_p.K284N|STAT6_ENST00000538913.2_Missense_Mutation_p.K174N	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	284					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TGGTCTGAGTCTTCAGTACCT	0.632																																					p.K284N		.											.	STAT6-849	0			c.G852T						.						38	43	41					12																	57499083		2203	4299	6502	SO:0001583	missense	6778	exon9			CTGAGTCTTCAGT	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"SH2 domain containing"	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.852G>T	12.37:g.57499083C>A	ENSP00000300134:p.Lys284Asn	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	105	18	NM_001178079	0	0	59	91	32	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943506	0.73672	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	D;D;D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2;-3.2;-3.2	4.64	3.76	0.43208	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.96488	0.8854	M	0.87328	2.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96356	0.9262	10	0.87932	D	0	-24.3606	10.4551	0.44546	0.0:0.9051:0.0:0.0949	.	284;284	A8K4S9;P42226	.;STAT6_HUMAN	N	284;174;174;284;284;174;284;174;284	ENSP00000300134:K284N;ENSP00000445409:K174N;ENSP00000438451:K284N;ENSP00000451742:K284N;ENSP00000444530:K174N;ENSP00000401486:K284N	ENSP00000300134:K284N	K	-	3	2	STAT6	55785350	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.775000	0.47702	1.178000	0.42870	0.561000	0.74099	AAG	.		0.632	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		A	57499083	C	A	57499083	3	1	6	1	0	0	0	0	1	0	0	0	15302	912	32	4	1747	4	STAT6	12	57499083	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	4401913	57499083	76352812	75	466											
GCN1L1	10985	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	120599294	120599294	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgcctccgtgtactcacCtccttcagctccagctcgat	7	11	7	16	2	2	0	2	0	0	0	6	1	5	0	5	0	4	3	5	0	2	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:120599294C>T	ENST00000300648.6	-	22	2448	c.2436G>A	c.(2434-2436)gaG>gaA	p.E812E		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	812					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GTGTACTCACCTCCTTCAGCT	0.512																																					p.E812E		.											.	GCN1L1-94	0			c.G2436A						.						166	169	168					12																	120599294		2172	4262	6434	SO:0001630	splice_region_variant	10985	exon22			ACTCACCTCCTTC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.2436+1G>A	12.37:g.120599294C>T		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	119	10	NM_006836	0	0	0	0	0	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			.		0.512	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		Silent	T	120599294	C	T	120599294	5	4	6	1	0	0	0	0	0	0	1	0	6319	695	24	2	5727	2	GCN1L1	12	120599294	Splice_Site	SNP	C	TCGA-A4-7585-01A-11D-2136-08	63100211	120599294	13252601	76	467											
MYO16	23026	hgsc.bcm.edu	37	chr13	109793009	109793009	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcatcgccgcccctgctccaCcgcgcgccggaggacgaggc	5	3	14	19	7	0	0	0	0	0	0	2	3	1	2	6	3	1	2	6	3	0	0	rs141423536	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr13:109793009C>T	ENST00000357550.2	+	31	4424	c.4383C>T	c.(4381-4383)caC>caT	p.H1461H	MYO16_ENST00000356711.2_Silent_p.H1461H	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCCTGCTCCACCGCGCGCCGG	0.761													C|||	89	0.0177716	0.0023	0.0317	5008	,	,		6208	0		0.0527	False		,,,				2504	0.0112				p.H1483H		.											.	MYO16-142	0			c.C4449T						.						1	2	2					13																	109793009		1243	2621	3864	SO:0001819	synonymous_variant	23026	exon32			GCTCCACCGCGCG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4383C>T	13.37:g.109793009C>T		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	6	4	NM_001198950	0	0	0	0	0		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			C|0.974;T|0.026		0.761	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109793009	C	T	109793009	2	4	6	1	0	0	0	0	0	0	0	1	10089	506	18	2		2	MYO16	13	109793009	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08		109793009	5376869	77	468											
NFKBIA	4792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	35871629	35871629	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaactccgtgaactctgActctgtgtcatagctctcct	7	14	8	12	1	4	3	1	3	3	0	6	3	5	3	2	0	3	1	2	0	3	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr14:35871629A>T	ENST00000216797.5	-	5	978	c.877T>A	c.(877-879)Tca>Aca	p.S293T	NFKBIA_ENST00000557389.1_Missense_Mutation_p.S203T|NFKBIA_ENST00000557140.1_Missense_Mutation_p.S250T|NFKBIA_ENST00000557100.1_5'Flank	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	293					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	GTGAACTCTGACTCTGTGTCA	0.562																																					p.S293T		.											.	NFKBIA-721	0			c.T877A						.						88	94	92					14																	35871629		2203	4300	6503	SO:0001583	missense	4792	exon5			ACTCTGACTCTGT		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"Ankyrin repeat domain containing"	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.877T>A	14.37:g.35871629A>T	ENSP00000216797:p.Ser293Thr	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	145	24	NM_020529	0	0	87	130	43	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.759198	0.49468	.	.	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	T;T;T	0.46063	0.88;0.89;1.06	5.9	4.73	0.59995	Ankyrin repeat-containing domain (1);	.	.	.	.	T	0.28400	0.0702	L	0.29908	0.895	0.34457	D	0.701352	B;B	0.32467	0.372;0.145	B;B	0.30316	0.114;0.034	T	0.36915	-0.9728	9	0.35671	T	0.21	0.4354	7.8624	0.29517	0.7845:0.1395:0.0759:0.0	.	250;293	G3V3I4;P25963	.;IKBA_HUMAN	T	293;250;203	ENSP00000216797:S293T;ENSP00000451257:S250T;ENSP00000450514:S203T	ENSP00000216797:S293T	S	-	1	0	NFKBIA	34941380	1.000000	0.71417	0.820000	0.32676	0.916000	0.54674	3.478000	0.53158	1.015000	0.39444	0.533000	0.62120	TCA	.		0.562	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		T	35871629	A	T	35871629	3	4	6	1	0	0	0	0	1	0	0	0	10403	275	10	5	84	5	NFKBIA	14	35871629	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		35871629	71477911	78	469											
SLC39A9	55334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	69866098	69866098	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagggcagaatggatgatttCatctccattagcctgctgtc	9	12	11	9	0	2	2	1	1	1	1	4	4	2	3	2	2	2	2	2	2	2	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr14:69866098C>T	ENST00000336643.5	+	1	690	c.12C>T	c.(10-12)ttC>ttT	p.F4F	ERH_ENST00000216520.6_5'Flank|SLC39A9_ENST00000555245.1_Intron|SLC39A9_ENST00000031146.4_Silent_p.F4F|ERH_ENST00000555373.1_5'Flank|SLC39A9_ENST00000557046.1_Silent_p.F4F|ERH_ENST00000557016.1_5'Flank|SLC39A9_ENST00000556605.1_Silent_p.F4F	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	4					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.F4F(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		TGGATGATTTCATCTCCATTA	0.438																																					p.F4F		.											.	SLC39A9-90	1	Substitution - coding silent(1)	endometrium(1)	c.C12T						.						224	200	208					14																	69866098		2203	4300	6503	SO:0001819	synonymous_variant	55334	exon1			TGATTTCATCTCC		CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"Solute carriers"	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.12C>T	14.37:g.69866098C>T		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	47	13	NM_001252150	0	0	20	35	15	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Silent	SNP	ENST00000336643.5	37	CCDS9795.1																																																																																			.		0.438	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375		T	69866098	C	T	69866098	2	4	6	1	0	0	0	0	0	0	0	1	14657	825	29	2		2	SLC39A9	14	69866098	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	33994469	69866098	37483442	79	470											
ATP10A	57194	broad.mit.edu	37	chr15	25953155	25953155	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggttggtctccaggcgaatgGcagactggaagaggagctcc	9	7	16	9	1	1	2	0	0	1	2	3	5	2	4	2	6	1	3	2	6	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:25953155G>A	ENST00000356865.6	-	12	2654	c.2543C>T	c.(2542-2544)gCc>gTc	p.A848V		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	848					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CAGGCGAATGGCAGACTGGAA	0.537																																					p.A848V													.	ATP10A-139	0			c.C2543T						.						78	69	72					15																	25953155		2203	4300	6503	SO:0001583	missense	57194	exon12			CGAATGGCAGACT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2543C>T	15.37:g.25953155G>A	ENSP00000349325:p.Ala848Val	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_024490	0	0	2	2	0	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.007574	0.93287	.	.	ENSG00000206190	ENST00000356865	T	0.12147	2.71	4.68	4.68	0.58851	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.33990	0.0882	M	0.62723	1.935	0.58432	D	0.999999	D	0.67145	0.996	D	0.72338	0.977	T	0.03130	-1.1069	10	0.25751	T	0.34	-32.1911	17.9745	0.89123	0.0:0.0:1.0:0.0	.	848	O60312	AT10A_HUMAN	V	848	ENSP00000349325:A848V	ENSP00000349325:A848V	A	-	2	0	ATP10A	23504248	1.000000	0.71417	0.504000	0.27639	0.994000	0.84299	9.090000	0.94144	2.311000	0.77944	0.655000	0.94253	GCC	.		0.537	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25953155	G	A	25953155	3	1	6	1	0	0	0	0	1	0	0	0	1117	1203	42	2	1996	2	ATP10A	15	25953155	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08		25953155	76578237	80	471											
SLC28A2	9153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	45561728	45561728	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagggagagaaacagtggAtttctgtaagtgacaatcca	14	10	12	5	0	1	3	0	2	1	1	2	6	2	5	1	2	1	1	1	2	3	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:45561728A>C	ENST00000347644.3	+	14	1626	c.1561A>C	c.(1561-1563)Att>Ctt	p.I521L	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	521					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	GAAACAGTGGATTTCTGTAAG	0.433																																					p.I521L	NSCLC(92;493 1501 26361 28917 47116)	.											.	SLC28A2-94	0			c.A1561C						.						96	90	92					15																	45561728		2198	4298	6496	SO:0001583	missense	9153	exon14			CAGTGGATTTCTG	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"Solute carriers"	11002	protein-coding gene	gene with protein product		606208	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.1561A>C	15.37:g.45561728A>C	ENSP00000315006:p.Ile521Leu	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	6	NM_004212	0	0	0	0	0	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	37	CCDS10121.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.475336	0.63737	.	.	ENSG00000137860	ENST00000347644	T	0.04454	3.62	6.17	3.87	0.44632	Na dependent nucleoside transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.05318	0.0141	N	0.20445	0.575	0.58432	D	0.999999	P	0.39551	0.678	P	0.46339	0.513	T	0.50381	-0.8835	10	0.48119	T	0.1	-12.9596	7.5865	0.27995	0.7845:0.1422:0.0733:0.0	.	521	O43868	S28A2_HUMAN	L	521	ENSP00000315006:I521L	ENSP00000315006:I521L	I	+	1	0	SLC28A2	43349020	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.369000	0.52365	0.559000	0.29153	0.533000	0.62120	ATT	.		0.433	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212		C	45561728	A	C	45561728	3	2	6	1	0	0	0	0	1	0	0	0	14564	333	12	5	1611	5	SLC28A2	15	45561728	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	19608573	45561728	56969664	81	472											
MTFMT	123263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65295424	65295424	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaatgcattgttgcatagcAacagtttttttctgcttctt	8	19	6	8	0	3	0	1	0	2	0	3	0	3	0	0	0	5	6	0	0	3	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:65295424A>C	ENST00000220058.4	-	9	1159	c.1146T>G	c.(1144-1146)gtT>gtG	p.V382V		NM_139242.3	NP_640335.2	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	382						mitochondrion (GO:0005739)	methionyl-tRNA formyltransferase activity (GO:0004479)			endometrium(1)|large_intestine(3)|lung(3)|ovary(3)	10					Tetrahydrofolic acid(DB00116)	GTTGCATAGCAACAGTTTTTT	0.348																																					p.V382V		.											.	MTFMT-24	0			c.T1146G						.						111	98	102					15																	65295424		1825	4084	5909	SO:0001819	synonymous_variant	123263	exon9			CATAGCAACAGTT	AK055688	CCDS45280.1	15q22.31	2006-11-29		2005-08-09		ENSG00000103707			29666	protein-coding gene	gene with protein product		611766				9614118	Standard	NM_139242		Approved	FMT1	uc002aof.4	Q96DP5		ENST00000220058.4:c.1146T>G	15.37:g.65295424A>C		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	56	9	NM_139242	0	0	9	14	5	B7Z734	Silent	SNP	ENST00000220058.4	37	CCDS45280.1																																																																																			.		0.348	MTFMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418155.1	NM_139242		C	65295424	A	C	65295424	2	2	6	1	0	0	0	0	0	0	0	1	9949	117	5	5		5	MTFMT	15	65295424	Silent	SNP	A	TCGA-A4-7585-01A-11D-2136-08	19733696	65295424	37235968	82	473											
C15orf27	123591	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	76484312	76484312	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccgtctccctccgcagtttGagatccggcagctgcgcgcg	4	8	12	17	6	1	1	0	1	1	1	4	2	3	1	4	1	2	4	4	1	0	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:76484312G>A	ENST00000388942.3	+	9	1048	c.772G>A	c.(772-774)Gag>Aag	p.E258K		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	258					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						TCCGCAGTTTGAGATCCGGCA	0.741																																					p.E258K		.											.	C15orf27-90	0			c.G772A						.						8	10	9					15																	76484312		2045	4020	6065	SO:0001583	missense	123591	exon9			CAGTTTGAGATCC	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.772G>A	15.37:g.76484312G>A	ENSP00000373594:p.Glu258Lys	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	49	9	NM_152335	0	0	0	0	0	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818369	0.71028	.	.	ENSG00000169758	ENST00000388942	T	0.47869	0.83	4.58	4.58	0.56647	.	0.123666	0.56097	D	0.000027	T	0.67392	0.2888	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.71674	0.998;0.996	D;D	0.80764	0.994;0.99	T	0.70590	-0.4830	10	0.52906	T	0.07	-5.2743	14.5154	0.67816	0.0:0.0:1.0:0.0	.	222;258	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	K	258	ENSP00000373594:E258K	ENSP00000373594:E258K	E	+	1	0	C15orf27	74271367	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	8.737000	0.91562	2.097000	0.63578	0.491000	0.48974	GAG	.		0.741	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335		A	76484312	G	A	76484312	3	1	6	1	0	0	0	0	1	0	0	0	1792	1291	45	2	802	2	C15orf27	15	76484312	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	11188888	76484312	26047080	83	474											
ANPEP	290	broad.mit.edu	37	chr15	90349269	90349269	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcatctgccaactccccctcGaactcgctgtccatctcata	8	11	4	18	2	3	0	2	0	2	0	8	1	5	0	4	0	3	1	4	0	3	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:90349269G>C	ENST00000300060.6	-	2	859	c.546C>G	c.(544-546)ttC>ttG	p.F182L		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	182	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	ACTCCCCCTCGAACTCGCTGT	0.607																																					p.F182L	NSCLC(30;827 977 2459 19669 26125)												.	ANPEP-94	0			c.C546G						.						91	86	87					15																	90349269		2200	4299	6499	SO:0001583	missense	290	exon2			CCCCTCGAACTCG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.546C>G	15.37:g.90349269G>C	ENSP00000300060:p.Phe182Leu	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	153	5	NM_001150	0	0	439	465	25	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	G	12.48	1.949569	0.34377	.	.	ENSG00000166825	ENST00000300060	T	0.03441	3.93	4.8	0.924	0.19418	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	H	0.98333	4.205	0.29499	N	0.855041	D	0.89917	1.0	D	0.97110	1.0	T	0.19418	-1.0306	10	0.87932	D	0	.	7.4046	0.26983	0.6447:0.0:0.3553:0.0	.	182	P15144	AMPN_HUMAN	L	182	ENSP00000300060:F182L	ENSP00000300060:F182L	F	-	3	2	ANPEP	88150273	0.003000	0.15002	0.035000	0.18076	0.018000	0.09664	0.045000	0.14013	0.310000	0.22990	0.563000	0.77884	TTC	.		0.607	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90349269	G	C	90349269	3	2	6	1	0	0	0	0	1	0	0	0	710	1049	37	4	2437	4	ANPEP	15	90349269	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	13864957	90349269	12182123	84	475											
CIITA	4261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	10992818	10992818	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtgatcggtgagagtaTggagatgccagcagaagttg	12	9	16	4	1	0	5	0	3	0	3	1	7	0	5	1	2	2	3	1	2	3	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:10992818T>C	ENST00000324288.8	+	5	528	c.395T>C	c.(394-396)aTg>aCg	p.M132T	CIITA_ENST00000381835.5_Missense_Mutation_p.M132T|CIITA_ENST00000537380.1_3'UTR	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	132	Asp/Glu-rich (acidic).|Required for acetyltransferase activity.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGTGAGAGTATGGAGATGCCA	0.483			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.M132T		.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA-226	0			c.T395C						.						183	172	176					16																	10992818		2197	4300	6497	SO:0001583	missense	4261	exon5			AGAGTATGGAGAT	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.395T>C	16.37:g.10992818T>C	ENSP00000316328:p.Met132Thr	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	137	15	NM_000246	0	0	11	11	0	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	T	5.450	0.268042	0.10349	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.70749	-0.51;1.78	3.81	2.68	0.31781	.	1.431470	0.05038	N	0.475874	T	0.52224	0.1721	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B	0.30824	0.296;0.01;0.017;0.017;0.052;0.109	B;B;B;B;B;B	0.28849	0.095;0.005;0.014;0.014;0.047;0.021	T	0.44283	-0.9338	10	0.30078	T	0.28	.	5.0256	0.14383	0.0:0.1558:0.0:0.8442	.	132;132;132;132;133;132	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	T	132;132;133;132	ENSP00000316328:M132T;ENSP00000371257:M132T	ENSP00000316328:M132T	M	+	2	0	CIITA	10900319	0.615000	0.27026	0.024000	0.17045	0.006000	0.05464	1.060000	0.30530	0.628000	0.30357	0.455000	0.32223	ATG	.		0.483	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		C	10992818	T	C	10992818	3	2	6	1	0	0	0	0	1	0	0	0	3434	1464	51	3	413	3	CIITA	16	10992818	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08		10992818	79361935	85	476											
ABCC11	85320	hgsc.bcm.edu;broad.mit.edu	37	chr16	48230229	48230229	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgtgagctgatgctccGgcactgggtcagggtagaag	7	9	16	9	1	1	3	1	2	0	1	2	3	2	3	2	3	2	4	2	3	2	1	rs531997909		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:48230229G>A	ENST00000394747.1	-	17	2667	c.2318C>T	c.(2317-2319)cCg>cTg	p.P773L	ABCC11_ENST00000394748.1_Missense_Mutation_p.P773L|ABCC11_ENST00000356608.2_Missense_Mutation_p.P773L|ABCC11_ENST00000353782.5_Missense_Mutation_p.P773L|ABCC11_ENST00000537808.1_Missense_Mutation_p.R741W	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	773					organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CTGATGCTCCGGCACTGGGTC	0.542													G|||	1	0.000199681	8e-04	0	5008	,	,		17131	0		0	False		,,,				2504	0				p.P773L		.											.	ABCC11-95	0			c.C2318T						.						92	67	75					16																	48230229		2201	4300	6501	SO:0001583	missense	85320	exon17			TGCTCCGGCACTG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2318C>T	16.37:g.48230229G>A	ENSP00000378230:p.Pro773Leu	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	52	3	NM_033151	0	0	0	0	0	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.096|8.096	0.775519|0.775519	0.16051|0.16051	.|.	.|.	ENSG00000121270|ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747|ENST00000537808	T;T;T;T|D	0.59083|0.93189	0.29;0.29;0.29;0.29|-3.18	5.24|5.24	-0.454|-0.454	0.12197|0.12197	.|.	1.019920|.	0.07799|.	N|.	0.956214|.	T|T	0.79947|0.79947	0.4534|0.4534	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.71692|0.71692	-0.4516|-0.4516	10|7	0.26408|0.72032	T|D	0.33|0.01	-0.0042|-0.0042	4.1543|4.1543	0.10252|0.10252	0.6596:0.0:0.2017:0.1387|0.6596:0.0:0.2017:0.1387	.|.	773;773|.	Q96J66-2;Q96J66|.	.;ABCCB_HUMAN|.	L|W	773|741	ENSP00000311326:P773L;ENSP00000349017:P773L;ENSP00000378231:P773L;ENSP00000378230:P773L|ENSP00000438530:R741W	ENSP00000311326:P773L|ENSP00000438530:R741W	P|R	-|-	2|1	0|2	ABCC11|ABCC11	46787730|46787730	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.054000|0.054000	0.15201|0.15201	-0.353000|-0.353000	0.07691|0.07691	-0.308000|-0.308000	0.08792|0.08792	-0.794000|-0.794000	0.03295|0.03295	CCG|CGG	.		0.542	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		A	48230229	G	A	48230229	3	1	6	1	0	0	0	0	1	0	0	0	51	1116	39	1	1882	1	ABCC11	16	48230229	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	37237411	48230229	42124524	86	477											
KIAA0174	9798	hgsc.bcm.edu;ucsc.edu	37	chr16	71956520	71956520	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaacggtgccaatgcccatGcccatgcccatgcctatgcc	8	7	10	16	1	0	0	0	0	0	0	0	1	0	1	6	2	7	0	6	2	3	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:71956520G>T	ENST00000378799.6	+	7	1052	c.696G>T	c.(694-696)atG>atT	p.M232I	RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000538850.1_Missense_Mutation_p.M84I|IST1_ENST00000606369.1_Missense_Mutation_p.M84I|IST1_ENST00000544564.1_Missense_Mutation_p.M232I|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000329908.8_Missense_Mutation_p.M232I|IST1_ENST00000378798.5_Missense_Mutation_p.M232I|IST1_ENST00000541571.2_Missense_Mutation_p.M232I|IST1_ENST00000535424.1_Missense_Mutation_p.M245I			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	230	Interaction with VPS37B.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										caatgcccatgcccatgccca	0.493																																					p.M245I		.											.	.	0			c.G735T						.						109	82	91					16																	71956520		2198	4300	6498	SO:0001583	missense	9798	exon8			GCCCATGCCCATG	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"KIAA0174"	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.696G>T	16.37:g.71956520G>T	ENSP00000368076:p.Met232Ile	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	84	13	NM_001270976	0	0	13	53	40	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Missense_Mutation	SNP	ENST00000378799.6	37	CCDS59272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.18|12.18	1.860092|1.860092	0.32884|0.32884	.|.	.|.	ENSG00000182149|ENSG00000182149	ENST00000541848|ENST00000535424;ENST00000378799;ENST00000538963;ENST00000329908;ENST00000538850;ENST00000378798;ENST00000456820	.|.	.|.	.|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.104309	.|0.85682	.|N	.|0.000000	T|T	0.41880|0.41880	0.1178|0.1178	N|N	0.22421|0.22421	0.69|0.69	0.43342|0.43342	D|D	0.995393|0.995393	.|B;B;B	.|0.26400	.|0.005;0.148;0.008	.|B;B;B	.|0.20955	.|0.013;0.032;0.01	T|T	0.27468|0.27468	-1.0073|-1.0073	5|9	.|0.23302	.|T	.|0.38	-12.5172|-12.5172	13.4407|13.4407	0.61112|0.61112	0.0:0.0:0.8434:0.1566|0.0:0.0:0.8434:0.1566	.|.	.|232;232;245	.|P53990-2;P53990-3;A8KAH5	.|.;.;.	F|I	119|245;232;221;232;84;232;170	.|.	.|ENSP00000330408:M232I	C|M	+|+	2|3	0|0	KIAA0174|KIAA0174	70514021|70514021	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	6.357000|6.357000	0.73051|0.73051	2.611000|2.611000	0.88343|0.88343	0.655000|0.655000	0.94253|0.94253	TGC|ATG	.		0.493	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761		T	71956520	G	T	71956520	3	4	6	1	0	0	0	0	1	0	0	0	8179	1319	46	4	718	4	KIAA0174	16	71956520	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	23726291	71956520	18398233	87	478											
GAN	8139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81411103	81411103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cactccttccatccgaccttCgccgtacaggatgtgcagcc	7	9	8	17	3	0	0	0	0	0	0	4	2	3	1	6	1	3	2	6	1	1	3	rs368372086		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:81411103C>T	ENST00000568107.2	+	11	1858	c.1696C>T	c.(1696-1698)Cgc>Tgc	p.R566C		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	566					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				ATCCGACCTTCGCCGTACAGG	0.493																																					p.R566C	GBM(106;1239 1507 7582 9741 33976)	.											.	GAN-92	0			c.C1696T						.	C	CYS/ARG	1,4401	2.1+/-5.4	0,1,2200	237	206	216		1696	5.6	0.9	16		216	0,8600		0,0,4300	no	missense	GAN	NM_022041.3	180	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	566/598	81411103	1,13001	2201	4300	6501	SO:0001583	missense	8139	exon11			GACCTTCGCCGTA	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1696C>T	16.37:g.81411103C>T	ENSP00000476795:p.Arg566Cys	Somatic	261	0		WXS	Illumina HiSeq	Phase_I	359	54	NM_022041	0	0	2	2	0		Missense_Mutation	SNP	ENST00000568107.2	37	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.524137	0.64747	2.27E-4	0.0	ENSG00000127688	ENST00000248272	T	0.76448	-1.02	5.58	5.58	0.84498	.	0.183579	0.47852	D	0.000209	T	0.70064	0.3181	N	0.14661	0.345	0.80722	D	1	D	0.69078	0.997	P	0.47470	0.548	T	0.70103	-0.4964	10	0.29301	T	0.29	.	19.5747	0.95438	0.0:1.0:0.0:0.0	.	566	Q9H2C0	GAN_HUMAN	C	566	ENSP00000248272:R566C	ENSP00000248272:R566C	R	+	1	0	GAN	79968604	1.000000	0.71417	0.950000	0.38849	0.726000	0.41606	4.573000	0.60893	2.631000	0.89168	0.467000	0.42956	CGC	.		0.493	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			T	81411103	C	T	81411103	3	4	6	1	0	0	0	0	1	0	0	0	6252	884	31	1	1738	1	GAN	16	81411103	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	9454583	81411103	8943650	88	479											
HSDL1	83693	hgsc.bcm.edu;broad.mit.edu	37	chr16	84158328	84158328	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaggcatatactgtgcaaaAagaaactaaaaatgaaagag	21	7	8	5	0	1	3	1	1	0	2	1	3	1	3	0	1	3	2	0	1	9	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:84158328A>C	ENST00000219439.4	-	6	1076	c.900T>G	c.(898-900)ctT>ctG	p.L300L	HSDL1_ENST00000434463.3_Silent_p.L245L|HSDL1_ENST00000565275.1_5'Flank	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	300						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						ACTGTGCAAAAAGAAACTAAA	0.433																																					p.L300L		.											.	HSDL1-90	0			c.T900G						.						78	71	73					16																	84158328		2200	4300	6500	SO:0001819	synonymous_variant	83693	exon6			TGCAAAAAGAAAC	AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	16475	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 12C, member 3"					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.900T>G	16.37:g.84158328A>C		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	63	11	NM_031463	0	0	1	1	0	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Silent	SNP	ENST00000219439.4	37	CCDS10942.1																																																																																			.		0.433	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463		C	84158328	A	C	84158328	2	2	6	1	0	0	0	0	0	0	0	1	7414	1	1	5		5	HSDL1	16	84158328	Silent	SNP	A	TCGA-A4-7585-01A-11D-2136-08	2747225	84158328	6196425	89	480											
NLE1	54475	broad.mit.edu	37	chr17	33464163	33464163	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcagttgtgtcccagatccGcacactgccatccttggagc	7	10	10	14	1	0	1	0	0	0	1	3	2	3	2	4	1	3	3	4	1	0	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:33464163G>A	ENST00000442241.4	-	7	724	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	NLE1_ENST00000586869.1_5'UTR|NLE1_ENST00000593176.1_5'UTR|NLE1_ENST00000360831.5_Missense_Mutation_p.R187W	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	229					hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				TCCCAGATCCGCACACTGCCA	0.617																																					p.R229W													.	NLE1-290	0			c.C685T						.						62	54	57					17																	33464163		2203	4300	6503	SO:0001583	missense	54475	exon7			AGATCCGCACACT		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"WD repeat domain containing"	19889	protein-coding gene	gene with protein product	"Notchless gene homolog, (Drosophila)"						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.685C>T	17.37:g.33464163G>A	ENSP00000413572:p.Arg229Trp	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_018096	0	0	9	9	0	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	37	CCDS11291.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848474	0.91277	.	.	ENSG00000073536	ENST00000442241;ENST00000537697	T	0.28454	1.61	4.51	4.51	0.55191	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.56891	0.2016	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.63637	-0.6592	10	0.87932	D	0	-25.4301	14.7766	0.69736	0.0:0.0:1.0:0.0	.	229	Q9NVX2	NLE1_HUMAN	W	229;205	ENSP00000413572:R229W	ENSP00000413572:R229W	R	-	1	2	NLE1	30488276	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.047000	0.76599	2.358000	0.79984	0.591000	0.81541	CGG	.		0.617	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096		A	33464163	G	A	33464163	3	1	6	1	0	0	0	0	1	0	0	0	10486	1086	38	1	800	1	NLE1	17	33464163	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08		33464163	47731047	90	481											
KRT9	3857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39726126	39726126	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctacctccttatgattcttCttgagggccatcagctcctc	6	14	6	15	0	3	2	1	2	2	0	6	2	5	2	5	1	2	1	5	1	2	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:39726126C>A	ENST00000246662.4	-	3	932	c.867G>T	c.(865-867)aaG>aaT	p.K289N	KRT9_ENST00000588431.1_Missense_Mutation_p.K56N	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	289	Coil 1B.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.K289N(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TATGATTCTTCTTGAGGGCCA	0.537																																					p.K289N		.											.	KRT9-92	1	Substitution - Missense(1)	lung(1)	c.G867T						.						100	101	101					17																	39726126		2200	4295	6495	SO:0001583	missense	3857	exon3			ATTCTTCTTGAGG		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.867G>T	17.37:g.39726126C>A	ENSP00000246662:p.Lys289Asn	Somatic	264	0		WXS	Illumina HiSeq	Phase_I	277	60	NM_000226	0	0	0	0	0	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974370	0.53720	.	.	ENSG00000171403	ENST00000246662	D	0.93547	-3.24	4.86	2.84	0.33178	Filament (1);	0.249082	0.20923	N	0.083245	D	0.95940	0.8678	M	0.86805	2.84	0.29942	N	0.821017	D	0.58268	0.982	P	0.59825	0.864	D	0.92785	0.6243	10	0.87932	D	0	.	11.0067	0.47637	0.0:0.8453:0.0:0.1547	.	289	P35527	K1C9_HUMAN	N	289	ENSP00000246662:K289N	ENSP00000246662:K289N	K	-	3	2	KRT9	36979652	1.000000	0.71417	0.925000	0.36789	0.365000	0.29674	1.620000	0.36976	0.452000	0.26830	0.491000	0.48974	AAG	.		0.537	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39726126	C	A	39726126	3	1	6	1	0	0	0	0	1	0	0	0	8522	912	32	4	1024	4	KRT9	17	39726126	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	6261963	39726126	41469084	91	482											
CACNA1G	8913	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	48692731	48692732	+	Frame_Shift_Del	DEL	GC	GC	-																															tgccccatcagaagcccagtGcaaaccttactactccgact																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:48692731_48692732delGC	ENST00000359106.5	+	27	4769_4770	c.4769_4770delGC	c.(4768-4770)tgcfs	p.C1590fs	CACNA1G_ENST00000513689.2_Frame_Shift_Del_p.C1545fs|CACNA1G_ENST00000507336.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000505165.1_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000502264.1_Frame_Shift_Del_p.C1567fs|CACNA1G_ENST00000510115.1_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000515765.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000360761.4_Frame_Shift_Del_p.C1567fs|CACNA1G_ENST00000507896.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000358244.5_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000515165.1_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000352832.5_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000510366.1_Frame_Shift_Del_p.C1538fs|CACNA1G_ENST00000429973.2_Frame_Shift_Del_p.C1572fs|CACNA1G_ENST00000515411.1_Frame_Shift_Del_p.C1572fs|CACNA1G_ENST00000514717.1_Frame_Shift_Del_p.C1533fs|CACNA1G_ENST00000514181.1_Frame_Shift_Del_p.C1572fs|CACNA1G_ENST00000513964.1_Frame_Shift_Del_p.C1545fs|CACNA1G_ENST00000512389.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000354983.4_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000507510.2_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000442258.2_Frame_Shift_Del_p.C1549fs|CACNA1G_ENST00000514079.1_Frame_Shift_Del_p.C1597fs|CACNA1G_ENST00000503485.1_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000507609.1_Frame_Shift_Del_p.C1590fs	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1590					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GAAGCCCAGTGCAAACCTTACT	0.629																																					p.1597_1597del		.											.	CACNA1G-67	0			c.4790_4791del						.																																			SO:0001589	frameshift_variant	8913	exon27			.	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4769_4770delGC	17.37:g.48692731_48692732delGC	ENSP00000352011:p.Cys1590fs	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	75	13	NM_001256325	0	0	0	0	0	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Frame_Shift_Del	DEL	ENST00000359106.5	37	CCDS45730.1																																																																																			.		0.629	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		-	48692732	GC	-	48692731	7	5	6	1	0	1	0	1	0	0	0	0	2550	1319	46	0	5142	0	CACNA1G	17	48692731	Frame_Shift_Del	DEL	GC	TCGA-A4-7585-01A-11D-2136-08	8966605	48692731	32502479	92	483											
PPM1D	8493	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58740446	58740446	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctcagagaattttttaGaggtttcagctgagatagct	10	15	9	7	0	2	3	2	1	1	3	3	5	2	3	1	1	2	3	1	1	3	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:58740446G>T	ENST00000305921.3	+	6	1583	c.1351G>T	c.(1351-1353)Gag>Tag	p.E451*	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	451					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)			GAATTTTTTAGAGGTTTCAGC	0.443											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.E451X		.											.	PPM1D-227	0			c.G1351T						.						100	99	100					17																	58740446		2203	4300	6503	SO:0001587	stop_gained	8493	exon6			TTTTTAGAGGTTT	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.1351G>T	17.37:g.58740446G>T	ENSP00000306682:p.Glu451*	Somatic	101	0	1033	WXS	Illumina HiSeq	Phase_I	142	42	NM_003620	0	0	11	46	35	Q53XP4|Q6P991|Q8IVR6	Nonsense_Mutation	SNP	ENST00000305921.3	37	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	G	39	7.470853	0.98306	.	.	ENSG00000170836	ENST00000305921	.	.	.	6.08	6.08	0.98989	.	0.064947	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-21.5774	13.8168	0.63297	0.0695:0.0:0.9305:0.0	.	.	.	.	X	451	.	ENSP00000306682:E451X	E	+	1	0	PPM1D	56095228	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.119000	0.64679	2.894000	0.99253	0.591000	0.81541	GAG	.		0.443	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		T	58740446	G	T	58740446	4	4	6	1	0	0	0	0	0	1	0	0	12366	943	33	4	1373	4	PPM1D	17	58740446	Nonsense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	10047715	58740446	22454764	93	484											
ABCA8	10351	hgsc.bcm.edu;bcgsc.ca	37	chr17	66928478	66928478	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtcatcaaggccttcatccTtttcctctctcttgtgacat	6	17	5	13	0	5	1	3	1	2	0	8	1	7	1	3	1	0	0	3	1	1	4	rs149928780	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:66928478T>C	ENST00000269080.2	-	6	885	c.748A>G	c.(748-750)Agg>Ggg	p.R250G	ABCA8_ENST00000430352.2_Missense_Mutation_p.R250G|ABCA8_ENST00000586539.1_Missense_Mutation_p.R250G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	250					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GCCTTCATCCTTTTCCTCTCT	0.393													T|||	2	0.000399361	0.0015	0	5008	,	,		20503	0		0	False		,,,				2504	0				p.R250G		.											.	ABCA8-93	0			c.A748G						.	T	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	89	82	84		748	1.2	0	17	dbSNP_134	84	0,8600		0,0,4300	no	missense	ABCA8	NM_007168.2	125	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	250/1582	66928478	1,13005	2203	4300	6503	SO:0001583	missense	10351	exon6			TCATCCTTTTCCT	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.748A>G	17.37:g.66928478T>C	ENSP00000269080:p.Arg250Gly	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	76	5	NM_007168	0	0	1	1	0	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	7.800	0.713528	0.15306	2.27E-4	0.0	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.84070	-1.8;-1.8	4.86	1.22	0.21188	.	0.865701	0.09871	N	0.744923	T	0.76550	0.4003	L	0.55481	1.735	0.09310	N	1	B;B;B;B;B	0.27951	0.195;0.157;0.044;0.109;0.034	B;B;B;B;B	0.29524	0.089;0.103;0.038;0.098;0.044	T	0.65253	-0.6213	10	0.56958	D	0.05	.	3.7768	0.08663	0.3317:0.0923:0.0:0.576	.	189;250;250;250;250	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	250;250;189;250	ENSP00000269080:R250G;ENSP00000402814:R250G	ENSP00000269080:R250G	R	-	1	2	ABCA8	64440073	0.000000	0.05858	0.002000	0.10522	0.197000	0.23852	0.098000	0.15189	0.065000	0.16485	0.460000	0.39030	AGG	T|1.000;C|0.000		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66928478	T	C	66928478	3	2	6	1	0	0	0	0	1	0	0	0	38	1608	56	3	4129	3	ABCA8	17	66928478	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	8188032	66928478	14266732	94	485											
ABCA5	23461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	67304486	67304486	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgaggaccagtactgagcagCctcacatgattttgaacagc	12	9	10	10	0	1	4	1	4	0	0	1	5	1	5	2	1	5	2	2	1	2	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:67304486C>G	ENST00000392676.3	-	5	557	c.493G>C	c.(493-495)Gct>Cct	p.A165P	ABCA5_ENST00000588877.1_Missense_Mutation_p.A165P|ABCA5_ENST00000392677.2_Missense_Mutation_p.A165P			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	165					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TACTGAGCAGCCTCACATGAT	0.378																																					p.A165P		.											.	ABCA5-93	0			c.G493C						.						98	103	101					17																	67304486		2203	4300	6503	SO:0001583	missense	23461	exon4			GAGCAGCCTCACA	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.493G>C	17.37:g.67304486C>G	ENSP00000376443:p.Ala165Pro	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	174	23	NM_018672	0	0	0	1	1	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710325	0.48517	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	T;T	0.39229	1.09;1.09	4.96	4.96	0.65561	.	0.108387	0.40908	D	0.000993	T	0.54727	0.1876	L	0.47190	1.495	0.49483	D	0.999799	D;D	0.63880	0.984;0.993	P;D	0.67725	0.877;0.953	T	0.51276	-0.8726	9	.	.	.	.	13.9115	0.63869	0.1528:0.8472:0.0:0.0	.	165;165	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	P	165	ENSP00000376444:A165P;ENSP00000376443:A165P	.	A	-	1	0	ABCA5	64816081	0.993000	0.37304	0.999000	0.59377	0.987000	0.75469	2.955000	0.49121	2.293000	0.77203	0.585000	0.79938	GCT	.		0.378	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		G	67304486	C	G	67304486	3	3	6	1	0	0	0	0	1	0	0	0	35	739	26	4	4575	4	ABCA5	17	67304486	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	376008	67304486	13890724	95	486											
TNRC6C	57690	broad.mit.edu	37	chr17	76046980	76046980	+	Frame_Shift_Del	DEL	A	A	-																															ttggacacttgggggatgggAaaaaaaatggatctggatgg																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:76046980delA	ENST00000588061.1	+	5	2564	c.1837delA	c.(1837-1839)aaafs	p.K614fs	TNRC6C_ENST00000541771.1_Frame_Shift_Del_p.K614fs|TNRC6C_ENST00000588847.1_Frame_Shift_Del_p.K614fs|TNRC6C_ENST00000335749.4_Frame_Shift_Del_p.K614fs|TNRC6C_ENST00000301624.4_Frame_Shift_Del_p.K614fs|TNRC6C_ENST00000544502.1_Frame_Shift_Del_p.K614fs			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	614	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GGGGGATGGGAAAAAAAATGG	0.522																																					p.K613fs													.	TNRC6C-24	0			c.1837delA						.		,	8,3764		1,6,1879	77	78	78		,	-0.2	0.8	17	dbSNP_130	79	42,7894		10,22,3936	no	frameshift,frameshift	TNRC6C	NM_018996.3,NM_001142640.1	,	11,28,5815	A1A1,A1R,RR		0.5292,0.2121,0.4271	,	,	76046980	50,11658	1966	4142	6108	SO:0001589	frameshift_variant	57690	exon4			GATGGGAAAAAAA	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"Trinucleotide (CAG) repeat containing"	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.1837delA	17.37:g.76046980delA	ENSP00000468647:p.Lys614fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	169	5	NM_018996	0	0	0	0	0	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Frame_Shift_Del	DEL	ENST00000588061.1	37	CCDS45798.1																																																																																			.		0.522	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		-	76046980	A	-	76046980	7	5	6	1	0	1	0	1	0	0	0	0	16374	247	9	0	1839	0	TNRC6C	17	76046980	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08	8742494	76046980	5148230	96	487											
GAA	2548	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	78085893	78085894	+	Frame_Shift_Del	DEL	CC	CC	-																															cctgaccgaagccatcgcctCccacaggtgagggccacgtc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:78085893_78085894delCC	ENST00000302262.3	+	12	1967_1968	c.1748_1749delCC	c.(1747-1749)tccfs	p.S583fs	GAA_ENST00000390015.3_Frame_Shift_Del_p.S583fs	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	583					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	GCCATCGCCTCCCACAGGTGAG	0.649																																					p.583_583del		.											.	GAA-91	0			c.1748_1749del	GRCh37	CM082761	GAA	M		.																																			SO:0001589	frameshift_variant	2548	exon13			.		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"Pompe disease", "glycogen storage disease type II"	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.1748_1749delCC	17.37:g.78085893_78085894delCC	ENSP00000305692:p.Ser583fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	107	20	NM_001079803	0	0	0	0	0	Q09GN4|Q14351|Q16302|Q8IWE7	Frame_Shift_Del	DEL	ENST00000302262.3	37	CCDS32760.1																																																																																			.		0.649	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1			-	78085894	CC	-	78085893	7	5	6	1	0	1	0	1	0	0	0	0	6166	855	30	0	1790	0	GAA	17	78085893	Frame_Shift_Del	DEL	CC	TCGA-A4-7585-01A-11D-2136-08	2038913	78085893	3109317	97	488											
CCDC57	284001	hgsc.bcm.edu	37	chr17	80115741	80115741	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcagccacctgcttccgcagCtccaaaacctccaggtgtac	9	8	7	17	1	1	0	1	0	0	0	4	0	4	0	6	1	5	4	6	1	3	2	rs367918124	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:80115741C>T	ENST00000389641.4	-	14	2160	c.2124G>A	c.(2122-2124)gaG>gaA	p.E708E	CCDC57_ENST00000392343.3_Silent_p.E708E|CCDC57_ENST00000327026.3_5'UTR|RP11-1376P16.1_ENST00000582774.1_RNA|CCDC57_ENST00000392347.1_Silent_p.E708E			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	708										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GCTTCCGCAGCTCCAAAACCT	0.657													C|||	5	0.000998403	0.0038	0	5008	,	,		17781	0		0	False		,,,				2504	0				p.E708E		.											.	CCDC57-24	0			c.G2124A						.	C		8,3916		0,8,1954	24	27	26		2124	2.2	0.6	17		26	0,8292		0,0,4146	no	coding-synonymous	CCDC57	NM_198082.2		0,8,6100	TT,TC,CC		0.0,0.2039,0.0655		708/916	80115741	8,12208	1962	4146	6108	SO:0001819	synonymous_variant	284001	exon14			CCGCAGCTCCAAA	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2124G>A	17.37:g.80115741C>T		Somatic	7	1		WXS	Illumina HiSeq	Phase_I	18	6	NM_198082	0	0	0	4	4	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37		.	.	.	.	.	.	.	.	.	.	C	5.340	0.247999	0.10130	0.002039	0.0	ENSG00000176155	ENST00000419322	.	.	.	3.19	2.15	0.27550	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.33073	D	0.535584	.	.	.	.	.	.	T	0.51973	-0.8637	4	.	.	.	-15.9417	8.1007	0.30854	0.0:0.7494:0.2506:0.0	.	.	.	.	T	54	.	.	A	-	1	0	CCDC57	77709030	0.989000	0.36119	0.584000	0.28653	0.660000	0.38997	0.614000	0.24314	0.612000	0.30071	0.462000	0.41574	GCT	.		0.657	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		T	80115741	C	T	80115741	2	4	6	1	0	0	0	0	0	0	0	1	2833	796	28	2		2	CCDC57	17	80115741	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	2029848	80115741	1079469	98	489											
PTPRS	5802	broad.mit.edu;bcgsc.ca	37	chr19	5231542	5231542	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagggccccgttgtgcgttTccggcggcggcgggcgccaa	3	6	17	15	7	0	0	0	0	0	0	1	0	1	0	5	5	1	2	5	5	1	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr19:5231542T>A	ENST00000587303.1	-	13	2033	c.1934A>T	c.(1933-1935)gAa>gTa	p.E645V	PTPRS_ENST00000262963.6_Missense_Mutation_p.E641V|PTPRS_ENST00000372412.4_Missense_Mutation_p.E646V|PTPRS_ENST00000588552.1_Intron|PTPRS_ENST00000357368.4_Missense_Mutation_p.E645V|PTPRS_ENST00000588012.1_Missense_Mutation_p.E632V|PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000348075.2_Missense_Mutation_p.E632V|PTPRS_ENST00000353284.2_Intron			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	645	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTTGTGCGTTTCCGGCGGCGG	0.662																																					p.E645V													.	PTPRS-357	0			c.A1934T						.						23	21	21					19																	5231542		2202	4297	6499	SO:0001583	missense	5802	exon14			TGCGTTTCCGGCG	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.1934A>T	19.37:g.5231542T>A	ENSP00000467537:p.Glu645Val	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	33	7	NM_002850	0	0	4	6	2	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	t	19.75	3.884856	0.72410	.	.	ENSG00000105426	ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	3.88	3.88	0.44766	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.085998	0.44902	U	0.000401	T	0.62708	0.2450	M	0.81239	2.535	0.80722	D	1	P;P	0.46457	0.878;0.481	P;B	0.48873	0.593;0.41	T	0.70252	-0.4923	10	0.72032	D	0.01	.	12.8515	0.57860	0.0:0.0:0.0:1.0	.	632;645	Q13332-6;Q13332	.;PTPRS_HUMAN	V	646;645;645;645;641;632	ENSP00000361489:E646V;ENSP00000349932:E645V;ENSP00000262963:E641V;ENSP00000269907:E632V	ENSP00000262963:E641V	E	-	2	0	PTPRS	5182542	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.631000	0.67812	1.618000	0.50286	0.449000	0.29647	GAA	.		0.662	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5231542	T	A	5231542	3	1	6	1	0	0	0	0	1	0	0	0	12843	1783	62	5	4012	5	PTPRS	19	5231542	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08		5231542	53897441	99	490											
ZNF681	148213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	23926507	23926507	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttttaggtttgtagagtttCtcaccagtatgaattttctt	8	20	7	6	0	2	2	1	1	2	1	3	2	2	2	1	1	0	4	1	1	4	9			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr19:23926507C>G	ENST00000402377.3	-	4	1986	c.1845G>C	c.(1843-1845)gaG>gaC	p.E615D	ZNF681_ENST00000395385.3_Missense_Mutation_p.E546D	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	615					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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TGTAGAGTTTCTCACCAGTAT	0.333																																					p.E615D		.											.	.	0			c.G1845C						.						60	61	61					19																	23926507		2202	4300	6502	SO:0001583	missense	148213	exon4			GAGTTTCTCACCA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1845G>C	19.37:g.23926507C>G	ENSP00000384000:p.Glu615Asp	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	27	4	NM_138286	0	0	8	8	0	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	8.238	0.806253	0.16467	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.34472	1.36;1.36	1.44	1.44	0.22558	Zinc finger, C2H2 (1);	.	.	.	.	T	0.31327	0.0793	L	0.49350	1.555	0.25356	N	0.988829	B	0.18013	0.025	B	0.17979	0.02	T	0.31447	-0.9943	9	0.62326	D	0.03	.	8.329	0.32175	0.0:1.0:0.0:0.0	.	615	Q96N22	ZN681_HUMAN	D	615;546	ENSP00000384000:E615D;ENSP00000378783:E546D	ENSP00000378783:E546D	E	-	3	2	ZNF681	23718347	0.416000	0.25424	0.017000	0.16124	0.114000	0.19823	0.067000	0.14510	0.754000	0.32968	0.205000	0.17691	GAG	.		0.333	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23926507	C	G	23926507	3	3	6	1	0	0	0	0	1	0	0	0	18120	912	32	4	96	4	ZNF681	19	23926507	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	18694965	23926507	35202476	100	491											
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39960028	39960028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatcatgcccaagcatgAggacctcaaggtgggtgccc	10	6	11	14	0	2	1	2	1	0	0	2	2	2	2	4	3	3	1	4	3	2	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr19:39960028A>G	ENST00000599117.1	+	17	1731	c.1364A>G	c.(1363-1365)gAg>gGg	p.E455G	SUPT5H_ENST00000598725.1_Missense_Mutation_p.E455G|SUPT5H_ENST00000432763.2_Missense_Mutation_p.E455G|SUPT5H_ENST00000359191.6_Missense_Mutation_p.E451G|SUPT5H_ENST00000402194.2_Missense_Mutation_p.E451G			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	455					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCCAAGCATGAGGACCTCAAG	0.592																																					p.E455G		.											.	SUPT5H-94	0			c.A1364G						.						85	67	73					19																	39960028		2203	4300	6503	SO:0001583	missense	6829	exon15			AGCATGAGGACCT	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.1364A>G	19.37:g.39960028A>G	ENSP00000470252:p.Glu455Gly	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_003169	0	0	0	0	0	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.711198	0.89112	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.69637	0.3133	L	0.49455	1.56	0.80722	D	1	D;D;D	0.71674	0.996;0.998;0.993	D;D;D	0.71184	0.919;0.972;0.909	T	0.68565	-0.5375	8	.	.	.	-20.9067	14.8931	0.70623	1.0:0.0:0.0:0.0	.	247;451;455	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	G	455;451;433;455	.	.	E	+	2	0	SUPT5H	44651868	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.040000	0.93783	2.169000	0.68431	0.528000	0.53228	GAG	.		0.592	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		G	39960028	A	G	39960028	3	3	6	1	0	0	0	0	1	0	0	0	15431	304	11	3	1422	3	SUPT5H	19	39960028	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	16033521	39960028	19168955	101	492											
POU2F2	5452	hgsc.bcm.edu	37	chr19	42599440	42599440	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggcgggctcttggtaccaTatgggggctgtagctggccg	5	9	17	10	2	1	0	0	0	1	0	1	0	1	0	2	6	2	5	2	6	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr19:42599440T>C	ENST00000526816.2	-	11	1144	c.1129A>G	c.(1129-1131)Atg>Gtg	p.M377V	POU2F2_ENST00000560398.1_Missense_Mutation_p.M383V|POU2F2_ENST00000533720.1_Missense_Mutation_p.M361V|POU2F2_ENST00000529952.1_Missense_Mutation_p.M377V|POU2F2_ENST00000389341.5_Missense_Mutation_p.M361V|POU2F2_ENST00000560558.1_Missense_Mutation_p.M322V|POU2F2_ENST00000342301.4_Missense_Mutation_p.M377V|POU2F2_ENST00000529067.1_Missense_Mutation_p.M361V			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	377					cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	CTTGGTACCATATGGGGGCTG	0.647																																					p.M377V		.											.	POU2F2-227	0			c.A1129G						.						16	19	18					19																	42599440		2201	4300	6501	SO:0001583	missense	5452	exon11			GTACCATATGGGG		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9213	protein-coding gene	gene with protein product		164176	"POU domain class 2, transcription factor 2"	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.1129A>G	19.37:g.42599440T>C	ENSP00000431603:p.Met377Val	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001207025	0	0	0	0	0	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	10.89	1.479093	0.26511	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;T;D	0.81908	-1.5;-1.54;-1.55;-1.32;-1.5	3.46	2.42	0.29668	.	1.165660	0.06364	N	0.712317	T	0.75591	0.3870	L	0.32530	0.975	0.34537	D	0.709819	B;B;B	0.28082	0.2;0.0;0.024	B;B;B	0.32022	0.139;0.001;0.061	T	0.73375	-0.4002	10	0.87932	D	0	.	4.4556	0.11642	0.1173:0.0:0.4065:0.4761	.	361;377;361	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	V	361;377;377;361;376;361;377	ENSP00000373992:M361V;ENSP00000339369:M377V;ENSP00000437221:M361V;ENSP00000437224:M361V;ENSP00000436988:M377V	ENSP00000292077:M377V	M	-	1	0	POU2F2	47291280	1.000000	0.71417	0.978000	0.43139	0.978000	0.69477	1.793000	0.38764	0.954000	0.37851	0.533000	0.62120	ATG	.		0.647	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			C	42599440	T	C	42599440	3	2	6	1	0	0	0	0	1	0	0	0	12298	1406	49	3	326	3	POU2F2	19	42599440	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	2639412	42599440	16529543	102	493											
SLC23A2	9962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	4855238	4855238	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacagggaacattttgaacAgctgtaacttgtacgcagtc	12	11	9	9	1	1	1	1	1	0	0	2	2	1	2	0	1	5	4	0	1	4	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr20:4855238A>T	ENST00000379333.1	-	10	1321	c.929T>A	c.(928-930)cTg>cAg	p.L310Q	SLC23A2_ENST00000424750.2_Missense_Mutation_p.L196Q|SLC23A2_ENST00000338244.1_Missense_Mutation_p.L310Q|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	310					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CATTTTGAACAGCTGTAACTT	0.383																																					p.L310Q		.											.	SLC23A2-92	0			c.T929A						.						195	187	190					20																	4855238		2203	4300	6503	SO:0001583	missense	9962	exon10			TTGAACAGCTGTA	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"Solute carriers"	10973	protein-coding gene	gene with protein product		603791	"solute carrier family 23 (nucleobase transporters), member 1"	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.929T>A	20.37:g.4855238A>T	ENSP00000368637:p.Leu310Gln	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	181	28	NM_203327	0	0	6	7	1	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	37	CCDS13085.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.811425	0.32053	.	.	ENSG00000089057	ENST00000379333;ENST00000338244;ENST00000424750	T;T;T	0.21543	2.0;2.0;2.0	5.44	5.44	0.79542	.	0.062992	0.64402	D	0.000005	T	0.40694	0.1127	M	0.62088	1.915	0.58432	D	0.999999	D;D;D	0.59767	0.986;0.976;0.976	P;P;P	0.60789	0.876;0.879;0.879	T	0.28996	-1.0026	10	0.87932	D	0	-14.7288	14.3204	0.66482	1.0:0.0:0.0:0.0	.	196;310;310	B4DJZ1;A0MSJ5;Q9UGH3	.;.;S23A2_HUMAN	Q	310;310;196	ENSP00000368637:L310Q;ENSP00000344322:L310Q;ENSP00000406601:L196Q	ENSP00000344322:L310Q	L	-	2	0	SLC23A2	4803238	1.000000	0.71417	0.998000	0.56505	0.004000	0.04260	9.339000	0.96797	2.063000	0.61619	0.533000	0.62120	CTG	.		0.383	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			T	4855238	A	T	4855238	3	4	6	1	0	0	0	0	1	0	0	0	14495	188	7	5	1055	5	SLC23A2	20	4855238	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		4855238	58170282	103	494											
BFSP1	631	hgsc.bcm.edu	37	chr20	17511868	17511869	+	Missense_Mutation	DNP	GC	GC	AA																															ccgccaggctcgttgccccaGcccagccctcgtcggccggg																								rs549462369|rs561046384	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr20:17511868_17511869GC>AA	ENST00000377873.3	-	1	145_146	c.106_107GC>TT	c.(106-108)GCt>TTt	p.A36F	BFSP1_ENST00000473415.1_Intron|BFSP1_ENST00000544874.1_Intron|BFSP1_ENST00000536626.1_Intron|BFSP1_ENST00000377868.2_Intron	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	36	Head.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CGTTGCCCCAGCCCAGCCCTCG	0.782																																					p.A36F		.											.	BFSP1	0			c.G106T						.																																			SO:0001583	missense	631	exon1			CCCCAGCCCAGCC	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"Intermediate filaments type VI, eye lens intermediate filaments"	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.106_107delinsAA	20.37:g.17511868_17511869delinsAA	ENSP00000367104:p.Ala36Phe	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	9	8		0	0	0	0	0	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Missense_Mutation	DNP	ENST00000377873.3	37	CCDS13126.1																																																																																			.		0.782	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195		AA	17511869	GC	AA	17511868	3	1	6	1	0	0	0	0	1	0	0	0	1416	971	34	2	1922	2	BFSP1	20	17511868	Missense_Mutation	DNP	GC	TCGA-A4-7585-01A-11D-2136-08	12656630	17511868	45513652	104	495											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50221537	50221537	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccgactcaaacagcagcagCgccccgtacatgatggtgct	10	7	10	14	3	1	1	1	1	0	0	2	2	2	1	3	1	6	4	3	1	2	1	rs376310810		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr20:50221537C>G	ENST00000338821.5	-	27	3090	c.2826G>C	c.(2824-2826)gcG>gcC	p.A942A	ATP9A_ENST00000402822.1_Silent_p.A821A|ATP9A_ENST00000311637.5_Silent_p.A806A	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	942					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						ACAGCAGCAGCGCCCCGTACA	0.602																																					p.A942A		.											.	ATP9A-94	0			c.G2826C						.						89	62	71					20																	50221537		2203	4300	6503	SO:0001819	synonymous_variant	10079	exon27			CAGCAGCGCCCCG	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.2826G>C	20.37:g.50221537C>G		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_006045	0	0	10	10	0	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			.		0.602	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		G	50221537	C	G	50221537	2	3	6	1	0	0	0	0	0	0	0	1	1199	755	27	4		4	ATP9A	20	50221537	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	32709669	50221537	12803983	105	496											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50224072	50224072	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccactcatccttaccttgatAgatgctaatcaaaacccata	14	11	3	13	0	2	2	2	1	0	1	3	2	3	2	4	0	3	1	4	0	6	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr20:50224072A>G	ENST00000338821.5	-	26	3061	c.2797T>C	c.(2797-2799)Tat>Cat	p.Y933H	ATP9A_ENST00000402822.1_Missense_Mutation_p.Y812H|ATP9A_ENST00000311637.5_Missense_Mutation_p.Y797H	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	933					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTACCTTGATAGATGCTAATC	0.483																																					p.Y933H		.											.	ATP9A-94	0			c.T2797C						.						87	66	73					20																	50224072		2203	4300	6503	SO:0001583	missense	10079	exon26			CTTGATAGATGCT	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"ATPases / P-type"	13540	protein-coding gene	gene with protein product		609126	"ATPase, Class II, type 9A"			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.2797T>C	20.37:g.50224072A>G	ENSP00000342481:p.Tyr933His	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_006045	0	0	0	0	0	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.524609	0.85600	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.74947	-0.89;-0.89;-0.89	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.88629	0.6488	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.75484	0.986;0.986	D	0.91299	0.5065	10	0.87932	D	0	-15.2899	14.9169	0.70805	1.0:0.0:0.0:0.0	.	812;933	O75110-2;O75110	.;ATP9A_HUMAN	H	797;933;812	ENSP00000309086:Y797H;ENSP00000342481:Y933H;ENSP00000385875:Y812H	ENSP00000309086:Y797H	Y	-	1	0	ATP9A	49657479	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.754000	0.91642	1.927000	0.55829	0.528000	0.53228	TAT	.		0.483	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		G	50224072	A	G	50224072	3	3	6	1	0	0	0	0	1	0	0	0	1199	420	15	3	358	3	ATP9A	20	50224072	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	2535	50224072	12801448	106	497											
ITSN1	6453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	35239577	35239577	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtaaagggatgccactctCtagttttatactgaagccta	11	13	9	8	0	1	1	0	1	1	0	2	2	1	2	2	1	3	2	2	1	7	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr21:35239577C>A	ENST00000381318.3	+	33	4403	c.4115C>A	c.(4114-4116)tCt>tAt	p.S1372Y	ITSN1_ENST00000399367.3_Missense_Mutation_p.S1367Y|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000437442.2_Missense_Mutation_p.S1367Y|ITSN1_ENST00000381285.4_Missense_Mutation_p.S1372Y|ITSN1_ENST00000399326.3_3'UTR	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1372	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						ATGCCACTCTCTAGTTTTATA	0.393																																					p.S1372Y		.											.	ITSN1-94	0			c.C4115A						.						151	144	146					21																	35239577		2203	4300	6503	SO:0001583	missense	6453	exon33			CACTCTCTAGTTT	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "EF-hand domain containing"	6183	protein-coding gene	gene with protein product	"SH3 domain protein-1A", "human intersectin-SH3 domain-containing protein SH3P17", "Src homology 3 domain-containing protein", "intersectin 1 short form variant, 11", "intersectin 1 short form variant 3", "intersectin short variant 12"	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4115C>A	21.37:g.35239577C>A	ENSP00000370719:p.Ser1372Tyr	Somatic	119	1		WXS	Illumina HiSeq	Phase_I	102	21	NM_003024	0	0	2	2	0	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756394	0.89843	.	.	ENSG00000205726	ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.51	5.51	0.81932	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.78654	0.4317	M	0.64630	1.985	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.983	T	0.79598	-0.1737	10	0.87932	D	0	.	19.7837	0.96428	0.0:1.0:0.0:0.0	.	1367;1367;1372	A8CTY3;A8CTX8;Q15811	.;.;ITSN1_HUMAN	Y	1372;1372;1301;1367;1367	ENSP00000370719:S1372Y;ENSP00000370685:S1372Y;ENSP00000382301:S1367Y;ENSP00000387377:S1367Y	ENSP00000370685:S1372Y	S	+	2	0	ITSN1	34161447	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	7.396000	0.79891	2.738000	0.93877	0.655000	0.94253	TCT	.		0.393	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		A	35239577	C	A	35239577	3	1	6	1	0	0	0	0	1	0	0	0	7947	913	32	4	4247	4	ITSN1	21	35239577	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		35239577	12890318	107	498											
MYO18B	84700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	26423002	26423002	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcagttcctgcgagtccctCttagaatccagaccgagcat	9	11	8	13	2	2	2	1	0	1	2	5	4	5	2	4	0	2	2	4	0	2	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr22:26423002C>G	ENST00000407587.2	+	43	7234	c.7065C>G	c.(7063-7065)ctC>ctG	p.L2355L	MYO18B_ENST00000335473.7_Silent_p.L2354L|MYO18B_ENST00000536101.1_Silent_p.L2354L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2354						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GCGAGTCCCTCTTAGAATCCA	0.572																																					p.L2354L		.											.	MYO18B-142	0			c.C7062G						.						86	94	91					22																	26423002		1936	4137	6073	SO:0001819	synonymous_variant	84700	exon43			GTCCCTCTTAGAA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7065C>G	22.37:g.26423002C>G		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	200	48	NM_032608	0	0	0	0	0	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	C	3.671	-0.067510	0.07273	.	.	ENSG00000133454	ENST00000543971	.	.	.	4.89	-0.276	0.12902	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.31595	N	0.653425	.	.	.	.	.	.	T	0.47100	-0.9143	4	.	.	.	.	8.3531	0.32314	0.0:0.4167:0.4883:0.095	.	.	.	.	C	304	.	.	S	+	2	0	MYO18B	24753002	0.045000	0.20229	0.019000	0.16419	0.647000	0.38526	-0.357000	0.07651	-0.215000	0.10063	0.462000	0.41574	TCT	.		0.572	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26423002	C	G	26423002	2	3	6	1	0	0	0	0	0	0	0	1	10091	900	32	4		4	MYO18B	22	26423002	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08		26423002	24881564	108	499											
PKDREJ	10343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46653660	46653660	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcttataagtaaatccatTggtactctcatctatagcct	12	14	6	9	0	2	0	1	0	2	0	4	0	3	0	2	2	2	3	2	2	7	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr22:46653660T>G	ENST00000253255.5	-	1	5559	c.5560A>C	c.(5560-5562)Aat>Cat	p.N1854H		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1854					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		GTAAATCCATTGGTACTCTCA	0.383																																					p.N1854H		.											.	PKDREJ-156	0			c.A5560C						.						133	136	135					22																	46653660		2203	4300	6503	SO:0001583	missense	10343	exon1			ATCCATTGGTACT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5560A>C	22.37:g.46653660T>G	ENSP00000253255:p.Asn1854His	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	137	34	NM_006071	0	0	0	0	0	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	4.903	0.167837	0.09339	.	.	ENSG00000130943	ENST00000253255	T	0.70045	-0.45	4.51	-2.95	0.05564	Polycystin cation channel, PKD1/PKD2 (1);	1.774300	0.02687	N	0.110187	T	0.44371	0.1290	N	0.11560	0.145	0.09310	N	1	B	0.12013	0.005	B	0.15052	0.012	T	0.20940	-1.0260	10	0.30078	T	0.28	-0.4113	5.5709	0.17196	0.0:0.3289:0.2649:0.4062	.	1854	Q9NTG1	PKDRE_HUMAN	H	1854	ENSP00000253255:N1854H	ENSP00000253255:N1854H	N	-	1	0	PKDREJ	45032324	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.516000	0.06282	-0.535000	0.06307	0.374000	0.22700	AAT	.		0.383	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		G	46653660	T	G	46653660	3	3	6	1	0	0	0	0	1	0	0	0	11996	1812	63	5	1205	5	PKDREJ	22	46653660	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	20230658	46653660	4650906	109	500											
SAPS2	9701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50878437	50878437	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccggtggacacagaatgcaGccatgctgagggcagccgga	10	5	15	11	2	0	2	0	1	0	1	1	4	1	4	3	4	4	3	3	4	1	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr22:50878437G>T	ENST00000216061.5	+	22	2703	c.2333G>T	c.(2332-2334)aGc>aTc	p.S778I	PPP6R2_ENST00000395744.3_Missense_Mutation_p.S751I|PPP6R2_ENST00000395741.3_Missense_Mutation_p.S752I|PPP6R2_ENST00000359139.3_Missense_Mutation_p.S752I			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	778						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						ACAGAATGCAGCCATGCTGAG	0.642																																					p.S778I		.											.	PPP6R2-92	0			c.G2333T						.						42	42	42					22																	50878437		2203	4300	6503	SO:0001583	missense	9701	exon21			AATGCAGCCATGC	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	19253	protein-coding gene	gene with protein product		610877	"KIAA0685", "SAPS domain family, member 2"	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2333G>T	22.37:g.50878437G>T	ENSP00000216061:p.Ser778Ile	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	69	13	NM_001242898	0	0	32	44	12	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	37		.	.	.	.	.	.	.	.	.	.	G	16.34	3.095777	0.56075	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.84	2.68	0.31781	.	0.269718	0.36628	N	0.002493	T	0.63153	0.2487	M	0.70275	2.135	0.09310	N	1	D;D;D;D;D;D	0.71674	0.993;0.992;0.986;0.998;0.996;0.998	P;D;P;D;D;D	0.70716	0.877;0.917;0.828;0.956;0.917;0.97	T	0.55296	-0.8163	10	0.72032	D	0.01	-11.7634	10.2693	0.43473	0.0:0.1469:0.7006:0.1524	.	311;778;778;752;751;752	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	I	752;752;751;778	ENSP00000352051:S752I;ENSP00000379090:S752I;ENSP00000379093:S751I;ENSP00000216061:S778I	ENSP00000216061:S778I	S	+	2	0	PPP6R2	49225303	0.020000	0.18652	0.001000	0.08648	0.015000	0.08874	1.601000	0.36773	0.523000	0.28482	0.561000	0.74099	AGC	.		0.642	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		T	50878437	G	T	50878437	3	4	6	1	0	0	0	0	1	0	0	0	13869	971	34	4	2322	4	SAPS2	22	50878437	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	4224777	50878437	426129	110	501											
PTCHD1	139411	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	23411958	23411959	+	Frame_Shift_Ins	INS	-	-	G																															tgctccaatgttatccacatINSttgttctgggcaaggatttc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:23411958_23411959insG	ENST00000379361.4	+	3	3183_3184	c.2323_2324insG	c.(2323-2325)tttfs	p.F775fs		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	775					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GTTATCCACATTTGTTCTGGGC	0.371																																					p.F775fs		.											.	PTCHD1-135	0			c.2323_2324insG						.																																			SO:0001589	frameshift_variant	139411	exon3			.	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	Exception_encountered	X.37:g.23411958_23411959insG	ENSP00000368666:p.Phe775fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	44	19	NM_173495	0	0	0	0	0	B4DQH0|Q0IJ60|Q6P6B8	Frame_Shift_Ins	INS	ENST00000379361.4	37	CCDS35215.2																																																																																			.		0.371	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		G	23411959	-	G	23411958	7	5	6	1	0	1	1	0	0	0	0	0	12761	1493	52	0	2333	0	PTCHD1	23	23411958	Frame_Shift_Ins	INS	-	TCGA-A4-7585-01A-11D-2136-08		23411958	131858602	111	502											
MAGEB4	4115	hgsc.bcm.edu	37	chrX	30260477	30260477	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctgctgctgcagctatGtcatgcactggatctgataa	9	12	9	11	0	3	1	1	1	2	0	3	2	3	2	1	1	5	5	1	1	2	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:30260477G>C	ENST00000378982.2	+	1	421	c.225G>C	c.(223-225)atG>atC	p.M75I	MAGEB1_ENST00000397550.1_5'Flank|MAGEB1_ENST00000378981.3_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	75										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						CTGCAGCTATGTCATGCACTG	0.527																																					p.M75I		.											.	MAGEB4-131	0			c.G225C						.						55	47	50					X																	30260477		2202	4300	6502	SO:0001583	missense	4115	exon1			AGCTATGTCATGC		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.225G>C	X.37:g.30260477G>C	ENSP00000368266:p.Met75Ile	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_002367	0	0	0	0	0	B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	37	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	G	6.088	0.384441	0.11524	.	.	ENSG00000120289	ENST00000378982	T	0.03580	3.88	3.13	0.709	0.18150	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.02455	0.0075	N	0.19112	0.55	0.09310	N	1	B	0.16802	0.019	B	0.20577	0.03	T	0.46665	-0.9175	9	0.36615	T	0.2	.	3.0253	0.06088	0.0:0.1527:0.2745:0.5729	.	75	O15481	MAGB4_HUMAN	I	75	ENSP00000368266:M75I	ENSP00000368266:M75I	M	+	3	0	MAGEB4	30170398	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-0.052000	0.11865	0.045000	0.15804	-0.490000	0.04691	ATG	.		0.527	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		C	30260477	G	C	30260477	3	2	6	1	0	0	0	0	1	0	0	0	9203	1377	48	4	227	4	MAGEB4	23	30260477	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	6848519	30260477	125010083	112	503											
SMC1A	8243	broad.mit.edu;bcgsc.ca	37	chrX	53442034	53442036	+	In_Frame_Del	DEL	ATC	ATC	-																															tgcccacaggagctccatggAtcaggtcccgcagggtcttt																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:53442034_53442036delATC	ENST00000322213.4	-	2	319_321	c.192_194delGAT	c.(190-195)ctgatc>ctc	p.I65del	SMC1A_ENST00000375340.6_In_Frame_Del_p.I65del	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	65					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						AGCTCCATGGATCAGGTCCCGCA	0.552																																					p.64_65del													.	SMC1A-232	0			c.192_194del						.																																			SO:0001651	inframe_deletion	8243	exon2			CCATGGATCAGGT	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.192_194delGAT	X.37:g.53442034_53442036delATC	ENSP00000323421:p.Ile65del	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	27	8	NM_006306	0	0	0	0	0	O14995|Q16351|Q2M228	In_Frame_Del	DEL	ENST00000322213.4	37	CCDS14352.1																																																																																			.		0.552	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		-	53442036	ATC	-	53442034	7	5	6	1	0	1	0	1	0	0	0	0	14813	333	12	0	3603	0	SMC1A	23	53442034	In_Frame_Del	DEL	ATC	TCGA-A4-7585-01A-11D-2136-08	23181557	53442034	101828526	113	504											
DACH2	117154	hgsc.bcm.edu	37	chrX	86087132	86087132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtaactattactgtttagaaAtggcacaacagttgtattca	14	14	7	6	0	1	1	1	0	0	1	1	1	1	1	0	1	3	5	0	1	7	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:86087132A>G	ENST00000373125.4	+	12	1774	c.1774A>G	c.(1774-1776)Atg>Gtg	p.M592V	DACH2_ENST00000510272.1_Missense_Mutation_p.M373V|DACH2_ENST00000373131.1_3'UTR|DACH2_ENST00000508860.1_Missense_Mutation_p.M425V	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	592					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						CTGTTTAGAAATGGCACAACA	0.338																																					p.M592V		.											.	DACH2-136	0			c.A1774G						.						97	87	90					X																	86087132		2203	4300	6503	SO:0001583	missense	117154	exon12			TTAGAAATGGCAC	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"dachshund homolog 2 (Drosophila)"				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1774A>G	X.37:g.86087132A>G	ENSP00000362217:p.Met592Val	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_053281	0	0	0	0	0	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	A	9.414	1.081366	0.20309	.	.	ENSG00000126733	ENST00000344497;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297	D	0.81996	-1.56	4.52	3.1	0.35709	.	0.202921	0.32952	N	0.005443	T	0.66665	0.2812	N	0.14661	0.345	0.23376	N	0.997808	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.54715	-0.8252	10	0.31617	T	0.26	.	9.0231	0.36213	0.8892:0.0:0.1108:0.0	.	458;592	Q1RMF5;Q96NX9	.;DACH2_HUMAN	V	592;592;425;373;425	ENSP00000362217:M592V	ENSP00000345134:M592V	M	+	1	0	DACH2	85973788	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.642000	0.54367	1.469000	0.48083	0.356000	0.21956	ATG	.		0.338	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		G	86087132	A	G	86087132	3	3	6	1	0	0	0	0	1	0	0	0	4227	101	4	3	1829	3	DACH2	23	86087132	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	32645098	86087132	69183428	114	505											
ARHGEF6	9459	broad.mit.edu	37	chrX	135754263	135754263	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ggagtaggacttgtggaatgGaatcttttcgagtacctaca	11	12	12	6	1	1	0	0	0	1	0	2	5	1	4	1	4	2	2	1	4	5	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:135754263G>C	ENST00000250617.6	-	20	3256	c.2051C>G	c.(2050-2052)tCc>tGc	p.S684C	ARHGEF6_ENST00000370620.1_Missense_Mutation_p.S530C|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.S530C|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.S557C	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	684					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TTGTGGAATGGAATCTTTTCG	0.448																																					p.S684C													.	ARHGEF6-227	0			c.C2051G						.						188	163	172					X																	135754263		2203	4300	6503	SO:0001583	missense	9459	exon20			GGAATGGAATCTT	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.2051C>G	X.37:g.135754263G>C	ENSP00000250617:p.Ser684Cys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	94	4	NM_004840	0	0	13	13	0	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	G	9.961	1.222904	0.22457	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.55234	0.53;0.64;0.64;0.53	5.84	5.84	0.93424	.	0.047019	0.85682	D	0.000000	T	0.43299	0.1241	N	0.20401	0.57	0.39802	D	0.972583	B;B	0.15719	0.014;0.012	B;B	0.18561	0.022;0.013	T	0.29761	-1.0001	10	0.49607	T	0.09	.	19.1327	0.93414	0.0:0.0:1.0:0.0	.	557;684	B7Z3C7;Q15052	.;ARHG6_HUMAN	C	684;530;530;530;557	ENSP00000250617:S684C;ENSP00000359654:S530C;ENSP00000359656:S530C;ENSP00000439483:S557C	ENSP00000250617:S684C	S	-	2	0	ARHGEF6	135581929	1.000000	0.71417	0.964000	0.40570	0.111000	0.19643	5.043000	0.64208	2.469000	0.83416	0.600000	0.82982	TCC	.		0.448	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		C	135754263	G	C	135754263	3	2	6	1	0	0	0	0	1	0	0	0	910	1174	41	4	291	4	ARHGEF6	23	135754263	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	49667131	135754263	19516297	115	506											
FMR1	2332	hgsc.bcm.edu;bcgsc.ca	37	chrX	147011651	147011651	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatttaaatcatttagtccaTcaatgaagtcacctcaaagc	16	12	4	9	0	4	1	4	1	0	0	5	1	5	1	2	0	1	0	2	0	7	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:147011651T>A	ENST00000370475.4	+	7	646	c.518T>A	c.(517-519)aTc>aAc	p.I173N	FMR1_ENST00000370470.1_Missense_Mutation_p.I173N|FMR1_ENST00000370471.3_Missense_Mutation_p.I173N|FMR1_ENST00000439526.2_Missense_Mutation_p.I173N|FMR1_ENST00000440235.2_5'Flank|FMR1_ENST00000218200.8_Missense_Mutation_p.I173N|FMR1_ENST00000370477.1_Missense_Mutation_p.I173N|FMR1_ENST00000334557.6_Missense_Mutation_p.I173N	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	173					central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					ATTTAGTCCATCAATGAAGTC	0.353									Fragile X syndrome																												p.I173N		.											.	FMR1-133	0			c.T518A						.						116	99	105					X																	147011651		2203	4300	6503	SO:0001583	missense	2332	exon7	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	AGTCCATCAATGA	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"premature ovarian failure 1"	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.518T>A	X.37:g.147011651T>A	ENSP00000359506:p.Ile173Asn	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	47	4	NM_002024	0	0	0	0	0	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	37	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	T	7.528	0.658159	0.14645	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.56103	1.25;0.48;1.26;1.26;1.56;1.27;1.28	5.12	5.12	0.69794	.	0.053956	0.85682	D	0.000000	T	0.40119	0.1104	N	0.02011	-0.69	0.80722	D	1	B;P;B;D;D	0.62365	0.0;0.88;0.007;0.991;0.98	B;B;B;P;P	0.59889	0.001;0.296;0.008;0.865;0.805	T	0.45760	-0.9239	10	0.17832	T	0.49	-24.9991	13.3209	0.60432	0.0:0.0:0.0:1.0	.	173;173;89;173;173	Q8IXW7;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	N	173	ENSP00000218200:I173N;ENSP00000359502:I173N;ENSP00000359508:I173N;ENSP00000359506:I173N;ENSP00000355115:I173N;ENSP00000395923:I173N;ENSP00000359501:I173N	ENSP00000218200:I173N	I	+	2	0	FMR1	146819343	1.000000	0.71417	0.999000	0.59377	0.830000	0.47004	6.149000	0.71795	1.808000	0.52836	0.430000	0.28490	ATC	.		0.353	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		A	147011651	T	A	147011651	3	1	6	1	0	0	0	0	1	0	0	0	5979	1435	50	5	544	5	FMR1	23	147011651	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	11257388	147011651	8258909	116	507											
TMEM200B	399474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	29447533	29447533	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgagctgctggggccccaaGgaggagctccccaaggccca	8	3	14	16	1	0	0	0	0	0	0	1	3	1	2	6	5	3	3	6	5	2	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:29447533G>A	ENST00000420504.2	-	2	965	c.808C>T	c.(808-810)Ctt>Ttt	p.L270F	TMEM200B_ENST00000521452.1_Missense_Mutation_p.L270F	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	270						integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		GGGGCCCCAAGGAGGAGCTCC	0.622																																					p.L270F		.											.	TMEM200B-68	0			c.C808T						.						23	25	25					1																	29447533		2202	4300	6502	SO:0001583	missense	399474	exon2			CCCCAAGGAGGAG		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.808C>T	1.37:g.29447533G>A	ENSP00000428544:p.Leu270Phe	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_001171868	0	0	4	11	7	Q6P2G8|Q6P2Q5	Missense_Mutation	SNP	ENST00000420504.2	37	CCDS30658.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565457	0.65651	.	.	ENSG00000253304	ENST00000521452;ENST00000420504	.	.	.	4.15	4.15	0.48705	.	0.000000	0.35903	U	0.002907	T	0.64681	0.2620	L	0.27053	0.805	0.35733	D	0.818101	D	0.89917	1.0	D	0.80764	0.994	T	0.75133	-0.3425	9	0.87932	D	0	.	15.9517	0.79843	0.0:0.0:1.0:0.0	.	270	Q69YZ2	T200B_HUMAN	F	270	.	ENSP00000428544:L270F	L	-	1	0	TMEM200B	29320120	0.952000	0.32445	1.000000	0.80357	0.996000	0.88848	2.717000	0.47227	2.288000	0.76882	0.655000	0.94253	CTT	.		0.622	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682		A	29447533	G	A	29447533	3	1	7	1	0	0	0	0	1	0	0	0	16156	1000	35	2	119	2	TMEM200B	1	29447533	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		29447533	219803088	1	508											
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94548962	94548962	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctccccaagatctcagattGataccttgagaacggctgtc	10	10	8	13	1	1	4	1	2	1	3	4	5	2	4	4	1	2	1	4	1	3	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:94548962G>A	ENST00000370225.3	-	7	890	c.804C>T	c.(802-804)atC>atT	p.I268I	ABCA4_ENST00000535735.1_Silent_p.I268I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	268					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		ATCTCAGATTGATACCTTGAG	0.348																																					p.I268I		.											.	ABCA4-162	0			c.C804T						.						188	206	200					1																	94548962		2203	4300	6503	SO:0001819	synonymous_variant	24	exon7			CAGATTGATACCT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.804C>T	1.37:g.94548962G>A		Somatic	393	1		WXS	Illumina HiSeq	Phase_I	257	119	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			.		0.348	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94548962	G	A	94548962	2	1	7	1	0	0	0	0	0	0	0	1	34	1280	45	2		2	ABCA4	1	94548962	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08	65101429	94548962	154701659	2	509											
PTPN22	26191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	114402065	114402065	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtctgccttgtacttggtAgattgccttttcagcttctg	4	19	9	9	0	3	1	1	0	2	1	3	1	3	1	2	1	4	3	2	1	2	9			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:114402065A>G	ENST00000359785.5	-	2	240	c.105T>C	c.(103-105)tcT>tcC	p.S35S	PTPN22_ENST00000534519.1_5'UTR|PTPN22_ENST00000538253.1_5'UTR|PTPN22_ENST00000528414.1_Silent_p.S35S|PTPN22_ENST00000460620.1_Silent_p.S35S|AP4B1-AS1_ENST00000419536.1_RNA|PTPN22_ENST00000525799.1_Silent_p.S35S|PTPN22_ENST00000420377.2_Silent_p.S35S	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	35	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTACTTGGTAGATTGCCTTT	0.373																																					p.S35S		.											.	PTPN22-227	0			c.T105C						.						151	151	151					1																	114402065		2203	4300	6503	SO:0001819	synonymous_variant	26191	exon2			CTTGGTAGATTGC	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.105T>C	1.37:g.114402065A>G		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	97	46	NM_001193431	0	0	0	0	0	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Silent	SNP	ENST00000359785.5	37	CCDS863.1																																																																																			.		0.373	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		G	114402065	A	G	114402065	2	3	7	1	0	0	0	0	0	0	0	1	12819	407	15	3		3	PTPN22	1	114402065	Silent	SNP	A	TCGA-A4-7732-01A-11D-2136-08	19853103	114402065	134848556	3	510											
CRNN	49860	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	152382377	152382391	+	In_Frame_Del	DEL	TCAGGGTTGCTCACT	TCAGGGTTGCTCACT	-																															ccggtactgtctctcctgccTcagggttgctcacttgcatc																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	TCAGGGTTGCTCACT	TCAGGGTTGCTCACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:152382377_152382391delTCAGGGTTGCTCACT	ENST00000271835.3	-	3	1229_1243	c.1167_1181delAGTGAGCAACCCTGA	c.(1165-1182)caagtgagcaaccctgag>cag	p.VSNPE390del	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	390					response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTCCTGCCTCAGGGTTGCTCACTTGCATCCATC	0.595																																					p.389_394del		.											.	CRNN-93	0			c.1167_1181del						.																																			SO:0001651	inframe_deletion	49860	exon3			.	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"EF-hand domain containing"	1230	protein-coding gene	gene with protein product		611312	"chromosome 1 open reading frame 10"	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.1167_1181delAGTGAGCAACCCTGA	1.37:g.152382377_152382391delTCAGGGTTGCTCACT	ENSP00000271835:p.Val390_Glu394del	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	73	23	NM_016190	0	0	0	0	0	B2RE60|Q8N613	In_Frame_Del	DEL	ENST00000271835.3	37	CCDS1010.1																																																																																			.		0.595	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		-	152382391	TCAGGGTTGCTCACT	-	152382377	7	5	7	1	0	1	0	1	0	0	0	0	3898	1551	54	0	310	0	CRNN	1	152382377	In_Frame_Del	DEL	TCAGGGTTGCTCACT	TCGA-A4-7732-01A-11D-2136-08	37980312	152382377	96868244	4	511											
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213244385	213244385	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccagaggatgtccaggaggTaacatttatatgaagatttt	13	13	10	5	0	0	3	0	1	0	2	2	5	2	5	2	3	1	1	2	3	4	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:213244385T>C	ENST00000366960.3	+	2	291		c.e2+2		RPS6KC1_ENST00000366959.3_Intron|RPS6KC1_ENST00000543470.1_Splice_Site|RPS6KC1_ENST00000543354.1_Intron	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1						signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GTCCAGGAGGTAACATTTATA	0.259																																					.		.											.	RPS6KC1-417	0			c.141+2T>C						.						43	44	44					1																	213244385		2197	4300	6497	SO:0001630	splice_region_variant	26750	exon2			AGGAGGTAACATT	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.141+2T>C	1.37:g.213244385T>C		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	11	2	NM_012424	0	0	0	0	0	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Splice_Site	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.471757	0.84533	.	.	ENSG00000136643	ENST00000366960	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3608	0.66771	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPS6KC1	211311008	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.630000	0.74272	2.061000	0.61500	0.528000	0.53228	.	.		0.259	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	Intron	C	213244385	T	C	213244385	5	2	7	1	0	0	0	0	0	0	1	0	13690	1652	57	3	149	3	RPS6KC1	1	213244385	Splice_Site	SNP	T	TCGA-A4-7732-01A-11D-2136-08	60862008	213244385	36006236	5	512											
CABC1	56997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	227174187	227174187	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacttggatgccatcctcAtcctgggggaggccttcgcc	5	9	11	16	1	1	0	1	0	0	0	4	2	3	2	6	4	1	0	6	4	0	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:227174187A>G	ENST00000366779.1	+	20	4464	c.1693A>G	c.(1693-1695)Atc>Gtc	p.I565V	ADCK3_ENST00000458507.2_Missense_Mutation_p.I286V|ADCK3_ENST00000433743.2_Missense_Mutation_p.I239V|ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000366778.1_Missense_Mutation_p.I513V|ADCK3_ENST00000366777.3_Missense_Mutation_p.I565V			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	565					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						TGCCATCCTCATCCTGGGGGA	0.592																																					p.I565V		.											.	ADCK3-361	0			c.A1693G						.						89	90	90					1																	227174187		2203	4300	6503	SO:0001583	missense	56997	exon15			ATCCTCATCCTGG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"coenzyme Q8 homolog (yeast)"	606980	"chaperone-ABC1 (activity of bc1 complex, S.pombe)-like", "chaperone, ABC1 activity of bc1 complex like (S. pombe)", "chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.1693A>G	1.37:g.227174187A>G	ENSP00000355741:p.Ile565Val	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	97	45	NM_020247	0	0	12	30	18	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Missense_Mutation	SNP	ENST00000366779.1	37	CCDS1557.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.198951	0.58126	.	.	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000458507;ENST00000366775;ENST00000405743;ENST00000433743	T;T;T;T;T;T;T	0.74737	-0.76;-0.73;-0.76;-0.87;-0.43;-0.83;-0.71	5.87	5.87	0.94306	.	0.044860	0.85682	D	0.000000	T	0.71117	0.3302	L	0.60012	1.86	0.80722	D	1	B;B	0.20550	0.001;0.046	B;B	0.19148	0.01;0.024	T	0.66101	-0.6007	10	0.24483	T	0.36	-21.7545	16.2688	0.82603	1.0:0.0:0.0:0.0	.	239;565	E7EVZ8;Q8NI60	.;ADCK3_HUMAN	V	565;513;565;490;286;410;516;239	ENSP00000355741:I565V;ENSP00000355740:I513V;ENSP00000355739:I565V;ENSP00000355738:I490V;ENSP00000403704:I286V;ENSP00000355737:I410V;ENSP00000404550:I239V	ENSP00000355737:I410V	I	+	1	0	ADCK3	225240810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.289000	0.96061	2.244000	0.73946	0.533000	0.62120	ATC	.		0.592	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247		G	227174187	A	G	227174187	3	3	7	1	0	0	0	0	1	0	0	0	2533	217	8	3	1747	3	CABC1	1	227174187	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	13929802	227174187	22076434	6	513											
PCNXL2	80003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	233134020	233134020	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttctctgtgtcccttcacagGatgacaccccgtgctgagca	7	11	9	14	1	2	2	1	2	1	0	4	3	3	3	3	1	2	2	3	1	0	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:233134020G>A	ENST00000258229.9	-	32	6002	c.5768C>T	c.(5767-5769)tCc>tTc	p.S1923F	PCNXL2_ENST00000344698.2_Missense_Mutation_p.S575F	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1923						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CCCTTCACAGGATGACACCCC	0.592																																					p.S1923F		.											.	PCNXL2-91	0			c.C5768T						.						43	46	45					1																	233134020		2040	4195	6235	SO:0001583	missense	80003	exon32			TCACAGGATGACA	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5768C>T	1.37:g.233134020G>A	ENSP00000258229:p.Ser1923Phe	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	18	9	NM_014801	0	0	8	10	2	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.779932	0.31502	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.24723	1.84;3.01	4.86	4.86	0.63082	.	1.450940	0.04437	N	0.370187	T	0.23410	0.0566	L	0.36672	1.1	0.25414	N	0.988333	P;B	0.40266	0.71;0.302	B;B	0.26614	0.071;0.047	T	0.43491	-0.9388	10	0.72032	D	0.01	.	15.136	0.72566	0.0:0.0:1.0:0.0	.	1923;575	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	F	575;1923	ENSP00000340759:S575F;ENSP00000258229:S1923F	ENSP00000258229:S1923F	S	-	2	0	PCNXL2	231200643	0.023000	0.18921	0.320000	0.25306	0.131000	0.20780	2.059000	0.41384	2.255000	0.74692	0.563000	0.77884	TCC	.		0.592	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233134020	G	A	233134020	3	1	7	1	0	0	0	0	1	0	0	0	11618	1174	41	2	657	2	PCNXL2	1	233134020	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	5959833	233134020	16116601	7	514											
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233225880	233225880	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacactcccaagaaatgggcTcaatggggtagaaaagattg	15	7	12	7	0	1	3	1	0	0	3	2	4	2	3	1	3	0	2	1	3	6	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:233225880T>C	ENST00000258229.9	-	23	4237	c.4003A>G	c.(4003-4005)Agc>Ggc	p.S1335G		NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1335						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				AGAAATGGGCTCAATGGGGTA	0.363																																					p.S1335G		.											.	PCNXL2-91	0			c.A4003G						.						105	101	102					1																	233225880		1852	4107	5959	SO:0001583	missense	80003	exon23			ATGGGCTCAATGG	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4003A>G	1.37:g.233225880T>C	ENSP00000258229:p.Ser1335Gly	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_014801	0	0	1	1	0	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	18.89	3.719025	0.68844	.	.	ENSG00000135749	ENST00000258229	T	0.09073	3.02	5.87	5.87	0.94306	.	0.122641	0.85682	D	0.000000	T	0.16938	0.0407	L	0.54323	1.7	0.80722	D	1	P	0.42871	0.792	P	0.47402	0.546	T	0.00106	-1.2054	10	0.72032	D	0.01	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1335	A6NKB5	PCX2_HUMAN	G	1335	ENSP00000258229:S1335G	ENSP00000258229:S1335G	S	-	1	0	PCNXL2	231292503	1.000000	0.71417	0.999000	0.59377	0.535000	0.34838	3.860000	0.55995	2.371000	0.80710	0.533000	0.62120	AGC	.		0.363	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		C	233225880	T	C	233225880	3	2	7	1	0	0	0	0	1	0	0	0	11618	1551	54	3	2458	3	PCNXL2	1	233225880	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	91860	233225880	16024741	8	515											
PREB	10113	bcgsc.ca	37	chr2	27355508	27355521	+	Frame_Shift_Del	DEL	TGGGTCCATTTTCT	TGGGTCCATTTTCT	-																															gtaaggtgtgctggaaaaggTgggtccattttcttgccagt																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	TGGGTCCATTTTCT	TGGGTCCATTTTCT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:27355508_27355521delTGGGTCCATTTTCT	ENST00000260643.2	-	5	955_968	c.702_715delAGAAAATGGACCCA	c.(700-717)caagaaaatggacccaccfs	p.QENGPT234fs	PREB_ENST00000416802.1_5'Flank|PREB_ENST00000406567.3_Frame_Shift_Del_p.QENGPT234fs	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	234					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGAAAAGGTGGGTCCATTTTCTTGCCAGTGCA	0.547																																					p.234_239del													.	PREB-91	0			c.702_715del						.																																			SO:0001589	frameshift_variant	10113	exon5			AAAAGGTGGGTCC		CCDS1738.1	2p23	2013-01-10			ENSG00000138073	ENSG00000138073		"WD repeat domain containing"	9356	protein-coding gene	gene with protein product		606395				10194769, 12735795	Standard	NM_013388		Approved	SEC12	uc002rix.1	Q9HCU5	OTTHUMG00000097076	ENST00000260643.2:c.702_715delAGAAAATGGACCCA	2.37:g.27355508_27355521delTGGGTCCATTTTCT	ENSP00000260643:p.Gln234fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_1	35	5	NM_013388	0	0	0	0	0	Q53SZ8|Q9UH94	Frame_Shift_Del	DEL	ENST00000260643.2	37	CCDS1738.1																																																																																			.		0.547	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388		-	27355521	TGGGTCCATTTTCT	-	27355508	7	5	7	1	0	1	0	1	0	0	0	0	12499	1696	59	0	558	0	PREB	2	27355508	Frame_Shift_Del	DEL	TGGGTCCATTTTCT	TCGA-A4-7732-01A-11D-2136-08		27355508	215843865	9	516											
USP34	9736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	61454345	61454345	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctctgataacacttcAacttgaggctaagttggaat	11	14	7	9	0	3	2	1	2	2	0	4	3	4	3	1	2	2	2	1	2	4	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:61454345A>C	ENST00000398571.2	-	62	7528	c.7452T>G	c.(7450-7452)gtT>gtG	p.V2484V		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2484					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATAACACTTCAACTTGAGGCT	0.363																																					p.V2484V		.											.	USP34-579	0			c.T7452G						.						52	44	46					2																	61454345		1830	4087	5917	SO:0001819	synonymous_variant	9736	exon62			CACTTCAACTTGA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.7452T>G	2.37:g.61454345A>C		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	11	6	NM_014709	0	0	0	0	0	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	A	8.176	0.792843	0.16327	.	.	ENSG00000115464	ENST00000411912	.	.	.	5.4	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9549	0.52976	0.7265:0.2735:0.0:0.0	.	.	.	.	G	244	.	.	X	-	1	0	USP34	61307849	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.203000	0.51075	0.902000	0.36520	-0.265000	0.10407	TGA	.		0.363	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61454345	A	C	61454345	2	2	7	1	0	0	0	0	0	0	0	1	17098	117	5	5		5	USP34	2	61454345	Silent	SNP	A	TCGA-A4-7732-01A-11D-2136-08	34098837	61454345	181745028	10	517											
C2orf3	6936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	75929399	75929399	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctcttttcatggtcatcaGgctcactctcagggtcatct	6	16	7	12	0	8	0	6	0	3	0	10	0	8	0	0	3	0	1	0	3	0	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:75929399G>T	ENST00000321027.3	-	3	678	c.545C>A	c.(544-546)cCt>cAt	p.P182H	GCFC2_ENST00000409857.3_Intron|GCFC2_ENST00000541687.1_Missense_Mutation_p.P182H|GCFC2_ENST00000470503.1_Missense_Mutation_p.P182H	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	182					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										ATGGTCATCAGGCTCACTCTC	0.418																																					p.P182H		.											.	.	0			c.C545A						.						196	185	189					2																	75929399		2203	4300	6503	SO:0001583	missense	6936	exon3			TCATCAGGCTCAC	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.545C>A	2.37:g.75929399G>T	ENSP00000318690:p.Pro182His	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	135	59	NM_001201335	0	0	2	5	3	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.505961	0.64410	.	.	ENSG00000005436	ENST00000321027;ENST00000541687	T;T	0.34072	2.49;1.38	4.85	4.85	0.62838	.	0.455607	0.22605	N	0.057903	T	0.54822	0.1882	M	0.66939	2.045	0.27164	N	0.961081	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.987	T	0.49031	-0.8981	10	0.56958	D	0.05	-15.8005	9.7929	0.40717	0.0967:0.0:0.9033:0.0	.	182;182	A4UHQ8;P16383	.;GCF_HUMAN	H	182	ENSP00000318690:P182H;ENSP00000437767:P182H	ENSP00000318690:P182H	P	-	2	0	C2orf3	75782907	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.496000	0.53288	2.620000	0.88729	0.591000	0.81541	CCT	.		0.418	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		T	75929399	G	T	75929399	3	4	7	1	0	0	0	0	1	0	0	0	2168	1000	35	4	1860	4	C2orf3	2	75929399	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	14475054	75929399	167269974	11	518											
NCAPH	23397	bcgsc.ca	37	chr2	97017653	97017654	+	Missense_Mutation	DNP	GA	GA	TT																															tgtccactctccactgccagGactacagaagtgaactgctg																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	GA	GA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:97017653_97017654GA>TT	ENST00000240423.4	+	7	848_849	c.805_806GA>TT	c.(805-807)GAc>TTc	p.D269F	NCAPH_ENST00000427946.1_Missense_Mutation_p.D133F|NCAPH_ENST00000455200.1_Missense_Mutation_p.D258F	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	269					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				CCACTGCCAGGACTACAGAAGT	0.49																																					p.D269F													.	NCAPH-228	0			c.A806T						.																																			SO:0001583	missense	23397	exon7			GCCAGGACTACAG	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"barren (Drosophila) homolog", "barren homolog (Drosophila)", "barren homolog 1 (Drosophila)"	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	Exception_encountered	2.37:g.97017653_97017654delinsTT	ENSP00000240423:p.Asp269Phe	Somatic	104	0		WXS	Illumina HiSeq	Phase_1	50	17	NM_015341	0	0	0	0	0	B4E189|Q8TB87	Missense_Mutation	DNP	ENST00000240423.4	37	CCDS2021.1																																																																																			.		0.49	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341		TT	97017654	GA	TT	97017653	3	4	7	1	0	0	0	0	1	0	0	0	10235	1174	41	4	831	4	NCAPH	2	97017653	Missense_Mutation	DNP	GA	TCGA-A4-7732-01A-11D-2136-08	21088254	97017653	146181720	12	519	5	2									
NCAPH	23397	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	97017659	97017669	+	Frame_Shift_Del	DEL	AGAAGTGAACT	AGAAGTGAACT	-																															ctctccactgccaggactacAgaagtgaactgctgtttccc																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	AGAAGTGAACT	AGAAGTGAACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:97017659_97017669delAGAAGTGAACT	ENST00000240423.4	+	7	854_864	c.811_821delAGAAGTGAACT	c.(811-822)agaagtgaactgfs	p.RSEL271fs	NCAPH_ENST00000427946.1_Frame_Shift_Del_p.RSEL135fs|NCAPH_ENST00000455200.1_Frame_Shift_Del_p.RSEL260fs	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	271					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				CCAGGACTACAGAAGTGAACTGCTGTTTCCC	0.479																																					p.271_274del		.											.	NCAPH-228	0			c.811_821del						.																																			SO:0001589	frameshift_variant	23397	exon7			.	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"barren (Drosophila) homolog", "barren homolog (Drosophila)", "barren homolog 1 (Drosophila)"	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.811_821delAGAAGTGAACT	2.37:g.97017659_97017669delAGAAGTGAACT	ENSP00000240423:p.Arg271fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	55	17	NM_015341	0	0	0	0	0	B4E189|Q8TB87	Frame_Shift_Del	DEL	ENST00000240423.4	37	CCDS2021.1																																																																																			.		0.479	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341		-	97017669	AGAAGTGAACT	-	97017659	7	5	7	1	0	1	0	1	0	0	0	0	10235	180	7	0	837	0	NCAPH	2	97017659	Frame_Shift_Del	DEL	AGAAGTGAACT	TCGA-A4-7732-01A-11D-2136-08	6	97017659	146181714	13	520	5	2									
IL1R1	3554	hgsc.bcm.edu	37	chr2	102792833	102792833	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acattgttgaggtcattaatGaaaacgtaaagaaaagcaga	19	9	9	4	1	1	4	1	2	0	2	1	4	1	4	0	1	2	3	0	1	7	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:102792833G>C	ENST00000410023.1	+	12	1642	c.1324G>C	c.(1324-1326)Gaa>Caa	p.E442Q	IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000233946.3_Missense_Mutation_p.E442Q|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000424272.1_3'UTR|IL1R1_ENST00000409929.1_Missense_Mutation_p.E411Q			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	442	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	GGTCATTAATGAAAACGTAAA	0.373																																					p.E442Q		.											.	IL1R1-523	0			c.G1324C						.						49	51	50					2																	102792833		2203	4300	6503	SO:0001583	missense	3554	exon11			ATTAATGAAAACG	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1324G>C	2.37:g.102792833G>C	ENSP00000386380:p.Glu442Gln	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_000877	0	0	8	8	0	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	37	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154988	0.78114	.	.	ENSG00000115594	ENST00000409929;ENST00000428279;ENST00000410023;ENST00000233946	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	5.61	4.73	0.59995	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.465576	0.25450	N	0.030588	T	0.33556	0.0867	M	0.77313	2.365	0.37504	D	0.916883	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.983	T	0.18808	-1.0325	10	0.62326	D	0.03	.	13.9351	0.64021	0.0726:0.0:0.9274:0.0	.	411;442	B8ZZW4;P14778	.;IL1R1_HUMAN	Q	411;298;442;442	ENSP00000386776:E411Q;ENSP00000410461:E298Q;ENSP00000386380:E442Q;ENSP00000233946:E442Q	ENSP00000233946:E442Q	E	+	1	0	IL1R1	102159265	1.000000	0.71417	0.947000	0.38551	0.951000	0.60555	4.341000	0.59335	2.646000	0.89796	0.563000	0.77884	GAA	.		0.373	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			C	102792833	G	C	102792833	3	2	7	1	0	0	0	0	1	0	0	0	7679	1291	45	4	1362	4	IL1R1	2	102792833	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	5775174	102792833	140406540	14	521											
HNMT	3176	hgsc.bcm.edu;broad.mit.edu	37	chr2	138771361	138771361	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggaagcagtggctgggaCaagctgtggaaaaagtacgg	14	5	16	6	1	0	0	0	0	0	0	0	3	0	3	0	5	3	4	0	5	5	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:138771361C>A	ENST00000280097.3	+	6	722	c.540C>A	c.(538-540)gaC>gaA	p.D180E	HNMT_ENST00000485653.1_3'UTR|HNMT_ENST00000410115.1_Missense_Mutation_p.D180E	NM_006895.2	NP_008826.1	P50135	HNMT_HUMAN	histamine N-methyltransferase	180					brain development (GO:0007420)|hyperosmotic response (GO:0006972)|respiratory gaseous exchange (GO:0007585)|response to amine (GO:0014075)|response to cocaine (GO:0042220)|response to glucocorticoid (GO:0051384)|response to interleukin-1 (GO:0070555)|response to tumor cell (GO:0002347)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	histamine N-methyltransferase activity (GO:0046539)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Chlorhexidine(DB00878)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	GTGGCTGGGACAAGCTGTGGA	0.443																																					p.D180E		.											.	HNMT-91	0			c.C540A						.						76	73	74					2																	138771361		2203	4300	6503	SO:0001583	missense	3176	exon6			CTGGGACAAGCTG		CCDS2181.1, CCDS33296.1, CCDS33297.1	2q22.1	2008-02-05			ENSG00000150540	ENSG00000150540	2.1.1.8		5028	protein-coding gene	gene with protein product		605238					Standard	NM_001024074		Approved		uc002tvf.3	P50135	OTTHUMG00000131751	ENST00000280097.3:c.540C>A	2.37:g.138771361C>A	ENSP00000280097:p.Asp180Glu	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	22	6	NM_006895	0	0	15	32	17	B2R9J3|Q546Z6|Q7Z7I2|Q8IU56|Q8WW98|Q9BRW6	Missense_Mutation	SNP	ENST00000280097.3	37	CCDS2181.1	.	.	.	.	.	.	.	.	.	.	C	6.154	0.396689	0.11638	.	.	ENSG00000150540	ENST00000410115;ENST00000280097	T;T	0.14391	2.51;2.51	5.98	2.07	0.26955	.	1.023760	0.07680	N	0.937009	T	0.07638	0.0192	N	0.14661	0.345	0.46167	D	0.998905	B	0.06786	0.001	B	0.08055	0.003	T	0.35201	-0.9798	10	0.02654	T	1	-12.4241	10.4716	0.44640	0.4747:0.4636:0.0:0.0617	.	180	P50135	HNMT_HUMAN	E	180	ENSP00000386940:D180E;ENSP00000280097:D180E	ENSP00000280097:D180E	D	+	3	2	HNMT	138487831	0.008000	0.16893	0.252000	0.24328	0.881000	0.50899	-0.112000	0.10791	0.098000	0.17522	0.591000	0.81541	GAC	.		0.443	HNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254673.1			A	138771361	C	A	138771361	3	1	7	1	0	0	0	0	1	0	0	0	7276	477	17	4	780	4	HNMT	2	138771361	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	35978528	138771361	104428012	15	522											
SCN2A	6326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	166210795	166210795	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgaaatgaataatctccagAttgctgtgggaaggatgcag	14	9	12	6	1	1	2	0	1	1	1	2	5	1	4	1	2	2	2	1	2	4	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:166210795A>C	ENST00000375437.2	+	17	3303	c.3013A>C	c.(3013-3015)Att>Ctt	p.I1005L	SCN2A_ENST00000357398.3_Missense_Mutation_p.I1005L|SCN2A_ENST00000375427.2_Missense_Mutation_p.I1005L|SCN2A_ENST00000283256.6_Missense_Mutation_p.I1005L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1005					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAATCTCCAGATTGCTGTGGG	0.383																																					p.I1005L		.											.	SCN2A-142	0			c.A3013C						.						146	151	149					2																	166210795		2203	4300	6503	SO:0001583	missense	6326	exon16			CTCCAGATTGCTG	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.3013A>C	2.37:g.166210795A>C	ENSP00000364586:p.Ile1005Leu	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	154	66	NM_001040143	0	0	0	0	0	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	13.51	2.257989	0.39896	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87	5.6	5.6	0.85130	Sodium ion transport-associated (1);	0.080914	0.52532	D	0.000063	D	0.83101	0.5181	L	0.53671	1.685	0.49915	D	0.999837	B;B	0.17268	0.021;0.005	B;B	0.25291	0.059;0.042	T	0.78513	-0.2175	10	0.30854	T	0.27	.	15.7718	0.78176	1.0:0.0:0.0:0.0	.	1005;1005	Q99250-2;Q99250	.;SCN2A_HUMAN	L	1005	ENSP00000364586:I1005L;ENSP00000349973:I1005L;ENSP00000283256:I1005L;ENSP00000364576:I1005L	ENSP00000283256:I1005L	I	+	1	0	SCN2A	165919041	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.572000	0.82409	2.110000	0.64415	0.482000	0.46254	ATT	.		0.383	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		C	166210795	A	C	166210795	3	2	7	1	0	0	0	0	1	0	0	0	13948	333	12	5	3171	5	SCN2A	2	166210795	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	27439434	166210795	76988578	16	523											
LASS6	253782	broad.mit.edu	37	chr2	169571584	169571584	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatatgtcaacaatatggCccgagtaggaacgctggtcc	11	10	10	10	2	2	0	2	0	0	0	3	2	3	1	2	3	2	2	2	3	6	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:169571584C>T	ENST00000305747.6	+	7	1270	c.683C>T	c.(682-684)gCc>gTc	p.A228V	CERS6_ENST00000392687.4_Missense_Mutation_p.A228V	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	228	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AACAATATGGCCCGAGTAGGA	0.363																																					p.A228V													.	.	0			c.C683T						.						220	207	212					2																	169571584		2203	4300	6503	SO:0001583	missense	253782	exon7			ATATGGCCCGAGT	BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"Homeoboxes / CERS class"	23826	protein-coding gene	gene with protein product		615336	"LAG1 longevity assurance homolog 6 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 6"	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.683C>T	2.37:g.169571584C>T	ENSP00000306579:p.Ala228Val	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	76	4	NM_001256126	0	0	0	0	0	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	.	.	.	.	.	.	.	.	.	.	C	5.941	0.357562	0.11239	.	.	ENSG00000172292	ENST00000305747;ENST00000392687	D;D	0.84589	-1.87;-1.87	5.46	2.58	0.30949	TRAM/LAG1/CLN8 homology domain (3);	0.337573	0.33980	N	0.004362	T	0.61223	0.2330	N	0.03194	-0.395	0.38507	D	0.948384	B;B	0.06786	0.001;0.001	B;B	0.16289	0.015;0.015	T	0.54748	-0.8247	10	0.02654	T	1	-6.119	8.2579	0.31766	0.0:0.6784:0.0:0.3216	.	228;228	Q32M63;Q6ZMG9	.;CERS6_HUMAN	V	228	ENSP00000306579:A228V;ENSP00000376453:A228V	ENSP00000306579:A228V	A	+	2	0	CERS6	169279830	0.992000	0.36948	0.997000	0.53966	0.985000	0.73830	0.532000	0.23067	0.237000	0.21200	0.655000	0.94253	GCC	.		0.363	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		T	169571584	C	T	169571584	3	4	7	1	0	0	0	0	1	0	0	0	8664	739	26	2	709	2	LASS6	2	169571584	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	3360789	169571584	73627789	17	524											
PDE11A	50940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178936278	178936278	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcatcaggaatgttgaccGtttctccatgctccccgaca	9	10	9	13	2	2	1	1	1	1	0	4	3	3	2	4	2	1	4	4	2	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:178936278G>T	ENST00000286063.6	-	1	1204	c.887C>A	c.(886-888)aCg>aAg	p.T296K	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	296	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	AATGTTGACCGTTTCTCCATG	0.537									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.T296K		.											.	PDE11A-93	0			c.C887A						.						153	132	139					2																	178936278		2203	4300	6503	SO:0001583	missense	50940	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TTGACCGTTTCTC	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.887C>A	2.37:g.178936278G>T	ENSP00000286063:p.Thr296Lys	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	100	52	NM_016953	0	0	0	0	0	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.521048	0.85495	.	.	ENSG00000128655	ENST00000286063	T	0.68181	-0.31	5.63	5.63	0.86233	GAF (2);	0.042243	0.85682	D	0.000000	D	0.82559	0.5063	M	0.82716	2.605	0.80722	D	1	D	0.64830	0.994	D	0.65140	0.932	T	0.82643	-0.0356	10	0.44086	T	0.13	.	18.6717	0.91514	0.0:0.0:1.0:0.0	.	296	Q9HCR9	PDE11_HUMAN	K	296	ENSP00000286063:T296K	ENSP00000286063:T296K	T	-	2	0	PDE11A	178644524	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	9.379000	0.97198	2.650000	0.89964	0.655000	0.94253	ACG	.		0.537	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			T	178936278	G	T	178936278	3	4	7	1	0	0	0	0	1	0	0	0	11657	1145	40	4	1994	4	PDE11A	2	178936278	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	9364694	178936278	64263095	18	525											
MARS2	92935	hgsc.bcm.edu;broad.mit.edu	37	chr2	198571900	198571900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacttggctggtgaaagccCaccggacctagaaactcagt	11	7	12	11	1	1	2	1	1	0	1	1	4	1	4	3	4	2	1	3	4	3	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:198571900C>T	ENST00000282276.6	+	1	1814	c.1771C>T	c.(1771-1773)Cac>Tac	p.H591Y	AC011997.1_ENST00000409845.1_Intron	NM_138395.3	NP_612404.1	Q96GW9	SYMM_HUMAN	methionyl-tRNA synthetase 2, mitochondrial	591					cell death (GO:0008219)|gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	22					L-Methionine(DB00134)	GGTGAAAGCCCACCGGACCTA	0.423																																					p.H591Y		.											.	MARS2-92	0			c.C1771T						.						62	64	63					2																	198571900		2203	4299	6502	SO:0001583	missense	92935	exon1			AAAGCCCACCGGA	BC009115	CCDS33358.1	2q33.1	2014-01-30	2007-02-26		ENSG00000247626	ENSG00000247626	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	25133	protein-coding gene	gene with protein product	"methionine tRNA ligase 2, mitochondrial"	609728				15274629	Standard	NM_138395		Approved	mtMetRS, SPAX3	uc002uuq.3	Q96GW9	OTTHUMG00000154487	ENST00000282276.6:c.1771C>T	2.37:g.198571900C>T	ENSP00000282276:p.His591Tyr	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	98	8	NM_138395	0	0	2	2	0	A0AVC3|Q76E79|Q8IW62|Q8N7N4	Missense_Mutation	SNP	ENST00000282276.6	37	CCDS33358.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624395	0.28889	.	.	ENSG00000247626	ENST00000282276;ENST00000499940	T	0.44083	0.93	4.93	4.93	0.64822	.	0.240489	0.32671	N	0.005784	T	0.28499	0.0705	L	0.29908	0.895	0.24793	N	0.992741	B	0.29909	0.261	B	0.23150	0.044	T	0.24799	-1.0150	10	0.66056	D	0.02	-13.272	9.1162	0.36760	0.0:0.903:0.0:0.097	.	591	Q96GW9	SYMM_HUMAN	Y	591;518	ENSP00000282276:H591Y	ENSP00000282276:H591Y	H	+	1	0	MARS2	198280145	0.989000	0.36119	0.998000	0.56505	0.981000	0.71138	2.152000	0.42272	2.553000	0.86117	0.557000	0.71058	CAC	.		0.423	MARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335477.1	NM_138395		T	198571900	C	T	198571900	3	4	7	1	0	0	0	0	1	0	0	0	9342	594	21	2	1773	2	MARS2	2	198571900	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	19635622	198571900	44627473	19	526											
PRKCD	5580	ucsc.edu	37	chr3	53212505	53212505	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccctgcaggccgaggacgagGcgaaccagcccttctgtgcc	7	5	13	16	3	1	0	0	0	1	0	1	4	1	1	5	3	4	1	5	3	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr3:53212505G>A	ENST00000394729.2	+	2	395	c.67G>A	c.(67-69)Gcg>Acg	p.A23T	PRKCD_ENST00000477794.2_3'UTR|PRKCD_ENST00000330452.3_Missense_Mutation_p.A23T	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	23	C2.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	CGAGGACGAGGCGAACCAGCC	0.662																																					p.A23T													.	PRKCD-1378	0			c.G67A						.						55	50	52					3																	53212505		2203	4300	6503	SO:0001583	missense	5580	exon2			GACGAGGCGAACC		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.67G>A	3.37:g.53212505G>A	ENSP00000378217:p.Ala23Thr	Somatic	86	0		WXS	Illumina HiSeq		43	4	NM_212539	0	0	1	1	0	B0KZ81|B2R834|Q15144|Q86XJ6	Missense_Mutation	SNP	ENST00000394729.2	37	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	G	5.282	0.237366	0.10023	.	.	ENSG00000163932	ENST00000478843;ENST00000394729;ENST00000330452;ENST00000487897;ENST00000464818	T;T;D	0.82711	-0.39;-0.39;-1.64	4.95	2.97	0.34412	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	1.056850	0.07276	N	0.870034	T	0.64951	0.2645	N	0.11560	0.145	0.09310	N	1	B;B	0.13145	0.007;0.002	B;B	0.11329	0.003;0.006	T	0.53436	-0.8439	10	0.16420	T	0.52	.	4.333	0.11073	0.21:0.1892:0.6008:0.0	.	23;23	C9K0E3;Q05655	.;KPCD_HUMAN	T	23	ENSP00000378217:A23T;ENSP00000331602:A23T;ENSP00000419629:A23T	ENSP00000331602:A23T	A	+	1	0	PRKCD	53187545	0.000000	0.05858	0.004000	0.12327	0.006000	0.05464	0.337000	0.19841	1.311000	0.45024	0.650000	0.86243	GCG	.		0.662	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1			A	53212505	G	A	53212505	3	1	7	1	0	0	0	0	1	0	0	0	12538	1203	42	2	69	2	PRKCD	3	53212505	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		53212505	144809925	20	527											
PARP9	83666	hgsc.bcm.edu	37	chr3	122259457	122259457	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taactctgtccttcctgggcTgataatttctgtgatggaga	8	15	10	8	0	2	3	0	2	2	1	4	4	4	3	2	2	1	1	2	2	2	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr3:122259457T>C	ENST00000360356.2	-	8	1959	c.1732A>G	c.(1732-1734)Agc>Ggc	p.S578G	PARP9_ENST00000492382.1_Missense_Mutation_p.S123G|PARP9_ENST00000471785.1_Missense_Mutation_p.S543G|PARP9_ENST00000462315.1_Missense_Mutation_p.S543G|PARP9_ENST00000477522.2_Missense_Mutation_p.S543G	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	578					cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		CTTCCTGGGCTGATAATTTCT	0.408																																					p.S578G		.											.	PARP9-525	0			c.A1732G						.						107	104	105					3																	122259457		2203	4300	6503	SO:0001583	missense	83666	exon8			CTGGGCTGATAAT	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"Poly (ADP-ribose) polymerases"	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.1732A>G	3.37:g.122259457T>C	ENSP00000353512:p.Ser578Gly	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_031458	0	0	22	22	0	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	.	.	.	.	.	.	.	.	.	.	T	2.053	-0.417329	0.04766	.	.	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457;ENST00000462315	T;T;T;T;T	0.18657	3.2;2.86;3.06;3.06;2.2	4.98	-0.548	0.11833	.	1.510340	0.03573	N	0.228962	T	0.17023	0.0409	L	0.46157	1.445	0.09310	N	1	B;B;B;B	0.32245	0.046;0.361;0.021;0.003	B;B;B;B	0.26969	0.007;0.075;0.031;0.004	T	0.19418	-1.0306	10	0.51188	T	0.08	.	2.8456	0.05542	0.3155:0.1796:0.0:0.5049	.	543;578;123;543	E9PFM7;Q8IXQ6;G5E9U8;Q8IXQ6-2	.;PARP9_HUMAN;.;.	G	578;123;543;543;501;543	ENSP00000353512:S578G;ENSP00000417664:S123G;ENSP00000419506:S543G;ENSP00000419001:S543G;ENSP00000418894:S543G	ENSP00000353512:S578G	S	-	1	0	PARP9	123742147	0.071000	0.21146	0.000000	0.03702	0.001000	0.01503	0.264000	0.18497	-0.227000	0.09884	0.528000	0.53228	AGC	.		0.408	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		C	122259457	T	C	122259457	3	2	7	1	0	0	0	0	1	0	0	0	11492	1580	55	3	901	3	PARP9	3	122259457	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	69046952	122259457	75762973	21	528											
KIAA0226	9711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	197427622	197427622	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagctggctctccccacCtccttcctggtcccctaagg	5	9	9	18	0	1	0	0	0	1	0	5	1	4	1	7	4	1	2	7	4	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr3:197427622C>G	ENST00000296343.5	-	7	1122	c.1123G>C	c.(1123-1125)Ggt>Cgt	p.G375R	KIAA0226_ENST00000389665.5_Missense_Mutation_p.G375R|KIAA0226_ENST00000273582.5_Missense_Mutation_p.G315R|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000449205.1_Missense_Mutation_p.G375R	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	375	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		CTCTCCCCACCTCCTTCCTGG	0.577																																					p.G375R	Esophageal Squamous(3;167 355 3763 15924)	.											.	KIAA0226-22	0			c.G1123C						.						57	61	60					3																	197427622		2021	4184	6205	SO:0001583	missense	9711	exon7			CCCCACCTCCTTC	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1123G>C	3.37:g.197427622C>G	ENSP00000296343:p.Gly375Arg	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	36	11	NM_014687	0	0	0	1	1	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	1.899|1.899|1.899	-0.453623|-0.453623|-0.453623	0.04540|0.04540|0.04540	.|.|.	.|.|.	ENSG00000145016|ENSG00000145016|ENSG00000145016	ENST00000415452|ENST00000273582;ENST00000296343;ENST00000389665;ENST00000447048;ENST00000449205|ENST00000413360	.|.|.	.|.|.	.|.|.	5.85|5.85|5.85	2.98|2.98|2.98	0.34508|0.34508|0.34508	.|.|.	.|0.954594|.	.|0.08839|.	.|N|.	.|0.886108|.	T|T|T	0.23886|0.23886|0.23886	0.0578|0.0578|0.0578	N|N|N	0.19112|0.19112|0.19112	0.55|0.55|0.55	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|P;P;P;P;B|.	.|0.52577|.	.|0.954;0.785;0.704;0.905;0.282|.	.|P;P;B;B;B|.	.|0.50192|.	.|0.634;0.49;0.299;0.394;0.051|.	T|T|T	0.20538|0.20538|0.20538	-1.0272|-1.0272|-1.0272	5|9|5	.|0.16896|.	.|T|.	.|0.51|.	.|.|.	7.6388|7.6388|7.6388	0.28282|0.28282|0.28282	0.0:0.5923:0.0:0.4077|0.0:0.5923:0.0:0.4077|0.0:0.5923:0.0:0.4077	.|.|.	.|375;208;375;315;375|.	.|E9PEM3;Q5HYI6;Q92622-3;Q92622-2;Q92622|.	.|.;.;.;.;RUBIC_HUMAN|.	D|R|T	133|315;375;375;7;375|353	.|.|.	.|ENSP00000273582:G315R|.	E|G|R	-|-|-	3|1|2	2|0|0	KIAA0226|KIAA0226|KIAA0226	198912019|198912019|198912019	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.010000|0.010000|0.010000	0.14722|0.14722|0.14722	0.364000|0.364000|0.364000	0.29643|0.29643|0.29643	0.779000|0.779000|0.779000	0.26746|0.26746|0.26746	0.756000|0.756000|0.756000	0.33013|0.33013|0.33013	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAG|GGT|AGG	.		0.577	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		G	197427622	C	G	197427622	3	3	7	1	0	0	0	0	1	0	0	0	8183	681	24	4	1900	4	KIAA0226	3	197427622	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	75168165	197427622	594808	22	529											
UGT2A3	79799	broad.mit.edu	37	chr4	69817176	69817177	+	Frame_Shift_Ins	INS	-	-	AA																															taactgattgccaggttgatINSaagcctggcaagacattcag																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr4:69817176_69817177insAA	ENST00000251566.4	-	1	332_333	c.302_303insTT	c.(301-303)ttafs	p.L101fs	UGT2A3_ENST00000420231.2_5'Flank	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	101					cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GCCAGGTTGATAAGCCTGGCAA	0.351																																					p.L101fs													.	UGT2A3-92	0			c.303_304insTT						.																																			SO:0001589	frameshift_variant	79799	exon1			GGTTGATAAGCCT		CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220		"UDP glucuronosyltransferases"	28528	protein-coding gene	gene with protein product							Standard	NM_024743		Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.301_302dupTT	4.37:g.69817177_69817178dupAA	ENSP00000251566:p.Leu101fs	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	45	9	NM_024743	0	0	0	0	0	Q9H6S4	Frame_Shift_Ins	INS	ENST00000251566.4	37	CCDS3525.1																																																																																			.		0.351	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251564.1	NM_024743		AA	69817177	-	AA	69817176	7	5	7	1	0	1	1	0	0	0	0	0	16988	1403	49	0	1304	0	UGT2A3	4	69817176	Frame_Shift_Ins	INS	-	TCGA-A4-7732-01A-11D-2136-08		69817176	121337100	23	530											
TRIO	7204	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	14387672	14387672	+	Frame_Shift_Del	DEL	T	T	-																															aagaggtacagagatttctcTctgcggatggagaagtacag																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr5:14387672delT	ENST00000344204.4	+	22	3720	c.3696delT	c.(3694-3696)tctfs	p.S1232fs	TRIO_ENST00000509967.2_Frame_Shift_Del_p.S1183fs|TRIO_ENST00000537187.1_Frame_Shift_Del_p.S1232fs	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1232					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GAGATTTCTCTCTGCGGATGG	0.433																																					p.S1232fs		.											.	TRIO-562	0			c.3696delT						.						118	132	127					5																	14387672		2203	4300	6503	SO:0001589	frameshift_variant	7204	exon22			.	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.3696delT	5.37:g.14387672delT	ENSP00000339299:p.Ser1232fs	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	94	38	NM_007118	0	0	0	0	0	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Frame_Shift_Del	DEL	ENST00000344204.4	37	CCDS3883.1																																																																																			.		0.433	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		-	14387672	T	-	14387672	7	5	7	1	0	1	0	1	0	0	0	0	16585	1538	54	0	3782	0	TRIO	5	14387672	Frame_Shift_Del	DEL	T	TCGA-A4-7732-01A-11D-2136-08		14387672	166527588	24	531											
PCDHGB7	56099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140798373	140798373	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaagaagtagaaagatataCgataaacatagaagcaaaag	23	6	9	3	1	0	5	0	1	0	4	0	6	0	5	0	0	3	2	0	0	12	5	rs200530054		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr5:140798373C>G	ENST00000398594.2	+	1	947	c.947C>G	c.(946-948)aCg>aGg	p.T316R	PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	316	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAAGATATACGATAAACATA	0.408																																					p.T316R		.											.	PCDHGB7-29	0			c.C947G						.						66	62	63					5																	140798373		1868	4100	5968	SO:0001583	missense	56099	exon1			GATATACGATAAA	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.947C>G	5.37:g.140798373C>G	ENSP00000381594:p.Thr316Arg	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	24	4	NM_018927	0	0	0	0	0	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	c	11.77	1.736942	0.30774	.	.	ENSG00000254122	ENST00000398594	T	0.51325	0.71	5.7	3.93	0.45458	Cadherin (5);Cadherin-like (1);	1.919090	0.04837	U	0.439841	T	0.56615	0.1997	L	0.49350	1.555	0.09310	N	1	D;D	0.54397	0.966;0.958	P;P	0.57204	0.815;0.795	T	0.26916	-1.0089	10	0.54805	T	0.06	.	4.1608	0.10282	0.1578:0.5582:0.0:0.284	.	316;316	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	R	316	ENSP00000381594:T316R	ENSP00000381594:T316R	T	+	2	0	PCDHGB7	140778557	0.000000	0.05858	0.048000	0.18961	0.684000	0.39900	0.516000	0.22817	0.776000	0.33473	0.561000	0.74099	ACG	C|0.999;T|0.000		0.408	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		G	140798373	C	G	140798373	3	3	7	1	0	0	0	0	1	0	0	0	11594	536	19	4	949	4	PCDHGB7	5	140798373	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	126410701	140798373	40116887	25	532											
ARHGEF37	389337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149006787	149006787	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcgtggccatccttcaaaAcaaggacaccaaaggcaaca	17	5	7	12	1	1	0	1	0	0	0	3	1	2	1	3	3	2	1	3	3	6	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr5:149006787A>G	ENST00000333677.6	+	11	1776	c.1613A>G	c.(1612-1614)aAc>aGc	p.N538S		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	538	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						ATCCTTCAAAACAAGGACACC	0.597																																					p.N538S		.											.	ARHGEF37-90	0			c.A1613G						.						82	94	90					5																	149006787		2091	4214	6305	SO:0001583	missense	389337	exon11			TTCAAAACAAGGA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1613A>G	5.37:g.149006787A>G	ENSP00000328083:p.Asn538Ser	Somatic	251	0		WXS	Illumina HiSeq	Phase_I	116	43	NM_001001669	0	0	1	2	1	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	A	11.15	1.553479	0.27739	.	.	ENSG00000183111	ENST00000333677	T	0.41065	1.01	5.11	3.94	0.45596	Src homology-3 domain (2);Variant SH3 (1);	0.646786	0.17386	N	0.176119	T	0.23965	0.0580	N	0.16478	0.41	0.28347	N	0.921071	B	0.23249	0.082	B	0.21151	0.033	T	0.19745	-1.0296	10	0.14656	T	0.56	.	8.9935	0.36039	0.8446:0.0:0.1554:0.0	.	538	A1IGU5	ARH37_HUMAN	S	538	ENSP00000328083:N538S	ENSP00000328083:N538S	N	+	2	0	ARHGEF37	148986980	0.615000	0.27026	1.000000	0.80357	0.932000	0.56968	3.659000	0.54489	0.785000	0.33685	-0.441000	0.05720	AAC	.		0.597	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		G	149006787	A	G	149006787	3	3	7	1	0	0	0	0	1	0	0	0	906	43	2	3	1651	3	ARHGEF37	5	149006787	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	8208414	149006787	31908473	26	533											
PRSS16	10279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	27222771	27222771	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctttctttccaggggacaCagacccctggcatgtgctaa	8	11	9	13	0	1	1	0	0	1	1	3	2	3	2	4	3	1	2	4	3	1	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr6:27222771C>T	ENST00000230582.3	+	11	1352	c.1337C>T	c.(1336-1338)aCa>aTa	p.T446I	PRSS16_ENST00000421826.2_Missense_Mutation_p.T189I|PRSS16_ENST00000377456.2_3'UTR	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	446					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CCAGGGGACACAGACCCCTGG	0.547																																					p.T446I	NSCLC(178;1118 2105 17078 23587 44429)	.											.	PRSS16-94	0			c.C1337T						.						123	127	126					6																	27222771		2203	4300	6503	SO:0001583	missense	10279	exon11			GGGACACAGACCC	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"Serine peptidases / Serine peptidases"	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1337C>T	6.37:g.27222771C>T	ENSP00000230582:p.Thr446Ile	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	184	83	NM_005865	0	0	0	0	0	O75416	Missense_Mutation	SNP	ENST00000230582.3	37	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	C	0.210	-1.036976	0.02013	.	.	ENSG00000112812	ENST00000421826;ENST00000230582	T;T	0.12039	2.72;2.72	4.64	-1.58	0.08479	.	0.476548	0.23981	N	0.042674	T	0.01222	0.0040	N	0.02011	-0.69	0.09310	N	1	B;B	0.15930	0.015;0.002	B;B	0.10450	0.005;0.001	T	0.46005	-0.9222	10	0.23302	T	0.38	0.0031	9.7619	0.40537	0.0:0.3092:0.0:0.6908	.	189;446	F2Z2N5;Q9NQE7	.;TSSP_HUMAN	I	189;446	ENSP00000404349:T189I;ENSP00000230582:T446I	ENSP00000230582:T446I	T	+	2	0	PRSS16	27330750	0.007000	0.16637	0.571000	0.28486	0.927000	0.56198	-0.021000	0.12504	-0.193000	0.10415	-0.267000	0.10333	ACA	.		0.547	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			T	27222771	C	T	27222771	3	4	7	1	0	0	0	0	1	0	0	0	12645	478	17	2	1379	2	PRSS16	6	27222771	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		27222771	143892296	27	534											
HIST1H1B	3009	broad.mit.edu	37	chr6	27835118	27835118	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctaaggccttcttaagggCtgccaaagaaaggccattgc	11	8	11	11	1	1	1	0	0	1	1	1	1	1	1	3	3	2	2	3	3	4	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr6:27835118C>A	ENST00000331442.3	-	1	241	c.190G>T	c.(190-192)Gcc>Tcc	p.A64S		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	64	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						TTCTTAAGGGCTGCCAAAGAA	0.602																																					p.A64S													.	HIST1H1B-585	0			c.G190T						.						88	98	94					6																	27835118		2203	4300	6503	SO:0001583	missense	3009	exon1			TAAGGGCTGCCAA	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"Histones / Replication-dependent"	4719	protein-coding gene	gene with protein product		142711	"H1 histone family, member 5", "histone 1, H1b"	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.190G>T	6.37:g.27835118C>A	ENSP00000330074:p.Ala64Ser	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	137	5	NM_005322	0	0	0	0	0	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.971156	0.74246	.	.	ENSG00000184357	ENST00000331442	T	0.11604	2.76	5.43	5.43	0.79202	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.109576	0.64402	D	0.000009	T	0.33177	0.0854	M	0.88842	2.985	0.80722	D	1	D	0.60160	0.987	D	0.67900	0.954	T	0.27054	-1.0085	10	0.87932	D	0	-13.976	18.6154	0.91300	0.0:1.0:0.0:0.0	.	64	P16401	H15_HUMAN	S	64	ENSP00000330074:A64S	ENSP00000330074:A64S	A	-	1	0	HIST1H1B	27943097	1.000000	0.71417	0.462000	0.27118	0.003000	0.03518	4.710000	0.61873	2.716000	0.92895	0.655000	0.94253	GCC	.		0.602	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		A	27835118	C	A	27835118	3	1	7	1	0	0	0	0	1	0	0	0	7144	797	28	4	494	4	HIST1H1B	6	27835118	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	612347	27835118	143279949	28	535											
HSPA1L	3305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31779708	31779708	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacacaggagtaggtggtGcccaggtcgatgcctatggc	8	7	14	12	1	0	0	0	0	0	0	1	2	0	1	3	5	2	1	3	5	2	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr6:31779708G>A	ENST00000375654.4	-	2	231	c.42C>T	c.(40-42)ggC>ggT	p.G14G	HSPA1L_ENST00000417199.3_Silent_p.G14G	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	14					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						AGTAGGTGGTGCCCAGGTCGA	0.557																																					p.G14G		.											.	HSPA1L-230	0			c.C42T						.						71	60	64					6																	31779708		2203	4300	6503	SO:0001819	synonymous_variant	3305	exon2			GGTGGTGCCCAGG	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.42C>T	6.37:g.31779708G>A		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	36	16	NM_005527	0	0	0	0	0	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Silent	SNP	ENST00000375654.4	37	CCDS34413.1																																																																																			.		0.557	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			A	31779708	G	A	31779708	2	1	7	1	0	0	0	0	0	0	0	1	7431	1306	46	2		2	HSPA1L	6	31779708	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08	3944590	31779708	139335359	29	536											
CD109	135228	hgsc.bcm.edu	37	chr6	74524713	74524713	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attttttacagctcaatgttGtatataatgtgaaggcttct	11	18	7	5	0	2	1	1	1	1	0	2	1	2	1	0	1	2	4	0	1	6	8			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr6:74524713G>C	ENST00000287097.5	+	30	3890	c.3778G>C	c.(3778-3780)Gta>Cta	p.V1260L	CD109_ENST00000437994.2_Missense_Mutation_p.V1243L|CD109_ENST00000422508.2_Missense_Mutation_p.V1183L			Q6YHK3	CD109_HUMAN	CD109 molecule	1260					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GCTCAATGTTGTATATAATGT	0.303																																					p.V1260L		.											.	CD109-155	0			c.G3778C						.						75	83	80					6																	74524713		2203	4299	6502	SO:0001583	missense	135228	exon30			AATGTTGTATATA	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3778G>C	6.37:g.74524713G>C	ENSP00000287097:p.Val1260Leu	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_133493	0	0	0	0	0	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	G	8.339	0.828370	0.16749	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.23348	1.91;2.15;1.94	5.45	-3.9	0.04181	.	0.491379	0.24204	N	0.040590	T	0.03011	0.0089	N	0.19112	0.55	0.22521	N	0.999021	B;B;B	0.13145	0.007;0.003;0.0	B;B;B	0.15052	0.012;0.003;0.004	T	0.43877	-0.9364	10	0.08179	T	0.78	.	8.0038	0.30313	0.4964:0.0:0.4003:0.1033	.	1183;1243;1260	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	L	1243;1183;1260	ENSP00000388062:V1243L;ENSP00000404475:V1183L;ENSP00000287097:V1260L	ENSP00000287097:V1260L	V	+	1	0	CD109	74581434	0.995000	0.38212	0.919000	0.36401	0.670000	0.39368	0.252000	0.18278	-0.595000	0.05828	-0.237000	0.12165	GTA	.		0.303	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74524713	G	C	74524713	3	2	7	1	0	0	0	0	1	0	0	0	2969	1377	48	4	3896	4	CD109	6	74524713	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	42745005	74524713	96590354	30	537											
SP8	221833	hgsc.bcm.edu	37	chr7	20824445	20824445	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggggagccccccagcggcgCcgaaggcccagcgctcaaca	8	1	14	18	5	1	0	1	0	0	0	1	2	1	1	5	4	4	1	5	4	2	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr7:20824445C>T	ENST00000361443.4	-	3	1174	c.937G>A	c.(937-939)Gcg>Acg	p.A313T	SP8_ENST00000418710.2_Missense_Mutation_p.A331T	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	313					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						CCCAGCGGCGCCGAAGGCCCA	0.756																																					p.A331T		.											.	SP8-91	0			c.G991A						.						2	2	2					7																	20824445		1078	2448	3526	SO:0001583	missense	221833	exon2			GCGGCGCCGAAGG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.937G>A	7.37:g.20824445C>T	ENSP00000354482:p.Ala313Thr	Somatic	4	2		WXS	Illumina HiSeq	Phase_I	4	3	NM_182700	0	0	0	0	0	Q7Z615|Q7Z616|Q96MJ1	Missense_Mutation	SNP	ENST00000361443.4	37	CCDS5372.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.208792	0.39003	.	.	ENSG00000164651	ENST00000297210;ENST00000418710;ENST00000361443	T;T	0.12147	2.71;2.72	4.01	4.01	0.46588	.	0.070349	0.56097	U	0.000034	T	0.11367	0.0277	L	0.28115	0.83	0.54753	D	0.999984	B;B	0.19935	0.04;0.04	B;B	0.18561	0.022;0.022	T	0.10636	-1.0621	10	0.33141	T	0.24	.	16.0853	0.81042	0.0:1.0:0.0:0.0	.	313;313	Q7Z615;Q8IXZ3	.;SP8_HUMAN	T	289;331;313	ENSP00000408792:A331T;ENSP00000354482:A313T	ENSP00000297210:A289T	A	-	1	0	SP8	20790970	0.990000	0.36364	0.995000	0.50966	0.807000	0.45602	1.553000	0.36255	1.949000	0.56562	0.491000	0.48974	GCG	.		0.756	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			T	20824445	C	T	20824445	3	4	7	1	0	0	0	0	1	0	0	0	15002	739	26	2	539	2	SP8	7	20824445	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		20824445	138314218	31	538											
WBSCR17	64409	broad.mit.edu;bcgsc.ca	37	chr7	71142235	71142235	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aagacgtctgcttggaccagGggccgctggagaaccacaca	11	5	13	12	2	1	2	0	0	1	2	1	4	1	3	3	4	2	2	3	4	2	1	rs546847548		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr7:71142235G>A	ENST00000333538.5	+	9	2078	c.1444G>A	c.(1444-1446)Ggg>Agg	p.G482R	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	482	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CTTGGACCAGGGGCCGCTGGA	0.532																																					p.G482R													.	WBSCR17-96	0			c.G1444A						.						231	229	229					7																	71142235		2203	4300	6503	SO:0001583	missense	64409	exon9			GACCAGGGGCCGC	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"Glycosyltransferase family 2 domain containing"	16347	protein-coding gene	gene with protein product	"polypeptide N-acetylgalactosaminyltransferase-like 3", "polypeptide GalNAc transferase 3"	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1444G>A	7.37:g.71142235G>A	ENSP00000329654:p.Gly482Arg	Somatic	457	0		WXS	Illumina HiSeq	Phase_I	517	16	NM_022479	0	0	0	0	0	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.048935	0.93740	.	.	ENSG00000185274	ENST00000333538	T	0.26373	1.74	5.2	5.2	0.72013	Ricin B-related lectin (1);Ricin B lectin (3);	0.114545	0.64402	D	0.000013	T	0.58163	0.2103	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63839	-0.6546	10	0.59425	D	0.04	.	17.9178	0.88957	0.0:0.0:1.0:0.0	.	482	Q6IS24	GLTL3_HUMAN	R	482	ENSP00000329654:G482R	ENSP00000329654:G482R	G	+	1	0	WBSCR17	70780171	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.109000	0.94291	2.692000	0.91855	0.650000	0.86243	GGG	.		0.532	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71142235	G	A	71142235	3	1	7	1	0	0	0	0	1	0	0	0	17297	1232	43	2	1478	2	WBSCR17	7	71142235	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	50317790	71142235	87996428	32	539											
SLC26A5	375611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	103029857	103029857	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggttgacaatcacaatGgccgacagcacagcctgaaa	14	7	9	11	1	2	2	2	2	0	0	2	3	2	2	2	2	2	2	2	2	3	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr7:103029857G>A	ENST00000306312.3	-	13	1587	c.1326C>T	c.(1324-1326)gcC>gcT	p.A442A	SLC26A5_ENST00000393727.1_Silent_p.A442A|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000393730.1_Intron|SLC26A5_ENST00000393723.1_Intron|SLC26A5_ENST00000432958.2_Intron|SLC26A5_ENST00000393729.1_Silent_p.A405A|SLC26A5_ENST00000339444.6_Silent_p.A442A|SLC26A5_ENST00000393735.2_Silent_p.A442A|SLC26A5_ENST00000356767.4_Intron	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	442					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						CAATCACAATGGCCGACAGCA	0.498																																					p.A442A		.											.	SLC26A5-91	0			c.C1326T						.						145	124	131					7																	103029857		2203	4300	6503	SO:0001819	synonymous_variant	375611	exon13			CACAATGGCCGAC	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1326C>T	7.37:g.103029857G>A		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	78	30	NM_206883	0	0	0	0	0	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1																																																																																			.		0.498	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		A	103029857	G	A	103029857	2	1	7	1	0	0	0	0	0	0	0	1	14552	1335	47	2		2	SLC26A5	7	103029857	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08	31887622	103029857	56108806	33	540											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241089	131241089	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcgttgacaacagtagcagCagcgccgagagcgccagcgc	10	3	15	13	5	0	2	0	1	0	1	0	3	0	2	2	1	6	4	2	1	2	2	rs116656523	byFrequency	TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr7:131241089C>T	ENST00000378555.3	-	1	277	c.30G>A	c.(28-30)ctG>ctA	p.L10L	PODXL_ENST00000322985.9_Silent_p.L10L|PODXL_ENST00000541194.1_Silent_p.L10L|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.L10L			O00592	PODXL_HUMAN	podocalyxin-like	10					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					ACAGTAGCAGCAGCGCCGAGA	0.746													C|||	49	0.00978435	0.0356	0.0029	5008	,	,		9741	0		0	False		,,,				2504	0				p.L10L		.											.	PODXL-136	0			c.G30A						.	C	,	89,4029		1,87,1971	6	9	8		30,30	-2.9	0	7	dbSNP_132	8	1,8107		0,1,4053	no	coding-synonymous,coding-synonymous	PODXL	NM_001018111.2,NM_005397.3	,	1,88,6024	TT,TC,CC		0.0123,2.1612,0.7361	,	10/559,10/527	131241089	90,12136	2059	4054	6113	SO:0001819	synonymous_variant	5420	exon1			TAGCAGCAGCGCC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.30G>A	7.37:g.131241089C>T		Somatic	5	2		WXS	Illumina HiSeq	Phase_I	14	7	NM_001018111	0	0	0	0	0	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			C|0.993;T|0.007		0.746	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		T	131241089	C	T	131241089	2	4	7	1	0	0	0	0	0	0	0	1	12206	697	25	2		2	PODXL	7	131241089	Silent	SNP	C	TCGA-A4-7732-01A-11D-2136-08	28211232	131241089	27897574	34	541											
ZNF707	286075	broad.mit.edu	37	chr8	144776267	144776267	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagaagaaccacacgcGcgagaagcccttctgctgcg	11	4	10	16	4	1	3	0	0	1	3	1	4	1	3	4	0	4	1	4	0	3	1	rs368360386		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr8:144776267G>A	ENST00000532205.1	+	8	1582	c.683G>A	c.(682-684)cGc>cAc	p.R228H	RP11-429J17.2_ENST00000531565.1_RNA|ZNF707_ENST00000532158.1_Missense_Mutation_p.R228H|ZNF707_ENST00000454097.1_Missense_Mutation_p.R228H|ZNF707_ENST00000418203.2_Missense_Mutation_p.R228H|ZNF707_ENST00000358656.4_Missense_Mutation_p.R228H			Q96C28	ZN707_HUMAN	zinc finger protein 707	228					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)	1	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;5.6e-41)|Epithelial(56;1.02e-39)|all cancers(56;9.65e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			AACCACACGCGCGAGAAGCCC	0.667													G|||	1	0.000199681	8e-04	0	5008	,	,		16764	0		0	False		,,,				2504	0				p.R228H													.	ZNF707-67	0			c.G683A						.	G	HIS/ARG,HIS/ARG,HIS/ARG	3,4207		0,3,2102	15	19	17		683,683,683	-2	0	8		17	0,8452		0,0,4226	no	missense,missense,missense	ZNF707	NM_001100598.1,NM_001100599.1,NM_173831.3	29,29,29	0,3,6328	AA,AG,GG		0.0,0.0713,0.0237	benign,benign,benign	228/372,228/372,228/372	144776267	3,12659	2105	4226	6331	SO:0001583	missense	286075	exon6			ACACGCGCGAGAA	AK001126	CCDS47932.1	8q24.3	2013-01-08				ENSG00000181135		"Zinc fingers, C2H2-type", "-"	27815	protein-coding gene	gene with protein product						12477932	Standard	NM_173831		Approved		uc010mfi.3	Q96C28		ENST00000532205.1:c.683G>A	8.37:g.144776267G>A	ENSP00000436212:p.Arg228His	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_001100598	0	0	8	8	0	A8K317|B3KNY1|D3DWK7	Missense_Mutation	SNP	ENST00000532205.1	37	CCDS47932.1	.	.	.	.	.	.	.	.	.	.	G	2.453	-0.325892	0.05350	7.13E-4	0.0	ENSG00000181135	ENST00000454097;ENST00000358656;ENST00000532158;ENST00000532205;ENST00000418203	T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22	2.99	-2.01	0.07410	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23249	0.0562	L	0.58354	1.805	0.09310	N	1	D;P	0.65815	0.995;0.942	P;B	0.53760	0.734;0.308	T	0.09530	-1.0670	8	.	.	.	-0.0611	6.335	0.21291	0.2932:0.1315:0.5754:0.0	.	153;228	B4DV46;Q96C28	.;ZN707_HUMAN	H	228	ENSP00000409029:R228H;ENSP00000351482:R228H;ENSP00000436250:R228H;ENSP00000436212:R228H;ENSP00000413215:R228H	.	R	+	2	0	ZNF707	144848255	0.002000	0.14202	0.000000	0.03702	0.005000	0.04900	0.739000	0.26173	-1.528000	0.01756	-2.578000	0.00169	CGC	.		0.667	ZNF707-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382197.1	NM_173831		A	144776267	G	A	144776267	3	1	7	1	0	0	0	0	1	0	0	0	18143	1087	38	1	697	1	ZNF707	8	144776267	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		144776267	1587755	35	542											
MAPK15	225689	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	144801161	144801161	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcctgcctcctctctgcAgccgtccaatgtgctcctgg	4	11	9	17	1	2	0	1	0	1	0	6	0	5	0	6	1	5	2	6	1	1	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr8:144801161A>T	ENST00000338033.4	+	6	536		c.e6-1		RP11-429J17.5_ENST00000527908.1_RNA|MAPK15_ENST00000395107.4_Splice_Site|MAPK15_ENST00000395108.2_Splice_Site	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15						MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TCCTCTCTGCAGCCGTCCAAT	0.711																																					.		.											.	MAPK15-1378	0			c.418-2A>T						.						21	19	20					8																	144801161		2202	4299	6501	SO:0001630	splice_region_variant	225689	exon6			CTCTGCAGCCGTC	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"Mitogen-activated protein kinase cascade / Kinases"	24667	protein-coding gene	gene with protein product	"extracellular signal regulated kinase 8"					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.418-1A>T	8.37:g.144801161A>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	12	7	NM_139021	0	0	0	8	8	Q2TCF9|Q8N362	Splice_Site	SNP	ENST00000338033.4	37	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	A	16.20	3.054752	0.55325	.	.	ENSG00000181085	ENST00000338033;ENST00000395107;ENST00000395108	.	.	.	4.02	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9881	0.24739	0.8928:0.0:0.1072:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAPK15	144873149	1.000000	0.71417	0.912000	0.35992	0.794000	0.44872	4.544000	0.60691	1.680000	0.50976	0.157000	0.16456	.	.		0.711	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	Intron	T	144801161	A	T	144801161	5	4	7	1	0	0	0	0	0	0	1	0	9302	202	7	5	438	5	MAPK15	8	144801161	Splice_Site	SNP	A	TCGA-A4-7732-01A-11D-2136-08	24894	144801161	1562861	36	543											
SLC1A1	6505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	4585458	4585458	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccttggaatccacaatccTtgacaacgaagactcagaca	14	8	7	12	1	1	3	1	1	0	2	3	5	3	4	3	1	2	0	3	1	4	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr9:4585458T>C	ENST00000262352.3	+	12	1711	c.1475T>C	c.(1474-1476)cTt>cCt	p.L492P		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	492					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	TCCACAATCCTTGACAACGAA	0.463																																					p.L492P		.											.	SLC1A1-514	0			c.T1475C						.						134	109	118					9																	4585458		2203	4300	6503	SO:0001583	missense	6505	exon12			CAATCCTTGACAA		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.1475T>C	9.37:g.4585458T>C	ENSP00000262352:p.Leu492Pro	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	56	27	NM_004170	0	0	9	18	9	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	ENST00000262352.3	37	CCDS6452.1	.	.	.	.	.	.	.	.	.	.	T	3.609	-0.079875	0.07141	.	.	ENSG00000106688	ENST00000262352	T	0.57752	0.38	5.71	3.33	0.38152	.	0.566440	0.18485	N	0.139812	T	0.28200	0.0696	N	0.08118	0	0.21878	N	0.999492	B	0.12013	0.005	B	0.11329	0.006	T	0.14420	-1.0473	10	0.35671	T	0.21	.	5.5545	0.17109	0.1284:0.1394:0.0:0.7322	.	492	P43005	EAA3_HUMAN	P	492	ENSP00000262352:L492P	ENSP00000262352:L492P	L	+	2	0	SLC1A1	4575458	0.890000	0.30428	0.013000	0.15412	0.092000	0.18411	3.193000	0.50997	0.417000	0.25871	0.460000	0.39030	CTT	.		0.463	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			C	4585458	T	C	4585458	3	2	7	1	0	0	0	0	1	0	0	0	14463	1609	56	3	1521	3	SLC1A1	9	4585458	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		4585458	136627973	37	544											
APTX	54840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	32988092	32988092	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacacctacctgctttacctTgacatatcccttgttacact	9	15	3	14	0	0	1	0	1	0	0	1	1	1	1	4	0	5	2	4	0	5	8			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr9:32988092T>A	ENST00000379819.1	-	3	210	c.211A>T	c.(211-213)Aag>Tag	p.K71*	APTX_ENST00000476858.1_Intron|APTX_ENST00000309615.3_Nonsense_Mutation_p.K71*|APTX_ENST00000379825.2_Nonsense_Mutation_p.K71*|APTX_ENST00000397172.3_Nonsense_Mutation_p.K71*|APTX_ENST00000436040.2_Nonsense_Mutation_p.K57*|APTX_ENST00000468275.1_Nonsense_Mutation_p.K57*|APTX_ENST00000463596.1_Nonsense_Mutation_p.K57*|APTX_ENST00000379813.3_Nonsense_Mutation_p.K57*|APTX_ENST00000379817.2_Nonsense_Mutation_p.K57*			Q7Z2E3	APTX_HUMAN	aprataxin	71	FHA-like.|Interactions with ADPRT and NCL.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|dephosphorylation (GO:0016311)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA ligation (GO:0006266)|double-strand break repair (GO:0006302)|polynucleotide 3' dephosphorylation (GO:0098506)|regulation of protein stability (GO:0031647)|response to hydrogen peroxide (GO:0042542)|single strand break repair (GO:0000012)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA 5'-adenosine monophosphate hydrolase activity (GO:0033699)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|phosphoglycolate phosphatase activity (GO:0008967)|phosphoprotein binding (GO:0051219)|polynucleotide 3'-phosphatase activity (GO:0046403)|protein N-terminus binding (GO:0047485)			endometrium(1)|lung(1)|ovary(2)|prostate(2)	6			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		TGCTTTACCTTGACATATCCC	0.388								Editing and processing nucleases																													p.K71X		.											.	APTX-91	0			c.A211T						.						136	132	134					9																	32988092		2203	4300	6503	SO:0001587	stop_gained	54840	exon3			TTACCTTGACATA	AK000164	CCDS47956.1, CCDS56568.1, CCDS75827.1	9p13.3	2014-01-28	2003-04-03		ENSG00000137074	ENSG00000137074			15984	protein-coding gene	gene with protein product		606350	"ataxia 1, early onset with hypoalbuminemia"	AXA1		11586299, 11586300	Standard	NM_175069		Approved	FLJ20157, AOA, AOA1, EAOH, EOAHA	uc003zry.3	Q7Z2E3	OTTHUMG00000019759	ENST00000379819.1:c.211A>T	9.37:g.32988092T>A	ENSP00000369147:p.Lys71*	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	76	25	NM_001195252	0	0	0	0	0	A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	Nonsense_Mutation	SNP	ENST00000379819.1	37		.	.	.	.	.	.	.	.	.	.	T	36	5.750052	0.96890	.	.	ENSG00000137074	ENST00000379825;ENST00000309615;ENST00000397172;ENST00000379817;ENST00000436040;ENST00000379819;ENST00000468275;ENST00000463596;ENST00000344355;ENST00000379813;ENST00000379812	.	.	.	5.16	5.16	0.70880	.	0.326514	0.35805	N	0.002978	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.792	12.9503	0.58397	0.0:0.0:0.0:1.0	.	.	.	.	X	71;71;71;57;57;71;57;57;71;57;71	.	ENSP00000311547:K71X	K	-	1	0	APTX	32978092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.233000	0.58651	1.957000	0.56846	0.455000	0.32223	AAG	.		0.388	APTX-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000052028.2	NM_017692		A	32988092	T	A	32988092	4	1	7	1	0	0	0	0	0	1	0	0	820	1821	63	5	892	5	APTX	9	32988092	Nonsense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	28402634	32988092	108225339	38	545											
PTCH1	5727	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	98268787	98268787	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggcccacaaccaagaacttgCcgcagtttttttgaatgtaa	12	11	8	10	1	0	2	0	1	0	1	0	2	0	2	3	1	3	3	3	1	5	5			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr9:98268787C>T	ENST00000331920.6	-	2	595	c.296G>A	c.(295-297)gGc>gAc	p.G99D	PTCH1_ENST00000437951.1_Missense_Mutation_p.G33D|PTCH1_ENST00000421141.1_5'UTR|RP11-435O5.5_ENST00000604104.1_RNA|PTCH1_ENST00000429896.2_5'UTR|PTCH1_ENST00000418258.1_5'UTR|PTCH1_ENST00000375274.2_Missense_Mutation_p.G98D|PTCH1_ENST00000430669.2_Missense_Mutation_p.G33D|PTCH1_ENST00000468211.2_Missense_Mutation_p.G33D	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	99					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.C98fs*13(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CAAGAACTTGCCGCAGTTTTT	0.537																																					p.G99D		.											.	PTCH1-3532	1	Deletion - Frameshift(1)	skin(1)	c.G296A						.						67	69	68					9																	98268787		2203	4300	6503	SO:0001583	missense	5727	exon2			AACTTGCCGCAGT	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"patched (Drosophila) homolog", "patched homolog (Drosophila)", "patched homolog 1 (Drosophila)"	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.296G>A	9.37:g.98268787C>T	ENSP00000332353:p.Gly99Asp	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_000264	0	0	0	0	0	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593802	0.86953	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000430669;ENST00000375274;ENST00000544247;ENST00000468211	D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	D	0.94056	0.8095	M	0.78916	2.43	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	D	0.93805	0.7104	10	0.40728	T	0.16	-11.9121	16.7843	0.85570	0.0:1.0:0.0:0.0	.	33;98;99	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	D	99;33;33;98;33;33	ENSP00000332353:G99D;ENSP00000389744:G33D;ENSP00000410287:G33D;ENSP00000364423:G98D;ENSP00000449745:G33D	ENSP00000332353:G99D	G	-	2	0	PTCH1	97308608	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.168000	0.77570	2.033000	0.60031	0.561000	0.74099	GGC	.		0.537	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		T	98268787	C	T	98268787	3	4	7	1	0	0	0	0	1	0	0	0	12759	739	26	2	4135	2	PTCH1	9	98268787	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	65280695	98268787	42944644	39	546											
ZMYND11	10771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	287963	287963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaacatttaatttccagatAcctaatcatgagctggtttg	14	14	6	7	0	1	2	1	1	0	1	2	2	2	2	2	1	3	2	2	1	5	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr10:287963A>G	ENST00000397962.3	+	10	1262	c.834A>G	c.(832-834)atA>atG	p.I278M	ZMYND11_ENST00000545619.1_Missense_Mutation_p.I158M|ZMYND11_ENST00000403354.1_Missense_Mutation_p.I198M|ZMYND11_ENST00000402736.1_Missense_Mutation_p.I247M|ZMYND11_ENST00000558098.2_Missense_Mutation_p.I278M|ZMYND11_ENST00000381602.4_Missense_Mutation_p.I238M|ZMYND11_ENST00000309776.4_Missense_Mutation_p.I238M|ZMYND11_ENST00000397959.3_Missense_Mutation_p.I193M|ZMYND11_ENST00000535374.1_Missense_Mutation_p.I73M|ZMYND11_ENST00000602682.1_Missense_Mutation_p.I193M|ZMYND11_ENST00000381604.4_Missense_Mutation_p.I238M|ZMYND11_ENST00000509513.2_Missense_Mutation_p.I277M|ZMYND11_ENST00000381584.1_Missense_Mutation_p.I261M|ZMYND11_ENST00000381591.1_Missense_Mutation_p.I278M|ZMYND11_ENST00000381607.4_Missense_Mutation_p.I184M			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	278					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ATTTCCAGATACCTAATCATG	0.328																																					p.I278M		.											.	ZMYND11-90	0			c.A834G						.						111	110	111					10																	287963		2203	4300	6503	SO:0001583	missense	10771	exon10			CCAGATACCTAAT	X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"Zinc fingers, MYND-type"	16966	protein-coding gene	gene with protein product		608668	"zinc finger, MYND domain containing 11"			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.834A>G	10.37:g.287963A>G	ENSP00000381053:p.Ile278Met	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	46	17	NM_006624	0	0	0	1	1	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Missense_Mutation	SNP	ENST00000397962.3	37	CCDS7052.2	.	.	.	.	.	.	.	.	.	.	A	16.71	3.199641	0.58126	.	.	ENSG00000015171	ENST00000397962;ENST00000309776;ENST00000381602;ENST00000509513;ENST00000397959;ENST00000381591;ENST00000403354;ENST00000381607;ENST00000402736;ENST00000381604;ENST00000381584;ENST00000545619;ENST00000535374	T;T;T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	6.17	5.03	0.67393	PWWP (2);	0.248837	0.46758	D	0.000271	T	0.59088	0.2168	N	0.08118	0	0.30416	N	0.778601	P;P;P;P;D;P;P;P;P;D	0.55800	0.918;0.921;0.727;0.727;0.973;0.832;0.918;0.882;0.927;0.973	P;P;P;P;P;P;P;B;B;P	0.49752	0.49;0.587;0.56;0.56;0.592;0.621;0.49;0.397;0.402;0.592	T	0.70839	-0.4763	9	0.46703	T	0.11	-28.5082	12.919	0.58222	0.8782:0.0:0.0:0.1218	.	238;278;193;223;278;198;207;224;224;247	Q15326;Q2LD45;B7Z293;B7Z2J6;Q2LD48;B0QZE2;B0QZE3;Q2LD46;Q2LD47;E7ENI9	ZMY11_HUMAN;.;.;.;.;.;.;.;.;.	M	278;238;238;278;193;278;198;184;247;238;261;158;73	ENSP00000381053:I278M;ENSP00000309992:I238M;ENSP00000371015:I238M;ENSP00000381050:I193M;ENSP00000371003:I278M;ENSP00000385484:I198M;ENSP00000371020:I184M;ENSP00000386010:I247M;ENSP00000371017:I238M;ENSP00000370996:I261M;ENSP00000438461:I158M;ENSP00000439587:I73M	ENSP00000309992:I238M	I	+	3	3	ZMYND11	277963	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.942000	0.40243	1.134000	0.42165	0.533000	0.62120	ATA	.		0.328	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624		G	287963	A	G	287963	3	3	7	1	0	0	0	0	1	0	0	0	17738	381	14	3	868	3	ZMYND11	10	287963	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08		287963	135246784	40	547											
PLXDC2	84898	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	20357165	20357165	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaatcactgtggcaaccGggggtaagtggttttctacc	9	11	13	8	1	2	1	1	1	1	0	2	1	2	1	2	4	2	3	2	4	4	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr10:20357165G>A	ENST00000377252.4	+	4	1379	c.538G>A	c.(538-540)Ggg>Agg	p.G180R	PLXDC2_ENST00000377238.2_3'UTR|RP11-575A19.2_ENST00000451584.1_RNA|PLXDC2_ENST00000377242.3_Missense_Mutation_p.G131R	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	180					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						TGTGGCAACCGGGGGTAAGTG	0.358																																					p.G180R													.	PLXDC2-93	0			c.G538A						.						74	70	71					10																	20357165		2203	4300	6503	SO:0001583	missense	84898	exon4			GCAACCGGGGGTA	AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.538G>A	10.37:g.20357165G>A	ENSP00000366460:p.Gly180Arg	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	29	4	NM_032812	0	0	0	0	0	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535127	0.85812	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	D;D	0.83335	-1.71;-1.71	5.85	5.85	0.93711	.	0.044468	0.85682	D	0.000000	D	0.91106	0.7200	M	0.75150	2.29	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68943	0.961;0.942	D	0.90862	0.4739	10	0.62326	D	0.03	.	20.2366	0.98359	0.0:0.0:1.0:0.0	.	131;180	Q6UX71-2;Q6UX71	.;PXDC2_HUMAN	R	180;131;43;166	ENSP00000366460:G180R;ENSP00000366450:G131R	ENSP00000366446:G43R	G	+	1	0	PLXDC2	20397171	1.000000	0.71417	1.000000	0.80357	0.540000	0.34992	8.884000	0.92432	2.793000	0.96121	0.558000	0.71614	GGG	.		0.358	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		A	20357165	G	A	20357165	3	1	7	1	0	0	0	0	1	0	0	0	12144	1116	39	1	552	1	PLXDC2	10	20357165	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	20069202	20357165	115177582	41	548											
PPRC1	23082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	103900396	103900396	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcagcaccccagctcctcGtggagtcagagtccttggac	7	9	11	14	1	2	1	2	0	0	1	5	3	4	3	4	2	2	3	4	2	0	2	rs17847386		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr10:103900396G>A	ENST00000278070.2	+	5	2170	c.2131G>A	c.(2131-2133)Gtg>Atg	p.V711M	PPRC1_ENST00000370012.1_5'Flank|PPRC1_ENST00000413464.2_Missense_Mutation_p.V711M	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	711					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CCAGCTCCTCGTGGAGTCAGA	0.532																																					p.V711M		.											.	PPRC1-227	0			c.G2131A						.						79	75	76					10																	103900396		2203	4300	6503	SO:0001583	missense	23082	exon5			CTCCTCGTGGAGT	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.2131G>A	10.37:g.103900396G>A	ENSP00000278070:p.Val711Met	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	64	6	NM_015062	0	0	3	3	0	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	g	8.673	0.903227	0.17760	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.24151	1.88;1.87	3.89	-0.341	0.12639	.	0.355194	0.16037	N	0.232573	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;P;B	0.41345	0.191;0.746;0.191	B;B;B	0.31191	0.036;0.125;0.036	T	0.22765	-1.0207	10	0.46703	T	0.11	.	5.7647	0.18219	0.0:0.3035:0.4867:0.2099	rs17847386	711;591;711	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	M	711	ENSP00000278070:V711M;ENSP00000399743:V711M	ENSP00000278070:V711M	V	+	1	0	PPRC1	103890386	0.000000	0.05858	0.006000	0.13384	0.068000	0.16541	-0.952000	0.03881	-0.046000	0.13446	-1.200000	0.01667	GTG	G|0.999;T|0.001		0.532	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		A	103900396	G	A	103900396	3	1	7	1	0	0	0	0	1	0	0	0	12439	1145	40	1	2149	1	PPRC1	10	103900396	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	83543231	103900396	31634351	42	549											
COPB1	1315	hgsc.bcm.edu	37	chr11	14510132	14510132	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtaatccaaagctcgatccTaaaaaaaataagaatatatt	21	10	4	6	1	0	1	0	0	0	1	3	2	2	1	2	0	1	2	2	0	10	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:14510132T>C	ENST00000249923.3	-	6	907		c.e6-2		COPB1_ENST00000439561.2_Splice_Site	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						AGCTCGATCCTAAAAAAAATA	0.294																																					.		.											.	COPB1-91	0			c.607-2A>G						.						39	40	39					11																	14510132		2199	4289	6488	SO:0001630	splice_region_variant	1315	exon7			CGATCCTAAAAAA	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.607-2A>G	11.37:g.14510132T>C		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	20	2	NM_001144062	0	0	0	0	0	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Splice_Site	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.100291	0.76983	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234	.	.	.	4.66	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3891	0.66965	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	COPB1	14466708	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.997000	0.88414	1.864000	0.54056	0.533000	0.62120	.	.		0.294	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451	Intron	C	14510132	T	C	14510132	5	2	7	1	0	0	0	0	0	0	1	0	3734	1536	53	3	2324	3	COPB1	11	14510132	Splice_Site	SNP	T	TCGA-A4-7732-01A-11D-2136-08		14510132	120496384	43	550											
SLC5A12	159963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	26743059	26743059	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacttcagaaggggtccccAggaccgtgacagctgacatg	11	6	13	11	1	1	4	1	2	0	2	2	5	2	5	3	3	1	1	3	3	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:26743059A>G	ENST00000396005.3	-	1	512	c.203T>C	c.(202-204)cTg>cCg	p.L68P	SLC5A12_ENST00000280467.6_Missense_Mutation_p.L68P	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	68					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						AGGGGTCCCCAGGACCGTGAC	0.522																																					p.L68P		.											.	SLC5A12-92	0			c.T203C						.						78	78	78					11																	26743059		2203	4299	6502	SO:0001583	missense	159963	exon1			GTCCCCAGGACCG	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.203T>C	11.37:g.26743059A>G	ENSP00000379326:p.Leu68Pro	Somatic	57	1		WXS	Illumina HiSeq	Phase_I	50	22	NM_178498	0	0	0	2	2	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	19.99	3.929498	0.73327	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.90324	-2.65;-2.65	5.59	5.59	0.84812	.	0.092595	0.45606	D	0.000357	D	0.96996	0.9019	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	D	0.98356	1.0546	10	0.87932	D	0	.	15.7638	0.78110	1.0:0.0:0.0:0.0	.	68;68	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	P	68	ENSP00000379326:L68P;ENSP00000280467:L68P	ENSP00000280467:L68P	L	-	2	0	SLC5A12	26699635	0.987000	0.35691	0.873000	0.34254	0.613000	0.37349	9.273000	0.95719	2.135000	0.66039	0.477000	0.44152	CTG	.		0.522	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26743059	A	G	26743059	3	3	7	1	0	0	0	0	1	0	0	0	14696	188	7	3	1713	3	SLC5A12	11	26743059	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	12232927	26743059	108263457	44	551											
SLC43A3	29015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57177469	57177469	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggctgatcacttgcaggaTgaaggtgaggtactggagag	10	8	17	6	1	1	4	1	3	0	1	1	6	1	5	0	5	2	3	0	5	2	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:57177469T>G	ENST00000395123.2	-	12	1490	c.1186A>C	c.(1186-1188)Atc>Ctc	p.I396L	SLC43A3_ENST00000529554.1_Missense_Mutation_p.I396L|SLC43A3_ENST00000352187.1_Missense_Mutation_p.I396L|SLC43A3_ENST00000395124.1_Missense_Mutation_p.I396L|RP11-872D17.8_ENST00000529411.1_Missense_Mutation_p.I40L|SLC43A3_ENST00000533524.1_Missense_Mutation_p.I409L	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	396					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						ACTTGCAGGATGAAGGTGAGG	0.632																																					p.I396L		.											.	SLC43A3-90	0			c.A1186C						.						93	72	79					11																	57177469		2201	4296	6497	SO:0001583	missense	29015	exon12			GCAGGATGAAGGT	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.1186A>C	11.37:g.57177469T>G	ENSP00000378555:p.Ile396Leu	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	24	7	NM_017611	0	0	5	5	0	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711618	0.68730	.	.	ENSG00000254979;ENSG00000134802;ENSG00000134802;ENSG00000134802;ENSG00000134802;ENSG00000134802	ENST00000529411;ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524	T;T;T;T;T;T	0.80123	-1.34;0.43;0.43;0.43;0.43;0.43	5.65	0.744	0.18353	Major facilitator superfamily domain, general substrate transporter (1);	0.373532	0.30235	N	0.010082	T	0.73218	0.3559	M	0.64997	1.995	0.35492	D	0.799026	B;B	0.22276	0.031;0.067	B;B	0.25614	0.062;0.062	T	0.64343	-0.6430	10	0.23891	T	0.37	-18.2579	8.0046	0.30317	0.0:0.353:0.0:0.647	.	409;396	E7EQD2;Q8NBI5	.;S43A3_HUMAN	L	40;396;396;396;396;409	ENSP00000431536:I40L;ENSP00000378555:I396L;ENSP00000378556:I396L;ENSP00000337561:I396L;ENSP00000436254:I396L;ENSP00000434515:I409L	ENSP00000431536:I40L	I	-	1	0	RP11-872D17.8;SLC43A3	56934045	0.962000	0.33011	0.995000	0.50966	0.953000	0.61014	-0.028000	0.12350	-0.110000	0.12022	0.533000	0.62120	ATC	.		0.632	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		G	57177469	T	G	57177469	3	3	7	1	0	0	0	0	1	0	0	0	14666	1464	51	5	301	5	SLC43A3	11	57177469	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	30434410	57177469	77829047	45	552											
USP28	57646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113705056	113705056	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attcaggcaattgaaagagaGactgaaataaagaaagaaag	22	6	10	3	0	1	6	1	2	0	4	1	7	1	6	0	1	0	1	0	1	7	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:113705056G>C	ENST00000003302.4	-	6	604	c.536C>G	c.(535-537)tCt>tGt	p.S179C	USP28_ENST00000545540.1_Splice_Site_p.S54C|USP28_ENST00000537706.1_Splice_Site_p.S179C|USP28_ENST00000542033.1_5'UTR|USP28_ENST00000260188.5_Splice_Site_p.S179C	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	179	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		TTGAAAGAGAGACTGAAATAA	0.313																																					p.S179C	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	.											.	USP28-706	0			c.C536G						.						83	78	80					11																	113705056		2201	4296	6497	SO:0001630	splice_region_variant	57646	exon6			AAGAGAGACTGAA	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.535-1C>G	11.37:g.113705056G>C		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	34	18	NM_020886	0	0	0	0	0	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470732	0.84533	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000545540;ENST00000537706	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.08	5.08	0.68730	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	L	0.55743	1.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.994;1.0;0.997;0.999	T	0.55147	-0.8186	10	0.87932	D	0	-14.6997	17.4468	0.87580	0.0:0.0:1.0:0.0	.	179;54;179;179	B4E2Q2;B4E3L3;Q6NZX9;Q96RU2	.;.;.;UBP28_HUMAN	C	179;179;54;179	ENSP00000003302:S179C;ENSP00000260188:S179C;ENSP00000444991:S54C;ENSP00000445743:S179C	ENSP00000003302:S179C	S	-	2	0	USP28	113210266	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.444000	0.97578	2.357000	0.79964	0.460000	0.39030	TCT	.		0.313	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		Missense_Mutation	C	113705056	G	C	113705056	5	2	7	1	0	0	0	0	0	0	1	0	17091	956	33	4	2777	4	USP28	11	113705056	Splice_Site	SNP	G	TCGA-A4-7732-01A-11D-2136-08	56527587	113705056	21301460	46	553											
SIDT2	51092	broad.mit.edu;bcgsc.ca	37	chr11	117063308	117063308	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agactcggggatcttccgccGcatcctccacgtgctctaca	7	9	9	16	4	2	1	0	0	2	1	6	2	5	2	4	2	2	2	4	2	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:117063308G>A	ENST00000324225.4	+	21	2531	c.2000G>A	c.(1999-2001)cGc>cAc	p.R667H	SIDT2_ENST00000532062.1_5'Flank|SIDT2_ENST00000431081.2_Missense_Mutation_p.R664H	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	667					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		ATCTTCCGCCGCATCCTCCAC	0.632																																					p.R667H													.	SIDT2-90	0			c.G2000A						.						79	64	69					11																	117063308		2201	4296	6497	SO:0001583	missense	51092	exon21			TCCGCCGCATCCT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.2000G>A	11.37:g.117063308G>A	ENSP00000314023:p.Arg667His	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	75	5	NM_001040455	0	0	9	9	0	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058195	0.93846	.	.	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081;ENST00000525478	T;T;T	0.20598	2.06;2.07;2.07	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.53834	0.1821	M	0.86953	2.85	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.994;0.997;0.999	T	0.62445	-0.6853	10	0.72032	D	0.01	-23.3667	18.2684	0.90060	0.0:0.0:1.0:0.0	.	688;664;667;688	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	H	667;688;664;5	ENSP00000314023:R667H;ENSP00000278951:R688H;ENSP00000399635:R664H	ENSP00000278951:R688H	R	+	2	0	SIDT2	116568518	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.674000	0.83992	2.549000	0.85964	0.563000	0.77884	CGC	.		0.632	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		A	117063308	G	A	117063308	3	1	7	1	0	0	0	0	1	0	0	0	14335	1087	38	1	2082	1	SIDT2	11	117063308	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	3358252	117063308	17943208	47	554											
DPAGT1	1798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118969112	118969112	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttatccacaggcctacttaCcagttgtggtagagcaatcc	10	11	8	12	0	0	1	0	0	0	1	2	1	2	1	4	2	3	3	4	2	5	5			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:118969112C>T	ENST00000409993.2	-	7	2280		c.e7+1		DPAGT1_ENST00000445653.1_5'Flank|H2AFX_ENST00000530167.1_5'Flank|DPAGT1_ENST00000432443.2_Splice_Site|DPAGT1_ENST00000354202.4_Splice_Site			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)						cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GGCCTACTTACCAGTTGTGGT	0.463																																					.		.											.	DPAGT1-221	0			c.728+1G>A						.						194	173	180					11																	118969112		2200	4295	6495	SO:0001630	splice_region_variant	1798	exon6			TACTTACCAGTTG	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.728+1G>A	11.37:g.118969112C>T		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	101	50	NM_001382	0	0	0	2	2	O15216|Q86WV9|Q9BWE6	Splice_Site	SNP	ENST00000409993.2	37	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.476893	0.84640	.	.	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2906	0.90129	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DPAGT1	118474322	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.570000	0.82390	2.788000	0.95919	0.650000	0.86243	.	.		0.463	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382	Intron	T	118969112	C	T	118969112	5	4	7	1	0	0	0	0	0	0	1	0	4721	521	18	2	517	2	DPAGT1	11	118969112	Splice_Site	SNP	C	TCGA-A4-7732-01A-11D-2136-08	1905804	118969112	16037404	48	555											
TFCP2	7024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	51495806	51495806	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agttaatttcaataaatctgCccctggaataaatataagaa	18	12	5	6	0	2	1	1	0	1	1	2	2	2	2	2	1	1	1	2	1	10	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:51495806C>T	ENST00000257915.5	-	11	1521	c.1063G>A	c.(1063-1065)Gca>Aca	p.A355T	TFCP2_ENST00000307660.4_Missense_Mutation_p.A304T|TFCP2_ENST00000549867.1_Intron|TFCP2_ENST00000548115.1_Missense_Mutation_p.A304T	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	355	DNA-binding.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AATAAATCTGCCCCTGGAATA	0.343																																					p.A355T		.											.	TFCP2-91	0			c.G1063A						.						51	53	52					12																	51495806		2202	4300	6502	SO:0001583	missense	7024	exon11			AATCTGCCCCTGG	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.1063G>A	12.37:g.51495806C>T	ENSP00000257915:p.Ala355Thr	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	65	15	NM_001173452	0	0	0	0	0	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	37	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089945	0.76756	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000548115;ENST00000548108	T;T;T;T	0.51325	2.11;0.71;0.74;2.09	5.19	4.31	0.51392	Sterile alpha motif/pointed domain (1);	0.000000	0.85682	D	0.000000	T	0.61689	0.2367	L	0.53729	1.69	0.58432	D	0.999995	D;B;B	0.67145	0.996;0.059;0.182	D;B;B	0.79784	0.993;0.059;0.177	T	0.61564	-0.7037	10	0.42905	T	0.14	-20.1909	12.9675	0.58492	0.0:0.9209:0.0:0.0791	.	304;355;355	Q12800-2;Q12800;Q12800-4	.;TFCP2_HUMAN;.	T	355;304;304;257	ENSP00000257915:A355T;ENSP00000304411:A304T;ENSP00000447991:A304T;ENSP00000449280:A257T	ENSP00000257915:A355T	A	-	1	0	TFCP2	49782073	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.576000	0.60915	1.574000	0.49760	0.563000	0.77884	GCA	.		0.343	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		T	51495806	C	T	51495806	3	4	7	1	0	0	0	0	1	0	0	0	15827	739	26	2	465	2	TFCP2	12	51495806	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		51495806	82356089	49	556											
SLC39A5	283375	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56626598	56626598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagccccctcgggcctggAcctccttcacaggcttctgt	4	9	10	18	1	2	0	1	0	1	0	4	1	3	1	6	3	1	1	6	3	0	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:56626598A>G	ENST00000266980.4	+	3	706	c.413A>G	c.(412-414)gAc>gGc	p.D138G	SLC39A5_ENST00000454355.2_Missense_Mutation_p.D138G	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	138					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCGGGCCTGGACCTCCTTCAC	0.612																																					p.D138G		.											.	SLC39A5-92	0			c.A413G						.						51	52	52					12																	56626598		2203	4300	6503	SO:0001583	missense	283375	exon5			GCCTGGACCTCCT		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"Solute carriers"	20502	protein-coding gene	gene with protein product		608730	"solute carrier family 39 (metal ion transporter), member 5"				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.413A>G	12.37:g.56626598A>G	ENSP00000266980:p.Asp138Gly	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	83	32	NM_173596	0	0	28	35	7	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	37	CCDS8912.2	.	.	.	.	.	.	.	.	.	.	A	10.38	1.334275	0.24253	.	.	ENSG00000139540	ENST00000419753;ENST00000454355;ENST00000436633;ENST00000266980	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	5.43	-4.08	0.03963	.	0.862131	0.10182	N	0.705702	T	0.15739	0.0379	N	0.25647	0.755	0.23473	N	0.997603	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.31668	-0.9935	9	.	.	.	-2.6848	13.1574	0.59524	0.4593:0.0:0.5407:0.0	.	138;29	Q6ZMH5;B4DPG8	S39A5_HUMAN;.	G	138;138;109;138	ENSP00000402891:D138G;ENSP00000405360:D138G;ENSP00000391711:D109G;ENSP00000266980:D138G	.	D	+	2	0	SLC39A5	54912865	0.782000	0.28689	0.322000	0.25334	0.858000	0.48976	-0.215000	0.09279	-0.637000	0.05516	-0.269000	0.10298	GAC	.		0.612	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		G	56626598	A	G	56626598	3	3	7	1	0	0	0	0	1	0	0	0	14653	275	10	3	419	3	SLC39A5	12	56626598	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	5130792	56626598	77225297	50	557											
GLI1	2735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57864354	57864354	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgcagcatccagcctggatCggataggtggtcttcccatg	7	10	12	12	1	1	0	0	0	1	0	4	2	3	2	3	4	3	2	3	4	1	2	rs368078339		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:57864354C>T	ENST00000228682.2	+	12	1922	c.1831C>T	c.(1831-1833)Cgg>Tgg	p.R611W	GLI1_ENST00000543426.1_Missense_Mutation_p.R483W|GLI1_ENST00000546141.1_Missense_Mutation_p.R570W	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	611					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			CAGCCTGGATCGGATAGGTGG	0.617																																					p.R611W	Pancreas(157;841 1936 10503 41495 50368)	.											.	GLI1-722	0			c.C1831T						.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405		0,1,2202	55	47	49		1447,1708,1831	3.9	1	12		49	0,8600		0,0,4300	no	missense,missense,missense	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	483/979,570/1066,611/1107	57864354	1,13005	2203	4300	6503	SO:0001583	missense	2735	exon12			CTGGATCGGATAG		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1831C>T	12.37:g.57864354C>T	ENSP00000228682:p.Arg611Trp	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	57	21	NM_005269	0	0	0	0	0	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.547626	0.27652	2.27E-4	0.0	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467	T;T;T;T	0.22336	2.12;1.96;2.06;2.06	3.86	3.86	0.44501	.	0.172694	0.28166	N	0.016347	T	0.21761	0.0524	M	0.64997	1.995	0.37842	D	0.929105	B	0.09022	0.002	B	0.04013	0.001	T	0.14839	-1.0458	10	0.87932	D	0	.	9.2479	0.37539	0.328:0.672:0.0:0.0	.	611	P08151	GLI1_HUMAN	W	483;611;570;570	ENSP00000437607:R483W;ENSP00000228682:R611W;ENSP00000441006:R570W;ENSP00000434408:R570W	ENSP00000228682:R611W	R	+	1	2	GLI1	56150621	0.021000	0.18746	0.995000	0.50966	0.883000	0.51084	0.653000	0.24902	2.436000	0.82500	0.491000	0.48974	CGG	.		0.617	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		T	57864354	C	T	57864354	3	4	7	1	0	0	0	0	1	0	0	0	6457	875	31	1	1873	1	GLI1	12	57864354	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	1237756	57864354	75987541	51	558											
CCDC41	51134	hgsc.bcm.edu	37	chr12	94769760	94769760	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgtagctctttttccaaacGttctgcccgtaaattagctg	8	16	7	10	2	2	0	0	0	2	0	3	0	3	0	2	0	4	5	2	0	5	7	rs79068264	byFrequency	TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:94769760G>A	ENST00000397809.5	-	8	1384	c.835C>T	c.(835-837)Cgt>Tgt	p.R279C	CCDC41_ENST00000397807.2_Missense_Mutation_p.R246C|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000339839.5_Missense_Mutation_p.R279C|CCDC41_ENST00000547575.1_Missense_Mutation_p.R279C	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		271					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						TTTTCCAAACGTTCTGCCCGT	0.284													G|||	19	0.00379393	0.0144	0	5008	,	,		14527	0		0	False		,,,				2504	0				p.R279C		.											.	CCDC41-90	0			c.C835T						.	G	CYS/ARG,CYS/ARG	5,3607		0,5,1801	75	70	71		835,835	5.4	1	12	dbSNP_131	71	1,8143		0,1,4071	yes	missense,missense	CCDC41	NM_001042399.1,NM_016122.2	180,180	0,6,5872	AA,AG,GG		0.0123,0.1384,0.051	probably-damaging,probably-damaging	279/702,279/702	94769760	6,11750	1806	4072	5878	SO:0001583	missense	51134	exon8			CCAAACGTTCTGC																												ENST00000397809.5:c.835C>T	12.37:g.94769760G>A	ENSP00000380911:p.Arg279Cys	Somatic	12	2		WXS	Illumina HiSeq	Phase_I	20	7	NM_016122	0	0	0	0	0	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.24	3.339819	0.60963	0.001384	1.23E-4	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807;ENST00000547575	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.42	5.42	0.78866	.	.	.	.	.	T	0.37758	0.1015	M	0.61703	1.905	0.49130	D	0.999759	D;D;D	0.76494	0.997;0.999;0.999	P;P;P	0.57283	0.817;0.8;0.817	T	0.36432	-0.9748	9	0.87932	D	0	0.1483	19.2202	0.93793	0.0:0.0:1.0:0.0	.	279;246;271	F8VYN8;Q9Y592-2;Q9Y592	.;.;CCD41_HUMAN	C	279;279;246;279	ENSP00000344655:R279C;ENSP00000380911:R279C;ENSP00000380909:R246C;ENSP00000448913:R279C	ENSP00000344655:R279C	R	-	1	0	CCDC41	93293891	1.000000	0.71417	0.998000	0.56505	0.383000	0.30230	6.050000	0.71063	2.563000	0.86464	0.455000	0.32223	CGT	G|0.998;A|0.002		0.284	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			A	94769760	G	A	94769760	3	1	7	1	0	0	0	0	1	0	0	0	2819	1145	40	1	1310	1	CCDC41	12	94769760	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	36905406	94769760	39082135	52	559											
NAA16	79612	hgsc.bcm.edu;bcgsc.ca	37	chr13	41894809	41894809	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttaacttaataggttggcAtgtatatggactcttgcagc	10	14	9	8	0	1	0	0	0	1	0	1	1	1	1	1	3	3	4	1	3	5	7			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr13:41894809A>T	ENST00000379406.3	+	4	575	c.251A>T	c.(250-252)cAt>cTt	p.H84L	NAA16_ENST00000379367.3_Missense_Mutation_p.H84L|NAA16_ENST00000403412.3_Missense_Mutation_p.H84L	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	84					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						ATAGGTTGGCATGTATATGGA	0.299																																					p.H84L		.											.	NAA16-90	0			c.A251T						.						76	79	78					13																	41894809		2203	4300	6503	SO:0001583	missense	79612	exon4			GTTGGCATGTATA	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.251A>T	13.37:g.41894809A>T	ENSP00000368716:p.His84Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	58	4	NM_001110798	0	0	0	0	0	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.530845	0.85706	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.58060	0.36;0.36;0.36	4.9	4.9	0.64082	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000001	T	0.80265	0.4591	H	0.95816	3.725	0.80722	D	1	D;P;D	0.76494	0.999;0.754;0.985	D;P;D	0.85130	0.997;0.673;0.943	D	0.86393	0.1737	10	0.72032	D	0.01	-17.5873	14.6766	0.68983	1.0:0.0:0.0:0.0	.	84;84;84	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	L	84	ENSP00000368674:H84L;ENSP00000368716:H84L;ENSP00000386103:H84L	ENSP00000368674:H84L	H	+	2	0	NAA16	40792809	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.523000	0.90576	2.048000	0.60808	0.533000	0.62120	CAT	.		0.299	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41894809	A	T	41894809	3	4	7	1	0	0	0	0	1	0	0	0	10144	217	8	5	265	5	NAA16	13	41894809	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08		41894809	73275069	53	560											
SEC23A	10484	broad.mit.edu;bcgsc.ca	37	chr14	39514526	39514526	+	Frame_Shift_Del	DEL	A	A	-																															gatcttcttaaatgaaacatAaactgtaagataaacacgta																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:39514526delA	ENST00000307712.6	-	16	2257	c.1740delT	c.(1738-1740)tttfs	p.F580fs	SEC23A_ENST00000537403.1_Frame_Shift_Del_p.F378fs|SEC23A_ENST00000536508.1_Frame_Shift_Del_p.F478fs|SEC23A_ENST00000545328.2_Frame_Shift_Del_p.F551fs	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	580					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		AATGAAACATAAACTGTAAGA	0.289																																					p.F580fs													.	SEC23A-95	0			c.1740delT						.						39	39	39					14																	39514526		2202	4299	6501	SO:0001589	frameshift_variant	10484	exon16			AAACATAAACTGT	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1740delT	14.37:g.39514526delA	ENSP00000306881:p.Phe580fs	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	25	8	NM_006364	0	0	0	0	0	B2R5P4|B3KXI2|Q8NE16	Frame_Shift_Del	DEL	ENST00000307712.6	37	CCDS9668.1																																																																																			.		0.289	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			-	39514526	A	-	39514526	7	5	7	1	0	1	0	1	0	0	0	0	14023	359	13	0	577	0	SEC23A	14	39514526	Frame_Shift_Del	DEL	A	TCGA-A4-7732-01A-11D-2136-08		39514526	67835014	54	561											
MDGA2	161357	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	47351354	47351354	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttagctctgtcaagttatatGtaattaattctcccttttga	10	19	5	7	0	3	1	1	1	2	0	4	1	3	1	1	0	1	3	1	0	6	8	rs369029916		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:47351354G>T	ENST00000399232.2	-	11	2466	c.2102C>A	c.(2101-2103)aCa>aAa	p.T701K	MDGA2_ENST00000439988.3_Missense_Mutation_p.T770K|MDGA2_ENST00000357362.3_Missense_Mutation_p.T472K|MDGA2_ENST00000399222.3_5'UTR|MDGA2_ENST00000426342.1_Missense_Mutation_p.T472K	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	701	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						CAAGTTATATGTAATTAATTC	0.368																																					p.T770K		.											.	MDGA2-95	0			c.C2309A						.						65	62	63					14																	47351354		1827	4086	5913	SO:0001583	missense	161357	exon11			TTATATGTAATTA	AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19835	protein-coding gene	gene with protein product		611128	"MAM domain containing 1"	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.2102C>A	14.37:g.47351354G>T	ENSP00000382178:p.Thr701Lys	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	29	7	NM_001113498	0	0	0	0	0	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	G	15.69	2.907198	0.52333	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.1	5.1	0.69264	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.52532	U	0.000066	T	0.49098	0.1537	L	0.36672	1.1	0.80722	D	1	P;B	0.35139	0.486;0.227	B;B	0.38755	0.281;0.146	T	0.52388	-0.8582	10	0.54805	T	0.06	.	17.4396	0.87562	0.0:0.0:1.0:0.0	.	472;701	F6W3S7;Q7Z553	.;MDGA2_HUMAN	K	701;472;770;472	ENSP00000400011:T701K;ENSP00000405456:T472K;ENSP00000382178:T770K;ENSP00000349925:T472K	ENSP00000349925:T472K	T	-	2	0	MDGA2	46421104	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.258000	0.72487	2.547000	0.85894	0.467000	0.42956	ACA	.		0.368	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47351354	G	T	47351354	3	4	7	1	0	0	0	0	1	0	0	0	9432	1377	48	4	796	4	MDGA2	14	47351354	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	7836828	47351354	59998186	55	562											
KCNK13	56659	hgsc.bcm.edu;broad.mit.edu	37	chr14	90528673	90528673	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccgccgtcttctccgcgctgGagctggcgcacgagcgccag	4	6	14	17	7	2	0	0	0	2	0	3	2	2	1	4	2	2	3	4	2	0	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:90528673G>A	ENST00000282146.4	+	1	565	c.124G>A	c.(124-126)Gag>Aag	p.E42K		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	42					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				CTCCGCGCTGGAGCTGGCGCA	0.721																																					p.E42K		.											.	KCNK13-91	0			c.G124A						.						4	5	4					14																	90528673		1987	3967	5954	SO:0001583	missense	56659	exon1			GCGCTGGAGCTGG	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.124G>A	14.37:g.90528673G>A	ENSP00000282146:p.Glu42Lys	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	7	4	NM_022054	0	0	0	0	0	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	35	5.521378	0.96416	.	.	ENSG00000152315	ENST00000282146	T	0.39787	1.06	4.0	4.0	0.46444	.	0.000000	0.32753	N	0.005686	T	0.71492	0.3346	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80843	-0.1201	10	0.87932	D	0	.	16.446	0.83932	0.0:0.0:1.0:0.0	.	42	Q9HB14	KCNKD_HUMAN	K	42	ENSP00000282146:E42K	ENSP00000282146:E42K	E	+	1	0	KCNK13	89598426	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	9.054000	0.93866	1.946000	0.56461	0.313000	0.20887	GAG	.		0.721	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		A	90528673	G	A	90528673	3	1	7	1	0	0	0	0	1	0	0	0	8082	1175	41	2	126	2	KCNK13	14	90528673	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	43177319	90528673	16820867	56	563											
DYNC1H1	1778	broad.mit.edu	37	chr14	102483550	102483550	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctgttcaacttggaaagtgGctggtgttgttctgtgatga	7	15	13	6	0	2	2	1	2	1	0	2	3	2	3	1	3	1	4	1	3	2	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:102483550G>T	ENST00000360184.4	+	39	8138	c.7974G>T	c.(7972-7974)tgG>tgT	p.W2658C		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2658	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TTGGAAAGTGGCTGGTGTTGT	0.458																																					p.W2658C													.	DYNC1H1-98	0			c.G7974T						.						122	121	121					14																	102483550		2203	4300	6503	SO:0001583	missense	1778	exon39			AAAGTGGCTGGTG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.7974G>T	14.37:g.102483550G>T	ENSP00000348965:p.Trp2658Cys	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	79	5	NM_001376	0	0	6	6	0	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.393294	0.83011	.	.	ENSG00000197102	ENST00000360184	T	0.62232	0.04	5.46	5.46	0.80206	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.86066	0.5844	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89742	0.3934	10	0.66056	D	0.02	.	19.3032	0.94151	0.0:0.0:1.0:0.0	.	2658	Q14204	DYHC1_HUMAN	C	2658	ENSP00000348965:W2658C	ENSP00000348965:W2658C	W	+	3	0	DYNC1H1	101553303	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.688000	0.98670	2.576000	0.86940	0.561000	0.74099	TGG	.		0.458	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102483550	G	T	102483550	3	4	7	1	0	0	0	0	1	0	0	0	4852	1212	42	4	8128	4	DYNC1H1	14	102483550	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	11954877	102483550	4865990	57	564											
TECPR2	9895	broad.mit.edu	37	chr14	102910132	102910132	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgtgagcagcttctgtccGgaaggcgagcagtggaagtg	8	7	18	8	3	1	1	0	1	1	0	2	4	2	3	1	4	3	3	1	4	2	1	rs202209194		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:102910132G>A	ENST00000359520.7	+	12	3127	c.2901G>A	c.(2899-2901)ccG>ccA	p.P967P	TECPR2_ENST00000558678.1_Silent_p.P967P	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	967					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						GCTTCTGTCCGGAAGGCGAGC	0.597																																					p.P967P													.	TECPR2-92	0			c.G2901A						.						78	65	69					14																	102910132		2203	4300	6503	SO:0001819	synonymous_variant	9895	exon12			CTGTCCGGAAGGC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.2901G>A	14.37:g.102910132G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	40	3	NM_001172631	0	0	7	7	0	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	37	CCDS32162.1																																																																																			G|0.999;C|0.000		0.597	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		A	102910132	G	A	102910132	2	1	7	1	0	0	0	0	0	0	0	1	15776	1103	39	1		1	TECPR2	14	102910132	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08	426582	102910132	4439408	58	565											
MAPKBP1	23005	ucsc.edu;bcgsc.ca	37	chr15	42117531	42117531	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtgctgtccagcccaggcaGcagccctggggctgtgggag	6	6	17	12	0	0	0	0	0	0	0	1	1	1	1	3	4	4	4	3	4	0	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr15:42117531G>A	ENST00000456763.2	+	32	4638	c.4442G>A	c.(4441-4443)aGc>aAc	p.S1481N	PLA2G4B_ENST00000542534.2_5'Flank|JMJD7_ENST00000397299.4_5'Flank|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.S1198N|JMJD7_ENST00000408047.1_5'Flank|JMJD7-PLA2G4B_ENST00000342159.4_5'Flank|JMJD7-PLA2G4B_ENST00000382448.4_5'Flank|RP11-23P13.4_ENST00000512295.1_RNA|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.S1475N|RP11-23P13.4_ENST00000510176.1_RNA|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.S1358N|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.S1314N	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1481										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AGCCCAGGCAGCAGCCCTGGG	0.612																																					p.S1481N													.	MAPKBP1-589	0			c.G4442A						.						28	31	30					15																	42117531		2202	4300	6502	SO:0001583	missense	23005	exon32			CAGGCAGCAGCCC	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.4442G>A	15.37:g.42117531G>A	ENSP00000393099:p.Ser1481Asn	Somatic	67	0		WXS	Illumina HiSeq		38	4	NM_001128608	0	0	5	5	0	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	.	5.446	0.267400	0.10294	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T;T	0.39229	1.27;1.43;1.09;1.32;1.36	4.49	4.49	0.54785	.	0.806241	0.11670	N	0.540965	T	0.25865	0.0630	L	0.27053	0.805	0.09310	N	1	B;B;B;B;B;B	0.10296	0.002;0.001;0.001;0.0;0.002;0.003	B;B;B;B;B;B	0.06405	0.001;0.001;0.001;0.001;0.0;0.002	T	0.21655	-1.0239	10	0.11485	T	0.65	-8.7742	6.4193	0.21734	0.1601:0.0:0.8399:0.0	.	1314;1356;1314;1198;1481;1475	F8WC21;O60336-3;B4DYK7;O60336-2;O60336;O60336-6	.;.;.;.;MABP1_HUMAN;.	N	1475;1358;1314;1481;1198	ENSP00000397570:S1475N;ENSP00000221214:S1358N;ENSP00000260357:S1314N;ENSP00000393099:S1481N;ENSP00000426154:S1198N	ENSP00000221214:S1358N	S	+	2	0	MAPKBP1	39904823	0.739000	0.28196	0.112000	0.21494	0.419000	0.31324	2.186000	0.42593	2.338000	0.79540	0.655000	0.94253	AGC	.		0.612	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42117531	G	A	42117531	3	1	7	1	0	0	0	0	1	0	0	0	9317	971	34	2	4564	2	MAPKBP1	15	42117531	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		42117531	60413861	59	566											
PKD1	5310	hgsc.bcm.edu;broad.mit.edu	37	chr16	2155927	2155927	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgctggggatcggcctgcCgcagcagccctgggagcaca	6	5	16	14	3	0	0	0	0	0	0	1	2	0	2	3	4	5	4	3	4	0	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr16:2155927C>G	ENST00000262304.4	-	20	8010	c.7802G>C	c.(7801-7803)cGg>cCg	p.R2601P	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Missense_Mutation_p.R2601P	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2601	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ATCGGCCTGCCGCAGCAGCCC	0.652																																					p.R2601P		.											.	PKD1-91	0			c.G7802C						.						40	44	43					16																	2155927		1404	2483	3887	SO:0001583	missense	5310	exon20			GCCTGCCGCAGCA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.7802G>C	16.37:g.2155927C>G	ENSP00000262304:p.Arg2601Pro	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	52	7	NM_000296	0	0	11	13	2	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	c	12.44	1.938417	0.34189	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.70045	-0.45;-0.45	4.7	2.54	0.30619	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	0.463918	0.23250	N	0.050258	T	0.66287	0.2774	L	0.47716	1.5	0.09310	N	1	D;D	0.60160	0.987;0.981	P;P	0.62184	0.785;0.899	T	0.54077	-0.8347	10	0.33940	T	0.23	.	2.443	0.04499	0.2323:0.4657:0.0:0.302	.	2601;2601	P98161-3;P98161	.;PKD1_HUMAN	P	2601;2601;1952;880	ENSP00000262304:R2601P;ENSP00000399501:R2601P	ENSP00000262304:R2601P	R	-	2	0	PKD1	2095928	0.709000	0.27886	0.342000	0.25602	0.058000	0.15608	1.983000	0.40648	1.203000	0.43233	0.538000	0.68166	CGG	.		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2155927	C	G	2155927	3	3	7	1	0	0	0	0	1	0	0	0	11989	652	23	4	5217	4	PKD1	16	2155927	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		2155927	88198826	60	567											
PRSS21	10942	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	2868950	2868950	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgctgggtgactggctgggGgtacatcaaagaggatgagg	9	8	18	6	0	1	3	1	2	0	1	1	4	1	4	0	6	2	3	0	6	2	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr16:2868950G>T	ENST00000005995.3	+	4	572	c.530G>T	c.(529-531)gGg>gTg	p.G177V	PRSS21_ENST00000575739.1_3'UTR|PRSS21_ENST00000455114.1_Missense_Mutation_p.G175V|PRSS21_ENST00000450020.3_Missense_Mutation_p.G177V			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	177	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						ACTGGCTGGGGGTACATCAAA	0.562																																					p.G177V		.											.	PRSS21-92	0			c.G530T						.						66	61	63					16																	2868950		2198	4300	6498	SO:0001583	missense	10942	exon4			GCTGGGGGTACAT	AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"Serine peptidases / Serine peptidases"	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.530G>T	16.37:g.2868950G>T	ENSP00000005995:p.Gly177Val	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	44	5	NM_144957	0	0	6	6	0	Q9NS34|Q9P2V6	Missense_Mutation	SNP	ENST00000005995.3	37	CCDS10478.1	.	.	.	.	.	.	.	.	.	.	g	16.73	3.204970	0.58234	.	.	ENSG00000007038	ENST00000455114;ENST00000450020;ENST00000005995	D;D;D	0.89810	-2.57;-2.57;-2.57	4.67	4.67	0.58626	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.33364	N	0.004994	D	0.96833	0.8966	H	0.98786	4.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98254	1.0495	10	0.87932	D	0	.	15.0995	0.72262	0.0:0.0:1.0:0.0	.	177;175;177	Q9Y6M0;Q9Y6M0-2;Q9Y6M0-3	TEST_HUMAN;.;.	V	175;177;177	ENSP00000400632:G175V;ENSP00000407741:G177V;ENSP00000005995:G177V	ENSP00000005995:G177V	G	+	2	0	PRSS21	2808951	1.000000	0.71417	0.971000	0.41717	0.203000	0.24098	5.319000	0.65835	2.394000	0.81467	0.586000	0.80456	GGG	.		0.562	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799		T	2868950	G	T	2868950	3	4	7	1	0	0	0	0	1	0	0	0	12647	1232	43	4	544	4	PRSS21	16	2868950	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	713023	2868950	87485803	61	568											
RRN3	54700	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	15159184	15159184	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgactggcagcatctggcgaTtgttcctctcaatgatggtg	7	13	12	9	1	2	2	1	2	2	0	4	3	3	2	1	3	1	3	1	3	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr16:15159184T>C	ENST00000198767.6	-	16	1681	c.1598A>G	c.(1597-1599)aAt>aGt	p.N533S	RRN3_ENST00000563559.1_Missense_Mutation_p.N533S|RRN3_ENST00000327307.7_Missense_Mutation_p.N500S|RRN3_ENST00000429751.2_Missense_Mutation_p.N503S|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000540462.1_Missense_Mutation_p.N351S	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	533	Interaction with TWISTNB.				cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						CATCTGGCGATTGTTCCTCTC	0.502																																					p.N533S		.											.	RRN3-91	0			c.A1598G						.						95	80	85					16																	15159184		2197	4300	6497	SO:0001583	missense	54700	exon16			TGGCGATTGTTCC	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"RRN3 RNA polymerase I transcription factor homolog (yeast)"			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.1598A>G	16.37:g.15159184T>C	ENSP00000198767:p.Asn533Ser	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	77	13	NM_018427	0	0	6	6	0	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	8.281	0.815443	0.16607	.	.	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307;ENST00000540462	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.39	3.07	0.35406	.	0.056806	0.64402	D	0.000003	T	0.35038	0.0918	L	0.48642	1.525	0.47123	D	0.999324	B;B;B	0.17038	0.004;0.02;0.01	B;B;B	0.27500	0.009;0.08;0.022	T	0.07849	-1.0751	10	0.23891	T	0.37	.	9.8617	0.41118	0.0:0.127:0.0:0.873	.	503;434;533	F5H148;B4DZL9;Q9NYV6	.;.;RRN3_HUMAN	S	533;503;500;351	ENSP00000198767:N533S;ENSP00000402027:N503S;ENSP00000318484:N500S;ENSP00000437963:N351S	ENSP00000198767:N533S	N	-	2	0	RRN3	15066685	1.000000	0.71417	0.993000	0.49108	0.185000	0.23345	3.207000	0.51106	0.410000	0.25675	0.482000	0.46254	AAT	.		0.502	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427		C	15159184	T	C	15159184	3	2	7	1	0	0	0	0	1	0	0	0	13716	1493	52	3	369	3	RRN3	16	15159184	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	12290234	15159184	75195569	62	569											
TMCO7	79613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	68909060	68909060	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tctctccattgtgccagcggGagcagctggtggaagtgatg	7	10	15	9	1	1	1	0	1	1	0	3	3	2	3	2	3	4	2	2	3	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr16:68909060G>T	ENST00000261778.1	+	5	1010	c.998G>T	c.(997-999)gGa>gTa	p.G333V		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	333						integral component of membrane (GO:0016021)											GTGCCAGCGGGAGCAGCTGGT	0.473																																					p.G333V		.											.	.	0			c.G998T						.						78	88	85					16																	68909060		2134	4251	6385	SO:0001583	missense	79613	exon5			CAGCGGGAGCAGC		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.998G>T	16.37:g.68909060G>T	ENSP00000261778:p.Gly333Val	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	37	17	NM_024562	0	0	0	0	0	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	37	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713100	0.48517	.	.	ENSG00000103047	ENST00000261778	T	0.69175	-0.38	4.94	4.94	0.65067	.	.	.	.	.	T	0.81138	0.4760	M	0.77820	2.39	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	D	0.83369	0.0006	9	0.59425	D	0.04	-8.1136	17.3079	0.87200	0.0:0.0:1.0:0.0	.	333	Q9C0B7	TMCO7_HUMAN	V	333	ENSP00000261778:G333V	ENSP00000261778:G333V	G	+	2	0	TMCO7	67466561	1.000000	0.71417	0.969000	0.41365	0.107000	0.19398	5.015000	0.64035	2.437000	0.82529	0.591000	0.81541	GGA	.		0.473	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68909060	G	T	68909060	3	4	7	1	0	0	0	0	1	0	0	0	16033	1174	41	4	1016	4	TMCO7	16	68909060	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	53749876	68909060	21445693	63	570											
KIAA0664	23277	hgsc.bcm.edu;broad.mit.edu	37	chr17	2601454	2601454	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtgccgcaggatcttgAggggccgactcgtgcgctcc	4	8	15	14	4	1	1	0	1	1	0	3	3	2	2	4	4	2	2	4	4	0	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:2601454A>G	ENST00000570628.2	-	10	1688	c.1583T>C	c.(1582-1584)cTc>cCc	p.L528P	CLUH_ENST00000435359.1_Missense_Mutation_p.L528P|CLUH_ENST00000538975.1_Missense_Mutation_p.L528P			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	528					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CAGGATCTTGAGGGGCCGACT	0.647																																					p.L528P		.											.	.	0			c.T1583C						.						37	48	44					17																	2601454		2169	4256	6425	SO:0001583	missense	23277	exon10			ATCTTGAGGGGCC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.1583T>C	17.37:g.2601454A>G	ENSP00000458986:p.Leu528Pro	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	9	7	NM_015229	0	0	5	27	22	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.819136	0.90873	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.87412	-2.25;-2.25	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.95098	0.8412	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96211	0.9153	10	0.87932	D	0	.	15.0034	0.71492	1.0:0.0:0.0:0.0	.	528;528	O75153;C9J6D7	K0664_HUMAN;.	P	528	ENSP00000388872:L528P;ENSP00000439628:L528P	ENSP00000320468:L528P	L	-	2	0	KIAA0664	2548204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.144000	0.66660	0.533000	0.62120	CTC	.		0.647	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		G	2601454	A	G	2601454	3	3	7	1	0	0	0	0	1	0	0	0	8210	304	11	3	2414	3	KIAA0664	17	2601454	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08		2601454	78593756	64	571											
DNAH9	1770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	11772554	11772554	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agtgaccgcagtcaccatctCccttgccaaccgcctggtga	8	8	9	16	2	2	2	1	2	1	0	3	2	2	2	6	1	2	1	6	1	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:11772554C>T	ENST00000262442.4	+	51	10105	c.10037C>T	c.(10036-10038)tCc>tTc	p.S3346F	DNAH9_ENST00000454412.2_Missense_Mutation_p.S3346F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3346					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GTCACCATCTCCCTTGCCAAC	0.498																																					p.S3346F		.											.	DNAH9-168	0			c.C10037T						.						93	83	87					17																	11772554		2203	4300	6503	SO:0001583	missense	1770	exon51			CCATCTCCCTTGC	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"Axonemal dyneins"	2953	protein-coding gene	gene with protein product		603330	"dynein, axonemal, heavy polypeptide 17-like", "dynein, axonemal, heavy polypeptide 9"	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10037C>T	17.37:g.11772554C>T	ENSP00000262442:p.Ser3346Phe	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	91	28	NM_001372	0	0	0	0	0	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.091444	0.55968	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.75589	-0.95;-0.95	4.54	4.54	0.55810	Dynein heavy chain, coiled coil stalk (1);	0.361482	0.29246	N	0.012706	D	0.84238	0.5428	M	0.87682	2.9	0.80722	D	1	P	0.44195	0.828	P	0.52554	0.702	D	0.87047	0.2144	10	0.66056	D	0.02	.	15.0338	0.71728	0.0:0.8577:0.1423:0.0	.	3346	Q9NYC9	DYH9_HUMAN	F	3346;3346;1928	ENSP00000262442:S3346F;ENSP00000414874:S3346F	ENSP00000262442:S3346F	S	+	2	0	DNAH9	11713279	0.799000	0.28903	1.000000	0.80357	0.588000	0.36517	1.816000	0.38992	2.510000	0.84645	0.643000	0.83706	TCC	.		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11772554	C	T	11772554	3	4	7	1	0	0	0	0	1	0	0	0	4619	855	30	2	10239	2	DNAH9	17	11772554	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	9171100	11772554	69422656	65	572											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305911	39305911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcttgcagcagctggggcGgcagcaggtggtcctgcagc	5	6	19	11	1	0	0	0	0	0	0	1	0	1	0	1	6	6	7	1	6	0	1	rs557154279|rs141058010	byFrequency	TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:39305911G>A	ENST00000343246.4	-	1	143	c.109C>T	c.(109-111)Cgc>Tgc	p.R37C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	37	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGGGCGGCAGCAGGTG	0.657																																					p.R37C		.											.	KRTAP4-5-90	0			c.C109T						.						25	29	27					17																	39305911		2176	4272	6448	SO:0001583	missense	85289	exon1			TGGGGCGGCAGCA	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.109C>T	17.37:g.39305911G>A	ENSP00000340546:p.Arg37Cys	Somatic	86	1		WXS	Illumina HiSeq	Phase_I	78	7	NM_033188	0	0	0	0	0		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	12.13	1.844454	0.32606	.	.	ENSG00000198271	ENST00000343246	T	0.01455	4.87	3.22	-1.8	0.07907	.	2.080600	0.03668	U	0.243553	T	0.02767	0.0083	L	0.57536	1.79	0.18873	N	0.999989	B	0.18461	0.028	B	0.12837	0.008	T	0.47045	-0.9147	10	0.56958	D	0.05	.	5.7249	0.18008	0.1011:0.0:0.4232:0.4757	.	37	Q9BYR2	KRA45_HUMAN	C	37	ENSP00000340546:R37C	ENSP00000340546:R37C	R	-	1	0	KRTAP4-5	36559437	0.000000	0.05858	0.674000	0.29902	0.928000	0.56348	-0.202000	0.09451	-0.272000	0.09259	0.556000	0.70494	CGC	G|1.000;A|0.000		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			A	39305911	G	A	39305911	3	1	7	1	0	0	0	0	1	0	0	0	8575	1116	39	1	440	1	KRTAP4-5	17	39305911	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	27533357	39305911	41889299	66	573											
SLC16A5	9121	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	73096278	73096278	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggaggggtaccttccttGtcttcggcgggatctttctc	3	14	13	11	2	3	0	0	0	3	0	6	2	4	2	2	5	1	2	2	5	1	5			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:73096278G>T	ENST00000450736.2	+	4	935	c.520G>T	c.(520-522)Gtc>Ttc	p.V174F	SLC16A5_ENST00000538213.2_Missense_Mutation_p.V214F|SLC16A5_ENST00000329783.4_Missense_Mutation_p.V174F|SLC16A5_ENST00000580123.1_Missense_Mutation_p.V174F			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	174					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	TACCTTCCTTGTCTTCGGCGG	0.642																																					p.V174F		.											.	SLC16A5-90	0			c.G520T						.						49	49	49					17																	73096278		2203	4300	6503	SO:0001583	missense	9121	exon5			TTCCTTGTCTTCG	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"Solute carriers"	10926	protein-coding gene	gene with protein product		603879	"solute carrier family 16 (monocarboxylic acid transporters), member 5", "solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.520G>T	17.37:g.73096278G>T	ENSP00000390564:p.Val174Phe	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	49	4	NM_001271765	0	0	0	1	1	B4E288	Missense_Mutation	SNP	ENST00000450736.2	37	CCDS11713.1	.	.	.	.	.	.	.	.	.	.	G	8.724	0.915027	0.17907	.	.	ENSG00000170190	ENST00000329783;ENST00000450736;ENST00000538213	T;T;T	0.59772	0.24;0.24;0.24	4.58	-5.33	0.02713	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.457119	0.24674	N	0.036522	T	0.53899	0.1825	L	0.39692	1.235	0.21740	N	0.99956	D;D	0.56287	0.975;0.975	P;P	0.58391	0.791;0.838	T	0.55933	-0.8062	10	0.66056	D	0.02	.	8.4103	0.32640	0.444:0.112:0.444:0.0	.	214;174	B4E288;O15375	.;MOT6_HUMAN	F	174;174;214	ENSP00000330141:V174F;ENSP00000390564:V174F;ENSP00000440212:V214F	ENSP00000330141:V174F	V	+	1	0	SLC16A5	70607873	0.006000	0.16342	0.067000	0.19924	0.636000	0.38137	0.220000	0.17660	-1.012000	0.03387	0.561000	0.74099	GTC	.		0.642	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695		T	73096278	G	T	73096278	3	4	7	1	0	0	0	0	1	0	0	0	14443	1377	48	4	530	4	SLC16A5	17	73096278	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	33790367	73096278	8098932	67	574											
FAM108A1	81926	hgsc.bcm.edu	37	chr19	1881550	1881550	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcagcagagctcactcaGcgacagcccattcatggcgg	10	5	13	13	2	3	1	3	0	0	1	3	3	3	1	1	3	4	3	1	3	0	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:1881550G>A	ENST00000292577.7	-	2	449	c.16C>T	c.(16-18)Ctg>Ttg	p.L6L	ABHD17A_ENST00000590661.1_Silent_p.L6L|ABHD17A_ENST00000250974.9_Silent_p.L6L	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	6						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										AGCTCACTCAGCGACAGCCCA	0.761																																					p.L6L		.											.	FAM108A1-90	0			c.C16T						.																																			SO:0001819	synonymous_variant	81926	exon2			CACTCAGCGACAG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"Abhydrolase domain containing"	28756	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 27", "family with sequence similarity 108, member A1"	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.16C>T	19.37:g.1881550G>A		Somatic	36	1		WXS	Illumina HiSeq	Phase_I	21	6	NM_031213	0	0	3	3	0	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Silent	SNP	ENST00000292577.7	37	CCDS45902.1																																																																																			.		0.761	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		A	1881550	G	A	1881550	2	1	7	1	0	0	0	0	0	0	0	1	5407	962	34	2		2	FAM108A1	19	1881550	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08		1881550	57247433	68	575											
MUC16	94025	broad.mit.edu	37	chr19	9088433	9088433	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtcatttgtggagtcagagCtgagcttgttccatctctag	8	14	11	8	0	3	2	2	1	1	1	5	3	4	3	1	1	2	3	1	1	1	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:9088433C>T	ENST00000397910.4	-	1	3585	c.3382G>A	c.(3382-3384)Gct>Act	p.A1128T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1128	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAGTCAGAGCTGAGCTTGTT	0.463																																					p.A1128T													.	MUC16-566	0			c.G3382A						.						127	123	125					19																	9088433		2096	4220	6316	SO:0001583	missense	94025	exon1			TCAGAGCTGAGCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.3382G>A	19.37:g.9088433C>T	ENSP00000381008:p.Ala1128Thr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	61	4	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	3.172	-0.169859	0.06461	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.04	-0.229	0.13094	.	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	.	.	.	D	0.55172	0.97	B	0.40602	0.334	T	0.48714	-0.9011	8	0.87932	D	0	.	4.9543	0.14031	0.0:0.5148:0.4852:0.0	.	1128	B5ME49	.	T	1128	ENSP00000381008:A1128T	ENSP00000381008:A1128T	A	-	1	0	MUC16	8949433	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	0.163000	0.16520	0.001000	0.14605	0.305000	0.20034	GCT	.		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9088433	C	T	9088433	3	4	7	1	0	0	0	0	1	0	0	0	9998	797	28	2	40477	2	MUC16	19	9088433	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	7206883	9088433	50040550	69	576											
ZNF439	90594	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	11978986	11978986	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcttttattctgccaagTcatttcaaagacatgaaaaa	16	12	6	7	0	3	2	2	1	1	1	3	2	3	2	1	1	1	1	1	1	6	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:11978986T>C	ENST00000304030.2	+	3	1302	c.1102T>C	c.(1102-1104)Tca>Cca	p.S368P	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.S232P	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	368					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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						TTCTGCCAAGTCATTTCAAAG	0.383																																					p.S368P		.											.	ZNF439-91	0			c.T1102C						.						65	66	66					19																	11978986		2203	4300	6503	SO:0001583	missense	90594	exon3			GCCAAGTCATTTC	AL833935	CCDS12268.1	19p13.13	2013-01-08			ENSG00000171291	ENSG00000171291		"Zinc fingers, C2H2-type", "-"	20873	protein-coding gene	gene with protein product							Standard	NM_152262		Approved	DKFZp571K0837	uc002mss.3	Q8NDP4	OTTHUMG00000156527	ENST00000304030.2:c.1102T>C	19.37:g.11978986T>C	ENSP00000305077:p.Ser368Pro	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	60	4	NM_152262	0	0	15	15	0	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	t	11.77	1.736704	0.30774	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.07908	3.15;3.15	0.575	0.575	0.17374	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24392	0.0591	M	0.84082	2.675	0.09310	N	1	P	0.49961	0.93	P	0.62885	0.908	T	0.03863	-1.0997	9	0.54805	T	0.06	.	6.7827	0.23654	0.0:0.0:0.0:1.0	.	368	Q8NDP4	ZN439_HUMAN	P	232;368	ENSP00000395632:S232P;ENSP00000305077:S368P	ENSP00000305077:S368P	S	+	1	0	ZNF439	11839986	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-1.393000	0.02521	0.485000	0.27652	0.163000	0.16589	TCA	.		0.383	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			C	11978986	T	C	11978986	3	2	7	1	0	0	0	0	1	0	0	0	17943	1667	58	3	1112	3	ZNF439	19	11978986	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	2890553	11978986	47149997	70	577											
ZNF226	7769	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	44680650	44680650	+	Frame_Shift_Del	DEL	T	T	-																															tcttcaatcccatcaaagagTtcatacaggagagaaaccat																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:44680650delT	ENST00000590089.1	+	7	1602	c.1235delT	c.(1234-1236)gttfs	p.V412fs	ZNF226_ENST00000454662.2_Frame_Shift_Del_p.V412fs|ZNF226_ENST00000337433.5_Frame_Shift_Del_p.V412fs|ZNF226_ENST00000588883.1_3'UTR			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	412					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)						Prostate(69;0.0352)|all_neural(266;0.202)				CATCAAAGAGTTCATACAGGA	0.433																																					p.V412fs	Pancreas(115;581 1665 13228 19278 50070)	.											.	.	0			c.1235delT						.						62	66	65					19																	44680650		2197	4300	6497	SO:0001589	frameshift_variant	7769	exon6			.	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.1235delT	19.37:g.44680650delT	ENSP00000465121:p.Val412fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	46	19	NM_001032372	0	0	0	0	0	Q8WWE6|Q96TE6|Q9NS44	Frame_Shift_Del	DEL	ENST00000590089.1	37	CCDS46102.1																																																																																			.		0.433	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			-	44680650	T	-	44680650	7	5	7	1	0	1	0	1	0	0	0	0	17812	1725	60	0	1303	0	ZNF226	19	44680650	Frame_Shift_Del	DEL	T	TCGA-A4-7732-01A-11D-2136-08	32701664	44680650	14448333	71	578											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44892065	44892065	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttcagaaatctgaagagaAatgcctgcccactcttcact	12	12	6	11	0	4	3	2	1	2	2	4	4	4	3	2	0	2	0	2	0	3	3	rs374886155		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:44892065A>C	ENST00000330997.4	-	4	406	c.342T>G	c.(340-342)atT>atG	p.I114M	ZNF285_ENST00000591679.1_Missense_Mutation_p.I121M|ZNF285_ENST00000544719.2_Missense_Mutation_p.I114M|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	114					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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TCTGAAGAGAAATGCCTGCCC	0.408																																					p.I114M		.											.	ZNF285-94	0			c.T342G						.						88	86	87					19																	44892065		2203	4300	6503	SO:0001583	missense	26974	exon4			AAGAGAAATGCCT	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.342T>G	19.37:g.44892065A>C	ENSP00000333595:p.Ile114Met	Somatic	163	2		WXS	Illumina HiSeq	Phase_I	114	6	NM_152354	0	0	0	0	0	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	A	4.441	0.081618	0.08533	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.06528	3.29	2.66	-4.03	0.04021	.	.	.	.	.	T	0.02230	0.0069	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42716	-0.9435	9	0.46703	T	0.11	.	2.2202	0.03971	0.1479:0.2063:0.4361:0.2097	.	138;114	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	M	137;114	ENSP00000333595:I114M	ENSP00000333595:I114M	I	-	3	3	ZNF285	49583905	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-4.542000	0.00218	-0.798000	0.04444	-1.783000	0.00646	ATT	.		0.408	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		C	44892065	A	C	44892065	3	2	7	1	0	0	0	0	1	0	0	0	17854	10	1	5	1434	5	ZNF285	19	44892065	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	211415	44892065	14236918	72	579											
KPTN	11133	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	47987312	47987312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagctccccgcgcccgcCggcgccgcctgccagcccgt	3	3	12	23	7	0	0	0	0	0	0	1	0	1	0	8	1	4	2	8	1	0	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:47987312C>T	ENST00000338134.3	-	1	213	c.106G>A	c.(106-108)Ggc>Agc	p.G36S	KPTN_ENST00000536339.1_5'UTR|NAPA-AS1_ENST00000594367.1_RNA|KPTN_ENST00000595484.1_5'UTR|NAPA-AS1_ENST00000593284.1_RNA	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	36					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		ccgcgcccgccggcgccgccT	0.697											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G36S		.											.	KPTN-91	0			c.G106A						.						16	20	19					19																	47987312		1778	3946	5724	SO:0001583	missense	11133	exon1			GCCCGCCGGCGCC	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"kaptin (actin-binding protein)"			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.106G>A	19.37:g.47987312C>T	ENSP00000337850:p.Gly36Ser	Somatic	64	0	951	WXS	Illumina HiSeq	Phase_I	43	17	NM_007059	0	0	0	0	0	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	37	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	C	5.953	0.359822	0.11296	.	.	ENSG00000118162	ENST00000338134	.	.	.	4.59	1.01	0.19927	.	0.822214	0.11218	N	0.586992	T	0.16041	0.0386	N	0.10874	0.06	0.22968	N	0.998498	B	0.12013	0.005	B	0.10450	0.005	T	0.30060	-0.9991	9	0.15952	T	0.53	-4.8928	5.1034	0.14772	0.0:0.5015:0.17:0.3285	.	36	Q9Y664	KPTN_HUMAN	S	36	.	ENSP00000337850:G36S	G	-	1	0	KPTN	52679124	0.103000	0.21917	0.979000	0.43373	0.439000	0.31926	1.690000	0.37711	0.509000	0.28195	0.313000	0.20887	GGC	.		0.697	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			T	47987312	C	T	47987312	3	4	7	1	0	0	0	0	1	0	0	0	8458	652	23	1	1252	1	KPTN	19	47987312	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	3095247	47987312	11141671	73	580											
SHANK1	50944	broad.mit.edu	37	chr19	51171508	51171508	+	Frame_Shift_Del	DEL	C	C	-																															ctccctccgggccgcccccaCcagggcggccccgaactggc																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:51171508delC	ENST00000293441.1	-	22	3727	c.3709delG	c.(3709-3711)gtgfs	p.V1237fs	SHANK1_ENST00000359082.3_Frame_Shift_Del_p.V1228fs|SHANK1_ENST00000391814.1_Frame_Shift_Del_p.V1245fs|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000391813.1_Frame_Shift_Del_p.V624fs	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1237					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		GCCGCCCCCACCAGGGCGGCC	0.781																																					p.V1237fs													.	SHANK1-153	0			c.3709delG						.						3	5	5					19																	51171508		883	1945	2828	SO:0001589	frameshift_variant	50944	exon22			CCCCCACCAGGGC	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15474	protein-coding gene	gene with protein product	"somatostatin receptor-interacting protein"	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.3709delG	19.37:g.51171508delC	ENSP00000293441:p.Val1237fs	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_016148	0	0	0	0	0	A8MXP5|B7WNY6|Q9NYW9	Frame_Shift_Del	DEL	ENST00000293441.1	37	CCDS12799.1																																																																																			.		0.781	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		-	51171508	C	-	51171508	7	5	7	1	0	1	0	1	0	0	0	0	14296	507	18	0	2784	0	SHANK1	19	51171508	Frame_Shift_Del	DEL	C	TCGA-A4-7732-01A-11D-2136-08	3184196	51171508	7957475	74	581											
LILRB4	11006	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55176288	55176288	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctcacccacaaggtccGtctcaacagctggtgagtct	8	8	10	15	1	3	1	2	1	2	0	5	1	4	1	3	3	2	1	3	3	2	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:55176288G>A	ENST00000391736.1	+	7	1009	c.694G>A	c.(694-696)Gtc>Atc	p.V232I	LILRB4_ENST00000391734.3_Missense_Mutation_p.V232I|LILRB4_ENST00000391733.3_Missense_Mutation_p.V232I|LILRB4_ENST00000270452.2_Missense_Mutation_p.V232I|LILRB4_ENST00000430952.2_Missense_Mutation_p.V232I	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	232					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CACAAGGTCCGTCTCAACAGC	0.557																																					p.V232I													.	LILRB4-93	0			c.G694A						.						68	59	62					19																	55176288		2203	4300	6503	SO:0001583	missense	11006	exon5			AGGTCCGTCTCAA	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.694G>A	19.37:g.55176288G>A	ENSP00000375616:p.Val232Ile	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	31	5	NM_006847	0	0	0	0	0	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	G	0.383	-0.927790	0.02377	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00472	7.29;7.29;7.29;7.24;7.31;7.19	2.47	-4.94	0.03057	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.18310	0.001;0.001;0.003;0.027;0.0	B;B;B;B;B	0.12837	0.001;0.001;0.003;0.008;0.001	T	0.32402	-0.9908	9	0.30854	T	0.27	.	0.9564	0.01386	0.2375:0.3417:0.2521:0.1687	.	232;232;232;232;232	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	I	232	ENSP00000375616:V232I;ENSP00000270452:V232I;ENSP00000408995:V232I;ENSP00000375614:V232I;ENSP00000375613:V232I;ENSP00000401962:V232I	ENSP00000270452:V232I	V	+	1	0	LILRB4	59868100	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.540000	0.06106	-1.610000	0.01583	-1.673000	0.00743	GTC	.		0.557	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			A	55176288	G	A	55176288	3	1	7	1	0	0	0	0	1	0	0	0	8815	1145	40	1	712	1	LILRB4	19	55176288	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	4004780	55176288	3952695	75	582											
NLRP13	126204	hgsc.bcm.edu	37	chr19	56416341	56416341	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcacacttggggtgagtcAgggccgcacacaatagcttt	10	8	13	10	1	1	1	1	1	0	0	1	1	1	1	1	4	1	3	1	4	2	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:56416341A>G	ENST00000342929.3	-	8	2584	c.2585T>C	c.(2584-2586)cTg>cCg	p.L862P	NLRP13_ENST00000588751.1_Missense_Mutation_p.L862P	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	862							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		GGGGTGAGTCAGGGCCGCACA	0.463																																					p.L862P		.											.	NLRP13-211	0			c.T2585C						.						121	98	106					19																	56416341		2203	4300	6503	SO:0001583	missense	126204	exon8			TGAGTCAGGGCCG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2585T>C	19.37:g.56416341A>G	ENSP00000343891:p.Leu862Pro	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_176810	0	0	0	0	0	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	10.91	1.483925	0.26598	.	.	ENSG00000173572	ENST00000342929	T	0.63417	-0.04	2.28	1.21	0.21127	.	.	.	.	.	T	0.78972	0.4368	M	0.91249	3.19	0.09310	N	0.999991	D	0.76494	0.999	D	0.74674	0.984	T	0.64854	-0.6309	9	0.87932	D	0	.	5.2371	0.15452	0.6965:0.3035:0.0:0.0	.	862	Q86W25	NAL13_HUMAN	P	862	ENSP00000343891:L862P	ENSP00000343891:L862P	L	-	2	0	NLRP13	61108153	0.303000	0.24463	0.014000	0.15608	0.005000	0.04900	3.240000	0.51368	0.304000	0.22809	0.533000	0.62120	CTG	.		0.463	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		G	56416341	A	G	56416341	3	3	7	1	0	0	0	0	1	0	0	0	10501	188	7	3	560	3	NLRP13	19	56416341	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	1240053	56416341	2712642	76	583											
MKKS	8195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	10385928	10385928	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaataacatatgaaagatcCaaaatcaaattggctgtctc	17	11	5	8	0	3	2	2	1	1	1	5	2	4	2	1	1	1	1	1	1	7	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr20:10385928C>A	ENST00000347364.3	-	6	2442	c.1680G>T	c.(1678-1680)ttG>ttT	p.L560F	MKKS_ENST00000399054.2_Missense_Mutation_p.L560F	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	560					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						ATGAAAGATCCAAAATCAAAT	0.393																																					p.L560F	Melanoma(79;1979 2212 6640)	.											.	MKKS-90	0			c.G1680T						.						32	31	31					20																	10385928		2203	4300	6503	SO:0001583	missense	8195	exon6			AAGATCCAAAATC	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"Heat Shock Proteins / Chaperonins"	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.1680G>T	20.37:g.10385928C>A	ENSP00000246062:p.Leu560Phe	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_170784	0	0	18	21	3	A8K7B0|D3DW18	Missense_Mutation	SNP	ENST00000347364.3	37	CCDS13111.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.843811	0.71488	.	.	ENSG00000125863	ENST00000347364;ENST00000399054	D;D	0.87966	-2.32;-2.32	6.07	2.82	0.32997	.	0.000000	0.64402	D	0.000001	D	0.91791	0.7403	M	0.77616	2.38	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.90008	0.4119	10	0.87932	D	0	-8.0737	8.1919	0.31374	0.0:0.6163:0.0:0.3837	.	560	Q9NPJ1	MKKS_HUMAN	F	560	ENSP00000246062:L560F;ENSP00000382008:L560F	ENSP00000246062:L560F	L	-	3	2	MKKS	10333928	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.884000	0.28214	0.279000	0.22186	0.655000	0.94253	TTG	.		0.393	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3			A	10385928	C	A	10385928	3	1	7	1	0	0	0	0	1	0	0	0	9625	593	21	4	36	4	MKKS	20	10385928	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		10385928	52639592	77	584											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60891744	60891744	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaaggcccagcctctgcTgttcctggagcatggcctct	6	9	10	16	0	2	0	0	0	2	0	3	1	3	1	5	3	3	3	5	3	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr20:60891744T>C	ENST00000252999.3	-	57	7805	c.7739A>G	c.(7738-7740)cAg>cGg	p.Q2580R		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2580	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CAGCCTCTGCTGTTCCTGGAG	0.672																																					p.Q2580R		.											.	LAMA5-93	0			c.A7739G						.						26	20	22					20																	60891744		2184	4279	6463	SO:0001583	missense	3911	exon57			CTCTGCTGTTCCT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7739A>G	20.37:g.60891744T>C	ENSP00000252999:p.Gln2580Arg	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_005560	0	0	27	27	0	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	9.586	1.124844	0.20959	.	.	ENSG00000130702	ENST00000252999	T	0.19394	2.15	3.79	2.68	0.31781	.	0.486771	0.21799	U	0.068955	T	0.18635	0.0447	L	0.60845	1.875	0.09310	N	0.999996	B	0.10296	0.003	B	0.06405	0.002	T	0.19353	-1.0308	10	0.49607	T	0.09	.	5.5906	0.17299	0.0:0.1285:0.0:0.8715	.	2580	O15230	LAMA5_HUMAN	R	2580	ENSP00000252999:Q2580R	ENSP00000252999:Q2580R	Q	-	2	0	LAMA5	60325139	0.002000	0.14202	0.010000	0.14722	0.034000	0.12701	0.444000	0.21661	0.526000	0.28541	0.255000	0.18592	CAG	.		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		C	60891744	T	C	60891744	3	2	7	1	0	0	0	0	1	0	0	0	8630	1580	55	3	3444	3	LAMA5	20	60891744	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	50505816	60891744	2133776	78	585											
GYG2	8908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	2772026	2772026	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgtctgttccagggtcaTcctctcgaaggtgttcgatg	7	13	11	10	2	3	0	1	0	2	0	7	2	5	0	2	2	0	2	2	2	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:2772026T>A	ENST00000381163.3	+	5	530	c.248T>A	c.(247-249)aTc>aAc	p.I83N	GYG2-AS1_ENST00000445107.1_RNA|GYG2_ENST00000398806.3_Missense_Mutation_p.I52N|GYG2_ENST00000338623.5_Missense_Mutation_p.I83N|GYG2_ENST00000381161.1_3'UTR|GYG2_ENST00000542787.1_Missense_Mutation_p.I83N	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	83					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCCAGGGTCATCCTCTCGAAG	0.507																																					p.I83N		.											.	GYG2-132	0			c.T248A						.						126	99	108					X																	2772026		2203	4298	6501	SO:0001583	missense	8908	exon5			GGGTCATCCTCTC	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"Glycosyltransferase family 8 domain containing"	4700	protein-coding gene	gene with protein product	"glycogenin glucosyltransferase"	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.248T>A	X.37:g.2772026T>A	ENSP00000370555:p.Ile83Asn	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	47	43	NM_003918	0	0	0	0	0	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.584140	0.28268	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787;ENST00000520904	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	3.59	2.41	0.29592	.	0.614533	0.14619	N	0.308517	T	0.37999	0.1024	L	0.39898	1.24	0.25836	N	0.984116	P;D;P;B;P	0.54964	0.731;0.969;0.847;0.378;0.489	P;P;P;B;P	0.49887	0.477;0.558;0.625;0.3;0.522	T	0.12016	-1.0564	10	0.41790	T	0.15	.	6.5	0.22164	0.0:0.2109:0.0:0.7891	.	83;43;52;52;83	O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;GLYG2_HUMAN	N	52;83;83;83;52	ENSP00000381786:I52N;ENSP00000370555:I83N;ENSP00000341273:I83N;ENSP00000446092:I83N;ENSP00000430764:I52N	ENSP00000341273:I83N	I	+	2	0	GYG2	2782026	0.959000	0.32827	0.051000	0.19133	0.019000	0.09904	1.290000	0.33319	1.271000	0.44313	0.481000	0.45027	ATC	.		0.507	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918		A	2772026	T	A	2772026	3	1	7	1	0	0	0	0	1	0	0	0	6927	1435	50	5	262	5	GYG2	23	2772026	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		2772026	152498534	79	586											
SYP	6855	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	49050637	49050638	+	Frame_Shift_Del	DEL	TG	TG	-																															actcaccagcatgggcccttTgttattctctcggtacttgt																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:49050637_49050638delTG	ENST00000263233.4	-	4	480_481	c.408_409delCA	c.(406-411)aacaaafs	p.N136fs	SYP_ENST00000538567.1_Frame_Shift_Del_p.N18fs|SYP_ENST00000479808.1_Frame_Shift_Del_p.N136fs	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	136	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular response to organic substance (GO:0071310)|endocytosis (GO:0006897)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle membrane organization (GO:0048499)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	cholesterol binding (GO:0015485)|protein self-association (GO:0043621)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)	15		all_lung(315;0.00016)				ATGGGCCCTTTGTTATTCTCTC	0.564																																					p.136_137del		.											.	SYP-556	0			c.408_409del						.																																			SO:0001589	frameshift_variant	6855	exon4			.	X06389	CCDS14321.1	Xp11.23-p11.22	2014-02-19			ENSG00000102003	ENSG00000102003			11506	protein-coding gene	gene with protein product		313475				3120152, 19377476	Standard	NM_003179		Approved	MRX96	uc004dmz.1	P08247	OTTHUMG00000034557	ENST00000263233.4:c.408_409delCA	X.37:g.49050637_49050638delTG	ENSP00000263233:p.Asn136fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	27	20	NM_003179	0	0	0	0	0	B2R7L6|B7Z359|Q6P2F7	Frame_Shift_Del	DEL	ENST00000263233.4	37	CCDS14321.1																																																																																			.		0.564	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179		-	49050638	TG	-	49050637	7	5	7	1	0	1	0	1	0	0	0	0	15493	1821	63	0	544	0	SYP	23	49050637	Frame_Shift_Del	DEL	TG	TCGA-A4-7732-01A-11D-2136-08	46278611	49050637	106219923	80	587	6	2									
SYP	6855	bcgsc.ca	37	chrX	49050639	49050639	+	Missense_Mutation	SNP	T	T	C																															tcaccagcatgggccctttgTtattctctcggtacttgttc																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:49050639T>C	ENST00000263233.4	-	4	479	c.407A>G	c.(406-408)aAc>aGc	p.N136S	SYP_ENST00000538567.1_Missense_Mutation_p.N18S|SYP_ENST00000479808.1_Missense_Mutation_p.N136S	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	136	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular response to organic substance (GO:0071310)|endocytosis (GO:0006897)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle membrane organization (GO:0048499)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	cholesterol binding (GO:0015485)|protein self-association (GO:0043621)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)	15		all_lung(315;0.00016)				GGGCCCTTTGTTATTCTCTCG	0.562																																					p.N136S													.	SYP-556	0			c.A407G						.						99	88	92					X																	49050639		2203	4300	6503	SO:0001583	missense	6855	exon4			CCTTTGTTATTCT	X06389	CCDS14321.1	Xp11.23-p11.22	2014-02-19			ENSG00000102003	ENSG00000102003			11506	protein-coding gene	gene with protein product		313475				3120152, 19377476	Standard	NM_003179		Approved	MRX96	uc004dmz.1	P08247	OTTHUMG00000034557	ENST00000263233.4:c.407A>G	X.37:g.49050639T>C	ENSP00000263233:p.Asn136Ser	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	25	19	NM_003179	0	0	3	3	0	B2R7L6|B7Z359|Q6P2F7	Missense_Mutation	SNP	ENST00000263233.4	37	CCDS14321.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.786962	0.49997	.	.	ENSG00000102003	ENST00000263233;ENST00000538567;ENST00000479808	T;T;T	0.25085	1.82;1.82;1.82	4.55	4.55	0.56014	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.37945	0.1022	L	0.43598	1.365	0.52099	D	0.999945	D	0.64830	0.994	D	0.64506	0.926	T	0.05869	-1.0859	10	0.30854	T	0.27	3.7056	12.0455	0.53477	0.0:0.0:0.0:1.0	.	136	P08247	SYPH_HUMAN	S	136;18;136	ENSP00000263233:N136S;ENSP00000437456:N18S;ENSP00000418169:N136S	ENSP00000263233:N136S	N	-	2	0	SYP	48937583	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.013000	0.64023	1.684000	0.51022	0.486000	0.48141	AAC	.		0.562	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179		C	49050639	T	C	49050639	3	2	7	1	0	0	0	0	1	0	0	0	15493	1725	60	3	546	3	SYP	23	49050639	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	2	49050639	106219921	81	588	6	2									
PHKA1	5255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	71829514	71829514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggttctggaggaagtcctaCtgtcaaatgtttctggtggg	8	13	14	6	0	3	0	1	0	2	0	4	2	4	2	1	5	1	2	1	5	3	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:71829514C>T	ENST00000373542.4	-	23	2725	c.2566G>A	c.(2566-2568)Gta>Ata	p.V856I	PHKA1_ENST00000541944.1_Missense_Mutation_p.V797I|PHKA1_ENST00000373539.3_Missense_Mutation_p.V856I|PHKA1_ENST00000373545.3_Missense_Mutation_p.V797I|PHKA1_ENST00000339490.3_Missense_Mutation_p.V856I	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	856					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GGAAGTCCTACTGTCAAATGT	0.453																																					p.V856I		.											.	PHKA1-134	0			c.G2566A						.						226	193	204					X																	71829514		2203	4300	6503	SO:0001583	missense	5255	exon23			GTCCTACTGTCAA		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2566G>A	X.37:g.71829514C>T	ENSP00000362643:p.Val856Ile	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	53	47	NM_002637	0	0	0	1	1	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.271260	0.80469	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98	5.65	5.65	0.86999	Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.95172	0.8435	M	0.84082	2.675	0.54753	D	0.999987	B;B;B	0.33637	0.118;0.389;0.42	B;P;B	0.48627	0.21;0.584;0.421	D	0.94813	0.7980	10	0.52906	T	0.07	-4.9016	15.893	0.79315	0.0:1.0:0.0:0.0	.	797;856;856	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	I	797;856;797;856;856	ENSP00000362646:V797I;ENSP00000362643:V856I;ENSP00000441251:V797I;ENSP00000342469:V856I;ENSP00000362640:V856I	ENSP00000342469:V856I	V	-	1	0	PHKA1	71746239	0.999000	0.42202	0.998000	0.56505	0.964000	0.63967	4.396000	0.59684	2.353000	0.79882	0.544000	0.68410	GTA	.		0.453	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			T	71829514	C	T	71829514	3	4	7	1	0	0	0	0	1	0	0	0	11869	565	20	2	1145	2	PHKA1	23	71829514	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	22778875	71829514	83441046	82	589											
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19181066	19181066	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggcccaggactcggaggCgatccacacggcgccagtga	9	4	15	13	4	0	1	0	1	0	0	2	5	1	3	3	5	0	0	3	5	0	0	rs201197024		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:19181066C>T	ENST00000375371.3	-	3	919	c.898G>A	c.(898-900)Gcc>Acc	p.A300T	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	300					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GACTCGGAGGCGATCCACACG	0.647													C|||	1	0.000199681	0	0.0014	5008	,	,		19322	0		0	False		,,,				2504	0				p.A300T		.											.	TAS1R2-93	0			c.G898A						.						56	54	55					1																	19181066		2203	4300	6503	SO:0001583	missense	80834	exon3			CGGAGGCGATCCA		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.898G>A	1.37:g.19181066C>T	ENSP00000364520:p.Ala300Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	64	21	NM_152232	0	0	0	0	0	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	23.7	4.444658	0.83993	.	.	ENSG00000179002	ENST00000375371	D	0.84730	-1.89	4.89	4.89	0.63831	Extracellular ligand-binding receptor (1);	0.000000	0.46145	D	0.000306	D	0.92756	0.7697	M	0.87971	2.92	0.42114	D	0.991391	D	0.89917	1.0	D	0.80764	0.994	D	0.92892	0.6332	10	0.44086	T	0.13	.	15.5821	0.76452	0.0:1.0:0.0:0.0	.	300	Q8TE23	TS1R2_HUMAN	T	300	ENSP00000364520:A300T	ENSP00000364520:A300T	A	-	1	0	TAS1R2	19053653	1.000000	0.71417	1.000000	0.80357	0.419000	0.31324	5.789000	0.69029	2.550000	0.86006	0.561000	0.74099	GCC	C|1.000;T|0.000		0.647	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19181066	C	T	19181066	3	4	8	1	0	0	0	0	1	0	0	0	15595	768	27	1	1637	1	TAS1R2	1	19181066	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08		19181066	230069555	1	590											
SLC35D1	23169	hgsc.bcm.edu	37	chr1	67515474	67515474	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacatcttacctggcagctAcaaaggctccaataatcatt	13	10	5	13	0	2	0	1	0	1	0	3	0	3	0	3	2	3	3	3	2	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:67515474A>G	ENST00000235345.5	-	6	609	c.524T>C	c.(523-525)gTa>gCa	p.V175A	SLC35D1_ENST00000506472.2_Missense_Mutation_p.V96A	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	175					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						CCTGGCAGCTACAAAGGCTCC	0.289																																					p.V175A		.											.	SLC35D1-90	0			c.T524C						.						61	63	62					1																	67515474		2203	4299	6502	SO:0001583	missense	23169	exon6			GCAGCTACAAAGG	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.524T>C	1.37:g.67515474A>G	ENSP00000235345:p.Val175Ala	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_015139	0	0	0	0	0	A8K185|B7Z3X2|Q52LU5|Q92548	Missense_Mutation	SNP	ENST00000235345.5	37	CCDS636.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.621853	0.87460	.	.	ENSG00000116704	ENST00000235345;ENST00000506472	T;T	0.66280	-0.2;0.25	5.29	5.29	0.74685	.	0.158134	0.56097	D	0.000027	T	0.69178	0.3082	M	0.86651	2.83	0.49483	D	0.999798	P;P	0.50156	0.932;0.806	P;P	0.53185	0.676;0.72	T	0.75445	-0.3315	10	0.54805	T	0.06	-7.0229	12.7442	0.57270	1.0:0.0:0.0:0.0	.	96;175	B7Z3X2;Q9NTN3	.;S35D1_HUMAN	A	175;96	ENSP00000235345:V175A;ENSP00000445189:V96A	ENSP00000235345:V175A	V	-	2	0	SLC35D1	67288062	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.193000	0.89719	2.000000	0.58554	0.533000	0.62120	GTA	.		0.289	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		G	67515474	A	G	67515474	3	3	8	1	0	0	0	0	1	0	0	0	14613	391	14	3	571	3	SLC35D1	1	67515474	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	48334408	67515474	181735147	2	591											
ZNF644	84146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	91406116	91406116	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttagtcataagaaattgaatGaactctttttggggatccca	13	14	8	6	0	2	3	1	2	1	1	3	4	3	4	1	2	1	0	1	2	5	5			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:91406116G>A	ENST00000370440.1	-	3	1012	c.795C>T	c.(793-795)ttC>ttT	p.F265F	ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000337393.5_Silent_p.F265F|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	265					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(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GAAATTGAATGAACTCTTTTT	0.353																																					p.F265F		.											.	ZNF644-155	0			c.C795T						.						106	105	105					1																	91406116		2202	4300	6502	SO:0001819	synonymous_variant	84146	exon3			TTGAATGAACTCT	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.795C>T	1.37:g.91406116G>A		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	144	57	NM_201269	0	0	8	15	7	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	37	CCDS731.1																																																																																			.		0.353	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91406116	G	A	91406116	2	1	8	1	0	0	0	0	0	0	0	1	18092	1281	45	2		2	ZNF644	1	91406116	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08	23890642	91406116	157844505	3	592											
KCND3	3752	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	112524716	112524716	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggcagctccttgctgccCgggaccgtgccgcacggcac	5	5	13	18	5	0	0	0	0	0	0	1	1	1	1	4	3	4	5	4	3	0	1	rs35131566	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:112524716C>T	ENST00000315987.2	-	2	1112	c.633G>A	c.(631-633)ccG>ccA	p.P211P	KCND3_ENST00000369697.1_Silent_p.P211P|KCND3_ENST00000302127.4_Silent_p.P211P	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	211					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CCTTGCTGCCCGGGACCGTGC	0.647																																					p.P211P		.											.	KCND3-155	0			c.G633A						.						27	28	28					1																	112524716		2203	4300	6503	SO:0001819	synonymous_variant	3752	exon2			GCTGCCCGGGACC	AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.633G>A	1.37:g.112524716C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	34	13	NM_004980	0	0	3	10	7	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Silent	SNP	ENST00000315987.2	37	CCDS843.1																																																																																			C|0.999;A|0.001		0.647	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		T	112524716	C	T	112524716	2	4	8	1	0	0	0	0	0	0	0	1	8041	639	23	1		1	KCND3	1	112524716	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	21118600	112524716	136725905	4	593											
YY1AP1	55249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155638446	155638446	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgtcaggagctctgttcAtgttgaggttcttgattctc	5	18	11	7	0	5	2	2	2	3	0	6	3	5	3	0	2	1	5	0	2	0	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:155638446A>T	ENST00000295566.4	-	9	1012	c.989T>A	c.(988-990)aTg>aAg	p.M330K	YY1AP1_ENST00000355499.4_Missense_Mutation_p.M284K|YY1AP1_ENST00000311573.5_Missense_Mutation_p.M253K|YY1AP1_ENST00000347088.5_Missense_Mutation_p.M284K|YY1AP1_ENST00000404643.1_Missense_Mutation_p.M264K|YY1AP1_ENST00000535662.1_Missense_Mutation_p.M130K|YY1AP1_ENST00000476093.1_5'Flank|YY1AP1_ENST00000407221.1_Missense_Mutation_p.M253K|YY1AP1_ENST00000361831.5_Missense_Mutation_p.M273K|YY1AP1_ENST00000368339.5_Missense_Mutation_p.M422K|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000368340.5_Missense_Mutation_p.M402K|YY1AP1_ENST00000405763.3_Missense_Mutation_p.M422K|YY1AP1_ENST00000359205.5_Missense_Mutation_p.M273K|YY1AP1_ENST00000368330.2_Missense_Mutation_p.M284K	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	330					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					AGCTCTGTTCATGTTGAGGTT	0.433																																					p.M422K		.											.	YY1AP1-93	0			c.T1265A						.						307	257	274					1																	155638446		2203	4300	6503	SO:0001583	missense	55249	exon8			CTGTTCATGTTGA	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.989T>A	1.37:g.155638446A>T	ENSP00000295566:p.Met330Lys	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	149	46	NM_001198903	0	0	36	60	24	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.419504	0.42918	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662;ENST00000405763	T;T;T;T;T;T;T;T;T;T;T;T	0.24151	1.9;1.9;1.92;1.9;1.9;1.9;1.91;1.9;1.92;1.93;1.87;1.93	3.4	-0.935	0.10423	.	0.476592	0.21278	N	0.077194	T	0.07999	0.0200	L	0.53249	1.67	0.80722	D	1	B;B;B;B;B;P;B	0.40211	0.12;0.103;0.169;0.297;0.034;0.707;0.088	B;B;B;B;B;B;B	0.36845	0.098;0.025;0.079;0.175;0.017;0.234;0.046	T	0.14671	-1.0464	10	0.32370	T	0.25	.	4.6279	0.12488	0.6197:0.0:0.0911:0.2892	.	350;422;264;422;330;284;402	B4DQQ0;B4DMP2;Q9H869-4;B0QZ55;Q9H869;Q9H869-2;Q5VYZ1	.;.;.;.;YYAP1_HUMAN;.;.	K	273;284;253;284;273;402;330;284;253;264;422;130;422	ENSP00000352134:M273K;ENSP00000347686:M284K;ENSP00000311138:M253K;ENSP00000316079:M284K;ENSP00000355298:M273K;ENSP00000357324:M402K;ENSP00000295566:M330K;ENSP00000357314:M284K;ENSP00000385791:M253K;ENSP00000385390:M264K;ENSP00000357323:M422K;ENSP00000437926:M130K	ENSP00000295566:M330K	M	-	2	0	YY1AP1	153905070	0.275000	0.24201	0.971000	0.41717	0.982000	0.71751	0.942000	0.29017	0.038000	0.15604	0.379000	0.24179	ATG	.		0.433	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		T	155638446	A	T	155638446	3	4	8	1	0	0	0	0	1	0	0	0	17541	217	8	5	1413	5	YY1AP1	1	155638446	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	43113730	155638446	93612175	5	594											
PVRL4	81607	hgsc.bcm.edu;bcgsc.ca	37	chr1	161049405	161049405	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcggagccgcagccgcgcCtggaagctgccggcggggaa	7	3	17	14	6	0	0	0	0	0	0	1	3	0	3	4	5	4	2	4	5	2	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:161049405C>T	ENST00000368012.3	-	2	716	c.414G>A	c.(412-414)caG>caA	p.Q138Q		NM_030916.2	NP_112178.2	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	138	Ig-like V-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|urinary_tract(1)	20	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			GCAGCCGCGCCTGGAAGCTGC	0.677																																					p.Q138Q	NSCLC(76;1160 1387 14476 16172 29359)	.											.	PVRL4-92	0			c.G414A						.						9	11	10					1																	161049405		2016	4029	6045	SO:0001819	synonymous_variant	81607	exon2			CCGCGCCTGGAAG	AF426163	CCDS1216.1	1q22-q23.2	2013-01-14			ENSG00000143217	ENSG00000143217		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	19688	protein-coding gene	gene with protein product		609607				11544254	Standard	NM_030916		Approved	nectin-4, PRR4, LNIR	uc001fxo.2	Q96NY8	OTTHUMG00000031475	ENST00000368012.3:c.414G>A	1.37:g.161049405C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_030916	0	0	0	0	0	B4DQW3|Q96K15	Silent	SNP	ENST00000368012.3	37	CCDS1216.1																																																																																			.		0.677	PVRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077074.1	NM_030916		T	161049405	C	T	161049405	2	4	8	1	0	0	0	0	0	0	0	1	12874	680	24	2		2	PVRL4	1	161049405	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	5410959	161049405	88201216	6	595											
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	21251317	21251317	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattttgttaatatctgcctGtgaaggactcctcatcaaca	12	14	6	9	0	3	1	2	1	1	0	4	2	4	2	2	1	2	1	2	1	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:21251317G>A	ENST00000233242.1	-	13	1838	c.1711C>T	c.(1711-1713)Cag>Tag	p.Q571*	APOB_ENST00000399256.4_Nonsense_Mutation_p.Q571*	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	571	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATATCTGCCTGTGAAGGACTC	0.438																																					p.Q571X		.											.	APOB-175	0			c.C1711T						.						131	133	132					2																	21251317		2203	4300	6503	SO:0001587	stop_gained	338	exon13			CTGCCTGTGAAGG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1711C>T	2.37:g.21251317G>A	ENSP00000233242:p.Gln571*	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	144	55	NM_000384	0	0	0	0	0	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	37	6.513092	0.97629	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	.	.	.	5.69	3.47	0.39725	.	0.330090	0.28688	N	0.014472	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	5.0861	0.14682	0.0975:0.133:0.632:0.1375	.	.	.	.	X	571	.	ENSP00000233242:Q571X	Q	-	1	0	APOB	21104822	0.134000	0.22483	0.496000	0.27539	0.194000	0.23727	0.571000	0.23669	0.602000	0.29896	0.655000	0.94253	CAG	.		0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21251317	G	A	21251317	4	1	8	1	0	0	0	0	0	1	0	0	785	1386	48	2	12048	2	APOB	2	21251317	Nonsense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08		21251317	221948056	7	596											
ITGA6	3655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	173352903	173352903	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggtacagttgttggcgagCaagctatgaaatctgaagat	13	10	13	5	1	1	3	0	2	1	1	1	5	1	3	0	2	3	5	0	2	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:173352903C>A	ENST00000264106.6	+	20	2772	c.2569C>A	c.(2569-2571)Caa>Aaa	p.Q857K	ITGA6_ENST00000343713.4_Missense_Mutation_p.Q813K|ITGA6_ENST00000375221.2_Missense_Mutation_p.Q857K|ITGA6_ENST00000409532.1_Missense_Mutation_p.Q699K|ITGA6_ENST00000409080.1_Missense_Mutation_p.Q818K|ITGA6_ENST00000264107.7_Missense_Mutation_p.Q818K|AC093818.1_ENST00000442417.1_RNA			P23229	ITA6_HUMAN	integrin, alpha 6	857					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TGTTGGCGAGCAAGCTATGAA	0.368																																					p.Q818K		.											.	ITGA6-227	0			c.C2452A						.						152	153	153					2																	173352903		2203	4300	6503	SO:0001583	missense	3655	exon19			GGCGAGCAAGCTA		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2569C>A	2.37:g.173352903C>A	ENSP00000264106:p.Gln857Lys	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	115	46	NM_000210	0	0	65	143	78	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		.	.	.	.	.	.	.	.	.	.	C	14.43	2.532122	0.45073	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.76	3.78	0.43462	.	0.192038	0.56097	D	0.000033	T	0.33904	0.0879	N	0.22421	0.69	0.31631	N	0.648993	B;B;B;B	0.16802	0.007;0.008;0.019;0.019	B;B;B;B	0.19666	0.015;0.026;0.026;0.016	T	0.36065	-0.9763	10	0.42905	T	0.14	.	12.9758	0.58537	0.3451:0.6549:0.0:0.0	.	813;857;818;818	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	K	699;818;857;857;813;818;857;813;43	ENSP00000386614:Q699K;ENSP00000264107:Q818K;ENSP00000264106:Q857K;ENSP00000364369:Q857K;ENSP00000341078:Q813K;ENSP00000386896:Q818K;ENSP00000406694:Q857K;ENSP00000394169:Q813K;ENSP00000388435:Q43K	ENSP00000264106:Q857K	Q	+	1	0	ITGA6	173061149	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	4.932000	0.63476	2.725000	0.93324	0.585000	0.79938	CAA	.		0.368	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				A	173352903	C	A	173352903	3	1	8	1	0	0	0	0	1	0	0	0	7901	711	25	4	2526	4	ITGA6	2	173352903	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	152101586	173352903	69846470	8	597											
ZNF385B	151126	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	180310448	180310448	+	Frame_Shift_Del	DEL	T	T	-																															gcttcaaccatggtcttgtgTttagatcctaagacagaaag																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:180310448delT	ENST00000410066.1	-	8	1527	c.924delA	c.(922-924)aaafs	p.K308fs	ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Frame_Shift_Del_p.K232fs|ZNF385B_ENST00000336917.5_Frame_Shift_Del_p.K206fs|ZNF385B_ENST00000409692.1_Frame_Shift_Del_p.K206fs	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	308	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TGGTCTTGTGTTTAGATCCTA	0.388																																					p.K308fs	Colon(155;204 2491 32774 51842)	.											.	ZNF385B-23	0			c.924delA						.						103	95	98					2																	180310448		2203	4300	6503	SO:0001589	frameshift_variant	151126	exon8			.	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.924delA	2.37:g.180310448delT	ENSP00000386845:p.Lys308fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	91	30	NM_152520	0	0	0	0	0	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Frame_Shift_Del	DEL	ENST00000410066.1	37	CCDS33339.1																																																																																			.		0.388	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		-	180310448	T	-	180310448	7	5	8	1	0	1	0	1	0	0	0	0	17909	1722	60	0	503	0	ZNF385B	2	180310448	Frame_Shift_Del	DEL	T	TCGA-A4-7734-01A-11D-2136-08	6957545	180310448	62888925	9	598											
OBSL1	23363	broad.mit.edu	37	chr2	220435527	220435528	+	Frame_Shift_Ins	INS	-	-	C																															gcacgtcagcaccacctccgINSccccccgcagcacccactgg																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:220435527_220435528insC	ENST00000404537.1	-	1	483_484	c.427_428insG	c.(427-429)gcgfs	p.A143fs	OBSL1_ENST00000491370.1_Intron|OBSL1_ENST00000373873.4_Frame_Shift_Ins_p.A143fs|OBSL1_ENST00000289656.3_Intron|OBSL1_ENST00000603926.1_Frame_Shift_Ins_p.A143fs|OBSL1_ENST00000373876.1_Frame_Shift_Ins_p.A143fs|INHA_ENST00000243786.2_5'Flank|INHA_ENST00000489456.1_Intron|OBSL1_ENST00000265318.4_Frame_Shift_Ins_p.A143fs	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	143	Ig-like 2.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CACCACCTCCGCCCCCCGCAGC	0.748																																					p.A143fs													.	OBSL1-71	0			c.428_429insG						.																																			SO:0001589	frameshift_variant	23363	exon1			ACCTCCGCCCCCC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.428dupG	2.37:g.220435533_220435533dupC	ENSP00000385636:p.Ala143fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001173431	0	0	0	0	0	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Frame_Shift_Ins	INS	ENST00000404537.1	37	CCDS46520.1																																																																																			.		0.748	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			C	220435528	-	C	220435527	7	5	8	1	0	1	1	0	0	0	0	0	10839	1087	38	0	5498	0	OBSL1	2	220435527	Frame_Shift_Ins	INS	-	TCGA-A4-7734-01A-11D-2136-08	40125079	220435527	22763846	10	599											
TOP2B	7155	broad.mit.edu	37	chr3	25678710	25678710	+	Frame_Shift_Del	DEL	T	T	-																															tgtgtttctagcatacctgcTtaaaactgtgtttgtattct																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr3:25678710delT	ENST00000264331.4	-	6	634	c.635delA	c.(634-636)aagfs	p.K212fs	TOP2B_ENST00000435706.2_Frame_Shift_Del_p.K207fs	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	212					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GCATACCTGCTTAAAACTGTG	0.333																																					p.K207fs													.	TOP2B-273	0			c.620delA						.						50	46	48					3																	25678710		1782	4022	5804	SO:0001589	frameshift_variant	7155	exon6			ACCTGCTTAAAAC	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.635delA	3.37:g.25678710delT	ENSP00000264331:p.Lys212fs	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_001068	0	0	0	0	0	Q13600|Q9UMG8|Q9UQP8	Frame_Shift_Del	DEL	ENST00000264331.4	37																																																																																				.		0.333	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				-	25678710	T	-	25678710	7	5	8	1	0	1	0	1	0	0	0	0	16399	1609	56	0	4369	0	TOP2B	3	25678710	Frame_Shift_Del	DEL	T	TCGA-A4-7734-01A-11D-2136-08		25678710	172343720	11	600											
NEK10	152110	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	27297798	27297799	+	Missense_Mutation	DNP	GA	GA	AT																															tgtccttaccaagaatacagGattgttccaaccacagaggt																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr3:27297798_27297799GA>AT	ENST00000429845.2	-	24	2440_2441	c.2078_2079TC>AT	c.(2077-2079)aTC>aAT	p.I693N	NEK10_ENST00000357467.2_Missense_Mutation_p.I90N|NEK10_ENST00000341435.5_Missense_Mutation_p.I693N			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	693	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AAGAATACAGGATTGTTCCAAC	0.342																																					p.I693N													.	NEK10-695	0			c.T2078A						.																																			SO:0001583	missense	152110	exon24			TACAGGATTGTTC	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2078_2079delinsAT	3.37:g.27297798_27297799delinsAT	ENSP00000395849:p.Ile693Asn	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	25	8	NM_199347	0	0	0	0	0	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	DNP	ENST00000429845.2	37																																																																																				.		0.342	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		AT	27297799	GA	AT	27297798	3	1	8	1	0	0	0	0	1	0	0	0	10348	1164	41	2	67	2	NEK10	3	27297798	Missense_Mutation	DNP	GA	TCGA-A4-7734-01A-11D-2136-08	1619088	27297798	170724632	12	601											
KBTBD5	131377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	42727131	42727131	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggcgctgggcttggagcaGgcggaggagcagcggttgta	7	7	20	7	3	0	0	0	0	0	0	0	3	0	3	0	7	3	6	0	7	1	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr3:42727131G>A	ENST00000287777.4	+	1	121	c.21G>A	c.(19-21)caG>caA	p.Q7Q		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	7					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)											GCTTGGAGCAGGCGGAGGAGC	0.647																																					p.Q7Q		.											.	.	0			c.G21A						.						29	23	25					3																	42727131		2198	4298	6496	SO:0001819	synonymous_variant	131377	exon1			GGAGCAGGCGGAG	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"Kelch-like", "BTB/POZ domain containing"	30372	protein-coding gene	gene with protein product	"sarcosynapsin", "nemaline myopathy type 8"	615340	"kelch repeat and BTB (POZ) domain containing 5", "kelch-like 40 (Drosophila)"	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.21G>A	3.37:g.42727131G>A		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	16	8	NM_152393	0	0	0	0	0	Q86SI1|Q96MR2	Silent	SNP	ENST00000287777.4	37	CCDS2703.1																																																																																			.		0.647	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393		A	42727131	G	A	42727131	2	1	8	1	0	0	0	0	0	0	0	1	8017	991	35	2		2	KBTBD5	3	42727131	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08	15429333	42727131	155295299	13	602											
HTR3D	200909	ucsc.edu	37	chr3	183756414	183756414	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccccacccacctgcccggTgagggaagtcatacttcctc	8	7	8	18	1	1	1	1	1	0	0	3	2	2	2	6	2	2	0	6	2	2	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr3:183756414T>A	ENST00000382489.3	+	7	1135		c.e7+2		HTR3D_ENST00000428798.2_Splice_Site|HTR3D_ENST00000334128.2_Splice_Site|HTR3D_ENST00000453435.1_Splice_Site	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	ACCTGCCCGGTGAGGGAAGTC	0.632																																					.													.	HTR3D-90	0			c.610+2T>A						.						20	24	23					3																	183756414		2199	4298	6497	SO:0001630	splice_region_variant	200909	exon5			GCCCGGTGAGGGA	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24004	protein-coding gene	gene with protein product		610122	"5-hydroxytryptamine (serotonin) receptor 3 family member D"			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1135+2T>A	3.37:g.183756414T>A		Somatic	22	0		WXS	Illumina HiSeq		23	4	NM_182537	0	0	0	0	0	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Splice_Site	SNP	ENST00000382489.3	37	CCDS54685.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.156539	0.38119	.	.	ENSG00000186090	ENST00000334128;ENST00000428798;ENST00000382489;ENST00000453435	.	.	.	3.77	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0732	0.36504	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HTR3D	185239108	0.592000	0.26832	0.793000	0.32043	0.128000	0.20619	2.138000	0.42140	1.706000	0.51276	0.379000	0.24179	.	.		0.632	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	Intron	A	183756414	T	A	183756414	5	1	8	1	0	0	0	0	0	0	1	0	7468	1710	59	5	1333	5	HTR3D	3	183756414	Splice_Site	SNP	T	TCGA-A4-7734-01A-11D-2136-08	141029283	183756414	14266016	14	603											
HERC5	51191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	89410409	89410409	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccacgtttgatctaacagtCagaaggaatcacttgattga	13	11	8	9	1	3	4	2	3	1	1	3	5	3	5	1	1	1	1	1	1	3	4	rs141289100	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr4:89410409C>G	ENST00000264350.3	+	16	2208	c.2055C>G	c.(2053-2055)gtC>gtG	p.V685V	HERC5_ENST00000508159.1_Silent_p.V323V	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	685					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		ATCTAACAGTCAGAAGGAATC	0.383																																					p.V685V	Esophageal Squamous(39;887 1012 34045 50514)	.											.	HERC5-664	0			c.C2055G						.						177	183	181					4																	89410409		2203	4300	6503	SO:0001819	synonymous_variant	51191	exon16			AACAGTCAGAAGG	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.2055C>G	4.37:g.89410409C>G		Somatic	259	0		WXS	Illumina HiSeq	Phase_I	220	98	NM_016323	0	0	3	14	11	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																			C|1.000;T|0.000		0.383	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		G	89410409	C	G	89410409	2	3	8	1	0	0	0	0	0	0	0	1	7082	813	29	4		4	HERC5	4	89410409	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08		89410409	101743867	15	604											
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	126411930	126411930	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacacaccaaaattttcaatCcagaggcacagtcccctagg	14	7	6	14	0	1	1	1	0	0	1	3	1	3	1	4	2	0	1	4	2	4	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr4:126411930C>A	ENST00000394329.3	+	17	13966	c.13953C>A	c.(13951-13953)atC>atA	p.I4651I	FAT4_ENST00000335110.5_Silent_p.I2892I	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4651					branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AATTTTCAATCCAGAGGCACA	0.502																																					p.I4651I		.											.	FAT4-108	0			c.C13953A						.						75	70	72					4																	126411930		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon17			TTCAATCCAGAGG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.13953C>A	4.37:g.126411930C>A		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	73	32	NM_024582	0	0	9	18	9	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.		0.502	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126411930	C	A	126411930	2	1	8	1	0	0	0	0	0	0	0	1	5711	845	30	4		4	FAT4	4	126411930	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	37001521	126411930	64742346	16	605											
NSUN2	54888	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	6620336	6620336	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccaccatgatgcaggggCtgctcagcctcttggcttga	7	10	12	12	0	2	3	1	3	1	0	2	3	2	3	3	3	3	4	3	3	0	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:6620336C>T	ENST00000264670.6	-	7	1009	c.698G>A	c.(697-699)aGc>aAc	p.S233N	NSUN2_ENST00000506139.1_Missense_Mutation_p.S198N|NSUN2_ENST00000505264.1_5'UTR|NSUN2_ENST00000539938.1_5'UTR	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	233					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						GATGCAGGGGCTGCTCAGCCT	0.502																																					p.S233N		.											.	NSUN2-91	0			c.G698A						.						99	99	99					5																	6620336		2203	4300	6503	SO:0001583	missense	54888	exon7			CAGGGGCTGCTCA	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.698G>A	5.37:g.6620336C>T	ENSP00000264670:p.Ser233Asn	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	144	9	NM_017755	0	0	26	26	0	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	C	36	5.656410	0.96724	.	.	ENSG00000037474	ENST00000264670;ENST00000506139	T;T	0.41065	1.01;1.04	6.02	6.02	0.97574	.	0.070917	0.85682	D	0.000000	T	0.67813	0.2933	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66571	-0.5890	10	0.56958	D	0.05	-41.3851	20.5407	0.99260	0.0:1.0:0.0:0.0	.	198;233	B4DQW2;Q08J23	.;NSUN2_HUMAN	N	233;198	ENSP00000264670:S233N;ENSP00000420957:S198N	ENSP00000264670:S233N	S	-	2	0	NSUN2	6673336	1.000000	0.71417	0.994000	0.49952	0.961000	0.63080	7.366000	0.79548	2.865000	0.98341	0.655000	0.94253	AGC	.		0.502	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6620336	C	T	6620336	3	4	8	1	0	0	0	0	1	0	0	0	10704	797	28	2	1657	2	NSUN2	5	6620336	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08		6620336	174294924	17	606											
FCHO2	115548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	72378596	72378596	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttattgcaggaatgcagAacaaatgaaagccttttgga	14	12	9	6	0	1	2	0	1	1	1	1	4	1	4	1	2	4	2	1	2	5	5			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:72378596A>C	ENST00000430046.2	+	24	2305	c.2189A>C	c.(2188-2190)gAa>gCa	p.E730A	FCHO2_ENST00000512348.1_Missense_Mutation_p.E697A|FCHO2_ENST00000341845.6_Missense_Mutation_p.E730A	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	730	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with DAB2, EPS15, EPS15R and ITSN1.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AGGAATGCAGAACAAATGAAA	0.308																																					p.E730A		.											.	FCHO2-23	0			c.A2189C						.						67	66	66					5																	72378596		1810	4076	5886	SO:0001583	missense	115548	exon24			ATGCAGAACAAAT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.2189A>C	5.37:g.72378596A>C	ENSP00000393776:p.Glu730Ala	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	14	9	NM_138782	0	0	0	0	0	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	37	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.309909	0.60414	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.54071	0.59;0.59;0.59	5.31	5.31	0.75309	Muniscin C-terminal mu homology domain (1);	0.172570	0.49305	D	0.000142	T	0.49081	0.1536	L	0.52364	1.645	0.58432	D	0.999996	B;B	0.10296	0.003;0.003	B;B	0.21151	0.01;0.033	T	0.43572	-0.9383	10	0.40728	T	0.16	-23.3471	14.6045	0.68466	1.0:0.0:0.0:0.0	.	697;730	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	A	730;730;697	ENSP00000393776:E730A;ENSP00000344034:E730A;ENSP00000427296:E697A	ENSP00000344034:E730A	E	+	2	0	FCHO2	72414352	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.460000	0.90369	2.231000	0.72958	0.533000	0.62120	GAA	.		0.308	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		C	72378596	A	C	72378596	3	2	8	1	0	0	0	0	1	0	0	0	5807	246	9	5	2283	5	FCHO2	5	72378596	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	65758260	72378596	108536664	18	607											
AP3B1	8546	hgsc.bcm.edu	37	chr5	77406161	77406161	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagatttttcattttccttcTccccatcttcagaatcacta	9	18	2	12	0	5	2	3	0	2	2	7	2	6	2	3	0	0	0	3	0	3	8			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:77406161T>C	ENST00000255194.6	-	20	2442	c.2267A>G	c.(2266-2268)gAg>gGg	p.E756G	AP3B1_ENST00000519295.1_Missense_Mutation_p.E707G	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	756	Glu/Ser-rich.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		ATTTTCCTTCTCCCCATCTTC	0.294									Hermansky-Pudlak syndrome																												p.E756G		.											.	AP3B1-90	0			c.A2267G						.						48	46	46					5																	77406161		2199	4296	6495	SO:0001583	missense	8546	exon20	Familial Cancer Database	HPS, HPS1-8	TCCTTCTCCCCAT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2267A>G	5.37:g.77406161T>C	ENSP00000255194:p.Glu756Gly	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	20	2	NM_003664	0	1	23	24	0	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.746589	0.30955	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.64803	-0.12;-0.12	5.68	4.52	0.55395	.	1.179390	0.05769	N	0.606283	T	0.48995	0.1531	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34725	-0.9817	10	0.22706	T	0.39	-1.7341	8.3059	0.32042	0.0:0.1581:0.0:0.8419	.	756	O00203	AP3B1_HUMAN	G	756;707;756	ENSP00000255194:E756G;ENSP00000430597:E707G	ENSP00000255194:E756G	E	-	2	0	AP3B1	77441917	0.060000	0.20803	0.105000	0.21289	0.972000	0.66771	2.151000	0.42263	0.978000	0.38470	0.533000	0.62120	GAG	.		0.294	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77406161	T	C	77406161	3	2	8	1	0	0	0	0	1	0	0	0	744	1551	54	3	1049	3	AP3B1	5	77406161	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	5027565	77406161	103509099	19	608											
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127419881	127419881	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcccaccccgagccagAgccgtttccaggtggacctg	6	6	14	15	2	0	1	0	0	0	1	1	3	1	2	7	4	2	1	7	4	0	1	rs557916029		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:127419881A>C	ENST00000262461.2	+	1	424	c.235A>C	c.(235-237)Agc>Cgc	p.S79R	SLC12A2_ENST00000343225.4_Missense_Mutation_p.S79R|CTC-228N24.3_ENST00000501702.2_lincRNA	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	79					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	CCCGAGCCAGAGCCGTTTCCA	0.816													A|||	1	0.000199681	0	0	5008	,	,		6545	0		0.001	False		,,,				2504	0				p.S79R		.											.	SLC12A2-94	0			c.A235C						.						1	2	1					5																	127419881		861	2057	2918	SO:0001583	missense	6558	exon1			AGCCAGAGCCGTT		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.235A>C	5.37:g.127419881A>C	ENSP00000262461:p.Ser79Arg	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	7	5	NM_001046	0	0	0	0	0	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	37	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.467578	0.84533	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.86865	-2.16;-2.18	4.11	2.95	0.34219	.	0.128217	0.50627	D	0.000110	D	0.89280	0.6670	L	0.47190	1.495	0.58432	D	0.99999	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	D	0.88787	0.3275	10	0.72032	D	0.01	.	8.7601	0.34669	0.9077:0.0:0.0923:0.0	.	79;79	P55011-3;P55011	.;S12A2_HUMAN	R	79	ENSP00000262461:S79R;ENSP00000340878:S79R	ENSP00000262461:S79R	S	+	1	0	SLC12A2	127447780	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.501000	0.60393	1.474000	0.48178	0.260000	0.18958	AGC	.		0.816	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		C	127419881	A	C	127419881	3	2	8	1	0	0	0	0	1	0	0	0	14415	304	11	5	237	5	SLC12A2	5	127419881	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	50013720	127419881	53495379	20	609											
HSPA4	3308	hgsc.bcm.edu	37	chr5	132425377	132425377	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggatttgccctatccagaTcctgctataggtaagtaaag	12	11	9	9	0	0	1	0	0	0	1	2	2	2	2	3	2	2	3	3	2	6	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:132425377T>C	ENST00000304858.2	+	11	1657	c.1368T>C	c.(1366-1368)gaT>gaC	p.D456D		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	456					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCTATCCAGATCCTGCTATAG	0.383																																					p.D456D	Colon(114;1299 1588 6063 12302 48757)	.											.	HSPA4-226	0			c.T1368C						.						38	35	36					5																	132425377		2203	4300	6503	SO:0001819	synonymous_variant	3308	exon11			TCCAGATCCTGCT	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"Heat shock proteins / HSP70"	5237	protein-coding gene	gene with protein product	"hsp70 RY"	601113	"heat shock 70kD protein 4"			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.1368T>C	5.37:g.132425377T>C		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_002154	0	0	0	0	0	O95756|Q2TAL4|Q9BUK9	Silent	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	T	9.025	0.985947	0.18889	.	.	ENSG00000170606	ENST00000537974	.	.	.	5.63	1.94	0.25998	.	.	.	.	.	T	0.52256	0.1723	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31280	-0.9949	5	0.21540	T	0.41	-23.0249	9.6052	0.39630	0.0:0.3421:0.0:0.6579	.	.	.	.	P	456	.	ENSP00000445221:S456P	S	+	1	0	HSPA4	132453276	0.748000	0.28294	1.000000	0.80357	0.977000	0.68977	-0.148000	0.10219	0.161000	0.19458	0.482000	0.46254	TCC	.		0.383	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		C	132425377	T	C	132425377	2	2	8	1	0	0	0	0	0	0	0	1	7433	1432	50	3		3	HSPA4	5	132425377	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	5005496	132425377	48489883	21	610											
CAMK2A	815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149644564	149644564	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gcagatgcgggcttcacgctCcagcttctgatggtctgaaa	8	10	12	11	2	3	3	1	2	2	1	4	3	4	3	1	2	2	4	1	2	1	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:149644564C>G	ENST00000348628.6	-	3	837	c.172G>C	c.(172-174)Gag>Cag	p.E58Q	CAMK2A_ENST00000398376.3_Missense_Mutation_p.E58Q	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	58	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTTCACGCTCCAGCTTCTGA	0.607																																					p.E58Q		.											.	CAMK2A-333	0			c.G172C						.						44	49	47					5																	149644564		2002	4186	6188	SO:0001583	missense	815	exon3			CACGCTCCAGCTT	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.172G>C	5.37:g.149644564C>G	ENSP00000261793:p.Glu58Gln	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	68	20	NM_171825	0	0	0	0	0	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	37	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	c	17.93	3.509651	0.64522	.	.	ENSG00000070808	ENST00000348628;ENST00000398376;ENST00000510347	T;T;T	0.24538	1.85;1.85;1.85	4.6	4.6	0.57074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067804	0.64402	U	0.000020	T	0.28863	0.0716	N	0.21448	0.665	0.58432	D	0.999997	B;B	0.29552	0.248;0.248	B;P	0.45099	0.307;0.469	T	0.27905	-1.0060	10	0.87932	D	0	.	13.2562	0.60081	0.0:1.0:0.0:0.0	.	58;58	Q9UQM7;A8K161	KCC2A_HUMAN;.	Q	58	ENSP00000261793:E58Q;ENSP00000381412:E58Q;ENSP00000426607:E58Q	ENSP00000261793:E58Q	E	-	1	0	CAMK2A	149624757	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.110000	0.71535	2.281000	0.76405	0.306000	0.20318	GAG	.		0.607	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		G	149644564	C	G	149644564	3	3	8	1	0	0	0	0	1	0	0	0	2605	864	30	4	1365	4	CAMK2A	5	149644564	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	17219187	149644564	31270696	22	611											
KIF13A	63971	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	17796913	17796913	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacaaacctgtcatgcagtgTtcttgtcttagcatgaagag	11	13	9	8	0	3	2	1	1	2	1	3	2	3	2	1	0	4	3	1	0	4	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr6:17796913T>G	ENST00000259711.6	-	23	3034	c.2929A>C	c.(2929-2931)Aca>Cca	p.T977P	KIF13A_ENST00000378814.5_Missense_Mutation_p.T977P|KIF13A_ENST00000378826.2_Missense_Mutation_p.T977P|KIF13A_ENST00000378843.2_Missense_Mutation_p.T977P|KIF13A_ENST00000378816.5_Missense_Mutation_p.T977P	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	977					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TCATGCAGTGTTCTTGTCTTA	0.507																																					p.T977P		.											.	KIF13A-137	0			c.A2929C						.						149	142	144					6																	17796913		1924	4131	6055	SO:0001583	missense	63971	exon23			GCAGTGTTCTTGT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.2929A>C	6.37:g.17796913T>G	ENSP00000259711:p.Thr977Pro	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	175	75	NM_001105567	0	0	16	24	8	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.3|24.3	4.513415|4.513415	0.85389|0.85389	.|.	.|.	ENSG00000137177|ENSG00000137177	ENST00000358380|ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816;ENST00000506044	.|T;T;T;T;T	.|0.72505	.|-0.62;-0.66;-0.62;-0.63;-0.62	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75939|0.75939	0.3918|0.3918	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.997;0.999;0.994;0.999	.|D;D;D;D	.|0.71184	.|0.947;0.962;0.922;0.972	T|T	0.79892|0.79892	-0.1611|-0.1611	5|10	.|0.87932	.|D	.|0	.|.	15.0983|15.0983	0.72253|0.72253	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|977;977;977;977	.|Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.|.;.;KI13A_HUMAN;.	D|P	370|977;977;977;977;977;37	.|ENSP00000368091:T977P;ENSP00000259711:T977P;ENSP00000368103:T977P;ENSP00000368120:T977P;ENSP00000368093:T977P	.|ENSP00000259711:T977P	E|T	-|-	3|1	2|0	KIF13A|KIF13A	17904892|17904892	1.000000|1.000000	0.71417|0.71417	0.959000|0.959000	0.39883|0.39883	0.984000|0.984000	0.73092|0.73092	5.938000|5.938000	0.70170|0.70170	2.019000|2.019000	0.59389|0.59389	0.460000|0.460000	0.39030|0.39030	GAA|ACA	.		0.507	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			G	17796913	T	G	17796913	3	3	8	1	0	0	0	0	1	0	0	0	8295	1725	60	5	2581	5	KIF13A	6	17796913	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		17796913	153318154	23	612											
DST	667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	56463337	56463337	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcctttttagactgttcTgcttttaaattaagctgttc	8	19	6	8	0	1	1	0	0	1	1	3	1	2	1	1	0	3	5	1	0	4	8			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr6:56463337T>C	ENST00000361203.3	-	42	11239	c.11232A>G	c.(11230-11232)gcA>gcG	p.A3744A	DST_ENST00000312431.6_Silent_p.A3744A|DST_ENST00000370788.2_Silent_p.A1658A|DST_ENST00000421834.2_Silent_p.A1658A|DST_ENST00000370769.4_Silent_p.A3746A|DST_ENST00000370754.5_Silent_p.A3924A|DST_ENST00000244364.6_Silent_p.A1332A|DST_ENST00000446842.2_Silent_p.A3420A			Q03001	DYST_HUMAN	dystonin	3744					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TAGACTGTTCTGCTTTTAAAT	0.353																																					p.A1332A		.											.	DST-523	0			c.A3996G						.						159	143	148					6																	56463337		1845	4078	5923	SO:0001819	synonymous_variant	667	exon27			CTGTTCTGCTTTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.11232A>G	6.37:g.56463337T>C		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	34	13	NM_015548	0	0	12	23	11	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				.		0.353	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56463337	T	C	56463337	2	2	8	1	0	0	0	0	0	0	0	1	4794	1567	55	3		3	DST	6	56463337	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	38666424	56463337	114651730	24	613											
BRP44L	51660	hgsc.bcm.edu	37	chr6	166778932	166778932	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattgttatgcagatgccgtTttagtcatcctggaaagaaa	12	13	9	7	1	1	2	1	0	0	2	2	3	2	3	2	1	2	3	2	1	4	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr6:166778932T>C	ENST00000360961.6	-	5	436	c.315A>G	c.(313-315)aaA>aaG	p.K105K	MPC1_ENST00000341756.6_Silent_p.K105K|MPC1_ENST00000487218.1_5'UTR	NM_001270879.1|NM_016098.3	NP_001257808.1|NP_057182.1	Q9Y5U8	MPC1_HUMAN	mitochondrial pyruvate carrier 1	105					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	pyruvate transmembrane transporter activity (GO:0050833)										CAGATGCCGTTTTAGTCATCC	0.393																																					p.K62K		.											.	.	0			c.A186G						.						94	80	85					6																	166778932		2202	4300	6502	SO:0001819	synonymous_variant	51660	exon5			TGCCGTTTTAGTC	AF125101	CCDS5293.1, CCDS75547.1	6q27	2012-08-01	2012-07-30	2012-07-30	ENSG00000060762	ENSG00000060762			21606	protein-coding gene	gene with protein product		614738	"brain protein 44-like"	BRP44L		22628558	Standard	NM_016098		Approved	dJ68L15.3, CGI-129	uc031sra.1	Q9Y5U8	OTTHUMG00000015999	ENST00000360961.6:c.315A>G	6.37:g.166778932T>C		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_001270879	0	0	1	1	0	B2R5I7|Q5TI66|Q9HB67|Q9UQN4	Silent	SNP	ENST00000360961.6	37	CCDS5293.1																																																																																			.		0.393	MPC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043052.1	NM_016098		C	166778932	T	C	166778932	2	2	8	1	0	0	0	0	0	0	0	1	1522	1838	64	3		3	BRP44L	6	166778932	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	110315595	166778932	4336135	25	614											
TYW1	55253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	66514966	66514966	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacagcaggaagagaagtctGgtttgttcaggaacatgggg	13	8	15	5	0	2	1	1	0	1	1	2	4	2	3	0	5	3	3	0	5	4	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:66514966G>T	ENST00000359626.5	+	8	1179	c.1015G>T	c.(1015-1017)Ggt>Tgt	p.G339C		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	339					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				AGAGAAGTCTGGTTTGTTCAG	0.383																																					p.G339C		.											.	TYW1-91	0			c.G1015T						.						45	47	47					7																	66514966		2203	4298	6501	SO:0001583	missense	55253	exon8			AAGTCTGGTTTGT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"	611243	"radical S-adenosyl methionine and flavodoxin domains 1"	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1015G>T	7.37:g.66514966G>T	ENSP00000352645:p.Gly339Cys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	92	18	NM_018264	0	0	42	55	13	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Missense_Mutation	SNP	ENST00000359626.5	37	CCDS5538.1	.	.	.	.	.	.	.	.	.	.	G	6.950	0.545036	0.13312	.	.	ENSG00000198874	ENST00000359626	T	0.17854	2.25	3.59	-7.17	0.01511	.	1.038170	0.07760	U	0.949947	T	0.14700	0.0355	L	0.39898	1.24	0.09310	N	1	P	0.39376	0.67	B	0.42112	0.376	T	0.31336	-0.9947	10	0.72032	D	0.01	.	9.461	0.38785	0.2223:0.1477:0.6299:0.0	.	339	Q9NV66	TYW1_HUMAN	C	339	ENSP00000352645:G339C	ENSP00000352645:G339C	G	+	1	0	TYW1	66152401	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.640000	0.00865	-1.521000	0.01771	-1.012000	0.02466	GGT	.		0.383	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		T	66514966	G	T	66514966	3	4	8	1	0	0	0	0	1	0	0	0	16851	1348	47	4	1045	4	TYW1	7	66514966	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08		66514966	92623697	26	615											
VPS37D	155382	broad.mit.edu	37	chr7	73083913	73083921	+	Splice_Site	DEL	GCGACTGGG	GCGACTGGG	-																															aactgcgcggacaagctgcaGcgactgggtgagggcacgtc																								rs199826922	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	GCGACTGGG	GCGACTGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:73083913_73083921delGCGACTGGG	ENST00000324941.4	+	2	437_444	c.303_310delGCGACTGGG	c.(301-312)cagcgactggga>caga	p.RLG102del	VPS37D_ENST00000451519.1_Intron	NM_001077621.1	NP_001071089.1			vacuolar protein sorting 37 homolog D (S. cerevisiae)											central_nervous_system(1)|ovary(1)	2		Lung NSC(55;0.0908)|all_lung(88;0.198)				ACAAGCTGCAGCGACTGGGTGAGGGCACG	0.675																																					p.101_104del													.	VPS37D-68	0			c.303_310del						.																																			SO:0001630	splice_region_variant	155382	exon2			GCTGCAGCGACTG	AY081952	CCDS43596.1	7q11.23	2007-07-27	2006-04-04	2005-08-18	ENSG00000176428	ENSG00000176428			18287	protein-coding gene	gene with protein product		610039	"Williams Beuren syndrome chromosome region 24", "vacuolar protein sorting 37D (yeast)"	WBSCR24		15218037	Standard	NM_001077621		Approved	MGC35352	uc003tyr.3	Q86XT2	OTTHUMG00000157227	ENST00000324941.4:c.310+1GCGACTGGG>-	7.37:g.73083913_73083921delGCGACTGGG		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_001077621	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000324941.4	37	CCDS43596.1																																																																																			.		0.675	VPS37D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348064.1	NM_152560	In_Frame_Del	-	73083921	GCGACTGGG	-	73083913	8	5	8	1	0	1	0	1	0	0	1	0	17241	962	34	0	309	0	VPS37D	7	73083913	Splice_Site	DEL	GCGACTGGG	TCGA-A4-7734-01A-11D-2136-08	6568947	73083913	86054750	27	616											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116423433	116423433	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgataaagaatactatagTgtacacaacaaaacaggtgc	19	9	7	6	0	0	2	0	1	0	1	0	2	0	2	0	1	5	1	0	1	11	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:116423433T>A	ENST00000318493.6	+	19	3949	c.3762T>A	c.(3760-3762)agT>agA	p.S1254R	MET_ENST00000539704.1_Missense_Mutation_p.S106R|MET_ENST00000397752.3_Missense_Mutation_p.S1236R			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AATACTATAGTGTACACAACA	0.383			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.S1254R		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.T3762A						.						99	95	96					7																	116423433		1861	4097	5958	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CTATAGTGTACAC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3762T>A	7.37:g.116423433T>A	ENSP00000317272:p.Ser1254Arg	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	105	62	NM_001127500	0	0	132	445	313	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.189759	0.38707	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.34072	1.38;1.38;1.38	5.46	-2.57	0.06248	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.30696	0.0773	N	0.03304	-0.355	0.54753	D	0.999982	P;D	0.89917	0.924;1.0	P;D	0.85130	0.574;0.997	T	0.26326	-1.0106	10	0.87932	D	0	.	11.8823	0.52581	0.0:0.4505:0.0:0.5495	.	1254;1236	P08581-2;P08581	.;MET_HUMAN	R	1236;1254;106	ENSP00000380860:S1236R;ENSP00000317272:S1254R;ENSP00000445020:S106R	ENSP00000317272:S1254R	S	+	3	2	MET	116210669	0.936000	0.31750	0.978000	0.43139	0.978000	0.69477	0.045000	0.14013	-0.366000	0.08064	0.460000	0.39030	AGT	.		0.383	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116423433	T	A	116423433	3	1	8	1	0	0	0	0	1	0	0	0	9510	1693	59	5	3832	5	MET	7	116423433	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	43339520	116423433	42715230	28	617											
SPAM1	6677	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr7	123599995	123599995	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattgttagtattttgtttcTtatcatttcttctgtagcga	7	22	6	6	1	4	0	1	0	3	0	4	1	4	0	0	0	1	4	0	0	4	10			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:123599995T>A	ENST00000439500.1	+	6	2115	c.1502T>A	c.(1501-1503)cTt>cAt	p.L501H	SPAM1_ENST00000223028.7_Missense_Mutation_p.L501H|SPAM1_ENST00000402183.2_Missense_Mutation_p.L501H|SPAM1_ENST00000460182.1_Missense_Mutation_p.L501H|SPAM1_ENST00000340011.5_Intron	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	501					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						ATTTTGTTTCTTATCATTTCT	0.353																																					p.L501H		.											.	SPAM1-94	0			c.T1502A						.						87	83	84					7																	123599995		2203	4300	6503	SO:0001583	missense	6677	exon5			TGTTTCTTATCAT	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1502T>A	7.37:g.123599995T>A	ENSP00000402123:p.Leu501His	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	97	54	NM_153189	0	0	0	0	0	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	37	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	T	9.524	1.109145	0.20714	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000439500;ENST00000223028	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	2.06	2.06	0.26882	.	.	.	.	.	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	P	0.49862	0.929	B	0.30316	0.114	T	0.22836	-1.0205	9	0.72032	D	0.01	.	6.1126	0.20110	0.0:0.0:0.0:1.0	.	501	P38567	HYALP_HUMAN	H	501	ENSP00000386028:L501H;ENSP00000417934:L501H;ENSP00000402123:L501H;ENSP00000223028:L501H	ENSP00000223028:L501H	L	+	2	0	SPAM1	123387231	0.016000	0.18221	0.004000	0.12327	0.009000	0.06853	2.479000	0.45197	1.210000	0.43336	0.528000	0.53228	CTT	.		0.353	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			A	123599995	T	A	123599995	3	1	8	1	0	0	0	0	1	0	0	0	15018	1609	56	5	1512	5	SPAM1	7	123599995	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	7176562	123599995	35538668	29	618											
SHH	6469	hgsc.bcm.edu	37	chr7	155595634	155595634	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccagcgggtgcagggccTcgctgtccaggagccaggtg	5	6	17	13	2	0	0	0	0	0	0	2	1	1	1	4	4	4	2	4	4	0	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:155595634T>C	ENST00000297261.2	-	3	1499	c.1349A>G	c.(1348-1350)gAg>gGg	p.E450G		NM_000193.2	NP_000184.1	Q15465	SHH_HUMAN	sonic hedgehog	450					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|artery development (GO:0060840)|axon guidance (GO:0007411)|Bergmann glial cell differentiation (GO:0060020)|blood coagulation (GO:0007596)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bud outgrowth involved in lung branching (GO:0060447)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway (GO:0060070)|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment (GO:0043369)|cell development (GO:0048468)|cell fate specification (GO:0001708)|cell-cell signaling (GO:0007267)|cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|cerebellar granule cell precursor proliferation (GO:0021930)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|dorsal/ventral neural tube patterning (GO:0021904)|dorsal/ventral pattern formation (GO:0009953)|ectoderm development (GO:0007398)|embryo development (GO:0009790)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal system development (GO:0048706)|endocytosis (GO:0006897)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|establishment of cell polarity (GO:0030010)|forebrain development (GO:0030900)|formation of anatomical boundary (GO:0048859)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|hindgut morphogenesis (GO:0007442)|inner ear development (GO:0048839)|intein-mediated protein splicing (GO:0016539)|intermediate filament organization (GO:0045109)|left lung development (GO:0060459)|limb bud formation (GO:0060174)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|lymphoid progenitor cell differentiation (GO:0002320)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal smoothened signaling pathway involved in prostate gland development (GO:0060783)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephros development (GO:0001656)|midbrain development (GO:0030901)|multicellular structure septum development (GO:0080125)|myoblast differentiation (GO:0045445)|myotube differentiation (GO:0014902)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of kidney smooth muscle cell differentiation (GO:2000357)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ureter smooth muscle cell differentiation (GO:2000062)|negative thymic T cell selection (GO:0045060)|neural crest cell migration (GO:0001755)|neuroblast proliferation (GO:0007405)|neuron fate commitment (GO:0048663)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|organ formation (GO:0048645)|osteoblast development (GO:0002076)|palate development (GO:0060021)|pancreas development (GO:0031016)|pattern specification process (GO:0007389)|patterning of blood vessels (GO:0001569)|polarity specification of anterior/posterior axis (GO:0009949)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of immature T cell proliferation in thymus (GO:0033092)|positive regulation of kidney smooth muscle cell differentiation (GO:2000358)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sclerotome development (GO:0061189)|positive regulation of skeletal muscle cell proliferation (GO:0014858)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureter smooth muscle cell differentiation (GO:2000063)|positive regulation of Wnt signaling pathway (GO:0030177)|positive thymic T cell selection (GO:0045059)|primary prostatic bud elongation (GO:0060516)|prostate epithelial cord elongation (GO:0060523)|prostate gland development (GO:0030850)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|regulation of mesenchymal cell proliferation involved in prostate gland development (GO:0060782)|regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900175)|regulation of odontogenesis (GO:0042481)|regulation of prostatic bud formation (GO:0060685)|regulation of protein localization to nucleus (GO:1900180)|regulation of proteolysis (GO:0030162)|renal system development (GO:0072001)|right lung development (GO:0060458)|salivary gland cavitation (GO:0060662)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|somite development (GO:0061053)|spinal cord dorsal/ventral patterning (GO:0021513)|spinal cord motor neuron differentiation (GO:0021522)|stem cell development (GO:0048864)|striated muscle tissue development (GO:0014706)|T cell differentiation in thymus (GO:0033077)|telencephalon regionalization (GO:0021978)|thalamus development (GO:0021794)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|trachea morphogenesis (GO:0060439)|vasculogenesis (GO:0001570)|ventral midline development (GO:0007418)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|laminin-1 binding (GO:0043237)|morphogen activity (GO:0016015)|patched binding (GO:0005113)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGCAGGGCCTCGCTGTCCAG	0.731																																					p.E450G		.											.	SHH-1134	0			c.A1349G						.						9	10	10					7																	155595634		1638	3497	5135	SO:0001583	missense	6469	exon3			AGGGCCTCGCTGT		CCDS5942.1	7q36	2010-06-25	2010-06-25		ENSG00000164690	ENSG00000164690			10848	protein-coding gene	gene with protein product		600725	"sonic hedgehog (Drosophila) homolog", "sonic hedgehog homolog (Drosophila)"	HPE3, HLP3		7590746	Standard	NM_000193		Approved	HHG1, SMMCI, TPT, TPTPS, MCOPCB5	uc003wmk.1	Q15465	OTTHUMG00000151349	ENST00000297261.2:c.1349A>G	7.37:g.155595634T>C	ENSP00000297261:p.Glu450Gly	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_000193	0	0	24	24	0	A4D247|Q75MC9	Missense_Mutation	SNP	ENST00000297261.2	37	CCDS5942.1	.	.	.	.	.	.	.	.	.	.	T	9.939	1.216860	0.22373	.	.	ENSG00000164690	ENST00000297261	D	0.99801	-6.81	3.89	2.71	0.32032	.	0.294987	0.32028	N	0.006695	D	0.98298	0.9436	L	0.32530	0.975	0.30779	N	0.742184	B;B	0.27498	0.039;0.18	B;B	0.19946	0.024;0.027	D	0.99969	1.1953	10	0.23302	T	0.38	.	9.1642	0.37041	0.0:0.0:0.1838:0.8162	.	450;453	Q15465;D9ZGF9	SHH_HUMAN;.	G	450	ENSP00000297261:E450G	ENSP00000297261:E450G	E	-	2	0	SHH	155288395	1.000000	0.71417	0.976000	0.42696	0.983000	0.72400	4.427000	0.59888	0.537000	0.28751	0.459000	0.35465	GAG	.		0.731	SHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322327.1	NM_000193		C	155595634	T	C	155595634	3	2	8	1	0	0	0	0	1	0	0	0	14311	1551	54	3	43	3	SHH	7	155595634	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	31995639	155595634	3543029	30	619											
PKHD1L1	93035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	110420393	110420393	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttcacactgaattgggatggGatcgcttctaagccactcac	10	11	9	11	1	3	1	2	1	1	0	4	3	3	3	1	2	1	1	1	2	2	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr8:110420393G>C	ENST00000378402.5	+	18	2033	c.1929G>C	c.(1927-1929)ggG>ggC	p.G643G		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	643					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATTGGGATGGGATCGCTTCTA	0.428										HNSCC(38;0.096)																											p.G643G		.											.	PKHD1L1-145	0			c.G1929C						.						121	121	121					8																	110420393		1946	4145	6091	SO:0001819	synonymous_variant	93035	exon18			GGATGGGATCGCT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.1929G>C	8.37:g.110420393G>C		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	58	12	NM_177531	0	0	0	0	0	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			.		0.428	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110420393	G	C	110420393	2	2	8	1	0	0	0	0	0	0	0	1	11998	1161	41	4		4	PKHD1L1	8	110420393	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08		110420393	35943629	31	620											
VPS28	51160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145651588	145651588	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagctccggcttgttcccaGgggctgcaagagaaggcaga	10	6	14	11	1	0	2	0	0	0	2	2	3	2	2	2	4	2	6	2	4	2	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr8:145651588G>T	ENST00000526054.1	-	2	78	c.41C>A	c.(40-42)cCt>cAt	p.P14H	VPS28_ENST00000526734.1_5'UTR|VPS28_ENST00000377348.2_Missense_Mutation_p.P14H|VPS28_ENST00000529182.1_Missense_Mutation_p.P14H|VPS28_ENST00000292510.4_Missense_Mutation_p.P14H			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)	14	VPS28 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00645}.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CTTGTTCCCAGGGGCTGCAAG	0.632																																					p.P14H		.											.	VPS28-90	0			c.C41A						.						20	19	20					8																	145651588		2194	4296	6490	SO:0001583	missense	51160	exon3			TTCCCAGGGGCTG	AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948			18178	protein-coding gene	gene with protein product		611952	"vacuolar protein sorting 28 (yeast)"				Standard	NM_183057		Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.41C>A	8.37:g.145651588G>T	ENSP00000434064:p.Pro14His	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	13	8	NM_016208	0	0	2	2	0	Q86VK0	Missense_Mutation	SNP	ENST00000526054.1	37	CCDS6425.1	.	.	.	.	.	.	.	.	.	.	g	19.57	3.851936	0.71719	.	.	ENSG00000160948	ENST00000529182;ENST00000526054;ENST00000292510;ENST00000377348;ENST00000533806;ENST00000531032;ENST00000530790	.	.	.	5.09	5.09	0.68999	Vacuolar protein sorting-associated, VPS28, N-terminal (1);	0.051939	0.85682	D	0.000000	T	0.52948	0.1766	N	0.08118	0	0.51482	D	0.999924	D;D	0.76494	0.999;0.986	D;P	0.66979	0.948;0.575	T	0.63120	-0.6708	9	0.62326	D	0.03	.	16.3554	0.83234	0.0:0.0:1.0:0.0	.	14;14	Q9UK41-2;Q9UK41	.;VPS28_HUMAN	H	14	.	ENSP00000292510:P14H	P	-	2	0	VPS28	145622396	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.858000	0.69532	2.515000	0.84797	0.650000	0.86243	CCT	.		0.632	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382694.1			T	145651588	G	T	145651588	3	4	8	1	0	0	0	0	1	0	0	0	17232	1000	35	4	770	4	VPS28	8	145651588	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	35231195	145651588	712434	32	621											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17394561	17394561	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggaaaatcggctgaaatcTtttgagaaaaggtcgagaaa	16	10	11	4	2	1	3	0	2	1	2	3	6	1	4	0	3	0	1	0	3	6	3	rs551838719		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:17394561T>C	ENST00000380647.3	+	15	2193	c.2109T>C	c.(2107-2109)tcT>tcC	p.S703S	CNTLN_ENST00000425824.1_Silent_p.S703S|CNTLN_ENST00000262360.5_Silent_p.S703S			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	703					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		GGCTGAAATCTTTTGAGAAAA	0.294													T|||	0	0	0	0	5008	,	,		16095	0		0	False		,,,				2504	0				p.S703S		.											.	CNTLN-91	0			c.T2109C						.						24	22	23					9																	17394561		1782	4045	5827	SO:0001819	synonymous_variant	54875	exon15			GAAATCTTTTGAG	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.2109T>C	9.37:g.17394561T>C		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_017738	0	0	8	8	0	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	37	CCDS43789.1																																																																																			.		0.294	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		C	17394561	T	C	17394561	2	2	8	1	0	0	0	0	0	0	0	1	3645	1596	56	3		3	CNTLN	9	17394561	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08		17394561	123818870	33	622											
KIAA1797	54914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	20990148	20990148	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacttcttcttgctgatattTgcaaccgcagtggttgcatg	7	15	10	9	1	2	1	0	1	2	0	2	2	2	1	1	1	4	5	1	1	2	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:20990148T>A	ENST00000380249.1	+	44	5395	c.5031T>A	c.(5029-5031)ttT>ttA	p.F1677L	FOCAD_ENST00000338382.6_Missense_Mutation_p.F1677L|FOCAD_ENST00000605086.1_Missense_Mutation_p.F1113L	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1677						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TGCTGATATTTGCAACCGCAG	0.488																																					p.F1677L		.											.	.	0			c.T5031A						.						89	79	82					9																	20990148		2203	4300	6503	SO:0001583	missense	54914	exon44			GATATTTGCAACC	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.5031T>A	9.37:g.20990148T>A	ENSP00000369599:p.Phe1677Leu	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	89	39	NM_017794	0	0	4	23	19	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.022456	0.54683	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	6.06	3.75	0.43078	.	0.052794	0.85682	D	0.000000	T	0.27489	0.0675	L	0.57536	1.79	0.54753	D	0.999988	P	0.42296	0.775	B	0.42738	0.396	T	0.01574	-1.1321	10	0.33141	T	0.24	-19.4576	10.2953	0.43620	0.0:0.1318:0.0:0.8682	.	1677	Q5VW36	K1797_HUMAN	L	1677	ENSP00000369599:F1677L;ENSP00000344307:F1677L	ENSP00000344307:F1677L	F	+	3	2	KIAA1797	20980148	1.000000	0.71417	0.998000	0.56505	0.834000	0.47266	1.862000	0.39448	0.543000	0.28864	0.533000	0.62120	TTT	.		0.488	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20990148	T	A	20990148	3	1	8	1	0	0	0	0	1	0	0	0	8279	1809	63	5	5193	5	KIAA1797	9	20990148	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	3595587	20990148	120223283	34	623											
SMC5	23137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	72913102	72913102	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aggcgaaataattgataagcGaagagagagggaaactctag	18	6	13	4	2	1	3	0	1	1	2	1	7	1	4	0	2	2	0	0	2	6	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:72913102G>C	ENST00000361138.5	+	9	1332	c.1274G>C	c.(1273-1275)cGa>cCa	p.R425P		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	425					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						ATTGATAAGCGAAGAGAGAGG	0.358																																					p.R425P		.											.	SMC5-229	0			c.G1274C						.						90	86	87					9																	72913102		2203	4300	6503	SO:0001583	missense	23137	exon9			ATAAGCGAAGAGA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.1274G>C	9.37:g.72913102G>C	ENSP00000354957:p.Arg425Pro	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	89	31	NM_015110	0	0	18	31	13	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524798	0.44969	.	.	ENSG00000198887	ENST00000361138	T	0.19669	2.13	5.72	-2.63	0.06133	RecF/RecN/SMC (1);	0.559219	0.18103	N	0.151640	T	0.17109	0.0411	L	0.46157	1.445	0.09310	N	1	P	0.48694	0.914	P	0.48840	0.592	T	0.11446	-1.0587	10	0.32370	T	0.25	-0.2642	2.2335	0.04002	0.3745:0.0877:0.3454:0.1924	.	425	Q8IY18	SMC5_HUMAN	P	425	ENSP00000354957:R425P	ENSP00000354957:R425P	R	+	2	0	SMC5	72102922	0.591000	0.26824	0.162000	0.22713	0.993000	0.82548	0.529000	0.23019	-0.132000	0.11557	0.591000	0.81541	CGA	.		0.358	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		C	72913102	G	C	72913102	3	2	8	1	0	0	0	0	1	0	0	0	14818	1058	37	4	1308	4	SMC5	9	72913102	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	51922954	72913102	68300329	35	624											
VPS13A	23230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	79981712	79981712	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaacaaaatggaggactgAttccagttcattctttaaat	16	12	6	7	0	2	1	1	1	1	0	3	3	3	3	1	2	1	1	1	2	6	5	rs566242673		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:79981712A>C	ENST00000360280.3	+	61	8655	c.8395A>C	c.(8395-8397)Att>Ctt	p.I2799L	VPS13A_ENST00000376636.3_Missense_Mutation_p.I2760L|VPS13A_ENST00000376634.4_Missense_Mutation_p.I2799L|VPS13A_ENST00000357409.5_Missense_Mutation_p.I2799L	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2799					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGGAGGACTGATTCCAGTTCA	0.313																																					p.I2799L		.											.	VPS13A-161	0			c.A8395C						.						66	69	68					9																	79981712		2203	4299	6502	SO:0001583	missense	23230	exon61			GGACTGATTCCAG	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.8395A>C	9.37:g.79981712A>C	ENSP00000353422:p.Ile2799Leu	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	42	20	NM_001018038	0	0	9	17	8	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.457324	0.43634	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.56	0.396	0.16309	.	0.303860	0.34178	N	0.004187	T	0.64757	0.2627	L	0.54323	1.7	0.80722	D	1	B;B;B;B	0.14438	0.001;0.002;0.01;0.004	B;B;B;B	0.15870	0.007;0.006;0.014;0.014	T	0.47005	-0.9150	9	.	.	.	.	3.193	0.06624	0.643:0.1183:0.1256:0.1131	.	2760;2799;2799;2799	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	L	2799;2760;2799;2799	ENSP00000365821:I2799L;ENSP00000365823:I2760L;ENSP00000353422:I2799L;ENSP00000349985:I2799L	.	I	+	1	0	VPS13A	79171532	1.000000	0.71417	0.083000	0.20561	0.958000	0.62258	3.532000	0.53553	-0.167000	0.10871	-0.376000	0.06991	ATT	.		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		C	79981712	A	C	79981712	3	2	8	1	0	0	0	0	1	0	0	0	17222	333	12	5	8637	5	VPS13A	9	79981712	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	7068610	79981712	61231719	36	625											
PDCL	5082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125582792	125582792	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actggagatctcaaaaacctGcttgaattggggccccttgt	10	11	10	10	0	1	2	1	1	1	1	2	3	1	2	3	3	2	1	3	3	3	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:125582792G>A	ENST00000259467.4	-	4	643	c.478C>T	c.(478-480)Cag>Tag	p.Q160*		NM_005388.4	NP_005379.3	Q13371	PHLP_HUMAN	phosducin-like	160					heterotrimeric G-protein complex assembly (GO:1902605)|intracellular signal transduction (GO:0035556)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10						TCAAAAACCTGCTTGAATTGG	0.443																																					p.Q160X		.											.	PDCL-90	0			c.C478T						.						104	102	102					9																	125582792		2203	4300	6503	SO:0001587	stop_gained	5082	exon4			AAACCTGCTTGAA	AF083325	CCDS6845.1	9q12-q13	2008-07-21			ENSG00000136940	ENSG00000136940			8770	protein-coding gene	gene with protein product		604421				10095058	Standard	NM_005388		Approved	PhLP, DKFZp564M1863	uc004bmz.2	Q13371	OTTHUMG00000020624	ENST00000259467.4:c.478C>T	9.37:g.125582792G>A	ENSP00000259467:p.Gln160*	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	162	56	NM_005388	0	0	20	29	9	Q4VXB6|Q96AF1|Q9UEW7|Q9UFL0|Q9UNX1|Q9UNX2	Nonsense_Mutation	SNP	ENST00000259467.4	37	CCDS6845.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440900	0.83993	.	.	ENSG00000136940	ENST00000259467	.	.	.	5.58	4.67	0.58626	.	0.160604	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.79	12.8162	0.57667	0.0:0.0:0.7031:0.2969	.	.	.	.	X	160	.	ENSP00000259467:Q160X	Q	-	1	0	PDCL	124622613	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.527000	0.45615	1.349000	0.45751	0.655000	0.94253	CAG	.		0.443	PDCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053956.1	NM_005388		A	125582792	G	A	125582792	4	1	8	1	0	0	0	0	0	1	0	0	11652	1328	46	2	431	2	PDCL	9	125582792	Nonsense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	45601080	125582792	15630639	37	626											
SLC2A8	29988	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130167105	130167105	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgcctgcaggtgtggtcAtggtgttcagcacgagtgcc	5	10	14	12	2	2	0	2	0	0	0	3	1	3	0	3	3	3	3	3	3	0	1			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:130167105A>G	ENST00000373371.3	+	8	1074	c.985A>G	c.(985-987)Atg>Gtg	p.M329V	SLC2A8_ENST00000485806.1_3'UTR|SLC2A8_ENST00000373360.3_Missense_Mutation_p.M329V|SLC2A8_ENST00000373352.1_Missense_Mutation_p.M66V	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	329					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						AGGTGTGGTCATGGTGTTCAG	0.697																																					p.M329V		.											.	SLC2A8-92	0			c.A985G						.						50	45	47					9																	130167105		2203	4297	6500	SO:0001583	missense	29988	exon8			GTGGTCATGGTGT	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"Solute carriers"	13812	protein-coding gene	gene with protein product		605245	"solute carrier family 2 (facilitated glucose transporter) member 8"			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.985A>G	9.37:g.130167105A>G	ENSP00000362469:p.Met329Val	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	64	14	NM_014580	0	0	0	1	1	Q8WUZ9|Q9NSC4	Missense_Mutation	SNP	ENST00000373371.3	37	CCDS6870.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.122981	0.56613	.	.	ENSG00000136856	ENST00000373371;ENST00000451404;ENST00000373352;ENST00000373360;ENST00000439597;ENST00000423934;ENST00000373350;ENST00000430147	T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.16	5.16	0.70880	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.071263	0.85682	D	0.000000	D	0.86585	0.5968	M	0.71036	2.16	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.80764	0.994;0.992	D	0.87560	0.2471	10	0.56958	D	0.05	.	14.2805	0.66208	1.0:0.0:0.0:0.0	.	329;329	Q5VVV9;Q9NY64	.;GTR8_HUMAN	V	329;166;66;329;168;194;194;168	ENSP00000362469:M329V;ENSP00000392434:M166V;ENSP00000362450:M66V;ENSP00000362458:M329V;ENSP00000404893:M168V;ENSP00000389070:M194V;ENSP00000391213:M168V	ENSP00000362448:M194V	M	+	1	0	SLC2A8	129206926	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	6.771000	0.74996	2.073000	0.62155	0.533000	0.62120	ATG	.		0.697	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580		G	130167105	A	G	130167105	3	3	8	1	0	0	0	0	1	0	0	0	14583	217	8	3	1015	3	SLC2A8	9	130167105	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	4584313	130167105	11046326	38	627											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	17127627	17127627	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtaggtgatatggaagccTtggtcactaatctgggagtc	11	11	13	6	0	2	1	1	1	1	0	3	3	2	3	1	4	1	1	1	4	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr10:17127627T>G	ENST00000377833.4	-	16	2144	c.2079A>C	c.(2077-2079)caA>caC	p.Q693H		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	693	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TATGGAAGCCTTGGTCACTAA	0.463																																					p.Q693H		.											.	CUBN-166	0			c.A2079C						.						117	123	121					10																	17127627		2203	4300	6503	SO:0001583	missense	8029	exon16			GAAGCCTTGGTCA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2079A>C	10.37:g.17127627T>G	ENSP00000367064:p.Gln693His	Somatic	227	1		WXS	Illumina HiSeq	Phase_I	180	69	NM_001081	0	0	2	2	0	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.021025	0.54576	.	.	ENSG00000107611	ENST00000377833	T	0.18502	2.21	5.73	-4.07	0.03975	CUB (5);	0.772213	0.10776	N	0.635427	T	0.15739	0.0379	L	0.45137	1.4	0.80722	D	1	P	0.48998	0.918	P	0.51355	0.667	T	0.50346	-0.8839	10	0.56958	D	0.05	.	0.6265	0.00787	0.2025:0.1691:0.2075:0.4209	.	693	O60494	CUBN_HUMAN	H	693	ENSP00000367064:Q693H	ENSP00000367064:Q693H	Q	-	3	2	CUBN	17167633	0.006000	0.16342	0.025000	0.17156	0.768000	0.43524	-0.278000	0.08490	-0.484000	0.06763	0.533000	0.62120	CAA	.		0.463	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17127627	T	G	17127627	3	3	8	1	0	0	0	0	1	0	0	0	4057	1606	56	5	9000	5	CUBN	10	17127627	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		17127627	118407120	39	628											
ARID5B	84159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	63852307	63852307	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattgcagggaaaaaggccCgggcagtgtctcccttagac	10	8	13	10	1	1	2	0	1	1	1	2	3	1	3	2	3	1	2	2	3	3	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr10:63852307C>A	ENST00000279873.7	+	10	3495	c.3085C>A	c.(3085-3087)Cgg>Agg	p.R1029R	ARID5B_ENST00000309334.5_Silent_p.R786R	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	1029					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)	p.R1029W(1)		NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					GAAAAAGGCCCGGGCAGTGTC	0.597																																					p.R1029R		.											.	ARID5B-94	1	Substitution - Missense(1)	large_intestine(1)	c.C3085A						.						62	70	67					10																	63852307		2203	4300	6503	SO:0001819	synonymous_variant	84159	exon10			AAGGCCCGGGCAG	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.3085C>A	10.37:g.63852307C>A		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	131	44	NM_032199	0	0	11	27	16	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	37	CCDS31208.1																																																																																			.		0.597	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		A	63852307	C	A	63852307	2	1	8	1	0	0	0	0	0	0	0	1	922	643	23	4		4	ARID5B	10	63852307	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	46724680	63852307	71682440	40	629											
PTPRJ	5795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	48181586	48181586	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccggaatggaccatcagagaTttcacagtgaaaaatgtaag	16	8	10	7	1	2	2	2	1	0	1	2	5	2	4	2	2	0	1	2	2	4	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr11:48181586T>A	ENST00000418331.2	+	22	3895	c.3543T>A	c.(3541-3543)gaT>gaA	p.D1181E		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	1181	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CCATCAGAGATTTCACAGTGA	0.393																																					p.D1181E		.											.	PTPRJ-541	0			c.T3543A						.						109	99	102					11																	48181586		2201	4298	6499	SO:0001583	missense	5795	exon22			CAGAGATTTCACA	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.3543T>A	11.37:g.48181586T>A	ENSP00000400010:p.Asp1181Glu	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	145	56	NM_002843	0	0	32	69	37	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277957	0.80692	.	.	ENSG00000149177	ENST00000418331	D	0.82526	-1.62	5.53	4.46	0.54185	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	.	.	.	.	T	0.59542	0.2201	N	0.02658	-0.545	0.80722	D	1	P	0.41131	0.739	B	0.44133	0.442	T	0.59537	-0.7436	9	0.07813	T	0.8	.	4.5662	0.12187	0.0:0.3223:0.0:0.6777	.	1181	Q12913	PTPRJ_HUMAN	E	1181	ENSP00000400010:D1181E	ENSP00000400010:D1181E	D	+	3	2	PTPRJ	48138162	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	0.202000	0.17295	1.076000	0.40961	0.529000	0.55759	GAT	.		0.393	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			A	48181586	T	A	48181586	3	1	8	1	0	0	0	0	1	0	0	0	12836	1490	52	5	3638	5	PTPRJ	11	48181586	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		48181586	86824930	41	630											
CAPN1	823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64974118	64974118	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgacttcgtgctgcgctTcttctcagagaagagtgctg	6	11	14	10	3	2	2	1	0	2	2	4	4	2	2	0	1	3	3	0	1	1	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr11:64974118T>G	ENST00000527323.1	+	12	1778	c.1538T>G	c.(1537-1539)tTc>tGc	p.F513C	CAPN1_ENST00000524773.1_Missense_Mutation_p.F513C|CAPN1_ENST00000279247.6_Missense_Mutation_p.F513C|CAPN1_ENST00000533820.1_Missense_Mutation_p.F513C|CAPN1_ENST00000533129.1_Missense_Mutation_p.F513C			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	513	Domain III.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		GTGCTGCGCTTCTTCTCAGAG	0.652																																					p.F513C		.											.	CAPN1-91	0			c.T1538G						.						30	34	33					11																	64974118		2089	4209	6298	SO:0001583	missense	823	exon13			TGCGCTTCTTCTC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"EF-hand domain containing"	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.1538T>G	11.37:g.64974118T>G	ENSP00000431984:p.Phe513Cys	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	53	12	NM_001198869	0	0	366	714	348	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.227125	0.79576	.	.	ENSG00000014216	ENST00000533820;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323	D;D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21;-2.21	5.06	5.06	0.68205	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.209169	0.43416	D	0.000576	D	0.88171	0.6365	L	0.33753	1.03	0.46774	D	0.999196	P	0.48350	0.909	P	0.59115	0.852	D	0.89382	0.3682	10	0.87932	D	0	.	12.7595	0.57356	0.0:0.0:0.0:1.0	.	513	P07384	CAN1_HUMAN	C	513;513;513;513;459;513	ENSP00000435272:F513C;ENSP00000431686:F513C;ENSP00000434176:F513C;ENSP00000279247:F513C;ENSP00000431984:F513C	ENSP00000259755:F459C	F	+	2	0	CAPN1	64730694	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	7.950000	0.87804	1.897000	0.54924	0.379000	0.24179	TTC	.		0.652	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1			G	64974118	T	G	64974118	3	3	8	1	0	0	0	0	1	0	0	0	2628	1783	62	5	1584	5	CAPN1	11	64974118	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	16792532	64974118	70032398	42	631											
RNF26	79102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119206410	119206410	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcctagcccacatttccaGcagtgctgtggccatggcca	7	10	9	15	0	0	0	0	0	0	0	2	0	2	0	5	2	3	2	5	2	1	3	rs200033048		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr11:119206410G>A	ENST00000311413.4	+	1	1174	c.578G>A	c.(577-579)aGc>aAc	p.S193N	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	193						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		CACATTTCCAGCAGTGCTGTG	0.622																																					p.S193N		.											.	RNF26-227	0			c.G578A						.	G	ASN/SER	0,4398		0,0,2199	115	95	102		578	5.1	1	11		102	1,8589	1.2+/-3.3	0,1,4294	no	missense	RNF26	NM_032015.3	46	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	193/434	119206410	1,12987	2199	4295	6494	SO:0001583	missense	79102	exon1			TTTCCAGCAGTGC	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"RING-type (C3HC4) zinc fingers"	14646	protein-coding gene	gene with protein product	"ring finger protein with leucine zipper"	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.578G>A	11.37:g.119206410G>A	ENSP00000312439:p.Ser193Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	69	28	NM_032015	0	0	20	36	16	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	37	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192453	0.58017	0.0	1.16E-4	ENSG00000173456	ENST00000311413	T	0.79653	-1.29	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.73613	0.3609	L	0.32530	0.975	0.47659	D	0.999484	D	0.53312	0.959	P	0.46940	0.532	T	0.71024	-0.4712	10	0.26408	T	0.33	-16.3913	11.0828	0.48070	0.0844:0.0:0.9156:0.0	.	193	Q9BY78	RNF26_HUMAN	N	193	ENSP00000312439:S193N	ENSP00000312439:S193N	S	+	2	0	RNF26	118711620	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.210000	0.65214	2.393000	0.81446	0.561000	0.74099	AGC	G|0.999;A|0.001		0.622	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		A	119206410	G	A	119206410	3	1	8	1	0	0	0	0	1	0	0	0	13518	971	34	2	580	2	RNF26	11	119206410	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	54232292	119206410	15800106	43	632											
H2AFJ	55766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	14927594	14927594	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtaccttacggcggagatcCtggagctggctggcaacgcc	8	7	14	12	3	0	1	0	0	0	1	1	3	1	2	3	5	4	4	3	5	3	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:14927594C>G	ENST00000544848.1	+	1	325	c.190C>G	c.(190-192)Ctg>Gtg	p.L64V		NM_177925.2	NP_808760.1	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	64						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|kidney(1)|ovary(1)|skin(1)	5						GGCGGAGATCCTGGAGCTGGC	0.632																																					p.L64V		.											.	H2AFJ-69	0			c.C190G						.						49	56	54					12																	14927594		2203	4300	6503	SO:0001583	missense	55766	exon1			GAGATCCTGGAGC	AK001765	CCDS31752.1	12p12.3	2012-09-11			ENSG00000246705	ENSG00000246705		"Histones / Replication-independent"	14456	protein-coding gene	gene with protein product							Standard	NM_177925		Approved	FLJ10903, MGC921	uc009zia.3	Q9BTM1	OTTHUMG00000168736	ENST00000544848.1:c.190C>G	12.37:g.14927594C>G	ENSP00000438553:p.Leu64Val	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	105	36	NM_177925	0	0	97	173	76	Q9NV63	Missense_Mutation	SNP	ENST00000544848.1	37	CCDS31752.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.387309	0.42308	.	.	ENSG00000246705	ENST00000544848;ENST00000228929	T;T	0.72282	-0.64;-0.64	4.67	3.78	0.43462	Histone-fold (2);Histone core (1);Histone H2A (2);	.	.	.	.	T	0.81489	0.4833	H	0.97158	3.95	0.45139	D	0.998151	B	0.22800	0.075	B	0.30251	0.113	D	0.84014	0.0350	9	0.87932	D	0	.	13.3675	0.60694	0.0:0.8405:0.1594:0.0	.	64	Q9BTM1	H2AJ_HUMAN	V	64	ENSP00000438553:L64V;ENSP00000228929:L64V	ENSP00000228929:L64V	L	+	1	2	H2AFJ	14818861	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.833000	0.55790	1.571000	0.49722	-0.156000	0.13503	CTG	.		0.632	H2AFJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400845.1	NM_177925		G	14927594	C	G	14927594	3	3	8	1	0	0	0	0	1	0	0	0	6947	680	24	4	192	4	H2AFJ	12	14927594	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08		14927594	118924301	44	633											
MRPS35	60488	hgsc.bcm.edu	37	chr12	27877051	27877051	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcattttccaattgaaattGacagcactgattatgtttca	13	15	6	7	0	1	3	1	3	0	0	2	3	2	3	1	0	2	3	1	0	3	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:27877051G>C	ENST00000081029.3	+	5	525	c.454G>C	c.(454-456)Gac>Cac	p.D152H	MRPS35_ENST00000538315.1_Missense_Mutation_p.D152H	NM_021821.3	NP_068593.2	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S35	0						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	6	Lung SC(9;0.0873)					AATTGAAATTGACAGCACTGA	0.363																																					p.D152H		.											.	MRPS35-90	0			c.G454C						.						83	77	79					12																	27877051		2203	4300	6503	SO:0001583	missense	60488	exon5			GAAATTGACAGCA	AF182422	CCDS8714.1, CCDS53769.1	12p11	2012-09-13			ENSG00000061794	ENSG00000061794		"Mitochondrial ribosomal proteins / small subunits"	16635	protein-coding gene	gene with protein product		611995				11279123	Standard	NM_021821		Approved	MRPS28, MDS023	uc001rih.3	P82673	OTTHUMG00000169215	ENST00000081029.3:c.454G>C	12.37:g.27877051G>C	ENSP00000081029:p.Asp152His	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_001190864	0	0	70	70	0	B2RDZ7|Q96Q21	Missense_Mutation	SNP	ENST00000081029.3	37	CCDS8714.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.246246	0.39697	.	.	ENSG00000061794	ENST00000081029;ENST00000321446;ENST00000538315	T;T	0.44881	0.94;0.91	5.73	4.83	0.62350	Ribosomal protein S24/S35, mitochondrial, conserved domain (1);	0.315846	0.38272	N	0.001760	T	0.38612	0.1047	N	0.25647	0.755	0.35298	D	0.78274	P;P	0.50710	0.938;0.915	P;P	0.51355	0.537;0.667	T	0.51576	-0.8688	10	0.46703	T	0.11	-28.0696	9.2958	0.37815	0.076:0.1453:0.7788:0.0	.	152;152	P82673-2;P82673	.;RT35_HUMAN	H	152	ENSP00000081029:D152H;ENSP00000445390:D152H	ENSP00000081029:D152H	D	+	1	0	MRPS35	27768318	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	3.238000	0.51352	1.411000	0.46957	0.655000	0.94253	GAC	.		0.363	MRPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402897.1	NM_021821		C	27877051	G	C	27877051	3	2	8	1	0	0	0	0	1	0	0	0	9869	1290	45	4	472	4	MRPS35	12	27877051	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	12949457	27877051	105974844	45	634											
CPM	1368	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	69326479	69326479	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcacagatttcccaatacTgtgtaagtgagtgacagaac	13	12	8	8	0	1	4	1	2	0	2	2	4	2	4	1	0	2	1	1	0	4	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:69326479T>A	ENST00000551568.1	-	2	199	c.139A>T	c.(139-141)Agt>Tgt	p.S47C	CPM_ENST00000546373.1_Missense_Mutation_p.S47C|CPM_ENST00000338356.3_Missense_Mutation_p.S47C	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	47					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TTCCCAATACTGTGTAAGTGA	0.473																																					p.S47C		.											.	CPM-650	0			c.A139T						.						117	109	112					12																	69326479		2203	4300	6503	SO:0001583	missense	1368	exon2			CAATACTGTGTAA	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"renal carboxypeptidase", "urinary carboxypeptidase B"	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.139A>T	12.37:g.69326479T>A	ENSP00000448517:p.Ser47Cys	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	104	53	NM_001005502	0	0	45	85	40	B2R800|Q9H2K9	Missense_Mutation	SNP	ENST00000551568.1	37	CCDS8987.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.981836	0.53827	.	.	ENSG00000135678	ENST00000551568;ENST00000338356;ENST00000546373;ENST00000548954;ENST00000548262;ENST00000549781	T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;3.2	4.24	4.24	0.50183	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	H	0.94183	3.505	0.58432	D	0.999997	B	0.28324	0.207	B	0.34418	0.182	T	0.18650	-1.0330	9	.	.	.	-17.8592	11.2744	0.49157	0.0:0.0:0.0:1.0	.	47	P14384	CBPM_HUMAN	C	47	ENSP00000448517:S47C;ENSP00000339157:S47C;ENSP00000447255:S47C;ENSP00000446799:S47C;ENSP00000449911:S47C;ENSP00000448078:S47C	.	S	-	1	0	CPM	67612746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.980000	0.49321	1.899000	0.54978	0.460000	0.39030	AGT	.		0.473	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320		A	69326479	T	A	69326479	3	1	8	1	0	0	0	0	1	0	0	0	3814	1580	55	5	1224	5	CPM	12	69326479	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	41449428	69326479	64525416	46	635											
DUSP6	1848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	89744677	89744677	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactcgatgtccgaggaagAgtcagagctgatccgcaggc	11	6	14	10	3	1	4	1	1	0	3	4	7	3	5	2	2	1	2	2	2	1	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:89744677A>G	ENST00000279488.7	-	2	1757	c.526T>C	c.(526-528)Tct>Cct	p.S176P	DUSP6_ENST00000308385.6_Intron|DUSP6_ENST00000547291.1_Missense_Mutation_p.S51P|DUSP6_ENST00000547140.1_5'UTR	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	176					cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						TCCGAGGAAGAGTCAGAGCTG	0.607																																					p.S176P	Colon(132;3456 5224)	.											.	DUSP6-846	0			c.T526C						.						53	48	50					12																	89744677		2203	4300	6503	SO:0001583	missense	1848	exon2			AGGAAGAGTCAGA	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.526T>C	12.37:g.89744677A>G	ENSP00000279488:p.Ser176Pro	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	63	28	NM_001946	0	0	98	156	58	O75109|Q53Y75|Q9BSH6	Missense_Mutation	SNP	ENST00000279488.7	37	CCDS9033.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.455071	0.63290	.	.	ENSG00000139318	ENST00000279488;ENST00000547291	T;T	0.03035	4.28;4.07	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.05090	0.0136	L	0.44542	1.39	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43940	-0.9360	10	0.22706	T	0.39	.	16.0353	0.80625	1.0:0.0:0.0:0.0	.	176	Q16828	DUS6_HUMAN	P	176;51	ENSP00000279488:S176P;ENSP00000449838:S51P	ENSP00000279488:S176P	S	-	1	0	DUSP6	88268808	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.624000	0.61254	2.178000	0.69098	0.533000	0.62120	TCT	.		0.607	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		G	89744677	A	G	89744677	3	3	8	1	0	0	0	0	1	0	0	0	4840	304	11	3	627	3	DUSP6	12	89744677	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	20418198	89744677	44107218	47	636											
PRPF39	55015	hgsc.bcm.edu	37	chr14	45579918	45579918	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatgccaaatcaaataatgaAtcttcattttatgctgtcaa	16	14	4	7	0	4	1	3	1	1	0	4	1	4	1	1	0	2	1	1	0	7	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr14:45579918A>G	ENST00000355765.6	+	10	1640	c.1470A>G	c.(1468-1470)gaA>gaG	p.E490E	SNORD127_ENST00000458892.1_RNA	NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	490					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						CAAATAATGAATCTTCATTTT	0.373																																					p.E490E		.											.	PRPF39-70	0			c.A1470G						.						31	27	29					14																	45579918		2200	4294	6494	SO:0001819	synonymous_variant	55015	exon10			TAATGAATCTTCA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.1470A>G	14.37:g.45579918A>G		Somatic	10	1		WXS	Illumina HiSeq	Phase_I	11	6	NM_017922	0	0	14	31	17	Q08AL1|Q08AL2|Q9NUU5	Silent	SNP	ENST00000355765.6	37	CCDS9682.2																																																																																			.		0.373	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			G	45579918	A	G	45579918	2	3	8	1	0	0	0	0	0	0	0	1	12598	98	4	3		3	PRPF39	14	45579918	Silent	SNP	A	TCGA-A4-7734-01A-11D-2136-08		45579918	61769622	48	637											
ABCD4	5826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	74756774	74756774	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagaatggcttttgtggcaGgaatagcaccccatggggcc	10	8	14	9	0	0	1	0	0	0	1	0	3	0	2	3	5	1	3	3	5	4	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr14:74756774G>T	ENST00000356924.4	-	13	1518	c.1375C>A	c.(1375-1377)Ctg>Atg	p.L459M	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_5'Flank|ABCD4_ENST00000298816.7_Missense_Mutation_p.L355M	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	459	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		TTTTGTGGCAGGAATAGCACC	0.592											OREG0022800	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L459M		.											.	ABCD4-292	0			c.C1375A						.						80	82	82					14																	74756774		2203	4300	6503	SO:0001583	missense	5826	exon13			GTGGCAGGAATAG	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"ATP binding cassette transporters / subfamily D"	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1375C>A	14.37:g.74756774G>T	ENSP00000349396:p.Leu459Met	Somatic	147	0	1155	WXS	Illumina HiSeq	Phase_I	105	36	NM_005050	0	0	13	28	15	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843870	0.71488	.	.	ENSG00000119688	ENST00000356924;ENST00000298816	D;D	0.95035	-2.78;-3.59	5.76	4.87	0.63330	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.64402	D	0.000001	D	0.96367	0.8815	M	0.66560	2.04	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	D	0.96434	0.9321	10	0.72032	D	0.01	.	11.9671	0.53042	0.1395:0.0:0.8605:0.0	.	355;459;459	F8W7M4;A8K5L7;O14678	.;.;ABCD4_HUMAN	M	459;355	ENSP00000349396:L459M;ENSP00000298816:L355M	ENSP00000298816:L355M	L	-	1	2	ABCD4	73826527	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.539000	0.60657	1.443000	0.47586	0.462000	0.41574	CTG	.		0.592	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050		T	74756774	G	T	74756774	3	4	8	1	0	0	0	0	1	0	0	0	63	991	35	4	473	4	ABCD4	14	74756774	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	29176856	74756774	32592766	49	638											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27271931	27271931	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtaattgacgttgacatttAtgttaacagcattggtcctg	10	15	9	7	2	0	2	0	2	0	0	1	2	1	2	1	1	2	4	1	1	3	7			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:27271931A>G	ENST00000333743.6	+	3	487	c.233A>G	c.(232-234)tAt>tGt	p.Y78C	GABRG3_ENST00000555083.1_Missense_Mutation_p.Y78C	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	78					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)	GTTGACATTTATGTTAACAGC	0.393																																					p.Y78C	NSCLC(114;800 1656 7410 37729 45293)	.											.	.	0			c.A233G						.						118	111	113					15																	27271931		1947	4162	6109	SO:0001583	missense	2567	exon3			ACATTTATGTTAA		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.233A>G	15.37:g.27271931A>G	ENSP00000331912:p.Tyr78Cys	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001270873	0	0	2	2	0	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.665142	0.67700	.	.	ENSG00000182256	ENST00000333743;ENST00000555083	T;T	0.78924	-1.22;-1.22	5.96	5.96	0.96718	Neurotransmitter-gated ion-channel ligand-binding (3);	0.261625	0.32533	N	0.005964	D	0.88897	0.6562	M	0.88105	2.93	0.45330	D	0.998323	D;D	0.71674	0.996;0.998	D;D	0.68621	0.95;0.959	D	0.90706	0.4624	10	0.87932	D	0	.	12.8256	0.57718	1.0:0.0:0.0:0.0	.	78;78	Q99928;G3V594	GBRG3_HUMAN;.	C	78	ENSP00000331912:Y78C;ENSP00000452244:Y78C	ENSP00000331912:Y78C	Y	+	2	0	GABRG3	24854677	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	4.829000	0.62737	2.270000	0.75569	0.533000	0.62120	TAT	.		0.393	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			G	27271931	A	G	27271931	3	3	8	1	0	0	0	0	1	0	0	0	6192	449	16	3	243	3	GABRG3	15	27271931	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08		27271931	75259461	50	639											
FSIP1	161835	hgsc.bcm.edu	37	chr15	40034075	40034075	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtatgaaacactgaggaaaAggtgtcttcctcctcatgag	13	10	10	8	0	2	3	1	3	1	0	4	4	4	4	2	2	1	1	2	2	4	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:40034075A>G	ENST00000350221.3	-	6	795	c.586T>C	c.(586-588)Ttt>Ctt	p.F196L	FSIP1_ENST00000559692.1_5'UTR	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	196										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		ACTGAGGAAAAGGTGTCTTCC	0.308																																					p.F196L		.											.	FSIP1-517	0			c.T586C						.						80	79	80					15																	40034075		2203	4298	6501	SO:0001583	missense	161835	exon6			AGGAAAAGGTGTC	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.586T>C	15.37:g.40034075A>G	ENSP00000280236:p.Phe196Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_152597	0	0	2	2	0	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.903946	0.33628	.	.	ENSG00000150667	ENST00000350221	T	0.24908	1.83	5.44	0.0699	0.14376	.	0.379516	0.22348	N	0.061248	T	0.14313	0.0346	L	0.31664	0.95	0.09310	N	1	B	0.13594	0.008	B	0.13407	0.009	T	0.22977	-1.0201	9	.	.	.	-2.6282	6.4892	0.22105	0.414:0.494:0.0919:0.0	.	196	Q8NA03	FSIP1_HUMAN	L	196	ENSP00000280236:F196L	.	F	-	1	0	FSIP1	37821367	0.499000	0.26083	0.008000	0.14137	0.003000	0.03518	1.386000	0.34419	0.037000	0.15575	-0.313000	0.08912	TTT	.		0.308	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		G	40034075	A	G	40034075	3	3	8	1	0	0	0	0	1	0	0	0	6093	72	3	3	1187	3	FSIP1	15	40034075	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	12762144	40034075	62497317	51	640											
NEDD4	4734	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	56208931	56208934	+	Frame_Shift_Del	DEL	CATG	CATG	-																															cgtgttggtcttttgaagcaCatgtgaacatggctatccaa																								rs1912403	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	CATG	CATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:56208931_56208934delCATG	ENST00000508342.1	-	1	395_398	c.96_99delCATG	c.(94-99)cacatgfs	p.HM32fs	NEDD4_ENST00000338963.2_Frame_Shift_Del_p.HM32fs|NEDD4_ENST00000506154.1_Frame_Shift_Del_p.HM32fs|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	32					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TTTTGAAGCACATGTGAACATGGC	0.436																																					p.32_33del		.											.	NEDD4-723	0			c.96_99del						.																																			SO:0001589	frameshift_variant	4734	exon1			.	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.96_99delCATG	15.37:g.56208931_56208934delCATG	ENSP00000424827:p.His32fs	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	214	67	NM_198400	0	0	0	0	0	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Frame_Shift_Del	DEL	ENST00000508342.1	37																																																																																				.		0.436	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		-	56208934	CATG	-	56208931	7	5	8	1	0	1	0	1	0	0	0	0	10336	478	17	0	3960	0	NEDD4	15	56208931	Frame_Shift_Del	DEL	CATG	TCGA-A4-7734-01A-11D-2136-08	16174856	56208931	46322461	52	641											
PPIB	5479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64454355	64454355	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgtaggtcaaaatacaccTgaggaaagagaccatttcca	15	9	8	9	1	1	2	1	1	0	1	3	4	2	3	3	2	1	1	3	2	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:64454355T>C	ENST00000300026.3	-	2	354		c.e2-2		PPIB_ENST00000558492.1_Intron	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)						bone development (GO:0060348)|chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|positive regulation of multicellular organism growth (GO:0040018)|protein peptidyl-prolyl isomerization (GO:0000413)|protein stabilization (GO:0050821)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(6)	10					L-Proline(DB00172)	AAAATACACCTGAGGAAAGAG	0.463																																					.	GBM(105;399 1481 32889 33051 36637)	.											.	PPIB-90	0			c.136-2A>G						.						132	141	138					15																	64454355		2203	4300	6503	SO:0001630	splice_region_variant	5479	exon3			TACACCTGAGGAA		CCDS10191.1	15q21-q22	2014-09-17			ENSG00000166794	ENSG00000166794	5.2.1.8		9255	protein-coding gene	gene with protein product		123841				2000394, 20089953	Standard	NM_000942		Approved	CYPB, OI9	uc002and.3	P23284	OTTHUMG00000133018	ENST00000300026.3:c.136-2A>G	15.37:g.64454355T>C		Somatic	220	0		WXS	Illumina HiSeq	Phase_I	187	80	NM_000942	0	0	0	2	2	A8K534|Q6IBH5|Q9BVK5	Splice_Site	SNP	ENST00000300026.3	37	CCDS10191.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.086591	0.76642	.	.	ENSG00000166794	ENST00000300026	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3959	0.74794	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PPIB	62241408	1.000000	0.71417	0.976000	0.42696	0.823000	0.46562	7.490000	0.81461	2.121000	0.65114	0.374000	0.22700	.	.		0.463	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256604.1		Intron	C	64454355	T	C	64454355	5	2	8	1	0	0	0	0	0	0	1	0	12348	1594	55	3	532	3	PPIB	15	64454355	Splice_Site	SNP	T	TCGA-A4-7734-01A-11D-2136-08	8245424	64454355	38077037	53	642											
ULK3	25989	hgsc.bcm.edu	37	chr15	75132966	75132966	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatcccacggggacatgtgTtgtgcgaaaccaaagtctgc	10	9	11	11	2	2	0	1	0	1	0	3	2	3	1	2	2	3	1	2	2	2	1			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:75132966T>C	ENST00000440863.2	-	5	577	c.486A>G	c.(484-486)caA>caG	p.Q162Q	ULK3_ENST00000569437.1_Silent_p.Q162Q|ULK3_ENST00000568667.1_Silent_p.Q173Q	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	162	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						GGGACATGTGTTGTGCGAAAC	0.612																																					p.Q162Q		.											.	ULK3-290	0			c.A486G						.						29	32	31					15																	75132966		2095	4222	6317	SO:0001819	synonymous_variant	25989	exon5			CATGTGTTGTGCG	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"unc-51-like kinase 3 (C. elegans)"				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.486A>G	15.37:g.75132966T>C		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	37	3	NM_001099436	0	0	30	30	0	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Silent	SNP	ENST00000440863.2	37	CCDS45305.1																																																																																			.		0.612	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518		C	75132966	T	C	75132966	2	2	8	1	0	0	0	0	0	0	0	1	17010	1722	60	3		3	ULK3	15	75132966	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	10678611	75132966	27398426	54	643											
CORO1A	11151	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	30198546	30198547	+	Splice_Site	INS	-	-	GA																															aaaggcactgtcgtagctgtINSgagtcgccatctaccctgac																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:30198546_30198547insGA	ENST00000219150.5	+	5	941		c.e5+2		RP11-455F5.5_ENST00000566144.1_RNA|CORO1A_ENST00000565497.1_Splice_Site|RP11-455F5.5_ENST00000568506.1_RNA|CORO1A_ENST00000570045.1_Splice_Site|RP11-455F5.5_ENST00000567153.1_RNA	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A						actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						GTCGTAGCTGTGAGTCGCCATC	0.589																																					.		.											.	CORO1A-226	0			c.636+2->GA						.																																			SO:0001630	splice_region_variant	11151	exon5			.	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"Coronins", "WD repeat domain containing"	2252	protein-coding gene	gene with protein product	"Clabp TACO"	605000	"coronin, actin-binding protein, 1A"			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.636+2->GA	16.37:g.30198547_30198548dupGA		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	74	21	NM_007074	0	0	0	0	0	B2RBL1|Q2YD73	Splice_Site	INS	ENST00000219150.5	37	CCDS10673.1																																																																																			.		0.589	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074	Intron	GA	30198547	-	GA	30198546	8	5	8	1	0	1	1	0	0	0	1	0	3759	1710	59	0	652	0	CORO1A	16	30198546	Splice_Site	INS	-	TCGA-A4-7734-01A-11D-2136-08		30198546	60156207	55	644											
GPR97	222487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57719830	57719830	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catctttgcacttttcaactCcttgcaaggtgaggcccctg	7	13	8	13	0	2	1	1	1	1	0	3	1	3	1	3	2	3	2	3	2	2	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:57719830C>T	ENST00000333493.4	+	11	1693	c.1532C>T	c.(1531-1533)tCc>tTc	p.S511F	RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000450388.3_Missense_Mutation_p.S391F|GPR97_ENST00000327655.6_Missense_Mutation_p.S301F	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	511					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CTTTTCAACTCCTTGCAAGGT	0.597																																					p.S511F		.											.	GPR97-91	0			c.C1532T						.						88	82	84					16																	57719830		2198	4300	6498	SO:0001583	missense	222487	exon11			TCAACTCCTTGCA	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"-", "GPCR / Class B : Orphans"	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1532C>T	16.37:g.57719830C>T	ENSP00000332900:p.Ser511Phe	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	120	52	NM_170776	0	0	0	0	0	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	37	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752027	0.69533	.	.	ENSG00000182885	ENST00000333493;ENST00000327655;ENST00000450388	T;T;T	0.56611	0.45;0.45;0.45	5.62	5.62	0.85841	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000025	T	0.80737	0.4680	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85478	0.1177	10	0.87932	D	0	.	18.6332	0.91368	0.0:1.0:0.0:0.0	.	511	Q86Y34	GPR97_HUMAN	F	511;301;391	ENSP00000332900:S511F;ENSP00000331199:S301F;ENSP00000404803:S391F	ENSP00000331199:S301F	S	+	2	0	GPR97	56277331	1.000000	0.71417	0.998000	0.56505	0.375000	0.29983	4.512000	0.60469	2.647000	0.89833	0.655000	0.94253	TCC	.		0.597	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		T	57719830	C	T	57719830	3	4	8	1	0	0	0	0	1	0	0	0	6741	855	30	2	1574	2	GPR97	16	57719830	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	27521284	57719830	32634923	56	645											
KIFC3	3801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57806198	57806198	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcttctccttcaggtgttcTacctgtgggcacagagtcag	7	12	11	11	0	4	1	2	0	2	1	5	1	4	1	2	2	2	3	2	2	1	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:57806198T>C	ENST00000379655.4	-	4	575	c.318A>G	c.(316-318)gtA>gtG	p.V106V	KIFC3_ENST00000540079.2_Silent_p.V4V|KIFC3_ENST00000421376.2_5'UTR|KIFC3_ENST00000445690.2_Silent_p.V106V|KIFC3_ENST00000566975.1_5'UTR|KIFC3_ENST00000543930.1_5'UTR|KIFC3_ENST00000562903.1_5'UTR|KIFC3_ENST00000465878.2_5'UTR|KIFC3_ENST00000539578.1_Silent_p.V48V|KIFC3_ENST00000541240.1_Silent_p.V128V	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	106					ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				TCAGGTGTTCTACCTGTGGGC	0.617																																					p.V106V		.											.	KIFC3-91	0			c.A318G						.						117	92	101					16																	57806198		2198	4300	6498	SO:0001819	synonymous_variant	3801	exon4			GTGTTCTACCTGT	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"Kinesins"	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.318A>G	16.37:g.57806198T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	79	31	NM_001130100	0	0	0	1	1	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Silent	SNP	ENST00000379655.4	37	CCDS10789.2																																																																																			.		0.617	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		C	57806198	T	C	57806198	2	2	8	1	0	0	0	0	0	0	0	1	8335	1509	53	3		3	KIFC3	16	57806198	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	86368	57806198	32548555	57	646											
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85706125	85706125	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcactggcctaggggctacCtgaagggatatcccaggtga	9	8	14	10	0	0	2	0	2	0	0	1	3	1	3	3	5	2	2	3	5	4	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:85706125C>T	ENST00000253458.7	+	16	3810	c.3634C>T	c.(3634-3636)Ctg>Ttg	p.L1212L	GSE1_ENST00000393243.1_Silent_p.L1139L|GSE1_ENST00000471070.1_3'UTR|GSE1_ENST00000405402.2_Silent_p.L1108L	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1212																	TAGGGGCTACCTGAAGGGATA	0.453																																					p.L1212L		.											.	.	0			c.C3634T						.						59	48	51					16																	85706125		2198	4300	6498	SO:0001819	synonymous_variant	23199	exon16			GGCTACCTGAAGG	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3634C>T	16.37:g.85706125C>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_014615	1	0	45	46	0	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1																																																																																			.		0.453	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		T	85706125	C	T	85706125	2	4	8	1	0	0	0	0	0	0	0	1	8180	680	24	2		2	KIAA0182	16	85706125	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	27899927	85706125	4648628	58	647											
MYO1C	4641	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	1370772	1370772	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggggccgcccgcgcctcAcctgccctggttgatgttga	3	8	14	16	4	1	2	1	2	0	0	1	2	1	2	6	3	1	2	6	3	0	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:1370772A>C	ENST00000575158.1	-	30	3137		c.e30+1		MYO1C_ENST00000438665.2_Splice_Site|MYO1C_ENST00000361007.2_Splice_Site|MYO1C_ENST00000359786.5_Splice_Site|MYO1C_ENST00000545534.2_Splice_Site			Q12965	MYO1E_HUMAN	myosin IC						actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCCGCGCCTCACCTGCCCTGG	0.677																																					.		.											.	MYO1C-90	0			c.2960+2T>G						.						64	58	60					17																	1370772		2203	4299	6502	SO:0001630	splice_region_variant	4641	exon31			CGCCTCACCTGCC	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"Myosins / Myosin superfamily : Class I"	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.2960+1T>G	17.37:g.1370772A>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	82	36	NM_033375	0	0	0	10	10	Q14778	Splice_Site	SNP	ENST00000575158.1	37	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	a	23.7	4.448047	0.84101	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5923	0.68373	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYO1C	1317522	1.000000	0.71417	0.994000	0.49952	0.936000	0.57629	9.119000	0.94362	2.231000	0.72958	0.456000	0.33151	.	.		0.677	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		Intron	C	1370772	A	C	1370772	5	2	8	1	0	0	0	0	0	0	1	0	10095	173	6	5	136	5	MYO1C	17	1370772	Splice_Site	SNP	A	TCGA-A4-7734-01A-11D-2136-08		1370772	79824438	59	648											
LUC7L3	51747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48818486	48818486	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagaagagctctcgtttcaTgaaagttggctatgagagag	12	11	13	5	1	2	5	1	3	1	3	3	7	2	5	0	1	1	4	0	1	3	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:48818486T>C	ENST00000505658.1	+	4	419	c.230T>C	c.(229-231)aTg>aCg	p.M77T	LUC7L3_ENST00000393227.2_Missense_Mutation_p.M77T|LUC7L3_ENST00000544170.1_Start_Codon_SNP_p.M1T|LUC7L3_ENST00000240304.1_Missense_Mutation_p.M77T			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	77					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						TCTCGTTTCATGAAAGTTGGC	0.383																																					p.M77T		.											.	LUC7L3-90	0			c.T230C						.						180	182	181					17																	48818486		2203	4300	6503	SO:0001583	missense	51747	exon4			GTTTCATGAAAGT		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.230T>C	17.37:g.48818486T>C	ENSP00000425092:p.Met77Thr	Somatic	306	0		WXS	Illumina HiSeq	Phase_I	310	87	NM_006107	0	0	67	94	27	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	37	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.064693	0.76187	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000505619;ENST00000544170;ENST00000510984	T;T;T;T;T	0.47528	1.31;1.31;1.31;1.03;0.84	5.95	4.83	0.62350	.	0.071512	0.85682	D	0.000000	T	0.39036	0.1063	L	0.31065	0.9	0.80722	D	1	D;B;B	0.53885	0.963;0.369;0.369	P;B;B	0.47786	0.557;0.171;0.237	T	0.11275	-1.0594	10	0.09338	T	0.73	-10.5258	13.4049	0.60906	0.0:0.0:0.1306:0.8694	.	1;77;77	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	T	77;77;77;77;126;1;1	ENSP00000425092:M77T;ENSP00000376919:M77T;ENSP00000240304:M77T;ENSP00000420933:M126T;ENSP00000444253:M1T	ENSP00000240304:M77T	M	+	2	0	LUC7L3	46173485	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.043000	0.64208	2.272000	0.75746	0.460000	0.39030	ATG	.		0.383	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		C	48818486	T	C	48818486	3	2	8	1	0	0	0	0	1	0	0	0	9109	1464	51	3	244	3	LUC7L3	17	48818486	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	47447714	48818486	32376724	60	649											
CLTC	1213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	57724783	57724783	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaaactcttcagatttttaAcattgaaatgaaaagtaaaa	20	12	5	4	0	2	3	1	2	1	1	2	4	2	3	0	0	2	1	0	0	8	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:57724783A>T	ENST00000269122.3	+	3	549	c.275A>T	c.(274-276)aAc>aTc	p.N92I	CLTC_ENST00000579456.1_Missense_Mutation_p.N92I|CLTC_ENST00000393043.1_Missense_Mutation_p.N92I	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	92	Globular terminal domain.|WD40-like repeat 2.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CAGATTTTTAACATTGAAATG	0.318			T	"ALK, TFE3"	"ALCL, renal "																																p.N92I		.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC-835	0			c.A275T						.						73	71	72					17																	57724783		2203	4300	6503	SO:0001583	missense	1213	exon3			TTTTTAACATTGA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.275A>T	17.37:g.57724783A>T	ENSP00000269122:p.Asn92Ile	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	91	28	NM_004859	0	0	212	297	85	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.244879	0.79912	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.27256	1.68;1.68	5.79	5.79	0.91817	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.043886	0.85682	D	0.000000	T	0.63390	0.2507	H	0.94222	3.51	0.31520	N	0.662492	D;D	0.76494	0.994;0.999	D;D	0.79784	0.993;0.993	T	0.77419	-0.2595	10	0.87932	D	0	.	16.1376	0.81497	1.0:0.0:0.0:0.0	.	92;92	Q00610;Q00610-2	CLH1_HUMAN;.	I	92	ENSP00000269122:N92I;ENSP00000376763:N92I	ENSP00000269122:N92I	N	+	2	0	CLTC	55079565	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.339000	0.96797	2.212000	0.71576	0.533000	0.62120	AAC	.		0.318	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		T	57724783	A	T	57724783	3	4	8	1	0	0	0	0	1	0	0	0	3572	43	2	5	285	5	CLTC	17	57724783	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	8906297	57724783	23470427	61	650											
BAHCC1	57597	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79425869	79425869	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggccgtgagccgcctgctgGaaagcttcgccgtggaggaa	7	6	17	11	4	0	1	0	1	0	0	1	4	0	4	4	4	3	2	4	4	2	1			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:79425869G>T	ENST00000307745.7	+	24	5479	c.5479G>T	c.(5479-5481)Gaa>Taa	p.E1827*	RP11-1055B8.8_ENST00000572590.1_RNA																							CCGCCTGCTGGAAAGCTTCGC	0.662																																					.													.	BAHCC1-23	0			.						.						17	22	20					17																	79425869		2091	4207	6298	SO:0001587	stop_gained	57597	.			CTGCTGGAAAGCT																												ENST00000307745.7:c.5479G>T	17.37:g.79425869G>T	ENSP00000303486:p.Glu1827*	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	38	9	.	0	0	4	6	2		Nonsense_Mutation	SNP	ENST00000307745.7	37		.	.	.	.	.	.	.	.	.	.	G	44	10.877947	0.99482	.	.	ENSG00000171282	ENST00000307745	.	.	.	3.69	3.69	0.42338	.	0.124501	0.34200	U	0.004171	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	10.7766	0.46353	0.0:0.194:0.806:0.0	.	.	.	.	X	1827	.	ENSP00000303486:E1827X	E	+	1	0	AC110285.1	77040464	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	2.589000	0.46145	1.765000	0.52091	0.455000	0.32223	GAA	.		0.662	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	79425869	G	T	79425869	4	4	8	1	0	0	0	0	0	1	0	0	1297	1175	41	4	5388	4	BAHCC1	17	79425869	Nonsense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	21701086	79425869	1769341	62	651											
SF4	57794	hgsc.bcm.edu	37	chr19	19387814	19387814	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgcggaacgcctcatacTcgtcgtcctccttggagagc	6	11	10	14	4	2	1	1	0	1	1	6	3	4	2	3	2	4	0	3	2	2	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:19387814T>C	ENST00000247001.5	-	13	2200	c.1853A>G	c.(1852-1854)gAg>gGg	p.E618G		NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	618					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						CGCCTCATACTCGTCGTCCTC	0.637																																					p.E618G		.											.	SUGP1-91	0			c.A1853G						.						39	39	39					19																	19387814		2203	4300	6503	SO:0001583	missense	57794	exon13			TCATACTCGTCGT	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"G patch domain containing"	18643	protein-coding gene	gene with protein product		607992	"splicing factor 4"	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.1853A>G	19.37:g.19387814T>C	ENSP00000247001:p.Glu618Gly	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_172231	0	0	34	34	0	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.240159	0.58995	.	.	ENSG00000105705	ENST00000247001	T	0.28454	1.61	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.51092	0.1654	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.53194	-0.8473	10	0.59425	D	0.04	.	12.9089	0.58169	0.0:0.0:0.0:1.0	.	618	Q8IWZ8	SUGP1_HUMAN	G	618	ENSP00000247001:E618G	ENSP00000247001:E618G	E	-	2	0	SUGP1	19248814	1.000000	0.71417	0.832000	0.32986	0.032000	0.12392	7.875000	0.87205	1.735000	0.51646	0.260000	0.18958	GAG	.		0.637	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		C	19387814	T	C	19387814	3	2	8	1	0	0	0	0	1	0	0	0	14187	1551	54	3	92	3	SF4	19	19387814	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		19387814	39741169	63	652											
TBCB	1155	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	36606528	36606528	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	agcagctccctcaacaccttCcgctccgagaagcgatacag	11	6	8	16	3	1	1	1	0	0	1	4	3	4	1	4	0	5	3	4	0	3	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:36606528C>G	ENST00000221855.3	+	1	641	c.66C>G	c.(64-66)ttC>ttG	p.F22L	TBCB_ENST00000586868.1_5'Flank|TBCB_ENST00000392178.4_3'UTR|POLR2I_ENST00000221859.4_5'Flank|TBCB_ENST00000589996.1_Missense_Mutation_p.F22L|TBCB_ENST00000585746.1_5'Flank	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	22					'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCAACACCTTCCGCTCCGAGA	0.667																																					p.F22L		.											.	TBCB-90	0			c.C66G						.						35	25	28					19																	36606528		2202	4298	6500	SO:0001583	missense	1155	exon1			CACCTTCCGCTCC	AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"cytoskeleton-associated protein 1", "cytoskeleton associated protein 1"	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.66C>G	19.37:g.36606528C>G	ENSP00000221855:p.Phe22Leu	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	28	10	NM_001281	0	0	102	181	79	O00111|O00674|O14728|Q6FGY5	Missense_Mutation	SNP	ENST00000221855.3	37	CCDS12488.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.391016	0.62066	.	.	ENSG00000105254	ENST00000221855;ENST00000392178	D	0.91068	-2.78	5.33	1.7	0.24286	.	0.000000	0.85682	D	0.000000	D	0.86916	0.6048	M	0.65498	2.005	0.80722	D	1	B	0.15473	0.013	B	0.20955	0.032	T	0.77035	-0.2737	10	0.28530	T	0.3	-21.5313	8.0558	0.30604	0.0:0.7565:0.0:0.2435	.	22	Q99426	TBCB_HUMAN	L	22	ENSP00000221855:F22L	ENSP00000221855:F22L	F	+	3	2	TBCB	41298368	1.000000	0.71417	0.999000	0.59377	0.866000	0.49608	1.041000	0.30291	0.088000	0.17205	0.484000	0.47621	TTC	.		0.667	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281		G	36606528	C	G	36606528	3	3	8	1	0	0	0	0	1	0	0	0	15662	854	30	4	68	4	TBCB	19	36606528	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	17218714	36606528	22522455	64	653											
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42795453	42795453	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacctgccccagcaccaGcccctgggaccaaggcagcg	8	3	12	18	1	0	0	0	0	0	0	0	1	0	1	7	3	4	3	7	3	1	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:42795453G>A	ENST00000575354.2	+	10	2573	c.2533G>A	c.(2533-2535)Gcc>Acc	p.A845T	CIC_ENST00000572681.2_Missense_Mutation_p.A1754T|CIC_ENST00000160740.3_Missense_Mutation_p.A845T	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	845	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCCAGCACCAGCCCCTGGGAC	0.677			"Mis, F, S"		oligodendroglioma																																p.A845T		.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC-591	0			c.G2533A						.						16	17	17					19																	42795453		2165	4211	6376	SO:0001583	missense	23152	exon10			GCACCAGCCCCTG	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.2533G>A	19.37:g.42795453G>A	ENSP00000458663:p.Ala845Thr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	45	19	NM_015125	0	0	31	52	21	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547541	0.45383	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.44	1.07	0.20283	.	.	.	.	.	T	0.20901	0.0503	N	0.08118	0	0.30059	N	0.811071	B	0.11235	0.004	B	0.04013	0.001	T	0.17319	-1.0373	8	0.87932	D	0	-7.4144	5.5731	0.17208	0.1937:0.1695:0.6368:0.0	.	845	Q96RK0	CIC_HUMAN	T	845	.	ENSP00000160740:A845T	A	+	1	0	CIC	47487293	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.094000	0.41719	0.553000	0.29044	0.561000	0.74099	GCC	.		0.677	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			A	42795453	G	A	42795453	3	1	8	1	0	0	0	0	1	0	0	0	3430	971	34	2	2571	2	CIC	19	42795453	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	6188925	42795453	16333530	65	654											
MYH14	79784	broad.mit.edu;ucsc.edu	37	chr19	50783389	50783389	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagaagcccagctgcaCgatgcccaggtgaccctgcc	10	4	11	16	1	0	2	0	1	0	1	0	3	0	2	4	1	6	3	4	1	1	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:50783389C>T	ENST00000596571.1	+	28	4005	c.4005C>T	c.(4003-4005)caC>caT	p.H1335H	MYH14_ENST00000376970.2_Silent_p.H1368H|MYH14_ENST00000601313.1_Silent_p.H1376H|MYH14_ENST00000598205.1_Silent_p.H1343H|MYH14_ENST00000440075.2_Silent_p.H1376H|MYH14_ENST00000262269.8_Silent_p.H1376H|MYH14_ENST00000425460.1_Silent_p.H1343H			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1335					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CCCAGCTGCACGATGCCCAGG	0.607																																					p.H1376H													.	MYH14-23	0			c.C4128T						.						55	63	60					19																	50783389		2188	4285	6473	SO:0001819	synonymous_variant	79784	exon31			GCTGCACGATGCC	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4005C>T	19.37:g.50783389C>T		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	9	3	NM_001145809	0	0	0	0	0	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			.		0.607	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50783389	C	T	50783389	2	4	8	1	0	0	0	0	0	0	0	1	10058	535	19	1		1	MYH14	19	50783389	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	7987936	50783389	8345594	66	655											
TUBB1	81027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	57597910	57597910	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctttcagttctgggagaTgattggtgaggaacacggga	9	11	15	6	1	2	3	1	2	1	1	2	6	2	5	0	4	2	2	0	4	1	3	rs374942824		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr20:57597910T>C	ENST00000217133.1	+	2	337	c.68T>C	c.(67-69)aTg>aCg	p.M23T		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	23					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	TTCTGGGAGATGATTGGTGAG	0.547																																					p.M23T		.											.	TUBB1-227	0			c.T68C						.	T	THR/MET	1,4405	2.1+/-5.4	0,1,2202	67	63	65		68	4.4	1	20		65	0,8600		0,0,4300	no	missense	TUBB1	NM_030773.3	81	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	23/452	57597910	1,13005	2203	4300	6503	SO:0001583	missense	81027	exon2			GGGAGATGATTGG	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.68T>C	20.37:g.57597910T>C	ENSP00000217133:p.Met23Thr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	88	51	NM_030773	0	0	0	0	0		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	T	12.98	2.099754	0.37048	2.27E-4	0.0	ENSG00000101162	ENST00000217133	T	0.68903	-0.36	4.36	4.36	0.52297	Tubulin/FtsZ, GTPase domain (3);	0.121035	0.56097	D	0.000037	T	0.31888	0.0811	N	0.00277	-1.72	0.37932	D	0.932041	B	0.02656	0.0	B	0.04013	0.001	T	0.41413	-0.9510	10	0.87932	D	0	.	13.0037	0.58692	0.0:0.0:0.0:1.0	.	23	Q9H4B7	TBB1_HUMAN	T	23	ENSP00000217133:M23T	ENSP00000217133:M23T	M	+	2	0	TUBB1	57031305	1.000000	0.71417	0.989000	0.46669	0.464000	0.32679	7.967000	0.87967	1.727000	0.51537	0.528000	0.53228	ATG	.		0.547	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		C	57597910	T	C	57597910	3	2	8	1	0	0	0	0	1	0	0	0	16786	1464	51	3	74	3	TUBB1	20	57597910	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		57597910	5427610	67	656											
SON	6651	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	34927198	34927198	+	Frame_Shift_Del	DEL	A	A	-																															agaggaagaagatctgtatcAaaagagaagcgcaaaagatc																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr21:34927198delA	ENST00000356577.4	+	3	6136	c.5661delA	c.(5659-5661)tcafs	p.S1887fs	SON_ENST00000290239.6_Frame_Shift_Del_p.S1887fs|SON_ENST00000381679.4_Frame_Shift_Del_p.S1887fs|SON_ENST00000300278.4_Frame_Shift_Del_p.S1887fs|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1887					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GATCTGTATCAAAAGAGAAGC	0.453																																					p.S1887fs		.											.	SON-97	0			c.5661delA						.						52	50	51					21																	34927198		2203	4300	6503	SO:0001589	frameshift_variant	6651	exon3			.	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.5661delA	21.37:g.34927198delA	ENSP00000348984:p.Ser1887fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	42	15	NM_032195	0	0	0	0	0	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Frame_Shift_Del	DEL	ENST00000356577.4	37	CCDS13629.1																																																																																			.		0.453	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		-	34927198	A	-	34927198	7	5	8	1	0	1	0	1	0	0	0	0	14958	117	5	0	5671	0	SON	21	34927198	Frame_Shift_Del	DEL	A	TCGA-A4-7734-01A-11D-2136-08		34927198	13202697	68	657											
RIPK4	54101	broad.mit.edu	37	chr21	43166867	43166867	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcggccgggctctgcacacGggcggcagctcggggcggtg	3	4	20	14	7	1	0	0	0	1	0	2	0	1	0	1	7	2	4	1	7	0	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr21:43166867G>C	ENST00000352483.2	-	5	802	c.738C>G	c.(736-738)ccC>ccG	p.P246P	RIPK4_ENST00000542057.1_Silent_p.P183P|RIPK4_ENST00000332512.3_Silent_p.P246P|RIPK4_ENST00000544709.1_Silent_p.P183P			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	246	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTCTGCACACGGGCGGCAGCT	0.657																																					p.P246P													.	RIPK4-947	0			c.C738G						.						62	62	62					21																	43166867		2203	4300	6503	SO:0001819	synonymous_variant	54101	exon5			GCACACGGGCGGC	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"Ankyrin repeat domain containing"	496	protein-coding gene	gene with protein product	"protein kinase C-associated kinase", "PKC-delta-interacting protein kinase"	605706	"ankyrin repeat domain 3"	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.738C>G	21.37:g.43166867G>C		Somatic	232	0		WXS	Illumina HiSeq	Phase_I	135	4	NM_020639	0	0	58	60	2	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				.		0.657	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		C	43166867	G	C	43166867	2	2	8	1	0	0	0	0	0	0	0	1	13415	1103	39	4		4	RIPK4	21	43166867	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08	8239669	43166867	4963028	69	658											
SLC37A1	54020	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43963563	43963563	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caggagaggtttgattatggGggtctggaactcccacacct	9	10	13	9	0	1	2	0	1	1	1	2	4	2	3	2	5	1	1	2	5	2	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr21:43963563G>A	ENST00000352133.2	+	8	1563	c.581G>A	c.(580-582)gGg>gAg	p.G194E	SLC37A1_ENST00000398341.3_Missense_Mutation_p.G194E			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	194					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						TTGATTATGGGGGTCTGGAAC	0.572																																					p.G194E		.											.	SLC37A1-90	0			c.G581A						.						165	155	158					21																	43963563		2203	4300	6503	SO:0001583	missense	54020	exon9			TTATGGGGGTCTG	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"Solute carriers"	11024	protein-coding gene	gene with protein product		608094	"solute carrier family 37 (glycerol-3-phosphate transporter), member 1"			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.581G>A	21.37:g.43963563G>A	ENSP00000344648:p.Gly194Glu	Somatic	320	0		WXS	Illumina HiSeq	Phase_I	243	75	NM_018964	0	0	10	19	9	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.732737	0.89482	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.66099	-0.19;-0.19	4.99	4.99	0.66335	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.177957	0.49916	D	0.000125	D	0.85292	0.5663	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89875	0.4026	10	0.87932	D	0	-14.7963	18.3114	0.90201	0.0:0.0:1.0:0.0	.	194	P57057	GLPT_HUMAN	E	194	ENSP00000381383:G194E;ENSP00000344648:G194E	ENSP00000344648:G194E	G	+	2	0	SLC37A1	42836632	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	9.423000	0.97461	2.324000	0.78689	0.650000	0.86243	GGG	.		0.572	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			A	43963563	G	A	43963563	3	1	8	1	0	0	0	0	1	0	0	0	14629	1232	43	2	607	2	SLC37A1	21	43963563	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	796696	43963563	4166332	70	659											
KLHL34	257240	hgsc.bcm.edu	37	chrX	21675434	21675434	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcgccagcagctcctgcAagtggctcacgatgcagcgc	7	5	12	17	4	1	0	1	0	0	0	2	1	2	0	3	1	5	5	3	1	1	0	rs145604187		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chrX:21675434A>G	ENST00000379499.2	-	1	1014	c.473T>C	c.(472-474)tTg>tCg	p.L158S		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	158	BACK.					extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						CAGCTCCTGCAAGTGGCTCAC	0.711													A|||	13	0.00344371	8e-04	0.0086	3775	,	,		10108	0		0.006	False		,,,				2504	0				p.L158S		.											.	KLHL34-131	0			c.T473C						.	A	SER/LEU	3,3293		0,2,1,1438,415	3	4	3		473	4.3	0.8	X	dbSNP_134	3	41,5735		0,28,13,2144,1419	yes	missense	KLHL34	NM_153270.1	145	0,30,14,3582,1834	GG,GA,G,AA,A		0.7098,0.091,0.485	possibly-damaging	158/645	21675434	44,9028	1856	3604	5460	SO:0001583	missense	257240	exon1			TCCTGCAAGTGGC	AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"Kelch-like", "BTB/POZ domain containing"	26634	protein-coding gene	gene with protein product			"kelch-like 34 (Drosophila)"				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.473T>C	X.37:g.21675434A>G	ENSP00000368813:p.Leu158Ser	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	8	5	NM_153270	0	0	1	1	0		Missense_Mutation	SNP	ENST00000379499.2	37	CCDS14199.1	6	0.003616636528028933	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	13.64	2.297650	0.40694	9.1E-4	0.007098	ENSG00000185915	ENST00000379499	T	0.70282	-0.47	4.35	4.35	0.52113	BTB/Kelch-associated (2);	0.155107	0.43579	D	0.000545	T	0.63640	0.2528	L	0.56769	1.78	0.24527	P	0.99413997	P	0.47191	0.891	P	0.45829	0.494	T	0.79685	-0.1700	9	0.87932	D	0	.	12.8899	0.58066	1.0:0.0:0.0:0.0	.	158	Q8N239	KLH34_HUMAN	S	158	ENSP00000368813:L158S	ENSP00000368813:L158S	L	-	2	0	KLHL34	21585355	1.000000	0.71417	0.829000	0.32907	0.226000	0.24999	8.854000	0.92228	1.610000	0.50200	0.345000	0.21793	TTG	A|0.996;G|0.004		0.711	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270		G	21675434	A	G	21675434	3	3	8	1	0	0	0	0	1	0	0	0	8408	131	5	3	1465	3	KLHL34	23	21675434	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08		21675434	133595126	71	660											
GPR174	84636	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	78427128	78427128	+	Frame_Shift_Del	DEL	G	G	-																															ctatattgtacctggaagacGgttttatcactgcaagataa																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chrX:78427128delG	ENST00000276077.1	+	1	660	c.624delG	c.(622-624)acgfs	p.T208fs		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CCTGGAAGACGGTTTTATCAC	0.438										HNSCC(63;0.18)																											p.T208fs		.											.	GPR174-130	0			c.624delG						.						97	93	94					X																	78427128		2203	4300	6503	SO:0001589	frameshift_variant	84636	exon1			.	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.624delG	X.37:g.78427128delG	ENSP00000276077:p.Thr208fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	151	60	NM_032553	0	0	0	0	0	Q2M3F7	Frame_Shift_Del	DEL	ENST00000276077.1	37	CCDS14443.1																																																																																			.		0.438	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		-	78427128	G	-	78427128	7	5	8	1	0	1	0	1	0	0	0	0	6692	1103	39	0	626	0	GPR174	23	78427128	Frame_Shift_Del	DEL	G	TCGA-A4-7734-01A-11D-2136-08	56751694	78427128	76843432	72	661											
MTOR	2475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11184573	11184573	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgaggtttttccgaagaGatgttgggtcattggccaga	9	12	13	7	1	1	3	1	1	0	2	2	5	2	3	3	3	0	2	3	3	1	4	rs587777894		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:11184573G>T	ENST00000361445.4	-	47	6720	c.6644C>A	c.(6643-6645)tCt>tAt	p.S2215Y	MTOR_ENST00000376838.1_Missense_Mutation_p.S420Y	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2215	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		S -> Y (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.S2215Y(4)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTTCCGAAGAGATGTTGGGTC	0.438																																					p.S2215Y		.											.	MTOR-1439	4	Substitution - Missense(4)	large_intestine(2)|kidney(1)|endometrium(1)	c.C6644A						.						101	98	99					1																	11184573		2203	4300	6503	SO:0001583	missense	2475	exon47			CGAAGAGATGTTG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6644C>A	1.37:g.11184573G>T	ENSP00000354558:p.Ser2215Tyr	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	71	24	NM_004958	0	0	9	11	2	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903707	0.92035	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.78364	-1.17;-1.17	5.8	5.8	0.92144	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.88862	0.6552	M	0.86651	2.83	0.80722	D	1	D	0.58970	0.984	P	0.60541	0.876	D	0.90182	0.4243	10	0.87932	D	0	-14.2436	18.2956	0.90145	0.0:0.0:1.0:0.0	.	2215	P42345	MTOR_HUMAN	Y	2215;420	ENSP00000354558:S2215Y;ENSP00000366034:S420Y	ENSP00000354558:S2215Y	S	-	2	0	MTOR	11107160	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.362000	0.97126	2.761000	0.94854	0.650000	0.86243	TCT	.		0.438	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11184573	G	T	11184573	3	4	9	1	0	0	0	0	1	0	0	0	9979	942	33	4	1053	4	MTOR	1	11184573	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		11184573	238066048	1	662											
BEST4	266675	hgsc.bcm.edu	37	chr1	45252159	45252159	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaccacgtgctccatggTggggaagcgcttaagcacgc	8	7	13	13	3	0	0	0	0	0	0	2	1	2	1	3	3	3	3	3	3	2	1	rs41306591	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:45252159T>C	ENST00000372207.3	-	3	456	c.457A>G	c.(457-459)Acc>Gcc	p.T153A		NM_153274.2	NP_695006.1	Q8NFU0	BEST4_HUMAN	bestrophin 4	153						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)					TGCTCCATGGTGGGGAAGCGC	0.736											OREG0013447	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	6	0.00119808	0	0.0014	5008	,	,		14773	0		0.005	False		,,,				2504	0				p.T153A		.											.	BEST4-91	0			c.A457G						.	T	ALA/THR	3,4269		0,3,2133	8	9	8		457	5.8	1	1	dbSNP_127	8	15,8343		0,15,4164	yes	missense	BEST4	NM_153274.2	58	0,18,6297	CC,CT,TT		0.1795,0.0702,0.1425	probably-damaging	153/474	45252159	18,12612	2136	4179	6315	SO:0001583	missense	266675	exon3			CCATGGTGGGGAA	AF440757	CCDS514.1	1p33-p32.3	2012-09-26	2006-10-18	2006-10-18	ENSG00000142959	ENSG00000142959		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17106	protein-coding gene	gene with protein product		607336	"vitelliform macular dystrophy 2-like 2"	VMD2L2		12032738, 16702355	Standard	NM_153274		Approved		uc001cmm.3	Q8NFU0	OTTHUMG00000008488	ENST00000372207.3:c.457A>G	1.37:g.45252159T>C	ENSP00000361281:p.Thr153Ala	Somatic	2	1	930	WXS	Illumina HiSeq	Phase_I	8	3	NM_153274	0	0	0	0	0	Q5JR93	Missense_Mutation	SNP	ENST00000372207.3	37	CCDS514.1	6	0.0027472527472527475	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	36	5.748484	0.96882	7.02E-4	0.001795	ENSG00000142959	ENST00000372207	D	0.98264	-4.83	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.98588	0.9528	M	0.93808	3.46	0.58432	D	0.999995	P	0.44281	0.831	P	0.55713	0.782	D	0.96014	0.9004	10	0.72032	D	0.01	-32.0345	14.8939	0.70630	0.0:0.0:0.0:1.0	rs41306591	153	Q8NFU0	BEST4_HUMAN	A	153	ENSP00000361281:T153A	ENSP00000361281:T153A	T	-	1	0	BEST4	45024746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.089000	0.71384	2.200000	0.70718	0.459000	0.35465	ACC	T|0.997;C|0.003		0.736	BEST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023425.1	NM_153274		C	45252159	T	C	45252159	3	2	9	1	0	0	0	0	1	0	0	0	1408	1696	59	3	992	3	BEST4	1	45252159	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	34067586	45252159	203998462	2	663											
C1orf175	374977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	55118778	55118778	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcttggctctcgttccagAtcttaatgattctttgagtc	6	17	9	9	1	3	3	0	2	3	1	6	3	4	3	1	2	0	3	1	2	1	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:55118778A>C	ENST00000421030.2	+	3	464	c.179A>C	c.(178-180)gAt>gCt	p.D60A	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000395690.2_Missense_Mutation_p.D60A|MROH7_ENST00000454855.2_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.D60A|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000339553.5_Missense_Mutation_p.D60A|MROH7_ENST00000409996.1_Intron	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	60						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CTCGTTCCAGATCTTAATGAT	0.567																																					p.D60A		.											.	.	0			c.A179C						.						77	78	77					1																	55118778		1918	4127	6045	SO:0001583	missense	374977	exon3			TTCCAGATCTTAA	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"maestro heat-like repeat containing"	24802	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 175", "HEAT repeat containing 8"	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.179A>C	1.37:g.55118778A>C	ENSP00000396622:p.Asp60Ala	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	148	46	NM_001039464	0	0	0	0	0	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	A	6.762	0.509542	0.12883	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.02974	4.62;4.09;4.11	3.58	1.19	0.21007	.	.	.	.	.	T	0.02012	0.0063	N	0.17082	0.46	0.09310	N	0.999998	B;B;P	0.46142	0.154;0.015;0.873	B;B;B	0.42495	0.053;0.018;0.389	T	0.47724	-0.9095	9	0.33141	T	0.24	.	3.5678	0.07907	0.6251:0.247:0.1279:0.0	.	60;60;60	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	A	60	ENSP00000396622:D60A;ENSP00000343211:D60A;ENSP00000379044:D60A	ENSP00000343211:D60A	D	+	2	0	HEATR8	54891366	0.027000	0.19231	0.058000	0.19502	0.109000	0.19521	0.013000	0.13310	0.238000	0.21222	0.459000	0.35465	GAT	.		0.567	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		C	55118778	A	C	55118778	3	2	9	1	0	0	0	0	1	0	0	0	2022	333	12	5	181	5	C1orf175	1	55118778	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	9866619	55118778	194131843	3	664											
TRIM33	51592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	114948195	114948195	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccaatccttgccgacctgtGcatgaggcttcgaattgggg	7	11	12	11	2	0	1	0	1	0	0	3	3	2	1	4	3	2	2	4	3	2	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:114948195G>A	ENST00000358465.2	-	15	2688	c.2605C>T	c.(2605-2607)Cac>Tac	p.H869Y	TRIM33_ENST00000450349.2_Missense_Mutation_p.H501Y|TRIM33_ENST00000476908.1_5'UTR|TRIM33_ENST00000369543.2_Missense_Mutation_p.H869Y	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	869					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCCGACCTGTGCATGAGGCTT	0.468			T	RET	papillary thyroid																																p.H869Y		.		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	.	TRIM33-1351	0			c.C2605T						.						218	196	203					1																	114948195		2203	4300	6503	SO:0001583	missense	51592	exon15			ACCTGTGCATGAG	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2605C>T	1.37:g.114948195G>A	ENSP00000351250:p.His869Tyr	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	243	65	NM_033020	0	0	3	5	2	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895312	0.72639	.	.	ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349	T;T;T	0.75589	-0.81;-0.71;-0.95	5.29	5.29	0.74685	Zinc finger, FYVE/PHD-type (1);	0.224309	0.50627	D	0.000108	T	0.66944	0.2841	N	0.19112	0.55	0.53688	D	0.999974	D;D;P;P;P	0.54601	0.967;0.957;0.952;0.952;0.92	P;B;B;P;B	0.53102	0.718;0.402;0.446;0.548;0.346	T	0.72261	-0.4345	10	0.59425	D	0.04	-10.5094	19.2948	0.94118	0.0:0.0:1.0:0.0	.	501;501;64;869;869	E7EN20;B3KN30;Q9HAL0;Q9UPN9-2;Q9UPN9	.;.;.;.;TRI33_HUMAN	Y	869;869;501	ENSP00000351250:H869Y;ENSP00000358556:H869Y;ENSP00000412077:H501Y	ENSP00000351250:H869Y	H	-	1	0	TRIM33	114749718	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.388000	0.73195	2.636000	0.89361	0.491000	0.48974	CAC	.		0.468	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		A	114948195	G	A	114948195	3	1	9	1	0	0	0	0	1	0	0	0	16540	1319	46	2	802	2	TRIM33	1	114948195	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	59829417	114948195	134302426	4	665											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228467538	228467538	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcagacatccccgtagtcctCacacggccgttggagcccaa	9	6	10	16	3	1	1	1	0	0	1	3	2	3	2	5	2	1	3	5	2	2	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:228467538C>G	ENST00000422127.1	+	28	7457	c.7413C>G	c.(7411-7413)ctC>ctG	p.L2471L	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000359599.6_Silent_p.L1318L|OBSCN_ENST00000284548.11_Silent_p.L2471L|OBSCN_ENST00000570156.2_Silent_p.L2900L|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2471	Ig-like 24.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCGTAGTCCTCACACGGCCGT	0.652																																					p.L2900L		.											.	OBSCN-403	0			c.C8700G						.						19	23	21					1																	228467538		2149	4246	6395	SO:0001819	synonymous_variant	84033	exon33			AGTCCTCACACGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.7413C>G	1.37:g.228467538C>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_001271223	0	0	1	1	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228467538	C	G	228467538	2	3	9	1	0	0	0	0	0	0	0	1	10838	813	29	4		4	OBSCN	1	228467538	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08	113519343	228467538	20783083	5	666											
RYR2	6262	hgsc.bcm.edu	37	chr1	237804221	237804221	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaggaggaggaagatgaCactatccacatggggaacgc	15	4	14	8	1	0	3	0	1	0	2	1	7	1	7	1	5	1	0	1	5	3	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:237804221C>G	ENST00000366574.2	+	47	7457	c.7140C>G	c.(7138-7140)gaC>gaG	p.D2380E	RYR2_ENST00000360064.6_Missense_Mutation_p.D2378E|RYR2_ENST00000542537.1_Missense_Mutation_p.D2364E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2380	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGAAGATGACACTATCCACA	0.428																																					p.D2380E		.											.	RYR2-158	0			c.C7140G						.						168	162	164					1																	237804221		2066	4233	6299	SO:0001583	missense	6262	exon47			AGATGACACTATC	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7140C>G	1.37:g.237804221C>G	ENSP00000355533:p.Asp2380Glu	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_001035	0	0	0	0	0	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.488252	0.26686	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.98474	-4.95;-4.95;-4.95	5.6	-2.13	0.07144	.	0.000000	0.64402	D	0.000003	D	0.90672	0.7074	N	0.04043	-0.29	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.77726	-0.2480	10	0.24483	T	0.36	-26.3529	6.6308	0.22855	0.1122:0.424:0.0:0.4638	.	2380	Q92736	RYR2_HUMAN	E	2380;2378;2364	ENSP00000355533:D2380E;ENSP00000353174:D2378E;ENSP00000443798:D2364E	ENSP00000353174:D2378E	D	+	3	2	RYR2	235870844	0.002000	0.14202	0.967000	0.41034	0.977000	0.68977	-1.210000	0.02999	-0.290000	0.09025	0.591000	0.81541	GAC	.		0.428	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237804221	C	G	237804221	3	3	9	1	0	0	0	0	1	0	0	0	13801	477	17	4	7326	4	RYR2	1	237804221	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	9336683	237804221	11446400	6	667											
APOB	338	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	21224920	21224921	+	Frame_Shift_Ins	INS	-	-	G																															tctctttcccttttccatctINSggatcggtaaggatgctaag																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:21224920_21224921insG	ENST00000233242.1	-	29	13500_13501	c.13373_13374insC	c.(13372-13374)ccafs	p.P4458fs	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4458					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTTTCCATCTGGATCGGTAAG	0.396																																					p.P4458fs		.											.	APOB-175	0			c.13374_13375insC						.																																			SO:0001589	frameshift_variant	338	exon29			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.13374dupC	2.37:g.21224922_21224922dupG	ENSP00000233242:p.Pro4458fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	117	33	NM_000384	0	0	0	0	0	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	37	CCDS1703.1																																																																																			.		0.396	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21224921	-	G	21224920	7	5	9	1	0	1	1	0	0	0	0	0	785	1567	55	0	321	0	APOB	2	21224920	Frame_Shift_Ins	INS	-	TCGA-A4-7828-01A-11D-2136-08		21224920	221974453	7	668											
DHRS9	10170	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	169938176	169938176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taaagattgaagacatcactGataagtacatttttatcact	16	14	5	6	0	2	4	2	2	0	2	2	4	2	4	0	0	1	1	0	0	6	7			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:169938176G>A	ENST00000327239.4	+	5	1589	c.85G>A	c.(85-87)Gat>Aat	p.D29N	DHRS9_ENST00000412271.1_Missense_Mutation_p.D29N|DHRS9_ENST00000436483.2_Missense_Mutation_p.D29N|DHRS9_ENST00000602501.1_Missense_Mutation_p.D29N|DHRS9_ENST00000428522.1_Missense_Mutation_p.D29N|DHRS9_ENST00000432060.2_Missense_Mutation_p.D89N|DHRS9_ENST00000421653.1_5'UTR|DHRS9_ENST00000357546.2_Missense_Mutation_p.D29N	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	29					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						AGACATCACTGATAAGTACAT	0.428																																					p.D29N		.											.	DHRS9-90	0			c.G85A						.						118	117	117					2																	169938176		2203	4300	6503	SO:0001583	missense	10170	exon5			ATCACTGATAAGT	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.85G>A	2.37:g.169938176G>A	ENSP00000316670:p.Asp29Asn	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	134	7	NM_005771	0	0	0	0	0	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	37	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099956	0.56183	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000450153;ENST00000436483;ENST00000412271	D;D;D;D;T;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;0.73;-2.53;-2.53	5.88	2.98	0.34508	NAD(P)-binding domain (1);	0.501056	0.24625	N	0.036936	T	0.77624	0.4158	N	0.11756	0.17	0.34824	D	0.738968	B;B	0.17268	0.021;0.013	B;B	0.19666	0.026;0.018	T	0.73550	-0.3947	10	0.30854	T	0.27	.	10.261	0.43427	0.228:0.0:0.772:0.0	.	89;29	B7Z416;Q9BPW9	.;DHRS9_HUMAN	N	29;29;89;29;29;29;29	ENSP00000316670:D29N;ENSP00000350154:D29N;ENSP00000389241:D89N;ENSP00000388564:D29N;ENSP00000391214:D29N;ENSP00000407167:D29N;ENSP00000407747:D29N	ENSP00000316670:D29N	D	+	1	0	DHRS9	169646422	0.316000	0.24580	0.753000	0.31225	0.908000	0.53690	0.839000	0.27586	0.752000	0.32923	0.655000	0.94253	GAT	.		0.428	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		A	169938176	G	A	169938176	3	1	9	1	0	0	0	0	1	0	0	0	4509	1290	45	2	87	2	DHRS9	2	169938176	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	148713256	169938176	73261197	8	669											
CDCA7	83879	bcgsc.ca	37	chr2	174231883	174231883	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acaatcctccttcagaactgGcattgcccgccttgtcgagg	8	10	9	14	2	1	1	1	0	0	1	4	2	3	1	4	2	2	1	4	2	2	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:174231883G>A	ENST00000347703.3	+	8	1098	c.954G>A	c.(952-954)tgG>tgA	p.W318*	CDCA7_ENST00000410019.3_Nonsense_Mutation_p.W276*|CDCA7_ENST00000306721.3_Nonsense_Mutation_p.W397*|CDCA7_ENST00000410101.3_Nonsense_Mutation_p.W353*|CDCA7_ENST00000392567.2_Nonsense_Mutation_p.W268*	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7	318	Mediates transcriptional activity.				apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			TTCAGAACTGGCATTGCCCGC	0.463																																					p.W397X													.	CDCA7-91	0			c.G1191A						.						121	116	118					2																	174231883		2203	4300	6503	SO:0001587	stop_gained	83879	exon9			GAACTGGCATTGC	BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.954G>A	2.37:g.174231883G>A	ENSP00000272789:p.Trp318*	Somatic	115	1		WXS	Illumina HiSeq	Phase_1	138	6	NM_031942	0	0	0	0	0	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Nonsense_Mutation	SNP	ENST00000347703.3	37	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	G	36	5.963895	0.97151	.	.	ENSG00000144354	ENST00000347703;ENST00000392567;ENST00000306721;ENST00000410101;ENST00000410019	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.1383	18.9676	0.92702	0.0:0.0:1.0:0.0	.	.	.	.	X	318;268;397;353;276	.	ENSP00000306968:W397X	W	+	3	0	CDCA7	173940129	1.000000	0.71417	0.999000	0.59377	0.772000	0.43724	9.785000	0.99042	2.473000	0.83533	0.563000	0.77884	TGG	.		0.463	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		A	174231883	G	A	174231883	4	1	9	1	0	0	0	0	0	1	0	0	3096	1212	42	2	1225	2	CDCA7	2	174231883	Nonsense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	4293707	174231883	68967490	9	670											
PGAP1	80055	hgsc.bcm.edu;broad.mit.edu	37	chr2	197781305	197781305	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttttctaagtgcaatggagCcaatagaacgaactgcagag	14	9	10	8	1	1	2	0	0	1	2	1	4	1	3	1	1	5	2	1	1	6	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:197781305C>A	ENST00000354764.4	-	3	428	c.314G>T	c.(313-315)gGc>gTc	p.G105V	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Missense_Mutation_p.G63V|PGAP1_ENST00000409475.1_Missense_Mutation_p.G105V	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	105					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TGCAATGGAGCCAATAGAACG	0.368																																					p.G105V		.											.	PGAP1-93	0			c.G314T						.						69	63	65					2																	197781305		2203	4300	6503	SO:0001583	missense	80055	exon3			ATGGAGCCAATAG		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.314G>T	2.37:g.197781305C>A	ENSP00000346809:p.Gly105Val	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	47	9	NM_024989	0	0	0	0	0	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.973928	0.74246	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.86097	-2.07;-2.07;-2.07	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.92361	0.7576	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	0.994;1.0	P;D	0.83275	0.844;0.996	D	0.92756	0.6220	10	0.72032	D	0.01	-10.0578	15.4815	0.75530	0.0:0.862:0.138:0.0	.	105;105	Q75T13-3;Q75T13	.;PGAP1_HUMAN	V	105;105;63	ENSP00000346809:G105V;ENSP00000387028:G105V;ENSP00000386802:G63V	ENSP00000346809:G105V	G	-	2	0	PGAP1	197489550	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.646000	0.67916	2.796000	0.96246	0.644000	0.83932	GGC	.		0.368	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		A	197781305	C	A	197781305	3	1	9	1	0	0	0	0	1	0	0	0	11803	739	26	4	2554	4	PGAP1	2	197781305	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	23549422	197781305	45418068	10	671											
SPAG16	79582	hgsc.bcm.edu	37	chr2	214204970	214204970	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgaatagtccaggaaaaaaAcaaattaattaatgacctca	20	8	6	7	1	1	1	1	1	0	0	2	3	2	2	2	1	1	0	2	1	8	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:214204970A>C	ENST00000331683.5	+	6	715	c.620A>C	c.(619-621)aAc>aCc	p.N207T	SPAG16_ENST00000272898.7_Missense_Mutation_p.N207T|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000413312.1_Missense_Mutation_p.N176T|SPAG16_ENST00000447990.1_Missense_Mutation_p.N207T|SPAG16_ENST00000374309.3_Missense_Mutation_p.N113T	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	207					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		CAGGAAAAAAACAAATTAATT	0.279																																					p.N207T		.											.	SPAG16-188	0			c.A620C						.						36	38	37					2																	214204970		2203	4296	6499	SO:0001583	missense	79582	exon6			AAAAAAACAAATT	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.620A>C	2.37:g.214204970A>C	ENSP00000332592:p.Asn207Thr	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_024532	0	0	2	2	0	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	A	14.13	2.443855	0.43429	.	.	ENSG00000144451	ENST00000331683;ENST00000413312;ENST00000272898;ENST00000447990;ENST00000374309	T;T	0.58506	0.36;0.33	5.96	3.55	0.40652	.	0.097154	0.64402	N	0.000002	T	0.55433	0.1920	M	0.67700	2.07	0.35052	D	0.760759	B;B;B;B;B	0.28512	0.004;0.214;0.176;0.008;0.004	B;B;B;B;B	0.29077	0.004;0.098;0.046;0.019;0.004	T	0.62909	-0.6754	10	0.62326	D	0.03	.	11.639	0.51222	0.718:0.282:0.0:0.0	.	113;58;176;147;207	B4DYB5;Q8N0X2-2;Q8N0X2-3;Q4G1A2;Q8N0X2	.;.;.;.;SPG16_HUMAN	T	207;176;207;207;113	ENSP00000332592:N207T;ENSP00000363428:N113T	ENSP00000272898:N207T	N	+	2	0	SPAG16	213913215	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.005000	0.49521	0.479000	0.27511	-0.313000	0.08912	AAC	.		0.279	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		C	214204970	A	C	214204970	3	2	9	1	0	0	0	0	1	0	0	0	15010	43	2	5	658	5	SPAG16	2	214204970	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	16423665	214204970	28994403	11	672											
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111983130	111983130	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatatgtatgtgcaggaatTagaagtccaaagaaagtaaa	20	9	9	3	0	0	2	0	0	0	2	1	3	1	3	1	1	1	3	1	1	10	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr3:111983130T>C	ENST00000305815.5	-	9	1191	c.939A>G	c.(937-939)ctA>ctG	p.L313L	SLC9C1_ENST00000487372.1_Intron	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	313					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										GTGCAGGAATTAGAAGTCCAA	0.244																																					p.L313L		.											.	.	0			c.A939G						.						27	29	28					3																	111983130		2171	4252	6423	SO:0001819	synonymous_variant	285335	exon9			AGGAATTAGAAGT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.939A>G	3.37:g.111983130T>C		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_183061	0	0	0	0	0	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																			.		0.244	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		C	111983130	T	C	111983130	2	2	9	1	0	0	0	0	0	0	0	1	14742	1741	61	3		3	SLC9A10	3	111983130	Silent	SNP	T	TCGA-A4-7828-01A-11D-2136-08		111983130	86039300	12	673											
CLCN2	1181	hgsc.bcm.edu	37	chr3	184075764	184075764	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agttacctctttgccaagcgGcatcccgctgcctagggcgc	6	9	11	15	3	1	0	0	0	1	0	2	0	2	0	4	2	4	3	4	2	3	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr3:184075764G>A	ENST00000265593.4	-	5	772	c.601C>T	c.(601-603)Ccg>Tcg	p.P201S	CLCN2_ENST00000457512.1_Missense_Mutation_p.P201S|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000434054.2_Missense_Mutation_p.P157S|CLCN2_ENST00000423355.2_5'UTR|CLCN2_ENST00000344937.7_Missense_Mutation_p.P201S	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	201					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	TTGCCAAGCGGCATCCCGCTG	0.597																																					p.P201S		.											.	CLCN2-90	0			c.C601T						.						57	55	56					3																	184075764		2203	4300	6503	SO:0001583	missense	1181	exon5			CAAGCGGCATCCC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.601C>T	3.37:g.184075764G>A	ENSP00000265593:p.Pro201Ser	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	100	5	NM_001171087	0	0	0	0	0	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	37	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	g	21.3	4.123267	0.77436	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87	4.58	4.58	0.56647	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.92450	0.7603	L	0.31926	0.97	0.80722	D	1	D;D;P;D;D	0.89917	0.999;1.0;0.915;0.976;0.992	D;D;P;P;D	0.97110	0.994;1.0;0.851;0.9;0.932	D	0.93567	0.6900	10	0.87932	D	0	-17.2281	16.3077	0.82855	0.0:0.0:1.0:0.0	.	201;157;201;201;201	B4DYE3;E9PBD9;E9PCD2;P51788-3;P51788	.;.;.;.;CLCN2_HUMAN	S	201;201;157;201	ENSP00000265593:P201S;ENSP00000345056:P201S;ENSP00000400425:P157S;ENSP00000391928:P201S	ENSP00000265593:P201S	P	-	1	0	CLCN2	185558458	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	9.595000	0.98260	2.378000	0.81104	0.561000	0.74099	CCG	.		0.597	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			A	184075764	G	A	184075764	3	1	9	1	0	0	0	0	1	0	0	0	3469	1203	42	2	2175	2	CLCN2	3	184075764	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	72092634	184075764	13946666	13	674											
POLR2B	5431	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	57888371	57888373	+	In_Frame_Del	DEL	AAG	AAG	-																															gtctaaaaaaggatttgatcAagaagaagtttttgagaagc																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr4:57888371_57888373delAAG	ENST00000381227.1	+	19	2887_2889	c.2474_2476delAAG	c.(2473-2478)caagaa>caa	p.E827del	POLR2B_ENST00000441246.2_In_Frame_Del_p.E820del|POLR2B_ENST00000431623.2_In_Frame_Del_p.E752del|POLR2B_ENST00000314595.5_In_Frame_Del_p.E827del			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	827					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GGATTTGATCAAGAAGAAGTTTT	0.34																																					p.825_826del		.											.	POLR2B-92	0			c.2474_2476del						.																																			SO:0001651	inframe_deletion	5431	exon18			.		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2474_2476delAAG	4.37:g.57888377_57888379delAAG	ENSP00000370625:p.Glu827del	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	81	13	NM_000938	0	0	0	0	0	A8K1A8|Q8IZ61	In_Frame_Del	DEL	ENST00000381227.1	37	CCDS3511.1																																																																																			.		0.34	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		-	57888373	AAG	-	57888371	7	5	9	1	0	1	0	1	0	0	0	0	12241	130	5	0	2544	0	POLR2B	4	57888371	In_Frame_Del	DEL	AAG	TCGA-A4-7828-01A-11D-2136-08		57888371	133265905	14	675											
ITGA2	3673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	52366069	52366069	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcaagcacagagttgcccCgagcacatcatttatataca	15	9	6	11	1	2	1	2	0	0	1	2	2	2	1	2	0	4	3	2	0	5	5	rs142557473		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:52366069C>G	ENST00000296585.5	+	17	2357	c.2214C>G	c.(2212-2214)ccC>ccG	p.P738P		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	738					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				AGAGTTGCCCCGAGCACATCA	0.398																																					p.P738P		.											.	ITGA2-226	0			c.C2214G						.						72	71	71					5																	52366069		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon17			TTGCCCCGAGCAC		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2214C>G	5.37:g.52366069C>G		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	114	34	NM_002203	0	0	6	11	5	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			C|1.000;T|0.000		0.398	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		G	52366069	C	G	52366069	2	3	9	1	0	0	0	0	0	0	0	1	7896	639	23	4		4	ITGA2	5	52366069	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08		52366069	128549191	15	676											
CMYA5	202333	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	79034426	79034426	+	Frame_Shift_Del	DEL	G	G	-																															accaaccgatagctgcagaaGgggaaatttggggaaagttt																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:79034426delG	ENST00000446378.2	+	2	9869	c.9838delG	c.(9838-9840)gggfs	p.G3280fs		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3280					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AGCTGCAGAAGGGGAAATTTG	0.453																																					p.G3280fs		.											.	CMYA5-77	0			c.9838delG						.						104	100	101					5																	79034426		1865	4114	5979	SO:0001589	frameshift_variant	202333	exon2			.	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9838delG	5.37:g.79034426delG	ENSP00000394770:p.Gly3280fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	144	25	NM_153610	0	0	0	0	0	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Frame_Shift_Del	DEL	ENST00000446378.2	37	CCDS47238.1																																																																																			.		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		-	79034426	G	-	79034426	7	5	9	1	0	1	0	1	0	0	0	0	3596	1000	35	0	9844	0	CMYA5	5	79034426	Frame_Shift_Del	DEL	G	TCGA-A4-7828-01A-11D-2136-08	26668357	79034426	101880834	16	677											
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128797258	128797258	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctcgggacctgtacctgctGctccggagagacggccgctt	5	9	13	14	4	1	1	0	0	1	1	3	4	2	3	4	3	3	4	4	3	1	2	rs147557427	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:128797258G>C	ENST00000274487.4	+	2	682	c.537G>C	c.(535-537)ctG>ctC	p.L179L	ADAMTS19-AS1_ENST00000502827.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	179	Pro-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TGTACCTGCTGCTCCGGAGAG	0.741													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		10775	0		0	False		,,,				2504	0				p.L179L		.											.	ADAMTS19-295	0			c.G537C						.	G		59,3989		0,59,1965	4	5	5		537	1.5	1	5	dbSNP_134	5	2,8144		0,2,4071	no	coding-synonymous	ADAMTS19	NM_133638.3		0,61,6036	CC,CG,GG		0.0246,1.4575,0.5002		179/1208	128797258	61,12133	2024	4073	6097	SO:0001819	synonymous_variant	171019	exon2			CCTGCTGCTCCGG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.537G>C	5.37:g.128797258G>C		Somatic	7	1		WXS	Illumina HiSeq	Phase_I	7	4	NM_133638	0	0	0	0	0		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			G|0.993;C|0.007		0.741	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128797258	G	C	128797258	2	2	9	1	0	0	0	0	0	0	0	1	264	1306	46	4		4	ADAMTS19	5	128797258	Silent	SNP	G	TCGA-A4-7828-01A-11D-2136-08	49762832	128797258	52118002	17	678											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139828840	139828840	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tacttgaagctggtgcagatCaagagcacaaaacagatgag	16	7	11	7	0	1	5	1	2	0	3	1	5	1	5	0	1	5	3	0	1	5	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:139828840C>G	ENST00000360839.2	+	7	1346	c.1192C>G	c.(1192-1194)Caa>Gaa	p.Q398E	ANKHD1_ENST00000394723.3_Missense_Mutation_p.Q398E|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.Q398E|ANKHD1_ENST00000394722.3_Missense_Mutation_p.Q387E|ANKHD1_ENST00000297183.6_Missense_Mutation_p.Q398E	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	398						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTGCAGATCAAGAGCACAA	0.348																																					p.Q398E		.											.	ANKHD1-185	0			c.C1192G						.						88	75	80					5																	139828840		2203	4300	6503	SO:0001583	missense	54882	exon7			GCAGATCAAGAGC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1192C>G	5.37:g.139828840C>G	ENSP00000354085:p.Gln398Glu	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_024668	0	0	10	10	0	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470542	0.63625	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	T;T;T;T;T;T	0.71103	-0.54;-0.54;2.43;2.43;2.43;-0.54	5.97	5.97	0.96955	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.73032	0.3535	N	0.11106	0.095	0.80722	D	1	B;D;D;B;B	0.59357	0.185;0.985;0.985;0.214;0.317	B;D;D;B;B	0.73708	0.205;0.981;0.981;0.089;0.205	T	0.74680	-0.3584	10	0.38643	T	0.18	.	20.4324	0.99085	0.0:1.0:0.0:0.0	.	398;398;398;387;398	Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.;.;ANKH1_HUMAN;.;.	E	398;412;398;398;398;398;387;398	ENSP00000354085:Q398E;ENSP00000297183:Q398E;ENSP00000394489:Q398E;ENSP00000378212:Q398E;ENSP00000378211:Q387E;ENSP00000432016:Q398E	ENSP00000432016:Q398E	Q	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139809024	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.833000	0.97629	0.585000	0.79938	CAA	.		0.348	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139828840	C	G	139828840	3	3	9	1	0	0	0	0	1	0	0	0	628	827	29	4	1218	4	ANKHD1	5	139828840	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	11031582	139828840	41086420	18	679											
PCDHAC1	56135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140307713	140307713	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcagatcagtgaataccaAgtcctgatcacggcctcaga	13	7	10	11	1	3	4	3	2	0	2	4	5	4	4	3	1	2	1	3	1	3	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:140307713A>G	ENST00000253807.2	+	1	1236	c.1236A>G	c.(1234-1236)caA>caG	p.Q412Q	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.Q412Q|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	412	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAATACCAAGTCCTGATCA	0.517																																					p.Q412Q		.											.	PCDHAC1-28	0			c.A1236G						.						81	79	80					5																	140307713		2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			ATACCAAGTCCTG	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"Cadherins / Protocadherins : Clustered"	8676	other	complex locus constituent	"PCDH-ALPHA-C1"	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1236A>G	5.37:g.140307713A>G		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	99	22	NM_031882	0	0	0	0	0	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			.		0.517	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		G	140307713	A	G	140307713	2	3	9	1	0	0	0	0	0	0	0	1	11558	69	3	3		3	PCDHAC1	5	140307713	Silent	SNP	A	TCGA-A4-7828-01A-11D-2136-08	478873	140307713	40607547	19	680											
DOCK2	1794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	169446069	169446069	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccataccaatcttcttcgAcatgatgctgtgtgaatatc	11	13	6	11	1	2	2	0	2	2	0	4	3	2	2	2	0	2	1	2	0	4	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:169446069A>G	ENST00000256935.8	+	33	3418	c.3338A>G	c.(3337-3339)gAc>gGc	p.D1113G	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Missense_Mutation_p.D174G|DOCK2_ENST00000520908.1_Missense_Mutation_p.D605G	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1113	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATCTTCTTCGACATGATGCTG	0.463																																					p.D1113G		.											.	DOCK2-97	0			c.A3338G						.						180	180	180					5																	169446069		2203	4300	6503	SO:0001583	missense	1794	exon33			TCTTCGACATGAT	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3338A>G	5.37:g.169446069A>G	ENSP00000256935:p.Asp1113Gly	Somatic	350	1		WXS	Illumina HiSeq	Phase_I	308	74	NM_004946	0	0	3	3	0	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.613086	0.87258	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.58060	0.36;0.36;0.36	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.66799	0.2826	M	0.91510	3.215	0.58432	D	0.999998	D;P	0.53151	0.958;0.688	P;B	0.46825	0.528;0.138	T	0.76432	-0.2961	10	0.56958	D	0.05	.	14.3619	0.66779	1.0:0.0:0.0:0.0	.	605;1113	E7ERW7;Q92608	.;DOCK2_HUMAN	G	1113;605;174	ENSP00000256935:D1113G;ENSP00000429283:D605G;ENSP00000438827:D174G	ENSP00000256935:D1113G	D	+	2	0	DOCK2	169378647	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.218000	0.95166	1.795000	0.52594	0.528000	0.53228	GAC	.		0.463	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169446069	A	G	169446069	3	3	9	1	0	0	0	0	1	0	0	0	4698	275	10	3	3468	3	DOCK2	5	169446069	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	29138356	169446069	11469191	20	681											
PKD1L1	168507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	47944905	47944905	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggcaaacacagttccatTtgtgtagacagagacggctg	11	10	12	8	1	0	2	0	0	0	2	1	3	1	2	1	2	1	4	1	2	2	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:47944905T>A	ENST00000289672.2	-	11	1590	c.1540A>T	c.(1540-1542)Aat>Tat	p.N514Y		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	514	PKD 1. {ECO:0000255|PROSITE- ProRule:PRU00151}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACAGTTCCATTTGTGTAGACA	0.443																																					p.N514Y		.											.	PKD1L1-145	0			c.A1540T						.						139	128	132					7																	47944905		2203	4300	6503	SO:0001583	missense	168507	exon11			TTCCATTTGTGTA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1540A>T	7.37:g.47944905T>A	ENSP00000289672:p.Asn514Tyr	Somatic	221	0		WXS	Illumina HiSeq	Phase_I	174	37	NM_138295	0	0	0	0	0	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518459	0.64634	.	.	ENSG00000158683	ENST00000289672	T	0.69435	-0.4	5.38	5.38	0.77491	PKD/Chitinase domain (1);	0.178382	0.36519	N	0.002559	T	0.72260	0.3438	L	0.29908	0.895	0.32501	N	0.53884	D	0.89917	1.0	D	0.75484	0.986	T	0.78435	-0.2205	10	0.59425	D	0.04	-24.3676	13.6779	0.62465	0.0:0.0:0.0:1.0	.	514	Q8TDX9	PK1L1_HUMAN	Y	514	ENSP00000289672:N514Y	ENSP00000289672:N514Y	N	-	1	0	PKD1L1	47911430	0.998000	0.40836	0.991000	0.47740	0.970000	0.65996	2.029000	0.41098	2.185000	0.69588	0.529000	0.55759	AAT	.		0.443	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47944905	T	A	47944905	3	1	9	1	0	0	0	0	1	0	0	0	11990	1841	64	5	7197	5	PKD1L1	7	47944905	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08		47944905	111193758	21	682											
ZKSCAN5	23660	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99129235	99129235	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcatcagagcgtgcacaGtggggagagacccttcaagt	11	7	13	10	1	3	2	3	0	0	2	3	4	3	3	1	2	3	2	1	2	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:99129235G>A	ENST00000394170.2	+	7	2134	c.1883G>A	c.(1882-1884)aGt>aAt	p.S628N	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.S628N|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.S628N	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	628					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AGCGTGCACAGTGGGGAGAGA	0.557																																					p.S628N		.											.	ZKSCAN5-91	0			c.G1883A						.						80	70	74					7																	99129235		2203	4300	6503	SO:0001583	missense	23660	exon7			TGCACAGTGGGGA	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"Zinc fingers, C2H2-type", "-", "-", "-"	12867	protein-coding gene	gene with protein product		611272	"zinc finger protein homologous to Zfp95 in mouse", "zinc finger protein 95 homolog (mouse)"	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.1883G>A	7.37:g.99129235G>A	ENSP00000377725:p.Ser628Asn	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	85	5	NM_145102	0	0	10	10	0	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852959	0.71719	.	.	ENSG00000196652	ENST00000537357;ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.19394	2.15;2.15;2.15	5.23	4.29	0.51040	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.091827	0.48767	D	0.000175	T	0.29389	0.0732	L	0.46885	1.475	0.35690	D	0.814761	P;P	0.49185	0.92;0.92	P;P	0.53313	0.598;0.723	T	0.14090	-1.0485	10	0.52906	T	0.07	.	11.8173	0.52218	0.0:0.2653:0.7347:0.0	.	628;628	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	N	628	ENSP00000322872:S628N;ENSP00000392104:S628N;ENSP00000377725:S628N	ENSP00000322872:S628N	S	+	2	0	ZKSCAN5	98967171	0.999000	0.42202	0.986000	0.45419	0.987000	0.75469	3.694000	0.54742	2.894000	0.99253	0.591000	0.81541	AGT	.		0.557	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		A	99129235	G	A	99129235	3	1	9	1	0	0	0	0	1	0	0	0	17722	1029	36	2	1905	2	ZKSCAN5	7	99129235	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	51184330	99129235	60009428	22	683											
VGF	7425	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	100806695	100806695	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccgcttccgcttctccTccacctcctcgatgatgctg	3	14	6	18	3	2	1	0	1	2	0	8	2	6	1	6	0	1	3	6	0	0	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:100806695T>A	ENST00000249330.2	-	2	1669	c.1430A>T	c.(1429-1431)gAg>gTg	p.E477V	VGF_ENST00000445482.2_Missense_Mutation_p.E477V	NM_003378.3	NP_003369.2	O15240	VGF_HUMAN	VGF nerve growth factor inducible	477					defense response to bacterium (GO:0042742)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|ovarian follicle development (GO:0001541)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to dietary excess (GO:0002021)|response to insulin (GO:0032868)|sexual reproduction (GO:0019953)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				cervix(1)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	9	Lung NSC(181;0.168)|all_lung(186;0.215)					CCGCTTCTCCTCCACCTCCTC	0.697																																					p.E477V		.											.	VGF-90	0			c.A1430T						.						58	61	60					7																	100806695		2203	4300	6503	SO:0001583	missense	7425	exon2			TTCTCCTCCACCT	Y12661	CCDS5712.1	7q22	2008-07-18			ENSG00000128564	ENSG00000128564			12684	protein-coding gene	gene with protein product	"neuro-endocrine specific protein VGF"	602186				9344675	Standard	NM_003378		Approved		uc003uxx.4	O15240	OTTHUMG00000157109	ENST00000249330.2:c.1430A>T	7.37:g.100806695T>A	ENSP00000249330:p.Glu477Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	56	15	NM_003378	0	0	0	0	0	Q9UDW8	Missense_Mutation	SNP	ENST00000249330.2	37	CCDS5712.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.386102	0.61956	.	.	ENSG00000128564	ENST00000249330;ENST00000445482	.	.	.	4.41	4.41	0.53225	.	0.000000	0.48286	U	0.000186	T	0.56307	0.1976	N	0.24115	0.695	0.40841	D	0.983675	D	0.76494	0.999	D	0.80764	0.994	T	0.61720	-0.7005	9	0.87932	D	0	-7.6164	10.0532	0.42228	0.0:0.0:0.0:1.0	.	477	O15240	VGF_HUMAN	V	477	.	ENSP00000249330:E477V	E	-	2	0	VGF	100593415	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.280000	0.51677	1.650000	0.50662	0.449000	0.29647	GAG	.		0.697	VGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347462.1	NM_003378		A	100806695	T	A	100806695	3	1	9	1	0	0	0	0	1	0	0	0	17190	1551	54	5	421	5	VGF	7	100806695	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	1677460	100806695	58331968	23	684											
TBXAS1	6916	hgsc.bcm.edu;bcgsc.ca	37	chr7	139719838	139719838	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttaggtaccgctgcagcTagaatccaaatctgccctag	11	11	8	11	1	1	1	0	0	1	1	2	1	2	1	3	1	4	4	3	1	6	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:139719838T>C	ENST00000411653.1	+	12	1505	c.1378T>C	c.(1378-1380)Tag>Cag	p.*460Q	TBXAS1_ENST00000436047.2_Missense_Mutation_p.L515P|TBXAS1_ENST00000448866.1_Missense_Mutation_p.L514P|TBXAS1_ENST00000425687.1_Missense_Mutation_p.L447P|TBXAS1_ENST00000263552.6_Missense_Mutation_p.L515P|TBXAS1_ENST00000414508.2_Nonstop_Mutation_p.*461Q|TBXAS1_ENST00000458722.1_Missense_Mutation_p.L560P|TBXAS1_ENST00000416849.2_Missense_Mutation_p.L561P|TBXAS1_ENST00000336425.5_Missense_Mutation_p.L514P			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	0					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	CCGCTGCAGCTAGAATCCAAA	0.453																																					p.X461Q		.											.	TBXAS1-155	0			c.T1381C						.						86	87	86					7																	139719838		2203	4300	6503	SO:0001578	stop_lost	6916	exon12			TGCAGCTAGAATC	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"Cytochrome P450s"	11609	protein-coding gene	gene with protein product	"cytochrome P450, family 5, subfamily A, polypeptide 1"	274180	"thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000411653.1:c.1378T>C	7.37:g.139719838T>C	ENSP00000411326:p.*460Glnext*6	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_030984	0	0	16	16	0	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000411653.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.44|16.44	3.125072|3.125072	0.56721|0.56721	.|.	.|.	ENSG00000059377|ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000448866;ENST00000458722|ENST00000414508;ENST00000411653	T;T;T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32;-0.32|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.70657|.	0.3249|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.999;1.0;1.0;0.996;0.996|.	T|.	0.69914|.	-0.5016|.	9|.	0.87932|.	D|.	0|.	.|.	14.324|14.324	0.66507|0.66507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	495;561;447;515;514|.	B4DVP1;E7EP08;E7ESB5;Q53F23;P24557|.	.;.;.;.;THAS_HUMAN|.	P|Q	447;515;514;561;515;514;560|461;460	ENSP00000388736:L447P;ENSP00000263552:L515P;ENSP00000338087:L514P;ENSP00000389414:L561P;ENSP00000392361:L515P;ENSP00000402536:L514P;ENSP00000411274:L560P|.	ENSP00000263552:L515P|.	L|X	+|+	2|1	0|0	TBXAS1|TBXAS1	139366307|139366307	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.872000|0.872000	0.50106|0.50106	5.929000|5.929000	0.70096|0.70096	2.187000|2.187000	0.69744|0.69744	0.459000|0.459000	0.35465|0.35465	CTA|TAG	.		0.453	TBXAS1-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348377.1			C	139719838	T	C	139719838	4	2	9	1	0	0	0	0	0	0	0	0	15696	1535	53	3	1736	3	TBXAS1	7	139719838	Nonstop_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	38913143	139719838	19418825	24	685											
CPA6	57094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	68397000	68397000	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caacatttttctcatggctgGgtcactcttatatgttagaa	10	16	7	8	0	3	1	2	0	2	1	4	1	3	1	0	2	1	2	0	2	5	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr8:68397000G>A	ENST00000297770.4	-	7	876	c.661C>T	c.(661-663)Cca>Tca	p.P221S	CPA6_ENST00000297769.4_Missense_Mutation_p.P73S|CPA6_ENST00000518549.1_Missense_Mutation_p.P221S	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	221						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			CTCATGGCTGGGTCACTCTTA	0.353																																					p.P221S		.											.	CPA6-92	0			c.C661T						.						92	81	84					8																	68397000		2203	4300	6503	SO:0001583	missense	57094	exon7			TGGCTGGGTCACT	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.661C>T	8.37:g.68397000G>A	ENSP00000297770:p.Pro221Ser	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	85	21	NM_020361	0	0	0	0	0	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	37	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689277	0.29962	.	.	ENSG00000165078	ENST00000297769;ENST00000297770;ENST00000518549	T;T;T	0.10860	2.83;2.83;2.83	5.25	4.36	0.52297	Peptidase M14, carboxypeptidase A (2);	0.112178	0.64402	D	0.000006	T	0.08980	0.0222	L	0.28115	0.83	0.44587	D	0.997554	P;P;B	0.48230	0.907;0.537;0.003	B;B;B	0.41691	0.364;0.203;0.013	T	0.26573	-1.0099	10	0.32370	T	0.25	.	13.3643	0.60674	0.0:0.1588:0.8412:0.0	.	221;73;221	Q8N4T0-2;Q8N4T0-3;Q8N4T0	.;.;CBPA6_HUMAN	S	73;221;221	ENSP00000297769:P73S;ENSP00000297770:P221S;ENSP00000431112:P221S	ENSP00000297769:P73S	P	-	1	0	CPA6	68559554	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.498000	0.66931	1.306000	0.44926	0.643000	0.83706	CCA	.		0.353	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		A	68397000	G	A	68397000	3	1	9	1	0	0	0	0	1	0	0	0	3800	1232	43	2	672	2	CPA6	8	68397000	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		68397000	77967022	25	686											
HEATR7A	727957	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr8	145267981	145267981	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccctgcacgtgctgctcCgcagcctgctgatctaacgg	5	9	11	16	3	1	1	0	1	1	0	2	1	2	1	3	1	7	5	3	1	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr8:145267981C>T	ENST00000528919.1	+	12	1262				MROH1_ENST00000398656.4_Intron|MROH1_ENST00000423230.2_Missense_Mutation_p.P409L|MROH1_ENST00000326134.5_Intron|MROH1_ENST00000534366.1_Intron|MROH1_ENST00000527071.1_Intron	NM_032450.2	NP_115826	Q8NDA8	MROH1_HUMAN	maestro heat-like repeat family member 1																		CGTGCTGCTCCGCAGCCTGCT	0.557																																					p.P409L		.											.	.	0			c.C1226T						.						93	104	100					8																	145267981		2144	4245	6389	SO:0001627	intron_variant	727957	exon13			CTGCTCCGCAGCC		CCDS47938.1, CCDS47939.1, CCDS75803.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000179832	ENSG00000179832		"maestro heat-like repeat containing"	26958	protein-coding gene	gene with protein product			"HEAT repeat containing 7A"	HEATR7A		11347906	Standard	NM_032450		Approved	KIAA1833	uc003zbk.4	Q8NDA8	OTTHUMG00000165781	ENST00000528919.1:c.1142-7522C>T	8.37:g.145267981C>T		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	118	21	NM_001099280	0	0	1	1	0	C9JWM5|D3DWL5|Q0P612|Q569G6|Q6NVW4|Q8N230|Q8NAD1|Q8ND95|Q96JJ4	Missense_Mutation	SNP	ENST00000528919.1	37	CCDS47938.1	.	.	.	.	.	.	.	.	.	.	C	2.586	-0.296322	0.05532	.	.	ENSG00000179832	ENST00000423230	T	0.15718	2.4	0.818	-1.64	0.08318	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40627	-0.9553	8	0.13470	T	0.59	.	1.5793	0.02631	0.3347:0.385:0.0:0.2803	.	409	Q8NDA8-4	.	L	409	ENSP00000388174:P409L	ENSP00000388174:P409L	P	+	2	0	HEATR7A	145339969	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.583000	0.23849	-0.788000	0.04504	0.460000	0.39030	CCG	.		0.557	MROH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386183.1	NM_032450		T	145267981	C	T	145267981	1	4	9	0	1	0	0	0	0	0	0	0	7055	652	23	1		1	HEATR7A	8	145267981	Intron	SNP	C	TCGA-A4-7828-01A-11D-2136-08	76870981	145267981	1096041	26	687											
WNK2	65268	hgsc.bcm.edu	37	chr9	96055159	96055159	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtcggcgtgggcgagccCgtgtccagcgactctgggga	5	6	19	11	5	1	0	0	0	1	0	3	4	2	1	2	5	2	0	2	5	0	0	rs56125631	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr9:96055159C>T	ENST00000297954.4	+	23	5523	c.5523C>T	c.(5521-5523)ccC>ccT	p.P1841P	WNK2_ENST00000349097.3_Silent_p.P1453P|WNK2_ENST00000356055.3_Silent_p.P168P|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000395477.2_Silent_p.P1804P|WNK2_ENST00000427277.2_Silent_p.P1416P	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1841					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TGGGCGAGCCCGTGTCCAGCG	0.726													C|||	34	0.00678914	0.0234	0.0043	5008	,	,		12809	0		0	False		,,,				2504	0				p.P1804P		.											.	WNK2-765	0			c.C5412T						.	C		78,4248		0,78,2085	7	8	8		5412	-10.5	0	9	dbSNP_129	8	0,8488		0,0,4244	no	coding-synonymous	WNK2	NM_006648.3		0,78,6329	TT,TC,CC		0.0,1.8031,0.6087		1804/2218	96055159	78,12736	2163	4244	6407	SO:0001819	synonymous_variant	65268	exon22			CGAGCCCGTGTCC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5523C>T	9.37:g.96055159C>T		Somatic	10	1		WXS	Illumina HiSeq	Phase_I	5	3	NM_006648	0	0	0	0	0	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.180|2.180	-0.387838|-0.387838	0.04932|0.04932	0.018031|0.018031	0.0|0.0	ENSG00000165238|ENSG00000165238	ENST00000432730;ENST00000448251;ENST00000453718|ENST00000411624	T;T;D|.	0.83075|.	-0.42;-0.66;-1.68|.	5.24|5.24	-10.5|-10.5	0.00291|0.00291	.|.	0.486738|.	0.22537|.	N|.	0.058779|.	T|T	0.20210|0.20210	0.0486|0.0486	.|.	.|.	.|.	0.26704|0.26704	N|N	0.971117|0.971117	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39313|0.39313	-0.9620|-0.9620	7|4	0.48119|.	T|.	0.1|.	.|.	13.7224|13.7224	0.62735|0.62735	0.0:0.1023:0.3462:0.5515|0.0:0.1023:0.3462:0.5515	rs56125631;rs61743448|rs56125631;rs61743448	.|.	.|.	.|.	L|C	1800;601;326|1408	ENSP00000415038:P1800L;ENSP00000390441:P601L;ENSP00000413325:P326L|.	ENSP00000415038:P1800L|.	P|R	+|+	2|1	0|0	WNK2|WNK2	95094980|95094980	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.299000|0.299000	0.27559|0.27559	-0.879000|-0.879000	0.04188|0.04188	-2.637000|-2.637000	0.00431|0.00431	-0.997000|-0.997000	0.02515|0.02515	CCG|CGT	C|0.986;T|0.014		0.726	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96055159	C	T	96055159	2	4	9	1	0	0	0	0	0	0	0	1	17411	639	23	1		1	WNK2	9	96055159	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08		96055159	45158272	27	688											
CCDC7	79741	broad.mit.edu	37	chr10	32854549	32854549	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aattgaaacaggctttacagGtaaaggatgtcatgtttctt	13	14	9	5	0	2	1	1	1	1	0	2	2	2	2	0	3	2	3	0	3	5	6			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr10:32854549G>T	ENST00000362006.5	+	15	1740		c.e15+1		C10orf68_ENST00000572165.1_Splice_Site|C10orf68_ENST00000375030.2_5'Flank|CCDC7_ENST00000277657.6_Splice_Site|C10orf68_ENST00000375028.3_5'Flank	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7											NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				GGCTTTACAGGTAAAGGATGT	0.328																																					.													.	CCDC7-90	0			c.1197+1G>T						.						44	43	44					10																	32854549		2203	4297	6500	SO:0001630	splice_region_variant	221016	exon15			TTACAGGTAAAGG	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 68"	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.1197+1G>T	10.37:g.32854549G>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_145023	0	0	0	0	0	Q5VW55|Q8IVQ0|Q8NEQ0	Splice_Site	SNP	ENST00000362006.5	37	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.262780	0.59431	.	.	ENSG00000216937	ENST00000277657;ENST00000362006;ENST00000435402	.	.	.	4.97	4.97	0.65823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7259	0.62759	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC7	32894555	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	3.819000	0.55686	2.276000	0.75962	0.563000	0.77884	.	.		0.328	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	Intron	T	32854549	G	T	32854549	5	4	9	1	0	0	0	0	0	0	1	0	2848	1275	44	4	1252	4	CCDC7	10	32854549	Splice_Site	SNP	G	TCGA-A4-7828-01A-11D-2136-08		32854549	102680198	28	689											
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999189	46999190	+	Frame_Shift_Del	DEL	CA	CA	-																															aatgtgtccaccatgggcggCagtgacctgtgtcgcctgcg																								rs71185249|rs3127678|rs3127679	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr10:46999189_46999190delCA	ENST00000374317.1	+	3	582_583	c.309_310delCA	c.(307-312)ggcagtfs	p.S104fs	GPRIN2_ENST00000374314.4_Frame_Shift_Del_p.S104fs	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	104			S -> G (in dbSNP:rs3127679). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581}.							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CCATGGGCGGCAGTGACCTGTG	0.653																																					p.103_104del		.											.	GPRIN2-90	0			c.309_310del						.																																			SO:0001589	frameshift_variant	9721	exon3			.	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.309_310delCA	10.37:g.46999189_46999190delCA	ENSP00000363436:p.Ser104fs	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	68	11	NM_014696	0	0	0	0	0	Q5SVF0	Frame_Shift_Del	DEL	ENST00000374317.1	37	CCDS31192.1																																																																																			.		0.653	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		-	46999190	CA	-	46999189	7	5	9	1	0	1	0	1	0	0	0	0	6751	697	25	0	311	0	GPRIN2	10	46999189	Frame_Shift_Del	DEL	CA	TCGA-A4-7828-01A-11D-2136-08	14144640	46999189	88535558	29	690											
ZNF488	118738	broad.mit.edu	37	chr10	48371023	48371023	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgagcaaagaagcgcctttaGcaaaccaaccaagcgaccag	16	4	9	12	2	0	2	0	1	0	1	0	3	0	2	4	0	6	2	4	0	6	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr10:48371023G>T	ENST00000395702.2	+	2	718	c.491G>T	c.(490-492)aGc>aTc	p.S164I	ZNF488_ENST00000586537.1_Missense_Mutation_p.S57I|ZNF488_ENST00000494156.1_3'UTR			Q96MN9	ZN488_HUMAN	zinc finger protein 488	164					negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte development (GO:0014003)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|ovary(2)	14						AGCGCCTTTAGCAAACCAACC	0.597																																					p.S164I													.	ZNF488-91	0			c.G491T						.						68	67	67					10																	48371023		2203	4300	6503	SO:0001583	missense	118738	exon2			CCTTTAGCAAACC	AK056666	CCDS73120.1	10q11.22	2014-04-10			ENSG00000165388	ENSG00000265763		"Zinc fingers, C2H2-type"	23535	protein-coding gene	gene with protein product							Standard	NM_153034		Approved	FLJ32104	uc001jex.3	Q96MN9	OTTHUMG00000188322	ENST00000395702.2:c.491G>T	10.37:g.48371023G>T	ENSP00000379054:p.Ser164Ile	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	88	5	NM_153034	0	0	0	0	0	Q05CE0	Missense_Mutation	SNP	ENST00000395702.2	37	CCDS7217.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.817368	0.70912	.	.	ENSG00000165388	ENST00000395702	T	0.31247	1.5	5.55	5.55	0.83447	.	0.159805	0.56097	D	0.000026	T	0.47710	0.1460	L	0.55481	1.735	0.30813	N	0.738595	D	0.71674	0.998	P	0.62014	0.897	T	0.53005	-0.8499	10	0.72032	D	0.01	.	14.1431	0.65331	0.0:0.1498:0.8502:0.0	.	164	Q96MN9	ZN488_HUMAN	I	164	ENSP00000379054:S164I	ENSP00000379054:S164I	S	+	2	0	ZNF488	47991029	1.000000	0.71417	0.997000	0.53966	0.374000	0.29953	4.688000	0.61715	2.613000	0.88420	0.561000	0.74099	AGC	.		0.597	ZNF488-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314632.1	NM_153034		T	48371023	G	T	48371023	3	4	9	1	0	0	0	0	1	0	0	0	17972	971	34	4	493	4	ZNF488	10	48371023	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	1371834	48371023	87163724	30	691											
C10orf137	26098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	127442312	127442312	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgcttctcctagtctcaAtcgagaagaagtgatgaaac	13	11	9	8	1	2	5	1	3	2	2	5	6	2	5	1	0	2	1	1	0	5	2	rs199695348		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr10:127442312A>G	ENST00000356792.4	+	24	3675	c.3443A>G	c.(3442-3444)aAt>aGt	p.N1148S	RP11-383C5.7_ENST00000602030.1_RNA|RP11-383C5.7_ENST00000594025.1_RNA|RP11-383C5.7_ENST00000593871.1_RNA|RP11-383C5.7_ENST00000601363.1_RNA|C10orf137_ENST00000337623.3_Missense_Mutation_p.N1114S	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		1148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				CCTAGTCTCAATCGAGAAGAA	0.393																																					p.N1148S		.											.	C10orf137-590	0			c.A3443G						.						153	143	146					10																	127442312		2203	4300	6503	SO:0001583	missense	26098	exon24			GTCTCAATCGAGA																												ENST00000356792.4:c.3443A>G	10.37:g.127442312A>G	ENSP00000349244:p.Asn1148Ser	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	120	42	NM_001202438	0	0	4	6	2	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	A	8.698	0.908981	0.17833	.	.	ENSG00000107938	ENST00000356792;ENST00000337623	T;T	0.42131	0.98;0.98	4.89	-2.12	0.07165	.	0.274294	0.39020	N	0.001485	T	0.14313	0.0346	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.18310	0.027;0.013;0.0	B;B;B	0.14578	0.009;0.011;0.003	T	0.26018	-1.0115	10	0.13470	T	0.59	.	6.4393	0.21841	0.5191:0.1277:0.3532:0.0	.	1148;495;1114	Q3B7T1;Q5VZQ1;Q3B7T1-5	EDRF1_HUMAN;.;.	S	1148;1114	ENSP00000349244:N1148S;ENSP00000336727:N1114S	ENSP00000336727:N1114S	N	+	2	0	C10orf137	127432302	0.081000	0.21417	0.000000	0.03702	0.099000	0.18886	1.651000	0.37302	-0.178000	0.10672	-0.274000	0.10170	AAT	A|0.999;G|0.001		0.393	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			G	127442312	A	G	127442312	3	3	9	1	0	0	0	0	1	0	0	0	1598	101	4	3	3431	3	C10orf137	10	127442312	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	79071289	127442312	8092435	31	692											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1268488	1268488	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccacacacgggcggtccctgCcccccagcagtccccacacg	7	3	9	22	3	0	0	0	0	0	0	2	0	2	0	7	2	2	1	7	2	0	0	rs200106077		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr11:1268488C>T	ENST00000529681.1	+	31	10436	c.10378C>T	c.(10378-10380)Ccc>Tcc	p.P3460S	MUC5B_ENST00000447027.1_Missense_Mutation_p.P3463S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3460	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCGGTCCCTGCCCCCCAGCAG	0.672																																					p.P3460S		.											.	.	0			c.C10378T						.						92	127	115					11																	1268488		2115	4227	6342	SO:0001583	missense	727897	exon31			TCCCTGCCCCCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.10378C>T	11.37:g.1268488C>T	ENSP00000436812:p.Pro3460Ser	Somatic	95	2		WXS	Illumina HiSeq	Phase_I	112	13	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	4.064	0.009588	0.07912	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21734	1.99;2.18	2.39	0.0952	0.14484	.	.	.	.	.	T	0.19565	0.0470	L	0.46157	1.445	0.09310	N	1	B;P	0.47841	0.274;0.901	B;P	0.44811	0.2;0.461	T	0.15178	-1.0446	9	0.87932	D	0	.	5.7781	0.18292	0.188:0.6856:0.0:0.1263	.	3988;3463	A7Y9J9;E9PBJ0	.;.	S	3460;3463;3432;3365	ENSP00000436812:P3460S;ENSP00000415793:P3463S	ENSP00000343037:P3432S	P	+	1	0	MUC5B	1225064	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.924000	0.00333	0.339000	0.23719	-0.642000	0.03964	CCC	.		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1268488	C	T	1268488	3	4	9	1	0	0	0	0	1	0	0	0	10004	739	26	2	10509	2	MUC5B	11	1268488	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08		1268488	133738028	32	693											
TCN1	6947	bcgsc.ca	37	chr11	59622265	59622265	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atatatgattgtgagtcaggAggtgtcacagttataggctc	11	13	12	5	0	2	2	2	2	0	0	3	3	2	3	0	3	0	2	0	3	4	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr11:59622265A>G	ENST00000257264.3	-	7	1085	c.981T>C	c.(979-981)ccT>ccC	p.P327P	TCN1_ENST00000532419.1_5'UTR	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	327	Flexible linker.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTGAGTCAGGAGGTGTCACAG	0.393																																					p.P327P													.	TCN1-92	0			c.T981C						.						114	108	110					11																	59622265		2201	4295	6496	SO:0001819	synonymous_variant	6947	exon7			GTCAGGAGGTGTC	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"haptocorin", "haptocorrin"	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.981T>C	11.37:g.59622265A>G		Somatic	94	0		WXS	Illumina HiSeq	Phase_1	150	5	NM_001062	0	0	121	121	0	A8KAC5|Q8WV77	Silent	SNP	ENST00000257264.3	37	CCDS7978.1																																																																																			.		0.393	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		G	59622265	A	G	59622265	2	3	9	1	0	0	0	0	0	0	0	1	15738	291	11	3		3	TCN1	11	59622265	Silent	SNP	A	TCGA-A4-7828-01A-11D-2136-08	58353777	59622265	75384251	33	694											
SLCO2B1	11309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74883496	74883496	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggtttcctcatcgctgccgGtgcagtggccctggctgcca	3	10	14	14	2	1	0	1	0	0	0	3	0	2	0	4	4	3	4	4	4	0	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr11:74883496G>C	ENST00000289575.5	+	7	1249	c.854G>C	c.(853-855)gGt>gCt	p.G285A	SLCO2B1_ENST00000526660.1_3'UTR|SLCO2B1_ENST00000454962.2_Missense_Mutation_p.G58A|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.G263A|SLCO2B1_ENST00000531756.1_Missense_Mutation_p.G30A|SLCO2B1_ENST00000341411.4_Missense_Mutation_p.G58A|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.G141A|SLCO2B1_ENST00000532236.1_Missense_Mutation_p.G169A	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	285					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	ATCGCTGCCGGTGCAGTGGCC	0.557																																					p.G285A		.											.	SLCO2B1-154	0			c.G854C						.						93	81	85					11																	74883496		2200	4293	6493	SO:0001583	missense	11309	exon7			CTGCCGGTGCAGT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.854G>C	11.37:g.74883496G>C	ENSP00000289575:p.Gly285Ala	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	103	30	NM_007256	0	0	10	10	0	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	37	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	G	5.226	0.227121	0.09916	.	.	ENSG00000137491	ENST00000289575;ENST00000341411;ENST00000532236;ENST00000531756;ENST00000525650;ENST00000454962;ENST00000428359	T;T;T;T;T;T;T	0.80033	0.41;-1.33;-1.33;-1.33;-1.33;-1.33;0.41	5.65	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);	0.406164	0.30347	N	0.009837	T	0.67979	0.2951	N	0.26092	0.79	0.19945	N	0.999945	B;B;B;B	0.19935	0.019;0.04;0.016;0.008	B;B;B;B	0.26969	0.034;0.075;0.02;0.015	T	0.51545	-0.8692	10	0.16896	T	0.51	.	10.9072	0.47086	0.0:0.1411:0.7122:0.1467	.	141;30;58;285	E9PPU8;E9PPJ4;O94956-2;O94956	.;.;.;SO2B1_HUMAN	A	285;58;169;30;141;58;263	ENSP00000289575:G285A;ENSP00000341286:G58A;ENSP00000434112:G169A;ENSP00000432650:G30A;ENSP00000436324:G141A;ENSP00000389653:G58A;ENSP00000388912:G263A	ENSP00000289575:G285A	G	+	2	0	SLCO2B1	74561144	0.897000	0.30589	0.001000	0.08648	0.003000	0.03518	3.898000	0.56281	0.903000	0.36546	0.655000	0.94253	GGT	.		0.557	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		C	74883496	G	C	74883496	3	2	9	1	0	0	0	0	1	0	0	0	14759	1261	44	4	880	4	SLCO2B1	11	74883496	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	15261231	74883496	60123020	34	695											
ARHGEF12	23365	broad.mit.edu	37	chr11	120300474	120300474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caaagattgctaaaagagatCcaagaggccaagaaacacat	20	5	8	8	0	0	4	0	0	0	4	1	5	1	4	2	1	2	1	2	1	6	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr11:120300474C>T	ENST00000397843.2	+	10	883	c.717C>T	c.(715-717)atC>atT	p.I239I	ARHGEF12_ENST00000532993.1_Silent_p.I136I|ARHGEF12_ENST00000356641.3_Silent_p.I220I	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	239					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TAAAAGAGATCCAAGAGGCCA	0.378			T	MLL	AML																																p.I239I				Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12-661	0			c.C717T						.						82	78	79					11																	120300474		1869	4099	5968	SO:0001819	synonymous_variant	23365	exon10			AGAGATCCAAGAG	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.717C>T	11.37:g.120300474C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	103	4	NM_015313	0	0	16	17	1	O15086|Q6P526	Silent	SNP	ENST00000397843.2	37	CCDS41727.1																																																																																			.		0.378	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120300474	C	T	120300474	2	4	9	1	0	0	0	0	0	0	0	1	897	845	30	2		2	ARHGEF12	11	120300474	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08	45416978	120300474	14706042	35	696											
GTSF1	121355	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54857070	54857070	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccaatttgcttgcaacAtcaggatgattctgtggaac	11	12	10	8	0	2	1	1	1	1	0	2	3	2	3	1	2	5	3	1	2	4	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr12:54857070A>G	ENST00000552397.1	-	4	1025	c.129T>C	c.(127-129)gaT>gaC	p.D43D	GTSF1_ENST00000305879.5_Silent_p.D43D|GTSF1_ENST00000552395.1_5'UTR|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1	43						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				TGCTTGCAACATCAGGATGAT	0.433																																					p.D43D		.											.	GTSF1-90	0			c.T129C						.						125	113	117					12																	54857070		2203	4300	6503	SO:0001819	synonymous_variant	121355	exon4			TGCAACATCAGGA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"family with sequence similarity 112, member B"	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.129T>C	12.37:g.54857070A>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	93	27	NM_144594	0	0	0	0	0	B3KQ60|Q0VGM4|Q8N778	Silent	SNP	ENST00000552397.1	37	CCDS8881.1																																																																																			.		0.433	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594		G	54857070	A	G	54857070	2	3	9	1	0	0	0	0	0	0	0	1	6907	214	8	3		3	GTSF1	12	54857070	Silent	SNP	A	TCGA-A4-7828-01A-11D-2136-08		54857070	78994825	36	697											
AGAP2	116986	hgsc.bcm.edu	37	chr12	58120409	58120409	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcgggggctgggcgtggCggtgatgctgggcgtggtgg	1	7	26	7	5	0	1	0	1	0	0	0	1	0	1	0	9	1	2	0	9	0	0	rs199546118	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr12:58120409C>T	ENST00000547588.1	-	19	3504	c.3505G>A	c.(3505-3507)Gcc>Acc	p.A1169T	AGAP2-AS1_ENST00000542466.2_Intron|RP11-571M6.8_ENST00000548410.2_RNA|AGAP2_ENST00000257897.3_Missense_Mutation_p.A813T	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	1169					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						CTGGGCGTGGCGGTGATGCTG	0.751											OREG0021951	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	71	0.0141773	0.0507	0.0043	5008	,	,		5966	0		0	False		,,,				2504	0.001				p.A1169T		.											.	AGAP2-716	0			c.G3505A						.						2	2	2					12																	58120409		1012	2358	3370	SO:0001583	missense	116986	exon19			GCGTGGCGGTGAT	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.3505G>A	12.37:g.58120409C>T	ENSP00000449241:p.Ala1169Thr	Somatic	3	0	1028	WXS	Illumina HiSeq	Phase_I	7	6	NM_001122772	0	0	0	0	0	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	37	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.51|15.51	2.855284|2.855284	0.51376|0.51376	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000257897;ENST00000547588|ENST00000328568	T;T|.	0.35605|.	1.5;1.3|.	2.6|2.6	2.6|2.6	0.31112|0.31112	.|.	.|.	.|.	.|.	.|.	T|T	0.42585|0.42585	0.1209|0.1209	N|N	0.22421|0.22421	0.69|0.69	0.34065|0.34065	D|D	0.657751|0.657751	B;D;D|.	0.57257|.	0.35;0.979;0.964|.	B;P;B|.	0.53006|.	0.006;0.715;0.42|.	T|T	0.52808|0.52808	-0.8526|-0.8526	9|5	0.54805|.	T|.	0.06|.	.|.	10.9754|10.9754	0.47463|0.47463	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	813;1169;1169|.	Q99490-2;F8VVT9;Q99490|.	.;.;AGAP2_HUMAN|.	T|H	813;1169|1012	ENSP00000257897:A813T;ENSP00000449241:A1169T|.	ENSP00000257897:A813T|.	A|R	-|-	1|2	0|0	AGAP2|AGAP2	56406676|56406676	0.997000|0.997000	0.39634|0.39634	0.993000|0.993000	0.49108|0.49108	0.429000|0.429000	0.31625|0.31625	0.614000|0.614000	0.24314|0.24314	1.783000|1.783000	0.52377|0.52377	0.305000|0.305000	0.20034|0.20034	GCC|CGC	.		0.751	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58120409	C	T	58120409	3	4	9	1	0	0	0	0	1	0	0	0	368	768	27	1	77	1	AGAP2	12	58120409	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	3263339	58120409	75731486	37	698											
NAV3	89795	hgsc.bcm.edu	37	chr12	78574710	78574710	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcagaaactggtaacacAgctaagcctactcggccacc	14	5	9	13	1	0	1	0	0	0	1	1	1	0	1	3	3	5	3	3	3	5	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr12:78574710A>G	ENST00000397909.2	+	30	5750	c.5577A>G	c.(5575-5577)acA>acG	p.T1859T	NAV3_ENST00000266692.7_Silent_p.T1660T|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000536525.2_Silent_p.T1837T|NAV3_ENST00000228327.6_Silent_p.T1837T			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1859						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTGGTAACACAGCTAAGCCTA	0.413										HNSCC(70;0.22)																											p.T1837T		.											.	NAV3-279	0			c.A5511G						.						93	94	94					12																	78574710		1965	4149	6114	SO:0001819	synonymous_variant	89795	exon29			TAACACAGCTAAG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5577A>G	12.37:g.78574710A>G		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_014903	0	0	0	0	0	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	A	8.767	0.925079	0.18056	.	.	ENSG00000067798	ENST00000552895	.	.	.	6.02	-12.0	0.00017	.	.	.	.	.	T	0.30448	0.0765	.	.	.	0.47994	D	0.999561	.	.	.	.	.	.	T	0.39702	-0.9601	4	.	.	.	-0.0484	1.2926	0.02063	0.2205:0.141:0.3103:0.3282	.	.	.	.	G	732	.	.	S	+	1	0	NAV3	77098841	0.000000	0.05858	0.000000	0.03702	0.921000	0.55340	-2.756000	0.00789	-2.540000	0.00486	-0.263000	0.10527	AGC	.		0.413	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78574710	A	G	78574710	2	3	9	1	0	0	0	0	0	0	0	1	10210	175	7	3		3	NAV3	12	78574710	Silent	SNP	A	TCGA-A4-7828-01A-11D-2136-08	20454301	78574710	55277185	38	699											
SHISA2	387914	hgsc.bcm.edu	37	chr13	26625047	26625047	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccgccagcagcgcagccaGcagcagctgcaggagcgaag	10	1	15	15	4	0	0	0	0	0	0	0	2	0	1	3	1	8	6	3	1	1	0	rs4770911	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr13:26625047G>A	ENST00000319420.3	-	1	122	c.67C>T	c.(67-69)Ctg>Ttg	p.L23L	LINC00415_ENST00000439079.1_lincRNA	NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	23					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						AGCGCAGCCAGCAGCAGCTGC	0.731													G|||	768	0.153355	0.1036	0.1167	5008	,	,		13796	0.1032		0.171	False		,,,				2504	0.2802				p.L23L		.											.	SHISA2-69	0			c.C67T						.	G		241,2763		3,235,1264	2	2	2		67	4.4	1	13	dbSNP_111	2	750,5346		25,700,2323	no	coding-synonymous	SHISA2	NM_001007538.1		28,935,3587	AA,AG,GG		12.3031,8.0226,10.8901		23/296	26625047	991,8109	1502	3048	4550	SO:0001819	synonymous_variant	387914	exon1			CAGCCAGCAGCAG		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.67C>T	13.37:g.26625047G>A		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_001007538	0	0	0	1	1	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	37	CCDS31951.1																																																																																			G|0.870;A|0.130		0.731	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		A	26625047	G	A	26625047	2	1	9	1	0	0	0	0	0	0	0	1	14312	962	34	2		2	SHISA2	13	26625047	Silent	SNP	G	TCGA-A4-7828-01A-11D-2136-08		26625047	88544831	39	700											
FRY	10129	bcgsc.ca	37	chr13	32811616	32811616	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaccaccagcggcaacaccGcaactgccgaacggagccgg	12	1	12	16	5	0	0	0	0	0	0	0	3	0	1	5	3	7	2	5	3	4	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr13:32811616G>A	ENST00000380250.3	+	44	6407	c.5911G>A	c.(5911-5913)Gca>Aca	p.A1971T		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1971						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGGCAACACCGCAACTGCCGA	0.537																																					p.A1971T													.	FRY-142	0			c.G5911A						.						60	69	66					13																	32811616		2020	4189	6209	SO:0001583	missense	10129	exon44			AACACCGCAACTG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5911G>A	13.37:g.32811616G>A	ENSP00000369600:p.Ala1971Thr	Somatic	86	1		WXS	Illumina HiSeq	Phase_1	84	6	NM_023037	0	0	4	4	0	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	9.183	1.023983	0.19433	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.21734	1.99	5.65	-5.39	0.02664	.	0.703225	0.13908	N	0.354457	T	0.09774	0.0240	N	0.11427	0.14	0.23936	N	0.996414	B	0.06786	0.001	B	0.01281	0.0	T	0.22173	-1.0224	10	0.23302	T	0.38	.	15.1608	0.72782	0.3067:0.0:0.6933:0.0	.	1971	Q5TBA9	FRY_HUMAN	T	1971;808	ENSP00000369600:A1971T	ENSP00000369600:A1971T	A	+	1	0	FRY	31709616	0.044000	0.20184	0.000000	0.03702	0.005000	0.04900	0.435000	0.21510	-1.087000	0.03081	-0.768000	0.03414	GCA	.		0.537	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32811616	G	A	32811616	3	1	9	1	0	0	0	0	1	0	0	0	6082	1087	38	1	6085	1	FRY	13	32811616	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	6186569	32811616	82358262	40	701											
MYH6	4624	hgsc.bcm.edu;broad.mit.edu	37	chr14	23859655	23859655	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccagctcctcgatgcgtgCctgggtcagacacaaagggc	8	7	12	14	2	1	1	1	0	0	1	4	2	3	1	3	2	3	1	3	2	1	0	rs375733891		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr14:23859655C>G	ENST00000356287.3	-	25	3372	c.3343G>C	c.(3343-3345)Gca>Cca	p.A1115P	MYH6_ENST00000405093.3_Splice_Site_p.A1115P|MIR208A_ENST00000362287.1_RNA			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1115					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		tcGATGCGTGCCTGGGTCAGA	0.627																																					p.A1115P		.											.	MYH6-94	0			c.G3343C						.						18	20	19					14																	23859655		2203	4298	6501	SO:0001630	splice_region_variant	4624	exon26			TGCGTGCCTGGGT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3343-1G>C	14.37:g.23859655C>G		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	43	14	NM_002471	0	0	0	0	0	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	c	26.1	4.701069	0.88924	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.80480	-1.38;-1.38	4.25	4.25	0.50352	Myosin tail (1);	.	.	.	.	D	0.92698	0.7679	H	0.95470	3.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95199	0.8315	9	0.87932	D	0	.	17.0442	0.86498	0.0:1.0:0.0:0.0	.	1115	P13533	MYH6_HUMAN	P	1115	ENSP00000386041:A1115P;ENSP00000348634:A1115P	ENSP00000348634:A1115P	A	-	1	0	MYH6	22929495	1.000000	0.71417	0.779000	0.31741	0.049000	0.14656	7.575000	0.82447	2.092000	0.63282	0.561000	0.74099	GCA	.		0.627	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		Missense_Mutation	G	23859655	C	G	23859655	5	3	9	1	0	0	0	0	0	0	1	0	10063	753	26	4	2532	4	MYH6	14	23859655	Splice_Site	SNP	C	TCGA-A4-7828-01A-11D-2136-08		23859655	83489885	41	702											
COCH	1690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31353851	31353851	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaggtttcagagggggtaAttccaatacaggtaagtaga	14	10	13	4	0	1	2	1	0	0	2	2	2	2	2	1	4	1	5	1	4	6	7			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr14:31353851A>C	ENST00000396618.3	+	9	778	c.722A>C	c.(721-723)aAt>aCt	p.N241T	RP11-829H16.3_ENST00000468444.2_RNA|RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000216361.4_Missense_Mutation_p.N241T|COCH_ENST00000475087.1_Missense_Mutation_p.N241T|COCH_ENST00000460581.2_Missense_Mutation_p.N129T|COCH_ENST00000382493.4_Missense_Mutation_p.N48T|RP11-829H16.3_ENST00000555421.1_RNA|RP11-829H16.3_ENST00000555108.1_RNA	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	241	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		AGAGGGGGTAATTCCAATACA	0.358																																					p.N241T		.											.	COCH-228	0			c.A722C						.						69	72	71					14																	31353851		2203	4299	6502	SO:0001583	missense	1690	exon9			GGGGTAATTCCAA		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.722A>C	14.37:g.31353851A>C	ENSP00000379862:p.Asn241Thr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	71	18	NM_004086	0	0	0	0	0	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	37	CCDS9640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.1|23.1	4.373608|4.373608	0.82573|0.82573	.|.	.|.	ENSG00000100473|ENSG00000100473	ENST00000468826|ENST00000216361;ENST00000396618;ENST00000475087;ENST00000555881;ENST00000460581;ENST00000542225;ENST00000382493	.|D;D;D;D;D;D	.|0.83075	.|-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.78|5.78	5.78|5.78	0.91487|0.91487	.|von Willebrand factor, type A (3);	.|0.040966	.|0.85682	.|D	.|0.000000	D|D	0.89114|0.89114	0.6623|0.6623	M|M	0.64676|0.64676	1.99|1.99	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.64830	.|0.994;0.992;0.975	.|D;P;P	.|0.67231	.|0.95;0.87;0.819	D|D	0.88337|0.88337	0.2972|0.2972	5|10	.|0.39692	.|T	.|0.17	-22.9226|-22.9226	16.1145|16.1145	0.81295|0.81295	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|48;241;241	.|E7EN67;Q96IU6;O43405	.|.;.;COCH_HUMAN	L|T	81|241;241;241;123;129;129;48	.|ENSP00000216361:N241T;ENSP00000379862:N241T;ENSP00000451528:N241T;ENSP00000452569:N123T;ENSP00000451713:N129T;ENSP00000371933:N48T	.|ENSP00000216361:N241T	I|N	+|+	1|2	0|0	COCH|COCH	30423602|30423602	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	8.474000|8.474000	0.90413|0.90413	2.205000|2.205000	0.71048|0.71048	0.454000|0.454000	0.30748|0.30748	ATT|AAT	.		0.358	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		C	31353851	A	C	31353851	3	2	9	1	0	0	0	0	1	0	0	0	3662	101	4	5	752	5	COCH	14	31353851	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	7494196	31353851	75995689	42	703											
C14orf126	112487	hgsc.bcm.edu	37	chr14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgggcctgaggaatccGgctaccctcagccatggctt	6	7	12	16	3	1	1	1	1	0	0	2	2	2	2	5	4	2	2	5	4	2	2	rs17097904	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	DTD2_ENST00000356180.4_Missense_Mutation_p.R6W|RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		.											.	.	1	Substitution - Missense(1)	skin(1)	c.C16T						.						12	12	12					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	11	1		WXS	Illumina HiSeq	Phase_I	11	2	NM_080664	0	0	2	4	2	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		A	31926584	G	A	31926584	3	1	9	1	0	0	0	0	1	0	0	0	1747	1115	39	1	502	1	C14orf126	14	31926584	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	572733	31926584	75422956	43	704											
TUBGCP5	114791	broad.mit.edu;bcgsc.ca	37	chr15	22872435	22872444	+	Frame_Shift_Del	DEL	AAACTGCCAT	AAACTGCCAT	-																															aaaatggaatctgattttaaAaactgccatatgtttcttgt																								rs201453400		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	AAACTGCCAT	AAACTGCCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr15:22872435_22872444delAAACTGCCAT	ENST00000283645.4	+	22	3094_3103	c.2964_2973delAAACTGCCAT	c.(2962-2973)aaaaactgccatfs	p.KNCH988fs	TUBGCP5_ENST00000453949.2_Frame_Shift_Del_p.KNCH988fs	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	988					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CTGATTTTAAAAACTGCCATATGTTTCTTG	0.324																																					p.988_991del													.	TUBGCP5-91	0			c.2964_2973del						.																																			SO:0001589	frameshift_variant	114791	exon22			TTTTAAAAACTGC	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"gamma-tubulin complex component GCP5"	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.2964_2973delAAACTGCCAT	15.37:g.22872435_22872444delAAACTGCCAT	ENSP00000283645:p.Lys988fs	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	114	8	NM_052903	0	0	0	0	0	E9PB12|Q6IQ52|Q96PY8	Frame_Shift_Del	DEL	ENST00000283645.4	37	CCDS10008.1																																																																																			.		0.324	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903		-	22872444	AAACTGCCAT	-	22872435	7	5	9	1	0	1	0	1	0	0	0	0	16802	11	1	0	3050	0	TUBGCP5	15	22872435	Frame_Shift_Del	DEL	AAACTGCCAT	TCGA-A4-7828-01A-11D-2136-08		22872435	79658957	44	705											
TRAF7	84231	hgsc.bcm.edu	37	chr16	2222231	2222231	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcaaactgaccgtggtggTgaacaacatcgcggtggccg	9	7	14	11	5	1	2	1	2	0	0	2	2	1	2	2	4	3	0	2	4	3	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr16:2222231T>G	ENST00000326181.6	+	8	647	c.515T>G	c.(514-516)gTg>gGg	p.V172G		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	172					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						ACCGTGGTGGTGAACAACATC	0.662																																					p.V172G		.											.	TRAF7-661	0			c.T515G						.						67	61	63					16																	2222231		2197	4300	6497	SO:0001583	missense	84231	exon8			TGGTGGTGAACAA	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"RING-type (C3HC4) zinc fingers", "WD repeat domain containing"	20456	protein-coding gene	gene with protein product		606692	"ring finger and WD repeat domain 1", "TNF receptor-associated factor 7"	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.515T>G	16.37:g.2222231T>G	ENSP00000318944:p.Val172Gly	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_032271	0	1	25	26	0	Q9H073	Missense_Mutation	SNP	ENST00000326181.6	37	CCDS10461.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.682097	0.47991	.	.	ENSG00000131653	ENST00000326181	T	0.54071	0.59	4.38	4.38	0.52667	Zinc finger, RING/FYVE/PHD-type (1);	0.132520	0.50627	D	0.000110	T	0.49270	0.1547	L	0.60455	1.87	0.80722	D	1	P	0.43477	0.808	B	0.39419	0.299	T	0.58222	-0.7674	10	0.87932	D	0	-16.0939	12.9098	0.58173	0.0:0.0:0.0:1.0	.	172	Q6Q0C0	TRAF7_HUMAN	G	172	ENSP00000318944:V172G	ENSP00000318944:V172G	V	+	2	0	TRAF7	2162232	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	6.127000	0.71642	1.837000	0.53436	0.459000	0.35465	GTG	.		0.662	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		G	2222231	T	G	2222231	3	3	9	1	0	0	0	0	1	0	0	0	16479	1696	59	5	541	5	TRAF7	16	2222231	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08		2222231	88132522	45	706											
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3081004	3081004	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcccgtgcccgttctcGcccactgtcctgctgctctg	2	10	12	17	3	2	0	0	0	2	0	4	1	3	0	4	1	3	3	4	1	0	1	rs199875074	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr16:3081004G>A	ENST00000572449.1	-	3	492	c.430C>T	c.(430-432)Cga>Tga	p.R144*	CCDC64B_ENST00000389347.4_Nonsense_Mutation_p.R144*|CCDC64B_ENST00000573514.1_5'UTR|RP11-473M20.5_ENST00000382225.3_RNA			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	144										breast(1)|endometrium(2)|large_intestine(1)	4						GCCCGTTCTCGCCCACTGTCC	0.721													G|||	6	0.00119808	0.0045	0	5008	,	,		15044	0		0	False		,,,				2504	0				p.R144X		.											.	.	0			c.C430T						.	G	stop/ARG	10,4056		0,10,2023	11	15	14		430	5.3	0.1	16		14	0,8340		0,0,4170	yes	stop-gained	CCDC64B	NM_001103175.1		0,10,6193	AA,AG,GG		0.0,0.2459,0.0806		144/509	3081004	10,12396	2033	4170	6203	SO:0001587	stop_gained	146439	exon2			GTTCTCGCCCACT	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.430C>T	16.37:g.3081004G>A	ENSP00000459043:p.Arg144*	Somatic	9	2		WXS	Illumina HiSeq	Phase_I	12	8	NM_001103175	0	0	0	0	0	Q658L9	Nonsense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036215	0.54896	0.002459	0.0	ENSG00000162069	ENST00000389347	.	.	.	5.28	5.28	0.74379	.	0.067706	0.53938	D	0.000041	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.426	11.4983	0.50422	0.0:0.0:0.8205:0.1795	.	.	.	.	X	144	.	ENSP00000373998:R144X	R	-	1	2	CCDC64B	3021005	0.996000	0.38824	0.087000	0.20705	0.341000	0.28922	2.452000	0.44961	2.477000	0.83638	0.561000	0.74099	CGA	.		0.721	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			A	3081004	G	A	3081004	4	1	9	1	0	0	0	0	0	1	0	0	2842	1095	38	1	1128	1	CCDC64B	16	3081004	Nonsense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	858773	3081004	87273749	46	707											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	373	57		WXS	Illumina HiSeq		404	64	NM_145301	0	0	0	14	14	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		T	15457087	C	T	15457087	3	4	9	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08		15457087	65738123	47	708											
ABCC3	8714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48734448	48734448	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtatgagcggctgcagggCgtacagtcttcgggggtcct	6	9	16	10	3	1	1	0	1	1	0	3	1	2	1	1	4	3	4	1	4	2	3	rs139452504	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr17:48734448C>T	ENST00000285238.8	+	4	470	c.390C>T	c.(388-390)ggC>ggT	p.G130G	ABCC3_ENST00000427699.1_Silent_p.G130G	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	130					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GGCTGCAGGGCGTACAGTCTT	0.587													C|||	9	0.00179712	8e-04	0	5008	,	,		18107	0.0079		0	False		,,,				2504	0				p.G130G		.											.	ABCC3-93	0			c.C390T						.						122	101	108					17																	48734448		2203	4300	6503	SO:0001819	synonymous_variant	8714	exon4			GCAGGGCGTACAG	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"ATP binding cassette transporters / subfamily C"	54	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter 2"	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.390C>T	17.37:g.48734448C>T		Somatic	118	1		WXS	Illumina HiSeq	Phase_I	137	27	NM_003786	0	0	8	10	2	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			C|0.998;T|0.002		0.587	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		T	48734448	C	T	48734448	2	4	9	1	0	0	0	0	0	0	0	1	54	755	27	1		1	ABCC3	17	48734448	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08	33277361	48734448	32460762	48	709											
SPAG9	9043	broad.mit.edu	37	chr17	49063070	49063071	+	Frame_Shift_Del	DEL	AA	AA	-																															aaaacttacacaatactgagAatcgaatctttaagtttaat																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr17:49063070_49063071delAA	ENST00000262013.7	-	23	3216_3217	c.3008_3009delTT	c.(3007-3009)attfs	p.I1003fs	SPAG9_ENST00000510283.1_Frame_Shift_Del_p.I846fs|SPAG9_ENST00000357122.4_Frame_Shift_Del_p.I989fs|SPAG9_ENST00000505279.1_Frame_Shift_Del_p.I993fs	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1003					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			CAATACTGAGAATCGAATCTTT	0.322																																					p.1003_1003del													.	SPAG9-659	0			c.3008_3009del						.																																			SO:0001589	frameshift_variant	9043	exon23			ACTGAGAATCGAA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3008_3009delTT	17.37:g.49063070_49063071delAA	ENSP00000262013:p.Ile1003fs	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	36	8	NM_001130528	0	0	0	0	0	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Frame_Shift_Del	DEL	ENST00000262013.7	37	CCDS45740.1																																																																																			.		0.322	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		-	49063071	AA	-	49063070	7	5	9	1	0	1	0	1	0	0	0	0	15017	242	9	0	988	0	SPAG9	17	49063070	Frame_Shift_Del	DEL	AA	TCGA-A4-7828-01A-11D-2136-08	328622	49063070	32132140	49	710											
EPX	8288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	56281634	56281634	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaagacagcgcaaggccctGagcagaatttccttgtctcg	12	8	10	11	2	1	3	0	1	1	2	3	3	2	3	2	1	2	2	2	1	4	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr17:56281634G>A	ENST00000225371.5	+	12	2108	c.1998G>A	c.(1996-1998)ctG>ctA	p.L666L		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	666					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	GCAAGGCCCTGAGCAGAATTT	0.502																																					p.L666L		.											.	EPX-92	0			c.G1998A						.						112	99	103					17																	56281634		2203	4300	6503	SO:0001819	synonymous_variant	8288	exon12			GGCCCTGAGCAGA	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.1998G>A	17.37:g.56281634G>A		Somatic	123	1		WXS	Illumina HiSeq	Phase_I	113	35	NM_000502	0	0	0	1	1	Q4TVP3	Silent	SNP	ENST00000225371.5	37	CCDS11602.1																																																																																			.		0.502	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502		A	56281634	G	A	56281634	2	1	9	1	0	0	0	0	0	0	0	1	5213	1277	45	2		2	EPX	17	56281634	Silent	SNP	G	TCGA-A4-7828-01A-11D-2136-08	7218564	56281634	24913576	50	711											
CCDC57	284001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80129603	80129603	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctgtcgaggtgcggacgCtgggctgagactcagcatga	7	9	15	10	3	2	2	1	2	1	1	4	5	2	3	0	3	2	3	0	3	0	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr17:80129603C>G	ENST00000389641.4	-	12	1892	c.1856G>C	c.(1855-1857)aGc>aCc	p.S619T	CCDC57_ENST00000327026.3_5'UTR|CCDC57_ENST00000392347.1_Missense_Mutation_p.S619T|CCDC57_ENST00000392343.3_Missense_Mutation_p.S619T			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	619										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GGTGCGGACGCTGGGCTGAGA	0.478																																					p.S619T		.											.	CCDC57-24	0			c.G1856C						.						95	99	98					17																	80129603		1929	4143	6072	SO:0001583	missense	284001	exon12			CGGACGCTGGGCT	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.1856G>C	17.37:g.80129603C>G	ENSP00000374292:p.Ser619Thr	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	90	15	NM_198082	0	0	3	3	0	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Missense_Mutation	SNP	ENST00000389641.4	37		.	.	.	.	.	.	.	.	.	.	C	10.52	1.371836	0.24857	.	.	ENSG00000176155	ENST00000389641;ENST00000392347;ENST00000327026;ENST00000392343	T;T;T	0.24538	3.02;3.02;1.85	2.92	-1.57	0.08506	.	2.029070	0.02447	N	0.085210	T	0.23846	0.0577	L	0.57536	1.79	0.09310	N	0.999995	P;P	0.44816	0.844;0.572	B;B	0.41088	0.347;0.122	T	0.19257	-1.0311	10	0.22109	T	0.4	5.4141	3.303	0.06989	0.0:0.3889:0.2116:0.3995	.	619;619	Q2TAC2-2;Q2TAC2	.;CCD57_HUMAN	T	619;619;127;619	ENSP00000374292:S619T;ENSP00000376158:S619T;ENSP00000376154:S619T	ENSP00000315967:S127T	S	-	2	0	CCDC57	77722892	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.431000	0.06965	-0.298000	0.08921	0.561000	0.74099	AGC	.		0.478	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		G	80129603	C	G	80129603	3	3	9	1	0	0	0	0	1	0	0	0	2833	797	28	4	915	4	CCDC57	17	80129603	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	23847969	80129603	1065607	51	712											
EPB41L3	23136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	5416056	5416056	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggttggtttcagaaaggtTggggaaagagaggtatccat	12	10	16	3	0	1	2	1	0	0	2	2	5	2	3	1	6	0	4	1	6	3	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr18:5416056T>A	ENST00000341928.2	-	13	2168	c.1828A>T	c.(1828-1830)Aac>Tac	p.N610Y	EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.N610Y|EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000542652.2_Intron	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	610	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TCAGAAAGGTTGGGGAAAGAG	0.532																																					p.N610Y		.											.	EPB41L3-95	0			c.A1828T						.						157	126	136					18																	5416056		2203	4300	6503	SO:0001583	missense	23136	exon13			AAAGGTTGGGGAA	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1828A>T	18.37:g.5416056T>A	ENSP00000343158:p.Asn610Tyr	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	138	37	NM_012307	0	0	0	0	0	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.558267	0.45590	.	.	ENSG00000082397	ENST00000341928;ENST00000342933	T;T	0.81415	-1.49;-1.49	5.74	4.55	0.56014	.	0.102804	0.64402	D	0.000003	T	0.77377	0.4121	L	0.57536	1.79	0.80722	D	1	P	0.49447	0.924	B	0.41088	0.347	T	0.78593	-0.2144	10	0.72032	D	0.01	.	12.8348	0.57767	0.0:0.0:0.1364:0.8636	.	610	Q9Y2J2	E41L3_HUMAN	Y	610	ENSP00000343158:N610Y;ENSP00000341138:N610Y	ENSP00000343158:N610Y	N	-	1	0	EPB41L3	5406056	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	0.958000	0.37956	0.460000	0.39030	AAC	.		0.532	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5416056	T	A	5416056	3	1	9	1	0	0	0	0	1	0	0	0	5167	1812	63	5	1475	5	EPB41L3	18	5416056	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08		5416056	72661192	52	713											
PRAM1	84106	hgsc.bcm.edu	37	chr19	8563524	8563524	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgcaggcagtgagctctCggaagcggagctggggagtg	7	5	20	9	3	1	1	0	1	1	0	2	4	1	4	1	6	3	4	1	6	1	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:8563524C>A	ENST00000423345.4	-	2	1688	c.1168G>T	c.(1168-1170)Gag>Tag	p.E390*	PRAM1_ENST00000255612.3_Nonsense_Mutation_p.E390*			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	438	Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						AGTGAGCTCTCGGAAGCGGAG	0.672																																					p.E390X		.											.	.	0			c.G1168T						.						9	12	11					19																	8563524		1967	4100	6067	SO:0001587	stop_gained	84106	exon2			AGCTCTCGGAAGC	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.1168G>T	19.37:g.8563524C>A	ENSP00000408342:p.Glu390*	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_032152	0	0	5	5	0	Q8N6W7	Nonsense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	C	28.9	4.959595	0.92791	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	.	.	.	4.06	4.06	0.47325	.	0.172051	0.28011	N	0.016953	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	11.0355	0.47797	0.1863:0.8136:0.0:0.0	.	.	.	.	X	390	.	ENSP00000255612:E390X	E	-	1	0	PRAM1	8469524	0.824000	0.29247	0.826000	0.32828	0.136000	0.21042	1.952000	0.40343	2.205000	0.71048	0.462000	0.41574	GAG	.		0.672	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		A	8563524	C	A	8563524	4	1	9	1	0	0	0	0	0	1	0	0	12452	893	31	4	877	4	PRAM1	19	8563524	Nonsense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08		8563524	50565459	53	714											
TMEM205	374882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11453637	11453637	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggtccttctctcgcagctGgcggtagggatcgggaccct	4	9	16	12	3	1	0	0	0	1	0	5	2	2	2	2	6	1	3	2	6	1	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:11453637G>T	ENST00000354882.5	-	3	850	c.424C>A	c.(424-426)Cag>Aag	p.Q142K	TMEM205_ENST00000586218.1_Missense_Mutation_p.Q81K|TMEM205_ENST00000447337.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000593256.2_Missense_Mutation_p.Q142K|TMEM205_ENST00000586956.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000589555.1_Missense_Mutation_p.Q142K|RAB3D_ENST00000589655.1_Intron|CCDC159_ENST00000588790.1_5'Flank|TMEM205_ENST00000588560.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000586590.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000587948.1_Missense_Mutation_p.Q142K			Q6UW68	TM205_HUMAN	transmembrane protein 205	142						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|lung(1)	2						TCTCGCAGCTGGCGGTAGGGA	0.627																																					p.Q142K		.											.	TMEM205-22	0			c.C424A						.						94	85	88					19																	11453637		2203	4300	6503	SO:0001583	missense	374882	exon4			GCAGCTGGCGGTA	AK127147	CCDS32909.1	19p13.2	2008-01-09				ENSG00000105518			29631	protein-coding gene	gene with protein product		613771				12975309	Standard	NM_198536		Approved	UNQ501, MBC3205	uc002mrb.2	Q6UW68		ENST00000354882.5:c.424C>A	19.37:g.11453637G>T	ENSP00000346954:p.Gln142Lys	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	149	48	NM_033408	0	0	128	226	98		Missense_Mutation	SNP	ENST00000354882.5	37	CCDS32909.1	.	.	.	.	.	.	.	.	.	.	G	6.199	0.404917	0.11754	.	.	ENSG00000105518	ENST00000354882;ENST00000447337	.	.	.	4.96	3.9	0.45041	.	0.240493	0.34245	U	0.004140	T	0.34250	0.0891	L	0.36672	1.1	0.30403	N	0.779844	B	0.12013	0.005	B	0.09377	0.004	T	0.26224	-1.0109	9	0.06365	T	0.9	-4.5936	14.6711	0.68945	0.0:0.1463:0.8537:0.0	.	142	Q6UW68	TM205_HUMAN	K	142	.	ENSP00000346954:Q142K	Q	-	1	0	TMEM205	11314637	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	3.726000	0.54977	1.193000	0.43086	0.655000	0.94253	CAG	.		0.627	TMEM205-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458743.1	NM_198536		T	11453637	G	T	11453637	3	4	9	1	0	0	0	0	1	0	0	0	16162	1357	47	4	149	4	TMEM205	19	11453637	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	2890113	11453637	47675346	54	715											
ANO8	57719	hgsc.bcm.edu	37	chr19	17439378	17439378	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccggagcccgcagtccaggaGgcccccttcctcgccctcct	4	6	10	21	3	0	0	0	0	0	0	4	2	3	2	8	3	1	1	8	3	0	1	rs73511896	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:17439378G>A	ENST00000159087.4	-	13	1977	c.1819C>T	c.(1819-1821)Ctc>Ttc	p.L607F		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	607	Glu-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						CAGTCCAGGAGGCccccttcc	0.731													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		7740	0		0	False		,,,				2504	0				p.L607F		.											.	ANO8-93	0			c.C1819T						.	G	PHE/LEU	87,4125		1,85,2020	9	7	7		1819	4	0.9	19	dbSNP_131	7	1,8251		0,1,4125	yes	missense	ANO8	NM_020959.2	22	1,86,6145	AA,AG,GG		0.0121,2.0655,0.706	probably-damaging	607/1233	17439378	88,12376	2106	4126	6232	SO:0001583	missense	57719	exon13			CCAGGAGGCCCCC	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	29329	protein-coding gene	gene with protein product		610216	"KIAA1623", "transmembrane protein 16H"	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.1819C>T	19.37:g.17439378G>A	ENSP00000159087:p.Leu607Phe	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_020959	0	0	1	1	0	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	37	CCDS32949.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	G	13.87	2.365625	0.41902	0.020655	1.21E-4	ENSG00000074855	ENST00000159087	T	0.70282	-0.47	5.06	4.03	0.46877	.	0.080524	0.48286	D	0.000196	T	0.57902	0.2085	M	0.78456	2.415	0.27653	N	0.947327	D	0.56746	0.977	P	0.60012	0.867	T	0.65368	-0.6185	10	0.72032	D	0.01	.	5.7041	0.17899	0.0985:0.0:0.7064:0.1951	.	607	Q9HCE9	ANO8_HUMAN	F	607	ENSP00000159087:L607F	ENSP00000159087:L607F	L	-	1	0	ANO8	17300378	0.998000	0.40836	0.921000	0.36526	0.416000	0.31233	1.549000	0.36212	2.372000	0.80975	0.484000	0.47621	CTC	G|0.992;A|0.008		0.731	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		A	17439378	G	A	17439378	3	1	9	1	0	0	0	0	1	0	0	0	703	1000	35	2	1903	2	ANO8	19	17439378	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	5985741	17439378	41689605	55	716											
CACNG8	59283	hgsc.bcm.edu	37	chr19	54485464	54485464	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tacttcggcgggctgtcgttCatcctggccgaggtgatagg	5	11	15	10	4	1	1	1	1	0	0	4	2	2	1	2	5	1	2	2	5	2	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:54485464C>G	ENST00000270458.2	+	4	742	c.639C>G	c.(637-639)ttC>ttG	p.F213L	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	213					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGCTGTCGTTCATCCTGGCCG	0.652																																					p.F213L		.											.	CACNG8-90	0			c.C639G						.						58	42	47					19																	54485464		2202	4298	6500	SO:0001583	missense	59283	exon4			GTCGTTCATCCTG	AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.639C>G	19.37:g.54485464C>G	ENSP00000270458:p.Phe213Leu	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_031895	0	0	0	0	0	Q9BXT0|Q9BY23	Missense_Mutation	SNP	ENST00000270458.2	37	CCDS33104.1	.	.	.	.	.	.	.	.	.	.	.	20.8	4.055205	0.75960	.	.	ENSG00000142408	ENST00000270458	D	0.89875	-2.58	1.91	1.91	0.25777	.	0.000000	0.64402	U	0.000003	D	0.92548	0.7633	M	0.83483	2.645	0.35646	D	0.811372	D	0.65815	0.995	D	0.80764	0.994	D	0.91889	0.5522	9	0.87932	D	0	-10.5923	4.4689	0.11703	0.0:0.7951:0.0:0.2048	.	213	Q8WXS5	CCG8_HUMAN	L	213	ENSP00000270458:F213L	ENSP00000270458:F213L	F	+	3	2	CACNG8	59177276	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	2.644000	0.46613	1.062000	0.40625	0.289000	0.19496	TTC	.		0.652	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			G	54485464	C	G	54485464	3	3	9	1	0	0	0	0	1	0	0	0	2569	825	29	4	653	4	CACNG8	19	54485464	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	37046086	54485464	4643519	56	717											
ISOC2	79763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55966664	55966664	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtccaccaccacatggacctGcagcccccggtctaggaggt	8	6	11	16	1	1	0	0	0	1	0	2	2	2	2	6	4	2	1	6	4	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:55966664G>A	ENST00000425675.2	-	4	442	c.382C>T	c.(382-384)Cag>Tag	p.Q128*	ISOC2_ENST00000438389.2_Nonsense_Mutation_p.Q58*|ISOC2_ENST00000085068.3_Nonsense_Mutation_p.Q144*			Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2	128					protein destabilization (GO:0031648)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			endometrium(1)|lung(4)|ovary(1)|stomach(1)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		ACATGGACCTGCAGCCCCCGG	0.662																																					p.Q144X		.											.	ISOC2-91	0			c.C430T						.						32	34	33					19																	55966664		2203	4300	6503	SO:0001587	stop_gained	79763	exon4			GGACCTGCAGCCC	AK027122	CCDS12925.1, CCDS46194.1, CCDS46195.1	19q13.42	2011-07-14			ENSG00000063241	ENSG00000063241			26278	protein-coding gene	gene with protein product		612928				17658461	Standard	NM_024710		Approved	FLJ23469	uc002qla.3	Q96AB3		ENST00000425675.2:c.382C>T	19.37:g.55966664G>A	ENSP00000401726:p.Gln128*	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	28	5	NM_024710	0	0	31	33	2	Q6ZN91|Q9H5G0	Nonsense_Mutation	SNP	ENST00000425675.2	37	CCDS46195.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324290	0.95708	.	.	ENSG00000063241	ENST00000085068;ENST00000425675;ENST00000438389	.	.	.	3.62	2.44	0.29823	.	0.212717	0.38436	N	0.001695	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-16.1072	10.4505	0.44520	0.0:0.2009:0.7991:0.0	.	.	.	.	X	144;128;58	.	ENSP00000085068:Q144X	Q	-	1	0	ISOC2	60658476	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.156000	0.50708	1.977000	0.57605	0.486000	0.48141	CAG	.		0.662	ISOC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453179.1	NM_024710		A	55966664	G	A	55966664	4	1	9	1	0	0	0	0	0	1	0	0	7884	1328	46	2	247	2	ISOC2	19	55966664	Nonsense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	1481200	55966664	3162319	57	718											
DHX35	60625	bcgsc.ca	37	chr20	37623476	37623476	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttttagattcagaaaaagCgaggggatcttcgattgatt	12	15	10	4	2	2	3	1	1	1	2	3	6	2	4	0	2	1	0	0	2	3	7			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr20:37623476C>A	ENST00000252011.3	+	8	628	c.595C>A	c.(595-597)Cga>Aga	p.R199R	DHX35_ENST00000373323.4_Silent_p.R168R|DHX35_ENST00000373325.2_Silent_p.R199R	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	199	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TCAGAAAAAGCGAGGGGATCT	0.383																																					p.R199R													.	DHX35-226	0			c.C595A						.						134	125	128					20																	37623476		2203	4300	6503	SO:0001819	synonymous_variant	60625	exon8			AAAAAGCGAGGGG	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.595C>A	20.37:g.37623476C>A		Somatic	144	0		WXS	Illumina HiSeq	Phase_1	170	6	NM_021931	0	0	0	0	0	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Silent	SNP	ENST00000252011.3	37	CCDS13310.1																																																																																			.		0.383	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		A	37623476	C	A	37623476	2	1	9	1	0	0	0	0	0	0	0	1	4519	760	27	4		4	DHX35	20	37623476	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08		37623476	25402044	58	719											
PTPRT	11122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	41306544	41306544	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtgaggggaggccctggcGgtcccgtacccccctcacct	4	7	14	16	2	1	1	1	1	0	0	2	2	2	2	6	6	1	1	6	6	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr20:41306544G>T	ENST00000373187.1	-	7	1114	c.1115C>A	c.(1114-1116)cCg>cAg	p.P372Q	PTPRT_ENST00000373184.1_Missense_Mutation_p.P372Q|PTPRT_ENST00000373198.4_Missense_Mutation_p.P372Q|PTPRT_ENST00000356100.2_Missense_Mutation_p.P372Q|PTPRT_ENST00000373193.3_Missense_Mutation_p.P372Q|PTPRT_ENST00000373201.1_Missense_Mutation_p.P372Q|PTPRT_ENST00000373190.1_Missense_Mutation_p.P372Q			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	372	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGGCCCTGGCGGTCCCGTACC	0.542																																					p.P372Q		.											.	PTPRT-664	0			c.C1115A						.						87	87	87					20																	41306544		1919	4125	6044	SO:0001583	missense	11122	exon7			CCTGGCGGTCCCG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1115C>A	20.37:g.41306544G>T	ENSP00000362283:p.Pro372Gln	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	150	42	NM_007050	0	0	0	0	0	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.737618	0.49045	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	5.42	5.42	0.78866	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81346	0.4803	L	0.29908	0.895	0.58432	D	0.999991	D;D	0.56746	0.971;0.977	P;P	0.55391	0.775;0.772	T	0.78523	-0.2171	10	0.28530	T	0.3	.	19.1814	0.93625	0.0:0.0:1.0:0.0	.	372;372	O14522-1;O14522	.;PTPRT_HUMAN	Q	372	ENSP00000362286:P372Q;ENSP00000362283:P372Q;ENSP00000362289:P372Q;ENSP00000348408:P372Q;ENSP00000362294:P372Q;ENSP00000362280:P372Q;ENSP00000362297:P372Q	ENSP00000348408:P372Q	P	-	2	0	PTPRT	40739958	1.000000	0.71417	0.973000	0.42090	0.948000	0.59901	5.469000	0.66749	2.705000	0.92388	0.655000	0.94253	CCG	.		0.542	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	41306544	G	T	41306544	3	4	9	1	0	0	0	0	1	0	0	0	12844	1116	39	4	3371	4	PTPRT	20	41306544	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	3683068	41306544	21718976	59	720											
TMEM189	387522	hgsc.bcm.edu	37	chr20	48770156	48770156	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagctgctggcccggccAgttctcggcgcccgccatgg	3	7	13	18	4	1	0	0	0	1	0	3	0	2	0	5	4	2	3	5	4	0	1	rs2026757	byFrequency	TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr20:48770156A>C	ENST00000341698.2	-	1	18	c.19T>G	c.(19-21)Tgg>Ggg	p.W7G	TMEM189_ENST00000371652.4_Missense_Mutation_p.W7G|TMEM189_ENST00000371650.5_Missense_Mutation_p.W7G|TMEM189_ENST00000557021.1_Missense_Mutation_p.W7G	NM_001257399.1	NP_001244328.1			TMEM189-UBE2V1 readthrough											breast(1)|endometrium(4)|large_intestine(6)|lung(6)	17			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)			TGGCCCGGCCAGTTCTCGGCG	0.776													C|||	602	0.120208	0.3903	0.036	5008	,	,		6116	0.0208		0.004	False		,,,				2504	0.0368				p.W7G		.											.	TMEM189-22	0			c.T19G						.	C	GLY/TRP,GLY/TRP,GLY/TRP	475,1843		15,445,699	2	2	2		19,19,19	3.8	0.5	20	dbSNP_94	2	6,4692		0,6,2343	no	missense,missense,missense	TMEM189,TMEM189-UBE2V1	NM_001162505.1,NM_199129.2,NM_199203.2	184,184,184	15,451,3042	CC,CA,AA		0.1277,20.4918,6.8558	benign,benign,benign	7/268,7/271,7/371	48770156	481,6535	1159	2349	3508	SO:0001583	missense	387521	exon1			CCGGCCAGTTCTC	U39361	CCDS13424.1	20q13.13	2011-05-31			ENSG00000124208	ENSG00000124208			33521	other	readthrough						11076860	Standard	NM_199203		Approved	Kua-UEV, CROC-1B	uc002xvf.3		OTTHUMG00000033085	ENST00000341698.2:c.19T>G	20.37:g.48770156A>C	ENSP00000344166:p.Trp7Gly	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	10	7	NM_199129	0	0	0	0	0		Missense_Mutation	SNP	ENST00000341698.2	37	CCDS13424.1	211	0.09661172161172162	166	0.33739837398373984	16	0.04419889502762431	22	0.038461538461538464	7	0.009234828496042216	C	0.099	-1.154825	0.01700	0.204918	0.001277	ENSG00000124208;ENSG00000240849;ENSG00000240849;ENSG00000240849	ENST00000341698;ENST00000557021;ENST00000371650;ENST00000371652	T;T;T;T	0.48836	0.8;0.8;1.06;1.06	3.81	3.81	0.43845	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	9.99999999995449E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37526	-0.9702	8	0.08599	T	0.76	.	8.6645	0.34112	0.2276:0.7724:0.0:0.0	rs2026757;rs57405958	7;7;7	Q5TGE1;A5PLL7;G3V2F7	.;TM189_HUMAN;.	G	7	ENSP00000344166:W7G;ENSP00000450635:W7G;ENSP00000360713:W7G;ENSP00000360715:W7G	ENSP00000360713:W7G	W	-	1	0	TMEM189-UBE2V1;TMEM189	48203563	0.998000	0.40836	0.481000	0.27354	0.065000	0.16274	1.462000	0.35266	0.820000	0.34516	-0.407000	0.06327	TGG	A|0.903;C|0.097		0.776	TMEM189-UBE2V1-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000080532.5			C	48770156	A	C	48770156	3	2	9	1	0	0	0	0	1	0	0	0	16143	188	7	5	817	5	TMEM189	20	48770156	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	7463612	48770156	14255364	60	721											
MYT1	4661	broad.mit.edu	37	chr20	62851191	62851191	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggtgtgaagtctcccgaCgcctcccagcgccacagcag	7	5	11	18	4	1	1	0	1	1	0	3	2	2	1	5	1	2	1	5	1	1	0	rs117853857		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr20:62851191C>T	ENST00000328439.1	+	13	2461	c.2097C>T	c.(2095-2097)gaC>gaT	p.D699D	MYT1_ENST00000360149.4_Silent_p.D401D|MYT1_ENST00000536311.1_Silent_p.D726D	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AGTCTCCCGACGCCTCCCAGC	0.657													C|||	1	0.000199681	0	0	5008	,	,		16055	0.001		0	False		,,,				2504	0				p.D699D	GBM(59;481 1041 20555 21139 33705)												.	MYT1-704	0			c.C2097T						.						38	39	39					20																	62851191		2203	4299	6502	SO:0001819	synonymous_variant	4661	exon13			TCCCGACGCCTCC	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.2097C>T	20.37:g.62851191C>T		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_004535	0	0	0	0	0	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	37	CCDS13558.1																																																																																			C|0.999;T|0.001		0.657	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62851191	C	T	62851191	2	4	9	1	0	0	0	0	0	0	0	1	10131	535	19	1		1	MYT1	20	62851191	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08	14081035	62851191	174329	61	722											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382372	24382373	+	IGR	DNP	AT	AT	GC																															cattttctgctgctgctgctAttgctgctgctgctgctgct																								rs371342199|rs35206911|rs2695489|rs201827126		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:24382372_24382373AT>GC								AC004552.1 (15349 upstream) : PDK3 (100964 downstream)																							tgctgctgctattgctgctgct	0.574																																					.		.											.	.	0			c.T1496C						.																																			SO:0001628	intergenic_variant	100130302	exon1			CTGCTATTGCTGC																													X.37:g.24382372_24382373delinsGC		Somatic	10	1		WXS	Illumina HiSeq	Phase_I	6	2		0	0	0	0	0		Missense_Mutation	DNP		37																																																																																				.	0	0.574									GC	24382373	AT	GC	24382372	1	3	9	0	1	0	0	0	0	0	0	0	5592	449	16	3		3	FAM48B1	23	24382372	IGR	DNP	AT	TCGA-A4-7828-01A-11D-2136-08		24382372	130888188	62	723											
FLJ44635	0	ucsc.edu	37	chrX	71379997	71379997	+	IGR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatgaaatcaatcaaaggCaaactggaagaacagagacc	20	5	8	8	0	2	3	2	1	0	2	2	5	2	4	1	2	3	1	1	2	7	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:71379997C>G								BX119917.1 (7733 upstream) : PIN4 (21528 downstream)																							CAATCAAAGGCAAACTGGAAG	0.378																																					p.G106G													.	FLJ44635-108	0			c.C318G						.						81	72	75					X																	71379997		2202	4300	6502	SO:0001628	intergenic_variant	0	exon2			CAAAGGCAAACTG																													X.37:g.71379997C>G		Somatic	122	0		WXS	Illumina HiSeq		117	1	NM_207422	0	0	0	4	4		Silent	SNP		37																																																																																				.	0	0.378									G	71379997	C	G	71379997	1	3	9	0	1	0	0	0	0	0	0	0	5950	697	25	4		4	FLJ44635	23	71379997	IGR	SNP	C	TCGA-A4-7828-01A-11D-2136-08	46997625	71379997	83890563	63	724											
RGAG1	57529	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	109695056	109695056	+	Frame_Shift_Del	DEL	G	G	-																															gatgtctgcaccaccagtaaGagctttagattctggagcaa																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:109695056delG	ENST00000465301.2	+	3	1457	c.1211delG	c.(1210-1212)agafs	p.R404fs	RGAG1_ENST00000540313.1_Frame_Shift_Del_p.R404fs	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	404										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CCACCAGTAAGAGCTTTAGAT	0.502																																					p.R404fs		.											.	RGAG1-132	0			c.1211delG						.						195	202	200					X																	109695056		2203	4300	6503	SO:0001589	frameshift_variant	57529	exon3			.	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1211delG	X.37:g.109695056delG	ENSP00000419786:p.Arg404fs	Somatic	585	0		WXS	Illumina HiSeq	Phase_I	661	185	NM_020769	0	0	0	0	0	Q9P2M8	Frame_Shift_Del	DEL	ENST00000465301.2	37	CCDS14552.1																																																																																			.		0.502	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		-	109695056	G	-	109695056	7	5	9	1	0	1	0	1	0	0	0	0	13306	942	33	0	1213	0	RGAG1	23	109695056	Frame_Shift_Del	DEL	G	TCGA-A4-7828-01A-11D-2136-08	38315059	109695056	45575504	64	725	7	2									
RGAG1	57529	bcgsc.ca	37	chrX	109695057	109695057	+	Missense_Mutation	SNP	A	A	T																															atgtctgcaccaccagtaagAgctttagattctggagcaat																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:109695057A>T	ENST00000465301.2	+	3	1458	c.1212A>T	c.(1210-1212)agA>agT	p.R404S	RGAG1_ENST00000540313.1_Missense_Mutation_p.R404S	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	404										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CACCAGTAAGAGCTTTAGATT	0.498																																					p.R404S													.	RGAG1-132	0			c.A1212T						.						195	202	200					X																	109695057		2203	4300	6503	SO:0001583	missense	57529	exon3			AGTAAGAGCTTTA	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.1212A>T	X.37:g.109695057A>T	ENSP00000419786:p.Arg404Ser	Somatic	579	0		WXS	Illumina HiSeq	Phase_1	647	180	NM_020769	0	0	0	0	0	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.954058	0.34471	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.49720	0.77;0.77	4.06	4.06	0.47325	.	0.000000	0.37809	N	0.001935	T	0.39332	0.1074	L	0.46741	1.465	0.09310	N	1	P	0.42296	0.775	B	0.39660	0.306	T	0.29579	-1.0007	9	.	.	.	-7.0542	10.3612	0.43994	1.0:0.0:0.0:0.0	.	404	Q8NET4	RGAG1_HUMAN	S	404	ENSP00000419786:R404S;ENSP00000441452:R404S	.	R	+	3	2	RGAG1	109581713	0.999000	0.42202	0.018000	0.16275	0.101000	0.19017	4.796000	0.62496	1.807000	0.52817	0.486000	0.48141	AGA	.		0.498	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		T	109695057	A	T	109695057	3	4	9	1	0	0	0	0	1	0	0	0	13306	301	11	5	1214	5	RGAG1	23	109695057	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	1	109695057	45575503	65	726	7	2									
MBNL3	55796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	131540269	131540269	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacttacaagtgatgacattTgagcgttttggagcataagc	12	12	11	6	1	0	3	0	3	0	0	0	5	0	4	0	1	4	2	0	1	3	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:131540269T>A	ENST00000370853.3	-	2	407	c.329A>T	c.(328-330)cAa>cTa	p.Q110L	MBNL3_ENST00000394311.2_Missense_Mutation_p.Q14L|RAP2C-AS1_ENST00000441399.2_RNA|MBNL3_ENST00000370857.3_Missense_Mutation_p.Q110L|MBNL3_ENST00000370839.3_Missense_Mutation_p.Q110L|MBNL3_ENST00000370849.3_Missense_Mutation_p.Q60L|RAP2C-AS1_ENST00000421483.2_RNA|MBNL3_ENST00000473364.1_5'UTR|MBNL3_ENST00000370844.1_Missense_Mutation_p.Q14L|MBNL3_ENST00000538204.1_Missense_Mutation_p.Q60L	NM_018388.3	NP_060858.2	Q9NUK0	MBNL3_HUMAN	muscleblind-like splicing regulator 3	110					mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|negative regulation of myoblast differentiation (GO:0045662)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)	16	Acute lymphoblastic leukemia(192;0.000127)					TGATGACATTTGAGCGTTTTG	0.453																																					p.Q110L		.											.	MBNL3-130	0			c.A329T						.						144	116	125					X																	131540269		2203	4300	6503	SO:0001583	missense	55796	exon2			GACATTTGAGCGT	AF491305	CCDS14633.1, CCDS14634.1, CCDS55492.1, CCDS55493.1, CCDS55494.1	Xq26.2	2013-01-18	2012-02-23		ENSG00000076770	ENSG00000076770		"Zinc fingers, CCCH-type domain containing"	20564	protein-coding gene	gene with protein product		300413	"muscleblind-like 3 (Drosophila)"			12297108, 10970838	Standard	NM_018388		Approved	CHCR, FLJ11316, MBLX39, MBXL	uc004ewv.4	Q9NUK0	OTTHUMG00000022426	ENST00000370853.3:c.329A>T	X.37:g.131540269T>A	ENSP00000359890:p.Gln110Leu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	183	62	NM_018388	0	0	0	0	0	Q5JXN8|Q5JXN9|Q5JXP4|Q6UDQ1|Q8IUR4|Q8TAD9|Q8TAF4|Q9H0Z7|Q9UF37	Missense_Mutation	SNP	ENST00000370853.3	37	CCDS14633.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.534641	0.27475	.	.	ENSG00000076770	ENST00000394311;ENST00000538204;ENST00000370857;ENST00000370853;ENST00000370849;ENST00000370839;ENST00000370844;ENST00000436215;ENST00000421707	T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.57	5.57	0.84162	.	0.086244	0.49916	D	0.000138	T	0.46328	0.1387	M	0.66939	2.045	0.49483	D	0.999793	B;B;B;P;P	0.35272	0.404;0.246;0.246;0.454;0.493	B;B;B;B;B	0.42771	0.287;0.346;0.286;0.397;0.157	T	0.38373	-0.9664	10	0.07644	T	0.81	-4.1668	14.7499	0.69516	0.0:0.0:0.0:1.0	.	60;110;110;60;14	Q9NUK0-4;Q9NUK0;Q9NUK0-2;Q9NUK0-3;Q8IUR4	.;MBNL3_HUMAN;.;.;.	L	14;60;110;110;60;110;14;14;14	ENSP00000377848:Q14L;ENSP00000439618:Q60L;ENSP00000359894:Q110L;ENSP00000359890:Q110L;ENSP00000359886:Q60L;ENSP00000359876:Q110L;ENSP00000359881:Q14L;ENSP00000406014:Q14L;ENSP00000402128:Q14L	ENSP00000359876:Q110L	Q	-	2	0	MBNL3	131367950	1.000000	0.71417	0.905000	0.35620	0.731000	0.41821	4.662000	0.61525	1.864000	0.54056	0.486000	0.48141	CAA	.		0.453	MBNL3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058319.1	NM_018388		A	131540269	T	A	131540269	3	1	9	1	0	0	0	0	1	0	0	0	9380	1812	63	5	824	5	MBNL3	23	131540269	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	21845212	131540269	23730291	66	727											
CDR1	1038	hgsc.bcm.edu	37	chrX	139866440	139866440	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtgtcttccaacaaaggtAcgtcttccaacaaaggtacg	12	11	8	10	2	2	0	0	0	2	0	4	0	4	0	2	2	4	2	2	2	6	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:139866440A>G	ENST00000370532.2	-	1	283	c.92T>C	c.(91-93)gTa>gCa	p.V31A		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	31	23 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				CAACAAAGGTACGTCTTCCAA	0.448																																					p.V31A		.											.	CDR1-130	0			c.T92C						.						171	162	165					X																	139866440		2203	4300	6503	SO:0001583	missense	1038	exon1			AAAGGTACGTCTT		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"Cerebellar degeneration-related protein-1 (34kD)"	302650	"cerebellar degeneration-related protein (34kD)"	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.92T>C	X.37:g.139866440A>G	ENSP00000359563:p.Val31Ala	Somatic	145	2		WXS	Illumina HiSeq	Phase_I	299	16	NM_004065	0	0	0	0	0	Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	CCDS14670.1	.	.	.	.	.	.	.	.	.	.	A	2.772	-0.255469	0.05829	.	.	ENSG00000184258	ENST00000370532	T	0.35048	1.33	1.84	-0.941	0.10402	.	.	.	.	.	T	0.15912	0.0383	N	0.19112	0.55	0.09310	N	1	P	0.35481	0.504	B	0.29598	0.104	T	0.14420	-1.0473	8	.	.	.	.	2.5052	0.04643	0.6001:0.0:0.1643:0.2356	.	31	P51861	CDR1_HUMAN	A	31	ENSP00000359563:V31A	.	V	-	2	0	CDR1	139694106	0.000000	0.05858	0.011000	0.14972	0.002000	0.02628	-0.414000	0.07114	-0.339000	0.08401	-1.671000	0.00744	GTA	.		0.448	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		G	139866440	A	G	139866440	3	3	9	1	0	0	0	0	1	0	0	0	3177	391	14	3	700	3	CDR1	23	139866440	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	8326171	139866440	15404120	67	728											
SLC6A8	6535	broad.mit.edu	37	chrX	152960547	152960547	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgctggcagcacctgaccCagcccatctggggcctccac	7	5	11	18	1	1	1	0	1	1	0	2	1	2	1	5	3	3	3	5	3	0	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:152960547C>T	ENST00000253122.5	+	13	2262	c.1786C>T	c.(1786-1788)Cag>Tag	p.Q596*	SLC6A8_ENST00000430077.2_Nonsense_Mutation_p.Q481*|SLC6A8_ENST00000485324.1_3'UTR	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	596					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	GCACCTGACCCAGCCCATCTG	0.652																																					p.Q596X													.	SLC6A8-131	0			c.C1786T						.						23	20	21					X																	152960547		2200	4296	6496	SO:0001587	stop_gained	6535	exon13			CTGACCCAGCCCA		CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.1786C>T	X.37:g.152960547C>T	ENSP00000253122:p.Gln596*	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	23	3	NM_005629	0	0	77	77	0	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Nonsense_Mutation	SNP	ENST00000253122.5	37	CCDS14726.1	.	.	.	.	.	.	.	.	.	.	c	38	6.723814	0.97792	.	.	ENSG00000130821	ENST00000253122;ENST00000430077;ENST00000328897	.	.	.	5.18	5.18	0.71444	.	0.415204	0.20801	U	0.085434	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	11.7212	0.51683	0.1766:0.8234:0.0:0.0	.	.	.	.	X	596;481;690	.	ENSP00000253122:Q596X	Q	+	1	0	SLC6A8	152613741	0.998000	0.40836	1.000000	0.80357	0.951000	0.60555	1.925000	0.40074	2.152000	0.67230	0.525000	0.51046	CAG	.		0.652	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			T	152960547	C	T	152960547	4	4	9	1	0	0	0	0	0	1	0	0	14722	595	21	2	1836	2	SLC6A8	23	152960547	Nonsense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	13094107	152960547	2310013	68	729											
ATP6AP1	537	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	153657422	153657422	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctcctgcggccgacactCatgaaggccacatcaccagc	9	5	11	16	2	2	1	2	1	0	0	3	2	3	1	4	3	2	1	4	3	1	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:153657422C>A	ENST00000369762.2	+	2	251	c.190C>A	c.(190-192)Cat>Aat	p.H64N		NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	64					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	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)					GGCCGACACTCATGAAGGCCA	0.617																																					p.H64N		.											.	ATP6AP1-138	0			c.C190A						.						87	75	79					X																	153657422		2203	4300	6503	SO:0001583	missense	537	exon2			GACACTCATGAAG	D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.190C>A	X.37:g.153657422C>A	ENSP00000358777:p.His64Asn	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	130	33	NM_001183	0	0	59	59	0	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	37	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756732	0.49362	.	.	ENSG00000071553	ENST00000369762;ENST00000422890;ENST00000449556	.	.	.	4.74	4.74	0.60224	.	0.240499	0.42420	D	0.000718	T	0.49133	0.1539	M	0.70275	2.135	0.09310	N	0.999994	B;B	0.30439	0.279;0.178	B;B	0.35813	0.18;0.211	T	0.43491	-0.9388	9	0.28530	T	0.3	-20.593	12.2641	0.54668	0.0:1.0:0.0:0.0	.	24;64	B3KR70;Q15904	.;VAS1_HUMAN	N	64	.	ENSP00000358777:H64N	H	+	1	0	ATP6AP1	153310616	0.775000	0.28604	0.966000	0.40874	0.457000	0.32468	1.869000	0.39519	1.939000	0.56221	0.529000	0.55759	CAT	.		0.617	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183		A	153657422	C	A	153657422	3	1	9	1	0	0	0	0	1	0	0	0	1166	826	29	4	196	4	ATP6AP1	23	153657422	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	696875	153657422	1613138	69	730											
PRDM16	63976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	3342300	3342300	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctcaagaagcacgagcAcgagaacgcaccaggtgggc	13	2	13	13	3	1	2	1	0	0	2	1	4	1	2	2	2	3	4	2	2	3	0			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:3342300A>G	ENST00000270722.5	+	13	3144	c.3095A>G	c.(3094-3096)cAc>cGc	p.H1032R	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378398.3_Missense_Mutation_p.H1032R|PRDM16_ENST00000378391.2_Missense_Mutation_p.H1032R|PRDM16_ENST00000511072.1_Missense_Mutation_p.H1033R|PRDM16_ENST00000441472.2_Missense_Mutation_p.H1031R|PRDM16_ENST00000514189.1_Missense_Mutation_p.H1032R|PRDM16_ENST00000442529.2_Missense_Mutation_p.H1031R			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	1032	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AAGCACGAGCACGAGAACGCA	0.667			T	EVI1	"MDS, AML"																																p.H1032R		.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16-660	0			c.A3095G						.						60	69	66					1																	3342300		2112	4203	6315	SO:0001583	missense	63976	exon13			ACGAGCACGAGAA	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.3095A>G	1.37:g.3342300A>G	ENSP00000270722:p.His1032Arg	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	123	24	NM_022114	0	0	0	0	0	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	A	15.68	2.904180	0.52333	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53;2.53;2.53;2.53;2.53	4.02	4.02	0.46733	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	U	0.000113	T	0.33702	0.0872	M	0.68317	2.08	0.51012	D	0.999906	D;D;B;D	0.60575	0.973;0.988;0.369;0.979	D;D;B;D	0.72982	0.921;0.979;0.364;0.953	T	0.08659	-1.0711	10	0.66056	D	0.02	.	12.9149	0.58200	1.0:0.0:0.0:0.0	.	1032;1032;1031;1031	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	R	1033;1032;1031;1031;1032;1032;1032;848;848;840	ENSP00000426975:H1033R;ENSP00000367651:H1032R;ENSP00000407968:H1031R;ENSP00000405253:H1031R;ENSP00000367643:H1032R;ENSP00000421400:H1032R;ENSP00000270722:H1032R;ENSP00000422504:H848R;ENSP00000425796:H840R	ENSP00000270722:H1032R	H	+	2	0	PRDM16	3332160	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	7.051000	0.76627	1.451000	0.47736	0.379000	0.24179	CAC	.		0.667	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		G	3342300	A	G	3342300	3	3	10	1	0	0	0	0	1	0	0	0	12486	159	6	3	3145	3	PRDM16	1	3342300	Missense_Mutation	SNP	A	TCGA-A4-7915-01A-11D-2201-08		3342300	245908321	1	731											
TAS1R1	80835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6639491	6639491	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaagtacctgcctgcggcCaacatgatggctgggctgag	8	7	15	11	1	0	2	0	2	0	0	0	2	0	2	3	4	4	4	3	4	3	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:6639491C>T	ENST00000333172.6	+	6	2566	c.2373C>T	c.(2371-2373)gcC>gcT	p.A791A	TAS1R1_ENST00000328191.4_3'UTR|ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000351136.3_Silent_p.A537A	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	791					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TGCCTGCGGCCAACATGATGG	0.587																																					p.A791A		.											.	TAS1R1-516	0			c.C2373T						.						97	86	90					1																	6639491		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon6			TGCGGCCAACATG		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.2373C>T	1.37:g.6639491C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	114	46	NM_138697	0	0	0	0	0	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	37	CCDS81.1																																																																																			.		0.587	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			T	6639491	C	T	6639491	2	4	10	1	0	0	0	0	0	0	0	1	15594	594	21	2		2	TAS1R1	1	6639491	Silent	SNP	C	TCGA-A4-7915-01A-11D-2201-08	3297191	6639491	242611130	2	732											
COL8A2	1296	hgsc.bcm.edu;bcgsc.ca	37	chr1	36564488	36564488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggcccacagctcctggcTcccccctggggcctggaact	4	8	12	17	0	0	0	0	0	0	0	2	1	2	1	6	5	2	2	6	5	1	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:36564488T>C	ENST00000397799.1	-	4	1018	c.794A>G	c.(793-795)gAg>gGg	p.E265G	COL8A2_ENST00000303143.4_Missense_Mutation_p.E265G|COL8A2_ENST00000481785.1_Missense_Mutation_p.E200G			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	265	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGCTCCTGGCTCCCCCCTGGG	0.657																																					p.E265G		.											.	COL8A2-90	0			c.A794G						.						14	17	16					1																	36564488		2193	4289	6482	SO:0001583	missense	1296	exon2			CCTGGCTCCCCCC	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"Collagens"	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.794A>G	1.37:g.36564488T>C	ENSP00000380901:p.Glu265Gly	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	65	4	NM_005202	0	0	0	0	0	Q5JV31|Q8TEJ5	Missense_Mutation	SNP	ENST00000397799.1	37	CCDS403.1	.	.	.	.	.	.	.	.	.	.	T	6.827	0.521652	0.13005	.	.	ENSG00000171812	ENST00000303143;ENST00000397799;ENST00000481785	D;D;D	0.93906	-3.31;-3.31;-3.31	3.91	3.91	0.45181	.	0.198447	0.43747	D	0.000533	D	0.88742	0.6519	L	0.52206	1.635	0.46298	D	0.998977	P	0.44877	0.845	B	0.40329	0.326	D	0.84976	0.0885	10	0.18276	T	0.48	.	8.5265	0.33309	0.1725:0.0:0.0:0.8275	.	265	P25067	CO8A2_HUMAN	G	265;265;200	ENSP00000305913:E265G;ENSP00000380901:E265G;ENSP00000436433:E200G	ENSP00000305913:E265G	E	-	2	0	COL8A2	36337075	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	3.987000	0.56944	1.639000	0.50556	0.334000	0.21626	GAG	.		0.657	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		C	36564488	T	C	36564488	3	2	10	1	0	0	0	0	1	0	0	0	3712	1551	54	3	1321	3	COL8A2	1	36564488	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08	29924997	36564488	212686133	3	733											
MACF1	23499	hgsc.bcm.edu	37	chr1	39908528	39908528	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	catgaaccaatgctgggagtCagtgttacagaaaacagagg	15	7	12	7	0	1	3	1	1	0	2	1	4	1	4	1	2	4	2	1	2	5	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:39908528C>G	ENST00000372915.3	+	77	19031	c.18944C>G	c.(18943-18945)tCa>tGa	p.S6315*	MACF1_ENST00000564288.1_Nonsense_Mutation_p.S6416*|MACF1_ENST00000539005.1_Nonsense_Mutation_p.S4227*|MACF1_ENST00000361689.2_Nonsense_Mutation_p.S4357*|MACF1_ENST00000545844.1_Nonsense_Mutation_p.S4357*|MACF1_ENST00000567887.1_Nonsense_Mutation_p.S6453*|MACF1_ENST00000289893.4_Nonsense_Mutation_p.S4859*|MACF1_ENST00000317713.7_Nonsense_Mutation_p.S4357*			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6315					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGCTGGGAGTCAGTGTTACAG	0.483																																					p.S4357X		.											.	MACF1-165	0			c.C13070G						.						63	54	57					1																	39908528		2203	4300	6503	SO:0001587	stop_gained	23499	exon75			GGGAGTCAGTGTT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18944C>G	1.37:g.39908528C>G	ENSP00000362006:p.Ser6315*	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_012090	0	0	43	43	0	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Nonsense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	50	16.952701	0.99876	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.	.	.	5.82	5.82	0.92795	.	0.129756	0.35495	N	0.003165	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	13.3128	0.60390	0.0:0.9281:0.0:0.0719	.	.	.	.	X	4357;6315;4357;4357;4227;4859	.	ENSP00000289893:S4859X	S	+	2	0	MACF1	39681115	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	2.693000	0.47027	2.752000	0.94435	0.655000	0.94253	TCA	.		0.483	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39908528	C	G	39908528	4	3	10	1	0	0	0	0	0	1	0	0	9169	838	29	4	19515	4	MACF1	1	39908528	Nonsense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	3344040	39908528	209342093	4	734											
NPR1	4881	hgsc.bcm.edu	37	chr1	153651704	153651704	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacctgacggtagccgtggtActgccgctggccaatacctc	8	8	11	14	3	0	1	0	1	0	0	1	1	0	1	5	3	5	3	5	3	5	3	rs375325568	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:153651704A>G	ENST00000368680.3	+	1	592	c.120A>G	c.(118-120)gtA>gtG	p.V40V		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	40					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TAGCCGTGGTACTGCCGCTGG	0.741													A|||	5	0.000998403	0.0038	0	5008	,	,		13275	0		0	False		,,,				2504	0				p.V40V	Pancreas(141;1349 1870 15144 15830 40702)	.											.	NPR1-393	0			c.A120G						.	A		10,3462		0,10,1726	5	5	5		120	1.6	1	1		5	0,6794		0,0,3397	no	coding-synonymous	NPR1	NM_000906.3		0,10,5123	GG,GA,AA		0.0,0.288,0.0974		40/1062	153651704	10,10256	1736	3397	5133	SO:0001819	synonymous_variant	4881	exon1			CGTGGTACTGCCG	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"guanylate cyclase A"	108960	"atrionatriuretic peptide receptor A", "natriuretic peptide receptor A"	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.120A>G	1.37:g.153651704A>G		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_000906	0	0	0	0	0	B0ZBF0|Q5SR08|Q6P4Q3	Silent	SNP	ENST00000368680.3	37	CCDS1051.1																																																																																			.		0.741	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		G	153651704	A	G	153651704	2	3	10	1	0	0	0	0	0	0	0	1	10620	378	14	3		3	NPR1	1	153651704	Silent	SNP	A	TCGA-A4-7915-01A-11D-2201-08	113743176	153651704	95598917	5	735											
PAPPA2	60676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	176809321	176809321	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccctacagcccttccaagcaGatggttggtgtgacactatc	9	10	9	13	0	0	2	0	1	0	1	2	2	1	2	3	2	3	2	3	2	3	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:176809321G>A	ENST00000367662.3	+	22	6379	c.5215G>A	c.(5215-5217)Gat>Aat	p.D1739N		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1739				D -> N (in Ref. 6; CAC11134). {ECO:0000305}.	bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CTTCCAAGCAGATGGTTGGTG	0.507																																					p.D1739N		.											.	PAPPA2-548	0			c.G5215A						.						155	155	155					1																	176809321		2032	4183	6215	SO:0001583	missense	60676	exon22			CAAGCAGATGGTT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.5215G>A	1.37:g.176809321G>A	ENSP00000356634:p.Asp1739Asn	Somatic	277	0		WXS	Illumina HiSeq	Phase_I	310	90	NM_020318	0	0	0	0	0	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	35	5.437435	0.96168	.	.	ENSG00000116183	ENST00000367662	D	0.91894	-2.93	5.44	5.44	0.79542	Notch domain (2);	0.000000	0.85682	D	0.000000	D	0.95674	0.8593	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95767	0.8805	10	0.66056	D	0.02	-17.6405	18.8699	0.92309	0.0:0.0:1.0:0.0	.	1739	Q9BXP8	PAPP2_HUMAN	N	1739	ENSP00000356634:D1739N	ENSP00000356634:D1739N	D	+	1	0	PAPPA2	175075944	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.729000	0.91490	2.544000	0.85801	0.655000	0.94253	GAT	.		0.507	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176809321	G	A	176809321	3	1	10	1	0	0	0	0	1	0	0	0	11459	942	33	2	5350	2	PAPPA2	1	176809321	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	23157617	176809321	72441300	6	736											
RYR2	6262	broad.mit.edu;bcgsc.ca	37	chr1	237604652	237604652	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	taggggtgagaaaagaagtaGatggcatgggaacatctgaa	16	7	15	3	0	1	4	0	2	1	3	1	6	1	5	0	4	1	2	0	4	7	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:237604652G>C	ENST00000366574.2	+	13	1356	c.1039G>C	c.(1039-1041)Gat>Cat	p.D347H	RYR2_ENST00000360064.6_Missense_Mutation_p.D345H|RYR2_ENST00000542537.1_Missense_Mutation_p.D331H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	347					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AAAAGAAGTAGATGGCATGGG	0.388																																					p.D347H													.	RYR2-158	0			c.G1039C						.						152	147	149					1																	237604652		1865	4108	5973	SO:0001583	missense	6262	exon13			GAAGTAGATGGCA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1039G>C	1.37:g.237604652G>C	ENSP00000355533:p.Asp347His	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	133	5	NM_001035	0	0	0	0	0	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.599191	0.66332	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.86497	-2.13;-2.13;-2.13	5.39	5.39	0.77823	MIR motif (1);MIR (2);	0.076275	0.48767	D	0.000165	D	0.90587	0.7049	L	0.33485	1.01	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.91523	0.5236	10	0.87932	D	0	.	19.5142	0.95155	0.0:0.0:1.0:0.0	.	347	Q92736	RYR2_HUMAN	H	347;345;331	ENSP00000355533:D347H;ENSP00000353174:D345H;ENSP00000443798:D331H	ENSP00000353174:D345H	D	+	1	0	RYR2	235671275	1.000000	0.71417	0.892000	0.35008	0.325000	0.28411	9.800000	0.99124	2.679000	0.91253	0.655000	0.94253	GAT	.		0.388	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237604652	G	C	237604652	3	2	10	1	0	0	0	0	1	0	0	0	13801	942	33	4	1089	4	RYR2	1	237604652	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	60795331	237604652	11645969	7	737											
GREB1	9687	broad.mit.edu;bcgsc.ca	37	chr2	11716612	11716612	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtattacctggtccgtaaTgcacaagggactctaaccaa	14	9	8	10	1	1	0	0	0	1	0	2	1	2	1	3	2	3	3	3	2	7	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr2:11716612T>A	ENST00000381486.2	+	5	888	c.588T>A	c.(586-588)aaT>aaA	p.N196K	GREB1_ENST00000389825.3_Missense_Mutation_p.N86K|GREB1_ENST00000234142.5_Missense_Mutation_p.N196K|GREB1_ENST00000381483.2_Missense_Mutation_p.N196K|GREB1_ENST00000263834.5_Missense_Mutation_p.N196K	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	196						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TGGTCCGTAATGCACAAGGGA	0.478																																					p.N196K	Ovarian(39;850 945 2785 23371 33093)												.	GREB1-91	0			c.T588A						.						126	120	122					2																	11716612		2203	4300	6503	SO:0001583	missense	9687	exon5			CCGTAATGCACAA		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.588T>A	2.37:g.11716612T>A	ENSP00000370896:p.Asn196Lys	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	182	7	NM_148903	0	0	0	0	0	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520760	0.64747	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000389825;ENST00000381483;ENST00000234142	T;D;D;D;T	0.82167	3.02;-1.58;-1.58;-1.58;3.02	5.08	-3.82	0.04281	.	0.000000	0.85682	D	0.000000	D	0.84428	0.5470	M	0.66939	2.045	0.58432	D	0.99999	P;D;P;D	0.54772	0.94;0.968;0.897;0.959	P;P;P;P	0.54889	0.625;0.763;0.465;0.526	T	0.82952	-0.0202	10	0.72032	D	0.01	-8.2171	13.0658	0.59032	0.0:0.4458:0.0:0.5542	.	196;86;196;196	Q4ZG55-2;F8W6E5;Q4ZG55-3;Q4ZG55	.;.;.;GREB1_HUMAN	K	196;196;86;196;196	ENSP00000370896:N196K;ENSP00000263834:N196K;ENSP00000374475:N86K;ENSP00000370892:N196K;ENSP00000234142:N196K	ENSP00000234142:N196K	N	+	3	2	GREB1	11634063	0.667000	0.27484	0.014000	0.15608	0.860000	0.49131	-0.199000	0.09491	-1.399000	0.02063	-1.139000	0.01908	AAT	.		0.478	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11716612	T	A	11716612	3	1	10	1	0	0	0	0	1	0	0	0	6781	1461	51	5	602	5	GREB1	2	11716612	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08		11716612	231482761	8	738											
GRM2	2912	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	51750001	51750001	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggcctacaatgtgctcCtcatcgcgctctgcacgctt	5	11	9	16	4	2	0	1	0	1	0	4	0	3	0	2	1	3	5	2	1	2	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:51750001C>T	ENST00000395052.3	+	4	2446	c.2212C>T	c.(2212-2214)Ctc>Ttc	p.L738F	GRM2_ENST00000442933.2_Intron|GRM2_ENST00000475478.1_3'UTR	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	738					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAATGTGCTCCTCATCGCGCT	0.577																																					p.L738F		.											.	GRM2-522	0			c.C2212T						.						120	94	103					3																	51750001		2203	4300	6503	SO:0001583	missense	2912	exon4			GTGCTCCTCATCG	L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.2212C>T	3.37:g.51750001C>T	ENSP00000378492:p.Leu738Phe	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	104	31	NM_000839	0	0	0	0	0	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937162	0.73557	.	.	ENSG00000164082	ENST00000395052	D	0.96365	-3.99	5.14	5.14	0.70334	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98604	0.9533	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98917	1.0782	10	0.87932	D	0	.	10.6161	0.45451	0.0:0.8753:0.0:0.1247	.	738	Q14416	GRM2_HUMAN	F	738	ENSP00000378492:L738F	ENSP00000378492:L738F	L	+	1	0	GRM2	51725041	1.000000	0.71417	0.998000	0.56505	0.864000	0.49448	5.989000	0.70587	2.567000	0.86603	0.549000	0.68633	CTC	.		0.577	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51750001	C	T	51750001	3	4	10	1	0	0	0	0	1	0	0	0	6818	681	24	2	2222	2	GRM2	3	51750001	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		51750001	146272429	9	739											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52678740	52678740	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcattcgaagacttgacttAgccatttcatgatgttcaat	11	15	6	9	1	3	3	3	2	0	1	4	4	3	3	1	0	1	1	1	0	3	5			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:52678740A>G	ENST00000296302.7	-	8	880	c.879T>C	c.(877-879)gcT>gcC	p.A293A	PBRM1_ENST00000409114.3_Silent_p.A293A|PBRM1_ENST00000356770.4_Silent_p.A293A|PBRM1_ENST00000410007.1_Silent_p.A293A|PBRM1_ENST00000337303.4_Silent_p.A293A|PBRM1_ENST00000409767.1_Silent_p.A293A|PBRM1_ENST00000409057.1_Silent_p.A293A|PBRM1_ENST00000394830.3_Silent_p.A293A			Q86U86	PB1_HUMAN	polybromo 1	293					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GACTTGACTTAGCCATTTCAT	0.383			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.A293A		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.T879C						.						113	98	103					3																	52678740		2202	4300	6502	SO:0001819	synonymous_variant	55193	exon9			TGACTTAGCCATT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.879T>C	3.37:g.52678740A>G		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_018313	0	0	4	4	0	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				.		0.383	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		G	52678740	A	G	52678740	2	3	10	1	0	0	0	0	0	0	0	1	11517	407	15	3		3	PBRM1	3	52678740	Silent	SNP	A	TCGA-A4-7915-01A-11D-2201-08	928739	52678740	145343690	10	740											
CADPS	8618	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	62477094	62477096	+	In_Frame_Del	DEL	AAC	AAC	-																															tccatcagatccacatatctAacaacaagtggggcaaacag																										TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:62477094_62477096delAAC	ENST00000383710.4	-	21	3293_3295	c.2944_2946delGTT	c.(2944-2946)gttdel	p.V982del	CADPS_ENST00000357948.3_In_Frame_Del_p.V952del|CADPS_ENST00000283269.9_In_Frame_Del_p.V992del	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	982	Interaction with DRD2.|MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CCACATATCTAACAACAAGTGGG	0.419																																					p.992_992del		.											.	CADPS-281	0			c.2974_2976del						.																																			SO:0001651	inframe_deletion	8618	exon20			.	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2944_2946delGTT	3.37:g.62477097_62477099delAAC	ENSP00000373215:p.Val982del	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	191	53	NM_183394	0	0	0	0	0	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	In_Frame_Del	DEL	ENST00000383710.4	37	CCDS46858.1																																																																																			.		0.419	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		-	62477096	AAC	-	62477094	7	5	10	1	0	1	0	1	0	0	0	0	2576	349	13	0	1155	0	CADPS	3	62477094	In_Frame_Del	DEL	AAC	TCGA-A4-7915-01A-11D-2201-08	9798354	62477094	135545336	11	741											
LMOD3	56203	hgsc.bcm.edu	37	chr3	69169080	69169080	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcatcttcttcatctgtTtcttggatattgctgctgcc	4	20	6	11	0	7	0	2	0	5	0	7	1	7	1	1	1	3	3	1	1	1	7	rs111848977	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:69169080T>C	ENST00000420581.2	-	2	605	c.426A>G	c.(424-426)gaA>gaG	p.E142E	LMOD3_ENST00000475434.1_Silent_p.E142E|LMOD3_ENST00000489031.1_Silent_p.E142E	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	142	Glu-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		cttcatctgtttcttGGATAT	0.358													T|||	36	0.0071885	0.0265	0.0014	5008	,	,		19320	0		0	False		,,,				2504	0				p.E142E		.											.	LMOD3-23	0			c.A426G						.	T		76,3864		3,70,1897	99	85	89		426	1.2	0.7	3	dbSNP_132	89	0,8242		0,0,4121	no	coding-synonymous	LMOD3	NM_198271.3		3,70,6018	CC,CT,TT		0.0,1.9289,0.6239		142/561	69169080	76,12106	1970	4121	6091	SO:0001819	synonymous_variant	56203	exon2			ATCTGTTTCTTGG	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.426A>G	3.37:g.69169080T>C		Somatic	6	1		WXS	Illumina HiSeq	Phase_I	7	4	NM_198271	0	0	0	0	0	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Silent	SNP	ENST00000420581.2	37	CCDS46862.1																																																																																			T|0.995;C|0.005		0.358	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529		C	69169080	T	C	69169080	2	2	10	1	0	0	0	0	0	0	0	1	8881	1838	64	3		3	LMOD3	3	69169080	Silent	SNP	T	TCGA-A4-7915-01A-11D-2201-08	6691986	69169080	128853350	12	742											
KIAA2018	205717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113376859	113376859	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agttgaatcctgtaaagatgCatttgatgttttaattccta	12	17	7	5	0	0	3	0	2	0	1	2	3	2	3	2	0	1	4	2	0	5	7			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:113376859C>A	ENST00000478658.1	-	5	3687	c.3670G>T	c.(3670-3672)Gca>Tca	p.A1224S	KIAA2018_ENST00000316407.4_Missense_Mutation_p.A1224S|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1224						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						TGTAAAGATGCATTTGATGTT	0.418																																					p.A1224S		.											.	KIAA2018-93	0			c.G3670T						.						86	83	84					3																	113376859		1945	4164	6109	SO:0001583	missense	205717	exon7			AAGATGCATTTGA	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.3670G>T	3.37:g.113376859C>A	ENSP00000420721:p.Ala1224Ser	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	101	29	NM_001009899	0	0	2	2	0	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	C	3.356	-0.131444	0.06753	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.14022	2.54;2.54	5.67	3.84	0.44239	.	0.282276	0.34386	N	0.004013	T	0.05547	0.0146	N	0.14661	0.345	0.28041	N	0.933755	B	0.15141	0.012	B	0.12156	0.007	T	0.38950	-0.9637	10	0.07030	T	0.85	-2.1301	2.9175	0.05757	0.3149:0.4409:0.1391:0.1051	.	1224	Q68DE3	K2018_HUMAN	S	1224	ENSP00000320794:A1224S;ENSP00000420721:A1224S	ENSP00000320794:A1224S	A	-	1	0	KIAA2018	114859549	0.971000	0.33674	0.911000	0.35937	0.515000	0.34225	0.248000	0.18198	0.701000	0.31803	0.561000	0.74099	GCA	.		0.418	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113376859	C	A	113376859	3	1	10	1	0	0	0	0	1	0	0	0	8289	710	25	4	3071	4	KIAA2018	3	113376859	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	44207779	113376859	84645571	13	743											
MUC20	200958	hgsc.bcm.edu	37	chr3	195456549	195456549	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtttcctcctcctgcggcTgagtgtggcttccccggaag	4	11	13	13	2	0	1	0	1	0	0	4	2	4	2	5	4	1	3	5	4	1	2	rs201857816	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:195456549T>C	ENST00000447234.2	+	3	2126	c.2000T>C	c.(1999-2001)cTg>cCg	p.L667P	MUC20_ENST00000445522.2_Missense_Mutation_p.L632P|MUC20_ENST00000436408.1_Missense_Mutation_p.L667P|MUC20_ENST00000320736.6_Missense_Mutation_p.L496P	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	667	Interaction with MET.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTCCTGCGGCTGAGTGTGGCT	0.577													.|||	18	0.00359425	0.0136	0	5008	,	,		29066	0		0	False		,,,				2504	0				p.L496P		.											.	.	0			c.T1487C						.		PRO/LEU,PRO/LEU	22,3968		0,22,1973	50	48	49		1382,1487	4.6	1	3		49	0,8354		0,0,4177	yes	missense,missense	MUC20	NM_001098516.1,NM_152673.2	98,98	0,22,6150	CC,CT,TT		0.0,0.5514,0.1782	probably-damaging,probably-damaging	461/504,496/539	195456549	22,12322	1995	4177	6172	SO:0001583	missense	200958	exon4			TGCGGCTGAGTGT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"Mucins"	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.2000T>C	3.37:g.195456549T>C	ENSP00000414350:p.Leu667Pro	Somatic	24	1		WXS	Illumina HiSeq	Phase_I	22	6	NM_152673	0	0	17	19	2	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	T	14.72	2.618589	0.46736	0.005514	0.0	ENSG00000176945	ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.44083	1.44;1.76;1.47;0.93	4.63	4.63	0.57726	.	0.000000	0.32258	N	0.006354	T	0.44808	0.1311	L	0.39245	1.2	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.51513	-0.8696	10	0.66056	D	0.02	-6.0446	10.3989	0.44218	0.0:0.0:0.0:1.0	.	496	E9PH32	.	P	478;667;496;667;632	ENSP00000414350:L667P;ENSP00000325431:L496P;ENSP00000396774:L667P;ENSP00000405629:L632P	ENSP00000325431:L496P	L	+	2	0	MUC20	196942220	0.750000	0.28316	0.986000	0.45419	0.443000	0.32047	3.128000	0.50492	1.943000	0.56356	0.456000	0.33151	CTG	.		0.577	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		C	195456549	T	C	195456549	3	2	10	1	0	0	0	0	1	0	0	0	10001	1580	55	3	1501	3	MUC20	3	195456549	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08	82079690	195456549	2565881	14	744											
ADAD1	132612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123305047	123305047	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aaataaaaaggagtctagatCcaatgcagcaaaattagctc	19	8	7	7	0	1	1	0	0	1	1	3	2	2	2	1	1	3	3	1	1	9	3			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr4:123305047C>G	ENST00000296513.2	+	5	640	c.455C>G	c.(454-456)tCc>tGc	p.S152C	ADAD1_ENST00000388725.2_Missense_Mutation_p.S134C|ADAD1_ENST00000388724.2_Missense_Mutation_p.S152C|ADAD1_ENST00000492454.1_3'UTR	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	152	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GAGTCTAGATCCAATGCAGCA	0.368																																					p.S152C		.											.	ADAD1-90	0			c.C455G						.						123	120	121					4																	123305047		2203	4300	6503	SO:0001583	missense	132612	exon5			CTAGATCCAATGC	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.455C>G	4.37:g.123305047C>G	ENSP00000296513:p.Ser152Cys	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	115	29	NM_139243	0	0	0	0	0	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	37	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.993627	0.74703	.	.	ENSG00000164113	ENST00000446706;ENST00000296513;ENST00000439307;ENST00000388724;ENST00000388725	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.84	5.84	0.93424	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.354445	0.30455	N	0.009587	T	0.82181	0.4981	L	0.29908	0.895	0.33397	D	0.576823	D;D	0.69078	0.996;0.997	D;D	0.66351	0.936;0.943	D	0.85408	0.1135	10	0.54805	T	0.06	-7.2127	18.912	0.92489	0.0:1.0:0.0:0.0	.	152;152	Q96M93-2;Q96M93	.;ADAD1_HUMAN	C	152;152;152;152;134	ENSP00000390510:S152C;ENSP00000296513:S152C;ENSP00000397254:S152C;ENSP00000373376:S152C;ENSP00000373377:S134C	ENSP00000296513:S152C	S	+	2	0	ADAD1	123524497	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.447000	0.35101	2.768000	0.95171	0.579000	0.79373	TCC	.		0.368	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		G	123305047	C	G	123305047	3	3	10	1	0	0	0	0	1	0	0	0	231	855	30	4	465	4	ADAD1	4	123305047	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		123305047	67849229	15	745											
PGBD1	84547	broad.mit.edu;bcgsc.ca	37	chr6	28269463	28269463	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatctagtgatgaacttcgCtgatgttcttttagagagag	12	14	10	5	1	2	5	0	3	2	2	3	6	2	5	0	0	1	2	0	0	4	5			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr6:28269463C>T	ENST00000405948.2	+	7	2252	c.1832C>T	c.(1831-1833)gCt>gTt	p.A611V	PGBD1_ENST00000259883.3_Missense_Mutation_p.A611V	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	611						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ATGAACTTCGCTGATGTTCTT	0.408																																					p.A611V													.	PGBD1-94	0			c.C1832T						.						159	158	158					6																	28269463		2203	4300	6503	SO:0001583	missense	84547	exon7			ACTTCGCTGATGT	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"-"	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1832C>T	6.37:g.28269463C>T	ENSP00000385213:p.Ala611Val	Somatic	250	0		WXS	Illumina HiSeq	Phase_I	272	9	NM_001184743	0	0	0	0	0	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	C	9.249	1.040200	0.19669	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.15487	2.42;2.42	4.66	3.79	0.43588	.	0.000000	0.48767	D	0.000165	T	0.02083	0.0065	N	0.05306	-0.075	0.27589	N	0.94933	B	0.20550	0.046	B	0.31869	0.137	T	0.46898	-0.9158	10	0.02654	T	1	-14.8085	8.97	0.35901	0.0:0.8988:0.0:0.1012	.	611	Q96JS3	PGBD1_HUMAN	V	611	ENSP00000385213:A611V;ENSP00000259883:A611V	ENSP00000259883:A611V	A	+	2	0	PGBD1	28377442	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.137000	0.31479	1.323000	0.45263	0.655000	0.94253	GCT	.		0.408	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28269463	C	T	28269463	3	4	10	1	0	0	0	0	1	0	0	0	11806	797	28	2	1854	2	PGBD1	6	28269463	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		28269463	142845604	16	746											
SLC35D3	340146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	137245376	137245376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtgtggtgaagagcatcGccaccatcacggtgggcatg	8	8	16	9	2	1	2	1	1	0	1	2	2	1	2	2	4	1	2	2	4	1	0			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr6:137245376G>A	ENST00000331858.4	+	2	958	c.793G>A	c.(793-795)Gcc>Acc	p.A265T		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	265					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		GAAGAGCATCGCCACCATCAC	0.592																																					p.A265T		.											.	SLC35D3-91	0			c.G793A						.						77	64	68					6																	137245376		2203	4300	6503	SO:0001583	missense	340146	exon2			AGCATCGCCACCA		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.793G>A	6.37:g.137245376G>A	ENSP00000333591:p.Ala265Thr	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	76	12	NM_001008783	0	0	0	0	0	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354459	0.82243	.	.	ENSG00000182747	ENST00000331858	T	0.64085	-0.08	5.68	5.68	0.88126	Domain of unknown function DUF250 (1);	0.056787	0.64402	D	0.000001	T	0.63034	0.2477	L	0.36672	1.1	0.58432	D	0.999995	D	0.67145	0.996	P	0.60682	0.878	T	0.58713	-0.7588	10	0.34782	T	0.22	-25.1818	19.7951	0.96477	0.0:0.0:1.0:0.0	.	265	Q5M8T2	S35D3_HUMAN	T	265	ENSP00000333591:A265T	ENSP00000333591:A265T	A	+	1	0	SLC35D3	137287069	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.777000	0.85628	2.698000	0.92095	0.561000	0.74099	GCC	.		0.592	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		A	137245376	G	A	137245376	3	1	10	1	0	0	0	0	1	0	0	0	14615	1087	38	1	799	1	SLC35D3	6	137245376	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	108975913	137245376	33869691	17	747											
IFNGR1	3459	broad.mit.edu;bcgsc.ca	37	chr6	137519461	137519461	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagtgatacgagtttaaagCgatgctgccaggttcagact	11	10	13	7	2	1	2	1	1	0	1	1	5	1	3	1	2	4	3	1	2	3	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr6:137519461C>A	ENST00000367739.4	-	7	1298	c.1177G>T	c.(1177-1179)Gct>Tct	p.A393S	IFNGR1_ENST00000543628.1_Missense_Mutation_p.A365S	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	393					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	GAGTTTAAAGCGATGCTGCCA	0.443																																					p.A393S													.	IFNGR1-91	0			c.G1177T						.						88	88	88					6																	137519461		2203	4300	6503	SO:0001583	missense	3459	exon7			TTAAAGCGATGCT		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"Interferons", "CD molecules"	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.1177G>T	6.37:g.137519461C>A	ENSP00000356713:p.Ala393Ser	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	101	5	NM_000416	1	0	72	73	0	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	37	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.776120	0.31411	.	.	ENSG00000027697	ENST00000367739;ENST00000543628	T;T	0.72394	-0.65;-0.49	6.06	-12.1	0.00011	.	2.161120	0.01880	N	0.037820	T	0.20577	0.0495	N	0.12182	0.205	0.09310	N	1	B;B	0.20164	0.031;0.042	B;B	0.22601	0.04;0.03	T	0.10917	-1.0609	10	0.27082	T	0.32	-0.1572	5.4548	0.16584	0.1953:0.5294:0.0993:0.176	.	365;393	F5H5M7;P15260	.;INGR1_HUMAN	S	393;365	ENSP00000356713:A393S;ENSP00000443282:A365S	ENSP00000356713:A393S	A	-	1	0	IFNGR1	137561154	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.897000	0.01603	-2.423000	0.00562	-1.202000	0.01658	GCT	.		0.443	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			A	137519461	C	A	137519461	3	1	10	1	0	0	0	0	1	0	0	0	7570	768	27	4	296	4	IFNGR1	6	137519461	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	274085	137519461	33595606	18	748											
RP9	6100	broad.mit.edu	37	chr7	33136131	33136131	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttttcatgtcgtttattGtctcgtatgatgtcatacat	7	20	6	8	2	3	1	2	1	1	0	6	1	4	1	1	0	1	2	1	0	3	7			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr7:33136131G>A	ENST00000297157.3	-	5	458	c.441C>T	c.(439-441)gaC>gaT	p.D147D		NM_203288.1	NP_976033.1	Q8TA86	RP9_HUMAN	retinitis pigmentosa 9 (autosomal dominant)	147	PIM1-binding. {ECO:0000250}.				cognition (GO:0050890)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|signal recognition particle receptor complex (GO:0005785)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|urinary_tract(1)	7			GBM - Glioblastoma multiforme(11;0.0403)			GTCGTTTATTGTCTCGTATGA	0.368																																					p.D147D													.	RP9-90	0			c.C441T						.						255	217	230					7																	33136131		2203	4300	6503	SO:0001819	synonymous_variant	6100	exon5			TTTATTGTCTCGT	AX016710	CCDS5440.1	7p14.3	2014-01-28			ENSG00000164610	ENSG00000164610			10288	protein-coding gene	gene with protein product	"Pim-1 kinase associated protein"	607331				8513323	Standard	NM_203288		Approved	PAP-1	uc003tdm.3	Q8TA86	OTTHUMG00000152988	ENST00000297157.3:c.441C>T	7.37:g.33136131G>A		Somatic	127	1		WXS	Illumina HiSeq	Phase_I	111	6	NM_203288	0	0	19	19	0		Silent	SNP	ENST00000297157.3	37	CCDS5440.1																																																																																			.		0.368	RP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328914.1	NM_203288		A	33136131	G	A	33136131	2	1	10	1	0	0	0	0	0	0	0	1	13567	1368	48	2		2	RP9	7	33136131	Silent	SNP	G	TCGA-A4-7915-01A-11D-2201-08		33136131	126002532	19	749											
LAMB1	3912	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107572810	107572810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaacaggaggcccctggggGtgttccacaggtctgcaaca	9	6	15	11	0	1	0	0	0	1	0	2	2	2	2	3	6	3	2	3	6	2	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr7:107572810G>A	ENST00000222399.6	-	28	4431	c.4201C>T	c.(4201-4203)Ccc>Tcc	p.P1401S	LAMB1_ENST00000474380.1_5'UTR|LAMB1_ENST00000393561.1_Missense_Mutation_p.P1425S	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1401	Domain alpha.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)	p.P1401T(1)		NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GCCCCTGGGGGTGTTCCACAG	0.592																																					p.P1401S		.											.	LAMB1-97	1	Substitution - Missense(1)	lung(1)	c.C4201T						.						67	64	65					7																	107572810		2203	4300	6503	SO:0001583	missense	3912	exon28			CTGGGGGTGTTCC	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.4201C>T	7.37:g.107572810G>A	ENSP00000222399:p.Pro1401Ser	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	152	45	NM_002291	0	0	0	0	0	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.918956	0.33908	.	.	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.29917	1.55;1.55	5.28	5.28	0.74379	.	.	.	.	.	T	0.24890	0.0604	L	0.37850	1.14	0.33891	D	0.637353	B;B	0.17667	0.023;0.014	B;B	0.17098	0.017;0.016	T	0.20042	-1.0287	9	0.45353	T	0.12	.	9.8304	0.40939	0.0744:0.1405:0.7851:0.0	.	1401;1425	P07942;G3XAI2	LAMB1_HUMAN;.	S	1425;1401	ENSP00000377191:P1425S;ENSP00000222399:P1401S	ENSP00000222399:P1401S	P	-	1	0	LAMB1	107360046	0.999000	0.42202	0.979000	0.43373	0.967000	0.64934	4.639000	0.61361	2.627000	0.88993	0.655000	0.94253	CCC	.		0.592	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107572810	G	A	107572810	3	1	10	1	0	0	0	0	1	0	0	0	8631	1261	44	2	1187	2	LAMB1	7	107572810	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	74436679	107572810	51565853	20	750											
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121653581	121653581	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaagtgtatcctcagacaGtcaaactggtatggacagaa	15	8	9	9	0	2	2	2	0	0	2	3	3	3	3	1	2	1	2	1	2	5	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr7:121653581G>T	ENST00000393386.2	+	12	4892	c.4481G>T	c.(4480-4482)aGt>aTt	p.S1494I	PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1494					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TCCTCAGACAGTCAAACTGGT	0.398																																					p.S1494I		.											.	PTPRZ1-699	0			c.G4481T						.						88	85	86					7																	121653581		2203	4300	6503	SO:0001583	missense	5803	exon12			CAGACAGTCAAAC	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.4481G>T	7.37:g.121653581G>T	ENSP00000377047:p.Ser1494Ile	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	91	29	NM_002851	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756857	0.49362	.	.	ENSG00000106278	ENST00000393386	T	0.54071	0.59	4.95	4.07	0.47477	.	0.299113	0.33057	N	0.005339	T	0.43456	0.1248	L	0.44542	1.39	0.80722	D	1	B	0.33379	0.41	B	0.35550	0.205	T	0.33394	-0.9870	10	0.37606	T	0.19	.	9.1534	0.36978	0.1675:0.0:0.8325:0.0	.	1494	P23471	PTPRZ_HUMAN	I	1494	ENSP00000377047:S1494I	ENSP00000377047:S1494I	S	+	2	0	PTPRZ1	121440817	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.448000	0.35112	1.215000	0.43411	0.555000	0.69702	AGT	.		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121653581	G	T	121653581	3	4	10	1	0	0	0	0	1	0	0	0	12846	1029	36	4	4527	4	PTPRZ1	7	121653581	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	14080771	121653581	37485082	21	751											
SHH	6469	hgsc.bcm.edu	37	chr7	155596098	155596098	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgaggccccagtgcgcccccGgaaggcggccccgagcccga	6	1	15	19	6	0	0	0	0	0	0	0	4	0	1	7	4	2	0	7	4	1	0	rs549625672	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr7:155596098G>A	ENST00000297261.2	-	3	1035	c.885C>T	c.(883-885)tcC>tcT	p.S295S		NM_000193.2	NP_000184.1	Q15465	SHH_HUMAN	sonic hedgehog	295					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|artery development (GO:0060840)|axon guidance (GO:0007411)|Bergmann glial cell differentiation (GO:0060020)|blood coagulation (GO:0007596)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bud outgrowth involved in lung branching (GO:0060447)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway (GO:0060070)|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment (GO:0043369)|cell development (GO:0048468)|cell fate specification (GO:0001708)|cell-cell signaling (GO:0007267)|cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|cerebellar granule cell precursor proliferation (GO:0021930)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|dorsal/ventral neural tube patterning (GO:0021904)|dorsal/ventral pattern formation (GO:0009953)|ectoderm development (GO:0007398)|embryo development (GO:0009790)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal system development (GO:0048706)|endocytosis (GO:0006897)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|establishment of cell polarity (GO:0030010)|forebrain development (GO:0030900)|formation of anatomical boundary (GO:0048859)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|hindgut morphogenesis (GO:0007442)|inner ear development (GO:0048839)|intein-mediated protein splicing (GO:0016539)|intermediate filament organization (GO:0045109)|left lung development (GO:0060459)|limb bud formation (GO:0060174)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|lymphoid progenitor cell differentiation (GO:0002320)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal smoothened signaling pathway involved in prostate gland development (GO:0060783)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephros development (GO:0001656)|midbrain development (GO:0030901)|multicellular structure septum development (GO:0080125)|myoblast differentiation (GO:0045445)|myotube differentiation (GO:0014902)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of kidney smooth muscle cell differentiation (GO:2000357)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ureter smooth muscle cell differentiation (GO:2000062)|negative thymic T cell selection (GO:0045060)|neural crest cell migration (GO:0001755)|neuroblast proliferation (GO:0007405)|neuron fate commitment (GO:0048663)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|organ formation (GO:0048645)|osteoblast development (GO:0002076)|palate development (GO:0060021)|pancreas development (GO:0031016)|pattern specification process (GO:0007389)|patterning of blood vessels (GO:0001569)|polarity specification of anterior/posterior axis (GO:0009949)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of immature T cell proliferation in thymus (GO:0033092)|positive regulation of kidney smooth muscle cell differentiation (GO:2000358)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sclerotome development (GO:0061189)|positive regulation of skeletal muscle cell proliferation (GO:0014858)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureter smooth muscle cell differentiation (GO:2000063)|positive regulation of Wnt signaling pathway (GO:0030177)|positive thymic T cell selection (GO:0045059)|primary prostatic bud elongation (GO:0060516)|prostate epithelial cord elongation (GO:0060523)|prostate gland development (GO:0030850)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|regulation of mesenchymal cell proliferation involved in prostate gland development (GO:0060782)|regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900175)|regulation of odontogenesis (GO:0042481)|regulation of prostatic bud formation (GO:0060685)|regulation of protein localization to nucleus (GO:1900180)|regulation of proteolysis (GO:0030162)|renal system development (GO:0072001)|right lung development (GO:0060458)|salivary gland cavitation (GO:0060662)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|somite development (GO:0061053)|spinal cord dorsal/ventral patterning (GO:0021513)|spinal cord motor neuron differentiation (GO:0021522)|stem cell development (GO:0048864)|striated muscle tissue development (GO:0014706)|T cell differentiation in thymus (GO:0033077)|telencephalon regionalization (GO:0021978)|thalamus development (GO:0021794)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|trachea morphogenesis (GO:0060439)|vasculogenesis (GO:0001570)|ventral midline development (GO:0007418)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|laminin-1 binding (GO:0043237)|morphogen activity (GO:0016015)|patched binding (GO:0005113)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGCGCCCCCGGAAGGCGGCC	0.776													G|||	13	0.00259585	0.0091	0.0014	5008	,	,		6904	0		0	False		,,,				2504	0				p.S295S		.											.	SHH-1134	0			c.C885T						.																																			SO:0001819	synonymous_variant	6469	exon3			GCCCCCGGAAGGC		CCDS5942.1	7q36	2010-06-25	2010-06-25		ENSG00000164690	ENSG00000164690			10848	protein-coding gene	gene with protein product		600725	"sonic hedgehog (Drosophila) homolog", "sonic hedgehog homolog (Drosophila)"	HPE3, HLP3		7590746	Standard	NM_000193		Approved	HHG1, SMMCI, TPT, TPTPS, MCOPCB5	uc003wmk.1	Q15465	OTTHUMG00000151349	ENST00000297261.2:c.885C>T	7.37:g.155596098G>A		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	5	4	NM_000193	0	0	0	0	0	A4D247|Q75MC9	Silent	SNP	ENST00000297261.2	37	CCDS5942.1																																																																																			.		0.776	SHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322327.1	NM_000193		A	155596098	G	A	155596098	2	1	10	1	0	0	0	0	0	0	0	1	14311	1103	39	1		1	SHH	7	155596098	Silent	SNP	G	TCGA-A4-7915-01A-11D-2201-08	33942517	155596098	3542565	22	752											
SCARA5	286133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	27737097	27737097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgccttaccttgcccgaatCgagctgtgcggtacacctcc	6	9	10	16	4	0	0	0	0	0	0	2	2	1	0	5	1	5	2	5	1	3	3			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr8:27737097C>T	ENST00000354914.3	-	8	1825	c.1340G>A	c.(1339-1341)cGa>cAa	p.R447Q	SCARA5_ENST00000380385.2_Missense_Mutation_p.R222Q	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	447	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)	p.R447P(1)		central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TTGCCCGAATCGAGCTGTGCG	0.622																																					p.R447Q		.											.	SCARA5-91	1	Substitution - Missense(1)	lung(1)	c.G1340A						.						142	110	121					8																	27737097		2203	4300	6503	SO:0001583	missense	286133	exon8			CCGAATCGAGCTG	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"scavenger receptor class A, member 5 (putative)"			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.1340G>A	8.37:g.27737097C>T	ENSP00000346990:p.Arg447Gln	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	187	49	NM_173833	0	0	0	0	0	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	37	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491434	0.44249	.	.	ENSG00000168079	ENST00000354914;ENST00000380385	T;T	0.44482	0.92;0.92	4.87	1.96	0.26148	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.165261	0.40554	N	0.001077	T	0.28732	0.0712	L	0.38649	1.16	0.80722	D	1	B;B	0.22851	0.003;0.076	B;B	0.15870	0.003;0.014	T	0.07501	-1.0769	10	0.46703	T	0.11	.	7.6192	0.28175	0.0:0.6991:0.0:0.3009	.	222;447	Q6ZMJ2-4;Q6ZMJ2	.;SCAR5_HUMAN	Q	447;222	ENSP00000346990:R447Q;ENSP00000369746:R222Q	ENSP00000346990:R447Q	R	-	2	0	SCARA5	27793016	0.174000	0.23070	0.360000	0.25837	0.505000	0.33919	1.411000	0.34702	0.536000	0.28733	0.591000	0.81541	CGA	.		0.622	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		T	27737097	C	T	27737097	3	4	10	1	0	0	0	0	1	0	0	0	13912	884	31	1	155	1	SCARA5	8	27737097	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		27737097	118626925	23	753											
RAD21	5885	broad.mit.edu;bcgsc.ca	37	chr8	117862960	117862960	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatatttggaggttcttctGggggaagctctacaggtggt	8	13	15	5	0	3	1	0	0	3	1	3	3	3	3	0	6	2	2	0	6	3	5			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr8:117862960G>A	ENST00000297338.2	-	12	1804	c.1517C>T	c.(1516-1518)cCa>cTa	p.P506L	RAD21_ENST00000518055.1_Missense_Mutation_p.P51L|RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000523986.1_Missense_Mutation_p.P10L	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	506	Pro-rich.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					AGGTTCTTCTGGGGGAAGCTC	0.378																																					p.P506L													.	RAD21-227	0			c.C1517T						.						131	130	130					8																	117862960		2203	4300	6503	SO:0001583	missense	5885	exon12			TCTTCTGGGGGAA	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"sister chromatid cohesion 1"	606462	"RAD21 (S. pombe) homolog"			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1517C>T	8.37:g.117862960G>A	ENSP00000297338:p.Pro506Leu	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	165	7	NM_006265	1	0	112	119	6	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.208572	0.58343	.	.	ENSG00000164754	ENST00000297338;ENST00000523986;ENST00000518055	T;T;T	0.80123	0.64;-1.34;-0.19	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.77585	0.4152	L	0.60455	1.87	0.80722	D	1	B	0.31318	0.319	B	0.27608	0.081	T	0.74262	-0.3722	10	0.22109	T	0.4	-6.1488	19.0827	0.93188	0.0:0.0:1.0:0.0	.	506	O60216	RAD21_HUMAN	L	506;10;51	ENSP00000297338:P506L;ENSP00000428513:P10L;ENSP00000428003:P51L	ENSP00000297338:P506L	P	-	2	0	RAD21	117932141	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.869000	0.87170	2.477000	0.83638	0.460000	0.39030	CCA	.		0.378	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117862960	G	A	117862960	3	1	10	1	0	0	0	0	1	0	0	0	13013	1348	47	2	390	2	RAD21	8	117862960	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	90125863	117862960	28501062	24	754											
FBXL6	26233	hgsc.bcm.edu	37	chr8	145581950	145581950	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgcgcggggccgggcggggCcgggttcggacagcaccagc	4	3	21	13	6	0	0	0	0	0	0	1	1	0	1	3	7	3	2	3	7	0	1	rs200282665	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr8:145581950C>G	ENST00000331890.5	-	1	222	c.158G>C	c.(157-159)gGc>gCc	p.G53A	FBXL6_ENST00000455319.2_Missense_Mutation_p.G53A|SLC52A2_ENST00000530047.1_5'Flank|SLC52A2_ENST00000329994.2_5'Flank|SLC52A2_ENST00000532887.1_5'Flank|SLC52A2_ENST00000526752.1_5'Flank|SLC52A2_ENST00000527078.1_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|FBXL6_ENST00000526524.1_5'Flank|SLC52A2_ENST00000540505.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	53	F-box.				protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			ccgggcggggccgggTTCGGA	0.791													C|||	85	0.0169728	0.0575	0.0101	5008	,	,		6467	0		0.001	False		,,,				2504	0.001				p.G53A		.											.	FBXL6-658	0			c.G158C						.	C	ALA/GLY,ALA/GLY	39,2553		0,39,1257	3	3	3		158,158	1.7	0	8		3	11,5933		0,11,2961	no	missense,missense	FBXL6	NM_012162.1,NM_024555.3	60,60	0,50,4218	GG,GC,CC		0.1851,1.5046,0.5858	benign,benign	53/540,53/534	145581950	50,8486	1296	2972	4268	SO:0001583	missense	26233	exon1			GCGGGGCCGGGTT	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"F-boxes / Leucine-rich repeats"	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.158G>C	8.37:g.145581950C>G	ENSP00000330098:p.Gly53Ala	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_024555	0	0	0	0	0	Q53G43|Q9H5W9|Q9UKC7	Missense_Mutation	SNP	ENST00000331890.5	37	CCDS6422.1	32	0.014652014652014652	27	0.054878048780487805	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	11.26	1.586411	0.28268	0.015046	0.001851	ENSG00000182325	ENST00000455319;ENST00000331890	T;T	0.25085	1.83;1.82	3.66	1.72	0.24424	.	0.566152	0.14975	U	0.287596	T	0.02455	0.0075	L	0.39898	1.24	0.09310	N	1	B;B	0.33171	0.279;0.4	B;B	0.32211	0.067;0.142	T	0.14671	-1.0464	10	0.20519	T	0.43	-16.4339	6.039	0.19724	0.0:0.7105:0.0:0.2895	.	53;53	Q8N531;Q8N531-2	FBXL6_HUMAN;.	A	53	ENSP00000403873:G53A;ENSP00000330098:G53A	ENSP00000330098:G53A	G	-	2	0	FBXL6	145552758	0.000000	0.05858	0.023000	0.16930	0.016000	0.09150	0.118000	0.15605	0.602000	0.29896	0.563000	0.77884	GGC	C|0.985;G|0.015		0.791	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555		G	145581950	C	G	145581950	3	3	10	1	0	0	0	0	1	0	0	0	5742	739	26	4	1497	4	FBXL6	8	145581950	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	27718990	145581950	782072	25	755											
CCIN	881	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	36170395	36170395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttcaatgatggagtgtttgCttatatcatccaggagaacc	11	13	10	7	0	2	2	2	1	0	1	3	4	3	3	2	2	2	3	2	2	4	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr9:36170395C>T	ENST00000335119.2	+	1	1007	c.896C>T	c.(895-897)gCt>gTt	p.A299V		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	299					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			GGAGTGTTTGCTTATATCATC	0.557																																					p.A299V		.											.	CCIN-92	0			c.C896T						.						79	75	76					9																	36170395		2203	4300	6503	SO:0001583	missense	881	exon1			TGTTTGCTTATAT	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.896C>T	9.37:g.36170395C>T	ENSP00000334996:p.Ala299Val	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	135	8	NM_005893	0	0	0	0	0	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	37	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502198	0.64298	.	.	ENSG00000185972	ENST00000335119	T	0.65732	-0.17	5.97	5.97	0.96955	Kelch-type beta propeller (1);	0.000000	0.56097	D	0.000024	T	0.66577	0.2803	L	0.29908	0.895	0.39812	D	0.972727	D	0.63880	0.993	D	0.68192	0.956	T	0.59386	-0.7464	10	0.12766	T	0.61	.	15.9243	0.79603	0.0:1.0:0.0:0.0	.	299	Q13939	CALI_HUMAN	V	299	ENSP00000334996:A299V	ENSP00000334996:A299V	A	+	2	0	CCIN	36160395	0.997000	0.39634	1.000000	0.80357	0.954000	0.61252	4.483000	0.60264	2.839000	0.97877	0.655000	0.94253	GCT	.		0.557	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36170395	C	T	36170395	3	4	10	1	0	0	0	0	1	0	0	0	2884	797	28	2	898	2	CCIN	9	36170395	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		36170395	105043036	26	756											
USP20	10868	hgsc.bcm.edu	37	chr9	132625508	132625508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggagtgtggcggcctggtgCgcacagataagaagccagcc	9	6	16	10	2	0	2	0	0	0	2	0	3	0	3	3	4	3	1	3	4	2	1	rs370020171		TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr9:132625508C>T	ENST00000315480.4	+	9	699	c.541C>T	c.(541-543)Cgc>Tgc	p.R181C	USP20_ENST00000358355.1_Missense_Mutation_p.R181C|USP20_ENST00000372429.3_Missense_Mutation_p.R181C			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	181	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CGGCCTGGTGCGCACAGATAA	0.597													C|||	1	0.000199681	8e-04	0	5008	,	,		12876	0		0	False		,,,				2504	0				p.R181C		.											.	USP20-658	0			c.C541T						.	C	CYS/ARG,CYS/ARG,CYS/ARG	1,3963		0,1,1981	21	23	22		541,541,541	5.7	1	9		22	0,8164		0,0,4082	no	missense,missense,missense	USP20	NM_001008563.3,NM_001110303.2,NM_006676.6	180,180,180	0,1,6063	TT,TC,CC		0.0,0.0252,0.0082	probably-damaging,probably-damaging,probably-damaging	181/915,181/915,181/915	132625508	1,12127	1982	4082	6064	SO:0001583	missense	10868	exon9			CTGGTGCGCACAG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.541C>T	9.37:g.132625508C>T	ENSP00000313811:p.Arg181Cys	Somatic	5	2		WXS	Illumina HiSeq	Phase_I	8	6	NM_001008563	0	0	6	10	4	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	C	35	5.446654	0.96205	2.52E-4	0.0	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.32272	1.46;1.46;1.46	5.65	5.65	0.86999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.098333	0.64402	D	0.000001	T	0.62600	0.2441	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67593	-0.5631	10	0.87932	D	0	.	18.7287	0.91726	0.0:1.0:0.0:0.0	.	181	Q9Y2K6	UBP20_HUMAN	C	181	ENSP00000361506:R181C;ENSP00000313811:R181C;ENSP00000351122:R181C	ENSP00000313811:R181C	R	+	1	0	USP20	131665329	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.052000	0.49893	2.655000	0.90218	0.655000	0.94253	CGC	.		0.597	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132625508	C	T	132625508	3	4	10	1	0	0	0	0	1	0	0	0	17085	768	27	1	567	1	USP20	9	132625508	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	96455113	132625508	8587923	27	757											
CDH23	64072	hgsc.bcm.edu	37	chr10	73454012	73454012	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caaccagaaaactggcatcgCcaccgtgagtgcgctcccct	10	6	9	16	3	0	2	0	1	0	1	2	2	1	2	5	1	3	2	5	1	3	0			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr10:73454012C>G	ENST00000224721.6	+	20	2305	c.2300C>G	c.(2299-2301)gCc>gGc	p.A767G	CDH23_ENST00000299366.7_Missense_Mutation_p.A807G	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	762	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ACTGGCATCGCCACCGTGAGT	0.642																																					p.A762G		.											.	CDH23-563	0			c.C2285G						.						47	58	54					10																	73454012		2119	4228	6347	SO:0001583	missense	64072	exon20			GCATCGCCACCGT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2300C>G	10.37:g.73454012C>G	ENSP00000224721:p.Ala767Gly	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_022124	0	0	0	0	0	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	26.2	4.709952	0.89018	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.55	4.64	0.57946	Cadherin (4);Cadherin-like (1);	0.139502	0.47093	D	0.000241	T	0.65026	0.2652	L	0.48642	1.525	0.80722	D	1	B;P;P	0.47350	0.349;0.747;0.894	B;P;P	0.56398	0.257;0.477;0.797	T	0.63559	-0.6610	9	0.37606	T	0.19	.	14.7666	0.69642	0.0:0.9301:0.0:0.0699	.	762;765;762	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	G	767;762;762;765;765;279	.	ENSP00000224721:A767G	A	+	2	0	CDH23	73124018	1.000000	0.71417	0.998000	0.56505	0.806000	0.45545	4.951000	0.63610	1.339000	0.45563	0.643000	0.83706	GCC	.		0.642	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		G	73454012	C	G	73454012	3	3	10	1	0	0	0	0	1	0	0	0	3114	739	26	4	2590	4	CDH23	10	73454012	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		73454012	62080735	28	758											
PAPSS2	9060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	89501012	89501012	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtgatggaaagtggggaCtggctggttggtggagacct	8	10	19	4	0	0	2	0	1	0	1	0	5	0	4	1	8	0	2	1	8	1	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr10:89501012C>T	ENST00000361175.4	+	9	1461	c.1092C>T	c.(1090-1092)gaC>gaT	p.D364D	PAPSS2_ENST00000427144.2_Silent_p.D368D|PAPSS2_ENST00000456849.1_Silent_p.D369D	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	364					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		AAAGTGGGGACTGGCTGGTTG	0.403																																					p.D369D		.											.	PAPSS2-493	0			c.C1107T						.						145	129	134					10																	89501012		2203	4300	6503	SO:0001819	synonymous_variant	9060	exon10			TGGGGACTGGCTG	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.1092C>T	10.37:g.89501012C>T		Somatic	155	1		WXS	Illumina HiSeq	Phase_I	119	34	NM_001015880	0	0	4	16	12	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Silent	SNP	ENST00000361175.4	37	CCDS7385.1																																																																																			.		0.403	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			T	89501012	C	T	89501012	2	4	10	1	0	0	0	0	0	0	0	1	11461	564	20	2		2	PAPSS2	10	89501012	Silent	SNP	C	TCGA-A4-7915-01A-11D-2201-08	16047000	89501012	46033735	29	759											
ANO5	203859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	22294380	22294380	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggcctcttttcctttggctCctcttcttgctctcataaat	4	19	5	13	0	4	0	1	0	4	0	7	0	6	0	3	2	1	2	3	2	2	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:22294380C>A	ENST00000324559.8	+	19	2397	c.2080C>A	c.(2080-2082)Cct>Act	p.P694T	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	694					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)	p.P694fs*7(1)		breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCTTTGGCTCCTCTTCTTGC	0.378																																					p.P694T		.											.	ANO5-515	1	Deletion - Frameshift(1)	breast(1)	c.C2080A						.						150	131	138					11																	22294380		2203	4300	6503	SO:0001583	missense	203859	exon19			TTGGCTCCTCTTC	AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	27337	protein-coding gene	gene with protein product		608662	"transmembrane protein 16E", "limb girdle muscular dystrophy 2L (autosomal recessive)"	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.2080C>A	11.37:g.22294380C>A	ENSP00000315371:p.Pro694Thr	Somatic	98	1		WXS	Illumina HiSeq	Phase_I	98	29	NM_213599	0	0	0	0	0		Missense_Mutation	SNP	ENST00000324559.8	37	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.087948	0.76642	.	.	ENSG00000171714	ENST00000324559	T	0.68025	-0.3	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.84606	0.5509	H	0.96748	3.875	0.80722	D	1	B	0.22276	0.067	B	0.39771	0.309	D	0.85101	0.0957	10	0.87932	D	0	.	19.9071	0.97012	0.0:1.0:0.0:0.0	.	694	Q75V66	ANO5_HUMAN	T	694	ENSP00000315371:P694T	ENSP00000315371:P694T	P	+	1	0	ANO5	22250956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.767000	0.85331	2.776000	0.95493	0.651000	0.88453	CCT	.		0.378	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		A	22294380	C	A	22294380	3	1	10	1	0	0	0	0	1	0	0	0	700	855	30	4	2154	4	ANO5	11	22294380	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		22294380	112712136	30	760											
HSD17B12	51144	hgsc.bcm.edu	37	chr11	43837920	43837920	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcaagaaaatgataaatatTaatattctttctgtttgtaa	17	17	4	3	0	3	2	1	1	2	1	3	2	3	2	0	0	0	2	0	0	9	8			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:43837920T>C	ENST00000278353.4	+	6	599	c.480T>C	c.(478-480)atT>atC	p.I160I	HSD17B12_ENST00000529261.1_3'UTR	NM_016142.2	NP_057226.1	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12	160					cellular lipid metabolic process (GO:0044255)|estrogen biosynthetic process (GO:0006703)|extracellular matrix organization (GO:0030198)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cell-substrate adhesion (GO:0010811)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|heparin binding (GO:0008201)			endometrium(2)|large_intestine(4)|lung(4)	10						TGATAAATATTAATATTCTTT	0.289																																					p.I160I	Ovarian(58;548 1143 13948 16572 34258)	.											.	HSD17B12-90	0			c.T480C						.						44	47	46					11																	43837920		2198	4291	6489	SO:0001819	synonymous_variant	51144	exon6			AAATATTAATATT	AF078850	CCDS7905.1	11q11	2011-09-20				ENSG00000149084	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	18646	protein-coding gene	gene with protein product	"3-ketoacyl-CoA reductase", "short chain dehydrogenase/reductase family 12C, member 1"	609574				12482854, 19027726	Standard	NM_016142		Approved	KAR, SDR12C1	uc001mxq.4	Q53GQ0		ENST00000278353.4:c.480T>C	11.37:g.43837920T>C		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	40	3	NM_016142	0	0	57	57	0	A8K9B0|D3DR23|Q96EA9|Q96JU2|Q9Y6G8	Silent	SNP	ENST00000278353.4	37	CCDS7905.1																																																																																			.		0.289	HSD17B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389594.1			C	43837920	T	C	43837920	2	2	10	1	0	0	0	0	0	0	0	1	7402	1742	61	3		3	HSD17B12	11	43837920	Silent	SNP	T	TCGA-A4-7915-01A-11D-2201-08	21543540	43837920	91168596	31	761											
RCOR2	283248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63679913	63679913	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccagattgaagcggcgcCggtagctcacaaagaaagtc	12	6	11	12	3	1	3	1	1	0	2	3	3	2	3	3	2	2	2	3	2	4	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:63679913C>A	ENST00000301459.4	-	11	1508	c.1121G>T	c.(1120-1122)cGg>cTg	p.R374L	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	374	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GAAGCGGCGCCGGTAGCTCAC	0.587																																					p.R374L		.											.	RCOR2-92	0			c.G1121T						.						64	76	72					11																	63679913		2201	4297	6498	SO:0001583	missense	283248	exon11			CGGCGCCGGTAGC	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.1121G>T	11.37:g.63679913C>A	ENSP00000301459:p.Arg374Leu	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	180	55	NM_173587	0	0	0	0	0	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	37	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040706	0.93685	.	.	ENSG00000167771	ENST00000301459	T	0.37411	1.2	4.55	4.55	0.56014	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	M	0.89287	3.02	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.74237	-0.3730	10	0.87932	D	0	.	16.6282	0.84992	0.0:1.0:0.0:0.0	.	374	Q8IZ40	RCOR2_HUMAN	L	374	ENSP00000301459:R374L	ENSP00000301459:R374L	R	-	2	0	RCOR2	63436489	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.314000	0.78988	2.536000	0.85505	0.561000	0.74099	CGG	.		0.587	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		A	63679913	C	A	63679913	3	1	10	1	0	0	0	0	1	0	0	0	13215	652	23	4	458	4	RCOR2	11	63679913	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	19841993	63679913	71326603	32	762											
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65346571	65346571	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agccagataagctggtggtgGtatggacccgtcggaaccga	10	7	15	9	3	0	1	0	0	0	1	1	4	0	3	3	5	3	2	3	5	3	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:65346571G>C	ENST00000309295.4	+	2	392	c.127G>C	c.(127-129)Gta>Cta	p.V43L		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	43						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						GCTGGTGGTGGTATGGACCCG	0.647																																					p.V43L		.											.	EHBP1L1-69	0			c.G127C						.						19	20	20					11																	65346571		1961	4141	6102	SO:0001583	missense	254102	exon2			GTGGTGGTATGGA	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.127G>C	11.37:g.65346571G>C	ENSP00000312671:p.Val43Leu	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	19	2	NM_001099409	0	0	13	13	0	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	G	32	5.108044	0.94292	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.45276	0.9;0.9	5.05	4.13	0.48395	.	0.000000	0.64402	D	0.000018	T	0.56031	0.1958	M	0.63428	1.95	0.80722	D	1	D	0.54772	0.968	D	0.64321	0.924	T	0.58896	-0.7555	10	0.87932	D	0	.	9.9196	0.41457	0.0986:0.0:0.9014:0.0	.	43	Q8N3D4	EH1L1_HUMAN	L	43	ENSP00000312671:V43L;ENSP00000431996:V43L	ENSP00000312671:V43L	V	+	1	0	EHBP1L1	65103147	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.685000	0.61693	2.345000	0.79718	0.561000	0.74099	GTA	.		0.647	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		C	65346571	G	C	65346571	3	2	10	1	0	0	0	0	1	0	0	0	4987	1261	44	4	133	4	EHBP1L1	11	65346571	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	1666658	65346571	69659945	33	763											
RBM4B	83759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66444485	66444485	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcaccttcccatactgctcGaagagtgagcgaatctcctg	10	9	9	13	2	1	2	0	1	1	1	4	4	2	2	3	0	4	2	3	0	3	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:66444485G>A	ENST00000525754.1	-	1	734	c.66C>T	c.(64-66)ttC>ttT	p.F22F	RBM4B_ENST00000531036.2_Silent_p.F22F|RBM4B_ENST00000310046.4_Silent_p.F22F|RBM4B_ENST00000524637.1_Silent_p.F22F|RBM4B_ENST00000531969.1_Silent_p.F22F			Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	22	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|entrainment of circadian clock by photoperiod (GO:0043153)|mRNA processing (GO:0006397)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)|urinary_tract(2)	10						CATACTGCTCGAAGAGTGAGC	0.512																																					p.F22F		.											.	RBM4B-90	0			c.C66T						.						91	91	91					11																	66444485		2200	4295	6495	SO:0001819	synonymous_variant	83759	exon2			CTGCTCGAAGAGT	AK095158	CCDS8149.1, CCDS66144.1	11q13	2013-02-12	2006-01-25	2006-01-25				"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	28842	protein-coding gene	gene with protein product			"RNA binding motif protein 30"	RBM30		12477932	Standard	XR_247213		Approved	MGC10871, ZCCHC15, RBM4L, ZCRB3B, ZCCHC21B	uc001ojb.3	Q9BQ04		ENST00000525754.1:c.66C>T	11.37:g.66444485G>A		Somatic	259	0		WXS	Illumina HiSeq	Phase_I	235	52	NM_031492	0	0	98	98	0	B3KT83	Silent	SNP	ENST00000525754.1	37	CCDS8149.1																																																																																			.		0.512	RBM4B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393851.1	NM_031492		A	66444485	G	A	66444485	2	1	10	1	0	0	0	0	0	0	0	1	13174	1049	37	1		1	RBM4B	11	66444485	Silent	SNP	G	TCGA-A4-7915-01A-11D-2201-08	1097914	66444485	68562031	34	764											
SLC36A4	120103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	92917687	92917687	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcataagagtttgtacaaatCtgaaaagtaaaagttgtaag	18	11	9	3	0	1	2	0	1	1	1	1	2	1	2	0	0	1	6	0	0	8	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:92917687C>A	ENST00000326402.4	-	3	310		c.e3-1		SLC36A4_ENST00000529184.1_Splice_Site	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4						L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGTACAAATCTGAAAAGTAA	0.313																																					.		.											.	SLC36A4-93	0			c.180-1G>T						.						99	105	103					11																	92917687		2201	4297	6498	SO:0001630	splice_region_variant	120103	exon4			ACAAATCTGAAAA	AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.180-1G>T	11.37:g.92917687C>A		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	135	50	NM_152313	0	0	0	0	0	Q86X30|Q8IVM5|Q8N8S6	Splice_Site	SNP	ENST00000326402.4	37	CCDS8291.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172159	0.78452	.	.	ENSG00000180773	ENST00000326402	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2544	0.98414	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC36A4	92557335	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.132000	0.71676	2.885000	0.99019	0.655000	0.94253	.	.		0.313	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2		Intron	A	92917687	C	A	92917687	5	1	10	1	0	0	0	0	0	0	1	0	14628	927	32	4	1371	4	SLC36A4	11	92917687	Splice_Site	SNP	C	TCGA-A4-7915-01A-11D-2201-08	26473202	92917687	42088829	35	765											
TEP1	7011	broad.mit.edu;bcgsc.ca	37	chr14	20840924	20840924	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgccgaacccttccgcagTttcacttgccactcgctgat	6	11	9	15	3	1	1	1	1	0	0	3	2	2	1	4	1	3	3	4	1	1	3			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr14:20840924T>C	ENST00000262715.5	-	49	7084	c.7044A>G	c.(7042-7044)aaA>aaG	p.K2348K	TEP1_ENST00000545983.1_Intron|TEP1_ENST00000556935.1_Silent_p.K2240K	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2348					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CCTTCCGCAGTTTCACTTGCC	0.507																																					p.K2348K													.	TEP1-95	0			c.A7044G						.						135	125	129					14																	20840924		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon49			CCGCAGTTTCACT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.7044A>G	14.37:g.20840924T>C		Somatic	229	1		WXS	Illumina HiSeq	Phase_I	186	7	NM_007110	0	0	14	15	1	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			.		0.507	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20840924	T	C	20840924	2	2	10	1	0	0	0	0	0	0	0	1	15791	1722	60	3		3	TEP1	14	20840924	Silent	SNP	T	TCGA-A4-7915-01A-11D-2201-08		20840924	86508616	36	766											
SLC9A3R2	9351	hgsc.bcm.edu	37	chr16	2077090	2077090	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcttccacctgcacggcgaGaagggccgccgcgggcagtt	6	5	16	14	5	0	1	0	0	0	1	1	2	1	1	4	4	1	4	4	4	1	2	rs73496087	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr16:2077090G>C	ENST00000424542.2	+	1	222	c.84G>C	c.(82-84)gaG>gaC	p.E28D	SLC9A3R2_ENST00000432365.2_Missense_Mutation_p.E28D|SLC9A3R2_ENST00000563587.1_5'Flank	NM_001130012.2|NM_004785.5	NP_001123484.1|NP_004776.3	Q15599	NHRF2_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2	28	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|protein complex assembly (GO:0006461)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatase binding (GO:0019902)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)	2						TGCACGGCGAGAAGGGCCGCC	0.781													G|||	174	0.0347444	0.1233	0.013	5008	,	,		5109	0		0.002	False		,,,				2504	0				p.E28D	Ovarian(69;105 1552 17724 23473)	.											.	SLC9A3R2-23	0			c.G84C						.	G	ASP/GLU,ASP/GLU	92,1620		0,92,764	1	1	1		84,84	2.6	1	16	dbSNP_131	1	1,4161		0,1,2080	no	missense,missense	SLC9A3R2	NM_001130012.1,NM_004785.4	45,45	0,93,2844	CC,CG,GG		0.024,5.3738,1.5832	probably-damaging,probably-damaging	28/338,28/327	2077090	93,5781	856	2081	2937	SO:0001583	missense	9351	exon1			CGGCGAGAAGGGC	AF004900	CCDS45382.1, CCDS45383.1, CCDS58407.1	16p13.3	2014-09-04	2012-03-22		ENSG00000065054	ENSG00000065054			11076	protein-coding gene	gene with protein product		606553	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 2", "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2"			9054412, 9671706	Standard	NM_001130012		Approved	SIP-1, TKA-1, NHERF-2, E3KARP	uc002coi.3	Q15599	OTTHUMG00000176956	ENST00000424542.2:c.84G>C	16.37:g.2077090G>C	ENSP00000408005:p.Glu28Asp	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_004785	0	0	0	0	0	D3DU84|D3DU85|H3BSV6|O00272|O00556|Q3KQY7	Missense_Mutation	SNP	ENST00000424542.2	37	CCDS45382.1	82	0.037545787545787544	71	0.1443089430894309	7	0.019337016574585635	4	0.006993006993006993	0	0.0	G	26.4	4.733652	0.89482	0.053738	2.4E-4	ENSG00000065054	ENST00000424542;ENST00000432365	T;T	0.51071	0.72;0.72	2.63	2.63	0.31362	PDZ/DHR/GLGF (4);	0.000000	0.85682	U	0.000000	T	0.00468	0.0015	N	0.16602	0.42	0.09310	P	1.0	D;D	0.89917	0.972;1.0	D;D	0.91635	0.912;0.999	T	0.15838	-1.0423	9	0.44086	T	0.13	-11.9793	12.2597	0.54642	0.0:0.0:1.0:0.0	.	28;28	D3DU85;Q15599	.;NHRF2_HUMAN	D	28	ENSP00000408005:E28D;ENSP00000402857:E28D	ENSP00000408005:E28D	E	+	3	2	SLC9A3R2	2017091	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.478000	0.35442	1.497000	0.48584	0.298000	0.19748	GAG	G|0.962;C|0.038		0.781	SLC9A3R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434448.1			C	2077090	G	C	2077090	3	2	10	1	0	0	0	0	1	0	0	0	14747	933	33	4	86	4	SLC9A3R2	16	2077090	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		2077090	88277663	37	767											
ITGAL	3683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30490672	30490672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatgtatcaagggcaacgtaGacctggtatttctgtttgat	11	14	10	6	1	2	2	1	1	1	1	2	2	2	2	1	2	1	5	1	2	6	5			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr16:30490672G>A	ENST00000356798.6	+	6	646	c.466G>A	c.(466-468)Gac>Aac	p.D156N	RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000433423.2_Intron|RP11-297C4.3_ENST00000562525.1_RNA|ITGAL_ENST00000454514.2_Intron|ITGAL_ENST00000358164.5_Intron	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	156	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GGGCAACGTAGACCTGGTATT	0.478																																					p.D156N	NSCLC(110;1462 1641 3311 33990 49495)	.											.	ITGAL-994	0			c.G466A						.						120	108	112					16																	30490672		2197	4300	6497	SO:0001583	missense	3683	exon6			AACGTAGACCTGG		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.466G>A	16.37:g.30490672G>A	ENSP00000349252:p.Asp156Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	101	43	NM_002209	0	0	2	2	0	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.796940	0.90453	.	.	ENSG00000005844	ENST00000356798	D	0.92149	-2.98	5.98	5.98	0.97165	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000021	D	0.94434	0.8209	M	0.73430	2.235	0.80722	D	1	P	0.44006	0.824	P	0.51193	0.662	D	0.94464	0.7679	10	0.72032	D	0.01	.	17.3632	0.87357	0.0:0.0:1.0:0.0	.	156	P20701	ITAL_HUMAN	N	156	ENSP00000349252:D156N	ENSP00000349252:D156N	D	+	1	0	ITGAL	30398173	1.000000	0.71417	0.978000	0.43139	0.941000	0.58515	4.655000	0.61476	2.838000	0.97847	0.514000	0.50259	GAC	.		0.478	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			A	30490672	G	A	30490672	3	1	10	1	0	0	0	0	1	0	0	0	7907	942	33	2	488	2	ITGAL	16	30490672	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	28413582	30490672	59864081	38	768											
DNAJA2	10294	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	47005807	47005807	+	Splice_Site	DEL	C	C	-																															aaaaaggtgcaaataacttaCtttgtctcctgcatttggat																										TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr16:47005807delC	ENST00000317089.5	-	2	354		c.e2+1		RP11-169E6.1_ENST00000562536.1_RNA	NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2						positive regulation of cell proliferation (GO:0008284)|protein refolding (GO:0042026)|response to heat (GO:0009408)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	14		all_cancers(37;0.00125)|all_lung(18;0.00338)|all_epithelial(9;0.00358)|Lung NSC(13;0.0309)|Breast(268;0.116)				AAATAACTTACTTTGTCTCCT	0.343																																					.		.											.	DNAJA2-226	0			c.138+1G>-						.						127	126	126					16																	47005807		2203	4300	6503	SO:0001630	splice_region_variant	10294	exon3			.	AF116720	CCDS10726.1	16q12.1	2011-09-02			ENSG00000069345	ENSG00000069345		"Heat shock proteins / DNAJ (HSP40)"	14884	protein-coding gene	gene with protein product		611322				9710638, 11147971	Standard	NM_005880		Approved	HIRIP4, DNAJ, CPR3, DNJ3	uc002eeo.2	O60884	OTTHUMG00000133104	ENST00000317089.5:c.138+1G>-	16.37:g.47005807delC		Somatic	179	0		WXS	Illumina HiSeq	Phase_I	155	47	NM_005880	0	0	0	0	0	B2R7L7|O14711	Splice_Site	DEL	ENST00000317089.5	37	CCDS10726.1																																																																																			.		0.343	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2		Intron	-	47005807	C	-	47005807	8	5	10	1	0	1	0	1	0	0	1	0	4623	579	20	0	1131	0	DNAJA2	16	47005807	Splice_Site	DEL	C	TCGA-A4-7915-01A-11D-2201-08	16515135	47005807	43348946	39	769											
MMP15	4324	hgsc.bcm.edu	37	chr16	58079306	58079306	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcgcaagggtgcgccaCgtgtcctgctttactgcaag	7	9	13	12	3	0	0	0	0	0	0	1	0	1	0	2	1	6	4	2	1	3	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr16:58079306C>T	ENST00000219271.3	+	10	2751	c.1966C>T	c.(1966-1968)Cgt>Tgt	p.R656C		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	656					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	GGGTGCGCCACGTGTCCTGCT	0.647																																					p.R656C		.											.	MMP15-713	0			c.C1966T						.						101	101	101					16																	58079306		2190	4290	6480	SO:0001583	missense	4324	exon10			GCGCCACGTGTCC	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.1966C>T	16.37:g.58079306C>T	ENSP00000219271:p.Arg656Cys	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	10	7	NM_002428	0	0	13	21	8	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.621358	0.28889	.	.	ENSG00000102996	ENST00000219271	T	0.41065	1.01	5.08	2.89	0.33648	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.219462	0.42294	D	0.000730	T	0.58409	0.2120	M	0.61703	1.905	0.30757	N	0.744488	D	0.89917	1.0	D	0.77557	0.99	T	0.62760	-0.6786	10	0.87932	D	0	.	11.7648	0.51924	0.4094:0.5906:0.0:0.0	.	656	P51511	MMP15_HUMAN	C	656	ENSP00000219271:R656C	ENSP00000219271:R656C	R	+	1	0	MMP15	56636807	0.077000	0.21312	0.513000	0.27749	0.005000	0.04900	1.011000	0.29911	1.139000	0.42245	-0.466000	0.05196	CGT	.		0.647	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		T	58079306	C	T	58079306	3	4	10	1	0	0	0	0	1	0	0	0	9679	536	19	1	2004	1	MMP15	16	58079306	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	11073499	58079306	32275447	40	770											
KRT10	3858	hgsc.bcm.edu	37	chr17	38975327	38975327	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgccgtggccgccgccgTggccgccgccggagcttccg	1	5	16	19	9	0	0	0	0	0	0	1	1	1	1	9	3	2	1	9	3	0	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr17:38975327T>G	ENST00000269576.5	-	7	1469	c.1460A>C	c.(1459-1461)cAc>cCc	p.H487P	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	487	Gly-rich.|Ser-rich.|Tail.		H -> Y (in dbSNP:rs17855579). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2448602, ECO:0000269|PubMed:2459124, ECO:0000269|PubMed:2464696}.	Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				gccgccgccgtggccgccgcc	0.786																																					p.H487P		.											.	KRT10-90	0			c.A1460C						.						1	2	1					17																	38975327		484	1205	1689	SO:0001583	missense	3858	exon7			CCGCCGTGGCCGC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1460A>C	17.37:g.38975327T>G	ENSP00000269576:p.His487Pro	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_000421	0	0	0	0	0	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	37	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.647306	0.47258	.	.	ENSG00000186395	ENST00000269576	D	0.91237	-2.81	4.29	1.08	0.20341	.	1.067520	0.07539	N	0.913467	T	0.78966	0.4367	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.64939	-0.6289	10	0.30078	T	0.28	.	6.1771	0.20449	0.0:0.2066:0.4458:0.3476	.	487	P13645	K1C10_HUMAN	P	487	ENSP00000269576:H487P	ENSP00000269576:H487P	H	-	2	0	KRT10	36228853	0.000000	0.05858	0.085000	0.20634	0.080000	0.17528	-3.816000	0.00359	0.303000	0.22785	-0.263000	0.10527	CAC	.		0.786	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		G	38975327	T	G	38975327	3	3	10	1	0	0	0	0	1	0	0	0	8469	1696	59	5	302	5	KRT10	17	38975327	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08		38975327	42219883	41	771											
C17orf82	388407	hgsc.bcm.edu	37	chr17	59489911	59489911	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctcacaggtccacgagatgGcgctgcaggccagggcccgg	7	4	15	15	3	1	1	1	0	0	1	2	2	2	1	4	5	1	2	4	5	0	0			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr17:59489911G>C	ENST00000335108.2	+	1	800	c.575G>C	c.(574-576)gGc>gCc	p.G192A	RP11-332H18.4_ENST00000592009.1_RNA	NM_203425.1	NP_982249	Q86X59	CQ082_HUMAN	chromosome 17 open reading frame 82	192										cervix(1)|lung(1)	2						CCACGAGATGGCGCTGCAGGC	0.751																																					p.G192A		.											.	C17orf82-226	0			c.G575C						.																																			SO:0001583	missense	388407	exon1			GAGATGGCGCTGC	BC046200	CCDS11628.1	17q23.2	2012-10-23			ENSG00000187013	ENSG00000187013			32699	protein-coding gene	gene with protein product							Standard	NM_203425		Approved		uc002izh.1	Q86X59	OTTHUMG00000180077	ENST00000335108.2:c.575G>C	17.37:g.59489911G>C	ENSP00000335229:p.Gly192Ala	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	13	4	NM_203425	0	0	0	0	0		Missense_Mutation	SNP	ENST00000335108.2	37	CCDS11628.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.718970	0.48622	.	.	ENSG00000187013	ENST00000335108	T	0.58358	0.34	4.29	2.08	0.27032	.	.	.	.	.	T	0.45736	0.1357	N	0.08118	0	0.21553	N	0.999642	D	0.76494	0.999	D	0.71414	0.973	T	0.22591	-1.0212	9	0.87932	D	0	.	3.225	0.06729	0.2203:0.0:0.57:0.2097	.	192	Q86X59	CQ082_HUMAN	A	192	ENSP00000335229:G192A	ENSP00000335229:G192A	G	+	2	0	C17orf82	56844693	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	1.447000	0.35101	1.101000	0.41535	0.448000	0.29417	GGC	.		0.751	C17orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449646.1	NM_203425		C	59489911	G	C	59489911	3	2	10	1	0	0	0	0	1	0	0	0	1892	1203	42	4	577	4	C17orf82	17	59489911	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	20514584	59489911	21705299	42	772											
LPIN2	9663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2951317	2951317	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taaagaactgatcttcagtaGgaattggtgaggtggcaagg	13	10	14	4	0	2	3	1	2	1	1	2	4	2	4	0	5	1	2	0	5	6	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr18:2951317G>T	ENST00000261596.4	-	4	564	c.326C>A	c.(325-327)cCt>cAt	p.P109H	RP11-737O24.2_ENST00000581488.1_RNA|RP11-737O24.2_ENST00000584431.1_RNA	NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	109					cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		ATCTTCAGTAGGAATTGGTGA	0.418																																					p.P109H		.											.	LPIN2-227	0			c.C326A						.						74	73	74					18																	2951317		2203	4300	6503	SO:0001583	missense	9663	exon4			TCAGTAGGAATTG	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.326C>A	18.37:g.2951317G>T	ENSP00000261596:p.Pro109His	Somatic	90	1		WXS	Illumina HiSeq	Phase_I	88	10	NM_014646	0	0	19	28	9	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704863	0.88924	.	.	ENSG00000101577	ENST00000261596;ENST00000455369	T	0.77098	-1.07	5.92	5.92	0.95590	Lipin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89743	0.6803	M	0.87900	2.915	0.80722	D	1	D	0.69078	0.997	D	0.73708	0.981	D	0.87681	0.2547	10	0.33141	T	0.24	-13.5139	20.3206	0.98668	0.0:0.0:1.0:0.0	.	109	Q92539	LPIN2_HUMAN	H	109	ENSP00000261596:P109H	ENSP00000261596:P109H	P	-	2	0	LPIN2	2941317	1.000000	0.71417	0.978000	0.43139	0.966000	0.64601	6.527000	0.73803	2.809000	0.96659	0.655000	0.94253	CCT	.		0.418	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		T	2951317	G	T	2951317	3	4	10	1	0	0	0	0	1	0	0	0	8944	1000	35	4	2432	4	LPIN2	18	2951317	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		2951317	75125931	43	773											
JSRP1	126306	hgsc.bcm.edu	37	chr19	2253780	2253780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccttcttgcgcgcggggAcgctccgagggcctgcgggg	2	6	19	14	7	1	0	0	0	1	0	2	2	2	1	3	5	2	1	3	5	0	2	rs10426549	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:2253780A>G	ENST00000300961.6	-	5	339	c.275T>C	c.(274-276)gTc>gCc	p.V92A	JSRP1_ENST00000586471.2_Missense_Mutation_p.V92A	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	92			V -> A (in dbSNP:rs10426549).		protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGCGCGGGGACGCTCCGAGG	0.761													G|||	1026	0.204872	0.5219	0.072	5008	,	,		11441	0.0734		0.0845	False		,,,				2504	0.1299				p.V92A		.											.	JSRP1-91	0			c.T275C						.	G	ALA/VAL	495,1775		30,435,670	2	4	3		275	0.1	0.4	19	dbSNP_119	3	248,4804		5,238,2283	no	missense	JSRP1	NM_144616.3	64	35,673,2953	GG,GA,AA		4.9089,21.8062,10.1475	benign	92/332	2253780	743,6579	1135	2526	3661	SO:0001583	missense	126306	exon5			GCGGGGACGCTCC	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.275T>C	19.37:g.2253780A>G	ENSP00000300961:p.Val92Ala	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_144616	0	0	0	0	0		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	362	0.16575091575091574	231	0.4695121951219512	21	0.058011049723756904	48	0.08391608391608392	62	0.08179419525065963	a	0.017	-1.492342	0.01009	0.218062	0.049089	ENSG00000167476	ENST00000300961	T	0.18657	2.2	3.74	0.0998	0.14504	.	1.682840	0.03947	N	0.287865	T	0.00012	0.0000	N	0.04508	-0.205	0.46927	P	7.479999999999709E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47560	-0.9108	9	0.18710	T	0.47	0.0096	4.6604	0.12639	0.3093:0.1591:0.5316:0.0	rs10426549;rs58800051	92	Q96MG2	JSPR1_HUMAN	A	92	ENSP00000300961:V92A	ENSP00000300961:V92A	V	-	2	0	JSRP1	2204780	0.001000	0.12720	0.427000	0.26684	0.036000	0.12997	-0.186000	0.09670	-0.634000	0.05538	-0.930000	0.02707	GTC	A|0.832;G|0.168		0.761	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		G	2253780	A	G	2253780	3	3	10	1	0	0	0	0	1	0	0	0	7987	275	10	3	732	3	JSRP1	19	2253780	Missense_Mutation	SNP	A	TCGA-A4-7915-01A-11D-2201-08		2253780	56875203	44	774											
MRPL54	116541	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	3762750	3762750	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggacgtgggccggctgggggGcctgggagctcctaaacccc	5	5	18	13	2	0	0	0	0	0	0	1	2	1	2	5	7	2	2	5	7	2	1	rs200308520		TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:3762750G>T	ENST00000330133.4	+	1	89	c.52G>T	c.(52-54)Gcc>Tcc	p.A18S	APBA3_ENST00000316757.3_5'Flank	NM_172251.2	NP_758455.1	Q6P161	RM54_HUMAN	mitochondrial ribosomal protein L54	18						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCTGGGGGGCCTGGGAGCT	0.617													G|||	1	0.000199681	0	0	5008	,	,		14484	0.001		0	False		,,,				2504	0				p.A18S		.											.	MRPL54-90	0			c.G52T						.																																			SO:0001583	missense	116541	exon1			TGGGGGGCCTGGG		CCDS12111.1	19p13.3	2012-11-14			ENSG00000183617	ENSG00000183617		"Mitochondrial ribosomal proteins / large subunits"	16685	protein-coding gene	gene with protein product		611858				11551941	Standard	NM_172251		Approved		uc002lyq.4	Q6P161	OTTHUMG00000180873	ENST00000330133.4:c.52G>T	19.37:g.3762750G>T	ENSP00000331849:p.Ala18Ser	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	140	42	NM_172251	0	0	40	65	25		Missense_Mutation	SNP	ENST00000330133.4	37	CCDS12111.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.41	1.629158	0.28978	.	.	ENSG00000183617	ENST00000330133	.	.	.	5.57	-7.27	0.01461	.	1.148870	0.06434	N	0.724730	T	0.15176	0.0366	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27502	-1.0072	9	0.09590	T	0.72	-1.6956	1.7102	0.02891	0.2105:0.3326:0.273:0.184	.	18	Q6P161	RM54_HUMAN	S	18	.	ENSP00000331849:A18S	A	+	1	0	MRPL54	3713750	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.357000	0.02607	-1.580000	0.01644	-1.134000	0.01955	GCC	G|0.999;T|0.000		0.617	MRPL54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453443.1	NM_172251		T	3762750	G	T	3762750	3	4	10	1	0	0	0	0	1	0	0	0	9843	1203	42	4	54	4	MRPL54	19	3762750	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	1508970	3762750	55366233	45	775											
SHD	56961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4290585	4290585	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactgccggtgcagggtgcCgagcatctggctctgctgta	5	9	14	13	2	2	0	0	0	2	0	2	1	2	0	3	3	5	5	3	3	1	1	rs111268424		TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:4290585C>T	ENST00000543264.2	+	6	2441	c.978C>T	c.(976-978)gcC>gcT	p.A326A	SHD_ENST00000599689.1_Silent_p.A286A	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	326	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.									breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCAGGGTGCCGAGCATCTGG	0.657																																					p.A326A		.											.	SHD-90	0			c.C978T						.						59	53	55					19																	4290585		2203	4300	6503	SO:0001819	synonymous_variant	56961	exon6			GGGTGCCGAGCAT	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"SH2 domain containing"	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.978C>T	19.37:g.4290585C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	107	42	NM_020209	0	0	0	0	0	Q96NC2	Silent	SNP	ENST00000543264.2	37	CCDS12125.1																																																																																			C|0.500;T|0.500		0.657	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209		T	4290585	C	T	4290585	2	4	10	1	0	0	0	0	0	0	0	1	14307	639	23	1		1	SHD	19	4290585	Silent	SNP	C	TCGA-A4-7915-01A-11D-2201-08	527835	4290585	54838398	46	776											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41025619	41025619	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgggcgccgagtggggcgCgctagctagcgcggctcagg	4	5	20	12	6	1	0	1	0	0	0	1	1	1	0	1	5	2	4	1	5	2	2	rs529933555	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:41025619C>G	ENST00000352632.3	+	16	3301	c.3215C>G	c.(3214-3216)gCg>gGg	p.A1072G	SPTBN4_ENST00000338932.3_Missense_Mutation_p.A1072G|SPTBN4_ENST00000595535.1_Missense_Mutation_p.A1072G|SPTBN4_ENST00000598249.1_Missense_Mutation_p.A1072G|SPTBN4_ENST00000344104.3_Missense_Mutation_p.A1072G			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1072					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GAGTGGGGCGCGCTAGCTAGC	0.746													C|||	9	0.00179712	0.0045	0.0029	5008	,	,		10299	0		0.001	False		,,,				2504	0				p.A1072G		.											.	SPTBN4-94	0			c.C3215G						.																																			SO:0001583	missense	57731	exon16			GGGGCGCGCTAGC	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.3215C>G	19.37:g.41025619C>G	ENSP00000263373:p.Ala1072Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_020971	0	0	0	0	0	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	5.929	0.355426	0.11239	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.78246	-1.02;1.3;-1.16	4.11	1.84	0.25277	.	0.292311	0.27554	N	0.018848	T	0.73079	0.3541	L	0.34521	1.04	0.52099	D	0.999943	P;B	0.47545	0.897;0.01	P;B	0.51701	0.677;0.006	T	0.66724	-0.5851	10	0.27785	T	0.31	.	11.1789	0.48616	0.3346:0.6654:0.0:0.0	.	1072;1072	Q9H254;Q71S06	SPTN4_HUMAN;.	G	1072	ENSP00000263373:A1072G;ENSP00000340345:A1072G;ENSP00000340741:A1072G	ENSP00000340345:A1072G	A	+	2	0	SPTBN4	45717459	0.501000	0.26099	0.095000	0.20976	0.212000	0.24457	1.342000	0.33919	0.328000	0.23435	0.462000	0.41574	GCG	.		0.746	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			G	41025619	C	G	41025619	3	3	10	1	0	0	0	0	1	0	0	0	15153	768	27	4	3273	4	SPTBN4	19	41025619	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	36735034	41025619	18103364	47	777											
ARHGAP35	2909	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	47422875	47422875	+	Frame_Shift_Del	DEL	C	C	-																															atgtctacctggaagggactCagaaagccaagaagctgttt																										TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:47422875delC	ENST00000404338.3	+	1	943	c.943delC	c.(943-945)cagfs	p.Q315fs		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	315	FF 1.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										GGAAGGGACTCAGAAAGCCAA	0.507																																					p.Q315fs		.											.	.	0			c.943delC						.						32	32	32					19																	47422875		1979	4167	6146	SO:0001589	frameshift_variant	2909	exon1			.	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"Rho GTPase activating proteins"	4591	protein-coding gene	gene with protein product		605277	"glucocorticoid receptor DNA binding factor 1"	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.943delC	19.37:g.47422875delC	ENSP00000385720:p.Gln315fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	46	13	NM_004491	0	0	0	0	0	A7E2A4|Q14452|Q9C0E1	Frame_Shift_Del	DEL	ENST00000404338.3	37	CCDS46127.1																																																																																			.		0.507	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		-	47422875	C	-	47422875	7	5	10	1	0	1	0	1	0	0	0	0	6816	827	29	0	945	0	ARHGAP35	19	47422875	Frame_Shift_Del	DEL	C	TCGA-A4-7915-01A-11D-2201-08	6397256	47422875	11706108	48	778											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945880	48945880	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacagctgctgcagcgcTgaggccgccccaccgcccgc	6	5	12	18	4	0	1	0	1	0	0	0	1	0	1	5	1	5	5	5	1	1	1	rs62130268	byFrequency	TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:48945880T>C	ENST00000263269.3	+	13	2785	c.2697T>C	c.(2695-2697)gcT>gcC	p.A899A		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	899					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTGCAGCGCTGAGGCCGCCC	0.781													c|||	3742	0.747204	0.6188	0.8545	5008	,	,		4716	0.6548		0.8887	False		,,,				2504	0.7945				p.A899A		.											.	GRIN2D-156	0			c.T2697C						.			1689,437		638,413,12	1	1	1		2697	-3.3	1	19	dbSNP_129	1	3712,202		1757,198,2	no	coding-synonymous	GRIN2D	NM_000836.2		2395,611,14	CC,CT,TT		5.161,20.555,10.5795		899/1337	48945880	5401,639	1063	1957	3020	SO:0001819	synonymous_variant	2906	exon13			CAGCGCTGAGGCC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2697T>C	19.37:g.48945880T>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_000836	0	0	0	0	0		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			T|0.245;C|0.755		0.781	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			C	48945880	T	C	48945880	2	2	10	1	0	0	0	0	0	0	0	1	6803	1567	55	3		3	GRIN2D	19	48945880	Silent	SNP	T	TCGA-A4-7915-01A-11D-2201-08	1523005	48945880	10183103	49	779											
TP53RK	112858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	45315804	45315804	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgaacagtcactgagcctTcaatttcttccatatataag	12	13	5	11	1	3	1	2	1	1	0	5	2	4	1	2	0	2	0	2	0	5	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr20:45315804T>C	ENST00000372102.3	-	2	380	c.355A>G	c.(355-357)Aag>Gag	p.K119E	RP1-28H20.3_ENST00000606362.1_lincRNA			Q96S44	PRPK_HUMAN	TP53 regulating kinase	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				lipopolysaccharide biosynthetic process (GO:0009103)|protein phosphorylation (GO:0006468)|tRNA processing (GO:0008033)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				CACTGAGCCTTCAATTTCTTC	0.418																																					p.E117G		.											.	TP53RK-333	0			c.A350G						.						151	172	165					20																	45315804		2202	4300	6502	SO:0001583	missense	112858	exon2			GAGCCTTCAATTT		CCDS13401.1	20q13.2	2014-05-14	2004-05-10	2004-05-12	ENSG00000172315	ENSG00000172315			16197	protein-coding gene	gene with protein product		608679	"chromosome 20 open reading frame 64"	C20orf64		11546806, 12914926	Standard	NM_033550		Approved	dJ101A2.2, prpk, Nori-2p, BUD32	uc002xsk.3	Q96S44	OTTHUMG00000085887	ENST00000372102.3:c.355A>G	20.37:g.45315804T>C	ENSP00000361174:p.Lys119Glu	Somatic	408	1		WXS	Illumina HiSeq	Phase_I	360	116	NM_033550	0	0	7	17	10	B3KU44|Q3T977|Q5JZ01|Q6NZ60|Q96FM7|Q9NQE6	Missense_Mutation	SNP	ENST00000372102.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.74|11.74	1.727453|1.727453	0.30593|0.30593	.|.	.|.	ENSG00000172315|ENSG00000172315	ENST00000372114|ENST00000372102	T|T	0.12361|0.47869	2.69|0.83	5.38|5.38	3.04|3.04	0.35103|0.35103	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.167964|.	0.52532|.	D|.	0.000073|.	T|T	0.33731|0.33731	0.0873|0.0873	L|L	0.39898|0.39898	1.24|1.24	0.23677|0.23677	N|N	0.997139|0.997139	P|B	0.49961|0.31548	0.93|0.328	P|B	0.53224|0.34242	0.721|0.178	T|T	0.25641|0.25641	-1.0126|-1.0126	10|9	0.42905|0.07644	T|T	0.14|0.81	-10.1094|-10.1094	6.7483|6.7483	0.23474|0.23474	0.1725:0.0:0.2393:0.5882|0.1725:0.0:0.2393:0.5882	.|.	117|119	Q96S44|Q5JZ02	PRPK_HUMAN|.	G|E	117|119	ENSP00000361186:E117G|ENSP00000361174:K119E	ENSP00000361186:E117G|ENSP00000361174:K119E	E|K	-|-	2|1	0|0	TP53RK|TP53RK	44749211|44749211	0.999000|0.999000	0.42202|0.42202	0.971000|0.971000	0.41717|0.41717	0.502000|0.502000	0.33828|0.33828	1.944000|1.944000	0.40263|0.40263	0.449000|0.449000	0.26747|0.26747	-0.313000|-0.313000	0.08912|0.08912	GAA|AAG	.		0.418	TP53RK-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000193688.1	NM_033550		C	45315804	T	C	45315804	3	2	10	1	0	0	0	0	1	0	0	0	16423	1783	62	3	415	3	TP53RK	20	45315804	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08		45315804	17709716	50	780											
C21orf63	59271	hgsc.bcm.edu	37	chr21	33785313	33785313	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagatctcagcgctcaccgActtctctggtaagagcgccc	9	8	10	14	3	3	2	2	0	2	2	5	4	3	2	2	1	2	2	2	1	1	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr21:33785313A>G	ENST00000300255.2	+	1	625	c.152A>G	c.(151-153)gAc>gGc	p.D51G	EVA1C_ENST00000401402.3_Missense_Mutation_p.D51G|EVA1C_ENST00000382699.3_Missense_Mutation_p.D51G	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	51						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										GCGCTCACCGACTTCTCTGGT	0.692																																					p.D51G		.											.	.	0			c.A152G						.						17	17	17					21																	33785313		2202	4299	6501	SO:0001583	missense	59271	exon1			TCACCGACTTCTC	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 64", "chromosome 21 open reading frame 63", "family with sequence similarity 176, member C"	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.152A>G	21.37:g.33785313A>G	ENSP00000300255:p.Asp51Gly	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_058187	0	0	1	1	0	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	37	CCDS13614.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824968	0.50739	.	.	ENSG00000166979	ENST00000300255;ENST00000401402;ENST00000382699	T;T;T	0.10099	2.91;3.01;2.92	4.17	4.17	0.49024	.	0.000000	0.85682	D	0.000000	T	0.11793	0.0287	L	0.59436	1.845	0.32695	N	0.513686	B;B;B	0.26445	0.01;0.149;0.114	B;B;B	0.24701	0.012;0.048;0.055	T	0.05068	-1.0908	10	0.37606	T	0.19	-13.1462	9.541	0.39251	1.0:0.0:0.0:0.0	.	51;51;51	A6ND58;P58658;B5MC74	.;CU063_HUMAN;.	G	51	ENSP00000300255:D51G;ENSP00000384594:D51G;ENSP00000372146:D51G	ENSP00000300255:D51G	D	+	2	0	C21orf63	32707184	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.857000	0.55972	1.735000	0.51646	0.528000	0.53228	GAC	.		0.692	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		G	33785313	A	G	33785313	3	3	10	1	0	0	0	0	1	0	0	0	2137	275	10	3	154	3	C21orf63	21	33785313	Missense_Mutation	SNP	A	TCGA-A4-7915-01A-11D-2201-08		33785313	14344582	51	781											
KDELR3	11015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38877225	38877225	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tctttggctcagatcctctgGactttctctatctatctgga	6	17	7	11	0	6	1	1	0	5	1	8	3	7	3	1	3	0	1	1	3	2	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr22:38877225G>A	ENST00000216014.4	+	4	532	c.360G>A	c.(358-360)tgG>tgA	p.W120*	KDELR3_ENST00000409006.3_Nonsense_Mutation_p.W120*|KDELR3_ENST00000471268.1_3'UTR	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	120					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					AGATCCTCTGGACTTTCTCTA	0.448																																					p.W120X	Ovarian(11;103 529 24120 28493 32980)	.											.	KDELR3-92	0			c.G360A						.						173	182	179					22																	38877225		2203	4300	6503	SO:0001587	stop_gained	11015	exon4			CCTCTGGACTTTC	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.360G>A	22.37:g.38877225G>A	ENSP00000216014:p.Trp120*	Somatic	285	0		WXS	Illumina HiSeq	Phase_I	282	79	NM_016657	0	0	0	0	0	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Nonsense_Mutation	SNP	ENST00000216014.4	37	CCDS13972.1	.	.	.	.	.	.	.	.	.	.	G	35	5.560833	0.96527	.	.	ENSG00000100196	ENST00000216014;ENST00000409006	.	.	.	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4255	0.90607	0.0:0.0:1.0:0.0	.	.	.	.	X	120	.	ENSP00000216014:W120X	W	+	3	0	KDELR3	37207171	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.657000	0.98554	2.595000	0.87683	0.650000	0.86243	TGG	.		0.448	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			A	38877225	G	A	38877225	4	1	10	1	0	0	0	0	0	1	0	0	8142	1183	41	2	374	2	KDELR3	22	38877225	Nonsense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		38877225	12427341	52	782											
MAP7D3	79649	broad.mit.edu	37	chrX	135312676	135312676	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgaataggcattattttatAaggaaaagaagtctgtggtg	14	14	11	2	0	1	2	0	1	1	1	1	3	1	3	0	3	0	1	0	3	8	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chrX:135312676A>G	ENST00000316077.9	-	10	1838	c.1618T>C	c.(1618-1620)Tat>Cat	p.Y540H	MAP7D3_ENST00000370663.5_Missense_Mutation_p.Y522H|MAP7D3_ENST00000370661.1_Missense_Mutation_p.Y505H|MAP7D3_ENST00000495432.1_5'Flank	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	540					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					ATTATTTTATAAGGAAAAGAA	0.363																																					p.Y540H													.	MAP7D3-110	0			c.T1618C						.						140	131	134					X																	135312676		1838	4080	5918	SO:0001583	missense	79649	exon10			TTTTATAAGGAAA	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1618T>C	X.37:g.135312676A>G	ENSP00000318086:p.Tyr540His	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	228	3	NM_024597	0	0	28	28	0	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	A	7.290	0.610842	0.14066	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.04194	4.29;3.68;3.68;3.68	4.96	-2.35	0.06684	.	1.832210	0.03370	N	0.198761	T	0.04588	0.0125	L	0.32530	0.975	0.09310	N	1	P;P;P;P	0.46512	0.59;0.879;0.59;0.713	B;B;B;B	0.41571	0.118;0.36;0.118;0.234	T	0.31752	-0.9932	10	0.36615	T	0.2	0.0869	4.3898	0.11334	0.34:0.0:0.1543:0.5057	.	522;499;540;505	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	H	505;540;522;499	ENSP00000359695:Y505H;ENSP00000318086:Y540H;ENSP00000359697:Y522H;ENSP00000359694:Y499H	ENSP00000318086:Y540H	Y	-	1	0	MAP7D3	135140342	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.213000	0.17521	-0.659000	0.05359	-1.378000	0.01179	TAT	.		0.363	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			G	135312676	A	G	135312676	3	3	10	1	0	0	0	0	1	0	0	0	9294	362	13	3	1048	3	MAP7D3	23	135312676	Missense_Mutation	SNP	A	TCGA-A4-7915-01A-11D-2201-08		135312676	19957884	53	783											
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	8674682	8674682	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgatgccaccggcagagAgcatgctggggggtcacaca	9	6	15	11	1	1	2	1	1	0	1	1	3	1	2	2	4	3	3	2	4	0	0			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:8674682A>T	ENST00000337907.3	-	5	1094	c.460T>A	c.(460-462)Tct>Act	p.S154T	RERE_ENST00000400907.2_Missense_Mutation_p.S154T|RERE_ENST00000400908.2_Missense_Mutation_p.S154T	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	154	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		ACCGGCAGAGAGCATGCTGGG	0.498																																					p.S154T		.											.	RERE-515	0			c.T460A						.						77	86	83					1																	8674682		2203	4300	6503	SO:0001583	missense	473	exon5			GCAGAGAGCATGC	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.460T>A	1.37:g.8674682A>T	ENSP00000338629:p.Ser154Thr	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	183	57	NM_012102	0	0	5	5	0	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.568378	0.45798	.	.	ENSG00000142599	ENST00000337907;ENST00000400907;ENST00000400908	T;T	0.43294	0.95;0.95	5.33	5.33	0.75918	Bromo adjacent homology (BAH) domain (3);	.	.	.	.	T	0.42314	0.1197	N	0.17631	0.505	0.80722	D	1	D	0.53885	0.963	D	0.67231	0.95	T	0.21827	-1.0234	9	0.07644	T	0.81	-16.2545	11.6091	0.51049	1.0:0.0:0.0:0.0	.	154	Q9P2R6	RERE_HUMAN	T	154	ENSP00000338629:S154T;ENSP00000383700:S154T	ENSP00000338629:S154T	S	-	1	0	RERE	8597269	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.525000	0.22956	2.234000	0.73211	0.533000	0.62120	TCT	.		0.498	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			T	8674682	A	T	8674682	3	4	11	1	0	0	0	0	1	0	0	0	13263	304	11	5	4320	5	RERE	1	8674682	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		8674682	240575939	1	784											
TNFRSF1B	7133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	12266986	12266986	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaggaatgtgcctttcggtCacagctggagacgccagaga	10	7	15	9	2	1	2	1	0	0	2	2	6	1	4	2	4	2	1	2	4	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:12266986C>T	ENST00000376259.3	+	10	1384	c.1295C>T	c.(1294-1296)tCa>tTa	p.S432L	TNFRSF1B_ENST00000492361.1_3'UTR	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	432					aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	GCCTTTCGGTCACAGCTGGAG	0.622																																					p.S432L		.											.	TNFRSF1B-1085	0			c.C1295T						.						100	96	98					1																	12266986		2203	4300	6503	SO:0001583	missense	7133	exon10			TTCGGTCACAGCT	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"Tumor necrosis factor receptor superfamily", "CD molecules"	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.1295C>T	1.37:g.12266986C>T	ENSP00000365435:p.Ser432Leu	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	116	34	NM_001066	0	0	31	34	3	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	CCDS145.1	.	.	.	.	.	.	.	.	.	.	C	8.806	0.934041	0.18206	.	.	ENSG00000028137	ENST00000376259	D	0.86865	-2.18	4.93	3.01	0.34805	.	3.844360	0.01082	N	0.005008	D	0.85366	0.5680	L	0.57536	1.79	0.09310	N	0.999998	B	0.30068	0.267	B	0.28139	0.086	T	0.66901	-0.5806	10	0.44086	T	0.13	-20.2744	6.4642	0.21973	0.1787:0.7264:0.0:0.0949	.	432	P20333	TNR1B_HUMAN	L	432	ENSP00000365435:S432L	ENSP00000365435:S432L	S	+	2	0	TNFRSF1B	12189573	0.043000	0.20138	0.045000	0.18777	0.005000	0.04900	2.194000	0.42668	0.564000	0.29238	0.561000	0.74099	TCA	.		0.622	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066		T	12266986	C	T	12266986	3	4	11	1	0	0	0	0	1	0	0	0	16326	838	29	2	1333	2	TNFRSF1B	1	12266986	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	3592304	12266986	236983635	2	785											
AGMAT	79814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15909721	15909721	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatacagccagctgctacaaTtttctcataggcctcttgaa	12	12	6	11	0	2	1	1	1	2	0	3	1	2	1	2	1	5	2	2	1	6	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:15909721T>A	ENST00000375826.3	-	2	584	c.442A>T	c.(442-444)Att>Ttt	p.I148F	RP4-680D5.2_ENST00000428945.1_RNA|DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	148					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGCTACAATTTTCTCATAG	0.502																																					p.I148F	NSCLC(126;1678 1780 25805 43508 49531)	.											.	AGMAT-91	0			c.A442T						.						60	62	61					1																	15909721		2203	4300	6503	SO:0001583	missense	79814	exon2			CTACAATTTTCTC	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.442A>T	1.37:g.15909721T>A	ENSP00000364986:p.Ile148Phe	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	59	24	NM_024758	0	0	39	67	28	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284549	0.40394	.	.	ENSG00000116771	ENST00000375826	D	0.86097	-2.07	5.17	4.0	0.46444	Ureohydrolase domain (1);	0.051325	0.85682	D	0.000000	D	0.85864	0.5796	M	0.88241	2.94	0.49483	D	0.99979	B	0.30914	0.3	B	0.28553	0.091	D	0.83786	0.0228	10	0.62326	D	0.03	-10.0798	10.1512	0.42794	0.0:0.0812:0.0:0.9188	.	148	Q9BSE5	SPEB_HUMAN	F	148	ENSP00000364986:I148F	ENSP00000364986:I148F	I	-	1	0	AGMAT	15782308	1.000000	0.71417	0.015000	0.15790	0.482000	0.33219	3.489000	0.53237	0.768000	0.33290	0.460000	0.39030	ATT	.		0.502	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		A	15909721	T	A	15909721	3	1	11	1	0	0	0	0	1	0	0	0	385	1493	52	5	640	5	AGMAT	1	15909721	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	3642735	15909721	233340900	3	786											
SLC5A9	200010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	48713171	48713171	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaacatcaatgctgtcCttttgctggccatcaacatc	9	13	6	13	0	3	0	2	0	1	0	5	0	4	0	2	1	5	3	2	1	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:48713171C>T	ENST00000438567.2	+	14	2054	c.2002C>T	c.(2002-2004)Ctt>Ttt	p.L668F	SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Missense_Mutation_p.L693F|SLC5A9_ENST00000533824.1_Missense_Mutation_p.L689F	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	668					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						CAATGCTGTCCTTTTGCTGGC	0.527																																					p.L693F		.											.	SLC5A9-93	0			c.C2077T						.						118	109	112					1																	48713171		2203	4300	6503	SO:0001583	missense	200010	exon15			GCTGTCCTTTTGC	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"Solute carriers"	22146	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 9"				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.2002C>T	1.37:g.48713171C>T	ENSP00000401730:p.Leu668Phe	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	131	36	NM_001135181	0	0	17	31	14	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633803	0.47049	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.89485	-2.46;-2.45;-2.52	4.91	-2.59	0.06209	.	0.427982	0.25433	N	0.030704	D	0.85208	0.5644	L	0.43646	1.37	0.80722	D	1	P;P;P	0.52577	0.883;0.954;0.954	P;P;P	0.50617	0.459;0.526;0.646	T	0.80341	-0.1423	10	0.28530	T	0.3	.	10.552	0.45095	0.6789:0.2512:0.0:0.0699	.	689;668;693	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	F	689;668;693	ENSP00000431900:L689F;ENSP00000401730:L668F;ENSP00000236495:L693F	ENSP00000236495:L693F	L	+	1	0	SLC5A9	48485758	0.564000	0.26602	0.314000	0.25224	0.881000	0.50899	-0.070000	0.11523	-0.340000	0.08388	0.561000	0.74099	CTT	.		0.527	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48713171	C	T	48713171	3	4	11	1	0	0	0	0	1	0	0	0	14704	681	24	2	2135	2	SLC5A9	1	48713171	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	32803450	48713171	200537450	4	787											
ZYG11B	79699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53287171	53287171	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagcatttatacaacatcaAagatcatgaacatactgatc	17	10	5	9	0	2	3	2	2	0	1	3	3	2	3	0	0	5	2	0	0	6	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:53287171A>G	ENST00000294353.6	+	14	2250	c.2105A>G	c.(2104-2106)aAa>aGa	p.K702R	ZYG11B_ENST00000443756.2_Missense_Mutation_p.K632R	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	702										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TACAACATCAAAGATCATGAA	0.418																																					p.K702R		.											.	ZYG11B-94	0			c.A2105G						.						98	85	89					1																	53287171		2203	4300	6503	SO:0001583	missense	79699	exon14			ACATCAAAGATCA	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.2105A>G	1.37:g.53287171A>G	ENSP00000294353:p.Lys702Arg	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	84	18	NM_024646	0	0	14	26	12	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	37	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.462431	0.26248	.	.	ENSG00000162378	ENST00000443756;ENST00000294353	T;T	0.48836	0.8;0.8	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.155352	0.56097	D	0.000023	T	0.25791	0.0628	N	0.08118	0	0.80722	D	1	B;B	0.16802	0.019;0.001	B;B	0.22753	0.041;0.001	T	0.13415	-1.0510	10	0.14656	T	0.56	.	9.8251	0.40908	0.9231:0.0:0.0769:0.0	.	632;702	B4DK95;Q9C0D3	.;ZY11B_HUMAN	R	632;702	ENSP00000400522:K632R;ENSP00000294353:K702R	ENSP00000294353:K702R	K	+	2	0	ZYG11B	53059759	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.218000	0.51192	2.019000	0.59389	0.482000	0.46254	AAA	.		0.418	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		G	53287171	A	G	53287171	3	3	11	1	0	0	0	0	1	0	0	0	18285	14	1	3	2159	3	ZYG11B	1	53287171	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	4574000	53287171	195963450	5	788											
USP24	23358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	55612677	55612677	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcacgattccagcccagAtacagagtagcttcttgcaa	11	10	9	11	1	1	2	0	0	1	2	2	3	2	2	2	1	4	4	2	1	3	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:55612677A>G	ENST00000294383.6	-	19	2174	c.2175T>C	c.(2173-2175)taT>taC	p.Y725Y	USP24_ENST00000407756.1_Silent_p.Y565Y	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	725					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TCCAGCCCAGATACAGAGTAG	0.393																																					p.Y725Y		.											.	USP24-521	0			c.T2175C						.						104	99	101					1																	55612677		1852	4098	5950	SO:0001819	synonymous_variant	23358	exon19			GCCCAGATACAGA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.2175T>C	1.37:g.55612677A>G		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	54	20	NM_015306	0	0	9	15	6	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			.		0.393	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55612677	A	G	55612677	2	3	11	1	0	0	0	0	0	0	0	1	17088	340	12	3		3	USP24	1	55612677	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	2325506	55612677	193637944	6	789											
INADL	10207	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	62365295	62365295	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaggcgaaggagaagaaactCcaaattttagccactggggt	15	7	12	7	1	0	2	0	0	0	2	1	4	1	2	2	4	2	0	2	4	6	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:62365295C>T	ENST00000371158.2	+	23	3286	c.3172C>T	c.(3172-3174)Cca>Tca	p.P1058S	INADL_ENST00000316485.6_Missense_Mutation_p.P1058S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1058					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AGAAGAAACTCCAAATTTTAG	0.398																																					p.P1058S		.											.	INADL-94	0			c.C3172T						.						179	177	178					1																	62365295		2203	4300	6503	SO:0001583	missense	10207	exon23			GAAACTCCAAATT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3172C>T	1.37:g.62365295C>T	ENSP00000360200:p.Pro1058Ser	Somatic	263	0		WXS	Illumina HiSeq	Phase_I	256	78	NM_176877	0	0	48	92	44	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626785	0.87560	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.13307	2.74;2.6	5.26	5.26	0.73747	PDZ/DHR/GLGF (1);	0.000000	0.64402	D	0.000001	T	0.39655	0.1086	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	0.991;0.999;1.0	D;D;D	0.85130	0.98;0.997;0.994	T	0.04915	-1.0918	10	0.34782	T	0.22	.	19.2911	0.94100	0.0:1.0:0.0:0.0	.	1058;1058;1058	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	1058	ENSP00000360200:P1058S;ENSP00000326199:P1058S	ENSP00000255202:P1058S	P	+	1	0	INADL	62137883	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.990000	0.63876	2.636000	0.89361	0.579000	0.79373	CCA	.		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62365295	C	T	62365295	3	4	11	1	0	0	0	0	1	0	0	0	7752	855	30	2	3258	2	INADL	1	62365295	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	6752618	62365295	186885326	7	790											
HIST2H2BE	8349	broad.mit.edu	37	chr1	149858178	149858178	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggggccggagcggattttgCcggttcaggcatggtaagac	8	8	17	8	3	1	1	1	0	0	1	1	3	1	3	2	7	2	3	2	7	1	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:149858178C>T	ENST00000369155.2	-	1	54	c.13G>A	c.(13-15)Gca>Aca	p.A5T	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	5				A -> S (in Ref. 7; AAH98112/AAH98289). {ECO:0000305}.	antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GCGGATTTTGCCGGTTCAGGC	0.507																																					p.A5T													.	HIST2H2BE-69	0			c.G13A						.						57	58	58					1																	149858178		2203	4300	6503	SO:0001583	missense	8349	exon1			ATTTTGCCGGTTC	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.13G>A	1.37:g.149858178C>T	ENSP00000358151:p.Ala5Thr	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	80	4	NM_003528	0	0	53	53	0	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	37	CCDS936.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.216193	0.79352	.	.	ENSG00000184678	ENST00000369155	T	0.18810	2.19	5.99	5.99	0.97316	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.15652	0.0377	L	0.59436	1.845	0.43218	D	0.99509	B	0.25904	0.137	B	0.13407	0.009	T	0.01266	-1.1401	10	0.66056	D	0.02	.	19.1154	0.93336	0.0:1.0:0.0:0.0	.	5	Q16778	H2B2E_HUMAN	T	5	ENSP00000358151:A5T	ENSP00000358151:A5T	A	-	1	0	HIST2H2BE	148124802	1.000000	0.71417	0.870000	0.34147	0.970000	0.65996	5.960000	0.70348	2.857000	0.98124	0.650000	0.86243	GCA	.		0.507	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		T	149858178	C	T	149858178	3	4	11	1	0	0	0	0	1	0	0	0	7200	739	26	2	371	2	HIST2H2BE	1	149858178	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	87492883	149858178	99392443	8	791											
TCHH	7062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152082279	152082279	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcctcttcctcccgatattgCctctccagctcctggcgcct	3	13	6	19	2	2	0	0	0	2	0	7	1	6	0	7	1	2	1	7	1	1	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:152082279C>T	ENST00000368804.1	-	2	3413	c.3414G>A	c.(3412-3414)agG>agA	p.R1138R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1138	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			cccgatattgcctctccagct	0.612																																					p.R1138R		.											.	TCHH-72	0			c.G3414A						.						91	90	90					1																	152082279		2000	4154	6154	SO:0001819	synonymous_variant	7062	exon3			ATATTGCCTCTCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3414G>A	1.37:g.152082279C>T		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	139	39	NM_007113	0	0	0	0	0	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																			.		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		T	152082279	C	T	152082279	2	4	11	1	0	0	0	0	0	0	0	1	15732	738	26	2		2	TCHH	1	152082279	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	2224101	152082279	97168342	9	792											
KCNN3	3782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154841688	154841688	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctttggggaaggtggtgctGctggcggtggtgccggcatg	3	10	21	7	2	0	0	0	0	0	0	0	1	0	1	1	8	3	4	1	8	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:154841688G>A	ENST00000271915.4	-	1	1068	c.753C>T	c.(751-753)agC>agT	p.S251S	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	256					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	AGGTGGTGCTGCTGGCGGTGG	0.567																																					p.S251S		.											.	KCNN3-91	0			c.C753T						.						109	104	106					1																	154841688		2203	4300	6503	SO:0001819	synonymous_variant	3782	exon1			GGTGCTGCTGGCG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.753C>T	1.37:g.154841688G>A		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	113	41	NM_001204087	0	0	4	4	0	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.		0.567	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		A	154841688	G	A	154841688	2	1	11	1	0	0	0	0	0	0	0	1	8101	1310	46	2		2	KCNN3	1	154841688	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	2759409	154841688	94408933	10	793											
EFNA1	1942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155104075	155104075	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacacctttcaccctgggcaAggagttcaaagaaggacaca	14	6	9	12	0	2	1	2	0	0	1	2	3	2	3	2	3	0	2	2	3	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:155104075A>G	ENST00000368407.3	+	2	871	c.353A>G	c.(352-354)aAg>aGg	p.K118R	EFNA1_ENST00000469878.1_3'UTR|EFNA1_ENST00000368406.2_Missense_Mutation_p.K118R	NM_004428.2	NP_004419.2	P20827	EFNA1_HUMAN	ephrin-A1	118	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1)	5	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			ACCCTGGGCAAGGAGTTCAAA	0.527																																					p.K118R		.											.	EFNA1-90	0			c.A353G						.						53	47	49					1																	155104075		2203	4300	6503	SO:0001583	missense	1942	exon2			TGGGCAAGGAGTT		CCDS1091.1, CCDS1092.1	1q21-q22	2011-03-09			ENSG00000169242	ENSG00000169242		"Ephrins"	3221	protein-coding gene	gene with protein product		191164		TNFAIP4, EPLG1		2233719, 8660976	Standard	NM_182685		Approved	LERK1, ECKLG	uc001fhh.3	P20827	OTTHUMG00000035312	ENST00000368407.3:c.353A>G	1.37:g.155104075A>G	ENSP00000357392:p.Lys118Arg	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	47	10	NM_182685	0	0	41	70	29	D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578	Missense_Mutation	SNP	ENST00000368407.3	37	CCDS1091.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.554194	0.86231	.	.	ENSG00000169242	ENST00000368407;ENST00000368406	T;T	0.43294	0.95;0.95	5.22	5.22	0.72569	Ephrin, conserved site (1);Cupredoxin (2);	0.045262	0.85682	D	0.000000	T	0.51500	0.1678	M	0.71581	2.175	0.53688	D	0.999973	D;D	0.76494	0.997;0.999	P;D	0.71184	0.9;0.972	T	0.51124	-0.8745	10	0.33940	T	0.23	-2.5539	13.3345	0.60509	1.0:0.0:0.0:0.0	.	118;118	P20827-2;P20827	.;EFNA1_HUMAN	R	118	ENSP00000357392:K118R;ENSP00000357391:K118R	ENSP00000357391:K118R	K	+	2	0	EFNA1	153370699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.204000	0.51082	2.097000	0.63578	0.533000	0.62120	AAG	.		0.527	EFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085428.1	NM_004428		G	155104075	A	G	155104075	3	3	11	1	0	0	0	0	1	0	0	0	4961	72	3	3	359	3	EFNA1	1	155104075	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	262387	155104075	94146546	11	794											
LRPPRC	10128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44139638	44139638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatttaatgagattgctgtAggtttcagcattaaacacaa	15	14	7	5	0	1	1	1	1	0	1	1	2	1	1	0	1	3	4	0	1	6	7			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:44139638A>G	ENST00000260665.7	-	30	3265	c.3208T>C	c.(3208-3210)Tac>Cac	p.Y1070H		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1070					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGATTGCTGTAGGTTTCAGCA	0.313																																					p.Y1070H		.											.	LRPPRC-93	0			c.T3208C						.						112	107	109					2																	44139638		2202	4297	6499	SO:0001583	missense	10128	exon30			TGCTGTAGGTTTC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.3208T>C	2.37:g.44139638A>G	ENSP00000260665:p.Tyr1070His	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	86	33	NM_133259	0	0	72	158	86	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.643279	0.67244	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	T	0.13420	2.59	5.78	5.78	0.91487	.	0.065106	0.64402	D	0.000006	T	0.40272	0.1110	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.27773	-1.0064	10	0.66056	D	0.02	-5.0562	15.7709	0.78167	1.0:0.0:0.0:0.0	.	970;1070	F5H4J6;P42704	.;LPPRC_HUMAN	H	970;1070	ENSP00000260665:Y1070H	ENSP00000260665:Y1070H	Y	-	1	0	LRPPRC	43993142	1.000000	0.71417	0.283000	0.24790	0.010000	0.07245	7.018000	0.76406	2.205000	0.71048	0.533000	0.62120	TAC	.		0.313	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		G	44139638	A	G	44139638	3	3	11	1	0	0	0	0	1	0	0	0	8990	420	15	3	1012	3	LRPPRC	2	44139638	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		44139638	199059735	12	795											
MTHFD2	10797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74441208	74441208	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttgtttctatgtaggaGtcagacaaaaagctgggtat	11	14	11	5	0	3	1	1	0	2	1	3	2	3	2	0	2	1	4	0	2	5	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:74441208G>A	ENST00000394053.2	+	8	972	c.892G>A	c.(892-894)Gtc>Atc	p.V298I	MTHFD2_ENST00000409804.1_Missense_Mutation_p.V170I|RP11-287D1.3_ENST00000451608.2_Intron|MTHFD2_ENST00000394050.3_Missense_Mutation_p.V134I|SLC4A5_ENST00000483195.1_5'Flank|MTHFD2_ENST00000409601.1_Missense_Mutation_p.V215I|MTHFD2_ENST00000264090.4_Missense_Mutation_p.V196I	NM_006636.3	NP_006627.2	P13995	MTDC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	298					folic acid-containing compound biosynthetic process (GO:0009396)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate metabolic process (GO:0046653)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	magnesium ion binding (GO:0000287)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|phosphate ion binding (GO:0042301)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6					Tetrahydrofolic acid(DB00116)	CTATGTAGGAGTCAGACAAAA	0.398																																					p.V298I		.											.	MTHFD2-90	0			c.G892A						.						110	119	116					2																	74441208		2029	4215	6244	SO:0001583	missense	10797	exon8			GTAGGAGTCAGAC	X16396	CCDS1935.2	2p13.1	2008-05-02			ENSG00000065911	ENSG00000065911			7434	protein-coding gene	gene with protein product		604887				2587219, 8218174	Standard	NR_027405		Approved		uc002skk.3	P13995	OTTHUMG00000129814	ENST00000394053.2:c.892G>A	2.37:g.74441208G>A	ENSP00000377617:p.Val298Ile	Somatic	274	0		WXS	Illumina HiSeq	Phase_I	244	71	NM_006636	0	0	0	0	0	Q53G90|Q53GV5|Q53S36|Q7Z650	Missense_Mutation	SNP	ENST00000394053.2	37	CCDS1935.2	.	.	.	.	.	.	.	.	.	.	G	24.5	4.540151	0.85917	.	.	ENSG00000065911	ENST00000394053;ENST00000409804;ENST00000264090;ENST00000394050;ENST00000409601	T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.37	5.58	5.58	0.84498	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.114477	0.64402	D	0.000017	T	0.78291	0.4260	M	0.82323	2.585	0.80722	D	1	D;D	0.71674	0.988;0.998	D;D	0.74023	0.919;0.982	T	0.80569	-0.1324	10	0.72032	D	0.01	.	17.4533	0.87599	0.0:0.0:1.0:0.0	.	215;298	B8ZZU9;P13995	.;MTDC_HUMAN	I	298;170;196;134;215	ENSP00000377617:V298I;ENSP00000386536:V170I;ENSP00000264090:V196I;ENSP00000377614:V134I;ENSP00000386542:V215I	ENSP00000264090:V196I	V	+	1	0	MTHFD2	74294716	1.000000	0.71417	0.821000	0.32701	0.724000	0.41520	9.415000	0.97375	2.813000	0.96785	0.655000	0.94253	GTC	.		0.398	MTHFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252045.2			A	74441208	G	A	74441208	3	1	11	1	0	0	0	0	1	0	0	0	9954	1029	36	2	922	2	MTHFD2	2	74441208	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	30301570	74441208	168758165	13	796											
IL1RL2	8808	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	102849533	102849533	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccgaggtgttggagagaCaatgtggatataagttgttt	10	13	14	4	1	0	1	0	0	0	1	0	5	0	3	1	3	1	3	1	3	3	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:102849533C>T	ENST00000264257.2	+	10	1372	c.1246C>T	c.(1246-1248)Caa>Taa	p.Q416*	IL1RL2_ENST00000539491.1_Nonsense_Mutation_p.Q416*|IL1RL2_ENST00000441515.2_Nonsense_Mutation_p.Q298*|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	416	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						GTTGGAGAGACAATGTGGATA	0.453																																					p.Q416X		.											.	IL1RL2-92	0			c.C1246T						.						116	111	113					2																	102849533		2203	4300	6503	SO:0001587	stop_gained	8808	exon10			GAGAGACAATGTG	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1246C>T	2.37:g.102849533C>T	ENSP00000264257:p.Gln416*	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	128	38	NM_003854	0	0	1	2	1	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Nonsense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	C	36	5.844802	0.97016	.	.	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	.	.	.	6.07	6.07	0.98685	.	0.205036	0.43919	D	0.000507	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	.	.	.	X	416;298;416	.	ENSP00000264257:Q416X	Q	+	1	0	IL1RL2	102215965	0.985000	0.35326	1.000000	0.80357	0.447000	0.32167	2.970000	0.49240	2.885000	0.99019	0.655000	0.94253	CAA	.		0.453	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		T	102849533	C	T	102849533	4	4	11	1	0	0	0	0	0	1	0	0	7685	479	17	2	1280	2	IL1RL2	2	102849533	Nonsense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	28408325	102849533	140349840	14	797											
KIF5C	3800	hgsc.bcm.edu	37	chr2	149850958	149850958	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaagccaagatcaagtctctGacagactacatgcagaacat	16	7	8	10	0	2	4	1	1	1	3	3	5	2	4	1	0	4	1	1	0	5	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:149850958G>C	ENST00000435030.1	+	17	2297	c.1929G>C	c.(1927-1929)ctG>ctC	p.L643L	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Silent_p.L548L|KIF5C_ENST00000397413.1_Silent_p.L411L			O60282	KIF5C_HUMAN	kinesin family member 5C	643					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TCAAGTCTCTGACAGACTACA	0.498																																					p.L643L		.											.	KIF5C-69	0			c.G1929C						.						34	36	36					2																	149850958		1969	4163	6132	SO:0001819	synonymous_variant	3800	exon17			GTCTCTGACAGAC	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.1929G>C	2.37:g.149850958G>C		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	11	3	NM_004522	0	0	0	0	0	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				.		0.498	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		C	149850958	G	C	149850958	2	2	11	1	0	0	0	0	0	0	0	1	8328	1277	45	4		4	KIF5C	2	149850958	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	47001425	149850958	93348415	15	798											
PSMD14	10213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	162227815	162227815	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtggttgtggatcccatTcagagtgtaaaaggaaaggt	12	10	14	5	0	1	1	1	0	0	1	2	3	2	3	1	4	0	3	1	4	3	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:162227815T>C	ENST00000409682.3	+	7	1148	c.444T>C	c.(442-444)atT>atC	p.I148I		NM_005805.5	NP_005796.1	O00487	PSDE_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	148					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K63-linked deubiquitination (GO:0070536)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, lid subcomplex (GO:0008541)	endopeptidase activator activity (GO:0061133)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|proteasome binding (GO:0070628)|ubiquitin thiolesterase activity (GO:0004221)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	12						TGGATCCCATTCAGAGTGTAA	0.408																																					p.I148I		.											.	PSMD14-433	0			c.T444C						.						121	120	121					2																	162227815		1930	4131	6061	SO:0001819	synonymous_variant	10213	exon7			TCCCATTCAGAGT	U86782	CCDS46437.1	2q14.3	2008-05-22			ENSG00000115233	ENSG00000115233		"Proteasome (prosome, macropain) subunits"	16889	protein-coding gene	gene with protein product		607173				9374539	Standard	NM_005805		Approved	POH1, pad1, Rpn11	uc002ubu.3	O00487	OTTHUMG00000153882	ENST00000409682.3:c.444T>C	2.37:g.162227815T>C		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	20	4	NM_005805	0	0	82	155	73	B3KNW2|O00176	Silent	SNP	ENST00000409682.3	37	CCDS46437.1																																																																																			.		0.408	PSMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332833.1	NM_005805		C	162227815	T	C	162227815	2	2	11	1	0	0	0	0	0	0	0	1	12726	1771	62	3		3	PSMD14	2	162227815	Silent	SNP	T	TCGA-A4-7996-01A-11D-2201-08	12376857	162227815	80971558	16	799											
COL5A2	1290	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	189898818	189898819	+	Frame_Shift_Ins	INS	-	-	TT																															cacaaaacaaactggcccaaINStttcaacgccgaattcctgg																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:189898818_189898819insTT	ENST00000374866.3	-	54	4751_4752	c.4477_4478insAA	c.(4477-4479)attfs	p.I1493fs		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1493	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			AACTGGCCCAATTTCAACGCCG	0.46																																					p.I1493fs		.											.	COL5A2-92	0			c.4478_4479insAA						.																																			SO:0001589	frameshift_variant	1290	exon54			.	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4476_4477dupAA	2.37:g.189898819_189898820dupTT	ENSP00000364000:p.Ile1493fs	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	68	15	NM_000393	0	0	0	0	0	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Frame_Shift_Ins	INS	ENST00000374866.3	37	CCDS33350.1																																																																																			.		0.46	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		TT	189898819	-	TT	189898818	7	5	11	1	0	1	1	0	0	0	0	0	3703	101	4	0	25	0	COL5A2	2	189898818	Frame_Shift_Ins	INS	-	TCGA-A4-7996-01A-11D-2201-08	27671003	189898818	53300555	17	800											
NBEAL1	65065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	204039877	204039877	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttccccacagatatgaaAattttgaggatcctatggga	12	14	8	7	0	0	3	0	2	0	1	2	5	2	5	3	2	0	0	3	2	4	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:204039877A>T	ENST00000449802.1	+	41	6577	c.6244A>T	c.(6244-6246)Aat>Tat	p.N2082Y		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2082	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.									NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CAGATATGAAAATTTTGAGGA	0.333																																					p.N2082Y		.											.	NBEAL1-92	0			c.A6244T						.						66	66	66					2																	204039877		1802	4060	5862	SO:0001583	missense	65065	exon41			TATGAAAATTTTG	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6244A>T	2.37:g.204039877A>T	ENSP00000399903:p.Asn2082Tyr	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	83	27	NM_001114132	0	0	0	0	0	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.547864	0.86022	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.80304	-1.36;-1.36	5.92	5.92	0.95590	BEACH domain (4);	0.091060	0.85682	D	0.000000	D	0.82300	0.5007	L	0.28649	0.875	0.54753	D	0.999985	P;P	0.48016	0.904;0.904	P;P	0.57371	0.819;0.748	T	0.82971	-0.0192	10	0.48119	T	0.1	.	16.0292	0.80564	1.0:0.0:0.0:0.0	.	2082;2071	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	Y	2082;2082;97	ENSP00000399903:N2082Y;ENSP00000388466:N97Y	ENSP00000344985:N2082Y	N	+	1	0	NBEAL1	203748122	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	9.287000	0.95975	2.254000	0.74563	0.528000	0.53228	AAT	.		0.333	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204039877	A	T	204039877	3	4	11	1	0	0	0	0	1	0	0	0	10213	14	1	5	6402	5	NBEAL1	2	204039877	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	14141059	204039877	39159496	18	801											
ANKZF1	55139	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	220099806	220099806	+	Frame_Shift_Del	DEL	C	C	-																															tttgctggatgaggccaaagCccctggtcagccagagctct																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:220099806delC	ENST00000323348.5	+	10	1637	c.1463delC	c.(1462-1464)gccfs	p.A488fs	GLB1L_ENST00000497855.1_5'Flank|ANKZF1_ENST00000409849.1_Frame_Shift_Del_p.A278fs|ANKZF1_ENST00000410034.3_Frame_Shift_Del_p.A488fs	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	488						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAGGCCAAAGCCCCTGGTCAG	0.587																																					p.A488fs		.											.	ANKZF1-92	0			c.1463delC						.						49	53	51					2																	220099806		1987	4163	6150	SO:0001589	frameshift_variant	55139	exon10			.	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1463delC	2.37:g.220099806delC	ENSP00000321617:p.Ala488fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_001042410	0	0	0	0	0	Q9NVZ4	Frame_Shift_Del	DEL	ENST00000323348.5	37	CCDS42821.1																																																																																			.		0.587	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		-	220099806	C	-	220099806	7	5	11	1	0	1	0	1	0	0	0	0	693	739	26	0	1497	0	ANKZF1	2	220099806	Frame_Shift_Del	DEL	C	TCGA-A4-7996-01A-11D-2201-08	16059929	220099806	23099567	19	802											
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233660917	233660917	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtattacaaagatcctcAgggagaaattcaaggcaagt	15	9	11	6	0	2	2	2	0	0	2	3	3	3	2	1	3	1	2	1	3	6	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:233660917A>G	ENST00000409547.1	+	16	1936	c.1625A>G	c.(1624-1626)cAg>cGg	p.Q542R	GIGYF2_ENST00000373566.3_Missense_Mutation_p.Q564R|GIGYF2_ENST00000409480.1_Missense_Mutation_p.Q564R|GIGYF2_ENST00000409451.3_Missense_Mutation_p.Q563R|GIGYF2_ENST00000409196.3_Missense_Mutation_p.Q536R|GIGYF2_ENST00000373563.4_Missense_Mutation_p.Q542R|GIGYF2_ENST00000452341.2_Missense_Mutation_p.Q373R	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	542	GYF. {ECO:0000255|PROSITE- ProRule:PRU00101}.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AAAGATCCTCAGGGAGAAATT	0.378																																					p.Q563R		.											.	GIGYF2-28	0			c.A1688G						.						121	117	118					2																	233660917		2203	4300	6503	SO:0001583	missense	26058	exon16			ATCCTCAGGGAGA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1625A>G	2.37:g.233660917A>G	ENSP00000386537:p.Gln542Arg	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	136	33	NM_001103147	0	0	19	38	19	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.654738	0.88056	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;D;T;T;T;T	0.81579	-1.35;-1.33;-1.35;-1.33;-1.51;-1.32;-1.35;-1.45;-1.27	5.68	5.68	0.88126	GYF (4);	0.000000	0.85682	D	0.000000	D	0.91529	0.7325	M	0.89658	3.05	0.80722	D	1	D;D;D;D	0.71674	0.994;0.998;0.997;0.969	D;D;D;D	0.83275	0.986;0.996;0.992;0.968	D	0.93157	0.6554	10	0.87932	D	0	-17.6236	16.2119	0.82168	1.0:0.0:0.0:0.0	.	373;563;542;536	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	R	564;485;542;564;542;542;485;536;563;536;373	ENSP00000362667:Q564R;ENSP00000362664:Q542R;ENSP00000386765:Q564R;ENSP00000386537:Q542R;ENSP00000404195:Q485R;ENSP00000387070:Q536R;ENSP00000387170:Q563R;ENSP00000410297:Q536R;ENSP00000411505:Q373R	ENSP00000362664:Q542R	Q	+	2	0	GIGYF2	233369161	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.288000	0.76882	0.482000	0.46254	CAG	.		0.378	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		G	233660917	A	G	233660917	3	3	11	1	0	0	0	0	1	0	0	0	6398	188	7	3	1741	3	GIGYF2	2	233660917	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	13561111	233660917	9538456	20	803											
CCR3	1232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46307340	46307340	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacgctgctgaggtgccccAgtaaaaaaaagtacaaggcc	16	5	10	10	1	0	1	0	1	0	0	0	1	0	1	3	2	4	4	3	2	7	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:46307340A>G	ENST00000357422.2	+	4	1234	c.691A>G	c.(691-693)Agt>Ggt	p.S231G	CCR3_ENST00000395940.2_Missense_Mutation_p.S231G|CCR3_ENST00000545097.1_Missense_Mutation_p.S252G|CCR3_ENST00000541018.1_Missense_Mutation_p.S231G|CCR3_ENST00000395942.2_Missense_Mutation_p.S231G			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	231					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		GAGGTGCCCCAGTAAAAAAAA	0.463																																					p.S252G		.											.	CCR3-660	0			c.A754G						.						73	72	72					3																	46307340		2203	4300	6503	SO:0001583	missense	1232	exon3			TGCCCCAGTAAAA	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.691A>G	3.37:g.46307340A>G	ENSP00000350003:p.Ser231Gly	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	62	28	NM_178328	0	0	0	0	0	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	37	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.712194	0.30322	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	5.96	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.34424	0.0897	N	0.21448	0.665	0.09310	N	1	B;B	0.14805	0.009;0.011	B;B	0.23150	0.036;0.044	T	0.31166	-0.9953	9	0.66056	D	0.02	.	9.5513	0.39313	0.8017:0.0:0.1983:0.0	.	252;231	F5GWL6;P51677	.;CCR3_HUMAN	G	231;252;231;231;231	ENSP00000350003:S231G;ENSP00000441600:S252G;ENSP00000440097:S231G;ENSP00000379271:S231G;ENSP00000379273:S231G	ENSP00000350003:S231G	S	+	1	0	CCR3	46282344	0.001000	0.12720	0.041000	0.18516	0.744000	0.42396	1.757000	0.38400	0.158000	0.19367	0.533000	0.62120	AGT	.		0.463	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			G	46307340	A	G	46307340	3	3	11	1	0	0	0	0	1	0	0	0	2948	188	7	3	760	3	CCR3	3	46307340	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		46307340	151715090	21	804											
PLXNB1	5364	ucsc.edu	37	chr3	48447207	48447207	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgaggtctccggagtagttcTagggaagaggccaaatgaaa	13	7	14	7	2	2	2	0	1	2	1	3	5	2	4	2	4	0	2	2	4	5	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:48447207T>C	ENST00000358536.4	-	37	6498		c.e37-2		PLXNB1_ENST00000456774.1_Splice_Site|PLXNB1_ENST00000296440.6_Splice_Site|PLXNB1_ENST00000448774.2_Splice_Site|PLXNB1_ENST00000358459.4_Splice_Site	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1						axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGAGTAGTTCTAGGGAAGAGG	0.612																																					.													.	PLXNB1-293	0			c.6229-2A>G						.						49	48	48					3																	48447207		2203	4300	6503	SO:0001630	splice_region_variant	5364	exon38			TAGTTCTAGGGAA	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.6229-2A>G	3.37:g.48447207T>C		Somatic	55	0		WXS	Illumina HiSeq		47	1	NM_002673	0	0	1	1	0	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Splice_Site	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.040651	0.55003	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000448774;ENST00000456774	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.461	0.67450	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLXNB1	48422211	1.000000	0.71417	0.991000	0.47740	0.495000	0.33615	6.184000	0.72008	2.021000	0.59480	0.528000	0.53228	.	.		0.612	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	Intron	C	48447207	T	C	48447207	5	2	11	1	0	0	0	0	0	0	1	0	12149	1536	53	3	188	3	PLXNB1	3	48447207	Splice_Site	SNP	T	TCGA-A4-7996-01A-11D-2201-08	2139867	48447207	149575223	22	805											
GNAI2	2771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50294280	50294280	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctagctgaggacgaggAgatggtgagaggatgagaga	12	6	20	3	1	0	5	0	3	0	3	0	11	0	7	0	5	2	2	0	5	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:50294280A>C	ENST00000313601.6	+	6	1103	c.719A>C	c.(718-720)gAg>gCg	p.E240A	GNAI2_ENST00000422163.1_Missense_Mutation_p.E224A|GNAI2_ENST00000491100.1_3'UTR|GNAI2_ENST00000451956.1_Missense_Mutation_p.E203A|GNAI2_ENST00000536647.1_Missense_Mutation_p.E159A|GNAI2_ENST00000440628.1_Missense_Mutation_p.E188A|GNAI2_ENST00000266027.5_Missense_Mutation_p.E224A	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	240					activation of MAPKK activity (GO:0000186)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of synaptic transmission (GO:0050805)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|regulation of calcium ion transport (GO:0051924)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|liver(2)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		GAGGACGAGGAGATGGTGAGA	0.577																																					p.E240A		.											.	GNAI2-417	0			c.A719C						.						113	107	109					3																	50294280		2203	4300	6503	SO:0001583	missense	2771	exon6			ACGAGGAGATGGT	X04828	CCDS2813.1, CCDS54587.1, CCDS63642.1, CCDS63644.1	3p21.31	2010-08-27			ENSG00000114353	ENSG00000114353			4385	protein-coding gene	gene with protein product	"GTP-binding regulatory protein Gi alpha-2 chain"	139360		GNAI2B		3100330, 1733849	Standard	NM_001166425		Approved	GIP	uc003cyq.1	P04899	OTTHUMG00000156940	ENST00000313601.6:c.719A>C	3.37:g.50294280A>C	ENSP00000312999:p.Glu240Ala	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	87	35	NM_002070	0	0	0	0	0	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	Missense_Mutation	SNP	ENST00000313601.6	37	CCDS2813.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703847	0.68501	.	.	ENSG00000114353	ENST00000422163;ENST00000313601;ENST00000536647;ENST00000540560;ENST00000440628;ENST00000451956;ENST00000266027	T;T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39	4.62	4.62	0.57501	.	0.117678	0.64402	D	0.000009	T	0.67924	0.2945	M	0.77103	2.36	0.80722	D	1	B;B;B;B	0.17852	0.002;0.007;0.024;0.019	B;B;B;B	0.23852	0.049;0.049;0.049;0.029	T	0.69928	-0.5012	10	0.72032	D	0.01	.	12.3095	0.54920	1.0:0.0:0.0:0.0	.	203;240;224;224	B4DYA0;P04899;B3KTZ0;P04899-2	.;GNAI2_HUMAN;.;.	A	224;240;159;240;188;203;224	ENSP00000406871:E224A;ENSP00000312999:E240A;ENSP00000444360:E159A;ENSP00000395736:E188A;ENSP00000406369:E203A;ENSP00000266027:E224A	ENSP00000266027:E224A	E	+	2	0	GNAI2	50269284	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.285000	0.78660	2.088000	0.63022	0.459000	0.35465	GAG	.		0.577	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070		C	50294280	A	C	50294280	3	2	11	1	0	0	0	0	1	0	0	0	6525	304	11	5	752	5	GNAI2	3	50294280	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	1847073	50294280	147728150	23	806											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376113	113376113	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgttgttgttgctgttgCtgctgctgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	8	13	0	0	0	5	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1472Q			Q68DE3	K2018_HUMAN	KIAA2018	1472	Gln-rich.					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						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		.											.	KIAA2018-93	0			c.G4416A						.						68	71	70					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	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.4416G>A	3.37:g.113376113C>T		Somatic	42	2		WXS	Illumina HiSeq	Phase_I	46	7	NM_001009899	0	0	8	9	1	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376113	C	T	113376113	2	4	11	1	0	0	0	0	0	0	0	1	8289	796	28	2		2	KIAA2018	3	113376113	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	63081833	113376113	84646317	24	807											
ZXDC	79364	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	126194470	126194470	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgccgccgtgcggcactTccagcagcaccaagaaagag	11	3	12	15	4	0	2	0	0	0	2	1	2	1	2	4	1	4	3	4	1	2	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:126194470T>C	ENST00000389709.3	-	1	292	c.239A>G	c.(238-240)gAa>gGa	p.E80G	ZXDC_ENST00000336332.5_Missense_Mutation_p.E80G	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	80					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		GTGCGGCACTTCCAGCAGCAC	0.766																																					p.E80G		.											.	ZXDC-91	0			c.A239G						.						10	11	10					3																	126194470		1178	2759	3937	SO:0001583	missense	79364	exon1			GGCACTTCCAGCA	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"Zinc fingers, C2H2-type"	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.239A>G	3.37:g.126194470T>C	ENSP00000374359:p.Glu80Gly	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	18	11	NM_025112	0	0	0	0	0	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Missense_Mutation	SNP	ENST00000389709.3	37	CCDS43145.1	.	.	.	.	.	.	.	.	.	.	T	7.919	0.738083	0.15574	.	.	ENSG00000070476	ENST00000389709;ENST00000336332	T;T	0.29142	1.58;1.58	3.22	1.97	0.26223	.	3.885840	0.01408	U	0.013872	T	0.25269	0.0614	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.10800	-1.0614	10	0.23891	T	0.37	-0.3189	3.4994	0.07668	0.0:0.1312:0.2352:0.6336	.	80;80	Q2QGD7-2;Q2QGD7	.;ZXDC_HUMAN	G	80	ENSP00000374359:E80G;ENSP00000337694:E80G	ENSP00000337694:E80G	E	-	2	0	ZXDC	127677160	0.000000	0.05858	0.272000	0.24630	0.077000	0.17291	0.070000	0.14573	0.233000	0.21120	0.358000	0.22013	GAA	.		0.766	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112		C	126194470	T	C	126194470	3	2	11	1	0	0	0	0	1	0	0	0	18284	1783	62	3	2383	3	ZXDC	3	126194470	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	12818357	126194470	71827960	25	808											
C4orf36	132989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	87809274	87809274	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaacttaaggaacttacAttctgcagaagggagcagtc	14	8	11	8	0	1	2	0	0	1	2	2	4	1	4	0	2	5	3	0	2	5	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr4:87809274A>T	ENST00000473559.1	-	6	883	c.220T>A	c.(220-222)Tct>Act	p.S74T	C4orf36_ENST00000295898.3_Splice_Site_p.S74T|C4orf36_ENST00000503001.1_5'Flank			Q96KX1	CD036_HUMAN	chromosome 4 open reading frame 36	74										breast(1)|kidney(1)|lung(1)|prostate(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		AGGAACTTACATTCTGCAGAA	0.363																																					p.S74T		.											.	C4orf36-90	0			c.T220A						.						65	66	66					4																	87809274		2203	4300	6503	SO:0001630	splice_region_variant	132989	exon3			ACTTACATTCTGC	BC016746	CCDS3615.1	4q21.3	2008-02-05			ENSG00000163633	ENSG00000163633			28386	protein-coding gene	gene with protein product						12477932	Standard	NM_144645		Approved	MGC26744	uc003hqe.4	Q96KX1	OTTHUMG00000130597	ENST00000473559.1:c.220+1T>A	4.37:g.87809274A>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	89	25	NM_144645	0	0	0	0	0		Missense_Mutation	SNP	ENST00000473559.1	37	CCDS3615.1	.	.	.	.	.	.	.	.	.	.	A	7.943	0.743153	0.15642	.	.	ENSG00000163633	ENST00000295898;ENST00000473559;ENST00000506308;ENST00000504008	T;T;T;T	0.38887	1.11;1.11;1.11;1.11	5.13	-6.29	0.02013	.	1.537520	0.03676	N	0.244784	T	0.22003	0.0530	N	0.17082	0.46	0.23249	N	0.99805	B	0.06786	0.001	B	0.08055	0.003	T	0.13764	-1.0497	9	.	.	.	0.0079	6.0792	0.19933	0.2272:0.2261:0.0:0.5468	.	74	Q96KX1	CD036_HUMAN	T	74	ENSP00000295898:S74T;ENSP00000420949:S74T;ENSP00000421141:S74T;ENSP00000422720:S74T	.	S	-	1	0	C4orf36	88028298	0.908000	0.30866	0.122000	0.21767	0.240000	0.25518	-0.311000	0.08124	-0.602000	0.05775	0.482000	0.46254	TCT	.		0.363	C4orf36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253045.2	NM_144645	Missense_Mutation	T	87809274	A	T	87809274	5	4	11	1	0	0	0	0	0	0	1	0	2272	231	8	5	141	5	C4orf36	4	87809274	Splice_Site	SNP	A	TCGA-A4-7996-01A-11D-2201-08		87809274	103345002	26	809											
PLK4	10733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	128812805	128812805	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaccctcacctactgacaaCatcagtaggtacagctttga	12	9	6	14	0	2	2	2	2	0	0	2	2	2	2	3	1	4	3	3	1	4	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr4:128812805C>A	ENST00000270861.5	+	9	2281	c.2007C>A	c.(2005-2007)aaC>aaA	p.N669K	PLK4_ENST00000507249.1_Missense_Mutation_p.N608K|PLK4_ENST00000515069.1_Missense_Mutation_p.N591K|PLK4_ENST00000513090.1_Missense_Mutation_p.N637K|PLK4_ENST00000514379.1_Missense_Mutation_p.N628K|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	669					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						CTACTGACAACATCAGTAGGT	0.318																																					p.N669K	Colon(135;508 1718 19061 31832 42879)	.											.	PLK4-333	0			c.C2007A						.						89	97	94					4																	128812805		2203	4300	6503	SO:0001583	missense	10733	exon9			TGACAACATCAGT	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2007C>A	4.37:g.128812805C>A	ENSP00000270861:p.Asn669Lys	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	176	59	NM_014264	0	0	1	1	0	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.175146	0.57692	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.07	2.4	0.29515	.	0.153463	0.56097	D	0.000021	T	0.32255	0.0823	L	0.51422	1.61	0.35092	D	0.764371	P;P	0.47762	0.9;0.839	P;B	0.48400	0.576;0.372	T	0.41360	-0.9513	10	0.59425	D	0.04	-4.1709	7.6088	0.28118	0.1342:0.724:0.0:0.1418	.	637;669	O00444-2;O00444	.;PLK4_HUMAN	K	669;591;637;608;628	ENSP00000270861:N669K;ENSP00000421774:N591K;ENSP00000427554:N637K;ENSP00000423412:N608K;ENSP00000423582:N628K	ENSP00000270861:N669K	N	+	3	2	PLK4	129032255	0.963000	0.33076	0.983000	0.44433	0.892000	0.51952	0.033000	0.13754	0.309000	0.22966	0.467000	0.42956	AAC	.		0.318	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			A	128812805	C	A	128812805	3	1	11	1	0	0	0	0	1	0	0	0	12124	477	17	4	2041	4	PLK4	4	128812805	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	41003531	128812805	62341471	27	810											
FHDC1	85462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	153896859	153896859	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaaggcggggaaggggatGgctccatgtcctctggggtt	7	8	19	7	1	1	0	0	0	1	0	3	3	3	3	2	9	0	2	2	9	2	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr4:153896859G>A	ENST00000511601.1	+	12	2604	c.2416G>A	c.(2416-2418)Ggc>Agc	p.G806S	FHDC1_ENST00000260008.3_Missense_Mutation_p.G806S			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	806									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					GGAAGGGGATGGCTCCATGTC	0.652																																					p.G806S		.											.	FHDC1-136	0			c.G2416A						.						51	61	58					4																	153896859		2203	4300	6503	SO:0001583	missense	85462	exon11			GGGGATGGCTCCA	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.2416G>A	4.37:g.153896859G>A	ENSP00000427567:p.Gly806Ser	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	139	52	NM_033393	0	0	3	6	3		Missense_Mutation	SNP	ENST00000511601.1	37	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	G	5.523	0.281358	0.10458	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.29917	1.55;1.55	4.95	3.16	0.36331	.	0.771246	0.12008	N	0.508193	T	0.16811	0.0404	L	0.29908	0.895	0.09310	N	1	P	0.39282	0.666	B	0.33339	0.162	T	0.07947	-1.0746	10	0.02654	T	1	.	10.0533	0.42230	0.0:0.1495:0.695:0.1555	.	806	Q9C0D6	FHDC1_HUMAN	S	806	ENSP00000427567:G806S;ENSP00000260008:G806S	ENSP00000260008:G806S	G	+	1	0	FHDC1	154116309	0.062000	0.20869	0.002000	0.10522	0.222000	0.24845	2.052000	0.41316	0.455000	0.26910	0.563000	0.77884	GGC	.		0.652	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		A	153896859	G	A	153896859	3	1	11	1	0	0	0	0	1	0	0	0	5895	1348	47	2	2458	2	FHDC1	4	153896859	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	25084054	153896859	37257417	28	811											
SLC12A7	10723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1074691	1074691	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcggtgctcacctccagttcTtggtgtgggggggaccgtgc	3	10	17	11	2	2	0	1	0	1	0	3	1	3	1	3	5	2	2	3	5	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:1074691T>G	ENST00000264930.5	-	16	2106	c.2063A>C	c.(2062-2064)aAg>aCg	p.K688T		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	688					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CCTCCAGTTCTTGGTGTGGGG	0.657																																					p.K688T		.											.	SLC12A7-138	0			c.A2063C						.						54	51	52					5																	1074691		2201	4299	6500	SO:0001583	missense	10723	exon16			CAGTTCTTGGTGT	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2063A>C	5.37:g.1074691T>G	ENSP00000264930:p.Lys688Thr	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	100	31	NM_006598	0	0	0	0	0	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	37	CCDS34129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	17.74|17.74	3.464117|3.464117	0.63513|0.63513	.|.	.|.	ENSG00000113504|ENSG00000113504	ENST00000264930|ENST00000513223	D|.	0.99186|.	-5.53|.	3.81|3.81	3.81|3.81	0.43845|0.43845	Amino acid permease domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86682|0.86682	0.5991|0.5991	H|H	0.97707|0.97707	4.06|4.06	0.58432|0.58432	D|D	0.999998|0.999998	P|.	0.46912|.	0.886|.	P|.	0.46339|.	0.513|.	D|D	0.89599|0.89599	0.3833|0.3833	10|5	0.87932|.	D|.	0|.	.|.	10.8081|10.8081	0.46529|0.46529	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	688|.	Q9Y666|.	S12A7_HUMAN|.	T|H	688|45	ENSP00000264930:K688T|.	ENSP00000264930:K688T|.	K|Q	-|-	2|3	0|2	SLC12A7|SLC12A7	1127691|1127691	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.335000|0.335000	0.28730|0.28730	7.076000|7.076000	0.76806|0.76806	1.501000|1.501000	0.48654|0.48654	0.260000|0.260000	0.18958|0.18958	AAG|CAA	.		0.657	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		G	1074691	T	G	1074691	3	3	11	1	0	0	0	0	1	0	0	0	14420	1609	56	5	1224	5	SLC12A7	5	1074691	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08		1074691	179840569	29	812											
PCDHA11	56138	hgsc.bcm.edu;bcgsc.ca	37	chr5	140250097	140250097	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaaggagaacaacccaccagGctgccacatcttcacagtgt	13	6	9	13	0	2	1	1	0	1	1	2	3	2	1	3	2	3	1	3	2	3	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:140250097G>C	ENST00000398640.2	+	1	1409	c.1409G>C	c.(1408-1410)gGc>gCc	p.G470A	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	470	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACCCACCAGGCTGCCACATC	0.667																																					p.G470A		.											.	PCDHA11-67	0			c.G1409C						.						105	109	108					5																	140250097		2203	4300	6503	SO:0001583	missense	56138	exon1			CACCAGGCTGCCA	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"Cadherins / Protocadherins : Clustered"	8665	other	complex locus constituent	"KIAA0345-like 3", "ortholog of mouse CNR7"	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1409G>C	5.37:g.140250097G>C	ENSP00000381636:p.Gly470Ala	Somatic	272	1		WXS	Illumina HiSeq	Phase_I	239	23	NM_018902	0	0	0	0	0	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.905417	0.52333	.	.	ENSG00000249158	ENST00000398640	T	0.69806	-0.43	5.55	5.55	0.83447	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.80565	0.4647	L	0.58428	1.81	0.51233	D	0.999911	D;D	0.89917	1.0;1.0	D;D	0.91635	0.986;0.999	T	0.81673	-0.0826	9	0.87932	D	0	.	19.1659	0.93557	0.0:0.0:1.0:0.0	.	470;470	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	A	470	ENSP00000381636:G470A	ENSP00000381636:G470A	G	+	2	0	PCDHA11	140230281	1.000000	0.71417	0.897000	0.35233	0.024000	0.10985	4.966000	0.63715	2.618000	0.88619	0.556000	0.70494	GGC	.		0.667	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		C	140250097	G	C	140250097	3	2	11	1	0	0	0	0	1	0	0	0	11547	1203	42	4	1411	4	PCDHA11	5	140250097	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	139175406	140250097	40665163	30	813											
MAT2B	27430	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	162940576	162940577	+	Frame_Shift_Ins	INS	-	-	A																															ctagccccatgttatagtacINSattgtgcagcagagagaaga																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:162940576_162940577insA	ENST00000321757.6	+	3	413_414	c.274_275insA	c.(274-276)catfs	p.H92fs	MAT2B_ENST00000518095.1_Frame_Shift_Ins_p.H92fs|MAT2B_ENST00000280969.5_Frame_Shift_Ins_p.H81fs	NM_013283.3	NP_037415.1	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta	92					cellular nitrogen compound metabolic process (GO:0034641)|extracellular polysaccharide biosynthetic process (GO:0045226)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|regulation of catalytic activity (GO:0050790)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|methionine adenosyltransferase complex (GO:0048269)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dTDP-4-dehydrorhamnose reductase activity (GO:0008831)|enzyme binding (GO:0019899)|methionine adenosyltransferase regulator activity (GO:0048270)			endometrium(3)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	14	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)	TGTTATAGTACATTGTGCAGCA	0.371																																					p.H92fs		.											.	MAT2B-91	0			c.274_275insA						.																																			SO:0001589	frameshift_variant	27430	exon3			.	AF182814	CCDS4364.1, CCDS4365.1	5q34-q35	2011-09-14			ENSG00000038274	ENSG00000038274		"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	6905	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 23E, member 1"	605527				9055605, 10644686, 19027726	Standard	NM_182796		Approved	MATIIbeta, SDR23E1	uc003lzk.4	Q9NZL9	OTTHUMG00000130379	ENST00000321757.6:c.275dupA	5.37:g.162940577_162940577dupA	ENSP00000325425:p.His92fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	104	37	NM_013283	0	0	0	0	0	B2R5Y6|Q1WAI7|Q27J92|Q3LIE8|Q567T7|Q6NYC7|Q9BS89|Q9H3E1|Q9UJ54	Frame_Shift_Ins	INS	ENST00000321757.6	37	CCDS4365.1																																																																																			.		0.371	MAT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252749.2	NM_013283		A	162940577	-	A	162940576	7	5	11	1	0	1	1	0	0	0	0	0	9356	478	17	0	318	0	MAT2B	5	162940576	Frame_Shift_Ins	INS	-	TCGA-A4-7996-01A-11D-2201-08	22690479	162940576	17974684	31	814											
CLTB	1212	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	175843340	175843342	+	In_Frame_Del	DEL	AGA	AGA	-																															ggcaccgctctccgacgacgAgaagaagccaaagtcatcag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:175843340_175843342delAGA	ENST00000310418.4	-	1	228_230	c.23_25delTCT	c.(22-27)ttctcg>tcg	p.F8del	CLTB_ENST00000345807.2_In_Frame_Del_p.F8del	NM_007097.3	NP_009028.1	P09497	CLCB_HUMAN	clathrin, light chain B	8					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	ciliary membrane (GO:0060170)|clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|trans-Golgi network (GO:0005802)	peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			lung(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.098)		TCCGACGACGAGAAGAAGCCAAA	0.724																																					p.8_9del		.											.	CLTB-90	0			c.23_25del						.																																			SO:0001651	inframe_deletion	1212	exon1			.	M20470	CCDS4402.1, CCDS4403.1	5q35.2	2010-05-11	2010-05-11		ENSG00000175416	ENSG00000175416			2091	protein-coding gene	gene with protein product		118970	"clathrin, light polypeptide (Lcb)"			7713494	Standard	NM_007097		Approved	Lcb	uc003meh.4	P09497	OTTHUMG00000130662	ENST00000310418.4:c.23_25delTCT	5.37:g.175843343_175843345delAGA	ENSP00000309415:p.Phe8del	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	36	15	NM_001834	0	0	0	0	0	Q53Y37|Q6FHW1	In_Frame_Del	DEL	ENST00000310418.4	37	CCDS4403.1																																																																																			.		0.724	CLTB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253153.1			-	175843342	AGA	-	175843340	7	5	11	1	0	1	0	1	0	0	0	0	3571	304	11	0	688	0	CLTB	5	175843340	In_Frame_Del	DEL	AGA	TCGA-A4-7996-01A-11D-2201-08	12902764	175843340	5071920	32	815											
F12	2161	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176831350	176831350	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcactgtgccaggtcgcagtActcccagctcagccggtcgc	6	7	12	16	3	1	0	1	0	0	0	4	0	2	0	3	2	4	4	3	2	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:176831350A>G	ENST00000253496.3	-	9	913	c.865T>C	c.(865-867)Tac>Cac	p.Y289H	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	289	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	AGGTCGCAGTACTCCCAGCTC	0.697									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y289H		.											.	F12-90	0			c.T865C						.						16	20	19					5																	176831350		2200	4296	6496	SO:0001583	missense	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	CGCAGTACTCCCA	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.865T>C	5.37:g.176831350A>G	ENSP00000253496:p.Tyr289His	Somatic	33	0	1934	WXS	Illumina HiSeq	Phase_I	36	15	NM_000505	0	0	1	5	4	P78339	Missense_Mutation	SNP	ENST00000253496.3	37	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.074641	0.76415	.	.	ENSG00000131187	ENST00000253496	T	0.66460	-0.21	5.45	5.45	0.79879	Kringle (5);Kringle-like fold (1);	0.000000	0.42682	D	0.000679	T	0.73497	0.3594	M	0.75150	2.29	0.80722	D	1	P	0.51537	0.946	P	0.54210	0.745	T	0.74548	-0.3629	10	0.41790	T	0.15	.	9.0885	0.36596	0.9168:0.0:0.0832:0.0	.	289	P00748	FA12_HUMAN	H	289	ENSP00000253496:Y289H	ENSP00000253496:Y289H	Y	-	1	0	F12	176763956	0.924000	0.31332	0.575000	0.28536	0.770000	0.43624	2.546000	0.45778	2.080000	0.62538	0.459000	0.35465	TAC	.		0.697	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			G	176831350	A	G	176831350	3	3	11	1	0	0	0	0	1	0	0	0	5352	391	14	3	1006	3	F12	5	176831350	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	988010	176831350	4083910	33	816											
SKIV2L	6499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31927082	31927082	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctttccccgtagtgctacccCctccagatcccctggaccta	6	10	6	19	1	0	1	0	0	0	1	3	2	3	2	8	1	2	2	8	1	3	4	rs563036739	byFrequency	TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:31927082C>A	ENST00000375394.2	+	2	144	c.31C>A	c.(31-33)Cct>Act	p.P11T	NELFE_ENST00000444811.2_5'Flank|MIR1236_ENST00000408340.1_RNA|NELFE_ENST00000375429.3_5'Flank|SKIV2L_ENST00000544581.1_5'UTR|NELFE_ENST00000375425.5_5'Flank|SKIV2L_ENST00000488648.1_3'UTR	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	11					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						AGTGCTACCCCCTCCAGATCC	0.602																																					p.P11T		.											.	SKIV2L-290	0			c.C31A						.						221	230	227					6																	31927082		2203	4299	6502	SO:0001583	missense	6499	exon2			CTACCCCCTCCAG		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.31C>A	6.37:g.31927082C>A	ENSP00000364543:p.Pro11Thr	Somatic	587	1		WXS	Illumina HiSeq	Phase_I	457	133	NM_006929	0	0	0	0	0	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	37	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	C	9.522	1.108545	0.20714	.	.	ENSG00000204351	ENST00000375394	T	0.45276	0.9	5.18	3.42	0.39159	.	0.176723	0.50627	D	0.000113	T	0.18130	0.0435	L	0.47716	1.5	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04900	-1.0919	10	0.40728	T	0.16	-13.5646	9.0377	0.36298	0.0:0.8274:0.0:0.1726	.	11	Q15477	SKIV2_HUMAN	T	11	ENSP00000364543:P11T	ENSP00000364543:P11T	P	+	1	0	SKIV2L	32035061	1.000000	0.71417	0.993000	0.49108	0.481000	0.33189	1.932000	0.40143	0.781000	0.33589	0.655000	0.94253	CCT	.		0.602	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31927082	C	A	31927082	3	1	11	1	0	0	0	0	1	0	0	0	14391	623	22	4	37	4	SKIV2L	6	31927082	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		31927082	139187985	34	817											
CYP21A2	1589	broad.mit.edu;bcgsc.ca	37	chr6	32007842	32007846	+	Frame_Shift_Del	DEL	CAGCC	CAGCC	-																															acatgctccaaggggtggcgCagccgagcatggaagagggc																								rs142028935	byFrequency	TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	CAGCC	CAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:32007842_32007846delCAGCC	ENST00000418967.2	+	7	957_961	c.799_803delCAGCC	c.(799-804)cagccgfs	p.QP267fs	CYP21A2_ENST00000435122.2_Frame_Shift_Del_p.QP237fs	NM_000500.7	NP_000491.4	P08686	CP21A_HUMAN	cytochrome P450, family 21, subfamily A, polypeptide 2	266					glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 21-monooxygenase activity (GO:0004509)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	11					Ketoconazole(DB01026)	AGGGGTGGCGCAGCCGAGCATGGAA	0.639																																					.	Melanoma(174;1669 1998 3915 34700 46447)												.	CYP21A2-68	0			.						.																																			SO:0001589	frameshift_variant	1589	.			GTGGCGCAGCCGA	X58906	CCDS4735.1, CCDS47406.1	6p21.3	2014-09-17	2003-01-14		ENSG00000231852	ENSG00000231852	1.14.99.10	"Cytochrome P450s"	2600	protein-coding gene	gene with protein product	"Steroid 21-monooxygenase"	613815	"cytochrome P450, subfamily XXIA (steroid 21-hydroxylase, congenital adrenal hyperplasia), polypeptide 2"	CYP21, CYP21B			Standard	NM_000500		Approved	P450c21B, CA21H, CPS1, CAH1	uc021yvd.1	P08686	OTTHUMG00000031069	ENST00000418967.2:c.799_803delCAGCC	6.37:g.32007842_32007846delCAGCC	ENSP00000408860:p.Gln267fs	Somatic	361	0		WXS	Illumina HiSeq	Phase_I	265	33	.	0	0	0	0	0	A2BHY6|P04033|Q01204|Q08AG8|Q16749|Q16806|Q5ST44|Q96NU8	Frame_Shift_Del	DEL	ENST00000418967.2	37	CCDS4735.1																																																																																			.		0.639	CYP21A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268768.2	NM_000500		-	32007846	CAGCC	-	32007842	7	5	11	1	0	1	0	1	0	0	0	0	4159	711	25	0	2346	0	CYP21A2	6	32007842	Frame_Shift_Del	DEL	CAGCC	TCGA-A4-7996-01A-11D-2201-08	80760	32007842	139107225	35	818											
AGPAT1	10554	broad.mit.edu	37	chr6	32139261	32139268	+	Frame_Shift_Del	DEL	GCCACAAA	GCCACAAA	-																															cagcagcatccatgcccctgGccacaaatccattctggcca																								rs529759736		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	GCCACAAA	GCCACAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:32139261_32139268delGCCACAAA	ENST00000395499.1	-	2	585_592	c.6_13delTTTGTGGC	c.(4-15)gatttgtggccafs	p.LWP3fs	AGPAT1_ENST00000412465.2_5'UTR|AGPAT1_ENST00000375104.2_Frame_Shift_Del_p.LWP3fs|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000395496.1_Frame_Shift_Del_p.LWP3fs|AGPAT1_ENST00000336984.6_Frame_Shift_Del_p.LWP3fs|AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000375107.3_Frame_Shift_Del_p.LWP3fs|AGPAT1_ENST00000395497.1_Frame_Shift_Del_p.LWP3fs			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	3					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						CATGCCCCTGGCCACAAATCCATTCTGG	0.606																																					p.2_5del													.	AGPAT1-90	0			c.6_13del						.																																			SO:0001589	frameshift_variant	10554	exon2			CCCCTGGCCACAA	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	324	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, alpha"	603099	"1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.6_13delTTTGTGGC	6.37:g.32139261_32139268delGCCACAAA	ENSP00000378877:p.Leu3fs	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	22	9	NM_006411	0	0	0	0	0	A2BFI5|Q5BL03	Frame_Shift_Del	DEL	ENST00000395499.1	37	CCDS4744.1																																																																																			.		0.606	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		-	32139268	GCCACAAA	-	32139261	7	5	11	1	0	1	0	1	0	0	0	0	386	1203	42	0	862	0	AGPAT1	6	32139261	Frame_Shift_Del	DEL	GCCACAAA	TCGA-A4-7996-01A-11D-2201-08	131419	32139261	138975806	36	819											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51930865	51930865	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccagtttctggaaacacAgataatatttctgcaagagt	13	12	7	9	0	2	2	0	0	2	2	3	3	3	3	1	1	2	2	1	1	4	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:51930865A>G	ENST00000371117.3	-	12	1064	c.789T>C	c.(787-789)tcT>tcC	p.S263S	PKHD1_ENST00000340994.4_Silent_p.S263S	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	263	IPT/TIG 3.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTGGAAACACAGATAATATTT	0.328																																					p.S263S		.											.	PKHD1-603	0			c.T789C						.						67	66	66					6																	51930865		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon12			AAACACAGATAAT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.789T>C	6.37:g.51930865A>G		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	53	15	NM_170724	0	0	1	1	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			.		0.328	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51930865	A	G	51930865	2	3	11	1	0	0	0	0	0	0	0	1	11997	175	7	3		3	PKHD1	6	51930865	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	19791604	51930865	119184202	37	820											
PARK2	5071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	162864432	162864432	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcgcttagcaaccacctcCttgagctggaagatgctggt	8	11	11	11	1	0	2	0	1	0	1	2	3	1	3	3	2	4	4	3	2	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:162864432C>T	ENST00000366898.1	-	2	183	c.81G>A	c.(79-81)aaG>aaA	p.K27K	PARK2_ENST00000366897.1_Silent_p.K27K|PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366896.1_Silent_p.K27K|PARK2_ENST00000366892.1_Silent_p.K27K|PARK2_ENST00000366894.1_5'UTR	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	27	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CAACCACCTCCTTGAGCTGGA	0.542																																					p.K27K		.											.	PARK2-91	0			c.G81A						.						163	138	146					6																	162864432		2203	4300	6503	SO:0001819	synonymous_variant	5071	exon2			CACCTCCTTGAGC		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"Parkinson disease"	8607	protein-coding gene	gene with protein product	"E3 ubiquitin ligase"	602544	"Parkinson disease (autosomal recessive, juvenile) 2, parkin", "parkinson protein 2, E3 ubiquitin protein ligase (parkin)"			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.81G>A	6.37:g.162864432C>T		Somatic	197	1		WXS	Illumina HiSeq	Phase_I	160	47	NM_004562	0	0	10	13	3	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Silent	SNP	ENST00000366898.1	37	CCDS5281.1																																																																																			.		0.542	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			T	162864432	C	T	162864432	2	4	11	1	0	0	0	0	0	0	0	1	11475	680	24	2		2	PARK2	6	162864432	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	110933567	162864432	8250635	38	821											
FSCN1	6624	hgsc.bcm.edu;broad.mit.edu	37	chr7	5633277	5633277	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggcgccgtcggggcccaGcggcacgctcaaggcgggca	5	3	17	16	6	1	0	1	0	0	0	2	0	1	0	3	6	1	3	3	6	1	0			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:5633277G>A	ENST00000382361.3	+	1	824	c.710G>A	c.(709-711)aGc>aAc	p.S237N	FSCN1_ENST00000340250.6_Missense_Mutation_p.S216N	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	237					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		TCGGGGCCCAGCGGCACGCTC	0.716																																					p.S237N		.											.	FSCN1-91	0			c.G710A						.						5	5	5					7																	5633277		1934	3850	5784	SO:0001583	missense	6624	exon1			GGCCCAGCGGCAC	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"Fascins"	11148	protein-coding gene	gene with protein product	"Singed, drosophila, homolog-like", "actin bundling protein"	602689	"singed (Drosophila)-like (sea urchin fascin homolog like)", "fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.710G>A	7.37:g.5633277G>A	ENSP00000371798:p.Ser237Asn	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	24	3	NM_003088	0	0	38	65	27	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Missense_Mutation	SNP	ENST00000382361.3	37	CCDS5342.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462789	0.43736	.	.	ENSG00000075618	ENST00000340250;ENST00000382361	T;T	0.44881	0.91;1.48	3.4	2.5	0.30297	Fascin domain (1);Actin cross-linking (1);	0.346255	0.27227	N	0.020326	T	0.38134	0.1029	L	0.56769	1.78	0.45307	D	0.998308	B	0.26809	0.16	B	0.24701	0.055	T	0.34775	-0.9815	10	0.87932	D	0	2.5978	10.5668	0.45177	0.0:0.0:0.805:0.195	.	237	Q16658	FSCN1_HUMAN	N	216;237	ENSP00000339729:S216N;ENSP00000371798:S237N	ENSP00000339729:S216N	S	+	2	0	FSCN1	5599803	0.943000	0.32029	0.992000	0.48379	0.996000	0.88848	0.989000	0.29629	0.627000	0.30340	0.462000	0.41574	AGC	.		0.716	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088		A	5633277	G	A	5633277	3	1	11	1	0	0	0	0	1	0	0	0	6086	971	34	2	712	2	FSCN1	7	5633277	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08		5633277	153505386	39	822											
MPP6	51678	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	24727063	24727075	+	Frame_Shift_Del	DEL	GACTTGAAGAAAA	GACTTGAAGAAAA	-																															aaactcttcaacaggactctGacttgaagaaaacagtggat																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	GACTTGAAGAAAA	GACTTGAAGAAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:24727063_24727075delGACTTGAAGAAAA	ENST00000222644.5	+	12	1703_1715	c.1453_1465delGACTTGAAGAAAA	c.(1453-1467)gacttgaagaaaacafs	p.DLKKT485fs	MPP6_ENST00000396475.2_Frame_Shift_Del_p.DLKKT485fs|MPP6_ENST00000409761.1_Frame_Shift_Del_p.DLKKT373fs			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						ACAGGACTCTGACTTGAAGAAAACAGTGGATGA	0.324																																					p.485_489del		.											.	MPP6-90	0			c.1453_1465del						.																																			SO:0001589	frameshift_variant	51678	exon13			.	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.1453_1465delGACTTGAAGAAAA	7.37:g.24727063_24727075delGACTTGAAGAAAA	ENSP00000222644:p.Asp485fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	142	50	NM_016447	0	0	0	0	0	B2RAF0	Frame_Shift_Del	DEL	ENST00000222644.5	37	CCDS5388.1																																																																																			.		0.324	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			-	24727075	GACTTGAAGAAAA	-	24727063	7	5	11	1	0	1	0	1	0	0	0	0	9763	1290	45	0	1495	0	MPP6	7	24727063	Frame_Shift_Del	DEL	GACTTGAAGAAAA	TCGA-A4-7996-01A-11D-2201-08	19093786	24727063	134411600	40	823											
ZMIZ2	83637	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	44807159	44807159	+	Frame_Shift_Del	DEL	G	G	-																															gatgagctactgtcctacttGggcccacccgacctccctac																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:44807159delG	ENST00000309315.4	+	19	2823	c.2700delG	c.(2698-2700)ttgfs	p.L900fs	ZMIZ2_ENST00000441627.1_Frame_Shift_Del_p.L900fs|ZMIZ2_ENST00000433667.1_Frame_Shift_Del_p.L868fs|ZMIZ2_ENST00000265346.7_Frame_Shift_Del_p.L874fs|ZMIZ2_ENST00000413916.1_Frame_Shift_Del_p.L842fs|ZMIZ2_ENST00000463931.1_3'UTR	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	900	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TGTCCTACTTGGGCCCACCCG	0.552																																					p.L900fs	NSCLC(20;604 852 1948 16908 50522)	.											.	ZMIZ2-137	0			c.2700delG						.						145	159	155					7																	44807159		2045	4190	6235	SO:0001589	frameshift_variant	83637	exon19			.	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"Zinc fingers, MIZ-type"	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2700delG	7.37:g.44807159delG	ENSP00000311778:p.Leu900fs	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	122	24	NM_031449	0	0	0	0	0	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Frame_Shift_Del	DEL	ENST00000309315.4	37	CCDS43576.1																																																																																			.		0.552	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		-	44807159	G	-	44807159	7	5	11	1	0	1	0	1	0	0	0	0	17729	1339	47	0	2770	0	ZMIZ2	7	44807159	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	20080096	44807159	114331504	41	824											
RELN	5649	broad.mit.edu	37	chr7	103159949	103159949	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagatccacagtgactaaTaatcgactacaaccctaaga	16	10	5	10	1	0	3	0	1	0	2	2	4	1	3	2	0	2	0	2	0	6	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:103159949T>C	ENST00000428762.1	-	49	7842	c.7683A>G	c.(7681-7683)ttA>ttG	p.L2561L	RELN_ENST00000424685.2_Silent_p.L2561L|RELN_ENST00000343529.5_Silent_p.L2561L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2561					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CAGTGACTAATAATCGACTAC	0.328																																					p.L2561L	NSCLC(146;835 1944 15585 22231 52158)												.	RELN-574	0			c.A7683G						.						84	74	78					7																	103159949		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon49			GACTAATAATCGA		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7683A>G	7.37:g.103159949T>C		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	98	5	NM_173054	0	0	34	37	3	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			.		0.328	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103159949	T	C	103159949	2	2	11	1	0	0	0	0	0	0	0	1	13252	1403	49	3		3	RELN	7	103159949	Silent	SNP	T	TCGA-A4-7996-01A-11D-2201-08	58352790	103159949	55978714	42	825											
DOCK4	9732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	111555869	111555869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaaaatcccagcttccttGttatggatactccatgagaa	12	13	7	9	0	0	2	0	2	0	1	3	4	3	3	3	1	2	2	3	1	5	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:111555869G>A	ENST00000437633.1	-	13	1413	c.1157C>T	c.(1156-1158)aCa>aTa	p.T386I	DOCK4_ENST00000428084.1_Missense_Mutation_p.T386I|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	386					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CAGCTTCCTTGTTATGGATAC	0.368																																					p.T386I		.											.	DOCK4-26	0			c.C1157T						.						57	53	54					7																	111555869		1820	4078	5898	SO:0001583	missense	9732	exon13			TTCCTTGTTATGG		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1157C>T	7.37:g.111555869G>A	ENSP00000404179:p.Thr386Ile	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	48	13	NM_014705	0	0	8	8	0	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.3|27.3	4.816438|4.816438	0.90790|0.90790	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	.|T;T	.|0.03580	.|3.88;3.88	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.19167	.|0.0460	M|M	0.74467|0.74467	2.265|2.265	0.80722|0.80722	D|D	1|1	.|D;D	.|0.69078	.|0.997;0.997	.|D;D	.|0.67103	.|0.949;0.949	.|T	.|0.00003	.|-1.2602	.|10	.|0.87932	.|D	.|0	.|.	19.3311|19.3311	0.94288|0.94288	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|386;386	.|Q149N5;Q8N1I0	.|.;DOCK4_HUMAN	X|I	374|374;386;386;374;385	.|ENSP00000410746:T386I;ENSP00000404179:T386I	.|ENSP00000345432:T374I	Q|T	-|-	1|2	0|0	DOCK4|DOCK4	111343105|111343105	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.960000|0.960000	0.62799|0.62799	8.322000|8.322000	0.90000|0.90000	2.868000|2.868000	0.98415|0.98415	0.555000|0.555000	0.69702|0.69702	CAA|ACA	.		0.368	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111555869	G	A	111555869	3	1	11	1	0	0	0	0	1	0	0	0	4700	1377	48	2	4903	2	DOCK4	7	111555869	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	8395920	111555869	47582794	43	826											
ABP1	26	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	150553627	150553627	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccatggcggagccctccccGgggactctgcccaggaaggc	6	4	15	16	2	1	0	0	0	1	0	2	3	2	3	5	6	2	0	5	6	1	0	rs186258416	byFrequency	TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:150553627G>C	ENST00000493429.1	+	4	653	c.69G>C	c.(67-69)ccG>ccC	p.P23P	AOC1_ENST00000467291.1_Silent_p.P23P|AOC1_ENST00000416793.2_Silent_p.P23P|AOC1_ENST00000360937.4_Silent_p.P23P			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	23					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	AGCCCTCCCCGGGGACTCTGC	0.632																																					p.P23P		.											.	ABP1-139	0			c.G69C						.						41	42	42					7																	150553627		1927	4136	6063	SO:0001819	synonymous_variant	26	exon2			CTCCCCGGGGACT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"diamine oxidase"	104610	"amiloride binding protein 1 (amine oxidase (copper-containing))"	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.69G>C	7.37:g.150553627G>C		Somatic	69	1		WXS	Illumina HiSeq	Phase_I	82	37	NM_001091	0	0	2	31	29	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			G|0.999;A|0.001		0.632	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		C	150553627	G	C	150553627	2	2	11	1	0	0	0	0	0	0	0	1	98	1103	39	4		4	ABP1	7	150553627	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	38997758	150553627	8585036	44	827											
KIF13B	23303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	28991695	28991695	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacacaaagtgggacagatgCtgtggcaacccagtagcttg	13	7	12	9	0	0	1	0	0	0	1	0	2	0	2	1	2	4	4	1	2	4	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:28991695C>G	ENST00000524189.1	-	22	2684	c.2646G>C	c.(2644-2646)caG>caC	p.Q882H	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	882					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		GGGACAGATGCTGTGGCAACC	0.488																																					p.Q882H		.											.	KIF13B-22	0			c.G2646C						.						81	81	81					8																	28991695		1901	4128	6029	SO:0001583	missense	23303	exon22			CAGATGCTGTGGC	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.2646G>C	8.37:g.28991695C>G	ENSP00000427900:p.Gln882His	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	122	45	NM_015254	0	0	21	33	12	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.235189	0.58886	.	.	ENSG00000197892	ENST00000524189	T	0.10382	2.88	5.28	2.49	0.30216	.	0.057734	0.64402	D	0.000001	T	0.23094	0.0558	M	0.68317	2.08	0.80722	D	1	D	0.60575	0.988	P	0.59221	0.854	T	0.00992	-1.1488	10	0.45353	T	0.12	.	10.5748	0.45221	0.0:0.7286:0.0:0.2714	.	882	F8VPJ2	.	H	882	ENSP00000427900:Q882H	ENSP00000427900:Q882H	Q	-	3	2	KIF13B	29047614	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.458000	0.21892	0.810000	0.34279	0.650000	0.86243	CAG	.		0.488	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			G	28991695	C	G	28991695	3	3	11	1	0	0	0	0	1	0	0	0	8296	796	28	4	2910	4	KIF13B	8	28991695	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		28991695	117372327	45	828											
RB1CC1	9821	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	53570007	53570007	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catctttccaactggacattCagagaagtatgatctccaaa	14	11	6	10	0	3	2	1	1	2	1	5	4	4	3	2	1	1	1	2	1	4	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:53570007C>T	ENST00000025008.5	-	15	2905	c.2382G>A	c.(2380-2382)ctG>ctA	p.L794L	RB1CC1_ENST00000435644.2_Silent_p.L794L|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Silent_p.L794L	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	794					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				ACTGGACATTCAGAGAAGTAT	0.378																																					p.L794L	GBM(180;1701 2102 13475 42023 52570)												.	RB1CC1-170	0			c.G2382A						.						162	150	154					8																	53570007		2203	4300	6503	SO:0001819	synonymous_variant	9821	exon15			GACATTCAGAGAA	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2382G>A	8.37:g.53570007C>T		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	166	58	NM_001083617	0	0	11	23	12	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	37	CCDS34892.1																																																																																			.		0.378	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		T	53570007	C	T	53570007	2	4	11	1	0	0	0	0	0	0	0	1	13131	813	29	2		2	RB1CC1	8	53570007	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	24578312	53570007	92794015	46	829											
C8orf46	254778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr8	67405943	67405943	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagttttcaccaccgtgatTccttccaagggtgagtgaaa	11	11	10	9	1	1	3	1	3	0	0	3	4	3	3	4	1	0	1	4	1	3	4	rs139160272	byFrequency	TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:67405943T>A	ENST00000305454.3	+	1	501	c.60T>A	c.(58-60)atT>atA	p.I20I	C8orf46_ENST00000521495.1_Silent_p.I20I|C8orf46_ENST00000482608.2_Intron|C8orf46_ENST00000522977.1_Silent_p.I20I|C8orf46_ENST00000480005.1_Silent_p.I20I	NM_152765.3	NP_689978.2	Q8TAG6	CH046_HUMAN	chromosome 8 open reading frame 46	20										endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(2)	6			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			CCACCGTGATTCCTTCCAAGG	0.502																																					p.I20I		.											.	C8orf46-92	0			c.T60A						.						124	98	107					8																	67405943		2203	4300	6503	SO:0001819	synonymous_variant	254778	exon1			CGTGATTCCTTCC	BC028400	CCDS6191.2	8q13.1	2005-08-09			ENSG00000169085	ENSG00000169085			28498	protein-coding gene	gene with protein product						12477932	Standard	NM_152765		Approved	MGC33510	uc003xwg.3	Q8TAG6	OTTHUMG00000156998	ENST00000305454.3:c.60T>A	8.37:g.67405943T>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	76	22	NM_152765	0	0	0	0	0	B2RDC3|B4DFU4|C9J814|C9JCS3	Silent	SNP	ENST00000305454.3	37	CCDS6191.2																																																																																			T|0.999;C|0.001		0.502	C8orf46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347010.1	NM_152765		A	67405943	T	A	67405943	2	1	11	1	0	0	0	0	0	0	0	1	2437	1771	62	5		5	C8orf46	8	67405943	Silent	SNP	T	TCGA-A4-7996-01A-11D-2201-08	13835936	67405943	78958079	47	830											
TRAPPC9	83696	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	141449171	141449172	+	Frame_Shift_Del	DEL	TT	TT	-																															ctccaagccacagaaagtcaTtcacagaacgcagcagctcc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:141449171_141449172delTT	ENST00000438773.2	-	3	842_843	c.709_710delAA	c.(709-711)aatfs	p.N237fs	TRAPPC9_ENST00000389327.3_Frame_Shift_Del_p.N237fs|TRAPPC9_ENST00000389328.4_Frame_Shift_Del_p.N335fs	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	237					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CAGAAAGTCATTCACAGAACGC	0.525																																					p.335_335del		.											.	TRAPPC9-228	0			c.1003_1004del						.																																			SO:0001589	frameshift_variant	83696	exon3			.	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.709_710delAA	8.37:g.141449171_141449172delTT	ENSP00000405060:p.Asn237fs	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	160	72	NM_031466	0	0	0	0	0	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Frame_Shift_Del	DEL	ENST00000438773.2	37	CCDS55278.1																																																																																			.		0.525	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		-	141449172	TT	-	141449171	7	5	11	1	0	1	0	1	0	0	0	0	16498	1493	52	0	2820	0	TRAPPC9	8	141449171	Frame_Shift_Del	DEL	TT	TCGA-A4-7996-01A-11D-2201-08	74043228	141449171	4914851	48	831											
KCNV2	169522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	2718279	2718279	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgggctgtgtccgcgccgCttcctggaggagctgggcta	4	8	17	12	4	0	0	0	0	0	0	2	3	2	2	3	4	1	4	3	4	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:2718279C>T	ENST00000382082.3	+	1	778	c.540C>T	c.(538-540)cgC>cgT	p.R180R		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	180					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GTCCGCGCCGCTTCCTGGAGG	0.657																																					p.R180R		.											.	KCNV2-515	0			c.C540T						.						19	17	18					9																	2718279		2200	4292	6492	SO:0001819	synonymous_variant	169522	exon1			GCGCCGCTTCCTG	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.540C>T	9.37:g.2718279C>T		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	17	6	NM_133497	0	0	0	0	0	Q5T6X0	Silent	SNP	ENST00000382082.3	37	CCDS6447.1																																																																																			.		0.657	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		T	2718279	C	T	2718279	2	4	11	1	0	0	0	0	0	0	0	1	8116	784	28	2		2	KCNV2	9	2718279	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08		2718279	138495152	49	832											
TLN1	7094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35699405	35699405	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacggaaccagccacacgCtttgaatgtcctgtcaactg	10	9	10	12	2	1	2	1	2	0	0	2	3	2	3	3	1	3	1	3	1	3	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:35699405C>A	ENST00000314888.9	-	51	7175	c.6822G>T	c.(6820-6822)aaG>aaT	p.K2274N	TLN1_ENST00000540444.1_Missense_Mutation_p.K2162N	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2274					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGCCACACGCTTTGAATGTC	0.562																																					p.K2274N		.											.	TLN1-609	0			c.G6822T						.						158	127	137					9																	35699405		2203	4300	6503	SO:0001583	missense	7094	exon51			CACACGCTTTGAA	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6822G>T	9.37:g.35699405C>A	ENSP00000316029:p.Lys2274Asn	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	99	32	NM_006289	0	1	171	286	114	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	c	18.95	3.732220	0.69189	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.69926	-0.44;-0.44	5.79	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.79028	0.4377	M	0.81239	2.535	0.58432	D	0.999996	D	0.67145	0.996	P	0.61397	0.888	T	0.81519	-0.0896	10	0.72032	D	0.01	-23.9158	10.9276	0.47199	0.0:0.8574:0.0:0.1426	.	2274	Q9Y490	TLN1_HUMAN	N	2274;2162	ENSP00000316029:K2274N;ENSP00000442981:K2162N	ENSP00000316029:K2274N	K	-	3	2	TLN1	35689405	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.766000	0.38491	1.472000	0.48140	0.651000	0.88453	AAG	.		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35699405	C	A	35699405	3	1	11	1	0	0	0	0	1	0	0	0	15979	796	28	4	831	4	TLN1	9	35699405	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	32981126	35699405	105514026	50	833											
OLFML2A	169611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	127572163	127572163	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtaccagggcgccttctaCtacaaccgcgccttcaccaa	9	8	8	16	3	2	0	1	0	1	0	2	0	2	0	5	1	4	1	5	1	5	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:127572163C>T	ENST00000373580.3	+	8	1431	c.1431C>T	c.(1429-1431)taC>taT	p.Y477Y	OLFML2A_ENST00000288815.5_Silent_p.Y263Y	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	477	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						GCGCCTTCTACTACAACCGCG	0.602																																					p.Y477Y		.											.	OLFML2A-68	0			c.C1431T						.						124	99	108					9																	127572163		2203	4300	6503	SO:0001819	synonymous_variant	169611	exon8			CTTCTACTACAAC	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.1431C>T	9.37:g.127572163C>T		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	96	32	NM_182487	0	0	1	2	1	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Silent	SNP	ENST00000373580.3	37	CCDS6857.2																																																																																			.		0.602	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		T	127572163	C	T	127572163	2	4	11	1	0	0	0	0	0	0	0	1	10883	576	20	2		2	OLFML2A	9	127572163	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	91872758	127572163	13641268	51	834											
CCBL1	883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131607633	131607633	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagcccagctggctcaccAggggttgtagtcgatcccgt	6	8	12	15	2	1	0	1	0	0	0	3	1	2	0	4	3	2	4	4	3	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:131607633A>T	ENST00000302586.3	-	2	214	c.52T>A	c.(52-54)Tgg>Agg	p.W18R	CCBL1_ENST00000320665.6_Splice_Site_p.W18R|CCBL1_ENST00000436267.2_Splice_Site_p.W112R|CCBL1_ENST00000483599.1_5'UTR	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	18					cellular amino acid biosynthetic process (GO:0008652)|cellular modified amino acid metabolic process (GO:0006575)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine catabolic process (GO:0097053)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|glutamine-phenylpyruvate transaminase activity (GO:0047316)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-glutamine:pyruvate aminotransferase activity (GO:0047945)|L-phenylalanine-oxaloacetate transaminase activity (GO:0036141)|L-phenylalanine:pyruvate aminotransferase activity (GO:0047312)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)	18					L-Glutamine(DB00130)	CTGGCTCACCAGGGGTTGTAG	0.602																																					p.W18R		.											.	CCBL1-91	0			c.T52A						.						53	62	59					9																	131607633		2053	4192	6245	SO:0001630	splice_region_variant	883	exon2			CTCACCAGGGGTT	Y17448	CCDS43884.1, CCDS48038.1, CCDS75915.1	9q34.11	2008-03-11	2008-03-11		ENSG00000171097	ENSG00000171097	2.6.1.64		1564	protein-coding gene	gene with protein product	"glutamine transaminase K", "kyneurenine aminotransferase"	600547	"cysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)"			7883047	Standard	NM_001122671		Approved	KATI, GTK	uc004bwh.3	Q16773	OTTHUMG00000020767	ENST00000302586.3:c.53+1T>A	9.37:g.131607633A>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	48	8	NM_001122672	0	0	0	0	0	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	37	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.458148	0.63401	.	.	ENSG00000171097	ENST00000302586;ENST00000372610;ENST00000320665;ENST00000436267;ENST00000451800;ENST00000416084;ENST00000427720	T;D;T;T;T	0.83075	-0.95;-1.68;-1.0;-0.87;0.85	5.28	5.28	0.74379	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.81917	0.4924	M	0.66378	2.025	0.80722	D	1	B;B;B;B;B	0.26081	0.141;0.047;0.018;0.047;0.019	B;B;B;B;B	0.24974	0.046;0.02;0.057;0.02;0.02	T	0.81256	-0.1015	10	0.72032	D	0.01	-3.8485	14.326	0.66521	1.0:0.0:0.0:0.0	.	112;18;18;18;18	B7Z4W5;A8K563;Q16773-2;Q16773;Q5T278	.;.;.;KAT1_HUMAN;.	R	18;19;18;112;18;18;19	ENSP00000302227:W18R;ENSP00000317342:W18R;ENSP00000399415:W112R;ENSP00000390377:W18R;ENSP00000412402:W18R	ENSP00000302227:W18R	W	-	1	0	CCBL1	130647454	0.996000	0.38824	0.998000	0.56505	0.955000	0.61496	3.509000	0.53386	2.120000	0.65058	0.460000	0.39030	TGG	.		0.602	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2		Missense_Mutation	T	131607633	A	T	131607633	5	4	11	1	0	0	0	0	0	0	1	0	2738	202	7	5	1264	5	CCBL1	9	131607633	Splice_Site	SNP	A	TCGA-A4-7996-01A-11D-2201-08	4035470	131607633	9605798	52	835											
PTCHD3	374308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	27687708	27687708	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgtacaaaacatatataaAgactacaaaatacttggact	20	10	5	6	0	0	1	0	0	0	1	0	3	0	2	0	1	4	1	0	1	11	7			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:27687708A>G	ENST00000438700.3	-	4	1936	c.1819T>C	c.(1819-1821)Ttt>Ctt	p.F607L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	607					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						ACATATATAAAGACTACAAAA	0.383																																					p.F607L		.											.	PTCHD3-94	0			c.T1819C						.						64	65	64					10																	27687708		2203	4300	6503	SO:0001583	missense	374308	exon4			ATATAAAGACTAC	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1819T>C	10.37:g.27687708A>G	ENSP00000417658:p.Phe607Leu	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	95	63	NM_001034842	0	0	0	0	0	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.996644	0.00044	.	.	ENSG00000182077	ENST00000438700	D	0.83914	-1.78	4.05	-0.446	0.12238	.	0.493132	0.20919	N	0.083307	T	0.41650	0.1168	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.48410	-0.9038	10	0.02654	T	1	-5.7246	0.1591	0.00101	0.2673:0.2583:0.2122:0.2622	.	607	Q3KNS1	PTHD3_HUMAN	L	607	ENSP00000417658:F607L	ENSP00000417658:F607L	F	-	1	0	PTCHD3	27727714	0.012000	0.17670	0.007000	0.13788	0.009000	0.06853	-0.796000	0.04575	-0.287000	0.09064	-0.425000	0.05940	TTT	.		0.383	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		G	27687708	A	G	27687708	3	3	11	1	0	0	0	0	1	0	0	0	12763	72	3	3	488	3	PTCHD3	10	27687708	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		27687708	107847039	53	836											
NCOA4	8031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	51585156	51585156	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctttgcagagtgtgtgtgtGatgagaattgtgagaaggag	10	12	17	2	0	0	4	0	3	0	3	0	7	0	5	0	1	1	2	0	1	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:51585156G>T	ENST00000443446.1	+	8	1484	c.1255G>T	c.(1255-1257)Gat>Tat	p.D419Y	NCOA4_ENST00000344348.6_Missense_Mutation_p.D419Y|NCOA4_ENST00000430396.2_Missense_Mutation_p.D319Y|NCOA4_ENST00000374087.4_Missense_Mutation_p.D419Y|NCOA4_ENST00000374082.1_Missense_Mutation_p.D419Y|NCOA4_ENST00000414907.2_Missense_Mutation_p.D253Y|NCOA4_ENST00000438493.1_Missense_Mutation_p.D435Y|NCOA4_ENST00000452682.1_Missense_Mutation_p.D435Y	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	419					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						GTGTGTGTGTGATGAGAATTG	0.483			T	RET	papillary thyroid																																p.D435Y		.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4-1042	0			c.G1303T						.						71	74	73					10																	51585156		2203	4300	6503	SO:0001583	missense	8031	exon9			GTGTGTGATGAGA	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1255G>T	10.37:g.51585156G>T	ENSP00000390713:p.Asp419Tyr	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	104	69	NM_001145261	0	0	117	545	428	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	37	CCDS7237.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.878324	0.91740	.	.	ENSG00000138293	ENST00000438493;ENST00000452682;ENST00000430396;ENST00000374087;ENST00000414907;ENST00000344348;ENST00000374082;ENST00000443446	T;T;T;T;T;T;T;T	0.30981	1.99;2.0;1.7;2.0;1.51;2.0;1.7;2.0	5.6	5.6	0.85130	.	0.334273	0.35805	N	0.002979	T	0.54983	0.1892	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.76494	0.999;0.994;0.994;0.997	D;P;P;P	0.63488	0.915;0.87;0.87;0.819	T	0.51593	-0.8686	9	.	.	.	-20.3172	19.608	0.95587	0.0:0.0:1.0:0.0	.	319;435;435;419	B4DF87;B4E260;E9PAV7;Q13772	.;.;.;NCOA4_HUMAN	Y	435;435;319;419;253;419;419;419	ENSP00000405146:D435Y;ENSP00000395465:D435Y;ENSP00000393053:D319Y;ENSP00000363200:D419Y;ENSP00000411018:D253Y;ENSP00000344552:D419Y;ENSP00000363195:D419Y;ENSP00000390713:D419Y	.	D	+	1	0	NCOA4	51255162	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.392000	0.97252	2.647000	0.89833	0.650000	0.86243	GAT	.		0.483	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		T	51585156	G	T	51585156	3	4	11	1	0	0	0	0	1	0	0	0	10257	1290	45	4	1333	4	NCOA4	10	51585156	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	23897448	51585156	83949591	54	837											
SLC29A3	55315	broad.mit.edu	37	chr10	73111339	73111339	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttgcagtccacatccgtgTcctggcctcactgacggtca	6	10	11	14	2	2	1	2	1	0	0	5	1	5	1	4	3	1	2	4	3	0	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:73111339T>A	ENST00000373189.5	+	4	456	c.404T>A	c.(403-405)gTc>gAc	p.V135D		NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	135					transmembrane transport (GO:0055085)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	15						CACATCCGTGTCCTGGCCTCA	0.602																																					p.V135D	Esophageal Squamous(200;1319 2142 18949 31248 39672)												.	SLC29A3-90	0			c.T404A						.						169	130	143					10																	73111339		2203	4300	6503	SO:0001583	missense	55315	exon4			TCCGTGTCCTGGC	AF326987	CCDS7310.1	10q22.2	2013-07-17	2013-07-17		ENSG00000198246	ENSG00000198246		"Solute carriers"	23096	protein-coding gene	gene with protein product		612373	"solute carrier family 29 (nucleoside transporters), member 3"			11396612	Standard	NM_018344		Approved	ENT3, FLJ11160	uc001jrr.4	Q9BZD2	OTTHUMG00000018424	ENST00000373189.5:c.404T>A	10.37:g.73111339T>A	ENSP00000362285:p.Val135Asp	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	86	4	NM_018344	0	0	15	15	0	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	37	CCDS7310.1	.	.	.	.	.	.	.	.	.	.	T	17.53	3.411418	0.62399	.	.	ENSG00000198246	ENST00000373189	T	0.59638	0.25	5.36	5.36	0.76844	.	0.355948	0.29924	N	0.010858	T	0.74566	0.3733	M	0.83012	2.62	0.36975	D	0.894034	D	0.56968	0.978	P	0.59703	0.862	T	0.82705	-0.0325	9	0.87932	D	0	-34.3891	14.2128	0.65776	0.0:0.0:0.0:1.0	.	135	Q9BZD2	S29A3_HUMAN	D	135	ENSP00000362285:V135D	ENSP00000362285:V135D	V	+	2	0	SLC29A3	72781345	1.000000	0.71417	0.838000	0.33150	0.023000	0.10783	5.964000	0.70379	2.166000	0.68216	0.454000	0.30748	GTC	.		0.602	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344		A	73111339	T	A	73111339	3	1	11	1	0	0	0	0	1	0	0	0	14568	1667	58	5	418	5	SLC29A3	10	73111339	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	21526183	73111339	62423408	55	838											
WAPAL	23063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	88259986	88259986	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaacttacaccccctttCtttgcctgattcaggccatc	8	12	4	17	0	2	1	1	1	1	0	3	1	2	1	5	1	3	0	5	1	2	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:88259986C>A	ENST00000298767.5	-	3	1486	c.1014G>T	c.(1012-1014)aaG>aaT	p.K338N		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	338	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						CACCCCCTTTCTTTGCCTGAT	0.448																																					p.K338N		.											.	WAPAL-91	0			c.G1014T						.						182	152	162					10																	88259986		2203	4300	6503	SO:0001583	missense	23063	exon3			CCCTTTCTTTGCC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1014G>T	10.37:g.88259986C>A	ENSP00000298767:p.Lys338Asn	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	166	117	NM_015045	0	0	13	84	71	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.653403	0.29425	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.29397	1.57	5.77	0.75	0.18387	.	0.497401	0.21168	N	0.079024	T	0.20901	0.0503	L	0.36672	1.1	0.80722	D	1	B;B;B	0.26809	0.099;0.099;0.16	B;B;B	0.28232	0.017;0.027;0.087	T	0.04708	-1.0932	10	0.52906	T	0.07	.	5.8006	0.18412	0.126:0.4044:0.0:0.4696	.	338;338;381	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	N	423;338;423	ENSP00000298767:K338N	ENSP00000298767:K338N	K	-	3	2	WAPAL	88249966	0.994000	0.37717	0.998000	0.56505	0.897000	0.52465	0.251000	0.18257	0.097000	0.17492	-0.145000	0.13849	AAG	.		0.448	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		A	88259986	C	A	88259986	3	1	11	1	0	0	0	0	1	0	0	0	17281	912	32	4	2626	4	WAPAL	10	88259986	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	15148647	88259986	47274761	56	839											
PAPSS2	9060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	89503313	89503313	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggatgaagcagcacgcggCtgtgctcgaggaaggggtcc	8	5	18	10	4	0	1	0	1	0	0	2	4	1	3	1	5	3	4	1	5	2	0			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:89503313C>T	ENST00000361175.4	+	10	1760	c.1391C>T	c.(1390-1392)gCt>gTt	p.A464V	PAPSS2_ENST00000427144.2_Missense_Mutation_p.A468V|PAPSS2_ENST00000456849.1_Missense_Mutation_p.A469V	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	464					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		CAGCACGCGGCTGTGCTCGAG	0.587																																					p.A469V		.											.	PAPSS2-493	0			c.C1406T						.						105	91	96					10																	89503313		2203	4300	6503	SO:0001583	missense	9060	exon11			ACGCGGCTGTGCT	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.1391C>T	10.37:g.89503313C>T	ENSP00000354436:p.Ala464Val	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	91	47	NM_001015880	0	4	4	74	66	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	37	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	C	31	5.099439	0.94197	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.34472	1.36;1.36;1.36	5.33	5.33	0.75918	Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.047627	0.85682	D	0.000000	T	0.56441	0.1985	M	0.62154	1.92	0.80722	D	1	D;D	0.63880	0.991;0.993	P;P	0.61201	0.885;0.773	T	0.54043	-0.8352	10	0.49607	T	0.09	-17.1332	19.2123	0.93760	0.0:1.0:0.0:0.0	.	464;469	O95340;O95340-2	PAPS2_HUMAN;.	V	464;469;468;468	ENSP00000354436:A464V;ENSP00000406157:A469V;ENSP00000397123:A468V	ENSP00000354436:A464V	A	+	2	0	PAPSS2	89493293	1.000000	0.71417	0.889000	0.34880	0.628000	0.37860	7.315000	0.78998	2.771000	0.95319	0.561000	0.74099	GCT	.		0.587	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			T	89503313	C	T	89503313	3	4	11	1	0	0	0	0	1	0	0	0	11461	797	28	2	1448	2	PAPSS2	10	89503313	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	1243327	89503313	46031434	57	840											
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	89717645	89717646	+	Frame_Shift_Del	DEL	AT	AT	-																															tctgccagctaaaggtgaagAtatattcctccaattcagga																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:89717645_89717646delAT	ENST00000371953.3	+	7	2027_2028	c.670_671delAT	c.(670-672)atafs	p.I224fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	224	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AAAGGTGAAGATATATTCCTCC	0.421		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.224_224del		.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN-17735	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.670_671del						.																																			SO:0001589	frameshift_variant	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.670_671delAT	10.37:g.89717649_89717650delAT	ENSP00000361021:p.Ile224fs	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	150	84	NM_000314	0	0	0	0	0	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	37	CCDS31238.1																																																																																			.		0.421	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89717646	AT	-	89717645	7	5	11	1	0	1	0	1	0	0	0	0	12767	333	12	0	696	0	PTEN	10	89717645	Frame_Shift_Del	DEL	AT	TCGA-A4-7996-01A-11D-2201-08	214332	89717645	45817102	58	841											
ABCC2	1244	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	101606844	101606844	+	Frame_Shift_Del	DEL	G	G	-																															ttgtggccagcctgcaacttGggttatcccacgaagtgaca																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:101606844delG	ENST00000370449.4	+	30	4386	c.4273delG	c.(4273-4275)gggfs	p.G1425fs		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1425	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.G1425W(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CCTGCAACTTGGGTTATCCCA	0.537																																					p.G1425fs		.											.	ABCC2-91	1	Substitution - Missense(1)	lung(1)	c.4273delG						.						104	97	99					10																	101606844		2203	4300	6503	SO:0001589	frameshift_variant	1244	exon30			.	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.4273delG	10.37:g.101606844delG	ENSP00000359478:p.Gly1425fs	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	150	101	NM_000392	0	0	0	0	0	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Frame_Shift_Del	DEL	ENST00000370449.4	37	CCDS7484.1																																																																																			.		0.537	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		-	101606844	G	-	101606844	7	5	11	1	0	1	0	1	0	0	0	0	53	1348	47	0	4391	0	ABCC2	10	101606844	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	11889199	101606844	33927903	59	842											
MMP21	118856	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	127455343	127455343	+	Frame_Shift_Del	DEL	T	T	-																															aggaattctgttgtttgtccTtgtcattaactaccttccag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:127455343delT	ENST00000368808.3	-	7	1597	c.1598delA	c.(1597-1599)aagfs	p.K533fs		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	533					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	TTGTTTGTCCTTGTCATTAAC	0.363																																					p.K533fs		.											.	MMP21-228	0			c.1598delA						.						131	131	131					10																	127455343		2203	4300	6503	SO:0001589	frameshift_variant	118856	exon7			.	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1598delA	10.37:g.127455343delT	ENSP00000357798:p.Lys533fs	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	119	63	NM_147191	0	0	0	0	0	Q5VZP9|Q8NG02	Frame_Shift_Del	DEL	ENST00000368808.3	37	CCDS7647.1																																																																																			.		0.363	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			-	127455343	T	-	127455343	7	5	11	1	0	1	0	1	0	0	0	0	9685	1609	56	0	115	0	MMP21	10	127455343	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08	25848499	127455343	8079404	60	843											
DOCK1	1793	ucsc.edu;bcgsc.ca	37	chr10	129209146	129209146	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagcgatttgaatattctcgGccaatccggaagggagagaa	13	8	12	8	3	1	2	0	1	1	1	3	6	2	4	2	3	1	0	2	3	5	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:129209146G>A	ENST00000280333.6	+	43	4432	c.4323G>A	c.(4321-4323)cgG>cgA	p.R1441R		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1441	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AATATTCTCGGCCAATCCGGA	0.403																																					p.R1441R													.	DOCK1-698	0			c.G4323A						.						69	67	67					10																	129209146		1868	4101	5969	SO:0001819	synonymous_variant	1793	exon43			TTCTCGGCCAATC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.4323G>A	10.37:g.129209146G>A		Somatic	45	0		WXS	Illumina HiSeq		39	4	NM_001380	0	0	131	131	0	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				.		0.403	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	129209146	G	A	129209146	2	1	11	1	0	0	0	0	0	0	0	1	4695	1190	42	2		2	DOCK1	10	129209146	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	1753803	129209146	6325601	61	844											
OR52K1	390036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4510932	4510932	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcatgcaccgtgtagccCgccatgctgcccctcgtgtc	5	9	10	17	3	1	0	1	0	0	0	3	0	1	0	5	0	4	3	5	0	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:4510932C>T	ENST00000307632.3	+	1	824	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C		NM_001005171.2	NP_001005171.2	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K, member 1	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R268S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(18)|skin(2)|stomach(1)	32		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)		CCGTGTAGCCCGCCATGCTGC	0.507																																					p.R268C		.											.	OR52K1-68	1	Substitution - Missense(1)	lung(1)	c.C802T						.						213	192	199					11																	4510932		2201	4298	6499	SO:0001583	missense	390036	exon1			GTAGCCCGCCATG	AB065790	CCDS31352.1	11p15.4	2012-08-09			ENSG00000196778	ENSG00000196778		"GPCR / Class A : Olfactory receptors"	15222	protein-coding gene	gene with protein product							Standard	NM_001005171		Approved		uc001lza.2	Q8NGK4	OTTHUMG00000165705	ENST00000307632.3:c.802C>T	11.37:g.4510932C>T	ENSP00000302422:p.Arg268Cys	Somatic	300	0		WXS	Illumina HiSeq	Phase_I	230	66	NM_001005171	0	0	0	0	0	B9EH54|Q6IFK5	Missense_Mutation	SNP	ENST00000307632.3	37	CCDS31352.1	.	.	.	.	.	.	.	.	.	.	C	3.130	-0.178651	0.06380	.	.	ENSG00000196778	ENST00000307632	T	0.37411	1.2	4.5	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.429234	0.17846	N	0.160035	T	0.28896	0.0717	L	0.42529	1.33	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.25328	-1.0135	10	0.87932	D	0	.	6.8973	0.24262	0.1728:0.7359:0.0:0.0912	.	268	Q8NGK4	O52K1_HUMAN	C	268	ENSP00000302422:R268C	ENSP00000302422:R268C	R	+	1	0	OR52K1	4467508	0.000000	0.05858	0.723000	0.30687	0.076000	0.17211	-0.593000	0.05740	1.235000	0.43724	0.411000	0.27672	CGC	.		0.507	OR52K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385846.1	NM_001005171		T	4510932	C	T	4510932	3	4	11	1	0	0	0	0	1	0	0	0	11149	652	23	1	804	1	OR52K1	11	4510932	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		4510932	130495584	62	845											
DENND5A	23258	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	9173965	9173965	+	Frame_Shift_Del	DEL	G	G	-																															gttgtcctgataatgtaacaGgtgggaccataaggctgatt																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:9173965delG	ENST00000328194.3	-	13	2781	c.2461delC	c.(2461-2463)ctgfs	p.L822fs	DENND5A_ENST00000527700.1_Frame_Shift_Del_p.L165fs|DENND5A_ENST00000530044.1_Frame_Shift_Del_p.L822fs	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	822	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TAATGTAACAGGTGGGACCAT	0.473																																					p.L821fs		.											.	DENND5A-91	0			c.2461delC						.						268	217	234					11																	9173965		2201	4296	6497	SO:0001589	frameshift_variant	23258	exon13			.	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"DENN/MADD domain containing"	19344	protein-coding gene	gene with protein product			"RAB6 interacting protein 1"	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.2461delC	11.37:g.9173965delG	ENSP00000328524:p.Leu822fs	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	188	58	NM_015213	0	0	0	0	0	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Frame_Shift_Del	DEL	ENST00000328194.3	37	CCDS31423.1																																																																																			.		0.473	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		-	9173965	G	-	9173965	7	5	11	1	0	1	0	1	0	0	0	0	4447	991	35	0	1446	0	DENND5A	11	9173965	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	4663033	9173965	125832551	63	846											
USP47	55031	hgsc.bcm.edu;broad.mit.edu	37	chr11	11942036	11942036	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacttttattgatgttgaaGatgaggtaaatatttgttat	12	19	9	1	0	0	4	0	3	0	1	0	4	0	4	0	1	1	4	0	1	7	9			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:11942036G>T	ENST00000399455.2	+	11	1393	c.1273G>T	c.(1273-1275)Gat>Tat	p.D425Y	USP47_ENST00000539466.1_5'UTR|USP47_ENST00000339865.5_Missense_Mutation_p.D337Y|USP47_ENST00000527733.1_Missense_Mutation_p.D405Y	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	425	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TGATGTTGAAGATGAGGTAAA	0.303																																					p.D337Y		.											.	USP47-660	0			c.G1009T						.						77	72	74					11																	11942036		1819	4070	5889	SO:0001583	missense	55031	exon9			GTTGAAGATGAGG	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1273G>T	11.37:g.11942036G>T	ENSP00000382382:p.Asp425Tyr	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	75	21	NM_017944	0	0	0	0	0	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	37		.	.	.	.	.	.	.	.	.	.	G	23.4	4.416072	0.83449	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455;ENST00000535588	T;T;T	0.32272	1.46;1.46;1.46	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.42040	0.1185	N	0.20986	0.625	0.80722	D	1	D;D	0.64830	0.991;0.994	P;P	0.62649	0.905;0.846	T	0.34850	-0.9812	10	0.59425	D	0.04	.	18.9869	0.92775	0.0:0.0:1.0:0.0	.	405;337	E9PM46;Q96K76-2	.;.	Y	337;405;425;425	ENSP00000339957:D337Y;ENSP00000433146:D405Y;ENSP00000382382:D425Y	ENSP00000339957:D337Y	D	+	1	0	USP47	11898612	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.591000	0.87537	0.563000	0.77884	GAT	.		0.303	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		T	11942036	G	T	11942036	3	4	11	1	0	0	0	0	1	0	0	0	17111	942	33	4	1043	4	USP47	11	11942036	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	2768071	11942036	123064480	64	847											
DDB1	1642	broad.mit.edu	37	chr11	61081866	61081866	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctggctgctattgcaggaGgccacactgatgttcttggc	7	11	12	11	0	1	1	0	1	1	0	1	2	1	2	2	4	2	4	2	4	1	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:61081866G>A	ENST00000301764.7	-	13	1900	c.1503C>T	c.(1501-1503)gcC>gcT	p.A501A	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	501	Interaction with CDT1.|WD repeat beta-propeller B; Interaction with CUL4A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						TATTGCAGGAGGCCACACTGA	0.532								Nucleotide excision repair (NER)																													p.A501A													.	DDB1-661	0			c.C1503T						.						157	147	150					11																	61081866		2203	4299	6502	SO:0001819	synonymous_variant	1642	exon13			GCAGGAGGCCACA	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.1503C>T	11.37:g.61081866G>A		Somatic	229	1		WXS	Illumina HiSeq	Phase_I	229	4	NM_001923	0	0	260	267	7	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent	SNP	ENST00000301764.7	37	CCDS31576.1																																																																																			.		0.532	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		A	61081866	G	A	61081866	2	1	11	1	0	0	0	0	0	0	0	1	4329	987	35	2		2	DDB1	11	61081866	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	49139830	61081866	73924650	65	848											
SLC25A45	283130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65144060	65144060	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcagtccatccatctgcaTccgggacttgatcatgtcta	8	13	7	13	1	4	1	2	1	3	0	8	2	7	2	3	1	1	1	3	1	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:65144060T>C	ENST00000527174.1	-	6	740	c.685A>G	c.(685-687)Atg>Gtg	p.M229V	SLC25A45_ENST00000534028.1_Missense_Mutation_p.M205V|SLC25A45_ENST00000417511.2_Missense_Mutation_p.M187V|RP11-867O8.5_ENST00000533886.1_RNA|SLC25A45_ENST00000294187.6_Missense_Mutation_p.M187V|SLC25A45_ENST00000398802.1_Missense_Mutation_p.M229V|SLC25A45_ENST00000377152.2_Missense_Mutation_p.M125V|SLC25A45_ENST00000360662.3_Missense_Mutation_p.M205V|SLC25A45_ENST00000526432.1_Missense_Mutation_p.M167V			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	229					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						TCCATCTGCATCCGGGACTTG	0.617																																					p.M229V		.											.	SLC25A45-68	0			c.A685G						.						92	97	95					11																	65144060		2158	4257	6415	SO:0001583	missense	283130	exon7			TCTGCATCCGGGA	BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"Solute carriers"	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.685A>G	11.37:g.65144060T>C	ENSP00000435489:p.Met229Val	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	121	33	NM_182556	0	0	0	0	0	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	T	17.61	3.433016	0.62844	.	.	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	T;T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	4.58	3.41	0.39046	Mitochondrial carrier domain (2);	.	.	.	.	T	0.72566	0.3476	L	0.37630	1.12	0.37087	D	0.899261	B;B;B	0.31256	0.316;0.056;0.122	B;B;B	0.35470	0.203;0.139;0.156	T	0.73943	-0.3823	9	0.72032	D	0.01	-0.0527	8.8454	0.35168	0.0:0.0:0.3728:0.6272	.	167;205;229	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	V	229;205;229;205;125;187;187;167	ENSP00000435489:M229V;ENSP00000431769:M205V;ENSP00000381782:M229V;ENSP00000353879:M205V;ENSP00000366357:M125V;ENSP00000294187:M187V;ENSP00000407530:M187V;ENSP00000435547:M167V	ENSP00000294187:M187V	M	-	1	0	SLC25A45	64900636	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.144000	0.42197	0.866000	0.35629	0.459000	0.35465	ATG	.		0.617	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556		C	65144060	T	C	65144060	3	2	11	1	0	0	0	0	1	0	0	0	14542	1435	50	3	185	3	SLC25A45	11	65144060	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	4062194	65144060	69862456	66	849											
RELA	5970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65423175	65423175	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttacctggcttggggacagaAgctgagctgcgggaaggcac	9	7	16	9	1	0	2	0	1	0	1	0	4	0	4	1	5	4	4	1	5	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:65423175A>G	ENST00000406246.3	-	10	1278	c.1017T>C	c.(1015-1017)gcT>gcC	p.A339A	RELA_ENST00000308639.9_Silent_p.A336A|RELA_ENST00000525693.1_Silent_p.A339A	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	339					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						TGGGGACAGAAGCTGAGCTGC	0.607																																					p.A339A		.											.	RELA-872	0			c.T1017C						.						79	75	77					11																	65423175		2201	4297	6498	SO:0001819	synonymous_variant	5970	exon10			GACAGAAGCTGAG	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1017T>C	11.37:g.65423175A>G		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	67	16	NM_021975	0	0	56	94	38	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	37	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	A	1.229	-0.624695	0.03636	.	.	ENSG00000173039	ENST00000426617	.	.	.	4.46	0.645	0.17782	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.817	0.18497	0.5244:0.0:0.4756:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RELA	65179751	0.675000	0.27558	0.008000	0.14137	0.234000	0.25298	0.116000	0.15561	0.141000	0.18875	0.454000	0.30748	.	.		0.607	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		G	65423175	A	G	65423175	2	3	11	1	0	0	0	0	0	0	0	1	13248	59	3	3		3	RELA	11	65423175	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	279115	65423175	69583341	67	850											
ANO1	55107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	69951883	69951883	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttttcgacagcaaaaccCggagcacgattgtaagtatc	12	10	8	11	3	0	0	0	0	0	0	2	3	0	1	2	1	3	4	2	1	4	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:69951883C>T	ENST00000355303.5	+	5	1041	c.736C>T	c.(736-738)Cgg>Tgg	p.R246W	ANO1_ENST00000530676.1_Missense_Mutation_p.R130W|ANO1_ENST00000398543.2_Missense_Mutation_p.R130W|ANO1_ENST00000316296.5_Missense_Mutation_p.R218W|ANO1_ENST00000531349.1_5'Flank|ANO1_ENST00000538023.1_Missense_Mutation_p.R246W	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	246					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CAGCAAAACCCGGAGCACGAT	0.488																																					p.R246W		.											.	ANO1-47	0			c.C736T						.						91	90	91					11																	69951883		1928	4129	6057	SO:0001583	missense	55107	exon5			AAAACCCGGAGCA	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	21625	protein-coding gene	gene with protein product		610108	"oral cancer overexpressed 2", "transmembrane protein 16A"	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.736C>T	11.37:g.69951883C>T	ENSP00000347454:p.Arg246Trp	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	47	15	NM_018043	0	0	0	0	0	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	37	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621448	0.46736	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000531604;ENST00000316296;ENST00000530676	T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.86965	0.6060	M	0.93720	3.45	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89503	0.3765	9	.	.	.	.	11.6143	0.51080	0.2839:0.7161:0.0:0.0	.	218;246	Q5XXA6-3;Q5XXA6	.;ANO1_HUMAN	W	246;246;130;30;213;218;130	ENSP00000347454:R246W;ENSP00000444689:R246W;ENSP00000381551:R130W;ENSP00000436392:R213W;ENSP00000319477:R218W;ENSP00000435797:R130W	.	R	+	1	2	ANO1	69629531	0.996000	0.38824	1.000000	0.80357	0.109000	0.19521	3.489000	0.53237	2.437000	0.82529	0.650000	0.86243	CGG	.		0.488	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		T	69951883	C	T	69951883	3	4	11	1	0	0	0	0	1	0	0	0	695	643	23	1	754	1	ANO1	11	69951883	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	4528708	69951883	65054633	68	851											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825431	95825431	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgttgctgctgttgctgTtgggtgtagtgtaggagaga	5	15	17	4	0	0	1	0	0	0	1	0	3	0	2	0	2	4	9	0	2	2	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:95825431T>C	ENST00000524717.1	-	2	3048	c.1764A>G	c.(1762-1764)caA>caG	p.Q588Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	588					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgTTGGGTGTAGT	0.522			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q588Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.A1764G						.																																			SO:0001819	synonymous_variant	84441	exon2			TTGCTGTTGGGTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1764A>G	11.37:g.95825431T>C		Somatic	12	2		WXS	Illumina HiSeq	Phase_I	8	2	NM_032427	0	0	44	44	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.522	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825431	T	C	95825431	2	2	11	1	0	0	0	0	0	0	0	1	9231	1722	60	3		3	MAML2	11	95825431	Silent	SNP	T	TCGA-A4-7996-01A-11D-2201-08	25873548	95825431	39181085	69	852											
ZC3H12C	85463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	110007683	110007683	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcagaacaattgggtagcaTttcagtagagccaggcttga	12	10	12	7	0	2	3	2	1	0	2	2	3	2	3	1	2	3	4	1	2	4	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:110007683T>C	ENST00000278590.3	+	2	368	c.317T>C	c.(316-318)aTt>aCt	p.I106T	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.I107T|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.I75T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	106							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		TTGGGTAGCATTTCAGTAGAG	0.448																																					p.I106T		.											.	ZC3H12C-68	0			c.T317C						.						42	41	41					11																	110007683		1893	4130	6023	SO:0001583	missense	85463	exon2			GTAGCATTTCAGT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.317T>C	11.37:g.110007683T>C	ENSP00000278590:p.Ile106Thr	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	27	15	NM_033390	0	0	1	1	0	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	t	0.015	-1.546583	0.00926	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.29917	1.55;1.55;1.56	5.42	4.29	0.51040	.	.	.	.	.	T	0.18759	0.0450	N	0.25647	0.755	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.11329	0.005;0.006;0.006	T	0.31475	-0.9942	9	0.13853	T	0.58	-1.7133	6.4988	0.22158	0.0:0.1421:0.1326:0.7254	.	107;106;106	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	T	106;107;75	ENSP00000278590:I106T;ENSP00000431821:I107T;ENSP00000413094:I75T	ENSP00000278590:I106T	I	+	2	0	ZC3H12C	109512893	0.003000	0.15002	0.297000	0.24988	0.069000	0.16628	0.578000	0.23773	0.902000	0.36520	0.528000	0.53228	ATT	.		0.448	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		C	110007683	T	C	110007683	3	2	11	1	0	0	0	0	1	0	0	0	17595	1493	52	3	323	3	ZC3H12C	11	110007683	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	14182252	110007683	24998833	70	853											
DRD2	1813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113295344	113295344	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcctctccagatcatcAtcataccaggacagattcag	11	11	6	13	0	6	2	4	0	2	2	7	3	6	3	3	1	2	0	3	1	1	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:113295344A>G	ENST00000362072.3	-	2	374	c.30T>C	c.(28-30)gaT>gaC	p.D10D	DRD2_ENST00000544518.1_Silent_p.D10D|DRD2_ENST00000535984.1_5'Flank|DRD2_ENST00000355319.2_Silent_p.D10D|DRD2_ENST00000346454.3_Silent_p.D10D|DRD2_ENST00000542968.1_Silent_p.D10D|DRD2_ENST00000538967.1_Silent_p.D10D	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	10					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CCAGATCATCATCATACCAGG	0.587																																					p.D10D		.											.	DRD2-92	0			c.T30C						.						116	103	107					11																	113295344		2201	4296	6497	SO:0001819	synonymous_variant	1813	exon2			ATCATCATCATAC	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.30T>C	11.37:g.113295344A>G		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	107	27	NM_016574	0	0	0	0	0	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	37	CCDS8361.1																																																																																			.		0.587	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		G	113295344	A	G	113295344	2	3	11	1	0	0	0	0	0	0	0	1	4768	214	8	3		3	DRD2	11	113295344	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	3287661	113295344	21711172	71	854											
FAM113B	91523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	47628909	47628909	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aataagttcgtggtcatcctGggggactctgtgcatagggc	8	11	14	8	1	2	0	1	0	1	0	4	1	3	1	1	4	1	2	1	4	3	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr12:47628909G>T	ENST00000546455.1	+	4	794	c.63G>T	c.(61-63)ctG>ctT	p.L21L	PCED1B_ENST00000432328.1_Silent_p.L21L|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	21							hydrolase activity (GO:0016787)										TGGTCATCCTGGGGGACTCTG	0.602																																					p.L21L		.											.	.	0			c.G63T						.						73	71	72					12																	47628909		2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			CATCCTGGGGGAC	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.63G>T	12.37:g.47628909G>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	74	24	NM_138371	0	0	12	12	0	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			.		0.602	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		T	47628909	G	T	47628909	2	4	11	1	0	0	0	0	0	0	0	1	5418	1335	47	4		4	FAM113B	12	47628909	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08		47628909	86222986	72	855											
TMEM120B	144404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	122190050	122190050	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaggttcgcctacaaggacGaatatgagaagttcaagctc	13	8	11	9	2	1	1	1	1	0	1	3	4	1	2	1	2	2	4	1	2	6	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr12:122190050G>A	ENST00000449592.2	+	5	483	c.382G>A	c.(382-384)Gaa>Aaa	p.E128K	TMEM120B_ENST00000540377.1_5'UTR	NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	128						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		CTACAAGGACGAATATGAGAA	0.577																																					p.E128K		.											.	TMEM120B-68	0			c.G382A						.						111	130	124					12																	122190050		2155	4240	6395	SO:0001583	missense	144404	exon5			AAGGACGAATATG	BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.382G>A	12.37:g.122190050G>A	ENSP00000404991:p.Glu128Lys	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	120	40	NM_001080825	0	0	9	15	6	A0PK01|B3KX33	Missense_Mutation	SNP	ENST00000449592.2	37	CCDS41852.1	.	.	.	.	.	.	.	.	.	.	G	32	5.129163	0.94473	.	.	ENSG00000188735	ENST00000449592;ENST00000541467	T;T	0.42513	0.97;0.97	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.73133	0.3548	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81391	-0.0954	10	0.87932	D	0	-29.3312	15.8383	0.78818	0.0:0.0:1.0:0.0	.	128	A0PK00	T120B_HUMAN	K	128;107	ENSP00000404991:E128K;ENSP00000442105:E107K	ENSP00000345152:E128K	E	+	1	0	TMEM120B	120674433	1.000000	0.71417	0.995000	0.50966	0.953000	0.61014	9.405000	0.97313	2.387000	0.81309	0.491000	0.48974	GAA	.		0.577	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825		A	122190050	G	A	122190050	3	1	11	1	0	0	0	0	1	0	0	0	16066	1059	37	1	400	1	TMEM120B	12	122190050	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	74561141	122190050	11661845	73	856											
DYNC1H1	1778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102500785	102500785	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcatgctgaaacgattcAataggtatgagctcgggtgc	11	10	11	9	2	2	2	2	2	0	0	3	3	2	2	1	2	4	3	1	2	4	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr14:102500785A>G	ENST00000360184.4	+	56	10914	c.10750A>G	c.(10750-10752)Aat>Gat	p.N3584D	RP11-1017G21.4_ENST00000557551.1_RNA|DYNC1H1_ENST00000556791.1_3'UTR|RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557242.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3584	AAA 5. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAAACGATTCAATAGGTATGA	0.473																																					p.N3584D		.											.	DYNC1H1-98	0			c.A10750G						.						94	85	88					14																	102500785		2203	4300	6503	SO:0001583	missense	1778	exon56			CGATTCAATAGGT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.10750A>G	14.37:g.102500785A>G	ENSP00000348965:p.Asn3584Asp	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	137	39	NM_001376	0	0	0	0	0	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.89|14.89	2.671516|2.671516	0.47781|0.47781	.|.	.|.	ENSG00000197102|ENSG00000197102	ENST00000360184|ENST00000553423	T|.	0.52057|.	0.68|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72358|0.72358	0.3450|0.3450	M|M	0.68728|0.68728	2.09|2.09	0.80722|0.80722	D|D	1|1	D|.	0.60160|.	0.987|.	D|.	0.63488|.	0.915|.	T|T	0.72491|0.72491	-0.4277|-0.4277	10|5	0.41790|.	T|.	0.15|.	.|.	15.2984|15.2984	0.73928|0.73928	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	3584|.	Q14204|.	DYHC1_HUMAN|.	D|R	3584|59	ENSP00000348965:N3584D|.	ENSP00000348965:N3584D|.	N|Q	+|+	1|2	0|0	DYNC1H1|DYNC1H1	101570538|101570538	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.411000|0.411000	0.31082|0.31082	7.417000|7.417000	0.80156|0.80156	2.090000|2.090000	0.63153|0.63153	0.482000|0.482000	0.46254|0.46254	AAT|CAA	.		0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102500785	A	G	102500785	3	3	11	1	0	0	0	0	1	0	0	0	4852	130	5	3	10972	3	DYNC1H1	14	102500785	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		102500785	4848755	74	857											
CALML4	91860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	68489823	68489823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagactcgtgagttttgaccGcaggtcggacgccatgacgt	8	9	13	11	5	0	4	0	3	0	1	2	5	0	5	2	2	0	2	2	2	0	2	rs201056051		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:68489823G>A	ENST00000467889.1	-	4	632	c.448C>T	c.(448-450)Cgg>Tgg	p.R150W	RP11-315D16.2_ENST00000562767.1_Missense_Mutation_p.A76V|CALML4_ENST00000540479.1_Missense_Mutation_p.R74W|CALML4_ENST00000448060.2_Missense_Mutation_p.R103W|CALML4_ENST00000395465.3_Intron	NM_033429.2	NP_219501.2	Q96GE6	CALL4_HUMAN	calmodulin-like 4	150	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4						AGTTTTGACCGCAGGTCGGAC	0.507													G|||	1	0.000199681	0	0	5008	,	,		20494	0		0.001	False		,,,				2504	0				p.R150W		.											.	CALML4-90	0			c.C448T						.						154	150	151					15																	68489823		1978	4138	6116	SO:0001583	missense	91860	exon4			TTGACCGCAGGTC	AF308287	CCDS10226.2, CCDS42052.1, CCDS66808.1	15q22.31	2013-01-10			ENSG00000129007	ENSG00000129007		"EF-hand domain containing"	18445	protein-coding gene	gene with protein product							Standard	NM_033429		Approved	MGC4809, NY-BR-20	uc002arb.3	Q96GE6	OTTHUMG00000133287	ENST00000467889.1:c.448C>T	15.37:g.68489823G>A	ENSP00000419081:p.Arg150Trp	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	136	45	NM_033429	0	0	148	277	129	B4DL15|F8W6Y4|Q6MZY3|Q6N048|Q9H286	Missense_Mutation	SNP	ENST00000467889.1	37	CCDS10226.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.57	3.161345	0.57368	.	.	ENSG00000129007	ENST00000478113;ENST00000448060;ENST00000395463;ENST00000540479;ENST00000467889	T;T;T	0.81247	-1.47;-1.47;-1.47	5.02	3.98	0.46160	EF-hand-like domain (1);	0.052342	0.64402	D	0.000001	D	0.92890	0.7738	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.94426	0.7645	10	0.87932	D	0	-25.9495	12.4925	0.55907	0.0:0.0:0.7081:0.2919	.	103;150	F8W6Y4;Q96GE6	.;CALL4_HUMAN	W	35;103;35;74;150	ENSP00000400755:R103W;ENSP00000438177:R74W;ENSP00000419081:R150W	ENSP00000435285:R35W	R	-	1	2	CALML4	66276877	1.000000	0.71417	0.996000	0.52242	0.473000	0.32948	1.955000	0.40372	2.501000	0.84356	0.491000	0.48974	CGG	G|0.999;A|0.000		0.507	CALML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257067.3	NM_033429		A	68489823	G	A	68489823	3	1	11	1	0	0	0	0	1	0	0	0	2594	1086	38	1	150	1	CALML4	15	68489823	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08		68489823	34041569	75	858											
NTRK3	4916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	88679229	88679229	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcactcgtcacattcaccaGcgtcaagttgatggcatgaa	11	10	8	12	2	4	2	4	2	0	0	5	2	4	2	1	1	1	2	1	1	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:88679229G>C	ENST00000360948.2	-	8	969	c.808C>G	c.(808-810)Ctg>Gtg	p.L270V	NTRK3_ENST00000542733.2_Missense_Mutation_p.L172V|NTRK3_ENST00000355254.2_Missense_Mutation_p.L270V|NTRK3_ENST00000540489.2_Missense_Mutation_p.L270V|NTRK3_ENST00000394480.2_Missense_Mutation_p.L270V|NTRK3_ENST00000317501.3_Missense_Mutation_p.L270V|NTRK3_ENST00000557856.1_Missense_Mutation_p.L270V|NTRK3_ENST00000357724.2_Missense_Mutation_p.L270V|NTRK3_ENST00000558676.1_Missense_Mutation_p.L270V	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	270	Ig-like C2-type 1.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L270M(1)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			ACATTCACCAGCGTCAAGTTG	0.478			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.L270V		.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3-3538	1	Substitution - Missense(1)	lung(1)	c.C808G						.						241	164	190					15																	88679229		2201	4299	6500	SO:0001583	missense	4916	exon9			TCACCAGCGTCAA	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.808C>G	15.37:g.88679229G>C	ENSP00000354207:p.Leu270Val	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	136	42	NM_001243101	0	0	2	2	0	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422428	0.62622	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	5.51	4.6	0.57074	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.072619	0.56097	D	0.000024	T	0.75982	0.3924	L	0.57536	1.79	0.47819	D	0.999528	D;D;P;D;D;P	0.71674	0.967;0.969;0.87;0.998;0.969;0.87	P;P;P;D;P;P	0.69824	0.808;0.645;0.777;0.966;0.594;0.718	T	0.76515	-0.2931	10	0.54805	T	0.06	.	10.3176	0.43747	0.1599:0.0:0.8401:0.0	.	172;270;270;270;270;270	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	V	270;270;270;270;172;270;270	ENSP00000377990:L270V;ENSP00000354207:L270V;ENSP00000350356:L270V;ENSP00000347397:L270V;ENSP00000437773:L172V;ENSP00000444673:L270V;ENSP00000318328:L270V	ENSP00000318328:L270V	L	-	1	2	NTRK3	86480233	1.000000	0.71417	0.940000	0.37924	0.891000	0.51852	4.245000	0.58734	1.336000	0.45506	-0.253000	0.11424	CTG	.		0.478	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88679229	G	C	88679229	3	2	11	1	0	0	0	0	1	0	0	0	10734	962	34	4	2021	4	NTRK3	15	88679229	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	20189406	88679229	13852163	76	859											
ACAN	176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	89398462	89398462	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtttcaggacaccttgacttCagtgggcagctgtcagggga	8	10	14	9	0	3	1	3	1	0	0	3	3	3	3	1	4	1	3	1	4	0	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:89398462C>T	ENST00000561243.1	+	11	2646	c.2646C>T	c.(2644-2646)ttC>ttT	p.F882F	ACAN_ENST00000439576.2_Silent_p.F882F|ACAN_ENST00000559004.1_Silent_p.F882F|ACAN_ENST00000352105.7_Silent_p.F882F			P16112	PGCA_HUMAN	aggrecan	881	CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			ACCTTGACTTCAGTGGGCAGC	0.597																																					p.F882F		.											.	ACAN-25	0			c.C2646T						.						59	65	63					15																	89398462		2009	4185	6194	SO:0001819	synonymous_variant	176	exon12			TGACTTCAGTGGG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2646C>T	15.37:g.89398462C>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	74	22	NM_001135	0	0	0	0	0	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			.		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89398462	C	T	89398462	2	4	11	1	0	0	0	0	0	0	0	1	117	825	29	2		2	ACAN	15	89398462	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	719233	89398462	13132930	77	860											
RHCG	51458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90026327	90026327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttaaggagaatgaactcatTcacagcgaagagggtcactt	14	9	11	7	1	3	3	3	1	0	2	3	5	3	3	0	2	2	1	0	2	4	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:90026327T>C	ENST00000268122.4	-	3	561	c.493A>G	c.(493-495)Aat>Gat	p.N165D	RHCG_ENST00000544600.1_Missense_Mutation_p.N165D	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	165					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					ATGAACTCATTCACAGCGAAG	0.537																																					p.N165D		.											.	RHCG-226	0			c.A493G						.						68	51	57					15																	90026327		2200	4299	6499	SO:0001583	missense	51458	exon3			ACTCATTCACAGC	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.493A>G	15.37:g.90026327T>C	ENSP00000268122:p.Asn165Asp	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	78	29	NM_016321	0	0	0	0	0	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	37	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811144	0.70797	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.23147	1.92;1.92	5.47	5.47	0.80525	Ammonium transporter AmtB-like (3);	0.089021	0.85682	D	0.000000	T	0.63570	0.2522	H	0.95611	3.695	0.58432	D	0.999999	D;D	0.69078	0.997;0.997	D;D	0.72075	0.976;0.976	T	0.76181	-0.3053	9	.	.	.	-18.2072	15.5452	0.76093	0.0:0.0:0.0:1.0	.	165;165	A8K4D4;Q9UBD6	.;RHCG_HUMAN	D	165;165;156	ENSP00000438123:N165D;ENSP00000268122:N165D	.	N	-	1	0	RHCG	87827331	1.000000	0.71417	0.940000	0.37924	0.612000	0.37316	5.740000	0.68629	2.076000	0.62316	0.533000	0.62120	AAT	.		0.537	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		C	90026327	T	C	90026327	3	2	11	1	0	0	0	0	1	0	0	0	13358	1783	62	3	978	3	RHCG	15	90026327	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	627865	90026327	12505065	78	861											
BAIAP3	8938	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	1398015	1398021	+	Splice_Site	DEL	ACTTGTG	ACTTGTG	-																															tgtatacgacgaactcttctActtgtgagtgtcctaagccc																								rs112608838		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	ACTTGTG	ACTTGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:1398015_1398021delACTTGTG	ENST00000324385.5	+	32	3409_3412	c.3251_3254delACTTGTG	c.(3250-3255)tacttg>tg	p.YL1084fs	BAIAP3_ENST00000397488.2_Splice_Site_p.YL1066fs|BAIAP3_ENST00000562208.1_Splice_Site_p.YL1026fs|BAIAP3_ENST00000421665.2_Splice_Site_p.YL1013fs|BAIAP3_ENST00000397489.1_Splice_Site_p.YL1066fs|BAIAP3_ENST00000426824.3_Splice_Site_p.YL1049fs|BAIAP3_ENST00000568887.1_Splice_Site_p.YL1021fs	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1084	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GAACTCTTCTACTTGTGAGTGTCCTAa	0.657																																					p.1084_1085del		.											.	BAIAP3-91	0			c.3251_3254del						.																																			SO:0001630	splice_region_variant	8938	exon32			.	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.3254+1ACTTGTG>-	16.37:g.1398015_1398021delACTTGTG		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	115	43	NM_003933	0	0	0	0	0	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Frame_Shift_Del	DEL	ENST00000324385.5	37	CCDS10434.1																																																																																			.		0.657	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		Frame_Shift_Del	-	1398021	ACTTGTG	-	1398015	8	5	11	1	0	1	0	1	0	0	1	0	1305	391	14	0	3377	0	BAIAP3	16	1398015	Splice_Site	DEL	ACTTGTG	TCGA-A4-7996-01A-11D-2201-08		1398015	88956738	79	862	8	2									
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1398016	1398016	+	Nonsense_Mutation	SNP	C	C	G																															gtatacgacgaactcttctaCttgtgagtgtcctaagcccc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:1398016C>G	ENST00000324385.5	+	32	3410	c.3252C>G	c.(3250-3252)taC>taG	p.Y1084*	BAIAP3_ENST00000397488.2_Nonsense_Mutation_p.Y1066*|BAIAP3_ENST00000562208.1_Nonsense_Mutation_p.Y1026*|BAIAP3_ENST00000421665.2_Nonsense_Mutation_p.Y1013*|BAIAP3_ENST00000397489.1_Nonsense_Mutation_p.Y1066*|BAIAP3_ENST00000426824.3_Nonsense_Mutation_p.Y1049*|BAIAP3_ENST00000568887.1_Nonsense_Mutation_p.Y1021*	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1084	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				AACTCTTCTACTTGTGAGTGT	0.652																																					p.Y1084X		.											.	BAIAP3-91	0			c.C3252G						.						50	50	50					16																	1398016		2198	4300	6498	SO:0001587	stop_gained	8938	exon32			CTTCTACTTGTGA	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.3252C>G	16.37:g.1398016C>G	ENSP00000324510:p.Tyr1084*	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	66	6	NM_003933	0	0	0	0	0	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Nonsense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	C	38	6.826251	0.97865	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	.	.	.	4.65	1.6	0.23607	.	0.402932	0.24625	N	0.036938	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.1567	6.7323	0.23390	0.0:0.6052:0.0:0.3948	.	.	.	.	X	1049;1066;1084;1066;1013	.	ENSP00000324510:Y1084X	Y	+	3	2	BAIAP3	1338017	0.998000	0.40836	0.998000	0.56505	0.087000	0.18053	0.792000	0.26929	0.068000	0.16574	-0.258000	0.10820	TAC	.		0.652	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			G	1398016	C	G	1398016	4	3	11	1	0	0	0	0	0	1	0	0	1305	576	20	4	3378	4	BAIAP3	16	1398016	Nonsense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	1	1398016	88956737	80	863	8	2									
PRSS22	64063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2905588	2905589	+	Missense_Mutation	DNP	GC	GC	AT																															gccgcacctccatcttggatGctcccccagcctgagatcca																								rs556704172		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:2905588_2905589GC>AT	ENST00000161006.3	-	4	610_611	c.545_546GC>AT	c.(544-546)aGC>aAT	p.S182N	LA16c-325D7.1_ENST00000577140.1_RNA|PRSS22_ENST00000574768.1_5'Flank|PRSS22_ENST00000571228.1_Intron	NM_022119.3	NP_071402.1	Q9GZN4	BSSP4_HUMAN	protease, serine, 22	182	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|skin(2)	10						CATCTTGGATGCTCCCCCAGCC	0.589																																					p.S182N		.											.	PRSS22	0			c.G545A						.																																			SO:0001583	missense	64063	exon4			TGGATGCTCCCCC	AF321182	CCDS10481.1	16p13.3	2010-05-07			ENSG00000005001	ENSG00000005001		"Serine peptidases / Serine peptidases"	14368	protein-coding gene	gene with protein product	"brain-specific serine protease 4"	609343				11602603, 15701722	Standard	XM_005255473		Approved	hBSSP-4, BSSP-4, SP001LA	uc002cry.1	Q9GZN4	OTTHUMG00000128961	ENST00000161006.3:c.545_546delinsAT	16.37:g.2905588_2905589delinsAT	ENSP00000161006:p.Ser182Asn	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	121	62		0	0	0	0	0	O43342|Q6UXE0	Missense_Mutation	DNP	ENST00000161006.3	37	CCDS10481.1																																																																																			.		0.589	PRSS22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250943.1	NM_022119		AT	2905589	GC	AT	2905588	3	1	11	1	0	0	0	0	1	0	0	0	12648	1310	46	2	419	2	PRSS22	16	2905588	Missense_Mutation	DNP	GC	TCGA-A4-7996-01A-11D-2201-08	1507572	2905588	87449165	81	864											
ZNF200	7752	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	3274128	3274128	+	Frame_Shift_Del	DEL	G	G	-																															actccgatgagaattctgacGgaagttttttccacactgag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:3274128delG	ENST00000431561.3	-	5	1564	c.952delC	c.(952-954)cgtfs	p.R318fs	ZNF200_ENST00000396871.4_Frame_Shift_Del_p.R317fs|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.R317fs|ZNF200_ENST00000414144.2_Frame_Shift_Del_p.R318fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.R317fs|ZNF200_ENST00000396868.3_Frame_Shift_Del_p.R317fs|AJ003147.9_ENST00000576468.1_RNA	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	318					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						GAATTCTGACGGAAGTTTTTT	0.393																																					p.R318fs		.											.	ZNF200-90	0			c.952delC						.						110	110	110					16																	3274128		2197	4300	6497	SO:0001589	frameshift_variant	7752	exon5			.	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.952delC	16.37:g.3274128delG	ENSP00000395723:p.Arg318fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	233	109	NM_003454	0	0	0	0	0	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	37	CCDS10497.1																																																																																			.		0.393	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			-	3274128	G	-	3274128	7	5	11	1	0	1	0	1	0	0	0	0	17794	1116	39	0	239	0	ZNF200	16	3274128	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	368540	3274128	87080625	82	865											
PSMB10	5699	hgsc.bcm.edu	37	chr16	67970649	67970649	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggctccagggctggcttcaGcatcttggggcaggcagagg	6	7	18	10	0	2	1	1	0	1	1	3	1	3	1	1	7	1	6	1	7	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:67970649G>C	ENST00000358514.4	-	1	341	c.4C>G	c.(4-6)Ctg>Gtg	p.L2V	CTC-479C5.12_ENST00000573493.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	2					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)|cell morphogenesis (GO:0000902)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|humoral immune response (GO:0006959)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	GCTGGCTTCAGCATCTTGGGG	0.657																																					p.L2V		.											.	PSMB10-90	0			c.C4G						.						6	9	8					16																	67970649		2068	4126	6194	SO:0001583	missense	5699	exon1			GCTTCAGCATCTT	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"Proteasome (prosome, macropain) subunits"	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.4C>G	16.37:g.67970649G>C	ENSP00000351314:p.Leu2Val	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	11	6	NM_002801	0	0	45	144	99	B2R5J4|Q5U098	Missense_Mutation	SNP	ENST00000358514.4	37	CCDS10853.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368139	0.61513	.	.	ENSG00000205220	ENST00000358514	T	0.29917	1.55	5.44	3.45	0.39498	.	0.789141	0.11429	N	0.564987	T	0.22322	0.0538	L	0.34521	1.04	0.31055	N	0.714774	B	0.21225	0.053	B	0.17722	0.019	T	0.14783	-1.0460	10	0.33940	T	0.23	-0.1279	7.6089	0.28118	0.1898:0.0:0.8102:0.0	.	2	P40306	PSB10_HUMAN	V	2	ENSP00000351314:L2V	ENSP00000351314:L2V	L	-	1	2	PSMB10	66528150	0.741000	0.28217	0.993000	0.49108	0.082000	0.17680	0.926000	0.28804	1.422000	0.47177	0.549000	0.68633	CTG	.		0.657	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801		C	67970649	G	C	67970649	3	2	11	1	0	0	0	0	1	0	0	0	12704	962	34	4	849	4	PSMB10	16	67970649	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	64696521	67970649	22384104	83	866											
KCNJ12	3768	broad.mit.edu;bcgsc.ca	37	chr17	21319584	21319584	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gaggccacagccatgaccacCcaggcccgcagctcctacct	9	4	9	19	1	0	1	0	1	0	0	1	2	1	1	7	2	3	2	7	2	1	1	rs548667759		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:21319584C>T	ENST00000583088.1	+	3	1825	c.930C>T	c.(928-930)acC>acT	p.T310T	KCNJ12_ENST00000331718.5_Silent_p.T310T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	310					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CCATGACCACCCAGGCCCGCA	0.607										Prostate(3;0.18)																											p.T310T													.	.	0			c.C930T						.						101	101	101					17																	21319584		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			GACCACCCAGGCC	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.930C>T	17.37:g.21319584C>T		Somatic	259	0		WXS	Illumina HiSeq	Phase_I	227	10	NM_001194958	0	0	3	3	0	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			.		0.607	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21319584	C	T	21319584	2	4	11	1	0	0	0	0	0	0	0	1	8067	610	22	2		2	KCNJ12	17	21319584	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08		21319584	59875626	84	867											
TRAF4	9618	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	27074242	27074243	+	Frame_Shift_Ins	INS	-	-	C																															catttcagtgaaggagtcttINScaagtgccctgaggaccagc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:27074242_27074243insC	ENST00000262395.5	+	2	284_285	c.155_156insC	c.(154-159)ttcaagfs	p.K53fs	AC010761.9_ENST00000577325.1_RNA|AC010761.10_ENST00000579468.1_RNA|TRAF4_ENST00000444415.3_Frame_Shift_Ins_p.K53fs|TRAF4_ENST00000262396.6_Frame_Shift_Ins_p.K53fs	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	53					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			GAAGGAGTCTTCAAGTGCCCTG	0.594																																					p.F52fs		.											.	TRAF4-660	0			c.155_156insC						.																																			SO:0001589	frameshift_variant	9618	exon2			.	X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"RING-type (C3HC4) zinc fingers"	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.156dupC	17.37:g.27074243_27074243dupC	ENSP00000262395:p.Lys53fs	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	158	82	NM_004295	0	0	0	0	0	O75615|Q14848|Q2KJU4|Q2PJN8	Frame_Shift_Ins	INS	ENST00000262395.5	37	CCDS11243.1																																																																																			.		0.594	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751		C	27074243	-	C	27074242	7	5	11	1	0	1	1	0	0	0	0	0	16476	1783	62	0	161	0	TRAF4	17	27074242	Frame_Shift_Ins	INS	-	TCGA-A4-7996-01A-11D-2201-08	5754658	27074242	54120968	85	868											
SSH2	85464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27975326	27975326	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggctgagcgactcaccccCattttgcagtgcacaaggca	10	7	11	13	1	1	1	1	1	0	0	1	3	1	1	2	2	3	4	2	2	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:27975326C>A	ENST00000269033.3	-	13	1333	c.1182G>T	c.(1180-1182)atG>atT	p.M394I	RP11-68I3.11_ENST00000582881.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.M421I	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	394	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GACTCACCCCCATTTTGCAGT	0.443																																					p.M394I		.											.	SSH2-92	0			c.G1182T						.						89	78	82					17																	27975326		2203	4300	6503	SO:0001583	missense	85464	exon13			CACCCCCATTTTG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.1182G>T	17.37:g.27975326C>A	ENSP00000269033:p.Met394Ile	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	85	46	NM_033389	0	0	23	45	22	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	36	5.803091	0.96960	.	.	ENSG00000141298	ENST00000269033;ENST00000540801;ENST00000394848	D;D	0.85411	-1.98;-1.98	5.95	5.95	0.96441	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.94611	0.8263	M	0.94101	3.495	0.80722	D	1	P;P;P	0.50710	0.526;0.895;0.938	P;P;D	0.65233	0.701;0.647;0.933	D	0.94987	0.8131	10	0.87932	D	0	-16.2523	20.3932	0.98965	0.0:1.0:0.0:0.0	.	421;394;394	F5H527;Q76I76-4;Q76I76	.;.;SSH2_HUMAN	I	394;421;394	ENSP00000269033:M394I;ENSP00000444743:M421I	ENSP00000269033:M394I	M	-	3	0	SSH2	24999452	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	ATG	.		0.443	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		A	27975326	C	A	27975326	3	1	11	1	0	0	0	0	1	0	0	0	15217	594	21	4	3101	4	SSH2	17	27975326	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	901084	27975326	53219884	86	869											
WIPF2	147179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38416825	38416825	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgagtagagatgagcaGcggggtcgaggcgccctctt	9	7	16	9	3	1	3	0	2	1	1	2	5	1	3	1	3	3	3	1	3	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:38416825G>A	ENST00000323571.4	+	3	342	c.102G>A	c.(100-102)caG>caA	p.Q34Q	WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000536600.1_Silent_p.Q34Q|WIPF2_ENST00000394103.3_Silent_p.Q34Q|WIPF2_ENST00000583130.1_Silent_p.Q34Q|WIPF2_ENST00000585043.1_Silent_p.Q34Q	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	34					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						GAGATGAGCAGCGGGGTCGAG	0.522										HNSCC(43;0.11)																											p.Q34Q		.											.	WIPF2-93	0			c.G102A						.						101	89	93					17																	38416825		2203	4300	6503	SO:0001819	synonymous_variant	147179	exon3			TGAGCAGCGGGGT	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.102G>A	17.37:g.38416825G>A		Somatic	158	0		WXS	Illumina HiSeq	Phase_I	161	38	NM_133264	0	0	40	59	19	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	37	CCDS11364.1																																																																																			.		0.522	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		A	38416825	G	A	38416825	2	1	11	1	0	0	0	0	0	0	0	1	17401	962	34	2		2	WIPF2	17	38416825	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	10441499	38416825	42778385	87	870											
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39191010	39191010	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttggctggcagcagctggAgccgcatgtcccactggtgg	5	8	16	12	1	0	0	0	0	0	0	1	1	1	1	2	5	3	6	2	5	0	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:39191010A>T	ENST00000344363.5	-	1	97	c.64T>A	c.(64-66)Tcc>Acc	p.S22T		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	22						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCAGCTGGAGCCGCATGTC	0.587																																					p.S22T		.											.	.	0			c.T64A						.						41	49	47					17																	39191010		1974	4168	6142	SO:0001583	missense	81850	exon1			AGCTGGAGCCGCA	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.64T>A	17.37:g.39191010A>T	ENSP00000344420:p.Ser22Thr	Somatic	80	2		WXS	Illumina HiSeq	Phase_I	97	9	NM_030966	0	0	0	0	0	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	A	9.615	1.132314	0.21041	.	.	ENSG00000221880	ENST00000344363	T	0.33216	1.42	4.31	0.846	0.18955	.	.	.	.	.	T	0.15652	0.0377	.	.	.	0.26468	N	0.975321	B	0.09022	0.002	B	0.15484	0.013	T	0.30060	-0.9991	8	0.21014	T	0.42	.	3.8262	0.08855	0.6175:0.1859:0.1966:0.0	.	22	Q8IUG1	KRA13_HUMAN	T	22	ENSP00000344420:S22T	ENSP00000344420:S22T	S	-	1	0	KRTAP1-3	36444536	.	.	0.993000	0.49108	0.724000	0.41520	.	.	0.093000	0.17368	-0.376000	0.06991	TCC	.		0.587	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			T	39191010	A	T	39191010	3	4	11	1	0	0	0	0	1	0	0	0	8524	304	11	5	443	5	KRTAP1-3	17	39191010	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	774185	39191010	42004200	88	871											
CDC27	996	hgsc.bcm.edu	37	chr17	45249300	45249300	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacttgctgagatcaacacaAcattttgcaagcaggtattt	13	13	7	8	0	1	1	1	1	0	1	1	2	1	1	0	1	6	4	0	1	5	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:45249300A>C	ENST00000066544.3	-	3	327	c.234T>G	c.(232-234)tgT>tgG	p.C78W	CDC27_ENST00000446365.2_Intron|CDC27_ENST00000527547.1_Missense_Mutation_p.C78W|CDC27_ENST00000528748.1_5'UTR|RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000531206.1_Missense_Mutation_p.C78W	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	78					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						GATCAACACAACATTTTGCAA	0.338																																					p.C78W		.											.	CDC27-291	0			c.T234G						.						38	38	38					17																	45249300		2202	4300	6502	SO:0001583	missense	996	exon3			AACACAACATTTT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.234T>G	17.37:g.45249300A>C	ENSP00000066544:p.Cys78Trp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	69	4	NM_001114091	0	0	48	48	0	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	18.65	3.668591	0.67814	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000527547;ENST00000526866	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	5.69	3.44	0.39384	Tetratricopeptide-like helical (1);	0.046528	0.85682	N	0.000000	D	0.83580	0.5285	M	0.82323	2.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.81143	-0.1067	10	0.87932	D	0	-31.1317	4.5705	0.12207	0.6658:0.1666:0.1676:0.0	.	78;78;78	G5EA36;G3V1C4;P30260	.;.;CDC27_HUMAN	W	78	ENSP00000066544:C78W;ENSP00000434614:C78W;ENSP00000437339:C78W;ENSP00000432105:C78W	ENSP00000066544:C78W	C	-	3	2	CDC27	42604299	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.381000	0.52455	0.421000	0.25980	0.482000	0.46254	TGT	.		0.338	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45249300	A	C	45249300	3	2	11	1	0	0	0	0	1	0	0	0	3072	41	2	5	2326	5	CDC27	17	45249300	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	6058290	45249300	35945910	89	872											
TLK2	11011	hgsc.bcm.edu	37	chr17	60650591	60650591	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctaggcaacaggaaaggatAaattcacagagggaagagat	18	6	12	5	0	2	2	1	0	1	2	2	6	2	5	0	4	1	1	0	4	6	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:60650591A>G	ENST00000326270.9	+	12	1252	c.984A>G	c.(982-984)atA>atG	p.I328M	TLK2_ENST00000343388.7_Missense_Mutation_p.I296M|TLK2_ENST00000582809.1_Missense_Mutation_p.I179M|TLK2_ENST00000346027.5_Missense_Mutation_p.I328M|TLK2_ENST00000542523.1_Missense_Mutation_p.I296M	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	328					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						AGGAAAGGATAAATTCACAGA	0.423																																					p.I328M		.											.	TLK2-464	0			c.A984G						.						39	36	37					17																	60650591		2203	4300	6503	SO:0001583	missense	11011	exon12			AAGGATAAATTCA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.984A>G	17.37:g.60650591A>G	ENSP00000316512:p.Ile328Met	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_006852	0	0	41	41	0	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	A	11.04	1.523127	0.27211	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.69926	-0.4;-0.44;-0.38;-0.44	6.08	6.08	0.98989	.	0.085573	0.85682	D	0.000000	T	0.77691	0.4168	M	0.75085	2.285	0.58432	D	0.999994	P;P;P;D	0.56968	0.955;0.553;0.712;0.978	P;B;B;P	0.54629	0.726;0.287;0.381;0.757	T	0.80721	-0.1256	10	0.87932	D	0	.	15.825	0.78698	1.0:0.0:0.0:0.0	.	328;296;328;328	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	M	328;296;328;296	ENSP00000275780:I328M;ENSP00000340800:I296M;ENSP00000316512:I328M;ENSP00000442311:I296M	ENSP00000316512:I328M	I	+	3	3	TLK2	58004323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.963000	0.40452	2.333000	0.79357	0.533000	0.62120	ATA	.		0.423	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		G	60650591	A	G	60650591	3	3	11	1	0	0	0	0	1	0	0	0	15976	352	13	3	1026	3	TLK2	17	60650591	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	15401291	60650591	20544619	90	873											
FAM59A	64762	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	29867256	29867256	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcttcactagcttctgggAaaaggtagtcgctcccacta	10	12	8	11	1	3	0	1	0	2	0	5	1	4	1	1	2	1	3	1	2	5	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr18:29867256A>G	ENST00000269209.6	-	4	1307	c.1304T>C	c.(1303-1305)tTc>tCc	p.F435S	GAREM_ENST00000399218.4_Missense_Mutation_p.F435S|GAREM_ENST00000578619.1_5'Flank|RP11-344B2.2_ENST00000579580.1_RNA			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	435					cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										AGCTTCTGGGAAAAGGTAGTC	0.557																																					p.F435S		.											.	.	0			c.T1304C						.						103	109	107					18																	29867256		2203	4300	6503	SO:0001583	missense	64762	exon4			TCTGGGAAAAGGT	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1304T>C	18.37:g.29867256A>G	ENSP00000269209:p.Phe435Ser	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	210	69	NM_022751	0	0	28	58	30	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	A	0.031	-1.336778	0.01287	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.13538	2.58;2.58	5.65	5.65	0.86999	.	0.136032	0.64402	D	0.000002	T	0.09468	0.0233	N	0.12182	0.205	0.58432	D	0.99999	B;B	0.17852	0.024;0.012	B;B	0.20577	0.03;0.019	T	0.28839	-1.0031	10	0.22109	T	0.4	-29.2932	16.1512	0.81624	1.0:0.0:0.0:0.0	.	435;435	Q9H706;Q9H706-3	FA59A_HUMAN;.	S	435	ENSP00000382165:F435S;ENSP00000269209:F435S	ENSP00000269209:F435S	F	-	2	0	FAM59A	28121254	1.000000	0.71417	1.000000	0.80357	0.104000	0.19210	7.042000	0.76565	2.275000	0.75901	0.459000	0.35465	TTC	.		0.557	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		G	29867256	A	G	29867256	3	3	11	1	0	0	0	0	1	0	0	0	5611	246	9	3	1335	3	FAM59A	18	29867256	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		29867256	48209992	91	874											
MBD1	4152	hgsc.bcm.edu;broad.mit.edu	37	chr18	47800703	47800703	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccccgcacttgcggttctgCcggcggttcgtgtagggctg	2	10	16	13	5	1	0	0	0	1	0	2	0	1	0	3	4	2	5	3	4	1	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr18:47800703C>T	ENST00000591416.1	-	11	1430	c.999G>A	c.(997-999)cgG>cgA	p.R333R	MBD1_ENST00000398495.2_Intron|MBD1_ENST00000424334.2_Silent_p.R384R|MBD1_ENST00000436910.1_Silent_p.R310R|MBD1_ENST00000590208.1_Silent_p.R333R|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000398493.1_Intron|MBD1_ENST00000353909.3_Silent_p.R284R|MBD1_ENST00000588937.1_Silent_p.R310R|MBD1_ENST00000382948.5_Silent_p.R333R|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000269468.5_Silent_p.R333R|MBD1_ENST00000339998.6_Silent_p.R333R|MBD1_ENST00000585672.1_Silent_p.R283R|MBD1_ENST00000591535.1_Silent_p.R310R|MBD1_ENST00000457839.2_Silent_p.R358R|MBD1_ENST00000585595.1_Silent_p.R358R|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000269471.5_Silent_p.R310R|MBD1_ENST00000398488.1_Intron			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	333					negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						TGCGGTTCTGCCGGCGGTTCG	0.642																																					p.R358R		.											.	MBD1-228	0			c.G1074A						.						23	23	23					18																	47800703		2202	4300	6502	SO:0001819	synonymous_variant	4152	exon12			GTTCTGCCGGCGG	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.999G>A	18.37:g.47800703C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_001204137	0	0	33	33	0	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	37	CCDS11943.1																																																																																			.		0.642	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846		T	47800703	C	T	47800703	2	4	11	1	0	0	0	0	0	0	0	1	9367	726	26	2		2	MBD1	18	47800703	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	17933447	47800703	30276545	92	875											
ZNF516	9658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	74154041	74154041	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gccggcgacgatcacctcctCctggaccacgttgttgatgg	6	9	12	14	4	1	1	1	1	0	0	3	4	3	2	5	3	0	2	5	3	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr18:74154041C>T	ENST00000443185.2	-	3	1287	c.970G>A	c.(970-972)Gag>Aag	p.E324K	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		ATCACCTCCTCCTGGACCACG	0.602																																					p.E324K		.											.	ZNF516-69	0			c.G970A						.						64	73	70					18																	74154041		2178	4264	6442	SO:0001583	missense	9658	exon3			CCTCCTCCTGGAC	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.970G>A	18.37:g.74154041C>T	ENSP00000394757:p.Glu324Lys	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	87	24	NM_014643	0	0	3	6	3		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	C	25.9	4.681412	0.88542	.	.	ENSG00000101493	ENST00000443185	T	0.11495	2.77	4.97	4.97	0.65823	.	0.095344	0.49916	D	0.000140	T	0.36138	0.0956	.	.	.	0.54753	D	0.999984	D	0.76494	0.999	D	0.80764	0.994	T	0.12604	-1.0541	9	0.62326	D	0.03	-3.4552	18.4275	0.90614	0.0:1.0:0.0:0.0	.	324	Q92618	ZN516_HUMAN	K	324	ENSP00000394757:E324K	ENSP00000394757:E324K	E	-	1	0	ZNF516	72283029	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.572000	0.67411	2.578000	0.87016	0.655000	0.94253	GAG	.		0.602	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		T	74154041	C	T	74154041	3	4	11	1	0	0	0	0	1	0	0	0	17992	864	30	2	2542	2	ZNF516	18	74154041	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	26353338	74154041	3923207	93	876											
CD209	30835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7810714	7810714	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agccaggtcagctcctggtaGatctcctgcagcttagattt	8	12	10	11	0	2	2	1	0	1	2	4	2	3	2	3	2	4	4	3	2	2	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:7810714G>A	ENST00000315599.7	-	4	460	c.438C>T	c.(436-438)atC>atT	p.I146I	CD209_ENST00000394173.4_Intron|CD209_ENST00000601951.1_Silent_p.I122I|CD209_ENST00000601256.1_Silent_p.I122I|CD209_ENST00000204801.8_Silent_p.I102I|CD209_ENST00000593821.1_Silent_p.I102I|CD209_ENST00000394161.5_Intron|CD209_ENST00000354397.6_Silent_p.I146I|CD209_ENST00000315591.8_Silent_p.I122I|CD209_ENST00000593660.1_Silent_p.I122I|CD209_ENST00000602261.1_Silent_p.I146I|CD209_ENST00000301357.8_Intron	NM_001144895.1|NM_001144897.1|NM_021155.3	NP_001138367.1|NP_001138369.1|NP_066978.1	Q9NNX6	CD209_HUMAN	CD209 molecule	146	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|heterophilic cell-cell adhesion (GO:0007157)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of T cell proliferation (GO:0042129)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|virion binding (GO:0046790)			endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GCTCCTGGTAGATCTCCTGCA	0.547																																					p.I146I		.											.	CD209-91	0			c.C438T						.						106	105	105					19																	7810714		2197	4299	6496	SO:0001819	synonymous_variant	30835	exon4			CTGGTAGATCTCC	M98457	CCDS12186.1, CCDS45949.1, CCDS45950.1, CCDS45951.1, CCDS45952.1, CCDS59344.1, CCDS59345.1	19p13	2011-08-30	2006-03-28			ENSG00000090659		"C-type lectin domain containing", "CD molecules"	1641	protein-coding gene	gene with protein product		604672	"CD209 antigen"			1518869	Standard	NM_021155		Approved	DC-SIGN, CDSIGN, DC-SIGN1, CLEC4L	uc002mht.2	Q9NNX6		ENST00000315599.7:c.438C>T	19.37:g.7810714G>A		Somatic	367	0		WXS	Illumina HiSeq	Phase_I	237	73	NM_021155	0	0	4	4	0	A8KAM4|A8MVQ9|G5E9C4|Q2TB19|Q96QP7|Q96QP8|Q96QP9|Q96QQ0|Q96QQ1|Q96QQ2|Q96QQ3|Q96QQ4|Q96QQ5|Q96QQ6|Q96QQ7|Q96QQ8	Silent	SNP	ENST00000315599.7	37	CCDS12186.1																																																																																			.		0.547	CD209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462241.1	NM_021155		A	7810714	G	A	7810714	2	1	11	1	0	0	0	0	0	0	0	1	2990	932	33	2		2	CD209	19	7810714	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08		7810714	51318269	94	877											
BRD4	23476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15350519	15350519	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccgggtgcttggggggCtccggccgcagcgaggggct	2	7	19	13	4	1	0	0	0	1	0	3	1	2	0	3	7	2	4	3	7	0	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:15350519C>T	ENST00000263377.2	-	16	3617	c.3396G>A	c.(3394-3396)gaG>gaA	p.E1132E		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1132	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GCTTGGGGGGCTCCGGCCGCA	0.711			T	C15orf55	lethal midline carcinoma of young people																																p.E1132E		.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4-767	0			c.G3396A						.						19	26	24					19																	15350519		2159	4231	6390	SO:0001819	synonymous_variant	23476	exon16			GGGGGGCTCCGGC	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3396G>A	19.37:g.15350519C>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	69	27	NM_058243	0	0	22	40	18	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																			.		0.711	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		T	15350519	C	T	15350519	2	4	11	1	0	0	0	0	0	0	0	1	1507	796	28	2		2	BRD4	19	15350519	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	7539805	15350519	43778464	95	878											
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40419757	40419757	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctgggggtccagcttgctAtggcactcccggaagggccc	5	7	14	15	1	0	0	0	0	0	0	2	1	2	1	4	5	2	3	4	5	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:40419757A>G	ENST00000221347.6	-	6	3244	c.3237T>C	c.(3235-3237)caT>caC	p.H1079H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1079	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCAGCTTGCTATGGCACTCCC	0.642																																					p.H1079H		.											.	FCGBP-98	0			c.T3237C						.						70	65	67					19																	40419757		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon6			CTTGCTATGGCAC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.3237T>C	19.37:g.40419757A>G		Somatic	181	0		WXS	Illumina HiSeq	Phase_I	162	44	NM_003890	0	0	24	24	0	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			.		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40419757	A	G	40419757	2	3	11	1	0	0	0	0	0	0	0	1	5797	446	16	3		3	FCGBP	19	40419757	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	25069238	40419757	18709226	96	879											
HRC	3270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49658077	49658077	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agctgagtcttccgtgtcttCactcccgtggcctctgtgcc	3	13	10	15	2	4	1	1	1	3	0	6	1	6	1	4	1	2	1	4	1	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:49658077C>G	ENST00000252825.4	-	1	604	c.418G>C	c.(418-420)Gaa>Caa	p.E140Q	TRPM4_ENST00000252826.5_5'Flank|HRC_ENST00000595625.1_Missense_Mutation_p.E140Q|TRPM4_ENST00000427978.2_5'Flank	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	140	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TCCGTGTCTTCACTCCCGTGG	0.597																																					p.E140Q	Melanoma(37;75 1097 24567 25669 30645)	.											.	HRC-91	0			c.G418C						.						176	128	144					19																	49658077		2203	4300	6503	SO:0001583	missense	3270	exon1			TGTCTTCACTCCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.418G>C	19.37:g.49658077C>G	ENSP00000252825:p.Glu140Gln	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	113	34	NM_002152	0	0	1	1	0	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.264155	0.59431	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.06933	3.24	2.6	2.6	0.31112	.	.	.	.	.	T	0.24624	0.0597	M	0.73217	2.22	0.23923	N	0.996455	D	0.89917	1.0	D	0.79108	0.992	T	0.03000	-1.1084	9	0.35671	T	0.21	-0.6964	11.3389	0.49520	0.0:1.0:0.0:0.0	.	140	P23327	SRCH_HUMAN	Q	140;110	ENSP00000252825:E140Q	ENSP00000252825:E140Q	E	-	1	0	HRC	54349889	0.062000	0.20869	0.037000	0.18230	0.019000	0.09904	1.982000	0.40638	1.775000	0.52247	0.462000	0.41574	GAA	.		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		G	49658077	C	G	49658077	3	3	11	1	0	0	0	0	1	0	0	0	7373	835	29	4	1705	4	HRC	19	49658077	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	9238320	49658077	9470906	97	880											
VN1R2	317701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53762787	53762787	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctgcagaagaaatagaCgattctttcatgatttcagg	12	13	9	7	1	4	4	2	1	2	3	4	5	4	4	0	1	2	2	0	1	3	4	rs374706531		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:53762787C>T	ENST00000341702.3	+	1	1243	c.1159C>T	c.(1159-1161)Cga>Tga	p.R387*	VN1R2_ENST00000598458.1_Intron	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	387					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		AAGAAATAGACGATTCTTTCA	0.433																																					p.R387X		.											.	VN1R2-90	0			c.C1159T						.						105	103	104					19																	53762787		2203	4300	6503	SO:0001587	stop_gained	317701	exon1			AATAGACGATTCT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.1159C>T	19.37:g.53762787C>T	ENSP00000351244:p.Arg387*	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	139	35	NM_173856	0	0	0	0	0	A1L411|Q8TDU4	Nonsense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024586	0.35701	.	.	ENSG00000196131	ENST00000341702	.	.	.	2.92	-5.84	0.02318	.	.	.	.	.	.	.	.	.	.	.	0.20764	N	0.999858	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.3458	0.04271	0.3322:0.4169:0.1115:0.1395	.	.	.	.	X	387	.	ENSP00000351244:R387X	R	+	1	2	VN1R2	58454599	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.676000	0.00396	-3.923000	0.00091	-0.582000	0.04134	CGA	C|1.000;T|0.000		0.433	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		T	53762787	C	T	53762787	4	4	11	1	0	0	0	0	0	1	0	0	17212	528	19	1	1161	1	VN1R2	19	53762787	Nonsense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	4104710	53762787	5366196	98	881											
SLC24A3	57419	hgsc.bcm.edu;ucsc.edu	37	chr20	19679325	19679325	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtggattacggatcctacGtaagtggttttctccaggac	8	13	11	9	2	1	0	0	0	1	0	3	3	2	3	2	4	2	2	2	4	3	5	rs201062990		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr20:19679325G>C	ENST00000328041.6	+	15	1916		c.e15+1		RP4-718D20.3_ENST00000600889.1_RNA|RP4-718D20.3_ENST00000435992.2_RNA|RP4-718D20.3_ENST00000609846.1_RNA|RP4-718D20.3_ENST00000598694.1_RNA|RP4-718D20.3_ENST00000593770.1_RNA	NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3						ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CGGATCCTACGTAAGTGGTTT	0.542																																					.		.											.	SLC24A3-91	0			c.1719+1G>C						.						79	63	68					20																	19679325		2203	4299	6502	SO:0001630	splice_region_variant	57419	exon15			TCCTACGTAAGTG	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1719+1G>C	20.37:g.19679325G>C		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_020689	0	0	0	3	3	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Splice_Site	SNP	ENST00000328041.6	37	CCDS13140.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120039	0.94385	.	.	ENSG00000185052	ENST00000328041	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8252	0.92115	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC24A3	19627325	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	9.869000	0.99810	2.758000	0.94735	0.561000	0.74099	.	G|0.999;A|0.000		0.542	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	Intron	C	19679325	G	C	19679325	5	2	11	1	0	0	0	0	0	0	1	0	14499	1159	40	4	1778	4	SLC24A3	20	19679325	Splice_Site	SNP	G	TCGA-A4-7996-01A-11D-2201-08		19679325	43346195	99	882											
MOCS3	8813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49576203	49576203	+	5'Flank	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcttacagtggcagctTgttgctctttgatgccctga	5	14	9	13	0	2	2	0	2	2	0	2	2	2	2	3	1	4	4	3	1	1	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr20:49576203T>G	ENST00000371588.5	-	0	0				MOCS3_ENST00000244051.1_Missense_Mutation_p.L275W|DPM1_ENST00000371582.4_5'Flank|DPM1_ENST00000371583.5_5'Flank|DPM1_ENST00000466152.1_5'Flank	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit						C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose metabolic process (GO:0019673)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|protein mannosylation (GO:0035268)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nucleus (GO:0005634)	alcohol binding (GO:0043178)|dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannose binding (GO:0005537)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	7						AGTGGCAGCTTGTTGCTCTTT	0.632																																					p.L275W		.											.	MOCS3-93	0			c.T824G						.						46	51	50					20																	49576203		2203	4300	6503	SO:0001631	upstream_gene_variant	27304	exon1			GCAGCTTGTTGCT	AF007875	CCDS13434.1	20q13.1	2013-02-26			ENSG00000000419	ENSG00000000419	2.4.1.83	"Glycosyltransferase family 2 domain containing"	3005	protein-coding gene	gene with protein product	"DPM synthase complex, catalytic subunit"	603503				9223280, 9535917	Standard	NM_003859		Approved	MPDS, CDGIE	uc002xvw.1	O60762	OTTHUMG00000032742		20.37:g.49576203T>G	Exception_encountered	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	120	63	NM_014484	0	0	10	37	27	O15157|Q6IB78|Q96HK0	Missense_Mutation	SNP	ENST00000371588.5	37	CCDS13434.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.243077	0.58995	.	.	ENSG00000124217	ENST00000244051	T	0.37058	1.22	5.27	5.27	0.74061	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);MoeZ/MoeB (1);	0.229560	0.37483	N	0.002066	T	0.75824	0.3902	H	0.98965	4.385	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	D	0.86356	0.1714	9	.	.	.	-5.0901	15.1888	0.73025	0.0:0.0:0.0:1.0	.	275	O95396	MOCS3_HUMAN	W	275	ENSP00000244051:L275W	.	L	+	2	0	MOCS3	49009610	1.000000	0.71417	0.918000	0.36340	0.234000	0.25298	5.437000	0.66544	1.992000	0.58205	0.459000	0.35465	TTG	.		0.632	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1	NM_003859		G	49576203	T	G	49576203	1	3	11	0	1	0	0	0	0	0	0	0	9717	1821	63	5		5	MOCS3	20	49576203	5'Flank	SNP	T	TCGA-A4-7996-01A-11D-2201-08	29896878	49576203	13449317	100	883											
NFATC2	4773	broad.mit.edu	37	chr20	50092014	50092014	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttgccctcatgttgttttTgggctccaagggtatctcca	5	15	10	11	1	2	0	1	0	1	0	4	0	3	0	3	2	1	5	3	2	2	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr20:50092014T>G	ENST00000396009.3	-	4	1735	c.1516A>C	c.(1516-1518)Aaa>Caa	p.K506Q	NFATC2_ENST00000610033.1_Missense_Mutation_p.K287Q|NFATC2_ENST00000609507.1_Missense_Mutation_p.K287Q|NFATC2_ENST00000414705.1_Missense_Mutation_p.K486Q|NFATC2_ENST00000609943.1_Missense_Mutation_p.K486Q|NFATC2_ENST00000371564.3_Missense_Mutation_p.K506Q	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	506	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K506Q(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					ATGTTGTTTTTGGGCTCCAAG	0.577																																					p.K506Q													.	NFATC2-92	1	Substitution - Missense(1)	prostate(1)	c.A1516C						.						181	186	184					20																	50092014		2203	4300	6503	SO:0001583	missense	4773	exon4			TGTTTTTGGGCTC	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1516A>C	20.37:g.50092014T>G	ENSP00000379330:p.Lys506Gln	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	240	3	NM_012340	0	0	3	3	0	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.597747	0.66332	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.45276	0.9;0.9;0.9	5.26	5.26	0.73747	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.57344	0.2047	L	0.43152	1.355	0.45528	D	0.998486	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.87578	0.998;0.988;0.998;0.998	T	0.60500	-0.7251	10	0.72032	D	0.01	-14.8818	15.1948	0.73078	0.0:0.0:0.0:1.0	.	486;486;506;506	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	Q	506;506;486	ENSP00000360619:K506Q;ENSP00000379330:K506Q;ENSP00000396471:K486Q	ENSP00000360619:K506Q	K	-	1	0	NFATC2	49525421	1.000000	0.71417	0.982000	0.44146	0.941000	0.58515	3.350000	0.52224	1.982000	0.57802	0.477000	0.44152	AAA	.		0.577	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		G	50092014	T	G	50092014	3	3	11	1	0	0	0	0	1	0	0	0	10388	1821	63	5	1337	5	NFATC2	20	50092014	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	515811	50092014	12933506	101	884											
ARVCF	421	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	19965495	19965495	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gcccaccttgttgtcagtgtCcttccggcccacagccgact	5	10	9	17	2	1	0	1	0	0	0	3	1	3	0	6	1	1	1	6	1	0	3	rs373958610		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr22:19965495C>G	ENST00000263207.3	-	8	1975	c.1684G>C	c.(1684-1686)Gac>Cac	p.D562H	ARVCF_ENST00000344269.3_Missense_Mutation_p.D499H|ARVCF_ENST00000406522.1_Missense_Mutation_p.D499H|ARVCF_ENST00000401994.1_Missense_Mutation_p.D499H|ARVCF_ENST00000406259.1_Missense_Mutation_p.D562H	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	562					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					TTGTCAGTGTCCTTCCGGCCC	0.652																																					p.D562H		.											.	ARVCF-91	0			c.G1684C						.						61	50	54					22																	19965495		2203	4300	6503	SO:0001583	missense	421	exon8			CAGTGTCCTTCCG		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1684G>C	22.37:g.19965495C>G	ENSP00000263207:p.Asp562His	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	58	16	NM_001670	0	0	0	2	2	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145373	0.77888	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	4.03	4.03	0.46877	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.973;0.999	D	0.89030	0.3441	9	.	.	.	-17.2062	17.0615	0.86548	0.0:1.0:0.0:0.0	.	562;84	O00192;E7EV58	ARVC_HUMAN;.	H	562;499;499;499;562	ENSP00000263207:D562H;ENSP00000342042:D499H;ENSP00000384341:D499H;ENSP00000384732:D499H;ENSP00000385444:D562H	.	D	-	1	0	ARVCF	18345495	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.569000	0.67391	2.541000	0.85698	0.655000	0.94253	GAC	.		0.652	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		G	19965495	C	G	19965495	3	3	11	1	0	0	0	0	1	0	0	0	1004	855	30	4	1252	4	ARVCF	22	19965495	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		19965495	31339071	102	885											
PKDREJ	10343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	46655720	46655720	+	Frame_Shift_Del	DEL	G	G	-																															accgtagatccacaggattaGggatcacaatcaccttggcc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr22:46655720delG	ENST00000253255.5	-	1	3499	c.3500delC	c.(3499-3501)cctfs	p.P1167fs		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1167					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CACAGGATTAGGGATCACAAT	0.493																																					p.P1167fs		.											.	PKDREJ-156	0			c.3500delC						.						160	152	155					22																	46655720		2203	4300	6503	SO:0001589	frameshift_variant	10343	exon1			.	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.3500delC	22.37:g.46655720delG	ENSP00000253255:p.Pro1167fs	Somatic	208	0		WXS	Illumina HiSeq	Phase_I	205	50	NM_006071	0	0	0	0	0	B1AJY3|O95850	Frame_Shift_Del	DEL	ENST00000253255.5	37	CCDS14073.1																																																																																			.		0.493	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		-	46655720	G	-	46655720	7	5	11	1	0	1	0	1	0	0	0	0	11996	1000	35	0	3265	0	PKDREJ	22	46655720	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	26690225	46655720	4648846	103	886											
TRAPPC2	6399	hgsc.bcm.edu	37	chrX	13732606	13732606	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aataggagaattgggttcatAaaatggattcattgaaaact	17	12	9	3	0	2	2	2	1	0	1	2	4	2	3	0	3	1	1	0	3	7	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chrX:13732606A>G	ENST00000380579.1	-	6	535	c.343T>C	c.(343-345)Tat>Cat	p.Y115H	TRAPPC2_ENST00000359680.5_Missense_Mutation_p.Y115H|TRAPPC2_ENST00000453655.2_Missense_Mutation_p.Y122H|TRAPPC2_ENST00000458511.2_Missense_Mutation_p.Y149H|TRAPPC2_ENST00000358231.5_Missense_Mutation_p.Y115H			P0DI81	TPC2A_HUMAN	trafficking protein particle complex 2	115					ER to Golgi vesicle-mediated transport (GO:0006888)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ion channel binding (GO:0044325)|transcription factor binding (GO:0008134)			kidney(1)	1						TTGGGTTCATAAAATGGATTC	0.303																																					p.Y149H		.											.	TRAPPC2-130	0			c.T445C						.						35	29	31					X																	13732606		1789	4040	5829	SO:0001583	missense	6399	exon6			GTTCATAAAATGG	AF157061	CCDS48082.1, CCDS48083.1, CCDS48083.2	Xp22	2011-10-10	2005-01-26		ENSG00000196459	ENSG00000196459		"Trafficking protein particle complex"	23068	protein-coding gene	gene with protein product		300202	"spondyloepiphyseal dysplasia, late"	SEDL		14597397	Standard	NM_014563		Approved	TRS20, SEDT, MIP-2A, ZNF547L, hYP38334	uc010nej.2	P0DI81	OTTHUMG00000021157	ENST00000380579.1:c.343T>C	X.37:g.13732606A>G	ENSP00000369953:p.Tyr115His	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_001128835	0	0	34	34	0	A6NEG0|O14582|Q9HD16	Missense_Mutation	SNP	ENST00000380579.1	37	CCDS48082.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.370361	0.82573	.	.	ENSG00000196459	ENST00000453655;ENST00000359680;ENST00000380579;ENST00000358231;ENST00000458511	D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93	5.68	5.68	0.88126	Longin-like (1);	0.000000	0.85682	D	0.000000	D	0.95828	0.8642	M	0.79693	2.465	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.95496	0.8573	10	0.42905	T	0.14	-25.1011	14.9504	0.71067	1.0:0.0:0.0:0.0	.	115	P0DI81	TPC2A_HUMAN	H	122;115;115;115;149	ENSP00000394629:Y122H;ENSP00000352708:Y115H;ENSP00000369953:Y115H;ENSP00000350966:Y115H;ENSP00000392495:Y149H	ENSP00000350966:Y115H	Y	-	1	0	TRAPPC2	13642527	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.251000	0.95483	1.913000	0.55393	0.417000	0.27973	TAT	.		0.303	TRAPPC2-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055805.2	NM_014563		G	13732606	A	G	13732606	3	3	11	1	0	0	0	0	1	0	0	0	16491	362	13	3	83	3	TRAPPC2	23	13732606	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		13732606	141537954	104	887											
FAM48B1	100130302	broad.mit.edu	37	chrX	24381695	24381695	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctggccaaaaagaagaaaGaaaagtaggtcagccttgtg	16	8	11	6	0	2	3	1	0	1	3	2	3	2	3	2	2	1	1	2	2	7	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chrX:24381695G>A								AC004552.1 (14672 upstream) : PDK3 (101642 downstream)																							AAAGAAGAAAGAAAAGTAGGT	0.512																																					p.R273K													.	.	0			c.G818A						.						101	86	90					X																	24381695		1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			AAGAAAGAAAAGT																													X.37:g.24381695G>A		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	97	4	NM_001136234	0	0	0	0	0		Missense_Mutation	SNP		37																																																																																				.	0	0.512									A	24381695	G	A	24381695	1	1	11	0	1	0	0	0	0	0	0	0	5592	942	33	2		2	FAM48B1	23	24381695	IGR	SNP	G	TCGA-A4-7996-01A-11D-2201-08	10649089	24381695	130888865	105	888											
RLIM	51132	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	73815805	73815805	+	Frame_Shift_Del	DEL	T	T	-																															ctttgtcattggaatctgagTtttccatattgatgaacaag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chrX:73815805delT	ENST00000332687.6	-	2	226	c.8delA	c.(7-9)aacfs	p.N3fs	RLIM_ENST00000349225.2_Frame_Shift_Del_p.N3fs	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	3					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GGAATCTGAGTTTTCCATATT	0.358																																					p.N3fs	Esophageal Squamous(169;1899 1923 14997 18818 32118)	.											.	RLIM-228	0			c.8delA						.						53	49	50					X																	73815805		2203	4300	6503	SO:0001589	frameshift_variant	51132	exon3			.	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.8delA	X.37:g.73815805delT	ENSP00000328059:p.Asn3fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	69	31	NM_183353	0	0	0	0	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Frame_Shift_Del	DEL	ENST00000332687.6	37	CCDS14427.1																																																																																			.		0.358	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		-	73815805	T	-	73815805	7	5	11	1	0	1	0	1	0	0	0	0	13422	1725	60	0	1878	0	RLIM	23	73815805	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08	49434110	73815805	81454755	106	889											
GLUD2	2747	ucsc.edu	37	chrX	120182436	120182436	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggaatgacaccagggtttAgagataaaacatttgttgtt	14	13	10	4	0	0	2	0	1	0	1	0	4	0	3	1	2	1	3	1	2	5	7			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chrX:120182436A>G	ENST00000328078.1	+	1	975	c.898A>G	c.(898-900)Aga>Gga	p.R300G		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	300					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						ACCAGGGTTTAGAGATAAAAC	0.413																																					p.R300G													.	GLUD2-131	0			c.A898G						.						189	170	177					X																	120182436		2203	4300	6503	SO:0001583	missense	2747	exon1			GGGTTTAGAGATA	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.898A>G	X.37:g.120182436A>G	ENSP00000327589:p.Arg300Gly	Somatic	302	0		WXS	Illumina HiSeq		210	1	NM_012084	0	0	4	917	913	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.462215	0.01062	.	.	ENSG00000182890	ENST00000328078	D	0.95272	-3.66	2.3	-1.33	0.09172	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (2);NAD(P)-binding domain (1);	0.376526	0.30093	N	0.010424	T	0.76983	0.4064	N	0.02247	-0.625	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.70048	-0.4979	10	0.02654	T	1	-8.2867	4.1877	0.10405	0.2739:0.2268:0.4994:0.0	.	300	P49448	DHE4_HUMAN	G	300	ENSP00000327589:R300G	ENSP00000327589:R300G	R	+	1	2	GLUD2	120010117	1.000000	0.71417	0.578000	0.28575	0.925000	0.55904	2.644000	0.46613	-0.680000	0.05211	-0.386000	0.06593	AGA	.		0.413	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		G	120182436	A	G	120182436	3	3	11	1	0	0	0	0	1	0	0	0	6497	412	15	3	900	3	GLUD2	23	120182436	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	46366631	120182436	35088124	107	890											
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	8422892	8422892	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcttcttccgaccactgcGtagtgtcgacatctgcccac	6	11	8	16	3	2	0	0	0	2	0	4	2	3	0	3	0	3	2	3	0	1	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:8422892G>T	ENST00000337907.3	-	17	2387	c.1753C>A	c.(1753-1755)Cgc>Agc	p.R585S	RERE_ENST00000400908.2_Missense_Mutation_p.R585S|RERE_ENST00000377464.1_Missense_Mutation_p.R317S|RERE_ENST00000476556.1_Missense_Mutation_p.R31S|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	585					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		CGACCACTGCGTAGTGTCGAC	0.617																																					p.R585S		.											.	RERE-515	0			c.C1753A						.						95	83	87					1																	8422892		2203	4300	6503	SO:0001583	missense	473	exon17			CACTGCGTAGTGT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1753C>A	1.37:g.8422892G>T	ENSP00000338629:p.Arg585Ser	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	92	29	NM_012102	0	0	0	0	0	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444981	0.83993	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T;T	0.05025	3.51;3.51;3.51;3.51	5.8	5.8	0.92144	.	.	.	.	.	T	0.21509	0.0518	M	0.67953	2.075	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.07481	-1.0770	9	0.06891	T	0.86	-30.1132	19.0501	0.93039	0.0:0.0:1.0:0.0	.	317;585	B1AKN3;Q9P2R6	.;RERE_HUMAN	S	585;317;31;585;5	ENSP00000338629:R585S;ENSP00000366684:R317S;ENSP00000422246:R31S;ENSP00000383700:R585S	ENSP00000338629:R585S	R	-	1	0	RERE	8345479	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.407000	0.97325	2.730000	0.93505	0.563000	0.77884	CGC	.		0.617	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			T	8422892	G	T	8422892	3	4	12	1	0	0	0	0	1	0	0	0	13263	1145	40	4	2979	4	RERE	1	8422892	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08		8422892	240827729	1	891											
UQCRHL	0	ucsc.edu	37	chr1	16133912	16133912	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgggccacgcaatggtccTttgcatgcaagaagtcaaag	11	9	12	9	1	1	1	1	0	0	1	2	1	2	1	2	2	2	3	2	2	4	1	rs570054582		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:16133912T>C								FBLIM1 (20823 upstream) : RP11-169K16.9 (26647 downstream)																							GCAATGGTCCTTTGCATGCAA	0.463													T|||	1	0.000199681	0	0.0014	5008	,	,		19503	0		0	False		,,,				2504	0				p.K78R													.	.	0			c.A233G						.						163	165	164					1																	16133912		2203	4300	6503	SO:0001628	intergenic_variant	0	exon1			TGGTCCTTTGCAT																													1.37:g.16133912T>C		Somatic	274	0		WXS	Illumina HiSeq		270	1	NM_001089591	0	0	0	0	0		Missense_Mutation	SNP		37																																																																																				.	0	0.463									C	16133912	T	C	16133912	1	2	12	0	1	0	0	0	0	0	0	0	17056	1609	56	3		3	UQCRHL	1	16133912	IGR	SNP	T	TCGA-A4-7997-01A-11D-2201-08	7711020	16133912	233116709	2	892											
SPEN	23013	broad.mit.edu	37	chr1	16203085	16203085	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggctagccaagcatctagaCccacaaggtcccctagcggc	10	6	10	15	1	1	1	0	0	1	1	2	1	2	1	4	3	3	2	4	3	5	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:16203085C>A	ENST00000375759.3	+	3	997	c.793C>A	c.(793-795)Ccc>Acc	p.P265T	SPEN_ENST00000471538.1_3'UTR	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	265	Arg-rich.|Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AGCATCTAGACCCACAAGGTC	0.527																																					p.P265T													.	SPEN-298	0			c.C793A						.						43	40	41					1																	16203085		2201	4290	6491	SO:0001583	missense	23013	exon3			TCTAGACCCACAA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.793C>A	1.37:g.16203085C>A	ENSP00000364912:p.Pro265Thr	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	95	4	NM_015001	0	0	18	18	0	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.76|13.76	2.332667|2.332667	0.41297|0.41297	.|.	.|.	ENSG00000065526|ENSG00000065526	ENST00000442985|ENST00000375759;ENST00000438066;ENST00000375753	.|T;T	.|0.31769	.|3.01;1.48	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|.	.|.	.|.	.|.	T|T	0.28366|0.28366	0.0701|0.0701	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|P	.|0.42692	.|0.787	.|B	.|0.40199	.|0.322	T|T	0.03933|0.03933	-1.0991|-1.0991	5|9	.|0.62326	.|D	.|0.03	-10.4615|-10.4615	20.0118|20.0118	0.97458|0.97458	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|265	.|Q96T58	.|MINT_HUMAN	E|T	5|265;224;224	.|ENSP00000364912:P265T;ENSP00000388021:P224T	.|ENSP00000364906:P224T	D|P	+|+	3|1	2|0	SPEN|SPEN	16075672|16075672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.463000|5.463000	0.66712|0.66712	2.744000|2.744000	0.94065|0.94065	0.563000|0.563000	0.77884|0.77884	GAC|CCC	.		0.527	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16203085	C	A	16203085	3	1	12	1	0	0	0	0	1	0	0	0	15070	507	18	4	803	4	SPEN	1	16203085	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	69173	16203085	233047536	3	893											
MAST2	23139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	46290209	46290209	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgacaactgagtcaggaTgattgtaagttatggagagg	13	9	14	5	1	1	3	1	2	0	1	1	6	1	4	0	3	2	2	0	3	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:46290209T>C	ENST00000361297.2	+	2	565	c.282T>C	c.(280-282)gaT>gaC	p.D94D	MAST2_ENST00000372009.2_Silent_p.D94D	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					TGAGTCAGGATGATTGTAAGT	0.398																																					p.D94D		.											.	MAST2-581	0			c.T282C						.						166	149	154					1																	46290209		1856	4094	5950	SO:0001819	synonymous_variant	23139	exon2			TCAGGATGATTGT	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.282T>C	1.37:g.46290209T>C		Somatic	282	0		WXS	Illumina HiSeq	Phase_I	265	88	NM_015112	0	0	3	6	3		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			.		0.398	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		C	46290209	T	C	46290209	2	2	12	1	0	0	0	0	0	0	0	1	9350	1461	51	3		3	MAST2	1	46290209	Silent	SNP	T	TCGA-A4-7997-01A-11D-2201-08	30087124	46290209	202960412	4	894											
WDR3	10885	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	118502024	118502024	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagccacttggaagagaagaAgaggaagaggaaaaagaggg	19	3	16	3	0	0	5	0	0	0	5	0	9	0	8	1	4	1	0	1	4	7	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:118502024A>G	ENST00000349139.5	+	27	2833	c.2786A>G	c.(2785-2787)aAg>aGg	p.K929R	SPAG17_ENST00000336338.5_Intron	NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3	929						nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		GAAGagaagaagaggaagagg	0.378																																					p.K929R		.											.	WDR3-91	0			c.A2786G						.						70	77	74					1																	118502024		2203	4300	6503	SO:0001583	missense	10885	exon27			AGAAGAAGAGGAA	AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183		"WD repeat domain containing"	12755	protein-coding gene	gene with protein product		604737				10395803	Standard	NM_006784		Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.2786A>G	1.37:g.118502024A>G	ENSP00000308179:p.Lys929Arg	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	66	24	NM_006784	0	0	20	46	26		Missense_Mutation	SNP	ENST00000349139.5	37	CCDS898.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502821	0.44558	.	.	ENSG00000065183	ENST00000349139	T	0.54479	0.57	5.47	4.35	0.52113	.	0.188191	0.56097	D	0.000032	T	0.15782	0.0380	N	0.08118	0	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.06734	-1.0810	10	0.28530	T	0.3	-11.5094	10.512	0.44868	0.9233:0.0:0.0767:0.0	.	929	Q9UNX4	WDR3_HUMAN	R	929	ENSP00000308179:K929R	ENSP00000308179:K929R	K	+	2	0	WDR3	118303547	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.417000	0.44653	2.091000	0.63221	0.496000	0.49642	AAG	.		0.378	WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2	NM_006784		G	118502024	A	G	118502024	3	3	12	1	0	0	0	0	1	0	0	0	17318	72	3	3	2888	3	WDR3	1	118502024	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	72211815	118502024	130748597	5	895											
PDZK1	5174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145761288	145761288	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagtctcaagtccaccagaTactacagaggaagtagatca	16	7	9	9	0	2	3	2	0	1	3	4	5	3	4	2	1	2	1	2	1	6	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:145761288T>C	ENST00000344770.2	+	7	1174	c.1101T>C	c.(1099-1101)gaT>gaC	p.D367D	PDZK1_ENST00000417171.1_Silent_p.D367D|PDZK1_ENST00000451928.2_Silent_p.D256D	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	367					carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			GTCCACCAGATACTACAGAGG	0.483																																					p.D367D		.											.	PDZK1-90	0			c.T1101C						.						91	96	94					1																	145761288		2201	4298	6499	SO:0001819	synonymous_variant	5174	exon8			ACCAGATACTACA	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.1101T>C	1.37:g.145761288T>C		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	184	69	NM_002614	0	0	345	693	348	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Silent	SNP	ENST00000344770.2	37	CCDS924.1																																																																																			.		0.483	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		C	145761288	T	C	145761288	2	2	12	1	0	0	0	0	0	0	0	1	11733	1403	49	3		3	PDZK1	1	145761288	Silent	SNP	T	TCGA-A4-7997-01A-11D-2201-08	27259264	145761288	103489333	6	896											
ASH1L	55870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155491175	155491175	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccgtttgcgaaggtcctcttCctcctttgtgtttttttcta	3	20	7	11	2	2	0	0	0	2	0	5	1	5	0	4	1	1	2	4	1	2	7			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:155491175C>T	ENST00000368346.3	-	2	775	c.136G>A	c.(136-138)Gaa>Aaa	p.E46K	ASH1L_ENST00000392403.3_Missense_Mutation_p.E46K|ASH1L_ENST00000548830.1_Missense_Mutation_p.E46K			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	46					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AGGTCCTCTTCCTCCTTTGTG	0.418																																					p.E46K		.											.	ASH1L-234	0			c.G136A						.						302	301	301					1																	155491175		2203	4300	6503	SO:0001583	missense	55870	exon2			CCTCTTCCTCCTT	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.136G>A	1.37:g.155491175C>T	ENSP00000357330:p.Glu46Lys	Somatic	518	0		WXS	Illumina HiSeq	Phase_I	495	164	NM_018489	0	0	10	33	23	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	C	36	5.771812	0.96922	.	.	ENSG00000116539	ENST00000368346;ENST00000392403;ENST00000548830	D;D	0.89875	-2.58;-2.58	5.51	5.51	0.81932	.	0.134693	0.48286	N	0.000192	T	0.73776	0.3630	N	0.08118	0	0.46874	D	0.999234	B;B	0.30281	0.18;0.275	B;B	0.28232	0.04;0.087	T	0.76487	-0.2941	10	0.72032	D	0.01	.	19.2027	0.93717	0.0:1.0:0.0:0.0	.	46;46	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	K	46	ENSP00000357330:E46K;ENSP00000376204:E46K	ENSP00000357330:E46K	E	-	1	0	ASH1L	153757799	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.059000	0.76684	2.868000	0.98415	0.557000	0.71058	GAA	.		0.418	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155491175	C	T	155491175	3	4	12	1	0	0	0	0	1	0	0	0	1042	864	30	2	8866	2	ASH1L	1	155491175	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	9729887	155491175	93759446	7	897											
TOR1AIP2	163590	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	179834038	179834038	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttttctaaccagtggaggacCcagaagaaatggatggcaag	14	8	12	7	0	1	2	0	0	1	2	1	5	1	5	2	4	1	1	2	4	4	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:179834038C>A	ENST00000553856.1	-	1	273	c.274G>T	c.(274-276)Ggt>Tgt	p.G92C	TOR1AIP2_ENST00000367612.3_Intron|TOR1AIP2_ENST00000609928.1_Intron|TOR1AIP2_ENST00000482587.1_5'UTR	NM_022347.3	NP_071742.1	Q9H496	IFG15_HUMAN		92																	AGTGGAGGACCCAGAAGAAAT	0.428																																					p.G92C		.											.	TOR1AIP2-69	0			c.G274T						.						130	126	128					1																	179834038		1854	4087	5941	SO:0001583	missense	163590	exon3			GAGGACCCAGAAG																												ENST00000553856.1:c.274G>T	1.37:g.179834038C>A	ENSP00000452581:p.Gly92Cys	Somatic	151	1		WXS	Illumina HiSeq	Phase_I	184	61	NM_022347	0	0	12	28	16	Q05BU2	Missense_Mutation	SNP	ENST00000553856.1	37	CCDS53439.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377210	0.42105	.	.	ENSG00000258664	ENST00000553856	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	T	0.50582	0.1624	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.47262	-0.9131	7	.	.	.	.	13.6483	0.62294	0.0:1.0:0.0:0.0	.	92	Q9H496	.	C	92	.	.	G	-	1	0	AL359853.3	178100661	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.906000	0.48735	2.941000	0.99782	0.655000	0.94253	GGT	.		0.428	IFRG15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	179834038	C	A	179834038	3	1	12	1	0	0	0	0	1	0	0	0	16406	623	22	4	1554	4	TOR1AIP2	1	179834038	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	24342863	179834038	69416583	8	898											
SLC41A1	254428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205770146	205770146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccccagcagcgcaggcaCtaggatgaagacctctgtca	11	5	12	13	1	2	2	1	1	1	1	2	4	2	3	3	2	3	3	3	2	2	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:205770146C>T	ENST00000367137.3	-	3	1429	c.415G>A	c.(415-417)Gtg>Atg	p.V139M	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	139					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			AGCGCAGGCACTAGGATGAAG	0.562																																					p.V139M		.											.	SLC41A1-92	0			c.G415A						.						109	105	106					1																	205770146		2203	4300	6503	SO:0001583	missense	254428	exon3			CAGGCACTAGGAT	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"Solute carriers"	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.415G>A	1.37:g.205770146C>T	ENSP00000356105:p.Val139Met	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	133	39	NM_173854	0	0	25	46	21	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Missense_Mutation	SNP	ENST00000367137.3	37	CCDS30988.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182269	0.94885	.	.	ENSG00000133065	ENST00000367137	T	0.29917	1.55	5.78	5.78	0.91487	MgtE magnesium transporter, integral membrane (1);	0.000000	0.85682	D	0.000000	T	0.68091	0.2963	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73538	-0.3951	10	0.51188	T	0.08	-13.616	19.9618	0.97254	0.0:1.0:0.0:0.0	.	139	Q8IVJ1	S41A1_HUMAN	M	139	ENSP00000356105:V139M	ENSP00000356105:V139M	V	-	1	0	SLC41A1	204036769	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.768000	0.85345	2.894000	0.99253	0.655000	0.94253	GTG	.		0.562	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1			T	205770146	C	T	205770146	3	4	12	1	0	0	0	0	1	0	0	0	14661	565	20	2	1162	2	SLC41A1	1	205770146	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	25936108	205770146	43480475	9	899											
PIGR	5284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207109097	207109097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccttacggttgtaggggCagagcacggccacagagcct	8	9	13	11	2	0	2	0	0	0	2	1	2	1	2	3	4	3	4	3	4	2	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:207109097C>T	ENST00000356495.4	-	5	1295	c.1112G>A	c.(1111-1113)tGc>tAc	p.C371Y		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	371	Ig-like V-type 4.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GTTGTAGGGGCAGAGCACGGC	0.622											OREG0014186	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C371Y		.											.	PIGR-92	0			c.G1112A						.						33	37	36					1																	207109097		2203	4300	6503	SO:0001583	missense	5284	exon5			TAGGGGCAGAGCA		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1112G>A	1.37:g.207109097C>T	ENSP00000348888:p.Cys371Tyr	Somatic	41	0	2165	WXS	Illumina HiSeq	Phase_I	43	17	NM_002644	8	19	2506	5529	2996	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.956538	0.53293	.	.	ENSG00000162896	ENST00000356495	T	0.40476	1.03	5.55	5.55	0.83447	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.75882	0.3910	H	0.96518	3.835	0.53005	D	0.999964	D	0.89917	1.0	D	0.97110	1.0	D	0.83757	0.0212	10	0.87932	D	0	-23.806	16.2203	0.82255	0.0:1.0:0.0:0.0	.	371	P01833	PIGR_HUMAN	Y	371	ENSP00000348888:C371Y	ENSP00000348888:C371Y	C	-	2	0	PIGR	205175720	1.000000	0.71417	0.930000	0.37139	0.097000	0.18754	4.383000	0.59600	2.614000	0.88457	0.655000	0.94253	TGC	.		0.622	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		T	207109097	C	T	207109097	3	4	12	1	0	0	0	0	1	0	0	0	11923	710	25	2	1210	2	PIGR	1	207109097	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	1338951	207109097	42141524	10	900											
IRF6	3664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	209974723	209974723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccacctgggccaccagccaGggctttagccggactctgcg	6	7	12	16	2	1	0	0	0	1	0	2	1	2	1	6	3	3	1	6	3	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:209974723G>A	ENST00000367021.3	-	3	208	c.36C>T	c.(34-36)ccC>ccT	p.P12P	IRF6_ENST00000542854.1_Intron	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	12					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CCACCAGCCAGGGCTTTAGCC	0.607										HNSCC(57;0.16)																											p.P12P		.											.	IRF6-92	0			c.C36T						.						55	63	60					1																	209974723		2202	4300	6502	SO:0001819	synonymous_variant	3664	exon3			CAGCCAGGGCTTT	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"Van der Woude syndrome"	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.36C>T	1.37:g.209974723G>A		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	151	46	NM_006147	0	0	23	30	7	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Silent	SNP	ENST00000367021.3	37	CCDS1492.1																																																																																			.		0.607	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147		A	209974723	G	A	209974723	2	1	12	1	0	0	0	0	0	0	0	1	7855	987	35	2		2	IRF6	1	209974723	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	2865626	209974723	39275898	11	901											
LEFTY2	7044	hgsc.bcm.edu;broad.mit.edu	37	chr1	226127230	226127230	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggctgccggggccggctcaGctgctgccagaagttcacgg	5	6	16	14	4	2	1	2	0	0	1	2	1	2	1	3	5	4	5	3	5	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:226127230G>A	ENST00000366820.5	-	3	916	c.568C>T	c.(568-570)Ctg>Ttg	p.L190L	RP4-559A3.6_ENST00000513672.1_RNA|LEFTY2_ENST00000420304.2_Silent_p.L156L|LEFTY2_ENST00000474493.1_5'UTR	NM_003240.3	NP_003231.2	O00292	LFTY2_HUMAN	left-right determination factor 2	190					blood coagulation (GO:0007596)|cell growth (GO:0016049)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16	Breast(184;0.197)					GGCCGGCTCAGCTGCTGCCAG	0.672																																					p.L190L	Colon(172;116 2643 9098 43333)	.											.	LEFTY2-90	0			c.C568T						.						12	16	15					1																	226127230		2166	4217	6383	SO:0001819	synonymous_variant	7044	exon3			GGCTCAGCTGCTG	U81523	CCDS1549.1, CCDS53479.1	1q42.1	2008-07-18	2004-11-17	2004-11-17	ENSG00000143768	ENSG00000143768			3122	protein-coding gene	gene with protein product	"transforming growth factor, beta-4 (endometrial bleeding-associated factor; LEFTY A)"	601877	"endometrial bleeding associated factor (left-right determination, factor A; transforming growth factor beta superfamily)"	TGFB4, EBAF		9153275	Standard	NM_001172425		Approved	LEFTA, LEFTYA	uc001hpt.2	O00292	OTTHUMG00000037441	ENST00000366820.5:c.568C>T	1.37:g.226127230G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	54	16	NM_003240	0	0	4	4	0	B3KNH4|B4E332|E9PDM4|O75611|Q5TE89|Q8NBQ9	Silent	SNP	ENST00000366820.5	37	CCDS1549.1																																																																																			.		0.672	LEFTY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091152.1	NM_003240		A	226127230	G	A	226127230	2	1	12	1	0	0	0	0	0	0	0	1	8737	962	34	2		2	LEFTY2	1	226127230	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	16152507	226127230	23123391	12	902											
EXOC8	149371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	231472205	231472205	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccctgtttctcaaaaatagCtcacaggccttcgtgcactg	9	11	8	13	1	2	0	2	0	1	0	4	0	2	0	2	1	2	3	2	1	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:231472205C>A	ENST00000360394.2	-	1	1373	c.1287G>T	c.(1285-1287)gaG>gaT	p.E429D	EXOC8_ENST00000366645.1_Missense_Mutation_p.E425D|SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank|SPRTN_ENST00000391858.4_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	429					cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				TCAAAAATAGCTCACAGGCCT	0.527																																					p.E429D		.											.	EXOC8-91	0			c.G1287T						.						48	49	49					1																	231472205		2203	4300	6503	SO:0001583	missense	149371	exon1			AAATAGCTCACAG	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.1287G>T	1.37:g.231472205C>A	ENSP00000353564:p.Glu429Asp	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	86	18	NM_175876	0	0	10	13	3	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	37	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.657151	0.29425	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.77098	-1.07;-1.07	5.97	5.05	0.67936	Cullin repeat-like-containing domain (1);	0.052227	0.85682	D	0.000000	T	0.67297	0.2878	L	0.31526	0.94	0.58432	D	0.999998	P	0.45957	0.869	B	0.43754	0.43	T	0.62431	-0.6856	10	0.15066	T	0.55	-29.5152	12.807	0.57619	0.0:0.8715:0.0:0.1285	.	429	Q8IYI6	EXOC8_HUMAN	D	429;425	ENSP00000353564:E429D;ENSP00000355605:E425D	ENSP00000353564:E429D	E	-	3	2	EXOC8	229538828	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.827000	0.55745	2.837000	0.97791	0.655000	0.94253	GAG	.		0.527	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472205	C	A	231472205	3	1	12	1	0	0	0	0	1	0	0	0	5324	796	28	4	894	4	EXOC8	1	231472205	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	5344975	231472205	17778416	13	903											
IRF2BP2	359948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	234744251	234744251	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aacaacctgcctgcagtcagGgccggctccttcttaaactt	9	10	8	14	1	2	0	1	0	1	0	3	0	3	0	4	2	5	2	4	2	4	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:234744251G>T	ENST00000366609.3	-	1	1020	c.990C>A	c.(988-990)gcC>gcA	p.A330A	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000366610.3_Silent_p.A330A|IRF2BP2_ENST00000491430.1_5'Flank	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CTGCAGTCAGGGCCGGCTCCT	0.637																																					p.A330A		.											.	IRF2BP2-90	0			c.C990A						.						22	21	21					1																	234744251		2201	4300	6501	SO:0001819	synonymous_variant	359948	exon1			AGTCAGGGCCGGC	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.990C>A	1.37:g.234744251G>T		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	39	15	NM_182972	0	1	30	57	26	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			.		0.637	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		T	234744251	G	T	234744251	2	4	12	1	0	0	0	0	0	0	0	1	7851	1219	43	4		4	IRF2BP2	1	234744251	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	3272046	234744251	14506370	14	904											
GPR113	165082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	26533773	26533773	+	Frame_Shift_Del	DEL	C	C	-																															atggccatggctagtaccagCccattcacgcctatgatggc																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:26533773delC	ENST00000311519.1	-	11	2822	c.2823delG	c.(2821-2823)gggfs	p.G941fs	GPR113_ENST00000541401.1_Frame_Shift_Del_p.G544fs|GPR113_ENST00000421160.2_Frame_Shift_Del_p.G872fs|GPR113_ENST00000333478.6_Frame_Shift_Del_p.G742fs|GPR113_ENST00000459892.1_5'UTR	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	941					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)					CTAGTACCAGCCCATTCACGC	0.597																																					p.G941fs		.											.	GPR113-94	0			c.2823delG						.						58	51	53					2																	26533773		2203	4300	6503	SO:0001589	frameshift_variant	165082	exon11			.	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.2823delG	2.37:g.26533773delC	ENSP00000307831:p.Gly941fs	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	39	18	NM_001145168	0	0	0	0	0	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Frame_Shift_Del	DEL	ENST00000311519.1	37	CCDS46239.1																																																																																			.		0.597	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		-	26533773	C	-	26533773	7	5	12	1	0	1	0	1	0	0	0	0	6650	726	26	0	517	0	GPR113	2	26533773	Frame_Shift_Del	DEL	C	TCGA-A4-7997-01A-11D-2201-08		26533773	216665600	15	905											
OTOF	9381	ucsc.edu;bcgsc.ca	37	chr2	26700635	26700635	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcctgtgaatcaggagtgtGggtgatgctgggccacagcc	7	10	15	9	0	1	2	1	2	0	0	2	3	2	3	3	3	2	1	3	3	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:26700635G>C	ENST00000272371.2	-	19	2341				OTOF_ENST00000339598.3_Intron|OTOF_ENST00000402415.3_Missense_Mutation_p.H43D|OTOF_ENST00000338581.6_Intron|OTOF_ENST00000403946.3_Intron	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAGGAGTGTGGGTGATGCTG	0.602																																					p.H43D	GBM(102;732 1451 20652 24062 31372)												.	OTOF-135	0			c.C127G						.						53	41	45					2																	26700635		2194	4294	6488	SO:0001627	intron_variant	9381	exon1			GAGTGTGGGTGAT	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2215-18C>G	2.37:g.26700635G>C		Somatic	42	0		WXS	Illumina HiSeq		35	15	NM_194322	0	0	0	0	0	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	G	7.354	0.623380	0.14193	.	.	ENSG00000115155	ENST00000402415	T	0.76709	-1.04	3.28	-1.12	0.09808	.	.	.	.	.	T	0.59307	0.2184	.	.	.	0.09310	N	1	B	0.15473	0.013	B	0.16289	0.015	T	0.36138	-0.9760	7	.	.	.	.	6.8786	0.24160	0.2752:0.1313:0.5935:0.0	.	43	Q9HC10-3	.	D	43	ENSP00000383906:H43D	.	H	-	1	0	OTOF	26554139	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.033000	0.13754	-0.801000	0.04427	-1.268000	0.01426	CAC	.		0.602	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			C	26700635	G	C	26700635	1	2	12	0	1	0	0	0	0	0	0	0	11329	1348	47	4		4	OTOF	2	26700635	Intron	SNP	G	TCGA-A4-7997-01A-11D-2201-08	166862	26700635	216498738	16	906											
C2orf73	129852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	54587528	54587528	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caacaaaattctcaggagctGttagagcctaaaactcactt	15	10	6	10	0	2	1	2	0	1	1	3	2	2	2	1	1	4	2	1	1	6	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:54587528G>T	ENST00000398634.2	+	5	735	c.693G>T	c.(691-693)ctG>ctT	p.L231L	C2orf73_ENST00000405749.1_Intron|C2orf73_ENST00000491538.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	231										breast(2)	2						CTCAGGAGCTGTTAGAGCCTA	0.493																																					p.L231L		.											.	.	0			c.G693T						.						35	34	35					2																	54587528		1907	4128	6035	SO:0001819	synonymous_variant	129852	exon5			GGAGCTGTTAGAG	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.693G>T	2.37:g.54587528G>T		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	31	8	NM_001100396	0	0	1	1	0	A0AV79|A0AV81|Q8N7V4	Silent	SNP	ENST00000398634.2	37	CCDS46285.1																																																																																			.		0.493	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396		T	54587528	G	T	54587528	2	4	12	1	0	0	0	0	0	0	0	1	2198	1364	48	4		4	C2orf73	2	54587528	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	27886893	54587528	188611845	17	907											
ZAP70	7535	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	98341626	98341626	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcattgctacgacggcccaCgagcggatgccctggtacca	8	7	11	15	4	1	0	1	0	0	0	1	3	1	1	3	3	5	2	3	3	2	3	rs56404668	byFrequency	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:98341626C>A	ENST00000264972.5	+	4	689	c.474C>A	c.(472-474)caC>caA	p.H158Q	ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Missense_Mutation_p.H32Q	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	158	Interdomain A.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|beta selection (GO:0043366)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative thymic T cell selection (GO:0045060)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell activation (GO:0042110)|T cell aggregation (GO:0070489)|T cell differentiation (GO:0030217)|T cell migration (GO:0072678)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	29						CGACGGCCCACGAGCGGATGC	0.637																																					p.H158Q		.											.	ZAP70-955	0			c.C474A						.						48	43	45					2																	98341626		2203	4300	6503	SO:0001583	missense	7535	exon4			GGCCCACGAGCGG	L05148	CCDS33254.1, CCDS33255.1	2q11-q13	2014-09-17	2002-08-29		ENSG00000115085	ENSG00000115085		"SH2 domain containing"	12858	protein-coding gene	gene with protein product		176947	"zeta-chain (TCR) associated protein kinase (70 kD)"	SRK		1423621	Standard	NM_001079		Approved	ZAP-70, STD	uc002syd.1	P43403	OTTHUMG00000153060	ENST00000264972.5:c.474C>A	2.37:g.98341626C>A	ENSP00000264972:p.His158Gln	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	75	36	NM_001079	0	0	0	0	0	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	37	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.642553	0.67244	.	.	ENSG00000115085	ENST00000264972;ENST00000442208	D;D	0.92858	-3.12;-3.12	5.37	1.01	0.19927	SH2 motif (1);	0.000000	0.50627	D	0.000112	D	0.93262	0.7853	L	0.58810	1.83	0.51012	D	0.999903	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	D	0.90788	0.4684	10	0.62326	D	0.03	.	6.7946	0.23719	0.0:0.491:0.0:0.509	.	158;32;158	B4E0E2;P43403-3;P43403	.;.;ZAP70_HUMAN	Q	158;32	ENSP00000264972:H158Q;ENSP00000411141:H32Q	ENSP00000264972:H158Q	H	+	3	2	ZAP70	97708058	0.004000	0.15560	1.000000	0.80357	0.763000	0.43281	-1.323000	0.02692	0.354000	0.24105	-0.216000	0.12614	CAC	C|0.998;T|0.002		0.637	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			A	98341626	C	A	98341626	3	1	12	1	0	0	0	0	1	0	0	0	17547	535	19	4	480	4	ZAP70	2	98341626	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	43754098	98341626	144857747	18	908											
SUMF1	285362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	4490972	4490972	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgttgaatattggtcttcActtgctcactcaacatgcct	8	15	6	12	0	4	1	3	1	1	0	4	1	4	1	2	1	3	2	2	1	3	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:4490972A>C	ENST00000272902.5	-	3	532	c.497T>G	c.(496-498)gTg>gGg	p.V166G	SUMF1_ENST00000405420.2_Missense_Mutation_p.V166G|SUMF1_ENST00000534863.1_Missense_Mutation_p.V166G|SUMF1_ENST00000458465.2_Intron|SUMF1_ENST00000383843.5_Intron	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	166					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		ATTGGTCTTCACTTGCTCACT	0.393																																					p.V166G		.											.	SUMF1-91	0			c.T497G						.						172	171	171					3																	4490972		2203	4300	6503	SO:0001583	missense	285362	exon3			GTCTTCACTTGCT	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.497T>G	3.37:g.4490972A>C	ENSP00000272902:p.Val166Gly	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	260	84	NM_001164675	0	0	42	81	39	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	37	CCDS2564.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.002331	0.74932	.	.	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000405420	D;D;D	0.97553	-4.43;-4.43;-4.43	5.53	5.53	0.82687	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.000000	0.85682	D	0.000000	D	0.97002	0.9021	L	0.41824	1.3	0.80722	D	1	D;P	0.67145	0.996;0.541	D;P	0.65684	0.937;0.566	D	0.96392	0.9290	10	0.32370	T	0.25	-14.8274	14.671	0.68945	1.0:0.0:0.0:0.0	.	166;166	E9PGL0;Q8NBK3	.;SUMF1_HUMAN	G	166	ENSP00000440421:V166G;ENSP00000272902:V166G;ENSP00000384977:V166G	ENSP00000272902:V166G	V	-	2	0	SUMF1	4465972	1.000000	0.71417	0.989000	0.46669	0.926000	0.56050	7.392000	0.79840	2.100000	0.63781	0.533000	0.62120	GTG	.		0.393	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760		C	4490972	A	C	4490972	3	2	12	1	0	0	0	0	1	0	0	0	15417	159	6	5	655	5	SUMF1	3	4490972	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		4490972	193531458	19	909											
ANO10	55129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	43618738	43618738	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcaattgtttccccaaagTagccacgaatactgtctata	13	11	7	10	1	1	0	0	0	1	0	2	2	2	0	3	0	3	3	3	0	7	6			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:43618738T>A	ENST00000292246.3	-	6	778	c.608A>T	c.(607-609)tAc>tTc	p.Y203F	ANO10_ENST00000451430.2_Missense_Mutation_p.Y92F|ANO10_ENST00000396091.3_Missense_Mutation_p.Y137F|ANO10_ENST00000414522.2_Missense_Mutation_p.Y203F|ANO10_ENST00000350459.4_Intron	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	203					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						TTCCCCAAAGTAGCCACGAAT	0.343																																					p.Y203F		.											.	ANO10-92	0			c.A608T						.						20	22	21					3																	43618738		2189	4296	6485	SO:0001583	missense	55129	exon6			CCAAAGTAGCCAC	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25519	protein-coding gene	gene with protein product		613726	"transmembrane protein 16K"	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.608A>T	3.37:g.43618738T>A	ENSP00000292246:p.Tyr203Phe	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_018075	0	0	9	21	12	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	37	CCDS2710.2	.	.	.	.	.	.	.	.	.	.	T	24.3	4.511689	0.85389	.	.	ENSG00000160746	ENST00000292246;ENST00000396091;ENST00000414522;ENST00000451430;ENST00000428472	T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.87577	0.6212	M	0.91354	3.2	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.90259	0.4299	10	0.87932	D	0	.	16.3127	0.82898	0.0:0.0:0.0:1.0	.	92;203;137;203	Q9NW15-4;C9JHS1;Q9NW15-3;Q9NW15	.;.;.;ANO10_HUMAN	F	203;137;203;92;92	ENSP00000292246:Y203F;ENSP00000379398:Y137F;ENSP00000396990:Y203F;ENSP00000394119:Y92F;ENSP00000416266:Y92F	ENSP00000292246:Y203F	Y	-	2	0	ANO10	43593742	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	8.040000	0.89188	2.246000	0.74042	0.533000	0.62120	TAC	.		0.343	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075		A	43618738	T	A	43618738	3	1	12	1	0	0	0	0	1	0	0	0	696	1638	57	5	1406	5	ANO10	3	43618738	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	39127766	43618738	154403692	20	910											
ARHGEF3	50650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56787577	56787577	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcaagtcttcttctccttgGgaaagctcaaagatcgcctg	10	12	8	11	1	5	1	2	0	3	1	7	2	5	2	2	1	1	1	2	1	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:56787577G>C	ENST00000296315.3	-	4	561	c.393C>G	c.(391-393)tcC>tcG	p.S131S	ARHGEF3_ENST00000498517.1_5'UTR|ARHGEF3_ENST00000495373.1_Silent_p.S131S|ARHGEF3_ENST00000413728.2_Silent_p.S137S|ARHGEF3_ENST00000496106.1_Silent_p.S137S|ARHGEF3_ENST00000497267.1_Silent_p.S102S|ARHGEF3_ENST00000338458.4_Silent_p.S163S	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	131	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		CTTCTCCTTGGGAAAGCTCAA	0.363																																					p.S163S		.											.	ARHGEF3-228	0			c.C489G						.						116	120	118					3																	56787577		2203	4300	6503	SO:0001819	synonymous_variant	50650	exon7			TCCTTGGGAAAGC	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"Rho guanine nucleotide exchange factors"	683	protein-coding gene	gene with protein product	"exchange factor found in platelets and leukemic and neuronal tissues, XPLN", "RhoGEF protein"	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.393C>G	3.37:g.56787577G>C		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	93	20	NM_001128615	0	0	30	47	17	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			.		0.363	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		C	56787577	G	C	56787577	2	2	12	1	0	0	0	0	0	0	0	1	904	1219	43	4		4	ARHGEF3	3	56787577	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	13168839	56787577	141234853	21	911											
TMF1	7110	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	69096768	69096770	+	In_Frame_Del	DEL	GAA	GAA	-																															ctgttttagactttggagttGaagaattaactataataggc																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:69096768_69096770delGAA	ENST00000398559.2	-	2	1302_1304	c.1086_1088delTTC	c.(1084-1089)tcttca>tca	p.362_363SS>S	CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|TMF1_ENST00000543976.1_In_Frame_Del_p.362_363SS>S|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	362					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CTTTGGAGTTGAAGAATTAACTA	0.355																																					p.362_363del		.											.	TMF1-90	0			c.1086_1088del						.																																			SO:0001651	inframe_deletion	7110	exon2			.		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.1086_1088delTTC	3.37:g.69096771_69096773delGAA	ENSP00000381567:p.Ser363del	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	98	27	NM_007114	0	0	0	0	0	B7ZLJ2|Q17R87|Q59GK0	In_Frame_Del	DEL	ENST00000398559.2	37	CCDS43105.1																																																																																			.		0.355	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		-	69096770	GAA	-	69096768	7	5	12	1	0	1	0	1	0	0	0	0	16260	1294	45	0	2257	0	TMF1	3	69096768	In_Frame_Del	DEL	GAA	TCGA-A4-7997-01A-11D-2201-08	12309191	69096768	128925662	22	912											
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69336931	69336931	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaggcctttgcattcaggAaaaacagctccacggtggtt	11	9	10	11	1	1	0	1	0	0	0	2	1	2	1	2	4	3	3	2	4	2	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:69336931A>G	ENST00000398540.3	-	5	556	c.473T>C	c.(472-474)tTc>tCc	p.F158S	FRMD4B_ENST00000542259.1_Missense_Mutation_p.F104S	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	158	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGCATTCAGGAAAAACAGCTC	0.443																																					p.F158S		.											.	FRMD4B-72	0			c.T473C						.						82	85	84					3																	69336931		1890	4113	6003	SO:0001583	missense	23150	exon5			TTCAGGAAAAACA	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.473T>C	3.37:g.69336931A>G	ENSP00000381549:p.Phe158Ser	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_015123	0	0	0	0	0	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.326829	0.81690	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000493880;ENST00000473029;ENST00000460709;ENST00000459638	D;D;D;D;D;D	0.84516	-1.52;-1.52;-1.52;-1.52;-1.52;-1.86	5.76	5.76	0.90799	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.055141	0.64402	D	0.000001	D	0.93294	0.7863	M	0.88570	2.965	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.81914	0.986;0.995	D	0.94402	0.7624	10	0.87932	D	0	-18.8637	15.0592	0.71939	1.0:0.0:0.0:0.0	.	263;158	Q6PEW6;Q9Y2L6	.;FRM4B_HUMAN	S	158;104;49;104;104;104	ENSP00000381549:F158S;ENSP00000437658:F104S;ENSP00000418962:F49S;ENSP00000418373:F104S;ENSP00000418023:F104S;ENSP00000417550:F104S	ENSP00000381549:F158S	F	-	2	0	FRMD4B	69419621	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	7.367000	0.79558	2.202000	0.70862	0.533000	0.62120	TTC	.		0.443	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			G	69336931	A	G	69336931	3	3	12	1	0	0	0	0	1	0	0	0	6071	246	9	3	2707	3	FRMD4B	3	69336931	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	240163	69336931	128685499	23	913											
EAF2	55840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121591418	121591418	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctagtctaatggaccagatGagtagttgtgatagttcatc	11	13	11	6	0	2	3	1	2	1	1	3	4	2	4	1	1	0	4	1	1	4	6			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:121591418G>A	ENST00000273668.2	+	5	590	c.519G>A	c.(517-519)atG>atA	p.M173I	EAF2_ENST00000451944.2_Missense_Mutation_p.M173I	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	173					apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	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)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TGGACCAGATGAGTAGTTGTG	0.313																																					p.M173I	Esophageal Squamous(194;1942 2097 24663 29345 31866)	.											.	EAF2-90	0			c.G519A						.						120	123	122					3																	121591418		2203	4300	6503	SO:0001583	missense	55840	exon5			CCAGATGAGTAGT	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.519G>A	3.37:g.121591418G>A	ENSP00000273668:p.Met173Ile	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	288	154	NM_018456	0	0	5	12	7	Q9NZ82	Missense_Mutation	SNP	ENST00000273668.2	37	CCDS3006.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.127060	0.56721	.	.	ENSG00000145088	ENST00000273668;ENST00000451944	.	.	.	4.74	4.74	0.60224	.	0.135191	0.64402	D	0.000004	T	0.62258	0.2413	M	0.77820	2.39	0.47862	D	0.999539	B	0.30406	0.278	B	0.27887	0.084	T	0.62243	-0.6895	9	0.29301	T	0.29	-9.0448	15.2478	0.73521	0.0:0.0:1.0:0.0	.	173	Q96CJ1	EAF2_HUMAN	I	173	.	ENSP00000273668:M173I	M	+	3	0	EAF2	123074108	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.397000	0.79903	2.456000	0.83038	0.305000	0.20034	ATG	.		0.313	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456		A	121591418	G	A	121591418	3	1	12	1	0	0	0	0	1	0	0	0	4887	1290	45	2	537	2	EAF2	3	121591418	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	52254487	121591418	76431012	24	914											
COL6A6	131873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	130287032	130287032	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accagatcgggtgcaaattgGtgtagtccagttcagcgaca	11	9	12	9	2	1	1	1	0	0	1	3	2	2	1	2	2	2	3	2	2	2	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:130287032G>A	ENST00000358511.6	+	5	2016	c.1985G>A	c.(1984-1986)gGt>gAt	p.G662D	COL6A6_ENST00000453409.2_Missense_Mutation_p.G662D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	662	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						GTGCAAATTGGTGTAGTCCAG	0.408																																					p.G662D		.											.	COL6A6-76	0			c.G1985A						.						176	171	173					3																	130287032		1915	4119	6034	SO:0001583	missense	131873	exon5			AAATTGGTGTAGT	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.1985G>A	3.37:g.130287032G>A	ENSP00000351310:p.Gly662Asp	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	297	79	NM_001102608	0	0	0	0	0	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654369	0.47467	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.82711	-1.64;-1.64	5.53	5.53	0.82687	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000018	D	0.93350	0.7880	H	0.94886	3.595	0.54753	D	0.999986	D	0.89917	1.0	D	0.87578	0.998	D	0.94709	0.7890	10	0.87932	D	0	.	14.6487	0.68780	0.0:0.1454:0.8546:0.0	.	662	A6NMZ7	CO6A6_HUMAN	D	662	ENSP00000351310:G662D;ENSP00000399236:G662D	ENSP00000351310:G662D	G	+	2	0	COL6A6	131769722	1.000000	0.71417	0.353000	0.25747	0.014000	0.08584	5.227000	0.65305	2.616000	0.88540	0.655000	0.94253	GGT	.		0.408	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130287032	G	A	130287032	3	1	12	1	0	0	0	0	1	0	0	0	3709	1261	44	2	2003	2	COL6A6	3	130287032	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	8695614	130287032	67735398	25	915											
CP	1356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	148930432	148930432	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagataaagggccttcttaTatagtctcccaattctatct	12	14	6	9	0	4	1	0	0	4	1	5	2	4	1	2	1	0	0	2	1	8	7	rs141532762		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:148930432T>C	ENST00000264613.6	-	2	462	c.200A>G	c.(199-201)tAt>tGt	p.Y67C		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	67	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GGCCTTCTTATATAGTCTCCC	0.388																																					p.Y67C		.											.	CP-515	0			c.A200G						.	T	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	74	73	73		200	5.4	0.5	3	dbSNP_134	73	0,8600		0,0,4300	no	missense	CP	NM_000096.3	194	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging	67/1066	148930432	1,13005	2203	4300	6503	SO:0001583	missense	1356	exon2			TTCTTATATAGTC	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.200A>G	3.37:g.148930432T>C	ENSP00000264613:p.Tyr67Cys	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	66	29	NM_000096	0	0	3	5	2	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.636271	0.67130	2.27E-4	0.0	ENSG00000047457	ENST00000264613;ENST00000455472	D;D	0.99277	-5.67;-5.67	5.42	5.42	0.78866	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	M	0.92784	3.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.984;0.993	D	0.98194	1.0464	10	0.87932	D	0	-24.6173	15.6278	0.76874	0.0:0.0:0.0:1.0	.	67;67	A8K5A4;P00450	.;CERU_HUMAN	C	67;107	ENSP00000264613:Y67C;ENSP00000426888:Y107C	ENSP00000264613:Y67C	Y	-	2	0	CP	150413122	1.000000	0.71417	0.500000	0.27589	0.701000	0.40568	7.525000	0.81892	2.280000	0.76307	0.460000	0.39030	TAT	T|1.000;C|0.000		0.388	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		C	148930432	T	C	148930432	3	2	12	1	0	0	0	0	1	0	0	0	3793	1406	49	3	3069	3	CP	3	148930432	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	18643400	148930432	49091998	26	916											
CLCN2	1181	hgsc.bcm.edu;broad.mit.edu	37	chr3	184071155	184071155	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgggctgggctcagctgggcCcccaacaatgccaccacctg	7	5	12	17	1	1	0	1	0	0	0	1	0	1	0	5	3	3	3	5	3	2	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:184071155C>A	ENST00000265593.4	-	17	2082	c.1911G>T	c.(1909-1911)ggG>ggT	p.G637G	CLCN2_ENST00000457512.1_Silent_p.G637G|CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000434054.2_Silent_p.G593G|CLCN2_ENST00000423355.2_3'UTR|CLCN2_ENST00000344937.7_Silent_p.G620G|EIF2B5_ENST00000444495.1_Intron	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	637	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	TCAGCTGGGCCCCCAACAATG	0.637																																					p.G637G		.											.	CLCN2-90	0			c.G1911T						.						29	31	31					3																	184071155		2201	4298	6499	SO:0001819	synonymous_variant	1181	exon17			CTGGGCCCCCAAC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.1911G>T	3.37:g.184071155C>A		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	68	31	NM_004366	0	0	6	21	15	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Silent	SNP	ENST00000265593.4	37	CCDS3263.1																																																																																			.		0.637	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			A	184071155	C	A	184071155	2	1	12	1	0	0	0	0	0	0	0	1	3469	610	22	4		4	CLCN2	3	184071155	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	35140723	184071155	13951275	27	917											
HTT	3064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	3156098	3156098	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggagaaagaaccaggagaaCaagcatctgtaccgttgagt	16	6	12	7	1	1	4	0	1	1	3	1	6	1	4	2	2	4	3	2	2	5	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:3156098C>A	ENST00000355072.5	+	27	3722	c.3577C>A	c.(3577-3579)Caa>Aaa	p.Q1193K		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1193					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ACCAGGAGAACAAGCATCTGT	0.498																																					p.Q1193K		.											.	HTT-281	0			c.C3577A						.						55	53	54					4																	3156098		2049	4207	6256	SO:0001583	missense	3064	exon27			GGAGAACAAGCAT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.3577C>A	4.37:g.3156098C>A	ENSP00000347184:p.Gln1193Lys	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	33	9	NM_002111	0	0	17	27	10	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.061554	0.36373	.	.	ENSG00000197386	ENST00000355072	T	0.05081	3.5	5.2	5.2	0.72013	.	0.378699	0.27906	N	0.017370	T	0.07683	0.0193	L	0.43152	1.355	0.27971	N	0.936396	B	0.20887	0.049	B	0.19148	0.024	T	0.21143	-1.0254	10	0.17832	T	0.49	.	16.9201	0.86162	0.0:1.0:0.0:0.0	.	1193	P42858	HD_HUMAN	K	1193	ENSP00000347184:Q1193K	ENSP00000347184:Q1193K	Q	+	1	0	HTT	3125896	0.989000	0.36119	0.644000	0.29465	0.961000	0.63080	3.195000	0.51013	2.430000	0.82344	0.557000	0.71058	CAA	.		0.498	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3156098	C	A	3156098	3	1	12	1	0	0	0	0	1	0	0	0	7478	479	17	4	3683	4	HTT	4	3156098	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		3156098	187998178	28	918											
TECRL	253017	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	65180367	65180367	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtgtgtgtatcacttactGtaccactgggtggcgtaatc	7	14	12	8	1	1	0	1	0	0	0	2	0	1	0	1	2	2	3	1	2	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:65180367G>A	ENST00000381210.3	-	5	660	c.550C>T	c.(550-552)Cac>Tac	p.H184Y	TECRL_ENST00000507440.1_Splice_Site_p.H184Y|TECRL_ENST00000513125.1_5'UTR	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	184					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						ATCACTTACTGTACCACTGGG	0.428																																					p.H184Y		.											.	TECRL-90	0			c.C550T						.						83	76	78					4																	65180367		2203	4300	6503	SO:0001630	splice_region_variant	253017	exon5			CTTACTGTACCAC	AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"glycoprotein, synaptic 2-like"					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.551+1C>T	4.37:g.65180367G>A		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	33	10	NM_001010874	0	0	0	0	0		Missense_Mutation	SNP	ENST00000381210.3	37	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191677	0.78902	.	.	ENSG00000205678	ENST00000507440;ENST00000381210	T;T	0.42900	0.96;0.96	5.7	5.7	0.88788	.	0.124523	0.52532	D	0.000077	T	0.64832	0.2634	M	0.85777	2.775	0.80722	D	1	D;D	0.67145	0.996;0.993	D;P	0.78314	0.991;0.866	T	0.63537	-0.6615	10	0.07644	T	0.81	-12.79	16.5536	0.84479	0.0:0.0:1.0:0.0	.	184;184	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	Y	184	ENSP00000426043:H184Y;ENSP00000370607:H184Y	ENSP00000370607:H184Y	H	-	1	0	TECRL	64862962	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	4.899000	0.63245	2.689000	0.91719	0.591000	0.81541	CAC	.		0.428	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	Missense_Mutation	A	65180367	G	A	65180367	5	1	12	1	0	0	0	0	0	0	1	0	15778	1391	48	2	573	2	TECRL	4	65180367	Splice_Site	SNP	G	TCGA-A4-7997-01A-11D-2201-08	62024269	65180367	125973909	29	919											
SEPT11	55752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	77941678	77941678	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaatgaaaatcattgcgatTttgtgaaacttcgagagatg	15	12	10	4	2	1	4	1	2	0	2	2	7	1	4	0	0	2	0	0	0	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:77941678T>G	ENST00000264893.6	+	7	1009	c.808T>G	c.(808-810)Ttt>Gtt	p.F270V	SEPT11_ENST00000502584.1_Missense_Mutation_p.F270V|SEPT11_ENST00000541121.1_Missense_Mutation_p.F280V|SEPT11_ENST00000512575.1_Intron|SEPT11_ENST00000505788.1_Missense_Mutation_p.F270V|SEPT11_ENST00000510515.1_Missense_Mutation_p.F280V	NM_018243.2	NP_060713.1	Q9NVA2	SEP11_HUMAN	septin 11	270	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)|protein heterooligomerization (GO:0051291)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|septin complex (GO:0031105)|stress fiber (GO:0001725)|synapse (GO:0045202)	GTP binding (GO:0005525)			endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	11						TCATTGCGATTTTGTGAAACT	0.468																																					p.F270V		.											.	SEPT11-68	0			c.T808G						.						96	93	94					4																	77941678		2203	4300	6503	SO:0001583	missense	55752	exon7			TGCGATTTTGTGA	AK001711	CCDS34018.1	4q21.1	2013-01-21			ENSG00000138758	ENSG00000138758		"Septins"	25589	protein-coding gene	gene with protein product		612887				14999297, 15140406	Standard	NM_018243		Approved	FLJ10849	uc003hkj.3	Q9NVA2	OTTHUMG00000160854	ENST00000264893.6:c.808T>G	4.37:g.77941678T>G	ENSP00000264893:p.Phe270Val	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	157	52	NM_018243	1	0	60	135	74	B7Z7Z6|E9KL32|Q4W5G1|Q7L4N1|Q96SP1|Q9UFY9	Missense_Mutation	SNP	ENST00000264893.6	37	CCDS34018.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.015347	0.93404	.	.	ENSG00000138758	ENST00000264893;ENST00000502584;ENST00000510641;ENST00000505788;ENST00000510515;ENST00000541121	T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35;-0.35	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.88724	0.6514	H	0.98388	4.22	0.58432	D	0.999996	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.80764	0.99;0.989;0.994	D	0.93076	0.6487	10	0.87932	D	0	.	15.1435	0.72630	0.0:0.0:0.0:1.0	.	280;262;270	Q9NVA2-2;D6RDU5;Q9NVA2	.;.;SEP11_HUMAN	V	270;270;262;270;280;280	ENSP00000264893:F270V;ENSP00000426344:F270V;ENSP00000420839:F262V;ENSP00000424925:F270V;ENSP00000422896:F280V;ENSP00000443701:F280V	ENSP00000264893:F270V	F	+	1	0	SEPT11	78160702	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	1.975000	0.57531	0.482000	0.46254	TTT	.		0.468	SEPT11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362676.1	NM_018243		G	77941678	T	G	77941678	3	3	12	1	0	0	0	0	1	0	0	0	14093	1841	64	5	834	5	SEPT11	4	77941678	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	12761311	77941678	113212598	30	920											
LARP1B	55132	hgsc.bcm.edu	37	chr4	128998994	128998994	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccacaaaatagaaaagaaAaagaagagaaggttgaaaag	25	3	10	3	0	0	5	0	1	0	4	0	6	0	5	1	1	1	1	1	1	11	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:128998994A>C	ENST00000326639.6	+	4	305	c.94A>C	c.(94-96)Aaa>Caa	p.K32Q	LARP1B_ENST00000512292.1_Missense_Mutation_p.K32Q|LARP1B_ENST00000427266.1_Missense_Mutation_p.K32Q|LARP1B_ENST00000354456.3_5'UTR|LARP1B_ENST00000264584.5_Missense_Mutation_p.K32Q|LARP1B_ENST00000432347.2_Missense_Mutation_p.K32Q|LARP1B_ENST00000441387.1_Missense_Mutation_p.K32Q|LARP1B_ENST00000394288.3_Missense_Mutation_p.K32Q	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	32						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TAGAAAAGAAAAAGAAGAGAA	0.363																																					p.K32Q		.											.	LARP1B-68	0			c.A94C						.						55	58	57					4																	128998994		2203	4300	6503	SO:0001583	missense	55132	exon4			AAAGAAAAAGAAG		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"La ribonucleoprotein domain containing"	24704	protein-coding gene	gene with protein product			"La ribonucleoprotein domain family, member 2"	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.94A>C	4.37:g.128998994A>C	ENSP00000321997:p.Lys32Gln	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_032239	0	0	53	53	0	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.170063	0.38315	.	.	ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000394288;ENST00000432347;ENST00000264584;ENST00000441387;ENST00000427266	T;T;T;T;T;T;T;T	0.48836	1.83;1.42;1.31;0.83;0.8;1.77;1.84;1.41	3.83	2.61	0.31194	.	0.451995	0.22773	N	0.055806	T	0.47857	0.1468	L	0.52573	1.65	0.80722	D	1	B;P;P;D	0.55800	0.22;0.934;0.796;0.973	B;P;B;P	0.51657	0.109;0.559;0.43;0.676	T	0.31251	-0.9950	10	0.22706	T	0.39	.	10.2386	0.43299	0.833:0.167:0.0:0.0	.	32;32;32;32	Q659C4;G3XAJ5;Q659C4-3;G3V0E9	LAR1B_HUMAN;.;.;.	Q	32	ENSP00000321997:K32Q;ENSP00000422850:K32Q;ENSP00000427281:K32Q;ENSP00000377829:K32Q;ENSP00000390395:K32Q;ENSP00000264584:K32Q;ENSP00000396521:K32Q;ENSP00000403586:K32Q	ENSP00000264584:K32Q	K	+	1	0	LARP1B	129218444	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.720000	0.38022	0.626000	0.30322	0.386000	0.25728	AAA	.		0.363	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078		C	128998994	A	C	128998994	3	2	12	1	0	0	0	0	1	0	0	0	8650	15	1	5	100	5	LARP1B	4	128998994	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	51057316	128998994	62155282	31	921											
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	36984988	36984988	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccataaaaaagcctgaagAaatcaaacaatgtaatgatg	20	8	6	7	0	1	3	1	2	0	1	2	3	2	3	2	0	2	1	2	0	8	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:36984988A>T	ENST00000282516.8	+	10	2205	c.1706A>T	c.(1705-1707)gAa>gTa	p.E569V	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Missense_Mutation_p.E569V	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	569					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AAGCCTGAAGAAATCAAACAA	0.393																																					p.E569V		.											.	NIPBL-293	0			c.A1706T						.						92	96	94					5																	36984988		2203	4300	6503	SO:0001583	missense	25836	exon10			CTGAAGAAATCAA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1706A>T	5.37:g.36984988A>T	ENSP00000282516:p.Glu569Val	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	179	72	NM_015384	0	0	18	29	11	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.974280	0.34848	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.94417	-3.41;-3.42	5.98	5.98	0.97165	.	0.120361	0.64402	D	0.000018	D	0.90933	0.7150	N	0.19112	0.55	0.42318	D	0.992241	P;P	0.48503	0.856;0.911	B;P	0.44561	0.266;0.453	D	0.91908	0.5537	10	0.49607	T	0.09	.	16.4781	0.84144	1.0:0.0:0.0:0.0	.	569;569	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	V	569	ENSP00000282516:E569V;ENSP00000406266:E569V	ENSP00000282516:E569V	E	+	2	0	NIPBL	37020745	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.883000	0.69721	2.288000	0.76882	0.528000	0.53228	GAA	.		0.393	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		T	36984988	A	T	36984988	3	4	12	1	0	0	0	0	1	0	0	0	10454	246	9	5	1740	5	NIPBL	5	36984988	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		36984988	143930272	32	922											
ARHGAP26	23092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	142416823	142416823	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatccatgctgtggaaaccAgaggtaaagtagtttaacag	14	9	11	7	0	0	1	0	0	0	1	1	2	1	2	2	2	3	5	2	2	5	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:142416823A>G	ENST00000274498.4	+	13	1585	c.1207A>G	c.(1207-1209)Aga>Gga	p.R403G	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.R403G	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	403	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTGGAAACCAGAGGTAAAGT	0.468																																					p.R403G		.											.	ARHGAP26-660	0			c.A1207G						.						127	106	113					5																	142416823		2203	4300	6503	SO:0001583	missense	23092	exon13			GAAACCAGAGGTA	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1207A>G	5.37:g.142416823A>G	ENSP00000274498:p.Arg403Gly	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	81	41	NM_015071	0	0	0	0	0	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.144516	0.77888	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.21031	2.03;2.03	5.84	4.64	0.57946	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.42268	0.1195	M	0.85945	2.785	0.58432	D	0.999996	P;D	0.53619	0.924;0.961	P;P	0.54590	0.508;0.756	T	0.42241	-0.9463	10	0.49607	T	0.09	.	12.0971	0.53761	0.856:0.144:0.0:0.0	.	403;403	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	G	403	ENSP00000274498:R403G;ENSP00000367243:R403G	ENSP00000274498:R403G	R	+	1	2	ARHGAP26	142397016	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.389000	0.52516	0.988000	0.38734	0.455000	0.32223	AGA	.		0.468	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		G	142416823	A	G	142416823	3	3	12	1	0	0	0	0	1	0	0	0	875	180	7	3	1257	3	ARHGAP26	5	142416823	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	105431835	142416823	38498437	33	923											
JAKMIP2	9832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	147000262	147000262	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagagcttgttttctgtaGtctagttcttcctccagata	8	17	7	9	0	4	2	1	0	3	2	6	2	6	2	2	0	1	4	2	0	4	8			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:147000262G>T	ENST00000265272.5	-	18	2576	c.2109C>A	c.(2107-2109)gaC>gaA	p.D703E	JAKMIP2_ENST00000333010.6_Missense_Mutation_p.D661E|JAKMIP2_ENST00000507386.1_Missense_Mutation_p.D682E	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	703						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTTTCTGTAGTCTAGTTCTT	0.388																																					p.D703E		.											.	JAKMIP2-154	0			c.C2109A						.						308	258	275					5																	147000262		2203	4300	6503	SO:0001583	missense	9832	exon18			TCTGTAGTCTAGT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.2109C>A	5.37:g.147000262G>T	ENSP00000265272:p.Asp703Glu	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	176	85	NM_001270941	0	0	0	0	0	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287394	0.59976	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.25912	1.8;1.77;1.78	5.66	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.41558	0.1164	M	0.64404	1.975	0.49389	D	0.999788	D;D;D;D	0.61697	0.99;0.99;0.99;0.99	D;D;D;D	0.70935	0.971;0.971;0.971;0.971	T	0.22347	-1.0219	10	0.15952	T	0.53	.	10.5305	0.44973	0.1413:0.0:0.8587:0.0	.	661;703;682;703	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	E	682;703;661;682	ENSP00000421398:D682E;ENSP00000265272:D703E;ENSP00000328989:D661E	ENSP00000265272:D703E	D	-	3	2	JAKMIP2	146980455	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.966000	0.40481	0.817000	0.34445	0.591000	0.81541	GAC	.		0.388	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		T	147000262	G	T	147000262	3	4	12	1	0	0	0	0	1	0	0	0	7962	1020	36	4	339	4	JAKMIP2	5	147000262	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	4583439	147000262	33914998	34	924											
C5orf41	153222	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	172518026	172518026	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agaaaaaagggatggagcctCttcaaggtcatgccactccc	13	7	10	11	0	3	1	2	0	1	1	4	3	4	3	3	3	2	0	3	3	4	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:172518026C>G	ENST00000296953.2	+	4	1163	c.844C>G	c.(844-846)Ctt>Gtt	p.L282V	CREBRF_ENST00000520420.1_Missense_Mutation_p.L282V|CREBRF_ENST00000522692.1_Missense_Mutation_p.L282V|CREBRF_ENST00000540014.1_Missense_Mutation_p.L282V	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	282					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GATGGAGCCTCTTCAAGGTCA	0.522																																					p.L282V		.											.	.	0			c.C844G						.						60	61	60					5																	172518026		2203	4300	6503	SO:0001583	missense	153222	exon4			GAGCCTCTTCAAG	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.844C>G	5.37:g.172518026C>G	ENSP00000296953:p.Leu282Val	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	96	26	NM_153607	0	0	9	21	12	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	37	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	C	3.060	-0.193550	0.06259	.	.	ENSG00000164463	ENST00000522692;ENST00000296953;ENST00000540014;ENST00000520420;ENST00000538538;ENST00000393776	T;T	0.43294	0.95;0.95	5.29	2.49	0.30216	.	0.733387	0.13308	N	0.397700	T	0.23766	0.0575	N	0.24115	0.695	0.09310	N	1	B;B	0.25609	0.039;0.13	B;B	0.24269	0.052;0.043	T	0.27191	-1.0081	10	0.07482	T	0.82	.	8.0149	0.30374	0.1291:0.7322:0.0:0.1387	.	282;282	Q8IUR6;Q8IUR6-2	CE041_HUMAN;.	V	282	ENSP00000296953:L282V;ENSP00000440075:L282V	ENSP00000296953:L282V	L	+	1	0	C5orf41	172450632	0.996000	0.38824	0.050000	0.19076	0.931000	0.56810	3.394000	0.52551	0.215000	0.20761	0.563000	0.77884	CTT	.		0.522	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		G	172518026	C	G	172518026	3	3	12	1	0	0	0	0	1	0	0	0	2306	913	32	4	854	4	C5orf41	5	172518026	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	25517764	172518026	8397234	35	925											
SPDEF	25803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	34512076	34512076	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtagaaggcggacaggccctGctcgggcgtggcgggtggac	6	5	20	10	4	0	1	0	0	0	1	1	3	0	3	1	7	1	2	1	7	2	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr6:34512076G>T	ENST00000374037.3	-	2	571	c.157C>A	c.(157-159)Cag>Aag	p.Q53K	SPDEF_ENST00000544425.1_Missense_Mutation_p.Q53K	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	53					cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						GACAGGCCCTGCTCGGGCGTG	0.687																																					p.Q53K		.											.	SPDEF-653	0			c.C157A						.						35	40	38					6																	34512076		2203	4300	6503	SO:0001583	missense	25803	exon2			GGCCCTGCTCGGG	AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"SAM pointed domain containing ets transcription factor"			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.157C>A	6.37:g.34512076G>T	ENSP00000363149:p.Gln53Lys	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	79	18	NM_001252294	0	0	0	0	0	B4DWH8|F5H778	Missense_Mutation	SNP	ENST00000374037.3	37	CCDS4794.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534021	0.45073	.	.	ENSG00000124664	ENST00000374037;ENST00000544425	T;T	0.14022	2.54;2.73	4.97	4.97	0.65823	.	0.498805	0.17278	N	0.180107	T	0.04452	0.0122	L	0.27053	0.805	0.28482	N	0.914903	B;B	0.25904	0.137;0.085	B;B	0.25140	0.058;0.026	T	0.26121	-1.0112	10	0.35671	T	0.21	.	13.5867	0.61935	0.0:0.1561:0.8439:0.0	.	53;53	F5H778;O95238	.;SPDEF_HUMAN	K	53	ENSP00000363149:Q53K;ENSP00000442715:Q53K	ENSP00000363149:Q53K	Q	-	1	0	SPDEF	34620054	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.798000	0.62510	2.286000	0.76751	0.591000	0.81541	CAG	.		0.687	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		T	34512076	G	T	34512076	3	4	12	1	0	0	0	0	1	0	0	0	15058	1328	46	4	870	4	SPDEF	6	34512076	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08		34512076	136602991	36	926											
SNX9	51429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	158288583	158288583	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctccactcctgataggctcGggttatgtatgattttgctg	6	16	10	9	1	1	2	0	2	1	0	4	2	2	2	2	2	1	4	2	2	3	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr6:158288583G>A	ENST00000392185.3	+	2	188	c.17G>A	c.(16-18)cGg>cAg	p.R6Q		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	6	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		TGATAGGCTCGGGTTATGTAT	0.393																																					p.R6Q		.											.	SNX9-226	0			c.G17A						.						171	140	150					6																	158288583		2203	4300	6503	SO:0001583	missense	51429	exon2			AGGCTCGGGTTAT	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.17G>A	6.37:g.158288583G>A	ENSP00000376024:p.Arg6Gln	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	72	23	NM_016224	0	0	0	0	0	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	37	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908097	0.52333	.	.	ENSG00000130340	ENST00000539592;ENST00000392185	T	0.24350	1.86	5.22	4.33	0.51752	Src homology-3 domain (3);	0.434714	0.25546	N	0.029934	T	0.11281	0.0275	L	0.42686	1.345	0.80722	D	1	B	0.29936	0.262	B	0.26770	0.073	T	0.03514	-1.1029	10	0.45353	T	0.12	-7.1352	12.8925	0.58080	0.0:0.164:0.836:0.0	.	6	Q9Y5X1	SNX9_HUMAN	Q	6	ENSP00000376024:R6Q	ENSP00000376024:R6Q	R	+	2	0	SNX9	158208571	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.078000	0.57606	1.204000	0.43247	0.655000	0.94253	CGG	.		0.393	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1			A	158288583	G	A	158288583	3	1	12	1	0	0	0	0	1	0	0	0	14941	1116	39	1	23	1	SNX9	6	158288583	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	123776507	158288583	12826484	37	927											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116417463	116417463	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcattttggttgtgtatatCatgggactttgttggacaat	8	17	12	4	0	1	0	1	0	0	0	1	2	1	2	0	4	0	4	0	4	3	7	rs121913244		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr7:116417463C>T	ENST00000318493.6	+	16	3521	c.3334C>T	c.(3334-3336)Cat>Tat	p.H1112Y	MET_ENST00000539704.1_5'UTR|MET_ENST00000397752.3_Missense_Mutation_p.H1094Y			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.H1112Y(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTGTGTATATCATGGGACTTT	0.343			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.H1112Y		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.C3334T	GRCh37	CM993668	MET	M	rs121913244	.						188	175	179					7																	116417463		1832	4086	5918	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GTATATCATGGGA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3334C>T	7.37:g.116417463C>T	ENSP00000317272:p.His1112Tyr	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	276	144	NM_001127500	0	0	280	825	545	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615896	0.87359	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.33654	1.4;1.4	5.29	5.29	0.74685	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43919	0.1269	N	0.11364	0.135	0.80722	D	1	P;D	0.89917	0.937;1.0	P;D	0.91635	0.854;0.999	T	0.52711	-0.8539	10	0.51188	T	0.08	-16.8984	19.2953	0.94119	0.0:1.0:0.0:0.0	.	1112;1094	P08581-2;P08581	.;MET_HUMAN	Y	1094;1112	ENSP00000380860:H1094Y;ENSP00000317272:H1112Y	ENSP00000317272:H1112Y	H	+	1	0	MET	116204699	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.628000	0.89032	0.655000	0.94253	CAT	.		0.343	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116417463	C	T	116417463	3	4	12	1	0	0	0	0	1	0	0	0	9510	826	29	2	3392	2	MET	7	116417463	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		116417463	42721200	38	928											
CTTNBP2	83992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	117365303	117365303	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgacgccattccacagcttaGacatccacctagcaggagag	12	7	9	13	1	0	3	0	1	0	2	2	4	2	3	4	1	2	2	4	1	2	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr7:117365303G>C	ENST00000160373.3	-	18	4155	c.4064C>G	c.(4063-4065)tCt>tGt	p.S1355C		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1355					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CCACAGCTTAGACATCCACCT	0.468																																					p.S1355C		.											.	CTTNBP2-94	0			c.C4064G						.						138	134	135					7																	117365303		2203	4300	6503	SO:0001583	missense	83992	exon18			AGCTTAGACATCC		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4064C>G	7.37:g.117365303G>C	ENSP00000160373:p.Ser1355Cys	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	326	72	NM_033427	0	0	0	0	0	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864762	0.51482	.	.	ENSG00000077063	ENST00000160373	D	0.91068	-2.78	5.72	5.72	0.89469	.	0.267144	0.43416	D	0.000578	D	0.87557	0.6207	L	0.41824	1.3	0.80722	D	1	B	0.14012	0.009	B	0.15484	0.013	T	0.81274	-0.1007	10	0.23891	T	0.37	9.6033	20.244	0.98389	0.0:0.0:1.0:0.0	.	1355	Q8WZ74	CTTB2_HUMAN	C	1355	ENSP00000160373:S1355C	ENSP00000160373:S1355C	S	-	2	0	CTTNBP2	117152539	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.149000	0.71795	2.865000	0.98341	0.655000	0.94253	TCT	.		0.468	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		C	117365303	G	C	117365303	3	2	12	1	0	0	0	0	1	0	0	0	4051	942	33	4	951	4	CTTNBP2	7	117365303	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	947840	117365303	41773360	39	929											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151917756	151917756	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaactgtaactgtgaggctCtgtaactgagtcatccctga	10	11	11	9	0	2	3	1	3	1	0	3	4	3	4	1	2	3	3	1	2	3	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr7:151917756C>A	ENST00000262189.6	-	23	3782	c.3564G>T	c.(3562-3564)caG>caT	p.Q1188H	KMT2C_ENST00000355193.2_Missense_Mutation_p.Q1188H	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1188					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CTGTGAGGCTCTGTAACTGAG	0.408																																					p.Q1188H		.											.	MLL3-1398	0			c.G3564T						.						72	69	70					7																	151917756		2203	4298	6501	SO:0001583	missense	58508	exon23			GAGGCTCTGTAAC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3564G>T	7.37:g.151917756C>A	ENSP00000262189:p.Gln1188His	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	163	71	NM_170606	0	0	15	25	10	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.948672	0.53186	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.85171	-1.95;-1.95	4.44	3.56	0.40772	.	0.000000	0.41605	U	0.000856	D	0.89763	0.6809	L	0.56769	1.78	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.75484	0.986;0.971	D	0.89849	0.4008	10	0.66056	D	0.02	.	12.545	0.56195	0.0:0.9173:0.0:0.0827	.	1188;249	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	H	1188	ENSP00000262189:Q1188H;ENSP00000347325:Q1188H	ENSP00000262189:Q1188H	Q	-	3	2	MLL3	151548689	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.614000	0.61183	0.976000	0.38417	0.484000	0.47621	CAG	.		0.408	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151917756	C	A	151917756	3	1	12	1	0	0	0	0	1	0	0	0	9647	912	32	4	11319	4	MLL3	7	151917756	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	34552453	151917756	7220907	40	930											
RP1L1	94137	broad.mit.edu	37	chr8	10470573	10470573	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgccgtgagggcgctggcCctgcccatcctccgggacca	4	6	14	17	3	0	1	0	1	0	0	2	2	2	2	6	3	2	2	6	3	0	0	rs73201157	byFrequency	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr8:10470573C>T	ENST00000382483.3	-	4	1258	c.1035G>A	c.(1033-1035)agG>agA	p.R345R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	345					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGGCGCTGGCCCTGCCCATCC	0.657													C|||	4	0.000798722	0	0	5008	,	,		16066	0		0.004	False		,,,				2504	0				p.R345R													.	RP1L1-139	0			c.G1035A						.	C		0,4218		0,0,2109	57	63	61		1035	4.3	0.7	8	dbSNP_130	61	6,8446		0,6,4220	no	coding-synonymous	RP1L1	NM_178857.5		0,6,6329	TT,TC,CC		0.071,0.0,0.0474		345/2401	10470573	6,12664	2109	4226	6335	SO:0001819	synonymous_variant	94137	exon4			GCTGGCCCTGCCC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1035G>A	8.37:g.10470573C>T		Somatic	169	1		WXS	Illumina HiSeq	Phase_I	132	5	NM_178857	0	0	0	0	0	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.999;T|0.001		0.657	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10470573	C	T	10470573	2	4	12	1	0	0	0	0	0	0	0	1	13565	622	22	2		2	RP1L1	8	10470573	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08		10470573	135893449	41	931											
FAM160B2	64760	broad.mit.edu	37	chr8	21953846	21953847	+	Splice_Site	DEL	AG	AG	-																															cttgtttcccaaacatcattAgatgaaagcacccccgccaa																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr8:21953846_21953847delAG	ENST00000289921.7	+	3	170		c.e3-1			NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2											endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						AAACATCATTAGATGAAAGCAC	0.564																																					.													.	.	0			.						.																																			SO:0001630	splice_region_variant	64760	.			ATCATTAGATGAA	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"retinoic acid induced 16"	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.125-1AG>-	8.37:g.21953846_21953847delAG		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	7	5	.	0	0	0	0	0	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Splice_Site	DEL	ENST00000289921.7	37	CCDS6021.2																																																																																			.		0.564	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		Intron	-	21953847	AG	-	21953846	8	5	12	1	0	1	0	1	0	0	1	0	5487	434	15	0	133	0	FAM160B2	8	21953846	Splice_Site	DEL	AG	TCGA-A4-7997-01A-11D-2201-08	11483273	21953846	124410176	42	932											
IDO2	169355	hgsc.bcm.edu	37	chr8	39862889	39862889	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgcaggcatccggatcttTctctctgggtaagtatagtt	8	15	10	8	1	3	0	0	0	3	0	5	1	4	1	1	3	1	5	1	3	4	6			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr8:39862889T>C	ENST00000389060.4	+	8	711	c.711T>C	c.(709-711)ttT>ttC	p.F237F	IDO2_ENST00000502986.2_Silent_p.F250F|IDO2_ENST00000343295.4_Intron			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	237					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						TCCGGATCTTTCTCTCTGGGT	0.398																																					p.F250F		.											.	IDO2-24	0			c.T750C						.						190	162	171					8																	39862889		1876	4108	5984	SO:0001819	synonymous_variant	169355	exon9			GATCTTTCTCTCT	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"indoleamine-pyrrole 2,3 dioxygenase-like 1"	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.711T>C	8.37:g.39862889T>C		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_194294	0	0	0	0	0	A4UD41	Silent	SNP	ENST00000389060.4	37																																																																																				.		0.398	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		C	39862889	T	C	39862889	2	2	12	1	0	0	0	0	0	0	0	1	7523	1780	62	3		3	IDO2	8	39862889	Silent	SNP	T	TCGA-A4-7997-01A-11D-2201-08	17909043	39862889	106501133	43	933											
CDH17	1015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	95201459	95201459	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggccttcataaatagaaaAtgtcatgggtttcaggggtc	11	13	11	6	0	3	1	3	0	0	1	4	1	3	1	1	4	0	1	1	4	5	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr8:95201459A>C	ENST00000027335.3	-	3	230	c.106T>G	c.(106-108)Ttt>Gtt	p.F36V	CDH17_ENST00000441892.2_Missense_Mutation_p.F36V|CDH17_ENST00000450165.2_Missense_Mutation_p.F36V	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	36	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TAAATAGAAAATGTCATGGGT	0.403																																					p.F36V		.											.	CDH17-96	0			c.T106G						.						118	120	119					8																	95201459		2203	4300	6503	SO:0001583	missense	1015	exon3			TAGAAAATGTCAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.106T>G	8.37:g.95201459A>C	ENSP00000027335:p.Phe36Val	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	97	76	NM_004063	0	0	1	17	16	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	37	CCDS6260.1	.	.	.	.	.	.	.	.	.	.	A	9.966	1.224134	0.22457	.	.	ENSG00000079112	ENST00000027335;ENST00000441892;ENST00000450165;ENST00000521491	T;T;T;T	0.60040	0.26;0.26;0.26;0.22	5.43	5.43	0.79202	Cadherin (1);Cadherin-like (1);	0.000000	0.49305	D	0.000150	T	0.59959	0.2232	L	0.39514	1.22	0.47374	D	0.999407	D;D	0.62365	0.979;0.991	P;P	0.56042	0.622;0.79	T	0.57365	-0.7824	10	0.30854	T	0.27	-19.528	11.8845	0.52594	1.0:0.0:0.0:0.0	.	36;36	E7EN24;Q12864	.;CAD17_HUMAN	V	36	ENSP00000027335:F36V;ENSP00000392811:F36V;ENSP00000401468:F36V;ENSP00000428189:F36V	ENSP00000027335:F36V	F	-	1	0	CDH17	95270635	0.957000	0.32711	0.996000	0.52242	0.606000	0.37113	2.732000	0.47352	2.057000	0.61298	0.482000	0.46254	TTT	.		0.403	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		C	95201459	A	C	95201459	3	2	12	1	0	0	0	0	1	0	0	0	3108	101	4	5	2456	5	CDH17	8	95201459	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	55338570	95201459	51162563	44	934											
BNC2	54796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	16419221	16419221	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaagctgctgaacataagAgatcctgaaacttcagcccc	14	7	8	12	0	1	3	1	2	0	1	2	5	2	3	3	0	5	2	3	0	4	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr9:16419221A>G	ENST00000380672.4	-	7	3123	c.3066T>C	c.(3064-3066)tcT>tcC	p.S1022S	BNC2_ENST00000380667.2_Silent_p.S955S|BNC2_ENST00000545497.1_Silent_p.S927S	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		TGAACATAAGAGATCCTGAAA	0.547																																					p.S1022S		.											.	BNC2-92	0			c.T3066C						.						81	72	75					9																	16419221		2203	4300	6503	SO:0001819	synonymous_variant	54796	exon7			CATAAGAGATCCT	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.3066T>C	9.37:g.16419221A>G		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	96	29	NM_017637	0	0	5	7	2		Silent	SNP	ENST00000380672.4	37	CCDS6482.2																																																																																			.		0.547	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		G	16419221	A	G	16419221	2	3	12	1	0	0	0	0	0	0	0	1	1476	291	11	3		3	BNC2	9	16419221	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08		16419221	124794210	45	935											
GRIN3A	116443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	104449145	104449145	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gaagttcagggggcatgaccCcaaactgggttgtaatttcg	10	10	13	8	1	1	1	1	1	0	0	2	2	1	1	2	3	1	4	2	3	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr9:104449145C>G	ENST00000361820.3	-	2	1637	c.1037G>C	c.(1036-1038)gGg>gCg	p.G346A		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	346					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	GGGCATGACCCCAAACTGGGT	0.507																																					p.G346A		.											.	GRIN3A-96	0			c.G1037C						.						66	64	65					9																	104449145		2203	4300	6503	SO:0001583	missense	116443	exon2			ATGACCCCAAACT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.1037G>C	9.37:g.104449145C>G	ENSP00000355155:p.Gly346Ala	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	68	33	NM_133445	0	0	0	0	0	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.696202	0.48202	.	.	ENSG00000198785	ENST00000361820	D	0.90732	-2.72	5.83	4.92	0.64577	.	0.942080	0.09021	N	0.860194	D	0.90017	0.6883	L	0.59436	1.845	0.58432	D	0.999992	B	0.28419	0.211	B	0.26864	0.074	D	0.83443	0.0044	10	0.66056	D	0.02	.	15.7632	0.78103	0.1471:0.8529:0.0:0.0	.	346	Q8TCU5	NMD3A_HUMAN	A	346	ENSP00000355155:G346A	ENSP00000355155:G346A	G	-	2	0	GRIN3A	103488966	1.000000	0.71417	0.885000	0.34714	0.653000	0.38743	4.782000	0.62396	1.403000	0.46800	0.563000	0.77884	GGG	.		0.507	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			G	104449145	C	G	104449145	3	3	12	1	0	0	0	0	1	0	0	0	6804	623	22	4	2342	4	GRIN3A	9	104449145	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	88029924	104449145	36764286	46	936											
SH2D3C	10044	hgsc.bcm.edu	37	chr9	130501166	130501166	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgcatctggaactccgtgctGaacacctccaggagctccgg	8	7	11	15	3	1	1	0	1	1	0	4	3	4	3	4	3	4	3	4	3	2	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr9:130501166G>C	ENST00000314830.8	-	12	2555	c.2442C>G	c.(2440-2442)ttC>ttG	p.F814L	SH2D3C_ENST00000373276.3_Missense_Mutation_p.F746L|SH2D3C_ENST00000420366.1_Missense_Mutation_p.F656L|SH2D3C_ENST00000429553.1_Missense_Mutation_p.F460L|SH2D3C_ENST00000373277.4_Missense_Mutation_p.F657L|SH2D3C_ENST00000373274.3_Missense_Mutation_p.F654L	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	814	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACTCCGTGCTGAACACCTCCA	0.637																																					p.F814L		.											.	SH2D3C-228	0			c.C2442G						.						34	30	32					9																	130501166		2198	4298	6496	SO:0001583	missense	10044	exon12			CGTGCTGAACACC	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"SH2 domain containing"	16884	protein-coding gene	gene with protein product		604722	"SH2 domain-containing 3C"			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.2442C>G	9.37:g.130501166G>C	ENSP00000317817:p.Phe814Leu	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	17	2	NM_170600	0	0	4	4	0	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	37	CCDS6877.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.684832	0.88639	.	.	ENSG00000095370	ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830	T;T;T;T;T;T	0.29142	2.42;2.41;2.1;2.43;1.58;2.33	5.76	5.76	0.90799	Guanine-nucleotide dissociation stimulator CDC25 (2);	0.090299	0.85682	D	0.000000	T	0.44350	0.1289	L	0.48174	1.505	0.80722	D	1	P;D;B;P;D	0.69078	0.918;0.997;0.45;0.507;0.996	P;P;B;B;D	0.62955	0.485;0.591;0.281;0.232;0.909	T	0.08027	-1.0742	10	0.28530	T	0.3	-8.9959	13.8642	0.63578	0.0:0.0:0.8475:0.1525	.	654;814;746;657;656	E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.;SH2D3_HUMAN;.;.;.	L	657;656;746;654;460;814	ENSP00000362374:F657L;ENSP00000388536:F656L;ENSP00000362373:F746L;ENSP00000362371:F654L;ENSP00000394632:F460L;ENSP00000317817:F814L	ENSP00000317817:F814L	F	-	3	2	SH2D3C	129540987	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.813000	0.86123	2.713000	0.92767	0.655000	0.94253	TTC	.		0.637	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		C	130501166	G	C	130501166	3	2	12	1	0	0	0	0	1	0	0	0	14266	1281	45	4	144	4	SH2D3C	9	130501166	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	26052021	130501166	10712265	47	937											
MASTL	84930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	27459483	27459483	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaatgatagcaaaaaaccTtatgtgtgaactcgatgaag	17	9	8	7	1	0	3	0	3	0	0	1	4	0	3	2	0	3	1	2	0	8	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr10:27459483T>C	ENST00000375940.4	+	8	1652	c.1595T>C	c.(1594-1596)cTt>cCt	p.L532P	MASTL_ENST00000477034.1_3'UTR|MASTL_ENST00000342386.6_Missense_Mutation_p.L532P|MASTL_ENST00000375946.4_Missense_Mutation_p.L532P			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	532	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCAAAAAACCTTATGTGTGAA	0.313																																					p.L532P		.											.	MASTL-522	0			c.T1595C						.						89	92	91					10																	27459483		2203	4300	6503	SO:0001583	missense	84930	exon8			AAAACCTTATGTG	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.1595T>C	10.37:g.27459483T>C	ENSP00000365107:p.Leu532Pro	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	132	46	NM_032844	0	0	3	5	2	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985988	0.53934	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.33654	1.4;1.4;1.4	5.67	5.67	0.87782	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61590	0.2359	M	0.75264	2.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65957	-0.6042	10	0.87932	D	0	-17.4573	15.9272	0.79628	0.0:0.0:0.0:1.0	.	532;532;532	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	P	532	ENSP00000365113:L532P;ENSP00000343446:L532P;ENSP00000365107:L532P	ENSP00000343446:L532P	L	+	2	0	MASTL	27499489	1.000000	0.71417	0.861000	0.33841	0.432000	0.31715	6.170000	0.71920	2.153000	0.67306	0.533000	0.62120	CTT	.		0.313	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		C	27459483	T	C	27459483	3	2	12	1	0	0	0	0	1	0	0	0	9353	1609	56	3	1625	3	MASTL	10	27459483	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		27459483	108075264	48	938											
UNC5B	219699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	73055666	73055666	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cacaacctgcgcctctccctCcatgacctcccccatgccca	7	7	4	23	1	1	1	0	1	1	0	4	1	3	1	8	0	3	0	8	0	1	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr10:73055666C>T	ENST00000335350.6	+	14	2690	c.2274C>T	c.(2272-2274)ctC>ctT	p.L758L	UNC5B_ENST00000373192.4_Silent_p.L747L	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	758	UPA domain. {ECO:0000250}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						GCCTCTCCCTCCATGACCTCC	0.612																																					p.L758L		.											.	UNC5B-228	0			c.C2274T						.						133	105	115					10																	73055666		2203	4300	6503	SO:0001819	synonymous_variant	219699	exon14			CTCCCTCCATGAC	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.2274C>T	10.37:g.73055666C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	116	46	NM_170744	0	0	2	2	0	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			.		0.612	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73055666	C	T	73055666	2	4	12	1	0	0	0	0	0	0	0	1	17025	842	30	2		2	UNC5B	10	73055666	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	45596183	73055666	62479081	49	939											
FUT11	170384	hgsc.bcm.edu	37	chr10	75532345	75532345	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgtggtggagcccagggcTattcccccacttcccgggag	5	8	14	14	1	0	0	0	0	0	0	2	2	2	2	4	4	1	2	4	4	1	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr10:75532345T>C	ENST00000372841.3	+	1	297	c.254T>C	c.(253-255)cTa>cCa	p.L85P	RMRPP1_ENST00000517236.1_RNA|AC022400.2_ENST00000595757.1_Missense_Mutation_p.S12G|FUT11_ENST00000394790.1_Missense_Mutation_p.L85P|FUT11_ENST00000465695.1_3'UTR	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	85					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					AGCCCAGGGCTATTCCCCCAC	0.746																																					p.L85P		.											.	FUT11-90	0			c.T254C						.						11	10	10					10																	75532345		2159	4225	6384	SO:0001583	missense	170384	exon1			CAGGGCTATTCCC	BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"Fucosyltransferases"	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.254T>C	10.37:g.75532345T>C	ENSP00000361932:p.Leu85Pro	Somatic	10	1		WXS	Illumina HiSeq	Phase_I	16	4	NM_173540	0	0	1	1	0	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	37	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560436	0.86335	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.23552	1.9;1.9	4.74	4.74	0.60224	.	0.152784	0.44285	D	0.000468	T	0.52468	0.1736	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.98;0.993	T	0.59182	-0.7502	10	0.72032	D	0.01	-17.3432	14.0401	0.64669	0.0:0.0:0.0:1.0	.	85;85;85	Q495W5;Q495W5-2;B2RC53	FUT11_HUMAN;.;.	P	85	ENSP00000361932:L85P;ENSP00000378270:L85P	ENSP00000361932:L85P	L	+	2	0	FUT11	75202351	1.000000	0.71417	0.893000	0.35052	0.927000	0.56198	4.480000	0.60243	1.995000	0.58328	0.379000	0.24179	CTA	.		0.746	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540		C	75532345	T	C	75532345	3	2	12	1	0	0	0	0	1	0	0	0	6122	1522	53	3	256	3	FUT11	10	75532345	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	2476679	75532345	60002402	50	940											
SEMA4G	57715	broad.mit.edu	37	chr10	102732887	102732887	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgttcctgctctccccagaGctctctgggacccggcactt	4	11	9	17	1	2	1	0	0	2	1	5	2	3	2	4	2	2	4	4	2	0	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr10:102732887G>A	ENST00000370250.4	+	2	499	c.126G>A	c.(124-126)gaG>gaA	p.E42E	SEMA4G_ENST00000517724.1_Splice_Site_p.E42E|SEMA4G_ENST00000519756.1_3'UTR|SEMA4G_ENST00000210633.3_Splice_Site_p.E42E|MIR608_ENST00000384820.1_RNA	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	42	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		TCTCCCCAGAGCTCTCTGGGA	0.622																																					p.E42E													.	SEMA4G-154	0			c.G126A						.						43	43	43					10																	102732887		2203	4300	6503	SO:0001630	splice_region_variant	57715	exon2			CCCAGAGCTCTCT	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.125-1G>A	10.37:g.102732887G>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	58	3	NM_001203244	0	0	0	0	0	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Silent	SNP	ENST00000370250.4	37																																																																																				.		0.622	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2		Silent	A	102732887	G	A	102732887	5	1	12	1	0	0	0	0	0	0	1	0	14068	985	34	2	132	2	SEMA4G	10	102732887	Splice_Site	SNP	G	TCGA-A4-7997-01A-11D-2201-08	27200542	102732887	32801860	51	941											
PIK3C2A	5286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	17124313	17124313	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattgtcattgtgtcgatcAcagatgcctaaaacataggt	13	13	8	7	1	2	1	2	0	0	1	3	2	2	1	1	1	2	0	1	1	4	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:17124313A>C	ENST00000265970.7	-	23	3746	c.3747T>G	c.(3745-3747)tgT>tgG	p.C1249W	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.C869W	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1249	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TGTGTCGATCACAGATGCCTA	0.383																																					p.C1249W		.											.	PIK3C2A-1310	0			c.T3747G						.						102	88	93					11																	17124313		2200	4293	6493	SO:0001583	missense	5286	exon23			TCGATCACAGATG	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3747T>G	11.37:g.17124313A>C	ENSP00000265970:p.Cys1249Trp	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	103	37	NM_002645	0	0	14	32	18	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420006	0.62622	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.80909	-1.43;-1.43	5.45	4.32	0.51571	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.89199	0.6647	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89599	0.3833	10	0.72032	D	0.01	-12.9025	11.3328	0.49485	0.9285:0.0:0.0715:0.0	.	1249	O00443	P3C2A_HUMAN	W	1249;869	ENSP00000265970:C1249W;ENSP00000438687:C869W	ENSP00000265970:C1249W	C	-	3	2	PIK3C2A	17080889	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.320000	0.51991	1.021000	0.39600	0.533000	0.62120	TGT	.		0.383	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		C	17124313	A	C	17124313	3	2	12	1	0	0	0	0	1	0	0	0	11935	157	6	5	1353	5	PIK3C2A	11	17124313	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		17124313	117882203	52	942											
PLAC1L	219990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	59811100	59811100	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtttatatatcttgttcgtGattgtggcatcaggacaagg	10	15	11	5	1	2	1	1	1	1	0	3	2	2	2	0	3	0	3	0	3	4	7			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:59811100G>A	ENST00000278855.2	+	2	408	c.223G>A	c.(223-225)Gat>Aat	p.D75N	PLAC1L_ENST00000532905.1_Missense_Mutation_p.D44N	NM_173801.3	NP_776162.2	Q86WS3	OOSP2_HUMAN		75						extracellular region (GO:0005576)				breast(1)|lung(9)|ovary(2)|prostate(2)|skin(1)	15						TCTTGTTCGTGATTGTGGCAT	0.338																																					p.D75N		.											.	PLAC1L-93	0			c.G223A						.						80	77	78					11																	59811100		2201	4295	6496	SO:0001583	missense	219990	exon2			GTTCGTGATTGTG																												ENST00000278855.2:c.223G>A	11.37:g.59811100G>A	ENSP00000278855:p.Asp75Asn	Somatic	53	1		WXS	Illumina HiSeq	Phase_I	64	26	NM_173801	0	0	0	0	0	E9PJA4|Q8N9U6	Missense_Mutation	SNP	ENST00000278855.2	37	CCDS7979.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.715783	0.30413	.	.	ENSG00000149507	ENST00000278855;ENST00000532905	D;D	0.82711	-1.64;-1.64	3.4	0.273	0.15650	.	1.719800	0.03545	N	0.224546	T	0.76765	0.4033	L	0.50333	1.59	0.09310	N	1	B	0.32160	0.358	B	0.24701	0.055	T	0.61964	-0.6954	10	0.59425	D	0.04	0.1876	5.3931	0.16255	0.1238:0.4285:0.4477:0.0	.	75	Q86WS3	PLACL_HUMAN	N	75;44	ENSP00000278855:D75N;ENSP00000433831:D44N	ENSP00000278855:D75N	D	+	1	0	PLAC1L	59567676	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.220000	0.17660	0.067000	0.16545	-0.312000	0.09012	GAT	.		0.338	PLAC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394411.1			A	59811100	G	A	59811100	3	1	12	1	0	0	0	0	1	0	0	0	12039	1290	45	2	229	2	PLAC1L	11	59811100	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	42686787	59811100	75195416	53	943											
ENDOD1	23052	hgsc.bcm.edu;broad.mit.edu	37	chr11	94823276	94823276	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtcagcgcgcggagggtgCtgagcgcttcgccaccctct	4	8	14	15	5	2	1	1	1	1	0	3	2	2	2	2	2	3	2	2	2	0	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:94823276C>T	ENST00000278505.4	+	1	303	c.185C>T	c.(184-186)gCt>gTt	p.A62V		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	62						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				GCGGAGGGTGCTGAGCGCTTC	0.716																																					p.A62V		.											.	ENDOD1-68	0			c.C185T						.						12	17	15					11																	94823276		1882	4102	5984	SO:0001583	missense	23052	exon1			AGGGTGCTGAGCG	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.185C>T	11.37:g.94823276C>T	ENSP00000278505:p.Ala62Val	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_015036	0	0	6	11	5	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.399463	0.42512	.	.	ENSG00000149218	ENST00000278505	T	0.69306	-0.39	4.43	1.23	0.21249	DNA/RNA non-specific endonuclease (1);Extracellular Endonuclease, subunit A (2);	1.135320	0.06834	N	0.794557	T	0.55800	0.1943	L	0.36672	1.1	0.09310	N	0.999999	B	0.33413	0.411	B	0.40165	0.321	T	0.50206	-0.8855	10	0.28530	T	0.3	-13.357	2.0739	0.03619	0.3599:0.396:0.1335:0.1106	.	62	O94919	ENDD1_HUMAN	V	62	ENSP00000278505:A62V	ENSP00000278505:A62V	A	+	2	0	ENDOD1	94462924	0.076000	0.21285	0.977000	0.42913	0.495000	0.33615	0.653000	0.24902	0.848000	0.35191	0.585000	0.79938	GCT	.		0.716	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		T	94823276	C	T	94823276	3	4	12	1	0	0	0	0	1	0	0	0	5127	797	28	2	187	2	ENDOD1	11	94823276	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	35012176	94823276	40183240	54	944											
MMP8	4317	hgsc.bcm.edu	37	chr11	102589165	102589165	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagatggcctgaatgccaTcgatgtcatcttgagggagt	10	11	12	8	1	2	3	1	2	1	1	3	5	2	4	2	2	1	0	2	2	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:102589165T>C	ENST00000236826.3	-	5	862	c.764A>G	c.(763-765)gAt>gGt	p.D255G		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	255					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	CTGAATGCCATCGATGTCATC	0.488																																					p.D255G		.											.	MMP8-229	0			c.A764G						.						109	90	96					11																	102589165		2203	4299	6502	SO:0001583	missense	4317	exon5			ATGCCATCGATGT	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.764A>G	11.37:g.102589165T>C	ENSP00000236826:p.Asp255Gly	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_002424	0	0	1	1	0	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	.	.	.	.	.	.	.	.	.	.	T	12.42	1.933886	0.34096	.	.	ENSG00000118113	ENST00000236826;ENST00000544383;ENST00000534942	T	0.21543	2.0	5.45	4.32	0.51571	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.282103	0.30800	N	0.008847	T	0.31765	0.0807	M	0.74467	2.265	0.23669	N	0.997152	B;B;B	0.33826	0.06;0.427;0.179	B;B;B	0.42138	0.037;0.377;0.114	T	0.24404	-1.0161	10	0.72032	D	0.01	.	10.3966	0.44205	0.0:0.1373:0.0:0.8627	.	255;190;255	A8K9E4;F5GXB5;P22894	.;.;MMP8_HUMAN	G	255;232;190	ENSP00000236826:D255G	ENSP00000236826:D255G	D	-	2	0	MMP8	102094375	1.000000	0.71417	0.785000	0.31869	0.680000	0.39746	3.827000	0.55745	1.001000	0.39076	0.533000	0.62120	GAT	.		0.488	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		C	102589165	T	C	102589165	3	2	12	1	0	0	0	0	1	0	0	0	9693	1435	50	3	663	3	MMP8	11	102589165	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	7765889	102589165	32417351	55	945											
ATM	472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	108155202	108155202	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacttattgggaaaacaggTatggcttcaatttttatgta	14	15	8	4	0	1	0	1	0	0	0	1	1	1	1	0	3	2	3	0	3	8	8			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:108155202T>C	ENST00000452508.2	+	27	4182		c.e27+2		ATM_ENST00000278616.4_Splice_Site			Q13315	ATM_HUMAN	ATM serine/threonine kinase						brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GGAAAACAGGTATGGCTTCAA	0.348			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											.		.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM-3419	0			c.3993+2T>C						.						93	90	91					11																	108155202		2201	4298	6499	SO:0001630	splice_region_variant	472	exon26	Familial Cancer Database	AT, Louis-Bar syndrome	AACAGGTATGGCT	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"TEL1, telomere maintenance 1, homolog (S. cerevisiae)"	607585	"ataxia telangiectasia mutated (includes complementation groups A, C and D)", "ataxia telangiectasia mutated"	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3993+2T>C	11.37:g.108155202T>C		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	96	34	NM_000051	0	0	0	0	0	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Splice_Site	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311730	0.60414	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508;ENST00000531525	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4694	0.75429	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATM	107660412	1.000000	0.71417	0.998000	0.56505	0.827000	0.46813	7.450000	0.80656	2.070000	0.61991	0.455000	0.32223	.	.		0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	Intron	C	108155202	T	C	108155202	5	2	12	1	0	0	0	0	0	0	1	0	1110	1652	57	3	4093	3	ATM	11	108155202	Splice_Site	SNP	T	TCGA-A4-7997-01A-11D-2201-08	5566037	108155202	26851314	56	946											
VWF	7450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6138619	6138619	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagactccaccacctcaaaGtgagtctcatccttcatggg	10	9	7	15	0	3	2	3	1	1	1	6	2	5	2	5	1	0	0	5	1	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:6138619G>A	ENST00000261405.5	-	22	3110	c.2856C>T	c.(2854-2856)caC>caT	p.H952H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	952	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCACCTCAAAGTGAGTCTCAT	0.572																																					p.H952H		.											.	VWF-163	0			c.C2856T						.						108	95	99					12																	6138619		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon22			CTCAAAGTGAGTC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2856C>T	12.37:g.6138619G>A		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	126	76	NM_000552	0	0	34	35	1	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			.		0.572	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6138619	G	A	6138619	2	1	12	1	0	0	0	0	0	0	0	1	17279	1020	36	2		2	VWF	12	6138619	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08		6138619	127713276	57	947											
LRRC23	10233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7014840	7014840	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagactctgagccagaccagGatgattctgagaaagaagag	16	6	12	7	0	2	7	0	3	2	5	2	9	2	8	2	1	1	0	2	1	3	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:7014840G>C	ENST00000007969.8	+	2	263	c.43G>C	c.(43-45)Gat>Cat	p.D15H	LRRC23_ENST00000429740.1_Missense_Mutation_p.D15H|LRRC23_ENST00000436789.1_Missense_Mutation_p.D15H|LRRC23_ENST00000449039.1_3'UTR|LRRC23_ENST00000443597.2_Missense_Mutation_p.D15H|LRRC23_ENST00000433346.1_Missense_Mutation_p.D15H|LRRC23_ENST00000323702.5_Missense_Mutation_p.D15H	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	15										NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						GCCAGACCAGGATGATTCTga	0.498																																					p.D15H		.											.	LRRC23-23	0			c.G43C						.						70	74	73					12																	7014840		2203	4300	6503	SO:0001583	missense	10233	exon2			GACCAGGATGATT	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.43G>C	12.37:g.7014840G>C	ENSP00000007969:p.Asp15His	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	148	43	NM_001135217	0	0	62	94	32	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.906459	0.33628	.	.	ENSG00000010626	ENST00000433346;ENST00000007969;ENST00000323702;ENST00000443597;ENST00000415834;ENST00000436789;ENST00000429740	T;T;T;T;T;T;T	0.71461	1.55;-0.26;-0.57;-0.26;0.55;1.6;1.19	4.74	4.74	0.60224	.	.	.	.	.	T	0.79088	0.4387	L	0.60455	1.87	0.47698	D	0.999497	D;D;D;D	0.69078	0.997;0.997;0.984;0.991	D;P;P;P	0.63877	0.919;0.884;0.769;0.769	T	0.80533	-0.1340	9	0.62326	D	0.03	-12.2314	13.0943	0.59182	0.0:0.0:1.0:0.0	.	15;15;15;15	E9PDZ4;Q53EV4-2;Q53EV4;C9JKE8	.;.;LRC23_HUMAN;.	H	15	ENSP00000402554:D15H;ENSP00000007969:D15H;ENSP00000317464:D15H;ENSP00000390932:D15H;ENSP00000408066:D15H;ENSP00000396049:D15H;ENSP00000397192:D15H	ENSP00000007969:D15H	D	+	1	0	LRRC23	6885101	0.995000	0.38212	0.960000	0.40013	0.183000	0.23260	2.632000	0.46511	2.452000	0.82932	0.561000	0.74099	GAT	.		0.498	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992		C	7014840	G	C	7014840	3	2	12	1	0	0	0	0	1	0	0	0	9003	1174	41	4	45	4	LRRC23	12	7014840	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	876221	7014840	126837055	58	948											
CMAS	55907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	22218064	22218064	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacttgataggaaatgaagTgtctgatgaagagtgcttga	13	13	12	3	0	1	6	0	5	1	1	1	7	1	7	0	1	2	1	0	1	5	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:22218064T>A	ENST00000229329.2	+	8	1254	c.1124T>A	c.(1123-1125)gTg>gAg	p.V375E		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	375					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						GGAAATGAAGTGTCTGATGAA	0.403																																					p.V375E		.											.	CMAS-93	0			c.T1124A						.						161	170	167					12																	22218064		2203	4300	6503	SO:0001583	missense	55907	exon8			ATGAAGTGTCTGA	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.1124T>A	12.37:g.22218064T>A	ENSP00000229329:p.Val375Glu	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	258	126	NM_018686	0	0	0	0	0	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	37	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	T	9.711	1.157024	0.21454	.	.	ENSG00000111726	ENST00000229329	T	0.24151	1.87	5.33	5.33	0.75918	HAD-like domain (2);	0.374692	0.26840	N	0.022237	T	0.17619	0.0423	L	0.32530	0.975	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09357	-1.0678	10	0.18276	T	0.48	-0.3894	8.8914	0.35437	0.2119:0.0:0.0:0.788	.	375	Q8NFW8	NEUA_HUMAN	E	375	ENSP00000229329:V375E	ENSP00000229329:V375E	V	+	2	0	CMAS	22109331	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.188000	0.50958	2.001000	0.58596	0.455000	0.32223	GTG	.		0.403	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		A	22218064	T	A	22218064	3	1	12	1	0	0	0	0	1	0	0	0	3581	1696	59	5	1154	5	CMAS	12	22218064	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	15203224	22218064	111633831	59	949											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49416134	49416134	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaacatgtagatgcctcgAttctagaaaggcagaggttg	12	9	13	7	2	1	3	0	0	1	3	2	5	1	4	1	3	2	3	1	3	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:49416134A>C	ENST00000301067.7	-	52	16340	c.16341T>G	c.(16339-16341)aaT>aaG	p.N5447K		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5447	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGATGCCTCGATTCTAGAAAG	0.512																																					p.N5447K		.											.	MLL2-612	0			c.T16341G						.						45	44	44					12																	49416134		2076	4217	6293	SO:0001583	missense	8085	exon52			GCCTCGATTCTAG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.16341T>G	12.37:g.49416134A>C	ENSP00000301067:p.Asn5447Lys	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	26	14	NM_003482	0	0	0	0	0	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109690	0.37242	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	T;T	0.80824	-1.42;-1.42	5.11	0.159	0.14968	SET domain (3);	0.000000	0.38326	N	0.001723	D	0.85013	0.5600	L	0.60067	1.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82888	-0.0234	10	0.87932	D	0	.	10.057	0.42250	0.4781:0.0:0.5219:0.0	.	5447	O14686	MLL2_HUMAN	K	5447;128	ENSP00000301067:N5447K;ENSP00000435714:N128K	ENSP00000301067:N5447K	N	-	3	2	MLL2	47702401	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	1.117000	0.31234	-0.129000	0.11620	-0.256000	0.11100	AAT	.		0.512	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49416134	A	C	49416134	3	2	12	1	0	0	0	0	1	0	0	0	9646	330	12	5	284	5	MLL2	12	49416134	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	27198070	49416134	84435761	60	950											
CLIP1	6249	broad.mit.edu	37	chr12	122812693	122812694	+	Frame_Shift_Ins	INS	-	-	T																															ctgacactggttgtggcttgINStttccattttcttttcctgc																								rs77289752	byFrequency	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:122812693_122812694insT	ENST00000540338.1	-	16	3090_3091	c.3049_3050insA	c.(3049-3051)acafs	p.T1017fs	CLIP1_ENST00000361654.4_Frame_Shift_Ins_p.T895fs|CLIP1_ENST00000545889.1_Frame_Shift_Ins_p.T592fs|CLIP1_ENST00000537178.1_Frame_Shift_Ins_p.T971fs|CLIP1_ENST00000302528.7_Frame_Shift_Ins_p.T1006fs|CLIP1_ENST00000358808.2_Frame_Shift_Ins_p.T1006fs			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1017					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		GTTGTGGCTTGTTTCCATTTTC	0.505																																					p.T1017fs													.	CLIP1-155	0			c.3050_3051insA						.																																			SO:0001589	frameshift_variant	6249	exon17			TGGCTTGTTTCCA		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"restin"	179838	"restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.3050dupA	12.37:g.122812696_122812696dupT	ENSP00000439093:p.Thr1017fs	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	280	8	NM_001247997	0	0	0	0	0	A0AVD3|Q17RS4|Q29RG0	Frame_Shift_Ins	INS	ENST00000540338.1	37	CCDS58285.1																																																																																			.		0.505	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		T	122812694	-	T	122812693	7	5	12	1	0	1	1	0	0	0	0	0	3538	1377	48	0	1306	0	CLIP1	12	122812693	Frame_Shift_Ins	INS	-	TCGA-A4-7997-01A-11D-2201-08	73396559	122812693	11039202	61	951											
ULK1	8408	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132405713	132405713	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcccacgctaccacaaggcCctgctgctcctggaggggct	6	7	12	16	1	0	0	0	0	0	0	2	1	2	1	4	4	3	4	4	4	2	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:132405713C>G	ENST00000321867.4	+	27	3381	c.3030C>G	c.(3028-3030)gcC>gcG	p.A1010A	ULK1_ENST00000540647.1_Silent_p.A255A	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	1010					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		ACCACAAGGCCCTGCTGCTCC	0.677																																					p.A1010A		.											.	ULK1-758	0			c.C3030G						.						54	52	53					12																	132405713		2203	4299	6502	SO:0001819	synonymous_variant	8408	exon27			CAAGGCCCTGCTG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.3030C>G	12.37:g.132405713C>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	96	53	NM_003565	0	0	21	42	21	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			.		0.677	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			G	132405713	C	G	132405713	2	3	12	1	0	0	0	0	0	0	0	1	17008	610	22	4		4	ULK1	12	132405713	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	9593020	132405713	1446182	62	952											
SSTR1	6751	hgsc.bcm.edu	37	chr14	38678657	38678657	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccccagcccgggcagctgCggcgaaggcggcggcagcag	7	1	18	15	5	0	0	0	0	0	0	0	1	0	0	3	5	5	4	3	5	1	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr14:38678657C>G	ENST00000267377.2	+	3	680	c.63C>G	c.(61-63)tgC>tgG	p.C21W		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	21					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.C21C(1)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)|Pasireotide(DB06663)	CGGGCAGCTGCGGCGAAGGCG	0.736																																					p.C21W		.											.	SSTR1-947	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C63G						.						12	13	13					14																	38678657		2183	4234	6417	SO:0001583	missense	6751	exon3			CAGCTGCGGCGAA		CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"GPCR / Class A : Somatostatin receptors"	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.63C>G	14.37:g.38678657C>G	ENSP00000267377:p.Cys21Trp	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_001049	0	0	1	1	0		Missense_Mutation	SNP	ENST00000267377.2	37	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.608924	0.28623	.	.	ENSG00000139874	ENST00000267377	T	0.70045	-0.45	5.17	1.05	0.20165	.	0.310059	0.23375	N	0.048870	T	0.36496	0.0969	N	0.08118	0	0.39683	D	0.970939	P	0.35700	0.516	B	0.24541	0.054	T	0.12528	-1.0544	10	0.37606	T	0.19	.	8.1652	0.31222	0.0:0.6547:0.0:0.3453	.	21	P30872	SSR1_HUMAN	W	21	ENSP00000267377:C21W	ENSP00000267377:C21W	C	+	3	2	SSTR1	37748408	0.002000	0.14202	0.877000	0.34402	0.931000	0.56810	0.205000	0.17356	0.016000	0.14998	0.563000	0.77884	TGC	.		0.736	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			G	38678657	C	G	38678657	3	3	12	1	0	0	0	0	1	0	0	0	15229	776	27	4	65	4	SSTR1	14	38678657	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		38678657	68670883	63	953											
EXOC5	10640	broad.mit.edu	37	chr14	57702498	57702498	+	Frame_Shift_Del	DEL	A	A	-																															cctcttctttgagcactggtAaactcctgaatcagctggca																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr14:57702498delA	ENST00000413566.2	-	7	959	c.600delT	c.(598-600)tttfs	p.F200fs	EXOC5_ENST00000340918.7_Frame_Shift_Del_p.F135fs	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	200					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						GAGCACTGGTAAACTCCTGAA	0.353																																					p.F200fs													.	EXOC5-137	0			c.600delT						.						55	49	51					14																	57702498		1853	4086	5939	SO:0001589	frameshift_variant	10640	exon7			ACTGGTAAACTCC	U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"SEC10 (S. cerevisiae)-like 1", "SEC10-like 1 (S. cerevisiae)"	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.600delT	14.37:g.57702498delA	ENSP00000389934:p.Phe200fs	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_006544	0	0	0	0	0	B2R6C5	Frame_Shift_Del	DEL	ENST00000413566.2	37	CCDS45111.1																																																																																			.		0.353	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544		-	57702498	A	-	57702498	7	5	12	1	0	1	0	1	0	0	0	0	5320	359	13	0	1574	0	EXOC5	14	57702498	Frame_Shift_Del	DEL	A	TCGA-A4-7997-01A-11D-2201-08	19023841	57702498	49647042	64	954											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58827678	58827678	+	Silent	SNP	G	G	T																															gagaggcagaagtcaaaacgGggacgacctcctttaaaatc																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr14:58827678G>T	ENST00000355431.3	+	19	2371	c.1998G>T	c.(1996-1998)cgG>cgT	p.R666R	ARID4A_ENST00000395168.3_Silent_p.R666R|ARID4A_ENST00000431317.2_Silent_p.R666R|ARID4A_ENST00000348476.3_Silent_p.R666R	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	666					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AGTCAAAACGGGGACGACCTC	0.433																																					p.R666R		.											.	ARID4A-231	0			c.G1998T						.						172	159	163					14																	58827678		2203	4300	6503	SO:0001819	synonymous_variant	5926	exon19			AAAACGGGGACGA	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.1998G>T	14.37:g.58827678G>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	97	13	NM_002892	0	0	10	10	0	Q15991|Q15992|Q15993	Silent	SNP	ENST00000355431.3	37	CCDS9732.1																																																																																			.		0.433	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		T	58827678	G	T	58827678	2	4	12	1	0	0	0	0	0	0	0	1	919	1219	43	4		4	ARID4A	14	58827678	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	1125180	58827678	48521862	65	955	9	2									
ARID4A	5926	hgsc.bcm.edu	37	chr14	58827680	58827680	+	Missense_Mutation	SNP	G	G	C																															gaggcagaagtcaaaacgggGacgacctcctttaaaatcaa																								rs145426502		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr14:58827680G>C	ENST00000355431.3	+	19	2373	c.2000G>C	c.(1999-2001)gGa>gCa	p.G667A	ARID4A_ENST00000395168.3_Missense_Mutation_p.G667A|ARID4A_ENST00000431317.2_Missense_Mutation_p.G667A|ARID4A_ENST00000348476.3_Missense_Mutation_p.G667A	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	667					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TCAAAACGGGGACGACCTCCT	0.443																																					p.G667A		.											.	ARID4A-231	0			c.G2000C						.						172	159	163					14																	58827680		2203	4300	6503	SO:0001583	missense	5926	exon19			AACGGGGACGACC	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2000G>C	14.37:g.58827680G>C	ENSP00000347602:p.Gly667Ala	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	99	14	NM_002892	0	0	15	15	0	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723941	0.89298	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	5.71	5.71	0.89125	Chromo domain-like (1);	0.105040	0.64402	D	0.000004	T	0.56124	0.1964	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.49790	-0.8902	10	0.35671	T	0.21	-26.8249	19.8505	0.96738	0.0:0.0:1.0:0.0	.	667;667;667	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	A	667;667;667;667;345	ENSP00000347602:G667A;ENSP00000344556:G667A;ENSP00000378597:G667A;ENSP00000397368:G667A;ENSP00000416053:G345A	ENSP00000344556:G667A	G	+	2	0	ARID4A	57897433	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.225000	0.78051	2.688000	0.91661	0.655000	0.94253	GGA	G|1.000;A|0.000		0.443	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58827680	G	C	58827680	3	2	12	1	0	0	0	0	1	0	0	0	919	1174	41	4	2070	4	ARID4A	14	58827680	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	2	58827680	48521860	66	956	9	2									
ARHGAP11A	9824	hgsc.bcm.edu;bcgsc.ca	37	chr15	32916475	32916475	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaactgccagagcccattctCccagctgatttgcatgaagc	10	9	9	13	0	1	3	0	2	1	1	2	4	1	3	3	0	6	2	3	0	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:32916475C>T	ENST00000361627.3	+	4	1121	c.399C>T	c.(397-399)ctC>ctT	p.L133L	ARHGAP11A_ENST00000567348.1_Silent_p.L133L|ARHGAP11A_ENST00000565905.1_5'UTR|ARHGAP11A_ENST00000543522.1_5'UTR|ARHGAP11A_ENST00000563864.1_Silent_p.L133L	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	133	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AGCCCATTCTCCCAGCTGATT	0.453																																					p.L133L	Colon(45;757 1134 30003 36652)	.											.	ARHGAP11A-292	0			c.C399T						.						35	35	35					15																	32916475		2200	4295	6495	SO:0001819	synonymous_variant	9824	exon4			CATTCTCCCAGCT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.399C>T	15.37:g.32916475C>T		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	142	31	NM_199357	0	0	0	2	2	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																			.		0.453	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32916475	C	T	32916475	2	4	12	1	0	0	0	0	0	0	0	1	863	842	30	2		2	ARHGAP11A	15	32916475	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08		32916475	69614917	67	957											
CDAN1	146059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43023981	43023981	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actcaacacatctggggcctCgcccaagacggtgcccccag	9	5	10	17	2	2	1	1	0	1	1	3	1	2	1	4	3	2	0	4	3	2	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:43023981C>T	ENST00000356231.3	-	11	1599	c.1576G>A	c.(1576-1578)Gag>Aag	p.E526K		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	526					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TCTGGGGCCTCGCCCAAGACG	0.587																																					p.E526K		.											.	CDAN1-92	0			c.G1576A						.						38	42	41					15																	43023981		2203	4299	6502	SO:0001583	missense	146059	exon11			GGGCCTCGCCCAA	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.1576G>A	15.37:g.43023981C>T	ENSP00000348564:p.Glu526Lys	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	103	35	NM_138477	0	0	4	4	0	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.074758	0.76415	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.90324	-2.65	5.9	4.99	0.66335	.	0.297879	0.39020	N	0.001487	D	0.92708	0.7682	M	0.65975	2.015	0.44432	D	0.997352	D	0.71674	0.998	P	0.54312	0.748	D	0.93041	0.6457	10	0.59425	D	0.04	-19.189	15.0277	0.71682	0.0:0.9321:0.0:0.0679	.	526	Q8IWY9	CDAN1_HUMAN	K	526;524	ENSP00000348564:E526K	ENSP00000267892:E524K	E	-	1	0	CDAN1	40811273	1.000000	0.71417	0.246000	0.24233	0.217000	0.24651	7.039000	0.76544	1.511000	0.48818	0.651000	0.88453	GAG	.		0.587	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43023981	C	T	43023981	3	4	12	1	0	0	0	0	1	0	0	0	3060	893	31	1	2179	1	CDAN1	15	43023981	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	10107506	43023981	59507411	68	958											
GNB5	10681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	52446239	52446239	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctggtcttcatgacaaactgCcccagggcctccacccgctc	7	8	8	18	1	2	1	1	1	1	0	4	1	3	1	5	2	2	1	5	2	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:52446239C>T	ENST00000261837.7	-	4	338	c.273G>A	c.(271-273)ggG>ggA	p.G91G	GNB5_ENST00000396335.4_Silent_p.G49G|GNB5_ENST00000358784.7_Silent_p.G49G|GNB5_ENST00000560116.1_Silent_p.G49G	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	91					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		TGACAAACTGCCCCAGGGCCT	0.572																																					p.G91G		.											.	GNB5-227	0			c.G273A						.						115	95	102					15																	52446239		2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			AAACTGCCCCAGG	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"WD repeat domain containing"	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.273G>A	15.37:g.52446239C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	57	17	NM_016194	0	0	27	52	25	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			.		0.572	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			T	52446239	C	T	52446239	2	4	12	1	0	0	0	0	0	0	0	1	6541	726	26	2		2	GNB5	15	52446239	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	9422258	52446239	50085153	69	959											
HERC1	8925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64021464	64021464	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctccaacactgccattcCaaggactttctttgagcaaa	11	13	5	12	0	2	1	0	1	2	0	4	2	3	2	3	1	3	1	3	1	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:64021464C>T	ENST00000443617.2	-	16	3212	c.3125G>A	c.(3124-3126)tGg>tAg	p.W1042*		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1042					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACTGCCATTCCAAGGACTTTC	0.363																																					p.W1042X		.											.	HERC1-666	0			c.G3125A						.						43	40	41					15																	64021464		1833	4095	5928	SO:0001587	stop_gained	8925	exon16			CCATTCCAAGGAC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.3125G>A	15.37:g.64021464C>T	ENSP00000390158:p.Trp1042*	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	25	4	NM_003922	0	0	7	8	1	Q8IW65	Nonsense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	41	8.909842	0.99000	.	.	ENSG00000103657	ENST00000443617	.	.	.	5.6	5.6	0.85130	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	19.6131	0.95618	0.0:1.0:0.0:0.0	.	.	.	.	X	1042	.	ENSP00000390158:W1042X	W	-	2	0	HERC1	61808517	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.840000	0.69402	2.652000	0.90054	0.561000	0.74099	TGG	.		0.363	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	64021464	C	T	64021464	4	4	12	1	0	0	0	0	0	1	0	0	7078	595	21	2	11712	2	HERC1	15	64021464	Nonsense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	11575225	64021464	38509928	70	960											
SYNM	23336	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	99672333	99672333	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgcaacagaagagtcagtGggtacccagacttctgtcag	11	10	11	9	0	3	3	2	0	1	3	3	3	3	3	1	1	3	2	1	1	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:99672333G>T	ENST00000336292.6	+	5	3885	c.3765G>T	c.(3763-3765)gtG>gtT	p.V1255V	SYNM_ENST00000560674.1_Intron|SYNM_ENST00000328642.7_Intron|SYNM_ENST00000561323.1_3'UTR|RP11-6O2.4_ENST00000566974.1_RNA	NM_145728.2	NP_663780.2	O15061	SYNEM_HUMAN	synemin, intermediate filament protein	1256	Interaction with DMD and UTRN.|Interaction with TLN1 and VCL.|Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						AAGAGTCAGTGGGTACCCAGA	0.478																																					.	Pancreas(125;1071 1762 21750 40003 40381)												.	SYNM-26	0			.						.						51	51	51					15																	99672333		1892	4113	6005	SO:0001819	synonymous_variant	23336	.			GTCAGTGGGTACC	AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"A-kinase anchor proteins", "Intermediate filaments type IV"	24466	protein-coding gene	gene with protein product	"synemin alpha", "synemin beta"	606087	"desmuslin"	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000336292.6:c.3765G>T	15.37:g.99672333G>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	93	33	.	0	0	0	2	2	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Silent	SNP	ENST00000336292.6	37																																																																																				.		0.478	SYNM-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_145728		T	99672333	G	T	99672333	2	4	12	1	0	0	0	0	0	0	0	1	15487	1335	47	4		4	SYNM	15	99672333	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	35650869	99672333	2859059	71	961											
AXIN1	8312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	396884	396884	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttaatgccaacaccttTcccggagcagaaactgtagc	12	9	7	13	1	0	1	0	0	0	1	1	2	1	2	4	1	5	2	4	1	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:396884T>G	ENST00000262320.3	-	2	513	c.142A>C	c.(142-144)Aaa>Caa	p.K48Q	AXIN1_ENST00000354866.3_Missense_Mutation_p.K48Q|AXIN1_ENST00000481769.1_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	48					activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCAACACCTTTCCCGGAGCAG	0.627											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K48Q		.											.	AXIN1-684	0			c.A142C						.						44	44	44					16																	396884		2202	4300	6502	SO:0001583	missense	8312	exon2			CACCTTTCCCGGA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.142A>C	16.37:g.396884T>G	ENSP00000262320:p.Lys48Gln	Somatic	59	0	588	WXS	Illumina HiSeq	Phase_I	70	39	NM_181050	0	0	11	28	17	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	37	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449477	0.63178	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.61980	0.06;0.07	5.34	5.34	0.76211	.	0.138741	0.64402	D	0.000005	T	0.77143	0.4087	M	0.74258	2.255	0.58432	D	0.999991	D;D	0.69078	0.997;0.996	D;P	0.63703	0.917;0.894	T	0.80051	-0.1544	10	0.62326	D	0.03	-17.2364	15.3197	0.74112	0.0:0.0:0.0:1.0	.	48;48	O15169-2;O15169	.;AXIN1_HUMAN	Q	48	ENSP00000262320:K48Q;ENSP00000346935:K48Q	ENSP00000262320:K48Q	K	-	1	0	AXIN1	336885	1.000000	0.71417	0.998000	0.56505	0.388000	0.30384	5.889000	0.69766	2.039000	0.60335	0.533000	0.62120	AAA	.		0.627	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			G	396884	T	G	396884	3	3	12	1	0	0	0	0	1	0	0	0	1237	1792	62	5	2486	5	AXIN1	16	396884	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		396884	89957869	72	962											
HAGH	3029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1869997	1869997	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcttgaccagtttctcAttcccgccagcatggtccct	6	12	7	16	1	1	1	1	1	1	0	5	1	4	1	5	1	2	3	5	1	0	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:1869997A>G	ENST00000397356.3	-	4	739	c.333T>C	c.(331-333)aaT>aaC	p.N111N	HAGH_ENST00000455446.2_Silent_p.N111N|HAGH_ENST00000566709.1_Silent_p.N63N|HAGH_ENST00000397353.2_Silent_p.N63N	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	111					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CCAGTTTCTCATTCCCGCCAG	0.617																																					p.N111N	Pancreas(55;1048 1176 25227 40124 41333)	.											.	HAGH-91	0			c.T333C						.						95	78	83					16																	1869997		2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			TTTCTCATTCCCG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"hydroxyacyl glutathione hydrolase"			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.333T>C	16.37:g.1869997A>G		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	135	26	NM_005326	0	0	107	157	50	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			.		0.617	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326		G	1869997	A	G	1869997	2	3	12	1	0	0	0	0	0	0	0	1	6966	214	8	3		3	HAGH	16	1869997	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08	1473113	1869997	88484756	73	963											
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3807907	3807907	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaacttatagactcgggatGtcttgcgattatagagccag	13	11	10	7	2	1	2	0	0	1	2	2	4	1	3	1	1	3	0	1	1	6	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:3807907G>A	ENST00000262367.5	-	18	4321	c.3512C>T	c.(3511-3513)aCa>aTa	p.T1171I	CREBBP_ENST00000382070.3_Missense_Mutation_p.T1133I	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1171	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.|Interaction with ASF1A. {ECO:0000269|PubMed:24616510}.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GACTCGGGATGTCTTGCGATT	0.502			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.T1171I		.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP-1807	0			c.C3512T	GRCh37	CI084721	CREBBP	I		.						148	125	133					16																	3807907		2197	4300	6497	SO:0001583	missense	1387	exon18			CGGGATGTCTTGC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3512C>T	16.37:g.3807907G>A	ENSP00000262367:p.Thr1171Ile	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	147	39	NM_004380	0	0	11	12	1	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.279568	0.59758	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	T;T	0.19669	2.13;2.13	5.59	5.59	0.84812	Bromodomain (6);	0.000000	0.85682	D	0.000000	T	0.45236	0.1332	L	0.56199	1.76	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.83275	0.996;0.996	T	0.26608	-1.0098	10	0.62326	D	0.03	-14.9891	19.5896	0.95503	0.0:0.0:1.0:0.0	.	1201;1171	Q4LE28;Q92793	.;CBP_HUMAN	I	1171;1201;1133	ENSP00000262367:T1171I;ENSP00000371502:T1133I	ENSP00000262367:T1171I	T	-	2	0	CREBBP	3747908	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	9.731000	0.98807	2.632000	0.89209	0.585000	0.79938	ACA	.		0.502	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3807907	G	A	3807907	3	1	12	1	0	0	0	0	1	0	0	0	3867	1377	48	2	3872	2	CREBBP	16	3807907	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	1937910	3807907	86546846	74	964											
GLYR1	84656	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4895118	4895118	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaagaagcatttctttcCgcgaggtttcttcaagtcct	10	13	7	11	2	3	1	1	0	2	1	5	2	5	1	2	1	1	2	2	1	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:4895118C>G	ENST00000321919.9	-	3	188	c.112G>C	c.(112-114)Gga>Cga	p.G38R	UBN1_ENST00000545171.1_5'Flank|GLYR1_ENST00000381983.3_Missense_Mutation_p.G38R|GLYR1_ENST00000436648.5_Missense_Mutation_p.G38R|GLYR1_ENST00000591451.1_Missense_Mutation_p.G38R|UBN1_ENST00000262376.6_5'Flank	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	38	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						CATTTCTTTCCGCGAGGTTTC	0.463																																					p.G38R		.											.	GLYR1-90	0			c.G112C						.						107	118	115					16																	4895118		2197	4300	6497	SO:0001583	missense	84656	exon3			TCTTTCCGCGAGG	AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632			24434	protein-coding gene	gene with protein product	"nuclear protein 60kDa"	610660				16352664	Standard	NM_032569		Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.112G>C	16.37:g.4895118C>G	ENSP00000322716:p.Gly38Arg	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	241	118	NM_032569	0	0	34	102	68	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	37	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062788	0.76187	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.70045	-0.45;-0.45;-0.45	5.25	5.25	0.73442	PWWP (2);	0.000000	0.85682	D	0.000000	T	0.72787	0.3504	N	0.25647	0.755	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.72424	-0.4298	10	0.37606	T	0.19	-9.014	17.6028	0.88030	0.0:1.0:0.0:0.0	.	38;38;38	Q49A26-5;Q49A26-3;Q49A26	.;.;GLYR1_HUMAN	R	38	ENSP00000322716:G38R;ENSP00000371413:G38R;ENSP00000390276:G38R	ENSP00000322716:G38R	G	-	1	0	GLYR1	4835119	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.931000	0.70113	2.451000	0.82905	0.491000	0.48974	GGA	.		0.463	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569		G	4895118	C	G	4895118	3	3	12	1	0	0	0	0	1	0	0	0	6503	661	23	4	1605	4	GLYR1	16	4895118	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	1087211	4895118	85459635	75	965											
PDXDC1	23042	hgsc.bcm.edu;broad.mit.edu	37	chr16	15122744	15122744	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttggtgtcagatccggtgtTtaaagccgtcccagtgccca	7	12	11	11	2	1	1	1	0	0	1	3	1	3	1	4	2	2	1	4	2	2	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:15122744T>G	ENST00000396410.4	+	15	1311	c.1214T>G	c.(1213-1215)tTt>tGt	p.F405C	PDXDC1_ENST00000563679.1_Missense_Mutation_p.F423C|PDXDC1_ENST00000450288.2_Missense_Mutation_p.F377C|PDXDC1_ENST00000535621.2_Missense_Mutation_p.F405C|PDXDC1_ENST00000447912.2_Missense_Mutation_p.F314C|PDXDC1_ENST00000569715.1_Missense_Mutation_p.F378C|PDXDC1_ENST00000455313.2_Missense_Mutation_p.F382C|PDXDC1_ENST00000325823.7_Missense_Mutation_p.F390C	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	405					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GATCCGGTGTTTAAAGCCGTC	0.552																																					p.F405C		.											.	PDXDC1-91	0			c.T1214G						.						93	84	87					16																	15122744		2197	4300	6497	SO:0001583	missense	23042	exon15			CGGTGTTTAAAGC	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1214T>G	16.37:g.15122744T>G	ENSP00000379691:p.Phe405Cys	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	102	6	NM_015027	0	0	0	0	0	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	T	7.666	0.685974	0.14973	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.28454	1.61;2.14;2.04;1.61;1.61;1.9	5.23	2.85	0.33270	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.687962	0.14343	N	0.325608	T	0.19805	0.0476	N	0.22421	0.69	0.09310	N	1	P;P;P;P;P;P	0.42357	0.614;0.614;0.777;0.777;0.614;0.562	B;B;B;B;B;B	0.42916	0.243;0.243;0.312;0.312;0.227;0.402	T	0.07214	-1.0784	10	0.42905	T	0.14	-0.7059	3.6422	0.08172	0.1651:0.1907:0.0:0.6442	.	377;314;405;377;405;382	E7EPL4;E7EMH5;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;PDXD1_HUMAN;.	C	390;314;405;405;377;111;382	ENSP00000322807:F390C;ENSP00000400310:F314C;ENSP00000437835:F405C;ENSP00000379691:F405C;ENSP00000391147:F377C;ENSP00000406703:F382C	ENSP00000322807:F390C	F	+	2	0	PDXDC1	15030245	0.000000	0.05858	0.230000	0.23976	0.025000	0.11179	-0.337000	0.07852	0.944000	0.37579	0.533000	0.62120	TTT	.		0.552	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		G	15122744	T	G	15122744	3	3	12	1	0	0	0	0	1	0	0	0	11722	1841	64	5	1272	5	PDXDC1	16	15122744	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	10227626	15122744	75232009	76	966											
PALB2	79728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23646368	23646368	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttgggcaactgccttcctaGacaagtcattatcttcagtg	9	13	8	11	0	3	1	2	0	1	1	4	1	4	1	2	1	2	1	2	1	4	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:23646368G>A	ENST00000261584.4	-	4	1651	c.1499C>T	c.(1498-1500)tCt>tTt	p.S500F		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	500	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		TGCCTTCCTAGACAAGTCATT	0.473			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.S500F		.	yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	.	PALB2-1351	0			c.C1499T						.						146	143	144					16																	23646368		2197	4300	6497	SO:0001583	missense	79728	exon4			TTCCTAGACAAGT		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.1499C>T	16.37:g.23646368G>A	ENSP00000261584:p.Ser500Phe	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	242	64	NM_024675	0	0	8	13	5	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	g	17.98	3.521575	0.64747	.	.	ENSG00000083093	ENST00000261584	T	0.17691	2.26	5.27	1.12	0.20585	.	0.782893	0.11510	N	0.556845	T	0.15955	0.0384	L	0.57536	1.79	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.27606	-1.0069	10	0.46703	T	0.11	-0.048	4.9673	0.14096	0.2567:0.1532:0.5902:0.0	.	500	Q86YC2	PALB2_HUMAN	F	500	ENSP00000261584:S500F	ENSP00000261584:S500F	S	-	2	0	PALB2	23553869	0.000000	0.05858	0.000000	0.03702	0.614000	0.37383	0.098000	0.15189	0.057000	0.16193	-0.121000	0.15023	TCT	.		0.473	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		A	23646368	G	A	23646368	3	1	12	1	0	0	0	0	1	0	0	0	11432	942	33	2	2101	2	PALB2	16	23646368	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	8523624	23646368	66708385	77	967											
CENPT	80152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67863889	67863889	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcgtgtaagggctctactTcatcttctccagagacacca	10	11	7	13	1	4	1	1	0	3	1	6	2	4	1	2	1	1	2	2	1	2	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:67863889T>A	ENST00000562787.1	-	12	1513	c.965A>T	c.(964-966)gAa>gTa	p.E322V	CENPT_ENST00000562947.1_5'Flank|CENPT_ENST00000219172.3_Missense_Mutation_p.E322V|CENPT_ENST00000440851.2_Missense_Mutation_p.E322V|CENPT_ENST00000564817.1_Missense_Mutation_p.E322V	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	322	Flexible stalk domain. {ECO:0000250}.				chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		GGGCTCTACTTCATCTTCTCC	0.532																																					p.E322V		.											.	CENPT-90	0			c.A965T						.						189	187	188					16																	67863889		2040	4195	6235	SO:0001583	missense	80152	exon12			TCTACTTCATCTT	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.965A>T	16.37:g.67863889T>A	ENSP00000457810:p.Glu322Val	Somatic	290	0		WXS	Illumina HiSeq	Phase_I	314	79	NM_025082	0	0	34	44	10	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	37	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502660	0.26949	.	.	ENSG00000102901	ENST00000440851;ENST00000436104;ENST00000219172	T;T	0.43294	0.95;0.95	4.08	-1.05	0.10036	.	0.294496	0.23852	N	0.043925	T	0.23249	0.0562	L	0.29908	0.895	0.26493	N	0.974919	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.001	T	0.07635	-1.0762	10	0.42905	T	0.14	.	3.7971	0.08744	0.1696:0.5023:0.0:0.3281	.	80;322;322	F5H5A6;Q96BT3;B3KPB2	.;CENPT_HUMAN;.	V	322;80;322	ENSP00000400140:E322V;ENSP00000219172:E322V	ENSP00000219172:E322V	E	-	2	0	CENPT	66421390	0.000000	0.05858	0.023000	0.16930	0.019000	0.09904	-1.893000	0.01609	0.003000	0.14656	-0.313000	0.08912	GAA	.		0.532	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67863889	T	A	67863889	3	1	12	1	0	0	0	0	1	0	0	0	3248	1783	62	5	740	5	CENPT	16	67863889	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	44217521	67863889	22490864	78	968											
KDM6B	23135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7755333	7755333	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggcccaggcgactgcgagtgGttcgcggtgcacgagcacta	7	6	16	12	5	0	0	0	0	0	0	1	3	0	0	1	4	3	3	1	4	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:7755333G>C	ENST00000448097.2	+	18	4561	c.4230G>C	c.(4228-4230)tgG>tgC	p.W1410C	KDM6B_ENST00000254846.5_Missense_Mutation_p.W1410C			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1410	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						ACTGCGAGTGGTTCGCGGTGC	0.627											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W1410C		.											.	KDM6B-205	0			c.G4230C						.						93	80	84					17																	7755333		2203	4300	6503	SO:0001583	missense	23135	exon18			CGAGTGGTTCGCG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.4230G>C	17.37:g.7755333G>C	ENSP00000412513:p.Trp1410Cys	Somatic	86	0	644	WXS	Illumina HiSeq	Phase_I	71	14	NM_001080424	0	0	30	48	18	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		.	.	.	.	.	.	.	.	.	.	G	14.04	2.416033	0.42817	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	D;D	0.86230	-2.09;-2.09	4.99	3.95	0.45737	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.062767	0.64402	D	0.000002	D	0.95194	0.8442	H	0.95780	3.72	0.80722	D	1	D;B	0.89917	1.0;0.058	D;B	0.97110	1.0;0.064	D	0.95975	0.8973	10	0.87932	D	0	-8.7797	15.1416	0.72615	0.0:0.1428:0.8572:0.0	.	1410;1410	O15054;O15054-1	KDM6B_HUMAN;.	C	1410	ENSP00000254846:W1410C;ENSP00000412513:W1410C	ENSP00000254846:W1410C	W	+	3	0	KDM6B	7696058	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.404000	0.79996	2.769000	0.95229	0.561000	0.74099	TGG	.		0.627	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		C	7755333	G	C	7755333	3	2	12	1	0	0	0	0	1	0	0	0	8159	1270	44	4	4288	4	KDM6B	17	7755333	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08		7755333	73439877	79	969											
KRT33A	3883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39505660	39505660	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcaccacaagcctggcattCtcagacttgctgcacaggat	10	9	9	13	0	1	1	1	0	1	1	2	2	1	2	2	2	4	4	2	2	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:39505660C>G	ENST00000007735.3	-	2	413	c.369G>C	c.(367-369)gaG>gaC	p.E123D		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	123	Coil 1B.|Rod.					extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				GCCTGGCATTCTCAGACTTGC	0.478																																					p.E123D		.											.	KRT33A-90	0			c.G369C						.						110	100	104					17																	39505660		2203	4300	6503	SO:0001583	missense	3883	exon2			GGCATTCTCAGAC	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"-", "Intermediate filaments type I, keratins (acidic)"	6450	protein-coding gene	gene with protein product	"hard keratin type I 3I"	602761	"keratin, hair, acidic, 3A"	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.369G>C	17.37:g.39505660C>G	ENSP00000007735:p.Glu123Asp	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	74	32	NM_004138	0	0	0	0	0	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	37	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920429	0.33908	.	.	ENSG00000006059	ENST00000007735	D	0.89617	-2.54	4.8	4.8	0.61643	Filament (1);	0.000000	0.64402	D	0.000019	D	0.84750	0.5541	L	0.42744	1.35	0.31832	N	0.624605	B	0.22211	0.066	B	0.34385	0.181	T	0.80443	-0.1380	10	0.27082	T	0.32	.	8.7524	0.34626	0.1523:0.572:0.2757:0.0	.	123	O76009	KT33A_HUMAN	D	123	ENSP00000007735:E123D	ENSP00000007735:E123D	E	-	3	2	KRT33A	36759186	0.937000	0.31787	1.000000	0.80357	0.994000	0.84299	0.006000	0.13152	2.643000	0.89663	0.655000	0.94253	GAG	.		0.478	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138		G	39505660	C	G	39505660	3	3	12	1	0	0	0	0	1	0	0	0	8490	912	32	4	869	4	KRT33A	17	39505660	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	31750327	39505660	41689550	80	970											
SCRN2	90507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45916322	45916322	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgcagctccgggtgttgggCcgagatgtccgtgccaatgc	5	8	15	13	4	0	1	0	0	0	1	2	2	2	1	5	2	3	3	5	2	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:45916322C>A	ENST00000290216.9	-	5	732	c.607G>T	c.(607-609)Gcc>Tcc	p.A203S	SCRN2_ENST00000584123.1_Missense_Mutation_p.A211S|SCRN2_ENST00000407215.3_Missense_Mutation_p.A203S	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	203						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						GGGTGTTGGGCCGAGATGTCC	0.592																																					p.A203S		.											.	SCRN2-91	0			c.G607T						.						85	89	88					17																	45916322		2203	4300	6503	SO:0001583	missense	90507	exon5			GTTGGGCCGAGAT	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.607G>T	17.37:g.45916322C>A	ENSP00000290216:p.Ala203Ser	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	177	57	NM_138355	0	0	42	82	40	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	37	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	C	1.216	-0.628224	0.03610	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.20881	2.04;2.04	5.52	5.52	0.82312	.	0.215480	0.47455	D	0.000225	T	0.15392	0.0371	L	0.37630	1.12	0.09310	N	1	B;B;B	0.25850	0.051;0.136;0.051	B;B;B	0.27608	0.081;0.081;0.081	T	0.25606	-1.0127	10	0.07482	T	0.82	-11.1584	11.6628	0.51356	0.0:0.9174:0.0:0.0825	.	203;203;203	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	S	203	ENSP00000290216:A203S;ENSP00000383935:A203S	ENSP00000290216:A203S	A	-	1	0	SCRN2	43271321	0.000000	0.05858	0.026000	0.17262	0.066000	0.16364	0.485000	0.22324	2.588000	0.87417	0.655000	0.94253	GCC	.		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45916322	C	A	45916322	3	1	12	1	0	0	0	0	1	0	0	0	13971	739	26	4	704	4	SCRN2	17	45916322	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	6410662	45916322	35278888	81	971											
AATK	9625	broad.mit.edu	37	chr17	79094413	79094413	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgttgccttctgatctcAgcggaaccggggtcagcagg	7	9	14	11	2	3	1	2	1	2	0	4	2	3	2	2	4	5	3	2	4	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:79094413A>C	ENST00000326724.4	-	11	3347	c.3323T>G	c.(3322-3324)cTg>cGg	p.L1108R	AATK_ENST00000417379.1_Missense_Mutation_p.L1005R	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1108	Pro-rich.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TTCTGATCTCAGCGGAACCGG	0.692																																					p.L1108R													.	AATK-933	0			c.T3323G						.						8	9	9					17																	79094413		1800	4036	5836	SO:0001583	missense	9625	exon11			GATCTCAGCGGAA	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.3323T>G	17.37:g.79094413A>C	ENSP00000324196:p.Leu1108Arg	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	13	3	NM_001080395	0	0	0	0	0	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.862|7.862	0.726238|0.726238	0.15439|0.15439	.|.	.|.	ENSG00000181409|ENSG00000181409	ENST00000326724|ENST00000417379	T|.	0.79033|.	-1.23|.	4.32|4.32	-1.87|-1.87	0.07737|0.07737	.|.	1.360170|.	0.05149|.	N|.	0.495650|.	T|.	0.21427|.	0.0516|.	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.14438|.	0.01|.	B|.	0.11329|.	0.006|.	T|.	0.29912|.	-0.9996|.	10|.	0.72032|.	D|.	0.01|.	.|.	5.5575|5.5575	0.17125|0.17125	0.6453:0.1626:0.1921:0.0|0.6453:0.1626:0.1921:0.0	.|.	1108|.	Q6ZMQ8|.	LMTK1_HUMAN|.	R|G	1108|1061	ENSP00000324196:L1108R|.	ENSP00000324196:L1108R|.	L|X	-|-	2|1	0|0	AATK|AATK	76709008|76709008	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.024000|0.024000	0.10985|0.10985	-0.610000|-0.610000	0.05629|0.05629	-0.443000|-0.443000	0.07180|0.07180	0.260000|0.260000	0.18958|0.18958	CTG|TGA	.		0.692	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		C	79094413	A	C	79094413	3	2	12	1	0	0	0	0	1	0	0	0	26	188	7	5	817	5	AATK	17	79094413	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	33178091	79094413	2100797	82	972											
NARF	26502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80443450	80443450	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgctgcagcctatggctttcGaaacatccagaacatgatcc	11	10	8	12	1	0	2	0	1	0	1	3	3	2	2	3	1	5	3	3	1	3	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:80443450G>A	ENST00000309794.11	+	10	1247	c.1049G>A	c.(1048-1050)cGa>cAa	p.R350Q	NARF_ENST00000457415.3_Missense_Mutation_p.R396Q|NARF_ENST00000345415.7_Missense_Mutation_p.R302Q|NARF-IT1_ENST00000584012.1_RNA|NARF_ENST00000390006.4_Missense_Mutation_p.R291Q	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	350						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			TATGGCTTTCGAAACATCCAG	0.493																																					p.R350Q		.											.	NARF-226	0			c.G1049A						.						151	133	139					17																	80443450		2203	4300	6503	SO:0001583	missense	26502	exon10			GCTTTCGAAACAT	BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.1049G>A	17.37:g.80443450G>A	ENSP00000309899:p.Arg350Gln	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	142	18	NM_012336	0	0	70	84	14	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Missense_Mutation	SNP	ENST00000309794.11	37	CCDS32777.1	.	.	.	.	.	.	.	.	.	.	.	16.94	3.261532	0.59431	.	.	ENSG00000141562	ENST00000390006;ENST00000374611;ENST00000309794;ENST00000345415	T;T;T	0.47177	0.85;0.85;0.85	5.32	5.32	0.75619	Iron hydrogenase, large subunit, C-terminal (1);Iron hydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.63355	0.2504	M	0.77406	2.37	0.80722	D	1	D;D;D;P	0.55605	0.972;0.972;0.961;0.895	P;P;P;P	0.54140	0.743;0.743;0.727;0.473	T	0.63332	-0.6661	10	0.33940	T	0.23	-19.4724	17.9724	0.89117	0.0:0.0:1.0:0.0	.	396;302;397;350	Q9UHQ1-2;Q9UHQ1-3;E9PH27;Q9UHQ1	.;.;.;NARF_HUMAN	Q	291;397;350;302	ENSP00000374656:R291Q;ENSP00000309899:R350Q;ENSP00000283996:R302Q	ENSP00000309899:R350Q	R	+	2	0	NARF	78036739	1.000000	0.71417	0.941000	0.38009	0.854000	0.48673	9.273000	0.95719	2.480000	0.83734	0.561000	0.74099	CGA	.		0.493	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		A	80443450	G	A	80443450	3	1	12	1	0	0	0	0	1	0	0	0	10192	1058	37	1	1229	1	NARF	17	80443450	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	1349037	80443450	751760	83	973											
EPB41L3	23136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	5394764	5394764	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatgtcagggtgctgctctTtggcctctttaattgcctga	6	15	10	10	0	3	1	1	1	2	0	3	1	3	1	2	2	3	2	2	2	1	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr18:5394764T>G	ENST00000341928.2	-	22	3522	c.3182A>C	c.(3181-3183)aAa>aCa	p.K1061T	EPB41L3_ENST00000542146.1_Missense_Mutation_p.K366T|EPB41L3_ENST00000540638.2_Missense_Mutation_p.K839T|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000427684.2_Missense_Mutation_p.K358T|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000342933.3_Missense_Mutation_p.K1061T|EPB41L3_ENST00000400111.3_Missense_Mutation_p.K839T	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1061	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GTGCTGCTCTTTGGCCTCTTT	0.498																																					p.K1061T		.											.	EPB41L3-95	0			c.A3182C						.						208	171	184					18																	5394764		2203	4300	6503	SO:0001583	missense	23136	exon22			TGCTCTTTGGCCT	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.3182A>C	18.37:g.5394764T>G	ENSP00000343158:p.Lys1061Thr	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	125	46	NM_012307	0	0	19	25	6	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.858556	0.91433	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;D;T;T;T;T	0.85339	-1.48;-1.97;-1.48;-1.48;-1.48;-1.48	5.82	5.82	0.92795	Band 4.1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89996	0.6877	L	0.49126	1.545	0.80722	D	1	D;D;D;D;P;D;P	0.89917	1.0;1.0;1.0;1.0;0.66;1.0;0.887	D;D;D;D;B;D;P	0.91635	0.996;0.99;0.994;0.998;0.376;0.999;0.809	D	0.88953	0.3388	10	0.36615	T	0.2	.	16.1814	0.81903	0.0:0.0:0.0:1.0	.	358;366;453;730;839;1061;296	E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;E41L3_HUMAN;.	T	1061;730;730;358;366;1061;839	ENSP00000343158:K1061T;ENSP00000442091:K730T;ENSP00000392195:K358T;ENSP00000442233:K366T;ENSP00000341138:K1061T;ENSP00000382981:K839T	ENSP00000343158:K1061T	K	-	2	0	EPB41L3	5384764	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.991000	0.88244	2.234000	0.73211	0.533000	0.62120	AAA	.		0.498	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		G	5394764	T	G	5394764	3	3	12	1	0	0	0	0	1	0	0	0	5167	1841	64	5	85	5	EPB41L3	18	5394764	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		5394764	72682484	84	974											
MEP1B	4225	broad.mit.edu;bcgsc.ca	37	chr18	29787415	29787415	+	Frame_Shift_Del	DEL	A	A	-																															actctgatctcctaaagttgAatcaactgtataactgctgt																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr18:29787415delA	ENST00000269202.6	+	8	795	c.748delA	c.(748-750)aatfs	p.N250fs	MEP1B_ENST00000581447.1_Frame_Shift_Del_p.N250fs	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	250	Metalloprotease.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CCTAAAGTTGAATCAACTGTA	0.398																																					p.N250fs													.	MEP1B-92	0			c.748delA						.						43	40	41					18																	29787415		1906	4127	6033	SO:0001589	frameshift_variant	4225	exon8			AAGTTGAATCAAC	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.748delA	18.37:g.29787415delA	ENSP00000269202:p.Asn250fs	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	24	8	NM_005925	0	0	0	0	0	B7ZM35|B9EGL6|Q670J1	Frame_Shift_Del	DEL	ENST00000269202.6	37	CCDS45846.1																																																																																			.		0.398	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		-	29787415	A	-	29787415	7	5	12	1	0	1	0	1	0	0	0	0	9501	246	9	0	778	0	MEP1B	18	29787415	Frame_Shift_Del	DEL	A	TCGA-A4-7997-01A-11D-2201-08	24392651	29787415	48289833	85	975											
STK11	6794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1223168	1223168	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acactcaggacttcacggtgCccggtgagtctggcgggggc	6	7	16	12	3	3	1	2	1	1	0	3	2	3	2	1	6	1	0	1	6	0	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:1223168C>T	ENST00000326873.7	+	8	2278	c.1105C>T	c.(1105-1107)Ccc>Tcc	p.P369S		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	369					activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCACGGTGCCCGGTGAGTC	0.642		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.P369S		.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	.	STK11-5227	20	Whole gene deletion(20)	cervix(14)|lung(2)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C1105T						.						36	45	42					19																	1223168		2094	4215	6309	SO:0001583	missense	6794	exon8	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	ACGGTGCCCGGTG	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.1105C>T	19.37:g.1223168C>T	ENSP00000324856:p.Pro369Ser	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_000455	0	0	0	0	0	B2RBX7|E7EW76	Missense_Mutation	SNP	ENST00000326873.7	37	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	.	15.23	2.770635	0.49680	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	T	0.68181	-0.31	3.66	3.66	0.41972	.	0.115197	0.64402	N	0.000011	T	0.62889	0.2465	M	0.71581	2.175	0.80722	D	1	P	0.40398	0.716	B	0.39339	0.297	T	0.62728	-0.6793	10	0.10636	T	0.68	-19.522	14.5402	0.67987	0.0:1.0:0.0:0.0	.	369	Q15831	STK11_HUMAN	S	369	ENSP00000324856:P369S	ENSP00000324856:P369S	P	+	1	0	STK11	1174168	1.000000	0.71417	1.000000	0.80357	0.216000	0.24613	7.025000	0.76449	1.884000	0.54569	0.313000	0.20887	CCC	.		0.642	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1223168	C	T	1223168	3	4	12	1	0	0	0	0	1	0	0	0	15319	739	26	2	1135	2	STK11	19	1223168	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		1223168	57905815	86	976											
ZNF433	163059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12126384	12126384	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtttgaaggagtgaggcaGatctgaaggctttcccacat	10	11	13	7	0	1	4	0	3	1	1	2	5	2	5	1	3	0	3	1	3	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:12126384G>T	ENST00000344980.6	-	4	1468	c.1298C>A	c.(1297-1299)tCt>tAt	p.S433Y	CTD-2006C1.2_ENST00000406892.2_RNA|ZNF433_ENST00000419886.2_Missense_Mutation_p.S398Y|CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	433					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)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						GAGTGAGGCAGATCTGAAGGC	0.418																																					p.S433Y		.											.	.	0			c.C1298A						.						93	97	96					19																	12126384		2202	4300	6502	SO:0001583	missense	163059	exon4			GAGGCAGATCTGA	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"Zinc fingers, C2H2-type", "-"	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.1298C>A	19.37:g.12126384G>T	ENSP00000339767:p.Ser433Tyr	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	118	34	NM_001080411	0	0	4	9	5	Q86VX3	Missense_Mutation	SNP	ENST00000344980.6	37	CCDS45983.1	.	.	.	.	.	.	.	.	.	.	G	1.694	-0.503274	0.04261	.	.	ENSG00000197647	ENST00000419886;ENST00000344980	T;T	0.06608	3.28;3.28	1.18	-2.37	0.06643	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06462	0.0166	L	0.45744	1.44	0.09310	N	1	D	0.56746	0.977	P	0.53224	0.721	T	0.16217	-1.0410	9	0.02654	T	1	.	0.9392	0.01351	0.1557:0.2904:0.2991:0.2549	.	433	Q8N7K0	ZN433_HUMAN	Y	398;433	ENSP00000393416:S398Y;ENSP00000339767:S433Y	ENSP00000339767:S433Y	S	-	2	0	ZNF433	11987384	0.000000	0.05858	0.000000	0.03702	0.881000	0.50899	-3.866000	0.00347	-1.541000	0.01727	0.298000	0.19748	TCT	.		0.418	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602		T	12126384	G	T	12126384	3	4	12	1	0	0	0	0	1	0	0	0	17939	942	33	4	727	4	ZNF433	19	12126384	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	10903216	12126384	47002599	87	977											
KIAA1683	80726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18368726	18368726	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgccaggtagccacggacgCccgcctggatagtgatcact	8	6	13	14	4	1	1	1	1	0	0	1	3	1	3	4	3	1	1	4	3	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:18368726C>G	ENST00000600328.3	-	4	3000	c.2807G>C	c.(2806-2808)gGc>gCc	p.G936A	KIAA1683_ENST00000392413.4_Missense_Mutation_p.G1123A|KIAA1683_ENST00000600359.3_Missense_Mutation_p.G890A|PDE4C_ENST00000355502.3_5'Flank|PDE4C_ENST00000596647.1_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	936	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCCACGGACGCCCGCCTGGAT	0.672																																					p.G1123A		.											.	KIAA1683-92	0			c.G3368C						.						51	53	52					19																	18368726		2201	4295	6496	SO:0001583	missense	80726	exon4			CGGACGCCCGCCT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2807G>C	19.37:g.18368726C>G	ENSP00000470780:p.Gly936Ala	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	127	41	NM_001145304	0	0	0	0	0	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	C	8.574	0.880834	0.17467	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.21932	1.98;1.98;1.98	4.33	-0.667	0.11395	.	0.473857	0.15866	N	0.240773	T	0.09992	0.0245	N	0.10972	0.075	0.09310	N	1	B;P	0.38148	0.101;0.62	B;P	0.45610	0.073;0.487	T	0.16988	-1.0384	10	0.16896	T	0.51	-0.3503	0.5212	0.00612	0.1866:0.3422:0.2124:0.2589	.	1123;936	E9PDE0;Q9H0B3	.;K1683_HUMAN	A	1123;936;890;200;550	ENSP00000376213:G1123A;ENSP00000352774:G936A;ENSP00000404501:G890A	ENSP00000352774:G936A	G	-	2	0	KIAA1683	18229726	0.000000	0.05858	0.002000	0.10522	0.074000	0.17049	0.457000	0.21875	0.249000	0.21456	0.313000	0.20887	GGC	.		0.672	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			G	18368726	C	G	18368726	3	3	12	1	0	0	0	0	1	0	0	0	8272	739	26	4	739	4	KIAA1683	19	18368726	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	6242342	18368726	40760257	88	978											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927139	23927139	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagtaaggtgtgaggactTgttaaaagctttgccacatt	11	14	10	6	0	1	1	0	1	1	0	1	2	1	2	1	2	2	3	1	2	4	6	rs1852431		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:23927139T>G	ENST00000402377.3	-	4	1354	c.1213A>C	c.(1213-1215)Aag>Cag	p.K405Q	ZNF681_ENST00000395385.3_Missense_Mutation_p.K336Q	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	405					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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TGTGAGGACTTGTTAAAAGCT	0.403																																					p.K405Q		.											.	.	0			c.A1213C						.						69	73	72					19																	23927139		2203	4300	6503	SO:0001583	missense	148213	exon4			AGGACTTGTTAAA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1213A>C	19.37:g.23927139T>G	ENSP00000384000:p.Lys405Gln	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	75	4	NM_138286	0	0	1	9	8	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	0	-2.720447	0.00092	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07444	3.19;3.19	1.51	-3.01	0.05463	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.02275	-0.615	0.09310	N	1	B	0.17465	0.022	B	0.15870	0.014	T	0.33033	-0.9884	9	0.02654	T	1	.	5.6438	0.17579	0.151:0.0:0.5623:0.2867	rs1852431	405	Q96N22	ZN681_HUMAN	Q	405;336	ENSP00000384000:K405Q;ENSP00000378783:K336Q	ENSP00000378783:K336Q	K	-	1	0	ZNF681	23718979	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.510000	0.00063	-2.559000	0.00474	-2.453000	0.00207	AAG	.		0.403	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23927139	T	G	23927139	3	3	12	1	0	0	0	0	1	0	0	0	18120	1821	63	5	728	5	ZNF681	19	23927139	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	5558413	23927139	35201844	89	979											
U2AF2	11338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56180114	56180114	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtgccacggggctctccaagGgctacgccttctgtgagtac	6	9	13	13	2	2	1	0	1	2	0	3	1	2	1	3	3	3	3	3	3	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:56180114G>A	ENST00000308924.4	+	9	941	c.901G>A	c.(901-903)Ggc>Agc	p.G301S	U2AF2_ENST00000590551.1_Missense_Mutation_p.G137S|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000450554.2_Missense_Mutation_p.G301S			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	301	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		GCTCTCCAAGGGCTACGCCTT	0.617																																					p.G301S		.											.	U2AF2-91	0			c.G901A						.						68	65	66					19																	56180114		2203	4300	6503	SO:0001583	missense	11338	exon9			TCCAAGGGCTACG	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"RNA binding motif (RRM) containing"	23156	protein-coding gene	gene with protein product	"U2 small nuclear ribonucleoprotein auxiliary factor (65kD)", "splicing factor U2AF 65 kD subunit", "U2 snRNP auxiliary factor large subunit"	191318	"U2 (RNU2) small nuclear RNA auxiliary factor 2"			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.901G>A	19.37:g.56180114G>A	ENSP00000307863:p.Gly301Ser	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	91	30	NM_001012478	0	0	72	163	91	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	37	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448539	0.96205	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	D;T	0.83419	-1.72;0.1	4.4	4.4	0.53042	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.94683	0.8285	H	0.98646	4.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96949	0.9693	10	0.87932	D	0	-32.268	16.1527	0.81634	0.0:0.0:1.0:0.0	.	301;301	P26368;P26368-2	U2AF2_HUMAN;.	S	301	ENSP00000307863:G301S;ENSP00000388475:G301S	ENSP00000307863:G301S	G	+	1	0	U2AF2	60871926	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.145000	0.94634	2.184000	0.69523	0.655000	0.94253	GGC	.		0.617	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		A	56180114	G	A	56180114	3	1	12	1	0	0	0	0	1	0	0	0	16856	1232	43	2	935	2	U2AF2	19	56180114	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	32252975	56180114	2948869	90	980											
TBC1D20	128637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	419913	419913	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atgtcacagtcacagtccagGacttcctgctcgcgatacaa	11	9	8	13	2	2	0	2	0	0	0	5	2	4	1	2	1	2	1	2	1	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:419913G>T	ENST00000354200.4	-	7	942	c.795C>A	c.(793-795)gtC>gtA	p.V265V	TBC1D20_ENST00000461188.1_5'UTR	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	265					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				CACAGTCCAGGACTTCCTGCT	0.562																																					p.V265V		.											.	TBC1D20-90	0			c.C795A						.						137	118	124					20																	419913		2203	4300	6503	SO:0001819	synonymous_variant	128637	exon7			GTCCAGGACTTCC	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.795C>A	20.37:g.419913G>T		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	81	48	NM_144628	0	0	22	51	29	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Silent	SNP	ENST00000354200.4	37	CCDS13002.1																																																																																			.		0.562	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		T	419913	G	T	419913	2	4	12	1	0	0	0	0	0	0	0	1	15641	1161	41	4		4	TBC1D20	20	419913	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08		419913	62605607	91	981											
FAM65C	140876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49219116	49219116	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcgctgtcagacaggtagctGaggatggaggtggcccttgg	7	9	17	8	1	1	2	1	1	0	1	2	4	1	4	1	6	1	3	1	6	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:49219116G>A	ENST00000327979.2	-	13	1551	c.1140C>T	c.(1138-1140)ctC>ctT	p.L380L	FAM65C_ENST00000535356.1_Silent_p.L384L|FAM65C_ENST00000045083.2_Silent_p.L380L			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	380										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACAGGTAGCTGAGGATGGAGG	0.637																																					p.L380L		.											.	FAM65C-92	0			c.C1140T						.						26	28	27					20																	49219116		2061	4109	6170	SO:0001819	synonymous_variant	140876	exon13			GTAGCTGAGGATG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1140C>T	20.37:g.49219116G>A		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	115	24	NM_080829	0	0	16	16	0	Q5QPB6|Q9NQQ2	Silent	SNP	ENST00000327979.2	37	CCDS13431.2																																																																																			.		0.637	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			A	49219116	G	A	49219116	2	1	12	1	0	0	0	0	0	0	0	1	5620	1277	45	2		2	FAM65C	20	49219116	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	48799203	49219116	13806404	92	982											
CYP24A1	1591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	52773943	52773943	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacccaacaaagagccaaaTgcagttgaagctctgctaat	15	9	7	10	0	1	2	0	1	1	1	1	2	1	2	2	0	6	4	2	0	6	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:52773943T>C	ENST00000216862.3	-	10	1811	c.1418A>G	c.(1417-1419)cAt>cGt	p.H473R	CYP24A1_ENST00000395954.3_Missense_Mutation_p.H331R|CYP24A1_ENST00000395955.3_Intron|CYP24A1_ENST00000460643.1_5'Flank	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	473					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	AAGAGCCAAATGCAGTTGAAG	0.423																																					p.H473R		.											.	CYP24A1-228	0			c.A1418G						.						81	76	78					20																	52773943		2203	4300	6503	SO:0001583	missense	1591	exon10			GCCAAATGCAGTT	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"Cytochrome P450s"	2602	protein-coding gene	gene with protein product		126065	"cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.1418A>G	20.37:g.52773943T>C	ENSP00000216862:p.His473Arg	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	85	42	NM_000782	0	0	45	143	98	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	t	15.34	2.805491	0.50315	.	.	ENSG00000019186	ENST00000216862;ENST00000395954	T;T	0.67345	-0.26;-0.26	5.2	4.06	0.47325	.	0.101356	0.64402	D	0.000001	T	0.63698	0.2533	N	0.25992	0.78	0.41376	D	0.987529	D;P	0.54964	0.969;0.934	P;B	0.55161	0.77;0.424	T	0.60979	-0.7155	10	0.33141	T	0.24	-19.4807	11.563	0.50788	0.0:0.0:0.1498:0.8502	.	473;331	Q07973;Q5I2W7	CP24A_HUMAN;.	R	473;331	ENSP00000216862:H473R;ENSP00000379284:H331R	ENSP00000216862:H473R	H	-	2	0	CYP24A1	52207350	1.000000	0.71417	0.969000	0.41365	0.303000	0.27691	4.744000	0.62118	0.884000	0.36064	0.451000	0.29950	CAT	.		0.423	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			C	52773943	T	C	52773943	3	2	12	1	0	0	0	0	1	0	0	0	4160	1464	51	3	134	3	CYP24A1	20	52773943	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	3554827	52773943	10251577	93	983											
LIME1	54923	broad.mit.edu	37	chr20	62369217	62369217	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaagagggcgcggaggcagCgggcgaggctgcagggcagt	8	2	23	8	4	0	1	0	0	0	1	0	4	0	3	0	7	2	4	0	7	1	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:62369217C>T	ENST00000309546.3	+	3	229	c.142C>T	c.(142-144)Cgg>Tgg	p.R48W	LIME1_ENST00000490824.1_3'UTR|RP4-583P15.15_ENST00000490623.2_3'UTR|SLC2A4RG_ENST00000266077.2_5'Flank|RP4-583P15.14_ENST00000467211.1_5'Flank	NM_017806.2	NP_060276.2	Q9H400	LIME1_HUMAN	Lck interacting transmembrane adaptor 1	48					B cell receptor signaling pathway (GO:0050853)|T cell receptor signaling pathway (GO:0050852)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|liver(1)	3	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GCGGAGGCAGCGGGCGAGGCT	0.756																																					p.R48W													.	LIME1-44	0			c.C142T						.						7	8	7					20																	62369217		2102	4177	6279	SO:0001583	missense	54923	exon3			AGGCAGCGGGCGA	AK000413	CCDS13536.1	20q13.33	2010-05-11			ENSG00000203896	ENSG00000203896			26016	protein-coding gene	gene with protein product		609809				12477932	Standard	NM_017806		Approved	FLJ20406, dJ583P15.4, LIME	uc002ygp.4	Q9H400	OTTHUMG00000032999	ENST00000309546.3:c.142C>T	20.37:g.62369217C>T	ENSP00000309521:p.Arg48Trp	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	29	4	NM_017806	0	0	36	36	0	E1P5K5|E1P5K6|Q5JWJ2|Q6XYB3|Q9NX69	Missense_Mutation	SNP	ENST00000309546.3	37	CCDS13536.1	.	.	.	.	.	.	.	.	.	.	c	12.37	1.916705	0.33815	.	.	ENSG00000203896	ENST00000444951;ENST00000309546	T;T	0.46063	0.88;0.88	4.09	0.988	0.19796	.	.	.	.	.	T	0.20780	0.0500	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.19063	-1.0317	9	0.66056	D	0.02	.	5.114	0.14825	0.0:0.5647:0.1546:0.2807	.	48	Q9H400	LIME1_HUMAN	W	48	ENSP00000414506:R48W;ENSP00000309521:R48W	ENSP00000309521:R48W	R	+	1	2	LIME1	61839661	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.255000	0.08769	0.325000	0.23359	-0.760000	0.03462	CGG	.		0.756	LIME1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080225.1	NM_017806		T	62369217	C	T	62369217	3	4	12	1	0	0	0	0	1	0	0	0	8822	759	27	1	148	1	LIME1	20	62369217	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	9595274	62369217	656303	94	984											
APP	351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	27348294	27348294	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgccttcttatcagctttAggcaagttctttgcttgacg	7	16	8	10	1	3	1	1	1	2	0	3	1	3	1	1	1	3	4	1	1	3	7			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr21:27348294A>C	ENST00000346798.3	-	10	1305	c.1272T>G	c.(1270-1272)ccT>ccG	p.P424P	APP_ENST00000354192.3_Silent_p.P293P|APP_ENST00000359726.3_Silent_p.P368P|APP_ENST00000357903.3_Silent_p.P405P|APP_ENST00000440126.3_Silent_p.P400P|APP_ENST00000439274.2_Silent_p.P368P|APP_ENST00000448388.2_Silent_p.P314P|APP_ENST00000348990.5_Silent_p.P349P|APP_ENST00000358918.3_Silent_p.P424P	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	424					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TATCAGCTTTAGGCAAGTTCT	0.383																																					p.P424P		.											.	APP-91	0			c.T1272G						.						249	199	216					21																	27348294		2203	4300	6503	SO:0001819	synonymous_variant	351	exon10			AGCTTTAGGCAAG	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1272T>G	21.37:g.27348294A>C		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	96	28	NM_000484	3	4	2245	5139	2887	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.472507	0.26423	.	.	ENSG00000142192	ENST00000448850;ENST00000415997	.	.	.	5.11	-5.12	0.02893	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.1356	2.2262	0.03985	0.1134:0.1931:0.3431:0.3504	.	.	.	.	E	327;159	.	.	X	-	1	0	APP	26270165	0.085000	0.21516	0.973000	0.42090	0.999000	0.98932	-0.688000	0.05150	-0.726000	0.04895	0.529000	0.55759	TAA	.		0.383	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27348294	A	C	27348294	2	2	12	1	0	0	0	0	0	0	0	1	815	407	15	5		5	APP	21	27348294	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08		27348294	20781601	95	985											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46930115	46930115	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcctgtcctcgcgcctgcaGgacctgtacagcatcgtgcg	5	10	11	15	4	0	0	0	0	0	0	4	1	2	1	4	1	4	3	4	1	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr21:46930115G>A	ENST00000359759.4	+	39	4899	c.4878G>A	c.(4876-4878)caG>caA	p.Q1626Q	SLC19A1_ENST00000567670.1_Intron|SLC19A1_ENST00000468508.1_5'Flank|COL18A1_ENST00000400337.2_Silent_p.Q1211Q|COL18A1_ENST00000355480.5_Silent_p.Q1391Q			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1626	Nonhelical region 11 (NC11).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CGCGCCTGCAGGACCTGTACA	0.726																																					p.Q1388Q		.											.	COL18A1-90	0			c.G4164A						.						8	11	10					21																	46930115		2006	4132	6138	SO:0001819	synonymous_variant	80781	exon40			CCTGCAGGACCTG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4878G>A	21.37:g.46930115G>A		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_030582	0	0	162	162	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	G	9.305	1.053998	0.19907	.	.	ENSG00000182871	ENST00000423214	.	.	.	4.46	1.57	0.23409	.	.	.	.	.	T	0.55721	0.1938	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48222	-0.9054	4	.	.	.	.	8.1174	0.30950	0.3609:0.0:0.6391:0.0	.	.	.	.	K	196	.	.	R	+	2	0	COL18A1	45754543	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	0.958000	0.29227	0.444000	0.26612	-0.137000	0.14449	AGG	.		0.726	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46930115	G	A	46930115	2	1	12	1	0	0	0	0	0	0	0	1	3681	991	35	2		2	COL18A1	21	46930115	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	19581821	46930115	1199780	96	986											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38150890	38150890	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcctccttgcagcctcccTccccctcgctcaccaccacc	5	8	3	25	1	1	0	1	0	0	0	6	0	5	0	9	0	2	2	9	0	0	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr22:38150890T>C	ENST00000406386.3	+	13	5641	c.5386T>C	c.(5386-5388)Tcc>Ccc	p.S1796P	TRIOBP_ENST00000403663.2_Missense_Mutation_p.S83P|TRIOBP_ENST00000407319.2_Missense_Mutation_p.S83P	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1796	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GCAGCCTCCCTCCCCCTCGCT	0.517																																					p.S1796P		.											.	TRIOBP-136	0			c.T5386C						.						204	151	169					22																	38150890		2203	4300	6503	SO:0001583	missense	11078	exon13			CCTCCCTCCCCCT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.5386T>C	22.37:g.38150890T>C	ENSP00000384312:p.Ser1796Pro	Somatic	102	1		WXS	Illumina HiSeq	Phase_I	108	7	NM_001039141	0	0	0	0	0	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.340653	0.41498	.	.	ENSG00000100106	ENST00000406386;ENST00000407319;ENST00000403663;ENST00000418339;ENST00000452519;ENST00000417857	T	0.21361	2.01	4.81	-2.04	0.07343	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	T	0.15998	0.0385	L	0.52905	1.665	0.09310	N	1	B;B;B	0.12013	0.0;0.0;0.005	B;B;B	0.12156	0.0;0.002;0.007	T	0.31194	-0.9952	9	0.36615	T	0.2	.	3.4612	0.07533	0.2773:0.2069:0.0:0.5157	.	83;83;1796	F8W6V6;F2Z2W0;Q9H2D6	.;.;TARA_HUMAN	P	1796;83;83;42;12;12	ENSP00000384312:S1796P	ENSP00000386026:S83P	S	+	1	0	TRIOBP	36480836	0.002000	0.14202	0.012000	0.15200	0.667000	0.39255	0.161000	0.16481	-0.406000	0.07588	0.533000	0.62120	TCC	.		0.517	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			C	38150890	T	C	38150890	3	2	12	1	0	0	0	0	1	0	0	0	16586	1551	54	3	5615	3	TRIOBP	22	38150890	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		38150890	13153676	97	987											
ARAF	369	hgsc.bcm.edu	37	chrX	47426120	47426120	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacagcgcatccgctccacgTccactcccaacgtccatatg	9	8	6	18	4	0	0	0	0	0	0	5	0	5	0	5	0	3	2	5	0	3	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chrX:47426120T>G	ENST00000377045.4	+	7	834	c.640T>G	c.(640-642)Tcc>Gcc	p.S214A	ARAF_ENST00000290277.6_Intron	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	214					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	CCGCTCCACGTCCACTCCCAA	0.662																																					p.S217A		.											.	ARAF-1557	0			c.T649G						.						71	57	62					X																	47426120		2203	4300	6503	SO:0001583	missense	369	exon7			TCCACGTCCACTC	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"v-raf murine sarcoma 3611 viral oncogene homolog 1"	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.640T>G	X.37:g.47426120T>G	ENSP00000366244:p.Ser214Ala	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001256196	0	0	57	58	1	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	37	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494658	0.64186	.	.	ENSG00000078061	ENST00000377045	T	0.75821	-0.97	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	M	0.78456	2.415	0.80722	D	1	B;P	0.39903	0.403;0.694	B;B	0.43018	0.142;0.405	T	0.80745	-0.1245	10	0.87932	D	0	.	12.2128	0.54389	0.0:0.0:0.0:1.0	.	214;80	P10398;B4DV85	ARAF_HUMAN;.	A	214	ENSP00000366244:S214A	ENSP00000366244:S214A	S	+	1	0	ARAF	47311064	1.000000	0.71417	0.887000	0.34795	0.944000	0.59088	7.542000	0.82095	1.788000	0.52465	0.441000	0.28932	TCC	.		0.662	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1			G	47426120	T	G	47426120	3	3	12	1	0	0	0	0	1	0	0	0	837	1667	58	5	662	5	ARAF	23	47426120	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		47426120	107844440	98	988											
TRO	7216	hgsc.bcm.edu	37	chrX	54948719	54948719	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acggatatagggtgcctctaTttcaggtgaggcctctctgc	7	12	12	10	1	3	1	1	1	2	0	4	2	3	2	2	4	2	0	2	4	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chrX:54948719T>G	ENST00000173898.7	+	2	152	c.40T>G	c.(40-42)Ttt>Gtt	p.F14V	TRO_ENST00000484031.1_3'UTR|TRO_ENST00000319167.8_Missense_Mutation_p.F14V|TRO_ENST00000375022.4_Missense_Mutation_p.F14V|TRO_ENST00000399736.1_Missense_Mutation_p.F14V|TRO_ENST00000375041.2_Missense_Mutation_p.F14V|TRO_ENST00000420798.2_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	14					embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						GGTGCCTCTATTTCAGGTGAG	0.507																																					p.F14V		.											.	TRO-131	0			c.T40G						.						127	114	118					X																	54948719		1971	4133	6104	SO:0001583	missense	7216	exon2			CCTCTATTTCAGG	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.40T>G	X.37:g.54948719T>G	ENSP00000173898:p.Phe14Val	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_016157	0	0	3	3	0	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	T	3.075	-0.190361	0.06299	.	.	ENSG00000067445	ENST00000442098;ENST00000173898;ENST00000319167;ENST00000375022;ENST00000399736;ENST00000319179;ENST00000431115;ENST00000375041;ENST00000440759;ENST00000416704	T;T;T;T;T;T;T;T;T	0.55930	0.49;3.3;3.17;3.17;2.62;1.81;3.62;0.5;0.5	3.15	1.93	0.25924	.	.	.	.	.	T	0.29749	0.0743	N	0.24115	0.695	0.26674	N	0.971676	B;B;B;P	0.43094	0.384;0.056;0.036;0.799	B;B;B;B	0.30782	0.078;0.004;0.014;0.12	T	0.15809	-1.0424	9	0.72032	D	0.01	.	5.5808	0.17248	0.0:0.0:0.2837:0.7163	.	14;14;14;14	B1AKE9;B1AKF1;Q96SX2;Q12816	.;.;.;TROP_HUMAN	V	14	ENSP00000404645:F14V;ENSP00000173898:F14V;ENSP00000318278:F14V;ENSP00000364162:F14V;ENSP00000382641:F14V;ENSP00000407996:F14V;ENSP00000364181:F14V;ENSP00000406574:F14V;ENSP00000404767:F14V	ENSP00000173898:F14V	F	+	1	0	TRO	54965444	0.669000	0.27502	0.342000	0.25602	0.080000	0.17528	0.843000	0.27640	0.419000	0.25927	0.417000	0.27973	TTT	.		0.507	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		G	54948719	T	G	54948719	3	3	12	1	0	0	0	0	1	0	0	0	16607	1493	52	5	42	5	TRO	23	54948719	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	7522599	54948719	100321841	99	989											
MYOM3	127294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	24416117	24416117	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctctcggatctcgctggCatggacattggttggcggtg	4	11	16	10	3	2	0	0	0	2	0	4	2	2	2	1	7	0	3	1	7	0	2	rs201031583		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:24416117C>G	ENST00000374434.3	-	14	1687	c.1525G>C	c.(1525-1527)Gcc>Ccc	p.A509P	MYOM3_ENST00000330966.7_Missense_Mutation_p.A510P|MYOM3_ENST00000329601.7_Missense_Mutation_p.A509P|MYOM3_ENST00000475306.1_5'UTR|RP11-293P20.2_ENST00000439239.2_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	509	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		ATCTCGCTGGCATGGACATTG	0.602																																					p.A509P		.											.	MYOM3-93	0			c.G1525C						.						34	38	37					1																	24416117		2019	4174	6193	SO:0001583	missense	127294	exon14			CGCTGGCATGGAC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	26679	protein-coding gene	gene with protein product			"myomesin family, member 3"			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1525G>C	1.37:g.24416117C>G	ENSP00000363557:p.Ala509Pro	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_152372	0	0	0	0	0	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.139059	0.56936	.	.	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.60548	0.18;0.18;0.18	5.5	5.5	0.81552	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.155897	0.56097	D	0.000027	T	0.72510	0.3469	M	0.67953	2.075	0.38183	D	0.939678	P;D;D	0.69078	0.784;0.997;0.994	P;D;D	0.71184	0.782;0.972;0.928	T	0.74057	-0.3787	10	0.40728	T	0.16	.	14.6425	0.68737	0.0:0.9282:0.0:0.0718	.	166;509;509	Q6ZU56;Q5VTT5-2;Q5VTT5	.;.;MYOM3_HUMAN	P	509;510;509	ENSP00000363557:A509P;ENSP00000332670:A510P;ENSP00000328415:A509P	ENSP00000328415:A509P	A	-	1	0	MYOM3	24288704	1.000000	0.71417	0.966000	0.40874	0.226000	0.24999	6.278000	0.72614	2.600000	0.87896	0.655000	0.94253	GCC	.		0.602	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		G	24416117	C	G	24416117	3	3	13	1	0	0	0	0	1	0	0	0	10118	710	25	4	2884	4	MYOM3	1	24416117	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08		24416117	224834504	1	990											
L1TD1	54596	hgsc.bcm.edu	37	chr1	62675665	62675665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctcagggctggaggaggagGaggaagagccctcagggctg	9	4	19	9	0	2	1	2	0	0	1	2	6	2	6	2	7	1	2	2	7	1	0	rs532563709		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:62675665G>A	ENST00000498273.1	+	4	1514	c.1219G>A	c.(1219-1221)Gag>Aag	p.E407K	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	407	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						ggaggaggaggaggaagagcc	0.552																																					p.E407K		.											.	L1TD1-92	0			c.G1219A						.						36	40	38					1																	62675665		2200	4299	6499	SO:0001583	missense	54596	exon5			GAGGAGGAGGAAG	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1219G>A	1.37:g.62675665G>A	ENSP00000419901:p.Glu407Lys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_001164835	0	0	0	0	0	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.064442	0.36470	.	.	ENSG00000240563	ENST00000498273	T	0.10192	2.9	3.4	1.41	0.22369	.	.	.	.	.	T	0.06508	0.0167	N	0.24115	0.695	0.09310	N	1	B	0.25235	0.121	B	0.19148	0.024	T	0.35001	-0.9806	9	0.56958	D	0.05	.	3.8632	0.09005	0.1308:0.0:0.6037:0.2655	.	407	Q5T7N2	LITD1_HUMAN	K	407	ENSP00000419901:E407K	ENSP00000419901:E407K	E	+	1	0	L1TD1	62448253	0.054000	0.20591	0.000000	0.03702	0.033000	0.12548	0.260000	0.18424	0.403000	0.25479	0.448000	0.29417	GAG	.		0.552	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		A	62675665	G	A	62675665	3	1	13	1	0	0	0	0	1	0	0	0	8610	1175	41	2	1225	2	L1TD1	1	62675665	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	38259548	62675665	186574956	2	991											
RBM15	64783	broad.mit.edu	37	chr1	110883162	110883162	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctaaccggacgctcttcttgGgcaacctagacatcactgta	10	10	8	13	2	3	1	1	0	2	1	3	2	3	2	2	2	2	3	2	2	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:110883162G>T	ENST00000369784.3	+	1	2035	c.1135G>T	c.(1135-1137)Ggc>Tgc	p.G379C	RBM15_ENST00000487146.2_Missense_Mutation_p.G379C|RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Missense_Mutation_p.G379C	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	379	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GCTCTTCTTGGGCAACCTAGA	0.522			T	MKL1	acute megakaryocytic leukemia																																p.G379C				Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15-661	0			c.G1135T						.						49	47	48					1																	110883162		2203	4300	6503	SO:0001583	missense	64783	exon1			TTCTTGGGCAACC	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.1135G>T	1.37:g.110883162G>T	ENSP00000358799:p.Gly379Cys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_022768	0	0	0	0	0	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.842591	0.71488	.	.	ENSG00000162775	ENST00000369784	T	0.11712	2.75	4.69	4.69	0.59074	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.45126	D	0.000395	T	0.27134	0.0665	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.97110	0.937;1.0	T	0.04307	-1.0961	10	0.87932	D	0	-12.0588	17.7957	0.88570	0.0:0.0:1.0:0.0	.	379;379	Q96T37-3;Q96T37	.;RBM15_HUMAN	C	379	ENSP00000358799:G379C	ENSP00000358799:G379C	G	+	1	0	RBM15	110684685	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.232000	0.95325	2.446000	0.82766	0.655000	0.94253	GGC	.		0.522	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		T	110883162	G	T	110883162	3	4	13	1	0	0	0	0	1	0	0	0	13148	1232	43	4	1137	4	RBM15	1	110883162	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	48207497	110883162	138367459	3	992											
NBPF9	0	broad.mit.edu	37	chr1	144615252	144615252	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcgtaaacctcaaagagaTgttttctaactcaactggcc	12	12	7	10	1	3	1	2	0	1	1	4	2	3	1	2	1	3	3	2	1	5	5	rs202192397		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:144615252T>A								RP11-640M9.2 (9361 upstream) : NBPF9 (196491 downstream)																							CTCAAAGAGATGTTTTCTAAC	0.463																																					.													.	.	0			.						.																																			SO:0001628	intergenic_variant	400818	.			AAGAGATGTTTTC																													1.37:g.144615252T>A		Somatic	263	1		WXS	Illumina HiSeq	Phase_I	172	6	.	0	0	0	0	0		Missense_Mutation	SNP		37																																																																																				A|0.500;G|0.500	0	0.463									A	144615252	T	A	144615252	1	1	13	0	1	0	0	0	0	0	0	0	10225	1464	51	5		5	NBPF9	1	144615252	IGR	SNP	T	TCGA-A4-8098-01A-11D-2396-08	33732090	144615252	104635369	4	993											
ITGA10	8515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145532515	145532515	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctttcctgagagaaattaGaactattgccagtgatccag	12	12	8	9	0	1	4	0	2	1	2	3	5	3	4	3	0	2	0	3	0	4	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:145532515G>A	ENST00000369304.3	+	9	1143	c.968G>A	c.(967-969)aGa>aAa	p.R323K	ITGA10_ENST00000539363.1_Missense_Mutation_p.R180K|ITGA10_ENST00000481236.1_3'UTR|ITGA10_ENST00000538811.1_Missense_Mutation_p.R192K	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	323	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AGAGAAATTAGAACTATTGCC	0.473																																					p.R323K		.											.	ITGA10-231	0			c.G968A						.						144	138	140					1																	145532515		2203	4300	6503	SO:0001583	missense	8515	exon9			AAATTAGAACTAT	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"Integrins"	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.968G>A	1.37:g.145532515G>A	ENSP00000358310:p.Arg323Lys	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	170	66	NM_003637	0	0	0	0	0	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	7.649	0.682583	0.14907	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	D;D;D	0.83914	-1.78;-1.78;-1.78	5.27	4.34	0.51931	von Willebrand factor, type A (3);	0.060779	0.64402	D	0.000004	T	0.34600	0.0903	N	0.01771	-0.73	0.35261	D	0.779612	B;B;B;B	0.18741	0.024;0.024;0.024;0.03	B;B;B;B	0.23150	0.021;0.021;0.044;0.036	T	0.39292	-0.9621	10	0.02654	T	1	.	7.3767	0.26833	0.1809:0.0:0.8191:0.0	.	289;192;180;323	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	K	323;289;180;192	ENSP00000358310:R323K;ENSP00000439894:R180K;ENSP00000440011:R192K	ENSP00000358310:R323K	R	+	2	0	ITGA10	144243872	1.000000	0.71417	0.974000	0.42286	0.966000	0.64601	5.786000	0.69006	2.653000	0.90120	0.561000	0.74099	AGA	.		0.473	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		A	145532515	G	A	145532515	3	1	13	1	0	0	0	0	1	0	0	0	7894	942	33	2	1002	2	ITGA10	1	145532515	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	917263	145532515	103718106	5	994											
SEMA6C	10500	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151109386	151109386	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcagagcggccatgcaggttCacaggcccagtcaaggcctg	9	5	14	13	1	2	1	2	0	0	1	2	1	2	1	3	4	2	3	3	4	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:151109386C>T	ENST00000341697.3	-	11	2612	c.921G>A	c.(919-921)gtG>gtA	p.V307V				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	307	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATGCAGGTTCACAGGCCCAG	0.542																																					p.V307V		.											.	SEMA6C-92	0			c.G921A						.						101	108	106					1																	151109386		2203	4300	6503	SO:0001819	synonymous_variant	10500	exon11			CAGGTTCACAGGC	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.921G>A	1.37:g.151109386C>T		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	165	47	NM_001178061	0	0	0	0	0	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Silent	SNP	ENST00000341697.3	37	CCDS984.1																																																																																			.		0.542	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151109386	C	T	151109386	2	4	13	1	0	0	0	0	0	0	0	1	14073	813	29	2		2	SEMA6C	1	151109386	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	5576871	151109386	98141235	6	995											
HRNR	388697	hgsc.bcm.edu	37	chr1	152190382	152190382	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcggccgcggctaggggaAtggccagatccagacccttg	7	7	15	12	3	0	2	0	0	0	2	2	3	1	3	4	5	0	1	4	5	2	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:152190382A>C	ENST00000368801.2	-	3	3798	c.3723T>G	c.(3721-3723)caT>caG	p.H1241Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1241					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCTAGGGGAATGGCCAGATC	0.632																																					p.H1241Q		.											.	HRNR-93	0			c.T3723G						.						11	1	7					1																	152190382		591	491	1082	SO:0001583	missense	388697	exon3			AGGGGAATGGCCA	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.3723T>G	1.37:g.152190382A>C	ENSP00000357791:p.His1241Gln	Somatic	30	1		WXS	Illumina HiSeq	Phase_I	31	3	NM_001009931	0	0	0	0	0	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	8.219	0.802011	0.16397	.	.	ENSG00000197915	ENST00000368801	T	0.01787	4.64	2.97	0.73	0.18271	.	.	.	.	.	T	0.00328	0.0010	N	0.03154	-0.405	0.53005	P	3.2999999999949736E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.26189	-1.0110	8	0.12766	T	0.61	.	9.7029	0.40198	0.5136:0.4864:0.0:0.0	.	1241	Q86YZ3	HORN_HUMAN	Q	1241	ENSP00000357791:H1241Q	ENSP00000357791:H1241Q	H	-	3	2	HRNR	150457006	0.000000	0.05858	0.075000	0.20258	0.012000	0.07955	-1.453000	0.02383	0.036000	0.15547	-0.232000	0.12228	CAT	.		0.632	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		C	152190382	A	C	152190382	3	2	13	1	0	0	0	0	1	0	0	0	7380	98	4	5	4833	5	HRNR	1	152190382	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	1080996	152190382	97060239	7	996											
PEAR1	375033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156877993	156877993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgactgcgccccggacgccCgttgcttcccggccaacggc	4	5	13	19	7	0	0	0	0	0	0	1	2	1	1	5	3	3	2	5	3	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:156877993C>T	ENST00000338302.3	+	10	1201	c.976C>T	c.(976-978)Cgt>Tgt	p.R326C	PEAR1_ENST00000292357.7_Missense_Mutation_p.R326C			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	326	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCGGACGCCCGTTGCTTCCC	0.692																																					p.R326C		.											.	PEAR1-71	0			c.C976T						.						21	26	24					1																	156877993		2202	4296	6498	SO:0001583	missense	375033	exon9			GACGCCCGTTGCT	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.976C>T	1.37:g.156877993C>T	ENSP00000344465:p.Arg326Cys	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	22	11	NM_001080471	0	0	0	0	0	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373658	0.82573	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	T;T	0.18016	2.24;2.24	4.33	4.33	0.51752	EGF-like, laminin (2);Epidermal growth factor-like, type 3 (1);	0.152429	0.30920	N	0.008604	T	0.30603	0.0770	M	0.72479	2.2	0.58432	D	0.999999	D;D	0.76494	0.998;0.999	D;D	0.70016	0.953;0.967	T	0.05582	-1.0876	10	0.62326	D	0.03	.	14.3643	0.66795	0.0:1.0:0.0:0.0	.	127;326	Q8N780;Q5VY43	.;PEAR1_HUMAN	C	326	ENSP00000344465:R326C;ENSP00000292357:R326C	ENSP00000292357:R326C	R	+	1	0	PEAR1	155144617	0.978000	0.34361	1.000000	0.80357	0.896000	0.52359	2.495000	0.45337	2.230000	0.72887	0.561000	0.74099	CGT	.		0.692	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156877993	C	T	156877993	3	4	13	1	0	0	0	0	1	0	0	0	11738	652	23	1	1006	1	PEAR1	1	156877993	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	4687611	156877993	92372628	8	997											
DUSP27	92235	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167096129	167096129	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctccgacgtcagcctgacAgcctaccaggcctggaagct	8	6	10	17	2	1	1	1	1	0	0	2	3	2	2	6	2	4	1	6	2	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:167096129A>G	ENST00000361200.2	+	6	1927	c.1761A>G	c.(1759-1761)acA>acG	p.T587T	DUSP27_ENST00000443333.1_Silent_p.T587T|DUSP27_ENST00000271385.5_Silent_p.T587T|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	587					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						TCAGCCTGACAGCCTACCAGG	0.597																																					p.T587T		.											.	DUSP27-71	0			c.A1761G						.						45	45	45					1																	167096129		2203	4300	6503	SO:0001819	synonymous_variant	92235	exon5			CCTGACAGCCTAC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1761A>G	1.37:g.167096129A>G		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	63	29	NM_001080426	0	0	0	0	0	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	37	CCDS30932.1																																																																																			.		0.597	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		G	167096129	A	G	167096129	2	3	13	1	0	0	0	0	0	0	0	1	4835	175	7	3		3	DUSP27	1	167096129	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10218136	167096129	82154492	9	998											
ATP1B1	481	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169100749	169100768	+	Frame_Shift_Del	DEL	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	-																															ttgggtacagtgagaaagacCgttttcagggacgttttgat																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:169100749_169100768delCGTTTTCAGGGACGTTTTGA	ENST00000367816.1	+	7	1397_1416	c.868_887delCGTTTTCAGGGACGTTTTGA	c.(868-888)cgttttcagggacgttttgatfs	p.RFQGRFD290fs	ATP1B1_ENST00000367815.4_Frame_Shift_Del_p.RFQGRFD290fs|ATP1B1_ENST00000367813.3_Frame_Shift_Del_p.RFQGRFD282fs|ATP1B1_ENST00000499679.3_Frame_Shift_Del_p.RFQGRFD234fs			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	290	immunoglobulin-like.				blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.R290S(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					TGAGAAAGACCGTTTTCAGGGACGTTTTGATGTAAAAATT	0.4																																					p.290_296del		.											.	ATP1B1-540	1	Substitution - Missense(1)	lung(1)	c.868_887del						.																																			SO:0001589	frameshift_variant	481	exon6			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.868_887delCGTTTTCAGGGACGTTTTGA	1.37:g.169100749_169100768delCGTTTTCAGGGACGTTTTGA	ENSP00000356790:p.Arg290fs	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	79	26	NM_001677	0	0	0	0	0	Q5TGZ3	Frame_Shift_Del	DEL	ENST00000367816.1	37	CCDS1276.1																																																																																			.		0.4	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			-	169100768	CGTTTTCAGGGACGTTTTGA	-	169100749	7	5	13	1	0	1	0	1	0	0	0	0	1133	652	23	0	890	0	ATP1B1	1	169100749	Frame_Shift_Del	DEL	CGTTTTCAGGGACGTTTTGA	TCGA-A4-8098-01A-11D-2396-08	2004620	169100749	80149872	10	999											
C1orf112	55732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169806133	169806133	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgtggcaacatatttcCttccaggcgttacctcctga	7	13	7	14	1	1	1	0	1	1	0	4	1	4	1	5	2	2	2	5	2	3	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:169806133C>T	ENST00000286031.6	+	17	2305	c.1605C>T	c.(1603-1605)tcC>tcT	p.S535S	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Silent_p.S535S	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	535										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AACATATTTCCTTCCAGGCGT	0.438																																					p.S535S		.											.	C1orf112-90	0			c.C1605T						.						73	69	71					1																	169806133		2203	4300	6503	SO:0001819	synonymous_variant	55732	exon17			TATTTCCTTCCAG	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1605C>T	1.37:g.169806133C>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	65	23	NM_018186	0	0	0	0	0	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																			.		0.438	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		T	169806133	C	T	169806133	2	4	13	1	0	0	0	0	0	0	0	1	1991	668	24	2		2	C1orf112	1	169806133	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	705384	169806133	79444488	11	1000											
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203025587	203025587	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcctcacccaggacgctgCggctagagaagcttggccac	8	7	11	15	2	1	1	1	0	0	1	2	3	2	2	3	3	2	3	3	3	2	3	rs549873910		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:203025587C>A	ENST00000447715.2	+	23	2566	c.2125C>A	c.(2125-2127)Cgg>Agg	p.R709R	PPFIA4_ENST00000295706.4_Silent_p.R225R|PPFIA4_ENST00000414050.2_Silent_p.R438R|PPFIA4_ENST00000599966.1_Silent_p.R225R|PPFIA4_ENST00000272198.6_Silent_p.R225R|PPFIA4_ENST00000367240.2_Silent_p.R710R			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	709					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.R856W(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CAGGACGCTGCGGCTAGAGAA	0.567																																					p.R225R		.											.	PPFIA4-230	1	Substitution - Missense(1)	large_intestine(1)	c.C673A						.						37	43	41					1																	203025587		2040	4173	6213	SO:0001819	synonymous_variant	8497	exon5			ACGCTGCGGCTAG	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2125C>A	1.37:g.203025587C>A		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_015053	0	0	0	0	0	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																				.		0.567	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203025587	C	A	203025587	2	1	13	1	0	0	0	0	0	0	0	1	12338	759	27	4		4	PPFIA4	1	203025587	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	33219454	203025587	46225034	12	1001											
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204219693	204219693	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catctgtgtcttgctcgtttAacttgtaggtgtggaggctg	5	16	13	7	1	2	0	0	0	2	0	3	1	2	1	0	3	2	4	0	3	2	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:204219693A>G	ENST00000272203.3	-	10	1890	c.1574T>C	c.(1573-1575)tTa>tCa	p.L525S	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.L545S	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	525										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			TTGCTCGTTTAACTTGTAGGT	0.602																																					p.L525S		.											.	PLEKHA6-654	0			c.T1574C						.						153	138	143					1																	204219693		2203	4300	6503	SO:0001583	missense	22874	exon10			TCGTTTAACTTGT	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.1574T>C	1.37:g.204219693A>G	ENSP00000272203:p.Leu525Ser	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_014935	0	0	0	0	0	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.711789	0.30322	.	.	ENSG00000143850	ENST00000272203;ENST00000414478;ENST00000450705;ENST00000543129;ENST00000454206;ENST00000367191;ENST00000430806	T;T	0.30981	1.51;1.51	5.68	5.68	0.88126	.	0.270585	0.30999	N	0.008448	T	0.26195	0.0639	N	0.25647	0.755	0.32133	N	0.586553	P;P;B;P;P;P	0.52842	0.763;0.828;0.215;0.804;0.493;0.956	B;B;B;B;B;P	0.47528	0.229;0.371;0.075;0.292;0.219;0.549	T	0.07158	-1.0787	10	0.07644	T	0.81	-2.4712	15.5805	0.76432	1.0:0.0:0.0:0.0	.	88;106;545;115;133;525	A5XEJ7;A5XEJ6;Q5VTI5;A5XEJ3;A5XEJ2;Q9Y2H5	.;.;.;.;.;PKHA6_HUMAN	S	525;545;133;115;106;88;86	ENSP00000272203:L525S;ENSP00000402046:L545S	ENSP00000272203:L525S	L	-	2	0	PLEKHA6	202486316	1.000000	0.71417	0.996000	0.52242	0.595000	0.36748	5.584000	0.67490	2.166000	0.68216	0.523000	0.50628	TTA	.		0.602	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		G	204219693	A	G	204219693	3	3	13	1	0	0	0	0	1	0	0	0	12086	372	13	3	1624	3	PLEKHA6	1	204219693	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	1194106	204219693	45030928	13	1002											
OTOF	9381	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	26693573	26693574	+	Frame_Shift_Ins	INS	-	-	C																															cttcttcttcttcttcttctINSccttctcctcctcagcctgc																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:26693573_26693574insC	ENST00000272371.2	-	32	4036_4037	c.3910_3911insG	c.(3910-3912)gagfs	p.E1304fs	OTOF_ENST00000339598.3_Frame_Shift_Ins_p.E537fs|OTOF_ENST00000403946.3_Frame_Shift_Ins_p.E1304fs|OTOF_ENST00000338581.6_Frame_Shift_Ins_p.E537fs|OTOF_ENST00000402415.3_Frame_Shift_Ins_p.E614fs	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1304	Poly-Lys.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cttcttcttctccttctcctcc	0.584																																					p.E1304fs	GBM(102;732 1451 20652 24062 31372)	.											.	OTOF-135	0			c.3911_3912insG						.																																			SO:0001589	frameshift_variant	9381	exon32			.	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"fer-1-like family member 2"	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3911dupG	2.37:g.26693575_26693575dupC	ENSP00000272371:p.Glu1304fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	84	14	NM_194248	0	0	0	0	0	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Frame_Shift_Ins	INS	ENST00000272371.2	37	CCDS1725.1																																																																																			.		0.584	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			C	26693574	-	C	26693573	7	5	13	1	0	1	1	0	0	0	0	0	11329	1551	54	0	2327	0	OTOF	2	26693573	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08		26693573	216505800	14	1003											
MAPRE3	22924	bcgsc.ca	37	chr2	27248500	27248500	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaaaacatgcagacctctggCcggctgagcaatgtggcccc	11	6	11	13	1	1	2	0	1	1	1	1	2	1	2	4	3	3	3	4	3	3	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:27248500C>T	ENST00000233121.2	+	5	717	c.519C>T	c.(517-519)ggC>ggT	p.G173G	MAPRE3_ENST00000402218.1_Silent_p.G158G|MAPRE3_ENST00000405074.3_Silent_p.G158G			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	173					mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGACCTCTGGCCGGCTGAGCA	0.577																																					p.G173G													.	MAPRE3-91	0			c.C519T						.						62	60	61					2																	27248500		2203	4300	6503	SO:0001819	synonymous_variant	22924	exon5			CTCTGGCCGGCTG	Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.519C>T	2.37:g.27248500C>T		Somatic	114	0		WXS	Illumina HiSeq	Phase_1	97	5	NM_012326	0	0	0	0	0	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Silent	SNP	ENST00000233121.2	37	CCDS1731.1																																																																																			.		0.577	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326		T	27248500	C	T	27248500	2	4	13	1	0	0	0	0	0	0	0	1	9321	726	26	2		2	MAPRE3	2	27248500	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	554927	27248500	215950873	15	1004											
EIF2AK2	5610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37365711	37365711	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtagtagcaaaagaaccagaGgacaggtagtcagatttctg	15	8	12	6	0	2	3	1	0	1	3	2	4	2	4	1	2	2	4	1	2	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:37365711G>A	ENST00000233057.4	-	7	856	c.534C>T	c.(532-534)tcC>tcT	p.S178S	EIF2AK2_ENST00000395127.2_Silent_p.S178S|EIF2AK2_ENST00000405334.1_Silent_p.S178S	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	178					activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				AAGAACCAGAGGACAGGTAGT	0.363																																					p.S178S		.											.	EIF2AK2-794	0			c.C534T						.						90	93	92					2																	37365711		2203	4300	6503	SO:0001819	synonymous_variant	5610	exon5			ACCAGAGGACAGG	BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 83"	176871	"protein kinase, interferon-inducible double stranded RNA dependent"	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.534C>T	2.37:g.37365711G>A		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	71	32	NM_001135652	0	0	0	0	0	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Silent	SNP	ENST00000233057.4	37	CCDS1786.1																																																																																			.		0.363	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759		A	37365711	G	A	37365711	2	1	13	1	0	0	0	0	0	0	0	1	5008	987	35	2		2	EIF2AK2	2	37365711	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10117211	37365711	205833662	16	1005											
ATOH8	84913	hgsc.bcm.edu	37	chr2	85981696	85981696	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacgccgccgccgccgccGcctcctgcgccccagagcca	4	2	10	25	7	0	1	0	0	0	1	1	1	1	1	11	0	2	0	11	0	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:85981696G>T	ENST00000306279.3	+	1	680	c.384G>T	c.(382-384)ccG>ccT	p.P128P		NM_032827.6	NP_116216.2	Q96SQ7	ATOH8_HUMAN	atonal homolog 8 (Drosophila)	128	Pro-rich.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CGCCGCCGCCGCCTCCTGCGC	0.766																																					p.P128P		.											.	ATOH8-90	0			c.G384T						.						2	2	2					2																	85981696		1216	2628	3844	SO:0001819	synonymous_variant	84913	exon1			GCCGCCGCCTCCT	AK074681	CCDS1985.1	2p11.2	2013-05-21			ENSG00000168874	ENSG00000168874		"Basic helix-loop-helix proteins"	24126	protein-coding gene	gene with protein product	"basic helix loop helix transcription factor 6"					12419857	Standard	NM_032827		Approved	HATH6, FLJ14708, bHLHa21	uc002sqn.3	Q96SQ7	OTTHUMG00000130178	ENST00000306279.3:c.384G>T	2.37:g.85981696G>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_032827	0	0	0	0	0	Q504S2|Q659B0	Silent	SNP	ENST00000306279.3	37	CCDS1985.1																																																																																			.		0.766	ATOH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252496.1	NM_032827		T	85981696	G	T	85981696	2	4	13	1	0	0	0	0	0	0	0	1	1115	1074	38	4		4	ATOH8	2	85981696	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	48615985	85981696	157217677	17	1006											
GPAT2	150763	hgsc.bcm.edu	37	chr2	96687959	96687959	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagtttttcctgattgtccAggctggcaaaagtaggggac	9	12	12	8	0	0	1	0	1	0	0	2	2	2	2	2	4	0	4	2	4	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:96687959A>T	ENST00000434632.1	-	23	2795	c.2336T>A	c.(2335-2337)cTg>cAg	p.L779Q	GPAT2_ENST00000359548.4_Missense_Mutation_p.L779Q|GPAT2_ENST00000453542.1_Missense_Mutation_p.L708Q|GPAT2_ENST00000377137.3_3'UTR|FAHD2CP_ENST00000607780.1_RNA			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	779					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)	p.L779Q(2)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						CTGATTGTCCAGGCTGGCAAA	0.567																																					p.L779Q		.											.	GPAT2-90	2	Substitution - Missense(2)	skin(2)	c.T2336A						.						30	30	30					2																	96687959		1847	4102	5949	SO:0001583	missense	150763	exon22			TTGTCCAGGCTGG	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"cancer/testis antigen 123"					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.2336T>A	2.37:g.96687959A>T	ENSP00000389395:p.Leu779Gln	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_207328	0	0	0	0	0	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	37	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	t	0.005	-2.199373	0.00299	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	T;T;T	0.74526	-0.85;-0.85;0.16	4.97	-1.85	0.07784	.	.	.	.	.	T	0.31857	0.0810	N	0.00483	-1.445	0.09310	N	0.999997	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39187	-0.9626	9	0.02654	T	1	-26.1951	5.7343	0.18057	0.1497:0.2636:0.0:0.5866	.	708;785;779;708	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	Q	779;779;708	ENSP00000352547:L779Q;ENSP00000389395:L779Q;ENSP00000393770:L708Q	ENSP00000352547:L779Q	L	-	2	0	GPAT2	96051686	0.001000	0.12720	0.375000	0.26029	0.081000	0.17604	-0.019000	0.12546	-0.483000	0.06772	-0.751000	0.03497	CTG	.		0.567	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328		T	96687959	A	T	96687959	3	4	13	1	0	0	0	0	1	0	0	0	6609	188	7	5	55	5	GPAT2	2	96687959	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10706263	96687959	146511414	18	1007											
CNNM4	26504	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97428127	97428127	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggatgccatgctggaggAgttcaagaagggtaaggcca	11	8	16	6	0	1	1	1	0	0	1	1	4	1	4	2	5	2	4	2	5	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:97428127A>G	ENST00000377075.2	+	1	1489	c.1391A>G	c.(1390-1392)gAg>gGg	p.E464G		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	464	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						ATGCTGGAGGAGTTCAAGAAG	0.517																																					p.E464G		.											.	CNNM4-154	0			c.A1391G						.						87	83	85					2																	97428127		2203	4300	6503	SO:0001583	missense	26504	exon1			TGGAGGAGTTCAA	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1391A>G	2.37:g.97428127A>G	ENSP00000366275:p.Glu464Gly	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	81	36	NM_020184	0	0	0	0	0	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937929	0.73557	.	.	ENSG00000158158	ENST00000377075	D	0.93712	-3.27	5.26	5.26	0.73747	Cystathionine beta-synthase, core (2);	0.000000	0.85682	D	0.000000	D	0.96623	0.8898	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97084	0.9786	10	0.66056	D	0.02	-1.1101	14.1805	0.65572	1.0:0.0:0.0:0.0	.	464	Q6P4Q7	CNNM4_HUMAN	G	464	ENSP00000366275:E464G	ENSP00000366275:E464G	E	+	2	0	CNNM4	96791854	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.281000	0.95811	1.996000	0.58369	0.533000	0.62120	GAG	.		0.517	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		G	97428127	A	G	97428127	3	3	13	1	0	0	0	0	1	0	0	0	3621	304	11	3	1393	3	CNNM4	2	97428127	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	740168	97428127	145771246	19	1008											
TMEM131	23505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	98413329	98413329	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtacaatcttttaacaaTgcttccgtgattttaaagcg	11	16	6	8	2	2	1	0	1	2	0	3	1	3	1	1	0	4	2	1	0	6	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:98413329T>A	ENST00000186436.5	-	27	3219	c.2991A>T	c.(2989-2991)gcA>gcT	p.A997A		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	997						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CTTTTAACAATGCTTCCGTGA	0.393																																					p.A997A		.											.	TMEM131-74	0			c.A2991T						.						109	108	109					2																	98413329		1899	4122	6021	SO:0001819	synonymous_variant	23505	exon27			TAACAATGCTTCC	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.2991A>T	2.37:g.98413329T>A		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	65	23	NM_015348	0	0	0	0	0		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																			.		0.393	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		A	98413329	T	A	98413329	2	1	13	1	0	0	0	0	0	0	0	1	16076	1451	51	5		5	TMEM131	2	98413329	Silent	SNP	T	TCGA-A4-8098-01A-11D-2396-08	985202	98413329	144786044	20	1009											
RGPD3	653489	broad.mit.edu;bcgsc.ca	37	chr2	107032393	107032393	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcactttttgtggtggaactGagcttctgaaccaattcttc	8	15	9	9	0	2	2	0	2	2	0	3	3	2	3	1	2	3	2	1	2	3	5	rs554062950		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:107032393G>A	ENST00000409886.3	-	21	5064	c.4977C>T	c.(4975-4977)ctC>ctT	p.L1659L	RGPD3_ENST00000304514.7_Silent_p.L1659L	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1659					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TGGTGGAACTGAGCTTCTGAA	0.388																																					p.L1659L													.	RGPD3-23	0			c.C4977T						.						72	67	68					2																	107032393		678	1556	2234	SO:0001819	synonymous_variant	653489	exon21			GGAACTGAGCTTC		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"Tetratricopeptide (TTC) repeat domain containing"	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.4977C>T	2.37:g.107032393G>A		Somatic	262	3		WXS	Illumina HiSeq	Phase_I	256	16	NM_001144013	0	0	0	0	0	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			.		0.388	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		A	107032393	G	A	107032393	2	1	13	1	0	0	0	0	0	0	0	1	13319	1277	45	2		2	RGPD3	2	107032393	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	8619064	107032393	136166980	21	1010											
GALNT5	11227	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	158115698	158115699	+	Frame_Shift_Ins	INS	-	-	T																															atagaagtgagatgtcttccINStcttcacttgctccacatag																								rs141648249		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:158115698_158115699insT	ENST00000259056.4	+	1	1589_1590	c.1104_1105insT	c.(1105-1107)tctfs	p.S369fs		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	369					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						AGATGTCTTCCTCTTCACTTGC	0.416																																					p.S368fs		.											.	GALNT5-290	0			c.1104_1105insT						.																																			SO:0001589	frameshift_variant	11227	exon1			.	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1105dupT	2.37:g.158115699_158115699dupT	ENSP00000259056:p.Ser369fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	147	49	NM_014568	0	0	0	0	0	A5PKZ1|Q9UGK7|Q9UHL6	Frame_Shift_Ins	INS	ENST00000259056.4	37	CCDS2203.1																																																																																			.		0.416	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		T	158115699	-	T	158115698	7	5	13	1	0	1	1	0	0	0	0	0	6236	668	24	0	1106	0	GALNT5	2	158115698	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	51083305	158115698	85083675	22	1011											
TTN	7273	hgsc.bcm.edu	37	chr2	179460425	179460425	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attcacgcttttcaatgacaTaattggtgattggagagcct	11	14	9	7	1	2	3	2	2	0	1	2	4	2	3	1	2	1	1	1	2	2	6	rs201541213		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:179460425T>A	ENST00000591111.1	-	245	52957	c.52733A>T	c.(52732-52734)tAt>tTt	p.Y17578F	TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Y10279F|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Y16651F|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Y19219F|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Y10154F|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Y10346F			Q8WZ42	TITIN_HUMAN	titin	17578	Fibronectin type-III 27. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCAATGACATAATTGGTGAT	0.463																																					p.Y19219F		.											.	TTN-636	0			c.A57656T						.	T	PHE/TYR,PHE/TYR,PHE/TYR,PHE/TYR	0,3818		0,0,1909	82	75	77		30461,49952,30836,31037	6.1	1	2		77	7,8255		0,7,4124	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	22,22,22,22	0,7,6033	AA,AT,TT		0.0847,0.0,0.0579	probably-damaging,probably-damaging,probably-damaging,probably-damaging	10154/26927,16651/33424,10279/27052,10346/27119	179460425	7,12073	1909	4131	6040	SO:0001583	missense	7273	exon295			ATGACATAATTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.52733A>T	2.37:g.179460425T>A	ENSP00000465570:p.Tyr17578Phe	Somatic	14	2		WXS	Illumina HiSeq	Phase_I	22	9	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	18.46	3.628597	0.67015	0.0	8.47E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31	6.05	6.05	0.98169	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89581	0.6756	M	0.73753	2.245	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	D	0.90542	0.4503	9	0.87932	D	0	.	16.5932	0.84781	0.0:0.0:0.0:1.0	.	10154;10279;10346;17578	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	16651;10154;10346;10279;10152	ENSP00000343764:Y16651F;ENSP00000434586:Y10154F;ENSP00000340554:Y10346F;ENSP00000352154:Y10279F	ENSP00000340554:Y10346F	Y	-	2	0	TTN	179168671	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.991000	0.88244	2.320000	0.78422	0.528000	0.53228	TAT	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179460425	T	A	179460425	3	1	13	1	0	0	0	0	1	0	0	0	16768	1406	49	5	50595	5	TTN	2	179460425	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	21344727	179460425	63738948	23	1012											
COL6A3	1293	ucsc.edu;bcgsc.ca	37	chr2	238280361	238280361	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccaaggagaacctccgaCgcccccatctcacctggagg	9	5	10	17	2	1	1	1	0	1	1	4	4	3	2	6	3	1	1	6	3	2	0	rs373893821		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:238280361C>T	ENST00000295550.4	-	9	4738				COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000392004.3_Silent_p.A1227A|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000346358.4_Intron|COL6A3_ENST00000392003.2_Silent_p.A1026A|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000409809.1_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A1227A(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GAACCTCCGACGCCCCCATCT	0.473																																					p.A1227A													.	COL6A3-526	1	Substitution - coding silent(1)	lung(1)	c.G3681A						.	C	,,,,	1,4405	2.1+/-5.4	0,1,2202	69	78	75		,3078,3681,,	-1.3	0	2		75	0,8600		0,0,4300	no	intron,coding-synonymous,coding-synonymous,intron,intron	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	,1026/1037,1227/1238,,	238280361	1,13005	2203	4300	6503	SO:0001627	intron_variant	1293	exon8			CTCCGACGCCCCC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4285+13G>A	2.37:g.238280361C>T		Somatic	138	0		WXS	Illumina HiSeq		165	52	NM_057165	0	0	0	0	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			.		0.473	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238280361	C	T	238280361	1	4	13	0	1	0	0	0	0	0	0	0	3707	523	19	1		1	COL6A3	2	238280361	Intron	SNP	C	TCGA-A4-8098-01A-11D-2396-08	58819936	238280361	4919012	24	1013											
CAPN7	23473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	15288921	15288921	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accccatctaccaattccatAtagaaaagactgggccgtta	14	9	6	12	1	1	2	0	0	1	2	2	2	2	2	5	1	1	1	5	1	7	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:15288921A>G	ENST00000253693.2	+	19	2414	c.2161A>G	c.(2161-2163)Ata>Gta	p.I721V		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	721	Domain N.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCAATTCCATATAGAAAAGAC	0.363																																					p.I721V		.											.	CAPN7-91	0			c.A2161G						.						84	84	84					3																	15288921		2203	4300	6503	SO:0001583	missense	23473	exon19			TTCCATATAGAAA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.2161A>G	3.37:g.15288921A>G	ENSP00000253693:p.Ile721Val	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	116	46	NM_014296	0	0	0	0	0		Missense_Mutation	SNP	ENST00000253693.2	37	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	A	7.495	0.651423	0.14516	.	.	ENSG00000131375	ENST00000253693	D	0.85629	-2.01	5.57	-3.39	0.04868	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.669254	0.16098	N	0.229700	T	0.62816	0.2459	N	0.16266	0.395	0.21105	N	0.999789	B	0.02656	0.0	B	0.12837	0.008	T	0.49244	-0.8960	10	0.15066	T	0.55	-2.6499	1.3262	0.02126	0.3616:0.1918:0.2926:0.154	.	721	Q9Y6W3	CAN7_HUMAN	V	721	ENSP00000253693:I721V	ENSP00000253693:I721V	I	+	1	0	CAPN7	15263925	0.062000	0.20869	0.564000	0.28396	0.978000	0.69477	-0.068000	0.11561	-0.127000	0.11661	0.533000	0.62120	ATA	.		0.363	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		G	15288921	A	G	15288921	3	3	13	1	0	0	0	0	1	0	0	0	2637	449	16	3	2235	3	CAPN7	3	15288921	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08		15288921	182733509	25	1014											
ARPP21	10777	bcgsc.ca	37	chr3	35756938	35756938	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttatttttcagtcagtttGctcccaggaaagcctttttg	7	19	7	8	0	2	0	2	0	0	0	3	1	3	1	2	1	2	2	2	1	2	7			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:35756938G>T	ENST00000187397.4	+	12	1361	c.905G>T	c.(904-906)tGc>tTc	p.C302F	ARPP21_ENST00000444190.1_Missense_Mutation_p.C268F|ARPP21_ENST00000337271.5_Missense_Mutation_p.C268F|ARPP21_ENST00000417925.1_Missense_Mutation_p.C268F|ARPP21_ENST00000458225.1_Missense_Mutation_p.C268F	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	302					cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						CAGTCAGTTTGCTCCCAGGAA	0.363																																					p.C302F													.	ARPP21-93	0			c.G905T						.						122	121	122					3																	35756938		2202	4300	6502	SO:0001583	missense	10777	exon12			CAGTTTGCTCCCA	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"R3H domain containing 3"	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.905G>T	3.37:g.35756938G>T	ENSP00000187397:p.Cys302Phe	Somatic	95	0		WXS	Illumina HiSeq	Phase_1	68	4	NM_016300	0	0	0	0	0	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.060897	0.76074	.	.	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925;ENST00000425289	T;T;T;T;T	0.25912	1.86;1.83;1.83;1.77;1.86	5.92	5.92	0.95590	.	0.253759	0.42682	D	0.000679	T	0.49949	0.1587	M	0.61703	1.905	0.58432	D	0.999999	D;D;D	0.69078	0.996;0.997;0.996	D;P;P	0.65010	0.931;0.795;0.899	T	0.37798	-0.9690	10	0.56958	D	0.05	-14.633	20.3343	0.98733	0.0:0.0:1.0:0.0	.	268;302;268	Q9UBL0-3;Q9UBL0;Q9UBL0-4	.;ARP21_HUMAN;.	F	268;268;268;302;268;73	ENSP00000414351:C268F;ENSP00000337792:C268F;ENSP00000405276:C268F;ENSP00000187397:C302F;ENSP00000412326:C268F	ENSP00000187397:C302F	C	+	2	0	ARPP21	35731942	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.098000	0.76974	2.822000	0.97130	0.650000	0.86243	TGC	.		0.363	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		T	35756938	G	T	35756938	3	4	13	1	0	0	0	0	1	0	0	0	979	1319	46	4	956	4	ARPP21	3	35756938	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	20468017	35756938	162265492	26	1015											
ACAA1	30	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38168151	38168151	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggtggtcacaggcacaaTctcagcttggaaacagccct	10	8	11	12	1	2	0	2	0	1	0	3	1	2	1	1	4	3	2	1	4	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:38168151T>G	ENST00000333167.8	-	8	839	c.667A>C	c.(667-669)Att>Ctt	p.I223L	ACAA1_ENST00000444607.2_3'UTR|ACAA1_ENST00000301810.7_Missense_Mutation_p.I190L|ACAA1_ENST00000450296.1_Missense_Mutation_p.I182L|ACAA1_ENST00000544624.1_Missense_Mutation_p.I71L|ACAA1_ENST00000480865.1_5'UTR|Y_RNA_ENST00000365095.1_RNA	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	223					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		ACAGGCACAATCTCAGCTTGG	0.612																																					p.I223L		.											.	ACAA1-91	0			c.A667C						.						146	120	129					3																	38168151		2203	4300	6503	SO:0001583	missense	30	exon8			GCACAATCTCAGC	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.667A>C	3.37:g.38168151T>G	ENSP00000333664:p.Ile223Leu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	125	54	NM_001607	0	0	0	0	0	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	37	CCDS2673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.183188|5.183188	0.94885|0.94885	.|.	.|.	ENSG00000060971|ENSG00000060971	ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122;ENST00000544624|ENST00000452171;ENST00000421218	D;D;D;D|.	0.93547|.	-3.11;-3.11;-3.24;-3.24|.	5.46|5.46	5.46|5.46	0.80206|0.80206	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78892|0.78892	0.4355|0.4355	M|M	0.84585|0.84585	2.705|2.705	0.80722|0.80722	D|D	1|1	P;D;D;D|.	0.71674|.	0.911;0.997;0.998;0.993|.	D;D;D;D|.	0.85130|.	0.926;0.914;0.997;0.956|.	T|T	0.81484|0.81484	-0.0912|-0.0912	10|5	0.87932|.	D|.	0|.	-10.3475|-10.3475	15.5417|15.5417	0.76057|0.76057	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	155;182;190;223|.	F5GXL8;C9JDE9;G5E935;P09110|.	.;.;.;THIK_HUMAN|.	L|S	223;190;182;155;71|95;112	ENSP00000333664:I223L;ENSP00000301810:I190L;ENSP00000395183:I182L;ENSP00000445710:I71L|.	ENSP00000301810:I190L|.	I|R	-|-	1|3	0|2	ACAA1|ACAA1	38143155|38143155	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.998000|0.998000	0.95712|0.95712	6.148000|6.148000	0.71788|0.71788	2.072000|2.072000	0.62099|0.62099	0.533000|0.533000	0.62120|0.62120	ATT|AGA	.		0.612	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38168151	T	G	38168151	3	3	13	1	0	0	0	0	1	0	0	0	104	1435	50	5	627	5	ACAA1	3	38168151	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	2411213	38168151	159854279	27	1016											
TGM4	7047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	44926858	44926858	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcttgaatcaggacaacGccgtttctcaccacacatgg	11	10	7	13	2	3	1	2	1	2	0	4	2	3	2	2	2	1	1	2	2	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:44926858G>T	ENST00000296125.4	+	2	129	c.61G>T	c.(61-63)Gcc>Tcc	p.A21S		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	21					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	TCAGGACAACGCCGTTTCTCA	0.522																																					p.A21S		.											.	TGM4-91	0			c.G61T						.						102	93	96					3																	44926858		2203	4300	6503	SO:0001583	missense	7047	exon2			GACAACGCCGTTT	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.61G>T	3.37:g.44926858G>T	ENSP00000296125:p.Ala21Ser	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_003241	0	0	0	0	0	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	9.481	1.098065	0.20552	.	.	ENSG00000163810	ENST00000296125	D	0.84873	-1.91	2.77	-1.63	0.08345	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.329666	0.20233	U	0.096458	T	0.70850	0.3271	L	0.33245	0.995	0.09310	N	1	B;P	0.36027	0.448;0.533	B;B	0.37047	0.24;0.1	T	0.62296	-0.6884	10	0.10902	T	0.67	.	6.6582	0.22998	0.4424:0.0:0.5576:0.0	.	21;21	P49221;B4YUQ1	TGM4_HUMAN;.	S	21	ENSP00000296125:A21S	ENSP00000296125:A21S	A	+	1	0	TGM4	44901862	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.711000	0.05019	-0.425000	0.07371	0.467000	0.42956	GCC	.		0.522	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		T	44926858	G	T	44926858	3	4	13	1	0	0	0	0	1	0	0	0	15864	1087	38	4	67	4	TGM4	3	44926858	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	6758707	44926858	153095572	28	1017											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47127778	47127778	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgacgttccagaaaggaCttcaggcaggactgtgagtg	11	8	13	9	1	1	3	1	2	0	1	2	5	2	5	2	3	0	2	2	3	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:47127778C>A	ENST00000409792.3	-	11	5346	c.5304G>T	c.(5302-5304)aaG>aaT	p.K1768N	snoU13_ENST00000516129.1_RNA|SETD2_ENST00000492397.1_5'Flank	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1768					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCAGAAAGGACTTCAGGCAGG	0.512			"N, F, S, Mis"		clear cell renal carcinoma																																p.K1768N		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.G5304T						.						127	110	116					3																	47127778		2203	4300	6503	SO:0001583	missense	29072	exon11			AAAGGACTTCAGG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5304G>T	3.37:g.47127778C>A	ENSP00000386759:p.Lys1768Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	57	22	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	20.4	3.988848	0.74589	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.90504	-2.68	5.47	4.52	0.55395	.	0.000000	0.56097	D	0.000025	D	0.93220	0.7840	M	0.62723	1.935	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.91914	0.5542	10	0.42905	T	0.14	.	9.269	0.37659	0.0:0.8236:0.0:0.1764	.	1768;1768	F2Z317;Q9BYW2	.;SETD2_HUMAN	N	1768	ENSP00000386759:K1768N	ENSP00000386759:K1768N	K	-	3	2	SETD2	47102782	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.865000	0.39479	1.167000	0.42706	0.650000	0.86243	AAG	.		0.512	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47127778	C	A	47127778	3	1	13	1	0	0	0	0	1	0	0	0	14163	564	20	4	2434	4	SETD2	3	47127778	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	2200920	47127778	150894652	29	1018											
CADPS	8618	hgsc.bcm.edu	37	chr3	62499343	62499343	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccatcacttgggaggccaAgcagaagacaggatgctcat	13	7	11	10	0	2	2	2	0	0	2	3	4	3	4	2	3	2	2	2	3	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:62499343A>G	ENST00000383710.4	-	17	2931				CADPS_ENST00000357948.3_Intron|CADPS_ENST00000283269.9_Silent_p.L874L	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator						catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TGGGAGGCCAAGCAGAAGACA	0.423																																					p.L874L		.											.	CADPS-281	0			c.T2620C						.						122	96	105					3																	62499343		2203	4299	6502	SO:0001627	intron_variant	8618	exon17			AGGCCAAGCAGAA	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"Pleckstrin homology (PH) domain containing"	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2582-900T>C	3.37:g.62499343A>G		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_183394	0	0	0	0	0	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	37	CCDS46858.1																																																																																			.		0.423	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		G	62499343	A	G	62499343	1	3	13	0	1	0	0	0	0	0	0	0	2576	69	3	3		3	CADPS	3	62499343	Intron	SNP	A	TCGA-A4-8098-01A-11D-2396-08	15371565	62499343	135523087	30	1019											
ZNF595	152687	bcgsc.ca	37	chr4	86145	86145	+	3'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgaacataagaaaattcatActggagagaaaccctacaaa	21	6	6	8	1	1	2	1	0	0	2	1	5	1	3	1	1	4	0	1	1	8	4	rs200927625		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:86145A>G	ENST00000339368.6	+	0	954							Q8IYB9	ZN595_HUMAN	zinc finger protein 595						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		GAAAATTCATACTGGAGAGAA	0.393																																					.													.	.	0			.						.						33	35	34					4																	86145		2130	4261	6391	SO:0001624	3_prime_UTR_variant	152687	.			ATTCATACTGGAG	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"Zinc fingers, C2H2-type", "-"	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000339368.6:c.*951A>G	4.37:g.86145A>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_1	44	6	.	0	0	0	0	0		RNA	SNP	ENST00000339368.6	37																																																																																				.		0.393	ZNF595-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000357814.2	NM_182524		G	86145	A	G	86145	1	3	13	0	1	0	0	0	0	0	0	0	18057	381	14	3		3	ZNF595	4	86145	3'UTR	SNP	A	TCGA-A4-8098-01A-11D-2396-08		86145	191068131	31	1020											
TMEM175	84286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	947053	947053	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcgctctgcccacagggctCtgtaccgacgacacgtcctg	7	7	11	16	4	2	0	0	0	2	0	3	2	3	0	3	1	3	3	3	1	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:947053C>G	ENST00000264771.4	+	8	723	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000515740.1_Missense_Mutation_p.L64V|TMEM175_ENST00000508204.1_Missense_Mutation_p.L98V	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	180						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCACAGGGCTCTGTACCGACG	0.617																																					p.L180V		.											.	TMEM175-90	0			c.C538G						.						120	100	107					4																	947053		2203	4300	6503	SO:0001583	missense	84286	exon8			AGGGCTCTGTACC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.538C>G	4.37:g.947053C>G	ENSP00000264771:p.Leu180Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	65	33	NM_032326	0	0	0	0	0	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	37	CCDS3341.1	.	.	.	.	.	.	.	.	.	.	c	0.044	-1.272845	0.01421	.	.	ENSG00000127419	ENST00000264771;ENST00000514453;ENST00000515492;ENST00000359768;ENST00000509508;ENST00000515740;ENST00000508204;ENST00000510493	T;T;T;T	0.46819	1.44;0.94;1.49;0.86	4.71	-0.169	0.13339	.	0.217286	0.39083	N	0.001461	T	0.31263	0.0791	L	0.54323	1.7	0.09310	N	1	B;B;B	0.20887	0.001;0.049;0.031	B;B;B	0.19666	0.001;0.026;0.005	T	0.11251	-1.0595	10	0.15499	T	0.54	-27.4926	1.8457	0.03158	0.1956:0.2847:0.3858:0.1339	.	98;180;98	D6RBE5;Q9BSA9;B3KR27	.;TM175_HUMAN;.	V	180;167;98;98;86;64;98;98	ENSP00000264771:L180V;ENSP00000425181:L167V;ENSP00000427039:L64V;ENSP00000423669:L98V	ENSP00000264771:L180V	L	+	1	2	TMEM175	937053	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.647000	0.24812	0.040000	0.15660	-0.322000	0.08575	CTG	.		0.617	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		G	947053	C	G	947053	3	3	13	1	0	0	0	0	1	0	0	0	16123	912	32	4	564	4	TMEM175	4	947053	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	860908	947053	190207223	32	1021											
DRD5	1816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	9784197	9784197	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtccagctcaactggcacAgggaccaggcggcctcttgg	7	6	14	14	2	2	0	1	0	1	0	3	1	3	1	3	6	2	2	3	6	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:9784197A>T	ENST00000304374.2	+	1	940	c.544A>T	c.(544-546)Agg>Tgg	p.R182W		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	182					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CAACTGGCACAGGGACCAGGC	0.617																																					p.R182W		.											.	DRD5-91	0			c.A544T						.						35	36	35					4																	9784197		2203	4299	6502	SO:0001583	missense	1816	exon1			TGGCACAGGGACC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.544A>T	4.37:g.9784197A>T	ENSP00000306129:p.Arg182Trp	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	84	33	NM_000798	0	0	0	0	0	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	a	16.35	3.098148	0.56183	.	.	ENSG00000169676	ENST00000304374	T	0.73047	-0.71	4.53	-6.0	0.02206	GPCR, rhodopsin-like superfamily (1);	0.214762	0.44483	D	0.000455	T	0.80088	0.4559	M	0.74881	2.28	0.37769	D	0.926595	D	0.71674	0.998	D	0.70935	0.971	T	0.82639	-0.0358	10	0.87932	D	0	.	17.6446	0.88145	0.2761:0.7239:0.0:0.0	.	182	P21918	DRD5_HUMAN	W	182	ENSP00000306129:R182W	ENSP00000306129:R182W	R	+	1	2	DRD5	9393295	1.000000	0.71417	0.162000	0.22713	0.673000	0.39480	3.173000	0.50839	-1.286000	0.02384	-0.973000	0.02599	AGG	.		0.617	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			T	9784197	A	T	9784197	3	4	13	1	0	0	0	0	1	0	0	0	4771	179	7	5	546	5	DRD5	4	9784197	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	8837144	9784197	181370079	33	1022											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68939702	68939702	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgataaatcgaccgcctacaGaagaatgtcgaaatatccta	16	9	7	9	3	0	3	0	1	0	2	3	5	1	3	3	0	1	0	3	0	8	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:68939702G>C	ENST00000356291.2	-	4	367	c.308C>G	c.(307-309)tCt>tGt	p.S103C	UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	103	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						ACCGCCTACAGAAGAATGTCG	0.239																																					p.S103C		.											.	TMPRSS11F-91	0			c.C308G						.						33	32	32					4																	68939702		2197	4294	6491	SO:0001583	missense	389208	exon4			CCTACAGAAGAAT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.308C>G	4.37:g.68939702G>C	ENSP00000348639:p.Ser103Cys	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_207407	0	0	0	0	0	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771982	0.49680	.	.	ENSG00000198092	ENST00000356291	T	0.40476	1.03	5.23	5.23	0.72850	SEA (3);	0.105172	0.43260	D	0.000593	T	0.59985	0.2234	M	0.72118	2.19	0.34918	D	0.748179	D	0.59767	0.986	P	0.61533	0.89	T	0.71368	-0.4614	10	0.52906	T	0.07	.	14.3036	0.66371	0.0:0.0:1.0:0.0	.	103	Q6ZWK6	TM11F_HUMAN	C	103	ENSP00000348639:S103C	ENSP00000348639:S103C	S	-	2	0	TMPRSS11F	68622297	0.999000	0.42202	1.000000	0.80357	0.446000	0.32137	2.553000	0.45837	2.457000	0.83068	0.655000	0.94253	TCT	.		0.239	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		C	68939702	G	C	68939702	3	2	13	1	0	0	0	0	1	0	0	0	16275	942	33	4	1036	4	TMPRSS11F	4	68939702	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	59155505	68939702	122214574	34	1023											
MRPL1	65008	hgsc.bcm.edu	37	chr4	78804410	78804411	+	Missense_Mutation	DNP	CA	CA	AC																															tttaaggtctgcaaagaaaaCaaaaaaaggtgctaaagaaa																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:78804410_78804411CA>AC	ENST00000315567.8	+	3	487_488	c.158_159CA>AC	c.(157-159)aCA>aAC	p.T53N	MRPL1_ENST00000506674.1_3'UTR	NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	53					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						GCAAAGAAAACAAAAAAAGGTG	0.282																																					p.T53N		.											.	MRPL1	0			c.A159C						.																																			SO:0001583	missense	65008	exon3			GAAAACAAAAAAA	AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"Mitochondrial ribosomal proteins / large subunits"	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	Exception_encountered	4.37:g.78804410_78804411delinsAC	ENSP00000315017:p.Thr53Asn	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	24	2		0	0	0	0	0	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Missense_Mutation	DNP	ENST00000315567.8	37	CCDS3583.2																																																																																			.		0.282	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236		AC	78804411	CA	AC	78804410	3	1	13	1	0	0	0	0	1	0	0	0	9799	478	17	4	168	4	MRPL1	4	78804410	Missense_Mutation	DNP	CA	TCGA-A4-8098-01A-11D-2396-08	9864708	78804410	112349866	35	1024											
ANK2	287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	114232517	114232517	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagttcctggatggtatgaaTtacctgcgatacagcttgga	10	12	11	8	1	0	1	0	1	0	0	1	4	1	3	2	3	4	3	2	3	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:114232517T>A	ENST00000357077.4	+	24	2708	c.2655T>A	c.(2653-2655)aaT>aaA	p.N885K	ANK2_ENST00000264366.6_Missense_Mutation_p.N885K|ANK2_ENST00000394537.3_Missense_Mutation_p.N885K|ANK2_ENST00000509550.1_Missense_Mutation_p.N94K|ANK2_ENST00000506722.1_Missense_Mutation_p.N864K	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	885					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATGGTATGAATTACCTGCGAT	0.438																																					p.N885K		.											.	ANK2-583	0			c.T2655A						.						163	134	144					4																	114232517		2203	4300	6503	SO:0001583	missense	287	exon24			TATGAATTACCTG	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2655T>A	4.37:g.114232517T>A	ENSP00000349588:p.Asn885Lys	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	73	39	NM_001148	0	0	0	0	0	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.511662	0.27036	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550	T;T;T;T;T;T;T;T	0.75154	-0.04;0.07;-0.13;-0.04;-0.12;-0.17;-0.2;-0.91	5.15	-2.52	0.06346	.	0.000000	0.53938	D	0.000056	T	0.53932	0.1827	L	0.27053	0.805	0.80722	D	1	B;P;B;P;B;B	0.44627	0.0;0.839;0.372;0.835;0.026;0.288	B;B;B;B;B;B	0.36719	0.001;0.231;0.058;0.228;0.029;0.081	T	0.51810	-0.8658	10	0.21014	T	0.42	.	14.3697	0.66830	0.0:0.6687:0.0:0.3313	.	94;885;885;885;864;864	E9PCH6;Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	.;ANK2_HUMAN;.;.;.;.	K	864;831;864;900;885;885;885;864;94	ENSP00000423799:N864K;ENSP00000421011:N831K;ENSP00000421067:N864K;ENSP00000424722:N900K;ENSP00000378044:N885K;ENSP00000349588:N885K;ENSP00000264366:N885K;ENSP00000426944:N94K	ENSP00000264366:N885K	N	+	3	2	ANK2	114451966	0.711000	0.27906	0.990000	0.47175	0.999000	0.98932	-0.123000	0.10611	-0.397000	0.07691	0.533000	0.62120	AAT	.		0.438	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114232517	T	A	114232517	3	1	13	1	0	0	0	0	1	0	0	0	621	1490	52	5	2774	5	ANK2	4	114232517	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	35428107	114232517	76921759	36	1025											
TRPC3	7222	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	122825594	122825594	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattttctatgaatttgtgAtcatatttgagcacaacgga	13	16	7	5	1	2	3	1	3	1	0	2	4	2	4	0	1	2	1	0	1	5	7			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:122825594A>C	ENST00000379645.3	-	8	2209	c.2136T>G	c.(2134-2136)gaT>gaG	p.D712E	TRPC3_ENST00000513531.1_Missense_Mutation_p.D584E|TRPC3_ENST00000264811.5_Missense_Mutation_p.D639E	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	627					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TGAATTTGTGATCATATTTGA	0.308																																					p.D712E		.											.	TRPC3-92	0			c.T2136G						.						89	86	87					4																	122825594		2203	4298	6501	SO:0001583	missense	7222	exon8			TTTGTGATCATAT	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2136T>G	4.37:g.122825594A>C	ENSP00000368966:p.Asp712Glu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	52	20	NM_001130698	0	0	0	0	0	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.982982	0.53827	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.75938	-0.76;-0.98;-0.92	5.77	0.478	0.16789	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.59622	0.2207	L	0.35487	1.065	0.43187	D	0.995017	B;B;B	0.19935	0.002;0.018;0.04	B;B;B	0.30716	0.057;0.057;0.119	T	0.39121	-0.9629	10	0.10111	T	0.7	-24.2756	9.899	0.41335	0.7445:0.0:0.2555:0.0	.	627;584;712	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	E	639;712;584	ENSP00000264811:D639E;ENSP00000368966:D712E;ENSP00000426899:D584E	ENSP00000264811:D639E	D	-	3	2	TRPC3	123045044	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.041000	0.30291	-0.050000	0.13356	0.533000	0.62120	GAT	.		0.308	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		C	122825594	A	C	122825594	3	2	13	1	0	0	0	0	1	0	0	0	16612	330	12	5	649	5	TRPC3	4	122825594	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	8593077	122825594	68328682	37	1026											
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167656109	167656109	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcatcaccaccatcatcaTcatccccttcatcttcatca	10	12	2	17	0	9	0	8	0	1	0	10	0	10	0	4	1	0	0	4	1	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:167656109T>C	ENST00000357154.3	-	12	1411	c.1274A>G	c.(1273-1275)gAt>gGt	p.D425G	SPOCK3_ENST00000511269.1_Missense_Mutation_p.D422G|SPOCK3_ENST00000541354.1_Missense_Mutation_p.D305G|SPOCK3_ENST00000510741.1_Missense_Mutation_p.D382G|SPOCK3_ENST00000512681.1_Missense_Mutation_p.D327G|SPOCK3_ENST00000511531.1_Missense_Mutation_p.D425G|SPOCK3_ENST00000504953.1_Missense_Mutation_p.D422G|SPOCK3_ENST00000421836.2_Missense_Mutation_p.D374G|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Missense_Mutation_p.D422G|SPOCK3_ENST00000502330.1_Missense_Mutation_p.D425G|SPOCK3_ENST00000534949.1_Missense_Mutation_p.D329G|SPOCK3_ENST00000535728.1_Missense_Mutation_p.D293G|SPOCK3_ENST00000506886.1_Missense_Mutation_p.D425G|SPOCK3_ENST00000541637.1_Missense_Mutation_p.D327G	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	425	Asp-rich.				negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		accatcatcatcatccccttc	0.323																																					p.D425G		.											.	SPOCK3-136	0			c.A1274G						.						170	161	164					4																	167656109		2203	4300	6503	SO:0001583	missense	50859	exon12			TCATCATCATCCC	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1274A>G	4.37:g.167656109T>C	ENSP00000349677:p.Asp425Gly	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_016950	0	0	0	0	0	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	T	10.25	1.298672	0.23650	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000510741;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000535728;ENST00000421836;ENST00000541637;ENST00000534949	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.1	5.1	0.69264	.	0.134505	0.47852	D	0.000214	T	0.80396	0.4615	L	0.32530	0.975	0.58432	D	0.999997	D;D;D;D;D;D;D	0.89917	0.993;0.996;1.0;1.0;1.0;0.996;0.993	D;D;D;D;D;D;D	0.80764	0.984;0.993;0.994;0.994;0.994;0.993;0.984	T	0.75531	-0.3285	10	0.13108	T	0.6	-23.1417	14.9101	0.70749	0.0:0.0:0.0:1.0	.	327;329;374;434;382;422;425	B4DGK5;F5H099;B4DHB4;B4DFW5;E7EP61;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;TICN3_HUMAN	G	425;422;422;425;425;425;382;305;327;422;293;374;327;329	ENSP00000349677:D425G;ENSP00000350153:D422G;ENSP00000425570:D422G;ENSP00000420920:D425G;ENSP00000423421:D425G;ENSP00000423606:D425G;ENSP00000426716:D382G;ENSP00000444789:D305G;ENSP00000426318:D327G;ENSP00000425502:D422G;ENSP00000441396:D293G;ENSP00000411344:D374G;ENSP00000445430:D327G;ENSP00000438142:D329G	ENSP00000349677:D425G	D	-	2	0	SPOCK3	167892684	1.000000	0.71417	1.000000	0.80357	0.055000	0.15305	4.684000	0.61686	2.060000	0.61445	0.514000	0.50259	GAT	.		0.323	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			C	167656109	T	C	167656109	3	2	13	1	0	0	0	0	1	0	0	0	15113	1435	50	3	40	3	SPOCK3	4	167656109	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	44830515	167656109	23498167	38	1027											
ADAM29	11086	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	175898831	175898832	+	Frame_Shift_Ins	INS	-	-	A																															tccatctgcaaaagaagaggINSaaaaaattcagcgtcgacct																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:175898831_175898832insA	ENST00000359240.3	+	5	2825_2826	c.2155_2156insA	c.(2155-2157)gaafs	p.E719fs	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Frame_Shift_Ins_p.E719fs|ADAM29_ENST00000404450.4_Frame_Shift_Ins_p.E719fs|ADAM29_ENST00000514159.1_Frame_Shift_Ins_p.E719fs	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	719					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E719K(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AAAAGAAGAGGAAAAAATTCAG	0.406																																					p.E719fs	Ovarian(140;1727 1835 21805 25838 41440)	.											.	ADAM29-729	1	Substitution - Missense(1)	NS(1)	c.2155_2156insA						.																																			SO:0001589	frameshift_variant	11086	exon4			.	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"ADAM metallopeptidase domain containing"	207	protein-coding gene	gene with protein product	"cancer/testis antigen 73"	604778	"a disintegrin and metalloproteinase domain 29"			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2161dupA	4.37:g.175898837_175898837dupA	ENSP00000352177:p.Glu719fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	73	46	NM_001130703	0	0	0	0	0	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Frame_Shift_Ins	INS	ENST00000359240.3	37	CCDS3823.1																																																																																			.		0.406	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175898832	-	A	175898831	7	5	13	1	0	1	1	0	0	0	0	0	247	1175	41	0	2157	0	ADAM29	4	175898831	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	8242722	175898831	15255445	39	1028											
MARCH6	10299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	10411600	10411600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agccatactccagcagggagGgcctgttggctttcagcctt	7	10	12	12	0	1	0	1	0	0	0	2	1	2	1	4	3	4	3	4	3	1	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:10411600G>A	ENST00000274140.5	+	19	1979	c.1847G>A	c.(1846-1848)gGg>gAg	p.G616E	MARCH6_ENST00000503788.1_Missense_Mutation_p.G511E|MARCH6_ENST00000510792.1_Missense_Mutation_p.G314E|MARCH6_ENST00000449913.2_Missense_Mutation_p.G568E	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	616					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						CAGCAGGGAGGGCCTGTTGGC	0.453																																					p.G616E		.											.	MARCH6-501	0			c.G1847A						.						73	70	71					5																	10411600		2203	4300	6503	SO:0001583	missense	10299	exon19			AGGGAGGGCCTGT	AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	30550	protein-coding gene	gene with protein product		613297	"membrane-associated ring finger (C3HC4) 6"			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.1847G>A	5.37:g.10411600G>A	ENSP00000274140:p.Gly616Glu	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	166	50	NM_005885	0	0	0	0	0	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249847	0.59212	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.42337	0.1198	L	0.40543	1.245	0.80722	D	1	P;P;D;D	0.76494	0.545;0.75;0.999;0.994	B;B;D;P	0.65987	0.136;0.154;0.94;0.795	T	0.08659	-1.0711	10	0.02654	T	1	-20.4936	19.599	0.95552	0.0:0.0:1.0:0.0	.	511;568;196;616	B4DKJ2;B4DT33;B2RBJ1;O60337	.;.;.;MARH6_HUMAN	E	568;511;616;314	ENSP00000414643:G568E;ENSP00000425930:G511E;ENSP00000274140:G616E;ENSP00000424512:G314E	ENSP00000274140:G616E	G	+	2	0	MARCH6	10464600	1.000000	0.71417	0.688000	0.30117	0.992000	0.81027	9.368000	0.97152	2.708000	0.92522	0.563000	0.77884	GGG	.		0.453	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885		A	10411600	G	A	10411600	3	1	13	1	0	0	0	0	1	0	0	0	9330	1232	43	2	1921	2	MARCH6	5	10411600	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08		10411600	170503660	40	1029											
CENPH	64946	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	68505552	68505552	+	Frame_Shift_Del	DEL	A	A	-																															agaaccttattttggggagtAaagtcaattgggcagaggat																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:68505552delA	ENST00000283006.2	+	9	757	c.670delA	c.(670-672)aaafs	p.K224fs	CENPH_ENST00000515001.1_Frame_Shift_Del_p.K205fs	NM_022909.3	NP_075060.1			centromere protein H											kidney(15)|large_intestine(2)|lung(3)	20		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.41e-56)|Epithelial(20;1.29e-52)|all cancers(19;3.15e-48)|Lung(70;0.0178)		TTTGGGGAGTAAAGTCAATTG	0.289																																					p.K224fs		.											.	CENPH-153	0			c.670delA						.						78	78	78					5																	68505552		2203	4300	6503	SO:0001589	frameshift_variant	64946	exon9			.	AB035124	CCDS3998.1	5p15.2	2013-11-05			ENSG00000153044	ENSG00000153044			17268	protein-coding gene	gene with protein product		605607				11092768, 15502821	Standard	NM_022909		Approved		uc003jvp.3	Q9H3R5	OTTHUMG00000097816	ENST00000283006.2:c.670delA	5.37:g.68505552delA	ENSP00000283006:p.Lys224fs	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	57	31	NM_022909	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000283006.2	37	CCDS3998.1																																																																																			.		0.289	CENPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215083.1			-	68505552	A	-	68505552	7	5	13	1	0	1	0	1	0	0	0	0	3238	363	13	0	704	0	CENPH	5	68505552	Frame_Shift_Del	DEL	A	TCGA-A4-8098-01A-11D-2396-08	58093952	68505552	112409708	41	1030											
GFM2	84340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	74026107	74026107	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtggcacgaactgagtttagGatggtctctcgatatgccac	9	11	12	9	2	1	1	0	1	1	0	3	4	1	2	1	3	2	2	1	3	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:74026107G>T	ENST00000296805.3	-	17	2161	c.1704C>A	c.(1702-1704)atC>atA	p.I568I	GFM2_ENST00000509430.1_Silent_p.I568I|GFM2_ENST00000515125.1_Intron|GFM2_ENST00000345239.2_Silent_p.I521I	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CTGAGTTTAGGATGGTCTCTC	0.413																																					p.I568I		.											.	GFM2-90	0			c.C1704A						.						106	100	102					5																	74026107		2203	4300	6503	SO:0001819	synonymous_variant	84340	exon17			GTTTAGGATGGTC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1704C>A	5.37:g.74026107G>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	114	32	NM_032380	0	0	0	0	0		Silent	SNP	ENST00000296805.3	37	CCDS4023.1																																																																																			.		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		T	74026107	G	T	74026107	2	4	13	1	0	0	0	0	0	0	0	1	6362	1164	41	4		4	GFM2	5	74026107	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	5520555	74026107	106889153	42	1031											
POC5	134359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	74981182	74981182	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctccgacggcggctggtggGgatggcagcagtggtgatgt	5	8	19	9	3	0	1	0	1	0	0	1	3	1	2	2	7	1	3	2	7	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:74981182G>C	ENST00000428202.2	-	10	1446	c.1257C>G	c.(1255-1257)tcC>tcG	p.S419S	POC5_ENST00000510798.1_Silent_p.S302S|POC5_ENST00000380475.2_Silent_p.S302S|POC5_ENST00000446329.2_Silent_p.S394S|POC5_ENST00000514838.2_Silent_p.S391S	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	419					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CGGCTGGTGGGGATGGCAGCA	0.557																																					p.S419S		.											.	POC5-45	0			c.C1257G						.						100	118	112					5																	74981182		2058	4209	6267	SO:0001819	synonymous_variant	134359	exon10			TGGTGGGGATGGC	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 37", "POC5 centriolar protein homolog (Chlamydomonas)"	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1257C>G	5.37:g.74981182G>C		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	199	47	NM_001099271	0	0	0	0	0	B4DJG7|Q494X7|Q494X9|Q6P085	Silent	SNP	ENST00000428202.2	37	CCDS47236.1																																																																																			.		0.557	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		C	74981182	G	C	74981182	2	2	13	1	0	0	0	0	0	0	0	1	12203	1219	43	4		4	POC5	5	74981182	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	955075	74981182	105934078	43	1032											
MSH3	4437	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	80160742	80160743	+	Frame_Shift_Ins	INS	-	-	GAAA																															gattcttggtcagtgaggatINSgaaagcaaactggatccagg																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:80160742_80160743insGAAA	ENST00000265081.6	+	22	3191_3192	c.3111_3112insGAAA	c.(3112-3114)gaafs	p.-1038fs		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3						ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCAGTGAGGATGAAAGCAAACT	0.396								Mismatch excision repair (MMR)																													p.D1037fs	Melanoma(88;1010 1399 13793 26548 36275)	.											.	MSH3-661	0			c.3111_3112insGAAA						.																																			SO:0001589	frameshift_variant	4437	exon22			.	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.3112_3115dupGAAA	5.37:g.80160743_80160746dupGAAA	ENSP00000265081:p.Glu1038fs	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	171	38	NM_002439	0	0	0	0	0	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Ins	INS	ENST00000265081.6	37	CCDS34195.1																																																																																			.		0.396	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		GAAA	80160743	-	GAAA	80160742	7	5	13	1	0	1	1	0	0	0	0	0	9896	1461	51	0	3197	0	MSH3	5	80160742	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	5179560	80160742	100754518	44	1033											
CHD1	1105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	98195710	98195710	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttttttaatagcatgcttaTataatttatgtaattttctt	11	23	4	3	0	1	0	0	0	1	0	1	0	1	0	0	0	2	4	0	0	7	13			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:98195710T>C	ENST00000284049.3	-	32	4639	c.4490A>G	c.(4489-4491)tAt>tGt	p.Y1497C		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1497					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AGCATGCTTATATAATTTATG	0.274																																					p.Y1497C		.											.	CHD1-274	0			c.A4490G						.						37	42	40					5																	98195710		2193	4275	6468	SO:0001583	missense	1105	exon32			TGCTTATATAATT	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4490A>G	5.37:g.98195710T>C	ENSP00000284049:p.Tyr1497Cys	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	67	42	NM_001270	0	0	0	0	0	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.048523	0.75846	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.97041	-4.22	5.09	5.09	0.68999	.	0.000000	0.31233	U	0.008011	D	0.98378	0.9461	M	0.83384	2.64	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99620	1.0983	10	0.87932	D	0	.	15.1564	0.72746	0.0:0.0:0.0:1.0	.	1497	O14646	CHD1_HUMAN	C	87;1497	ENSP00000284049:Y1497C	ENSP00000284049:Y1497C	Y	-	2	0	CHD1	98223610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.671000	0.83941	2.036000	0.60181	0.533000	0.62120	TAT	.		0.274	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		C	98195710	T	C	98195710	3	2	13	1	0	0	0	0	1	0	0	0	3329	1406	49	3	658	3	CHD1	5	98195710	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	18034968	98195710	82719550	45	1034											
GIN1	54826	hgsc.bcm.edu	37	chr5	102442521	102442521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctccactgtcattttcatGgcattctcttaagactttct	8	17	5	11	0	4	1	2	0	2	1	6	1	5	1	1	1	1	2	1	1	1	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:102442521G>A	ENST00000399004.2	-	3	326	c.232C>T	c.(232-234)Cat>Tat	p.H78Y	GIN1_ENST00000511400.1_5'Flank|GIN1_ENST00000508629.1_Missense_Mutation_p.H78Y	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	78					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		TCATTTTCATGGCATTCTCTT	0.358																																					p.H78Y		.											.	GIN1-92	0			c.C232T						.						103	95	97					5																	102442521		1844	4093	5937	SO:0001583	missense	54826	exon3			TTTCATGGCATTC	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.232C>T	5.37:g.102442521G>A	ENSP00000381970:p.His78Tyr	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	44	11	NM_017676	0	0	0	0	0	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511057	0.85389	.	.	ENSG00000145723	ENST00000399004;ENST00000508629	T;T	0.34859	1.34;1.34	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000007	T	0.43523	0.1251	N	0.08118	0	0.50813	D	0.999895	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.53528	-0.8426	10	0.72032	D	0.01	-23.322	18.8203	0.92094	0.0:0.0:1.0:0.0	.	78;78	Q9NXP7-3;Q9NXP7	.;GIN1_HUMAN	Y	78	ENSP00000381970:H78Y;ENSP00000427162:H78Y	ENSP00000381970:H78Y	H	-	1	0	GIN1	102470420	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.069000	0.71209	2.880000	0.98712	0.650000	0.86243	CAT	.		0.358	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		A	102442521	G	A	102442521	3	1	13	1	0	0	0	0	1	0	0	0	6406	1348	47	2	1360	2	GIN1	5	102442521	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	4246811	102442521	78472739	46	1035											
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140724210	140724210	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgggccctggaccgtgagAaaaaagaaattcaccagctt	14	6	11	10	2	1	2	1	1	0	2	1	4	1	3	3	2	2	1	3	2	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:140724210A>T	ENST00000253812.6	+	1	610	c.610A>T	c.(610-612)Aaa>Taa	p.K204*	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	204	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCGTGAGAAAAAAGAAAT	0.537																																					p.K204X		.											.	PCDHGA3-68	0			c.A610T						.						48	51	50					5																	140724210		2151	4270	6421	SO:0001587	stop_gained	56112	exon1			CGTGAGAAAAAAG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.610A>T	5.37:g.140724210A>T	ENSP00000253812:p.Lys204*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	136	39	NM_032011	0	0	0	0	0	Q9Y5D4	Nonsense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	16.89	3.246840	0.59103	.	.	ENSG00000254245	ENST00000253812	.	.	.	5.65	1.35	0.21983	.	0.498029	0.14302	U	0.328230	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	5.4155	0.16372	0.3545:0.1525:0.4931:0.0	.	.	.	.	X	204	.	ENSP00000253812:K204X	K	+	1	0	PCDHGA3	140704394	0.000000	0.05858	0.941000	0.38009	0.356000	0.29392	0.140000	0.16056	0.282000	0.22254	0.533000	0.62120	AAA	.		0.537	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140724210	A	T	140724210	4	4	13	1	0	0	0	0	0	1	0	0	11581	247	9	5	612	5	PCDHGA3	5	140724210	Nonsense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	38281689	140724210	40191050	47	1036											
PCDH1	5097	hgsc.bcm.edu	37	chr5	141233788	141233788	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggggccgttttggtgttcCggtcttccggggggctgggg	0	11	21	9	4	1	0	0	0	1	0	3	0	3	0	3	9	0	3	3	9	0	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:141233788C>T	ENST00000287008.3	-	5	3680	c.3533G>A	c.(3532-3534)cGg>cAg	p.R1178Q	PCDH1_ENST00000503492.1_3'UTR	NM_032420.2	NP_115796.2	Q08174	PCDH1_HUMAN	protocadherin 1	0					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TTTGGTGTTCCGGTCTTCCGG	0.652																																					p.R1178Q	Ovarian(132;1609 1739 4190 14731 45037)	.											.	PCDH1-95	0			c.G3533A						.						20	22	21					5																	141233788		2202	4299	6501	SO:0001583	missense	5097	exon5			GTGTTCCGGTCTT	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"Cadherins / Protocadherins : Non-clustered"	8655	protein-coding gene	gene with protein product		603626	"protocadherin 1 (cadherin-like 1)"			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000287008.3:c.3533G>A	5.37:g.141233788C>T	ENSP00000287008:p.Arg1178Gln	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_032420	0	0	0	0	0	Q8IUP2	Missense_Mutation	SNP	ENST00000287008.3	37	CCDS4267.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.490764	0.44249	.	.	ENSG00000156453	ENST00000287008	T	0.53423	0.62	4.78	3.9	0.45041	.	1.032420	0.07798	U	0.956009	T	0.40886	0.1135	L	0.40543	1.245	0.80722	D	1	P	0.50443	0.935	B	0.38755	0.281	T	0.20472	-1.0274	10	0.41790	T	0.15	.	13.0535	0.58967	0.0:0.8367:0.1633:0.0	.	1178	Q08174-2	.	Q	1178	ENSP00000287008:R1178Q	ENSP00000287008:R1178Q	R	-	2	0	PCDH1	141213972	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.887000	0.48586	1.131000	0.42111	0.448000	0.29417	CGG	.		0.652	PCDH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320587.2	NM_032420		T	141233788	C	T	141233788	3	4	13	1	0	0	0	0	1	0	0	0	11532	652	23	1	184	1	PCDH1	5	141233788	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	509578	141233788	39681472	48	1037											
MAML1	821	hgsc.bcm.edu	37	chr5	179160185	179160185	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcggtcatggagcgccttcgCcggcgcatcgagctgtgccg	4	7	16	14	7	1	0	1	0	0	0	3	2	1	1	3	3	3	2	3	3	0	1	rs76621265	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:179160185C>T	ENST00000247461.4	+	0	4260				MAML1_ENST00000292599.3_Silent_p.R24R	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin						aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	AGCGCCTTCGCCGGCGCATCG	0.756													C|||	115	0.0229633	0.0862	0.0014	5008	,	,		6237	0		0	False		,,,				2504	0				p.R24R		.											.	MAML1-848	0			c.C72T						.	C		163,3143		1,161,1491	3	2	2		72	3.8	1	5	dbSNP_131	2	5,6517		0,5,3256	no	coding-synonymous	MAML1	NM_014757.4		1,166,4747	TT,TC,CC		0.0767,4.9304,1.7094		24/1017	179160185	168,9660	1653	3261	4914	SO:0001628	intergenic_variant	9794	exon1			CCTTCGCCGGCGC	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"major histocompatibility complex class I antigen-binding protein p88"	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910		5.37:g.179160185C>T		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	8	7	NM_014757	0	0	0	0	0	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Silent	SNP	ENST00000247461.4	37	CCDS4447.1	40	0.018315018315018316	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	13.00	2.107428	0.37145	0.049304	7.67E-4	ENSG00000161021	ENST00000376951	.	.	.	3.79	3.79	0.43588	.	.	.	.	.	T	0.17323	0.0416	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53556	-0.8422	5	0.66056	D	0.02	-10.5307	11.6476	0.51269	0.0:0.9087:0.0:0.0913	.	.	.	.	V	107	.	ENSP00000366150:A107V	A	+	2	0	MAML1	179092791	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.489000	0.45285	1.958000	0.56883	0.465000	0.42564	GCC	C|0.982;T|0.018		0.756	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		T	179160185	C	T	179160185	1	4	13	0	1	0	0	0	0	0	0	0	9230	726	26	2		2	MAML1	5	179160185	IGR	SNP	C	TCGA-A4-8098-01A-11D-2396-08	37926397	179160185	1755075	49	1038											
SLC26A8	116369	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	35923086	35923086	+	Frame_Shift_Del	DEL	T	T	-																															caggcagtcctggtgagctgTttcttgatgagttattagga																								rs200648238		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:35923086delT	ENST00000490799.1	-	17	2428	c.2075delA	c.(2074-2076)aacfs	p.N692fs	SLC26A8_ENST00000355574.2_Frame_Shift_Del_p.N692fs|SLC26A8_ENST00000394602.2_Frame_Shift_Del_p.N587fs	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						TGGTGAGCTGTTTCTTGATGA	0.507																																					p.N692fs		.											.	SLC26A8-92	0			c.2075delA						.						194	187	190					6																	35923086		2203	4300	6503	SO:0001589	frameshift_variant	116369	exon17			.	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2075delA	6.37:g.35923086delT	ENSP00000417638:p.Asn692fs	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	108	45	NM_052961	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000490799.1	37	CCDS4813.1																																																																																			.		0.507	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			-	35923086	T	-	35923086	7	5	13	1	0	1	0	1	0	0	0	0	14555	1725	60	0	853	0	SLC26A8	6	35923086	Frame_Shift_Del	DEL	T	TCGA-A4-8098-01A-11D-2396-08		35923086	135191981	50	1039											
SLC22A7	10864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43266249	43266249	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcccaccgatgtgccctGccgggtgcccctgccaactt	4	8	10	19	2	0	0	0	0	0	0	0	1	0	0	8	1	6	0	8	1	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:43266249G>A	ENST00000372585.5	+	1	248	c.153G>A	c.(151-153)ctG>ctA	p.L51L	SLC22A7_ENST00000372574.3_Silent_p.L51L|SLC22A7_ENST00000372589.3_Silent_p.L51L|SLC22A7_ENST00000487175.1_Intron	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	51					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GATGTGCCCTGCCGGGTGCCC	0.662																																					p.L51L		.											.	SLC22A7-90	0			c.G153A						.						51	51	51					6																	43266249		2203	4300	6503	SO:0001819	synonymous_variant	10864	exon1			TGCCCTGCCGGGT	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.153G>A	6.37:g.43266249G>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	89	35	NM_006672	0	0	0	0	0	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	37	CCDS4893.2																																																																																			G|1.000;T|0.000		0.662	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			A	43266249	G	A	43266249	2	1	13	1	0	0	0	0	0	0	0	1	14491	1306	46	2		2	SLC22A7	6	43266249	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	7343163	43266249	127848818	51	1040											
LRRC1	55227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	53660212	53660212	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctccgcgagctgcccgAggtaagggtccggcctcacc	6	5	13	17	4	1	0	1	0	0	0	3	2	3	0	6	3	3	3	6	3	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:53660212A>T	ENST00000370888.1	+	1	435	c.158A>T	c.(157-159)gAg>gTg	p.E53V	LRRC1_ENST00000370882.1_Splice_Site_p.E53V|RP13-476E20.1_ENST00000429053.1_RNA	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	53						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		GAGCTGCCCGAGGTAAGGGTC	0.682																																					p.E53V		.											.	LRRC1-91	0			c.A158T						.						28	28	28					6																	53660212		2203	4300	6503	SO:0001630	splice_region_variant	55227	exon1			TGCCCGAGGTAAG	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.159+1A>T	6.37:g.53660212A>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	31	9	NM_018214	0	0	0	0	0	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	37	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737840	0.69304	.	.	ENSG00000137269	ENST00000370888;ENST00000370882	T;T	0.58797	0.31;0.31	4.88	3.68	0.42216	.	0.264852	0.37623	N	0.002013	T	0.35008	0.0917	N	0.25380	0.74	0.39279	D	0.96452	B	0.32467	0.372	B	0.42319	0.383	T	0.38373	-0.9664	10	0.87932	D	0	.	9.613	0.39674	0.914:0.0:0.086:0.0	.	53	Q9BTT6	LRRC1_HUMAN	V	53	ENSP00000359925:E53V;ENSP00000359919:E53V	ENSP00000359919:E53V	E	+	2	0	LRRC1	53768171	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	8.227000	0.89787	0.660000	0.30964	0.460000	0.39030	GAG	.		0.682	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	Missense_Mutation	T	53660212	A	T	53660212	5	4	13	1	0	0	0	0	0	0	1	0	8991	318	11	5	160	5	LRRC1	6	53660212	Splice_Site	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10393963	53660212	117454855	52	1041											
CD109	135228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	74407130	74407130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggaactctttaggcctcggTttctggtgacagccccaggg	6	10	14	11	1	2	1	0	1	2	0	3	2	2	2	3	5	2	1	3	5	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:74407130T>C	ENST00000287097.5	+	2	194	c.82T>C	c.(82-84)Ttt>Ctt	p.F28L	CD109_ENST00000437994.2_Missense_Mutation_p.F28L|RP11-553A21.3_ENST00000428865.2_RNA|CD109_ENST00000422508.2_Missense_Mutation_p.F28L			Q6YHK3	CD109_HUMAN	CD109 molecule	28					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TAGGCCTCGGTTTCTGGTGAC	0.507																																					p.F28L		.											.	CD109-155	0			c.T82C						.						103	101	102					6																	74407130		2203	4300	6503	SO:0001583	missense	135228	exon2			CCTCGGTTTCTGG	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"CD molecules"	21685	protein-coding gene	gene with protein product		608859	"CD109 antigen (Gov platelet alloantigens)"			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.82T>C	6.37:g.74407130T>C	ENSP00000287097:p.Phe28Leu	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	118	49	NM_133493	0	0	0	0	0	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192857	0.78902	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.35421	1.86;1.31;1.86	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000004	T	0.29850	0.0746	N	0.19112	0.55	0.23555	N	0.997424	D;D;D;D	0.69078	0.965;0.997;0.986;0.985	P;D;P;P	0.66716	0.63;0.946;0.84;0.873	T	0.19516	-1.0303	10	0.72032	D	0.01	.	12.8889	0.58058	0.0:0.0:0.0:1.0	.	28;28;28;28	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	L	28	ENSP00000388062:F28L;ENSP00000404475:F28L;ENSP00000287097:F28L	ENSP00000287097:F28L	F	+	1	0	CD109	74463851	0.998000	0.40836	0.964000	0.40570	0.607000	0.37147	4.263000	0.58853	2.243000	0.73865	0.533000	0.62120	TTT	.		0.507	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74407130	T	C	74407130	3	2	13	1	0	0	0	0	1	0	0	0	2969	1725	60	3	88	3	CD109	6	74407130	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	20746918	74407130	96707937	53	1042											
PHIP	55023	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	79724879	79724879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcatgaccagcagaaaagaGaactctaggatcgaacgggt	16	6	11	8	2	2	3	1	1	1	2	3	6	2	4	1	2	3	1	1	2	5	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:79724879G>A	ENST00000275034.4	-	15	1611	c.1444C>T	c.(1444-1446)Ctc>Ttc	p.L482F		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	482					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GCAGAAAAGAGAACTCTAGGA	0.358																																					p.L482F		.											.	PHIP-579	0			c.C1444T						.						101	94	96					6																	79724879		2203	4300	6503	SO:0001583	missense	55023	exon15			AAAAGAGAACTCT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	15673	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 14"	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1444C>T	6.37:g.79724879G>A	ENSP00000275034:p.Leu482Phe	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	82	10	NM_017934	0	0	0	0	0	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033289	0.75504	.	.	ENSG00000146247	ENST00000275034	T	0.68479	-0.33	5.23	5.23	0.72850	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.52532	D	0.000061	T	0.60586	0.2280	N	0.21194	0.64	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.61093	-0.7132	9	.	.	.	-5.5196	11.6141	0.51078	0.0821:0.0:0.9179:0.0	.	482;482	A7J992;Q8WWQ0	.;PHIP_HUMAN	F	482	ENSP00000275034:L482F	.	L	-	1	0	PHIP	79781598	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.663000	0.54518	2.586000	0.87340	0.460000	0.39030	CTC	.		0.358	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79724879	G	A	79724879	3	1	13	1	0	0	0	0	1	0	0	0	11868	942	33	2	4125	2	PHIP	6	79724879	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	5317749	79724879	91390188	54	1043											
KIAA0776	23376	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	96996102	96996102	+	Frame_Shift_Del	DEL	C	C	-																															ttgaagattttttaagaaaaCacatacaagatgcccctgag																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:96996102delC	ENST00000369278.4	+	13	1531	c.1465delC	c.(1465-1467)cacfs	p.H489fs		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	489					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										TTTAAGAAAACACATACAAGA	0.308																																					p.H489fs		.											.	.	0			c.1465delC						.						57	59	58					6																	96996102		2202	4300	6502	SO:0001589	frameshift_variant	23376	exon13			.	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"novel LZAP-binding protein", "Regulator of CDK5RAP3 and DDRGK1"	613372	"KIAA0776"	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1465delC	6.37:g.96996102delC	ENSP00000358283:p.His489fs	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	35	17	NM_015323	0	0	0	0	0	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Frame_Shift_Del	DEL	ENST00000369278.4	37	CCDS5034.1																																																																																			.		0.308	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		-	96996102	C	-	96996102	7	5	13	1	0	1	0	1	0	0	0	0	8214	478	17	0	1515	0	KIAA0776	6	96996102	Frame_Shift_Del	DEL	C	TCGA-A4-8098-01A-11D-2396-08	17271223	96996102	74118965	55	1044											
TNRC18	84629	broad.mit.edu	37	chr7	5396802	5396803	+	Frame_Shift_Ins	INS	-	-	G																															ccagcactgtccgaaaacttINSgaagggcgacttcaacttgt																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:5396802_5396803insG	ENST00000430969.1	-	16	5286_5287	c.4938_4939insC	c.(4936-4941)ttcaagfs	p.K1647fs	TNRC18_ENST00000399537.4_Frame_Shift_Ins_p.K1647fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1647							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TCCGAAAACTTGAAGGGCGACT	0.559																																					p.K1647fs													.	TNRC18-46	0			c.4939_4940insC						.																																			SO:0001589	frameshift_variant	84629	exon16			AAAACTTGAAGGG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4939dupC	7.37:g.5396803_5396803dupG	ENSP00000395538:p.Lys1647fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	13	6	NM_001080495	0	0	0	0	0	A8MX41|Q96JH1|Q96K91	Frame_Shift_Ins	INS	ENST00000430969.1	37	CCDS47534.1																																																																																			.		0.559	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5396803	-	G	5396802	7	5	13	1	0	1	1	0	0	0	0	0	16371	1821	63	0	4027	0	TNRC18	7	5396802	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08		5396802	153741861	56	1045											
DNAH11	8701	broad.mit.edu;bcgsc.ca	37	chr7	21908512	21908512	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggctttacaattgactctgGaaaattccacaatgtgtctt	11	15	7	8	0	2	1	0	1	2	0	3	2	3	2	1	2	1	1	1	2	5	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:21908512G>T	ENST00000409508.3	+	73	11901	c.11870G>T	c.(11869-11871)gGa>gTa	p.G3957V	DNAH11_ENST00000328843.6_Missense_Mutation_p.G3964V	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3964	AAA 6. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ATTGACTCTGGAAAATTCCAC	0.498									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						120	117	118					7																	21908512		1914	4130	6044	SO:0001583	missense	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACTCTGGAAAATT	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.11870G>T	7.37:g.21908512G>T	ENSP00000475939:p.Gly3957Val	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	121	11	.	0	0	0	0	0	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	28.7	4.945078	0.92593	.	.	ENSG00000105877	ENST00000328843	T	0.08370	3.1	5.85	5.85	0.93711	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.29321	0.0730	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00161	-1.1972	9	0.30078	T	0.28	.	20.1527	0.98091	0.0:0.0:1.0:0.0	.	3964	Q96DT5	DYH11_HUMAN	V	3964	ENSP00000330671:G3964V	ENSP00000330671:G3964V	G	+	2	0	DNAH11	21875037	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.770000	0.95276	0.579000	0.79373	GGA	.		0.498	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		T	21908512	G	T	21908512	3	4	13	1	0	0	0	0	1	0	0	0	4610	1174	41	4	12182	4	DNAH11	7	21908512	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	16511710	21908512	137230151	57	1046											
GPNMB	10457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	23306207	23306207	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagattaacagatatggcCactttcaagccaccatcaca	14	8	6	13	0	2	2	2	0	0	2	2	2	2	2	4	1	2	0	4	1	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:23306207C>A	ENST00000381990.2	+	7	1287	c.1126C>A	c.(1126-1128)Cac>Aac	p.H376N	GPNMB_ENST00000453162.2_Missense_Mutation_p.H318N|GPNMB_ENST00000258733.4_Missense_Mutation_p.H364N|GPNMB_ENST00000539136.1_Missense_Mutation_p.H265N	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	376					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			CAGATATGGCCACTTTCAAGC	0.478																																					p.H376N		.											.	GPNMB-580	0			c.C1126A						.						82	71	75					7																	23306207		2203	4300	6503	SO:0001583	missense	10457	exon7			TATGGCCACTTTC	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1126C>A	7.37:g.23306207C>A	ENSP00000371420:p.His376Asn	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	52	19	NM_001005340	0	0	0	0	0	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	6.226	0.409829	0.11812	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.13657	2.58;2.58;2.57;2.58	5.89	-0.668	0.11392	PKD/Chitinase domain (1);	0.606085	0.16307	N	0.220182	T	0.12518	0.0304	L	0.47716	1.5	0.09310	N	0.999998	D;P;P;P	0.53745	0.962;0.82;0.913;0.744	B;B;B;B	0.43990	0.438;0.351;0.345;0.275	T	0.29212	-1.0019	10	0.22706	T	0.39	-12.8359	11.5467	0.50698	0.0:0.5539:0.0:0.4461	.	265;318;376;364	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	N	364;411;376;259;265;318	ENSP00000258733:H364N;ENSP00000371420:H376N;ENSP00000445266:H265N;ENSP00000405586:H318N	ENSP00000258733:H364N	H	+	1	0	GPNMB	23272732	0.759000	0.28416	0.042000	0.18584	0.021000	0.10359	1.106000	0.31098	-0.061000	0.13110	-0.781000	0.03364	CAC	.		0.478	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		A	23306207	C	A	23306207	3	1	13	1	0	0	0	0	1	0	0	0	6640	594	21	4	1152	4	GPNMB	7	23306207	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	1397695	23306207	135832456	58	1047											
GLI3	2737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	42063171	42063171	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgctttcatctttgtcccCttcctccttgacaagggttg	4	18	7	12	0	2	1	1	1	1	0	5	1	5	1	4	1	1	2	4	1	1	6	rs35488756	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:42063171C>T	ENST00000395925.3	-	10	1477	c.1393G>A	c.(1393-1395)Ggg>Agg	p.G465R	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	465					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TCTTTGTCCCCTTCCTCCTTG	0.542									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.G465R		.											.	GLI3-1149	0			c.G1393A						.						152	118	129					7																	42063171		2203	4300	6503	SO:0001583	missense	2737	exon10	Familial Cancer Database	;	TGTCCCCTTCCTC		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1393G>A	7.37:g.42063171C>T	ENSP00000379258:p.Gly465Arg	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	102	41	NM_000168	0	0	0	0	0	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727028	0.69074	.	.	ENSG00000106571	ENST00000395925	T	0.69306	-0.39	5.81	5.81	0.92471	.	0.043845	0.85682	D	0.000000	T	0.66713	0.2817	L	0.57536	1.79	0.80722	D	1	B	0.16396	0.017	B	0.14023	0.01	T	0.60762	-0.7199	10	0.42905	T	0.14	.	20.0912	0.97820	0.0:1.0:0.0:0.0	.	465	P10071	GLI3_HUMAN	R	465	ENSP00000379258:G465R	ENSP00000379258:G465R	G	-	1	0	GLI3	42029696	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.975000	0.70475	2.746000	0.94184	0.591000	0.81541	GGG	C|0.997;G|0.003		0.542	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42063171	C	T	42063171	3	4	13	1	0	0	0	0	1	0	0	0	6459	681	24	2	3373	2	GLI3	7	42063171	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	18756964	42063171	117075492	59	1048											
CLIP2	7461	broad.mit.edu	37	chr7	73790237	73790239	+	In_Frame_Del	DEL	GTC	GTC	-																															ctgaccacagtggccgagaaGtcgcgcgtgctgcagctgga																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	GTC	GTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:73790237_73790239delGTC	ENST00000395060.1	+	9	1506_1508	c.1506_1508delGTC	c.(1504-1509)aagtcg>aag	p.S503del	CLIP2_ENST00000361545.5_In_Frame_Del_p.S468del|CLIP2_ENST00000223398.6_In_Frame_Del_p.S503del			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	503						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						TGGCCGAGAAGTCGCGCGTGCTG	0.67																																					p.502_503del													.	CLIP2-93	0			c.1506_1508del						.																																			SO:0001651	inframe_deletion	7461	exon10			CGAGAAGTCGCGC	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.1506_1508delGTC	7.37:g.73790237_73790239delGTC	ENSP00000378500:p.Ser503del	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	14	5	NM_003388	0	0	0	0	0	O14527|O43611	In_Frame_Del	DEL	ENST00000395060.1	37	CCDS5569.1																																																																																			.		0.67	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		-	73790239	GTC	-	73790237	7	5	13	1	0	1	0	1	0	0	0	0	3539	1020	36	0	1540	0	CLIP2	7	73790237	In_Frame_Del	DEL	GTC	TCGA-A4-8098-01A-11D-2396-08	31727066	73790237	85348426	60	1049											
PILRA	29992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99971777	99971777	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctccttctattaccccTgggagttagccacagctccc	6	12	6	17	0	2	0	0	0	2	0	4	1	3	1	6	1	3	2	6	1	3	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:99971777T>G	ENST00000198536.2	+	2	387	c.175T>G	c.(175-177)Tgg>Ggg	p.W59G	PILRA_ENST00000453419.1_Missense_Mutation_p.W59G|PILRA_ENST00000350573.2_Missense_Mutation_p.W59G|PILRA_ENST00000474013.1_3'UTR|PILRA_ENST00000394000.2_Missense_Mutation_p.W59G	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	59	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTATTACCCCTGGGAGTTAGC	0.547																																					p.W59G		.											.	PILRA-91	0			c.T175G						.						65	73	70					7																	99971777		2203	4300	6503	SO:0001583	missense	29992	exon2			TACCCCTGGGAGT	AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"Immunoglobulin superfamily / V-set domain containing"	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.175T>G	7.37:g.99971777T>G	ENSP00000198536:p.Trp59Gly	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	101	9	NM_013439	0	0	0	0	0	Q8NHI1	Missense_Mutation	SNP	ENST00000198536.2	37	CCDS5691.1	.	.	.	.	.	.	.	.	.	.	T	7.824	0.718406	0.15372	.	.	ENSG00000085514	ENST00000432297;ENST00000198536;ENST00000453419;ENST00000394000;ENST00000350573	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	3.28	0.423	0.16463	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.575166	0.14763	N	0.299864	T	0.36220	0.0959	L	0.35542	1.07	0.09310	N	1	P;B;B;B;P	0.47841	0.465;0.091;0.074;0.014;0.901	B;B;B;B;P	0.49421	0.166;0.046;0.047;0.014;0.61	T	0.18903	-1.0322	9	.	.	.	.	8.3067	0.32047	0.0:0.0:0.5403:0.4597	.	59;59;59;59;59	C9JJ79;C9JGG1;Q9UKJ1-4;Q9UKJ1-3;Q9UKJ1	.;.;.;.;PILRA_HUMAN	G	59	ENSP00000415111:W59G;ENSP00000198536:W59G;ENSP00000390026:W59G;ENSP00000377569:W59G;ENSP00000340109:W59G	.	W	+	1	0	PILRA	99809713	0.011000	0.17503	0.078000	0.20375	0.106000	0.19336	0.017000	0.13399	0.052000	0.16007	0.260000	0.18958	TGG	.		0.547	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439		G	99971777	T	G	99971777	3	3	13	1	0	0	0	0	1	0	0	0	11951	1580	55	5	181	5	PILRA	7	99971777	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	26181540	99971777	59166886	61	1050											
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121651018	121651018	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attcaacttcatcaggttcaGaagaatcactaaaggatcct	15	11	6	9	0	5	2	5	0	0	2	6	3	6	3	1	2	1	1	1	2	5	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:121651018G>C	ENST00000393386.2	+	12	2329	c.1918G>C	c.(1918-1920)Gaa>Caa	p.E640Q	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E640Q	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	640					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ATCAGGTTCAGAAGAATCACT	0.418																																					p.E640Q		.											.	PTPRZ1-699	0			c.G1918C						.						60	58	59					7																	121651018		2203	4300	6503	SO:0001583	missense	5803	exon12			GGTTCAGAAGAAT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.1918G>C	7.37:g.121651018G>C	ENSP00000377047:p.Glu640Gln	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	105	45	NM_001206838	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952906	0.34471	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.50548	0.8;0.74	5.87	5.87	0.94306	.	0.470308	0.21679	N	0.070741	T	0.61274	0.2334	M	0.67953	2.075	0.27751	N	0.944151	P;P;D	0.63880	0.779;0.671;0.993	B;B;P	0.55713	0.277;0.143;0.782	T	0.60182	-0.7313	10	0.59425	D	0.04	.	14.976	0.71273	0.0:0.0:0.8573:0.1427	.	640;640;640	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	Q	640	ENSP00000377047:E640Q;ENSP00000410000:E640Q	ENSP00000377047:E640Q	E	+	1	0	PTPRZ1	121438254	0.993000	0.37304	0.945000	0.38365	0.967000	0.64934	3.265000	0.51561	2.778000	0.95560	0.655000	0.94253	GAA	.		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121651018	G	C	121651018	3	2	13	1	0	0	0	0	1	0	0	0	12846	943	33	4	1964	4	PTPRZ1	7	121651018	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	21679241	121651018	37487645	62	1051											
LRRC67	286187	hgsc.bcm.edu	37	chr8	67900719	67900719	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atttagatcaattttccacaGcttcatcaacttgttcagta	12	16	4	9	0	4	1	4	0	0	1	5	1	5	1	1	0	2	3	1	0	4	8			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:67900719G>C	ENST00000324682.5	-	6	730	c.586C>G	c.(586-588)Ctg>Gtg	p.L196V	PPP1R42_ENST00000522909.1_Missense_Mutation_p.L196V	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	196					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										ATTTTCCACAGCTTCATCAAC	0.333																																					p.L196V		.											.	.	0			c.C586G						.						63	60	61					8																	67900719		2202	4298	6500	SO:0001583	missense	286187	exon6			TCCACAGCTTCAT	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	33732	protein-coding gene	gene with protein product	"testis leucine-rich repeat"		"leucine rich repeat containing 67"	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.586C>G	8.37:g.67900719G>C	ENSP00000315035:p.Leu196Val	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_001013626	0	0	0	0	0		Missense_Mutation	SNP	ENST00000324682.5	37	CCDS34902.1	.	.	.	.	.	.	.	.	.	.	G	16.49	3.137817	0.56936	.	.	ENSG00000178125	ENST00000522909;ENST00000421742;ENST00000324682	T;T	0.65178	1.11;-0.14	5.37	-9.13E-4	0.14036	.	0.067900	0.64402	D	0.000010	T	0.79684	0.4488	H	0.94264	3.515	0.45366	D	0.998359	D	0.76494	0.999	D	0.73708	0.981	T	0.75964	-0.3132	10	0.72032	D	0.01	-0.3165	6.0082	0.19559	0.2809:0.0:0.5996:0.1195	.	196	Q7Z4L9-2	.	V	196	ENSP00000429721:L196V;ENSP00000315035:L196V	ENSP00000315035:L196V	L	-	1	2	LRRC67	68063273	0.998000	0.40836	0.889000	0.34880	0.908000	0.53690	1.394000	0.34509	-0.222000	0.09958	-0.355000	0.07637	CTG	.		0.333	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		C	67900719	G	C	67900719	3	2	13	1	0	0	0	0	1	0	0	0	9044	962	34	4	104	4	LRRC67	8	67900719	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08		67900719	78463303	63	1052											
NCOA2	10499	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	71039066	71039067	+	Frame_Shift_Ins	INS	-	-	AAAC																															ccgtagtttggaggaaatggINSaaactgctgtgcatttgcct																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:71039066_71039067insAAAC	ENST00000452400.2	-	19	4078_4079	c.3897_3898insGTTT	c.(3895-3900)tttccafs	p.P1300fs	NCOA2_ENST00000267974.4_Frame_Shift_Ins_p.P388fs	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1300					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GGAGGAAATGGAAACTGCTGTG	0.53			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P1300fs		.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2-639	0			c.3898_3899insGTTT						.																																			SO:0001589	frameshift_variant	10499	exon19			.	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.3894_3897dupGTTT	8.37:g.71039067_71039070dupAAAC	ENSP00000399968:p.Pro1300fs	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	50	11	NM_006540	0	0	0	0	0	Q14CD2	Frame_Shift_Ins	INS	ENST00000452400.2	37	CCDS47872.1																																																																																			.		0.53	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			AAAC	71039067	-	AAAC	71039066	7	5	13	1	0	1	1	0	0	0	0	0	10255	1174	41	0	516	0	NCOA2	8	71039066	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	3138347	71039066	75324956	64	1053											
DENND3	22898	hgsc.bcm.edu	37	chr8	142146788	142146788	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagagaagcccagaccagagCagtggaagggcctcccgggg	11	2	17	11	1	0	3	0	0	0	3	1	6	1	4	4	4	2	1	4	4	2	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:142146788C>G	ENST00000262585.2	+	2	321	c.43C>G	c.(43-45)Cag>Gag	p.Q15E	DENND3_ENST00000518347.1_Missense_Mutation_p.Q95E|DENND3_ENST00000424248.1_Missense_Mutation_p.Q15E|DENND3_ENST00000519811.1_Missense_Mutation_p.Q95E	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	15	UDENN.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGACCAGAGCAGTGGAAGGG	0.647																																					p.Q15E		.											.	DENND3-91	0			c.C43G						.						18	22	20					8																	142146788		2203	4300	6503	SO:0001583	missense	22898	exon2			CCAGAGCAGTGGA	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.43C>G	8.37:g.142146788C>G	ENSP00000262585:p.Gln15Glu	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_014957	0	0	0	0	0	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.940|2.940	-0.219046|-0.219046	0.06101|0.06101	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000519291;ENST00000518347;ENST00000262585;ENST00000424248;ENST00000519811;ENST00000520986;ENST00000523058	.|T;T;T;T;T;T	.|0.40756	.|1.02;3.03;2.62;1.02;1.02;1.02	5.61|5.61	0.916|0.916	0.19373|0.19373	.|uDENN (1);	.|2.092340	.|0.01515	.|N	.|0.018084	T|T	0.21145|0.21145	0.0509|0.0509	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.19817	.|0.026;0.012;0.039;0.017	.|B;B;B;B	.|0.14023	.|0.001;0.001;0.01;0.004	T|T	0.14896|0.14896	-1.0456|-1.0456	5|10	.|0.09843	.|T	.|0.71	-11.1125|-11.1125	4.0219|4.0219	0.09670|0.09670	0.1871:0.4918:0.2347:0.0864|0.1871:0.4918:0.2347:0.0864	.|.	.|95;15;95;95	.|E9PF32;A2RUS2;E5RHH2;E5RIR7	.|.;DEND3_HUMAN;.;.	G|E	71|28;95;15;15;95;95;95	.|ENSP00000430695:Q95E;ENSP00000262585:Q15E;ENSP00000410594:Q15E;ENSP00000428714:Q95E;ENSP00000429780:Q95E;ENSP00000430786:Q95E	.|ENSP00000262585:Q15E	A|Q	+|+	2|1	0|0	DENND3|DENND3	142215970|142215970	0.007000|0.007000	0.16637|0.16637	0.004000|0.004000	0.12327|0.12327	0.004000|0.004000	0.04260|0.04260	0.021000|0.021000	0.13489|0.13489	0.204000|0.204000	0.20548|0.20548	0.650000|0.650000	0.86243|0.86243	GCA|CAG	.		0.647	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		G	142146788	C	G	142146788	3	3	13	1	0	0	0	0	1	0	0	0	4443	711	25	4	45	4	DENND3	8	142146788	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	71107722	142146788	4217234	65	1054											
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144942527	144942527	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aggtttctttcccgaacattCctgctttgaacgcctcctcc	6	14	6	15	2	1	1	0	1	1	0	5	2	5	1	5	1	3	2	5	1	2	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:144942527C>G	ENST00000525985.1	-	2	4966	c.4895G>C	c.(4894-4896)gGa>gCa	p.G1632A				P58107	EPIPL_HUMAN	epiplakin 1	1632						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCCGAACATTCCTGCTTTGAA	0.627																																					p.G1632A		.											.	EPPK1-25	0			c.G4895C						.						74	83	80					8																	144942527		2037	4184	6221	SO:0001583	missense	83481	exon1			AACATTCCTGCTT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4895G>C	8.37:g.144942527C>G	ENSP00000436337:p.Gly1632Ala	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	128	42	NM_031308	0	0	0	0	0	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	13.25	2.180920	0.38511	.	.	ENSG00000227184	ENST00000525985	D	0.85411	-1.98	4.41	4.41	0.53225	.	.	.	.	.	D	0.93798	0.8017	M	0.92317	3.295	0.09310	N	1	D	0.89917	1.0	D	0.72338	0.977	D	0.87143	0.2204	9	0.72032	D	0.01	.	14.5607	0.68133	0.0:1.0:0.0:0.0	.	1632	E9PPU0	.	A	1632	ENSP00000436337:G1632A	ENSP00000436337:G1632A	G	-	2	0	EPPK1	145014515	0.004000	0.15560	0.114000	0.21550	0.403000	0.30841	1.625000	0.37029	2.280000	0.76307	0.591000	0.81541	GGA	.		0.627	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144942527	C	G	144942527	3	3	13	1	0	0	0	0	1	0	0	0	5203	855	30	4	2371	4	EPPK1	8	144942527	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	2795739	144942527	1421495	66	1055											
CEP110	11064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	123900898	123900898	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcccttggaaaagcccagTtctcagaagaaaaggagcaa	16	6	10	9	0	1	2	1	0	1	2	2	4	1	4	2	2	3	2	2	2	6	2	rs566495778		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:123900898T>G	ENST00000373855.1	+	16	2538	c.2278T>G	c.(2278-2280)Ttc>Gtc	p.F760V	CNTRL_ENST00000373847.1_Missense_Mutation_p.F208V|CNTRL_ENST00000238341.5_Missense_Mutation_p.F760V|CNTRL_ENST00000373850.1_Missense_Mutation_p.F208V			Q7Z7A1	CNTRL_HUMAN	centriolin	760					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AAAAGCCCAGTTCTCAGAAGA	0.418																																					p.F760V		.											.	CNTRL-661	0			c.T2278G						.						97	98	98					9																	123900898		2203	4300	6503	SO:0001583	missense	11064	exon14			GCCCAGTTCTCAG	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.2278T>G	9.37:g.123900898T>G	ENSP00000362962:p.Phe760Val	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	101	42	NM_007018	0	0	0	0	0	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.248769	0.39797	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.76	2.4	0.29515	.	.	.	.	.	T	0.24236	0.0587	N	0.14661	0.345	0.23731	N	0.996993	B;B;B	0.24483	0.049;0.082;0.104	B;B;B	0.21708	0.016;0.036;0.024	T	0.20338	-1.0278	9	0.27082	T	0.32	.	8.6368	0.33953	0.0:0.3003:0.0:0.6997	.	760;760;760	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	V	760;760;760;242;208;208	ENSP00000362962:F760V;ENSP00000238341:F760V;ENSP00000362956:F208V;ENSP00000362953:F208V	ENSP00000238341:F760V	F	+	1	0	CNTRL	122940719	0.982000	0.34865	0.996000	0.52242	0.970000	0.65996	0.049000	0.14099	0.269000	0.21961	0.533000	0.62120	TTC	.		0.418	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123900898	T	G	123900898	3	3	13	1	0	0	0	0	1	0	0	0	3251	1725	60	5	2332	5	CEP110	9	123900898	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08		123900898	17312533	67	1056											
DNM1	1759	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130985083	130985083	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacacagatggagtttgaTgagaaggaactccgaaggga	14	8	13	6	1	1	3	0	2	1	2	2	8	2	6	1	3	2	1	1	3	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:130985083T>A	ENST00000372923.3	+	9	1232	c.1140T>A	c.(1138-1140)gaT>gaA	p.D380E	DNM1_ENST00000393594.3_Missense_Mutation_p.D380E|DNM1_ENST00000341179.7_Missense_Mutation_p.D380E|DNM1_ENST00000475805.1_Missense_Mutation_p.D380E|DNM1_ENST00000486160.1_Missense_Mutation_p.D380E	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	380					endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						TGGAGTTTGATGAGAAGGAAC	0.547																																					.	GBM(113;146 1575 2722 28670 29921)												.	DNM1-228	0			.						.						91	93	93					9																	130985083		2203	4300	6503	SO:0001583	missense	1759	.			GTTTGATGAGAAG	L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"Pleckstrin homology (PH) domain containing"	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.1140T>A	9.37:g.130985083T>A	ENSP00000362014:p.Asp380Glu	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	115	43	.	0	0	0	0	0	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Missense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.803679	0.50315	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393589;ENST00000393594;ENST00000486160	T;T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72;-0.72	5.74	-7.32	0.01436	Dynamin central domain (1);	0.000000	0.85682	D	0.000000	T	0.78874	0.4352	M	0.71871	2.18	0.80722	D	1	D;D;D	0.69078	0.997;0.996;0.974	D;D;P	0.80764	0.994;0.99;0.84	T	0.83247	-0.0055	10	0.54805	T	0.06	-2.1403	16.7993	0.85610	0.0:0.4642:0.0:0.5358	.	380;380;380	Q05193;Q05193-3;Q05193-2	DYN1_HUMAN;.;.	E	380;380;380;375;380;380	ENSP00000419225:D380E;ENSP00000345680:D380E;ENSP00000362014:D380E;ENSP00000377219:D380E;ENSP00000420045:D380E	ENSP00000345680:D380E	D	+	3	2	DNM1	130024904	0.950000	0.32346	0.481000	0.27354	0.831000	0.47069	0.027000	0.13621	-2.077000	0.00874	-1.447000	0.01057	GAT	.		0.547	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408		A	130985083	T	A	130985083	3	1	13	1	0	0	0	0	1	0	0	0	4681	1461	51	5	1174	5	DNM1	9	130985083	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	7084185	130985083	10228348	68	1057											
ADAMTS13	11093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	136305499	136305499	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggcgctatgtcgtggctggGaagatgagcatctcccctaa	8	9	14	10	2	1	2	0	1	1	1	3	3	1	3	2	3	1	3	2	3	3	2	rs371209152		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:136305499G>T	ENST00000371929.3	+	16	2265	c.1821G>T	c.(1819-1821)ggG>ggT	p.G607G	ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.G576G|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000355699.2_Silent_p.G607G|ADAMTS13_ENST00000536611.1_Silent_p.G279G	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	607	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCGTGGCTGGGAAGATGAGCA	0.642																																					p.G607G		.											.	ADAMTS13-229	0			c.G1821T						.						138	98	111					9																	136305499		2203	4300	6503	SO:0001819	synonymous_variant	11093	exon16			GGCTGGGAAGATG	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"ADAM metallopeptidases with thrombospondin type 1 motif"	1366	protein-coding gene	gene with protein product		604134	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1821G>T	9.37:g.136305499G>T		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	103	32	NM_139027	0	0	0	0	0	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			.		0.642	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		T	136305499	G	T	136305499	2	4	13	1	0	0	0	0	0	0	0	1	258	1161	41	4		4	ADAMTS13	9	136305499	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	5320416	136305499	4907932	69	1058											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139391440	139391440	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgccgccatctcgggcttggCcgccacgttcaggtgcccga	4	7	13	17	6	2	0	1	0	1	0	3	1	2	0	5	3	1	2	5	3	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:139391440C>T	ENST00000277541.6	-	34	6826	c.6751G>A	c.(6751-6753)Gcc>Acc	p.A2251T		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2251					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TCGGGCTTGGCCGCCACGTTC	0.706			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.A2251T		.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1-5459	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.G6751A						.						12	15	14					9																	139391440		1983	4126	6109	SO:0001583	missense	4851	exon34			GCTTGGCCGCCAC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6751G>A	9.37:g.139391440C>T	ENSP00000277541:p.Ala2251Thr	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_017617	0	0	0	0	0	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	4.536	0.099550	0.08681	.	.	ENSG00000148400	ENST00000277541	D	0.81821	-1.54	5.55	2.72	0.32119	.	0.379586	0.27841	N	0.017627	T	0.60261	0.2255	N	0.15975	0.35	0.30523	N	0.768211	B	0.12013	0.005	B	0.09377	0.004	T	0.49670	-0.8915	10	0.12766	T	0.61	.	8.1541	0.31158	0.0:0.693:0.0:0.307	.	2251	P46531	NOTC1_HUMAN	T	2251	ENSP00000277541:A2251T	ENSP00000277541:A2251T	A	-	1	0	NOTCH1	138511261	.	.	0.413000	0.26509	0.292000	0.27327	.	.	0.390000	0.25115	0.655000	0.94253	GCC	.		0.706	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		T	139391440	C	T	139391440	3	4	13	1	0	0	0	0	1	0	0	0	10573	739	26	2	920	2	NOTCH1	9	139391440	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	3085941	139391440	1821991	70	1059											
C10orf18	54906	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	5790239	5790239	+	Frame_Shift_Del	DEL	T	T	-																															aaagcagtcagaaccatctcTttcccggtgatttgaaaaca																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:5790239delT	ENST00000328090.5	+	15	5480	c.4855delT	c.(4855-4857)tttfs	p.F1619fs		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1619																	GAACCATCTCTTTCCCGGTGA	0.453																																					p.F1619fs		.											.	.	0			c.4855delT						.						65	65	65					10																	5790239		1964	4151	6115	SO:0001589	frameshift_variant	54906	exon15			.	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.4855delT	10.37:g.5790239delT	ENSP00000328426:p.Phe1619fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	133	29	NM_017782	0	0	0	0	0	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Frame_Shift_Del	DEL	ENST00000328090.5	37	CCDS41485.1																																																																																			.		0.453	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		-	5790239	T	-	5790239	7	5	13	1	0	1	0	1	0	0	0	0	1600	1609	56	0	4901	0	C10orf18	10	5790239	Frame_Shift_Del	DEL	T	TCGA-A4-8098-01A-11D-2396-08		5790239	129744508	71	1060											
SLC18A3	6572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	50819621	50819621	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctcgggccaacctgccagtgGgcactcccatccaccgcctc	6	6	9	20	2	0	0	0	0	0	0	4	0	2	0	7	2	2	1	7	2	1	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:50819621G>C	ENST00000374115.3	+	1	1275	c.835G>C	c.(835-837)Ggc>Cgc	p.G279R	CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000339797.1_Intron|CHAT_ENST00000395559.2_5'Flank|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000351556.3_5'Flank|CHAT_ENST00000455728.2_5'Flank	NM_003055.2	NP_003046.2	Q16572	VACHT_HUMAN	solute carrier family 18 (vesicular acetylcholine transporter), member 3	279					acetylcholine transport (GO:0015870)|cation transmembrane transport (GO:0098655)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)			endometrium(6)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	43						CCTGCCAGTGGGCACTCCCAT	0.647																																					p.G279R		.											.	SLC18A3-92	0			c.G835C						.						45	42	43					10																	50819621		2202	4300	6502	SO:0001583	missense	6572	exon1			CCAGTGGGCACTC	BC007765	CCDS7231.1	10q11.2	2013-07-18	2013-07-18		ENSG00000187714	ENSG00000187714		"Solute carriers"	10936	protein-coding gene	gene with protein product		600336				8071310	Standard	NM_003055		Approved	VACHT	uc001jhw.3	Q16572	OTTHUMG00000018196	ENST00000374115.3:c.835G>C	10.37:g.50819621G>C	ENSP00000363229:p.Gly279Arg	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	126	31	NM_003055	0	0	0	0	0	B2R7S1	Missense_Mutation	SNP	ENST00000374115.3	37	CCDS7231.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749750	0.89753	.	.	ENSG00000187714	ENST00000374115	T	0.80393	-1.37	5.42	5.42	0.78866	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	U	0.000001	D	0.91408	0.7289	M	0.86420	2.815	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.92566	0.6062	10	0.87932	D	0	0.7852	19.2158	0.93778	0.0:0.0:1.0:0.0	.	279	Q16572	VACHT_HUMAN	R	279	ENSP00000363229:G279R	ENSP00000363229:G279R	G	+	1	0	SLC18A3	50489627	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.824000	0.99380	2.552000	0.86080	0.561000	0.74099	GGC	.		0.647	SLC18A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047995.1	NM_003055		C	50819621	G	C	50819621	3	2	13	1	0	0	0	0	1	0	0	0	14459	1232	43	4	837	4	SLC18A3	10	50819621	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	45029382	50819621	84715126	72	1061											
TET1	80312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	70450862	70450862	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgatggccctggcaTttcacagcttggcgaagtgg	6	11	14	10	1	1	1	1	1	0	0	1	2	1	1	1	4	3	4	1	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:70450862T>G	ENST00000373644.4	+	12	5911	c.5702T>G	c.(5701-5703)aTt>aGt	p.I1901S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1901					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GGCCCTGGCATTTCACAGCTT	0.572																																					p.I1901S		.											.	TET1-663	0			c.T5702G						.						70	66	67					10																	70450862		2203	4300	6503	SO:0001583	missense	80312	exon12			CTGGCATTTCACA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5702T>G	10.37:g.70450862T>G	ENSP00000362748:p.Ile1901Ser	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	167	91	NM_030625	0	0	0	0	0	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	9.058	0.993658	0.19043	.	.	ENSG00000138336	ENST00000373644	T	0.06849	3.25	5.34	2.89	0.33648	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	5.533840	0.00166	N	0.000001	T	0.11024	0.0269	L	0.41710	1.295	0.09310	N	1	P	0.38729	0.644	B	0.40329	0.326	T	0.22382	-1.0218	10	0.49607	T	0.09	.	5.5383	0.17023	0.0:0.152:0.1458:0.7022	.	1901	Q8NFU7	TET1_HUMAN	S	1901	ENSP00000362748:I1901S	ENSP00000362748:I1901S	I	+	2	0	TET1	70120868	0.002000	0.14202	0.006000	0.13384	0.050000	0.14768	0.124000	0.15728	0.300000	0.22699	0.533000	0.62120	ATT	.		0.572	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70450862	T	G	70450862	3	3	13	1	0	0	0	0	1	0	0	0	15801	1493	52	5	5744	5	TET1	10	70450862	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	19631241	70450862	65083885	73	1062											
H2AFY2	55506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	71868875	71868875	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctccgacaaatgtgaagaaCagcttgaagagaccatcaaa	17	6	9	9	1	1	4	1	2	0	2	2	6	2	4	2	0	2	2	2	0	5	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:71868875C>A	ENST00000373255.4	+	8	1129	c.865C>A	c.(865-867)Cag>Aag	p.Q289K	AIFM2_ENST00000373248.1_Intron	NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	289	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						ATGTGAAGAACAGCTTGAAGA	0.557																																					p.Q289K		.											.	H2AFY2-91	0			c.C865A						.						89	82	84					10																	71868875		2203	4300	6503	SO:0001583	missense	55506	exon8			GAAGAACAGCTTG	AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"Histones / Replication-independent"	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.865C>A	10.37:g.71868875C>A	ENSP00000362352:p.Gln289Lys	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	167	24	NM_018649	0	0	0	0	0	Q5SQT2	Missense_Mutation	SNP	ENST00000373255.4	37	CCDS7296.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.119095	0.77323	.	.	ENSG00000099284	ENST00000373255;ENST00000395046;ENST00000455786	T;T	0.21031	2.03;2.03	6.03	6.03	0.97812	Appr-1-p processing (2);	0.000000	0.85682	D	0.000000	T	0.16769	0.0403	N	0.17723	0.515	0.80722	D	1	P	0.43231	0.801	B	0.38842	0.283	T	0.02553	-1.1142	10	0.25751	T	0.34	.	20.177	0.98182	0.0:1.0:0.0:0.0	.	289	Q9P0M6	H2AW_HUMAN	K	289;223;223	ENSP00000362352:Q289K;ENSP00000404584:Q223K	ENSP00000362352:Q289K	Q	+	1	0	H2AFY2	71538881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.830000	0.62745	2.854000	0.98071	0.655000	0.94253	CAG	.		0.557	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649		A	71868875	C	A	71868875	3	1	13	1	0	0	0	0	1	0	0	0	6951	479	17	4	891	4	H2AFY2	10	71868875	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	1418013	71868875	63665872	74	1063											
TRIM8	81603	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	104415049	104415049	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctgctctttgataagacGgaggatgtcagcttcatgaa	11	11	11	8	1	3	3	2	2	1	1	3	5	3	5	0	2	3	3	0	2	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:104415049G>A	ENST00000302424.7	+	3	1001	c.879G>A	c.(877-879)acG>acA	p.T293T	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	293					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TTGATAAGACGGAGGATGTCA	0.597																																					p.T293T		.											.	TRIM8-227	0			c.G879A						.						31	34	33					10																	104415049		2202	4300	6502	SO:0001819	synonymous_variant	81603	exon3			TAAGACGGAGGAT	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.879G>A	10.37:g.104415049G>A		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	92	8	NM_030912	0	0	0	0	0	A6NI31|Q9C028	Silent	SNP	ENST00000302424.7	37	CCDS31274.1																																																																																			.		0.597	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		A	104415049	G	A	104415049	2	1	13	1	0	0	0	0	0	0	0	1	16581	1103	39	1		1	TRIM8	10	104415049	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	32546174	104415049	31119698	75	1064											
NRAP	4892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115372127	115372127	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttggcatgcaccagggCggccatgtccaacggcagat	8	8	12	13	2	1	1	0	0	1	1	2	1	2	1	3	4	2	3	3	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:115372127C>G	ENST00000359988.3	-	30	3608	c.3364G>C	c.(3364-3366)Gcc>Ccc	p.A1122P	NRAP_ENST00000360478.3_Missense_Mutation_p.A1087P|NRAP_ENST00000369360.3_Missense_Mutation_p.A1095P|NRAP_ENST00000369358.4_Missense_Mutation_p.A1130P	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.A1122T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGCACCAGGGCGGCCATGTCC	0.532																																					p.A1122P		.											.	NRAP-522	1	Substitution - Missense(1)	large_intestine(1)	c.G3364C						.						106	93	97					10																	115372127		2203	4300	6503	SO:0001583	missense	4892	exon30			CCAGGGCGGCCAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3364G>C	10.37:g.115372127C>G	ENSP00000353078:p.Ala1122Pro	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	157	44	NM_001261463	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467717	0.26335	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.62	4.42	0.53409	.	0.222981	0.47852	D	0.000215	T	0.18923	0.0454	L	0.27053	0.805	0.19775	N	0.999954	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.16335	-1.0406	10	0.30078	T	0.28	.	6.6353	0.22879	0.0:0.0846:0.2726:0.6428	.	1122;1087;1122	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	P	1130;1095;1122;1087	ENSP00000358365:A1130P;ENSP00000358367:A1095P;ENSP00000353078:A1122P;ENSP00000353666:A1087P	ENSP00000353078:A1122P	A	-	1	0	NRAP	115362117	0.827000	0.29292	0.788000	0.31933	0.559000	0.35586	1.269000	0.33074	0.978000	0.38470	-0.345000	0.07892	GCC	.		0.532	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		G	115372127	C	G	115372127	3	3	13	1	0	0	0	0	1	0	0	0	10664	768	27	4	1880	4	NRAP	10	115372127	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	10957078	115372127	20162620	76	1065											
UEVLD	55293	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	18568448	18568448	+	Frame_Shift_Del	DEL	G	G	-																															tggttgagatgcaacgagcaGgacactgtgttgactataat																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:18568448delG	ENST00000396197.3	-	8	893	c.865delC	c.(865-867)ctgfs	p.L290fs	UEVLD_ENST00000379387.4_Frame_Shift_Del_p.L268fs|UEVLD_ENST00000543987.1_Frame_Shift_Del_p.L290fs|UEVLD_ENST00000320750.6_Frame_Shift_Del_p.L268fs|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000535484.1_Frame_Shift_Del_p.L252fs|UEVLD_ENST00000541984.1_Intron	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GCAACGAGCAGGACACTGTGT	0.403																																					p.L289fs		.											.	UEVLD-226	0			c.865delC						.						142	133	136					11																	18568448		2199	4293	6492	SO:0001589	frameshift_variant	55293	exon8			.	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.865delC	11.37:g.18568448delG	ENSP00000379500:p.Leu290fs	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	98	35	NM_001040697	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000396197.3	37	CCDS41624.1																																																																																			.		0.403	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314		-	18568448	G	-	18568448	7	5	13	1	0	1	0	1	0	0	0	0	16966	991	35	0	570	0	UEVLD	11	18568448	Frame_Shift_Del	DEL	G	TCGA-A4-8098-01A-11D-2396-08		18568448	116438068	77	1066											
NELL1	4745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	21594920	21594920	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagtggctcagtgtggacgAtggctggatctccctgcaca	7	11	13	10	1	2	0	1	0	1	0	3	3	2	2	1	4	1	3	1	4	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:21594920A>T	ENST00000357134.5	+	19	2499	c.2347A>T	c.(2347-2349)Atg>Ttg	p.M783L	NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000532434.1_Missense_Mutation_p.M736L|NELL1_ENST00000298925.5_Missense_Mutation_p.M811L|NELL1_ENST00000325319.5_Missense_Mutation_p.M726L	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	783					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGTGTGGACGATGGCTGGATC	0.488																																					p.M783L		.											.	NELL1-155	0			c.A2347T						.						165	145	152					11																	21594920		2203	4300	6503	SO:0001583	missense	4745	exon19			TGGACGATGGCTG	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.2347A>T	11.37:g.21594920A>T	ENSP00000349654:p.Met783Leu	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	211	75	NM_006157	0	0	0	0	0	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	5.365	0.252558	0.10185	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.78481	-1.18;-1.15;-1.07;-1.06	5.73	4.59	0.56863	.	0.047962	0.85682	N	0.000000	T	0.66655	0.2811	L	0.46157	1.445	0.34190	D	0.671993	P;B;B;B;P	0.37370	0.592;0.0;0.001;0.001;0.457	B;B;B;B;B	0.33254	0.16;0.0;0.002;0.007;0.077	T	0.68561	-0.5376	10	0.10636	T	0.68	-16.3644	12.2052	0.54348	0.872:0.0:0.0:0.1279	.	726;811;328;736;783	F5H6I3;B3KXR2;Q8N9Z6;Q92832-2;Q92832	.;.;.;.;NELL1_HUMAN	L	811;783;726;736	ENSP00000298925:M811L;ENSP00000349654:M783L;ENSP00000317837:M726L;ENSP00000437170:M736L	ENSP00000298925:M811L	M	+	1	0	NELL1	21551496	1.000000	0.71417	0.995000	0.50966	0.203000	0.24098	5.967000	0.70403	0.983000	0.38602	0.454000	0.30748	ATG	.		0.488	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		T	21594920	A	T	21594920	3	4	13	1	0	0	0	0	1	0	0	0	10359	333	12	5	2421	5	NELL1	11	21594920	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	3026472	21594920	113411596	78	1067											
LGR4	55366	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	27412675	27412676	+	In_Frame_Ins	INS	-	-	AAG																															ctcagccctcgaatggcttcINSactgggtactgttttcaact																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:27412675_27412676insAAG	ENST00000379214.4	-	4	809_810	c.366_367insCTT	c.(364-369)agtgaa>agtCTTgaa	p.122_123SE>SLE	LGR4_ENST00000389858.4_In_Frame_Ins_p.98_99SE>SLE|LGR4_ENST00000480977.2_Intron	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	122					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CGAATGGCTTCACTGGGTACTG	0.366																																					p.E123delinsLE		.											.	LGR4-91	0			c.367_368insCTT						.																																			SO:0001652	inframe_insertion	55366	exon4			.	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.366_367insCTT	11.37:g.27412675_27412676insAAG	ENSP00000368516:p.Ser122_Glu123insLeu	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	82	21	NM_018490	0	0	0	0	0	A6NCH3|G5E9B3|Q8N537|Q9NYD1	In_Frame_Ins	INS	ENST00000379214.4	37	CCDS31449.1																																																																																			.		0.366	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		AAG	27412676	-	AAG	27412675	7	5	13	1	0	1	1	0	0	0	0	0	8778	835	29	0	2548	0	LGR4	11	27412675	In_Frame_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	5817755	27412675	107593841	79	1068											
IMMP1L	196294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	31482191	31482191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttggataccataaaaaTgtcgactaagattttctgca	14	13	6	8	1	1	1	0	0	1	1	2	3	1	2	2	1	2	1	2	1	5	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:31482191T>C	ENST00000278200.1	-	4	371	c.176A>G	c.(175-177)cAt>cGt	p.H59R	IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000532287.1_Missense_Mutation_p.H59R|IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000528161.1_Intron|IMMP1L_ENST00000534812.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	59					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					ACCATAAAAATGTCGACTAAG	0.318																																					p.H59R		.											.	IMMP1L-90	0			c.A176G						.						67	69	68					11																	31482191		2202	4295	6497	SO:0001583	missense	196294	exon4			TAAAAATGTCGAC		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.176A>G	11.37:g.31482191T>C	ENSP00000278200:p.His59Arg	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	36	11	NM_144981	0	0	0	0	0	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	37	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	T	8.728	0.915998	0.17907	.	.	ENSG00000148950	ENST00000532287;ENST00000278200;ENST00000529749;ENST00000530023	.	.	.	5.58	5.58	0.84498	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.046287	0.85682	D	0.000000	T	0.32102	0.0818	N	0.02403	-0.565	0.80722	D	1	P;B	0.38300	0.626;0.0	P;B	0.45232	0.474;0.006	T	0.36187	-0.9758	9	0.02654	T	1	-14.2458	16.0334	0.80603	0.0:0.0:0.0:1.0	.	59;59	E9PIG6;Q96LU5	.;IMP1L_HUMAN	R	59	.	ENSP00000278200:H59R	H	-	2	0	IMMP1L	31438767	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.245000	0.65405	2.243000	0.73865	0.533000	0.62120	CAT	.		0.318	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		C	31482191	T	C	31482191	3	2	13	1	0	0	0	0	1	0	0	0	7737	1464	51	3	340	3	IMMP1L	11	31482191	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	4069516	31482191	103524325	80	1069											
CCDC73	493860	hgsc.bcm.edu	37	chr11	32676507	32676507	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttatcaagtctgaggctgcTttttttagttccttaataag	9	19	7	6	0	2	1	1	1	1	0	3	1	3	1	1	1	1	3	1	1	5	9			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:32676507T>C	ENST00000335185.5	-	10	700	c.657A>G	c.(655-657)aaA>aaG	p.K219K	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	219										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					CTGAGGCTGCTTTTTTTAGTT	0.303																																					p.D219E		.											.	CCDC73-91	0			c.T657G						.						80	67	71					11																	32676507		1809	4051	5860	SO:0001819	synonymous_variant	493860	exon10			GGCTGCTTTTTTT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.657A>G	11.37:g.32676507T>C		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_001008391	0	0	0	0	0	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1																																																																																			.		0.303	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		C	32676507	T	C	32676507	2	2	13	1	0	0	0	0	0	0	0	1	2852	1606	56	3		3	CCDC73	11	32676507	Silent	SNP	T	TCGA-A4-8098-01A-11D-2396-08	1194316	32676507	102330009	81	1070											
PRR5L	79899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	36472765	36472765	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttcattttccagagtgttCacgagcccacaggcccaagt	9	11	9	12	1	2	1	2	0	0	1	3	2	3	1	3	1	1	2	3	1	1	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:36472765C>T	ENST00000378867.3	+	9	947	c.592C>T	c.(592-594)Cac>Tac	p.H198Y	PRR5L_ENST00000311599.5_Missense_Mutation_p.H125Y|PRR5L_ENST00000530639.1_Missense_Mutation_p.H198Y|PRR5L_ENST00000527487.1_Intron|PRR5L_ENST00000389693.3_3'UTR	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	198					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)	p.H198Y(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						CCAGAGTGTTCACGAGCCCAC	0.502																																					p.H198Y		.											.	PRR5L-91	1	Substitution - Missense(1)	cervix(1)	c.C592T						.						170	157	162					11																	36472765		2202	4298	6500	SO:0001583	missense	79899	exon9			AGTGTTCACGAGC		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"protein observed with Rictor-2"	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.592C>T	11.37:g.36472765C>T	ENSP00000368144:p.His198Tyr	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	156	67	NM_024841	0	0	0	0	0	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	37	CCDS31463.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049026	0.75846	.	.	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867	T;T;T	0.36157	1.27;1.5;1.27	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.80982	2.52	0.58432	D	0.999995	D;D	0.71674	0.989;0.998	D;D	0.77557	0.979;0.99	T	0.69815	-0.5043	10	0.87932	D	0	-17.9831	17.9793	0.89136	0.0:1.0:0.0:0.0	.	70;198	Q6MZQ0-3;Q6MZQ0	.;PRR5L_HUMAN	Y	198;125;198	ENSP00000435050:H198Y;ENSP00000310103:H125Y;ENSP00000368144:H198Y	ENSP00000310103:H125Y	H	+	1	0	PRR5L	36429341	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.758000	0.68776	2.345000	0.79718	0.313000	0.20887	CAC	.		0.502	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841		T	36472765	C	T	36472765	3	4	13	1	0	0	0	0	1	0	0	0	12631	826	29	2	624	2	PRR5L	11	36472765	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	3796258	36472765	98533751	82	1071											
CKAP5	9793	broad.mit.edu	37	chr11	46804912	46804912	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttgtgagaaagccattgAcacaacctgaaaagggaaaa	17	8	9	7	0	0	3	0	3	0	1	0	5	0	4	2	1	2	0	2	1	6	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:46804912A>G	ENST00000529230.1	-	18	2207	c.2161T>C	c.(2161-2163)Tca>Cca	p.S721P	CKAP5_ENST00000415402.1_Missense_Mutation_p.S721P|CKAP5_ENST00000312055.5_Missense_Mutation_p.S721P|CKAP5_ENST00000354558.3_Missense_Mutation_p.S721P			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	721					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						AAAGCCATTGACACAACCTGA	0.348																																					p.S721P	Ovarian(4;85 273 2202 4844 13323)												.	CKAP5-92	0			c.T2161C						.						80	77	78					11																	46804912		2201	4299	6500	SO:0001583	missense	9793	exon18			CCATTGACACAAC		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.2161T>C	11.37:g.46804912A>G	ENSP00000432768:p.Ser721Pro	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_001008938	0	0	0	0	0	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	A	12.38	1.920823	0.33908	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.25	5.25	0.73442	Armadillo-type fold (1);	0.184073	0.49305	D	0.000149	T	0.56337	0.1978	L	0.34521	1.04	0.53005	D	0.999962	B;P;B	0.39883	0.305;0.693;0.214	B;B;B	0.41332	0.162;0.354;0.063	T	0.55749	-0.8092	10	0.32370	T	0.25	-4.3512	10.7838	0.46393	0.8291:0.1709:0.0:0.0	.	721;721;721	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	P	721	ENSP00000432768:S721P;ENSP00000395302:S721P;ENSP00000310227:S721P;ENSP00000346566:S721P	ENSP00000310227:S721P	S	-	1	0	CKAP5	46761488	1.000000	0.71417	1.000000	0.80357	0.391000	0.30476	5.799000	0.69101	1.989000	0.58080	0.528000	0.53228	TCA	.		0.348	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		G	46804912	A	G	46804912	3	3	13	1	0	0	0	0	1	0	0	0	3451	275	10	3	4045	3	CKAP5	11	46804912	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10332147	46804912	88201604	83	1072											
GSTP1	2950	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67352235	67352235	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catcctgcgtcacctgggccGcacccttggtgagtcttgaa	6	10	11	14	2	2	2	1	2	1	0	3	2	3	2	4	2	1	1	4	2	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:67352235G>A	ENST00000398606.3	+	4	473	c.224G>A	c.(223-225)cGc>cAc	p.R75H	GSTP1_ENST00000498765.1_3'UTR|GSTP1_ENST00000398603.1_Missense_Mutation_p.R75H	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	75	GST N-terminal.				cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	CACCTGGGCCGCACCCTTGGT	0.617																																					p.R75H		.											.	GSTP1-91	0			c.G224A						.						65	72	70					11																	67352235		1984	4154	6138	SO:0001583	missense	2950	exon4			TGGGCCGCACCCT	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"Glutathione S-transferases / Soluble"	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.224G>A	11.37:g.67352235G>A	ENSP00000381607:p.Arg75His	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	125	59	NM_000852	0	0	0	0	0	O00460|Q15690|Q5TZY3	Missense_Mutation	SNP	ENST00000398606.3	37	CCDS41679.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.827181	0.32329	.	.	ENSG00000084207	ENST00000398606;ENST00000398603	T;T	0.08634	3.07;3.07	5.55	2.56	0.30785	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (1);	0.225561	0.37623	N	0.002005	T	0.10337	0.0253	M	0.79614	2.46	0.41117	D	0.985788	P	0.35700	0.516	B	0.33521	0.165	T	0.06232	-1.0838	9	0.52906	T	0.07	-16.5031	5.4855	0.16747	0.1699:0.0:0.6726:0.1576	.	75	P09211	GSTP1_HUMAN	H	75	ENSP00000381607:R75H;ENSP00000381604:R75H	ENSP00000381604:R75H	R	+	2	0	GSTP1	67108811	1.000000	0.71417	0.910000	0.35882	0.001000	0.01503	5.167000	0.64972	0.721000	0.32231	-0.142000	0.14014	CGC	.		0.617	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852		A	67352235	G	A	67352235	3	1	13	1	0	0	0	0	1	0	0	0	6865	1087	38	1	238	1	GSTP1	11	67352235	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	20547323	67352235	67654281	84	1073											
C11orf67	28971	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	77580812	77580812	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatgtgaaggaagttgttgaGaagggtgtacagactcttgt	11	12	15	3	0	1	3	0	2	1	2	1	6	1	4	0	2	1	3	0	2	4	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:77580812G>A	ENST00000526415.1	+	4	350	c.177G>A	c.(175-177)gaG>gaA	p.E59E	AAMDC_ENST00000532481.1_Silent_p.E59E|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000393427.2_Silent_p.E59E|AAMDC_ENST00000525034.1_Silent_p.E78E|AAMDC_ENST00000525409.1_Intron|AAMDC_ENST00000527134.1_Silent_p.E59E|AAMDC_ENST00000533193.1_Silent_p.E105E|RP11-91P24.6_ENST00000530972.1_RNA|AAMDC_ENST00000304716.8_Silent_p.E59E			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	59	MTH138-like domain. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)											AAGTTGTTGAGAAGGGTGTAC	0.493																																					p.E59E		.											.	.	0			c.G177A						.						349	322	331					11																	77580812		2200	4292	6492	SO:0001819	synonymous_variant	28971	exon3			TGTTGAGAAGGGT	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 67"	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.177G>A	11.37:g.77580812G>A		Somatic	338	0		WXS	Illumina HiSeq	Phase_I	264	91	NM_024684	0	0	0	0	0	Q96AQ4|Q9Y6B1	Silent	SNP	ENST00000526415.1	37	CCDS8254.1																																																																																			.		0.493	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684		A	77580812	G	A	77580812	2	1	13	1	0	0	0	0	0	0	0	1	1661	933	33	2		2	C11orf67	11	77580812	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10228577	77580812	57425704	85	1074											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877724	82877724	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagttccaagtctgccaaAagatggaaatctggttggga	14	9	11	7	0	2	1	0	0	2	1	3	3	3	3	2	3	1	2	2	3	5	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:82877724A>G	ENST00000298281.4	+	5	2237	c.1785A>G	c.(1783-1785)aaA>aaG	p.K595K		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	595					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AGTCTGCCAAAAGATGGAAAT	0.348																																					p.K595K		.											.	PCF11-23	0			c.A1785G						.						73	75	74					11																	82877724		1755	3856	5611	SO:0001819	synonymous_variant	51585	exon5			TGCCAAAAGATGG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1785A>G	11.37:g.82877724A>G		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	125	55	NM_015885	0	0	0	0	0	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			.		0.348	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877724	A	G	82877724	2	3	13	1	0	0	0	0	0	0	0	1	11599	11	1	3		3	PCF11	11	82877724	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	5296912	82877724	52128792	86	1075											
PCF11	51585	hgsc.bcm.edu	37	chr11	82878487	82878487	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttagcatctggtgaaattAcacaggatgacttccttgtt	10	15	9	7	0	1	2	0	2	1	0	2	3	2	3	1	2	2	3	1	2	3	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:82878487A>G	ENST00000298281.4	+	7	2484	c.2032A>G	c.(2032-2034)Aca>Gca	p.T678A		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	678					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TGGTGAAATTACACAGGATGA	0.333																																					p.T678A		.											.	PCF11-23	0			c.A2032G						.						67	58	61					11																	82878487		1857	4097	5954	SO:0001583	missense	51585	exon7			GAAATTACACAGG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2032A>G	11.37:g.82878487A>G	ENSP00000298281:p.Thr678Ala	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_015885	0	0	0	0	0	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607403	0.28623	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.50277	1.71;0.78;0.75	5.98	3.51	0.40186	.	0.214364	0.33144	N	0.005224	T	0.33381	0.0861	L	0.27053	0.805	0.36008	D	0.837853	P;B	0.44090	0.826;0.089	B;B	0.40825	0.341;0.037	T	0.36089	-0.9762	9	.	.	.	.	11.0037	0.47622	0.7513:0.0:0.0:0.2487	.	678;678	E9PQ01;O94913	.;PCF11_HUMAN	A	678	ENSP00000298281:T678A;ENSP00000434540:T678A;ENSP00000431567:T678A	.	T	+	1	0	PCF11	82556135	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.208000	0.58486	1.056000	0.40484	-0.468000	0.05107	ACA	.		0.333	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82878487	A	G	82878487	3	3	13	1	0	0	0	0	1	0	0	0	11599	391	14	3	2058	3	PCF11	11	82878487	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	763	82878487	52128029	87	1076											
PCSK7	9159	hgsc.bcm.edu	37	chr11	117077797	117077797	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acccacctttgtctgtccctGatgtctactgcactccacac	7	12	5	17	0	2	1	0	1	2	0	4	1	4	1	4	0	2	1	4	0	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:117077797G>A	ENST00000320934.3	-	15	2496	c.1866C>T	c.(1864-1866)atC>atT	p.I622I	PCSK7_ENST00000529458.1_Intron|PCSK7_ENST00000540028.1_3'UTR	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	622					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		GTCTGTCCCTGATGTCTACTG	0.607			T	IGH@	MLCLS																																p.I622I		.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7-658	0			c.C1866T						.						79	72	74					11																	117077797		2201	4293	6494	SO:0001819	synonymous_variant	9159	exon15			GTCCCTGATGTCT	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1866C>T	11.37:g.117077797G>A		Somatic	248	0		WXS	Illumina HiSeq	Phase_I	239	45	NM_004716	0	0	0	0	0	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	G	9.730	1.161985	0.21538	.	.	ENSG00000160613	ENST00000543900	.	.	.	5.01	3.14	0.36123	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-31.6552	3.4196	0.07388	0.0833:0.1475:0.4652:0.304	.	.	.	.	X	574	.	ENSP00000445538:Q574X	Q	-	1	0	PCSK7	116583007	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.991000	0.40727	0.698000	0.31739	-0.183000	0.12914	CAG	.		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		A	117077797	G	A	117077797	2	1	13	1	0	0	0	0	0	0	0	1	11631	1280	45	2		2	PCSK7	11	117077797	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	34199310	117077797	17928719	88	1077											
ARHGAP32	9743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	128840894	128840894	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggtgcagcagcgggaccCgggcaccgtcccgcactttc	6	5	14	16	4	0	0	0	0	0	0	2	1	1	1	3	3	3	5	3	3	0	1	rs530219324		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:128840894C>T	ENST00000310343.9	-	22	4171	c.4172G>A	c.(4171-4173)cGg>cAg	p.R1391Q	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.R1042Q|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.R1042Q	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1391	Interaction with GAB2.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						CAGCGGGACCCGGGCACCGTC	0.632													C|||	1	0.000199681	0	0	5008	,	,		17039	0		0.001	False		,,,				2504	0				p.R1391Q		.											.	ARHGAP32-231	0			c.G4172A						.						45	47	47					11																	128840894		2201	4297	6498	SO:0001583	missense	9743	exon22			GGGACCCGGGCAC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.4172G>A	11.37:g.128840894C>T	ENSP00000310561:p.Arg1391Gln	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	61	25	NM_001142685	0	0	0	0	0	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168938	0.78339	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.11712	2.77;2.75;2.75	5.71	5.71	0.89125	.	0.112572	0.56097	D	0.000024	T	0.19805	0.0476	M	0.69823	2.125	0.32214	N	0.576128	D	0.58620	0.983	P	0.44422	0.449	T	0.09207	-1.0685	10	0.37606	T	0.19	.	19.8599	0.96779	0.0:1.0:0.0:0.0	.	1391	A7KAX9	RHG32_HUMAN	Q	1391;1042;1042	ENSP00000310561:R1391Q;ENSP00000376425:R1042Q;ENSP00000432862:R1042Q	ENSP00000310561:R1391Q	R	-	2	0	ARHGAP32	128346104	0.998000	0.40836	0.932000	0.37286	0.291000	0.27294	3.773000	0.55333	2.710000	0.92621	0.655000	0.94253	CGG	.		0.632	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128840894	C	T	128840894	3	4	13	1	0	0	0	0	1	0	0	0	881	652	23	1	2095	1	ARHGAP32	11	128840894	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	11763097	128840894	6165622	89	1078											
AKAP3	10566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	4737430	4737430	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcaaagtggacttgtatTtcaaatttgggggactttgt	9	17	10	5	0	3	0	2	0	1	0	3	2	3	2	0	3	0	1	0	3	3	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:4737430T>G	ENST00000545990.2	-	5	1162	c.638A>C	c.(637-639)aAa>aCa	p.K213T	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.K213T	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	213					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GGACTTGTATTTCAAATTTGG	0.468																																					p.K213T		.											.	AKAP3-292	0			c.A638C						.						99	99	99					12																	4737430		2203	4300	6503	SO:0001583	missense	10566	exon4			TTGTATTTCAAAT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.638A>C	12.37:g.4737430T>G	ENSP00000440994:p.Lys213Thr	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	202	121	NM_006422	0	0	0	0	0	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.224438	0.39300	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.09255	3.0;3.0	4.87	1.27	0.21489	A-kinase anchor 110kDa, C-terminal (1);	0.332965	0.25968	N	0.027150	T	0.20861	0.0502	M	0.63428	1.95	0.09310	N	1	D	0.63046	0.992	P	0.60415	0.874	T	0.03651	-1.1016	10	0.87932	D	0	-14.2358	6.9349	0.24461	0.0:0.2845:0.0:0.7155	.	213	O75969	AKAP3_HUMAN	T	213	ENSP00000228850:K213T;ENSP00000440994:K213T	ENSP00000228850:K213T	K	-	2	0	AKAP3	4607691	0.949000	0.32298	0.109000	0.21407	0.693000	0.40251	1.094000	0.30951	0.121000	0.18284	0.528000	0.53228	AAA	.		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		G	4737430	T	G	4737430	3	3	13	1	0	0	0	0	1	0	0	0	452	1841	64	5	1931	5	AKAP3	12	4737430	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08		4737430	129114465	90	1079											
GTSF1	121355	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54856511	54856511	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctcctggtttggttgacTgcaagacaataaagattgga	12	11	12	6	0	0	3	0	1	0	2	1	4	1	4	1	4	1	4	1	4	4	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:54856511T>A	ENST00000552397.1	-	5	1141		c.e5-2		GTSF1_ENST00000305879.5_Splice_Site|GTSF1_ENST00000552395.1_Splice_Site|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1							cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				TTTGGTTGACTGCAAGACAAT	0.483																																					.		.											.	GTSF1-90	0			c.245-2A>T						.						92	91	92					12																	54856511		2203	4300	6503	SO:0001630	splice_region_variant	121355	exon6			GTTGACTGCAAGA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"family with sequence similarity 112, member B"	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.245-2A>T	12.37:g.54856511T>A		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	168	46	NM_144594	0	0	0	0	0	B3KQ60|Q0VGM4|Q8N778	Splice_Site	SNP	ENST00000552397.1	37	CCDS8881.1	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220561	0.22457	.	.	ENSG00000170627	ENST00000552397;ENST00000305879	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3935	0.55373	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTSF1	53142778	1.000000	0.71417	0.971000	0.41717	0.231000	0.25187	4.551000	0.60740	2.183000	0.69458	0.533000	0.62120	.	.		0.483	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594	Intron	A	54856511	T	A	54856511	5	1	13	1	0	0	0	0	0	0	1	0	6907	1594	55	5	276	5	GTSF1	12	54856511	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08	50119081	54856511	78995384	91	1080											
WIF1	11197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	65460514	65460514	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catacatcgtggggtacaaaGggcttatagggagagagaac	14	7	14	6	1	0	2	0	0	0	2	1	4	0	2	0	4	3	2	0	4	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:65460514G>T	ENST00000286574.4	-	6	1011	c.637C>A	c.(637-639)Ctt>Att	p.L213I		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	213	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		GGGGTACAAAGGGCTTATAGG	0.433			T	HMGA2	pleomorphic salivary gland adenoma																																p.L213I	Esophageal Squamous(148;1595 1816 48559 49439 49664)	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1-1110	0			c.C637A						.						75	72	73					12																	65460514		2203	4300	6503	SO:0001583	missense	11197	exon6			TACAAAGGGCTTA	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.637C>A	12.37:g.65460514G>T	ENSP00000286574:p.Leu213Ile	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	54	14	NM_007191	0	0	0	0	0	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	37	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572822	0.45798	.	.	ENSG00000156076	ENST00000286574	T	0.03035	4.07	5.23	4.34	0.51931	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.068823	0.64402	D	0.000016	T	0.02455	0.0075	N	0.05306	-0.075	0.53688	D	0.999978	B	0.19935	0.04	B	0.25291	0.059	T	0.54675	-0.8258	9	.	.	.	.	14.326	0.66521	0.0722:0.0:0.9278:0.0	.	213	Q9Y5W5	WIF1_HUMAN	I	213	ENSP00000286574:L213I	.	L	-	1	0	WIF1	63746781	1.000000	0.71417	0.998000	0.56505	0.123000	0.20343	4.824000	0.62701	1.530000	0.49136	0.655000	0.94253	CTT	.		0.433	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			T	65460514	G	T	65460514	3	4	13	1	0	0	0	0	1	0	0	0	17399	1000	35	4	522	4	WIF1	12	65460514	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10604003	65460514	68391381	92	1081											
DDX51	317781	hgsc.bcm.edu	37	chr12	132628412	132628412	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcccctggcgcctcctcgCtgctccctgcgctgggctcc	0	9	11	21	3	0	0	0	0	0	0	5	0	4	0	6	2	2	5	6	2	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:132628412C>T	ENST00000397333.3	-	2	385	c.347G>A	c.(346-348)aGc>aAc	p.S116N	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	116					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CGCCTCCTCGCTGCTCCCTGC	0.766																																					p.S116N		.											.	DDX51-227	0			c.G347A						.						2	3	3					12																	132628412		1500	3477	4977	SO:0001583	missense	317781	exon2			TCCTCGCTGCTCC	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.347G>A	12.37:g.132628412C>T	ENSP00000380495:p.Ser116Asn	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	16	2	NM_175066	0	0	0	0	0	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	.	.	.	.	.	.	.	.	.	.	c	3.403	-0.121875	0.06795	.	.	ENSG00000185163	ENST00000397333	T	0.01933	4.55	1.88	-2.2	0.06994	.	0.671970	0.14773	U	0.299291	T	0.01287	0.0042	N	0.22421	0.69	0.09310	N	1	B	0.22604	0.072	B	0.16722	0.016	T	0.47911	-0.9080	10	0.16896	T	0.51	.	3.3245	0.07062	0.0:0.274:0.2471:0.4789	.	116	Q8N8A6	DDX51_HUMAN	N	116	ENSP00000380495:S116N	ENSP00000380495:S116N	S	-	2	0	DDX51	131194365	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.480000	0.22244	-0.320000	0.08640	-1.201000	0.01664	AGC	.		0.766	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		T	132628412	C	T	132628412	3	4	13	1	0	0	0	0	1	0	0	0	4375	797	28	2	1709	2	DDX51	12	132628412	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	67167898	132628412	1223483	93	1082											
PARP4	143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	25029240	25029240	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgcttggcttgcaagaaTgtcacaccctccatggaact	10	12	8	11	0	1	1	1	0	0	1	2	2	2	2	2	2	3	3	2	2	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr13:25029240T>C	ENST00000381989.3	-	22	2778	c.2673A>G	c.(2671-2673)acA>acG	p.T891T	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	891	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTTGCAAGAATGTCACACCCT	0.502																																					p.T891T		.											.	PARP4-94	0			c.A2673G						.						261	222	235					13																	25029240		2203	4300	6503	SO:0001819	synonymous_variant	143	exon22			CAAGAATGTCACA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2673A>G	13.37:g.25029240T>C		Somatic	257	0		WXS	Illumina HiSeq	Phase_I	286	104	NM_006437	0	0	0	0	0	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			.		0.502	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		C	25029240	T	C	25029240	2	2	13	1	0	0	0	0	0	0	0	1	11489	1451	51	3		3	PARP4	13	25029240	Silent	SNP	T	TCGA-A4-8098-01A-11D-2396-08		25029240	90140638	94	1083											
CPB2	1361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	46658419	46658419	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatcagatgcatttacaaaAaaatggacttgttttttctt	14	16	5	6	0	2	1	1	0	1	1	2	2	2	2	0	1	2	2	0	1	4	7			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr13:46658419A>C	ENST00000181383.4	-	3	226	c.210T>G	c.(208-210)ttT>ttG	p.F70L	CPB2-AS1_ENST00000415033.2_RNA|CPB2_ENST00000439329.3_Missense_Mutation_p.F70L|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000606351.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	70					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		CATTTACAAAAAAATGGACTT	0.368																																					p.F70L		.											.	CPB2-92	0			c.T210G						.						151	139	143					13																	46658419		2203	4300	6503	SO:0001583	missense	1361	exon3			TACAAAAAAATGG	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"thrombin-activatable fibrinolysis inhibitor", "carboxypeptidase U", "plasma carboxypeptidase B", "carboxypeptidase R"	603101	"carboxypeptidase B2 (plasma, carboxypeptidase U)"			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.210T>G	13.37:g.46658419A>C	ENSP00000181383:p.Phe70Leu	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	171	74	NM_001872	0	0	0	0	0	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	37	CCDS9401.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.740893	0.49151	.	.	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.13538	2.58;2.58	5.41	-2.81	0.05805	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.050842	0.85682	D	0.000000	T	0.12646	0.0307	L	0.42245	1.32	0.40335	D	0.978972	B;P	0.49253	0.337;0.921	B;P	0.46320	0.162;0.512	T	0.03875	-1.0996	10	0.44086	T	0.13	.	10.4812	0.44695	0.4897:0.0:0.5103:0.0	.	70;70	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	L	70	ENSP00000181383:F70L;ENSP00000400714:F70L	ENSP00000181383:F70L	F	-	3	2	CPB2	45556420	0.999000	0.42202	0.991000	0.47740	0.819000	0.46315	0.355000	0.20163	-0.389000	0.07786	-0.263000	0.10527	TTT	.		0.368	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872		C	46658419	A	C	46658419	3	2	13	1	0	0	0	0	1	0	0	0	3803	11	1	5	1097	5	CPB2	13	46658419	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	21629179	46658419	68511459	95	1084											
AP1G2	8906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24032848	24032848	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgtttggttggagcaaacCtaggggatatatggctcatc	10	11	13	7	1	1	0	1	0	0	0	2	2	1	2	1	5	3	4	1	5	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:24032848C>T	ENST00000308724.5	-	12	1988		c.e12-1		AP1G2_ENST00000556277.1_5'Flank|RP11-66N24.3_ENST00000555968.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000397120.3_Splice_Site	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit						intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TGGAGCAAACCTAGGGGATAT	0.567											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		.											.	AP1G2-45	0			c.1233-1G>A						.						138	109	119					14																	24032848		2203	4300	6503	SO:0001630	splice_region_variant	8906	exon14			GCAAACCTAGGGG	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1233-1G>A	14.37:g.24032848C>T		Somatic	103	0	768	WXS	Illumina HiSeq	Phase_I	68	46	NM_003917	0	0	0	0	0	D3DS51|O75504	Splice_Site	SNP	ENST00000308724.5	37	CCDS9602.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691409	0.48097	.	.	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000545295;ENST00000535852	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7542	0.69552	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AP1G2	23102688	1.000000	0.71417	0.997000	0.53966	0.613000	0.37349	4.964000	0.63701	2.314000	0.78098	0.557000	0.71058	.	.		0.567	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	Intron	T	24032848	C	T	24032848	5	4	13	1	0	0	0	0	0	0	1	0	733	695	24	2	1165	2	AP1G2	14	24032848	Splice_Site	SNP	C	TCGA-A4-8098-01A-11D-2396-08		24032848	83316692	96	1085											
TGM1	7051	hgsc.bcm.edu	37	chr14	24718666	24718666	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagagctgtgggctgtccaaGctggcaatgagctggcgggg	7	7	19	8	1	0	2	0	1	0	1	1	3	1	2	1	5	3	5	1	5	2	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:24718666G>T	ENST00000206765.6	-	15	2430	c.2307C>A	c.(2305-2307)agC>agA	p.S769R	TGM1_ENST00000544573.1_Missense_Mutation_p.S327R	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	769					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	GGCTGTCCAAGCTGGCAATGA	0.622																																					p.S769R		.											.	TGM1-91	0			c.C2307A						.						65	58	61					14																	24718666		2203	4300	6503	SO:0001583	missense	7051	exon15			GTCCAAGCTGGCA	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"Transglutaminases"	11777	protein-coding gene	gene with protein product	"K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"	190195	"transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.2307C>A	14.37:g.24718666G>T	ENSP00000206765:p.Ser769Arg	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_000359	0	0	0	0	0	B4DWR7|Q197M4	Missense_Mutation	SNP	ENST00000206765.6	37	CCDS9622.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631726	0.67015	.	.	ENSG00000092295	ENST00000206765;ENST00000544573	T;T	0.69435	-0.4;-0.4	4.97	0.986	0.19784	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.106857	0.64402	D	0.000006	T	0.78227	0.4250	M	0.80982	2.52	0.39093	D	0.961146	D	0.89917	1.0	D	0.77557	0.99	T	0.77811	-0.2449	10	0.66056	D	0.02	-37.3875	8.3138	0.32088	0.4692:0.0:0.5308:0.0	.	769	P22735	TGM1_HUMAN	R	769;327	ENSP00000206765:S769R;ENSP00000439446:S327R	ENSP00000206765:S769R	S	-	3	2	TGM1	23788506	0.988000	0.35896	0.998000	0.56505	0.996000	0.88848	0.096000	0.15147	0.277000	0.22141	0.655000	0.94253	AGC	.		0.622	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359		T	24718666	G	T	24718666	3	4	13	1	0	0	0	0	1	0	0	0	15861	962	34	4	150	4	TGM1	14	24718666	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	685818	24718666	82630874	97	1086											
C14orf106	55320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	45711249	45711249	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcccacctgattttttttAagtccatttgtaacagtttg	8	20	5	8	0	0	1	0	1	0	0	2	1	2	1	3	0	1	2	3	0	2	8			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:45711249A>C	ENST00000310806.4	-	4	1589	c.1131T>G	c.(1129-1131)ctT>ctG	p.L377L	MIS18BP1_ENST00000492652.1_5'UTR	NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	377					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						GATTTTTTTTAAGTCCATTTG	0.308																																					p.L377L		.											.	MIS18BP1-90	0			c.T1131G						.						57	66	63					14																	45711249		2202	4294	6496	SO:0001819	synonymous_variant	55320	exon4			TTTTTTAAGTCCA	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1131T>G	14.37:g.45711249A>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	47	30	NM_018353	0	0	0	0	0	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	37	CCDS9684.1																																																																																			.		0.308	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			C	45711249	A	C	45711249	2	2	13	1	0	0	0	0	0	0	0	1	1742	349	13	5		5	C14orf106	14	45711249	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	20992583	45711249	61638291	98	1087											
NEK9	91754	hgsc.bcm.edu	37	chr14	75593497	75593497	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gttcctcctgctccgccgcgCcgccgccggctcgcggcccc	0	6	12	23	8	0	0	0	0	0	0	4	0	3	0	9	2	1	3	9	2	0	1	rs78524303	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:75593497C>G	ENST00000238616.5	-	1	286	c.128G>C	c.(127-129)gGc>gCc	p.G43A	RP11-950C14.7_ENST00000556236.1_RNA	NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	43					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		CTccgccgcgccgccgccggc	0.721													C|||	90	0.0179712	0.0666	0.0029	5008	,	,		13180	0		0	False		,,,				2504	0				p.G43A		.											.	NEK9-359	0			c.G128C						.	C	ALA/GLY	99,3617		1,97,1760	5	7	7		128	3.3	1	14	dbSNP_131	7	1,7139		0,1,3569	no	missense	NEK9	NM_033116.4	60	1,98,5329	GG,GC,CC		0.014,2.6642,0.9211	benign	43/980	75593497	100,10756	1858	3570	5428	SO:0001583	missense	91754	exon1			GCCGCGCCGCCGC	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.128G>C	14.37:g.75593497C>G	ENSP00000238616:p.Gly43Ala	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_033116	0	0	0	0	0	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	37	CCDS9839.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	16.06	3.016730	0.54468	0.026642	1.4E-4	ENSG00000119638	ENST00000238616	T	0.70986	-0.53	3.34	3.34	0.38264	.	0.228496	0.38217	N	0.001761	T	0.03053	0.0090	N	0.14661	0.345	0.33726	D	0.617613	B	0.10296	0.003	B	0.12156	0.007	T	0.25710	-1.0124	10	0.20519	T	0.43	.	12.956	0.58427	0.0:1.0:0.0:0.0	.	43	Q8TD19	NEK9_HUMAN	A	43	ENSP00000238616:G43A	ENSP00000238616:G43A	G	-	2	0	NEK9	74663250	0.995000	0.38212	1.000000	0.80357	0.974000	0.67602	0.878000	0.28126	1.837000	0.53436	0.462000	0.41574	GGC	C|0.979;G|0.021		0.721	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		G	75593497	C	G	75593497	3	3	13	1	0	0	0	0	1	0	0	0	10357	739	26	4	2899	4	NEK9	14	75593497	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	29882248	75593497	31756043	99	1088											
AHNAK2	113146	ucsc.edu	37	chr14	105410343	105410343	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggacttgcctggggcagaCaccccaaatgacggcatctt	10	8	11	12	1	1	2	0	1	1	1	1	3	1	3	3	4	1	2	3	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:105410343C>A	ENST00000333244.5	-	7	11564	c.11445G>T	c.(11443-11445)gtG>gtT	p.V3815V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3815						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTGGGGCAGACACCCCAAATG	0.587																																					p.V3815V													.	AHNAK2-47	0			c.G11445T						.						238	236	236					14																	105410343		1996	4157	6153	SO:0001819	synonymous_variant	113146	exon7			GGCAGACACCCCA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.11445G>T	14.37:g.105410343C>A		Somatic	392	0		WXS	Illumina HiSeq		263	5	NM_138420	0	0	0	0	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.		0.587	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105410343	C	A	105410343	2	1	13	1	0	0	0	0	0	0	0	1	415	465	17	4		4	AHNAK2	14	105410343	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	29816846	105410343	1939197	100	1089											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75985432	75985432	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcaggcgtccagagtagagCtgcagcaggaggtggtcagc	9	6	17	9	1	1	2	1	0	0	2	2	3	2	3	1	4	5	5	1	4	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr15:75985432C>A	ENST00000308508.5	-	2	323	c.231G>T	c.(229-231)caG>caT	p.Q77H		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	77	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CAGAGTAGAGCTGCAGCAGGA	0.627																																					p.Q77H		.											.	CSPG4-229	0			c.G231T						.						10	8	9					15																	75985432		2185	4240	6425	SO:0001583	missense	1464	exon2			GTAGAGCTGCAGC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.231G>T	15.37:g.75985432C>A	ENSP00000312506:p.Gln77His	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	35	6	NM_001897	0	0	0	0	0	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	19.47	3.833556	0.71258	.	.	ENSG00000173546	ENST00000308508	T	0.76709	-1.04	4.78	-2.86	0.05717	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.384482	0.21631	N	0.071486	T	0.80904	0.4713	L	0.58101	1.795	0.42024	D	0.990993	D	0.67145	0.996	D	0.64877	0.93	T	0.79591	-0.1740	10	0.72032	D	0.01	.	10.2802	0.43534	0.0:0.415:0.0:0.585	.	77	Q6UVK1	CSPG4_HUMAN	H	77	ENSP00000312506:Q77H	ENSP00000312506:Q77H	Q	-	3	2	CSPG4	73772487	0.236000	0.23804	0.916000	0.36221	0.977000	0.68977	-0.283000	0.08433	-0.376000	0.07943	-0.266000	0.10368	CAG	.		0.627	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		A	75985432	C	A	75985432	3	1	13	1	0	0	0	0	1	0	0	0	3966	796	28	4	6773	4	CSPG4	15	75985432	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08		75985432	26545960	101	1090											
LRRK1	79705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	101529603	101529603	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagttatccgggaaaaacAgtgagtagtcactgcctgtg	12	9	12	8	1	1	1	1	1	0	0	2	2	2	2	2	1	3	3	2	1	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr15:101529603A>G	ENST00000388948.3	+	6	1121	c.762A>G	c.(760-762)acA>acG	p.T254T	LRRK1_ENST00000532029.2_Silent_p.T254T|LRRK1_ENST00000284395.5_Splice_Site_p.T251T	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CGGGAAAAACAGTGAGTAGTC	0.433																																					p.T254T		.											.	LRRK1-602	0			c.A762G						.						80	79	79					15																	101529603		1890	4124	6014	SO:0001630	splice_region_variant	79705	exon6			AAAAACAGTGAGT	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.762+1A>G	15.37:g.101529603A>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	64	30	NM_024652	0	0	0	0	0		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			.		0.433	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	Silent	G	101529603	A	G	101529603	5	3	13	1	0	0	0	0	0	0	1	0	9057	202	7	3	780	3	LRRK1	15	101529603	Splice_Site	SNP	A	TCGA-A4-8098-01A-11D-2396-08	25544171	101529603	1001789	102	1091											
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	570232	570232	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaggagtaccacagccgCgcccgggagagcgagctgga	9	3	16	13	4	0	1	0	0	0	1	0	5	0	3	3	3	5	3	3	3	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:570232C>T	ENST00000262305.4	+	12	2359	c.1971C>T	c.(1969-1971)cgC>cgT	p.R657R	RAB11FIP3_ENST00000450428.1_Silent_p.R361R|RAB11FIP3_ENST00000457159.1_Silent_p.R702R	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	657					cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				ACCACAGCCGCGCCCGGGAGA	0.682																																					p.R657R	Melanoma(160;2366 2595 4474 8099)	.											.	RAB11FIP3-90	0			c.C1971T						.						5	9	8					16																	570232		2086	4138	6224	SO:0001819	synonymous_variant	9727	exon12			CAGCCGCGCCCGG	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"EF-hand domain containing"	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1971C>T	16.37:g.570232C>T		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	11	6	NM_014700	0	0	0	0	0	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																			.		0.682	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		T	570232	C	T	570232	2	4	13	1	0	0	0	0	0	0	0	1	12927	755	27	1		1	RAB11FIP3	16	570232	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08		570232	89784521	103	1092											
MYH11	4629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	15880497	15880497	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccactcaccgtgatacttGtgtctttcttgcccttgtgg	4	16	9	12	1	3	1	1	1	2	0	3	1	3	1	3	1	3	0	3	1	1	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:15880497G>T	ENST00000300036.5	-	5	732	c.623C>A	c.(622-624)aCa>aAa	p.T208K	MYH11_ENST00000396324.3_Missense_Mutation_p.T208K|MYH11_ENST00000576790.2_Missense_Mutation_p.T208K|MYH11_ENST00000452625.2_Missense_Mutation_p.T208K	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	208	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CGTGATACTTGTGTCTTTCTT	0.527			T	CBFB	AML																																p.T208K		.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11-666	0			c.C623A						.						210	155	173					16																	15880497		2197	4300	6497	SO:0001583	missense	4629	exon5			ATACTTGTGTCTT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.623C>A	16.37:g.15880497G>T	ENSP00000300036:p.Thr208Lys	Somatic	64	1		WXS	Illumina HiSeq	Phase_I	63	23	NM_001040114	0	0	0	0	0	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	4.212	0.038077	0.08148	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.71461	-0.57;-0.57;-0.56;-0.56	5.25	3.25	0.37280	Myosin head, motor domain (2);	0.379952	0.28322	N	0.015761	T	0.46367	0.1389	N	0.05177	-0.1	0.40126	D	0.97666	B;B;B;B;B	0.10296	0.001;0.0;0.0;0.0;0.003	B;B;B;B;B	0.11329	0.002;0.002;0.002;0.002;0.006	T	0.27365	-1.0076	10	0.37606	T	0.19	.	8.2051	0.31449	0.0889:0.1663:0.7448:0.0	.	208;208;208;208;208	Q4G140;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	K	208	ENSP00000300036:T208K;ENSP00000345136:T208K;ENSP00000379616:T208K;ENSP00000407821:T208K	ENSP00000300036:T208K	T	-	2	0	MYH11	15787998	1.000000	0.71417	0.610000	0.28997	0.808000	0.45660	3.511000	0.53400	0.584000	0.29591	0.549000	0.68633	ACA	.		0.527	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15880497	G	T	15880497	3	4	13	1	0	0	0	0	1	0	0	0	10056	1377	48	4	5503	4	MYH11	16	15880497	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	15310265	15880497	74474256	104	1093											
ARL6IP1	23204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	18810023	18810023	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatctaatagctcacttacAgaaacaccaaagaaaccaca	20	7	3	11	0	2	2	1	0	1	2	2	2	2	2	2	0	4	1	2	0	7	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:18810023A>G	ENST00000304414.7	-	2	381	c.170T>C	c.(169-171)cTg>cCg	p.L57P	ARL6IP1_ENST00000562819.1_Intron|RP11-1035H13.3_ENST00000567078.2_Splice_Site_p.L57P|ARL6IP1_ENST00000546206.2_Splice_Site_p.L28P	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	57					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)				breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						GCTCACTTACAGAAACACCAA	0.413																																					p.L57P		.											.	ARL6IP1-90	0			c.T170C						.						132	115	121					16																	18810023		2197	4300	6497	SO:0001630	splice_region_variant	23204	exon2			ACTTACAGAAACA	BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"ADP-ribosylation factor-like 6 interacting protein"	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.170+1T>C	16.37:g.18810023A>G		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	168	63	NM_015161	0	0	0	0	0		Missense_Mutation	SNP	ENST00000304414.7	37	CCDS10572.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.394667	0.83011	.	.	ENSG00000170540	ENST00000304414;ENST00000545430;ENST00000546206	T;T	0.52754	0.65;0.65	5.07	5.07	0.68467	.	0.320357	0.30930	N	0.008581	T	0.64182	0.2575	M	0.65498	2.005	0.80722	D	1	D	0.58970	0.984	D	0.64237	0.923	T	0.64841	-0.6312	9	.	.	.	-0.7325	14.7838	0.69787	1.0:0.0:0.0:0.0	.	57	Q15041	AR6P1_HUMAN	P	57;9;28	ENSP00000306788:L57P;ENSP00000440048:L28P	.	L	-	2	0	ARL6IP1	18717524	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.476000	0.81055	2.016000	0.59253	0.533000	0.62120	CTG	.		0.413	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161	Missense_Mutation	G	18810023	A	G	18810023	5	3	13	1	0	0	0	0	0	0	1	0	943	202	7	3	461	3	ARL6IP1	16	18810023	Splice_Site	SNP	A	TCGA-A4-8098-01A-11D-2396-08	2929526	18810023	71544730	105	1094											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	18882177	18882177	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcatgtagactgctgcatGcctgcagacagatattcaca	12	9	10	10	0	1	3	1	0	0	3	1	4	1	3	1	0	5	5	1	0	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:18882177G>A	ENST00000446231.2	-	17	2748	c.2336C>T	c.(2335-2337)gCa>gTa	p.A779V	SMG1_ENST00000389467.3_Missense_Mutation_p.A779V|snoU13_ENST00000459248.1_RNA			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	779	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ACTGCTGCATGCCTGCAGACA	0.373																																					p.A779V		.											.	SMG1-1160	0			c.C2336T						.						7	6	7					16																	18882177		1113	2424	3537	SO:0001583	missense	23049	exon17			CTGCATGCCTGCA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2336C>T	16.37:g.18882177G>A	ENSP00000402515:p.Ala779Val	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	19	8	NM_015092	0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120890	0.37436	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.73575	-0.76;-0.76	5.42	5.42	0.78866	Armadillo-type fold (1);	0.000000	0.52532	U	0.000061	T	0.52709	0.1751	N	0.12569	0.235	0.37999	D	0.934166	P	0.39809	0.689	B	0.28553	0.091	T	0.59521	-0.7439	10	0.09843	T	0.71	.	19.2253	0.93816	0.0:0.0:1.0:0.0	.	779	Q96Q15	SMG1_HUMAN	V	779	ENSP00000402515:A779V;ENSP00000374118:A779V	ENSP00000374118:A779V	A	-	2	0	SMG1	18789678	1.000000	0.71417	0.983000	0.44433	0.913000	0.54294	7.379000	0.79691	2.555000	0.86185	0.555000	0.69702	GCA	.		0.373	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18882177	G	A	18882177	3	1	13	1	0	0	0	0	1	0	0	0	14827	1319	46	2	8837	2	SMG1	16	18882177	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	72154	18882177	71472576	106	1095											
SEPHS2	22928	broad.mit.edu	37	chr16	30456699	30456699	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacgcaggagtccatcccgAtgcccagggctggaaaggtg	9	6	15	11	2	0	1	0	1	0	0	2	4	2	3	3	4	1	2	3	4	1	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:30456699A>T	ENST00000478753.2	-	1	803	c.350T>A	c.(349-351)aTc>aAc	p.I117N	SEPHS2_ENST00000500504.2_Missense_Mutation_p.I117N|SEPHS2_ENST00000542752.1_Missense_Mutation_p.I60N			Q99611	SPS2_HUMAN	selenophosphate synthetase 2	117					selenocysteine biosynthetic process (GO:0016260)		ATP binding (GO:0005524)|selenide, water dikinase activity (GO:0004756)			breast(3)|cervix(1)|kidney(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	10						GTCCATCCCGATGCCCAGGGC	0.677																																					.	Esophageal Squamous(81;1142 1261 11202 24614 35697)												.	SEPHS2-138	0			.						.						16	18	17					16																	30456699		1874	4092	5966	SO:0001583	missense	22928	.			ATCCCGATGCCCA	BC002381		16p11.2	2013-02-15			ENSG00000179918	ENSG00000179918			19686	protein-coding gene	gene with protein product		606218				10608886	Standard	NM_012248		Approved	SPS2, SPS2b	uc021tgl.1	Q99611	OTTHUMG00000176988	ENST00000478753.2:c.350T>A	16.37:g.30456699A>T	ENSP00000418669:p.Ile117Asn	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	27	10	.	0	0	0	0	0	Q9BUQ2	Missense_Mutation	SNP	ENST00000478753.2	37		.	.	.	.	.	.	.	.	.	.	A	18.26	3.583754	0.65992	.	.	ENSG00000179918	ENST00000478753;ENST00000542752;ENST00000418751;ENST00000500504	T;T;T	0.51071	0.72;0.8;0.75	5.64	4.54	0.55810	PurM, N-terminal-like (1);	0.087451	0.49305	D	0.000154	T	0.45397	0.1340	N	0.08118	0	0.80722	D	1	D;D	0.65815	0.992;0.995	P;D	0.65140	0.899;0.932	T	0.53913	-0.8371	10	0.87932	D	0	-18.3636	11.3411	0.49533	0.8474:0.1526:0.0:0.0	.	117;60	Q99611;F5H8F9	SPS2_HUMAN;.	N	117;60;68;117	ENSP00000418669:I117N;ENSP00000443601:I60N;ENSP00000426234:I117N	ENSP00000390233:I68N	I	-	2	0	SEPHS2	30364200	1.000000	0.71417	0.977000	0.42913	0.796000	0.44982	8.813000	0.91963	1.059000	0.40554	-0.313000	0.08912	ATC	.		0.677	SEPHS2-001	KNOWN	basic|seleno	protein_coding	protein_coding	OTTHUMT00000109640.11	NM_012248		T	30456699	A	T	30456699	3	4	13	1	0	0	0	0	1	0	0	0	14087	333	12	5	1000	5	SEPHS2	16	30456699	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	11574522	30456699	59898054	107	1096											
PRSS53	339105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31098021	31098021	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggggaagcgatgggcgggCtggggcaggcagaggggtgt	8	4	24	5	2	0	1	0	0	0	1	0	3	0	2	0	9	1	3	0	9	2	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:31098021C>T	ENST00000280606.6	-	4	594	c.441G>A	c.(439-441)caG>caA	p.Q147Q		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	147	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						GATGGGCGGGCTGGGGCAGGC	0.657																																					p.Q147Q		.											.	PRSS53-68	0			c.G441A						.						30	38	35					16																	31098021		1927	4114	6041	SO:0001819	synonymous_variant	339105	exon4			GGCGGGCTGGGGC		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"Serine peptidases / Serine peptidases"	34407	protein-coding gene	gene with protein product	"polyserase 3"	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.441G>A	16.37:g.31098021C>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	94	44	NM_001039503	0	0	0	0	0		Silent	SNP	ENST00000280606.6	37	CCDS42153.1																																																																																			.		0.657	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268		T	31098021	C	T	31098021	2	4	13	1	0	0	0	0	0	0	0	1	12661	796	28	2		2	PRSS53	16	31098021	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	641322	31098021	59256732	108	1097											
OGFOD1	55239	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	56485680	56485680	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggacgccgttcagtcacggTaaccgggtgctctcagggag	8	7	15	11	4	3	0	3	0	1	0	4	2	3	2	2	4	2	3	2	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:56485680T>C	ENST00000566157.1	+	1	277		c.e1+2		NUDT21_ENST00000300291.5_5'Flank|OGFOD1_ENST00000568397.1_Splice_Site	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1						cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	TCAGTCACGGTAACCGGGTGC	0.632																																					.		.											.	OGFOD1-69	0			c.154+2T>C						.						28	31	30					16																	56485680		2198	4300	6498	SO:0001630	splice_region_variant	55239	exon1			TCACGGTAACCGG	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.154+2T>C	16.37:g.56485680T>C		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	57	21	NM_018233	0	0	0	0	0	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Splice_Site	SNP	ENST00000566157.1	37	CCDS10761.2	.	.	.	.	.	.	.	.	.	.	T	20.2	3.952175	0.73787	.	.	ENSG00000087263	ENST00000336111	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6838	0.62504	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	OGFOD1	55043181	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	4.939000	0.63526	2.227000	0.72691	0.460000	0.39030	.	.		0.632	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	Intron	C	56485680	T	C	56485680	5	2	13	1	0	0	0	0	0	0	1	0	10867	1652	57	3	158	3	OGFOD1	16	56485680	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08	25387659	56485680	33869073	109	1098											
DDX19B	11269	hgsc.bcm.edu	37	chr16	70346536	70346536	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaacttgcatcttaaggaaGagaaaatcaaaccagatacc	18	7	7	9	0	2	2	1	0	1	2	2	4	2	3	2	1	4	2	2	1	7	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:70346536G>C	ENST00000288071.6	+	2	327	c.82G>C	c.(82-84)Gag>Cag	p.E28Q	DDX19B_ENST00000355992.3_Missense_Mutation_p.E28Q|RP11-529K1.3_ENST00000567706.1_Missense_Mutation_p.E28Q|DDX19B_ENST00000451014.3_Missense_Mutation_p.E33Q|DDX19B_ENST00000393657.2_Intron|DDX19B_ENST00000570055.1_3'UTR|DDX19B_ENST00000563206.1_Missense_Mutation_p.E33Q|DDX19B_ENST00000563392.1_Intron|DDX19B_ENST00000568625.1_Intron	NM_007242.5	NP_009173.1	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B	28	N-terminal lobe.				mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)	9		Ovarian(137;0.0694)				TCTTAAGGAAGAGAAAATCAA	0.378																																					p.E33Q	Esophageal Squamous(26;382 757 1343 9728 15939)	.											.	DDX19B-226	0			c.G97C						.						100	94	96					16																	70346536		2198	4300	6498	SO:0001583	missense	11269	exon2			AAGGAAGAGAAAA	AJ237946	CCDS10888.1, CCDS32475.1, CCDS42187.1, CCDS58478.1	16q22.3	2012-02-23	2012-02-23	2005-07-13	ENSG00000157349	ENSG00000157349		"DEAD-boxes"	2742	protein-coding gene	gene with protein product		605812	"DEAD (Asp-Glu-Ala-As) box polypeptide 19", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (Dbp5, yeast, homolog)"	DDX19		10428971	Standard	NM_007242		Approved	DBP5	uc002eyo.4	Q9UMR2	OTTHUMG00000137577	ENST00000288071.6:c.82G>C	16.37:g.70346536G>C	ENSP00000288071:p.Glu28Gln	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_001257172	0	0	0	0	0	B3KNE9|B4DXS6|E7EMK4|Q6FIB7|Q6IAE0|Q96KE7|Q9H0U0	Missense_Mutation	SNP	ENST00000288071.6	37	CCDS10888.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.714638	0.48622	.	.	ENSG00000157349	ENST00000451014;ENST00000355992;ENST00000288071	T;T;T	0.62639	3.73;0.01;0.01	5.24	5.24	0.73138	.	0.047526	0.85682	D	0.000000	T	0.50360	0.1611	L	0.31845	0.965	0.43000	D	0.994511	B;B;P;B	0.36535	0.085;0.259;0.557;0.006	B;B;B;B	0.33620	0.015;0.11;0.167;0.01	T	0.53436	-0.8439	10	0.42905	T	0.14	.	14.1874	0.65614	0.0:0.0:1.0:0.0	.	33;28;28;28	E7EMK4;Q7Z4W5;Q9UMR2-2;Q9UMR2	.;.;.;DD19B_HUMAN	Q	33;28;28	ENSP00000392639:E33Q;ENSP00000348271:E28Q;ENSP00000288071:E28Q	ENSP00000288071:E28Q	E	+	1	0	DDX19B	68904037	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.261000	0.65496	2.732000	0.93576	0.655000	0.94253	GAG	.		0.378	DDX19B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268965.3	NM_007242		C	70346536	G	C	70346536	3	2	13	1	0	0	0	0	1	0	0	0	4353	943	33	4	88	4	DDX19B	16	70346536	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	13860856	70346536	20008217	110	1099											
AP1G1	164	broad.mit.edu	37	chr16	71768532	71768533	+	Frame_Shift_Ins	INS	-	-	A																															ttctgagggttcagaactttINSaatgacttgtgtgatggtcc																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:71768532_71768533insA	ENST00000299980.4	-	22	2787_2788	c.2346_2347insT	c.(2344-2349)attaaafs	p.K783fs	AP1G1_ENST00000569748.1_Frame_Shift_Ins_p.K783fs|AP1G1_ENST00000393512.3_Frame_Shift_Ins_p.K786fs|AP1G1_ENST00000433195.2_Frame_Shift_Ins_p.K806fs|AP1G1_ENST00000423132.2_Frame_Shift_Ins_p.K786fs|AP1G1_ENST00000564155.1_Frame_Shift_Ins_p.K208fs	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	783	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TTCAGAACTTTAATGACTTGTG	0.45																																					p.K786_V787delinsX													.	AP1G1-92	0			c.2356_2357insT						.																																			SO:0001589	frameshift_variant	164	exon23			GAACTTTAATGAC	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2347dupT	16.37:g.71768534_71768534dupA	ENSP00000299980:p.Lys783fs	Somatic	465	0		WXS	Illumina HiSeq	Phase_I	477	7	NM_001030007	0	0	0	0	0	O75709|O75842|Q9UG09|Q9Y3U4	Nonsense_Mutation	INS	ENST00000299980.4	37	CCDS32480.1																																																																																			.		0.45	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71768533	-	A	71768532	7	5	13	1	0	1	1	0	0	0	0	0	732	1763	61	0	129	0	AP1G1	16	71768532	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	1421996	71768532	18586221	111	1100											
TXNL4B	54957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72120699	72120699	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaacttagtgtgatctggaGatctagacagcatagaagag	15	9	11	6	0	2	5	0	1	2	4	2	6	2	5	0	1	2	1	0	1	5	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:72120699G>T	ENST00000268483.3	-	4	608	c.287C>A	c.(286-288)tCt>tAt	p.S96Y	TXNL4B_ENST00000426362.2_Missense_Mutation_p.S96Y|RP11-384M15.3_ENST00000561827.1_RNA|TXNL4B_ENST00000423037.1_Missense_Mutation_p.S96Y	NM_001142318.1|NM_017853.2	NP_001135790.1|NP_060323.1	Q9NX01	TXN4B_HUMAN	thioredoxin-like 4B	96					mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)				cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)	8						GTGATCTGGAGATCTAGACAG	0.358																																					p.S96Y		.											.	TXNL4B-91	0			c.C287A						.						68	65	66					16																	72120699		2198	4300	6498	SO:0001583	missense	54957	exon4			TCTGGAGATCTAG	BC009646	CCDS10906.1	16q22.2	2012-11-19			ENSG00000140830	ENSG00000140830			26041	protein-coding gene	gene with protein product						15161931	Standard	NM_017853		Approved	FLJ20511, DLP, Dim2	uc010vmn.2	Q9NX01	OTTHUMG00000173453	ENST00000268483.3:c.287C>A	16.37:g.72120699G>T	ENSP00000268483:p.Ser96Tyr	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	61	26	NM_001142318	0	0	0	0	0	D3DWS6	Missense_Mutation	SNP	ENST00000268483.3	37	CCDS10906.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824185	0.90955	.	.	ENSG00000140830	ENST00000268483;ENST00000426362;ENST00000423037	.	.	.	5.87	5.87	0.94306	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.60345	0.873	T	0.66594	-0.5884	9	0.87932	D	0	.	18.0718	0.89410	0.0:0.0:1.0:0.0	.	96	Q9NX01	TXN4B_HUMAN	Y	96	.	ENSP00000268483:S96Y	S	-	2	0	TXNL4B	70678200	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	TCT	.		0.358	TXNL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269007.2	NM_017853		T	72120699	G	T	72120699	3	4	13	1	0	0	0	0	1	0	0	0	16839	942	33	4	166	4	TXNL4B	16	72120699	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	352167	72120699	18234054	112	1101											
HSBP1	3281	hgsc.bcm.edu	37	chr16	83842931	83842931	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatgatatgagtagtcgcaTtgatgatctggaaaagaata	15	12	11	3	1	1	6	0	5	1	1	2	7	1	7	0	1	0	2	0	1	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:83842931T>C	ENST00000433866.2	+	3	368	c.134T>C	c.(133-135)aTt>aCt	p.I45T	RP11-483P21.2_ENST00000561599.1_RNA|HSBP1_ENST00000570259.1_Missense_Mutation_p.I45T	NM_001537.3	NP_001528.1	O75506	HSBP1_HUMAN	heat shock factor binding protein 1	45					muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)						all_cancers(2;0.00573)|all_epithelial(2;0.0309)		BRCA - Breast invasive adenocarcinoma(80;0.0404)		AGTAGTCGCATTGATGATCTG	0.468																																					p.I45T		.											.	.	0			c.T134C						.						71	67	69					16																	83842931		1993	4159	6152	SO:0001583	missense	3281	exon3			GTCGCATTGATGA	AF068754	CCDS45534.1	16q23.3	2008-02-05				ENSG00000230989			5203	protein-coding gene	gene with protein product		604553				9649501, 9493008	Standard	NM_001537		Approved		uc002fgy.2	O75506		ENST00000433866.2:c.134T>C	16.37:g.83842931T>C	ENSP00000392896:p.Ile45Thr	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	20	2	NM_001537	0	0	0	0	0	Q53XA8|Q7Z5Z3	Missense_Mutation	SNP	ENST00000433866.2	37	CCDS45534.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.936726	0.52972	.	.	ENSG00000230989	ENST00000433866	.	.	.	4.82	3.7	0.42460	Four-helical cytokine, core (1);	0.000000	0.85682	D	0.000000	T	0.61627	0.2362	.	.	.	0.80722	D	1	B	0.24675	0.109	B	0.37451	0.25	T	0.61108	-0.7129	8	0.66056	D	0.02	-9.5504	10.0348	0.42122	0.1511:0.0:0.0:0.8488	.	45	O75506	HSBP1_HUMAN	T	45	.	ENSP00000392896:I45T	I	+	2	0	HSBP1	82400432	1.000000	0.71417	0.977000	0.42913	0.922000	0.55478	6.881000	0.75584	0.771000	0.33359	0.460000	0.39030	ATT	.		0.468	HSBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433004.1	NM_001537		C	83842931	T	C	83842931	3	2	13	1	0	0	0	0	1	0	0	0	7394	1493	52	3	144	3	HSBP1	16	83842931	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	11722232	83842931	6511822	113	1102											
SLC2A4	6517	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	7189210	7189210	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcaacttcatcattggcatgGgtttccagtatgttgcggta	8	14	11	8	1	2	0	2	0	0	0	3	0	3	0	1	3	2	6	1	3	3	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:7189210G>C	ENST00000317370.8	+	10	1577	c.1309G>C	c.(1309-1311)Ggt>Cgt	p.G437R	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000571308.1_Missense_Mutation_p.G437R|SLC2A4_ENST00000424875.2_Missense_Mutation_p.G427R	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	437					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CATTGGCATGGGTTTCCAGTA	0.627																																					p.G437R		.											.	SLC2A4-90	0			c.G1309C						.						88	72	77					17																	7189210		2203	4300	6503	SO:0001583	missense	6517	exon10			GGCATGGGTTTCC	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"Solute carriers"	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.1309G>C	17.37:g.7189210G>C	ENSP00000320935:p.Gly437Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	71	24	NM_001042	0	0	0	0	0	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	37	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851854	0.51270	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.74002	-0.8;-0.8	5.09	1.72	0.24424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.256239	0.39834	N	0.001255	T	0.72162	0.3426	M	0.67569	2.06	0.46654	D	0.999149	P;P	0.40144	0.539;0.704	P;B	0.48488	0.579;0.443	T	0.65463	-0.6162	10	0.30854	T	0.27	.	3.2542	0.06826	0.2014:0.0:0.4319:0.3667	.	437;427	P14672;F5H081	GTR4_HUMAN;.	R	437;427	ENSP00000320935:G437R;ENSP00000396887:G427R	ENSP00000320935:G437R	G	+	1	0	SLC2A4	7129934	0.224000	0.23674	0.998000	0.56505	0.998000	0.95712	-0.437000	0.06914	0.677000	0.31305	0.563000	0.77884	GGT	.		0.627	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			C	7189210	G	C	7189210	3	2	13	1	0	0	0	0	1	0	0	0	14578	1232	43	4	1347	4	SLC2A4	17	7189210	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08		7189210	74006000	114	1103											
POLR2A	5430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7399344	7399344	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcttggggggctgatggacCcgaggcagggggtgattgag	7	7	21	6	1	0	3	0	3	0	0	0	5	0	4	1	7	1	3	1	7	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:7399344C>G	ENST00000322644.6	+	2	577	c.178C>G	c.(178-180)Ccg>Gcg	p.P60A	POLR2A_ENST00000572844.1_Missense_Mutation_p.P60A	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	60					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCTGATGGACCCGAGGCAGGG	0.612																																					p.P60A		.											.	POLR2A-91	0			c.C178G						.						42	48	46					17																	7399344		2202	4299	6501	SO:0001583	missense	5430	exon2			ATGGACCCGAGGC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.178C>G	17.37:g.7399344C>G	ENSP00000314949:p.Pro60Ala	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	100	36	NM_000937	0	0	0	0	0	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.134164	0.77662	.	.	ENSG00000181222	ENST00000322644	T	0.21734	1.99	5.33	5.33	0.75918	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	T	0.48927	-0.8991	10	0.87932	D	0	.	17.783	0.88529	0.0:1.0:0.0:0.0	.	60;60	P24928;Q6NX41	RPB1_HUMAN;.	A	60	ENSP00000314949:P60A	ENSP00000314949:P60A	P	+	1	0	SLC35G6	7340068	1.000000	0.71417	0.995000	0.50966	0.853000	0.48598	7.142000	0.77339	2.499000	0.84300	0.467000	0.42956	CCG	.		0.612	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		G	7399344	C	G	7399344	3	3	13	1	0	0	0	0	1	0	0	0	12240	623	22	4	184	4	POLR2A	17	7399344	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	210134	7399344	73795866	115	1104											
GAS2L2	246176	hgsc.bcm.edu;broad.mit.edu	37	chr17	34077159	34077159	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgctggcggcgaggggtcGggcgggggcagggccagctc	3	3	24	11	5	0	0	0	0	0	0	2	1	0	0	1	9	1	3	1	9	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:34077159G>C	ENST00000254466.6	-	2	591	c.564C>G	c.(562-564)ccC>ccG	p.P188P	GAS2L2_ENST00000587565.1_Intron	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	188					cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GCGAGGGGTCGGGCGGGGGCA	0.746																																					p.P188P		.											.	GAS2L2-227	0			c.C564G						.						22	29	26					17																	34077159		2190	4283	6473	SO:0001819	synonymous_variant	246176	exon2			GGGGTCGGGCGGG	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.564C>G	17.37:g.34077159G>C		Somatic	86	1		WXS	Illumina HiSeq	Phase_I	84	26	NM_139285	0	0	0	0	0	Q8NHY4	Silent	SNP	ENST00000254466.6	37	CCDS11298.1																																																																																			.		0.746	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		C	34077159	G	C	34077159	2	2	13	1	0	0	0	0	0	0	0	1	6267	1103	39	4		4	GAS2L2	17	34077159	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	26677815	34077159	47118051	116	1105											
TAF15	8148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34172014	34172014	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggctacggaggagaccgaGgtggctatggaggcaaaatg	11	5	19	6	2	0	1	0	0	0	1	0	5	0	3	1	8	1	3	1	8	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:34172014G>T	ENST00000588240.1	+	15	1826	c.1711G>T	c.(1711-1713)Ggt>Tgt	p.G571C	TAF15_ENST00000592237.1_Missense_Mutation_p.E375D|TAF15_ENST00000311979.3_Missense_Mutation_p.G568C	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AGGAGACCGAGGTGGCTATGG	0.527			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.G571C		.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15-723	0			c.G1711T						.						76	89	85					17																	34172014		2203	4300	6503	SO:0001583	missense	8148	exon15			GACCGAGGTGGCT	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1711G>T	17.37:g.34172014G>T	ENSP00000466950:p.Gly571Cys	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	165	55	NM_139215	0	0	0	0	0	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	37	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911288	0.52439	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	D	0.94862	-3.54	5.07	4.09	0.47781	.	.	.	.	.	D	0.94424	0.8206	L	0.34521	1.04	0.39114	D	0.961521	D;D	0.89917	1.0;1.0	D;D	0.69479	0.92;0.964	D	0.94444	0.7661	9	0.87932	D	0	-3.2622	10.8882	0.46978	0.0922:0.0:0.9078:0.0	.	571;568	Q92804;Q92804-2	RBP56_HUMAN;.	C	571;374	ENSP00000309558:G571C	ENSP00000309558:G571C	G	+	1	0	TAF15	31196127	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.652000	0.61454	2.520000	0.84964	0.591000	0.81541	GGT	.		0.527	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		T	34172014	G	T	34172014	3	4	13	1	0	0	0	0	1	0	0	0	15550	1000	35	4	1769	4	TAF15	17	34172014	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	94855	34172014	47023196	117	1106											
RPRML	388394	hgsc.bcm.edu;broad.mit.edu	37	chr17	45056017	45056017	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacccagatggcgctcagtaCagccccaggatggctgcgcc	8	5	13	15	2	1	1	1	0	0	1	1	3	1	2	4	3	3	3	4	3	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:45056017C>T	ENST00000322329.3	-	1	597	c.357G>A	c.(355-357)ctG>ctA	p.L119L	GOSR2_ENST00000439730.2_Intron|RP11-156P1.2_ENST00000571841.1_Intron|LRRC37A17P_ENST00000570478.1_RNA	NM_203400.4	NP_981945.1	Q8N4K4	RPRML_HUMAN	reprimo-like	119						integral component of membrane (GO:0016021)				lung(1)	1						GCGCTCAGTACAGCCCCAGGA	0.682																																					p.L119L		.											.	RPRML-68	0			c.G357A						.						18	19	19					17																	45056017		2200	4299	6499	SO:0001819	synonymous_variant	388394	exon1			TCAGTACAGCCCC	BC033942	CCDS11508.1	17q21.32	2006-09-26				ENSG00000179673			32422	protein-coding gene	gene with protein product							Standard	NM_203400		Approved	MGC43894	uc002ilb.3	Q8N4K4		ENST00000322329.3:c.357G>A	17.37:g.45056017C>T		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	20	8	NM_203400	0	0	0	0	0		Silent	SNP	ENST00000322329.3	37	CCDS11508.1																																																																																			.		0.682	RPRML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440919.1	NM_203400		T	45056017	C	T	45056017	2	4	13	1	0	0	0	0	0	0	0	1	13651	465	17	2		2	RPRML	17	45056017	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	10884003	45056017	36139193	118	1107											
LRRC46	90506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45914207	45914207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctgctgaggatggagatGcagcccaccctcaccgacct	9	6	10	16	1	1	2	1	1	0	1	1	5	1	3	5	2	3	2	5	2	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:45914207G>A	ENST00000269025.4	+	8	1050	c.687G>A	c.(685-687)atG>atA	p.M229I		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	229										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGATGGAGATGCAGCCCACCC	0.667																																					p.M229I		.											.	LRRC46-91	0			c.G687A						.						54	56	55					17																	45914207		2203	4300	6503	SO:0001583	missense	90506	exon8			GGAGATGCAGCCC		CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.687G>A	17.37:g.45914207G>A	ENSP00000269025:p.Met229Ile	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	132	38	NM_033413	0	0	0	0	0	A8K9Q0	Missense_Mutation	SNP	ENST00000269025.4	37	CCDS11518.1	.	.	.	.	.	.	.	.	.	.	G	6.561	0.471736	0.12461	.	.	ENSG00000141294	ENST00000269025	T	0.72167	-0.63	5.53	-11.1	0.00147	.	1.132520	0.06682	N	0.768096	T	0.41558	0.1164	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47623	-0.9103	10	0.37606	T	0.19	0.4736	6.5183	0.22260	0.1084:0.4274:0.3331:0.131	.	229;229	A8K9Q0;Q96FV0	.;LRC46_HUMAN	I	229	ENSP00000269025:M229I	ENSP00000269025:M229I	M	+	3	0	LRRC46	43269206	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.635000	0.00058	-4.674000	0.00036	-1.325000	0.01285	ATG	.		0.667	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413		A	45914207	G	A	45914207	3	1	13	1	0	0	0	0	1	0	0	0	9028	1319	46	2	717	2	LRRC46	17	45914207	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	858190	45914207	35281003	119	1108											
ACSF2	80221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48549793	48549793	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccatcctgtcccaggcccGgatcatgaacatggaggcag	9	6	13	13	1	1	1	1	1	0	0	3	3	3	3	4	5	1	1	4	5	1	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:48549793G>A	ENST00000300441.4	+	12	1432	c.1328G>A	c.(1327-1329)cGg>cAg	p.R443Q	ACSF2_ENST00000506085.1_Intron|ACSF2_ENST00000427954.2_Missense_Mutation_p.R468Q|ACSF2_ENST00000504392.1_Missense_Mutation_p.R400Q|ACSF2_ENST00000541920.1_Missense_Mutation_p.R283Q|ACSF2_ENST00000502667.1_Missense_Mutation_p.R430Q	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	443					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCCCAGGCCCGGATCATGAAC	0.612																																					p.R443Q		.											.	ACSF2-68	0			c.G1328A						.						50	48	49					17																	48549793		2203	4300	6503	SO:0001583	missense	80221	exon12			AGGCCCGGATCAT	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1328G>A	17.37:g.48549793G>A	ENSP00000300441:p.Arg443Gln	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	53	31	NM_025149	0	0	0	0	0	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	37	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.851859	0.32699	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.09	1.7	0.24286	AMP-dependent synthetase/ligase (1);	0.312695	0.37393	N	0.002103	T	0.26810	0.0656	L	0.28192	0.835	0.24361	N	0.994876	B;B;B;B	0.15930	0.003;0.015;0.003;0.003	B;B;B;B	0.12156	0.007;0.007;0.007;0.007	T	0.18085	-1.0348	10	0.52906	T	0.07	-5.2723	7.7408	0.28841	0.7438:0.0:0.2562:0.0	.	430;468;400;443	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	Q	443;283;400;468;430	ENSP00000300441:R443Q;ENSP00000437987:R283Q;ENSP00000425964:R400Q;ENSP00000401831:R468Q;ENSP00000421884:R430Q	ENSP00000300441:R443Q	R	+	2	0	ACSF2	45904792	1.000000	0.71417	0.994000	0.49952	0.237000	0.25408	4.324000	0.59228	0.295000	0.22570	-0.378000	0.06908	CGG	.		0.612	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		A	48549793	G	A	48549793	3	1	13	1	0	0	0	0	1	0	0	0	175	1116	39	1	1374	1	ACSF2	17	48549793	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	2635586	48549793	32645417	120	1109											
PITPNC1	26207	hgsc.bcm.edu;broad.mit.edu	37	chr17	65665781	65665781	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaacaatttgtacacaaggTaagtggtccaacagcagttc	14	9	10	8	0	0	0	0	0	0	0	2	1	1	1	1	3	4	4	1	3	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:65665781T>C	ENST00000581322.1	+	7	618		c.e7+2		PITPNC1_ENST00000335257.6_Splice_Site|PITPNC1_ENST00000299954.9_Splice_Site|PITPNC1_ENST00000580974.1_Splice_Site			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1						phospholipid transport (GO:0015914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)			breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			GTACACAAGGTAAGTGGTCCA	0.468																																					.		.											.	PITPNC1-226	0			c.618+2T>C						.						64	68	67					17																	65665781		1987	4159	6146	SO:0001630	splice_region_variant	26207	exon7			ACAAGGTAAGTGG	AF171102	CCDS58587.1, CCDS58588.1	17q24.3	2008-02-05							21045	protein-coding gene	gene with protein product		605134				10531358	Standard	NM_012417		Approved	RDGBB1, RDGBB, RDGB-BETA	uc002jgc.4	Q9UKF7		ENST00000581322.1:c.618+2T>C	17.37:g.65665781T>C		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	20	12	NM_181671	0	0	0	0	0	A8K473|J3QR20|Q96I07	Splice_Site	SNP	ENST00000581322.1	37	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.709581	0.68730	.	.	ENSG00000154217	ENST00000335257;ENST00000299954	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0556	0.80801	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PITPNC1	63096243	1.000000	0.71417	0.955000	0.39395	0.604000	0.37047	7.880000	0.87243	2.239000	0.73571	0.533000	0.62120	.	.		0.468	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417	Intron	C	65665781	T	C	65665781	5	2	13	1	0	0	0	0	0	0	1	0	11975	1652	57	3	646	3	PITPNC1	17	65665781	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08	17115988	65665781	15529429	121	1110											
DNAH17	8632	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	76491997	76491997	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaggcagctccgcgcgtcCggcgtacccagggttcatgg	5	7	14	15	5	2	0	2	0	0	0	4	0	4	0	3	4	2	4	3	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:76491997C>G	ENST00000585328.1	-	38	5972	c.5848G>C	c.(5848-5850)Gga>Cga	p.G1950R	RP11-559N14.5_ENST00000591373.1_RNA|DNAH17-AS1_ENST00000598378.1_5'Flank|DNAH17_ENST00000389840.5_Missense_Mutation_p.G1941R|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1941	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TCCGCGCGTCCGGCGTACCCA	0.557																																					p.G1955R		.											.	DNAH17-142	0			c.G5863C						.						93	94	94					17																	76491997		2059	4237	6296	SO:0001583	missense	8632	exon38			CGCGTCCGGCGTA	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.5848G>C	17.37:g.76491997C>G	ENSP00000465516:p.Gly1950Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	82	20	NM_173628	0	0	0	0	0	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	c	16.89	3.247501	0.59103	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.17528	2.27	4.49	4.49	0.54785	.	.	.	.	.	T	0.57902	0.2085	H	0.96833	3.89	0.58432	D	0.999995	.	.	.	.	.	.	T	0.74910	-0.3503	7	0.87932	D	0	.	17.7846	0.88533	0.0:1.0:0.0:0.0	.	.	.	.	R	1950;1941	ENSP00000374490:G1941R	ENSP00000300671:G1950R	G	-	1	0	DNAH17	74003592	1.000000	0.71417	0.121000	0.21740	0.087000	0.18053	7.472000	0.80996	2.501000	0.84356	0.537000	0.68136	GGA	.		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76491997	C	G	76491997	3	3	13	1	0	0	0	0	1	0	0	0	4612	661	23	4	7701	4	DNAH17	17	76491997	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	10826216	76491997	4703213	122	1111											
GNAL	2774	hgsc.bcm.edu	37	chr18	11689823	11689823	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgagtgccgaggagcgcgaGgcggccaaggagcgcgaggc	8	2	20	11	6	0	1	0	1	0	0	0	6	0	3	2	5	3	0	2	5	1	0	rs181443061	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr18:11689823G>A	ENST00000334049.6	+	1	869	c.261G>A	c.(259-261)gaG>gaA	p.E87E		NM_182978.3	NP_892023.1	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	88					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						AGGAGCGCGAGGCGGCCAAGG	0.706													G|||	93	0.0185703	0.0666	0.0072	5008	,	,		8793	0		0	False		,,,				2504	0				p.E87E		.											.	GNAL-228	0			c.G261A						.	G		169,3865		3,163,1851	6	5	5		261	3.3	1	18		5	3,8023		0,3,4010	no	coding-synonymous	GNAL	NM_182978.2		3,166,5861	AA,AG,GG		0.0374,4.1894,1.4262		87/459	11689823	172,11888	2017	4013	6030	SO:0001819	synonymous_variant	2774	exon1			GCGCGAGGCGGCC	AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000334049.6:c.261G>A	18.37:g.11689823G>A		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	10	6	NM_182978	0	0	0	0	0	B7ZA26|Q86XU3	Silent	SNP	ENST00000334049.6	37	CCDS11851.1																																																																																			G|0.989;A|0.011		0.706	GNAL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254560.2	NM_182978, NM_002071		A	11689823	G	A	11689823	2	1	13	1	0	0	0	0	0	0	0	1	6527	991	35	2		2	GNAL	18	11689823	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08		11689823	66387425	123	1112											
TJP3	27134	ucsc.edu	37	chr19	3730391	3730391	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatccacctgcccgccacCaaagccagcccctccagccc	9	3	7	22	1	0	0	0	0	0	0	2	1	2	1	10	1	4	0	10	1	1	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:3730391C>G	ENST00000541714.2	+	5	762	c.300C>G	c.(298-300)acC>acG	p.T100T	TJP3_ENST00000587686.1_Silent_p.T119T|TJP3_ENST00000539908.2_Silent_p.T64T|TJP3_ENST00000589378.1_Silent_p.T109T|TJP3_ENST00000262968.9_Silent_p.T119T|TJP3_ENST00000382008.3_Silent_p.T100T	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	100					regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCCCGCCACCAAAGCCAGCC	0.672																																					p.T109T													.	TJP3-92	0			c.C327G						.						14	17	16					19																	3730391		2176	4276	6452	SO:0001819	synonymous_variant	27134	exon5			CGCCACCAAAGCC	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"zona occludens 3"	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.300C>G	19.37:g.3730391C>G		Somatic	10	0		WXS	Illumina HiSeq		11	3	NM_001267561	0	0	0	0	0	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			.		0.672	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			G	3730391	C	G	3730391	2	3	13	1	0	0	0	0	0	0	0	1	15963	581	21	4		4	TJP3	19	3730391	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08		3730391	55398592	124	1113											
PNPLA6	10908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7615223	7615223	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtgtggtgctgagtgcggcGcacacggtggcagccaggat	7	7	18	9	3	0	1	0	1	0	0	0	2	0	2	1	5	3	3	1	5	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:7615223G>A	ENST00000221249.6	+	18	2168	c.1737G>A	c.(1735-1737)gcG>gcA	p.A579A	PNPLA6_ENST00000414982.3_Silent_p.A627A|PNPLA6_ENST00000600737.1_Silent_p.A618A|PNPLA6_ENST00000594864.1_3'UTR|PNPLA6_ENST00000545201.2_Silent_p.A553A|PNPLA6_ENST00000450331.3_Silent_p.A579A	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	618					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						TGAGTGCGGCGCACACGGTGG	0.637																																					p.A627A		.											.	PNPLA6-47	0			c.G1881A						.						61	58	59					19																	7615223		2202	4290	6492	SO:0001819	synonymous_variant	10908	exon17			TGCGGCGCACACG	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1737G>A	19.37:g.7615223G>A		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	149	53	NM_001166111	0	0	0	0	0	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																			.		0.637	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		A	7615223	G	A	7615223	2	1	13	1	0	0	0	0	0	0	0	1	12195	1074	38	1		1	PNPLA6	19	7615223	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	3884832	7615223	51513760	125	1114											
STXBP2	6813	hgsc.bcm.edu	37	chr19	7712339	7712339	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcggtgtggccatgtcagaGatgagggccgcctacgaggt	7	7	18	9	3	1	2	1	1	0	1	1	4	1	2	3	5	1	0	3	5	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:7712339G>C	ENST00000221283.5	+	18	1669	c.1638G>C	c.(1636-1638)gaG>gaC	p.E546D	STXBP2_ENST00000414284.2_Missense_Mutation_p.E543D|STXBP2_ENST00000602355.1_Missense_Mutation_p.E81D|STXBP2_ENST00000441779.2_Missense_Mutation_p.E557D	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	546					leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						CCATGTCAGAGATGAGGGCCG	0.647																																					p.E557D		.											.	STXBP2-91	0			c.G1671C						.						23	26	25					19																	7712339		2202	4300	6502	SO:0001583	missense	6813	exon18			GTCAGAGATGAGG	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.1638G>C	19.37:g.7712339G>C	ENSP00000221283:p.Glu546Asp	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_001272034	0	0	0	0	0	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	37	CCDS12181.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437346	0.83885	.	.	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902	D;D;D	0.99129	-5.46;-5.46;-5.46	5.26	0.768	0.18487	.	0.112267	0.64402	D	0.000015	D	0.99187	0.9718	M	0.91972	3.26	0.52501	D	0.999954	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.99387	1.0924	10	0.87932	D	0	7.1221	8.2082	0.31467	0.3433:0.0:0.6567:0.0	.	557;512;543;546	E7EQD5;B4DY46;Q15833-2;Q15833	.;.;.;STXB2_HUMAN	D	546;543;557;546	ENSP00000221283:E546D;ENSP00000409471:E543D;ENSP00000413606:E557D	ENSP00000221283:E546D	E	+	3	2	STXBP2	7618339	1.000000	0.71417	0.994000	0.49952	0.971000	0.66376	2.075000	0.41538	-0.005000	0.14395	0.555000	0.69702	GAG	.		0.647	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949		C	7712339	G	C	7712339	3	2	13	1	0	0	0	0	1	0	0	0	15385	933	33	4	1708	4	STXBP2	19	7712339	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	97116	7712339	51416644	126	1115											
JUNB	3726	hgsc.bcm.edu;broad.mit.edu	37	chr19	12902787	12902787	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggcggcggtggcggcagcTacttttctggtcagggctcg	4	9	18	10	4	2	0	1	0	1	0	3	0	2	0	0	7	2	3	0	7	1	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:12902787T>C	ENST00000302754.4	+	1	478	c.202T>C	c.(202-204)Tac>Cac	p.Y68H		NM_002229.2	NP_002220.1	P17275	JUNB_HUMAN	jun B proto-oncogene	68					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|decidualization (GO:0046697)|embryonic process involved in female pregnancy (GO:0060136)|gene expression (GO:0010467)|labyrinthine layer blood vessel development (GO:0060716)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|osteoclast differentiation (GO:0030316)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|kidney(1)|lung(3)	6						TGGCGGCAGCTACTTTTCTGG	0.672																																					p.Y68H		.											.	JUNB-846	0			c.T202C						.						12	13	13					19																	12902787		2200	4294	6494	SO:0001583	missense	3726	exon1			GGCAGCTACTTTT	M29039	CCDS12280.1	19p13.13	2013-01-10				ENSG00000171223		"basic leucine zipper proteins"	6205	protein-coding gene	gene with protein product		165161				2513129	Standard	NM_002229		Approved		uc002mvc.3	P17275		ENST00000302754.4:c.202T>C	19.37:g.12902787T>C	ENSP00000303315:p.Tyr68His	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	31	13	NM_002229	0	0	0	0	0	Q96GH3	Missense_Mutation	SNP	ENST00000302754.4	37	CCDS12280.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192125	0.38707	.	.	ENSG00000171223	ENST00000302754	T	0.29142	1.58	4.97	4.97	0.65823	Jun-like transcription factor (1);	1.243760	0.05788	U	0.609862	T	0.21103	0.0508	N	0.22421	0.69	0.34616	D	0.718126	B	0.18166	0.026	B	0.11329	0.006	T	0.28681	-1.0036	10	0.15499	T	0.54	-6.7954	6.385	0.21556	0.0:0.1805:0.0:0.8195	.	68	P17275	JUNB_HUMAN	H	68	ENSP00000303315:Y68H	ENSP00000303315:Y68H	Y	+	1	0	JUNB	12763787	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.617000	0.36943	1.865000	0.54081	0.448000	0.29417	TAC	.		0.672	JUNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451015.1	NM_002229		C	12902787	T	C	12902787	3	2	13	1	0	0	0	0	1	0	0	0	7991	1522	53	3	204	3	JUNB	19	12902787	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	5190448	12902787	46226196	127	1116											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927139	23927139	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagtaaggtgtgaggactTgttaaaagctttgccacatt	11	14	10	6	0	1	1	0	1	1	0	1	2	1	2	1	2	2	3	1	2	4	6	rs1852431		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:23927139T>G	ENST00000402377.3	-	4	1354	c.1213A>C	c.(1213-1215)Aag>Cag	p.K405Q	ZNF681_ENST00000395385.3_Missense_Mutation_p.K336Q	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	405					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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TGTGAGGACTTGTTAAAAGCT	0.403																																					p.K405Q		.											.	.	0			c.A1213C						.						69	73	72					19																	23927139		2203	4300	6503	SO:0001583	missense	148213	exon4			AGGACTTGTTAAA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1213A>C	19.37:g.23927139T>G	ENSP00000384000:p.Lys405Gln	Somatic	46	1		WXS	Illumina HiSeq	Phase_I	59	3	NM_138286	0	0	0	0	0	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	0	-2.720447	0.00092	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07444	3.19;3.19	1.51	-3.01	0.05463	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.02275	-0.615	0.09310	N	1	B	0.17465	0.022	B	0.15870	0.014	T	0.33033	-0.9884	9	0.02654	T	1	.	5.6438	0.17579	0.151:0.0:0.5623:0.2867	rs1852431	405	Q96N22	ZN681_HUMAN	Q	405;336	ENSP00000384000:K405Q;ENSP00000378783:K336Q	ENSP00000378783:K336Q	K	-	1	0	ZNF681	23718979	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.510000	0.00063	-2.559000	0.00474	-2.453000	0.00207	AAG	.		0.403	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23927139	T	G	23927139	3	3	13	1	0	0	0	0	1	0	0	0	18120	1821	63	5	728	5	ZNF681	19	23927139	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	11024352	23927139	35201844	128	1117											
LSM14A	26065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	34712486	34712486	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcccacttcgtccaaaccGtggccgtgggggatacagag	10	7	12	12	3	0	1	0	0	0	1	3	2	2	2	4	3	2	0	4	3	3	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:34712486G>T	ENST00000433627.5	+	9	1286	c.1211G>T	c.(1210-1212)cGt>cTt	p.R404L	LSM14A_ENST00000544216.3_Missense_Mutation_p.R404L|LSM14A_ENST00000540746.2_Missense_Mutation_p.R363L	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	404					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					CGTCCAAACCGTGGCCGTGGG	0.507																																					p.R404L		.											.	LSM14A-91	0			c.G1211T						.						96	71	79					19																	34712486		2203	4300	6503	SO:0001583	missense	26065	exon9			CAAACCGTGGCCG	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.1211G>T	19.37:g.34712486G>T	ENSP00000413964:p.Arg404Leu	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	63	20	NM_001114093	0	0	0	0	0	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	g	28.6	4.933243	0.92458	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.18657	2.2;2.2;2.2	5.96	4.93	0.64822	.	0.104479	0.64402	D	0.000004	T	0.40297	0.1111	M	0.76002	2.32	0.80722	D	1	P;D;D	0.56287	0.889;0.958;0.975	B;P;P	0.55824	0.396;0.614;0.785	T	0.26503	-1.0101	10	0.37606	T	0.19	-9.5825	15.0274	0.71680	0.0679:0.0:0.9321:0.0	.	363;404;404	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	L	404;404;363	ENSP00000446271:R404L;ENSP00000413964:R404L;ENSP00000446451:R363L	ENSP00000314768:R404L	R	+	2	0	LSM14A	39404326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.382000	0.97209	1.533000	0.49186	0.655000	0.94253	CGT	.		0.507	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		T	34712486	G	T	34712486	3	4	13	1	0	0	0	0	1	0	0	0	9079	1145	40	4	1245	4	LSM14A	19	34712486	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10785347	34712486	24416497	129	1118											
SIPA1L3	23094	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	38572702	38572702	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggcagggccttcctcccccTtcggcaccgcagcagcagcg	5	5	12	19	4	0	0	0	0	0	0	3	0	2	0	5	3	3	5	5	3	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:38572702T>C	ENST00000222345.6	+	3	1006	c.497T>C	c.(496-498)cTt>cCt	p.L166P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	166					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TTCCTCCCCCTTCGGCACCGC	0.711																																					p.L166P		.											.	SIPA1L3-91	0			c.T497C						.						46	56	53					19																	38572702		2203	4299	6502	SO:0001583	missense	23094	exon3			TCCCCCTTCGGCA	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.497T>C	19.37:g.38572702T>C	ENSP00000222345:p.Leu166Pro	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	125	52	NM_015073	0	0	0	0	0	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.672868	0.67928	.	.	ENSG00000105738	ENST00000222345	T	0.80994	-1.44	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000006	D	0.83737	0.5319	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.85925	0.1448	10	0.87932	D	0	-15.4086	14.0813	0.64925	0.0:0.0:0.0:1.0	.	166	O60292	SI1L3_HUMAN	P	166	ENSP00000222345:L166P	ENSP00000222345:L166P	L	+	2	0	SIPA1L3	43264542	0.433000	0.25562	0.937000	0.37676	0.960000	0.62799	3.929000	0.56514	1.971000	0.57363	0.460000	0.39030	CTT	.		0.711	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		C	38572702	T	C	38572702	3	2	13	1	0	0	0	0	1	0	0	0	14363	1609	56	3	499	3	SIPA1L3	19	38572702	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	3860216	38572702	20556281	130	1119											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41018832	41018832	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgagctgggcgggcggcgAgcgttgctgcagcaggccct	4	5	20	12	5	0	0	0	0	0	0	0	2	0	0	1	5	5	5	1	5	0	1	rs814533	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:41018832A>G	ENST00000352632.3	+	14	2222	c.2136A>G	c.(2134-2136)cgA>cgG	p.R712R	SPTBN4_ENST00000338932.3_Silent_p.R712R|SPTBN4_ENST00000595535.1_Silent_p.R712R|SPTBN4_ENST00000344104.3_Silent_p.R712R|SPTBN4_ENST00000598249.1_Silent_p.R712R			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	712					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGGGCGGCGAGCGTTGCTGC	0.751													G|||	1110	0.221645	0.4758	0.1239	5008	,	,		9743	0.1052		0.1372	False		,,,				2504	0.1544				p.R712R		.											.	SPTBN4-94	0			c.A2136G						.	G		502,1916		17,468,724	1	2	2		2136	3.2	1	19	dbSNP_86	2	282,4934		4,274,2330	no	coding-synonymous	SPTBN4	NM_020971.2		21,742,3054	GG,GA,AA		5.4064,20.761,10.2698		712/2565	41018832	784,6850	1209	2608	3817	SO:0001819	synonymous_variant	57731	exon14			GCGGCGAGCGTTG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.2136A>G	19.37:g.41018832A>G		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_020971	0	0	0	0	0	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			A|0.806;G|0.194		0.751	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			G	41018832	A	G	41018832	2	3	13	1	0	0	0	0	0	0	0	1	15153	291	11	3		3	SPTBN4	19	41018832	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	2446130	41018832	18110151	131	1120											
FKRP	79147	hgsc.bcm.edu	37	chr19	47259238	47259238	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaacgtcagcctgcgagaGtggaccgcccgctatggcgc	7	6	14	14	5	1	2	1	1	0	1	1	4	1	3	3	2	3	1	3	2	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:47259238G>A	ENST00000318584.5	+	4	828	c.531G>A	c.(529-531)gaG>gaA	p.E177E	FKRP_ENST00000391909.3_Silent_p.E177E|FKRP_ENST00000600646.1_Intron	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	177					glycoprotein biosynthetic process (GO:0009101)|protein processing (GO:0016485)	dystrophin-associated glycoprotein complex (GO:0016010)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)	transferase activity (GO:0016740)			NS(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		GCCTGCGAGAGTGGACCGCCC	0.731																																					p.E177E		.											.	FKRP-91	0			c.G531A						.						4	4	4					19																	47259238		1916	3734	5650	SO:0001819	synonymous_variant	79147	exon4			GCGAGAGTGGACC	AJ314847	CCDS12691.1	19q13.32	2014-09-17			ENSG00000181027	ENSG00000181027			17997	protein-coding gene	gene with protein product		606596				11592034, 11741828	Standard	NM_024301		Approved	LGMD2I, MDC1C	uc002pfp.2	Q9H9S5		ENST00000318584.5:c.531G>A	19.37:g.47259238G>A		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_024301	0	0	0	0	0	A8K5G7	Silent	SNP	ENST00000318584.5	37	CCDS12691.1																																																																																			.		0.731	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301		A	47259238	G	A	47259238	2	1	13	1	0	0	0	0	0	0	0	1	5936	1020	36	2		2	FKRP	19	47259238	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	6240406	47259238	11869745	132	1121											
RUVBL2	10856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49510337	49510337	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgccggcagtgaaatcttcTccctggagatgagcaagacc	10	8	11	12	2	2	4	0	2	2	2	4	5	2	4	3	2	1	2	3	2	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:49510337T>C	ENST00000595090.1	+	5	792	c.328T>C	c.(328-330)Tcc>Ccc	p.S110P	RUVBL2_ENST00000413176.2_Missense_Mutation_p.S65P|RUVBL2_ENST00000601968.1_Missense_Mutation_p.S65P	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	110					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		TGAAATCTTCTCCCTGGAGAT	0.657																																					p.S110P		.											.	RUVBL2-227	0			c.T328C						.						41	46	44					19																	49510337		2026	4182	6208	SO:0001583	missense	10856	exon5			ATCTTCTCCCTGG	AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"INO80 complex subunits", "ATPases / AAA-type"	10475	protein-coding gene	gene with protein product	"reptin", "INO80 complex subunit J"	604788	"RuvB (E coli homolog)-like 2", "RuvB-like 2 (E. coli)"			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.328T>C	19.37:g.49510337T>C	ENSP00000473172:p.Ser110Pro	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	116	43	NM_006666	0	0	0	0	0	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	37	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.040844	0.93685	.	.	ENSG00000183207	ENST00000221413;ENST00000413176	T;T	0.68903	-0.36;0.06	5.61	5.61	0.85477	TIP49, C-terminal (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.89336	0.6686	H	0.99225	4.475	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93330	0.6700	10	0.87932	D	0	-29.1189	14.0551	0.64764	0.0:0.0:0.0:1.0	.	110;110;76	B4DW30;Q9Y230;B3KNL2	.;RUVB2_HUMAN;.	P	110;65	ENSP00000221413:S110P;ENSP00000413890:S65P	ENSP00000221413:S110P	S	+	1	0	RUVBL2	54202149	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.598000	0.67585	2.271000	0.75665	0.459000	0.35465	TCC	.		0.657	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1			C	49510337	T	C	49510337	3	2	13	1	0	0	0	0	1	0	0	0	13785	1551	54	3	346	3	RUVBL2	19	49510337	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	2251099	49510337	9618646	133	1122											
SYT3	84258	hgsc.bcm.edu	37	chr19	51133415	51133415	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgctgggtgaggggtcgggGcagggctgggtacctgtagg	4	8	22	7	1	0	1	0	1	0	0	1	1	0	1	1	8	2	5	1	8	2	2	rs371022999		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:51133415G>A	ENST00000338916.4	-	3	1321	c.688C>T	c.(688-690)Ccc>Tcc	p.P230S	SYT3_ENST00000593901.1_Missense_Mutation_p.P230S|SYT3_ENST00000544769.1_Missense_Mutation_p.P230S|SYT3_ENST00000600079.1_Missense_Mutation_p.P230S	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	230					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		AGGGGTCGGGGCAGGGCTGGG	0.657																																					p.P230S		.											.	SYT3-155	0			c.C688T						.						11	13	12					19																	51133415		2200	4286	6486	SO:0001583	missense	84258	exon3			GTCGGGGCAGGGC	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.688C>T	19.37:g.51133415G>A	ENSP00000340914:p.Pro230Ser	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_032298	0	0	0	0	0	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	37	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.467406	0.43839	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.58797	0.31;0.31	4.29	4.29	0.51040	.	0.226024	0.27072	U	0.021075	T	0.40570	0.1122	N	0.19112	0.55	0.41103	D	0.985685	P	0.43477	0.808	B	0.36244	0.22	T	0.49872	-0.8893	10	0.54805	T	0.06	.	14.1182	0.65169	0.0:0.0:1.0:0.0	.	230	Q9BQG1	SYT3_HUMAN	S	230	ENSP00000340914:P230S;ENSP00000438883:P230S	ENSP00000340914:P230S	P	-	1	0	SYT3	55825227	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.435000	0.52849	2.382000	0.81193	0.655000	0.94253	CCC	.		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		A	51133415	G	A	51133415	3	1	13	1	0	0	0	0	1	0	0	0	15507	1203	42	2	1108	2	SYT3	19	51133415	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	1623078	51133415	7995568	134	1123											
ADRA1D	146	hgsc.bcm.edu	37	chr20	4229281	4229281	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggttacctgccacggccatAaggatgaaggctgccaggaa	12	6	13	10	1	0	1	0	1	0	0	0	3	0	3	4	5	3	2	4	5	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:4229281A>G	ENST00000379453.4	-	1	440	c.324T>C	c.(322-324)ctT>ctC	p.L108L		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	108					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CCACGGCCATAAGGATGAAGG	0.672																																					p.L108L		.											.	ADRA1D-522	0			c.T324C						.						34	36	36					20																	4229281		2203	4299	6502	SO:0001819	synonymous_variant	146	exon1			GGCCATAAGGATG	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"GPCR / Class A : Adrenoceptors : alpha"	280	protein-coding gene	gene with protein product		104219	"adrenergic, alpha-1D-, receptor"			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.324T>C	20.37:g.4229281A>G		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_000678	0	0	0	0	0	Q9NPY0	Silent	SNP	ENST00000379453.4	37	CCDS13079.1																																																																																			.		0.672	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		G	4229281	A	G	4229281	2	3	13	1	0	0	0	0	0	0	0	1	336	349	13	3		3	ADRA1D	20	4229281	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08		4229281	58796239	135	1124											
MYL9	10398	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	35177592	35177592	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccattgataagaaaggcaaCttcaactacgtggagttcac	14	9	8	10	1	2	2	2	1	0	1	2	3	2	3	1	2	3	2	1	2	5	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:35177592C>T	ENST00000279022.2	+	4	563	c.459C>T	c.(457-459)aaC>aaT	p.N153N	MYL9_ENST00000346786.2_Silent_p.N99N|RP5-977B1.7_ENST00000425233.1_RNA|RP5-977B1.7_ENST00000439595.1_RNA|RP5-977B1.11_ENST00000561134.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	153	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				AGAAAGGCAACTTCAACTACG	0.592																																					p.N153N		.											.	MYL9-90	0			c.C459T						.						112	95	101					20																	35177592		2203	4300	6503	SO:0001819	synonymous_variant	10398	exon4			AGGCAACTTCAAC	J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"Myosins / Light chain", "EF-hand domain containing"	15754	protein-coding gene	gene with protein product	"myosin regulatory light chain 2, smooth muscle isoform", "myosin regulatory light chain 1"	609905	"myosin, light polypeptide 9, regulatory"			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.459C>T	20.37:g.35177592C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	69	20	NM_006097	0	0	0	0	0	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Silent	SNP	ENST00000279022.2	37	CCDS13276.1																																																																																			.		0.592	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097		T	35177592	C	T	35177592	2	4	13	1	0	0	0	0	0	0	0	1	10079	564	20	2		2	MYL9	20	35177592	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	30948311	35177592	27847928	136	1125											
TGIF2	60436	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	35219568	35219569	+	Frame_Shift_Ins	INS	-	-	A																															agcccctttcccacgtggggINSagctggagtctcccaagccc																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:35219568_35219569insA	ENST00000373874.2	+	3	647_648	c.448_449insA	c.(448-450)gagfs	p.E150fs	TGIF2-C20orf24_ENST00000558530.1_Intron|TGIF2_ENST00000373872.4_Frame_Shift_Ins_p.E150fs|RP5-977B1.11_ENST00000561134.1_RNA	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	150	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CCCACGTGGGGAGCTGGAGTCT	0.629																																					p.E150fs		.											.	TGIF2-92	0			c.448_449insA						.																																			SO:0001589	frameshift_variant	60436	exon3			.	AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"Homeoboxes / TALE class"	15764	protein-coding gene	gene with protein product		607294	"TGFB-induced factor 2 (TALE family homeobox)"			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.449dupA	20.37:g.35219569_35219569dupA	ENSP00000362981:p.Glu150fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	104	42	NM_021809	0	0	0	0	0	B2R9U3|E1P5T9|H0YNI0	Frame_Shift_Ins	INS	ENST00000373874.2	37	CCDS13278.1																																																																																			.		0.629	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809		A	35219569	-	A	35219568	7	5	13	1	0	1	1	0	0	0	0	0	15858	1175	41	0	454	0	TGIF2	20	35219568	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	41976	35219568	27805952	137	1126											
RRP1	8568	hgsc.bcm.edu	37	chr21	45209575	45209575	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcctggcggggaatgagcAggtgacccgggaccgggcgg	6	3	21	11	5	0	2	0	2	0	0	0	4	0	4	3	7	1	1	3	7	1	0	rs530432421	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr21:45209575A>G	ENST00000497547.1	+	1	182	c.65A>G	c.(64-66)cAg>cGg	p.Q22R		NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		GGGAATGAGCAGGTGACCCGG	0.711													A|||	2	0.000399361	0.0015	0	5008	,	,		12178	0		0	False		,,,				2504	0				p.Q22R		.											.	RRP1-90	0			c.A65G						.																																			SO:0001583	missense	8568	exon1			ATGAGCAGGTGAC	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"DNA segment on chromosome 21 (unique) 2056 expressed sequence", "Nnp1 homolog, nucleolar protein (Drosophila)"	610653	"ribosomal RNA processing 1 homolog (S. cerevisiae)"			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.65A>G	21.37:g.45209575A>G	ENSP00000417464:p.Gln22Arg	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	8	5	NM_003683	0	0	0	0	0	A6NIB2	Missense_Mutation	SNP	ENST00000497547.1	37	CCDS42951.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.746588	0.69418	.	.	ENSG00000160214	ENST00000497547;ENST00000400387	T	0.41400	1.0	4.41	4.41	0.53225	.	0.195056	0.47455	D	0.000238	T	0.27349	0.0671	N	0.15975	0.35	0.34121	D	0.664176	P;B	0.34462	0.454;0.309	B;B	0.34931	0.192;0.138	T	0.47724	-0.9095	10	0.87932	D	0	.	11.1628	0.48526	1.0:0.0:0.0:0.0	.	22;22	B4DZM3;P56182	.;RRP1_HUMAN	R	22	ENSP00000417464:Q22R	ENSP00000383237:Q22R	Q	+	2	0	RRP1	44034003	0.996000	0.38824	1.000000	0.80357	0.869000	0.49853	2.387000	0.44389	1.624000	0.50355	0.402000	0.26972	CAG	.		0.711	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683		G	45209575	A	G	45209575	3	3	13	1	0	0	0	0	1	0	0	0	13717	188	7	3	67	3	RRP1	21	45209575	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08		45209575	2920320	138	1127											
TPST2	8459	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	26937461	26937461	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagctcctcctgctcaggccGcatggccccccgggggctcc	3	6	12	20	2	1	0	1	0	0	0	4	0	4	0	7	4	2	4	7	4	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr22:26937461G>A	ENST00000338754.4	-	3	406	c.136C>T	c.(136-138)Cgg>Tgg	p.R46W	TPST2_ENST00000403880.1_Missense_Mutation_p.R46W|TPST2_ENST00000398110.2_Missense_Mutation_p.R46W	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	46					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TGCTCAGGCCGCATGGCCCCC	0.701																																					p.R46W		.											.	TPST2-90	0			c.C136T						.						45	39	41					22																	26937461		2185	4257	6442	SO:0001583	missense	8459	exon3			CAGGCCGCATGGC	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"Sulfotransferases, membrane-bound"	12021	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog B (Drosophila)"	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.136C>T	22.37:g.26937461G>A	ENSP00000339813:p.Arg46Trp	Somatic	54	1		WXS	Illumina HiSeq	Phase_I	39	5	NM_001008566	0	0	0	0	0	B3KQA7|Q6FI98|Q9H0V4	Missense_Mutation	SNP	ENST00000338754.4	37	CCDS13839.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.299440	0.23650	.	.	ENSG00000128294	ENST00000338754;ENST00000398110;ENST00000403880;ENST00000442495;ENST00000454778;ENST00000440953;ENST00000453117;ENST00000450022	.	.	.	4.95	1.41	0.22369	.	0.398194	0.20982	N	0.082188	T	0.38374	0.1038	N	0.24115	0.695	0.38148	D	0.938657	B	0.06786	0.001	B	0.01281	0.0	T	0.26744	-1.0094	9	0.66056	D	0.02	-23.8602	6.5609	0.22485	0.0907:0.0:0.3942:0.5151	.	46	O60704	TPST2_HUMAN	W	46	.	ENSP00000339813:R46W	R	-	1	2	TPST2	25267461	0.999000	0.42202	0.997000	0.53966	0.209000	0.24338	1.285000	0.33261	0.479000	0.27511	-0.192000	0.12808	CGG	.		0.701	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595		A	26937461	G	A	26937461	3	1	13	1	0	0	0	0	1	0	0	0	16461	1086	38	1	1013	1	TPST2	22	26937461	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08		26937461	24367105	139	1128											
NF2	4771	broad.mit.edu	37	chr22	30069467	30069470	+	Frame_Shift_Del	DEL	AGAG	AGAG	-																															ctgaagatggctgaggagtcAgagaggaggtgagggggcac																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr22:30069467_30069470delAGAG	ENST00000338641.4	+	12	1773_1776	c.1332_1335delAGAG	c.(1330-1335)tcagagfs	p.SE444fs	NF2_ENST00000403435.1_Frame_Shift_Del_p.SE415fs|NF2_ENST00000403999.3_Frame_Shift_Del_p.SE444fs|NF2_ENST00000397789.3_Frame_Shift_Del_p.SE444fs|NF2_ENST00000353887.4_Frame_Shift_Del_p.SE361fs|NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Frame_Shift_Del_p.SE402fs|NF2_ENST00000334961.7_Frame_Shift_Del_p.SE361fs|NF2_ENST00000361452.4_Frame_Shift_Del_p.SE403fs|NF2_ENST00000347330.5_Intron|NF2_ENST00000361166.4_Frame_Shift_Del_p.SE444fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	444	Glu-rich.				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.?(4)|p.E445fs*9(3)|p.R446fs*48(1)|p.R446fs*49(1)		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						CTGAGGAGTCAGAGAGGAGGTGAG	0.637			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.444_445del			yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	9	Unknown(4)|Deletion - Frameshift(4)|Insertion - Frameshift(1)	meninges(4)|soft_tissue(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)	c.1332_1335del	GRCh37	CD962110|CI983171	NF2	D|I		.																																			SO:0001589	frameshift_variant	4771	exon12	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GGAGTCAGAGAGG	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.1332_1335delAGAG	22.37:g.30069467_30069470delAGAG	ENSP00000344666:p.Ser444fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	8	5	NM_000268	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	37	CCDS13861.1																																																																																			.		0.637	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		-	30069470	AGAG	-	30069467	7	5	13	1	0	1	0	1	0	0	0	0	10383	175	7	0	1378	0	NF2	22	30069467	Frame_Shift_Del	DEL	AGAG	TCGA-A4-8098-01A-11D-2396-08	3132006	30069467	21235099	140	1129											
RFPL2	10739	hgsc.bcm.edu	37	chr22	32598365	32598365	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaaagtcccagtggccaCacaatacagcacatagacag	15	5	8	13	0	0	1	0	0	0	1	1	1	1	1	2	1	3	2	2	1	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr22:32598365C>G	ENST00000400237.1	-	2	1009	c.74G>C	c.(73-75)tGt>tCt	p.C25S	RFPL2_ENST00000248983.4_5'UTR|RP1-90G24.10_ENST00000434942.1_RNA|RFPL2_ENST00000400236.3_5'UTR			O75678	RFPL2_HUMAN	ret finger protein-like 2	25							zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						ccagtggccacacaatacagc	0.517																																					p.C25S		.											.	RFPL2-91	0			c.G74C						.						93	83	86					22																	32598365		1568	3582	5150	SO:0001583	missense	10739	exon2			TGGCCACACAATA	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.74G>C	22.37:g.32598365C>G	ENSP00000383096:p.Cys25Ser	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_001098527	0	0	0	0	0		Missense_Mutation	SNP	ENST00000400237.1	37	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	C	7.446	0.641751	0.14451	.	.	ENSG00000128253	ENST00000400237	T	0.55930	0.49	.	.	.	.	.	.	.	.	T	0.27866	0.0686	N	0.08118	0	0.22240	N	0.999265	P	0.34662	0.462	B	0.32762	0.152	T	0.17653	-1.0362	7	0.87932	D	0	.	.	.	.	.	25	O75678	RFPL2_HUMAN	S	25	ENSP00000383096:C25S	ENSP00000383096:C25S	C	-	2	0	RFPL2	30928365	0.011000	0.17503	0.259000	0.24435	0.261000	0.26267	0.571000	0.23669	0.088000	0.17205	0.089000	0.15464	TGT	.		0.517	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		G	32598365	C	G	32598365	3	3	13	1	0	0	0	0	1	0	0	0	13286	478	17	4	1160	4	RFPL2	22	32598365	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	2528898	32598365	18706201	141	1130											
UBA1	7317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	47069022	47069022	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtttgctctgtctgcagTgggctcgggatgagtttgaa	5	15	14	7	1	3	2	0	2	3	0	4	3	3	3	0	2	2	5	0	2	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:47069022T>G	ENST00000335972.6	+	17	2122	c.1939T>G	c.(1939-1941)Tgg>Ggg	p.W647G	UBA1_ENST00000377269.3_Missense_Mutation_p.W95G|UBA1_ENST00000377351.4_Splice_Site_p.W647G	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	647					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CTGTCTGCAGTGGGCTCGGGA	0.498																																					p.W647G		.											.	UBA1-227	0			c.T1939G						.						122	93	103					X																	47069022		2203	4300	6503	SO:0001630	splice_region_variant	7317	exon17			CTGCAGTGGGCTC	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"Ubiquitin-like modifier activating enzymes"	12469	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog (yeast)", "POC20 centriolar protein homolog (Chlamydomonas)"	314370	"ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)", "ubiquitin-activating enzyme E1"	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.1939-1T>G	X.37:g.47069022T>G		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	32	26	NM_153280	0	0	0	0	0	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.009850	0.75046	.	.	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.51817	0.69;0.69;0.69	5.22	5.22	0.72569	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-activating enzyme (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.111594	0.64402	D	0.000003	T	0.79782	0.4505	H	0.98577	4.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86491	0.1797	10	0.87932	D	0	-10.8017	11.8816	0.52579	0.0:0.0:0.0:1.0	.	95;647	Q5JRR6;P22314	.;UBA1_HUMAN	G	647;647;95	ENSP00000366568:W647G;ENSP00000338413:W647G;ENSP00000366481:W95G	ENSP00000338413:W647G	W	+	1	0	UBA1	46953966	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.580000	0.82523	1.860000	0.53959	0.427000	0.28365	TGG	.		0.498	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	Missense_Mutation	G	47069022	T	G	47069022	5	3	13	1	0	0	0	0	0	0	1	0	16860	1710	59	5	2001	5	UBA1	23	47069022	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08		47069022	108201538	142	1131											
FAAH2	158584	hgsc.bcm.edu	37	chrX	57313330	57313330	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggctttctcataggcttagtAggccgagcagctttagtctt	7	14	11	9	1	2	0	1	0	2	0	3	1	2	0	1	3	2	5	1	3	4	7			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:57313330A>G	ENST00000374900.4	+	1	192	c.72A>G	c.(70-72)gtA>gtG	p.V24V		NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	24						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						TAGGCTTAGTAGGCCGAGCAG	0.567										HNSCC(52;0.14)																											p.V24V		.											.	FAAH2-133	0			c.A72G						.						41	36	38					X																	57313330		2203	4299	6502	SO:0001819	synonymous_variant	158584	exon1			CTTAGTAGGCCGA	AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"amidase domain containing"	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.72A>G	X.37:g.57313330A>G		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	17	2	NM_174912	0	0	0	0	0	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																			.		0.567	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912		G	57313330	A	G	57313330	2	3	13	1	0	0	0	0	0	0	0	1	5370	407	15	3		3	FAAH2	23	57313330	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10244308	57313330	97957230	143	1132											
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	123211859	123211862	+	Frame_Shift_Del	DEL	AGAT	AGAT	-																															aacaatgagtaaaacaaggcAgatagacaaaattcagtgtg																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	AGAT	AGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:123211859_123211862delAGAT	ENST00000371160.1	+	27	3016_3019	c.2726_2729delAGAT	c.(2725-2730)cagatafs	p.QI909fs	STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000371157.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000371145.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000354548.5_Frame_Shift_Del_p.QI840fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	909					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AAAACAAGGCAGATAGACAAAATT	0.314																																					p.909_910del		.											.	STAG2-134	0			c.2726_2729del						.																																			SO:0001589	frameshift_variant	10735	exon27			.	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2726_2729delAGAT	X.37:g.123211859_123211862delAGAT	ENSP00000360202:p.Gln909fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	58	45	NM_001042749	0	0	0	0	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	37	CCDS14607.1																																																																																			.		0.314	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123211862	AGAT	-	123211859	7	5	13	1	0	1	0	1	0	0	0	0	15275	188	7	0	2824	0	STAG2	23	123211859	Frame_Shift_Del	DEL	AGAT	TCGA-A4-8098-01A-11D-2396-08	65898529	123211859	32058701	144	1133											
PLXNB3	5365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	153037078	153037078	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgtgcccgccgggggctgtgGagctgctgtgtcctgcgccc	1	9	17	14	3	0	0	0	0	0	0	1	1	1	1	4	3	4	3	4	3	0	0	rs375202688		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:153037078G>C	ENST00000361971.5	+	14	2599	c.2485G>C	c.(2485-2487)Gag>Cag	p.E829Q	PLXNB3_ENST00000538776.1_Missense_Mutation_p.E482Q|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538282.1_Missense_Mutation_p.E439Q|PLXNB3_ENST00000538966.1_Missense_Mutation_p.E852Q	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	829	PSI 3.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGGGCTGTGGAGCTGCTGTG	0.692																																					p.E852Q		.											.	PLXNB3-130	0			c.G2554C						.						20	20	20					X																	153037078		2180	4292	6472	SO:0001583	missense	5365	exon15			GCTGTGGAGCTGC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.2485G>C	X.37:g.153037078G>C	ENSP00000355378:p.Glu829Gln	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	12	12	NM_001163257	0	0	0	0	0	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.404697	0.25378	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.66460	5.33;5.29;4.71;-0.21	5.01	-0.321	0.12717	.	.	.	.	.	T	0.59945	0.2231	L	0.55103	1.725	0.09310	N	1	B;B;B;B	0.23128	0.001;0.08;0.009;0.003	B;B;B;B	0.17098	0.005;0.017;0.008;0.005	T	0.43718	-0.9374	9	0.12103	T	0.63	.	17.8542	0.88758	0.0:0.6872:0.3128:0.0	.	482;511;852;829	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	Q	852;829;482;439	ENSP00000442736:E852Q;ENSP00000355378:E829Q;ENSP00000445569:E482Q;ENSP00000441919:E439Q	ENSP00000355378:E829Q	E	+	1	0	PLXNB3	152690272	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.736000	0.26130	-0.636000	0.05524	-0.347000	0.07816	GAG	.		0.692	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			C	153037078	G	C	153037078	3	2	13	1	0	0	0	0	1	0	0	0	12151	1175	41	4	2653	4	PLXNB3	23	153037078	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	29825219	153037078	2233482	145	1134											
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153037467	153037467	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctctctctaccgcacgtcggCccggtgaggcacttggaggg	5	8	14	14	4	2	1	0	1	2	0	4	2	2	2	2	5	1	2	2	5	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:153037467C>T	ENST00000361971.5	+	15	2780	c.2666C>T	c.(2665-2667)gCc>gTc	p.A889V	PLXNB3_ENST00000538776.1_Missense_Mutation_p.A542V|PLXNB3_ENST00000538543.1_3'UTR|PLXNB3_ENST00000538282.1_Missense_Mutation_p.A499V|PLXNB3_ENST00000538966.1_Missense_Mutation_p.A912V	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	889	IPT/TIG 1.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CGCACGTCGGCCCGGTGAGGC	0.672																																					p.A912V		.											.	PLXNB3-130	0			c.C2735T						.						35	35	35					X																	153037467		2195	4292	6487	SO:0001583	missense	5365	exon16			CGTCGGCCCGGTG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"Plexins"	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.2666C>T	X.37:g.153037467C>T	ENSP00000355378:p.Ala889Val	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_001163257	0	0	0	0	0	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.809753	0.31961	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	4.96	4.96	0.65561	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.469786	0.22002	N	0.065995	T	0.60958	0.2309	N	0.10782	0.045	0.22354	N	0.999179	B;P;B;B	0.36483	0.188;0.555;0.257;0.343	B;B;B;B	0.39935	0.314;0.257;0.149;0.314	T	0.53885	-0.8375	10	0.27082	T	0.32	.	9.9877	0.41852	0.2018:0.7982:0.0:0.0	.	542;571;912;889	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	V	912;889;542;499	ENSP00000442736:A912V;ENSP00000355378:A889V;ENSP00000445569:A542V;ENSP00000441919:A499V	ENSP00000355378:A889V	A	+	2	0	PLXNB3	152690661	0.013000	0.17824	0.441000	0.26858	0.020000	0.10135	1.775000	0.38584	2.035000	0.60131	0.513000	0.50165	GCC	.		0.672	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153037467	C	T	153037467	3	4	13	1	0	0	0	0	1	0	0	0	12151	739	26	2	2838	2	PLXNB3	23	153037467	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	389	153037467	2233093	146	1135											
FBXO42	54455	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	16577319	16577320	+	Frame_Shift_Ins	INS	-	-	TATTAAA																															aggtccaaccacagaactgcINStattaaatactttccatttg																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:16577319_16577320insTATTAAA	ENST00000375592.3	-	10	2215_2216	c.1999_2000insTTTAATA	c.(1999-2001)agcfs	p.S667fs		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	667										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		CACAGAACTGCTATTAAATACT	0.475																																					p.S667_S668delinsIX		.											.	FBXO42-228	0			c.2000_2001insTTTAATA						.																																			SO:0001589	frameshift_variant	54455	exon10			.	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"F-boxes /  "other""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1993_1999dupTTTAATA	1.37:g.16577320_16577326dupTATTAAA	ENSP00000364742:p.Ser667fs	Somatic	262	0		WXS	Illumina HiSeq	Phase_I	221	35	NM_018994	0	0	0	0	0	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Nonsense_Mutation	INS	ENST00000375592.3	37	CCDS30613.1																																																																																			.		0.475	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			TATTAAA	16577320	-	TATTAAA	16577319	7	5	14	1	0	1	1	0	0	0	0	0	5770	797	28	0	157	0	FBXO42	1	16577319	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08		16577319	232673302	1	1136											
ARHGEF10L	55160	bcgsc.ca	37	chr1	17939552	17939552	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctggccgcttggggctccaGctttctccagacctgactag	5	10	11	15	1	1	2	0	1	1	1	3	2	2	2	5	3	1	3	5	3	1	3	rs76330277		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:17939552G>T	ENST00000361221.3	+	8	768		c.e8-1		ARHGEF10L_ENST00000375420.3_Intron|ARHGEF10L_ENST00000452522.1_Intron|ARHGEF10L_ENST00000375415.1_Intron|ARHGEF10L_ENST00000434513.1_Splice_Site	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like							cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		TGGGGCTCCAGCTTTCTCCAG	0.557																																					.													.	ARHGEF10L-292	0			c.610-1G>T						.						110	113	112					1																	17939552		2203	4300	6503	SO:0001630	splice_region_variant	55160	exon8			GCTCCAGCTTTCT	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.610-1G>T	1.37:g.17939552G>T		Somatic	195	0		WXS	Illumina HiSeq	Phase_1	166	6	NM_018125	0	0	0	0	0	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Splice_Site	SNP	ENST00000361221.3	37	CCDS182.1	.	.	.	.	.	.	.	.	.	.	g	19.87	3.906931	0.72868	.	.	ENSG00000074964	ENST00000361221;ENST00000434513	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8542	0.70323	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGEF10L	17812139	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.141000	0.89618	2.279000	0.76181	0.558000	0.71614	.	.		0.557	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	Intron	T	17939552	G	T	17939552	5	4	14	1	0	0	0	0	0	0	1	0	895	985	34	4	635	4	ARHGEF10L	1	17939552	Splice_Site	SNP	G	TCGA-A4-8310-01A-11D-2396-08	1362233	17939552	231311069	2	1137											
ASAP3	55616	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	23779230	23779231	+	Frame_Shift_Ins	INS	-	-	GG																															ccccttcatcagactgtccaINSgggggaaagagacaatgttg																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:23779230_23779231insGG	ENST00000336689.3	-	4	426_427	c.382_383insCC	c.(382-384)ctgfs	p.L128fs	ASAP3_ENST00000437606.2_Frame_Shift_Ins_p.L128fs	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	128					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						CAGACTGTCCAGGGGGAAAGAG	0.559																																					p.L128fs		.											.	ASAP3-155	0			c.383_384insCC						.																																			SO:0001589	frameshift_variant	55616	exon4			.	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.381_382dupCC	1.37:g.23779233_23779234dupGG	ENSP00000338769:p.Leu128fs	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	214	80	NM_001143778	0	0	0	0	0	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Frame_Shift_Ins	INS	ENST00000336689.3	37	CCDS235.1																																																																																			.		0.559	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		GG	23779231	-	GG	23779230	7	5	14	1	0	1	1	0	0	0	0	0	1013	188	7	0	2439	0	ASAP3	1	23779230	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08	5839678	23779230	225471391	3	1138											
LDLRAP1	26119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	25889193	25889193	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgcctttgagttttggcAggtgtccaaggaaggtgaga	9	11	15	6	1	0	2	0	2	0	1	2	4	1	3	2	4	0	2	2	4	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:25889193A>G	ENST00000374338.4	+	5	637	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	173	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTTTTGGCAGGTGTCCAAG	0.572																																					p.Q173R		.											.	LDLRAP1-91	0			c.A518G						.						139	124	129					1																	25889193		2203	4300	6503	SO:0001583	missense	26119	exon5			TTTGGCAGGTGTC	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.518A>G	1.37:g.25889193A>G	ENSP00000363458:p.Gln173Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	68	28	NM_015627	0	0	0	0	0	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Missense_Mutation	SNP	ENST00000374338.4	37	CCDS30639.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858315	0.71834	.	.	ENSG00000157978	ENST00000374338	T	0.64260	-0.09	5.56	5.56	0.83823	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.65101	0.2659	L	0.49350	1.555	0.58432	D	0.999998	B	0.25105	0.118	B	0.39339	0.297	T	0.63950	-0.6521	10	0.45353	T	0.12	-17.9581	14.8888	0.70590	1.0:0.0:0.0:0.0	.	173	Q5SW96	ARH_HUMAN	R	173	ENSP00000363458:Q173R	ENSP00000363458:Q173R	Q	+	2	0	LDLRAP1	25761780	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.809000	0.91944	2.117000	0.64856	0.454000	0.30748	CAG	.		0.572	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627		G	25889193	A	G	25889193	3	3	14	1	0	0	0	0	1	0	0	0	8729	188	7	3	536	3	LDLRAP1	1	25889193	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	2109963	25889193	223361428	4	1139											
GTF2B	2959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	89325567	89325567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaagctaaaaacttacctTtaaatgtcctaggaacccct	16	10	4	11	0	0	0	0	0	0	0	1	1	1	1	4	1	4	1	4	1	9	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:89325567T>C	ENST00000370500.5	-	5	651	c.533A>G	c.(532-534)aAa>aGa	p.K178R	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	178					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		AAACTTACCTTTAAATGTCCT	0.418																																					p.K178R		.											.	GTF2B-154	0			c.A533G						.						118	124	122					1																	89325567		2203	4300	6503	SO:0001583	missense	2959	exon5			TTACCTTTAAATG	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.533A>G	1.37:g.89325567T>C	ENSP00000359531:p.Lys178Arg	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	101	46	NM_001514	0	0	0	0	0	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	37	CCDS715.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308867	0.81247	.	.	ENSG00000137947	ENST00000370500;ENST00000448623;ENST00000418217	T;T;T	0.51574	0.77;0.7;0.7	5.52	5.52	0.82312	Transcription factor TFIIB, cyclin-related (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.52933	0.1765	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.50171	-0.8859	10	0.34782	T	0.22	-32.0439	15.9344	0.79691	0.0:0.0:0.0:1.0	.	178	Q00403	TF2B_HUMAN	R	178;177;173	ENSP00000359531:K178R;ENSP00000415741:K177R;ENSP00000402345:K173R	ENSP00000359531:K178R	K	-	2	0	GTF2B	89098155	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.587000	0.82613	2.214000	0.71695	0.482000	0.46254	AAA	.		0.418	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514		C	89325567	T	C	89325567	3	2	14	1	0	0	0	0	1	0	0	0	6876	1841	64	3	429	3	GTF2B	1	89325567	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	63436374	89325567	159925054	5	1140											
CCDC18	343099	hgsc.bcm.edu;broad.mit.edu	37	chr1	93680444	93680444	+	Frame_Shift_Del	DEL	C	C	-																															tgatttgaaggttaacatggCtcacagaactagtcagtttc																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:93680444delC	ENST00000343253.7	+	12	2139	c.1637delC	c.(1636-1638)gctfs	p.A546fs	CCDC18_ENST00000338949.4_Frame_Shift_Del_p.A346fs|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000401026.3_Frame_Shift_Del_p.A547fs|CCDC18_ENST00000557479.1_Frame_Shift_Del_p.A665fs			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	546										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		GTTAACATGGCTCACAGAACT	0.388																																					p.A547fs		.											.	CCDC18-138	0			c.1640delC						.						51	48	49					1																	93680444		1844	4098	5942	SO:0001589	frameshift_variant	343099	exon12			.			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1637delC	1.37:g.93680444delC	ENSP00000343377:p.Ala546fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	33	11	NM_206886	0	0	0	0	0	Q6ZU17	Frame_Shift_Del	DEL	ENST00000343253.7	37																																																																																				.		0.388	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		-	93680444	C	-	93680444	7	5	14	1	0	1	0	1	0	0	0	0	2800	797	28	0	2040	0	CCDC18	1	93680444	Frame_Shift_Del	DEL	C	TCGA-A4-8310-01A-11D-2396-08	4354877	93680444	155570177	6	1141											
TARS2	80222	hgsc.bcm.edu	37	chr1	150469382	150469382	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcactagtggcgtttatcAgggtaaggggacccaggtct	9	10	14	8	1	2	0	1	0	1	0	2	1	2	1	1	5	1	3	1	5	3	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:150469382A>T	ENST00000369064.3	+	9	1052	c.1018A>T	c.(1018-1020)Agg>Tgg	p.R340W	TARS2_ENST00000606933.1_Intron|TARS2_ENST00000369054.2_Intron|TARS2_ENST00000463555.1_Intron|TARS2_ENST00000438568.2_3'UTR	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	340					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GGCGTTTATCAGGGTAAGGGG	0.542																																					p.R340W		.											.	TARS2-91	0			c.A1018T						.						57	50	52					1																	150469382		2203	4300	6503	SO:0001583	missense	80222	exon9			TTTATCAGGGTAA	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1018A>T	1.37:g.150469382A>T	ENSP00000358060:p.Arg340Trp	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_025150	0	0	0	0	0	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	37	CCDS952.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522343	0.85600	.	.	ENSG00000143374	ENST00000369064	T	0.71934	-0.61	5.39	4.23	0.50019	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.113939	0.64402	D	0.000016	T	0.78997	0.4372	M	0.85197	2.74	0.80722	D	1	D	0.67145	0.996	D	0.64687	0.928	T	0.82760	-0.0298	10	0.87932	D	0	-1.4334	11.7094	0.51616	0.722:0.278:0.0:0.0	.	340	Q9BW92	SYTM_HUMAN	W	340	ENSP00000358060:R340W	ENSP00000358060:R340W	R	+	1	2	TARS2	148736006	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.446000	0.60014	1.012000	0.39366	0.533000	0.62120	AGG	.		0.542	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		T	150469382	A	T	150469382	3	4	14	1	0	0	0	0	1	0	0	0	15592	179	7	5	1052	5	TARS2	1	150469382	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	56788938	150469382	98781239	7	1142											
GOLPH3L	55204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150634375	150634375	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcatccagtaaaacatcAcctgttgggctgtctgactt	9	14	8	10	0	3	1	2	1	1	0	4	1	4	1	2	1	1	4	2	1	2	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:150634375A>T	ENST00000271732.3	-	4	389	c.345T>A	c.(343-345)ggT>ggA	p.G115G	GOLPH3L_ENST00000540514.1_Silent_p.G71G	NM_018178.5	NP_060648.2	Q9H4A5	GLP3L_HUMAN	golgi phosphoprotein 3-like	115					Golgi organization (GO:0007030)|positive regulation of protein secretion (GO:0050714)	Golgi membrane (GO:0000139)|trans-Golgi network membrane (GO:0032588)	phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			GTAAAACATCACCTGTTGGGC	0.383																																					p.G115G		.											.	GOLPH3L-91	0			c.T345A						.						167	160	162					1																	150634375		2203	4300	6503	SO:0001819	synonymous_variant	55204	exon4			AACATCACCTGTT	AJ296153	CCDS966.1	1q21	2008-02-05			ENSG00000143457	ENSG00000143457			24882	protein-coding gene	gene with protein product		612208					Standard	NM_018178		Approved	GPP34R	uc001evj.2	Q9H4A5	OTTHUMG00000035009	ENST00000271732.3:c.345T>A	1.37:g.150634375A>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	110	39	NM_018178	0	0	1	7	6	B1AN09|B7Z6N3|Q9NVK0	Silent	SNP	ENST00000271732.3	37	CCDS966.1																																																																																			.		0.383	GOLPH3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084734.1	NM_018178		T	150634375	A	T	150634375	2	4	14	1	0	0	0	0	0	0	0	1	6589	146	6	5		5	GOLPH3L	1	150634375	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08	164993	150634375	98616246	8	1143											
RPTN	126638	broad.mit.edu	37	chr1	152127881	152127884	+	Frame_Shift_Del	DEL	TGTC	TGTC	-																															cataatgatagctctggcctTgtctgtctgtctgaccgtag																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:152127881_152127884delTGTC	ENST00000316073.3	-	3	1755_1758	c.1691_1694delGACA	c.(1690-1695)agacaafs	p.RQ564fs		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	564	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GCTCTGGCCTTGTCTGTCTGTCTG	0.485																																					p.564_565del													.	RPTN-68	0			c.1691_1694del						.																																			SO:0001589	frameshift_variant	126638	exon3			TGGCCTTGTCTGT	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1691_1694delGACA	1.37:g.152127889_152127892delTGTC	ENSP00000317895:p.Arg564fs	Somatic	695	0		WXS	Illumina HiSeq	Phase_I	758	6	NM_001122965	0	0	0	0	0	B7ZBZ3	Frame_Shift_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																			.		0.485	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		-	152127884	TGTC	-	152127881	7	5	14	1	0	1	0	1	0	0	0	0	13696	1812	63	0	664	0	RPTN	1	152127881	Frame_Shift_Del	DEL	TGTC	TCGA-A4-8310-01A-11D-2396-08	1493506	152127881	97122740	9	1144											
DENND4B	9909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153915526	153915526	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccggggcctggaggggccAggtttgctgagtggctgtag	4	8	20	9	1	0	1	0	1	0	0	0	2	0	2	3	7	1	4	3	7	1	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:153915526A>T	ENST00000361217.4	-	3	816	c.398T>A	c.(397-399)cTg>cAg	p.L133Q		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	133	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGAGGGGCCAGGTTTGCTGA	0.637																																					p.L133Q		.											.	DENND4B-69	0			c.T398A						.						62	73	70					1																	153915526		1957	4140	6097	SO:0001583	missense	9909	exon3			GGGGCCAGGTTTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.398T>A	1.37:g.153915526A>T	ENSP00000354597:p.Leu133Gln	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	74	26	NM_014856	0	0	9	12	3	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.259272	0.80246	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.24908	1.83;1.83	4.69	4.69	0.59074	MABP domain (1);	.	.	.	.	T	0.36690	0.0976	L	0.61218	1.895	0.58432	D	0.999992	D	0.76494	0.999	D	0.68765	0.96	T	0.28004	-1.0057	9	0.87932	D	0	-3.5699	13.2559	0.60079	1.0:0.0:0.0:0.0	.	133	O75064	DEN4B_HUMAN	Q	133;144	ENSP00000354597:L133Q;ENSP00000357635:L144Q	ENSP00000354597:L133Q	L	-	2	0	DENND4B	152182150	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.891000	0.92485	1.946000	0.56461	0.460000	0.39030	CTG	.		0.637	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		T	153915526	A	T	153915526	3	4	14	1	0	0	0	0	1	0	0	0	4445	188	7	5	4196	5	DENND4B	1	153915526	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	1787645	153915526	95335095	10	1145											
FAM5C	339479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	190068039	190068039	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcaggcttgcagagcccctgGctgagcatgtagccggtgtt	6	10	14	11	1	1	2	1	1	0	1	1	2	1	2	3	3	4	6	3	3	1	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:190068039G>C	ENST00000367462.3	-	8	1641	c.1410C>G	c.(1408-1410)agC>agG	p.S470R	BRINP3_ENST00000534846.1_Missense_Mutation_p.S368R	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	470					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											AGAGCCCCTGGCTGAGCATGT	0.577																																					p.S470R		.											.	FAM5C-228	0			c.C1410G						.						100	101	101					1																	190068039		2203	4300	6503	SO:0001583	missense	339479	exon8			CCCCTGGCTGAGC	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"family with sequence similarity 5, member C"	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1410C>G	1.37:g.190068039G>C	ENSP00000356432:p.Ser470Arg	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	170	40	NM_199051	0	0	0	0	0	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	9.011	0.982421	0.18889	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.42131	0.98;0.98	5.75	3.56	0.40772	Epidermal growth factor-like (1);	0.146558	0.64402	D	0.000008	T	0.35219	0.0924	L	0.53249	1.67	0.45883	D	0.998734	P;P	0.43701	0.815;0.718	B;B	0.39258	0.295;0.154	T	0.12218	-1.0556	10	0.25751	T	0.34	-10.9852	11.0596	0.47940	0.177:0.0:0.823:0.0	.	368;470	B7Z260;Q76B58	.;FAM5C_HUMAN	R	470;368	ENSP00000356432:S470R;ENSP00000438022:S368R	ENSP00000356432:S470R	S	-	3	2	FAM5C	188334662	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	1.416000	0.34759	1.440000	0.47531	-0.229000	0.12294	AGC	.		0.577	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		C	190068039	G	C	190068039	3	2	14	1	0	0	0	0	1	0	0	0	5613	1194	42	4	894	4	FAM5C	1	190068039	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	36152513	190068039	59182582	11	1146											
PCNXL2	80003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	233190130	233190130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcaatcgccagagctgtagTtgccccaacgtccaagaact	12	7	9	13	2	0	2	0	0	0	2	2	2	1	2	4	0	5	4	4	0	5	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:233190130T>C	ENST00000258229.9	-	25	4469	c.4235A>G	c.(4234-4236)aAc>aGc	p.N1412S	PCNXL2_ENST00000344698.2_Missense_Mutation_p.N64S	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1412						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				AGAGCTGTAGTTGCCCCAACG	0.438																																					p.N1412S		.											.	PCNXL2-91	0			c.A4235G						.						67	65	66					1																	233190130		1887	4122	6009	SO:0001583	missense	80003	exon25			CTGTAGTTGCCCC	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4235A>G	1.37:g.233190130T>C	ENSP00000258229:p.Asn1412Ser	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	43	19	NM_014801	0	0	3	3	0	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.437330	0.62955	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.24151	1.87;3.01	4.97	2.65	0.31530	.	0.042018	0.85682	D	0.000000	T	0.23846	0.0577	L	0.42487	1.325	0.80722	D	1	B;P	0.52692	0.434;0.955	B;P	0.45449	0.263;0.481	T	0.02705	-1.1121	10	0.87932	D	0	.	8.878	0.35356	0.0:0.154:0.0:0.846	.	1412;64	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	S	64;1412	ENSP00000340759:N64S;ENSP00000258229:N1412S	ENSP00000258229:N1412S	N	-	2	0	PCNXL2	231256753	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.826000	0.62715	0.862000	0.35528	0.533000	0.62120	AAC	.		0.438	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		C	233190130	T	C	233190130	3	2	14	1	0	0	0	0	1	0	0	0	11618	1725	60	3	2218	3	PCNXL2	1	233190130	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	43122091	233190130	16060491	12	1147											
TEKT4	150483	ucsc.edu;bcgsc.ca	37	chr2	95540716	95540716	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaggagctggaggacgcgcgGtacaagctgcatcaccacct	10	5	14	12	3	1	0	1	0	0	0	1	4	1	3	2	4	4	4	2	4	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:95540716G>A	ENST00000295201.4	+	4	1046	c.909G>A	c.(907-909)cgG>cgA	p.R303R	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	303					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						AGGACGCGCGGTACAAGCTGC	0.662																																					p.R303R													.	TEKT4-155	0			c.G909A						.						26	33	31					2																	95540716		2197	4299	6496	SO:0001819	synonymous_variant	150483	exon4			CGCGCGGTACAAG	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.909G>A	2.37:g.95540716G>A		Somatic	40	0		WXS	Illumina HiSeq		20	4	NM_144705	0	0	0	0	0		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			.		0.662	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		A	95540716	G	A	95540716	2	1	14	1	0	0	0	0	0	0	0	1	15787	1248	44	2		2	TEKT4	2	95540716	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08		95540716	147658657	13	1148											
NCKAP5	344148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	133721438	133721438	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctctcttcctctgacagcTtttcctgaagcaagaaagaa	11	13	6	11	0	3	4	0	2	3	2	6	4	5	4	2	0	2	2	2	0	4	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:133721438T>G	ENST00000409261.1	-	8	807	c.434A>C	c.(433-435)aAg>aCg	p.K145T	NCKAP5_ENST00000409213.1_Missense_Mutation_p.K145T|NCKAP5_ENST00000405974.3_Missense_Mutation_p.K145T|NCKAP5_ENST00000317721.6_Missense_Mutation_p.K145T	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	145										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						CTCTGACAGCTTTTCCTGAAG	0.428																																					p.K145T		.											.	.	0			c.A434C						.						142	136	138					2																	133721438		1861	4093	5954	SO:0001583	missense	344148	exon8			GACAGCTTTTCCT	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.434A>C	2.37:g.133721438T>G	ENSP00000387128:p.Lys145Thr	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	105	38	NM_207481	0	0	0	0	0	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.913961	0.33815	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834	T;T;T;T	0.48522	2.8;0.81;2.8;0.81	5.0	-0.271	0.12922	.	.	.	.	.	T	0.25717	0.0626	N	0.14661	0.345	0.09310	N	1	B;B;B	0.24823	0.0;0.001;0.112	B;B;B	0.24394	0.002;0.003;0.053	T	0.17440	-1.0369	9	0.38643	T	0.18	.	4.4156	0.11454	0.0:0.1923:0.3253:0.4823	.	120;145;145	O14513-3;O14513-2;O14513	.;.;NCKP5_HUMAN	T	145;145;145;145;145;120	ENSP00000387128:K145T;ENSP00000386952:K145T;ENSP00000380603:K145T;ENSP00000385692:K145T	ENSP00000380603:K145T	K	-	2	0	NCKAP5	133437908	0.968000	0.33430	0.029000	0.17559	0.554000	0.35429	1.269000	0.33074	-0.107000	0.12088	-0.321000	0.08615	AAG	.		0.428	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		G	133721438	T	G	133721438	3	3	14	1	0	0	0	0	1	0	0	0	10249	1609	56	5	5347	5	NCKAP5	2	133721438	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	38180722	133721438	109477935	14	1149											
ACMSD	130013	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	135659397	135659398	+	Frame_Shift_Ins	INS	-	-	T																															aagccggcaatgccctggcaINStttttgggtcttgagagaaa																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:135659397_135659398insT	ENST00000356140.5	+	10	1114_1115	c.978_979insT	c.(979-981)tttfs	p.F327fs	AC016725.4_ENST00000428857.1_RNA|AC016725.4_ENST00000413962.1_RNA|AC016725.4_ENST00000537615.1_RNA|ACMSD_ENST00000392928.1_Frame_Shift_Ins_p.F269fs|AC016725.4_ENST00000392929.2_RNA|ACMSD_ENST00000283054.4_Frame_Shift_Ins_p.F269fs	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	327					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		ATGCCCTGGCATTTTTGGGTCT	0.297																																					p.A326fs		.											.	ACMSD-91	0			c.978_979insT						.																																			SO:0001589	frameshift_variant	130013	exon10			.	AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.983dupT	2.37:g.135659402_135659402dupT	ENSP00000348459:p.Phe327fs	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	42	18	NM_138326	0	0	0	0	0	Q3B7X3|Q53SR5|Q96KY2	Frame_Shift_Ins	INS	ENST00000356140.5	37	CCDS2173.2																																																																																			.		0.297	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			T	135659398	-	T	135659397	7	5	14	1	0	1	1	0	0	0	0	0	144	204	8	0	1016	0	ACMSD	2	135659397	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08	1937959	135659397	107539976	15	1150											
ACVR2A	92	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	148677893	148677893	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatttgaggctggcaagtctGcaggcgatacccatggacag	11	8	13	9	1	1	1	0	1	1	0	1	3	1	2	1	4	2	3	1	4	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:148677893G>A	ENST00000241416.7	+	8	1693	c.1057G>A	c.(1057-1059)Gca>Aca	p.A353T	ACVR2A_ENST00000535787.1_Missense_Mutation_p.A245T|ACVR2A_ENST00000404590.1_Missense_Mutation_p.A353T	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	353	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGGCAAGTCTGCAGGCGATAC	0.383																																					p.A353T		.											.	ACVR2A-831	0			c.G1057A						.						87	89	89					2																	148677893		2203	4300	6503	SO:0001583	missense	92	exon8			AAGTCTGCAGGCG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1057G>A	2.37:g.148677893G>A	ENSP00000241416:p.Ala353Thr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	94	34	NM_001616	0	0	1	4	3	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	37	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039512	0.55003	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.65732	-0.17;-0.17;-0.17	5.42	5.42	0.78866	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.38188	0.1031	N	0.02345	-0.59	0.80722	D	1	B	0.11235	0.004	B	0.13407	0.009	T	0.26849	-1.0091	10	0.34782	T	0.22	.	15.113	0.72375	0.0:0.1411:0.8589:0.0	.	353	P27037	AVR2A_HUMAN	T	353;245;353	ENSP00000241416:A353T;ENSP00000439988:A245T;ENSP00000384338:A353T	ENSP00000241416:A353T	A	+	1	0	ACVR2A	148394363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.587000	0.67510	2.699000	0.92147	0.655000	0.94253	GCA	.		0.383	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		A	148677893	G	A	148677893	3	1	14	1	0	0	0	0	1	0	0	0	223	1319	46	2	1087	2	ACVR2A	2	148677893	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	13018496	148677893	94521480	16	1151											
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	152482148	152482148	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcccaggcttctgtgtatAagcgctgtgaaggataaaaa	12	11	11	7	1	1	1	0	1	1	0	2	2	2	2	1	2	1	3	1	2	6	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:152482148A>G	ENST00000172853.10	-	67	9770	c.9623T>C	c.(9622-9624)tTa>tCa	p.L3208S	NEB_ENST00000604864.1_Missense_Mutation_p.L3451S|NEB_ENST00000427231.2_Missense_Mutation_p.L3451S|NEB_ENST00000603639.1_Missense_Mutation_p.L3451S|NEB_ENST00000409198.1_Missense_Mutation_p.L3208S|NEB_ENST00000397345.3_Missense_Mutation_p.L3451S			P20929	NEBU_HUMAN	nebulin	3208					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTCTGTGTATAAGCGCTGTGA	0.358																																					p.L3451S		.											.	NEB-145	0			c.T10352C						.						74	67	69					2																	152482148		1835	4090	5925	SO:0001583	missense	4703	exon71			GTGTATAAGCGCT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.9623T>C	2.37:g.152482148A>G	ENSP00000172853:p.Leu3208Ser	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	28	10	NM_001271208	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	A	18.62	3.662545	0.67700	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	4.98	4.98	0.66077	.	0.086330	0.48286	D	0.000195	T	0.66366	0.2782	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.70285	-0.4914	10	0.72032	D	0.01	.	14.6222	0.68594	1.0:0.0:0.0:0.0	.	3208	P20929	NEBU_HUMAN	S	3208;3451;3451;3208	ENSP00000386259:L3208S;ENSP00000380505:L3451S;ENSP00000416578:L3451S;ENSP00000172853:L3208S	ENSP00000172853:L3208S	L	-	2	0	NEB	152190394	0.060000	0.20803	1.000000	0.80357	0.993000	0.82548	2.165000	0.42396	1.996000	0.58369	0.455000	0.32223	TTA	.		0.358	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152482148	A	G	152482148	3	3	14	1	0	0	0	0	1	0	0	0	10328	372	13	3	15782	3	NEB	2	152482148	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	3804255	152482148	90717225	17	1152											
SSFA2	6744	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	182778659	182778659	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctatcccttaatcatcttcAggtaaaattttctgttctaa	11	17	3	10	0	5	0	2	0	3	0	6	0	6	0	2	1	0	2	2	1	5	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:182778659A>T	ENST00000431877.2	+	10	1753	c.1574A>T	c.(1573-1575)cAg>cTg	p.Q525L	SSFA2_ENST00000409136.1_Splice_Site_p.Q34L|SSFA2_ENST00000320370.7_Splice_Site_p.Q525L|SSFA2_ENST00000409001.1_Splice_Site_p.Q525L|SSFA2_ENST00000428267.2_Splice_Site_p.Q372L	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	525						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			AATCATCTTCAGGTAAAATTT	0.318																																					p.Q525L		.											.	SSFA2-153	0			c.A1574T						.						90	83	85					2																	182778659		2203	4300	6503	SO:0001630	splice_region_variant	6744	exon10			ATCTTCAGGTAAA	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.1575+1A>T	2.37:g.182778659A>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	43	22	NM_001130445	0	0	0	0	0	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.458095	0.43634	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.15834	2.64;2.41;2.64;2.64;2.39	5.13	2.62	0.31277	.	0.553772	0.19548	N	0.111640	T	0.15565	0.0375	L	0.45581	1.43	0.58432	D	0.999999	B;B;B;B	0.19583	0.037;0.011;0.011;0.021	B;B;B;B	0.22386	0.039;0.009;0.009;0.009	T	0.05115	-1.0905	10	0.27785	T	0.31	-4.9981	10.8683	0.46869	0.7739:0.0:0.0:0.2261	.	372;525;525;525	E7END2;E9PHV5;P28290;P28290-3	.;.;SSFA2_HUMAN;.	L	525;525;525;372;34	ENSP00000388731:Q525L;ENSP00000314669:Q525L;ENSP00000387319:Q525L;ENSP00000409867:Q372L;ENSP00000386916:Q34L	ENSP00000314669:Q525L	Q	+	2	0	SSFA2	182486904	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.823000	0.69272	0.310000	0.22990	0.455000	0.32223	CAG	.		0.318	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	Missense_Mutation	T	182778659	A	T	182778659	5	4	14	1	0	0	0	0	0	0	1	0	15215	202	7	5	1612	5	SSFA2	2	182778659	Splice_Site	SNP	A	TCGA-A4-8310-01A-11D-2396-08	30296511	182778659	60420714	18	1153											
ICOS	29851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	204822592	204822592	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcagtgaacacagccaaaaAatctagactcacaggtatga	18	6	8	9	0	2	3	1	2	1	1	2	3	2	3	1	1	3	2	1	1	6	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:204822592A>C	ENST00000316386.6	+	4	639	c.572A>C	c.(571-573)aAa>aCa	p.K191T	ICOS_ENST00000435193.1_Intron	NM_012092.3	NP_036224.1	Q9Y6W8	ICOS_HUMAN	inducible T-cell co-stimulator	191					immune response (GO:0006955)|single organismal cell-cell adhesion (GO:0016337)|T cell costimulation (GO:0031295)|T cell tolerance induction (GO:0002517)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6						ACAGCCAAAAAATCTAGACTC	0.388																																					p.K191T		.											.	ICOS-90	0			c.A572C						.						86	85	86					2																	204822592		2203	4300	6503	SO:0001583	missense	29851	exon4			CCAAAAAATCTAG	AB023135	CCDS2363.1	2q33	2014-09-17			ENSG00000163600	ENSG00000163600		"CD molecules"	5351	protein-coding gene	gene with protein product	"activation-inducible lymphocyte immunomediatory molecule"	604558				9930702, 10617205	Standard	NM_012092		Approved	AILIM, CD278	uc002vam.3	Q9Y6W8	OTTHUMG00000132880	ENST00000316386.6:c.572A>C	2.37:g.204822592A>C	ENSP00000319476:p.Lys191Thr	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	86	36	NM_012092	0	0	0	0	0	Q8N6W8	Missense_Mutation	SNP	ENST00000316386.6	37	CCDS2363.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.581135	0.65992	.	.	ENSG00000163600	ENST00000316386	.	.	.	5.73	3.24	0.37175	.	0.180516	0.37577	N	0.002037	T	0.41696	0.1170	M	0.72118	2.19	0.09310	N	0.999993	B;B	0.19583	0.037;0.037	B;B	0.17433	0.018;0.018	T	0.33979	-0.9847	9	0.30078	T	0.28	-32.144	5.7144	0.17952	0.6551:0.157:0.0:0.188	.	191;191	Q53QY6;Q9Y6W8	.;ICOS_HUMAN	T	191	.	ENSP00000319476:K191T	K	+	2	0	ICOS	204530837	0.794000	0.28838	0.002000	0.10522	0.508000	0.34012	1.387000	0.34430	0.383000	0.24910	0.383000	0.25322	AAA	.		0.388	ICOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256369.1	NM_012092		C	204822592	A	C	204822592	3	2	14	1	0	0	0	0	1	0	0	0	7507	14	1	5	586	5	ICOS	2	204822592	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	22043933	204822592	38376781	19	1154											
ACADL	33	hgsc.bcm.edu	37	chr2	211068079	211068079	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgagcaactgttttgccAaaagcttttctttgtttaac	10	16	8	7	0	1	1	0	1	1	0	1	1	1	1	1	1	5	4	1	1	4	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:211068079A>C	ENST00000233710.3	-	8	1187	c.960T>G	c.(958-960)ttT>ttG	p.F320L	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	320					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		CTGTTTTGCCAAAAGCTTTTC	0.368																																					p.F320L		.											.	ACADL-90	0			c.T960G						.						111	97	102					2																	211068079		2203	4300	6503	SO:0001583	missense	33	exon8			TTTGCCAAAAGCT	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.960T>G	2.37:g.211068079A>C	ENSP00000233710:p.Phe320Leu	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_001608	0	0	12	12	0	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.372516	0.82573	.	.	ENSG00000115361	ENST00000233710	D	0.97328	-4.34	5.43	5.43	0.79202	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.98871	0.9618	H	0.97103	3.94	0.58432	D	0.999998	D	0.61697	0.99	P	0.62014	0.897	D	0.99521	1.0958	10	0.87932	D	0	.	15.4826	0.75539	1.0:0.0:0.0:0.0	.	320	P28330	ACADL_HUMAN	L	320	ENSP00000233710:F320L	ENSP00000233710:F320L	F	-	3	2	ACADL	210776324	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.209000	0.42806	2.055000	0.61198	0.332000	0.21555	TTT	.		0.368	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		C	211068079	A	C	211068079	3	2	14	1	0	0	0	0	1	0	0	0	112	127	5	5	348	5	ACADL	2	211068079	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	6245487	211068079	32131294	20	1155											
DNPEP	23549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220239739	220239739	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggggtgtcattccggaccatGagatcctagggagagcagga	10	7	16	8	1	1	2	1	1	0	2	3	6	3	4	3	5	1	1	3	5	1	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:220239739G>A	ENST00000273075.4	-	14	1465	c.1245C>T	c.(1243-1245)ctC>ctT	p.L415L	DNPEP_ENST00000490371.1_5'UTR|DNPEP_ENST00000373972.1_Silent_p.L340L|DNPEP_ENST00000523282.1_Silent_p.L423L	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	405					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCGGACCATGAGATCCTAGG	0.582																																					p.L415L		.											.	DNPEP-90	0			c.C1245T						.						54	57	56					2																	220239739		1995	4197	6192	SO:0001819	synonymous_variant	23549	exon14			GACCATGAGATCC		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.1245C>T	2.37:g.220239739G>A		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	60	23	NM_012100	0	0	0	0	0	Q9BW44|Q9NUV5	Silent	SNP	ENST00000273075.4	37	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	G	9.087	1.000674	0.19121	.	.	ENSG00000123992	ENST00000337010	.	.	.	5.38	4.5	0.54988	.	.	.	.	.	T	0.72518	0.3470	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72830	-0.4174	4	.	.	.	-23.6962	16.3965	0.83607	0.0:0.1313:0.8686:0.0	.	.	.	.	L	415	.	.	S	-	2	0	DNPEP	219947983	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.609000	0.54117	1.492000	0.48499	0.655000	0.94253	TCA	.		0.582	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100		A	220239739	G	A	220239739	2	1	14	1	0	0	0	0	0	0	0	1	4690	1277	45	2		2	DNPEP	2	220239739	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	9171660	220239739	22959634	21	1156											
GOLGB1	2804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121433805	121433805	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaaattggctaatttctttgGatttttgctggagctgatct	8	18	10	5	0	2	1	0	1	2	0	2	4	2	3	0	3	2	3	0	3	2	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr3:121433805G>A	ENST00000340645.5	-	10	1417	c.1292C>T	c.(1291-1293)tCc>tTc	p.S431F	GOLGB1_ENST00000393667.3_Missense_Mutation_p.S436F	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	431					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AATTTCTTTGGATTTTTGCTG	0.328																																					p.S436F		.											.	GOLGB1-161	0			c.C1307T						.						121	122	122					3																	121433805		2203	4300	6503	SO:0001583	missense	2804	exon10			TCTTTGGATTTTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.1292C>T	3.37:g.121433805G>A	ENSP00000341848:p.Ser431Phe	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	64	32	NM_001256486	0	0	6	11	5	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.900|8.900	0.956079|0.956079	0.18507|0.18507	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000489400|ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.|T;T;T	.|0.25414	.|2.39;2.39;1.8	4.95|4.95	2.09|2.09	0.27110|0.27110	.|.	.|0.423391	.|0.20726	.|N	.|0.086819	T|T	0.43787|0.43787	0.1263|0.1263	M|M	0.68317|0.68317	2.08|2.08	0.25739|0.25739	N|N	0.985181|0.985181	.|D;D;D;D;D	.|0.89917	.|1.0;0.999;1.0;0.999;1.0	.|D;D;D;D;D	.|0.87578	.|0.998;0.996;0.998;0.996;0.998	T|T	0.18053|0.18053	-1.0349|-1.0349	5|10	.|0.51188	.|T	.|0.08	.|.	8.2496|8.2496	0.31708|0.31708	0.0:0.3271:0.5037:0.1692|0.0:0.3271:0.5037:0.1692	.|.	.|356;395;436;436;431	.|F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.|.;.;.;.;GOGB1_HUMAN	S|F	302|431;436;395;243	.|ENSP00000341848:S431F;ENSP00000377275:S436F;ENSP00000418231:S395F	.|ENSP00000341848:S431F	P|S	-|-	1|2	0|0	GOLGB1|GOLGB1	122916495|122916495	0.949000|0.949000	0.32298|0.32298	0.256000|0.256000	0.24389|0.24389	0.478000|0.478000	0.33099|0.33099	1.453000|1.453000	0.35167|0.35167	0.231000|0.231000	0.21079|0.21079	-0.188000|-0.188000	0.12872|0.12872	CCA|TCC	.		0.328	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121433805	G	A	121433805	3	1	14	1	0	0	0	0	1	0	0	0	6585	1174	41	2	8539	2	GOLGB1	3	121433805	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		121433805	76588625	22	1157											
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128606	147128606	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatcgagcccgagcagctggCcaaccccaaaaagtcgtgca	12	4	11	14	3	0	0	0	0	0	0	2	3	0	0	4	1	5	3	4	1	3	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr3:147128606C>G	ENST00000282928.4	+	1	1436	c.707C>G	c.(706-708)gCc>gGc	p.A236G		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	236					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GAGCAGCTGGCCAACCCCAAA	0.587																																					p.A236G		.											.	ZIC1-91	0			c.C707G						.						74	69	71					3																	147128606		2203	4300	6503	SO:0001583	missense	7545	exon1			AGCTGGCCAACCC	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.707C>G	3.37:g.147128606C>G	ENSP00000282928:p.Ala236Gly	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_003412	0	0	0	0	0	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298325	0.40694	.	.	ENSG00000152977	ENST00000282928	D	0.96396	-4.0	3.86	3.86	0.44501	.	0.190591	0.44688	D	0.000432	D	0.91713	0.7380	N	0.12182	0.205	0.43000	D	0.994515	B	0.17038	0.02	B	0.32211	0.142	D	0.87772	0.2606	10	0.18276	T	0.48	.	16.1416	0.81528	0.0:1.0:0.0:0.0	.	236	Q15915	ZIC1_HUMAN	G	236	ENSP00000282928:A236G	ENSP00000282928:A236G	A	+	2	0	ZIC1	148611296	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.066000	0.50002	1.857000	0.53885	0.561000	0.74099	GCC	.		0.587	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		G	147128606	C	G	147128606	3	3	14	1	0	0	0	0	1	0	0	0	17710	739	26	4	709	4	ZIC1	3	147128606	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	25694801	147128606	50893824	23	1158											
TNIP2	79155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	2746482	2746482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgggccgtcctggaggccGccagctcctgcttcacttcg	3	8	12	18	4	1	0	1	0	0	0	4	1	3	1	6	3	2	2	6	3	0	2	rs150823075		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:2746482G>A	ENST00000315423.7	-	4	934	c.848C>T	c.(847-849)gCg>gTg	p.A283V	TNIP2_ENST00000510267.1_Missense_Mutation_p.A176V|TNIP2_ENST00000505186.1_5'UTR|TNIP2_ENST00000503235.1_Intron	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCTGGAGGCCGCCAGCTCCTG	0.607																																					p.A283V		.											.	TNIP2-90	0			c.C848T						.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	44	50	48		527,848	2.7	0.6	4	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TNIP2	NM_001161527.1,NM_024309.3	64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	176/323,283/430	2746482	1,13005	2203	4300	6503	SO:0001583	missense	79155	exon4			GAGGCCGCCAGCT	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.848C>T	4.37:g.2746482G>A	ENSP00000321203:p.Ala283Val	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	107	46	NM_024309	0	0	24	42	18		Missense_Mutation	SNP	ENST00000315423.7	37	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671911	0.29693	0.0	1.16E-4	ENSG00000168884	ENST00000510267;ENST00000315423	T;T	0.46063	0.88;0.88	5.66	2.71	0.32032	.	0.165365	0.52532	D	0.000076	T	0.24928	0.0605	L	0.35723	1.085	0.80722	D	1	P	0.35155	0.487	B	0.19666	0.026	T	0.05435	-1.0885	10	0.42905	T	0.14	-8.1276	7.0861	0.25257	0.0878:0.0:0.3927:0.5195	.	283	Q8NFZ5	TNIP2_HUMAN	V	176;283	ENSP00000427613:A176V;ENSP00000321203:A283V	ENSP00000321203:A283V	A	-	2	0	TNIP2	2716280	0.729000	0.28090	0.600000	0.28864	0.114000	0.19823	1.029000	0.30140	0.754000	0.32968	0.555000	0.69702	GCG	G|1.000;A|0.000		0.607	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		A	2746482	G	A	2746482	3	1	14	1	0	0	0	0	1	0	0	0	16347	1087	38	1	453	1	TNIP2	4	2746482	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		2746482	188407794	24	1159											
DCUN1D4	23142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr4	52765463	52765463	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaacagaaaaactcagaaaTactttggattacttaagatc	19	10	5	7	0	1	3	1	0	0	3	2	4	1	4	0	1	4	0	0	1	7	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:52765463T>C	ENST00000334635.5	+	8	714	c.534T>C	c.(532-534)aaT>aaC	p.N178N	DCUN1D4_ENST00000381437.4_Silent_p.N118N|DCUN1D4_ENST00000451288.2_Silent_p.N222N|DCUN1D4_ENST00000381441.3_Silent_p.N178N	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4	178	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					nucleus (GO:0005634)				endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			AACTCAGAAATACTTTGGATT	0.299																																					p.N178N		.											.	DCUN1D4-92	0			c.T534C						.						39	41	41					4																	52765463		2201	4297	6498	SO:0001819	synonymous_variant	23142	exon8			CAGAAATACTTTG	D87466	CCDS3487.2, CCDS33982.1, CCDS75123.1	4q11	2013-06-10	2013-06-10		ENSG00000109184	ENSG00000109184			28998	protein-coding gene	gene with protein product		612977	"DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"			15988528	Standard	XM_005265731		Approved	KIAA0276	uc003gze.3	Q92564	OTTHUMG00000128700	ENST00000334635.5:c.534T>C	4.37:g.52765463T>C		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	25	10	NM_015115	0	0	3	4	1	B4DH25|Q7Z3F3|Q7Z6B8	Silent	SNP	ENST00000334635.5	37	CCDS33982.1																																																																																			.		0.299	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	NM_015115		C	52765463	T	C	52765463	2	2	14	1	0	0	0	0	0	0	0	1	4322	1403	49	3		3	DCUN1D4	4	52765463	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	50018981	52765463	138388813	25	1160											
PDE5A	8654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	120446828	120446828	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcagtaattttaagggtcTgggcagatggcaccacagca	12	9	12	8	0	2	1	1	0	1	1	2	1	2	1	1	3	1	4	1	3	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:120446828T>A	ENST00000354960.3	-	12	1974	c.1655A>T	c.(1654-1656)cAg>cTg	p.Q552L	RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000512739.1_5'UTR|PDE5A_ENST00000264805.5_Missense_Mutation_p.Q510L|PDE5A_ENST00000394439.1_Missense_Mutation_p.Q500L	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	552					blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TTTAAGGGTCTGGGCAGATGG	0.413																																					p.Q552L		.											.	PDE5A-90	0			c.A1655T						.						105	101	103					4																	120446828		2203	4300	6503	SO:0001583	missense	8654	exon12			AGGGTCTGGGCAG	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1655A>T	4.37:g.120446828T>A	ENSP00000347046:p.Gln552Leu	Somatic	61	1		WXS	Illumina HiSeq	Phase_I	104	41	NM_001083	0	0	0	0	0	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	T	19.29	3.799045	0.70567	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	T;T;T	0.49720	0.77;0.77;0.77	5.06	5.06	0.68205	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.114545	0.64402	D	0.000012	T	0.36880	0.0983	L	0.31065	0.9	0.80722	D	1	B;B	0.16396	0.017;0.015	B;B	0.15870	0.014;0.011	T	0.12477	-1.0546	10	0.28530	T	0.3	.	14.82	0.70065	0.0:0.0:0.0:1.0	.	552;510	O76074;O76074-2	PDE5A_HUMAN;.	L	552;500;510	ENSP00000347046:Q552L;ENSP00000377957:Q500L;ENSP00000264805:Q510L	ENSP00000264805:Q510L	Q	-	2	0	PDE5A	120666276	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.906000	0.55180	0.533000	0.62120	CAG	.		0.413	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		A	120446828	T	A	120446828	3	1	14	1	0	0	0	0	1	0	0	0	11670	1580	55	5	1012	5	PDE5A	4	120446828	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	67681365	120446828	70707448	26	1161											
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141590820	141590820	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactcctcgggagaccgccGccgatacatggtcatcaggg	9	6	13	13	4	2	1	2	0	0	1	4	4	3	1	4	3	2	0	4	3	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:141590820G>T	ENST00000442267.2	-	8	1479	c.1405C>A	c.(1405-1407)Cgg>Agg	p.R469R		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	469							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GGAGACCGCCGCCGATACATG	0.493																																					p.R469R		.											.	TBC1D9-23	0			c.C1405A						.						49	55	53					4																	141590820		2044	4169	6213	SO:0001819	synonymous_variant	23158	exon8			ACCGCCGCCGATA	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1405C>A	4.37:g.141590820G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_015130	0	0	11	11	0	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			.		0.493	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		T	141590820	G	T	141590820	2	4	14	1	0	0	0	0	0	0	0	1	15659	1086	38	4		4	TBC1D9	4	141590820	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	21143992	141590820	49563456	27	1162											
HMGB2	3148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	174254247	174254247	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttaggagcattggggtccTttttcttccccttcttatca	5	19	7	10	0	3	0	1	0	2	0	5	1	5	1	3	3	1	1	3	3	2	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:174254247T>C	ENST00000296503.5	-	3	1142	c.269A>G	c.(268-270)aAg>aGg	p.K90R	HMGB2_ENST00000438704.2_Missense_Mutation_p.K90R|HMGB2_ENST00000446922.2_Missense_Mutation_p.K90R			P26583	HMGB2_HUMAN	high mobility group box 2	90					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cell chemotaxis (GO:0060326)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to lipopolysaccharide (GO:0071222)|chromatin organization (GO:0006325)|DNA ligation involved in DNA repair (GO:0051103)|DNA topological change (GO:0006265)|male gonad development (GO:0008584)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive chemotaxis (GO:0050918)|positive regulation of DNA binding (GO:0043388)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of nuclease activity (GO:0032075)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to steroid hormone (GO:0048545)|spermatid nucleus differentiation (GO:0007289)|V(D)J recombination (GO:0033151)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	chemoattractant activity (GO:0042056)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription regulatory region DNA binding (GO:0044212)	p.K90R(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		ATTGGGGTCCTTTTTCTTCCC	0.398																																					p.K90R		.											.	HMGB2-650	1	Substitution - Missense(1)	endometrium(1)	c.A269G						.						222	233	229					4																	174254247		2203	4300	6503	SO:0001583	missense	3148	exon2			GGGTCCTTTTTCT		CCDS3816.1	4q31	2011-07-01	2011-04-05	2002-08-16	ENSG00000164104	ENSG00000164104		"High-mobility group / Canonical"	5000	protein-coding gene	gene with protein product		163906	"high-mobility group (nonhistone chromosomal) protein 2", "high-mobility group box 2"	HMG2		1754403	Standard	NM_002129		Approved		uc011ckc.1	P26583	OTTHUMG00000160799	ENST00000296503.5:c.269A>G	4.37:g.174254247T>C	ENSP00000296503:p.Lys90Arg	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	276	104	NM_001130689	0	0	41	65	24	B2R4K8|D3DP37|Q5U072	Missense_Mutation	SNP	ENST00000296503.5	37	CCDS3816.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.451760	0.43531	.	.	ENSG00000164104	ENST00000296503;ENST00000446922;ENST00000438704;ENST00000506267	D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49	5.06	5.06	0.68205	High mobility group, superfamily (1);	0.000000	0.64402	D	0.000001	D	0.96883	0.8982	M	0.81802	2.56	0.58432	D	0.99999	P	0.48350	0.909	D	0.65987	0.94	D	0.96930	0.9680	10	0.51188	T	0.08	.	14.1447	0.65344	0.0:0.0:0.0:1.0	.	90	P26583	HMGB2_HUMAN	R	90	ENSP00000296503:K90R;ENSP00000393448:K90R;ENSP00000404912:K90R;ENSP00000423001:K90R	ENSP00000296503:K90R	K	-	2	0	HMGB2	174490822	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	7.626000	0.83164	2.122000	0.65172	0.460000	0.39030	AAG	.		0.398	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		C	174254247	T	C	174254247	3	2	14	1	0	0	0	0	1	0	0	0	7247	1609	56	3	372	3	HMGB2	4	174254247	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	32663427	174254247	16900029	28	1163											
SNX25	83891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	186188140	186188140	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tagtcttgaagccggtagtgGagttactgagtaatccagat	11	12	12	6	1	1	3	0	2	1	1	2	4	2	4	2	2	2	3	2	2	5	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:186188140G>A	ENST00000504273.1	+	5	724	c.430G>A	c.(430-432)Gag>Aag	p.E144K	SNX25_ENST00000264694.8_Missense_Mutation_p.E144K			Q9H3E2	SNX25_HUMAN	sorting nexin 25	144	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.E144Q(1)		NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		GCCGGTAGTGGAGTTACTGAG	0.423																																					p.E144K		.											.	SNX25-273	1	Substitution - Missense(1)	lung(1)	c.G430A						.						78	72	74					4																	186188140		2203	4300	6503	SO:0001583	missense	83891	exon5			GTAGTGGAGTTAC	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"Sorting nexins"	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.430G>A	4.37:g.186188140G>A	ENSP00000426255:p.Glu144Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	95	39	NM_031953	0	0	1	3	2	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860679	0.51482	.	.	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.10192	2.9;2.9	5.16	4.32	0.51571	Phox-associated domain (2);	0.188926	0.44688	D	0.000437	T	0.14227	0.0344	L	0.53249	1.67	0.42561	D	0.993145	P	0.35493	0.505	B	0.38803	0.282	T	0.04140	-1.0974	10	0.36615	T	0.2	-5.5611	13.8858	0.63708	0.0734:0.0:0.9266:0.0	.	144	Q9H3E2	SNX25_HUMAN	K	144	ENSP00000426255:E144K;ENSP00000264694:E144K	ENSP00000264694:E144K	E	+	1	0	SNX25	186425134	1.000000	0.71417	0.427000	0.26684	0.993000	0.82548	7.437000	0.80417	1.402000	0.46780	0.591000	0.81541	GAG	.		0.423	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		A	186188140	G	A	186188140	3	1	14	1	0	0	0	0	1	0	0	0	14928	1175	41	2	444	2	SNX25	4	186188140	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	11933893	186188140	4966136	29	1164											
CLPTM1L	81037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1323010	1323010	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accgttgacgaagctgttgaTtaaccaggagtaccagctga	12	9	11	9	2	0	3	0	3	0	0	0	5	0	4	3	1	4	5	3	1	3	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:1323010T>C	ENST00000320895.5	-	13	1554	c.1297A>G	c.(1297-1299)Atc>Gtc	p.I433V	CLPTM1L_ENST00000507807.1_Missense_Mutation_p.I264V|CLPTM1L_ENST00000506641.1_5'UTR|CLPTM1L_ENST00000320927.6_Missense_Mutation_p.I397V	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	433					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)		AAGCTGTTGATTAACCAGGAG	0.388																																					p.I433V		.											.	CLPTM1L-153	0			c.A1297G						.						152	150	151					5																	1323010		2203	4300	6503	SO:0001583	missense	81037	exon13			TGTTGATTAACCA	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.1297A>G	5.37:g.1323010T>C	ENSP00000313854:p.Ile433Val	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	143	42	NM_030782	0	0	18	34	16	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	37	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.947015	0.34377	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.51817	0.69;0.8;0.78	4.58	3.39	0.38822	.	0.047837	0.85682	D	0.000000	T	0.32556	0.0833	N	0.26042	0.785	0.54753	D	0.999983	B;B	0.06786	0.001;0.001	B;B	0.14023	0.005;0.01	T	0.07009	-1.0795	10	0.35671	T	0.21	-39.5635	9.5543	0.39328	0.0:0.087:0.0:0.913	.	433;264	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	V	433;264;397	ENSP00000313854:I433V;ENSP00000423321:I264V;ENSP00000315196:I397V	ENSP00000313854:I433V	I	-	1	0	CLPTM1L	1376010	1.000000	0.71417	0.825000	0.32803	0.932000	0.56968	4.256000	0.58810	0.694000	0.31654	0.402000	0.26972	ATC	.		0.388	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782		C	1323010	T	C	1323010	3	2	14	1	0	0	0	0	1	0	0	0	3561	1493	52	3	339	3	CLPTM1L	5	1323010	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		1323010	179592250	30	1165											
ADAMTS16	170690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	5240027	5240027	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaccaaccaacgagacaCtgattgtggaggtaaagtcc	13	7	11	10	1	0	2	0	1	0	1	1	5	1	4	3	3	2	1	3	3	4	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:5240027C>G	ENST00000274181.7	+	16	2650	c.2512C>G	c.(2512-2514)Ctg>Gtg	p.L838V		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	838	Spacer.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						CAACGAGACACTGATTGTGGA	0.478																																					p.L838V		.											.	ADAMTS16-275	0			c.C2512G						.						86	83	84					5																	5240027		1878	4117	5995	SO:0001583	missense	170690	exon16			GAGACACTGATTG	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2512C>G	5.37:g.5240027C>G	ENSP00000274181:p.Leu838Val	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	135	15	NM_139056	0	0	0	0	0	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.325582	0.41197	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.61742	0.08	5.56	3.45	0.39498	ADAM-TS Spacer 1 (1);	0.000000	0.64402	D	0.000013	T	0.70325	0.3211	M	0.62266	1.93	0.48452	D	0.999658	D;D	0.89917	1.0;0.991	D;D	0.87578	0.998;0.919	T	0.69450	-0.5142	10	0.36615	T	0.2	.	12.5248	0.56079	0.0:0.8343:0.0:0.1657	.	838;838	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	V	838	ENSP00000274181:L838V	ENSP00000274181:L838V	L	+	1	2	ADAMTS16	5293027	0.864000	0.29904	0.134000	0.22075	0.299000	0.27559	1.676000	0.37565	1.352000	0.45808	0.655000	0.94253	CTG	.		0.478	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		G	5240027	C	G	5240027	3	3	14	1	0	0	0	0	1	0	0	0	261	564	20	4	2574	4	ADAMTS16	5	5240027	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	3917017	5240027	175675233	31	1166											
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	32059458	32059458	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccaagatggagagcaacCtgaggtttgttgtttgcctg	8	12	14	7	0	0	3	0	1	0	2	0	4	0	3	3	3	3	4	3	3	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:32059458C>A	ENST00000438447.1	+	13	2702	c.2314C>A	c.(2314-2316)Ctg>Atg	p.L772M	PDZD2_ENST00000282493.3_Missense_Mutation_p.L772M			O15018	PDZD2_HUMAN	PDZ domain containing 2	772	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGAGAGCAACCTGAGGTTTGT	0.448																																					p.L772M		.											.	PDZD2-563	0			c.C2314A						.						102	88	93					5																	32059458		2203	4300	6503	SO:0001583	missense	23037	exon12			AGCAACCTGAGGT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.2314C>A	5.37:g.32059458C>A	ENSP00000402033:p.Leu772Met	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	53	20	NM_178140	0	0	0	0	0	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930044	0.73327	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.50001	0.76;0.76	5.79	3.98	0.46160	PDZ/DHR/GLGF (4);	0.000000	0.36268	N	0.002696	T	0.71896	0.3394	M	0.91249	3.19	0.40854	D	0.983775	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77292	-0.2642	10	0.72032	D	0.01	.	10.7091	0.45973	0.0:0.8633:0.0:0.1367	.	598;772	B4E3P2;O15018	.;PDZD2_HUMAN	M	772;591;772	ENSP00000402033:L772M;ENSP00000282493:L772M	ENSP00000282493:L772M	L	+	1	2	PDZD2	32095215	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	2.741000	0.47426	2.726000	0.93360	0.655000	0.94253	CTG	.		0.448	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32059458	C	A	32059458	3	1	14	1	0	0	0	0	1	0	0	0	11727	680	24	4	2360	4	PDZD2	5	32059458	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	26819431	32059458	148855802	32	1167											
C5orf42	65250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	37181023	37181023	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agttccacctggagttgctaCtgcaactgaaccgccagcat	10	9	9	13	1	0	1	0	1	0	0	1	2	1	2	4	1	6	5	4	1	3	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:37181023C>T	ENST00000508244.1	-	26	5599	c.5506G>A	c.(5506-5508)Gta>Ata	p.V1836I	C5orf42_ENST00000425232.2_Missense_Mutation_p.V1836I|C5orf42_ENST00000274258.7_Missense_Mutation_p.V717I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1836						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GGAGTTGCTACTGCAACTGAA	0.403																																					p.V1836I		.											.	C5orf42-94	0			c.G5506A						.						72	67	69					5																	37181023		2203	4300	6503	SO:0001583	missense	65250	exon27			TTGCTACTGCAAC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5506G>A	5.37:g.37181023C>T	ENSP00000421690:p.Val1836Ile	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	65	24	NM_023073	0	0	0	0	0	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	12.91	2.078569	0.36662	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.20200	2.09;2.09;2.09;2.09	5.91	1.94	0.25998	.	2.430320	0.01888	N	0.038363	T	0.19604	0.0471	L	0.40543	1.245	0.09310	N	1	P;B	0.34724	0.465;0.386	B;B	0.31101	0.124;0.124	T	0.29119	-1.0022	10	0.26408	T	0.33	.	9.6655	0.39981	0.0:0.5185:0.4071:0.0744	.	1836;717	E9PH94;Q9H799	.;CE042_HUMAN	I	1836;1836;717;884;717	ENSP00000421690:V1836I;ENSP00000389014:V1836I;ENSP00000274258:V717I;ENSP00000424223:V884I	ENSP00000274258:V717I	V	-	1	0	C5orf42	37216780	0.021000	0.18746	0.000000	0.03702	0.019000	0.09904	0.036000	0.13819	0.067000	0.16545	0.655000	0.94253	GTA	.		0.403	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37181023	C	T	37181023	3	4	14	1	0	0	0	0	1	0	0	0	2307	565	20	2	4191	2	C5orf42	5	37181023	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	5121565	37181023	143734237	33	1168											
DAB2	1601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	39390645	39390645	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatcacgggcaatgaaagaAatcttatttactggatgttc	14	12	8	7	1	2	2	1	1	1	1	3	3	2	3	0	2	1	2	0	2	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:39390645A>G	ENST00000320816.6	-	5	830	c.363T>C	c.(361-363)atT>atC	p.I121I	DAB2_ENST00000509337.1_Silent_p.I121I|DAB2_ENST00000545653.1_Silent_p.I121I|DAB2_ENST00000339788.6_Silent_p.I121I|DAB2_ENST00000512525.1_5'UTR	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	121	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			CAATGAAAGAAATCTTATTTA	0.398																																					p.I121I		.											.	DAB2-227	0			c.T363C						.						74	78	76					5																	39390645		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon5			GAAAGAAATCTTA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.363T>C	5.37:g.39390645A>G		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	78	34	NM_001343	0	0	32	52	20	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	CCDS34149.1																																																																																			.		0.398	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		G	39390645	A	G	39390645	2	3	14	1	0	0	0	0	0	0	0	1	4224	10	1	3		3	DAB2	5	39390645	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08	2209622	39390645	141524615	34	1169											
DAB2	1601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	39394411	39394411	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggttgcacttgtttctacTtcgttagacatggcaagaag	9	15	10	7	1	1	2	0	0	1	2	2	2	1	2	0	2	2	5	0	2	4	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:39394411T>C	ENST00000320816.6	-	2	479	c.12A>G	c.(10-12)gaA>gaG	p.E4E	DAB2_ENST00000509337.1_Silent_p.E4E|DAB2_ENST00000545653.1_Silent_p.E4E|DAB2_ENST00000339788.6_Silent_p.E4E|DAB2_ENST00000512525.1_5'Flank	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	4					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TTGTTTCTACTTCGTTAGACA	0.478																																					p.E4E		.											.	DAB2-227	0			c.A12G						.						147	131	137					5																	39394411		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon2			TTCTACTTCGTTA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.12A>G	5.37:g.39394411T>C		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	81	32	NM_001343	0	0	20	46	26	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	CCDS34149.1																																																																																			.		0.478	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		C	39394411	T	C	39394411	2	2	14	1	0	0	0	0	0	0	0	1	4224	1606	56	3		3	DAB2	5	39394411	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	3766	39394411	141520849	35	1170											
PLK2	10769	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr5	57753133	57753133	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggacggcattgtataccttgCttcccttatgcacctataag	9	13	8	11	1	0	0	0	0	0	0	1	1	1	1	3	2	3	4	3	2	5	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:57753133C>T	ENST00000274289.3	-	7	1183	c.883G>A	c.(883-885)Gca>Aca	p.A295T	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	295	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GTATACCTTGCTTCCCTTATG	0.433																																					p.A295T		.											.	PLK2-409	0			c.G883A						.						79	76	77					5																	57753133		2203	4300	6503	SO:0001583	missense	10769	exon7			ACCTTGCTTCCCT		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"serum-inducible kinase"	607023	"polo-like kinase 2 (Drosophila)"				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.883G>A	5.37:g.57753133C>T	ENSP00000274289:p.Ala295Thr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	48	14	NM_006622	0	0	11	16	5	O60679|Q96CV7|Q9UE61	Missense_Mutation	SNP	ENST00000274289.3	37	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	C	35	5.479369	0.96307	.	.	ENSG00000145632	ENST00000274289;ENST00000537944;ENST00000442330	T	0.64618	-0.11	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70055	0.3180	L	0.33624	1.015	0.80722	D	1	D	0.64830	0.994	D	0.65140	0.932	T	0.69363	-0.5165	10	0.40728	T	0.16	-15.6861	18.9292	0.92558	0.0:1.0:0.0:0.0	.	295	Q9NYY3	PLK2_HUMAN	T	295;295;281	ENSP00000274289:A295T	ENSP00000274289:A295T	A	-	1	0	PLK2	57788890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.388000	0.79795	2.461000	0.83175	0.655000	0.94253	GCA	.		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		T	57753133	C	T	57753133	3	4	14	1	0	0	0	0	1	0	0	0	12122	797	28	2	1206	2	PLK2	5	57753133	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	18358722	57753133	123162127	36	1171											
GPR98	84059	hgsc.bcm.edu	37	chr5	89949707	89949707	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatggtataatcgaattctAcctggatggaaatgcaatgc	13	11	11	6	1	1	0	0	0	1	0	2	4	1	3	1	4	3	2	1	4	6	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:89949707A>G	ENST00000405460.2	+	20	4412	c.4316A>G	c.(4315-4317)tAc>tGc	p.Y1439C		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1439					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATCGAATTCTACCTGGATGGA	0.408																																					p.Y1439C		.											.	GPR98-103	0			c.A4316G						.						36	33	34					5																	89949707		1860	4083	5943	SO:0001583	missense	84059	exon20			AATTCTACCTGGA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4316A>G	5.37:g.89949707A>G	ENSP00000384582:p.Tyr1439Cys	Somatic	14	1		WXS	Illumina HiSeq	Phase_I	9	2	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392953	0.62066	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	D	0.88354	-2.37	5.38	5.38	0.77491	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.169125	0.53938	D	0.000057	D	0.93128	0.7812	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.93579	0.6911	10	0.87932	D	0	.	11.1862	0.48657	0.8624:0.0:0.0:0.1376	.	1439	Q8WXG9	GPR98_HUMAN	C	1439	ENSP00000384582:Y1439C	ENSP00000296619:Y1439C	Y	+	2	0	GPR98	89985463	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.831000	0.69330	2.044000	0.60594	0.528000	0.53228	TAC	.		0.408	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	89949707	A	G	89949707	3	3	14	1	0	0	0	0	1	0	0	0	6742	391	14	3	4394	3	GPR98	5	89949707	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	32196574	89949707	90965553	37	1172											
FBN2	2201	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	127641530	127641530	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attaccttcacaaaccaacaGcaggtcattgtaactgaatc	15	10	5	11	0	2	1	2	1	0	0	3	1	2	1	2	1	5	2	2	1	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:127641530G>C	ENST00000508053.1	-	49	6507	c.5533C>G	c.(5533-5535)Ctg>Gtg	p.L1845V	FBN2_ENST00000262464.4_Missense_Mutation_p.L1845V			P35556	FBN2_HUMAN	fibrillin 2	1845	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CAAACCAACAGCAGGTCATTG	0.363																																					p.L1845V		.											.	FBN2-146	0			c.C5533G						.						123	118	120					5																	127641530		2203	4300	6503	SO:0001583	missense	2201	exon43			CCAACAGCAGGTC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"fibrillin 5"	612570	"congenital contractural arachnodactyly"	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.5533C>G	5.37:g.127641530G>C	ENSP00000424571:p.Leu1845Val	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	122	11	NM_001999	0	0	0	0	0	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015309	0.75161	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.95554	-3.74;-3.74	5.24	5.24	0.73138	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.53938	D	0.000045	D	0.95548	0.8553	L	0.50333	1.59	0.35026	D	0.758342	D	0.55605	0.972	P	0.54346	0.749	D	0.94672	0.7857	10	0.16896	T	0.51	.	19.3745	0.94503	0.0:0.0:1.0:0.0	.	1845	P35556	FBN2_HUMAN	V	1845	ENSP00000262464:L1845V;ENSP00000424571:L1845V	ENSP00000262464:L1845V	L	-	1	2	FBN2	127669429	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.312000	0.72840	2.880000	0.98712	0.650000	0.86243	CTG	.		0.363	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		C	127641530	G	C	127641530	3	2	14	1	0	0	0	0	1	0	0	0	5722	962	34	4	3297	4	FBN2	5	127641530	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	37691823	127641530	53273730	38	1173											
RUFY1	80230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	178987050	178987050	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagtgccagatgatggaggAgcgtgccaacctgatgcaca	12	7	13	9	1	0	3	0	2	0	1	0	5	0	5	3	2	5	1	3	2	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:178987050A>G	ENST00000319449.4	+	2	347	c.335A>G	c.(334-336)gAg>gGg	p.E112G	RUFY1_ENST00000393438.2_Missense_Mutation_p.E4G|RUFY1_ENST00000377001.2_Missense_Mutation_p.E112G|RUFY1_ENST00000437570.2_Missense_Mutation_p.E4G	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	112					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATGATGGAGGAGCGTGCCAAC	0.597										HNSCC(44;0.11)																											p.E112G		.											.	RUFY1-157	0			c.A335G						.						82	59	67					5																	178987050		2203	4300	6503	SO:0001583	missense	80230	exon2			TGGAGGAGCGTGC	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"Zinc fingers, FYVE domain containing"	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.335A>G	5.37:g.178987050A>G	ENSP00000325594:p.Glu112Gly	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	32	17	NM_025158	0	0	2	3	1	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	ENST00000319449.4	37	CCDS4445.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.405080|5.405080	0.96051|0.96051	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000319449;ENST00000377001;ENST00000437570;ENST00000393438|ENST00000502984	T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.098275|.	0.64402|.	D|.	0.000002|.	T|T	0.77082|0.77082	0.4078|0.4078	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.78663|0.78663	-0.2116|-0.2116	10|5	0.87932|.	D|.	0|.	-27.8219|-27.8219	15.7239|15.7239	0.77736|0.77736	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	112|.	Q96T51|.	RUFY1_HUMAN|.	G|G	112;112;4;4|70	ENSP00000325594:E112G;ENSP00000366200:E112G;ENSP00000390025:E4G;ENSP00000377087:E4G|.	ENSP00000325594:E112G|.	E|S	+|+	2|1	0|0	RUFY1|RUFY1	178919656|178919656	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.223000|7.223000	0.78033|0.78033	2.128000|2.128000	0.65567|0.65567	0.459000|0.459000	0.35465|0.35465	GAG|AGC	.		0.597	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		G	178987050	A	G	178987050	3	3	14	1	0	0	0	0	1	0	0	0	13770	304	11	3	341	3	RUFY1	5	178987050	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	51345520	178987050	1928210	39	1174											
KIF13A	63971	hgsc.bcm.edu	37	chr6	17771374	17771374	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcacgtttgctattgtgttCtactggcatgctgctgccat	5	16	9	11	1	2	0	1	0	1	0	2	0	2	0	1	1	5	6	1	1	2	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:17771374C>G	ENST00000259711.6	-	38	4657	c.4552G>C	c.(4552-4554)Gaa>Caa	p.E1518Q	KIF13A_ENST00000378814.5_Intron|KIF13A_ENST00000378816.5_Intron|KIF13A_ENST00000378826.2_Intron|KIF13A_ENST00000378843.2_Intron	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1518					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			CTATTGTGTTCTACTGGCATG	0.483																																					p.E1518Q		.											.	KIF13A-137	0			c.G4552C						.						158	152	154					6																	17771374		2012	4187	6199	SO:0001583	missense	63971	exon38			TGTGTTCTACTGG	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.4552G>C	6.37:g.17771374C>G	ENSP00000259711:p.Glu1518Gln	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_022113	0	0	6	6	0	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621578	0.87460	.	.	ENSG00000137177	ENST00000502297;ENST00000259711	T;T	0.73469	1.71;-0.75	6.03	6.03	0.97812	.	0.495687	0.20555	N	0.090024	T	0.48333	0.1494	N	0.24115	0.695	0.80722	D	1	P	0.35363	0.497	B	0.26202	0.067	T	0.51826	-0.8656	10	0.21540	T	0.41	.	20.1519	0.98089	0.0:1.0:0.0:0.0	.	1518	Q9H1H9	KI13A_HUMAN	Q	522;1518	ENSP00000425616:E522Q;ENSP00000259711:E1518Q	ENSP00000259711:E1518Q	E	-	1	0	KIF13A	17879353	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.911000	0.56378	2.861000	0.98227	0.655000	0.94253	GAA	.		0.483	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			G	17771374	C	G	17771374	3	3	14	1	0	0	0	0	1	0	0	0	8295	922	32	4	898	4	KIF13A	6	17771374	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08		17771374	153343693	40	1175											
DDAH2	23564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31696435	31696435	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcctcaccggtgaagagaaCgtcagtgccatccagcgtcg	10	6	12	13	4	2	2	2	1	0	1	4	3	3	2	4	1	4	0	4	1	2	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:31696435C>T	ENST00000375789.2	-	2	1015	c.385G>A	c.(385-387)Gtt>Att	p.V129I	DDAH2_ENST00000375792.3_Missense_Mutation_p.V129I|DDAH2_ENST00000480913.1_5'UTR|DDAH2_ENST00000375787.2_Missense_Mutation_p.V129I			O95865	DDAH2_HUMAN	dimethylarginine dimethylaminohydrolase 2	129					arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|negative regulation of apoptotic process (GO:0043066)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of nitric oxide biosynthetic process (GO:0045429)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	11					L-Citrulline(DB00155)	GTGAAGAGAACGTCAGTGCCA	0.572																																					p.V129I		.											.	DDAH2-90	0			c.G385A						.						71	55	61					6																	31696435		1511	2709	4220	SO:0001583	missense	23564	exon3			AGAGAACGTCAGT	AF070667	CCDS4718.1	6p21	2010-02-17			ENSG00000213722	ENSG00000213722	3.5.3.18		2716	protein-coding gene	gene with protein product		604744				10493931	Standard	XM_005248974		Approved		uc003nwq.3	O95865	OTTHUMG00000031212	ENST00000375789.2:c.385G>A	6.37:g.31696435C>T	ENSP00000364945:p.Val129Ile	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_013974	0	0	1	2	1	A2BEZ7	Missense_Mutation	SNP	ENST00000375789.2	37	CCDS4718.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.08|13.08	2.130498|2.130498	0.37630|0.37630	.|.	.|.	ENSG00000213722|ENSG00000213722	ENST00000437288|ENST00000375789;ENST00000375787;ENST00000375792;ENST00000416410;ENST00000436437	.|.	.|.	.|.	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	.|0.130895	.|0.50627	.|D	.|0.000101	T|T	0.32041|0.32041	0.0816|0.0816	L|L	0.45051|0.45051	1.395|1.395	0.40188|0.40188	D|D	0.977377|0.977377	.|B	.|0.33477	.|0.413	.|B	.|0.31290	.|0.127	T|T	0.28808|0.28808	-1.0032|-1.0032	5|9	.|0.38643	.|T	.|0.18	-22.272|-22.272	9.2267|9.2267	0.37412|0.37412	0.0:0.9044:0.0:0.0956|0.0:0.9044:0.0:0.0956	.|.	.|129	.|O95865	.|DDAH2_HUMAN	H|I	34|129	.|.	.|ENSP00000364943:V129I	R|V	-|-	2|1	0|0	DDAH2|DDAH2	31804414|31804414	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.892000|0.892000	0.51952|0.51952	3.286000|3.286000	0.51724|0.51724	2.585000|2.585000	0.87301|0.87301	0.655000|0.655000	0.94253|0.94253	CGT|GTT	.		0.572	DDAH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076432.2			T	31696435	C	T	31696435	3	4	14	1	0	0	0	0	1	0	0	0	4328	536	19	1	492	1	DDAH2	6	31696435	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	13925061	31696435	139418632	41	1176											
GSTA1	2938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	52658943	52658943	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttcaaaggcagggaagtAgcgattttttattttctctt	9	19	8	5	1	2	0	1	0	1	0	3	2	2	1	0	2	1	2	0	2	4	9			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:52658943A>G	ENST00000334575.5	-	5	549	c.394T>C	c.(394-396)Tac>Cac	p.Y132H	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	132	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	GCAGGGAAGTAGCGATTTTTT	0.433																																					p.Y132H		.											.	GSTA1-91	0			c.T394C						.						249	246	247					6																	52658943		2203	4300	6503	SO:0001583	missense	2938	exon5			GGAAGTAGCGATT		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"Glutathione S-transferases / Soluble"	4626	protein-coding gene	gene with protein product		138359	"glutathione S-transferase A1"			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.394T>C	6.37:g.52658943A>G	ENSP00000335620:p.Tyr132His	Somatic	263	0		WXS	Illumina HiSeq	Phase_I	342	114	NM_145740	0	0	1	1	0	Q14750|Q5GHF8|Q5SZC1	Missense_Mutation	SNP	ENST00000334575.5	37	CCDS4945.1	.	.	.	.	.	.	.	.	.	.	a	13.85	2.359274	0.41801	.	.	ENSG00000243955	ENST00000334575	T	0.02103	4.45	2.58	2.58	0.30949	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.157818	0.43579	D	0.000559	T	0.04679	0.0127	M	0.76727	2.345	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.12811	-1.0533	10	0.87932	D	0	.	9.4793	0.38891	1.0:0.0:0.0:0.0	.	132	P08263	GSTA1_HUMAN	H	132	ENSP00000335620:Y132H	ENSP00000335620:Y132H	Y	-	1	0	GSTA1	52766902	0.951000	0.32395	0.003000	0.11579	0.017000	0.09413	5.478000	0.66806	0.928000	0.37168	0.164000	0.16699	TAC	.		0.433	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1			G	52658943	A	G	52658943	3	3	14	1	0	0	0	0	1	0	0	0	6851	420	15	3	286	3	GSTA1	6	52658943	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	20962508	52658943	118456124	42	1177											
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73332281	73332281	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtacaacgtgctggagagaCcccgcggctgggcgttcatc	7	8	14	12	4	1	1	1	0	0	1	2	3	1	2	2	3	3	4	2	3	2	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:73332281C>G	ENST00000370398.1	+	1	473	c.364C>G	c.(364-366)Ccc>Gcc	p.P122A	KCNQ5_ENST00000414165.2_Missense_Mutation_p.P122A|KCNQ5_ENST00000370392.1_Missense_Mutation_p.P122A|KCNQ5_ENST00000355635.3_Missense_Mutation_p.P122A|KCNQ5_ENST00000342056.2_Missense_Mutation_p.P122A|KCNQ5_ENST00000403813.2_Missense_Mutation_p.P122A|KCNQ5_ENST00000355194.4_Missense_Mutation_p.P122A|KCNQ5_ENST00000402622.2_Missense_Mutation_p.P122A	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	122					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GCTGGAGAGACCCCGCGGCTG	0.662																																					p.P122A	GBM(142;1375 1859 14391 23261 44706)	.											.	KCNQ5-158	0			c.C364G						.						30	32	31					6																	73332281		2203	4300	6503	SO:0001583	missense	56479	exon1			GAGAGACCCCGCG	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.364C>G	6.37:g.73332281C>G	ENSP00000359425:p.Pro122Ala	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_001160132	0	0	0	0	0	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997483	0.54147	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000370392;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D;D	0.99511	-5.96;-5.96;-5.95;-5.91;-5.97;-5.95;-5.98;-6.05	4.58	3.69	0.42338	.	0.298816	0.24866	N	0.034965	D	0.99309	0.9758	M	0.75447	2.3	0.51233	D	0.999914	P;D;D;D;D;D	0.71674	0.825;0.998;0.974;0.984;0.989;0.982	P;D;P;D;D;P	0.74023	0.76;0.982;0.829;0.918;0.915;0.885	D	0.99023	1.0818	10	0.87932	D	0	-7.2859	14.5401	0.67987	0.0:0.8525:0.1475:0.0	.	122;122;122;122;122;122	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82;Q9NR82-4	.;.;.;.;KCNQ5_HUMAN;.	A	122	ENSP00000345055:P122A;ENSP00000347326:P122A;ENSP00000359425:P122A;ENSP00000359419:P122A;ENSP00000385501:P122A;ENSP00000347853:P122A;ENSP00000384453:P122A;ENSP00000409861:P122A	ENSP00000345055:P122A	P	+	1	0	KCNQ5	73389002	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	5.571000	0.67404	0.911000	0.36747	-0.305000	0.09177	CCC	.		0.662	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		G	73332281	C	G	73332281	3	3	14	1	0	0	0	0	1	0	0	0	8107	507	18	4	366	4	KCNQ5	6	73332281	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	20673338	73332281	97782786	43	1178											
IBTK	25998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	82904254	82904254	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcaattctgttactgggaaTaggctgtggagcagatattt	11	14	11	5	0	2	1	1	0	1	1	2	3	2	3	0	3	2	3	0	3	5	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:82904254T>G	ENST00000306270.7	-	23	3829	c.3280A>C	c.(3280-3282)Att>Ctt	p.I1094L	IBTK_ENST00000503631.1_Missense_Mutation_p.I893L|IBTK_ENST00000510291.1_Missense_Mutation_p.I1079L	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1094					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TTACTGGGAATAGGCTGTGGA	0.368																																					p.I1094L		.											.	IBTK-92	0			c.A3280C						.						92	95	94					6																	82904254		2203	4300	6503	SO:0001583	missense	25998	exon23			TGGGAATAGGCTG	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3280A>C	6.37:g.82904254T>G	ENSP00000305721:p.Ile1094Leu	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	49	21	NM_015525	0	0	18	30	12	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.873221	0.72180	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.38240	1.63;1.15;1.6	5.3	4.14	0.48551	.	0.226344	0.45126	D	0.000398	T	0.41511	0.1162	M	0.66939	2.045	0.45541	D	0.998499	P;P;D;D;P	0.69078	0.677;0.937;0.997;0.962;0.937	B;P;D;P;P	0.83275	0.243;0.506;0.996;0.701;0.506	T	0.30563	-0.9974	10	0.23302	T	0.38	-15.758	11.0232	0.47730	0.0:0.0732:0.0:0.9268	.	893;1079;45;1094;1094	E9PDR5;E7EPI0;B3KX60;Q9P2D0-2;Q9P2D0	.;.;.;.;IBTK_HUMAN	L	1094;893;1079	ENSP00000305721:I1094L;ENSP00000422762:I893L;ENSP00000426405:I1079L	ENSP00000305721:I1094L	I	-	1	0	IBTK	82960973	1.000000	0.71417	0.992000	0.48379	0.918000	0.54935	3.615000	0.54167	0.963000	0.38082	0.482000	0.46254	ATT	.		0.368	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		G	82904254	T	G	82904254	3	3	14	1	0	0	0	0	1	0	0	0	7497	1406	49	5	809	5	IBTK	6	82904254	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	9571973	82904254	88210813	44	1179											
KLHL32	114792	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	97562031	97562031	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagctggctcccatgcctGtgggaaggagccaccattgt	7	9	14	11	0	0	1	0	1	0	0	1	3	1	3	4	3	3	2	4	3	1	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:97562031G>T	ENST00000369261.4	+	7	1363	c.1000G>T	c.(1000-1002)Gtg>Ttg	p.V334L	KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000536676.1_Missense_Mutation_p.V298L|KLHL32_ENST00000539200.1_Missense_Mutation_p.V265L	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	334										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		TCCCATGCCTGTGGGAAGGAG	0.562																																					p.V334L		.											.	KLHL32-94	0			c.G1000T						.						88	84	85					6																	97562031		2203	4300	6503	SO:0001583	missense	114792	exon7			ATGCCTGTGGGAA	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"Kelch-like", "BTB/POZ domain containing"	21221	protein-coding gene	gene with protein product			"BTB and kelch domain containing 5", "KIAA1900", "kelch-like 32 (Drosophila)"	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1000G>T	6.37:g.97562031G>T	ENSP00000358265:p.Val334Leu	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	101	7	NM_052904	0	0	4	4	0	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.750577	0.49257	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.65916	-0.18;-0.18;-0.18	5.36	5.36	0.76844	Kelch-type beta propeller (1);	0.173711	0.52532	D	0.000077	T	0.48187	0.1486	M	0.64997	1.995	0.80722	D	1	B;B;B;B	0.11235	0.001;0.002;0.001;0.004	B;B;B;B	0.12156	0.001;0.003;0.004;0.007	T	0.48703	-0.9012	10	0.45353	T	0.12	.	14.5444	0.68017	0.0719:0.0:0.9281:0.0	.	265;298;334;334	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	L	334;298;265	ENSP00000358265:V334L;ENSP00000440382:V298L;ENSP00000441527:V265L	ENSP00000358265:V334L	V	+	1	0	KLHL32	97668752	1.000000	0.71417	0.982000	0.44146	0.985000	0.73830	4.839000	0.62810	2.763000	0.94921	0.655000	0.94253	GTG	.		0.562	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		T	97562031	G	T	97562031	3	4	14	1	0	0	0	0	1	0	0	0	8407	1377	48	4	1022	4	KLHL32	6	97562031	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	14657777	97562031	73553036	45	1180											
USP45	85015	hgsc.bcm.edu	37	chr6	99956502	99956502	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctggaagccacacttgAggcacaaccaaatatcagaa	16	7	7	11	0	1	2	1	1	0	1	1	3	1	3	3	2	3	1	3	2	6	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:99956502A>G	ENST00000327681.6	-	3	789	c.257T>C	c.(256-258)cTc>cCc	p.L86P	USP45_ENST00000369232.2_5'UTR|USP45_ENST00000392738.2_5'UTR|USP45_ENST00000472914.2_Missense_Mutation_p.L86P|USP45_ENST00000369231.3_Missense_Mutation_p.L86P|USP45_ENST00000500704.2_Missense_Mutation_p.L86P|USP45_ENST00000329966.6_Missense_Mutation_p.L86P|USP45_ENST00000369233.2_Missense_Mutation_p.L86P	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	86					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		GCCACACTTGAGGCACAACCA	0.368																																					p.L86P		.											.	USP45-637	0			c.T257C						.						103	102	103					6																	99956502		2203	4300	6503	SO:0001583	missense	85015	exon3			CACTTGAGGCACA	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.257T>C	6.37:g.99956502A>G	ENSP00000333376:p.Leu86Pro	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_001080481	0	0	1	1	0	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107156	0.77096	.	.	ENSG00000123552	ENST00000500704;ENST00000327681;ENST00000369233;ENST00000329966;ENST00000472914;ENST00000369231	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.35	5.35	0.76521	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.000000	0.64402	D	0.000001	D	0.84147	0.5408	H	0.97265	3.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90020	0.4127	10	0.87932	D	0	.	14.9824	0.71321	1.0:0.0:0.0:0.0	.	86;86	D6RBV3;Q70EL2	.;UBP45_HUMAN	P	86	ENSP00000424372:L86P;ENSP00000333376:L86P;ENSP00000358236:L86P;ENSP00000330540:L86P;ENSP00000423993:L86P;ENSP00000358234:L86P	ENSP00000333376:L86P	L	-	2	0	USP45	100063223	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.371000	0.90123	2.036000	0.60181	0.402000	0.26972	CTC	.		0.368	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		G	99956502	A	G	99956502	3	3	14	1	0	0	0	0	1	0	0	0	17109	304	11	3	2251	3	USP45	6	99956502	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	2394471	99956502	71158565	46	1181											
RGS17	26575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	153332802	153332802	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagaatctctgtgcattaaAgtatatatctgaagttgggc	14	13	9	5	0	2	2	0	1	2	1	3	2	2	2	0	1	1	3	0	1	8	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:153332802A>T	ENST00000367225.2	-	4	564	c.540T>A	c.(538-540)acT>acA	p.T180T	RGS17_ENST00000206262.1_Silent_p.T180T			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	180	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		TGTGCATTAAAGTATATATCT	0.353																																					p.T180T	Esophageal Squamous(78;500 1236 6775 24364 49058)	.											.	RGS17-227	0			c.T540A						.						59	60	59					6																	153332802		2203	4300	6503	SO:0001819	synonymous_variant	26575	exon5			CATTAAAGTATAT	AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"Regulators of G-protein signaling"	14088	protein-coding gene	gene with protein product		607191	"regulator of G-protein signalling 17"			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.540T>A	6.37:g.153332802A>T		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	44	10	NM_012419	0	0	0	1	1	Q5TF49|Q8TD61|Q9UJS8	Silent	SNP	ENST00000367225.2	37	CCDS5244.1																																																																																			.		0.353	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2			T	153332802	A	T	153332802	2	4	14	1	0	0	0	0	0	0	0	1	13331	59	3	5		5	RGS17	6	153332802	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08	53376300	153332802	17782265	47	1182											
PPIA	5478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44839397	44839397	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctaaagcatacgggtcctGgcatcttgtccatggcaaat	10	11	9	11	1	1	0	0	0	1	0	4	0	4	0	3	3	2	3	3	3	4	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr7:44839397G>T	ENST00000468812.1	+	4	331	c.286G>T	c.(286-288)Ggc>Tgc	p.G96C	PPIA_ENST00000355968.6_Missense_Mutation_p.G36C|PPIA_ENST00000451562.1_Missense_Mutation_p.G96C|PPIA_ENST00000489459.1_Missense_Mutation_p.G36C|PPIA_ENST00000480603.1_3'UTR	NM_021130.3	NP_066953.1	P62937	PPIA_HUMAN	peptidylprolyl isomerase A (cyclophilin A)	96	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				blood coagulation (GO:0007596)|entry into host cell (GO:0030260)|establishment of integrated proviral latency (GO:0075713)|leukocyte migration (GO:0050900)|lipid particle organization (GO:0034389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of protein secretion (GO:0050714)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of viral genome replication (GO:0045069)|RNA-dependent DNA replication (GO:0006278)|uncoating of virus (GO:0019061)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral release from host cell (GO:0019076)|virion assembly (GO:0019068)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Cyclosporine(DB00091)|L-Proline(DB00172)	TACGGGTCCTGGCATCTTGTC	0.483																																					p.G96C	Pancreas(95;605 727 734 1731 12572 23104 24406 38694 39103 44805)	.											.	PPIA-90	0			c.G286T						.						85	81	82					7																	44839397		2203	4298	6501	SO:0001583	missense	5478	exon4			GGTCCTGGCATCT	X52851	CCDS5494.1, CCDS75592.1	7p13	2010-03-23			ENSG00000196262	ENSG00000196262	5.2.1.8		9253	protein-coding gene	gene with protein product		123840				1989998, 2197089	Standard	XM_005249791		Approved	CYPA	uc003tlw.3	P62937	OTTHUMG00000023687	ENST00000468812.1:c.286G>T	7.37:g.44839397G>T	ENSP00000419425:p.Gly96Cys	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	126	23	NM_021130	1	1	1692	2445	751	A8K220|P05092|Q3KQW3|Q567Q0|Q6IBU5|Q96IX3|Q9BRU4|Q9BTY9|Q9UC61	Missense_Mutation	SNP	ENST00000468812.1	37	CCDS5494.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909500	0.92107	.	.	ENSG00000196262	ENST00000451562;ENST00000468812;ENST00000489459;ENST00000355968;ENST00000244636	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.24	5.24	0.73138	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	U	0.000000	D	0.83027	0.5165	H	0.99425	4.56	0.80722	D	1	D	0.67145	0.996	D	0.74348	0.983	D	0.90988	0.4833	10	0.87932	D	0	.	18.4613	0.90739	0.0:0.0:1.0:0.0	.	96	P62937	PPIA_HUMAN	C	96;96;36;36;36	ENSP00000405975:G96C;ENSP00000419425:G96C;ENSP00000427976:G36C;ENSP00000430817:G36C	ENSP00000442606:G36C	G	+	1	0	PPIA	44805922	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.601000	0.98297	2.449000	0.82847	0.563000	0.77884	GGC	.		0.483	PPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251293.1	NM_021130		T	44839397	G	T	44839397	3	4	14	1	0	0	0	0	1	0	0	0	12342	1348	47	4	300	4	PPIA	7	44839397	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		44839397	114299266	48	1183											
LOC441294	441294	hgsc.bcm.edu	37	chr7	143270001	143270001	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaatcttcagactcaacaagCatctttgcaatcagaaaaca	18	9	4	10	0	5	2	3	0	2	2	5	2	5	2	0	0	4	2	0	0	6	2	rs201104924	byFrequency	TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr7:143270001C>T	ENST00000420911.2	+	1	1108	c.1091C>T	c.(1090-1092)gCa>gTa	p.A364V	RNU6-162P_ENST00000516228.1_RNA	NM_001008747.1	NP_001008747.1	A4D2H0	CTGEF_HUMAN	CTAGE family, member 15	364						integral component of membrane (GO:0016021)											ACTCAACAAGCATCTTTGCAA	0.299													.|||	1090	0.217652	0.171	0.3213	5008	,	,		25006	0.1002		0.3419	False		,,,				2504	0.2004				p.A364V		.											.	.	0			c.C1091T						.						2	2	2					7																	143270001		1060	2315	3375	SO:0001583	missense	441294	exon1			AACAAGCATCTTT		CCDS64788.1	7q35	2013-02-25	2013-02-25	2013-02-25	ENSG00000176227	ENSG00000271079			37295	protein-coding gene	gene with protein product			"CTAGE family, member 15, pseudogene"	CTAGE15P			Standard	NM_001008747		Approved		uc011kth.3	A4D2H0	OTTHUMG00000153233	ENST00000420911.2:c.1091C>T	7.37:g.143270001C>T	ENSP00000474204:p.Ala364Val	Somatic	28	2		WXS	Illumina HiSeq	Phase_I	57	11	NM_001008747	0	0	18	21	3	A6H8Z8	Missense_Mutation	SNP	ENST00000420911.2	37																																																																																				C|0.500;A|0.500		0.299	CTAGE15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330280.2	NM_001008747		T	143270001	C	T	143270001	3	4	14	1	0	0	0	0	1	0	0	0	8905	710	25	2	1093	2	LOC441294	7	143270001	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	98430604	143270001	15868662	49	1184											
CUL1	8454	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	148495672	148495672	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcttgatagtaagaaatTaagggttaacatcaatgtgc	14	15	8	4	0	2	2	1	1	1	1	2	2	2	2	0	1	2	2	0	1	6	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr7:148495672T>C	ENST00000325222.4	+	20	2318	c.2039T>C	c.(2038-2040)tTa>tCa	p.L680S	CUL1_ENST00000409469.1_Missense_Mutation_p.L680S|CUL1_ENST00000602748.1_Missense_Mutation_p.L680S	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	680					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AGTAAGAAATTAAGGGTTAAC	0.383																																					p.L680S		.											.	CUL1-226	0			c.T2039C						.						122	116	118					7																	148495672		2203	4300	6503	SO:0001583	missense	8454	exon20			AGAAATTAAGGGT	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.2039T>C	7.37:g.148495672T>C	ENSP00000326804:p.Leu680Ser	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	80	47	NM_003592	0	0	0	0	0	D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	37	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	.	23.0	4.360805	0.82353	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000433865	T;T	0.74209	-0.82;-0.82	4.91	4.91	0.64330	Winged helix-turn-helix transcription repressor DNA-binding (1);Cullin homology (1);	0.156457	0.44483	D	0.000453	T	0.78220	0.4249	M	0.70903	2.155	0.80722	D	1	B;P	0.52316	0.148;0.952	B;P	0.49752	0.103;0.621	T	0.77411	-0.2598	10	0.29301	T	0.29	-6.0639	14.5579	0.68115	0.0:0.0:0.0:1.0	.	607;680	E7EWR0;Q13616	.;CUL1_HUMAN	S	680;680;607	ENSP00000387160:L680S;ENSP00000326804:L680S	ENSP00000326804:L680S	L	+	2	0	CUL1	148126605	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	7.693000	0.84214	1.844000	0.53588	0.379000	0.24179	TTA	.		0.383	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		C	148495672	T	C	148495672	3	2	14	1	0	0	0	0	1	0	0	0	4060	1764	61	3	2113	3	CUL1	7	148495672	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	5225671	148495672	10642991	50	1185											
MLL3	58508	hgsc.bcm.edu	37	chr7	151945349	151945349	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaattttctttctgttcctTttctccttgtagcctttcta	5	22	4	10	0	4	1	0	0	4	1	6	1	5	1	3	0	1	2	3	0	3	10	rs201039690		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr7:151945349T>A	ENST00000262189.6	-	14	2388	c.2170A>T	c.(2170-2172)Aag>Tag	p.K724*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.K724*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	724					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K724*(4)									TTCTGTTCCTTTTCTCCTTGT	0.398																																					p.K724X		.											.	MLL3-1398	4	Substitution - Nonsense(4)	kidney(2)|skin(2)	c.A2170T						.						70	69	69					7																	151945349		2203	4300	6503	SO:0001587	stop_gained	58508	exon14			GTTCCTTTTCTCC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2170A>T	7.37:g.151945349T>A	ENSP00000262189:p.Lys724*	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	173	13	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	37	6.120169	0.97300	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.13	-1.83	0.07833	.	0.648456	0.13994	N	0.348586	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	1.3853	0.02239	0.12:0.2536:0.2465:0.3799	.	.	.	.	X	724	.	ENSP00000262189:K724X	K	-	1	0	MLL3	151576282	0.000000	0.05858	0.029000	0.17559	0.083000	0.17756	-0.061000	0.11693	-0.613000	0.05694	-0.321000	0.08615	AAG	.		0.398	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151945349	T	A	151945349	4	1	14	1	0	0	0	0	0	1	0	0	9647	1850	64	5	12749	5	MLL3	7	151945349	Nonsense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	3449677	151945349	7193314	51	1186											
MFHAS1	9258	hgsc.bcm.edu;broad.mit.edu	37	chr8	8654999	8654999	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tctgggctgactcagcaactCccctgtaggaggagagagaa	11	7	13	10	0	2	3	1	1	1	2	3	6	3	4	2	3	2	3	2	3	3	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:8654999C>G	ENST00000276282.6	-	2	3587	c.3001G>C	c.(3001-3003)Gag>Cag	p.E1001Q	MFHAS1_ENST00000520091.1_5'UTR	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	1001		Breakpoint for translocation to form chimeric MASL1.								endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CTCAGCAACTCCCCTGTAGGA	0.552																																					p.E1001Q	Melanoma(103;1201 2045 17515 28966)	.											.	MFHAS1-90	0			c.G3001C						.						81	68	72					8																	8654999		2203	4300	6503	SO:0001583	missense	9258	exon2			GCAACTCCCCTGT	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.3001G>C	8.37:g.8654999C>G	ENSP00000276282:p.Glu1001Gln	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_004225	0	0	0	0	0	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529145	0.64860	.	.	ENSG00000147324	ENST00000276282	T	0.38401	1.14	5.73	5.73	0.89815	.	0.068346	0.56097	D	0.000026	T	0.56292	0.1975	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.43956	-0.9359	10	0.29301	T	0.29	.	18.882	0.92358	0.0:1.0:0.0:0.0	.	1001	Q9Y4C4	MFHA1_HUMAN	Q	1001	ENSP00000276282:E1001Q	ENSP00000276282:E1001Q	E	-	1	0	MFHAS1	8692409	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.251000	0.78297	2.703000	0.92315	0.551000	0.68910	GAG	.		0.552	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		G	8654999	C	G	8654999	3	3	14	1	0	0	0	0	1	0	0	0	9546	864	30	4	165	4	MFHAS1	8	8654999	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08		8654999	137709023	52	1187											
SLC7A2	6542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	17419589	17419589	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctcaccatctggaggcaGccccagaatcagcaaaaagt	13	7	9	12	0	3	1	2	0	2	1	4	2	3	2	3	2	2	3	3	2	3	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:17419589G>A	ENST00000494857.1	+	11	1859	c.1641G>A	c.(1639-1641)caG>caA	p.Q547Q	SLC7A2_ENST00000004531.10_Silent_p.Q587Q|SLC7A2_ENST00000470360.1_Silent_p.Q586Q|SLC7A2_ENST00000398090.3_Silent_p.Q586Q|SLC7A2_ENST00000522656.1_Silent_p.Q547Q	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	547			Q -> L (in dbSNP:rs1981498).		amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TCTGGAGGCAGCCCCAGAATC	0.468																																					p.Q587Q		.											.	SLC7A2-93	0			c.G1761A						.						89	79	83					8																	17419589		2203	4300	6503	SO:0001819	synonymous_variant	6542	exon10			GAGGCAGCCCCAG	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"Solute carriers"	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1641G>A	8.37:g.17419589G>A		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	67	32	NM_001164771	0	0	0	0	0	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Silent	SNP	ENST00000494857.1	37	CCDS34852.1																																																																																			.		0.468	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		A	17419589	G	A	17419589	2	1	14	1	0	0	0	0	0	0	0	1	14729	962	34	2		2	SLC7A2	8	17419589	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	8764590	17419589	128944433	53	1188											
KIAA0196	9897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	126085409	126085409	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattacctgagtctgctgtaTgaagcatcagccatcggatg	10	11	10	10	1	2	2	1	2	1	0	3	3	2	3	2	1	4	3	2	1	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:126085409T>G	ENST00000318410.7	-	9	1485	c.1136A>C	c.(1135-1137)cAt>cCt	p.H379P	KIAA0196_ENST00000517845.1_Missense_Mutation_p.H231P	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	379					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			GTCTGCTGTATGAAGCATCAG	0.448																																					p.H379P		.											.	KIAA0196-92	0			c.A1136C						.						117	101	106					8																	126085409		2203	4300	6503	SO:0001583	missense	9897	exon9			GCTGTATGAAGCA		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"strumpellin"	610657	"spastic paraplegia 8 (autosomal dominant)"	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.1136A>C	8.37:g.126085409T>G	ENSP00000318016:p.His379Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	90	39	NM_014846	0	0	0	0	0	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178175	0.78564	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.89552	-2.53;-2.53	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.95211	0.8447	M	0.87971	2.92	0.80722	D	1	D	0.67145	0.996	D	0.78314	0.991	D	0.95703	0.8751	10	0.87932	D	0	-28.8795	16.8222	0.85835	0.0:0.0:0.0:1.0	.	379	Q12768	STRUM_HUMAN	P	379;231	ENSP00000318016:H379P;ENSP00000429676:H231P	ENSP00000318016:H379P	H	-	2	0	KIAA0196	126154591	1.000000	0.71417	0.164000	0.22755	0.692000	0.40212	7.950000	0.87804	2.371000	0.80710	0.533000	0.62120	CAT	.		0.448	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		G	126085409	T	G	126085409	3	3	14	1	0	0	0	0	1	0	0	0	8182	1464	51	5	2427	5	KIAA0196	8	126085409	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	108665820	126085409	20278613	54	1189											
ADCY8	114	hgsc.bcm.edu;broad.mit.edu	37	chr8	132052526	132052526	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccggccgggggcgtcgggtgGatggtgtagagttcctcgct	3	9	19	10	5	0	1	0	0	0	1	3	2	1	2	3	6	0	3	3	6	1	2	rs529228094	byFrequency	TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:132052526G>A	ENST00000286355.5	-	1	2146	c.54C>T	c.(52-54)atC>atT	p.I18I	ADCY8_ENST00000377928.3_Silent_p.I18I	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	18					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCGTCGGGTGGATGGTGTAGA	0.697										HNSCC(32;0.087)																											p.I18I		.											.	ADCY8-157	0			c.C54T						.						5	6	5					8																	132052526		2067	4086	6153	SO:0001819	synonymous_variant	114	exon1			CGGGTGGATGGTG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.54C>T	8.37:g.132052526G>A		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	7	4	NM_001115	0	0	0	0	0		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			.		0.697	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132052526	G	A	132052526	2	1	14	1	0	0	0	0	0	0	0	1	300	1164	41	2		2	ADCY8	8	132052526	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	5967117	132052526	14311496	55	1190											
BAI1	575	hgsc.bcm.edu;broad.mit.edu	37	chr8	143623373	143623373	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgaagcggccgtctctgcccGaggaggagaagctgaagctg	9	6	16	10	3	1	3	0	2	1	1	2	6	1	4	2	3	4	2	2	3	3	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:143623373G>C	ENST00000517894.1	+	28	4672	c.3778G>C	c.(3778-3780)Gag>Cag	p.E1260Q	BAI1_ENST00000323289.5_Missense_Mutation_p.E1260Q			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1260					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GTCTCTGCCCGAGGAGGAGAA	0.682																																					p.E1260Q		.											.	BAI1-1129	0			c.G3778C						.						11	14	13					8																	143623373		2083	4183	6266	SO:0001583	missense	575	exon27			CTGCCCGAGGAGG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3778G>C	8.37:g.143623373G>C	ENSP00000430945:p.Glu1260Gln	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_001702	0	0	1	1	0		Missense_Mutation	SNP	ENST00000517894.1	37		.	.	.	.	.	.	.	.	.	.	g	15.14	2.743642	0.49151	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.28255	1.62;1.62	4.26	4.26	0.50523	.	0.341183	0.26349	U	0.024892	T	0.20414	0.0491	N	0.24115	0.695	0.20821	N	0.999846	P	0.43578	0.811	B	0.34301	0.179	T	0.16217	-1.0410	10	0.66056	D	0.02	.	15.6704	0.77270	0.0:0.0:1.0:0.0	.	1260	E9PBK0	.	Q	1260	ENSP00000430945:E1260Q;ENSP00000313046:E1260Q	ENSP00000313046:E1260Q	E	+	1	0	BAI1	143620375	1.000000	0.71417	0.807000	0.32361	0.825000	0.46686	7.460000	0.80816	1.910000	0.55303	0.586000	0.80456	GAG	.		0.682	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		C	143623373	G	C	143623373	3	2	14	1	0	0	0	0	1	0	0	0	1299	1059	37	4	3884	4	BAI1	8	143623373	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	11570847	143623373	2740649	56	1191											
CYP11B1	1584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	143957217	143957217	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgctggctgcggcggccagGctctcctggcgcagggcctg	3	7	17	14	3	1	0	0	0	1	0	2	0	1	0	3	6	2	4	3	6	0	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:143957217G>A	ENST00000292427.4	-	6	1064	c.1032C>T	c.(1030-1032)agC>agT	p.S344S	CYP11B1_ENST00000377675.3_Silent_p.S415S|CYP11B1_ENST00000517471.1_Silent_p.S344S	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	344					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CGGCGGCCAGGCTCTCCTGGC	0.652									Familial Hyperaldosteronism type I																												p.S344S		.											.	CYP11B1-94	0			c.C1032T						.						70	73	72					8																	143957217		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GGCCAGGCTCTCC	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.1032C>T	8.37:g.143957217G>A		Somatic	267	0		WXS	Illumina HiSeq	Phase_I	169	70	NM_000497	0	0	0	0	0	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			.		0.652	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			A	143957217	G	A	143957217	2	1	14	1	0	0	0	0	0	0	0	1	4151	1194	42	2		2	CYP11B1	8	143957217	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	333844	143957217	2406805	57	1192											
NFX1	4799	bcgsc.ca	37	chr9	33307212	33307212	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaggtaaagaatcctgagTggagcagaaatgaaattcca	17	7	11	6	0	0	4	0	2	0	2	2	5	2	5	2	2	1	3	2	2	6	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:33307212T>C	ENST00000379540.3	+	5	1353	c.1291T>C	c.(1291-1293)Tgg>Cgg	p.W431R	NFX1_ENST00000318524.6_Missense_Mutation_p.W431R|NFX1_ENST00000379521.4_Missense_Mutation_p.W431R	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	431					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GAATCCTGAGTGGAGCAGAAA	0.413																																					p.W431R													.	NFX1-91	0			c.T1291C						.						148	147	147					9																	33307212		2203	4300	6503	SO:0001583	missense	4799	exon5			CCTGAGTGGAGCA	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1291T>C	9.37:g.33307212T>C	ENSP00000368856:p.Trp431Arg	Somatic	117	0		WXS	Illumina HiSeq	Phase_1	141	6	NM_147134	0	0	10	10	0	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	37	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.223848	0.79576	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.12879	2.64;2.64;2.64	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.48642	1.525	0.58432	D	0.999999	D;D;P;D;B	0.76494	0.999;0.998;0.459;0.997;0.39	D;D;B;D;B	0.71414	0.973;0.926;0.218;0.966;0.176	T	0.00975	-1.1494	10	0.33940	T	0.23	-5.1452	13.5049	0.61479	0.0:0.0:0.0:1.0	.	431;315;431;431;431	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	R	431	ENSP00000368856:W431R;ENSP00000368836:W431R;ENSP00000317695:W431R	ENSP00000317695:W431R	W	+	1	0	NFX1	33297212	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.751000	0.85126	2.092000	0.63282	0.477000	0.44152	TGG	.		0.413	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			C	33307212	T	C	33307212	3	2	14	1	0	0	0	0	1	0	0	0	10413	1696	59	3	1309	3	NFX1	9	33307212	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		33307212	107906219	58	1193											
FAM75A6	389730	broad.mit.edu;bcgsc.ca	37	chr9	43626666	43626666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccctggatagattttgtgggGtctcacccagaatttgcccc	7	12	10	12	0	1	2	1	0	1	2	2	3	1	3	4	3	1	0	4	3	2	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:43626666G>A	ENST00000332857.6	-	4	2049	c.2021C>T	c.(2020-2022)aCc>aTc	p.T674I	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	674					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ATTTTGTGGGGTCTCACCCAG	0.542																																					p.T674I													.	.	0			c.C2021T						.						2	2	2					9																	43626666		473	1329	1802	SO:0001583	missense	389730	exon4			TGTGGGGTCTCAC		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A6"	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.2021C>T	9.37:g.43626666G>A	ENSP00000329825:p.Thr674Ile	Somatic	275	1		WXS	Illumina HiSeq	Phase_I	295	126	NM_001145196	0	0	0	0	0		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	G	0.406	-0.916016	0.02415	.	.	ENSG00000185775	ENST00000332857	T	0.04970	3.52	2.27	-4.54	0.03452	.	1.619430	0.03668	N	0.243514	T	0.03434	0.0099	N	0.17082	0.46	0.09310	N	1	B	0.13145	0.007	B	0.12837	0.008	T	0.38887	-0.9640	10	0.32370	T	0.25	-0.2923	0.3687	0.00376	0.392:0.1913:0.2271:0.1896	.	674	Q5VVP1	F75A6_HUMAN	I	674	ENSP00000329825:T674I	ENSP00000329825:T674I	T	-	2	0	FAM75A6	43566662	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.551000	0.23361	-1.054000	0.03214	0.383000	0.25322	ACC	.		0.542	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196		A	43626666	G	A	43626666	3	1	14	1	0	0	0	0	1	0	0	0	5641	1261	44	2	2014	2	FAM75A6	9	43626666	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	10319454	43626666	97586765	59	1194											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73255487	73255487	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactctaccggccactgttGcccgtaaataaagatctggc	11	10	8	12	2	2	1	0	0	2	1	2	1	2	1	3	2	3	2	3	2	6	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:73255487G>C	ENST00000377111.2	-	10	1678	c.1435C>G	c.(1435-1437)Caa>Gaa	p.Q479E	TRPM3_ENST00000357533.2_Missense_Mutation_p.Q481E|TRPM3_ENST00000377110.3_Missense_Mutation_p.Q479E|TRPM3_ENST00000396285.1_Missense_Mutation_p.Q326E|TRPM3_ENST00000423814.3_Missense_Mutation_p.Q506E|TRPM3_ENST00000396280.5_Missense_Mutation_p.Q326E|TRPM3_ENST00000360823.2_Missense_Mutation_p.Q351E|TRPM3_ENST00000396292.4_Missense_Mutation_p.Q351E|TRPM3_ENST00000377105.1_Missense_Mutation_p.Q326E|TRPM3_ENST00000358082.3_Missense_Mutation_p.Q351E|TRPM3_ENST00000377106.1_Missense_Mutation_p.Q351E|TRPM3_ENST00000408909.2_Missense_Mutation_p.Q326E	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	504					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						GGCCACTGTTGCCCGTAAATA	0.517											OREG0019249	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q479E		.											.	TRPM3-521	0			c.C1435G						.						73	64	67					9																	73255487		2203	4300	6503	SO:0001583	missense	80036	exon10			ACTGTTGCCCGTA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.1435C>G	9.37:g.73255487G>C	ENSP00000366315:p.Gln479Glu	Somatic	33	0	1143	WXS	Illumina HiSeq	Phase_I	32	2	NM_001007471	0	0	0	0	0	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.9|27.9	4.870372|4.870372	0.91587|0.91587	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	.|T;T;T;T;T;T;T;T;T;T;T	.|0.35605	.|1.3;1.3;1.3;1.3;1.3;1.3;1.3;1.3;1.3;1.3;1.3	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60379|0.60379	0.2264|0.2264	M|M	0.83774|0.83774	2.66|2.66	0.54753|0.54753	D|D	0.999985|0.999985	.|P;P;B;B;B;B;B;D;B	.|0.54601	.|0.478;0.876;0.36;0.392;0.401;0.413;0.392;0.967;0.03	.|B;P;B;B;B;B;B;P;B	.|0.56042	.|0.191;0.596;0.138;0.086;0.19;0.269;0.086;0.79;0.057	T|T	0.60541|0.60541	-0.7243|-0.7243	5|10	.|0.44086	.|T	.|0.13	-14.0359|-14.0359	20.1731|20.1731	0.98165|0.98165	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|504;479;479;479;481;351;326;479;326	.|Q9HCF6;Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|TRPM3_HUMAN;.;.;.;.;.;.;.;.	G|E	325|479;479;351;351;326;481;326;326;351;351;506	.|ENSP00000366315:Q479E;ENSP00000366314:Q479E;ENSP00000366310:Q351E;ENSP00000354066:Q351E;ENSP00000366309:Q326E;ENSP00000350140:Q481E;ENSP00000386127:Q326E;ENSP00000379581:Q326E;ENSP00000379587:Q351E;ENSP00000350791:Q351E;ENSP00000389542:Q506E	.|ENSP00000350140:Q481E	A|Q	-|-	2|1	0|0	TRPM3|TRPM3	72445307|72445307	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.476000|9.476000	0.97823|0.97823	2.768000|2.768000	0.95171|0.95171	0.655000|0.655000	0.94253|0.94253	GCA|CAA	.		0.517	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		C	73255487	G	C	73255487	3	2	14	1	0	0	0	0	1	0	0	0	16620	1328	46	4	3792	4	TRPM3	9	73255487	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	29628821	73255487	67957944	60	1195											
HNRNPK	3190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	86587099	86587099	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgcacgtcctttgatGggagactaaaaacagagatg	12	9	13	7	1	0	3	0	1	0	2	1	5	1	3	1	2	2	2	1	2	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:86587099G>T	ENST00000376264.2	-	11	909	c.651C>A	c.(649-651)ccC>ccA	p.P217P	RP11-575L7.8_ENST00000448389.1_RNA|HNRNPK_ENST00000360384.5_Silent_p.P217P|HNRNPK_ENST00000376263.3_Silent_p.P217P|MIR7-1_ENST00000384871.1_RNA|HNRNPK_ENST00000376281.4_Silent_p.P217P|HNRNPK_ENST00000351839.3_Silent_p.P217P	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	217	2 X 22 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|Interaction with ZIK1. {ECO:0000250}.|Necessary for interaction with DDX1.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|single-stranded DNA binding (GO:0003697)			endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						GTCCTTTGATGGGAGACTAAA	0.403																																					p.P217P		.											.	HNRNPK-227	0			c.C651A						.						48	47	48					9																	86587099		2203	4300	6503	SO:0001819	synonymous_variant	3190	exon11			TTTGATGGGAGAC		CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"transformation upregulated nuclear protein"	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.651C>A	9.37:g.86587099G>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	75	35	NM_031262	0	0	0	0	0	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Silent	SNP	ENST00000376264.2	37	CCDS6667.1																																																																																			.		0.403	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2			T	86587099	G	T	86587099	2	4	14	1	0	0	0	0	0	0	0	1	7290	1335	47	4		4	HNRNPK	9	86587099	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	13331612	86587099	54626332	61	1196											
FNBP1	23048	hgsc.bcm.edu	37	chr9	132719674	132719674	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttgtgacattgatgtcagCgtccattttctcaaagtact	9	17	7	8	1	2	2	2	2	1	0	4	2	3	2	1	0	2	1	1	0	2	6	rs200418146		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:132719674C>G	ENST00000446176.2	-	6	664	c.478G>C	c.(478-480)Gct>Cct	p.A160P	FNBP1_ENST00000355681.3_Missense_Mutation_p.A160P|FNBP1_ENST00000420781.1_Missense_Mutation_p.A160P	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	160	F-BAR domain.|Interaction with microtubules. {ECO:0000250}.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		TTGATGTCAGCGTCCATTTTC	0.483			T	MLL	AML																																p.A160P		.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	.	.	0			c.G478C						.						129	126	127					9																	132719674		2056	4206	6262	SO:0001583	missense	23048	exon6			TGTCAGCGTCCAT	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.478G>C	9.37:g.132719674C>G	ENSP00000413625:p.Ala160Pro	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_015033	0	0	2	2	0	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	37	CCDS48040.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.260778	0.80246	.	.	ENSG00000187239	ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000355681	T;T;T	0.46819	0.86;0.86;0.86	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.67487	0.2898	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.996;1.0;0.992;0.999;1.0;0.995;0.999	P;D;P;D;D;P;D	0.72625	0.833;0.978;0.802;0.963;0.978;0.903;0.96	T	0.66548	-0.5896	10	0.38643	T	0.18	-19.6827	17.3082	0.87201	0.0:1.0:0.0:0.0	.	160;160;160;160;121;160;160	B7ZL12;B7ZL13;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3	.;.;.;.;.;.;FNBP1_HUMAN	P	160	ENSP00000413625:A160P;ENSP00000407548:A160P;ENSP00000347907:A160P	ENSP00000347907:A160P	A	-	1	0	FNBP1	131759495	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	4.632000	0.61311	2.434000	0.82447	0.479000	0.44913	GCT	C|1.000;T|0.000		0.483	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2			G	132719674	C	G	132719674	3	3	14	1	0	0	0	0	1	0	0	0	5984	768	27	4	1423	4	FNBP1	9	132719674	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	46132575	132719674	8493757	62	1197											
SNAPC4	6621	hgsc.bcm.edu;broad.mit.edu	37	chr9	139272475	139272475	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gacagcaggcccaggtccagGgcccccttctcaggcccagg	7	4	13	17	0	1	0	1	0	1	0	3	1	2	0	5	5	1	1	5	5	0	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:139272475G>T	ENST00000298532.2	-	21	4172	c.3804C>A	c.(3802-3804)gcC>gcA	p.A1268A		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CCAGGTCCAGGGCCCCCTTCT	0.731																																					p.A1268A		.											.	SNAPC4-90	0			c.C3804A						.						4	5	5					9																	139272475		1776	3616	5392	SO:0001819	synonymous_variant	6621	exon21			GTCCAGGGCCCCC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.3804C>A	9.37:g.139272475G>T		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	24	8	NM_003086	0	0	1	2	1		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			.		0.731	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		T	139272475	G	T	139272475	2	4	14	1	0	0	0	0	0	0	0	1	14869	1219	43	4		4	SNAPC4	9	139272475	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	6552801	139272475	1940956	63	1198											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	17157562	17157562	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgtcatatttggatgcacActggggtccgtacgtctcag	7	12	12	10	3	2	0	2	0	1	0	5	1	3	1	1	3	2	2	1	3	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:17157562A>G	ENST00000377833.4	-	7	693	c.628T>C	c.(628-630)Tgt>Cgt	p.C210R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	210	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTGGATGCACACTGGGGTCCG	0.542																																					p.C210R		.											.	CUBN-166	0			c.T628C						.						147	123	131					10																	17157562		2203	4300	6503	SO:0001583	missense	8029	exon7			ATGCACACTGGGG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.628T>C	10.37:g.17157562A>G	ENSP00000367064:p.Cys210Arg	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	110	37	NM_001081	0	0	3	9	6	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.003508	0.54254	.	.	ENSG00000107611	ENST00000377833	D	0.91521	-2.86	5.75	5.75	0.90469	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.50627	D	0.000104	D	0.97362	0.9137	H	0.98276	4.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98939	1.0790	10	0.87932	D	0	.	15.7034	0.77558	1.0:0.0:0.0:0.0	.	210	O60494	CUBN_HUMAN	R	210	ENSP00000367064:C210R	ENSP00000367064:C210R	C	-	1	0	CUBN	17197568	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	7.574000	0.82434	2.197000	0.70478	0.533000	0.62120	TGT	.		0.542	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17157562	A	G	17157562	3	3	14	1	0	0	0	0	1	0	0	0	4057	159	6	3	10487	3	CUBN	10	17157562	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		17157562	118377185	64	1199											
COMMD3	23412	hgsc.bcm.edu	37	chr10	22605388	22605388	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaaaggcttccagatgctGgcggatccccgctccttcga	8	8	11	14	3	0	2	0	0	0	2	4	4	3	3	4	3	1	3	4	3	1	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:22605388G>A	ENST00000376836.3	+	1	486	c.42G>A	c.(40-42)ctG>ctA	p.L14L	COMMD3-BMI1_ENST00000463409.2_3'UTR|COMMD3-BMI1_ENST00000602390.1_Silent_p.L14L	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	14										kidney(2)|lung(2)|ovary(1)	5						TCCAGATGCTGGCGGATCCCC	0.647																																					p.L14L		.											.	.	0			c.G42A						.						58	36	43					10																	22605388		2072	4086	6158	SO:0001819	synonymous_variant	0	exon1			GATGCTGGCGGAT	AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 8"	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.42G>A	10.37:g.22605388G>A		Somatic	2	2		WXS	Illumina HiSeq	Phase_I	8	6	NM_001204062	0	0	17	32	15	D3DRU7|Q5T8Y9	Silent	SNP	ENST00000376836.3	37	CCDS7137.1	.	.	.	.	.	.	.	.	.	.	G	5.041	0.193236	0.09599	.	.	ENSG00000148444	ENST00000456711;ENST00000444869	.	.	.	4.8	3.89	0.44902	.	.	.	.	.	T	0.58892	0.2154	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56257	-0.8009	4	.	.	.	-21.0468	8.8553	0.35225	0.1748:0.0:0.8252:0.0	.	.	.	.	S	15;14	.	.	G	+	1	0	COMMD3	22645394	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	0.939000	0.28978	1.384000	0.46424	-0.140000	0.14226	GGC	.		0.647	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		A	22605388	G	A	22605388	2	1	14	1	0	0	0	0	0	0	0	1	3723	1335	47	2		2	COMMD3	10	22605388	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	5447826	22605388	112929359	65	1200											
MYO3A	53904	hgsc.bcm.edu	37	chr10	26459400	26459400	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaattgttgacatgaaaaaCacagcagtaacaaccattca	19	8	6	8	0	1	2	1	2	0	0	1	3	1	2	1	0	4	3	1	0	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:26459400C>A	ENST00000265944.5	+	29	3496	c.3330C>A	c.(3328-3330)aaC>aaA	p.N1110K	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1110	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ACATGAAAAACACAGCAGTAA	0.328																																					p.N1110K		.											.	MYO3A-1007	0			c.C3330A						.						70	65	66					10																	26459400		2203	4299	6502	SO:0001583	missense	53904	exon29			GAAAAACACAGCA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"Myosins / Myosin superfamily : Class III"	7601	protein-coding gene	gene with protein product		606808	"deafness, autosomal recessive 30"	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3330C>A	10.37:g.26459400C>A	ENSP00000265944:p.Asn1110Lys	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_017433	0	0	0	0	0	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	C	4.358	0.066012	0.08388	.	.	ENSG00000095777	ENST00000265944	T	0.75821	-0.97	5.03	-1.66	0.08265	.	0.221408	0.52532	D	0.000064	T	0.59582	0.2204	L	0.55481	1.735	0.09310	N	1	B	0.34264	0.446	B	0.32677	0.15	T	0.50816	-0.8783	10	0.44086	T	0.13	.	3.6725	0.08279	0.101:0.4666:0.0993:0.333	.	1110	Q8NEV4	MYO3A_HUMAN	K	1110	ENSP00000265944:N1110K	ENSP00000265944:N1110K	N	+	3	2	MYO3A	26499406	0.060000	0.20803	0.001000	0.08648	0.062000	0.15995	0.198000	0.17217	0.023000	0.15187	-0.136000	0.14681	AAC	.		0.328	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26459400	C	A	26459400	3	1	14	1	0	0	0	0	1	0	0	0	10101	477	17	4	3436	4	MYO3A	10	26459400	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	3854012	26459400	109075347	66	1201											
HECTD2	143279	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	93252242	93252243	+	Splice_Site	INS	-	-	T																															atttttcatccagattatggINStaagtatgtaatctaatttt																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:93252242_93252243insT	ENST00000298068.5	+	13	1526		c.e13+1		HECTD2_ENST00000371667.1_Splice_Site|HECTD2_ENST00000536715.1_Splice_Site|HECTD2_ENST00000446394.1_Splice_Site	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2						protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						CCAGATTATGGTAAGTATGTAA	0.312																																					.	NSCLC(12;376 469 1699 39910 41417)	.											.	HECTD2-658	0			c.1432+1->T						.																																			SO:0001630	splice_region_variant	143279	exon13			.	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"HECT domain containing 2"			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.1432+1->T	10.37:g.93252243_93252243dupT		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	38	14	NM_182765	0	0	0	0	0	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Splice_Site	INS	ENST00000298068.5	37	CCDS7414.1																																																																																			.		0.312	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		Intron	T	93252243	-	T	93252242	8	5	14	1	0	1	1	0	0	0	1	0	7061	1275	44	0	1507	0	HECTD2	10	93252242	Splice_Site	INS	-	TCGA-A4-8310-01A-11D-2396-08	66792842	93252242	42282505	67	1202											
IDE	3416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	94239044	94239044	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtacttacatacatcccaTagatggtattttggagatca	12	13	9	7	0	1	2	1	0	0	2	2	3	2	2	1	3	3	2	1	3	5	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:94239044T>C	ENST00000265986.6	-	15	1930	c.1874A>G	c.(1873-1875)tAt>tGt	p.Y625C	IDE_ENST00000371581.5_Missense_Mutation_p.Y70C|IDE_ENST00000496903.1_Intron	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	625					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	ATACATCCCATAGATGGTATT	0.408																																					p.Y625C		.											.	IDE-92	0			c.A1874G						.						172	149	157					10																	94239044		2203	4300	6503	SO:0001583	missense	3416	exon15			ATCCCATAGATGG	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1874A>G	10.37:g.94239044T>C	ENSP00000265986:p.Tyr625Cys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	140	57	NM_004969	0	0	0	0	0	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.522510	0.44866	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.40756	1.02;1.02	5.64	5.64	0.86602	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.140820	0.49305	D	0.000142	T	0.40956	0.1138	M	0.64170	1.965	0.80722	D	1	P	0.38370	0.628	B	0.33890	0.172	T	0.34601	-0.9822	10	0.38643	T	0.18	-12.9568	15.5248	0.75894	0.0:0.0:0.0:1.0	.	625	P14735	IDE_HUMAN	C	625;70	ENSP00000265986:Y625C;ENSP00000360637:Y70C	ENSP00000265986:Y625C	Y	-	2	0	IDE	94229024	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.152000	0.67230	0.533000	0.62120	TAT	.		0.408	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94239044	T	C	94239044	3	2	14	1	0	0	0	0	1	0	0	0	7514	1406	49	3	1229	3	IDE	10	94239044	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	986802	94239044	41295703	68	1203											
SLC22A8	9376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62782340	62782340	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaggttgtggttggccaTgttgaggatcgggaggccca	7	9	17	8	1	0	1	0	1	0	0	1	3	0	3	2	6	1	4	2	6	0	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:62782340T>C	ENST00000336232.2	-	2	226	c.91A>G	c.(91-93)Atg>Gtg	p.M31V	SLC22A8_ENST00000545207.1_Intron|SLC22A8_ENST00000311438.8_Missense_Mutation_p.M31V|SLC22A8_ENST00000535878.1_Intron|SLC22A8_ENST00000430500.2_Missense_Mutation_p.M31V	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	31					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGGTTGGCCATGTTGAGGATC	0.617																																					p.M31V		.											.	SLC22A8-93	0			c.A91G						.						183	179	181					11																	62782340		2201	4298	6499	SO:0001583	missense	9376	exon2			TGGCCATGTTGAG	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.91A>G	11.37:g.62782340T>C	ENSP00000337335:p.Met31Val	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	256	85	NM_001184732	0	0	0	0	0	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	37	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009360	0.35415	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000311438;ENST00000430500	T;T;T	0.53206	0.63;0.63;0.63	4.76	2.38	0.29361	.	0.446155	0.25666	N	0.029103	T	0.26484	0.0647	N	0.21282	0.65	0.24143	N	0.995726	B;B	0.18968	0.032;0.01	B;B	0.21917	0.037;0.016	T	0.23726	-1.0180	10	0.08381	T	0.77	.	6.2794	0.20999	0.153:0.0:0.1774:0.6696	.	31;31	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	V	31	ENSP00000337335:M31V;ENSP00000311463:M31V;ENSP00000398548:M31V	ENSP00000311463:M31V	M	-	1	0	SLC22A8	62538916	0.007000	0.16637	0.736000	0.30914	0.989000	0.77384	0.313000	0.19415	0.303000	0.22785	0.533000	0.62120	ATG	.		0.617	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		C	62782340	T	C	62782340	3	2	14	1	0	0	0	0	1	0	0	0	14492	1464	51	3	1577	3	SLC22A8	11	62782340	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		62782340	72224176	69	1204											
PITPNM1	9600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67263727	67263727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcgatggcctggaactTcggggccagcaggggctcga	6	6	19	10	3	0	0	0	0	0	0	2	3	0	1	2	8	2	2	2	8	1	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:67263727T>C	ENST00000534749.1	-	14	2427	c.2239A>G	c.(2239-2241)Aag>Gag	p.K747E	PITPNM1_ENST00000526450.1_5'Flank|PITPNM1_ENST00000436757.2_Missense_Mutation_p.K746E|PITPNM1_ENST00000356404.3_Missense_Mutation_p.K747E			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	747	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						GCCTGGAACTTCGGGGCCAGC	0.642																																					p.K747E	GBM(28;144 709 4607 5525)	.											.	PITPNM1-227	0			c.A2239G						.						41	42	42					11																	67263727		2200	4294	6494	SO:0001583	missense	9600	exon15			GGAACTTCGGGGC	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.2239A>G	11.37:g.67263727T>C	ENSP00000437286:p.Lys747Glu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	73	36	NM_004910	0	0	9	30	21	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	37	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.758047	0.31137	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404	T;T;T	0.39787	1.06;1.06;1.06	4.43	3.29	0.37713	DDHD (2);	0.329601	0.26757	N	0.022648	T	0.26195	0.0639	N	0.13235	0.315	0.28852	N	0.896001	P;P	0.36712	0.51;0.566	B;B	0.40702	0.228;0.338	T	0.10086	-1.0645	10	0.46703	T	0.11	-28.7945	6.0013	0.19521	0.0:0.089:0.1682:0.7428	.	746;747	O00562-2;O00562	.;PITM1_HUMAN	E	747;746;747	ENSP00000437286:K747E;ENSP00000398787:K746E;ENSP00000348772:K747E	ENSP00000348772:K747E	K	-	1	0	PITPNM1	67020303	0.737000	0.28175	1.000000	0.80357	0.378000	0.30076	0.802000	0.27069	0.837000	0.34925	-0.429000	0.05907	AAG	.		0.642	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		C	67263727	T	C	67263727	3	2	14	1	0	0	0	0	1	0	0	0	11976	1792	62	3	1535	3	PITPNM1	11	67263727	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	4481387	67263727	67742789	70	1205											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877237	82877237	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaaaaaaggataaagatgAgcacatgaagtcatccgaac	21	5	9	6	1	1	4	1	2	0	2	2	6	2	5	1	1	2	1	1	1	7	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:82877237A>G	ENST00000298281.4	+	5	1750	c.1298A>G	c.(1297-1299)gAg>gGg	p.E433G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	433	Lys-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GATAAAGATGAGCACATGAAG	0.348																																					p.E433G		.											.	PCF11-23	0			c.A1298G						.						80	77	78					11																	82877237		1876	4113	5989	SO:0001583	missense	51585	exon5			AAGATGAGCACAT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1298A>G	11.37:g.82877237A>G	ENSP00000298281:p.Glu433Gly	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_015885	0	0	3	3	0	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.881854	0.72294	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.53640	1.6;0.61;0.61	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000012	T	0.57227	0.2039	L	0.32530	0.975	0.49299	D	0.999772	D;B	0.76494	0.999;0.083	D;B	0.75484	0.986;0.077	T	0.54403	-0.8299	9	.	.	.	.	14.3816	0.66914	1.0:0.0:0.0:0.0	.	433;433	E9PQ01;O94913	.;PCF11_HUMAN	G	433	ENSP00000298281:E433G;ENSP00000434540:E433G;ENSP00000431567:E433G	.	E	+	2	0	PCF11	82554885	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.999000	0.88496	2.326000	0.78906	0.533000	0.62120	GAG	.		0.348	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877237	A	G	82877237	3	3	14	1	0	0	0	0	1	0	0	0	11599	304	11	3	1316	3	PCF11	11	82877237	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	15613510	82877237	52129279	71	1206											
ALG9	79796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	111715419	111715419	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaattcagaaatccattaAttaaatagaaataccagggt	19	11	6	5	0	1	3	1	1	0	2	2	3	2	3	2	1	1	0	2	1	8	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:111715419A>G	ENST00000531154.1	-	9	882	c.410T>C	c.(409-411)aTt>aCt	p.I137T	ALG9_ENST00000398006.2_Missense_Mutation_p.I137T|ALG9_ENST00000524880.1_3'UTR|ALG9_ENST00000527228.1_5'UTR	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	308					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		AAATCCATTAATTAAATAGAA	0.393																																					p.I308T		.											.	ALG9-91	0			c.T923C						.						91	86	88					11																	111715419		1836	4091	5927	SO:0001583	missense	79796	exon10			CCATTAATTAAAT		CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	15672	protein-coding gene	gene with protein product	"dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase", "dol-P-Man dependent alpha-1,2-mannosyltransferase"	606941	"disrupted in bipolar affective disorder 1", "asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)", "asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)", "asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000531154.1:c.410T>C	11.37:g.111715419A>G	ENSP00000435517:p.Ile137Thr	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	83	38	NM_001077690	0	0	3	6	3	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Missense_Mutation	SNP	ENST00000531154.1	37	CCDS41714.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.077619	0.55753	.	.	ENSG00000086848	ENST00000531154;ENST00000398006;ENST00000428306	T;T	0.63417	-0.04;-0.04	5.69	5.69	0.88448	.	0.149147	0.64402	D	0.000012	T	0.67878	0.2940	L	0.60455	1.87	0.51767	D	0.999935	P;B;B;P	0.41080	0.549;0.068;0.055;0.737	B;B;B;P	0.49301	0.272;0.068;0.076;0.606	T	0.63782	-0.6559	10	0.22109	T	0.4	-13.3791	15.9548	0.79880	1.0:0.0:0.0:0.0	.	137;308;541;308	B4DQI3;Q9H6U8-3;B4DYW0;Q9H6U8	.;.;.;ALG9_HUMAN	T	137;137;541	ENSP00000435517:I137T;ENSP00000381090:I137T	ENSP00000381090:I137T	I	-	2	0	ALG9	111220629	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.161000	0.77505	2.171000	0.68590	0.528000	0.53228	ATT	.		0.393	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		G	111715419	A	G	111715419	3	3	14	1	0	0	0	0	1	0	0	0	524	101	4	3	961	3	ALG9	11	111715419	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	28838182	111715419	23291097	72	1207											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2795428	2795428	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcccttgcatctggttcAtcatcaggtagctcacactt	7	13	7	14	0	5	0	4	0	1	0	5	0	5	0	2	2	3	4	2	2	1	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr12:2795428A>G	ENST00000347598.4	+	47	5921	c.5921A>G	c.(5920-5922)cAt>cGt	p.H1974R	CACNA1C_ENST00000399595.1_Missense_Mutation_p.H1934R|CACNA1C_ENST00000399603.1_Missense_Mutation_p.H1926R|CACNA1C_ENST00000399621.1_Missense_Mutation_p.H1945R|CACNA1C_ENST00000399617.1_Missense_Mutation_p.H1961R|CACNA1C_ENST00000406454.3_Missense_Mutation_p.H1997R|CACNA1C_ENST00000399606.1_Missense_Mutation_p.H1946R|CACNA1C_ENST00000399638.1_Missense_Mutation_p.H1954R|CACNA1C_ENST00000327702.7_Missense_Mutation_p.H1961R|CACNA1C_ENST00000399634.1_Missense_Mutation_p.H1997R|CACNA1C_ENST00000335762.5_Missense_Mutation_p.H1951R|CACNA1C_ENST00000399649.1_Missense_Mutation_p.H1932R|CACNA1C_ENST00000399644.1_Missense_Mutation_p.H1926R|CACNA1C_ENST00000402845.3_Missense_Mutation_p.H1945R|CACNA1C_ENST00000399629.1_Missense_Mutation_p.H1943R|CACNA1C_ENST00000399597.1_Missense_Mutation_p.H1926R|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000344100.3_Missense_Mutation_p.H1967R|CACNA1C_ENST00000399591.1_Missense_Mutation_p.H1934R|CACNA1C_ENST00000399641.1_Missense_Mutation_p.H1926R|CACNA1C_ENST00000399637.1_Missense_Mutation_p.H1945R|CACNA1C_ENST00000399601.1_Missense_Mutation_p.H1926R|CACNA1C_ENST00000399655.1_Missense_Mutation_p.H1926R	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	2009					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CATCTGGTTCATCATCAGGTA	0.567																																					p.H2009R		.											.	CACNA1C-34	0			c.A6026G						.						93	96	95					12																	2795428		1976	4136	6112	SO:0001583	missense	775	exon48			TGGTTCATCATCA	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5921A>G	12.37:g.2795428A>G	ENSP00000266376:p.His1974Arg	Somatic	172	2		WXS	Illumina HiSeq	Phase_I	215	11	NM_199460	0	0	0	1	1	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.137578	0.77775	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64;0.64	4.82	4.82	0.62117	.	0.600028	0.16837	N	0.197501	T	0.66761	0.2822	M	0.65975	2.015	0.44149	D	0.996944	P;D;D;B;D;D;D;D;D;B;D;D;D;D;D;D;D;P;D;B;D;D;D;D;D	0.71674	0.902;0.997;0.984;0.315;0.99;0.997;0.993;0.997;0.976;0.36;0.998;0.991;0.996;0.995;0.973;0.995;0.996;0.877;0.994;0.006;0.964;0.997;0.997;0.998;0.984	P;P;D;B;D;D;P;D;P;B;D;P;D;D;D;D;D;P;D;B;P;D;D;D;D	0.81914	0.63;0.85;0.964;0.109;0.983;0.995;0.879;0.995;0.792;0.069;0.995;0.84;0.99;0.995;0.921;0.967;0.99;0.533;0.983;0.012;0.786;0.995;0.995;0.969;0.964	T	0.68614	-0.5362	10	0.62326	D	0.03	.	14.527	0.67894	1.0:0.0:0.0:0.0	.	617;1967;1923;2009;1961;1945;1926;1943;1954;1926;1946;1926;1957;1974;1926;1961;1997;1934;1932;1934;1915;1945;1945;1926;1926	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	R	1951;1926;1926;1954;1926;1945;1945;1934;1926;1974;1946;1926;1967;1943;1961;1932;1945;1926;1997;1961;1997;1934;1827	ENSP00000336982:H1951R;ENSP00000382563:H1926R;ENSP00000382552:H1926R;ENSP00000382547:H1954R;ENSP00000382506:H1926R;ENSP00000382530:H1945R;ENSP00000382546:H1945R;ENSP00000382500:H1934R;ENSP00000382549:H1926R;ENSP00000266376:H1974R;ENSP00000382515:H1946R;ENSP00000382510:H1926R;ENSP00000341092:H1967R;ENSP00000382537:H1943R;ENSP00000329877:H1961R;ENSP00000382557:H1932R;ENSP00000385724:H1945R;ENSP00000382512:H1926R;ENSP00000382542:H1997R;ENSP00000382526:H1961R;ENSP00000385896:H1997R;ENSP00000382504:H1934R	ENSP00000323129:H1827R	H	+	2	0	CACNA1C	2665689	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.652000	0.91083	2.023000	0.59567	0.477000	0.44152	CAT	.		0.567	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		G	2795428	A	G	2795428	3	3	14	1	0	0	0	0	1	0	0	0	2546	217	8	3	6664	3	CACNA1C	12	2795428	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		2795428	131056467	73	1208											
NCAPD2	9918	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6638743	6638743	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtggaaaagctgtgtcagCggttccgcacatcccggtat	8	10	13	10	3	1	0	1	0	0	0	3	1	3	1	2	4	2	4	2	4	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr12:6638743C>A	ENST00000315579.5	+	28	4436	c.3637C>A	c.(3637-3639)Cgg>Agg	p.R1213R	NCAPD2_ENST00000545962.1_Silent_p.R1168R|RP5-940J5.3_ENST00000537921.1_RNA	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1213					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						GCTGTGTCAGCGGTTCCGCAC	0.602																																					p.R1213R		.											.	NCAPD2-660	0			c.C3637A						.						95	82	86					12																	6638743		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon28			TGTCAGCGGTTCC	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"chromosome condensation related SMC associated protein 1"	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.3637C>A	12.37:g.6638743C>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	114	20	NM_014865	0	0	23	32	9	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			.		0.602	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		A	6638743	C	A	6638743	2	1	14	1	0	0	0	0	0	0	0	1	10231	759	27	4		4	NCAPD2	12	6638743	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	3843315	6638743	127213152	74	1209											
OS9	10956	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	58087952	58087952	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggaacgaaagatggcggCggaaacgctgctgtccagtt	11	6	16	8	4	0	1	0	0	0	1	1	4	1	3	1	5	3	3	1	5	3	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr12:58087952C>T	ENST00000315970.7	+	1	49	c.8C>T	c.(7-9)gCg>gTg	p.A3V	OS9_ENST00000389146.6_Missense_Mutation_p.A3V|OS9_ENST00000551035.1_Missense_Mutation_p.A3V|OS9_ENST00000439210.2_Missense_Mutation_p.A3V|OS9_ENST00000389142.5_Missense_Mutation_p.A3V|OS9_ENST00000257966.8_Missense_Mutation_p.A3V|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000413095.2_Missense_Mutation_p.A3V|OS9_ENST00000435406.2_Missense_Mutation_p.A3V|OS9_ENST00000552285.1_Missense_Mutation_p.A3V	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	3					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			AAGATGGCGGCGGAAACGCTG	0.582																																					p.A3V		.											.	OS9-493	0			c.C8T						.						135	134	134					12																	58087952		2203	4300	6503	SO:0001583	missense	10956	exon1			TGGCGGCGGAAAC	AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"endoplasmic reticulum lectin 2", "erlectin 2"	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.8C>T	12.37:g.58087952C>T	ENSP00000318165:p.Ala3Val	Somatic	192	1		WXS	Illumina HiSeq	Phase_I	253	70	NM_001261423	0	0	11	15	4	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Missense_Mutation	SNP	ENST00000315970.7	37	CCDS31843.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205750	0.79127	.	.	ENSG00000135506	ENST00000552285;ENST00000315970;ENST00000547079;ENST00000439210;ENST00000389146;ENST00000413095;ENST00000551035;ENST00000257966;ENST00000435406;ENST00000550372;ENST00000389142	T;T;T;T;T;T;T;T;T;T	0.51574	1.54;1.55;0.7;1.42;1.48;1.3;1.73;1.54;1.69;1.48	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.52597	0.1744	N	0.19112	0.55	0.47949	D	0.999556	D;D;D;B;B;B;B;B	0.76494	0.998;0.999;0.995;0.002;0.004;0.001;0.002;0.003	P;D;P;B;B;B;B;B	0.64506	0.845;0.926;0.772;0.005;0.002;0.002;0.001;0.001	T	0.56475	-0.7973	10	0.62326	D	0.03	-0.3422	16.1626	0.81731	0.0:1.0:0.0:0.0	.	3;3;3;3;3;3;3;3	E7EW91;F8VUH2;B4E321;G3XA88;E9PEY5;Q9BW99;A6NLB2;Q13438	.;.;.;.;.;.;.;OS9_HUMAN	V	3	ENSP00000450010:A3V;ENSP00000318165:A3V;ENSP00000447031:A3V;ENSP00000407360:A3V;ENSP00000373798:A3V;ENSP00000413112:A3V;ENSP00000447866:A3V;ENSP00000257966:A3V;ENSP00000389632:A3V;ENSP00000373794:A3V	ENSP00000257966:A3V	A	+	2	0	OS9	56374219	0.963000	0.33076	1.000000	0.80357	0.894000	0.52154	1.435000	0.34969	2.756000	0.94617	0.563000	0.77884	GCG	.		0.582	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812		T	58087952	C	T	58087952	3	4	14	1	0	0	0	0	1	0	0	0	11298	768	27	1	10	1	OS9	12	58087952	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	51449209	58087952	75763943	75	1210											
ESD	2098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	47345616	47345616	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaggttgcaatgaagtagtAgctatgatcataaccctaga	16	10	9	6	0	1	3	1	2	0	1	1	3	1	3	1	1	3	5	1	1	8	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr13:47345616A>G	ENST00000378720.3	-	10	966	c.784T>C	c.(784-786)Tac>Cac	p.Y262H	ESD_ENST00000378697.1_Missense_Mutation_p.Y233H	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	262					formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	ATGAAGTAGTAGCTATGATCA	0.328																																					p.Y262H		.											.	ESD-91	0			c.T784C						.						152	154	153					13																	47345616		2203	4296	6499	SO:0001583	missense	2098	exon10			AGTAGTAGCTATG	M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"S-formylglutathione hydrolase"	133280	"esterase D/formylglutathione hydrolase"				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.784T>C	13.37:g.47345616A>G	ENSP00000367992:p.Tyr262His	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	83	21	NM_001984	0	0	111	208	97	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Missense_Mutation	SNP	ENST00000378720.3	37	CCDS9404.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.686182	0.88639	.	.	ENSG00000139684	ENST00000378720;ENST00000378697	T;T	0.37584	1.19;1.19	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81052	-0.1107	10	0.87932	D	0	-15.2421	16.0034	0.80327	1.0:0.0:0.0:0.0	.	262	P10768	ESTD_HUMAN	H	262;233	ENSP00000367992:Y262H;ENSP00000367969:Y233H	ENSP00000367969:Y233H	Y	-	1	0	ESD	46243617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.060000	0.93907	2.371000	0.80710	0.533000	0.62120	TAC	.		0.328	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1			G	47345616	A	G	47345616	3	3	14	1	0	0	0	0	1	0	0	0	5263	420	15	3	68	3	ESD	13	47345616	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		47345616	67824262	76	1211											
ATP7B	540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	52511445	52511445	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcccaaccaggttataaaTcagtgccaggaccaggttga	13	9	9	10	0	1	1	1	1	0	0	2	2	2	2	4	3	2	2	4	3	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr13:52511445T>G	ENST00000242839.4	-	19	4144	c.3988A>C	c.(3988-3990)Att>Ctt	p.I1330L	ATP7B_ENST00000400366.3_Missense_Mutation_p.I1219L|ATP7B_ENST00000448424.2_Missense_Mutation_p.I1252L|ATP7B_ENST00000418097.2_Missense_Mutation_p.I1265L|ATP7B_ENST00000400370.3_Missense_Mutation_p.I900L|ATP7B_ENST00000417240.2_Missense_Mutation_p.I541L|ATP7B_ENST00000344297.5_Missense_Mutation_p.I1123L	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1330					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGGTTATAAATCAGTGCCAGG	0.532									Wilson disease																												p.I1330L		.											.	ATP7B-92	0			c.A3988C						.						104	109	107					13																	52511445		2043	4195	6238	SO:0001583	missense	540	exon19	Familial Cancer Database		TATAAATCAGTGC	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3988A>C	13.37:g.52511445T>G	ENSP00000242839:p.Ile1330Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	76	33	NM_000053	0	0	6	9	3	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459608	0.63401	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.99158	-5.5;-5.5;-5.5;-2.36;-5.5;-5.5;-5.5	5.34	5.34	0.76211	HAD-like domain (1);	0.000000	0.85682	D	0.000000	D	0.98689	0.9560	L	0.42008	1.315	0.80722	D	1	D;B;D;B;D;P;D;D	0.56521	0.974;0.191;0.976;0.447;0.976;0.678;0.976;0.974	D;B;P;B;P;P;P;P	0.66716	0.946;0.145;0.741;0.285;0.741;0.646;0.741;0.677	D	0.99474	1.0946	10	0.40728	T	0.16	-22.351	15.6255	0.76851	0.0:0.0:0.0:1.0	.	1252;1282;1265;541;900;1219;1123;1330	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	L	1330;1219;1123;541;1252;900;1265	ENSP00000242839:I1330L;ENSP00000383217:I1219L;ENSP00000342559:I1123L;ENSP00000390360:I541L;ENSP00000416738:I1252L;ENSP00000383221:I900L;ENSP00000393343:I1265L	ENSP00000242839:I1330L	I	-	1	0	ATP7B	51409446	1.000000	0.71417	0.983000	0.44433	0.966000	0.64601	6.243000	0.72384	2.144000	0.66660	0.533000	0.62120	ATT	.		0.532	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		G	52511445	T	G	52511445	3	3	14	1	0	0	0	0	1	0	0	0	1192	1435	50	5	421	5	ATP7B	13	52511445	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	5165829	52511445	62658433	77	1212											
STK24	8428	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	99114124	99114125	+	Frame_Shift_Ins	INS	-	-	C																															tccagtccccagaatcactgINSccccccgaggcttggccatc																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr13:99114124_99114125insC	ENST00000376547.3	-	8	1137_1138	c.992_993insG	c.(991-993)ggcfs	p.G331fs	STK24_ENST00000397517.2_Frame_Shift_Ins_p.G319fs|STK24_ENST00000539966.1_Frame_Shift_Ins_p.G300fs	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	331					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CAGAATCACTGCCCCCCGAGGC	0.535																																					p.G331fs		.											.	STK24-979	0			c.993_994insG						.																																			SO:0001589	frameshift_variant	8428	exon8			.	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"STE20-like kinase 3", "sterile 20-like kinase 3"	604984	"serine/threonine kinase 24 (Ste20, yeast homolog)"			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.993dupG	13.37:g.99114130_99114130dupC	ENSP00000365730:p.Gly331fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	113	41	NM_003576	0	0	0	0	0	O14840|Q5JV92	Frame_Shift_Ins	INS	ENST00000376547.3	37	CCDS9488.1																																																																																			.		0.535	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576		C	99114125	-	C	99114124	7	5	14	1	0	1	1	0	0	0	0	0	15325	1306	46	0	354	0	STK24	13	99114124	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08	46602679	99114124	16055754	78	1213											
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35270380	35270380	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tataacttgcaagagtctgtTtattagcaacattgtcctcc	11	15	6	9	0	1	1	0	0	1	1	3	1	3	1	2	0	4	3	2	0	6	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr14:35270380T>G	ENST00000382422.2	-	7	1208	c.881A>C	c.(880-882)aAa>aCa	p.K294T	AL355885.1_ENST00000581314.1_RNA|BAZ1A_ENST00000360310.1_Missense_Mutation_p.K294T|BAZ1A_ENST00000358716.4_Missense_Mutation_p.K294T			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	294					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		AAGAGTCTGTTTATTAGCAAC	0.308																																					p.K294T		.											.	BAZ1A-291	0			c.A881C						.						79	78	78					14																	35270380		2203	4297	6500	SO:0001583	missense	11177	exon8			GTCTGTTTATTAG	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.881A>C	14.37:g.35270380T>G	ENSP00000371859:p.Lys294Thr	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_182648	0	0	4	4	0	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019343	0.54576	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310	T;T;T	0.61158	0.13;0.13;0.13	5.13	3.89	0.44902	.	0.581293	0.17894	N	0.158411	T	0.43433	0.1247	L	0.47716	1.5	0.51482	D	0.999924	P;P	0.47910	0.902;0.651	B;B	0.33392	0.163;0.078	T	0.51236	-0.8731	10	0.59425	D	0.04	.	9.6276	0.39761	0.0:0.0:0.1753:0.8247	.	294;294	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	T	294	ENSP00000351555:K294T;ENSP00000371859:K294T;ENSP00000353458:K294T	ENSP00000351555:K294T	K	-	2	0	BAZ1A	34340131	0.997000	0.39634	0.990000	0.47175	0.462000	0.32619	1.307000	0.33516	2.054000	0.61138	0.377000	0.23210	AAA	.		0.308	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35270380	T	G	35270380	3	3	14	1	0	0	0	0	1	0	0	0	1330	1841	64	5	3869	5	BAZ1A	14	35270380	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		35270380	72079160	79	1214											
SERPINA10	51156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	94756790	94756790	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgctcatcttcctcttcCtccttgggagcctgcactac	4	14	6	17	0	3	0	1	0	2	0	7	1	7	1	5	1	4	2	5	1	1	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr14:94756790C>T	ENST00000393096.1	-	2	606	c.141G>A	c.(139-141)gaG>gaA	p.E47E	SERPINA10_ENST00000261994.4_Silent_p.E47E|SERPINA10_ENST00000554723.1_Silent_p.E87E|SERPINA10_ENST00000554173.1_Silent_p.E47E	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	47					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	33		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CTTCCTCTTCCTCCTTGGGAG	0.622																																					p.E47E		.											.	SERPINA10-228	0			c.G141A						.						39	38	38					14																	94756790		2203	4300	6503	SO:0001819	synonymous_variant	51156	exon2			CTCTTCCTCCTTG	AF181467	CCDS9923.1	14q32.13	2014-02-18	2005-08-18		ENSG00000140093	ENSG00000140093		"Serine (or cysteine) peptidase inhibitors"	15996	protein-coding gene	gene with protein product		605271	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10"			10460162, 9689066, 24172014	Standard	NM_016186		Approved	PZI, ZPI	uc001yct.3	Q9UK55	OTTHUMG00000171345	ENST00000393096.1:c.141G>A	14.37:g.94756790C>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	33	13	NM_001100607	0	0	0	0	0	A5Z2A5|Q6UWX9|Q86U20	Silent	SNP	ENST00000393096.1	37	CCDS9923.1																																																																																			.		0.622	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		T	94756790	C	T	94756790	2	4	14	1	0	0	0	0	0	0	0	1	14119	680	24	2		2	SERPINA10	14	94756790	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	59486410	94756790	12592750	80	1215											
MYO1E	4643	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	59515313	59515313	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttgaagctgatgtttccCaggtggagaatacccgccac	9	11	10	11	1	1	3	0	2	1	1	2	4	2	3	3	2	2	2	3	2	3	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr15:59515313C>G	ENST00000288235.4	-	9	1254	c.855G>C	c.(853-855)ctG>ctC	p.L285L	MYO1E_ENST00000558814.1_5'UTR	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	285	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TGATGTTTCCCAGGTGGAGAA	0.507																																					p.L285L													.	MYO1E-514	0			c.G855C						.						110	88	96					15																	59515313		2190	4290	6480	SO:0001819	synonymous_variant	4643	exon9			GTTTCCCAGGTGG	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.855G>C	15.37:g.59515313C>G		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	59	8	NM_004998	0	0	31	37	6	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			.		0.507	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		G	59515313	C	G	59515313	2	3	14	1	0	0	0	0	0	0	0	1	10097	581	21	4		4	MYO1E	15	59515313	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08		59515313	43016079	81	1216											
RORA	6095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	60849084	60849084	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttgtacttccttatctTccttttgtgaatatggtggc	6	19	8	8	0	1	1	0	1	1	0	3	1	3	1	2	2	1	2	2	2	4	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr15:60849084T>C	ENST00000335670.6	-	3	297				RORA_ENST00000261523.5_Missense_Mutation_p.E88G|RORA_ENST00000449337.2_Intron|RORA_ENST00000560004.1_Intron|RORA_ENST00000309157.4_Intron|RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000558235.1_RNA	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A						angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						TTCCTTATCTTCCTTTTGTGA	0.403																																					p.E88G		.											.	RORA-290	0			c.A263G						.						325	278	294					15																	60849084		2203	4300	6503	SO:0001627	intron_variant	6095	exon3			TTATCTTCCTTTT	U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"Nuclear hormone receptors"	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.197-25034A>G	15.37:g.60849084T>C		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	169	83	NM_134260	0	0	0	0	0	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	37	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.566201	0.27915	.	.	ENSG00000069667	ENST00000261523	D	0.94457	-3.43	4.3	3.17	0.36434	.	2.259680	0.02344	N	0.075239	D	0.87815	0.6272	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.77749	-0.2471	10	0.22706	T	0.39	.	7.854	0.29472	0.0:0.0:0.2396:0.7604	.	88	P35398	RORA_HUMAN	G	88	ENSP00000261523:E88G	ENSP00000261523:E88G	E	-	2	0	RORA	58636376	0.028000	0.19301	0.012000	0.15200	0.033000	0.12548	0.610000	0.24253	0.985000	0.38656	0.533000	0.62120	GAA	.		0.403	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			C	60849084	T	C	60849084	1	2	14	0	1	0	0	0	0	0	0	0	13560	1783	62	3		3	RORA	15	60849084	Intron	SNP	T	TCGA-A4-8310-01A-11D-2396-08	1333771	60849084	41682308	82	1217											
DENND4A	10260	hgsc.bcm.edu	37	chr15	66010115	66010115	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taaaactatgcagtcactcaCcttgtagggcaaagagagag	15	8	10	8	0	2	2	2	0	0	2	2	3	2	2	1	1	2	3	1	1	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr15:66010115C>G	ENST00000431932.2	-	13	2016		c.e13+1		DENND4A_ENST00000443035.3_Splice_Site|MIR4511_ENST00000582784.1_RNA	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A						positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						CAGTCACTCACCTTGTAGGGC	0.383																																					.		.											.	DENND4A-229	0			c.1807+1G>C						.						53	54	53					15																	66010115		1852	4108	5960	SO:0001630	splice_region_variant	10260	exon14			CACTCACCTTGTA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.1807+1G>C	15.37:g.66010115C>G		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_001144823	0	0	0	0	0	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Splice_Site	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768120	0.69878	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0056	0.92849	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DENND4A	63797169	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	7.814000	0.86154	2.464000	0.83262	0.467000	0.42956	.	.		0.383	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	Intron	G	66010115	C	G	66010115	5	3	14	1	0	0	0	0	0	0	1	0	4444	521	18	4	3996	4	DENND4A	15	66010115	Splice_Site	SNP	C	TCGA-A4-8310-01A-11D-2396-08	5161031	66010115	36521277	83	1218											
C15orf39	56905	bcgsc.ca	37	chr15	75499127	75499127	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagcaatgtctgaggggccCtcaagtccttggacccagct	9	8	11	13	0	2	1	1	1	1	0	3	2	3	2	3	3	2	2	3	3	3	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr15:75499127C>A	ENST00000360639.2	+	2	1058	c.738C>A	c.(736-738)ccC>ccA	p.P246P	C15orf39_ENST00000394987.4_Silent_p.P246P|C15orf39_ENST00000567617.1_Silent_p.P246P			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	246						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CTGAGGGGCCCTCAAGTCCTT	0.637																																					p.P246P													.	C15orf39-90	0			c.C738A						.						41	45	43					15																	75499127		2197	4295	6492	SO:0001819	synonymous_variant	56905	exon2			GGGGCCCTCAAGT	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.738C>A	15.37:g.75499127C>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_1	67	4	NM_015492	0	0	2	2	0	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Silent	SNP	ENST00000360639.2	37	CCDS10276.1																																																																																			.		0.637	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		A	75499127	C	A	75499127	2	1	14	1	0	0	0	0	0	0	0	1	1797	668	24	4		4	C15orf39	15	75499127	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	9489012	75499127	27032265	84	1219											
GFER	2671	hgsc.bcm.edu	37	chr16	2034408	2034408	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccgattctcctgtcgccgaGgacgcctcccggaggcggcc	4	7	13	17	6	1	0	0	0	1	0	5	4	3	2	6	4	0	0	6	4	0	1	rs375792737	byFrequency	TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:2034408G>C	ENST00000248114.6	+	1	195	c.189G>C	c.(187-189)gaG>gaC	p.E63D	NOXO1_ENST00000354249.4_5'Flank|NOXO1_ENST00000356120.4_5'Flank|GFER_ENST00000567719.1_5'Flank|AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000569451.1_Missense_Mutation_p.E63D	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	63					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	CTGTCGCCGAGGACGCCTCCC	0.746													g|||	3	0.000599042	0	0.0014	5008	,	,		7495	0		0.002	False		,,,				2504	0				p.E63D		.											.	GFER-90	0			c.G189C						.		ASP/GLU	1,2865		0,1,1432	2	2	2		189	2.9	0	16		2	2,6508		0,2,3253	no	missense	GFER	NM_005262.2	45	0,3,4685	CC,CG,GG		0.0307,0.0349,0.032	benign	63/206	2034408	3,9373	1433	3255	4688	SO:0001583	missense	2671	exon1			CGCCGAGGACGCC	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.189G>C	16.37:g.2034408G>C	ENSP00000248114:p.Glu63Asp	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	9	7	NM_005262	0	0	2	10	8	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Missense_Mutation	SNP	ENST00000248114.6	37	CCDS32368.1	.	.	.	.	.	.	.	.	.	.	g	9.647	1.140479	0.21205	3.49E-4	3.07E-4	ENSG00000127554	ENST00000248114	T	0.64085	-0.08	3.85	2.87	0.33458	.	.	.	.	.	T	0.43567	0.1253	N	0.22421	0.69	0.24325	N	0.995023	B	0.24186	0.099	B	0.19946	0.027	T	0.20140	-1.0284	9	0.12430	T	0.62	.	10.074	0.42349	0.0:0.0:0.7985:0.2015	.	63	P55789	ALR_HUMAN	D	63	ENSP00000248114:E63D	ENSP00000248114:E63D	E	+	3	2	GFER	1974409	0.000000	0.05858	0.002000	0.10522	0.164000	0.22412	-0.657000	0.05335	0.791000	0.33826	0.493000	0.49557	GAG	.		0.746	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		C	2034408	G	C	2034408	3	2	14	1	0	0	0	0	1	0	0	0	6358	991	35	4	191	4	GFER	16	2034408	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		2034408	88320345	85	1220			1	6		3	3	1560	N	T_G_A	1.583717e-05
GFER	2671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2035934	2035934	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggctgtgccacctgcacAatgaagtgaaccgcaagctg	11	7	12	11	1	0	2	0	2	0	0	0	2	0	2	3	1	4	4	3	1	4	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:2035934A>C	ENST00000248114.6	+	3	529	c.523A>C	c.(523-525)Aat>Cat	p.N175H	GFER_ENST00000567719.1_Missense_Mutation_p.N100H|AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000569451.1_Missense_Mutation_p.Q109P	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	175	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	CCACCTGCACAATGAAGTGAA	0.587																																					p.N175H		.											.	GFER-90	0			c.A523C						.						95	91	92					16																	2035934		2198	4299	6497	SO:0001583	missense	2671	exon3			CTGCACAATGAAG	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.523A>C	16.37:g.2035934A>C	ENSP00000248114:p.Asn175His	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	201	121	NM_005262	0	0	13	47	34	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Missense_Mutation	SNP	ENST00000248114.6	37	CCDS32368.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	19.71|19.71	3.878702|3.878702	0.72294|0.72294	.|.	.|.	ENSG00000127554|ENSG00000127554	ENST00000248114|ENST00000425414	T|.	0.79454|.	-1.27|.	4.43|4.43	4.43|4.43	0.53597|0.53597	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87799|0.87799	0.6268|0.6268	H|H	0.97852|0.97852	4.09|4.09	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.91675|0.91675	0.5353|0.5353	10|6	0.87932|0.72032	D|D	0|0.01	-22.5825|-22.5825	13.1409|13.1409	0.59434|0.59434	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	101;175|.	Q9UQK8;P55789|.	.;ALR_HUMAN|.	H|P	175|94	ENSP00000248114:N175H|.	ENSP00000248114:N175H|ENSP00000396950:Q94P	N|Q	+|+	1|2	0|0	GFER|GFER	1975935|1975935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.444000|0.444000	0.32077|0.32077	6.743000|6.743000	0.74848|0.74848	1.763000|1.763000	0.52060|0.52060	0.418000|0.418000	0.28097|0.28097	AAT|CAA	.		0.587	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		C	2035934	A	C	2035934	3	2	14	1	0	0	0	0	1	0	0	0	6358	130	5	5	533	5	GFER	16	2035934	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	1526	2035934	88318819	86	1221			1	6		3	3	1560	N	T_G_A	1.583717e-05
GFER	2671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2035967	2035967	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaagctgggcaagcctgacTtcgactgctcaaaagtggat	11	8	12	10	1	1	1	1	1	0	0	2	3	1	2	1	2	3	4	1	2	4	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:2035967T>A	ENST00000248114.6	+	3	562	c.556T>A	c.(556-558)Ttc>Atc	p.F186I	GFER_ENST00000567719.1_Missense_Mutation_p.F111I|AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000569451.1_3'UTR	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	186	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	CAAGCCTGACTTCGACTGCTC	0.612																																					p.F186I		.											.	GFER-90	0			c.T556A						.						93	87	89					16																	2035967		2198	4300	6498	SO:0001583	missense	2671	exon3			CCTGACTTCGACT	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.556T>A	16.37:g.2035967T>A	ENSP00000248114:p.Phe186Ile	Somatic	182	1		WXS	Illumina HiSeq	Phase_I	171	101	NM_005262	0	0	13	57	44	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Missense_Mutation	SNP	ENST00000248114.6	37	CCDS32368.1	.	.	.	.	.	.	.	.	.	.	t	33	5.218249	0.95104	.	.	ENSG00000127554	ENST00000248114	T	0.64803	-0.12	4.43	4.43	0.53597	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);	0.000000	0.85682	D	0.000000	D	0.84951	0.5586	H	0.97077	3.935	0.80722	D	1	D;D	0.89917	0.985;1.0	D;D	0.81914	0.982;0.995	D	0.89667	0.3881	10	0.87932	D	0	-13.6696	13.1409	0.59434	0.0:0.0:0.0:1.0	.	112;186	Q9UQK8;P55789	.;ALR_HUMAN	I	186	ENSP00000248114:F186I	ENSP00000248114:F186I	F	+	1	0	GFER	1975968	1.000000	0.71417	0.993000	0.49108	0.876000	0.50452	7.301000	0.78850	1.763000	0.52060	0.418000	0.28097	TTC	.		0.612	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		A	2035967	T	A	2035967	3	1	14	1	0	0	0	0	1	0	0	0	6358	1609	56	5	566	5	GFER	16	2035967	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	33	2035967	88318786	87	1222			1	6		3	3	1560	N	T_G_A	1.583717e-05
BFAR	51283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	14755823	14755823	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggctgagtctgctctacctGtacctgtttgactacaccga	8	12	9	12	1	2	2	0	2	2	0	2	3	2	2	3	1	4	4	3	1	3	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:14755823G>T	ENST00000261658.2	+	6	1135	c.858G>T	c.(856-858)ctG>ctT	p.L286L	BFAR_ENST00000426842.2_Silent_p.L158L|BFAR_ENST00000563971.1_Silent_p.L161L	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	286					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						TGCTCTACCTGTACCTGTTTG	0.567																																					p.L286L		.											.	BFAR-92	0			c.G858T						.						237	201	213					16																	14755823		2197	4300	6497	SO:0001819	synonymous_variant	51283	exon6			CTACCTGTACCTG	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"RING-type (C3HC4) zinc fingers", "Sterile alpha motif (SAM) domain containing"	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.858G>T	16.37:g.14755823G>T		Somatic	211	0		WXS	Illumina HiSeq	Phase_I	280	161	NM_016561	0	0	15	50	35	A8K4Z9|B4DUT0|D3DUG8	Silent	SNP	ENST00000261658.2	37	CCDS10554.1																																																																																			.		0.567	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		T	14755823	G	T	14755823	2	4	14	1	0	0	0	0	0	0	0	1	1415	1364	48	4		4	BFAR	16	14755823	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	12719856	14755823	75598930	88	1223											
XYLT1	64131	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	17202725	17202725	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caacgagtccagccatccctCcagcgctgtgcccgtggagg	7	6	12	16	3	0	0	0	0	0	0	3	2	3	1	5	2	4	1	5	2	1	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:17202725C>A	ENST00000261381.6	-	12	2791	c.2707G>T	c.(2707-2709)Gag>Tag	p.E903*		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	903					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)	p.E903Q(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGCCATCCCTCCAGCGCTGTG	0.667																																					p.E903X		.											.	XYLT1-94	2	Substitution - Missense(2)	lung(2)	c.G2707T						.						71	63	66					16																	17202725		2197	4300	6497	SO:0001587	stop_gained	64131	exon12			ATCCCTCCAGCGC	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2707G>T	16.37:g.17202725C>A	ENSP00000261381:p.Glu903*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	125	9	NM_022166	0	0	9	9	0	Q9H1B6	Nonsense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	C	40	8.341779	0.98769	.	.	ENSG00000103489	ENST00000261381	.	.	.	5.7	5.7	0.88788	.	0.042979	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-47.0445	18.8196	0.92090	0.0:1.0:0.0:0.0	.	.	.	.	X	903	.	ENSP00000261381:E903X	E	-	1	0	XYLT1	17110226	1.000000	0.71417	0.995000	0.50966	0.811000	0.45836	5.784000	0.68990	2.675000	0.91044	0.655000	0.94253	GAG	.		0.667	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		A	17202725	C	A	17202725	4	1	14	1	0	0	0	0	0	1	0	0	17496	864	30	4	176	4	XYLT1	16	17202725	Nonsense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	2446902	17202725	73152028	89	1224											
SLC12A4	6560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67982000	67982000	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accggggccgccagttggggGtcctcaggagtgtctgcacc	5	7	16	13	2	2	0	1	0	1	0	3	1	3	1	5	5	1	2	5	5	0	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:67982000G>A	ENST00000316341.3	-	14	1951	c.1811C>T	c.(1810-1812)aCc>aTc	p.T604I	SLC12A4_ENST00000537830.2_Missense_Mutation_p.T598I|SLC12A4_ENST00000541864.2_Missense_Mutation_p.T573I|SLC12A4_ENST00000338335.3_Missense_Mutation_p.T604I|SLC12A4_ENST00000572037.1_Missense_Mutation_p.T556I|SLC12A4_ENST00000576616.1_Missense_Mutation_p.T604I|SLC12A4_ENST00000422611.2_Missense_Mutation_p.T606I	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	604					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAGTTGGGGGTCCTCAGGAG	0.617																																					p.T606I		.											.	SLC12A4-91	0			c.C1817T						.						86	87	87					16																	67982000		2198	4300	6498	SO:0001583	missense	6560	exon13			TTGGGGGTCCTCA		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1811C>T	16.37:g.67982000G>A	ENSP00000318557:p.Thr604Ile	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	263	64	NM_001145962	0	0	31	53	22	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	G	35	5.548568	0.96488	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98	5.82	5.82	0.92795	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.98957	0.9645	M	0.79805	2.47	0.80722	D	1	B;P;D;P;P;P	0.69078	0.338;0.917;0.997;0.511;0.511;0.76	B;P;D;B;B;P	0.71184	0.373;0.783;0.972;0.373;0.281;0.507	D	0.99808	1.1039	10	0.87932	D	0	.	20.0953	0.97838	0.0:0.0:1.0:0.0	.	606;604;573;598;604;604	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	I	606;573;598;604;604	ENSP00000395983:T606I;ENSP00000438334:T573I;ENSP00000445962:T598I;ENSP00000343374:T604I;ENSP00000318557:T604I	ENSP00000318557:T604I	T	-	2	0	SLC12A4	66539501	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.807000	0.99171	2.767000	0.95098	0.655000	0.94253	ACC	.		0.617	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		A	67982000	G	A	67982000	3	1	14	1	0	0	0	0	1	0	0	0	14417	1261	44	2	1490	2	SLC12A4	16	67982000	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	50779275	67982000	22372753	90	1225											
CNTNAP4	85445	bcgsc.ca	37	chr16	76389341	76389341	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagctccaactgggtgaccaGctacctcctgatgttcagtg	8	11	10	12	0	1	2	1	2	0	0	3	2	3	2	4	1	4	3	4	1	3	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:76389341G>C	ENST00000476707.1	+	2	471	c.332G>C	c.(331-333)aGc>aCc	p.S111T	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.S107T|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.S83T|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.S107T			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	108	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TGGGTGACCAGCTACCTCCTG	0.488																																					p.S83T													.	CNTNAP4-70	0			c.G248C						.						99	89	92					16																	76389341		2198	4300	6498	SO:0001583	missense	85445	exon3			TGACCAGCTACCT	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.332G>C	16.37:g.76389341G>C	ENSP00000417628:p.Ser111Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	153	5	NM_138994	0	0	0	0	0	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	G	20.6	4.022868	0.75275	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	D;D;D;D	0.98264	-4.83;-4.83;-4.83;-4.83	4.8	4.8	0.61643	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.137286	0.33438	N	0.004903	D	0.98807	0.9598	.	.	.	0.36845	D	0.8876	D;D;P;D	0.76494	0.992;0.999;0.949;0.99	D;D;P;D	0.75484	0.959;0.986;0.883;0.969	D	0.99953	1.1571	9	0.59425	D	0.04	.	15.7228	0.77728	0.0:0.0:1.0:0.0	.	83;111;83;108	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	T	107;107;83;111	ENSP00000306893:S107T;ENSP00000439733:S107T;ENSP00000418741:S83T;ENSP00000417628:S111T	ENSP00000306893:S107T	S	+	2	0	CNTNAP4	74946842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.268000	0.58883	2.655000	0.90218	0.591000	0.81541	AGC	.		0.488	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		C	76389341	G	C	76389341	3	2	14	1	0	0	0	0	1	0	0	0	3655	971	34	4	346	4	CNTNAP4	16	76389341	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	8407341	76389341	13965412	91	1226											
KIAA0664	23277	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	2595388	2595388	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tagactcgggcgacaaggtgGtggctgccgggaggcgcggc	6	5	20	10	5	0	1	0	0	0	1	1	3	0	2	1	7	1	1	1	7	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:2595388G>T	ENST00000570628.2	-	23	3552	c.3447C>A	c.(3445-3447)caC>caA	p.H1149Q	CLUH_ENST00000435359.1_Missense_Mutation_p.H1149Q|CLUH_ENST00000538975.1_Missense_Mutation_p.H1149Q			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1149					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CGACAAGGTGGTGGCTGCCGG	0.687																																					p.H1149Q		.											.	.	0			c.C3447A						.						9	10	10					17																	2595388		1998	4151	6149	SO:0001583	missense	23277	exon23			AAGGTGGTGGCTG	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.3447C>A	17.37:g.2595388G>T	ENSP00000458986:p.His1149Gln	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	13	9	NM_015229	0	0	0	0	0	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.989729	0.74589	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.93953	-3.32;-3.32	4.81	4.81	0.61882	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.94961	0.8370	L	0.49350	1.555	0.58432	D	0.999994	P;D	0.61697	0.629;0.99	P;D	0.66351	0.542;0.943	D	0.95039	0.8176	10	0.59425	D	0.04	.	15.1886	0.73025	0.0:0.0:1.0:0.0	.	1149;1150	O75153;C9J6D7	K0664_HUMAN;.	Q	1149;1150;1149	ENSP00000388872:H1149Q;ENSP00000439628:H1149Q	ENSP00000320468:H1150Q	H	-	3	2	KIAA0664	2542138	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.158000	0.50723	2.494000	0.84150	0.549000	0.68633	CAC	.		0.687	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		T	2595388	G	T	2595388	3	4	14	1	0	0	0	0	1	0	0	0	8210	1252	44	4	498	4	KIAA0664	17	2595388	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		2595388	78599822	92	1227											
NDEL1	81565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	8350137	8350137	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttagaagatgatttaagTcagactcgggccattaagga	13	11	12	5	1	1	4	1	1	0	3	2	5	1	5	1	2	0	1	1	2	4	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:8350137T>C	ENST00000334527.7	+	4	503	c.306T>C	c.(304-306)agT>agC	p.S102S	NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000299734.7_Silent_p.S102S|NDEL1_ENST00000380025.4_Silent_p.S102S|NDEL1_ENST00000402554.3_Silent_p.S102S	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	102	Interaction with KATNB1. {ECO:0000250}.|Self-association. {ECO:0000250}.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						ATGATTTAAGTCAGACTCGGG	0.463																																					p.S102S		.											.	NDEL1-90	0			c.T306C						.						114	104	107					17																	8350137		2203	4300	6503	SO:0001819	synonymous_variant	81565	exon4			TTTAAGTCAGACT	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.306T>C	17.37:g.8350137T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	115	60	NM_001025579	0	0	1	9	8	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Silent	SNP	ENST00000334527.7	37	CCDS11143.1																																																																																			.		0.463	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		C	8350137	T	C	8350137	2	2	14	1	0	0	0	0	0	0	0	1	10270	1664	58	3		3	NDEL1	17	8350137	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	5754749	8350137	72845073	93	1228											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	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_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000584811.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y	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	265	268					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	216	34		WXS	Illumina HiSeq		443	56	NM_145301	0	0	3	38	35	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		T	15457087	C	T	15457087	3	4	14	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	7106950	15457087	65738123	94	1229											
SLFN12	55106	bcgsc.ca	37	chr17	33749975	33749975	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttttttcctactgttctCtccaagagtgactcttccca	7	17	4	13	0	2	2	0	1	2	1	6	2	5	2	3	0	1	1	3	0	2	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:33749975C>A	ENST00000394562.1	-	4	596	c.73G>T	c.(73-75)Gag>Tag	p.E25*	SLFN12_ENST00000452764.3_Nonsense_Mutation_p.E25*|SLFN12_ENST00000460530.1_5'Flank|SLFN12_ENST00000304905.5_Nonsense_Mutation_p.E25*			Q8IYM2	SLN12_HUMAN	schlafen family member 12	25							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTACTGTTCTCTCCAAGAGTG	0.433																																					p.E25X													.	SLFN12-91	0			c.G73T						.						144	133	137					17																	33749975		2203	4300	6503	SO:0001587	stop_gained	55106	exon2			TGTTCTCTCCAAG	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.73G>T	17.37:g.33749975C>A	ENSP00000378063:p.Glu25*	Somatic	156	0		WXS	Illumina HiSeq	Phase_1	236	7	NM_018042	0	0	3	3	0	A8K711|Q9NP47	Nonsense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	.	.	.	.	.	.	.	.	.	.	c	25.5	4.647477	0.87958	.	.	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764;ENST00000447040;ENST00000445092	.	.	.	3.2	1.06	0.20224	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	5.4878	0.16759	0.0:0.7164:0.0:0.2836	.	.	.	.	X	25	.	ENSP00000302077:E25X	E	-	1	0	SLFN12	30774088	0.000000	0.05858	0.007000	0.13788	0.332000	0.28634	0.103000	0.15292	0.163000	0.19507	0.436000	0.28706	GAG	.		0.433	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		A	33749975	C	A	33749975	4	1	14	1	0	0	0	0	0	1	0	0	14766	922	32	4	1675	4	SLFN12	17	33749975	Nonsense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	18292888	33749975	47445235	95	1230											
IGFBP4	3487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38612795	38612795	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctggagccaaagggggAgctggactgccaccagctgg	8	4	18	11	0	0	0	0	0	0	0	0	3	0	3	4	6	4	2	4	6	1	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:38612795A>G	ENST00000269593.4	+	4	1012	c.737A>G	c.(736-738)gAg>gGg	p.E246G	IGFBP4_ENST00000542955.1_Missense_Mutation_p.E146G	NM_001552.2	NP_001543.2	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	246	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|DNA metabolic process (GO:0006259)|inflammatory response (GO:0006954)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			CCAAAGGGGGAGCTGGACTGC	0.657																																					p.E246G	GBM(160;940 3581 26177)	.											.	IGFBP4-522	0			c.A737G						.						37	41	40					17																	38612795		2202	4300	6502	SO:0001583	missense	3487	exon4			AGGGGGAGCTGGA	M38177	CCDS11367.1	17q21.2	2014-09-16	2001-11-28		ENSG00000141753	ENSG00000141753			5473	protein-coding gene	gene with protein product	"IGF-binding protein 4"	146733	"insulin-like growth factor-binding protein 4"			1707125, 1704481	Standard	NM_001552		Approved	IBP4, BP-4, HT29-IGFBP, IGFBP-4	uc002hus.3	P22692	OTTHUMG00000133326	ENST00000269593.4:c.737A>G	17.37:g.38612795A>G	ENSP00000269593:p.Glu246Gly	Somatic	116	1		WXS	Illumina HiSeq	Phase_I	108	24	NM_001552	1	0	187	257	69	A0N9W2|B4E351|Q5U012|Q9UCL6	Missense_Mutation	SNP	ENST00000269593.4	37	CCDS11367.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.158984	0.78226	.	.	ENSG00000141753	ENST00000542955;ENST00000269593	T;T	0.65549	-0.16;-0.16	5.29	5.29	0.74685	Thyroglobulin type-1 (5);	0.117947	0.56097	D	0.000022	T	0.63022	0.2476	L	0.49350	1.555	0.43417	D	0.995564	P	0.43231	0.801	P	0.46510	0.519	T	0.65833	-0.6072	10	0.54805	T	0.06	-21.3132	12.7751	0.57443	1.0:0.0:0.0:0.0	.	246	P22692	IBP4_HUMAN	G	146;246	ENSP00000437734:E146G;ENSP00000269593:E246G	ENSP00000269593:E246G	E	+	2	0	IGFBP4	35866321	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.850000	0.86915	1.991000	0.58162	0.533000	0.62120	GAG	.		0.657	IGFBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257134.1	NM_001552		G	38612795	A	G	38612795	3	3	14	1	0	0	0	0	1	0	0	0	7602	304	11	3	751	3	IGFBP4	17	38612795	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	4862820	38612795	42582415	96	1231											
ACLY	47	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40025023	40025023	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggctccaatgtcaatataTtcatcagcttcctccctgca	10	12	6	13	0	3	0	3	0	0	0	6	0	6	0	3	1	2	3	3	1	4	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:40025023T>C	ENST00000352035.2	-	28	3280	c.3150A>G	c.(3148-3150)gaA>gaG	p.E1050E	ACLY_ENST00000393896.2_Silent_p.E1040E|ACLY_ENST00000588779.1_5'UTR|ACLY_ENST00000537919.1_Silent_p.E779E|ACLY_ENST00000590151.1_Silent_p.E1050E|ACLY_ENST00000353196.1_Silent_p.E1040E	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	1050					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				TGTCAATATATTCATCAGCTT	0.438																																					p.E1050E	Colon(64;807 1396 15971 30971)	.											.	ACLY-228	0			c.A3150G						.						157	139	145					17																	40025023		2203	4300	6503	SO:0001819	synonymous_variant	47	exon28			AATATATTCATCA	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.3150A>G	17.37:g.40025023T>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	180	46	NM_001096	0	0	103	148	45	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	37	CCDS11412.1																																																																																			.		0.438	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		C	40025023	T	C	40025023	2	2	14	1	0	0	0	0	0	0	0	1	143	1490	52	3		3	ACLY	17	40025023	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	1412228	40025023	41170187	97	1232											
NACA2	342538	ucsc.edu	37	chr17	59668191	59668191	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaaaactatgtaggcatcCgaagcagggctcttgtagac	13	8	10	10	1	1	1	0	0	1	1	2	2	2	1	2	2	2	5	2	2	6	4	rs373217743		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:59668191C>T	ENST00000521764.1	-	1	372	c.351G>A	c.(349-351)tcG>tcA	p.S117S		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	117	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TGTAGGCATCCGAAGCAGGGC	0.443																																					p.S117S													.	NACA2-91	0			c.G351A						.						168	168	168					17																	59668191		2203	4300	6503	SO:0001819	synonymous_variant	342538	exon1			GGCATCCGAAGCA	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.351G>A	17.37:g.59668191C>T		Somatic	209	1		WXS	Illumina HiSeq		378	1	NM_199290	0	0	0	0	0	Q2VIR9	Silent	SNP	ENST00000521764.1	37	CCDS11630.1																																																																																			.		0.443	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		T	59668191	C	T	59668191	2	4	14	1	0	0	0	0	0	0	0	1	10159	639	23	1		1	NACA2	17	59668191	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	19643168	59668191	21527019	98	1233											
CSNK1D	1453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80202675	80202675	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcatcggtgcacgacagaCtgaagaccactggaagccac	12	6	10	13	2	1	3	1	1	1	2	3	5	1	4	2	2	2	1	2	2	2	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:80202675C>T	ENST00000314028.6	-	9	1579	c.1230G>A	c.(1228-1230)caG>caA	p.Q410Q	CSNK1D_ENST00000392334.2_3'UTR|CSNK1D_ENST00000398519.5_Intron	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	410					circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			GCACGACAGACTGAAGACCAC	0.557											OREG0024822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q410Q		.											.	CSNK1D-909	0			c.G1230A						.						115	85	95					17																	80202675		2203	4300	6503	SO:0001819	synonymous_variant	1453	exon9			GACAGACTGAAGA		CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551			2452	protein-coding gene	gene with protein product		600864				7797465	Standard	NM_001893		Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.1230G>A	17.37:g.80202675C>T		Somatic	92	0	1196	WXS	Illumina HiSeq	Phase_I	98	47	NM_001893	0	0	31	105	74	A2I2P2|Q96KZ6|Q9BTN5	Silent	SNP	ENST00000314028.6	37	CCDS11805.1																																																																																			.		0.557	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442632.1	NM_139062		T	80202675	C	T	80202675	2	4	14	1	0	0	0	0	0	0	0	1	3958	564	20	2		2	CSNK1D	17	80202675	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	20534484	80202675	992535	99	1234											
DSG3	1830	hgsc.bcm.edu	37	chr18	29054160	29054160	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgaccactaagcttggAgcagccactgaatctggagg	13	7	12	9	0	1	2	0	2	1	0	1	5	1	4	2	3	3	2	2	3	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr18:29054160A>G	ENST00000257189.4	+	15	2261	c.2178A>G	c.(2176-2178)ggA>ggG	p.G726G		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	726					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTAAGCTTGGAGCAGCCACTG	0.507																																					p.G726G		.											.	DSG3-98	0			c.A2178G						.						99	85	90					18																	29054160		2203	4300	6503	SO:0001819	synonymous_variant	1830	exon15			GCTTGGAGCAGCC	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2178A>G	18.37:g.29054160A>G		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	49	3	NM_001944	0	0	1	1	0	A8K2V2	Silent	SNP	ENST00000257189.4	37	CCDS11898.1																																																																																			.		0.507	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		G	29054160	A	G	29054160	2	3	14	1	0	0	0	0	0	0	0	1	4789	291	11	3		3	DSG3	18	29054160	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08		29054160	49023088	100	1235											
SETBP1	26040	hgsc.bcm.edu	37	chr18	42532691	42532691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgggccttggtgacatgcAgccttctctgaaccctccca	7	10	9	15	0	1	2	0	2	1	0	3	2	2	2	4	2	3	1	4	2	1	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr18:42532691A>G	ENST00000282030.5	+	4	3682	c.3386A>G	c.(3385-3387)cAg>cGg	p.Q1129R		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1129						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GGTGACATGCAGCCTTCTCTG	0.532									Schinzel-Giedion syndrome																												p.Q1129R		.											.	SETBP1-155	0			c.A3386G						.						108	87	94					18																	42532691		2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ACATGCAGCCTTC	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3386A>G	18.37:g.42532691A>G	ENSP00000282030:p.Gln1129Arg	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_015559	0	0	5	5	0	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	A	10.09	1.254514	0.22965	.	.	ENSG00000152217	ENST00000282030	T	0.68765	-0.35	5.88	4.72	0.59763	.	0.141871	0.52532	D	0.000074	T	0.49406	0.1555	L	0.29908	0.895	0.31120	N	0.708952	P	0.41848	0.763	B	0.36608	0.229	T	0.51325	-0.8720	10	0.09084	T	0.74	.	13.285	0.60237	0.8676:0.1324:0.0:0.0	.	1129	Q9Y6X0	SETBP_HUMAN	R	1129	ENSP00000282030:Q1129R	ENSP00000282030:Q1129R	Q	+	2	0	SETBP1	40786689	1.000000	0.71417	0.996000	0.52242	0.940000	0.58332	6.468000	0.73551	1.043000	0.40175	0.459000	0.35465	CAG	.		0.532	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		G	42532691	A	G	42532691	3	3	14	1	0	0	0	0	1	0	0	0	14161	188	7	3	3589	3	SETBP1	18	42532691	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	13478531	42532691	35544557	101	1236											
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11132430	11132430	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtacatgattgtggacgaAggtcaccgcatgaagaacca	15	7	11	8	2	1	3	1	2	0	1	1	5	1	4	2	2	2	2	2	2	5	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr19:11132430A>T	ENST00000429416.3	+	20	2927	c.2646A>T	c.(2644-2646)gaA>gaT	p.E882D	SMARCA4_ENST00000590574.1_Missense_Mutation_p.E882D|SMARCA4_ENST00000589677.1_Missense_Mutation_p.E882D|SMARCA4_ENST00000344626.4_Missense_Mutation_p.E882D|SMARCA4_ENST00000444061.3_Missense_Mutation_p.E882D|SMARCA4_ENST00000541122.2_Missense_Mutation_p.E882D|SMARCA4_ENST00000450717.3_Missense_Mutation_p.E882D|SMARCA4_ENST00000358026.2_Missense_Mutation_p.E882D|SMARCA4_ENST00000413806.3_Missense_Mutation_p.E882D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	882	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TTGTGGACGAAGGTCACCGCA	0.632			"F, N, Mis"		NSCLC																																p.E882D		.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.A2646T						.						77	61	67					19																	11132430		2202	4300	6502	SO:0001583	missense	6597	exon19			GGACGAAGGTCAC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2646A>T	19.37:g.11132430A>T	ENSP00000395654:p.Glu882Asp	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	34	11	NM_003072	0	0	24	40	16	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825530	0.71143	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.99652	-6.3;-6.3;-6.3;-6.3;-6.3;-6.3;-6.3	4.66	-2.31	0.06765	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99778	0.9908	H	0.99825	4.815	0.50313	D	0.999868	D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;0.999;1.0;0.999;0.999	D;D;D;D;D;D;D;D	0.97110	0.994;0.994;0.994;0.992;0.981;1.0;0.994;0.994	D	0.98030	1.0376	10	0.87932	D	0	-29.2033	10.9557	0.47356	0.5266:0.0:0.4734:0.0	.	882;882;882;882;882;102;882;882	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	D	882;882;946;882;882;882;882;882	ENSP00000395654:E882D;ENSP00000350720:E882D;ENSP00000343896:E882D;ENSP00000445036:E882D;ENSP00000392837:E882D;ENSP00000397783:E882D;ENSP00000414727:E882D	ENSP00000343896:E882D	E	+	3	2	SMARCA4	10993430	0.554000	0.26522	0.953000	0.39169	0.784000	0.44337	-0.089000	0.11180	-0.861000	0.04094	-0.256000	0.11100	GAA	.		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11132430	A	T	11132430	3	4	14	1	0	0	0	0	1	0	0	0	14802	69	3	5	2716	5	SMARCA4	19	11132430	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		11132430	47996553	102	1237											
SAPS1	22870	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	55752903	55752903	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcgggcgtagggcgtgcAaggcgcccacactggacaca	8	3	16	14	5	0	0	0	0	0	0	0	1	0	1	2	4	1	2	2	4	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr19:55752903A>T	ENST00000412770.2	-	8	1516	c.950T>A	c.(949-951)tTg>tAg	p.L317*	PPP6R1_ENST00000587283.1_Nonsense_Mutation_p.L317*	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	317	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						TAGGGCGTGCAAGGCGCCCAC	0.672																																					p.L317X		.											.	PPP6R1-67	0			c.T950A						.						16	20	19					19																	55752903		2009	4156	6165	SO:0001587	stop_gained	22870	exon8			GCGTGCAAGGCGC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.950T>A	19.37:g.55752903A>T	ENSP00000414202:p.Leu317*	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	15	4	NM_014931	0	0	35	35	0	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Nonsense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	A	36	5.920878	0.97105	.	.	ENSG00000105063	ENST00000412770	.	.	.	4.31	4.31	0.51392	.	0.000000	0.41938	D	0.000783	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.1454	11.7405	0.51790	1.0:0.0:0.0:0.0	.	.	.	.	X	317	.	ENSP00000414202:L317X	L	-	2	0	PPP6R1	60444715	1.000000	0.71417	0.898000	0.35279	0.236000	0.25371	4.122000	0.57910	1.937000	0.56155	0.379000	0.24179	TTG	.		0.672	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		T	55752903	A	T	55752903	4	4	14	1	0	0	0	0	0	1	0	0	13868	131	5	5	1763	5	SAPS1	19	55752903	Nonsense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	44620473	55752903	3376080	103	1238											
DNMT3B	1789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31375212	31375212	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggggggcatggagtccccGcaggtggaggcagacagtgg	8	4	20	9	1	0	1	0	0	0	1	1	3	1	3	2	8	0	3	2	8	0	0	rs376501500		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr20:31375212G>A	ENST00000328111.2	+	6	930	c.609G>A	c.(607-609)ccG>ccA	p.P203P	DNMT3B_ENST00000456297.2_Silent_p.P127P|DNMT3B_ENST00000201963.3_Silent_p.P215P|DNMT3B_ENST00000443239.3_Silent_p.P161P|DNMT3B_ENST00000348286.2_Silent_p.P203P|DNMT3B_ENST00000353855.2_Silent_p.P203P|DNMT3B_ENST00000344505.4_Silent_p.P203P|DNMT3B_ENST00000375623.4_Silent_p.P161P	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	203	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGGAGTCCCCGCAGGTGGAGG	0.637																																					p.P215P		.											.	DNMT3B-660	0			c.G645A						.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	52	51	51		483,381,609,609,609,645	-7.6	0	20		51	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	,,,,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,,,,	161/729,127/695,203/854,203/834,203/771,215/846	31375212	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1789	exon6			GTCCCCGCAGGTG		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.609G>A	20.37:g.31375212G>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	87	50	NM_175850	0	0	0	5	5	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																			.		0.637	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31375212	G	A	31375212	2	1	14	1	0	0	0	0	0	0	0	1	4688	1074	38	1		1	DNMT3B	20	31375212	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08		31375212	31650308	104	1239											
NCOA6	23054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33330861	33330861	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actctgttgcatgggcattcTctgggagtcggggttcaggg	5	12	16	8	1	3	0	1	0	2	0	5	1	3	1	0	5	1	4	0	5	0	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr20:33330861T>C	ENST00000374796.2	-	12	5769	c.3199A>G	c.(3199-3201)Aga>Gga	p.R1067G	NCOA6_ENST00000359003.2_Missense_Mutation_p.R1067G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1067	NCOA1-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						ATGGGCATTCTCTGGGAGTCG	0.537																																					p.R1067G		.											.	NCOA6-292	0			c.A3199G						.						112	117	115					20																	33330861		2203	4300	6503	SO:0001583	missense	23054	exon11			GCATTCTCTGGGA	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.3199A>G	20.37:g.33330861T>C	ENSP00000363929:p.Arg1067Gly	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	349	214	NM_014071	0	0	2	16	14	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.067284	0.55539	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.52526	0.66;0.66	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000001	T	0.56396	0.1982	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.54827	-0.8235	10	0.38643	T	0.18	-10.3259	12.8878	0.58053	0.0:0.0:0.1444:0.8556	.	1067	Q14686	NCOA6_HUMAN	G	1067	ENSP00000363929:R1067G;ENSP00000351894:R1067G	ENSP00000351894:R1067G	R	-	1	2	NCOA6	32794522	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.049000	0.57397	2.225000	0.72522	0.460000	0.39030	AGA	.		0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33330861	T	C	33330861	3	2	14	1	0	0	0	0	1	0	0	0	10259	1559	54	3	3012	3	NCOA6	20	33330861	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	1955649	33330861	29694659	105	1240											
ARFGEF2	10564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47628617	47628617	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatacgtctctgagaggcCtcgggttcgtttttccccac	7	12	9	13	3	1	1	0	1	1	1	5	2	2	1	3	2	1	2	3	2	2	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr20:47628617C>A	ENST00000371917.4	+	28	3914	c.3914C>A	c.(3913-3915)cCt>cAt	p.P1305H		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1305					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TCTGAGAGGCCTCGGGTTCGT	0.512																																					p.P1305H	Esophageal Squamous(176;1738 1974 26285 33069 35354)	.											.	ARFGEF2-358	0			c.C3914A						.						93	88	90					20																	47628617		2203	4300	6503	SO:0001583	missense	10564	exon28			AGAGGCCTCGGGT	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.3914C>A	20.37:g.47628617C>A	ENSP00000360985:p.Pro1305His	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	215	55	NM_006420	0	0	0	0	0	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767327	0.90020	.	.	ENSG00000124198	ENST00000371917	T	0.56611	0.45	5.46	5.46	0.80206	Armadillo-type fold (1);	0.050275	0.85682	D	0.000000	T	0.77246	0.4102	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.81337	-0.0978	10	0.87932	D	0	.	19.3208	0.94237	0.0:1.0:0.0:0.0	.	1305	Q9Y6D5	BIG2_HUMAN	H	1305	ENSP00000360985:P1305H	ENSP00000360985:P1305H	P	+	2	0	ARFGEF2	47062024	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	7.747000	0.85070	2.557000	0.86248	0.561000	0.74099	CCT	.		0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47628617	C	A	47628617	3	1	14	1	0	0	0	0	1	0	0	0	853	681	24	4	4024	4	ARFGEF2	20	47628617	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	14297756	47628617	15396903	106	1241											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26166902	26166902	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaagggtgagactttggaTtgatgctgacaaaaccatca	14	9	12	6	0	1	3	1	3	0	1	1	6	1	5	1	3	2	1	1	3	3	2	rs201482451		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr22:26166902T>A	ENST00000407587.2	+	6	1812	c.1643T>A	c.(1642-1644)aTt>aAt	p.I548N	MYO18B_ENST00000335473.7_Missense_Mutation_p.I548N|MYO18B_ENST00000536101.1_Missense_Mutation_p.I548N			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	548						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGACTTTGGATTGATGCTGAC	0.577																																					p.I548N		.											.	MYO18B-142	0			c.T1643A						.						66	76	73					22																	26166902		2043	4039	6082	SO:0001583	missense	84700	exon6			TTTGGATTGATGC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1643T>A	22.37:g.26166902T>A	ENSP00000386096:p.Ile548Asn	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_032608	0	0	0	0	0	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	T	11.73	1.726167	0.30593	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	T;T;T	0.72051	-0.62;-0.62;-0.62	4.74	3.7	0.42460	.	0.683074	0.13008	N	0.421139	T	0.74489	0.3723	M	0.61703	1.905	0.28366	N	0.920238	P;P;D;D	0.53151	0.925;0.93;0.958;0.958	P;P;P;P	0.54312	0.667;0.564;0.748;0.748	T	0.66444	-0.5922	10	0.87932	D	0	.	5.9265	0.19114	0.0:0.0907:0.1667:0.7426	.	61;548;548;548	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	N	548	ENSP00000441229:I548N;ENSP00000334563:I548N;ENSP00000386096:I548N	ENSP00000334563:I548N	I	+	2	0	MYO18B	24496902	0.459000	0.25768	0.173000	0.22940	0.081000	0.17604	3.482000	0.53186	0.676000	0.31285	0.260000	0.18958	ATT	.		0.577	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26166902	T	A	26166902	3	1	14	1	0	0	0	0	1	0	0	0	10091	1493	52	5	1661	5	MYO18B	22	26166902	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		26166902	25137664	107	1242											
APOL6	80830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	36055131	36055131	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctggaaagattatctataatCttagaaacaccttgaagtat	16	13	6	6	0	2	3	0	1	2	2	2	4	2	4	1	1	1	1	1	1	8	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr22:36055131C>G	ENST00000409652.4	+	3	796	c.520C>G	c.(520-522)Ctt>Gtt	p.L174V		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	174					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TATCTATAATCTTAGAAACAC	0.493																																					p.L174V		.											.	APOL6-90	0			c.C520G						.						61	63	62					22																	36055131		2203	4300	6503	SO:0001583	missense	80830	exon3			TATAATCTTAGAA	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"Apolipoproteins"	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.520C>G	22.37:g.36055131C>G	ENSP00000386280:p.Leu174Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	72	8	NM_030641	0	0	3	3	0	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Missense_Mutation	SNP	ENST00000409652.4	37	CCDS13919.1	.	.	.	.	.	.	.	.	.	.	C	0.284	-0.984328	0.02180	.	.	ENSG00000221963	ENST00000409652	T	0.03124	4.04	4.05	-3.17	0.05202	.	1.542230	0.03383	N	0.200606	T	0.01489	0.0048	N	0.01482	-0.84	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46331	-0.9199	10	0.11182	T	0.66	-11.6376	7.5122	0.27579	0.0:0.1896:0.5669:0.2435	.	174	Q9BWW8	APOL6_HUMAN	V	174	ENSP00000386280:L174V	ENSP00000386280:L174V	L	+	1	0	APOL6	34385077	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.171000	0.09883	-0.392000	0.07751	-1.127000	0.01993	CTT	.		0.493	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		G	36055131	C	G	36055131	3	3	14	1	0	0	0	0	1	0	0	0	810	913	32	4	526	4	APOL6	22	36055131	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	9888229	36055131	15249435	108	1243											
BCOR	54880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	39932880	39932880	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccatctgcattggcattgggGgcgggtgatgcggaggctgg	5	9	19	8	2	1	1	0	1	1	0	1	2	1	2	1	7	2	3	1	7	0	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:39932880G>T	ENST00000378444.4	-	4	1947	c.1719C>A	c.(1717-1719)gcC>gcA	p.A573A	BCOR_ENST00000378455.4_Silent_p.A573A|BCOR_ENST00000342274.4_Silent_p.A573A|BCOR_ENST00000397354.3_Silent_p.A573A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	573					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TGGCATTGGGGGCGGGTGATG	0.617			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.A573A		.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR-229	0			c.C1719A						.						72	62	65					X																	39932880		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			ATTGGGGGCGGGT	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1719C>A	X.37:g.39932880G>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	38	32	NM_001123385	0	0	0	9	9	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			.		0.617	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39932880	G	T	39932880	2	4	14	1	0	0	0	0	0	0	0	1	1387	1219	43	4		4	BCOR	23	39932880	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08		39932880	115337680	109	1244											
CXorf38	159013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	40506303	40506303	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccagcggcccggccggcAgtttccccagtgcacatctc	5	6	13	17	3	1	0	0	0	1	0	3	0	2	0	5	4	2	3	5	4	0	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:40506303A>G	ENST00000327877.5	-	2	333	c.307T>C	c.(307-309)Tgc>Cgc	p.C103R	CXorf38_ENST00000378418.2_Missense_Mutation_p.C103R|CXorf38_ENST00000378421.1_5'UTR|CXorf38_ENST00000378426.1_5'UTR|CXorf38_ENST00000440784.2_Intron	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	103										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						CCCGGCCGGCAGTTTCCCCAG	0.622																																					p.C103R		.											.	CXorf38-131	0			c.T307C						.						26	27	26					X																	40506303		2202	4300	6502	SO:0001583	missense	159013	exon2			GCCGGCAGTTTCC	AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.307T>C	X.37:g.40506303A>G	ENSP00000330488:p.Cys103Arg	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	22	14	NM_144970	0	0	0	2	2	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	37	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	a	22.0	4.230190	0.79688	.	.	ENSG00000185753	ENST00000327877;ENST00000378418	T;T	0.70516	-0.49;-0.49	5.26	4.06	0.47325	.	0.123229	0.56097	D	0.000040	T	0.79003	0.4373	M	0.66939	2.045	0.80722	D	1	D	0.55385	0.971	P	0.60473	0.875	T	0.78976	-0.1991	10	0.87932	D	0	-4.1854	10.4684	0.44622	0.8383:0.1617:0.0:0.0	.	103	Q8TB03	CX038_HUMAN	R	103	ENSP00000330488:C103R;ENSP00000367674:C103R	ENSP00000330488:C103R	C	-	1	0	CXorf38	40391247	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	7.258000	0.78371	0.627000	0.30340	0.483000	0.47432	TGC	.		0.622	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		G	40506303	A	G	40506303	3	3	14	1	0	0	0	0	1	0	0	0	4113	188	7	3	672	3	CXorf38	23	40506303	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	573423	40506303	114764257	110	1245											
GJB1	2705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70444364	70444364	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgccgcagccctggcacCggggctgggctggctgaaaa	6	5	16	14	3	0	1	0	1	0	0	0	1	0	1	3	5	2	5	3	5	2	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:70444364C>T	ENST00000374022.3	+	2	902	c.807C>T	c.(805-807)acC>acT	p.T269T	GJB1_ENST00000361726.6_Silent_p.T269T|GJB1_ENST00000374029.1_Silent_p.T269T	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	269					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					GCCCTGGCACCGGGGCTGGGC	0.637																																					p.T269T		.											.	GJB1-193	0			c.C807T						.						7	7	7					X																	70444364		2162	4203	6365	SO:0001819	synonymous_variant	2705	exon2			TGGCACCGGGGCT	X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"Ion channels / Gap junction proteins (connexins)"	4283	protein-coding gene	gene with protein product	"Charcot-Marie-Tooth neuropathy, X-linked", "connexin 32"	304040	"gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32)"	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.807C>T	X.37:g.70444364C>T		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	10	7	NM_000166	0	0	24	32	8	B2R8R2|D3DVV2|Q5U0S4	Silent	SNP	ENST00000374022.3	37	CCDS14408.1																																																																																			.		0.637	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166		T	70444364	C	T	70444364	2	4	14	1	0	0	0	0	0	0	0	1	6427	639	23	1		1	GJB1	23	70444364	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	29938061	70444364	84826196	111	1246											
PASD1	139135	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chrX	150828200	150828200	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacaggaccaaattgatattGcagaggttgagcagtatgga	14	10	12	5	0	0	3	0	2	0	1	0	5	0	5	1	3	3	4	1	3	4	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:150828200G>T	ENST00000370357.4	+	10	978	c.733G>T	c.(733-735)Gca>Tca	p.A245S		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	245						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					AATTGATATTGCAGAGGTTGA	0.373																																					p.A245S		.											.	PASD1-133	0			c.G733T						.						200	160	173					X																	150828200		2203	4300	6503	SO:0001583	missense	139135	exon10			GATATTGCAGAGG	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"cancer/testis antigen 63"					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.733G>T	X.37:g.150828200G>T	ENSP00000359382:p.Ala245Ser	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	40	4	NM_173493	0	0	0	0	0	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	g	8.919	0.960719	0.18583	.	.	ENSG00000166049	ENST00000370357	T	0.70399	-0.48	3.46	-4.06	0.03986	.	.	.	.	.	T	0.44850	0.1313	N	0.14661	0.345	0.09310	N	1	B	0.26876	0.162	B	0.19666	0.026	T	0.16897	-1.0387	9	0.27082	T	0.32	-10.8623	5.9292	0.19130	0.6076:0.0:0.245:0.1474	.	245	Q8IV76	PASD1_HUMAN	S	245	ENSP00000359382:A245S	ENSP00000359382:A245S	A	+	1	0	PASD1	150578856	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.030000	0.03581	-1.424000	0.01999	-0.925000	0.02716	GCA	.		0.373	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		T	150828200	G	T	150828200	3	4	14	1	0	0	0	0	1	0	0	0	11497	1319	46	4	767	4	PASD1	23	150828200	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	80383836	150828200	4442360	112	1247											
HES4	57801	hgsc.bcm.edu	37	chr1	934488	934488	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggccctgcggccccgccCtgggggcggcgggcagcgcc	1	2	19	19	6	0	0	0	0	0	0	0	0	0	0	6	6	2	1	6	6	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:934488C>G	ENST00000304952.6	-	4	754	c.617G>C	c.(616-618)aGg>aCg	p.R206T	HES4_ENST00000484667.2_Missense_Mutation_p.R174T|HES4_ENST00000428771.2_Missense_Mutation_p.R232T|RP11-54O7.17_ENST00000606034.1_lincRNA			Q9HCC6	HES4_HUMAN	hes family bHLH transcription factor 4	206	Pro-rich.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			lung(2)	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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;9.36e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.41e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00237)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		cggccccgccctgggggcggc	0.796																																					p.R232T		.											.	HES4-226	0			c.G695C						.																																			SO:0001583	missense	57801	exon3			CCCGCCCTGGGGG	BC012351	CCDS5.1, CCDS44034.1	1p36	2013-10-17	2013-10-17		ENSG00000188290	ENSG00000188290		"Basic helix-loop-helix proteins"	24149	protein-coding gene	gene with protein product		608060	"hairy and enhancer of split 4 (Drosophila)"			11260262, 15254753	Standard	NM_021170		Approved	bHLHb42	uc001aci.2	Q9HCC6	OTTHUMG00000040758	ENST00000304952.6:c.617G>C	1.37:g.934488C>G	ENSP00000304595:p.Arg206Thr	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_001142467	0	0	0	0	0	Q5SVA5	Missense_Mutation	SNP	ENST00000304952.6	37	CCDS5.1	.	.	.	.	.	.	.	.	.	.	C	3.404	-0.121669	0.06838	.	.	ENSG00000188290	ENST00000428771;ENST00000304952;ENST00000484667	T;T;T	0.59502	0.26;0.26;1.53	2.88	1.95	0.26073	.	.	.	.	.	T	0.36193	0.0958	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.18429	-1.0337	9	0.24483	T	0.36	.	4.8453	0.13510	0.0:0.4879:0.3756:0.1365	.	232;206	E9PB28;Q9HCC6	.;HES4_HUMAN	T	232;206;174	ENSP00000393198:R232T;ENSP00000304595:R206T;ENSP00000425085:R174T	ENSP00000304595:R206T	R	-	2	0	HES4	924351	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.923000	0.04000	0.413000	0.25759	0.393000	0.25936	AGG	.		0.796	HES4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097944.1	NM_021170		G	934488	C	G	934488	3	3	15	1	0	0	0	0	1	0	0	0	7089	681	24	4	52	4	HES4	1	934488	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08		934488	248316133	1	1248											
PEX14	5195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10678475	10678475	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctttcaccagctctacaagGtgagtcacccccagcggctg	8	8	10	15	1	3	1	2	1	1	0	3	1	3	1	3	2	3	3	3	2	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:10678475G>A	ENST00000356607.4	+	5	464		c.e5+1		RN7SL614P_ENST00000461850.2_RNA|PEX14_ENST00000538836.1_Splice_Site	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14						microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		GCTCTACAAGGTGAGTCACCC	0.627																																					.		.											.	PEX14-90	0			c.384+1G>A						.						70	62	64					1																	10678475		2203	4300	6503	SO:0001630	splice_region_variant	5195	exon5			TACAAGGTGAGTC	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.384+1G>A	1.37:g.10678475G>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	36	16	NM_004565	0	0	0	0	0	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Splice_Site	SNP	ENST00000356607.4	37	CCDS30582.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.726384	0.89298	.	.	ENSG00000142655	ENST00000356607;ENST00000538836	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.856	0.88762	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PEX14	10601062	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	9.430000	0.97488	2.195000	0.70347	0.655000	0.94253	.	.		0.627	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		Intron	A	10678475	G	A	10678475	5	1	15	1	0	0	0	0	0	0	1	0	11768	1275	44	2	403	2	PEX14	1	10678475	Splice_Site	SNP	G	TCGA-A4-8311-01A-11D-2396-08	9743987	10678475	238572146	2	1249											
EIF2C4	192670	hgsc.bcm.edu;broad.mit.edu	37	chr1	36316582	36316582	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcgctcagtctctattcCagcccctgcatattatgccc	7	12	5	17	1	2	0	1	0	1	0	5	0	3	0	4	0	3	2	4	0	3	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:36316582C>A	ENST00000373210.3	+	17	2650	c.2405C>A	c.(2404-2406)cCa>cAa	p.P802Q	AGO4_ENST00000488778.1_3'UTR	NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	802	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										GTCTCTATTCCAGCCCCTGCA	0.478																																					p.P802Q		.											.	.	0			c.C2405A						.						100	87	91					1																	36316582		2203	4300	6503	SO:0001583	missense	192670	exon17			CTATTCCAGCCCC	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"Argonaute/PIWI family"	18424	protein-coding gene	gene with protein product	"argonaute 4"	607356	"eukaryotic translation initiation factor 2C, 4"	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.2405C>A	1.37:g.36316582C>A	ENSP00000362306:p.Pro802Gln	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	48	3	NM_017629	0	0	0	0	0	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	37	CCDS397.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473642	0.84640	.	.	ENSG00000134698	ENST00000373210	T	0.57907	0.37	5.22	5.22	0.72569	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	D	0.84042	0.5385	H	0.98466	4.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90316	0.4341	10	0.62326	D	0.03	-9.3183	18.7904	0.91971	0.0:1.0:0.0:0.0	.	802	Q9HCK5	AGO4_HUMAN	Q	802	ENSP00000362306:P802Q	ENSP00000362306:P802Q	P	+	2	0	EIF2C4	36089169	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.417000	0.82017	0.591000	0.81541	CCA	.		0.478	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629		A	36316582	C	A	36316582	3	1	15	1	0	0	0	0	1	0	0	0	5019	594	21	4	2471	4	EIF2C4	1	36316582	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	25638107	36316582	212934039	3	1250											
ZCCHC11	23318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52961169	52961169	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctagtcagagatgagccaTacaacctaagtgaacattct	15	10	7	9	0	3	3	1	2	2	1	3	4	3	3	2	0	4	0	2	0	5	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:52961169T>C	ENST00000371544.3	-	6	1458	c.1196A>G	c.(1195-1197)tAt>tGt	p.Y399C	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.Y399C|ZCCHC11_ENST00000371541.1_5'UTR	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	399					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						AGATGAGCCATACAACCTAAG	0.338																																					p.Y399C		.											.	ZCCHC11-93	0			c.A1196G						.						56	58	57					1																	52961169		2203	4299	6502	SO:0001583	missense	23318	exon6			GAGCCATACAACC	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.1196A>G	1.37:g.52961169T>C	ENSP00000360599:p.Tyr399Cys	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	65	28	NM_001009881	0	0	2	7	5	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.180486	0.78677	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.90494	0.7022	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.998	D	0.91443	0.5175	10	0.87932	D	0	.	15.929	0.79646	0.0:0.0:0.0:1.0	.	158;399;399	E9PKX1;Q5TAX3-2;Q5TAX3	.;.;TUT4_HUMAN	C	399;399;399;158	ENSP00000257177:Y399C;ENSP00000360599:Y399C;ENSP00000433486:Y399C;ENSP00000435256:Y158C	ENSP00000257177:Y399C	Y	-	2	0	ZCCHC11	52733757	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.780000	0.62382	2.243000	0.73865	0.533000	0.62120	TAT	.		0.338	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		C	52961169	T	C	52961169	3	2	15	1	0	0	0	0	1	0	0	0	17612	1406	49	3	3841	3	ZCCHC11	1	52961169	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	16644587	52961169	196289452	4	1251											
LEPR	3953	hgsc.bcm.edu	37	chr1	66087101	66087101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccagtaattatttcctctTccatcttattgcttggaaca	9	17	5	10	0	2	0	0	0	2	0	4	1	4	1	3	1	3	2	3	1	4	7			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:66087101T>C	ENST00000349533.6	+	18	2742	c.2557T>C	c.(2557-2559)Tcc>Ccc	p.S853P	LEPR_ENST00000371060.3_Missense_Mutation_p.S853P|LEPR_ENST00000371059.3_Missense_Mutation_p.S853P|LEPR_ENST00000344610.8_Missense_Mutation_p.S853P|LEPR_ENST00000371058.1_Missense_Mutation_p.S853P|LEPR_ENST00000406510.3_Intron	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TATTTCCTCTTCCATCTTATT	0.338																																					p.S853P		.											.	LEPR-91	0			c.T2557C						.						162	151	155					1																	66087101		2203	4297	6500	SO:0001583	missense	3953	exon18			TCCTCTTCCATCT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2557T>C	1.37:g.66087101T>C	ENSP00000330393:p.Ser853Pro	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_001003680	0	0	4	4	0	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.175705	0.38413	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.60171	0.28;0.21;0.28;0.31;0.28	5.13	5.13	0.70059	.	0.310582	0.36374	N	0.002625	T	0.57533	0.2060	M	0.66939	2.045	0.52099	D	0.99994	P;P;D	0.55385	0.882;0.928;0.971	P;P;P	0.56278	0.629;0.795;0.736	T	0.61806	-0.6987	10	0.45353	T	0.12	-2.4259	10.2523	0.43377	0.0:0.0:0.1661:0.8338	.	853;853;853	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	P	853	ENSP00000340884:S853P;ENSP00000330393:S853P;ENSP00000360099:S853P;ENSP00000360098:S853P;ENSP00000360097:S853P	ENSP00000340884:S853P	S	+	1	0	LEPR	65859689	0.968000	0.33430	0.715000	0.30552	0.225000	0.24961	2.752000	0.47516	2.056000	0.61249	0.482000	0.46254	TCC	.		0.338	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		C	66087101	T	C	66087101	3	2	15	1	0	0	0	0	1	0	0	0	8749	1783	62	3	2619	3	LEPR	1	66087101	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	13125932	66087101	183163520	5	1252											
ABCA4	24	hgsc.bcm.edu	37	chr1	94485270	94485270	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctgggacgaaggacatggaGaaaatcacgcagatggcaac	15	4	14	8	2	1	2	1	0	0	2	1	6	1	4	0	4	1	3	0	4	4	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:94485270G>C	ENST00000370225.3	-	36	5150	c.5064C>G	c.(5062-5064)ttC>ttG	p.F1688L	ABCA4_ENST00000536513.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1688					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AGGACATGGAGAAAATCACGC	0.547																																					p.F1688L		.											.	ABCA4-162	0			c.C5064G						.						74	66	69					1																	94485270		2203	4300	6503	SO:0001583	missense	24	exon36			CATGGAGAAAATC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5064C>G	1.37:g.94485270G>C	ENSP00000359245:p.Phe1688Leu	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.290922	0.80914	.	.	ENSG00000198691	ENST00000546054;ENST00000370225	D	0.86956	-2.19	5.38	-3.17	0.05202	.	0.099805	0.64402	N	0.000001	D	0.85221	0.5647	M	0.62209	1.925	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.82792	-0.0282	10	0.44086	T	0.13	.	7.1314	0.25504	0.654:0.0:0.2065:0.1395	.	1688	P78363	ABCA4_HUMAN	L	480;1688	ENSP00000359245:F1688L	ENSP00000359245:F1688L	F	-	3	2	ABCA4	94257858	0.800000	0.28916	0.981000	0.43875	0.978000	0.69477	-0.121000	0.10643	-0.418000	0.07450	0.655000	0.94253	TTC	.		0.547	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		C	94485270	G	C	94485270	3	2	15	1	0	0	0	0	1	0	0	0	34	933	33	4	1817	4	ABCA4	1	94485270	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	28398169	94485270	154765351	6	1253											
GPR161	23432	hgsc.bcm.edu	37	chr1	168066462	168066462	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acaccatggggtacaggacaGcatagtagctagaaaaggga	16	5	13	7	0	0	1	0	0	0	1	0	3	0	3	1	4	3	4	1	4	6	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:168066462G>A	ENST00000367838.1	-	5	696	c.383C>T	c.(382-384)gCt>gTt	p.A128V	GPR161_ENST00000537209.1_Missense_Mutation_p.A148V|GPR161_ENST00000367836.1_5'UTR|GPR161_ENST00000546300.1_Missense_Mutation_p.A14V|GPR161_ENST00000361697.2_Missense_Mutation_p.A128V|GPR161_ENST00000271357.5_Missense_Mutation_p.A128V|GPR161_ENST00000367835.1_Missense_Mutation_p.A128V|GPR161_ENST00000539777.1_Missense_Mutation_p.A50V	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	128					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					GTACAGGACAGCATAGTAGCT	0.567																																					p.A148V		.											.	GPR161-90	0			c.C443T						.						63	58	59					1																	168066462		2201	4298	6499	SO:0001583	missense	23432	exon4			AGGACAGCATAGT	AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"GPCR / Class A : Orphans"	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.383C>T	1.37:g.168066462G>A	ENSP00000356812:p.Ala128Val	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_001267609	0	0	0	0	0	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Missense_Mutation	SNP	ENST00000367838.1	37	CCDS1268.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922844	0.92319	.	.	ENSG00000143147	ENST00000367838;ENST00000271357;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697	T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.62088	1.915	0.49299	D	0.999773	D;D;D;D;D;D	0.89917	0.99;0.978;1.0;1.0;0.988;1.0	D;D;D;D;P;D	0.91635	0.914;0.946;0.997;0.999;0.81;0.999	T	0.65651	-0.6116	9	0.87932	D	0	-17.0027	18.2107	0.89869	0.0:0.0:1.0:0.0	.	148;14;50;148;128;128	F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8-2;Q8N6U8	.;.;.;.;.;GP161_HUMAN	V	128;128;128;14;50;148;128	ENSP00000356812:A128V;ENSP00000271357:A128V;ENSP00000356809:A128V;ENSP00000444348:A14V;ENSP00000437576:A50V;ENSP00000441039:A148V;ENSP00000355194:A128V	ENSP00000271357:A128V	A	-	2	0	GPR161	166333086	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.634000	0.98435	2.490000	0.84030	0.561000	0.74099	GCT	.		0.567	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369		A	168066462	G	A	168066462	3	1	15	1	0	0	0	0	1	0	0	0	6685	971	34	2	1222	2	GPR161	1	168066462	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	73581192	168066462	81184159	7	1254											
GALNT2	2590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	230372159	230372159	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcttggtggatgactacagCaatgatcgtgagtactgaca	12	11	11	7	1	1	4	0	4	1	0	2	5	1	5	0	2	3	2	0	2	3	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:230372159C>T	ENST00000366672.4	+	5	606	c.534C>T	c.(532-534)agC>agT	p.S178S	GALNT2_ENST00000543760.1_Silent_p.S140S|GALNT2_ENST00000541865.1_Silent_p.S88S	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	178	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				ATGACTACAGCAATGATCGTG	0.448																																					p.S178S		.											.	GALNT2-92	0			c.C534T						.						79	77	78					1																	230372159		2203	4300	6503	SO:0001819	synonymous_variant	2590	exon5			CTACAGCAATGAT	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.534C>T	1.37:g.230372159C>T		Somatic	73	1		WXS	Illumina HiSeq	Phase_I	67	21	NM_004481	0	0	0	0	0	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Silent	SNP	ENST00000366672.4	37	CCDS1582.1																																																																																			.		0.448	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		T	230372159	C	T	230372159	2	4	15	1	0	0	0	0	0	0	0	1	6233	709	25	2		2	GALNT2	1	230372159	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	62305697	230372159	18878462	8	1255											
KIDINS220	57498	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	8872073	8872073	+	Frame_Shift_Del	DEL	A	A	-																															ttcaatactggaatcctgggAattgagactcgaaagacttg																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:8872073delA	ENST00000256707.3	-	30	4274	c.4093delT	c.(4093-4095)tccfs	p.S1365fs	KIDINS220_ENST00000473731.1_Frame_Shift_Del_p.S1346fs|KIDINS220_ENST00000427284.1_Frame_Shift_Del_p.S1346fs|KIDINS220_ENST00000418530.1_Frame_Shift_Del_p.S1266fs	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1365					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GAATCCTGGGAATTGAGACTC	0.363																																					p.S1365fs		.											.	KIDINS220-93	0			c.4093delT						.						81	77	78					2																	8872073		1825	4096	5921	SO:0001589	frameshift_variant	57498	exon30			.	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4093delT	2.37:g.8872073delA	ENSP00000256707:p.Ser1365fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	129	43	NM_020738	0	0	0	0	0	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Frame_Shift_Del	DEL	ENST00000256707.3	37	CCDS42650.1																																																																																			.		0.363	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		-	8872073	A	-	8872073	7	5	15	1	0	1	0	1	0	0	0	0	8292	246	9	0	1226	0	KIDINS220	2	8872073	Frame_Shift_Del	DEL	A	TCGA-A4-8311-01A-11D-2396-08		8872073	234327300	9	1256											
SRBD1	55133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	45616665	45616665	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtggcattctcaactttGcctgtaagaactgtcccaat	11	12	8	10	0	1	2	1	0	1	2	3	2	2	2	2	1	3	2	2	1	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:45616665G>C	ENST00000263736.4	-	21	2834	c.2772C>G	c.(2770-2772)ggC>ggG	p.G924G	SRBD1_ENST00000535761.1_Silent_p.G443G|SRBD1_ENST00000490133.1_5'UTR	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	924	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			TCTCAACTTTGCCTGTAAGAA	0.378																																					p.G924G		.											.	SRBD1-90	0			c.C2772G						.						66	64	64					2																	45616665		2202	4300	6502	SO:0001819	synonymous_variant	55133	exon21			AACTTTGCCTGTA	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2772C>G	2.37:g.45616665G>C		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	65	17	NM_018079	0	0	6	7	1	Q53T56|Q96TA4|Q9NW11	Silent	SNP	ENST00000263736.4	37	CCDS1823.1																																																																																			.		0.378	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		C	45616665	G	C	45616665	2	2	15	1	0	0	0	0	0	0	0	1	15165	1306	46	4		4	SRBD1	2	45616665	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	36744592	45616665	197582708	10	1257											
ZNF514	84874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95815137	95815137	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtttctctccagtgtgaaAtctgtaatgttgagtgagag	9	14	13	5	0	2	3	0	3	2	1	4	4	3	3	1	1	0	3	1	1	2	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:95815137A>C	ENST00000295208.2	-	5	1555	c.1093T>G	c.(1093-1095)Ttt>Gtt	p.F365V	ZNF514_ENST00000411425.1_Missense_Mutation_p.F365V|MRPS5_ENST00000475040.1_5'UTR	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	365					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)			large_intestine(4)|lung(6)|urinary_tract(1)	11						CCAGTGTGAAATCTGTAATGT	0.398																																					p.F365V		.											.	ZNF514-90	0			c.T1093G						.						78	72	74					2																	95815137		2203	4300	6503	SO:0001583	missense	84874	exon5			TGTGAAATCTGTA	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.1093T>G	2.37:g.95815137A>C	ENSP00000295208:p.Phe365Val	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	74	33	NM_032788	0	0	11	21	10	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	37	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.864411	0.32977	.	.	ENSG00000144026	ENST00000295208;ENST00000411425	T;T	0.28454	1.61;1.61	2.74	1.57	0.23409	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.00611	-1.325	0.23572	N	0.997388	B;B	0.14805	0.011;0.0	B;B	0.14578	0.011;0.002	T	0.26326	-1.0106	9	0.35671	T	0.21	.	2.3501	0.04281	0.6187:0.0:0.1395:0.2419	.	365;184	Q96K75;Q658L7	ZN514_HUMAN;.	V	365	ENSP00000295208:F365V;ENSP00000405509:F365V	ENSP00000295208:F365V	F	-	1	0	ZNF514	95178864	0.001000	0.12720	0.999000	0.59377	0.996000	0.88848	0.606000	0.24194	0.454000	0.26884	0.533000	0.62120	TTT	.		0.398	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		C	95815137	A	C	95815137	3	2	15	1	0	0	0	0	1	0	0	0	17991	101	4	5	113	5	ZNF514	2	95815137	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	50198472	95815137	147384236	11	1258											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198266726	198266726	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacctttcctctgtgttggcGgatacccttccataaaggct	7	14	8	12	1	1	0	0	0	1	0	3	1	3	1	4	3	2	2	4	3	4	6	rs78164940		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:198266726G>T	ENST00000335508.6	-	15	2297	c.2206C>A	c.(2206-2208)Cgc>Agc	p.R736S	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	736					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.R736C(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTGTGTTGGCGGATACCCTTC	0.373			Mis		myelodysplastic syndrome																																p.R736S		.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	1	Substitution - Missense(1)	endometrium(1)	c.C2206A						.						92	88	89					2																	198266726		2203	4300	6503	SO:0001583	missense	23451	exon15			GTTGGCGGATACC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2206C>A	2.37:g.198266726G>T	ENSP00000335321:p.Arg736Ser	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	64	4	NM_012433	0	0	85	85	0	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006500	0.54361	.	.	ENSG00000115524	ENST00000335508	T	0.63913	-0.07	5.47	5.47	0.80525	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67496	0.2899	M	0.76574	2.34	0.80722	D	1	B	0.33857	0.429	B	0.36335	0.222	T	0.69525	-0.5122	10	0.52906	T	0.07	.	19.3674	0.94469	0.0:0.0:1.0:0.0	.	736	O75533	SF3B1_HUMAN	S	736	ENSP00000335321:R736S	ENSP00000335321:R736S	R	-	1	0	SF3B1	197974971	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.892000	0.56235	2.567000	0.86603	0.650000	0.86243	CGC	.		0.373	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198266726	G	T	198266726	3	4	15	1	0	0	0	0	1	0	0	0	14181	1116	39	4	1752	4	SF3B1	2	198266726	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	102451589	198266726	44932647	12	1259											
UGT1A3	54659	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	234638329	234638329	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagactttaagggcacacAgtgtccaaacccttcctcct	10	12	6	13	0	0	1	0	0	0	1	3	1	3	1	4	1	1	1	4	1	3	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:234638329A>G	ENST00000482026.1	+	1	576	c.557A>G	c.(556-558)cAg>cGg	p.Q186R	UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.Q186R|UGT1A6_ENST00000406651.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	186					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	AAGGGCACACAGTGTCCAAAC	0.458																																					p.Q186R		.											.	UGT1A3-24	0			c.A557G						.						184	182	183					2																	234638329		2203	4300	6503	SO:0001583	missense	54659	exon1			GCACACAGTGTCC	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"UDP glucuronosyltransferases"	12535	other	complex locus constituent		606428	"UDP glycosyltransferase 1 family, polypeptide A3"			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.557A>G	2.37:g.234638329A>G	ENSP00000418532:p.Gln186Arg	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	254	122	NM_019093	0	0	0	0	0	B8K287	Missense_Mutation	SNP	ENST00000482026.1	37	CCDS2509.1	.	.	.	.	.	.	.	.	.	.	a	8.706	0.910893	0.17833	.	.	ENSG00000243135	ENST00000482026	T	0.61392	0.11	4.13	-0.128	0.13506	.	.	.	.	.	T	0.52403	0.1732	L	0.41961	1.31	0.26480	N	0.975128	P;P	0.38863	0.65;0.65	P;P	0.49140	0.601;0.601	T	0.46275	-0.9203	9	0.13108	T	0.6	.	6.8323	0.23917	0.6376:0.2835:0.0789:0.0	.	186;186	Q5DT01;P35503	.;UD13_HUMAN	R	186	ENSP00000418532:Q186R	ENSP00000418532:Q186R	Q	+	2	0	UGT1A3	234303068	0.618000	0.27051	0.013000	0.15412	0.284000	0.27059	2.244000	0.43124	-0.332000	0.08489	-0.359000	0.07587	CAG	.		0.458	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		G	234638329	A	G	234638329	3	3	15	1	0	0	0	0	1	0	0	0	16979	188	7	3	559	3	UGT1A3	2	234638329	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	36371603	234638329	8561044	13	1260											
SCLY	51540	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	238990470	238990470	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccaacaatgagactggcaTtgtcatggtgagtcggcctt	9	10	13	9	1	1	2	1	2	0	1	2	3	1	2	2	4	1	1	2	4	2	2	rs548740545		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:238990470T>C	ENST00000555827.1	+	5	669	c.605T>C	c.(604-606)aTt>aCt	p.I202T	SCLY_ENST00000429612.2_Intron|SCLY_ENST00000254663.6_Missense_Mutation_p.I210T|SCLY_ENST00000422984.2_Missense_Mutation_p.I108T|SCLY_ENST00000409736.2_Missense_Mutation_p.I202T|SCLY_ENST00000373332.3_Missense_Mutation_p.I120T			Q96I15	SCLY_HUMAN	selenocysteine lyase	202					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GAGACTGGCATTGTCATGGTG	0.572													T|||	1	0.000199681	0	0	5008	,	,		19116	0		0	False		,,,				2504	0.001				p.I210T	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	.											.	SCLY-92	0			c.T629C						.						95	77	83					2																	238990470		2203	4300	6503	SO:0001583	missense	51540	exon5			CTGGCATTGTCAT	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"putative selenocysteine lyase"	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.605T>C	2.37:g.238990470T>C	ENSP00000450613:p.Ile202Thr	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	50	19	NM_016510	0	0	0	1	1	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		.	.	.	.	.	.	.	.	.	.	T	5.647	0.303939	0.10678	.	.	ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965	D;D;D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97	5.84	4.67	0.58626	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.126390	0.52532	D	0.000062	T	0.61874	0.2382	N	0.00996	-1.065	0.80722	D	1	B;B;B	0.24043	0.036;0.096;0.006	B;B;B	0.31751	0.132;0.135;0.016	T	0.61426	-0.7065	10	0.02654	T	1	-27.8716	12.3833	0.55320	0.0:0.0:0.1409:0.8591	.	108;202;202	E7ESG3;Q96I15;Q96I15-2	.;SCLY_HUMAN;.	T	210;202;120;116;202;108;32	ENSP00000254663:I210T;ENSP00000450613:I202T;ENSP00000362429:I120T;ENSP00000414165:I116T;ENSP00000387162:I202T;ENSP00000416865:I108T;ENSP00000414053:I32T	ENSP00000254663:I202T	I	+	2	0	SCLY	238655209	1.000000	0.71417	0.002000	0.10522	0.045000	0.14185	7.953000	0.87836	1.020000	0.39573	0.533000	0.62120	ATT	.		0.572	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510		C	238990470	T	C	238990470	3	2	15	1	0	0	0	0	1	0	0	0	13939	1493	52	3	623	3	SCLY	2	238990470	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	4352141	238990470	4208903	14	1261											
ANKRD28	23243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	15751227	15751227	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagtattcagcagaaggtTtaggcactccaaattcctat	13	11	7	10	0	1	1	1	0	0	1	3	1	3	1	3	2	1	4	3	2	5	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:15751227T>C	ENST00000399451.2	-	13	1631	c.1264A>G	c.(1264-1266)Aac>Gac	p.N422D	ANKRD28_ENST00000383777.1_Missense_Mutation_p.N455D|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	422						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						AGCAGAAGGTTTAGGCACTCC	0.323																																					p.N422D		.											.	ANKRD28-135	0			c.A1264G						.						68	60	62					3																	15751227		1816	4070	5886	SO:0001583	missense	23243	exon13			GAAGGTTTAGGCA	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1264A>G	3.37:g.15751227T>C	ENSP00000382379:p.Asn422Asp	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	15	9	NM_015199	0	0	0	4	4	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.992948	0.54041	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.63744	-0.06;-0.06;-0.06	5.96	5.96	0.96718	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.44746	0.1308	N	0.05608	-0.01	0.80722	D	1	B;B;B	0.19817	0.039;0.019;0.003	B;B;B	0.20184	0.028;0.012;0.013	T	0.34950	-0.9808	10	0.32370	T	0.25	.	16.4311	0.83844	0.0:0.0:0.0:1.0	.	455;452;422	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	D	422;455;422	ENSP00000382379:N422D;ENSP00000373287:N455D;ENSP00000397341:N422D	ENSP00000373287:N455D	N	-	1	0	ANKRD28	15726231	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.972000	0.88022	2.277000	0.76020	0.528000	0.53228	AAC	.		0.323	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		C	15751227	T	C	15751227	3	2	15	1	0	0	0	0	1	0	0	0	656	1841	64	3	1961	3	ANKRD28	3	15751227	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08		15751227	182271203	15	1262											
SACM1L	22908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	45780273	45780273	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tttcttcctttctgttctagGattccatagacttatttctt	6	22	4	9	0	4	1	0	0	4	1	6	2	6	2	2	1	0	1	2	1	3	10			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:45780273G>A	ENST00000389061.5	+	18	1681	c.1477G>A	c.(1477-1479)Gat>Aat	p.D493N	SACM1L_ENST00000541314.1_Splice_Site_p.D432N|SACM1L_ENST00000418611.1_Splice_Site_p.D390N	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	493					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TCTGTTCTAGGATTCCATAGA	0.363																																					p.D493N		.											.	SACM1L-91	0			c.G1477A						.						145	139	141					3																	45780273		2203	4300	6503	SO:0001630	splice_region_variant	22908	exon18			TTCTAGGATTCCA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1477-1G>A	3.37:g.45780273G>A		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	55	31	NM_014016	0	0	0	0	0	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226777	0.95173	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314;ENST00000433336	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	6.05	6.05	0.98169	.	0.091827	0.85682	D	0.000000	T	0.27629	0.0679	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.995	D;D;P	0.87578	0.918;0.998;0.831	T	0.00063	-1.2155	9	.	.	.	-4.7089	13.7549	0.62930	0.0698:0.0:0.9302:0.0	.	432;136;493	B4DK71;B3KX17;Q9NTJ5	.;.;SAC1_HUMAN	N	390;493;432;170	ENSP00000396387:D390N;ENSP00000373713:D493N;ENSP00000443373:D432N;ENSP00000412883:D170N	.	D	+	1	0	SACM1L	45755277	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.455000	0.80726	2.878000	0.98634	0.650000	0.86243	GAT	.		0.363	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016	Missense_Mutation	A	45780273	G	A	45780273	5	1	15	1	0	0	0	0	0	0	1	0	13835	1188	41	2	1547	2	SACM1L	3	45780273	Splice_Site	SNP	G	TCGA-A4-8311-01A-11D-2396-08	30029046	45780273	152242157	16	1263											
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73673578	73673578	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccactggccgcgcgtcgcaGgcgtcgcgcatgtgcgcctc	3	6	14	18	8	0	0	0	0	0	0	3	0	0	0	3	2	1	2	3	2	0	0	rs6763344	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:73673578G>C	ENST00000263666.4	-	1	513	c.399C>G	c.(397-399)gcC>gcG	p.A133A	PDZRN3-AS1_ENST00000608304.1_RNA|PDZRN3-AS1_ENST00000478988.1_RNA|PDZRN3-AS1_ENST00000608743.1_RNA|PDZRN3_ENST00000308537.4_Silent_p.A133A	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	133					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GCGCGTCGCAGGCGTCGCGCA	0.776													C|||	4619	0.922324	0.9781	0.8977	5008	,	,		6325	0.9385		0.8757	False		,,,				2504	0.8957				p.A133A		.											.	PDZRN3-232	0			c.C399G						.						1	1	1					3																	73673578		356	609	965	SO:0001819	synonymous_variant	23024	exon1			GTCGCAGGCGTCG	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.399C>G	3.37:g.73673578G>C		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_015009	0	0	0	0	0	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			G|0.119;C|0.881		0.776	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		C	73673578	G	C	73673578	2	2	15	1	0	0	0	0	0	0	0	1	11735	987	35	4		4	PDZRN3	3	73673578	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	27893305	73673578	124348852	17	1264											
ACPL2	92370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	140979087	140979087	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctttgtgagcctcagcCtgcagttctgtgagtagagc	6	12	13	10	0	2	3	1	2	1	1	2	3	2	3	3	1	4	3	3	1	1	3	rs367551091	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:140979087C>A	ENST00000286353.4	+	2	207	c.70C>A	c.(70-72)Ctg>Atg	p.L24M	ACPL2_ENST00000504264.1_5'Flank|ACPL2_ENST00000393010.2_Missense_Mutation_p.L24M|ACPL2_ENST00000502783.1_5'UTR	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		24						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)			endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						GAGCCTCAGCCTGCAGTTCTG	0.517																																					p.L24M		.											.	ACPL2-91	0			c.C70A						.						49	56	53					3																	140979087		2203	4300	6503	SO:0001583	missense	92370	exon4			CTCAGCCTGCAGT																												ENST00000286353.4:c.70C>A	3.37:g.140979087C>A	ENSP00000286353:p.Leu24Met	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	46	22	NM_152282	0	0	0	0	0	D3DNF5|Q49AJ2|W0TR04	Missense_Mutation	SNP	ENST00000286353.4	37	CCDS3116.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845120	0.51164	.	.	ENSG00000155893	ENST00000505013;ENST00000286353;ENST00000393010;ENST00000514680	T;T	0.25085	1.82;1.82	5.87	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.47021	0.1423	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.42832	-0.9428	10	0.49607	T	0.09	.	13.2927	0.60280	0.0:0.9233:0.0:0.0767	.	24	Q8TE99	ACPL2_HUMAN	M	24	ENSP00000286353:L24M;ENSP00000376733:L24M	ENSP00000286353:L24M	L	+	1	2	ACPL2	142461777	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.962000	0.63687	1.628000	0.50416	-0.150000	0.13652	CTG	.		0.517	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2			A	140979087	C	A	140979087	3	1	15	1	0	0	0	0	1	0	0	0	166	680	24	4	72	4	ACPL2	3	140979087	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	67305509	140979087	57043343	18	1265											
ZNF721	170960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	437056	437056	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgcagtaaggtttgttgaActattaaaggctttgccaca	11	14	10	6	0	0	1	0	1	0	0	0	1	0	1	1	2	3	5	1	2	5	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:437056A>G	ENST00000338977.5	-	2	1212	c.1164T>C	c.(1162-1164)agT>agC	p.S388S	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_Silent_p.S400S|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	388				NS -> VC (in Ref. 1; CAH10687). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						GGTTTGTTGAACTATTAAAGG	0.428																																					p.M400I		.											.	ZNF721-47	0			c.G1200C						.						92	96	95					4																	437056		2109	4254	6363	SO:0001819	synonymous_variant	170960	exon3			TGTTGAACTATTA	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1164T>C	4.37:g.437056A>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	56	24	NM_133474	8	0	1	12	3	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37																																																																																				.		0.428	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	437056	A	G	437056	2	3	15	1	0	0	0	0	0	0	0	1	18154	40	2	3		3	ZNF721	4	437056	Silent	SNP	A	TCGA-A4-8311-01A-11D-2396-08		437056	190717220	19	1266											
SLC26A1	10861	hgsc.bcm.edu;broad.mit.edu	37	chr4	983983	983983	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcgcagcaggctcagccaTgtgaggaccaccatgccggg	8	4	14	15	3	1	1	1	1	0	0	1	2	1	2	5	3	3	3	5	3	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:983983T>C	ENST00000361661.2	-	4	1121	c.744A>G	c.(742-744)acA>acG	p.T248T	SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398516.2_Silent_p.T248T|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398520.2_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	248					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCTCAGCCATGTGAGGACCA	0.697																																					p.T248T		.											.	SLC26A1-91	0			c.A744G						.						10	12	11					4																	983983		2134	4181	6315	SO:0001819	synonymous_variant	10861	exon3			CAGCCATGTGAGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.744A>G	4.37:g.983983T>C		Somatic	9	0		WXS	Illumina HiSeq	Phase_I	7	5	NM_022042	0	0	3	5	2	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	37	CCDS33934.1																																																																																			.		0.697	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		C	983983	T	C	983983	2	2	15	1	0	0	0	0	0	0	0	1	14546	1451	51	3		3	SLC26A1	4	983983	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	546927	983983	190170293	20	1267											
SH3BP2	6452	broad.mit.edu	37	chr4	2824661	2824661	+	Splice_Site	DEL	G	G	-																															tgcccttgccacctcccacaGggcccctgcgctttgtcatc																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:2824661delG	ENST00000356331.5	+	3	397		c.e3-1		SH3BP2_ENST00000435136.2_Splice_Site|SH3BP2_ENST00000442312.2_Splice_Site|SH3BP2_ENST00000389838.2_Splice_Site|SH3BP2_ENST00000511747.1_Splice_Site|SH3BP2_ENST00000503393.2_Splice_Site|SH3BP2_ENST00000452765.2_Splice_Site	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2						positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		ACCTCCCACAGGGCCCCTGCG	0.622									Cherubism																												.													.	SH3BP2-514	0			c.137-1G>-						.						63	51	55					4																	2824661		2203	4300	6503	SO:0001630	splice_region_variant	6452	exon3	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCCACAGGGCCCC	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.137-1G>-	4.37:g.2824661delG		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	27	11	NM_001122681	0	0	0	0	0	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Splice_Site	DEL	ENST00000356331.5	37	CCDS33944.1																																																																																			.		0.622	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	Intron	-	2824661	G	-	2824661	8	5	15	1	0	1	0	1	0	0	1	0	14277	1014	35	0	401	0	SH3BP2	4	2824661	Splice_Site	DEL	G	TCGA-A4-8311-01A-11D-2396-08	1840678	2824661	188329615	21	1268	10	2									
SH3BP2	6452	hgsc.bcm.edu;bcgsc.ca	37	chr4	2824664	2824664	+	Missense_Mutation	SNP	C	C	T																															ccttgccacctcccacagggCccctgcgctttgtcatcatc																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:2824664C>T	ENST00000356331.5	+	3	400	c.139C>T	c.(139-141)Ccc>Tcc	p.P47S	SH3BP2_ENST00000435136.2_Missense_Mutation_p.P47S|SH3BP2_ENST00000442312.2_Missense_Mutation_p.P75S|SH3BP2_ENST00000389838.2_Missense_Mutation_p.P47S|SH3BP2_ENST00000511747.1_Missense_Mutation_p.P47S|SH3BP2_ENST00000503393.2_Missense_Mutation_p.P104S|SH3BP2_ENST00000452765.2_Missense_Mutation_p.P47S	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	47	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)	p.P47S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		TCCCACAGGGCCCCTGCGCTT	0.627									Cherubism																												p.P104S		.											.	SH3BP2-514	1	Substitution - Missense(1)	prostate(1)	c.C310T						.						64	52	56					4																	2824664		2203	4300	6503	SO:0001583	missense	6452	exon3	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	ACAGGGCCCCTGC	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.139C>T	4.37:g.2824664C>T	ENSP00000348685:p.Pro47Ser	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	33	14	NM_001145856	0	0	0	0	0	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	37	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553572	0.65425	.	.	ENSG00000087266	ENST00000452765;ENST00000389838;ENST00000503219;ENST00000504294;ENST00000508385;ENST00000512014;ENST00000513095;ENST00000442312;ENST00000502260;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	T;T;T;T;T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	3.94	3.94	0.45596	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.20373	0.0490	L	0.31207	0.915	0.58432	D	0.999997	P;D;P;P	0.61080	0.863;0.989;0.939;0.939	P;D;P;P	0.64595	0.524;0.927;0.666;0.666	T	0.02877	-1.1099	10	0.52906	T	0.07	-4.9102	15.9158	0.79517	0.0:1.0:0.0:0.0	.	75;75;104;47	B4DT04;B7Z9B6;D6R919;P78314	.;.;.;3BP2_HUMAN	S	47;47;47;47;47;47;47;75;47;47;47;104;47	ENSP00000409746:P47S;ENSP00000374488:P47S;ENSP00000422796:P47S;ENSP00000423275:P47S;ENSP00000424917:P47S;ENSP00000424105:P47S;ENSP00000423823:P47S;ENSP00000388152:P75S;ENSP00000425537:P47S;ENSP00000403231:P47S;ENSP00000424846:P47S;ENSP00000422168:P104S;ENSP00000348685:P47S	ENSP00000348685:P47S	P	+	1	0	SH3BP2	2794462	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.870000	0.75526	1.927000	0.55829	0.491000	0.48974	CCC	.		0.627	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		T	2824664	C	T	2824664	3	4	15	1	0	0	0	0	1	0	0	0	14277	739	26	2	404	2	SH3BP2	4	2824664	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	3	2824664	188329612	22	1269	10	2									
MFSD10	10227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	2934166	2934166	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggcaaaccagggtgccAtttccaggggcagggaggct	9	5	17	10	0	0	0	0	0	0	0	1	1	1	1	3	6	2	4	3	6	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:2934166A>G	ENST00000329687.4	-	5	1139	c.605T>C	c.(604-606)aTg>aCg	p.M202T	MFSD10_ENST00000355443.4_Missense_Mutation_p.M202T|MFSD10_ENST00000514800.1_Missense_Mutation_p.M202T|MFSD10_ENST00000508221.1_Missense_Mutation_p.M202T|MFSD10_ENST00000507555.1_Missense_Mutation_p.M202T|NOP14-AS1_ENST00000505731.1_RNA|NOP14-AS1_ENST00000507999.1_RNA	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	202					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCAGGGTGCCATTTCCAGGGG	0.632																																					p.M202T		.											.	MFSD10-68	0			c.T605C						.						52	58	56					4																	2934166		2203	4300	6503	SO:0001583	missense	10227	exon5			GGTGCCATTTCCA	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"tetracycline transporter like protein"	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.605T>C	4.37:g.2934166A>G	ENSP00000332646:p.Met202Thr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	64	26	NM_001120	0	0	52	120	68	Q07706	Missense_Mutation	SNP	ENST00000329687.4	37	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	A	0.137	-1.106537	0.01828	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	4.69	-2.4	0.06583	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.719668	0.14277	N	0.329747	T	0.14141	0.0342	N	0.00890	-1.11	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.23762	-1.0179	10	0.15066	T	0.55	-26.4194	2.158	0.03818	0.4585:0.122:0.2967:0.1227	.	202;202;202;202	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	T	202	ENSP00000426907:M202T;ENSP00000347619:M202T;ENSP00000332646:M202T;ENSP00000425757:M202T;ENSP00000423402:M202T	ENSP00000332646:M202T	M	-	2	0	MFSD10	2903964	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.615000	0.05597	-0.477000	0.06832	-0.417000	0.06048	ATG	.		0.632	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120		G	2934166	A	G	2934166	3	3	15	1	0	0	0	0	1	0	0	0	9553	217	8	3	794	3	MFSD10	4	2934166	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	109502	2934166	188220110	23	1270											
SEC24D	9871	bcgsc.ca	37	chr4	119666217	119666217	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcccaggacagtctgctgccTaaaaaaaaaaaaaaacccaa	20	5	5	11	0	1	0	0	0	1	0	2	1	2	1	3	1	3	1	3	1	9	1	rs78494615|rs35951660		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:119666217T>A	ENST00000280551.6	-	14	1946		c.e14-2		SEC24D_ENST00000419654.2_Splice_Site|SEC24D_ENST00000511481.1_Splice_Site|SEC24D_ENST00000429811.2_Splice_Site|SEC24D_ENST00000505134.1_Splice_Site|SEC24D_ENST00000379735.5_Splice_Site			O94855	SC24D_HUMAN	SEC24 family member D						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GTCTGCTGCCTAAAAAAAAAA	0.383																																					.													.	SEC24D-90	0			c.1708-2A>T						.						57	62	60					4																	119666217		2203	4300	6503	SO:0001630	splice_region_variant	9871	exon15			GCTGCCTAAAAAA	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"SEC24 (S. cerevisiae) related gene family, member D", "SEC24 family, member D (S. cerevisiae)"			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.1708-2A>T	4.37:g.119666217T>A		Somatic	64	3		WXS	Illumina HiSeq	Phase_1	68	9	NM_014822	0	0	0	0	0	Q8IYI7	Splice_Site	SNP	ENST00000280551.6	37	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	T	19.52	3.843690	0.71488	.	.	ENSG00000150961	ENST00000280551;ENST00000379735;ENST00000429811;ENST00000511481;ENST00000419654	.	.	.	5.59	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9966	0.53206	0.1298:0.0:0.0:0.8702	.	.	.	.	.	-1	.	.	.	-	.	.	SEC24D	119885665	1.000000	0.71417	0.977000	0.42913	0.934000	0.57294	7.994000	0.88315	0.917000	0.36895	0.533000	0.62120	.	.		0.383	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		Intron	A	119666217	T	A	119666217	5	1	15	1	0	0	0	0	0	0	1	0	14029	1536	53	5	1432	5	SEC24D	4	119666217	Splice_Site	SNP	T	TCGA-A4-8311-01A-11D-2396-08	116732051	119666217	71488059	24	1271											
TKTL2	84076	hgsc.bcm.edu	37	chr4	164394649	164394649	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcagcatagaggataggagCagcatgtcccctggagagga	13	5	15	8	0	0	2	0	0	0	2	1	6	1	5	2	4	4	4	2	4	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:164394649C>A	ENST00000280605.3	-	1	398	c.238G>T	c.(238-240)Gct>Tct	p.A80S		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	80						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				AGGATAGGAGCAGCATGTCCC	0.532																																					p.A80S		.											.	TKTL2-95	0			c.G238T						.						172	116	135					4																	164394649		2203	4300	6503	SO:0001583	missense	84076	exon1			TAGGAGCAGCATG	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"similar to transketolase"					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.238G>T	4.37:g.164394649C>A	ENSP00000280605:p.Ala80Ser	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_032136	0	0	0	0	0	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	6.285	0.420662	0.11928	.	.	ENSG00000151005	ENST00000280605	T	0.21191	2.02	4.02	2.25	0.28309	Transketolase, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.20088	0.0483	L	0.37561	1.115	0.48341	D	0.999636	B	0.27416	0.178	B	0.42214	0.38	T	0.06499	-1.0823	10	0.18710	T	0.47	-7.0095	7.6308	0.28238	0.0:0.7376:0.1665:0.0959	.	80	Q9H0I9	TKTL2_HUMAN	S	80	ENSP00000280605:A80S	ENSP00000280605:A80S	A	-	1	0	TKTL2	164614099	0.986000	0.35501	0.024000	0.17045	0.011000	0.07611	2.894000	0.48640	0.630000	0.30394	-0.332000	0.08345	GCT	.		0.532	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136		A	164394649	C	A	164394649	3	1	15	1	0	0	0	0	1	0	0	0	15968	710	25	4	1646	4	TKTL2	4	164394649	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	44728432	164394649	26759627	25	1272											
ZFR	51663	hgsc.bcm.edu	37	chr5	32407029	32407029	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgttgcagcagcagcagcAgctgctgctgctgcctgctt	5	10	13	13	0	0	0	0	0	0	0	0	0	0	0	1	0	11	12	1	0	0	2	rs139769264		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:32407029A>T	ENST00000265069.8	-	6	984	c.882T>A	c.(880-882)gcT>gcA	p.A294A		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	294	Ala-rich.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A294A(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		cagcagcagcagctgctgctg	0.483																																					p.A294A		.											.	ZFR-90	1	Substitution - coding silent(1)	endometrium(1)	c.T882A						.	A		0,4406		0,0,2203	35	36	36		882	-7.9	1	5	dbSNP_134	36	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZFR	NM_016107.3		0,1,6502	TT,TA,AA		0.0116,0.0,0.0077		294/1075	32407029	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51663	exon6			AGCAGCAGCTGCT	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.882T>A	5.37:g.32407029A>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_016107	0	1	11	12	0	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Silent	SNP	ENST00000265069.8	37	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.711849	0.30322	0.0	1.16E-4	ENSG00000056097	ENST00000416900	.	.	.	5.89	-7.9	0.01169	.	.	.	.	.	T	0.27731	0.0682	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33292	-0.9874	5	0.08179	T	0.78	.	8.2119	0.31488	0.2876:0.1859:0.0:0.5266	.	.	.	.	S	175	.	ENSP00000393243:C175S	C	-	1	0	ZFR	32442786	0.089000	0.21612	0.989000	0.46669	0.998000	0.95712	-1.076000	0.03420	-0.596000	0.05821	0.454000	0.30748	TGC	A|1.000;T|0.000		0.483	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			T	32407029	A	T	32407029	2	4	15	1	0	0	0	0	0	0	0	1	17691	175	7	5		5	ZFR	5	32407029	Silent	SNP	A	TCGA-A4-8311-01A-11D-2396-08		32407029	148508231	26	1273											
SLCO6A1	133482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	101834204	101834204	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctcaccttgacatatgagCaggatgcagtagaaaatcat	14	9	10	8	0	2	3	2	2	0	1	2	4	2	4	1	2	2	4	1	2	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:101834204C>A	ENST00000506729.1	-	1	516	c.345G>T	c.(343-345)ctG>ctT	p.L115L	SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000389019.3_Silent_p.L115L|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000513675.1_Silent_p.L115L|SLCO6A1_ENST00000379810.1_Silent_p.L115L|SLCO6A1_ENST00000379807.3_Silent_p.L115L			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	115	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		GACATATGAGCAGGATGCAGT	0.572																																					p.L115L		.											.	SLCO6A1-96	0			c.G345T						.						59	60	60					5																	101834204		2203	4300	6503	SO:0001819	synonymous_variant	133482	exon1			TATGAGCAGGATG	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.345G>T	5.37:g.101834204C>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	73	35	NM_173488	0	0	0	0	0	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																			.		0.572	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101834204	C	A	101834204	2	1	15	1	0	0	0	0	0	0	0	1	14764	697	25	4		4	SLCO6A1	5	101834204	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	69427175	101834204	79081056	27	1274											
IL9	3578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	135228124	135228124	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcttttctttctggaaaaTttccagaagactcttcagaa	12	15	5	9	0	5	3	1	0	4	3	6	4	6	4	1	1	0	0	1	1	4	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:135228124T>C	ENST00000274520.1	-	5	401	c.391A>G	c.(391-393)Att>Gtt	p.I131V		NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	interleukin 9	131					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-5 biosynthetic process (GO:0045407)	extracellular space (GO:0005615)				large_intestine(3)|lung(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCTGGAAAATTTCCAGAAGA	0.368																																					p.I131V		.											.	IL9-90	0			c.A391G						.						66	73	71					5																	135228124		2203	4300	6503	SO:0001583	missense	3578	exon5			GGAAAATTTCCAG	S63356	CCDS4189.1	5q31-q35	2008-07-18			ENSG00000145839	ENSG00000145839		"Interleukins and interleukin receptors"	6029	protein-coding gene	gene with protein product	"p40 T-cell and mast cell growth factor", "T-cell growth factor p40", "p40 cytokine", "homolog of mouse T cell and mast cell growth factor 40"	146931				8379467	Standard	NM_000590		Approved	IL-9, HP40, P40	uc003lbb.1	P15248	OTTHUMG00000129147	ENST00000274520.1:c.391A>G	5.37:g.135228124T>C	ENSP00000274520:p.Ile131Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	49	23	NM_000590	0	0	0	0	0		Missense_Mutation	SNP	ENST00000274520.1	37	CCDS4189.1	.	.	.	.	.	.	.	.	.	.	T	0.246	-1.010364	0.02095	.	.	ENSG00000145839	ENST00000274520	T	0.42131	0.98	5.48	-7.84	0.01196	.	1.696530	0.03303	N	0.189306	T	0.12944	0.0314	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25916	-1.0118	10	0.08179	T	0.78	-2.0474	8.7041	0.34343	0.0:0.3821:0.1035:0.5144	.	131	P15248	IL9_HUMAN	V	131	ENSP00000274520:I131V	ENSP00000274520:I131V	I	-	1	0	IL9	135256023	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.778000	0.04664	-1.878000	0.01128	-1.601000	0.00813	ATT	.		0.368	IL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251210.1	NM_000590		C	135228124	T	C	135228124	3	2	15	1	0	0	0	0	1	0	0	0	7728	1493	52	3	47	3	IL9	5	135228124	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	33393920	135228124	45687136	28	1275											
SLC35A4	113829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	139947279	139947279	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagtccccctccagcagcTgctgccagccccatgcccct	5	6	7	23	0	0	0	0	0	0	0	2	0	2	0	9	0	6	3	9	0	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:139947279T>A	ENST00000514199.1	+	2	2211	c.525T>A	c.(523-525)gcT>gcA	p.A175A	APBB3_ENST00000507279.1_Intron|SLC35A4_ENST00000323146.3_Silent_p.A175A			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	175	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCAGCAGCTGCTGCCAGCC	0.622																																					p.A175A		.											.	SLC35A4-90	0			c.T525A						.						59	57	58					5																	139947279		2203	4300	6503	SO:0001819	synonymous_variant	113829	exon3			AGCAGCTGCTGCC	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"Solute carriers"	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.525T>A	5.37:g.139947279T>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	73	35	NM_080670	0	0	19	36	17	A8K013	Silent	SNP	ENST00000514199.1	37	CCDS4231.1																																																																																			.		0.622	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670		A	139947279	T	A	139947279	2	1	15	1	0	0	0	0	0	0	0	1	14605	1567	55	5		5	SLC35A4	5	139947279	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	4719155	139947279	40967981	29	1276											
TREM2	54209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	41129014	41129014	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcacctgccagcacctcCaccaggaccttcctgagggt	8	7	8	18	0	1	1	1	1	0	0	3	2	3	2	7	2	2	1	7	2	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr6:41129014C>T	ENST00000373113.3	-	2	471	c.378G>A	c.(376-378)gtG>gtA	p.V126V	TREM2_ENST00000338469.3_Silent_p.V126V|TREM2_ENST00000373122.4_Silent_p.V126V	NM_018965.2	NP_061838.1	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	126					axon guidance (GO:0007411)|dendritic cell differentiation (GO:0097028)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of C-C chemokine receptor CCR7 signaling pathway (GO:1903082)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of CD40 signaling pathway (GO:2000350)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to plasma membrane (GO:1903078)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	11	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCAGCACCTCCACCAGGACCT	0.612																																					p.V126V		.											.	TREM2-91	0			c.G378A						.						43	41	42					6																	41129014		2203	4300	6503	SO:0001819	synonymous_variant	54209	exon2			CACCTCCACCAGG	AF213457	CCDS4852.1, CCDS64422.1	6p21.1	2014-09-17	2002-08-15		ENSG00000095970	ENSG00000095970		"Immunoglobulin superfamily / V-set domain containing"	17761	protein-coding gene	gene with protein product		605086	"triggering receptor expressed on myeloid cells 2a"			10799849, 12080485	Standard	NM_001271821		Approved	TREM-2, Trem2a, Trem2b, Trem2c	uc003opy.3	Q9NZC2	OTTHUMG00000014671	ENST00000373113.3:c.378G>A	6.37:g.41129014C>T		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	42	13	NM_018965	0	0	0	0	0	Q8N5H8|Q8WYN6	Silent	SNP	ENST00000373113.3	37	CCDS4852.1																																																																																			.		0.612	TREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040499.1	NM_018965		T	41129014	C	T	41129014	2	4	15	1	0	0	0	0	0	0	0	1	16504	581	21	2		2	TREM2	6	41129014	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08		41129014	129986053	30	1277											
TJAP1	93643	hgsc.bcm.edu	37	chr6	43466779	43466779	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctaagaaaccctaccgtaagGcaccaccagagcatcgggag	14	4	10	13	2	0	2	0	0	0	2	1	3	0	3	4	2	3	3	4	2	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr6:43466779G>C	ENST00000372445.5	+	4	416	c.40G>C	c.(40-42)Gca>Cca	p.A14P	TJAP1_ENST00000438588.2_Missense_Mutation_p.A14P|TJAP1_ENST00000372444.2_Missense_Mutation_p.A14P|TJAP1_ENST00000372449.1_Missense_Mutation_p.A14P|TJAP1_ENST00000259751.1_Missense_Mutation_p.A14P|TJAP1_ENST00000372452.1_Missense_Mutation_p.A14P|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Missense_Mutation_p.A14P	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	14					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)		p.A14S(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CTACCGTAAGGCACCACCAGA	0.587																																					p.A14P		.											.	TJAP1-90	1	Substitution - Missense(1)	lung(1)	c.G40C						.						92	77	82					6																	43466779		2203	4300	6503	SO:0001583	missense	93643	exon4			CGTAAGGCACCAC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.40G>C	6.37:g.43466779G>C	ENSP00000361522:p.Ala14Pro	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	51	4	NM_080604	0	0	8	8	0	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	37	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	G	34	5.300029	0.95574	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.56426	0.1984	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.60188	-0.7312	10	0.87932	D	0	-0.0171	17.1606	0.86802	0.0:0.0:1.0:0.0	.	14;14;14	E2QRK7;Q5JTD0;Q5JTD0-2	.;TJAP1_HUMAN;.	P	14	ENSP00000361521:A14P;ENSP00000361522:A14P;ENSP00000407080:A14P;ENSP00000390981:A14P;ENSP00000259751:A14P;ENSP00000361530:A14P;ENSP00000361527:A14P;ENSP00000408769:A14P	ENSP00000259751:A14P	A	+	1	0	TJAP1	43574757	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.903000	0.87398	2.495000	0.84180	0.655000	0.94253	GCA	.		0.587	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		C	43466779	G	C	43466779	3	2	15	1	0	0	0	0	1	0	0	0	15960	1203	42	4	42	4	TJAP1	6	43466779	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	2337765	43466779	127648288	31	1278											
LCA5	167691	hgsc.bcm.edu	37	chr6	80197555	80197555	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaagatgccttttctttttgCtttttatcaagttcttctct	7	22	4	8	0	4	1	1	0	3	1	5	1	4	1	1	0	2	2	1	0	3	9	rs141642284		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr6:80197555C>T	ENST00000392959.1	-	9	1871	c.1260G>A	c.(1258-1260)aaG>aaA	p.K420K	LCA5_ENST00000369846.4_Silent_p.K420K|LCA5_ENST00000467898.3_3'UTR	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	420					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		TTTCTTTTTGCTTTTTATCAA	0.308													C|||	1	0.000199681	0	0	5008	,	,		15674	0		0.001	False		,,,				2504	0				p.K420K		.											.	LCA5-90	0			c.G1260A						.	C	,	1,4401		0,1,2200	77	78	77		1260,1260	1.5	0.9	6	dbSNP_134	77	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	LCA5	NM_001122769.2,NM_181714.3	,	0,5,6495	TT,TC,CC		0.0465,0.0227,0.0385	,	420/698,420/698	80197555	5,12995	2201	4299	6500	SO:0001819	synonymous_variant	167691	exon8			TTTTTGCTTTTTA		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"lebercilin"	611408	"chromosome 6 open reading frame 152"	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1260G>A	6.37:g.80197555C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_001122769	0	0	2	2	0	E1P542|Q9BWX7	Silent	SNP	ENST00000392959.1	37	CCDS4990.1																																																																																			C|1.000;T|0.000		0.308	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		T	80197555	C	T	80197555	2	4	15	1	0	0	0	0	0	0	0	1	8677	796	28	2		2	LCA5	6	80197555	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	36730776	80197555	90917512	32	1279											
TMEM120A	5447	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	75617074	75617074	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgccgctcgcccagcgccCgcaggcggtagaggcagccg	5	4	16	16	6	0	1	0	0	0	1	1	1	0	1	4	3	3	4	4	3	1	1	rs201249328		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr7:75617074C>T	ENST00000461988.1	+	0	2522				TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase						carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCCCAGCGCCCGCAGGCGGTA	0.672																																					.													.	.	0			.						.	C	GLN/ARG	0,4056		0,0,2028	19	26	24		746	2.7	0.9	7		24	3,8299		0,3,4148	yes	missense	TMEM120A	NM_031925.2	43	0,3,6176	TT,TC,CC		0.0361,0.0,0.0243	probably-damaging	249/344	75617074	3,12355	2028	4151	6179	SO:0001628	intergenic_variant	83862	.			AGCGCCCGCAGGC	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413		7.37:g.75617074C>T		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	36	9	.	0	0	30	46	16	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	37	CCDS5579.1																																																																																			.		0.672	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		T	75617074	C	T	75617074	1	4	15	0	1	0	0	0	0	0	0	0	16065	652	23	1		1	TMEM120A	7	75617074	IGR	SNP	C	TCGA-A4-8311-01A-11D-2396-08		75617074	83521589	33	1280											
WDR91	29062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	134873248	134873248	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaactccacagagtagacCtccccgtagtgggccctcca	9	7	9	16	1	0	3	0	1	0	2	3	3	3	3	6	1	1	2	6	1	3	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr7:134873248C>T	ENST00000354475.4	-	13	1849	c.1818G>A	c.(1816-1818)gaG>gaA	p.E606E	WDR91_ENST00000423565.1_Silent_p.E571E|WDR91_ENST00000344400.5_Intron	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	606										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						CAGAGTAGACCTCCCCGTAGT	0.592																																					p.E606E		.											.	WDR91-137	0			c.G1818A						.						177	161	167					7																	134873248		2203	4300	6503	SO:0001819	synonymous_variant	29062	exon13			GTAGACCTCCCCG	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.1818G>A	7.37:g.134873248C>T		Somatic	217	0		WXS	Illumina HiSeq	Phase_I	304	64	NM_014149	0	0	76	119	43	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Silent	SNP	ENST00000354475.4	37	CCDS34758.1																																																																																			.		0.592	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		T	134873248	C	T	134873248	2	4	15	1	0	0	0	0	0	0	0	1	17371	680	24	2		2	WDR91	7	134873248	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	59256174	134873248	24265415	34	1281											
PRKDC	5591	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	48744423	48744423	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctggcatacatcaaactGagcttctcctggtccctcat	8	14	6	13	0	4	1	2	1	2	0	6	1	5	1	2	2	3	2	2	2	2	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr8:48744423G>T	ENST00000314191.2	-	61	8270	c.8214C>A	c.(8212-8214)ctC>ctA	p.L2738L	PRKDC_ENST00000338368.3_Silent_p.L2738L|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2739	KIP-binding.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	ACATCAAACTGAGCTTCTCCT	0.532								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)												.	PRKDC-1515	0			.						.						193	198	196					8																	48744423		1984	4172	6156	SO:0001819	synonymous_variant	5591	.			CAAACTGAGCTTC		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.8214C>A	8.37:g.48744423G>T		Somatic	221	0		WXS	Illumina HiSeq	Phase_I	196	76	.	0	0	4	7	3	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Silent	SNP	ENST00000314191.2	37																																																																																				.		0.532	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		T	48744423	G	T	48744423	2	4	15	1	0	0	0	0	0	0	0	1	12550	1277	45	4		4	PRKDC	8	48744423	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		48744423	97619599	35	1282											
VCPIP1	80124	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	67577113	67577113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttgttttctgtccagtaAgaataattttagttgggagc	9	19	9	4	0	1	1	0	0	1	1	2	2	2	2	1	1	1	3	1	1	4	9			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr8:67577113A>G	ENST00000310421.4	-	1	2339	c.2081T>C	c.(2080-2082)cTt>cCt	p.L694P	C8orf44-SGK3_ENST00000519289.1_5'Flank|C8orf44_ENST00000521889.1_5'Flank|C8orf44_ENST00000519561.1_5'Flank	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	694					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			CTGTCCAGTAAGAATAATTTT	0.373																																					p.L694P	NSCLC(179;265 2915 6144 43644)	.											.	VCPIP1-662	0			c.T2081C						.						133	142	139					8																	67577113		2203	4300	6503	SO:0001583	missense	80124	exon1			CCAGTAAGAATAA	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"OTU domain containing"	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.2081T>C	8.37:g.67577113A>G	ENSP00000309031:p.Leu694Pro	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	151	58	NM_025054	0	0	2	3	1	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	37	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	A	16.13	3.036462	0.54896	.	.	ENSG00000175073	ENST00000310421	T	0.46063	0.88	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.61160	0.2325	L	0.56769	1.78	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	T	0.64778	-0.6327	10	0.87932	D	0	-11.0176	15.447	0.75238	1.0:0.0:0.0:0.0	.	694	Q96JH7	VCIP1_HUMAN	P	694	ENSP00000309031:L694P	ENSP00000309031:L694P	L	-	2	0	VCPIP1	67739667	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.244000	0.95423	2.091000	0.63221	0.533000	0.62120	CTT	.		0.373	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			G	67577113	A	G	67577113	3	3	15	1	0	0	0	0	1	0	0	0	17174	72	3	3	1599	3	VCPIP1	8	67577113	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	18832690	67577113	78786909	36	1283											
TAF2	6873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	120816142	120816142	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tagaattttgatacccacaaGagaaaacatgagcacctctc	16	9	6	10	0	1	4	0	2	1	2	2	5	1	4	2	0	3	1	2	0	6	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr8:120816142G>A	ENST00000378164.2	-	5	834	c.536C>T	c.(535-537)tCt>tTt	p.S179F		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	179					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ATACCCACAAGAGAAAACATG	0.333																																					p.S179F		.											.	TAF2-274	0			c.C536T						.						138	140	139					8																	120816142		2203	4300	6503	SO:0001583	missense	6873	exon5			CCACAAGAGAAAA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.536C>T	8.37:g.120816142G>A	ENSP00000367406:p.Ser179Phe	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	160	75	NM_003184	0	0	0	0	0	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198064	0.94997	.	.	ENSG00000064313	ENST00000378164	T	0.05855	3.38	5.89	5.89	0.94794	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24431	0.0592	L	0.56769	1.78	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.00024	-1.2327	10	0.87932	D	0	-13.5961	20.2617	0.98447	0.0:0.0:1.0:0.0	.	179	Q6P1X5	TAF2_HUMAN	F	179	ENSP00000367406:S179F	ENSP00000367406:S179F	S	-	2	0	TAF2	120885323	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.814000	0.99346	2.793000	0.96121	0.655000	0.94253	TCT	.		0.333	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		A	120816142	G	A	120816142	3	1	15	1	0	0	0	0	1	0	0	0	15556	942	33	2	3151	2	TAF2	8	120816142	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	53239029	120816142	25547880	37	1284											
TNFSF15	9966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	117552848	117552848	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaggagaacatggctccgaGgtagatgggctggaaccagt	12	6	15	8	1	0	2	0	0	0	2	1	5	1	3	2	5	2	3	2	5	4	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:117552848G>A	ENST00000374045.4	-	4	753	c.640C>T	c.(640-642)Ctc>Ttc	p.L214F	AL390240.1_ENST00000408807.1_RNA|TNFSF15_ENST00000374044.1_Missense_Mutation_p.L137F	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	214					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						ATGGCTCCGAGGTAGATGGGC	0.493																																					p.L214F		.											.	TNFSF15-227	0			c.C640T						.						155	135	142					9																	117552848		2203	4300	6503	SO:0001583	missense	9966	exon4			CTCCGAGGTAGAT	AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"Tumor necrosis factor (ligand) superfamily"	11931	protein-coding gene	gene with protein product	"vascular endothelial cell growth inhibitor", "TNF superfamily ligand TL1A", "TNF ligand-related molecule 1", "vascular endothelial growth inhibitor-192A"	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.640C>T	9.37:g.117552848G>A	ENSP00000363157:p.Leu214Phe	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	91	39	NM_005118	0	0	0	0	0	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	37	CCDS6809.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.299347	0.60195	.	.	ENSG00000181634	ENST00000374045;ENST00000374044	T;T	0.67523	-0.27;-0.27	6.03	4.2	0.49525	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.000000	0.64402	D	0.000009	T	0.77896	0.4199	M	0.73372	2.23	0.46203	D	0.998926	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.76539	-0.2922	10	0.48119	T	0.1	-26.8042	8.9914	0.36026	0.3322:0.0:0.6678:0.0	.	214;155	O95150;O95150-2	TNF15_HUMAN;.	F	214;137	ENSP00000363157:L214F;ENSP00000363156:L137F	ENSP00000363156:L137F	L	-	1	0	TNFSF15	116592669	0.994000	0.37717	0.997000	0.53966	0.967000	0.64934	0.902000	0.28459	0.885000	0.36088	0.655000	0.94253	CTC	.		0.493	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118		A	117552848	G	A	117552848	3	1	15	1	0	0	0	0	1	0	0	0	16340	1000	35	2	119	2	TNFSF15	9	117552848	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08		117552848	23660583	38	1285											
TNC	3371	hgsc.bcm.edu	37	chr9	117853282	117853282	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagacacctgccaacagctGagtcatggcccccatggtgg	11	6	11	13	0	1	2	1	1	0	1	1	2	1	2	4	3	3	1	4	3	2	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:117853282G>C	ENST00000350763.4	-	2	427	c.16C>G	c.(16-18)Cag>Gag	p.Q6E	TNC_ENST00000542877.1_Missense_Mutation_p.Q6E|TNC_ENST00000535648.1_Missense_Mutation_p.Q6E|TNC_ENST00000346706.3_Missense_Mutation_p.Q6E|TNC_ENST00000345230.3_Missense_Mutation_p.Q6E|TNC_ENST00000340094.3_Missense_Mutation_p.Q6E|TNC_ENST00000537320.1_Missense_Mutation_p.Q6E|TNC_ENST00000423613.2_Missense_Mutation_p.Q6E|TNC_ENST00000341037.4_Missense_Mutation_p.Q6E	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	6					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						GCCAACAGCTGAGTCATGGCC	0.567																																					p.Q6E		.											.	TNC-517	0			c.C16G						.						32	33	33					9																	117853282		2203	4300	6503	SO:0001583	missense	3371	exon2			ACAGCTGAGTCAT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.16C>G	9.37:g.117853282G>C	ENSP00000265131:p.Gln6Glu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_002160	0	0	7	7	0	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.488221	0.26686	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877;ENST00000534839	T;T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.54	-0.0359	0.13891	.	1.121870	0.06517	N	0.738965	T	0.22437	0.0541	L	0.44542	1.39	0.09310	N	1	B;B	0.33103	0.397;0.031	B;B	0.32928	0.155;0.034	T	0.22103	-1.0226	10	0.33141	T	0.24	.	2.2322	0.03999	0.2935:0.1119:0.467:0.1276	.	6;6	E9PC84;P24821	.;TENA_HUMAN	E	6	ENSP00000344400:Q6E;ENSP00000438152:Q6E;ENSP00000344555:Q6E;ENSP00000345861:Q6E;ENSP00000265131:Q6E;ENSP00000339553:Q6E;ENSP00000411406:Q6E;ENSP00000443478:Q6E;ENSP00000442242:Q6E;ENSP00000443469:Q6E	ENSP00000344400:Q6E	Q	-	1	0	TNC	116893103	0.005000	0.15991	0.001000	0.08648	0.005000	0.04900	0.717000	0.25851	-0.293000	0.08986	0.456000	0.33151	CAG	.		0.567	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		C	117853282	G	C	117853282	3	2	15	1	0	0	0	0	1	0	0	0	16302	1299	45	4	6697	4	TNC	9	117853282	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	300434	117853282	23360149	39	1286											
PIP5KL1	138429	hgsc.bcm.edu;broad.mit.edu	37	chr9	130684238	130684238	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccacaggtgctccagcCgcttgcggagcccgtagact	6	9	11	15	3	1	1	0	0	1	1	3	2	3	2	4	2	4	3	4	2	1	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:130684238C>T	ENST00000388747.4	-	10	1117	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q	PIP5KL1_ENST00000300432.3_Missense_Mutation_p.R155Q	NM_001135219.1	NP_001128691.1	Q5T9C9	PI5L1_HUMAN	phosphatidylinositol-4-phosphate 5-kinase-like 1	358	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)	8						GTGCTCCAGCCGCTTGCGGAG	0.687											OREG0019512	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R358Q		.											.	PIP5KL1-240	0			c.G1073A						.						21	21	21					9																	130684238		2183	4276	6459	SO:0001583	missense	138429	exon10			TCCAGCCGCTTGC	BC042184	CCDS6885.1, CCDS48030.1	9q34.13	2008-02-05			ENSG00000167103	ENSG00000167103			28711	protein-coding gene	gene with protein product		612865				12477932	Standard	NM_001135219		Approved	bA203J24.5, MGC46424	uc011mao.2	Q5T9C9	OTTHUMG00000020719	ENST00000388747.4:c.1073G>A	9.37:g.130684238C>T	ENSP00000373399:p.Arg358Gln	Somatic	12	0	1582	WXS	Illumina HiSeq	Phase_I	5	4	NM_001135219	0	0	0	0	0	Q8IVS3	Missense_Mutation	SNP	ENST00000388747.4	37	CCDS48030.1	.	.	.	.	.	.	.	.	.	.	C	36	5.911299	0.97093	.	.	ENSG00000167103	ENST00000388747;ENST00000300432	T;T	0.35605	1.3;1.3	5.32	5.32	0.75619	Phosphatidylinositol-4-phosphate 5-kinase, core (2);	0.000000	0.85682	D	0.000000	T	0.54240	0.1846	L	0.48260	1.515	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.56013	-0.8049	10	0.87932	D	0	-38.4281	16.4798	0.84155	0.0:1.0:0.0:0.0	.	358	Q5T9C9	PI5L1_HUMAN	Q	358;155	ENSP00000373399:R358Q;ENSP00000300432:R155Q	ENSP00000300432:R155Q	R	-	2	0	PIP5KL1	129724059	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.211000	0.51137	2.473000	0.83533	0.555000	0.69702	CGG	.		0.687	PIP5KL1-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054289.2	NM_173492		T	130684238	C	T	130684238	3	4	15	1	0	0	0	0	1	0	0	0	11968	652	23	1	115	1	PIP5KL1	9	130684238	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	12830956	130684238	10529193	40	1287											
C9orf69	90120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139008421	139008421	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagcagctcgttcaccaggCggaagtccacgcgccggcgg	7	4	15	15	7	1	0	1	0	0	0	3	2	2	1	3	4	2	3	3	4	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:139008421C>T	ENST00000418388.1	-	2	828	c.326G>A	c.(325-327)cGc>cAc	p.R109H	C9orf69_ENST00000561457.1_Missense_Mutation_p.A134T			H0YL14	CI069_HUMAN	chromosome 9 open reading frame 69	109					cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of viral process (GO:0048524)|viral process (GO:0016032)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)			endometrium(1)	1		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.58e-07)|Epithelial(140;6.42e-06)		GTTCACCAGGCGGAAGTCCAC	0.657																																					p.R109H		.											.	.	0			c.G326A						.						13	18	16					9																	139008421		2159	4244	6403	SO:0001583	missense	90120	exon2			ACCAGGCGGAAGT		CCDS59155.1	9q34.3	2012-11-26	2012-07-05	2012-07-05	ENSG00000238227	ENSG00000238227			31009	protein-coding gene	gene with protein product						21667337	Standard	NM_152833		Approved	bA83N9.1	uc004cgx.5	H0YL14	OTTHUMG00000020922	ENST00000418388.1:c.326G>A	9.37:g.139008421C>T	ENSP00000453019:p.Arg109His	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	24	12	NM_152833	0	0	6	11	5		Missense_Mutation	SNP	ENST00000418388.1	37	CCDS59155.1																																																																																			.		0.657	C9orf69-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055043.3	NM_152833		T	139008421	C	T	139008421	3	4	15	1	0	0	0	0	1	0	0	0	2498	768	27	1	11	1	C9orf69	9	139008421	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	8324183	139008421	2205010	41	1288											
TMEM72	643236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	45429133	45429133	+	5'UTR	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtaagggagaaagcccactgGctgggctgcttccagaagtt	10	8	14	9	0	0	2	0	0	0	2	1	3	1	2	2	3	2	5	2	3	3	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr10:45429133G>C	ENST00000544540.1	+	0	388				TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						AAGCCCACTGGCTGGGCTGCT	0.602																																					p.W86C		.											.	TMEM72-90	0			c.G258C						.						54	58	57					10																	45429133		1568	3582	5150	SO:0001623	5_prime_UTR_variant	643236	exon4			CCACTGGCTGGGC	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 127"	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.-97G>C	10.37:g.45429133G>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	53	25	NM_001123376	0	0	0	0	0	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	37		.	.	.	.	.	.	.	.	.	.	G	17.68	3.448729	0.63178	.	.	ENSG00000187783	ENST00000389583	.	.	.	5.59	4.68	0.58851	.	0.407067	0.24354	N	0.039259	T	0.67439	0.2893	M	0.62723	1.935	0.80722	D	1	D	0.69078	0.997	D	0.63192	0.912	T	0.65512	-0.6150	9	0.42905	T	0.14	-9.242	9.7258	0.40330	0.0925:0.0:0.9075:0.0	.	86	A0PK05	TMM72_HUMAN	C	86	.	ENSP00000374234:W86C	W	+	3	0	TMEM72	44749139	0.995000	0.38212	1.000000	0.80357	0.867000	0.49689	0.969000	0.29370	2.793000	0.96121	0.655000	0.94253	TGG	.		0.602	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		C	45429133	G	C	45429133	1	2	15	0	1	0	0	0	0	0	0	0	16233	1212	42	4		4	TMEM72	10	45429133	5'UTR	SNP	G	TCGA-A4-8311-01A-11D-2396-08		45429133	90105614	42	1289											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119049810	119049814	+	Frame_Shift_Del	DEL	AGACG	AGACG	-																															acccatcagttgactggacaAgacgaagtgtaagtccaaca																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	AGACG	AGACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr10:119049810_119049814delAGACG	ENST00000334464.5	-	4	1383_1387	c.1144_1148delCGTCT	c.(1144-1149)cgtcttfs	p.RL382fs	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	382	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TGACTGGACAAGACGAAGTGTAAGT	0.41																																					p.382_383del		.											.	PDZD8-90	0			c.1144_1148del						.																																			SO:0001589	frameshift_variant	118987	exon4			.	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1144_1148delCGTCT	10.37:g.119049810_119049814delAGACG	ENSP00000334642:p.Arg382fs	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_173791	0	0	0	0	0	Q86WE0|Q86WE5|Q9UFF1	Frame_Shift_Del	DEL	ENST00000334464.5	37	CCDS7600.1																																																																																			.		0.41	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		-	119049814	AGACG	-	119049810	7	5	15	1	0	1	0	1	0	0	0	0	11731	72	3	0	2324	0	PDZD8	10	119049810	Frame_Shift_Del	DEL	AGACG	TCGA-A4-8311-01A-11D-2396-08	73620677	119049810	16484937	43	1290											
MUC5B	727897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1275533	1275533	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcatccactacaagtccatGgatatcgtcctcactgtcac	11	10	6	14	1	2	0	2	0	0	0	6	1	5	1	3	1	2	1	3	1	3	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:1275533G>C	ENST00000529681.1	+	34	15487	c.15429G>C	c.(15427-15429)atG>atC	p.M5143I	MUC5B_ENST00000447027.1_Missense_Mutation_p.M5146I	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5143	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACAAGTCCATGGATATCGTCC	0.642																																					p.M5143I		.											.	.	0			c.G15429C						.						34	41	39					11																	1275533		2164	4260	6424	SO:0001583	missense	727897	exon34			GTCCATGGATATC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.15429G>C	11.37:g.1275533G>C	ENSP00000436812:p.Met5143Ile	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	53	21	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789191	0.31685	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.15952	2.38;2.58	4.31	-3.06	0.05379	.	.	.	.	.	T	0.09113	0.0225	L	0.29908	0.895	0.09310	N	1	P;P	0.34462	0.454;0.454	B;B	0.31191	0.125;0.125	T	0.29792	-1.0000	9	0.87932	D	0	.	2.4091	0.04420	0.4222:0.118:0.3402:0.1197	.	5480;5146	A7Y9J9;E9PBJ0	.;.	I	5143;5146;5087;42;4855	ENSP00000436812:M5143I;ENSP00000415793:M5146I	ENSP00000343037:M5087I	M	+	3	0	MUC5B	1232109	0.000000	0.05858	0.003000	0.11579	0.609000	0.37215	-0.057000	0.11768	-0.168000	0.10853	0.400000	0.26472	ATG	.		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1275533	G	C	1275533	3	2	15	1	0	0	0	0	1	0	0	0	10004	1348	47	4	15572	4	MUC5B	11	1275533	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08		1275533	133730983	44	1291											
LGALS12	85329	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	63273900	63273900	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gggggcagggctcctggaacGaggatctacagttggagttg	8	8	18	7	1	1	0	0	0	1	0	2	4	2	3	1	6	2	4	1	6	2	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:63273900G>C	ENST00000394618.3	+	1	327	c.36G>C	c.(34-36)acG>acC	p.T12T	LGALS12_ENST00000415491.2_5'Flank|LGALS12_ENST00000340246.5_Silent_p.T12T|LGALS12_ENST00000425950.2_5'Flank|LGALS12_ENST00000255684.5_Silent_p.T12T	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	12					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						CTCCTGGAACGAGGATCTACA	0.572																																					p.T12T		.											.	LGALS12-92	0			c.G36C						.						126	114	118					11																	63273900		2201	4298	6499	SO:0001819	synonymous_variant	85329	exon1			TGGAACGAGGATC	AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.36G>C	11.37:g.63273900G>C		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	86	5	NM_001142535	0	0	0	0	0	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent	SNP	ENST00000394618.3	37	CCDS8045.1																																																																																			.		0.572	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101		C	63273900	G	C	63273900	2	2	15	1	0	0	0	0	0	0	0	1	8760	1045	37	4		4	LGALS12	11	63273900	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	61998367	63273900	71732616	45	1292											
CATSPER1	117144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65788966	65788966	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgggagccgtggccactgaCctgagcctccgcaggacccg	6	5	15	15	3	0	2	0	2	0	0	1	4	1	4	6	3	2	1	6	3	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:65788966C>T	ENST00000312106.5	-	4	1829		c.e4+1			NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1						calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TGGCCACTGACCTGAGCCTCC	0.627																																					.		.											.	CATSPER1-92	0			c.1691+1G>A						.						41	45	44					11																	65788966		2201	4296	6497	SO:0001630	splice_region_variant	117144	exon5			CACTGACCTGAGC	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"Voltage-gated ion channels / Cation channels, sperm associated"	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1691+1G>A	11.37:g.65788966C>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	29	16	NM_053054	0	0	0	0	0	Q96P76	Splice_Site	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.826703	0.32329	.	.	ENSG00000175294	ENST00000312106	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4667	0.61258	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CATSPER1	65545542	1.000000	0.71417	0.985000	0.45067	0.197000	0.23852	4.738000	0.62073	2.227000	0.72691	0.561000	0.74099	.	.		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	Intron	T	65788966	C	T	65788966	5	4	15	1	0	0	0	0	0	0	1	0	2693	521	18	2	686	2	CATSPER1	11	65788966	Splice_Site	SNP	C	TCGA-A4-8311-01A-11D-2396-08	2515066	65788966	69217550	46	1293											
C11orf52	91894	hgsc.bcm.edu	37	chr11	111796415	111796415	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cactgaagccgcagccacaaCagctgcagcagaatctccca	13	4	8	16	1	1	2	0	1	1	1	2	2	1	2	3	0	6	4	3	0	3	0	rs202170534		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:111796415C>G	ENST00000278601.5	+	3	205	c.109C>G	c.(109-111)Cag>Gag	p.Q37E	HSPB2-C11orf52_ENST00000534100.1_3'UTR|CRYAB_ENST00000527950.1_5'Flank|RNA5SP351_ENST00000459480.1_RNA|DIXDC1_ENST00000529225.1_5'Flank|C11orf52_ENST00000527286.1_3'UTR	NM_080659.2	NP_542390.2	Q96A22	CK052_HUMAN	chromosome 11 open reading frame 52	37						extracellular vesicular exosome (GO:0070062)		p.Q37*(1)		lung(2)|ovary(1)	3		all_cancers(61;8.8e-15)|all_epithelial(67;6.27e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.63e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.7e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		GCAGCCACAACAGCTGCAGCA	0.512													C|||	1	0.000199681	0	0	5008	,	,		21658	0		0.001	False		,,,				2504	0				p.Q37E		.											.	C11orf52-91	1	Substitution - Nonsense(1)	ovary(1)	c.C109G						.	C	GLU/GLN	0,4402		0,0,2201	74	82	79		109	1.1	0.1	11		79	3,8591	3.7+/-12.6	0,3,4294	yes	missense	C11orf52	NM_080659.2	29	0,3,6495	GG,GC,CC		0.0349,0.0,0.0231	benign	37/124	111796415	3,12993	2201	4297	6498	SO:0001583	missense	91894	exon3			CCACAACAGCTGC	AK057948	CCDS8353.1	11q23.1	2006-02-06	2006-02-06		ENSG00000149300	ENSG00000149300			30531	protein-coding gene	gene with protein product							Standard	NM_080659		Approved	MGC14839, FLJ25219		Q96A22	OTTHUMG00000166888	ENST00000278601.5:c.109C>G	11.37:g.111796415C>G	ENSP00000278601:p.Gln37Glu	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_080659	0	0	25	25	0		Missense_Mutation	SNP	ENST00000278601.5	37	CCDS8353.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.03	2.115309	0.37339	0.0	3.49E-4	ENSG00000149300	ENST00000529342;ENST00000278601	T;T	0.44881	0.91;0.91	4.38	1.08	0.20341	.	0.574067	0.15833	N	0.242382	T	0.30166	0.0756	L	0.39898	1.24	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.25502	-1.0130	10	0.62326	D	0.03	-0.2206	6.4554	0.21926	0.3722:0.4467:0.1811:0.0	.	37	Q96A22	CK052_HUMAN	E	37	ENSP00000436268:Q37E;ENSP00000278601:Q37E	ENSP00000278601:Q37E	Q	+	1	0	C11orf52	111301625	0.728000	0.28080	0.108000	0.21378	0.186000	0.23388	1.389000	0.34453	0.543000	0.28864	0.561000	0.74099	CAG	C|0.999;G|0.000		0.512	C11orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391673.1	NM_080659		G	111796415	C	G	111796415	3	3	15	1	0	0	0	0	1	0	0	0	1651	479	17	4	119	4	C11orf52	11	111796415	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	46007449	111796415	23210101	47	1294											
BCL9L	283149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118771983	118771983	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccatcacgccactgctgttCtgggcccgaacccgggccat	6	7	10	18	3	2	0	1	0	1	0	2	1	2	0	5	2	2	2	5	2	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:118771983C>T	ENST00000334801.3	-	6	3433	c.2469G>A	c.(2467-2469)caG>caA	p.Q823Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	823	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CACTGCTGTTCTGGGCCCGAA	0.652																																					p.Q823Q		.											.	BCL9L-229	0			c.G2469A						.						49	49	49					11																	118771983		2200	4295	6495	SO:0001819	synonymous_variant	283149	exon6			GCTGTTCTGGGCC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2469G>A	11.37:g.118771983C>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	92	38	NM_182557	0	0	4	12	8	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			.		0.652	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118771983	C	T	118771983	2	4	15	1	0	0	0	0	0	0	0	1	1383	912	32	2		2	BCL9L	11	118771983	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	6975568	118771983	16234533	48	1295											
CBL	867	bcgsc.ca	37	chr11	119156157	119156157	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctgccccaagttccagtgatCcctggacaggaagagaatta	12	8	10	11	0	0	2	0	1	0	1	2	5	2	4	4	2	1	1	4	2	4	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:119156157C>T	ENST00000264033.4	+	11	2198	c.1822C>T	c.(1822-1824)Ccc>Tcc	p.P608S		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	608	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TTCCAGTGATCCCTGGACAGG	0.557			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.P608S				"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL-4020	0			c.C1822T						.						67	67	67					11																	119156157		2199	4295	6494	SO:0001583	missense	867	exon11	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	AGTGATCCCTGGA	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"RING-type (C3HC4) zinc fingers"	1541	protein-coding gene	gene with protein product	"oncogene CBL2"	165360	"Cas-Br-M (murine) ecotropic retroviral transforming sequence"	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1822C>T	11.37:g.119156157C>T	ENSP00000264033:p.Pro608Ser	Somatic	91	0		WXS	Illumina HiSeq	Phase_1	68	4	NM_005188	0	0	3	3	0	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	C	7.137	0.581011	0.13686	.	.	ENSG00000110395	ENST00000264033	T	0.76839	-1.05	5.34	3.48	0.39840	.	0.541904	0.21736	N	0.069893	T	0.68531	0.3011	L	0.36672	1.1	0.30177	N	0.800794	B	0.23442	0.085	B	0.19666	0.026	T	0.66432	-0.5925	10	0.56958	D	0.05	-36.4407	12.6911	0.56974	0.1315:0.7423:0.1262:0.0	.	608	P22681	CBL_HUMAN	S	608	ENSP00000264033:P608S	ENSP00000264033:P608S	P	+	1	0	CBL	118661367	1.000000	0.71417	0.955000	0.39395	0.335000	0.28730	3.388000	0.52509	0.825000	0.34637	-0.127000	0.14921	CCC	.		0.557	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		T	119156157	C	T	119156157	3	4	15	1	0	0	0	0	1	0	0	0	2706	855	30	2	1864	2	CBL	11	119156157	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	384174	119156157	15850359	49	1296											
ARHGEF12	23365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	120352127	120352127	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agaatactcactccgatgggGcaatttcaccattcaccccc	11	9	6	15	1	3	1	3	0	0	1	4	2	4	1	4	2	1	1	4	2	3	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:120352127G>T	ENST00000397843.2	+	39	4562	c.4396G>T	c.(4396-4398)Gca>Tca	p.A1466S	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.A1447S|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.A1363S	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1466					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		CTCCGATGGGGCAATTTCACC	0.537			T	MLL	AML																																p.A1466S		.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12-661	0			c.G4396T						.						91	92	92					11																	120352127		1937	4149	6086	SO:0001583	missense	23365	exon39			GATGGGGCAATTT	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.4396G>T	11.37:g.120352127G>T	ENSP00000380942:p.Ala1466Ser	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	83	28	NM_015313	0	1	16	28	11	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.820487	0.32145	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.66099	-0.08;-0.19;-0.08	6.08	3.08	0.35506	.	0.599101	0.14093	N	0.341889	T	0.43233	0.1238	N	0.19112	0.55	0.18873	N	0.999987	B	0.23377	0.084	B	0.21708	0.036	T	0.22103	-1.0226	10	0.13108	T	0.6	-1.3411	10.087	0.42423	0.0683:0.2579:0.6738:0.0	.	1466	Q9NZN5	ARHGC_HUMAN	S	1466;1447;1363	ENSP00000380942:A1466S;ENSP00000349056:A1447S;ENSP00000432984:A1363S	ENSP00000349056:A1447S	A	+	1	0	ARHGEF12	119857337	1.000000	0.71417	0.695000	0.30226	0.341000	0.28922	3.420000	0.52735	0.398000	0.25338	0.655000	0.94253	GCA	.		0.537	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120352127	G	T	120352127	3	4	15	1	0	0	0	0	1	0	0	0	897	1203	42	4	4550	4	ARHGEF12	11	120352127	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	1195970	120352127	14654389	50	1297											
LARP4	113251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	50847454	50847454	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttactttgaaacaccacTggtaagtgagatccttacaa	14	11	6	10	0	0	2	0	2	0	1	1	3	1	2	3	1	3	1	3	1	5	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr12:50847454T>C	ENST00000398473.2	+	9	1128	c.1016T>C	c.(1015-1017)cTg>cCg	p.L339P	LARP4_ENST00000522085.1_Splice_Site_p.L339P|LARP4_ENST00000347328.5_Intron|LARP4_ENST00000429001.3_Splice_Site_p.L345P|LARP4_ENST00000518444.1_Splice_Site_p.L338P|LARP4_ENST00000518561.1_Splice_Site_p.L269P|LARP4_ENST00000293618.8_Splice_Site_p.L339P	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	339					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						GAAACACCACTGGTAAGTGAG	0.353																																					p.L339P		.											.	LARP4-91	0			c.T1016C						.						143	119	126					12																	50847454		1844	4078	5922	SO:0001630	splice_region_variant	113251	exon9			CACCACTGGTAAG	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1017+1T>C	12.37:g.50847454T>C		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	123	59	NM_001170808	0	0	0	0	0	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	37	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760444	0.69763	.	.	ENSG00000161813	ENST00000293618;ENST00000429001;ENST00000398473;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000518561;ENST00000520064	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	4.05	4.05	0.47172	.	0.000000	0.64402	D	0.000005	T	0.57784	0.2077	M	0.71581	2.175	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.911;1.0;1.0;1.0	D;P;D;D;D	0.91635	0.997;0.756;0.999;0.996;0.996	T	0.61739	-0.7001	10	0.54805	T	0.06	.	13.6919	0.62550	0.0:0.0:0.0:1.0	.	240;338;339;339;345	Q71RC2-2;Q71RC2-3;G3XAA8;Q71RC2;Q71RC2-4	.;.;.;LARP4_HUMAN;.	P	339;345;339;339;339;338;269;240	ENSP00000293618:L339P;ENSP00000415464:L345P;ENSP00000381490:L339P;ENSP00000429781:L339P;ENSP00000429077:L338P;ENSP00000430851:L269P	ENSP00000293618:L339P	L	+	2	0	LARP4	49133721	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.487000	0.81328	1.793000	0.52555	0.402000	0.26972	CTG	.		0.353	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	Missense_Mutation	C	50847454	T	C	50847454	5	2	15	1	0	0	0	0	0	0	1	0	8651	1594	55	3	1050	3	LARP4	12	50847454	Splice_Site	SNP	T	TCGA-A4-8311-01A-11D-2396-08		50847454	83004441	51	1298											
GRASP	160622	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	52401016	52401016	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgagctgtaccgcgcgctCgccgtgtccgggggcaccct	3	6	15	17	7	0	0	0	0	0	0	2	1	1	0	5	2	2	4	5	2	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr12:52401016C>A	ENST00000293662.4	+	1	293	c.213C>A	c.(211-213)ctC>ctA	p.L71L		NM_181711.2	NP_859062.1	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	71					protein localization (GO:0008104)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACCGCGCGCTCGCCGTGTCCG	0.741																																					p.L71L		.											.	GRASP-91	0			c.C213A						.						8	9	9					12																	52401016		1938	4028	5966	SO:0001819	synonymous_variant	160622	exon1			CGCGCTCGCCGTG	AC019244	CCDS8817.1, CCDS61124.1	12q13.13	2011-09-02			ENSG00000161835	ENSG00000161835			18707	protein-coding gene	gene with protein product		612027				10828067	Standard	NM_001271856		Approved		uc001rzo.2	Q7Z6J2	OTTHUMG00000169595	ENST00000293662.4:c.213C>A	12.37:g.52401016C>A		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	25	14	NM_181711	0	0	0	0	0	Q6PIF8|Q7Z741	Silent	SNP	ENST00000293662.4	37	CCDS8817.1																																																																																			.		0.741	GRASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404972.1			A	52401016	C	A	52401016	2	1	15	1	0	0	0	0	0	0	0	1	6776	871	31	4		4	GRASP	12	52401016	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	1553562	52401016	81450879	52	1299											
PCDH17	27253	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	58208351	58208351	+	Frame_Shift_Del	DEL	G	G	-																															aaggtgcttgctaaggactcGggggcgcccgcgcacttgga																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr13:58208351delG	ENST00000377918.3	+	1	1697	c.1671delG	c.(1669-1671)tcgfs	p.S557fs		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	557	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CTAAGGACTCGGGGGCGCCCG	0.592																																					p.S557fs	Melanoma(72;952 1291 1619 12849 33676)	.											.	PCDH17-97	0			c.1671delG						.						39	41	40					13																	58208351		2203	4300	6503	SO:0001589	frameshift_variant	27253	exon1			.	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"Cadherins / Protocadherins : Non-clustered"	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1671delG	13.37:g.58208351delG	ENSP00000367151:p.Ser557fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	93	21	NM_001040429	0	0	0	0	0	A8K1R5|Q5VVW9|Q5VVX0	Frame_Shift_Del	DEL	ENST00000377918.3	37	CCDS31986.1																																																																																			.		0.592	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		-	58208351	G	-	58208351	7	5	15	1	0	1	0	1	0	0	0	0	11538	1103	39	0	1673	0	PCDH17	13	58208351	Frame_Shift_Del	DEL	G	TCGA-A4-8311-01A-11D-2396-08		58208351	56961527	53	1300											
MTHFD1	4522	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	64914978	64914979	+	Frame_Shift_Del	DEL	AA	AA	-																															cttcagtaacttgaagaaacAaattgaaaatgccagaatgt																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr14:64914978_64914979delAA	ENST00000545908.1	+	23	2619_2620	c.2390_2391delAA	c.(2389-2391)caafs	p.Q797fs	MTHFD1_ENST00000216605.8_Frame_Shift_Del_p.Q741fs|CTD-2555O16.2_ENST00000556640.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	741	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	TTGAAGAAACAAATTGAAAATG	0.401																																					p.741_741del	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	.											.	MTHFD1-92	0			c.2222_2223del						.																																			SO:0001589	frameshift_variant	4522	exon23			.	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2390_2391delAA	14.37:g.64914978_64914979delAA	ENSP00000438588:p.Gln797fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	47	16	NM_005956	0	0	0	0	0	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Frame_Shift_Del	DEL	ENST00000545908.1	37																																																																																				.		0.401	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			-	64914979	AA	-	64914978	7	5	15	1	0	1	0	1	0	0	0	0	9952	130	5	0	2312	0	MTHFD1	14	64914978	Frame_Shift_Del	DEL	AA	TCGA-A4-8311-01A-11D-2396-08		64914978	42434562	54	1301											
YY1	7528	bcgsc.ca	37	chr14	100705945	100705945	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgacgactcggacgggctgCgcgccgaggacggcttcgag	6	4	18	13	9	0	0	0	0	0	0	2	6	0	2	1	4	1	2	1	4	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr14:100705945C>T	ENST00000262238.4	+	1	624	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	RP11-638I2.4_ENST00000554537.1_RNA	NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN	YY1 transcription factor	122	Interaction with the SMAD1/SMAD4 complex.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|cell differentiation (GO:0030154)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromosome organization (GO:0051276)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to prostaglandin F (GO:0034696)|response to UV-C (GO:0010225)|RNA localization (GO:0006403)|spermatogenesis (GO:0007283)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|four-way junction DNA binding (GO:0000400)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11		Melanoma(154;0.152)				GGACGGGCTGCGCGCCGAGGA	0.697																																					p.R122C													.	YY1-226	0			c.C364T						.						35	38	37					14																	100705945		2195	4298	6493	SO:0001583	missense	7528	exon1			GGGCTGCGCGCCG	BC020324	CCDS9957.1	14q	2013-01-08			ENSG00000100811	ENSG00000100811		"INO80 complex subunits", "Zinc fingers, C2H2-type"	12856	protein-coding gene	gene with protein product	"INO80 complex subunit S", "Yin and Yang 1 protein"	600013				1655281, 7912122	Standard	NM_003403		Approved	NF-E1, DELTA, UCRBP, YIN-YANG-1, INO80S	uc001ygy.2	P25490	OTTHUMG00000150479	ENST00000262238.4:c.364C>T	14.37:g.100705945C>T	ENSP00000262238:p.Arg122Cys	Somatic	122	0		WXS	Illumina HiSeq	Phase_1	104	6	NM_003403	0	0	8	8	0	Q14935	Missense_Mutation	SNP	ENST00000262238.4	37	CCDS9957.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593967	0.86953	.	.	ENSG00000100811	ENST00000262238	T	0.10960	2.82	2.34	2.34	0.29019	.	0.145303	0.45867	U	0.000332	T	0.08313	0.0207	N	0.22421	0.69	0.58432	D	0.999999	D	0.58620	0.983	B	0.43575	0.424	T	0.25916	-1.0118	10	0.51188	T	0.08	.	11.574	0.50850	0.0:1.0:0.0:0.0	.	122	P25490	TYY1_HUMAN	C	122	ENSP00000262238:R122C	ENSP00000262238:R122C	R	+	1	0	YY1	99775698	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	6.051000	0.71072	1.305000	0.44909	0.549000	0.68633	CGC	.		0.697	YY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318277.1	NM_003403		T	100705945	C	T	100705945	3	4	15	1	0	0	0	0	1	0	0	0	17540	768	27	1	366	1	YY1	14	100705945	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	35790967	100705945	6643595	55	1302											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41864763	41864763	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggattggggagaacccctttGtgagtacctggtgtgggggt	6	11	18	6	0	0	2	0	1	0	1	0	4	0	3	3	6	2	1	3	6	2	3	rs200965082		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr15:41864763G>A	ENST00000263798.3	+	15	2099		c.e15+1		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GAACCCCTTTGTGAGTACCTG	0.612																																					.		.											.	TYRO3-1388	0			c.1875+1G>A						.						45	40	42					15																	41864763		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon15			CCCTTTGTGAGTA	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1875+1G>A	15.37:g.41864763G>A		Somatic	73	2		WXS	Illumina HiSeq	Phase_I	55	4	NM_006293	0	0	0	0	0	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.398910	0.83120	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4658	0.94939	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39652055	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.858000	0.99539	2.599000	0.87857	0.655000	0.94253	.	G|0.999;T|0.001		0.612	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron	A	41864763	G	A	41864763	5	1	15	1	0	0	0	0	0	0	1	0	16847	1391	48	2	1934	2	TYRO3	15	41864763	Splice_Site	SNP	G	TCGA-A4-8311-01A-11D-2396-08		41864763	60666629	56	1303											
MAPK6	5597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	52338881	52338881	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattagaagacttgaccatgAtaacattgtgaaagtgtttg	14	14	9	4	0	0	5	0	3	0	2	0	5	0	5	1	0	1	1	1	0	5	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr15:52338881A>G	ENST00000261845.5	+	2	1031	c.224A>G	c.(223-225)gAt>gGt	p.D75G		NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	75	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTTGACCATGATAACATTGTG	0.398																																					p.D75G		.											.	MAPK6-1403	0			c.A224G						.						95	94	94					15																	52338881		2195	4293	6488	SO:0001583	missense	5597	exon2			ACCATGATAACAT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.224A>G	15.37:g.52338881A>G	ENSP00000261845:p.Asp75Gly	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	119	45	NM_002748	0	0	7	9	2	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189988	0.78789	.	.	ENSG00000069956	ENST00000261845	T	0.43688	0.94	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	L	0.56199	1.76	0.80722	D	1	D	0.60575	0.988	D	0.79784	0.993	T	0.63646	-0.6590	10	0.87932	D	0	-21.6017	15.4537	0.75297	1.0:0.0:0.0:0.0	.	75	Q16659	MK06_HUMAN	G	75	ENSP00000261845:D75G	ENSP00000261845:D75G	D	+	2	0	MAPK6	50126173	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.249000	0.95470	2.067000	0.61834	0.529000	0.55759	GAT	.		0.398	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		G	52338881	A	G	52338881	3	3	15	1	0	0	0	0	1	0	0	0	9306	333	12	3	226	3	MAPK6	15	52338881	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	10474118	52338881	50192511	57	1304											
SLTM	79811	hgsc.bcm.edu	37	chr15	59186365	59186365	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatcattttctttcttcaTttctttcttagagggatcac	7	21	4	9	0	8	1	4	0	4	1	8	2	8	2	0	1	0	0	0	1	1	8			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr15:59186365T>C	ENST00000380516.2	-	11	1492	c.1405A>G	c.(1405-1407)Atg>Gtg	p.M469V	AC025918.2_ENST00000452467.1_RNA|SLTM_ENST00000536328.1_Missense_Mutation_p.M38V	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	469					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TCTTTCTTCATTTCTTTCTTA	0.294																																					p.M469V		.											.	SLTM-91	0			c.A1405G						.						85	80	82					15																	59186365		2188	4289	6477	SO:0001583	missense	79811	exon11			TCTTCATTTCTTT	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.1405A>G	15.37:g.59186365T>C	ENSP00000369887:p.Met469Val	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_024755	0	0	19	19	0	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	37	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	T	11.67	1.708574	0.30322	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328;ENST00000249736	D;T	0.86956	-2.19;2.86	5.46	0.551	0.17225	.	0.132360	0.33610	N	0.004722	T	0.69214	0.3086	N	0.14661	0.345	0.22737	N	0.998798	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.51957	-0.8639	10	0.10636	T	0.68	.	5.9184	0.19067	0.2961:0.0:0.3918:0.3121	.	469;38	Q9NWH9;A8K5V8	SLTM_HUMAN;.	V	469;62;38;451	ENSP00000369887:M469V;ENSP00000249736:M451V	ENSP00000249736:M451V	M	-	1	0	SLTM	56973657	0.052000	0.20516	0.988000	0.46212	0.993000	0.82548	0.155000	0.16362	-0.156000	0.11079	0.528000	0.53228	ATG	.		0.294	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		C	59186365	T	C	59186365	3	2	15	1	0	0	0	0	1	0	0	0	14786	1493	52	3	1743	3	SLTM	15	59186365	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	6847484	59186365	43345027	58	1305											
RAB11FIP3	9727	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	568988	568988	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaactccggtcctgcacGccctgtctgaaggccaacat	9	8	10	14	2	1	2	0	2	1	0	3	2	3	2	4	2	3	1	4	2	3	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:568988G>A	ENST00000262305.4	+	10	2074	c.1686G>A	c.(1684-1686)acG>acA	p.T562T	RAB11FIP3_ENST00000450428.1_Silent_p.T266T|RAB11FIP3_ENST00000457159.1_Silent_p.T607T	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	562	ARF-binding domain (ABD).				cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				GGTCCTGCACGCCCTGTCTGA	0.612																																					p.T562T	Melanoma(160;2366 2595 4474 8099)	.											.	RAB11FIP3-90	0			c.G1686A						.						142	124	130					16																	568988		2201	4300	6501	SO:0001819	synonymous_variant	9727	exon10			CTGCACGCCCTGT	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"EF-hand domain containing"	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1686G>A	16.37:g.568988G>A		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	129	34	NM_014700	0	0	48	68	20	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																			.		0.612	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		A	568988	G	A	568988	2	1	15	1	0	0	0	0	0	0	0	1	12927	1074	38	1		1	RAB11FIP3	16	568988	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		568988	89785765	59	1306											
MRPS34	65993	hgsc.bcm.edu	37	chr16	1822947	1822947	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaggcggctctcgcggcgCacgtcggcccaggcccggac	6	3	16	16	7	1	1	0	0	1	1	3	2	1	2	2	6	0	2	2	6	1	0	rs1076695	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:1822947C>G	ENST00000397375.2	-	1	209	c.174G>C	c.(172-174)gtG>gtC	p.V58V	MRPS34_ENST00000177742.3_Silent_p.V58V|EME2_ENST00000568449.1_5'Flank|NME3_ENST00000219302.3_5'Flank|NME3_ENST00000563498.1_5'Flank|EME2_ENST00000307394.7_5'Flank	NM_023936.1	NP_076425.1	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34	58						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|skin(2)	3						TCTCGCGGCGCACGTCGGCCC	0.726													C|||	251	0.0501198	0.0061	0.0965	5008	,	,		10499	0.002		0.1421	False		,,,				2504	0.0317				p.V58V		.											.	MRPS34-92	0			c.G174C						.	C		25,2311		0,25,1143	1	2	2		174	1.7	1	16	dbSNP_86	2	405,4871		9,387,2242	no	coding-synonymous	MRPS34	NM_023936.1		9,412,3385	GG,GC,CC		7.6763,1.0702,5.649		58/219	1822947	430,7182	1168	2638	3806	SO:0001819	synonymous_variant	65993	exon1			GCGGCGCACGTCG	BC001182	CCDS10444.1, CCDS73805.1	16p13.3	2012-09-13			ENSG00000074071	ENSG00000074071		"Mitochondrial ribosomal proteins / small subunits"	16618	protein-coding gene	gene with protein product		611994					Standard	NM_023936		Approved	MRP-S12, MGC2616	uc002cmo.3	P82930	OTTHUMG00000128636	ENST00000397375.2:c.174G>C	16.37:g.1822947C>G		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	2	NM_023936	0	0	2	7	5	Q9BVI7	Silent	SNP	ENST00000397375.2	37	CCDS10444.1																																																																																			C|0.923;G|0.077		0.726	MRPS34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250506.1	NM_023936		G	1822947	C	G	1822947	2	3	15	1	0	0	0	0	0	0	0	1	9868	697	25	4		4	MRPS34	16	1822947	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	1253959	1822947	88531806	60	1307											
ZNF263	10127	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	3339974	3339974	+	Frame_Shift_Del	DEL	T	T	-																															cgcacactggggagaagcccTacaagtgccctgagtgtggg																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:3339974delT	ENST00000219069.5	+	6	2344	c.1468delT	c.(1468-1470)tacfs	p.Y490fs	ZNF263_ENST00000538765.1_Frame_Shift_Del_p.Y138fs	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	490					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						GGAGAAGCCCTACAAGTGCCC	0.537																																					p.Y490fs		.											.	ZNF263-94	0			c.1468delT						.						69	67	68					16																	3339974		2197	4300	6497	SO:0001589	frameshift_variant	10127	exon6			.	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1468delT	16.37:g.3339974delT	ENSP00000219069:p.Tyr490fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	68	19	NM_005741	0	0	0	0	0	B2R634|O43387|Q96H95	Frame_Shift_Del	DEL	ENST00000219069.5	37	CCDS10499.1																																																																																			.		0.537	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			-	3339974	T	-	3339974	7	5	15	1	0	1	0	1	0	0	0	0	17835	1522	53	0	1490	0	ZNF263	16	3339974	Frame_Shift_Del	DEL	T	TCGA-A4-8311-01A-11D-2396-08	1517027	3339974	87014779	61	1308											
PPP4C	5531	hgsc.bcm.edu	37	chr16	30087732	30087732	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gcgacctggaccggcagatcGagcagctgcgtcgctgcgag	7	5	16	13	6	0	1	0	0	0	1	2	5	0	2	2	2	4	4	2	2	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:30087732G>C	ENST00000279387.7	+	2	202	c.34G>C	c.(34-36)Gag>Cag	p.E12Q	PPP4C_ENST00000561610.1_Missense_Mutation_p.E12Q	NM_002720.1	NP_002711.1	P60510	PP4C_HUMAN	protein phosphatase 4, catalytic subunit	12					dephosphorylation (GO:0016311)|NIK/NF-kappaB signaling (GO:0038061)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase 4 complex (GO:0030289)	metal ion binding (GO:0046872)|NF-kappaB-inducing kinase activity (GO:0004704)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(2)|pancreas(1)|skin(1)|urinary_tract(1)	9						CCGGCAGATCGAGCAGCTGCG	0.706																																					p.E12Q		.											.	PPP4C-226	0			c.G34C						.						28	26	27					16																	30087732		2197	4299	6496	SO:0001583	missense	5531	exon2			CAGATCGAGCAGC		CCDS10669.1	16p11.2	2010-03-17	2010-03-05		ENSG00000149923	ENSG00000149923	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9319	protein-coding gene	gene with protein product	"protein phosphatase X, catalytic subunit"	602035	"protein phosphatase 4 (formerly X), catalytic subunit"			9177794	Standard	NM_002720		Approved	PP4, PPX	uc002dwf.3	P60510	OTTHUMG00000132113	ENST00000279387.7:c.34G>C	16.37:g.30087732G>C	ENSP00000279387:p.Glu12Gln	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_002720	0	0	75	77	2	P33172	Missense_Mutation	SNP	ENST00000279387.7	37	CCDS10669.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700379	0.88924	.	.	ENSG00000149923	ENST00000279387	T	0.06608	3.28	6.16	4.18	0.49190	.	0.047590	0.85682	D	0.000000	T	0.12603	0.0306	M	0.86268	2.805	0.80722	D	1	B	0.17268	0.021	B	0.14023	0.01	T	0.01982	-1.1235	10	0.62326	D	0.03	-5.1047	11.8243	0.52259	0.068:0.1226:0.8094:0.0	.	12	P60510	PP4C_HUMAN	Q	12	ENSP00000279387:E12Q	ENSP00000279387:E12Q	E	+	1	0	PPP4C	29995233	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.378000	0.66190	1.600000	0.50102	0.650000	0.86243	GAG	.		0.706	PPP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255155.2	NM_002720		C	30087732	G	C	30087732	3	2	15	1	0	0	0	0	1	0	0	0	12431	1059	37	4	36	4	PPP4C	16	30087732	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	26747758	30087732	60267021	62	1309											
ALOX15	246	hgsc.bcm.edu	37	chr17	4542864	4542864	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttaaggaggtgccgtttGcgcagtttcacaaacagcag	10	10	11	10	2	1	0	1	0	0	0	2	1	2	1	2	2	4	4	2	2	2	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:4542864G>A	ENST00000570836.1	-	3	294	c.198C>T	c.(196-198)cgC>cgT	p.R66R	ALOX15_ENST00000574640.1_Intron|ALOX15_ENST00000545513.1_Silent_p.R88R|ALOX15_ENST00000293761.3_Silent_p.R66R			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	66	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		GGTGCCGTTTGCGCAGTTTCA	0.627																																					p.R66R		.											.	ALOX15-229	0			c.C198T						.						42	42	42					17																	4542864		2203	4300	6503	SO:0001819	synonymous_variant	246	exon2			CCGTTTGCGCAGT	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"Arachidonate lipoxygenases"	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.198C>T	17.37:g.4542864G>A		Somatic	47	2		WXS	Illumina HiSeq	Phase_I	69	5	NM_001140	0	0	0	0	0	A8K2P4|B7ZA11|Q8N6R7|Q99657	Silent	SNP	ENST00000570836.1	37	CCDS11049.1																																																																																			.		0.627	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2			A	4542864	G	A	4542864	2	1	15	1	0	0	0	0	0	0	0	1	538	1306	46	2		2	ALOX15	17	4542864	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		4542864	76652346	63	1310											
ULK2	9706	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	19770705	19770705	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacgagatccctcttgctgTactcgaagtcacccaccacc	9	8	6	18	2	2	1	1	0	1	1	4	3	3	1	5	0	2	2	5	0	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:19770705T>A	ENST00000395544.4	-	1	525	c.26A>T	c.(25-27)tAc>tTc	p.Y9F	ULK2_ENST00000361658.2_Missense_Mutation_p.Y9F	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	9	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CCTCTTGCTGTACTCGAAGTC	0.771																																					p.Y9F		.											.	ULK2-334	0			c.A26T						.						21	21	21					17																	19770705		2197	4295	6492	SO:0001583	missense	9706	exon1			TTGCTGTACTCGA	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"unc-51 (C. elegans)-like kinase 2", "unc-51-like kinase 2 (C. elegans)"			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.26A>T	17.37:g.19770705T>A	ENSP00000378914:p.Tyr9Phe	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	51	29	NM_001142610	0	0	0	0	0	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	37	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.181057	0.38511	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.30981	1.51;1.51	4.71	3.61	0.41365	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067152	0.64402	D	0.000007	T	0.39860	0.1094	L	0.42744	1.35	0.49687	D	0.999814	D	0.76494	0.999	D	0.79108	0.992	T	0.21724	-1.0237	10	0.09590	T	0.72	-10.0083	9.917	0.41442	0.1526:0.0:0.0:0.8474	.	9	Q8IYT8	ULK2_HUMAN	F	9	ENSP00000354877:Y9F;ENSP00000378914:Y9F	ENSP00000354877:Y9F	Y	-	2	0	ULK2	19711297	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.963000	0.56773	0.633000	0.30452	0.472000	0.43445	TAC	.		0.771	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		A	19770705	T	A	19770705	3	1	15	1	0	0	0	0	1	0	0	0	17009	1638	57	5	3192	5	ULK2	17	19770705	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	15227841	19770705	61424505	64	1311											
EVI2A	2123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	29645740	29645740	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggactgttgctgacgacagAaggtatataaagctcctgtt	12	11	11	7	1	0	2	0	1	0	1	1	4	1	3	1	2	2	5	1	2	5	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:29645740A>T	ENST00000462804.2	-	2	691	c.292T>A	c.(292-294)Tct>Act	p.S98T	NF1_ENST00000581113.2_Intron|EVI2A_ENST00000247270.3_Missense_Mutation_p.S121T|NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron|EVI2A_ENST00000461237.1_Missense_Mutation_p.S98T|CTD-2370N5.3_ENST00000578584.1_Missense_Mutation_p.F37Y	NM_014210.3	NP_055025.2	P22794	EVI2A_HUMAN	ecotropic viral integration site 2A	98					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.0?(8)|p.?(3)|p.S121P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;5.94e-13)|Epithelial(4;7.98e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.4e-12)|GBM - Glioblastoma multiforme(4;0.18)		CTGACGACAGAAGGTATATAA	0.368																																					p.S121T		.											.	EVI2A-136	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)|liver(1)	c.T361A						.						153	153	153					17																	29645740		2203	4300	6503	SO:0001583	missense	2123	exon3			CGACAGAAGGTAT	M55267	CCDS32608.1, CCDS42293.1	17q11.2	2008-07-18			ENSG00000126860	ENSG00000126860			3499	protein-coding gene	gene with protein product		158380		EVI2		2117566	Standard	NM_014210		Approved	EVDA	uc002hgm.3	P22794	OTTHUMG00000159306	ENST00000462804.2:c.292T>A	17.37:g.29645740A>T	ENSP00000420557:p.Ser98Thr	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	196	116	NM_001003927	0	0	1	1	0	B2R5X2|B4DHX8	Missense_Mutation	SNP	ENST00000462804.2	37	CCDS42293.1	.	.	.	.	.	.	.	.	.	.	A	7.116	0.577064	0.13686	.	.	ENSG00000126860	ENST00000394755;ENST00000462804;ENST00000461237;ENST00000247270	.	.	.	4.67	-0.204	0.13200	.	1.194170	0.05806	N	0.613220	T	0.23249	0.0562	L	0.50333	1.59	0.19300	N	0.99998	B;B	0.33318	0.058;0.408	B;B	0.29785	0.091;0.107	T	0.12400	-1.0549	9	0.07175	T	0.84	.	0.9302	0.01333	0.421:0.1575:0.2688:0.1527	.	98;121	P22794;P22794-2	EVI2A_HUMAN;.	T	98;94;98;121	.	ENSP00000247270:S121T	S	-	1	0	EVI2A	26669866	0.000000	0.05858	0.002000	0.10522	0.601000	0.36947	0.005000	0.13129	-0.022000	0.13986	0.459000	0.35465	TCT	.		0.368	EVI2A-001	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354491.3	NM_014210		T	29645740	A	T	29645740	3	4	15	1	0	0	0	0	1	0	0	0	5300	246	9	5	422	5	EVI2A	17	29645740	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	9875035	29645740	51549470	65	1312											
HNF1B	6928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	36099582	36099582	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccctctgggggatgttgtgTtgctgcatgtaacccttgat	5	15	12	9	0	1	1	0	1	1	0	2	2	2	2	2	2	3	5	2	2	1	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:36099582T>C	ENST00000225893.4	-	2	754	c.393A>G	c.(391-393)caA>caG	p.Q131Q	HNF1B_ENST00000560016.1_Silent_p.Q131Q|HNF1B_ENST00000561193.1_Silent_p.Q131Q|HNF1B_ENST00000427275.2_Silent_p.Q131Q	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	131					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GGATGTTGTGTTGCTGCATGT	0.547																																					p.Q131Q	Colon(71;102 1179 9001 27917 43397)	.											.	HNF1B-71	0			c.A393G						.						101	86	92					17																	36099582		2203	4300	6503	SO:0001819	synonymous_variant	6928	exon2			GTTGTGTTGCTGC	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.393A>G	17.37:g.36099582T>C		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	68	42	NM_001165923	0	0	26	88	62	B4DKM3|E0YMJ9	Silent	SNP	ENST00000225893.4	37	CCDS11324.1																																																																																			.		0.547	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		C	36099582	T	C	36099582	2	2	15	1	0	0	0	0	0	0	0	1	7273	1722	60	3		3	HNF1B	17	36099582	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	6453842	36099582	45095628	66	1313											
KRT26	353288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38926071	38926071	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgttttaattcggtcagctCatttctggctgctgtggctg	4	16	12	9	2	3	0	2	0	1	0	4	0	3	0	0	3	2	5	0	3	1	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:38926071C>A	ENST00000335552.4	-	5	952	c.904G>T	c.(904-906)Gag>Tag	p.E302*		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				TCGGTCAGCTCATTTCTGGCT	0.463																																					p.E302X		.											.	KRT26-90	0			c.G904T						.						174	159	164					17																	38926071		2203	4300	6503	SO:0001587	stop_gained	353288	exon5			TCAGCTCATTTCT	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"-", "Intermediate filaments type I, keratins (acidic)"	30840	protein-coding gene	gene with protein product			"keratin 25B"	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.904G>T	17.37:g.38926071C>A	ENSP00000334798:p.Glu302*	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	214	68	NM_181539	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000335552.4	37	CCDS11374.1	.	.	.	.	.	.	.	.	.	.	C	36	5.661653	0.96734	.	.	ENSG00000186393	ENST00000335552	.	.	.	5.24	4.24	0.50183	.	0.102432	0.42821	D	0.000643	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.7173	0.77677	0.0:0.7423:0.2577:0.0	.	.	.	.	X	302	.	ENSP00000334798:E302X	E	-	1	0	KRT26	36179597	0.424000	0.25490	1.000000	0.80357	0.917000	0.54804	1.023000	0.30065	1.292000	0.44672	0.655000	0.94253	GAG	.		0.463	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		A	38926071	C	A	38926071	4	1	15	1	0	0	0	0	0	1	0	0	8484	835	29	4	518	4	KRT26	17	38926071	Nonsense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	2826489	38926071	42269139	67	1314											
NARF	26502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80443514	80443514	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccattccactttgtggaggtCctcgcctgtgctggaggtga	5	12	13	11	1	0	1	0	1	0	0	3	3	2	3	4	4	1	1	4	4	0	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:80443514C>T	ENST00000309794.11	+	10	1311	c.1113C>T	c.(1111-1113)gtC>gtT	p.V371V	NARF_ENST00000345415.7_Silent_p.V323V|NARF-IT1_ENST00000584012.1_RNA|NARF_ENST00000457415.3_Silent_p.V417V|NARF_ENST00000390006.4_Silent_p.V312V	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	371						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			TTGTGGAGGTCCTCGCCTGTG	0.572																																					p.V371V		.											.	NARF-226	0			c.C1113T						.						106	93	97					17																	80443514		2203	4300	6503	SO:0001819	synonymous_variant	26502	exon10			GGAGGTCCTCGCC	BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.1113C>T	17.37:g.80443514C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	123	86	NM_012336	0	0	26	60	34	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Silent	SNP	ENST00000309794.11	37	CCDS32777.1																																																																																			.		0.572	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		T	80443514	C	T	80443514	2	4	15	1	0	0	0	0	0	0	0	1	10192	842	30	2		2	NARF	17	80443514	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	41517443	80443514	751696	68	1315											
MEP1B	4225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	29788204	29788204	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttcccagggggccagagAgtgatcactccaacatgggc	10	6	14	11	0	1	2	1	1	0	1	3	3	3	2	3	4	1	1	3	4	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr18:29788204A>T	ENST00000269202.6	+	9	936	c.889A>T	c.(889-891)Agt>Tgt	p.S297C	MEP1B_ENST00000581447.1_Missense_Mutation_p.S297C	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	297	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GGGGCCAGAGAGTGATCACTC	0.478																																					p.S297C		.											.	MEP1B-92	0			c.A889T						.						83	86	85					18																	29788204		1915	4116	6031	SO:0001583	missense	4225	exon9			CCAGAGAGTGATC	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.889A>T	18.37:g.29788204A>T	ENSP00000269202:p.Ser297Cys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	83	36	NM_005925	0	0	0	0	0	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103407	0.56291	.	.	ENSG00000141434	ENST00000269202	T	0.02369	4.32	5.48	4.33	0.51752	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.625246	0.18028	N	0.154004	T	0.11965	0.0291	M	0.77313	2.365	0.09310	N	1	P	0.51791	0.948	P	0.59948	0.866	T	0.02047	-1.1223	10	0.62326	D	0.03	-5.1783	10.7622	0.46272	0.9255:0.0:0.0745:0.0	.	297	Q16820	MEP1B_HUMAN	C	297	ENSP00000269202:S297C	ENSP00000269202:S297C	S	+	1	0	MEP1B	28042202	0.761000	0.28439	0.207000	0.23584	0.486000	0.33341	6.024000	0.70857	2.078000	0.62432	0.459000	0.35465	AGT	.		0.478	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		T	29788204	A	T	29788204	3	4	15	1	0	0	0	0	1	0	0	0	9501	304	11	5	923	5	MEP1B	18	29788204	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08		29788204	48289044	69	1316											
PQLC1	80148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	77679262	77679262	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcttcggtcagcacagccAggaagcccagggtctccaca	9	6	12	14	1	2	0	1	0	1	0	4	1	2	1	3	4	3	2	3	4	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr18:77679262A>T	ENST00000397778.2	-	5	712	c.530T>A	c.(529-531)cTg>cAg	p.L177Q	PQLC1_ENST00000409073.1_Missense_Mutation_p.L94Q|PQLC1_ENST00000357575.4_Missense_Mutation_p.L159Q|PQLC1_ENST00000590381.1_Intron	NM_025078.4	NP_079354.2	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1	177						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	9		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)		CAGCACAGCCAGGAAGCCCAG	0.652																																					p.L177Q		.											.	PQLC1-154	0			c.T530A						.						88	75	79					18																	77679262		2203	4300	6503	SO:0001583	missense	80148	exon5			ACAGCCAGGAAGC	AK123870	CCDS12020.1, CCDS54192.1, CCDS54193.1	18q23	2004-01-14			ENSG00000122490	ENSG00000122490			26188	protein-coding gene	gene with protein product						12477932	Standard	NM_025078		Approved	FLJ22378	uc002lnl.2	Q8N2U9	OTTHUMG00000132921	ENST00000397778.2:c.530T>A	18.37:g.77679262A>T	ENSP00000380880:p.Leu177Gln	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	50	18	NM_025078	0	0	12	17	5	B7Z7D9|G5E989|Q9H6D0	Missense_Mutation	SNP	ENST00000397778.2	37	CCDS12020.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453736	0.84209	.	.	ENSG00000122490	ENST00000397778;ENST00000409073;ENST00000357575	D;D;D	0.98531	-4.98;-4.98;-4.98	5.1	3.95	0.45737	.	0.000000	0.64402	D	0.000002	D	0.98707	0.9566	M	0.85197	2.74	0.80722	D	1	D;P	0.89917	1.0;0.937	D;P	0.81914	0.995;0.71	D	0.98869	1.0765	10	0.56958	D	0.05	-19.803	10.2033	0.43099	0.9213:0.0:0.0786:0.0	.	177;159	Q8N2U9;G5E989	PQLC1_HUMAN;.	Q	177;94;159	ENSP00000380880:L177Q;ENSP00000387221:L94Q;ENSP00000350188:L159Q	ENSP00000350188:L159Q	L	-	2	0	PQLC1	75780250	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	6.181000	0.71988	1.917000	0.55516	0.533000	0.62120	CTG	.		0.652	PQLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256434.1	NM_025078		T	77679262	A	T	77679262	3	4	15	1	0	0	0	0	1	0	0	0	12447	188	7	5	293	5	PQLC1	18	77679262	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	47891058	77679262	397986	70	1317											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1046944	1046944	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatggggctcagccgcgCggtgctctggctaggctggt	3	8	17	13	4	2	0	1	0	1	0	2	0	2	0	2	6	2	4	2	6	1	1	rs144979723|rs142076058|rs375206158	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:1046944C>G	ENST00000263094.6	+	14	1997	c.1766C>G	c.(1765-1767)gCg>gGg	p.A589G	ABCA7_ENST00000533574.1_Intron|ABCA7_ENST00000435683.2_Missense_Mutation_p.A451G|ABCA7_ENST00000433129.1_Missense_Mutation_p.A589G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	589					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCAGCCGCGCGGTGCTCTGG	0.692													C|||	5	0.000998403	0	0	5008	,	,		13253	0.002		0	False		,,,				2504	0.0031				p.A589G		.											.	ABCA7-98	0			c.C1766G						.						17	18	18					19																	1046944		2170	4265	6435	SO:0001583	missense	10347	exon14			GCCGCGCGGTGCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1766C>G	19.37:g.1046944C>G	ENSP00000263094:p.Ala589Gly	Somatic	8	1		WXS	Illumina HiSeq	Phase_I	10	3	NM_019112	0	0	2	3	1	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	c	0.005	-2.154384	0.00325	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.80909	-1.43;-1.43	4.68	0.595	0.17490	.	.	.	.	.	T	0.60183	0.2249	N	0.03948	-0.315	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.21546	0.015;0.035	T	0.30357	-0.9981	9	0.09590	T	0.72	.	16.2636	0.82563	0.0:0.5375:0.4625:0.0	.	451;589	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	G	589	ENSP00000263094:A589G;ENSP00000414062:A589G	ENSP00000263094:A589G	A	+	2	0	ABCA7	997944	0.806000	0.28996	0.000000	0.03702	0.012000	0.07955	1.386000	0.34419	0.054000	0.16065	-1.338000	0.01255	GCG	C|0.999;T|0.001		0.692	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		G	1046944	C	G	1046944	3	3	15	1	0	0	0	0	1	0	0	0	37	768	27	4	1816	4	ABCA7	19	1046944	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08		1046944	58082039	71	1318											
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2416797	2416797	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccggatggggaaatacgcaGgaaggaaatggtgagcgctg	12	6	17	6	3	0	1	0	1	0	0	1	5	1	5	1	6	2	2	1	6	4	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:2416797G>A	ENST00000332578.3	+	11	1905	c.1905G>A	c.(1903-1905)caG>caA	p.Q635Q		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	635	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAATACGCAGGAAGGAAATG	0.592																																					p.Q635Q		.											.	TMPRSS9-91	0			c.G1905A						.						31	35	34					19																	2416797		2203	4299	6502	SO:0001819	synonymous_variant	360200	exon11			TACGCAGGAAGGA	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1905G>A	19.37:g.2416797G>A		Somatic	44	1		WXS	Illumina HiSeq	Phase_I	39	2	NM_182973	0	0	0	0	0	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			.		0.592	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		A	2416797	G	A	2416797	2	1	15	1	0	0	0	0	0	0	0	1	16285	991	35	2		2	TMPRSS9	19	2416797	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	1369853	2416797	56712186	72	1319											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9077786	9077786	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatttctcacagtggacctGatctctgggctgatgctggg	7	12	13	9	0	2	2	1	2	2	0	4	4	2	3	1	3	1	2	1	3	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:9077786G>T	ENST00000397910.4	-	3	9863	c.9660C>A	c.(9658-9660)atC>atA	p.I3220I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3221	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTGGACCTGATCTCTGGGC	0.498																																					p.I3220I		.											.	MUC16-566	0			c.C9660A						.						142	140	140					19																	9077786		1965	4150	6115	SO:0001819	synonymous_variant	94025	exon3			GGACCTGATCTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9660C>A	19.37:g.9077786G>T		Somatic	162	0		WXS	Illumina HiSeq	Phase_I	157	71	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			.		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9077786	G	T	9077786	2	4	15	1	0	0	0	0	0	0	0	1	9998	1280	45	4		4	MUC16	19	9077786	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	6660989	9077786	50051197	73	1320											
ANGPTL6	83854	broad.mit.edu	37	chr19	10206815	10206815	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggacgcgttgagcacgCgctccccgagcagcgccagc	6	3	15	17	8	0	1	0	1	0	0	1	3	1	2	3	2	4	4	3	2	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:10206815C>T	ENST00000253109.4	-	2	663	c.425G>A	c.(424-426)cGc>cAc	p.R142H	ANGPTL6_ENST00000592641.1_Missense_Mutation_p.R142H|ANGPTL6_ENST00000589181.1_Missense_Mutation_p.R142H	NM_031917.2	NP_114123.2	Q8NI99	ANGL6_HUMAN	angiopoietin-like 6	142					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)	12			OV - Ovarian serous cystadenocarcinoma(20;3.58e-08)|Epithelial(33;2.5e-05)|all cancers(31;5.96e-05)			GTTGAGCACGCGCTCCCCGAG	0.771																																					p.R142H													.	ANGPTL6-90	0			c.G425A						.						4	4	4					19																	10206815		1659	3270	4929	SO:0001583	missense	83854	exon2			AGCACGCGCTCCC	AB054064	CCDS12224.1	19p13.2	2013-02-06				ENSG00000130812		"Fibrinogen C domain containing"	23140	protein-coding gene	gene with protein product	"angiopoietin-related protein 5"	609336				12871997	Standard	NM_031917		Approved	ARP5, AGF	uc002mmy.1	Q8NI99		ENST00000253109.4:c.425G>A	19.37:g.10206815C>T	ENSP00000253109:p.Arg142His	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_031917	0	0	0	0	0	A5PKV7|Q9BZZ0	Missense_Mutation	SNP	ENST00000253109.4	37	CCDS12224.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.214259	0.79352	.	.	ENSG00000130812	ENST00000253109	T	0.56776	0.44	4.36	2.11	0.27256	.	0.730444	0.12789	N	0.438963	T	0.40546	0.1121	L	0.39245	1.2	0.30614	N	0.75922	B	0.12630	0.006	B	0.06405	0.002	T	0.43032	-0.9416	10	0.54805	T	0.06	.	6.8988	0.24271	0.0:0.6789:0.0:0.3211	.	142	Q8NI99	ANGL6_HUMAN	H	142	ENSP00000253109:R142H	ENSP00000253109:R142H	R	-	2	0	ANGPTL6	10067815	0.995000	0.38212	1.000000	0.80357	0.884000	0.51177	0.382000	0.20635	1.030000	0.39839	0.455000	0.32223	CGC	.		0.771	ANGPTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451142.1	NM_031917		T	10206815	C	T	10206815	3	4	15	1	0	0	0	0	1	0	0	0	618	768	27	1	1007	1	ANGPTL6	19	10206815	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	1129029	10206815	48922168	74	1321											
MAST3	23031	hgsc.bcm.edu	37	chr19	18257754	18257754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccatcaaggtgggccccGcccggaagaatgtggccaag	9	5	13	14	2	1	1	1	0	0	1	2	2	2	2	6	4	0	0	6	4	4	0	rs372265542		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:18257754G>A	ENST00000262811.6	+	25	3139	c.3139G>A	c.(3139-3141)Gcc>Acc	p.A1047T	AC007192.6_ENST00000600364.2_RNA	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	1047							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						GGTGGGCCCCGCCCGGAAGAA	0.672																																					p.A1047T		.											.	MAST3-502	0			c.G3139A						.		THR/ALA	0,3852		0,0,1926	20	22	21		3139	4.4	0.2	19		21	1,8143		0,1,4071	no	missense	MAST3	NM_015016.1	58	0,1,5997	AA,AG,GG		0.0123,0.0,0.0083	probably-damaging	1047/1310	18257754	1,11995	1926	4072	5998	SO:0001583	missense	23031	exon25			GGCCCCGCCCGGA	AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308			19036	protein-coding gene	gene with protein product		612258					Standard	NM_015016		Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.3139G>A	19.37:g.18257754G>A	ENSP00000262811:p.Ala1047Thr	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	4	3	NM_015016	0	0	1	1	0	Q7LDZ8|Q9UPI0	Missense_Mutation	SNP	ENST00000262811.6	37	CCDS46014.1	.	.	.	.	.	.	.	.	.	.	g	26.0	4.698857	0.88830	0.0	1.23E-4	ENSG00000099308	ENST00000262811	T	0.69561	-0.41	4.38	4.38	0.52667	.	0.000000	0.85682	D	0.000000	D	0.83022	0.5164	M	0.85542	2.76	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	D	0.85721	0.1325	10	0.52906	T	0.07	-27.2754	15.9367	0.79717	0.0:0.0:1.0:0.0	.	1047	O60307	MAST3_HUMAN	T	1047	ENSP00000262811:A1047T	ENSP00000262811:A1047T	A	+	1	0	MAST3	18118754	1.000000	0.71417	0.187000	0.23214	0.712000	0.41017	9.712000	0.98738	1.985000	0.57927	0.486000	0.48141	GCC	.		0.672	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150		A	18257754	G	A	18257754	3	1	15	1	0	0	0	0	1	0	0	0	9351	1087	38	1	3237	1	MAST3	19	18257754	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	8050939	18257754	40871229	75	1322											
KIAA0892	23383	hgsc.bcm.edu	37	chr19	19431719	19431719	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggcggcggcccaggctgcGcaggccgaggcggccgactc	4	2	19	16	7	0	0	0	0	0	0	1	2	0	0	3	7	1	2	3	7	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:19431719G>C	ENST00000392313.6	+	1	230	c.51G>C	c.(49-51)gcG>gcC	p.A17A	SUGP1_ENST00000585763.1_5'Flank|SUGP1_ENST00000247001.5_5'Flank|MAU2_ENST00000262815.8_Silent_p.A17A|SUGP1_ENST00000334782.5_5'Flank	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	17	Ala-rich.|Sufficient for interaction with NIPBL.				maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						cccaggctgcgcaggccgagg	0.716																																					p.A17A		.											.	MAU2-91	0			c.G51C						.						4	5	5					19																	19431719		1710	3860	5570	SO:0001819	synonymous_variant	23383	exon1			GGCTGCGCAGGCC	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.51G>C	19.37:g.19431719G>C		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	6	5	NM_015329	0	0	2	8	6	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Silent	SNP	ENST00000392313.6	37	CCDS32969.2																																																																																			.		0.716	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		C	19431719	G	C	19431719	2	2	15	1	0	0	0	0	0	0	0	1	8217	1074	38	4		4	KIAA0892	19	19431719	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	1173965	19431719	39697264	76	1323											
LMTK3	114783	hgsc.bcm.edu;broad.mit.edu	37	chr19	49000760	49000760	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgtctccgctgagtgccGtgtctccgccggccctgctg	1	9	12	19	5	2	1	0	1	2	0	4	1	2	1	7	1	2	2	7	1	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:49000760G>A	ENST00000600059.1	-	11	3793	c.3566C>T	c.(3565-3567)aCg>aTg	p.T1189M	LMTK3_ENST00000270238.3_Missense_Mutation_p.T1218M			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	1189	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GCTGAGTGCCGTGTCTCCGCC	0.726																																					p.T1218M		.											.	LMTK3-1357	0			c.C3653T						.						20	22	22					19																	49000760		1899	4097	5996	SO:0001583	missense	114783	exon12			AGTGCCGTGTCTC	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 101"						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.3566C>T	19.37:g.49000760G>A	ENSP00000472020:p.Thr1189Met	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	36	3	NM_001080434	0	0	4	4	0	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	37		.	.	.	.	.	.	.	.	.	.	G	3.648	-0.072072	0.07228	.	.	ENSG00000142235	ENST00000270238	T	0.75821	-0.97	3.8	1.65	0.23941	.	0.769546	0.11439	N	0.563997	T	0.47637	0.1456	N	0.08118	0	0.20489	N	0.999892	B	0.13145	0.007	B	0.08055	0.003	T	0.26710	-1.0095	10	0.25751	T	0.34	.	2.6431	0.04976	0.2569:0.0:0.513:0.2301	.	1189	Q96Q04	LMTK3_HUMAN	M	1218	ENSP00000270238:T1218M	ENSP00000270238:T1218M	T	-	2	0	LMTK3	53692572	0.094000	0.21725	1.000000	0.80357	0.292000	0.27327	-0.331000	0.07914	0.919000	0.36945	0.563000	0.77884	ACG	.		0.726	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		A	49000760	G	A	49000760	3	1	15	1	0	0	0	0	1	0	0	0	8883	1145	40	1	836	1	LMTK3	19	49000760	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	29569041	49000760	10128223	77	1324											
LENG9	94059	hgsc.bcm.edu	37	chr19	54974538	54974538	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcggcggcttcttggcccCggcctccggctgcgcctcgc	1	7	14	19	6	1	0	0	0	1	0	3	0	2	0	5	5	2	2	5	5	0	2	rs202206879	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:54974538C>T	ENST00000333834.4	-	1	356	c.238G>A	c.(238-240)Ggg>Agg	p.G80R		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	80							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		TTCTTGGCCCCGGCCTCCGGC	0.776													C|||	18	0.00359425	8e-04	0.013	5008	,	,		8860	0		0.008	False		,,,				2504	0				p.G80R		.											.	LENG9-68	0			c.G238A						.	C	ARG/GLY	3,2029		0,3,1013	1	1	1		238	-0.5	0	19		1	17,4149		0,17,2066	no	missense	LENG9	NM_198988.1	125	0,20,3079	TT,TC,CC		0.4081,0.1476,0.3227	benign	80/502	54974538	20,6178	1016	2083	3099	SO:0001583	missense	94059	exon1			TGGCCCCGGCCTC	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.238G>A	19.37:g.54974538C>T	ENSP00000331647:p.Gly80Arg	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_198988	0	0	0	0	0	B2VAM3	Missense_Mutation	SNP	ENST00000333834.4	37	CCDS12895.2	.	.	.	.	.	.	.	.	.	.	C	6.063	0.379917	0.11466	0.001476	0.004081	ENSG00000182909	ENST00000333834	T	0.32988	1.43	3.31	-0.497	0.12023	.	1.586810	0.03704	N	0.249105	T	0.15219	0.0367	N	0.11064	0.09	0.09310	N	1	B	0.16802	0.019	B	0.10450	0.005	T	0.17077	-1.0381	10	0.13470	T	0.59	-0.0431	5.1691	0.15101	0.0:0.6056:0.1681:0.2264	.	80	Q96B70	LENG9_HUMAN	R	80	ENSP00000331647:G80R	ENSP00000331647:G80R	G	-	1	0	LENG9	59666350	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.192000	0.17096	-0.111000	0.12001	-0.362000	0.07510	GGG	.		0.776	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988		T	54974538	C	T	54974538	3	4	15	1	0	0	0	0	1	0	0	0	8746	652	23	1	1271	1	LENG9	19	54974538	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	5973778	54974538	4154445	78	1325											
SNTA1	6640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	32026771	32026771	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acaaaaagggcctctgtctgGtcagctgccaatcccttgaa	11	9	9	12	0	3	1	1	1	2	0	4	1	4	1	3	2	2	1	3	2	4	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:32026771G>A	ENST00000217381.2	-	2	643	c.372C>T	c.(370-372)gaC>gaT	p.D124D		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	124	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)			breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						CCTCTGTCTGGTCAGCTGCCA	0.527																																					p.D124D		.											.	SNTA1-91	0			c.C372T						.						123	121	122					20																	32026771		2203	4300	6503	SO:0001819	synonymous_variant	6640	exon2			TGTCTGGTCAGCT	U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"pro-TGF-alpha cytoplasmic domain-interacting protein 1", "dystrophin-associated protein A1, 59kDa, acidic component"	601017	"syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.372C>T	20.37:g.32026771G>A		Somatic	178	1		WXS	Illumina HiSeq	Phase_I	235	74	NM_003098	0	0	0	1	1	A8K7H9|B4DX40|E1P5N1|Q16438	Silent	SNP	ENST00000217381.2	37	CCDS13220.1																																																																																			.		0.527	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098		A	32026771	G	A	32026771	2	1	15	1	0	0	0	0	0	0	0	1	14903	1252	44	2		2	SNTA1	20	32026771	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		32026771	30998749	79	1326											
RALGAPB	57148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37153507	37153507	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttattctaaactctcctcCtttgttctgctgtgacttga	6	18	6	11	1	3	2	0	2	3	0	5	2	4	2	2	0	2	3	2	0	3	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:37153507C>A	ENST00000262879.6	+	11	1990	c.1706C>A	c.(1705-1707)cCt>cAt	p.P569H	RALGAPB_ENST00000397038.1_Missense_Mutation_p.P347H|RALGAPB_ENST00000397042.3_Missense_Mutation_p.P569H|RALGAPB_ENST00000397040.1_Missense_Mutation_p.P569H			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	569					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						AACTCTCCTCCTTTGTTCTGC	0.393																																					p.P569H		.											.	RALGAPB-92	0			c.C1706A						.						301	273	283					20																	37153507		2203	4300	6503	SO:0001583	missense	57148	exon11			CTCCTCCTTTGTT	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"KIAA1219"	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1706C>A	20.37:g.37153507C>A	ENSP00000262879:p.Pro569His	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	247	151	NM_020336	0	0	4	8	4	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249579	0.59212	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	T;T	0.66280	-0.2;-0.2	5.51	4.54	0.55810	.	0.099219	0.64402	D	0.000001	T	0.49423	0.1556	N	0.22421	0.69	0.49299	D	0.999778	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.06405	0.001;0.002;0.002;0.002	T	0.46707	-0.9172	10	0.48119	T	0.1	.	15.7457	0.77939	0.1369:0.8631:0.0:0.0	.	397;569;569;569	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	H	569;569;569;347;569;397	ENSP00000262879:P569H;ENSP00000380233:P569H	ENSP00000262879:P569H	P	+	2	0	RALGAPB	36586921	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.977000	0.70492	2.587000	0.87381	0.561000	0.74099	CCT	.		0.393	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		A	37153507	C	A	37153507	3	1	15	1	0	0	0	0	1	0	0	0	13047	681	24	4	1744	4	RALGAPB	20	37153507	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	5126736	37153507	25872013	80	1327											
SULF2	55959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	46291842	46291842	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtctgtgttgagatcaaagTactctaggaagccagttgca	11	11	12	7	0	3	1	1	1	2	1	3	3	3	2	1	2	3	4	1	2	4	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:46291842T>A	ENST00000359930.4	-	17	3193	c.2342A>T	c.(2341-2343)tAc>tTc	p.Y781F	SULF2_ENST00000467815.1_Missense_Mutation_p.Y781F|SULF2_ENST00000484875.1_Missense_Mutation_p.Y781F|SULF2_ENST00000361612.4_Missense_Mutation_p.Y781F	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	781					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GAGATCAAAGTACTCTAGGAA	0.547											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y781F		.											.	SULF2-293	0			c.A2342T						.						155	142	147					20																	46291842		2203	4300	6503	SO:0001583	missense	55959	exon17			TCAAAGTACTCTA	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.2342A>T	20.37:g.46291842T>A	ENSP00000353007:p.Tyr781Phe	Somatic	89	0	938	WXS	Illumina HiSeq	Phase_I	98	51	NM_001161841	0	0	68	195	127	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.42|19.42	3.824660|3.824660	0.71143|0.71143	.|.	.|.	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|D;D;D;D	.|0.96073	.|-3.9;-3.9;-3.9;-3.9	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	.|0.054592	.|0.85682	.|D	.|0.000000	D|D	0.95956|0.95956	0.8683|0.8683	L|L	0.41356|0.41356	1.27|1.27	0.54753|0.54753	D|D	0.999982|0.999982	.|D;D	.|0.89917	.|1.0;0.998	.|D;D	.|0.87578	.|0.998;0.99	D|D	0.94418|0.94418	0.7638|0.7638	5|10	.|0.19147	.|T	.|0.46	-23.4617|-23.4617	15.4799|15.4799	0.75517|0.75517	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|781;781	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	S|F	136|781;781;781;200;781	.|ENSP00000353007:Y781F;ENSP00000418290:Y781F;ENSP00000354662:Y781F;ENSP00000418442:Y781F	.|ENSP00000353007:Y781F	T|Y	-|-	1|2	0|0	SULF2|SULF2	45725249|45725249	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	8.040000|8.040000	0.89188|0.89188	2.068000|2.068000	0.61886|0.61886	0.454000|0.454000	0.30748|0.30748	ACT|TAC	.		0.547	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		A	46291842	T	A	46291842	3	1	15	1	0	0	0	0	1	0	0	0	15403	1638	57	5	290	5	SULF2	20	46291842	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	9138335	46291842	16733678	81	1328											
DDX27	55661	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	47835928	47835928	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacgacgaggaggctgcgaAaagttaagggccggaccgca	13	3	16	9	5	0	1	0	0	0	1	0	6	0	3	2	4	1	3	2	4	3	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:47835928A>C	ENST00000371764.4	+	1	45	c.36A>C	c.(34-36)gaA>gaC	p.E12D	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	12						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAGGCTGCGAAAAGTTAAGGG	0.607																																					p.E12D		.											.	DDX27-537	0			c.A36C						.						78	66	70					20																	47835928		2203	4300	6503	SO:0001583	missense	55661	exon1			CTGCGAAAAGTTA	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"DEAD-boxes"	15837	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.36A>C	20.37:g.47835928A>C	ENSP00000360828:p.Glu12Asp	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	49	14	NM_017895	0	0	1	1	0	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	A	8.891	0.954106	0.18431	.	.	ENSG00000124228	ENST00000535160;ENST00000371764	T	0.01446	4.88	5.04	-4.9E-5	0.14040	.	2.187840	0.02319	N	0.072815	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.46830	-0.9163	10	0.87932	D	0	4.3423	3.5735	0.07926	0.5451:0.0:0.2933:0.1616	.	12	Q96GQ7	DDX27_HUMAN	D	12	ENSP00000360828:E12D	ENSP00000360828:E12D	E	+	3	2	DDX27	47269335	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.050000	0.14120	-0.113000	0.11958	0.533000	0.62120	GAA	.		0.607	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			C	47835928	A	C	47835928	3	2	15	1	0	0	0	0	1	0	0	0	4360	11	1	5	38	5	DDX27	20	47835928	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	1544086	47835928	15189592	82	1329											
CRYAA	1409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	44589374	44589374	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccagtccctcttccgcacCgtgctggactccggcatctc	4	9	9	19	4	2	0	0	0	2	0	6	1	5	1	5	2	1	3	5	2	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr21:44589374C>G	ENST00000291554.2	+	1	257	c.165C>G	c.(163-165)acC>acG	p.T55T	CRYAA_ENST00000398132.1_5'Flank|CRYAA_ENST00000398133.1_5'Flank|CRYAA_ENST00000482775.1_3'UTR	NM_000394.2	NP_000385.1	P02489	CRYAA_HUMAN	crystallin, alpha A	55					negative regulation of apoptotic process (GO:0043066)|negative regulation of intracellular transport (GO:0032387)|protein homooligomerization (GO:0051260)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural constituent of eye lens (GO:0005212)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						TCTTCCGCACCGTGCTGGACT	0.622																																					p.T55T		.											.	CRYAA-289	0			c.C165G						.						130	118	122					21																	44589374		2203	4300	6503	SO:0001819	synonymous_variant	1409	exon1			CCGCACCGTGCTG		CCDS13695.1	21q22.3	2011-09-05			ENSG00000160202	ENSG00000160202		"Heat shock proteins / HSPB"	2388	protein-coding gene	gene with protein product		123580		CRYA1			Standard	XM_005261093		Approved	HSPB4	uc002zdd.1	P02489	OTTHUMG00000086842	ENST00000291554.2:c.165C>G	21.37:g.44589374C>G		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	183	92	NM_000394	0	0	0	0	0	Q53X53	Silent	SNP	ENST00000291554.2	37	CCDS13695.1																																																																																			.		0.622	CRYAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195562.1			G	44589374	C	G	44589374	2	3	15	1	0	0	0	0	0	0	0	1	3911	639	23	4		4	CRYAA	21	44589374	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08		44589374	3540521	83	1330											
DIP2A	23181	hgsc.bcm.edu	37	chr21	47958481	47958481	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgtcagcctcagctcactGcgcatgctgattgtggccga	7	9	12	13	3	3	1	3	1	0	0	3	3	3	1	2	1	4	3	2	1	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr21:47958481G>A	ENST00000417564.2	+	16	1908	c.1887G>A	c.(1885-1887)ctG>ctA	p.L629L	DIP2A_ENST00000466639.1_Silent_p.L586L|Metazoa_SRP_ENST00000607098.1_RNA|DIP2A_ENST00000427143.2_Silent_p.L565L|DIP2A_ENST00000400274.1_Silent_p.L625L|DIP2A_ENST00000318711.7_Silent_p.L630L|DIP2A_ENST00000435722.3_Silent_p.L629L|DIP2A_ENST00000457905.3_Silent_p.L629L			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	629					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCAGCTCACTGCGCATGCTGA	0.617																																					p.L629L		.											.	DIP2A-24	0			c.G1887A						.						40	49	46					21																	47958481		2154	4215	6369	SO:0001819	synonymous_variant	23181	exon16			CTCACTGCGCATG	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.1887G>A	21.37:g.47958481G>A		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	10	6	NM_206891	0	0	2	10	8	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			.		0.617	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		A	47958481	G	A	47958481	2	1	15	1	0	0	0	0	0	0	0	1	4538	1306	46	2		2	DIP2A	21	47958481	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	3369107	47958481	171414	84	1331											
MED15	51586	hgsc.bcm.edu	37	chr22	20920816	20920816	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagctccaacaacagcaacaGcagcagcagcagcagcagca	16	1	9	15	0	0	0	0	0	0	0	1	0	1	0	1	0	12	9	1	0	3	0	rs535773989	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:20920816G>A	ENST00000263205.7	+	7	822	c.753G>A	c.(751-753)caG>caA	p.Q251Q	MED15_ENST00000292733.7_Silent_p.Q251Q|MED15_ENST00000406969.1_Silent_p.Q225Q|MED15_ENST00000542773.1_Silent_p.Q56Q|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000425759.2_Silent_p.Q140Q|MED15_ENST00000541476.1_Silent_p.Q225Q|MED15_ENST00000382974.2_Silent_p.Q180Q	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	251	Poly-Gln.			Missing (in Ref. 3; BAB85034). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			aacagcaacagcagcagcagc	0.592																																					p.Q251Q		.											.	MED15-211	0			c.G753A						.						19	25	23					22																	20920816		2129	4141	6270	SO:0001819	synonymous_variant	51586	exon7			GCAACAGCAGCAG	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"trinucleotide repeat containing 7", "PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.753G>A	22.37:g.20920816G>A		Somatic	56	2		WXS	Illumina HiSeq	Phase_I	46	5	NM_015889	0	0	23	23	0	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	37	CCDS33602.1	.	.	.	.	.	.	.	.	.	.	G	3.627	-0.076441	0.07184	.	.	ENSG00000099917	ENST00000423862	.	.	.	0.998	0.998	0.19857	.	.	.	.	.	T	0.51839	0.1698	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39143	-0.9628	4	.	.	.	.	5.6489	0.17604	0.0:0.0:1.0:0.0	.	.	.	.	T	192	.	.	A	+	1	0	MED15	19250816	0.894000	0.30519	0.949000	0.38748	0.643000	0.38383	0.816000	0.27267	0.293000	0.22520	0.298000	0.19748	GCA	.		0.592	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		A	20920816	G	A	20920816	2	1	15	1	0	0	0	0	0	0	0	1	9458	962	34	2		2	MED15	22	20920816	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		20920816	30383750	85	1332											
UQCR10	29796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30163434	30163434	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attgtactccctgctgttccGcaggacctccaccttcgccc	5	11	7	18	2	0	0	0	0	0	0	4	1	3	1	6	1	2	4	6	1	1	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:30163434G>A	ENST00000330029.6	+	1	77	c.47G>A	c.(46-48)cGc>cAc	p.R16H	ZMAT5_ENST00000397781.3_5'Flank|ZMAT5_ENST00000344318.3_5'Flank|UQCR10_ENST00000401406.3_Missense_Mutation_p.R16H	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X	16					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						CTGCTGTTCCGCAGGACCTCC	0.612																																					p.R16H		.											.	UQCR10-23	0			c.G47A						.						54	62	59					22																	30163434		2053	4195	6248	SO:0001583	missense	29796	exon1			TGTTCCGCAGGAC	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"Mitochondrial respiratory chain complex / Complex III"	30863	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa", "complex III subunit 9"	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	ENST00000330029.6:c.47G>A	22.37:g.30163434G>A	ENSP00000332887:p.Arg16His	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	60	29	NM_001003684	0	0	96	175	79	B5MCM5|Q9T2V6	Missense_Mutation	SNP	ENST00000330029.6	37	CCDS46680.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541323	0.85917	.	.	ENSG00000184076	ENST00000332801;ENST00000330029;ENST00000401406;ENST00000406782	T;T	0.61158	0.13;0.13	5.73	5.73	0.89815	.	0.000000	0.42821	D	0.000649	T	0.76485	0.3994	.	.	.	0.51482	D	0.999921	B;D	0.89917	0.403;1.0	B;D	0.85130	0.152;0.997	T	0.78137	-0.2321	9	0.62326	D	0.03	-4.8723	15.4576	0.75327	0.0:0.0:1.0:0.0	.	16;16	Q9UDW1;Q9UDW1-2	QCR9_HUMAN;.	H	16	ENSP00000332887:R16H;ENSP00000384962:R16H	ENSP00000332887:R16H	R	+	2	0	UQCR10	28493434	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.728000	0.62000	2.720000	0.93068	0.558000	0.71614	CGC	.		0.612	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387		A	30163434	G	A	30163434	3	1	15	1	0	0	0	0	1	0	0	0	17049	1087	38	1	49	1	UQCR10	22	30163434	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	9242618	30163434	21141132	86	1333											
SEC14L3	266629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30866522	30866522	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgtagaaggaaataatcAtcagggttgggcagggcagg	13	6	16	6	1	2	1	2	0	0	1	2	2	2	2	0	5	1	4	0	5	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:30866522A>T	ENST00000215812.4	-	2	192	c.102T>A	c.(100-102)gaT>gaA	p.D34E	SEC14L3_ENST00000415957.2_5'UTR|SEC14L3_ENST00000539629.1_5'UTR|SEC14L3_ENST00000540910.1_5'UTR|SEC14L3_ENST00000402286.1_5'UTR|SEC14L3_ENST00000403066.1_5'UTR|SEC14L3_ENST00000401751.1_5'UTR	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	34						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	GGAAATAATCATCAGGGTTGG	0.567																																					p.D34E	Esophageal Squamous(108;290 1516 3584 23771 37333)	.											.	SEC14L3-95	0			c.T102A						.						131	111	118					22																	30866522		2203	4300	6503	SO:0001583	missense	266629	exon2			ATAATCATCAGGG	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.102T>A	22.37:g.30866522A>T	ENSP00000215812:p.Asp34Glu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	63	31	NM_174975	0	0	0	0	0	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.81|17.81	3.481554|3.481554	0.63849|0.63849	.|.	.|.	ENSG00000100012|ENSG00000100012	ENST00000215812|ENST00000435069	D|.	0.87729|.	-2.29|.	5.39|5.39	0.515|0.515	0.17013|0.17013	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);|.	0.223524|.	0.46145|.	D|.	0.000308|.	T|.	0.77890|.	0.4198|.	M|M	0.92367|0.92367	3.3|3.3	0.80722|0.80722	D|D	1|1	P|.	0.47253|.	0.892|.	P|.	0.58391|.	0.838|.	T|.	0.77958|.	-0.2392|.	10|.	0.59425|.	D|.	0.04|.	-19.4435|-19.4435	9.2711|9.2711	0.37673|0.37673	0.5993:0.0:0.4007:0.0|0.5993:0.0:0.4007:0.0	.|.	34|.	Q9UDX4|.	S14L3_HUMAN|.	E|R	34|15	ENSP00000215812:D34E|.	ENSP00000215812:D34E|.	D|X	-|-	3|1	2|0	SEC14L3|SEC14L3	29196522|29196522	0.999000|0.999000	0.42202|0.42202	0.999000|0.999000	0.59377|0.59377	0.890000|0.890000	0.51754|0.51754	0.735000|0.735000	0.26115|0.26115	0.058000|0.058000	0.16222|0.16222	0.528000|0.528000	0.53228|0.53228	GAT|TGA	.		0.567	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		T	30866522	A	T	30866522	3	4	15	1	0	0	0	0	1	0	0	0	14015	214	8	5	1144	5	SEC14L3	22	30866522	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	703088	30866522	20438044	87	1334											
SUN2	25777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	39138452	39138452	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agccccttgccgcagctccaGacgttccagccgcatggcct	6	7	10	18	3	0	1	0	0	0	1	2	1	2	1	7	1	4	4	7	1	0	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:39138452G>A	ENST00000405510.1	-	10	1280	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	SUN2_ENST00000411587.2_Silent_p.L297L|RP3-508I15.14_ENST00000416406.1_RNA|RP3-508I15.22_ENST00000607991.1_RNA|SUN2_ENST00000216064.4_Silent_p.L308L|RP3-508I15.21_ENST00000609212.1_RNA|SUN2_ENST00000405018.1_Silent_p.L329L|SUN2_ENST00000406622.1_Silent_p.L308L	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	308					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CGCAGCTCCAGACGTTCCAGC	0.647																																					p.L329L		.											.	SUN2-154	0			c.C985T						.						30	30	30					22																	39138452		2203	4300	6503	SO:0001819	synonymous_variant	25777	exon9			GCTCCAGACGTTC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.922C>T	22.37:g.39138452G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	43	19	NM_001199579	0	0	16	23	7	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	37	CCDS13978.1																																																																																			.		0.647	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		A	39138452	G	A	39138452	2	1	15	1	0	0	0	0	0	0	0	1	15424	933	33	2		2	SUN2	22	39138452	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	8271930	39138452	12166114	88	1335											
TMEM27	57393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	15682860	15682860	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggttgacagagttcagcAtgaatggcagtcaccagaaa	13	8	11	9	0	2	4	2	2	0	2	2	4	2	4	2	2	1	4	2	2	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chrX:15682860A>G	ENST00000380342.3	-	1	294	c.39T>C	c.(37-39)caT>caC	p.H13H		NM_020665.4	NP_065716.1	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27	13					positive regulation of amino acid transport (GO:0051957)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of SNARE complex assembly (GO:0035543)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)			endometrium(3)|lung(4)|ovary(1)	8	Hepatocellular(33;0.183)					AGAGTTCAGCATGAATGGCAG	0.373																																					p.H13H		.											.	TMEM27-131	0			c.T39C						.						58	53	55					X																	15682860		2203	4299	6502	SO:0001819	synonymous_variant	57393	exon1			TTCAGCATGAATG	AF229179	CCDS14170.1	Xp22	2012-04-13			ENSG00000147003	ENSG00000147003			29437	protein-coding gene	gene with protein product	"collectrin"	300631				11278314	Standard	NM_020665		Approved	NX17	uc004cxc.2	Q9HBJ8	OTTHUMG00000021181	ENST00000380342.3:c.39T>C	X.37:g.15682860A>G		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	34	26	NM_020665	0	0	1	134	133	B2R9M1|Q6UW07	Silent	SNP	ENST00000380342.3	37	CCDS14170.1																																																																																			.		0.373	TMEM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055879.1	NM_020665		G	15682860	A	G	15682860	2	3	15	1	0	0	0	0	0	0	0	1	16184	214	8	3		3	TMEM27	23	15682860	Silent	SNP	A	TCGA-A4-8311-01A-11D-2396-08		15682860	139587700	89	1336											
THOC2	57187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	122756985	122756985	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtactgctttcatccgatTtagatgcacttcctattgat	9	16	6	10	1	1	2	1	1	0	1	3	3	3	2	2	0	3	3	2	0	3	7			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chrX:122756985T>A	ENST00000245838.8	-	29	3684	c.3653A>T	c.(3652-3654)aAa>aTa	p.K1218I	THOC2_ENST00000491737.1_Missense_Mutation_p.K1103I|THOC2_ENST00000355725.4_Missense_Mutation_p.K1218I|THOC2_ENST00000497887.1_5'Flank	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1218					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TTCATCCGATTTAGATGCACT	0.403																																					p.K1218I		.											.	THOC2-133	0			c.A3653T						.						100	89	93					X																	122756985		1868	4105	5973	SO:0001583	missense	57187	exon29			TCCGATTTAGATG	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3653A>T	X.37:g.122756985T>A	ENSP00000245838:p.Lys1218Ile	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	67	60	NM_001081550	0	0	0	19	19	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.82|15.82	2.945939|2.945939	0.53079|0.53079	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000438358	T;T;T|.	0.48836|.	0.8;0.8;0.8|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|.	0.53850|.	0.1822|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.80764|.	0.994|.	T|.	0.52155|.	-0.8613|.	10|.	0.44086|.	T|.	0.13|.	-18.2877|-18.2877	11.3724|11.3724	0.49708|0.49708	0.0:0.0733:0.0:0.9266|0.0:0.0733:0.0:0.9266	.|.	1218|.	Q8NI27|.	THOC2_HUMAN|.	I|Y	1218;1218;1103|312	ENSP00000245838:K1218I;ENSP00000347959:K1218I;ENSP00000419795:K1103I|.	ENSP00000245838:K1218I|.	K|X	-|-	2|3	0|2	THOC2|THOC2	122584666|122584666	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	2.582000|2.582000	0.46085|0.46085	2.011000|2.011000	0.59026|0.59026	0.437000|0.437000	0.28790|0.28790	AAA|TAA	.		0.403	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			A	122756985	T	A	122756985	3	1	15	1	0	0	0	0	1	0	0	0	15897	1841	64	5	1168	5	THOC2	23	122756985	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	107074125	122756985	32513575	90	1337											
FLNA	2316	hgsc.bcm.edu	37	chrX	153592962	153592962	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggggctgaggcggatgtcttCgctgttgcacagcacgtgaa	7	9	16	9	3	1	2	0	2	1	0	2	3	1	3	0	4	2	5	0	4	1	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chrX:153592962C>G	ENST00000369850.3	-	13	2190	c.1954G>C	c.(1954-1956)Gaa>Caa	p.E652Q	FLNA_ENST00000422373.1_Missense_Mutation_p.E652Q|FLNA_ENST00000360319.4_Missense_Mutation_p.E652Q|FLNA_ENST00000344736.4_Missense_Mutation_p.E652Q	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	652					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)					CGGATGTCTTCGCTGTTGCAC	0.607																																					p.E652Q		.											.	FLNA-599	0			c.G1954C						.						53	58	56					X																	153592962		2179	4245	6424	SO:0001583	missense	2316	exon13			TGTCTTCGCTGTT	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1954G>C	X.37:g.153592962C>G	ENSP00000358866:p.Glu652Gln	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	49	3	NM_001456	0	0	45	45	0	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919545	0.73098	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87	4.95	4.95	0.65309	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.070140	0.53938	D	0.000053	D	0.89570	0.6753	L	0.47016	1.485	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.69479	0.964;0.959	D	0.89925	0.4062	10	0.49607	T	0.09	.	17.4666	0.87634	0.0:1.0:0.0:0.0	.	652;652	P21333-2;P21333	.;FLNA_HUMAN	Q	652;625;652;652;652	ENSP00000353467:E652Q;ENSP00000416926:E652Q;ENSP00000358866:E652Q;ENSP00000358863:E652Q	ENSP00000358863:E652Q	E	-	1	0	FLNA	153246156	1.000000	0.71417	0.767000	0.31495	0.823000	0.46562	6.022000	0.70839	2.049000	0.60858	0.525000	0.51046	GAA	.		0.607	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			G	153592962	C	G	153592962	3	3	15	1	0	0	0	0	1	0	0	0	5952	893	31	4	6133	4	FLNA	23	153592962	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	30835977	153592962	1677598	91	1338											
TCTEX1D4	343521	hgsc.bcm.edu	37	chr1	45271914	45271914	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccagccgcgcggcctcgtCgctggagtagcacgcgtcgt	5	6	14	16	8	0	0	0	0	0	0	3	1	0	1	3	2	2	3	3	2	1	1	rs17886308	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:45271914C>A	ENST00000339355.2	-	1	433	c.427G>T	c.(427-429)Gac>Tac	p.D143Y	BTBD19_ENST00000450269.1_5'Flank|TCTEX1D4_ENST00000372200.1_Missense_Mutation_p.D143Y|BTBD19_ENST00000409335.2_5'Flank|BTBD19_ENST00000453418.1_5'Flank			Q5JR98	TC1D4_HUMAN	Tctex1 domain containing 4	143						acrosomal vesicle (GO:0001669)|axoneme (GO:0005930)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)	protein phosphatase 1 binding (GO:0008157)			pancreas(1)	1	Acute lymphoblastic leukemia(166;0.155)					GCGGCCTCGTCGCTGGAGTAG	0.726													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		10391	0		0	False		,,,				2504	0				p.D143Y		.											.	TCTEX1D4-91	0			c.G427T						.	C	TYR/ASP	20,3036		0,20,1508	2	3	3		427	-11.1	0	1	dbSNP_124	3	1,6517		0,1,3258	no	missense	TCTEX1D4	NM_001013632.2	160	0,21,4766	AA,AC,CC		0.0153,0.6545,0.2193	benign	143/222	45271914	21,9553	1528	3259	4787	SO:0001583	missense	343521	exon2			CCTCGTCGCTGGA	BC092499	CCDS30699.1	1p34.1	2007-12-17				ENSG00000188396			32315	protein-coding gene	gene with protein product	"novel Tctex-1 family domain-containing protein"	611713				12477932	Standard	XM_006710614		Approved		uc001cmp.3	Q5JR98		ENST00000339355.2:c.427G>T	1.37:g.45271914C>A	ENSP00000341803:p.Asp143Tyr	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	6	2	NM_001013632	0	0	0	0	0		Missense_Mutation	SNP	ENST00000339355.2	37	CCDS30699.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	14.07	2.425354	0.43020	0.006545	1.53E-4	ENSG00000188396	ENST00000339355;ENST00000372200	T;T	0.31769	1.48;1.48	5.54	-11.1	0.00147	.	1.665700	0.03319	N	0.191643	T	0.08846	0.0219	N	0.12746	0.255	0.09310	N	1	B	0.13594	0.008	B	0.23150	0.044	T	0.27020	-1.0086	10	0.48119	T	0.1	0.2504	0.8024	0.01077	0.3558:0.1086:0.1938:0.3418	rs17886308	143	Q5JR98	TC1D4_HUMAN	Y	143	ENSP00000341803:D143Y;ENSP00000361274:D143Y	ENSP00000341803:D143Y	D	-	1	0	TCTEX1D4	45044501	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.985000	0.00319	-3.696000	0.00119	-0.263000	0.10527	GAC	C|0.997;A|0.003		0.726	TCTEX1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023733.1	NM_001013632		A	45271914	C	A	45271914	3	1	16	1	0	0	0	0	1	0	0	0	15753	884	31	4	242	4	TCTEX1D4	1	45271914	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		45271914	203978707	1	1339											
AKR1A1	10327	hgsc.bcm.edu	37	chr1	46033809	46033809	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacagtcggcagattgatgAcatactcagtgtggcctccg	10	9	11	11	2	1	3	1	2	0	1	3	3	2	3	2	2	2	1	2	2	2	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:46033809A>G	ENST00000372070.3	+	6	1259	c.512A>G	c.(511-513)gAc>gGc	p.D171G	AKR1A1_ENST00000473038.1_3'UTR|AKR1A1_ENST00000351829.4_Missense_Mutation_p.D171G	NM_001202413.1|NM_001202414.1|NM_006066.3	NP_001189342.1|NP_001189343.1|NP_006057.1	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1 (aldehyde reductase)	171					aldehyde catabolic process (GO:0046185)|cellular aldehyde metabolic process (GO:0006081)|D-glucuronate catabolic process (GO:0042840)|glucose metabolic process (GO:0006006)|L-ascorbic acid biosynthetic process (GO:0019853)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|L-glucuronate reductase activity (GO:0047939)			lung(3)|prostate(1)|urinary_tract(1)	5	Acute lymphoblastic leukemia(166;0.155)				Doxorubicin(DB00997)	CAGATTGATGACATACTCAGT	0.567																																					p.D171G		.											.	AKR1A1-226	0			c.A512G						.						89	73	78					1																	46033809		2203	4300	6503	SO:0001583	missense	10327	exon6			TTGATGACATACT	J04794	CCDS523.1	1p33-p32	2010-04-08			ENSG00000117448	ENSG00000117448	1.1.1.2	"Aldo-keto reductases"	380	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 3"	103830				2498333, 10393438	Standard	NM_001202414		Approved	ALR, DD3	uc001coe.3	P14550	OTTHUMG00000007740	ENST00000372070.3:c.512A>G	1.37:g.46033809A>G	ENSP00000361140:p.Asp171Gly	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_006066	0	0	110	110	0	A8KAL8|D3DQ04|Q6IAZ4	Missense_Mutation	SNP	ENST00000372070.3	37	CCDS523.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.012973	0.93346	.	.	ENSG00000117448	ENST00000372070;ENST00000351829	T;T	0.24908	1.83;1.83	5.75	5.75	0.90469	NADP-dependent oxidoreductase domain (3);	0.041179	0.85682	N	0.000000	T	0.49609	0.1567	M	0.73962	2.25	0.80722	D	1	D	0.61080	0.989	D	0.63192	0.912	T	0.48779	-0.9005	10	0.46703	T	0.11	.	16.1191	0.81329	1.0:0.0:0.0:0.0	.	171	P14550	AK1A1_HUMAN	G	171	ENSP00000361140:D171G;ENSP00000312606:D171G	ENSP00000312606:D171G	D	+	2	0	AKR1A1	45806396	1.000000	0.71417	0.982000	0.44146	0.881000	0.50899	9.249000	0.95470	2.204000	0.70986	0.529000	0.55759	GAC	.		0.567	AKR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020851.1	NM_006066		G	46033809	A	G	46033809	3	3	16	1	0	0	0	0	1	0	0	0	465	275	10	3	526	3	AKR1A1	1	46033809	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08	761895	46033809	203216812	2	1340											
FAM40A	85369	hgsc.bcm.edu	37	chr1	110583300	110583300	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgaggaagcctgccatcTccctggctgacagcacagac	9	7	11	14	0	1	3	0	2	1	1	2	4	1	4	3	2	3	2	3	2	1	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:110583300T>C	ENST00000369795.3	+	6	647	c.625T>C	c.(625-627)Tcc>Ccc	p.S209P	STRIP1_ENST00000369796.1_Missense_Mutation_p.S114P	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	209					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)											GCCTGCCATCTCCCTGGCTGA	0.567																																					p.S209P		.											.	.	0			c.T625C						.						33	28	30					1																	110583300		2203	4300	6503	SO:0001583	missense	85369	exon6			GCCATCTCCCTGG	AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog A (yeast)"		"family with sequence similarity 40, member A"	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.625T>C	1.37:g.110583300T>C	ENSP00000358810:p.Ser209Pro	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_033088	0	0	1	1	0	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Missense_Mutation	SNP	ENST00000369795.3	37	CCDS30798.1	.	.	.	.	.	.	.	.	.	.	T	34	5.317204	0.95682	.	.	ENSG00000143093	ENST00000369796;ENST00000369795	T;T	0.50813	0.73;0.73	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.66867	0.2833	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79108	0.982;0.992	T	0.69075	-0.5241	10	0.37606	T	0.19	-27.1676	16.6438	0.85155	0.0:0.0:0.0:1.0	.	114;209	Q5VSL9-2;Q5VSL9	.;FA40A_HUMAN	P	114;209	ENSP00000358811:S114P;ENSP00000358810:S209P	ENSP00000358810:S209P	S	+	1	0	FAM40A	110384823	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.534000	0.82004	2.333000	0.79357	0.533000	0.62120	TCC	.		0.567	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088		C	110583300	T	C	110583300	3	2	16	1	0	0	0	0	1	0	0	0	5579	1551	54	3	647	3	FAM40A	1	110583300	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	64549491	110583300	138667321	3	1341											
DUSP27	92235	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167097085	167097085	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcccgcagtaattcccagaAacctgaaacagacacatgct	14	8	6	13	1	0	3	0	1	0	2	2	3	2	3	3	0	3	3	3	0	3	3	rs377480316		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:167097085A>C	ENST00000361200.2	+	6	2883	c.2717A>C	c.(2716-2718)aAa>aCa	p.K906T	DUSP27_ENST00000271385.5_Missense_Mutation_p.K906T|DUSP27_ENST00000443333.1_Missense_Mutation_p.K906T|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	906	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AATTCCCAGAAACCTGAAACA	0.493																																					p.K906T		.											.	DUSP27-71	0			c.A2717C						.	A	THR/LYS	0,4406		0,0,2203	87	77	81		2717	1.5	1	1		81	1,8599	1.2+/-3.3	0,1,4299	no	missense	DUSP27	NM_001080426.1	78	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	probably-damaging	906/1159	167097085	1,13005	2203	4300	6503	SO:0001583	missense	92235	exon5			CCCAGAAACCTGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2717A>C	1.37:g.167097085A>C	ENSP00000354483:p.Lys906Thr	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	56	5	NM_001080426	0	0	0	0	0	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.356232	0.41700	0.0	1.16E-4	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.04454	3.62;3.62;3.62	5.25	1.46	0.22682	.	0.874767	0.09948	N	0.735044	T	0.01905	0.0060	M	0.65975	2.015	0.09310	N	1	P	0.35433	0.501	B	0.27608	0.081	T	0.42899	-0.9424	10	0.87932	D	0	-19.6906	5.4857	0.16749	0.6201:0.1386:0.2413:0.0	.	906	Q5VZP5	DUS27_HUMAN	T	906	ENSP00000354483:K906T;ENSP00000271385:K906T;ENSP00000404874:K906T	ENSP00000271385:K906T	K	+	2	0	DUSP27	165363709	0.258000	0.24033	0.973000	0.42090	0.754000	0.42855	1.679000	0.37597	0.315000	0.23110	-0.269000	0.10298	AAA	.		0.493	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		C	167097085	A	C	167097085	3	2	16	1	0	0	0	0	1	0	0	0	4835	14	1	5	2735	5	DUSP27	1	167097085	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08	56513785	167097085	82153536	4	1342											
C1orf106	55765	hgsc.bcm.edu	37	chr1	200860815	200860815	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcaggcgggcggcgccagAgctccatgggacaggtaagc	8	3	19	11	3	0	1	0	0	0	1	1	2	1	2	2	6	2	3	2	6	1	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:200860815A>G	ENST00000367342.4	+	1	347	c.147A>G	c.(145-147)agA>agG	p.R49R		NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	49										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GCGGCGCCAGAGCTCCATGGG	0.692																																					p.R63R		.											.	C1orf106-93	0			c.A189G						.						14	15	15					1																	200860815		2194	4288	6482	SO:0001819	synonymous_variant	55765	exon1			CGCCAGAGCTCCA	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.147A>G	1.37:g.200860815A>G		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	8	2	NM_018265	0	0	0	0	0	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				.		0.692	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		G	200860815	A	G	200860815	2	3	16	1	0	0	0	0	0	0	0	1	1986	301	11	3		3	C1orf106	1	200860815	Silent	SNP	A	TCGA-A4-8312-01A-11D-2396-08	33763730	200860815	48389806	5	1343											
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234744215	234744215	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctttagacccgttggccccGttggcctcgaaacccaacaa	9	8	9	15	3	0	1	0	0	0	1	1	2	0	1	5	2	2	3	5	2	4	4			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:234744215G>A	ENST00000366609.3	-	1	1056	c.1026C>T	c.(1024-1026)aaC>aaT	p.N342N	IRF2BP2_ENST00000491430.1_5'Flank|RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000366610.3_Intron	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	342					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CGTTGGCCCCGTTGGCCTCGA	0.617																																					p.N342N		.											.	IRF2BP2-90	0			c.C1026T						.						19	20	20					1																	234744215		2202	4298	6500	SO:0001819	synonymous_variant	359948	exon1			GGCCCCGTTGGCC	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1026C>T	1.37:g.234744215G>A		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_182972	0	0	66	66	0	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			.		0.617	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		A	234744215	G	A	234744215	2	1	16	1	0	0	0	0	0	0	0	1	7851	1136	40	1		1	IRF2BP2	1	234744215	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	33883400	234744215	14506406	6	1344											
HOXD1	3231	hgsc.bcm.edu	37	chr2	177053728	177053728	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaccctcgccttcgcccccgGccgcccccgcgcggccgtcc	1	4	11	25	8	0	0	0	0	0	0	3	1	1	0	9	2	0	0	9	2	0	1	rs570567019|rs577155560	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr2:177053728G>C	ENST00000331462.4	+	1	422	c.199G>C	c.(199-201)Gcc>Ccc	p.A67P	HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000452365.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	67					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		ttcgcccccggccgcccccgc	0.786													G|||	304	0.0607029	0.2247	0.0101	5008	,	,		9078	0		0	False		,,,				2504	0				p.A67P		.											.	HOXD1-90	0			c.G199C						.						1	1	1					2																	177053728		630	1487	2117	SO:0001583	missense	3231	exon1			CCCCCGGCCGCCC		CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"Homeoboxes / ANTP class : HOXL subclass"	5132	protein-coding gene	gene with protein product		142987	"homeo box D1"	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.199G>C	2.37:g.177053728G>C	ENSP00000328598:p.Ala67Pro	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_024501	0	0	0	0	0	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.553|7.553	0.663178|0.663178	0.14710|0.14710	.|.	.|.	ENSG00000128645|ENSG00000128645	ENST00000331462|ENST00000375170	D|.	0.91237|.	-2.81|.	3.58|3.58	-0.609|-0.609	0.11608|0.11608	.|.	0.713207|.	0.11548|.	N|.	0.553047|.	T|T	0.20414|0.20414	0.0491|0.0491	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.06405|.	0.002;0.002|.	T|T	0.28267|0.28267	-1.0049|-1.0049	9|5	0.28530|0.87932	T|D	0.3|0	.|.	0.59|0.59	0.00726|0.00726	0.3692:0.1717:0.2845:0.1746|0.3692:0.1717:0.2845:0.1746	.|.	67;67|.	Q96CA4;Q9GZZ0|.	.;HXD1_HUMAN|.	P|A	67|42	ENSP00000328598:A67P|.	ENSP00000328598:A67P|ENSP00000364313:G42A	A|G	+|+	1|2	0|0	HOXD1|HOXD1	176761974|176761974	0.180000|0.180000	0.23148|0.23148	0.001000|0.001000	0.08648|0.08648	0.050000|0.050000	0.14768|0.14768	0.444000|0.444000	0.21661|0.21661	-0.414000|-0.414000	0.07495|0.07495	0.491000|0.491000	0.48974|0.48974	GCC|GGC	.		0.786	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			C	177053728	G	C	177053728	3	2	16	1	0	0	0	0	1	0	0	0	7339	1203	42	4	201	4	HOXD1	2	177053728	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08		177053728	66145645	7	1345											
SMARCAL1	50485	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	217279802	217279802	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcactggaatctctcctccCttggcacaaagtcctccaga	9	10	6	16	0	2	1	1	0	1	1	7	2	6	2	4	2	0	1	4	2	2	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr2:217279802C>G	ENST00000357276.4	+	3	705	c.375C>G	c.(373-375)ccC>ccG	p.P125P	SMARCAL1_ENST00000358207.5_Silent_p.P125P|AC098820.2_ENST00000457694.1_RNA	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	125					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		TCTCTCCTCCCTTGGCACAAA	0.507									Schimke Immuno-Osseous Dysplasia																												p.P125P		.											.	SMARCAL1-293	0			c.C375G						.						88	80	82					2																	217279802		2203	4300	6503	SO:0001819	synonymous_variant	50485	exon3	Familial Cancer Database	SIOD	TCCTCCCTTGGCA	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.375C>G	2.37:g.217279802C>G		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	109	44	NM_014140	0	0	7	7	0	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	37	CCDS2403.1																																																																																			.		0.507	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			G	217279802	C	G	217279802	2	3	16	1	0	0	0	0	0	0	0	1	14805	668	24	4		4	SMARCAL1	2	217279802	Silent	SNP	C	TCGA-A4-8312-01A-11D-2396-08	40226074	217279802	25919571	8	1346											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52431781	52431781	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgcctgagatctttggccTgcatgacaatgccaacatca	11	11	8	11	0	2	2	1	2	1	1	2	3	2	2	3	1	4	1	3	1	3	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr3:52431781T>A	ENST00000420323.2	+	74	12107	c.11846T>A	c.(11845-11847)cTg>cAg	p.L3949Q		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	4014					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATCTTTGGCCTGCATGACAAT	0.552																																					p.L3949Q		.											.	DNAH1-67	0			c.T11846A						.						107	108	108					3																	52431781		2079	4206	6285	SO:0001583	missense	25981	exon74			TTGGCCTGCATGA	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11846T>A	3.37:g.52431781T>A	ENSP00000401514:p.Leu3949Gln	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_015512	0	0	6	6	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.289114	0.80914	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.23147	1.92	5.28	5.28	0.74379	.	0.000000	0.53938	D	0.000047	T	0.51822	0.1697	M	0.76328	2.33	0.54753	D	0.999986	D;D	0.89917	1.0;0.976	D;P	0.91635	0.999;0.741	T	0.55147	-0.8186	10	0.62326	D	0.03	.	15.3898	0.74735	0.0:0.0:0.0:1.0	.	3949;4014	C9JXH6;Q9P2D7-2	.;.	Q	3949;702	ENSP00000401514:L3949Q	ENSP00000273600:L702Q	L	+	2	0	DNAH1	52406821	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	4.805000	0.62561	2.232000	0.73038	0.533000	0.62120	CTG	.		0.552	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52431781	T	A	52431781	3	1	16	1	0	0	0	0	1	0	0	0	4608	1580	55	5	12136	5	DNAH1	3	52431781	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08		52431781	145590649	9	1347											
VPS8	23355	hgsc.bcm.edu	37	chr3	184717520	184717520	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cactcattctgcctacaaaaCaaagaatgcactgtggaatt	15	10	6	10	0	2	1	1	0	1	1	2	2	2	2	1	1	4	1	1	1	6	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr3:184717520C>G	ENST00000437079.3	+	45	4044	c.3873C>G	c.(3871-3873)aaC>aaG	p.N1291K	VPS8_ENST00000446204.2_Missense_Mutation_p.N1199K|VPS8_ENST00000436792.2_Missense_Mutation_p.N1289K|VPS8_ENST00000287546.4_Missense_Mutation_p.N1291K	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1291							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			GCCTACAAAACAAAGAATGCA	0.358																																					p.N1291K		.											.	VPS8-91	0			c.C3873G						.						86	79	81					3																	184717520		1890	4135	6025	SO:0001583	missense	23355	exon44			ACAAAACAAAGAA	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3873C>G	3.37:g.184717520C>G	ENSP00000397879:p.Asn1291Lys	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_001009921	0	0	38	38	0	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	C	6.399	0.441748	0.12164	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.62	4.73	0.59995	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.435447	0.28908	N	0.013759	T	0.35711	0.0941	N	0.04880	-0.145	0.29946	N	0.820688	B;B;B	0.15141	0.0;0.012;0.0	B;B;B	0.20384	0.001;0.029;0.001	T	0.27606	-1.0069	10	0.10111	T	0.7	-27.2808	8.6758	0.34179	0.0:0.7772:0.0:0.2228	.	1291;1199;1289	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	K	1291;1291;1289;1199	ENSP00000287546:N1291K;ENSP00000397879:N1291K;ENSP00000404704:N1289K;ENSP00000405483:N1199K	ENSP00000287546:N1291K	N	+	3	2	VPS8	186200214	0.998000	0.40836	1.000000	0.80357	0.974000	0.67602	0.570000	0.23653	1.344000	0.45657	0.609000	0.83330	AAC	.		0.358	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		G	184717520	C	G	184717520	3	3	16	1	0	0	0	0	1	0	0	0	17251	477	17	4	4043	4	VPS8	3	184717520	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08	132285739	184717520	13304910	10	1348											
LYRM7	90624	hgsc.bcm.edu	37	chr5	130517930	130517930	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctctttgtagcagccagaAtaaagataaatgaagaattc	16	12	7	6	0	1	4	0	1	1	3	3	4	1	4	1	0	2	2	1	0	8	6	rs200336982	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr5:130517930A>C	ENST00000379380.4	+	3	311	c.100A>C	c.(100-102)Ata>Cta	p.I34L	LYRM7_ENST00000507584.1_Missense_Mutation_p.I34L|LYRM7_ENST00000510516.1_Intron	NM_181705.2	NP_859056.2	Q5U5X0	LYRM7_HUMAN	LYR motif containing 7	34						mitochondrion (GO:0005739)				upper_aerodigestive_tract(1)	1		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCAGCCAGAATAAAGATAAA	0.249													A|||	2	0.000399361	8e-04	0	5008	,	,		15990	0		0.001	False		,,,				2504	0				p.I34L		.											.	LYRM7-68	0			c.A100C						.	A	LEU/ILE	2,4038		0,2,2018	10	11	10		100	2.3	1	5		10	3,8299		0,3,4148	yes	missense	LYRM7	NM_181705.2	5	0,5,6166	CC,CA,AA		0.0361,0.0495,0.0405	benign	34/105	130517930	5,12337	2020	4151	6171	SO:0001583	missense	90624	exon3			GCCAGAATAAAGA	BC047079	CCDS4148.1	5q31.1	2013-05-24	2012-10-23	2006-10-17	ENSG00000186687	ENSG00000186687		"LYR motif containing"	28072	protein-coding gene	gene with protein product		615831	"chromosome 5 open reading frame 31", "Lyrm7 homolog (mouse)"	C5orf31		23168492	Standard	NM_181705		Approved	FLJ20796, MZM1L	uc003kvg.1	Q5U5X0	OTTHUMG00000128994	ENST00000379380.4:c.100A>C	5.37:g.130517930A>C	ENSP00000368688:p.Ile34Leu	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	27	6	NM_181705	0	0	0	0	0	A8MPQ9|Q86Y68	Missense_Mutation	SNP	ENST00000379380.4	37	CCDS4148.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	A	10.18	1.278672	0.23307	4.95E-4	3.61E-4	ENSG00000186687	ENST00000379380;ENST00000507584	T;T	0.68331	-0.32;-0.32	4.67	2.33	0.28932	.	0.563855	0.18398	N	0.142452	T	0.28001	0.0690	N	0.00538	-1.39	0.23430	N	0.997698	B	0.02656	0.0	B	0.01281	0.0	T	0.24119	-1.0169	10	0.26408	T	0.33	-13.1777	5.7836	0.18320	0.7863:0.0:0.2137:0.0	.	34	Q5U5X0	LYRM7_HUMAN	L	34	ENSP00000368688:I34L;ENSP00000423991:I34L	ENSP00000368688:I34L	I	+	1	0	LYRM7	130545829	0.969000	0.33509	1.000000	0.80357	0.992000	0.81027	0.633000	0.24598	0.548000	0.28955	0.533000	0.62120	ATA	A|0.999;C|0.001		0.249	LYRM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250983.1	NM_181705		C	130517930	A	C	130517930	3	2	16	1	0	0	0	0	1	0	0	0	9148	101	4	5	110	5	LYRM7	5	130517930	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08		130517930	50397330	11	1349											
ANXA6	309	hgsc.bcm.edu	37	chr5	150518240	150518240	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacacccccacttcttaccGagatggcatctttaatttct	10	14	4	13	1	3	1	0	0	3	1	3	2	3	1	3	1	2	1	3	1	3	6	rs188111044	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr5:150518240G>T	ENST00000354546.5	-	5	544	c.317C>A	c.(316-318)tCg>tAg	p.S106*	ANXA6_ENST00000523714.1_Splice_Site_p.S74*|ANXA6_ENST00000521512.1_Intron|ANXA6_ENST00000356496.5_Splice_Site_p.S106*|ANXA6_ENST00000377751.5_Intron	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	106					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTTCTTACCGAGATGGCATC	0.488																																					p.S106X		.											.	ANXA6-22	0			c.C317A						.						105	105	105					5																	150518240		1955	4147	6102	SO:0001630	splice_region_variant	309	exon5			CTTACCGAGATGG	J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"Annexins"	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.318+1C>A	5.37:g.150518240G>T		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_001155	0	0	0	0	0	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Nonsense_Mutation	SNP	ENST00000354546.5	37	CCDS47315.1	.	.	.	.	.	.	.	.	.	.	G	36	5.932215	0.97116	.	.	ENSG00000197043	ENST00000354546;ENST00000523714;ENST00000356496;ENST00000517486;ENST00000521749;ENST00000517757;ENST00000523164	.	.	.	5.77	5.77	0.91146	.	0.237963	0.42294	D	0.000738	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	14.2952	0.66308	0.0:0.0:0.8508:0.1492	.	.	.	.	X	106;74;106;106;74;74;106	.	ENSP00000346550:S106X	S	-	2	0	ANXA6	150498433	0.982000	0.34865	1.000000	0.80357	0.565000	0.35776	3.083000	0.50136	2.724000	0.93272	0.561000	0.74099	TCG	G|0.999;A|0.001		0.488	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155	Nonsense_Mutation	T	150518240	G	T	150518240	5	4	16	1	0	0	0	0	0	0	1	0	722	1072	37	4	1792	4	ANXA6	5	150518240	Splice_Site	SNP	G	TCGA-A4-8312-01A-11D-2396-08	20000310	150518240	30397020	12	1350											
PPIL1	51645	hgsc.bcm.edu;broad.mit.edu	37	chr6	36842542	36842542	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccaggaatctgggggaattgCcgccatagcgaagccggcgg	9	5	16	11	4	1	0	0	0	1	0	1	3	1	2	4	5	3	0	4	5	4	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr6:36842542C>T	ENST00000373699.5	-	1	258	c.7G>A	c.(7-9)Gca>Aca	p.A3T	C6orf89_ENST00000510325.2_Intron|C6orf89_ENST00000359359.2_Intron	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	3					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						GGGGGAATTGCCGCCATAGCG	0.637																																					p.A3T		.											.	PPIL1-91	0			c.G7A						.						27	31	30					6																	36842542		2203	4300	6503	SO:0001583	missense	51645	exon1			GAATTGCCGCCAT	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.7G>A	6.37:g.36842542C>T	ENSP00000362803:p.Ala3Thr	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	27	3	NM_016059	0	0	22	22	0	O15001|Q5TDC9	Missense_Mutation	SNP	ENST00000373699.5	37	CCDS4826.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142423	0.77888	.	.	ENSG00000137168	ENST00000373699	T	0.24151	1.87	5.49	5.49	0.81192	.	0.059397	0.64402	D	0.000004	T	0.09818	0.0241	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05257	-1.0896	10	0.72032	D	0.01	.	16.8702	0.86038	0.0:1.0:0.0:0.0	.	3	Q9Y3C6	PPIL1_HUMAN	T	3	ENSP00000362803:A3T	ENSP00000362803:A3T	A	-	1	0	PPIL1	36950520	1.000000	0.71417	0.994000	0.49952	0.675000	0.39556	6.986000	0.76200	2.596000	0.87737	0.557000	0.71058	GCA	.		0.637	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1			T	36842542	C	T	36842542	3	4	16	1	0	0	0	0	1	0	0	0	12355	739	26	2	509	2	PPIL1	6	36842542	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		36842542	134272525	13	1351											
TYW1	55253	hgsc.bcm.edu	37	chr7	66474575	66474575	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttttggtcctattagggattCgcaacagttcttgctgaagc	8	15	10	8	1	1	1	0	1	1	0	3	2	2	2	1	2	3	3	1	2	4	7	rs376806090		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr7:66474575C>T	ENST00000359626.5	+	4	443	c.279C>T	c.(277-279)ttC>ttT	p.F93F		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	93	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				ATTAGGGATTCGCAACAGTTC	0.398																																					p.F93F		.											.	TYW1-91	0			c.C279T						.						134	119	124					7																	66474575		2203	4300	6503	SO:0001819	synonymous_variant	55253	exon4			GGGATTCGCAACA	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"	611243	"radical S-adenosyl methionine and flavodoxin domains 1"	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.279C>T	7.37:g.66474575C>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	99	5	NM_018264	0	0	0	0	0	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			.		0.398	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		T	66474575	C	T	66474575	2	4	16	1	0	0	0	0	0	0	0	1	16851	883	31	1		1	TYW1	7	66474575	Silent	SNP	C	TCGA-A4-8312-01A-11D-2396-08		66474575	92664088	14	1352											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83023612	83023612	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acacacacacacagaacttaCccgctttgaagaaatctcca	16	7	4	14	1	1	3	0	1	1	2	2	3	1	3	2	0	2	1	2	0	4	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr7:83023612C>G	ENST00000307792.3	-	13	1968		c.e13+1		SEMA3E_ENST00000427262.1_Splice_Site	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E						axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				acaGAACTTACCCGCTTTGAA	0.318																																					.		.											.	SEMA3E-93	0			c.1500+1G>C						.						45	45	45					7																	83023612		2203	4297	6500	SO:0001630	splice_region_variant	9723	exon14			AACTTACCCGCTT	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10727	protein-coding gene	gene with protein product	"M-sema H"	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1500+1G>C	7.37:g.83023612C>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_012431	0	0	0	0	0	B4E1P1|Q75M94|Q75M97	Splice_Site	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677971	0.88445	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4324	0.99085	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA3E	82861548	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	6.793000	0.75130	2.833000	0.97629	0.585000	0.79938	.	.		0.318	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	Intron	G	83023612	C	G	83023612	5	3	16	1	0	0	0	0	0	0	1	0	14060	521	18	4	846	4	SEMA3E	7	83023612	Splice_Site	SNP	C	TCGA-A4-8312-01A-11D-2396-08	16549037	83023612	76115051	15	1353											
MBLAC1	255374	hgsc.bcm.edu	37	chr7	99725439	99725439	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcacgacttctgccttcccGgaggccgctacctgccccac	5	7	9	20	4	1	0	0	0	1	0	2	2	2	1	6	2	3	2	6	2	1	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr7:99725439G>A	ENST00000398075.2	+	2	820	c.421G>A	c.(421-423)Gga>Aga	p.G141R	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	141							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						CTGCCTTCCCGGAGGCCGCTA	0.736																																					p.G141R		.											.	MBLAC1-135	0			c.G421A						.						10	12	11					7																	99725439		1895	4100	5995	SO:0001583	missense	255374	exon2			CTTCCCGGAGGCC	BC031288	CCDS43620.1	7q22	2014-02-12	2009-04-08		ENSG00000214309	ENSG00000214309			22180	protein-coding gene	gene with protein product							Standard	XM_005250250		Approved	MGC49416	uc003utp.3	A4D2B0	OTTHUMG00000154846	ENST00000398075.2:c.421G>A	7.37:g.99725439G>A	ENSP00000381150:p.Gly141Arg	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_203397	0	0	3	3	0	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	37	CCDS43620.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600780	0.66332	.	.	ENSG00000214309	ENST00000398075	T	0.79454	-1.27	4.35	4.35	0.52113	Beta-lactamase-like (2);	0.096661	0.40302	U	0.001124	T	0.65575	0.2704	N	0.20574	0.59	0.31698	N	0.641087	P	0.52061	0.95	P	0.45099	0.469	T	0.65602	-0.6128	10	0.14252	T	0.57	.	14.7701	0.69671	0.0:0.0:1.0:0.0	.	141	A4D2B0	MBLC1_HUMAN	R	141	ENSP00000381150:G141R	ENSP00000381150:G141R	G	+	1	0	MBLAC1	99563375	1.000000	0.71417	0.993000	0.49108	0.885000	0.51271	4.846000	0.62860	2.440000	0.82611	0.561000	0.74099	GGA	.		0.736	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397		A	99725439	G	A	99725439	3	1	16	1	0	0	0	0	1	0	0	0	9376	1117	39	1	423	1	MBLAC1	7	99725439	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08	16701827	99725439	59413224	16	1354											
FBXW2	26190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	123527053	123527053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgtacaggtagcggttGtcaaacagcagggcaaagat	14	8	13	6	1	1	2	1	1	0	1	1	2	1	2	0	3	4	5	0	3	4	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr9:123527053G>A	ENST00000608872.1	-	8	1336	c.1149C>T	c.(1147-1149)gaC>gaT	p.D383D	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Silent_p.D318D	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	383					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						GGTAGCGGTTGTCAAACAGCA	0.502																																					p.D383D		.											.	FBXW2-227	0			c.C1149T						.						92	90	91					9																	123527053		1949	4160	6109	SO:0001819	synonymous_variant	26190	exon8			GCGGTTGTCAAAC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1149C>T	9.37:g.123527053G>A		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	125	11	NM_012164	0	0	27	29	2	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Silent	SNP	ENST00000608872.1	37	CCDS43872.1																																																																																			.		0.502	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			A	123527053	G	A	123527053	2	1	16	1	0	0	0	0	0	0	0	1	5785	1368	48	2		2	FBXW2	9	123527053	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08		123527053	17686378	17	1355											
TAF10	6881	hgsc.bcm.edu	37	chr11	6632632	6632632	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactcacatgcgtgggtctgAggcctcaaagccagcacggt	9	8	12	12	2	3	1	2	1	1	0	3	1	3	1	2	3	4	1	2	3	2	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr11:6632632A>G	ENST00000299424.4	-	3	916	c.439T>C	c.(439-441)Tca>Cca	p.S147P	RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'UTR	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa	147					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CGTGGGTCTGAGGCCTCAAAG	0.488																																					p.S147P		.											.	TAF10-90	0			c.T439C						.						87	83	84					11																	6632632		2201	4296	6497	SO:0001583	missense	6881	exon3			GGTCTGAGGCCTC	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402	ENST00000299424.4:c.439T>C	11.37:g.6632632A>G	ENSP00000299424:p.Ser147Pro	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	49	3	NM_006284	0	0	0	0	0	O00703|Q13175|Q6FH13	Missense_Mutation	SNP	ENST00000299424.4	37	CCDS7769.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082995	0.76642	.	.	ENSG00000166337	ENST00000299424	T	0.47869	0.83	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.42698	0.1214	L	0.33189	0.99	0.80722	D	1	P	0.42248	0.774	P	0.44897	0.463	T	0.34153	-0.9840	10	0.42905	T	0.14	-5.9082	12.7863	0.57507	1.0:0.0:0.0:0.0	.	147	Q12962	TAF10_HUMAN	P	147	ENSP00000299424:S147P	ENSP00000299424:S147P	S	-	1	0	TAF10	6589208	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.372000	0.73123	2.116000	0.64780	0.482000	0.46254	TCA	.		0.488	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284		G	6632632	A	G	6632632	3	3	16	1	0	0	0	0	1	0	0	0	15546	304	11	3	229	3	TAF10	11	6632632	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08		6632632	128373884	18	1356											
LRFN4	78999	hgsc.bcm.edu	37	chr11	66627272	66627272	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgctgccggcctcgccccTgtgccacgccctgcaggccc	3	5	11	22	4	0	0	0	0	0	0	1	0	0	0	7	2	3	2	7	2	0	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr11:66627272T>A	ENST00000309602.4	+	2	1757	c.1514T>A	c.(1513-1515)cTg>cAg	p.L505Q	LRFN4_ENST00000393952.3_Intron|PC_ENST00000393955.2_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393960.1_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	505						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						GCCTCGCCCCTGTGCCACGCC	0.706																																					p.L505Q		.											.	LRFN4-90	0			c.T1514A						.						28	23	25					11																	66627272		2190	4291	6481	SO:0001583	missense	78999	exon2			CGCCCCTGTGCCA	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1514T>A	11.37:g.66627272T>A	ENSP00000312535:p.Leu505Gln	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_024036	0	0	27	27	0	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Missense_Mutation	SNP	ENST00000309602.4	37	CCDS8153.1	.	.	.	.	.	.	.	.	.	.	T	3.096	-0.185884	0.06340	.	.	ENSG00000173621	ENST00000309602	T	0.45276	0.9	4.71	4.71	0.59529	.	0.279394	0.19674	N	0.108672	T	0.13798	0.0334	N	0.01168	-0.975	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.12268	-1.0554	10	0.08837	T	0.75	.	7.7816	0.29068	0.1863:0.0:0.0:0.8137	.	505	Q6PJG9	LRFN4_HUMAN	Q	505	ENSP00000312535:L505Q	ENSP00000312535:L505Q	L	+	2	0	LRFN4	66383848	0.002000	0.14202	0.997000	0.53966	0.717000	0.41224	-0.124000	0.10595	1.771000	0.52183	0.379000	0.24179	CTG	.		0.706	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		A	66627272	T	A	66627272	3	1	16	1	0	0	0	0	1	0	0	0	8965	1580	55	5	1520	5	LRFN4	11	66627272	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	59994640	66627272	68379244	19	1357											
MMP13	4322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102826393	102826393	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcagggcccgacaatgagtCcagctcaagaagaggaaggc	13	3	15	10	1	1	3	1	1	0	2	2	5	2	4	2	4	1	2	2	4	4	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr11:102826393C>A	ENST00000260302.3	-	1	70	c.42G>T	c.(40-42)tgG>tgT	p.W14C	MMP13_ENST00000340273.4_Missense_Mutation_p.W14C	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	14					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	GACAATGAGTCCAGCTCAAGA	0.507																																					p.W14C		.											.	MMP13-229	0			c.G42T						.						94	94	94					11																	102826393		2202	4299	6501	SO:0001583	missense	4322	exon1			ATGAGTCCAGCTC	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.42G>T	11.37:g.102826393C>A	ENSP00000260302:p.Trp14Cys	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	101	10	NM_002427	0	0	0	0	0	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	6.549	0.469578	0.12461	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.15139	2.64;2.45	5.87	5.87	0.94306	.	0.442712	0.26311	N	0.025120	T	0.11024	0.0269	N	0.14661	0.345	0.47994	D	0.999562	P	0.48640	0.913	B	0.40741	0.339	T	0.03306	-1.1050	10	0.45353	T	0.12	.	11.7621	0.51910	0.1372:0.7305:0.1323:0.0	.	14	P45452	MMP13_HUMAN	C	14	ENSP00000260302:W14C;ENSP00000339672:W14C	ENSP00000260302:W14C	W	-	3	0	MMP13	102331603	0.998000	0.40836	0.987000	0.45799	0.168000	0.22595	1.956000	0.40382	2.941000	0.99782	0.655000	0.94253	TGG	.		0.507	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		A	102826393	C	A	102826393	3	1	16	1	0	0	0	0	1	0	0	0	9677	856	30	4	1413	4	MMP13	11	102826393	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08	36199121	102826393	32180123	20	1358											
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123448255	123448255	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgcagctgctcctcccaGtccggccggagcggcggcaa	6	4	14	17	5	0	0	0	0	0	0	3	1	3	1	4	4	4	4	4	4	1	0	rs374298813		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr11:123448255G>A	ENST00000529750.1	+	2	531	c.204G>A	c.(202-204)caG>caA	p.Q68Q	GRAMD1B_ENST00000322282.7_Silent_p.Q68Q|GRAMD1B_ENST00000456860.2_Silent_p.Q68Q	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	68						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		GCTCCTCCCAGTCCGGCCGGA	0.662											OREG0021454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q68Q		.											.	GRAMD1B-69	0			c.G204A						.	G		1,4051		0,1,2025	13	18	16		204	4.9	1	11		16	0,8346		0,0,4173	no	coding-synonymous	GRAMD1B	NM_020716.1		0,1,6198	AA,AG,GG		0.0,0.0247,0.0081		68/739	123448255	1,12397	2026	4173	6199	SO:0001819	synonymous_variant	57476	exon2			CTCCCAGTCCGGC	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.204G>A	11.37:g.123448255G>A		Somatic	5	2	1526	WXS	Illumina HiSeq	Phase_I	8	3	NM_020716	0	0	1	1	0	Q6UW85|Q9ULL9	Silent	SNP	ENST00000529750.1	37	CCDS53720.1																																																																																			.		0.662	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		A	123448255	G	A	123448255	2	1	16	1	0	0	0	0	0	0	0	1	6769	1020	36	2		2	GRAMD1B	11	123448255	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	20621862	123448255	11558261	21	1359											
CACNA1C	775	hgsc.bcm.edu;broad.mit.edu	37	chr12	2614092	2614092	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cattttttgtacttaacttgGttctcggtgtgcttagcggg	5	18	11	7	2	1	0	0	0	1	0	2	0	1	0	0	3	4	3	0	3	3	8			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:2614092G>T	ENST00000347598.4	+	8	1198	c.1198G>T	c.(1198-1200)Gtt>Ttt	p.V400F	CACNA1C_ENST00000480911.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000491104.1_Intron|CACNA1C_ENST00000399601.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399606.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399595.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000402845.3_Missense_Mutation_p.V400F|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000344100.3_Missense_Mutation_p.V400F|CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399637.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000327702.7_Missense_Mutation_p.V400F|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399621.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399597.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399629.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399591.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000335762.5_Missense_Mutation_p.V400F|CACNA1C_ENST00000399644.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399649.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399655.1_Missense_Mutation_p.V400F|CACNA1C_ENST00000399638.1_Missense_Mutation_p.V400F	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	400					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACTTAACTTGGTTCTCGGTGT	0.398																																					p.V400F		.											.	CACNA1C-34	0			c.G1198T						.						111	106	108					12																	2614092		1895	4137	6032	SO:0001583	missense	775	exon8			AACTTGGTTCTCG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1198G>T	12.37:g.2614092G>T	ENSP00000266376:p.Val400Phe	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	22	8	NM_001129831	0	0	0	0	0	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221092	0.79464	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399595	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96104	-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91;-3.91	5.27	5.27	0.74061	Ion transport (1);	.	.	.	.	D	0.96247	0.8776	L	0.35249	1.045	0.80722	D	1	D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.995;0.999;1.0;1.0;1.0;0.659;0.997;1.0;0.999;0.998;0.999;0.987;0.998;1.0;1.0;0.998;1.0	D;D;D;D;D;D;D;P;D;D;D;D;D;P;D;D;D;D;D	0.91635	0.996;0.997;0.934;0.995;0.999;0.997;0.999;0.835;0.975;0.999;0.999;0.925;0.998;0.805;0.991;0.999;0.999;0.991;0.997	D	0.96063	0.9040	9	0.46703	T	0.11	.	19.0978	0.93260	0.0:0.0:1.0:0.0	.	400;397;400;400;400;400;400;400;400;400;400;400;400;400;400;400;400;400;400	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-11;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	F	400	ENSP00000336982:V400F;ENSP00000382563:V400F;ENSP00000437936:V400F;ENSP00000382552:V400F;ENSP00000382547:V400F;ENSP00000382506:V400F;ENSP00000382530:V400F;ENSP00000382546:V400F;ENSP00000382500:V400F;ENSP00000266376:V400F;ENSP00000382515:V400F;ENSP00000382510:V400F;ENSP00000341092:V400F;ENSP00000382537:V400F;ENSP00000329877:V400F;ENSP00000382557:V400F;ENSP00000385724:V400F;ENSP00000382504:V400F	ENSP00000329877:V400F	V	+	1	0	CACNA1C	2484353	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.735000	0.93741	0.655000	0.94253	GTT	.		0.398	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2614092	G	T	2614092	3	4	16	1	0	0	0	0	1	0	0	0	2546	1261	44	4	1336	4	CACNA1C	12	2614092	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08		2614092	131237803	22	1360											
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	11	7	6	17	1	1	0	0	0	1	0	2	0	2	0	5	1	5	2	5	1	4	3	rs121913529		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	.	KRAS-92875	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						.						91	81	85					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	37	19	NM_004985	0	0	6	10	4	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	16	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08	22784192	25398284	108453611	23	1361											
BICD1	636	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	32491723	32491724	+	Frame_Shift_Del	DEL	AT	AT	-																															cttggatctcctgcaagacaAttttcaccttccctttgtga																										TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:32491723_32491724delAT	ENST00000281474.5	+	8	2677_2678	c.2574_2575delAT	c.(2572-2577)caatttfs	p.QF858fs	BICD1_ENST00000548411.1_Intron	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	858					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			CTGCAAGACAATTTTCACCTTC	0.406																																					p.858_859del		.											.	BICD1-153	0			c.2574_2575del						.																																			SO:0001589	frameshift_variant	636	exon8			.	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"Bicaudal D (Drosophila) homolog 1"			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2574_2575delAT	12.37:g.32491723_32491724delAT	ENSP00000281474:p.Gln858fs	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	182	62	NM_001714	0	0	0	0	0	A8K2C3|F8W113|O43892|O43893	Frame_Shift_Del	DEL	ENST00000281474.5	37	CCDS8726.1																																																																																			.		0.406	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		-	32491724	AT	-	32491723	7	5	16	1	0	1	0	1	0	0	0	0	1429	98	4	0	2604	0	BICD1	12	32491723	Frame_Shift_Del	DEL	AT	TCGA-A4-8312-01A-11D-2396-08	7093439	32491723	101360172	24	1362											
TUBA1B	10376	hgsc.bcm.edu	37	chr12	49522587	49522587	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctggggtgctgggtaaatGgagaactccagcttggactt	9	10	14	8	0	0	1	0	0	0	1	1	3	1	2	2	5	3	3	2	5	3	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:49522587G>A	ENST00000336023.5	-	4	604	c.510C>T	c.(508-510)tcC>tcT	p.S170S	RP11-386G11.10_ENST00000547387.1_RNA|RP11-386G11.10_ENST00000547712.1_RNA|RP11-386G11.10_ENST00000548149.1_RNA|RP11-386G11.10_ENST00000551496.1_RNA|RP11-386G11.10_ENST00000552893.1_RNA	NM_006082.2	NP_006073.2	P68363	TBA1B_HUMAN	tubulin, alpha 1b	170					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(4)	12						CTGGGTAAATGGAGAACTCCA	0.532																																					p.S170S		.											.	TUBA1B-90	0			c.C510T						.						44	62	56					12																	49522587		2203	4296	6499	SO:0001819	synonymous_variant	10376	exon4			GTAAATGGAGAAC	AF081484	CCDS31792.1	12q13.12	2007-02-12				ENSG00000123416		"Tubulins"	18809	protein-coding gene	gene with protein product	"tubulin, alpha, ubiquitous"	602530				12054644, 6646120	Standard	NM_006082		Approved	K-ALPHA-1	uc001rtm.3	P68363	OTTHUMG00000170410	ENST00000336023.5:c.510C>T	12.37:g.49522587G>A		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	96	5	NM_006082	0	0	1	1	0	P04687|P05209|Q27I68|Q8WU19	Silent	SNP	ENST00000336023.5	37	CCDS31792.1																																																																																			.		0.532	TUBA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409005.1	NM_006082		A	49522587	G	A	49522587	2	1	16	1	0	0	0	0	0	0	0	1	16777	1335	47	2		2	TUBA1B	12	49522587	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	17030864	49522587	84329308	25	1363											
RAD9B	144715	hgsc.bcm.edu	37	chr12	110960047	110960047	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccctggaatgtatttcaaAaaaagcagcaccaagaaggc	16	6	10	9	0	1	1	1	0	0	1	1	2	1	2	2	3	2	3	2	3	7	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:110960047A>C	ENST00000409778.3	+	8	773	c.749A>C	c.(748-750)aAa>aCa	p.K250T	RAD9B_ENST00000409246.1_Missense_Mutation_p.K247T|RAD9B_ENST00000409425.1_Missense_Mutation_p.K247T|RAD9B_ENST00000409300.1_Missense_Mutation_p.K319T|RAD9B_ENST00000392672.4_Missense_Mutation_p.K319T			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	316					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						TGTATTTCAAAAAAAGCAGCA	0.408																																					p.K319T		.											.	RAD9B-228	0			c.A956C						.						43	42	42					12																	110960047		2203	4300	6503	SO:0001583	missense	144715	exon10			TTTCAAAAAAAGC		CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.749A>C	12.37:g.110960047A>C	ENSP00000386697:p.Lys250Thr	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_152442	0	0	1	1	0	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Missense_Mutation	SNP	ENST00000409778.3	37		.	.	.	.	.	.	.	.	.	.	G	8.034	0.762320	0.15914	.	.	ENSG00000151164	ENST00000409246;ENST00000392672;ENST00000409300;ENST00000409425;ENST00000409778	T;T;T;T;T	0.23754	1.89;2.22;2.22;1.89;2.15	5.12	2.05	0.26809	.	0.435152	0.23142	N	0.051460	T	0.10766	0.0263	N	0.19112	0.55	0.09310	N	1	B;B;B	0.12013	0.0;0.005;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.21930	-1.0231	10	0.12103	T	0.63	-10.2776	1.3704	0.02210	0.1914:0.1717:0.4596:0.1774	.	250;319;316	B4DYM6;B4DX60;Q6WBX8	.;.;RAD9B_HUMAN	T	247;319;319;247;250	ENSP00000387329:K247T;ENSP00000376440:K319T;ENSP00000386434:K319T;ENSP00000386629:K247T;ENSP00000386697:K250T	ENSP00000376440:K319T	K	+	2	0	RAD9B	109444430	0.111000	0.22076	0.035000	0.18076	0.357000	0.29423	0.805000	0.27112	0.647000	0.30713	-0.215000	0.12644	AAA	.		0.408	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442		C	110960047	A	C	110960047	3	2	16	1	0	0	0	0	1	0	0	0	13028	14	1	5	994	5	RAD9B	12	110960047	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08	61437460	110960047	22891848	26	1364											
MTUS2	23281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	29599704	29599704	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgaatttgactttggcatCgaaggaaatcccaagtaaac	14	11	8	8	1	1	2	0	2	1	0	3	4	2	3	1	2	1	2	1	2	6	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr13:29599704C>T	ENST00000431530.3	+	1	957	c.899C>T	c.(898-900)tCg>tTg	p.S300L		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	290						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.S300L(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						ACTTTGGCATCGAAGGAAATC	0.507																																					p.S300L		.											.	MTUS2-218	2	Substitution - Missense(2)	endometrium(1)|central_nervous_system(1)	c.C899T						.						40	40	40					13																	29599704		2007	4188	6195	SO:0001583	missense	23281	exon1			TGGCATCGAAGGA	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.899C>T	13.37:g.29599704C>T	ENSP00000392057:p.Ser300Leu	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_001033602	0	0	0	0	0	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	c	10.58	1.391325	0.25118	.	.	ENSG00000132938	ENST00000431530	T	0.13089	2.62	5.49	0.716	0.18191	.	0.981254	0.08305	N	0.966293	T	0.06096	0.0158	N	0.03115	-0.41	0.09310	N	1	B	0.21309	0.054	B	0.12156	0.007	T	0.44128	-0.9348	9	.	.	.	.	10.4835	0.44708	0.0:0.587:0.0:0.413	.	290	Q5JR59	MTUS2_HUMAN	L	300	ENSP00000392057:S300L	.	S	+	2	0	MTUS2	28497704	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.040000	0.13905	0.015000	0.14971	0.561000	0.74099	TCG	.		0.507	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29599704	C	T	29599704	3	4	16	1	0	0	0	0	1	0	0	0	9991	893	31	1	901	1	MTUS2	13	29599704	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		29599704	85570174	27	1365											
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24879003	24879003	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcacctgcagctcccaaagTacctgtgacccccagagtct	10	7	8	16	0	1	2	0	1	1	1	2	2	2	2	5	0	4	4	5	0	2	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:24879003T>C	ENST00000382554.3	+	4	2321	c.2003T>C	c.(2002-2004)gTa>gCa	p.V668A		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	668					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GCTCCCAAAGTACCTGTGACC	0.567																																					p.V668A		.											.	NYNRIN-3	0			c.T2003C						.						40	45	43					14																	24879003		1944	4140	6084	SO:0001583	missense	57523	exon4			CCAAAGTACCTGT	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.2003T>C	14.37:g.24879003T>C	ENSP00000371994:p.Val668Ala	Somatic	24	1		WXS	Illumina HiSeq	Phase_I	26	4	NM_025081	0	0	1	1	0	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	T	2.483	-0.319315	0.05386	.	.	ENSG00000205978	ENST00000382554	T	0.07688	3.17	3.23	2.32	0.28847	.	.	.	.	.	T	0.03477	0.0100	N	0.04508	-0.205	0.21355	N	0.999711	B	0.02656	0.0	B	0.01281	0.0	T	0.46148	-0.9212	9	0.12103	T	0.63	.	7.9246	0.29867	0.0:0.8644:0.0:0.1356	.	668	Q9P2P1	NYNRI_HUMAN	A	668	ENSP00000371994:V668A	ENSP00000371994:V668A	V	+	2	0	NYNRIN	23948843	0.993000	0.37304	0.508000	0.27688	0.206000	0.24218	1.627000	0.37050	0.904000	0.36572	-0.366000	0.07423	GTA	.		0.567	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			C	24879003	T	C	24879003	3	2	16	1	0	0	0	0	1	0	0	0	10822	1638	57	3	2013	3	NYNRIN	14	24879003	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08		24879003	82470537	28	1366											
ARHGAP5	394	hgsc.bcm.edu	37	chr14	32561433	32561433	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataaaatgagtgaaattcatAcagttctgagtgaagaacct	17	11	8	5	0	2	5	1	4	1	1	2	5	2	5	1	0	2	1	1	0	6	4			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:32561433A>G	ENST00000345122.3	+	2	1873	c.1558A>G	c.(1558-1560)Aca>Gca	p.T520A	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.T520A|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.T520A|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.T520A	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	520	FF 4.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.T520A(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TGAAATTCATACAGTTCTGAG	0.333																																					p.T520A	NSCLC(9;77 350 3443 29227 41353)	.											.	ARHGAP5-94	1	Substitution - Missense(1)	urinary_tract(1)	c.A1558G						.						30	30	30					14																	32561433		2201	4292	6493	SO:0001583	missense	394	exon2			ATTCATACAGTTC	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1558A>G	14.37:g.32561433A>G	ENSP00000371897:p.Thr520Ala	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	55	7	NM_001173	0	0	4	4	0	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	A	2.843	-0.240070	0.05944	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.27104	1.69;1.69;1.69;1.69	6.02	6.02	0.97574	FF domain (2);	0.265604	0.44688	D	0.000429	T	0.08403	0.0209	N	0.01352	-0.895	0.28157	N	0.929162	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.14117	-1.0484	10	0.27785	T	0.31	.	6.4383	0.21835	0.8146:0.0:0.1854:0.0	.	520;520	Q13017-2;Q13017	.;RHG05_HUMAN	A	520	ENSP00000452222:T520A;ENSP00000441692:T520A;ENSP00000371897:T520A;ENSP00000393307:T520A	ENSP00000371897:T520A	T	+	1	0	ARHGAP5	31631184	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.726000	0.47302	2.299000	0.77371	0.528000	0.53228	ACA	.		0.333	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		G	32561433	A	G	32561433	3	3	16	1	0	0	0	0	1	0	0	0	886	391	14	3	1560	3	ARHGAP5	14	32561433	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08	7682430	32561433	74788107	29	1367											
SLC8A3	6547	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	70527578	70527578	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attccacgttccatccatttCggttcaccaagggcaatgaa	11	11	7	12	2	1	1	1	1	0	0	5	1	4	1	4	2	0	3	4	2	3	4	rs376675749		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:70527578C>T	ENST00000381269.2	-	3	2616	c.1863G>A	c.(1861-1863)ccG>ccA	p.P621P	SLC8A3_ENST00000216568.7_5'UTR|SLC8A3_ENST00000528359.1_Intron|SLC8A3_ENST00000356921.2_Silent_p.P621P|SLC8A3_ENST00000533899.1_5'UTR|SLC8A3_ENST00000394330.2_Intron|SLC8A3_ENST00000357887.3_Intron|SLC8A3_ENST00000533541.1_Intron|SLC8A3_ENST00000534137.1_Silent_p.P621P	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	621					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CCATCCATTTCGGTTCACCAA	0.343																																					p.P621P		.											.	SLC8A3-225	0			c.G1863A						.	C	,,,,,	2,4404	4.2+/-10.8	0,2,2201	167	144	152		,,1863,1863,,1863	5.9	1	14		152	0,8600		0,0,4300	no	utr-5,intron,coding-synonymous,coding-synonymous,intron,coding-synonymous	SLC8A3	NM_001130417.1,NM_033262.3,NM_058240.2,NM_182932.1,NM_182936.1,NM_183002.1	,,,,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,,,,	,,621/925,621/922,,621/928	70527578	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon3			CCATTTCGGTTCA	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1863G>A	14.37:g.70527578C>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	71	22	NM_183002	0	0	0	0	0	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																			.		0.343	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70527578	C	T	70527578	2	4	16	1	0	0	0	0	0	0	0	1	14740	871	31	1		1	SLC8A3	14	70527578	Silent	SNP	C	TCGA-A4-8312-01A-11D-2396-08	37966145	70527578	36821962	30	1368											
TRIP11	9321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	92470654	92470654	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcacctgctgcttccactcTtccattttctttacttgctg	5	18	4	14	0	3	0	1	0	2	0	5	0	5	0	3	0	4	3	3	0	1	7			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:92470654T>A	ENST00000267622.4	-	11	4039	c.3666A>T	c.(3664-3666)gaA>gaT	p.E1222D		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1222					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GCTTCCACTCTTCCATTTTCT	0.443			T	PDGFRB	AML																																p.E1222D	Ovarian(84;609 1888 9852 42686)	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11-1400	0			c.A3666T						.						79	72	75					14																	92470654		2203	4300	6503	SO:0001583	missense	9321	exon11			CCACTCTTCCATT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.3666A>T	14.37:g.92470654T>A	ENSP00000267622:p.Glu1222Asp	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	64	28	NM_004239	0	0	7	11	4	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.88|11.88	1.771464|1.771464	0.31320|0.31320	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.05786|.	3.39|.	5.46|5.46	-4.33|-4.33	0.03677|0.03677	.|.	0.112824|.	0.64402|.	D|.	0.000015|.	T|.	0.44664|.	0.1304|.	L|L	0.32530|0.32530	0.975|0.975	0.41458|0.41458	D|D	0.988026|0.988026	D;D|.	0.89917|.	0.986;1.0|.	P;D|.	0.91635|.	0.78;0.999|.	T|.	0.32745|.	-0.9895|.	10|.	0.52906|.	T|.	0.07|.	.|.	8.2632|8.2632	0.31797|0.31797	0.119:0.4845:0.0:0.3964|0.119:0.4845:0.0:0.3964	.|.	958;1222|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	D|X	1222;958|938	ENSP00000267622:E1222D|.	ENSP00000267622:E1222D|.	E|R	-|-	3|1	2|2	TRIP11|TRIP11	91540407|91540407	0.238000|0.238000	0.23825|0.23825	0.822000|0.822000	0.32727|0.32727	0.150000|0.150000	0.21749|0.21749	-0.435000|-0.435000	0.06931|0.06931	-1.215000|-1.215000	0.02610|0.02610	-0.624000|-0.624000	0.04008|0.04008	GAA|AGA	.		0.443	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			A	92470654	T	A	92470654	3	1	16	1	0	0	0	0	1	0	0	0	16588	1606	56	5	2317	5	TRIP11	14	92470654	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	21943076	92470654	14878886	31	1369											
ATP10A	57194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	25972305	25972305	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgccaggtgcccgagcctAcctgcgtagatgacaatgcc	8	7	13	13	2	0	2	0	1	0	1	0	3	0	2	5	2	6	1	5	2	3	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr15:25972305A>T	ENST00000356865.6	-	4	959		c.e4+1			NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCCCGAGCCTACCTGCGTAGA	0.517																																					.		.											.	ATP10A-139	0			c.847+2T>A						.						102	81	88					15																	25972305		2203	4300	6503	SO:0001630	splice_region_variant	57194	exon5			GAGCCTACCTGCG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.847+1T>A	15.37:g.25972305A>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	81	36	NM_024490	0	0	0	0	0	Q4G0S9|Q969I4	Splice_Site	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514606	0.85389	.	.	ENSG00000206190	ENST00000356865	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3129	0.74048	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP10A	23523398	1.000000	0.71417	0.995000	0.50966	0.813000	0.45954	8.600000	0.90860	2.033000	0.60031	0.460000	0.39030	.	.		0.517	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	Intron	T	25972305	A	T	25972305	5	4	16	1	0	0	0	0	0	0	1	0	1117	405	14	5	3722	5	ATP10A	15	25972305	Splice_Site	SNP	A	TCGA-A4-8312-01A-11D-2396-08		25972305	76559087	32	1370											
AMDHD2	752014	hgsc.bcm.edu	37	chr16	2580428	2580428	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgaggctccctgaacagcttCgaggcgggtgggcttctgga	6	9	16	10	2	1	2	0	2	1	0	3	4	2	3	1	5	2	3	1	5	1	2	rs141294706	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:2580428C>T	ENST00000567119.1	-	1	981	c.647G>A	c.(646-648)cGa>cAa	p.R216Q	CEMP1_ENST00000565480.1_Intron|MIR3178_ENST00000581887.1_RNA|AMDHD2_ENST00000302956.4_3'UTR|AMDHD2_ENST00000565570.1_3'UTR|CEMP1_ENST00000382350.1_Missense_Mutation_p.R216Q|AMDHD2_ENST00000413459.3_Nonsense_Mutation_p.R485*	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	216						cytoplasm (GO:0005737)				lung(1)|skin(1)	2						TGAACAGCTTCGAGGCGGGTG	0.612													C|||	2	0.000399361	0.0015	0	5008	,	,		18808	0		0	False		,,,				2504	0				p.R485X		.											.	AMDHD2-155	0			c.C1453T						.	C	stop/ARG,GLN/ARG	7,3973		0,7,1983	42	46	45		1453,647	-3.4	0	16	dbSNP_134	45	0,8348		0,0,4174	yes	stop-gained,missense	AMDHD2,CEMP1	NM_001145815.1,NM_001048212.3	,43	0,7,6157	TT,TC,CC		0.0,0.1759,0.0568	,benign	485/595,216/248	2580428	7,12321	1990	4174	6164	SO:0001583	missense	51005	exon11			CAGCTTCGAGGCG	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"cementum protein-23"	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.647G>A	16.37:g.2580428C>T	ENSP00000457380:p.Arg216Gln	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	48	4	NM_001145815	0	0	5	7	2	B2RUY1	Nonsense_Mutation	SNP	ENST00000567119.1	37	CCDS42108.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	36|36	5.917064|5.917064	0.97099|0.97099	0.001759|0.001759	0.0|0.0	ENSG00000205923|ENSG00000162066	ENST00000382350|ENST00000413459	T|.	0.55588|.	0.51|.	1.71|1.71	-3.43|-3.43	0.04810|0.04810	.|.	.|.	.|.	.|.	.|.	T|.	0.09158|.	0.0226|.	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.01281|.	0.0|.	T|.	0.32851|.	-0.9891|.	9|.	0.87932|0.02654	D|T	0|1	.|.	7.5486|7.5486	0.27781|0.27781	0.0:0.7123:0.0:0.2877|0.0:0.7123:0.0:0.2877	.|.	216|.	Q6PRD7|.	CEMP1_HUMAN|.	Q|X	216|485	ENSP00000371787:R216Q|.	ENSP00000371787:R216Q|ENSP00000391596:R485X	R|R	-|+	2|1	0|2	CEMP1|AMDHD2	2520429|2520429	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	-2.151000|-2.151000	0.01289|0.01289	-0.863000|-0.863000	0.04084|0.04084	-0.416000|-0.416000	0.06073|0.06073	CGA|CGA	C|0.998;T|0.002		0.612	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212		T	2580428	C	T	2580428	3	4	16	1	0	0	0	0	1	0	0	0	568	885	31	1	1533	1	AMDHD2	16	2580428	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		2580428	87774325	33	1371											
SMG1	23049	hgsc.bcm.edu	37	chr16	18849419	18849419	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctgcttgctctcggcctGctggccacctccaccataga	5	10	9	17	1	2	1	0	0	2	1	4	1	3	1	5	2	3	4	5	2	1	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:18849419G>C	ENST00000446231.2	-	45	7742	c.7330C>G	c.(7330-7332)Cag>Gag	p.Q2444E	SMG1_ENST00000389467.3_Missense_Mutation_p.Q2444E			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2444	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CTCTCGGCCTGCTGGCCACCT	0.587																																					p.Q2444E		.											.	SMG1-1160	0			c.C7330G						.																																			SO:0001583	missense	23049	exon45			CGGCCTGCTGGCC	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.7330C>G	16.37:g.18849419G>C	ENSP00000402515:p.Gln2444Glu	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_015092	0	0	7	7	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.862987	0.71949	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01076	5.37;5.37	5.72	5.72	0.89469	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.64402	D	0.000004	T	0.02767	0.0083	N	0.17474	0.49	0.50467	D	0.999876	P	0.49447	0.924	P	0.62298	0.9	T	0.76542	-0.2921	10	0.18276	T	0.48	.	20.244	0.98389	0.0:0.0:1.0:0.0	.	2444	Q96Q15	SMG1_HUMAN	E	2444	ENSP00000402515:Q2444E;ENSP00000374118:Q2444E	ENSP00000374118:Q2444E	Q	-	1	0	SMG1	18756920	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.793000	0.99091	2.865000	0.98341	0.655000	0.94253	CAG	.		0.587	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18849419	G	C	18849419	3	2	16	1	0	0	0	0	1	0	0	0	14827	1328	46	4	3731	4	SMG1	16	18849419	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08	16268991	18849419	71505334	34	1372											
LOC100132247	100132247	broad.mit.edu	37	chr16	22545578	22545580	+	In_Frame_Del	DEL	ATA	ATA	-																															gcttccaccctcagcggatgAtaatctcaagacaccttccg																										TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:22545578_22545580delATA	ENST00000517539.1	+	8	1349_1351	c.1274_1276delATA	c.(1273-1278)gataat>gat	p.N426del	NPIPB5_ENST00000424340.1_In_Frame_Del_p.N426del|NPIPB5_ENST00000415654.1_3'UTR			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	426	Pro-rich.					integral component of membrane (GO:0016021)											TCAGCGGATGATAATCTCAAGAC	0.586																																					p.425_426del													.	.	0			c.1274_1276del						.			72,304		29,14,145							0			1	29,645		11,7,319	no	coding	LOC100132247	NM_001135865.1		40,21,464	A1A1,A1R,RR		4.3027,19.1489,9.619				101,949				SO:0001651	inframe_deletion	0	exon7			CGGATGATAATCT		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1274_1276delATA	16.37:g.22545578_22545580delATA	ENSP00000430633:p.Asn426del	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	180	3	NM_001135865	0	0	0	0	0	B4DK13	In_Frame_Del	DEL	ENST00000517539.1	37	CCDS45443.1																																																																																			.		0.586	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374343.2	NM_001135865		-	22545580	ATA	-	22545578	7	5	16	1	0	1	0	1	0	0	0	0	8891	333	12	0	1300	0	LOC100132247	16	22545578	In_Frame_Del	DEL	ATA	TCGA-A4-8312-01A-11D-2396-08	3696159	22545578	67809175	35	1373											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30718524	30718524	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaggccgagatcgagactcgGattgctgagctgcggaagga	10	6	17	8	4	0	3	0	1	0	2	2	9	0	6	1	4	3	2	1	4	1	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:30718524G>T	ENST00000262518.4	+	5	712	c.327G>T	c.(325-327)cgG>cgT	p.R109R	SRCAP_ENST00000344771.4_Silent_p.R109R|SRCAP_ENST00000395059.2_Silent_p.R109R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	109					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TCGAGACTCGGATTGCTGAGC	0.547																																					p.R109R		.											.	SRCAP-94	0			c.G327T						.						69	69	69					16																	30718524		1987	4166	6153	SO:0001819	synonymous_variant	10847	exon5			GACTCGGATTGCT	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.327G>T	16.37:g.30718524G>T		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	90	34	NM_006662	0	0	4	6	2	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.547	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30718524	G	T	30718524	2	4	16	1	0	0	0	0	0	0	0	1	15167	1161	41	4		4	SRCAP	16	30718524	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	8172946	30718524	59636229	36	1374											
SRCAP	10847	bcgsc.ca	37	chr16	30727477	30727477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttatccgctgcaggctcTccaagcgtcaacgctgtctc	7	11	9	14	3	3	0	1	0	2	0	6	0	4	0	2	1	3	5	2	1	3	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:30727477T>C	ENST00000262518.4	+	17	2969	c.2584T>C	c.(2584-2586)Tcc>Ccc	p.S862P	SRCAP_ENST00000344771.4_Missense_Mutation_p.S862P|SRCAP_ENST00000395059.2_Missense_Mutation_p.S862P	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	862					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CTGCAGGCTCTCCAAGCGTCA	0.517																																					p.S862P													.	SRCAP-94	0			c.T2584C						.						137	119	125					16																	30727477		2197	4300	6497	SO:0001583	missense	10847	exon17			AGGCTCTCCAAGC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.2584T>C	16.37:g.30727477T>C	ENSP00000262518:p.Ser862Pro	Somatic	103	0		WXS	Illumina HiSeq	Phase_1	112	5	NM_006662	0	0	5	5	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735012	0.69189	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	T;T;T	0.79749	-1.3;-1.3;-1.3	5.25	5.25	0.73442	SNF2-related (1);	0.000000	0.53938	D	0.000054	D	0.89577	0.6755	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.90981	0.4827	10	0.87932	D	0	-15.3089	14.2776	0.66191	0.0:0.0:0.0:1.0	.	862;862;862	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	P	862	ENSP00000262518:S862P;ENSP00000378499:S862P;ENSP00000343042:S862P	ENSP00000262518:S862P	S	+	1	0	SRCAP	30634978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.712000	0.84684	2.201000	0.70794	0.459000	0.35465	TCC	.		0.517	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30727477	T	C	30727477	3	2	16	1	0	0	0	0	1	0	0	0	15167	1551	54	3	2642	3	SRCAP	16	30727477	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	8953	30727477	59627276	37	1375											
TBC1D29	26083	hgsc.bcm.edu	37	chr17	28890334	28890334	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actcctgcagactcctccaaGggtgccaggacaacaagcct	11	6	9	15	0	0	1	0	0	0	1	3	2	3	2	5	2	4	1	5	2	3	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:28890334G>A	ENST00000580161.1	+	6	2841	c.344G>A	c.(343-345)aGg>aAg	p.R115K	RP11-218M11.1_ENST00000563063.1_lincRNA|TBC1D29_ENST00000579181.1_Missense_Mutation_p.R115K|TBC1D29_ENST00000584297.1_3'UTR			Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	115							Rab GTPase activator activity (GO:0005097)			breast(1)|kidney(1)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Myeloproliferative disorder(56;0.0255)				ACTCCTCCAAGGGTGCCAGGA	0.572																																					p.R115K		.											.	TBC1D29-22	0			c.G344A						.						64	57	60					17																	28890334		2203	4300	6503	SO:0001583	missense	26083	exon5			CTCCAAGGGTGCC	BC096718	CCDS32606.1	17q11.2	2014-09-04			ENSG00000266733	ENSG00000266733			24509	protein-coding gene	gene with protein product						12618308	Standard	XM_006721805		Approved	DKFZP434O047	uc002hfh.3	Q9UFV1	OTTHUMG00000178857	ENST00000580161.1:c.344G>A	17.37:g.28890334G>A	ENSP00000462799:p.Arg115Lys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	76	4	NM_015594	0	0	0	0	0		Missense_Mutation	SNP	ENST00000580161.1	37	CCDS32606.1	.	.	.	.	.	.	.	.	.	.	.	11.00	1.509043	0.27036	.	.	ENSG00000197689	ENST00000329040	.	.	.	.	.	.	.	.	.	.	.	T	0.11410	0.0278	N	0.08118	0	0.18873	N	0.999982	B	0.28667	0.219	B	0.32090	0.14	T	0.31888	-0.9927	7	0.06625	T	0.88	.	2.665	0.05041	0.4896:0.0:0.5104:0.0	.	115	Q9UFV1	TBC29_HUMAN	K	115	.	ENSP00000330052:R115K	R	+	2	0	TBC1D29	25914460	0.034000	0.19679	0.031000	0.17742	0.031000	0.12232	0.975000	0.29449	0.107000	0.17824	0.109000	0.15622	AGG	.		0.572	TBC1D29-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443632.1	NM_015594		A	28890334	G	A	28890334	3	1	16	1	0	0	0	0	1	0	0	0	15650	1000	35	2	362	2	TBC1D29	17	28890334	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08		28890334	52304876	38	1376											
LYZL6	57151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34261844	34261844	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtagaagagtggccggcCtgaacagtgcaacctccatt	11	7	11	12	1	0	3	0	1	0	2	1	3	1	3	5	2	3	2	5	2	4	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:34261844C>T	ENST00000585556.1	-	5	737	c.403G>A	c.(403-405)Ggc>Agc	p.G135S	LYZL6_ENST00000492340.2_5'Flank|LYZL6_ENST00000394523.3_Missense_Mutation_p.G135S|LYZL6_ENST00000293274.4_Missense_Mutation_p.G135S			O75951	LYZL6_HUMAN	lysozyme-like 6	135					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGTGGCCGGCCTGAACAGTGC	0.542																																					p.G135S		.											.	LYZL6-90	0			c.G403A						.						89	82	85					17																	34261844		2203	4300	6503	SO:0001583	missense	57151	exon4			GCCGGCCTGAACA	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.403G>A	17.37:g.34261844C>T	ENSP00000468094:p.Gly135Ser	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	77	19	NM_020426	0	0	0	0	0	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	37	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.410784	0.62399	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.51325	0.71;0.71	4.65	4.65	0.58169	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000004	T	0.66336	0.2779	M	0.87547	2.89	0.23988	N	0.996253	D	0.57257	0.979	P	0.56088	0.791	T	0.63844	-0.6545	10	0.62326	D	0.03	-0.303	13.7598	0.62959	0.0:1.0:0.0:0.0	.	135	O75951	LYZL6_HUMAN	S	135	ENSP00000293274:G135S;ENSP00000378031:G135S	ENSP00000293274:G135S	G	-	1	0	LYZL6	31285957	0.058000	0.20735	0.004000	0.12327	0.101000	0.19017	2.826000	0.48104	2.518000	0.84900	0.563000	0.77884	GGC	.		0.542	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426		T	34261844	C	T	34261844	3	4	16	1	0	0	0	0	1	0	0	0	9159	681	24	2	47	2	LYZL6	17	34261844	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08	5371510	34261844	46933366	39	1377											
CDC27	996	hgsc.bcm.edu	37	chr17	45234324	45234324	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggtcctcctaataaacttCgaccagtttttggtttattt	8	18	6	9	1	0	0	0	0	0	0	3	1	2	0	3	2	1	2	3	2	4	8			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:45234324C>T	ENST00000066544.3	-	7	890	c.797G>A	c.(796-798)cGa>cAa	p.R266Q	CDC27_ENST00000446365.2_Missense_Mutation_p.R205Q|CDC27_ENST00000531206.1_Missense_Mutation_p.R266Q|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000527547.1_Missense_Mutation_p.R266Q	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	266					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAATAAACTTCGACCAGTTTT	0.358																																					p.R266Q		.											.	CDC27-291	0			c.G797A						.						60	65	63					17																	45234324		2200	4293	6493	SO:0001583	missense	996	exon7			AAACTTCGACCAG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.797G>A	17.37:g.45234324C>T	ENSP00000066544:p.Arg266Gln	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	93	6	NM_001114091	0	0	8	8	0	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.328146	0.81690	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.69806	-0.43;-0.4;-0.17;-0.43;0.52	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	L	0.34521	1.04	0.58432	D	0.999999	D;D;D;P	0.89917	1.0;1.0;0.991;0.921	D;D;P;B	0.72338	0.95;0.977;0.724;0.153	T	0.69975	-0.4999	10	0.30854	T	0.27	-17.5002	17.2083	0.86924	0.0:1.0:0.0:0.0	.	205;266;266;266	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	Q	266;266;205;266;266	ENSP00000066544:R266Q;ENSP00000434614:R266Q;ENSP00000392802:R205Q;ENSP00000437339:R266Q;ENSP00000432105:R266Q	ENSP00000066544:R266Q	R	-	2	0	CDC27	42589323	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.320000	0.79064	2.665000	0.90641	0.460000	0.39030	CGA	.		0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			T	45234324	C	T	45234324	3	4	16	1	0	0	0	0	1	0	0	0	3072	884	31	1	1747	1	CDC27	17	45234324	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08	10972480	45234324	35960886	40	1378											
PHOSPHO1	162466	broad.mit.edu	37	chr17	47302352	47302352	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcgcggcgcgccctgcgcGgccatcctgccgtcctggga	4	5	15	17	7	0	0	0	0	0	0	2	1	2	1	5	3	3	0	5	3	1	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:47302352G>T	ENST00000310544.4	-	3	187	c.60C>A	c.(58-60)gcC>gcA	p.A20A	PHOSPHO1_ENST00000514112.1_Silent_p.A45A|PHOSPHO1_ENST00000413580.1_Silent_p.A45A			Q8TCT1	PHOP1_HUMAN	phosphatase, orphan 1	20					bone mineralization involved in bone maturation (GO:0035630)|dephosphorylation (GO:0016311)|endochondral ossification (GO:0001958)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of bone mineralization (GO:0030500)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|phosphocholine phosphatase activity (GO:0052731)|phosphoethanolamine phosphatase activity (GO:0052732)|pyrophosphatase activity (GO:0016462)							Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)		Choline(DB00122)	CGCCCTGCGCGGCCATCCTGC	0.716																																					p.A45A													.	PHOSPHO1-90	0			c.C135A						.						5	5	5					17																	47302352		2144	4141	6285	SO:0001819	synonymous_variant	162466	exon3			CTGCGCGGCCATC	AJ457189	CCDS11547.1, CCDS45726.1	17q21.32	2008-05-02				ENSG00000173868			16815	protein-coding gene	gene with protein product						12464021	Standard	NM_178500		Approved		uc010wlv.1	Q8TCT1		ENST00000310544.4:c.60C>A	17.37:g.47302352G>T		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001143804	0	0	0	0	0	E9PAM0|Q17RU6	Silent	SNP	ENST00000310544.4	37	CCDS11547.1																																																																																			.		0.716	PHOSPHO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364467.2			T	47302352	G	T	47302352	2	4	16	1	0	0	0	0	0	0	0	1	11882	1103	39	4		4	PHOSPHO1	17	47302352	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	2068028	47302352	33892858	41	1379											
MYCBPAP	84073	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48600413	48600413	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatttggtatgactggcgAcggcagcaccagccggacac	9	6	13	13	3	0	1	0	1	0	0	0	3	0	2	3	4	2	3	3	4	1	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:48600413A>T	ENST00000323776.5	+	11	1662	c.1500A>T	c.(1498-1500)cgA>cgT	p.R500R	MYCBPAP_ENST00000436259.2_Silent_p.R463R	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ATGACTGGCGACGGCAGCACC	0.507																																					p.R500R		.											.	MYCBPAP-230	0			c.A1500T						.						108	105	106					17																	48600413		2203	4300	6503	SO:0001819	synonymous_variant	84073	exon11			CTGGCGACGGCAG	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.1500A>T	17.37:g.48600413A>T		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	144	54	NM_032133	0	0	0	0	0		Silent	SNP	ENST00000323776.5	37	CCDS32680.2																																																																																			.		0.507	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		T	48600413	A	T	48600413	2	4	16	1	0	0	0	0	0	0	0	1	10044	262	10	5		5	MYCBPAP	17	48600413	Silent	SNP	A	TCGA-A4-8312-01A-11D-2396-08	1298061	48600413	32594797	42	1380											
GRIN2D	2906	ucsc.edu;bcgsc.ca	37	chr19	48908457	48908457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtttgcagtgcgctcggctgGctggcgggatgacctggctc	3	10	17	11	3	0	1	0	1	0	0	2	2	0	2	1	5	2	6	1	5	0	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:48908457G>A	ENST00000263269.3	+	3	1020	c.932G>A	c.(931-933)gGc>gAc	p.G311D		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	311					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGCTCGGCTGGCTGGCGGGAT	0.706																																					p.G311D													.	GRIN2D-156	0			c.G932A						.						11	13	12					19																	48908457		2149	4203	6352	SO:0001583	missense	2906	exon3			CGGCTGGCTGGCG	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.932G>A	19.37:g.48908457G>A	ENSP00000263269:p.Gly311Asp	Somatic	19	0		WXS	Illumina HiSeq		13	5	NM_000836	0	0	0	0	0		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028978	0.75504	.	.	ENSG00000105464	ENST00000263269	T	0.05025	3.51	4.45	4.45	0.53987	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.11452	0.0279	N	0.16602	0.42	0.58432	D	0.999995	D	0.89917	1.0	D	0.75484	0.986	T	0.44205	-0.9343	10	0.13470	T	0.59	.	16.2466	0.82448	0.0:0.0:1.0:0.0	.	311	O15399	NMDE4_HUMAN	D	311	ENSP00000263269:G311D	ENSP00000263269:G311D	G	+	2	0	GRIN2D	53600269	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.462000	0.66707	2.199000	0.70637	0.561000	0.74099	GGC	.		0.706	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48908457	G	A	48908457	3	1	16	1	0	0	0	0	1	0	0	0	6803	1203	42	2	938	2	GRIN2D	19	48908457	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08		48908457	10220526	43	1381											
ZNF816A	125893	hgsc.bcm.edu;bcgsc.ca	37	chr19	53454065	53454065	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggatgacttctcactgaaGgtcttgccacactcattaca	11	11	8	11	0	3	2	2	2	2	0	4	3	3	3	1	2	2	0	1	2	2	3	rs560657768	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:53454065G>A	ENST00000357666.4	-	5	1263	c.963C>T	c.(961-963)acC>acT	p.T321T	ZNF816_ENST00000444460.2_Silent_p.T321T|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000434371.2_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	321					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)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						TCTCACTGAAGGTCTTGCCAC	0.438													g|||	48	0.00958466	0.034	0.0043	5008	,	,		22622	0		0	False		,,,				2504	0				p.T321T		.											.	ZNF816-68	0			c.C963T						.						165	169	168					19																	53454065		2202	4300	6502	SO:0001819	synonymous_variant	125893	exon4			ACTGAAGGTCTTG	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"Zinc fingers, C2H2-type", "-"	26995	protein-coding gene	gene with protein product			"zinc finger protein 816A"	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.963C>T	19.37:g.53454065G>A		Somatic	140	2		WXS	Illumina HiSeq	Phase_I	135	11	NM_001202457	0	0	4	4	0	A8K7H5|Q3KR39|Q659B3	Silent	SNP	ENST00000357666.4	37	CCDS33096.1																																																																																			.		0.438	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		A	53454065	G	A	53454065	2	1	16	1	0	0	0	0	0	0	0	1	18209	987	35	2		2	ZNF816A	19	53454065	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	4545608	53454065	5674918	44	1382											
ZNF497	162968	hgsc.bcm.edu	37	chr19	58867849	58867849	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcagtcggcgcaggcgaaggGcttggcgcccgagtgcgtgc	5	5	19	12	6	0	0	0	0	0	0	1	2	0	0	1	4	2	3	1	4	1	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:58867849G>C	ENST00000311044.3	-	3	1341	c.1153C>G	c.(1153-1155)Ccc>Gcc	p.P385A	A1BG-AS1_ENST00000595302.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|ZNF497_ENST00000425453.3_Missense_Mutation_p.P385A|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG_ENST00000263100.3_5'Flank|CTD-2619J13.9_ENST00000599952.1_RNA	NM_198458.2	NP_940860.2	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|lung(3)|skin(2)	7		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0278)		CAGGCGAAGGGCTTGGCGCCC	0.711																																					p.P385A		.											.	ZNF497-90	0			c.C1153G						.						5	5	5					19																	58867849		2122	4162	6284	SO:0001583	missense	162968	exon2			CGAAGGGCTTGGC	AK126727	CCDS12977.1	19q13.43	2013-01-08			ENSG00000174586	ENSG00000174586		"Zinc fingers, C2H2-type"	23714	protein-coding gene	gene with protein product							Standard	NM_198458		Approved	FLJ44773	uc002qsi.2	Q6ZNH5		ENST00000311044.3:c.1153C>G	19.37:g.58867849G>C	ENSP00000311183:p.Pro385Ala	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	10	4	NM_001207009	0	0	0	3	3	Q05AG8|Q0VF48|Q6ZTD2|Q9UIA8	Missense_Mutation	SNP	ENST00000311044.3	37	CCDS12977.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.787030	0.49997	.	.	ENSG00000174586	ENST00000311044;ENST00000425453;ENST00000391697	T;T	0.28255	1.62;1.62	0.658	0.658	0.17855	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.54046	0.1834	M	0.83483	2.645	0.24694	N	0.993296	D	0.89917	1.0	D	0.97110	1.0	T	0.37572	-0.9700	9	0.87932	D	0	.	8.7378	0.34539	0.0:0.0:1.0:0.0	.	385	Q6ZNH5	ZN497_HUMAN	A	385;385;174	ENSP00000311183:P385A;ENSP00000402815:P385A	ENSP00000311183:P385A	P	-	1	0	ZNF497	63559661	0.999000	0.42202	0.006000	0.13384	0.073000	0.16967	4.986000	0.63851	0.613000	0.30089	0.205000	0.17691	CCC	.		0.711	ZNF497-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466942.2	NM_198458		C	58867849	G	C	58867849	3	2	16	1	0	0	0	0	1	0	0	0	17978	1203	42	4	347	4	ZNF497	19	58867849	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08	5413784	58867849	261134	45	1383											
SLMO2	51012	hgsc.bcm.edu	37	chr20	57611524	57611524	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accaagaagcagcctcacttActttactagcatttgaggat	13	11	7	10	0	1	2	1	1	0	1	1	3	1	3	2	1	5	2	2	1	5	5			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr20:57611524A>C	ENST00000355937.4	-	5	644		c.e5+1		SLMO2_ENST00000371033.5_Splice_Site	NM_016045.2	NP_057129.2	Q9Y3B1	SLMO2_HUMAN	slowmo homolog 2 (Drosophila)						phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(1)|lung(2)|skin(2)	5	all_lung(29;0.00711)		Colorectal(105;0.109)			AGCCTCACTTACTTTACTAGC	0.453																																					.		.											.	SLMO2-45	0			c.465+2T>G						.						110	100	103					20																	57611524		1975	4184	6159	SO:0001630	splice_region_variant	51012	exon6			TCACTTACTTTAC	AF151865	CCDS42893.1, CCDS58783.1	20q13.32	2008-10-22	2007-02-06	2007-02-06	ENSG00000101166	ENSG00000101166			15892	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 45"	C20orf45			Standard	NM_016045		Approved	dJ543J19.5, PRELID3B	uc002yam.3	Q9Y3B1	OTTHUMG00000032856	ENST00000355937.4:c.465+1T>G	20.37:g.57611524A>C		Somatic	106	1		WXS	Illumina HiSeq	Phase_I	82	7	NM_016045	0	0	0	0	0	E1P5I8|Q5JX17|Q9NUL0	Splice_Site	SNP	ENST00000355937.4	37	CCDS42893.1	.	.	.	.	.	.	.	.	.	.	A	17.35	3.366553	0.61513	.	.	ENSG00000101166	ENST00000355937;ENST00000371033	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8858	0.63708	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLMO2	57044919	1.000000	0.71417	0.995000	0.50966	0.611000	0.37282	8.880000	0.92407	1.935000	0.56089	0.533000	0.62120	.	.		0.453	SLMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079897.2	NM_016045	Intron	C	57611524	A	C	57611524	5	2	16	1	0	0	0	0	0	0	1	0	14783	405	14	5	125	5	SLMO2	20	57611524	Splice_Site	SNP	A	TCGA-A4-8312-01A-11D-2396-08		57611524	5413996	46	1384											
SLMO2	51012	hgsc.bcm.edu	37	chr20	57611629	57611629	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttcttgtgtcaaaacagttCtggaacaaaacatattcaca	15	12	5	9	0	4	0	2	0	2	0	4	1	4	1	0	1	3	1	0	1	6	5			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr20:57611629C>T	ENST00000355937.4	-	5	541		c.e5-1		SLMO2_ENST00000371033.5_Splice_Site	NM_016045.2	NP_057129.2	Q9Y3B1	SLMO2_HUMAN	slowmo homolog 2 (Drosophila)						phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(1)|lung(2)|skin(2)	5	all_lung(29;0.00711)		Colorectal(105;0.109)			CAAAACAGTTCTGGAACAAAA	0.368																																					.		.											.	SLMO2-45	0			c.363-1G>A						.						98	88	91					20																	57611629		1868	4102	5970	SO:0001630	splice_region_variant	51012	exon6			ACAGTTCTGGAAC	AF151865	CCDS42893.1, CCDS58783.1	20q13.32	2008-10-22	2007-02-06	2007-02-06	ENSG00000101166	ENSG00000101166			15892	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 45"	C20orf45			Standard	NM_016045		Approved	dJ543J19.5, PRELID3B	uc002yam.3	Q9Y3B1	OTTHUMG00000032856	ENST00000355937.4:c.363-1G>A	20.37:g.57611629C>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	76	4	NM_016045	0	0	0	0	0	E1P5I8|Q5JX17|Q9NUL0	Splice_Site	SNP	ENST00000355937.4	37	CCDS42893.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.102231	0.76983	.	.	ENSG00000101166	ENST00000355937;ENST00000371033	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2862	0.87142	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLMO2	57045024	1.000000	0.71417	0.999000	0.59377	0.924000	0.55760	7.421000	0.80204	2.389000	0.81357	0.655000	0.94253	.	.		0.368	SLMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079897.2	NM_016045	Intron	T	57611629	C	T	57611629	5	4	16	1	0	0	0	0	0	0	1	0	14783	927	32	2	230	2	SLMO2	20	57611629	Splice_Site	SNP	C	TCGA-A4-8312-01A-11D-2396-08	105	57611629	5413891	47	1385											
PHKA2	5256	bcgsc.ca	37	chrX	18972370	18972370	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacagctgtcagtcactattAcctgctccagctcgtaggcc	8	11	8	14	1	2	0	2	0	0	0	4	0	3	0	3	1	5	4	3	1	4	4			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chrX:18972370A>G	ENST00000379942.4	-	2	903		c.e2+1			NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)						carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					AGTCACTATTACCTGCTCCAG	0.537																																					.													.	PHKA2-131	0			c.237+2T>C						.						138	107	117					X																	18972370		2203	4300	6503	SO:0001630	splice_region_variant	5256	exon3			ACTATTACCTGCT		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.237+1T>C	X.37:g.18972370A>G		Somatic	71	0		WXS	Illumina HiSeq	Phase_1	92	4	NM_000292	0	0	0	0	0	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Splice_Site	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.266542	0.59540	.	.	ENSG00000044446	ENST00000379942	.	.	.	5.54	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0604	0.47944	0.8588:0.0:0.0:0.1412	.	.	.	.	.	-1	.	.	.	-	.	.	PHKA2	18882291	1.000000	0.71417	0.991000	0.47740	0.625000	0.37756	9.284000	0.95882	0.713000	0.32060	0.486000	0.48141	.	.		0.537	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	Intron	G	18972370	A	G	18972370	5	3	16	1	0	0	0	0	0	0	1	0	11870	405	14	3	3596	3	PHKA2	23	18972370	Splice_Site	SNP	A	TCGA-A4-8312-01A-11D-2396-08		18972370	136298190	48	1386											
RNF128	79589	hgsc.bcm.edu	37	chrX	106031218	106031218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaaatgatttggtacgcaTcttaacgtgcaagtaagttt	13	13	8	7	2	1	1	0	1	1	0	1	1	1	1	1	1	3	5	1	1	5	5			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chrX:106031218T>C	ENST00000255499.2	+	4	1125	c.875T>C	c.(874-876)aTc>aCc	p.I292T	RNF128_ENST00000324342.3_Missense_Mutation_p.I266T	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	292					negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						TTGGTACGCATCTTAACGTGC	0.343																																					p.I292T		.											.	RNF128-227	0			c.T875C						.						207	163	178					X																	106031218		2202	4300	6502	SO:0001583	missense	79589	exon4			TACGCATCTTAAC	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.875T>C	X.37:g.106031218T>C	ENSP00000255499:p.Ile292Thr	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_194463	0	0	0	0	0	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Missense_Mutation	SNP	ENST00000255499.2	37	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.328438	0.60743	.	.	ENSG00000133135	ENST00000418562;ENST00000324342;ENST00000255499	T;T;T	0.68479	-0.33;1.08;1.08	5.26	5.26	0.73747	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.060185	0.64402	D	0.000003	T	0.67869	0.2939	N	0.17312	0.475	0.53688	D	0.999978	D;P	0.65815	0.995;0.875	D;P	0.68039	0.955;0.729	T	0.72014	-0.4418	10	0.56958	D	0.05	.	12.9945	0.58638	0.0:0.0:0.0:1.0	.	292;266	Q8TEB7;Q8TEB7-2	RN128_HUMAN;.	T	239;266;292	ENSP00000412610:I239T;ENSP00000316127:I266T;ENSP00000255499:I292T	ENSP00000255499:I292T	I	+	2	0	RNF128	105917874	1.000000	0.71417	0.997000	0.53966	0.759000	0.43091	7.188000	0.77739	1.745000	0.51790	0.481000	0.45027	ATC	.		0.343	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		C	106031218	T	C	106031218	3	2	16	1	0	0	0	0	1	0	0	0	13468	1435	50	3	1299	3	RNF128	23	106031218	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	87058848	106031218	49239342	49	1387											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27107195	27107195	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtatcaccgttgatgaactCattggtttcacaagtcattt	10	15	8	8	1	4	2	4	2	0	0	4	2	4	2	1	2	1	3	1	2	3	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:27107195C>A	ENST00000324856.7	+	20	7177	c.6806C>A	c.(6805-6807)tCa>tAa	p.S2269*	ARID1A_ENST00000540690.1_Nonsense_Mutation_p.S597*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.S1886*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.S2052*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2269					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.S2269*(1)|p.S2269L(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TTGATGAACTCATTGGTTTCA	0.532			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S2269X		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	2	Substitution - Missense(1)|Substitution - Nonsense(1)	urinary_tract(1)|endometrium(1)	c.C6806A						.						126	99	109					1																	27107195		2203	4300	6503	SO:0001587	stop_gained	8289	exon20			TGAACTCATTGGT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6806C>A	1.37:g.27107195C>A	ENSP00000320485:p.Ser2269*	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	118	47	NM_006015	0	0	11	27	16	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	42	9.499439	0.99187	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	.	.	.	4.6	4.6	0.57074	.	0.216209	0.40385	N	0.001101	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.9686	13.6859	0.62515	0.0:0.8453:0.1547:0.0	.	.	.	.	X	2269;2052;1886;597	.	ENSP00000320485:S2269X	S	+	2	0	ARID1A	26979782	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	5.627000	0.67784	2.552000	0.86080	0.591000	0.81541	TCA	.		0.532	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27107195	C	A	27107195	4	1	17	1	0	0	0	0	0	1	0	0	913	838	29	4	6884	4	ARID1A	1	27107195	Nonsense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08		27107195	222143426	1	1388											
AMY1A	277	hgsc.bcm.edu	37	chr1	104231690	104231691	+	Frame_Shift_Ins	INS	-	-	A																															ggccatccactacattgcggINSaaattaaccatgttcctaaa																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:104231690_104231691insA	ENST00000330330.5	-	10	1529_1530	c.1235_1236insT	c.(1234-1236)ttcfs	p.F412fs	AMY1B_ENST00000370080.3_Frame_Shift_Ins_p.F412fs	NM_001008218.1	NP_001008219.1	P04745	AMY1_HUMAN	amylase, alpha 1B (salivary)	412					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)	2		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)		CTACATTGCGGAAATTAACCAT	0.356																																					p.F412fs		.											.	.	0			c.1236_1237insT						.																																			SO:0001589	frameshift_variant	278	exon10			.		CCDS30783.1	1p21	2012-10-02	2007-05-03		ENSG00000174876	ENSG00000174876	3.2.1.1		475	protein-coding gene	gene with protein product		104701	"amylase, alpha 1B; salivary"	AMY1			Standard	XM_005270758		Approved			P04745	OTTHUMG00000011021	ENST00000330330.5:c.1236dupT	1.37:g.104231693_104231693dupA	ENSP00000330484:p.Phe412fs	Somatic	315	0		WXS	Illumina HiSeq	Phase_I	357	54	NM_001008219	0	0	0	0	0	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Ins	INS	ENST00000330330.5	37	CCDS30783.1																																																																																			.		0.356	AMY1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030309.1	NM_001008218		A	104231691	-	A	104231690	7	5	17	1	0	1	1	0	0	0	0	0	591	1165	41	0	1883	0	AMY1A	1	104231690	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	77124495	104231690	145018931	2	1389											
C1orf194	127003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109649721	109649721	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttgtacaaggctgctaagcgGaagtccaggtcatcctttgg	9	11	12	9	1	1	0	1	0	0	0	3	1	3	1	2	4	3	3	2	4	4	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:109649721G>A	ENST00000369948.3	-	3	297	c.222C>T	c.(220-222)ttC>ttT	p.F74F	C1orf194_ENST00000369945.3_Silent_p.F35F|C1orf194_ENST00000369949.4_Silent_p.F62F			Q5T5A4	CA194_HUMAN	chromosome 1 open reading frame 194	74										large_intestine(2)|lung(2)|ovary(2)	6						CTGCTAAGCGGAAGTCCAGGT	0.483																																					p.F62F		.											.	C1orf194-23	0			c.C186T						.						210	178	188					1																	109649721		1568	3582	5150	SO:0001819	synonymous_variant	127003	exon3			TAAGCGGAAGTCC		CCDS41364.1	1p13.3	2011-03-31			ENSG00000179902	ENSG00000179902			32331	protein-coding gene	gene with protein product							Standard	NM_001122961		Approved		uc009wew.3	Q5T5A4	OTTHUMG00000011735	ENST00000369948.3:c.222C>T	1.37:g.109649721G>A		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	217	93	NM_001122961	0	0	1	1	0	Q5T5A3	Silent	SNP	ENST00000369948.3	37																																																																																				.		0.483	C1orf194-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000032416.2	NM_001122961		A	109649721	G	A	109649721	2	1	17	1	0	0	0	0	0	0	0	1	2031	1165	41	2		2	C1orf194	1	109649721	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	5418031	109649721	139600900	3	1390											
RFX5	5993	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151314667	151314667	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccccacagacctgtatcatgGgggtgttgcttttgggtctt	5	14	12	10	0	2	1	1	0	1	1	2	1	2	1	3	3	1	3	3	3	1	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:151314667G>T	ENST00000290524.4	-	11	2024	c.1846C>A	c.(1846-1848)Cca>Aca	p.P616T	RFX5_ENST00000368870.2_Missense_Mutation_p.P616T|RFX5_ENST00000452513.2_Missense_Mutation_p.P576T|RFX5_ENST00000478564.1_5'Flank|RFX5_ENST00000452671.2_Missense_Mutation_p.P616T|RP11-126K1.8_ENST00000422153.1_RNA	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	616					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CTGTATCATGGGGGTGTTGCT	0.453																																					p.P616T		.											.	RFX5-91	0			c.C1846A						.						133	126	128					1																	151314667		2203	4300	6503	SO:0001583	missense	5993	exon11			ATCATGGGGGTGT		CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.1846C>A	1.37:g.151314667G>T	ENSP00000290524:p.Pro616Thr	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	94	47	NM_000449	0	0	20	44	24	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	37	CCDS994.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686722	0.68157	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513	T;T;T;T	0.74632	-0.68;-0.68;-0.68;-0.86	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	T	0.76111	0.3942	L	0.36672	1.1	0.35535	D	0.8026	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.941	T	0.79593	-0.1739	10	0.87932	D	0	.	14.4852	0.67611	0.0:0.0:1.0:0.0	.	576;616	B7Z848;P48382	.;RFX5_HUMAN	T	616;616;616;576	ENSP00000290524:P616T;ENSP00000357864:P616T;ENSP00000389130:P616T;ENSP00000398388:P576T	ENSP00000290524:P616T	P	-	1	0	RFX5	149581291	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.473000	0.60196	2.806000	0.96561	0.591000	0.81541	CCA	.		0.453	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		T	151314667	G	T	151314667	3	4	17	1	0	0	0	0	1	0	0	0	13298	1232	43	4	8	4	RFX5	1	151314667	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	41664946	151314667	97935954	4	1391											
ASH1L	55870	broad.mit.edu	37	chr1	155324299	155324299	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcatctcggcagatcccaTtccaacgggtatataatgat	12	11	7	11	2	2	2	1	1	1	1	5	2	4	2	2	2	1	2	2	2	4	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:155324299T>C	ENST00000368346.3	-	16	7832	c.7193A>G	c.(7192-7194)aAt>aGt	p.N2398S	ASH1L_ENST00000392403.3_Missense_Mutation_p.N2393S			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2398					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GCAGATCCCATTCCAACGGGT	0.413																																					p.N2393S													.	ASH1L-234	0			c.A7178G						.						232	207	216					1																	155324299		2203	4300	6503	SO:0001583	missense	55870	exon16			ATCCCATTCCAAC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.7193A>G	1.37:g.155324299T>C	ENSP00000357330:p.Asn2398Ser	Somatic	280	0		WXS	Illumina HiSeq	Phase_I	269	7	NM_018489	0	0	7	8	1	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	T	17.01	3.279551	0.59758	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88124	-2.34;-2.34	5.5	4.37	0.52481	Bromodomain (1);	0.103984	0.64402	D	0.000003	T	0.61060	0.2317	N	0.24115	0.695	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.56829	-0.7914	10	0.14656	T	0.56	.	8.5176	0.33255	0.0:0.1495:0.0:0.8505	.	2398;2393	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	S	2398;2393	ENSP00000357330:N2398S;ENSP00000376204:N2393S	ENSP00000357330:N2398S	N	-	2	0	ASH1L	153590923	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.914000	0.48797	1.096000	0.41439	0.533000	0.62120	AAT	.		0.413	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155324299	T	C	155324299	3	2	17	1	0	0	0	0	1	0	0	0	1042	1493	52	3	1768	3	ASH1L	1	155324299	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	4009632	155324299	93926322	5	1392											
CENPL	91687	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	173772191	173772191	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaattttgaaatgtctatgGaaatgtgaataaaggcaatc	16	13	9	3	0	1	3	0	3	1	0	2	4	1	4	0	2	0	1	0	2	8	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:173772191G>T	ENST00000345664.6	-	4	1086	c.873C>A	c.(871-873)ttC>ttA	p.F291L	CENPL_ENST00000356198.2_Missense_Mutation_p.F337L|CENPL_ENST00000367710.3_Missense_Mutation_p.F291L	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	291					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						AATGTCTATGGAAATGTGAAT	0.393																																					p.F337L		.											.	CENPL-90	0			c.C1011A						.						89	90	90					1																	173772191		2203	4300	6503	SO:0001583	missense	91687	exon6			TCTATGGAAATGT	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"chromosome 1 open reading frame 155"	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.873C>A	1.37:g.173772191G>T	ENSP00000323543:p.Phe291Leu	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	84	8	NM_001127181	0	0	1	1	0	Q5TEL5|Q96ND4	Missense_Mutation	SNP	ENST00000345664.6	37	CCDS30938.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.218984	0.58560	.	.	ENSG00000120334	ENST00000356198;ENST00000345664;ENST00000367710	T;T;T	0.49720	1.37;0.77;0.77	5.56	0.81	0.18732	.	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	L	0.54323	1.7	0.49051	D	0.99974	D;D	0.89917	0.999;1.0	D;D	0.87578	0.986;0.998	T	0.51108	-0.8747	10	0.87932	D	0	-5.3901	8.6851	0.34232	0.4999:0.0:0.5001:0.0	.	337;291	Q8N0S6-2;Q8N0S6	.;CENPL_HUMAN	L	337;291;291	ENSP00000348527:F337L;ENSP00000323543:F291L;ENSP00000356683:F291L	ENSP00000323543:F291L	F	-	3	2	CENPL	172038814	1.000000	0.71417	0.995000	0.50966	0.901000	0.52897	1.311000	0.33562	0.257000	0.21650	-0.302000	0.09304	TTC	.		0.393	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		T	173772191	G	T	173772191	3	4	17	1	0	0	0	0	1	0	0	0	3242	1165	41	4	169	4	CENPL	1	173772191	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	18447892	173772191	75478430	6	1393											
PIK3C2B	5287	bcgsc.ca	37	chr1	204412626	204412626	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccagcactggcggttaaaCtcttctctcagccccttgcc	7	10	8	16	1	3	0	1	0	2	0	4	0	3	0	4	2	5	2	4	2	2	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:204412626C>A	ENST00000367187.3	-	20	3523	c.2967G>T	c.(2965-2967)gaG>gaT	p.E989D	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.E961D	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	989					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GGCGGTTAAACTCTTCTCTCA	0.597																																					p.E989D													.	PIK3C2B-1310	0			c.G2967T						.						82	85	84					1																	204412626		2203	4300	6503	SO:0001583	missense	5287	exon20			GTTAAACTCTTCT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2967G>T	1.37:g.204412626C>A	ENSP00000356155:p.Glu989Asp	Somatic	262	1		WXS	Illumina HiSeq	Phase_1	190	57	NM_002646	0	0	2	2	0	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467982	0.84533	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.80909	-1.43;-1.43	5.79	3.59	0.41128	Phosphoinositide 3-kinase, accessory (PIK) domain (1);Protein kinase-like domain (1);	0.050509	0.85682	D	0.000000	T	0.78685	0.4322	M	0.71581	2.175	0.33052	D	0.532882	B;P	0.42296	0.289;0.775	B;B	0.39706	0.307;0.306	D	0.84478	0.0603	10	0.41790	T	0.15	.	13.435	0.61079	0.0:0.8484:0.0:0.1516	.	961;989	F5GWN5;O00750	.;P3C2B_HUMAN	D	989;961	ENSP00000356155:E989D;ENSP00000400561:E961D	ENSP00000356155:E989D	E	-	3	2	PIK3C2B	202679249	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.157000	0.50716	1.455000	0.47813	0.591000	0.81541	GAG	.		0.597	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		A	204412626	C	A	204412626	3	1	17	1	0	0	0	0	1	0	0	0	11936	564	20	4	1997	4	PIK3C2B	1	204412626	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	30640435	204412626	44837995	7	1394											
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	216017693	216017693	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaataaacgacccaggcacAttcattccagtcttgtagag	14	9	8	10	1	2	2	1	0	1	2	3	3	3	2	2	1	1	2	2	1	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:216017693A>T	ENST00000307340.3	-	46	9587	c.9201T>A	c.(9199-9201)aaT>aaA	p.N3067K	USH2A_ENST00000366943.2_Missense_Mutation_p.N3067K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3067	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACCCAGGCACATTCATTCCAG	0.393										HNSCC(13;0.011)																											p.N3067K		.											.	USH2A-115	0			c.T9201A						.						98	99	99					1																	216017693		2203	4300	6503	SO:0001583	missense	7399	exon46			AGGCACATTCATT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9201T>A	1.37:g.216017693A>T	ENSP00000305941:p.Asn3067Lys	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	77	24	NM_206933	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	8.287	0.816795	0.16607	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53423	0.62;0.62	6.04	0.803	0.18691	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.298923	0.23197	N	0.050821	T	0.29749	0.0743	L	0.35723	1.085	0.19775	N	0.999957	B	0.13594	0.008	B	0.08055	0.003	T	0.15578	-1.0432	10	0.17832	T	0.49	.	6.0414	0.19736	0.4009:0.2965:0.3026:0.0	.	3067	O75445	USH2A_HUMAN	K	3067	ENSP00000305941:N3067K;ENSP00000355910:N3067K	ENSP00000305941:N3067K	N	-	3	2	USH2A	214084316	0.008000	0.16893	0.941000	0.38009	0.993000	0.82548	0.037000	0.13840	0.158000	0.19367	0.529000	0.55759	AAT	.		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216017693	A	T	216017693	3	4	17	1	0	0	0	0	1	0	0	0	17069	214	8	5	6515	5	USH2A	1	216017693	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	11605067	216017693	33232928	8	1395											
SIPA1L2	57568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	232650317	232650317	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataatctaatcctgagatgcGgacaaattctcccctagaaa	15	10	6	10	1	2	2	0	1	2	2	4	4	3	3	3	1	1	0	3	1	5	4	rs371322486		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:232650317G>A	ENST00000366630.1	-	2	1127	c.769C>T	c.(769-771)Cgc>Tgc	p.R257C	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R257C			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	257					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CCTGAGATGCGGACAAATTCT	0.502																																					p.R257C		.											.	SIPA1L2-95	0			c.C769T						.	G	CYS/ARG	1,3767		0,1,1883	68	67	67		769	5.4	1	1		67	0,8236		0,0,4118	no	missense	SIPA1L2	NM_020808.3	180	0,1,6001	AA,AG,GG		0.0,0.0265,0.0083	benign	257/1723	232650317	1,12003	1884	4118	6002	SO:0001583	missense	57568	exon1			AGATGCGGACAAA	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.769C>T	1.37:g.232650317G>A	ENSP00000355589:p.Arg257Cys	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	115	44	NM_020808	0	0	1	1	0	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.588865	0.28357	2.65E-4	0.0	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.79749	-1.3;-1.3	5.44	5.44	0.79542	.	0.117092	0.56097	D	0.000023	T	0.69187	0.3083	N	0.25647	0.755	0.49483	D	0.999794	B	0.19935	0.04	B	0.12837	0.008	T	0.63963	-0.6518	10	0.37606	T	0.19	-23.1003	12.1037	0.53798	0.0:0.0:0.7162:0.2838	.	257	Q9P2F8	SI1L2_HUMAN	C	257	ENSP00000355589:R257C;ENSP00000262861:R257C	ENSP00000262861:R257C	R	-	1	0	SIPA1L2	230716940	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.388000	0.59633	2.834000	0.97654	0.650000	0.86243	CGC	.		0.502	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232650317	G	A	232650317	3	1	17	1	0	0	0	0	1	0	0	0	14362	1116	39	1	4483	1	SIPA1L2	1	232650317	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	16632624	232650317	16600304	9	1396											
C2orf71	388939	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	29297095	29297096	+	Frame_Shift_Ins	INS	-	-	A																															cactctttgcaacgctgtttINSacaaggtcactgtgtgaagg																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:29297095_29297096insA	ENST00000331664.5	-	1	31_32	c.32_33insT	c.(31-33)gtafs	p.V11fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	11					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CAACGCTGTTTACAAGGTCACT	0.45																																					p.V11fs		.											.	C2orf71-91	0			c.33_34insT						.																																			SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.33dupT	2.37:g.29297096_29297096dupA	ENSP00000332809:p.Val11fs	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	93	48	NM_001029883	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000331664.5	37	CCDS42669.1																																																																																			.		0.45	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29297096	-	A	29297095	7	5	17	1	0	1	1	0	0	0	0	0	2197	1741	61	0	3841	0	C2orf71	2	29297095	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08		29297095	213902278	10	1397											
PELI1	57162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	64323347	64323347	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctctccatattccaggcttgGagtcttctgtgaacccattg	7	14	8	12	0	3	1	0	1	3	0	5	2	4	2	3	2	1	1	3	2	2	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:64323347G>A	ENST00000358912.4	-	6	1044	c.602C>T	c.(601-603)tCc>tTc	p.S201F		NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	201					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S201Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						TCCAGGCTTGGAGTCTTCTGT	0.453																																					p.S201F		.											.	PELI1-91	1	Substitution - Missense(1)	lung(1)	c.C602T						.						166	151	156					2																	64323347		2203	4300	6503	SO:0001583	missense	57162	exon6			GGCTTGGAGTCTT		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"Pellino homologs"	8827	protein-coding gene	gene with protein product		614797	"pellino (Drosophila) homolog 1", "pellino homolog 1 (Drosophila)"			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.602C>T	2.37:g.64323347G>A	ENSP00000351789:p.Ser201Phe	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	124	45	NM_020651	0	0	6	10	4	Q96SM0|Q9GZY5|Q9HCX0	Missense_Mutation	SNP	ENST00000358912.4	37	CCDS1876.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.917014	0.92249	.	.	ENSG00000197329	ENST00000358912	T	0.53423	0.62	5.65	5.65	0.86999	.	0.096296	0.64402	D	0.000001	T	0.62720	0.2451	M	0.74881	2.28	0.80722	D	1	P	0.48911	0.917	P	0.50490	0.642	T	0.66044	-0.6021	10	0.72032	D	0.01	-12.6236	20.0965	0.97849	0.0:0.0:1.0:0.0	.	201	Q96FA3	PELI1_HUMAN	F	201	ENSP00000351789:S201F	ENSP00000351789:S201F	S	-	2	0	PELI1	64176851	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.813000	0.99286	2.824000	0.97209	0.655000	0.94253	TCC	.		0.453	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651		A	64323347	G	A	64323347	3	1	17	1	0	0	0	0	1	0	0	0	11747	1174	41	2	662	2	PELI1	2	64323347	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	35026252	64323347	178876026	11	1398											
NCK2	8440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	106498221	106498221	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcgagaagggggagaccAtggaggtgattgagaagccg	12	6	17	6	2	0	4	0	2	0	3	1	8	0	5	2	4	1	0	2	4	2	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:106498221A>G	ENST00000233154.4	+	4	1106	c.664A>G	c.(664-666)Atg>Gtg	p.M222V	NCK2_ENST00000522586.1_Intron|NCK2_ENST00000393349.2_Missense_Mutation_p.M222V|NCK2_ENST00000451463.2_Intron	NM_003581.4	NP_003572.2	O43639	NCK2_HUMAN	NCK adaptor protein 2	222	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|lamellipodium assembly (GO:0030032)|negative regulation of cell proliferation (GO:0008285)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of translation (GO:0006417)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|lung(3)|ovary(1)	5						GGGGGAGACCATGGAGGTGAT	0.607																																					p.M222V		.											.	NCK2-415	0			c.A664G						.						79	87	84					2																	106498221		2203	4300	6503	SO:0001583	missense	8440	exon3			GAGACCATGGAGG	AF043119	CCDS33266.1	2q12	2013-02-14			ENSG00000071051	ENSG00000071051		"SH2 domain containing"	7665	protein-coding gene	gene with protein product		604930				9737977, 16752908	Standard	NM_001004720		Approved	NCKbeta	uc002tdi.3	O43639	OTTHUMG00000153116	ENST00000233154.4:c.664A>G	2.37:g.106498221A>G	ENSP00000233154:p.Met222Val	Somatic	198	1		WXS	Illumina HiSeq	Phase_I	178	71	NM_001004720	0	0	60	104	44	D3DVK1|Q9BWN9|Q9UIC3	Missense_Mutation	SNP	ENST00000233154.4	37	CCDS33266.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.000019	0.74818	.	.	ENSG00000071051	ENST00000233154;ENST00000393349	T;T	0.44482	0.92;0.92	5.51	5.51	0.81932	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.37679	0.1012	N	0.12443	0.215	0.80722	D	1	P	0.41420	0.749	P	0.48334	0.574	T	0.42430	-0.9452	10	0.72032	D	0.01	.	15.9183	0.79539	1.0:0.0:0.0:0.0	.	222	O43639	NCK2_HUMAN	V	222	ENSP00000233154:M222V;ENSP00000377018:M222V	ENSP00000233154:M222V	M	+	1	0	NCK2	105864653	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.848000	0.92172	2.225000	0.72522	0.379000	0.24179	ATG	.		0.607	NCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329634.1	NM_003581		G	106498221	A	G	106498221	3	3	17	1	0	0	0	0	1	0	0	0	10246	217	8	3	670	3	NCK2	2	106498221	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	42174874	106498221	136701152	12	1399											
ZC3H6	376940	ucsc.edu	37	chr2	113069433	113069433	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtcgtggacgtggcttgccGaagaaaatcaaacgaaaaga	15	6	13	7	4	1	2	1	0	0	2	2	5	1	3	1	3	2	1	1	3	6	1	rs529964785		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:113069433G>A	ENST00000409871.1	+	5	1067	c.666G>A	c.(664-666)ccG>ccA	p.P222P	ZC3H6_ENST00000343936.4_Silent_p.P222P	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	222							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						GTGGCTTGCCGAAGAAAATCA	0.348													G|||	1	0.000199681	0	0	5008	,	,		15850	0		0	False		,,,				2504	0.001				p.P222P													.	ZC3H6-93	0			c.G666A						.						71	73	72					2																	113069433		1829	4080	5909	SO:0001819	synonymous_variant	376940	exon5			CTTGCCGAAGAAA	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.666G>A	2.37:g.113069433G>A		Somatic	28	0		WXS	Illumina HiSeq		37	4	NM_198581	0	0	6	6	0	A9JR71|Q6ZW96	Silent	SNP	ENST00000409871.1	37	CCDS46393.1																																																																																			.		0.348	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		A	113069433	G	A	113069433	2	1	17	1	0	0	0	0	0	0	0	1	17603	1045	37	1		1	ZC3H6	2	113069433	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	6571212	113069433	130129940	13	1400											
CCDC108	255101	bcgsc.ca	37	chr2	219886565	219886565	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagaggcggtaatagagggTgcagttgccgtcattcagga	10	9	16	6	2	2	2	2	0	0	2	2	3	2	3	1	4	2	4	1	4	3	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:219886565T>G	ENST00000341552.5	-	18	3150	c.3067A>C	c.(3067-3069)Acc>Ccc	p.T1023P	CCDC108_ENST00000441968.1_Missense_Mutation_p.T1023P|CCDC108_ENST00000453220.1_Missense_Mutation_p.T1023P	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1023						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TAATAGAGGGTGCAGTTGCCG	0.612																																					p.T1023P													.	CCDC108-94	0			c.A3067C						.						139	141	140					2																	219886565		2203	4300	6503	SO:0001583	missense	255101	exon18			AGAGGGTGCAGTT	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.3067A>C	2.37:g.219886565T>G	ENSP00000340776:p.Thr1023Pro	Somatic	308	3		WXS	Illumina HiSeq	Phase_1	232	72	NM_194302	0	0	0	0	0	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	T	17.88	3.496937	0.64186	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.06068	3.35;3.35;3.35	5.04	2.38	0.29361	.	0.284822	0.25244	N	0.032071	T	0.11281	0.0275	M	0.67953	2.075	0.80722	D	1	D	0.54601	0.967	P	0.54372	0.75	T	0.35773	-0.9775	10	0.16896	T	0.51	-15.8016	4.6117	0.12406	0.137:0.1925:0.0:0.6705	.	1023	Q6ZU64	CC108_HUMAN	P	1023	ENSP00000340776:T1023P;ENSP00000413377:T1023P;ENSP00000409117:T1023P	ENSP00000340776:T1023P	T	-	1	0	CCDC108	219594809	0.652000	0.27349	0.997000	0.53966	0.931000	0.56810	0.091000	0.15046	0.290000	0.22444	0.533000	0.62120	ACC	.		0.612	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		G	219886565	T	G	219886565	3	3	17	1	0	0	0	0	1	0	0	0	2749	1696	59	5	2782	5	CCDC108	2	219886565	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	106817132	219886565	23312808	14	1401											
COL4A4	1286	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	227872789	227872789	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtctgcggacatggggggAtggactggtcctggctgtgc	5	9	19	8	1	1	0	0	0	1	0	2	3	2	3	1	8	2	1	1	8	0	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:227872789A>G	ENST00000396625.3	-	47	4961	c.4754T>C	c.(4753-4755)aTc>aCc	p.I1585T	COL4A4_ENST00000329662.7_Missense_Mutation_p.I1582T	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1585	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		ACATGGGGGGATGGACTGGTC	0.622																																					p.I1585T													.	COL4A4-142	0			c.T4754C						.						29	33	31					2																	227872789		1950	4146	6096	SO:0001583	missense	1286	exon47			GGGGGGATGGACT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4754T>C	2.37:g.227872789A>G	ENSP00000379866:p.Ile1585Thr	Somatic	80	2		WXS	Illumina HiSeq	Phase_I	50	17	NM_000092	0	0	2	7	5	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	A	17.00	3.276850	0.59758	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.95035	-3.59;-3.59	5.91	5.91	0.95273	C-type lectin fold (1);	.	.	.	.	D	0.94647	0.8274	M	0.81942	2.565	0.44890	D	0.997901	P	0.42941	0.794	B	0.40825	0.341	D	0.95012	0.8152	9	0.66056	D	0.02	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	1585	P53420	CO4A4_HUMAN	T	1585;1582	ENSP00000379866:I1585T;ENSP00000328553:I1582T	ENSP00000328553:I1582T	I	-	2	0	COL4A4	227581033	1.000000	0.71417	0.904000	0.35570	0.725000	0.41563	6.102000	0.71486	2.254000	0.74563	0.533000	0.62120	ATC	.		0.622	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		G	227872789	A	G	227872789	3	3	17	1	0	0	0	0	1	0	0	0	3699	333	12	3	326	3	COL4A4	2	227872789	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	7986224	227872789	15326584	15	1402											
RAD18	56852	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	8955405	8955406	+	Splice_Site	INS	-	-	TG																															tctcgaactatttcagcagcINStgttaaaataagaaaataac																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:8955405_8955406insTG	ENST00000264926.2	-	8	1006		c.e8-1			NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase						DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		ATTTCAGCAGCTGTTAAAATAA	0.317								Rad6 pathway																													.		.											.	RAD18-663	0			c.890-1->CA						.																																			SO:0001630	splice_region_variant	56852	exon9			.		CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.890-1->CA	3.37:g.8955406_8955407dupTG		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	23	13	NM_020165	0	0	0	0	0	Q58F55|Q9NRT6	Splice_Site	INS	ENST00000264926.2	37	CCDS2571.1																																																																																			.		0.317	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165	Intron	TG	8955406	-	TG	8955405	8	5	17	1	0	1	1	0	0	0	1	0	13012	811	28	0	622	0	RAD18	3	8955405	Splice_Site	INS	-	TCGA-A4-8515-01A-11D-2396-08		8955405	189067025	16	1403											
IQSEC1	9922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	12957106	12957106	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacataccggctttttcccCacaatgagcttctccacctt	8	13	4	16	1	2	1	1	1	1	0	4	1	3	1	5	1	2	2	5	1	2	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:12957106C>T	ENST00000273221.4	-	7	2406	c.2190G>A	c.(2188-2190)gtG>gtA	p.V730V		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	730					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCTTTTTCCCCACAATGAGCT	0.602																																					p.V730V		.											.	IQSEC1-91	0			c.G2190A						.						187	140	156					3																	12957106		2203	4300	6503	SO:0001819	synonymous_variant	9922	exon7			TTTCCCCACAATG	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2190G>A	3.37:g.12957106C>T		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	94	22	NM_014869	0	0	0	0	0	O94863|Q96D85	Silent	SNP	ENST00000273221.4	37	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	C	8.705	0.910574	0.17833	.	.	ENSG00000144711	ENST00000450726	.	.	.	4.54	3.59	0.41128	.	.	.	.	.	T	0.46132	0.1377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43393	-0.9394	4	.	.	.	.	3.2074	0.06671	0.1579:0.5539:0.1539:0.1342	.	.	.	.	R	731	.	.	G	-	1	0	IQSEC1	12932106	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	0.932000	0.28884	2.229000	0.72834	0.655000	0.94253	GGG	.		0.602	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		T	12957106	C	T	12957106	2	4	17	1	0	0	0	0	0	0	0	1	7838	581	21	2		2	IQSEC1	3	12957106	Silent	SNP	C	TCGA-A4-8515-01A-11D-2396-08	4001701	12957106	185065324	17	1404											
GOLGA4	2803	broad.mit.edu;bcgsc.ca	37	chr3	37369907	37369907	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtacatttttattactcagAcaggagcaggaagatcttga	13	12	10	6	0	2	3	1	1	1	2	2	5	2	5	0	3	3	2	0	3	4	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:37369907A>G	ENST00000361924.2	+	15	6314	c.5940A>G	c.(5938-5940)aaA>aaG	p.K1980K	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Splice_Site_p.K2002K	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1980	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TATTACTCAGACAGGAGCAGG	0.413																																					p.K2002K													.	GOLGA4-93	0			c.A6006G						.						152	156	155					3																	37369907		2203	4300	6503	SO:0001630	splice_region_variant	2803	exon16			ACTCAGACAGGAG	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5940-1A>G	3.37:g.37369907A>G		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	180	8	NM_001172713	0	0	0	0	0	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	37	CCDS2666.1																																																																																			.		0.413	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	Silent	G	37369907	A	G	37369907	5	3	17	1	0	0	0	0	0	0	1	0	6575	289	10	3	6068	3	GOLGA4	3	37369907	Splice_Site	SNP	A	TCGA-A4-8515-01A-11D-2396-08	24412801	37369907	160652523	18	1405											
PLXNB1	5364	bcgsc.ca	37	chr3	48451952	48451952	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagaatgaggtgcccggccAccccagaccgccactctgca	11	4	10	16	2	1	3	0	1	1	2	1	3	1	3	6	2	2	1	6	2	2	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:48451952A>C	ENST00000358536.4	-	30	5701	c.5432T>G	c.(5431-5433)gTg>gGg	p.V1811G	PLXNB1_ENST00000358459.4_Missense_Mutation_p.V1628G|PLXNB1_ENST00000456774.1_Missense_Mutation_p.V1628G|PLXNB1_ENST00000296440.6_Missense_Mutation_p.V1811G|PLXNB1_ENST00000448774.2_Missense_Mutation_p.V422G	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1811					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.V1811G(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTGCCCGGCCACCCCAGACCG	0.592																																					p.V1811G													.	PLXNB1-293	1	Substitution - Missense(1)	pancreas(1)	c.T5432G						.						42	46	44					3																	48451952		2203	4300	6503	SO:0001583	missense	5364	exon30			CCGGCCACCCCAG	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.5432T>G	3.37:g.48451952A>C	ENSP00000351338:p.Val1811Gly	Somatic	85	2		WXS	Illumina HiSeq	Phase_1	43	19	NM_001130082	0	0	88	89	1	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.907203	0.52333	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000448774;ENST00000456774	T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79	4.56	4.56	0.56223	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.148520	0.45867	D	0.000337	T	0.17365	0.0417	N	0.24115	0.695	0.80722	D	1	D;P	0.69078	0.997;0.5	D;B	0.70487	0.969;0.266	T	0.09684	-1.0663	10	0.22706	T	0.39	.	13.1259	0.59354	1.0:0.0:0.0:0.0	.	1811;1628	O43157;O43157-2	PLXB1_HUMAN;.	G	1811;1628;1811;422;1628	ENSP00000296440:V1811G;ENSP00000351242:V1628G;ENSP00000351338:V1811G;ENSP00000389320:V422G;ENSP00000414199:V1628G	ENSP00000296440:V1811G	V	-	2	0	PLXNB1	48426956	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	7.451000	0.80668	1.683000	0.51011	0.460000	0.39030	GTG	.		0.592	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		C	48451952	A	C	48451952	3	2	17	1	0	0	0	0	1	0	0	0	12149	159	6	5	1011	5	PLXNB1	3	48451952	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	11082045	48451952	149570478	19	1406											
UGDH	7358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39515753	39515753	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcatcaatattggtagAaaaaaaaagattttttcctc	16	13	6	6	0	2	2	2	0	0	2	4	2	3	2	1	2	0	2	1	2	7	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr4:39515753A>G	ENST00000316423.6	-	3	556	c.214T>C	c.(214-216)Tct>Cct	p.S72P	UGDH_ENST00000501493.2_Missense_Mutation_p.S72P|UGDH_ENST00000506179.1_Missense_Mutation_p.S72P|UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000507089.1_5'UTR	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	72					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)	p.S72fs*18(1)		breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						ATATTGGTAGAAAAAAAAAGA	0.299																																					p.S72P		.											.	UGDH-156	1	Deletion - Frameshift(1)	large_intestine(1)	c.T214C						.						64	75	72					4																	39515753		2201	4290	6491	SO:0001583	missense	7358	exon3			TGGTAGAAAAAAA	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"UDP-glucose dehydrogenase"			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.214T>C	4.37:g.39515753A>G	ENSP00000319501:p.Ser72Pro	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	98	40	NM_003359	0	0	11	25	14	B3KUU2|B4DN25|O60589	Missense_Mutation	SNP	ENST00000316423.6	37	CCDS3455.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.642875	0.87859	.	.	ENSG00000109814	ENST00000316423;ENST00000501493;ENST00000506179;ENST00000515021;ENST00000514106;ENST00000509391;ENST00000505698	T;T;T;T;T;T;T	0.78003	-1.14;-1.13;-1.14;-1.14;-1.14;-1.14;-1.14	5.66	5.66	0.87406	UDP-glucose/GDP-mannose dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90700	0.7082	M	0.93197	3.39	0.80722	D	1	D;P	0.71674	0.998;0.752	D;B	0.73708	0.981;0.32	D	0.92839	0.6287	10	0.66056	D	0.02	-3.2805	15.077	0.72084	1.0:0.0:0.0:0.0	.	72;72	B3KUU2;O60701	.;UGDH_HUMAN	P	72;72;72;85;72;72;72	ENSP00000319501:S72P;ENSP00000422909:S72P;ENSP00000421757:S72P;ENSP00000421954:S85P;ENSP00000425834:S72P;ENSP00000422603:S72P;ENSP00000422565:S72P	ENSP00000319501:S72P	S	-	1	0	UGDH	39192148	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.263000	0.89864	2.148000	0.66965	0.454000	0.30748	TCT	.		0.299	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		G	39515753	A	G	39515753	3	3	17	1	0	0	0	0	1	0	0	0	16973	246	9	3	1310	3	UGDH	4	39515753	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		39515753	151638523	20	1407											
NAF1	92345	broad.mit.edu	37	chr4	164050124	164050124	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggtggagggggagggggTgggggtagggagtatggtaa	8	7	26	0	0	0	0	0	0	0	0	0	3	0	3	0	10	0	3	0	10	3	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr4:164050124T>G	ENST00000274054.2	-	8	1603	c.1410A>C	c.(1408-1410)ccA>ccC	p.P470P	NAF1_ENST00000509434.1_Intron|NAF1_ENST00000422287.2_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	470	Pro-rich.				pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				ggggagggggtgggggtaggg	0.522																																					p.P470P													.	NAF1-70	0			c.A1410C						.						10	10	10					4																	164050124		2188	4274	6462	SO:0001819	synonymous_variant	92345	exon8			AGGGGGTGGGGGT		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.1410A>C	4.37:g.164050124T>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	20	9	NM_138386	0	0	3	3	0	D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	37	CCDS3803.1																																																																																			.		0.522	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		G	164050124	T	G	164050124	2	3	17	1	0	0	0	0	0	0	0	1	10165	1683	59	5		5	NAF1	4	164050124	Silent	SNP	T	TCGA-A4-8515-01A-11D-2396-08	124534371	164050124	27104152	21	1408											
CCDC110	256309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	186380257	186380257	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgtattcttctgttttaCttaacttagactgaatagta	10	19	6	6	0	2	2	0	1	2	1	2	2	2	2	0	0	3	4	0	0	7	9			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr4:186380257C>A	ENST00000307588.3	-	6	1559	c.1484G>T	c.(1483-1485)aGt>aTt	p.S495I	CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.S458I|CCDC110_ENST00000510617.1_Missense_Mutation_p.S495I	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	495						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TTCTGTTTTACTTAACTTAGA	0.284																																					p.S495I		.											.	CCDC110-90	0			c.G1484T						.						30	30	30					4																	186380257		2201	4278	6479	SO:0001583	missense	256309	exon6			GTTTTACTTAACT	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1484G>T	4.37:g.186380257C>A	ENSP00000306776:p.Ser495Ile	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	31	12	NM_152775	0	0	5	5	0	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	.	.	.	.	.	.	.	.	.	.	C	1.946	-0.442479	0.04604	.	.	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.07444	3.19;3.2;3.2	5.96	-8.17	0.01057	.	2.119420	0.01685	N	0.026366	T	0.03178	0.0093	N	0.02539	-0.55	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.002	T	0.41466	-0.9507	10	0.32370	T	0.25	0.1051	8.9096	0.35546	0.3181:0.3017:0.3802:0.0	.	495;458;495	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	I	458;495;495	ENSP00000377172:S458I;ENSP00000306776:S495I;ENSP00000427246:S495I	ENSP00000306776:S495I	S	-	2	0	CCDC110	186617251	0.023000	0.18921	0.005000	0.12908	0.210000	0.24377	-0.152000	0.10159	-0.952000	0.03649	-0.266000	0.10368	AGT	.		0.284	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		A	186380257	C	A	186380257	3	1	17	1	0	0	0	0	1	0	0	0	2753	565	20	4	1025	4	CCDC110	4	186380257	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	22330133	186380257	4774019	22	1409											
SORBS2	8470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	186545386	186545386	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gacttgactttcgggtccggGaagctatcgcagtcgtcgtt	6	12	13	10	5	0	1	0	1	0	0	5	3	1	2	1	2	1	3	1	2	2	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr4:186545386G>T	ENST00000284776.7	-	13	1694	c.1185C>A	c.(1183-1185)ttC>ttA	p.F395L	SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000355634.5_Missense_Mutation_p.F495L|SORBS2_ENST00000431808.1_Missense_Mutation_p.F395L|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.F299L	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	395					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TCGGGTCCGGGAAGCTATCGC	0.577																																					p.F495L	Esophageal Squamous(153;41 2433 9491 36028)	.											.	SORBS2-91	0			c.C1485A						.						62	58	59					4																	186545386		2203	4300	6503	SO:0001583	missense	8470	exon16			GTCCGGGAAGCTA		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1185C>A	4.37:g.186545386G>T	ENSP00000284776:p.Phe395Leu	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	70	30	NM_001270771	0	0	0	0	0	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	G	1.601	-0.526481	0.04141	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.35236	1.43;1.43;1.32;1.42	5.72	-0.19	0.13256	.	0.433914	0.25001	N	0.033913	T	0.23572	0.0570	L	0.50333	1.59	0.24909	N	0.992056	P;P;B	0.35612	0.512;0.512;0.329	B;B;B	0.35073	0.195;0.18;0.084	T	0.29822	-0.9999	10	0.10111	T	0.7	-15.4985	5.7099	0.17929	0.4632:0.2512:0.2856:0.0	.	299;495;395	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	L	395;395;299;495	ENSP00000284776:F395L;ENSP00000411764:F395L;ENSP00000397482:F299L;ENSP00000347852:F495L	ENSP00000284776:F395L	F	-	3	2	SORBS2	186782380	0.867000	0.29959	0.659000	0.29680	0.299000	0.27559	-0.021000	0.12504	-0.396000	0.07703	0.558000	0.71614	TTC	.		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186545386	G	T	186545386	3	4	17	1	0	0	0	0	1	0	0	0	14960	1165	41	4	2153	4	SORBS2	4	186545386	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	165129	186545386	4608890	23	1410											
MTRR	4552	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	7886796	7886796	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttacctggtgtcttgaaAtccgagcaattcctaaaaag	12	14	7	8	1	1	1	0	1	1	0	3	2	3	1	3	1	2	1	3	1	6	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr5:7886796A>G	ENST00000264668.2	+	8	1237	c.1207A>G	c.(1207-1209)Atc>Gtc	p.I403V	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Missense_Mutation_p.I376V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	403	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GTGTCTTGAAATCCGAGCAAT	0.363																																					p.I403V		.											.	MTRR-91	0			c.A1207G						.						129	124	126					5																	7886796		2203	4300	6503	SO:0001583	missense	4552	exon8			CTTGAAATCCGAG	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1207A>G	5.37:g.7886796A>G	ENSP00000264668:p.Ile403Val	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	79	5	NM_024010	0	0	27	28	1	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176144	0.78564	.	.	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.42900	0.96;0.96	5.37	5.37	0.77165	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.047649	0.85682	D	0.000000	T	0.59851	0.2224	M	0.72353	2.195	0.80722	D	1	D	0.64830	0.994	P	0.62649	0.905	T	0.62756	-0.6787	10	0.54805	T	0.06	-26.3682	12.5449	0.56193	0.8615:0.1384:0.0:0.0	.	403	Q9UBK8	MTRR_HUMAN	V	403;376	ENSP00000264668:I403V;ENSP00000402510:I376V	ENSP00000264668:I403V	I	+	1	0	MTRR	7939796	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.194000	0.65125	2.038000	0.60285	0.533000	0.62120	ATC	.		0.363	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7886796	A	G	7886796	3	3	17	1	0	0	0	0	1	0	0	0	9986	101	4	3	1237	3	MTRR	5	7886796	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		7886796	173028464	24	1411											
P4HA2	8974	broad.mit.edu	37	chr5	131546092	131546092	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgtggtggcctcctccccGgcatcaagctgctttagcac	5	11	11	14	1	1	0	1	0	0	0	3	0	3	0	4	3	3	5	4	3	2	3	rs147510145		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr5:131546092G>T	ENST00000401867.1	-	7	1162	c.594C>A	c.(592-594)gcC>gcA	p.A198A	P4HA2_ENST00000379086.1_Silent_p.A198A|P4HA2_ENST00000360568.3_Silent_p.A198A|P4HA2_ENST00000379104.2_Silent_p.A198A|P4HA2_ENST00000379100.2_Silent_p.A198A|P4HA2_ENST00000166534.4_Silent_p.A198A			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	198					peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|procollagen-proline 4-dioxygenase complex (GO:0016222)	electron carrier activity (GO:0009055)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	CCTCCTCCCCGGCATCAAGCT	0.577																																					p.A198A	Esophageal Squamous(68;117 1135 17362 19256 34242)												.	P4HA2-68	0			c.C594A						.						208	190	196					5																	131546092		2203	4300	6503	SO:0001819	synonymous_variant	8974	exon6			CTCCCCGGCATCA	U90441	CCDS4151.1, CCDS34230.1	5q31	2008-12-09	2008-12-09		ENSG00000072682	ENSG00000072682	1.14.11.2		8547	protein-coding gene	gene with protein product	"4-PH alpha 2", "collagen prolyl 4-hydroxylase alpha(II)"	600608	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II"			9211872, 9149945	Standard	NM_001142598		Approved	C-P4Halpha(II)	uc003kwl.3	O15460	OTTHUMG00000059647	ENST00000401867.1:c.594C>A	5.37:g.131546092G>T		Somatic	245	0		WXS	Illumina HiSeq	Phase_I	264	5	NM_001017974	0	0	53	53	0	D3DQ85|D3DQ86|Q8WWN0	Silent	SNP	ENST00000401867.1	37	CCDS4151.1																																																																																			A|0.000;G|1.000		0.577	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4	NM_004199		T	131546092	G	T	131546092	2	4	17	1	0	0	0	0	0	0	0	1	11383	1103	39	4		4	P4HA2	5	131546092	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	123659296	131546092	49369168	25	1412											
HLA-B	3106	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31323288	31323288	+	Frame_Shift_Del	DEL	G	G	-																															aggtcagtgtgatctccgcaGggtagaaacccagggcccag																								rs74428022		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:31323288delG	ENST00000412585.2	-	4	729	c.701delC	c.(700-702)cctfs	p.P234fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	234	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GATCTCCGCAGGGTAGAAACC	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.P234fs		.											.	HLA-B-90	0			c.701delC						.						83	82	82					6																	31323288		2203	4298	6501	SO:0001589	frameshift_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.701delC	6.37:g.31323288delG	ENSP00000399168:p.Pro234fs	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	162	72	NM_005514	0	0	0	0	0	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			.		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		-	31323288	G	-	31323288	7	5	17	1	0	1	0	1	0	0	0	0	7217	1000	35	0	403	0	HLA-B	6	31323288	Frame_Shift_Del	DEL	G	TCGA-A4-8515-01A-11D-2396-08		31323288	139791779	26	1413											
FAM46A	55603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	82461655	82461655	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccagccgctgcacttgctcCcagttcagcacattgcagtg	7	10	9	15	1	1	0	1	0	0	0	3	0	3	0	3	0	5	6	3	0	0	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:82461655C>A	ENST00000320172.6	-	2	518	c.204G>T	c.(202-204)tgG>tgT	p.W68C	FAM46A_ENST00000369756.3_Missense_Mutation_p.W149C|FAM46A_ENST00000369754.3_Missense_Mutation_p.W87C	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	68					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		GCACTTGCTCCCAGTTCAGCA	0.647																																					p.W68C		.											.	FAM46A-90	0			c.G204T						.						57	52	54					6																	82461655		2184	4283	6467	SO:0001583	missense	55603	exon2			TTGCTCCCAGTTC	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.204G>T	6.37:g.82461655C>A	ENSP00000318298:p.Trp68Cys	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	124	61	NM_017633	0	0	1	3	2	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Missense_Mutation	SNP	ENST00000320172.6	37	CCDS34489.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404404	0.62288	.	.	ENSG00000112773	ENST00000369754;ENST00000320172;ENST00000369756	T;T;T	0.23147	1.92;1.92;1.92	5.44	5.44	0.79542	Domain of unknown function DUF1693 (1);	0.056200	0.85682	D	0.000000	T	0.47600	0.1454	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.36114	-0.9761	9	.	.	.	-2.8137	19.0555	0.93062	0.0:1.0:0.0:0.0	.	68;87	Q96IP4;Q96IP4-2	FA46A_HUMAN;.	C	87;68;149	ENSP00000358769:W87C;ENSP00000318298:W68C;ENSP00000358771:W149C	.	W	-	3	0	FAM46A	82518374	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	5.897000	0.69831	2.837000	0.97791	0.655000	0.94253	TGG	.		0.647	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			A	82461655	C	A	82461655	3	1	17	1	0	0	0	0	1	0	0	0	5584	624	22	4	1132	4	FAM46A	6	82461655	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	51138367	82461655	88653412	27	1414											
MDN1	23195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90411386	90411386	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgagacagtctgaactTctttgtaatatctttaaagg	11	16	8	6	0	4	2	0	2	4	1	4	3	4	2	0	1	1	2	0	1	5	7			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:90411386T>A	ENST00000369393.3	-	55	8433	c.8318A>T	c.(8317-8319)gAa>gTa	p.E2773V	MDN1_ENST00000428876.1_Missense_Mutation_p.E2773V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2773					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGTCTGAACTTCTTTGTAATA	0.418																																					p.E2773V		.											.	MDN1-100	0			c.A8318T						.						40	41	41					6																	90411386		2203	4300	6503	SO:0001583	missense	23195	exon55			TGAACTTCTTTGT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.8318A>T	6.37:g.90411386T>A	ENSP00000358400:p.Glu2773Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	52	26	NM_014611	0	0	0	0	0	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.355386	0.61293	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03801	3.8;3.8	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.05686	0.0149	L	0.27053	0.805	0.53688	D	0.999978	D	0.71674	0.998	P	0.59115	0.852	T	0.49679	-0.8914	10	0.44086	T	0.13	.	16.1255	0.81392	0.0:0.0:0.0:1.0	.	2773	Q9NU22	MDN1_HUMAN	V	2773	ENSP00000358400:E2773V;ENSP00000413970:E2773V	ENSP00000358400:E2773V	E	-	2	0	MDN1	90468107	1.000000	0.71417	0.919000	0.36401	0.880000	0.50808	7.197000	0.77814	2.205000	0.71048	0.477000	0.44152	GAA	.		0.418	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90411386	T	A	90411386	3	1	17	1	0	0	0	0	1	0	0	0	9440	1783	62	5	8664	5	MDN1	6	90411386	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	7949731	90411386	80703681	28	1415											
ECHDC1	55862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	127611395	127611395	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatctctttgtggacgaaTctgatcttactctctggagt	7	15	8	11	1	4	1	0	1	4	0	6	4	4	3	1	2	1	0	1	2	2	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:127611395T>C	ENST00000531967.1	-	6	1046	c.543A>G	c.(541-543)agA>agG	p.R181R	ECHDC1_ENST00000488087.1_5'UTR|ECHDC1_ENST00000430841.2_Silent_p.R175R|ECHDC1_ENST00000368291.2_3'UTR|ECHDC1_ENST00000309620.9_Silent_p.R158R|ECHDC1_ENST00000368289.2_3'UTR|ECHDC1_ENST00000454859.3_Silent_p.R175R|ECHDC1_ENST00000474289.2_Silent_p.R175R|ECHDC1_ENST00000454591.2_Silent_p.R100R|ECHDC1_ENST00000528402.1_3'UTR	NM_001139510.1	NP_001132982.1	Q9NTX5	ECHD1_HUMAN	enoyl CoA hydratase domain containing 1	181						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxy-lyase activity (GO:0016831)|methylmalonyl-CoA decarboxylase activity (GO:0004492)			large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)		TGTGGACGAATCTGATCTTAC	0.408																																					p.R181R		.											.	ECHDC1-90	0			c.A543G						.						65	58	60					6																	127611395		1869	4110	5979	SO:0001819	synonymous_variant	55862	exon6			GACGAATCTGATC	AK025796	CCDS34530.1, CCDS43504.1, CCDS47471.1, CCDS47472.1, CCDS55054.1	6q22.33	2011-12-12	2010-04-30		ENSG00000093144	ENSG00000093144			21489	protein-coding gene	gene with protein product		612136	"enoyl Coenzyme A hydratase domain containing 1"			22016388	Standard	NM_001002030		Approved	dJ351K20.2	uc003qax.3	Q9NTX5	OTTHUMG00000015523	ENST00000531967.1:c.543A>G	6.37:g.127611395T>C		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	93	37	NM_001139510	0	0	28	46	18	A6NFJ5|B7Z8S0|E9PEN7|E9PR31|F8W851|Q5TEF6|Q5TEF7|Q5TEG0|Q5TEG4|Q9NZ30|V9HW18	Silent	SNP	ENST00000531967.1	37	CCDS47471.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.430675	0.25726	.	.	ENSG00000093144	ENST00000436638;ENST00000460558	.	.	.	5.65	2.0	0.26442	.	.	.	.	.	T	0.44829	0.1312	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36578	-0.9742	4	.	.	.	.	9.6944	0.40147	0.0:0.2675:0.0:0.7325	.	.	.	.	G	189;54	.	.	D	-	2	0	ECHDC1	127653088	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.054000	0.30455	0.414000	0.25790	0.533000	0.62120	GAT	.		0.408	ECHDC1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042131.2			C	127611395	T	C	127611395	2	2	17	1	0	0	0	0	0	0	0	1	4904	1432	50	3		3	ECHDC1	6	127611395	Silent	SNP	T	TCGA-A4-8515-01A-11D-2396-08	37200009	127611395	43503672	29	1416											
RSPH3	83861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	159401839	159401839	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atcataaaagtagccactatCcctgaggctgccaaaaacag	16	7	7	11	0	1	1	1	1	0	0	2	1	2	1	3	1	3	2	3	1	6	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:159401839C>T	ENST00000252655.1	-	6	1441	c.1252G>A	c.(1252-1254)Gat>Aat	p.D418N	RSPH3_ENST00000367069.2_Missense_Mutation_p.D276N|RSPH3_ENST00000449822.1_Missense_Mutation_p.D180N|RSPH3_ENST00000297262.3_Missense_Mutation_p.D322N	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	418										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TAGCCACTATCCCTGAGGCTG	0.408																																					p.D418N		.											.	RSPH3-92	0			c.G1252A						.						126	104	111					6																	159401839		2203	4300	6503	SO:0001583	missense	83861	exon6			CACTATCCCTGAG	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1252G>A	6.37:g.159401839C>T	ENSP00000252655:p.Asp418Asn	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_031924	0	0	11	27	16	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914542	0.52546	.	.	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.81	4.94	0.65067	.	0.362264	0.33938	N	0.004405	T	0.05502	0.0145	L	0.38175	1.15	0.38862	D	0.9565	P;B	0.36010	0.532;0.091	B;B	0.30943	0.122;0.065	T	0.28586	-1.0039	10	0.23302	T	0.38	-23.6685	12.7512	0.57310	0.0:0.9196:0.0:0.0804	.	322;418	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	N	276;180;418;322	ENSP00000356036:D276N;ENSP00000393195:D180N;ENSP00000252655:D418N;ENSP00000297262:D322N	ENSP00000252655:D418N	D	-	1	0	RSPH3	159321827	1.000000	0.71417	0.838000	0.33150	0.987000	0.75469	3.471000	0.53107	1.431000	0.47355	0.591000	0.81541	GAT	.		0.408	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		T	159401839	C	T	159401839	3	4	17	1	0	0	0	0	1	0	0	0	13737	855	30	2	442	2	RSPH3	6	159401839	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	31790444	159401839	11713228	30	1417											
TMEM184A	202915	broad.mit.edu	37	chr7	1586662	1586663	+	In_Frame_Ins	INS	-	-	GCC																															ctcccgccggagccgccgctINSggggtgggtgccgggcctgg																								rs3837151|rs3779607	byFrequency	TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:1586662_1586663insGCC	ENST00000297477.5	-	9	1483_1484	c.1167_1168insGGC	c.(1165-1170)cccagc>cccGGCagc	p.389_390PS>PGS	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	389			S -> G (in dbSNP:rs3779607). {ECO:0000269|PubMed:15489334}.		germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GAGCCGCCGCTGGGGTGGGTGC	0.703																																					p.S390delinsGS													.	TMEM184A-90	0			c.1168_1169insGGC						.			1912,2170		535,842,664						-3.6	0		dbSNP_132	17	3872,4214		1028,1816,1199	no	coding	TMEM184A	NM_001097620.1		1563,2658,1863	A1A1,A1R,RR		47.8852,46.8398,47.5345				5784,6384				SO:0001652	inframe_insertion	202915	exon9			CGCCGCTGGGGTG		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.1167_1168insGGC	7.37:g.1586662_1586663insGCC	ENSP00000297477:p.Pro389_Ser390insGly	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	85	11	NM_001097620	0	0	0	0	0	Q8TBQ6	In_Frame_Ins	INS	ENST00000297477.5	37	CCDS43537.1																																																																																			.		0.703	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		GCC	1586663	-	GCC	1586662	7	5	17	1	0	1	1	0	0	0	0	0	16136	1580	55	0	77	0	TMEM184A	7	1586662	In_Frame_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08		1586662	157552001	31	1418											
C7orf26	79034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	6639468	6639468	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtttgcagatgacctcAttccacctatggacttgctt	7	16	7	11	0	1	2	1	1	0	1	2	3	2	3	3	1	2	3	3	1	1	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:6639468A>T	ENST00000344417.5	+	4	856	c.589A>T	c.(589-591)Att>Ttt	p.I197F	C7orf26_ENST00000472693.1_3'UTR|C7orf26_ENST00000359073.5_Missense_Mutation_p.I178F	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	197										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		AGATGACCTCATTCCACCTAT	0.498																																					p.I197F		.											.	C7orf26-91	0			c.A589T						.						172	159	164					7																	6639468		2203	4300	6503	SO:0001583	missense	79034	exon4			GACCTCATTCCAC	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.589A>T	7.37:g.6639468A>T	ENSP00000340220:p.Ile197Phe	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	218	126	NM_024067	0	0	0	0	0	Q9BQ43	Missense_Mutation	SNP	ENST00000344417.5	37	CCDS5353.1	.	.	.	.	.	.	.	.	.	.	A	8.056	0.767095	0.15983	.	.	ENSG00000146576	ENST00000344417;ENST00000359073	T;T	0.42900	0.96;0.96	5.08	3.89	0.44902	.	0.136974	0.64402	D	0.000003	T	0.28764	0.0713	L	0.43152	1.355	0.40382	D	0.979454	B;B	0.32160	0.358;0.358	B;B	0.30495	0.116;0.116	T	0.06789	-1.0807	10	0.17369	T	0.5	-23.9783	5.9553	0.19269	0.7464:0.1654:0.0882:0.0	.	178;197	Q96N11-2;Q96N11	.;CG026_HUMAN	F	197;178	ENSP00000340220:I197F;ENSP00000351974:I178F	ENSP00000340220:I197F	I	+	1	0	C7orf26	6605993	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	4.865000	0.62998	0.995000	0.38917	0.454000	0.30748	ATT	.		0.498	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067		T	6639468	A	T	6639468	3	4	17	1	0	0	0	0	1	0	0	0	2387	217	8	5	603	5	C7orf26	7	6639468	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	5052806	6639468	152499195	32	1419											
HDAC9	9734	broad.mit.edu;bcgsc.ca	37	chr7	18625059	18625059	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcagcagcaacaaatcCagaagcagcttctgatagca	15	6	8	12	0	1	2	0	1	1	1	3	2	3	2	2	0	7	6	2	0	4	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:18625059C>T	ENST00000432645.2	+	2	178	c.178C>T	c.(178-180)Cag>Tag	p.Q60*	HDAC9_ENST00000417496.2_Nonsense_Mutation_p.Q102*|HDAC9_ENST00000524023.1_Nonsense_Mutation_p.Q29*|HDAC9_ENST00000406072.1_Nonsense_Mutation_p.Q88*|HDAC9_ENST00000476135.1_3'UTR|HDAC9_ENST00000441542.2_Nonsense_Mutation_p.Q60*|HDAC9_ENST00000405010.3_Nonsense_Mutation_p.Q60*|HDAC9_ENST00000401921.1_Nonsense_Mutation_p.Q60*|HDAC9_ENST00000406451.4_Nonsense_Mutation_p.Q60*|HDAC9_ENST00000456174.2_Nonsense_Mutation_p.Q29*|HDAC9_ENST00000428307.2_Nonsense_Mutation_p.Q60*	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	60					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	GCAACAAATCCAGAAGCAGCT	0.493																																					p.Q102X													.	HDAC9-227	0			c.C304T						.						59	61	61					7																	18625059		2006	4193	6199	SO:0001587	stop_gained	9734	exon5			CAAATCCAGAAGC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.178C>T	7.37:g.18625059C>T	ENSP00000410337:p.Gln60*	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	100	6	NM_001204144	0	0	9	10	1	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Nonsense_Mutation	SNP	ENST00000432645.2	37	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041834	0.93685	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000413509;ENST00000413380;ENST00000430454;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000441986;ENST00000456174;ENST00000524023;ENST00000341009	.	.	.	5.93	5.93	0.95920	.	0.000000	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-28.9728	20.3368	0.98748	0.0:1.0:0.0:0.0	.	.	.	.	X	102;105;60;60;29;60;60;60;88;60;60;60;29;29;29;60	.	ENSP00000262069:Q105X	Q	+	1	0	HDAC9	18591584	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.805000	0.96524	0.655000	0.94253	CAG	.		0.493	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18625059	C	T	18625059	4	4	17	1	0	0	0	0	0	1	0	0	7035	595	21	2	184	2	HDAC9	7	18625059	Nonsense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	11985591	18625059	140513604	33	1420											
HERPUD2	64224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	35707133	35707133	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatccttctgaggaagaAcccacagctaaagacaaggt	15	7	8	11	0	2	3	1	1	1	2	3	4	3	4	2	2	2	1	2	2	6	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:35707133A>G	ENST00000396081.1	-	4	1209	c.405T>C	c.(403-405)ggT>ggC	p.G135G	HERPUD2_ENST00000426180.1_5'UTR|HERPUD2_ENST00000311350.3_Silent_p.G135G	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	135	Ser-rich.				response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						CTGAGGAAGAACCCACAGCTA	0.398																																					p.G135G		.											.	HERPUD2-93	0			c.T405C						.						143	130	134					7																	35707133		2203	4300	6503	SO:0001819	synonymous_variant	64224	exon5			GGAAGAACCCACA	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.405T>C	7.37:g.35707133A>G		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	179	111	NM_022373	0	0	9	38	29	A4D1Y8|Q9H6F9	Silent	SNP	ENST00000396081.1	37	CCDS5446.1																																																																																			.		0.398	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		G	35707133	A	G	35707133	2	3	17	1	0	0	0	0	0	0	0	1	7085	30	2	3		3	HERPUD2	7	35707133	Silent	SNP	A	TCGA-A4-8515-01A-11D-2396-08	17082074	35707133	123431530	34	1421											
EPHB4	2050	broad.mit.edu;bcgsc.ca	37	chr7	100404084	100404104	+	In_Frame_Del	DEL	CATCACCTCCCACATCACAAT	CATCACCTCCCACATCACAAT	-																															tacggcctctccccaaatgaCatcacctcccacatcacaat																								rs199910843		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	CATCACCTCCCACATCACAAT	CATCACCTCCCACATCACAAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:100404084_100404104delCATCACCTCCCACATCACAAT	ENST00000358173.3	-	14	2890_2910	c.2422_2442delATTGTGATGTGGGAGGTGATG	c.(2422-2442)attgtgatgtgggaggtgatgdel	p.IVMWEVM808del	EPHB4_ENST00000360620.3_In_Frame_Del_p.IVMWEVM808del	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	808	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCCAAATGACATCACCTCCCACATCACAATCCCGTAACTC	0.552																																					p.808_814del	GBM(200;2113 3072 25865 52728)												.	EPHB4-1446	0			c.2422_2442del						.																																			SO:0001651	inframe_deletion	2050	exon14			AAATGACATCACC	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.2422_2442delATTGTGATGTGGGAGGTGATG	7.37:g.100404084_100404104delCATCACCTCCCACATCACAAT	ENSP00000350896:p.Ile808_Met814del	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	159	14	NM_004444	0	0	0	0	0	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	In_Frame_Del	DEL	ENST00000358173.3	37	CCDS5706.1																																																																																			.		0.552	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		-	100404104	CATCACCTCCCACATCACAAT	-	100404084	7	5	17	1	0	1	0	1	0	0	0	0	5190	478	17	0	537	0	EPHB4	7	100404084	In_Frame_Del	DEL	CATCACCTCCCACATCACAAT	TCGA-A4-8515-01A-11D-2396-08	64696951	100404084	58734579	35	1422											
MUC17	140453	broad.mit.edu	37	chr7	100681919	100681919	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtgtgcctgtcagcaccatgCcggtggtcagttctgaggct	5	11	14	11	1	3	1	2	1	1	0	3	1	3	1	3	3	3	3	3	3	0	1	rs200222893		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:100681919C>T	ENST00000306151.4	+	3	7286	c.7222C>T	c.(7222-7224)Ccg>Tcg	p.P2408S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2408	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CAGCACCATGCCGGTGGTCAG	0.512																																					p.P2408S													.	MUC17-95	0			c.C7222T						.						380	361	367					7																	100681919		2203	4300	6503	SO:0001583	missense	140453	exon3			ACCATGCCGGTGG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.7222C>T	7.37:g.100681919C>T	ENSP00000302716:p.Pro2408Ser	Somatic	585	0		WXS	Illumina HiSeq	Phase_I	841	6	NM_001040105	0	0	0	0	0	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	4.830	0.154397	0.09236	.	.	ENSG00000169876	ENST00000306151	T	0.03152	4.03	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.05456	0.0144	L	0.34521	1.04	0.09310	N	1	D	0.57571	0.98	P	0.59424	0.857	T	0.25082	-1.0142	9	0.07813	T	0.8	.	5.9248	0.19104	0.0:0.9993:0.0:7.0E-4	.	2408	Q685J3	MUC17_HUMAN	S	2408	ENSP00000302716:P2408S	ENSP00000302716:P2408S	P	+	1	0	MUC17	100468639	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.185000	0.00567	0.132000	0.18615	0.134000	0.15878	CCG	.		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100681919	C	T	100681919	3	4	17	1	0	0	0	0	1	0	0	0	9999	739	26	2	7232	2	MUC17	7	100681919	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	277835	100681919	58456744	36	1423											
PCMTD1	115294	broad.mit.edu	37	chr8	52733204	52733204	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccccttggcctgcatctcatCatttatgaaatttctaagtg	9	15	6	11	0	3	1	2	1	2	0	4	1	3	1	3	1	1	1	3	1	3	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr8:52733204C>G	ENST00000360540.5	-	7	1187	c.781G>C	c.(781-783)Gat>Cat	p.D261H	PCMTD1_ENST00000544451.1_Missense_Mutation_p.D185H|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Missense_Mutation_p.D261H	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	261						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				TGCATCTCATCATTTATGAAA	0.403																																					p.D261H													.	PCMTD1-68	0			c.G781C						.						88	92	91					8																	52733204		2203	4300	6503	SO:0001583	missense	115294	exon6			TCTCATCATTTAT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.781G>C	8.37:g.52733204C>G	ENSP00000353739:p.Asp261His	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	197	9	NM_052937	0	0	29	29	0	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.278887	0.80692	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.42513	0.97;0.97;0.97	5.77	5.77	0.91146	.	0.053651	0.85682	D	0.000000	T	0.51176	0.1659	N	0.22421	0.69	0.58432	D	0.999999	P;D;B	0.69078	0.895;0.997;0.26	P;D;B	0.63192	0.498;0.912;0.104	T	0.50363	-0.8837	10	0.49607	T	0.09	-23.9815	19.9832	0.97338	0.0:1.0:0.0:0.0	.	131;185;261	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	H	261;185;261	ENSP00000353739:D261H;ENSP00000444026:D185H;ENSP00000428099:D261H	ENSP00000353739:D261H	D	-	1	0	PCMTD1	52895757	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.317000	0.65822	2.722000	0.93159	0.655000	0.94253	GAT	.		0.403	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		G	52733204	C	G	52733204	3	3	17	1	0	0	0	0	1	0	0	0	11612	826	29	4	296	4	PCMTD1	8	52733204	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08		52733204	93630818	37	1424											
NSMAF	8439	broad.mit.edu	37	chr8	59498243	59498243	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtattctctcactgatttttGctccaaggaggtcccaaacg	9	13	8	11	1	2	1	1	1	1	0	5	2	4	2	2	2	2	2	2	2	3	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr8:59498243G>T	ENST00000038176.3	-	30	2839	c.2627C>A	c.(2626-2628)gCa>gAa	p.A876E	NSMAF_ENST00000427130.2_Missense_Mutation_p.A907E	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	876					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				ACTGATTTTTGCTCCAAGGAG	0.448																																					p.A907E													.	NSMAF-91	0			c.C2720A						.						109	99	102					8																	59498243		2203	4300	6503	SO:0001583	missense	8439	exon30			ATTTTTGCTCCAA	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"WD repeat domain containing"	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.2627C>A	8.37:g.59498243G>T	ENSP00000038176:p.Ala876Glu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	125	5	NM_001144772	0	0	15	15	0	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	37	CCDS6173.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.039039	0.35989	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.28895	1.59;1.59	5.64	3.74	0.42951	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.224726	0.46758	D	0.000264	T	0.21550	0.0519	N	0.22421	0.69	0.38053	D	0.935829	B;B	0.30361	0.277;0.03	B;B	0.29942	0.109;0.018	T	0.09596	-1.0667	9	.	.	.	.	15.672	0.77286	0.0:0.6781:0.3219:0.0	.	907;876	Q92636-2;Q92636	.;FAN_HUMAN	E	876;907	ENSP00000038176:A876E;ENSP00000411012:A907E	.	A	-	2	0	NSMAF	59660797	1.000000	0.71417	0.991000	0.47740	0.881000	0.50899	2.836000	0.48183	1.527000	0.49086	0.563000	0.77884	GCA	.		0.448	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		T	59498243	G	T	59498243	3	4	17	1	0	0	0	0	1	0	0	0	10700	1319	46	4	134	4	NSMAF	8	59498243	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	6765039	59498243	86865779	38	1425											
WWP1	11059	ucsc.edu	37	chr8	87392964	87392964	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgtctgttagtttctagtgCcaaacttaaaagaaaaaaga	16	13	7	5	0	2	2	0	0	2	2	2	2	2	2	1	0	2	2	1	0	8	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr8:87392964C>A	ENST00000517970.1	+	4	387	c.80C>A	c.(79-81)gCc>gAc	p.A27D	WWP1_ENST00000349423.2_Intron|WWP1_ENST00000265428.4_Missense_Mutation_p.A27D|WWP1_ENST00000341922.2_Missense_Mutation_p.A27D|WWP1_ENST00000523863.1_3'UTR	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	27	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						GTTTCTAGTGCCAAACTTAAA	0.338																																					p.A27D													.	WWP1-659	0			c.C80A						.						60	58	58					8																	87392964		2203	4300	6503	SO:0001583	missense	11059	exon4			CTAGTGCCAAACT	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.80C>A	8.37:g.87392964C>A	ENSP00000427793:p.Ala27Asp	Somatic	25	0		WXS	Illumina HiSeq		40	4	NM_007013	0	0	0	0	0	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780760	0.70222	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000436619	T;T;T	0.80994	-1.44;-1.44;-1.44	5.8	5.8	0.92144	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.91284	0.7252	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91473	0.5198	10	0.62326	D	0.03	.	20.0503	0.97624	0.0:1.0:0.0:0.0	.	27	Q9H0M0	WWP1_HUMAN	D	27	ENSP00000427793:A27D;ENSP00000265428:A27D;ENSP00000340564:A27D	ENSP00000265428:A27D	A	+	2	0	WWP1	87462080	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.926000	0.75835	2.736000	0.93811	0.591000	0.81541	GCC	.		0.338	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		A	87392964	C	A	87392964	3	1	17	1	0	0	0	0	1	0	0	0	17448	739	26	4	86	4	WWP1	8	87392964	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	27894721	87392964	58971058	39	1426											
TAF1L	138474	bcgsc.ca	37	chr9	32635283	32635283	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcttctgtactcctaatccAcccttcatcatttaccaagg	10	14	3	14	0	4	0	2	0	2	0	6	0	6	0	4	1	2	1	4	1	4	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:32635283A>C	ENST00000242310.4	-	1	384	c.295T>G	c.(295-297)Tgg>Ggg	p.W99G	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	99					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTCCTAATCCACCCTTCATCA	0.522																																					p.W99G													.	TAF1L-870	0			c.T295G						.						235	223	227					9																	32635283		2203	4300	6503	SO:0001583	missense	138474	exon1			TAATCCACCCTTC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.295T>G	9.37:g.32635283A>C	ENSP00000418379:p.Trp99Gly	Somatic	312	3		WXS	Illumina HiSeq	Phase_1	229	62	NM_153809	0	0	0	0	0	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.191108	0.38707	.	.	ENSG00000122728	ENST00000242310	T	0.08008	3.14	1.16	1.16	0.20824	.	0.000000	0.85682	D	0.000000	T	0.10208	0.0250	M	0.67953	2.075	0.42246	D	0.991958	P	0.38395	0.629	B	0.43331	0.416	T	0.13629	-1.0502	10	0.31617	T	0.26	.	3.0458	0.06153	0.7174:0.0:0.2826:0.0	.	99	Q8IZX4	TAF1L_HUMAN	G	99	ENSP00000418379:W99G	ENSP00000418379:W99G	W	-	1	0	TAF1L	32625283	1.000000	0.71417	0.951000	0.38953	0.358000	0.29455	2.430000	0.44766	0.505000	0.28104	0.329000	0.21502	TGG	.		0.522	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			C	32635283	A	C	32635283	3	2	17	1	0	0	0	0	1	0	0	0	15555	159	6	5	5189	5	TAF1L	9	32635283	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		32635283	108578148	40	1427											
RUSC2	9853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35560975	35560975	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggctcccctcggactggctGagcctggacaagtccatgtt	7	9	12	13	1	0	1	0	1	0	0	3	3	2	3	4	4	1	3	4	4	1	1			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:35560975G>A	ENST00000455600.1	+	11	4799	c.4230G>A	c.(4228-4230)ctG>ctA	p.L1410L	FAM166B_ENST00000492890.1_5'Flank	NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1410						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			CGGACTGGCTGAGCCTGGACA	0.662																																					p.L1410L		.											.	RUSC2-91	0			c.G4230A						.						33	39	37					9																	35560975		2203	4300	6503	SO:0001819	synonymous_variant	9853	exon11			CTGGCTGAGCCTG	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.4230G>A	9.37:g.35560975G>A		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	52	24	NM_014806	0	0	18	32	14	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Silent	SNP	ENST00000455600.1	37	CCDS35008.1																																																																																			.		0.662	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		A	35560975	G	A	35560975	2	1	17	1	0	0	0	0	0	0	0	1	13783	1277	45	2		2	RUSC2	9	35560975	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	2925692	35560975	105652456	41	1428											
TRIM14	9830	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	100862406	100862406	+	Frame_Shift_Del	DEL	A	A	-																															gtagtaatctgagttcagtgAatttccccttcagccaggtt																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:100862406delA	ENST00000341469.2	-	3	353	c.344delT	c.(343-345)ttcfs	p.F115fs	TRIM14_ENST00000375098.3_Frame_Shift_Del_p.F115fs|TRIM14_ENST00000342043.3_Frame_Shift_Del_p.F115fs	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	115					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				GAGTTCAGTGAATTTCCCCTT	0.433																																					p.F115fs	Colon(14;460 597 13826 51781)	.											.	TRIM14-226	0			c.344delT						.						113	105	108					9																	100862406		2203	4300	6503	SO:0001589	frameshift_variant	9830	exon3			.	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"Tripartite motif containing / Tripartite motif containing"	16283	protein-coding gene	gene with protein product		606556	"tripartite motif-containing 14"			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.344delT	9.37:g.100862406delA	ENSP00000344208:p.Phe115fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	111	52	NM_033219	0	0	0	0	0	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Frame_Shift_Del	DEL	ENST00000341469.2	37	CCDS6734.1																																																																																			.		0.433	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788		-	100862406	A	-	100862406	7	5	17	1	0	1	0	1	0	0	0	0	16522	246	9	0	1000	0	TRIM14	9	100862406	Frame_Shift_Del	DEL	A	TCGA-A4-8515-01A-11D-2396-08	65301431	100862406	40351025	42	1429											
GAPVD1	26130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	128117063	128117063	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaatcgatactttaccactGtctgtgtgagattactgctt	9	15	7	10	1	1	1	0	1	1	1	2	3	1	1	2	0	4	1	2	0	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:128117063G>A	ENST00000495955.1	+	24	4044	c.3754G>A	c.(3754-3756)Gtc>Atc	p.V1252I	GAPVD1_ENST00000312123.9_Missense_Mutation_p.V1213I|GAPVD1_ENST00000470056.1_Missense_Mutation_p.V1207I|GAPVD1_ENST00000394083.2_Missense_Mutation_p.V1186I|GAPVD1_ENST00000297933.6_Missense_Mutation_p.V1234I|GAPVD1_ENST00000394104.2_Missense_Mutation_p.V1252I|GAPVD1_ENST00000265956.4_Missense_Mutation_p.V1226I|GAPVD1_ENST00000394105.2_Missense_Mutation_p.V1261I			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1252					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CTTTACCACTGTCTGTGTGAG	0.423																																					p.V1261I		.											.	GAPVD1-93	0			c.G3781A						.						176	176	176					9																	128117063		2203	4300	6503	SO:0001583	missense	26130	exon23			ACCACTGTCTGTG		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.3754G>A	9.37:g.128117063G>A	ENSP00000419063:p.Val1252Ile	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	177	70	NM_015635	0	0	11	20	9	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	G	27.7	4.856083	0.91355	.	.	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.63546	0.2520	L	0.47716	1.5	0.80722	D	1	P;P;P;P;P;P	0.39404	0.542;0.604;0.672;0.672;0.672;0.528	B;B;B;B;B;B	0.42282	0.213;0.205;0.382;0.382;0.382;0.382	T	0.62124	-0.6920	9	0.48119	T	0.1	.	19.6603	0.95864	0.0:0.0:1.0:0.0	.	1252;267;1207;1213;1234;1261	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	I	1207;1261;1252;1226;1186;1252;1234;1213	.	ENSP00000265956:V1226I	V	+	1	0	GAPVD1	127156884	1.000000	0.71417	0.981000	0.43875	0.965000	0.64279	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	GTC	.		0.423	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128117063	G	A	128117063	3	1	17	1	0	0	0	0	1	0	0	0	6259	1377	48	2	3867	2	GAPVD1	9	128117063	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	27254657	128117063	13096368	43	1430											
ARRDC1	92714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	140508526	140508526	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaagaagttctcctacaagCtggtgaagacgggcagcgtg	11	7	13	10	2	1	3	0	1	1	2	2	3	1	3	2	2	3	3	2	2	5	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:140508526C>A	ENST00000371421.4	+	5	542	c.478C>A	c.(478-480)Ctg>Atg	p.L160M	ARRDC1_ENST00000491911.1_3'UTR|C9orf37_ENST00000496793.1_5'Flank	NM_152285.2	NP_689498.1	Q8N5I2	ARRD1_HUMAN	arrestin domain containing 1	160						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000273)|Epithelial(140;0.000464)		CTCCTACAAGCTGGTGAAGAC	0.637																																					p.L160M		.											.	ARRDC1-90	0			c.C478A						.						99	95	96					9																	140508526		2203	4300	6503	SO:0001583	missense	92714	exon5			TACAAGCTGGTGA	AJ420420	CCDS7049.1	9q34.3	2013-10-11			ENSG00000197070	ENSG00000197070			28633	protein-coding gene	gene with protein product	"alpha-arrestin 1"					23886940	Standard	XM_005266119		Approved	MGC40555	uc004cns.3	Q8N5I2	OTTHUMG00000020993	ENST00000371421.4:c.478C>A	9.37:g.140508526C>A	ENSP00000360475:p.Leu160Met	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	183	61	NM_152285	0	0	44	82	38		Missense_Mutation	SNP	ENST00000371421.4	37	CCDS7049.1	.	.	.	.	.	.	.	.	.	.	c	19.88	3.909911	0.72983	.	.	ENSG00000197070	ENST00000371421;ENST00000431925	T;T	0.53206	3.16;0.63	5.47	4.38	0.52667	Immunoglobulin E-set (1);	0.141252	0.49305	D	0.000154	T	0.67411	0.2890	M	0.76838	2.35	0.51767	D	0.999938	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.66756	-0.5843	10	0.36615	T	0.2	-7.9494	14.2819	0.66219	0.0:0.9154:0.0:0.0846	.	49;177;160	Q59FD7;Q5T371;Q8N5I2	.;.;ARRD1_HUMAN	M	160;177	ENSP00000360475:L160M;ENSP00000406247:L177M	ENSP00000360475:L160M	L	+	1	2	ARRDC1	139628347	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.922000	0.40045	2.582000	0.87167	0.555000	0.69702	CTG	.		0.637	ARRDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055358.1	NM_152285		A	140508526	C	A	140508526	3	1	17	1	0	0	0	0	1	0	0	0	983	796	28	4	496	4	ARRDC1	9	140508526	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	12391463	140508526	704905	44	1431											
UNC5B	219699	bcgsc.ca	37	chr10	73050759	73050759	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcctcatggcggtgggggTggtggtgtaccgccgcaact	6	9	16	10	3	1	0	1	0	0	0	2	0	2	0	3	6	2	2	3	6	3	1	rs117156661		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr10:73050759T>G	ENST00000335350.6	+	9	1603	c.1187T>G	c.(1186-1188)gTg>gGg	p.V396G	UNC5B_ENST00000373192.4_Missense_Mutation_p.V385G	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	396					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						GCGGTGGGGGTGGTGGTGTAC	0.627																																					p.V396G													.	UNC5B-228	0			c.T1187G						.						176	172	173					10																	73050759		2203	4300	6503	SO:0001583	missense	219699	exon9			TGGGGGTGGTGGT	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"Immunoglobulin superfamily / I-set domain containing"	12568	protein-coding gene	gene with protein product		607870	"unc5 (C.elegans homolog) b"				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1187T>G	10.37:g.73050759T>G	ENSP00000334329:p.Val396Gly	Somatic	675	46		WXS	Illumina HiSeq	Phase_1	333	147	NM_170744	0	0	0	0	0	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.510623	0.85389	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.55760	0.6;0.5	5.26	5.26	0.73747	.	0.062472	0.64402	D	0.000004	T	0.69557	0.3124	M	0.73217	2.22	0.80722	D	1	D;D	0.76494	0.999;0.998	D;P	0.66351	0.943;0.878	T	0.71364	-0.4615	10	0.46703	T	0.11	-20.6219	15.1633	0.72801	0.0:0.0:0.0:1.0	.	385;396	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	G	396;385	ENSP00000334329:V396G;ENSP00000362288:V385G	ENSP00000334329:V396G	V	+	2	0	UNC5B	72720765	1.000000	0.71417	0.929000	0.37066	0.557000	0.35523	4.283000	0.58977	1.996000	0.58369	0.460000	0.39030	GTG	T|0.999;G|0.001		0.627	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		G	73050759	T	G	73050759	3	3	17	1	0	0	0	0	1	0	0	0	17025	1696	59	5	1221	5	UNC5B	10	73050759	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08		73050759	62483988	45	1432											
GBF1	8729	bcgsc.ca	37	chr10	104120011	104120011	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctcatctccctcaccaaTccacacgaccgccataactc	10	9	2	20	2	3	0	2	0	1	0	7	1	5	0	6	0	1	0	6	0	2	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr10:104120011T>C	ENST00000369983.3	+	12	1508	c.1248T>C	c.(1246-1248)aaT>aaC	p.N416N	GBF1_ENST00000476019.1_Intron	NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	416					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCCTCACCAATCCACACGACC	0.577																																					p.N417N													.	GBF1-91	0			c.T1251C						.						251	250	251					10																	104120011		2203	4300	6503	SO:0001819	synonymous_variant	8729	exon12			CACCAATCCACAC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.1248T>C	10.37:g.104120011T>C		Somatic	633	7		WXS	Illumina HiSeq	Phase_1	397	76	NM_001199378	0	0	16	16	0	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	37	CCDS7533.1																																																																																			.		0.577	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			C	104120011	T	C	104120011	2	2	17	1	0	0	0	0	0	0	0	1	6291	1432	50	3		3	GBF1	10	104120011	Silent	SNP	T	TCGA-A4-8515-01A-11D-2396-08	31069252	104120011	31414736	46	1433											
CDHR5	53841	broad.mit.edu	37	chr11	618807	618807	+	Frame_Shift_Del	DEL	G	G	-																															gaggtgctggttcccatactGgggggcatcggctgagaggt																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:618807delG	ENST00000358353.3	-	14	2074	c.1752delC	c.(1750-1752)cccfs	p.P584fs	IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000330243.5_5'Flank|CDHR5_ENST00000397542.2_Frame_Shift_Del_p.P584fs|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000349570.7_Intron			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	584	4 X 31 AA approximate tandem repeats.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						TTCCCATACTGGGGGGCATCG	0.677																																					p.P584fs													.	CDHR5-90	0			c.1752delC						.						103	110	108					11																	618807		2203	4300	6503	SO:0001589	frameshift_variant	53841	exon13			CATACTGGGGGGC	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1752delC	11.37:g.618807delG	ENSP00000351118:p.Pro584fs	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	254	7	NM_021924	0	0	0	0	0	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Frame_Shift_Del	DEL	ENST00000358353.3	37	CCDS7707.1																																																																																			.		0.677	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		-	618807	G	-	618807	7	5	17	1	0	1	0	1	0	0	0	0	3128	1335	47	0	797	0	CDHR5	11	618807	Frame_Shift_Del	DEL	G	TCGA-A4-8515-01A-11D-2396-08		618807	134387709	47	1434											
NAV2	89797	broad.mit.edu	37	chr11	19954837	19954837	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtacctcctcggccatcccGcagcccggtgcagccaccaa	8	5	9	19	3	0	0	0	0	0	0	3	0	2	0	7	2	4	3	7	2	2	1	rs143560669		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:19954837G>A	ENST00000396087.3	+	8	1215	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	NAV2_ENST00000396085.1_Silent_p.P349P|NAV2_ENST00000540292.1_Silent_p.P303P|NAV2_ENST00000527559.2_Silent_p.P301P|NAV2_ENST00000360655.4_Silent_p.P285P|NAV2_ENST00000349880.4_Silent_p.P349P	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	372					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CGGCCATCCCGCAGCCCGGTG	0.627													G|||	1	0.000199681	0	0	5008	,	,		17564	0		0.001	False		,,,				2504	0				p.P372P													.	NAV2-96	0			c.G1116A						.	G	,,	0,4398		0,0,2199	131	133	132		855,1047,1047	2.6	1	11	dbSNP_134	132	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	0,1,6491	AA,AG,GG		0.0116,0.0,0.0077	,,	285/2366,349/2430,349/2433	19954837	1,12983	2199	4293	6492	SO:0001819	synonymous_variant	89797	exon8			CATCCCGCAGCCC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.1116G>A	11.37:g.19954837G>A		Somatic	435	0		WXS	Illumina HiSeq	Phase_I	430	5	NM_001244963	0	0	2	2	0	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			G|0.999;A|0.000		0.627	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	19954837	G	A	19954837	2	1	17	1	0	0	0	0	0	0	0	1	10209	1074	38	1		1	NAV2	11	19954837	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	19336030	19954837	115051679	48	1435											
FNBP4	23360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47745663	47745663	+	Missense_Mutation	SNP	G	G	T																															ccactgcagtgctaatttctGtagctttcctctttattcct																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:47745663G>T	ENST00000263773.5	-	14	2393	c.2381C>A	c.(2380-2382)aCa>aAa	p.T794K	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	794			T -> A (in dbSNP:rs35040940).			nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						GCTAATTTCTGTAGCTTTCCT	0.428																																					p.T794K		.											.	FNBP4-91	0			c.C2381A						.						132	133	133					11																	47745663		1886	4120	6006	SO:0001583	missense	23360	exon14			ATTTCTGTAGCTT	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.2381C>A	11.37:g.47745663G>T	ENSP00000263773:p.Thr794Lys	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	79	30	NM_015308	0	0	13	13	0	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	37	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.707845	0.48412	.	.	ENSG00000109920	ENST00000263773	T	0.50277	0.75	5.28	5.28	0.74379	.	0.468912	0.23563	N	0.046835	T	0.42337	0.1198	L	0.53249	1.67	0.28016	N	0.934697	B	0.31125	0.309	B	0.25140	0.058	T	0.47749	-0.9093	10	0.56958	D	0.05	-4.17	12.4896	0.55893	0.0803:0.0:0.9197:0.0	.	794	Q8N3X1	FNBP4_HUMAN	K	794	ENSP00000263773:T794K	ENSP00000263773:T794K	T	-	2	0	FNBP4	47702239	0.027000	0.19231	1.000000	0.80357	0.870000	0.49936	2.261000	0.43276	2.483000	0.83821	0.561000	0.74099	ACA	.		0.428	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47745663	G	T	47745663	3	4	17	1	0	0	0	0	1	0	0	0	5986	1377	48	4	688	4	FNBP4	11	47745663	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	27790826	47745663	87260853	49	1436	11	2									
FNBP4	23360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47745665	47745665	+	Silent	SNP	A	A	G																															actgcagtgctaatttctgtAgctttcctctttattccttt																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:47745665A>G	ENST00000263773.5	-	14	2391	c.2379T>C	c.(2377-2379)gcT>gcC	p.A793A	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	793						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						TAATTTCTGTAGCTTTCCTCT	0.428																																					p.A793A		.											.	FNBP4-91	0			c.T2379C						.						131	132	132					11																	47745665		1883	4121	6004	SO:0001819	synonymous_variant	23360	exon14			TTCTGTAGCTTTC	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.2379T>C	11.37:g.47745665A>G		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	75	29	NM_015308	0	0	11	11	0	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	37	CCDS41644.1																																																																																			.		0.428	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			G	47745665	A	G	47745665	2	3	17	1	0	0	0	0	0	0	0	1	5986	407	15	3		3	FNBP4	11	47745665	Silent	SNP	A	TCGA-A4-8515-01A-11D-2396-08	2	47745665	87260851	50	1437	11	2									
PTPRJ	5795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	48142761	48142761	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcatatgtattctccatcActccaggaataggcaatgag	12	12	7	10	0	3	1	2	1	1	0	5	2	4	2	2	2	0	2	2	2	5	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:48142761A>G	ENST00000418331.2	+	4	911	c.559A>G	c.(559-561)Act>Gct	p.T187A	PTPRJ_ENST00000440289.2_Missense_Mutation_p.T187A	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	187	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ATTCTCCATCACTCCAGGAAT	0.428																																					p.T187A		.											.	PTPRJ-541	0			c.A559G						.						129	120	123					11																	48142761		2201	4298	6499	SO:0001583	missense	5795	exon4			TCCATCACTCCAG	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.559A>G	11.37:g.48142761A>G	ENSP00000400010:p.Thr187Ala	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	69	20	NM_001098503	0	0	9	15	6	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.875810	0.33162	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000534219	T;T;T	0.76448	0.49;0.49;-1.02	5.05	0.487	0.16842	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70649	0.3248	L	0.44542	1.39	0.09310	N	1	B;P	0.36086	0.131;0.536	B;B	0.43623	0.068;0.425	T	0.57033	-0.7880	9	0.15066	T	0.55	.	8.4715	0.32988	0.4929:0.0:0.0:0.507	.	187;187	Q12913;Q6P4H4	PTPRJ_HUMAN;.	A	187;187;187;108	ENSP00000400010:T187A;ENSP00000409733:T187A;ENSP00000432686:T108A	ENSP00000278456:T187A	T	+	1	0	PTPRJ	48099337	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.045000	0.14013	0.206000	0.20587	0.482000	0.46254	ACT	.		0.428	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			G	48142761	A	G	48142761	3	3	17	1	0	0	0	0	1	0	0	0	12836	159	6	3	573	3	PTPRJ	11	48142761	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	397096	48142761	86863755	51	1438											
GAB2	9846	bcgsc.ca	37	chr11	77937657	77937657	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgacttggcttgggggggCggggtgggggagctatggct	3	9	22	7	1	0	1	0	1	0	0	0	2	0	2	1	9	1	3	1	9	1	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:77937657C>G	ENST00000361507.4	-	4	1146	c.1061G>C	c.(1060-1062)cGc>cCc	p.R354P	GAB2_ENST00000340149.2_Missense_Mutation_p.R316P|GAB2_ENST00000526030.1_5'Flank	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	354					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			CTTGGGGGGGCGGGGTGGGGG	0.582																																					p.R354P													.	GAB2-663	0			c.G1061C						.						46	52	50					11																	77937657		2200	4292	6492	SO:0001583	missense	9846	exon4			GGGGGGCGGGGTG	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1061G>C	11.37:g.77937657C>G	ENSP00000354952:p.Arg354Pro	Somatic	144	1		WXS	Illumina HiSeq	Phase_1	99	46	NM_080491	0	0	2	2	0	A2RRM2|A6NEW9|A7MD36|O60317	Missense_Mutation	SNP	ENST00000361507.4	37	CCDS8259.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.749568	0.69533	.	.	ENSG00000033327	ENST00000340149;ENST00000361507	T;T	0.33865	1.39;1.39	5.21	5.21	0.72293	.	0.000000	0.85682	U	0.000000	T	0.63803	0.2542	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61237	-0.7103	10	0.25106	T	0.35	-15.5922	19.1199	0.93358	0.0:1.0:0.0:0.0	.	354	Q9UQC2	GAB2_HUMAN	P	316;354	ENSP00000343959:R316P;ENSP00000354952:R354P	ENSP00000343959:R316P	R	-	2	0	GAB2	77615305	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.403000	0.79983	2.598000	0.87819	0.561000	0.74099	CGC	.		0.582	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		G	77937657	C	G	77937657	3	3	17	1	0	0	0	0	1	0	0	0	6168	768	27	4	997	4	GAB2	11	77937657	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	29794896	77937657	57068859	52	1439											
NCAM1	4684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113103986	113103986	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcaaatacaaagctgagtGgagagcagttggtgaagaag	15	7	13	6	0	1	4	1	2	0	2	1	5	1	4	1	2	3	3	1	2	5	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:113103986G>T	ENST00000533760.1	+	12	1855	c.1256G>T	c.(1255-1257)tGg>tTg	p.W419L	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.W546L|NCAM1_ENST00000316851.7_Missense_Mutation_p.W537L	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	547	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AAAGCTGAGTGGAGAGCAGTT	0.532																																					p.W573L		.											.	NCAM1-23	0			c.G1718T						.						78	81	80					11																	113103986		2079	4205	6284	SO:0001583	missense	4684	exon15			CTGAGTGGAGAGC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1256G>T	11.37:g.113103986G>T	ENSP00000473281:p.Trp419Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	42	16	NM_001242607	0	0	0	0	0	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	G	28.8	4.953276	0.92660	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.56103	0.48;0.48	6.06	6.06	0.98353	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.75459	0.3852	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.73808	-0.3866	9	0.49607	T	0.09	-34.0768	20.6208	0.99490	0.0:0.0:1.0:0.0	.	547;537;547;537	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	L	419;546;537	ENSP00000384055:W546L;ENSP00000318472:W537L	ENSP00000318472:W537L	W	+	2	0	NCAM1	112609196	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.476000	0.97823	2.882000	0.98803	0.655000	0.94253	TGG	.		0.532	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		T	113103986	G	T	113103986	3	4	17	1	0	0	0	0	1	0	0	0	10228	1357	47	4	1691	4	NCAM1	11	113103986	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	35166329	113103986	21902530	53	1440											
CADM1	23705	bcgsc.ca	37	chr11	115049423	115049423	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagcatggcgaacaccAccaccgccacgacgccaccg	12	1	9	19	5	0	0	0	0	0	0	0	2	0	0	6	1	3	2	6	1	1	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:115049423A>C	ENST00000452722.3	-	9	1171	c.1151T>G	c.(1150-1152)gTg>gGg	p.V384G	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000542447.2_Missense_Mutation_p.V356G|CADM1_ENST00000331581.6_Missense_Mutation_p.V413G|CADM1_ENST00000536727.1_Missense_Mutation_p.V385G|CADM1_ENST00000537058.1_Missense_Mutation_p.V395G	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		GGCGAACACCACCACCGCCAC	0.532																																					p.V384G													.	CADM1-92	0			c.T1151G						.						129	113	118					11																	115049423		2201	4296	6497	SO:0001583	missense	23705	exon9			AACACCACCACCG	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5951	protein-coding gene	gene with protein product	"nectin-like 2"	605686	"tumor suppressor in lung cancer 1", "immunoglobulin superfamily, member 4"	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.1151T>G	11.37:g.115049423A>C	ENSP00000395359:p.Val384Gly	Somatic	264	8		WXS	Illumina HiSeq	Phase_1	114	38	NM_014333	1	0	35	36	0		Missense_Mutation	SNP	ENST00000452722.3	37	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531606	0.64972	.	.	ENSG00000182985	ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581;ENST00000541325	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000001	D	0.83110	0.5183	M	0.84846	2.72	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.998	D;D;D;D	0.91635	0.999;0.991;0.979;0.981	D	0.86298	0.1678	10	0.87932	D	0	.	14.8691	0.70441	1.0:0.0:0.0:0.0	.	395;357;384;356	F5H0J4;A4FVB5;Q9BY67;A0A4Z1	.;.;CADM1_HUMAN;.	G	356;384;395;385;315;413;69	ENSP00000439176:V356G;ENSP00000395359:V384G;ENSP00000439817:V395G;ENSP00000440322:V385G;ENSP00000329797:V413G	ENSP00000329797:V413G	V	-	2	0	CADM1	114554633	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.761000	0.91691	2.115000	0.64714	0.533000	0.62120	GTG	.		0.532	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		C	115049423	A	C	115049423	3	2	17	1	0	0	0	0	1	0	0	0	2572	159	6	5	185	5	CADM1	11	115049423	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	1945437	115049423	19957093	54	1441											
CEP164	22897	bcgsc.ca	37	chr11	117280516	117280516	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaccctaagagcacccccAcccccacctactatggctcc	9	5	7	20	0	0	1	0	0	0	1	1	2	1	2	7	2	2	2	7	2	3	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:117280516A>C	ENST00000278935.3	+	30	4078	c.3931A>C	c.(3931-3933)Acc>Ccc	p.T1311P	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1311					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GAGCACCCCCACCCCCACCTA	0.662																																					p.T1311P													.	CEP164-69	0			c.A3931C						.						93	97	96					11																	117280516		2201	4296	6497	SO:0001583	missense	22897	exon30			ACCCCCACCCCCA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.3931A>C	11.37:g.117280516A>C	ENSP00000278935:p.Thr1311Pro	Somatic	408	7		WXS	Illumina HiSeq	Phase_1	231	44	NM_014956	0	0	8	8	0	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	9.089	1.001310	0.19121	.	.	ENSG00000110274	ENST00000278935	T	0.23950	1.88	4.19	-2.4	0.06583	.	2.488380	0.01670	N	0.025578	T	0.19565	0.0470	L	0.36672	1.1	0.09310	N	1	P;P	0.35982	0.531;0.531	B;B	0.34779	0.189;0.189	T	0.14559	-1.0468	10	0.34782	T	0.22	8.6364	5.5918	0.17305	0.342:0.0:0.4794:0.1786	.	1311;1306	Q9UPV0;Q9UPV0-2	CE164_HUMAN;.	P	1311	ENSP00000278935:T1311P	ENSP00000278935:T1311P	T	+	1	0	CEP164	116785726	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-1.319000	0.02702	-0.488000	0.06726	0.402000	0.26972	ACC	.		0.662	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		C	117280516	A	C	117280516	3	2	17	1	0	0	0	0	1	0	0	0	3255	159	6	5	4041	5	CEP164	11	117280516	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	2231093	117280516	17726000	55	1442											
PUS3	83480	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	125765906	125765922	+	Frame_Shift_Del	DEL	TCTCTTCAATGGTATTA	TCTCTTCAATGGTATTA	-																															ggttagagcttcaaacagttTctcttcaatggtattatttg																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	TCTCTTCAATGGTATTA	TCTCTTCAATGGTATTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:125765906_125765922delTCTCTTCAATGGTATTA	ENST00000530811.1	-	1	303_319	c.258_274delTAATACCATTGAAGAGA	c.(256-276)aataataccattgaagagaaafs	p.NNTIEE86fs	PUS3_ENST00000227474.3_Frame_Shift_Del_p.NNTIEE86fs|HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000425380.2_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	86					tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		TCAAACAGTTTCTCTTCAATGGTATTATTTGTGTTTT	0.447																																					p.86_92del		.											.	PUS3-91	0			c.258_274del						.																																			SO:0001589	frameshift_variant	83480	exon2			.	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.258_274delTAATACCATTGAAGAGA	11.37:g.125765906_125765922delTCTCTTCAATGGTATTA	ENSP00000432386:p.Asn86fs	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	194	60	NM_031307	0	0	0	0	0	B2RAM0|Q96D17|Q96J23|Q96NB4	Frame_Shift_Del	DEL	ENST00000530811.1	37	CCDS8466.1																																																																																			.		0.447	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307		-	125765922	TCTCTTCAATGGTATTA	-	125765906	7	5	17	1	0	1	0	1	0	0	0	0	12864	1792	62	0	1183	0	PUS3	11	125765906	Frame_Shift_Del	DEL	TCTCTTCAATGGTATTA	TCGA-A4-8515-01A-11D-2396-08	8485390	125765906	9240610	56	1443											
LAG3	3902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6886460	6886460	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atcctttgggtcacctggatCcctggggaagctgctttgtg	5	13	13	10	0	1	0	1	0	0	0	3	2	3	2	3	4	2	2	3	4	1	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:6886460C>G	ENST00000203629.2	+	6	1421	c.1088C>G	c.(1087-1089)tCc>tGc	p.S363C		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	363	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TCACCTGGATCCCTGGGGAAG	0.517																																					p.S363C		.											.	LAG3-90	0			c.C1088G						.						112	111	111					12																	6886460		2203	4300	6503	SO:0001583	missense	3902	exon6			CTGGATCCCTGGG		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1088C>G	12.37:g.6886460C>G	ENSP00000203629:p.Ser363Cys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	158	67	NM_002286	0	0	0	0	0	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658513	0.47467	.	.	ENSG00000089692	ENST00000203629	T	0.15603	2.41	4.55	1.61	0.23674	.	0.653989	0.15030	N	0.284515	T	0.18509	0.0444	L	0.27053	0.805	0.19300	N	0.999976	D	0.71674	0.998	P	0.57371	0.819	T	0.10800	-1.0614	10	0.36615	T	0.2	-8.8465	6.2866	0.21037	0.2301:0.4544:0.3155:0.0	.	363	P18627	LAG3_HUMAN	C	363	ENSP00000203629:S363C	ENSP00000203629:S363C	S	+	2	0	LAG3	6756721	0.507000	0.26146	0.578000	0.28575	0.907000	0.53573	0.505000	0.22642	0.136000	0.18733	0.561000	0.74099	TCC	.		0.517	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			G	6886460	C	G	6886460	3	3	17	1	0	0	0	0	1	0	0	0	8621	855	30	4	1110	4	LAG3	12	6886460	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08		6886460	126965435	57	1444											
PRB4	5545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	11461501	11461501	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggtggtctttctggctttCctggaggaggtgggggacgg	3	11	21	6	1	2	0	0	0	2	0	3	3	3	3	1	10	0	1	1	10	0	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:11461501C>A	ENST00000535904.1	-	3	449	c.416G>T	c.(415-417)gGa>gTa	p.G139V	PRB4_ENST00000445719.2_Intron|PRB4_ENST00000279575.1_Missense_Mutation_p.G139V			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	160	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).			extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TTCTGGCTTTCCTGGAGGAGG	0.602										HNSCC(22;0.051)																											p.G139V		.											.	PRB4-91	0			c.G416T						.						176	197	190					12																	11461501		2202	4300	6502	SO:0001583	missense	5545	exon3			GGCTTTCCTGGAG		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.416G>T	12.37:g.11461501C>A	ENSP00000442834:p.Gly139Val	Somatic	531	0		WXS	Illumina HiSeq	Phase_I	566	232	NM_002723	0	0	0	0	0	A1L439|O00600|P02813|P10161|P10162|P81489	Missense_Mutation	SNP	ENST00000535904.1	37	CCDS8641.1	.	.	.	.	.	.	.	.	.	.	.	5.316	0.243693	0.10077	.	.	ENSG00000230657	ENST00000279575;ENST00000535904	T;T	0.08546	3.08;3.08	0.849	0.849	0.18972	.	.	.	.	.	T	0.22437	0.0541	M	0.78456	2.415	0.09310	N	0.999999	D	0.89917	1.0	D	0.66979	0.948	T	0.05178	-1.0901	9	0.87932	D	0	.	5.0427	0.14467	0.0:1.0:0.0:0.0	.	139	E9PAL0	.	V	139	ENSP00000279575:G139V;ENSP00000442834:G139V	ENSP00000279575:G139V	G	-	2	0	PRB4	11352768	0.002000	0.14202	0.003000	0.11579	0.004000	0.04260	0.087000	0.14958	0.744000	0.32741	0.502000	0.49764	GGA	.		0.602	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		A	11461501	C	A	11461501	3	1	17	1	0	0	0	0	1	0	0	0	12474	855	30	4	331	4	PRB4	12	11461501	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	4575041	11461501	122390394	58	1445											
KRR1	11103	hgsc.bcm.edu	37	chr12	75900389	75900560	+	Splice_Site	DEL	CCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	CCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	-																															atcctgaagaattcgtactgCcttttgcaaaaaaaaaaaaa																								rs35071517|rs371478640|rs200776725|rs140710432|rs201846221|rs562964328|rs398020160|rs201412928	byFrequency	TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	CCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	CCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:75900389_75900560delCCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	ENST00000229214.4	-	4	417	c.394delTAAATCTAGAATTACAGAGACTTTGCTTTGTTTGCATCAGTGTTAACCTATAACATCCCACCATCAAGTTTTCATATTTGTGCTTAGGTAACAATAGCGTGGGCCTGGAAAATGAATGTAATTGTAAAAAATGTTGATAATGTCTTCTTTTTTTTTTTTTTTTTGCAAAAGG	c.(394-396)taa>aa	p.*132fs	KRR1_ENST00000438169.2_Splice_Site_p.*132fs	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	132					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						ATTCGTACTGCCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTACCTGTTCAAA	0.331																																					p.132_132del		.											.	KRR1-92	0			c.394_394del						.																																			SO:0001630	splice_region_variant	11103	exon4			.	U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"HIV-1 rev binding protein 2", "HIV-1 Rev binding protein 2"	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.394-1TAAATCTAGAATTACAGAGACTTTGCTTTGTTTGCATCAGTGTTAACCTATAACATCCCACCATCAAGTTTTCATATTTGTGCTTAGGTAACAATAGCGTGGGCCTGGAAAATGAATGTAATTGTAAAAAATGTTGATAATGTCTTCTTTTTTTTTTTTTTTTTGCAAAAGG>-	12.37:g.75900389_75900560delCCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	117	20	NM_007043	0	0	0	0	0	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Frame_Shift_Del	DEL	ENST00000229214.4	37	CCDS9012.1																																																																																			.		0.331	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043	Frame_Shift_Del	-	75900560	CCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	-	75900389	8	5	17	1	0	1	0	1	0	0	1	0	8467	753	26	0	779	0	KRR1	12	75900389	Splice_Site	DEL	CCTTTTGCAAAAAAAAAAAAAAAAAGAAGACATTATCAACATTTTTTACAATTACATTCATTTTCCAGGCCCACGCTATTGTTACCTAAGCACAAATATGAAAACTTGATGGTGGGATGTTATAGGTTAACACTGATGCAAACAAAGCAAAGTCTCTGTAATTCTAGATTTA	TCGA-A4-8515-01A-11D-2396-08	64438888	75900389	57951506	59	1446											
TMTC2	160335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	83290130	83290130	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggagaacattgttgttctGtctttatctttgttaatcat	9	19	7	6	1	4	1	1	0	3	1	4	2	4	1	0	1	1	3	0	1	3	7			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:83290130G>A	ENST00000321196.3	+	3	1895	c.1188G>A	c.(1186-1188)ctG>ctA	p.L396L	TMTC2_ENST00000549919.1_Silent_p.L390L|TMTC2_ENST00000548305.1_Silent_p.L396L	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	396					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TTGTTGTTCTGTCTTTATCTT	0.393																																					p.L396L		.											.	TMTC2-92	0			c.G1188A						.						191	193	192					12																	83290130		2203	4300	6503	SO:0001819	synonymous_variant	160335	exon3			TGTTCTGTCTTTA	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1188G>A	12.37:g.83290130G>A		Somatic	214	0		WXS	Illumina HiSeq	Phase_I	208	96	NM_152588	0	0	18	32	14	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	37	CCDS9025.1																																																																																			.		0.393	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		A	83290130	G	A	83290130	2	1	17	1	0	0	0	0	0	0	0	1	16293	1364	48	2		2	TMTC2	12	83290130	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	7389741	83290130	50561765	60	1447											
BTG1	694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	92537939	92537939	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccttacagctgattcggcTgtctaccatttgcacgttgg	6	14	9	12	2	1	1	0	1	1	0	3	1	2	1	2	2	4	4	2	2	2	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:92537939T>C	ENST00000256015.3	-	2	794	c.433A>G	c.(433-435)Agc>Ggc	p.S145G	C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000549802.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	145					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CTGATTCGGCTGTCTACCATT	0.473			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S145G		.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1-683	0			c.A433G						.						109	92	98					12																	92537939		2203	4300	6503	SO:0001583	missense	694	exon2			TTCGGCTGTCTAC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.433A>G	12.37:g.92537939T>C	ENSP00000256015:p.Ser145Gly	Somatic	117	0	1291	WXS	Illumina HiSeq	Phase_I	116	56	NM_001731	0	0	90	174	84	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	T	6.001	0.368520	0.11352	.	.	ENSG00000133639	ENST00000256015;ENST00000552315	T;T	0.34275	1.79;1.37	5.8	5.8	0.92144	.	0.037276	0.85682	D	0.000000	T	0.31734	0.0806	L	0.36672	1.1	0.80722	D	1	B	0.12630	0.006	B	0.15484	0.013	T	0.04203	-1.0969	10	0.33141	T	0.24	-7.3735	16.1508	0.81622	0.0:0.0:0.0:1.0	.	145	P62324	BTG1_HUMAN	G	145;70	ENSP00000256015:S145G;ENSP00000447551:S70G	ENSP00000256015:S145G	S	-	1	0	BTG1	91062070	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.649000	0.83500	2.207000	0.71202	0.528000	0.53228	AGC	.		0.473	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			C	92537939	T	C	92537939	3	2	17	1	0	0	0	0	1	0	0	0	1556	1580	55	3	86	3	BTG1	12	92537939	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	9247809	92537939	41313956	61	1448											
TMCC3	57458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	94976205	94976205	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtctgcagtgagtttgaccTtgtggaagtccaggatgcca	8	12	13	8	0	1	2	0	2	1	0	2	4	2	4	3	2	2	2	3	2	1	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:94976205T>A	ENST00000261226.4	-	2	319	c.188A>T	c.(187-189)aAg>aTg	p.K63M	TMCC3_ENST00000551457.1_Missense_Mutation_p.K32M	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	63						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GAGTTTGACCTTGTGGAAGTC	0.483																																					p.K63M		.											.	TMCC3-92	0			c.A188T						.						150	147	148					12																	94976205		2203	4300	6503	SO:0001583	missense	57458	exon2			TTGACCTTGTGGA	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.188A>T	12.37:g.94976205T>A	ENSP00000261226:p.Lys63Met	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	146	62	NM_020698	0	0	6	11	5	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	37	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457648	0.63401	.	.	ENSG00000057704	ENST00000261226;ENST00000551457;ENST00000548918	T;T	0.51574	1.34;0.7	5.91	5.91	0.95273	.	0.099394	0.64402	D	0.000002	T	0.67211	0.2869	M	0.61703	1.905	0.46203	D	0.998924	D	0.89917	1.0	D	0.91635	0.999	T	0.69555	-0.5114	10	0.72032	D	0.01	-45.39	16.3889	0.83525	0.0:0.0:0.0:1.0	.	63	Q9ULS5	TMCC3_HUMAN	M	63;32;32	ENSP00000261226:K63M;ENSP00000449888:K32M	ENSP00000261226:K63M	K	-	2	0	TMCC3	93500336	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	0.917000	0.28665	2.276000	0.75962	0.397000	0.26171	AAG	.		0.483	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		A	94976205	T	A	94976205	3	1	17	1	0	0	0	0	1	0	0	0	16026	1609	56	5	1257	5	TMCC3	12	94976205	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	2438266	94976205	38875690	62	1449											
ABCC4	10257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	95886864	95886865	+	Splice_Site	DNP	CT	CT	AG																															taatgctgaatgtcacttacCttccgataaatcatatggca																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr13:95886864_95886865CT>AG	ENST00000376887.4	-	4	644_645	c.530_531AG>CT	c.(529-531)aAG>aCT	p.K177T	ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000412704.1_Splice_Site_p.K177T|ABCC4_ENST00000536256.1_Intron|ABCC4_ENST00000431522.1_Splice_Site_p.K177T	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	177	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	TGTCACTTACCTTCCGATAAAT	0.391																																					p.K177T		.											.	ABCC4	0			c.A530C						.																																			SO:0001630	splice_region_variant	10257	exon4			CTTACCTTCCGAT	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.530_531delinsAG	13.37:g.95886864_95886865delinsAG		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	47	20		0	0	0	0	0	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	DNP	ENST00000376887.4	37	CCDS9474.1																																																																																			.		0.391	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	Missense_Mutation	AG	95886865	CT	AG	95886864	5	1	17	1	0	0	0	0	0	0	1	0	55	695	24	4	3607	4	ABCC4	13	95886864	Splice_Site	DNP	CT	TCGA-A4-8515-01A-11D-2396-08		95886864	19283014	63	1450											
TMCO3	55002	bcgsc.ca	37	chr13	114188424	114188425	+	In_Frame_Ins	INS	-	-	TTTTTTTTTTTT																															tcttttttcactagcggcggINStttttcttttatgtcttgtt																								rs141899812		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr13:114188424_114188425insTTTTTTTTTTTT	ENST00000434316.2	+	9	1767_1768	c.1408_1409insTTTTTTTTTTTT	c.(1408-1410)gtt>gTTTTTTTTTTTTtt	p.470_471insFFFF	TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	470						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			ACTAGCGGCGGTTTTTCTTTTA	0.406																																					p.V470delinsVFFFF													.	TMCO3-90	0			c.1408_1409insTTTTTTTTTTTT						.																																			SO:0001652	inframe_insertion	55002	exon9			GCGGCGGTTTTTC	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 11"	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	Exception_encountered	13.37:g.114188424_114188425insTTTTTTTTTTTT	ENSP00000389399:p.Val470_Phe471insPhePhePhePhe	Somatic	117	0		WXS	Illumina HiSeq	Phase_1	123	9	NM_017905	0	0	0	0	0	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	In_Frame_Ins	INS	ENST00000434316.2	37	CCDS9537.1																																																																																			.		0.406	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905		TTTTTTTTTTTT	114188425	-	TTTTTTTTTTTT	114188424	7	5	17	1	0	1	1	0	0	0	0	0	16029	1261	44	0	1438	0	TMCO3	13	114188424	In_Frame_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	18301560	114188424	981454	64	1451											
DENND4A	10260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	66031104	66031104	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggcagagggtatttgctAtttgatggccaacattcaat	12	12	10	7	0	1	2	1	1	0	1	1	2	1	2	1	3	2	3	1	3	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr15:66031104A>G	ENST00000431932.2	-	6	949	c.741T>C	c.(739-741)aaT>aaC	p.N247N	DENND4A_ENST00000443035.3_Silent_p.N247N	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	247	UDENN.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GGTATTTGCTATTTGATGGCC	0.363																																					p.N247N		.											.	DENND4A-229	0			c.T741C						.						117	113	114					15																	66031104		1819	4084	5903	SO:0001819	synonymous_variant	10260	exon6			TTTGCTATTTGAT	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.741T>C	15.37:g.66031104A>G		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	122	49	NM_001144823	0	0	1	3	2	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			.		0.363	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		G	66031104	A	G	66031104	2	3	17	1	0	0	0	0	0	0	0	1	4444	446	16	3		3	DENND4A	15	66031104	Silent	SNP	A	TCGA-A4-8515-01A-11D-2396-08		66031104	36500288	65	1452											
SENP8	123228	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	72432229	72432229	+	Frame_Shift_Del	DEL	G	G	-																															acaagagagttgtatttttaGccatcaatgataactccaac																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr15:72432229delG	ENST00000542035.2	+	2	598	c.265delG	c.(265-267)gccfs	p.A89fs	SENP8_ENST00000544411.1_Frame_Shift_Del_p.A89fs|RP11-2I17.4_ENST00000568984.1_RNA|SENP8_ENST00000544171.1_Frame_Shift_Del_p.A89fs|SENP8_ENST00000340912.4_Frame_Shift_Del_p.A89fs	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	89	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						TGTATTTTTAGCCATCAATGA	0.448																																					p.A89fs		.											.	SENP8-660	0			c.265delG						.						100	99	99					15																	72432229		2199	4297	6496	SO:0001589	frameshift_variant	123228	exon2			.	BC031411	CCDS10240.1	15q22.33	2005-08-17	2005-08-17	2004-01-30	ENSG00000166192	ENSG00000166192			22992	protein-coding gene	gene with protein product	"NEDD8-specific protease 1", "sentrin/SUMO-specific protease SENP8", "deneddylase 1"	608659	"protease, cysteine, 2 (NEDD8 specific)", "SUMO/sentrin specific protease family member 8"	PRSC2		12730221, 12759362	Standard	NM_145204		Approved	NEDP1, DEN1, HsT17512	uc021spt.1	Q96LD8	OTTHUMG00000133441	ENST00000542035.2:c.265delG	15.37:g.72432229delG	ENSP00000446057:p.Ala89fs	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	114	53	NM_001166340	0	0	0	0	0	Q96QA4	Frame_Shift_Del	DEL	ENST00000542035.2	37	CCDS10240.1																																																																																			.		0.448	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204		-	72432229	G	-	72432229	7	5	17	1	0	1	0	1	0	0	0	0	14084	971	34	0	267	0	SENP8	15	72432229	Frame_Shift_Del	DEL	G	TCGA-A4-8515-01A-11D-2396-08	6401125	72432229	30099163	66	1453											
C15orf59	388135	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	74032301	74032301	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctagtggctgtgtagggcAgaaccgtctgcgtgctcttg	5	12	15	9	2	3	1	0	0	3	1	3	1	3	1	1	2	3	4	1	2	3	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr15:74032301A>T	ENST00000569673.1	-	3	2043	c.839T>A	c.(838-840)cTg>cAg	p.L280Q	C15orf59_ENST00000379822.4_Missense_Mutation_p.L280Q|C15orf59_ENST00000558834.1_5'UTR			Q2T9L4	CO059_HUMAN	chromosome 15 open reading frame 59	280										breast(1)|endometrium(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGTGTAGGGCAGAACCGTCTG	0.572																																					p.L280Q		.											.	C15orf59-91	0			c.T839A						.						92	99	97					15																	74032301		2198	4297	6495	SO:0001583	missense	388135	exon2			TAGGGCAGAACCG		CCDS32289.1	15q24.1	2012-09-27			ENSG00000205363	ENSG00000205363			33753	protein-coding gene	gene with protein product							Standard	XM_005254369		Approved	MGC131524, LOC388135	uc002avy.3	Q2T9L4	OTTHUMG00000172556	ENST00000569673.1:c.839T>A	15.37:g.74032301A>T	ENSP00000457205:p.Leu280Gln	Somatic	250	0		WXS	Illumina HiSeq	Phase_I	163	72	NM_001039614	0	0	10	18	8		Missense_Mutation	SNP	ENST00000569673.1	37	CCDS32289.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207083	0.79127	.	.	ENSG00000205363	ENST00000379822	T	0.57907	0.37	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000003	T	0.67933	0.2946	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71434	-0.4594	10	0.87932	D	0	.	14.5288	0.67909	1.0:0.0:0.0:0.0	.	280	Q2T9L4	CO059_HUMAN	Q	280	ENSP00000369150:L280Q	ENSP00000369150:L280Q	L	-	2	0	C15orf59	71819354	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	8.572000	0.90756	1.906000	0.55180	0.459000	0.35465	CTG	.		0.572	C15orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419077.2	NM_001039614		T	74032301	A	T	74032301	3	4	17	1	0	0	0	0	1	0	0	0	1811	188	7	5	46	5	C15orf59	15	74032301	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	1600072	74032301	28499091	67	1454											
ACSM1	116285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20682868	20682868	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctaccttcctgggaaggagGgttgtaaggccaacccatgg	9	8	13	11	0	0	0	0	0	0	0	1	2	1	2	5	5	2	2	5	5	4	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr16:20682868G>T	ENST00000307493.4	-	4	804	c.737C>A	c.(736-738)cCc>cAc	p.P246H	ACSM1_ENST00000520010.1_Missense_Mutation_p.P246H|ACSM1_ENST00000219151.4_5'UTR	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	246					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						TGGGAAGGAGGGTTGTAAGGC	0.527																																					p.P246H		.											.	ACSM1-91	0			c.C737A						.						99	83	89					16																	20682868		2201	4300	6501	SO:0001583	missense	116285	exon4			AAGGAGGGTTGTA	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.737C>A	16.37:g.20682868G>T	ENSP00000301956:p.Pro246His	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	111	36	NM_052956	0	0	37	45	8	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	37	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	G	2.027	-0.423437	0.04734	.	.	ENSG00000166743	ENST00000307493;ENST00000520010	T;T	0.47177	0.85;0.85	4.95	1.81	0.25067	AMP-dependent synthetase/ligase (1);	1.028510	0.07746	N	0.947678	T	0.28300	0.0699	N	0.12471	0.22	0.09310	N	0.999995	B	0.06786	0.001	B	0.08055	0.003	T	0.22556	-1.0213	10	0.45353	T	0.12	.	5.2282	0.15406	0.0815:0.1431:0.6274:0.148	.	246	Q08AH1	ACSM1_HUMAN	H	246	ENSP00000301956:P246H;ENSP00000428047:P246H	ENSP00000301956:P246H	P	-	2	0	ACSM1	20590369	0.351000	0.24887	0.000000	0.03702	0.001000	0.01503	3.098000	0.50259	0.238000	0.21222	0.603000	0.83216	CCC	.		0.527	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		T	20682868	G	T	20682868	3	4	17	1	0	0	0	0	1	0	0	0	182	1232	43	4	1036	4	ACSM1	16	20682868	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08		20682868	69671885	68	1455											
APOB48R	55911	hgsc.bcm.edu	37	chr16	28507273	28507273	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaggaagccaggacaaTctcaggcggggaggaggctg	10	4	20	7	1	1	0	1	0	1	0	2	5	1	5	1	9	1	1	1	9	2	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr16:28507273T>C	ENST00000431282.1	+	2	921	c.911T>C	c.(910-912)aTc>aCc	p.I304T	APOBR_ENST00000328423.5_Missense_Mutation_p.I304T|CLN3_ENST00000569430.1_5'Flank|CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000564831.1_Missense_Mutation_p.I304T			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	304	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GCCAGGACAATCTCAGGCGGG	0.652																																					p.I304T		.											.	APOBR-90	0			c.T911C						.						25	27	27					16																	28507273		1953	4120	6073	SO:0001583	missense	55911	exon2			GGACAATCTCAGG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.911T>C	16.37:g.28507273T>C	ENSP00000416094:p.Ile304Thr	Somatic	53	1		WXS	Illumina HiSeq	Phase_I	68	5	NM_018690	0	0	0	0	0	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	T	7.813	0.716146	0.15306	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.60920	0.15;0.15	3.64	-0.321	0.12717	.	.	.	.	.	T	0.31765	0.0807	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.16217	-1.0410	9	0.14252	T	0.57	.	1.54	0.02553	0.1605:0.4546:0.1586:0.2263	.	295	Q9NS13	.	T	304	ENSP00000327669:I304T;ENSP00000416094:I304T	ENSP00000327669:I304T	I	+	2	0	APOBR	28414774	0.000000	0.05858	0.000000	0.03702	0.239000	0.25481	0.243000	0.18106	0.149000	0.19098	-0.320000	0.08662	ATC	.		0.652	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		C	28507273	T	C	28507273	3	2	17	1	0	0	0	0	1	0	0	0	786	1435	50	3	917	3	APOB48R	16	28507273	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	7824405	28507273	61847480	69	1456											
AP1G1	164	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	71768532	71768533	+	Frame_Shift_Ins	INS	-	-	A																															ttctgagggttcagaactttINSaatgacttgtgtgatggtcc																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr16:71768532_71768533insA	ENST00000299980.4	-	22	2787_2788	c.2346_2347insT	c.(2344-2349)attaaafs	p.K783fs	AP1G1_ENST00000393512.3_Frame_Shift_Ins_p.K786fs|AP1G1_ENST00000569748.1_Frame_Shift_Ins_p.K783fs|AP1G1_ENST00000433195.2_Frame_Shift_Ins_p.K806fs|AP1G1_ENST00000423132.2_Frame_Shift_Ins_p.K786fs|AP1G1_ENST00000564155.1_Frame_Shift_Ins_p.K208fs	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	783	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TTCAGAACTTTAATGACTTGTG	0.45																																					p.K786_V787delinsX		.											.	AP1G1-92	0			c.2356_2357insT						.																																			SO:0001589	frameshift_variant	164	exon23			.	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2347dupT	16.37:g.71768534_71768534dupA	ENSP00000299980:p.Lys783fs	Somatic	376	0		WXS	Illumina HiSeq	Phase_I	657	369	NM_001030007	0	0	0	0	0	O75709|O75842|Q9UG09|Q9Y3U4	Nonsense_Mutation	INS	ENST00000299980.4	37	CCDS32480.1																																																																																			.		0.45	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71768533	-	A	71768532	7	5	17	1	0	1	1	0	0	0	0	0	732	1763	61	0	129	0	AP1G1	16	71768532	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	43261259	71768532	18586221	70	1457											
WDR81	124997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	1633711	1633711	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtccgctggctgtctgccaaGctcggccccacagtggcctc	4	8	12	17	2	1	0	0	0	1	0	4	0	2	0	5	3	2	3	5	3	1	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:1633711G>A	ENST00000409644.1	+	2	3705	c.3705G>A	c.(3703-3705)aaG>aaA	p.K1235K	WDR81_ENST00000446363.1_Intron|WDR81_ENST00000437219.2_Silent_p.K32K|WDR81_ENST00000419248.1_Silent_p.K8K|WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000309182.5_Silent_p.K184K|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1235					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGTCTGCCAAGCTCGGCCCCA	0.642																																					p.K1235K		.											.	WDR81-91	0			c.G3705A						.						33	31	32					17																	1633711		2203	4299	6502	SO:0001819	synonymous_variant	124997	exon2			TGCCAAGCTCGGC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3705G>A	17.37:g.1633711G>A		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	69	15	NM_001163809	0	0	9	11	2	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			.		0.642	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		A	1633711	G	A	1633711	2	1	17	1	0	0	0	0	0	0	0	1	17363	962	34	2		2	WDR81	17	1633711	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08		1633711	79561499	71	1458											
ZZEF1	23140	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	3924472	3924472	+	Frame_Shift_Del	DEL	T	T	-																															ggccctcaagggggtccagcTttttctgctctgggtcgcca																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:3924472delT	ENST00000381638.2	-	45	7479	c.7355delA	c.(7354-7356)aagfs	p.K2452fs		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2452							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GGGGTCCAGCTTTTTCTGCTC	0.582																																					p.K2452fs		.											.	ZZEF1-93	0			c.7355delA						.						113	109	110					17																	3924472		2203	4300	6503	SO:0001589	frameshift_variant	23140	exon45			.	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.7355delA	17.37:g.3924472delT	ENSP00000371051:p.Lys2452fs	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	375	106	NM_015113	0	0	0	0	0	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Frame_Shift_Del	DEL	ENST00000381638.2	37	CCDS11043.1																																																																																			.		0.582	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		-	3924472	T	-	3924472	7	5	17	1	0	1	0	1	0	0	0	0	18287	1609	56	0	1574	0	ZZEF1	17	3924472	Frame_Shift_Del	DEL	T	TCGA-A4-8515-01A-11D-2396-08	2290761	3924472	77270738	72	1459											
MYBBP1A	10514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4445915	4445915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccccaacactcaccgggTgccgggagaagaggctgagg	10	3	16	12	2	1	3	1	1	0	2	1	4	1	3	4	5	2	1	4	5	2	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:4445915T>C	ENST00000254718.4	-	21	3320	c.3014A>G	c.(3013-3015)cAc>cGc	p.H1005R	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.H1005R			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1005					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						ACTCACCGGGTGCCGGGAGAA	0.627																																					p.H1005R		.											.	MYBBP1A-92	0			c.A3014G						.						99	98	98					17																	4445915		2203	4300	6503	SO:0001583	missense	10514	exon21			ACCGGGTGCCGGG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3014A>G	17.37:g.4445915T>C	ENSP00000254718:p.His1005Arg	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	189	115	NM_014520	0	0	0	0	0	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.527626	0.64860	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.19532	2.14;2.14	5.53	4.44	0.53790	Armadillo-type fold (1);	0.481948	0.24846	N	0.035136	T	0.23965	0.0580	L	0.54323	1.7	0.25888	N	0.9835	P;P	0.47106	0.824;0.89	B;P	0.46796	0.327;0.527	T	0.07309	-1.0779	10	0.26408	T	0.33	-19.5303	8.7411	0.34558	0.1687:0.0:0.0:0.8313	.	1005;1005	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	R	1005	ENSP00000370968:H1005R;ENSP00000254718:H1005R	ENSP00000254718:H1005R	H	-	2	0	MYBBP1A	4392664	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	3.604000	0.54081	0.910000	0.36722	0.533000	0.62120	CAC	.		0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		C	4445915	T	C	4445915	3	2	17	1	0	0	0	0	1	0	0	0	10033	1696	59	3	1036	3	MYBBP1A	17	4445915	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	521443	4445915	76749295	73	1460											
ALOX15B	247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7948982	7948982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggctaccctgcgtcagctgcCccactgccaccctctcttca	5	9	7	20	1	3	0	2	0	1	0	4	0	3	0	5	1	5	2	5	1	1	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:7948982C>T	ENST00000380183.4	+	8	1317	c.1178C>T	c.(1177-1179)cCc>cTc	p.P393L	ALOX15B_ENST00000572022.1_Missense_Mutation_p.P393L|ALOX15B_ENST00000380173.2_Missense_Mutation_p.P393L|ALOX15B_ENST00000573359.1_Missense_Mutation_p.P393L	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	393	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						CGTCAGCTGCCCCACTGCCAC	0.612																																					p.P393L		.											.	ALOX15B-227	0			c.C1178T						.						66	51	56					17																	7948982		2203	4300	6503	SO:0001583	missense	247	exon8			AGCTGCCCCACTG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"Arachidonate lipoxygenases"	434	protein-coding gene	gene with protein product		603697	"arachidonate 15-lipoxygenase, second type"			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1178C>T	17.37:g.7948982C>T	ENSP00000369530:p.Pro393Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	78	38	NM_001141	0	0	2	2	0	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929812	0.92389	.	.	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	D;D	0.91521	-2.86;-2.86	4.53	4.53	0.55603	Lipoxygenase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.96062	0.8717	M	0.89658	3.05	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97047	0.9761	10	0.87932	D	0	-23.6176	16.3899	0.83531	0.0:1.0:0.0:0.0	.	393;393;393;393	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	L	393	ENSP00000369520:P393L;ENSP00000369530:P393L	ENSP00000344337:P393L	P	+	2	0	ALOX15B	7889707	1.000000	0.71417	0.989000	0.46669	0.971000	0.66376	7.516000	0.81772	2.225000	0.72522	0.563000	0.77884	CCC	.		0.612	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			T	7948982	C	T	7948982	3	4	17	1	0	0	0	0	1	0	0	0	539	623	22	2	1208	2	ALOX15B	17	7948982	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	3503067	7948982	73246228	74	1461											
MYH2	4620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10433386	10433386	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgcatcagccaagccttcGgcttccttaagttggaaaca	10	11	8	12	1	2	0	1	0	1	0	4	1	3	1	3	2	4	3	3	2	3	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:10433386G>A	ENST00000245503.5	-	23	3087	c.2703C>T	c.(2701-2703)gcC>gcT	p.A901A	MYH2_ENST00000532183.2_Intron|MYH2_ENST00000397183.2_Silent_p.A901A|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	901					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CCAAGCCTTCGGCTTCCTTAA	0.398																																					p.A901A		.											.	MYH2-194	0			c.C2703T						.						124	121	122					17																	10433386		2203	4300	6503	SO:0001819	synonymous_variant	4620	exon23			GCCTTCGGCTTCC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.2703C>T	17.37:g.10433386G>A		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	254	82	NM_017534	0	0	0	0	0	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			.		0.398	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10433386	G	A	10433386	2	1	17	1	0	0	0	0	0	0	0	1	10060	1103	39	1		1	MYH2	17	10433386	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	2484404	10433386	70761824	75	1462											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	301	46		WXS	Illumina HiSeq		471	79	NM_145301	0	0	7	50	43	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		T	15457087	C	T	15457087	3	4	17	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	5023701	15457087	65738123	76	1463											
TRIM37	4591	broad.mit.edu;bcgsc.ca	37	chr17	57078973	57078974	+	Frame_Shift_Del	DEL	TG	TG	-																															ctgcaccttcatccgggggcTgtgtcatgaccatgaaggag																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:57078973_57078974delTG	ENST00000262294.7	-	23	3056_3057	c.2797_2798delCA	c.(2797-2799)cagfs	p.Q933fs	TRIM37_ENST00000393066.3_Frame_Shift_Del_p.Q933fs|TRIM37_ENST00000376149.3_Intron|TRIM37_ENST00000393065.2_Frame_Shift_Del_p.Q899fs	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	933					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					ATCCGGGGGCTGTGTCATGACC	0.485									Mulibrey Nanism																												p.933_933del													.	TRIM37-660	0			c.2797_2798del						.																																			SO:0001589	frameshift_variant	4591	exon23	Familial Cancer Database	Perheentupa syndrome	GGGGGCTGTGTCA	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.2797_2798delCA	17.37:g.57078975_57078976delTG	ENSP00000262294:p.Gln933fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	188	20	NM_015294	0	0	0	0	0	Q7Z3E6|Q8IYF7|Q8WYF7	Frame_Shift_Del	DEL	ENST00000262294.7	37	CCDS32694.1																																																																																			.		0.485	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		-	57078974	TG	-	57078973	7	5	17	1	0	1	0	1	0	0	0	0	16544	1580	55	0	112	0	TRIM37	17	57078973	Frame_Shift_Del	DEL	TG	TCGA-A4-8515-01A-11D-2396-08	41621886	57078973	24116237	77	1464											
ACE	1636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61561775	61561775	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgccctggatgcccagccGctgctcaagtacttccagcc	7	8	10	16	1	1	0	1	0	0	0	2	2	2	1	5	1	6	3	5	1	2	2	rs137910205		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:61561775G>C	ENST00000290866.4	+	12	1818	c.1794G>C	c.(1792-1794)ccG>ccC	p.P598P	ACE_ENST00000490216.2_5'Flank|ACE_ENST00000290863.6_5'Flank|ACE_ENST00000428043.1_Silent_p.P598P|ACE_ENST00000577647.1_5'Flank|ACE_ENST00000421982.2_5'Flank|ACE_ENST00000413513.3_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	598	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	ATGCCCAGCCGCTGCTCAAGT	0.657																																					p.P598P		.											.	ACE-94	0			c.G1794C						.						44	32	36					17																	61561775		2203	4300	6503	SO:0001819	synonymous_variant	1636	exon12			CCAGCCGCTGCTC	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1794G>C	17.37:g.61561775G>C		Somatic	50	1		WXS	Illumina HiSeq	Phase_I	57	27	NM_000789	0	0	10	36	26	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	37	CCDS11637.1																																																																																			G|1.000;A|0.000		0.657	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			C	61561775	G	C	61561775	2	2	17	1	0	0	0	0	0	0	0	1	136	1074	38	4		4	ACE	17	61561775	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	4482802	61561775	19633435	78	1465											
SMCHD1	23347	broad.mit.edu	37	chr18	2666935	2666935	+	Frame_Shift_Del	DEL	C	C	-																															caatcagttactactgacagCtacgaaagaacgaattgact																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr18:2666935delC	ENST00000320876.6	+	3	667	c.329delC	c.(328-330)gctfs	p.A110fs	SMCHD1_ENST00000261598.8_Frame_Shift_Del_p.A110fs	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	110					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						CTACTGACAGCTACGAAAGAA	0.388																																					p.A110fs													.	SMCHD1-46	0			c.329delC						.						113	100	104					18																	2666935		1920	4143	6063	SO:0001589	frameshift_variant	23347	exon3			TGACAGCTACGAA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.329delC	18.37:g.2666935delC	ENSP00000326603:p.Ala110fs	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	21	8	NM_015295	0	0	0	0	0	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Frame_Shift_Del	DEL	ENST00000320876.6	37	CCDS45822.1																																																																																			.		0.388	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			-	2666935	C	-	2666935	7	5	17	1	0	1	0	1	0	0	0	0	14820	797	28	0	339	0	SMCHD1	18	2666935	Frame_Shift_Del	DEL	C	TCGA-A4-8515-01A-11D-2396-08		2666935	75410313	79	1466											
EPB41L3	23136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	5406855	5406855	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgggggaggtggaaagcctcTtctcccattcattcgttacg	7	11	12	11	3	3	0	1	0	2	0	5	2	3	2	2	4	2	1	2	4	2	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr18:5406855T>C	ENST00000341928.2	-	16	2610	c.2270A>G	c.(2269-2271)aAg>aGg	p.K757R	EPB41L3_ENST00000400111.3_Missense_Mutation_p.K576R|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000342933.3_Missense_Mutation_p.K757R|EPB41L3_ENST00000544123.1_Missense_Mutation_p.K588R|EPB41L3_ENST00000427684.2_Missense_Mutation_p.K29R|EPB41L3_ENST00000542146.1_Missense_Mutation_p.K29R|EPB41L3_ENST00000540638.2_Missense_Mutation_p.K576R	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	757	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GGAAAGCCTCTTCTCCCATTC	0.512																																					p.K757R		.											.	EPB41L3-95	0			c.A2270G						.						179	143	155					18																	5406855		2203	4300	6503	SO:0001583	missense	23136	exon16			AGCCTCTTCTCCC	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2270A>G	18.37:g.5406855T>C	ENSP00000343158:p.Lys757Arg	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	116	49	NM_012307	0	0	21	43	22	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245271	0.80024	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	D;D;D;D;D;D	0.89875	-2.12;-2.58;-1.59;-1.5;-2.12;-2.37	5.78	5.78	0.91487	SAB (1);	0.043558	0.85682	D	0.000000	D	0.93360	0.7883	M	0.62266	1.93	0.58432	D	0.999999	D;D;D;D;D;D;D;D	0.89917	0.99;0.999;0.999;0.977;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.979;0.996;0.996;0.98;0.995;0.97;0.999;0.998	D	0.93204	0.6594	10	0.48119	T	0.1	.	16.1138	0.81283	0.0:0.0:0.0:1.0	.	588;29;29;149;467;576;757;29	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	R	757;467;588;467;29;29;757;576	ENSP00000343158:K757R;ENSP00000441174:K588R;ENSP00000392195:K29R;ENSP00000442233:K29R;ENSP00000341138:K757R;ENSP00000382981:K576R	ENSP00000343158:K757R	K	-	2	0	EPB41L3	5396855	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	7.698000	0.84413	2.220000	0.72140	0.533000	0.62120	AAG	.		0.512	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5406855	T	C	5406855	3	2	17	1	0	0	0	0	1	0	0	0	5167	1609	56	3	1021	3	EPB41L3	18	5406855	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	2739920	5406855	72670393	80	1467											
CABLES1	91768	broad.mit.edu	37	chr18	20716015	20716023	+	In_Frame_Del	DEL	GGCGCCGGC	GGCGCCGGC	-																															agggcggcgcggccaagccgGgcgccggcggcgcctgcggc																								rs201595073|rs139352344	byFrequency	TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	GGCGCCGGC	GGCGCCGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr18:20716015_20716023delGGCGCCGGC	ENST00000256925.7	+	1	289_297	c.289_297delGGCGCCGGC	c.(289-297)ggcgccggcdel	p.GAG97del	CABLES1_ENST00000400473.2_Intron|AC105247.1_ENST00000411067.1_RNA	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	97	Ala-rich.|Interacts with TDRD7. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ggccaagccgggcgccggcggcgcctgcg	0.785														1123	0.224241	0.2602	0.17	5008	,	,		3844	0.244		0.2048	False		,,,				2504	0.2137				p.97_99del													.	CABLES1-522	0			c.289_297del						.																																			SO:0001651	inframe_deletion	91768	exon1			AAGCCGGGCGCCG	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.289_297delGGCGCCGGC	18.37:g.20716015_20716023delGGCGCCGGC	ENSP00000256925:p.Gly97_Gly99del	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	9	7	NM_001100619	0	0	0	0	0	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	In_Frame_Del	DEL	ENST00000256925.7	37	CCDS42417.1																																																																																			.		0.785	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		-	20716023	GGCGCCGGC	-	20716015	7	5	17	1	0	1	0	1	0	0	0	0	2535	1232	43	0	291	0	CABLES1	18	20716015	In_Frame_Del	DEL	GGCGCCGGC	TCGA-A4-8515-01A-11D-2396-08	15309160	20716015	57361233	81	1468											
DSC2	1824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	28660278	28660278	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcttcattaactacaccaAtttgcaagatcatctgttgc	12	13	6	10	0	3	1	2	0	1	1	3	2	3	1	1	0	5	3	1	0	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr18:28660278A>C	ENST00000280904.6	-	10	1747	c.1304T>G	c.(1303-1305)aTt>aGt	p.I435S	DSC2_ENST00000251081.6_Missense_Mutation_p.I435S	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	435	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			AACTACACCAATTTGCAAGAT	0.378																																					p.I435S		.											.	DSC2-517	0			c.T1304G						.						159	138	145					18																	28660278		2203	4300	6503	SO:0001583	missense	1824	exon10			ACACCAATTTGCA	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.1304T>G	18.37:g.28660278A>C	ENSP00000280904:p.Ile435Ser	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	70	30	NM_024422	0	0	9	19	10		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.006051	0.54361	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.48836	0.8;0.8	5.92	5.92	0.95590	Cadherin (5);Cadherin-like (1);	0.000000	0.32884	N	0.005536	T	0.78997	0.4372	H	0.97491	4.015	0.54753	D	0.999989	D;D	0.69078	0.997;0.996	D;D	0.65443	0.934;0.935	D	0.86616	0.1876	10	0.87932	D	0	.	15.3456	0.74334	1.0:0.0:0.0:0.0	.	435;435	Q02487;Q02487-2	DSC2_HUMAN;.	S	435;435;201;448	ENSP00000251081:I435S;ENSP00000280904:I435S	ENSP00000251081:I435S	I	-	2	0	DSC2	26914276	1.000000	0.71417	0.226000	0.23910	0.115000	0.19883	7.733000	0.84916	2.266000	0.75297	0.533000	0.62120	ATT	.		0.378	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28660278	A	C	28660278	3	2	17	1	0	0	0	0	1	0	0	0	4777	101	4	5	1469	5	DSC2	18	28660278	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	7944263	28660278	49416970	82	1469											
ICAM5	7087	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10403449	10403449	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagctaaatgccaccgagAacgacgacagacgcagcttc	13	6	9	13	4	1	2	1	0	0	2	2	5	1	2	2	0	4	3	2	0	3	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr19:10403449A>G	ENST00000221980.4	+	5	1186	c.1123A>G	c.(1123-1125)Aac>Gac	p.N375D		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	375	Ig-like C2-type 4.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			TGCCACCGAGAACGACGACAG	0.622																																					p.N375D		.											.	ICAM5-153	0			c.A1123G						.						52	54	53					19																	10403449		2203	4300	6503	SO:0001583	missense	7087	exon5			ACCGAGAACGACG	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1123A>G	19.37:g.10403449A>G	ENSP00000221980:p.Asn375Asp	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	56	8	NM_003259	0	0	0	0	0	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	A	7.911	0.736583	0.15574	.	.	ENSG00000105376	ENST00000221980	T	0.05382	3.45	5.46	-10.9	0.00192	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.463300	0.03856	N	0.273164	T	0.02230	0.0069	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34354	-0.9832	10	0.16420	T	0.52	-0.0897	4.6077	0.12385	0.1132:0.1885:0.5112:0.1871	.	375	Q9UMF0	ICAM5_HUMAN	D	375	ENSP00000221980:N375D	ENSP00000221980:N375D	N	+	1	0	ICAM5	10264449	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-1.105000	0.03323	-3.113000	0.00241	-0.441000	0.05720	AAC	.		0.622	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		G	10403449	A	G	10403449	3	3	17	1	0	0	0	0	1	0	0	0	7504	246	9	3	1141	3	ICAM5	19	10403449	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		10403449	48725534	83	1470											
ZSWIM4	65249	ucsc.edu	37	chr19	13919690	13919690	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcaggaatcgaggacgcCaactgctggcacctggacga	10	4	15	12	4	0	0	0	0	0	0	1	5	0	3	2	5	2	3	2	5	2	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr19:13919690C>A	ENST00000254323.2	+	4	942	c.753C>A	c.(751-753)gcC>gcA	p.A251A	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	251							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			TCGAGGACGCCAACTGCTGGC	0.657																																					p.A251A													.	ZSWIM4-90	0			c.C753A						.						23	22	22					19																	13919690		2195	4296	6491	SO:0001819	synonymous_variant	65249	exon4			GGACGCCAACTGC	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.753C>A	19.37:g.13919690C>A		Somatic	30	0		WXS	Illumina HiSeq		35	4	NM_023072	0	0	2	2	0		Silent	SNP	ENST00000254323.2	37	CCDS32924.1																																																																																			.		0.657	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		A	13919690	C	A	13919690	2	1	17	1	0	0	0	0	0	0	0	1	18275	581	21	4		4	ZSWIM4	19	13919690	Silent	SNP	C	TCGA-A4-8515-01A-11D-2396-08	3516241	13919690	45209293	84	1471											
PEG3	5178	broad.mit.edu	37	chr19	57326548	57326548	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtctgagccttgaatgaCagggtcttcaattgtctcct	8	14	9	10	0	4	3	1	3	3	0	5	3	4	3	2	1	1	0	2	1	2	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr19:57326548C>A	ENST00000326441.9	-	10	3625	c.3262G>T	c.(3262-3264)Gtc>Ttc	p.V1088F	ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.V1088F|PEG3_ENST00000593695.1_Missense_Mutation_p.V962F|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.V964F|ZIM2_ENST00000599935.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1088					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CCTTGAATGACAGGGTCTTCA	0.517																																					p.V1088F													.	PEG3-164	0			c.G3262T						.						128	120	123					19																	57326548		2203	4300	6503	SO:0001583	missense	5178	exon9			GAATGACAGGGTC	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3262G>T	19.37:g.57326548C>A	ENSP00000326581:p.Val1088Phe	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	102	4	NM_001146184	0	0	0	0	0	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	4.117	0.019819	0.08006	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02446	4.29;4.29	3.15	1.71	0.24356	.	0.658998	0.13424	N	0.388972	T	0.06462	0.0166	L	0.57536	1.79	.	.	.	B;D;D	0.76494	0.012;0.999;0.981	B;D;P	0.66196	0.007;0.942;0.786	T	0.11842	-1.0571	9	0.02654	T	1	-9.2719	4.6601	0.12637	0.0:0.7375:0.0:0.2625	.	964;1088;1023	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	F	1088	ENSP00000326581:V1088F;ENSP00000403051:V1088F	ENSP00000326581:V1088F	V	-	1	0	ZIM2	62018360	0.000000	0.05858	0.001000	0.08648	0.944000	0.59088	-0.128000	0.10531	0.545000	0.28902	0.655000	0.94253	GTC	.		0.517	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57326548	C	A	57326548	3	1	17	1	0	0	0	0	1	0	0	0	11746	478	17	4	1508	4	PEG3	19	57326548	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	43406858	57326548	1802435	85	1472											
CPNE1	8904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34215310	34215310	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acttggggcagggcttggcgGtaggcatccacaatgccctg	7	8	15	11	1	0	0	0	0	0	0	1	0	1	0	2	6	1	4	2	6	2	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr20:34215310G>T	ENST00000317619.3	-	16	1522	c.1128C>A	c.(1126-1128)taC>taA	p.Y376*	CPNE1_ENST00000397443.1_Nonsense_Mutation_p.Y376*|CPNE1_ENST00000397446.1_Nonsense_Mutation_p.Y376*|CPNE1_ENST00000397445.1_Nonsense_Mutation_p.Y376*|CPNE1_ENST00000317677.5_Nonsense_Mutation_p.Y381*|CPNE1_ENST00000352393.4_Nonsense_Mutation_p.Y376*|CPNE1_ENST00000397442.1_Nonsense_Mutation_p.Y376*			Q99829	CPNE1_HUMAN	copine I	376	VWFA.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GGGCTTGGCGGTAGGCATCCA	0.562																																					p.Y381X		.											.	CPNE1-91	0			c.C1143A						.						96	88	91					20																	34215310		2203	4300	6503	SO:0001587	stop_gained	8904	exon14			TTGGCGGTAGGCA	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.1128C>A	20.37:g.34215310G>T	ENSP00000326126:p.Tyr376*	Somatic	112	1		WXS	Illumina HiSeq	Phase_I	110	49	NM_003915	0	0	48	55	7	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Nonsense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	17.22|17.22	3.333654|3.333654	0.60853|0.60853	.|.	.|.	ENSG00000214078|ENSG00000214078	ENST00000415920|ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570	.|.	.|.	.|.	4.88|4.88	0.0193|0.0193	0.14120|0.14120	.|.	.|0.000000	.|0.64402	.|U	.|0.000001	T|.	0.16385|.	0.0394|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40831|.	-0.9542|.	3|.	.|0.02654	.|T	.|1	-11.8283|-11.8283	8.2202|8.2202	0.31537|0.31537	0.5071:0.0:0.4929:0.0|0.5071:0.0:0.4929:0.0	.|.	.|.	.|.	.|.	N|X	15|376;381;376;376;376;376;376;376;352	.|.	.|ENSP00000326126:Y376X	T|Y	-|-	2|3	0|2	CPNE1|CPNE1	33678724|33678724	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.869000|0.869000	0.49853|0.49853	1.060000|1.060000	0.30530|0.30530	0.146000|0.146000	0.19002|0.19002	-0.213000|-0.213000	0.12676|0.12676	ACC|TAC	.		0.562	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930		T	34215310	G	T	34215310	4	4	17	1	0	0	0	0	0	1	0	0	3817	1256	44	4	497	4	CPNE1	20	34215310	Nonsense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08		34215310	28810210	86	1473											
ROMO1	140823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34288799	34288799	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcacctttggcacattcAtggccattgggatgggcatc	7	10	13	11	1	1	0	1	0	0	0	2	1	1	1	2	5	0	3	2	5	0	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr20:34288799A>G	ENST00000374078.1	+	3	391	c.211A>G	c.(211-213)Atg>Gtg	p.M71V	NFS1_ENST00000374092.4_5'Flank|ROMO1_ENST00000336695.4_Missense_Mutation_p.M71V|NFS1_ENST00000397425.1_5'Flank|NFS1_ENST00000541387.1_5'Flank|ROMO1_ENST00000374077.3_Missense_Mutation_p.M71V|ROMO1_ENST00000397416.1_Missense_Mutation_p.M71V|NFS1_ENST00000374085.1_5'Flank|ROMO1_ENST00000374072.1_3'UTR|NFS1_ENST00000540053.1_5'Flank|NFS1_ENST00000306750.3_5'Flank	NM_080748.2	NP_542786.1	P60602	ROMO1_HUMAN	reactive oxygen species modulator 1	71					cellular response to reactive oxygen species (GO:0034614)|defense response to bacterium (GO:0042742)|positive regulation of cell proliferation (GO:0008284)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|replicative cell aging (GO:0001302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				cervix(1)	1						TGGCACATTCATGGCCATTGG	0.517																																					p.M71V		.											.	ROMO1-90	0			c.A211G						.						124	86	99					20																	34288799		2203	4300	6503	SO:0001583	missense	140823	exon3			ACATTCATGGCCA	AK000548	CCDS13264.1	20q11.22	2008-09-30	2008-09-30	2008-09-30	ENSG00000125995	ENSG00000125995			16185	protein-coding gene	gene with protein product	"mitochondrial targeting GXXXG protein"		"chromosome 20 open reading frame 52"	C20orf52		18313394, 17537404, 16842742	Standard	NM_080748		Approved	bA353C18.2, MTGMP	uc002xdy.3	P60602	OTTHUMG00000032360	ENST00000374078.1:c.211A>G	20.37:g.34288799A>G	ENSP00000363191:p.Met71Val	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	127	49	NM_080748	0	0	105	215	110	A7M872|E1P5R9|E9KL28|Q3MHD5|Q5QP16|Q9CQ98|Q9H1N2	Missense_Mutation	SNP	ENST00000374078.1	37	CCDS13264.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.442280	0.63067	.	.	ENSG00000125995	ENST00000374078;ENST00000374077;ENST00000397416;ENST00000336695	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	4.68	4.68	0.58851	.	0.039506	0.85682	D	0.000000	T	0.48059	0.1479	.	.	.	0.80722	D	1	B	0.25351	0.124	B	0.25506	0.061	T	0.52124	-0.8617	9	0.87932	D	0	.	14.3539	0.66722	1.0:0.0:0.0:0.0	.	71	P60602	ROMO1_HUMAN	V	71	ENSP00000363191:M71V;ENSP00000363190:M71V;ENSP00000380561:M71V;ENSP00000338293:M71V	ENSP00000338293:M71V	M	+	1	0	ROMO1	33752213	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.080000	0.94040	1.982000	0.57802	0.529000	0.55759	ATG	.		0.517	ROMO1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000126404.1	NM_080748		G	34288799	A	G	34288799	3	3	17	1	0	0	0	0	1	0	0	0	13554	217	8	3	217	3	ROMO1	20	34288799	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	73489	34288799	28736721	87	1474											
TAF4	6874	hgsc.bcm.edu	37	chr20	60639811	60639811	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgccgccgggggcgccgcCtgcaccaccctcttgggcga	3	5	15	18	6	1	0	0	0	1	0	1	1	1	0	6	3	2	1	6	3	0	1	rs545583149	byFrequency	TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr20:60639811C>A	ENST00000252996.4	-	1	1055	c.1056G>T	c.(1054-1056)caG>caT	p.Q352H	hsa-mir-3195_ENST00000585001.1_RNA	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	352					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			GGGGCGCCGCCTGCACCACCC	0.816													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		2060	0		0	False		,,,				2504	0				p.Q352H		.											.	TAF4-93	0			c.G1056T						.						1	2	2					20																	60639811		361	897	1258	SO:0001583	missense	6874	exon1			CGCCGCCTGCACC	Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1056G>T	20.37:g.60639811C>A	ENSP00000252996:p.Gln352His	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	9	6	NM_003185	0	0	0	0	0	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	.	.	.	.	.	.	.	.	.	.	c	6.786	0.514007	0.12944	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.26223	1.75;1.77	2.3	1.19	0.21007	.	11.033200	0.01102	U	0.005396	T	0.21962	0.0529	N	0.24115	0.695	0.09310	N	0.999997	P	0.39576	0.679	B	0.38562	0.276	T	0.32052	-0.9921	10	0.44086	T	0.13	.	9.8974	0.41327	0.0:0.7883:0.2117:0.0	.	352	O00268	TAF4_HUMAN	H	352;216	ENSP00000252996:Q352H;ENSP00000399091:Q216H	ENSP00000252996:Q352H	Q	-	3	2	TAF4	60073206	0.523000	0.26274	0.074000	0.20217	0.091000	0.18340	0.327000	0.19663	-0.099000	0.12263	0.177000	0.17058	CAG	.		0.816	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60639811	C	A	60639811	3	1	17	1	0	0	0	0	1	0	0	0	15558	680	24	4	2261	4	TAF4	20	60639811	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	26351012	60639811	2385709	88	1475											
SON	6651	hgsc.bcm.edu	37	chr21	34948684	34948684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgaataggtattgagaaatgGagcccttaccagacccaatt	14	10	9	8	0	0	3	0	2	0	2	0	5	0	4	3	2	2	1	3	2	6	5	rs397829693|rs34377180		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr21:34948684G>A	ENST00000356577.4	+	12	7710	c.7235G>A	c.(7234-7236)gGa>gAa	p.G2412E	SON_ENST00000381692.2_Missense_Mutation_p.G440E|SON_ENST00000290239.6_3'UTR|DONSON_ENST00000303113.6_Intron|AP000304.1_ENST00000595468.1_5'Flank|SON_ENST00000470533.1_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2412	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TTGAGAAATGGAGCCCTTACC	0.338																																					p.G2412E		.											.	SON-97	0			c.G7235A						.						55	55	55					21																	34948684		2201	4295	6496	SO:0001583	missense	6651	exon12			GAAATGGAGCCCT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.7235G>A	21.37:g.34948684G>A	ENSP00000348984:p.Gly2412Glu	Somatic	32	2		WXS	Illumina HiSeq	Phase_I	58	10	NM_138927	0	0	0	0	0	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434360	0.43224	.	.	ENSG00000159140	ENST00000356577;ENST00000381692	T;T	0.69306	-0.39;-0.39	5.42	5.42	0.78866	Double-stranded RNA-binding-like (1);	0.000000	0.51477	D	0.000097	T	0.71134	0.3304	M	0.69823	2.125	0.80722	D	1	D;P	0.59767	0.986;0.799	P;B	0.50970	0.655;0.435	T	0.75127	-0.3427	10	0.87932	D	0	.	9.3335	0.38036	0.0788:0.1457:0.7755:0.0	.	440;2412	Q6ZRV7;P18583	.;SON_HUMAN	E	2412;440	ENSP00000348984:G2412E;ENSP00000371111:G440E	ENSP00000348984:G2412E	G	+	2	0	SON	33870554	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.898000	0.48672	2.560000	0.86352	0.555000	0.69702	GGA	.		0.338	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		A	34948684	G	A	34948684	3	1	17	1	0	0	0	0	1	0	0	0	14958	1174	41	2	7540	2	SON	21	34948684	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08		34948684	13181211	89	1476											
FAM48B1	100130302	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	24381817	24381817	+	IGR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtggagaaacttgctaaaGggtatcagtccgtcacagct	12	10	11	8	1	2	1	2	0	0	1	3	2	3	1	1	2	3	3	1	2	4	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chrX:24381817G>T								AC004552.1 (14794 upstream) : PDK3 (101520 downstream)																							ACTTGCTAAAGGGTATCAGTC	0.537																																					p.G314W		.											.	.	0			c.G940T						.						141	117	125					X																	24381817		1568	3578	5146	SO:0001628	intergenic_variant	100130302	exon1			GCTAAAGGGTATC																													X.37:g.24381817G>T		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	181	119	NM_001136234	0	0	0	0	0		Missense_Mutation	SNP		37																																																																																				.	0	0.537									T	24381817	G	T	24381817	1	4	17	0	1	0	0	0	0	0	0	0	5592	1000	35	4		4	FAM48B1	23	24381817	IGR	SNP	G	TCGA-A4-8515-01A-11D-2396-08		24381817	130888743	90	1477											
ZXDB	158586	hgsc.bcm.edu	37	chrX	57618845	57618845	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgtgttgagggaggaggccGaggagggcccggggctccag	6	5	21	9	2	0	1	0	1	0	0	1	5	1	4	3	7	0	2	3	7	0	1	rs199513692		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chrX:57618845G>A	ENST00000374888.1	+	1	577	c.364G>A	c.(364-366)Gag>Aag	p.E122K		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	122					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.E122K(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						GGAGGAGGCCGAGGAGGGCCC	0.756																																					p.E122K		.											.	ZXDB-130	1	Substitution - Missense(1)	skin(1)	c.G364A						.						3	4	4					X																	57618845		1773	3669	5442	SO:0001583	missense	158586	exon1			GAGGCCGAGGAGG	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.364G>A	X.37:g.57618845G>A	ENSP00000364023:p.Glu122Lys	Somatic	9	2		WXS	Illumina HiSeq	Phase_I	18	6	NM_007157	0	0	0	0	0	A8K151|Q9UBB3	Missense_Mutation	SNP	ENST00000374888.1	37	CCDS35313.1	.	.	.	.	.	.	.	.	.	.	.	8.440	0.850716	0.17034	.	.	ENSG00000198455	ENST00000374888	T	0.33865	1.39	2.93	2.93	0.34026	.	1.203730	0.05881	N	0.626423	T	0.25827	0.0629	L	0.27053	0.805	0.09310	N	0.999999	B	0.32071	0.355	B	0.19946	0.027	T	0.13710	-1.0499	10	0.28530	T	0.3	.	11.3184	0.49405	0.0:0.0:1.0:0.0	.	122	P98169	ZXDB_HUMAN	K	122	ENSP00000364023:E122K	ENSP00000364023:E122K	E	+	1	0	ZXDB	57635570	0.001000	0.12720	0.635000	0.29338	0.079000	0.17450	0.974000	0.29436	1.402000	0.46780	0.556000	0.70494	GAG	.		0.756	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		A	57618845	G	A	57618845	3	1	17	1	0	0	0	0	1	0	0	0	18283	1059	37	1	366	1	ZXDB	23	57618845	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	33237028	57618845	97651715	91	1478											
GLUD2	2747	ucsc.edu	37	chrX	120182120	120182120	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaatcccaagaactatacCgaaaatgaattggaaaagat	20	8	6	7	1	1	3	1	1	0	2	2	5	2	4	2	1	2	0	2	1	10	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chrX:120182120C>T	ENST00000328078.1	+	1	659	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	194					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						AGAACTATACCGAAAATGAAT	0.453																																					p.T194T													.	GLUD2-131	0			c.C582T						.						123	96	105					X																	120182120		2203	4300	6503	SO:0001819	synonymous_variant	2747	exon1			CTATACCGAAAAT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.582C>T	X.37:g.120182120C>T		Somatic	112	0		WXS	Illumina HiSeq		92	2	NM_012084	0	0	2	2	0	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																			.		0.453	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		T	120182120	C	T	120182120	2	4	17	1	0	0	0	0	0	0	0	1	6497	639	23	1		1	GLUD2	23	120182120	Silent	SNP	C	TCGA-A4-8515-01A-11D-2396-08	62563275	120182120	35088440	92	1479											
SDC3	9672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	31347253	31347253	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcccgggcgggcacccttGggcagtgtcccaggtggaga	5	5	19	12	2	0	1	0	0	0	1	1	2	1	1	3	6	0	2	3	6	0	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:31347253G>T	ENST00000339394.6	-	4	1227	c.1053C>A	c.(1051-1053)ccC>ccA	p.P351P	SDC3_ENST00000336798.7_Silent_p.P293P|SDC3_ENST00000471567.1_5'Flank	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	351					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GGGCACCCTTGGGCAGTGTCC	0.632																																					p.P351P		.											.	SDC3-227	0			c.C1053A						.						76	83	81					1																	31347253		2203	4300	6503	SO:0001819	synonymous_variant	9672	exon4			ACCCTTGGGCAGT	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"Proteoglycans / Cell Surface : Syndecans"	10660	protein-coding gene	gene with protein product	"syndecan proteoglycan 3"	186357	"syndecan 3 (N-syndecan)"			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.1053C>A	1.37:g.31347253G>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	96	31	NM_014654	0	0	13	15	2	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			.		0.632	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		T	31347253	G	T	31347253	2	4	18	1	0	0	0	0	0	0	0	1	13985	1335	47	4		4	SDC3	1	31347253	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08		31347253	217903368	1	1480											
PPIE	10450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40211152	40211152	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgctcctgcgttctgatGtcgtgcccatgacagcaggt	7	11	12	11	2	1	3	0	2	1	1	3	3	2	3	2	1	4	3	2	1	0	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:40211152G>A	ENST00000324379.5	+	7	509	c.490G>A	c.(490-492)Gtc>Atc	p.V164I	PPIE_ENST00000480169.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.V164I|PPIE_ENST00000372830.1_Missense_Mutation_p.V164I|PPIE_ENST00000470213.1_Intron	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	164	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GCGTTCTGATGTCGTGCCCAT	0.572																																					p.V164I		.											.	PPIE-90	0			c.G490A						.						67	55	59					1																	40211152		2203	4300	6503	SO:0001583	missense	10450	exon7			TCTGATGTCGTGC	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"RNA binding motif (RRM) containing"	9258	protein-coding gene	gene with protein product	"peptidyl-prolyl cis-trans isomerase E", "cyclophilin 33", "cyclophilin E", "PPIase E", "rotamase E", "peptidylprolyl isomerase E, isoform 1"	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.490G>A	1.37:g.40211152G>A	ENSP00000312769:p.Val164Ile	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	36	20	NM_006112	0	0	27	42	15	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	37	CCDS443.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839855	0.32513	.	.	ENSG00000084072	ENST00000324379;ENST00000356511;ENST00000497370;ENST00000372835;ENST00000372830	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.0	0.793	0.18632	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.135859	0.50627	D	0.000102	T	0.11750	0.0286	N	0.20357	0.565	0.47862	D	0.999531	B;B;B;B	0.17667	0.001;0.023;0.001;0.001	B;B;B;B	0.21917	0.01;0.037;0.005;0.009	T	0.13710	-1.0499	10	0.28530	T	0.3	-14.2927	8.5189	0.33264	0.4795:0.0:0.5205:0.0	.	85;164;164;164	B4E3F2;Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;.;PPIE_HUMAN	I	164;164;98;113;164	ENSP00000312769:V164I;ENSP00000348904:V164I;ENSP00000433475:V98I;ENSP00000361925:V113I;ENSP00000361918:V164I	ENSP00000312769:V164I	V	+	1	0	PPIE	39983739	0.996000	0.38824	0.443000	0.26883	0.786000	0.44442	2.773000	0.47686	0.320000	0.23234	-0.251000	0.11542	GTC	.		0.572	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112		A	40211152	G	A	40211152	3	1	18	1	0	0	0	0	1	0	0	0	12351	1377	48	2	516	2	PPIE	1	40211152	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	8863899	40211152	209039469	2	1481											
CAP1	5538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40536545	40536545	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaccatatccatcaacaaaaCagatggctgccatgcttacc	15	8	5	13	0	1	1	1	0	0	1	2	1	2	1	4	1	6	2	4	1	6	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:40536545C>T	ENST00000433473.3	-	0	2740				CAP1_ENST00000340450.3_Missense_Mutation_p.T412I|CAP1_ENST00000372802.1_Missense_Mutation_p.T412I|PPT1_ENST00000372775.2_5'Flank|CAP1_ENST00000372797.3_Missense_Mutation_p.T413I|CAP1_ENST00000372798.1_Missense_Mutation_p.T412I|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000372805.3_Missense_Mutation_p.T413I|CAP1_ENST00000372792.2_Missense_Mutation_p.T413I	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ATCAACAAAACAGATGGCTGC	0.463																																					p.T413I		.											.	CAP1-91	0			c.C1238T						.						138	126	130					1																	40536545		1891	4123	6014	SO:0001628	intergenic_variant	10487	exon12			ACAAAACAGATGG	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 1, infantile"	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40536545C>T		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	128	48	NM_006367	0	0	121	188	67	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	37	CCDS447.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618558	0.87460	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805	T;T;T;T;T;T	0.10382	2.89;2.88;2.89;2.88;2.88;2.89	5.55	5.55	0.83447	CARP motif (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);Adenylate cyclase-associated CAP, C-terminal (2);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.989	T	0.04467	-1.0949	10	0.56958	D	0.05	-5.8536	18.6642	0.91483	0.0:1.0:0.0:0.0	.	360;413	E7ENY9;Q01518	.;CAP1_HUMAN	I	413;412;413;390;412;412;413	ENSP00000361883:T413I;ENSP00000361888:T412I;ENSP00000361878:T413I;ENSP00000361884:T412I;ENSP00000344832:T412I;ENSP00000361891:T413I	ENSP00000344832:T412I	T	+	2	0	CAP1	40309132	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.511000	0.81718	2.890000	0.99128	0.585000	0.79938	ACA	.		0.463	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		T	40536545	C	T	40536545	1	4	18	0	1	0	0	0	0	0	0	0	2625	478	17	2		2	CAP1	1	40536545	IGR	SNP	C	TCGA-A4-8517-01A-11D-2396-08	325393	40536545	208714076	3	1482											
ZNF642	339559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40961061	40961061	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttcagatgtaaggaatGtggaagggcctttagtcaaa	13	11	11	6	0	2	1	2	0	0	1	2	3	2	3	2	3	0	1	2	3	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:40961061G>T	ENST00000372706.1	+	6	1917	c.911G>T	c.(910-912)tGt>tTt	p.C304F	ZFP69_ENST00000372705.3_Missense_Mutation_p.C304F|RP11-656D10.3_ENST00000450713.1_RNA			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	304					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGTAAGGAATGTGGAAGGGCC	0.388																																					p.C304F		.											.	.	0			c.G911T						.						60	58	59					1																	40961061		2203	4300	6503	SO:0001583	missense	339559	exon6			AGGAATGTGGAAG	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"Zinc fingers, C2H2-type", "-", "-", "-"	24708	protein-coding gene	gene with protein product	"ZFP69 zinc finger protein A"		"zinc finger protein 642"	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.911G>T	1.37:g.40961061G>T	ENSP00000361791:p.Cys304Phe	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	66	22	NM_198494	0	0	3	4	1	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	37	CCDS30686.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.804872	0.70682	.	.	ENSG00000187815	ENST00000372706;ENST00000372705	D;D	0.85861	-2.04;-2.04	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000241	D	0.95326	0.8483	H	0.98155	4.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96405	0.9300	10	0.87932	D	0	-9.3418	16.1533	0.81636	0.0:0.0:1.0:0.0	.	304	Q49AA0	ZN642_HUMAN	F	304	ENSP00000361791:C304F;ENSP00000361790:C304F	ENSP00000361790:C304F	C	+	2	0	ZNF642	40733648	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.601000	0.98297	2.941000	0.99782	0.655000	0.94253	TGT	.		0.388	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494		T	40961061	G	T	40961061	3	4	18	1	0	0	0	0	1	0	0	0	18090	1377	48	4	929	4	ZNF642	1	40961061	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	424516	40961061	208289560	4	1483											
NRD1	114883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52256297	52256297	+	IGR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggtgggtatcctcacactCcttcagcttgatgagagctg	9	11	11	10	0	2	2	2	2	0	1	4	3	4	2	2	2	2	3	2	2	2	3	rs147279713		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:52256297C>A	ENST00000428468.1	+	0	2893				NRD1_ENST00000354831.7_Nonsense_Mutation_p.E1094*|NRD1_ENST00000539524.1_Nonsense_Mutation_p.E962*|NRD1_ENST00000352171.7_Nonsense_Mutation_p.E1026*|NRD1_ENST00000485608.1_5'UTR			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9						lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						TCCTCACACTCCTTCAGCTTG	0.527																																					p.E1094X		.											.	NRD1-90	0			c.G3280T						.						151	113	126					1																	52256297		2203	4300	6503	SO:0001628	intergenic_variant	4898	exon31			CACACTCCTTCAG	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234		1.37:g.52256297C>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	58	26	NM_002525	0	0	38	47	9	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Nonsense_Mutation	SNP	ENST00000428468.1	37	CCDS41332.3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.320771|6.320771	0.97471|0.97471	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665;ENST00000546169|ENST00000440943	.|.	.|.	.|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.050156|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75598	.|0.3871	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72590	.|-0.4247	.|4	0.02654|.	T|.	1|.	-15.9931|-15.9931	19.6556|19.6556	0.95837|0.95837	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|V	1026;1094;962;428;1026|412	.|.	ENSP00000262679:E1026X|.	E|G	-|-	1|2	0|0	NRD1|NRD1	52028885|52028885	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.287000|7.287000	0.78681|0.78681	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	GAG|GGA	C|0.999;T|0.000		0.527	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4			A	52256297	C	A	52256297	1	1	18	0	1	0	0	0	0	0	0	0	10671	864	30	4		4	NRD1	1	52256297	IGR	SNP	C	TCGA-A4-8517-01A-11D-2396-08	11295236	52256297	196994324	5	1484											
PRMT6	55170	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	107600260	107600260	+	Frame_Shift_Del	DEL	C	C	-																															ggagaaacccctggtgctgtCcacctcgccttttcacccgg																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:107600260delC	ENST00000370078.1	+	1	960	c.923delC	c.(922-924)tccfs	p.S308fs	PRMT6_ENST00000361318.5_Frame_Shift_Del_p.S249fs			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	308	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		CTGGTGCTGTCCACCTCGCCT	0.607																																					p.S308fs		.											.	PRMT6-90	0			c.923delC						.						44	48	47					1																	107600260		1973	4160	6133	SO:0001589	frameshift_variant	55170	exon1			.	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.923delC	1.37:g.107600260delC	ENSP00000359095:p.Ser308fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	83	37	NM_018137	0	0	0	0	0	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Frame_Shift_Del	DEL	ENST00000370078.1	37	CCDS41360.2																																																																																			.		0.607	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		-	107600260	C	-	107600260	7	5	18	1	0	1	0	1	0	0	0	0	12569	855	30	0	925	0	PRMT6	1	107600260	Frame_Shift_Del	DEL	C	TCGA-A4-8517-01A-11D-2396-08	55343963	107600260	141650361	6	1485											
AHCYL1	10768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110561173	110561173	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actgtgctttcttcctttcaGaccagcctccgcactccgga	6	12	7	16	2	2	1	1	0	1	1	5	2	5	2	5	1	2	2	5	1	0	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:110561173G>A	ENST00000369799.5	+	13	1585		c.e13-1		AHCYL1_ENST00000359172.3_Splice_Site|AHCYL1_ENST00000393614.4_Splice_Site	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1						mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		CTTCCTTTCAGACCAGCCTCC	0.498																																					.		.											.	AHCYL1-91	0			c.1219-1G>A						.						77	62	67					1																	110561173		2203	4300	6503	SO:0001630	splice_region_variant	10768	exon13			CTTTCAGACCAGC	U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"inositol 1,4,5-trisphosphate receptor-binding protein", "protein phosphatase 1, regulatory subunit 78"	607826	"S-adenosylhomocysteine hydrolase-like 1"			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.1219-1G>A	1.37:g.110561173G>A		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	39	16	NM_006621	0	0	0	0	0	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Splice_Site	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444478	0.83993	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2323	0.93845	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AHCYL1	110362696	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.869000	0.99810	2.541000	0.85698	0.655000	0.94253	.	.		0.498	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1		Intron	A	110561173	G	A	110561173	5	1	18	1	0	0	0	0	0	0	1	0	410	956	33	2	1268	2	AHCYL1	1	110561173	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	2960913	110561173	138689448	7	1486											
POLR3C	10623	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	145592731	145592731	+	Frame_Shift_Del	DEL	G	G	-																															ctcaatgtaagactccagcaGgaagatggtttcgtccacct																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:145592731delG	ENST00000334163.3	-	15	1724	c.1564delC	c.(1564-1566)ctgfs	p.L523fs	POLR3C_ENST00000369294.1_3'UTR	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	523					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			GACTCCAGCAGGAAGATGGTT	0.438																																					p.L522fs		.											.	POLR3C-91	0			c.1564delC						.						124	107	113					1																	145592731		2203	4300	6503	SO:0001589	frameshift_variant	10623	exon15			.	AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"RNA polymerase subunits"	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.1564delC	1.37:g.145592731delG	ENSP00000334564:p.Leu523fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	83	30	NM_006468	0	0	0	0	0	O15317|Q9Y3R6	Frame_Shift_Del	DEL	ENST00000334163.3	37	CCDS921.1																																																																																			.		0.438	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468		-	145592731	G	-	145592731	7	5	18	1	0	1	0	1	0	0	0	0	12256	991	35	0	44	0	POLR3C	1	145592731	Frame_Shift_Del	DEL	G	TCGA-A4-8517-01A-11D-2396-08	35031558	145592731	103657890	8	1487											
SF3B4	10262	broad.mit.edu	37	chr1	149897857	149897857	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggaggcataggtggtggggGcatggctgggggtatcccag	7	7	21	6	0	0	0	0	0	0	0	1	1	1	1	1	9	0	4	1	9	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:149897857G>A	ENST00000271628.8	-	4	1368	c.784C>T	c.(784-786)Ccc>Tcc	p.P262S	MTMR11_ENST00000492824.1_5'Flank	NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	262	Poly-Pro.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GGTGGTGGGGGCATGGCTGGG	0.637																																					p.P262S													.	SF3B4-91	0			c.C784T						.						18	18	18					1																	149897857		2200	4298	6498	SO:0001583	missense	10262	exon4			GTGGGGGCATGGC	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"RNA binding motif (RRM) containing"	10771	protein-coding gene	gene with protein product		605593	"splicing factor 3b, subunit 4, 49kD"			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.784C>T	1.37:g.149897857G>A	ENSP00000271628:p.Pro262Ser	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	44	4	NM_005850	0	0	58	58	0	Q5SZ63	Missense_Mutation	SNP	ENST00000271628.8	37	CCDS941.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.947232	0.53186	.	.	ENSG00000143368	ENST00000271628	T	0.29142	1.58	4.33	4.33	0.51752	.	0.000000	0.64402	D	0.000001	T	0.34745	0.0908	L	0.47016	1.485	0.58432	D	0.999994	D;P	0.63880	0.993;0.909	D;P	0.70227	0.968;0.641	T	0.02301	-1.1180	10	0.27082	T	0.32	.	14.0104	0.64493	0.0:0.0:1.0:0.0	.	262;262	Q53FG6;Q15427	.;SF3B4_HUMAN	S	262	ENSP00000271628:P262S	ENSP00000271628:P262S	P	-	1	0	SF3B4	148164481	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.536000	0.60636	2.387000	0.81309	0.462000	0.41574	CCC	.		0.637	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850		A	149897857	G	A	149897857	3	1	18	1	0	0	0	0	1	0	0	0	14185	1203	42	2	502	2	SF3B4	1	149897857	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	4305126	149897857	99352764	9	1488											
HRNR	388697	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	152188167	152188167	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgaccggagccagactcatAtgggccacggctggaagacc	10	5	14	12	2	1	3	1	1	0	2	1	5	1	5	4	4	1	1	4	4	2	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:152188167A>G	ENST00000368801.2	-	3	6013	c.5938T>C	c.(5938-5940)Tat>Cat	p.Y1980H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1980					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCAGACTCATATGGGCCACGG	0.592																																					p.Y1980H		.											.	HRNR-93	0			c.T5938C						.						141	245	210					1																	152188167		2174	4288	6462	SO:0001583	missense	388697	exon3			ACTCATATGGGCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5938T>C	1.37:g.152188167A>G	ENSP00000357791:p.Tyr1980His	Somatic	1429	1		WXS	Illumina HiSeq	Phase_I	1470	83	NM_001009931	0	0	1	1	0	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	5.689	0.311642	0.10789	.	.	ENSG00000197915	ENST00000368801	T	0.01538	4.79	3.19	-1.26	0.09376	.	.	.	.	.	T	0.00241	0.0007	N	0.03050	-0.425	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33471	-0.9867	9	0.14656	T	0.56	.	3.9881	0.09525	0.3563:0.3518:0.2919:0.0	.	1980	Q86YZ3	HORN_HUMAN	H	1980	ENSP00000357791:Y1980H	ENSP00000357791:Y1980H	Y	-	1	0	HRNR	150454791	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.676000	0.05221	-0.112000	0.11979	-0.394000	0.06481	TAT	.		0.592	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		G	152188167	A	G	152188167	3	3	18	1	0	0	0	0	1	0	0	0	7380	449	16	3	2618	3	HRNR	1	152188167	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	2290310	152188167	97062454	10	1489											
COPA	1314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160305059	160305059	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaacgtggtgcgaatataAtctaagtgcccaagcaatgt	16	9	9	7	2	1	0	0	0	1	0	1	1	1	0	1	1	4	1	1	1	8	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:160305059A>G	ENST00000241704.7	-	4	511	c.282T>C	c.(280-282)gaT>gaC	p.D94D	COPA_ENST00000368069.3_Silent_p.D94D	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	94					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGCGAATATAATCTAAGTGCC	0.388																																					p.D94D		.											.	COPA-92	0			c.T282C						.						65	58	61					1																	160305059		2203	4300	6503	SO:0001819	synonymous_variant	1314	exon4			AATATAATCTAAG	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"WD repeat domain containing", "Endogenous ligands"	2230	protein-coding gene	gene with protein product	"proxenin", "xenin"	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.282T>C	1.37:g.160305059A>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	28	14	NM_001098398	0	0	20	34	14	Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	37	CCDS1202.1																																																																																			.		0.388	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		G	160305059	A	G	160305059	2	3	18	1	0	0	0	0	0	0	0	1	3733	98	4	3		3	COPA	1	160305059	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	8116892	160305059	88945562	11	1490											
ASAP2	8853	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	9515054	9515054	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggatcttacggaaaaaaTcccactggccaacggacatg	13	8	10	10	2	1	0	0	0	1	0	2	3	2	3	2	4	2	0	2	4	5	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:9515054T>C	ENST00000281419.3	+	17	2067	c.1727T>C	c.(1726-1728)aTc>aCc	p.I576T	ASAP2_ENST00000315273.4_Missense_Mutation_p.I576T	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	576					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ACGGAAAAAATCCCACTGGCC	0.473																																					p.I576T		.											.	ASAP2-90	0			c.T1727C						.						86	87	86					2																	9515054		2203	4300	6503	SO:0001583	missense	8853	exon17			AAAAAATCCCACT	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1727T>C	2.37:g.9515054T>C	ENSP00000281419:p.Ile576Thr	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	126	51	NM_001135191	0	0	2	4	2	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	37	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.279137	0.80692	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.66099	-0.19;-0.19	5.4	5.4	0.78164	Ankyrin repeat-containing domain (1);	0.146210	0.64402	D	0.000013	T	0.73401	0.3582	L	0.47716	1.5	0.80722	D	1	D;D	0.65815	0.986;0.995	P;D	0.77004	0.904;0.989	T	0.74074	-0.3782	10	0.48119	T	0.1	.	15.4253	0.75045	0.0:0.0:0.0:1.0	.	576;576	O43150-2;O43150	.;ASAP2_HUMAN	T	576	ENSP00000281419:I576T;ENSP00000316404:I576T	ENSP00000281419:I576T	I	+	2	0	ASAP2	9432505	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.691000	0.84191	2.039000	0.60335	0.533000	0.62120	ATC	.		0.473	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9515054	T	C	9515054	3	2	18	1	0	0	0	0	1	0	0	0	1012	1435	50	3	1793	3	ASAP2	2	9515054	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		9515054	233684319	12	1491											
TCF23	150921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27373231	27373231	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgctacttgcaccctctcAaggtaagtcacaagccctgg	9	9	8	15	1	2	0	2	0	1	0	4	0	3	0	3	2	3	3	3	2	4	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:27373231A>T	ENST00000296096.5	+	2	593	c.463A>T	c.(463-465)Aag>Tag	p.K155*		NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN	transcription factor 23	155					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	nucleus (GO:0005634)				large_intestine(2)|lung(11)|prostate(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACCCTCTCAAGGTAAGTCA	0.622																																					p.K155X		.											.	TCF23-90	0			c.A463T						.						100	109	106					2																	27373231		2203	4300	6503	SO:0001587	stop_gained	150921	exon2			CCTCTCAAGGTAA	AC013403	CCDS33163.1	2p23.3	2013-05-21			ENSG00000163792	ENSG00000163792		"Basic helix-loop-helix proteins"	18602	protein-coding gene	gene with protein product		609635				11701948, 10652346	Standard	NM_175769		Approved	OUT, bHLHa24	uc010ylg.2	Q7RTU1	OTTHUMG00000152031	ENST00000296096.5:c.463A>T	2.37:g.27373231A>T	ENSP00000296096:p.Lys155*	Somatic	391	0		WXS	Illumina HiSeq	Phase_I	260	107	NM_175769	0	0	0	0	0	B2RNZ3	Nonsense_Mutation	SNP	ENST00000296096.5	37	CCDS33163.1	.	.	.	.	.	.	.	.	.	.	A	37	6.018528	0.97205	.	.	ENSG00000163792	ENST00000296096	.	.	.	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.5975	13.8444	0.63459	1.0:0.0:0.0:0.0	.	.	.	.	X	155	.	ENSP00000296096:K155X	K	+	1	0	TCF23	27226735	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.489000	0.90461	2.164000	0.68074	0.459000	0.35465	AAG	.		0.622	TCF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324980.1	NM_175769		T	27373231	A	T	27373231	4	4	18	1	0	0	0	0	0	1	0	0	15724	131	5	5	469	5	TCF23	2	27373231	Nonsense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	17858177	27373231	215826142	13	1492											
SPTBN1	6711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	54852000	54852000	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggctttgcggaatgagctCataagacaggagaaactgga	13	8	13	7	1	1	3	1	1	0	2	1	6	1	5	0	4	3	2	0	4	3	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:54852000C>T	ENST00000356805.4	+	11	1523	c.1242C>T	c.(1240-1242)ctC>ctT	p.L414L	SPTBN1_ENST00000333896.5_Silent_p.L401L	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	414					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GGAATGAGCTCATAAGACAGG	0.493																																					p.L414L		.											.	SPTBN1-140	0			c.C1242T						.						76	73	74					2																	54852000		2203	4300	6503	SO:0001819	synonymous_variant	6711	exon11			TGAGCTCATAAGA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1242C>T	2.37:g.54852000C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	58	10	NM_003128	0	0	43	54	11	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			.		0.493	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54852000	C	T	54852000	2	4	18	1	0	0	0	0	0	0	0	1	15151	813	29	2		2	SPTBN1	2	54852000	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	27478769	54852000	188347373	14	1493											
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109380509	109380509	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgatgatgacggtcctcacTttgagcctgtagtacctctt	8	14	9	10	1	2	4	1	4	1	0	3	4	3	4	3	1	2	2	3	1	2	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:109380509T>G	ENST00000283195.6	+	20	3640	c.3514T>G	c.(3514-3516)Ttt>Gtt	p.F1172V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1172	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CGGTCCTCACTTTGAGCCTGT	0.428																																					p.F1172V		.											.	RANBP2-675	0			c.T3514G						.						117	109	112					2																	109380509		2203	4299	6502	SO:0001583	missense	5903	exon20			CCTCACTTTGAGC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3514T>G	2.37:g.109380509T>G	ENSP00000283195:p.Phe1172Val	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	148	58	NM_006267	0	0	1	2	1	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.034233	0.54896	.	.	ENSG00000153201	ENST00000283195	T	0.39787	1.06	5.57	5.57	0.84162	Pleckstrin homology-type (1);Ran binding protein 1 (2);	.	.	.	.	T	0.64951	0.2645	M	0.74258	2.255	0.50039	D	0.999845	D	0.76494	0.999	D	0.79784	0.993	T	0.67684	-0.5607	9	0.54805	T	0.06	-23.4766	15.7401	0.77887	0.0:0.0:0.0:1.0	.	1172	P49792	RBP2_HUMAN	V	1172	ENSP00000283195:F1172V	ENSP00000283195:F1172V	F	+	1	0	RANBP2	108746941	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.040000	0.89188	2.107000	0.64212	0.528000	0.53228	TTT	.		0.428	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109380509	T	G	109380509	3	3	18	1	0	0	0	0	1	0	0	0	13060	1609	56	5	3592	5	RANBP2	2	109380509	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	54528509	109380509	133818864	15	1494											
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141816463	141816463	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccacttacctgttggttgaGttcttttttgataaattcgg	7	18	8	8	1	1	2	0	2	1	0	2	2	1	2	2	2	1	3	2	2	3	9			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:141816463G>C	ENST00000389484.3	-	9	2368	c.1397C>G	c.(1396-1398)aCt>aGt	p.T466S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	466					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGTTGGTTGAGTTCTTTTTTG	0.353										TSP Lung(27;0.18)																											p.T466S	Colon(99;50 2074 2507 20106)	.											.	LRP1B-311	0			c.C1397G						.						83	82	82					2																	141816463		2201	4298	6499	SO:0001583	missense	53353	exon9			GGTTGAGTTCTTT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1397C>G	2.37:g.141816463G>C	ENSP00000374135:p.Thr466Ser	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	31	14	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	7.474	0.647368	0.14516	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.97575	-4.44	5.45	2.69	0.31865	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.247105	0.32028	U	0.006685	D	0.93032	0.7782	L	0.33245	0.995	0.09310	N	1	B	0.17038	0.02	B	0.16722	0.016	D	0.84920	0.0853	10	0.40728	T	0.16	.	9.4538	0.38743	0.2856:0.0:0.7144:0.0	.	466	Q9NZR2	LRP1B_HUMAN	S	466;404	ENSP00000374135:T466S	ENSP00000374135:T466S	T	-	2	0	LRP1B	141532933	0.582000	0.26749	0.952000	0.39060	0.309000	0.27889	1.212000	0.32394	0.287000	0.22375	0.462000	0.41574	ACT	.		0.353	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141816463	G	C	141816463	3	2	18	1	0	0	0	0	1	0	0	0	8980	1029	36	4	12734	4	LRP1B	2	141816463	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	32435954	141816463	101382910	16	1495			1	7		2	2	14	N	G_A	4.199323e-05
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141816476	141816476	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggttgagttcttttttgatAaattcggattccccaagcat	9	17	8	7	1	1	2	0	2	1	0	3	3	2	3	2	2	1	3	2	2	3	8			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:141816476A>T	ENST00000389484.3	-	9	2355	c.1384T>A	c.(1384-1386)Tat>Aat	p.Y462N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	462					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTTTTTTGATAAATTCGGATT	0.343										TSP Lung(27;0.18)																											p.Y462N	Colon(99;50 2074 2507 20106)	.											.	LRP1B-311	0			c.T1384A						.						82	82	82					2																	141816476		2201	4297	6498	SO:0001583	missense	53353	exon9			TTTGATAAATTCG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1384T>A	2.37:g.141816476A>T	ENSP00000374135:p.Tyr462Asn	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	30	10	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	17.26	3.345446	0.61073	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.97404	-4.37	5.45	5.45	0.79879	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	U	0.000004	D	0.98588	0.9528	M	0.89095	3.005	0.58432	D	0.999994	D	0.76494	0.999	D	0.83275	0.996	D	0.99589	1.0975	10	0.62326	D	0.03	.	15.5201	0.75859	1.0:0.0:0.0:0.0	.	462	Q9NZR2	LRP1B_HUMAN	N	462;400	ENSP00000374135:Y462N	ENSP00000374135:Y462N	Y	-	1	0	LRP1B	141532946	1.000000	0.71417	0.974000	0.42286	0.256000	0.26092	8.865000	0.92300	2.080000	0.62538	0.379000	0.24179	TAT	.		0.343	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141816476	A	T	141816476	3	4	18	1	0	0	0	0	1	0	0	0	8980	362	13	5	12747	5	LRP1B	2	141816476	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	13	141816476	101382897	17	1496			1	7		2	2	14	N	G_A	4.199323e-05
FBXO36	130888	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	230861514	230861516	+	In_Frame_Del	DEL	AAT	AAT	-																															gaatattagactatgtcatcAatttgtgcaaaggtaaattt																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:230861514_230861516delAAT	ENST00000283946.3	+	3	271_273	c.253_255delAAT	c.(253-255)aatdel	p.N85del	FBXO36_ENST00000373652.3_In_Frame_Del_p.N54del|FBXO36_ENST00000409992.1_Intron	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	85										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTATGTCATCAATTTGTGCAAAG	0.355																																					p.85_85del		.											.	FBXO36-227	0			c.253_255del						.																																			SO:0001651	inframe_deletion	130888	exon3			.	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.253_255delAAT	2.37:g.230861514_230861516delAAT	ENSP00000283946:p.Asn85del	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	115	47	NM_174899	0	0	0	0	0	B3KVQ6|Q53TE6|Q8WWD4	In_Frame_Del	DEL	ENST00000283946.3	37	CCDS2472.1																																																																																			.		0.355	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		-	230861516	AAT	-	230861514	7	5	18	1	0	1	0	1	0	0	0	0	5764	130	5	0	263	0	FBXO36	2	230861514	In_Frame_Del	DEL	AAT	TCGA-A4-8517-01A-11D-2396-08	89045038	230861514	12337859	18	1497											
HYAL2	8692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50357591	50357591	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acacgtttctgcagcatcttCcggtgtgcccaaaggctgac	8	10	10	13	2	2	1	0	1	2	0	3	1	3	1	2	2	3	4	2	2	1	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:50357591C>T	ENST00000447092.1	-	1	2622	c.330G>A	c.(328-330)cgG>cgA	p.R110R	HYAL2_ENST00000442581.1_Silent_p.R110R|HYAL2_ENST00000357750.4_Silent_p.R110R|TUSC2_ENST00000462137.1_5'UTR|HYAL2_ENST00000395139.3_Silent_p.R110R			Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	110					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|defense response to virus (GO:0051607)|fusion of virus membrane with host plasma membrane (GO:0019064)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|kidney development (GO:0001822)|monocyte activation (GO:0042117)|multicellular organismal aging (GO:0010259)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|transformation of host cell by virus (GO:0019087)|viral entry into host cell (GO:0046718)	anchored component of external side of plasma membrane (GO:0031362)|anchored component of plasma membrane (GO:0046658)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|lysosome (GO:0005764)|membrane raft (GO:0045121)|microvillus (GO:0005902)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|hyaluronic acid binding (GO:0005540)|hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)|receptor signaling protein tyrosine kinase inhibitor activity (GO:0030294)|receptor tyrosine kinase binding (GO:0030971)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)			breast(1)|endometrium(2)|kidney(1)|ovary(1)|prostate(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCAGCATCTTCCGGTGTGCCC	0.597																																					p.R110R		.											.	HYAL2-279	0			c.G330A						.						79	71	74					3																	50357591		2203	4300	6503	SO:0001819	synonymous_variant	8692	exon3			CATCTTCCGGTGT	AJ000099	CCDS2818.1	3p21.3	2008-07-18			ENSG00000068001	ENSG00000068001			5321	protein-coding gene	gene with protein product	"lysosomal hyaluronidase", "PH-20 homolog", "hyaluronidase 2"	603551				9712871, 9790770	Standard	NM_003773		Approved	LuCa-2, LUCA2	uc003czv.3	Q12891	OTTHUMG00000156876	ENST00000447092.1:c.330G>A	3.37:g.50357591C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	87	30	NM_033158	0	0	21	36	15	B3KRZ2|O15177|Q9BW29	Silent	SNP	ENST00000447092.1	37	CCDS2818.1																																																																																			.		0.597	HYAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346391.1	NM_003773		T	50357591	C	T	50357591	2	4	18	1	0	0	0	0	0	0	0	1	7485	842	30	2		2	HYAL2	3	50357591	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08		50357591	147664839	19	1498											
CACNA1D	776	broad.mit.edu	37	chr3	53808687	53808687	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccagacgtttccccaggCggtgctgctgctcttcaggt	4	12	11	14	2	2	1	1	0	1	1	4	1	4	1	3	3	3	4	3	3	0	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:53808687C>T	ENST00000350061.5	+	34	4695	c.4184C>T	c.(4183-4185)gCg>gTg	p.A1395V	CACNA1D_ENST00000540742.1_Missense_Mutation_p.A287V|CACNA1D_ENST00000288139.4_Missense_Mutation_p.A1415V|CACNA1D_ENST00000422281.2_Missense_Mutation_p.A1380V	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	1395					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)	p.A1415V(1)		breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TTTCCCCAGGCGGTGCTGCTG	0.547																																					p.A1415V													.	CACNA1D-100	1	Substitution - Missense(1)	prostate(1)	c.C4244T						.						113	112	112					3																	53808687		2203	4300	6503	SO:0001583	missense	776	exon35			CCCAGGCGGTGCT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.4184C>T	3.37:g.53808687C>T	ENSP00000288133:p.Ala1395Val	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	103	4	NM_000720	0	0	10	10	0	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	37	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	C	35	5.440507	0.96168	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000540742	D;D;D;D;D	0.98901	-5.22;-5.22;-5.22;-5.22;-5.22	6.17	6.17	0.99709	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99606	0.9857	H	0.98818	4.34	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.985;0.998;0.995;0.999	D	0.97737	1.0206	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1380;287;1088;1395;1415	B0FYA3;F5H313;Q59GD8;Q01668;Q01668-2	.;.;.;CAC1D_HUMAN;.	V	1395;1415;1380;1088;287	ENSP00000288133:A1395V;ENSP00000288139:A1415V;ENSP00000409174:A1380V;ENSP00000418014:A1088V;ENSP00000438229:A287V	ENSP00000288139:A1415V	A	+	2	0	CACNA1D	53783727	1.000000	0.71417	0.989000	0.46669	0.895000	0.52256	7.800000	0.85949	2.941000	0.99782	0.655000	0.94253	GCG	.		0.547	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		T	53808687	C	T	53808687	3	4	18	1	0	0	0	0	1	0	0	0	2547	768	27	1	4490	1	CACNA1D	3	53808687	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	3451096	53808687	144213743	20	1499											
MITF	4286	ucsc.edu	37	chr3	69988280	69988280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgaagagcaaaacagggCagagagcgagtgcccaggca	14	4	15	8	1	0	3	0	1	0	2	0	5	0	3	1	2	4	4	1	2	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:69988280C>T	ENST00000448226.2	+	4	741	c.614C>T	c.(613-615)gCa>gTa	p.A205V	MITF_ENST00000328528.6_Missense_Mutation_p.A204V|MITF_ENST00000314557.6_Missense_Mutation_p.A98V|MITF_ENST00000394355.2_Missense_Mutation_p.A180V|MITF_ENST00000472437.1_Missense_Mutation_p.A153V|MITF_ENST00000314589.5_Missense_Mutation_p.A189V|MITF_ENST00000531774.1_Missense_Mutation_p.A42V|MITF_ENST00000394351.3_Missense_Mutation_p.A98V|MITF_ENST00000352241.4_Missense_Mutation_p.A205V			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	205					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		CAAAACAGGGCAGAGAGCGAG	0.418			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.A205V	Melanoma(29;269 969 31479 41502 42961)			Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF-524	0			c.C614T						.						102	98	99					3																	69988280		2203	4300	6503	SO:0001583	missense	4286	exon4			ACAGGGCAGAGAG		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.614C>T	3.37:g.69988280C>T	ENSP00000391803:p.Ala205Val	Somatic	38	0		WXS	Illumina HiSeq		36	4	NM_198159	0	0	17	17	0	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	C	9.959	1.222404	0.22457	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000433517;ENST00000472437;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351;ENST00000531774	T;T;T;T;T;T;T;T;T;T	0.23348	2.74;2.24;2.52;2.73;1.91;2.73;2.74;2.52;1.92;2.5	5.98	0.676	0.17958	.	0.791935	0.11257	N	0.583025	T	0.12135	0.0295	N	0.08118	0	0.21147	N	0.999773	B;B;B;B;B;B;B	0.09022	0.0;0.001;0.001;0.0;0.002;0.001;0.0	B;B;B;B;B;B;B	0.08055	0.001;0.003;0.002;0.002;0.001;0.001;0.0	T	0.35301	-0.9794	9	.	.	.	.	10.3394	0.43868	0.0:0.5304:0.0:0.4696	.	153;98;98;180;189;204;205	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	V	205;205;97;153;204;189;189;180;98;98;42	ENSP00000295600:A205V;ENSP00000391803:A205V;ENSP00000418845:A153V;ENSP00000327867:A204V;ENSP00000398639:A189V;ENSP00000324443:A189V;ENSP00000377884:A180V;ENSP00000324246:A98V;ENSP00000377880:A98V;ENSP00000435909:A42V	.	A	+	2	0	MITF	70070970	0.007000	0.16637	0.657000	0.29651	0.370000	0.29829	-0.088000	0.11198	0.048000	0.15891	-0.133000	0.14855	GCA	.		0.418	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69988280	C	T	69988280	3	4	18	1	0	0	0	0	1	0	0	0	9621	710	25	2	849	2	MITF	3	69988280	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	16179593	69988280	128034150	21	1500											
CEP63	80254	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	134267996	134267996	+	Frame_Shift_Del	DEL	A	A	-																															gatggaagcacataacaatgAatacaaagcagagattaaga																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:134267996delA	ENST00000337090.3	+	10	1333	c.1160delA	c.(1159-1161)gaafs	p.E387fs	CEP63_ENST00000513612.2_Frame_Shift_Del_p.E387fs|CEP63_ENST00000606977.1_Frame_Shift_Del_p.E387fs|CEP63_ENST00000354446.3_Frame_Shift_Del_p.E341fs|CEP63_ENST00000383229.3_Frame_Shift_Del_p.E387fs|CEP63_ENST00000332047.5_Frame_Shift_Del_p.E341fs			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	387					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CATAACAATGAATACAAAGCA	0.373																																					p.E387fs		.											.	CEP63-493	0			c.1160delA						.						98	89	92					3																	134267996		2203	4300	6503	SO:0001589	frameshift_variant	80254	exon11			.	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1160delA	3.37:g.134267996delA	ENSP00000336524:p.Glu387fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	52	16	NM_025180	0	0	0	0	0	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Frame_Shift_Del	DEL	ENST00000337090.3	37	CCDS3086.1																																																																																			.		0.373	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		-	134267996	A	-	134267996	7	5	18	1	0	1	0	1	0	0	0	0	3263	246	9	0	1194	0	CEP63	3	134267996	Frame_Shift_Del	DEL	A	TCGA-A4-8517-01A-11D-2396-08	64279716	134267996	63754434	22	1501											
MFN1	55669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179076735	179076735	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctaagtgttgaaggaactgAtggagataaagcctatctta	14	11	10	6	0	1	3	0	2	1	1	1	5	1	4	2	2	2	1	2	2	7	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:179076735A>C	ENST00000471841.1	+	4	482	c.356A>C	c.(355-357)gAt>gCt	p.D119A	MFN1_ENST00000280653.7_Missense_Mutation_p.D119A|MFN1_ENST00000263969.5_Missense_Mutation_p.D119A	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	119	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GAAGGAACTGATGGAGATAAA	0.378																																					p.D119A		.											.	MFN1-155	0			c.A356C						.						150	139	143					3																	179076735		2203	4300	6503	SO:0001583	missense	55669	exon4			GAACTGATGGAGA	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.356A>C	3.37:g.179076735A>C	ENSP00000420617:p.Asp119Ala	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	81	27	NM_033540	0	0	10	15	5	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	37	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.824508	0.71143	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000467174;ENST00000263969	D;D;D;D	0.96830	-4.14;-4.14;-4.14;-4.14	5.86	5.86	0.93980	Dynamin, GTPase domain (1);	0.045333	0.85682	D	0.000000	D	0.97932	0.9320	M	0.80508	2.5	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.71656	0.974;0.964	D	0.97957	1.0335	10	0.42905	T	0.14	-26.3212	16.5602	0.84551	1.0:0.0:0.0:0.0	.	147;119	Q4AEJ4;Q8IWA4	.;MFN1_HUMAN	A	119	ENSP00000420617:D119A;ENSP00000280653:D119A;ENSP00000419134:D119A;ENSP00000263969:D119A	ENSP00000263969:D119A	D	+	2	0	MFN1	180559429	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	8.904000	0.92590	2.367000	0.80283	0.528000	0.53228	GAT	.		0.378	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		C	179076735	A	C	179076735	3	2	18	1	0	0	0	0	1	0	0	0	9548	333	12	5	366	5	MFN1	3	179076735	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	44808739	179076735	18945695	23	1502											
USP13	8975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179426711	179426711	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatgggctacccactagcCgtgaaactgggaaccatcac	12	6	10	13	1	1	1	1	1	0	0	1	3	1	2	3	2	4	1	3	2	4	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:179426711C>A	ENST00000263966.3	+	6	1242	c.771C>A	c.(769-771)gcC>gcA	p.A257A	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Silent_p.A192A	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	257					autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			ACCCACTAGCCGTGAAACTGG	0.547																																					p.A257A		.											.	USP13-659	0			c.C771A						.						75	70	71					3																	179426711		2203	4300	6503	SO:0001819	synonymous_variant	8975	exon6			ACTAGCCGTGAAA	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.771C>A	3.37:g.179426711C>A		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	73	33	NM_003940	0	0	1	2	1	A8K2S3|B4DYF3|D3DNS2|Q96B25	Silent	SNP	ENST00000263966.3	37	CCDS3235.1																																																																																			.		0.547	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179426711	C	A	179426711	2	1	18	1	0	0	0	0	0	0	0	1	17077	639	23	4		4	USP13	3	179426711	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	349976	179426711	18595719	24	1503											
CPN2	1370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	194062198	194062198	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggagccgatcggtgtactGctgcagccagttgaagaggt	9	8	15	9	2	0	2	0	1	0	1	1	4	0	3	2	3	5	4	2	3	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:194062198G>T	ENST00000323830.3	-	2	1323	c.1234C>A	c.(1234-1236)Cag>Aag	p.Q412K	CPN2_ENST00000429275.1_Missense_Mutation_p.Q412K	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	412	LRRCT.				protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		TCGGTGTACTGCTGCAGCCAG	0.602																																					p.Q412K		.											.	CPN2-73	0			c.C1234A						.						62	64	63					3																	194062198		2203	4300	6503	SO:0001583	missense	1370	exon2			TGTACTGCTGCAG	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"carboxypeptidase N, polypeptide 2, 83kD"	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.1234C>A	3.37:g.194062198G>T	ENSP00000319464:p.Gln412Lys	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	76	28	NM_001080513	0	0	1	2	1	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	G	2.132	-0.398880	0.04865	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.24151	1.87;1.87	5.56	1.46	0.22682	Cysteine-rich flanking region, C-terminal (1);	0.280456	0.19931	N	0.102851	T	0.10981	0.0268	N	0.25094	0.71	0.09310	N	1	B	0.21071	0.051	B	0.16722	0.016	T	0.32955	-0.9887	10	0.05436	T	0.98	.	4.2056	0.10486	0.0732:0.3827:0.2364:0.3077	.	412	P22792	CPN2_HUMAN	K	412	ENSP00000319464:Q412K;ENSP00000402232:Q412K	ENSP00000319464:Q412K	Q	-	1	0	CPN2	195543893	0.000000	0.05858	0.002000	0.10522	0.124000	0.20399	-0.469000	0.06648	0.787000	0.33731	-0.165000	0.13383	CAG	.		0.602	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		T	194062198	G	T	194062198	3	4	18	1	0	0	0	0	1	0	0	0	3816	1328	46	4	407	4	CPN2	3	194062198	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	14635487	194062198	3960232	25	1504											
ODAM	54959	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	71064324	71064324	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgtattctccttcaaaaTgcctcaagagcaaggacagg	13	10	8	10	0	3	1	2	0	1	1	4	2	3	2	2	2	2	2	2	2	6	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:71064324T>A	ENST00000396094.2	+	5	452	c.404T>A	c.(403-405)aTg>aAg	p.M135K		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	135	Gln-rich.				biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						TCCTTCAAAATGCCTCAAGAG	0.378																																					p.M135K		.											.	ODAM-134	0			c.T404A						.						120	116	118					4																	71064324		2203	4300	6503	SO:0001583	missense	54959	exon5			TCAAAATGCCTCA	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.404T>A	4.37:g.71064324T>A	ENSP00000379401:p.Met135Lys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	91	6	NM_017855	0	0	0	0	0	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	37	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	T	13.87	2.366377	0.41902	.	.	ENSG00000109205	ENST00000396094;ENST00000510709;ENST00000514097	T;T	0.48522	0.81;0.81	4.82	3.65	0.41850	.	0.949132	0.08736	N	0.901245	T	0.37972	0.1023	L	0.42245	1.32	0.22754	N	0.998773	P	0.38020	0.615	B	0.32805	0.153	T	0.30592	-0.9973	10	0.72032	D	0.01	-0.3936	7.1176	0.25424	0.0:0.101:0.0:0.899	.	135	A1E959	ODAM_HUMAN	K	135;121;88	ENSP00000379401:M135K;ENSP00000426106:M88K	ENSP00000379401:M135K	M	+	2	0	ODAM	71098913	0.773000	0.28580	0.893000	0.35052	0.676000	0.39594	0.800000	0.27042	0.987000	0.38709	0.374000	0.22700	ATG	.		0.378	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855		A	71064324	T	A	71064324	3	1	18	1	0	0	0	0	1	0	0	0	10850	1464	51	5	422	5	ODAM	4	71064324	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		71064324	120089952	26	1505											
SLC4A4	8671	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	72429564	72429564	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaaattccaatggacatcAtggaacagcaacctttccta	15	11	5	10	0	1	0	1	0	0	0	3	2	3	2	3	2	3	1	3	2	6	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:72429564A>G	ENST00000264485.5	+	24	3271	c.3154A>G	c.(3154-3156)Atg>Gtg	p.M1052V	SLC4A4_ENST00000340595.3_Missense_Mutation_p.M1008V|SLC4A4_ENST00000425175.1_Intron|SLC4A4_ENST00000351898.6_Missense_Mutation_p.M968V	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	1052					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.M1008V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	AATGGACATCATGGAACAGCA	0.358																																					p.M1052V		.											.	SLC4A4-95	1	Substitution - Missense(1)	large_intestine(1)	c.A3154G						.						152	158	156					4																	72429564		2203	4300	6503	SO:0001583	missense	8671	exon24			GACATCATGGAAC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.3154A>G	4.37:g.72429564A>G	ENSP00000264485:p.Met1052Val	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	122	45	NM_001098484	0	0	12	29	17	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	A	7.750	0.703080	0.15172	.	.	ENSG00000080493	ENST00000264485;ENST00000351898;ENST00000340595	T;T;T	0.75154	-0.91;-0.58;-0.91	5.46	4.25	0.50352	.	0.037886	0.85682	D	0.000000	T	0.56572	0.1994	N	0.24115	0.695	0.80722	D	1	B;B;B	0.20164	0.012;0.042;0.025	B;B;B	0.21546	0.017;0.035;0.01	T	0.49643	-0.8918	10	0.02654	T	1	.	12.5178	0.56042	0.8603:0.1397:0.0:0.0	.	968;1008;1052	Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	V	1052;968;1008	ENSP00000264485:M1052V;ENSP00000307349:M968V;ENSP00000344272:M1008V	ENSP00000264485:M1052V	M	+	1	0	SLC4A4	72648428	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.988000	0.76212	0.885000	0.36088	-0.619000	0.04042	ATG	.		0.358	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		G	72429564	A	G	72429564	3	3	18	1	0	0	0	0	1	0	0	0	14688	217	8	3	3365	3	SLC4A4	4	72429564	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	1365240	72429564	118724712	27	1506											
SHROOM3	57619	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	77661360	77661360	+	Frame_Shift_Del	DEL	G	G	-																															ctgagaagacacagcagcctGgagctaggccggggaaccca																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:77661360delG	ENST00000296043.6	+	5	2987	c.2034delG	c.(2032-2034)ctgfs	p.L678fs		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	678					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ACAGCAGCCTGGAGCTAGGCC	0.602																																					p.L678fs		.											.	SHROOM3-93	0			c.2034delG						.						46	58	54					4																	77661360		2203	4300	6503	SO:0001589	frameshift_variant	57619	exon5			.	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.2034delG	4.37:g.77661360delG	ENSP00000296043:p.Leu678fs	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	165	83	NM_020859	0	0	0	0	0	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Frame_Shift_Del	DEL	ENST00000296043.6	37	CCDS3579.2																																																																																			.		0.602	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		-	77661360	G	-	77661360	7	5	18	1	0	1	0	1	0	0	0	0	14327	1335	47	0	2052	0	SHROOM3	4	77661360	Frame_Shift_Del	DEL	G	TCGA-A4-8517-01A-11D-2396-08	5231796	77661360	113492916	28	1507											
EXOSC9	5393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	122724130	122724130	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgtctaagaaattcgaaGtgtatagacactgagtctct	14	12	9	6	1	2	4	0	1	2	3	4	5	2	4	0	0	0	1	0	0	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:122724130G>A	ENST00000243498.5	+	4	450	c.342G>A	c.(340-342)aaG>aaA	p.K114K	EXOSC9_ENST00000379663.3_Silent_p.K114K|EXOSC9_ENST00000509980.1_3'UTR|EXOSC9_ENST00000512454.1_Silent_p.K98K	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	114	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GAAATTCGAAGTGTATAGACA	0.393																																					p.K114K		.											.	EXOSC9-90	0			c.G342A						.						126	118	121					4																	122724130		2203	4300	6503	SO:0001819	synonymous_variant	5393	exon4			TTCGAAGTGTATA	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.342G>A	4.37:g.122724130G>A		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	69	32	NM_001034194	0	0	10	14	4	Q12883|Q4W5P5|Q86Y41|Q86Y48	Silent	SNP	ENST00000243498.5	37	CCDS3722.2																																																																																			.		0.393	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		A	122724130	G	A	122724130	2	1	18	1	0	0	0	0	0	0	0	1	5334	1020	36	2		2	EXOSC9	4	122724130	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	45062770	122724130	68430146	29	1508											
BDP1	55814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	70813231	70813231	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatgaaaatcaaagtcaggTggttcttgtagaaaaccttc	14	12	9	6	0	3	2	2	1	1	1	4	2	3	2	1	2	1	3	1	2	7	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:70813231T>A	ENST00000358731.4	+	22	5206	c.4943T>A	c.(4942-4944)gTg>gAg	p.V1648E	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1648					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CAAAGTCAGGTGGTTCTTGTA	0.308																																					p.V1648E		.											.	BDP1-92	0			c.T4943A						.						70	70	70					5																	70813231		1812	4074	5886	SO:0001583	missense	55814	exon22			GTCAGGTGGTTCT	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.4943T>A	5.37:g.70813231T>A	ENSP00000351575:p.Val1648Glu	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	76	32	NM_018429	0	0	0	0	0	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	T	2.499	-0.315545	0.05422	.	.	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.11495	2.77	3.38	-3.81	0.04294	.	1.408380	0.05200	N	0.504767	T	0.08846	0.0219	L	0.54323	1.7	0.09310	N	0.999996	B;B	0.25955	0.037;0.138	B;B	0.18561	0.008;0.022	T	0.41662	-0.9496	10	0.56958	D	0.05	.	0.473	0.00535	0.1852:0.283:0.1887:0.3431	.	1648;1648	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1648;1228	ENSP00000351575:V1648E	ENSP00000351575:V1648E	V	+	2	0	BDP1	70848987	0.000000	0.05858	0.004000	0.12327	0.069000	0.16628	-0.026000	0.12392	-0.363000	0.08101	0.383000	0.25322	GTG	.		0.308	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		A	70813231	T	A	70813231	3	1	18	1	0	0	0	0	1	0	0	0	1396	1696	59	5	5029	5	BDP1	5	70813231	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		70813231	110102029	30	1509											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82836395	82836395	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagtttccaagaccgtttcAgggaattcgaggattccacc	10	11	10	10	2	1	1	1	0	0	1	4	4	3	3	4	2	0	3	4	2	3	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:82836395A>T	ENST00000265077.3	+	8	8138	c.7573A>T	c.(7573-7575)Agg>Tgg	p.R2525W	VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.R1538W|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2525	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AGACCGTTTCAGGGAATTCGA	0.403																																					p.R2525W		.											.	VCAN-238	0			c.A7573T						.						53	54	54					5																	82836395		2203	4300	6503	SO:0001583	missense	1462	exon8			CGTTTCAGGGAAT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7573A>T	5.37:g.82836395A>T	ENSP00000265077:p.Arg2525Trp	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	56	21	NM_004385	0	0	22	34	12	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370274	0.24771	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.34072	1.38;1.38	6.17	-11.7	0.00046	.	1.888030	0.01961	N	0.043346	T	0.17577	0.0422	N	0.16478	0.41	0.09310	N	1	B;B	0.12630	0.006;0.004	B;B	0.11329	0.006;0.003	T	0.16808	-1.0390	10	0.54805	T	0.06	.	4.6375	0.12531	0.2227:0.3575:0.3326:0.0872	.	1538;2525	P13611-2;P13611	.;CSPG2_HUMAN	W	2525;1538	ENSP00000265077:R2525W;ENSP00000340062:R1538W	ENSP00000265077:R2525W	R	+	1	2	VCAN	82872151	0.000000	0.05858	0.000000	0.03702	0.260000	0.26232	-0.702000	0.05069	-2.549000	0.00480	0.533000	0.62120	AGG	.		0.403	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82836395	A	T	82836395	3	4	18	1	0	0	0	0	1	0	0	0	17171	179	7	5	7599	5	VCAN	5	82836395	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	12023164	82836395	98078865	31	1510											
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140724915	140724915	+	Missense_Mutation	SNP	A	A	C																															tgtccacagaaactcacatcAccctgcatgtgattgacatc																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:140724915A>C	ENST00000253812.6	+	1	1315	c.1315A>C	c.(1315-1317)Acc>Ccc	p.T439P	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	439	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACTCACATCACCCTGCATGT	0.507																																					p.T439P		.											.	PCDHGA3-68	0			c.A1315C						.						99	110	106					5																	140724915		2101	4254	6355	SO:0001583	missense	56112	exon1			CACATCACCCTGC	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1315A>C	5.37:g.140724915A>C	ENSP00000253812:p.Thr439Pro	Somatic	170	1		WXS	Illumina HiSeq	Phase_I	187	32	NM_032011	0	0	1	1	0	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	0.302	-0.973094	0.02215	.	.	ENSG00000254245	ENST00000253812	T	0.02552	4.25	5.59	-3.1	0.05315	Cadherin (4);Cadherin-like (1);	1.180670	0.06999	U	0.823041	T	0.03827	0.0108	M	0.75777	2.31	0.09310	N	1	B;B	0.15141	0.004;0.012	B;B	0.17979	0.008;0.02	T	0.48581	-0.9023	10	0.36615	T	0.2	.	1.0414	0.01559	0.2895:0.3371:0.17:0.2033	.	439;439	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	P	439	ENSP00000253812:T439P	ENSP00000253812:T439P	T	+	1	0	PCDHGA3	140705099	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.672000	0.05244	-0.115000	0.11915	-0.331000	0.08364	ACC	.		0.507	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		C	140724915	A	C	140724915	3	2	18	1	0	0	0	0	1	0	0	0	11581	159	6	5	1317	5	PCDHGA3	5	140724915	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	57888520	140724915	40190345	32	1511	12	2									
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140724920	140724920	+	Silent	SNP	G	G	T																															acagaaactcacatcaccctGcatgtgattgacatcaatga																								rs567477411		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:140724920G>T	ENST00000253812.6	+	1	1320	c.1320G>T	c.(1318-1320)ctG>ctT	p.L440L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	440	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATCACCCTGCATGTGATTG	0.502																																					p.L440L		.											.	PCDHGA3-68	0			c.G1320T						.						103	114	110					5																	140724920		2107	4256	6363	SO:0001819	synonymous_variant	56112	exon1			CACCCTGCATGTG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1320G>T	5.37:g.140724920G>T		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	205	36	NM_032011	0	0	0	0	0	Q9Y5D4	Silent	SNP	ENST00000253812.6	37	CCDS47290.1																																																																																			.		0.502	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140724920	G	T	140724920	2	4	18	1	0	0	0	0	0	0	0	1	11581	1306	46	4		4	PCDHGA3	5	140724920	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	5	140724920	40190340	33	1512	12	2									
TNIP1	10318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	150444534	150444534	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gctttacctaacatctttatCccttgcattttttccttcag	7	19	3	12	0	2	0	1	0	1	0	4	0	4	0	3	0	3	2	3	0	3	10			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:150444534C>G	ENST00000389378.2	-	2	711	c.123G>C	c.(121-123)ggG>ggC	p.G41G	TNIP1_ENST00000520931.1_Intron|TNIP1_ENST00000315050.7_Silent_p.G41G|TNIP1_ENST00000523200.1_Silent_p.G41G|TNIP1_ENST00000524280.1_Silent_p.G41G|TNIP1_ENST00000522226.1_Silent_p.G41G|TNIP1_ENST00000523338.1_Silent_p.G41G|TNIP1_ENST00000518977.1_Silent_p.G41G|TNIP1_ENST00000521591.1_Silent_p.G41G	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	41					defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACATCTTTATCCCTTGCATTT	0.567																																					p.G41G		.											.	TNIP1-91	0			c.G123C						.						170	164	166					5																	150444534		2203	4300	6503	SO:0001819	synonymous_variant	10318	exon2			CTTTATCCCTTGC	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"virion-associated nuclear-shuttling protein", "Nef-associated factor 1 SNP"	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.123G>C	5.37:g.150444534C>G		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	128	45	NM_001252385	0	0	0	0	0	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Silent	SNP	ENST00000389378.2	37	CCDS34280.1																																																																																			.		0.567	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		G	150444534	C	G	150444534	2	3	18	1	0	0	0	0	0	0	0	1	16346	842	30	4		4	TNIP1	5	150444534	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	9719614	150444534	30470726	34	1513											
WWC1	23286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	167833322	167833322	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaaaaggaaaagcaagAtctcattaaggtatgcaagt	17	8	12	4	0	1	1	1	0	1	1	2	3	1	3	0	4	2	3	0	4	8	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:167833322A>C	ENST00000265293.4	+	6	1212	c.710A>C	c.(709-711)gAt>gCt	p.D237A	WWC1_ENST00000521089.1_Missense_Mutation_p.D237A	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	237					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GAAAAGCAAGATCTCATTAAG	0.458																																					p.D237A		.											.	WWC1-157	0			c.A710C						.						189	179	182					5																	167833322		2203	4300	6503	SO:0001583	missense	23286	exon6			AGCAAGATCTCAT	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.710A>C	5.37:g.167833322A>C	ENSP00000265293:p.Asp237Ala	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	165	70	NM_015238	0	0	0	0	0	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.503944|4.503944	0.85176|0.85176	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089|ENST00000393895;ENST00000524228	T;T|.	0.07800|.	3.16;3.18|.	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	0.057843|.	0.64402|.	D|.	0.000002|.	T|T	0.75910|0.75910	0.3914|0.3914	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.60160|.	0.987;0.972;0.978;0.963|.	P;P;P;P|.	0.59012|.	0.85;0.737;0.796;0.63|.	T|T	0.77225|0.77225	-0.2666|-0.2666	10|5	0.52906|.	T|.	0.07|.	.|.	15.5264|15.5264	0.75910|0.75910	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	237;143;143;237|.	Q8IX03-2;F5H498;B3KX05;Q8IX03|.	.;.;.;KIBRA_HUMAN|.	A|S	237|198;13	ENSP00000265293:D237A;ENSP00000427772:D237A|.	ENSP00000265293:D237A|.	D|R	+|+	2|3	0|2	WWC1|WWC1	167765900|167765900	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.251000|9.251000	0.95483|0.95483	2.078000|2.078000	0.62432|0.62432	0.459000|0.459000	0.35465|0.35465	GAT|AGA	.		0.458	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		C	167833322	A	C	167833322	3	2	18	1	0	0	0	0	1	0	0	0	17444	333	12	5	732	5	WWC1	5	167833322	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	17388788	167833322	13081938	35	1514											
DDR1	780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30865203	30865203	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtcgaggctcaaggaccCaaacatcattcggctgctgg	10	8	11	12	2	2	0	2	0	0	0	4	2	2	1	1	4	2	3	1	4	2	1	rs541302814		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:30865203C>A	ENST00000324771.8	+	17	2593	c.2045C>A	c.(2044-2046)cCa>cAa	p.P682Q	DDR1_ENST00000513240.1_Missense_Mutation_p.P688Q|DDR1_ENST00000454612.2_Missense_Mutation_p.P645Q|DDR1_ENST00000418800.2_Missense_Mutation_p.P645Q|DDR1_ENST00000376570.4_Missense_Mutation_p.P645Q|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000361741.4_Missense_Mutation_p.P349Q|DDR1_ENST00000376569.3_Missense_Mutation_p.P645Q|DDR1_ENST00000452441.1_Missense_Mutation_p.P682Q|DDR1_ENST00000508312.1_Missense_Mutation_p.P663Q|DDR1_ENST00000376568.3_Missense_Mutation_p.P682Q|DDR1_ENST00000376575.3_Missense_Mutation_p.P688Q|DDR1_ENST00000376567.2_Missense_Mutation_p.P645Q			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	682	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CTCAAGGACCCAAACATCATT	0.547																																					p.P688Q		.											.	DDR1-1403	0			c.C2063A						.						103	93	97					6																	30865203		2203	4300	6503	SO:0001583	missense	780	exon14			AGGACCCAAACAT	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.2045C>A	6.37:g.30865203C>A	ENSP00000318217:p.Pro682Gln	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	70	25	NM_013994	0	1	157	296	138	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.6|28.6	4.933034|4.933034	0.92458|0.92458	.|.	.|.	ENSG00000204580|ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240;ENST00000417521;ENST00000361741|ENST00000484556	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.91407|.	-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84|.	5.39|5.39	5.39|5.39	0.77823|0.77823	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.060949|.	0.64402|.	D|.	0.000003|.	T|T	0.65852|0.65852	0.2731|0.2731	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;P;D;D;D|.	0.89917|.	1.0;0.792;1.0;0.981;1.0|.	D;P;D;P;D|.	0.97110|.	0.999;0.643;0.999;0.888;1.0|.	T|T	0.64491|0.64491	-0.6395|-0.6395	10|5	0.56958|.	D|.	0.05|.	.|.	16.6419|16.6419	0.85128|0.85128	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	663;146;414;688;682|.	B7Z2K0;A2ABL4;A2ABM8;Q08345-5;Q08345|.	.;.;.;.;DDR1_HUMAN|.	Q|K	682;645;645;645;688;645;682;682;663;645;688;414;349|39	ENSP00000318217:P682Q;ENSP00000407699:P645Q;ENSP00000406091:P645Q;ENSP00000365753:P645Q;ENSP00000365759:P688Q;ENSP00000365754:P645Q;ENSP00000365752:P682Q;ENSP00000405039:P682Q;ENSP00000422442:P663Q;ENSP00000365751:P645Q;ENSP00000427552:P688Q;ENSP00000398682:P414Q;ENSP00000354844:P349Q|.	ENSP00000318217:P682Q|.	P|Q	+|+	2|1	0|0	DDR1|DDR1	30973182|30973182	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.974000|0.974000	0.67602|0.67602	5.959000|5.959000	0.70339|0.70339	2.525000|2.525000	0.85131|0.85131	0.462000|0.462000	0.41574|0.41574	CCA|CAA	.		0.547	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		A	30865203	C	A	30865203	3	1	18	1	0	0	0	0	1	0	0	0	4342	594	21	4	2117	4	DDR1	6	30865203	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08		30865203	140249864	36	1515											
BAT4	7918	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31632033	31632035	+	In_Frame_Del	DEL	TTC	TTC	-																															tgctgctggtgccttcattaTtcttcttttctttctctttc																								rs367920721		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:31632033_31632035delTTC	ENST00000375906.1	-	3	905_907	c.221_223delGAA	c.(220-225)agaata>ata	p.R74del	CSNK2B_ENST00000375882.2_5'Flank|GPANK1_ENST00000375896.4_In_Frame_Del_p.R74del|GPANK1_ENST00000375900.4_In_Frame_Del_p.R74del|Y_RNA_ENST00000364337.1_RNA|CSNK2B_ENST00000375865.2_5'Flank|GPANK1_ENST00000375895.2_In_Frame_Del_p.R74del|GPANK1_ENST00000375893.2_In_Frame_Del_p.R74del|CSNK2B_ENST00000375885.4_5'Flank|CSNK2B_ENST00000375866.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	74							nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						GCCTTCATTATTCTTCTTTTCTT	0.507																																					p.74_75del		.											.	GPANK1-91	0			c.221_223del						.		,,,,	3,4259		1,1,2129					,,,,	-2.1	0			84	2,8250		0,2,4124	no	coding,coding,coding,coding,coding	GPANK1	NM_033177.3,NM_001199240.1,NM_001199239.1,NM_001199238.1,NM_001199237.1	,,,,	1,3,6253	A1A1,A1R,RR		0.0242,0.0704,0.04	,,,,	,,,,		5,12509				SO:0001651	inframe_deletion	7918	exon3			.		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"Ankyrin repeat domain containing", "G patch domain containing"	13920	protein-coding gene	gene with protein product	"G patch domain containing 10", "ankyrin repeat domain 59"	142610	"HLA-B associated transcript 4"	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.221_223delGAA	6.37:g.31632036_31632038delTTC	ENSP00000365071:p.Arg74del	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	92	34	NM_001199238	0	0	0	0	0	A6NG25|B0UXA2|Q5SQ49	In_Frame_Del	DEL	ENST00000375906.1	37	CCDS4711.1																																																																																			.		0.507	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177		-	31632035	TTC	-	31632033	7	5	18	1	0	1	0	1	0	0	0	0	1324	1493	52	0	855	0	BAT4	6	31632033	In_Frame_Del	DEL	TTC	TCGA-A4-8517-01A-11D-2396-08	766830	31632033	139483034	37	1516											
KIFC1	3833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33365943	33365943	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggcctggagcctgagaaGgtgagctgggcatggagagc	9	6	19	7	0	0	3	0	2	0	2	0	7	0	4	2	5	3	2	2	5	1	0			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:33365943G>T	ENST00000428849.2	+	2	600	c.150G>T	c.(148-150)aaG>aaT	p.K50N		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	50					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						AGCCTGAGAAGGTGAGCTGGG	0.542																																					p.K50N		.											.	KIFC1-90	0			c.G150T						.						60	62	61					6																	33365943		2203	4300	6503	SO:0001630	splice_region_variant	3833	exon2			TGAGAAGGTGAGC	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"Kinesins"	6389	protein-coding gene	gene with protein product		603763	"kinesin-like 2"	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.150+1G>T	6.37:g.33365943G>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	49	15	NM_002263	0	0	0	0	0	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035950	0.75617	.	.	ENSG00000237649	ENST00000428849;ENST00000450504	T	0.75260	-0.92	4.78	4.78	0.61160	.	0.217099	0.39274	N	0.001409	T	0.54334	0.1852	L	0.34521	1.04	0.43010	D	0.994544	P;P	0.43094	0.799;0.799	B;B	0.40901	0.343;0.343	T	0.61865	-0.6975	10	0.46703	T	0.11	-16.7844	13.1674	0.59579	0.0:0.0:1.0:0.0	.	50;50	B4E063;Q9BW19	.;KIFC1_HUMAN	N	50	ENSP00000393963:K50N	ENSP00000393963:K50N	K	+	3	2	KIFC1	33473921	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.761000	0.62243	2.493000	0.84123	0.455000	0.32223	AAG	.		0.542	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	Missense_Mutation	T	33365943	G	T	33365943	5	4	18	1	0	0	0	0	0	0	1	0	8333	1014	35	4	156	4	KIFC1	6	33365943	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	1733910	33365943	137749124	38	1517											
CUL9	23113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43153712	43153713	+	Missense_Mutation	DNP	TC	TC	CT																															gatcccaggaaagctgctttTctccttggtgaagcgctacc																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:43153712_43153713TC>CT	ENST00000252050.4	+	4	854_855	c.770_771TC>CT	c.(769-771)tTC>tCT	p.F257S	CUL9_ENST00000372647.2_Missense_Mutation_p.F257S|CUL9_ENST00000354495.3_Missense_Mutation_p.F257S	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	257					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						AAGCTGCTTTTCTCCTTGGTGA	0.53																																					p.F257S		.											.	CUL9	0			c.C771T						.																																			SO:0001583	missense	23113	exon4			GCTTTTCTCCTTG	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	Exception_encountered	6.37:g.43153712_43153713delinsCT	ENSP00000252050:p.Phe257Ser	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	71	30		0	0	0	0	0	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	DNP	ENST00000252050.4	37	CCDS4890.1																																																																																			.		0.53	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		CT	43153713	TC	CT	43153712	3	2	18	1	0	0	0	0	1	0	0	0	4067	1783	62	3	780	3	CUL9	6	43153712	Missense_Mutation	DNP	TC	TCGA-A4-8517-01A-11D-2396-08	9787769	43153712	127961355	39	1518											
PLEKHG1	57480	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	151117019	151117019	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agttccacatttatacccagTattgcactaactatccaagg	13	12	5	11	0	0	0	0	0	0	0	2	0	2	0	3	1	3	3	3	1	6	8			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:151117019T>G	ENST00000358517.2	+	5	821	c.610T>G	c.(610-612)Tat>Gat	p.Y204D	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.Y204D			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	204	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						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)		TTATACCCAGTATTGCACTAA	0.358																																					p.Y204D		.											.	PLEKHG1-92	0			c.T610G						.						161	148	152					6																	151117019		2203	4300	6503	SO:0001583	missense	57480	exon6			ACCCAGTATTGCA	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.610T>G	6.37:g.151117019T>G	ENSP00000351318:p.Tyr204Asp	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	114	48	NM_001029884	0	0	0	0	0	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.310648	0.81358	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	D;D	0.82255	-1.59;-1.59	5.58	5.58	0.84498	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.94503	0.8230	H	0.98818	4.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96775	0.9571	10	0.87932	D	0	.	15.756	0.78025	0.0:0.0:0.0:1.0	.	11;204;204	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	D	204	ENSP00000356297:Y204D;ENSP00000351318:Y204D	ENSP00000351318:Y204D	Y	+	1	0	PLEKHG1	151158712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.649000	0.83500	2.131000	0.65755	0.533000	0.62120	TAT	.		0.358	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151117019	T	G	151117019	3	3	18	1	0	0	0	0	1	0	0	0	12094	1638	57	5	624	5	PLEKHG1	6	151117019	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	107963307	151117019	19998048	40	1519											
MLLT4	4301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	168349109	168349109	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtggccaaattatgaggAaaagccacatatgcacacag	16	6	9	10	0	0	1	0	1	0	0	0	2	0	2	3	2	2	1	3	2	5	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:168349109A>T	ENST00000447894.2	+	28	3761	c.3761A>T	c.(3760-3762)gAa>gTa	p.E1254V	MLLT4_ENST00000366806.2_Missense_Mutation_p.E1254V|MLLT4_ENST00000400822.3_Missense_Mutation_p.E1253V|MLLT4_ENST00000344191.4_Missense_Mutation_p.E1254V|MLLT4_ENST00000392108.3_Missense_Mutation_p.E1254V|MLLT4_ENST00000392112.1_Missense_Mutation_p.E1237V|MLLT4_ENST00000351017.4_Missense_Mutation_p.E1261V			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1254					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		AATTATGAGGAAAAGCCACAT	0.448			T	MLL	AL																																p.E1254V		.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4-685	0			c.A3761T						.						90	84	86					6																	168349109		2203	4300	6503	SO:0001583	missense	4301	exon28			ATGAGGAAAAGCC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3761A>T	6.37:g.168349109A>T	ENSP00000404595:p.Glu1254Val	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	53	24	NM_001040000	0	0	8	8	0	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	A	17.88	3.496251	0.64186	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.04970	3.73;3.62;3.72;3.72;3.52;3.62;3.62	5.52	5.52	0.82312	.	0.343079	0.30392	N	0.009726	T	0.05686	0.0149	L	0.57536	1.79	0.46954	D	0.999266	P;P;P;B	0.40376	0.556;0.683;0.715;0.305	B;B;B;B	0.40602	0.179;0.334;0.244;0.133	T	0.09164	-1.0687	10	0.62326	D	0.03	-23.1008	15.6454	0.77046	1.0:0.0:0.0:0.0	.	1254;1253;1254;1238	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	V	1254;1261;1254;1254;1237;1254;1253;1254	ENSP00000341118:E1254V;ENSP00000252692:E1261V;ENSP00000375956:E1254V;ENSP00000355771:E1254V;ENSP00000375960:E1237V;ENSP00000383623:E1253V;ENSP00000404595:E1254V	ENSP00000345834:E1254V	E	+	2	0	MLLT4	168091958	1.000000	0.71417	0.894000	0.35097	0.875000	0.50365	5.595000	0.67563	2.084000	0.62774	0.533000	0.62120	GAA	.		0.448	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168349109	A	T	168349109	3	4	18	1	0	0	0	0	1	0	0	0	9654	246	9	5	3871	5	MLLT4	6	168349109	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	17232090	168349109	2765958	41	1520											
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44747234	44747234	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtgcagaagtaccccaaTgctgagctggcctggtgcca	9	7	14	11	0	0	2	0	1	0	1	0	3	0	2	4	3	5	4	4	3	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:44747234T>C	ENST00000222673.5	+	22	2892	c.2850T>C	c.(2848-2850)aaT>aaC	p.N950N	OGDH_ENST00000449767.1_Silent_p.N946N|OGDH_ENST00000444676.1_Silent_p.N965N|OGDH_ENST00000439616.2_Silent_p.N800N|OGDH_ENST00000447398.1_Silent_p.N961N|OGDH_ENST00000543843.1_Silent_p.N901N	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	950					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	AGTACCCCAATGCTGAGCTGG	0.567																																					p.N950N		.											.	OGDH-228	0			c.T2850C						.						130	115	120					7																	44747234		2203	4300	6503	SO:0001819	synonymous_variant	4967	exon22			CCCCAATGCTGAG	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.2850T>C	7.37:g.44747234T>C		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	239	66	NM_002541	0	0	77	114	37	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	37	CCDS34627.1																																																																																			.		0.567	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			C	44747234	T	C	44747234	2	2	18	1	0	0	0	0	0	0	0	1	10865	1461	51	3		3	OGDH	7	44747234	Silent	SNP	T	TCGA-A4-8517-01A-11D-2396-08		44747234	114391429	42	1521											
GTF2IRD1	9569	hgsc.bcm.edu;broad.mit.edu	37	chr7	73932549	73932549	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagggctgctggccgtgcagGggctgcccgaaggcctggcc	4	5	18	14	2	0	0	0	0	0	0	0	1	0	0	4	6	3	4	4	6	1	0			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:73932549G>A	ENST00000265755.3	+	5	895	c.502G>A	c.(502-504)Ggg>Agg	p.G168R	GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.G168R|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.G200R|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.G168R	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	168					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGCCGTGCAGGGGCTGCCCGA	0.662																																					p.G200R		.											.	GTF2IRD1-94	0			c.G598A						.						21	21	21					7																	73932549		2200	4297	6497	SO:0001583	missense	9569	exon5			GTGCAGGGGCTGC	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"binding factor for early enhancer"	604318	"GTF2I repeat domain-containing 1"	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.502G>A	7.37:g.73932549G>A	ENSP00000265755:p.Gly168Arg	Somatic	37	1		WXS	Illumina HiSeq	Phase_I	48	3	NM_001199207	0	0	6	6	0	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.047225	0.93740	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	D	0.88786	0.6531	M	0.82823	2.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.90625	0.4562	10	0.72032	D	0.01	-30.8558	16.9169	0.86153	0.0:0.0:1.0:0.0	.	200;168;168;168	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	R	168;200;168;168	ENSP00000265755:G168R;ENSP00000397566:G200R;ENSP00000408477:G168R;ENSP00000418383:G168R	ENSP00000265755:G168R	G	+	1	0	GTF2IRD1	73570485	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.179000	0.94861	2.301000	0.77427	0.650000	0.86243	GGG	.		0.662	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		A	73932549	G	A	73932549	3	1	18	1	0	0	0	0	1	0	0	0	6889	1232	43	2	516	2	GTF2IRD1	7	73932549	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	29185315	73932549	85206114	43	1522											
SSPO	23145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	149502569	149502569	+	RNA	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccttgccccgggagggggCcctggctggcgcagtcgttc	2	8	17	14	3	0	0	0	0	0	0	2	1	0	1	4	5	2	3	4	5	0	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:149502569C>A	ENST00000378016.2	+	0	8382							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGGGAGGGGGCCCTGGCTGGC	0.677																																					p.G2794G		.											.	.	0			c.C8382A						.						35	41	39					7																	149502569		1903	4106	6009			23145	exon57			AGGGGGCCCTGGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149502569C>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	85	16	NM_198455	0	0	0	0	0	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				.		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149502569	C	A	149502569	1	1	18	0	1	0	0	0	0	0	0	0	15221	726	26	4		4	SSPO	7	149502569	RNA	SNP	C	TCGA-A4-8517-01A-11D-2396-08	75570020	149502569	9636094	44	1523											
UBE3C	9690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	156963038	156963038	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgatcgctgtgctacctTgtcacagtccgggggcgctt	5	13	12	11	3	1	1	1	1	0	0	3	1	2	1	2	2	2	3	2	2	1	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:156963038T>A	ENST00000348165.5	+	4	596	c.236T>A	c.(235-237)tTg>tAg	p.L79*	UBE3C_ENST00000389103.4_Nonsense_Mutation_p.L36*	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	79					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TGTGCTACCTTGTCACAGTCC	0.393																																					p.L79X		.											.	UBE3C-704	0			c.T236A						.						157	154	155					7																	156963038		2203	4300	6503	SO:0001587	stop_gained	9690	exon4			CTACCTTGTCACA	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.236T>A	7.37:g.156963038T>A	ENSP00000309198:p.Leu79*	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	158	43	NM_014671	0	0	26	30	4	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Nonsense_Mutation	SNP	ENST00000348165.5	37	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	T	8.672	0.903131	0.17760	.	.	ENSG00000009335	ENST00000348165;ENST00000389103	.	.	.	4.82	1.18	0.20946	.	0.609361	0.15952	N	0.236699	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	6.478	0.22047	0.0:0.3795:0.0:0.6205	.	.	.	.	X	79;36	.	ENSP00000309198:L79X	L	+	2	0	UBE3C	156655799	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	1.040000	0.30278	-0.027000	0.13873	0.528000	0.53228	TTG	.		0.393	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		A	156963038	T	A	156963038	4	1	18	1	0	0	0	0	0	1	0	0	16914	1821	63	5	250	5	UBE3C	7	156963038	Nonsense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	7460469	156963038	2175625	45	1524											
KIF13B	23303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	28991587	28991587	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcaaagacaaccatgcagtgCggctccttgctgacggaaga	12	7	11	11	2	1	3	1	1	0	2	2	4	2	4	2	2	4	3	2	2	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr8:28991587C>T	ENST00000524189.1	-	22	2792	c.2754G>A	c.(2752-2754)ccG>ccA	p.P918P	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	918					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CCATGCAGTGCGGCTCCTTGC	0.458																																					p.P918P		.											.	KIF13B-22	0			c.G2754A						.						60	60	60					8																	28991587		1999	4166	6165	SO:0001819	synonymous_variant	23303	exon22			GCAGTGCGGCTCC	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.2754G>A	8.37:g.28991587C>T		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	52	19	NM_015254	0	0	3	6	3	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	37	CCDS55217.1																																																																																			.		0.458	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			T	28991587	C	T	28991587	2	4	18	1	0	0	0	0	0	0	0	1	8296	755	27	1		1	KIF13B	8	28991587	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08		28991587	117372435	46	1525											
DDX58	23586	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	32467853	32467868	+	Frame_Shift_Del	DEL	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	-																															aatgccttcatcagcaactgAggtggcaatcagaatattgt																								rs61757209	byFrequency	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr9:32467853_32467868delAGGTGGCAATCAGAAT	ENST00000379883.2	-	15	2234_2249	c.2077_2092delATTCTGATTGCCACCT	c.(2077-2094)attctgattgccacctcafs	p.ILIATS693fs	DDX58_ENST00000542096.1_Frame_Shift_Del_p.ILIATS622fs|DDX58_ENST00000379868.1_Frame_Shift_Del_p.ILIATS490fs|DDX58_ENST00000379882.1_Frame_Shift_Del_p.ILIATS648fs|DDX58_ENST00000545044.1_Frame_Shift_Del_p.ILIATS490fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	693	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with ZC3HAV1.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TCAGCAACTGAGGTGGCAATCAGAATATTGTGATCT	0.435																																					p.693_698del		.											.	DDX58-230	0			c.2077_2092del						.																																			SO:0001589	frameshift_variant	23586	exon15			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2077_2092delATTCTGATTGCCACCT	9.37:g.32467853_32467868delAGGTGGCAATCAGAAT	ENSP00000369213:p.Ile693fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	54	21	NM_014314	0	0	0	0	0	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	37	CCDS6526.1																																																																																			.		0.435	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		-	32467868	AGGTGGCAATCAGAAT	-	32467853	7	5	18	1	0	1	0	1	0	0	0	0	4381	304	11	0	701	0	DDX58	9	32467853	Frame_Shift_Del	DEL	AGGTGGCAATCAGAAT	TCGA-A4-8517-01A-11D-2396-08		32467853	108745578	47	1526											
SPTLC1	10558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	94821490	94821490	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcgatctcttgttcttttaGtagtcgctcgaggtcagcca	6	16	9	10	3	3	0	1	0	2	0	7	2	3	0	1	1	1	3	1	1	2	6			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr9:94821490G>A	ENST00000262554.2	-	7	666	c.661C>T	c.(661-663)Cta>Tta	p.L221L	SPTLC1_ENST00000482632.1_5'UTR	NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	221					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	TGTTCTTTTAGTAGTCGCTCG	0.353																																					p.L221L		.											.	SPTLC1-154	0			c.C661T						.						82	76	78					9																	94821490		2203	4300	6503	SO:0001819	synonymous_variant	10558	exon7			CTTTTAGTAGTCG	Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	"hereditary sensory neuropathy, type 1"	HSN1		9363775	Standard	NM_006415		Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.661C>T	9.37:g.94821490G>A		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	25	10	NM_006415	0	0	20	37	17	A8K681|Q5VWB4|Q96IX6	Silent	SNP	ENST00000262554.2	37	CCDS6692.1																																																																																			.		0.353	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	NM_006415		A	94821490	G	A	94821490	2	1	18	1	0	0	0	0	0	0	0	1	15155	1020	36	2		2	SPTLC1	9	94821490	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	62353637	94821490	46391941	48	1527											
OR1L8	138881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125330116	125330116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtatataagagaaagcaatgCagagaaaacgagtcaccaaa	21	5	9	6	1	1	2	1	0	0	2	1	5	1	2	1	0	3	3	1	0	8	3	rs377120372		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr9:125330116C>T	ENST00000304865.2	-	1	722	c.641G>A	c.(640-642)tGc>tAc	p.C214Y		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GAAAGCAATGCAGAGAAAACG	0.438																																					p.C214Y		.											.	OR1L8-70	0			c.G641A						.						77	67	71					9																	125330116		2203	4300	6503	SO:0001583	missense	138881	exon1			GCAATGCAGAGAA		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"GPCR / Class A : Olfactory receptors"	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.641G>A	9.37:g.125330116C>T	ENSP00000306607:p.Cys214Tyr	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	48	23	NM_001004454	0	0	0	0	0	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	37	CCDS35124.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720346	0.30503	.	.	ENSG00000171496	ENST00000304865	T	0.37411	1.2	4.49	-1.53	0.08611	GPCR, rhodopsin-like superfamily (1);	0.418105	0.20181	N	0.097537	T	0.49745	0.1575	L	0.55213	1.73	0.28899	N	0.893404	P	0.38167	0.621	P	0.55871	0.786	T	0.58387	-0.7645	10	0.59425	D	0.04	-12.7197	15.5399	0.76035	0.7908:0.2092:0.0:0.0	.	214	Q8NGR8	OR1L8_HUMAN	Y	214	ENSP00000306607:C214Y	ENSP00000306607:C214Y	C	-	2	0	OR1L8	124369937	0.000000	0.05858	0.169000	0.22859	0.363000	0.29612	0.406000	0.21032	-0.042000	0.13535	0.449000	0.29647	TGC	.		0.438	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1			T	125330116	C	T	125330116	3	4	18	1	0	0	0	0	1	0	0	0	10993	710	25	2	292	2	OR1L8	9	125330116	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	30508626	125330116	15883315	49	1528											
RBM17	84991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	6157469	6157469	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacgggtggtaaaagcatgtTtctacaatttggacaaattc	13	12	10	6	1	1	0	0	0	1	0	2	2	1	1	0	3	2	3	0	3	5	5	rs200401715		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:6157469T>C	ENST00000446108.1	+	12	1800	c.1156T>C	c.(1156-1158)Ttc>Ctc	p.F386L	RBM17_ENST00000476706.1_3'UTR|RBM17_ENST00000379888.4_Missense_Mutation_p.F386L	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	386					alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						AAAAGCATGTTTCTACAATTT	0.398																																					p.F386L		.											.	RBM17-90	0			c.T1156C						.						191	186	188					10																	6157469		2203	4300	6503	SO:0001583	missense	84991	exon12			GCATGTTTCTACA	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"RNA binding motif (RRM) containing", "G patch domain containing"	16944	protein-coding gene	gene with protein product	"splicing factor 45kDa"	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.1156T>C	10.37:g.6157469T>C	ENSP00000388638:p.Phe386Leu	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	186	84	NM_001145547	0	0	18	32	14	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	37	CCDS7077.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	28.4	4.917499	0.92249	.	.	ENSG00000134453	ENST00000379888;ENST00000446108	.	.	.	5.09	5.09	0.68999	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.77525	0.4143	M	0.71296	2.17	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	T	0.79112	-0.1937	9	0.51188	T	0.08	-11.255	15.189	0.73028	0.0:0.0:0.0:1.0	.	386	Q96I25	SPF45_HUMAN	L	386	.	ENSP00000369218:F386L	F	+	1	0	RBM17	6197475	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.290000	0.78711	2.038000	0.60285	0.533000	0.62120	TTC	T|1.000;C|0.000		0.398	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905		C	6157469	T	C	6157469	3	2	18	1	0	0	0	0	1	0	0	0	13151	1841	64	3	1198	3	RBM17	10	6157469	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		6157469	129377278	50	1529											
NUDT5	11164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	12226925	12226925	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atccatgtacgttgttttttCaagcttgacccattttcctt	7	19	5	10	1	1	1	1	1	0	0	3	1	3	1	3	0	2	4	3	0	2	9			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:12226925C>G	ENST00000491614.1	-	3	489	c.94G>C	c.(94-96)Gaa>Caa	p.E32Q	NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378927.3_Missense_Mutation_p.E32Q|NUDT5_ENST00000378937.3_Missense_Mutation_p.E32Q|NUDT5_ENST00000537776.1_Missense_Mutation_p.E32Q|NUDT5_ENST00000378940.3_Missense_Mutation_p.E32Q			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	32					D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				GTTGTTTTTTCAAGCTTGACC	0.313																																					p.E32Q		.											.	NUDT5-92	0			c.G94C						.						95	90	92					10																	12226925		2203	4299	6502	SO:0001583	missense	11164	exon3			TTTTTTCAAGCTT	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"Nudix motif containing"	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.94G>C	10.37:g.12226925C>G	ENSP00000419628:p.Glu32Gln	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	35	16	NM_014142	0	0	22	32	10	A8K516|Q6IAG0|Q9UH49	Missense_Mutation	SNP	ENST00000491614.1	37	CCDS7089.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.614095	0.46631	.	.	ENSG00000165609	ENST00000491614;ENST00000378929;ENST00000378937;ENST00000537776;ENST00000378940;ENST00000378927;ENST00000444732	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	5.87	5.87	0.94306	NUDIX hydrolase domain (1);NUDIX hydrolase domain-like (1);	0.044865	0.85682	D	0.000000	T	0.45377	0.1339	L	0.39514	1.22	0.45914	D	0.998752	D;D	0.65815	0.995;0.993	P;P	0.54889	0.763;0.647	T	0.08289	-1.0729	10	0.17832	T	0.49	-36.1269	13.3498	0.60595	0.0:0.9242:0.0:0.0758	.	32;32	A6NCQ0;Q9UKK9	.;NUDT5_HUMAN	Q	32	ENSP00000419628:E32Q;ENSP00000368219:E32Q;ENSP00000445116:E32Q;ENSP00000368222:E32Q;ENSP00000368209:E32Q	ENSP00000368209:E32Q	E	-	1	0	NUDT5	12266931	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.053000	0.57427	2.941000	0.99782	0.655000	0.94253	GAA	.		0.313	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			G	12226925	C	G	12226925	3	3	18	1	0	0	0	0	1	0	0	0	10768	835	29	4	597	4	NUDT5	10	12226925	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	6069456	12226925	123307822	51	1530											
HSPA14	51182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	14896200	14896200	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgaagtagcgaaacatTctttgtcaaccttgggaagt	11	12	11	7	1	2	1	1	1	1	0	2	3	2	2	1	1	4	2	1	1	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:14896200T>A	ENST00000378372.3	+	9	1050	c.811T>A	c.(811-813)Tct>Act	p.S271T		NM_016299.2	NP_057383.2	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14	271					'de novo' cotranslational protein folding (GO:0051083)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)			breast(4)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)	17						AGCGAAACATTCTTTGTCAAC	0.373																																					p.S271T		.											.	HSPA14-291	0			c.T811A						.						154	147	149					10																	14896200		2203	4300	6503	SO:0001583	missense	51182	exon9			AAACATTCTTTGT	AF112210	CCDS7103.1, CCDS60487.1	10p13	2011-09-02			ENSG00000187522	ENSG00000187522		"Heat shock proteins / HSP70"	29526	protein-coding gene	gene with protein product		610369				12477932	Standard	NM_016299		Approved	HSP70-4, HSP70L1	uc001ind.4	Q0VDF9	OTTHUMG00000017712	ENST00000378372.3:c.811T>A	10.37:g.14896200T>A	ENSP00000367623:p.Ser271Thr	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	91	12	NM_016299	0	0	9	10	1	A8K8F8|B0YIY9|Q9P0X2|Q9UI07	Missense_Mutation	SNP	ENST00000378372.3	37	CCDS7103.1	.	.	.	.	.	.	.	.	.	.	T	4.451	0.083454	0.08533	.	.	ENSG00000187522	ENST00000378372	T	0.00949	5.51	5.53	4.37	0.52481	.	0.173267	0.52532	D	0.000061	T	0.00468	0.0015	N	0.01515	-0.825	0.80722	D	1	B	0.14438	0.01	B	0.17433	0.018	T	0.46803	-0.9165	10	0.02654	T	1	-8.9176	11.4861	0.50354	0.0:0.0:0.2868:0.7132	.	271	Q0VDF9	HSP7E_HUMAN	T	271	ENSP00000367623:S271T	ENSP00000367623:S271T	S	+	1	0	HSPA14	14936206	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	2.499000	0.45372	0.916000	0.36871	0.533000	0.62120	TCT	.		0.373	HSPA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046910.1	NM_016299		A	14896200	T	A	14896200	3	1	18	1	0	0	0	0	1	0	0	0	7428	1783	62	5	845	5	HSPA14	10	14896200	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	2669275	14896200	120638547	52	1531											
FAM13C	220965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61112192	61112192	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcgcgtgctcttctacCagagcccctgcgtcggggta	4	8	15	14	5	2	1	0	0	2	1	3	1	2	1	3	4	4	2	3	4	2	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:61112192C>A	ENST00000373868.2	-	3	249	c.162G>T	c.(160-162)ctG>ctT	p.L54L	FAM13C_ENST00000419214.2_Silent_p.L54L|FAM13C_ENST00000422313.2_Silent_p.L54L|FAM13C_ENST00000442566.3_Silent_p.L54L|FAM13C_ENST00000277705.6_Silent_p.L54L|FAM13C_ENST00000435852.2_Silent_p.L54L|FAM13C_ENST00000468840.2_5'UTR|FAM13C_ENST00000373867.3_5'UTR	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	54										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCTCTTCTACCAGAGCCCCTG	0.502																																					p.L54L		.											.	FAM13C-70	0			c.G162T						.						30	33	32					10																	61112192		2203	4300	6503	SO:0001819	synonymous_variant	220965	exon3			TTCTACCAGAGCC	U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"family with sequence similarity 13, member C1"	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.162G>T	10.37:g.61112192C>A		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	37	13	NM_198215	0	0	0	0	0	B7ZB77|Q5T631|Q6P2M3|Q99787	Silent	SNP	ENST00000373868.2	37	CCDS7255.1																																																																																			.		0.502	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			A	61112192	C	A	61112192	2	1	18	1	0	0	0	0	0	0	0	1	5470	581	21	4		4	FAM13C	10	61112192	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	46215992	61112192	74422555	53	1532											
CPEB3	22849	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	93999658	93999658	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggccgatctgcggggagaaAgtgcctccgaagactgggtt	9	7	16	9	3	1	2	0	0	1	2	2	5	2	2	3	4	2	1	3	4	2	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:93999658A>C	ENST00000265997.4	-	2	622	c.450T>G	c.(448-450)acT>acG	p.T150T	CPEB3_ENST00000412050.4_Silent_p.T150T	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	150	Pro-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				GCGGGGAGAAAGTGCCTCCGA	0.677																																					p.T150T		.											.	CPEB3-90	0			c.T450G						.						39	36	37					10																	93999658		2203	4300	6503	SO:0001819	synonymous_variant	22849	exon2			GGAGAAAGTGCCT	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.450T>G	10.37:g.93999658A>C		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	30	9	NM_014912	0	0	0	2	2	Q5T389|Q9NQJ7|Q9Y2E9	Silent	SNP	ENST00000265997.4	37	CCDS31246.1																																																																																			.		0.677	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		C	93999658	A	C	93999658	2	2	18	1	0	0	0	0	0	0	0	1	3808	59	3	5		5	CPEB3	10	93999658	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	32887466	93999658	41535089	54	1533											
TLL2	7093	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	98145849	98145849	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	caaacacttcaaactgaaggGagatccggtactgagcgggg	13	6	13	9	2	1	3	1	2	0	1	2	4	2	3	1	4	4	1	1	4	4	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:98145849G>C	ENST00000357947.3	-	15	2201	c.1976C>G	c.(1975-1977)tCc>tGc	p.S659C		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	659	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		AAACTGAAGGGAGATCCGGTA	0.517																																					p.S659C		.											.	TLL2-93	0			c.C1976G						.						99	94	95					10																	98145849		2203	4300	6503	SO:0001583	missense	7093	exon15			TGAAGGGAGATCC	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1976C>G	10.37:g.98145849G>C	ENSP00000350630:p.Ser659Cys	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	71	14	NM_012465	0	0	0	0	0	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617588	0.87359	.	.	ENSG00000095587	ENST00000357947	T	0.19669	2.13	4.77	4.77	0.60923	CUB (5);	0.000000	0.45126	D	0.000385	T	0.49406	0.1555	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.48269	-0.9050	10	0.42905	T	0.14	.	17.3218	0.87238	0.0:0.0:1.0:0.0	.	659	Q9Y6L7	TLL2_HUMAN	C	659	ENSP00000350630:S659C	ENSP00000350630:S659C	S	-	2	0	TLL2	98135839	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.601000	0.98297	2.651000	0.90000	0.585000	0.79938	TCC	.		0.517	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			C	98145849	G	C	98145849	3	2	18	1	0	0	0	0	1	0	0	0	15978	1174	41	4	1099	4	TLL2	10	98145849	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	4146191	98145849	37388898	55	1534											
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104139057	104139057	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagttgctagacctgatgcAcaccctgcacacgcgggcag	9	7	11	14	2	0	2	0	1	0	1	0	2	0	2	2	1	3	5	2	1	2	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:104139057A>G	ENST00000369983.3	+	34	4768	c.4508A>G	c.(4507-4509)cAc>cGc	p.H1503R		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1503					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GACCTGATGCACACCCTGCAC	0.587																																					p.H1503R		.											.	GBF1-91	0			c.A4508G						.						71	64	66					10																	104139057		2203	4300	6503	SO:0001583	missense	8729	exon34			TGATGCACACCCT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4508A>G	10.37:g.104139057A>G	ENSP00000359000:p.His1503Arg	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	107	13	NM_004193	0	0	31	38	7	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.132469	0.77662	.	.	ENSG00000107862	ENST00000369983	T	0.12039	2.72	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.36524	0.0970	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.981	D;D;D	0.69824	0.959;0.961;0.966	T	0.12889	-1.0530	10	0.72032	D	0.01	-12.8919	15.3201	0.74115	1.0:0.0:0.0:0.0	.	1499;1499;1503	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	R	1503	ENSP00000359000:H1503R	ENSP00000359000:H1503R	H	+	2	0	GBF1	104129047	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.097000	0.94193	2.200000	0.70718	0.459000	0.35465	CAC	.		0.587	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104139057	A	G	104139057	3	3	18	1	0	0	0	0	1	0	0	0	6291	159	6	3	4638	3	GBF1	10	104139057	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	5993208	104139057	31395690	56	1535											
OR5M3	219482	broad.mit.edu	37	chr11	56237295	56237295	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgccttccttctgctgagcGcattcgcagaatggcaatga	8	11	10	12	2	1	3	0	2	1	1	3	3	2	3	2	1	3	4	2	1	2	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:56237295G>A	ENST00000312240.2	-	1	719	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					TCTGCTGAGCGCATTCGCAGA	0.418																																					p.R227C													.	OR5M3-70	0			c.C679T						.						62	60	61					11																	56237295		2201	4292	6493	SO:0001583	missense	219482	exon1			CTGAGCGCATTCG	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.679C>T	11.37:g.56237295G>A	ENSP00000312208:p.Arg227Cys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	97	4	NM_001004742	0	0	0	0	0	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	G	4.920	0.170929	0.09391	.	.	ENSG00000174937	ENST00000312240	T	0.40225	1.04	5.08	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	0.719989	0.11980	N	0.510873	T	0.46600	0.1401	M	0.83223	2.63	0.09310	N	1	B	0.11235	0.004	B	0.13407	0.009	T	0.46386	-0.9195	10	0.59425	D	0.04	0.0056	7.8533	0.29468	0.1885:0.0:0.8115:0.0	.	227	Q8NGP4	OR5M3_HUMAN	C	227	ENSP00000312208:R227C	ENSP00000312208:R227C	R	-	1	0	OR5M3	55993871	0.000000	0.05858	0.100000	0.21137	0.125000	0.20455	0.066000	0.14489	1.122000	0.41944	0.549000	0.68633	CGC	.		0.418	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		A	56237295	G	A	56237295	3	1	18	1	0	0	0	0	1	0	0	0	11201	1087	38	1	246	1	OR5M3	11	56237295	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08		56237295	78769221	57	1536											
LRRC55	219527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	56949791	56949792	+	Missense_Mutation	DNP	AA	AA	TC																															aggtgctggatttgcacaacAactccttaatggagctgccc																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:56949791_56949792AA>TC	ENST00000497933.1	+	1	571_572	c.424_425AA>TC	c.(424-426)AAc>TCc	p.N142S		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	112					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						TTTGCACAACAACTCCTTAATG	0.584																																					p.N142S		.											.	LRRC55	0			c.A425C						.																																			SO:0001583	missense	219527	exon1			ACAACAACTCCTT		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	Exception_encountered	11.37:g.56949791_56949792delinsTC	ENSP00000419542:p.Asn142Ser	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	41	16		0	0	0	0	0	A7E2U7|B2RN81	Missense_Mutation	DNP	ENST00000497933.1	37	CCDS31539.1																																																																																			.		0.584	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210		TC	56949792	AA	TC	56949791	3	4	18	1	0	0	0	0	1	0	0	0	9036	130	5	5	426	5	LRRC55	11	56949791	Missense_Mutation	DNP	AA	TCGA-A4-8517-01A-11D-2396-08	712496	56949791	78056725	58	1537											
PGA3	643834	hgsc.bcm.edu	37	chr11	60975055	60975055	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctacggcaccggcagcAtgacaggcatcctcggatac	10	6	10	15	3	1	1	1	1	0	0	3	2	2	2	3	4	3	4	3	4	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:60975055A>G	ENST00000325558.6	+	4	609	c.424A>G	c.(424-426)Atg>Gtg	p.M142V	PGA3_ENST00000543125.1_5'Flank	NM_001079807.1	NP_001073275.1	P0DJD8	PEPA3_HUMAN	pepsinogen 3, group I (pepsinogen A)	142					digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|lung(1)|ovary(1)|skin(2)	5						CACCGGCAGCATGACAGGCAT	0.587																																					p.M142V		.											.	PGA3-24	0			c.A424G						.						1	1	1					11																	60975055		814	1066	1880	SO:0001583	missense	643834	exon4			GGCAGCATGACAG	AL832946	CCDS31574.1	11q13	2006-12-13			ENSG00000229859	ENSG00000229859	3.4.23.1		8885	protein-coding gene	gene with protein product		169710				6300126	Standard	NM_001079807		Approved		uc001nqx.3	P0DJD8	OTTHUMG00000168071	ENST00000325558.6:c.424A>G	11.37:g.60975055A>G	ENSP00000322192:p.Met142Val	Somatic	598	0		WXS	Illumina HiSeq	Phase_I	575	67	NM_001079807	0	0	0	0	0	A8K749|B2R7D6|B7ZW75|P00790|Q7M4R0|Q8N1E3	Missense_Mutation	SNP	ENST00000325558.6	37	CCDS31574.1	.	.	.	.	.	.	.	.	.	.	A	14.42	2.528985	0.44969	.	.	ENSG00000229859	ENST00000325558;ENST00000439843;ENST00000543609;ENST00000543349;ENST00000543505	T;T;T	0.55052	0.54;0.54;0.54	3.59	2.46	0.29980	.	0.055879	0.64402	D	0.000002	T	0.36110	0.0955	N	0.25286	0.73	0.80722	D	1	B	0.29253	0.239	B	0.31191	0.125	T	0.15954	-1.0419	10	0.49607	T	0.09	.	8.7363	0.34530	0.9076:0.0:0.0924:0.0	.	142	F8WAB4	.	V	142;142;1;69;69	ENSP00000322192:M142V;ENSP00000442525:M69V;ENSP00000443732:M69V	ENSP00000322192:M142V	M	+	1	0	PGA3	60731631	1.000000	0.71417	0.104000	0.21259	0.506000	0.33950	4.784000	0.62411	0.587000	0.29643	0.254000	0.18369	ATG	.		0.587	PGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397955.2	NM_001079807		G	60975055	A	G	60975055	3	3	18	1	0	0	0	0	1	0	0	0	11797	217	8	3	438	3	PGA3	11	60975055	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	4025264	60975055	74031461	59	1538											
ALDH3B1	221	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67787234	67787234	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggagacggggcagctgctAgagcacaggttcgactacat	11	6	14	10	2	0	2	0	0	0	2	1	4	0	2	0	4	4	5	0	4	2	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:67787234A>T	ENST00000539229.1	+	7	644	c.528A>T	c.(526-528)ctA>ctT	p.L176L	ALDH3B1_ENST00000316367.6_Silent_p.L176L|ALDH3B1_ENST00000007633.8_Silent_p.L176L|ALDH3B1_ENST00000342456.6_Silent_p.L140L|ALDH3B1_ENST00000434449.1_3'UTR	NM_001161473.1	NP_001154945.1	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1	177					alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										GGCAGCTGCTAGAGCACAGGT	0.657																																					.													.	.	0			.						.						97	111	107					11																	67787234		2200	4294	6494	SO:0001819	synonymous_variant	221	.			GCTGCTAGAGCAC	U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"Aldehyde dehydrogenases"	410	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 7", "aldehyde dehydrogenase 3B1"	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000539229.1:c.528A>T	11.37:g.67787234A>T		Somatic	216	1		WXS	Illumina HiSeq	Phase_I	199	82	.	0	0	32	47	15	A3FMP9|Q53XL5|Q8N515|Q96CK8	Silent	SNP	ENST00000539229.1	37																																																																																				.		0.657	ALDH3B1-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000694		T	67787234	A	T	67787234	2	4	18	1	0	0	0	0	0	0	0	1	499	407	15	5		5	ALDH3B1	11	67787234	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	6812179	67787234	67219282	60	1539											
RAB38	23682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	87908439	87908439	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccacgccgattgtggcccgGtagtgcgaagagaagttctg	8	9	14	10	4	1	1	0	0	1	1	2	4	2	1	3	2	1	2	3	2	3	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:87908439G>A	ENST00000243662.6	-	1	196	c.114C>T	c.(112-114)taC>taT	p.Y38Y	MIR3166_ENST00000577344.1_RNA	NM_022337.2	NP_071732.1	P57729	RAB38_HUMAN	RAB38, member RAS oncogene family	38					endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome acidification (GO:0090383)|platelet dense granule organization (GO:0060155)|protein localization to membrane (GO:0072657)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)			large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGTGGCCCGGTAGTGCGAAG	0.612																																					p.Y38Y		.											.	RAB38-290	0			c.C114T						.						109	78	88					11																	87908439		2201	4299	6500	SO:0001819	synonymous_variant	23682	exon1			GGCCCGGTAGTGC	AF235022	CCDS8281.1	11q14	2008-05-14			ENSG00000123892	ENSG00000123892		"RAB, member RAS oncogene"	9776	protein-coding gene	gene with protein product		606281				10910072	Standard	NM_022337		Approved	NY-MEL-1	uc001pcj.2	P57729	OTTHUMG00000167288	ENST00000243662.6:c.114C>T	11.37:g.87908439G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	53	20	NM_022337	0	0	0	0	0	Q53XK7	Silent	SNP	ENST00000243662.6	37	CCDS8281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.90|19.90	3.912749|3.912749	0.72983|0.72983	.|.	.|.	ENSG00000123892|ENSG00000123892	ENST00000531138|ENST00000526372	.|.	.|.	.|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	.|.	.|.	.|.	.|.	T|T	0.74846|0.74846	0.3770|0.3770	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.73173|0.73173	-0.4066|-0.4066	4|4	.|.	.|.	.|.	-2.7885|-2.7885	18.9316|18.9316	0.92568|0.92568	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|I	55|55	.|.	.|.	P|T	-|-	1|2	0|0	RAB38|RAB38	87548087|87548087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.504000|6.504000	0.73704|0.73704	2.691000|2.691000	0.91804|0.91804	0.655000|0.655000	0.94253|0.94253	CCG|ACC	.		0.612	RAB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394015.2			A	87908439	G	A	87908439	2	1	18	1	0	0	0	0	0	0	0	1	12960	1256	44	2		2	RAB38	11	87908439	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	20121205	87908439	47098077	61	1540											
FAM55D	54827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	114450961	114450961	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcattttgactgtagccaaaCtacaggagacaggattccat	13	11	8	9	0	1	2	1	1	0	1	2	4	2	3	2	2	3	1	2	2	3	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:114450961C>T	ENST00000375478.3	-	5	1172	c.992G>A	c.(991-993)aGt>aAt	p.S331N	NXPE4_ENST00000424261.2_Missense_Mutation_p.S47N	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	331						extracellular vesicular exosome (GO:0070062)											TGTAGCCAAACTACAGGAGAC	0.443																																					p.S331N		.											.	.	0			c.G992A						.						187	175	179					11																	114450961		1880	4122	6002	SO:0001583	missense	54827	exon5			GCCAAACTACAGG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 33", "family with sequence similarity 55, member D"	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.992G>A	11.37:g.114450961C>T	ENSP00000364627:p.Ser331Asn	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	134	54	NM_001077639	0	0	0	0	0	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	C	7.005	0.555720	0.13436	.	.	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.13901	2.55;2.81	5.31	-0.797	0.10909	.	0.305202	0.31519	N	0.007506	T	0.07098	0.0180	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36553	-0.9743	10	0.09338	T	0.73	.	2.9753	0.05935	0.3243:0.2745:0.0:0.4012	.	331	Q6UWF7	FA55D_HUMAN	N	47;331	ENSP00000401503:S47N;ENSP00000364627:S331N	ENSP00000364627:S331N	S	-	2	0	FAM55D	113956171	0.159000	0.22864	0.003000	0.11579	0.936000	0.57629	0.469000	0.22067	0.168000	0.19655	0.655000	0.94253	AGT	.		0.443	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		T	114450961	C	T	114450961	3	4	18	1	0	0	0	0	1	0	0	0	5606	565	20	2	650	2	FAM55D	11	114450961	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	26542522	114450961	20555555	62	1541											
DSCAML1	57453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117308640	117308640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcttggcctcgatgatcTcgctgatgcgcccagagccc	5	9	13	14	3	2	3	0	2	2	1	4	4	2	3	3	2	2	1	3	2	0	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:117308640T>C	ENST00000321322.6	-	25	4584	c.4583A>G	c.(4582-4584)gAg>gGg	p.E1528G	DSCAML1_ENST00000527706.1_Missense_Mutation_p.E1258G	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1468	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CTCGATGATCTCGCTGATGCG	0.657																																					p.E1528G		.											.	DSCAML1-159	0			c.A4583G						.						80	62	68					11																	117308640		2201	4296	6497	SO:0001583	missense	57453	exon25			ATGATCTCGCTGA		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4583A>G	11.37:g.117308640T>C	ENSP00000315465:p.Glu1528Gly	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	28	12	NM_020693	0	0	1	2	1	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465316	0.63513	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.56444	0.46;0.46	4.18	4.18	0.49190	Fibronectin, type III (2);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60170	0.2248	M	0.86740	2.835	0.80722	D	1	B	0.18461	0.028	B	0.24394	0.053	T	0.65878	-0.6061	9	0.72032	D	0.01	.	13.7305	0.62785	0.0:0.0:0.0:1.0	.	1468	Q8TD84	DSCL1_HUMAN	G	1258;1528;1235	ENSP00000434335:E1258G;ENSP00000315465:E1528G	ENSP00000315465:E1528G	E	-	2	0	DSCAML1	116813850	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.785000	0.85724	1.878000	0.54408	0.454000	0.30748	GAG	.		0.657	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		C	117308640	T	C	117308640	3	2	18	1	0	0	0	0	1	0	0	0	4780	1551	54	3	1794	3	DSCAML1	11	117308640	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	2857679	117308640	17697876	63	1542											
FOXJ2	55810	broad.mit.edu	37	chr12	8200558	8200560	+	In_Frame_Del	DEL	CAG	CAG	-																															agcagccaccgccacctcaaCagcagcagcagcagcagcag																								rs372118289		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr12:8200558_8200560delCAG	ENST00000162391.3	+	7	2043_2045	c.898_900delCAG	c.(898-900)cagdel	p.Q306del	FOXJ2_ENST00000428177.2_In_Frame_Del_p.Q306del	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	306	Poly-Gln.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		gccacctcaacagcagcagcagc	0.64																																					p.300_300del													.	FOXJ2-230	0			c.898_900del						.																																			SO:0001651	inframe_deletion	55810	exon7			CCTCAACAGCAGC	AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"Forkhead boxes"	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.898_900delCAG	12.37:g.8200567_8200569delCAG	ENSP00000162391:p.Gln306del	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	100	9	NM_018416	0	0	0	0	0	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	In_Frame_Del	DEL	ENST00000162391.3	37	CCDS8587.1																																																																																			.		0.64	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416		-	8200560	CAG	-	8200558	7	5	18	1	0	1	0	1	0	0	0	0	6031	479	17	0	920	0	FOXJ2	12	8200558	In_Frame_Del	DEL	CAG	TCGA-A4-8517-01A-11D-2396-08		8200558	125651337	64	1543											
ARF3	377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49334777	49334777	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccccgagtttcagcttgtaTaggatggtggtctttcctgc	5	15	11	10	1	2	0	1	0	1	0	4	2	4	1	3	3	2	3	3	3	2	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr12:49334777T>C	ENST00000256682.4	-	2	436	c.102A>G	c.(100-102)ctA>ctG	p.L34L	ARF3_ENST00000447318.2_Silent_p.L34L|ARF3_ENST00000541967.1_5'Flank|ARF3_ENST00000541959.1_Silent_p.L34L|AC073610.5_ENST00000537495.1_5'Flank|RP11-302B13.5_ENST00000398092.4_Silent_p.L34L	NM_001659.2	NP_001650.1	P61204	ARF3_HUMAN	ADP-ribosylation factor 3	34					GTP catabolic process (GO:0006184)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|skin(1)	4						TCAGCTTGTATAGGATGGTGG	0.552																																					p.L34L	Pancreas(189;1862 2134 4419 30933 49364)	.											.	ARF3-227	0			c.A102G						.						246	205	219					12																	49334777		2203	4300	6503	SO:0001819	synonymous_variant	377	exon2			CTTGTATAGGATG	M74491	CCDS8774.1	12q13.12	2013-01-22			ENSG00000134287	ENSG00000134287		"ADP-ribosylation factors"	654	protein-coding gene	gene with protein product	"small GTP binding protein"	103190				8661066	Standard	NM_001659		Approved		uc001rsr.2	P61204	OTTHUMG00000168080	ENST00000256682.4:c.102A>G	12.37:g.49334777T>C		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	295	98	NM_001659	0	0	0	0	0	A8K6G8|B7ZB63|P16587	Silent	SNP	ENST00000256682.4	37	CCDS8774.1																																																																																			.		0.552	ARF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258242.2	NM_001659		C	49334777	T	C	49334777	2	2	18	1	0	0	0	0	0	0	0	1	845	1393	49	3		3	ARF3	12	49334777	Silent	SNP	T	TCGA-A4-8517-01A-11D-2396-08	41134219	49334777	84517118	65	1544											
KCNH3	23416	broad.mit.edu	37	chr12	49951572	49951572	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggggctaggactgggcccGcagagcctgtgagccaggct	8	5	17	11	1	0	2	0	1	0	1	0	3	0	3	3	5	2	3	3	5	2	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr12:49951572G>A	ENST00000257981.6	+	15	3348	c.3088G>A	c.(3088-3090)Gca>Aca	p.A1030T	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	1030	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GACTGGGCCCGCAGAGCCTGT	0.682																																					p.A1030T													.	KCNH3-90	0			c.G3088A						.						23	25	24					12																	49951572		2203	4300	6503	SO:0001583	missense	23416	exon15			GGGCCCGCAGAGC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.3088G>A	12.37:g.49951572G>A	ENSP00000257981:p.Ala1030Thr	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	84	4	NM_012284	0	0	1	1	0	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.113917	0.56398	.	.	ENSG00000135519	ENST00000257981	D	0.98617	-5.03	5.02	2.2	0.27929	.	0.179966	0.27340	N	0.019813	D	0.92437	0.7599	N	0.08118	0	0.35870	D	0.828135	B	0.02656	0.0	B	0.01281	0.0	D	0.84384	0.0551	10	0.19590	T	0.45	.	2.103	0.03684	0.1596:0.5137:0.1544:0.1723	.	1030	Q9ULD8	KCNH3_HUMAN	T	1030	ENSP00000257981:A1030T	ENSP00000257981:A1030T	A	+	1	0	KCNH3	48237839	0.025000	0.19082	0.264000	0.24511	0.986000	0.74619	-0.005000	0.12855	0.042000	0.15717	-0.216000	0.12614	GCA	.		0.682	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		A	49951572	G	A	49951572	3	1	18	1	0	0	0	0	1	0	0	0	8054	1087	38	1	3146	1	KCNH3	12	49951572	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	616795	49951572	83900323	66	1545											
CHD8	57680	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	21870158	21870158	+	Frame_Shift_Del	DEL	G	G	-																															ccttcagattcaatggtgatGgttgtagttcgtcttaacaa																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr14:21870158delG	ENST00000557364.1	-	20	4283	c.4020delC	c.(4018-4020)accfs	p.T1340fs	CHD8_ENST00000430710.3_Frame_Shift_Del_p.T1061fs|CHD8_ENST00000555962.1_5'UTR|CHD8_ENST00000399982.2_Frame_Shift_Del_p.T1340fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1340					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CAATGGTGATGGTTGTAGTTC	0.428																																					p.T1340fs		.											.	CHD8-277	0			c.4020delC						.						175	170	172					14																	21870158		2022	4216	6238	SO:0001589	frameshift_variant	57680	exon19			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.4020delC	14.37:g.21870158delG	ENSP00000451601:p.Thr1340fs	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	141	63	NM_001170629	0	0	0	0	0	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	37	CCDS53885.1																																																																																			.		0.428	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21870158	G	-	21870158	7	5	18	1	0	1	0	1	0	0	0	0	3337	1335	47	0	3801	0	CHD8	14	21870158	Frame_Shift_Del	DEL	G	TCGA-A4-8517-01A-11D-2396-08		21870158	85479382	67	1546											
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64633956	64633956	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttttaaaaatagaatcaTgtgctggcactgacagccca	14	12	7	8	0	1	2	1	1	0	1	1	2	1	2	1	1	2	2	1	1	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr14:64633956T>A	ENST00000344113.4	+	91	16823	c.16611T>A	c.(16609-16611)caT>caA	p.H5537Q	SYNE2_ENST00000394768.2_Missense_Mutation_p.H1922Q|SYNE2_ENST00000554584.1_Missense_Mutation_p.H5412Q|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.H2171Q|SYNE2_ENST00000358025.3_Missense_Mutation_p.H5537Q|SYNE2_ENST00000357395.3_Missense_Mutation_p.H1922Q	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5537					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AATAGAATCATGTGCTGGCAC	0.378																																					p.H5537Q		.											.	SYNE2-164	0			c.T16611A						.						46	47	46					14																	64633956		2203	4300	6503	SO:0001583	missense	23224	exon91			GAATCATGTGCTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16611T>A	14.37:g.64633956T>A	ENSP00000341781:p.His5537Gln	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	51	14	NM_182914	0	0	0	0	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	3.587	-0.084487	0.07097	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.55234	0.84;4.13;0.83;0.53;4.19;4.13	5.78	-2.01	0.07410	.	0.246206	0.28241	N	0.016071	T	0.32224	0.0822	L	0.39245	1.2	0.58432	D	0.999999	B;B;B;B	0.25772	0.004;0.112;0.008;0.134	B;B;B;B	0.26864	0.007;0.032;0.011;0.074	T	0.04053	-1.0981	10	0.17369	T	0.5	.	3.6697	0.08269	0.1137:0.4232:0.1908:0.2723	.	1922;5412;5537;5537	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	Q	5537;1922;5537;5412;5418;2171;1922	ENSP00000350719:H5537Q;ENSP00000349969:H1922Q;ENSP00000341781:H5537Q;ENSP00000452570:H5412Q;ENSP00000450831:H2171Q;ENSP00000378249:H1922Q	ENSP00000261678:H5418Q	H	+	3	2	SYNE2	63703709	0.000000	0.05858	0.820000	0.32676	0.932000	0.56968	-3.318000	0.00514	-0.265000	0.09352	0.533000	0.62120	CAT	.		0.378	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64633956	T	A	64633956	3	1	18	1	0	0	0	0	1	0	0	0	15478	1461	51	5	16969	5	SYNE2	14	64633956	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	42763798	64633956	42715584	68	1547											
FBLN5	10516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	92349359	92349359	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcaggagcagaagtatgtGccgggctggttcacacactc	9	7	15	10	1	1	1	1	0	0	1	2	2	1	2	1	4	2	5	1	4	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr14:92349359G>T	ENST00000342058.4	-	8	1394	c.801C>A	c.(799-801)ggC>ggA	p.G267G	FBLN5_ENST00000267620.10_Silent_p.G308G|FBLN5_ENST00000556154.1_Silent_p.G272G	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	267	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				AGAAGTATGTGCCGGGCTGGT	0.562																																					p.G267G		.											.	FBLN5-134	0			c.C801A						.						140	120	126					14																	92349359		2203	4300	6503	SO:0001819	synonymous_variant	10516	exon8			GTATGTGCCGGGC	AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"Fibulins"	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.801C>A	14.37:g.92349359G>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	93	39	NM_006329	0	0	6	7	1	O75966|Q6IAL4|Q6UWA3	Silent	SNP	ENST00000342058.4	37	CCDS9898.1																																																																																			.		0.562	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1			T	92349359	G	T	92349359	2	4	18	1	0	0	0	0	0	0	0	1	5719	1306	46	4		4	FBLN5	14	92349359	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	27715403	92349359	15000181	69	1548											
VPS39	23339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42462024	42462024	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aactgctttctgtagtctgtGggcagcaggtcagggtacag	8	11	14	8	0	3	0	1	0	2	0	3	0	3	0	0	3	4	5	0	3	3	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr15:42462024G>T	ENST00000348544.4	-	13	1163	c.1164C>A	c.(1162-1164)ccC>ccA	p.P388P	VPS39_ENST00000318006.5_Silent_p.P377P			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	388					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		TGTAGTCTGTGGGCAGCAGGT	0.493																																					p.P377P		.											.	VPS39-229	0			c.C1131A						.						110	104	106					15																	42462024		2203	4299	6502	SO:0001819	synonymous_variant	23339	exon12			GTCTGTGGGCAGC	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1164C>A	15.37:g.42462024G>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	73	33	NM_015289	0	0	16	26	10	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Silent	SNP	ENST00000348544.4	37	CCDS10083.1																																																																																			.		0.493	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		T	42462024	G	T	42462024	2	4	18	1	0	0	0	0	0	0	0	1	17242	1335	47	4		4	VPS39	15	42462024	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08		42462024	60069368	70	1549											
SCAPER	49855	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	76726602	76726603	+	Frame_Shift_Ins	INS	-	-	TA																															caagccttcaaaaacttgttINStatttgtatttctccccaaa																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr15:76726602_76726603insTA	ENST00000563290.1	-	26	3222_3223	c.3127_3128insTA	c.(3127-3129)aaafs	p.K1043fs	SCAPER_ENST00000538941.2_Frame_Shift_Ins_p.K797fs|SCAPER_ENST00000324767.7_Frame_Shift_Ins_p.K1043fs			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1043						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						AAAAACTTGTTTATTTGTATTT	0.371																																					p.K1043fs		.											.	SCAPER-137	0			c.3128_3129insTA						.																																			SO:0001589	frameshift_variant	49855	exon25			.	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.3126_3127dupTA	15.37:g.76726603_76726604dupTA	ENSP00000454973:p.Lys1043fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	95	36	NM_020843	0	0	0	0	0	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Frame_Shift_Ins	INS	ENST00000563290.1	37	CCDS53962.1																																																																																			.		0.371	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		TA	76726603	-	TA	76726602	7	5	18	1	0	1	1	0	0	0	0	0	13910	1841	64	0	1102	0	SCAPER	15	76726602	Frame_Shift_Ins	INS	-	TCGA-A4-8517-01A-11D-2396-08	34264578	76726602	25804790	71	1550											
AGPHD1	123688	hgsc.bcm.edu;broad.mit.edu	37	chr15	78807316	78807316	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttccatccatttagatagtgGctctgaaatcaaaagctact	13	13	6	9	0	2	2	1	1	1	1	4	2	4	2	2	1	2	2	2	1	6	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr15:78807316G>A	ENST00000569878.1	+	2	344	c.344G>A	c.(343-345)gGc>gAc	p.G115D	HYKK_ENST00000566332.1_Missense_Mutation_p.G115D|HYKK_ENST00000408962.2_Missense_Mutation_p.G115D|HYKK_ENST00000388988.4_Missense_Mutation_p.G115D|HYKK_ENST00000563233.1_Missense_Mutation_p.G115D|HYKK_ENST00000360519.3_Missense_Mutation_p.G115D			A2RU49	HYKK_HUMAN	hydroxylysine kinase	115						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)										TTAGATAGTGGCTCTGAAATC	0.378																																					p.G115D		.											.	AGPHD1-90	0			c.G344A						.						37	34	35					15																	78807316		1823	4075	5898	SO:0001583	missense	123688	exon3			ATAGTGGCTCTGA	BC132753, BC144383, BM045979	CCDS42063.1, CCDS45318.1	15q25.1	2013-06-11	2013-06-11	2013-06-11	ENSG00000188266	ENSG00000188266	2.7.1.81		34403	protein-coding gene	gene with protein product	"5-hydroxylysine kinase"	614681	"aminoglycoside phosphotransferase domain containing 1"	AGPHD1		18780872, 22241472	Standard	NM_001013619		Approved	LOC123688	uc010unc.2	A2RU49		ENST00000569878.1:c.344G>A	15.37:g.78807316G>A	ENSP00000455459:p.Gly115Asp	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	21	6	NM_001013619	0	0	0	0	0	B7ZMA5|F8W6X5|Q6ZTN0	Missense_Mutation	SNP	ENST00000569878.1	37	CCDS42063.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.768497	0.49680	.	.	ENSG00000188266	ENST00000408962;ENST00000388988;ENST00000360519	.	.	.	5.72	4.79	0.61399	Aminoglycoside phosphotransferase (1);Protein kinase-like domain (1);	0.054660	0.64402	D	0.000001	T	0.61527	0.2354	M	0.69823	2.125	0.53688	D	0.999975	B;B	0.29301	0.002;0.241	B;B	0.31245	0.02;0.126	T	0.62378	-0.6867	9	0.51188	T	0.08	-16.0178	11.2908	0.49250	0.0692:0.1272:0.8036:0.0	.	115;115	A2RU49;A2RU49-3	AGPD1_HUMAN;.	D	115	.	ENSP00000353710:G115D	G	+	2	0	AGPHD1	76594371	1.000000	0.71417	0.709000	0.30452	0.972000	0.66771	4.688000	0.61715	1.395000	0.46643	0.561000	0.74099	GGC	.		0.378	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619		A	78807316	G	A	78807316	3	1	18	1	0	0	0	0	1	0	0	0	393	1203	42	2	350	2	AGPHD1	15	78807316	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	2080714	78807316	23724076	72	1551											
POLG	5428	hgsc.bcm.edu;broad.mit.edu	37	chr15	89865055	89865055	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttggggcaggatggccccaTagaggccttcctcatcatag	8	9	12	12	0	2	1	2	0	0	1	3	2	3	2	4	5	0	1	4	5	2	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr15:89865055T>C	ENST00000268124.5	-	16	2843	c.2510A>G	c.(2509-2511)tAt>tGt	p.Y837C	POLG_ENST00000442287.2_Missense_Mutation_p.Y837C	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	837					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			GATGGCCCCATAGAGGCCTTC	0.627								DNA polymerases (catalytic subunits)																													p.Y837C	Colon(73;648 1203 11348 18386 27782)	.											.	POLG-228	0			c.A2510G						.						58	60	59					15																	89865055		2200	4299	6499	SO:0001583	missense	5428	exon16			GCCCCATAGAGGC	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.2510A>G	15.37:g.89865055T>C	ENSP00000268124:p.Tyr837Cys	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	111	6	NM_002693	0	0	20	22	2	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739682	0.49045	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.98400	-4.91;-4.91	5.37	4.24	0.50183	DNA-directed DNA polymerase, family A, palm domain (1);	0.113436	0.64402	N	0.000007	D	0.97040	0.9033	M	0.70595	2.14	0.80722	D	1	B	0.29301	0.241	B	0.33042	0.157	D	0.95347	0.8443	10	0.56958	D	0.05	-8.8443	10.8623	0.46833	0.0:0.0742:0.0:0.9258	.	837	P54098	DPOG1_HUMAN	C	837	ENSP00000268124:Y837C;ENSP00000399851:Y837C	ENSP00000268124:Y837C	Y	-	2	0	POLG	87666059	1.000000	0.71417	0.862000	0.33874	0.941000	0.58515	4.816000	0.62642	0.893000	0.36288	0.459000	0.35465	TAT	.		0.627	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		C	89865055	T	C	89865055	3	2	18	1	0	0	0	0	1	0	0	0	12226	1406	49	3	1241	3	POLG	15	89865055	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	11057739	89865055	12666337	73	1552											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	18856931	18856931	+	Frame_Shift_Del	DEL	C	C	-																															gcaaatacgatgggcttcatCaaagctgtgtgcttctccct																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:18856931delC	ENST00000446231.2	-	39	6451	c.6039delG	c.(6037-6039)ttgfs	p.L2013fs	SMG1_ENST00000389467.3_Frame_Shift_Del_p.L2013fs			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2013					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGGGCTTCATCAAAGCTGTGT	0.388																																					p.L2013fs		.											.	SMG1-1160	0			c.6039delG						.						130	120	123					16																	18856931		1903	4130	6033	SO:0001589	frameshift_variant	23049	exon39			.	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6039delG	16.37:g.18856931delC	ENSP00000402515:p.Leu2013fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	140	84	NM_015092	0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Frame_Shift_Del	DEL	ENST00000446231.2	37	CCDS45430.1																																																																																			.		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		-	18856931	C	-	18856931	7	5	18	1	0	1	0	1	0	0	0	0	14827	825	29	0	5046	0	SMG1	16	18856931	Frame_Shift_Del	DEL	C	TCGA-A4-8517-01A-11D-2396-08		18856931	71497822	74	1553											
LOC100132247	100132247	broad.mit.edu	37	chr16	22545580	22545585	+	In_Frame_Del	DEL	AATCTC	AATCTC	-																															ttccaccctcagcggatgatAatctcaagacaccttccgag																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AATCTC	AATCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:22545580_22545585delAATCTC	ENST00000517539.1	+	8	1351_1356	c.1276_1281delAATCTC	c.(1276-1281)aatctcdel	p.NL426del	NPIPB5_ENST00000415654.1_3'UTR|NPIPB5_ENST00000424340.1_In_Frame_Del_p.NL426del			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	426	Pro-rich.					integral component of membrane (GO:0016021)											AGCGGATGATAATCTCAAGACACCTT	0.597																																					p.426_427del													.	.	0			c.1276_1281del						.			2,380		1,0,190							0			1	16,654		5,6,324	no	coding	LOC100132247	NM_001135865.1		6,6,514	A1A1,A1R,RR		2.3881,0.5236,1.711				18,1034				SO:0001651	inframe_deletion	0	exon7			GATGATAATCTCA		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1276_1281delAATCTC	16.37:g.22545580_22545585delAATCTC	ENSP00000430633:p.Asn426_Leu427del	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	203	6	NM_001135865	0	0	0	0	0	B4DK13	In_Frame_Del	DEL	ENST00000517539.1	37	CCDS45443.1																																																																																			.		0.597	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374343.2	NM_001135865		-	22545585	AATCTC	-	22545580	7	5	18	1	0	1	0	1	0	0	0	0	8891	362	13	0	1302	0	LOC100132247	16	22545580	In_Frame_Del	DEL	AATCTC	TCGA-A4-8517-01A-11D-2396-08	3688649	22545580	67809173	75	1554											
NOL3	8996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67208730	67208730	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctctaaagaggctgaaccgGagccggagccagagccagag	12	3	14	12	2	1	4	0	1	1	3	1	6	1	6	5	3	4	1	5	3	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:67208730G>A	ENST00000568146.1	+	3	545	c.492G>A	c.(490-492)cgG>cgA	p.R164R	NOL3_ENST00000268605.7_Missense_Mutation_p.E168K|KIAA0895L_ENST00000563831.2_5'Flank|NOL3_ENST00000432069.2_Missense_Mutation_p.E168K|NOL3_ENST00000564053.1_Missense_Mutation_p.E230K			O60936	NOL3_HUMAN	nucleolar protein 3 (apoptosis repressor with CARD domain)	164					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		GGctgaaccggagccggagcc	0.682																																					p.E230K		.											.	NOL3-227	0			c.G688A						.						20	30	26					16																	67208730		2034	4211	6245	SO:0001819	synonymous_variant	8996	exon5			GAACCGGAGCCGG	AF043244	CCDS42176.1, CCDS58473.1, CCDS61960.1	16q22.1	2008-08-27				ENSG00000140939			7869	protein-coding gene	gene with protein product		605235				9560245	Standard	NM_001276312		Approved	ARC, NOP30, MYP, CARD2	uc010vjd.3	O60936		ENST00000568146.1:c.492G>A	16.37:g.67208730G>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	36	5	NM_001276319	0	0	83	93	10	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000568146.1	37	CCDS58473.1	.	.	.	.	.	.	.	.	.	.	g	11.53	1.665514	0.29604	.	.	ENSG00000140939	ENST00000432069;ENST00000268605	T;T	0.72167	-0.63;-0.63	1.38	0.29	0.15728	.	2.201480	0.01451	N	0.015497	T	0.50205	0.1602	.	.	.	0.09310	N	1	B	0.23854	0.092	B	0.12837	0.008	T	0.29912	-0.9996	9	0.17369	T	0.5	-9.4969	4.2104	0.10509	0.2347:0.0:0.7653:0.0	.	230	B4DFL0	.	K	168	ENSP00000399831:E168K;ENSP00000268605:E168K	ENSP00000268605:E168K	E	+	1	0	NOL3	65766231	0.024000	0.19004	0.003000	0.11579	0.030000	0.12068	0.709000	0.25734	0.155000	0.19261	0.430000	0.28490	GAG	.		0.682	NOL3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422746.1			A	67208730	G	A	67208730	2	1	18	1	0	0	0	0	0	0	0	1	10549	1175	41	2		2	NOL3	16	67208730	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	44663150	67208730	23146023	76	1555											
CDYL2	124359	hgsc.bcm.edu;broad.mit.edu	37	chr16	80654830	80654830	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcgccggacttctttcatGatctgccggcagagatgaat	8	11	11	11	3	3	3	1	2	2	1	4	5	3	4	2	2	1	2	2	2	1	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:80654830G>T	ENST00000570137.2	-	4	992	c.837C>A	c.(835-837)atC>atA	p.I279I	CDYL2_ENST00000562812.1_Silent_p.I280I|CDYL2_ENST00000566173.1_Silent_p.I280I|CDYL2_ENST00000563890.1_Silent_p.I280I	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	279						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						CTTCTTTCATGATCTGCCGGC	0.582																																					p.I279I		.											.	CDYL2-90	0			c.C837A						.						38	33	35					16																	80654830		2203	4300	6503	SO:0001819	synonymous_variant	124359	exon4			TTTCATGATCTGC	AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"chromodomain Y-like protein 2"			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.837C>A	16.37:g.80654830G>T		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	32	7	NM_152342	0	0	0	0	0	Q7Z5I8	Silent	SNP	ENST00000570137.2	37	CCDS32493.1																																																																																			.		0.582	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		T	80654830	G	T	80654830	2	4	18	1	0	0	0	0	0	0	0	1	3192	1280	45	4		4	CDYL2	16	80654830	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	13446100	80654830	9699923	77	1556											
ADAD2	161931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	84228709	84228709	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgagcagcgctgcgcagcGttggtgagcgccggctttga	6	8	16	11	5	0	3	0	3	0	0	0	3	0	3	1	2	5	5	1	2	0	2	rs369199969		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:84228709G>A	ENST00000315906.5	+	4	694	c.642G>A	c.(640-642)gcG>gcA	p.A214A	ADAD2_ENST00000268624.3_Silent_p.A286A|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	214					RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						GCTGCGCAGCGTTGGTGAGCG	0.637																																					p.A286A		.											.	ADAD2-68	0			c.G858A						.						45	47	46					16																	84228709		2200	4300	6500	SO:0001819	synonymous_variant	161931	exon5			CGCAGCGTTGGTG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.642G>A	16.37:g.84228709G>A		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	86	21	NM_139174	0	0	0	0	0	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			.		0.637	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84228709	G	A	84228709	2	1	18	1	0	0	0	0	0	0	0	1	232	1132	40	1		1	ADAD2	16	84228709	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	3573879	84228709	6126044	78	1557											
C17orf62	79415	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	80405459	80405459	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggggggtgctttacctcCgctgtagtaggcagcagcca	6	8	16	11	2	0	0	0	0	0	0	1	0	1	0	3	5	4	6	3	5	3	4	rs142773924		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr17:80405459C>T	ENST00000437807.2	-	4	441	c.124G>A	c.(124-126)Gga>Aga	p.G42R	C17orf62_ENST00000585064.1_Missense_Mutation_p.G42R|C17orf62_ENST00000577436.1_Intron|C17orf62_ENST00000578913.1_Missense_Mutation_p.G42R|C17orf62_ENST00000583617.1_Missense_Mutation_p.G42R|C17orf62_ENST00000306645.5_Missense_Mutation_p.G42R|C17orf62_ENST00000342572.8_Intron|C17orf62_ENST00000434650.2_Intron|C17orf62_ENST00000336995.7_5'UTR|C17orf62_ENST00000578919.1_Missense_Mutation_p.G42R|C17orf62_ENST00000577732.1_Missense_Mutation_p.G42R|C17orf62_ENST00000583359.1_5'UTR|C17orf62_ENST00000585080.1_Missense_Mutation_p.G42R	NM_001193653.1|NM_001193657.1	NP_001180582.1|NP_001180586.1	Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62	42						integral component of membrane (GO:0016021)				breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GCTTTACCTCCGCTGTAGTAG	0.542													C|||	1	0.000199681	0	0	5008	,	,		13456	0.001		0	False		,,,				2504	0				p.G42R		.											.	C17orf62-90	0			c.G124A						.						21	19	19					17																	80405459		2201	4293	6494	SO:0001583	missense	79415	exon4			TACCTCCGCTGTA	AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927			28672	protein-coding gene	gene with protein product							Standard	NM_001100407		Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000437807.2:c.124G>A	17.37:g.80405459C>T	ENSP00000388909:p.Gly42Arg	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	42	11	NM_001193657	0	0	0	0	0	E1B6X3|Q96NR1	Missense_Mutation	SNP	ENST00000437807.2	37	CCDS32776.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	15.31	2.795825	0.50208	.	.	ENSG00000178927	ENST00000437807;ENST00000306645	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	T	0.60340	0.2261	L	0.56769	1.78	0.80722	D	1	D	0.62365	0.991	P	0.53518	0.728	T	0.56854	-0.7910	8	0.21540	T	0.41	.	9.7894	0.40697	0.0:0.9038:0.0:0.0962	.	42	Q9BQA9	CQ062_HUMAN	R	42	.	ENSP00000307765:G42R	G	-	1	0	C17orf62	77998748	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	3.580000	0.53907	2.113000	0.64589	0.561000	0.74099	GGA	A|0.000;C|1.000;T|0.000		0.542	C17orf62-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443260.1	NM_001033046		T	80405459	C	T	80405459	3	4	18	1	0	0	0	0	1	0	0	0	1875	661	23	1	459	1	C17orf62	17	80405459	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08		80405459	789751	79	1558											
NCLN	56926	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	3192650	3192650	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccgccgtgccccaggacGtcgtccgggtgagcgtctgc	3	7	16	15	6	1	1	0	1	1	0	3	2	2	2	5	3	3	0	5	3	0	0	rs200277850		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:3192650G>A	ENST00000246117.4	+	2	798	c.367G>A	c.(367-369)Gtc>Atc	p.V123I	NCLN_ENST00000590671.1_Missense_Mutation_p.V49I	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	123					regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCCAGGACGTCGTCCGGGT	0.697													G|||	1	0.000199681	0	0.0014	5008	,	,		12285	0		0	False		,,,				2504	0				p.V123I		.											.	NCLN-90	0			c.G367A						.	G	ILE/VAL	1,4293		0,1,2146	11	12	12		367	2.1	0.7	19		12	0,8446		0,0,4223	no	missense	NCLN	NM_020170.3	29	0,1,6369	AA,AG,GG		0.0,0.0233,0.0078	benign	123/564	3192650	1,12739	2147	4223	6370	SO:0001583	missense	56926	exon2			CAGGACGTCGTCC	BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"nicastrin-like protein"	609156	"nicalin homolog (zebrafish)"			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.367G>A	19.37:g.3192650G>A	ENSP00000246117:p.Val123Ile	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	23	11	NM_020170	0	0	0	0	0	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Missense_Mutation	SNP	ENST00000246117.4	37	CCDS32869.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	G	10.20	1.283531	0.23392	2.33E-4	0.0	ENSG00000125912	ENST00000246117	T	0.30448	1.53	4.24	2.09	0.27110	.	0.344674	0.29715	N	0.011386	T	0.11922	0.0290	N	0.12831	0.26	0.30808	N	0.739163	B	0.09022	0.002	B	0.04013	0.001	T	0.32877	-0.9890	10	0.02654	T	1	-15.9979	6.4264	0.21772	0.3116:0.0:0.6884:0.0	.	123	Q969V3	NCLN_HUMAN	I	123	ENSP00000246117:V123I	ENSP00000246117:V123I	V	+	1	0	NCLN	3143650	1.000000	0.71417	0.696000	0.30242	0.916000	0.54674	3.340000	0.52143	0.770000	0.33336	0.555000	0.69702	GTC	G|0.998;A|0.002		0.697	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170		A	3192650	G	A	3192650	3	1	18	1	0	0	0	0	1	0	0	0	10253	1145	40	1	373	1	NCLN	19	3192650	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08		3192650	55936333	80	1559											
PIP5K1C	23396	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	3653310	3653310	+	Frame_Shift_Del	DEL	T	T	-																															ggcagtcccgctgcagcgtcTtgaccagggcgctgaaggtg																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:3653310delT	ENST00000335312.3	-	7	987	c.899delA	c.(898-900)aagfs	p.K300fs	PIP5K1C_ENST00000587482.1_5'UTR|PIP5K1C_ENST00000589578.1_Frame_Shift_Del_p.K300fs|PIP5K1C_ENST00000539785.1_Frame_Shift_Del_p.K300fs|PIP5K1C_ENST00000537021.1_Frame_Shift_Del_p.K300fs	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	300	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		CTGCAGCGTCTTGACCAGGGC	0.692																																					p.K300fs	Esophageal Squamous(135;99 1744 12852 27186 39851)	.											.	PIP5K1C-267	0			c.899delA						.						39	27	31					19																	3653310		2203	4297	6500	SO:0001589	frameshift_variant	23396	exon7			.	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.899delA	19.37:g.3653310delT	ENSP00000335333:p.Lys300fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	67	24	NM_001195733	0	0	0	0	0	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Frame_Shift_Del	DEL	ENST00000335312.3	37	CCDS32872.1																																																																																			.		0.692	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398		-	3653310	T	-	3653310	7	5	18	1	0	1	0	1	0	0	0	0	11967	1609	56	0	1155	0	PIP5K1C	19	3653310	Frame_Shift_Del	DEL	T	TCGA-A4-8517-01A-11D-2396-08	460660	3653310	55475673	81	1560											
ZNF709	163051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12576137	12576137	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgaaggccttcccacatTccttacattcataaggtttc	12	13	5	11	0	1	1	1	1	0	0	4	1	3	1	3	2	1	1	3	2	4	6			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:12576137T>G	ENST00000397732.3	-	4	770	c.599A>C	c.(598-600)gAa>gCa	p.E200A	ZNF709_ENST00000428311.1_Missense_Mutation_p.E200A|CTD-3105H18.18_ENST00000598753.1_Intron	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	200					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						CTTCCCACATTCCTTACATTC	0.413																																					p.E200A	GBM(33;565 669 12371 29134 51667)	.											.	ZNF709-90	0			c.A599C						.						94	100	98					19																	12576137		2202	4300	6502	SO:0001583	missense	163051	exon4			CCACATTCCTTAC	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.599A>C	19.37:g.12576137T>G	ENSP00000380840:p.Glu200Ala	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	81	30	NM_152601	4	0	9	13	0	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	37	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.399242	0.62177	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.06933	3.24;3.24	2.86	0.618	0.17624	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12305	0.0299	L	0.58354	1.805	0.09310	N	1	B	0.26002	0.139	B	0.40101	0.319	T	0.42378	-0.9455	9	0.59425	D	0.04	.	4.2166	0.10537	0.1786:0.1098:0.0:0.7115	.	200	Q8N972	ZN709_HUMAN	A	200	ENSP00000380840:E200A;ENSP00000404127:E200A	ENSP00000404127:E200A	E	-	2	0	ZNF709;CTD-2192J16.17	12437137	0.001000	0.12720	0.001000	0.08648	0.909000	0.53808	1.145000	0.31577	0.059000	0.16252	0.260000	0.18958	GAA	.		0.413	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		G	12576137	T	G	12576137	3	3	18	1	0	0	0	0	1	0	0	0	18145	1783	62	5	1330	5	ZNF709	19	12576137	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	8922827	12576137	46552846	82	1561											
PKN1	5585	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	14581037	14581037	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggagttcctggcccctgagGtgctgacggacacgtcgtac	6	8	14	13	4	0	2	0	2	0	0	2	4	1	4	3	4	2	3	3	4	1	2	rs149980109		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:14581037G>T	ENST00000242783.6	+	19	2521	c.2356G>T	c.(2356-2358)Gtg>Ttg	p.V786L	PKN1_ENST00000342216.4_Missense_Mutation_p.V792L	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	786	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						GGCCCCTGAGGTGCTGACGGA	0.647																																					p.V792L	NSCLC(185;2539 2965 10733 52867)												.	PKN1-1481	0			c.G2374T						.						87	97	94					19																	14581037		2203	4300	6503	SO:0001583	missense	5585	exon19			CCTGAGGTGCTGA	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"protein kinase C-like 1"	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.2356G>T	19.37:g.14581037G>T	ENSP00000242783:p.Val786Leu	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	65	7	NM_213560	0	0	203	275	72	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	37	CCDS42513.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186864	0.78789	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.68479	-0.33;-0.33	3.91	3.91	0.45181	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000012	T	0.74023	0.3662	L	0.39326	1.205	0.41792	D	0.989871	D;D	0.63046	0.99;0.992	D;D	0.76071	0.978;0.987	T	0.77582	-0.2534	10	0.87932	D	0	-29.2807	13.7643	0.62986	0.0:0.0:1.0:0.0	.	792;786	Q16512-2;Q16512	.;PKN1_HUMAN	L	786;792	ENSP00000242783:V786L;ENSP00000343325:V792L	ENSP00000242783:V786L	V	+	1	0	PKN1	14442037	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.709000	0.84645	2.184000	0.69523	0.491000	0.48974	GTG	G|0.999;A|0.000		0.647	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560		T	14581037	G	T	14581037	3	4	18	1	0	0	0	0	1	0	0	0	12005	1261	44	4	2473	4	PKN1	19	14581037	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	2004900	14581037	44547946	83	1562											
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15303027	15303027	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggcaggagcagaggaaGcgtccatcgggccccactga	9	4	17	11	2	0	2	0	1	0	1	2	4	1	4	3	5	2	2	3	5	1	0	rs116044239		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:15303027G>T	ENST00000263388.2	-	4	498	c.423C>A	c.(421-423)cgC>cgA	p.R141R		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	141	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> C (in CADASIL). {ECO:0000269|PubMed:10227618, ECO:0000269|PubMed:10371548, ECO:0000269|PubMed:10854111, ECO:0000269|PubMed:11102981, ECO:0000269|PubMed:11755616, ECO:0000269|PubMed:15229130, ECO:0000269|PubMed:15364702, ECO:0000269|PubMed:16009764, ECO:0000269|PubMed:9388399}.		forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AGCAGAGGAAGCGTCCATCGG	0.701																																					p.R141R		.											.	NOTCH3-855	0			c.C423A						.						20	22	22					19																	15303027		2201	4296	6497	SO:0001819	synonymous_variant	4854	exon4			GAGGAAGCGTCCA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.423C>A	19.37:g.15303027G>T		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	28	10	NM_000435	0	0	3	3	0	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																			G|0.995;A|0.005		0.701	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15303027	G	T	15303027	2	4	18	1	0	0	0	0	0	0	0	1	10576	958	34	4		4	NOTCH3	19	15303027	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	721990	15303027	43825956	84	1563											
CLIP3	25999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36515358	36515358	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagtgcgctaagcatgagAttgcctgggacgttgtcata	9	10	12	10	2	1	1	1	1	0	1	1	3	1	2	2	1	3	3	2	1	2	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:36515358A>C	ENST00000360535.4	-	7	1085	c.858T>G	c.(856-858)aaT>aaG	p.N286K	AC002116.7_ENST00000586962.1_RNA|CLIP3_ENST00000593074.1_Missense_Mutation_p.N286K	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	286					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TAAGCATGAGATTGCCTGGGA	0.617																																					p.N286K		.											.	CLIP3-94	0			c.T858G						.						122	105	111					19																	36515358		2203	4300	6503	SO:0001583	missense	25999	exon6			CATGAGATTGCCT	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"Ankyrin repeat domain containing"	24314	protein-coding gene	gene with protein product	"CLIP-170-related", "restin-like 1"	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.858T>G	19.37:g.36515358A>C	ENSP00000353732:p.Asn286Lys	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	70	30	NM_001199570	0	0	0	0	0	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	37	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	A	8.190	0.795873	0.16327	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	T	0.74842	-0.88	5.88	0.203	0.15195	Cytoskeleton-associated protein, Gly-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.47173	0.1431	N	0.17082	0.46	0.52099	D	0.999948	B	0.32781	0.384	B	0.33196	0.159	T	0.46596	-0.9180	10	0.02654	T	1	-19.5733	5.4011	0.16297	0.3499:0.1781:0.472:0.0	.	286	Q96DZ5	CLIP3_HUMAN	K	286;168;262	ENSP00000353732:N286K	ENSP00000353732:N286K	N	-	3	2	CLIP3	41207198	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	0.954000	0.29175	-0.068000	0.12953	0.482000	0.46254	AAT	.		0.617	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526		C	36515358	A	C	36515358	3	2	18	1	0	0	0	0	1	0	0	0	3540	330	12	5	817	5	CLIP3	19	36515358	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	21212331	36515358	22613625	85	1564											
CHMP2A	27243	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	59063432	59063433	+	Frame_Shift_Ins	INS	-	-	T																															tccccatacctctcctcttcINSatcttcctcatcacccatgg																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:59063432_59063433insT	ENST00000600118.1	-	3	893_894	c.468_469insA	c.(466-471)gatgaafs	p.E157fs	CHMP2A_ENST00000601220.1_Frame_Shift_Ins_p.E157fs|CHMP2A_ENST00000312547.2_Frame_Shift_Ins_p.E157fs			O43633	CHM2A_HUMAN	charged multivesicular body protein 2A	157	Interaction with VPS4B.				endosomal transport (GO:0016197)|establishment of protein localization (GO:0045184)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	7		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CTCTCCTCTTCATCTTCCTCAT	0.505																																					p.E157fs		.											.	CHMP2A-90	0			c.469_470insA						.																																			SO:0001589	frameshift_variant	27243	exon4			.	AF042384	CCDS12986.1	19q13.43	2014-09-04	2011-09-21		ENSG00000130724	ENSG00000130724		"Charged multivesicular body proteins"	30216	protein-coding gene	gene with protein product	"putative breast adenocarcinoma marker (32kD)", "VPS2 homolog A (S. cerevisiae)"	610893	"chromatin modifying protein 2A"			15173323, 11559748	Standard	XM_005258746		Approved	BC-2, CHMP2, VPS2, VPS2A	uc002qtk.3	O43633	OTTHUMG00000183547	ENST00000600118.1:c.468_469insA	19.37:g.59063432_59063433insT	ENSP00000469240:p.Glu157fs	Somatic	281	0		WXS	Illumina HiSeq	Phase_I	216	80	NM_198426	0	0	0	0	0	B2R4W6|Q3ZTT0	Frame_Shift_Ins	INS	ENST00000600118.1	37	CCDS12986.1																																																																																			.		0.505	CHMP2A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467088.1	NM_014453		T	59063433	-	T	59063432	7	5	18	1	0	1	1	0	0	0	0	0	3360	835	29	0	211	0	CHMP2A	19	59063432	Frame_Shift_Ins	INS	-	TCGA-A4-8517-01A-11D-2396-08	22548074	59063432	65551	86	1565											
PYGB	5834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	25271238	25271238	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcttcctggagaactaccGtgtgtccttggctgagaaag	9	11	12	9	1	1	2	0	1	1	2	3	5	3	2	3	2	2	1	3	2	3	3	rs139162483		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:25271238G>A	ENST00000216962.4	+	16	2059	c.1949G>A	c.(1948-1950)cGt>cAt	p.R650H		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	650					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GAGAACTACCGTGTGTCCTTG	0.552																																					p.R650H		.											.	PYGB-91	0			c.G1949A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	225	198	207		1949	4.1	0.9	20	dbSNP_134	207	0,8600		0,0,4300	no	missense	PYGB	NM_002862.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	650/844	25271238	1,13005	2203	4300	6503	SO:0001583	missense	5834	exon16			ACTACCGTGTGTC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"Glycogen phosphorylases"	9723	protein-coding gene	gene with protein product	"glycogen phosphorylase, brain form"	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1949G>A	20.37:g.25271238G>A	ENSP00000216962:p.Arg650His	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	272	161	NM_002862	0	0	57	225	168	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.5|28.5	4.923497|4.923497	0.92319|0.92319	2.27E-4|2.27E-4	0.0|0.0	ENSG00000100994|ENSG00000100994	ENST00000216962|ENST00000428458	D|.	0.93488|.	-3.23|.	4.1|4.1	4.1|4.1	0.47936|0.47936	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86447|0.86447	0.5935|0.5935	H|H	0.94698|0.94698	3.57|3.57	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.68483|.	0.958|.	D|D	0.90808|0.90808	0.4699|0.4699	10|5	0.66056|.	D|.	0.02|.	-11.4783|-11.4783	16.4812|16.4812	0.84158|0.84158	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	650|.	P11216|.	PYGB_HUMAN|.	H|M	650|69	ENSP00000216962:R650H|.	ENSP00000216962:R650H|.	R|V	+|+	2|1	0|0	PYGB|PYGB	25219238|25219238	1.000000|1.000000	0.71417|0.71417	0.947000|0.947000	0.38551|0.38551	0.941000|0.941000	0.58515|0.58515	7.643000|7.643000	0.83403|0.83403	2.286000|2.286000	0.76751|0.76751	0.563000|0.563000	0.77884|0.77884	CGT|GTG	G|1.000;A|0.000		0.552	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862		A	25271238	G	A	25271238	3	1	18	1	0	0	0	0	1	0	0	0	12892	1145	40	1	2011	1	PYGB	20	25271238	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08		25271238	37754282	87	1566											
KIF3B	9371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	30897803	30897803	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcagtttgaactgtacgatGagacgttccgaccacttgtt	10	12	10	9	3	0	2	0	2	0	1	1	5	1	2	2	0	3	5	2	0	2	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:30897803G>A	ENST00000375712.3	+	2	390	c.223G>A	c.(223-225)Gag>Aag	p.E75K	KIF3B_ENST00000418717.2_5'Flank	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	75	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)			NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACTGTACGATGAGACGTTCCG	0.488																																					p.E75K		.											.	KIF3B-517	0			c.G223A						.						157	136	143					20																	30897803		2203	4300	6503	SO:0001583	missense	9371	exon2			TACGATGAGACGT	AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"Kinesins"	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.223G>A	20.37:g.30897803G>A	ENSP00000364864:p.Glu75Lys	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	149	84	NM_004798	0	0	7	37	30	B2RMP4|B4DSR5|E1P5M5	Missense_Mutation	SNP	ENST00000375712.3	37	CCDS13200.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493801	0.84962	.	.	ENSG00000101350	ENST00000375712	T	0.74842	-0.88	4.76	4.76	0.60689	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.72471	0.3464	L	0.39692	1.235	0.80722	D	1	B;P	0.42620	0.02;0.785	B;P	0.44990	0.023;0.466	T	0.73464	-0.3974	10	0.42905	T	0.14	.	18.3265	0.90256	0.0:0.0:1.0:0.0	.	75;75	B4DYF2;O15066	.;KIF3B_HUMAN	K	75	ENSP00000364864:E75K	ENSP00000364864:E75K	E	+	1	0	KIF3B	30361464	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.601000	0.98297	2.630000	0.89119	0.561000	0.74099	GAG	.		0.488	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798		A	30897803	G	A	30897803	3	1	18	1	0	0	0	0	1	0	0	0	8322	1291	45	2	225	2	KIF3B	20	30897803	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	5626565	30897803	32127717	88	1567											
C20orf132	140699	broad.mit.edu;ucsc.edu	37	chr20	35800375	35800375	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttctcaacaatggcctcActgagcgggtcctgttgggt	7	12	12	10	1	2	1	2	1	1	0	4	1	3	1	2	3	2	2	2	3	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:35800375A>T	ENST00000400441.3	-	4	464	c.465T>A	c.(463-465)agT>agA	p.S155R	MROH8_ENST00000441008.2_Missense_Mutation_p.S141R|MROH8_ENST00000217333.8_Missense_Mutation_p.S70R			Q9H579	MROH8_HUMAN	maestro heat-like repeat family member 8	75																	CAATGGCCTCACTGAGCGGGT	0.468																																					.													.	.	0			.						.						67	67	67					20																	35800375		1957	4141	6098	SO:0001583	missense	140699	.			GGCCTCACTGAGC	AL136172		20q11.22	2012-12-19	2012-12-19	2012-12-19	ENSG00000101353	ENSG00000101353		"maestro heat-like repeat containing"	16125	protein-coding gene	gene with protein product	"hypothetical protein LOC140699"		"chromosome 20 open reading frame 131", "chromosome 20 open reading frame 132"	C20orf131, C20orf132		11780052, 15635413	Standard	NM_152503		Approved	dJ621N11.4, dJ621N11.3	uc010zvu.2	Q9H579	OTTHUMG00000032407	ENST00000400441.3:c.465T>A	20.37:g.35800375A>T	ENSP00000383291:p.Ser155Arg	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	20	11	.	0	0	1	4	3	Q5JYQ6	Missense_Mutation	SNP	ENST00000400441.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	12.30|12.30|12.30	1.896945|1.896945|1.896945	0.33535|0.33535|0.33535	.|.|.	.|.|.	ENSG00000101353|ENSG00000101353|ENSG00000101353	ENST00000441008;ENST00000400441;ENST00000217333|ENST00000343811;ENST00000400440|ENST00000421643	T;T;T|.|.	0.03831|.|.	4.08;4.36;3.79|.|.	5.08|5.08|5.08	-5.56|-5.56|-5.56	0.02529|0.02529|0.02529	.|.|.	2.060200|.|.	0.01818|.|.	N|.|.	0.033895|.|.	T|T|.	0.30947|0.30947|.	0.0781|0.0781|.	L|L|L	0.40543|0.40543|0.40543	1.245|1.245|1.245	0.09310|0.09310|0.09310	N|N|N	1|1|1	B;B;B|.|.	0.26002|.|.	0.139;0.067;0.032|.|.	B;B;B|.|.	0.26969|.|.	0.055;0.074;0.075|.|.	T|T|.	0.31971|0.31971|.	-0.9924|-0.9924|.	10|5|.	0.15952|.|.	T|.|.	0.53|.|.	2.848|2.848|2.848	7.2508|7.2508|7.2508	0.26148|0.26148|0.26148	0.3825:0.0:0.4868:0.1307|0.3825:0.0:0.4868:0.1307|0.3825:0.0:0.4868:0.1307	.|.|.	155;75;165|.|.	E7ETR9;Q9H579;Q6PF12|.|.	.;CT132_HUMAN;.|.|.	R|E|R	141;155;70|182;186|192	ENSP00000392144:S141R;ENSP00000383291:S155R;ENSP00000217333:S70R|.|.	ENSP00000217333:S70R|.|.	S|V|X	-|-|-	3|2|1	2|0|0	C20orf132|C20orf132|C20orf132	35233789|35233789|35233789	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.018000|0.018000|0.018000	0.09664|0.09664|0.09664	-1.008000|-1.008000|-1.008000	0.03663|0.03663|0.03663	-1.661000|-1.661000|-1.661000	0.01484|0.01484|0.01484	-0.669000|-0.669000|-0.669000	0.03829|0.03829|0.03829	AGT|GTG|TGA	.		0.468	MROH8-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152503		T	35800375	A	T	35800375	3	4	18	1	0	0	0	0	1	0	0	0	2092	156	6	5	2759	5	C20orf132	20	35800375	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	4902572	35800375	27225145	89	1568											
SDC4	6385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	43959164	43959164	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gttcggtggggacttggctcCcagaccctgccctctcaggg	4	9	14	14	1	1	1	1	0	1	1	4	2	2	2	3	5	1	2	3	5	0	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:43959164C>A	ENST00000372733.3	-	4	326	c.287G>T	c.(286-288)gGg>gTg	p.G96V	SDC4_ENST00000537976.1_Missense_Mutation_p.G24V	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	96					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)	p.G96E(1)	SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				GACTTGGCTCCCAGACCCTGC	0.532			T	ROS1	NSCLC																																p.G96V		.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4-90	1	Substitution - Missense(1)	endometrium(1)	c.G287T						.						86	73	77					20																	43959164		2203	4300	6503	SO:0001583	missense	6385	exon4			TGGCTCCCAGACC	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"Proteoglycans / Cell Surface : Syndecans"	10661	protein-coding gene	gene with protein product	"syndecan proteoglycan 4"	600017	"syndecan 4 (amphiglycan, ryudocan)"			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.287G>T	20.37:g.43959164C>A	ENSP00000361818:p.Gly96Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	66	17	NM_002999	1	0	316	442	125	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	1.625	-0.520393	0.04171	.	.	ENSG00000124145	ENST00000372733;ENST00000537976	T	0.29917	1.55	5.68	3.56	0.40772	.	0.486350	0.18834	N	0.129888	T	0.25457	0.0619	L	0.44542	1.39	0.25579	N	0.986817	B	0.10296	0.003	B	0.14023	0.01	T	0.13469	-1.0508	10	0.29301	T	0.29	-21.9327	11.2249	0.48877	0.143:0.7246:0.1323:0.0	.	96	P31431	SDC4_HUMAN	V	96;24	ENSP00000361818:G96V	ENSP00000361818:G96V	G	-	2	0	SDC4	43392578	0.042000	0.20092	0.902000	0.35471	0.284000	0.27059	0.780000	0.26760	1.334000	0.45468	0.561000	0.74099	GGG	.		0.532	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		A	43959164	C	A	43959164	3	1	18	1	0	0	0	0	1	0	0	0	13986	623	22	4	317	4	SDC4	20	43959164	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	8158789	43959164	19066356	90	1569											
ARFGEF2	10564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47628619	47628619	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatacgtctctgagaggcctCgggttcgtttttccccacct	6	13	9	13	3	1	1	0	1	1	1	5	2	2	1	4	2	1	2	4	2	2	4	rs371146257		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:47628619C>A	ENST00000371917.4	+	28	3916	c.3916C>A	c.(3916-3918)Cgg>Agg	p.R1306R		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1306					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TGAGAGGCCTCGGGTTCGTTT	0.512																																					p.R1306R	Esophageal Squamous(176;1738 1974 26285 33069 35354)	.											.	ARFGEF2-358	0			c.C3916A						.						89	85	86					20																	47628619		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon28			AGGCCTCGGGTTC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.3916C>A	20.37:g.47628619C>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	109	61	NM_006420	0	0	0	0	0	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			.		0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47628619	C	A	47628619	2	1	18	1	0	0	0	0	0	0	0	1	853	875	31	4		4	ARFGEF2	20	47628619	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	3669455	47628619	15396901	91	1570											
CDH26	60437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	58569544	58569544	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggaagttggggagaaattggGgtgagtttttgtattggtta	9	15	17	0	0	0	2	0	1	0	1	0	4	0	3	0	6	0	4	0	6	4	7			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:58569544G>C	ENST00000244047.5	+	11	1977	c.1666G>C	c.(1666-1668)Ggt>Cgt	p.G556R	CDH26_ENST00000350849.6_5'Flank|CDH26_ENST00000244049.3_5'Flank|CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000348616.4_Splice_Site_p.G556R			Q8IXH8	CAD26_HUMAN	cadherin 26	556					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GAGAAATTGGGGTGAGTTTTT	0.433																																					p.G556R		.											.	CDH26-93	0			c.G1666C						.						34	33	33					20																	58569544		2203	4300	6503	SO:0001630	splice_region_variant	60437	exon11			AATTGGGGTGAGT	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"Cadherins / Major cadherins"	15902	protein-coding gene	gene with protein product			"cadherin-like 26"				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1666+1G>C	20.37:g.58569544G>C		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	74	24	NM_177980	0	0	0	0	0	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	37		.	.	.	.	.	.	.	.	.	.	G	16.64	3.180551	0.57800	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.72835	-0.69;-0.69	4.35	4.35	0.52113	Cadherin-like (1);	0.391569	0.24463	N	0.038317	D	0.83436	0.5254	M	0.74258	2.255	0.49687	D	0.999815	D;D	0.89917	0.999;1.0	D;D	0.85130	0.973;0.997	D	0.86131	0.1575	10	0.87932	D	0	.	15.6637	0.77209	0.0:0.0:1.0:0.0	.	556;556	Q8IXH8;Q8IXH8-4	CAD26_HUMAN;.	R	556	ENSP00000244047:G556R;ENSP00000339390:G556R	ENSP00000244047:G556R	G	+	1	0	CDH26	58002939	1.000000	0.71417	0.388000	0.26195	0.582000	0.36321	5.190000	0.65104	1.954000	0.56735	0.655000	0.94253	GGT	.		0.433	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	Missense_Mutation	C	58569544	G	C	58569544	5	2	18	1	0	0	0	0	0	0	1	0	3116	1246	43	4	1708	4	CDH26	20	58569544	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	10940925	58569544	4455976	92	1571											
NCAM2	4685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	22849618	22849618	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattgctttcacagaaagatAaggaagaccaatggctagag	16	9	10	6	0	1	4	1	0	0	4	1	5	1	5	1	2	1	2	1	2	6	5	rs201923816		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr21:22849618A>G	ENST00000400546.1	+	15	2152	c.1903A>G	c.(1903-1905)Aag>Gag	p.K635E	NCAM2_ENST00000284894.7_Missense_Mutation_p.K493E	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	635	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		ACAGAAAGATAAGGAAGACCA	0.338																																					p.K635E		.											.	NCAM2-94	0			c.A1903G						.						80	74	76					21																	22849618		1822	4085	5907	SO:0001583	missense	4685	exon15			AAAGATAAGGAAG		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1903A>G	21.37:g.22849618A>G	ENSP00000383392:p.Lys635Glu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	36	12	NM_004540	0	0	0	0	0	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069133	0.76301	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.51574	0.7;0.7	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	N	0.15975	0.35	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.81914	0.995;0.995	T	0.58912	-0.7552	10	0.56958	D	0.05	-27.6898	14.9715	0.71238	1.0:0.0:0.0:0.0	.	493;635	B7Z5K2;O15394	.;NCAM2_HUMAN	E	635;493	ENSP00000383392:K635E;ENSP00000284894:K493E	ENSP00000284894:K493E	K	+	1	0	NCAM2	21771489	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.306000	0.72810	2.213000	0.71641	0.528000	0.53228	AAG	A|0.999;G|0.001		0.338	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		G	22849618	A	G	22849618	3	3	18	1	0	0	0	0	1	0	0	0	10229	363	13	3	1961	3	NCAM2	21	22849618	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08		22849618	25280277	93	1572											
MRPL40	64976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	19423455	19423455	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtacaatgacatcaccaaGgtgtacacacaagtggagtt	15	8	10	8	0	1	1	1	1	0	0	1	2	1	2	1	3	2	3	1	3	5	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:19423455G>T	ENST00000333130.3	+	4	1244	c.591G>T	c.(589-591)aaG>aaT	p.K197N	HIRA_ENST00000541063.1_Intron|MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000546308.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	197					anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					ACATCACCAAGGTGTACACAC	0.502																																					p.K197N		.											.	MRPL40-90	0			c.G591T						.						116	106	109					22																	19423455		2203	4300	6503	SO:0001583	missense	64976	exon4			CACCAAGGTGTAC	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"Mitochondrial ribosomal proteins / large subunits"	14491	protein-coding gene	gene with protein product		605089	"nuclear localization signal deleted in velocardiofacial syndrome"	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.591G>T	22.37:g.19423455G>T	ENSP00000333401:p.Lys197Asn	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	63	23	NM_003776	0	0	56	85	29	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	37	CCDS13760.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392258	0.42410	.	.	ENSG00000185608	ENST00000333130	T	0.52983	0.64	5.53	2.23	0.28157	.	0.102989	0.64402	D	0.000005	T	0.66247	0.2770	M	0.85542	2.76	0.45502	D	0.998462	D	0.76494	0.999	D	0.77557	0.99	T	0.67473	-0.5662	10	0.72032	D	0.01	-26.3156	7.4919	0.27466	0.4243:0.0:0.5757:0.0	.	197	Q9NQ50	RM40_HUMAN	N	197	ENSP00000333401:K197N	ENSP00000333401:K197N	K	+	3	2	MRPL40	17803455	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	1.675000	0.37555	0.898000	0.36418	0.655000	0.94253	AAG	.		0.502	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776		T	19423455	G	T	19423455	3	4	18	1	0	0	0	0	1	0	0	0	9829	991	35	4	605	4	MRPL40	22	19423455	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08		19423455	31881111	94	1573											
KLHL22	84861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	20796432	20796432	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagaggcaaagtccgggtcGgcctggctgcggtcaggggt	6	7	18	10	3	2	1	2	0	0	1	4	1	3	1	2	7	1	2	2	7	1	0	rs149300605		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:20796432G>C	ENST00000328879.4	-	7	1989	c.1833C>G	c.(1831-1833)gcC>gcG	p.A611A	KLHL22_ENST00000440659.2_Silent_p.A468A	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	611					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			AGTCCGGGTCGGCCTGGCTGC	0.647																																					p.A611A		.											.	KLHL22-278	0			c.C1833G						.						29	30	30					22																	20796432		2203	4300	6503	SO:0001819	synonymous_variant	84861	exon7			CGGGTCGGCCTGG		CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"Kelch-like", "BTB/POZ domain containing"	25888	protein-coding gene	gene with protein product			"kelch-like 22 (Drosophila)"			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1833C>G	22.37:g.20796432G>C		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	67	26	NM_032775	0	0	6	14	8	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Silent	SNP	ENST00000328879.4	37	CCDS13780.1																																																																																			G|1.000;A|0.000		0.647	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775		C	20796432	G	C	20796432	2	2	18	1	0	0	0	0	0	0	0	1	8398	1103	39	4		4	KLHL22	22	20796432	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	1372977	20796432	30508134	95	1574											
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46765598	46765598	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacactcacgattataacAgctccgatgggccccgcaaa	12	6	7	16	3	1	0	1	0	0	0	2	2	2	0	4	1	2	2	4	1	3	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:46765598A>G	ENST00000262738.3	-	26	7862	c.7863T>C	c.(7861-7863)gcT>gcC	p.A2621A		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2621					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CGATTATAACAGCTCCGATGG	0.627																																					p.A2621A		.											.	CELSR1-525	0			c.T7863C						.						55	54	54					22																	46765598		2203	4300	6503	SO:0001819	synonymous_variant	9620	exon26			TATAACAGCTCCG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.7863T>C	22.37:g.46765598A>G		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	63	24	NM_014246	0	0	0	0	0	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			.		0.627	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46765598	A	G	46765598	2	3	18	1	0	0	0	0	0	0	0	1	3227	175	7	3		3	CELSR1	22	46765598	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	25969166	46765598	4538968	96	1575											
MIOX	55586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50926723	50926723	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gactggttccacctcgtcggGctcctgcacgacctggggaa	6	8	13	14	3	0	0	0	0	0	0	4	3	2	1	4	4	1	3	4	4	1	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:50926723G>T	ENST00000216075.6	+	5	434	c.360G>T	c.(358-360)ggG>ggT	p.G120G	MIOX_ENST00000395732.3_Silent_p.G120G|MIOX_ENST00000395733.3_Missense_Mutation_p.G131V	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	120					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		ACCTCGTCGGGCTCCTGCACG	0.652																																					p.G120G		.											.	MIOX-90	0			c.G360T						.						57	55	56					22																	50926723		2203	4300	6503	SO:0001819	synonymous_variant	55586	exon5			CGTCGGGCTCCTG	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"kidney-specific protein 32"	606774	"aldehyde reductase (aldose reductase) like 6"	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.360G>T	22.37:g.50926723G>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	38	16	NM_017584	0	1	355	755	399	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	37	CCDS14092.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.277251	0.40294	.	.	ENSG00000100253	ENST00000395733	.	.	.	4.4	2.3	0.28687	.	0.000000	0.85682	D	0.000000	T	0.42988	0.1227	.	.	.	0.80722	D	1	B	0.20671	0.047	B	0.17979	0.02	T	0.37150	-0.9718	8	0.87932	D	0	-5.0893	3.2524	0.06819	0.2255:0.0:0.5677:0.2069	.	131	Q9UGB7-2	.	V	131	.	ENSP00000379082:G131V	G	+	2	0	MIOX	49273589	0.998000	0.40836	0.980000	0.43619	0.906000	0.53458	0.593000	0.23999	0.468000	0.27243	0.436000	0.28706	GGC	.		0.652	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584		T	50926723	G	T	50926723	2	4	18	1	0	0	0	0	0	0	0	1	9615	1190	42	4		4	MIOX	22	50926723	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	4161125	50926723	377843	97	1576											
WWC3	55841	broad.mit.edu;bcgsc.ca	37	chrX	10094307	10094307	+	Frame_Shift_Del	DEL	C	C	-																															ctgaagtcacttcagttataCgtgtgttcagtgactccgca																								rs199701428		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chrX:10094307delC	ENST00000380861.4	+	15	2458	c.2067delC	c.(2065-2067)tacfs	p.Y689fs	WWC3_ENST00000454666.1_Frame_Shift_Del_p.Y689fs	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	689	C2.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TTCAGTTATACGTGTGTTCAG	0.572																																					p.Y689X													.	WWC3-134	0			c.2067delC						.						114	95	101					X																	10094307		2203	4300	6503	SO:0001589	frameshift_variant	55841	exon15			GTTATACGTGTGT	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.2067delC	X.37:g.10094307delC	ENSP00000370242:p.Tyr689fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	75	11	NM_015691	0	0	0	0	0	A8KA96|Q659C1|Q9BTQ1	Nonsense_Mutation	DEL	ENST00000380861.4	37	CCDS14136.1																																																																																			.		0.572	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		-	10094307	C	-	10094307	7	5	18	1	0	1	0	1	0	0	0	0	17446	547	19	0	2121	0	WWC3	23	10094307	Frame_Shift_Del	DEL	C	TCGA-A4-8517-01A-11D-2396-08		10094307	145176253	98	1577											
NXT2	55916	hgsc.bcm.edu;broad.mit.edu	37	chrX	108780250	108780250	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcccagatggccacgtctctGgtgagtgcctgggccgtggc	4	9	15	13	2	1	2	0	1	1	1	3	2	2	2	4	4	1	0	4	4	0	0			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chrX:108780250G>A	ENST00000372106.1	+	1	146	c.15G>A	c.(13-15)ctG>ctA	p.L5L	NXT2_ENST00000372103.1_5'Flank|NXT2_ENST00000372107.1_5'UTR|NXT2_ENST00000218004.1_Splice_Site_p.L60L	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2	5					mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						CCACGTCTCTGGTGAGTGCCT	0.642																																					p.L60L		.											.	NXT2-109	0			c.G180A						.						50	33	39					X																	108780250		2203	4300	6503	SO:0001630	splice_region_variant	55916	exon2			GTCTCTGGTGAGT	AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185	ENST00000372106.1:c.15+1G>A	X.37:g.108780250G>A		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	15	6	NM_018698	0	0	0	0	0	D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Silent	SNP	ENST00000372106.1	37	CCDS56605.1																																																																																			.		0.642	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057886.1	NM_018698	Silent	A	108780250	G	A	108780250	5	1	18	1	0	0	0	0	0	0	1	0	10821	1362	47	2	186	2	NXT2	23	108780250	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	98685943	108780250	46490310	99	1578											
THOC2	57187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	122755201	122755201	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggggacagtggtcttaaaTttctcatctttagctttttc	7	19	8	7	0	3	0	1	0	3	0	5	1	3	1	0	3	1	1	0	3	3	7			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chrX:122755201T>A	ENST00000245838.8	-	31	4054	c.4023A>T	c.(4021-4023)aaA>aaT	p.K1341N	THOC2_ENST00000491737.1_Missense_Mutation_p.K1226N|THOC2_ENST00000355725.4_Missense_Mutation_p.K1341N|THOC2_ENST00000497887.1_5'Flank	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1341	Lys-rich.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TGGTCTTAAATTTCTCATCTT	0.373																																					p.K1341N		.											.	THOC2-133	0			c.A4023T						.						259	229	239					X																	122755201		1871	4088	5959	SO:0001583	missense	57187	exon31			CTTAAATTTCTCA	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.4023A>T	X.37:g.122755201T>A	ENSP00000245838:p.Lys1341Asn	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	68	56	NM_001081550	0	0	0	15	15	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.36|12.36	1.915943|1.915943	0.33815|0.33815	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000441692	T;T;T|.	0.22539|.	1.95;1.95;1.95|.	5.32|5.32	4.16|4.16	0.48862|0.48862	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.51126|0.51126	0.1656|0.1656	L|L	0.36672|0.36672	1.1|1.1	0.53688|0.53688	D|D	0.999974|0.999974	P|.	0.43094|.	0.799|.	B|.	0.42692|.	0.395|.	T|T	0.40194|0.40194	-0.9576|-0.9576	9|5	.|.	.|.	.|.	-12.8428|-12.8428	8.5327|8.5327	0.33344|0.33344	0.0:0.2225:0.0:0.7775|0.0:0.2225:0.0:0.7775	.|.	1341|.	Q8NI27|.	THOC2_HUMAN|.	N|I	1341;1341;1226|109	ENSP00000245838:K1341N;ENSP00000347959:K1341N;ENSP00000419795:K1226N|.	.|.	K|N	-|-	3|2	2|0	THOC2|THOC2	122582882|122582882	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	1.873000|1.873000	0.39558|0.39558	0.776000|0.776000	0.33473|0.33473	0.486000|0.486000	0.48141|0.48141	AAA|AAT	.		0.373	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			A	122755201	T	A	122755201	3	1	18	1	0	0	0	0	1	0	0	0	15897	1490	52	5	790	5	THOC2	23	122755201	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	13974951	122755201	32515359	100	1579											
RBMX	27316	hgsc.bcm.edu	37	chrX	135960073	135960073	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaggtccacgcaagttattaCccatgtgtcctccccgtgag	8	10	10	13	2	0	1	0	1	0	0	3	2	3	1	5	1	1	2	5	1	3	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chrX:135960073C>T	ENST00000320676.7	-	4	543		c.e4+1		RBMX_ENST00000570135.1_Intron|RBMX_ENST00000565438.1_Splice_Site|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000562646.1_Splice_Site|SNORD61_ENST00000384252.1_RNA	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked						cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAAGTTATTACCCATGTGTCC	0.537																																					.		.											.	RBMX-131	0			c.388+1G>A						.						66	64	65					X																	135960073		2203	4300	6503	SO:0001630	splice_region_variant	27316	exon5			TTATTACCCATGT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"RNA binding motif (RRM) containing"	9910	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein G"	300199	"RNA binding motif protein, X chromosome"			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.388+1G>A	X.37:g.135960073C>T		Somatic	44	1		WXS	Illumina HiSeq	Phase_I	50	4	NM_002139	0	0	0	0	0	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Splice_Site	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901881	0.52227	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	.	.	.	4.04	4.04	0.47022	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5997	0.68432	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RBMX	135787739	.	.	1.000000	0.80357	0.740000	0.42216	.	.	2.272000	0.75746	0.504000	0.49776	.	.		0.537	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	Intron	T	135960073	C	T	135960073	5	4	18	1	0	0	0	0	0	0	1	0	13183	521	18	2	865	2	RBMX	23	135960073	Splice_Site	SNP	C	TCGA-A4-8517-01A-11D-2396-08	13204872	135960073	19310487	101	1580											
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	18023490	18023490	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaagccagacgggcaggCacacgagcccatgcccgata	12	2	13	14	3	0	1	0	0	0	1	0	4	0	2	3	3	3	2	3	3	2	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:18023490C>G	ENST00000361221.3	+	29	3614	c.3455C>G	c.(3454-3456)gCa>gGa	p.A1152G	ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A1113G|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A925G|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A855G|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A1113G	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	1152						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GACGGGCAGGCACACGAGCCC	0.687											OREG0013156	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A1152G		.											.	ARHGEF10L-292	0			c.C3455G						.						22	22	22					1																	18023490		2199	4295	6494	SO:0001583	missense	55160	exon29			GGCAGGCACACGA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.3455C>G	1.37:g.18023490C>G	ENSP00000355060:p.Ala1152Gly	Somatic	32	0	722	WXS	Illumina HiSeq	Phase_I	30	2	NM_018125	0	0	21	21	0	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	.	.	.	.	.	.	.	.	.	.	C	0.151	-1.091069	0.01858	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000375415;ENST00000375408;ENST00000457829;ENST00000167825	T;T;T;T;T	0.59906	0.5;0.5;0.5;0.23;2.49	5.11	2.11	0.27256	.	0.854734	0.10305	N	0.690747	T	0.38825	0.1055	N	0.25647	0.755	0.09310	N	1	B;B;B;B;B;B;B	0.27823	0.081;0.19;0.003;0.016;0.0;0.0;0.0	B;B;B;B;B;B;B	0.24006	0.044;0.05;0.005;0.01;0.0;0.0;0.0	T	0.21827	-1.0234	10	0.24483	T	0.36	-2.8352	5.2153	0.15338	0.1484:0.6263:0.1435:0.0819	.	925;925;855;913;1108;1113;1152	Q5VXI4;B4DTL3;Q9HCE6-4;B3KX74;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;.;.;.;ARGAL_HUMAN	G	1152;1113;1113;925;925;855	ENSP00000355060:A1152G;ENSP00000399401:A1113G;ENSP00000364564:A1113G;ENSP00000364557:A925G;ENSP00000167825:A855G	ENSP00000167825:A855G	A	+	2	0	ARHGEF10L	17896077	0.000000	0.05858	0.012000	0.15200	0.001000	0.01503	0.830000	0.27462	0.149000	0.19098	-0.905000	0.02835	GCA	.		0.687	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		G	18023490	C	G	18023490	3	3	19	1	0	0	0	0	1	0	0	0	895	710	25	4	3565	4	ARHGEF10L	1	18023490	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		18023490	231227131	1	1581											
IL22RA1	58985	bcgsc.ca	37	chr1	24447843	24447843	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctgtccggagtggcttGaggggcataggaggaaggct	8	7	18	8	1	0	1	0	1	0	0	1	4	1	4	2	7	1	4	2	7	2	2	rs75716137		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:24447843G>T	ENST00000270800.1	-	7	1215	c.1177C>A	c.(1177-1179)Caa>Aaa	p.Q393K		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	393					cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GGAGTGGCTTGAGGGGCATAG	0.582																																					p.Q393K													.	IL22RA1-91	0			c.C1177A						.						59	62	61					1																	24447843		2203	4300	6503	SO:0001583	missense	58985	exon7			TGGCTTGAGGGGC	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"Interleukins and interleukin receptors"	13700	protein-coding gene	gene with protein product		605457	"interleukin 22 receptor"	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.1177C>A	1.37:g.24447843G>T	ENSP00000270800:p.Gln393Lys	Somatic	173	0		WXS	Illumina HiSeq	Phase_1	109	34	NM_021258	0	0	2	2	0	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	37	CCDS247.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726456	0.48833	.	.	ENSG00000142677	ENST00000270800	T	0.14144	2.53	4.9	4.9	0.64082	.	0.870285	0.09673	N	0.770867	T	0.09992	0.0245	L	0.27053	0.805	0.09310	N	0.999995	P;P	0.42908	0.793;0.793	B;B	0.35114	0.196;0.126	T	0.13176	-1.0519	10	0.17369	T	0.5	-27.4158	13.499	0.61442	0.0:0.0:1.0:0.0	.	325;393	B4E2V9;Q8N6P7	.;I22R1_HUMAN	K	393	ENSP00000270800:Q393K	ENSP00000270800:Q393K	Q	-	1	0	IL22RA1	24320430	0.673000	0.27539	0.083000	0.20561	0.136000	0.21042	4.235000	0.58666	2.562000	0.86427	0.558000	0.71614	CAA	.		0.582	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			T	24447843	G	T	24447843	3	4	19	1	0	0	0	0	1	0	0	0	7694	1299	45	4	551	4	IL22RA1	1	24447843	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	6424353	24447843	224802778	2	1582											
PPCS	79717	bcgsc.ca	37	chr1	42922310	42922310	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggctgaggttatggctcGcttcgcggccaggctgggcg	3	9	18	11	4	0	1	0	1	0	0	2	1	0	1	1	6	0	5	1	6	1	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:42922310G>C	ENST00000372561.3	+	1	81	c.74G>C	c.(73-75)cGc>cCc	p.R25P	ZMYND12_ENST00000433602.2_5'Flank|ZMYND12_ENST00000372565.3_5'Flank|PPCS_ENST00000372560.3_Missense_Mutation_p.R25P|PPCS_ENST00000455780.1_Intron|PPCS_ENST00000372556.3_Intron|PPCS_ENST00000372562.1_Intron|PPCS_ENST00000472013.1_3'UTR	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	25					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTTATGGCTCGCTTCGCGGCC	0.721																																					p.R25P													.	PPCS-90	0			c.G74C						.						10	13	12					1																	42922310		1817	3983	5800	SO:0001583	missense	79717	exon1			TGGCTCGCTTCGC	AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.74G>C	1.37:g.42922310G>C	ENSP00000361642:p.Arg25Pro	Somatic	71	0		WXS	Illumina HiSeq	Phase_1	24	16	NM_024664	0	0	4	4	0	Q3KQT2|Q5VVM0	Missense_Mutation	SNP	ENST00000372561.3	37	CCDS41311.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.619808	0.46736	.	.	ENSG00000127125	ENST00000372560;ENST00000372561	.	.	.	5.22	4.28	0.50868	DNA/pantothenate metabolism flavoprotein, C-terminal (2);	0.273869	0.41001	D	0.000961	T	0.39733	0.1089	N	0.24115	0.695	0.80722	D	1	B	0.24675	0.109	B	0.20384	0.029	T	0.32613	-0.9900	9	0.48119	T	0.1	-1.0833	8.2516	0.31730	0.1746:0.0:0.8254:0.0	.	25	Q9HAB8	PPCS_HUMAN	P	25	.	ENSP00000361641:R25P	R	+	2	0	PPCS	42694897	0.903000	0.30736	1.000000	0.80357	0.985000	0.73830	1.162000	0.31786	2.712000	0.92718	0.563000	0.77884	CGC	.		0.721	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664		C	42922310	G	C	42922310	3	2	19	1	0	0	0	0	1	0	0	0	12331	1087	38	4	76	4	PPCS	1	42922310	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	18474467	42922310	206328311	3	1583											
PTPRF	5792	bcgsc.ca	37	chr1	44070598	44070598	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaagaacttccgggtggCggctgcaatgaagacgtctg	9	8	14	10	3	1	3	0	1	1	2	2	3	2	3	2	3	3	2	2	3	4	1	rs147874335		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:44070598C>T	ENST00000359947.4	+	17	3402	c.3062C>T	c.(3061-3063)gCg>gTg	p.A1021V	PTPRF_ENST00000372414.3_Missense_Mutation_p.A1021V|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Missense_Mutation_p.A1012V|PTPRF_ENST00000422171.2_Missense_Mutation_p.A369V|PTPRF_ENST00000372413.3_Missense_Mutation_p.A1012V	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1021	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TTCCGGGTGGCGGCTGCAATG	0.562													C|||	1	0.000199681	8e-04	0	5008	,	,		21066	0		0	False		,,,				2504	0				p.A1021V													.	PTPRF-232	0			c.C3062T						.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	117	120	119		3062,3035	1.3	0.9	1	dbSNP_134	119	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	PTPRF	NM_002840.3,NM_130440.2	64,64	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	benign,benign	1021/1908,1012/1899	44070598	5,13001	2203	4300	6503	SO:0001583	missense	5792	exon17			GGGTGGCGGCTGC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.3062C>T	1.37:g.44070598C>T	ENSP00000353030:p.Ala1021Val	Somatic	149	0		WXS	Illumina HiSeq	Phase_1	124	6	NM_002840	0	0	56	56	0	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.87|14.87	2.665441|2.665441	0.47677|0.47677	0.0|0.0	5.81E-4|5.81E-4	ENSG00000142949|ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407|ENST00000429895	T;T;T;T;T;T|.	0.51574|.	0.7;0.7;0.7;0.7;0.7;0.71|.	4.91|4.91	1.28|1.28	0.21552|0.21552	Fibronectin, type III (3);Immunoglobulin-like fold (1);|.	0.259629|.	0.20302|.	N|.	0.095002|.	T|T	0.26085|0.26085	0.0636|0.0636	N|N	0.14661|0.14661	0.345|0.345	0.29885|0.29885	N|N	0.825714|0.825714	B;B;B;D;P|.	0.69078|.	0.007;0.0;0.01;0.997;0.531|.	B;B;B;P;B|.	0.55345|.	0.003;0.001;0.006;0.774;0.109|.	T|T	0.29150|0.29150	-1.0021|-1.0021	10|5	0.27785|.	T|.	0.31|.	.|.	9.2697|9.2697	0.37664|0.37664	0.6451:0.2479:0.107:0.0|0.6451:0.2479:0.107:0.0	.|.	666;369;587;1012;1021|.	Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586|.	.;.;.;.;PTPRF_HUMAN|.	V|W	1021;1012;1021;1012;369;82|667	ENSP00000353030:A1021V;ENSP00000398822:A1012V;ENSP00000361491:A1021V;ENSP00000361490:A1012V;ENSP00000387885:A369V;ENSP00000361484:A82V|.	ENSP00000353030:A1021V|.	A|R	+|+	2|1	0|2	PTPRF|PTPRF	43843185|43843185	0.540000|0.540000	0.26410|0.26410	0.896000|0.896000	0.35187|0.35187	0.967000|0.967000	0.64934|0.64934	1.325000|1.325000	0.33724|0.33724	0.546000|0.546000	0.28920|0.28920	0.491000|0.491000	0.48974|0.48974	GCG|CGG	C|1.000;T|0.000		0.562	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44070598	C	T	44070598	3	4	19	1	0	0	0	0	1	0	0	0	12833	768	27	1	3120	1	PTPRF	1	44070598	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	1148288	44070598	205180023	4	1584											
KIAA1324	57535	bcgsc.ca	37	chr1	109735398	109735398	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atattgaccgagattcaggaAcctgccactcctgccccact	10	9	7	15	1	1	2	1	1	0	1	2	4	2	3	6	1	3	0	6	1	2	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:109735398A>C	ENST00000369939.3	+	14	2032	c.1849A>C	c.(1849-1851)Acc>Ccc	p.T617P	KIAA1324_ENST00000529753.1_Missense_Mutation_p.T530P|KIAA1324_ENST00000369938.1_3'UTR	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	617					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		AGATTCAGGAACCTGCCACTC	0.562																																					p.T617P													.	KIAA1324-157	0			c.A1849C						.						154	148	150					1																	109735398		2203	4300	6503	SO:0001583	missense	57535	exon14			TCAGGAACCTGCC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.1849A>C	1.37:g.109735398A>C	ENSP00000358955:p.Thr617Pro	Somatic	286	32		WXS	Illumina HiSeq	Phase_1	227	80	NM_020775	0	0	0	0	0	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	37	CCDS794.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.130791	0.37630	.	.	ENSG00000116299	ENST00000369939;ENST00000457623;ENST00000529753	T;T;T	0.64618	-0.11;-0.11;-0.11	4.81	3.54	0.40534	Growth factor, receptor (1);	0.505379	0.23247	N	0.050290	T	0.24160	0.0585	N	0.14661	0.345	0.32545	N	0.533146	B;P;B;B	0.42692	0.21;0.787;0.21;0.21	B;B;B;B	0.41619	0.192;0.361;0.124;0.124	T	0.06734	-1.0810	10	0.35671	T	0.21	-15.6136	5.7003	0.17879	0.7307:0.0:0.2692:0.0	.	617;530;617;617	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	P	617;567;530	ENSP00000358955:T617P;ENSP00000393964:T567P;ENSP00000434595:T530P	ENSP00000358955:T617P	T	+	1	0	KIAA1324	109536921	0.000000	0.05858	1.000000	0.80357	0.816000	0.46133	0.706000	0.25690	0.999000	0.39023	0.528000	0.53228	ACC	.		0.562	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		C	109735398	A	C	109735398	3	2	19	1	0	0	0	0	1	0	0	0	8244	43	2	5	1903	5	KIAA1324	1	109735398	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	65664800	109735398	139515223	5	1585											
KCNC4	3749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110774916	110774916	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctccaactgctgggactctGttcctgccacattgaggaag	8	10	10	13	0	1	1	0	1	1	0	3	3	3	3	4	2	3	2	4	2	2	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:110774916G>A	ENST00000369787.3	+	4	1920	c.1893G>A	c.(1891-1893)ctG>ctA	p.L631L	KCNC4_ENST00000438661.2_Intron|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000413138.3_Intron	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	631					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		CTGGGACTCTGTTCCTGCCAC	0.562																																					p.L631L		.											.	KCNC4-154	0			c.G1893A						.						74	54	61					1																	110774916		2203	4300	6503	SO:0001819	synonymous_variant	3749	exon4			GACTCTGTTCCTG	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.1893G>A	1.37:g.110774916G>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	32	10	NM_004978	0	0	0	0	0	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	37	CCDS821.1																																																																																			.		0.562	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		A	110774916	G	A	110774916	2	1	19	1	0	0	0	0	0	0	0	1	8038	1364	48	2		2	KCNC4	1	110774916	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08	1039518	110774916	138475705	6	1586											
DENND2D	79961	hgsc.bcm.edu	37	chr1	111739853	111739853	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgcagtacactttgggaAggcgagggccagggccggca	9	6	17	9	2	0	1	0	1	0	0	0	3	0	2	2	5	2	3	2	5	2	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:111739853A>G	ENST00000357640.4	-	5	678	c.449T>C	c.(448-450)cTt>cCt	p.L150P	DENND2D_ENST00000369752.5_Missense_Mutation_p.L147P|DENND2D_ENST00000473682.1_5'UTR	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	150	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		CACTTTGGGAAGGCGAGGGCC	0.597																																					p.L150P		.											.	DENND2D-227	0			c.T449C						.						46	41	43					1																	111739853		2203	4300	6503	SO:0001583	missense	79961	exon5			TTGGGAAGGCGAG		CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"DENN/MADD domain containing"	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.449T>C	1.37:g.111739853A>G	ENSP00000350266:p.Leu150Pro	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_024901	0	0	21	21	0	Q5T5V6|Q9BSU0	Missense_Mutation	SNP	ENST00000357640.4	37	CCDS831.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.323695	0.81580	.	.	ENSG00000162777	ENST00000357640;ENST00000369752	T;T	0.12774	2.65;2.65	5.59	5.59	0.84812	DENN (3);	0.236682	0.39544	N	0.001326	T	0.10766	0.0263	M	0.66378	2.025	0.80722	D	1	B;P	0.35411	0.445;0.5	B;B	0.35770	0.134;0.21	T	0.01432	-1.1356	10	0.87932	D	0	-19.5041	13.9922	0.64374	1.0:0.0:0.0:0.0	.	147;150	Q9H6A0-2;Q9H6A0	.;DEN2D_HUMAN	P	150;147	ENSP00000350266:L150P;ENSP00000358767:L147P	ENSP00000350266:L150P	L	-	2	0	DENND2D	111541376	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	3.995000	0.57001	2.250000	0.74265	0.533000	0.62120	CTT	.		0.597	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901		G	111739853	A	G	111739853	3	3	19	1	0	0	0	0	1	0	0	0	4442	72	3	3	998	3	DENND2D	1	111739853	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	964937	111739853	137510768	7	1587											
VANGL1	81839	bcgsc.ca	37	chr1	116226631	116226631	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgctcggcgcagggactCaagccacaacgagttgtatt	10	8	12	11	3	1	0	1	0	0	0	2	2	1	1	1	2	4	5	1	2	3	3	rs74117015		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:116226631C>A	ENST00000355485.2	+	6	1284	c.1013C>A	c.(1012-1014)tCa>tAa	p.S338*	VANGL1_ENST00000369509.1_Nonsense_Mutation_p.S338*|VANGL1_ENST00000474344.1_3'UTR|VANGL1_ENST00000310260.3_Nonsense_Mutation_p.S338*|VANGL1_ENST00000369510.4_Nonsense_Mutation_p.S336*	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	338					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CGCAGGGACTCAAGCCACAAC	0.527																																					p.S338X													.	VANGL1-226	0			c.C1013A						.						75	68	70					1																	116226631		2203	4300	6503	SO:0001587	stop_gained	81839	exon6			GGGACTCAAGCCA	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.1013C>A	1.37:g.116226631C>A	ENSP00000347672:p.Ser338*	Somatic	81	2		WXS	Illumina HiSeq	Phase_1	66	29	NM_001172412	0	0	3	3	0	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Nonsense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	33	5.254362	0.95336	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	.	.	.	4.58	4.58	0.56647	.	0.244948	0.41938	D	0.000799	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	4.8415	12.6952	0.56999	0.1648:0.8352:0.0:0.0	.	.	.	.	X	338;336;338;338	.	ENSP00000310800:S338X	S	+	2	0	VANGL1	116028154	1.000000	0.71417	0.934000	0.37439	0.464000	0.32679	2.734000	0.47368	2.366000	0.80165	0.551000	0.68910	TCA	C|0.500;A|0.500		0.527	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			A	116226631	C	A	116226631	4	1	19	1	0	0	0	0	0	1	0	0	17152	838	29	4	1031	4	VANGL1	1	116226631	Nonsense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	4486778	116226631	133023990	8	1588											
NBPF14	25832	hgsc.bcm.edu	37	chr1	148015634	148015634	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggtactcaccatccatgtTaacagccaagccaacacgct	14	7	6	14	1	1	0	1	0	0	0	2	0	2	0	4	1	5	3	4	1	5	2	rs200156420	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:148015634T>C	ENST00000369219.1	-	8	1013	c.997A>G	c.(997-999)Aac>Gac	p.N333D				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	333	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.			N -> D (in Ref. 3; AAO15399). {ECO:0000305}.		cytoplasm (GO:0005737)		p.N333D(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					CCATCCATGTTAACAGCCAAG	0.463													-|||	445	0.0888578	0.146	0.0778	5008	,	,		13640	0.0675		0.0408	False		,,,				2504	0.091				p.N333D		.											.	NBPF14-91	1	Substitution - Missense(1)	skin(1)	c.A997G						.						4	3	4					1																	148015634		718	1612	2330	SO:0001583	missense	25832	exon8			CCATGTTAACAGC	AK092351		1q21.1	2013-01-17			ENSG00000122497			"neuroblastoma breakpoint family"	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.997A>G	1.37:g.148015634T>C	ENSP00000358221:p.Asn333Asp	Somatic	46	1		WXS	Illumina HiSeq	Phase_I	58	3	NM_015383	0	0	0	0	0	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	-	0	-2.747081	0.00086	.	.	ENSG00000122497	ENST00000369219	T	0.04234	3.67	.	.	.	DUF1220 (2);	.	.	.	.	T	0.00210	0.0006	N	0.00028	-2.63	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43686	-0.9376	7	0.02654	T	1	.	.	.	.	.	333	Q5TI25	NBPFE_HUMAN	D	333	ENSP00000358221:N333D	ENSP00000358221:N333D	N	-	1	0	NBPF14	146482258	0.402000	0.25311	0.002000	0.10522	0.000000	0.00434	-1.348000	0.02629	0.357000	0.24183	0.000000	0.15137	AAC	.		0.463	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		C	148015634	T	C	148015634	3	2	19	1	0	0	0	0	1	0	0	0	10220	1754	61	3	1828	3	NBPF14	1	148015634	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	31789003	148015634	101234987	9	1589											
ZNF687	5298	bcgsc.ca	37	chr1	151263397	151263397	+	IGR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgcctcgactgtggcttGtgctttgcctcccctggctc	2	13	11	15	1	0	0	0	0	0	0	3	1	1	0	4	2	3	3	4	2	0	2	rs77014701		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:151263397G>T	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_3'UTR			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			ACTGTGGCTTGTGCTTTGCCT	0.632																																					p.L1142F	Colon(154;765 1838 9854 28443 37492)												.	ZNF687-92	0			c.G3426T						.						92	78	82					1																	151263397		2203	4300	6503	SO:0001628	intergenic_variant	57592	exon9			TGGCTTGTGCTTT	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		1.37:g.151263397G>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_1	82	24	NM_020832	0	0	10	11	1	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	Missense_Mutation	SNP	ENST00000368873.1	37		.	.	.	.	.	.	.	.	.	.	G	18.69	3.677234	0.68042	.	.	ENSG00000143373	ENST00000336715;ENST00000324048	T;T	0.29142	1.58;1.58	5.27	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.25885	N	0.027675	T	0.30103	0.0754	M	0.66939	2.045	0.80722	D	1	D	0.64830	0.994	P	0.60886	0.88	T	0.08411	-1.0723	10	0.48119	T	0.1	-4.0316	5.4057	0.16320	0.1897:0.2541:0.5562:0.0	.	1142	Q8N1G0	ZN687_HUMAN	F	1142	ENSP00000336620:L1142F;ENSP00000319829:L1142F	ENSP00000319829:L1142F	L	+	3	2	ZNF687	149530021	0.694000	0.27738	1.000000	0.80357	0.996000	0.88848	0.651000	0.24873	0.810000	0.34279	0.563000	0.77884	TTG	C|1.000		0.632	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		T	151263397	G	T	151263397	1	4	19	0	1	0	0	0	0	0	0	0	18124	1368	48	4		4	ZNF687	1	151263397	IGR	SNP	G	TCGA-A4-8518-01A-11D-2396-08	3247763	151263397	97987224	10	1590											
LINGO4	339398	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	151774638	151774638	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccagggtgagggtgctcaaCttggctagccctgcaaaggc	8	8	14	11	0	1	1	1	1	0	0	2	1	2	1	2	4	4	3	2	4	3	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:151774638C>G	ENST00000368820.3	-	2	1480	c.543G>C	c.(541-543)aaG>aaC	p.K181N		NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	181						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GGGTGCTCAACTTGGCTAGCC	0.612																																					p.K181N		.											.	LINGO4-90	0			c.G543C						.						37	43	41					1																	151774638		2203	4299	6502	SO:0001583	missense	339398	exon2			GCTCAACTTGGCT		CCDS30855.1	1q21.3	2013-01-11	2007-02-01	2007-02-01	ENSG00000213171	ENSG00000213171		"Immunoglobulin superfamily / I-set domain containing"	31814	protein-coding gene	gene with protein product		609794	"leucine rich repeat neuronal 6D"	LRRN6D			Standard	NM_001004432		Approved		uc001ezf.1	Q6UY18	OTTHUMG00000013059	ENST00000368820.3:c.543G>C	1.37:g.151774638C>G	ENSP00000357810:p.Lys181Asn	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	101	6	NM_001004432	0	0	0	0	0		Missense_Mutation	SNP	ENST00000368820.3	37	CCDS30855.1	.	.	.	.	.	.	.	.	.	.	C	3.774	-0.047078	0.07407	.	.	ENSG00000213171	ENST00000368820	T	0.54071	0.59	5.13	2.23	0.28157	.	0.401034	0.21238	N	0.077871	T	0.09024	0.0223	N	0.05351	-0.065	0.20926	N	0.999823	B	0.06786	0.001	B	0.06405	0.002	T	0.39375	-0.9617	10	0.07482	T	0.82	.	8.7903	0.34845	0.0:0.748:0.0:0.252	.	181	Q6UY18	LIGO4_HUMAN	N	181	ENSP00000357810:K181N	ENSP00000357810:K181N	K	-	3	2	LINGO4	150041262	0.037000	0.19845	0.017000	0.16124	0.866000	0.49608	-0.213000	0.09305	0.328000	0.23435	0.462000	0.41574	AAG	.		0.612	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387		G	151774638	C	G	151774638	3	3	19	1	0	0	0	0	1	0	0	0	8840	564	20	4	1242	4	LINGO4	1	151774638	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	511241	151774638	97475983	11	1591											
CACNA1S	779	bcgsc.ca	37	chr1	201017805	201017805	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggggcatgttcatgcccAccagccgctgtacagggaga	9	7	13	12	1	2	1	2	0	0	1	2	2	2	1	3	3	3	4	3	3	1	2	rs79011683		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:201017805A>C	ENST00000362061.3	-	36	4572	c.4346T>G	c.(4345-4347)gTg>gGg	p.V1449G	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V1430G	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1449					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GTTCATGCCCACCAGCCGCTG	0.627																																					p.V1449G													.	CACNA1S-94	0			c.T4346G						.						68	55	59					1																	201017805		2203	4300	6503	SO:0001583	missense	779	exon36			ATGCCCACCAGCC	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4346T>G	1.37:g.201017805A>C	ENSP00000355192:p.Val1449Gly	Somatic	66	6		WXS	Illumina HiSeq	Phase_1	65	36	NM_000069	0	0	0	0	0	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	27.4	4.824332	0.90955	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.10288	2.89;2.89	5.15	5.15	0.70609	.	0.116960	0.64402	D	0.000018	T	0.36054	0.0953	M	0.89904	3.07	0.80722	D	1	D	0.56746	0.977	P	0.57960	0.83	T	0.46190	-0.9209	10	0.87932	D	0	.	15.2557	0.73582	1.0:0.0:0.0:0.0	.	1449	Q13698	CAC1S_HUMAN	G	1449;1430	ENSP00000355192:V1449G;ENSP00000356307:V1430G	ENSP00000355192:V1449G	V	-	2	0	CACNA1S	199284428	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.242000	0.95408	2.060000	0.61445	0.455000	0.32223	GTG	.		0.627	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		C	201017805	A	C	201017805	3	2	19	1	0	0	0	0	1	0	0	0	2553	159	6	5	1311	5	CACNA1S	1	201017805	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	49243167	201017805	48232816	12	1592											
OBSCN	84033	bcgsc.ca	37	chr1	228430947	228430947	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgcaggctgaggcaggggCcagtgccacgctgagctgcg	6	5	19	11	2	0	2	0	2	0	0	0	2	0	2	2	5	4	5	2	5	0	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:228430947C>G	ENST00000422127.1	+	10	3037	c.2993C>G	c.(2992-2994)gCc>gGc	p.A998G	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1090G|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A998G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	998	Ig-like 10.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAGGCAGGGGCCAGTGCCACG	0.592																																					p.A1090G													.	OBSCN-403	0			c.C3269G						.						24	25	25					1																	228430947		1997	4166	6163	SO:0001583	missense	84033	exon11			CAGGGGCCAGTGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2993C>G	1.37:g.228430947C>G	ENSP00000409493:p.Ala998Gly	Somatic	37	0		WXS	Illumina HiSeq	Phase_1	29	20	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	2.996	-0.207096	0.06180	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.04275	3.66;3.66	4.99	-1.36	0.09085	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);	2.441030	0.02358	N	0.076594	T	0.02494	0.0076	N	0.04297	-0.235	0.21675	N	0.999593	B;B	0.15473	0.013;0.008	B;B	0.22386	0.039;0.015	T	0.41342	-0.9514	10	0.23302	T	0.38	.	2.6595	0.05023	0.3558:0.2476:0.3066:0.09	.	998;998	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	998	ENSP00000284548:A998G;ENSP00000409493:A998G	ENSP00000284548:A998G	A	+	2	0	OBSCN	226497570	0.709000	0.27886	0.093000	0.20910	0.160000	0.22226	-0.229000	0.09098	0.123000	0.18342	0.460000	0.39030	GCC	.		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228430947	C	G	228430947	3	3	19	1	0	0	0	0	1	0	0	0	10838	739	26	4	3027	4	OBSCN	1	228430947	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	27413142	228430947	20819674	13	1593											
OBSCN	84033	bcgsc.ca	37	chr1	228434292	228434292	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgcggactgaggcaggggCcagtgccacactgagctgtg	7	6	18	10	1	0	2	0	2	0	0	0	3	0	3	2	5	3	2	2	5	0	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:228434292C>G	ENST00000422127.1	+	13	3865	c.3821C>G	c.(3820-3822)gCc>gGc	p.A1274G	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1366G|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A1274G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1274	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAGGCAGGGGCCAGTGCCACA	0.592																																					p.A1366G													.	OBSCN-403	0			c.C4097G						.						71	71	71					1																	228434292		2010	4164	6174	SO:0001583	missense	84033	exon14			CAGGGGCCAGTGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3821C>G	1.37:g.228434292C>G	ENSP00000409493:p.Ala1274Gly	Somatic	148	0		WXS	Illumina HiSeq	Phase_1	95	41	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	.	1.723	-0.496196	0.04291	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.04275	3.66;3.66	4.66	1.5	0.22942	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.534254	0.18563	N	0.137542	T	0.02119	0.0066	N	0.04335	-0.225	0.20196	N	0.99992	B;B	0.13594	0.002;0.008	B;B	0.18871	0.01;0.023	T	0.47761	-0.9092	10	0.22706	T	0.39	.	6.3266	0.21246	0.3995:0.3372:0.2632:0.0	.	1274;1274	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	1274	ENSP00000284548:A1274G;ENSP00000409493:A1274G	ENSP00000284548:A1274G	A	+	2	0	OBSCN	226500915	0.391000	0.25221	0.138000	0.22173	0.004000	0.04260	1.310000	0.33551	0.898000	0.36418	0.563000	0.77884	GCC	.		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228434292	C	G	228434292	3	3	19	1	0	0	0	0	1	0	0	0	10838	739	26	4	3867	4	OBSCN	1	228434292	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	3345	228434292	20816329	14	1594											
ABCB10	23456	hgsc.bcm.edu	37	chr1	229685147	229685147	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagaaaggggcagacatggaGataacactggacatcgtgag	16	5	14	6	1	0	4	0	1	0	3	1	6	0	5	0	4	1	1	0	4	3	1	rs138482043	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:229685147G>C	ENST00000344517.4	-	2	594	c.552C>G	c.(550-552)atC>atG	p.I184M	RNA5SP78_ENST00000364622.1_RNA	NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	184	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				CAGACATGGAGATAACACTGG	0.527																																					p.I184M		.											.	ABCB10-153	0			c.C552G						.						85	79	81					1																	229685147		2203	4300	6503	SO:0001583	missense	23456	exon2			CATGGAGATAACA	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.552C>G	1.37:g.229685147G>C	ENSP00000355637:p.Ile184Met	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_012089	0	0	2	2	0	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	37	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.746671	0.49257	.	.	ENSG00000135776	ENST00000344517	D	0.89681	-2.55	5.53	3.33	0.38152	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.250753	0.42294	D	0.000732	D	0.85548	0.5722	L	0.39633	1.23	0.50813	D	0.99989	B	0.25850	0.136	B	0.35727	0.209	D	0.83456	0.0051	10	0.49607	T	0.09	-15.9883	11.715	0.51647	0.2162:0.0:0.7838:0.0	.	184	Q9NRK6	ABCBA_HUMAN	M	184	ENSP00000355637:I184M	ENSP00000355637:I184M	I	-	3	3	ABCB10	227751770	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	1.474000	0.35398	1.351000	0.45789	0.591000	0.81541	ATC	G|0.993;A|0.007		0.527	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		C	229685147	G	C	229685147	3	2	19	1	0	0	0	0	1	0	0	0	41	932	33	4	1712	4	ABCB10	1	229685147	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	1250855	229685147	19565474	15	1595											
EXO1	9156	bcgsc.ca	37	chr1	242020734	242020734	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaacaaagcgggaattgtgCaagccataattacagaggac	16	8	10	7	1	0	1	0	0	0	1	0	3	0	3	1	2	5	1	1	2	6	4	rs78172944|rs369069198		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:242020734C>A	ENST00000366548.3	+	7	1086	c.493C>A	c.(493-495)Caa>Aaa	p.Q165K	EXO1_ENST00000348581.5_Missense_Mutation_p.Q165K|EXO1_ENST00000493702.1_3'UTR|EXO1_ENST00000518483.1_Missense_Mutation_p.Q165K	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	165	I-domain.|Interaction with MSH3.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			GGGAATTGTGCAAGCCATAAT	0.458								Editing and processing nucleases																													p.Q165K													.	EXO1-661	0			c.C493A						.						96	99	98					1																	242020734		2203	4300	6503	SO:0001583	missense	9156	exon7			ATTGTGCAAGCCA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.493C>A	1.37:g.242020734C>A	ENSP00000355506:p.Gln165Lys	Somatic	118	3		WXS	Illumina HiSeq	Phase_1	110	62	NM_130398	0	0	0	0	0	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.057200	0.55325	.	.	ENSG00000174371	ENST00000366548;ENST00000423131;ENST00000348581;ENST00000366547;ENST00000518483;ENST00000437497	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.93	4.99	0.66335	XPG/RAD2 endonuclease (2);	0.215165	0.49305	D	0.000141	T	0.75649	0.3878	M	0.84683	2.71	0.80722	D	1	D;P;D	0.56521	0.959;0.949;0.976	P;B;P	0.49276	0.55;0.333;0.605	T	0.78999	-0.1982	10	0.48119	T	0.1	0.0222	15.2098	0.73214	0.0:0.7373:0.2627:0.0	.	165;165;165	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	K	165;125;165;125;165;122	ENSP00000355506:Q165K;ENSP00000415531:Q125K;ENSP00000311873:Q165K;ENSP00000430251:Q165K;ENSP00000412041:Q122K	ENSP00000311873:Q165K	Q	+	1	0	EXO1	240087357	0.999000	0.42202	0.998000	0.56505	0.517000	0.34286	3.939000	0.56591	2.813000	0.96785	0.650000	0.86243	CAA	.		0.458	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027		A	242020734	C	A	242020734	3	1	19	1	0	0	0	0	1	0	0	0	5313	711	25	4	507	4	EXO1	1	242020734	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	12335587	242020734	7229887	16	1596											
PLB1	151056	hgsc.bcm.edu	37	chr2	28772929	28772929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactacctgaccagactgcAgaaaccccaagacaagcttg	15	5	7	14	0	0	4	0	1	0	3	0	4	0	4	4	0	5	2	4	0	5	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr2:28772929A>G	ENST00000327757.5	+	16	1105	c.1061A>G	c.(1060-1062)cAg>cGg	p.Q354R	PLB1_ENST00000422425.2_Missense_Mutation_p.Q365R|PLB1_ENST00000329020.6_Missense_Mutation_p.Q42R	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	354	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					ACCAGACTGCAGAAACCCCAA	0.463																																					p.Q365R		.											.	PLB1-141	0			c.A1094G						.						89	77	81					2																	28772929		2203	4300	6503	SO:0001583	missense	151056	exon16			GACTGCAGAAACC		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.1061A>G	2.37:g.28772929A>G	ENSP00000330442:p.Gln354Arg	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001170585	0	0	0	0	0	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.653|5.653	0.305110|0.305110	0.10678|0.10678	.|.	.|.	ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000436544;ENST00000329020|ENST00000404858	T;T;T;T|.	0.11821|.	2.74;2.74;2.74;2.75|.	4.83|4.83	-9.66|-9.66	0.00534|0.00534	.|.	2.571820|.	0.01222|.	N|.	0.008128|.	T|T	0.11067|0.11067	0.0270|0.0270	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B;B|.	0.25272|.	0.122;0.046;0.002|.	B;B;B|.	0.34824|.	0.19;0.011;0.008|.	T|T	0.14172|0.14172	-1.0482|-1.0482	10|5	0.15952|.	T|.	0.53|.	13.3363|13.3363	2.0146|2.0146	0.03495|0.03495	0.4036:0.1057:0.0955:0.3951|0.4036:0.1057:0.0955:0.3951	.|.	365;42;354|.	Q6P1J6-3;Q6P1J6-2;Q6P1J6|.	.;.;PLB1_HUMAN|.	R|G	354;365;64;42|364	ENSP00000330442:Q354R;ENSP00000416440:Q365R;ENSP00000392493:Q64R;ENSP00000330729:Q42R|.	ENSP00000330442:Q354R|.	Q|R	+|+	2|1	0|2	PLB1|PLB1	28626433|28626433	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-2.790000|-2.790000	0.00767|0.00767	-1.769000|-1.769000	0.01297|0.01297	-0.396000|-0.396000	0.06452|0.06452	CAG|AGA	.		0.463	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			G	28772929	A	G	28772929	3	3	19	1	0	0	0	0	1	0	0	0	12050	188	7	3	1156	3	PLB1	2	28772929	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		28772929	214426444	17	1597											
GALM	130589	bcgsc.ca	37	chr2	38908566	38908566	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatagtcaactacagagcaCaagccagtcaggccacacca	15	5	7	14	0	3	1	3	0	0	1	3	1	3	1	3	1	4	1	3	1	4	2	rs74917735		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr2:38908566C>A	ENST00000272252.5	+	3	742	c.490C>A	c.(490-492)Caa>Aaa	p.Q164K	GALM_ENST00000410063.1_Intron	NM_138801.2	NP_620156.1	Q96C23	GALM_HUMAN	galactose mutarotase (aldose 1-epimerase)	164					galactose metabolic process (GO:0006012)|glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldose 1-epimerase activity (GO:0004034)|carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	14		all_hematologic(82;0.248)				CTACAGAGCACAAGCCAGTCA	0.512																																					p.Q164K													.	GALM-90	0			c.C490A						.																																			SO:0001583	missense	130589	exon3			AGAGCACAAGCCA		CCDS1797.1	2p22.3	2008-02-05			ENSG00000143891	ENSG00000143891			24063	protein-coding gene	gene with protein product	"aldose 1 epimerase"	608883				12753898	Standard	NM_138801		Approved		uc002rqy.3	Q96C23	OTTHUMG00000102077	ENST00000272252.5:c.490C>A	2.37:g.38908566C>A	ENSP00000272252:p.Gln164Lys	Somatic	180	1		WXS	Illumina HiSeq	Phase_1	130	41	NM_138801	0	0	100	106	6	Q53RY1|Q8NIA2|V9HWA8	Missense_Mutation	SNP	ENST00000272252.5	37	CCDS1797.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.978033	0.53720	.	.	ENSG00000143891	ENST00000272252;ENST00000434934	T;T	0.38722	1.12;1.12	5.4	5.4	0.78164	Glycoside hydrolase-type carbohydrate-binding, subgroup (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.065779	0.64402	D	0.000004	T	0.30386	0.0763	N	0.16602	0.42	0.80722	D	1	B	0.30193	0.272	B	0.24155	0.051	T	0.06789	-1.0807	10	0.39692	T	0.17	-18.4737	19.1893	0.93658	0.0:1.0:0.0:0.0	.	164	Q96C23	GALM_HUMAN	K	164;44	ENSP00000272252:Q164K;ENSP00000399473:Q44K	ENSP00000272252:Q164K	Q	+	1	0	GALM	38762070	0.999000	0.42202	0.997000	0.53966	0.572000	0.35998	4.169000	0.58223	2.527000	0.85204	0.561000	0.74099	CAA	.		0.512	GALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219891.2	NM_138801		A	38908566	C	A	38908566	3	1	19	1	0	0	0	0	1	0	0	0	6225	479	17	4	500	4	GALM	2	38908566	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	10135637	38908566	204290807	18	1598											
ABCG5	64240	hgsc.bcm.edu	37	chr2	44049984	44049984	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcaacaacgctgaaggggAggacgtgcagtgcataggcc	11	5	16	9	2	0	1	0	1	0	0	0	3	0	3	1	5	4	4	1	5	4	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr2:44049984A>G	ENST00000260645.1	-	10	1554	c.1415T>C	c.(1414-1416)cTc>cCc	p.L472P	ABCG5_ENST00000543989.1_Missense_Mutation_p.L77P|ABCG5_ENST00000405322.1_Missense_Mutation_p.L301P	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	472	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	GCTGAAGGGGAGGACGTGCAG	0.597																																					p.L472P		.											.	ABCG5-92	0			c.T1415C						.						111	78	89					2																	44049984		2203	4300	6503	SO:0001583	missense	64240	exon10			AAGGGGAGGACGT	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"ATP binding cassette transporters / subfamily G"	13886	protein-coding gene	gene with protein product	"sterolin 1"	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1415T>C	2.37:g.44049984A>G	ENSP00000260645:p.Leu472Pro	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_022436	0	0	0	0	0	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	37	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	a	14.70	2.613097	0.46631	.	.	ENSG00000138075	ENST00000260645;ENST00000405322;ENST00000543989	T;T;T	0.74947	-0.89;-0.89;-0.89	4.9	4.9	0.64082	ABC-2 type transporter (1);	2.503810	0.01622	N	0.023076	D	0.87931	0.6302	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.99	T	0.72174	-0.4370	10	0.87932	D	0	.	14.347	0.66672	1.0:0.0:0.0:0.0	.	301;472	E7EX35;Q9H222	.;ABCG5_HUMAN	P	472;301;77	ENSP00000260645:L472P;ENSP00000384513:L301P;ENSP00000445107:L77P	ENSP00000260645:L472P	L	-	2	0	ABCG5	43903488	1.000000	0.71417	0.159000	0.22649	0.049000	0.14656	8.648000	0.91062	2.038000	0.60285	0.456000	0.33151	CTC	.		0.597	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436		G	44049984	A	G	44049984	3	3	19	1	0	0	0	0	1	0	0	0	71	304	11	3	556	3	ABCG5	2	44049984	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	5141418	44049984	199149389	19	1599											
SLC16A14	151473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	230910735	230910735	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagtcggctatgacgcccagGatcacttttccaaagatgtg	11	10	10	10	2	1	2	1	1	0	1	3	3	2	3	2	2	0	1	2	2	3	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr2:230910735G>A	ENST00000295190.4	-	4	1565	c.1107C>T	c.(1105-1107)atC>atT	p.I369I		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	369						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.I369I(1)		NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		TGACGCCCAGGATCACTTTTC	0.433																																					p.I369I		.											.	SLC16A14-96	1	Substitution - coding silent(1)	ovary(1)	c.C1107T						.						98	87	91					2																	230910735		2203	4300	6503	SO:0001819	synonymous_variant	151473	exon4			GCCCAGGATCACT	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.1107C>T	2.37:g.230910735G>A		Somatic	101	1		WXS	Illumina HiSeq	Phase_I	105	23	NM_152527	0	0	0	1	1	A8KA08|Q53R92|Q96NI7	Silent	SNP	ENST00000295190.4	37	CCDS2473.1																																																																																			.		0.433	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		A	230910735	G	A	230910735	2	1	19	1	0	0	0	0	0	0	0	1	14439	1164	41	2		2	SLC16A14	2	230910735	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08	186860751	230910735	12288638	20	1600											
AGAP1	116987	hgsc.bcm.edu	37	chr2	236839507	236839507	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaccagcgctcctactcaGtctccagtgccgaccagtgg	7	8	10	16	2	2	0	1	0	1	0	4	1	3	0	5	1	4	2	5	1	1	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr2:236839507G>A	ENST00000304032.8	+	12	2003	c.1423G>A	c.(1423-1425)Gtc>Atc	p.V475I	AGAP1_ENST00000336665.5_Intron|AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000428334.2_Missense_Mutation_p.V314I	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	475	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						CTCCTACTCAGTCTCCAGTGC	0.612																																					p.V475I		.											.	AGAP1-93	0			c.G1423A						.						71	60	63					2																	236839507		2203	4300	6503	SO:0001583	missense	116987	exon12			TACTCAGTCTCCA	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1423G>A	2.37:g.236839507G>A	ENSP00000307634:p.Val475Ile	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_001037131	0	0	8	8	0	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.42|16.42	3.117268|3.117268	0.56505|0.56505	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025|ENST00000304032;ENST00000428334	T|T;T	0.76709|0.77358	-1.04|-1.09;-1.09	5.36|5.36	5.36|5.36	0.76844|0.76844	.|Pleckstrin homology domain (3);	.|0.420852	.|0.20846	.|N	.|0.084619	D|D	0.84252|0.84252	0.5431|0.5431	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	D|D	1|1	.|D	.|0.63046	.|0.992	.|D	.|0.77004	.|0.989	T|T	0.79022|0.79022	-0.1973|-0.1973	7|10	0.24483|0.18710	T|T	0.36|0.47	.|.	19.0672|19.0672	0.93116|0.93116	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|475	.|Q9UPQ3	.|AGAP1_HUMAN	N|I	108|475;314	ENSP00000403482:S108N|ENSP00000307634:V475I;ENSP00000411824:V314I	ENSP00000403482:S108N|ENSP00000307634:V475I	S|V	+|+	2|1	0|0	AGAP1|AGAP1	236504246|236504246	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.996000|0.996000	0.88848|0.88848	9.388000|9.388000	0.97237|0.97237	2.676000|2.676000	0.91093|0.91093	0.655000|0.655000	0.94253|0.94253	AGT|GTC	.		0.612	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		A	236839507	G	A	236839507	3	1	19	1	0	0	0	0	1	0	0	0	366	1029	36	2	1469	2	AGAP1	2	236839507	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	5928772	236839507	6359866	21	1601											
KCNH8	131096	hgsc.bcm.edu;broad.mit.edu	37	chr3	19389246	19389246	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtagataaaccagcatttccGgagtataaagtttctgatgc	13	12	9	7	1	1	2	0	1	1	1	2	3	2	3	2	1	3	4	2	1	6	6			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:19389246G>A	ENST00000328405.2	+	5	866	c.600G>A	c.(598-600)ccG>ccA	p.P200P	KCNH8_ENST00000475063.1_3'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	200					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						CAGCATTTCCGGAGTATAAAG	0.358																																					p.P200P	NSCLC(124;1625 1765 8018 24930 42026)	.											.	KCNH8-524	0			c.G600A						.						123	117	119					3																	19389246		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon5			ATTTCCGGAGTAT	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.600G>A	3.37:g.19389246G>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	121	7	NM_144633	0	0	0	0	0	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																			.		0.358	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		A	19389246	G	A	19389246	2	1	19	1	0	0	0	0	0	0	0	1	8059	1103	39	1		1	KCNH8	3	19389246	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08		19389246	178633184	22	1602											
USP19	10869	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	49148785	49148785	+	Frame_Shift_Del	DEL	C	C	-																															gcttcacttggatgctggtaCccaggcacagcagctgtgtg																										TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:49148785delC	ENST00000398888.2	-	21	3240	c.2922delG	c.(2920-2922)gggfs	p.G974fs	USP19_ENST00000434032.2_Frame_Shift_Del_p.G1075fs|USP19_ENST00000398898.2_Frame_Shift_Del_p.G1014fs|USP19_ENST00000417901.1_Frame_Shift_Del_p.G1077fs|USP19_ENST00000398892.3_Frame_Shift_Del_p.G1014fs|USP19_ENST00000453664.1_Frame_Shift_Del_p.G1065fs|USP19_ENST00000398896.1_Frame_Shift_Del_p.G782fs	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	974	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GATGCTGGTACCCAGGCACAG	0.532																																					p.G1077fs		.											.	USP19-663	0			c.3231delG						.						101	106	105					3																	49148785		2047	4201	6248	SO:0001589	frameshift_variant	10869	exon22			.	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2922delG	3.37:g.49148785delC	ENSP00000381863:p.Gly974fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	105	20	NM_001199161	0	0	0	0	0	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Frame_Shift_Del	DEL	ENST00000398888.2	37	CCDS43090.1																																																																																			.		0.532	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		-	49148785	C	-	49148785	7	5	19	1	0	1	0	1	0	0	0	0	17083	494	18	0	1058	0	USP19	3	49148785	Frame_Shift_Del	DEL	C	TCGA-A4-8518-01A-11D-2396-08	29759539	49148785	148873645	23	1603											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376113	113376113	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgttgttgttgctgttgCtgctgctgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	8	13	0	0	0	5	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000316407.4_Silent_p.Q1472Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1472	Gln-rich.					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						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		.											.	KIAA2018-93	0			c.G4416A						.						68	71	70					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	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.4416G>A	3.37:g.113376113C>T		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_001009899	0	0	1	1	0	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376113	C	T	113376113	2	4	19	1	0	0	0	0	0	0	0	1	8289	796	28	2		2	KIAA2018	3	113376113	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	64227328	113376113	84646317	24	1604											
AP2M1	1173	bcgsc.ca	37	chr3	183898702	183898702	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attggctggcggcgagagggTatcaagtatcgtcggaatga	10	9	16	6	4	1	2	1	1	0	1	3	4	1	3	0	5	0	3	0	5	4	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:183898702T>G	ENST00000292807.5	+	6	643	c.495T>G	c.(493-495)ggT>ggG	p.G165G	AP2M1_ENST00000439647.1_Silent_p.G163G|AP2M1_ENST00000382456.3_Silent_p.G163G|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000411763.2_Silent_p.G190G|AP2M1_ENST00000461733.1_3'UTR	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	165					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGCGAGAGGGTATCAAGTATC	0.532																																					p.G163G													.	AP2M1-90	0			c.T489G						.						131	144	140					3																	183898702		2052	4189	6241	SO:0001819	synonymous_variant	1173	exon5			AGAGGGTATCAAG	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, medium 1", "plasma membrane adaptor AP-2 50kDA protein", "clathrin coat adaptor protein AP50", "clathrin adaptor complex AP2, mu subunit", "HA2 50 kDA subunit", "clathrin assembly protein complex 2 medium chain", "AP-2 mu 2 chain"	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.495T>G	3.37:g.183898702T>G		Somatic	306	3		WXS	Illumina HiSeq	Phase_1	288	71	NM_001025205	1	1	221	237	14	A6NE12|D3DNT1|P20172|P53679	Silent	SNP	ENST00000292807.5	37	CCDS43177.1																																																																																			.		0.532	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068		G	183898702	T	G	183898702	2	3	19	1	0	0	0	0	0	0	0	1	742	1638	57	5		5	AP2M1	3	183898702	Silent	SNP	T	TCGA-A4-8518-01A-11D-2396-08	70522589	183898702	14123728	25	1605											
KIAA0226	9711	bcgsc.ca	37	chr3	197410204	197410204	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggcatcatgctccgggaCaagccactccagctccgagg	9	5	13	14	2	1	0	1	0	0	0	4	2	4	1	4	4	3	3	4	4	1	0	rs80094312		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:197410204C>A	ENST00000296343.5	-	13	1953	c.1954G>T	c.(1954-1956)Gtc>Ttc	p.V652F	KIAA0226_ENST00000273582.5_Missense_Mutation_p.V607F|KIAA0226_ENST00000389665.5_Missense_Mutation_p.V677F	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	652					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		TGCTCCGGGACAAGCCACTCC	0.597																																					p.V652F	Esophageal Squamous(3;167 355 3763 15924)												.	KIAA0226-22	0			c.G1954T						.						56	63	61					3																	197410204		1978	4151	6129	SO:0001583	missense	9711	exon13			CCGGGACAAGCCA	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1954G>T	3.37:g.197410204C>A	ENSP00000296343:p.Val652Phe	Somatic	132	8		WXS	Illumina HiSeq	Phase_1	104	50	NM_014687	0	0	0	0	0	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	20.2|20.2|20.2	3.946469|3.946469|3.946469	0.73672|0.73672|0.73672	.|.|.	.|.|.	ENSG00000145016|ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452|ENST00000273582;ENST00000296343;ENST00000389665	.|T|T;T;T	.|0.47869|0.48522	.|0.83|0.81;0.81;0.81	5.46|5.46|5.46	5.46|5.46|5.46	0.80206|0.80206|0.80206	.|.|.	.|.|0.147664	.|.|0.45126	.|.|D	.|.|0.000400	T|T|T	0.70544|0.70544|0.70544	0.3236|0.3236|0.3236	M|M|M	0.74467|0.74467|0.74467	2.265|2.265|2.265	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0	.|.|D;D;D	.|.|0.80764	.|.|0.992;0.994;0.99	T|T|T	0.73585|0.73585|0.73585	-0.3936|-0.3936|-0.3936	5|6|10	.|.|0.87932	.|.|D	.|.|0	.|.|.	19.2993|19.2993|19.2993	0.94136|0.94136|0.94136	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|677;607;652	.|.|Q92622-3;Q92622-2;Q92622	.|.|.;.;RUBIC_HUMAN	F|F|F	613|435|607;652;677	.|ENSP00000409618:L435F|ENSP00000273582:V607F;ENSP00000296343:V652F;ENSP00000374316:V677F	.|.|ENSP00000273582:V607F	C|L|V	-|-|-	2|3|1	0|2|0	KIAA0226|KIAA0226|KIAA0226	198894601|198894601|198894601	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.931000|0.931000|0.931000	0.37212|0.37212|0.37212	0.101000|0.101000|0.101000	0.19017|0.19017|0.19017	7.783000|7.783000|7.783000	0.85696|0.85696|0.85696	2.580000|2.580000|2.580000	0.87095|0.87095|0.87095	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	TGT|TTG|GTC	C|0.999;A|0.001		0.597	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197410204	C	A	197410204	3	1	19	1	0	0	0	0	1	0	0	0	8183	478	17	4	996	4	KIAA0226	3	197410204	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	13511502	197410204	612226	26	1606											
LMLN	89782	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	197687183	197687183	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggccggagccggtggcgcTggagcgggtctgtgtgggtc	2	7	22	10	5	1	0	0	0	1	0	2	2	1	2	2	7	2	1	2	7	0	0	rs375365578		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:197687183T>A	ENST00000330198.4	+	1	113	c.91T>A	c.(91-93)Tgg>Agg	p.W31R	IQCG_ENST00000265239.6_5'Flank|LMLN_ENST00000420910.2_Missense_Mutation_p.W31R|IQCG_ENST00000480302.1_5'Flank|LMLN_ENST00000482695.1_Missense_Mutation_p.L19Q|LMLN_ENST00000332636.5_Missense_Mutation_p.L19Q	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	31					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CCGGTGGCGCTGGAGCGGGTC	0.687																																					p.W31R		.											.	LMLN-91	0			c.T91A						.	T	ARG/TRP,ARG/TRP	1,4405	2.1+/-5.4	0,1,2202	30	36	34		91,91	-0.9	0	3		34	0,8596		0,0,4298	no	missense,missense	LMLN	NM_033029.3,NM_001136049.2	101,101	0,1,6500	AA,AT,TT		0.0,0.0227,0.0077	benign,benign	31/656,31/693	197687183	1,13001	2203	4298	6501	SO:0001583	missense	89782	exon1			TGGCGCTGGAGCG	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.91T>A	3.37:g.197687183T>A	ENSP00000328829:p.Trp31Arg	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	97	19	NM_001136049	0	0	1	1	0	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	37	CCDS3332.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.21|12.21	1.869215|1.869215	0.32977|0.32977	2.27E-4|2.27E-4	0.0|0.0	ENSG00000185621|ENSG00000185621	ENST00000482695;ENST00000332636|ENST00000330198;ENST00000420910	T;T|T;T	0.47528|0.41400	0.85;0.84|1.01;1.0	4.02|4.02	-0.95|-0.95	0.10372|0.10372	.|.	.|0.745603	.|0.11975	.|N	.|0.511342	T|T	0.22322|0.22322	0.0538|0.0538	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B|B;B	0.24963|0.02656	0.115;0.115|0.0;0.0	B;B|B;B	0.28709|0.04013	0.093;0.093|0.0;0.001	T|T	0.24512|0.24512	-1.0158|-1.0158	9|10	0.13853|0.18276	T|T	0.58|0.48	-0.5349|-0.5349	7.0655|7.0655	0.25149|0.25149	0.0:0.4606:0.0:0.5394|0.0:0.4606:0.0:0.5394	.|.	19;19|31;31	F8WCE5;Q96KR4-2|Q96KR4;F8WB28	.;.|LMLN_HUMAN;.	Q|R	19|31	ENSP00000418324:L19Q;ENSP00000328611:L19Q|ENSP00000328829:W31R;ENSP00000410926:W31R	ENSP00000328611:L19Q|ENSP00000328829:W31R	L|W	+|+	2|1	0|0	LMLN|LMLN	199171580|199171580	0.031000|0.031000	0.19500|0.19500	0.003000|0.003000	0.11579|0.11579	0.735000|0.735000	0.41995|0.41995	0.079000|0.079000	0.14782|0.14782	-0.032000|-0.032000	0.13758|0.13758	0.374000|0.374000	0.22700|0.22700	CTG|TGG	.		0.687	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197687183	T	A	197687183	3	1	19	1	0	0	0	0	1	0	0	0	8870	1580	55	5	93	5	LMLN	3	197687183	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	276979	197687183	335247	27	1607											
ANAPC4	29945	bcgsc.ca	37	chr4	25398292	25398292	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtttggatagtggctcGgagtctttattataccattt	7	18	9	7	1	2	0	0	0	2	0	3	2	2	2	1	3	1	2	1	3	4	7	rs34015658	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr4:25398292G>C	ENST00000315368.3	+	15	1210	c.1068G>C	c.(1066-1068)tcG>tcC	p.S356S	ANAPC4_ENST00000510092.1_Silent_p.S356S	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	356					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				ATAGTGGCTCGGAGTCTTTAT	0.358																																					p.S356S													.	ANAPC4-293	0			c.G1068C						.						74	80	78					4																	25398292		2203	4300	6503	SO:0001819	synonymous_variant	29945	exon15			TGGCTCGGAGTCT	AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.1068G>C	4.37:g.25398292G>C		Somatic	78	1		WXS	Illumina HiSeq	Phase_1	58	19	NM_013367	0	0	0	0	0	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Silent	SNP	ENST00000315368.3	37	CCDS3434.1																																																																																			G|0.963;A|0.037		0.358	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		C	25398292	G	C	25398292	2	2	19	1	0	0	0	0	0	0	0	1	604	1103	39	4		4	ANAPC4	4	25398292	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08		25398292	165755984	28	1608											
SLC10A7	84068	hgsc.bcm.edu	37	chr4	147363940	147363940	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actatgtttacttaccaaaaAacttccaaaggctgaattaa	17	12	4	8	0	0	1	0	1	0	0	1	1	1	1	2	1	3	2	2	1	9	6			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr4:147363940A>G	ENST00000507030.1	-	5	429	c.430T>C	c.(430-432)Ttt>Ctt	p.F144L	SLC10A7_ENST00000432059.2_Intron|SLC10A7_ENST00000264986.3_3'UTR|SLC10A7_ENST00000394059.4_Missense_Mutation_p.F144L|SLC10A7_ENST00000511374.1_3'UTR|SLC10A7_ENST00000394062.3_Missense_Mutation_p.F144L|SLC10A7_ENST00000511315.1_5'UTR|SLC10A7_ENST00000335472.7_Missense_Mutation_p.F144L			Q0GE19	NTCP7_HUMAN	solute carrier family 10, member 7	144					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|skin(1)	16	all_hematologic(180;0.151)					CTTACCAAAAAACTTCCAAAG	0.284																																					p.F144L		.											.	SLC10A7-22	0			c.T430C						.						44	43	43					4																	147363940		2195	4288	6483	SO:0001583	missense	84068	exon5			CCAAAAAACTTCC	AY346324	CCDS3768.1, CCDS34073.1, CCDS75198.1	4q31.2	2013-07-18	2013-07-18	2006-12-19	ENSG00000120519	ENSG00000120519		"Solute carriers"	23088	protein-coding gene	gene with protein product		611459	"chromosome 4 open reading frame 13"	C4orf13		15932064	Standard	NM_032128		Approved	MGC25043, DKFZp566M114, DKFZp313H0531, DKFZp779O2438	uc003ikr.2	Q0GE19	OTTHUMG00000161437	ENST00000507030.1:c.430T>C	4.37:g.147363940A>G	ENSP00000421275:p.Phe144Leu	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_032128	0	0	0	0	0	A7E2E6|A7MAX9|Q0VAP9|Q45NG1|Q45NG2|Q5H9S6|Q6P4E6|Q8IZ62|Q8NBP8|Q9H0M9	Missense_Mutation	SNP	ENST00000507030.1	37	CCDS34073.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.027891	0.35797	.	.	ENSG00000120519	ENST00000335472;ENST00000507030;ENST00000394062;ENST00000394059	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.42517	0.1206	N	0.12471	0.22	0.80722	D	1	B;B;B	0.34147	0.438;0.384;0.337	B;B;B	0.40782	0.34;0.066;0.175	T	0.38243	-0.9670	9	0.02654	T	1	-23.5223	16.4221	0.83766	1.0:0.0:0.0:0.0	.	144;144;144	Q0GE19;Q0GE19-5;Q0GE19-2	NTCP7_HUMAN;.;.	L	144	.	ENSP00000334594:F144L	F	-	1	0	SLC10A7	147583390	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.778000	0.75043	2.283000	0.76528	0.477000	0.44152	TTT	.		0.284	SLC10A7-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366932.1	NM_032128		G	147363940	A	G	147363940	3	3	19	1	0	0	0	0	1	0	0	0	14411	14	1	3	669	3	SLC10A7	4	147363940	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	121965648	147363940	43790336	29	1609											
CMYA5	202333	bcgsc.ca	37	chr5	79029464	79029464	+	Missense_Mutation	SNP	G	G	A																															ctttggaacctgagaagaaaGacaagccacaccaaccgttg																								rs74757618		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr5:79029464G>A	ENST00000446378.2	+	2	4907	c.4876G>A	c.(4876-4878)Gac>Aac	p.D1626N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1626					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TGAGAAGAAAGACAAGCCACA	0.443																																					p.D1626N													.	CMYA5-77	0			c.G4876A						.						85	88	87					5																	79029464		1855	4103	5958	SO:0001583	missense	202333	exon2			AAGAAAGACAAGC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.4876G>A	5.37:g.79029464G>A	ENSP00000394770:p.Asp1626Asn	Somatic	151	2		WXS	Illumina HiSeq	Phase_1	117	26	NM_153610	0	0	0	0	0	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	9.307	1.054490	0.19907	.	.	ENSG00000164309	ENST00000446378	T	0.56776	0.44	4.34	2.5	0.30297	.	1.235380	0.05940	N	0.636733	T	0.43590	0.1254	L	0.39898	1.24	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.27400	-1.0075	10	0.14656	T	0.56	.	9.9471	0.41616	0.1937:0.0:0.8063:0.0	.	1626	Q8N3K9	CMYA5_HUMAN	N	1626	ENSP00000394770:D1626N	ENSP00000394770:D1626N	D	+	1	0	CMYA5	79065220	0.005000	0.15991	0.001000	0.08648	0.025000	0.11179	0.252000	0.18278	0.318000	0.23185	-1.134000	0.01955	GAC	.		0.443	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79029464	G	A	79029464	3	1	19	1	0	0	0	0	1	0	0	0	3596	942	33	2	4882	2	CMYA5	5	79029464	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08		79029464	101885796	30	1610	13	2									
CMYA5	202333	bcgsc.ca	37	chr5	79029466	79029466	+	Missense_Mutation	SNP	C	C	A																															ttggaacctgagaagaaagaCaagccacaccaaccgttgga																								rs79207557		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr5:79029466C>A	ENST00000446378.2	+	2	4909	c.4878C>A	c.(4876-4878)gaC>gaA	p.D1626E		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1626					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AGAAGAAAGACAAGCCACACC	0.443																																					p.D1626E													.	CMYA5-77	0			c.C4878A						.						92	94	94					5																	79029466		1855	4102	5957	SO:0001583	missense	202333	exon2			GAAAGACAAGCCA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.4878C>A	5.37:g.79029466C>A	ENSP00000394770:p.Asp1626Glu	Somatic	154	4		WXS	Illumina HiSeq	Phase_1	122	40	NM_153610	0	0	0	0	0	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015143	0.35511	.	.	ENSG00000164309	ENST00000446378	T	0.55760	0.5	4.47	-3.73	0.04398	.	1.235380	0.05940	N	0.636733	T	0.34542	0.0901	L	0.39898	1.24	0.09310	N	1	B	0.27625	0.183	B	0.20184	0.028	T	0.15178	-1.0446	10	0.33141	T	0.24	.	1.6141	0.02700	0.1485:0.2814:0.1289:0.4412	.	1626	Q8N3K9	CMYA5_HUMAN	E	1626	ENSP00000394770:D1626E	ENSP00000394770:D1626E	D	+	3	2	CMYA5	79065222	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.428000	0.02439	-0.622000	0.05626	-0.176000	0.13171	GAC	.		0.443	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79029466	C	A	79029466	3	1	19	1	0	0	0	0	1	0	0	0	3596	477	17	4	4884	4	CMYA5	5	79029466	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	2	79029466	101885794	31	1611	13	2									
BRD8	10902	bcgsc.ca	37	chr5	137503737	137503737	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgtactgttcaggtggcCagaagccacagccatttcac	10	9	9	13	0	2	1	2	0	0	1	2	1	2	1	4	2	3	2	4	2	2	3	rs370927725		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr5:137503737C>A	ENST00000254900.5	-	9	1044	c.673G>T	c.(673-675)Ggc>Tgc	p.G225C	BRD8_ENST00000455658.2_Missense_Mutation_p.G184C|BRD8_ENST00000411594.2_Missense_Mutation_p.G298C|BRD8_ENST00000402931.1_Missense_Mutation_p.G225C|BRD8_ENST00000230901.5_Missense_Mutation_p.G298C	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	225					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTCAGGTGGCCAGAAGCCACA	0.517																																					p.G298C													.	BRD8-91	0			c.G892T						.						75	74	75					5																	137503737		2203	4300	6503	SO:0001583	missense	10902	exon10			GGTGGCCAGAAGC	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.673G>T	5.37:g.137503737C>A	ENSP00000254900:p.Gly225Cys	Somatic	200	2		WXS	Illumina HiSeq	Phase_1	121	44	NM_001164326	0	0	3	3	0	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	37	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846551	0.51164	.	.	ENSG00000112983	ENST00000254900;ENST00000454473;ENST00000418329;ENST00000230901;ENST00000402931;ENST00000411594;ENST00000239899;ENST00000455658;ENST00000453824	T;T;T;T;T;T;T	0.34472	1.7;1.36;1.36;1.49;1.48;1.36;1.47	5.29	2.52	0.30459	.	0.528222	0.22011	N	0.065867	T	0.40670	0.1126	N	0.24115	0.695	0.48395	D	0.999647	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.963;1.0;1.0;1.0	D;D;D;D;P;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.654;1.0;1.0;1.0	T	0.23868	-1.0176	10	0.72032	D	0.01	-3.3377	7.0587	0.25113	0.1403:0.7116:0.0:0.1481	.	184;209;184;298;298;158;298;225	F8W820;B4DN43;B4DEG9;A8K1N6;Q9H0E9-4;Q9H0E9-3;Q9H0E9-2;Q9H0E9	.;.;.;.;.;.;.;BRD8_HUMAN	C	225;293;293;298;225;298;158;184;113	ENSP00000254900:G225C;ENSP00000398067:G293C;ENSP00000398873:G293C;ENSP00000230901:G298C;ENSP00000384845:G225C;ENSP00000394330:G298C;ENSP00000408396:G184C	ENSP00000230901:G298C	G	-	1	0	BRD8	137531636	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.504000	0.53347	0.365000	0.24400	0.591000	0.81541	GGC	.		0.517	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		A	137503737	C	A	137503737	3	1	19	1	0	0	0	0	1	0	0	0	1509	594	21	4	3174	4	BRD8	5	137503737	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	58474271	137503737	43411523	32	1612											
NRG2	9542	hgsc.bcm.edu	37	chr5	139422525	139422525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctcctgctgctgctgcCgctctcgctgctgctgctgc	0	12	12	17	2	1	0	0	0	1	0	3	0	2	0	2	0	9	10	2	0	0	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr5:139422525C>T	ENST00000361474.1	-	1	354	c.130G>A	c.(130-132)Ggc>Agc	p.G44S	NRG2_ENST00000358522.3_Missense_Mutation_p.G44S|NRG2_ENST00000545385.1_Missense_Mutation_p.G44S|NRG2_ENST00000541337.1_Missense_Mutation_p.G44S|NRG2_ENST00000289422.7_Missense_Mutation_p.G44S|NRG2_ENST00000394770.1_Missense_Mutation_p.G44S|NRG2_ENST00000289409.4_Missense_Mutation_p.G44S	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	44	Poly-Ser.				embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctgctgctgccgctctcgctg	0.706																																					p.G44S		.											.	NRG2-526	0			c.G130A						.						4	3	3					5																	139422525		1307	2784	4091	SO:0001583	missense	9542	exon1			TGCTGCCGCTCTC		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"Immunoglobulin superfamily / I-set domain containing"	7998	protein-coding gene	gene with protein product	"neural- and thymus-derived activator for ErbB kinases", "divergent of neuregulin-1"	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.130G>A	5.37:g.139422525C>T	ENSP00000354910:p.Gly44Ser	Somatic	6	1		WXS	Illumina HiSeq	Phase_I	5	2	NM_013982	0	0	0	0	0		Missense_Mutation	SNP	ENST00000361474.1	37	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	C	0.048	-1.259663	0.01445	.	.	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000394770;ENST00000289409;ENST00000358522;ENST00000378238	T;T;T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	3.8	-1.94	0.07571	.	.	.	.	.	T	0.48241	0.1489	N	0.08118	0	0.21762	N	0.999559	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40997	-0.9533	9	0.05525	T	0.97	0.2815	5.3685	0.16127	0.1349:0.3857:0.0:0.4795	.	44;44;44;44	O14511-2;O14511;O14511-4;O14511-3	.;NRG2_HUMAN;.;.	S	44	ENSP00000444235:G44S;ENSP00000289422:G44S;ENSP00000354910:G44S;ENSP00000438753:G44S;ENSP00000378251:G44S;ENSP00000289409:G44S;ENSP00000351323:G44S;ENSP00000367483:G44S	ENSP00000289409:G44S	G	-	1	0	NRG2	139402709	0.693000	0.27728	0.766000	0.31476	0.487000	0.33371	-0.501000	0.06398	-0.217000	0.10033	0.491000	0.48974	GGC	.		0.706	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		T	139422525	C	T	139422525	3	4	19	1	0	0	0	0	1	0	0	0	10674	652	23	1	2553	1	NRG2	5	139422525	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	1918788	139422525	41492735	33	1613											
FAT2	2196	bcgsc.ca	37	chr5	150948147	150948147	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggcttggatgatgagggTgtagctgtctcgcacctctc	5	13	14	9	1	2	2	0	2	2	0	4	3	2	3	1	3	1	4	1	3	1	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr5:150948147T>G	ENST00000261800.5	-	1	358	c.346A>C	c.(346-348)Acc>Ccc	p.T116P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	116	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATGATGAGGGTGTAGCTGTCT	0.502																																					p.T116P													.	FAT2-96	0			c.A346C						.						137	135	136					5																	150948147		2203	4300	6503	SO:0001583	missense	2196	exon1			TGAGGGTGTAGCT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.346A>C	5.37:g.150948147T>G	ENSP00000261800:p.Thr116Pro	Somatic	228	15		WXS	Illumina HiSeq	Phase_1	215	64	NM_001447	0	0	0	0	0	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.853594	0.51270	.	.	ENSG00000086570	ENST00000261800	T	0.62105	0.05	5.45	5.45	0.79879	Cadherin (3);Cadherin-like (1);	0.170932	0.41500	D	0.000865	T	0.67552	0.2905	M	0.82823	2.61	0.38714	D	0.953294	P	0.50710	0.938	P	0.45971	0.499	T	0.72814	-0.4179	10	0.35671	T	0.21	.	11.5219	0.50555	0.0:0.0:0.1496:0.8504	.	116	Q9NYQ8	FAT2_HUMAN	P	116	ENSP00000261800:T116P	ENSP00000261800:T116P	T	-	1	0	FAT2	150928340	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	1.690000	0.37711	2.065000	0.61736	0.454000	0.30748	ACC	.		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150948147	T	G	150948147	3	3	19	1	0	0	0	0	1	0	0	0	5709	1696	59	5	12795	5	FAT2	5	150948147	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	11525622	150948147	29967113	34	1614											
C6orf27	80737	bcgsc.ca	37	chr6	31733787	31733787	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccgctgaatctgggaccTccagccacaggcggccccag	7	4	14	16	2	1	1	0	1	1	0	2	2	2	2	6	4	1	1	6	4	1	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:31733787T>C	ENST00000375688.4	-	16	2572	c.2372A>G	c.(2371-2373)gAg>gGg	p.E791G	VWA7_ENST00000375686.3_Missense_Mutation_p.E791G|VWA7_ENST00000467576.1_5'Flank|SAPCD1-AS1_ENST00000419679.1_RNA			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	791						extracellular region (GO:0005576)											ATCTGGGACCTCCAGCCACAG	0.627																																					p.E791G													.	.	0			c.A2372G						.						87	112	103					6																	31733787		1507	2707	4214	SO:0001583	missense	80737	exon16			GGGACCTCCAGCC		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.2372A>G	6.37:g.31733787T>C	ENSP00000364840:p.Glu791Gly	Somatic	363	1		WXS	Illumina HiSeq	Phase_1	192	30	NM_025258	0	0	14	14	0	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	T	17.36	3.369798	0.61624	.	.	ENSG00000204396	ENST00000375688;ENST00000375686	T;T	0.15139	2.66;2.45	4.75	4.75	0.60458	.	0.149328	0.42821	D	0.000658	T	0.06050	0.0157	L	0.29908	0.895	0.80722	D	1	B	0.33238	0.403	B	0.33890	0.172	T	0.22312	-1.0220	10	0.33940	T	0.23	-11.7908	10.8128	0.46557	0.0:0.0:0.0:1.0	.	791	Q9Y334	G7C_HUMAN	G	791	ENSP00000364840:E791G;ENSP00000364838:E791G	ENSP00000364838:E791G	E	-	2	0	C6orf27	31841766	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.761000	0.26489	2.125000	0.65367	0.460000	0.39030	GAG	.		0.627	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		C	31733787	T	C	31733787	3	2	19	1	0	0	0	0	1	0	0	0	2368	1551	54	3	310	3	C6orf27	6	31733787	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08		31733787	139381280	35	1615											
C6orf222	389384	bcgsc.ca	37	chr6	36294451	36294451	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaggttctcttgaggcttGtctttttctcttgggatttc	3	21	10	7	0	3	2	0	2	3	0	6	3	3	3	0	3	0	2	0	3	0	8			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:36294451G>T	ENST00000437635.2	-	5	1049	c.872C>A	c.(871-873)aCa>aAa	p.T291K		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	291										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						CTTGAGGCTTGTCTTTTTCTC	0.562																																					p.T291K													.	C6orf222-93	0			c.C872A						.						173	182	179					6																	36294451		2203	4300	6503	SO:0001583	missense	389384	exon5			AGGCTTGTCTTTT		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.872C>A	6.37:g.36294451G>T	ENSP00000418983:p.Thr291Lys	Somatic	262	0		WXS	Illumina HiSeq	Phase_1	233	26	NM_001010903	0	0	0	0	0	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	37	CCDS34439.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.803436	0.50315	.	.	ENSG00000189325	ENST00000437635	T	0.45276	0.9	3.92	3.92	0.45320	.	1.008970	0.07961	N	0.982350	T	0.18257	0.0438	L	0.29908	0.895	0.09310	N	1	P	0.38020	0.615	B	0.34722	0.188	T	0.10497	-1.0627	10	0.66056	D	0.02	.	11.7334	0.51750	0.0:0.0:1.0:0.0	.	291	P0C671	CF222_HUMAN	K	291	ENSP00000418983:T291K	ENSP00000418983:T291K	T	-	2	0	C6orf222	36402429	0.058000	0.20735	0.006000	0.13384	0.036000	0.12997	3.731000	0.55013	2.483000	0.83821	0.455000	0.32223	ACA	.		0.562	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		T	36294451	G	T	36294451	3	4	19	1	0	0	0	0	1	0	0	0	2362	1377	48	4	1118	4	C6orf222	6	36294451	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	4560664	36294451	134820616	36	1616											
PIM1	5292	bcgsc.ca	37	chr6	37139029	37139029	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctgatcctggagaggccCgagccggtgcaagatctctt	7	9	13	12	2	1	3	0	1	1	2	4	5	3	3	4	3	2	1	4	3	1	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:37139029C>G	ENST00000373509.5	+	4	742	c.369C>G	c.(367-369)ccC>ccG	p.P123P		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	214					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	TGGAGAGGCCCGAGCCGGTGC	0.622			T	BCL6	NHL																																p.P214P				Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1-1493	0			c.C642G						.						78	92	87					6																	37139029		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GAGGCCCGAGCCG		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"pim-1 oncogene"	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.369C>G	6.37:g.37139029C>G		Somatic	345	1		WXS	Illumina HiSeq	Phase_1	220	57	NM_001243186	0	0	10	11	1	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.		0.622	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			G	37139029	C	G	37139029	2	3	19	1	0	0	0	0	0	0	0	1	11953	639	23	4		4	PIM1	6	37139029	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	844578	37139029	133976038	37	1617											
KCNK5	8645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	39161945	39161945	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcagaggcagggactcacCggccacaaagtcaccgaagc	13	2	13	13	2	2	1	2	0	0	1	2	3	2	2	3	4	1	2	3	4	2	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:39161945C>T	ENST00000359534.3	-	4	972	c.634G>A	c.(634-636)Ggt>Agt	p.G212S		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	212					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						AGGGACTCACCGGCCACAAAG	0.542																																					p.G212S		.											.	KCNK5-227	0			c.G634A						.						92	79	84					6																	39161945		2203	4300	6503	SO:0001630	splice_region_variant	8645	exon4			ACTCACCGGCCAC	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.634+1G>A	6.37:g.39161945C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	78	20	NM_003740	0	0	0	1	1	B2RAQ6|B5TJL2|Q5VV76	Missense_Mutation	SNP	ENST00000359534.3	37	CCDS4841.1	.	.	.	.	.	.	.	.	.	.	C	34	5.402436	0.96030	.	.	ENSG00000164626	ENST00000359534	T	0.30448	1.53	5.68	5.68	0.88126	Ion transport 2 (1);	0.101608	0.64402	D	0.000002	T	0.39911	0.1096	L	0.52759	1.655	0.80722	D	1	P	0.46512	0.879	P	0.58820	0.846	T	0.01909	-1.1249	9	.	.	.	.	19.7891	0.96450	0.0:1.0:0.0:0.0	.	212	O95279	KCNK5_HUMAN	S	212	ENSP00000352527:G212S	.	G	-	1	0	KCNK5	39269923	1.000000	0.71417	0.981000	0.43875	0.542000	0.35054	7.747000	0.85070	2.692000	0.91855	0.561000	0.74099	GGT	.		0.542	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740	Missense_Mutation	T	39161945	C	T	39161945	5	4	19	1	0	0	0	0	0	0	1	0	8090	666	23	1	873	1	KCNK5	6	39161945	Splice_Site	SNP	C	TCGA-A4-8518-01A-11D-2396-08	2022916	39161945	131953122	38	1618											
YIPF3	25844	hgsc.bcm.edu	37	chr6	43481182	43481182	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggtccatagagttcacctGcaattttctgtcaatatacc	11	13	7	10	0	3	1	2	0	1	1	4	2	4	1	3	1	2	2	3	1	5	6			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:43481182G>C	ENST00000372422.2	-	5	631	c.449C>G	c.(448-450)gCa>gGa	p.A150G	YIPF3_ENST00000506469.1_Missense_Mutation_p.A156G|LRRC73_ENST00000372441.1_5'Flank	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	150					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			GAGTTCACCTGCAATTTTCTG	0.488																																					p.A150G		.											.	YIPF3-90	0			c.C449G						.						99	103	101					6																	43481182		2203	4300	6503	SO:0001583	missense	25844	exon5			TCACCTGCAATTT	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.449C>G	6.37:g.43481182G>C	ENSP00000361499:p.Ala150Gly	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_015388	0	0	0	0	0	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Missense_Mutation	SNP	ENST00000372422.2	37	CCDS4899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.4|23.4	4.417351|4.417351	0.83449|0.83449	.|.	.|.	ENSG00000137207|ENSG00000137207	ENST00000372422;ENST00000504851;ENST00000506469;ENST00000503972|ENST00000500090	T;T;T|.	0.41065|.	1.01;1.01;1.01|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53594|0.53594	0.1806|0.1806	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	P;D;D;D|.	0.67145|.	0.874;0.994;0.996;0.996|.	P;D;D;D|.	0.77557|.	0.546;0.955;0.99;0.99|.	T|T	0.57573|0.57573	-0.7788|-0.7788	10|6	0.49607|0.02654	T|T	0.09|1	-12.2644|-12.2644	18.2414|18.2414	0.89968|0.89968	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	99;156;115;150|.	D6RED8;E7EQR8;Q5JTD5;Q9GZM5|.	.;.;.;YIPF3_HUMAN|.	G|E	150;99;156;150|88	ENSP00000361499:A150G;ENSP00000425494:A156G;ENSP00000421461:A150G|.	ENSP00000361499:A150G|ENSP00000259737:Q135E	A|Q	-|-	2|1	0|0	YIPF3|YIPF3	43589160|43589160	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.990000|0.990000	0.78478|0.78478	7.666000|7.666000	0.83877|0.83877	2.755000|2.755000	0.94549|0.94549	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.		0.488	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		C	43481182	G	C	43481182	3	2	19	1	0	0	0	0	1	0	0	0	17512	1319	46	4	623	4	YIPF3	6	43481182	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	4319237	43481182	127633885	39	1619											
TDRD6	221400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	46658247	46658247	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtgtcagctgaccaggaaCatacaaggacttaaaactct	14	9	9	9	0	2	1	1	1	1	0	2	3	2	3	1	3	4	1	1	3	5	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:46658247C>G	ENST00000316081.6	+	1	2382	c.2382C>G	c.(2380-2382)aaC>aaG	p.N794K	TDRD6_ENST00000544460.1_Missense_Mutation_p.N794K|RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	794					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TGACCAGGAACATACAAGGAC	0.428																																					p.N794K		.											.	TDRD6-138	0			c.C2382G						.						81	83	82					6																	46658247		2203	4300	6503	SO:0001583	missense	221400	exon1			CAGGAACATACAA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.2382C>G	6.37:g.46658247C>G	ENSP00000346065:p.Asn794Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	79	10	NM_001168359	0	0	0	0	0	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444596	0.25987	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.12879	2.64;2.64	5.75	3.93	0.45458	Maternal tudor protein (1);	0.375482	0.34178	N	0.004185	T	0.07143	0.0181	L	0.41356	1.27	0.19575	N	0.999962	P;P	0.40834	0.548;0.73	B;P	0.51415	0.439;0.669	T	0.31024	-0.9958	10	0.24483	T	0.36	-13.6225	7.3207	0.26526	0.1058:0.6679:0.1027:0.1236	.	794;794	F5H5M3;O60522	.;TDRD6_HUMAN	K	794	ENSP00000443299:N794K;ENSP00000346065:N794K	ENSP00000346065:N794K	N	+	3	2	TDRD6	46766206	0.072000	0.21174	0.342000	0.25602	0.870000	0.49936	0.453000	0.21811	0.342000	0.23796	-0.797000	0.03246	AAC	.		0.428	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		G	46658247	C	G	46658247	3	3	19	1	0	0	0	0	1	0	0	0	15766	477	17	4	2384	4	TDRD6	6	46658247	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	3177065	46658247	124456820	40	1620											
ULBP1	80329	bcgsc.ca	37	chr6	150290454	150290454	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggattgtaagatgtggcttGaagaatttttgatgtactgg	10	15	14	2	0	0	4	0	2	0	2	0	5	0	5	0	3	1	3	0	3	4	6	rs75999880		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:150290454G>T	ENST00000229708.3	+	3	626	c.583G>T	c.(583-585)Gaa>Taa	p.E195*		NM_025218.2	NP_079494.1	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	195	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			large_intestine(3)|lung(5)|pancreas(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)		GATGTGGCTTGAAGAATTTTT	0.448																																					p.E195X													.	ULBP1-91	0			c.G583T						.						97	99	99					6																	150290454		2203	4300	6503	SO:0001587	stop_gained	80329	exon3			TGGCTTGAAGAAT	AF304377	CCDS5223.1	6q25	2003-04-29			ENSG00000111981	ENSG00000111981			14893	protein-coding gene	gene with protein product		605697				11239445, 11827464	Standard	XM_005267151		Approved	RAET1I	uc003qnp.3	Q9BZM6	OTTHUMG00000015810	ENST00000229708.3:c.583G>T	6.37:g.150290454G>T	ENSP00000229708:p.Glu195*	Somatic	176	0		WXS	Illumina HiSeq	Phase_1	157	37	NM_025218	0	0	0	0	0	Q5VY81|Q8IZW3|Q8IZX6	Nonsense_Mutation	SNP	ENST00000229708.3	37	CCDS5223.1	.	.	.	.	.	.	.	.	.	.	g	12.52	1.961165	0.34565	.	.	ENSG00000111981	ENST00000367345;ENST00000229708	.	.	.	2.13	-0.927	0.10451	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	2.6859	0.05107	0.3243:0.2633:0.4125:0.0	.	.	.	.	X	195	.	ENSP00000229708:E195X	E	+	1	0	ULBP1	150332147	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-2.984000	0.00661	-0.252000	0.09528	0.195000	0.17529	GAA	.		0.448	ULBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042677.2			T	150290454	G	T	150290454	4	4	19	1	0	0	0	0	0	1	0	0	17005	1291	45	4	593	4	ULBP1	6	150290454	Nonsense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	103632207	150290454	20824613	41	1621											
FBXO24	26261	bcgsc.ca	37	chr7	100192051	100192051	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaatgagacccagcttgAccagccacgctcctacacgg	11	6	10	14	2	0	3	0	3	0	1	1	4	1	3	4	1	3	2	4	1	2	2	rs200752657		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr7:100192051A>C	ENST00000241071.6	+	6	1161	c.839A>C	c.(838-840)gAc>gCc	p.D280A	FBXO24_ENST00000465843.1_Missense_Mutation_p.D266A|FBXO24_ENST00000360609.2_Missense_Mutation_p.D266A|FBXO24_ENST00000468962.1_Missense_Mutation_p.D268A|PCOLCE-AS1_ENST00000442166.2_RNA|FBXO24_ENST00000427939.2_Missense_Mutation_p.D318A|PCOLCE-AS1_ENST00000544873.1_RNA	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	280					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					ACCCAGCTTGACCAGCCACGC	0.552																																					p.D318A													.	FBXO24-229	0			c.A953C						.						111	97	102					7																	100192051		2203	4300	6503	SO:0001583	missense	26261	exon6			AGCTTGACCAGCC	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.839A>C	7.37:g.100192051A>C	ENSP00000241071:p.Asp280Ala	Somatic	120	0		WXS	Illumina HiSeq	Phase_1	104	34	NM_012172	0	0	0	0	0	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582482	0.46006	.	.	ENSG00000106336	ENST00000241071;ENST00000360609;ENST00000465843;ENST00000468962;ENST00000427939	T;T;T;T;T	0.80123	-1.34;0.6;0.6;-1.34;-1.34	5.03	5.03	0.67393	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.080894	0.50627	D	0.000102	T	0.59500	0.2198	N	0.08118	0	0.41980	D	0.990791	P;P;P;B	0.39782	0.524;0.688;0.524;0.4	B;B;B;B	0.33960	0.095;0.095;0.095;0.173	T	0.62501	-0.6841	10	0.19147	T	0.46	-18.0956	12.7928	0.57543	1.0:0.0:0.0:0.0	.	268;318;280;266	B4DY42;B4DX91;O75426;O75426-2	.;.;FBX24_HUMAN;.	A	280;266;266;268;318	ENSP00000241071:D280A;ENSP00000353821:D266A;ENSP00000419602:D266A;ENSP00000420239:D268A;ENSP00000416558:D318A	ENSP00000241071:D280A	D	+	2	0	FBXO24	100029987	0.997000	0.39634	1.000000	0.80357	0.939000	0.58152	2.681000	0.46926	2.137000	0.66172	0.392000	0.25879	GAC	.		0.552	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			C	100192051	A	C	100192051	3	2	19	1	0	0	0	0	1	0	0	0	5754	275	10	5	1018	5	FBXO24	7	100192051	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		100192051	58946612	42	1622											
PREX2	80243	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	68995502	68995502	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggaagtcgggaaaaagAtttttgctattaatggtgac	13	12	12	4	1	0	2	0	1	0	1	1	4	0	4	0	3	1	2	0	3	5	4			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr8:68995502A>T	ENST00000288368.4	+	18	2183	c.1906A>T	c.(1906-1908)Att>Ttt	p.I636F	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	636	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CGGGAAAAAGATTTTTGCTAT	0.318																																					p.I636F		.											.	PREX2-390	0			c.A1906T						.						93	94	93					8																	68995502		2203	4300	6503	SO:0001583	missense	80243	exon18			AAAAAGATTTTTG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1906A>T	8.37:g.68995502A>T	ENSP00000288368:p.Ile636Phe	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	78	6	NM_025170	0	0	1	1	0	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358895	0.82353	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.37235	1.21	5.77	5.77	0.91146	PDZ/DHR/GLGF (3);	0.144361	0.50627	D	0.000115	T	0.50718	0.1632	L	0.52573	1.65	0.54753	D	0.999989	P;P;P	0.52692	0.906;0.955;0.906	P;P;P	0.57101	0.578;0.781;0.813	T	0.51553	-0.8691	10	0.87932	D	0	.	16.3948	0.83586	1.0:0.0:0.0:0.0	.	636;636;636	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	F	636	ENSP00000288368:I636F	ENSP00000288368:I636F	I	+	1	0	PREX2	69158056	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.744000	0.55112	2.326000	0.78906	0.533000	0.62120	ATT	.		0.318	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	68995502	A	T	68995502	3	4	19	1	0	0	0	0	1	0	0	0	12506	333	12	5	1976	5	PREX2	8	68995502	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		68995502	77368520	43	1623											
ASPN	54829	hgsc.bcm.edu	37	chr9	95237063	95237063	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcatcatcatcatcatcAtcatctgtgtcttccatatc	10	16	2	13	0	10	0	8	0	2	0	12	0	11	0	1	0	0	0	1	0	1	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr9:95237063A>T	ENST00000375544.3	-	2	360	c.117T>A	c.(115-117)gaT>gaA	p.D39E	CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_Missense_Mutation_p.D39E|ASPN_ENST00000450139.2_Missense_Mutation_p.D11E|ASPN_ENST00000395538.3_Missense_Mutation_p.D39E	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	39	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						catcatcatcatcatcTGTGT	0.403																																					p.D39E		.											.	ASPN-514	0			c.T117A						.						102	97	99					9																	95237063		2203	4300	6503	SO:0001583	missense	54829	exon2			ATCATCATCATCT	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.117T>A	9.37:g.95237063A>T	ENSP00000364694:p.Asp39Glu	Somatic	40	1		WXS	Illumina HiSeq	Phase_I	44	5	NM_001193335	0	0	0	0	0	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	37		.	.	.	.	.	.	.	.	.	.	A	1.685	-0.505411	0.04261	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538;ENST00000450139	T;T;T	0.53857	0.6;0.78;0.78	.	.	.	.	.	.	.	.	T	0.42426	0.1202	M	0.61703	1.905	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.33033	-0.9884	7	0.15952	T	0.53	.	.	.	.	.	39;39	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	E	39;39;39;11	ENSP00000364694:D39E;ENSP00000364693:D39E;ENSP00000378909:D39E	ENSP00000364693:D39E	D	-	3	2	ASPN	94276884	0.422000	0.25473	0.022000	0.16811	0.452000	0.32318	0.163000	0.16520	0.064000	0.16427	0.063000	0.15292	GAT	.		0.403	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		T	95237063	A	T	95237063	3	4	19	1	0	0	0	0	1	0	0	0	1058	214	8	5	1053	5	ASPN	9	95237063	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		95237063	45976368	44	1624											
FAM120A	23196	bcgsc.ca	37	chr9	96326681	96326681	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggagcacgggtgacgccagGgcccccagccactctgaaag	9	3	15	14	2	1	2	0	2	1	0	1	3	1	3	4	3	2	1	4	3	1	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr9:96326681G>C	ENST00000277165.6	+	18	3410	c.3216G>C	c.(3214-3216)agG>agC	p.R1072S	AL353629.1_ENST00000582353.1_RNA|FAM120A_ENST00000340893.4_Missense_Mutation_p.R1026S|FAM120A_ENST00000333936.5_Missense_Mutation_p.R1100S	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	1072	RNA binding.					cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GTGACGCCAGGGCCCCCAGCC	0.542																																					p.R1072S													.	FAM120A-90	0			c.G3216C						.						49	54	52					9																	96326681		2203	4299	6502	SO:0001583	missense	23196	exon18			CGCCAGGGCCCCC	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"DNA polymerase-transactivated protein 1", "oxidative stess-associated Src activator"	612265	"chromosome 9 open reading frame 10"	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.3216G>C	9.37:g.96326681G>C	ENSP00000277165:p.Arg1072Ser	Somatic	142	0		WXS	Illumina HiSeq	Phase_1	98	27	NM_014612	0	0	18	18	0	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782024	0.31502	.	.	ENSG00000048828	ENST00000277165;ENST00000333936;ENST00000340893;ENST00000427765	T;T;T;T	0.46063	1.45;1.43;1.46;0.88	5.45	4.54	0.55810	.	0.000000	0.64402	D	0.000001	T	0.30603	0.0770	L	0.27053	0.805	0.49798	D	0.999822	P;P;B	0.36837	0.546;0.571;0.106	B;B;B	0.34722	0.188;0.163;0.069	T	0.05209	-1.0899	10	0.31617	T	0.26	-19.3611	14.6358	0.68689	0.0716:0.0:0.9284:0.0	.	1026;1100;1072	Q9NZB2-4;Q9NZB2-6;Q9NZB2	.;.;F120A_HUMAN	S	1072;1100;1026;448	ENSP00000277165:R1072S;ENSP00000334918:R1100S;ENSP00000344698:R1026S;ENSP00000412440:R448S	ENSP00000277165:R1072S	R	+	3	2	FAM120A	95366502	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	6.446000	0.73460	1.270000	0.44297	0.591000	0.81541	AGG	.		0.542	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		C	96326681	G	C	96326681	3	2	19	1	0	0	0	0	1	0	0	0	5431	1223	43	4	3286	4	FAM120A	9	96326681	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	1089618	96326681	44886750	45	1625											
SLC25A25	114789	bcgsc.ca	37	chr9	130854243	130854243	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgatcgtgaagtcagaggcAccccagcccctgcctggaga	10	5	12	14	2	1	3	1	1	0	2	2	5	1	3	5	2	2	1	5	2	1	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr9:130854243A>C	ENST00000373066.5	+	1	501	c.94A>C	c.(94-96)Acc>Ccc	p.T32P	SLC25A25_ENST00000432073.2_Missense_Mutation_p.T32P|SLC25A25_ENST00000373069.5_Intron|SLC25A25_ENST00000373068.2_Intron|RP11-379C10.4_ENST00000453870.1_RNA	NM_001265614.2	NP_001252543.1	Q6KCM7	SCMC2_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25	0					adipose tissue development (GO:0060612)|ATP metabolic process (GO:0046034)|calcium ion transmembrane transport (GO:0070588)|camera-type eye development (GO:0043010)|cellular respiration (GO:0045333)|multicellular organism growth (GO:0035264)|response to activity (GO:0014823)|response to dietary excess (GO:0002021)|response to food (GO:0032094)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)	10						AGTCAGAGGCACCCCAGCCCC	0.582																																					p.T32P													.	SLC25A25-90	0			c.A94C						.						99	114	109					9																	130854243		1935	4132	6067	SO:0001583	missense	114789	exon1			AGAGGCACCCCAG	AJ619963	CCDS6890.1, CCDS35151.1, CCDS48031.1, CCDS59146.1	9q34	2013-05-22			ENSG00000148339	ENSG00000148339		"Solute carriers", "EF-hand domain containing"	20663	protein-coding gene	gene with protein product		608745				15123600	Standard	NM_052901		Approved	KIAA1896, PCSCL, MCSC	uc004btb.4	Q6KCM7	OTTHUMG00000020736	ENST00000373066.5:c.94A>C	9.37:g.130854243A>C	ENSP00000362157:p.Thr32Pro	Somatic	326	4		WXS	Illumina HiSeq	Phase_1	202	45	NM_001006642	0	0	0	0	0	Q5SYW7|Q5SYW8|Q5SYX3|Q5VWU2|Q5VWU3|Q5VWU4|Q6KCM4|Q6KCM6|Q6UX48|Q705K2|Q96PZ1|Q9BSA6	Missense_Mutation	SNP	ENST00000373066.5	37	CCDS59146.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.318171	0.40996	.	.	ENSG00000148339	ENST00000432073;ENST00000373066	T;T	0.80738	-1.15;-1.41	6.07	4.87	0.63330	.	.	.	.	.	T	0.72637	0.3485	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.69851	-0.5033	8	0.52906	T	0.07	.	11.1225	0.48298	0.8459:0.154:0.0:0.0	.	32;32	Q6KCM7-5;Q6KCM7-4	.;.	P	32	ENSP00000410053:T32P;ENSP00000362157:T32P	ENSP00000362157:T32P	T	+	1	0	SLC25A25	129894064	0.558000	0.26554	1.000000	0.80357	0.976000	0.68499	0.739000	0.26173	2.326000	0.78906	0.533000	0.62120	ACC	.		0.582	SLC25A25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054406.1	NM_052901		C	130854243	A	C	130854243	3	2	19	1	0	0	0	0	1	0	0	0	14520	159	6	5	361	5	SLC25A25	9	130854243	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	34527562	130854243	10359188	46	1626											
ZER1	10444	hgsc.bcm.edu	37	chr9	131515582	131515582	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgcctgagaggtccaaggCagccagggagttaagcggcc	11	5	15	10	1	0	1	0	1	0	1	1	3	1	2	4	4	3	2	4	4	3	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr9:131515582C>G	ENST00000291900.2	-	4	1013	c.607G>C	c.(607-609)Gcc>Ccc	p.A203P	ZER1_ENST00000494461.1_5'Flank	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	203					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						AGGTCCAAGGCAGCCAGGGAG	0.617																																					p.A203P		.											.	ZER1-91	0			c.G607C						.						47	37	41					9																	131515582		2202	4300	6502	SO:0001583	missense	10444	exon4			CCAAGGCAGCCAG	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.607G>C	9.37:g.131515582C>G	ENSP00000291900:p.Ala203Pro	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_006336	0	0	24	24	0	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	37	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939837	0.52972	.	.	ENSG00000160445	ENST00000291900	T	0.17691	2.26	5.32	4.43	0.53597	.	0.053817	0.64402	D	0.000001	T	0.15176	0.0366	L	0.36672	1.1	0.58432	D	0.999999	B	0.30021	0.265	B	0.31191	0.125	T	0.05084	-1.0907	10	0.36615	T	0.2	-26.2778	13.2885	0.60258	0.0:0.9243:0.0:0.0757	.	203	Q7Z7L7	ZER1_HUMAN	P	203	ENSP00000291900:A203P	ENSP00000291900:A203P	A	-	1	0	ZER1	130555403	0.980000	0.34600	0.888000	0.34837	0.488000	0.33401	2.530000	0.45641	1.475000	0.48197	0.655000	0.94253	GCC	.		0.617	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		G	131515582	C	G	131515582	3	3	19	1	0	0	0	0	1	0	0	0	17657	710	25	4	1745	4	ZER1	9	131515582	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	661339	131515582	9697849	47	1627											
PDE6C	5146	hgsc.bcm.edu	37	chr10	95396764	95396764	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattttagaaatttcaagagAagttaaatgttgatgtaatt	16	16	7	2	0	1	3	1	1	0	2	1	4	1	3	0	0	0	3	0	0	7	7			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr10:95396764A>G	ENST00000371447.3	+	11	1564	c.1426A>G	c.(1426-1428)Aag>Gag	p.K476E		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	476					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ATTTCAAGAGAAGTTAAATGT	0.308																																					p.K476E		.											.	PDE6C-94	0			c.A1426G						.						76	78	77					10																	95396764		2201	4299	6500	SO:0001583	missense	5146	exon11			CAAGAGAAGTTAA	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"Phosphodiesterases"	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1426A>G	10.37:g.95396764A>G	ENSP00000360502:p.Lys476Glu	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_006204	0	0	0	0	0	A6NCR6|Q5VY29	Missense_Mutation	SNP	ENST00000371447.3	37	CCDS7429.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.167376	0.57476	.	.	ENSG00000095464	ENST00000371447	T	0.64260	-0.09	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.67757	0.2927	M	0.83852	2.665	0.58432	D	0.999993	D	0.58268	0.982	P	0.44732	0.459	T	0.72272	-0.4342	10	0.36615	T	0.2	.	15.1703	0.72869	1.0:0.0:0.0:0.0	.	476	P51160	PDE6C_HUMAN	E	476	ENSP00000360502:K476E	ENSP00000360502:K476E	K	+	1	0	PDE6C	95386754	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.900000	0.75687	2.231000	0.72958	0.459000	0.35465	AAG	.		0.308	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		G	95396764	A	G	95396764	3	3	19	1	0	0	0	0	1	0	0	0	11673	247	9	3	1468	3	PDE6C	10	95396764	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		95396764	40137983	48	1628											
DNMBP	23268	bcgsc.ca	37	chr10	101646368	101646368	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatttaagggggagatgaCaagccgctctgtcctctcct	8	11	11	11	1	2	3	0	2	2	1	4	4	3	3	3	2	1	1	3	2	2	2	rs201493282		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr10:101646368C>A	ENST00000324109.4	-	13	3398	c.3307G>T	c.(3307-3309)Gtc>Ttc	p.V1103F	DNMBP_ENST00000342239.3_Missense_Mutation_p.V1127F|DNMBP_ENST00000540316.1_Missense_Mutation_p.V39F|DNMBP_ENST00000543621.1_Missense_Mutation_p.V349F|DNMBP_ENST00000472036.1_5'UTR	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1103	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		GGGGAGATGACAAGCCGCTCT	0.478																																					p.V1103F													.	DNMBP-233	0			c.G3307T						.						83	80	81					10																	101646368		2203	4300	6503	SO:0001583	missense	23268	exon13			AGATGACAAGCCG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.3307G>T	10.37:g.101646368C>A	ENSP00000315659:p.Val1103Phe	Somatic	162	0		WXS	Illumina HiSeq	Phase_1	122	33	NM_015221	0	0	1	2	1	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	C	34	5.379696	0.95945	.	.	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.82	5.82	0.92795	BAR (3);	0.000000	0.43747	D	0.000531	D	0.84266	0.5434	M	0.82823	2.61	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.85588	0.1244	10	0.87932	D	0	-24.1351	19.7034	0.96065	0.0:1.0:0.0:0.0	.	1103;349;1127	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	F	1127;1103;349;349;39	ENSP00000344914:V1127F;ENSP00000315659:V1103F;ENSP00000443657:V349F;ENSP00000443573:V39F	ENSP00000315659:V1103F	V	-	1	0	DNMBP	101636358	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.815000	0.86186	2.756000	0.94617	0.561000	0.74099	GTC	.		0.478	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		A	101646368	C	A	101646368	3	1	19	1	0	0	0	0	1	0	0	0	4685	478	17	4	1446	4	DNMBP	10	101646368	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	6249604	101646368	33888379	49	1629											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1258389	1258389	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccttcgccgcctgccgcTcccaggtggggctctggtct	2	9	12	18	3	2	0	0	0	2	0	4	0	3	0	6	4	1	2	6	4	0	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:1258389T>G	ENST00000529681.1	+	25	3350	c.3292T>G	c.(3292-3294)Tcc>Gcc	p.S1098A	MUC5B_ENST00000447027.1_Missense_Mutation_p.S1101A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1098	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGCCTGCCGCTCCCAGGTGGG	0.682																																					p.S1098A		.											.	.	0			c.T3292G						.						10	15	13					11																	1258389		1897	4084	5981	SO:0001583	missense	727897	exon25			TGCCGCTCCCAGG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3292T>G	11.37:g.1258389T>G	ENSP00000436812:p.Ser1098Ala	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	5.715	0.316511	0.10845	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76839	-1.05;-1.05	4.38	-4.2	0.03823	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.59473	0.2196	N	0.10645	0.015	0.27479	N	0.952642	B;P;P	0.48089	0.026;0.905;0.905	B;P;P	0.47376	0.027;0.545;0.545	T	0.57613	-0.7781	9	0.87932	D	0	.	6.1245	0.20172	0.0:0.2029:0.3546:0.4425	.	1098;1791;1101	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	A	1098;1101;1099;1168	ENSP00000436812:S1098A;ENSP00000415793:S1101A	ENSP00000343037:S1099A	S	+	1	0	MUC5B	1214965	0.000000	0.05858	0.074000	0.20217	0.008000	0.06430	-0.169000	0.09911	-0.576000	0.05974	-0.648000	0.03929	TCC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1258389	T	G	1258389	3	3	19	1	0	0	0	0	1	0	0	0	10004	1551	54	5	3399	5	MUC5B	11	1258389	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08		1258389	133748127	50	1630											
MRVI1	10335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	10626061	10626061	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccagagtgtagctgtcatttCtaaaggccaaggacagttgc	11	10	11	9	0	2	1	1	0	1	1	2	2	2	2	2	2	2	3	2	2	4	4	rs374023004		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:10626061C>G	ENST00000436272.1	-	12	1631	c.1553G>C	c.(1552-1554)aGa>aCa	p.R518T	MRVI1_ENST00000424001.1_Missense_Mutation_p.R230T|MRVI1_ENST00000558540.1_Missense_Mutation_p.R230T|MRVI1_ENST00000531107.1_Missense_Mutation_p.R537T|MRVI1_ENST00000552103.1_Missense_Mutation_p.R454T|LYVE1_ENST00000531706.1_Intron|MRVI1_ENST00000541483.1_Missense_Mutation_p.R339T|MRVI1_ENST00000547195.1_Missense_Mutation_p.R454T|MRVI1_ENST00000423302.2_Missense_Mutation_p.R545T|MRVI1_ENST00000534266.2_Missense_Mutation_p.R230T|MRVI1_ENST00000421747.1_Missense_Mutation_p.R536T|MRVI1_ENST00000545852.1_Missense_Mutation_p.R230T|MRVI1_ENST00000527509.2_Missense_Mutation_p.R454T			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	518	Interaction with ITPR1. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GCTGTCATTTCTAAAGGCCAA	0.488																																					p.R545T		.											.	MRVI1-25	0			c.G1634C						.						173	166	168					11																	10626061		1964	4161	6125	SO:0001583	missense	10335	exon13			TCATTTCTAAAGG	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1553G>C	11.37:g.10626061C>G	ENSP00000412229:p.Arg518Thr	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	82	18	NM_130385	0	0	1	1	0	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	37		.	.	.	.	.	.	.	.	.	.	C	27.5	4.839467	0.91117	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.40956	0.1138	L	0.57536	1.79	0.80722	D	1	D;D;D;D	0.89917	0.996;1.0;1.0;1.0	D;D;D;D	0.87578	0.99;0.998;0.998;0.997	T	0.13980	-1.0489	10	0.56958	D	0.05	-13.6185	19.0062	0.92852	0.0:1.0:0.0:0.0	.	339;518;537;536	F5H6A1;Q9Y6F6;E9PQY6;Q9Y6F6-4	.;MRVI1_HUMAN;.;.	T	536;519;518;454;454;230;230;545;339;537;454	ENSP00000414598:R536T;ENSP00000412229:R518T;ENSP00000448278:R454T;ENSP00000446764:R454T;ENSP00000441971:R230T;ENSP00000401205:R230T;ENSP00000412130:R545T;ENSP00000437784:R339T;ENSP00000432436:R537T;ENSP00000432067:R454T	ENSP00000307885:R519T	R	-	2	0	MRVI1	10582637	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.538000	0.67193	2.553000	0.86117	0.563000	0.77884	AGA	.		0.488	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		G	10626061	C	G	10626061	3	3	19	1	0	0	0	0	1	0	0	0	9878	913	32	4	1140	4	MRVI1	11	10626061	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	9367672	10626061	124380455	51	1631											
USH1C	10083	bcgsc.ca	37	chr11	17542427	17542427	+	Silent	SNP	G	G	T																															tgaaacttacactttggcttGcgaaggggtactgggtgtac																										TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:17542427G>T	ENST00000318024.4	-	14	1308	c.1200C>A	c.(1198-1200)cgC>cgA	p.R400R	USH1C_ENST00000527720.1_Silent_p.R369R|USH1C_ENST00000527020.1_Silent_p.R381R|USH1C_ENST00000005226.7_Silent_p.R400R	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	400					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						ACTTTGGCTTGCGAAGGGGTA	0.512																																					p.R400R													.	USH1C-91	0			c.C1200A						.						251	239	243					11																	17542427		2200	4293	6493	SO:0001819	synonymous_variant	10083	exon14			TGGCTTGCGAAGG	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1200C>A	11.37:g.17542427G>T		Somatic	427	0		WXS	Illumina HiSeq	Phase_1	313	51	NM_005709	0	0	0	0	0	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			.		0.512	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		T	17542427	G	T	17542427	2	4	19	1	0	0	0	0	0	0	0	1	17067	1306	46	4		4	USH1C	11	17542427	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08	6916366	17542427	117464089	52	1632	14	2									
USH1C	10083	bcgsc.ca	37	chr11	17542436	17542436	+	Silent	SNP	T	T	G																															cactttggcttgcgaaggggTactgggtgtacctcagcagt																										TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:17542436T>G	ENST00000318024.4	-	14	1299	c.1191A>C	c.(1189-1191)gtA>gtC	p.V397V	USH1C_ENST00000527720.1_Silent_p.V366V|USH1C_ENST00000527020.1_Silent_p.V378V|USH1C_ENST00000005226.7_Silent_p.V397V	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	397					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						TGCGAAGGGGTACTGGGTGTA	0.517																																					p.V397V													.	USH1C-91	0			c.A1191C						.						282	265	271					11																	17542436		2200	4293	6493	SO:0001819	synonymous_variant	10083	exon14			AAGGGGTACTGGG	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1191A>C	11.37:g.17542436T>G		Somatic	481	2		WXS	Illumina HiSeq	Phase_1	344	83	NM_005709	0	0	23	25	2	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			.		0.517	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		G	17542436	T	G	17542436	2	3	19	1	0	0	0	0	0	0	0	1	17067	1625	57	5		5	USH1C	11	17542436	Silent	SNP	T	TCGA-A4-8518-01A-11D-2396-08	9	17542436	117464080	53	1633	14	2									
MAML2	84441	hgsc.bcm.edu	37	chr11	95825431	95825431	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgttgctgctgttgctgTtgggtgtagtgtaggagaga	5	15	17	4	0	0	1	0	0	0	1	0	3	0	2	0	2	4	9	0	2	2	5			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:95825431T>C	ENST00000524717.1	-	2	3048	c.1764A>G	c.(1762-1764)caA>caG	p.Q588Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	588					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgTTGGGTGTAGT	0.522			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q588Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.A1764G						.																																			SO:0001819	synonymous_variant	84441	exon2			TTGCTGTTGGGTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1764A>G	11.37:g.95825431T>C		Somatic	12	2		WXS	Illumina HiSeq	Phase_I	6	2	NM_032427	0	0	7	7	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.522	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825431	T	C	95825431	2	2	19	1	0	0	0	0	0	0	0	1	9231	1722	60	3		3	MAML2	11	95825431	Silent	SNP	T	TCGA-A4-8518-01A-11D-2396-08	78282995	95825431	39181085	54	1634											
PPHLN1	51535	hgsc.bcm.edu	37	chr12	42840394	42840394	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttgttgtttactaattctagGatgtaaagccagaaaacaag	15	13	8	5	0	1	1	0	0	1	1	1	2	1	2	1	1	3	3	1	1	8	8			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr12:42840394G>C	ENST00000395568.2	+	13	1435	c.1351G>C	c.(1351-1353)Gat>Cat	p.D451H	PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000256678.8_Splice_Site_p.D356H|PPHLN1_ENST00000432191.2_Splice_Site_p.D427H	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	451					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		ctaattctaggatgtaaagcc	0.393																																					p.D451H		.											.	PPHLN1-154	0			c.G1351C						.						54	55	54					12																	42840394		2203	4300	6503	SO:0001630	splice_region_variant	51535	exon13			TTCTAGGATGTAA	AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.1351-1G>C	12.37:g.42840394G>C		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_016488	0	0	0	0	0	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320402	0.23994	.	.	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	.	.	.	.	T	0.61098	0.2320	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.58970	0.984;0.972;0.984;0.972	D;P;D;P	0.65323	0.934;0.861;0.934;0.861	T	0.61173	-0.7116	7	0.87932	D	0	.	.	.	.	.	356;402;427;451	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	H	451;356;427	.	ENSP00000256678:D356H	D	+	1	0	PPHLN1	41126661	0.332000	0.24722	0.224000	0.23877	0.223000	0.24884	0.251000	0.18257	0.202000	0.20498	0.205000	0.17691	GAT	.		0.393	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515	Missense_Mutation	C	42840394	G	C	42840394	5	2	19	1	0	0	0	0	0	0	1	0	12341	1188	41	4	1607	4	PPHLN1	12	42840394	Splice_Site	SNP	G	TCGA-A4-8518-01A-11D-2396-08		42840394	91011501	55	1635											
KRT1	3848	bcgsc.ca	37	chr12	53069392	53069392	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgatggtggtgtggcttGtgctcacagctgcaagagga	8	10	15	8	0	1	2	1	1	0	1	1	3	1	3	0	4	3	4	0	4	1	1	rs75007002		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr12:53069392G>T	ENST00000252244.3	-	9	1578	c.1520C>A	c.(1519-1521)aCa>aAa	p.T507K		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	507	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						GGTGTGGCTTGTGCTCACAGC	0.562																																					p.T507K													.	KRT1-92	0			c.C1520A						.						61	58	59					12																	53069392		2203	4300	6503	SO:0001583	missense	3848	exon9			TGGCTTGTGCTCA	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1520C>A	12.37:g.53069392G>T	ENSP00000252244:p.Thr507Lys	Somatic	107	0		WXS	Illumina HiSeq	Phase_1	125	52	NM_006121	0	0	0	0	0	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.827529	0.32329	.	.	ENSG00000167768	ENST00000252244	D	0.90620	-2.7	4.61	2.57	0.30868	.	.	.	.	.	T	0.81446	0.4824	N	0.14661	0.345	0.31022	N	0.718014	P	0.39480	0.675	B	0.33960	0.173	T	0.80188	-0.1486	9	0.59425	D	0.04	.	13.6984	0.62593	0.0:0.5685:0.4315:0.0	.	507	P04264	K2C1_HUMAN	K	507	ENSP00000252244:T507K	ENSP00000252244:T507K	T	-	2	0	KRT1	51355659	0.004000	0.15560	1.000000	0.80357	0.904000	0.53231	0.012000	0.13287	1.036000	0.39998	0.462000	0.41574	ACA	.		0.562	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		T	53069392	G	T	53069392	3	4	19	1	0	0	0	0	1	0	0	0	8468	1377	48	4	418	4	KRT1	12	53069392	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	10228998	53069392	80782503	56	1636											
ANAPC7	51434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	110813921	110813921	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctgatactcattgacagcTacaaggaaatctcctaggat	13	11	7	10	0	2	2	1	2	1	0	4	4	3	4	2	2	3	1	2	2	5	4			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr12:110813921T>C	ENST00000455511.3	-	10	1560	c.1560A>G	c.(1558-1560)gtA>gtG	p.V520V	ANAPC7_ENST00000481473.1_5'UTR|ANAPC7_ENST00000450008.2_Silent_p.V520V	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	520					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						CATTGACAGCTACAAGGAAAT	0.498																																					p.V520V		.											.	ANAPC7-226	0			c.A1560G						.						141	119	126					12																	110813921		2203	4300	6503	SO:0001819	synonymous_variant	51434	exon10			GACAGCTACAAGG	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1560A>G	12.37:g.110813921T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	75	14	NM_016238	0	0	40	51	11	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Silent	SNP	ENST00000455511.3	37	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	T	10.12	1.263642	0.23136	.	.	ENSG00000196510	ENST00000552087	.	.	.	5.55	2.43	0.29744	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50415	-0.8831	4	.	.	.	-22.9206	9.4319	0.38615	0.0:0.3125:0.0:0.6875	.	.	.	.	G	70	.	.	S	-	1	0	ANAPC7	109298304	0.916000	0.31088	1.000000	0.80357	0.998000	0.95712	-0.028000	0.12350	0.179000	0.19938	0.459000	0.35465	AGC	.		0.498	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		C	110813921	T	C	110813921	2	2	19	1	0	0	0	0	0	0	0	1	606	1509	53	3		3	ANAPC7	12	110813921	Silent	SNP	T	TCGA-A4-8518-01A-11D-2396-08	57744529	110813921	23037974	57	1637											
BRAP	8315	bcgsc.ca	37	chr12	112098449	112098449	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttattttcttctactggctcGggcgtttgacagtaccggca	6	15	10	10	3	2	1	0	1	2	0	3	1	2	1	1	3	2	4	1	3	3	7	rs201734278		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr12:112098449G>C	ENST00000327551.6	-	7	977	c.837C>G	c.(835-837)ccC>ccG	p.P279P	BRAP_ENST00000539060.1_Silent_p.P130P|BRAP_ENST00000419234.4_Silent_p.P309P			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	203					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						CTACTGGCTCGGGCGTTTGAC	0.408																																					p.P309P	Pancreas(146;846 1904 7830 25130 26065)												.	BRAP-710	0			c.C927G						.						157	152	154					12																	112098449		2203	4300	6503	SO:0001819	synonymous_variant	8315	exon7			TGGCTCGGGCGTT	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.837C>G	12.37:g.112098449G>C		Somatic	201	1		WXS	Illumina HiSeq	Phase_1	149	28	NM_006768	0	0	2	2	0	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Silent	SNP	ENST00000327551.6	37																																																																																				G|0.999;C|0.001		0.408	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			C	112098449	G	C	112098449	2	2	19	1	0	0	0	0	0	0	0	1	1500	1103	39	4		4	BRAP	12	112098449	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08	1284528	112098449	21753446	58	1638											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124414245	124414245	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgaacacgtacttaacgaAagccttccagcaacgggacc	13	7	8	13	3	1	1	0	1	1	0	2	3	2	2	3	1	6	2	3	1	5	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr12:124414245A>G	ENST00000409039.3	+	71	12222	c.12197A>G	c.(12196-12198)aAa>aGa	p.K4066R	CCDC92_ENST00000544798.1_Intron|DNAH10OS_ENST00000514254.2_3'UTR	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4066					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TACTTAACGAAAGCCTTCCAG	0.512																																					p.K4066R		.											.	DNAH10-95	0			c.A12197G						.						46	45	45					12																	124414245		1895	4111	6006	SO:0001583	missense	196385	exon71			TAACGAAAGCCTT	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.12197A>G	12.37:g.124414245A>G	ENSP00000386770:p.Lys4066Arg	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_207437	0	0	1	1	0	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912785	0.52439	.	.	ENSG00000197653	ENST00000409039	T	0.08634	3.07	5.06	5.06	0.68205	Dynein heavy chain (1);	0.112207	0.64402	D	0.000016	T	0.22322	0.0538	L	0.54965	1.715	0.80722	D	1	D	0.63880	0.993	D	0.63381	0.914	T	0.00351	-1.1796	10	0.56958	D	0.05	.	15.1038	0.72303	1.0:0.0:0.0:0.0	.	4066	Q8IVF4	DYH10_HUMAN	R	4066	ENSP00000386770:K4066R	ENSP00000386770:K4066R	K	+	2	0	DNAH10	122980198	1.000000	0.71417	0.965000	0.40720	0.157000	0.22087	7.196000	0.77805	2.038000	0.60285	0.533000	0.62120	AAA	.		0.512	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			G	124414245	A	G	124414245	3	3	19	1	0	0	0	0	1	0	0	0	4609	14	1	3	12479	3	DNAH10	12	124414245	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	12315796	124414245	9437650	59	1639											
SHISA2	387914	hgsc.bcm.edu	37	chr13	26625047	26625047	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccgccagcagcgcagccaGcagcagctgcaggagcgaag	10	1	15	15	4	0	0	0	0	0	0	0	2	0	1	3	1	8	6	3	1	1	0	rs4770911	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr13:26625047G>A	ENST00000319420.3	-	1	122	c.67C>T	c.(67-69)Ctg>Ttg	p.L23L	LINC00415_ENST00000439079.1_lincRNA	NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	23					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						AGCGCAGCCAGCAGCAGCTGC	0.731													G|||	768	0.153355	0.1036	0.1167	5008	,	,		13796	0.1032		0.171	False		,,,				2504	0.2802				p.L23L		.											.	SHISA2-69	0			c.C67T						.	G		241,2763		3,235,1264	2	2	2		67	4.4	1	13	dbSNP_111	2	750,5346		25,700,2323	no	coding-synonymous	SHISA2	NM_001007538.1		28,935,3587	AA,AG,GG		12.3031,8.0226,10.8901		23/296	26625047	991,8109	1502	3048	4550	SO:0001819	synonymous_variant	387914	exon1			CAGCCAGCAGCAG		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.67C>T	13.37:g.26625047G>A		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	4	3	NM_001007538	0	0	0	0	0	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	37	CCDS31951.1																																																																																			G|0.870;A|0.130		0.731	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		A	26625047	G	A	26625047	2	1	19	1	0	0	0	0	0	0	0	1	14312	962	34	2		2	SHISA2	13	26625047	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08		26625047	88544831	60	1640											
MYO16	23026	hgsc.bcm.edu	37	chr13	109792825	109792825	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgcgctgcccccggcggCgcctccgggtgacgaggacg	3	4	18	16	8	0	1	0	1	0	0	1	3	1	2	4	4	2	1	4	4	0	0	rs199777754	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr13:109792825C>T	ENST00000357550.2	+	31	4240	c.4199C>T	c.(4198-4200)gCg>gTg	p.A1400V	MYO16_ENST00000356711.2_Missense_Mutation_p.A1400V	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCCCCGGCGGCGCCTCCGGGT	0.776													C|||	29	0.00579073	0.0015	0.0086	5008	,	,		6517	0		0.0179	False		,,,				2504	0.0031				p.A1422V		.											.	MYO16-142	0			c.C4265T						.	C	VAL/ALA,VAL/ALA	6,3528		0,6,1761	3	4	3		4265,4199	-6.2	0	13		3	61,7069		0,61,3504	yes	missense,missense	MYO16	NM_001198950.1,NM_015011.1	64,64	0,67,5265	TT,TC,CC		0.8555,0.1698,0.6283	benign,benign	1422/1881,1400/1859	109792825	67,10597	1767	3565	5332	SO:0001583	missense	23026	exon32			CGGCGGCGCCTCC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4199C>T	13.37:g.109792825C>T	ENSP00000350160:p.Ala1400Val	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	12	10	NM_001198950	0	0	0	0	0		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	C	2.716	-0.267762	0.05754	0.001698	0.008555	ENSG00000041515	ENST00000356711;ENST00000357550	T;T	0.80909	-1.43;-1.43	4.18	-6.23	0.02052	.	1.421560	0.05654	U	0.585757	T	0.44456	0.1294	N	0.08118	0	0.09310	N	0.999997	B	0.22414	0.069	B	0.14578	0.011	T	0.34950	-0.9808	9	.	.	.	.	1.1331	0.01749	0.2674:0.1192:0.1351:0.4783	.	1400	Q9Y6X6	MYO16_HUMAN	V	1400	ENSP00000349145:A1400V;ENSP00000350160:A1400V	.	A	+	2	0	MYO16	108590826	0.972000	0.33761	0.000000	0.03702	0.005000	0.04900	2.028000	0.41088	-0.850000	0.04152	0.313000	0.20887	GCG	.		0.776	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109792825	C	T	109792825	3	4	19	1	0	0	0	0	1	0	0	0	10089	768	27	1	4321	1	MYO16	13	109792825	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	83167778	109792825	5377053	61	1641											
SQRDL	58472	bcgsc.ca	37	chr15	45968443	45968443	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaaaacctcattgaagtcCgagccgataaacaagaggct	17	6	9	9	2	1	3	1	1	0	2	2	5	2	3	3	1	3	1	3	1	6	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr15:45968443C>G	ENST00000260324.7	+	6	1185	c.799C>G	c.(799-801)Cga>Gga	p.R267G	SQRDL_ENST00000568606.1_Missense_Mutation_p.R267G|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.R267G	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	267					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		CATTGAAGTCCGAGCCGATAA	0.483																																					p.R267G													.	SQRDL-91	0			c.C799G						.						112	112	112					15																	45968443		2198	4297	6495	SO:0001583	missense	58472	exon6			GAAGTCCGAGCCG	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.799C>G	15.37:g.45968443C>G	ENSP00000260324:p.Arg267Gly	Somatic	199	1		WXS	Illumina HiSeq	Phase_1	124	38	NM_021199	0	0	27	27	0	Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	37	CCDS10127.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.011089	0.75046	.	.	ENSG00000137767	ENST00000260324	T	0.41065	1.01	5.74	4.77	0.60923	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.56426	0.1984	M	0.86268	2.805	0.80722	D	1	P	0.34562	0.457	B	0.43478	0.421	T	0.61357	-0.7079	10	0.52906	T	0.07	.	14.3248	0.66512	0.1489:0.8511:0.0:0.0	.	267	Q9Y6N5	SQRD_HUMAN	G	267	ENSP00000260324:R267G	ENSP00000260324:R267G	R	+	1	2	SQRDL	43755735	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.318000	0.43779	2.715000	0.92844	0.655000	0.94253	CGA	.		0.483	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2			G	45968443	C	G	45968443	3	3	19	1	0	0	0	0	1	0	0	0	15161	644	23	4	817	4	SQRDL	15	45968443	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		45968443	56562949	62	1642											
DMXL2	23312	bcgsc.ca	37	chr15	51766637	51766637	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attatttaatgggtgggctgCaagccgaaataattcactgg	12	12	11	6	1	1	0	1	0	0	0	1	1	1	0	1	3	2	2	1	3	5	5	rs374313651|rs371331405		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr15:51766637C>A	ENST00000251076.5	-	28	7401	c.7114G>T	c.(7114-7116)Gca>Tca	p.A2372S	DMXL2_ENST00000449909.3_Missense_Mutation_p.A1736S|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.A2373S	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2372						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GGGTGGGCTGCAAGCCGAAAT	0.383																																					p.A2373S													.	DMXL2-99	0			c.G7117T						.						59	60	60					15																	51766637		2196	4293	6489	SO:0001583	missense	23312	exon28			GGGCTGCAAGCCG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.7114G>T	15.37:g.51766637C>A	ENSP00000251076:p.Ala2372Ser	Somatic	68	0		WXS	Illumina HiSeq	Phase_1	58	27	NM_001174116	0	0	0	0	0	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089982	0.76756	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.25085	1.97;1.97;1.82	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.44074	0.1276	L	0.39245	1.2	0.80722	D	1	D;D;D;B	0.69078	0.997;0.994;0.997;0.25	D;D;D;B	0.75020	0.909;0.97;0.985;0.041	T	0.08700	-1.0709	10	0.36615	T	0.2	.	19.5897	0.95503	0.0:1.0:0.0:0.0	.	2373;1736;2372;2373	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	S	2372;2373;1736	ENSP00000251076:A2372S;ENSP00000441858:A2373S;ENSP00000400855:A1736S	ENSP00000251076:A2372S	A	-	1	0	DMXL2	49553929	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.757000	0.68766	2.635000	0.89317	0.655000	0.94253	GCA	.		0.383	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51766637	C	A	51766637	3	1	19	1	0	0	0	0	1	0	0	0	4606	710	25	4	2060	4	DMXL2	15	51766637	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	5798194	51766637	50764755	63	1643											
CCNB2	9133	bcgsc.ca	37	chr15	59406999	59406999	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcctagtggattggctggTacaagtccactccaagttta	10	12	9	10	0	0	0	0	0	0	0	3	1	3	1	3	3	1	3	3	3	5	5	rs200615810		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr15:59406999T>G	ENST00000288207.2	+	5	712	c.521T>G	c.(520-522)gTa>gGa	p.V174G	CCNB2_ENST00000559622.1_Missense_Mutation_p.V93G	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	174					G2/M transition of mitotic cell cycle (GO:0000086)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				kidney(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9						GATTGGCTGGTACAAGTCCAC	0.453																																					p.V174G													.	CCNB2-226	0			c.T521G						.						192	180	184					15																	59406999		2191	4291	6482	SO:0001583	missense	9133	exon5			GGCTGGTACAAGT	AF002822	CCDS10170.1	15q21.3	2004-01-19			ENSG00000157456	ENSG00000157456			1580	protein-coding gene	gene with protein product		602755					Standard	NM_004701		Approved	HsT17299	uc002afz.3	O95067	OTTHUMG00000132715	ENST00000288207.2:c.521T>G	15.37:g.59406999T>G	ENSP00000288207:p.Val174Gly	Somatic	265	11		WXS	Illumina HiSeq	Phase_1	249	66	NM_004701	0	0	2	2	0	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	37	CCDS10170.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.078656	0.76528	.	.	ENSG00000157456	ENST00000288207	T	0.13538	2.58	5.54	5.54	0.83059	Cyclin, N-terminal (2);Cyclin-like (3);	0.056803	0.64402	D	0.000001	T	0.43166	0.1235	M	0.91090	3.175	0.80722	D	1	D;D	0.61080	0.989;0.978	P;P	0.61070	0.883;0.844	T	0.55444	-0.8140	10	0.87932	D	0	.	14.8548	0.70329	0.0:0.0:0.0:1.0	.	174;174	Q53HG9;O95067	.;CCNB2_HUMAN	G	174	ENSP00000288207:V174G	ENSP00000288207:V174G	V	+	2	0	CCNB2	57194291	1.000000	0.71417	0.950000	0.38849	0.791000	0.44710	8.040000	0.89188	2.103000	0.63969	0.533000	0.62120	GTA	.		0.453	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701		G	59406999	T	G	59406999	3	3	19	1	0	0	0	0	1	0	0	0	2919	1638	57	5	539	5	CCNB2	15	59406999	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	7640362	59406999	43124393	64	1644											
TRIP4	9325	hgsc.bcm.edu	37	chr15	64692969	64692969	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcatgaggaacaagatattTtacagcgtgactcaaacaag	16	9	8	8	1	2	3	2	2	0	1	2	4	2	4	0	1	4	0	0	1	6	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr15:64692969T>C	ENST00000261884.3	+	5	706	c.646T>C	c.(646-648)Tta>Cta	p.L216L	TRIP4_ENST00000559565.1_3'UTR|RN7SL595P_ENST00000582065.1_RNA	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	216					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						ACAAGATATTTTACAGCGTGA	0.363																																					p.L216L		.											.	TRIP4-188	0			c.T646C						.						96	94	95					15																	64692969		2203	4300	6503	SO:0001819	synonymous_variant	9325	exon5			GATATTTTACAGC	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.646T>C	15.37:g.64692969T>C		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_016213	0	0	7	7	0	B2RAS0|Q96ED7|Q9UKH0	Silent	SNP	ENST00000261884.3	37	CCDS10194.1																																																																																			.		0.363	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		C	64692969	T	C	64692969	2	2	19	1	0	0	0	0	0	0	0	1	16591	1838	64	3		3	TRIP4	15	64692969	Silent	SNP	T	TCGA-A4-8518-01A-11D-2396-08	5285970	64692969	37838423	65	1645											
AKAP13	11214	bcgsc.ca	37	chr15	86287035	86287035	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaaaaaaagaagaacaaaAccagccgctctcagcccggt	19	3	8	11	2	1	3	1	0	1	3	2	3	1	3	3	1	4	1	3	1	8	0	rs79101360		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr15:86287035A>C	ENST00000394518.2	+	36	8466	c.8371A>C	c.(8371-8373)Acc>Ccc	p.T2791P	AKAP13_ENST00000361243.2_Missense_Mutation_p.T2795P|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Missense_Mutation_p.T1036P|RP11-158M2.3_ENST00000558375.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2791	Interaction with ESR1.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						GAAGAACAAAACCAGCCGCTC	0.542																																					p.T2795P	Melanoma(94;603 1453 3280 32295 32951)												.	AKAP13-258	0			c.A8383C						.						34	37	36					15																	86287035		2196	4288	6484	SO:0001583	missense	11214	exon36			AACAAAACCAGCC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.8371A>C	15.37:g.86287035A>C	ENSP00000378026:p.Thr2791Pro	Somatic	81	4		WXS	Illumina HiSeq	Phase_1	50	23	NM_006738	0	0	3	4	1	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.974617	0.34848	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.48201	0.82;0.82;0.82	5.59	3.7	0.42460	.	.	.	.	.	T	0.26268	0.0641	N	0.08118	0	0.23962	N	0.996336	B;P	0.34977	0.347;0.478	B;B	0.26416	0.031;0.069	T	0.09335	-1.0679	9	0.66056	D	0.02	.	11.4408	0.50096	0.1299:0.0:0.8701:0.0	.	2791;2795	Q12802;Q12802-2	AKP13_HUMAN;.	P	2795;2791;2794;2770;1036	ENSP00000354718:T2795P;ENSP00000378026:T2791P;ENSP00000378018:T1036P	ENSP00000354718:T2795P	T	+	1	0	AKAP13	84088039	1.000000	0.71417	0.827000	0.32855	0.425000	0.31504	4.301000	0.59086	0.702000	0.31825	-0.899000	0.02877	ACC	.		0.542	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86287035	A	C	86287035	3	2	19	1	0	0	0	0	1	0	0	0	449	43	2	5	8579	5	AKAP13	15	86287035	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08	21594066	86287035	16244357	66	1646											
PKD1	5310	hgsc.bcm.edu	37	chr16	2164808	2164808	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggagaggtacggggccCggggaccagggtggccggga	6	3	23	9	4	0	1	0	0	0	1	0	4	0	3	3	10	1	1	3	10	1	1	rs40433	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr16:2164808C>T	ENST00000262304.4	-	11	2424	c.2216G>A	c.(2215-2217)cGg>cAg	p.R739Q	PKD1_ENST00000423118.1_Missense_Mutation_p.R739Q|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	739			R -> Q (in dbSNP:rs40433). {ECO:0000269|PubMed:11857740, ECO:0000269|PubMed:18837007, ECO:0000269|PubMed:7663510}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GTACGGGGCCCGGGGACCAGG	0.711													t|||	4904	0.979233	0.9947	0.964	5008	,	,		11377	1		0.9453	False		,,,				2504	0.9826				p.R739Q		.											.	PKD1-91	0			c.G2216A						.						1	1	1					16																	2164808		369	697	1066	SO:0001583	missense	5310	exon11			GGGGCCCGGGGAC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.2216G>A	16.37:g.2164808C>T	ENSP00000262304:p.Arg739Gln	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_000296	0	0	0	12	12	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	1980	0.9065934065934066	441	0.8963414634146342	337	0.930939226519337	535	0.9353146853146853	667	0.8799472295514512	t	0.012	-1.660303	0.00772	.	.	ENSG00000008710	ENST00000262304;ENST00000423118	T;T	0.36157	1.27;1.27	5.39	-2.55	0.06288	Polycystin cation channel (1);	3.669600	0.00744	N	0.001030	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B;B	0.13145	0.005;0.007	B;B	0.04013	0.0;0.001	T	0.38735	-0.9647	9	0.02654	T	1	.	3.0572	0.06188	0.1042:0.3245:0.3205:0.2508	rs40433;rs3895634	739;739	P98161-3;P98161	.;PKD1_HUMAN	Q	739	ENSP00000262304:R739Q;ENSP00000399501:R739Q	ENSP00000262304:R739Q	R	-	2	0	PKD1	2104809	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.091000	0.15046	-0.934000	0.03733	-1.862000	0.00560	CGG	T|1.000;|0.000		0.711	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			T	2164808	C	T	2164808	3	4	19	1	0	0	0	0	1	0	0	0	11989	652	23	1	10839	1	PKD1	16	2164808	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		2164808	88189945	67	1647											
MYLK3	91807	bcgsc.ca	37	chr16	46744687	46744687	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgtttcccctagaaatgggGacaagccactgagtctatag	11	10	10	10	0	1	2	0	1	1	1	2	3	2	3	3	2	1	1	3	2	5	4	rs150139689|rs200890698		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr16:46744687G>A	ENST00000394809.4	-	11	2244	c.2129C>T	c.(2128-2130)tCc>tTc	p.S710F	MYLK3_ENST00000562104.1_5'UTR|MYLK3_ENST00000536476.1_Missense_Mutation_p.S369F	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	710	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TAGAAATGGGGACAAGCCACT	0.468																																					p.S710F													.	MYLK3-374	0			c.C2129T						.						79	88	85					16																	46744687		2203	4300	6503	SO:0001583	missense	91807	exon11			AATGGGGACAAGC	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.2129C>T	16.37:g.46744687G>A	ENSP00000378288:p.Ser710Phe	Somatic	249	4		WXS	Illumina HiSeq	Phase_1	180	58	NM_182493	0	0	0	0	0	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	G	28.7	4.944148	0.92593	.	.	ENSG00000140795	ENST00000394809;ENST00000536476	T;T	0.39229	1.09;1.09	6.03	6.03	0.97812	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.35378	N	0.003248	T	0.60011	0.2236	L	0.39467	1.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59064	-0.7524	10	0.87932	D	0	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	710	Q32MK0	MYLK3_HUMAN	F	710;369	ENSP00000378288:S710F;ENSP00000439297:S369F	ENSP00000378288:S710F	S	-	2	0	MYLK3	45302188	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.799000	0.99117	2.861000	0.98227	0.655000	0.94253	TCC	.		0.468	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		A	46744687	G	A	46744687	3	1	19	1	0	0	0	0	1	0	0	0	10083	1174	41	2	342	2	MYLK3	16	46744687	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08	44579879	46744687	43610066	68	1648											
FLII	2314	hgsc.bcm.edu	37	chr17	18154306	18154306	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtagtagatctcccagttgAgggagccgctgtcatccaga	10	9	12	10	1	2	3	1	1	1	2	4	4	3	4	3	1	1	4	3	1	2	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:18154306A>G	ENST00000327031.4	-	14	1847	c.1622T>C	c.(1621-1623)cTc>cCc	p.L541P	FLII_ENST00000379450.4_Missense_Mutation_p.L455P|FLII_ENST00000579294.1_Missense_Mutation_p.L530P|FLII_ENST00000545457.2_Missense_Mutation_p.L486P|FLII_ENST00000584444.1_5'Flank|FLII_ENST00000578558.1_Missense_Mutation_p.L540P	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	541	Interaction with ACTL6A.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CTCCCAGTTGAGGGAGCCGCT	0.587																																					p.L541P		.											.	FLII-91	0			c.T1622C						.						62	63	63					17																	18154306		2203	4300	6503	SO:0001583	missense	2314	exon14			CAGTTGAGGGAGC	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.1622T>C	17.37:g.18154306A>G	ENSP00000324573:p.Leu541Pro	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	50	3	NM_002018	0	0	68	68	0	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.530941	0.85706	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.19250	2.16;2.16	5.91	5.91	0.95273	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.974;0.974;0.974;0.995;0.999	T	0.55289	-0.8164	10	0.87932	D	0	-17.0341	16.3436	0.83110	1.0:0.0:0.0:0.0	.	455;455;541;541;510	E7EPM0;B4DIL0;F5H407;Q13045;B4DIX0	.;.;.;FLII_HUMAN;.	P	541;541;455	ENSP00000324573:L541P;ENSP00000368763:L455P	ENSP00000324573:L541P	L	-	2	0	FLII	18095031	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.944000	0.92980	2.269000	0.75478	0.533000	0.62120	CTC	.		0.587	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		G	18154306	A	G	18154306	3	3	19	1	0	0	0	0	1	0	0	0	5944	304	11	3	2255	3	FLII	17	18154306	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		18154306	63040904	69	1649											
ITGB3	3690	hgsc.bcm.edu	37	chr17	45361999	45361999	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttcggggcatttgtggaCaagcctgtgtcaccatacat	8	11	12	10	1	1	0	1	0	0	0	2	1	1	1	2	4	2	2	2	4	2	3	rs202100960		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:45361999C>A	ENST00000559488.1	+	4	568	c.552C>A	c.(550-552)gaC>gaA	p.D184E	ITGB3_ENST00000571680.1_Missense_Mutation_p.D184E|ITGB3_ENST00000560629.1_Missense_Mutation_p.Q173K|ITGB3_ENST00000435993.2_Missense_Mutation_p.D137E	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	184	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CATTTGTGGACAAGCCTGTGT	0.552																																					p.D184E		.											.	ITGB3-714	0			c.C552A						.						128	134	132					17																	45361999		2203	4300	6503	SO:0001583	missense	3690	exon4			TGTGGACAAGCCT		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.552C>A	17.37:g.45361999C>A	ENSP00000452786:p.Asp184Glu	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	281	15	NM_000212	0	0	22	24	2	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.385128	0.42308	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.98400	-4.91	5.86	4.87	0.63330	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.98043	0.9355	M	0.66560	2.04	0.80722	D	1	D;D	0.64830	0.994;0.962	D;D	0.76575	0.988;0.954	D	0.97929	1.0319	10	0.02654	T	1	.	11.3787	0.49743	0.0:0.9067:0.0:0.0933	.	184;184	P05106;Q2YFE1	ITB3_HUMAN;.	E	184;137	ENSP00000407801:D137E	ENSP00000262017:D184E	D	+	3	2	C17orf57	42716998	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.226000	0.32563	1.399000	0.46721	0.655000	0.94253	GAC	.		0.552	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		A	45361999	C	A	45361999	3	1	19	1	0	0	0	0	1	0	0	0	7916	477	17	4	566	4	ITGB3	17	45361999	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	27207693	45361999	35833211	70	1650											
SPATA20	64847	bcgsc.ca	37	chr17	48628511	48628511	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcccggaagcatcggccCaagccgcacctggacagcaa	11	2	12	16	3	0	0	0	0	0	0	1	2	0	2	4	4	3	3	4	4	3	0	rs149572077		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:48628511C>A	ENST00000356488.4	+	11	1571	c.1488C>A	c.(1486-1488)ccC>ccA	p.P496P	SPATA20_ENST00000393244.3_Silent_p.P452P|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Silent_p.P512P	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	496					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			AGCATCGGCCCAAGCCGCACC	0.622											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P512P													.	SPATA20-90	0			c.C1536A						.						16	15	15					17																	48628511		2176	4270	6446	SO:0001819	synonymous_variant	64847	exon12			TCGGCCCAAGCCG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1488C>A	17.37:g.48628511C>A		Somatic	59	0	119	WXS	Illumina HiSeq	Phase_1	26	7	NM_022827	0	0	43	44	1	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	37	CCDS58563.1																																																																																			.		0.622	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48628511	C	A	48628511	2	1	19	1	0	0	0	0	0	0	0	1	15038	581	21	4		4	SPATA20	17	48628511	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	3266512	48628511	32566699	71	1651											
HELZ	9931	hgsc.bcm.edu	37	chr17	65212033	65212033	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	accatgtctacaatcttcatCagcttgcacataatttttct	11	16	3	11	0	5	0	2	0	3	0	5	0	5	0	1	0	3	2	1	0	3	6			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:65212033C>G	ENST00000358691.5	-	5	395	c.229G>C	c.(229-231)Gat>Cat	p.D77H	HELZ_ENST00000580168.1_Missense_Mutation_p.D77H|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	77						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CAATCTTCATCAGCTTGCACA	0.284																																					p.D77H		.											.	HELZ-92	0			c.G229C						.						61	57	59					17																	65212033		1805	4071	5876	SO:0001583	missense	9931	exon5			CTTCATCAGCTTG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.229G>C	17.37:g.65212033C>G	ENSP00000351524:p.Asp77His	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_014877	0	0	3	3	0	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.324423	0.41197	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.73681	-0.77;-0.77	4.86	4.86	0.63082	.	0.046573	0.85682	D	0.000000	T	0.80193	0.4578	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	0.999;0.992;1.0	D;P;D	0.81914	0.995;0.863;0.993	T	0.82690	-0.0332	10	0.62326	D	0.03	-7.5014	18.0445	0.89328	0.0:1.0:0.0:0.0	.	77;77;77	B7ZLW2;F8WBX6;P42694	.;.;HELZ_HUMAN	H	77	ENSP00000351524:D77H;ENSP00000411144:D77H	ENSP00000351524:D77H	D	-	1	0	HELZ	62642495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.757000	0.74924	2.260000	0.74910	0.539000	0.68188	GAT	.		0.284	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65212033	C	G	65212033	3	3	19	1	0	0	0	0	1	0	0	0	7070	826	29	4	5715	4	HELZ	17	65212033	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	16583522	65212033	15983177	72	1652											
FADS6	283985	hgsc.bcm.edu	37	chr17	72878831	72878831	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgtgctctgcagtgaaggCtgtgcacacctagaggaggg	8	7	17	9	1	1	2	0	1	1	1	1	3	1	3	1	4	3	4	1	4	2	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:72878831C>G	ENST00000310226.6	-	3	381	c.367G>C	c.(367-369)Gcc>Ccc	p.A123P		NM_178128.3	NP_835229.2	Q8N9I5	FADS6_HUMAN	fatty acid desaturase 6	129					fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|lung(4)	8	all_lung(278;0.172)|Lung NSC(278;0.207)					GCAGTGAAGGCTGTGCACACC	0.612																																					p.A123P		.											.	FADS6-22	0			c.G367C						.						55	58	57					17																	72878831		2175	4273	6448	SO:0001583	missense	283985	exon3			TGAAGGCTGTGCA	AK094411	CCDS54163.1	17q25.1	2014-07-17	2013-01-25			ENSG00000172782		"Fatty acid desaturases"	30459	protein-coding gene	gene with protein product			"fatty acid desaturase domain family, member 6"				Standard	XM_005257224		Approved		uc002jmd.1	Q8N9I5		ENST00000310226.6:c.367G>C	17.37:g.72878831C>G	ENSP00000307821:p.Ala123Pro	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_178128	0	0	0	0	0	Q17RQ7|Q6XYE1	Missense_Mutation	SNP	ENST00000310226.6	37	CCDS54163.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.03|16.03	3.006645|3.006645	0.54361|0.54361	.|.	.|.	ENSG00000172782|ENSG00000172782	ENST00000310226|ENST00000413142	T|.	0.17054|.	2.3|.	5.26|5.26	-3.94|-3.94	0.04130|0.04130	Fatty acid desaturase, type 1 (1);|.	0.512064|.	0.21539|.	N|.	0.072933|.	T|T	0.41627|0.41627	0.1167|0.1167	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	P|B	0.50819|0.02656	0.939|0.0	P|B	0.55455|0.04013	0.776|0.001	T|T	0.42565|0.42565	-0.9444|-0.9444	10|8	0.46703|0.54805	T|T	0.11|0.06	-26.0152|-26.0152	13.8207|13.8207	0.63318|0.63318	0.5539:0.386:0.0:0.0601|0.5539:0.386:0.0:0.0601	.|.	129|39	Q8N9I5|B4DEP0	FADS6_HUMAN|.	P|H	123|39	ENSP00000307821:A123P|.	ENSP00000307821:A123P|ENSP00000396743:Q39H	A|Q	-|-	1|3	0|2	FADS6|FADS6	70390426|70390426	0.059000|0.059000	0.20769|0.20769	0.064000|0.064000	0.19789|0.19789	0.030000|0.030000	0.12068|0.12068	0.551000|0.551000	0.23361|0.23361	-0.693000|-0.693000	0.05121|0.05121	-0.797000|-0.797000	0.03246|0.03246	GCC|CAG	.		0.612	FADS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445219.1			G	72878831	C	G	72878831	3	3	19	1	0	0	0	0	1	0	0	0	5384	797	28	4	701	4	FADS6	17	72878831	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	7666798	72878831	8316379	73	1653											
FOXK2	3607	hgsc.bcm.edu	37	chr17	80559303	80559303	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggatcaagacagaagacggCgagggcatcgtcattgccct	11	6	13	11	4	2	3	2	0	0	3	3	5	2	4	1	3	1	1	1	3	2	1	rs201366286		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:80559303C>A	ENST00000335255.5	+	9	2085	c.1911C>A	c.(1909-1911)ggC>ggA	p.G637G	FOXK2_ENST00000529652.1_3'UTR|RP13-638C3.4_ENST00000576912.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	637					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			CAGAAGACGGCGAGGGCATCG	0.607																																					p.G637G		.											.	FOXK2-226	0			c.C1911A						.						59	51	54					17																	80559303		2203	4300	6503	SO:0001819	synonymous_variant	3607	exon9			AGACGGCGAGGGC	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1911C>A	17.37:g.80559303C>A		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_004514	0	0	14	14	0	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			C|0.999;T|0.001		0.607	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		A	80559303	C	A	80559303	2	1	19	1	0	0	0	0	0	0	0	1	6034	755	27	4		4	FOXK2	17	80559303	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	7680472	80559303	635907	74	1654											
POTEC	388468	bcgsc.ca	37	chr18	14533088	14533088	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgactagaaacagcatactCtctggccgtctgtccagata	12	10	8	11	1	2	3	0	1	2	2	4	3	3	3	2	1	3	1	2	1	4	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr18:14533088C>T	ENST00000358970.5	-	5	1026	c.1027G>A	c.(1027-1029)Gag>Aag	p.E343K	POTEC_ENST00000389891.4_5'UTR|RNU6-1021P_ENST00000363262.1_RNA	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	343										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						ACAGCATACTCTCTGGCCGTC	0.353																																					p.E343K													.	POTEC-3	0			c.G1027A						.																																			SO:0001583	missense	388468	exon5			CATACTCTCTGGC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33894	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 6"		"ANKRD26-like family B, member 2"	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1027G>A	18.37:g.14533088C>T	ENSP00000351856:p.Glu343Lys	Somatic	308	0		WXS	Illumina HiSeq	Phase_1	400	49	NM_001137671	0	0	0	0	0		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	C	3.226	-0.158502	0.06544	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.63913	-0.07	1.09	1.09	0.20402	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.46464	0.1394	L	0.41415	1.275	0.09310	N	1	P	0.43938	0.822	B	0.37550	0.253	T	0.38045	-0.9679	9	0.52906	T	0.07	.	5.5934	0.17313	0.0:1.0:0.0:0.0	.	343	B2RU33	POTEC_HUMAN	K	343	ENSP00000351856:E343K	ENSP00000351856:E343K	E	-	1	0	POTEC	14523088	0.002000	0.14202	0.018000	0.16275	0.080000	0.17528	0.255000	0.18333	0.927000	0.37143	0.194000	0.17425	GAG	.		0.353	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		T	14533088	C	T	14533088	3	4	19	1	0	0	0	0	1	0	0	0	12288	922	32	2	629	2	POTEC	18	14533088	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		14533088	63544160	75	1655											
SBNO2	22904	hgsc.bcm.edu	37	chr19	1122146	1122146	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccagcaggatacgacgccctCgaaggcctccccacaccagt	10	4	9	18	3	0	0	0	0	0	0	2	3	1	1	6	2	2	1	6	2	2	1	rs192343149	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:1122146C>G	ENST00000361757.3	-	11	1378	c.1141G>C	c.(1141-1143)Gag>Cag	p.E381Q	SBNO2_ENST00000438103.2_Missense_Mutation_p.E324Q|SBNO2_ENST00000587024.1_Missense_Mutation_p.E381Q	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	381					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGACGCCCTCGAAGGCCTCC	0.677													C|||	4	0.000798722	8e-04	0.0014	5008	,	,		15103	0		0.002	False		,,,				2504	0				p.E381Q		.											.	.	0			c.G1141C						.	C	GLN/GLU,GLN/GLU	1,4079		0,1,2039	17	20	19		970,1141	3.5	0.9	19		19	22,8226		0,22,4102	yes	missense,missense	SBNO2	NM_001100122.1,NM_014963.2	29,29	0,23,6141	GG,GC,CC		0.2667,0.0245,0.1866	benign,benign	324/1310,381/1367	1122146	23,12305	2040	4124	6164	SO:0001583	missense	22904	exon11			CGCCCTCGAAGGC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.1141G>C	19.37:g.1122146C>G	ENSP00000354733:p.Glu381Gln	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	5	2	NM_014963	0	0	0	0	0	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	37	CCDS45894.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.33	3.806906	0.70797	2.45E-4	0.002667	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	D;D	0.93307	-3.2;-3.2	3.5	3.5	0.40072	.	0.056732	0.64402	D	0.000001	D	0.92296	0.7556	L	0.46157	1.445	0.45076	D	0.998091	P;B;P;P	0.42908	0.793;0.023;0.793;0.754	P;B;B;B	0.47075	0.536;0.08;0.433;0.306	D	0.93015	0.6435	10	0.59425	D	0.04	-18.1776	14.5373	0.67969	0.0:1.0:0.0:0.0	.	324;381;381;324	B4DL53;B4DV91;Q9Y2G9;Q9Y2G9-3	.;.;SBNO2_HUMAN;.	Q	381;324;405	ENSP00000354733:E381Q;ENSP00000400762:E324Q	ENSP00000250872:E405Q	E	-	1	0	SBNO2	1073146	1.000000	0.71417	0.932000	0.37286	0.907000	0.53573	7.439000	0.80444	1.939000	0.56221	0.561000	0.74099	GAG	C|0.999;G|0.001		0.677	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		G	1122146	C	G	1122146	3	3	19	1	0	0	0	0	1	0	0	0	13895	893	31	4	3047	4	SBNO2	19	1122146	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		1122146	58006837	76	1656											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2193778	2193778	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacatcccggccaagtatgCggaggtgagcggatctgagg	10	6	16	9	3	1	3	0	2	1	1	2	5	2	5	2	5	2	1	2	5	2	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:2193778C>T	ENST00000398665.3	+	6	620	c.584C>T	c.(583-585)gCg>gTg	p.A195V		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	195	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCAAGTATGCGGAGGTGAGC	0.607																																					p.A195V		.											.	DOT1L-132	0			c.C584T						.						87	90	89					19																	2193778		2179	4268	6447	SO:0001583	missense	84444	exon6			AGTATGCGGAGGT	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.584C>T	19.37:g.2193778C>T	ENSP00000381657:p.Ala195Val	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_032482	0	0	0	0	0	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817061	0.90790	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.37235	1.21;1.21	4.34	4.34	0.51931	.	0.112447	0.64402	D	0.000012	T	0.68329	0.2989	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.78375	-0.2228	10	0.87932	D	0	-11.0759	15.988	0.80176	0.0:1.0:0.0:0.0	.	195	Q8TEK3-2	.	V	195;195;171	ENSP00000381657:A195V;ENSP00000404284:A171V	ENSP00000221482:A195V	A	+	2	0	DOT1L	2144778	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.528000	0.67129	2.249000	0.74217	0.561000	0.74099	GCG	.		0.607	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2193778	C	T	2193778	3	4	19	1	0	0	0	0	1	0	0	0	4720	768	27	1	606	1	DOT1L	19	2193778	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	1071632	2193778	56935205	77	1657											
PTPRS	5802	hgsc.bcm.edu	37	chr19	5220167	5220167	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagatgtcctggatgagcTgcgggaacagagtcatgggt	9	9	17	6	1	1	3	1	2	0	2	2	6	2	5	1	3	3	1	1	3	1	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:5220167T>A	ENST00000587303.1	-	21	3649		c.e21-2		PTPRS_ENST00000372412.4_Splice_Site|PTPRS_ENST00000353284.2_Splice_Site|PTPRS_ENST00000357368.4_Splice_Site|PTPRS_ENST00000592099.1_Splice_Site|PTPRS_ENST00000588012.1_Splice_Site|PTPRS_ENST00000262963.6_Splice_Site|PTPRS_ENST00000588552.1_Splice_Site|PTPRS_ENST00000348075.2_Splice_Site			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S						cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	CTGGATGAGCTGCGGGAACAG	0.632																																					.		.											.	PTPRS-357	0			c.3550-2A>T						.						25	27	26					19																	5220167		2203	4300	6503	SO:0001630	splice_region_variant	5802	exon23			ATGAGCTGCGGGA	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.3550-2A>T	19.37:g.5220167T>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_002850	0	0	0	0	0	O75255|O75870|Q15718|Q16341|Q2M3R7	Splice_Site	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.150456	0.57151	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	.	.	.	3.75	3.75	0.43078	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6563	0.56790	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTPRS	5171167	1.000000	0.71417	0.947000	0.38551	0.648000	0.38561	6.953000	0.75995	1.583000	0.49898	0.533000	0.62120	.	.		0.632	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		Intron	A	5220167	T	A	5220167	5	1	19	1	0	0	0	0	0	0	1	0	12843	1594	55	5	2366	5	PTPRS	19	5220167	Splice_Site	SNP	T	TCGA-A4-8518-01A-11D-2396-08	3026389	5220167	53908816	78	1658											
DNMT1	1786	bcgsc.ca	37	chr19	10270719	10270719	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcatgactgttttggcgCgagccatttttttctccgtt	5	18	9	9	3	2	1	1	1	1	0	3	2	2	1	2	1	1	3	2	1	0	7	rs201945078		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:10270719C>G	ENST00000340748.4	-	14	1251	c.1016G>C	c.(1015-1017)cGc>cCc	p.R339P	DNMT1_ENST00000359526.4_Missense_Mutation_p.R355P|DNMT1_ENST00000540357.1_Missense_Mutation_p.R339P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	339	DNA replication foci-targeting sequence. {ECO:0000250}.|Homodimerization.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R339P(2)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	TGTTTTGGCGCGAGCCATTTT	0.478																																					p.R355P													.	DNMT1-660	2	Substitution - Missense(2)	prostate(2)	c.G1064C						.						66	78	74					19																	10270719		2202	4300	6502	SO:0001583	missense	1786	exon15			TTGGCGCGAGCCA	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1016G>C	19.37:g.10270719C>G	ENSP00000345739:p.Arg339Pro	Somatic	186	1		WXS	Illumina HiSeq	Phase_1	133	29	NM_001130823	0	0	5	5	0	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525134	0.27299	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.80393	-1.37;1.54;1.54	3.95	0.695	0.18070	.	0.911290	0.09314	N	0.819141	T	0.64638	0.2616	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.001;0.004;0.0	T	0.47787	-0.9090	10	0.25106	T	0.35	.	5.6138	0.17420	0.0:0.639:0.0:0.361	.	339;355;339	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	P	355;339;339;207	ENSP00000352516:R355P;ENSP00000440457:R339P;ENSP00000345739:R339P	ENSP00000345739:R339P	R	-	2	0	DNMT1	10131719	0.095000	0.21747	0.032000	0.17829	0.368000	0.29767	0.288000	0.18939	0.251000	0.21505	0.650000	0.86243	CGC	.		0.478	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		G	10270719	C	G	10270719	3	3	19	1	0	0	0	0	1	0	0	0	4686	768	27	4	3942	4	DNMT1	19	10270719	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	5050552	10270719	48858264	79	1659											
CDC37	11140	bcgsc.ca	37	chr19	10506724	10506724	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgcgcagctgctgtgcctcGgcctgcaggcgctccagctc	3	9	13	16	3	0	0	0	0	0	0	3	0	1	0	3	2	6	6	3	2	0	1	rs140896014	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:10506724G>C	ENST00000222005.2	-	2	311	c.258C>G	c.(256-258)gcC>gcG	p.A86A		NM_007065.3	NP_008996.1	Q16543	CDC37_HUMAN	cell division cycle 37	86					protein targeting (GO:0006605)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	16			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		GCTGTGCCTCGGCCTGCAGGC	0.657																																					p.A86A													.	CDC37-522	0			c.C258G						.						104	98	100					19																	10506724		2203	4300	6503	SO:0001819	synonymous_variant	11140	exon2			TGCCTCGGCCTGC	U63131	CCDS12237.1	19p13.2	2013-01-17	2013-01-17		ENSG00000105401	ENSG00000105401			1735	protein-coding gene	gene with protein product	"CDC37 cell division cycle 37 homolog", "Hsp90 co-chaperone Cdc37", "CDC37 (cell division cycle 37, S. cerevisiae, homolog)"	605065	"CDC37 (cell division cycle 37, S. cerevisiae, homolog)", "CDC37 cell division cycle 37 homolog (S. cerevisiae)", "cell division cycle 37 homolog (S. cerevisiae)"			8703009, 8666233	Standard	NM_007065		Approved	P50CDC37	uc002mof.1	Q16543		ENST00000222005.2:c.258C>G	19.37:g.10506724G>C		Somatic	222	1		WXS	Illumina HiSeq	Phase_1	170	50	NM_007065	0	0	81	82	1	Q53YA2	Silent	SNP	ENST00000222005.2	37	CCDS12237.1																																																																																			G|0.999;A|0.001		0.657	CDC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451987.1	NM_007065		C	10506724	G	C	10506724	2	2	19	1	0	0	0	0	0	0	0	1	3074	1103	39	4		4	CDC37	19	10506724	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08	236005	10506724	48622259	80	1660											
C19orf44	84167	bcgsc.ca	37	chr19	16614154	16614154	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaggctgagactgtggaCgagccagtctcagaaggtgc	10	7	16	8	1	1	3	1	2	1	2	2	6	1	4	1	3	2	1	1	3	1	0	rs202132782		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:16614154C>G	ENST00000221671.3	+	3	1194	c.1038C>G	c.(1036-1038)gaC>gaG	p.D346E	CTD-3222D19.2_ENST00000409035.1_Intron|C19orf44_ENST00000594035.1_Missense_Mutation_p.D346E	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	346										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						AGACTGTGGACGAGCCAGTCT	0.557																																					p.D346E													.	C19orf44-90	0			c.C1038G						.						56	56	56					19																	16614154		2203	4300	6503	SO:0001583	missense	84167	exon3			TGTGGACGAGCCA	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.1038C>G	19.37:g.16614154C>G	ENSP00000221671:p.Asp346Glu	Somatic	115	2		WXS	Illumina HiSeq	Phase_1	67	30	NM_032207	0	0	1	1	0	Q8N6Y7	Missense_Mutation	SNP	ENST00000221671.3	37	CCDS12345.1	.	.	.	.	.	.	.	.	.	.	C	0.379	-0.929661	0.02359	.	.	ENSG00000105072	ENST00000221671	.	.	.	4.66	-9.33	0.00639	.	0.774565	0.11603	N	0.547535	T	0.12475	0.0303	N	0.21097	0.63	0.09310	N	1	B;B;B	0.19583	0.017;0.037;0.033	B;B;B	0.20384	0.016;0.019;0.029	T	0.34900	-0.9810	9	0.02654	T	1	0.0565	2.6963	0.05136	0.1427:0.2354:0.1275:0.4944	.	346;19;346	Q9H6X5;B4DN63;Q9H6X5-2	CS044_HUMAN;.;.	E	346	.	ENSP00000221671:D346E	D	+	3	2	C19orf44	16475154	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.817000	0.00751	-2.754000	0.00373	-2.167000	0.00324	GAC	.		0.557	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		G	16614154	C	G	16614154	3	3	19	1	0	0	0	0	1	0	0	0	1933	535	19	4	1044	4	C19orf44	19	16614154	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	6107430	16614154	42514829	81	1661											
GDF15	9518	bcgsc.ca	37	chr19	18499106	18499106	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcccacagtgcggctgggAtccggcggccacctgcacct	5	7	12	17	3	0	0	0	0	0	0	2	1	2	1	5	4	2	2	5	4	0	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:18499106A>G	ENST00000252809.3	+	2	320	c.288A>G	c.(286-288)ggA>ggG	p.G96G	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	96					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						TGCGGCTGGGATCCGGCGGCC	0.667											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G96G													.	GDF15-650	0			c.A288G						.						20	24	23					19																	18499106		2178	4275	6453	SO:0001819	synonymous_variant	9518	exon2			GCTGGGATCCGGC	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.288A>G	19.37:g.18499106A>G		Somatic	96	0	726	WXS	Illumina HiSeq	Phase_1	55	13	NM_004864	0	0	1	1	0	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																			.		0.667	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		G	18499106	A	G	18499106	2	3	19	1	0	0	0	0	0	0	0	1	6333	320	12	3		3	GDF15	19	18499106	Silent	SNP	A	TCGA-A4-8518-01A-11D-2396-08	1884952	18499106	40629877	82	1662											
PHLDB3	653583	hgsc.bcm.edu	37	chr19	43991217	43991217	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcggggggatcctctctggCtccccctctccccccttttc	1	12	9	19	1	2	0	0	0	2	0	8	1	4	1	6	4	0	1	6	4	0	2	rs138387298	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:43991217C>T	ENST00000292140.5	-	10	1568	c.1208G>A	c.(1207-1209)aGc>aAc	p.S403N		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	403							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				TCCTCTCTGGCTCCCCCTCTC	0.582													C|||	28	0.00559105	0	0.0058	5008	,	,		15086	0		0.004	False		,,,				2504	0.0204				p.S403N		.											.	PHLDB3-68	0			c.G1208A						.	C	ASN/SER	5,3761		0,5,1878	13	15	14		1208	2.2	0.6	19	dbSNP_134	14	58,8136		0,58,4039	yes	missense	PHLDB3	NM_198850.3	46	0,63,5917	TT,TC,CC		0.7078,0.1328,0.5268	possibly-damaging	403/641	43991217	63,11897	1883	4097	5980	SO:0001583	missense	653583	exon10			CTCTGGCTCCCCC		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"Pleckstrin homology (PH) domain containing"	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1208G>A	19.37:g.43991217C>T	ENSP00000292140:p.Ser403Asn	Somatic	3	2		WXS	Illumina HiSeq	Phase_I	11	4	NM_198850	0	0	0	0	0	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	11.07	1.530742	0.27387	0.001328	0.007078	ENSG00000176531	ENST00000292140	T	0.46819	0.86	4.47	2.25	0.28309	.	.	.	.	.	T	0.25938	0.0632	L	0.29908	0.895	0.09310	N	0.999999	B;B	0.31318	0.319;0.01	B;B	0.31751	0.135;0.002	T	0.20174	-1.0283	9	0.56958	D	0.05	.	6.1303	0.20201	0.0:0.703:0.1911:0.1059	.	107;403	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	N	403	ENSP00000292140:S403N	ENSP00000292140:S403N	S	-	2	0	PHLDB3	48683057	0.980000	0.34600	0.609000	0.28983	0.559000	0.35586	1.647000	0.37260	0.421000	0.25980	0.281000	0.19383	AGC	C|0.997;T|0.003		0.582	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			T	43991217	C	T	43991217	3	4	19	1	0	0	0	0	1	0	0	0	11879	797	28	2	742	2	PHLDB3	19	43991217	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	25492111	43991217	15137766	83	1663											
PVRL2	5819	bcgsc.ca	37	chr19	45381871	45381871	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcacggcgggcagtttaTgtgtgacctggacacagaca	10	9	12	10	2	1	2	1	1	1	1	2	3	1	3	1	3	0	2	1	3	1	2	rs199691943		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:45381871T>C	ENST00000252483.5	+	6	1042				PVRL2_ENST00000252485.4_Silent_p.Y478Y	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)						acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		GGGCAGTTTATGTGTGACCTG	0.627																																					p.Y478Y													.	PVRL2-90	0			c.T1434C						.						42	40	40					19																	45381871		2203	4297	6500	SO:0001627	intron_variant	5819	exon6			AGTTTATGTGTGA	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1043-3597T>C	19.37:g.45381871T>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_1	74	5	NM_002856	0	0	29	29	0	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			T|0.999;C|0.001		0.627	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		C	45381871	T	C	45381871	1	2	19	0	1	0	0	0	0	0	0	0	12872	1471	51	3		3	PVRL2	19	45381871	Intron	SNP	T	TCGA-A4-8518-01A-11D-2396-08	1390654	45381871	13747112	84	1664											
AP2A1	160	broad.mit.edu	37	chr19	50305818	50305818	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gagccgcctgcccccgagagCcccatggctttgctggctga	5	7	13	16	2	0	2	0	1	0	1	0	4	0	2	6	2	4	3	6	2	0	1	rs200480269	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:50305818C>T	ENST00000359032.5	+	16	2142	c.2142C>T	c.(2140-2142)agC>agT	p.S714S	AP2A1_ENST00000354293.5_Intron	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	714					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		CCCCCGAGAGCCCCATGGCTT	0.667													C|||	3	0.000599042	0	0.0029	5008	,	,		10699	0		0	False		,,,				2504	0.001				p.S714S													.	AP2A1-92	0			c.C2142T						.	C	,	1,3771		0,1,1885	13	14	14		2142,	5.1	1	19		14	13,8155		0,13,4071	no	coding-synonymous,intron	AP2A1	NM_014203.2,NM_130787.2	,	0,14,5956	TT,TC,CC		0.1592,0.0265,0.1173	,	714/978,	50305818	14,11926	1886	4084	5970	SO:0001819	synonymous_variant	160	exon16			CGAGAGCCCCATG	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.2142C>T	19.37:g.50305818C>T		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_014203	0	0	0	0	0	Q96CI7|Q96PP6|Q96PP7|Q9H070	Silent	SNP	ENST00000359032.5	37	CCDS46148.1																																																																																			C|1.000;T|0.000		0.667	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			T	50305818	C	T	50305818	2	4	19	1	0	0	0	0	0	0	0	1	739	738	26	2		2	AP2A1	19	50305818	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	4923947	50305818	8823165	85	1665											
PTPRT	11122	bcgsc.ca	37	chr20	40710579	40710579	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttcacgatgtggaacacGtcaatgatgttttgctgctg	8	15	11	7	2	2	1	2	1	0	0	2	3	2	2	0	1	3	4	0	1	2	4			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr20:40710579G>A	ENST00000373187.1	-	30	4214	c.4215C>T	c.(4213-4215)gaC>gaT	p.D1405D	PTPRT_ENST00000356100.2_Silent_p.D1414D|PTPRT_ENST00000373193.3_Silent_p.D1408D|PTPRT_ENST00000373184.1_Silent_p.D1415D|PTPRT_ENST00000373201.1_Silent_p.D1395D|PTPRT_ENST00000373190.1_Silent_p.D1404D|PTPRT_ENST00000373198.4_Silent_p.D1424D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1405	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGTGGAACACGTCAATGATGT	0.498																																					p.D1424D													.	PTPRT-664	0			c.C4272T						.						185	184	184					20																	40710579		2110	4236	6346	SO:0001819	synonymous_variant	11122	exon31			GAACACGTCAATG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.4215C>T	20.37:g.40710579G>A		Somatic	88	1		WXS	Illumina HiSeq	Phase_1	145	7	NM_133170	0	0	0	0	0	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			.		0.498	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40710579	G	A	40710579	2	1	19	1	0	0	0	0	0	0	0	1	12844	1136	40	1		1	PTPRT	20	40710579	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08		40710579	22314941	86	1666											
KCNE2	9992	hgsc.bcm.edu	37	chr21	35743147	35743147	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggttcaaaatgtcccccTgataagggagaaaggcacca	13	7	11	10	0	1	2	1	1	0	1	2	3	2	2	3	3	0	2	3	3	4	2	rs45610936		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr21:35743147T>C	ENST00000290310.3	+	2	510	c.370T>C	c.(370-372)Tga>Cga	p.*124R	AP000320.6_ENST00000440403.1_RNA	NM_172201.1	NP_751951.1	Q9Y6J6	KCNE2_HUMAN	potassium voltage-gated channel, Isk-related family, member 2	0					aging (GO:0007568)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular protein localization (GO:0034613)|cellular response to drug (GO:0035690)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|positive regulation of proteasomal protein catabolic process (GO:1901800)|potassium ion export (GO:0071435)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of cyclic nucleotide-gated ion channel activity (GO:1902159)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of inward rectifier potassium channel activity (GO:1901979)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|tongue development (GO:0043586)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|large_intestine(1)	2						AATGTCCCCCTGATAAGGGAG	0.473																																					p.X124R		.											.	KCNE2-68	0			c.T370C						.						36	33	34					21																	35743147		2203	4300	6503	SO:0001578	stop_lost	9992	exon2			TCCCCCTGATAAG	AF071002	CCDS13635.1	21q22.1	2014-09-17			ENSG00000159197	ENSG00000159197		"Potassium channels"	6242	protein-coding gene	gene with protein product		603796				10219239	Standard	NM_172201		Approved	MiRP1, LQT6	uc002ytt.1	Q9Y6J6	OTTHUMG00000086189	ENST00000290310.3:c.370T>C	21.37:g.35743147T>C	ENSP00000290310:p.*124Argext*1	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_172201	0	0	2	2	0	A5H1P3|D3DSF8|Q52LJ5	Missense_Mutation	SNP	ENST00000290310.3	37	CCDS13635.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869146	0.72065	.	.	ENSG00000159197	ENST00000290310	.	.	.	5.63	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7923	0.18367	0.0:0.0866:0.2254:0.6879	.	.	.	.	R	124	.	.	X	+	1	0	KCNE2	34665017	0.960000	0.32886	0.792000	0.32020	0.672000	0.39443	1.194000	0.32174	2.143000	0.66587	0.529000	0.55759	TGA	.		0.473	KCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194068.2			C	35743147	T	C	35743147	4	2	19	1	0	0	0	0	0	0	0	0	8044	1593	55	3	372	3	KCNE2	21	35743147	Nonstop_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08		35743147	12386748	87	1667											
BAIAP2L2	80115	ucsc.edu	37	chr22	38483204	38483204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaggtcatgggggtcaCgggggtcatgggattcacgg	7	8	19	7	2	4	0	4	0	0	0	4	2	4	2	0	8	0	0	0	8	0	1	rs201090429	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr22:38483204C>T	ENST00000381669.3	-	11	1330	c.1186G>A	c.(1186-1188)Gtg>Atg	p.V396M	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	396					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					atgggggtcacgggggtcatg	0.627													C|||	25	0.00499201	0.0068	0	5008	,	,		13610	0.003		0.005	False		,,,				2504	0.0082				p.V396M													.	BAIAP2L2-91	0			c.G1186A						.						37	45	42					22																	38483204		1928	4122	6050	SO:0001583	missense	80115	exon11			GGGTCACGGGGGT	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1186G>A	22.37:g.38483204C>T	ENSP00000371085:p.Val396Met	Somatic	65	0		WXS	Illumina HiSeq		43	1	NM_025045	0	0	31	31	0	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	.	.	.	.	.	.	.	.	.	.	C	7.609	0.674489	0.14841	.	.	ENSG00000128298	ENST00000381669;ENST00000402500;ENST00000428572	T;T	0.21932	1.98;1.98	3.32	-3.36	0.04913	.	1.502590	0.04754	N	0.425150	T	0.11110	0.0271	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33240	-0.9876	10	0.45353	T	0.12	-10.8299	4.4703	0.11708	0.2523:0.4451:0.0:0.3026	.	396	Q6UXY1	BI2L2_HUMAN	M	396;396;87	ENSP00000371085:V396M;ENSP00000410074:V87M	ENSP00000371085:V396M	V	-	1	0	BAIAP2L2	36813150	.	.	0.275000	0.24674	0.069000	0.16628	.	.	-0.339000	0.08401	-1.449000	0.01048	GTG	C|0.997;T|0.003		0.627	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		T	38483204	C	T	38483204	3	4	19	1	0	0	0	0	1	0	0	0	1304	536	19	1	419	1	BAIAP2L2	22	38483204	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		38483204	12821362	88	1668											
PCDH19	57526	hgsc.bcm.edu	37	chrX	99661616	99661616	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcgagagcaggggacaagtaGattaggacgagagcagaggc	14	4	17	6	2	0	4	0	0	0	4	1	8	0	6	0	4	2	3	0	4	3	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chrX:99661616G>C	ENST00000373034.4	-	1	3655	c.1980C>G	c.(1978-1980)atC>atG	p.I660M	PCDH19_ENST00000255531.7_Missense_Mutation_p.I660M|PCDH19_ENST00000420881.2_Missense_Mutation_p.I660M	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	660	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GGGACAAGTAGATTAGGACGA	0.547																																					p.I660M		.											.	PCDH19-110	0			c.C1980G						.						67	66	66					X																	99661616		2065	4185	6250	SO:0001583	missense	57526	exon1			CAAGTAGATTAGG	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"Cadherins / Protocadherins : Non-clustered"	14270	protein-coding gene	gene with protein product		300460	"epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1980C>G	X.37:g.99661616G>C	ENSP00000362125:p.Ile660Met	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_001184880	0	0	0	0	0	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	8.605	0.887772	0.17540	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.68025	-0.3;-0.3;-0.3	5.84	4.06	0.47325	Cadherin (4);Cadherin-like (1);	0.185233	0.49305	D	0.000142	D	0.83257	0.5215	M	0.88979	2.995	0.51767	D	0.99993	D;D;D	0.60575	0.988;0.973;0.979	D;P;D	0.63703	0.917;0.859;0.913	D	0.85025	0.0914	10	0.66056	D	0.02	.	16.0391	0.80651	0.0:0.0:0.602:0.398	.	660;660;660	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	M	660	ENSP00000400327:I660M;ENSP00000362125:I660M;ENSP00000255531:I660M	ENSP00000255531:I660M	I	-	3	3	PCDH19	99548272	1.000000	0.71417	0.985000	0.45067	0.678000	0.39670	0.814000	0.27239	0.223000	0.20920	-1.471000	0.01009	ATC	.		0.547	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		C	99661616	G	C	99661616	3	2	19	1	0	0	0	0	1	0	0	0	11540	932	33	4	1490	4	PCDH19	23	99661616	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08		99661616	55608944	89	1669											
KCNE1L	23630	bcgsc.ca	37	chrX	108868162	108868163	+	Missense_Mutation	DNP	CC	CC	AA																															gctgggacgagggccagcgcCcaagccgctggcattacccc																								rs200894798		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	CC	CC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chrX:108868162_108868163CC>AA	ENST00000372101.2	-	1	230_231	c.87_88GG>TT	c.(85-90)ttGGgc>ttTTgc	p.29_30LG>FC		NM_012282.2	NP_036414.1	Q9UJ90	KCE1L_HUMAN	KCNE1-like	29					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						GGGCCAGCGCCCAAGCCGCTGG	0.663																																					p.LG29FC													.	KCNE1L-130	0			c.G87T						.																																			SO:0001583	missense	23630	exon1			AGCGCCCAAGCCG	AJ012743	CCDS14547.1	Xq22.3	2008-02-05	2004-06-09		ENSG00000176076	ENSG00000176076		"Potassium channels"	6241	protein-coding gene	gene with protein product		300328	"potassium voltage-gated channel, Isk-related family, member 1-like"			10493825	Standard	NM_012282		Approved		uc004eoh.3	Q9UJ90	OTTHUMG00000022189	ENST00000372101.2:c.87_88delinsAA	X.37:g.108868162_108868163delinsAA	ENSP00000361173:p.L29_G30delinsFC	Somatic	34	4		WXS	Illumina HiSeq	Phase_1	12	8	NM_012282	0	0	0	0	0		Missense_Mutation	DNP	ENST00000372101.2	37	CCDS14547.1																																																																																			.		0.663	KCNE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057892.1	NM_012282		AA	108868163	CC	AA	108868162	3	1	19	1	0	0	0	0	1	0	0	0	8043	623	22	4	344	4	KCNE1L	23	108868162	Missense_Mutation	DNP	CC	TCGA-A4-8518-01A-11D-2396-08	9206546	108868162	46402398	90	1670											
PRRG3	79057	hgsc.bcm.edu	37	chrX	150869296	150869296	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggtgctggggcccagtCgggggggcaggaccacagtc	6	5	20	10	1	0	0	0	0	0	0	2	1	0	1	2	8	1	2	2	8	0	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chrX:150869296C>A	ENST00000370353.3	+	4	877	c.487C>A	c.(487-489)Cgg>Agg	p.R163R	PRRG3_ENST00000538575.1_Silent_p.R163R			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	163						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGCCCAGTCGGGGGGGCAG	0.672																																					p.R163R		.											.	PRRG3-134	0			c.C487A						.						30	28	29					X																	150869296		2202	4298	6500	SO:0001819	synonymous_variant	79057	exon4			CCCAGTCGGGGGG	AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.487C>A	X.37:g.150869296C>A		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_024082	0	0	0	0	0	A1A523|A1A575|Q8N2N6	Silent	SNP	ENST00000370353.3	37	CCDS14699.1																																																																																			.		0.672	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	NM_024082		A	150869296	C	A	150869296	2	1	19	1	0	0	0	0	0	0	0	1	12636	875	31	4		4	PRRG3	23	150869296	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	42001134	150869296	4401264	91	1671											
FATE1	89885	bcgsc.ca	37	chrX	150891105	150891105	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgactcctctgcagctgtaTgcagtcaaccggcgtctgcg	6	11	11	13	3	3	1	1	1	2	0	4	1	4	1	2	1	5	4	2	1	2	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chrX:150891105T>G	ENST00000370350.3	+	5	511	c.426T>G	c.(424-426)taT>taG	p.Y142*		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	142						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					TGCAGCTGTATGCAGTCAACC	0.612																																					p.Y142X													.	FATE1-131	0			c.T426G						.						57	64	62					X																	150891105		2203	4298	6501	SO:0001587	stop_gained	89885	exon5			GCTGTATGCAGTC	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.426T>G	X.37:g.150891105T>G	ENSP00000359375:p.Tyr142*	Somatic	82	0		WXS	Illumina HiSeq	Phase_1	98	4	NM_033085	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000370350.3	37	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.329167	0.24167	.	.	ENSG00000147378	ENST00000370350	.	.	.	4.55	-9.11	0.00711	.	2.770910	0.01081	N	0.004990	.	.	.	.	.	.	0.54753	D	0.99998	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	11.7727	2.708	0.05166	0.2388:0.3595:0.2921:0.1096	.	.	.	.	X	142	.	ENSP00000359375:Y142X	Y	+	3	2	FATE1	150641761	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.221000	0.00140	-4.843000	0.00030	-1.019000	0.02448	TAT	.		0.612	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085		G	150891105	T	G	150891105	4	3	19	1	0	0	0	0	0	1	0	0	5712	1471	51	5	444	5	FATE1	23	150891105	Nonsense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	21809	150891105	4379455	92	1672											
SSU72	29101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1480325	1480325	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagttctggaatctttctggCcggggcttgattctcttatt	5	17	10	9	1	4	1	0	1	4	0	5	2	4	2	1	4	0	2	1	4	2	6	rs138912153		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:1480325C>T	ENST00000291386.3	-	3	593	c.282G>A	c.(280-282)cgG>cgA	p.R94R		NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	94					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		ATCTTTCTGGCCGGGGCTTGA	0.478																																					p.R94R		.											.	SSU72-90	0			c.G282A						.						183	192	189					1																	1480325		2203	4300	6503	SO:0001819	synonymous_variant	29101	exon3			TTCTGGCCGGGGC	AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075			25016	protein-coding gene	gene with protein product			"Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)"			15125841, 15659578	Standard	NM_014188		Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.282G>A	1.37:g.1480325C>T		Somatic	265	0		WXS	Illumina HiSeq	Phase_I	197	71	NM_014188	0	0	100	166	66	Q9BZS6|Q9H933	Silent	SNP	ENST00000291386.3	37	CCDS32.1																																																																																			C|1.000;A|0.000		0.478	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001366.1	NM_014188		T	1480325	C	T	1480325	2	4	20	1	0	0	0	0	0	0	0	1	15234	726	26	2		2	SSU72	1	1480325	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08		1480325	247770296	1	1673											
TMEM52	339456	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1849335	1849335	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctccttcaaggggcaccagGgctacaaggtggtagttgag	9	8	14	10	0	1	1	1	1	0	0	2	1	2	1	3	5	1	4	3	5	4	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:1849335G>T	ENST00000310991.3	-	5	623	c.616C>A	c.(616-618)Cct>Act	p.P206T	TMEM52_ENST00000378602.3_Missense_Mutation_p.P191T	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	206						integral component of membrane (GO:0016021)				NS(1)|prostate(1)|stomach(1)	3	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGGGCACCAGGGCTACAAGGT	0.617																																					p.P206T		.											.	TMEM52-68	0			c.C616A						.						94	106	102					1																	1849335		2203	4300	6503	SO:0001583	missense	339456	exon5			CACCAGGGCTACA	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.616C>A	1.37:g.1849335G>T	ENSP00000311122:p.Pro206Thr	Somatic	165	1		WXS	Illumina HiSeq	Phase_I	150	53	NM_178545	0	0	1	4	3	Q4VXS6|Q6UX25	Missense_Mutation	SNP	ENST00000310991.3	37	CCDS35.1	.	.	.	.	.	.	.	.	.	.	.	14.32	2.500213	0.44455	.	.	ENSG00000178821	ENST00000378602;ENST00000310991	T;T	0.38560	1.13;1.34	3.67	1.68	0.24146	.	1.510860	0.05074	N	0.482172	T	0.23330	0.0564	N	0.08118	0	0.09310	N	1	B;B	0.30709	0.035;0.291	B;B	0.26693	0.017;0.072	T	0.25467	-1.0131	10	0.87932	D	0	1.4905	4.9634	0.14078	0.118:0.0:0.6558:0.2262	.	206;191	Q8NDY8;Q8NDY8-2	TMM52_HUMAN;.	T	191;206	ENSP00000367865:P191T;ENSP00000311122:P206T	ENSP00000311122:P206T	P	-	1	0	TMEM52	1839195	0.047000	0.20315	0.006000	0.13384	0.013000	0.08279	0.367000	0.20382	0.273000	0.22049	-1.334000	0.01262	CCT	.		0.617	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545		T	1849335	G	T	1849335	3	4	20	1	0	0	0	0	1	0	0	0	16210	1232	43	4	17	4	TMEM52	1	1849335	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	369010	1849335	247401286	2	1674											
CELA3B	23436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22310247	22310247	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgggagacgccgtccagctCgcctcactccctccggctgg	4	7	12	18	4	1	1	1	0	0	1	5	2	4	1	5	3	1	2	5	3	0	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:22310247C>T	ENST00000337107.6	+	5	442	c.423C>T	c.(421-423)ctC>ctT	p.L141L		NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	141	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CCGTCCAGCTCGCCTCACTCC	0.632																																					p.L141L		.											.	CELA3B-91	0			c.C423T						.						96	77	83					1																	22310247		2203	4300	6503	SO:0001819	synonymous_variant	23436	exon5			CCAGCTCGCCTCA	M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"proteinase E", "elastase 1", "cholesterol-binding pancreatic protease", "pancreatic endopeptidase E"		"elastase 3B, pancreatic"	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.423C>T	1.37:g.22310247C>T		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	119	38	NM_007352	0	0	0	0	0	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Silent	SNP	ENST00000337107.6	37	CCDS219.1																																																																																			.		0.632	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		T	22310247	C	T	22310247	2	4	20	1	0	0	0	0	0	0	0	1	3220	871	31	1		1	CELA3B	1	22310247	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	20460912	22310247	226940374	3	1675											
ASAP3	55616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	23759922	23759922	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggctgggacccaccttcTcttcctcatcctcctcactg	5	11	7	18	0	3	0	2	0	1	0	7	1	6	1	5	2	0	1	5	2	0	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:23759922T>A	ENST00000336689.3	-	21	2167	c.2123A>T	c.(2122-2124)gAg>gTg	p.E708V	ASAP3_ENST00000437606.2_Missense_Mutation_p.E699V|ASAP3_ENST00000495646.1_Missense_Mutation_p.E212V	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	708					cell migration (GO:0016477)|positive regulation of ARF GTPase activity (GO:0032850)|regulation of stress fiber assembly (GO:0051492)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	24						ACCCACCTTCTCTTCCTCATC	0.622																																					p.E708V		.											.	ASAP3-155	0			c.A2123T						.						73	72	72					1																	23759922		2203	4300	6503	SO:0001583	missense	55616	exon21			ACCTTCTCTTCCT	AK000206	CCDS235.1, CCDS44087.1	1p36.13	2013-01-10	2008-10-09	2008-09-22	ENSG00000088280	ENSG00000088280		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	14987	protein-coding gene	gene with protein product	"centaurin, beta 6"		"development and differentiation enhancing factor-like 1"	DDEFL1		14654939	Standard	NM_017707		Approved	FLJ20199, UPLC1, CENTB6	uc001bha.2	Q8TDY4	OTTHUMG00000003234	ENST00000336689.3:c.2123A>T	1.37:g.23759922T>A	ENSP00000338769:p.Glu708Val	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	90	47	NM_017707	0	0	1	2	1	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	37	CCDS235.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.453556	0.84209	.	.	ENSG00000088280	ENST00000538685;ENST00000495646;ENST00000336689;ENST00000465372;ENST00000437606	T;T;T	0.56941	1.77;0.43;0.43	4.69	4.69	0.59074	.	3.712730	0.00567	N	0.000291	T	0.65228	0.2671	L	0.27053	0.805	0.58432	D	0.999999	D;D;D;D	0.76494	0.996;0.996;0.981;0.999	P;D;P;P	0.65874	0.892;0.939;0.77;0.905	T	0.50215	-0.8854	10	0.72032	D	0.01	.	13.4102	0.60938	0.0:0.0:0.0:1.0	.	699;577;231;708	Q8TDY4-3;B4DRP2;Q9NXH7;Q8TDY4	.;.;.;ASAP3_HUMAN	V	231;212;708;35;699	ENSP00000436150:E212V;ENSP00000338769:E708V;ENSP00000408826:E699V	ENSP00000338769:E708V	E	-	2	0	ASAP3	23632509	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.415000	0.80131	2.104000	0.64026	0.459000	0.35465	GAG	.		0.622	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		A	23759922	T	A	23759922	3	1	20	1	0	0	0	0	1	0	0	0	1013	1551	54	5	608	5	ASAP3	1	23759922	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	1449675	23759922	225490699	4	1676											
CSMD2	114784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	33985175	33985175	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcgctggccatgatgtcTgtgggctggatgttgcggtc	3	12	16	10	2	1	1	0	1	1	0	3	2	1	2	2	4	1	3	2	4	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:33985175T>A	ENST00000373381.4	-	70	11015	c.10839A>T	c.(10837-10839)acA>acT	p.T3613T		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3469						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CCATGATGTCTGTGGGCTGGA	0.592																																					p.T3469T		.											.	CSMD2-103	0			c.A10407T						.						287	241	256					1																	33985175		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon69			GATGTCTGTGGGC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.10839A>T	1.37:g.33985175T>A		Somatic	330	0		WXS	Illumina HiSeq	Phase_I	235	90	NM_052896	0	0	0	0	0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																				.		0.592	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	33985175	T	A	33985175	2	1	20	1	0	0	0	0	0	0	0	1	3951	1567	55	5		5	CSMD2	1	33985175	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	10225253	33985175	215265446	5	1677											
YBX1	4904	hgsc.bcm.edu	37	chr1	43166452	43166452	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tttgacaccgttcattgcagGggccctcctcgccaaagaca	9	9	9	14	2	1	2	1	1	0	1	3	2	2	2	4	2	1	2	4	2	1	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:43166452G>A	ENST00000321358.7	+	7	880	c.741G>A	c.(739-741)agG>agA	p.R247R		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	247					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TTCATTGCAGGGGCCCTCCTC	0.483																																					p.R247R		.											.	YBX1-95	0			c.G741A						.						26	24	25					1																	43166452		2203	4300	6503	SO:0001630	splice_region_variant	4904	exon7			TTGCAGGGGCCCT	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.741-1G>A	1.37:g.43166452G>A		Somatic	20	1		WXS	Illumina HiSeq	Phase_I	24	5	NM_004559	0	0	2	2	0	P16990|P16991|Q14972|Q15325|Q5FVF0	Silent	SNP	ENST00000321358.7	37	CCDS470.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.823775	0.32237	.	.	ENSG00000065978	ENST00000318612;ENST00000436427	.	.	.	5.35	3.41	0.39046	.	.	.	.	.	T	0.58278	0.2111	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52155	-0.8613	4	.	.	.	.	8.8138	0.34983	0.1925:0.0:0.8075:0.0	.	.	.	.	E	238;297	.	.	G	+	2	0	YBX1	42939039	1.000000	0.71417	0.998000	0.56505	0.858000	0.48976	4.943000	0.63554	0.571000	0.29365	0.552000	0.68991	GGG	.		0.483	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559	Silent	A	43166452	G	A	43166452	5	1	20	1	0	0	0	0	0	0	1	0	17502	1246	43	2	767	2	YBX1	1	43166452	Splice_Site	SNP	G	TCGA-A4-8630-01A-11D-2396-08	9181277	43166452	206084169	6	1678											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122273	117122273	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtccgctctgttgggtcGtcgtcgtcgtcgtcgtcctc	0	13	13	15	8	1	0	0	0	1	0	10	0	3	0	3	1	0	2	3	1	0	1	rs562520690|rs114783166	byFrequency	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:117122273G>A	ENST00000369486.3	-	10	3840	c.3075C>T	c.(3073-3075)gaC>gaT	p.D1025D	IGSF3_ENST00000369483.1_Silent_p.D1045D|IGSF3_ENST00000318837.6_Silent_p.D1045D	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1025	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		CTGTTGGgtcgtcgtcgtcgt	0.637																																					p.D1045D		.											.	IGSF3-92	0			c.C3135T						.	G	,	0,4406		0,0,2203	30	30	30		3075,3135	-6	0	1	dbSNP_133	30	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	IGSF3	NM_001007237.1,NM_001542.2	,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,	1025/1195,1045/1215	117122273	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	3321	exon11			TGGGTCGTCGTCG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3075C>T	1.37:g.117122273G>A		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_001542	0	0	11	11	0	A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	37	CCDS30813.1																																																																																			G|1.000;A|0.000		0.637	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117122273	G	A	117122273	2	1	20	1	0	0	0	0	0	0	0	1	7622	1136	40	1		1	IGSF3	1	117122273	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	73955821	117122273	132128348	7	1679											
TTF2	8458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	117618867	117618867	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cagaagttgatcaaacaaatCcaggagctggaggaagtact	16	7	11	7	0	1	2	1	1	0	1	2	5	2	5	1	3	3	3	1	3	5	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:117618867C>G	ENST00000369466.4	+	6	1385	c.1341C>G	c.(1339-1341)atC>atG	p.I447M		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	447					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		TCAAACAAATCCAGGAGCTGG	0.478																																					p.I447M		.											.	TTF2-91	0			c.C1341G						.						101	95	97					1																	117618867		2203	4300	6503	SO:0001583	missense	8458	exon6			ACAAATCCAGGAG	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.1341C>G	1.37:g.117618867C>G	ENSP00000358478:p.Ile447Met	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_003594	0	0	2	5	3	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109329	0.37242	.	.	ENSG00000116830	ENST00000369466	D	0.88975	-2.45	5.41	-4.64	0.03349	.	0.000000	0.37906	N	0.001883	D	0.84379	0.5459	M	0.70595	2.14	0.34103	D	0.662138	D;D	0.67145	0.996;0.979	P;P	0.61800	0.894;0.857	T	0.77988	-0.2380	10	0.72032	D	0.01	-12.3789	1.4425	0.02357	0.2154:0.3707:0.1077:0.3062	.	447;447	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	M	447	ENSP00000358478:I447M	ENSP00000358478:I447M	I	+	3	3	TTF2	117420390	0.918000	0.31147	0.794000	0.32065	0.071000	0.16799	-0.183000	0.09712	-0.727000	0.04888	0.561000	0.74099	ATC	.		0.478	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			G	117618867	C	G	117618867	3	3	20	1	0	0	0	0	1	0	0	0	16752	845	30	4	1363	4	TTF2	1	117618867	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	496594	117618867	131631754	8	1680											
S100A3	6274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153520171	153520171	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcagaggctactgggagcagGggggctctgaggggcagtcc	7	5	20	9	0	1	2	0	1	1	1	2	3	2	3	1	7	2	5	1	7	1	1	rs199928185		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:153520171G>C	ENST00000368713.3	-	3	489	c.293C>G	c.(292-294)cCc>cGc	p.P98R	S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000368714.1_Intron|S100A4_ENST00000368716.4_5'Flank|S100A3_ENST00000368712.1_Missense_Mutation_p.P98R|S100A4_ENST00000368715.1_5'Flank	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	98						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGGGAGCAGGGGGGCTCTGA	0.612																																					p.P98R		.											.	S100A3-90	0			c.C293G						.						87	84	85					1																	153520171		2203	4300	6503	SO:0001583	missense	6274	exon3			GAGCAGGGGGGCT	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"S100 calcium binding proteins"	10493	protein-coding gene	gene with protein product		176992	"S100 calcium-binding protein A3"	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.293C>G	1.37:g.153520171G>C	ENSP00000357702:p.Pro98Arg	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	105	52	NM_002960	0	0	1	2	1	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.31	1.599880	0.28534	.	.	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.12569	2.67;2.67	5.02	4.1	0.47936	EF-hand-like domain (1);	0.459781	0.18636	N	0.135449	T	0.04634	0.0126	L	0.40543	1.245	0.32452	N	0.545297	P	0.41313	0.745	B	0.33295	0.161	T	0.16660	-1.0395	10	0.87932	D	0	.	11.2746	0.49159	0.0:0.0:0.8178:0.1822	.	98	P33764	S10A3_HUMAN	R	98	ENSP00000357702:P98R;ENSP00000357701:P98R	ENSP00000357701:P98R	P	-	2	0	S100A3	151786795	1.000000	0.71417	0.975000	0.42487	0.086000	0.17979	2.842000	0.48230	1.208000	0.43306	0.655000	0.94253	CCC	G|0.999;C|0.001		0.612	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960		C	153520171	G	C	153520171	3	2	20	1	0	0	0	0	1	0	0	0	13811	1232	43	4	16	4	S100A3	1	153520171	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	35901304	153520171	95730450	9	1681											
SMG5	23381	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	156221203	156221203	+	Frame_Shift_Del	DEL	G	G	-																															taaaatgttaccaggcatctGcatcctgcctcttcagctta																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:156221203delG	ENST00000361813.5	-	20	2963	c.2819delC	c.(2818-2820)gcafs	p.A940fs	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	940	PINc.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					CCAGGCATCTGCATCCTGCCT	0.552																																					p.A940fs		.											.	SMG5-231	0			c.2819delC						.						224	214	217					1																	156221203		2203	4300	6503	SO:0001589	frameshift_variant	23381	exon20			.	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.2819delC	1.37:g.156221203delG	ENSP00000355261:p.Ala940fs	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	197	69	NM_015327	0	0	0	0	0	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Frame_Shift_Del	DEL	ENST00000361813.5	37	CCDS1137.1																																																																																			.		0.552	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		-	156221203	G	-	156221203	7	5	20	1	0	1	0	1	0	0	0	0	14828	1319	46	0	243	0	SMG5	1	156221203	Frame_Shift_Del	DEL	G	TCGA-A4-8630-01A-11D-2396-08	2701032	156221203	93029418	10	1682											
C1orf66	51093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156706431	156706431	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctttctcccaggtttccaTgctgagctcctgcccatctt	4	14	6	17	0	2	1	0	1	2	0	5	1	4	1	5	1	3	3	5	1	0	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:156706431T>C	ENST00000368216.4	+	8	1944	c.1314T>C	c.(1312-1314)caT>caC	p.H438H	RRNAD1_ENST00000476229.1_Missense_Mutation_p.C154R|MRPL24_ENST00000478899.1_5'Flank|RRNAD1_ENST00000481920.1_Intron|RRNAD1_ENST00000368218.4_Missense_Mutation_p.C277R	NM_015997.3	NP_057081.3	Q96FB5	RRNAD_HUMAN	ribosomal RNA adenine dimethylase domain containing 1	438						integral component of membrane (GO:0016021)	rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)	9						CAGGTTTCCATGCTGAGCTCC	0.532																																					p.C277R		.											.	RRNAD1-90	0			c.T829C						.						132	123	126					1																	156706431		2203	4300	6503	SO:0001819	synonymous_variant	51093	exon7			TTTCCATGCTGAG	BC011382	CCDS1154.1, CCDS44246.1	1q23.1	2011-01-28	2011-01-28	2011-01-28	ENSG00000143303	ENSG00000143303			24273	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 66"	C1orf66		10810093, 310876	Standard	NM_015997		Approved	CGI-41	uc001fpu.3	Q96FB5	OTTHUMG00000041302	ENST00000368216.4:c.1314T>C	1.37:g.156706431T>C		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	135	52	NM_001142560	0	0	8	9	1	D3DVC7|Q4VX71|Q5SZ03|Q9Y358	Missense_Mutation	SNP	ENST00000368216.4	37	CCDS1154.1	.	.	.	.	.	.	.	.	.	.	T	13.71	2.319855	0.41096	.	.	ENSG00000143303	ENST00000368218;ENST00000476229	.	.	.	5.87	0.792	0.18625	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.36802	D	0.885409	B	0.06786	0.001	B	0.01281	0.0	T	0.08638	-1.0712	7	0.87932	D	0	-4.8252	4.626	0.12479	0.0:0.2522:0.2302:0.5176	.	277	Q4VX71	.	R	277;154	.	ENSP00000357201:C277R	C	+	1	0	RRNAD1	154973055	0.996000	0.38824	1.000000	0.80357	0.386000	0.30323	0.158000	0.16422	0.158000	0.19367	0.533000	0.62120	TGC	.		0.532	RRNAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098973.1	NM_015997		C	156706431	T	C	156706431	2	2	20	1	0	0	0	0	0	0	0	1	2062	1464	51	3		3	C1orf66	1	156706431	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	485228	156706431	92544190	11	1683											
BAT2L2	23215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171482181	171482181	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggaaaagtcggtatttcaCggcgtatgcctccacctgct	8	12	10	11	3	1	0	1	0	0	0	3	1	2	1	3	3	2	3	3	3	4	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:171482181C>G	ENST00000338920.4	+	3	391	c.154C>G	c.(154-156)Cgg>Ggg	p.R52G	PRRC2C_ENST00000426496.2_Missense_Mutation_p.R52G|PRRC2C_ENST00000367742.3_Missense_Mutation_p.R54G|PRRC2C_ENST00000392078.3_Missense_Mutation_p.R54G|PRRC2C_ENST00000476522.1_3'UTR	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	52					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CGGTATTTCACGGCGTATGCC	0.403																																					p.R52G		.											.	.	0			c.C154G						.						115	110	112					1																	171482181		2203	4300	6503	SO:0001583	missense	23215	exon3			ATTTCACGGCGTA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.154C>G	1.37:g.171482181C>G	ENSP00000343629:p.Arg52Gly	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	56	20	NM_015172	0	0	6	15	9	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993708	0.35131	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.82	2.79	0.32731	BAT2, N-terminal (1);	0.000000	0.43579	D	0.000551	T	0.61110	0.2321	M	0.81341	2.54	0.54753	D	0.999983	D;D;D	0.89917	0.999;1.0;0.98	D;D;P	0.79108	0.943;0.992;0.749	T	0.69665	-0.5084	10	0.87932	D	0	.	15.4227	0.75025	0.5817:0.4183:0.0:0.0	.	52;54;52	Q9Y520-4;E7EPN9;Q9Y520	.;.;PRC2C_HUMAN	G	54;52;52;54;52	ENSP00000375928:R54G;ENSP00000410219:R52G;ENSP00000356716:R54G;ENSP00000343629:R52G	ENSP00000343629:R52G	R	+	1	2	PRRC2C	169748805	0.984000	0.35163	0.999000	0.59377	0.992000	0.81027	2.586000	0.46119	0.312000	0.23038	-0.169000	0.13324	CGG	.		0.403	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171482181	C	G	171482181	3	3	20	1	0	0	0	0	1	0	0	0	1322	527	19	4	160	4	BAT2L2	1	171482181	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	14775750	171482181	77768440	12	1684											
TRIM11	81559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228584695	228584695	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtcccgggaccctgcacacgGtcctcagctccataggcaca	8	6	10	17	2	1	0	1	0	0	0	4	1	4	1	4	3	2	3	4	3	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:228584695G>T	ENST00000284551.6	-	5	1090	c.812C>A	c.(811-813)aCc>aAc	p.T271N	TRIM11_ENST00000366699.3_Missense_Mutation_p.T271N|TRIM11_ENST00000460651.1_5'UTR|RP11-245P10.8_ENST00000602963.1_RNA|TRIM11_ENST00000493030.2_Missense_Mutation_p.T146N	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	271	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				CCTGCACACGGTCCTCAGCTC	0.627																																					p.T271N		.											.	TRIM11-658	0			c.C812A						.						85	85	85					1																	228584695		2203	4300	6503	SO:0001583	missense	81559	exon5			CACACGGTCCTCA	AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16281	protein-coding gene	gene with protein product		607868	"tripartite motif-containing 11"			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.812C>A	1.37:g.228584695G>T	ENSP00000284551:p.Thr271Asn	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	80	35	NM_145214	0	0	5	8	3	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.549179	0.65311	.	.	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.06768	3.26;3.26	4.97	4.97	0.65823	B30.2/SPRY domain (1);	0.000000	0.41605	D	0.000853	T	0.19127	0.0459	L	0.41079	1.255	0.34988	D	0.754698	D;D;P	0.89917	1.0;1.0;0.781	D;D;B	0.97110	1.0;1.0;0.248	T	0.11108	-1.0601	10	0.26408	T	0.33	.	14.103	0.65070	0.0:0.0:1.0:0.0	.	270;271;271	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	N	271	ENSP00000284551:T271N;ENSP00000355660:T271N	ENSP00000284551:T271N	T	-	2	0	TRIM11	226651318	0.932000	0.31603	0.909000	0.35828	0.546000	0.35178	1.634000	0.37123	2.482000	0.83794	0.313000	0.20887	ACC	.		0.627	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214		T	228584695	G	T	228584695	3	4	20	1	0	0	0	0	1	0	0	0	16520	1261	44	4	602	4	TRIM11	1	228584695	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	57102514	228584695	20665926	13	1685											
AGBL5	60509	hgsc.bcm.edu	37	chr2	27291528	27291528	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcactcttgtcctctggAgacaaaccagaggctgtcat	9	11	9	12	0	4	2	2	0	2	2	5	3	5	2	2	2	2	2	2	2	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:27291528A>G	ENST00000360131.4	+	13	2430	c.2271A>G	c.(2269-2271)ggA>ggG	p.G757G		NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	757					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTCCTCTGGAGACAAACCAG	0.512																																					p.G757G		.											.	AGBL5-154	0			c.A2271G						.						78	79	79					2																	27291528		2203	4300	6503	SO:0001819	synonymous_variant	60509	exon13			CTCTGGAGACAAA	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.2271A>G	2.37:g.27291528A>G		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_021831	0	0	20	20	0	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Silent	SNP	ENST00000360131.4	37	CCDS1732.3																																																																																			.		0.512	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		G	27291528	A	G	27291528	2	3	20	1	0	0	0	0	0	0	0	1	378	291	11	3		3	AGBL5	2	27291528	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08		27291528	215907845	14	1686											
SLC8A1	6546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	40405590	40405590	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaagaaggtcttgttttTctcatactcctcatcatcaa	12	14	6	9	0	5	1	4	0	2	1	7	2	6	2	1	2	1	1	1	2	5	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:40405590T>C	ENST00000403092.1	-	3	1885	c.1852A>G	c.(1852-1854)Aaa>Gaa	p.K618E	SLC8A1_ENST00000406785.2_Intron|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000332839.4_Missense_Mutation_p.K618E|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1_ENST00000405901.3_Missense_Mutation_p.K618E|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1_ENST00000542024.1_Intron|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1_ENST00000402441.1_Intron|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1_ENST00000405269.1_Intron|SLC8A1_ENST00000408028.2_Intron|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.K618E|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1_ENST00000406391.2_Intron			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	618	Calx-beta 2.				blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	GTCTTGTTTTTCTCATACTCC	0.468																																					p.K618E		.											.	SLC8A1-93	0			c.A1852G						.						239	235	237					2																	40405590		2203	4300	6503	SO:0001583	missense	6546	exon2			TGTTTTTCTCATA		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1852A>G	2.37:g.40405590T>C	ENSP00000384763:p.Lys618Glu	Somatic	270	0		WXS	Illumina HiSeq	Phase_I	241	108	NM_021097	0	0	0	0	0	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.338174	0.81911	.	.	ENSG00000183023	ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000332839	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.39	5.39	0.77823	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	L	0.52011	1.625	0.80722	D	1	P;D	0.89917	0.917;1.0	P;D	0.91635	0.721;0.999	T	0.50800	-0.8785	10	0.87932	D	0	.	13.3557	0.60627	0.0:0.0:0.0:1.0	.	618;618	F6VPY9;P32418	.;NAC1_HUMAN	E	618	ENSP00000440727:K618E;ENSP00000384763:K618E;ENSP00000385678:K618E;ENSP00000332931:K618E	ENSP00000332931:K618E	K	-	1	0	SLC8A1	40259094	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.587000	0.82613	2.028000	0.59812	0.482000	0.46254	AAA	.		0.468	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		C	40405590	T	C	40405590	3	2	20	1	0	0	0	0	1	0	0	0	14738	1792	62	3	1213	3	SLC8A1	2	40405590	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	13114062	40405590	202793783	15	1687											
FBXO11	80204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	48049436	48049436	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatttccattaaatatagaAtttcccctataattatgcga	14	16	4	7	1	0	2	0	1	0	1	2	3	2	2	3	0	1	0	3	0	8	8			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:48049436A>C	ENST00000403359.3	-	13	1695	c.1623T>G	c.(1621-1623)aaT>aaG	p.N541K	FBXO11_ENST00000402508.1_Missense_Mutation_p.N457K|FBXO11_ENST00000434523.2_5'UTR|FBXO11_ENST00000316377.4_Missense_Mutation_p.N457K	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	541					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TAAATATAGAATTTCCCCTAT	0.343			"Mis, F, D"		DLBCL																																p.N541K		.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11-659	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1623G						.						51	51	51					2																	48049436		2202	4298	6500	SO:0001583	missense	80204	exon13			TATAGAATTTCCC	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.1623T>G	2.37:g.48049436A>C	ENSP00000384823:p.Asn541Lys	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	54	19	NM_001190274	0	0	0	0	0	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	37	CCDS54357.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.6|20.6	4.023026|4.023026	0.75275|0.75275	.|.	.|.	ENSG00000138081|ENSG00000138081	ENST00000493962|ENST00000402508;ENST00000403359;ENST00000316377	.|D;D;D	.|0.89485	.|-2.52;-1.81;-2.52	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);F-box domain, Skp2-like (1);Pectin lyase fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93135|0.93135	0.7814|0.7814	M|M	0.92459|0.92459	3.31|3.31	0.80722|0.80722	D|D	1|1	.|B	.|0.26258	.|0.145	.|B	.|0.37304	.|0.246	D|D	0.92695|0.92695	0.6170|0.6170	5|10	.|0.66056	.|D	.|0.02	-16.8508|-16.8508	15.4471|15.4471	0.75238|0.75238	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|541	.|Q86XK2	.|FBX11_HUMAN	V|K	333|457;541;457	.|ENSP00000385398:N457K;ENSP00000384823:N541K;ENSP00000323822:N457K	.|ENSP00000323822:N457K	F|N	-|-	1|3	0|2	FBXO11|FBXO11	47902940|47902940	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	4.344000|4.344000	0.59354|0.59354	2.039000|2.039000	0.60335|0.60335	0.533000|0.533000	0.62120|0.62120	TTC|AAT	.		0.343	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		C	48049436	A	C	48049436	3	2	20	1	0	0	0	0	1	0	0	0	5746	98	4	5	1294	5	FBXO11	2	48049436	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08	7643846	48049436	195149937	16	1688											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	179429832	179429834	+	In_Frame_Del	DEL	AAT	AAT	-																															gttgtatctcgcttctctacAatgtagttgcttatttggca																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:179429832_179429834delAAT	ENST00000591111.1	-	276	76326_76328	c.76102_76104delATT	c.(76102-76104)attdel	p.I25368del	TTN_ENST00000460472.2_In_Frame_Del_p.I17944del|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342175.6_In_Frame_Del_p.I18136del|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_In_Frame_Del_p.I24441del|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000589042.1_In_Frame_Del_p.I27009del|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_In_Frame_Del_p.I18069del			Q8WZ42	TITIN_HUMAN	titin	25368	Fibronectin type-III 84. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTTCTCTACAATGTAGTTGCTT	0.443																																					p.27009_27009del		.											.	TTN-636	0			c.81025_81027del						.																																			SO:0001651	inframe_deletion	7273	exon326			.	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76102_76104delATT	2.37:g.179429832_179429834delAAT	ENSP00000465570:p.Ile25368del	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	138	58	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	In_Frame_Del	DEL	ENST00000591111.1	37																																																																																				.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179429834	AAT	-	179429832	7	5	20	1	0	1	0	1	0	0	0	0	16768	126	5	0	27100	0	TTN	2	179429832	In_Frame_Del	DEL	AAT	TCGA-A4-8630-01A-11D-2396-08	131380396	179429832	63769541	17	1689											
CTLA4	1493	hgsc.bcm.edu	37	chr2	204735645	204735645	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cataggcaacggaacccagaTttatgtaattggtgagcaaa	15	9	10	7	1	0	2	0	1	0	1	0	3	0	3	1	3	3	3	1	3	6	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:204735645T>C	ENST00000302823.3	+	2	603	c.446T>C	c.(445-447)aTt>aCt	p.I149T	CTLA4_ENST00000427473.2_Missense_Mutation_p.I112T|CTLA4_ENST00000295854.6_Missense_Mutation_p.I149T|CTLA4_ENST00000487393.1_Intron|CTLA4_ENST00000472206.1_Intron	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	149					B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	GGAACCCAGATTTATGTAATT	0.473																																					p.I149T		.											.	CTLA4-90	0			c.T446C						.						56	53	54					2																	204735645		2203	4300	6503	SO:0001583	missense	1493	exon2			CCCAGATTTATGT		CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	2505	protein-coding gene	gene with protein product		123890	"celiac disease 3", "insulin-dependent diabetes mellitus 12"	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.446T>C	2.37:g.204735645T>C	ENSP00000303939:p.Ile149Thr	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_005214	0	0	0	0	0	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Missense_Mutation	SNP	ENST00000302823.3	37	CCDS2362.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.501240	0.44455	.	.	ENSG00000163599	ENST00000302823;ENST00000295854;ENST00000427473	T;T;T	0.46063	0.88;0.88;0.88	5.34	5.34	0.76211	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.124068	0.52532	D	0.000063	T	0.65585	0.2705	M	0.77616	2.38	0.40810	D	0.983413	D;D	0.89917	0.999;1.0	D;D	0.97110	1.0;0.997	T	0.71656	-0.4527	10	0.87932	D	0	-14.9442	14.4845	0.67606	0.0:0.0:0.0:1.0	.	149;149	Q8TDA6;P16410	.;CTLA4_HUMAN	T	149;149;112	ENSP00000303939:I149T;ENSP00000295854:I149T;ENSP00000409707:I112T	ENSP00000295854:I149T	I	+	2	0	CTLA4	204443890	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	5.303000	0.65738	2.015000	0.59207	0.533000	0.62120	ATT	.		0.473	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214		C	204735645	T	C	204735645	3	2	20	1	0	0	0	0	1	0	0	0	4017	1493	52	3	452	3	CTLA4	2	204735645	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	25305813	204735645	38463728	18	1690											
VGLL4	10533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	11600049	11600049	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttcaggagaccacagaggggGagtgactgtggctgaccatg	10	7	16	8	0	1	4	1	2	0	2	1	6	1	5	2	4	0	1	2	4	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr3:11600049G>A	ENST00000354449.3	+	0	4959				VGLL4_ENST00000451674.2_Missense_Mutation_p.S205F|VGLL4_ENST00000413604.1_Missense_Mutation_p.S226F|VGLL4_ENST00000424529.2_Missense_Mutation_p.S201F|VGLL4_ENST00000404339.1_Missense_Mutation_p.S290F|VGLL4_ENST00000273038.3_Missense_Mutation_p.S285F|VGLL4_ENST00000430365.2_Missense_Mutation_p.S291F	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7						adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CACAGAGGGGGAGTGACTGTG	0.572																																					p.S291F		.											.	VGLL4-91	0			c.C872T						.						43	49	47					3																	11600049		2203	4299	6502	SO:0001628	intergenic_variant	9686	exon5			GAGGGGGAGTGAC	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740		3.37:g.11600049G>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	101	18	NM_001128219	0	0	55	64	9	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	37	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347047	0.61183	.	.	ENSG00000144560	ENST00000273038;ENST00000413604;ENST00000451674;ENST00000424529;ENST00000430365;ENST00000404339	T;T;T	0.60672	0.23;0.26;0.17	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.74696	0.3750	M	0.62723	1.935	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.998;0.998;0.998;0.998	T	0.77851	-0.2434	10	0.87932	D	0	-39.5652	18.3059	0.90180	0.0:0.0:1.0:0.0	.	291;205;201;290;285	G5E9M7;Q14135-6;Q14135-5;G5E9F4;Q14135	.;.;.;.;VGLL4_HUMAN	F	285;226;205;201;291;290	ENSP00000273038:S285F;ENSP00000404251:S291F;ENSP00000384705:S290F	ENSP00000273038:S285F	S	-	2	0	VGLL4	11575049	1.000000	0.71417	0.967000	0.41034	0.519000	0.34347	7.672000	0.83956	2.321000	0.78463	0.563000	0.77884	TCC	.		0.572	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		A	11600049	G	A	11600049	1	1	20	0	1	0	0	0	0	0	0	0	17194	1174	41	2		2	VGLL4	3	11600049	IGR	SNP	G	TCGA-A4-8630-01A-11D-2396-08		11600049	186422381	19	1691											
B4GALT4	8702	bcgsc.ca	37	chr3	118945881	118945881	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtttgaaaatgagcttgctCtggcctcctacaatgaacat	11	12	9	9	0	1	3	0	3	1	0	2	3	2	3	2	2	4	3	2	2	5	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr3:118945881C>T	ENST00000483209.1	-	4	902	c.261G>A	c.(259-261)caG>caA	p.Q87Q	B4GALT4-AS1_ENST00000470790.1_RNA|B4GALT4_ENST00000359213.3_Silent_p.Q87Q|B4GALT4_ENST00000467604.1_Silent_p.Q87Q|B4GALT4_ENST00000471675.1_Silent_p.Q40Q|B4GALT4_ENST00000393765.2_Silent_p.Q87Q|B4GALT4_ENST00000460321.1_5'UTR			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	87					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	TGAGCTTGCTCTGGCCTCCTA	0.443																																					p.Q87Q													.	B4GALT4-90	0			c.G261A						.						91	90	90					3																	118945881		2203	4300	6503	SO:0001819	synonymous_variant	8702	exon5			CTTGCTCTGGCCT	AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"Beta 4-glycosyltransferases"	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.261G>A	3.37:g.118945881C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_1	77	4	NM_212543	0	0	0	0	0	Q68D68|Q9BSW3|Q9C078	Silent	SNP	ENST00000483209.1	37	CCDS2986.1																																																																																			.		0.443	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778		T	118945881	C	T	118945881	2	4	20	1	0	0	0	0	0	0	0	1	1274	912	32	2		2	B4GALT4	3	118945881	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	107345832	118945881	79076549	20	1692											
ITGB5	3693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	124487860	124487860	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtggcagcacactcacCgatggtgtccacccatgtga	8	8	13	12	1	1	1	1	1	0	0	2	2	2	1	3	4	1	2	3	4	0	0	rs375122712		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr3:124487860C>T	ENST00000296181.4	-	12	2313	c.2017G>A	c.(2017-2019)Gtg>Atg	p.V673M	ITGB5_ENST00000461306.1_5'UTR	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	673					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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		GCACACTCACCGATGGTGTCC	0.587																																					p.V673M		.											.	ITGB5-227	0			c.G2017A						.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	131	113	119		2017	4.3	1	3		119	0,8600		0,0,4300	no	missense-near-splice	ITGB5	NM_002213.3	21	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	673/800	124487860	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	3693	exon12			ACTCACCGATGGT	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.2017+1G>A	3.37:g.124487860C>T		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	101	29	NM_002213	0	0	0	1	1	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	37	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633900	0.47049	2.27E-4	0.0	ENSG00000082781	ENST00000296181	D	0.90261	-2.64	5.29	4.34	0.51931	Integrin beta subunit, tail (2);	0.762691	0.12573	N	0.457111	D	0.83151	0.5192	L	0.29908	0.895	0.38470	D	0.94744	B	0.20052	0.041	B	0.18561	0.022	T	0.76046	-0.3102	9	.	.	.	.	8.2832	0.31913	0.0:0.8282:0.0:0.1718	.	673	P18084	ITB5_HUMAN	M	673	ENSP00000296181:V673M	.	V	-	1	0	ITGB5	125970550	0.915000	0.31059	1.000000	0.80357	0.994000	0.84299	1.262000	0.32992	2.761000	0.94854	0.655000	0.94253	GTG	.		0.587	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	Missense_Mutation	T	124487860	C	T	124487860	5	4	20	1	0	0	0	0	0	0	1	0	7919	666	23	1	398	1	ITGB5	3	124487860	Splice_Site	SNP	C	TCGA-A4-8630-01A-11D-2396-08	5541979	124487860	73534570	21	1693											
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1807787	1807787	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttccccagtgcatccacAgggacctggctgcccgcaat	7	7	9	18	1	0	0	0	0	0	0	2	1	2	1	6	2	2	3	6	2	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:1807787A>G	ENST00000260795.2	+	13	1948	c.1846A>G	c.(1846-1848)Agg>Ggg	p.R616G	FGFR3_ENST00000412135.2_Missense_Mutation_p.R504G|FGFR3_ENST00000340107.4_Missense_Mutation_p.R618G|FGFR3_ENST00000481110.2_Missense_Mutation_p.R617G|FGFR3_ENST00000352904.1_Missense_Mutation_p.R504G|FGFR3_ENST00000440486.2_Missense_Mutation_p.R616G			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	616	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	GTGCATCCACAGGGACCTGGC	0.642		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.R618G		.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	0			c.A1852G						.						39	39	39					4																	1807787		2202	4300	6502	SO:0001583	missense	2261	exon14	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	ATCCACAGGGACC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1846A>G	4.37:g.1807787A>G	ENSP00000260795:p.Arg616Gly	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	27	11	NM_001163213	0	0	0	0	0	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	a	13.53	2.264914	0.40095	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	4.18	1.28	0.21552	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93559	0.7944	M	0.82433	2.59	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.998	D;D;D;D	0.97110	1.0;0.997;1.0;0.973	D	0.93158	0.6555	10	0.87932	D	0	.	11.472	0.50275	0.5856:0.4144:0.0:0.0	.	618;504;616;617	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	G	617;618;616;504;616;504	ENSP00000420533:R617G;ENSP00000339824:R618G;ENSP00000414914:R616G;ENSP00000412903:R504G;ENSP00000260795:R616G;ENSP00000231803:R504G	ENSP00000260795:R616G	R	+	1	2	FGFR3	1777585	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	1.293000	0.33353	0.540000	0.28808	0.241000	0.17934	AGG	.		0.642	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1807787	A	G	1807787	3	3	20	1	0	0	0	0	1	0	0	0	5886	179	7	3	2051	3	FGFR3	4	1807787	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08		1807787	189346489	22	1694											
SLAIN2	57606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48384849	48384849	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaatagaatatagtagagTgtccccacagcctatgatta	14	10	10	7	0	0	3	0	1	0	2	1	4	1	4	3	1	1	1	3	1	8	6			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:48384849T>A	ENST00000264313.6	+	5	1545	c.1127T>A	c.(1126-1128)gTg>gAg	p.V376E	SLAIN2_ENST00000512093.1_Missense_Mutation_p.V183E	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	376					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						TATAGTAGAGTGTCCCCACAG	0.473																																					p.V376E		.											.	.	0			c.T1127A						.						89	89	89					4																	48384849		1998	4164	6162	SO:0001583	missense	57606	exon5			GTAGAGTGTCCCC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"KIAA1458"	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1127T>A	4.37:g.48384849T>A	ENSP00000264313:p.Val376Glu	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	46	23	NM_020846	0	0	12	20	8	A8K4P1|Q8N5R3	Missense_Mutation	SNP	ENST00000264313.6	37	CCDS47051.1	.	.	.	.	.	.	.	.	.	.	T	4.898	0.166911	0.09339	.	.	ENSG00000109171	ENST00000264313;ENST00000512093	.	.	.	5.77	3.24	0.37175	.	0.222330	0.45867	D	0.000335	T	0.39306	0.1073	N	0.24115	0.695	0.43000	D	0.994515	B;B	0.25609	0.13;0.096	B;B	0.23574	0.047;0.026	T	0.24548	-1.0157	9	0.42905	T	0.14	-4.6941	7.659	0.28392	0.0:0.0736:0.141:0.7854	.	46;376	Q9H705;Q9P270	.;SLAI2_HUMAN	E	376;183	.	ENSP00000264313:V376E	V	+	2	0	SLAIN2	48079606	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	1.779000	0.38624	1.026000	0.39733	0.533000	0.62120	GTG	.		0.473	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846		A	48384849	T	A	48384849	3	1	20	1	0	0	0	0	1	0	0	0	14398	1696	59	5	1145	5	SLAIN2	4	48384849	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	46577062	48384849	142769427	23	1695											
MANBA	4126	hgsc.bcm.edu	37	chr4	103590185	103590185	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttggataaagggcacaggCaaacataaaatcctgccata	17	7	9	8	0	0	0	0	0	0	0	1	1	1	1	2	3	2	3	2	3	6	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:103590185C>G	ENST00000226578.4	-	10	1351	c.1252G>C	c.(1252-1254)Gcc>Ccc	p.A418P	MANBA_ENST00000505239.1_Missense_Mutation_p.A361P	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	418					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		AGGGCACAGGCAAACATAAAA	0.398																																					p.A418P		.											.	MANBA-91	0			c.G1252C						.						63	58	60					4																	103590185		2203	4300	6503	SO:0001583	missense	4126	exon10			CACAGGCAAACAT		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.1252G>C	4.37:g.103590185C>G	ENSP00000226578:p.Ala418Pro	Somatic	36	1		WXS	Illumina HiSeq	Phase_I	29	2	NM_005908	0	0	14	14	0	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963262	0.92791	.	.	ENSG00000109323	ENST00000226578;ENST00000505239	D;D	0.91407	-2.84;-2.84	4.82	4.82	0.62117	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 2, TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.97018	0.9026	H	0.96015	3.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98440	1.0586	10	0.87932	D	0	-26.6486	18.2864	0.90115	0.0:1.0:0.0:0.0	.	361;418	E9PFW2;O00462	.;MANBA_HUMAN	P	418;361	ENSP00000226578:A418P;ENSP00000427322:A361P	ENSP00000226578:A418P	A	-	1	0	MANBA	103809233	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.027000	0.76463	2.377000	0.81083	0.460000	0.39030	GCC	.		0.398	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			G	103590185	C	G	103590185	3	3	20	1	0	0	0	0	1	0	0	0	9244	710	25	4	1419	4	MANBA	4	103590185	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	55205336	103590185	87564091	24	1696											
TBCK	93627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	106967781	106967781	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggctttattttattaatGccaccatctagaatacagat	12	16	6	7	0	1	2	0	0	1	2	1	2	1	2	2	1	2	2	2	1	6	8			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:106967781G>A	ENST00000273980.5	-	27	3075	c.2628C>T	c.(2626-2628)ggC>ggT	p.G876G	TBCK_ENST00000394708.2_Silent_p.G876G|TBCK_ENST00000361687.4_Silent_p.G813G|TBCK_ENST00000432496.2_Silent_p.G876G|TBCK_ENST00000394706.3_Silent_p.G837G					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTTTATTAATGCCACCATCTA	0.393																																					p.G876G		.											.	TBCK-336	0			c.C2628T						.						120	116	117					4																	106967781		2203	4300	6503	SO:0001819	synonymous_variant	93627	exon26			ATTAATGCCACCA		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.2628C>T	4.37:g.106967781G>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	50	15	NM_001163436	0	0	24	40	16		Silent	SNP	ENST00000273980.5	37	CCDS54788.1																																																																																			.		0.393	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		A	106967781	G	A	106967781	2	1	20	1	0	0	0	0	0	0	0	1	15668	1306	46	2		2	TBCK	4	106967781	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	3377596	106967781	84186495	25	1697											
LARP7	51574	hgsc.bcm.edu	37	chr4	113578403	113578403	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgatttatttctctttagTtaatcaccaaagctgaaaag	13	17	5	6	0	2	2	1	2	1	0	3	2	2	2	1	0	1	2	1	0	6	7			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:113578403T>C	ENST00000344442.5	+	13	1947	c.1669T>C	c.(1669-1671)Tta>Cta	p.L557L	LARP7_ENST00000324052.6_Splice_Site_p.L557L|LARP7_ENST00000503898.1_3'UTR|LARP7_ENST00000509061.1_Splice_Site_p.L564L	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	557					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		TTCTCTTTAGTTAATCACCAA	0.303																																					p.L564L		.											.	LARP7-93	0			c.T1690C						.						32	35	34					4																	113578403		2199	4292	6491	SO:0001630	splice_region_variant	51574	exon15			CTTTAGTTAATCA	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.1669-1T>C	4.37:g.113578403T>C		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_001267039	0	0	2	2	0	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Silent	SNP	ENST00000344442.5	37	CCDS3701.2																																																																																			.		0.303	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648	Silent	C	113578403	T	C	113578403	5	2	20	1	0	0	0	0	0	0	1	0	8654	1739	60	3	1715	3	LARP7	4	113578403	Splice_Site	SNP	T	TCGA-A4-8630-01A-11D-2396-08	6610622	113578403	77575873	26	1698											
FRG1	2483	hgsc.bcm.edu;broad.mit.edu	37	chr4	190874221	190874221	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaaatgttttttctccaatAgttgatgagggccctagtcc	9	15	8	9	0	2	2	1	2	1	0	4	2	3	2	3	1	0	2	3	1	4	6			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:190874221A>G	ENST00000226798.4	+	4	481		c.e4-1		FRG1_ENST00000514482.1_Splice_Site	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1						mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TTTCTCCAATAGTTGATGAGG	0.294																																					.		.											.	FRG1-90	0			c.260-2A>G						.						11	11	11					4																	190874221		2069	4178	6247	SO:0001630	splice_region_variant	2483	exon4			TCCAATAGTTGAT	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.260-1A>G	4.37:g.190874221A>G		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	62	5	NM_004477	0	0	0	0	0	A8K775	Splice_Site	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	N	14.42	2.528819	0.44969	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	.	.	.	3.71	3.71	0.42584	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0497	0.47880	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRG1	191111215	1.000000	0.71417	0.923000	0.36655	0.650000	0.38633	5.850000	0.69473	1.645000	0.50612	0.514000	0.50259	.	.		0.294	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	Intron	G	190874221	A	G	190874221	5	3	20	1	0	0	0	0	0	0	1	0	6065	434	15	3	272	3	FRG1	4	190874221	Splice_Site	SNP	A	TCGA-A4-8630-01A-11D-2396-08	77295818	190874221	280055	27	1699											
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1210657	1210657	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaactccttccaggagcctCtgccctggagcgactgcccg	6	8	10	17	2	2	0	1	0	1	0	4	3	4	2	5	2	5	0	5	2	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:1210657C>A	ENST00000304460.10	+	3	498	c.442C>A	c.(442-444)Ctg>Atg	p.L148M		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	148					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CCAGGAGCCTCTGCCCTGGAG	0.552																																					p.L148M		.											.	SLC6A19-90	0			c.C442A						.						87	78	81					5																	1210657		2203	4300	6503	SO:0001583	missense	340024	exon3			GAGCCTCTGCCCT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.442C>A	5.37:g.1210657C>A	ENSP00000305302:p.Leu148Met	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	58	3	NM_001003841	0	0	5	5	0	A8K446	Missense_Mutation	SNP	ENST00000304460.10	37	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	c	19.97	3.924889	0.73213	.	.	ENSG00000174358	ENST00000304460	D	0.83837	-1.77	4.28	4.28	0.50868	.	0.000000	0.64402	D	0.000001	D	0.92831	0.7720	H	0.95437	3.67	0.52501	D	0.999952	D	0.89917	1.0	D	0.91635	0.999	D	0.93912	0.7198	10	0.87932	D	0	.	10.736	0.46126	0.0:0.911:0.0:0.089	.	148	Q695T7	S6A19_HUMAN	M	148	ENSP00000305302:L148M	ENSP00000305302:L148M	L	+	1	2	SLC6A19	1263657	0.904000	0.30761	0.875000	0.34327	0.897000	0.52465	1.923000	0.40055	2.100000	0.63781	0.472000	0.43445	CTG	.		0.552	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		A	1210657	C	A	1210657	3	1	20	1	0	0	0	0	1	0	0	0	14714	912	32	4	452	4	SLC6A19	5	1210657	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		1210657	179704603	28	1700											
JMY	133746	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	78610483	78610483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccccctcccccaccacCaccacctctgcctgttgcta	5	9	3	24	0	1	0	0	0	1	0	4	0	4	0	10	0	2	2	10	0	1	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:78610483C>T	ENST00000396137.4	+	9	2930	c.2468C>T	c.(2467-2469)cCa>cTa	p.P823L	JMY_ENST00000412001.1_Intron	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	823	Pro-rich.				'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		cccccaccaccaccacctcTG	0.547																																					p.P823L		.											.	JMY-227	0			c.C2468T						.						17	17	17					5																	78610483		1826	4036	5862	SO:0001583	missense	133746	exon9			CACCACCACCACC	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.2468C>T	5.37:g.78610483C>T	ENSP00000379441:p.Pro823Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	20	7	NM_152405	0	0	1	2	1	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340022	0.41398	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.33654	1.4	4.69	3.8	0.43715	.	0.871791	0.09687	N	0.768999	T	0.55065	0.1897	L	0.54323	1.7	0.52099	D	0.999943	D	0.89917	1.0	D	0.91635	0.999	T	0.29458	-1.0011	10	0.25106	T	0.35	.	13.6524	0.62318	0.1565:0.8435:0.0:0.0	.	823	Q8N9B5	JMY_HUMAN	L	812;823	ENSP00000379441:P823L	ENSP00000282259:P812L	P	+	2	0	JMY	78646239	0.992000	0.36948	0.018000	0.16275	0.297000	0.27493	7.110000	0.77069	0.928000	0.37168	0.650000	0.86243	CCA	.		0.547	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		T	78610483	C	T	78610483	3	4	20	1	0	0	0	0	1	0	0	0	7978	594	21	2	2502	2	JMY	5	78610483	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	77399826	78610483	102304777	29	1701											
CHSY3	337876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	129241299	129241299	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtatgagtggttcatgcgCgccgacgacgatgtctacat	10	10	12	9	5	2	1	1	1	1	0	2	4	2	1	1	1	2	2	1	1	3	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:129241299C>T	ENST00000305031.4	+	1	1135	c.777C>T	c.(775-777)cgC>cgT	p.R259R	CTC-575N7.1_ENST00000503616.1_RNA|CTC-575N7.1_ENST00000515569.1_RNA	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	259					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GGTTCATGCGCGCCGACGACG	0.562																																					p.R259R		.											.	CHSY3-25	0			c.C777T						.						105	108	107					5																	129241299		2203	4300	6503	SO:0001819	synonymous_variant	337876	exon1			CATGCGCGCCGAC	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.777C>T	5.37:g.129241299C>T		Somatic	177	2		WXS	Illumina HiSeq	Phase_I	133	40	NM_175856	0	0	0	0	0	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																			.		0.562	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		T	129241299	C	T	129241299	2	4	20	1	0	0	0	0	0	0	0	1	3419	755	27	1		1	CHSY3	5	129241299	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	50630816	129241299	51673961	30	1702											
RAD50	10111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131953819	131953819	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagaaatcataatttggcAttagggcgacagaaaggtta	18	9	10	4	1	1	2	1	0	0	2	1	3	1	2	0	3	0	2	0	3	7	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:131953819A>G	ENST00000265335.6	+	21	3609	c.3222A>G	c.(3220-3222)gcA>gcG	p.A1074A	RAD50_ENST00000378823.3_Silent_p.A935A			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1074					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATAATTTGGCATTAGGGCGAC	0.318								Homologous recombination																													p.A1074A		.											.	RAD50-229	0			c.A3222G						.						140	163	155					5																	131953819		2203	4299	6502	SO:0001819	synonymous_variant	10111	exon21			TTTGGCATTAGGG	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.3222A>G	5.37:g.131953819A>G		Somatic	226	0		WXS	Illumina HiSeq	Phase_I	249	110	NM_005732	0	0	16	36	20	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Silent	SNP	ENST00000265335.6	37	CCDS34233.1																																																																																			.		0.318	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		G	131953819	A	G	131953819	2	3	20	1	0	0	0	0	0	0	0	1	13016	204	8	3		3	RAD50	5	131953819	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08	2712520	131953819	48961441	31	1703											
ZNF346	23567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176471535	176471535	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcagtccactaaggtggaagGtactggttttcctgagtagt	9	12	13	7	0	0	1	0	1	0	0	2	2	2	2	2	4	1	4	2	4	4	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:176471535G>C	ENST00000358149.3	+	4	560		c.e4+1		ZNF346_ENST00000506693.1_Intron|ZNF346_ENST00000503425.1_Splice_Site|ZNF346_ENST00000503039.1_Splice_Site|ZNF346_ENST00000261948.4_Splice_Site|ZNF346_ENST00000512315.1_Intron|ZNF346_ENST00000511834.1_Splice_Site	NM_012279.2	NP_036411.1	Q9UL40	ZN346_HUMAN	zinc finger protein 346						positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGGTGGAAGGTACTGGTTTT	0.552																																					.		.											.	ZNF346-90	0			c.517+1G>C						.						117	109	112					5																	176471535		2203	4300	6503	SO:0001630	splice_region_variant	23567	exon4			TGGAAGGTACTGG	AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761			16403	protein-coding gene	gene with protein product		605308				10488071	Standard	NM_012279		Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000358149.3:c.517+1G>C	5.37:g.176471535G>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	80	28	NM_012279	0	0	0	1	1	B7Z367|Q68CV9|Q6ZMW1	Splice_Site	SNP	ENST00000358149.3	37	CCDS4409.1	.	.	.	.	.	.	.	.	.	.	G	5.228	0.227622	0.09916	.	.	ENSG00000113761	ENST00000358149;ENST00000503425;ENST00000261948;ENST00000511834;ENST00000503039	.	.	.	4.55	3.68	0.42216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.8977	0.35474	0.1045:0.0:0.8955:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF346	176404141	1.000000	0.71417	1.000000	0.80357	0.051000	0.14879	7.687000	0.84139	1.051000	0.40369	-0.160000	0.13428	.	.		0.552	ZNF346-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253415.2	NM_012279	Intron	C	176471535	G	C	176471535	5	2	20	1	0	0	0	0	0	0	1	0	17892	1275	44	4	532	4	ZNF346	5	176471535	Splice_Site	SNP	G	TCGA-A4-8630-01A-11D-2396-08	44517716	176471535	4443725	32	1704											
PECI	10455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	4117677	4117677	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttctttccaaaaataagcatCtctgttgcctgaaatgaaaa	15	13	5	8	0	2	2	0	2	2	0	4	2	3	2	2	0	2	2	2	0	6	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr6:4117677C>G	ENST00000380118.3	-	9	930	c.894G>C	c.(892-894)gaG>gaC	p.E298D	C6orf201_ENST00000333388.5_Intron|C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000465828.1_Missense_Mutation_p.E268D|C6orf201_ENST00000430835.2_Intron|ECI2_ENST00000413766.2_Missense_Mutation_p.E131D|ECI2_ENST00000361538.2_Missense_Mutation_p.E268D|ECI2_ENST00000380125.2_Missense_Mutation_p.E268D			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	298	ECH-like.				fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						AAATAAGCATCTCTGTTGCCT	0.393																																					p.E298D		.											.	ECI2-90	0			c.G894C						.						86	90	89					6																	4117677		2203	4300	6503	SO:0001583	missense	10455	exon9			AAGCATCTCTGTT	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"acyl-Coenzyme A binding domain containing 2", " Hepatocellular carcinoma-associated antigen 88"	608024	"peroxisomal D3,D2-enoyl-CoA isomerase"	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.894G>C	6.37:g.4117677C>G	ENSP00000369461:p.Glu298Asp	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	83	29	NM_206836	0	0	3	3	0	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	37	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129965	0.77549	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000413766;ENST00000361538;ENST00000465828	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43	6.16	4.39	0.52855	Crotonase, core (1);	0.145207	0.64402	D	0.000008	T	0.63498	0.2516	M	0.74389	2.26	0.80722	D	1	P	0.41524	0.753	P	0.47705	0.555	T	0.68965	-0.5270	10	0.54805	T	0.06	.	11.2609	0.49083	0.0:0.8536:0.0:0.1464	.	298	O75521	ECI2_HUMAN	D	298;268;131;268;268	ENSP00000369461:E298D;ENSP00000369468:E268D;ENSP00000406969:E131D;ENSP00000354737:E268D;ENSP00000420309:E268D	ENSP00000354737:E268D	E	-	3	2	ECI2	4062676	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.699000	0.37804	1.627000	0.50400	0.650000	0.86243	GAG	.		0.393	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117		G	4117677	C	G	4117677	3	3	20	1	0	0	0	0	1	0	0	0	11742	912	32	4	298	4	PECI	6	4117677	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		4117677	166997390	33	1705											
CDYL	9425	hgsc.bcm.edu	37	chr6	4891972	4891972	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggattgttgacaaaaggaAaaataaaaaagggaagacag	23	5	11	2	0	0	2	0	1	0	1	0	5	0	5	0	3	0	1	0	3	9	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr6:4891972A>G	ENST00000328908.5	+	4	343	c.212A>G	c.(211-213)aAa>aGa	p.K71R	CDYL_ENST00000472453.1_Intron|CDYL_ENST00000397588.3_Missense_Mutation_p.K17R|CDYL_ENST00000449732.2_5'UTR|CDYL_ENST00000343762.5_5'UTR			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	71	Chromo. {ECO:0000255|PROSITE- ProRule:PRU00053}.|Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		GACAAAAGGAAAAATAAAAAA	0.393																																					p.K17R		.											.	CDYL-90	0			c.A50G						.						40	40	40					6																	4891972		2203	4300	6503	SO:0001583	missense	9425	exon2			AAAGGAAAAATAA	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"CDY-like, autosomal", "testis-specific chromodomain Y-like protein"	603778	"chromodomain protein, Y chromosome-like"			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.212A>G	6.37:g.4891972A>G	ENSP00000330512:p.Lys71Arg	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	40	2	NM_004824	0	0	3	3	0	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		.	.	.	.	.	.	.	.	.	.	A	15.58	2.875807	0.51695	.	.	ENSG00000153046	ENST00000328908;ENST00000397588	T;T	0.73152	-0.72;-0.72	5.64	4.49	0.54785	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.150382	0.56097	D	0.000021	T	0.43344	0.1243	N	0.20685	0.6	0.80722	D	1	B;P	0.39737	0.289;0.685	B;B	0.42245	0.17;0.381	T	0.46190	-0.9209	10	0.38643	T	0.18	.	10.7779	0.46361	0.926:0.0:0.074:0.0	.	17;71	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	R	71;17	ENSP00000330512:K71R;ENSP00000380718:K17R	ENSP00000330512:K71R	K	+	2	0	CDYL	4836971	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.505000	0.53356	0.970000	0.38263	0.528000	0.53228	AAA	.		0.393	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		G	4891972	A	G	4891972	3	3	20	1	0	0	0	0	1	0	0	0	3191	14	1	3	56	3	CDYL	6	4891972	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08	774295	4891972	166223095	34	1706											
TAP1	6890	broad.mit.edu;bcgsc.ca	37	chr6	32813531	32813531	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcactgagcgggagtacCgctcagggctttcgtacagg	9	7	15	10	3	1	1	1	1	0	0	2	3	1	2	1	3	4	5	1	3	3	3	rs200753447	byFrequency	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr6:32813531C>G	ENST00000354258.4	-	11	2413	c.2252G>C	c.(2251-2253)cGg>cCg	p.R751P	PSMB8_ENST00000395339.3_5'Flank|PSMB8_ENST00000374881.2_5'Flank|TAPSAR1_ENST00000453426.1_lincRNA|PSMB9_ENST00000395330.1_Intron|PSMB8_ENST00000374882.3_5'Flank|TAP1_ENST00000425148.2_Missense_Mutation_p.R490P	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	751	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	GCGGGAGTACCGCTCAGGGCT	0.617																																					p.R751P													.	TAP1-91	0			c.G2252C						.						42	42	42					6																	32813531		1509	2708	4217	SO:0001583	missense	6890	exon11			GAGTACCGCTCAG		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.2252G>C	6.37:g.32813531C>G	ENSP00000346206:p.Arg751Pro	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	46	4	NM_000593	0	0	107	107	0	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	C	5.711	0.315657	0.10789	.	.	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.88354	-2.37;-2.36	5.85	4.07	0.47477	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.321554	0.21864	N	0.067993	T	0.73690	0.3619	L	0.52905	1.665	0.09310	N	1	B	0.33739	0.422	B	0.26969	0.075	T	0.65442	-0.6167	10	0.48119	T	0.1	-4.2561	9.0813	0.36554	0.0:0.8313:0.0:0.1687	.	751	Q03518	TAP1_HUMAN	P	751;490	ENSP00000346206:R751P;ENSP00000401919:R490P	ENSP00000346206:R751P	R	-	2	0	TAP1	32921509	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.193000	0.17116	0.814000	0.34374	0.643000	0.83706	CGG	C|0.999;G|0.001		0.617	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		G	32813531	C	G	32813531	3	3	20	1	0	0	0	0	1	0	0	0	15582	652	23	4	178	4	TAP1	6	32813531	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	27921559	32813531	138301536	35	1707											
TIAM2	26230	bcgsc.ca	37	chr6	155566798	155566798	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctctttcctttattacgcGgaccactttaaactgtacag	9	14	7	11	2	1	0	0	0	1	0	2	1	2	1	2	2	3	2	2	2	5	7	rs201618143		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr6:155566798G>A	ENST00000461783.3	+	21	4858	c.3585G>A	c.(3583-3585)gcG>gcA	p.A1195A	TIAM2_ENST00000275246.7_Silent_p.A120A|TIAM2_ENST00000318981.5_Silent_p.A1195A|TIAM2_ENST00000456877.2_Silent_p.A507A|TIAM2_ENST00000529824.2_Silent_p.A1195A|TIAM2_ENST00000456144.1_Silent_p.A1195A|TIAM2_ENST00000360366.4_Silent_p.A1219A|TIAM2_ENST00000528391.2_Silent_p.A531A|TIAM2_ENST00000367174.2_Silent_p.A571A			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1195	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TTTATTACGCGGACCACTTTA	0.403																																					p.A1195A													.	TIAM2-93	0			c.G3585A						.						231	245	240					6																	155566798		2203	4300	6503	SO:0001819	synonymous_variant	26230	exon18			TTACGCGGACCAC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3585G>A	6.37:g.155566798G>A		Somatic	337	0		WXS	Illumina HiSeq	Phase_1	270	7	NM_012454	0	0	0	0	0	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			G|0.999;A|0.001		0.403	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		A	155566798	G	A	155566798	2	1	20	1	0	0	0	0	0	0	0	1	15923	1103	39	1		1	TIAM2	6	155566798	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	122753267	155566798	15548269	36	1708											
WDR27	253769	hgsc.bcm.edu	37	chr6	170047892	170047892	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtactggatgcagcatacaCgtgtgcaggtgggggcggca	9	7	17	8	2	0	0	0	0	0	0	0	1	0	1	0	5	5	5	0	5	2	2	rs567696107		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr6:170047892C>T	ENST00000448612.1	-	16	1743	c.1634G>A	c.(1633-1635)cGt>cAt	p.R545H	WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000333572.6_Missense_Mutation_p.R545H|WDR27_ENST00000423258.1_Missense_Mutation_p.R418H	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	515						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GCAGCATACACGTGTGCAGGT	0.597													C|||	1	0.000199681	0	0	5008	,	,		13974	0		0.001	False		,,,				2504	0				p.R545H		.											.	WDR27-69	0			c.G1634A						.						9	12	11					6																	170047892		2013	4158	6171	SO:0001583	missense	253769	exon16			CATACACGTGTGC	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1634G>A	6.37:g.170047892C>T	ENSP00000416289:p.Arg545His	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	12	8	NM_182552	0	0	5	7	2	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.93|11.93	1.787047|1.787047	0.31593|0.31593	.|.	.|.	ENSG00000184465|ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258|ENST00000441385	T;T;D|.	0.95885|.	1.04;0.98;-3.84|.	0.235|0.235	0.235|0.235	0.15431|0.15431	.|.	0.305391|.	0.24530|.	N|.	0.037737|.	T|T	0.09335|0.09335	0.0230|0.0230	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	D;D;D|.	0.71674|.	0.983;0.998;0.998|.	B;P;P|.	0.58660|.	0.353;0.843;0.738|.	T|T	0.35276|0.35276	-0.9795|-0.9795	9|4	0.46703|.	T|.	0.11|.	0.6156|0.6156	.|.	.|.	.|.	.|.	545;418;545|.	F2Z2U5;A2RRH5-2;C9JGV0|.	.;.;.|.	H|M	545;545;418|179	ENSP00000416289:R545H;ENSP00000330265:R545H;ENSP00000397869:R418H|.	ENSP00000330265:R545H|.	R|V	-|-	2|1	0|0	WDR27|WDR27	169789817|169789817	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	-0.419000|-0.419000	0.07071|0.07071	0.308000|0.308000	0.22923|0.22923	0.313000|0.313000	0.20887|0.20887	CGT|GTG	.		0.597	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		T	170047892	C	T	170047892	3	4	20	1	0	0	0	0	1	0	0	0	17317	536	19	1	979	1	WDR27	6	170047892	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	14481094	170047892	1067175	37	1709											
AMPH	273	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	38431574	38431574	+	Frame_Shift_Del	DEL	A	A	-																															tcgttttctccttcctcttcAtggttggaggcaggctctat																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr7:38431574delA	ENST00000356264.2	-	19	1868	c.1653delT	c.(1651-1653)catfs	p.H551fs	AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000428293.2_Frame_Shift_Del_p.H509fs|AMPH_ENST00000325590.5_Frame_Shift_Del_p.H509fs	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	551					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CTTCCTCTTCATGGTTGGAGG	0.587																																					p.H551fs		.											.	AMPH-95	0			c.1653delT						.						66	65	66					7																	38431574		2203	4300	6503	SO:0001589	frameshift_variant	273	exon19			.		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1653delT	7.37:g.38431574delA	ENSP00000348602:p.His551fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	90	55	NM_001635	0	0	0	0	0	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Frame_Shift_Del	DEL	ENST00000356264.2	37	CCDS5456.1																																																																																			.		0.587	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		-	38431574	A	-	38431574	7	5	20	1	0	1	0	1	0	0	0	0	588	214	8	0	446	0	AMPH	7	38431574	Frame_Shift_Del	DEL	A	TCGA-A4-8630-01A-11D-2396-08		38431574	120707089	38	1710											
ASNS	440	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	97482647	97482647	+	Frame_Shift_Del	DEL	C	C	-																															ctcatttctggtggcagagaCaagtaataggaagaaaatcg																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr7:97482647delC	ENST00000394309.3	-	11	1761	c.1290delG	c.(1288-1290)ttgfs	p.L430fs	ASNS_ENST00000175506.4_Frame_Shift_Del_p.L430fs|ASNS_ENST00000444334.1_Frame_Shift_Del_p.L409fs|ASNS_ENST00000437628.1_Frame_Shift_Del_p.L347fs|ASNS_ENST00000422745.1_Frame_Shift_Del_p.L409fs|ASNS_ENST00000394308.3_Frame_Shift_Del_p.L430fs|ASNS_ENST00000455086.1_Frame_Shift_Del_p.L347fs	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	430	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	GTGGCAGAGACAAGTAATAGG	0.343																																					p.L430fs	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	.											.	ASNS-91	0			c.1290delG						.						73	75	75					7																	97482647		2203	4300	6503	SO:0001589	frameshift_variant	440	exon11			.	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1290delG	7.37:g.97482647delC	ENSP00000377846:p.Leu430fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	109	25	NM_133436	0	0	0	0	0	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Frame_Shift_Del	DEL	ENST00000394309.3	37	CCDS5652.1																																																																																			.		0.343	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		-	97482647	C	-	97482647	7	5	20	1	0	1	0	1	0	0	0	0	1049	477	17	0	407	0	ASNS	7	97482647	Frame_Shift_Del	DEL	C	TCGA-A4-8630-01A-11D-2396-08	59051073	97482647	61656016	39	1711											
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138738764	138738764	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcttctttatcttttcaatCttgaaatttttcatggaagc	10	20	4	7	0	6	1	2	1	4	0	6	2	6	2	0	1	1	0	0	1	4	8			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr7:138738764C>A	ENST00000242351.5	-	11	2581	c.2265G>T	c.(2263-2265)aaG>aaT	p.K755N	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.K877N	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	755	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						TCTTTTCAATCTTGAAATTTT	0.343																																					p.K755N		.											.	ZC3HAV1-91	0			c.G2265T						.						81	81	81					7																	138738764		2203	4300	6503	SO:0001583	missense	56829	exon11			TTCAATCTTGAAA	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	23721	protein-coding gene	gene with protein product	"zinc finger antiviral protein", " CCCH-type zinc finger antiviral protein"	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2265G>T	7.37:g.138738764C>A	ENSP00000242351:p.Lys755Asn	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_020119	0	0	16	16	0	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613704	0.66672	.	.	ENSG00000105939	ENST00000242351;ENST00000464606	T;T	0.14640	2.49;2.49	4.7	1.71	0.24356	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.296935	0.24492	N	0.038050	T	0.17066	0.0410	L	0.52573	1.65	0.80722	D	1	D	0.64830	0.994	P	0.57057	0.812	T	0.16541	-1.0399	10	0.24483	T	0.36	.	2.67	0.05064	0.1933:0.5174:0.1869:0.1024	.	755	Q7Z2W4	ZCCHV_HUMAN	N	755;877	ENSP00000242351:K755N;ENSP00000418385:K877N	ENSP00000242351:K755N	K	-	3	2	ZC3HAV1	138389304	0.967000	0.33354	1.000000	0.80357	0.941000	0.58515	0.249000	0.18216	1.156000	0.42514	0.655000	0.94253	AAG	.		0.343	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		A	138738764	C	A	138738764	3	1	20	1	0	0	0	0	1	0	0	0	17607	912	32	4	455	4	ZC3HAV1	7	138738764	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	41256117	138738764	20399899	40	1712											
SGK223	157285	hgsc.bcm.edu;broad.mit.edu	37	chr8	8176328	8176328	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggctgcggggctgagagtgCcaccagcaggcggggcggca	6	3	20	12	4	0	1	0	1	0	1	0	2	0	1	2	7	3	4	2	7	0	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr8:8176328C>T	ENST00000520004.1	-	6	3821	c.3557G>A	c.(3556-3558)gGc>gAc	p.G1186D	SGK223_ENST00000330777.4_Missense_Mutation_p.G1186D			Q86YV5	SG223_HUMAN		1190	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCTGAGAGTGCCACCAGCAGG	0.766																																					p.G1186D	GBM(34;731 755 10259 33573 33867)	.											.	.	0			c.G3557A						.						5	6	5					8																	8176328		1668	3707	5375	SO:0001583	missense	0	exon5			AGAGTGCCACCAG																												ENST00000520004.1:c.3557G>A	8.37:g.8176328C>T	ENSP00000428054:p.Gly1186Asp	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	14	4	NM_001080826	0	0	1	2	1	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	4.965	0.179191	0.09443	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.60920	0.15;0.15	3.89	-7.79	0.01218	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	3.081050	0.01799	N	0.032764	T	0.37865	0.1019	N	0.14661	0.345	0.09310	N	1	B	0.33919	0.432	B	0.34093	0.175	T	0.40739	-0.9547	10	0.42905	T	0.14	.	9.7595	0.40524	0.1401:0.288:0.5719:0.0	.	1186	Q86YV5	SG223_HUMAN	D	1186	ENSP00000330930:G1186D;ENSP00000428054:G1186D	ENSP00000330930:G1186D	G	-	2	0	AC068353.1	8213738	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.392000	0.01056	-2.066000	0.00886	0.467000	0.42956	GGC	.		0.766	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8176328	C	T	8176328	3	4	20	1	0	0	0	0	1	0	0	0	14242	739	26	2	655	2	SGK223	8	8176328	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		8176328	138187694	41	1713											
ADAM7	8756	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	24339727	24339728	+	Frame_Shift_Ins	INS	-	-	TA																															acatgaagataaaatagaacINStatattcaaatatagaaact																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr8:24339727_24339728insTA	ENST00000175238.6	+	9	861_862	c.778_779insTA	c.(778-780)ctafs	p.L260fs	ADAM7_ENST00000520720.1_Frame_Shift_Ins_p.L32fs|ADAM7_ENST00000380789.1_Frame_Shift_Ins_p.L260fs|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	260	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		TAAAATAGAACTATATTCAAAT	0.307																																					p.L260fs		.											.	ADAM7-230	0			c.778_779insTA						.																																			SO:0001589	frameshift_variant	8756	exon9			.	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.781_782dupTA	8.37:g.24339730_24339731dupTA	ENSP00000175238:p.Leu260fs	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	101	27	NM_003817	0	0	0	0	0	A8K8X7|O75959|Q6PEJ6	Frame_Shift_Ins	INS	ENST00000175238.6	37	CCDS6045.1																																																																																			.		0.307	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		TA	24339728	-	TA	24339727	7	5	20	1	0	1	1	0	0	0	0	0	251	564	20	0	812	0	ADAM7	8	24339727	Frame_Shift_Ins	INS	-	TCGA-A4-8630-01A-11D-2396-08	16163399	24339727	122024295	42	1714											
B4GALT1	2683	bcgsc.ca	37	chr9	33135275	33135275	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtacttgaggtgctcctgcCggttgcggaatggaatgatg	8	11	15	7	2	0	2	0	2	0	0	1	4	1	4	2	4	4	3	2	4	3	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr9:33135275C>T	ENST00000379731.4	-	2	746	c.560G>A	c.(559-561)cGg>cAg	p.R187Q	B4GALT1_ENST00000535206.1_Missense_Mutation_p.R187Q	NM_001497.3	NP_001488.2	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	187	UDP-alpha-D-galactose binding.				acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250)			endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)	14			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	GTGCTCCTGCCGGTTGCGGAA	0.562																																					p.R187Q													.	B4GALT1-90	0			c.G560A						.						104	94	97					9																	33135275		2203	4300	6503	SO:0001583	missense	2683	exon2			TCCTGCCGGTTGC	X14085	CCDS6535.1	9p13	2013-02-19			ENSG00000086062	ENSG00000086062	2.4.1.22	"Beta 4-glycosyltransferases"	924	protein-coding gene	gene with protein product		137060		GGTB2		9597550	Standard	NM_001497		Approved	beta4Gal-T1	uc003zsg.2	P15291	OTTHUMG00000019764	ENST00000379731.4:c.560G>A	9.37:g.33135275C>T	ENSP00000369055:p.Arg187Gln	Somatic	102	0		WXS	Illumina HiSeq	Phase_1	63	4	NM_001497	0	0	72	72	0	B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523	Missense_Mutation	SNP	ENST00000379731.4	37	CCDS6535.1	.	.	.	.	.	.	.	.	.	.	C	36	5.753105	0.96890	.	.	ENSG00000086062	ENST00000535206;ENST00000379731;ENST00000541701	T;T	0.37915	1.17;1.17	5.18	5.18	0.71444	.	0.056828	0.64402	N	0.000001	T	0.70631	0.3246	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78003	-0.2374	10	0.59425	D	0.04	-19.9582	16.5567	0.84487	0.0:1.0:0.0:0.0	.	187	P15291	B4GT1_HUMAN	Q	187;187;144	ENSP00000440341:R187Q;ENSP00000369055:R187Q	ENSP00000369055:R187Q	R	-	2	0	B4GALT1	33125275	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.609000	0.82925	2.848000	0.98002	0.655000	0.94253	CGG	.		0.562	B4GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052039.1	NM_001497		T	33135275	C	T	33135275	3	4	20	1	0	0	0	0	1	0	0	0	1271	652	23	1	656	1	B4GALT1	9	33135275	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		33135275	108078156	43	1715											
AGTPBP1	23287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	88284416	88284416	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactttataagactggaatTcttcttactaaatggtccaa	13	15	5	8	0	3	1	1	0	2	1	4	2	4	2	1	2	1	0	1	2	7	7			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr9:88284416T>G	ENST00000357081.3	-	8	790	c.646A>C	c.(646-648)Aat>Cat	p.N216H	AGTPBP1_ENST00000432218.1_Missense_Mutation_p.N54H|AGTPBP1_ENST00000376080.1_Missense_Mutation_p.N158H|AGTPBP1_ENST00000491784.1_5'UTR|AGTPBP1_ENST00000376081.4_Missense_Mutation_p.N216H|AGTPBP1_ENST00000337006.4_Missense_Mutation_p.N158H|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.N268H|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.N216H			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	216					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGACTGGAATTCTTCTTACTA	0.368																																					p.N216H		.											.	AGTPBP1-158	0			c.A646C						.						94	86	89					9																	88284416		2203	4298	6501	SO:0001583	missense	23287	exon8			TGGAATTCTTCTT	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.646A>C	9.37:g.88284416T>G	ENSP00000349592:p.Asn216His	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	65	26	NM_015239	0	0	0	3	3	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	T	12.67	2.007766	0.35415	.	.	ENSG00000135049	ENST00000337006;ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218;ENST00000376081;ENST00000376080	T;T;T;T;T;T;T	0.52754	1.94;1.94;0.65;0.65;1.94;1.94;1.94	5.76	5.76	0.90799	Armadillo-like helical (1);Armadillo-type fold (1);	0.081135	0.85682	D	0.000000	T	0.54886	0.1886	L	0.32530	0.975	0.54753	D	0.999983	D;D;D;B	0.89917	0.998;1.0;1.0;0.235	D;D;D;B	0.77004	0.949;0.962;0.989;0.102	T	0.46830	-0.9163	10	0.08837	T	0.75	-33.4404	16.087	0.81065	0.0:0.0:0.0:1.0	.	268;216;54;216	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	H	158;216;216;268;54;216;158	ENSP00000338512:N158H;ENSP00000349592:N216H;ENSP00000365251:N216H;ENSP00000365277:N268H;ENSP00000402804:N54H;ENSP00000365249:N216H;ENSP00000365248:N158H	ENSP00000338512:N158H	N	-	1	0	AGTPBP1	87474236	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.376000	0.79658	2.202000	0.70862	0.533000	0.62120	AAT	.		0.368	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88284416	T	G	88284416	3	3	20	1	0	0	0	0	1	0	0	0	400	1783	62	5	2990	5	AGTPBP1	9	88284416	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	55149141	88284416	52929015	44	1716											
CCBL1	883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131597888	131597888	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgcgggaactgcacaaagTagctgctgggttggcggaag	9	7	16	9	2	0	0	0	0	0	0	0	2	0	2	1	4	5	5	1	4	4	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr9:131597888T>A	ENST00000302586.3	-	10	1076	c.914A>T	c.(913-915)tAc>tTc	p.Y305F	CCBL1_ENST00000320665.6_Missense_Mutation_p.Y255F|CCBL1_ENST00000436267.2_Missense_Mutation_p.Y399F|CCBL1_ENST00000483599.1_5'UTR	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	305					cellular amino acid biosynthetic process (GO:0008652)|cellular modified amino acid metabolic process (GO:0006575)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine catabolic process (GO:0097053)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|glutamine-phenylpyruvate transaminase activity (GO:0047316)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-glutamine:pyruvate aminotransferase activity (GO:0047945)|L-phenylalanine-oxaloacetate transaminase activity (GO:0036141)|L-phenylalanine:pyruvate aminotransferase activity (GO:0047312)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)	18					L-Glutamine(DB00130)	CTGCACAAAGTAGCTGCTGGG	0.597																																					p.Y305F		.											.	CCBL1-91	0			c.A914T						.						56	58	57					9																	131597888		2103	4222	6325	SO:0001583	missense	883	exon10			ACAAAGTAGCTGC	Y17448	CCDS43884.1, CCDS48038.1, CCDS75915.1	9q34.11	2008-03-11	2008-03-11		ENSG00000171097	ENSG00000171097	2.6.1.64		1564	protein-coding gene	gene with protein product	"glutamine transaminase K", "kyneurenine aminotransferase"	600547	"cysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)"			7883047	Standard	NM_001122671		Approved	KATI, GTK	uc004bwh.3	Q16773	OTTHUMG00000020767	ENST00000302586.3:c.914A>T	9.37:g.131597888T>A	ENSP00000302227:p.Tyr305Phe	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	57	23	NM_001122671	0	0	4	13	9	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	37	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.960807	0.74016	.	.	ENSG00000171097	ENST00000302586;ENST00000320665;ENST00000436267	D;D;D	0.90261	-2.64;-2.64;-2.64	5.3	5.3	0.74995	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.93304	0.7866	L	0.52364	1.645	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.999	D	0.92808	0.6262	10	0.40728	T	0.16	-2.7503	14.4079	0.67096	0.0:0.0:0.0:1.0	.	399;305;255;305	B7Z4W5;A8K563;Q16773-2;Q16773	.;.;.;KAT1_HUMAN	F	305;255;399	ENSP00000302227:Y305F;ENSP00000317342:Y255F;ENSP00000399415:Y399F	ENSP00000302227:Y305F	Y	-	2	0	CCBL1	130637709	1.000000	0.71417	1.000000	0.80357	0.429000	0.31625	7.196000	0.77805	1.997000	0.58415	0.358000	0.22013	TAC	.		0.597	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2			A	131597888	T	A	131597888	3	1	20	1	0	0	0	0	1	0	0	0	2738	1638	57	5	370	5	CCBL1	9	131597888	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	43313472	131597888	9615543	45	1717											
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670920	131670920	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcgctggccttcctgcgtGagaacctgcgggcgctgcac	4	7	14	16	5	0	1	0	1	0	1	1	2	1	1	4	2	4	3	4	2	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr9:131670920G>T	ENST00000259324.5	+	3	2000	c.1477G>T	c.(1477-1479)Gag>Tag	p.E493*	LRRC8A_ENST00000372599.3_Nonsense_Mutation_p.E493*|LRRC8A_ENST00000372600.4_Nonsense_Mutation_p.E493*	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	493					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						CTTCCTGCGTGAGAACCTGCG	0.617																																					p.E493X		.											.	LRRC8A-90	0			c.G1477T						.						23	23	23					9																	131670920		2202	4300	6502	SO:0001587	stop_gained	56262	exon3			CTGCGTGAGAACC	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"leucine rich repeat containing 8"	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1477G>T	9.37:g.131670920G>T	ENSP00000259324:p.Glu493*	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001127244	0	0	23	23	0	Q6UXM2|Q8NCI0|Q9P2B1	Nonsense_Mutation	SNP	ENST00000259324.5	37	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	G	41	8.754277	0.98941	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	18.4034	0.90525	0.0:0.0:1.0:0.0	.	.	.	.	X	493	.	ENSP00000259324:E493X	E	+	1	0	LRRC8A	130710741	1.000000	0.71417	0.963000	0.40424	0.832000	0.47134	9.869000	0.99810	2.595000	0.87683	0.561000	0.74099	GAG	.		0.617	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		T	131670920	G	T	131670920	4	4	20	1	0	0	0	0	0	1	0	0	9046	1291	45	4	1479	4	LRRC8A	9	131670920	Nonsense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	73032	131670920	9542511	46	1718											
NFKB2	4791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104158555	104158555	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaccttctcccagcccttcGggggtggctcccacatgggt	4	9	11	17	1	1	0	0	0	1	0	4	0	2	0	5	4	1	1	5	4	0	2	rs45580031		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr10:104158555G>A	ENST00000369966.3	+	12	1301	c.1051G>A	c.(1051-1053)Ggg>Agg	p.G351R	NFKB2_ENST00000336486.5_3'UTR|NFKB2_ENST00000189444.6_Missense_Mutation_p.G351R|NFKB2_ENST00000428099.1_Missense_Mutation_p.G351R	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	351	GRR.|Gly-rich.		G -> R (in dbSNP:rs45580031). {ECO:0000269|Ref.7}.		extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	CCAGCCCTTCGGGGGTGGCTC	0.627			T	IGH@	B-NHL																																p.G351R		.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2-522	0			c.G1051A						.						23	25	24					10																	104158555		1910	4115	6025	SO:0001583	missense	4791	exon12			CCCTTCGGGGGTG	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.1051G>A	10.37:g.104158555G>A	ENSP00000358983:p.Gly351Arg	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	35	16	NM_001077494	0	0	15	25	10	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691545	0.48097	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	D;D;D	0.86164	-2.08;-2.08;-2.08	4.56	4.56	0.56223	Immunoglobulin E-set (1);	0.220426	0.45126	D	0.000387	D	0.90686	0.7078	L	0.42245	1.32	0.48341	D	0.999631	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89788	0.3966	10	0.36615	T	0.2	.	17.5171	0.87777	0.0:0.0:1.0:0.0	.	351;351;351	D3DR86;Q00653;A8K9D9	.;NFKB2_HUMAN;.	R	351	ENSP00000410256:G351R;ENSP00000358983:G351R;ENSP00000189444:G351R	ENSP00000189444:G351R	G	+	1	0	NFKB2	104148545	1.000000	0.71417	0.993000	0.49108	0.956000	0.61745	4.681000	0.61663	2.387000	0.81309	0.561000	0.74099	GGG	G|0.993;C|0.007		0.627	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104158555	G	A	104158555	3	1	20	1	0	0	0	0	1	0	0	0	10402	1116	39	1	1093	1	NFKB2	10	104158555	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		104158555	31376192	47	1719											
SMC3	9126	hgsc.bcm.edu	37	chr10	112342364	112342364	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagaaaaatccagacaattAagagatgctcagcaggatgc	17	6	11	7	0	1	3	1	0	0	3	2	6	2	4	1	2	3	2	1	2	4	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr10:112342364A>G	ENST00000361804.4	+	10	894	c.768A>G	c.(766-768)ttA>ttG	p.L256L		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	256					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		CCAGACAATTAAGAGATGCTC	0.323																																					p.L256L		.											.	SMC3-92	0			c.A768G						.						76	76	76					10																	112342364		2203	4300	6503	SO:0001819	synonymous_variant	9126	exon10			ACAATTAAGAGAT	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.768A>G	10.37:g.112342364A>G		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_005445	0	0	26	26	0	A8K156|O60464|Q5T482	Silent	SNP	ENST00000361804.4	37	CCDS31285.1																																																																																			.		0.323	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		G	112342364	A	G	112342364	2	3	20	1	0	0	0	0	0	0	0	1	14816	359	13	3		3	SMC3	10	112342364	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08	8183809	112342364	23192383	48	1720											
TCERG1L	256536	broad.mit.edu	37	chr10	133058651	133058651	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccatggcagcggcggcggCggtggcgatggcaatggcgg	6	4	21	10	6	0	0	0	0	0	0	0	2	0	0	1	9	1	2	1	9	1	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr10:133058651C>T	ENST00000368642.4	-	4	812	c.727G>A	c.(727-729)Gcc>Acc	p.A243T		NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	243	Poly-Ala.									cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		gcggcggcggcggtggcgatg	0.677																																					p.A243T													.	TCERG1L-138	0			c.G727A						.						16	18	17					10																	133058651		2197	4281	6478	SO:0001583	missense	256536	exon4			CGGCGGCGGTGGC	AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.727G>A	10.37:g.133058651C>T	ENSP00000357631:p.Ala243Thr	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_174937	0	0	0	0	0	Q5VWI2|Q86XM8	Missense_Mutation	SNP	ENST00000368642.4	37	CCDS7662.2	.	.	.	.	.	.	.	.	.	.	C	8.982	0.975564	0.18736	.	.	ENSG00000176769	ENST00000368642	T	0.25749	1.78	2.46	1.55	0.23275	.	0.337771	0.24623	N	0.036941	T	0.13415	0.0325	L	0.29908	0.895	0.09310	N	1	B	0.27264	0.173	B	0.13407	0.009	T	0.17048	-1.0382	9	.	.	.	-7.7013	5.3468	0.16014	0.0:0.8345:0.0:0.1655	.	243	Q5VWI1	TCRGL_HUMAN	T	243	ENSP00000357631:A243T	.	A	-	1	0	TCERG1L	132948641	0.023000	0.18921	0.003000	0.11579	0.001000	0.01503	0.210000	0.17455	0.577000	0.29470	-0.150000	0.13652	GCC	.		0.677	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937		T	133058651	C	T	133058651	3	4	20	1	0	0	0	0	1	0	0	0	15718	768	27	1	1069	1	TCERG1L	10	133058651	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	20716287	133058651	2476096	49	1721											
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60702116	60702116	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcacctgcttggccccgaCtggctgctagacgtgtccca	6	8	11	16	3	0	1	0	0	0	1	1	2	1	1	4	2	2	4	4	2	1	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr11:60702116C>G	ENST00000453848.2	+	9	1874	c.1716C>G	c.(1714-1716)gaC>gaG	p.D572E	TMEM132A_ENST00000005286.4_Missense_Mutation_p.D573E			Q24JP5	T132A_HUMAN	transmembrane protein 132A	572						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						TTGGCCCCGACTGGCTGCTAG	0.741																																					p.D573E		.											.	TMEM132A-227	0			c.C1719G						.						8	11	10					11																	60702116		2098	4120	6218	SO:0001583	missense	54972	exon9			CCCCGACTGGCTG	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.1716C>G	11.37:g.60702116C>G	ENSP00000405823:p.Asp572Glu	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_017870	0	0	5	5	0	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.00|15.00	2.704676|2.704676	0.48412|0.48412	.|.	.|.	ENSG00000006118|ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286|ENST00000540112	T;T|.	0.18657|.	2.2;2.2|.	4.16|4.16	0.0201|0.0201	0.14123|0.14123	.|.	0.415295|.	0.22719|.	N|.	0.056480|.	T|T	0.43055|0.43055	0.1230|0.1230	M|M	0.66297|0.66297	2.02|2.02	0.23693|0.23693	N|N	0.99709|0.99709	P;P|.	0.48230|.	0.884;0.907|.	P;P|.	0.53490|.	0.636;0.727|.	T|T	0.37911|0.37911	-0.9685|-0.9685	10|5	0.87932|.	D|.	0|.	.|.	5.2995|5.2995	0.15770|0.15770	0.0:0.4215:0.2573:0.3212|0.0:0.4215:0.2573:0.3212	.|.	572;573|.	Q24JP5;Q24JP5-2|.	T132A_HUMAN;.|.	E|S	323;572;573|1	ENSP00000405823:D572E;ENSP00000005286:D573E|.	ENSP00000005286:D573E|.	D|T	+|+	3|2	2|0	TMEM132A|TMEM132A	60458692|60458692	0.278000|0.278000	0.24230|0.24230	0.275000|0.275000	0.24674|0.24674	0.253000|0.253000	0.25986|0.25986	-0.198000|-0.198000	0.09505|0.09505	0.018000|0.018000	0.15052|0.15052	0.467000|0.467000	0.42956|0.42956	GAC|ACT	.		0.741	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		G	60702116	C	G	60702116	3	3	20	1	0	0	0	0	1	0	0	0	16077	564	20	4	1753	4	TMEM132A	11	60702116	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		60702116	74304400	50	1722											
CTSC	1075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	88045694	88045694	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattgtctcgttgcagtaaGtggtcaccttgctgccctct	5	15	9	12	1	4	0	2	0	2	0	5	0	4	0	2	1	3	4	2	1	1	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr11:88045694G>C	ENST00000227266.5	-	3	461	c.347C>G	c.(346-348)aCt>aGt	p.T116S		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	116					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTTGCAGTAAGTGGTCACCTT	0.458																																					p.T116S		.											.	CTSC-90	0			c.C347G						.						204	192	196					11																	88045694		2201	4299	6500	SO:0001583	missense	1075	exon3			CAGTAAGTGGTCA	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"Cathepsins"	2528	protein-coding gene	gene with protein product	"dipeptidyl peptidase 1"	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.347C>G	11.37:g.88045694G>C	ENSP00000227266:p.Thr116Ser	Somatic	316	0		WXS	Illumina HiSeq	Phase_I	283	119	NM_001814	0	0	333	613	280	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	37	CCDS8282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.162|0.162	-1.079798|-1.079798	0.01888|0.01888	.|.	.|.	ENSG00000109861|ENSG00000109861	ENST00000527018|ENST00000393302;ENST00000227266	.|D	.|0.84442	.|-1.85	5.97|5.97	4.11|4.11	0.48088|0.48088	.|Cathepsin C exclusion (1);	.|0.073747	.|0.85682	.|N	.|0.000000	T|T	0.48259|0.48259	0.1490|0.1490	N|N	0.00050|0.00050	-2.41|-2.41	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.54036|0.54036	-0.8353|-0.8353	5|9	.|.	.|.	.|.	.|.	12.6204|12.6204	0.56600|0.56600	0.1313:0.7414:0.1273:0.0|0.1313:0.7414:0.1273:0.0	.|.	.|116	.|P53634	.|CATC_HUMAN	V|S	73|99;116	.|ENSP00000227266:T116S	.|.	L|T	-|-	1|2	0|0	CTSC|CTSC	87685342|87685342	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.133000|0.133000	0.20885|0.20885	3.944000|3.944000	0.56629|0.56629	0.878000|0.878000	0.35920|0.35920	-0.783000|-0.783000	0.03347|0.03347	CTT|ACT	.		0.458	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		C	88045694	G	C	88045694	3	2	20	1	0	0	0	0	1	0	0	0	4037	1029	36	4	1064	4	CTSC	11	88045694	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	27343578	88045694	46960822	51	1723											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825424	95825424	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctgctgctgttgctgctGttgctgttgggtgtagtgta	2	17	15	7	0	0	0	0	0	0	0	0	0	0	0	0	1	6	11	0	1	2	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr11:95825424G>T	ENST00000524717.1	-	2	3055	c.1771C>A	c.(1771-1773)Cag>Aag	p.Q591K		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	591					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				tgttgctgctgttgctgTTGG	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q591K		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.C1771A						.						53	58	56					11																	95825424		2172	4257	6429	SO:0001583	missense	84441	exon2			GCTGCTGTTGCTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1771C>A	11.37:g.95825424G>T	ENSP00000434552:p.Gln591Lys	Somatic	10	2		WXS	Illumina HiSeq	Phase_I	6	2	NM_032427	0	0	9	9	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	.	.	.	.	.	.	.	.	.	.	G	6.985	0.551899	0.13374	.	.	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.75154	-0.91;-0.91	4.16	4.16	0.48862	.	0.641420	0.14538	N	0.313463	T	0.65719	0.2718	L	0.48642	1.525	0.36744	D	0.882387	B	0.23316	0.083	B	0.18871	0.023	T	0.62695	-0.6800	10	0.09084	T	0.74	-0.3554	14.8068	0.69962	0.0:0.0:1.0:0.0	.	591	Q8IZL2	MAML2_HUMAN	K	591	ENSP00000434552:Q591K;ENSP00000412394:Q591K	ENSP00000412394:Q591K	Q	-	1	0	MAML2	95465072	1.000000	0.71417	0.944000	0.38274	0.017000	0.09413	3.476000	0.53143	2.151000	0.67156	0.555000	0.69702	CAG	.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825424	G	T	95825424	3	4	20	1	0	0	0	0	1	0	0	0	9231	1386	48	4	1715	4	MAML2	11	95825424	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	7779730	95825424	39181092	52	1724											
ROBO3	64221	hgsc.bcm.edu	37	chr11	124739923	124739923	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgtagcctccaacatggCgggagaacgggagagtgcgg	9	5	18	9	4	0	2	0	0	0	2	1	4	1	2	2	4	5	1	2	4	3	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr11:124739923C>T	ENST00000397801.1	+	4	917	c.725C>T	c.(724-726)gCg>gTg	p.A242V	ROBO3_ENST00000538940.1_Missense_Mutation_p.A220V	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	242	Ig-like C2-type 2.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TCCAACATGGCGGGAGAACGG	0.522																																					p.A242V		.											.	ROBO3-113	0			c.C725T						.						75	94	88					11																	124739923		2061	4202	6263	SO:0001583	missense	64221	exon4			ACATGGCGGGAGA	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13433	protein-coding gene	gene with protein product		608630	"roundabout (axon guidance receptor, Drosophila) homolog 3", "horizontal gaze palsy with progressive scoliosis"	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.725C>T	11.37:g.124739923C>T	ENSP00000380903:p.Ala242Val	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_022370	0	0	0	0	0		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457128	0.26161	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.66995	-0.24;-0.24	4.72	4.72	0.59763	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.33309	U	0.005056	T	0.38983	0.1061	N	0.16743	0.435	0.80722	D	1	P	0.35923	0.528	B	0.31495	0.131	T	0.46965	-0.9153	10	0.02654	T	1	.	6.8425	0.23971	0.0:0.7707:0.0:0.2293	.	242	Q96MS0	ROBO3_HUMAN	V	242;220	ENSP00000380903:A242V;ENSP00000441797:A220V	ENSP00000380903:A242V	A	+	2	0	ROBO3	124245133	1.000000	0.71417	0.997000	0.53966	0.794000	0.44872	4.851000	0.62896	2.340000	0.79590	0.462000	0.41574	GCG	.		0.522	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		T	124739923	C	T	124739923	3	4	20	1	0	0	0	0	1	0	0	0	13547	768	27	1	739	1	ROBO3	11	124739923	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	28914499	124739923	10266593	53	1725											
FGF6	2251	hgsc.bcm.edu	37	chr12	4554425	4554425	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcgtgggtcccgctgatccgGccgtcggggagcacctggag	4	7	17	13	5	0	1	0	1	0	0	4	3	2	3	4	5	1	2	4	5	0	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:4554425G>A	ENST00000228837.2	-	1	355	c.312C>T	c.(310-312)ggC>ggT	p.G104G		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	104					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			CGCTGATCCGGCCGTCGGGGA	0.622																																					p.G104G		.											.	FGF6-659	0			c.C312T						.						37	34	35					12																	4554425		2203	4300	6503	SO:0001819	synonymous_variant	2251	exon1			GATCCGGCCGTCG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"Endogenous ligands"	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.312C>T	12.37:g.4554425G>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_020996	0	0	0	0	0	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																			.		0.622	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		A	4554425	G	A	4554425	2	1	20	1	0	0	0	0	0	0	0	1	5875	1190	42	2		2	FGF6	12	4554425	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08		4554425	129297470	54	1726											
DIP2B	57609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	51102296	51102296	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggttgcggaacaaagacCtgatgcttctgaggaagata	12	9	14	6	1	1	4	0	2	1	2	1	6	1	6	1	4	3	2	1	4	4	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:51102296C>A	ENST00000301180.5	+	22	2634	c.2600C>A	c.(2599-2601)cCt>cAt	p.P867H		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	867						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						GAACAAAGACCTGATGCTTCT	0.502																																					p.P867H		.											.	DIP2B-95	0			c.C2600A						.						262	192	215					12																	51102296		2203	4300	6503	SO:0001583	missense	57609	exon22			AAAGACCTGATGC	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.2600C>A	12.37:g.51102296C>A	ENSP00000301180:p.Pro867His	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_173602	0	0	4	8	4	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337555	0.81911	.	.	ENSG00000066084	ENST00000301180	T	0.12465	2.68	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.44953	0.1318	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48581	-0.9023	10	0.66056	D	0.02	-15.6463	18.0462	0.89332	0.0:1.0:0.0:0.0	.	867	Q9P265	DIP2B_HUMAN	H	867	ENSP00000301180:P867H	ENSP00000301180:P867H	P	+	2	0	DIP2B	49388563	1.000000	0.71417	0.968000	0.41197	0.855000	0.48748	5.912000	0.69948	2.826000	0.97356	0.491000	0.48974	CCT	.		0.502	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51102296	C	A	51102296	3	1	20	1	0	0	0	0	1	0	0	0	4539	681	24	4	2686	4	DIP2B	12	51102296	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	46547871	51102296	82749599	55	1727											
LETMD1	25875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	51450186	51450186	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacctgcctcctcccttgttGagacatcgtttgaagactca	8	13	7	13	1	1	3	1	2	0	2	4	4	3	3	4	0	2	2	4	0	2	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:51450186G>A	ENST00000262055.4	+	7	855	c.816G>A	c.(814-816)ttG>ttA	p.L272L	LETMD1_ENST00000550929.1_Silent_p.L216L|LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000547008.1_Silent_p.L148L|LETMD1_ENST00000380123.2_3'UTR|LETMD1_ENST00000552739.1_Silent_p.L155L|LETMD1_ENST00000418425.2_Silent_p.L285L	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	272	LETM1.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						CTCCCTTGTTGAGACATCGTT	0.493																																					p.L285L		.											.	LETMD1-90	0			c.G855A						.						174	148	156					12																	51450186		2203	4300	6503	SO:0001819	synonymous_variant	25875	exon7			CTTGTTGAGACAT	AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"cervical cancer 1 protooncogene"					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.816G>A	12.37:g.51450186G>A		Somatic	230	0		WXS	Illumina HiSeq	Phase_I	171	71	NM_001243689	0	0	44	76	32	A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Silent	SNP	ENST00000262055.4	37	CCDS8806.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347756	0.61183	.	.	ENSG00000050426	ENST00000553043	.	.	.	5.49	3.69	0.42338	.	.	.	.	.	T	0.47192	0.1432	.	.	.	0.80722	D	1	B;B	0.14438	0.01;0.001	B;B	0.14578	0.011;0.004	T	0.44345	-0.9334	7	0.87932	D	0	-8.0385	7.6315	0.28243	0.3175:0.0:0.6825:0.0	.	110;110	B7Z9A7;F8W6J0	.;.	K	41	.	ENSP00000369478:E110K	E	+	1	0	LETMD1	49736453	1.000000	0.71417	0.675000	0.29917	0.599000	0.36880	1.036000	0.30228	0.822000	0.34565	-0.137000	0.14449	GAG	.		0.493	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416		A	51450186	G	A	51450186	2	1	20	1	0	0	0	0	0	0	0	1	8757	1281	45	2		2	LETMD1	12	51450186	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	347890	51450186	82401709	56	1728											
OR6C1	390321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	55714436	55714436	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctgggattaacagatgAcccaaattttcaggttgtaa	12	14	8	7	0	3	2	1	1	2	1	3	3	3	3	1	2	1	2	1	2	3	6			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:55714436A>G	ENST00000379668.2	+	1	91	c.53A>G	c.(52-54)gAc>gGc	p.D18G		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						TTAACAGATGACCCAAATTTT	0.413																																					p.D18G		.											.	OR6C1-69	0			c.A53G						.						76	76	76					12																	55714436		2203	4300	6503	SO:0001583	missense	390321	exon1			CAGATGACCCAAA	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"GPCR / Class A : Olfactory receptors"	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.53A>G	12.37:g.55714436A>G	ENSP00000368990:p.Asp18Gly	Somatic	135	1		WXS	Illumina HiSeq	Phase_I	119	42	NM_001005182	0	0	0	0	0	B2RNM0	Missense_Mutation	SNP	ENST00000379668.2	37	CCDS31818.1	.	.	.	.	.	.	.	.	.	.	a	12.44	1.937163	0.34189	.	.	ENSG00000205330	ENST00000379668	T	0.01335	5.0	5.21	5.21	0.72293	.	0.092850	0.46442	D	0.000284	T	0.03220	0.0094	M	0.64567	1.98	0.30407	N	0.779456	B	0.34372	0.451	B	0.41946	0.371	T	0.01524	-1.1333	10	0.87932	D	0	.	9.7369	0.40392	0.7226:0.2774:0.0:0.0	.	18	Q96RD1	OR6C1_HUMAN	G	18	ENSP00000368990:D18G	ENSP00000368990:D18G	D	+	2	0	OR6C1	54000703	0.000000	0.05858	0.981000	0.43875	0.598000	0.36846	0.070000	0.14573	2.185000	0.69588	0.374000	0.22700	GAC	.		0.413	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182		G	55714436	A	G	55714436	3	3	20	1	0	0	0	0	1	0	0	0	11216	275	10	3	55	3	OR6C1	12	55714436	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08	4264250	55714436	78137459	57	1729											
STAB2	55576	hgsc.bcm.edu	37	chr12	104139037	104139037	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacggggtggacaggccccTcgtgtgacactcaggcaggt	9	6	15	11	2	1	1	1	1	0	0	2	2	1	2	2	6	1	1	2	6	1	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:104139037T>C	ENST00000388887.2	+	57	6322	c.6118T>C	c.(6118-6120)Tcg>Ccg	p.S2040P	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GACAGGCCCCTCGTGTGACAC	0.597																																					p.S2040P		.											.	STAB2-104	0			c.T6118C						.						63	53	56					12																	104139037		2203	4300	6503	SO:0001583	missense	55576	exon57			GGCCCCTCGTGTG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.6118T>C	12.37:g.104139037T>C	ENSP00000373539:p.Ser2040Pro	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_017564	0	0	0	0	0		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	T	7.308	0.614348	0.14129	.	.	ENSG00000136011	ENST00000388887;ENST00000258495	T	0.35421	1.31	4.31	4.31	0.51392	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	1.146940	0.06472	U	0.731372	T	0.35653	0.0939	M	0.65677	2.01	0.21445	N	0.999682	B	0.32160	0.358	B	0.30495	0.116	T	0.32613	-0.9900	10	0.29301	T	0.29	.	5.0961	0.14735	0.0:0.2553:0.0:0.7447	.	2040	Q8WWQ8	STAB2_HUMAN	P	2040;727	ENSP00000373539:S2040P	ENSP00000258495:S727P	S	+	1	0	STAB2	102663167	0.559000	0.26562	0.974000	0.42286	0.006000	0.05464	0.318000	0.19504	1.716000	0.51395	0.451000	0.29950	TCG	.		0.597	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104139037	T	C	104139037	3	2	20	1	0	0	0	0	1	0	0	0	15270	1551	54	3	6344	3	STAB2	12	104139037	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	48424601	104139037	29712858	58	1730											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124887102	124887102	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgttgttgCtgctgctgtcagaccccggg	2	13	14	12	1	1	1	1	0	0	1	1	1	1	1	2	1	7	9	2	1	0	2	rs7488825		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:124887102C>T	ENST00000405201.1	-	14	1488	c.1488G>A	c.(1486-1488)caG>caA	p.Q496Q	NCOR2_ENST00000356219.3_Silent_p.Q496Q|NCOR2_ENST00000404121.2_Silent_p.Q66Q|NCOR2_ENST00000397355.1_Silent_p.Q496Q|NCOR2_ENST00000404621.1_Silent_p.Q495Q|NCOR2_ENST00000429285.2_Silent_p.Q495Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	496	Poly-Gln.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gctgttgttgctgctgctgTC	0.627																																					p.Q496Q		.											.	NCOR2-229	0			c.G1488A						.						9	10	9					12																	124887102		2049	4171	6220	SO:0001819	synonymous_variant	9612	exon16			TTGTTGCTGCTGC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1488G>A	12.37:g.124887102C>T		Somatic	12	1		WXS	Illumina HiSeq	Phase_I	10	2	NM_006312	0	0	0	0	0	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			.		0.627	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124887102	C	T	124887102	2	4	20	1	0	0	0	0	0	0	0	1	10262	796	28	2		2	NCOR2	12	124887102	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	20748065	124887102	8964793	59	1731											
TDRD3	81550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	61034625	61034625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcgattacagatgactgatGgtcatataagttgcacagca	13	11	10	7	1	1	3	1	2	0	1	1	4	1	3	0	1	4	3	0	1	3	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr13:61034625G>A	ENST00000196169.3	+	4	813	c.25G>A	c.(25-27)Ggt>Agt	p.G9S	TDRD3_ENST00000463109.1_3'UTR|TDRD3_ENST00000377881.2_Missense_Mutation_p.G9S|TDRD3_ENST00000377894.2_Missense_Mutation_p.G9S|TDRD3_ENST00000535286.1_Missense_Mutation_p.G102S	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	9					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GATGACTGATGGTCATATAAG	0.358																																					p.G102S	Colon(36;164 906 35820 50723)	.											.	TDRD3-516	0			c.G304A						.						123	111	115					13																	61034625		2203	4300	6503	SO:0001583	missense	81550	exon4			ACTGATGGTCATA	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.25G>A	13.37:g.61034625G>A	ENSP00000196169:p.Gly9Ser	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	111	23	NM_001146070	0	0	6	7	1	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652402	0.96724	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286;ENST00000377882	D;D;D;D	0.99924	-7.4;-7.4;-7.4;-8.02	6.06	6.06	0.98353	.	0.048957	0.85682	N	0.000000	D	0.99937	0.9972	M	0.91920	3.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96414	0.9306	10	0.87932	D	0	-15.3725	20.6397	0.99537	0.0:0.0:1.0:0.0	.	102;9;9	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	S	9;9;9;102;9	ENSP00000196169:G9S;ENSP00000367113:G9S;ENSP00000367126:G9S;ENSP00000440190:G102S	ENSP00000196169:G9S	G	+	1	0	TDRD3	59932626	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.880000	0.98712	0.650000	0.86243	GGT	.		0.358	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61034625	G	A	61034625	3	1	20	1	0	0	0	0	1	0	0	0	15764	1348	47	2	318	2	TDRD3	13	61034625	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		61034625	54135253	60	1732											
SUPT16H	11198	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	21821646	21821648	+	Splice_Site	DEL	CCT	CCT	-																															aaacaacacatttttaaaaaCcttttcgggcttcttcctcc																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr14:21821646_21821648delCCT	ENST00000216297.2	-	25	3335_3337	c.2997_2999delAGG	c.(2995-3000)aaaggg>aag	p.G1000del		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	1000	Glu-rich (acidic).				DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TTTTTAAAAACCTTTTCGGGCTT	0.34																																					p.999_1000del		.											.	SUPT16H-90	0			c.2997_2998del						.																																			SO:0001630	splice_region_variant	11198	exon25			.	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.2998+1AGG>-	14.37:g.21821646_21821648delCCT		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	62	24	NM_007192	0	0	0	0	0	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Frame_Shift_Del	DEL	ENST00000216297.2	37	CCDS9569.1																																																																																			.		0.34	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		In_Frame_Del	-	21821648	CCT	-	21821646	8	5	20	1	0	1	0	1	0	0	1	0	15428	521	18	0	152	0	SUPT16H	14	21821646	Splice_Site	DEL	CCT	TCGA-A4-8630-01A-11D-2396-08		21821646	85527894	61	1733											
RALGAPA1	253959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	36104756	36104756	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttggagcagtgtctttagagGtaaggccatgatccagtcca	10	11	12	8	0	1	2	0	1	1	1	3	3	3	3	3	3	1	2	3	3	2	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr14:36104756G>C	ENST00000389698.3	-	31	4597	c.4207C>G	c.(4207-4209)Cct>Gct	p.P1403A	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.P1450A|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.P1403A|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.P1416A	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1403	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GTCTTTAGAGGTAAGGCCATG	0.363																																					p.P1403A		.											.	RALGAPA1-138	0			c.C4207G						.						49	46	47					14																	36104756		2203	4296	6499	SO:0001583	missense	253959	exon31			TTAGAGGTAAGGC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4207C>G	14.37:g.36104756G>C	ENSP00000374348:p.Pro1403Ala	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	33	15	NM_194301	0	0	2	3	1	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520063	0.85495	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;1.52;-0.2;-0.2	5.41	5.41	0.78517	.	0.100260	0.64402	D	0.000001	T	0.81187	0.4770	M	0.81112	2.525	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;0.98;0.855	D;D;P;P	0.91635	0.999;0.999;0.885;0.667	T	0.81604	-0.0857	10	0.51188	T	0.08	-15.3316	19.5739	0.95434	0.0:0.0:1.0:0.0	.	1450;1416;1403;1403	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	A	1403;1403;1403;1450;41;1416;1450	ENSP00000374348:P1403A;ENSP00000302647:P1403A;ENSP00000258840:P1450A;ENSP00000451133:P41A;ENSP00000371803:P1416A;ENSP00000451877:P1450A	ENSP00000258840:P1450A	P	-	1	0	RALGAPA1	35174507	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.934000	0.92915	2.691000	0.91804	0.563000	0.77884	CCT	.		0.363	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36104756	G	C	36104756	3	2	20	1	0	0	0	0	1	0	0	0	13045	1261	44	4	2096	4	RALGAPA1	14	36104756	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	14283110	36104756	71244784	62	1734											
PSMC6	5706	hgsc.bcm.edu	37	chr14	53194309	53194309	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgattctaagaagctggagTctaaattggactacaaacct	14	11	8	8	0	2	2	0	1	2	1	2	4	2	4	1	2	3	1	1	2	6	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr14:53194309T>G	ENST00000606149.1	+	14	1160	c.1144T>G	c.(1144-1146)Tct>Gct	p.S382A	PSMC6_ENST00000445930.2_Missense_Mutation_p.S396A|STYX_ENST00000442123.2_5'Flank|PSMC6_ENST00000557557.1_3'UTR|STYX_ENST00000354586.4_5'Flank	NM_002806.3	NP_002797.3	P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	382					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)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					GAAGCTGGAGTCTAAATTGGA	0.353																																					p.S396A		.											.	PSMC6-91	0			c.T1186G						.						86	86	86					14																	53194309		2203	4300	6503	SO:0001583	missense	5706	exon14			CTGGAGTCTAAAT		CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9553	protein-coding gene	gene with protein product		602708				8674546, 9473509	Standard	NM_002806		Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000606149.1:c.1144T>G	14.37:g.53194309T>G	ENSP00000475721:p.Ser382Ala	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	85	5	NM_002806	0	0	46	46	0	B2R975|P49719|Q6IBU3|Q92524	Missense_Mutation	SNP	ENST00000606149.1	37		.	.	.	.	.	.	.	.	.	.	T	16.47	3.131801	0.56828	.	.	ENSG00000100519	ENST00000445930	D	0.93659	-3.26	5.3	5.3	0.74995	.	0.101354	0.64402	D	0.000001	D	0.90696	0.7081	L	0.42581	1.335	0.80722	D	1	B	0.16603	0.018	B	0.24848	0.056	D	0.87242	0.2267	10	0.35671	T	0.21	.	15.5436	0.76077	0.0:0.0:0.0:1.0	.	382	P62333	PRS10_HUMAN	A	396	ENSP00000401802:S396A	ENSP00000401802:S396A	S	+	1	0	PSMC6	52264059	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.627000	0.83176	2.123000	0.65237	0.528000	0.53228	TCT	.		0.353	PSMC6-018	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470741.1	NM_002806		G	53194309	T	G	53194309	3	3	20	1	0	0	0	0	1	0	0	0	12720	1667	58	5	1240	5	PSMC6	14	53194309	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	17089553	53194309	54155231	63	1735											
UBE3A	7337	hgsc.bcm.edu	37	chr15	25615995	25615995	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcattaataaactcttcaaaAgggataagtggttttcgaca	15	13	7	6	1	3	0	2	0	1	0	4	2	3	1	0	2	1	1	0	2	6	6			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr15:25615995A>G	ENST00000397954.2	-	4	1334	c.1335T>C	c.(1333-1335)ccT>ccC	p.P445P	UBE3A_ENST00000232165.3_Silent_p.P442P|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000438097.1_Silent_p.P422P|UBE3A_ENST00000566215.1_Silent_p.P422P|UBE3A_ENST00000428984.2_Silent_p.P422P			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	445	Interaction with HCV core protein.				androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		ACTCTTCAAAAGGGATAAGTG	0.358																																					p.P445P		.											.	UBE3A-660	0			c.T1335C						.						33	33	33					15																	25615995		2202	4298	6500	SO:0001819	synonymous_variant	7337	exon7			TTCAAAAGGGATA	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1335T>C	15.37:g.25615995A>G		Somatic	58	1		WXS	Illumina HiSeq	Phase_I	40	2	NM_000462	0	0	9	9	0	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Silent	SNP	ENST00000397954.2	37	CCDS45192.1																																																																																			.		0.358	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		G	25615995	A	G	25615995	2	3	20	1	0	0	0	0	0	0	0	1	16912	59	3	3		3	UBE3A	15	25615995	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08		25615995	76915397	64	1736											
MGA	23269	hgsc.bcm.edu	37	chr15	42041519	42041519	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tacattgaccctgaggatttCtcctcctgaaccacaaagct	11	11	6	13	0	1	3	0	3	1	0	3	4	2	4	4	1	3	1	4	1	3	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr15:42041519C>G	ENST00000570161.1	+	16	5714	c.5714C>G	c.(5713-5715)tCt>tGt	p.S1905C	MGA_ENST00000545763.1_Missense_Mutation_p.S1696C|MGA_ENST00000219905.7_Missense_Mutation_p.S1905C|MGA_ENST00000566586.1_Missense_Mutation_p.S1696C|MGA_ENST00000389936.4_Missense_Mutation_p.S1866C			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTGAGGATTTCTCCTCCTGAA	0.458																																					p.S1905C		.											.	MGA-522	0			c.C5714G						.						86	78	81					15																	42041519		1894	4107	6001	SO:0001583	missense	23269	exon17			GGATTTCTCCTCC	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5714C>G	15.37:g.42041519C>G	ENSP00000457035:p.Ser1905Cys	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_001164273	0	0	8	8	0	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999116	0.54147	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.28454	1.61;1.61;1.61	5.72	5.72	0.89469	.	0.000000	0.49305	D	0.000156	T	0.39937	0.1097	N	0.19112	0.55	0.27919	N	0.938318	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.79784	0.972;0.988;0.993;0.993	T	0.30475	-0.9977	10	0.87932	D	0	.	13.1246	0.59346	0.0:0.927:0.0:0.073	.	521;1696;1905;1866	B4DVS1;F5H7K2;E7ENI0;Q8IWI9	.;.;.;MGAP_HUMAN	C	1905;1866;1696	ENSP00000219905:S1905C;ENSP00000374586:S1866C;ENSP00000442467:S1696C	ENSP00000219905:S1905C	S	+	2	0	MGA	39828811	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.086000	0.57664	2.704000	0.92352	0.563000	0.77884	TCT	.		0.458	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42041519	C	G	42041519	3	3	20	1	0	0	0	0	1	0	0	0	9565	913	32	4	5776	4	MGA	15	42041519	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	16425524	42041519	60489873	65	1737											
DUOXA2	405753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	45410080	45410080	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcaggccgctctcccagaCttaaaatgtatcaccactaa	14	8	6	13	1	2	1	1	0	1	1	3	1	2	1	3	1	1	3	3	1	5	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr15:45410080C>A	ENST00000323030.5	+	6	1221	c.936C>A	c.(934-936)gaC>gaA	p.D312E	DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000559014.1_Intron|DUOXA1_ENST00000558996.1_3'UTR|DUOXA1_ENST00000267803.4_Intron	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	312					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		CTCTCCCAGACTTAAAATGTA	0.627											OREG0023102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D312E		.											.	DUOXA2-226	0			c.C936A						.						56	67	63					15																	45410080		2198	4298	6496	SO:0001583	missense	405753	exon6			CCCAGACTTAAAA	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.936C>A	15.37:g.45410080C>A	ENSP00000319705:p.Asp312Glu	Somatic	140	0	931	WXS	Illumina HiSeq	Phase_I	113	48	NM_207581	0	0	0	0	0	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	37	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747884	0.30955	.	.	ENSG00000140274	ENST00000323030	T	0.58060	0.36	4.74	1.8	0.24995	.	0.658067	0.14730	N	0.301826	T	0.27278	0.0669	N	0.08118	0	0.09310	N	0.999998	B	0.06786	0.001	B	0.08055	0.003	T	0.13737	-1.0498	10	0.44086	T	0.13	-18.3106	4.3109	0.10971	0.1793:0.6307:0.0:0.19	.	312	Q1HG44	DOXA2_HUMAN	E	312	ENSP00000319705:D312E	ENSP00000319705:D312E	D	+	3	2	DUOXA2	43197372	0.001000	0.12720	0.004000	0.12327	0.047000	0.14425	0.068000	0.14531	0.310000	0.22990	0.561000	0.74099	GAC	.		0.627	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581		A	45410080	C	A	45410080	3	1	20	1	0	0	0	0	1	0	0	0	4814	564	20	4	958	4	DUOXA2	15	45410080	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	3368561	45410080	57121312	66	1738											
MYO9A	4649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72172105	72172105	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatattctgccgaaatTccttcagggcttttttaaat	11	16	7	7	1	2	2	1	1	1	1	3	3	3	2	2	1	1	1	2	1	5	7			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr15:72172105T>C	ENST00000356056.5	-	30	6168	c.5696A>G	c.(5695-5697)gAa>gGa	p.E1899G	MYO9A_ENST00000444904.1_Missense_Mutation_p.E1880G|MYO9A_ENST00000424560.1_Missense_Mutation_p.E1970G|MYO9A_ENST00000564571.1_Missense_Mutation_p.E1899G	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1899	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTGCCGAAATTCCTTCAGGGC	0.363																																					p.E1899G		.											.	MYO9A-93	0			c.A5696G						.						108	106	107					15																	72172105		2199	4297	6496	SO:0001583	missense	4649	exon30			CGAAATTCCTTCA	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5696A>G	15.37:g.72172105T>C	ENSP00000348349:p.Glu1899Gly	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	76	35	NM_006901	0	0	4	5	1	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.414821	0.83449	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.14893	2.47;2.47;2.47	4.73	4.73	0.59995	.	.	.	.	.	T	0.42899	0.1223	M	0.79258	2.445	0.58432	D	0.999997	D;D	0.89917	1.0;0.997	D;P	0.79108	0.992;0.848	T	0.43956	-0.9359	9	0.62326	D	0.03	.	14.5012	0.67722	0.0:0.0:0.0:1.0	.	1970;1899	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	G	1899;1970;1880	ENSP00000348349:E1899G;ENSP00000399162:E1970G;ENSP00000398250:E1880G	ENSP00000348349:E1899G	E	-	2	0	MYO9A	69959159	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.593000	0.82686	1.903000	0.55091	0.528000	0.53228	GAA	.		0.363	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72172105	T	C	72172105	3	2	20	1	0	0	0	0	1	0	0	0	10109	1783	62	3	2002	3	MYO9A	15	72172105	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	26762025	72172105	30359287	67	1739											
TMEM204	79652	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1604905	1604905	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggcggcagccatgctcAtctggaacattctccacaag	9	8	10	14	2	3	0	1	0	2	0	4	1	3	1	2	3	3	3	2	3	2	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:1604905A>T	ENST00000566264.1	+	3	1262	c.559A>T	c.(559-561)Atc>Ttc	p.I187F	TMEM204_ENST00000253934.5_Missense_Mutation_p.I187F|IFT140_ENST00000426508.2_Intron|IFT140_ENST00000439987.2_Intron	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	187					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				AGCCATGCTCATCTGGAACAT	0.597																																					p.I187F		.											.	TMEM204-90	0			c.A559T						.						57	62	60					16																	1604905		2025	4177	6202	SO:0001583	missense	79652	exon3			ATGCTCATCTGGA		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"chromosome 16 open reading frame 30"	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.559A>T	16.37:g.1604905A>T	ENSP00000454945:p.Ile187Phe	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	85	23	NM_024600	0	0	2	2	0	D3DU76|Q3KRC1|Q9H7G5	Missense_Mutation	SNP	ENST00000566264.1	37	CCDS42098.1	.	.	.	.	.	.	.	.	.	.	a	19.43	3.826453	0.71143	.	.	ENSG00000131634	ENST00000253934	T	0.56275	0.47	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.63212	0.2492	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66925	-0.5800	10	0.87932	D	0	-17.5451	16.269	0.82606	1.0:0.0:0.0:0.0	.	187	Q9BSN7	TM204_HUMAN	F	187	ENSP00000253934:I187F	ENSP00000253934:I187F	I	+	1	0	TMEM204	1544906	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.882000	0.92420	2.241000	0.73720	0.529000	0.55759	ATC	.		0.597	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600		T	1604905	A	T	1604905	3	4	20	1	0	0	0	0	1	0	0	0	16161	217	8	5	569	5	TMEM204	16	1604905	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08		1604905	88749848	68	1740											
SCNN1B	6338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23387095	23387095	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttccaagaccacatgatcCgtaactgcaactgtggccac	11	8	8	14	1	0	2	0	1	0	1	2	2	2	2	4	1	3	3	4	1	3	2	rs372303239		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:23387095C>T	ENST00000343070.2	+	8	1365	c.1189C>T	c.(1189-1191)Cgt>Tgt	p.R397C	SCNN1B_ENST00000568923.1_Missense_Mutation_p.R370C|SCNN1B_ENST00000307331.5_Missense_Mutation_p.R442C|SCNN1B_ENST00000568085.1_Missense_Mutation_p.R361C	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	397					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CCACATGATCCGTAACTGCAA	0.597																																					p.R397C		.											.	SCNN1B-157	0			c.C1189T						.		CYS/ARG	1,4393	2.1+/-5.4	0,1,2196	191	152	165		1189	2.5	0.7	16		165	0,8600		0,0,4300	no	missense	SCNN1B	NM_000336.2	180	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	possibly-damaging	397/641	23387095	1,12993	2197	4300	6497	SO:0001583	missense	6338	exon8			ATGATCCGTAACT	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.1189C>T	16.37:g.23387095C>T	ENSP00000345751:p.Arg397Cys	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	179	42	NM_000336	0	0	0	0	0	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	37	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	c	11.77	1.739120	0.30774	2.28E-4	0.0	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.64618	-0.11;-0.11	4.65	2.53	0.30540	Na+ channel, amiloride-sensitive, conserved site (1);	1.865040	0.02752	N	0.117609	T	0.67832	0.2935	L	0.48642	1.525	0.09310	N	1	P	0.36171	0.541	P	0.46275	0.51	T	0.58031	-0.7708	10	0.87932	D	0	-11.3583	9.6889	0.40116	0.0:0.7032:0.2048:0.0921	.	397	P51168	SCNNB_HUMAN	C	397;442	ENSP00000345751:R397C;ENSP00000302874:R442C	ENSP00000302874:R442C	R	+	1	0	SCNN1B	23294596	0.007000	0.16637	0.690000	0.30148	0.144000	0.21451	1.280000	0.33202	1.065000	0.40693	0.651000	0.88453	CGT	.		0.597	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			T	23387095	C	T	23387095	3	4	20	1	0	0	0	0	1	0	0	0	13960	652	23	1	1215	1	SCNN1B	16	23387095	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	21782190	23387095	66967658	69	1741											
ELMO3	79767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67236622	67236622	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaaggtgaatgcgctcacTtatggggaggtgctgcggct	8	9	15	9	2	1	1	1	1	0	0	1	2	1	2	1	5	3	3	1	5	3	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:67236622T>A	ENST00000360833.1	+	14	1656	c.1599T>A	c.(1597-1599)acT>acA	p.T533T	ELMO3_ENST00000477898.1_Silent_p.T384T|ELMO3_ENST00000393997.2_Silent_p.T550T|MIR328_ENST00000385213.1_RNA			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	497					apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		ATGCGCTCACTTATGGGGAGG	0.647																																					p.T550T		.											.	ELMO3-90	0			c.T1650A						.						42	49	46					16																	67236622		2076	4215	6291	SO:0001819	synonymous_variant	79767	exon15			GCTCACTTATGGG		CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"Engulfment and cell motility proteins"	17289	protein-coding gene	gene with protein product		606422	"engulfment and cell motility 3 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.1599T>A	16.37:g.67236622T>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	69	44	NM_024712	0	0	6	25	19	B4DV86|Q9H8A5	Silent	SNP	ENST00000360833.1	37																																																																																				.		0.647	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712		A	67236622	T	A	67236622	2	1	20	1	0	0	0	0	0	0	0	1	5080	1596	56	5		5	ELMO3	16	67236622	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	43849527	67236622	23118131	70	1742											
DEF8	54849	hgsc.bcm.edu;broad.mit.edu	37	chr16	90023966	90023966	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctgcggcaggcgatcgaGgagtgcaagcaggtgattct	9	7	16	9	3	1	1	0	1	1	0	2	4	1	2	0	4	4	4	0	4	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:90023966G>A	ENST00000268676.7	+	5	542	c.453G>A	c.(451-453)gaG>gaA	p.E151E	DEF8_ENST00000418391.2_Silent_p.E90E|DEF8_ENST00000569453.1_Silent_p.E90E|DEF8_ENST00000563795.1_Silent_p.E90E|DEF8_ENST00000567874.1_Silent_p.E30E|DEF8_ENST00000563594.1_Silent_p.E90E|DEF8_ENST00000570182.1_Silent_p.E80E	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	151					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		AGGCGATCGAGGAGTGCAAGC	0.647																																					p.E151E		.											.	DEF8-68	0			c.G453A						.						27	24	25					16																	90023966		2185	4291	6476	SO:0001819	synonymous_variant	54849	exon5			GATCGAGGAGTGC	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.453G>A	16.37:g.90023966G>A		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	16	5	NM_207514	0	0	43	56	13	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			.		0.647	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		A	90023966	G	A	90023966	2	1	20	1	0	0	0	0	0	0	0	1	4393	991	35	2		2	DEF8	16	90023966	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	22787344	90023966	330787	71	1743											
TEKT1	83659	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	6703554	6703554	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctaaagtttccttcaatCtaggagaaagggaagaagag	15	8	13	5	0	2	3	1	0	1	3	3	5	3	4	1	3	0	2	1	3	7	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:6703554C>A	ENST00000338694.2	-	8	1179		c.e8-1		TEKT1_ENST00000535086.1_Splice_Site	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1							cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				TTCCTTCAATCTAGGAGAAAG	0.463																																					.		.											.	TEKT1-92	0			c.1050-1G>T						.						55	53	53					17																	6703554		2203	4300	6503	SO:0001630	splice_region_variant	83659	exon9			TTCAATCTAGGAG		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.1050-1G>T	17.37:g.6703554C>A		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	101	29	NM_053285	0	0	0	0	0	D3DTM7	Splice_Site	SNP	ENST00000338694.2	37	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.558722	0.45590	.	.	ENSG00000167858	ENST00000338694;ENST00000535086	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8163	0.88635	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TEKT1	6644278	1.000000	0.71417	0.148000	0.22405	0.065000	0.16274	5.783000	0.68982	2.885000	0.99019	0.655000	0.94253	.	.		0.463	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	Intron	A	6703554	C	A	6703554	5	1	20	1	0	0	0	0	0	0	1	0	15784	927	32	4	211	4	TEKT1	17	6703554	Splice_Site	SNP	C	TCGA-A4-8630-01A-11D-2396-08		6703554	74491656	72	1744											
POLR2A	5430	bcgsc.ca	37	chr17	7402776	7402776	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggacacactcacagcagtgcGcaaattcaccaagagagacg	15	4	10	12	2	2	2	2	0	0	2	2	4	2	3	1	1	2	2	1	1	2	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:7402776G>A	ENST00000322644.6	+	10	2036	c.1637G>A	c.(1636-1638)cGc>cAc	p.R546H	POLR2A_ENST00000572844.1_Missense_Mutation_p.R546H	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	546					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ACAGCAGTGCGCAAATTCACC	0.577																																					p.R546H													.	POLR2A-91	0			c.G1637A						.						103	91	95					17																	7402776		2203	4300	6503	SO:0001583	missense	5430	exon10			CAGTGCGCAAATT			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.1637G>A	17.37:g.7402776G>A	ENSP00000314949:p.Arg546His	Somatic	53	0		WXS	Illumina HiSeq	Phase_1	79	5	NM_000937	0	0	62	62	0	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375047	0.95923	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.78816	-1.21	6.04	6.04	0.98038	RNA polymerase Rpb1, domain 3 (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90181	0.6931	M	0.89968	3.075	0.80722	D	1	D;D	0.76494	0.958;0.999	P;D	0.64776	0.657;0.929	D	0.91231	0.5014	10	0.87932	D	0	-10.3575	19.3663	0.94464	0.0:0.0:1.0:0.0	.	546;546	P24928;Q6NX41	RPB1_HUMAN;.	H	502;546	ENSP00000314949:R546H	ENSP00000314949:R546H	R	+	2	0	SLC35G6	7343500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.165000	0.94761	2.873000	0.98535	0.563000	0.77884	CGC	.		0.577	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		A	7402776	G	A	7402776	3	1	20	1	0	0	0	0	1	0	0	0	12240	1087	38	1	1675	1	POLR2A	17	7402776	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	699222	7402776	73792434	73	1745											
RAI1	10743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17701717	17701717	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggcagagcccggcggggagGcccaggagcactgggtgcat	7	3	19	12	3	0	1	0	0	0	1	0	3	0	3	2	7	3	3	2	7	0	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:17701717G>A	ENST00000353383.1	+	3	5924	c.5455G>A	c.(5455-5457)Gcc>Acc	p.A1819T	RAI1_ENST00000261641.6_Intron	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1819					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CGGCGGGGAGGCCCAGGAGCA	0.692																																					p.A1819T		.											.	RAI1-91	0			c.G5455A						.						15	17	16					17																	17701717		2196	4296	6492	SO:0001583	missense	10743	exon3			GGGGAGGCCCAGG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.5455G>A	17.37:g.17701717G>A	ENSP00000323074:p.Ala1819Thr	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	26	17	NM_030665	0	0	4	26	22	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	3.249	-0.153699	0.06585	.	.	ENSG00000108557	ENST00000353383;ENST00000395776	T	0.65364	-0.15	4.42	0.819	0.18785	.	0.164676	0.41605	N	0.000849	T	0.24928	0.0605	N	0.01576	-0.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04900	-1.0919	10	0.09843	T	0.71	.	5.4772	0.16702	0.6904:0.146:0.1635:0.0	.	1819	Q7Z5J4	RAI1_HUMAN	T	1819	ENSP00000323074:A1819T	ENSP00000323074:A1819T	A	+	1	0	RAI1	17642442	1.000000	0.71417	0.989000	0.46669	0.093000	0.18481	3.093000	0.50217	-0.047000	0.13423	-0.367000	0.07326	GCC	.		0.692	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		A	17701717	G	A	17701717	3	1	20	1	0	0	0	0	1	0	0	0	13039	1203	42	2	5457	2	RAI1	17	17701717	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	10298941	17701717	63493493	74	1746											
ALDH3A2	224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	19566808	19566808	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatgtattttcgcataaccAtaaggtaagctttagagaga	14	14	8	5	1	0	2	0	0	0	2	1	3	0	2	1	1	2	4	1	1	6	9			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:19566808A>G	ENST00000176643.6	+	7	1549	c.1103A>G	c.(1102-1104)cAt>cGt	p.H368R	ALDH3A2_ENST00000571163.1_Missense_Mutation_p.H41R|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.H368R|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.H368R|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.H368R|SNORA31_ENST00000516540.1_RNA|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.H368R			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	368					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					TCGCATAACCATAAGGTAAGC	0.358																																					p.H368R		.											.	ALDH3A2-228	0			c.A1103G						.						77	76	76					17																	19566808		2203	4300	6503	SO:0001583	missense	224	exon7			ATAACCATAAGGT	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"Aldehyde dehydrogenases"	403	protein-coding gene	gene with protein product	"fatty aldehyde dehydrogenase"	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.1103A>G	17.37:g.19566808A>G	ENSP00000176643:p.His368Arg	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	82	37	NM_001031806	0	0	1	1	0	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	.	.	.	.	.	.	.	.	.	.	A	6.134	0.392977	0.11638	.	.	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	T;T;T	0.75367	-0.93;-0.93;-0.93	5.12	2.89	0.33648	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.561400	0.20786	N	0.085705	T	0.41581	0.1165	N	0.01003	-1.06	0.09310	N	0.99999	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.33163	-0.9879	10	0.33141	T	0.24	-1.3235	7.2008	0.25879	0.7763:0.147:0.0766:0.0	.	368;368	P51648;P51648-2	AL3A2_HUMAN;.	R	368	ENSP00000176643:H368R;ENSP00000378942:H368R;ENSP00000345774:H368R	ENSP00000176643:H368R	H	+	2	0	ALDH3A2	19507400	0.592000	0.26832	0.274000	0.24659	0.402000	0.30811	2.992000	0.49417	0.289000	0.22422	0.455000	0.32223	CAT	.		0.358	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			G	19566808	A	G	19566808	3	3	20	1	0	0	0	0	1	0	0	0	498	217	8	3	1129	3	ALDH3A2	17	19566808	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08	1865091	19566808	61628402	75	1747											
ACCN1	40	hgsc.bcm.edu	37	chr17	31618997	31618997	+	Intron	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctggcccctgcagcgccCgctcgccgcctctgccgccc	1	5	10	25	5	1	0	0	0	1	0	2	0	1	0	9	1	3	2	9	1	0	0	rs112647385	byFrequency	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:31618997C>A	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Missense_Mutation_p.R46L	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CTGCAGCGCCCGCTCGCCGCC	0.806													C|||	1091	0.217851	0.112	0.1902	5008	,	,		5226	0.3194		0.2664	False		,,,				2504	0.226				p.R46L		.											.	.	0			c.G137T						.						1	2	2					17																	31618997		903	2226	3129	SO:0001627	intron_variant	40	exon1			AGCGCCCGCTCGC	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179912G>T	17.37:g.31618997C>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_183377	0	0	0	0	0	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	37	CCDS42296.1	567	0.25961538461538464	84	0.17073170731707318	81	0.22375690607734808	197	0.34440559440559443	205	0.2704485488126649	C	13.69	2.313571	0.40996	.	.	ENSG00000108684	ENST00000225823	T	0.65178	-0.14	4.45	-0.0635	0.13776	.	1.386070	0.04769	N	0.427624	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.17038	0.02	B	0.10450	0.005	T	0.17715	-1.0360	9	0.29301	T	0.29	-24.8125	4.0823	0.09932	0.0:0.3667:0.3479:0.2854	.	46	E9PBX2	.	L	46	ENSP00000225823:R46L	ENSP00000225823:R46L	R	-	2	0	ACCN1	28643110	0.458000	0.25760	0.926000	0.36857	0.865000	0.49528	1.119000	0.31258	0.274000	0.22072	0.306000	0.20318	CGG	C|0.740;A|0.260		0.806	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		A	31618997	C	A	31618997	1	1	20	0	1	0	0	0	0	0	0	0	128	652	23	4		4	ACCN1	17	31618997	Intron	SNP	C	TCGA-A4-8630-01A-11D-2396-08	12052189	31618997	49576213	76	1748											
TAF15	8148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34171754	34171754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggctatggaggagatcgagGtggctatggaggagaccgag	10	7	19	5	2	0	2	0	0	0	2	1	8	0	4	1	7	0	2	1	7	2	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:34171754G>A	ENST00000588240.1	+	15	1566	c.1451G>A	c.(1450-1452)gGt>gAt	p.G484D	TAF15_ENST00000592237.1_Intron|TAF15_ENST00000311979.3_Missense_Mutation_p.G481D	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		ggagatcgaggtggctatgga	0.617			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.G484D		.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15-723	0			c.G1451A						.						69	59	62					17																	34171754		2203	4300	6503	SO:0001583	missense	8148	exon15			ATCGAGGTGGCTA	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1451G>A	17.37:g.34171754G>A	ENSP00000466950:p.Gly484Asp	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_139215	0	0	68	199	131	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	37	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.613730	0.46631	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	D	0.95171	-3.63	4.33	3.36	0.38483	.	.	.	.	.	D	0.88250	0.6386	N	0.22421	0.69	0.35491	D	0.798963	P;P	0.39282	0.536;0.666	B;B	0.35240	0.097;0.198	D	0.89286	0.3615	9	0.87932	D	0	.	9.8408	0.40998	0.1042:0.0:0.8958:0.0	.	484;481	Q92804;Q92804-2	RBP56_HUMAN;.	D	484;287	ENSP00000309558:G484D	ENSP00000309558:G484D	G	+	2	0	TAF15	31195867	0.956000	0.32656	0.753000	0.31225	0.954000	0.61252	3.509000	0.53386	0.943000	0.37553	0.467000	0.42956	GGT	.		0.617	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		A	34171754	G	A	34171754	3	1	20	1	0	0	0	0	1	0	0	0	15550	1261	44	2	1509	2	TAF15	17	34171754	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	2552757	34171754	47023456	77	1749											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305510	39305510	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcacagcacaaggggcggggGcaggtggagatgacacaggt	11	3	19	8	1	0	2	0	1	0	1	0	3	0	2	0	7	1	3	0	7	1	0	rs539184974	byFrequency	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:39305510G>A	ENST00000343246.4	-	1	544	c.510C>T	c.(508-510)tgC>tgT	p.C170C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	170					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGGGGCGGGGGCAGGTGGAGA	0.537													G|||	3	0.000599042	0	0.0014	5008	,	,		20131	0		0.002	False		,,,				2504	0				p.C170C		.											.	KRTAP4-5-90	0			c.C510T						.						38	29	32					17																	39305510		2203	4300	6503	SO:0001819	synonymous_variant	85289	exon1			GCGGGGGCAGGTG	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.510C>T	17.37:g.39305510G>A		Somatic	31	2		WXS	Illumina HiSeq	Phase_I	27	3	NM_033188	0	0	0	0	0		Silent	SNP	ENST00000343246.4	37	CCDS32650.1																																																																																			.		0.537	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			A	39305510	G	A	39305510	2	1	20	1	0	0	0	0	0	0	0	1	8575	1195	42	2		2	KRTAP4-5	17	39305510	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	5133756	39305510	41889700	78	1750											
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65074431	65074431	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctaggctcagttcctggaaGagagacagagggtcgctact	10	8	13	10	1	1	3	1	0	0	3	3	5	2	4	2	3	1	3	2	3	3	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:65074431G>A	ENST00000358691.5	-	33	5932	c.5766C>T	c.(5764-5766)ctC>ctT	p.L1922L	HELZ_ENST00000580168.1_Silent_p.L1923L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1922						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GTTCCTGGAAGAGAGACAGAG	0.522																																					p.L1922L		.											.	HELZ-92	0			c.C5766T						.						44	46	45					17																	65074431		1860	4094	5954	SO:0001819	synonymous_variant	9931	exon33			CTGGAAGAGAGAC	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.5766C>T	17.37:g.65074431G>A		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	124	35	NM_014877	0	0	4	7	3	I6L9H4	Silent	SNP	ENST00000358691.5	37	CCDS42374.1																																																																																			.		0.522	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65074431	G	A	65074431	2	1	20	1	0	0	0	0	0	0	0	1	7070	929	33	2		2	HELZ	17	65074431	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	25768921	65074431	16120779	79	1751											
SMCHD1	23347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2718194	2718194	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agattatttcgcatattagtCaacatggaggaaaatggcct	14	12	9	6	1	1	1	1	0	0	1	2	3	1	3	1	3	1	1	1	3	6	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr18:2718194C>T	ENST00000320876.6	+	18	2637	c.2299C>T	c.(2299-2301)Caa>Taa	p.Q767*	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Nonsense_Mutation_p.Q767*	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	767					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GCATATTAGTCAACATGGAGG	0.284																																					p.Q767X		.											.	SMCHD1-46	0			c.C2299T						.						91	85	87					18																	2718194		1809	4065	5874	SO:0001587	stop_gained	23347	exon18			ATTAGTCAACATG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2299C>T	18.37:g.2718194C>T	ENSP00000326603:p.Gln767*	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	46	19	NM_015295	0	0	0	0	0	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Nonsense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313068	0.81358	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	.	.	.	5.62	5.62	0.85841	.	0.063495	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.072	19.6473	0.95784	0.0:1.0:0.0:0.0	.	.	.	.	X	767	.	ENSP00000261598:Q767X	Q	+	1	0	SMCHD1	2708194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.933000	0.70130	2.650000	0.89964	0.591000	0.81541	CAA	.		0.284	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2718194	C	T	2718194	4	4	20	1	0	0	0	0	0	1	0	0	14820	827	29	2	2369	2	SMCHD1	18	2718194	Nonsense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		2718194	75359054	80	1752											
TCF4	6925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	52921812	52921812	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccattatgagaaggtccAatgattccatgcatgtcccc	10	11	8	12	0	0	2	0	2	0	1	4	3	4	2	5	1	1	2	5	1	3	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr18:52921812A>G	ENST00000356073.4	-	15	1877	c.1266T>C	c.(1264-1266)atT>atC	p.I422I	TCF4_ENST00000570287.2_Silent_p.I262I|TCF4_ENST00000564228.1_Silent_p.I351I|TCF4_ENST00000564999.1_Silent_p.I422I|TCF4_ENST00000544241.2_Silent_p.I351I|TCF4_ENST00000565018.2_Silent_p.I422I|TCF4_ENST00000568740.1_Silent_p.I397I|TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000566279.1_Silent_p.I362I|TCF4_ENST00000457482.3_Silent_p.I262I|TCF4_ENST00000537578.1_Silent_p.I398I|TCF4_ENST00000566286.1_Silent_p.I419I|TCF4_ENST00000567880.1_Silent_p.I362I|TCF4_ENST00000398339.1_Silent_p.I524I|TCF4_ENST00000568673.1_Silent_p.I398I|TCF4_ENST00000561831.3_Silent_p.I262I|TCF4_ENST00000354452.3_Silent_p.I422I|TCF4_ENST00000561992.1_Silent_p.I292I|TCF4_ENST00000537856.3_Silent_p.I292I|TCF4_ENST00000564403.2_Silent_p.I428I|TCF4_ENST00000570177.2_Silent_p.I292I|TCF4_ENST00000543082.1_Silent_p.I380I|TCF4_ENST00000540999.1_Silent_p.I398I	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	422					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GAGAAGGTCCAATGATTCCAT	0.493																																					p.I524I		.											.	TCF4-523	0			c.T1572C						.						118	106	110					18																	52921812		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon16			AGGTCCAATGATT	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1266T>C	18.37:g.52921812A>G		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	53	22	NM_001243226	0	0	0	0	0	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	37	CCDS11960.1																																																																																			.		0.493	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		G	52921812	A	G	52921812	2	3	20	1	0	0	0	0	0	0	0	1	15727	126	5	3		3	TCF4	18	52921812	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08	50203618	52921812	25155436	81	1753											
APC2	10297	hgsc.bcm.edu	37	chr19	1460857	1460857	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acagtgaggagctccaccagGtacagggcggggtgctggga	9	5	18	9	1	0	1	0	1	0	0	1	3	1	3	2	6	3	3	2	6	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:1460857G>T	ENST00000535453.1	+	11	3234		c.e11+1		APC2_ENST00000238483.4_Splice_Site|APC2_ENST00000233607.2_Splice_Site|CTB-25B13.12_ENST00000588225.1_RNA			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2						cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCCACCAGGTACAGGGCGG	0.697																																					.		.											.	APC2-290	0			c.1521+1G>T						.						23	27	26					19																	1460857		2200	4295	6495	SO:0001630	splice_region_variant	10297	exon12			CACCAGGTACAGG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.1521+1G>T	19.37:g.1460857G>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_005883	0	0	11	11	0	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Splice_Site	SNP	ENST00000535453.1	37	CCDS12068.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.794659	0.31777	.	.	ENSG00000115266	ENST00000233607;ENST00000238483;ENST00000535453	.	.	.	4.07	1.92	0.25849	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.8948	0.35458	0.1893:0.0:0.8107:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	APC2	1411857	1.000000	0.71417	0.989000	0.46669	0.477000	0.33069	5.418000	0.66429	0.384000	0.24942	-0.251000	0.11542	.	.		0.697	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	Intron	T	1460857	G	T	1460857	5	4	20	1	0	0	0	0	0	0	1	0	764	1275	44	4	1564	4	APC2	19	1460857	Splice_Site	SNP	G	TCGA-A4-8630-01A-11D-2396-08		1460857	57668126	82	1754											
KHSRP	8570	hgsc.bcm.edu	37	chr19	6420477	6420477	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccctgtactcttctgtcattGaagtcctgtaaagagacacg	10	12	8	11	1	3	2	1	1	2	1	4	3	4	2	2	0	1	2	2	0	4	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:6420477G>C	ENST00000398148.3	-	5	523	c.431C>G	c.(430-432)tCa>tGa	p.S144*		NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	144	Gly-rich.|KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						TTCTGTCATTGAAGTCCTGTA	0.577																																					p.S144X	Colon(55;593 1006 2067 9135 22980)	.											.	KHSRP-226	0			c.C431G						.						59	64	62					19																	6420477		2038	4196	6234	SO:0001587	stop_gained	8570	exon5			GTCATTGAAGTCC	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"FUSE binding protein 2"	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.431C>G	19.37:g.6420477G>C	ENSP00000381216:p.Ser144*	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_003685	0	0	2	2	0	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Nonsense_Mutation	SNP	ENST00000398148.3	37	CCDS45936.1	.	.	.	.	.	.	.	.	.	.	G	36	5.747406	0.96882	.	.	ENSG00000088247	ENST00000398148;ENST00000201886;ENST00000424942	.	.	.	4.88	3.85	0.44370	.	0.391333	0.26478	N	0.024152	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	11.8559	0.52437	0.0857:0.0:0.9143:0.0	.	.	.	.	X	144;144;100	.	ENSP00000201886:S144X	S	-	2	0	KHSRP	6371477	0.995000	0.38212	0.891000	0.34965	0.736000	0.42039	3.476000	0.53143	1.266000	0.44231	0.655000	0.94253	TCA	.		0.577	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			C	6420477	G	C	6420477	4	2	20	1	0	0	0	0	0	1	0	0	8172	1294	45	4	1768	4	KHSRP	19	6420477	Nonsense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	4959620	6420477	52708506	83	1755											
FBN3	84467	hgsc.bcm.edu	37	chr19	8203361	8203361	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcacctgcccctgtcacagCagcactgcctgcgagtgtag	8	7	11	15	1	1	0	1	0	0	0	1	1	1	0	4	0	6	4	4	0	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:8203361C>A	ENST00000600128.1	-	9	1367	c.953G>T	c.(952-954)tGc>tTc	p.C318F	FBN3_ENST00000270509.2_Missense_Mutation_p.C318F|FBN3_ENST00000601739.1_Missense_Mutation_p.C318F			Q75N90	FBN3_HUMAN	fibrillin 3	318	TB 2.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCTGTCACAGCAGCACTGCCT	0.662																																					p.C318F		.											.	FBN3-100	0			c.G953T						.						26	29	28					19																	8203361		2203	4298	6501	SO:0001583	missense	84467	exon8			TCACAGCAGCACT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.953G>T	19.37:g.8203361C>A	ENSP00000470498:p.Cys318Phe	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_032447	0	0	0	0	0	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	c	19.80	3.895457	0.72639	.	.	ENSG00000142449	ENST00000270509	D	0.99875	-7.4	4.06	4.06	0.47325	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	U	0.000000	D	0.99883	0.9944	M	0.92738	3.34	0.49483	D	0.999794	D	0.89917	1.0	D	0.91635	0.999	D	0.96243	0.9177	10	0.56958	D	0.05	.	16.1794	0.81889	0.0:1.0:0.0:0.0	.	318	Q75N90	FBN3_HUMAN	F	318	ENSP00000270509:C318F	ENSP00000270509:C318F	C	-	2	0	FBN3	8109361	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	7.232000	0.78116	1.974000	0.57490	0.556000	0.70494	TGC	.		0.662	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8203361	C	A	8203361	3	1	20	1	0	0	0	0	1	0	0	0	5723	710	25	4	7700	4	FBN3	19	8203361	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	1782884	8203361	50925622	84	1756											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9056220	9056220	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttgataagcacttgtcactGttcccagctcaacgctctct	8	13	6	14	1	3	1	2	1	1	0	5	1	4	1	1	0	3	4	1	0	2	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:9056220G>C	ENST00000397910.4	-	3	31429	c.31226C>G	c.(31225-31227)aCa>aGa	p.T10409R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10411	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACTTGTCACTGTTCCCAGCTC	0.473																																					p.T10409R		.											.	MUC16-566	0			c.C31226G						.						201	199	200					19																	9056220		2020	4181	6201	SO:0001583	missense	94025	exon3			GTCACTGTTCCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31226C>G	19.37:g.9056220G>C	ENSP00000381008:p.Thr10409Arg	Somatic	268	0		WXS	Illumina HiSeq	Phase_I	246	94	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	7.773	0.707853	0.15239	.	.	ENSG00000181143	ENST00000397910	T	0.02525	4.26	3.94	-6.08	0.02151	.	.	.	.	.	T	0.01489	0.0048	N	0.19112	0.55	.	.	.	B	0.33044	0.395	B	0.27076	0.076	T	0.43798	-0.9369	8	0.87932	D	0	.	0.9223	0.01318	0.1739:0.2499:0.196:0.3802	.	10409	B5ME49	.	R	10409	ENSP00000381008:T10409R	ENSP00000381008:T10409R	T	-	2	0	MUC16	8917220	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.198000	0.01239	-1.038000	0.03279	-0.181000	0.13052	ACA	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9056220	G	C	9056220	3	2	20	1	0	0	0	0	1	0	0	0	9998	1377	48	4	12625	4	MUC16	19	9056220	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	852859	9056220	50072763	85	1757											
ZNF93	81931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	20044771	20044771	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacacataagagaattcataCtggagagaaaccatacaagt	19	8	7	7	0	1	2	1	0	0	2	1	5	1	3	1	1	4	0	1	1	7	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:20044771C>T	ENST00000343769.5	+	4	1035	c.1007C>T	c.(1006-1008)aCt>aTt	p.T336I	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						AGAATTCATACTGGAGAGAAA	0.378																																					p.T336I		.											.	ZNF93-91	0			c.C1007T						.						57	57	57					19																	20044771		2203	4300	6503	SO:0001583	missense	81931	exon4			TTCATACTGGAGA	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"Zinc fingers, C2H2-type", "-"	13169	protein-coding gene	gene with protein product		603975	"zinc finger protein 505", "zinc finger protein 93 (HTF34)"	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.1007C>T	19.37:g.20044771C>T	ENSP00000342002:p.Thr336Ile	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	53	21	NM_031218	0	0	27	28	1	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	.	.	.	.	.	.	.	.	.	.	c	17.57	3.422998	0.62733	.	.	ENSG00000184635	ENST00000343769;ENST00000427325	T	0.25749	1.78	0.85	0.85	0.18980	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46521	0.1397	M	0.77103	2.36	0.28256	N	0.925036	D	0.71674	0.998	D	0.76575	0.988	T	0.30208	-0.9986	9	0.87932	D	0	.	6.9971	0.24789	0.0:1.0:0.0:0.0	.	336	P35789	ZNF93_HUMAN	I	336	ENSP00000342002:T336I	ENSP00000342002:T336I	T	+	2	0	ZNF93	19905771	0.931000	0.31567	0.796000	0.32109	0.795000	0.44927	1.895000	0.39778	0.192000	0.20272	0.195000	0.17529	ACT	.		0.378	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		T	20044771	C	T	20044771	3	4	20	1	0	0	0	0	1	0	0	0	18234	565	20	2	1021	2	ZNF93	19	20044771	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	10988551	20044771	39084212	86	1758											
ZNF585A	199704	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	37642652	37642653	+	Missense_Mutation	DNP	GC	GC	TA																															acactcagcacacacgtaagGcttctctccagtgtgaattc																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:37642652_37642653GC>TA	ENST00000356958.4	-	5	2406_2407	c.2148_2149GC>TA	c.(2146-2151)aaGCct>aaTAct	p.716_717KP>NT	ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.661_662KP>NT|ZNF585A_ENST00000292841.5_Missense_Mutation_p.661_662KP>NT|ZNF585A_ENST00000355533.2_Missense_Mutation_p.353_354KP>NT			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	716					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CACACGTAAGGCTTCTCTCCAG	0.45																																					p.KP716NT		.											.	ZNF585A	0			c.G1983T						.																																			SO:0001583	missense	199704	exon6			GTAAGGCTTCTCT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.2148_2149delinsTA	19.37:g.37642652_37642653delinsTA	ENSP00000349440:p.K716_P717delinsNT	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	106	46		0	0	0	0	0	Q8TE95|Q96MV3	Missense_Mutation	DNP	ENST00000356958.4	37																																																																																				.		0.45	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		TA	37642653	GC	TA	37642652	3	4	20	1	0	0	0	0	1	0	0	0	18049	1203	42	4	164	4	ZNF585A	19	37642652	Missense_Mutation	DNP	GC	TCGA-A4-8630-01A-11D-2396-08	17597881	37642652	21486331	87	1759											
KCNB1	3745	hgsc.bcm.edu	37	chr20	48098853	48098853	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcggagcttgcccagccgCgtgcggggcaggcggtccag	4	5	18	14	6	0	0	0	0	0	0	2	1	1	1	3	5	4	2	3	5	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr20:48098853C>G	ENST00000371741.4	-	1	331	c.165G>C	c.(163-165)acG>acC	p.T55T		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	55					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	TGCCCAGCCGCGTGCGGGGCA	0.672																																					p.T55T		.											.	KCNB1-92	0			c.G165C						.						15	15	15					20																	48098853		2167	4240	6407	SO:0001819	synonymous_variant	3745	exon1			CAGCCGCGTGCGG	AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.165G>C	20.37:g.48098853C>G		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_004975	0	0	1	1	0	Q14193	Silent	SNP	ENST00000371741.4	37	CCDS13418.1																																																																																			.		0.672	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		G	48098853	C	G	48098853	2	3	20	1	0	0	0	0	0	0	0	1	8033	755	27	4		4	KCNB1	20	48098853	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08		48098853	14926667	88	1760											
C20orf20	55257	hgsc.bcm.edu	37	chr20	61427956	61427956	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccaccagcccggcggaggaGacagtggtgtggagccccga	8	3	17	13	3	0	1	0	0	0	1	0	5	0	3	5	5	2	0	5	5	0	0	rs374837545		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr20:61427956G>A	ENST00000370487.3	+	1	152	c.81G>A	c.(79-81)gaG>gaA	p.E27E		NM_018270.4	NP_060740.1	Q9NV56	MRGBP_HUMAN	MRG/MORF4L binding protein	27					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	H4/H2A histone acetyltransferase complex (GO:0043189)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGGCGGAGGAGACAGTGGTGT	0.776																																					p.E27E		.											.	.	0			c.G81A						.	G		0,4168		0,0,2084	16	16	16		81	0.7	1	20		16	4,8196		0,4,4096	no	coding-synonymous	C20orf20	NM_018270.4		0,4,6180	AA,AG,GG		0.0488,0.0,0.0323		27/205	61427956	4,12364	2084	4100	6184	SO:0001819	synonymous_variant	55257	exon1			GGAGGAGACAGTG	AK001776	CCDS13503.1	20q13.33	2012-10-29	2012-10-29	2012-10-29	ENSG00000101189	ENSG00000101189			15866	protein-coding gene	gene with protein product		611157	"chromosome 20 open reading frame 20"	C20orf20		12963728	Standard	NM_018270		Approved	FLJ10914, MRG15BP, Eaf7	uc002ydi.3	Q9NV56	OTTHUMG00000032940	ENST00000370487.3:c.81G>A	20.37:g.61427956G>A		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_018270	0	0	4	9	5	A8C4L5	Silent	SNP	ENST00000370487.3	37	CCDS13503.1																																																																																			.		0.776	MRGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080080.1	NM_018270		A	61427956	G	A	61427956	2	1	20	1	0	0	0	0	0	0	0	1	2109	933	33	2		2	C20orf20	20	61427956	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	13329103	61427956	1597564	89	1761											
SYNJ1	8867	hgsc.bcm.edu	37	chr21	34029042	34029042	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcaaactgctgcagaagcTcatcaatcaaggcatcatca	14	9	7	11	0	5	1	5	0	0	1	5	1	5	1	0	1	5	5	0	1	4	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr21:34029042T>C	ENST00000322229.7	-	20	2749	c.2750A>G	c.(2749-2751)gAg>gGg	p.E917G	SYNJ1_ENST00000382491.3_Missense_Mutation_p.E912G|SYNJ1_ENST00000382499.2_Missense_Mutation_p.E956G|SYNJ1_ENST00000433931.2_Missense_Mutation_p.E956G|SYNJ1_ENST00000464778.1_5'UTR|SYNJ1_ENST00000357345.3_Missense_Mutation_p.E917G			O43426	SYNJ1_HUMAN	synaptojanin 1	917	Pro-rich.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						CTGCAGAAGCTCATCAATCAA	0.333																																					p.E956G		.											.	SYNJ1-232	0			c.A2867G						.						43	44	43					21																	34029042		2202	4300	6502	SO:0001583	missense	8867	exon21			AGAAGCTCATCAA	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.2750A>G	21.37:g.34029042T>C	ENSP00000322234:p.Glu917Gly	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_203446	0	0	4	4	0	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.517716	0.64634	.	.	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229	D;D;D;D;D	0.94417	-2.55;-3.41;-3.42;-2.63;-2.64	5.35	5.35	0.76521	Domain of unknown function DUF1866 (1);Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.146900	0.64402	D	0.000012	D	0.93687	0.7983	L	0.55481	1.735	0.58432	D	0.999999	B;P;B;P;P	0.39480	0.17;0.607;0.218;0.607;0.675	B;B;B;B;B	0.43155	0.124;0.41;0.167;0.41;0.23	D	0.94197	0.7446	10	0.72032	D	0.01	.	15.3206	0.74117	0.0:0.0:0.0:1.0	.	912;956;917;917;917	B9EGN3;C9JFZ1;O43426-2;O43426;O43426-4	.;.;.;SYNJ1_HUMAN;.	G	912;917;956;956;917	ENSP00000371931:E912G;ENSP00000349903:E917G;ENSP00000371939:E956G;ENSP00000409667:E956G;ENSP00000322234:E917G	ENSP00000322234:E917G	E	-	2	0	SYNJ1	32950913	1.000000	0.71417	0.999000	0.59377	0.971000	0.66376	6.109000	0.71528	2.027000	0.59764	0.402000	0.26972	GAG	.		0.333	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				C	34029042	T	C	34029042	3	2	20	1	0	0	0	0	1	0	0	0	15484	1551	54	3	2044	3	SYNJ1	21	34029042	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08		34029042	14100853	90	1762											
DNMT3L	29947	hgsc.bcm.edu	37	chr21	45668957	45668957	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cgcggacagcattctgcaagGatccgccgtggacatctggg	8	7	14	12	4	2	0	0	0	2	0	3	3	3	3	2	4	2	2	2	4	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr21:45668957G>C	ENST00000418993.1	-	11	1430	c.947C>G	c.(946-948)tCc>tGc	p.S316C	AP001059.5_ENST00000442785.1_RNA|DNMT3L_ENST00000270172.3_Missense_Mutation_p.S316C	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	316					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		ATTCTGCAAGGATCCGCCGTG	0.637																																					p.S316C		.											.	DNMT3L-228	0			c.C947G						.						59	46	50					21																	45668957		2203	4300	6503	SO:0001583	missense	29947	exon11			TGCAAGGATCCGC	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"cytosine-5-methyltransferase 3-like protein", "human cytosine-5-methyltransferase 3-like protein"	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.947C>G	21.37:g.45668957G>C	ENSP00000412862:p.Ser316Cys	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_013369	0	0	1	1	0	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.458|8.458	0.854735|0.854735	0.17106|0.17106	.|.	.|.	ENSG00000142182|ENSG00000142182	ENST00000436357|ENST00000270172;ENST00000418993	.|T;T	.|0.35605	.|1.3;1.3	3.03|3.03	-3.77|-3.77	0.04346|0.04346	.|.	.|1.415870	.|0.04503	.|N	.|0.381631	T|T	0.17280|0.17280	0.0415|0.0415	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.21452	.|0.056;0.056	.|B;B	.|0.08055	.|0.003;0.003	T|T	0.21930|0.21930	-1.0231|-1.0231	5|10	.|0.72032	.|D	.|0.01	-3.1172|-3.1172	4.5041|4.5041	0.11879|0.11879	0.6019:0.0:0.2301:0.168|0.6019:0.0:0.2301:0.168	.|.	.|316;316	.|Q9UJW3-2;Q9UJW3	.|.;DNM3L_HUMAN	A|C	111|316	.|ENSP00000270172:S316C;ENSP00000412862:S316C	.|ENSP00000270172:S316C	P|S	-|-	1|2	0|0	DNMT3L|DNMT3L	44493385|44493385	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.047000|-0.047000	0.11963|0.11963	-0.950000|-0.950000	0.03659|0.03659	-0.244000|-0.244000	0.11960|0.11960	CCT|TCC	.		0.637	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369		C	45668957	G	C	45668957	3	2	20	1	0	0	0	0	1	0	0	0	4689	1174	41	4	224	4	DNMT3L	21	45668957	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	11639915	45668957	2460938	91	1763											
SBF1	6305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50903300	50903300	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgtgacgcaggacacgctggGggtggttctcatccgcccgc	5	7	15	14	5	1	1	1	1	1	0	3	2	2	2	2	4	0	3	2	4	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr22:50903300G>A	ENST00000390679.3	-	13	1563	c.1379C>T	c.(1378-1380)cCc>cTc	p.P460L	SBF1_ENST00000380817.3_Missense_Mutation_p.P460L|SBF1_ENST00000348911.6_Missense_Mutation_p.P461L			O95248	MTMR5_HUMAN	SET binding factor 1	460					cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GACACGCTGGGGGTGGTTCTC	0.642																																					p.P460L		.											.	SBF1-90	0			c.C1379T						.						46	51	49					22																	50903300		2127	4220	6347	SO:0001583	missense	6305	exon13			CGCTGGGGGTGGT	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.1379C>T	22.37:g.50903300G>A	ENSP00000375097:p.Pro460Leu	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	68	25	NM_002972	0	0	9	22	13	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	G	19.24	3.789727	0.70337	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	D;D;D	0.86769	-2.16;-2.16;-2.17	4.17	4.17	0.49024	.	0.269330	0.29767	N	0.011248	D	0.87822	0.6274	L	0.49126	1.545	0.58432	D	0.999996	B;P;D	0.56746	0.021;0.873;0.977	B;P;P	0.55923	0.029;0.466;0.787	D	0.86760	0.1966	10	0.44086	T	0.13	.	9.8481	0.41039	0.0:0.0:0.6463:0.3537	.	460;461;460	O95248;G5E933;O95248-4	MTMR5_HUMAN;.;.	L	460;461;471;470;460	ENSP00000370196:P460L;ENSP00000252027:P461L;ENSP00000375097:P460L	ENSP00000336522:P470L	P	-	2	0	SBF1	49250166	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.603000	0.54074	2.156000	0.67533	0.591000	0.81541	CCC	.		0.642	SBF1-201	KNOWN	basic	protein_coding	protein_coding				A	50903300	G	A	50903300	3	1	20	1	0	0	0	0	1	0	0	0	13890	1232	43	2	4418	2	SBF1	22	50903300	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		50903300	401266	92	1764											
GPR64	10149	hgsc.bcm.edu	37	chrX	19026233	19026233	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcaggagcttgggtttcCagagaaacctgaaaatcaag	13	10	10	8	0	2	2	2	1	1	1	4	4	3	3	2	2	2	2	2	2	4	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chrX:19026233C>G	ENST00000379869.3	-	19	1594	c.1431G>C	c.(1429-1431)ctG>ctC	p.L477L	GPR64_ENST00000340581.3_Intron|GPR64_ENST00000379873.2_Silent_p.L477L|GPR64_ENST00000357991.3_Silent_p.L474L|GPR64_ENST00000379878.3_Silent_p.L461L|GPR64_ENST00000357544.3_Silent_p.L447L|GPR64_ENST00000360279.4_Silent_p.L455L|GPR64_ENST00000356606.4_Silent_p.L463L|GPR64_ENST00000354791.3_Silent_p.L461L|GPR64_ENST00000379876.1_Silent_p.L453L	NM_001079858.2|NM_005756.3	NP_001073327.1|NP_005747.2	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64	477					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)|spermatogenesis (GO:0007283)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(18)|stomach(1)|urinary_tract(1)	42	Hepatocellular(33;0.183)					CTTGGGTTTCCAGAGAAACCT	0.393																																					p.L477L		.											.	GPR64-130	0			c.G1431C						.						64	59	61					X																	19026233		2203	4300	6503	SO:0001819	synonymous_variant	10149	exon19			GGTTTCCAGAGAA	X81892	CCDS14191.1, CCDS43921.1, CCDS43922.1, CCDS43923.1, CCDS55376.1, CCDS55377.1, CCDS55378.1, CCDS55379.1	Xp22.13	2014-08-08			ENSG00000173698	ENSG00000173698		"-", "GPCR / Class B : Orphans"	4516	protein-coding gene	gene with protein product	"epididymal protein 6"	300572				9739419, 9150425	Standard	NM_005756		Approved	HE6, TM7LN2, EDDM6	uc004cyx.3	Q8IZP9	OTTHUMG00000021223	ENST00000379869.3:c.1431G>C	X.37:g.19026233C>G		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_001184834	0	0	0	0	0	B1AWB3|B1AWB4|B1AWB6|B1AWB7|O00406|Q14CE0|Q8IWT2|Q8IZE4|Q8IZE5|Q8IZE6|Q8IZE7|Q8IZP3|Q8IZP4	Silent	SNP	ENST00000379869.3	37	CCDS43923.1																																																																																			.		0.393	GPR64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055970.2			G	19026233	C	G	19026233	2	3	20	1	0	0	0	0	0	0	0	1	6725	581	21	4		4	GPR64	23	19026233	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08		19026233	136244327	93	1765											
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20206637	20206637	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttaacttgatgtgaccttcTtcatcaagaagtatactgaa	13	14	7	7	0	3	4	2	3	1	1	3	4	3	4	1	0	2	2	1	0	6	6			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chrX:20206637T>C	ENST00000379565.3	-	8	816	c.609A>G	c.(607-609)gaA>gaG	p.E203E	RPS6KA3_ENST00000544447.1_Silent_p.E175E|RPS6KA3_ENST00000540702.1_Silent_p.E175E|RPS6KA3_ENST00000379548.4_Silent_p.E174E	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	203	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TGTGACCTTCTTCATCAAGAA	0.274																																					p.E203E		.											.	RPS6KA3-1504	0			c.A609G						.						23	21	21					X																	20206637		2176	4273	6449	SO:0001819	synonymous_variant	6197	exon8			ACCTTCTTCATCA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.609A>G	X.37:g.20206637T>C		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_004586	0	0	21	21	0	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Silent	SNP	ENST00000379565.3	37	CCDS14197.1																																																																																			.		0.274	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20206637	T	C	20206637	2	2	20	1	0	0	0	0	0	0	0	1	13684	1606	56	3		3	RPS6KA3	23	20206637	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	1180404	20206637	135063923	94	1766											
CXorf26	51260	hgsc.bcm.edu	37	chrX	75394774	75394774	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaatgcagcatgctgaagTctattacaaggtgagttgtc	12	11	11	7	0	1	2	0	2	1	0	2	2	1	2	0	1	5	5	0	1	5	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chrX:75394774T>C	ENST00000373358.3	+	3	349	c.146T>C	c.(145-147)gTc>gCc	p.V49A	PBDC1_ENST00000373357.3_Missense_Mutation_p.V49A	NM_016500.3	NP_057584.2	Q9BVG4	PBDC1_HUMAN	polysaccharide biosynthesis domain containing 1	49																	CATGCTGAAGTCTATTACAAG	0.408																																					p.V49A		.											.	.	0			c.T146C						.						142	114	124					X																	75394774		2203	4300	6503	SO:0001583	missense	51260	exon3			CTGAAGTCTATTA	BC001220	CCDS14432.1, CCDS75995.1	Xq13.2	2012-11-28	2012-11-28	2012-11-28	ENSG00000102390	ENSG00000102390			28790	protein-coding gene	gene with protein product			"chromosome X open reading frame 26"	CXorf26		11042152	Standard	NM_016500		Approved	MGC874	uc004ecl.1	Q9BVG4	OTTHUMG00000021876	ENST00000373358.3:c.146T>C	X.37:g.75394774T>C	ENSP00000362456:p.Val49Ala	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_016500	0	0	2	2	0		Missense_Mutation	SNP	ENST00000373358.3	37	CCDS14432.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.299549	0.60195	.	.	ENSG00000102390	ENST00000373358;ENST00000373357	.	.	.	5.48	5.48	0.80851	Yst0336-like domain (1);	0.057515	0.64402	D	0.000002	T	0.53190	0.1781	L	0.60957	1.885	0.52501	D	0.999953	P	0.36483	0.555	B	0.34301	0.179	T	0.58115	-0.7693	9	0.56958	D	0.05	-14.3814	12.5925	0.56451	0.0:0.0:0.0:1.0	.	49	Q9BVG4	CX026_HUMAN	A	49	.	ENSP00000362455:V49A	V	+	2	0	CXorf26	75311176	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	4.464000	0.60134	1.949000	0.56562	0.486000	0.48141	GTC	.		0.408	PBDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057294.1	NM_016500		C	75394774	T	C	75394774	3	2	20	1	0	0	0	0	1	0	0	0	4110	1667	58	3	156	3	CXorf26	23	75394774	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	55188137	75394774	79875786	95	1767											
COL4A6	1288	hgsc.bcm.edu	37	chrX	107447618	107447618	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtagatggtggaggtcctgCtgggccagggaggccaacat	9	7	17	8	0	0	1	0	0	0	1	1	3	1	3	3	6	2	2	3	6	2	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chrX:107447618C>G	ENST00000372216.4	-	12	815	c.715G>C	c.(715-717)Gca>Cca	p.A239P	COL4A6_ENST00000538570.1_Missense_Mutation_p.A238P|COL4A6_ENST00000545689.1_Missense_Mutation_p.A238P|COL4A6_ENST00000394872.2_Missense_Mutation_p.A236P|COL4A6_ENST00000334504.7_Missense_Mutation_p.A238P	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	239	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						GGAGGTCCTGCTGGGCCAGGG	0.468									Alport syndrome with Diffuse Leiomyomatosis																												p.A239P	Melanoma(87;1895 1945 2589 7165)	.											.	COL4A6-199	0			c.G715C						.						59	54	56					X																	107447618		2203	4300	6503	SO:0001583	missense	1288	exon12	Familial Cancer Database		GTCCTGCTGGGCC	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.715G>C	X.37:g.107447618C>G	ENSP00000361290:p.Ala239Pro	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_001847	0	0	2	2	0	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	37	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.481671	0.44147	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.94417	-3.42;-3.42;-3.3;-3.42;-3.42	5.21	5.21	0.72293	.	0.185432	0.26428	N	0.024425	D	0.88592	0.6478	N	0.00996	-1.065	0.38781	D	0.954768	D;D;D;D	0.76494	0.997;0.999;0.994;0.997	D;D;P;D	0.64410	0.925;0.925;0.844;0.925	D	0.85714	0.1321	10	0.02654	T	1	.	15.1797	0.72945	0.0:1.0:0.0:0.0	.	238;238;239;238	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	P	239;238;236;238;238;238	ENSP00000361290:A239P;ENSP00000334733:A238P;ENSP00000378340:A236P;ENSP00000443707:A238P;ENSP00000445236:A238P	ENSP00000334733:A238P	A	-	1	0	COL4A6	107334274	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.056000	0.41355	2.498000	0.84270	0.600000	0.82982	GCA	.		0.468	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			G	107447618	C	G	107447618	3	3	20	1	0	0	0	0	1	0	0	0	3701	797	28	4	4496	4	COL4A6	23	107447618	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	32052844	107447618	47822942	96	1768											
PLCH2	9651	broad.mit.edu	37	chr1	2426375	2426375	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcctcgtcgtgggaagcttCtccaggcgcaaggtccggcg	5	7	15	14	6	1	0	0	0	1	0	5	1	2	1	3	4	1	2	3	4	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:2426375C>T	ENST00000419816.2	+	12	2014	c.1740C>T	c.(1738-1740)ttC>ttT	p.F580F	PLCH2_ENST00000378486.3_Silent_p.F580F|PLCH2_ENST00000378488.3_Silent_p.F580F|PLCH2_ENST00000288766.5_Intron|PLCH2_ENST00000449969.1_Silent_p.F553F|RP3-395M20.2_ENST00000424657.1_RNA|RP3-395M20.3_ENST00000442305.1_RNA			O75038	PLCH2_HUMAN	phospholipase C, eta 2	580					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		TGGGAAGCTTCTCCAGGCGCA	0.687																																					p.F580F													.	PLCH2-229	0			c.C1740T						.						23	34	31					1																	2426375		2069	4185	6254	SO:0001819	synonymous_variant	9651	exon12			AAGCTTCTCCAGG	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.1740C>T	1.37:g.2426375C>T		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_014638	0	0	0	0	0	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37																																																																																				.		0.687	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		T	2426375	C	T	2426375	2	4	21	1	0	0	0	0	0	0	0	1	12064	912	32	2		2	PLCH2	1	2426375	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		2426375	246824246	1	1769											
NPHP4	261734	broad.mit.edu	37	chr1	5927943	5927943	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgatgggcttgccaccactcGctcggaacaagacctgtgag	9	7	12	13	3	0	2	0	1	0	1	2	4	0	3	3	2	2	2	3	2	2	1	rs139767853	byFrequency	TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:5927943G>C	ENST00000378156.4	-	24	3594	c.3329C>G	c.(3328-3330)gCg>gGg	p.A1110G	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	1110					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GCCACCACTCGCTCGGAACAA	0.607																																					p.A1110G													.	NPHP4-515	0			c.C3329G						.						47	56	53					1																	5927943		2159	4255	6414	SO:0001583	missense	261734	exon24			CCACTCGCTCGGA	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3329C>G	1.37:g.5927943G>C	ENSP00000367398:p.Ala1110Gly	Somatic	134	8		WXS	Illumina HiSeq	Phase_I	178	19	NM_015102	0	0	6	6	0	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	G	9.250	1.040526	0.19669	.	.	ENSG00000131697	ENST00000378156	T	0.68331	-0.32	5.57	-1.27	0.09347	.	0.553031	0.17272	N	0.180335	T	0.44912	0.1316	L	0.28740	0.885	0.09310	N	1	B;B	0.23058	0.079;0.007	B;B	0.22880	0.042;0.011	T	0.25984	-1.0116	10	0.13853	T	0.58	.	6.6143	0.22769	0.2804:0.3411:0.3785:0.0	.	52;1110	Q6ZSL3;O75161	.;NPHP4_HUMAN	G	1110	ENSP00000367398:A1110G	ENSP00000367398:A1110G	A	-	2	0	NPHP4	5850530	0.000000	0.05858	0.001000	0.08648	0.061000	0.15899	0.028000	0.13644	-0.214000	0.10078	-0.258000	0.10820	GCG	G|0.998;A|0.002		0.607	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			C	5927943	G	C	5927943	3	2	21	1	0	0	0	0	1	0	0	0	10607	1087	38	4	979	4	NPHP4	1	5927943	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	3501568	5927943	243322678	2	1770											
H6PD	9563	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	9324818	9324818	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgaagcgtgagatcaccAcgctggtgagccgggtgggc	8	6	18	9	3	1	3	1	3	0	1	1	5	1	4	2	4	2	1	2	4	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:9324818A>G	ENST00000377403.2	+	5	2568	c.2266A>G	c.(2266-2268)Acg>Gcg	p.T756A	H6PD_ENST00000602477.1_Missense_Mutation_p.T767A	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	756	6-phosphogluconolactonase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TGAGATCACCACGCTGGTGAG	0.637																																					p.T756A		.											.	H6PD-90	0			c.A2266G						.						33	30	31					1																	9324818		2203	4297	6500	SO:0001583	missense	9563	exon5			ATCACCACGCTGG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.2266A>G	1.37:g.9324818A>G	ENSP00000366620:p.Thr756Ala	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	259	61	NM_004285	0	0	5	6	1	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.467516	0.01053	.	.	ENSG00000049239	ENST00000377403	T	0.39406	1.08	5.45	-10.9	0.00192	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.671970	0.15660	N	0.250971	T	0.16257	0.0391	N	0.11560	0.145	0.09310	N	1	B	0.28128	0.201	B	0.28385	0.089	T	0.14896	-1.0456	10	0.35671	T	0.21	-7.8807	9.3226	0.37973	0.6541:0.1684:0.1206:0.057	.	756	O95479	G6PE_HUMAN	A	756	ENSP00000366620:T756A	ENSP00000366620:T756A	T	+	1	0	H6PD	9247405	0.002000	0.14202	0.001000	0.08648	0.225000	0.24961	0.628000	0.24522	-3.386000	0.00174	-2.411000	0.00221	ACG	.		0.637	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		G	9324818	A	G	9324818	3	3	21	1	0	0	0	0	1	0	0	0	6957	159	6	3	2280	3	H6PD	1	9324818	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	3396875	9324818	239925803	3	1771											
DHRS3	9249	broad.mit.edu;ucsc.edu	37	chr1	12628411	12628411	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatgcaggtgtaggttccTgagaatttgtggatctcctc	7	15	11	8	0	2	1	1	1	1	1	5	3	3	2	2	3	1	3	2	3	2	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:12628411T>C	ENST00000376223.2	-	6	1250	c.867A>G	c.(865-867)tcA>tcG	p.S289S	RNU6ATAC18P_ENST00000408413.1_RNA	NM_004753.4	NP_004744.2	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3	289					bone morphogenesis (GO:0060349)|cardiac septum morphogenesis (GO:0060411)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|phototransduction, visible light (GO:0007603)|regulation of ossification (GO:0030278)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|photoreceptor outer segment membrane (GO:0042622)	electron carrier activity (GO:0009055)|NADP-retinol dehydrogenase activity (GO:0052650)|nucleotide binding (GO:0000166)|retinol dehydrogenase activity (GO:0004745)			cervix(1)|large_intestine(4)|lung(2)|prostate(1)|skin(1)	9	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	TGTAGGTTCCTGAGAATTTGT	0.537																																					p.S289S													.	DHRS3-91	0			c.A867G						.						213	187	195					1																	12628411		2203	4300	6503	SO:0001819	synonymous_variant	9249	exon6			GGTTCCTGAGAAT	AF061741	CCDS146.1	1p36.1	2011-09-20			ENSG00000162496	ENSG00000162496	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	17693	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 16C, member 1"	612830				9705317, 12226107, 19027726	Standard	XM_005263533		Approved	retSDR1, Rsdr1, SDR1, RDH17, SDR16C1	uc001auc.3	O75911	OTTHUMG00000001885	ENST00000376223.2:c.867A>G	1.37:g.12628411T>C		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	196	5	NM_004753	0	0	157	180	23	B2R7F3|Q5VUY3|Q6UY38|Q9BUC8	Silent	SNP	ENST00000376223.2	37	CCDS146.1																																																																																			.		0.537	DHRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005318.1	NM_004753		C	12628411	T	C	12628411	2	2	21	1	0	0	0	0	0	0	0	1	4502	1567	55	3		3	DHRS3	1	12628411	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	3303593	12628411	236622210	4	1772											
SCP2	6342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53416459	53416459	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgggcagagggctatctatCacagtttgggaatgactgga	10	10	15	6	0	2	2	1	1	1	1	2	4	2	4	0	4	0	3	0	4	3	3	rs371605573		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:53416459C>T	ENST00000371514.3	+	4	400	c.232C>T	c.(232-234)Cac>Tac	p.H78Y	SCP2_ENST00000371513.5_Intron|SCP2_ENST00000528311.1_5'UTR|SCP2_ENST00000371509.4_Intron|SCP2_ENST00000407246.2_Missense_Mutation_p.H54Y	NM_002979.4	NP_002970.2	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	0					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						GGCTATCTATCACAGTTTGGG	0.393																																					p.H78Y		.											.	SCP2-153	0			c.C232T						.						164	155	158					1																	53416459		2203	4300	6503	SO:0001583	missense	6342	exon4			ATCTATCACAGTT	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000371514.3:c.232C>T	1.37:g.53416459C>T	ENSP00000360569:p.His78Tyr	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	118	25	NM_002979	0	0	9	13	4	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000371514.3	37	CCDS572.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184073	0.57800	.	.	ENSG00000116171	ENST00000371514;ENST00000407246	D;D	0.94138	-2.66;-3.36	5.09	5.09	0.68999	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.095236	0.64402	D	0.000001	D	0.96015	0.8702	M	0.76838	2.35	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69307	0.96;0.963	D	0.94185	0.7435	10	0.17832	T	0.49	-12.7756	17.4125	0.87489	0.0:1.0:0.0:0.0	.	54;78	C9JC79;P22307	.;NLTP_HUMAN	Y	78;54	ENSP00000360569:H78Y;ENSP00000384569:H54Y	ENSP00000360569:H78Y	H	+	1	0	SCP2	53189047	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.914000	0.75764	2.629000	0.89072	0.563000	0.77884	CAC	.		0.393	SCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024740.2	NM_002979		T	53416459	C	T	53416459	3	4	21	1	0	0	0	0	1	0	0	0	13966	826	29	2	246	2	SCP2	1	53416459	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	40788048	53416459	195834162	5	1773											
PODN	127435	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53535630	53535630	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggatttggccgaagtggcGgccacagcctgagccccgaa	9	5	14	13	3	0	1	0	1	0	0	0	4	0	2	5	4	2	0	5	4	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:53535630G>T	ENST00000312553.5	+	2	254	c.247G>T	c.(247-249)Ggc>Tgc	p.G83C	RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000371500.3_Missense_Mutation_p.G64C|PODN_ENST00000395871.2_Missense_Mutation_p.G83C	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	35	LRRNT.				negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CCGAAGTGGCGGCCACAGCCT	0.697																																					p.G83C		.											.	PODN-92	0			c.G247T						.						10	14	13					1																	53535630		2187	4283	6470	SO:0001583	missense	127435	exon2			AGTGGCGGCCACA	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	23174	protein-coding gene	gene with protein product	"podocan proteoglycan"	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.247G>T	1.37:g.53535630G>T	ENSP00000308315:p.Gly83Cys	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	50	23	NM_153703	0	0	0	0	0	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Missense_Mutation	SNP	ENST00000312553.5	37	CCDS573.1	.	.	.	.	.	.	.	.	.	.	G	9.986	1.229555	0.22542	.	.	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.59502	0.91;0.26;1.02	4.19	-3.33	0.04958	.	1.673490	0.03184	N	0.172477	T	0.54532	0.1864	N	0.08118	0	0.09310	N	1	D;P;P	0.65815	0.995;0.545;0.545	D;B;B	0.65010	0.931;0.209;0.306	T	0.53927	-0.8369	10	0.56958	D	0.05	.	10.02	0.42037	0.6741:0.0:0.3259:0.0	.	83;64;83	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	C	64;83;83	ENSP00000360555:G64C;ENSP00000379212:G83C;ENSP00000308315:G83C	ENSP00000308315:G83C	G	+	1	0	PODN	53308218	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-1.213000	0.02991	-0.646000	0.05452	-0.424000	0.05967	GGC	.		0.697	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703		T	53535630	G	T	53535630	3	4	21	1	0	0	0	0	1	0	0	0	12204	1116	39	4	253	4	PODN	1	53535630	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	119171	53535630	195714991	6	1774											
WLS	79971	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	68697907	68697910	+	Frame_Shift_Del	DEL	TTTG	TTTG	-																															tcccaccagaaaggcgatgaTttggaacacgagcagaatcc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TTTG	TTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:68697907_68697910delTTTG	ENST00000262348.4	-	1	326_329	c.73_76delCAAA	c.(73-78)caaatcfs	p.QI25fs	WLS_ENST00000540432.1_Frame_Shift_Del_p.QI25fs|WLS_ENST00000354777.2_Frame_Shift_Del_p.QI25fs|WLS_ENST00000370971.1_Frame_Shift_Del_p.QI25fs|WLS_ENST00000370976.3_Frame_Shift_Del_p.QI25fs	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	25					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						AAGGCGATGATTTGGAACACGAGC	0.505																																					p.25_26del		.											.	WLS-90	0			c.73_76del						.																																			SO:0001589	frameshift_variant	79971	exon1			.	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"wntless homolog"	611514	"chromosome 1 open reading frame 139", "G protein-coupled receptor 177", "wntless homolog (Drosophila)"	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.73_76delCAAA	1.37:g.68697907_68697910delTTTG	ENSP00000262348:p.Gln25fs	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	131	34	NM_001002292	0	0	0	0	0	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Frame_Shift_Del	DEL	ENST00000262348.4	37	CCDS642.1																																																																																			.		0.505	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911		-	68697910	TTTG	-	68697907	7	5	21	1	0	1	0	1	0	0	0	0	17409	1493	52	0	1723	0	WLS	1	68697907	Frame_Shift_Del	DEL	TTTG	TCGA-A4-A48D-01A-11D-A25F-10	15162277	68697907	180552714	7	1775											
NEXN	91624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	78395127	78395127	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgaaaaaaggaaagcagaaGaagaagccagaaggagaata	24	2	12	3	0	0	6	0	1	0	5	0	8	0	7	1	2	2	1	1	2	10	1	rs533331740		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:78395127G>C	ENST00000334785.7	+	9	1175	c.991G>C	c.(991-993)Gaa>Caa	p.E331Q	NEXN_ENST00000457030.1_Missense_Mutation_p.E317Q|NEXN_ENST00000330010.8_Missense_Mutation_p.E267Q	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		gaaagcagaagaagaagccag	0.388																																					p.E331Q		.											.	NEXN-92	0			c.G991C						.						91	91	91					1																	78395127		1854	4094	5948	SO:0001583	missense	91624	exon9			GCAGAAGAAGAAG	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.991G>C	1.37:g.78395127G>C	ENSP00000333938:p.Glu331Gln	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	98	28	NM_144573	0	0	0	0	0		Missense_Mutation	SNP	ENST00000334785.7	37	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.32|13.32	2.200748|2.200748	0.38905|0.38905	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000401035;ENST00000457030;ENST00000330010;ENST00000334785;ENST00000440324|ENST00000342754	T;T;T;T;T|.	0.69175|.	-0.38;0.01;0.03;0.1;-0.33|.	4.98|4.98	4.05|4.05	0.47172|0.47172	.|.	0.289025|.	0.24238|.	N|.	0.040288|.	T|T	0.49029|0.49029	0.1533|0.1533	L|L	0.49455|0.49455	1.56|1.56	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.16603|.	0.006;0.018;0.011;0.006|.	B;B;B;B|.	0.18263|.	0.021;0.016;0.016;0.016|.	T|T	0.48375|0.48375	-0.9041|-0.9041	10|5	0.30078|.	T|.	0.28|.	-4.9227|-4.9227	13.6045|13.6045	0.62039|0.62039	0.0:0.156:0.844:0.0|0.0:0.156:0.844:0.0	.|.	267;317;331;267|.	D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7|.	.;.;NEXN_HUMAN;.|.	Q|N	267;317;267;331;317|230	ENSP00000383814:E267Q;ENSP00000388048:E317Q;ENSP00000327363:E267Q;ENSP00000333938:E331Q;ENSP00000411902:E317Q|.	ENSP00000327363:E267Q|.	E|K	+|+	1|3	0|2	NEXN|NEXN	78167715|78167715	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.850000|0.850000	0.48378|0.48378	4.893000|4.893000	0.63199|0.63199	1.207000|1.207000	0.43291|0.43291	0.591000|0.591000	0.81541|0.81541	GAA|AAG	.		0.388	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		C	78395127	G	C	78395127	3	2	21	1	0	0	0	0	1	0	0	0	10381	943	33	4	1021	4	NEXN	1	78395127	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	9697220	78395127	170855494	8	1776											
SLC6A17	388662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110734657	110734657	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cccaggtcttctttgccttgGgcctgggctttggtggtgtc	1	15	14	11	0	2	0	0	0	2	0	3	0	2	0	3	5	1	1	3	5	0	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:110734657G>A	ENST00000331565.4	+	7	1413	c.928G>A	c.(928-930)Ggc>Agc	p.G310S		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	310					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CTTTGCCTTGGGCCTGGGCTT	0.552																																					p.G310S		.											.	SLC6A17-92	0			c.G928A						.						146	144	145					1																	110734657		2203	4300	6503	SO:0001583	missense	388662	exon7			GCCTTGGGCCTGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.928G>A	1.37:g.110734657G>A	ENSP00000330199:p.Gly310Ser	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	200	46	NM_001010898	0	0	0	0	0	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205508	0.79127	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.71579	-0.58	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	L	0.52823	1.66	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.75929	-0.3144	10	0.38643	T	0.18	.	18.2409	0.89967	0.0:0.0:1.0:0.0	.	310	Q9H1V8	S6A17_HUMAN	S	310	ENSP00000330199:G310S	ENSP00000330199:G310S	G	+	1	0	SLC6A17	110536180	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.414000	0.97362	2.298000	0.77334	0.650000	0.86243	GGC	.		0.552	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110734657	G	A	110734657	3	1	21	1	0	0	0	0	1	0	0	0	14712	1232	43	2	950	2	SLC6A17	1	110734657	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	32339530	110734657	138515964	9	1777											
SLC16A4	9122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110921516	110921516	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcatccatgatgtcaatcCccagtgttttggctctggct	7	13	10	11	0	2	1	1	1	1	0	4	1	4	1	3	3	0	4	3	3	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:110921516C>A	ENST00000369779.4	-	6	1238	c.989G>T	c.(988-990)gGg>gTg	p.G330V	SLC16A4_ENST00000437429.2_Missense_Mutation_p.G220V|SLC16A4_ENST00000497687.1_5'Flank|SLC16A4_ENST00000541986.1_Missense_Mutation_p.G268V|SLC16A4_ENST00000369781.4_Intron|SLC16A4_ENST00000472422.2_Missense_Mutation_p.G282V	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	330					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	GATGTCAATCCCCAGTGTTTT	0.418																																					p.G330V		.											.	SLC16A4-93	0			c.G989T						.						108	105	106					1																	110921516		2203	4300	6503	SO:0001583	missense	9122	exon6			TCAATCCCCAGTG	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"Solute carriers"	10925	protein-coding gene	gene with protein product		603878	"solute carrier family 16 (monocarboxylic acid transporters), member 4", "solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.989G>T	1.37:g.110921516C>A	ENSP00000358794:p.Gly330Val	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	157	47	NM_004696	0	0	37	65	28	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	37	CCDS823.1	.	.	.	.	.	.	.	.	.	.	c	19.00	3.741081	0.69304	.	.	ENSG00000168679	ENST00000369779;ENST00000472422;ENST00000437429;ENST00000541986;ENST00000467986	D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22	6.08	3.23	0.37069	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.367376	0.34156	N	0.004216	D	0.91005	0.7171	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.997;0.999	D;D;D;D	0.79784	0.993;0.986;0.982;0.986	D	0.91070	0.4892	10	0.87932	D	0	.	10.0556	0.42244	0.0:0.7928:0.0:0.2072	.	220;268;282;330	E7EPY8;B4DJ67;G3V175;O15374	.;.;.;MOT5_HUMAN	V	330;282;220;268;97	ENSP00000358794:G330V;ENSP00000432495:G282V;ENSP00000394790:G220V;ENSP00000446087:G268V;ENSP00000435768:G97V	ENSP00000358794:G330V	G	-	2	0	SLC16A4	110723039	0.996000	0.38824	0.271000	0.24616	0.894000	0.52154	3.296000	0.51802	0.463000	0.27118	-0.156000	0.13503	GGG	.		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		A	110921516	C	A	110921516	3	1	21	1	0	0	0	0	1	0	0	0	14442	623	22	4	490	4	SLC16A4	1	110921516	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	186859	110921516	138329105	10	1778											
ZNF687	57592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151261140	151261140	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccaattttcagacccatcTccgggaggcctgtctgcacg	8	9	10	14	2	3	1	1	0	2	1	4	2	3	2	4	2	2	1	4	2	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:151261140T>G	ENST00000368879.2	+	3	2350	c.2252T>G	c.(2251-2253)cTc>cGc	p.L751R		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	751					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CAGACCCATCTCCGGGAGGCC	0.582																																					p.L751R		.											.	ZNF687-92	0			c.T2252G						.						124	110	115					1																	151261140		2203	4300	6503	SO:0001583	missense	57592	exon3			CCCATCTCCGGGA		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.2252T>G	1.37:g.151261140T>G	ENSP00000357874:p.Leu751Arg	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	146	36	NM_020832	0	0	6	9	3	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.623891|4.623891	0.87460|0.87460	.|.	.|.	ENSG00000143373|ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879|ENST00000426871	T;T;T|.	0.02032|.	4.49;4.49;4.49|.	4.98|4.98	4.98|4.98	0.66077|0.66077	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	0.000000|.	0.32068|.	N|.	0.006627|.	T|T	0.51126|0.51126	0.1656|0.1656	L|L	0.48986|0.48986	1.54|1.54	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.991|.	T|T	0.51084|0.51084	-0.8750|-0.8750	10|5	0.66056|.	D|.	0.02|.	.|.	13.7947|13.7947	0.63164|0.63164	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	751;751|.	Q8N1G0-2;Q8N1G0|.	.;ZN687_HUMAN|.	R|A	751|354	ENSP00000336620:L751R;ENSP00000319829:L751R;ENSP00000357874:L751R|.	ENSP00000319829:L751R|.	L|S	+|+	2|1	0|0	ZNF687|ZNF687	149527764|149527764	0.994000|0.994000	0.37717|0.37717	0.765000|0.765000	0.31456|0.31456	0.997000|0.997000	0.91878|0.91878	7.803000|7.803000	0.85983|0.85983	2.098000|2.098000	0.63641|0.63641	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.		0.582	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		G	151261140	T	G	151261140	3	3	21	1	0	0	0	0	1	0	0	0	18124	1551	54	5	2258	5	ZNF687	1	151261140	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	40339624	151261140	97989481	11	1779											
ADAR	103	broad.mit.edu	37	chr1	154574370	154574370	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgctggttccaagcctgagCtgagactgcaataaaaggct	11	9	12	9	0	0	2	0	2	0	1	1	3	1	2	2	2	4	5	2	2	4	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:154574370C>A	ENST00000368474.4	-	2	947	c.748G>T	c.(748-750)Gct>Tct	p.A250S	ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000471068.1_5'Flank|ADAR_ENST00000292205.5_Missense_Mutation_p.A293S	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	250					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		CAAGCCTGAGCTGAGACTGCA	0.512																																					p.A250S													.	ADAR-157	0			c.G748T						.						120	124	122					1																	154574370		2203	4300	6503	SO:0001583	missense	103	exon2			CCTGAGCTGAGAC	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.748G>T	1.37:g.154574370C>A	ENSP00000357459:p.Ala250Ser	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	244	6	NM_001111	0	0	12	12	0	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.281003	0.23392	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.11712	2.75;2.76;2.79	2.09	-0.586	0.11694	.	1.204520	0.07030	U	0.828319	T	0.01222	0.0040	N	0.14661	0.345	0.09310	N	1	B;B;B	0.17667	0.023;0.023;0.013	B;B;B	0.14023	0.01;0.01;0.005	T	0.44590	-0.9318	10	0.06236	T	0.91	.	5.6522	0.17622	0.5699:0.4301:0.0:0.0	.	250;250;250	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	S	293;250;245	ENSP00000292205:A293S;ENSP00000357459:A250S;ENSP00000431794:A245S	ENSP00000292205:A293S	A	-	1	0	ADAR	152840994	0.635000	0.27199	0.134000	0.22075	0.149000	0.21700	0.000000	0.12993	0.145000	0.18977	0.491000	0.48974	GCT	.		0.512	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		A	154574370	C	A	154574370	3	1	21	1	0	0	0	0	1	0	0	0	281	797	28	4	2988	4	ADAR	1	154574370	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	3313230	154574370	94676251	12	1780											
DCST1	149095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155015935	155015935	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccggctggagtgggccctGgggctgctgcacgtgctgct	2	8	18	13	2	0	0	0	0	0	0	0	1	0	1	2	5	4	6	2	5	0	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:155015935G>T	ENST00000295542.1	+	10	1218	c.1122G>T	c.(1120-1122)ctG>ctT	p.L374L	DCST1_ENST00000423025.2_Silent_p.L349L|DCST1_ENST00000368419.2_Silent_p.L374L|DCST1_ENST00000392480.1_Silent_p.L374L|RP11-307C12.11_ENST00000452962.1_RNA	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	374						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			AGTGGGCCCTGGGGCTGCTGC	0.687																																					p.L374L		.											.	DCST1-92	0			c.G1122T						.						51	52	52					1																	155015935		2203	4299	6502	SO:0001819	synonymous_variant	149095	exon10			GGCCCTGGGGCTG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1122G>T	1.37:g.155015935G>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	70	21	NM_152494	0	0	0	0	0	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Silent	SNP	ENST00000295542.1	37	CCDS1083.1																																																																																			.		0.687	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		T	155015935	G	T	155015935	2	4	21	1	0	0	0	0	0	0	0	1	4308	1335	47	4		4	DCST1	1	155015935	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	441565	155015935	94234686	13	1781											
ADCY10	55811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167825476	167825476	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagatgtcgttaggctgtaCtgcaccaatgacaatgtagg	11	10	13	7	1	0	2	0	1	0	1	1	3	0	2	1	3	2	5	1	3	5	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:167825476C>T	ENST00000367851.4	-	17	2282	c.2098G>A	c.(2098-2100)Gta>Ata	p.V700I	ADCY10_ENST00000367848.1_Missense_Mutation_p.V608I|ADCY10_ENST00000545172.1_Missense_Mutation_p.V547I	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	700					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						TTAGGCTGTACTGCACCAATG	0.458																																					p.V700I		.											.	ADCY10-493	0			c.G2098A						.						315	265	282					1																	167825476		2203	4300	6503	SO:0001583	missense	55811	exon17			GCTGTACTGCACC	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2098G>A	1.37:g.167825476C>T	ENSP00000356825:p.Val700Ile	Somatic	240	0		WXS	Illumina HiSeq	Phase_I	284	89	NM_018417	0	0	0	0	0	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	C	4.303	0.055518	0.08291	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.26223	1.76;1.75;1.76	5.16	-9.58	0.00559	.	0.951722	0.08707	N	0.905544	T	0.03695	0.0105	N	0.13043	0.29	0.21527	N	0.999654	B;B;B	0.19583	0.037;0.018;0.006	B;B;B	0.16289	0.015;0.007;0.003	T	0.43032	-0.9416	9	0.54805	T	0.06	-0.402	8.8296	0.35076	0.0:0.1525:0.2062:0.6412	.	547;608;700	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	I	547;700;608	ENSP00000441992:V547I;ENSP00000356825:V700I;ENSP00000356822:V608I	ENSP00000356822:V608I	V	-	1	0	ADCY10	166092100	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.529000	0.00945	-1.853000	0.01165	-0.440000	0.05779	GTA	.		0.458	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167825476	C	T	167825476	3	4	21	1	0	0	0	0	1	0	0	0	293	565	20	2	2802	2	ADCY10	1	167825476	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	12809541	167825476	81425145	14	1782											
KCNT2	343450	broad.mit.edu;bcgsc.ca	37	chr1	196227503	196227503	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccactgcatgctttttctcCgcagcaagggatggtccgac	7	10	10	14	2	1	0	0	0	1	0	3	2	2	1	3	2	3	4	3	2	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:196227503C>T	ENST00000294725.9	-	26	3947	c.3032G>A	c.(3031-3033)cGg>cAg	p.R1011Q	KCNT2_ENST00000367431.4_Missense_Mutation_p.R945Q|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000609185.1_Missense_Mutation_p.R944Q|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367433.5_Missense_Mutation_p.R987Q			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1011					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GCTTTTTCTCCGCAGCAAGGG	0.517																																					p.R1011Q													.	KCNT2-159	0			c.G3032A						.						169	140	150					1																	196227503		2203	4300	6503	SO:0001583	missense	343450	exon26			TTTCTCCGCAGCA	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18866	protein-coding gene	gene with protein product	"sodium and chloride activated ATP sensitive potassium channel"	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.3032G>A	1.37:g.196227503C>T	ENSP00000294725:p.Arg1011Gln	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	165	8	NM_198503	0	0	0	0	0	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507711	0.64410	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.36699	1.37;1.24;1.88	5.74	4.83	0.62350	.	0.000000	0.53938	D	0.000058	T	0.61999	0.2392	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.987;0.995;0.987;0.988	T	0.67799	-0.5577	10	0.66056	D	0.02	-9.2458	14.7148	0.69259	0.0:0.9307:0.0:0.0693	.	976;987;944;1011	Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	Q	987;945;1011	ENSP00000356403:R987Q;ENSP00000356401:R945Q;ENSP00000294725:R1011Q	ENSP00000294725:R1011Q	R	-	2	0	KCNT2	194494126	1.000000	0.71417	0.995000	0.50966	0.305000	0.27757	7.487000	0.81328	1.437000	0.47472	-0.148000	0.13756	CGG	.		0.517	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196227503	C	T	196227503	3	4	21	1	0	0	0	0	1	0	0	0	8113	652	23	1	387	1	KCNT2	1	196227503	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	28402027	196227503	53023118	15	1783											
ASPM	259266	ucsc.edu;bcgsc.ca	37	chr1	197069639	197069639	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttacttctagcttgaataatGataacactgcttctgatctg	11	16	6	8	0	3	3	0	3	3	0	3	3	3	3	0	0	4	2	0	0	5	7			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:197069639G>A	ENST00000367409.4	-	18	8998	c.8742C>T	c.(8740-8742)atC>atT	p.I2914I	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2914	IQ 33. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.I2914I(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						CTTGAATAATGATAACACTGC	0.294																																					p.I2914I													.	ASPM-615	1	Substitution - coding silent(1)	lung(1)	c.C8742T						.						59	61	60					1																	197069639		2203	4296	6499	SO:0001819	synonymous_variant	259266	exon18			AATAATGATAACA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8742C>T	1.37:g.197069639G>A		Somatic	38	0		WXS	Illumina HiSeq		42	4	NM_018136	0	0	0	0	0	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			.		0.294	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197069639	G	A	197069639	2	1	21	1	0	0	0	0	0	0	0	1	1057	1280	45	2		2	ASPM	1	197069639	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	842136	197069639	52180982	16	1784											
CHI3L1	1116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	203151959	203151959	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccctggctgggcttcctTtataaattcggccttcattt	5	18	7	11	1	1	0	1	0	0	0	4	0	3	0	3	3	0	2	3	3	3	8			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:203151959T>C	ENST00000255409.3	-	6	612	c.487A>G	c.(487-489)Aag>Gag	p.K163E		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	163					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						TGGGCTTCCTTTATAAATTCG	0.537																																					p.K163E		.											.	CHI3L1-515	0			c.A487G						.						67	62	64					1																	203151959		2203	4300	6503	SO:0001583	missense	1116	exon6			CTTCCTTTATAAA	BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.487A>G	1.37:g.203151959T>C	ENSP00000255409:p.Lys163Glu	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	108	29	NM_001276	0	0	33	34	1	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	37	CCDS1435.1	.	.	.	.	.	.	.	.	.	.	T	4.508	0.094296	0.08632	.	.	ENSG00000133048	ENST00000255409	T	0.05996	3.36	5.51	-0.134	0.13481	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.813254	0.10863	N	0.625821	T	0.03959	0.0111	N	0.17723	0.515	0.09310	N	1	B	0.16802	0.019	B	0.19391	0.025	T	0.48547	-0.9026	10	0.12430	T	0.62	-9.5251	8.5461	0.33421	0.0:0.0823:0.5959:0.3217	.	163	P36222	CH3L1_HUMAN	E	163	ENSP00000255409:K163E	ENSP00000255409:K163E	K	-	1	0	CHI3L1	201418582	0.000000	0.05858	0.037000	0.18230	0.460000	0.32559	-0.071000	0.11505	0.013000	0.14918	0.459000	0.35465	AAG	.		0.537	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276		C	203151959	T	C	203151959	3	2	21	1	0	0	0	0	1	0	0	0	3346	1850	64	3	684	3	CHI3L1	1	203151959	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	6082320	203151959	46098662	17	1785											
CENPF	1063	broad.mit.edu	37	chr1	214820384	214820384	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agttgctacaaggccttgatGaggccaaaaataattatatt	15	12	8	6	0	0	2	0	2	0	0	0	2	0	2	2	2	2	2	2	2	7	7			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:214820384G>A	ENST00000366955.3	+	13	7639	c.7471G>A	c.(7471-7473)Gag>Aag	p.E2491K		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2587	2 X 177 AA tandem repeats.|Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGGCCTTGATGAGGCCAAAAA	0.403																																					p.E2491K	Colon(80;575 1284 11000 14801 43496)												.	CENPF-567	0			c.G7471A						.						63	72	69					1																	214820384		2202	4300	6502	SO:0001583	missense	1063	exon13			CTTGATGAGGCCA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7471G>A	1.37:g.214820384G>A	ENSP00000355922:p.Glu2491Lys	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	103	5	NM_016343	0	0	1	1	0	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427652	0.25726	.	.	ENSG00000117724	ENST00000366955	T	0.03831	3.79	4.74	2.83	0.33086	.	0.195147	0.25205	N	0.032342	T	0.07234	0.0183	M	0.63843	1.955	0.09310	N	1	B	0.24533	0.105	B	0.26614	0.071	T	0.18587	-1.0332	10	0.48119	T	0.1	.	10.4803	0.44689	0.0743:0.1349:0.7907:0.0	.	2587	P49454	CENPF_HUMAN	K	2491	ENSP00000355922:E2491K	ENSP00000355922:E2491K	E	+	1	0	CENPF	212887007	1.000000	0.71417	0.009000	0.14445	0.023000	0.10783	2.868000	0.48436	0.666000	0.31087	-0.235000	0.12190	GAG	.		0.403	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		A	214820384	G	A	214820384	3	1	21	1	0	0	0	0	1	0	0	0	3237	1291	45	2	7517	2	CENPF	1	214820384	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	11668425	214820384	34430237	18	1786											
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	21227463	21227463	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catatttgccatcttcttcaTattctgcactgaagtcacgg	9	15	6	11	1	5	1	2	1	3	0	5	1	5	1	1	1	2	1	1	1	3	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:21227463T>C	ENST00000233242.1	-	27	12000	c.11873A>G	c.(11872-11874)tAt>tGt	p.Y3958C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3958					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATCTTCTTCATATTCTGCACT	0.363																																					p.Y3958C		.											.	APOB-175	0			c.A11873G						.						155	147	150					2																	21227463		2203	4300	6503	SO:0001583	missense	338	exon27			TCTTCATATTCTG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11873A>G	2.37:g.21227463T>C	ENSP00000233242:p.Tyr3958Cys	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	159	39	NM_000384	0	0	0	0	0	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.236382	0.39498	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.20200	2.09	5.99	5.99	0.97316	.	0.000000	0.56097	D	0.000034	T	0.44623	0.1302	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.45086	-0.9285	10	0.87932	D	0	.	10.0499	0.42210	0.0:0.0741:0.0:0.9259	.	3958	P04114	APOB_HUMAN	C	3958	ENSP00000233242:Y3958C	ENSP00000233242:Y3958C	Y	-	2	0	APOB	21080968	0.999000	0.42202	0.067000	0.19924	0.123000	0.20343	3.693000	0.54735	2.291000	0.77112	0.533000	0.62120	TAT	.		0.363	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21227463	T	C	21227463	3	2	21	1	0	0	0	0	1	0	0	0	785	1406	49	3	1830	3	APOB	2	21227463	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		21227463	221971910	19	1787											
C2orf71	388939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	29295663	29295663	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtcttcctcctcctcctctgGgctgctgtcctcgctgtcac	1	14	8	18	1	3	0	1	0	2	0	9	0	8	0	5	1	1	3	5	1	0	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:29295663G>A	ENST00000331664.5	-	1	1464	c.1465C>T	c.(1465-1467)Cca>Tca	p.P489S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	489					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TCCTCCTCTGGGCTGCTGTCC	0.527																																					p.P489S		.											.	C2orf71-91	0			c.C1465T						.						83	86	85					2																	29295663		2105	4227	6332	SO:0001583	missense	388939	exon1			CCTCTGGGCTGCT		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1465C>T	2.37:g.29295663G>A	ENSP00000332809:p.Pro489Ser	Somatic	208	0		WXS	Illumina HiSeq	Phase_I	254	80	NM_001029883	0	0	0	0	0		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	G	1.537	-0.542885	0.04053	.	.	ENSG00000179270	ENST00000331664	T	0.18016	2.24	5.3	-0.867	0.10655	.	0.860292	0.10501	N	0.667309	T	0.05227	0.0139	N	0.05199	-0.095	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.40117	-0.9580	10	0.05525	T	0.97	-0.0051	2.483	0.04592	0.3929:0.1103:0.3836:0.1132	.	489	A6NGG8	CB071_HUMAN	S	489	ENSP00000332809:P489S	ENSP00000332809:P489S	P	-	1	0	C2orf71	29149167	0.015000	0.18098	0.442000	0.26870	0.446000	0.32137	0.072000	0.14617	-0.228000	0.09869	-1.036000	0.02392	CCA	.		0.527	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29295663	G	A	29295663	3	1	21	1	0	0	0	0	1	0	0	0	2197	1232	43	2	2409	2	C2orf71	2	29295663	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	8068200	29295663	213903710	20	1788											
FAM123C	205147	broad.mit.edu	37	chr2	131521382	131521382	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccacaggcctgctcgcCggagagagcaaggccctcgg	8	3	15	15	3	0	1	0	0	0	1	2	3	0	2	4	5	2	3	4	5	1	0	rs200984217	byFrequency	TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:131521382C>A	ENST00000423981.1	+	2	1847	c.1737C>A	c.(1735-1737)gcC>gcA	p.A579A	AMER3_ENST00000321420.4_Silent_p.A579A	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	579					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.A579A(1)									GCCTGCTCGCCGGAGAGAGCA	0.662													C|||	3	0.000599042	0	0	5008	,	,		14229	0.003		0	False		,,,				2504	0				p.A579A													.	.	1	Substitution - coding silent(1)	lung(1)	c.C1737A						.	C	,,,	0,4406		0,0,2203	30	36	34		1737,1737,1737,1737	-8.8	0	2		34	2,8594	1.2+/-3.3	0,2,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	,,,	0,2,6499	AA,AC,CC		0.0233,0.0,0.0154	,,,	579/862,579/862,579/862,579/862	131521382	2,13000	2203	4298	6501	SO:0001819	synonymous_variant	205147	exon2			GCTCGCCGGAGAG	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1737C>A	2.37:g.131521382C>A		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	56	8	NM_152698	0	0	0	0	0	B7ZLH6	Silent	SNP	ENST00000423981.1	37	CCDS2164.1																																																																																			C|0.999;A|0.001		0.662	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131521382	C	A	131521382	2	1	21	1	0	0	0	0	0	0	0	1	5440	639	23	4		4	FAM123C	2	131521382	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	102225719	131521382	111677991	21	1789											
BAZ2B	29994	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160206728	160206728	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tagatttgtgttatctttttCtttaagatcttccttttgtt	6	25	5	5	0	3	2	0	0	3	2	4	2	4	2	1	0	0	2	1	0	3	11			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:160206728C>T	ENST00000392783.2	-	28	4849	c.4354G>A	c.(4354-4356)Gaa>Aaa	p.E1452K	BAZ2B_ENST00000355831.2_Missense_Mutation_p.E1418K|BAZ2B_ENST00000343439.5_Missense_Mutation_p.E1352K|BAZ2B_ENST00000392782.1_Missense_Mutation_p.E1416K	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TTATCTTTTTCTTTAAGATCT	0.368																																					p.E1452K													.	BAZ2B-94	0			c.G4354A						.						66	58	60					2																	160206728		1809	4073	5882	SO:0001583	missense	29994	exon28			CTTTTTCTTTAAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.4354G>A	2.37:g.160206728C>T	ENSP00000376534:p.Glu1452Lys	Somatic	73	1		WXS	Illumina HiSeq	Phase_I	70	15	NM_013450	0	0	1	1	0	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	14.62	2.590148	0.46214	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.06768	3.26;3.26;3.26;3.26	5.76	5.76	0.90799	.	0.000000	0.37577	U	0.002035	T	0.23451	0.0567	L	0.54323	1.7	0.51482	D	0.999923	D;P	0.71674	0.998;0.533	D;B	0.63488	0.915;0.076	T	0.00048	-1.2206	10	0.32370	T	0.25	-21.567	18.5021	0.90886	0.0:1.0:0.0:0.0	.	1416;1452	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	K	1416;1452;1418;1352	ENSP00000376533:E1416K;ENSP00000376534:E1452K;ENSP00000348087:E1418K;ENSP00000339670:E1352K	ENSP00000339670:E1352K	E	-	1	0	BAZ2B	159914974	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.954000	0.63631	2.876000	0.98609	0.643000	0.83706	GAA	.		0.368	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160206728	C	T	160206728	3	4	21	1	0	0	0	0	1	0	0	0	1333	922	32	2	2192	2	BAZ2B	2	160206728	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	28685346	160206728	82992645	22	1790											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170012842	170012842	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgtgaagccatcagcacaGacacactcataacttccttt	13	9	6	13	1	2	2	2	1	0	1	3	3	3	2	2	0	3	1	2	0	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:170012842G>T	ENST00000263816.3	-	65	12378	c.12093C>A	c.(12091-12093)gtC>gtA	p.V4031V		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4031	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CATCAGCACAGACACACTCAT	0.438																																					p.V4031V		.											.	LRP2-175	0			c.C12093A						.						199	183	188					2																	170012842		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon65			AGCACAGACACAC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12093C>A	2.37:g.170012842G>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	174	40	NM_004525	0	0	38	80	42	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			.		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170012842	G	T	170012842	2	4	21	1	0	0	0	0	0	0	0	1	8981	929	33	4		4	LRP2	2	170012842	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	9806114	170012842	73186531	23	1791											
USP37	57695	broad.mit.edu;bcgsc.ca	37	chr2	219330816	219330816	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcatactgctggagccaatCaacttctccctgagatcctt	10	12	6	13	0	3	1	2	1	1	1	5	3	4	2	3	1	4	1	3	1	3	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:219330816C>T	ENST00000258399.3	-	21	2795	c.2383G>A	c.(2383-2385)Gat>Aat	p.D795N	USP37_ENST00000454775.1_Missense_Mutation_p.D795N|USP37_ENST00000418019.1_Missense_Mutation_p.D795N|USP37_ENST00000415516.1_Missense_Mutation_p.D701N	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	795	USP.				G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TGGAGCCAATCAACTTCTCCC	0.428																																					p.D795N													.	USP37-661	0			c.G2383A						.						180	172	175					2																	219330816		2203	4300	6503	SO:0001583	missense	57695	exon21			GCCAATCAACTTC	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"Ubiquitin-specific peptidases"	20063	protein-coding gene	gene with protein product			"ubiquitin specific protease 37"			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.2383G>A	2.37:g.219330816C>T	ENSP00000258399:p.Asp795Asn	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	95	6	NM_020935	0	0	0	0	0	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Missense_Mutation	SNP	ENST00000258399.3	37	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.660499	0.88154	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	T;T;T;T	0.50277	0.81;0.81;0.75;0.81	5.46	5.46	0.80206	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.047245	0.85682	D	0.000000	T	0.59542	0.2201	L	0.44542	1.39	0.80722	D	1	D;D	0.56746	0.971;0.977	P;P	0.59703	0.783;0.862	T	0.54879	-0.8227	10	0.42905	T	0.14	-17.9037	19.5125	0.95148	0.0:1.0:0.0:0.0	.	701;795	Q86T82-2;Q86T82	.;UBP37_HUMAN	N	795;795;701;795	ENSP00000258399:D795N;ENSP00000393662:D795N;ENSP00000400902:D701N;ENSP00000396585:D795N	ENSP00000258399:D795N	D	-	1	0	USP37	219039060	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.192000	0.77771	2.840000	0.97914	0.655000	0.94253	GAT	.		0.428	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		T	219330816	C	T	219330816	3	4	21	1	0	0	0	0	1	0	0	0	17101	826	29	2	580	2	USP37	2	219330816	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	49317974	219330816	23868557	24	1792											
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	233676027	233676029	+	In_Frame_Del	DEL	CTT	CTT	-																															agcagcagcagcagttggcaCttcttcttcaacagtttcag																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:233676027_233676029delCTT	ENST00000409547.1	+	19	2283_2285	c.1972_1974delCTT	c.(1972-1974)cttdel	p.L660del	GIGYF2_ENST00000452341.2_In_Frame_Del_p.L491del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.L681del|GIGYF2_ENST00000373566.3_In_Frame_Del_p.L682del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.L660del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.L654del|GIGYF2_ENST00000409480.1_In_Frame_Del_p.L682del	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	660	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GCAGTTGGCACTTCTTCTTCAAC	0.414																																					p.679_679del		.											.	GIGYF2-28	0			c.2035_2037del						.																																			SO:0001651	inframe_deletion	26058	exon19			.	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1972_1974delCTT	2.37:g.233676033_233676035delCTT	ENSP00000386537:p.Leu660del	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	167	47	NM_001103147	0	0	0	0	0	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	In_Frame_Del	DEL	ENST00000409547.1	37	CCDS33401.1																																																																																			.		0.414	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		-	233676029	CTT	-	233676027	7	5	21	1	0	1	0	1	0	0	0	0	6398	565	20	0	2100	0	GIGYF2	2	233676027	In_Frame_Del	DEL	CTT	TCGA-A4-A48D-01A-11D-A25F-10	14345211	233676027	9523346	25	1793											
ITPR1	3708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	4878618	4878618	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcggaattaaaggatcAggtaaagaaagaaaatccca	18	7	10	6	1	1	2	1	0	0	2	3	4	2	4	1	3	0	2	1	3	8	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:4878618A>C	ENST00000443694.2	+	58	8144	c.8144A>C	c.(8143-8145)cAg>cCg	p.Q2715P	AC018816.3_ENST00000449914.1_Intron|ITPR1_ENST00000357086.4_Splice_Site_p.Q2682P|ITPR1_ENST00000456211.2_Splice_Site_p.Q2667P|ITPR1_ENST00000302640.8_Splice_Site_p.Q2715P|AC018816.3_ENST00000441894.1_Intron|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000544951.1_Splice_Site_p.Q693P|ITPR1_ENST00000354582.6_Splice_Site_p.Q2715P|ITPR1_ENST00000423119.2_Splice_Site_p.Q2682P			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2730					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTAAAGGATCAGGTAAAGAAA	0.488																																					p.Q2715P		.											.	ITPR1-710	0			c.A8144C						.						43	42	42					3																	4878618		1916	4131	6047	SO:0001630	splice_region_variant	3708	exon60			AGGATCAGGTAAA	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.8145+1A>C	3.37:g.4878618A>C		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	59	13	NM_001168272	0	0	0	0	0	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.802091	0.90538	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.91996	-2.94;-2.95;-2.95;-2.95;-2.95;-1.79;-2.94	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.95928	0.8674	M	0.77486	2.375	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	D;P;D	0.78314	0.979;0.893;0.991	D	0.95864	0.8885	10	0.54805	T	0.06	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	693;2730;2682	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	P	2730;2715;2715;2682;1176;2682;2667;693;2715	ENSP00000306253:Q2715P;ENSP00000346595:Q2715P;ENSP00000405934:Q2682P;ENSP00000349597:Q2682P;ENSP00000397885:Q2667P;ENSP00000440564:Q693P;ENSP00000401671:Q2715P	ENSP00000306253:Q2715P	Q	+	2	0	ITPR1	4853618	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	9.243000	0.95416	2.324000	0.78689	0.533000	0.62120	CAG	.		0.488	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	Missense_Mutation	C	4878618	A	C	4878618	5	2	21	1	0	0	0	0	0	0	1	0	7941	202	7	5	8423	5	ITPR1	3	4878618	Splice_Site	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		4878618	193143812	26	1794											
NUP210	23225	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	13399893	13399893	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttccccaccgacagggcgatGacctggtagggcacagtgaa	10	6	13	12	2	0	2	0	2	0	0	1	4	1	2	4	3	0	2	4	3	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:13399893G>A	ENST00000254508.5	-	16	2239	c.2157C>T	c.(2155-2157)gtC>gtT	p.V719V		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	719					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					ACAGGGCGATGACCTGGTAGG	0.612																																					p.V719V													.	NUP210-256	0			c.C2157T						.						49	50	49					3																	13399893		2203	4300	6503	SO:0001819	synonymous_variant	23225	exon16			GGCGATGACCTGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.2157C>T	3.37:g.13399893G>A		Somatic	162	0		WXS	Illumina HiSeq	Phase_I	206	25	NM_024923	0	0	0	0	0	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			.		0.612	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13399893	G	A	13399893	2	1	21	1	0	0	0	0	0	0	0	1	10786	1277	45	2		2	NUP210	3	13399893	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	8521275	13399893	184622537	27	1795											
SH3BP5	9467	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	15298471	15298471	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagggctgggcagatccaGgctgccaggcctcacaaccg	9	4	13	15	1	1	1	1	0	0	1	2	1	2	1	4	4	2	3	4	4	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:15298471G>A	ENST00000383791.3	-	8	1259	c.1039C>T	c.(1039-1041)Ctg>Ttg	p.L347L	SH3BP5_ENST00000408919.3_Silent_p.L190L|SH3BP5_ENST00000253688.5_Silent_p.L190L|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5_ENST00000426925.1_Silent_p.L190L	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	347	Ser-rich.				intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						GGCAGATCCAGGCTGCCAGGC	0.587																																					p.L347L		.											.	SH3BP5-90	0			c.C1039T						.						73	63	67					3																	15298471		2203	4300	6503	SO:0001819	synonymous_variant	9467	exon8			GATCCAGGCTGCC	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"SH3 binding protein"	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.1039C>T	3.37:g.15298471G>A		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	221	46	NM_004844	0	0	26	26	0	B3KQW6|Q5JWV9	Silent	SNP	ENST00000383791.3	37	CCDS2625.2																																																																																			.		0.587	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		A	15298471	G	A	15298471	2	1	21	1	0	0	0	0	0	0	0	1	14279	991	35	2		2	SH3BP5	3	15298471	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	1898578	15298471	182723959	28	1796											
ANKRD28	23243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	15765925	15765925	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaaggtacttgactacgctGatcattccactagaggctgc	11	10	10	10	1	1	4	1	2	0	2	2	4	2	4	1	2	3	3	1	2	4	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:15765925G>A	ENST00000399451.2	-	7	1024	c.657C>T	c.(655-657)atC>atT	p.I219I	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Silent_p.I252I	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	219						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TGACTACGCTGATCATTCCAC	0.363																																					p.I219I		.											.	ANKRD28-135	0			c.C657T						.						56	53	54					3																	15765925		1940	4139	6079	SO:0001819	synonymous_variant	23243	exon7			TACGCTGATCATT	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.657C>T	3.37:g.15765925G>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	134	18	NM_015199	0	0	2	3	1	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Silent	SNP	ENST00000399451.2	37	CCDS46769.1																																																																																			.		0.363	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		A	15765925	G	A	15765925	2	1	21	1	0	0	0	0	0	0	0	1	656	1280	45	2		2	ANKRD28	3	15765925	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	467454	15765925	182256505	29	1797											
SLC22A13	9390	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38316203	38316203	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatggccctgcgctttgcTgtggctactgccgtcgctgg	3	12	13	13	3	0	0	0	0	0	0	1	0	0	0	2	3	5	4	2	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:38316203T>C	ENST00000311856.4	+	3	640	c.591T>C	c.(589-591)gcT>gcC	p.A197A	SLC22A13_ENST00000450935.2_Intron	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	197					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		TGCGCTTTGCTGTGGCTACTG	0.617																																					p.A197A		.											.	SLC22A13-91	0			c.T591C						.						72	68	69					3																	38316203		2203	4300	6503	SO:0001819	synonymous_variant	9390	exon3			CTTTGCTGTGGCT	AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.591T>C	3.37:g.38316203T>C		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	189	71	NM_004256	0	0	0	2	2	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	37	CCDS2676.1																																																																																			.		0.617	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38316203	T	C	38316203	2	2	21	1	0	0	0	0	0	0	0	1	14476	1567	55	3		3	SLC22A13	3	38316203	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	22550278	38316203	159706227	30	1798											
SCN10A	6336	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38755540	38755540	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccacttcagaatattccAgaatcttcgctgtgagactt	11	12	8	10	1	2	3	1	1	1	3	4	5	3	3	2	0	1	1	2	0	3	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:38755540A>C	ENST00000449082.2	-	21	3712	c.3713T>G	c.(3712-3714)cTg>cGg	p.L1238R		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1238					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGAATATTCCAGAATCTTCGC	0.527																																					p.L1238R													.	SCN10A-99	0			c.T3713G						.						119	116	117					3																	38755540		2203	4300	6503	SO:0001583	missense	6336	exon21			TATTCCAGAATCT	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3713T>G	3.37:g.38755540A>C	ENSP00000390600:p.Leu1238Arg	Somatic	48	1		WXS	Illumina HiSeq	Phase_I	80	27	NM_006514	0	0	0	0	0	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.911020	0.52439	.	.	ENSG00000185313	ENST00000449082	D	0.98701	-5.08	4.23	4.23	0.50019	Ion transport (1);	0.545385	0.16081	N	0.230526	D	0.98369	0.9458	M	0.92122	3.275	0.39492	D	0.968069	P	0.35714	0.517	B	0.37989	0.262	D	0.99961	1.1734	10	0.87932	D	0	.	10.3535	0.43950	0.8353:0.1647:0.0:0.0	.	1238	Q9Y5Y9	SCNAA_HUMAN	R	1238	ENSP00000390600:L1238R	ENSP00000390600:L1238R	L	-	2	0	SCN10A	38730544	0.994000	0.37717	0.640000	0.29408	0.574000	0.36063	7.332000	0.79203	1.770000	0.52166	0.338000	0.21704	CTG	.		0.527	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		C	38755540	A	C	38755540	3	2	21	1	0	0	0	0	1	0	0	0	13944	188	7	5	2185	5	SCN10A	3	38755540	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	439337	38755540	159266890	31	1799											
VIPR1	7433	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	42577629	42577629	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgctggcacctgcagggCgtcctgggctggaaccccaa	6	5	15	15	3	0	0	0	0	0	0	1	1	1	1	4	5	2	4	4	5	2	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:42577629C>T	ENST00000325123.4	+	13	1343	c.1230C>T	c.(1228-1230)ggC>ggT	p.G410G	VIPR1_ENST00000543411.1_Silent_p.G362G|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1_ENST00000438259.2_Silent_p.G200G|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1_ENST00000433647.1_Silent_p.G369G	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	410					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		ACCTGCAGGGCGTCCTGGGCT	0.682																																					p.G410G		.											.	VIPR1-91	0			c.C1230T						.						14	17	16					3																	42577629		2190	4293	6483	SO:0001819	synonymous_variant	7433	exon13			GCAGGGCGTCCTG	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12694	protein-coding gene	gene with protein product	"VIP and PACAP receptor 1"	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.1230C>T	3.37:g.42577629C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	121	51	NM_004624	0	0	2	2	0	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																			.		0.682	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		T	42577629	C	T	42577629	2	4	21	1	0	0	0	0	0	0	0	1	17202	755	27	1		1	VIPR1	3	42577629	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	3822089	42577629	155444801	32	1800											
FLNB	2317	broad.mit.edu;bcgsc.ca	37	chr3	58154281	58154281	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggaaacacctgaagggtAcaaagtcatgtacaccccca	15	5	8	13	0	1	1	1	1	0	0	1	2	1	2	4	2	3	2	4	2	5	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:58154281A>G	ENST00000295956.4	+	44	7478	c.7313A>G	c.(7312-7314)tAc>tGc	p.Y2438C	FLNB_ENST00000484981.1_3'UTR|FLNB_ENST00000357272.4_3'UTR|FLNB_ENST00000429972.2_Missense_Mutation_p.Y2427C|FLNB_ENST00000419752.2_Missense_Mutation_p.Y2258C|FLNB_ENST00000348383.5_Missense_Mutation_p.Y2397C|FLNB_ENST00000490882.1_Missense_Mutation_p.Y2469C|FLNB_ENST00000493452.1_Missense_Mutation_p.Y2245C|FLNB-AS1_ENST00000488720.1_RNA|FLNB_ENST00000358537.3_Missense_Mutation_p.Y2414C	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2438	Interaction with INPPL1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCTGAAGGGTACAAAGTCATG	0.522																																					p.Y2469C													.	FLNB-593	0			c.A7406G						.						107	89	95					3																	58154281		2203	4300	6503	SO:0001583	missense	2317	exon45			AAGGGTACAAAGT	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.7313A>G	3.37:g.58154281A>G	ENSP00000295956:p.Tyr2438Cys	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	208	7	NM_001164317	0	0	57	61	4	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.304102	0.81136	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64;-2.64;-2.64;-2.64	4.67	4.67	0.58626	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.062472	0.64402	D	0.000003	D	0.93334	0.7875	L	0.52266	1.64	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.988;1.0;0.991;0.999;0.999	D	0.93660	0.6981	10	0.56958	D	0.05	.	14.3123	0.66424	1.0:0.0:0.0:0.0	.	2414;2469;2245;2258;2427;2438	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	C	2438;2469;2414;2427;2397;2245;2258	ENSP00000295956:Y2438C;ENSP00000420213:Y2469C;ENSP00000351339:Y2414C;ENSP00000415599:Y2427C;ENSP00000232447:Y2397C;ENSP00000418510:Y2245C;ENSP00000414532:Y2258C	ENSP00000295956:Y2438C	Y	+	2	0	FLNB	58129321	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.139000	0.94554	1.966000	0.57179	0.460000	0.39030	TAC	.		0.522	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58154281	A	G	58154281	3	3	21	1	0	0	0	0	1	0	0	0	5953	391	14	3	7584	3	FLNB	3	58154281	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	15576652	58154281	139868149	33	1801											
ROPN1	54763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	123695737	123695737	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgcaggatctttaacagctCaggtgttagctctgcccggt	8	12	11	10	1	3	0	1	0	2	0	3	1	3	1	1	3	5	4	1	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:123695737C>G	ENST00000184183.4	-	4	548	c.208G>C	c.(208-210)Gag>Cag	p.E70Q	ROPN1_ENST00000405845.3_Missense_Mutation_p.E70Q	NM_017578.2	NP_060048.2	Q9HAT0	ROP1A_HUMAN	rhophilin associated tail protein 1	70						cytoplasm (GO:0005737)|nucleus (GO:0005634)				lung(2)|ovary(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.148)		TTTAACAGCTCAGGTGTTAGC	0.542																																					p.E70Q		.											.	ROPN1-92	0			c.G208C						.						97	86	90					3																	123695737		2203	4300	6503	SO:0001583	missense	54763	exon4			ACAGCTCAGGTGT	AF231410	CCDS3026.1	3q21.1	2011-01-20	2011-01-20			ENSG00000065371			17692	protein-coding gene	gene with protein product	"cancer/testis antigen 91"	611757	"ropporin, rhophilin associated protein 1"			10591629	Standard	NM_017578		Approved	ODF6, ropporin, ROPN1A, CT91	uc003eha.3	Q9HAT0		ENST00000184183.4:c.208G>C	3.37:g.123695737C>G	ENSP00000184183:p.Glu70Gln	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	235	40	NM_017578	0	0	0	0	0	D3DN99|Q9UF38	Missense_Mutation	SNP	ENST00000184183.4	37	CCDS3026.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599790	0.46318	.	.	ENSG00000065371	ENST00000184183;ENST00000405845;ENST00000467907;ENST00000460743;ENST00000495336;ENST00000496145	T;T;T;T	0.31247	1.99;1.99;1.99;1.5	4.37	4.37	0.52481	.	0.000000	0.56097	D	0.000025	T	0.22282	0.0537	N	0.22421	0.69	0.80722	D	1	P	0.41313	0.745	B	0.38803	0.282	T	0.04870	-1.0921	10	0.46703	T	0.11	-26.3117	14.1277	0.65233	0.0:1.0:0.0:0.0	.	70	Q9HAT0	ROP1A_HUMAN	Q	70	ENSP00000184183:E70Q;ENSP00000385919:E70Q;ENSP00000417067:E70Q;ENSP00000420310:E70Q	ENSP00000184183:E70Q	E	-	1	0	ROPN1	125178427	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	4.230000	0.58632	2.304000	0.77564	0.551000	0.68910	GAG	.		0.542	ROPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356188.2	NM_017578		G	123695737	C	G	123695737	3	3	21	1	0	0	0	0	1	0	0	0	13555	835	29	4	446	4	ROPN1	3	123695737	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	65541456	123695737	74326693	34	1802											
MME	4311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	154855893	154855893	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctatttttttcttgcaggcTtgtacagcatatgtggattt	7	19	9	6	0	1	0	0	0	1	0	1	1	1	1	0	2	3	5	0	2	3	9			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:154855893T>A	ENST00000460393.1	+	9	843	c.723T>A	c.(721-723)gcT>gcA	p.A241A	MME_ENST00000492661.1_Silent_p.A241A|MME_ENST00000462745.1_Silent_p.A241A|MME_ENST00000360490.2_Silent_p.A241A|MME_ENST00000493237.1_Silent_p.A241A	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	241					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	TCTTGCAGGCTTGTACAGCAT	0.323																																					p.A241A		.											.	MME-516	0			c.T723A						.						153	163	160					3																	154855893		2203	4300	6503	SO:0001819	synonymous_variant	4311	exon9			GCAGGCTTGTACA		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.723T>A	3.37:g.154855893T>A		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	161	70	NM_007287	0	0	0	0	0	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	37	CCDS3172.1																																																																																			.		0.323	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154855893	T	A	154855893	2	1	21	1	0	0	0	0	0	0	0	1	9670	1596	56	5		5	MME	3	154855893	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	31160156	154855893	43166537	35	1803											
GPR125	166647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	22436990	22436990	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttcaatcatttctgccaCaaatataacatccattttgt	12	18	2	9	0	3	0	2	0	1	0	4	0	4	0	2	0	2	0	2	0	4	7	rs146147575		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:22436990C>G	ENST00000334304.5	-	10	1656	c.1387G>C	c.(1387-1389)Gtg>Ctg	p.V463L	GPR125_ENST00000502482.1_Missense_Mutation_p.V463L|GPR125_ENST00000508133.1_Missense_Mutation_p.V237L|GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	463					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				ATTTCTGCCACAAATATAACA	0.388																																					p.V463L		.											.	GPR125-91	0			c.G1387C						.	C	LEU/VAL	1,4405	2.1+/-5.4	0,1,2202	81	80	80		1387	5.4	1	4	dbSNP_134	80	0,8600		0,0,4300	no	missense	GPR125	NM_145290.2	32	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	possibly-damaging	463/1322	22436990	1,13005	2203	4300	6503	SO:0001583	missense	166647	exon10			CTGCCACAAATAT	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1387G>C	4.37:g.22436990C>G	ENSP00000334952:p.Val463Leu	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	203	47	NM_145290	0	0	0	1	1	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434578	0.62955	2.27E-4	0.0	ENSG00000152990	ENST00000334304;ENST00000508133;ENST00000502482	T;T;T	0.41400	1.0;1.0;1.0	5.42	5.42	0.78866	.	0.063133	0.64402	D	0.000006	T	0.45955	0.1368	L	0.38175	1.15	0.58432	D	0.999998	D;B;P;D	0.53312	0.957;0.448;0.851;0.959	P;B;P;P	0.49561	0.615;0.283;0.546;0.556	T	0.38243	-0.9670	10	0.48119	T	0.1	-35.6945	19.2098	0.93749	0.0:1.0:0.0:0.0	.	338;463;237;463	Q8IWK6-3;Q8IWK6-2;Q8IWK6-4;Q8IWK6	.;.;.;GP125_HUMAN	L	463;237;463	ENSP00000334952:V463L;ENSP00000422606:V237L;ENSP00000421006:V463L	ENSP00000334952:V463L	V	-	1	0	GPR125	22046088	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.377000	0.59562	2.528000	0.85240	0.563000	0.77884	GTG	C|1.000;G|0.000		0.388	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			G	22436990	C	G	22436990	3	3	21	1	0	0	0	0	1	0	0	0	6659	478	17	4	2618	4	GPR125	4	22436990	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		22436990	168717286	36	1804											
TMEM156	80008	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	38988027	38988027	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaagagaacagatgtaggtTtgtctctatgacctattccc	11	14	8	8	0	1	3	0	1	1	2	3	4	2	3	2	1	1	2	2	1	5	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:38988027T>A	ENST00000381938.3	-	5	859	c.752A>T	c.(751-753)aAa>aTa	p.K251I		NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	251						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						AGATGTAGGTTTGTCTCTATG	0.373																																					p.K251I		.											.	TMEM156-91	0			c.A752T						.						97	87	90					4																	38988027		2203	4300	6503	SO:0001583	missense	80008	exon5			GTAGGTTTGTCTC	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.752A>T	4.37:g.38988027T>A	ENSP00000371364:p.Lys251Ile	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	53	10	NM_024943	0	0	0	0	0	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	37	CCDS3448.1	.	.	.	.	.	.	.	.	.	.	T	9.849	1.193176	0.22037	.	.	ENSG00000121895	ENST00000381938	T	0.26660	1.72	5.08	-0.654	0.11443	.	0.927636	0.09222	N	0.831791	T	0.25457	0.0619	L	0.48642	1.525	0.09310	N	1	P	0.43701	0.815	P	0.46389	0.515	T	0.20874	-1.0262	10	0.54805	T	0.06	-3.0832	4.5798	0.12253	0.0:0.1723:0.3153:0.5124	.	251	Q8N614	TM156_HUMAN	I	251	ENSP00000371364:K251I	ENSP00000371364:K251I	K	-	2	0	TMEM156	38664422	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.171000	0.16685	-0.126000	0.11682	0.379000	0.24179	AAA	.		0.373	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943		A	38988027	T	A	38988027	3	1	21	1	0	0	0	0	1	0	0	0	16105	1841	64	5	146	5	TMEM156	4	38988027	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	16551037	38988027	152166249	37	1805											
CLOCK	9575	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	56301748	56301748	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttgagggattcccatggAgcaacctagaagtctaaaaa	15	8	11	7	0	1	2	0	1	1	1	2	5	2	4	2	2	2	2	2	2	6	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:56301748A>G	ENST00000309964.4	-	22	2625	c.2375T>C	c.(2374-2376)cTc>cCc	p.L792P	CLOCK_ENST00000513440.1_Missense_Mutation_p.L792P|CLOCK_ENST00000381322.1_Missense_Mutation_p.L792P	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	792	Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			ATTCCCATGGAGCAACCTAGA	0.453																																					p.L792P													.	CLOCK-515	0			c.T2375C						.						191	178	183					4																	56301748		2203	4300	6503	SO:0001583	missense	9575	exon23			CCATGGAGCAACC	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.2375T>C	4.37:g.56301748A>G	ENSP00000308741:p.Leu792Pro	Somatic	192	2		WXS	Illumina HiSeq	Phase_I	193	53	NM_004898	0	0	0	2	2	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.404140	0.62288	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.10763	2.84;2.84;2.84	5.83	5.83	0.93111	.	1.213080	0.05401	N	0.540818	T	0.32102	0.0818	M	0.71206	2.165	0.80722	D	1	D	0.58970	0.984	P	0.55161	0.77	T	0.00292	-1.1842	10	0.42905	T	0.14	.	16.2025	0.82095	1.0:0.0:0.0:0.0	.	792	O15516	CLOCK_HUMAN	P	792	ENSP00000308741:L792P;ENSP00000370723:L792P;ENSP00000426983:L792P	ENSP00000308741:L792P	L	-	2	0	CLOCK	55996505	1.000000	0.71417	0.996000	0.52242	0.942000	0.58702	8.096000	0.89537	2.231000	0.72958	0.459000	0.35465	CTC	.		0.453	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		G	56301748	A	G	56301748	3	3	21	1	0	0	0	0	1	0	0	0	3555	304	11	3	169	3	CLOCK	4	56301748	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	17313721	56301748	134852528	38	1806											
PPP3CA	5530	broad.mit.edu;bcgsc.ca	37	chr4	102030234	102030236	+	Splice_Site	DEL	AAC	AAC	-																															tgtccatgaatgtccccacaAactgaaagaaacaaaattca																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:102030234_102030236delAAC	ENST00000394854.3	-	3	943_944	c.260_261delGTT	c.(259-261)ggt>g	p.G87del	PPP3CA_ENST00000323055.6_Splice_Site_p.G87del|PPP3CA_ENST00000507176.1_5'UTR|PPP3CA_ENST00000510292.1_5'UTR|PPP3CA_ENST00000523694.2_Splice_Site_p.G20del|PPP3CA_ENST00000394853.4_Splice_Site_p.G87del|PPP3CA_ENST00000512215.1_Intron	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	87	Catalytic.				calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		TGTCCCCACAAACTGAAAGAAAC	0.33																																					p.87_87del													.	PPP3CA-227	0			c.260_261del						.																																			SO:0001630	splice_region_variant	5530	exon3			CCCACAAACTGAA		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9314	protein-coding gene	gene with protein product	"calcineurin A alpha", "protein phosphatase 2B, catalytic subunit, alpha isoform"	114105	"protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)", "protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.260-1GTT>-	4.37:g.102030234_102030236delAAC		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	52	9	NM_000944	0	0	0	0	0	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Frame_Shift_Del	DEL	ENST00000394854.3	37	CCDS34037.1																																																																																			.		0.33	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944	In_Frame_Del	-	102030236	AAC	-	102030234	8	5	21	1	0	1	0	1	0	0	1	0	12426	28	1	0	1352	0	PPP3CA	4	102030234	Splice_Site	DEL	AAC	TCGA-A4-A48D-01A-11D-A25F-10	45728486	102030234	89124042	39	1807											
HSPA4L	22824	broad.mit.edu;bcgsc.ca	37	chr4	128726257	128726266	+	Frame_Shift_Del	DEL	GAAATTGTAG	GAAATTGTAG	-																															gtgaagacattagtagtataGaaattgtaggaggagcaaca																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	GAAATTGTAG	GAAATTGTAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:128726257_128726266delGAAATTGTAG	ENST00000296464.4	+	9	1426_1435	c.1015_1024delGAAATTGTAG	c.(1015-1026)gaaattgtaggafs	p.EIVG339fs	HSPA4L_ENST00000508776.1_Frame_Shift_Del_p.EIVG339fs|HSPA4L_ENST00000439123.2_Frame_Shift_Del_p.EIVG370fs|HSPA4L_ENST00000505726.1_Frame_Shift_Del_p.EIVG313fs	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	339					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TAGTAGTATAGAAATTGTAGGAGGAGCAAC	0.333																																					p.339_342del													.	HSPA4L-228	0			c.1015_1024del						.																																			SO:0001589	frameshift_variant	22824	exon9			AGTATAGAAATTG	AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.1015_1024delGAAATTGTAG	4.37:g.128726257_128726266delGAAATTGTAG	ENSP00000296464:p.Glu339fs	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	134	16	NM_014278	0	0	0	0	0	A2ICT2|Q4W5M5|Q8IWA2	Frame_Shift_Del	DEL	ENST00000296464.4	37	CCDS3734.1																																																																																			.		0.333	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		-	128726266	GAAATTGTAG	-	128726257	7	5	21	1	0	1	0	1	0	0	0	0	7434	943	33	0	1049	0	HSPA4L	4	128726257	Frame_Shift_Del	DEL	GAAATTGTAG	TCGA-A4-A48D-01A-11D-A25F-10	26696023	128726257	62428019	40	1808											
TBC1D9	23158	broad.mit.edu;bcgsc.ca	37	chr4	141590874	141590874	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggacgctgttgccatttaGgttaaactggcgctctccat	7	12	12	10	2	1	0	0	0	1	0	2	1	1	1	2	4	2	4	2	4	3	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:141590874G>A	ENST00000442267.2	-	8	1425	c.1351C>T	c.(1351-1353)Cta>Tta	p.L451L		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	451							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TTGCCATTTAGGTTAAACTGG	0.577																																					p.L451L													.	TBC1D9-23	0			c.C1351T						.						63	70	68					4																	141590874		2094	4216	6310	SO:0001819	synonymous_variant	23158	exon8			CATTTAGGTTAAA	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1351C>T	4.37:g.141590874G>A		Somatic	205	0		WXS	Illumina HiSeq	Phase_I	243	9	NM_015130	0	0	2	2	0	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			.		0.577	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141590874	G	A	141590874	2	1	21	1	0	0	0	0	0	0	0	1	15659	991	35	2		2	TBC1D9	4	141590874	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	12864617	141590874	49563402	41	1809											
TIGD4	201798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	153691183	153691183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgatatttgattttaaggCttttaataacaccttgtttc	10	19	6	6	1	0	1	0	1	0	0	2	2	0	1	1	1	1	2	1	1	4	9			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:153691183C>T	ENST00000304337.2	-	2	1794	c.974G>A	c.(973-975)aGc>aAc	p.S325N		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	325	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					GATTTTAAGGCTTTTAATAAC	0.323																																					p.S325N		.											.	TIGD4-91	0			c.G974A						.						75	78	77					4																	153691183		2203	4300	6503	SO:0001583	missense	201798	exon2			TTAAGGCTTTTAA	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.974G>A	4.37:g.153691183C>T	ENSP00000355162:p.Ser325Asn	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	140	32	NM_145720	0	0	0	0	0	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487660	0.04352	.	.	ENSG00000169989	ENST00000304337	T	0.45276	0.9	6.03	4.22	0.49857	.	0.326215	0.26620	N	0.023365	T	0.25938	0.0632	N	0.21448	0.665	0.27351	N	0.956258	B	0.17268	0.021	B	0.16289	0.015	T	0.12863	-1.0531	10	0.21540	T	0.41	-2.7406	8.7415	0.34560	0.0:0.7308:0.1218:0.1475	.	325	Q8IY51	TIGD4_HUMAN	N	325	ENSP00000355162:S325N	ENSP00000355162:S325N	S	-	2	0	TIGD4	153910633	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	1.186000	0.32078	1.465000	0.48006	-0.345000	0.07892	AGC	.		0.323	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		T	153691183	C	T	153691183	3	4	21	1	0	0	0	0	1	0	0	0	15930	797	28	2	568	2	TIGD4	4	153691183	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	12100309	153691183	37463093	42	1810											
FASTKD3	79072	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7867846	7867846	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttccatcgtgcttataaaActtagcacttcttctgatga	10	16	6	9	1	2	2	0	2	2	0	4	2	3	2	1	0	3	3	1	0	4	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:7867846A>G	ENST00000264669.5	-	2	487	c.351T>C	c.(349-351)agT>agC	p.S117S	MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	117					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGCTTATAAAACTTAGCACTT	0.423																																					p.S117S													.	FASTKD3-156	0			c.T351C						.						55	53	54					5																	7867846		2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			TATAAAACTTAGC	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.351T>C	5.37:g.7867846A>G		Somatic	116	1		WXS	Illumina HiSeq	Phase_I	126	55	NM_024091	0	0	1	1	0	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			.		0.423	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867846	A	G	7867846	2	3	21	1	0	0	0	0	0	0	0	1	5706	40	2	3		3	FASTKD3	5	7867846	Silent	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		7867846	173047414	43	1811											
CDH9	1007	broad.mit.edu	37	chr5	26988231	26988231	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttgcctacatattgtgtGtcagtacctgtgtactcttc	7	16	7	11	0	2	0	1	0	1	0	3	0	2	0	3	0	4	2	3	0	4	7			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:26988231G>T	ENST00000231021.4	-	2	382	c.210C>A	c.(208-210)gaC>gaA	p.D70E		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	70	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CATATTGTGTGTCAGTACCTG	0.393																																					p.D70E	Melanoma(8;187 585 15745 40864 52829)												.	CDH9-99	0			c.C210A						.																																			SO:0001583	missense	1007	exon2			TTGTGTGTCAGTA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.210C>A	5.37:g.26988231G>T	ENSP00000231021:p.Asp70Glu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	102	5	NM_016279	0	0	0	0	0	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.355301	0.41700	.	.	ENSG00000113100	ENST00000231021;ENST00000513289;ENST00000511822	T;T;T	0.00584	6.4;6.4;6.4	5.64	3.87	0.44632	Cadherin (1);Cadherin-like (1);	0.049238	0.85682	D	0.000000	T	0.00552	0.0018	N	0.05306	-0.075	0.41042	D	0.98523	D;B	0.54207	0.965;0.04	P;B	0.53760	0.734;0.059	D	0.85933	0.1453	9	.	.	.	.	7.5213	0.27629	0.3198:0.0:0.6802:0.0	.	70;70	E7EPN0;Q9ULB4	.;CADH9_HUMAN	E	70	ENSP00000231021:D70E;ENSP00000426239:D70E;ENSP00000422538:D70E	.	D	-	3	2	CDH9	27023988	0.999000	0.42202	1.000000	0.80357	0.985000	0.73830	0.662000	0.25038	0.745000	0.32763	0.591000	0.81541	GAC	.		0.393	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26988231	G	T	26988231	3	4	21	1	0	0	0	0	1	0	0	0	3123	1368	48	4	2203	4	CDH9	5	26988231	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	19120385	26988231	153927029	44	1812											
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	37017244	37017247	+	Frame_Shift_Del	DEL	ATAG	ATAG	-																															gcaaaatggatcaaggatctAtagaacgcattttaaaacag																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	ATAG	ATAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:37017244_37017247delATAG	ENST00000282516.8	+	24	5399_5402	c.4900_4903delATAG	c.(4900-4905)atagaafs	p.IE1634fs	NIPBL_ENST00000448238.2_Frame_Shift_Del_p.IE1634fs	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1634					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.E1635K(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TCAAGGATCTATAGAACGCATTTT	0.333																																					p.1634_1635del		.											.	NIPBL-293	2	Substitution - Missense(2)	lung(2)	c.4900_4903del						.																																			SO:0001589	frameshift_variant	25836	exon24			.	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4900_4903delATAG	5.37:g.37017244_37017247delATAG	ENSP00000282516:p.Ile1634fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	173	76	NM_015384	0	0	0	0	0	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	37	CCDS3920.1																																																																																			.		0.333	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	37017247	ATAG	-	37017244	7	5	21	1	0	1	0	1	0	0	0	0	10454	449	16	0	4990	0	NIPBL	5	37017244	Frame_Shift_Del	DEL	ATAG	TCGA-A4-A48D-01A-11D-A25F-10	10029013	37017244	143898016	45	1813											
MAST4	375449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	66449317	66449318	+	Missense_Mutation	DNP	CA	CA	AT																															aggaagtccggcatgccaggCaggactgaaggctggagatc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:66449317_66449318CA>AT	ENST00000403625.2	+	26	3852_3853	c.3557_3558CA>AT	c.(3556-3558)gCA>gAT	p.A1186D	MAST4_ENST00000404260.3_Missense_Mutation_p.A1189D|MAST4_ENST00000261569.7_Missense_Mutation_p.A992D|MAST4_ENST00000403666.1_Missense_Mutation_p.A997D|MAST4_ENST00000405643.1_Missense_Mutation_p.A1007D	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1189	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GCATGCCAGGCAGGACTGAAGG	0.441																																					p.A1189D		.											.	MAST4-647	0			c.A2991T						.																																			SO:0001583	missense	375449	exon25			CCAGGCAGGACTG	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	Exception_encountered	5.37:g.66449317_66449318delinsAT	ENSP00000385727:p.Ala1186Asp	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	73	14	NM_015183	0	0	0	0	0	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	DNP	ENST00000403625.2	37	CCDS54861.1																																																																																			.		0.441	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			AT	66449318	CA	AT	66449317	3	1	21	1	0	0	0	0	1	0	0	0	9352	710	25	4	3789	4	MAST4	5	66449317	Missense_Mutation	DNP	CA	TCGA-A4-A48D-01A-11D-A25F-10	29432073	66449317	114465943	46	1814											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82808190	82808191	+	Missense_Mutation	DNP	CA	CA	GC																															ggcttccctccccctgatagCagatttgatgcctactgctt																								rs558902507		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:82808190_82808191CA>GC	ENST00000265077.3	+	6	1582_1583	c.1017_1018CA>GC	c.(1015-1020)agCAga>agGCga	p.S339R	VCAN_ENST00000512590.2_Missense_Mutation_p.S291R|VCAN_ENST00000513984.1_Missense_Mutation_p.S339R|VCAN_ENST00000343200.5_Missense_Mutation_p.S339R|VCAN_ENST00000342785.4_Missense_Mutation_p.S339R|VCAN_ENST00000502527.2_Missense_Mutation_p.S339R	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	339	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCCCTGATAGCAGATTTGATGC	0.446																																					p.S339R		.											.	VCAN-238	0			c.A1018C						.																																			SO:0001583	missense	1462	exon6			GATAGCAGATTTG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	Exception_encountered	5.37:g.82808190_82808191delinsGC	ENSP00000265077:p.Ser339Arg	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	109	34	NM_001126336	0	0	0	0	0	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	DNP	ENST00000265077.3	37	CCDS4060.1																																																																																			.		0.446	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		GC	82808191	CA	GC	82808190	3	3	21	1	0	0	0	0	1	0	0	0	17171	709	25	4	1035	4	VCAN	5	82808190	Missense_Mutation	DNP	CA	TCGA-A4-A48D-01A-11D-A25F-10	16358873	82808190	98107070	47	1815											
GPR98	84059	broad.mit.edu	37	chr5	89971181	89971181	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaaatcaggttattggtcatCcgtgcacagggacttctggg	9	11	13	8	1	3	0	2	0	1	0	4	2	4	1	1	4	1	2	1	4	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:89971181C>T	ENST00000405460.2	+	24	5328	c.5232C>T	c.(5230-5232)atC>atT	p.I1744I	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1744	Calx-beta 12. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TATTGGTCATCCGTGCACAGG	0.507																																					p.I1744I													.	GPR98-103	0			c.C5232T						.						90	95	94					5																	89971181		2027	4195	6222	SO:0001819	synonymous_variant	84059	exon24			GGTCATCCGTGCA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5232C>T	5.37:g.89971181C>T		Somatic	254	0		WXS	Illumina HiSeq	Phase_I	350	6	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			.		0.507	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89971181	C	T	89971181	2	4	21	1	0	0	0	0	0	0	0	1	6742	845	30	2		2	GPR98	5	89971181	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	7162991	89971181	90944079	48	1816											
GIN1	54826	broad.mit.edu	37	chr5	102432357	102432357	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccactttctgtaatataGtctatgacacaaggaccaac	14	11	5	11	0	2	1	0	1	2	0	3	2	3	2	2	1	1	1	2	1	6	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:102432357G>C	ENST00000399004.2	-	7	1276	c.1182C>G	c.(1180-1182)gaC>gaG	p.D394E	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	394					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		CTGTAATATAGTCTATGACAC	0.398																																					p.D394E													.	GIN1-92	0			c.C1182G						.						246	232	236					5																	102432357		1869	4105	5974	SO:0001583	missense	54826	exon7			AATATAGTCTATG	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.1182C>G	5.37:g.102432357G>C	ENSP00000381970:p.Asp394Glu	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	162	4	NM_017676	0	0	2	2	0	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.659656	0.67586	.	.	ENSG00000145723	ENST00000399004	T	0.17054	2.3	5.68	3.91	0.45181	.	0.000000	0.43110	U	0.000610	T	0.24699	0.0599	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.02208	-1.1195	10	0.25751	T	0.34	-17.0316	8.8545	0.35221	0.2495:0.0:0.7505:0.0	.	394	Q9NXP7	GIN1_HUMAN	E	394	ENSP00000381970:D394E	ENSP00000381970:D394E	D	-	3	2	GIN1	102460256	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	1.738000	0.38207	0.754000	0.32968	0.655000	0.94253	GAC	.		0.398	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		C	102432357	G	C	102432357	3	2	21	1	0	0	0	0	1	0	0	0	6406	1020	36	4	394	4	GIN1	5	102432357	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	12461176	102432357	78482903	49	1817											
TXNDC15	79770	broad.mit.edu;bcgsc.ca	37	chr5	134223683	134223688	+	In_Frame_Del	DEL	TGGCGC	TGGCGC	-																															gagagccttttctctctggaTggcgctggagcacacttccc																								rs144331590		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TGGCGC	TGGCGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:134223683_134223688delTGGCGC	ENST00000358387.4	+	2	1027_1032	c.402_407delTGGCGC	c.(400-408)gatggcgct>gat	p.GA137del	TXNDC15_ENST00000546290.1_In_Frame_Del_p.GA114del	NM_024715.3	NP_078991.3	Q96J42	TXD15_HUMAN	thioredoxin domain containing 15	137					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.G135G(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCTCTCTGGATGGCGCTGGAGCACAC	0.558																																					p.134_136del													.	TXNDC15-154	1	Substitution - coding silent(1)	endometrium(1)	c.402_407del						.																																			SO:0001651	inframe_deletion	79770	exon2			TCTGGATGGCGCT	AK026278	CCDS4180.1	5q31.1	2008-02-05	2007-08-16	2007-08-16	ENSG00000113621	ENSG00000113621			20652	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 14"	C5orf14			Standard	NM_024715		Approved	2310047H23Rik, FLJ22625	uc003lac.1	Q96J42	OTTHUMG00000129115	ENST00000358387.4:c.402_407delTGGCGC	5.37:g.134223683_134223688delTGGCGC	ENSP00000351157:p.Gly137_Ala138del	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	186	27	NM_024715	0	0	0	0	0	D3DQA9|Q96MT2|Q9H639	In_Frame_Del	DEL	ENST00000358387.4	37	CCDS4180.1																																																																																			.		0.558	TXNDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251160.1	NM_024715		-	134223688	TGGCGC	-	134223683	7	5	21	1	0	1	0	1	0	0	0	0	16827	1461	51	0	408	0	TXNDC15	5	134223683	In_Frame_Del	DEL	TGGCGC	TCGA-A4-A48D-01A-11D-A25F-10	31791326	134223683	46691577	50	1818											
WNT8A	7478	broad.mit.edu	37	chr5	137426733	137426733	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcacgctccccaggcagtGcccagtccctgggtaagggc	6	5	14	16	2	0	0	0	0	0	0	2	0	2	0	4	3	1	4	4	3	1	1	rs568267809		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:137426733G>T	ENST00000398754.1	+	6	1032	c.1027G>T	c.(1027-1029)Gcc>Tcc	p.A343S	WNT8A_ENST00000506684.1_Missense_Mutation_p.A361S	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	343					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.A343S(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CCCAGGCAGTGCCCAGTCCCT	0.507																																					p.A343S													.	WNT8A-524	2	Substitution - Missense(2)	endometrium(1)|skin(1)	c.G1027T						.						93	88	90					5																	137426733		2003	4184	6187	SO:0001583	missense	7478	exon6			GGCAGTGCCCAGT	AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"Wingless-type MMTV integration sites"	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.1027G>T	5.37:g.137426733G>T	ENSP00000381739:p.Ala343Ser	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	105	9	NM_058244	0	0	0	0	0	Q96S51	Missense_Mutation	SNP	ENST00000398754.1	37	CCDS43368.1	.	.	.	.	.	.	.	.	.	.	G	9.870	1.198599	0.22121	.	.	ENSG00000061492	ENST00000506684;ENST00000398754	T;T	0.75477	-0.84;-0.94	4.58	0.217	0.15264	.	1.018450	0.07797	N	0.955811	T	0.55909	0.1950	N	0.19112	0.55	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.14023	0.01;0.003	T	0.40001	-0.9586	10	0.33141	T	0.24	.	4.8751	0.13653	0.1839:0.0:0.5089:0.3072	.	361;343	D6RF47;Q9H1J5	.;WNT8A_HUMAN	S	361;343	ENSP00000426653:A361S;ENSP00000381739:A343S	ENSP00000354726:A343S	A	+	1	0	WNT8A	137454632	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.381000	0.20619	0.172000	0.19760	0.557000	0.71058	GCC	.		0.507	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244		T	137426733	G	T	137426733	3	4	21	1	0	0	0	0	1	0	0	0	17429	1319	46	4	1049	4	WNT8A	5	137426733	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	3203050	137426733	43488527	51	1819											
BRD8	10902	broad.mit.edu;bcgsc.ca	37	chr5	137506838	137506838	+	Frame_Shift_Del	DEL	C	C	-																															ccaccacttctcccttttcaCctcgtttccgtctgtggaaa																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:137506838delC	ENST00000254900.5	-	5	619	c.248delG	c.(247-249)ggtfs	p.G83fs	BRD8_ENST00000455658.2_Frame_Shift_Del_p.G42fs|BRD8_ENST00000411594.2_Frame_Shift_Del_p.G83fs|BRD8_ENST00000230901.5_Frame_Shift_Del_p.G83fs|BRD8_ENST00000402931.1_Frame_Shift_Del_p.G83fs	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	83					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCCCTTTTCACCTCGTTTCCG	0.353																																					p.G83fs													.	BRD8-91	0			c.248delG						.						98	99	99					5																	137506838		2203	4300	6503	SO:0001589	frameshift_variant	10902	exon5			TTTTCACCTCGTT	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.248delG	5.37:g.137506838delC	ENSP00000254900:p.Gly83fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	136	19	NM_001164326	0	0	0	0	0	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Frame_Shift_Del	DEL	ENST00000254900.5	37	CCDS4198.1																																																																																			.		0.353	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		-	137506838	C	-	137506838	7	5	21	1	0	1	0	1	0	0	0	0	1509	507	18	0	3838	0	BRD8	5	137506838	Frame_Shift_Del	DEL	C	TCGA-A4-A48D-01A-11D-A25F-10	80105	137506838	43408422	52	1820											
NMUR2	56923	broad.mit.edu;bcgsc.ca	37	chr5	151784506	151784506	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgccaatgacccccaccaCaaaaattggcacatacacca	16	6	4	15	0	0	1	0	1	0	0	0	1	0	1	5	1	2	1	5	1	4	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:151784506C>A	ENST00000255262.3	-	1	334	c.169G>T	c.(169-171)Gtg>Ttg	p.V57L	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	57					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			ACCCCCACCACAAAAATTGGC	0.572																																					p.V57L													.	NMUR2-526	0			c.G169T						.						103	95	98					5																	151784506		2203	4300	6503	SO:0001583	missense	56923	exon1			CCACCACAAAAAT	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.169G>T	5.37:g.151784506C>A	ENSP00000255262:p.Val57Leu	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	238	9	NM_020167	0	0	0	0	0	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	C	4.823	0.153028	0.09185	.	.	ENSG00000132911	ENST00000255262	T	0.34667	1.35	5.54	2.68	0.31781	.	0.692044	0.13884	N	0.356069	T	0.22205	0.0535	N	0.17631	0.505	0.33114	D	0.540968	B	0.06786	0.001	B	0.04013	0.001	T	0.23940	-1.0174	10	0.22109	T	0.4	-3.2666	10.015	0.42010	0.0:0.5382:0.3902:0.0716	.	57	Q9GZQ4	NMUR2_HUMAN	L	57	ENSP00000255262:V57L	ENSP00000255262:V57L	V	-	1	0	NMUR2	151764699	0.604000	0.26932	0.985000	0.45067	0.114000	0.19823	-0.013000	0.12678	0.691000	0.31592	0.655000	0.94253	GTG	.		0.572	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		A	151784506	C	A	151784506	3	1	21	1	0	0	0	0	1	0	0	0	10533	478	17	4	1094	4	NMUR2	5	151784506	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	14277668	151784506	29130754	53	1821											
HUS1B	135458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	656335	656335	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggtttccaagatttttaaAataactttgaatggacacca	15	13	7	6	0	0	2	0	1	0	1	1	3	1	3	2	2	1	1	2	2	5	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:656335A>T	ENST00000380907.2	-	1	628	c.610T>A	c.(610-612)Ttt>Att	p.F204I	EXOC2_ENST00000448181.3_Intron|EXOC2_ENST00000230449.4_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	204					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		AGATTTTTAAAATAACTTTGA	0.532																																					p.F204I		.											.	HUS1B-227	0			c.T610A						.						96	107	103					6																	656335		2203	4300	6503	SO:0001583	missense	135458	exon1			TTTTAAAATAACT	AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"HUS1 (S. pombe) checkpoint homolog b"			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.610T>A	6.37:g.656335A>T	ENSP00000370293:p.Phe204Ile	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	103	27	NM_148959	0	0	0	0	0	Q5T4Z2	Missense_Mutation	SNP	ENST00000380907.2	37	CCDS4470.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279334	0.59758	.	.	ENSG00000188996	ENST00000380907	T	0.17854	2.25	3.61	2.42	0.29668	.	0.143577	0.46442	U	0.000298	T	0.21801	0.0525	M	0.79011	2.435	0.58432	D	0.999996	D	0.69078	0.997	D	0.63381	0.914	T	0.02104	-1.1213	10	0.59425	D	0.04	.	5.756	0.18172	0.871:0.0:0.129:0.0	.	204	Q8NHY5	HUS1B_HUMAN	I	204	ENSP00000370293:F204I	ENSP00000370293:F204I	F	-	1	0	HUS1B	601335	0.999000	0.42202	0.011000	0.14972	0.048000	0.14542	1.596000	0.36718	0.560000	0.29169	0.533000	0.62120	TTT	.		0.532	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959		T	656335	A	T	656335	3	4	21	1	0	0	0	0	1	0	0	0	7481	14	1	5	230	5	HUS1B	6	656335	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		656335	170458732	54	1822											
SERPINB6	5269	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	2948772	2948772	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagaagtctgccttgccCagctcgaaggcatcagtcat	10	8	10	13	1	3	1	2	0	1	1	4	3	3	1	3	1	3	2	3	1	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:2948772C>A	ENST00000380520.1	-	6	2885	c.891G>T	c.(889-891)ctG>ctT	p.L297L	SERPINB6_ENST00000380529.1_Silent_p.L297L|SERPINB6_ENST00000380524.1_Silent_p.L297L|SERPINB6_ENST00000380539.1_Silent_p.L297L|SERPINB6_ENST00000335686.5_Silent_p.L297L|SERPINB6_ENST00000380546.3_Silent_p.L297L			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	297					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	CTGCCTTGCCCAGCTCGAAGG	0.552																																					p.L316L													.	SERPINB6-226	0			c.G948T						.						127	118	121					6																	2948772		2203	4300	6503	SO:0001819	synonymous_variant	5269	exon7			CTTGCCCAGCTCG	Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"Serine (or cysteine) peptidase inhibitors"	8950	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase"	173321	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6", "deafness, autosomal recessive 91"	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.891G>T	6.37:g.2948772C>A		Somatic	158	1		WXS	Illumina HiSeq	Phase_I	201	48	NM_001271823	0	0	52	73	21	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Silent	SNP	ENST00000380520.1	37	CCDS4479.1	.	.	.	.	.	.	.	.	.	.	C	3.561	-0.089585	0.07053	.	.	ENSG00000124570	ENST00000380500	.	.	.	5.17	0.173	0.15036	.	.	.	.	.	T	0.10380	0.0254	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.34329	-0.9833	4	.	.	.	.	5.7342	0.18057	0.0:0.4744:0.2553:0.2702	.	.	.	.	L	102	.	.	W	-	2	0	SERPINB6	2893771	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.049000	0.00629	0.100000	0.17581	0.558000	0.71614	TGG	.		0.552	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1			A	2948772	C	A	2948772	2	1	21	1	0	0	0	0	0	0	0	1	14137	581	21	4		4	SERPINB6	6	2948772	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	2292437	2948772	168166295	55	1823											
C6orf27	80737	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31735431	31735431	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatccagaagctgctgatgTctccgtggatccggactgtg	7	11	13	10	2	1	3	0	2	1	1	4	5	3	5	3	2	2	2	3	2	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:31735431T>C	ENST00000375688.4	-	11	1804	c.1604A>G	c.(1603-1605)gAc>gGc	p.D535G	VWA7_ENST00000447450.1_Missense_Mutation_p.D535G|VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.D535G|SAPCD1-AS1_ENST00000419679.1_RNA			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	535						extracellular region (GO:0005576)											GCTGCTGATGTCTCCGTGGAT	0.572																																					p.D535G													.	.	0			c.A1604G						.						161	162	162					6																	31735431		2203	4300	6503	SO:0001583	missense	80737	exon11			CTGATGTCTCCGT		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"chromosome 6 open reading frame 27"	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.1604A>G	6.37:g.31735431T>C	ENSP00000364840:p.Asp535Gly	Somatic	130	1		WXS	Illumina HiSeq	Phase_I	133	40	NM_025258	0	0	6	10	4	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	T	10.52	1.374412	0.24857	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.31769	2.69;2.47;1.48	4.95	4.95	0.65309	.	0.672013	0.15404	N	0.264144	T	0.12944	0.0314	L	0.40543	1.245	0.32873	D	0.50954	B	0.22146	0.065	B	0.21546	0.035	T	0.08027	-1.0742	10	0.29301	T	0.29	-3.0526	12.6028	0.56506	0.0:0.0:0.0:1.0	.	535	Q9Y334	G7C_HUMAN	G	535	ENSP00000364840:D535G;ENSP00000364838:D535G;ENSP00000390554:D535G	ENSP00000364838:D535G	D	-	2	0	C6orf27	31843410	0.997000	0.39634	0.399000	0.26333	0.155000	0.21991	4.327000	0.59247	2.070000	0.61991	0.459000	0.35465	GAC	.		0.572	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		C	31735431	T	C	31735431	3	2	21	1	0	0	0	0	1	0	0	0	2368	1667	58	3	1098	3	C6orf27	6	31735431	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	28786659	31735431	139379636	56	1824											
RHAG	6005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	49586991	49586991	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagcaacgagtaggttgataCccacactgctgaagccatat	13	8	9	11	1	0	2	0	2	0	0	0	3	0	2	2	1	5	4	2	1	5	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:49586991C>T	ENST00000371175.4	-	2	268	c.242G>A	c.(241-243)gGt>gAt	p.G81D	RHAG_ENST00000229810.7_Missense_Mutation_p.G81D	NM_000324.2	NP_000315.2	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	81					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|carbon dioxide transport (GO:0015670)|cellular ion homeostasis (GO:0006873)|erythrocyte development (GO:0048821)|multicellular organismal iron ion homeostasis (GO:0060586)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	39	Lung NSC(77;0.0255)					TAGGTTGATACCCACACTGCT	0.443																																					p.G81D	Ovarian(176;476 2003 7720 43408 44749)	.											.	RHAG-154	0			c.G242A						.						112	95	101					6																	49586991		2203	4300	6503	SO:0001583	missense	6005	exon2			TTGATACCCACAC		CCDS4927.1	6p12.3	2014-07-19	2006-02-23		ENSG00000112077	ENSG00000112077		"CD molecules", "Blood group antigens", "Solute carriers"	10006	protein-coding gene	gene with protein product		180297	"Rhesus blood group-associated glycoprotein"			9479501	Standard	NM_000324		Approved	RH50A, CD241, SLC42A1	uc003ozk.4	Q02094	OTTHUMG00000016377	ENST00000371175.4:c.242G>A	6.37:g.49586991C>T	ENSP00000360217:p.Gly81Asp	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	130	30	NM_000324	0	0	0	0	0	B2R8T8|O43514|O43515|Q7L8L3|Q9H454	Missense_Mutation	SNP	ENST00000371175.4	37	CCDS4927.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972877	0.74246	.	.	ENSG00000112077	ENST00000371175;ENST00000229810;ENST00000418071;ENST00000539403	T;T	0.24538	1.85;1.85	5.62	5.62	0.85841	Ammonium transporter AmtB-like (3);	0.043100	0.85682	D	0.000000	T	0.59211	0.2177	H	0.94658	3.565	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76071	0.987;0.987;0.983	T	0.71497	-0.4575	10	0.87932	D	0	-11.5221	18.6546	0.91448	0.0:1.0:0.0:0.0	.	81;81;81	O43515;Q9UHG9;Q02094	.;.;RHAG_HUMAN	D	81	ENSP00000360217:G81D;ENSP00000229810:G81D	ENSP00000229810:G81D	G	-	2	0	RHAG	49694950	1.000000	0.71417	0.938000	0.37757	0.238000	0.25445	7.792000	0.85828	2.640000	0.89533	0.591000	0.81541	GGT	.		0.443	RHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043806.1			T	49586991	C	T	49586991	3	4	21	1	0	0	0	0	1	0	0	0	13347	507	18	2	1023	2	RHAG	6	49586991	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	17851560	49586991	121528076	57	1825											
CD164	8763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	109690201	109690201	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaggttgtgaggttggagtCacagtgttatttgttgtacc	8	15	13	5	0	1	1	1	1	0	0	1	2	1	2	1	3	1	5	1	3	2	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:109690201C>T	ENST00000310786.4	-	6	512	c.447G>A	c.(445-447)gtG>gtA	p.V149V	CD164_ENST00000275080.7_Silent_p.V136V|CD164_ENST00000504373.1_Silent_p.V115V|CD164_ENST00000368961.5_Silent_p.V117V|CD164_ENST00000512821.1_Intron|CD164_ENST00000506649.1_5'UTR|CD164_ENST00000413644.2_Silent_p.V149V|CD164_ENST00000324953.5_Silent_p.V130V	NM_001142404.1|NM_006016.4	NP_001135876.1|NP_006007.2	Q04900	MUC24_HUMAN	CD164 molecule, sialomucin	149	Thr-rich.				cell adhesion (GO:0007155)|hemopoiesis (GO:0030097)|heterophilic cell-cell adhesion (GO:0007157)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(1)|lung(2)	3		all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175)		Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16)		AGGTTGGAGTCACAGTGTTAT	0.408																																					p.V149V		.											.	CD164-90	0			c.G447A						.						114	96	102					6																	109690201		2203	4300	6503	SO:0001819	synonymous_variant	8763	exon6			TGGAGTCACAGTG	AF106518	CCDS5073.1, CCDS47462.1, CCDS47463.1, CCDS47464.1, CCDS47465.1	6q21	2014-09-05	2006-03-28		ENSG00000135535	ENSG00000135535		"CD molecules"	1632	protein-coding gene	gene with protein product		603356	"CD164 antigen, sialomucin"			9680353, 9763543	Standard	NM_006016		Approved	MUC-24, MGC-24	uc003pte.3	Q04900	OTTHUMG00000015339	ENST00000310786.4:c.447G>A	6.37:g.109690201C>T		Somatic	194	0		WXS	Illumina HiSeq	Phase_I	177	39	NM_006016	0	0	78	136	58	B4DQ85|E1P5E7|E1P5E8|E1P5E9|O95413|Q5JSU6|Q9BPV0|Q9NR26	Silent	SNP	ENST00000310786.4	37	CCDS5073.1																																																																																			.		0.408	CD164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041742.1	NM_006016		T	109690201	C	T	109690201	2	4	21	1	0	0	0	0	0	0	0	1	2975	813	29	2		2	CD164	6	109690201	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	60103210	109690201	61424866	58	1826											
SNX9	51429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	158330822	158330822	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatatcagctaacacctacTgtaagtatccacgttatcaa	15	11	5	10	1	2	0	2	0	0	0	3	1	3	0	2	0	3	4	2	0	8	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:158330822T>G	ENST00000392185.3	+	8	1002	c.831T>G	c.(829-831)acT>acG	p.T277T		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	277	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		TAACACCTACTGTAAGTATCC	0.393																																					p.T277T		.											.	SNX9-226	0			c.T831G						.						172	168	169					6																	158330822		2203	4300	6503	SO:0001630	splice_region_variant	51429	exon8			ACCTACTGTAAGT	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.831+1T>G	6.37:g.158330822T>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	104	26	NM_016224	0	0	0	0	0	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Silent	SNP	ENST00000392185.3	37	CCDS5253.1																																																																																			.		0.393	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1		Silent	G	158330822	T	G	158330822	5	3	21	1	0	0	0	0	0	0	1	0	14941	1594	55	5	861	5	SNX9	6	158330822	Splice_Site	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	48640621	158330822	12784245	59	1827											
MICALL2	79778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	1478499	1478499	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtttgccctgaaggtgaggtTtcttctcctcctccttccag	4	15	9	13	0	2	2	0	2	2	0	6	2	5	2	5	2	1	2	5	2	1	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:1478499T>G	ENST00000297508.7	-	10	2274	c.2099A>C	c.(2098-2100)aAa>aCa	p.K700T	MICALL2_ENST00000471899.1_5'UTR|MICALL2_ENST00000405088.4_Missense_Mutation_p.K488T	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	700	Forms an intramolecular interaction with the N-terminal CH and LIM zinc-binding domains-containing region keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		AAGGTGAGGTTTCTTCTCCTC	0.632																																					p.K700T		.											.	MICALL2-90	0			c.A2099C						.						80	79	79					7																	1478499		2203	4300	6503	SO:0001583	missense	79778	exon10			TGAGGTTTCTTCT	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"junctional Rab13-binding protein"					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2099A>C	7.37:g.1478499T>G	ENSP00000297508:p.Lys700Thr	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	43	13	NM_182924	0	0	2	3	1	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	T	7.035	0.561374	0.13498	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.71698	2.33;-0.59	1.61	-2.18	0.07037	.	0.219361	0.22804	N	0.055427	T	0.42449	0.1203	N	0.24115	0.695	0.09310	N	1	B;P	0.42908	0.267;0.793	B;B	0.37601	0.039;0.254	T	0.41822	-0.9487	10	0.24483	T	0.36	.	1.4582	0.02390	0.3162:0.2383:0.0:0.4454	.	700;488	Q8IY33;D3YTD2	MILK2_HUMAN;.	T	488;700	ENSP00000385928:K488T;ENSP00000297508:K700T	ENSP00000297508:K700T	K	-	2	0	MICALL2	1445025	0.000000	0.05858	0.003000	0.11579	0.171000	0.22731	-0.124000	0.10595	-0.123000	0.11745	0.260000	0.18958	AAA	.		0.632	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		G	1478499	T	G	1478499	3	3	21	1	0	0	0	0	1	0	0	0	9599	1841	64	5	647	5	MICALL2	7	1478499	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		1478499	157660164	60	1828											
HIBADH	11112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	27582616	27582616	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaacagctccacagtacacCacgttggagcccatgcaccc	11	5	7	18	1	0	0	0	0	0	0	1	1	1	1	5	1	5	4	5	1	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:27582616C>G	ENST00000265395.2	-	5	794	c.588G>C	c.(586-588)gtG>gtC	p.V196V		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	196					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			CACAGTACACCACGTTGGAGC	0.468																																					p.V196V		.											.	HIBADH-92	0			c.G588C						.						97	87	91					7																	27582616		2203	4300	6503	SO:0001819	synonymous_variant	11112	exon5			GTACACCACGTTG	AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	1.1.1.31		4907	protein-coding gene	gene with protein product		608475					Standard	NM_152740		Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.588G>C	7.37:g.27582616C>G		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	142	34	NM_152740	0	0	58	122	64	Q546Z2|Q9UDN3	Silent	SNP	ENST00000265395.2	37	CCDS5414.1	.	.	.	.	.	.	.	.	.	.	C	7.289	0.610641	0.14066	.	.	ENSG00000106049	ENST00000425715	.	.	.	6.02	4.21	0.49690	.	.	.	.	.	T	0.58104	0.2099	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53760	-0.8393	4	.	.	.	-2.1097	7.8405	0.29395	0.1159:0.6925:0.0:0.1916	.	.	.	.	S	139	.	.	W	-	2	0	HIBADH	27549141	0.993000	0.37304	0.856000	0.33681	0.715000	0.41141	0.664000	0.25068	0.865000	0.35603	0.655000	0.94253	TGG	.		0.468	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740		G	27582616	C	G	27582616	2	3	21	1	0	0	0	0	0	0	0	1	7120	581	21	4		4	HIBADH	7	27582616	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	26104117	27582616	131556047	61	1829											
HECW1	23072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	43508701	43508701	+	Frame_Shift_Del	DEL	A	A	-																															atcaaaacggaccagcagggAaaggtgagtgtgacccacgt																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:43508701delA	ENST00000395891.2	+	16	3701	c.3096delA	c.(3094-3096)ggafs	p.G1032fs	HECW1_ENST00000453890.1_Frame_Shift_Del_p.G998fs	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1032	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						ACCAGCAGGGAAAGGTGAGTG	0.577																																					p.G1032fs		.											.	HECW1-669	0			c.3096delA						.						61	61	61					7																	43508701		1982	4167	6149	SO:0001589	frameshift_variant	23072	exon16			.	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3096delA	7.37:g.43508701delA	ENSP00000379228:p.Gly1032fs	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	110	36	NM_015052	0	0	0	0	0	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Frame_Shift_Del	DEL	ENST00000395891.2	37	CCDS5469.2																																																																																			.		0.577	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		-	43508701	A	-	43508701	7	5	21	1	0	1	0	1	0	0	0	0	7063	233	9	0	3150	0	HECW1	7	43508701	Frame_Shift_Del	DEL	A	TCGA-A4-A48D-01A-11D-A25F-10	15926085	43508701	115629962	62	1830											
CYP3A43	64816	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99434139	99434139	+	Frame_Shift_Del	DEL	T	T	-																															cctgggccaacccctctgccTtttctgggaactattttgtt																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:99434139delT	ENST00000354829.2	+	2	238	c.135delT	c.(133-135)cctfs	p.P45fs	CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000421837.2_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000222382.5_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000415413.1_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000417625.1_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000312017.5_Frame_Shift_Del_p.P45fs	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	45			YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	CCCCTCTGCCTTTTCTGGGAA	0.393																																					p.P45fs		.											.	CYP3A43-92	0			c.135delT						.						95	93	94					7																	99434139		2203	4300	6503	SO:0001589	frameshift_variant	64816	exon2			.	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.135delT	7.37:g.99434139delT	ENSP00000346887:p.Pro45fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	88	21	NM_057096	0	0	0	0	0	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Frame_Shift_Del	DEL	ENST00000354829.2	37	CCDS5676.1																																																																																			.		0.393	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			-	99434139	T	-	99434139	7	5	21	1	0	1	0	1	0	0	0	0	4185	1596	56	0	141	0	CYP3A43	7	99434139	Frame_Shift_Del	DEL	T	TCGA-A4-A48D-01A-11D-A25F-10	55925438	99434139	59704524	63	1831											
ZAN	7455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100344177	100344177	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acaggtggctgctacatgctCctggaccccaagaatgcaag	11	7	11	12	0	0	1	0	0	0	1	1	2	1	2	3	3	4	4	3	3	4	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:100344177C>T	ENST00000348028.3	+	0	948				ZAN_ENST00000349350.6_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000546292.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCTACATGCTCCTGGACCCCA	0.577																																					.													.	ZAN-142	0			.						.						51	58	56					7																	100344177		2028	4180	6208			7455	.			CATGCTCCTGGAC	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100344177C>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	113	30	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Silent	SNP	ENST00000348028.3	37																																																																																				.		0.577	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100344177	C	T	100344177	1	4	21	0	1	0	0	0	0	0	0	0	17546	842	30	2		2	ZAN	7	100344177	RNA	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	910038	100344177	58794486	64	1832											
PPP1R3A	5506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	113519562	113519562	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggaaattttttctttgttTttcattaacacctaaatata	12	21	3	5	0	2	0	1	0	1	0	2	1	2	1	1	1	1	1	1	1	6	11			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:113519562T>C	ENST00000284601.3	-	4	1653	c.1585A>G	c.(1585-1587)Aaa>Gaa	p.K529E		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	529					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTTCTTTGTTTTTCATTAACA	0.343																																					p.K529E		.											.	PPP1R3A-832	0			c.A1585G						.						77	71	73					7																	113519562		2203	4300	6503	SO:0001583	missense	5506	exon4			TTTGTTTTTCATT	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9291	protein-coding gene	gene with protein product	"glycogen-associated regulatory subunit of protein phosphatase-1", "protein phosphatase 1 regulatory subunit GM"	600917	"protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)", "protein phosphatase 1, regulatory (inhibitor) subunit 3A"	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1585A>G	7.37:g.113519562T>C	ENSP00000284601:p.Lys529Glu	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	90	11	NM_002711	0	0	0	0	0	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.404017	0.25291	.	.	ENSG00000154415	ENST00000284601	T	0.17054	2.3	6.02	4.81	0.61882	.	0.792728	0.11805	N	0.527776	T	0.14830	0.0358	M	0.63428	1.95	0.09310	N	1	P	0.44734	0.842	B	0.31442	0.13	T	0.30179	-0.9987	10	0.52906	T	0.07	-0.2155	6.933	0.24451	0.1335:0.0719:0.0:0.7946	.	529	Q16821	PPR3A_HUMAN	E	529	ENSP00000284601:K529E	ENSP00000284601:K529E	K	-	1	0	PPP1R3A	113306798	0.941000	0.31946	0.713000	0.30519	0.230000	0.25150	1.271000	0.33098	2.311000	0.77944	0.533000	0.62120	AAA	.		0.343	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		C	113519562	T	C	113519562	3	2	21	1	0	0	0	0	1	0	0	0	12400	1850	64	3	1787	3	PPP1R3A	7	113519562	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	13175385	113519562	45619101	65	1833											
CTTNBP2	83992	bcgsc.ca	37	chr7	117375372	117375372	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgattttcaagaggtgcCaaaaagtccctcaataactc	13	10	7	11	1	2	1	2	0	0	1	4	2	3	1	2	1	3	0	2	1	5	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:117375372C>T	ENST00000160373.3	-	15	3730	c.3639G>A	c.(3637-3639)ttG>ttA	p.L1213L		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1213			L -> V (in dbSNP:rs62617115). {ECO:0000269|PubMed:11707066}.		brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CAAGAGGTGCCAAAAAGTCCC	0.393																																					p.L1213L													.	CTTNBP2-94	0			c.G3639A						.						65	70	68					7																	117375372		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon15			AGGTGCCAAAAAG		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3639G>A	7.37:g.117375372C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_1	39	4	NM_033427	0	0	0	0	0	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	C	9.301	1.053182	0.19907	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.52	4.63	0.57726	.	.	.	.	.	T	0.57932	0.2087	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53872	-0.8377	4	.	.	.	-2.1882	8.2124	0.31492	0.1376:0.7331:0.0:0.1293	.	.	.	.	S	701	.	.	G	-	1	0	CTTNBP2	117162608	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	1.035000	0.30216	2.745000	0.94114	0.655000	0.94253	GGC	.		0.393	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		T	117375372	C	T	117375372	2	4	21	1	0	0	0	0	0	0	0	1	4051	593	21	2		2	CTTNBP2	7	117375372	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	3855810	117375372	41763291	66	1834											
PAXIP1	22976	broad.mit.edu	37	chr7	154754041	154754041	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctgtcttacatgctgtgaaCatggctttcctcctggtggg	5	15	11	10	0	2	1	0	1	2	0	4	1	4	1	2	3	3	2	2	3	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:154754041C>T	ENST00000404141.1	-	10	2271	c.2117G>A	c.(2116-2118)tGt>tAt	p.C706Y	PAXIP1_ENST00000397192.1_Missense_Mutation_p.C706Y|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	706	BRCT 4. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		ATGCTGTGAACATGGCTTTCC	0.493																																					p.C706Y													.	PAXIP1-228	0			c.G2117A						.						184	186	185					7																	154754041		1973	4143	6116	SO:0001583	missense	22976	exon10			TGTGAACATGGCT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2117G>A	7.37:g.154754041C>T	ENSP00000384048:p.Cys706Tyr	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	188	5	NM_007349	0	0	0	0	0	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992709	0.54041	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.40756	1.02;1.02	4.91	4.91	0.64330	BRCT (2);	0.000000	0.64402	U	0.000009	T	0.64702	0.2622	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.99;0.985;0.999	T	0.68648	-0.5353	10	0.87932	D	0	-19.2775	18.4584	0.90729	0.0:1.0:0.0:0.0	.	659;672;706	B4DEQ6;Q6ZW49-1;Q6ZW49	.;.;PAXI1_HUMAN	Y	706;706;530;659	ENSP00000384048:C706Y;ENSP00000380376:C706Y	ENSP00000319149:C659Y	C	-	2	0	PAXIP1	154384974	1.000000	0.71417	0.075000	0.20258	0.673000	0.39480	7.158000	0.77470	2.426000	0.82243	0.467000	0.42956	TGT	.		0.493	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		T	154754041	C	T	154754041	3	4	21	1	0	0	0	0	1	0	0	0	11513	478	17	2	1140	2	PAXIP1	7	154754041	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	37378669	154754041	4384622	67	1835											
PTPRN2	5799	broad.mit.edu;bcgsc.ca	37	chr7	157369349	157369349	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaggaggaagggactcctcgGtcataccaactcaggaagtg	12	6	14	9	1	2	0	2	0	0	0	4	5	3	4	2	5	2	0	2	5	4	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:157369349G>C	ENST00000389418.4	-	19	2748	c.2739C>G	c.(2737-2739)gaC>gaG	p.D913E	PTPRN2_ENST00000389413.3_Missense_Mutation_p.D884E|PTPRN2_ENST00000404321.2_Missense_Mutation_p.D936E|PTPRN2_ENST00000389416.4_Missense_Mutation_p.D896E|MIR153-2_ENST00000385225.1_RNA|PTPRN2_ENST00000409483.1_Missense_Mutation_p.D875E	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	913	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GGACTCCTCGGTCATACCAAC	0.632																																					p.D913E													.	PTPRN2-295	0			c.C2739G						.						84	66	72					7																	157369349		2203	4300	6503	SO:0001583	missense	5799	exon19			TCCTCGGTCATAC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2739C>G	7.37:g.157369349G>C	ENSP00000374069:p.Asp913Glu	Somatic	95	1		WXS	Illumina HiSeq	Phase_I	92	7	NM_002847	0	0	0	0	0	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577030	0.65878	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	5.44	5.44	0.79542	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	T	0.24661	0.0598	L	0.38838	1.175	0.47065	D	0.999308	B;B;B;P;B	0.45078	0.027;0.034;0.027;0.85;0.034	B;B;B;P;B	0.49276	0.038;0.093;0.056;0.605;0.064	T	0.02326	-1.1176	10	0.02654	T	1	.	13.0262	0.58817	0.0829:0.0:0.9171:0.0	.	936;875;884;896;913	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	E	875;884;896;913;936	ENSP00000387114:D875E;ENSP00000374064:D884E;ENSP00000374067:D896E;ENSP00000374069:D913E;ENSP00000385464:D936E	ENSP00000374064:D884E	D	-	3	2	PTPRN2	157062110	1.000000	0.71417	1.000000	0.80357	0.698000	0.40448	4.368000	0.59505	2.546000	0.85860	0.650000	0.86243	GAC	.		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			C	157369349	G	C	157369349	3	2	21	1	0	0	0	0	1	0	0	0	12840	1252	44	4	328	4	PTPRN2	7	157369349	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	2615308	157369349	1769314	68	1836											
MTMR9	66036	broad.mit.edu	37	chr8	11180146	11180146	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcaataggtattttcctacGttggaatagatcctctaagt	11	16	7	7	1	2	1	1	0	1	1	4	2	4	2	2	2	1	2	2	2	7	9	rs375789918		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:11180146G>A	ENST00000221086.3	+	10	1972	c.1499G>A	c.(1498-1500)cGt>cAt	p.R500H	MTMR9_ENST00000526292.1_Missense_Mutation_p.R415H|AF131216.6_ENST00000498997.2_RNA	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	500						cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		ATTTTCCTACGTTGGAATAGA	0.294																																					p.R500H													.	MTMR9-226	0			c.G1499A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	55	60	59		1499	5.5	1	8		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	MTMR9	NM_015458.3	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	500/550	11180146	2,13004	2203	4300	6503	SO:0001583	missense	66036	exon10			TCCTACGTTGGAA	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	14596	protein-coding gene	gene with protein product		606260	"myotubularin related protein 8"	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.1499G>A	8.37:g.11180146G>A	ENSP00000221086:p.Arg500His	Somatic	183	1		WXS	Illumina HiSeq	Phase_I	165	4	NM_015458	0	0	0	0	0	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Missense_Mutation	SNP	ENST00000221086.3	37	CCDS5979.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.478961	0.63849	2.27E-4	1.16E-4	ENSG00000104643	ENST00000221086;ENST00000526292	D;D	0.91843	-2.92;-2.92	5.46	5.46	0.80206	.	0.050859	0.85682	D	0.000000	D	0.93242	0.7847	M	0.81942	2.565	0.80722	D	1	D	0.60575	0.988	P	0.45232	0.474	D	0.94240	0.7484	10	0.72032	D	0.01	.	18.2845	0.90110	0.0:0.0:1.0:0.0	.	500	Q96QG7	MTMR9_HUMAN	H	500;415	ENSP00000221086:R500H;ENSP00000433239:R415H	ENSP00000221086:R500H	R	+	2	0	MTMR9	11217556	1.000000	0.71417	0.983000	0.44433	0.602000	0.36980	9.247000	0.95444	2.562000	0.86427	0.655000	0.94253	CGT	.		0.294	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458		A	11180146	G	A	11180146	3	1	21	1	0	0	0	0	1	0	0	0	9975	1145	40	1	1537	1	MTMR9	8	11180146	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		11180146	135183876	69	1837											
DEFB136	613210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	11831570	11831570	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gacacccgaagaaacatacgGctttctggctagtgcaggtg	11	8	12	10	2	1	1	0	0	1	1	1	3	1	1	1	3	3	3	1	3	4	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:11831570G>A	ENST00000382209.2	-	2	112	c.113C>T	c.(112-114)gCc>gTc	p.A38V		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	38					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(4)	7			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)		GAAACATACGGCTTTCTGGCT	0.453																																					p.A38V		.											.	DEFB136-90	0			c.C113T						.						162	168	166					8																	11831570		2014	4183	6197	SO:0001583	missense	613210	exon2			CATACGGCTTTCT	DQ012026	CCDS43709.1	8p23.1	2011-07-19			ENSG00000205884	ENSG00000205884		"Defensins, beta"	34433	protein-coding gene	gene with protein product						16033865	Standard	NM_001033018		Approved	DEFB137	uc011kxm.2	Q30KP8	OTTHUMG00000158720	ENST00000382209.2:c.113C>T	8.37:g.11831570G>A	ENSP00000371644:p.Ala38Val	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	182	50	NM_001033018	0	0	0	0	0	Q4QY36	Missense_Mutation	SNP	ENST00000382209.2	37	CCDS43709.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863779	0.51482	.	.	ENSG00000205884	ENST00000382209	T	0.18960	2.18	4.06	3.18	0.36537	.	0.135690	0.34435	N	0.003978	T	0.17066	0.0410	.	.	.	0.09310	N	1	P	0.35982	0.531	B	0.35353	0.201	T	0.14282	-1.0478	9	0.66056	D	0.02	-1.9327	9.761	0.40532	0.0:0.7758:0.2242:0.0	.	38	Q30KP8	DB136_HUMAN	V	38	ENSP00000371644:A38V	ENSP00000371644:A38V	A	-	2	0	DEFB136	11868979	0.022000	0.18835	0.045000	0.18777	0.001000	0.01503	1.228000	0.32588	1.290000	0.44636	-0.321000	0.08615	GCC	.		0.453	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018		A	11831570	G	A	11831570	3	1	21	1	0	0	0	0	1	0	0	0	4431	1203	42	2	125	2	DEFB136	8	11831570	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	651424	11831570	134532452	70	1838											
SCARA3	51435	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	27516084	27516084	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccagagatccgaaaactgCaggaggagctggagggaatt	13	5	16	7	1	0	1	0	0	0	1	1	7	1	5	2	5	3	2	2	5	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:27516084C>T	ENST00000301904.3	+	5	417	c.397C>T	c.(397-399)Cag>Tag	p.Q133*	SCARA3_ENST00000337221.4_Nonsense_Mutation_p.Q133*	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	133					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		CCGAAAACTGCAGGAGGAGCT	0.562																																					p.Q133X		.											.	SCARA3-228	0			c.C397T						.						96	103	101					8																	27516084		2203	4300	6503	SO:0001587	stop_gained	51435	exon5			AAACTGCAGGAGG	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"macrophage scavenger receptor-like 1"	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.397C>T	8.37:g.27516084C>T	ENSP00000301904:p.Gln133*	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	93	7	NM_182826	0	0	9	9	0	Q9UM15|Q9UM16	Nonsense_Mutation	SNP	ENST00000301904.3	37	CCDS34871.1	.	.	.	.	.	.	.	.	.	.	C	38	7.138755	0.98088	.	.	ENSG00000168077	ENST00000337221;ENST00000301904	.	.	.	6.04	6.04	0.98038	.	0.106561	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-19.8686	18.073	0.89417	0.0:1.0:0.0:0.0	.	.	.	.	X	133	.	ENSP00000301904:Q133X	Q	+	1	0	SCARA3	27572003	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.363000	0.66104	2.873000	0.98535	0.561000	0.74099	CAG	.		0.562	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240		T	27516084	C	T	27516084	4	4	21	1	0	0	0	0	0	1	0	0	13911	711	25	2	415	2	SCARA3	8	27516084	Nonsense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	15684514	27516084	118847938	71	1839											
KCNU1	157855	broad.mit.edu	37	chr8	36703123	36703123	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatactaaatccacctccaCaagtgaggatacgtaagaac	16	8	7	10	1	0	3	0	2	0	1	2	4	2	4	3	1	3	1	3	1	7	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:36703123C>A	ENST00000399881.3	+	17	1766	c.1729C>A	c.(1729-1731)Caa>Aaa	p.Q577K		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	577					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TCCACCTCCACAAGTGAGGAT	0.383																																					p.Q577K													.	KCNU1-23	0			c.C1729A						.						120	113	115					8																	36703123		1854	4107	5961	SO:0001583	missense	157855	exon17			CCTCCACAAGTGA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1729C>A	8.37:g.36703123C>A	ENSP00000382770:p.Gln577Lys	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	104	3	NM_001031836	0	0	0	0	0		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	5.188	0.220288	0.09863	.	.	ENSG00000215262	ENST00000399881	T	0.29142	1.58	5.53	2.5	0.30297	.	0.000000	0.36519	U	0.002552	T	0.21145	0.0509	L	0.47716	1.5	0.80722	D	1	B	0.21381	0.055	B	0.18561	0.022	T	0.05666	-1.0871	10	0.22109	T	0.4	-5.5205	4.9734	0.14127	0.2651:0.5326:0.1288:0.0736	.	577	A8MYU2	KCNU1_HUMAN	K	577	ENSP00000382770:Q577K	ENSP00000382770:Q577K	Q	+	1	0	KCNU1	36822281	0.196000	0.23350	0.914000	0.36105	0.096000	0.18686	0.582000	0.23834	0.760000	0.33108	0.655000	0.94253	CAA	.		0.383	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36703123	C	A	36703123	3	1	21	1	0	0	0	0	1	0	0	0	8114	479	17	4	1795	4	KCNU1	8	36703123	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	9187039	36703123	109660899	72	1840											
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	37730035	37730036	+	Frame_Shift_Ins	INS	-	-	T																															agctgcatccctggctttgcINStctccacaagagacccagcc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:37730035_37730036insT	ENST00000330843.4	-	4	2296_2297	c.2284_2285insA	c.(2284-2286)agcfs	p.S762fs	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	762					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)			CCTGGCTTTGCTCTCCACAAGA	0.569																																					p.S762fs		.											.	RAB11FIP1-92	0			c.2285_2286insA						.																																			SO:0001589	frameshift_variant	80223	exon4			.	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.2285dupA	8.37:g.37730036_37730036dupT	ENSP00000331342:p.Ser762fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	128	27	NM_001002814	0	0	0	0	0	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Frame_Shift_Ins	INS	ENST00000330843.4	37	CCDS34882.1																																																																																			.		0.569	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		T	37730036	-	T	37730035	7	5	21	1	0	1	1	0	0	0	0	0	12925	797	28	0	1578	0	RAB11FIP1	8	37730035	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	1026912	37730035	108633987	73	1841											
HNF4G	3174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	76463728	76463728	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgaagttcggtctcgccAggtacctgtggcacggcagc	7	8	14	12	3	1	1	0	1	1	0	3	1	1	1	2	4	3	5	2	4	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:76463728A>G	ENST00000354370.1	+	5	617	c.347A>G	c.(346-348)cAg>cGg	p.Q116R	HNF4G_ENST00000396423.2_Splice_Site_p.Q153R			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	116					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)			CGGTCTCGCCAGGTACCTGTG	0.423																																					p.Q153R		.											.	HNF4G-187	0			c.A458G						.						114	86	96					8																	76463728		2203	4300	6503	SO:0001630	splice_region_variant	3174	exon4			CTCGCCAGGTACC		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.348+1A>G	8.37:g.76463728A>G		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	67	10	NM_004133	0	0	0	0	0	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	A	19.16	3.774742	0.70107	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94687	-3.49;-3.49	5.07	5.07	0.68467	Nuclear hormone receptor, ligand-binding (2);	0.485181	0.25587	N	0.029651	D	0.94853	0.8337	M	0.79258	2.445	0.80722	D	1	B;B	0.29571	0.249;0.249	B;B	0.38106	0.191;0.265	D	0.93931	0.7214	10	0.41790	T	0.15	.	15.1246	0.72472	1.0:0.0:0.0:0.0	.	153;116	F1D8Q4;Q14541	.;HNF4G_HUMAN	R	116;153	ENSP00000346339:Q116R;ENSP00000379701:Q153R	ENSP00000346339:Q116R	Q	+	2	0	HNF4G	76626283	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.152000	0.94680	2.026000	0.59711	0.528000	0.53228	CAG	.		0.423	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	Missense_Mutation	G	76463728	A	G	76463728	5	3	21	1	0	0	0	0	0	0	1	0	7275	202	7	3	472	3	HNF4G	8	76463728	Splice_Site	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	38733693	76463728	69900294	74	1842											
CA1	759	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	86250502	86250502	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgatcggttatcgttgtcctCaaaatttacatggaaggaat	12	14	9	6	2	1	1	1	1	0	0	4	3	2	3	1	3	1	2	1	3	6	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:86250502C>T	ENST00000523953.1	-	4	1260	c.214G>A	c.(214-216)Gag>Aag	p.E72K	CA1_ENST00000542576.1_Missense_Mutation_p.E72K|CA1_ENST00000523022.1_Missense_Mutation_p.E72K|CA1_ENST00000256119.5_Missense_Mutation_p.E72K|CA1_ENST00000432364.2_Missense_Mutation_p.E72K|CA1_ENST00000431316.1_Missense_Mutation_p.E72K|CA1_ENST00000518341.1_5'UTR|CA1_ENST00000522389.1_Intron			P00915	CAH1_HUMAN	carbonic anhydrase I	72					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	13		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methocarbamol(DB00423)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	TCGTTGTCCTCAAAATTTACA	0.388																																					p.E72K		.											.	CA1-91	0			c.G214A						.						222	221	222					8																	86250502		2203	4300	6503	SO:0001583	missense	759	exon2			TGTCCTCAAAATT	M33987	CCDS6237.1	8q21.2	2006-03-10				ENSG00000133742	4.2.1.1	"Carbonic anhydrases"	1368	protein-coding gene	gene with protein product		114800				1916821	Standard	NM_001164830		Approved	Car1	uc003ydi.3	P00915		ENST00000523953.1:c.214G>A	8.37:g.86250502C>T	ENSP00000430656:p.Glu72Lys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	100	8	NM_001164830	0	0	0	0	0		Missense_Mutation	SNP	ENST00000523953.1	37	CCDS6237.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.641247	0.47153	.	.	ENSG00000133742	ENST00000523953;ENST00000256119;ENST00000431316;ENST00000542576;ENST00000432364;ENST00000523022;ENST00000517618;ENST00000517590;ENST00000521846;ENST00000522579;ENST00000522814;ENST00000522662;ENST00000523858	T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.53	3.74	0.42951	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.620194	0.17999	N	0.154974	T	0.60011	0.2236	L	0.42632	1.34	0.37858	D	0.929602	P	0.45715	0.865	B	0.42692	0.395	T	0.63323	-0.6663	10	0.59425	D	0.04	-2.5698	10.6538	0.45663	0.0:0.8437:0.0:0.1563	.	72	P00915	CAH1_HUMAN	K	72	ENSP00000430656:E72K;ENSP00000256119:E72K;ENSP00000392338:E72K;ENSP00000443517:E72K;ENSP00000401551:E72K;ENSP00000429798:E72K;ENSP00000430861:E72K;ENSP00000429843:E72K;ENSP00000430471:E72K;ENSP00000427852:E72K;ENSP00000430737:E72K;ENSP00000430372:E72K;ENSP00000430975:E72K	ENSP00000256119:E72K	E	-	1	0	CA1	86437754	0.998000	0.40836	0.108000	0.21378	0.434000	0.31775	2.575000	0.46025	0.706000	0.31912	0.591000	0.81541	GAG	.		0.388	CA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381067.1	NM_001738		T	86250502	C	T	86250502	3	4	21	1	0	0	0	0	1	0	0	0	2516	835	29	2	595	2	CA1	8	86250502	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	9786774	86250502	60113520	75	1843											
DECR1	1666	hgsc.bcm.edu;bcgsc.ca	37	chr8	91029497	91029498	+	Frame_Shift_Ins	INS	-	-	A																															gggggaggtactggccttggINStaaaggaatgacaactcttc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:91029497_91029498insA	ENST00000220764.2	+	2	303_304	c.215_216insA	c.(214-219)ggtaaafs	p.K73fs	DECR1_ENST00000519007.1_3'UTR|DECR1_ENST00000522161.1_Frame_Shift_Ins_p.K64fs	NM_001359.1	NP_001350.1	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1, mitochondrial	73					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|NADPH binding (GO:0070402)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	15			BRCA - Breast invasive adenocarcinoma(11;0.00953)			ACTGGCCTTGGTAAAGGAATGA	0.45																																					p.G72fs		.											.	DECR1-90	0			c.215_216insA						.																																			SO:0001589	frameshift_variant	1666	exon2			.	L26050	CCDS6250.1	8q21.3	2011-09-14			ENSG00000104325	ENSG00000104325		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2753	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 18C, member 1"	222745		DECR		7818482, 19027726	Standard	NM_001359		Approved	SDR18C1	uc003yek.1	Q16698	OTTHUMG00000163829	Exception_encountered	8.37:g.91029497_91029498insA	ENSP00000220764:p.Lys73fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	127	44	NM_001359	0	0	0	0	0	B7Z6B8|Q2M304|Q93085	Frame_Shift_Ins	INS	ENST00000220764.2	37	CCDS6250.1																																																																																			.		0.45	DECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375822.1			A	91029498	-	A	91029497	7	5	21	1	0	1	1	0	0	0	0	0	4388	1261	44	0	221	0	DECR1	8	91029497	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	4778995	91029497	55334525	76	1844											
RGS22	26166	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	101076121	101076121	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtttcttttcaaggtatactCtcagaagagcttgagaagga	12	13	10	6	0	3	3	2	1	2	3	4	5	3	4	0	2	2	3	0	2	5	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:101076121C>G	ENST00000360863.6	-	8	1069	c.875G>C	c.(874-876)aGa>aCa	p.R292T	RGS22_ENST00000523437.1_Missense_Mutation_p.R280T|RGS22_ENST00000523287.1_Missense_Mutation_p.R111T	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	292					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			AAGGTATACTCTCAGAAGAGC	0.343																																					p.R292T		.											.	RGS22-140	0			c.G875C						.						79	79	79					8																	101076121		1823	4073	5896	SO:0001583	missense	26166	exon8			TATACTCTCAGAA	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.875G>C	8.37:g.101076121C>G	ENSP00000354109:p.Arg292Thr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	62	7	NM_015668	0	0	0	0	0	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240381	0.58995	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.32988	1.44;1.43;1.44	5.86	4.98	0.66077	.	0.202669	0.37809	N	0.001934	T	0.25531	0.0621	M	0.64997	1.995	0.25094	N	0.990833	P;P;P	0.38597	0.506;0.506;0.639	B;B;B	0.30029	0.051;0.051;0.11	T	0.41215	-0.9521	10	0.66056	D	0.02	.	7.6392	0.28284	0.1248:0.6867:0.1208:0.0677	.	280;292;111	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	T	292;280;111;280	ENSP00000354109:R292T;ENSP00000429382:R111T;ENSP00000428212:R280T	ENSP00000354109:R292T	R	-	2	0	RGS22	101145297	0.590000	0.26815	0.978000	0.43139	0.698000	0.40448	1.435000	0.34969	2.937000	0.99478	0.650000	0.86243	AGA	.		0.343	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	101076121	C	G	101076121	3	3	21	1	0	0	0	0	1	0	0	0	13337	913	32	4	2999	4	RGS22	8	101076121	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	10046624	101076121	45287901	77	1845											
ZNF572	137209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	125988719	125988719	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagcatgaggatgcaaaagAaatgccactgacatgggttc	15	8	11	7	0	0	3	0	2	0	1	1	4	0	4	1	2	3	3	1	2	4	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:125988719A>C	ENST00000319286.5	+	3	363	c.209A>C	c.(208-210)gAa>gCa	p.E70A		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	70					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	31	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			GATGCAAAAGAAATGCCACTG	0.378										HNSCC(60;0.17)																											p.E70A		.											.	ZNF572-154	0			c.A209C						.						91	89	90					8																	125988719		2203	4300	6503	SO:0001583	missense	137209	exon3			CAAAAGAAATGCC	BX537876	CCDS6354.1	8q24.13	2013-09-20			ENSG00000180938	ENSG00000180938		"Zinc fingers, C2H2-type"	26758	protein-coding gene	gene with protein product							Standard	NM_152412		Approved	FLJ38002	uc003yrr.3	Q7Z3I7	OTTHUMG00000164988	ENST00000319286.5:c.209A>C	8.37:g.125988719A>C	ENSP00000319305:p.Glu70Ala	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	54	13	NM_152412	0	0	0	0	0	A1L4F1|Q8N1Q0	Missense_Mutation	SNP	ENST00000319286.5	37	CCDS6354.1	.	.	.	.	.	.	.	.	.	.	A	9.984	1.229005	0.22542	.	.	ENSG00000180938	ENST00000319286	T	0.08634	3.07	4.06	2.92	0.33932	.	0.160607	0.29293	N	0.012574	T	0.05273	0.0140	N	0.24115	0.695	0.09310	N	0.999998	B	0.27823	0.19	B	0.27608	0.081	T	0.36456	-0.9747	10	0.27082	T	0.32	-9.0575	7.4137	0.27032	0.8925:0.0:0.1075:0.0	.	70	Q7Z3I7	ZN572_HUMAN	A	70	ENSP00000319305:E70A	ENSP00000319305:E70A	E	+	2	0	ZNF572	126057900	0.024000	0.19004	0.541000	0.28102	0.914000	0.54420	0.846000	0.27682	1.841000	0.53522	0.459000	0.35465	GAA	.		0.378	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		C	125988719	A	C	125988719	3	2	21	1	0	0	0	0	1	0	0	0	18036	246	9	5	215	5	ZNF572	8	125988719	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	24912598	125988719	20375303	78	1846											
KCNK9	51305	broad.mit.edu;bcgsc.ca	37	chr8	140631226	140631231	+	In_Frame_Del	DEL	TGTTCA	TGTTCA	-																															cagcaggtagcgcacgaaggTgttcatgcgctcgcccaggc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TGTTCA	TGTTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:140631226_140631231delTGTTCA	ENST00000520439.1	-	2	458_463	c.395_400delTGAACA	c.(394-402)atgaacacc>acc	p.MN132del	KCNK9_ENST00000303015.1_In_Frame_Del_p.MN132del|KCNK9_ENST00000523477.1_5'Flank	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	132					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CGCACGAAGGTGTTCATGCGCTCGCC	0.587																																					p.132_134del													.	KCNK9-93	0			c.395_400del						.																																			SO:0001651	inframe_deletion	51305	exon2			CGAAGGTGTTCAT	AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.395_400delTGAACA	8.37:g.140631226_140631231delTGTTCA	ENSP00000430676:p.Met132_Asn133del	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	213	0	NM_016601	0	0	0	0	0	Q2M290|Q540F2	In_Frame_Del	DEL	ENST00000520439.1	37	CCDS6377.1																																																																																			.		0.587	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		-	140631231	TGTTCA	-	140631226	7	5	21	1	0	1	0	1	0	0	0	0	8093	1696	59	0	728	0	KCNK9	8	140631226	In_Frame_Del	DEL	TGTTCA	TCGA-A4-A48D-01A-11D-A25F-10	14642507	140631226	5732796	79	1847											
ZNF251	90987	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	145947050	145947050	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaaaatgtctttcttggaaAatcttcttgatatgaataaa	16	16	5	4	0	4	2	0	2	4	0	4	3	4	3	0	1	0	0	0	1	9	7			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:145947050A>T	ENST00000292562.7	-	5	2270	c.1995T>A	c.(1993-1995)atT>atA	p.I665I	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	665					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)			autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		TTTCTTGGAAAATCTTCTTGA	0.358																																					p.I665I		.											.	ZNF251-68	0			c.T1995A						.						44	44	44					8																	145947050		1901	4119	6020	SO:0001819	synonymous_variant	90987	exon5			TTGGAAAATCTTC	AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"Zinc fingers, C2H2-type", "-"	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.1995T>A	8.37:g.145947050A>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	90	28	NM_138367	0	0	1	1	0	Q2M219	Silent	SNP	ENST00000292562.7	37	CCDS47944.1																																																																																			.		0.358	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367		T	145947050	A	T	145947050	2	4	21	1	0	0	0	0	0	0	0	1	17828	10	1	5		5	ZNF251	8	145947050	Silent	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	5315824	145947050	416972	80	1848											
TLN1	7094	broad.mit.edu	37	chr9	35704480	35704480	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	attcccagcctggagcgcagCcaggacgtgggagacctggg	8	5	16	12	2	0	1	0	0	0	1	1	4	1	3	4	4	3	1	4	4	0	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr9:35704480C>T	ENST00000314888.9	-	45	6249	c.5896G>A	c.(5896-5898)Gct>Act	p.A1966T	TLN1_ENST00000540444.1_Missense_Mutation_p.A1860T|TLN1_ENST00000464379.1_5'UTR	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1966				A -> R (in Ref. 1; AAD13152). {ECO:0000305}.	activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGGAGCGCAGCCAGGACGTGG	0.582																																					p.A1966T													.	TLN1-609	0			c.G5896A						.						59	54	56					9																	35704480		2203	4300	6503	SO:0001583	missense	7094	exon45			GCGCAGCCAGGAC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5896G>A	9.37:g.35704480C>T	ENSP00000316029:p.Ala1966Thr	Somatic	120	1		WXS	Illumina HiSeq	Phase_I	145	5	NM_006289	0	0	103	112	9	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.196475	0.79015	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.36520	1.25;1.25	4.87	4.87	0.63330	Vinculin-binding site-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.57621	0.2066	M	0.76170	2.325	0.80722	D	1	D	0.63046	0.992	D	0.67900	0.954	T	0.61559	-0.7038	10	0.62326	D	0.03	-7.2257	13.0408	0.58897	0.161:0.839:0.0:0.0	.	1966	Q9Y490	TLN1_HUMAN	T	1966;1860	ENSP00000316029:A1966T;ENSP00000442981:A1860T	ENSP00000316029:A1966T	A	-	1	0	TLN1	35694480	1.000000	0.71417	0.996000	0.52242	0.874000	0.50279	2.532000	0.45659	2.250000	0.74265	0.462000	0.41574	GCT	.		0.582	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35704480	C	T	35704480	3	4	21	1	0	0	0	0	1	0	0	0	15979	739	26	2	1781	2	TLN1	9	35704480	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		35704480	105508951	81	1849											
BAAT	570	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	104125253	104125253	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatagatagtccaatctgTactccttgacatacagagac	13	10	7	11	0	1	3	0	1	1	2	3	4	3	3	3	0	2	1	3	0	5	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr9:104125253T>C	ENST00000395051.3	-	3	784	c.714A>G	c.(712-714)gtA>gtG	p.V238V	BAAT_ENST00000259407.2_Silent_p.V238V			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	238					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	GTCCAATCTGTACTCCTTGAC	0.393																																					p.V238V		.											.	BAAT-228	0			c.A714G						.						90	91	91					9																	104125253		2202	4300	6502	SO:0001819	synonymous_variant	570	exon4			AATCTGTACTCCT	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"glycine N-choloyltransferase"	602938	"bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)", "bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.714A>G	9.37:g.104125253T>C		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	59	16	NM_001127610	0	0	0	0	0	Q3B7W9|Q96L31	Silent	SNP	ENST00000395051.3	37	CCDS6752.1																																																																																			.		0.393	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1			C	104125253	T	C	104125253	2	2	21	1	0	0	0	0	0	0	0	1	1281	1625	57	3		3	BAAT	9	104125253	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	68420773	104125253	37088178	82	1850											
GPR107	57720	broad.mit.edu;bcgsc.ca	37	chr9	132845879	132845879	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagaagtacagtggattcaAaggtaagaactaaccaccct	18	7	8	8	0	1	2	1	0	0	2	1	3	1	3	2	2	3	2	2	2	7	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr9:132845879A>G	ENST00000372406.1	+	6	1069	c.562A>G	c.(562-564)Aag>Gag	p.K188E	GPR107_ENST00000347136.6_Missense_Mutation_p.K188E|GPR107_ENST00000372410.3_Missense_Mutation_p.K188E	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	188						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				AGTGGATTCAAAGGTAAGAAC	0.348																																					p.K188E													.	GPR107-91	0			c.A562G						.						196	174	181					9																	132845879		2203	4300	6503	SO:0001583	missense	57720	exon6			GATTCAAAGGTAA	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"GPCR / Unclassified : 7TM orphan receptors"	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.562A>G	9.37:g.132845879A>G	ENSP00000361483:p.Lys188Glu	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	223	11	NM_001136557	0	0	0	0	0	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Missense_Mutation	SNP	ENST00000372406.1	37	CCDS48041.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.828233	0.50845	.	.	ENSG00000148358	ENST00000372406;ENST00000347136;ENST00000372410;ENST00000455412	T;T;T	0.22336	1.96;1.97;1.96	5.63	4.42	0.53409	.	0.148254	0.46758	D	0.000276	T	0.14874	0.0359	L	0.42245	1.32	0.32954	D	0.520166	P;P;P	0.40083	0.702;0.696;0.57	B;B;B	0.37650	0.255;0.214;0.255	T	0.05533	-1.0879	10	0.08837	T	0.75	-12.6956	9.084	0.36570	0.8151:0.1849:0.0:0.0	.	188;188;188	G5E994;Q5VW38;Q5VW38-2	.;GP107_HUMAN;.	E	188	ENSP00000361483:K188E;ENSP00000336988:K188E;ENSP00000361487:K188E	ENSP00000336988:K188E	K	+	1	0	GPR107	131885700	0.952000	0.32445	1.000000	0.80357	0.980000	0.70556	0.795000	0.26972	2.145000	0.66743	0.533000	0.62120	AAG	.		0.348	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2			G	132845879	A	G	132845879	3	3	21	1	0	0	0	0	1	0	0	0	6643	15	1	3	584	3	GPR107	9	132845879	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	28720626	132845879	8367552	83	1851											
ANK3	288	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61829526	61829526	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgttagtggctgctgctgAtttctccagggagccactac	6	12	13	10	0	1	1	0	1	1	0	2	2	1	2	2	3	4	4	2	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:61829526A>C	ENST00000280772.2	-	37	11304	c.11113T>G	c.(11113-11115)Tca>Gca	p.S3705A	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3705					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GCTGCTGCTGATTTCTCCAGG	0.512																																					p.S3705A													.	ANK3-107	0			c.T11113G						.						83	98	92					10																	61829526		2203	4300	6503	SO:0001583	missense	288	exon37			CTGCTGATTTCTC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11113T>G	10.37:g.61829526A>C	ENSP00000280772:p.Ser3705Ala	Somatic	136	1		WXS	Illumina HiSeq	Phase_I	136	28	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	A	4.423	0.078237	0.08485	.	.	ENSG00000151150	ENST00000280772	T	0.16324	2.35	5.52	-11.0	0.00169	.	0.998150	0.08104	N	0.997186	T	0.07052	0.0179	N	0.08118	0	0.31643	N	0.647774	B	0.02656	0.0	B	0.01281	0.0	T	0.37150	-0.9718	10	0.34782	T	0.22	.	12.7032	0.57045	0.258:0.6191:0.0549:0.0681	.	3705	Q12955	ANK3_HUMAN	A	3705	ENSP00000280772:S3705A	ENSP00000280772:S3705A	S	-	1	0	ANK3	61499532	0.247000	0.23920	0.021000	0.16686	0.899000	0.52679	-0.268000	0.08607	-2.908000	0.00309	-1.389000	0.01157	TCA	.		0.512	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61829526	A	C	61829526	3	2	21	1	0	0	0	0	1	0	0	0	622	333	12	5	2361	5	ANK3	10	61829526	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		61829526	73705221	84	1852											
NUDT13	25961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74884990	74884990	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcccttccaataatataatcTattatccacaggtaattatt	14	15	3	9	0	1	0	0	0	1	0	3	0	3	0	3	1	0	1	3	1	8	9			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:74884990T>G	ENST00000357321.4	+	6	698	c.580T>G	c.(580-582)Tat>Gat	p.Y194D	RP11-152N13.16_ENST00000608444.1_RNA|NUDT13_ENST00000372997.3_Missense_Mutation_p.Y194D|SNORA11_ENST00000408237.1_RNA|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000544879.1_Missense_Mutation_p.Y68D|NUDT13_ENST00000537969.1_5'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.Y194D	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					TAATATAATCTATTATCCACA	0.478																																					p.Y194D		.											.	NUDT13-90	0			c.T580G						.						68	70	69					10																	74884990		2203	4300	6503	SO:0001583	missense	25961	exon6			ATAATCTATTATC	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.580T>G	10.37:g.74884990T>G	ENSP00000349874:p.Tyr194Asp	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	101	25	NM_015901	0	0	0	0	0		Missense_Mutation	SNP	ENST00000357321.4	37	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580430	0.86645	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000544879;ENST00000372997	T;T;T;T	0.44083	0.93;1.36;0.93;1.43	5.97	5.97	0.96955	NUDIX hydrolase domain (1);Zinc ribbon, NADH pyrophosphatase (1);NUDIX hydrolase domain-like (1);	0.108901	0.64402	D	0.000004	T	0.57902	0.2085	L	0.42245	1.32	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.979	D;D;P	0.79108	0.992;0.984;0.821	T	0.57556	-0.7791	10	0.52906	T	0.07	.	16.43	0.83839	0.0:0.0:0.0:1.0	.	194;194;194	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	D	194;194;68;194	ENSP00000349874:Y194D;ENSP00000335326:Y194D;ENSP00000440760:Y68D;ENSP00000362088:Y194D	ENSP00000335326:Y194D	Y	+	1	0	NUDT13	74554996	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.758000	0.68776	2.283000	0.76528	0.533000	0.62120	TAT	.		0.478	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		G	74884990	T	G	74884990	3	3	21	1	0	0	0	0	1	0	0	0	10755	1522	53	5	598	5	NUDT13	10	74884990	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	13055464	74884990	60649757	85	1853											
MAT1A	4143	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	82039973	82039973	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggggaggaggccggagcGcctgaggtctgccatccggg	6	4	19	12	3	1	1	0	1	1	0	2	4	2	4	5	7	2	0	5	7	0	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:82039973G>T	ENST00000372213.3	-	5	765	c.505C>A	c.(505-507)Cgc>Agc	p.R169S		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	169					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	AGGCCGGAGCGCCTGAGGTCT	0.582																																					p.R169S		.											.	MAT1A-90	0			c.C505A						.						71	79	76					10																	82039973		2203	4300	6503	SO:0001583	missense	4143	exon5			CGGAGCGCCTGAG		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.505C>A	10.37:g.82039973G>T	ENSP00000361287:p.Arg169Ser	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	86	7	NM_000429	0	0	0	0	0	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	37	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441355	0.43326	.	.	ENSG00000151224	ENST00000372213;ENST00000372206;ENST00000455001	D;D	0.82619	-1.63;-1.63	4.91	4.01	0.46588	S-adenosylmethionine synthetase, central domain (1);S-adenosylmethionine synthetase superfamily (1);	0.097389	0.64402	N	0.000001	D	0.91835	0.7416	M	0.93854	3.465	0.80722	D	1	D	0.60160	0.987	D	0.62955	0.909	D	0.93004	0.6426	10	0.87932	D	0	-22.5394	11.6157	0.51088	0.0885:0.0:0.9115:0.0	.	169	Q00266	METK1_HUMAN	S	169;169;106	ENSP00000361287:R169S;ENSP00000414961:R106S	ENSP00000361280:R169S	R	-	1	0	MAT1A	82029953	1.000000	0.71417	0.858000	0.33744	0.028000	0.11728	6.335000	0.72949	1.217000	0.43442	-0.123000	0.14984	CGC	.		0.582	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		T	82039973	G	T	82039973	3	4	21	1	0	0	0	0	1	0	0	0	9354	1087	38	4	702	4	MAT1A	10	82039973	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	7154983	82039973	53494774	86	1854											
NRG3	10718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	83635455	83635455	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcctctccaagcccagctCtttccccaaggccatggaga	8	9	7	17	0	2	1	0	0	2	1	5	2	4	1	6	2	2	1	6	2	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:83635455C>G	ENST00000404547.1	+	1	359	c.359C>G	c.(358-360)tCt>tGt	p.S120C	NRG3_ENST00000556918.1_5'Flank|NRG3_ENST00000372141.2_Missense_Mutation_p.S120C|NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000404576.2_5'Flank			P56975	NRG3_HUMAN	neuregulin 3	120	Ser/Thr-rich.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		AAGCCCAGCTCTTTCCCCAAG	0.662																																					p.S120C		.											.	NRG3-522	0			c.C359G						.						71	78	75					10																	83635455		2203	4300	6503	SO:0001583	missense	10718	exon1			CCAGCTCTTTCCC	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.359C>G	10.37:g.83635455C>G	ENSP00000384796:p.Ser120Cys	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	113	29	NM_001165972	0	0	0	0	0	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	c	19.30	3.801788	0.70682	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.35973	1.28;1.29	2.97	2.97	0.34412	.	.	.	.	.	T	0.41119	0.1145	N	0.19112	0.55	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66847	0.947;0.947	T	0.42361	-0.9456	9	0.72032	D	0.01	-10.7268	11.8419	0.52359	0.0:1.0:0.0:0.0	.	120;120	B9EGV5;P56975-4	.;.	C	120	ENSP00000361214:S120C;ENSP00000384796:S120C	ENSP00000361214:S120C	S	+	2	0	NRG3	83625435	0.970000	0.33590	1.000000	0.80357	0.995000	0.86356	2.334000	0.43920	1.680000	0.50976	0.459000	0.35465	TCT	.		0.662	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		G	83635455	C	G	83635455	3	3	21	1	0	0	0	0	1	0	0	0	10675	913	32	4	361	4	NRG3	10	83635455	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	1595482	83635455	51899292	87	1855											
LRIT2	340745	ucsc.edu;bcgsc.ca	37	chr10	85984556	85984556	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgaagagccagctcagggAgtgcatcaatcttgttgcgt	10	11	12	8	1	3	2	2	1	1	1	3	3	3	3	1	1	4	3	1	1	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:85984556A>T	ENST00000372113.4	-	2	430	c.425T>A	c.(424-426)cTc>cAc	p.L142H	LRIT2_ENST00000538192.1_Missense_Mutation_p.L142H	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	142						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						CAGCTCAGGGAGTGCATCAAT	0.522																																					p.L142H													.	LRIT2-92	0			c.T425A						.						129	124	126					10																	85984556		2203	4300	6503	SO:0001583	missense	340745	exon2			TCAGGGAGTGCAT		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"Immunoglobulin superfamily / I-set domain containing"	23443	protein-coding gene	gene with protein product			"leucine rich repeat containing 22"	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.425T>A	10.37:g.85984556A>T	ENSP00000361185:p.Leu142His	Somatic	183	2		WXS	Illumina HiSeq		195	54	NM_001017924	0	0	0	0	0	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	.	.	.	.	.	.	.	.	.	.	A	16.26	3.073041	0.55646	.	.	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.20069	2.1;2.1	5.91	4.76	0.60689	.	0.127000	0.53938	N	0.000047	T	0.56978	0.2022	H	0.95679	3.705	0.52501	D	0.999952	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.99	T	0.67898	-0.5551	10	0.87932	D	0	.	11.5781	0.50875	0.8661:0.0:0.0:0.1339	.	142;142	B7ZME6;A6NDA9	.;LRIT2_HUMAN	H	142	ENSP00000361185:L142H;ENSP00000438264:L142H	ENSP00000361185:L142H	L	-	2	0	LRIT2	85974536	1.000000	0.71417	0.014000	0.15608	0.456000	0.32438	7.105000	0.77031	1.025000	0.39708	0.533000	0.62120	CTC	.		0.522	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697		T	85984556	A	T	85984556	3	4	21	1	0	0	0	0	1	0	0	0	8973	304	11	5	1235	5	LRIT2	10	85984556	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	2349101	85984556	49550191	88	1856											
BMPR1A	657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	88681453	88681453	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcgtcgttgtatcacaggagGtgggagtttgagtagtttct	7	15	14	5	2	2	1	1	1	1	0	4	3	2	3	0	3	0	5	0	3	2	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:88681453G>A	ENST00000372037.3	+	11	1879		c.e11+1			NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA						BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						ATCACAGGAGGTGGGAGTTTG	0.388			"Mis, N, F"			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												.	Ovarian(190;603 2086 22044 30335 47971)	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"bone morphogenetic protein receptor, type IA"		E	.	BMPR1A-1619	0			c.1342+1G>A						.						112	108	110					10																	88681453		2203	4300	6503	SO:0001630	splice_region_variant	657	exon11	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	CAGGAGGTGGGAG	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"CD molecules"	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.1342+1G>A	10.37:g.88681453G>A		Somatic	163	0		WXS	Illumina HiSeq	Phase_I	155	44	NM_004329	0	0	0	9	9	A8K6U9|Q8NEN8	Splice_Site	SNP	ENST00000372037.3	37	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039456	0.75617	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	.	.	.	5.63	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3472	0.83146	0.0:0.0:0.867:0.133	.	.	.	.	.	-1	.	.	.	+	.	.	BMPR1A	88671433	1.000000	0.71417	0.989000	0.46669	0.789000	0.44602	9.738000	0.98835	1.511000	0.48818	0.655000	0.94253	.	.		0.388	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329	Intron	A	88681453	G	A	88681453	5	1	21	1	0	0	0	0	0	0	1	0	1470	1275	44	2	1377	2	BMPR1A	10	88681453	Splice_Site	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	2696897	88681453	46853294	89	1857											
CDHR5	53841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	621148	621148	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgtagccatctgagaaggTgcagggcaggaaccacgggg	11	4	17	9	2	1	1	0	1	1	1	1	4	1	2	2	5	3	3	2	5	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:621148T>C	ENST00000358353.3	-	8	1043	c.721A>G	c.(721-723)Acc>Gcc	p.T241A	CDHR5_ENST00000397542.2_Missense_Mutation_p.T241A|CDHR5_ENST00000349570.7_Missense_Mutation_p.T241A			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	241					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						TCTGAGAAGGTGCAGGGCAGG	0.652																																					p.T241A		.											.	CDHR5-90	0			c.A721G						.						68	64	66					11																	621148		2203	4300	6503	SO:0001583	missense	53841	exon7			AGAAGGTGCAGGG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.721A>G	11.37:g.621148T>C	ENSP00000351118:p.Thr241Ala	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	154	34	NM_031264	0	2	87	126	37	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	37	CCDS7707.1	.	.	.	.	.	.	.	.	.	.	T	3.798	-0.042254	0.07452	.	.	ENSG00000099834	ENST00000397542;ENST00000358353;ENST00000326366;ENST00000349570	T;T;T	0.45668	0.89;0.89;0.89	4.08	-8.15	0.01065	.	2.323100	0.02445	N	0.084999	T	0.12092	0.0294	N	0.02357	-0.585	0.09310	N	1	B;B;B;B;B	0.13594	0.0;0.005;0.002;0.002;0.008	B;B;B;B;B	0.09377	0.003;0.004;0.004;0.004;0.004	T	0.22977	-1.0201	10	0.10377	T	0.69	-2.285	0.0745	0.00025	0.3221:0.1617:0.2125:0.3037	.	241;241;234;241;241	Q58EZ6;Q9HBB8-4;B4DV98;Q9HBB8-2;Q9HBB8	.;.;.;.;CDHR5_HUMAN	A	241	ENSP00000380676:T241A;ENSP00000351118:T241A;ENSP00000345726:T241A	ENSP00000326527:T241A	T	-	1	0	CDHR5	611148	0.000000	0.05858	0.000000	0.03702	0.184000	0.23303	-1.800000	0.01744	-2.416000	0.00567	-0.496000	0.04628	ACC	.		0.652	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		C	621148	T	C	621148	3	2	21	1	0	0	0	0	1	0	0	0	3128	1696	59	3	1852	3	CDHR5	11	621148	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		621148	134385368	90	1858											
MUC2	4583	broad.mit.edu	37	chr11	1093271	1093271	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caccggcacacagaccccaaCatcgacacccatcaccacca	14	2	4	21	2	1	1	1	0	0	1	2	2	1	1	6	1	1	1	6	1	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:1093271C>G	ENST00000441003.2	+	30	5117	c.5090C>G	c.(5089-5091)aCa>aGa	p.T1697R	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1664R|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1697R(2)|p.T1664R(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cagaccccaacatcgacaccc	0.637																																					p.T1697R													.	MUC2-90	4	Substitution - Missense(4)	kidney(2)|skin(2)	c.C5090G						.						126	165	151					11																	1093271		1844	3338	5182	SO:0001583	missense	4583	exon30			CCCCAACATCGAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5090C>G	11.37:g.1093271C>G	ENSP00000415183:p.Thr1697Arg	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	70	4	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	5.778	0.327961	0.10956	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.93;2.58	1.43	1.43	0.22495	.	27.718000	0.04275	U	0.342784	T	0.27027	0.0662	.	.	.	0.20307	N	0.999915	D	0.64830	0.994	D	0.67725	0.953	T	0.19647	-1.0299	9	0.30078	T	0.28	.	6.2291	0.20724	0.0:1.0:0.0:0.0	.	1697	E7EUV1	.	R	1697;1664	ENSP00000415183:T1697R;ENSP00000351956:T1664R	ENSP00000351956:T1664R	T	+	2	0	MUC2	1083271	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.752000	0.26362	0.796000	0.33947	0.184000	0.17185	ACA	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093271	C	G	1093271	3	3	21	1	0	0	0	0	1	0	0	0	10000	478	17	4	5208	4	MUC2	11	1093271	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	472123	1093271	133913245	91	1859											
MUC5B	727897	broad.mit.edu	37	chr11	1268538	1268538	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctggacttcggccacctcGggcatcttgggcaccaccca	6	7	11	17	2	1	0	0	0	1	0	3	1	1	1	5	4	0	2	5	4	0	2	rs367868062		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:1268538G>A	ENST00000529681.1	+	31	10486	c.10428G>A	c.(10426-10428)tcG>tcA	p.S3476S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.S3479S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3476	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGGCCACCTCGGGCATCTTGG	0.667																																					p.S3476S													.	.	0			c.G10428A						.	G		6,4250		0,6,2122	61	87	78		10428	-2.2	0	11		78	0,8416		0,0,4208	no	coding-synonymous	MUC5B	NM_002458.2		0,6,6330	AA,AG,GG		0.0,0.141,0.0473		3476/5763	1268538	6,12666	2128	4208	6336	SO:0001819	synonymous_variant	727897	exon31			CACCTCGGGCATC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.10428G>A	11.37:g.1268538G>A		Somatic	181	1		WXS	Illumina HiSeq	Phase_I	243	7	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1268538	G	A	1268538	2	1	21	1	0	0	0	0	0	0	0	1	10004	1103	39	1		1	MUC5B	11	1268538	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	175267	1268538	133737978	92	1860											
OR52D1	390066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	5510196	5510196	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgcccaagatgctggccaTtttgtggctccatgctggtg	5	13	13	10	0	0	1	0	0	0	1	1	1	1	1	3	3	3	3	3	3	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:5510196T>C	ENST00000322641.5	+	1	282	c.260T>C	c.(259-261)aTt>aCt	p.I87T	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	87					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGCTGGCCATTTTGTGGCTC	0.498																																					p.I87T		.											.	OR52D1-68	0			c.T260C						.						164	135	144					11																	5510196		2201	4297	6498	SO:0001583	missense	390066	exon1			TGGCCATTTTGTG	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"GPCR / Class A : Olfactory receptors"	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.260T>C	11.37:g.5510196T>C	ENSP00000326232:p.Ile87Thr	Somatic	413	1		WXS	Illumina HiSeq	Phase_I	419	115	NM_001005163	0	0	0	0	0	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650929	0.67472	.	.	ENSG00000181609	ENST00000322641	T	0.00384	7.6	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.088930	0.48767	D	0.000161	T	0.00936	0.0031	M	0.73372	2.23	0.41835	D	0.990092	D	0.89917	1.0	D	0.85130	0.997	T	0.73582	-0.3937	10	0.87932	D	0	.	14.7065	0.69194	0.0:0.0:0.0:1.0	.	87	Q9H346	O52D1_HUMAN	T	87	ENSP00000326232:I87T	ENSP00000326232:I87T	I	+	2	0	OR52D1	5466772	0.008000	0.16893	1.000000	0.80357	0.593000	0.36681	1.557000	0.36299	2.340000	0.79590	0.528000	0.53228	ATT	.		0.498	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		C	5510196	T	C	5510196	3	2	21	1	0	0	0	0	1	0	0	0	11140	1493	52	3	262	3	OR52D1	11	5510196	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	4241658	5510196	129496320	93	1861											
SUV420H1	51111	broad.mit.edu	37	chr11	67925405	67925405	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagagagaaagaggatcaCtgcagcacaccccattttca	15	6	8	12	0	2	3	2	0	0	3	2	5	2	4	3	1	2	2	3	1	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:67925405C>A	ENST00000304363.4	-	11	2761	c.2408G>T	c.(2407-2409)aGt>aTt	p.S803I		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	803					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						AAGAGGATCACTGCAGCACAC	0.438																																					p.S803I													.	SUV420H1-228	0			c.G2408T						.						191	206	201					11																	67925405		2200	4294	6494	SO:0001583	missense	51111	exon11			GGATCACTGCAGC	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.2408G>T	11.37:g.67925405C>A	ENSP00000305899:p.Ser803Ile	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	123	4	NM_017635	0	0	3	3	0	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	37	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.714362	0.30413	.	.	ENSG00000110066	ENST00000304363	T	0.47528	0.84	5.71	3.59	0.41128	.	0.364252	0.30869	N	0.008709	T	0.32912	0.0845	N	0.24115	0.695	0.09310	N	1	P	0.43169	0.8	B	0.41088	0.347	T	0.29427	-1.0012	10	0.87932	D	0	-9.2091	9.1236	0.36801	0.0:0.7325:0.1423:0.1252	.	803	Q4FZB7	SV421_HUMAN	I	803	ENSP00000305899:S803I	ENSP00000305899:S803I	S	-	2	0	SUV420H1	67681981	0.002000	0.14202	0.014000	0.15608	0.954000	0.61252	1.668000	0.37481	2.710000	0.92621	0.491000	0.48974	AGT	.		0.438	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		A	67925405	C	A	67925405	3	1	21	1	0	0	0	0	1	0	0	0	15446	565	20	4	253	4	SUV420H1	11	67925405	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	62415209	67925405	67081111	94	1862											
MRPL21	219927	broad.mit.edu	37	chr11	68660882	68660883	+	Frame_Shift_Ins	INS	-	-	T																															gccattacccgaggagtggcINSttgccaagcagcgtgaagtt																								rs368654836		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:68660882_68660883insT	ENST00000362034.2	-	5	446_447	c.437_438insA	c.(436-438)aagfs	p.K146fs	MRPL21_ENST00000567045.1_Frame_Shift_Ins_p.K61fs|MRPL21_ENST00000450904.2_Frame_Shift_Ins_p.K61fs	NM_181514.1|NM_181515.1	NP_852615.1|NP_852616.1	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21	146					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(6)|prostate(1)	8			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CGAGGAGTGGCTTGCCAAGCAG	0.54																																					p.K146fs													.	MRPL21-90	0			c.438_439insA						.																																			SO:0001589	frameshift_variant	219927	exon5			GAGTGGCTTGCCA	AK096756	CCDS8186.1, CCDS44662.1	11q13.3	2012-09-13			ENSG00000197345	ENSG00000197345		"Mitochondrial ribosomal proteins / large subunits"	14479	protein-coding gene	gene with protein product		611834				11551941	Standard	NM_181514		Approved		uc001ooi.3	Q7Z2W9	OTTHUMG00000167893	ENST00000362034.2:c.438dupA	11.37:g.68660884_68660884dupT	ENSP00000354580:p.Lys146fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	141	7	NM_181514	0	0	0	0	0	A6NKU0|C9JPR2	Frame_Shift_Ins	INS	ENST00000362034.2	37	CCDS8186.1																																																																																			.		0.54	MRPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396856.1	NM_181512		T	68660883	-	T	68660882	7	5	21	1	0	1	1	0	0	0	0	0	9812	796	28	0	191	0	MRPL21	11	68660882	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	735477	68660882	66345634	95	1863											
PRSS23	11098	broad.mit.edu	37	chr11	86519059	86519059	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agggtcttcaggaaagtctcGaaggaagcggcagatttatg	12	9	14	6	2	3	1	1	0	2	1	4	4	3	3	0	4	1	1	0	4	4	3	rs368713993		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:86519059G>A	ENST00000280258.5	+	2	799	c.374G>A	c.(373-375)cGa>cAa	p.R125Q	PRSS23_ENST00000533902.2_Intron|PRSS23_ENST00000441050.1_Missense_Mutation_p.R93Q	NM_007173.4	NP_009104.1	O95084	PRS23_HUMAN	protease, serine, 23	125						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGAAAGTCTCGAAGGAAGCGG	0.527																																					p.R125Q													.	PRSS23-515	0			c.G374A						.	G	GLN/ARG	0,4402		0,0,2201	81	76	77		374	5.8	1	11		77	1,8597	1.2+/-3.3	0,1,4298	no	missense	PRSS23	NM_007173.4	43	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/384	86519059	1,12999	2201	4299	6500	SO:0001583	missense	11098	exon2			AGTCTCGAAGGAA	AF015287	CCDS8278.1	11q14.2	2010-05-12			ENSG00000150687	ENSG00000150687		"Serine peptidases / Serine peptidases"	14370	protein-coding gene	gene with protein product							Standard	XM_005273727		Approved	SPUVE, SIG13	uc001pcb.3	O95084		ENST00000280258.5:c.374G>A	11.37:g.86519059G>A	ENSP00000280258:p.Arg125Gln	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	180	5	NM_007173	0	0	5	5	0	B2RDJ1|B4E2J3|Q6IBI0	Missense_Mutation	SNP	ENST00000280258.5	37	CCDS8278.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733287	0.89482	0.0	1.16E-4	ENSG00000150687	ENST00000527521;ENST00000280258;ENST00000441050	.	.	.	5.8	5.8	0.92144	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	D	0.82930	0.5144	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.80764	0.994;0.86	T	0.82047	-0.0651	8	.	.	.	-23.2305	20.0545	0.97645	0.0:0.0:1.0:0.0	.	93;125	B4E2J3;O95084	.;PRS23_HUMAN	Q	125;125;93	.	.	R	+	2	0	PRSS23	86196707	1.000000	0.71417	0.995000	0.50966	0.768000	0.43524	4.754000	0.62191	2.748000	0.94277	0.655000	0.94253	CGA	.		0.527	PRSS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393805.2	NM_007173		A	86519059	G	A	86519059	3	1	21	1	0	0	0	0	1	0	0	0	12649	1058	37	1	376	1	PRSS23	11	86519059	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	17858177	86519059	48487457	96	1864											
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	108381937	108381941	+	Frame_Shift_Del	DEL	CTTCT	CTTCT	-																															ttgggaatttccaatattaaCttctgaaagagctggaagac																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	CTTCT	CTTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:108381937_108381941delCTTCT	ENST00000265843.4	-	6	4403_4407	c.4293_4297delAGAAG	c.(4291-4299)tcagaagttfs	p.EV1432fs	EXPH5_ENST00000525344.1_Frame_Shift_Del_p.EV1425fs|EXPH5_ENST00000428840.1_Frame_Shift_Del_p.EV1356fs|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Frame_Shift_Del_p.EV1244fs	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1432					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CCAATATTAACTTCTGAAAGAGCTG	0.395																																					p.1431_1433del		.											.	EXPH5-95	0			c.4293_4297del						.																																			SO:0001589	frameshift_variant	23086	exon6			.		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4293_4297delAGAAG	11.37:g.108381937_108381941delCTTCT	ENSP00000265843:p.Glu1432fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	123	26	NM_015065	0	0	0	0	0	Q2KHM1|Q9Y4D6	Frame_Shift_Del	DEL	ENST00000265843.4	37	CCDS8341.1																																																																																			.		0.395	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		-	108381941	CTTCT	-	108381937	7	5	21	1	0	1	0	1	0	0	0	0	5335	565	20	0	1676	0	EXPH5	11	108381937	Frame_Shift_Del	DEL	CTTCT	TCGA-A4-A48D-01A-11D-A25F-10	21862878	108381937	26624579	97	1865											
SIK3	23387	broad.mit.edu	37	chr11	116729111	116729111	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggccggtgagcgaatgccGgggagaaagcagtccttgaa	10	6	17	8	3	0	3	0	2	0	1	1	5	1	3	3	4	3	1	3	4	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:116729111G>A	ENST00000292055.4	-	20	2787	c.2752C>T	c.(2752-2754)Cgg>Tgg	p.R918W	SIK3_ENST00000375288.1_Missense_Mutation_p.R253W|SIK3_ENST00000375300.1_Missense_Mutation_p.R976W|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000542607.1_Missense_Mutation_p.R858W|SIK3_ENST00000446921.2_Missense_Mutation_p.R916W|SIK3_ENST00000434315.2_Missense_Mutation_p.R757W|SIK3_ENST00000488337.1_5'UTR	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	918	Gln-rich.				protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						AGCGAATGCCGGGGAGAAAGC	0.592																																					p.R918W													.	SIK3-919	0			c.C2752T						.						105	96	99					11																	116729111		2201	4296	6497	SO:0001583	missense	23387	exon20			AATGCCGGGGAGA	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.2752C>T	11.37:g.116729111G>A	ENSP00000292055:p.Arg918Trp	Somatic	281	1		WXS	Illumina HiSeq	Phase_I	385	6	NM_025164	0	0	12	12	0	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.9|26.9	4.785267|4.785267	0.90282|0.90282	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000445177;ENST00000446921|ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315	T;T|T;T;T;T;T	0.70869|0.34072	1.2;-0.52|1.38;1.38;1.38;1.38;1.38	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.000000	.|0.38326	.|U	.|0.001724	T|T	0.52789|0.52789	0.1756|0.1756	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|1.0;0.999;0.999;0.999;0.999	T|T	0.54153|0.54153	-0.8336|-0.8336	7|10	0.87932|0.87932	D|D	0|0	.|.	19.7711|19.7711	0.96366|0.96366	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|918;858;757;918;253	.|Q9Y2K2-3;A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2	.|.;.;.;SIK3_HUMAN;.	L|W	1017;880|976;918;253;858;757	ENSP00000391295:P1017L;ENSP00000390442:P880L|ENSP00000364449:R976W;ENSP00000292055:R918W;ENSP00000364437:R253W;ENSP00000438108:R858W;ENSP00000415873:R757W	ENSP00000391295:P1017L|ENSP00000292055:R918W	P|R	-|-	2|1	0|2	SIK3|SIK3	116234321|116234321	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	8.979000|8.979000	0.93455|0.93455	2.654000|2.654000	0.90174|0.90174	0.655000|0.655000	0.94253|0.94253	CCG|CGG	.		0.592	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		A	116729111	G	A	116729111	3	1	21	1	0	0	0	0	1	0	0	0	14351	1115	39	1	1055	1	SIK3	11	116729111	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	8347174	116729111	18277405	98	1866											
SIK3	23387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	116741113	116741113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaggggtaactgctggcActgcctgaagagagacagga	12	5	14	10	0	0	3	0	1	0	2	0	5	0	4	2	4	3	3	2	4	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:116741113A>G	ENST00000292055.4	-	14	1603	c.1568T>C	c.(1567-1569)gTg>gCg	p.V523A	SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000375300.1_Missense_Mutation_p.V581A|SIK3_ENST00000542607.1_Missense_Mutation_p.V475A|SIK3_ENST00000446921.2_Missense_Mutation_p.V533A|SIK3_ENST00000434315.2_Missense_Mutation_p.V422A|SIK3_ENST00000488337.1_5'Flank	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	523					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						AACTGCTGGCACTGCCTGAAG	0.542											OREG0003489	type=REGULATORY REGION|Gene=BC063887|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V523A		.											.	SIK3-919	0			c.T1568C						.						76	67	70					11																	116741113		2201	4296	6497	SO:0001583	missense	23387	exon14			GCTGGCACTGCCT	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.1568T>C	11.37:g.116741113A>G	ENSP00000292055:p.Val523Ala	Somatic	88	0	1475	WXS	Illumina HiSeq	Phase_I	114	25	NM_025164	0	0	0	0	0	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.516700	0.64634	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.72615	-0.62;-0.65;-0.67;-0.23	5.79	4.66	0.58398	Protein kinase-like domain (1);	0.000000	0.36134	U	0.002766	T	0.66499	0.2795	L	0.29908	0.895	0.80722	D	1	D;P;P	0.53312	0.959;0.929;0.857	P;P;B	0.50192	0.634;0.48;0.396	T	0.68401	-0.5418	10	0.62326	D	0.03	.	11.844	0.52374	0.9311:0.0:0.0689:0.0	.	475;422;523	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	A	581;523;475;422	ENSP00000364449:V581A;ENSP00000292055:V523A;ENSP00000438108:V475A;ENSP00000415873:V422A	ENSP00000292055:V523A	V	-	2	0	SIK3	116246323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.658000	0.68003	1.011000	0.39340	0.482000	0.46254	GTG	.		0.542	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		G	116741113	A	G	116741113	3	3	21	1	0	0	0	0	1	0	0	0	14351	159	6	3	2263	3	SIK3	11	116741113	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	12002	116741113	18265403	99	1867											
USP5	8078	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	6974373	6974374	+	Frame_Shift_Del	DEL	TG	TG	-																															tcacatgggcacctctaccaTgtgtggtcactacgtctgcc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:6974373_6974374delTG	ENST00000229268.8	+	19	2496_2497	c.2444_2445delTG	c.(2443-2445)atgfs	p.M815fs	TPI1_ENST00000396705.5_5'Flank|TPI1_ENST00000229270.4_5'Flank|USP5_ENST00000389231.5_Frame_Shift_Del_p.M792fs|TPI1_ENST00000488464.2_5'Flank|TPI1_ENST00000535434.1_5'Flank	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	815	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						ACCTCTACCATGTGTGGTCACT	0.5																																					p.815_815del		.											.	USP5-659	0			c.2444_2445del						.																																			SO:0001589	frameshift_variant	8078	exon19			.	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.2444_2445delTG	12.37:g.6974377_6974378delTG	ENSP00000229268:p.Met815fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	182	32	NM_001098536	0	0	0	0	0	D3DUS7|D3DUS8|Q96J22	Frame_Shift_Del	DEL	ENST00000229268.8	37	CCDS41743.1																																																																																			.		0.5	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			-	6974374	TG	-	6974373	7	5	21	1	0	1	0	1	0	0	0	0	17114	1464	51	0	2518	0	USP5	12	6974373	Frame_Shift_Del	DEL	TG	TCGA-A4-A48D-01A-11D-A25F-10		6974373	126877522	100	1868											
ATF7IP	55729	broad.mit.edu;bcgsc.ca	37	chr12	14577475	14577475	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgatcccacctctagtgatcCcatcccaggtgaaccggtcc	8	9	8	16	1	1	3	0	3	1	0	5	3	5	3	6	2	1	0	6	2	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:14577475C>G	ENST00000540793.1	+	1	781	c.626C>G	c.(625-627)cCc>cGc	p.P209R	ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000544627.1_Missense_Mutation_p.P217R|ATF7IP_ENST00000536444.1_Missense_Mutation_p.P209R|ATF7IP_ENST00000261168.4_Missense_Mutation_p.P209R|ATF7IP_ENST00000543189.1_Missense_Mutation_p.P209R			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	209					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						TCTAGTGATCCCATCCCAGGT	0.522																																					p.P209R													.	ATF7IP-252	0			c.C626G						.						146	120	129					12																	14577475		2203	4300	6503	SO:0001583	missense	55729	exon2			GTGATCCCATCCC	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.626C>G	12.37:g.14577475C>G	ENSP00000444589:p.Pro209Arg	Somatic	360	0		WXS	Illumina HiSeq	Phase_I	411	14	NM_018179	0	0	6	6	0	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.501942	0.44455	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.22945	2.25;2.26;2.26;2.25;1.93;2.25	5.85	-1.72	0.08107	.	1.330470	0.05048	N	0.477590	T	0.16896	0.0406	L	0.36672	1.1	0.09310	N	1	P;P;B;B;B	0.45078	0.85;0.85;0.432;0.432;0.432	B;B;B;B;B	0.40285	0.325;0.325;0.165;0.165;0.246	T	0.10590	-1.0623	10	0.35671	T	0.21	6.3808	0.7923	0.01059	0.2337:0.3111:0.1143:0.3409	.	217;209;209;209;209	B4E2A2;B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;.;MCAF1_HUMAN;.	R	209;209;209;217;209;209	ENSP00000261168:P209R;ENSP00000443179:P209R;ENSP00000445955:P209R;ENSP00000440440:P217R;ENSP00000379575:P209R;ENSP00000444589:P209R	ENSP00000261168:P209R	P	+	2	0	ATF7IP	14468742	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.082000	0.11304	-0.541000	0.06257	-0.150000	0.13652	CCC	.		0.522	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		G	14577475	C	G	14577475	3	3	21	1	0	0	0	0	1	0	0	0	1088	623	22	4	628	4	ATF7IP	12	14577475	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	7603102	14577475	119274420	101	1869											
LRRK2	120892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	40713882	40713882	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctttcaaaaaaaaggaaAtttccaaagaactacatgtc	18	12	4	7	0	2	1	1	0	1	1	4	2	3	2	1	1	2	0	1	1	8	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:40713882A>T	ENST00000298910.7	+	34	4978	c.4920A>T	c.(4918-4920)aaA>aaT	p.K1640N		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1640					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AAAAAAGGAAATTTCCAAAGA	0.358											OREG0003827	type=REGULATORY REGION|Gene=LOC486608|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K1640N		.											.	LRRK2-533	0			c.A4920T						.						52	62	59					12																	40713882		2199	4296	6495	SO:0001583	missense	120892	exon34			AAGGAAATTTCCA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4920A>T	12.37:g.40713882A>T	ENSP00000298910:p.Lys1640Asn	Somatic	52	0	895	WXS	Illumina HiSeq	Phase_I	54	13	NM_198578	0	0	0	0	0	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.234808	0.39498	.	.	ENSG00000188906	ENST00000298910	T	0.71698	-0.59	5.55	4.4	0.53042	.	0.305891	0.37393	N	0.002104	T	0.52451	0.1735	L	0.27053	0.805	0.36820	D	0.886366	B;B	0.24823	0.112;0.005	B;B	0.15484	0.013;0.004	T	0.50233	-0.8852	10	0.17832	T	0.49	.	9.2446	0.37518	0.842:0.0:0.158:0.0	.	1640;1640	Q17RV3;Q5S007	.;LRRK2_HUMAN	N	1640	ENSP00000298910:K1640N	ENSP00000298910:K1640N	K	+	3	2	LRRK2	39000149	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	3.468000	0.53086	0.932000	0.37266	0.482000	0.46254	AAA	.		0.358	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40713882	A	T	40713882	3	4	21	1	0	0	0	0	1	0	0	0	9058	98	4	5	5054	5	LRRK2	12	40713882	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	26136407	40713882	93138013	102	1870											
LRRK2	120892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	40745358	40745358	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggtctttgacattttgaaTtcagctgaattagtctgtct	9	17	8	7	0	4	3	1	3	3	0	4	3	4	3	0	1	1	1	0	1	3	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:40745358T>A	ENST00000298910.7	+	44	6457	c.6399T>A	c.(6397-6399)aaT>aaA	p.N2133K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				ACATTTTGAATTCAGCTGAAT	0.343																																					p.N2133K		.											.	LRRK2-533	0			c.T6399A						.						48	48	48					12																	40745358		2203	4300	6503	SO:0001583	missense	120892	exon44			TTTGAATTCAGCT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6399T>A	12.37:g.40745358T>A	ENSP00000298910:p.Asn2133Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	56	6	NM_198578	0	0	18	24	6	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.514495	0.64522	.	.	ENSG00000188906	ENST00000298910	T	0.71817	-0.6	6.02	1.09	0.20402	Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53658	0.1810	N	0.21583	0.68	0.44492	D	0.997434	P;P	0.42692	0.476;0.787	B;B	0.40982	0.246;0.345	T	0.47947	-0.9077	10	0.41790	T	0.15	.	9.6792	0.40059	0.0:0.4062:0.0:0.5938	.	2133;2133	Q17RV3;Q5S007	.;LRRK2_HUMAN	K	2133	ENSP00000298910:N2133K	ENSP00000298910:N2133K	N	+	3	2	LRRK2	39031625	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	0.493000	0.22451	0.196000	0.20367	0.529000	0.55759	AAT	.		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		A	40745358	T	A	40745358	3	1	21	1	0	0	0	0	1	0	0	0	9058	1490	52	5	6573	5	LRRK2	12	40745358	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	31476	40745358	93106537	103	1871											
KRT79	338785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53225246	53225246	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgagctctgagtccagcctCccccgctcgctctgaagtct	5	10	9	17	2	3	3	0	3	3	0	6	3	5	3	4	0	2	3	4	0	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:53225246C>A	ENST00000330553.5	-	2	676	c.642G>T	c.(640-642)ggG>ggT	p.G214G		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	214	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGTCCAGCCTCCCCCGCTCGC	0.617																																					p.G214G		.											.	KRT79-72	0			c.G642T						.						114	114	114					12																	53225246		2203	4300	6503	SO:0001819	synonymous_variant	338785	exon2			CAGCCTCCCCCGC	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"-", "Intermediate filaments type II, keratins (basic)"	28930	protein-coding gene	gene with protein product	"keratin 6-like"	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.642G>T	12.37:g.53225246C>A		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	111	27	NM_175834	0	0	0	0	0	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	37	CCDS8839.1																																																																																			.		0.617	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		A	53225246	C	A	53225246	2	1	21	1	0	0	0	0	0	0	0	1	8513	842	30	4		4	KRT79	12	53225246	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	12479888	53225246	80626649	104	1872											
TIMELESS	8914	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	56827702	56827703	+	Frame_Shift_Ins	INS	-	-	CACG																															aaatagcggatcagatccttINScacgctctcttcagagacag																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:56827702_56827703insCACG	ENST00000553532.1	-	3	255_256	c.105_106insCGTG	c.(103-108)gtgaagfs	p.K36fs	TIMELESS_ENST00000229201.4_Frame_Shift_Ins_p.K36fs|TIMELESS_ENST00000554616.1_Frame_Shift_Ins_p.K36fs					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						ATCAGATCCTTCACGCTCTCTT	0.52																																					p.K36fs		.											.	TIMELESS-159	0			c.106_107insCGTG						.																																			SO:0001589	frameshift_variant	8914	exon3			.	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.102_105dupCGTG	12.37:g.56827703_56827706dupCACG	ENSP00000450607:p.Lys36fs	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	156	30	NM_003920	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000553532.1	37	CCDS8918.1																																																																																			.		0.52	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		CACG	56827703	-	CACG	56827702	7	5	21	1	0	1	1	0	0	0	0	0	15936	1792	62	0	3628	0	TIMELESS	12	56827702	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	3602456	56827702	77024193	105	1873											
GPR182	11318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57389791	57389791	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgtgcgcctacgtggccgtCtttgtcatgtgctggctgcc	2	13	13	13	3	2	0	1	0	1	0	2	0	2	0	3	2	4	2	3	2	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:57389791C>G	ENST00000300098.1	+	2	1017	c.798C>G	c.(796-798)gtC>gtG	p.V266V	RP11-474N8.5_ENST00000556850.1_RNA|HBCBP_ENST00000600202.1_5'Flank	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	266					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						ACGTGGCCGTCTTTGTCATGT	0.617																																					p.V266V		.											.	GPR182-500	0			c.C798G						.						168	145	153					12																	57389791		2203	4300	6503	SO:0001819	synonymous_variant	11318	exon2			GGCCGTCTTTGTC	Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"GPCR / Class A : Orphans"	13708	protein-coding gene	gene with protein product		605307	"adrenomedullin receptor"	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.798C>G	12.37:g.57389791C>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	67	18	NM_007264	0	0	0	0	0		Silent	SNP	ENST00000300098.1	37	CCDS8927.1																																																																																			.		0.617	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264		G	57389791	C	G	57389791	2	3	21	1	0	0	0	0	0	0	0	1	6697	900	32	4		4	GPR182	12	57389791	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	562089	57389791	76462104	106	1874											
KIF5A	3798	broad.mit.edu	37	chr12	57965901	57965901	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcgggagctgagccacctgCaatcagagaacgatgccgct	11	5	13	12	3	1	2	1	1	0	1	1	5	1	3	3	1	6	3	3	1	2	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:57965901C>T	ENST00000455537.2	+	14	1694	c.1420C>T	c.(1420-1422)Caa>Taa	p.Q474*	KIF5A_ENST00000286452.5_Nonsense_Mutation_p.Q385*	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	474					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						GAGCCACCTGCAATCAGAGAA	0.582																																					p.Q474X													.	KIF5A-517	0			c.C1420T						.						81	73	76					12																	57965901		2202	4300	6502	SO:0001587	stop_gained	3798	exon14			CACCTGCAATCAG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1420C>T	12.37:g.57965901C>T	ENSP00000408979:p.Gln474*	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	112	5	NM_004984	0	0	0	0	0	A6H8M5|Q4LE26	Nonsense_Mutation	SNP	ENST00000455537.2	37	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	C	40	8.293642	0.98747	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	17.4472	0.87581	0.0:1.0:0.0:0.0	.	.	.	.	X	474;385	.	ENSP00000286452:Q385X	Q	+	1	0	KIF5A	56252168	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.651000	0.83577	2.749000	0.94314	0.655000	0.94253	CAA	.		0.582	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57965901	C	T	57965901	4	4	21	1	0	0	0	0	0	1	0	0	8326	711	25	2	1474	2	KIF5A	12	57965901	Nonsense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	576110	57965901	75885994	107	1875											
TMEM132B	114795	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	126138829	126138830	+	In_Frame_Ins	INS	-	-	CAA																															tttgctgtgagtgagcagggINScaacatcccccattcccacg																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:126138829_126138830insCAA	ENST00000299308.3	+	9	2818_2819	c.2810_2811insCAA	c.(2809-2814)ggcaac>ggCAAcaac	p.938_939insN	TMEM132B_ENST00000535886.1_In_Frame_Ins_p.450_451insN	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	938						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		AGTGAGCAGGGCAACATCCCCC	0.51																																					p.G937delinsGN		.											.	TMEM132B-185	0			c.2810_2811insCAA						.																																			SO:0001652	inframe_insertion	114795	exon9			.	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2811_2813dupCAA	12.37:g.126138830_126138832dupCAA	ENSP00000299308:p.Asn938_Asn938dup	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	171	27	NM_052907	0	0	0	0	0	A2RRG8|Q8NA73|Q96JN9|Q96PY1	In_Frame_Ins	INS	ENST00000299308.3	37	CCDS41859.1																																																																																			.		0.51	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		CAA	126138830	-	CAA	126138829	7	5	21	1	0	1	1	0	0	0	0	0	16078	1203	42	0	2844	0	TMEM132B	12	126138829	In_Frame_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	68172928	126138829	7713066	108	1876											
IFT88	8100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	21163994	21163994	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagttactagacctatagcTactggatatggggtaggttt	10	13	12	6	0	0	1	0	0	0	1	0	2	0	2	1	4	3	5	1	4	7	8			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr13:21163994T>C	ENST00000319980.6	+	6	552	c.225T>C	c.(223-225)gcT>gcC	p.A75A	IFT88_ENST00000382778.4_Silent_p.A75A|IFT88_ENST00000351808.5_Silent_p.A66A|IFT88_ENST00000537103.1_Intron	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	75					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GACCTATAGCTACTGGATATG	0.328																																					p.A75A		.											.	IFT88-91	0			c.T225C						.						81	82	82					13																	21163994		2203	4299	6502	SO:0001819	synonymous_variant	8100	exon6			TATAGCTACTGGA	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.225T>C	13.37:g.21163994T>C		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	56	6	NM_175605	0	0	0	0	0	A2A491|B4DUS2|Q5SZJ6|Q8N719	Silent	SNP	ENST00000319980.6	37	CCDS31944.1																																																																																			.		0.328	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		C	21163994	T	C	21163994	2	2	21	1	0	0	0	0	0	0	0	1	7587	1509	53	3		3	IFT88	13	21163994	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		21163994	94005884	109	1877											
USP12	219333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	27664060	27664060	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgcgacactcttcacagtAatacttgtattcactgcaca	11	12	6	12	1	3	0	2	0	1	0	3	1	3	0	0	0	3	4	0	0	3	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr13:27664060A>T	ENST00000282344.6	-	6	950	c.694T>A	c.(694-696)Tac>Aac	p.Y232N		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	232	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		TCTTCACAGTAATACTTGTAT	0.338																																					p.Y232N	Ovarian(37;808 911 7590 44442 44991)	.											.	USP12-522	0			c.T694A						.						63	62	62					13																	27664060		2203	4300	6503	SO:0001583	missense	219333	exon6			CACAGTAATACTT	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"Ubiquitin-specific peptidases"	20485	protein-coding gene	gene with protein product			"ubiquitin specific protease 12 like 1", "ubiquitin specific protease 12"	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.694T>A	13.37:g.27664060A>T	ENSP00000282344:p.Tyr232Asn	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	115	39	NM_182488	0	0	1	2	1	A8K0X0|Q5VZV3|Q8TC49	Missense_Mutation	SNP	ENST00000282344.6	37	CCDS31952.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459009	0.84317	.	.	ENSG00000152484	ENST00000282344	T	0.05649	3.41	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.16085	0.0387	L	0.42686	1.345	0.80722	D	1	D	0.57571	0.98	P	0.60541	0.876	T	0.00575	-1.1663	10	0.49607	T	0.09	-15.958	15.4004	0.74834	1.0:0.0:0.0:0.0	.	232	O75317	UBP12_HUMAN	N	232	ENSP00000282344:Y232N	ENSP00000282344:Y232N	Y	-	1	0	USP12	26562060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.803000	0.91915	2.113000	0.64589	0.482000	0.46254	TAC	.		0.338	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		T	27664060	A	T	27664060	3	4	21	1	0	0	0	0	1	0	0	0	17076	362	13	5	434	5	USP12	13	27664060	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	6500066	27664060	87505818	110	1878											
DIAPH3	81624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	60686191	60686191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcattctctgacagtggctTtggaaagttctccatcatct	8	16	7	10	0	5	1	2	1	3	0	7	2	5	2	1	2	0	2	1	2	1	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr13:60686191T>C	ENST00000400324.4	-	3	563	c.343A>G	c.(343-345)Aag>Gag	p.K115E	DIAPH3_ENST00000377908.2_Missense_Mutation_p.K104E|DIAPH3_ENST00000267215.4_Missense_Mutation_p.K115E|DIAPH3_ENST00000400319.1_Intron|DIAPH3_ENST00000400330.1_Missense_Mutation_p.K115E|DIAPH3_ENST00000400320.1_Missense_Mutation_p.K104E	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	115	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GACAGTGGCTTTGGAAAGTTC	0.403																																					p.K115E		.											.	DIAPH3-516	0			c.A343G						.						162	151	154					13																	60686191		1840	4095	5935	SO:0001583	missense	81624	exon3			GTGGCTTTGGAAA	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.343A>G	13.37:g.60686191T>C	ENSP00000383178:p.Lys115Glu	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	88	21	NM_001042517	0	0	0	0	0	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	T	6.162	0.398114	0.11696	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000377908;ENST00000400320;ENST00000267215;ENST00000453990	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-1.93;-2.52	5.82	5.82	0.92795	GTPase-binding/formin homology 3 (1);Diaphanous GTPase-binding (1);	0.059630	0.64402	D	0.000004	D	0.82467	0.5043	N	0.25647	0.755	0.33949	D	0.644161	P;P;P	0.50819	0.704;0.485;0.939	B;B;P	0.45753	0.084;0.266;0.492	T	0.82212	-0.0569	10	0.02654	T	1	.	15.1658	0.72825	0.0:0.0:0.0:1.0	.	104;104;115	C9JL55;C9JDG1;Q9NSV4	.;.;DIAP3_HUMAN	E	115;115;104;104;104;104;115;115	ENSP00000383178:K115E;ENSP00000383184:K115E;ENSP00000367141:K104E;ENSP00000383174:K104E;ENSP00000267215:K115E	ENSP00000267215:K115E	K	-	1	0	DIAPH3	59584192	1.000000	0.71417	0.998000	0.56505	0.220000	0.24768	4.210000	0.58500	2.228000	0.72767	0.533000	0.62120	AAG	.		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		C	60686191	T	C	60686191	3	2	21	1	0	0	0	0	1	0	0	0	4531	1850	64	3	3362	3	DIAPH3	13	60686191	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	33022131	60686191	54483687	111	1879											
JUB	84962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23444254	23444254	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggatgccatccaggcacttGttgcaaacaatgcatcggaa	12	8	11	10	1	0	0	0	0	0	0	2	2	1	2	2	3	4	4	2	3	3	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr14:23444254G>A	ENST00000262713.2	-	5	1674	c.1299C>T	c.(1297-1299)aaC>aaT	p.N433N	AJUBA_ENST00000361265.4_Silent_p.N433N|RP11-298I3.5_ENST00000555074.1_Intron|AJUBA_ENST00000397388.3_Silent_p.N16N	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	433	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										CCAGGCACTTGTTGCAAACAA	0.522																																					p.N433N		.											.	.	0			c.C1299T						.						149	136	141					14																	23444254		2203	4300	6503	SO:0001819	synonymous_variant	84962	exon5			GCACTTGTTGCAA	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"jub, ajuba homolog (Xenopus laevis)"	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.1299C>T	14.37:g.23444254G>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	75	23	NM_032876	0	0	2	7	5	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	37	CCDS9581.1																																																																																			.		0.522	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2			A	23444254	G	A	23444254	2	1	21	1	0	0	0	0	0	0	0	1	7989	1368	48	2		2	JUB	14	23444254	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		23444254	83905286	112	1880											
SAV1	60485	broad.mit.edu	37	chr14	51132275	51132275	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggcattagggcttgaatctgGaagacagatatcagttcgtc	11	11	12	7	1	2	3	1	1	1	2	4	4	2	4	0	3	0	3	0	3	4	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr14:51132275G>A	ENST00000324679.4	-	2	520	c.157C>T	c.(157-159)Cca>Tca	p.P53S	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	53					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					CTTGAATCTGGAAGACAGATA	0.368																																					p.P53S													.	SAV1-658	0			c.C157T						.						40	40	40					14																	51132275		2203	4299	6502	SO:0001583	missense	60485	exon2			AATCTGGAAGACA	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.157C>T	14.37:g.51132275G>A	ENSP00000324729:p.Pro53Ser	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	164	4	NM_021818	0	0	6	6	0	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Missense_Mutation	SNP	ENST00000324679.4	37	CCDS9701.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315813	0.60524	.	.	ENSG00000151748	ENST00000324679;ENST00000535862	T	0.40756	1.02	5.14	5.14	0.70334	.	0.052841	0.85682	D	0.000000	T	0.31575	0.0801	L	0.34521	1.04	0.80722	D	1	P	0.37781	0.608	B	0.30401	0.115	T	0.08554	-1.0716	10	0.28530	T	0.3	-3.0154	17.5884	0.87989	0.0:0.0:1.0:0.0	.	53	Q9H4B6	SAV1_HUMAN	S	53;20	ENSP00000324729:P53S	ENSP00000324729:P53S	P	-	1	0	SAV1	50202025	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.405000	0.97313	2.397000	0.81536	0.563000	0.77884	CCA	.		0.368	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			A	51132275	G	A	51132275	3	1	21	1	0	0	0	0	1	0	0	0	13888	1174	41	2	1010	2	SAV1	14	51132275	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	27688021	51132275	56217265	113	1881											
C14orf102	55051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	90769186	90769186	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttttgatatcgaaaaggtaCtaaactggctctggcaaaat	14	13	8	6	1	1	1	0	1	1	0	2	2	1	1	0	3	2	3	0	3	8	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr14:90769186C>T	ENST00000354366.3	-	6	1521	c.1289G>A	c.(1288-1290)aGt>aAt	p.S430N	NRDE2_ENST00000357904.3_Missense_Mutation_p.S199N	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	430																	CGAAAAGGTACTAAACTGGCT	0.423																																					p.S430N		.											.	.	0			c.G1289A						.						69	72	71					14																	90769186		2203	4300	6503	SO:0001583	missense	55051	exon6			AAGGTACTAAACT	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.1289G>A	14.37:g.90769186C>T	ENSP00000346335:p.Ser430Asn	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	97	16	NM_017970	0	0	2	3	1	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	37	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364312	0.82463	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.35973	1.69;1.28	5.51	5.51	0.81932	Domain of unknown function DUF1740 (1);	0.041947	0.85682	D	0.000000	T	0.55986	0.1955	M	0.69185	2.1	0.53005	D	0.999965	D	0.61697	0.99	D	0.63381	0.914	T	0.52124	-0.8617	10	0.38643	T	0.18	-16.8351	16.4406	0.83900	0.0:0.8691:0.1309:0.0	.	430	Q9H7Z3	CN102_HUMAN	N	430;199	ENSP00000346335:S430N;ENSP00000350579:S199N	ENSP00000346335:S430N	S	-	2	0	C14orf102	89838939	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.785000	0.68998	2.586000	0.87340	0.650000	0.86243	AGT	.		0.423	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		T	90769186	C	T	90769186	3	4	21	1	0	0	0	0	1	0	0	0	1739	565	20	2	2241	2	C14orf102	14	90769186	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	39636911	90769186	16580354	114	1882											
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	39886356	39886356	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggaaagatttcaccgcctaCagatggcgtctcagccacag	11	8	10	12	2	2	2	2	0	1	2	3	3	2	3	3	2	2	0	3	2	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr15:39886356C>A	ENST00000260356.5	+	20	3489	c.3324C>A	c.(3322-3324)taC>taA	p.Y1108*	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1108	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TCACCGCCTACAGATGGCGTC	0.478																																					p.Y1108X		.											.	THBS1-653	0			c.C3324A						.						63	61	62					15																	39886356		2200	4297	6497	SO:0001587	stop_gained	7057	exon20			CGCCTACAGATGG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3324C>A	15.37:g.39886356C>A	ENSP00000260356:p.Tyr1108*	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	194	47	NM_003246	0	0	2	2	0	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Nonsense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	44	10.984739	0.99499	.	.	ENSG00000137801	ENST00000260356	.	.	.	5.83	4.92	0.64577	.	0.000000	0.32852	N	0.005571	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.5548	14.6654	0.68904	0.0:0.9305:0.0:0.0695	.	.	.	.	X	1108	.	ENSP00000260356:Y1108X	Y	+	3	2	THBS1	37673648	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.078000	0.57606	1.468000	0.48064	0.655000	0.94253	TAC	.		0.478	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39886356	C	A	39886356	4	1	21	1	0	0	0	0	0	1	0	0	15885	489	17	4	3398	4	THBS1	15	39886356	Nonsense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		39886356	62645036	115	1883											
MYO9A	4649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72190908	72190908	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggagactgaaggccttcAggcaccaattctgtagacca	11	8	11	11	1	2	3	1	1	1	2	2	4	2	3	3	3	0	2	3	3	3	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr15:72190908A>G	ENST00000356056.5	-	25	4408	c.3936T>C	c.(3934-3936)ccT>ccC	p.P1312P	MYO9A_ENST00000444904.1_Silent_p.P1293P|MYO9A_ENST00000564571.1_Silent_p.P1312P|MYO9A_ENST00000424560.1_Silent_p.P1312P|MYO9A_ENST00000566885.1_Silent_p.P932P|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1312	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GAAGGCCTTCAGGCACCAATT	0.453																																					p.P1312P		.											.	MYO9A-93	0			c.T3936C						.						113	113	113					15																	72190908		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon25			GCCTTCAGGCACC	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.3936T>C	15.37:g.72190908A>G		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	120	41	NM_006901	0	0	0	0	0	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	37	CCDS10239.1																																																																																			.		0.453	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72190908	A	G	72190908	2	3	21	1	0	0	0	0	0	0	0	1	10109	175	7	3		3	MYO9A	15	72190908	Silent	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	32304552	72190908	30340484	116	1884											
CLK3	1198	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	74912367	74912371	+	Frame_Shift_Del	DEL	ACCAG	ACCAG	-																															cagccatgaccgcctgccctAccagaggaggtaccgggagc																								rs373663118|rs371419854		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	ACCAG	ACCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr15:74912367_74912371delACCAG	ENST00000395066.3	+	3	1075_1079	c.614_618delACCAG	c.(613-618)taccagfs	p.YQ205fs	CLK3_ENST00000352989.5_Frame_Shift_Del_p.YQ57fs|CLK3_ENST00000348245.3_Frame_Shift_Del_p.YQ57fs|CLK3_ENST00000345005.4_Frame_Shift_Del_p.YQ57fs	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3	205	Arg-rich.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CGCCTGCCCTACCAGAGGAGGTACC	0.58																																					p.205_206del	Ovarian(133;694 1754 28950 29027 31859)	.											.	CLK3-358	0			c.614_618del						.																																			SO:0001589	frameshift_variant	1198	exon3			.	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.614_618delACCAG	15.37:g.74912367_74912371delACCAG	ENSP00000378505:p.Tyr205fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	176	41	NM_001130028	0	0	0	0	0	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Frame_Shift_Del	DEL	ENST00000395066.3	37	CCDS45304.1																																																																																			.		0.58	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3			-	74912371	ACCAG	-	74912367	7	5	21	1	0	1	0	1	0	0	0	0	3544	391	14	0	624	0	CLK3	15	74912367	Frame_Shift_Del	DEL	ACCAG	TCGA-A4-A48D-01A-11D-A25F-10	2721459	74912367	27619025	117	1885											
NUBP2	3483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1837701	1837701	+	IGR	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgataaagcagtttgtgtccGacgtggcctggggggagctg	7	10	17	7	2	0	1	0	1	0	0	1	3	1	2	2	4	2	3	2	4	2	2	rs533118487		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:1837701G>T	ENST00000215539.3	-	0	2116				NUBP2_ENST00000565134.1_Missense_Mutation_p.D120Y|NUBP2_ENST00000543305.1_5'UTR|NUBP2_ENST00000568706.1_5'UTR|NUBP2_ENST00000262302.9_Missense_Mutation_p.D120Y|NUBP2_ENST00000565987.1_Missense_Mutation_p.D60Y			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						GTTTGTGTCCGACGTGGCCTG	0.662																																					p.D120Y		.											.	NUBP2-90	0			c.G358T						.						80	83	82					16																	1837701		2199	4300	6499	SO:0001628	intergenic_variant	10101	exon4			GTGTCCGACGTGG	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638		16.37:g.1837701G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	105	33	NM_012225	0	1	47	80	32	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468399	0.84533	.	.	ENSG00000095906	ENST00000262302	T	0.42131	0.98	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.70885	0.3275	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79500	-0.1778	10	0.87932	D	0	-5.4419	15.1837	0.72982	0.0:0.0:1.0:0.0	.	120	Q9Y5Y2	NUBP2_HUMAN	Y	120	ENSP00000262302:D120Y	ENSP00000262302:D120Y	D	+	1	0	NUBP2	1777702	1.000000	0.71417	0.736000	0.30914	0.976000	0.68499	6.078000	0.71282	2.167000	0.68274	0.561000	0.74099	GAC	.		0.662	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			T	1837701	G	T	1837701	1	4	21	0	1	0	0	0	0	0	0	0	10742	1058	37	4		4	NUBP2	16	1837701	IGR	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		1837701	88517052	118	1886											
OR1F1	4992	broad.mit.edu	37	chr16	3254884	3254884	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgatcaccccatttctttGcatcctggcttcttatatgc	7	16	5	13	0	3	1	1	1	2	0	4	1	4	1	3	1	2	2	3	1	2	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:3254884G>T	ENST00000304646.2	+	1	638	c.638G>T	c.(637-639)tGc>tTc	p.C213F	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	213					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						CCATTTCTTTGCATCCTGGCT	0.512																																					p.C213F													.	OR1F1-68	0			c.G638T						.						184	157	166					16																	3254884		2197	4300	6497	SO:0001583	missense	4992	exon1			TTCTTTGCATCCT	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"GPCR / Class A : Olfactory receptors"	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.638G>T	16.37:g.3254884G>T	ENSP00000305424:p.Cys213Phe	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	321	8	NM_012360	0	0	1	1	0	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	.	.	.	.	.	.	.	.	.	.	G	8.341	0.828811	0.16749	.	.	ENSG00000168124	ENST00000304646	T	0.36157	1.27	5.06	4.11	0.48088	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000007	T	0.25901	0.0631	N	0.20530	0.585	0.34276	D	0.681611	B	0.21905	0.062	B	0.34418	0.182	T	0.29579	-1.0007	10	0.54805	T	0.06	.	6.4906	0.22113	0.094:0.0:0.727:0.179	.	213	O43749	OR1F1_HUMAN	F	213	ENSP00000305424:C213F	ENSP00000305424:C213F	C	+	2	0	OR1F1	3194885	0.028000	0.19301	0.901000	0.35422	0.473000	0.32948	2.234000	0.43035	1.119000	0.41883	0.393000	0.25936	TGC	.		0.512	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1			T	3254884	G	T	3254884	3	4	21	1	0	0	0	0	1	0	0	0	10982	1319	46	4	640	4	OR1F1	16	3254884	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	1417183	3254884	87099869	119	1887											
HMOX2	3163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4557884	4557884	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaaactgggaggagcaggtGcagtgccccaaggctgccca	11	4	15	11	0	0	0	0	0	0	0	0	3	0	2	3	4	5	3	3	4	3	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:4557884G>T	ENST00000570646.1	+	4	980	c.375G>T	c.(373-375)gtG>gtT	p.V125V	HMOX2_ENST00000219700.6_Silent_p.V125V|HMOX2_ENST00000575120.1_Silent_p.V96V|HMOX2_ENST00000458134.3_Silent_p.V125V|HMOX2_ENST00000406590.2_Silent_p.V125V|HMOX2_ENST00000398595.3_Silent_p.V125V|HMOX2_ENST00000414777.1_Silent_p.V125V	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	125					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						AGGAGCAGGTGCAGTGCCCCA	0.582																																					p.V125V		.											.	HMOX2-90	0			c.G375T						.						59	55	57					16																	4557884		2197	4300	6497	SO:0001819	synonymous_variant	3163	exon4			GCAGGTGCAGTGC		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.375G>T	16.37:g.4557884G>T		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	254	39	NM_001127205	0	0	89	112	23	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	37	CCDS10517.1																																																																																			.		0.582	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			T	4557884	G	T	4557884	2	4	21	1	0	0	0	0	0	0	0	1	7265	1306	46	4		4	HMOX2	16	4557884	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	1303000	4557884	85796869	120	1888											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	18861438	18861438	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcctagggtcatcctcaTctaaaggaatctaagagtga	13	9	10	9	0	4	2	2	1	2	1	5	3	5	3	2	2	1	1	2	2	5	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:18861438T>C	ENST00000446231.2	-	35	5706	c.5294A>G	c.(5293-5295)gAt>gGt	p.D1765G	SMG1_ENST00000389467.3_Missense_Mutation_p.D1765G			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1765	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GTCATCCTCATCTAAAGGAAT	0.388																																					p.D1765G		.											.	SMG1-1160	0			c.A5294G						.						64	62	63					16																	18861438		1955	4154	6109	SO:0001583	missense	23049	exon35			TCCTCATCTAAAG	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.5294A>G	16.37:g.18861438T>C	ENSP00000402515:p.Asp1765Gly	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	298	99	NM_015092	0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.398251	0.62177	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.68479	-0.33;-0.33	5.83	5.83	0.93111	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.68265	0.2982	N	0.14661	0.345	0.50313	D	0.999861	D;D	0.67145	0.996;0.993	D;D	0.74674	0.981;0.984	T	0.68187	-0.5475	10	0.27785	T	0.31	.	16.1982	0.82046	0.0:0.0:0.0:1.0	.	1625;1765	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	G	1765	ENSP00000402515:D1765G;ENSP00000374118:D1765G	ENSP00000374118:D1765G	D	-	2	0	SMG1	18768939	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	5.891000	0.69782	2.226000	0.72624	0.533000	0.62120	GAT	.		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18861438	T	C	18861438	3	2	21	1	0	0	0	0	1	0	0	0	14827	1435	50	3	5807	3	SMG1	16	18861438	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	14303554	18861438	71493315	121	1889											
ACSM2B	348158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20559488	20559488	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccctccagcgaggcagttctGtagatgggggaacttgtaac	9	9	13	10	1	1	1	0	0	1	1	2	3	2	2	2	3	3	4	2	3	3	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:20559488G>A	ENST00000329697.6	-	8	1162	c.994C>T	c.(994-996)Cag>Tag	p.Q332*	ACSM2B_ENST00000567001.1_Nonsense_Mutation_p.Q332*|ACSM2B_ENST00000565232.1_Nonsense_Mutation_p.Q332*|ACSM2B_ENST00000567288.1_5'UTR|ACSM2B_ENST00000565322.1_Nonsense_Mutation_p.Q253*	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	332					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						AGGCAGTTCTGTAGATGGGGG	0.522																																					p.Q332X		.											.	ACSM2B-94	0			c.C994T						.						118	124	122					16																	20559488		2201	4300	6501	SO:0001587	stop_gained	348158	exon9			AGTTCTGTAGATG	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"Acyl-CoA synthetase family"	30931	protein-coding gene	gene with protein product	"xenobiotic/medium chain fatty acid:CoA ligase"	614359	"acyl-CoA synthetase medium-chain family member 2"	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.994C>T	16.37:g.20559488G>A	ENSP00000327453:p.Gln332*	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	146	39	NM_182617	1	0	181	196	14	Q86YT1	Nonsense_Mutation	SNP	ENST00000329697.6	37	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	G	31	5.065183	0.93898	.	.	ENSG00000066813	ENST00000329697	.	.	.	3.37	-1.99	0.07457	.	1.249910	0.05709	N	0.595506	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-0.7319	14.1154	0.65149	0.0:0.0:0.2719:0.7281	.	.	.	.	X	332	.	ENSP00000327453:Q332X	Q	-	1	0	ACSM2B	20466989	0.000000	0.05858	0.015000	0.15790	0.297000	0.27493	-0.804000	0.04535	-0.475000	0.06852	-0.407000	0.06327	CAG	.		0.522	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617		A	20559488	G	A	20559488	4	1	21	1	0	0	0	0	0	1	0	0	184	1386	48	2	767	2	ACSM2B	16	20559488	Nonsense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	1698050	20559488	69795265	122	1890											
LOC100132247	100132247	broad.mit.edu	37	chr16	22545744	22545755	+	In_Frame_Del	DEL	TCCACCCTCAGC	TCCACCCTCAGC	-																															gagcgtcagctcactcccctTccaccctcagctccaccctc																								rs373344256		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TCCACCCTCAGC	TCCACCCTCAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:22545744_22545755delTCCACCCTCAGC	ENST00000517539.1	+	8	1515_1526	c.1440_1451delTCCACCCTCAGC	c.(1438-1452)cttccaccctcagct>ctt	p.PPSA485del	NPIPB5_ENST00000424340.1_In_Frame_Del_p.PPSA485del|NPIPB5_ENST00000415654.1_3'UTR			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	485	Pro-rich.					integral component of membrane (GO:0016021)											TCACTCCCCTTCCACCCTCAGCTCCACCCTCA	0.571																																					p.480_484del													.	.	0			c.1440_1451del						.			15,1619		1,13,803							0			1	14,2538		3,8,1265	no	coding	LOC100132247	NM_001135865.1		4,21,2068	A1A1,A1R,RR		0.5486,0.918,0.6928				29,4157				SO:0001651	inframe_deletion	0	exon7			TCCCCTTCCACCC		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1440_1451delTCCACCCTCAGC	16.37:g.22545744_22545755delTCCACCCTCAGC	ENSP00000430633:p.Pro485_Ala488del	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	74	20	NM_001135865	0	0	0	0	0	B4DK13	In_Frame_Del	DEL	ENST00000517539.1	37	CCDS45443.1																																																																																			.		0.571	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374343.2	NM_001135865		-	22545755	TCCACCCTCAGC	-	22545744	7	5	21	1	0	1	0	1	0	0	0	0	8891	1770	62	0	1466	0	LOC100132247	16	22545744	In_Frame_Del	DEL	TCCACCCTCAGC	TCGA-A4-A48D-01A-11D-A25F-10	1986256	22545744	67809009	123	1891											
SLC7A6OS	84138	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	68338097	68338097	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaatcgctcacggatcaaCtctacagaattgcagaggat	13	9	9	10	2	4	2	3	0	1	2	5	4	4	4	0	2	3	2	0	2	4	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:68338097C>G	ENST00000263997.6	-	3	528	c.510G>C	c.(508-510)gaG>gaC	p.E170D		NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	170					hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		CACGGATCAACTCTACAGAAT	0.458																																					p.E170D													.	SLC7A6OS-91	0			c.G510C						.						160	150	153					16																	68338097		2198	4300	6498	SO:0001583	missense	84138	exon3			GATCAACTCTACA		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.510G>C	16.37:g.68338097C>G	ENSP00000263997:p.Glu170Asp	Somatic	208	1		WXS	Illumina HiSeq	Phase_I	300	101	NM_032178	0	0	4	7	3	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	37	CCDS10865.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156070	0.78114	.	.	ENSG00000103061	ENST00000263997	T	0.19105	2.17	5.72	3.74	0.42951	.	0.190127	0.53938	D	0.000045	T	0.22244	0.0536	M	0.64997	1.995	0.35818	D	0.824418	P	0.35272	0.493	B	0.36845	0.234	T	0.18116	-1.0347	10	0.49607	T	0.09	-16.8805	8.1366	0.31058	0.0:0.7519:0.0:0.2481	.	170	Q96CW6	S7A6O_HUMAN	D	170	ENSP00000263997:E170D	ENSP00000263997:E170D	E	-	3	2	SLC7A6OS	66895598	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	2.762000	0.47597	0.754000	0.32968	0.505000	0.49811	GAG	.		0.458	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178		G	68338097	C	G	68338097	3	3	21	1	0	0	0	0	1	0	0	0	14734	564	20	4	431	4	SLC7A6OS	16	68338097	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	45792353	68338097	22016656	124	1892											
KLHDC4	54758	broad.mit.edu	37	chr16	87764193	87764193	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagccaccaaacaggatcaaTtgtctcttccaggccaccat	13	8	6	14	0	2	0	1	0	1	0	4	1	3	1	5	2	2	0	5	2	3	2	rs191241806		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:87764193T>C	ENST00000270583.5	-	6	622	c.564A>G	c.(562-564)caA>caG	p.Q188Q	KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Silent_p.Q131Q|KLHDC4_ENST00000347925.5_Intron	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	188										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		ACAGGATCAATTGTCTCTTCC	0.428													T|||	1	0.000199681	8e-04	0	5008	,	,		18118	0		0	False		,,,				2504	0				p.Q188Q													.	KLHDC4-182	0			c.A564G						.	T	,,	1,4395	2.1+/-5.4	0,1,2197	148	128	134		393,,564	-5	0	16		134	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous	KLHDC4	NM_001184854.1,NM_001184856.1,NM_017566.3	,,	0,1,6497	CC,CT,TT		0.0,0.0227,0.0077	,,	131/464,,188/521	87764193	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	54758	exon6			GATCAATTGTCTC	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.564A>G	16.37:g.87764193T>C		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	159	3	NM_017566	0	0	29	29	0	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Silent	SNP	ENST00000270583.5	37	CCDS10963.1																																																																																			T|0.999;C|0.000		0.428	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		C	87764193	T	C	87764193	2	2	21	1	0	0	0	0	0	0	0	1	8379	1490	52	3		3	KLHDC4	16	87764193	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	19426096	87764193	2590560	125	1893											
BANP	54971	hgsc.bcm.edu	37	chr16	88105728	88105728	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctcggaccccgcggcggcGggcgtggatgggtcgccact	3	6	17	15	7	0	0	0	0	0	0	3	2	1	2	4	6	0	0	4	6	0	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:88105728G>A	ENST00000393207.1	+	13	1619	c.1398G>A	c.(1396-1398)gcG>gcA	p.A466A	BANP_ENST00000355022.4_Silent_p.A416A|BANP_ENST00000538234.1_Silent_p.A455A|BANP_ENST00000393208.2_Silent_p.A438A|BANP_ENST00000355163.5_Silent_p.A444A|BANP_ENST00000479780.2_Silent_p.A413A|BANP_ENST00000286122.7_Silent_p.A466A|BANP_ENST00000481948.1_3'UTR	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	466					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		CCGCGGCGGCGGGCGTGGATG	0.711																																					p.A466A		.											.	BANP-226	0			c.G1398A						.						13	15	14					16																	88105728		2187	4283	6470	SO:0001819	synonymous_variant	54971	exon13			GGCGGCGGGCGTG	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.1398G>A	16.37:g.88105728G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	7	6	NM_001173543	0	0	5	7	2	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			.		0.711	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		A	88105728	G	A	88105728	2	1	21	1	0	0	0	0	0	0	0	1	1311	1103	39	1		1	BANP	16	88105728	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	341535	88105728	2249025	126	1894											
SMCR8	140775	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18226353	18226353	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccccatgctcaggtttgActatgtccccagctttttgt	6	14	7	14	0	1	1	1	1	0	0	2	1	2	1	5	1	2	3	5	1	1	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr17:18226353A>T	ENST00000406438.3	+	2	3263	c.2783A>T	c.(2782-2784)gAc>gTc	p.D928V	RP1-178F10.3_ENST00000577764.1_lincRNA	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	928						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CTCAGGTTTGACTATGTCCCC	0.547																																					p.D928V													.	SMCR8-91	0			c.A2783T						.						62	61	61					17																	18226353		1930	4148	6078	SO:0001583	missense	140775	exon2			GGTTTGACTATGT	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2783A>T	17.37:g.18226353A>T	ENSP00000385025:p.Asp928Val	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	200	43	NM_144775	0	0	1	2	1	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	A	19.81	3.896068	0.72639	.	.	ENSG00000176994	ENST00000406438	T	0.27890	1.64	5.37	5.37	0.77165	.	0.152719	0.41823	U	0.000810	T	0.46054	0.1373	L	0.47716	1.5	0.80722	D	1	D	0.71674	0.998	P	0.60682	0.878	T	0.44682	-0.9312	10	0.87932	D	0	-21.3723	15.3395	0.74284	1.0:0.0:0.0:0.0	.	928	Q8TEV9	SMCR8_HUMAN	V	928	ENSP00000385025:D928V	ENSP00000385025:D928V	D	+	2	0	SMCR8	18167078	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.156000	0.50708	2.171000	0.68590	0.460000	0.39030	GAC	.		0.547	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		T	18226353	A	T	18226353	3	4	21	1	0	0	0	0	1	0	0	0	14824	275	10	5	2789	5	SMCR8	17	18226353	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		18226353	62968857	127	1895											
C17orf37	84299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37886504	37886504	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactgctccttcacagcacTggccagctccaggtaggtcg	8	9	10	14	1	1	0	1	0	0	0	4	0	3	0	3	3	4	4	3	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr17:37886504T>C	ENST00000394231.3	-	2	421	c.130A>G	c.(130-132)Agt>Ggt	p.S44G	ERBB2_ENST00000584888.1_3'UTR|MIEN1_ENST00000577810.1_Missense_Mutation_p.S44G|MIEN1_ENST00000474210.1_Intron			Q9BRT3	MIEN1_HUMAN	migration and invasion enhancer 1	44					apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell migration (GO:0030335)|positive regulation of filopodium assembly (GO:0051491)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	selenium binding (GO:0008430)										TTCACAGCACTGGCCAGCTCC	0.657											OREG0024383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S44G		.											.	.	0			c.A130G						.						28	31	30					17																	37886504		2202	4300	6502	SO:0001583	missense	84299	exon2			CAGCACTGGCCAG	AJ308025	CCDS11344.1	17q12	2011-09-21	2011-09-21	2011-09-21	ENSG00000141741	ENSG00000141741			28230	protein-coding gene	gene with protein product		611802	"chromosome 17 open reading frame 37"	C17orf37		17121940, 12739007, 17503775, 21628459	Standard	NM_032339		Approved	MGC14832, ORB3, XTP4, C35, Rdx12	uc002hsq.3	Q9BRT3	OTTHUMG00000133252	ENST00000394231.3:c.130A>G	17.37:g.37886504T>C	ENSP00000377778:p.Ser44Gly	Somatic	59	0	874	WXS	Illumina HiSeq	Phase_I	64	18	NM_032339	0	1	39	61	21		Missense_Mutation	SNP	ENST00000394231.3	37	CCDS11344.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.505978	0.64410	.	.	ENSG00000141741	ENST00000394231	T	0.43688	0.94	4.91	4.91	0.64330	.	0.105490	0.64402	D	0.000008	T	0.34948	0.0915	L	0.39898	1.24	0.38895	D	0.957206	B	0.26935	0.164	B	0.22880	0.042	T	0.27773	-1.0064	10	0.48119	T	0.1	-18.1594	13.6518	0.62314	0.0:0.0:0.0:1.0	.	44	Q9BRT3	MIEN1_HUMAN	G	44	ENSP00000377778:S44G	ENSP00000377778:S44G	S	-	1	0	C17orf37	35140030	1.000000	0.71417	0.993000	0.49108	0.973000	0.67179	5.252000	0.65445	2.069000	0.61940	0.402000	0.26972	AGT	.		0.657	MIEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257020.3	NM_032339		C	37886504	T	C	37886504	3	2	21	1	0	0	0	0	1	0	0	0	1859	1580	55	3	229	3	C17orf37	17	37886504	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	19660151	37886504	43308706	128	1896											
AKAP1	8165	broad.mit.edu	37	chr17	55183277	55183277	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tctagagtgccccctttcatCcccaaagggtgtactattct	8	13	7	13	0	3	1	1	0	2	1	4	1	4	1	4	1	2	1	4	1	4	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr17:55183277C>T	ENST00000337714.3	+	2	685	c.452C>T	c.(451-453)tCc>tTc	p.S151F	AKAP1_ENST00000539273.1_Missense_Mutation_p.S151F|AKAP1_ENST00000572557.1_Missense_Mutation_p.S151F|AKAP1_ENST00000571629.1_Missense_Mutation_p.S151F|AKAP1_ENST00000314126.3_Missense_Mutation_p.S151F	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	151					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					CCCCTTTCATCCCCAAAGGGT	0.537																																					p.S151F													.	AKAP1-227	0			c.C452T						.						87	89	89					17																	55183277		2203	4300	6503	SO:0001583	missense	8165	exon3			TTTCATCCCCAAA	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Tudor domain containing"	367	protein-coding gene	gene with protein product	"protein kinase anchoring protein 1", "dual specificity A-kinase-anchoring protein 1", "protein phosphatase 1, regulatory subunit 43", "tudor domain containing 17"	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.452C>T	17.37:g.55183277C>T	ENSP00000337736:p.Ser151Phe	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	135	3	NM_001242902	0	0	8	8	0	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.767508	0.49574	.	.	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.17370	2.28;2.28;2.28	5.91	2.77	0.32553	.	1.150570	0.06086	N	0.662796	T	0.15696	0.0378	L	0.44542	1.39	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33266	-0.9875	10	0.54805	T	0.06	-0.4379	3.9811	0.09495	0.1674:0.5686:0.0:0.264	.	151	Q92667	AKAP1_HUMAN	F	151;151;193;151	ENSP00000337736:S151F;ENSP00000314075:S151F;ENSP00000443139:S151F	ENSP00000314075:S151F	S	+	2	0	AKAP1	52538276	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	0.616000	0.24344	0.357000	0.24183	0.655000	0.94253	TCC	.		0.537	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			T	55183277	C	T	55183277	3	4	21	1	0	0	0	0	1	0	0	0	445	855	30	2	454	2	AKAP1	17	55183277	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	17296773	55183277	26011933	129	1897											
SMCHD1	23347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2703754	2703754	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactgtcatgagaagtatgAtaaacaaataaaatttacac	19	10	7	5	0	1	2	1	2	0	1	1	4	1	3	0	1	2	1	0	1	8	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr18:2703754A>C	ENST00000320876.6	+	13	2050	c.1712A>C	c.(1711-1713)gAt>gCt	p.D571A	SMCHD1_ENST00000261598.8_Missense_Mutation_p.D571A|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	571					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GAGAAGTATGATAAACAAATA	0.343																																					p.D571A		.											.	SMCHD1-46	0			c.A1712C						.						74	75	75					18																	2703754		1821	4085	5906	SO:0001583	missense	23347	exon13			AGTATGATAAACA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.1712A>C	18.37:g.2703754A>C	ENSP00000326603:p.Asp571Ala	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	123	28	NM_015295	0	0	0	0	0	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.577974	0.45902	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.64260	-0.09;-0.06	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.76385	0.3980	L	0.59436	1.845	0.48288	D	0.999625	D	0.89917	1.0	D	0.83275	0.996	T	0.78949	-0.2002	10	0.87932	D	0	-11.3702	15.6552	0.77129	1.0:0.0:0.0:0.0	.	571	A6NHR9	SMHD1_HUMAN	A	571	ENSP00000326603:D571A;ENSP00000261598:D571A	ENSP00000261598:D571A	D	+	2	0	SMCHD1	2693754	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.503000	0.90509	2.088000	0.63022	0.460000	0.39030	GAT	.		0.343	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			C	2703754	A	C	2703754	3	2	21	1	0	0	0	0	1	0	0	0	14820	333	12	5	1762	5	SMCHD1	18	2703754	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		2703754	75373494	130	1898											
PIK3C3	5289	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	39542509	39542509	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacctgcccaggaatgccCaagtggccctcaccatatgg	9	7	10	15	0	1	1	1	1	0	0	1	2	1	2	5	3	2	0	5	3	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr18:39542509C>A	ENST00000262039.4	+	3	399	c.313C>A	c.(313-315)Caa>Aaa	p.Q105K	PIK3C3_ENST00000586545.1_Missense_Mutation_p.Q105K|PIK3C3_ENST00000398870.3_Missense_Mutation_p.Q42K	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	105	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CAGGAATGCCCAAGTGGCCCT	0.433										TSP Lung(28;0.18)																											p.Q105K	NSCLC(37;552 1060 2683 16430 37914)	.											.	PIK3C3-1312	0			c.C313A						.						101	91	94					18																	39542509		2203	4300	6503	SO:0001583	missense	5289	exon3			AATGCCCAAGTGG	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"phosphoinositide-3-kinase, class 3"			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.313C>A	18.37:g.39542509C>A	ENSP00000262039:p.Gln105Lys	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	139	7	NM_002647	0	0	3	3	0	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	C	31	5.104641	0.94245	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.76709	-1.04;-1.04	5.88	5.88	0.94601	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	T	0.81079	0.4748	M	0.78285	2.405	0.58432	D	0.999994	B;B	0.29341	0.073;0.242	B;B	0.33196	0.067;0.159	T	0.76887	-0.2793	9	.	.	.	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	42;105	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	K	105;42	ENSP00000262039:Q105K;ENSP00000381845:Q42K	.	Q	+	1	0	PIK3C3	37796507	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.805000	0.69143	2.789000	0.95967	0.591000	0.81541	CAA	.		0.433	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		A	39542509	C	A	39542509	3	1	21	1	0	0	0	0	1	0	0	0	11938	595	21	4	323	4	PIK3C3	18	39542509	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	36838755	39542509	38534739	131	1899											
MYO1F	4542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8642191	8642191	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacccttgaaggacttacCatggtggggggctggtgtct	6	10	14	11	0	1	1	0	1	1	0	1	2	1	2	3	6	1	1	3	6	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:8642191C>G	ENST00000338257.8	-	1	270	c.3G>C	c.(1-3)atG>atC	p.M1I	MYO1F_ENST00000595046.1_5'UTR	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	1					defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						AAGGACTTACCATGGTGGGGG	0.587																																					p.M1I		.											.	MYO1F-93	0			c.G3C						.						44	45	44					19																	8642191		1908	4116	6024	SO:0001630	splice_region_variant	4542	exon1			ACTTACCATGGTG	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"Myosins / Myosin superfamily : Class I"	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.3+1G>C	19.37:g.8642191C>G		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	80	24	NM_012335	0	0	0	0	0	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.237181	0.22711	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.86164	-2.08	3.64	3.64	0.41730	.	0.629994	0.14357	N	0.324717	T	0.78597	0.4308	.	.	.	0.80722	D	1	B;B;B	0.20261	0.0;0.009;0.043	B;B;B	0.14023	0.001;0.003;0.01	T	0.71590	-0.4547	8	.	.	.	.	11.03	0.47767	0.0:1.0:0.0:0.0	.	1;1;1	B4DVP3;B0I1T1;O00160	.;.;MYO1F_HUMAN	I	46;1	ENSP00000344871:M1I	.	M	-	3	0	MYO1F	8548191	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	3.368000	0.52357	2.028000	0.59812	0.462000	0.41574	ATG	.		0.587	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		Missense_Mutation	G	8642191	C	G	8642191	5	3	21	1	0	0	0	0	0	0	1	0	10098	608	21	4	3405	4	MYO1F	19	8642191	Splice_Site	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		8642191	50486792	132	1900											
ZNF101	94039	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	19790040	19790040	+	Frame_Shift_Del	DEL	A	A	-																															agaagggaatgaacacagagAaactttcagccagattcctg																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:19790040delA	ENST00000592502.1	+	4	352	c.242delA	c.(241-243)gaafs	p.E81fs	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_5'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	81	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						GAACACAGAGAAACTTTCAGC	0.413																																					p.E81fs		.											.	ZNF101-92	0			c.242delA						.						88	82	84					19																	19790040		2203	4300	6503	SO:0001589	frameshift_variant	94039	exon4			.	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.242delA	19.37:g.19790040delA	ENSP00000468049:p.Glu81fs	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	150	39	NM_033204	0	0	0	0	0	C9JU83|Q0VDG9	Frame_Shift_Del	DEL	ENST00000592502.1	37	CCDS32971.1																																																																																			.		0.413	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		-	19790040	A	-	19790040	7	5	21	1	0	1	0	1	0	0	0	0	17746	246	9	0	256	0	ZNF101	19	19790040	Frame_Shift_Del	DEL	A	TCGA-A4-A48D-01A-11D-A25F-10	11147849	19790040	39338943	133	1901											
GAPDHS	26330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36029207	36029207	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctgtctgtccctggccAgatttggacgcatcggtcgc	4	12	11	14	3	1	1	0	0	1	1	5	2	3	2	3	3	0	1	3	3	0	2	rs111871741		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:36029207A>C	ENST00000222286.4	+	3	361		c.e3-1		AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000590125.1_RNA|AD000090.2_ENST00000589137.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic						carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GTCCCTGGCCAGATTTGGACG	0.567																																					.		.											.	GAPDHS-226	0			c.246-2A>C						.						59	40	46					19																	36029207		2203	4300	6503	SO:0001630	splice_region_variant	26330	exon3			CTGGCCAGATTTG	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.246-1A>C	19.37:g.36029207A>C		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	147	34	NM_014364	0	0	0	0	0	B2RC82|O60823|Q6JTT9|Q9HCU6	Splice_Site	SNP	ENST00000222286.4	37	CCDS12465.1	.	.	.	.	.	.	.	.	.	.	A	19.98	3.927280	0.73327	.	.	ENSG00000105679	ENST00000222286	.	.	.	5.3	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0531	0.36389	0.9122:0.0:0.0878:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAPDHS	40721047	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	8.908000	0.92640	0.848000	0.35191	0.533000	0.62120	.	.		0.567	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364	Intron	C	36029207	A	C	36029207	5	2	21	1	0	0	0	0	0	0	1	0	6257	202	7	5	254	5	GAPDHS	19	36029207	Splice_Site	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	16239167	36029207	23099776	134	1902											
LRRC4B	94030	bcgsc.ca	37	chr19	51022541	51022541	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccgtggtcagccggttGtcaaaaagctccagcgtgtt	8	9	13	11	3	2	0	2	0	0	0	3	0	3	0	3	3	3	4	3	3	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:51022541G>T	ENST00000599957.1	-	3	626	c.429C>A	c.(427-429)gaC>gaA	p.D143E	LRRC4B_ENST00000389201.3_Missense_Mutation_p.D143E			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	143					positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		TCAGCCGGTTGTCAAAAAGCT	0.627																																					p.D143E													.	LRRC4B-205	0			c.C429A						.						52	56	55					19																	51022541		2200	4298	6498	SO:0001583	missense	94030	exon3			CCGGTTGTCAAAA	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"Immunoglobulin superfamily / I-set domain containing", "Endogenous ligands"	25042	protein-coding gene	gene with protein product	"netrin-G3 ligand"		"leucine-rich repeats and immunoglobulin-like domains 4"	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.429C>A	19.37:g.51022541G>T	ENSP00000471502:p.Asp143Glu	Somatic	78	0		WXS	Illumina HiSeq	Phase_1	123	6	NM_001080457	0	0	0	0	0	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	37	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028580	0.75390	.	.	ENSG00000131409	ENST00000389201;ENST00000535879	D	0.90955	-2.76	3.96	3.96	0.45880	.	0.000000	0.64402	U	0.000004	D	0.84437	0.5472	L	0.38649	1.16	0.58432	D	0.999995	P	0.44659	0.84	B	0.38296	0.27	D	0.83865	0.0270	10	0.30078	T	0.28	.	13.9104	0.63864	0.0:0.0:1.0:0.0	.	143	Q9NT99	LRC4B_HUMAN	E	143	ENSP00000373853:D143E	ENSP00000373853:D143E	D	-	3	2	LRRC4B	55714353	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.637000	0.67854	2.235000	0.73313	0.491000	0.48974	GAC	.		0.627	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		T	51022541	G	T	51022541	3	4	21	1	0	0	0	0	1	0	0	0	9032	1368	48	4	1716	4	LRRC4B	19	51022541	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	14993334	51022541	8106442	135	1903											
C20orf46	55321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	1161648	1161648	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggacgaaggtcctccggcgGtacagctcgcccttgcacag	7	6	14	14	4	0	0	0	0	0	0	3	2	2	1	3	4	3	3	3	4	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr20:1161648G>A	ENST00000381894.3	-	2	1286	c.615C>T	c.(613-615)taC>taT	p.Y205Y	TMEM74B_ENST00000481747.1_5'Flank	NM_018354.1	NP_060824.1	Q9NUR3	TM74B_HUMAN	transmembrane protein 74B	205						integral component of membrane (GO:0016021)											TCCTCCGGCGGTACAGCTCGC	0.652																																					p.Y205Y		.											.	.	0			c.C615T						.						56	50	52					20																	1161648		2203	4300	6503	SO:0001819	synonymous_variant	55321	exon2			CCGGCGGTACAGC	AK002052	CCDS13011.1	20p13	2011-11-23	2011-11-23	2011-11-23	ENSG00000125895	ENSG00000125895			15893	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 46"	C20orf46			Standard	XM_005260748		Approved	FLJ11190	uc002weq.1	Q9NUR3	OTTHUMG00000031655	ENST00000381894.3:c.615C>T	20.37:g.1161648G>A		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	86	18	NM_018354	0	0	0	0	0	D3DVW5	Silent	SNP	ENST00000381894.3	37	CCDS13011.1																																																																																			.		0.652	TMEM74B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077496.2	NM_018354		A	1161648	G	A	1161648	2	1	21	1	0	0	0	0	0	0	0	1	2119	1256	44	2		2	C20orf46	20	1161648	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		1161648	61863872	136	1904											
SRC	6714	broad.mit.edu	37	chr20	36026154	36026154	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accgtgtgccccacgtccaaGccgcagactcagggcctggc	7	5	12	17	3	1	1	1	0	0	1	2	1	2	1	6	2	2	1	6	2	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr20:36026154G>T	ENST00000373578.2	+	9	1105	c.756G>T	c.(754-756)aaG>aaT	p.K252N	SRC_ENST00000373558.2_Missense_Mutation_p.K258N|SRC_ENST00000477066.1_3'UTR|SRC_ENST00000445403.1_Missense_Mutation_p.K252N|SRC_ENST00000373567.2_Missense_Mutation_p.K252N|SRC_ENST00000360723.4_Missense_Mutation_p.K258N|SRC_ENST00000358208.4_Missense_Mutation_p.K252N	NM_198291.1	NP_938033.1	P12931	SRC_HUMAN	SRC proto-oncogene, non-receptor tyrosine kinase	252					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cellular response to progesterone stimulus (GO:0071393)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|membrane organization (GO:0061024)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of protein homooligomerization (GO:0032463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oogenesis (GO:0048477)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of integrin activation (GO:0033625)|positive regulation of podosome assembly (GO:0071803)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone receptor signaling pathway (GO:0050847)|protein autophosphorylation (GO:0046777)|Ras protein signal transduction (GO:0007265)|regulation of bone resorption (GO:0045124)|regulation of caveolin-mediated endocytosis (GO:2001286)|regulation of cell-cell adhesion (GO:0022407)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of epithelial cell migration (GO:0010632)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of protein binding (GO:0043393)|regulation of vascular permeability (GO:0043114)|response to interleukin-1 (GO:0070555)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|T cell costimulation (GO:0031295)|transforming growth factor beta receptor signaling pathway (GO:0007179)|uterus development (GO:0060065)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|growth factor receptor binding (GO:0070851)|heme binding (GO:0020037)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(16)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)			Bosutinib(DB06616)|Dasatinib(DB01254)|Ponatinib(DB08901)	CCACGTCCAAGCCGCAGACTC	0.677																																					p.K252N													.	SRC-2731	0			c.G756T						.						44	42	43					20																	36026154		2203	4300	6503	SO:0001583	missense	6714	exon9			GTCCAAGCCGCAG	AF077754	CCDS13294.1	20q12-q13	2014-06-25	2014-06-25		ENSG00000197122	ENSG00000197122		"SH2 domain containing"	11283	protein-coding gene	gene with protein product		190090	"v-src avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog"	SRC1		2582238	Standard	NM_005417		Approved	ASV, c-src	uc002xgy.3	P12931	OTTHUMG00000032417	ENST00000373578.2:c.756G>T	20.37:g.36026154G>T	ENSP00000362680:p.Lys252Asn	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_005417	0	0	15	15	0	E1P5V4|Q76P87|Q86VB9|Q9H5A8	Missense_Mutation	SNP	ENST00000373578.2	37	CCDS13294.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.508256	0.27036	.	.	ENSG00000197122	ENST00000445403;ENST00000373578;ENST00000360723;ENST00000358208;ENST00000373567;ENST00000373558	T;T;T;T;T;T	0.75260	-0.9;-0.9;-0.92;-0.9;-0.9;-0.92	4.53	3.58	0.41010	SH2 motif (1);	0.000000	0.85682	D	0.000000	T	0.71169	0.3308	M	0.70275	2.135	0.80722	D	1	P	0.37276	0.589	B	0.36922	0.236	T	0.71879	-0.4459	10	0.51188	T	0.08	.	10.2811	0.43541	0.0976:0.0:0.9024:0.0	.	252	P12931	SRC_HUMAN	N	252;252;258;252;252;258	ENSP00000408503:K252N;ENSP00000362680:K252N;ENSP00000353950:K258N;ENSP00000350941:K252N;ENSP00000362668:K252N;ENSP00000362659:K258N	ENSP00000350941:K252N	K	+	3	2	SRC	35459568	1.000000	0.71417	0.998000	0.56505	0.116000	0.19942	3.875000	0.56108	1.125000	0.41998	0.462000	0.41574	AAG	.		0.677	SRC-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268142.1	NM_005417		T	36026154	G	T	36026154	3	4	21	1	0	0	0	0	1	0	0	0	15166	962	34	4	778	4	SRC	20	36026154	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	34864506	36026154	26999366	137	1905											
MYBL2	4605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42310472	42310472	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttggacagcaggactggAagttcctggccagccacttc	9	9	12	11	0	0	0	0	0	0	0	2	3	1	3	3	4	2	3	3	4	1	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr20:42310472A>G	ENST00000217026.4	+	3	290	c.163A>G	c.(163-165)Aag>Gag	p.K55E	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	55	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GCAGGACTGGAAGTTCCTGGC	0.602																																					p.K55E		.											.	MYBL2-415	0			c.A163G						.						64	52	56					20																	42310472		2203	4300	6503	SO:0001583	missense	4605	exon3			GACTGGAAGTTCC		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.163A>G	20.37:g.42310472A>G	ENSP00000217026:p.Lys55Glu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	144	41	NM_002466	0	0	1	1	0	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	A	32	5.164691	0.94727	.	.	ENSG00000101057	ENST00000217026	T	0.15718	2.4	5.61	5.61	0.85477	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.33089	0.0851	L	0.46567	1.45	0.80722	D	1	D	0.60160	0.987	D	0.62955	0.909	T	0.01613	-1.1312	10	0.54805	T	0.06	-37.5596	15.101	0.72276	1.0:0.0:0.0:0.0	.	55	P10244	MYBB_HUMAN	E	55	ENSP00000217026:K55E	ENSP00000217026:K55E	K	+	1	0	MYBL2	41743886	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.926000	0.92839	2.281000	0.76405	0.533000	0.62120	AAG	.		0.602	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		G	42310472	A	G	42310472	3	3	21	1	0	0	0	0	1	0	0	0	10035	247	9	3	173	3	MYBL2	20	42310472	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	6284318	42310472	20715048	138	1906											
SGSM3	27352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40800334	40800334	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcggtggcaggcccacCtggagttcacccataaccac	8	6	12	15	1	1	0	1	0	0	0	1	1	1	1	4	5	2	3	4	5	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr22:40800334C>T	ENST00000248929.9	+	5	430	c.241C>T	c.(241-243)Ctg>Ttg	p.L81L	SGSM3_ENST00000454798.2_Silent_p.L14L	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						GCAGGCCCACCTGGAGTTCAC	0.627																																					p.L81L		.											.	SGSM3-494	0			c.C241T						.						53	49	51					22																	40800334		2203	4300	6503	SO:0001819	synonymous_variant	27352	exon5			GCCCACCTGGAGT	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.241C>T	22.37:g.40800334C>T		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	90	24	NM_015705	0	0	0	3	3		Silent	SNP	ENST00000248929.9	37	CCDS14002.1																																																																																			.		0.627	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		T	40800334	C	T	40800334	2	4	21	1	0	0	0	0	0	0	0	1	14256	680	24	2		2	SGSM3	22	40800334	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		40800334	10504232	139	1907											
SGSM3	27352	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40802147	40802147	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgtggtggacatcaagctgCtcctgcgcatctgggacctg	6	9	14	12	2	2	0	1	0	1	0	3	2	3	2	2	3	3	3	2	3	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr22:40802147C>T	ENST00000248929.9	+	9	1069	c.880C>T	c.(880-882)Ctc>Ttc	p.L294F	SGSM3_ENST00000454798.2_Missense_Mutation_p.L227F	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						CATCAAGCTGCTCCTGCGCAT	0.617																																					p.L294F													.	SGSM3-494	0			c.C880T						.						106	89	95					22																	40802147		2203	4300	6503	SO:0001583	missense	27352	exon9			AAGCTGCTCCTGC	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.880C>T	22.37:g.40802147C>T	ENSP00000248929:p.Leu294Phe	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	234	9	NM_015705	0	0	13	17	4		Missense_Mutation	SNP	ENST00000248929.9	37	CCDS14002.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305342	0.60305	.	.	ENSG00000100359	ENST00000457767;ENST00000248929;ENST00000545416;ENST00000454798	T;T;T	0.25085	1.82;1.82;1.82	5.25	4.22	0.49857	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.54886	0.1886	M	0.88979	2.995	0.80722	D	1	D;D;D;D;D	0.71674	0.998;0.998;0.995;0.996;0.996	D;D;D;D;D	0.79108	0.989;0.992;0.947;0.979;0.979	T	0.62483	-0.6845	10	0.87932	D	0	.	12.4289	0.55563	0.0:0.8653:0.0:0.1347	.	231;227;294;294;294	B4DVE3;B4DMS2;Q96HU1-2;B9A6J5;Q96HU1	.;.;.;.;SGSM3_HUMAN	F	227;294;237;227	ENSP00000399249:L227F;ENSP00000248929:L294F;ENSP00000390998:L227F	ENSP00000248929:L294F	L	+	1	0	SGSM3	39132093	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	3.568000	0.53820	2.636000	0.89361	0.313000	0.20887	CTC	.		0.617	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		T	40802147	C	T	40802147	3	4	21	1	0	0	0	0	1	0	0	0	14256	797	28	2	910	2	SGSM3	22	40802147	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	1813	40802147	10502419	140	1908											
MKL1	57591	broad.mit.edu;bcgsc.ca	37	chr22	40825749	40825750	+	Missense_Mutation	DNP	GA	GA	AG																															agcttcagctgcttggcctgGagggatggctcagccgaggt																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr22:40825749_40825750GA>AG	ENST00000355630.3	-	7	751_752	c.161_162TC>CT	c.(160-162)cTC>cCT	p.L54P	MKL1_ENST00000396617.3_Missense_Mutation_p.L54P|MKL1_ENST00000402630.1_Missense_Mutation_p.L54P|MKL1_ENST00000402042.1_Missense_Mutation_p.L54P|MKL1_ENST00000407029.1_Missense_Mutation_p.L54P	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	54	Mediates interaction with SCAI and ACTB. {ECO:0000250}.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L54L(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GCTTGGCCTGGAGGGATGGCTC	0.579			T	RBM15	acute megakaryocytic leukemia																																p.L54P				Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T161C						.																																			SO:0001583	missense	57591	exon7			GCCTGGAGGGATG	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.161_162delinsAG	22.37:g.40825749_40825750delinsAG	ENSP00000347847:p.Leu54Pro	Somatic	99	2		WXS	Illumina HiSeq	Phase_I	124	35	NM_020831	0	0	0	0	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	DNP	ENST00000355630.3	37	CCDS14003.1																																																																																			.		0.579	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		AG	40825750	GA	AG	40825749	3	1	21	1	0	0	0	0	1	0	0	0	9626	1161	41	2	2669	2	MKL1	22	40825749	Missense_Mutation	DNP	GA	TCGA-A4-A48D-01A-11D-A25F-10	23602	40825749	10478817	141	1909											
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	44922715	44922716	+	Nonsense_Mutation	DNP	GG	GG	TA																															gatctactggaattcctaatGggccaacagctgactcatca																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chrX:44922715_44922716GG>TA	ENST00000377967.4	+	16	1617_1618	c.1576_1577GG>TA	c.(1576-1578)GGg>TAg	p.G526*	KDM6A_ENST00000536777.1_Nonsense_Mutation_p.G481*|KDM6A_ENST00000382899.4_Nonsense_Mutation_p.G533*|KDM6A_ENST00000543216.1_Nonsense_Mutation_p.G447*	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	526	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AATTCCTAATGGGCCAACAGCT	0.485			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.G533*	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.G1577A						.																																			SO:0001587	stop_gained	7403	exon16			CTAATGGGCCAAC	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	Exception_encountered	X.37:g.44922715_44922716delinsTA	ENSP00000367203:p.Gly526*	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	28	18	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Nonsense_Mutation	DNP	ENST00000377967.4	37	CCDS14265.1																																																																																			.		0.485	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		TA	44922716	GG	TA	44922715	4	4	21	1	0	0	0	0	0	1	0	0	8158	1348	47	4	1638	4	KDM6A	23	44922715	Nonsense_Mutation	DNP	GG	TCGA-A4-A48D-01A-11D-A25F-10		44922715	110347845	142	1910											
RAB41	407	bcgsc.ca	37	chrX	69502407	69502407	+	IGR	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagacatccatcatcagccGcttcatgtacaacagcttcg	12	9	7	13	2	3	1	3	0	0	1	5	2	4	1	2	0	4	3	2	0	3	3	rs375268434		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chrX:69502407G>T	ENST00000307959.8	+	0	1292				RAB41_ENST00000276066.4_Missense_Mutation_p.R49L|RAB41_ENST00000374473.2_Missense_Mutation_p.R50L	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)						endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						ATCATCAGCCGCTTCATGTAC	0.537																																					p.R49L													.	RAB41-229	0			c.G146T						.						100	71	81					X																	69502407		2203	4300	6503	SO:0001628	intergenic_variant	347517	exon2			TCAGCCGCTTCAT		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768		X.37:g.69502407G>T		Somatic	196	3		WXS	Illumina HiSeq	Phase_1	186	94	NM_001032726	0	0	0	0	0	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Missense_Mutation	SNP	ENST00000307959.8	37	CCDS14399.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.328288	0.60743	.	.	ENSG00000147127	ENST00000374473;ENST00000276066	D;D	0.82081	-1.57;-1.57	4.51	-5.54	0.02544	Small GTP-binding protein domain (1);	0.000000	0.49916	U	0.000122	D	0.89928	0.6857	H	0.94542	3.55	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	T	0.82297	-0.0527	10	0.87932	D	0	.	5.8878	0.18892	0.4471:0.2274:0.3255:0.0	.	49;50	Q5JT25-2;Q5JT25	.;RAB41_HUMAN	L	50;49	ENSP00000363597:R50L;ENSP00000276066:R49L	ENSP00000276066:R49L	R	+	2	0	RAB41	69419132	0.608000	0.26966	0.000000	0.03702	0.006000	0.05464	0.836000	0.27545	-1.214000	0.02614	-0.380000	0.06706	CGC	.		0.537	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		T	69502407	G	T	69502407	1	4	21	0	1	0	0	0	0	0	0	0	12975	1087	38	4		4	RAB41	23	69502407	IGR	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	24579692	69502407	85768153	143	1911											
IRS4	8471	ucsc.edu	37	chrX	107977151	107977151	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagggtttggtagagagaaGtaggagctccaacttttgga	13	10	14	4	0	0	2	0	0	0	2	1	5	1	4	1	4	2	4	1	4	5	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chrX:107977151G>A	ENST00000372129.2	-	1	2500	c.2424C>T	c.(2422-2424)taC>taT	p.Y808Y	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	808					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GTAGAGAGAAGTAGGAGCTCC	0.502																																					p.Y808Y													.	IRS4-623	0			c.C2424T						.						136	144	141					X																	107977151		2203	4300	6503	SO:0001819	synonymous_variant	8471	exon1			AGAGAAGTAGGAG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.2424C>T	X.37:g.107977151G>A		Somatic	48	0		WXS	Illumina HiSeq		33	4	NM_003604	0	0	0	0	0		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			.		0.502	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107977151	G	A	107977151	2	1	21	1	0	0	0	0	0	0	0	1	7863	1024	36	2		2	IRS4	23	107977151	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	38474744	107977151	47293409	144	1912											
KIAA1751	85452	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	1891408	1891409	+	IGR	DEL	GC	GC	-																															gcccctctgactcaccatcgGcttgaaggtgacaagcactt																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:1891408_1891409delGC								TMEM52 (40696 upstream) : C1orf222 (28153 downstream)																							CTCACCATCGGCTTGAAGGTGA	0.619											OREG0013001	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.585_586del		.											.	KIAA1751-69	0			c.1755_1756del						.																																			SO:0001628	intergenic_variant	85452	exon15			.																													1.37:g.1891408_1891409delGC		Somatic	259	0	599	WXS	Illumina HiSeq	Phase_I	214	77	NM_001080484	0	0	0	0	0		Frame_Shift_Del	DEL		37																																																																																				.	0	0.619									-	1891409	GC	-	1891408	6	5	22	0	1	1	0	1	0	0	0	0	8277	1203	42	0		0	KIAA1751	1	1891408	IGR	DEL	GC	TCGA-A4-A4ZT-01A-11D-A26P-10		1891408	247359213	1	1913											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	19524166	19524172	+	Frame_Shift_Del	DEL	ATTACGA	ATTACGA	-																															cactgtgaagcaccttacccAttacgaacagcagtggcatc																								rs200068490		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	ATTACGA	ATTACGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:19524166_19524172delATTACGA	ENST00000375254.3	-	7	912_918	c.885_891delTCGTAAT	c.(883-891)gttcgtaatfs	p.VRN295fs	UBR4_ENST00000375226.2_Frame_Shift_Del_p.VRN295fs|UBR4_ENST00000375267.2_Frame_Shift_Del_p.VRN295fs|UBR4_ENST00000375217.2_Frame_Shift_Del_p.VRN295fs	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	295					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CACCTTACCCATTACGAACAGCAGTGG	0.464																																					p.295_297del		.											.	UBR4-612	0			c.885_891del						.																																			SO:0001589	frameshift_variant	23352	exon7			.	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.885_891delTCGTAAT	1.37:g.19524166_19524172delATTACGA	ENSP00000364403:p.Val295fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	77	28	NM_020765	0	0	0	0	0	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Frame_Shift_Del	DEL	ENST00000375254.3	37	CCDS189.1																																																																																			.		0.464	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		-	19524172	ATTACGA	-	19524166	7	5	22	1	0	1	0	1	0	0	0	0	16937	214	8	0	15060	0	UBR4	1	19524166	Frame_Shift_Del	DEL	ATTACGA	TCGA-A4-A4ZT-01A-11D-A26P-10	17632758	19524166	229726455	2	1914											
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32266188	32266191	+	Frame_Shift_Del	DEL	CCAG	CCAG	-																															ctggccgtggctgatggcccCcaggagctggatcactggcc																								rs369969025		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	CCAG	CCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:32266188_32266191delCCAG	ENST00000360482.2	-	4	1582_1585	c.1453_1456delCTGG	c.(1453-1458)ctggggfs	p.LG485fs	SPOCD1_ENST00000533231.1_Frame_Shift_Del_p.LG485fs|SPOCD1_ENST00000257100.3_5'UTR|SPOCD1_ENST00000373648.2_Intron	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	485					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CTGATGGCCCCCAGGAGCTGGATC	0.662																																					p.485_486del		.											.	SPOCD1-158	0			c.1453_1456del						.			0,4264		0,0,2132						5	1			16	1,8253		0,1,4126	no	frameshift	SPOCD1	NM_144569.4		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12517				SO:0001589	frameshift_variant	90853	exon4			.	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 146"					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.1453_1456delCTGG	1.37:g.32266188_32266191delCCAG	ENSP00000353670:p.Leu485fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	122	55	NM_144569	0	0	0	0	0	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Frame_Shift_Del	DEL	ENST00000360482.2	37	CCDS347.1																																																																																			.		0.662	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		-	32266191	CCAG	-	32266188	7	5	22	1	0	1	0	1	0	0	0	0	15110	623	22	0	2246	0	SPOCD1	1	32266188	Frame_Shift_Del	DEL	CCAG	TCGA-A4-A4ZT-01A-11D-A26P-10	12742022	32266188	216984433	3	1915											
CSMD2	114784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	34052133	34052133	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgggggtggtccttcaaacTgcaggtaggttccaagtttg	7	12	14	8	1	1	0	1	0	0	0	4	0	3	0	2	5	2	4	2	5	3	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:34052133T>A	ENST00000373381.4	-	46	7198	c.7022A>T	c.(7021-7023)cAg>cTg	p.Q2341L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2343	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCCTTCAAACTGCAGGTAGGT	0.493																																					p.Q2343L		.											.	CSMD2-103	0			c.A7028T						.						105	96	99					1																	34052133		2203	4300	6503	SO:0001583	missense	114784	exon47			TCAAACTGCAGGT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7022A>T	1.37:g.34052133T>A	ENSP00000362479:p.Gln2341Leu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	230	98	NM_052896	0	0	0	0	0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	T	18.56	3.650854	0.67472	.	.	ENSG00000121904	ENST00000373381	T	0.66815	-0.23	5.83	5.83	0.93111	Complement control module (2);Sushi/SCR/CCP (3);	0.061993	0.64402	D	0.000004	T	0.65565	0.2703	M	0.64260	1.97	0.80722	D	1	B;B	0.11235	0.004;0.004	B;B	0.24006	0.05;0.029	T	0.60682	-0.7215	10	0.27082	T	0.32	.	15.3817	0.74661	0.0:0.0:0.0:1.0	.	2343;2341	Q7Z408;E7EUA6	CSMD2_HUMAN;.	L	2341	ENSP00000362479:Q2341L	ENSP00000241312:Q2343L	Q	-	2	0	CSMD2	33824720	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.018000	0.70811	2.227000	0.72691	0.528000	0.53228	CAG	.		0.493	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34052133	T	A	34052133	3	1	22	1	0	0	0	0	1	0	0	0	3951	1580	55	5	3527	5	CSMD2	1	34052133	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	1785945	34052133	215198488	4	1916											
KIAA0754	643314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	39878312	39878312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgagctgaatgtggcatcatCagagggaggggagatggaaa	13	7	17	4	0	2	4	2	2	0	2	2	7	2	6	0	5	1	2	0	5	2	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:39878312C>T	ENST00000530275.1	+	1	2162	c.1967C>T	c.(1966-1968)tCa>tTa	p.S656L	MACF1_ENST00000317713.7_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000539005.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	656										central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GTGGCATCATCAGAGGGAGGG	0.428																																					p.S792L		.											.	.	0			c.C2375T						.						85	83	84					1																	39878312		1910	4132	6042	SO:0001583	missense	643314	exon1			CATCATCAGAGGG			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.1967C>T	1.37:g.39878312C>T	ENSP00000431179:p.Ser656Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	57	17	NM_015038	0	0	0	3	3	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	C	10.93	1.491329	0.26774	.	.	ENSG00000255103	ENST00000530275	D	0.86230	-2.09	5.48	-0.479	0.12089	.	.	.	.	.	T	0.74489	0.3723	N	0.24115	0.695	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.63047	-0.6724	9	0.87932	D	0	.	2.2667	0.04080	0.1278:0.5256:0.1262:0.2204	.	656	O94854	K0754_HUMAN	L	656	ENSP00000431179:S656L	ENSP00000431179:S656L	S	+	2	0	RP4-562N20.1	39650899	0.000000	0.05858	0.032000	0.17829	0.874000	0.50279	-0.517000	0.06275	0.188000	0.20168	0.655000	0.94253	TCA	.		0.428	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39878312	C	T	39878312	3	4	22	1	0	0	0	0	1	0	0	0	8213	838	29	2	2377	2	KIAA0754	1	39878312	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	5826179	39878312	209372309	5	1917											
FNDC7	163479	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	109265207	109265229	+	Splice_Site	DEL	GAAAACTGGTATGTAAACAAGAG	GAAAACTGGTATGTAAACAAGAG	-																															tcatcttcagcaatgaccctGaaaactggtatgtaaacaag																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GAAAACTGGTATGTAAACAAGAG	GAAAACTGGTATGTAAACAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:109265207_109265229delGAAAACTGGTATGTAAACAAGAG	ENST00000370017.3	+	5	1126_1133	c.849_856delGAAAACTGGTATGTAAACAAGAG	c.(847-858)ctgaaaactggt>ctgt	p.KTG284fs	FNDC7_ENST00000271311.2_Splice_Site_p.KTG285fs	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	284	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		CAATGACCCTGAAAACTGGTATGTAAACAAGAGTGAGACTGCT	0.439																																					p.283_286del		.											.	FNDC7-92	0			c.849_856del						.																																			SO:0001630	splice_region_variant	163479	exon5			.		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"Fibronectin type III domain containing"	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.856+1GAAAACTGGTATGTAAACAAGAG>-	1.37:g.109265207_109265229delGAAAACTGGTATGTAAACAAGAG		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	54	13	NM_001144937	0	0	0	0	0	A1L468|E9PAZ5|Q6PF16|Q8NA51	Frame_Shift_Del	DEL	ENST00000370017.3	37	CCDS44185.1																																																																																			.		0.439	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	Frame_Shift_Del	-	109265229	GAAAACTGGTATGTAAACAAGAG	-	109265207	8	5	22	1	0	1	0	1	0	0	1	0	5992	1277	45	0	867	0	FNDC7	1	109265207	Splice_Site	DEL	GAAAACTGGTATGTAAACAAGAG	TCGA-A4-A4ZT-01A-11D-A26P-10	69386895	109265207	139985414	6	1918											
STXBP3	6814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109338856	109338856	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aatattttattttcattaagGacctggcacttggaactgat	12	16	7	6	0	1	1	1	1	0	0	1	3	1	3	1	3	1	1	1	3	5	7			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:109338856G>C	ENST00000370008.3	+	14	1161	c.1111G>C	c.(1111-1113)Gac>Cac	p.D371H		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	371					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		TTTCATTAAGGACCTGGCACT	0.358																																					p.D371H		.											.	STXBP3-93	0			c.G1111C						.						54	54	54					1																	109338856		2203	4300	6503	SO:0001630	splice_region_variant	6814	exon14			ATTAAGGACCTGG	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1111-1G>C	1.37:g.109338856G>C		Somatic	156	0		WXS	Illumina HiSeq	Phase_I	205	53	NM_007269	0	0	0	0	0	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	37	CCDS790.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.298070	0.81025	.	.	ENSG00000116266	ENST00000370008	T	0.79247	-1.25	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.89114	0.6623	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88884	0.3341	9	.	.	.	-7.6976	20.1392	0.98050	0.0:0.0:1.0:0.0	.	371	O00186	STXB3_HUMAN	H	371	ENSP00000359025:D371H	.	D	+	1	0	STXBP3	109140379	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	8.716000	0.91420	2.751000	0.94390	0.591000	0.81541	GAC	.		0.358	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	Missense_Mutation	C	109338856	G	C	109338856	5	2	22	1	0	0	0	0	0	0	1	0	15386	1188	41	4	1165	4	STXBP3	1	109338856	Splice_Site	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	73649	109338856	139911765	7	1919											
ATP6V1B1	525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	71188132	71188132	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accatgacgacaacttcgccAtcgtctttgcagccatgggg	9	9	10	13	3	1	1	0	1	1	0	3	2	1	1	3	2	3	1	3	2	1	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:71188132A>T	ENST00000234396.4	+	7	740	c.667A>T	c.(667-669)Atc>Ttc	p.I223F	ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.I223F|AC007040.11_ENST00000606025.1_Intron	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	223					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						CAACTTCGCCATCGTCTTTGC	0.587																																					p.I223F		.											.	ATP6V1B1-91	0			c.A667T						.						94	63	74					2																	71188132		2203	4300	6503	SO:0001583	missense	525	exon7			TTCGCCATCGTCT	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"ATPases / V-type"	853	protein-coding gene	gene with protein product	"Renal tubular acidosis with deafness"	192132	"vacuolar proton pump 3"	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.667A>T	2.37:g.71188132A>T	ENSP00000234396:p.Ile223Phe	Somatic	219	1		WXS	Illumina HiSeq	Phase_I	279	158	NM_001692	0	0	0	5	5	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.541872	0.85917	.	.	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314;ENST00000454446	D;D;D	0.81908	-1.55;-1.55;-1.55	5.04	5.04	0.67666	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.64402	D	0.000011	D	0.91036	0.7180	M	0.84585	2.705	0.80722	D	1	D;D;D	0.67145	0.996;0.979;0.979	D;D;D	0.74674	0.984;0.93;0.93	D	0.92308	0.5855	10	0.87932	D	0	-35.7839	12.7736	0.57436	1.0:0.0:0.0:0.0	.	198;223;223	B4DWH7;C9JL73;P15313	.;.;VATB1_HUMAN	F	223;198;223;240	ENSP00000234396:I223F;ENSP00000388353:I223F;ENSP00000408361:I240F	ENSP00000234396:I223F	I	+	1	0	ATP6V1B1	71041640	1.000000	0.71417	0.999000	0.59377	0.683000	0.39861	7.140000	0.77322	2.133000	0.65898	0.533000	0.62120	ATC	.		0.587	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692		T	71188132	A	T	71188132	3	4	22	1	0	0	0	0	1	0	0	0	1179	217	8	5	693	5	ATP6V1B1	2	71188132	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		71188132	172011241	8	1920											
CCDC74A	90557	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	132290624	132290624	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttccccaaggtctccaccaAgagcctctccaagaaatggt	11	9	7	14	0	2	2	0	0	2	2	5	2	3	2	6	2	1	0	6	2	4	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:132290624A>G	ENST00000295171.6	+	7	1127	c.989A>G	c.(988-990)aAg>aGg	p.K330R	CCDC74A_ENST00000467992.2_3'UTR|CCDC74A_ENST00000409856.3_Missense_Mutation_p.K264R	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	330										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						GTCTCCACCAAGAGCCTCTCC	0.637																																					p.K330R		.											.	CCDC74A-69	0			c.A989G						.						55	62	60					2																	132290624		2202	4280	6482	SO:0001583	missense	90557	exon7			CCACCAAGAGCCT		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.989A>G	2.37:g.132290624A>G	ENSP00000295171:p.Lys330Arg	Somatic	456	0		WXS	Illumina HiSeq	Phase_I	473	177	NM_138770	0	0	42	66	24	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	9.783	1.175737	0.21704	.	.	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.32988	1.43;1.43	3.07	3.07	0.35406	.	0.000000	0.34603	U	0.003821	T	0.46229	0.1382	L	0.56769	1.78	0.32221	N	0.57519	D;P	0.67145	0.996;0.927	D;D	0.75484	0.986;0.953	T	0.55379	-0.8150	10	0.66056	D	0.02	.	7.967	0.30104	1.0:0.0:0.0:0.0	.	264;330	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	R	330;264	ENSP00000295171:K330R;ENSP00000387009:K264R	ENSP00000295171:K330R	K	+	2	0	CCDC74A	132007094	0.982000	0.34865	0.108000	0.21378	0.014000	0.08584	1.298000	0.33412	1.179000	0.42884	0.352000	0.21897	AAG	.		0.637	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770		G	132290624	A	G	132290624	3	3	22	1	0	0	0	0	1	0	0	0	2853	72	3	3	1015	3	CCDC74A	2	132290624	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	61102492	132290624	110908749	9	1921											
METTL8	79828	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	172195861	172195862	+	Missense_Mutation	DNP	GA	GA	AG																															tttttcatcaggcacagtagGacagtgcattcttgagaaac																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:172195861_172195862GA>AG	ENST00000375258.4	-	4	653_654	c.438_439TC>CT	c.(436-441)tgTCct>tgCTct	p.P147S		NM_024770.3	NP_079046.2	Q9H825	METL8_HUMAN	methyltransferase like 8	147						cytoplasm (GO:0005737)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	11						GGCACAGTAGGACAGTGCATTC	0.366																																					p.P147S													.	METTL8-91	0			.						.																																			SO:0001583	missense	79828	.			AGTAGGACAGTGC	AK024046	CCDS2242.1, CCDS2242.2	2q31.1	2012-06-12			ENSG00000123600	ENSG00000123600			25856	protein-coding gene	gene with protein product	"tension-induced/inhibited protein"	609525				15992539	Standard	NM_024770		Approved	FLJ13984, TIP	uc010zdo.2	Q9H825	OTTHUMG00000132261	ENST00000375258.4:c.438_439delinsAG	2.37:g.172195861_172195862delinsAG	ENSP00000364407:p.Pro147Ser	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	98	22	.	0	0	0	0	0	Q53TM9|Q53TQ0	Missense_Mutation	DNP	ENST00000375258.4	37																																																																																				.		0.366	METTL8-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255345.3	NM_024770		AG	172195862	GA	AG	172195861	3	1	22	1	0	0	0	0	1	0	0	0	9532	1174	41	2	812	2	METTL8	2	172195861	Missense_Mutation	DNP	GA	TCGA-A4-A4ZT-01A-11D-A26P-10	39905237	172195861	71003512	10	1922											
PTPRN	5798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220161482	220161482	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactcacaatggggctggCgttgatgtaatcgctccgag	8	9	13	11	3	1	1	1	1	0	0	3	2	2	1	2	3	0	4	2	3	2	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:220161482C>T	ENST00000295718.2	-	16	2539	c.2299G>A	c.(2299-2301)Gcc>Acc	p.A767T	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.A677T|PTPRN_ENST00000497977.1_5'Flank|MIR153-1_ENST00000384914.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.A738T	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	767	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		ATGGGGCTGGCGTTGATGTAA	0.607																																					p.A767T		.											.	PTPRN-229	0			c.G2299A						.						116	99	104					2																	220161482		2203	4300	6503	SO:0001583	missense	5798	exon16			GGCTGGCGTTGAT		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.2299G>A	2.37:g.220161482C>T	ENSP00000295718:p.Ala767Thr	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	199	46	NM_002846	0	0	0	0	0	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590157	0.86851	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.59364	0.27;0.27;0.27	4.24	4.24	0.50183	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.151418	0.41938	D	0.000789	D	0.85221	0.5647	H	0.98594	4.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.956;0.998	D	0.91588	0.5284	10	0.87932	D	0	.	16.4513	0.83991	0.0:1.0:0.0:0.0	.	738;767	Q6NSL1;Q16849	.;PTPRN_HUMAN	T	738;767;738;677	ENSP00000386638:A738T;ENSP00000295718:A767T;ENSP00000444244:A677T	ENSP00000295718:A767T	A	-	1	0	PTPRN	219869726	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.198000	0.77823	2.187000	0.69744	0.563000	0.77884	GCC	.		0.607	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			T	220161482	C	T	220161482	3	4	22	1	0	0	0	0	1	0	0	0	12839	768	27	1	672	1	PTPRN	2	220161482	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	47965621	220161482	23037891	11	1923											
DOCK10	55619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	225688235	225688235	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taccttgagaaatctggcaaCgctgtggtttgcccttcttg	7	14	10	10	1	2	1	0	1	2	1	2	2	2	1	2	2	3	3	2	2	3	5	rs371861682		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:225688235C>T	ENST00000258390.7	-	28	3233	c.3166G>A	c.(3166-3168)Gtt>Att	p.V1056I	DOCK10_ENST00000409592.3_Missense_Mutation_p.V1050I	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1056					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V1054F(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AATCTGGCAACGCTGTGGTTT	0.413																																					p.V1056I		.											.	DOCK10-92	1	Substitution - Missense(1)	breast(1)	c.G3166A						.	C	ILE/VAL	0,3770		0,0,1885	191	181	184		3166	4.2	0.8	2		184	2,8232		0,2,4115	no	missense	DOCK10	NM_014689.2	29	0,2,6000	TT,TC,CC		0.0243,0.0,0.0167	benign	1056/2187	225688235	2,12002	1885	4117	6002	SO:0001583	missense	55619	exon28			TGGCAACGCTGTG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3166G>A	2.37:g.225688235C>T	ENSP00000258390:p.Val1056Ile	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	224	121	NM_014689	0	0	3	3	0	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292507	0.40594	0.0	2.43E-4	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.67171	3.85;-0.25	6.0	4.2	0.49525	.	0.302824	0.35349	N	0.003275	T	0.55146	0.1902	L	0.38838	1.175	0.21933	N	0.999469	B;B	0.12013	0.005;0.001	B;B	0.08055	0.002;0.003	T	0.49542	-0.8929	10	0.49607	T	0.09	.	10.9896	0.47541	0.0:0.7834:0.0:0.2166	.	1056;1050	Q96BY6;B3FL70	DOC10_HUMAN;.	I	1050;1056	ENSP00000386694:V1050I;ENSP00000258390:V1056I	ENSP00000258390:V1056I	V	-	1	0	DOCK10	225396479	0.057000	0.20700	0.828000	0.32881	0.970000	0.65996	0.541000	0.23207	0.862000	0.35528	0.643000	0.83706	GTT	.		0.413	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225688235	C	T	225688235	3	4	22	1	0	0	0	0	1	0	0	0	4696	536	19	1	3510	1	DOCK10	2	225688235	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	5526753	225688235	17511138	12	1924											
SP140L	93349	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	231264856	231264856	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctagatgagaaacttggaTgagtgtgaggtgtgccggga	10	11	16	4	1	1	4	0	3	1	2	1	7	1	6	1	3	2	0	1	3	2	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:231264856T>A	ENST00000415673.2	+	15	1298	c.1212T>A	c.(1210-1212)gaT>gaA	p.D404E	SP140L_ENST00000396563.4_Missense_Mutation_p.D369E|SP140L_ENST00000243810.6_Missense_Mutation_p.D404E|SP140L_ENST00000444636.1_Missense_Mutation_p.D404E	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	404						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GAAACTTGGATGAGTGTGAGG	0.512																																					p.D404E		.											.	SP140L-23	0			c.T1212A						.						181	183	182					2																	231264856		2043	4208	6251	SO:0001583	missense	93349	exon15			CTTGGATGAGTGT	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1212T>A	2.37:g.231264856T>A	ENSP00000397911:p.Asp404Glu	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	389	213	NM_138402	0	0	0	1	1	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.883793	0.51908	.	.	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	3.5	-2.37	0.06643	.	.	.	.	.	T	0.81235	0.4780	L	0.52126	1.63	0.09310	N	1	P;P	0.45044	0.849;0.663	B;P	0.45794	0.382;0.493	T	0.71507	-0.4572	9	0.72032	D	0.01	.	0.2987	0.00269	0.1938:0.243:0.1988:0.3644	.	369;404	Q9H930-2;Q9H930-4	.;.	E	404;404;404;369	ENSP00000395195:D404E;ENSP00000397911:D404E;ENSP00000243810:D404E;ENSP00000379811:D369E	ENSP00000243810:D404E	D	+	3	2	SP140L	230973100	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-1.650000	0.01991	-0.178000	0.10672	-0.415000	0.06103	GAT	.		0.512	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		A	231264856	T	A	231264856	3	1	22	1	0	0	0	0	1	0	0	0	14995	1461	51	5	1270	5	SP140L	2	231264856	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	5576621	231264856	11934517	13	1925											
OXTR	5021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	8809352	8809352	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacctcgcgcagagagaaGatgtgcacctgcggcgcgct	8	5	14	14	5	0	3	0	0	0	3	1	4	0	3	3	1	2	3	3	1	1	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr3:8809352G>T	ENST00000316793.3	-	3	1146	c.522C>A	c.(520-522)atC>atA	p.I174I	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	174					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	GCAGAGAGAAGATGTGCACCT	0.692																																					p.I174I		.											.	OXTR-68	0			c.C522A						.						34	39	37					3																	8809352		2203	4300	6503	SO:0001819	synonymous_variant	5021	exon3			AGAGAAGATGTGC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"GPCR / Class A : Vasopressin and oxytocin receptors"	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.522C>A	3.37:g.8809352G>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	187	101	NM_000916	0	0	0	0	0	Q15071	Silent	SNP	ENST00000316793.3	37	CCDS2570.1																																																																																			.		0.692	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2			T	8809352	G	T	8809352	2	4	22	1	0	0	0	0	0	0	0	1	11364	932	33	4		4	OXTR	3	8809352	Silent	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		8809352	189213078	14	1926											
FNDC3B	64778	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	171969140	171969140	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaactgaaagaccgccagaTcgatcgccagaaccgcctca	15	4	8	14	4	1	4	1	1	0	3	3	5	1	4	5	0	2	0	5	0	4	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr3:171969140T>A	ENST00000336824.4	+	6	698	c.599T>A	c.(598-600)aTc>aAc	p.I200N	FNDC3B_ENST00000416957.1_Missense_Mutation_p.I200N|FNDC3B_ENST00000415807.2_Missense_Mutation_p.I200N	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	200					cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GACCGCCAGATCGATCGCCAG	0.463																																					p.I200N													.	FNDC3B-155	0			c.T599A						.						66	67	67					3																	171969140		2203	4300	6503	SO:0001583	missense	64778	exon6			GCCAGATCGATCG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.599T>A	3.37:g.171969140T>A	ENSP00000338523:p.Ile200Asn	Somatic	111	1		WXS	Illumina HiSeq	Phase_I	162	92	NM_001135095	0	0	5	14	9	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.805927	0.50421	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957;ENST00000443501	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.78	4.43	0.53597	.	0.228496	0.44483	D	0.000441	T	0.24005	0.0581	L	0.40543	1.245	0.80722	D	1	B;B	0.32160	0.358;0.147	B;B	0.30179	0.112;0.063	T	0.04537	-1.0944	10	0.27082	T	0.32	-20.4035	12.3626	0.55211	0.0:0.0762:0.0:0.9238	.	200;200	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	N	200;200;200;173	ENSP00000411242:I200N;ENSP00000338523:I200N;ENSP00000389094:I200N;ENSP00000389064:I173N	ENSP00000338523:I200N	I	+	2	0	FNDC3B	173451834	1.000000	0.71417	0.982000	0.44146	0.988000	0.76386	3.590000	0.53979	2.205000	0.71048	0.482000	0.46254	ATC	.		0.463	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		A	171969140	T	A	171969140	3	1	22	1	0	0	0	0	1	0	0	0	5989	1435	50	5	617	5	FNDC3B	3	171969140	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	163159788	171969140	26053290	15	1927											
PARL	55486	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183558378	183558378	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcaccaagtgatggtccatAtcttcctgtggcaactttac	9	13	8	11	0	1	1	0	1	1	0	3	1	3	1	3	2	3	2	3	2	4	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr3:183558378A>G	ENST00000317096.4	-	7	868	c.808T>C	c.(808-810)Tat>Cat	p.Y270H	PARL_ENST00000435888.1_Missense_Mutation_p.Y220H|PARL_ENST00000311101.5_Missense_Mutation_p.Y220H	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	270					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GATGGTCCATATCTTCCTGTG	0.279																																					p.Y270H													.	PARL-90	0			c.T808C						.						58	54	56					3																	183558378		2203	4300	6503	SO:0001583	missense	55486	exon7			GTCCATATCTTCC	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"rhomboid 7 homolog 1 (Drosophila)"	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.808T>C	3.37:g.183558378A>G	ENSP00000325421:p.Tyr270His	Somatic	157	1		WXS	Illumina HiSeq	Phase_I	192	65	NM_018622	0	0	36	48	12	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	37	CCDS3248.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.32|12.32	1.901679|1.901679	0.33535|0.33535	.|.	.|.	ENSG00000175193|ENSG00000175193	ENST00000417784;ENST00000449306|ENST00000317096;ENST00000311101;ENST00000450375;ENST00000435888	.|T;T;T;T	.|0.11930	.|2.73;2.73;2.73;2.73	5.08|5.08	5.08|5.08	0.68730|0.68730	.|Peptidase S54, rhomboid domain (1);	.|0.202877	.|0.43579	.|D	.|0.000542	T|T	0.08537|0.08537	0.0212|0.0212	N|N	0.12471|0.12471	0.22|0.22	0.41648|0.41648	D|D	0.989116|0.989116	.|B;B	.|0.12013	.|0.005;0.0	.|B;B	.|0.11329	.|0.006;0.001	T|T	0.26503|0.26503	-1.0101|-1.0101	5|10	.|0.16420	.|T	.|0.52	-14.7906|-14.7906	15.1375|15.1375	0.72579|0.72579	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|220;270	.|Q9H300-2;Q9H300	.|.;PARL_HUMAN	T|H	61;133|270;220;50;220	.|ENSP00000325421:Y270H;ENSP00000310676:Y220H;ENSP00000402689:Y50H;ENSP00000402137:Y220H	.|ENSP00000310676:Y220H	I|Y	-|-	2|1	0|0	PARL|PARL	185041072|185041072	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.953000|0.953000	0.61014|0.61014	5.259000|5.259000	0.65485|0.65485	2.042000|2.042000	0.60477|0.60477	0.460000|0.460000	0.39030|0.39030	ATA|TAT	.		0.279	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		G	183558378	A	G	183558378	3	3	22	1	0	0	0	0	1	0	0	0	11477	449	16	3	347	3	PARL	3	183558378	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	11589238	183558378	14464052	16	1928											
WDR1	9948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	10099338	10099338	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtaagttcacttacgccAattgtgaacttgaacttgaa	15	12	7	7	1	1	3	1	3	0	0	1	3	1	3	1	0	3	2	1	0	7	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:10099338A>G	ENST00000499869.2	-	5	748	c.555T>C	c.(553-555)atT>atC	p.I185I	WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382452.2_Silent_p.I185I|WDR1_ENST00000382451.2_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	185			I -> V (in dbSNP:rs13441). {ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CACTTACGCCAATTGTGAACT	0.507																																					p.I185I		.											.	WDR1-48	0			c.T555C						.						62	66	65					4																	10099338		1963	4144	6107	SO:0001819	synonymous_variant	9948	exon5			TACGCCAATTGTG	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.555T>C	4.37:g.10099338A>G		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	124	48	NM_017491	0	0	0	0	0	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Silent	SNP	ENST00000499869.2	37	CCDS54740.1																																																																																			.		0.507	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			G	10099338	A	G	10099338	2	3	22	1	0	0	0	0	0	0	0	1	17305	126	5	3		3	WDR1	4	10099338	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		10099338	181054938	17	1929											
UBA6	55236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	68536260	68536261	+	Frame_Shift_Ins	INS	-	-	T																															aaacttcaaattcatcaccgINSaaatcacaaaataaccttga																								rs140398587		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:68536260_68536261insT	ENST00000322244.5	-	8	655_656	c.596_597insA	c.(595-597)ttcfs	p.F199fs	UBA6_ENST00000420827.2_Frame_Shift_Ins_p.F199fs	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	199					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						ATTCATCACCGAAATCACAAAA	0.267																																					p.F199fs		.											.	UBA6-90	0			c.597_598insA						.																																			SO:0001589	frameshift_variant	55236	exon8			.	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"Ubiquitin-like modifier activating enzymes"	25581	protein-coding gene	gene with protein product	"UBA6, ubiquitin-activating enzyme E1"	611361	"ubiquitin-activating enzyme E1-like 2"	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.596_597insA	4.37:g.68536260_68536261insT	ENSP00000313454:p.Phe199fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	96	23	NM_018227	0	0	0	0	0	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Frame_Shift_Ins	INS	ENST00000322244.5	37	CCDS3516.1																																																																																			.		0.267	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		T	68536261	-	T	68536260	7	5	22	1	0	1	1	0	0	0	0	0	16865	1049	37	0	2665	0	UBA6	4	68536260	Frame_Shift_Ins	INS	-	TCGA-A4-A4ZT-01A-11D-A26P-10	58436922	68536260	122618016	18	1930	15	2									
UBA6	55236	hgsc.bcm.edu	37	chr4	68536261	68536261	+	Frame_Shift_Del	DEL	A	A	-																															aaacttcaaattcatcaccgAaatcacaaaataaccttgac																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:68536261delA	ENST00000322244.5	-	8	655	c.596delT	c.(595-597)ttcfs	p.F199fs	UBA6_ENST00000420827.2_Frame_Shift_Del_p.F199fs	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	199					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						TTCATCACCGAAATCACAAAA	0.269																																					p.F199fs		.											.	UBA6-90	0			c.596delT						.						91	94	93					4																	68536261		2203	4294	6497	SO:0001589	frameshift_variant	55236	exon8			.	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"Ubiquitin-like modifier activating enzymes"	25581	protein-coding gene	gene with protein product	"UBA6, ubiquitin-activating enzyme E1"	611361	"ubiquitin-activating enzyme E1-like 2"	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.596delT	4.37:g.68536261delA	ENSP00000313454:p.Phe199fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	96	21	NM_018227	0	0	0	0	0	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Frame_Shift_Del	DEL	ENST00000322244.5	37	CCDS3516.1																																																																																			.		0.269	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		-	68536261	A	-	68536261	7	5	22	1	0	1	0	1	0	0	0	0	16865	246	9	0	2666	0	UBA6	4	68536261	Frame_Shift_Del	DEL	A	TCGA-A4-A4ZT-01A-11D-A26P-10	1	68536261	122618015	19	1931	15	2									
FAM13A	10144	bcgsc.ca	37	chr4	89772288	89772288	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcagatagctctggttgcAgtactctgtgggcctgaata	9	12	11	9	0	3	2	1	1	2	1	3	2	3	2	1	2	3	4	1	2	4	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:89772288A>G	ENST00000264344.5	-	7	1097	c.890T>C	c.(889-891)cTg>cCg	p.L297P	FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000502459.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	297					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						CTCTGGTTGCAGTACTCTGTG	0.448																																					p.L297P													.	FAM13A-70	0			c.T890C						.						120	125	123					4																	89772288		2203	4300	6503	SO:0001583	missense	10144	exon7			GGTTGCAGTACTC	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.890T>C	4.37:g.89772288A>G	ENSP00000264344:p.Leu297Pro	Somatic	60	0		WXS	Illumina HiSeq	Phase_1	70	4	NM_014883	0	0	0	0	0	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	A	8.362	0.833254	0.16820	.	.	ENSG00000138640	ENST00000264344	T	0.19250	2.16	4.42	2.28	0.28536	.	0.539992	0.17335	N	0.177970	T	0.06325	0.0163	N	0.01352	-0.895	0.21184	N	0.999769	B	0.02656	0.0	B	0.01281	0.0	T	0.30031	-0.9992	10	0.37606	T	0.19	.	5.2731	0.15636	0.3336:0.0:0.6664:0.0	.	297	O94988	FA13A_HUMAN	P	297	ENSP00000264344:L297P	ENSP00000264344:L297P	L	-	2	0	FAM13A	89991311	0.961000	0.32948	0.011000	0.14972	0.284000	0.27059	1.335000	0.33839	0.561000	0.29186	-0.248000	0.11899	CTG	.		0.448	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			G	89772288	A	G	89772288	3	3	22	1	0	0	0	0	1	0	0	0	5468	188	7	3	2286	3	FAM13A	4	89772288	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	21236027	89772288	101381988	20	1932											
ANK2	287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	114277121	114277121	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagaagataactcttcacaCaaaacccctgattctctgga	14	10	5	12	0	3	3	1	1	2	2	4	4	3	4	2	1	2	0	2	1	5	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:114277121C>A	ENST00000357077.4	+	38	7400	c.7347C>A	c.(7345-7347)caC>caA	p.H2449Q	ANK2_ENST00000506722.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.H2416Q|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2449					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ACTCTTCACACAAAACCCCTG	0.502																																					p.H2449Q		.											.	ANK2-583	0			c.C7347A						.						75	74	74					4																	114277121		2203	4300	6503	SO:0001583	missense	287	exon38			TTCACACAAAACC	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.7347C>A	4.37:g.114277121C>A	ENSP00000349588:p.His2449Gln	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	80	28	NM_001148	0	0	0	0	0	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734944	0.48939	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.70516	-0.48;-0.49	5.85	5.01	0.66863	.	0.000000	0.64402	D	0.000013	T	0.69015	0.3064	L	0.54323	1.7	0.80722	D	1	B;P	0.41848	0.144;0.763	B;P	0.44990	0.053;0.466	T	0.67665	-0.5612	9	.	.	.	.	11.2279	0.48895	0.0:0.8096:0.0:0.1904	.	2416;2449	Q01484;Q01484-4	ANK2_HUMAN;.	Q	2449;2416	ENSP00000349588:H2449Q;ENSP00000264366:H2416Q	.	H	+	3	2	ANK2	114496570	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.444000	0.21661	1.488000	0.48433	0.655000	0.94253	CAC	.		0.502	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114277121	C	A	114277121	3	1	22	1	0	0	0	0	1	0	0	0	621	477	17	4	7562	4	ANK2	4	114277121	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	24504833	114277121	76877155	21	1933											
AHRR	57491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	353963	353963	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcctgacatcatctccaagCtggacaagctttctgtcctg	8	11	8	14	1	3	1	1	1	2	0	5	2	4	2	3	1	2	2	3	1	2	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr5:353963C>T	ENST00000505113.1	+	3	237	c.193C>T	c.(193-195)Ctg>Ttg	p.L65L	AHRR_ENST00000515206.1_Silent_p.L61L|AHRR_ENST00000316418.5_Silent_p.L65L|AHRR_ENST00000512529.1_Intron	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	65	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.L61V(2)		breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			CATCTCCAAGCTGGACAAGCT	0.592																																					p.L65L		.											.	AHRR-225	2	Substitution - Missense(2)	lung(2)	c.C193T						.						102	115	111					5																	353963		2130	4244	6374	SO:0001819	synonymous_variant	57491	exon3			TCCAAGCTGGACA	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"Basic helix-loop-helix proteins"	346	protein-coding gene	gene with protein product		606517	"aryl hydrocarbon receptor regulator"	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.193C>T	5.37:g.353963C>T		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	193	67	NM_001242412	0	0	0	0	0	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Silent	SNP	ENST00000505113.1	37	CCDS56355.1																																																																																			.		0.592	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		T	353963	C	T	353963	2	4	22	1	0	0	0	0	0	0	0	1	417	796	28	2		2	AHRR	5	353963	Silent	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10		353963	180561297	22	1934											
C5orf44	80006	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	64956553	64956553	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgtttgggtcaagagcataTttgcaaccaatggatacacg	13	10	10	8	2	1	1	1	0	0	1	1	2	1	2	1	2	4	3	1	2	5	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr5:64956553T>G	ENST00000399438.3	+	10	1071	c.726T>G	c.(724-726)taT>taG	p.Y242*	TRAPPC13_ENST00000505553.1_Nonsense_Mutation_p.Y236*|TRAPPC13_ENST00000545191.1_Nonsense_Mutation_p.Y243*|TRAPPC13_ENST00000231526.4_Nonsense_Mutation_p.Y236*|TRAPPC13_ENST00000438419.2_Nonsense_Mutation_p.Y242*	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	242																	CAAGAGCATATTTGCAACCAA	0.408																																					p.Y242X													.	.	0			c.T726G						.						83	77	79					5																	64956553		1878	4116	5994	SO:0001587	stop_gained	80006	exon10			AGCATATTTGCAA		CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597			25828	protein-coding gene	gene with protein product	"Trs65-related"		"chromosome 5 open reading frame 44"	C5orf44		12477932	Standard	NM_024941		Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.726T>G	5.37:g.64956553T>G	ENSP00000382367:p.Tyr242*	Somatic	243	1		WXS	Illumina HiSeq	Phase_I	234	86	NM_001093755	0	0	5	8	3	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	Nonsense_Mutation	SNP	ENST00000399438.3	37	CCDS47222.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.200295	0.79015	.	.	ENSG00000113597	ENST00000399438;ENST00000438419;ENST00000231526;ENST00000505553;ENST00000545191	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.6909	9.5899	0.39539	0.0:0.091:0.0:0.909	.	.	.	.	X	242;242;236;236;243	.	ENSP00000231526:Y236X	Y	+	3	2	C5orf44	64992309	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.129000	0.31381	1.913000	0.55393	0.379000	0.24179	TAT	.		0.408	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370113.1	NM_024941		G	64956553	T	G	64956553	4	3	22	1	0	0	0	0	0	1	0	0	2309	1500	52	5	764	5	C5orf44	5	64956553	Nonsense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	64602590	64956553	115958707	23	1935											
LIX1	167410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	96443096	96443096	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tactgcttcctgaacactttCcataatgaattccttggtga	10	15	6	10	0	0	3	0	3	0	0	3	3	3	3	3	1	3	1	3	1	4	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr5:96443096C>A	ENST00000274382.4	-	3	650	c.355G>T	c.(355-357)Gaa>Taa	p.E119*	CTD-2215E18.1_ENST00000509481.1_Intron	NM_153234.4	NP_694966.3	Q8N485	LIX1_HUMAN	Lix1 homolog (chicken)	119										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)	10		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)		TGAACACTTTCCATAATGAAT	0.527																																					p.E119X		.											.	LIX1-92	0			c.G355T						.						109	102	105					5																	96443096		2203	4300	6503	SO:0001587	stop_gained	167410	exon3			CACTTTCCATAAT		CCDS4088.1	5q15	2008-03-06	2008-03-06	2005-02-07	ENSG00000145721	ENSG00000145721			18581	protein-coding gene	gene with protein product		610466	"chromosome 5 open reading frame 11", "Lix1 homolog (mouse)"	C5orf11		11731258	Standard	NM_153234		Approved		uc003kmy.4	Q8N485	OTTHUMG00000128720	ENST00000274382.4:c.355G>T	5.37:g.96443096C>A	ENSP00000274382:p.Glu119*	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	137	38	NM_153234	0	0	3	5	2	A8K4R9|Q8N7I2	Nonsense_Mutation	SNP	ENST00000274382.4	37	CCDS4088.1	.	.	.	.	.	.	.	.	.	.	C	37	6.428078	0.97559	.	.	ENSG00000145721	ENST00000274382	.	.	.	6.17	6.17	0.99709	.	0.186655	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.9396	13.6552	0.62333	0.0:0.9294:0.0:0.0706	.	.	.	.	X	119	.	ENSP00000274382:E119X	E	-	1	0	LIX1	96468852	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.753000	0.38359	2.941000	0.99782	0.655000	0.94253	GAA	.		0.527	LIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250625.1	NM_153234		A	96443096	C	A	96443096	4	1	22	1	0	0	0	0	0	1	0	0	8854	864	30	4	509	4	LIX1	5	96443096	Nonsense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	31486543	96443096	84472164	24	1936											
HIST1H2BN	8341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	27806755	27806755	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcgcctgctgctgccagggGagctggccaagcacgcggtg	5	6	17	13	3	0	0	0	0	0	0	0	1	0	1	3	4	6	4	3	4	1	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr6:27806755G>A	ENST00000396980.3	+	1	316	c.316G>A	c.(316-318)Gag>Aag	p.E106K	HIST1H2AK_ENST00000330180.2_5'Flank|HIST1H2BN_ENST00000606613.1_Missense_Mutation_p.E106K	NM_003520.3	NP_003511.1	Q99877	H2B1N_HUMAN	histone cluster 1, H2bn	106					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(3)|lung(3)|prostate(1)	8						GCTGCCAGGGGAGCTGGCCAA	0.677																																					p.E106K		.											.	HIST1H2BN-68	0			c.G316A						.						57	61	60					6																	27806755		2203	4299	6502	SO:0001583	missense	8341	exon1			CCAGGGGAGCTGG	Z83336	CCDS4633.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000233822	ENSG00000233822		"Histones / Replication-dependent"	4749	protein-coding gene	gene with protein product		602801	"H2B histone family, member D", "histone 1, H2bn"	H2BFD		9439656, 12408966	Standard	NM_003520		Approved	H2B/d	uc003njv.3	Q99877	OTTHUMG00000016397	ENST00000396980.3:c.316G>A	6.37:g.27806755G>A	ENSP00000380177:p.Glu106Lys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	62	23	NM_003520	0	0	0	0	0	B2R5L4|Q494S8|Q96FB7	Missense_Mutation	SNP	ENST00000396980.3	37	CCDS4633.1	.	.	.	.	.	.	.	.	.	.	.	14.44	2.536027	0.45176	.	.	ENSG00000233822	ENST00000449538;ENST00000396980	T;T	0.78126	-1.15;-1.15	4.71	4.71	0.59529	Histone-fold (2);	0.000000	0.43747	U	0.000529	T	0.78710	0.4326	M	0.93106	3.38	0.37318	D	0.90942	B;B	0.28713	0.014;0.22	B;B	0.26202	0.009;0.067	D	0.83433	0.0039	10	0.87932	D	0	.	17.5855	0.87980	0.0:0.0:1.0:0.0	.	106;106	Q99877;B2R4S9	H2B1N_HUMAN;.	K	106	ENSP00000446031:E106K;ENSP00000380177:E106K	ENSP00000380177:E106K	E	+	1	0	HIST1H2BN	27914734	1.000000	0.71417	1.000000	0.80357	0.301000	0.27625	7.723000	0.84788	2.537000	0.85549	0.650000	0.86243	GAG	.		0.677	HIST1H2BN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043840.2	NM_003520		A	27806755	G	A	27806755	3	1	22	1	0	0	0	0	1	0	0	0	7174	1175	41	2	318	2	HIST1H2BN	6	27806755	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		27806755	143308312	25	1937											
PPP1R10	5514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30572781	30572781	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcccataccttggcagccGtaggtgacagtacttttttt	8	13	10	10	1	0	1	0	1	0	0	0	2	0	1	3	2	4	3	3	2	3	7			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr6:30572781G>A	ENST00000376511.2	-	11	1496	c.944C>T	c.(943-945)aCg>aTg	p.T315M		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	315	Interaction with TOX4. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						CTTGGCAGCCGTAGGTGACAG	0.468																																					p.T315M		.											.	PPP1R10-660	0			c.C944T						.						47	57	53					6																	30572781		1511	2709	4220	SO:0001583	missense	5514	exon11			GCAGCCGTAGGTG	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.944C>T	6.37:g.30572781G>A	ENSP00000365694:p.Thr315Met	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	89	29	NM_002714	0	0	3	4	1	O00405	Missense_Mutation	SNP	ENST00000376511.2	37	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084609	0.55861	.	.	ENSG00000204569	ENST00000376511	T	0.62498	0.02	5.06	5.06	0.68205	.	0.049773	0.85682	D	0.000000	T	0.61362	0.2341	N	0.19112	0.55	0.58432	D	0.999997	D	0.89917	1.0	D	0.83275	0.996	T	0.66799	-0.5832	10	0.56958	D	0.05	-10.3518	17.3696	0.87372	0.0:0.0:1.0:0.0	.	315	Q96QC0	PP1RA_HUMAN	M	315	ENSP00000365694:T315M	ENSP00000365694:T315M	T	-	2	0	PPP1R10	30680760	1.000000	0.71417	0.995000	0.50966	0.762000	0.43233	6.222000	0.72249	2.642000	0.89623	0.561000	0.74099	ACG	.		0.468	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		A	30572781	G	A	30572781	3	1	22	1	0	0	0	0	1	0	0	0	12381	1145	40	1	1918	1	PPP1R10	6	30572781	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	2766026	30572781	140542286	26	1938											
UNC5CL	222643	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	40999454	40999454	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatggtgacaatgatctcaTtggttagtgctgaacagtcc	10	12	11	8	0	1	3	1	3	1	0	3	3	2	3	1	2	2	3	1	2	3	2	rs145811250	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr6:40999454T>A	ENST00000373164.1	-	5	1145	c.1085A>T	c.(1084-1086)aAt>aTt	p.N362I	UNC5CL_ENST00000470102.1_Intron|UNC5CL_ENST00000244565.3_Missense_Mutation_p.N362I			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	362	Interaction with RELA and NFKB1.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					AATGATCTCATTGGTTAGTGC	0.547																																					p.N362I		.											.	UNC5CL-92	0			c.A1085T						.						196	174	181					6																	40999454		2203	4300	6503	SO:0001583	missense	222643	exon6			ATCTCATTGGTTA	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1085A>T	6.37:g.40999454T>A	ENSP00000362258:p.Asn362Ile	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	170	64	NM_173561	0	0	7	10	3	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	37	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.024767	0.35701	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	T;T	0.14391	2.51;2.51	4.52	3.34	0.38264	.	0.124350	0.36482	N	0.002565	T	0.02649	0.0080	N	0.24115	0.695	0.37746	D	0.925799	B	0.11235	0.004	B	0.09377	0.004	T	0.35549	-0.9784	10	0.22109	T	0.4	-8.9542	6.7625	0.23548	0.0:0.1071:0.0:0.8929	.	362	Q8IV45	UN5CL_HUMAN	I	362	ENSP00000244565:N362I;ENSP00000362258:N362I	ENSP00000244565:N362I	N	-	2	0	UNC5CL	41107432	1.000000	0.71417	0.996000	0.52242	0.944000	0.59088	0.406000	0.21032	0.770000	0.33336	0.383000	0.25322	AAT	T|0.998;C|0.002		0.547	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		A	40999454	T	A	40999454	3	1	22	1	0	0	0	0	1	0	0	0	17027	1493	52	5	487	5	UNC5CL	6	40999454	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	10426673	40999454	130115613	27	1939											
ACTB	60	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5567473	5567473	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggacagcgaggccaggAtggagccgccgatccacacg	10	3	16	12	4	0	0	0	0	0	0	1	5	1	3	4	5	2	0	4	5	0	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr7:5567473A>G	ENST00000331789.5	-	6	1225	c.1034T>C	c.(1033-1035)aTc>aCc	p.I345T	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'UTR	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	345					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		CGAGGCCAGGATGGAGCCGCC	0.612																																					p.I345T		.											.	ACTB-226	0			c.T1034C						.						67	70	69					7																	5567473		2203	4300	6503	SO:0001583	missense	60	exon6			GCCAGGATGGAGC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.1034T>C	7.37:g.5567473A>G	ENSP00000349960:p.Ile345Thr	Somatic	230	1		WXS	Illumina HiSeq	Phase_I	407	193	NM_001101	1	1	1389	2570	1178	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.232891	0.58777	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713	D	0.95788	-3.81	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000013	D	0.98535	0.9511	H	0.94886	3.595	0.53005	D	0.99996	P	0.40032	0.699	D	0.79108	0.992	D	0.99293	1.0899	10	0.87932	D	0	.	14.9227	0.70851	1.0:0.0:0.0:0.0	.	345	P60709	ACTB_HUMAN	T	345;321;317;264	ENSP00000349960:I345T	ENSP00000440549:I264T	I	-	2	0	ACTB	5533999	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.991000	0.93514	2.114000	0.64651	0.529000	0.55759	ATC	.		0.612	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		G	5567473	A	G	5567473	3	3	22	1	0	0	0	0	1	0	0	0	193	333	12	3	97	3	ACTB	7	5567473	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		5567473	153571190	28	1940											
AGK	55750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	141352597	141352597	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttctccccagggagcaggggGctcttttagcattgacagtg	7	11	13	10	0	2	1	0	1	2	0	3	2	2	2	2	3	2	3	2	3	1	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr7:141352597G>C	ENST00000355413.4	+	16	1402	c.1142G>C	c.(1141-1143)gGc>gCc	p.G381A	AGK_ENST00000473247.1_Missense_Mutation_p.G353A|RP5-894A10.2_ENST00000467537.1_RNA	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	381					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					GGAGCAGGGGGCTCTTTTAGC	0.502																																					p.G381A		.											.	AGK-290	0			c.G1142C						.						111	104	107					7																	141352597		2203	4300	6503	SO:0001583	missense	55750	exon16			CAGGGGGCTCTTT	BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.1142G>C	7.37:g.141352597G>C	ENSP00000347581:p.Gly381Ala	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	189	89	NM_018238	0	0	5	13	8	Q75KN1|Q96GC3|Q9NP48	Missense_Mutation	SNP	ENST00000355413.4	37	CCDS5865.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331077	0.81690	.	.	ENSG00000006530	ENST00000355413;ENST00000473247	T;T	0.12984	2.63;2.63	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.16428	0.0395	L	0.49126	1.545	0.80722	D	1	P	0.37663	0.604	B	0.32533	0.147	T	0.01848	-1.1261	10	0.72032	D	0.01	.	19.2669	0.93990	0.0:0.0:1.0:0.0	.	381	Q53H12	AGK_HUMAN	A	381;353	ENSP00000347581:G381A;ENSP00000420776:G353A	ENSP00000347581:G381A	G	+	2	0	AGK	140999066	1.000000	0.71417	0.986000	0.45419	0.515000	0.34225	8.920000	0.92779	2.549000	0.85964	0.655000	0.94253	GGC	.		0.502	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		C	141352597	G	C	141352597	3	2	22	1	0	0	0	0	1	0	0	0	383	1203	42	4	1200	4	AGK	7	141352597	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	135785124	141352597	17786066	29	1941											
C8orf80	389643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	27913490	27913490	+	Missense_Mutation	SNP	T	T	G																															ctattaactcaccttcagttTttccttgagaattctagtcc																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr8:27913490T>G	ENST00000413272.2	-	10	1340	c.1198A>C	c.(1198-1200)Aaa>Caa	p.K400Q	NUGGC_ENST00000341513.6_Missense_Mutation_p.K400Q	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	400					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										ACCTTCAGTTTTTCCTTGAGA	0.373																																					p.K400Q		.											.	.	0			c.A1198C						.						94	88	89					8																	27913490		1840	4086	5926	SO:0001583	missense	389643	exon10			TCAGTTTTTCCTT	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1198A>C	8.37:g.27913490T>G	ENSP00000408697:p.Lys400Gln	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	37	13	NM_001010906	0	0	0	0	0	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.739734	0.69304	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.15952	2.38;2.38	5.37	5.37	0.77165	.	0.192094	0.43919	D	0.000520	T	0.14485	0.0350	L	0.32530	0.975	0.37961	D	0.932984	P	0.47350	0.894	B	0.40444	0.329	T	0.05517	-1.0880	10	0.66056	D	0.02	-18.4502	11.7885	0.52055	0.0:0.0:0.0:1.0	.	400	Q68CJ6	SLIP_HUMAN	Q	400	ENSP00000408697:K400Q;ENSP00000345031:K400Q	ENSP00000345031:K400Q	K	-	1	0	C8orf80	27969409	0.999000	0.42202	0.999000	0.59377	0.985000	0.73830	2.663000	0.46774	2.030000	0.59900	0.455000	0.32223	AAA	.		0.373	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		G	27913490	T	G	27913490	3	3	22	1	0	0	0	0	1	0	0	0	2445	1850	64	5	1232	5	C8orf80	8	27913490	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10		27913490	118450532	30	1942	16	2									
C8orf80	389643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	27913492	27913492	+	Missense_Mutation	SNP	T	T	C																															attaactcaccttcagttttTccttgagaattctagtcctt																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr8:27913492T>C	ENST00000413272.2	-	10	1338	c.1196A>G	c.(1195-1197)gAa>gGa	p.E399G	NUGGC_ENST00000341513.6_Missense_Mutation_p.E399G	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	399					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										CTTCAGTTTTTCCTTGAGAAT	0.368																																					p.E399G		.											.	.	0			c.A1196G						.						93	87	88					8																	27913492		1839	4084	5923	SO:0001583	missense	389643	exon10			AGTTTTTCCTTGA	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1196A>G	8.37:g.27913492T>C	ENSP00000408697:p.Glu399Gly	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	36	13	NM_001010906	0	0	0	0	0	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.686312	0.47991	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.17054	2.3;2.32	5.37	4.2	0.49525	.	0.367956	0.29205	N	0.012835	T	0.12178	0.0296	L	0.32530	0.975	0.35309	D	0.783741	B	0.32245	0.361	B	0.25140	0.058	T	0.14952	-1.0454	10	0.59425	D	0.04	-7.5105	9.3405	0.38076	0.0:0.0:0.1808:0.8192	.	399	Q68CJ6	SLIP_HUMAN	G	399	ENSP00000408697:E399G;ENSP00000345031:E399G	ENSP00000345031:E399G	E	-	2	0	C8orf80	27969411	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.756000	0.38390	0.851000	0.35264	0.455000	0.32223	GAA	.		0.368	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		C	27913492	T	C	27913492	3	2	22	1	0	0	0	0	1	0	0	0	2445	1783	62	3	1234	3	C8orf80	8	27913492	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	2	27913492	118450530	31	1943	16	2									
ENPP2	5168	bcgsc.ca	37	chr8	120628549	120628549	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attaaatttctctcgccctcGcagatgaaaagtggcatcaa	13	11	7	10	2	2	2	1	1	1	1	5	2	2	2	1	1	0	2	1	1	5	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr8:120628549G>T	ENST00000075322.6	-	8	791	c.733C>A	c.(733-735)Cga>Aga	p.R245R	ENPP2_ENST00000427067.2_Silent_p.R241R|ENPP2_ENST00000259486.6_Silent_p.R245R|ENPP2_ENST00000522826.1_Silent_p.R245R	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	245	Substrate binding. {ECO:0000250}.				cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TCTCGCCCTCGCAGATGAAAA	0.373																																					p.R245R	Melanoma(20;305 879 2501 4818 31020)												.	ENPP2-292	0			c.C733A						.						123	110	114					8																	120628549		2203	4300	6503	SO:0001819	synonymous_variant	5168	exon8			GCCCTCGCAGATG	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.733C>A	8.37:g.120628549G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	57	4	NM_001130863	0	0	6	6	0	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			.		0.373	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			T	120628549	G	T	120628549	2	4	22	1	0	0	0	0	0	0	0	1	5143	1095	38	4		4	ENPP2	8	120628549	Silent	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	92715057	120628549	25735473	32	1944											
NUP188	23511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131735460	131735460	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccaccagcactgcatgcAtgtgtgtctatggactgctc	8	10	10	13	0	1	0	0	0	1	0	2	1	1	1	2	1	4	5	2	1	1	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr9:131735460A>G	ENST00000372577.2	+	12	1156	c.1135A>G	c.(1135-1137)Atg>Gtg	p.M379V		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	379					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CACTGCATGCATGTGTGTCTA	0.493																																					p.M379V		.											.	NUP188-207	0			c.A1135G						.						166	127	140					9																	131735460		2203	4300	6503	SO:0001583	missense	23511	exon12			GCATGCATGTGTG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.1135A>G	9.37:g.131735460A>G	ENSP00000361658:p.Met379Val	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	57	16	NM_015354	0	0	0	2	2	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.706341	0.30232	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.64618	-0.11	5.01	5.01	0.66863	.	0.175989	0.64402	D	0.000006	T	0.44623	0.1302	N	0.19112	0.55	0.40933	D	0.984408	B	0.11235	0.004	B	0.09377	0.004	T	0.39143	-0.9628	10	0.34782	T	0.22	0.8656	9.6632	0.39967	0.8449:0.0:0.0:0.1551	.	379	Q5SRE5	NU188_HUMAN	V	268;379	ENSP00000361658:M379V	ENSP00000349125:M268V	M	+	1	0	NUP188	130775281	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	3.448000	0.52943	2.014000	0.59158	0.451000	0.29950	ATG	.		0.493	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			G	131735460	A	G	131735460	3	3	22	1	0	0	0	0	1	0	0	0	10784	217	8	3	1181	3	NUP188	9	131735460	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		131735460	9477971	33	1945											
CSGALNACT2	55454	broad.mit.edu	37	chr10	43659419	43659419	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggacaagggagaggtcttGatgtttttctgtgatgttga	8	15	15	3	0	2	4	0	3	2	1	2	6	2	5	0	3	0	2	0	3	1	4	rs79064394		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:43659419G>T	ENST00000374466.3	+	5	1421	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	362					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.L362F(5)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GAGAGGTCTTGATGTTTTTCT	0.433																																					p.L362F													.	CSGALNACT2-69	5	Substitution - Missense(5)	endometrium(4)|kidney(1)	c.G1086T						.						223	221	222					10																	43659419		2203	4300	6503	SO:0001583	missense	55454	exon5			GGTCTTGATGTTT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1086G>T	10.37:g.43659419G>T	ENSP00000363590:p.Leu362Phe	Somatic	143	1		WXS	Illumina HiSeq	Phase_I	134	4	NM_018590	0	0	3	3	0	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499782	0.85176	.	.	ENSG00000169826	ENST00000374466	T	0.27256	1.68	6.08	5.17	0.71159	.	0.064535	0.64402	D	0.000004	T	0.57359	0.2048	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63721	-0.6573	10	0.87932	D	0	-11.7375	14.8306	0.70146	0.0683:0.0:0.9317:0.0	.	362	Q8N6G5	CGAT2_HUMAN	F	362	ENSP00000363590:L362F	ENSP00000363590:L362F	L	+	3	2	CSGALNACT2	42979425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.894000	0.99253	0.591000	0.81541	TTG	.		0.433	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43659419	G	T	43659419	3	4	22	1	0	0	0	0	1	0	0	0	3945	1281	45	4	1100	4	CSGALNACT2	10	43659419	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		43659419	91875328	34	1946											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	61832051	61832054	+	Frame_Shift_Del	DEL	TTGT	TTGT	-																															gtttttctttctgagacttaTtgttagtggctcccgaactc																								rs371964932		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	TTGT	TTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:61832051_61832054delTTGT	ENST00000280772.2	-	37	8776_8779	c.8585_8588delACAA	c.(8584-8589)aacaatfs	p.NN2862fs	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2862					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTGAGACTTATTGTTAGTGGCTCC	0.402																																					p.2862_2863del		.											.	ANK3-107	0			c.8585_8588del						.																																			SO:0001589	frameshift_variant	288	exon37			.	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8585_8588delACAA	10.37:g.61832051_61832054delTTGT	ENSP00000280772:p.Asn2862fs	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	85	13	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	37	CCDS7258.1																																																																																			.		0.402	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61832054	TTGT	-	61832051	7	5	22	1	0	1	0	1	0	0	0	0	622	1493	52	0	4886	0	ANK3	10	61832051	Frame_Shift_Del	DEL	TTGT	TCGA-A4-A4ZT-01A-11D-A26P-10	18172632	61832051	73702696	35	1947	17	3									
ANK3	288	hgsc.bcm.edu	37	chr10	61832052	61832061	+	Frame_Shift_Del	DEL	TGTTAGTGGC	TGTTAGTGGC	-																															tttttctttctgagacttatTgttagtggctcccgaactct																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	TGTTAGTGGC	TGTTAGTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:61832052_61832061delTGTTAGTGGC	ENST00000280772.2	-	37	8769_8778	c.8578_8587delGCCACTAACA	c.(8578-8589)gccactaacaatfs	p.ATNN2860fs	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2860					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TGAGACTTATTGTTAGTGGCTCCCGAACTC	0.41																																					p.2860_2863del		.											.	ANK3-107	0			c.8578_8587del						.																																			SO:0001589	frameshift_variant	288	exon37			.	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8578_8587delGCCACTAACA	10.37:g.61832052_61832061delTGTTAGTGGC	ENSP00000280772:p.Ala2860fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	87	18	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	37	CCDS7258.1																																																																																			.		0.41	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61832061	TGTTAGTGGC	-	61832052	7	5	22	1	0	1	0	1	0	0	0	0	622	1812	63	0	4887	0	ANK3	10	61832052	Frame_Shift_Del	DEL	TGTTAGTGGC	TCGA-A4-A4ZT-01A-11D-A26P-10	1	61832052	73702695	36	1948	17	3									
ANK3	288	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	61832057	61832061	+	Frame_Shift_Del	DEL	GTGGC	GTGGC	-																															ctttctgagacttattgttaGtggctcccgaactctcccat																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GTGGC	GTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:61832057_61832061delGTGGC	ENST00000280772.2	-	37	8769_8773	c.8578_8582delGCCAC	c.(8578-8583)gccactfs	p.AT2860fs	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2860					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTTATTGTTAGTGGCTCCCGAACTC	0.415																																					p.2860_2861del		.											.	ANK3-107	0			c.8578_8582del						.																																			SO:0001589	frameshift_variant	288	exon37			.	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8578_8582delGCCAC	10.37:g.61832057_61832061delGTGGC	ENSP00000280772:p.Ala2860fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	78	13	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	37	CCDS7258.1																																																																																			.		0.415	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61832061	GTGGC	-	61832057	7	5	22	1	0	1	0	1	0	0	0	0	622	1029	36	0	4892	0	ANK3	10	61832057	Frame_Shift_Del	DEL	GTGGC	TCGA-A4-A4ZT-01A-11D-A26P-10	5	61832057	73702690	37	1949	17	3									
AIFM2	84883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	71874678	71874678	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acatggggcctctcttacccGgcttgtaggcctggagaggc	6	9	14	12	1	1	1	0	0	1	1	2	2	1	1	3	6	1	2	3	6	2	3	rs376374471		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:71874678G>A	ENST00000307864.1	-	8	1181	c.968C>T	c.(967-969)cCg>cTg	p.P323L	AIFM2_ENST00000373248.1_Missense_Mutation_p.P323L|AIFM2_ENST00000482166.1_5'UTR	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	323					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						TCTCTTACCCGGCTTGTAGGC	0.547																																					p.P323L		.											.	AIFM2-90	0			c.C968T						.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	29	30	30		968,968	5.8	1	10		30	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	AIFM2	NM_001198696.1,NM_032797.5	98,98	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	323/374,323/374	71874678	2,13004	2203	4300	6503	SO:0001583	missense	84883	exon8			TTACCCGGCTTGT	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.968C>T	10.37:g.71874678G>A	ENSP00000312370:p.Pro323Leu	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	60	16	NM_001198696	0	0	0	0	0	B3KXI0|Q63Z39	Missense_Mutation	SNP	ENST00000307864.1	37	CCDS7297.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.594868	0.66219	0.0	2.33E-4	ENSG00000042286	ENST00000373248;ENST00000307864;ENST00000395039	T;T	0.35421	1.31;1.31	5.8	5.8	0.92144	.	0.052232	0.85682	D	0.000000	T	0.32255	0.0823	M	0.64567	1.98	0.80722	D	1	P	0.39748	0.686	B	0.29598	0.104	T	0.17077	-1.0381	10	0.12766	T	0.61	-6.747	17.8576	0.88771	0.0:0.0:1.0:0.0	.	323	Q9BRQ8	AIFM2_HUMAN	L	323;323;286	ENSP00000362345:P323L;ENSP00000312370:P323L	ENSP00000312370:P323L	P	-	2	0	AIFM2	71544684	1.000000	0.71417	0.996000	0.52242	0.199000	0.23934	8.579000	0.90781	2.758000	0.94735	0.563000	0.77884	CCG	.		0.547	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797		A	71874678	G	A	71874678	3	1	22	1	0	0	0	0	1	0	0	0	427	1116	39	1	161	1	AIFM2	10	71874678	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	10042621	71874678	63660069	38	1950											
ZMYND17	118490	hgsc.bcm.edu;bcgsc.ca	37	chr10	75185695	75185695	+	Frame_Shift_Del	DEL	T	T	-																															gccaggttccaggggtgaagTtgaggtgctctgtgaaaagc																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:75185695delT	ENST00000372912.1	-	4	945	c.943delA	c.(943-945)actfs	p.T315fs	MSS51_ENST00000299432.2_Frame_Shift_Del_p.T315fs|AL353731.1_ENST00000584907.1_RNA			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	315					social behavior (GO:0035176)		metal ion binding (GO:0046872)										AGGGGTGAAGTTGAGGTGCTC	0.542																																					p.T315fs		.											.	.	0			c.943delA						.						85	75	78					10																	75185695		2203	4300	6503	SO:0001589	frameshift_variant	118490	exon5			.	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.943delA	10.37:g.75185695delT	ENSP00000362003:p.Thr315fs	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	140	33	NM_001024593	0	0	0	0	0	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Frame_Shift_Del	DEL	ENST00000372912.1	37	CCDS31221.1																																																																																			.		0.542	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		-	75185695	T	-	75185695	7	5	22	1	0	1	0	1	0	0	0	0	17741	1725	60	0	451	0	ZMYND17	10	75185695	Frame_Shift_Del	DEL	T	TCGA-A4-A4ZT-01A-11D-A26P-10	3311017	75185695	60349052	39	1951											
FERMT3	83706	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63990576	63990576	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccaacaaccgactgatccGcatcgacttggccgtgggcg	8	6	12	15	6	0	1	0	1	0	0	2	3	1	1	4	2	2	1	4	2	2	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr11:63990576G>T	ENST00000279227.5	+	14	1834	c.1739G>T	c.(1738-1740)cGc>cTc	p.R580L	TRPT1_ENST00000540472.1_5'Flank|FERMT3_ENST00000345728.5_Missense_Mutation_p.R576L	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	580					integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						CGACTGATCCGCATCGACTTG	0.622																																					p.R580L		.											.	FERMT3-23	0			c.G1739T						.						109	83	92					11																	63990576		2201	4296	6497	SO:0001583	missense	83706	exon14			TGATCCGCATCGA	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"Fermitins", "Pleckstrin homology (PH) domain containing"	23151	protein-coding gene	gene with protein product	"kindlin-3"	607901	"fermitin family homolog 3 (Drosophila)"				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1739G>T	11.37:g.63990576G>T	ENSP00000279227:p.Arg580Leu	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	170	65	NM_178443	0	0	17	17	0	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	.	.	.	.	.	.	.	.	.	.	G	35	5.437985	0.96168	.	.	ENSG00000149781	ENST00000345728;ENST00000279227;ENST00000545896	T;T;T	0.73575	-0.76;-0.76;-0.76	5.19	5.19	0.71726	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.86908	0.6046	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.993	D	0.87510	0.2439	10	0.52906	T	0.07	-23.8856	17.8551	0.88760	0.0:0.0:1.0:0.0	.	576;580	Q86UX7-2;Q86UX7	.;URP2_HUMAN	L	576;580;97	ENSP00000339950:R576L;ENSP00000279227:R580L;ENSP00000440209:R97L	ENSP00000279227:R580L	R	+	2	0	FERMT3	63747152	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	9.411000	0.97342	2.591000	0.87537	0.561000	0.74099	CGC	.		0.622	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		T	63990576	G	T	63990576	3	4	22	1	0	0	0	0	1	0	0	0	5838	1087	38	4	1789	4	FERMT3	11	63990576	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		63990576	71015940	40	1952											
SLCO1B3	28234	ucsc.edu	37	chr12	21030729	21030729	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccagtctttgaaaagcAtccttaccaatcccctgtat	10	15	4	12	0	1	1	0	1	1	0	4	1	4	1	5	0	2	2	5	0	5	5			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr12:21030729A>G	ENST00000381545.3	+	10	1213	c.994A>G	c.(994-996)Atc>Gtc	p.I332V	SLCO1B3_ENST00000261196.2_Missense_Mutation_p.I332V|LST3_ENST00000381541.3_Intron|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000540229.1_Missense_Mutation_p.I332V|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.I332V	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	332					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TTTGAAAAGCATCCTTACCAA	0.249																																					p.I332V													.	SLCO1B3-155	0			c.A994G						.						104	100	101					12																	21030729		2203	4300	6503	SO:0001583	missense	28234	exon10			AAAAGCATCCTTA		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.994A>G	12.37:g.21030729A>G	ENSP00000370956:p.Ile332Val	Somatic	47	0		WXS	Illumina HiSeq		44	4	NM_019844	0	0	0	0	0	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	.	8.568	0.879456	0.17467	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000261196;ENST00000381545;ENST00000553473;ENST00000544370;ENST00000540229	T;T;T;T;T	0.80304	0.38;0.38;0.38;-1.36;0.38	3.13	-1.66	0.08265	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.224065	0.38058	N	0.001824	T	0.76485	0.3994	M	0.77820	2.39	0.80722	D	1	B;B;B	0.32409	0.37;0.001;0.001	B;B;B	0.35727	0.209;0.016;0.016	T	0.66244	-0.5972	10	0.49607	T	0.09	.	7.0333	0.24979	0.4897:0.4173:0.093:0.0	.	332;332;332	Q5JAR4;B3KP78;Q9NPD5	.;.;SO1B3_HUMAN	V	332;332;332;156;332	ENSP00000261196:I332V;ENSP00000370956:I332V;ENSP00000451758:I332V;ENSP00000443225:I156V;ENSP00000441269:I332V	ENSP00000441269:I332V	I	+	1	0	SLCO1B3;RP11-545J16.1	20921996	0.102000	0.21896	0.884000	0.34674	0.142000	0.21351	0.482000	0.22276	-0.498000	0.06632	-2.470000	0.00202	ATC	.		0.249	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		G	21030729	A	G	21030729	3	3	22	1	0	0	0	0	1	0	0	0	14756	217	8	3	1024	3	SLCO1B3	12	21030729	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		21030729	112821166	41	1953											
TIMELESS	8914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56814422	56814422	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactgttcgttttccatggcTtcctcattttcctctgtgag	5	18	7	11	1	2	1	1	1	1	0	6	1	5	1	3	1	1	3	3	1	1	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr12:56814422T>G	ENST00000553532.1	-	26	3309	c.3159A>C	c.(3157-3159)gaA>gaC	p.E1053D	TIMELESS_ENST00000554616.1_Missense_Mutation_p.E550D|TIMELESS_ENST00000229201.4_Missense_Mutation_p.E1052D					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TTTCCATGGCTTCCTCATTTT	0.507																																					p.E1053D		.											.	TIMELESS-159	0			c.A3159C						.						133	109	117					12																	56814422		2203	4300	6503	SO:0001583	missense	8914	exon26			CATGGCTTCCTCA	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1"	603887	"timeless (Drosophila) homolog", "timeless homolog (Drosophila)"			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.3159A>C	12.37:g.56814422T>G	ENSP00000450607:p.Glu1053Asp	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	270	135	NM_003920	0	0	1	8	7		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	T	9.732	1.162558	0.21538	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.15487	2.42;2.42;2.42	5.34	2.91	0.33838	Timeless C-terminal (1);	0.056591	0.64402	D	0.000002	T	0.11024	0.0269	L	0.41961	1.31	0.23589	N	0.99734	B	0.09022	0.002	B	0.14578	0.011	T	0.21348	-1.0248	10	0.15066	T	0.55	-17.0728	4.1508	0.10237	0.3164:0.094:0.0:0.5895	.	1053	Q9UNS1	TIM_HUMAN	D	1052;1053;550	ENSP00000229201:E1052D;ENSP00000450607:E1053D;ENSP00000450848:E550D	ENSP00000229201:E1053D	E	-	3	2	TIMELESS	55100689	0.994000	0.37717	1.000000	0.80357	0.959000	0.62525	0.126000	0.15769	2.150000	0.67090	0.459000	0.35465	GAA	.		0.507	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		G	56814422	T	G	56814422	3	3	22	1	0	0	0	0	1	0	0	0	15936	1606	56	5	483	5	TIMELESS	12	56814422	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	35783693	56814422	77037473	42	1954											
SLC6A15	55117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	85279278	85279278	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggttgctgaaaagactgAgaaaaataaaacaaactcca	20	6	9	6	0	0	3	0	2	0	2	1	4	1	3	1	2	3	2	1	2	7	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr12:85279278A>G	ENST00000266682.5	-	4	1051	c.510T>C	c.(508-510)tcT>tcC	p.S170S	SLC6A15_ENST00000552192.1_Silent_p.S63S|SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000450363.3_Silent_p.S170S	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	170					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						GAAAAGACTGAGAAAAATAAA	0.368																																					p.S170S		.											.	SLC6A15-93	0			c.T510C						.						95	94	94					12																	85279278		2203	4300	6503	SO:0001819	synonymous_variant	55117	exon4			AGACTGAGAAAAA	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"Solute carriers"	13621	protein-coding gene	gene with protein product	"homolog of rat orphan transporter v7-3", "sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"	607971	"solute carrier family 6 (neurotransmitter transporter), member 15"			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.510T>C	12.37:g.85279278A>G		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	232	62	NM_018057	0	0	0	0	0	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	37	CCDS9026.1																																																																																			.		0.368	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		G	85279278	A	G	85279278	2	3	22	1	0	0	0	0	0	0	0	1	14710	291	11	3		3	SLC6A15	12	85279278	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	28464856	85279278	48572617	43	1955											
GOLGA3	2802	broad.mit.edu	37	chr12	133359035	133359035	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaacttcttgtttgactcCtcaaggcgttttatcttctt	6	18	6	11	1	4	1	1	1	3	0	5	1	5	1	2	1	1	2	2	1	3	7			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr12:133359035C>T	ENST00000450791.2	-	16	3495	c.3312G>A	c.(3310-3312)gaG>gaA	p.E1104E	GOLGA3_ENST00000204726.3_Silent_p.E1104E|GOLGA3_ENST00000456883.2_Silent_p.E1104E			Q08378	GOGA3_HUMAN	golgin A3	1104					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TGTTTGACTCCTCAAGGCGTT	0.473																																					p.E1104E													.	GOLGA3-95	0			c.G3312A						.						151	148	149					12																	133359035		2203	4300	6503	SO:0001819	synonymous_variant	2802	exon17			TGACTCCTCAAGG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"SY2/SY10 protein", "Golgi complex-associated protein of 170 kD"	602581	"golgi autoantigen, golgin subfamily a, 3"			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.3312G>A	12.37:g.133359035C>T		Somatic	144	0		WXS	Illumina HiSeq	Phase_I	175	4	NM_005895	0	0	2	2	0	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			.		0.473	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		T	133359035	C	T	133359035	2	4	22	1	0	0	0	0	0	0	0	1	6574	680	24	2		2	GOLGA3	12	133359035	Silent	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	48079757	133359035	492860	44	1956											
KIAA0564	23078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	42185853	42185853	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctttgccacccaggcctGccgtgtctcttccccctgga	3	11	8	19	1	1	0	0	0	1	0	4	1	3	1	7	2	2	0	7	2	0	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr13:42185853G>C	ENST00000379310.3	-	39	4804	c.4736C>G	c.(4735-4737)gCa>gGa	p.A1579G		NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1579						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										ACCCAGGCCTGCCGTGTCTCT	0.522																																					p.A1579G		.											.	.	0			c.C4736G						.						53	56	55					13																	42185853		1917	4129	6046	SO:0001583	missense	23078	exon39			AGGCCTGCCGTGT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.4736C>G	13.37:g.42185853G>C	ENSP00000368612:p.Ala1579Gly	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	108	33	NM_015058	0	0	4	11	7	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015419	0.93404	.	.	ENSG00000102763	ENST00000251030;ENST00000379310	T	0.16457	2.34	5.95	5.95	0.96441	.	0.110644	0.64402	D	0.000012	T	0.46521	0.1397	M	0.87180	2.865	0.80722	D	1	D	0.67145	0.996	P	0.58266	0.836	T	0.50931	-0.8769	10	0.87932	D	0	.	19.9739	0.97296	0.0:0.0:1.0:0.0	.	1579	A3KMH1	K0564_HUMAN	G	1483;1579	ENSP00000368612:A1579G	ENSP00000251030:A1483G	A	-	2	0	KIAA0564	41083853	1.000000	0.71417	0.920000	0.36463	0.903000	0.53119	9.577000	0.98196	2.826000	0.97356	0.563000	0.77884	GCA	.		0.522	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		C	42185853	G	C	42185853	3	2	22	1	0	0	0	0	1	0	0	0	8206	1319	46	4	1009	4	KIAA0564	13	42185853	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		42185853	72984025	45	1957											
TUBGCP3	10426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	113140459	113140459	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taacaccaaaaactgctgcaCgataccctaaaaagaagcaa	20	5	5	11	1	0	1	0	0	0	1	0	2	0	1	2	0	6	3	2	0	9	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr13:113140459C>G	ENST00000261965.3	-	22	2758	c.2572G>C	c.(2572-2574)Gtg>Ctg	p.V858L		NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	858					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					AACTGCTGCACGATACCCTAA	0.458																																					p.V858L		.											.	TUBGCP3-90	0			c.G2572C						.						26	24	25					13																	113140459		2203	4297	6500	SO:0001583	missense	10426	exon22			GCTGCACGATACC	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"spindle pole body protein"					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.2572G>C	13.37:g.113140459C>G	ENSP00000261965:p.Val858Leu	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	281	103	NM_006322	0	0	3	3	0	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	37	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786517	0.31593	.	.	ENSG00000126216	ENST00000261965	T	0.21932	1.98	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	L	0.58669	1.825	0.80722	D	1	P;P	0.45827	0.867;0.732	B;B	0.41946	0.371;0.371	T	0.08166	-1.0735	10	0.07990	T	0.79	-24.5804	17.6998	0.88291	0.0:1.0:0.0:0.0	.	848;858	B4DYP7;Q96CW5	.;GCP3_HUMAN	L	858	ENSP00000261965:V858L	ENSP00000261965:V858L	V	-	1	0	TUBGCP3	112188460	1.000000	0.71417	0.894000	0.35097	0.023000	0.10783	7.085000	0.76875	2.216000	0.71823	0.655000	0.94253	GTG	.		0.458	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		G	113140459	C	G	113140459	3	3	22	1	0	0	0	0	1	0	0	0	16800	536	19	4	155	4	TUBGCP3	13	113140459	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	70954606	113140459	2029419	46	1958											
PRKD1	5587	bcgsc.ca	37	chr14	30068292	30068292	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtttgaggtcacagtgaaCgatatttttaaaatgaaggt	13	14	11	3	1	1	3	1	3	0	0	1	4	1	3	0	3	1	1	0	3	5	5			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr14:30068292C>T	ENST00000331968.5	-	15	2336	c.2107G>A	c.(2107-2109)Gtt>Att	p.V703I	PRKD1_ENST00000415220.2_Missense_Mutation_p.V711I	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	703	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.V703I(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TCACAGTGAACGATATTTTTA	0.388																																					p.V703I													.	PRKD1-1534	2	Substitution - Missense(2)	large_intestine(2)	c.G2107A						.						129	128	128					14																	30068292		2203	4300	6503	SO:0001583	missense	5587	exon15			AGTGAACGATATT		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"Pleckstrin homology (PH) domain containing"	9407	protein-coding gene	gene with protein product		605435	"protein kinase C, mu"	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2107G>A	14.37:g.30068292C>T	ENSP00000333568:p.Val703Ile	Somatic	74	0		WXS	Illumina HiSeq	Phase_1	69	4	NM_002742	0	0	23	23	0	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	C	35	5.505666	0.96371	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	D;D	0.81579	-1.51;-1.51	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.81451	0.4825	N	0.13140	0.3	0.80722	D	1	D	0.58970	0.984	P	0.60886	0.88	D	0.84005	0.0345	10	0.62326	D	0.03	-15.9558	19.9348	0.97133	0.0:1.0:0.0:0.0	.	703	Q15139	KPCD1_HUMAN	I	703;711	ENSP00000333568:V703I;ENSP00000390535:V711I	ENSP00000333568:V703I	V	-	1	0	PRKD1	29138043	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.720000	0.84759	2.789000	0.95967	0.591000	0.81541	GTT	.		0.388	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		T	30068292	C	T	30068292	3	4	22	1	0	0	0	0	1	0	0	0	12547	536	19	1	647	1	PRKD1	14	30068292	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10		30068292	77281248	47	1959											
LTK	4058	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41798200	41798200	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccaaaggcaccatggcccagGgctctgcaggaagacacgtt	11	5	12	13	1	1	1	0	0	1	1	1	2	1	2	3	4	1	4	3	4	2	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr15:41798200G>T	ENST00000263800.6	-	12	1641	c.1545C>A	c.(1543-1545)gcC>gcA	p.A515A	LTK_ENST00000453182.2_Intron|LTK_ENST00000561619.1_Silent_p.A213A|LTK_ENST00000355166.5_Silent_p.A454A	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	515	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CATGGCCCAGGGCTCTGCAGG	0.597										TSP Lung(18;0.14)																											p.A515A													.	LTK-1377	0			c.C1545A						.						67	64	65					15																	41798200		2203	4300	6503	SO:0001819	synonymous_variant	4058	exon12			GCCCAGGGCTCTG	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1545C>A	15.37:g.41798200G>T		Somatic	146	1		WXS	Illumina HiSeq	Phase_I	137	65	NM_002344	0	0	0	0	0	A6NNJ8|B4DL89|E9PFX4	Silent	SNP	ENST00000263800.6	37	CCDS10077.1																																																																																			.		0.597	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			T	41798200	G	T	41798200	2	4	22	1	0	0	0	0	0	0	0	1	9105	1219	43	4		4	LTK	15	41798200	Silent	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		41798200	60733192	48	1960											
CHTF18	63922	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	839242	839242	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aacggcctaggctgcaggtgGtcaagaggctgaacttcaga	11	7	14	9	1	2	3	2	1	0	2	2	3	2	3	1	5	3	3	1	5	4	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr16:839242G>T	ENST00000262315.9	+	3	382	c.319G>T	c.(319-321)Gtc>Ttc	p.V107F	RPUSD1_ENST00000565809.1_5'Flank|RPUSD1_ENST00000561734.1_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.V304F|CHTF18_ENST00000491530.1_3'UTR|CHTF18_ENST00000455171.2_Missense_Mutation_p.V135F|RPUSD1_ENST00000567114.1_5'Flank|RPUSD1_ENST00000007264.2_5'Flank	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	107					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GCTGCAGGTGGTCAAGAGGCT	0.692																																					p.V107F													.	CHTF18-227	0			c.G319T						.						12	15	14					16																	839242		1934	4078	6012	SO:0001583	missense	63922	exon3			CAGGTGGTCAAGA	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.319G>T	16.37:g.839242G>T	ENSP00000262315:p.Val107Phe	Somatic	188	1		WXS	Illumina HiSeq	Phase_I	270	141	NM_022092	0	0	0	1	1	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	G	10.20	1.285452	0.23478	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.13089	2.67;2.62;2.76	5.07	3.09	0.35607	.	1.527240	0.04025	N	0.300464	T	0.11196	0.0273	L	0.39397	1.21	0.21915	N	0.999474	P;B;B	0.45428	0.858;0.046;0.03	B;B;B	0.36845	0.234;0.04;0.017	T	0.26052	-1.0114	10	0.09590	T	0.72	-22.4866	8.536	0.33364	0.0813:0.0:0.7654:0.1532	.	107;135;107	B4DEY3;Q8WVB6-2;Q8WVB6	.;.;CTF18_HUMAN	F	304;135;107	ENSP00000313029:V304F;ENSP00000406252:V135F;ENSP00000262315:V107F	ENSP00000262315:V107F	V	+	1	0	CHTF18	779243	0.968000	0.33430	0.048000	0.18961	0.065000	0.16274	3.655000	0.54460	0.528000	0.28580	0.511000	0.50034	GTC	.		0.692	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		T	839242	G	T	839242	3	4	22	1	0	0	0	0	1	0	0	0	3420	1261	44	4	329	4	CHTF18	16	839242	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		839242	89515511	49	1961											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	18849889	18849889	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctttttcaaagcaaacAttgtaatctatgtgaacaac	15	14	4	8	0	2	1	1	1	1	0	2	1	2	1	1	0	5	2	1	0	7	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr16:18849889A>G	ENST00000446231.2	-	43	7480	c.7068T>C	c.(7066-7068)aaT>aaC	p.N2356N	SMG1_ENST00000389467.3_Silent_p.N2356N			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2356	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CAAAGCAAACATTGTAATCTA	0.328																																					p.N2356N		.											.	SMG1-1160	0			c.T7068C						.						147	136	139					16																	18849889		1828	4078	5906	SO:0001819	synonymous_variant	23049	exon43			GCAAACATTGTAA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.7068T>C	16.37:g.18849889A>G		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	177	42	NM_015092	0	0	4	5	1	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			.		0.328	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		G	18849889	A	G	18849889	2	3	22	1	0	0	0	0	0	0	0	1	14827	214	8	3		3	SMG1	16	18849889	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	18010647	18849889	71504864	50	1962											
CCDC113	29070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	58292369	58292370	+	Missense_Mutation	DNP	GG	GG	CT																															agccatatccaagaagaaagGgagtattttggccactcaga																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr16:58292369_58292370GG>CT	ENST00000219299.4	+	4	567_568	c.488_489GG>CT	c.(487-489)gGG>gCT	p.G163A	CCDC113_ENST00000443128.2_Missense_Mutation_p.G109A	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	163						cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)				large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						AAGAAGAAAGGGAGTATTTTGG	0.416																																					p.G163A		.											.	CCDC113-90	0			c.G327T						.																																			SO:0001583	missense	29070	exon3			GAAAGGGAGTATT	AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021			25002	protein-coding gene	gene with protein product						11230166, 11042152	Standard	NM_014157		Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	Exception_encountered	16.37:g.58292369_58292370delinsCT	ENSP00000219299:p.Gly163Ala	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	128	53	NM_001142302	0	0	0	0	0	B2RAQ7|B4DR20|Q9NZX2	Missense_Mutation	DNP	ENST00000219299.4	37	CCDS10795.1																																																																																			.		0.416	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257387.2	NM_014157		CT	58292370	GG	CT	58292369	3	2	22	1	0	0	0	0	1	0	0	0	2756	1232	43	4	502	4	CCDC113	16	58292369	Missense_Mutation	DNP	GG	TCGA-A4-A4ZT-01A-11D-A26P-10	39442480	58292369	32062384	51	1963											
PRDM7	11105	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	90127013	90127013	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggttctgctcttcatcatcCcgggcacagttcacatacct	8	12	7	14	1	5	0	3	0	2	0	6	0	6	0	2	2	2	4	2	2	1	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr16:90127013C>A	ENST00000449207.2	-	9	988	c.969G>T	c.(967-969)cgG>cgT	p.R323R	PRDM7_ENST00000407825.1_Intron|PRDM7_ENST00000325921.6_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	323	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)			lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CTTCATCATCCCGGGCACAGT	0.542																																					p.R323R													.	PRDM7-92	0			c.G969T						.						76	75	75					16																	90127013		1940	4123	6063	SO:0001819	synonymous_variant	11105	exon9			ATCATCCCGGGCA	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"Zinc fingers, C2H2-type", "-"	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.969G>T	16.37:g.90127013C>A		Somatic	349	1		WXS	Illumina HiSeq	Phase_I	417	111	NM_001098173	0	0	0	0	0	A4Q9G8|Q08EM4|Q9NQW4	Silent	SNP	ENST00000449207.2	37	CCDS45557.1																																																																																			.		0.542	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1			A	90127013	C	A	90127013	2	1	22	1	0	0	0	0	0	0	0	1	12490	610	22	4		4	PRDM7	16	90127013	Silent	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	31834644	90127013	227740	52	1964											
CAMTA2	23125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4872081	4872081	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtcccggctggggaagcccTtccagctcctggttctgctt	4	11	12	14	1	1	0	0	0	1	0	4	1	4	1	4	4	3	4	4	4	1	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:4872081T>A	ENST00000348066.3	-	23	3702	c.3579A>T	c.(3577-3579)gaA>gaT	p.E1193D	CAMTA2_ENST00000414043.3_Missense_Mutation_p.R1216W|SPAG7_ENST00000571023.1_5'Flank|CAMTA2_ENST00000361571.5_Missense_Mutation_p.E1192D|CAMTA2_ENST00000358183.4_Missense_Mutation_p.E1186D|SPAG7_ENST00000573366.1_5'Flank|SPAG7_ENST00000206020.3_5'Flank|RP5-1050D4.3_ENST00000576752.1_RNA|CAMTA2_ENST00000381311.5_Missense_Mutation_p.E1188D|CAMTA2_ENST00000572543.1_Missense_Mutation_p.E1198D|SPAG7_ENST00000575142.1_5'Flank	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	1193					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GGGGAAGCCCTTCCAGCTCCT	0.612																																					p.R1216W		.											.	CAMTA2-91	0			c.A3646T						.						51	56	55					17																	4872081		2203	4300	6503	SO:0001583	missense	23125	exon23			AAGCCCTTCCAGC	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.3579A>T	17.37:g.4872081T>A	ENSP00000321813:p.Glu1193Asp	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	88	24	NM_001171167	0	0	9	21	12	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	37	CCDS11063.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.8|20.8	4.044334|4.044334	0.75732|0.75732	.|.	.|.	ENSG00000108509|ENSG00000108509	ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066|ENST00000414043	T;T;T;T|T	0.40756|0.13538	1.4;1.02;1.4;1.05|2.58	4.7|4.7	-0.79|-0.79	0.10932|0.10932	.|.	0.542415|.	0.14944|.	N|.	0.289350|.	T|T	0.06508|0.06508	0.0167|0.0167	L|L	0.27053|0.27053	0.805|0.805	0.24084|0.24084	N|N	0.995937|0.995937	D;P;D|P	0.56035|0.41643	0.974;0.956;0.974|0.758	D;D;D|B	0.70487|0.30251	0.969;0.931;0.953|0.113	T|T	0.30238|0.30238	-0.9985|-0.9985	10|9	0.62326|0.87932	D|D	0.03|0	0.022|0.022	3.8552|3.8552	0.08973|0.08973	0.0:0.2518:0.4031:0.3451|0.0:0.2518:0.4031:0.3451	.|.	1188;1193;1192|1216	O94983-3;O94983;O94983-4|E7EWU5	.;CMTA2_HUMAN;.|.	D|W	1188;1192;1186;1193|1216	ENSP00000370712:E1188D;ENSP00000354828:E1192D;ENSP00000350910:E1186D;ENSP00000321813:E1193D|ENSP00000412886:R1216W	ENSP00000321813:E1193D|ENSP00000412886:R1216W	E|R	-|-	3|1	2|2	CAMTA2|CAMTA2	4812805|4812805	0.276000|0.276000	0.24211|0.24211	0.999000|0.999000	0.59377|0.59377	0.928000|0.928000	0.56348|0.56348	0.041000|0.041000	0.13927|0.13927	0.162000|0.162000	0.19483|0.19483	0.460000|0.460000	0.39030|0.39030	GAA|AGG	.		0.612	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		A	4872081	T	A	4872081	3	1	22	1	0	0	0	0	1	0	0	0	2620	1609	56	5	83	5	CAMTA2	17	4872081	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10		4872081	76323129	53	1965											
SSH2	85464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27958364	27958364	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atttggcgagagaagctgagCgcctcatttgggatggtttg	8	12	15	6	2	1	2	1	1	0	1	1	5	1	3	1	3	2	2	1	3	1	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:27958364C>T	ENST00000269033.3	-	15	3918	c.3767G>A	c.(3766-3768)cGc>cAc	p.R1256H	SSH2_ENST00000540801.1_Missense_Mutation_p.R1283H|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	1256					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGAAGCTGAGCGCCTCATTTG	0.532																																					p.R1256H		.											.	SSH2-92	0			c.G3767A						.						103	102	102					17																	27958364		2203	4300	6503	SO:0001583	missense	85464	exon15			GCTGAGCGCCTCA	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.3767G>A	17.37:g.27958364C>T	ENSP00000269033:p.Arg1256His	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	136	81	NM_033389	0	0	3	10	7	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.991842	0.54041	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.45668	0.89;0.89	6.17	5.19	0.71726	.	0.253540	0.39407	N	0.001375	T	0.34337	0.0894	L	0.39397	1.21	0.80722	D	1	P;B	0.35192	0.489;0.357	B;B	0.29663	0.105;0.048	T	0.17592	-1.0364	10	0.54805	T	0.06	-7.483	14.755	0.69557	0.0:0.9289:0.0:0.0711	.	1283;1256	F5H527;Q76I76	.;SSH2_HUMAN	H	1256;1283	ENSP00000269033:R1256H;ENSP00000444743:R1283H	ENSP00000269033:R1256H	R	-	2	0	SSH2	24982490	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.058000	0.57463	1.560000	0.49568	0.655000	0.94253	CGC	.		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		T	27958364	C	T	27958364	3	4	22	1	0	0	0	0	1	0	0	0	15217	768	27	1	508	1	SSH2	17	27958364	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	23086283	27958364	53236846	54	1966											
SLFN13	146857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33772567	33772567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacgcggcccgtataactcTcgccctctcttggtctctct	5	12	7	17	4	4	0	0	0	4	0	7	0	4	0	2	2	1	1	2	2	2	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:33772567T>C	ENST00000285013.6	-	3	408	c.133A>G	c.(133-135)Aga>Gga	p.R45G	SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000526861.1_Missense_Mutation_p.R45G|SLFN13_ENST00000533791.1_Missense_Mutation_p.R45G|SLFN13_ENST00000542635.1_Missense_Mutation_p.R45G|SLFN13_ENST00000360502.2_Intron	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	45						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CGTATAACTCTCGCCCTCTCT	0.498																																					p.R45G		.											.	SLFN13-91	0			c.A133G						.						108	111	110					17																	33772567		2203	4300	6503	SO:0001583	missense	146857	exon3			TAACTCTCGCCCT	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.133A>G	17.37:g.33772567T>C	ENSP00000285013:p.Arg45Gly	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	88	46	NM_144682	0	0	2	7	5	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.611668	0.28712	.	.	ENSG00000154760	ENST00000285013;ENST00000526861;ENST00000542635;ENST00000524511	T;T;T;T	0.23950	4.48;4.48;4.48;1.88	3.28	3.28	0.37604	.	0.641780	0.12846	U	0.434341	T	0.22820	0.0551	M	0.62723	1.935	0.09310	N	1	B	0.33694	0.421	B	0.24006	0.05	T	0.13202	-1.0518	10	0.46703	T	0.11	.	8.1521	0.31148	0.0:0.0:0.0:1.0	.	45	Q68D06	SLN13_HUMAN	G	45	ENSP00000285013:R45G;ENSP00000434439:R45G;ENSP00000444016:R45G;ENSP00000433181:R45G	ENSP00000285013:R45G	R	-	1	2	SLFN13	30796680	0.001000	0.12720	0.000000	0.03702	0.122000	0.20287	1.012000	0.29924	1.481000	0.48307	0.172000	0.16884	AGA	.		0.498	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		C	33772567	T	C	33772567	3	2	22	1	0	0	0	0	1	0	0	0	14768	1559	54	3	2576	3	SLFN13	17	33772567	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	5814203	33772567	47422643	55	1967											
LASP1	3927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37070728	37070728	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acatcccgaccagtgccccgGgtgagtgcaggtcctgttgg	6	8	14	13	2	0	1	0	1	0	0	2	2	2	1	5	3	2	2	5	3	0	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:37070728G>A	ENST00000318008.6	+	5	839	c.508G>A	c.(508-510)Gtt>Att	p.V170I	LASP1_ENST00000435347.3_Splice_Site_p.V170I|LASP1_ENST00000433206.2_Splice_Site_p.V114I	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	170					ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						CAGTGCCCCGGGTGAGTGCAG	0.657			T	MLL	AML																																p.V170I		.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	.	LASP1-522	0			c.G508A						.						24	30	28					17																	37070728		2202	4299	6501	SO:0001630	splice_region_variant	3927	exon5			GCCCCGGGTGAGT		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.508+1G>A	17.37:g.37070728G>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	100	50	NM_006148	0	0	0	0	0	B4DGQ0|Q96ED2|Q96IG0	Missense_Mutation	SNP	ENST00000318008.6	37	CCDS11331.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080367	0.76528	.	.	ENSG00000002834	ENST00000318008;ENST00000433206;ENST00000435347;ENST00000419929	T;T;T;T	0.39997	1.17;1.05;1.17;2.67	5.24	5.24	0.73138	.	0.969776	0.08459	N	0.942649	T	0.33411	0.0862	N	0.24115	0.695	0.41878	D	0.990301	B;B	0.32302	0.363;0.018	B;B	0.24701	0.055;0.016	T	0.11397	-1.0589	10	0.31617	T	0.26	.	17.3957	0.87444	0.0:0.0:1.0:0.0	.	114;170	B4DGQ0;Q14847	.;LASP1_HUMAN	I	170;114;170;134	ENSP00000325240:V170I;ENSP00000401048:V114I;ENSP00000392853:V170I;ENSP00000391897:V134I	ENSP00000325240:V170I	V	+	1	0	LASP1	34324254	1.000000	0.71417	0.713000	0.30519	0.712000	0.41017	4.856000	0.62932	2.431000	0.82371	0.563000	0.77884	GTT	.		0.657	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	Missense_Mutation	A	37070728	G	A	37070728	5	1	22	1	0	0	0	0	0	0	1	0	8658	1246	43	2	526	2	LASP1	17	37070728	Splice_Site	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	3298161	37070728	44124482	56	1968											
KRT35	3886	hgsc.bcm.edu	37	chr17	39633816	39633816	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggtacgtgttgatctcacActccagccgggcccggacgt	6	8	12	15	5	1	1	1	1	1	0	3	2	2	2	4	3	2	2	4	3	1	2	rs200529540		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:39633816A>C	ENST00000393989.1	-	6	1216	c.1174T>G	c.(1174-1176)Tgt>Ggt	p.C392G	KRT35_ENST00000246639.2_Missense_Mutation_p.C362G	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	392	Coil 2.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				TTGATCTCACACTCCAGCCGG	0.602													A|||	1	0.000199681	8e-04	0	5008	,	,		17752	0		0	False		,,,				2504	0				p.C392G		.											.	KRT35-92	0			c.T1174G						.						69	69	69					17																	39633816		2203	4300	6503	SO:0001583	missense	3886	exon6			TCTCACACTCCAG	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.1174T>G	17.37:g.39633816A>C	ENSP00000377558:p.Cys392Gly	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	119	6	NM_002280	0	0	0	0	0	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	1.976	-0.435352	0.04669	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.88586	-2.4;-2.4	4.95	-9.89	0.00464	Filament (1);	0.589135	0.17355	N	0.177272	T	0.76033	0.3931	L	0.27053	0.805	0.20196	N	0.999928	B	0.06786	0.001	B	0.06405	0.002	T	0.50849	-0.8779	10	0.22706	T	0.39	.	14.2893	0.66265	0.116:0.7368:0.0646:0.0826	.	392	Q92764	KRT35_HUMAN	G	362;392	ENSP00000246639:C362G;ENSP00000377558:C392G	ENSP00000246639:C362G	C	-	1	0	KRT35	36887342	0.000000	0.05858	0.054000	0.19295	0.517000	0.34286	-3.318000	0.00514	-2.252000	0.00699	-0.460000	0.05396	TGT	A|0.999;C|0.000		0.602	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		C	39633816	A	C	39633816	3	2	22	1	0	0	0	0	1	0	0	0	8493	159	6	5	201	5	KRT35	17	39633816	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	2563088	39633816	41561394	57	1969											
KRT13	3860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39661375	39661375	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcagggctagctgggctcTgcttcaggtgccagtcacgg	5	9	15	12	1	4	0	3	0	1	0	4	0	4	0	1	4	3	5	1	4	1	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:39661375T>A	ENST00000246635.3	-	1	474	c.428A>T	c.(427-429)cAg>cTg	p.Q143L	KRT13_ENST00000336861.3_Missense_Mutation_p.Q143L|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000587544.1_Missense_Mutation_p.Q143L|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	143	Linker 1.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				AGCTGGGCTCTGCTTCAGGTG	0.617																																					p.Q143L		.											.	KRT13-95	0			c.A428T						.						112	104	107					17																	39661375		2203	4300	6503	SO:0001583	missense	3860	exon1			GGGCTCTGCTTCA		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.428A>T	17.37:g.39661375T>A	ENSP00000246635:p.Gln143Leu	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	248	155	NM_002274	0	0	0	0	0	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	37	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.448953	0.43531	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	D;D	0.89196	-2.48;-2.48	4.9	4.9	0.64082	Filament (1);	0.152962	0.30244	N	0.010071	D	0.94663	0.8279	M	0.87381	2.88	0.35788	D	0.822162	D;D;D;D	0.67145	0.979;0.996;0.989;0.996	P;D;D;D	0.71870	0.905;0.975;0.925;0.975	D	0.97698	1.0183	10	0.62326	D	0.03	.	14.6956	0.69118	0.0:0.0:0.0:1.0	.	131;143;143;143	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	L	143;143;131	ENSP00000246635:Q143L;ENSP00000336604:Q143L	ENSP00000157775:Q131L	Q	-	2	0	KRT13	36914901	0.975000	0.34042	0.999000	0.59377	0.052000	0.14988	3.295000	0.51794	2.073000	0.62155	0.533000	0.62120	CAG	.		0.617	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39661375	T	A	39661375	3	1	22	1	0	0	0	0	1	0	0	0	8471	1580	55	5	980	5	KRT13	17	39661375	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	27559	39661375	41533835	58	1970											
SCRN2	90507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45918192	45918192	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcaggaacatggggagtcAgggctcgacgacgccatctg	9	6	15	11	4	2	0	1	0	1	0	4	4	2	2	1	4	1	2	1	4	1	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:45918192A>G	ENST00000290216.9	-	2	143	c.18T>C	c.(16-18)ccT>ccC	p.P6P	SCRN2_ENST00000584123.1_Silent_p.P14P|SCRN2_ENST00000407215.3_Silent_p.P6P	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	6						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						ATGGGGAGTCAGGGCTCGACG	0.662																																					p.P6P		.											.	SCRN2-91	0			c.T18C						.						25	31	29					17																	45918192		2203	4299	6502	SO:0001819	synonymous_variant	90507	exon2			GGAGTCAGGGCTC	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.18T>C	17.37:g.45918192A>G		Somatic	188	0		WXS	Illumina HiSeq	Phase_I	243	48	NM_138355	0	0	18	21	3	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	37	CCDS11519.1																																																																																			.		0.662	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		G	45918192	A	G	45918192	2	3	22	1	0	0	0	0	0	0	0	1	13971	175	7	3		3	SCRN2	17	45918192	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	6256817	45918192	35277018	59	1971											
AP3D1	8943	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	2130440	2130440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccagcttctccttcagccGgggaaaggcagggcgcagcg	7	6	14	14	3	2	0	1	0	1	0	4	1	3	1	3	4	3	3	3	4	1	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr19:2130440G>A	ENST00000345016.5	-	6	790	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	AP3D1_ENST00000350812.6_Intron|AP3D1_ENST00000590683.1_5'Flank|AP3D1_ENST00000355272.6_Missense_Mutation_p.R187W|AP3D1_ENST00000356926.4_Intron	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	187					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCTTCAGCCGGGGAAAGGCA	0.597																																					p.R187W		.											.	AP3D1-90	0			c.C559T						.						90	101	97					19																	2130440		2034	4183	6217	SO:0001583	missense	8943	exon6			TCAGCCGGGGAAA	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.559C>T	19.37:g.2130440G>A	ENSP00000344055:p.Arg187Trp	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	106	6	NM_001261826	0	0	45	48	3	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	37	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333240	0.81801	.	.	ENSG00000065000	ENST00000345016;ENST00000355272;ENST00000343722	T;T	0.28255	1.62;1.62	4.61	4.61	0.57282	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	M	0.92459	3.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.95;0.989	T	0.76187	-0.3051	10	0.87932	D	0	-30.4076	16.444	0.83910	0.0:0.0:1.0:0.0	.	187;187	O14617-5;O14617	.;AP3D1_HUMAN	W	187	ENSP00000344055:R187W;ENSP00000347416:R187W	ENSP00000341579:R187W	R	-	1	2	AP3D1	2081440	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	6.998000	0.76277	2.116000	0.64780	0.542000	0.68232	CGG	.		0.597	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			A	2130440	G	A	2130440	3	1	22	1	0	0	0	0	1	0	0	0	746	1115	39	1	3160	1	AP3D1	19	2130440	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		2130440	56998543	60	1972											
ZNF564	163050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12639471	12639471	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaaagcccactcctcaaGtgtgaagttcacagccacat	13	7	7	14	0	2	1	2	1	0	0	3	1	3	1	3	0	3	2	3	0	3	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr19:12639471G>T	ENST00000339282.7	-	2	239	c.43C>A	c.(43-45)Ctt>Att	p.L15I	CTD-2192J16.21_ENST00000601420.1_RNA|CTD-2192J16.20_ENST00000593682.1_3'UTR|ZNF709_ENST00000428311.1_Intron	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						CACTCCTCAAGTGTGAAGTTC	0.468																																					p.L15I		.											.	ZNF564-91	0			c.C43A						.						91	92	91					19																	12639471		2203	4300	6503	SO:0001583	missense	163050	exon2			CCTCAAGTGTGAA	BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.43C>A	19.37:g.12639471G>T	ENSP00000340004:p.Leu15Ile	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	86	18	NM_144976	0	0	1	1	0	B9EGT4|Q6P1K6	Missense_Mutation	SNP	ENST00000339282.7	37	CCDS42505.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.387425	0.25031	.	.	ENSG00000249709	ENST00000339282	T	0.01838	4.61	1.99	0.862	0.19056	Krueppel-associated box (4);	.	.	.	.	T	0.04724	0.0128	M	0.84683	2.71	0.20926	N	0.999823	B	0.29909	0.261	B	0.33196	0.159	T	0.28235	-1.0050	9	0.52906	T	0.07	.	4.2715	0.10789	0.0:0.2591:0.4772:0.2636	.	15	Q8TBZ8	ZN564_HUMAN	I	15	ENSP00000340004:L15I	ENSP00000340004:L15I	L	-	1	0	ZNF564	12500471	0.000000	0.05858	0.452000	0.26994	0.655000	0.38815	-0.253000	0.08794	0.174000	0.19809	0.442000	0.29010	CTT	.		0.468	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		T	12639471	G	T	12639471	3	4	22	1	0	0	0	0	1	0	0	0	18027	1029	36	4	1630	4	ZNF564	19	12639471	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	10509031	12639471	46489512	61	1973											
ZNF493	284443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	21606232	21606232	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccttactacacataagagAattcatactggacagaaacc	18	8	5	10	0	1	2	1	0	0	2	1	4	1	3	2	1	5	0	2	1	7	5			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr19:21606232A>C	ENST00000355504.4	+	2	653	c.387A>C	c.(385-387)agA>agC	p.R129S	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.R257S	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	129					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)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CACATAAGAGAATTCATACTG	0.378																																					p.R257S		.											.	ZNF493-516	0			c.A771C						.						38	41	40					19																	21606232		2203	4296	6499	SO:0001583	missense	284443	exon4			TAAGAGAATTCAT	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.387A>C	19.37:g.21606232A>C	ENSP00000347691:p.Arg129Ser	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	72	38	NM_001076678	0	0	3	6	3	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	9.658	1.143276	0.21205	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.24151	1.87;1.87	0.927	-1.44	0.08856	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41581	0.1165	M	0.79258	2.445	0.80722	D	1	D;P	0.71674	0.998;0.932	D;B	0.66084	0.941;0.317	T	0.34204	-0.9838	9	0.66056	D	0.02	.	5.0403	0.14456	0.7906:0.0:0.2094:0.0	.	129;257	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	S	257;129	ENSP00000376110:R257S;ENSP00000347691:R129S	ENSP00000347691:R129S	R	+	3	2	ZNF493	21398072	0.000000	0.05858	0.035000	0.18076	0.033000	0.12548	-4.038000	0.00308	-0.593000	0.05844	-0.586000	0.04128	AGA	.		0.378	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		C	21606232	A	C	21606232	3	2	22	1	0	0	0	0	1	0	0	0	17976	243	9	5	848	5	ZNF493	19	21606232	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	8966761	21606232	37522751	62	1974											
ACSS1	84532	broad.mit.edu;bcgsc.ca	37	chr20	25028726	25028755	+	In_Frame_Del	DEL	GGTGATCCTCACTTCCGTTCCAGGCTCATC	GGTGATCCTCACTTCCGTTCCAGGCTCATC	-																															tcgagggcacagtacctgtaGgtgatcctcacttccgttcc																								rs144423103|rs191234596|rs559373176	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GGTGATCCTCACTTCCGTTCCAGGCTCATC	GGTGATCCTCACTTCCGTTCCAGGCTCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr20:25028726_25028755delGGTGATCCTCACTTCCGTTCCAGGCTCATC	ENST00000323482.4	-	2	476_505	c.397_426delGATGAGCCTGGAACGGAAGTGAGGATCACC	c.(397-426)gatgagcctggaacggaagtgaggatcaccdel	p.DEPGTEVRIT133del	ACSS1_ENST00000376726.3_In_Frame_Del_p.DEPGTEVRIT133del|ACSS1_ENST00000432802.2_In_Frame_Del_p.DEPGTEVRIT133del	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	133					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)	p.D133A(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AGTACCTGTAGGTGATCCTCACTTCCGTTCCAGGCTCATCGCGCTCCCAG	0.574																																					p.133_142del													.	ACSS1-92	1	Substitution - Missense(1)	lung(1)	c.397_426del						.																																			SO:0001651	inframe_deletion	84532	exon2			CCTGTAGGTGATC		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"Acyl-CoA synthetase family"	16091	protein-coding gene	gene with protein product		614355	"acetyl-Coenzyme A synthetase 2 (AMP forming)-like"	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.397_426delGATGAGCCTGGAACGGAAGTGAGGATCACC	20.37:g.25028726_25028755delGGTGATCCTCACTTCCGTTCCAGGCTCATC	ENSP00000316924:p.Asp133_Thr142del	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	67	7	NM_001252677	0	0	0	0	0	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	In_Frame_Del	DEL	ENST00000323482.4	37	CCDS13167.1																																																																																			.		0.574	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		-	25028755	GGTGATCCTCACTTCCGTTCCAGGCTCATC	-	25028726	7	5	22	1	0	1	0	1	0	0	0	0	188	987	35	0	1695	0	ACSS1	20	25028726	In_Frame_Del	DEL	GGTGATCCTCACTTCCGTTCCAGGCTCATC	TCGA-A4-A4ZT-01A-11D-A26P-10		25028726	37996794	63	1975											
KIAA0406	9675	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	36641648	36641648	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagttcatccaatgaccttgGatggtcctgacaatcacact	12	11	7	11	0	2	2	2	2	0	0	4	3	4	3	3	2	0	1	3	2	3	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr20:36641648G>C	ENST00000373448.2	-	3	809	c.571C>G	c.(571-573)Cca>Gca	p.P191A	TTI1_ENST00000373447.3_Missense_Mutation_p.P191A|TTI1_ENST00000487362.1_Intron|TTI1_ENST00000449821.1_Missense_Mutation_p.P191A	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	191					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						AATGACCTTGGATGGTCCTGA	0.423																																					p.P191A		.											.	TTI1-94	0			c.C571G						.						61	62	62					20																	36641648		2203	4300	6503	SO:0001583	missense	9675	exon3			ACCTTGGATGGTC	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.571C>G	20.37:g.36641648G>C	ENSP00000362547:p.Pro191Ala	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	64	20	NM_014657	0	0	2	5	3	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	G	9.292	1.050781	0.19827	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.13307	2.6;2.6;2.6	5.32	5.32	0.75619	Armadillo-like helical (1);Armadillo-type fold (1);	0.056167	0.64402	D	0.000001	T	0.20455	0.0492	M	0.63428	1.95	0.31399	N	0.676886	D	0.56521	0.976	P	0.49085	0.6	T	0.07443	-1.0772	10	0.07813	T	0.8	-22.5589	16.312	0.82874	0.0:0.0:1.0:0.0	.	191	O43156	TTI1_HUMAN	A	191	ENSP00000362547:P191A;ENSP00000362546:P191A;ENSP00000407270:P191A	ENSP00000362546:P191A	P	-	1	0	TTI1	36075062	0.927000	0.31430	1.000000	0.80357	0.958000	0.62258	1.398000	0.34554	2.767000	0.95098	0.555000	0.69702	CCA	.		0.423	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		C	36641648	G	C	36641648	3	2	22	1	0	0	0	0	1	0	0	0	8194	1174	41	4	2726	4	KIAA0406	20	36641648	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	11612922	36641648	26383872	64	1976											
TSHZ2	128553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	51871576	51871576	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaaatactgtcaccacaGccatcaacaaagcccaaaac	18	5	5	13	0	2	0	2	0	0	0	2	1	2	1	3	1	5	0	3	1	7	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr20:51871576G>A	ENST00000371497.5	+	2	2466	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A524T|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A524T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	527					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			TGTCACCACAGCCATCAACAA	0.522																																					p.A527T		.											.	TSHZ2-232	0			c.G1579A						.						50	54	53					20																	51871576		2203	4300	6503	SO:0001583	missense	128553	exon2			ACCACAGCCATCA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.1579G>A	20.37:g.51871576G>A	ENSP00000360552:p.Ala527Thr	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	67	24	NM_173485	0	0	0	0	0	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.906244	0.92107	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.50001	0.76;0.76	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.73678	-0.3907	10	0.87932	D	0	-23.9458	20.3655	0.98876	0.0:0.0:1.0:0.0	.	527	Q9NRE2	TSH2_HUMAN	T	527;524;53	ENSP00000360552:A527T;ENSP00000333114:A524T	ENSP00000333114:A524T	A	+	1	0	TSHZ2	51304983	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.470000	0.97683	2.822000	0.97130	0.643000	0.83706	GCC	.		0.522	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51871576	G	A	51871576	3	1	22	1	0	0	0	0	1	0	0	0	16657	971	34	2	1585	2	TSHZ2	20	51871576	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	15229928	51871576	11153944	65	1977											
IFNAR1	3454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34725063	34725063	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgatttaattatattttctaGagaaaaattatcgagaaaaa	19	15	5	2	1	1	3	0	1	1	2	2	5	1	3	0	0	0	0	0	0	9	8			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr21:34725063G>A	ENST00000270139.3	+	9	1295		c.e9-1		IFNAR1_ENST00000442357.2_Splice_Site|IFNAR1_ENST00000416947.2_Splice_Site	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1						cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""Interferon Alfa-2a(DB00034)|""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"	ATATTTTCTAGAGAAAAATTA	0.328																																					.	Esophageal Squamous(73;817 1211 32990 35667 42746)	.											.	IFNAR1-91	0			c.1144-1G>A						.						34	39	38					21																	34725063		2200	4297	6497	SO:0001630	splice_region_variant	3454	exon9			TTTCTAGAGAAAA		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"Interferons"	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.1144-1G>A	21.37:g.34725063G>A		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	18	14	NM_000629	0	0	0	0	0	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Splice_Site	SNP	ENST00000270139.3	37	CCDS13624.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650324	0.47362	.	.	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	.	.	.	5.48	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3702	0.55250	0.0:0.1684:0.8316:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IFNAR1	33646933	0.956000	0.32656	0.594000	0.28785	0.331000	0.28603	4.213000	0.58520	2.562000	0.86427	0.650000	0.86243	.	.		0.328	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		Intron	A	34725063	G	A	34725063	5	1	22	1	0	0	0	0	0	0	1	0	7565	956	33	2	1177	2	IFNAR1	21	34725063	Splice_Site	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		34725063	13404832	66	1978											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119757	38119757	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcccaacagaaccactcaAcgagagaattccagaacatc	16	6	5	14	1	2	3	1	0	1	3	5	5	3	3	3	0	4	0	3	0	5	1	rs71322688|rs67890459|rs199535040|rs55745992	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr22:38119757A>T	ENST00000406386.3	+	7	1449	c.1194A>T	c.(1192-1194)caA>caT	p.Q398H		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACCACTCAACGAGAGAATT	0.547																																					p.Q398H		.											.	TRIOBP-136	0			c.A1194T						.						118	99	106					22																	38119757		1848	3567	5415	SO:0001583	missense	11078	exon7			CACTCAACGAGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1194A>T	22.37:g.38119757A>T	ENSP00000384312:p.Gln398His	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	13	6	NM_001039141	0	0	0	0	0	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.346788	0.41599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.34275	1.37	2.47	-1.65	0.08291	.	.	.	.	.	T	0.42177	0.1191	L	0.44542	1.39	0.09310	N	0.999998	D	0.54964	0.969	P	0.62382	0.901	T	0.32402	-0.9908	9	0.49607	T	0.09	.	6.5071	0.22202	0.6093:0.0:0.3907:0.0	.	398	Q9H2D6	TARA_HUMAN	H	398	ENSP00000384312:Q398H	ENSP00000384312:Q398H	Q	+	3	2	TRIOBP	36449703	.	.	0.034000	0.17996	0.078000	0.17371	.	.	-0.503000	0.06586	0.113000	0.15668	CAA	.		0.547	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38119757	A	T	38119757	3	4	22	1	0	0	0	0	1	0	0	0	16586	40	2	5	1212	5	TRIOBP	22	38119757	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		38119757	13184809	67	1979											
SMC1B	27127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	45748333	45748333	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagcttttgtgaccttacctGtgcacagcaaacaggagagc	11	10	10	10	0	0	2	0	1	0	1	0	3	0	2	2	1	6	3	2	1	3	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr22:45748333G>T	ENST00000357450.4	-	22	3422	c.3423C>A	c.(3421-3423)caC>caA	p.H1141Q	SMC1B_ENST00000404354.3_Intron	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1141	Ala/Asp-rich (DA-box).				meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.H1143Q(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GACCTTACCTGTGCACAGCAA	0.443																																					p.H1141Q		.											.	SMC1B-229	1	Substitution - Missense(1)	ovary(1)	c.C3423A						.						74	73	74					22																	45748333		1908	4110	6018	SO:0001583	missense	27127	exon22			TTACCTGTGCACA	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.3423C>A	22.37:g.45748333G>T	ENSP00000350036:p.His1141Gln	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	113	32	NM_148674	0	0	0	0	0	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092182	0.76756	.	.	ENSG00000077935	ENST00000357450	T	0.65549	-0.16	6.17	1.52	0.23074	.	0.090318	0.48767	D	0.000179	T	0.64349	0.2590	L	0.59912	1.85	0.80722	D	1	D	0.57257	0.979	P	0.54026	0.74	T	0.65038	-0.6265	10	0.56958	D	0.05	.	8.4322	0.32764	0.1878:0.111:0.7013:0.0	.	1141	Q8NDV3-3	.	Q	1141	ENSP00000350036:H1141Q	ENSP00000350036:H1141Q	H	-	3	2	SMC1B	44126997	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.612000	0.61169	0.948000	0.37687	0.655000	0.94253	CAC	.		0.443	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		T	45748333	G	T	45748333	3	4	22	1	0	0	0	0	1	0	0	0	14814	1368	48	4	300	4	SMC1B	22	45748333	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	7628576	45748333	5556233	68	1980											
TIMM17B	10245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	48751030	48751031	+	Missense_Mutation	DNP	GC	GC	CT																															cctcagtggtactgctgataGctggggtagcctggggccgg																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chrX:48751030_48751031GC>CT	ENST00000376582.3	-	7	648_649	c.500_501GC>AG	c.(499-501)aGC>aAG	p.S167K	TIMM17B_ENST00000465150.2_Missense_Mutation_p.S217K|TIMM17B_ENST00000396779.3_Missense_Mutation_p.S217K|TIMM17B_ENST00000472645.1_5'UTR|TIMM17B_ENST00000495490.2_Missense_Mutation_p.S187K	NM_005834.3	NP_005825.1	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17 homolog B (yeast)	167					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)	6						ACTGCTGATAGCTGGGGTAGCC	0.629																																					p.S217K		.											.	TIMM17B-131	0			c.G650A						.																																			SO:0001583	missense	10245	exon8			TGATAGCTGGGGT	AF034790	CCDS14308.1, CCDS55411.1	Xp11.23	2008-02-05			ENSG00000126768	ENSG00000126768			17310	protein-coding gene	gene with protein product		300249				10339406	Standard	NM_001167947		Approved	DXS9822, JM3	uc004dla.2	O60830	OTTHUMG00000034498	ENST00000376582.3:c.500_501delinsCT	X.37:g.48751030_48751031delinsCT	ENSP00000365766:p.Ser167Lys	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	92	29	NM_001167947	0	0	0	0	0	A8K2E2|J3KPV3|Q9UJV0	Missense_Mutation	DNP	ENST00000376582.3	37	CCDS14308.1																																																																																			.		0.629	TIMM17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083411.2	NM_005834		CT	48751031	GC	CT	48751030	3	2	22	1	0	0	0	0	1	0	0	0	15941	962	34	4	21	4	TIMM17B	23	48751030	Missense_Mutation	DNP	GC	TCGA-A4-A4ZT-01A-11D-A26P-10		48751030	106519530	69	1981											
PNMA3	29944	broad.mit.edu	37	chrX	152226011	152226011	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcaggtgcccgagggggAaaagaggcggaggctgatgg	9	4	22	6	2	0	2	0	1	0	1	0	5	0	4	1	8	1	2	1	8	2	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chrX:152226011A>G	ENST00000370264.4	+	1	625	c.599A>G	c.(598-600)gAa>gGa	p.E200G	PNMA3_ENST00000370265.4_Missense_Mutation_p.E200G|PNMA3_ENST00000447306.1_Missense_Mutation_p.E200G			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	200					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					cccgagggggaaaagaggcgg	0.587																																					p.E200G													.	PNMA3-600	0			c.A599G						.						65	64	64					X																	152226011		2203	4300	6503	SO:0001583	missense	29944	exon2			AGGGGGAAAAGAG	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"Paraneoplastic Ma antigens"	18742	protein-coding gene	gene with protein product	"paraneoplastic cancer-testis-brain antigen"	300675	"paraneoplastic antigen MA3"			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.599A>G	X.37:g.152226011A>G	ENSP00000359286:p.Glu200Gly	Somatic	58	3		WXS	Illumina HiSeq	Phase_I	80	12	NM_013364	0	0	0	0	0	D3DWT7|Q9H0A4	Missense_Mutation	SNP	ENST00000370264.4	37	CCDS35435.2	.	.	.	.	.	.	.	.	.	.	a	13.68	2.310689	0.40895	.	.	ENSG00000183837	ENST00000370265;ENST00000447306;ENST00000370264	T;T;T	0.13538	2.58;2.58;2.58	1.98	1.98	0.26296	.	.	.	.	.	T	0.31827	0.0809	M	0.75447	2.3	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04693	-1.0933	9	0.87932	D	0	.	5.4244	0.16417	1.0:0.0:0.0:0.0	.	200	Q9UL41	PNMA3_HUMAN	G	200	ENSP00000359288:E200G;ENSP00000407642:E200G;ENSP00000359286:E200G	ENSP00000359286:E200G	E	+	2	0	PNMA3	151976667	0.302000	0.24454	0.007000	0.13788	0.009000	0.06853	2.310000	0.43708	1.055000	0.40461	0.378000	0.23410	GAA	.		0.587	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		G	152226011	A	G	152226011	3	3	22	1	0	0	0	0	1	0	0	0	12181	246	9	3	601	3	PNMA3	23	152226011	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	103474981	152226011	3044549	70	1982											
KIAA0562	9731	ucsc.edu;bcgsc.ca	37	chr1	3747716	3747716	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaggtgaactgaagagtttGctttcaatggctgcaccagg	10	10	12	9	0	1	3	1	2	0	1	1	3	1	3	2	3	3	4	2	3	3	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:3747716G>A	ENST00000378230.3	-	13	2054	c.1730C>T	c.(1729-1731)gCa>gTa	p.A577V	CEP104_ENST00000460038.1_5'UTR	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	577						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						TGAAGAGTTTGCTTTCAATGG	0.473																																					p.A577V													.	CEP104-92	0			c.C1730T						.						110	109	109					1																	3747716		2203	4300	6503	SO:0001583	missense	9731	exon13			GAGTTTGCTTTCA	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"glycine, glutamate, thienylcyclohexylpiperidine binding protein"		"KIAA0562"	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.1730C>T	1.37:g.3747716G>A	ENSP00000367476:p.Ala577Val	Somatic	211	2		WXS	Illumina HiSeq		145	103	NM_014704	0	0	0	5	5	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	9.961	1.222704	0.22457	.	.	ENSG00000116198	ENST00000378230	T	0.23147	1.92	5.33	3.25	0.37280	Armadillo-like helical (1);Armadillo-type fold (1);	0.892982	0.09774	N	0.757615	T	0.23289	0.0563	L	0.54323	1.7	0.09310	N	0.999998	P	0.34724	0.465	B	0.31101	0.124	T	0.12218	-1.0556	10	0.29301	T	0.29	.	9.3751	0.38278	0.083:0.0:0.7643:0.1527	.	577	O60308	CE104_HUMAN	V	577	ENSP00000367476:A577V	ENSP00000367476:A577V	A	-	2	0	CEP104	3737576	0.986000	0.35501	0.005000	0.12908	0.103000	0.19146	4.565000	0.60836	1.246000	0.43901	0.643000	0.83706	GCA	.		0.473	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		A	3747716	G	A	3747716	3	1	23	1	0	0	0	0	1	0	0	0	8205	1319	46	2	1087	2	KIAA0562	1	3747716	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		3747716	245502905	1	1983											
H6PD	9563	hgsc.bcm.edu	37	chr1	9324338	9324338	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcggggggctcgagccccGtggccctgttccagcagctg	3	8	16	14	3	0	0	0	0	0	0	3	1	1	0	4	4	3	4	4	4	0	1	rs200978401	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:9324338G>A	ENST00000377403.2	+	5	2088	c.1786G>A	c.(1786-1788)Gtg>Atg	p.V596M	H6PD_ENST00000602477.1_Missense_Mutation_p.V607M	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	596	6-phosphogluconolactonase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CTCGAGCCCCGTGGCCCTGTT	0.672													G|||	6	0.00119808	0	0.0058	5008	,	,		17060	0.002		0	False		,,,				2504	0				p.V596M		.											.	H6PD-90	0			c.G1786A						.																																			SO:0001583	missense	9563	exon5			AGCCCCGTGGCCC	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1786G>A	1.37:g.9324338G>A	ENSP00000366620:p.Val596Met	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_004285	0	0	0	3	3	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	G	12.24	1.877814	0.33162	.	.	ENSG00000049239	ENST00000377403	T	0.42900	0.96	5.67	-1.43	0.08884	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.555420	0.18251	N	0.146951	T	0.36082	0.0954	M	0.64997	1.995	0.09310	N	1	D	0.53462	0.96	B	0.43990	0.438	T	0.30268	-0.9984	10	0.59425	D	0.04	-5.044	5.9469	0.19223	0.4614:0.0:0.4156:0.123	.	596	O95479	G6PE_HUMAN	M	596	ENSP00000366620:V596M	ENSP00000366620:V596M	V	+	1	0	H6PD	9246925	0.014000	0.17966	0.001000	0.08648	0.459000	0.32528	0.207000	0.17395	-0.632000	0.05553	0.561000	0.74099	GTG	G|0.999;A|0.001		0.672	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		A	9324338	G	A	9324338	3	1	23	1	0	0	0	0	1	0	0	0	6957	1145	40	1	1800	1	H6PD	1	9324338	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	5576622	9324338	239926283	2	1984											
PRAMEF12	390999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	12835789	12835789	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggccctgagtaagagaCgaacagcagggaactgtcca	14	4	13	10	1	0	3	0	1	0	2	1	6	1	4	2	2	3	2	2	2	3	1	rs201386508		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:12835789C>T	ENST00000357726.4	+	2	418	c.391C>T	c.(391-393)Cga>Tga	p.R131*		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	131					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTAAGAGACGAACAGCAGG	0.542																																					p.R131X		.											.	PRAMEF12-25	0			c.C391T						.	C	stop/ARG	1,4345		0,1,2172	109	123	118		391	-2.5	0	1		118	0,8588		0,0,4294	no	stop-gained	PRAMEF12	NM_001080830.1		0,1,6466	TT,TC,CC		0.0,0.023,0.0077		131/484	12835789	1,12933	2173	4294	6467	SO:0001587	stop_gained	390999	exon2			AAGAGACGAACAG		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.391C>T	1.37:g.12835789C>T	ENSP00000350358:p.Arg131*	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	126	49	NM_001080830	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000357726.4	37	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	14.34	2.507496	0.44558	2.3E-4	0.0	ENSG00000116726	ENST00000357726	.	.	.	2.8	-2.45	0.06481	.	6.292790	0.00896	N	0.002291	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	5.4193	0.16392	0.3728:0.2852:0.3419:0.0	.	.	.	.	X	131	.	ENSP00000350358:R131X	R	+	1	2	PRAMEF12	12758376	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.908000	0.00700	-0.506000	0.06558	0.313000	0.20887	CGA	C|0.999;A|0.001		0.542	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12835789	C	T	12835789	4	4	23	1	0	0	0	0	0	1	0	0	12457	528	19	1	397	1	PRAMEF12	1	12835789	Nonsense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	3511451	12835789	236414832	3	1985											
ARHGEF10L	55160	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	17907127	17907127	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcctccacagcctgccataGgtaccgtacccagggcttcc	7	8	8	18	1	0	0	0	0	0	0	3	0	3	0	7	2	4	3	7	2	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:17907127G>T	ENST00000361221.3	+	2	196	c.37G>T	c.(37-39)Gga>Tga	p.G13*	ARHGEF10L_ENST00000452522.1_Splice_Site_p.G13*|ARHGEF10L_ENST00000375415.1_Splice_Site_p.G13*|ARHGEF10L_ENST00000434513.1_Splice_Site_p.G13*	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	13						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GCCTGCCATAGGTACCGTACC	0.622																																					p.G13X													.	ARHGEF10L-292	0			c.G37T						.						100	76	84					1																	17907127		2203	4300	6503	SO:0001630	splice_region_variant	55160	exon2			GCCATAGGTACCG	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.37+1G>T	1.37:g.17907127G>T		Somatic	90	1		WXS	Illumina HiSeq	Phase_I	90	31	NM_018125	0	0	0	1	1	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Nonsense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	.	.	.	.	.	.	.	.	.	.	G	37	6.567216	0.97671	.	.	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415	.	.	.	4.28	4.28	0.50868	.	0.199425	0.33382	N	0.004971	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-0.8805	12.3935	0.55373	0.0:0.0:1.0:0.0	.	.	.	.	X	13	.	ENSP00000355060:G13X	G	+	1	0	ARHGEF10L	17779714	1.000000	0.71417	0.972000	0.41901	0.830000	0.47004	3.990000	0.56965	2.382000	0.81193	0.462000	0.41574	GGA	.		0.622	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	Nonsense_Mutation	T	17907127	G	T	17907127	5	4	23	1	0	0	0	0	0	0	1	0	895	1014	35	4	39	4	ARHGEF10L	1	17907127	Splice_Site	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	5071338	17907127	231343494	4	1986											
MYCL1	4610	hgsc.bcm.edu	37	chr1	40366677	40366677	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgcccagcggacagggggCggcgggcgccgggttgccgg	3	4	21	13	7	0	0	0	0	0	0	1	1	0	1	3	7	2	1	3	7	0	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:40366677C>T	ENST00000372816.2	-	1	877	c.430G>A	c.(430-432)Gcc>Acc	p.A144T	MYCL_ENST00000429311.1_Missense_Mutation_p.A144T|MYCL_ENST00000372815.1_Missense_Mutation_p.A174T|RP1-118J21.5_ENST00000418255.1_RNA|MYCL_ENST00000397332.2_Missense_Mutation_p.A174T			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	144						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GGACAGGGGGCGGCGGGCGCC	0.761																																					p.A174T		.											.	MYCL1-847	0			c.G520A						.																																			SO:0001583	missense	4610	exon2			AGGGGGCGGCGGG		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"Basic helix-loop-helix proteins"	7555	protein-coding gene	gene with protein product	"l-myc protein", "myc-related gene from lung cancer", "oncogene lmyc"	164850	"v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.430G>A	1.37:g.40366677C>T	ENSP00000361903:p.Ala144Thr	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	7	4	NM_005376	0	0	0	0	0	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Missense_Mutation	SNP	ENST00000372816.2	37	CCDS30682.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.711171	0.30322	.	.	ENSG00000116990	ENST00000397332;ENST00000372816;ENST00000372815;ENST00000429311	T;T;T;T	0.78003	-0.93;-1.14;1.92;1.51	5.05	1.59	0.23543	.	0.621427	0.17026	N	0.189921	T	0.57814	0.2079	N	0.22421	0.69	0.22531	N	0.999018	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.003	T	0.44050	-0.9353	10	0.41790	T	0.15	-27.6027	2.4699	0.04561	0.233:0.4938:0.1472:0.126	.	144;144	P12524-2;P12524	.;MYCL1_HUMAN	T	174;144;174;144	ENSP00000380494:A174T;ENSP00000361903:A144T;ENSP00000361902:A174T;ENSP00000389358:A144T	ENSP00000361902:A174T	A	-	1	0	MYCL1	40139264	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.103000	0.31062	0.575000	0.29434	0.563000	0.77884	GCC	.		0.761	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082		T	40366677	C	T	40366677	3	4	23	1	0	0	0	0	1	0	0	0	10045	768	27	1	797	1	MYCL1	1	40366677	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	22459550	40366677	208883944	5	1987											
FOXD2	2306	hgsc.bcm.edu;broad.mit.edu	37	chr1	47905224	47905224	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acattcgcctctcgcatcccGgggacgcgctgctgtcctca	5	9	10	17	5	2	0	1	0	1	0	6	1	4	1	3	2	1	3	3	2	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:47905224G>A	ENST00000334793.5	+	1	3536	c.1417G>A	c.(1417-1419)Ggg>Agg	p.G473R		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	473					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		CTCGCATCCCGGGGACGCGCT	0.701																																					p.G473R		.											.	FOXD2-226	0			c.G1417A						.						5	6	6					1																	47905224		2116	4208	6324	SO:0001583	missense	2306	exon1			CATCCCGGGGACG	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"Forkhead boxes"	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.1417G>A	1.37:g.47905224G>A	ENSP00000335493:p.Gly473Arg	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	34	21	NM_004474	0	0	0	0	0	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	37	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990550	0.54041	.	.	ENSG00000186564	ENST00000334793	T	0.61627	0.09	4.99	4.06	0.47325	.	0.529712	0.18195	U	0.148720	T	0.32010	0.0815	N	0.14661	0.345	0.28578	N	0.910271	P	0.38992	0.653	B	0.19946	0.027	T	0.31052	-0.9957	10	0.51188	T	0.08	.	9.9291	0.41512	0.0969:0.0:0.9031:0.0	.	473	O60548	FOXD2_HUMAN	R	473	ENSP00000335493:G473R	ENSP00000335493:G473R	G	+	1	0	FOXD2	47677811	0.000000	0.05858	1.000000	0.80357	0.936000	0.57629	0.303000	0.19210	2.280000	0.76307	0.561000	0.74099	GGG	.		0.701	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474		A	47905224	G	A	47905224	3	1	23	1	0	0	0	0	1	0	0	0	6016	1116	39	1	1419	1	FOXD2	1	47905224	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	7538547	47905224	201345397	6	1988											
C1orf51	148523	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	150256865	150256882	+	In_Frame_Del	DEL	ATGGACAGGATCCAGCGT	ATGGACAGGATCCAGCGT	-																															gttttcagcagagtgtggcaAtggacaggatccagcgtatt																								rs137955605	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	ATGGACAGGATCCAGCGT	ATGGACAGGATCCAGCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:150256865_150256882delATGGACAGGATCCAGCGT	ENST00000290363.5	+	3	921_938	c.472_489delATGGACAGGATCCAGCGT	c.(472-489)atggacaggatccagcgtdel	p.MDRIQR158del	C1orf51_ENST00000469255.1_3'UTR|C1orf51_ENST00000369095.1_In_Frame_Del_p.MDRIQR158del|C1orf51_ENST00000369094.1_In_Frame_Del_p.MDRIQR70del	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		158					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)	p.R163H(1)		endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGTGTGGCAATGGACAGGATCCAGCGTATTGTAGGTG	0.459																																					p.158_163del		.											.	C1orf51-90	1	Substitution - Missense(1)	urinary_tract(1)	c.472_489del						.																																			SO:0001651	inframe_deletion	148523	exon3			.																												ENST00000290363.5:c.472_489delATGGACAGGATCCAGCGT	1.37:g.150256865_150256882delATGGACAGGATCCAGCGT	ENSP00000290363:p.Met158_Arg163del	Somatic	262	0		WXS	Illumina HiSeq	Phase_I	171	27	NM_144697	0	0	0	0	0	B2RD43|D3DV01|Q8N795|Q96MG6	In_Frame_Del	DEL	ENST00000290363.5	37	CCDS949.1																																																																																			.		0.459	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			-	150256882	ATGGACAGGATCCAGCGT	-	150256865	7	5	23	1	0	1	0	1	0	0	0	0	2049	101	4	0	482	0	C1orf51	1	150256865	In_Frame_Del	DEL	ATGGACAGGATCCAGCGT	TCGA-A4-A57E-01A-11D-A26P-10	102351641	150256865	98993756	7	1989											
PRUNE	58497	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	151001408	151001408	+	Frame_Shift_Del	DEL	A	A	-																															attttctgtccccatgtggcActccaaacaacggtgagtct																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:151001408delA	ENST00000271620.3	+	7	1077	c.921delA	c.(919-921)gcafs	p.A307fs	PRUNE_ENST00000368937.1_Intron|PRUNE_ENST00000467771.1_3'UTR|PRUNE_ENST00000368936.1_Frame_Shift_Del_p.A125fs|PRUNE_ENST00000368935.1_Intron|PRUNE_ENST00000368934.1_Intron|PRUNE_ENST00000271619.8_Intron	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	307						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCCATGTGGCACTCCAAACAA	0.502																																					p.A307fs		.											.	PRUNE-91	0			c.921delA						.						129	94	106					1																	151001408		2203	4300	6503	SO:0001589	frameshift_variant	58497	exon7			.	U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"prune homolog (Drosophila)"			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.921delA	1.37:g.151001408delA	ENSP00000271620:p.Ala307fs	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	114	43	NM_021222	0	0	0	0	0	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Frame_Shift_Del	DEL	ENST00000271620.3	37	CCDS977.1																																																																																			.		0.502	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222		-	151001408	A	-	151001408	7	5	23	1	0	1	0	1	0	0	0	0	12669	146	6	0	947	0	PRUNE	1	151001408	Frame_Shift_Del	DEL	A	TCGA-A4-A57E-01A-11D-A26P-10	744543	151001408	98249213	8	1990											
IVL	3713	broad.mit.edu	37	chr1	152883242	152883242	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcagcaggaggggcagccTaagcatctggagcagcagga	12	3	17	9	0	1	0	0	0	1	0	1	4	1	3	1	5	6	6	1	5	1	1	rs576967368	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:152883242T>G	ENST00000368764.3	+	2	1033	c.969T>G	c.(967-969)ccT>ccG	p.P323P	IVL_ENST00000392667.2_Silent_p.P177P			P07476	INVO_HUMAN	involucrin	323	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			aggggcagcctaagcatctgg	0.652													G|||	5	0.000998403	0	0.0014	5008	,	,		17882	0.004		0	False		,,,				2504	0				p.P323P													.	IVL-93	0			c.T969G						.						18	17	17					1																	152883242		2109	4146	6255	SO:0001819	synonymous_variant	3713	exon2			GCAGCCTAAGCAT	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.969T>G	1.37:g.152883242T>G		Somatic	95	1		WXS	Illumina HiSeq	Phase_I	180	10	NM_005547	0	0	0	0	0	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			.		0.652	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		G	152883242	T	G	152883242	2	3	23	1	0	0	0	0	0	0	0	1	7950	1509	53	5		5	IVL	1	152883242	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	1881834	152883242	96367379	9	1991											
PRDX6	9588	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	173454563	173454563	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttttcccatcatcgatgatAggaatcgggagcttgccatc	9	12	9	11	2	1	1	1	1	0	0	5	4	2	3	2	2	2	1	2	2	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:173454563A>G	ENST00000340385.5	+	3	448	c.316A>G	c.(316-318)Agg>Ggg	p.R106G	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	106	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						CATCGATGATAGGAATCGGGA	0.453																																					p.R106G		.											.	PRDX6-186	0			c.A316G						.						141	133	136					1																	173454563		2203	4300	6503	SO:0001583	missense	9588	exon3			GATGATAGGAATC	D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.316A>G	1.37:g.173454563A>G	ENSP00000342026:p.Arg106Gly	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	109	44	NM_004905	0	0	300	685	385	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Missense_Mutation	SNP	ENST00000340385.5	37	CCDS1307.1	.	.	.	.	.	.	.	.	.	.	A	5.323	0.244994	0.10077	.	.	ENSG00000117592	ENST00000340385	T	0.30182	1.54	5.27	1.5	0.22942	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);	0.924235	0.09408	N	0.806253	T	0.05318	0.0141	N	0.13299	0.325	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35847	-0.9772	10	0.35671	T	0.21	-4.8805	2.931	0.05800	0.3634:0.413:0.086:0.1375	.	106	P30041	PRDX6_HUMAN	G	106	ENSP00000342026:R106G	ENSP00000342026:R106G	R	+	1	2	PRDX6	171721186	0.000000	0.05858	0.966000	0.40874	0.149000	0.21700	0.209000	0.17435	0.911000	0.36747	0.528000	0.53228	AGG	.		0.453	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		G	173454563	A	G	173454563	3	3	23	1	0	0	0	0	1	0	0	0	12498	411	15	3	326	3	PRDX6	1	173454563	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	20571321	173454563	75796058	10	1992											
SIPA1L2	57568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	232600607	232600607	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	actaatcgctgaacaatttcCctgatgtcttcagcacagtt	11	13	6	11	1	2	2	1	2	1	0	4	2	3	2	1	0	2	3	1	0	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:232600607C>G	ENST00000366630.1	-	8	3157	c.2799G>C	c.(2797-2799)agG>agC	p.R933S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R933S|SIPA1L2_ENST00000308942.4_5'Flank			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	933					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GAACAATTTCCCTGATGTCTT	0.408																																					p.R933S		.											.	SIPA1L2-95	0			c.G2799C						.						63	58	60					1																	232600607		1902	4124	6026	SO:0001583	missense	57568	exon7			AATTTCCCTGATG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2799G>C	1.37:g.232600607C>G	ENSP00000355589:p.Arg933Ser	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	95	37	NM_020808	0	0	0	1	1	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859942	0.32884	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.79554	-1.28;-1.28	6.07	1.09	0.20402	.	0.000000	0.85682	D	0.000000	T	0.81163	0.4765	L	0.52759	1.655	0.51233	D	0.999913	P	0.51351	0.944	P	0.55455	0.776	T	0.77197	-0.2676	10	0.46703	T	0.11	-29.1302	10.0474	0.42195	0.0:0.3607:0.0:0.6393	.	933	Q9P2F8	SI1L2_HUMAN	S	933	ENSP00000355589:R933S;ENSP00000262861:R933S	ENSP00000262861:R933S	R	-	3	2	SIPA1L2	230667230	0.443000	0.25641	0.814000	0.32528	0.705000	0.40729	-0.151000	0.10175	-0.062000	0.13088	-0.136000	0.14681	AGG	.		0.408	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		G	232600607	C	G	232600607	3	3	23	1	0	0	0	0	1	0	0	0	14362	622	22	4	2429	4	SIPA1L2	1	232600607	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	59146044	232600607	16650014	11	1993											
SNTG2	54221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	1241762	1241763	+	Missense_Mutation	DNP	CA	CA	AT																															tggctgcgggcggtctcagcCaacatcagggagctgacact																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:1241762_1241763CA>AT	ENST00000308624.5	+	10	951_952	c.822_823CA>AT	c.(820-825)gcCAac>gcATac	p.N275Y	SNTG2_ENST00000407292.1_Missense_Mutation_p.N148Y	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	275					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CGGTCTCAGCCAACATCAGGGA	0.55																																					p.N275Y		.											.	SNTG2-136	0			c.A823T						.																																			SO:0001583	missense	54221	exon10			TCAGCCAACATCA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	Exception_encountered	2.37:g.1241762_1241763delinsAT	ENSP00000311837:p.Asn275Tyr	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	47	31	NM_018968	0	0	0	0	0	Q05AH5	Missense_Mutation	DNP	ENST00000308624.5	37	CCDS46220.1																																																																																			.		0.55	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		AT	1241763	CA	AT	1241762	3	1	23	1	0	0	0	0	1	0	0	0	14907	581	21	4	860	4	SNTG2	2	1241762	Missense_Mutation	DNP	CA	TCGA-A4-A57E-01A-11D-A26P-10		1241762	241957611	12	1994											
IL1A	3552	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	113540317	113540317	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcagagacagatgatcaatGgaggaactgtcttcttcatt	12	13	9	7	0	5	3	3	1	2	2	5	6	5	5	0	2	1	0	0	2	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:113540317G>T	ENST00000263339.3	-	3	227	c.72C>A	c.(70-72)tcC>tcA	p.S24S		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	24					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	GATGATCAATGGAGGAACTGT	0.373																																					p.S24S		.											.	IL1A-522	0			c.C72A						.						243	215	224					2																	113540317		2203	4300	6503	SO:0001819	synonymous_variant	3552	exon3			ATCAATGGAGGAA	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"Interleukins and interleukin receptors", "Endogenous ligands"	5991	protein-coding gene	gene with protein product	"preinterleukin 1 alpha", "hematopoietin-1", "pro-interleukin-1-alpha"	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.72C>A	2.37:g.113540317G>T		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	124	25	NM_000575	0	0	0	0	0	Q53QF9|Q7RU02	Silent	SNP	ENST00000263339.3	37	CCDS2101.1																																																																																			.		0.373	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575		T	113540317	G	T	113540317	2	4	23	1	0	0	0	0	0	0	0	1	7671	1335	47	4		4	IL1A	2	113540317	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	112298555	113540317	129659056	13	1995											
SLC35F5	80255	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	114487016	114487016	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaacttgtcttctctatctActtttctcttaatcataaca	10	18	1	12	0	5	0	1	0	4	0	7	0	5	0	1	0	3	0	1	0	5	8			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:114487016A>C	ENST00000245680.2	-	11	1465	c.1052T>G	c.(1051-1053)gTa>gGa	p.V351G	SLC35F5_ENST00000470204.2_5'UTR	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	351					transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						TTCTCTATCTACTTTTCTCTT	0.348																																					p.V351G													.	SLC35F5-90	0			c.T1052G						.						73	70	71					2																	114487016		2203	4299	6502	SO:0001583	missense	80255	exon11			CTATCTACTTTTC	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.1052T>G	2.37:g.114487016A>C	ENSP00000245680:p.Val351Gly	Somatic	123	2		WXS	Illumina HiSeq	Phase_I	131	85	NM_025181	0	0	7	18	11	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	37	CCDS2119.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.0|23.0	4.364234|4.364234	0.82463|0.82463	.|.	.|.	ENSG00000115084|ENSG00000115084	ENST00000447673|ENST00000245680;ENST00000409106	.|T;T	.|0.53640	.|0.61;0.61	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.67429|0.67429	0.2892|0.2892	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.76071	.|0.987	T|T	0.69591|0.69591	-0.5104|-0.5104	5|10	.|0.59425	.|D	.|0.04	-13.7299|-13.7299	16.0957|16.0957	0.81123|0.81123	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|351	.|Q8WV83	.|S35F5_HUMAN	R|G	113|351;345	.|ENSP00000245680:V351G;ENSP00000386754:V345G	.|ENSP00000245680:V351G	S|V	-|-	3|2	2|0	SLC35F5|SLC35F5	114203486|114203486	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.692000|8.692000	0.91284|0.91284	2.199000|2.199000	0.70637|0.70637	0.533000|0.533000	0.62120|0.62120	AGT|GTA	.		0.348	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		C	114487016	A	C	114487016	3	2	23	1	0	0	0	0	1	0	0	0	14624	391	14	5	539	5	SLC35F5	2	114487016	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	946699	114487016	128712357	14	1996											
FAM168B	130074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	131812937	131812937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcagggtacaccgttgcaGgcatgccgttgggctgcacc	7	7	15	12	2	0	0	0	0	0	0	0	1	0	0	3	3	5	8	3	3	1	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:131812937G>A	ENST00000409185.1	-	5	490	c.383C>T	c.(382-384)cCt>cTt	p.P128L	FAM168B_ENST00000389915.3_Missense_Mutation_p.P128L	NM_001009993.2	NP_001009993.2	A1KXE4	F168B_HUMAN	family with sequence similarity 168, member B	128						cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|lung(2)	5						CACCGTTGCAGGCATGCCGTT	0.622																																					p.P128L		.											.	FAM168B-90	0			c.C383T						.						153	170	164					2																	131812937		2164	4258	6422	SO:0001583	missense	130074	exon5			GTTGCAGGCATGC		CCDS42755.1	2q21.1	2008-08-08			ENSG00000152102	ENSG00000152102			27016	protein-coding gene	gene with protein product							Standard	NM_001009993		Approved	KIAA0280L	uc002tsd.3	A1KXE4	OTTHUMG00000153473	ENST00000409185.1:c.383C>T	2.37:g.131812937G>A	ENSP00000387051:p.Pro128Leu	Somatic	196	1		WXS	Illumina HiSeq	Phase_I	241	154	NM_001009993	0	0	8	26	18	Q2TAZ6|Q6NZ40	Missense_Mutation	SNP	ENST00000409185.1	37	CCDS42755.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849158	0.91277	.	.	ENSG00000152102	ENST00000409185;ENST00000389915	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.70364	-0.4892	9	0.87932	D	0	-5.3044	16.8479	0.85986	0.0:0.0:1.0:0.0	.	128	A1KXE4	F168B_HUMAN	L	128	.	ENSP00000374565:P128L	P	-	2	0	FAM168B	131529407	1.000000	0.71417	0.971000	0.41717	0.857000	0.48899	9.249000	0.95470	2.640000	0.89533	0.655000	0.94253	CCT	.		0.622	FAM168B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331299.2	NM_001009993		A	131812937	G	A	131812937	3	1	23	1	0	0	0	0	1	0	0	0	5502	1000	35	2	212	2	FAM168B	2	131812937	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	17325921	131812937	111386436	15	1997											
CLK1	1195	broad.mit.edu;bcgsc.ca	37	chr2	201719790	201719790	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctatgctccagacatcacaTggttgggaccaccctagggc	9	8	10	14	0	1	1	1	0	0	1	2	2	2	2	4	3	1	2	4	3	2	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:201719790T>G	ENST00000321356.4	-	10	1212	c.1077A>C	c.(1075-1077)ccA>ccC	p.P359P	CLK1_ENST00000409769.2_Silent_p.P182P|CLK1_ENST00000434813.2_Silent_p.P401P	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	359	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						AGACATCACATGGTTGGGACC	0.348																																					p.P401P													.	CLK1-784	0			c.A1203C						.						88	85	86					2																	201719790		2203	4300	6503	SO:0001819	synonymous_variant	1195	exon10			ATCACATGGTTGG	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.1077A>C	2.37:g.201719790T>G		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	327	12	NM_001162407	0	0	44	44	0	B4DFW7|Q0P694|Q8N5V8	Silent	SNP	ENST00000321356.4	37	CCDS2331.1																																																																																			.		0.348	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			G	201719790	T	G	201719790	2	3	23	1	0	0	0	0	0	0	0	1	3542	1451	51	5		5	CLK1	2	201719790	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	69906853	201719790	41479583	16	1998											
RAPH1	65059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	204304798	204304798	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acacccttgttggagaactcCaggaaggttgactccagaaa	13	8	10	10	0	0	3	0	1	0	2	2	5	2	4	3	3	1	2	3	3	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:204304798C>G	ENST00000319170.5	-	14	3414	c.3115G>C	c.(3115-3117)Gga>Cga	p.G1039R	RAPH1_ENST00000374493.3_Missense_Mutation_p.G1091R|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1039					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGGAGAACTCCAGGAAGGTTG	0.552																																					p.G1039R		.											.	RAPH1-1151	0			c.G3115C						.						45	52	50					2																	204304798		2203	4300	6503	SO:0001583	missense	65059	exon14			GAACTCCAGGAAG	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3115G>C	2.37:g.204304798C>G	ENSP00000316543:p.Gly1039Arg	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	92	27	NM_213589	0	0	2	2	0	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432725	0.43224	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.43294	0.95;0.96	4.46	1.62	0.23740	.	.	.	.	.	T	0.19327	0.0464	N	0.08118	0	0.09310	N	0.999998	B	0.31125	0.309	B	0.25884	0.064	T	0.16541	-1.0399	9	0.26408	T	0.33	.	7.532	0.27689	0.0:0.4758:0.0:0.5242	.	1039	Q70E73	RAPH1_HUMAN	R	1039;1091	ENSP00000316543:G1039R;ENSP00000363617:G1091R	ENSP00000316543:G1039R	G	-	1	0	RAPH1	204013043	0.026000	0.19158	0.000000	0.03702	0.668000	0.39293	0.417000	0.21214	0.104000	0.17725	0.467000	0.42956	GGA	.		0.552	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		G	204304798	C	G	204304798	3	3	23	1	0	0	0	0	1	0	0	0	13082	603	21	4	641	4	RAPH1	2	204304798	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	2585008	204304798	38894575	17	1999											
ZDBF2	57683	broad.mit.edu	37	chr2	207169686	207169686	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaaaactggagaagggacAgcagcagcccttggagtttg	13	7	13	8	0	1	1	1	0	0	1	1	4	1	3	1	3	4	3	1	3	3	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:207169686A>G	ENST00000374423.3	+	5	820	c.434A>G	c.(433-435)cAg>cGg	p.Q145R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	145							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GAGAAGGGACAGCAGCAGCCC	0.423																																					p.Q145R													.	ZDBF2-3	0			c.A434G						.						57	53	54					2																	207169686		1874	4116	5990	SO:0001583	missense	57683	exon5			AGGGACAGCAGCA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.434A>G	2.37:g.207169686A>G	ENSP00000363545:p.Gln145Arg	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	91	3	NM_020923	0	0	0	0	0	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997018	0.54147	.	.	ENSG00000204186	ENST00000374423	T	0.16324	2.35	5.16	2.82	0.32997	.	0.498096	0.14995	N	0.286492	T	0.15176	0.0366	L	0.53249	1.67	0.24874	N	0.992264	P	0.41673	0.759	B	0.35899	0.213	T	0.09400	-1.0676	10	0.48119	T	0.1	.	8.9296	0.35661	0.8486:0.0:0.1514:0.0	.	145	Q9HCK1	ZDBF2_HUMAN	R	145	ENSP00000363545:Q145R	ENSP00000363545:Q145R	Q	+	2	0	ZDBF2	206877931	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.547000	0.36190	0.810000	0.34279	-0.263000	0.10527	CAG	.		0.423	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207169686	A	G	207169686	3	3	23	1	0	0	0	0	1	0	0	0	17631	188	7	3	444	3	ZDBF2	2	207169686	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	2864888	207169686	36029687	18	2000											
ZFAND2B	130617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220072714	220072714	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatcaagcaccggcatccaCtggaccatgattgctctggg	9	8	11	13	1	2	1	1	1	1	0	3	2	3	2	3	3	2	4	3	3	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:220072714C>T	ENST00000289528.5	+	4	583	c.388C>T	c.(388-390)Ctg>Ttg	p.L130L	ZFAND2B_ENST00000409319.1_Silent_p.L130L|ZFAND2B_ENST00000409412.1_Silent_p.L130L|ZFAND2B_ENST00000409217.1_Silent_p.L130L|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000409206.1_Silent_p.L130L|ZFAND2B_ENST00000444522.2_Silent_p.L130L|ZFAND2B_ENST00000409097.1_Silent_p.L130L|ZFAND2B_ENST00000409594.1_Silent_p.L130L|ZFAND2B_ENST00000409336.1_Silent_p.L130L	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	130						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGGCATCCACTGGACCATGA	0.552																																					p.L130L		.											.	ZFAND2B-68	0			c.C388T						.						80	86	84					2																	220072714		2203	4300	6503	SO:0001819	synonymous_variant	130617	exon4			CATCCACTGGACC	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"Zinc fingers, AN1-type domain containing"	25206	protein-coding gene	gene with protein product	"arsenite inducible RNA associated protein-like"	613474	"zinc finger, AN1-type 2B"			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.388C>T	2.37:g.220072714C>T		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	156	107	NM_138802	0	0	3	34	31	Q8NB98	Silent	SNP	ENST00000289528.5	37	CCDS2435.1																																																																																			.		0.552	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		T	220072714	C	T	220072714	2	4	23	1	0	0	0	0	0	0	0	1	17660	564	20	2		2	ZFAND2B	2	220072714	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	12903028	220072714	23126659	19	2001											
CUL3	8452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	225422463	225422463	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaccattgtatatgcattTctatagagctcctcaaaact	15	13	4	9	0	2	1	1	0	1	1	3	1	3	1	2	0	4	3	2	0	8	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:225422463T>G	ENST00000264414.4	-	2	515	c.177A>C	c.(175-177)agA>agC	p.R59S	CUL3_ENST00000344951.4_Intron|CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409096.1_Missense_Mutation_p.R35S|CUL3_ENST00000409777.1_Missense_Mutation_p.R35S	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	59					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TATATGCATTTCTATAGAGCT	0.338																																					p.R65S		.											.	CUL3-229	0			c.A195C						.						99	97	98					2																	225422463		2203	4298	6501	SO:0001583	missense	8452	exon2			TGCATTTCTATAG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.177A>C	2.37:g.225422463T>G	ENSP00000264414:p.Arg59Ser	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	36	24	NM_001257198	0	0	0	5	5	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.79|16.79	3.221692|3.221692	0.58560|0.58560	.|.	.|.	ENSG00000036257|ENSG00000036257	ENST00000436172|ENST00000264414;ENST00000409096;ENST00000409777	.|T;T;T	.|0.29917	.|1.55;1.55;1.55	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55641|0.55641	0.1933|0.1933	M|M	0.86420|0.86420	2.815|2.815	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.67725	.|0.953;0.953	T|T	0.62511|0.62511	-0.6839|-0.6839	5|10	.|0.72032	.|D	.|0.01	.|.	8.148|8.148	0.31124|0.31124	0.0:0.1903:0.0:0.8097|0.0:0.1903:0.0:0.8097	.|.	.|37;59	.|Q53S54;Q13618	.|.;CUL3_HUMAN	Q|S	80|59;35;35	.|ENSP00000264414:R59S;ENSP00000387200:R35S;ENSP00000386525:R35S	.|ENSP00000264414:R59S	K|R	-|-	1|3	0|2	CUL3|CUL3	225130707|225130707	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.980000|1.980000	0.40618|0.40618	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	AAA|AGA	.		0.338	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			G	225422463	T	G	225422463	3	3	23	1	0	0	0	0	1	0	0	0	4062	1780	62	5	2189	5	CUL3	2	225422463	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	5349749	225422463	17776910	20	2002											
KIF1A	547	hgsc.bcm.edu;bcgsc.ca	37	chr2	241658528	241658528	+	Frame_Shift_Del	DEL	G	G	-																															ctgttgtacatgtaggcataGgggcgccgcaccaccacgaa																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:241658528delG	ENST00000320389.7	-	45	4964	c.4806delC	c.(4804-4806)cccfs	p.P1602fs	KIF1A_ENST00000498729.2_Frame_Shift_Del_p.P1703fs	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1602	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TGTAGGCATAGGGGCGCCGCA	0.622																																					p.P1703fs		.											.	KIF1A-91	0			c.5109delC						.						87	100	96					2																	241658528		2166	4274	6440	SO:0001589	frameshift_variant	547	exon47			.	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.4806delC	2.37:g.241658528delG	ENSP00000322791:p.Pro1602fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	289	95	NM_001244008	0	0	0	0	0	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Frame_Shift_Del	DEL	ENST00000320389.7	37	CCDS46561.1																																																																																			.		0.622	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		-	241658528	G	-	241658528	7	5	23	1	0	1	0	1	0	0	0	0	8304	987	35	0	278	0	KIF1A	2	241658528	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	16236065	241658528	1540845	21	2003											
CMTM7	112616	hgsc.bcm.edu	37	chr3	32433539	32433539	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccgcacccacgcggccctGctgaaagtggcgcaaatggt	8	5	12	16	4	0	1	0	1	0	0	0	1	0	1	4	3	1	3	4	3	2	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr3:32433539G>C	ENST00000334983.5	+	1	377	c.141G>C	c.(139-141)ctG>ctC	p.L47L	CMTM7_ENST00000349718.4_Silent_p.L47L	NM_138410.2	NP_612419.1	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing 7	47	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(1)|lung(2)	4						ACGCGGCCCTGCTGAAAGTGG	0.756																																					p.L47L		.											.	CMTM7-226	0			c.G141C						.						2	2	2					3																	32433539		1638	3364	5002	SO:0001819	synonymous_variant	112616	exon1			GGCCCTGCTGAAA	AF479263	CCDS33730.1, CCDS33731.1	3p22.2	2005-11-08	2005-11-08	2005-11-08	ENSG00000153551	ENSG00000153551			19178	protein-coding gene	gene with protein product		607890	"chemokine-like factor super family 7", "chemokine-like factor superfamily 7"	CKLFSF7			Standard	NM_138410		Approved	FLJ30992	uc003cey.1	Q96FZ5	OTTHUMG00000155869	ENST00000334983.5:c.141G>C	3.37:g.32433539G>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_138410	0	0	0	0	0	Q5VLK1	Silent	SNP	ENST00000334983.5	37	CCDS33730.1																																																																																			.		0.756	CMTM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342084.1			C	32433539	G	C	32433539	2	2	23	1	0	0	0	0	0	0	0	1	3594	1306	46	4		4	CMTM7	3	32433539	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		32433539	165588891	22	2004											
FAIM	55179	ucsc.edu	37	chr3	138340383	138340383	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtatatgtagatggaaaggTaggaagaaaatatgttactt	17	12	11	1	0	0	2	0	0	0	2	0	4	0	4	0	3	1	4	0	3	10	7			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr3:138340383T>A	ENST00000393035.2	+	2	220		c.e2+2		FAIM_ENST00000338446.4_Splice_Site|FAIM_ENST00000393034.2_Splice_Site|FAIM_ENST00000360570.3_Splice_Site|FAIM_ENST00000464668.1_Splice_Site	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule						apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						GATGGAAAGGTAGGAAGAAAA	0.343																																					.													.	FAIM-227	0			c.111+2T>A						.						89	88	89					3																	138340383		2203	4300	6503	SO:0001630	splice_region_variant	55179	exon2			GAAAGGTAGGAAG	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.111+2T>A	3.37:g.138340383T>A		Somatic	66	0		WXS	Illumina HiSeq		4245	10	NM_001033032	0	0	0	0	0	Q6IAN2	Splice_Site	SNP	ENST00000393035.2	37	CCDS3103.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.819193	0.50633	.	.	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	.	.	.	4.59	3.39	0.38822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7803	0.34787	0.1691:0.0:0.0:0.8309	.	.	.	.	.	-1	.	.	.	+	.	.	FAIM	139823073	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.777000	0.85628	0.856000	0.35383	0.383000	0.25322	.	.		0.343	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	Intron	A	138340383	T	A	138340383	5	1	23	1	0	0	0	0	0	0	1	0	5391	1652	57	5	269	5	FAIM	3	138340383	Splice_Site	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	105906844	138340383	59682047	23	2005											
KIT	3815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	55570036	55570036	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acttttggatcagcaaatgtCacaacaaccttggaagtagt	14	11	8	8	0	2	0	2	0	0	0	2	2	2	2	1	2	3	2	1	2	5	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr4:55570036C>G	ENST00000288135.5	+	5	1000	c.903C>G	c.(901-903)gtC>gtG	p.V301V		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	301	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCAAATGTCACAACAACCT	0.348		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.V301V		.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"L, M, O, E"	.	KIT-20166	0			c.C903G						.						168	163	165					4																	55570036		2203	4300	6503	SO:0001819	synonymous_variant	3815	exon5	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	AAATGTCACAACA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6342	protein-coding gene	gene with protein product		164920	"piebald trait"	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.903C>G	4.37:g.55570036C>G		Somatic	162	0		WXS	Illumina HiSeq	Phase_I	164	58	NM_000222	0	0	0	0	0	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																			.		0.348	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55570036	C	G	55570036	2	3	23	1	0	0	0	0	0	0	0	1	8350	813	29	4		4	KIT	4	55570036	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		55570036	135584240	24	2006											
ADAMTS3	9508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	73148995	73148995	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagccatttgtgaagctgaaCtgaggtggaccctcttggtg	8	11	13	9	0	1	3	0	3	1	0	1	4	1	4	2	3	3	1	2	3	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr4:73148995C>T	ENST00000286657.4	-	22	3512	c.3476G>A	c.(3475-3477)aGt>aAt	p.S1159N		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	1159					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGAAGCTGAACTGAGGTGGAC	0.498																																					p.S1159N	NSCLC(168;1941 2048 2918 13048 43078)	.											.	ADAMTS3-651	0			c.G3476A						.						195	172	180					4																	73148995		2203	4300	6503	SO:0001583	missense	9508	exon22			GCTGAACTGAGGT	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.3476G>A	4.37:g.73148995C>T	ENSP00000286657:p.Ser1159Asn	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	157	51	NM_014243	0	0	5	8	3	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.777427	0.00080	.	.	ENSG00000156140	ENST00000286657	T	0.61040	0.14	5.23	-10.5	0.00291	.	1.555640	0.04150	N	0.321125	T	0.22282	0.0537	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	10	0.09084	T	0.74	.	11.9585	0.52995	0.0:0.5187:0.2677:0.2136	.	1159	O15072	ATS3_HUMAN	N	1159	ENSP00000286657:S1159N	ENSP00000286657:S1159N	S	-	2	0	ADAMTS3	73367859	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.403000	0.01046	-2.504000	0.00508	-0.423000	0.05987	AGT	.		0.498	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73148995	C	T	73148995	3	4	23	1	0	0	0	0	1	0	0	0	267	565	20	2	145	2	ADAMTS3	4	73148995	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	17578959	73148995	118005281	25	2007											
DMXL1	1657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	118451949	118451949	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaacaatcccaaggagaaAttgacttttcttttgtgtat	15	14	6	6	0	1	2	0	1	1	1	2	3	2	2	1	1	1	1	1	1	6	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:118451949A>T	ENST00000311085.8	+	7	741	c.661A>T	c.(661-663)Att>Ttt	p.I221F	DMXL1_ENST00000539542.1_Missense_Mutation_p.I221F	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	221			I -> M (in dbSNP:rs7700801).							breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CCAAGGAGAAATTGACTTTTC	0.403																																					p.I221F		.											.	DMXL1-92	0			c.A661T						.						136	130	132					5																	118451949		2202	4300	6502	SO:0001583	missense	1657	exon7			GGAGAAATTGACT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.661A>T	5.37:g.118451949A>T	ENSP00000309690:p.Ile221Phe	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	95	27	NM_005509	0	0	0	2	2		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.554283	0.45487	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.66815	1.93;-0.23;2.94	4.96	2.25	0.28309	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.551167	0.19764	N	0.106592	T	0.46328	0.1387	L	0.28400	0.85	0.25888	N	0.983509	B;B	0.22541	0.071;0.042	B;B	0.23018	0.043;0.019	T	0.17930	-1.0353	10	0.24483	T	0.36	-0.2952	3.3933	0.07297	0.3747:0.2296:0.3958:0.0	.	221;221	F5H269;Q9Y485	.;DMXL1_HUMAN	F	221	ENSP00000427692:I221F;ENSP00000309690:I221F;ENSP00000439479:I221F	ENSP00000309690:I221F	I	+	1	0	DMXL1	118479848	1.000000	0.71417	0.979000	0.43373	0.953000	0.61014	1.200000	0.32247	0.842000	0.35045	0.533000	0.62120	ATT	.		0.403	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118451949	A	T	118451949	3	4	23	1	0	0	0	0	1	0	0	0	4605	101	4	5	687	5	DMXL1	5	118451949	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10		118451949	62463311	26	2008											
ARAP3	64411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141035313	141035313	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgtcgtaagaccactggctGctggtcatcgtgctggtggg	5	10	16	10	3	1	1	1	0	0	1	3	1	1	1	1	4	2	4	1	4	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:141035313G>C	ENST00000239440.4	-	31	4050	c.3985C>G	c.(3985-3987)Cag>Gag	p.Q1329E	ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000508305.1_Missense_Mutation_p.Q1160E|ARAP3_ENST00000513878.1_Missense_Mutation_p.Q991E	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1329					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						ACCACTGGCTGCTGGTCATCG	0.617																																					p.Q1329E		.											.	ARAP3-291	0			c.C3985G						.						84	79	81					5																	141035313		2203	4300	6503	SO:0001583	missense	64411	exon31			CTGGCTGCTGGTC	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3985C>G	5.37:g.141035313G>C	ENSP00000239440:p.Gln1329Glu	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	195	58	NM_022481	0	0	2	2	0	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782249	0.31502	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.14893	2.47;3.19;3.04	5.66	5.66	0.87406	Pleckstrin homology-type (1);	0.184808	0.46442	D	0.000286	T	0.14960	0.0361	N	0.24115	0.695	0.36230	D	0.852566	P;P;P	0.46220	0.65;0.874;0.637	B;B;B	0.40375	0.306;0.327;0.087	T	0.06844	-1.0804	10	0.35671	T	0.21	.	19.3334	0.94303	0.0:0.0:1.0:0.0	.	991;1160;1329	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	E	1160;1329;991	ENSP00000421826:Q1160E;ENSP00000239440:Q1329E;ENSP00000421468:Q991E	ENSP00000239440:Q1329E	Q	-	1	0	ARAP3	141015497	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	5.807000	0.69157	2.675000	0.91044	0.655000	0.94253	CAG	.		0.617	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		C	141035313	G	C	141035313	3	2	23	1	0	0	0	0	1	0	0	0	840	1328	46	4	661	4	ARAP3	5	141035313	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	22583364	141035313	39879947	27	2009											
PCDH12	51294	hgsc.bcm.edu;bcgsc.ca	37	chr5	141334867	141334868	+	Frame_Shift_Ins	INS	-	-	A																															tcctctgcctgggatggttgINSaaaaggaggttgaccgtgtc																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:141334867_141334868insA	ENST00000231484.3	-	1	3759_3760	c.2549_2550insT	c.(2548-2550)ttcfs	p.F850fs	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	850					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGATGGTTGAAAAGGAGGTT	0.629																																					p.F850fs		.											.	PCDH12-93	0			c.2550_2551insT						.																																			SO:0001589	frameshift_variant	51294	exon1			.	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2550dupT	5.37:g.141334871_141334871dupA	ENSP00000231484:p.Phe850fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	158	47	NM_016580	0	0	0	0	0	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Frame_Shift_Ins	INS	ENST00000231484.3	37	CCDS4269.1																																																																																			.		0.629	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141334868	-	A	141334867	7	5	23	1	0	1	1	0	0	0	0	0	11536	1281	45	0	1020	0	PCDH12	5	141334867	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	299554	141334867	39580393	28	2010											
ADAMTS2	9509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	178567002	178567002	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtcccgtttgaggatgtcaGgtgtcagccagatgcagtgt	7	11	14	9	2	2	2	2	1	0	1	3	3	3	3	2	2	2	2	2	2	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:178567002G>A	ENST00000251582.7	-	11	1765	c.1664C>T	c.(1663-1665)cCt>cTt	p.P555L		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	555	Disintegrin.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GAGGATGTCAGGTGTCAGCCA	0.607																																					p.P555L		.											.	ADAMTS2-228	0			c.C1664T						.						162	170	167					5																	178567002		2203	4300	6503	SO:0001583	missense	9509	exon11			ATGTCAGGTGTCA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1664C>T	5.37:g.178567002G>A	ENSP00000251582:p.Pro555Leu	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	190	56	NM_014244	0	0	1	1	0		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.362637	0.41902	.	.	ENSG00000087116	ENST00000251582	T	0.61274	0.12	4.92	4.92	0.64577	.	0.000000	0.53938	D	0.000058	T	0.62841	0.2461	N	0.20685	0.6	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	T	0.67201	-0.5730	10	0.52906	T	0.07	.	17.1242	0.86710	0.0:0.0:1.0:0.0	.	555	O95450	ATS2_HUMAN	L	555	ENSP00000251582:P555L	ENSP00000251582:P555L	P	-	2	0	ADAMTS2	178499608	1.000000	0.71417	0.117000	0.21633	0.227000	0.25037	9.282000	0.95840	2.281000	0.76405	0.561000	0.74099	CCT	.		0.607	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178567002	G	A	178567002	3	1	23	1	0	0	0	0	1	0	0	0	265	1000	35	2	2019	2	ADAMTS2	5	178567002	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	37232135	178567002	2348258	29	2011											
GCM2	9247	broad.mit.edu	37	chr6	10877442	10877442	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggaaccgtcgggcagggTgcaggcctgtgtacacacca	8	5	16	12	3	0	0	0	0	0	0	1	1	0	1	3	4	3	3	3	4	2	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:10877442T>G	ENST00000379491.4	-	2	421	c.274A>C	c.(274-276)Acc>Ccc	p.T92P	RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron	NM_004752.3	NP_004743.1	O75603	GCM2_HUMAN	glial cells missing homolog 2 (Drosophila)	92					cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to organic substance (GO:0071310)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|parathyroid gland development (GO:0060017)|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 (GO:0043565)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	30	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				TCGGGCAGGGTGCAGGCCTGT	0.642																																					p.T92P													.	GCM2-92	0			c.A274C						.						84	73	77					6																	10877442		2203	4300	6503	SO:0001583	missense	9247	exon2			GCAGGGTGCAGGC	AF079550	CCDS4517.1	6p24.2	2008-08-29	2001-11-28	2002-09-27	ENSG00000124827	ENSG00000124827			4198	protein-coding gene	gene with protein product		603716	"glial cells missing (Drosophila) homolog b"	GCMB		9928992	Standard	NM_004752		Approved	hGCMb	uc003mzn.4	O75603	OTTHUMG00000014249	ENST00000379491.4:c.274A>C	6.37:g.10877442T>G	ENSP00000368805:p.Thr92Pro	Somatic	41	10		WXS	Illumina HiSeq	Phase_I	84	20	NM_004752	0	0	0	0	0	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	t	9.347	1.064491	0.20067	.	.	ENSG00000124827	ENST00000379491	T	0.73897	-0.79	5.41	-7.21	0.01490	.	1.296560	0.04939	N	0.458294	T	0.53029	0.1771	L	0.50333	1.59	0.35726	D	0.817526	P	0.37612	0.602	B	0.39617	0.305	T	0.52373	-0.8584	10	0.48119	T	0.1	1.9185	12.6703	0.56864	0.0797:0.3284:0.0:0.5919	.	92	O75603	GCM2_HUMAN	P	92	ENSP00000368805:T92P	ENSP00000368805:T92P	T	-	1	0	GCM2	10985428	0.004000	0.15560	0.030000	0.17652	0.355000	0.29361	-0.858000	0.04281	-1.786000	0.01269	-2.592000	0.00164	ACC	.		0.642	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			G	10877442	T	G	10877442	3	3	23	1	0	0	0	0	1	0	0	0	6318	1696	59	5	1262	5	GCM2	6	10877442	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10		10877442	160237625	30	2012											
ABT1	29777	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	26597328	26597328	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaagcggcctgtggcagcAagaaacgggtagtgccaggt	12	5	16	8	2	0	2	0	0	0	2	0	2	0	2	2	4	4	3	2	4	5	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:26597328A>T	ENST00000274849.1	+	1	149	c.118A>T	c.(118-120)Aag>Tag	p.K40*		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	40					regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CTGTGGCAGCAAGAAACGGGT	0.627																																					p.K40X													.	ABT1-91	0			c.A118T						.						69	79	76					6																	26597328		2203	4300	6503	SO:0001587	stop_gained	29777	exon1			GGCAGCAAGAAAC	AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.118A>T	6.37:g.26597328A>T	ENSP00000274849:p.Lys40*	Somatic	170	1		WXS	Illumina HiSeq	Phase_I	184	72	NM_013375	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000274849.1	37	CCDS4616.1	.	.	.	.	.	.	.	.	.	.	A	16.60	3.169046	0.57584	.	.	ENSG00000146109	ENST00000274849	.	.	.	4.27	1.81	0.25067	.	0.269435	0.26828	N	0.022284	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4501	3.5569	0.07867	0.6006:0.1975:0.2019:0.0	.	.	.	.	X	40	.	ENSP00000274849:K40X	K	+	1	0	ABT1	26705307	1.000000	0.71417	0.836000	0.33094	0.107000	0.19398	4.161000	0.58170	0.399000	0.25367	0.533000	0.62120	AAG	.		0.627	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1			T	26597328	A	T	26597328	4	4	23	1	0	0	0	0	0	1	0	0	101	131	5	5	120	5	ABT1	6	26597328	Nonsense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	15719886	26597328	144517739	31	2013											
COL21A1	81578	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	55925556	55925557	+	Frame_Shift_Ins	INS	-	-	A																															acctcttattacatctgtgcINSaaacttgtcgaataaattgt																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:55925556_55925557insA	ENST00000244728.5	-	27	2786_2787	c.2389_2390insT	c.(2389-2391)tgcfs	p.C797fs	COL21A1_ENST00000370819.1_Frame_Shift_Ins_p.C794fs|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000535941.1_Frame_Shift_Ins_p.C797fs|COL21A1_ENST00000370808.2_Frame_Shift_Ins_p.C197fs	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	797					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TACATCTGTGCAAACTTGTCGA	0.297																																					p.C797fs		.											.	COL21A1-24	0			c.2390_2391insT						.																																			SO:0001589	frameshift_variant	81578	exon27			.	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2390dupT	6.37:g.55925559_55925559dupA	ENSP00000244728:p.Cys797fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	47	14	NM_030820	0	0	0	0	0	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Frame_Shift_Ins	INS	ENST00000244728.5	37	CCDS55025.1																																																																																			.		0.297	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	55925557	-	A	55925556	7	5	23	1	0	1	1	0	0	0	0	0	3686	710	25	0	499	0	COL21A1	6	55925556	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	29328228	55925556	115189511	32	2014											
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	129766960	129766960	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccaagctcggaaacaagcCaattctgtaagttcttttta	14	12	6	9	1	2	0	0	0	2	0	3	1	2	1	2	1	4	3	2	1	7	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:129766960C>T	ENST00000421865.2	+	45	6472	c.6423C>T	c.(6421-6423)gcC>gcT	p.A2141A		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2141	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGAAACAAGCCAATTCTGTAA	0.368																																					p.A2141A		.											.	LAMA2-162	0			c.C6423T						.						53	48	50					6																	129766960		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon45			ACAAGCCAATTCT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.6423C>T	6.37:g.129766960C>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	45	19	NM_000426	0	0	0	0	0	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			.		0.368	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129766960	C	T	129766960	2	4	23	1	0	0	0	0	0	0	0	1	8627	581	21	2		2	LAMA2	6	129766960	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	73841404	129766960	41348107	33	2015											
TAAR9	134860	broad.mit.edu	37	chr6	132859485	132859485	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtgttacaagaacgtgaaCgaatcctgcattaaaactcc	14	10	7	10	2	0	2	0	1	0	1	2	3	2	2	2	0	5	2	2	0	7	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:132859485C>T	ENST00000434551.1	+	0	57					NM_175057.3	NP_778227.3	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9 (gene/pseudogene)						G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)					Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		AGAACGTGAACGAATCCTGCA	0.458																																					.	Colon(10;433 445 15992 45047 47213)												.	.	0			.						.						87	84	85					6																	132859485		1991	4182	6173			134860	.			CGTGAACGAATCC	AF380189	CCDS75520.1	6q23.2	2013-10-02	2010-03-12	2005-02-24	ENSG00000237110	ENSG00000237110		"GPCR / Class A : Trace amine associated receptors"	20977	protein-coding gene	gene with protein product		608282	"trace amine receptor 3", "trace amine associated receptor 9"	TRAR3		15718104	Standard	NM_175057		Approved	TA3, TAR3	uc011eci.2	Q96RI9	OTTHUMG00000015578		6.37:g.132859485C>T		Somatic	215	0		WXS	Illumina HiSeq	Phase_I	228	6	.	0	0	0	0	0		Silent	SNP	ENST00000434551.1	37																																																																																				.		0.458	TAAR9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000042254.2	NM_175057		T	132859485	C	T	132859485	1	4	23	0	1	0	0	0	0	0	0	0	15526	535	19	1		1	TAAR9	6	132859485	RNA	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	3092525	132859485	38255582	34	2016											
REPS1	85021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	139235873	139235873	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggaggcactgcaggaggatgGgcaacaactccagcctgttg	10	6	15	10	0	0	0	0	0	0	0	1	3	1	3	2	5	4	4	2	5	2	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:139235873G>T	ENST00000450536.2	-	15	2320	c.1746C>A	c.(1744-1746)gcC>gcA	p.A582A	REPS1_ENST00000409812.2_Silent_p.A491A|REPS1_ENST00000415951.2_Silent_p.A555A|REPS1_ENST00000367663.4_Silent_p.A555A|REPS1_ENST00000258062.5_Silent_p.A581A			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	582	Pro-rich.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		CAGGAGGATGGGCAACAACTC	0.398																																					p.A581A		.											.	REPS1-522	0			c.C1743A						.						142	141	142					6																	139235873		2203	4300	6503	SO:0001819	synonymous_variant	85021	exon15			AGGATGGGCAACA		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1746C>A	6.37:g.139235873G>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	74	33	NM_031922	0	0	16	24	8	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Silent	SNP	ENST00000450536.2	37																																																																																				.		0.398	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			T	139235873	G	T	139235873	2	4	23	1	0	0	0	0	0	0	0	1	13260	1219	43	4		4	REPS1	6	139235873	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	6376388	139235873	31879194	35	2017											
MEOX2	4223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	15725867	15725867	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caaacatgccctcttcgttgGggtatcccgcgattatgcaa	9	11	9	12	3	1	0	0	0	1	0	3	1	2	0	2	2	3	3	2	2	4	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:15725867G>C	ENST00000262041.5	-	1	570	c.161C>G	c.(160-162)cCc>cGc	p.P54R	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	54					angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		CTCTTCGTTGGGGTATCCCGC	0.572																																					p.P54R	Esophageal Squamous(140;197 1769 16409 18257 29929)	.											.	MEOX2-515	0			c.C161G						.						59	53	55					7																	15725867		2203	4300	6503	SO:0001583	missense	4223	exon1			TCGTTGGGGTATC		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.161C>G	7.37:g.15725867G>C	ENSP00000262041:p.Pro54Arg	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	161	43	NM_005924	0	0	0	0	0	B2R8I7|O75263|Q9UPL6	Missense_Mutation	SNP	ENST00000262041.5	37	CCDS34605.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877795	0.51801	.	.	ENSG00000106511	ENST00000262041	D	0.91068	-2.78	4.88	4.88	0.63580	.	0.233514	0.43919	D	0.000502	D	0.89269	0.6667	L	0.54323	1.7	0.54753	D	0.999981	B	0.23891	0.093	B	0.26517	0.07	D	0.86520	0.1815	10	0.44086	T	0.13	-23.5827	18.4725	0.90779	0.0:0.0:1.0:0.0	.	54	P50222	MEOX2_HUMAN	R	54	ENSP00000262041:P54R	ENSP00000262041:P54R	P	-	2	0	MEOX2	15692392	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.705000	0.91357	2.424000	0.82194	0.650000	0.86243	CCC	.		0.572	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		C	15725867	G	C	15725867	3	2	23	1	0	0	0	0	1	0	0	0	9499	1232	43	4	765	4	MEOX2	7	15725867	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		15725867	143412796	36	2018											
HDAC9	9734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	18975517	18975517	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggacatgatctcacagcCatctgtgatgcatcagaagc	12	8	11	10	0	3	3	2	2	2	1	4	5	3	5	1	2	3	1	1	2	1	0	rs534633020		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:18975517C>T	ENST00000432645.2	+	22	2880	c.2880C>T	c.(2878-2880)gcC>gcT	p.A960A	HDAC9_ENST00000401921.1_Silent_p.A919A|HDAC9_ENST00000441542.2_Silent_p.A963A|HDAC9_ENST00000406451.4_Silent_p.A960A	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	960	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	ATCTCACAGCCATCTGTGATG	0.433																																					p.A963A		.											.	HDAC9-227	0			c.C2889T						.						200	193	195					7																	18975517		1929	4145	6074	SO:0001819	synonymous_variant	9734	exon22			CACAGCCATCTGT	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2880C>T	7.37:g.18975517C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	203	48	NM_178425	0	0	0	0	0	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			.		0.433	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18975517	C	T	18975517	2	4	23	1	0	0	0	0	0	0	0	1	7035	581	21	2		2	HDAC9	7	18975517	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	3249650	18975517	140163146	37	2019											
C7orf46	340277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	23728992	23728992	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagggcttacctttatgtccCcttgaatggtagccagccca	8	11	9	13	0	0	1	0	1	0	0	1	1	1	1	5	2	3	2	5	2	4	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:23728992C>G	ENST00000344962.4	+	3	433	c.344C>G	c.(343-345)cCc>cGc	p.P115R	FAM221A_ENST00000409653.1_Missense_Mutation_p.P57R|FAM221A_ENST00000409192.3_Missense_Mutation_p.P115R|FAM221A_ENST00000409994.3_Missense_Mutation_p.P57R	NM_199136.3	NP_954587.2	A4D161	F221A_HUMAN	family with sequence similarity 221, member A	115																	CTTTATGTCCCCTTGAATGGT	0.493																																					p.P115R		.											.	.	0			c.C344G						.						86	78	81					7																	23728992		2203	4300	6503	SO:0001583	missense	340277	exon3			ATGTCCCCTTGAA		CCDS5385.1, CCDS47561.1, CCDS47562.1, CCDS75570.1	7p15.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000188732	ENSG00000188732			27977	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 46"	C7orf46		12477932	Standard	XR_242080		Approved	FLJ45875, MGC72075, DKFZp686F0810	uc003swo.4	A4D161	OTTHUMG00000128463	ENST00000344962.4:c.344C>G	7.37:g.23728992C>G	ENSP00000342576:p.Pro115Arg	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	124	34	NM_199136	0	0	2	2	0	Q05CG4|Q4G0Q7|Q6P519	Missense_Mutation	SNP	ENST00000344962.4	37	CCDS5385.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896270	0.72639	.	.	ENSG00000188732	ENST00000409192;ENST00000344962;ENST00000409653;ENST00000409994	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.58	5.58	0.84498	.	0.051181	0.85682	D	0.000000	T	0.57272	0.2042	M	0.90650	3.135	0.53005	D	0.999968	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.94;0.996;0.996	T	0.65841	-0.6070	10	0.87932	D	0	-12.9907	19.5733	0.95430	0.0:1.0:0.0:0.0	.	57;115;115	A4D161-3;A4D161-2;A4D161	.;.;CG046_HUMAN	R	115;115;57;57	ENSP00000386927:P115R;ENSP00000342576:P115R;ENSP00000386900:P57R;ENSP00000386631:P57R	ENSP00000342576:P115R	P	+	2	0	C7orf46	23695517	1.000000	0.71417	0.971000	0.41717	0.755000	0.42902	5.491000	0.66887	2.622000	0.88805	0.585000	0.79938	CCC	.		0.493	FAM221A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250261.1	NM_199136		G	23728992	C	G	23728992	3	3	23	1	0	0	0	0	1	0	0	0	2402	623	22	4	354	4	C7orf46	7	23728992	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	4753475	23728992	135409671	38	2020											
NEUROD6	63974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	31377935	31377935	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggctgcgcagatgtaagtcGtaagggaagtggctgtcggt	8	10	17	6	3	0	1	0	0	0	1	2	2	0	2	0	4	1	5	0	4	3	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:31377935G>A	ENST00000297142.3	-	2	1270	c.948C>T	c.(946-948)taC>taT	p.Y316Y		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	316					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.Y316Y(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GATGTAAGTCGTAAGGGAAGT	0.453																																					p.Y316Y		.											.	NEUROD6-92	1	Substitution - coding silent(1)	endometrium(1)	c.C948T						.						82	81	81					7																	31377935		2203	4300	6503	SO:0001819	synonymous_variant	63974	exon2			TAAGTCGTAAGGG	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.948C>T	7.37:g.31377935G>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	107	53	NM_022728	0	0	0	0	0	Q548T9|Q9H3H6	Silent	SNP	ENST00000297142.3	37	CCDS5434.1																																																																																			.		0.453	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		A	31377935	G	A	31377935	2	1	23	1	0	0	0	0	0	0	0	1	10377	1140	40	1		1	NEUROD6	7	31377935	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	7648943	31377935	127760728	39	2021											
SAMD9L	219285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92764048	92764048	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaatgtaccagtcatagtAtgaattatccagtgagtctc	14	12	8	7	0	2	3	1	2	1	1	4	3	3	3	2	0	1	2	2	0	7	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:92764048A>T	ENST00000318238.4	-	5	2453	c.1237T>A	c.(1237-1239)Tac>Aac	p.Y413N	SAMD9L_ENST00000411955.1_Missense_Mutation_p.Y413N|SAMD9L_ENST00000437805.1_Missense_Mutation_p.Y413N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	413					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGTCATAGTATGAATTATCC	0.358																																					p.Y413N		.											.	SAMD9L-94	0			c.T1237A						.						136	138	137					7																	92764048		2203	4299	6502	SO:0001583	missense	219285	exon5			CATAGTATGAATT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1237T>A	7.37:g.92764048A>T	ENSP00000326247:p.Tyr413Asn	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	25	7	NM_152703	0	0	7	10	3	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892471	0.52121	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.13538	2.58;2.58;2.58	4.74	4.74	0.60224	.	0.088161	0.46442	D	0.000299	T	0.31104	0.0786	L	0.51422	1.61	0.42354	D	0.992381	D	0.89917	1.0	D	0.77557	0.99	T	0.03514	-1.1029	10	0.72032	D	0.01	-9.3295	14.0508	0.64734	1.0:0.0:0.0:0.0	.	413	Q8IVG5	SAM9L_HUMAN	N	413	ENSP00000326247:Y413N;ENSP00000405760:Y413N;ENSP00000408796:Y413N	ENSP00000326247:Y413N	Y	-	1	0	SAMD9L	92601984	0.688000	0.27680	0.999000	0.59377	0.977000	0.68977	2.301000	0.43628	1.991000	0.58162	0.377000	0.23210	TAC	.		0.358	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		T	92764048	A	T	92764048	3	4	23	1	0	0	0	0	1	0	0	0	13859	449	16	5	3521	5	SAMD9L	7	92764048	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	61386113	92764048	66374615	40	2022											
CCDC132	55610	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	92953019	92953019	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttattacttgtatgcaatatAtaccttttttggtcggaatg	10	19	7	5	1	0	0	0	0	0	0	1	1	0	1	1	2	3	2	1	2	8	10			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:92953019A>T	ENST00000305866.5	+	21	2080	c.1952A>T	c.(1951-1953)tAt>tTt	p.Y651F	CCDC132_ENST00000535481.1_Missense_Mutation_p.Y371F|CCDC132_ENST00000544910.1_Missense_Mutation_p.Y621F|CCDC132_ENST00000541136.1_Missense_Mutation_p.Y462F	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	651						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TATGCAATATATACCTTTTTT	0.279																																					p.Y651F		.											.	CCDC132-90	0			c.A1952T						.						77	71	73					7																	92953019		1800	4052	5852	SO:0001583	missense	55610	exon21			CAATATATACCTT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1952A>T	7.37:g.92953019A>T	ENSP00000307666:p.Tyr651Phe	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_017667	0	0	6	8	2	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071795	0.76301	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481	.	.	.	4.68	4.68	0.58851	.	0.061363	0.64402	D	0.000002	T	0.53158	0.1779	N	0.12853	0.265	0.80722	D	1	D;D;D	0.64830	0.993;0.994;0.993	D;D;D	0.68192	0.956;0.915;0.956	T	0.57768	-0.7754	9	0.41790	T	0.15	-9.4515	14.0796	0.64912	1.0:0.0:0.0:0.0	.	371;621;651	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	F	651;621;462;371	.	ENSP00000307666:Y651F	Y	+	2	0	CCDC132	92790955	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.058000	0.93896	1.877000	0.54381	0.402000	0.26972	TAT	.		0.279	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		T	92953019	A	T	92953019	3	4	23	1	0	0	0	0	1	0	0	0	2773	449	16	5	2076	5	CCDC132	7	92953019	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	188971	92953019	66185644	41	2023											
MUC17	140453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100676808	100676808	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacactggtggccagttctgAggctagcaccctttcaacaa	10	9	9	13	0	2	1	1	1	1	0	2	1	2	1	2	3	2	3	2	3	3	3	rs71517134		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:100676808A>G	ENST00000306151.4	+	3	2175	c.2111A>G	c.(2110-2112)gAg>gGg	p.E704G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	704	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GCCAGTTCTGAGGCTAGCACC	0.502																																					p.E704G		.											.	MUC17-95	0			c.A2111G						.						340	344	343					7																	100676808		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2111A>G	7.37:g.100676808A>G	ENSP00000302716:p.Glu704Gly	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	234	54	NM_001040105	0	0	0	0	0	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.191	-0.635436	0.03584	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	1.07	-0.378	0.12497	.	.	.	.	.	T	0.01189	0.0039	N	0.11560	0.145	0.09310	N	1	P	0.47604	0.898	B	0.31686	0.134	T	0.51458	-0.8703	9	0.25751	T	0.34	.	5.6279	0.17492	0.4094:0.5906:0.0:0.0	.	704	Q685J3	MUC17_HUMAN	G	704	ENSP00000302716:E704G	ENSP00000302716:E704G	E	+	2	0	MUC17	100463528	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.400000	0.07241	-0.070000	0.12908	-0.949000	0.02662	GAG	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100676808	A	G	100676808	3	3	23	1	0	0	0	0	1	0	0	0	9999	304	11	3	2121	3	MUC17	7	100676808	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	7723789	100676808	58461855	42	2024											
TRPV5	56302	hgsc.bcm.edu;broad.mit.edu	37	chr7	142606703	142606703	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattcgcacccacagatcccGgagcgaggccacaggcagcg	11	3	12	15	4	0	1	0	0	0	1	2	3	1	2	3	3	2	2	3	3	1	1	rs368151896	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:142606703G>A	ENST00000265310.1	-	14	2196	c.1848C>T	c.(1846-1848)tcC>tcT	p.S616S		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	616					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					CACAGATCCCGGAGCGAGGCC	0.597													G|||	7	0.00139776	0	0	5008	,	,		20437	0		0	False		,,,				2504	0.0072				p.S616S		.											.	TRPV5-177	0			c.C1848T						.						79	70	73					7																	142606703		2203	4300	6503	SO:0001819	synonymous_variant	56302	exon14			GATCCCGGAGCGA	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1848C>T	7.37:g.142606703G>A		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	112	6	NM_019841	0	0	0	0	0	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	37	CCDS5875.1																																																																																			.		0.597	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142606703	G	A	142606703	2	1	23	1	0	0	0	0	0	0	0	1	16632	1103	39	1		1	TRPV5	7	142606703	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	41929895	142606703	16531960	43	2025											
DCAF13	25879	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	104432588	104432588	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actggaacgagtatttgcaaAaccattccttgcttcgctgg	10	12	9	10	2	0	0	0	0	0	0	2	2	1	1	2	2	4	4	2	2	4	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:104432588A>C	ENST00000297579.5	+	2	900	c.623A>C	c.(622-624)aAa>aCa	p.K208T	DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000519682.1_Missense_Mutation_p.K52T|DCAF13_ENST00000521716.1_Missense_Mutation_p.K52T|DCAF13_ENST00000521971.1_Missense_Mutation_p.K52T	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	56					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						GTATTTGCAAAACCATTCCTT	0.453																																					p.K208T													.	DCAF13-135	0			c.A623C						.						112	102	105					8																	104432588		2203	4300	6503	SO:0001583	missense	25879	exon2			TTGCAAAACCATT	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.623A>C	8.37:g.104432588A>C	ENSP00000297579:p.Lys208Thr	Somatic	178	2		WXS	Illumina HiSeq	Phase_I	146	56	NM_015420	0	0	9	25	16	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751423	0.89753	.	.	ENSG00000164934	ENST00000297579;ENST00000521716;ENST00000521971;ENST00000388778;ENST00000519682	T;T;T;T	0.01279	5.06;5.06;5.06;5.06	5.2	5.2	0.72013	.	0.091849	0.64402	D	0.000001	T	0.08802	0.0218	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00855	-1.1539	10	0.87932	D	0	-21.8419	15.0602	0.71947	1.0:0.0:0.0:0.0	.	56	B3KME9	.	T	208;52;52;56;52	ENSP00000297579:K208T;ENSP00000430645:K52T;ENSP00000430883:K52T;ENSP00000430411:K52T	ENSP00000297579:K208T	K	+	2	0	DCAF13	104501764	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.759000	0.91667	1.960000	0.56953	0.533000	0.62120	AAA	.		0.453	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		C	104432588	A	C	104432588	3	2	23	1	0	0	0	0	1	0	0	0	4272	14	1	5	629	5	DCAF13	8	104432588	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10		104432588	41931434	44	2026											
COL22A1	169044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	139707076	139707076	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acaagagactcaccggttccCcaggcaggcctggatcgccc	9	5	11	16	2	1	1	1	0	0	1	3	3	2	2	5	4	0	2	5	4	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:139707076C>T	ENST00000303045.6	-	33	3085	c.2639G>A	c.(2638-2640)gGg>gAg	p.G880E	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.G880E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	880	Collagen-like 7.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CACCGGTTCCCCAGGCAGGCC	0.602										HNSCC(7;0.00092)																											p.G880E		.											.	COL22A1-103	0			c.G2639A						.						104	98	100					8																	139707076		2203	4300	6503	SO:0001583	missense	169044	exon33			GGTTCCCCAGGCA	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2639G>A	8.37:g.139707076C>T	ENSP00000303153:p.Gly880Glu	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	90	38	NM_152888	0	0	0	0	0	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	9.130	1.011213	0.19277	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99353	-5.77;-5.77	4.06	3.19	0.36642	.	0.000000	0.48286	U	0.000190	D	0.99489	0.9818	H	0.96518	3.835	0.43412	D	0.995558	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99078	1.0836	10	0.87932	D	0	.	7.6856	0.28538	0.0:0.883:0.0:0.117	.	880;880	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	880;880;593	ENSP00000303153:G880E;ENSP00000387655:G880E	ENSP00000303153:G880E	G	-	2	0	COL22A1	139776258	0.931000	0.31567	0.745000	0.31077	0.080000	0.17528	3.173000	0.50839	1.056000	0.40484	0.551000	0.68910	GGG	.		0.602	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139707076	C	T	139707076	3	4	23	1	0	0	0	0	1	0	0	0	3687	623	22	2	2373	2	COL22A1	8	139707076	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	35274488	139707076	6656946	45	2027											
TOP1MT	116447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144397926	144397926	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccatccccttgggctttGtgctcagccctcgccctcct	2	13	8	18	1	1	0	1	0	0	0	4	0	3	0	6	1	3	2	6	1	0	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:144397926G>C	ENST00000329245.4	-	12	1558	c.1524C>G	c.(1522-1524)caC>caG	p.H508Q	TOP1MT_ENST00000521193.1_Missense_Mutation_p.H410Q|TOP1MT_ENST00000523676.1_Missense_Mutation_p.H410Q|AC087793.1_ENST00000585120.1_RNA|TOP1MT_ENST00000519148.1_Missense_Mutation_p.H410Q	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	508					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	CTTGGGCTTTGTGCTCAGCCC	0.662																																					p.H508Q		.											.	TOP1MT-91	0			c.C1524G						.						131	84	100					8																	144397926		2203	4300	6503	SO:0001583	missense	116447	exon12			GGCTTTGTGCTCA	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1524C>G	8.37:g.144397926G>C	ENSP00000328835:p.His508Gln	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	75	35	NM_052963	0	0	10	21	11	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	37	CCDS6400.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.192|1.192	-0.634970|-0.634970	0.03584|0.03584	.|.	.|.	ENSG00000184428|ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676|ENST00000519977	T;T;T;T|.	0.42131|.	0.98;0.98;0.98;0.98|.	3.56|3.56	-0.755|-0.755	0.11061|0.11061	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (1);DNA topoisomerases I, dispensable insert, eukaryotic-type (1);|.	1.222760|.	0.06298|.	U|.	0.700351|.	T|T	0.41119|0.41119	0.1145|0.1145	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	P;B|.	0.43826|.	0.818;0.437|.	B;B|.	0.43194|.	0.411;0.131|.	T|T	0.38308|0.38308	-0.9667|-0.9667	10|5	0.18276|.	T|.	0.48|.	.|.	4.746|4.746	0.13038|0.13038	0.4744:0.1621:0.3634:0.0|0.4744:0.1621:0.3634:0.0	.|.	303;508|.	E7ESI1;Q969P6|.	.;TOP1M_HUMAN|.	Q|E	508;410;410;410|18	ENSP00000328835:H508Q;ENSP00000428369:H410Q;ENSP00000429169:H410Q;ENSP00000429181:H410Q|.	ENSP00000328835:H508Q|.	H|Q	-|-	3|1	2|0	TOP1MT|TOP1MT	144469301|144469301	0.018000|0.018000	0.18449|0.18449	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.132000|0.132000	0.15891|0.15891	-0.145000|-0.145000	0.11294|0.11294	-0.351000|-0.351000	0.07748|0.07748	CAC|CAA	.		0.662	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		C	144397926	G	C	144397926	3	2	23	1	0	0	0	0	1	0	0	0	16397	1368	48	4	293	4	TOP1MT	8	144397926	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	4690850	144397926	1966096	46	2028											
KCNT1	57582	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	138649177	138649177	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctgcggaacctgttcatcCccgtctttctgaactgctgg	5	12	10	14	3	3	1	1	1	2	0	4	2	4	2	3	2	4	3	3	2	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr9:138649177C>G	ENST00000263604.3	+	9	652	c.652C>G	c.(652-654)Ccc>Gcc	p.P218A	KCNT1_ENST00000298480.5_Missense_Mutation_p.P237A|KCNT1_ENST00000371757.2_Missense_Mutation_p.P237A|KCNT1_ENST00000488444.2_Missense_Mutation_p.P218A|KCNT1_ENST00000486577.2_Missense_Mutation_p.P198A|KCNT1_ENST00000490355.2_Missense_Mutation_p.P218A|KCNT1_ENST00000491806.2_Missense_Mutation_p.P204A|KCNT1_ENST00000487664.1_Missense_Mutation_p.P189A			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	218					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CCTGTTCATCCCCGTCTTTCT	0.667																																					p.P237A		.											.	KCNT1-137	0			c.C709G						.						51	58	55					9																	138649177		2203	4300	6503	SO:0001583	missense	57582	exon9			TTCATCCCCGTCT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.652C>G	9.37:g.138649177C>G	ENSP00000263604:p.Pro218Ala	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	55	18	NM_020822	0	0	0	0	0	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	37		.	.	.	.	.	.	.	.	.	.	.	23.4	4.416656	0.83449	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;D;T	0.97186	1.86;1.86;1.86;-4.28;1.86	4.63	4.63	0.57726	.	0.000000	0.85682	U	0.000000	D	0.98337	0.9448	M	0.79926	2.475	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.91635	0.999;0.989;0.992	D	0.99577	1.0972	10	0.72032	D	0.01	-28.7902	16.4704	0.84109	0.0:1.0:0.0:0.0	.	204;237;189	C9JYL2;B9EGP2;G5E9V0	.;.;.	A	189;237;237;184;198;204;218;218;218	ENSP00000417851:P189A;ENSP00000298480:P237A;ENSP00000360822:P237A;ENSP00000420764:P184A;ENSP00000263604:P218A	ENSP00000263604:P218A	P	+	1	0	KCNT1	137788998	1.000000	0.71417	0.995000	0.50966	0.866000	0.49608	7.427000	0.80284	2.124000	0.65301	0.460000	0.39030	CCC	.		0.667	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		G	138649177	C	G	138649177	3	3	23	1	0	0	0	0	1	0	0	0	8112	623	22	4	743	4	KCNT1	9	138649177	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		138649177	2564254	47	2029											
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999193	46999193	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtccaccatgggcggcagtGacctgtgtcgcctgcgggcc	4	8	15	14	3	0	1	0	1	0	0	2	1	1	1	5	3	1	1	5	3	0	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:46999193G>A	ENST00000374317.1	+	3	586	c.313G>A	c.(313-315)Gac>Aac	p.D105N	GPRIN2_ENST00000374314.4_Missense_Mutation_p.D105N	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	105										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GGGCGGCAGTGACCTGTGTCG	0.652																																					p.D105N		.											.	GPRIN2-90	0			c.G313A						.						30	29	29					10																	46999193		2196	4288	6484	SO:0001583	missense	9721	exon3			GGCAGTGACCTGT	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"KIAA0514"	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.313G>A	10.37:g.46999193G>A	ENSP00000363436:p.Asp105Asn	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	23	8	NM_014696	0	0	0	0	0	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.467432	0.63625	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03982	3.74;3.74	5.11	5.11	0.69529	.	0.279617	0.25830	N	0.028026	T	0.11495	0.0280	L	0.54323	1.7	0.09310	N	1	D	0.56746	0.977	P	0.52957	0.714	T	0.04678	-1.0934	10	0.45353	T	0.12	-14.3008	14.245	0.65983	0.0:0.0:1.0:0.0	.	105	O60269	GRIN2_HUMAN	N	105	ENSP00000363436:D105N;ENSP00000363433:D105N	ENSP00000363433:D105N	D	+	1	0	GPRIN2	46419199	0.655000	0.27376	0.709000	0.30452	0.969000	0.65631	3.163000	0.50763	2.833000	0.97629	0.650000	0.86243	GAC	.		0.652	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		A	46999193	G	A	46999193	3	1	23	1	0	0	0	0	1	0	0	0	6751	1290	45	2	315	2	GPRIN2	10	46999193	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		46999193	88535554	48	2030											
JMJD1C	221037	broad.mit.edu	37	chr10	64973409	64973409	+	Frame_Shift_Del	DEL	G	G	-																															tccaagaagatgaggtgactGgtgctgtaacaactgttgtt																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:64973409delG	ENST00000399262.2	-	8	2736	c.2518delC	c.(2518-2520)cagfs	p.Q840fs	JMJD1C_ENST00000399251.1_Frame_Shift_Del_p.Q621fs|JMJD1C_ENST00000542921.1_Frame_Shift_Del_p.Q658fs|JMJD1C_ENST00000489372.2_5'Flank|JMJD1C_ENST00000402544.1_Frame_Shift_Del_p.Q621fs	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	840					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TGAGGTGACTGGTGCTGTAAC	0.473																																					p.Q840fs													.	JMJD1C-275	0			c.2518delC						.						92	92	92					10																	64973409		2111	4238	6349	SO:0001589	frameshift_variant	221037	exon8			GTGACTGGTGCTG	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.2518delC	10.37:g.64973409delG	ENSP00000382204:p.Gln840fs	Somatic	292	0		WXS	Illumina HiSeq	Phase_I	321	7	NM_032776	0	0	0	0	0	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Frame_Shift_Del	DEL	ENST00000399262.2	37	CCDS41532.1																																																																																			.		0.473	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		-	64973409	G	-	64973409	7	5	23	1	0	1	0	1	0	0	0	0	7971	1357	47	0	5180	0	JMJD1C	10	64973409	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	17974216	64973409	70561338	49	2031											
PNLIPRP1	5407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	118357347	118357347	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctcttttagggttggaTcctgtagaagcaagtttcga	9	15	10	7	1	2	1	1	0	1	1	5	3	3	2	1	2	1	4	1	2	4	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:118357347T>C	ENST00000528052.1	+	7	653	c.582T>C	c.(580-582)gaT>gaC	p.D194D	PNLIPRP1_ENST00000358834.4_Silent_p.D194D|PNLIPRP1_ENST00000534537.1_Silent_p.D194D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	194					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		TAGGGTTGGATCCTGTAGAAG	0.507																																					p.D194D		.											.	PNLIPRP1-154	0			c.T582C						.						149	129	136					10																	118357347		2203	4300	6503	SO:0001819	synonymous_variant	5407	exon7			GTTGGATCCTGTA	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.582T>C	10.37:g.118357347T>C		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	149	57	NM_006229	0	0	0	0	0	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Silent	SNP	ENST00000528052.1	37	CCDS7595.1																																																																																			.		0.507	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		C	118357347	T	C	118357347	2	2	23	1	0	0	0	0	0	0	0	1	12176	1432	50	3		3	PNLIPRP1	10	118357347	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	53383938	118357347	17177400	50	2032											
MUC2	4583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1094686	1094686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccccactcgcggtaccaCgaccgggtcatcttcagccc	7	6	8	20	4	3	0	2	0	1	0	4	1	3	0	5	2	2	1	5	2	1	2	rs375767205		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:1094686C>T	ENST00000441003.2	+	31	5801	c.5774C>T	c.(5773-5775)aCg>aTg	p.T1925M	MUC2_ENST00000333592.6_Missense_Mutation_p.T213M|MUC2_ENST00000361558.6_Missense_Mutation_p.T63M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4287					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CGCGGTACCACGACCGGGTCA	0.637													C|||	1	0.000199681	0	0	5008	,	,		16685	0		0	False		,,,				2504	0.001				p.T1921M		.											.	MUC2-90	0			c.C5762T						.		MET/THR	3,4229		0,3,2113	70	87	82		5759	-0.2	0	11		82	1,8447		0,1,4223	no	missense	MUC2	NM_002457.2	81	0,4,6336	TT,TC,CC		0.0118,0.0709,0.0315	benign	1920/2813	1094686	4,12676	2116	4224	6340	SO:0001583	missense	4583	exon32			GTACCACGACCGG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5774C>T	11.37:g.1094686C>T	ENSP00000415183:p.Thr1925Met	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	165	64	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	7.600	0.672559	0.14776	7.09E-4	1.18E-4	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.51071	2.55;0.72;3.15	2.06	-0.251	0.13003	.	.	.	.	.	T	0.40094	0.1103	M	0.65975	2.015	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.40869	-0.9540	9	0.62326	D	0.03	.	3.434	0.07438	0.2454:0.5996:0.0:0.155	.	1925	E7EUV1	.	M	1925;63;213	ENSP00000415183:T1925M;ENSP00000354885:T63M;ENSP00000331373:T213M	ENSP00000331373:T213M	T	+	2	0	MUC2	1084686	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.419000	0.21247	-0.196000	0.10366	-0.354000	0.07668	ACG	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1094686	C	T	1094686	3	4	23	1	0	0	0	0	1	0	0	0	10000	536	19	1	5888	1	MUC2	11	1094686	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		1094686	133911830	51	2033											
MUC5B	727897	broad.mit.edu	37	chr11	1271547	1271547	+	Frame_Shift_Del	DEL	A	A	-																															caggcaactgctggcaccccAcatgtgagcaccacggccac																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:1271547delA	ENST00000529681.1	+	31	13495	c.13437delA	c.(13435-13437)ccafs	p.P4479fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Del_p.P4482fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4479	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CTGGCACCCCACATGTGAGCA	0.647																																					p.P4479fs													.	.	0			c.13437delA						.						57	78	71					11																	1271547		2110	4218	6328	SO:0001589	frameshift_variant	727897	exon31			CACCCCACATGTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13437delA	11.37:g.1271547delA	ENSP00000436812:p.Pro4479fs	Somatic	391	0		WXS	Illumina HiSeq	Phase_I	804	7	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	37	CCDS44515.2																																																																																			.		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1271547	A	-	1271547	7	5	23	1	0	1	0	1	0	0	0	0	10004	146	6	0	13568	0	MUC5B	11	1271547	Frame_Shift_Del	DEL	A	TCGA-A4-A57E-01A-11D-A26P-10	176861	1271547	133734969	52	2034											
MRGPRX3	117195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	18159591	18159591	+	Frame_Shift_Del	DEL	G	G	-																															cgtgggctcctttaggcagcGtcaaaataggcagaacctga																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:18159591delG	ENST00000396275.2	+	3	1203	c.842delG	c.(841-843)cgtfs	p.R281fs		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	281				R -> L (in Ref. 2; AAL86879). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTTAGGCAGCGTCAAAATAGG	0.517																																					p.R281fs		.											.	MRGPRX3-92	0			c.842delG						.						56	60	58					11																	18159591		2200	4290	6490	SO:0001589	frameshift_variant	117195	exon3			.		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.842delG	11.37:g.18159591delG	ENSP00000379571:p.Arg281fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	65	26	NM_054031	0	0	0	0	0	B0M0L1|Q8TDE0|Q8TDE1	Frame_Shift_Del	DEL	ENST00000396275.2	37	CCDS7830.1																																																																																			.		0.517	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		-	18159591	G	-	18159591	7	5	23	1	0	1	0	1	0	0	0	0	9793	1145	40	0	844	0	MRGPRX3	11	18159591	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	16888044	18159591	116846925	53	2035											
OR4C3	256144	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	48347236	48347236	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctacattgtcatcctgtaCtccttgaggtcccacagtgc	7	13	7	14	0	1	1	1	1	0	0	5	1	5	1	4	1	3	1	4	1	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:48347236C>T	ENST00000319856.4	+	1	765	c.744C>T	c.(742-744)taC>taT	p.Y248Y		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						TCATCCTGTACTCCTTGAGGT	0.493																																					p.Y248Y		.											.	OR4C3-69	0			c.C744T						.						268	192	218					11																	48347236		2201	4298	6499	SO:0001819	synonymous_variant	256144	exon1			CCTGTACTCCTTG	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"GPCR / Class A : Olfactory receptors"	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.744C>T	11.37:g.48347236C>T		Somatic	267	0		WXS	Illumina HiSeq	Phase_I	280	46	NM_001004702	0	0	0	0	0	B2RNF2|Q6IFB3	Silent	SNP	ENST00000319856.4	37	CCDS31489.1																																																																																			.		0.493	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		T	48347236	C	T	48347236	2	4	23	1	0	0	0	0	0	0	0	1	11076	576	20	2		2	OR4C3	11	48347236	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	30187645	48347236	86659280	54	2036											
RPS6KA4	8986	hgsc.bcm.edu	37	chr11	64136019	64136019	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcttttctgtgtgtcgccGctgccgccagcgccagagcg	4	9	13	15	5	1	1	0	0	1	1	2	1	1	1	4	0	4	2	4	0	0	2	rs199674030		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:64136019G>A	ENST00000334205.4	+	11	1345	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	RPS6KA4_ENST00000528057.1_Missense_Mutation_p.R420H|MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000294261.4_Intron	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	427	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GTGTGTCGCCGCTGCCGCCAG	0.701													G|||	1	0.000199681	0	0	5008	,	,		9970	0		0.001	False		,,,				2504	0				p.R427H		.											.	RPS6KA4-1036	0			c.G1280A						.	G	HIS/ARG,HIS/ARG	1,4357		0,1,2178	9	11	11		1262,1280	4.5	1	11		11	12,8514		0,12,4251	yes	missense,missense	RPS6KA4	NM_001006944.1,NM_003942.2	29,29	0,13,6429	AA,AG,GG		0.1407,0.0229,0.1009	probably-damaging,probably-damaging	421/767,427/773	64136019	13,12871	2179	4263	6442	SO:0001583	missense	8986	exon11			GTCGCCGCTGCCG	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"ribosomal protein S6 kinase, 90kD, polypeptide 4"			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.1280G>A	11.37:g.64136019G>A	ENSP00000333896:p.Arg427His	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	13	10	NM_003942	0	0	15	20	5	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	37	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	g	17.24	3.339473	0.60963	2.29E-4	0.001407	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000530504	T;T;T	0.42513	0.97;0.97;0.97	4.5	4.5	0.54988	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.221656	0.37530	N	0.002053	T	0.47451	0.1446	L	0.33339	1.005	0.09310	N	0.999995	D;D;D	0.69078	0.963;0.997;0.984	P;D;P	0.65323	0.616;0.934;0.843	T	0.32214	-0.9915	10	0.72032	D	0.01	.	8.538	0.33375	0.108:0.0:0.892:0.0	.	420;427;421	E9PJN1;O75676;O75676-2	.;KS6A4_HUMAN;.	H	420;427;405	ENSP00000435580:R420H;ENSP00000333896:R427H;ENSP00000432945:R405H	ENSP00000333896:R427H	R	+	2	0	RPS6KA4	63892595	0.333000	0.24731	0.997000	0.53966	0.668000	0.39293	2.159000	0.42339	2.059000	0.61396	0.462000	0.41574	CGC	.		0.701	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942		A	64136019	G	A	64136019	3	1	23	1	0	0	0	0	1	0	0	0	13685	1087	38	1	1322	1	RPS6KA4	11	64136019	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	15788783	64136019	70870497	55	2037											
ALDH3B1	221	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67789010	67789010	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccaagcacctgacacctGtcaccctggagctggggggc	7	5	13	16	1	1	1	1	1	0	0	1	2	1	2	5	4	2	2	5	4	1	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:67789010G>T	ENST00000539229.1	+	8	732	c.616G>T	c.(616-618)Gtc>Ttc	p.V206F	ALDH3B1_ENST00000316367.6_Intron|ALDH3B1_ENST00000434449.1_3'UTR|ALDH3B1_ENST00000342456.6_Missense_Mutation_p.V170F|ALDH3B1_ENST00000007633.8_Missense_Mutation_p.V206F	NM_001161473.1	NP_001154945.1	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1	207					alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										CCTGACACCTGTCACCCTGGA	0.622											OREG0021141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	0			.						.						107	114	111					11																	67789010		2200	4294	6494	SO:0001583	missense	221	.			ACACCTGTCACCC	U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"Aldehyde dehydrogenases"	410	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 7", "aldehyde dehydrogenase 3B1"	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000539229.1:c.616G>T	11.37:g.67789010G>T	ENSP00000474034:p.Val206Phe	Somatic	86	0	1102	WXS	Illumina HiSeq	Phase_I	158	9	.	0	0	25	27	2	A3FMP9|Q53XL5|Q8N515|Q96CK8	Missense_Mutation	SNP	ENST00000539229.1	37																																																																																				.		0.622	ALDH3B1-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000694		T	67789010	G	T	67789010	3	4	23	1	0	0	0	0	1	0	0	0	499	1377	48	4	640	4	ALDH3B1	11	67789010	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	3652991	67789010	67217506	56	2038											
FGF19	9965	broad.mit.edu	37	chr11	69514314	69514314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atctgggcggatctcctcctCgaaagcacagtcttcctccg	7	10	9	15	3	3	0	0	0	3	0	8	2	6	1	4	2	1	1	4	2	1	1	rs377419016		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:69514314C>T	ENST00000294312.3	-	3	1132	c.367G>A	c.(367-369)Gag>Aag	p.E123K		NM_005117.2	NP_005108.1	O95750	FGF19_HUMAN	fibroblast growth factor 19	123					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bile acid biosynthetic process (GO:0070858)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of JNK cascade (GO:0046330)	extracellular region (GO:0005576)	fibroblast growth factor receptor binding (GO:0005104)			large_intestine(2)|lung(2)|skin(2)	6	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			ATCTCCTCCTCGAAAGCACAG	0.562																																					p.E123K													.	FGF19-658	0			c.G367A						.	C	LYS/GLU	0,4400		0,0,2200	51	47	48		367	2.8	1	11		48	1,8587	1.2+/-3.3	0,1,4293	no	missense	FGF19	NM_005117.2	56	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	123/217	69514314	1,12987	2200	4294	6494	SO:0001583	missense	9965	exon3			CCTCCTCGAAAGC	AB018122	CCDS8193.1	11q13.1	2008-02-01			ENSG00000162344	ENSG00000162344			3675	protein-coding gene	gene with protein product		603891				9931477, 10525310	Standard	NM_005117		Approved		uc001opf.3	O95750	OTTHUMG00000167886	ENST00000294312.3:c.367G>A	11.37:g.69514314C>T	ENSP00000294312:p.Glu123Lys	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	110	5	NM_005117	0	0	0	0	0		Missense_Mutation	SNP	ENST00000294312.3	37	CCDS8193.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.258639	0.23051	0.0	1.16E-4	ENSG00000162344	ENST00000294312	T	0.80304	-1.36	4.9	2.82	0.32997	.	0.379197	0.28659	N	0.014570	T	0.49423	0.1556	N	0.11341	0.13	0.34812	D	0.737793	P	0.40376	0.715	B	0.25759	0.063	T	0.61955	-0.6956	10	0.02654	T	1	-19.2795	7.4934	0.27475	0.0:0.7302:0.166:0.1038	.	123	O95750	FGF19_HUMAN	K	123	ENSP00000294312:E123K	ENSP00000294312:E123K	E	-	1	0	FGF19	69223495	0.833000	0.29383	0.979000	0.43373	0.961000	0.63080	1.017000	0.29989	0.323000	0.23307	0.555000	0.69702	GAG	.		0.562	FGF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396833.1	NM_005117		T	69514314	C	T	69514314	3	4	23	1	0	0	0	0	1	0	0	0	5866	893	31	1	287	1	FGF19	11	69514314	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	1725304	69514314	65492202	57	2039											
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	108384826	108384826	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaatctcctctgttctcCgcttcgtccaaaggtattgc	7	14	6	14	2	3	0	0	0	3	0	8	0	5	0	4	1	1	3	4	1	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:108384826C>T	ENST00000265843.4	-	6	1518	c.1408G>A	c.(1408-1410)Gga>Aga	p.G470R	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.G394R|EXPH5_ENST00000443411.1_Missense_Mutation_p.G282R|EXPH5_ENST00000525344.1_Missense_Mutation_p.G463R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	470					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTCTGTTCTCCGCTTCGTCCA	0.433																																					p.G470R		.											.	EXPH5-95	0			c.G1408A						.						130	127	128					11																	108384826		2201	4298	6499	SO:0001583	missense	23086	exon6			GTTCTCCGCTTCG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1408G>A	11.37:g.108384826C>T	ENSP00000265843:p.Gly470Arg	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	109	27	NM_015065	0	0	0	0	0	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	1.713	-0.498555	0.04291	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03152	4.59;4.53;4.37;4.59;4.47;4.03	5.8	4.61	0.57282	.	0.279252	0.31461	N	0.007616	T	0.00815	0.0027	N	0.00104	-2.125	0.19945	N	0.999949	B	0.06786	0.001	B	0.06405	0.002	T	0.43877	-0.9364	10	0.02654	T	1	-6.2184	9.3795	0.38304	0.0:0.0824:0.0:0.9176	.	470	Q8NEV8	EXPH5_HUMAN	R	470;394;282;463;314;394;282	ENSP00000265843:G470R;ENSP00000391966:G394R;ENSP00000411390:G282R;ENSP00000432546:G463R;ENSP00000432683:G394R;ENSP00000446434:G282R	ENSP00000265843:G470R	G	-	1	0	EXPH5	107890036	0.012000	0.17670	0.950000	0.38849	0.930000	0.56654	0.504000	0.22626	1.011000	0.39340	-0.423000	0.05987	GGA	.		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108384826	C	T	108384826	3	4	23	1	0	0	0	0	1	0	0	0	5335	661	23	1	4565	1	EXPH5	11	108384826	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	38870512	108384826	26621690	58	2040											
ABCG4	64137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119027153	119027153	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtgccaagctctttgagatGtttgacaaggtgagtgtctc	9	13	12	7	0	2	3	0	3	2	1	3	4	2	3	1	1	2	2	1	1	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:119027153G>T	ENST00000449422.2	+	7	989	c.801G>T	c.(799-801)atG>atT	p.M267I	ABCG4_ENST00000531739.1_Missense_Mutation_p.M267I|ABCG4_ENST00000307417.3_Missense_Mutation_p.M267I	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	267	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		TCTTTGAGATGTTTGACAAGG	0.577																																					p.M267I		.											.	ABCG4-92	0			c.G801T						.						141	137	138					11																	119027153		2200	4295	6495	SO:0001583	missense	64137	exon7			TGAGATGTTTGAC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.801G>T	11.37:g.119027153G>T	ENSP00000406874:p.Met267Ile	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	231	131	NM_022169	0	0	0	0	0	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255972	0.59321	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.34667	1.35;1.35;1.35	4.82	4.82	0.62117	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.037537	0.85682	D	0.000000	T	0.25382	0.0617	N	0.19112	0.55	0.80722	D	1	B	0.32245	0.361	B	0.25140	0.058	T	0.05971	-1.0853	10	0.38643	T	0.18	-32.7477	18.0972	0.89494	0.0:0.0:1.0:0.0	.	267	Q9H172	ABCG4_HUMAN	I	267	ENSP00000304111:M267I;ENSP00000406874:M267I;ENSP00000434318:M267I	ENSP00000304111:M267I	M	+	3	0	ABCG4	118532363	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.808000	0.86044	2.502000	0.84385	0.655000	0.94253	ATG	.		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119027153	G	T	119027153	3	4	23	1	0	0	0	0	1	0	0	0	70	1377	48	4	823	4	ABCG4	11	119027153	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	10642327	119027153	15979363	59	2041											
GAPDH	2597	ucsc.edu	37	chr12	6645958	6645958	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcaccatcttccaggagTgagtggaagacagaatggaa	14	7	11	9	0	2	3	1	1	1	2	3	6	3	6	3	3	0	0	3	3	3	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:6645958T>C	ENST00000229239.5	+	4	902		c.e4+2		GAPDH_ENST00000396856.1_5'UTR|GAPDH_ENST00000396858.1_Splice_Site|RP5-940J5.9_ENST00000602946.1_RNA|GAPDH_ENST00000396859.1_Splice_Site|GAPDH_ENST00000396861.1_Splice_Site	NM_002046.4	NP_002037.2	P04406	G3P_HUMAN	glyceraldehyde-3-phosphate dehydrogenase						carbohydrate metabolic process (GO:0005975)|cellular response to interferon-gamma (GO:0071346)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of translation (GO:0017148)|neuron apoptotic process (GO:0051402)|peptidyl-cysteine S-trans-nitrosylation (GO:0035606)|protein stabilization (GO:0050821)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GAIT complex (GO:0097452)|lipid particle (GO:0005811)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|identical protein binding (GO:0042802)|microtubule binding (GO:0008017)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|peptidyl-cysteine S-nitrosylase activity (GO:0035605)			central_nervous_system(1)|cervix(1)|endometrium(1)|lung(4)	7						CTTCCAGGAGTGAGTGGAAGA	0.488																																					.													.	GAPDH-226	0			c.236+2T>C						.						102	99	100					12																	6645958		2203	4300	6503	SO:0001630	splice_region_variant	2597	exon4			CAGGAGTGAGTGG	AF261085	CCDS8549.1, CCDS58201.1	12p13.31	2012-10-02		2005-05-06	ENSG00000111640	ENSG00000111640	1.2.1.12		4141	protein-coding gene	gene with protein product		138400		GAPD		3170585	Standard	NM_002046		Approved		uc001qop.2	P04406	OTTHUMG00000137379	ENST00000229239.5:c.236+2T>C	12.37:g.6645958T>C		Somatic	190	1		WXS	Illumina HiSeq		182	1	NM_002046	0	0	14	14	0	E7EUT4|P00354|Q53X65	Splice_Site	SNP	ENST00000229239.5	37	CCDS8549.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.530649	0.85706	.	.	ENSG00000111640	ENST00000229239;ENST00000450282;ENST00000396861;ENST00000396859;ENST00000396858	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8869	0.70575	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAPDH	6516219	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	5.011000	0.64011	1.924000	0.55735	0.459000	0.35465	.	.		0.488	GAPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268059.1	NM_002046	Intron	C	6645958	T	C	6645958	5	2	23	1	0	0	0	0	0	0	1	0	6256	1710	59	3	248	3	GAPDH	12	6645958	Splice_Site	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10		6645958	127205937	60	2042											
PIK3C2G	5288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	18435382	18435382	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacctcaaaatacgaataaaGaatgctcctggggaagcccc	16	6	8	11	1	1	1	1	0	0	1	2	3	2	2	4	2	4	1	4	2	9	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:18435382G>A	ENST00000266497.5	+	1	405	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.E123K|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.E123K|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.E123K|RERGL_ENST00000541632.1_Intron			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	123					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TACGAATAAAGAATGCTCCTG	0.398																																					p.E123K		.											.	PIK3C2G-1312	0			c.G367A						.						69	69	69					12																	18435382		1829	4080	5909	SO:0001583	missense	5288	exon2			AATAAAGAATGCT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.367G>A	12.37:g.18435382G>A	ENSP00000266497:p.Glu123Lys	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	44	6	NM_004570	0	0	0	0	0	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.480900	0.44044	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.62788	1.35;-0.0;-0.0;-0.0	4.79	2.91	0.33838	.	.	.	.	.	T	0.44138	0.1279	N	0.24115	0.695	0.09310	N	1	B;B	0.31548	0.328;0.22	B;B	0.28011	0.085;0.039	T	0.15809	-1.0424	9	0.15952	T	0.53	-4.9931	11.4633	0.50223	0.0:0.3511:0.6488:0.0	.	123;123	F5H369;O75747	.;P3C2G_HUMAN	K	123	ENSP00000443850:E123K;ENSP00000404845:E123K;ENSP00000266497:E123K;ENSP00000445381:E123K	ENSP00000266497:E123K	E	+	1	0	PIK3C2G	18326649	0.022000	0.18835	0.006000	0.13384	0.083000	0.17756	0.866000	0.27954	0.897000	0.36392	0.655000	0.94253	GAA	.		0.398	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18435382	G	A	18435382	3	1	23	1	0	0	0	0	1	0	0	0	11937	943	33	2	369	2	PIK3C2G	12	18435382	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	11789424	18435382	115416513	61	2043											
PKP2	5318	hgsc.bcm.edu;broad.mit.edu	37	chr12	33031889	33031889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttttaggaacaggggaacGgcctccaacaaaatcatttt	13	10	10	8	1	1	0	1	0	0	0	2	2	2	2	2	5	3	1	2	5	6	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:33031889G>A	ENST00000070846.6	-	2	325	c.301C>T	c.(301-303)Cgt>Tgt	p.R101C	PKP2_ENST00000340811.4_Missense_Mutation_p.R101C	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	101					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					ACAGGGGAACGGCCTCCAACA	0.378																																					p.R101C		.											.	PKP2-92	0			c.C301T						.						96	91	93					12																	33031889		2203	4300	6503	SO:0001583	missense	5318	exon2			GGGAACGGCCTCC	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.301C>T	12.37:g.33031889G>A	ENSP00000070846:p.Arg101Cys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	72	4	NM_004572	0	0	0	0	0	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126134	0.56721	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81163	-1.46;-1.42	5.7	3.72	0.42706	.	1.351310	0.04721	N	0.419289	T	0.76076	0.3937	L	0.47716	1.5	0.09310	N	1	B;B;B	0.21381	0.055;0.033;0.033	B;B;B	0.10450	0.005;0.002;0.003	T	0.60835	-0.7184	10	0.52906	T	0.07	-0.1096	8.3857	0.32499	0.0822:0.0:0.7645:0.1533	.	101;101;101	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	C	101	ENSP00000342800:R101C;ENSP00000070846:R101C	ENSP00000070846:R101C	R	-	1	0	PKP2	32923156	0.000000	0.05858	0.010000	0.14722	0.864000	0.49448	0.261000	0.18442	2.679000	0.91253	0.650000	0.86243	CGT	.		0.378	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		A	33031889	G	A	33031889	3	1	23	1	0	0	0	0	1	0	0	0	12011	1116	39	1	2396	1	PKP2	12	33031889	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	14596507	33031889	100820006	62	2044											
KRT86	3892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52700004	52700004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggaggtgatgaactccaAgctgggcctggacatcgaga	11	6	14	10	1	0	3	0	2	0	1	2	6	1	5	3	4	2	1	3	4	2	0	rs542735645		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:52700004A>G	ENST00000423955.2	+	9	1365	c.1187A>G	c.(1186-1188)aAg>aGg	p.K396R	KRT86_ENST00000544024.1_Missense_Mutation_p.K396R|KRT86_ENST00000293525.5_Missense_Mutation_p.K396R|RP11-845M18.6_ENST00000552441.1_RNA			O43790	KRT86_HUMAN	keratin 86	396	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATGAACTCCAAGCTGGGCCTG	0.637											OREG0021845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1	0.000199681	0	0.0014	5008	,	,		18796	0		0	False		,,,				2504	0				p.K396R		.											.	KRT86-91	0			c.A1187G						.						78	77	77					12																	52700004		2203	4295	6498	SO:0001583	missense	3892	exon7			ACTCCAAGCTGGG	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"-", "Intermediate filaments type II, keratins (basic)"	6463	protein-coding gene	gene with protein product	"hard keratin type II 6"	601928	"keratin, hair, basic, 6 (monilethrix)"	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.1187A>G	12.37:g.52700004A>G	ENSP00000444533:p.Lys396Arg	Somatic	97	0	987	WXS	Illumina HiSeq	Phase_I	170	52	NM_002284	0	0	0	0	0	P78387	Missense_Mutation	SNP	ENST00000423955.2	37	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.954205	0.92726	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	D;D;D	0.94376	-3.41;-3.41;-3.41	5.35	5.35	0.76521	Filament (1);	0.000000	0.43747	U	0.000525	D	0.97179	0.9078	M	0.91300	3.195	0.43399	D	0.99552	D	0.89917	1.0	D	0.80764	0.994	D	0.98008	1.0364	10	0.87932	D	0	.	13.9101	0.63862	1.0:0.0:0.0:0.0	.	396	O43790	KRT86_HUMAN	R	396	ENSP00000443169:K396R;ENSP00000444533:K396R;ENSP00000293525:K396R	ENSP00000293525:K396R	K	+	2	0	AC021066.1;KRT86	50986271	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.425000	0.80255	2.020000	0.59435	0.454000	0.30748	AAG	.		0.637	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		G	52700004	A	G	52700004	3	3	23	1	0	0	0	0	1	0	0	0	8521	72	3	3	1213	3	KRT86	12	52700004	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	19668115	52700004	81151891	63	2045											
CYP27B1	1594	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	58158227	58158227	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaacagtggctgaggggtagGcactggagccagggctcagg	9	5	19	8	0	1	1	1	1	0	0	1	3	1	2	1	7	2	4	1	7	2	1	rs142446425	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:58158227G>A	ENST00000228606.4	-	6	1279	c.1070C>T	c.(1069-1071)gCc>gTc	p.A357V	CYP27B1_ENST00000546496.1_5'Flank	NM_000785.3	NP_000776.1	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B, polypeptide 1	357					bone mineralization (GO:0030282)|calcitriol biosynthetic process from calciol (GO:0036378)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|decidualization (GO:0046697)|G1 to G0 transition (GO:0070314)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of bone mineralization (GO:0030500)|response to estrogen (GO:0043627)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	calcidiol 1-monooxygenase activity (GO:0004498)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|urinary_tract(1)	15	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Alfacalcidol(DB01436)|Calcidiol(DB00146)|Corticotropin(DB01285)|Ergocalciferol(DB00153)	TGAGGGGTAGGCACTGGAGCC	0.597																																					p.A357V													.	CYP27B1-514	0			c.C1070T						.						112	117	115					12																	58158227		2203	4300	6503	SO:0001583	missense	1594	exon6			GGGTAGGCACTGG	AB006987	CCDS8954.1	12q14.1	2013-11-13	2003-01-14		ENSG00000111012	ENSG00000111012		"Cytochrome P450s"	2606	protein-coding gene	gene with protein product	"VDDR I", "1alpha(OH)ase", "25-Hydroxyvitamin D3 1alpha-hydroxylase"	609506	"cytochrome P450, subfamily XXVIIB (25-hydroxyvitamin D-1-alpha-hydroxylase), polypeptide 1"	VDD1, PDDR		9295274, 9344864	Standard	NM_000785		Approved	CYP1, P450c1	uc001spz.1	O15528	OTTHUMG00000170457	ENST00000228606.4:c.1070C>T	12.37:g.58158227G>A	ENSP00000228606:p.Ala357Val	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	121	47	NM_000785	0	0	1	2	1	B2RC61|Q548T3	Missense_Mutation	SNP	ENST00000228606.4	37	CCDS8954.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.233980	0.22626	.	.	ENSG00000111012	ENST00000228606;ENST00000546567	T;T	0.68903	-0.36;-0.36	4.79	2.91	0.33838	.	1.026450	0.07685	N	0.937680	T	0.57770	0.2076	L	0.33245	0.995	0.09310	N	1	B	0.06786	0.001	B	0.13407	0.009	T	0.44574	-0.9319	10	0.30078	T	0.28	-0.3466	12.7694	0.57412	0.0:0.3168:0.6832:0.0	.	357	O15528	CP27B_HUMAN	V	357;122	ENSP00000228606:A357V;ENSP00000449472:A122V	ENSP00000228606:A357V	A	-	2	0	CYP27B1	56444494	0.001000	0.12720	0.003000	0.11579	0.902000	0.53008	0.202000	0.17295	0.604000	0.29930	0.462000	0.41574	GCC	G|1.000;C|0.000		0.597	CYP27B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409248.1	NM_000785		A	58158227	G	A	58158227	3	1	23	1	0	0	0	0	1	0	0	0	4165	1203	42	2	472	2	CYP27B1	12	58158227	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	5458223	58158227	75693668	64	2046											
SRGAP1	57522	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	64491125	64491125	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aaaaccccctctttcctaagGaaagatttaacgatctgatt	14	12	5	10	1	2	2	0	1	2	1	3	4	3	3	3	1	2	0	3	1	5	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:64491125G>C	ENST00000355086.3	+	15	2307	c.1783G>C	c.(1783-1785)Gaa>Caa	p.E595Q	RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000543397.1_Missense_Mutation_p.E532Q|SRGAP1_ENST00000357825.3_Missense_Mutation_p.E572Q	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	595	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTTTCCTAAGGAAAGATTTAA	0.398																																					p.E595Q		.											.	SRGAP1-653	0			c.G1783C						.						89	86	87					12																	64491125		2203	4300	6503	SO:0001583	missense	57522	exon15			CCTAAGGAAAGAT	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1783G>C	12.37:g.64491125G>C	ENSP00000347198:p.Glu595Gln	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	54	18	NM_020762	0	0	0	0	0	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095528	0.94197	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.48201	0.82;0.82;0.82	5.48	5.48	0.80851	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.36002	U	0.002860	T	0.62636	0.2444	L	0.53561	1.675	0.80722	D	1	P;P	0.52463	0.953;0.946	P;P	0.59825	0.864;0.786	T	0.57266	-0.7841	9	.	.	.	.	19.7379	0.96215	0.0:0.0:1.0:0.0	.	595;532	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	Q	595;572;532	ENSP00000347198:E595Q;ENSP00000350480:E572Q;ENSP00000437948:E532Q	.	E	+	1	0	SRGAP1	62777392	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.748000	0.98867	2.733000	0.93635	0.655000	0.94253	GAA	.		0.398	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			C	64491125	G	C	64491125	3	2	23	1	0	0	0	0	1	0	0	0	15177	1175	41	4	1841	4	SRGAP1	12	64491125	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	6332898	64491125	69360770	65	2047											
C12orf12	196477	hgsc.bcm.edu	37	chr12	91347593	91347593	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcgacctcttcctcctcAtcttcgacctcttcttcctc	3	17	2	19	2	6	0	1	0	5	0	12	2	9	0	5	0	0	0	5	0	0	5	rs137989103		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:91347593A>C	ENST00000358859.2	-	1	1360	c.927T>G	c.(925-927)gaT>gaG	p.D309E	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	309	Glu-rich.																cttcctcctcatcttcgacct	0.527																																					p.D309E		.											.	.	0			c.T927G						.						221	189	200					12																	91347593		2203	4300	6503	SO:0001583	missense	196477	exon1			CTCCTCATCTTCG	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 12"	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.927T>G	12.37:g.91347593A>C	ENSP00000351727:p.Asp309Glu	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	101	9	NM_152638	0	0	0	0	0	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	37	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	A	0.040	-1.288355	0.01387	.	.	ENSG00000197651	ENST00000358859	T	0.15139	2.45	4.85	-9.69	0.00524	.	1.727330	0.03768	N	0.259267	T	0.05686	0.0149	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37934	-0.9684	10	0.02654	T	1	-2.4783	8.0014	0.30299	0.6481:0.1314:0.0:0.2205	.	309	Q8TC90	CL012_HUMAN	E	309	ENSP00000351727:D309E	ENSP00000351727:D309E	D	-	3	2	C12orf12	89871724	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.544000	0.06077	-1.269000	0.02436	0.378000	0.23410	GAT	.		0.527	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		C	91347593	A	C	91347593	3	2	23	1	0	0	0	0	1	0	0	0	1680	214	8	5	297	5	C12orf12	12	91347593	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	26856468	91347593	42504302	66	2048											
TBX5	6910	hgsc.bcm.edu	37	chr12	114841566	114841566	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtctccttacctgctgggtGaaggcggcctgcggggacga	5	8	17	11	3	1	1	0	1	1	0	2	3	1	2	3	6	3	1	3	6	2	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:114841566G>A	ENST00000310346.4	-	2	804	c.138C>T	c.(136-138)ttC>ttT	p.F46F	TBX5_ENST00000526441.1_Silent_p.F46F|TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000405440.2_Silent_p.F46F	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	46				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		CCTGCTGGGTGAAGGCGGCCT	0.632																																					p.F46F	NSCLC(152;1358 1980 4050 23898 40356)	.											.	TBX5-98	0			c.C138T						.						42	52	48					12																	114841566		2199	4299	6498	SO:0001819	synonymous_variant	6910	exon2			CTGGGTGAAGGCG	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"T-boxes"	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.138C>T	12.37:g.114841566G>A		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	29	10	NM_000192	0	0	0	0	0	A6ND77|O15301|Q96TB0|Q9Y4I2	Silent	SNP	ENST00000310346.4	37	CCDS9173.1																																																																																			.		0.632	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		A	114841566	G	A	114841566	2	1	23	1	0	0	0	0	0	0	0	1	15693	1281	45	2		2	TBX5	12	114841566	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	23493973	114841566	19010329	67	2049											
LRRC43	254050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	122669246	122669246	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagacagtttcctgagagaaTtggccatccggaacccgctg	11	8	11	11	2	0	3	0	1	0	2	2	5	2	4	4	2	1	2	4	2	3	2	rs373684289		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:122669246T>C	ENST00000339777.4	+	2	359	c.331T>C	c.(331-333)Ttg>Ctg	p.L111L	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	111										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CCTGAGAGAATTGGCCATCCG	0.592													T|||	1	0.000199681	8e-04	0	5008	,	,		20729	0		0	False		,,,				2504	0				p.L111L		.											.	LRRC43-135	0			c.T331C						.	T	,	1,3991		0,1,1995	51	53	52		331,	4.2	0.8	12		52	0,8312		0,0,4156	no	coding-synonymous,utr-5	LRRC43	NM_001098519.1,NM_152759.4	,	0,1,6151	CC,CT,TT		0.0,0.0251,0.0081	,	111/657,	122669246	1,12303	1996	4156	6152	SO:0001819	synonymous_variant	254050	exon2			AGAGAATTGGCCA	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.331T>C	12.37:g.122669246T>C		Somatic	181	0		WXS	Illumina HiSeq	Phase_I	213	92	NM_001098519	0	0	2	7	5	Q6ZVT9	Silent	SNP	ENST00000339777.4	37	CCDS45001.1																																																																																			.		0.592	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		C	122669246	T	C	122669246	2	2	23	1	0	0	0	0	0	0	0	1	9026	1490	52	3		3	LRRC43	12	122669246	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	7827680	122669246	11182649	68	2050											
DNAH10	196385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	124335495	124335495	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcttcatcaccatgaaccccGgctacgcaggccgcacggag	9	6	10	16	4	3	1	2	1	1	0	3	2	3	2	4	3	2	3	4	3	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:124335495G>A	ENST00000409039.3	+	34	5834	c.5809G>A	c.(5809-5811)Ggc>Agc	p.G1937S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1937	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CATGAACCCCGGCTACGCAGG	0.582																																					p.G1937S		.											.	DNAH10-95	0			c.G5809A						.						40	45	44					12																	124335495		2155	4286	6441	SO:0001583	missense	196385	exon34			AACCCCGGCTACG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"Axonemal dyneins"	2941	protein-coding gene	gene with protein product		605884	"dynein, axonemal, heavy polypeptide 10"				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.5809G>A	12.37:g.124335495G>A	ENSP00000386770:p.Gly1937Ser	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	94	51	NM_207437	0	0	0	0	0	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	35	5.476132	0.96291	.	.	ENSG00000197653	ENST00000409039	T	0.16743	2.32	5.48	5.48	0.80851	ATPase, AAA+ type, core (1);	0.000000	0.64402	U	0.000001	T	0.53546	0.1803	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64232	-0.6456	10	0.87932	D	0	.	19.3709	0.94484	0.0:0.0:1.0:0.0	.	1937	Q8IVF4	DYH10_HUMAN	S	1937	ENSP00000386770:G1937S	ENSP00000386770:G1937S	G	+	1	0	DNAH10	122901448	1.000000	0.71417	0.956000	0.39512	0.972000	0.66771	8.010000	0.88615	2.576000	0.86940	0.655000	0.94253	GGC	.		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124335495	G	A	124335495	3	1	23	1	0	0	0	0	1	0	0	0	4609	1116	39	1	5943	1	DNAH10	12	124335495	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1666249	124335495	9516400	69	2051											
BRI3BP	140707	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	125509696	125509696	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgttcggccgcttcttctGgatcgtgcgggtcgtcctgt	1	14	15	11	5	2	0	0	0	2	0	6	1	3	1	2	4	1	2	2	4	0	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:125509696G>T	ENST00000341446.8	+	3	567	c.476G>T	c.(475-477)tGg>tTg	p.W159L		NM_080626.5	NP_542193.3			BRI3 binding protein									p.W159S(1)		large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		CGCTTCTTCTGGATCGTGCGG	0.622																																					p.W159L													.	BRI3BP-91	1	Substitution - Missense(1)	lung(1)	c.G476T						.						131	99	110					12																	125509696		2203	4300	6503	SO:0001583	missense	140707	exon3			TCTTCTGGATCGT	AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.476G>T	12.37:g.125509696G>T	ENSP00000340761:p.Trp159Leu	Somatic	59	1		WXS	Illumina HiSeq	Phase_I	90	41	NM_080626	0	0	2	7	5		Missense_Mutation	SNP	ENST00000341446.8	37	CCDS9262.1	.	.	.	.	.	.	.	.	.	.	g	29.4	5.001126	0.93227	.	.	ENSG00000184992	ENST00000341446	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79841	-0.1633	9	0.87932	D	0	-1.2314	18.495	0.90861	0.0:0.0:1.0:0.0	.	159	Q8WY22	BRI3B_HUMAN	L	159	.	ENSP00000340761:W159L	W	+	2	0	BRI3BP	124075649	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	9.284000	0.95882	2.344000	0.79699	0.556000	0.70494	TGG	.		0.622	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626		T	125509696	G	T	125509696	3	4	23	1	0	0	0	0	1	0	0	0	1516	1357	47	4	486	4	BRI3BP	12	125509696	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1174201	125509696	8342199	70	2052											
TBC1D4	9882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	75923415	75923415	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtactgaaggcctgtttCagagtcagcattacctcatc	9	11	9	12	1	3	2	3	1	0	1	4	2	3	2	3	1	3	3	3	1	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr13:75923415C>A	ENST00000377636.3	-	5	1645	c.1299G>T	c.(1297-1299)ctG>ctT	p.L433L	TBC1D4_ENST00000377625.2_Silent_p.L433L|TBC1D4_ENST00000431480.2_Silent_p.L433L|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	433	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		AGGCCTGTTTCAGAGTCAGCA	0.473																																					p.L433L		.											.	TBC1D4-95	0			c.G1299T						.						57	58	58					13																	75923415		1948	4168	6116	SO:0001819	synonymous_variant	9882	exon5			CTGTTTCAGAGTC	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"Akt substrate of 160 kDa"	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.1299G>T	13.37:g.75923415C>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	48	25	NM_014832	0	0	1	3	2	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																			.		0.473	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		A	75923415	C	A	75923415	2	1	23	1	0	0	0	0	0	0	0	1	15654	813	29	4		4	TBC1D4	13	75923415	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		75923415	39246463	71	2053											
TEP1	7011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20846267	20846267	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagccatggtgggcagggaaGgcagccagccgtgccccttc	8	5	15	13	1	0	0	0	0	0	0	1	1	0	1	5	4	4	2	5	4	2	1	rs201698574		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:20846267G>C	ENST00000262715.5	-	39	5677	c.5637C>G	c.(5635-5637)gcC>gcG	p.A1879A	TEP1_ENST00000556935.1_Silent_p.A1771A|TEP1_ENST00000545983.1_Silent_p.A217A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1879					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GGGCAGGGAAGGCAGCCAGCC	0.632																																					p.A1879A		.											.	TEP1-95	0			c.C5637G						.						87	85	86					14																	20846267		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon39			AGGGAAGGCAGCC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5637C>G	14.37:g.20846267G>C		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	119	40	NM_007110	0	0	0	0	0	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			G|0.999;A|0.000		0.632	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20846267	G	C	20846267	2	2	23	1	0	0	0	0	0	0	0	1	15791	987	35	4		4	TEP1	14	20846267	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		20846267	86503273	72	2054											
KCNH5	27133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	63447729	63447729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgggccccacgaaagtcGtgtgaaaatttaaaacgatg	14	7	10	10	4	0	1	0	1	0	0	1	3	0	1	3	1	1	0	3	1	5	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:63447729G>A	ENST00000322893.7	-	6	1071	c.803C>T	c.(802-804)aCg>aTg	p.T268M	KCNH5_ENST00000420622.2_Missense_Mutation_p.T268M|KCNH5_ENST00000394968.1_Missense_Mutation_p.T210M|KCNH5_ENST00000394964.2_Missense_Mutation_p.T210M	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	268					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CACGAAAGTCGTGTGAAAATT	0.423																																					p.T268M		.											.	KCNH5-98	0			c.C803T						.						70	71	71					14																	63447729		2203	4300	6503	SO:0001583	missense	27133	exon6			AAAGTCGTGTGAA	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.803C>T	14.37:g.63447729G>A	ENSP00000321427:p.Thr268Met	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	94	40	NM_172375	0	0	0	0	0	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325830	0.81580	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76	5.54	5.54	0.83059	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	M	0.90542	3.125	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;1.0;1.0;1.0	D	0.98956	1.0796	10	0.87932	D	0	.	19.4888	0.95042	0.0:0.0:1.0:0.0	.	210;210;268;268	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	M	268;268;210;210	ENSP00000321427:T268M;ENSP00000395439:T268M;ENSP00000378419:T210M;ENSP00000378415:T210M	ENSP00000321427:T268M	T	-	2	0	KCNH5	62517482	1.000000	0.71417	0.992000	0.48379	0.740000	0.42216	9.799000	0.99117	2.607000	0.88179	0.585000	0.79938	ACG	.		0.423	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63447729	G	A	63447729	3	1	23	1	0	0	0	0	1	0	0	0	8056	1145	40	1	2221	1	KCNH5	14	63447729	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	42601462	63447729	43901811	73	2055											
C14orf50	145376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	65053588	65053588	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatacacagaaagactggaaGttctttgaggtgagtcactt	13	11	11	6	0	2	4	1	2	1	2	2	6	2	5	0	2	1	1	0	2	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:65053588G>A	ENST00000298705.1	+	9	798	c.702G>A	c.(700-702)aaG>aaA	p.K234K	RP11-973N13.3_ENST00000556634.1_RNA|RP11-973N13.3_ENST00000554454.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	234					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AAGACTGGAAGTTCTTTGAGG	0.353																																					p.K234K		.											.	.	0			c.G702A						.						134	126	128					14																	65053588		2203	4300	6503	SO:0001819	synonymous_variant	145376	exon9			CTGGAAGTTCTTT		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.702G>A	14.37:g.65053588G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	51	11	NM_172365	0	0	0	0	0	Q6NTH6	Silent	SNP	ENST00000298705.1	37	CCDS9767.1																																																																																			.		0.353	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		A	65053588	G	A	65053588	2	1	23	1	0	0	0	0	0	0	0	1	1781	1020	36	2		2	C14orf50	14	65053588	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1605859	65053588	42295952	74	2056											
GALC	2581	hgsc.bcm.edu;broad.mit.edu	37	chr14	88454869	88454870	+	Splice_Site	INS	-	-	A																															tagaagtcgggaggttgcctINSaaaaaaaaaagttttcaaaa																								rs561184126	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:88454869_88454870insA	ENST00000261304.2	-	2	302		c.e2-2		GALC_ENST00000393569.2_Splice_Site|GALC_ENST00000554916.1_Splice_Site|GALC_ENST00000544807.2_Splice_Site|GALC_ENST00000393568.4_Intron	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase						carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGAGGTTGCCTAAAAAAAAAAG	0.351																																					.		.											.	GALC-90	0			c.118-2->T						.																																			SO:0001630	splice_region_variant	2581	exon3			.	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.196-2->T	14.37:g.88454879_88454879dupA		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	39	18	NM_001201402	0	0	0	0	0	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Splice_Site	INS	ENST00000261304.2	37	CCDS9878.2																																																																																			.		0.351	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		Intron	A	88454870	-	A	88454869	8	5	23	1	0	1	1	0	0	0	1	0	6221	1536	53	0	1990	0	GALC	14	88454869	Splice_Site	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	23401281	88454869	18894671	75	2057											
RIN3	79890	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	93117951	93117952	+	Frame_Shift_Ins	INS	-	-	T																															tgggactcctcgctgaatccINStccacaagaaagagggaagc																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:93117951_93117952insT	ENST00000216487.7	+	6	716_717	c.557_558insT	c.(556-561)cctccafs	p.P187fs	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	187					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				TCGCTGAATCCTCCACAAGAAA	0.629																																					p.P186fs		.											.	RIN3-522	0			c.557_558insT						.																																			SO:0001589	frameshift_variant	79890	exon6			.	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.558dupT	14.37:g.93117952_93117952dupT	ENSP00000216487:p.Pro187fs	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	39	24	NM_024832	0	0	0	0	0	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Frame_Shift_Ins	INS	ENST00000216487.7	37	CCDS32144.1																																																																																			.		0.629	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			T	93117952	-	T	93117951	7	5	23	1	0	1	1	0	0	0	0	0	13405	681	24	0	579	0	RIN3	14	93117951	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	4663082	93117951	14231589	76	2058											
RTL1	388015	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	101350131	101350136	+	In_Frame_Del	DEL	TCGTTG	TCGTTG	-																															atagatagtgcctgatctccTcgttgagcccctggcacaag																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TCGTTG	TCGTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350131_101350136delTCGTTG	ENST00000534062.1	-	1	1048_1053	c.990_995delCAACGA	c.(988-996)ctcaacgag>ctg	p.NE331del	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	331					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CCTGATCTCCTCGTTGAGCCCCTGGC	0.563																																					p.330_332del		.											.	RTL1-46	0			c.990_995del						.																																			SO:0001651	inframe_deletion	388015	exon1			.		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.990_995delCAACGA	14.37:g.101350131_101350136delTCGTTG	ENSP00000435342:p.Asn331_Glu332del	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	46	14	NM_001134888	0	0	0	0	0	E9PKS8	In_Frame_Del	DEL	ENST00000534062.1	37	CCDS53910.1																																																																																			.		0.563	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		-	101350136	TCGTTG	-	101350131	7	5	23	1	0	1	0	1	0	0	0	0	13756	1551	54	0	3085	0	RTL1	14	101350131	In_Frame_Del	DEL	TCGTTG	TCGA-A4-A57E-01A-11D-A26P-10	8232180	101350131	5999409	77	2059	18	2									
RTL1	388015	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	101350138	101350138	+	Frame_Shift_Del	DEL	G	G	-																															gtgcctgatctcctcgttgaGcccctggcacaagtgggcct																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350138delG	ENST00000534062.1	-	1	1046	c.988delC	c.(988-990)ctcfs	p.L330fs	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	330					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TCCTCGTTGAGCCCCTGGCAC	0.572																																					p.L330fs		.											.	RTL1-46	0			c.988delC						.						70	67	68					14																	101350138		692	1591	2283	SO:0001589	frameshift_variant	388015	exon1			.		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.988delC	14.37:g.101350138delG	ENSP00000435342:p.Leu330fs	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	45	14	NM_001134888	0	0	0	0	0	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	37	CCDS53910.1																																																																																			.		0.572	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		-	101350138	G	-	101350138	7	5	23	1	0	1	0	1	0	0	0	0	13756	971	34	0	3092	0	RTL1	14	101350138	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	7	101350138	5999402	78	2060	18	2									
ARHGAP11A	9824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	32929467	32929467	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataaaagtcaagtcacctctTaagtttcagcgtactcctgt	12	13	6	10	1	4	0	3	0	1	0	5	0	5	0	2	0	2	2	2	0	5	4	rs373558097		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:32929467T>C	ENST00000361627.3	+	12	3215	c.2493T>C	c.(2491-2493)ctT>ctC	p.L831L	ARHGAP11A_ENST00000543522.1_Silent_p.L642L|ARHGAP11A_ENST00000565905.1_Silent_p.L642L	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	831					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AGTCACCTCTTAAGTTTCAGC	0.388																																					p.L831L	Colon(45;757 1134 30003 36652)	.											.	ARHGAP11A-292	0			c.T2493C						.						99	103	101					15																	32929467		2201	4300	6501	SO:0001819	synonymous_variant	9824	exon12			ACCTCTTAAGTTT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.2493T>C	15.37:g.32929467T>C		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	117	52	NM_014783	0	0	3	4	1	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																			.		0.388	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		C	32929467	T	C	32929467	2	2	23	1	0	0	0	0	0	0	0	1	863	1741	61	3		3	ARHGAP11A	15	32929467	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10		32929467	69601925	79	2061											
ZNF770	54989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	35275620	35275620	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctttagcatttttaaatTgttttcagccatcatattct	11	20	3	7	0	4	0	2	0	2	0	4	0	4	0	1	0	2	2	1	0	5	10			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:35275620T>A	ENST00000356321.4	-	3	360	c.16A>T	c.(16-18)Aat>Tat	p.N6Y		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	6					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		ATTTTTAAATTGTTTTCAGCC	0.313																																					p.N6Y		.											.	ZNF770-91	0			c.A16T						.						68	62	64					15																	35275620		2201	4298	6499	SO:0001583	missense	54989	exon3			TTAAATTGTTTTC	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"Zinc fingers, C2H2-type"	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.16A>T	15.37:g.35275620T>A	ENSP00000348673:p.Asn6Tyr	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	74	27	NM_014106	0	0	1	3	2	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	T	4.657	0.122204	0.08931	.	.	ENSG00000198146	ENST00000356321	T	0.09538	2.97	4.27	3.14	0.36123	.	0.420309	0.21769	N	0.069391	T	0.05227	0.0139	N	0.14661	0.345	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.32481	-0.9905	10	0.66056	D	0.02	-8.2947	0.8062	0.01084	0.1598:0.1796:0.1664:0.4942	.	6	Q6IQ21	ZN770_HUMAN	Y	6	ENSP00000348673:N6Y	ENSP00000348673:N6Y	N	-	1	0	ZNF770	33062912	1.000000	0.71417	0.962000	0.40283	0.306000	0.27790	1.749000	0.38319	0.959000	0.37980	-0.297000	0.09499	AAT	.		0.313	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		A	35275620	T	A	35275620	3	1	23	1	0	0	0	0	1	0	0	0	18175	1812	63	5	2063	5	ZNF770	15	35275620	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	2346153	35275620	67255772	80	2062											
PRTG	283659	broad.mit.edu;bcgsc.ca	37	chr15	55931987	55931988	+	Frame_Shift_Ins	INS	-	-	C																															agccttcgcatagagatggtINSggggtggtggtggaggaggg																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931987_55931988insC	ENST00000389286.4	-	13	2223_2224	c.2176_2177insG	c.(2176-2178)cacfs	p.H726fs		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ATAGAGATGGTGGGGTGGTGGT	0.455																																					p.H726fs													.	PRTG-92	0			c.2177_2178insG						.																																			SO:0001589	frameshift_variant	283659	exon13			AGATGGTGGGGTG	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2176_2177insG	15.37:g.55931987_55931988insC	ENSP00000373937:p.His726fs	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	138	18	NM_173814	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000389286.4	37	CCDS42040.1																																																																																			.		0.455	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55931988	-	C	55931987	7	5	23	1	0	1	1	0	0	0	0	0	12667	1696	59	0	1307	0	PRTG	15	55931987	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	20656367	55931987	46599405	81	2063	19	3									
PRTG	283659	ucsc.edu	37	chr15	55931988	55931988	+	Missense_Mutation	SNP	G	G	C																															agccttcgcatagagatggtGgggtggtggtggaggaggga																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931988G>C	ENST00000389286.4	-	13	2223	c.2176C>G	c.(2176-2178)Cac>Gac	p.H726D		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TAGAGATGGTGGGGTGGTGGT	0.458																																					p.H726D													.	PRTG-92	0			c.C2176G						.						154	167	163					15																	55931988		2049	4184	6233	SO:0001583	missense	283659	exon13			GATGGTGGGGTGG	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2176C>G	15.37:g.55931988G>C	ENSP00000373937:p.His726Asp	Somatic	170	1		WXS	Illumina HiSeq		138	19	NM_173814	0	0	0	0	0		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.586149	0.46110	.	.	ENSG00000166450	ENST00000389286	T	0.56776	0.44	5.81	5.81	0.92471	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	L	0.35854	1.095	0.80722	D	1	B	0.18741	0.03	B	0.21360	0.034	T	0.33752	-0.9856	10	0.12430	T	0.62	-23.4452	19.072	0.93143	0.0:0.0:1.0:0.0	.	726	Q2VWP7	PRTG_HUMAN	D	726	ENSP00000373937:H726D	ENSP00000373937:H726D	H	-	1	0	PRTG	53719280	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.866000	0.69590	2.741000	0.93983	0.655000	0.94253	CAC	.		0.458	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55931988	G	C	55931988	3	2	23	1	0	0	0	0	1	0	0	0	12667	1348	47	4	1308	4	PRTG	15	55931988	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1	55931988	46599404	82	2064	19	3									
PRTG	283659	hgsc.bcm.edu	37	chr15	55931991	55931992	+	Frame_Shift_Ins	INS	-	-	TGGTGGG																															ttcgcatagagatggtggggINStggtggtggaggagggacca																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931991_55931992insTGGTGGG	ENST00000389286.4	-	13	2219_2220	c.2172_2173insCCCACCA	c.(2170-2175)ccacccfs	p.-725fs		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		AGATGGTGGGGTGGTGGTGGAG	0.45																																					p.P725fs		.											.	PRTG-92	0			c.2173_2174insCCCACCA						.																																			SO:0001589	frameshift_variant	283659	exon13			.	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2172_2173insCCCACCA	15.37:g.55931991_55931992insTGGTGGG	ENSP00000373937:p.Pro725fs	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	132	20	NM_173814	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000389286.4	37	CCDS42040.1																																																																																			.		0.45	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		TGGTGGG	55931992	-	TGGTGGG	55931991	7	5	23	1	0	1	1	0	0	0	0	0	12667	1261	44	0	1311	0	PRTG	15	55931991	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	3	55931991	46599401	83	2065	19	3									
DNAH3	55567	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21156633	21156633	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgttggcgatggaatcactgGgtccacggtggtgatgctgt	6	12	16	7	2	1	1	1	1	0	0	2	3	2	2	1	5	1	2	1	5	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:21156633G>A	ENST00000261383.3	-	3	316	c.317C>T	c.(316-318)cCc>cTc	p.P106L	DNAH3_ENST00000415178.1_Missense_Mutation_p.P106L|DNAH3_ENST00000575491.1_5'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	106	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGAATCACTGGGTCCACGGTG	0.542																																					p.P106L													.	DNAH3-167	0			c.C317T						.						183	133	150					16																	21156633		2201	4300	6501	SO:0001583	missense	55567	exon3			TCACTGGGTCCAC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.317C>T	16.37:g.21156633G>A	ENSP00000261383:p.Pro106Leu	Somatic	249	1		WXS	Illumina HiSeq	Phase_I	406	114	NM_017539	0	0	0	0	0	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001163	0.93227	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.27402	1.67;1.7	5.81	5.81	0.92471	.	2.329690	0.01929	N	0.041117	T	0.58552	0.2130	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	T	0.18461	-1.0336	10	0.66056	D	0.02	.	17.5613	0.87908	0.0:0.0:1.0:0.0	.	106;77	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	L	106;106;77	ENSP00000261383:P106L;ENSP00000394245:P106L	ENSP00000261383:P106L	P	-	2	0	DNAH3	21064134	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.942000	0.75928	2.755000	0.94549	0.655000	0.94253	CCC	.		0.542	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21156633	G	A	21156633	3	1	23	1	0	0	0	0	1	0	0	0	4614	1232	43	2	12272	2	DNAH3	16	21156633	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		21156633	69198120	84	2066											
GTF3C1	2975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27473632	27473632	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctggagcaactccagcaCggcgacgggctgcaggaccc	9	3	13	16	3	0	0	0	0	0	0	1	3	1	2	3	4	4	4	3	4	1	0	rs143019604		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:27473632C>T	ENST00000356183.4	-	36	6115	c.6100G>A	c.(6100-6102)Gtg>Atg	p.V2034M	GTF3C1_ENST00000567806.1_5'Flank|GTF3C1_ENST00000561623.1_Missense_Mutation_p.V2009M	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	2034					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						AACTCCAGCACGGCGACGGGC	0.667													c|||	1	0.000199681	0	0.0014	5008	,	,		18038	0		0	False		,,,				2504	0				p.V2034M		.											.	GTF3C1-94	0			c.G6100A						.		MET/VAL	0,4300		0,0,2150	49	41	44		6100	5.1	1	16	dbSNP_134	44	1,8483		0,1,4241	yes	missense	GTF3C1	NM_001520.3	21	0,1,6391	TT,TC,CC		0.0118,0.0,0.0078	probably-damaging	2034/2110	27473632	1,12783	2150	4242	6392	SO:0001583	missense	2975	exon36			CCAGCACGGCGAC	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.6100G>A	16.37:g.27473632C>T	ENSP00000348510:p.Val2034Met	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	81	23	NM_001520	0	0	19	31	12	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	c	19.56	3.849945	0.71603	0.0	1.18E-4	ENSG00000077235	ENST00000356183	T	0.30182	1.54	5.09	5.09	0.68999	.	0.077050	0.51477	D	0.000092	T	0.52435	0.1734	M	0.70595	2.14	0.40258	D	0.978142	D;D	0.89917	1.0;1.0	D;D	0.69479	0.964;0.964	T	0.56944	-0.7895	10	0.66056	D	0.02	-15.7857	12.9995	0.58667	0.0:0.8379:0.1621:0.0	.	2034;2009	Q12789;Q12789-3	TF3C1_HUMAN;.	M	2034	ENSP00000348510:V2034M	ENSP00000348510:V2034M	V	-	1	0	GTF3C1	27381133	0.991000	0.36638	0.998000	0.56505	0.968000	0.65278	2.903000	0.48711	2.369000	0.80426	0.457000	0.33378	GTG	C|1.000;T|0.000		0.667	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27473632	C	T	27473632	3	4	23	1	0	0	0	0	1	0	0	0	6893	536	19	1	237	1	GTF3C1	16	27473632	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	6316999	27473632	62881121	85	2067											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31473812	31473812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgcccagggcctgattcGgcctgcactgggcaatgctg	5	9	15	12	1	0	1	0	1	0	0	1	1	0	1	3	3	3	3	3	3	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:31473812G>A	ENST00000563544.1	+	4	1490	c.944G>A	c.(943-945)cGg>cAg	p.R315Q	ARMC5_ENST00000268314.4_Missense_Mutation_p.R315Q|ARMC5_ENST00000408912.3_Missense_Mutation_p.R410Q|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000538189.1_Missense_Mutation_p.R347Q|ARMC5_ENST00000412665.2_Intron|ARMC5_ENST00000457010.2_Missense_Mutation_p.R315Q			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	315										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GGCCTGATTCGGCCTGCACTG	0.652																																					p.R315Q		.											.	ARMC5-24	0			c.G944A						.						33	37	36					16																	31473812		2058	4214	6272	SO:0001583	missense	79798	exon3			TGATTCGGCCTGC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.944G>A	16.37:g.31473812G>A	ENSP00000456877:p.Arg315Gln	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	73	34	NM_024742	0	0	1	3	2	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	g	19.23	3.787652	0.70337	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	4.51	4.51	0.55191	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43411	0.1246	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.996;0.996	T	0.35968	-0.9767	10	0.54805	T	0.06	-20.0021	14.7442	0.69477	0.0:0.0:1.0:0.0	.	347;410;315;315	F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;ARMC5_HUMAN;.	Q	410;347;315;315	ENSP00000386125:R410Q;ENSP00000443995:R347Q;ENSP00000268314:R315Q;ENSP00000399561:R315Q	ENSP00000268314:R315Q	R	+	2	0	ARMC5	31381313	1.000000	0.71417	0.970000	0.41538	0.216000	0.24613	5.851000	0.69481	2.060000	0.61445	0.450000	0.29827	CGG	.		0.652	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		A	31473812	G	A	31473812	3	1	23	1	0	0	0	0	1	0	0	0	955	1116	39	1	954	1	ARMC5	16	31473812	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	4000180	31473812	58880941	86	2068											
TMCO7	79613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	68941414	68941414	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggccgggtggagcatctcgGggacttgctgtcccactgcc	4	8	16	13	2	1	0	0	0	1	0	3	2	2	2	3	5	3	2	3	5	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:68941414G>T	ENST00000261778.1	+	10	1748	c.1736G>T	c.(1735-1737)gGg>gTg	p.G579V		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	579						integral component of membrane (GO:0016021)											GAGCATCTCGGGGACTTGCTG	0.488																																					p.G579V		.											.	.	0			c.G1736T						.						93	92	92					16																	68941414		1892	4105	5997	SO:0001583	missense	79613	exon10			ATCTCGGGGACTT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.1736G>T	16.37:g.68941414G>T	ENSP00000261778:p.Gly579Val	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	147	46	NM_024562	0	0	5	7	2	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	37	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.982626	0.34942	.	.	ENSG00000103047	ENST00000261778	.	.	.	5.95	3.84	0.44239	Armadillo-type fold (1);	0.334836	0.36444	N	0.002597	T	0.30541	0.0768	N	0.11724	0.165	0.51012	D	0.999904	B	0.19706	0.038	B	0.17433	0.018	T	0.08391	-1.0724	9	0.12766	T	0.61	-9.4786	11.0925	0.48123	0.0:0.0:0.5339:0.4661	.	579	Q9C0B7	TMCO7_HUMAN	V	579	.	ENSP00000261778:G579V	G	+	2	0	TMCO7	67498915	1.000000	0.71417	0.996000	0.52242	0.835000	0.47333	2.559000	0.45888	1.483000	0.48342	0.655000	0.94253	GGG	.		0.488	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68941414	G	T	68941414	3	4	23	1	0	0	0	0	1	0	0	0	16033	1232	43	4	1774	4	TMCO7	16	68941414	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	37467602	68941414	21413339	87	2069											
AP1G1	164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	71779166	71779166	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccaacaaatccaataaaTcattggcctaaacaaggtaa	18	8	4	11	0	1	0	1	0	0	0	3	0	3	0	3	2	2	1	3	2	9	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:71779166T>G	ENST00000299980.4	-	19	2321	c.1880A>C	c.(1879-1881)gAt>gCt	p.D627A	AP1G1_ENST00000433195.2_Missense_Mutation_p.D650A|AP1G1_ENST00000393512.3_Missense_Mutation_p.D630A|AP1G1_ENST00000569748.1_Missense_Mutation_p.D627A|AP1G1_ENST00000564155.1_Missense_Mutation_p.D52A|AP1G1_ENST00000423132.2_Missense_Mutation_p.D630A	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	627					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				ATCCAATAAATCATTGGCCTA	0.358																																					p.D630A		.											.	AP1G1-92	0			c.A1889C						.						87	81	83					16																	71779166		2198	4300	6498	SO:0001583	missense	164	exon20			AATAAATCATTGG	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.1880A>C	16.37:g.71779166T>G	ENSP00000299980:p.Asp627Ala	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	112	74	NM_001030007	0	0	1	1	0	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	37	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	T	11.24	1.579662	0.28180	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.15718	2.41;2.41;2.42;2.4	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.10551	0.0258	N	0.13198	0.31	0.80722	D	1	B;B;B	0.14012	0.001;0.002;0.009	B;B;B	0.17098	0.001;0.004;0.017	T	0.11542	-1.0583	10	0.08599	T	0.76	-12.6522	15.3832	0.74676	0.0:0.0:0.0:1.0	.	627;650;630	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	A	627;630;630;650	ENSP00000299980:D627A;ENSP00000377148:D630A;ENSP00000409153:D630A;ENSP00000403259:D650A	ENSP00000299980:D627A	D	-	2	0	AP1G1	70336667	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.054000	0.61138	0.459000	0.35465	GAT	.		0.358	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			G	71779166	T	G	71779166	3	3	23	1	0	0	0	0	1	0	0	0	732	1435	50	5	608	5	AP1G1	16	71779166	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	2837752	71779166	18575587	88	2070											
MLKL	197259	bcgsc.ca	37	chr16	74716659	74716659	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgagttcacagtactccatGacaatggagaattgaggcgg	12	8	12	9	2	1	3	1	2	0	1	2	5	2	3	2	3	1	2	2	3	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:74716659G>T	ENST00000308807.7	-	6	1309	c.846C>A	c.(844-846)gtC>gtA	p.V282V	MLKL_ENST00000306247.7_Intron	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						AGTACTCCATGACAATGGAGA	0.572																																					p.V282V													.	MLKL-561	0			c.C846A						.						58	50	53					16																	74716659		2198	4300	6498	SO:0001819	synonymous_variant	197259	exon6			CTCCATGACAATG	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.846C>A	16.37:g.74716659G>T		Somatic	117	4		WXS	Illumina HiSeq	Phase_1	155	92	NM_152649	0	0	7	11	4		Silent	SNP	ENST00000308807.7	37	CCDS32487.1																																																																																			.		0.572	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		T	74716659	G	T	74716659	2	4	23	1	0	0	0	0	0	0	0	1	9644	1277	45	4		4	MLKL	16	74716659	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	2937493	74716659	15638094	89	2071											
WDR81	124997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	1630298	1630298	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aggtgaccagctgggctcctCcagtcaagcgtcccctggac	7	7	12	15	1	1	1	1	1	0	0	4	2	4	2	5	3	2	2	5	3	1	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:1630298C>T	ENST00000409644.1	+	1	2045	c.2045C>T	c.(2044-2046)tCc>tTc	p.S682F	WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000446363.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	682					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CTGGGCTCCTCCAGTCAAGCG	0.607																																					p.S682F		.											.	WDR81-91	0			c.C2045T						.						12	14	14					17																	1630298		691	1588	2279	SO:0001583	missense	124997	exon1			GCTCCTCCAGTCA	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.2045C>T	17.37:g.1630298C>T	ENSP00000386609:p.Ser682Phe	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	45	31	NM_001163809	0	0	0	1	1	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	2.791	-0.251404	0.05867	.	.	ENSG00000167716	ENST00000409644	T	0.56444	0.46	5.5	4.5	0.54988	.	.	.	.	.	T	0.52158	0.1717	.	.	.	0.29534	N	0.85255	.	.	.	.	.	.	T	0.50180	-0.8858	6	0.37606	T	0.19	.	11.6034	0.51017	0.0:0.8056:0.1247:0.0697	.	.	.	.	F	682	ENSP00000386609:S682F	ENSP00000386609:S682F	S	+	2	0	WDR81	1577048	0.044000	0.20184	0.251000	0.24312	0.026000	0.11368	0.643000	0.24750	2.580000	0.87095	0.561000	0.74099	TCC	.		0.607	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1630298	C	T	1630298	3	4	23	1	0	0	0	0	1	0	0	0	17363	855	30	2	2109	2	WDR81	17	1630298	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		1630298	79564912	90	2072											
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7577559	7577559	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ggttcatgccgcccatgcagGaactgttacacatgtagttg	9	11	11	10	1	1	0	1	0	0	0	1	1	1	1	2	2	4	5	2	2	3	4	rs397516437|rs28934573		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:7577559G>C	ENST00000269305.4	-	7	911	c.722C>G	c.(721-723)tCc>tGc	p.S241C	TP53_ENST00000445888.2_Missense_Mutation_p.S241C|TP53_ENST00000420246.2_Missense_Mutation_p.S241C|TP53_ENST00000359597.4_Missense_Mutation_p.S241C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Missense_Mutation_p.S241C|TP53_ENST00000455263.2_Missense_Mutation_p.S241C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	241	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		S -> A (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|S -> C (in sporadic cancers; somatic mutation).|S -> F (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934573). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228}.|S -> P (in sporadic cancers; somatic mutation).|S -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.S241F(85)|p.S241C(26)|p.0?(8)|p.S241Y(8)|p.C242fs*5(6)|p.?(5)|p.S241del(5)|p.S148F(4)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.S148C(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCCATGCAGGAACTGTTACA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S241C	Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53-70225	160	Substitution - Missense(124)|Deletion - In frame(13)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(5)|Complex - deletion inframe(1)	urinary_tract(19)|large_intestine(18)|breast(17)|endometrium(15)|ovary(15)|lung(12)|skin(9)|biliary_tract(8)|central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(7)|upper_aerodigestive_tract(6)|stomach(6)|oesophagus(5)|bone(5)|liver(3)|pancreas(3)|eye(2)|thyroid(1)|kidney(1)	c.C722G	GRCh37	CM920673	TP53	M	rs28934573	.						139	108	118					17																	7577559		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATGCAGGAACTGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.722C>G	17.37:g.7577559G>C	ENSP00000269305:p.Ser241Cys	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	98	72	NM_000546	0	0	2	17	15	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276619	0.59758	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99857	-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22	4.62	3.64	0.41730	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.120078	0.56097	D	0.000022	D	0.99871	0.9939	M	0.92784	3.345	0.51233	D	0.999916	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0;0.999	D	0.96551	0.9408	10	0.87932	D	0	-35.4617	12.8645	0.57932	0.0:0.1651:0.8349:0.0	.	241;241;148;241;241;241	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	C	241;241;241;241;241;241;230;148;109;148	ENSP00000410739:S241C;ENSP00000352610:S241C;ENSP00000269305:S241C;ENSP00000398846:S241C;ENSP00000391127:S241C;ENSP00000391478:S241C;ENSP00000425104:S109C;ENSP00000423862:S148C	ENSP00000269305:S241C	S	-	2	0	TP53	7518284	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.346000	0.44027	1.295000	0.44724	0.462000	0.41574	TCC	G|1.000;|0.000		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577559	G	C	7577559	3	2	23	1	0	0	0	0	1	0	0	0	16414	1174	41	4	568	4	TP53	17	7577559	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	5947261	7577559	73617651	91	2073											
SSH2	85464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27958146	27958146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcacaatacactctgttgTtgtgagttgttctacaaaag	11	14	8	8	0	2	1	0	1	2	0	2	1	2	1	0	0	3	5	0	0	5	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:27958146T>C	ENST00000269033.3	-	15	4136	c.3985A>G	c.(3985-3987)Aca>Gca	p.T1329A	SSH2_ENST00000540801.1_Missense_Mutation_p.T1356A|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	1329					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CACTCTGTTGTTGTGAGTTGT	0.532																																					p.T1329A		.											.	SSH2-92	0			c.A3985G						.						57	50	52					17																	27958146		2203	4300	6503	SO:0001583	missense	85464	exon15			CTGTTGTTGTGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.3985A>G	17.37:g.27958146T>C	ENSP00000269033:p.Thr1329Ala	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	133	33	NM_033389	0	0	1	6	5	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.576881	0.45902	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.58506	0.33;0.33	6.17	6.17	0.99709	.	0.593826	0.17897	N	0.158323	T	0.58509	0.2127	M	0.64997	1.995	0.80722	D	1	P;P	0.41131	0.739;0.622	B;B	0.40782	0.34;0.183	T	0.62234	-0.6897	10	0.59425	D	0.04	-13.774	13.2295	0.59933	0.0:0.0:0.1323:0.8677	.	1356;1329	F5H527;Q76I76	.;SSH2_HUMAN	A	1329;1356	ENSP00000269033:T1329A;ENSP00000444743:T1356A	ENSP00000269033:T1329A	T	-	1	0	SSH2	24982272	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	2.987000	0.49378	2.371000	0.80710	0.533000	0.62120	ACA	.		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		C	27958146	T	C	27958146	3	2	23	1	0	0	0	0	1	0	0	0	15217	1725	60	3	290	3	SSH2	17	27958146	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	20380587	27958146	53237064	92	2074											
CCDC55	84081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	28512533	28512533	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cacagactcacagaggaaggGcaagagaagggtaaagaaca	19	2	13	7	0	1	4	1	0	0	4	1	6	1	5	0	3	1	2	0	3	6	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:28512533G>T	ENST00000247026.5	+	7	1581	c.1518G>T	c.(1516-1518)ggG>ggT	p.G506G	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	506					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						CAGAGGAAGGGCAAGAGAAGG	0.433																																					p.G506G		.											.	NSRP1-91	0			c.G1518T						.						103	101	102					17																	28512533		2203	4300	6503	SO:0001819	synonymous_variant	84081	exon7			GGAAGGGCAAGAG	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.1518G>T	17.37:g.28512533G>T		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	170	95	NM_032141	0	0	9	28	19	Q6FI71	Silent	SNP	ENST00000247026.5	37	CCDS11255.1																																																																																			.		0.433	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		T	28512533	G	T	28512533	2	4	23	1	0	0	0	0	0	0	0	1	2831	1190	42	4		4	CCDC55	17	28512533	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	554387	28512533	52682677	93	2075											
SAMD14	201191	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	48191564	48191565	+	Frame_Shift_Del	DEL	TG	TG	-																															tgctcacctcatctgaagacTgagacagcgtgtggtagggg																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:48191564_48191565delTG	ENST00000330175.4	-	8	1245_1246	c.928_929delCA	c.(928-930)cagfs	p.Q310fs	SAMD14_ENST00000503734.1_5'Flank|SAMD14_ENST00000503131.1_Frame_Shift_Del_p.Q338fs	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	310								p.Q338P(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						ATCTGAAGACTGAGACAGCGTG	0.624																																					p.338_338del		.											.	SAMD14-68	1	Substitution - Missense(1)	large_intestine(1)	c.1012_1013del						.																																			SO:0001589	frameshift_variant	201191	exon9			.		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.928_929delCA	17.37:g.48191564_48191565delTG	ENSP00000329144:p.Gln310fs	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	219	58	NM_174920	0	0	0	0	0	A5D8V1|Q8N2X0	Frame_Shift_Del	DEL	ENST00000330175.4	37	CCDS58562.1																																																																																			.		0.624	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		-	48191565	TG	-	48191564	7	5	23	1	0	1	0	1	0	0	0	0	13851	1580	55	0	336	0	SAMD14	17	48191564	Frame_Shift_Del	DEL	TG	TCGA-A4-A57E-01A-11D-A26P-10	19679031	48191564	33003646	94	2076											
SBNO2	22904	hgsc.bcm.edu	37	chr19	1132140	1132140	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctgggacatggtcccGgcgctcggggggccaggggt	4	6	20	11	3	0	0	0	0	0	0	2	1	1	1	2	8	2	3	2	8	0	0	rs377714018	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:1132140G>A	ENST00000361757.3	-	5	517				SBNO2_ENST00000438103.2_Silent_p.A19A|SBNO2_ENST00000587024.1_Intron	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)						bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACATGGTCCCGGCGCTCGGGG	0.731													G|||	2	0.000399361	0	0	5008	,	,		11813	0		0.002	False		,,,				2504	0				p.A19A		.											.	.	0			c.C57T						.	G	,	2,3470		0,2,1734	5	6	6		57,	1.7	0	19		6	23,7859		0,23,3918	no	coding-synonymous,intron	SBNO2	NM_001100122.1,NM_014963.2	,	0,25,5652	AA,AG,GG		0.2918,0.0576,0.2202	,	19/1310,	1132140	25,11329	1736	3941	5677	SO:0001627	intron_variant	22904	exon1			GGTCCCGGCGCTC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"KIAA0963"	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.280-4376C>T	19.37:g.1132140G>A		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	9	6	NM_001100122	0	0	0	0	0	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			.		0.731	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		A	1132140	G	A	1132140	1	1	23	0	1	0	0	0	0	0	0	0	13895	1103	39	1		1	SBNO2	19	1132140	Intron	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		1132140	57996843	95	2077											
REXO1	57455	hgsc.bcm.edu	37	chr19	1827197	1827197	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctcggcacccctggccctgCggcctcgtcctcactctcgt	2	9	10	20	4	2	0	1	0	1	0	6	0	3	0	5	3	1	2	5	3	0	0	rs78977406	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:1827197C>T	ENST00000170168.4	-	2	1685	c.1591G>A	c.(1591-1593)Gca>Aca	p.A531T	CTB-31O20.4_ENST00000593201.1_RNA|REXO1_ENST00000587524.1_5'Flank|CTB-31O20.4_ENST00000587741.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	531	Interacts with TCEB3.					nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGCCCTGCGGCCTCGTCC	0.701													.|||	13	0.00259585	0	0.0043	5008	,	,		9187	0		0.0099	False		,,,				2504	0				p.A531T		.											.	REXO1-90	0			c.G1591A						.	C	THR/ALA	12,4044		0,12,2016	6	6	6		1591	-6.9	0	19	dbSNP_131	6	100,7964		0,100,3932	no	missense	REXO1	NM_020695.3	58	0,112,5948	TT,TC,CC		1.2401,0.2959,0.9241	benign	531/1222	1827197	112,12008	2028	4032	6060	SO:0001583	missense	57455	exon2			GCCCTGCGGCCTC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1591G>A	19.37:g.1827197C>T	ENSP00000170168:p.Ala531Thr	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	10	6	NM_020695	0	0	2	3	1	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	1.950	-0.441470	0.04604	0.002959	0.012401	ENSG00000079313	ENST00000170168	T	0.11495	2.77	3.44	-6.88	0.01665	.	0.575271	0.17178	N	0.184019	T	0.02119	0.0066	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34675	-0.9819	10	0.14252	T	0.57	.	5.9946	0.19487	0.1669:0.5959:0.1378:0.0994	.	531	Q8N1G1	REXO1_HUMAN	T	531	ENSP00000170168:A531T	ENSP00000170168:A531T	A	-	1	0	REXO1	1778197	0.001000	0.12720	0.000000	0.03702	0.049000	0.14656	0.297000	0.19101	-1.688000	0.01435	-0.463000	0.05309	GCA	C|0.995;T|0.005		0.701	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		T	1827197	C	T	1827197	3	4	23	1	0	0	0	0	1	0	0	0	13273	768	27	1	2134	1	REXO1	19	1827197	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	695057	1827197	57301786	96	2078											
TPM4	7171	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	16199862	16199862	+	Frame_Shift_Del	DEL	G	G	-																															tgtctttgtgcagaaaatgtGgtgacctggaagaagaactc																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:16199862delG	ENST00000300933.4	+	5	723	c.463delG	c.(463-465)ggtfs	p.G155fs	TPM4_ENST00000538887.1_Frame_Shift_Del_p.G191fs|TPM4_ENST00000344824.6_Frame_Shift_Del_p.G191fs	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	155					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						CAGAAAATGTGGTGACCTGGA	0.428			T	ALK	ALCL						OREG0025329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G191fs		.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4-316	0			c.571delG						.						125	113	117					19																	16199862		2203	4300	6503	SO:0001589	frameshift_variant	7171	exon6			.		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"Tropomyosins"	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.463delG	19.37:g.16199862delG	ENSP00000300933:p.Gly155fs	Somatic	101	0	708	WXS	Illumina HiSeq	Phase_I	80	32	NM_001145160	0	0	0	0	0	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Frame_Shift_Del	DEL	ENST00000300933.4	37	CCDS12338.1																																																																																			.		0.428	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		-	16199862	G	-	16199862	7	5	23	1	0	1	0	1	0	0	0	0	16441	1348	47	0	729	0	TPM4	19	16199862	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	14372665	16199862	42929121	97	2079											
YJEFN3	374887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19640278	19640278	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacaggcctggggaaggcaGtcatggctagagcagatttg	12	7	15	7	0	1	2	1	0	0	2	1	3	1	3	1	5	2	3	1	5	3	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:19640278G>T	ENST00000514277.4	+	2	203	c.165G>T	c.(163-165)caG>caT	p.Q55H	CTC-260F20.3_ENST00000555938.1_Intron|YJEFN3_ENST00000608404.1_Intron|CTC-260F20.3_ENST00000586674.1_3'UTR|NDUFA13_ENST00000512771.3_Missense_Mutation_p.Q177H|YJEFN3_ENST00000436027.5_Intron	NM_198537.3	NP_940939.2	A6XGL0	YJEN3_HUMAN	YjeF N-terminal domain containing 3	55										NS(1)|breast(1)|lung(3)	5						GGGGAAGGCAGTCATGGCTAG	0.577																																					p.Q55H		.											.	YJEFN3-90	0			c.G165T						.						53	58	56					19																	19640278		2035	4179	6214	SO:0001583	missense	374887	exon2			AAGGCAGTCATGG		CCDS42530.1, CCDS54236.1	19p13.11	2014-09-11			ENSG00000250067	ENSG00000250067			24785	protein-coding gene	gene with protein product						17533573	Standard	NM_198537		Approved	hYjeF_N3-19p13.11, FLJ44968	uc002nmt.2	A6XGL0	OTTHUMG00000162251	ENST00000514277.4:c.165G>T	19.37:g.19640278G>T	ENSP00000426964:p.Gln55His	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	172	39	NM_198537	0	0	1	1	0	A6XGK9|Q4G1C0	Missense_Mutation	SNP	ENST00000514277.4	37	CCDS42530.1	.	.	.	.	.	.	.	.	.	.	G	9.605	1.129720	0.21041	.	.	ENSG00000250067	ENST00000397179;ENST00000514277	T	0.48201	0.82	2.12	2.12	0.27331	.	.	.	.	.	T	0.20981	0.0505	N	0.08118	0	0.58432	D	0.999999	P;B	0.39831	0.69;0.191	B;B	0.35353	0.201;0.008	T	0.02991	-1.1085	9	0.15952	T	0.53	.	7.8598	0.29504	0.0:0.0:1.0:0.0	.	177;55	B4DF76;A6XGL0	.;YJEN3_HUMAN	H	55	ENSP00000426964:Q55H	ENSP00000380364:Q55H	Q	+	3	2	YJEFN3	19501278	0.071000	0.21146	0.059000	0.19551	0.062000	0.15995	1.327000	0.33746	1.530000	0.49136	0.555000	0.69702	CAG	.		0.577	YJEFN3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368157.5	NM_198537		T	19640278	G	T	19640278	3	4	23	1	0	0	0	0	1	0	0	0	17517	1020	36	4	171	4	YJEFN3	19	19640278	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	3440416	19640278	39488705	98	2080											
TSHZ3	57616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	31769063	31769063	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcatggatgctgggatagcCcccccagctaggagtgccgt	7	7	15	12	1	0	0	0	0	0	0	0	3	0	3	4	4	4	3	4	4	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:31769063C>T	ENST00000240587.4	-	2	1963	c.1636G>A	c.(1636-1638)Ggc>Agc	p.G546S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	546					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTGGGATAGCCCCCCCAGCTA	0.557																																					p.G546S		.											.	TSHZ3-232	0			c.G1636A						.						120	120	120					19																	31769063		2203	4300	6503	SO:0001583	missense	57616	exon2			GATAGCCCCCCCA	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1636G>A	19.37:g.31769063C>T	ENSP00000240587:p.Gly546Ser	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	171	83	NM_020856	0	0	0	0	0	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689081	0.88735	.	.	ENSG00000121297	ENST00000240587	T	0.59502	0.26	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.75221	0.3820	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77054	-0.2730	10	0.72032	D	0.01	-41.0424	19.1896	0.93660	0.0:1.0:0.0:0.0	.	546	Q63HK5	TSH3_HUMAN	S	546	ENSP00000240587:G546S	ENSP00000240587:G546S	G	-	1	0	TSHZ3	36460903	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.461000	0.80834	2.519000	0.84933	0.655000	0.94253	GGC	.		0.557	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31769063	C	T	31769063	3	4	23	1	0	0	0	0	1	0	0	0	16658	623	22	2	1613	2	TSHZ3	19	31769063	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	12128785	31769063	27359920	99	2081											
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39019255	39019255	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggcaccgggcatgtaacAtgttcctggagagctacaag	11	7	13	10	1	0	1	0	0	0	1	1	2	1	1	2	3	3	6	2	3	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:39019255A>T	ENST00000359596.3	+	75	10954	c.10954A>T	c.(10954-10956)Atg>Ttg	p.M3652L	AC067969.1_ENST00000597015.1_RNA|RYR1_ENST00000355481.4_Missense_Mutation_p.M3647L|RYR1_ENST00000360985.3_Missense_Mutation_p.M3652L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3652					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCATGTAACATGTTCCTGGA	0.612																																					p.M3652L		.											.	RYR1-100	0			c.A10954T						.						106	87	93					19																	39019255		2203	4300	6503	SO:0001583	missense	6261	exon75			TGTAACATGTTCC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10954A>T	19.37:g.39019255A>T	ENSP00000352608:p.Met3652Leu	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	219	76	NM_000540	0	0	0	0	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.262183	0.39995	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.95518	-3.73;-3.73;-3.73	5.43	5.43	0.79202	.	0.000000	0.85682	U	0.000000	D	0.88901	0.6563	N	0.16307	0.4	0.36251	D	0.853928	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.10450	0.005;0.001;0.001	D	0.84199	0.0449	10	0.02654	T	1	.	14.4595	0.67440	1.0:0.0:0.0:0.0	.	3652;3647;3652	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	L	3652;3647;3652;572	ENSP00000352608:M3652L;ENSP00000347667:M3647L;ENSP00000354254:M3652L	ENSP00000347667:M3647L	M	+	1	0	RYR1	43711095	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.641000	0.46587	2.074000	0.62210	0.459000	0.35465	ATG	.		0.612	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39019255	A	T	39019255	3	4	23	1	0	0	0	0	1	0	0	0	13800	217	8	5	11252	5	RYR1	19	39019255	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	7250192	39019255	20109728	100	2082											
MED25	81857	broad.mit.edu	37	chr19	50333366	50333366	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgggggtggctcagccccagGccccctccagtcaaagcagc	7	5	13	16	0	2	0	2	0	0	0	3	0	3	0	5	4	3	2	5	4	1	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:50333366G>C	ENST00000312865.6	+	7	763	c.710G>C	c.(709-711)gGc>gCc	p.G237A	MED25_ENST00000538643.1_Intron	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	237	Pro-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		TCAGCCCCAGGCCCCCTCCAG	0.642																																					p.G237A	GBM(51;894 1657 37868)												.	MED25-91	0			c.G710C						.						48	61	57					19																	50333366		2179	4263	6442	SO:0001583	missense	81857	exon7			CCCCAGGCCCCCT	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.710G>C	19.37:g.50333366G>C	ENSP00000326767:p.Gly237Ala	Somatic	28	1		WXS	Illumina HiSeq	Phase_I	43	6	NM_030973	0	0	10	10	0	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Missense_Mutation	SNP	ENST00000312865.6	37	CCDS33075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.981|9.981	1.228097|1.228097	0.22542|0.22542	.|.	.|.	ENSG00000104973|ENSG00000104973	ENST00000355584;ENST00000377077;ENST00000312881;ENST00000312865;ENST00000456294;ENST00000542221|ENST00000544580	D|.	0.84589|.	-1.87|.	4.98|4.98	3.95|3.95	0.45737|0.45737	Mediator complex, subunit Med25, synapsin 1 (1);|.	0.054579|.	0.64402|.	D|.	0.000001|.	T|T	0.46014|0.46014	0.1371|0.1371	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	D;P|.	0.59767|.	0.986;0.77|.	P;B|.	0.56612|.	0.802;0.353|.	T|T	0.49532|0.49532	-0.8930|-0.8930	10|6	0.15952|0.72032	T|D	0.53|0.01	.|.	9.6428|9.6428	0.39850|0.39850	0.1689:0.0:0.8311:0.0|0.1689:0.0:0.8311:0.0	.|.	237;237|.	B5ME50;Q71SY5|.	.;MED25_HUMAN|.	A|S	237|236	ENSP00000326767:G237A|.	ENSP00000326767:G237A|ENSP00000444765:R236S	G|R	+|+	2|3	0|2	MED25|MED25	55025178|55025178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.633000|0.633000	0.38033|0.38033	2.878000|2.878000	0.48515|0.48515	1.477000|1.477000	0.48234|0.48234	-0.136000|-0.136000	0.14681|0.14681	GGC|AGG	.		0.642	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973		C	50333366	G	C	50333366	3	2	23	1	0	0	0	0	1	0	0	0	9468	1203	42	4	736	4	MED25	19	50333366	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	11314111	50333366	8795617	101	2083											
POLD1	5424	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50918079	50918079	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctccctcccaggtctactTcccatacctgcttatcagca	7	11	6	17	0	2	0	1	0	1	0	5	0	5	0	4	2	4	3	4	2	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:50918079T>A	ENST00000440232.2	+	20	2449	c.2396T>A	c.(2395-2397)tTc>tAc	p.F799Y	POLD1_ENST00000599857.1_Missense_Mutation_p.F799Y|CTD-2545M3.6_ENST00000599632.1_5'Flank|POLD1_ENST00000595904.1_Missense_Mutation_p.F825Y	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	799					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CAGGTCTACTTCCCATACCTG	0.642								DNA polymerases (catalytic subunits)			OREG0025635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F799Y		.											.	POLD1-840	0			c.T2396A						.						55	54	54					19																	50918079		2203	4300	6503	SO:0001583	missense	5424	exon20			TCTACTTCCCATA		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2396T>A	19.37:g.50918079T>A	ENSP00000406046:p.Phe799Tyr	Somatic	75	0	973	WXS	Illumina HiSeq	Phase_I	96	34	NM_002691	0	0	0	0	0	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657494	0.47467	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.16597	2.33	4.84	4.84	0.62591	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.060647	0.64402	D	0.000003	T	0.12305	0.0299	N	0.17764	0.52	0.46521	D	0.999085	B;B	0.12013	0.005;0.002	B;B	0.20384	0.029;0.013	T	0.10636	-1.0621	10	0.27785	T	0.31	-24.2344	13.7358	0.62817	0.0:0.0:0.0:1.0	.	825;799	E7EVW0;P28340	.;DPOD1_HUMAN	Y	799;800	ENSP00000406046:F799Y	ENSP00000366129:F800Y	F	+	2	0	POLD1	55609891	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	2.937000	0.48979	1.970000	0.57323	0.449000	0.29647	TTC	.		0.642	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			A	50918079	T	A	50918079	3	1	23	1	0	0	0	0	1	0	0	0	12216	1783	62	5	2470	5	POLD1	19	50918079	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	584713	50918079	8210904	102	2084											
ZNF548	147694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57908473	57908473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggaggagtgggggcacCttgatgaggctcagagattg	9	7	17	8	0	1	3	1	2	0	1	1	6	1	5	2	5	0	2	2	5	0	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:57908473C>T	ENST00000366197.5	+	2	323	c.73C>T	c.(73-75)Ctt>Ttt	p.L25F	ZNF548_ENST00000598895.1_Missense_Mutation_p.L37F|AC003002.6_ENST00000596400.1_Intron|ZNF548_ENST00000336128.7_Missense_Mutation_p.L37F|ZNF548_ENST00000597400.1_Missense_Mutation_p.L37F|AC003002.6_ENST00000600421.1_3'UTR|AC003002.4_ENST00000597658.1_Intron|AC004076.7_ENST00000597410.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	25	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTGGGGGCACCTTGATGAGGC	0.512																																					p.L37F		.											.	ZNF548-67	0			c.C109T						.						377	349	358					19																	57908473		2203	4300	6503	SO:0001583	missense	147694	exon3			GGGCACCTTGATG	AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"Zinc fingers, C2H2-type", "-"	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		ENST00000366197.5:c.73C>T	19.37:g.57908473C>T	ENSP00000379482:p.Leu25Phe	Somatic	331	0		WXS	Illumina HiSeq	Phase_I	321	126	NM_001172773	0	0	0	0	0	Q96M05	Missense_Mutation	SNP	ENST00000366197.5	37	CCDS46209.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220274	0.58560	.	.	ENSG00000188785	ENST00000336128;ENST00000366197	T;T	0.18960	2.18;2.18	2.55	2.55	0.30701	Krueppel-associated box (4);	.	.	.	.	T	0.61640	0.2363	H	0.99286	4.5	0.21782	N	0.999543	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.55933	-0.8062	9	0.66056	D	0.02	.	8.7465	0.34589	0.0:1.0:0.0:0.0	.	37;25	Q8NEK5-2;Q8NEK5	.;ZN548_HUMAN	F	37;25	ENSP00000337555:L37F;ENSP00000379482:L25F	ENSP00000337555:L37F	L	+	1	0	ZNF548	62600285	0.277000	0.24220	0.716000	0.30569	0.995000	0.86356	1.271000	0.33098	1.763000	0.52060	0.563000	0.77884	CTT	.		0.512	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1	NM_152909		T	57908473	C	T	57908473	3	4	23	1	0	0	0	0	1	0	0	0	18012	681	24	2	119	2	ZNF548	19	57908473	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	6990394	57908473	1220510	103	2085											
PAK7	57144	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	9525075	9525076	+	Missense_Mutation	DNP	CC	CC	AT																															catccagtagggagtgccaaCcaatgatttcctcttcggca																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:9525075_9525076CC>AT	ENST00000378429.3	-	9	2355_2356	c.1809_1810GG>AT	c.(1807-1812)ttGGtt>ttATtt	p.V604F	PAK7_ENST00000378423.1_Missense_Mutation_p.V604F|PAK7_ENST00000353224.5_Missense_Mutation_p.V604F	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.V604I(1)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			GGAGTGCCAACCAATGATTTCC	0.475																																					p.V604F													.	PAK7-1434	1	Substitution - Missense(1)	skin(1)	c.G1809A						.																																			SO:0001583	missense	57144	exon8			GCCAACCAATGAT	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"p21(CDKN1A)-activated kinase 7"			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1809_1810delinsAT	20.37:g.9525075_9525076delinsAT	ENSP00000367686:p.Val604Phe	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	98	31	NM_177990	0	0	0	0	0	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	DNP	ENST00000378429.3	37	CCDS13107.1																																																																																			.		0.475	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			AT	9525076	CC	AT	9525075	3	1	23	1	0	0	0	0	1	0	0	0	11431	507	18	4	361	4	PAK7	20	9525075	Missense_Mutation	DNP	CC	TCGA-A4-A57E-01A-11D-A26P-10		9525075	53500445	104	2086											
KIAA1755	85449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	36869309	36869309	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctgagctgcaccatattCtctgggtttcctagaggtcc	6	12	11	12	0	1	2	0	1	1	1	4	2	3	2	4	3	2	3	4	3	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:36869309C>A	ENST00000279024.4	-	3	1495	c.1224G>T	c.(1222-1224)gaG>gaT	p.E408D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	408										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCACCATATTCTCTGGGTTTC	0.577																																					p.E408D		.											.	KIAA1755-95	0			c.G1224T						.						67	67	67					20																	36869309		2203	4300	6503	SO:0001583	missense	85449	exon3			CATATTCTCTGGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1224G>T	20.37:g.36869309C>A	ENSP00000279024:p.Glu408Asp	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	53	23	NM_001029864	0	0	0	0	0	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582898	0.28268	.	.	ENSG00000149633	ENST00000279024	T	0.61040	0.14	4.64	0.4	0.16331	.	0.300502	0.24046	N	0.042048	T	0.62221	0.2410	M	0.67953	2.075	0.09310	N	1	D	0.67145	0.996	P	0.58266	0.836	T	0.53823	-0.8384	10	0.30078	T	0.28	.	7.1114	0.25392	0.0:0.5955:0.0:0.4045	.	408	Q5JYT7	K1755_HUMAN	D	408	ENSP00000279024:E408D	ENSP00000279024:E408D	E	-	3	2	KIAA1755	36302723	0.001000	0.12720	0.026000	0.17262	0.036000	0.12997	-0.298000	0.08265	-0.072000	0.12864	0.655000	0.94253	GAG	.		0.577	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36869309	C	A	36869309	3	1	23	1	0	0	0	0	1	0	0	0	8278	912	32	4	2426	4	KIAA1755	20	36869309	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	27344234	36869309	26156211	105	2087											
SGK2	10110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42199308	42199308	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctggagccccgggccaggTtctacgctgctgaggtggcc	4	8	15	14	2	1	1	0	1	1	0	2	2	2	2	5	5	3	3	5	5	1	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:42199308T>C	ENST00000341458.4	+	6	811	c.592T>C	c.(592-594)Ttc>Ctc	p.F198L	SGK2_ENST00000373077.1_Missense_Mutation_p.F137L|SGK2_ENST00000426287.1_Missense_Mutation_p.F164L|SGK2_ENST00000373092.3_Missense_Mutation_p.F138L|SGK2_ENST00000373100.1_Missense_Mutation_p.F138L|SGK2_ENST00000423407.3_Missense_Mutation_p.F138L|SGK2_ENST00000485914.1_3'UTR	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	198	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCGGGCCAGGTTCTACGCTGC	0.627																																					p.F198L		.											.	SGK2-990	0			c.T592C						.						57	60	59					20																	42199308		2203	4300	6503	SO:0001583	missense	10110	exon6			GCCAGGTTCTACG	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.592T>C	20.37:g.42199308T>C	ENSP00000340608:p.Phe198Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	67	15	NM_016276	0	0	20	35	15	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	T	34	5.328708	0.95733	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.13	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75243	0.3823	L	0.59912	1.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.77448	-0.2584	10	0.62326	D	0.03	.	14.235	0.65919	0.0:0.0:0.0:1.0	.	164;198;138	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	L	138;138;137;137;138;198;164	ENSP00000362192:F138L;ENSP00000362184:F138L;ENSP00000362168:F137L;ENSP00000396222:F137L;ENSP00000392795:F138L;ENSP00000340608:F198L;ENSP00000412214:F164L	ENSP00000340608:F198L	F	+	1	0	SGK2	41632722	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.860000	0.86993	2.148000	0.66965	0.533000	0.62120	TTC	.		0.627	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			C	42199308	T	C	42199308	3	2	23	1	0	0	0	0	1	0	0	0	14241	1725	60	3	614	3	SGK2	20	42199308	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	5329999	42199308	20826212	106	2088											
SREBF2	6721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42289163	42289163	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagcctgtgtggccccgagCacagtgctgttcctgactcc	6	9	12	14	1	0	2	0	1	0	1	2	3	2	2	5	1	3	3	5	1	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr22:42289163C>A	ENST00000361204.4	+	12	2417	c.2251C>A	c.(2251-2253)Cac>Aac	p.H751N	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	751					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						TGGCCCCGAGCACAGTGCTGT	0.612																																					p.H751N		.											.	SREBF2-154	0			c.C2251A						.						77	77	77					22																	42289163		2203	4300	6503	SO:0001583	missense	6721	exon12			CCCGAGCACAGTG	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2251C>A	22.37:g.42289163C>A	ENSP00000354476:p.His751Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	78	41	NM_004599	0	0	10	21	11	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	C	5.682	0.310364	0.10733	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.07216	3.21	5.42	4.36	0.52297	.	0.494236	0.23861	N	0.043856	T	0.03959	0.0111	N	0.03608	-0.345	0.26458	N	0.975491	B	0.14438	0.01	B	0.11329	0.006	T	0.39440	-0.9614	10	0.14252	T	0.57	-3.4319	13.8968	0.63778	0.1516:0.8484:0.0:0.0	.	751	Q12772	SRBP2_HUMAN	N	751	ENSP00000354476:H751N	ENSP00000354476:H751N	H	+	1	0	SREBF2	40619109	0.993000	0.37304	0.234000	0.24042	0.412000	0.31113	2.219000	0.42899	2.543000	0.85770	0.650000	0.86243	CAC	.		0.612	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		A	42289163	C	A	42289163	3	1	23	1	0	0	0	0	1	0	0	0	15174	710	25	4	2297	4	SREBF2	22	42289163	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		42289163	9015403	107	2089											
MED14	9282	broad.mit.edu	37	chrX	40586008	40586008	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaactcaccgcacattttTccactttgccagcattatta	10	16	3	12	1	1	0	1	0	0	0	2	0	2	0	3	0	3	2	3	0	3	7			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chrX:40586008T>C	ENST00000324817.1	-	3	456	c.338A>G	c.(337-339)gAa>gGa	p.E113G		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	113					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGCACATTTTTCCACTTTGCC	0.328																																					p.E113G													.	MED14-289	0			c.A338G						.						50	46	47					X																	40586008		2203	4300	6503	SO:0001583	missense	9282	exon3			CATTTTTCCACTT	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.338A>G	X.37:g.40586008T>C	ENSP00000323720:p.Glu113Gly	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_004229	0	0	0	0	0	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	37	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.982017	0.74474	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.53077	0.1774	L	0.39633	1.23	0.80722	D	1	B	0.34349	0.45	B	0.39738	0.308	T	0.52442	-0.8575	9	0.35671	T	0.21	.	13.9069	0.63841	0.0:0.0:0.0:1.0	.	113	O60244	MED14_HUMAN	G	113	.	ENSP00000323720:E113G	E	-	2	0	MED14	40470952	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.519000	0.81809	1.809000	0.52856	0.441000	0.28932	GAA	.		0.328	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		C	40586008	T	C	40586008	3	2	23	1	0	0	0	0	1	0	0	0	9457	1783	62	3	4142	3	MED14	23	40586008	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10		40586008	114684552	108	2090											
TAS1R1	80835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6639633	6639633	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggactacacgaggcgctgcGgctccacctgaccagtgggt	8	6	14	13	3	0	1	0	1	0	0	1	3	1	2	3	4	2	2	3	4	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:6639633G>A	ENST00000333172.6	+	6	2708	c.2515G>A	c.(2515-2517)Ggc>Agc	p.G839S	ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000328191.4_3'UTR|TAS1R1_ENST00000351136.3_Missense_Mutation_p.G585S	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	839					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		GAGGCGCTGCGGCTCCACCTG	0.632																																					p.G839S		.											.	TAS1R1-516	0			c.G2515A						.						41	41	41					1																	6639633		2203	4299	6502	SO:0001583	missense	80835	exon6			CGCTGCGGCTCCA		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14448	protein-coding gene	gene with protein product		606225	"G protein-coupled receptor 70"	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.2515G>A	1.37:g.6639633G>A	ENSP00000331867:p.Gly839Ser	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	32	12	NM_138697	0	0	0	0	0	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	.	.	.	.	.	.	.	.	.	.	G	2.898	-0.228154	0.06022	.	.	ENSG00000173662	ENST00000333172;ENST00000351136	D;D	0.90900	-2.37;-2.75	5.18	-0.747	0.11091	.	0.840078	0.10725	N	0.641242	T	0.80188	0.4577	N	0.22421	0.69	0.18873	N	0.999982	B;B	0.18310	0.027;0.003	B;B	0.12156	0.007;0.004	T	0.64050	-0.6498	10	0.25751	T	0.34	.	5.538	0.17021	0.3891:0.1411:0.4698:0.0	.	585;839	Q7RTX1-2;Q7RTX1	.;TS1R1_HUMAN	S	839;585	ENSP00000331867:G839S;ENSP00000312558:G585S	ENSP00000331867:G839S	G	+	1	0	TAS1R1	6562220	0.000000	0.05858	0.059000	0.19551	0.071000	0.16799	-0.005000	0.12855	-0.027000	0.13873	-0.216000	0.12614	GGC	.		0.632	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			A	6639633	G	A	6639633	3	1	24	1	0	0	0	0	1	0	0	0	15594	1116	39	1	2537	1	TAS1R1	1	6639633	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		6639633	242610988	1	2091											
KIAA0467	23334	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	43902958	43902958	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgatccgagtccattcaCgcctcaaaatggggcccagc	9	8	10	14	2	2	1	2	1	0	0	4	2	4	1	4	2	1	0	4	2	2	1	rs534888615		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:43902958C>T	ENST00000562955.1	+	42	5980	c.5980C>T	c.(5980-5982)Cgc>Tgc	p.R1994C	SZT2_ENST00000372442.1_Missense_Mutation_p.R1152C	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2051					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						AGTCCATTCACGCCTCAAAAT	0.572													C|||	1	0.000199681	0	0	5008	,	,		19955	0.001		0	False		,,,				2504	0				p.R1994C													.	SZT2-144	0			c.C5980T						.						97	96	96					1																	43902958		2203	4300	6503	SO:0001583	missense	23334	exon42			CATTCACGCCTCA	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"seizure threshold 2 homolog A (mouse)", "seizure threshold 2 homolog B (mouse)"	615463	"chromosome 1 open reading frame 84", "KIAA0467"	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.5980C>T	1.37:g.43902958C>T	ENSP00000457168:p.Arg1994Cys	Somatic	123	1		WXS	Illumina HiSeq	Phase_I	107	52	NM_015284	0	0	0	4	4	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584433	0.86748	.	.	ENSG00000198198	ENST00000372442	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.78604	0.4309	L	0.57536	1.79	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.78137	-0.2321	9	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1994	Q5T011-5	.	C	1152	.	ENSP00000361519:R1152C	R	+	1	0	SZT2	43675545	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.735000	0.84939	2.884000	0.98904	0.655000	0.94253	CGC	.		0.572	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43902958	C	T	43902958	3	4	24	1	0	0	0	0	1	0	0	0	8199	536	19	1	3556	1	KIAA0467	1	43902958	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	37263325	43902958	205347663	2	2092											
NOTCH2	4853	bcgsc.ca	37	chr1	120539926	120539926	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atttgcacagggatgagacaGgcaggcatccgtccattggc	10	8	13	10	1	0	1	0	1	0	1	2	3	2	2	2	4	1	3	2	4	0	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:120539926G>C	ENST00000256646.2	-	4	664	c.445C>G	c.(445-447)Ctg>Gtg	p.L149V	NOTCH2_ENST00000602566.1_Missense_Mutation_p.L110V	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	149	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGATGAGACAGGCAGGCATCC	0.498			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.L149V				Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2-1441	0			c.C445G						.						123	98	107					1																	120539926		2201	4299	6500	SO:0001583	missense	4853	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GAGACAGGCAGGC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.445C>G	1.37:g.120539926G>C	ENSP00000256646:p.Leu149Val	Somatic	350	3		WXS	Illumina HiSeq	Phase_1	362	33	NM_024408	0	0	0	0	0	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.493005	0.26774	.	.	ENSG00000134250	ENST00000256646;ENST00000539617;ENST00000401649;ENST00000369342	T	0.50548	0.74	5.71	4.61	0.57282	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.29799	U	0.011171	T	0.31231	0.0790	N	0.25957	0.775	0.33759	D	0.621659	P;B;P	0.45715	0.698;0.248;0.865	B;B;P	0.60012	0.338;0.206;0.867	T	0.20538	-1.0272	10	0.20046	T	0.44	.	4.9587	0.14056	0.0883:0.1371:0.6152:0.1595	.	110;149;149	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	V	149;110;122;110	ENSP00000256646:L149V	ENSP00000256646:L149V	L	-	1	2	NOTCH2	120341449	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.758000	0.38410	2.686000	0.91538	0.585000	0.79938	CTG	.		0.498	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		C	120539926	G	C	120539926	3	2	24	1	0	0	0	0	1	0	0	0	10574	991	35	4	7094	4	NOTCH2	1	120539926	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	76636968	120539926	128710695	3	2093											
RORC	6097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151785765	151785765	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgccttcaaaaaagaccGtgcggttgtcagcattgtag	11	12	10	8	2	2	1	2	0	0	1	2	1	2	1	2	1	3	3	2	1	4	5			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:151785765G>A	ENST00000318247.6	-	8	1231	c.1124C>T	c.(1123-1125)aCg>aTg	p.T375M	RORC_ENST00000356728.6_Missense_Mutation_p.T354M|RORC_ENST00000480719.1_5'UTR|RORC_ENST00000392697.3_Missense_Mutation_p.T429M	NM_005060.3	NP_005051.2	P51449	RORG_HUMAN	RAR-related orphan receptor C	375	Ligand-binding.				adipose tissue development (GO:0060612)|cellular response to sterol (GO:0036315)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lymph node development (GO:0048535)|negative regulation of thymocyte apoptotic process (GO:0070244)|Peyer's patch development (GO:0048541)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of fat cell differentiation (GO:0045598)|regulation of gamma-delta T cell differentiation (GO:0045586)|regulation of glucose metabolic process (GO:0010906)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|T cell differentiation in thymus (GO:0033077)|T-helper 17 cell differentiation (GO:0072539)|T-helper cell differentiation (GO:0042093)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|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)			autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AAAAAAGACCGTGCGGTTGTC	0.557																																					p.T375M		.											.	RORC-227	0			c.C1124T						.						236	234	235					1																	151785765		2203	4300	6503	SO:0001583	missense	6097	exon8			AAGACCGTGCGGT	U16997	CCDS1004.1, CCDS30856.1	1q21	2013-01-16			ENSG00000143365	ENSG00000143365		"Nuclear hormone receptors"	10260	protein-coding gene	gene with protein product		602943				7811290	Standard	NM_005060		Approved	RZRG, RORG, NR1F3, TOR	uc001ezh.3	P51449	OTTHUMG00000013053	ENST00000318247.6:c.1124C>T	1.37:g.151785765G>A	ENSP00000327025:p.Thr375Met	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	97	41	NM_005060	0	0	7	13	6	Q5SZR9|Q8N5V7|Q8NCY8	Missense_Mutation	SNP	ENST00000318247.6	37	CCDS1004.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.478730	0.84747	.	.	ENSG00000143365	ENST00000356728;ENST00000392697;ENST00000318247	D;D;D	0.96427	-4.01;-4.01;-4.01	4.62	4.62	0.57501	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.64402	U	0.000012	D	0.97532	0.9192	M	0.71920	2.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	D	0.98360	1.0548	10	0.87932	D	0	.	16.1933	0.82006	0.0:0.0:1.0:0.0	.	375;429;375;354	B6ZGS6;B4DPR1;P51449;F1D8P6	.;.;RORG_HUMAN;.	M	354;429;375	ENSP00000349164:T354M;ENSP00000376461:T429M;ENSP00000327025:T375M	ENSP00000327025:T375M	T	-	2	0	RORC	150052389	1.000000	0.71417	0.997000	0.53966	0.914000	0.54420	9.469000	0.97679	2.391000	0.81399	0.563000	0.77884	ACG	.		0.557	RORC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036626.1			A	151785765	G	A	151785765	3	1	24	1	0	0	0	0	1	0	0	0	13562	1145	40	1	448	1	RORC	1	151785765	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	31245839	151785765	97464856	4	2094											
FASLG	356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	172634980	172634980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatccccaggatctggtgAtgatggaggggaagatgatg	11	9	16	5	0	1	4	0	3	1	1	2	7	2	7	2	5	0	1	2	5	2	1	rs111238176		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:172634980A>G	ENST00000367721.2	+	4	854	c.670A>G	c.(670-672)Atg>Gtg	p.M224V	FASLG_ENST00000340030.3_3'UTR	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	224					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						GGATCTGGTGATGATGGAGGG	0.507																																					p.M224V	Ovarian(28;486 876 30334 44033)	.											.	FASLG-618	0			c.A670G						.						107	102	104					1																	172634980		2203	4300	6503	SO:0001583	missense	356	exon4			CTGGTGATGATGG	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"Tumor necrosis factor (ligand) superfamily", "CD molecules", "Endogenous ligands"	11936	protein-coding gene	gene with protein product		134638	"tumor necrosis factor (ligand) superfamily, member 6"	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.670A>G	1.37:g.172634980A>G	ENSP00000356694:p.Met224Val	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	103	46	NM_000639	0	0	0	0	0	Q9BZP9	Missense_Mutation	SNP	ENST00000367721.2	37	CCDS1304.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.431408	0.43122	.	.	ENSG00000117560	ENST00000367721	D	0.94457	-3.43	5.34	4.41	0.53225	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.257132	0.32624	N	0.005854	T	0.78033	0.4220	N	0.02539	-0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.75068	-0.3448	10	0.66056	D	0.02	-4.9683	13.2687	0.60150	0.1797:0.8202:0.0:0.0	.	224	P48023	TNFL6_HUMAN	V	224	ENSP00000356694:M224V	ENSP00000356694:M224V	M	+	1	0	FASLG	170901603	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.680000	0.25306	1.203000	0.43233	0.528000	0.53228	ATG	A|0.500;G|0.500		0.507	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1			G	172634980	A	G	172634980	3	3	24	1	0	0	0	0	1	0	0	0	5701	333	12	3	684	3	FASLG	1	172634980	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	20849215	172634980	76615641	5	2095											
SEC16B	89866	broad.mit.edu	37	chr1	177902408	177902408	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggggatgcgttcttggtggGcttcgatcgaaaccagctga	7	10	16	8	3	1	1	0	1	1	0	3	4	1	2	1	4	3	3	1	4	1	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:177902408G>T	ENST00000308284.6	-	22	2853	c.2764C>A	c.(2764-2766)Ccc>Acc	p.P922T	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000495165.1_5'UTR	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	922					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						TTCTTGGTGGGCTTCGATCGA	0.577																																					p.P922T													.	SEC16B-93	0			c.C2764A						.						30	38	35					1																	177902408		1977	4172	6149	SO:0001583	missense	89866	exon22			TGGTGGGCTTCGA	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"regucalcin gene promotor region related protein"	612855	"leucine zipper transcription regulator 2"	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2764C>A	1.37:g.177902408G>T	ENSP00000308339:p.Pro922Thr	Somatic	136	2		WXS	Illumina HiSeq	Phase_I	160	9	NM_033127	0	0	14	14	0	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.433855	0.43224	.	.	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.21543	2.0	5.65	4.73	0.59995	.	0.084911	0.51477	D	0.000082	T	0.41259	0.1151	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;P;D	0.85130	0.997;0.997;0.895;0.997	T	0.17440	-1.0369	10	0.62326	D	0.03	-20.473	9.517	0.39111	0.0931:0.0:0.9069:0.0	.	477;923;922;619	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	T	922;606;637	ENSP00000308339:P922T	ENSP00000239472:P637T	P	-	1	0	AL359075.1	176169031	1.000000	0.71417	0.987000	0.45799	0.049000	0.14656	3.299000	0.51826	2.659000	0.90383	0.655000	0.94253	CCC	.		0.577	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		T	177902408	G	T	177902408	3	4	24	1	0	0	0	0	1	0	0	0	14019	1203	42	4	438	4	SEC16B	1	177902408	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	5267428	177902408	71348213	6	2096											
PIGR	5284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207112530	207112530	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgcccaggccacacttgtAgcgcccggagtcatcctggc	7	7	12	15	2	1	0	1	0	0	0	2	2	2	1	4	3	2	1	4	3	1	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:207112530A>G	ENST00000356495.4	-	3	505	c.322T>C	c.(322-324)Tac>Cac	p.Y108H		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	108	Ig-like V-type 1.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CCACACTTGTAGCGCCCGGAG	0.577																																					p.Y108H		.											.	PIGR-92	0			c.T322C						.						75	64	68					1																	207112530		2203	4300	6503	SO:0001583	missense	5284	exon3			ACTTGTAGCGCCC		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.322T>C	1.37:g.207112530A>G	ENSP00000348888:p.Tyr108His	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	158	56	NM_002644	0	0	14	32	18	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035080	0.75617	.	.	ENSG00000162896	ENST00000356495	D	0.94537	-3.45	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	D	0.97939	0.9322	H	0.95004	3.61	0.44890	D	0.997906	D	0.89917	1.0	D	0.97110	1.0	D	0.98953	1.0795	10	0.87932	D	0	-20.6353	13.9439	0.64073	1.0:0.0:0.0:0.0	.	108	P01833	PIGR_HUMAN	H	108	ENSP00000348888:Y108H	ENSP00000348888:Y108H	Y	-	1	0	PIGR	205179153	1.000000	0.71417	0.979000	0.43373	0.686000	0.39977	5.514000	0.67043	2.288000	0.76882	0.533000	0.62120	TAC	.		0.577	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		G	207112530	A	G	207112530	3	3	24	1	0	0	0	0	1	0	0	0	11923	420	15	3	2008	3	PIGR	1	207112530	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	29210122	207112530	42138091	7	2097											
RAB3GAP2	25782	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	220324630	220324630	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atatggcttccacagcttcaAtgaggtgtaaggctagacca	12	10	10	9	0	1	2	1	1	0	1	2	2	2	2	2	3	1	4	2	3	4	5	rs376300719		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:220324630A>G	ENST00000358951.2	-	35	4261	c.4145T>C	c.(4144-4146)aTt>aCt	p.I1382T		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	1382					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		CACAGCTTCAATGAGGTGTAA	0.348																																					p.I1382T		.											.	RAB3GAP2-90	0			c.T4145C						.	A	THR/ILE	0,4406		0,0,2203	115	113	114		4145	0.9	0	1		114	1,8599	1.2+/-3.3	0,1,4299	no	missense	RAB3GAP2	NM_012414.3	89	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	1382/1394	220324630	1,13005	2203	4300	6503	SO:0001583	missense	25782	exon35			GCTTCAATGAGGT	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.4145T>C	1.37:g.220324630A>G	ENSP00000351832:p.Ile1382Thr	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	113	8	NM_012414	0	0	1	1	0	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	A	11.29	1.596066	0.28445	0.0	1.16E-4	ENSG00000118873	ENST00000358951	T	0.32753	1.44	5.84	0.898	0.19264	.	0.368085	0.29286	N	0.012581	T	0.23210	0.0561	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.19516	-1.0303	10	0.52906	T	0.07	.	8.7515	0.34618	0.7065:0.0:0.2935:0.0	.	1382	Q9H2M9	RBGPR_HUMAN	T	1382	ENSP00000351832:I1382T	ENSP00000351832:I1382T	I	-	2	0	RAB3GAP2	218391253	0.956000	0.32656	0.003000	0.11579	0.894000	0.52154	2.838000	0.48199	0.145000	0.18977	0.533000	0.62120	ATT	.		0.348	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		G	220324630	A	G	220324630	3	3	24	1	0	0	0	0	1	0	0	0	12968	101	4	3	40	3	RAB3GAP2	1	220324630	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	13212100	220324630	28925991	8	2098											
DISC1	27185	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	231931003	231931003	+	Frame_Shift_Del	DEL	A	A	-																															tccagcctccaggaaagaatAaaatccctcaacttgtcact																										TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:231931003delA	ENST00000602281.1	+	7	1703	c.1650delA	c.(1648-1650)atafs	p.I550fs	DISC1_ENST00000535983.1_Frame_Shift_Del_p.I550fs|DISC1_ENST00000537876.1_Intron|DISC1_ENST00000539444.1_Frame_Shift_Del_p.I550fs|DISC1_ENST00000439617.2_Frame_Shift_Del_p.I550fs|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000366636.4_Frame_Shift_Del_p.I550fs|DISC1_ENST00000366633.3_Frame_Shift_Del_p.I550fs|DISC1_ENST00000366637.3_5'UTR	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	550	Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.|Required for localization to punctate cytoplasmic foci.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				AGGAAAGAATAAAATCCCTCA	0.358																																					p.I582fs		.											.	DISC1-91	0			c.1746delA						.						84	85	85					1																	231931003		2203	4300	6503	SO:0001589	frameshift_variant	27185	exon8			.	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1650delA	1.37:g.231931003delA	ENSP00000473425:p.Ile550fs	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	59	27	NM_001164537	0	0	0	0	0	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Frame_Shift_Del	DEL	ENST00000602281.1	37	CCDS59205.1																																																																																			.		0.358	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		-	231931003	A	-	231931003	7	5	24	1	0	1	0	1	0	0	0	0	4549	352	13	0	2049	0	DISC1	1	231931003	Frame_Shift_Del	DEL	A	TCGA-A4-A5DU-01A-11D-A28G-10	11606373	231931003	17319618	9	2099											
GALNT14	79623	broad.mit.edu	37	chr2	31154974	31154974	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tccatcagggaaaacgtaggGgtgcttcttccggaagacgt	10	9	13	9	3	2	1	1	0	1	1	4	3	4	3	2	4	2	2	2	4	4	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:31154974G>T	ENST00000349752.5	-	10	1657	c.1018C>A	c.(1018-1020)Ccc>Acc	p.P340T	GALNT14_ENST00000420311.2_Missense_Mutation_p.P305T|GALNT14_ENST00000324589.5_Missense_Mutation_p.P345T|GALNT14_ENST00000356174.3_Missense_Mutation_p.P307T|GALNT14_ENST00000406653.1_Missense_Mutation_p.P320T|GALNT14_ENST00000486564.1_5'UTR	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	340					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					AAAACGTAGGGGTGCTTCTTC	0.602																																					p.P345T													.	GALNT14-93	0			c.C1033A						.						93	86	88					2																	31154974		2203	4300	6503	SO:0001583	missense	79623	exon11			CGTAGGGGTGCTT	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"Glycosyltransferase family 2 domain containing"	22946	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 14"	608225	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.1018C>A	2.37:g.31154974G>T	ENSP00000288988:p.Pro340Thr	Somatic	61	1		WXS	Illumina HiSeq	Phase_I	107	5	NM_001253826	0	0	50	50	0	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	G	27.3	4.819624	0.90873	.	.	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311;ENST00000430167	T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.92509	0.7621	M	0.93420	3.415	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;0.999	D	0.94523	0.7729	10	0.87932	D	0	.	18.2582	0.90025	0.0:0.0:1.0:0.0	.	305;307;345;340;320	F5H263;Q96FL9-2;Q96FL9-3;Q96FL9;B3KV89	.;.;.;GLT14_HUMAN;.	T	340;345;320;307;305;307	ENSP00000288988:P340T;ENSP00000314500:P345T;ENSP00000385435:P320T;ENSP00000348497:P307T;ENSP00000415514:P305T;ENSP00000406399:P307T	ENSP00000314500:P345T	P	-	1	0	GALNT14	31008478	1.000000	0.71417	0.990000	0.47175	0.874000	0.50279	9.869000	0.99810	2.315000	0.78130	0.561000	0.74099	CCC	.		0.602	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572		T	31154974	G	T	31154974	3	4	24	1	0	0	0	0	1	0	0	0	6232	1232	43	4	664	4	GALNT14	2	31154974	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		31154974	212044399	10	2100											
PPM1B	5495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44457731	44457731	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagctgccacagctacttcTtcgaacagtgatgctggaaa	11	9	9	12	1	1	1	0	1	1	0	2	3	1	2	2	1	6	3	2	1	3	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:44457731T>C	ENST00000282412.4	+	6	1726	c.1314T>C	c.(1312-1314)tcT>tcC	p.S438S	PPM1B_ENST00000378540.4_Intron|PPM1B_ENST00000345249.4_Silent_p.S151S|PPM1B_ENST00000409432.3_3'UTR|PPM1B_ENST00000378551.2_Intron	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	438					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CAGCTACTTCTTCGAACAGTG	0.473																																					p.S438S		.											.	PPM1B-227	0			c.T1314C						.						76	74	75					2																	44457731		2203	4300	6503	SO:0001819	synonymous_variant	5495	exon6			TACTTCTTCGAAC	AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9276	protein-coding gene	gene with protein product	"protein phosphatase 2C, beta isoform"	603770	"protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.1314T>C	2.37:g.44457731T>C		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	197	131	NM_002706	0	0	5	19	14	Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Silent	SNP	ENST00000282412.4	37	CCDS1817.1																																																																																			.		0.473	PPM1B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250672.1	NM_002706		C	44457731	T	C	44457731	2	2	24	1	0	0	0	0	0	0	0	1	12365	1596	56	3		3	PPM1B	2	44457731	Silent	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10	13302757	44457731	198741642	11	2101											
PRKCE	5581	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	45879246	45879246	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccgccccgaccatggtaGtgttcaatggccttcttaag	7	11	9	14	2	2	0	1	0	1	0	3	1	3	0	6	2	0	2	6	2	3	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:45879246G>C	ENST00000306156.3	+	1	334	c.7G>C	c.(7-9)Gtg>Ctg	p.V3L		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	3	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	GACCATGGTAGTGTTCAATGG	0.652																																					p.V3L		.											.	PRKCE-1019	0			c.G7C						.						31	36	35					2																	45879246		2196	4297	6493	SO:0001583	missense	5581	exon1			ATGGTAGTGTTCA		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.7G>C	2.37:g.45879246G>C	ENSP00000306124:p.Val3Leu	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	55	28	NM_005400	0	0	1	1	0	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Missense_Mutation	SNP	ENST00000306156.3	37	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.565679	0.65651	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	T;T	0.08458	3.09;3.09	4.71	4.71	0.59529	C2 membrane targeting protein (1);C2 calcium/lipid-binding domain, CaLB (1);	0.080242	0.47852	D	0.000211	T	0.09202	0.0227	L	0.40543	1.245	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.19192	-1.0313	10	0.20519	T	0.43	.	17.673	0.88224	0.0:0.0:1.0:0.0	.	3	Q02156	KPCE_HUMAN	L	3	ENSP00000394574:V3L;ENSP00000306124:V3L	ENSP00000306124:V3L	V	+	1	0	PRKCE	45732750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.766000	0.98957	2.152000	0.67230	0.561000	0.74099	GTG	.		0.652	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			C	45879246	G	C	45879246	3	2	24	1	0	0	0	0	1	0	0	0	12540	1029	36	4	9	4	PRKCE	2	45879246	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	1421515	45879246	197320127	12	2102											
ABCA12	26154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	215865727	215865727	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gtgccagcttctgttagaagGaagcttaaaaataacaccta	15	10	8	8	0	1	1	0	0	1	1	1	2	1	2	2	1	4	3	2	1	8	5			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:215865727G>C	ENST00000272895.7	-	22	3100	c.2881C>G	c.(2881-2883)Cct>Gct	p.P961A	ABCA12_ENST00000389661.4_Missense_Mutation_p.P643A	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	961					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTGTTAGAAGGAAGCTTAAAA	0.403																																					p.P961A	Ovarian(66;664 1488 5121 34295)	.											.	ABCA12-99	0			c.C2881G						.						55	58	57					2																	215865727		2202	4300	6502	SO:0001583	missense	26154	exon22			TAGAAGGAAGCTT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.2881C>G	2.37:g.215865727G>C	ENSP00000272895:p.Pro961Ala	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_173076	0	0	0	0	0	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749673	0.69533	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.86627	-2.15;-2.15	5.9	5.9	0.94986	.	0.627251	0.15788	N	0.244589	D	0.92221	0.7533	L	0.46947	1.48	0.80722	D	1	D;D	0.89917	1.0;0.984	D;P	0.87578	0.998;0.885	D	0.91505	0.5222	10	0.59425	D	0.04	.	20.2664	0.98460	0.0:0.0:1.0:0.0	.	961;643	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	A	961;643	ENSP00000272895:P961A;ENSP00000374312:P643A	ENSP00000272895:P961A	P	-	1	0	ABCA12	215573972	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.627000	0.67784	2.786000	0.95864	0.561000	0.74099	CCT	.		0.403	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215865727	G	C	215865727	3	2	24	1	0	0	0	0	1	0	0	0	30	1174	41	4	5034	4	ABCA12	2	215865727	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	169986481	215865727	27333646	13	2103											
TNS1	7145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	218713569	218713569	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcccgcttctcctggggactCaaggcagcagtggcactgga	7	8	13	13	1	2	0	1	0	1	0	4	2	3	2	2	5	1	4	2	5	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:218713569C>G	ENST00000171887.4	-	17	1748	c.1296G>C	c.(1294-1296)ttG>ttC	p.L432F	TNS1_ENST00000430930.1_Missense_Mutation_p.L432F|TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000419504.1_Missense_Mutation_p.L432F	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	432					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CCTGGGGACTCAAGGCAGCAG	0.642																																					p.L432F		.											.	TNS1-156	0			c.G1296C						.						64	67	66					2																	218713569		2203	4300	6503	SO:0001583	missense	7145	exon17			GGGACTCAAGGCA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1296G>C	2.37:g.218713569C>G	ENSP00000171887:p.Leu432Phe	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	125	47	NM_022648	0	0	6	10	4	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454564	0.43634	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.95447	-3.48;-3.47;-3.49;-3.71	4.79	3.9	0.45041	.	0.172150	0.40469	N	0.001094	D	0.96929	0.8997	M	0.76328	2.33	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.996;1.0;0.999;0.999	D;D;D;D;D	0.85130	0.997;0.943;0.974;0.994;0.981	D	0.96213	0.9154	10	0.46703	T	0.11	.	10.7558	0.46237	0.0:0.8443:0.0:0.1557	.	432;486;432;432;432	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	F	432;432;432;557	ENSP00000171887:L432F;ENSP00000408724:L432F;ENSP00000406016:L432F;ENSP00000405460:L557F	ENSP00000171887:L432F	L	-	3	2	TNS1	218421814	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	1.405000	0.34635	1.227000	0.43598	0.561000	0.74099	TTG	.		0.642	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218713569	C	G	218713569	3	3	24	1	0	0	0	0	1	0	0	0	16375	825	29	4	3979	4	TNS1	2	218713569	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	2847842	218713569	24485804	14	2104											
NISCH	11188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52526011	52526011	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgagccagagaaggcccCagccctcagcatcctgctgt	8	6	12	15	0	1	2	1	1	0	1	2	3	2	2	5	2	4	3	5	2	1	0	rs369447186		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr3:52526011C>T	ENST00000479054.1	+	22	4100	c.4028C>T	c.(4027-4029)cCa>cTa	p.P1343L	NISCH_ENST00000345716.4_Missense_Mutation_p.P1343L			Q9Y2I1	NISCH_HUMAN	nischarin	1343					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	GAGAAGGCCCCAGCCCTCAGC	0.627																																					p.P1343L		.											.	NISCH-93	0			c.C4028T						.	C	LEU/PRO	0,4406		0,0,2203	71	73	72		4028	4.7	0.1	3		72	2,8598	2.2+/-6.3	0,2,4298	no	missense	NISCH	NM_007184.3	98	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	1343/1505	52526011	2,13004	2203	4300	6503	SO:0001583	missense	11188	exon21			AGGCCCCAGCCCT	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.4028C>T	3.37:g.52526011C>T	ENSP00000418232:p.Pro1343Leu	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	137	36	NM_007184	0	0	21	33	12	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	37	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744827	0.49151	0.0	2.33E-4	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000414197	T;T	0.07908	3.15;3.15	5.6	4.7	0.59300	.	0.353140	0.30277	N	0.009998	T	0.07458	0.0188	N	0.24115	0.695	0.09310	N	0.999995	B	0.06786	0.001	B	0.09377	0.004	T	0.24728	-1.0152	10	0.62326	D	0.03	-9.2061	14.0883	0.64973	0.4654:0.5346:0.0:0.0	.	1343	Q9Y2I1	NISCH_HUMAN	L	1343;1343;267;687	ENSP00000418232:P1343L;ENSP00000339958:P1343L	ENSP00000339958:P1343L	P	+	2	0	NISCH	52501051	0.002000	0.14202	0.052000	0.19188	0.991000	0.79684	1.108000	0.31123	1.309000	0.44985	0.491000	0.48974	CCA	.		0.627	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52526011	C	T	52526011	3	4	24	1	0	0	0	0	1	0	0	0	10458	594	21	2	4110	2	NISCH	3	52526011	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		52526011	145496419	15	2105											
ZNF721	170960	hgsc.bcm.edu;bcgsc.ca	37	chr4	436799	436801	+	In_Frame_Del	DEL	GAG	GAG	-																															tcttatgtttagcaaagcttGaggatgaggtaatgactttg																										TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr4:436799_436801delGAG	ENST00000338977.5	-	2	1467_1469	c.1419_1421delCTC	c.(1417-1422)tcctca>tca	p.473_474SS>S	ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_In_Frame_Del_p.485_486SS>S|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGCAAAGCTTGAGGATGAGGTAA	0.369																																					p.485_486del		.											.	ZNF721-47	0			c.1455_1457del						.			2,3976		1,0,1988						0.4	0.1			78	1,8109		0,1,4054	no	coding	ZNF721	NM_133474.2		1,1,6042	A1A1,A1R,RR		0.0123,0.0503,0.0248				3,12085				SO:0001651	inframe_deletion	170960	exon3			.	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1419_1421delCTC	4.37:g.436799_436801delGAG	ENSP00000340524:p.Ser475del	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	80	23	NM_133474	0	0	0	0	0	Q69YG7	In_Frame_Del	DEL	ENST00000338977.5	37																																																																																				.		0.369	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		-	436801	GAG	-	436799	7	5	24	1	0	1	0	1	0	0	0	0	18154	1294	45	0	1318	0	ZNF721	4	436799	In_Frame_Del	DEL	GAG	TCGA-A4-A5DU-01A-11D-A28G-10		436799	190717477	16	2106											
CC2D2A	57545	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	15552558	15552558	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctactgaagaagtggagtttAgcagtaatcagcatgtgaca	14	10	11	6	0	1	3	1	2	0	1	1	4	1	4	0	1	3	4	0	1	5	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr4:15552558A>G	ENST00000503292.1	+	19	2473	c.2293A>G	c.(2293-2295)Agc>Ggc	p.S765G	CC2D2A_ENST00000389652.5_Missense_Mutation_p.S716G|CC2D2A_ENST00000424120.1_Missense_Mutation_p.S765G|CC2D2A_ENST00000413206.1_Missense_Mutation_p.S765G	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	765					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						AGTGGAGTTTAGCAGTAATCA	0.453																																					p.S765G													.	CC2D2A-25	0			c.A2293G						.						99	91	94					4																	15552558		1929	4162	6091	SO:0001583	missense	57545	exon19			GAGTTTAGCAGTA	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.2293A>G	4.37:g.15552558A>G	ENSP00000421809:p.Ser765Gly	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	67	31	NM_001080522	0	0	0	4	4	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	37	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702496	0.88924	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000503292;ENST00000389652	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	5.3	5.3	0.74995	.	0.091915	0.85682	D	0.000000	T	0.74261	0.3693	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77603	-0.2526	10	0.87932	D	0	.	15.2238	0.73333	1.0:0.0:0.0:0.0	.	765;716	Q9P2K1;Q9P2K1-2	C2D2A_HUMAN;.	G	765;765;716;716;765;716	ENSP00000403465:S765G;ENSP00000398391:S765G;ENSP00000421809:S765G;ENSP00000374303:S716G	ENSP00000374303:S716G	S	+	1	0	CC2D2A	15161656	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.979000	0.93455	2.013000	0.59113	0.460000	0.39030	AGC	.		0.453	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		G	15552558	A	G	15552558	3	3	24	1	0	0	0	0	1	0	0	0	2734	420	15	3	2562	3	CC2D2A	4	15552558	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	15115759	15552558	175601718	17	2107											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537224	88537232	+	In_Frame_Del	DEL	ACAGCAGCA	ACAGCAGCA	-																															cgacagcagtgatagcagtgAcagcagcaacagcagtgaca																								rs201608130|rs140656082|rs200679221|rs564674887	byFrequency	TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	ACAGCAGCA	ACAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr4:88537224_88537232delACAGCAGCA	ENST00000282478.7	+	4	3443_3451	c.3410_3418delACAGCAGCA	c.(3409-3420)gacagcagcaac>gac	p.SSN1138del	DSPP_ENST00000399271.1_In_Frame_Del_p.SSN1138del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1138	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gatagcagtgacagcagcaacagcagtga	0.569																																					p.1137_1140del		.											.	DSPP-90	0			c.3410_3418del						.																																			SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3410_3418delACAGCAGCA	4.37:g.88537224_88537232delACAGCAGCA	ENSP00000282478:p.Ser1138_Asn1140del	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	250	114	NM_014208	0	0	0	0	0	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.569	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537232	ACAGCAGCA	-	88537224	7	5	24	1	0	1	0	1	0	0	0	0	4793	275	10	0	3424	0	DSPP	4	88537224	In_Frame_Del	DEL	ACAGCAGCA	TCGA-A4-A5DU-01A-11D-A28G-10	72984666	88537224	102617052	18	2108											
IL6ST	3572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	55237637	55237637	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatacatttgatcttttgaaTtaaaattgtgctaaggaaga	16	15	7	3	0	1	3	0	2	1	1	1	4	1	4	0	1	2	1	0	1	7	7			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr5:55237637T>A	ENST00000381298.2	-	17	2342	c.2030A>T	c.(2029-2031)aAt>aTt	p.N677I	IL6ST_ENST00000381294.3_Missense_Mutation_p.N616I|IL6ST_ENST00000502326.3_Missense_Mutation_p.N677I|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.N677I|IL6ST_ENST00000381293.2_Missense_Mutation_p.I190F|IL6ST_ENST00000381286.3_Missense_Mutation_p.I53F|IL6ST_ENST00000536319.1_3'UTR|CTD-2031P19.5_ENST00000576302.1_RNA	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	677					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ATCTTTTGAATTAAAATTGTG	0.343			O		hepatocellular ca																																p.N677I		.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST-290	0			c.A2030T						.						43	47	46					5																	55237637		2199	4298	6497	SO:0001583	missense	3572	exon17			TTTGAATTAAAAT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.2030A>T	5.37:g.55237637T>A	ENSP00000370698:p.Asn677Ile	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	135	55	NM_002184	0	0	0	0	0	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.125|9.125	1.009945|1.009945	0.19277|0.19277	.|.	.|.	ENSG00000134352|ENSG00000134352	ENST00000381293;ENST00000381286|ENST00000381298;ENST00000336909;ENST00000381294	T;T|T;T;T	0.56611|0.40225	1.87;0.45|1.31;1.31;1.04	5.68|5.68	1.97|1.97	0.26223|0.26223	.|.	.|0.501171	.|0.23920	.|N	.|0.043246	T|T	0.37732|0.37732	0.1014|0.1014	N|N	0.19112|0.19112	0.55|0.55	0.41896|0.41896	D|D	0.990396|0.990396	P|P;D;P	0.39216|0.60160	0.664|0.822;0.987;0.822	B|B;P;P	0.36030|0.56216	0.216|0.406;0.794;0.534	T|T	0.03608|0.03608	-1.1020|-1.1020	9|10	0.87932|0.22706	D|T	0|0.39	.|.	11.3078|11.3078	0.49345|0.49345	0.0:0.2696:0.0:0.7304|0.0:0.2696:0.0:0.7304	.|.	190|677;616;677	Q5FC05|Q17RA0;Q5FC04;P40189	.|.;.;IL6RB_HUMAN	F|I	190;53|677;677;616	ENSP00000370693:I190F;ENSP00000370686:I53F|ENSP00000370698:N677I;ENSP00000338799:N677I;ENSP00000370694:N616I	ENSP00000370686:I53F|ENSP00000338799:N677I	I|N	-|-	1|2	0|0	IL6ST|IL6ST	55273394|55273394	0.905000|0.905000	0.30787|0.30787	0.932000|0.932000	0.37286|0.37286	0.603000|0.603000	0.37013|0.37013	0.092000|0.092000	0.15066|0.15066	-0.059000|-0.059000	0.13154|0.13154	-1.162000|-1.162000	0.01777|0.01777	ATT|AAT	.		0.343	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		A	55237637	T	A	55237637	3	1	24	1	0	0	0	0	1	0	0	0	7724	1493	52	5	730	5	IL6ST	5	55237637	Missense_Mutation	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10		55237637	125677623	19	2109											
ZNF474	133923	broad.mit.edu	37	chr5	121487938	121487938	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cggaaagccagcttagccccCctgtgatcccggcccgcagg	7	5	12	17	3	0	1	0	1	0	0	1	2	1	2	6	3	3	2	6	3	2	1	rs143759385	byFrequency	TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr5:121487938C>T	ENST00000296600.4	+	2	636	c.253C>T	c.(253-255)Cct>Tct	p.P85S	CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA|ZNF474_ENST00000514925.1_Intron	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	85							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		GCTTAGCCCCCCTGTGATCCC	0.478																																					p.P85S													.	ZNF474-90	0			c.C253T						.						82	94	90					5																	121487938		2203	4300	6503	SO:0001583	missense	133923	exon2			AGCCCCCCTGTGA	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"Zinc fingers, C2H2-type"	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.253C>T	5.37:g.121487938C>T	ENSP00000296600:p.Pro85Ser	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	48	3	NM_207317	0	0	0	0	0	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.737799	0.30774	.	.	ENSG00000164185	ENST00000296600	T	0.55052	0.54	5.58	5.58	0.84498	.	0.000000	0.48286	U	0.000193	T	0.47581	0.1453	L	0.36672	1.1	0.48511	D	0.999669	P	0.36438	0.553	B	0.35899	0.213	T	0.47686	-0.9098	10	0.49607	T	0.09	-13.0415	19.1747	0.93599	0.0:1.0:0.0:0.0	.	85	Q6S9Z5	ZN474_HUMAN	S	85	ENSP00000296600:P85S	ENSP00000296600:P85S	P	+	1	0	ZNF474	121515837	0.995000	0.38212	0.967000	0.41034	0.012000	0.07955	5.490000	0.66881	2.624000	0.88883	0.655000	0.94253	CCT	C|1.000;G|0.000		0.478	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		T	121487938	C	T	121487938	3	4	24	1	0	0	0	0	1	0	0	0	17964	623	22	2	255	2	ZNF474	5	121487938	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	66250301	121487938	59427322	20	2110											
BAT3	7917	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31612378	31612378	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaccaggctgtgtgccagaAtctgggcagggagacagaga	11	5	15	10	0	1	3	0	0	1	3	1	5	1	3	3	3	1	2	3	3	1	0			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr6:31612378A>T	ENST00000375964.6	-	11	1702	c.1389T>A	c.(1387-1389)gaT>gaA	p.D463E	BAG6_ENST00000211379.5_Splice_Site_p.D457E|BAG6_ENST00000404765.2_Splice_Site_p.D457E|BAG6_ENST00000375976.4_Splice_Site_p.D457E|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000362049.6_Splice_Site_p.D457E|BAG6_ENST00000439687.2_Splice_Site_p.D457E	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	463	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						GTGTGCCAGAATCTGGGCAGG	0.597																																					p.D463E													.	BAG6-154	0			c.T1389A						.						50	35	41					6																	31612378		1509	2708	4217	SO:0001630	splice_region_variant	7917	exon11			GCCAGAATCTGGG	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"HLA-B associated transcript 3"	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1388-1T>A	6.37:g.31612378A>T		Somatic	66	1		WXS	Illumina HiSeq	Phase_I	70	30	NM_004639	0	0	0	0	0	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	37	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	a	17.87	3.494104	0.64186	.	.	ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049;ENST00000437771;ENST00000438149;ENST00000436214;ENST00000435080	T;T;T;T;T;T;T;T	0.53423	1.47;1.48;1.47;1.2;0.91;1.48;0.62;0.91	4.66	3.46	0.39613	.	0.115441	0.56097	D	0.000026	T	0.32852	0.0843	L	0.32530	0.975	0.33181	D	0.5495	P;P;D;P;P	0.69078	0.953;0.756;0.997;0.841;0.902	P;P;D;P;P	0.72338	0.739;0.893;0.977;0.846;0.893	T	0.11767	-1.0574	10	0.13853	T	0.58	.	7.1945	0.25845	0.8977:0.0:0.1023:0.0	.	457;457;457;463;457	E7EMZ4;F8VXY4;B0UX85;P46379;P46379-2	.;.;.;BAG6_HUMAN;.	E	457;463;457;457;457;457;457;51;71;457	ENSP00000365143:D457E;ENSP00000365131:D463E;ENSP00000211379:D457E;ENSP00000384494:D457E;ENSP00000402856:D457E;ENSP00000354875:D457E;ENSP00000397978:D457E;ENSP00000410280:D51E	ENSP00000211379:D457E	D	-	3	2	BAG6	31720357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.019000	0.41001	0.769000	0.33313	0.525000	0.51046	GAT	.		0.597	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	Missense_Mutation	T	31612378	A	T	31612378	5	4	24	1	0	0	0	0	0	0	1	0	1323	115	4	5	2069	5	BAT3	6	31612378	Splice_Site	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10		31612378	139502689	21	2111											
FHL5	9457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	97051597	97051597	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttacatgttatgatcgtgtAttttctaactattgcgagga	10	17	9	5	2	1	1	0	1	1	0	2	3	1	2	0	1	3	3	0	1	5	8			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr6:97051597A>G	ENST00000326771.2	+	3	488	c.108A>G	c.(106-108)gtA>gtG	p.V36V	FHL5_ENST00000541107.1_Silent_p.V36V	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	36					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		ATGATCGTGTATTTTCTAACT	0.363																																					p.V36V		.											.	FHL5-92	0			c.A108G						.						166	146	153					6																	97051597		2203	4300	6503	SO:0001819	synonymous_variant	9457	exon3			TCGTGTATTTTCT	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.108A>G	6.37:g.97051597A>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	73	28	NM_020482	0	0	0	0	0	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			.		0.363	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		G	97051597	A	G	97051597	2	3	24	1	0	0	0	0	0	0	0	1	5900	436	16	3		3	FHL5	6	97051597	Silent	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	65439219	97051597	74063470	22	2112											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5372499	5372499	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttccgggccttgcgcccCttctccaccgccagcttggc	3	9	10	19	3	1	0	0	0	1	0	3	0	2	0	7	2	3	2	7	2	0	4	rs113405524	byFrequency	TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:5372499C>T	ENST00000430969.1	-	19	6249	c.5901G>A	c.(5899-5901)aaG>aaA	p.K1967K	TNRC18_ENST00000399537.4_Silent_p.K1967K	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1967							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCTTGCGCCCCTTCTCCACCG	0.771													C|||	67	0.0133786	0	0.0086	5008	,	,		9553	0		0.0149	False		,,,				2504	0.047				p.K1967K		.											.	TNRC18-46	0			c.G5901A						.	C		2,2776		0,2,1387	3	4	3		5901	3.2	1	7	dbSNP_132	3	19,6349		0,19,3165	no	coding-synonymous	TNRC18	NM_001080495.2		0,21,4552	TT,TC,CC		0.2984,0.072,0.2296		1967/2969	5372499	21,9125	1389	3184	4573	SO:0001819	synonymous_variant	84629	exon19			GCGCCCCTTCTCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5901G>A	7.37:g.5372499C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	25	9	NM_001080495	0	0	4	5	1	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1	23	0.010531135531135532	7	0.014227642276422764	3	0.008287292817679558	2	0.0034965034965034965	11	0.014511873350923483	.	9.698	1.153785	0.21371	7.2E-4	0.002984	ENSG00000182095	ENST00000455076	.	.	.	4.35	3.21	0.36854	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51957	-0.8639	4	.	.	.	.	9.2245	0.37398	0.0:0.8174:0.0:0.1826	.	.	.	.	K	4	.	.	R	-	2	0	TNRC18	5339025	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	0.720000	0.25896	1.955000	0.56771	0.555000	0.69702	AGG	C|0.989;T|0.011		0.771	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	5372499	C	T	5372499	2	4	24	1	0	0	0	0	0	0	0	1	16371	680	24	2		2	TNRC18	7	5372499	Silent	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		5372499	153766164	23	2113											
ZMIZ2	83637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44796552	44796552	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgcttcctcataggttttgGggaaccccatgggccctgca	6	11	11	13	0	1	0	1	0	0	0	2	1	2	1	4	4	3	3	4	4	2	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:44796552G>A	ENST00000309315.4	+	4	295	c.172G>A	c.(172-174)Ggg>Agg	p.G58R	ZMIZ2_ENST00000265346.7_Missense_Mutation_p.G58R|ZMIZ2_ENST00000413916.1_Intron|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.G58R|ZMIZ2_ENST00000433667.1_Intron	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	58	Gly-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						ATAGGTTTTGGGGAACCCCAT	0.592																																					p.G58R	NSCLC(20;604 852 1948 16908 50522)	.											.	ZMIZ2-137	0			c.G172A						.						112	114	113					7																	44796552		1971	4146	6117	SO:0001583	missense	83637	exon3			GTTTTGGGGAACC	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"Zinc fingers, MIZ-type"	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.172G>A	7.37:g.44796552G>A	ENSP00000311778:p.Gly58Arg	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	97	43	NM_174929	0	0	7	7	0	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707309	0.89018	.	.	ENSG00000122515	ENST00000457123;ENST00000309315;ENST00000441627;ENST00000265346;ENST00000414051	D;D;D;D	0.97731	-4.51;-4.51;-4.51;-4.51	4.8	4.8	0.61643	.	0.000000	0.56097	D	0.000030	D	0.98466	0.9489	M	0.71036	2.16	0.54753	D	0.999989	D;D	0.89917	0.999;1.0	D;D	0.79108	0.962;0.992	D	0.99771	1.1024	10	0.87932	D	0	-8.5125	17.6515	0.88165	0.0:0.0:1.0:0.0	.	58;58	Q8NF64-2;Q8NF64	.;ZMIZ2_HUMAN	R	58	ENSP00000415501:G58R;ENSP00000311778:G58R;ENSP00000414723:G58R;ENSP00000265346:G58R	ENSP00000265346:G58R	G	+	1	0	ZMIZ2	44763077	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.810000	0.91950	2.485000	0.83878	0.655000	0.94253	GGG	.		0.592	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		A	44796552	G	A	44796552	3	1	24	1	0	0	0	0	1	0	0	0	17729	1232	43	2	182	2	ZMIZ2	7	44796552	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	39424053	44796552	114342111	24	2114											
AUTS2	26053	broad.mit.edu;bcgsc.ca	37	chr7	70229864	70229864	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgcacagcttcacacccacCctccagccccccgcacactc	8	5	4	24	1	1	0	1	0	0	0	3	0	2	0	6	0	3	3	6	0	0	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:70229864C>G	ENST00000342771.4	+	8	1662	c.1341C>G	c.(1339-1341)acC>acG	p.T447T	AUTS2_ENST00000406775.2_Silent_p.T447T	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	447										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		tcacacccaccctccagcccc	0.652																																					p.T447T													.	AUTS2-92	0			c.C1341G						.						78	66	70					7																	70229864		2203	4300	6503	SO:0001819	synonymous_variant	26053	exon8			ACCCACCCTCCAG	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1341C>G	7.37:g.70229864C>G		Somatic	97	1		WXS	Illumina HiSeq	Phase_I	224	121	NM_001127231	0	0	0	0	0	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1																																																																																			.		0.652	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			G	70229864	C	G	70229864	2	3	24	1	0	0	0	0	0	0	0	1	1226	610	22	4		4	AUTS2	7	70229864	Silent	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	25433312	70229864	88908799	25	2115											
PON2	5445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	95040981	95040981	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtaccttggaagaagctcatGtttgactgttttcagatgca	10	14	10	7	0	2	3	2	1	0	2	2	4	2	4	1	1	3	5	1	1	3	5			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:95040981G>T	ENST00000222572.3	-	5	724	c.478C>A	c.(478-480)Cat>Aat	p.H160N	PON2_ENST00000536183.1_Missense_Mutation_p.H181N|PON2_ENST00000433091.2_Missense_Mutation_p.H148N|PON2_ENST00000483292.1_5'UTR			Q15165	PON2_HUMAN	paraoxonase 2	160					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			AGAAGCTCATGTTTGACTGTT	0.358																																					p.H160N	GBM(42;803 823 13649 23368 31463)	.											.	PON2-90	0			c.C478A						.						76	78	78					7																	95040981		2203	4300	6503	SO:0001583	missense	5445	exon5			GCTCATGTTTGAC	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"Paraoxonases"	9205	protein-coding gene	gene with protein product	"paraoxonase nirs", "arylesterase 2"	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.478C>A	7.37:g.95040981G>T	ENSP00000222572:p.His160Asn	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	98	47	NM_000305	0	1	52	81	28	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921121	0.33908	.	.	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.40476	2.34;1.03;2.34	4.94	3.1	0.35709	Six-bladed beta-propeller, TolB-like (1);	0.093511	0.85682	D	0.000000	T	0.60077	0.2241	M	0.83118	2.625	0.52501	D	0.999956	D;D	0.76494	0.998;0.999	D;D	0.69824	0.946;0.966	T	0.60944	-0.7162	10	0.14252	T	0.57	-9.4713	10.7179	0.46023	0.0717:0.132:0.7963:0.0	.	160;160	A4D1H7;Q15165	.;PON2_HUMAN	N	181;158;148;160	ENSP00000440282:H181N;ENSP00000404622:H148N;ENSP00000222572:H160N	ENSP00000222572:H160N	H	-	1	0	PON2	94878917	1.000000	0.71417	0.894000	0.35097	0.062000	0.15995	7.184000	0.77705	0.774000	0.33427	-0.157000	0.13467	CAT	.		0.358	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		T	95040981	G	T	95040981	3	4	24	1	0	0	0	0	1	0	0	0	12275	1377	48	4	606	4	PON2	7	95040981	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	24811117	95040981	64097682	26	2116											
SLC35B4	84912	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	133984905	133984905	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttcaggaagttgcttacaTtataaaacaaagcctccttg	13	12	8	8	0	1	0	1	0	0	0	2	1	2	1	2	2	4	3	2	2	6	6	rs570322971		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:133984905T>C	ENST00000378509.4	-	7	895	c.596A>G	c.(595-597)aAt>aGt	p.N199S		NM_032826.4	NP_116215.1	Q969S0	S35B4_HUMAN	solute carrier family 35 (UDP-xylose/UDP-N-acetylglucosamine transporter), member B4	199					carbohydrate transport (GO:0008643)|regulation of gluconeogenesis (GO:0006111)|transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine transport (GO:0015788)|UDP-xylose transport (GO:0015790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)|UDP-xylose transmembrane transporter activity (GO:0005464)			large_intestine(1)|lung(2)|skin(1)|stomach(1)	5						GTTGCTTACATTATAAAACAA	0.378													T|||	1	0.000199681	0	0	5008	,	,		18423	0		0	False		,,,				2504	0.001				p.N199S													.	SLC35B4-91	0			c.A596G						.						91	91	91					7																	133984905		2203	4300	6503	SO:0001630	splice_region_variant	84912	exon7			CTTACATTATAAA	AB052892	CCDS34756.1	7q33	2013-07-17	2013-07-17		ENSG00000205060	ENSG00000205060		"Solute carriers"	20584	protein-coding gene	gene with protein product		610923	"solute carrier family 35, member B4"				Standard	NM_032826		Approved	FLJ14697, YEA4	uc003vrn.3	Q969S0	OTTHUMG00000155321	ENST00000378509.4:c.597+1A>G	7.37:g.133984905T>C		Somatic	69	1		WXS	Illumina HiSeq	Phase_I	120	56	NM_032826	0	0	1	2	1	A4D1P3|A6NNS4|Q53GQ7|Q8TCU7|Q96K33	Missense_Mutation	SNP	ENST00000378509.4	37	CCDS34756.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.337875	0.60963	.	.	ENSG00000205060	ENST00000378509	T	0.25579	1.79	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.15176	0.0366	N	0.13352	0.335	0.80722	D	1	B;B;B	0.20164	0.034;0.034;0.042	B;B;B	0.21917	0.022;0.022;0.037	T	0.05937	-1.0855	10	0.05436	T	0.98	-14.4544	16.0396	0.80654	0.0:0.0:0.0:1.0	.	199;199;199	Q969S0-3;Q969S0-2;Q969S0	.;.;S35B4_HUMAN	S	199	ENSP00000367770:N199S	ENSP00000367770:N199S	N	-	2	0	SLC35B4	133635445	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	7.927000	0.87577	2.277000	0.76020	0.528000	0.53228	AAT	.		0.378	SLC35B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339444.2	NM_032826	Missense_Mutation	C	133984905	T	C	133984905	5	2	24	1	0	0	0	0	0	0	1	0	14610	1507	52	3	415	3	SLC35B4	7	133984905	Splice_Site	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10	38943924	133984905	25153758	27	2117											
PDP1	54704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	94934633	94934633	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccttggatttgacagcaatCagctgcctgcaaatgcaccc	10	10	8	13	0	1	1	1	1	0	0	2	2	2	2	3	1	5	4	3	1	2	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr8:94934633C>T	ENST00000297598.4	+	2	615	c.346C>T	c.(346-348)Cag>Tag	p.Q116*	PDP1_ENST00000517764.1_Nonsense_Mutation_p.Q116*|PDP1_ENST00000520728.1_Nonsense_Mutation_p.Q116*|PDP1_ENST00000396200.3_Nonsense_Mutation_p.Q141*	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	116				NVSSILGFDSNQ -> MSVLSLDLTAIK (in Ref. 1; AAF67480). {ECO:0000305}.	cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TGACAGCAATCAGCTGCCTGC	0.463																																					p.Q141X		.											.	PDP1-229	0			c.C421T						.						88	92	90					8																	94934633		2203	4300	6503	SO:0001587	stop_gained	54704	exon3			AGCAATCAGCTGC	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.346C>T	8.37:g.94934633C>T	ENSP00000297598:p.Gln116*	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	81	37	NM_001161780	0	0	1	4	3	B3KX71|J3KPU0|Q5U5K1	Nonsense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	C	33	5.196332	0.94960	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000518573;ENST00000517764;ENST00000518827;ENST00000521144	.	.	.	6.03	6.03	0.97812	.	0.120323	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-14.0857	20.5753	0.99366	0.0:1.0:0.0:0.0	.	.	.	.	X	116;116;141;116;116;116;116	.	ENSP00000297598:Q116X	Q	+	1	0	PDP1	95003809	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.792000	0.85828	2.868000	0.98415	0.557000	0.71058	CAG	.		0.463	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		T	94934633	C	T	94934633	4	4	24	1	0	0	0	0	0	1	0	0	11711	827	29	2	529	2	PDP1	8	94934633	Nonsense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		94934633	51429389	28	2118											
VPS13B	157680	broad.mit.edu	37	chr8	100729543	100729543	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtaaacacagcgggaatcCaggcccagaacaatccatac	15	5	9	12	1	0	1	0	0	0	1	2	2	2	2	3	2	4	1	3	2	6	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr8:100729543C>G	ENST00000358544.2	+	37	6785	c.6674C>G	c.(6673-6675)cCa>cGa	p.P2225R	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.P2200R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2225					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AGCGGGAATCCAGGCCCAGAA	0.418																																					p.P2225R	Colon(161;2205 2542 7338 31318)												.	VPS13B-301	0			c.C6674G						.						97	91	93					8																	100729543		2203	4300	6503	SO:0001583	missense	157680	exon37			GGAATCCAGGCCC	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6674C>G	8.37:g.100729543C>G	ENSP00000351346:p.Pro2225Arg	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	141	7	NM_017890	0	0	0	0	0	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.229592	0.39399	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.68903	-0.36;-0.36	5.27	3.48	0.39840	.	0.130594	0.50627	D	0.000112	T	0.75332	0.3835	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.993	D;P	0.67382	0.951;0.844	T	0.76113	-0.3078	10	0.72032	D	0.01	.	11.9882	0.53159	0.0:0.8584:0.0:0.1416	.	2200;2225	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	R	2200;2225	ENSP00000349685:P2200R;ENSP00000351346:P2225R	ENSP00000349685:P2200R	P	+	2	0	VPS13B	100798719	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	3.399000	0.52586	0.704000	0.31869	-0.150000	0.13652	CCA	.		0.418	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100729543	C	G	100729543	3	3	24	1	0	0	0	0	1	0	0	0	17223	594	21	4	7010	4	VPS13B	8	100729543	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	5794910	100729543	45634479	29	2119											
ENPP2	5168	broad.mit.edu;bcgsc.ca	37	chr8	120580455	120580455	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggaaccatattggttacaagGaatgcatcatatttagcctc	13	12	8	8	0	1	0	1	0	0	0	2	2	1	2	2	3	4	2	2	3	7	6			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr8:120580455G>A	ENST00000075322.6	-	22	2149	c.2091C>T	c.(2089-2091)ttC>ttT	p.F697F	ENPP2_ENST00000522826.1_Silent_p.F722F|ENPP2_ENST00000427067.2_Silent_p.F718F|ENPP2_ENST00000522167.1_Silent_p.F332F|ENPP2_ENST00000259486.6_Silent_p.F749F	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	697					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGGTTACAAGGAATGCATCAT	0.294																																					p.F749F	Melanoma(20;305 879 2501 4818 31020)												.	ENPP2-292	0			c.C2247T						.						131	136	134					8																	120580455		2203	4298	6501	SO:0001819	synonymous_variant	5168	exon23			TACAAGGAATGCA	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"autotaxin"	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2091C>T	8.37:g.120580455G>A		Somatic	359	0		WXS	Illumina HiSeq	Phase_I	348	11	NM_006209	0	0	3	3	0	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			.		0.294	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			A	120580455	G	A	120580455	2	1	24	1	0	0	0	0	0	0	0	1	5143	1165	41	2		2	ENPP2	8	120580455	Silent	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	19850912	120580455	25783567	30	2120											
NOTCH1	4851	broad.mit.edu	37	chr9	139417461	139417462	+	Frame_Shift_Ins	INS	-	-	G																															gagccgacctcgttgtggcaINSggtgcctccgtggcggcaaa																								rs146350322		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr9:139417461_139417462insG	ENST00000277541.6	-	4	657_658	c.582_583insC	c.(580-585)acctgcfs	p.C195fs	NOTCH1_ENST00000491649.1_5'UTR	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	195	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TCGTTGTGGCAGGTGCCTCCGT	0.698			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.C195fs				Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1-5459	0			c.583_584insC						.																																			SO:0001589	frameshift_variant	4851	exon4			TGTGGCAGGTGCC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.583dupC	9.37:g.139417463_139417463dupG	ENSP00000277541:p.Cys195fs	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	145	4	NM_017617	0	0	0	0	0	Q59ED8|Q5SXM3	Frame_Shift_Ins	INS	ENST00000277541.6	37	CCDS43905.1																																																																																			.		0.698	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		G	139417462	-	G	139417461	7	5	24	1	0	1	1	0	0	0	0	0	10573	188	7	0	7208	0	NOTCH1	9	139417461	Frame_Shift_Ins	INS	-	TCGA-A4-A5DU-01A-11D-A28G-10		139417461	1795970	31	2121											
DDX50	79009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	70670106	70670106	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagccttctccaattttcCtatttctgaagagactataa	12	14	6	9	0	2	2	0	1	2	1	4	4	3	3	3	1	1	0	3	1	5	7			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr10:70670106C>A	ENST00000373585.3	+	3	535	c.428C>A	c.(427-429)cCt>cAt	p.P143H	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	143						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TCCAATTTTCCTATTTCTGAA	0.378																																					p.P143H		.											.	DDX50-91	0			c.C428A						.						129	133	132					10																	70670106		2203	4300	6503	SO:0001583	missense	79009	exon3			ATTTTCCTATTTC	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.428C>A	10.37:g.70670106C>A	ENSP00000362687:p.Pro143His	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	39	11	NM_024045	0	0	3	3	0	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	37	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489203	0.64074	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.21543	2.0	5.23	5.23	0.72850	RNA helicase, DEAD-box type, Q motif (1);	0.210307	0.43110	D	0.000611	T	0.19005	0.0456	L	0.32530	0.975	0.35802	D	0.82318	P;P	0.48016	0.904;0.604	B;B	0.42882	0.401;0.396	T	0.11891	-1.0569	10	0.48119	T	0.1	-3.6785	13.2098	0.59817	0.1588:0.8412:0.0:0.0	.	143;143	Q9BQ39;B4DED6	DDX50_HUMAN;.	H	143	ENSP00000362687:P143H	ENSP00000362687:P143H	P	+	2	0	DDX50	70340112	0.366000	0.25014	1.000000	0.80357	0.993000	0.82548	1.963000	0.40452	2.585000	0.87301	0.555000	0.69702	CCT	.		0.378	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		A	70670106	C	A	70670106	3	1	24	1	0	0	0	0	1	0	0	0	4374	681	24	4	438	4	DDX50	10	70670106	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		70670106	64864641	32	2122											
SLC5A12	159963	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	26720060	26720060	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caccagaatgatccagagacCcagcaagttaaaatacaagg	18	5	8	10	0	0	3	0	1	0	2	1	4	1	3	3	1	2	2	3	1	6	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr11:26720060C>A	ENST00000396005.3	-	7	1153	c.844G>T	c.(844-846)Ggt>Tgt	p.G282C	SLC5A12_ENST00000280467.6_Missense_Mutation_p.G282C	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	282					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						ATCCAGAGACCCAGCAAGTTA	0.453																																					p.G282C													.	SLC5A12-92	0			c.G844T						.						120	108	112					11																	26720060		2203	4299	6502	SO:0001583	missense	159963	exon7			AGAGACCCAGCAA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.844G>T	11.37:g.26720060C>A	ENSP00000379326:p.Gly282Cys	Somatic	137	1		WXS	Illumina HiSeq	Phase_I	142	80	NM_178498	0	0	0	0	0	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454419	0.84209	.	.	ENSG00000148942	ENST00000396005;ENST00000280467;ENST00000533617	D;D;D	0.87729	-2.29;-2.29;-2.29	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.94489	0.8226	M	0.84683	2.71	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.987;1.0	D	0.93232	0.6618	10	0.45353	T	0.12	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	282;282	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	C	282;282;94	ENSP00000379326:G282C;ENSP00000280467:G282C;ENSP00000435053:G94C	ENSP00000280467:G282C	G	-	1	0	SLC5A12	26676636	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.669000	0.83911	2.890000	0.99128	0.650000	0.86243	GGT	.		0.453	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		A	26720060	C	A	26720060	3	1	24	1	0	0	0	0	1	0	0	0	14696	623	22	4	1048	4	SLC5A12	11	26720060	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		26720060	108286456	33	2123											
INCENP	3619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	61897408	61897408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagctgccgcggctaccatgGcattggctgcaccttcttca	6	10	10	15	2	2	0	1	0	1	0	2	0	2	0	3	3	4	5	3	3	1	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr11:61897408G>A	ENST00000394818.3	+	4	611	c.409G>A	c.(409-411)Gca>Aca	p.A137T	INCENP_ENST00000278849.4_Missense_Mutation_p.A137T	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	137			A -> V (in dbSNP:rs34441559).		chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GGCTACCATGGCATTGGCTGC	0.627																																					p.A137T		.											.	INCENP-227	0			c.G409A						.						60	60	60					11																	61897408		2201	4299	6500	SO:0001583	missense	3619	exon4			ACCATGGCATTGG	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.409G>A	11.37:g.61897408G>A	ENSP00000378295:p.Ala137Thr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	72	29	NM_001040694	0	0	0	0	0	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	G	9.095	1.002664	0.19121	.	.	ENSG00000149503	ENST00000394818;ENST00000533896;ENST00000278849	T;T;T	0.23754	2.52;1.89;2.51	3.14	-3.13	0.05266	.	2.075460	0.02904	N	0.135798	T	0.13884	0.0336	N	0.22421	0.69	0.09310	N	1	B;B;B	0.11235	0.004;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.001	T	0.14671	-1.0464	10	0.10636	T	0.68	.	4.1359	0.10170	0.3443:0.3363:0.3194:0.0	.	137;137;137	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	T	137	ENSP00000378295:A137T;ENSP00000433100:A137T;ENSP00000278849:A137T	ENSP00000278849:A137T	A	+	1	0	INCENP	61653984	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.779000	0.04659	-0.725000	0.04901	-0.459000	0.05422	GCA	.		0.627	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61897408	G	A	61897408	3	1	24	1	0	0	0	0	1	0	0	0	7754	1203	42	2	419	2	INCENP	11	61897408	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	35177348	61897408	73109108	34	2124											
PDE2A	5138	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	72293520	72293520	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcctcgggcagggaacgagGggtataggtgaaacttgcaa	12	7	15	7	2	0	1	0	1	0	0	2	3	1	2	1	5	3	3	1	5	5	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr11:72293520G>T	ENST00000334456.5	-	21	2064	c.1819C>A	c.(1819-1821)Cct>Act	p.P607T	RP11-169D4.2_ENST00000545254.1_RNA|PDE2A_ENST00000418754.2_Missense_Mutation_p.P492T|PDE2A_ENST00000540345.1_Missense_Mutation_p.P598T|PDE2A_ENST00000376450.3_Missense_Mutation_p.P351T|PDE2A_ENST00000544570.1_Missense_Mutation_p.P600T|PDE2A_ENST00000444035.2_Missense_Mutation_p.P598T	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	607					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	AGGGAACGAGGGGTATAGGTG	0.517																																					p.P607T													.	PDE2A-156	0			c.C1819A						.						103	83	90					11																	72293520		2200	4293	6493	SO:0001583	missense	5138	exon21			AACGAGGGGTATA	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"Phosphodiesterases"	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.1819C>A	11.37:g.72293520G>T	ENSP00000334910:p.Pro607Thr	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	108	56	NM_002599	0	0	0	0	0	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Missense_Mutation	SNP	ENST00000334456.5	37	CCDS8216.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039400	0.75617	.	.	ENSG00000186642	ENST00000334456;ENST00000376450;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345;ENST00000441209;ENST00000542223	T;T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	4.74	4.74	0.60224	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.245967	0.32952	N	0.005459	D	0.84786	0.5549	M	0.75777	2.31	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D	0.79108	0.982;0.981;0.981;0.992;0.981;0.986	D	0.85408	0.1135	10	0.46703	T	0.11	.	14.4911	0.67651	0.0:0.0:1.0:0.0	.	492;607;598;600;607;351	E9PEF1;O00408;E9PGI1;F6W5Z0;B2R646;Q6ZMR1	.;PDE2A_HUMAN;.;.;.;.	T	607;351;598;676;600;492;598;148;38	ENSP00000334910:P607T;ENSP00000365633:P351T;ENSP00000411657:P598T;ENSP00000442256:P600T;ENSP00000410310:P492T;ENSP00000446399:P598T;ENSP00000392457:P148T;ENSP00000440834:P38T	ENSP00000334910:P607T	P	-	1	0	PDE2A	71971168	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	8.586000	0.90806	2.197000	0.70478	0.563000	0.77884	CCT	.		0.517	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599		T	72293520	G	T	72293520	3	4	24	1	0	0	0	0	1	0	0	0	11662	1232	43	4	1050	4	PDE2A	11	72293520	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	10396112	72293520	62712996	35	2125											
SSPN	8082	hgsc.bcm.edu	37	chr12	26348668	26348668	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccgccggccgcggacgcCgctgggcccgacgacatgga	5	2	17	17	8	0	0	0	0	0	0	0	4	0	2	5	5	0	1	5	5	0	0	rs200655450	byFrequency	TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr12:26348668C>G	ENST00000242729.2	+	1	240	c.63C>G	c.(61-63)gcC>gcG	p.A21A	SSPN_ENST00000535504.1_Silent_p.A21A|SSPN_ENST00000422622.2_Intron|SSPN_ENST00000540266.1_Intron	NM_005086.4	NP_005077.2	Q14714	SSPN_HUMAN	sarcospan	21					cell adhesion (GO:0007155)|muscle contraction (GO:0006936)	cell junction (GO:0030054)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10	Colorectal(261;0.0847)					ccgcggacgccgctgggcccg	0.756													C|||	11	0.00219649	8e-04	0.0029	5008	,	,		8179	0		0.007	False		,,,				2504	0.001				p.A21A		.											.	SSPN-90	0			c.C63G						.						2	3	2					12																	26348668		1476	3051	4527	SO:0001819	synonymous_variant	8082	exon1			GGACGCCGCTGGG	AF016028	CCDS8707.1, CCDS44850.1	12p11.2	2014-09-17	2012-03-14			ENSG00000123096			11322	protein-coding gene	gene with protein product		601599	"Kras oncogene-associated gene"	KRAG		9395445, 8661122	Standard	NM_005086		Approved	SPN1, SPN2	uc001rhe.3	Q14714		ENST00000242729.2:c.63C>G	12.37:g.26348668C>G		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	16	6	NM_005086	0	0	0	0	0	B3KS67	Silent	SNP	ENST00000242729.2	37	CCDS8707.1																																																																																			C|0.997;G|0.003		0.756	SSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402654.2	NM_005086		G	26348668	C	G	26348668	2	3	24	1	0	0	0	0	0	0	0	1	15220	639	23	4		4	SSPN	12	26348668	Silent	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		26348668	107503227	36	2126											
SLC25A3	5250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	98995295	98995295	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctctgaagaagaagcttgggTtaactcagtagttagatcaa	14	11	10	6	0	3	4	2	1	1	3	3	4	3	4	0	1	2	4	0	1	7	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr12:98995295T>A	ENST00000228318.3	+	8	1198	c.1078T>A	c.(1078-1080)Tta>Ata	p.L360I	SLC25A3_ENST00000548847.1_Missense_Mutation_p.L322I|SLC25A3_ENST00000552981.1_Missense_Mutation_p.L359I|SLC25A3_ENST00000401722.3_Missense_Mutation_p.L359I|SNORA53_ENST00000391141.1_RNA|SLC25A3_ENST00000188376.5_Missense_Mutation_p.L359I|SLC25A3_ENST00000549338.1_Missense_Mutation_p.L359I|SLC25A3_ENST00000551917.1_Missense_Mutation_p.L360I	NM_005888.3	NP_005879.1	Q00325	MPCP_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3	360					generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293)			breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		GAAGCTTGGGTTAACTCAGTA	0.433																																					p.L360I		.											.	SLC25A3-90	0			c.T1078A						.						83	79	80					12																	98995295		2203	4300	6503	SO:0001583	missense	5250	exon8			CTTGGGTTAACTC		CCDS9065.1, CCDS9066.1	12q23.1	2013-05-22			ENSG00000075415	ENSG00000075415		"Solute carriers"	10989	protein-coding gene	gene with protein product		600370		PHC		8168843	Standard	NM_213611		Approved		uc001tfo.3	Q00325	OTTHUMG00000170212	ENST00000228318.3:c.1078T>A	12.37:g.98995295T>A	ENSP00000228318:p.Leu360Ile	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	76	48	NM_005888	1	0	229	573	343	B3KS34|Q7Z7N7|Q96A03	Missense_Mutation	SNP	ENST00000228318.3	37	CCDS9066.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008501	0.75046	.	.	ENSG00000075415	ENST00000401722;ENST00000188376;ENST00000228318;ENST00000551917;ENST00000552981;ENST00000549338;ENST00000548847	T;T;T;T;T;T;T	0.78126	-1.15;-1.15;-0.89;-0.89;-1.15;-1.15;-1.13	5.48	3.14	0.36123	.	0.132239	0.49305	D	0.000142	T	0.72112	0.3420	N	0.17674	0.51	0.51012	D	0.999902	B;P;P;B	0.52842	0.135;0.956;0.598;0.135	B;D;B;B	0.65010	0.121;0.931;0.19;0.145	T	0.66324	-0.5952	10	0.09590	T	0.72	-0.9242	7.4149	0.27038	0.0:0.3411:0.0:0.6589	.	322;359;360;359	F8VVM2;B2RE88;Q00325;Q00325-2	.;.;MPCP_HUMAN;.	I	359;359;360;360;359;359;322	ENSP00000383898:L359I;ENSP00000188376:L359I;ENSP00000228318:L360I;ENSP00000447310:L360I;ENSP00000448708:L359I;ENSP00000447740:L359I;ENSP00000449166:L322I	ENSP00000188376:L359I	L	+	1	2	SLC25A3	97519426	0.996000	0.38824	1.000000	0.80357	0.956000	0.61745	0.932000	0.28884	1.022000	0.39626	0.533000	0.62120	TTA	.		0.433	SLC25A3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407989.1	NM_005888		A	98995295	T	A	98995295	3	1	24	1	0	0	0	0	1	0	0	0	14525	1722	60	5	1230	5	SLC25A3	12	98995295	Missense_Mutation	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10	72646627	98995295	34856600	37	2127											
RPGRIP1	57096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21793036	21793036	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttatctgtggggccacagccCctctatgacttcacctccca	7	11	7	16	0	3	1	1	1	2	0	4	1	4	1	5	2	1	0	5	2	2	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr14:21793036C>T	ENST00000400017.2	+	14	2022	c.2022C>T	c.(2020-2022)ccC>ccT	p.P674P	RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000553500.1_Intron|RPGRIP1_ENST00000557771.1_Silent_p.P636P|RPGRIP1_ENST00000307974.4_Silent_p.P33P|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000206660.6_Silent_p.P674P	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	674					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GGCCACAGCCCCTCTATGACT	0.512																																					p.P674P		.											.	RPGRIP1-140	0			c.C2022T						.						169	159	162					14																	21793036		1949	4136	6085	SO:0001819	synonymous_variant	57096	exon14			ACAGCCCCTCTAT	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2022C>T	14.37:g.21793036C>T		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	126	46	NM_020366	0	0	0	0	0	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																			.		0.512	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21793036	C	T	21793036	2	4	24	1	0	0	0	0	0	0	0	1	13581	610	22	2		2	RPGRIP1	14	21793036	Silent	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		21793036	85556504	38	2128											
POMT2	29954	broad.mit.edu;bcgsc.ca	37	chr14	77769260	77769260	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggggtcaaggaggatgtActgggacagagtgaggcatc	11	7	18	5	0	1	2	1	1	0	1	2	6	1	5	0	6	1	2	0	6	2	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr14:77769260A>G	ENST00000261534.4	-	5	776	c.574T>C	c.(574-576)Tac>Cac	p.Y192H	POMT2_ENST00000556880.1_5'UTR	NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	192						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		AGGAGGATGTACTGGGACAGA	0.532																																					p.Y192H													.	POMT2-91	0			c.T574C						.						94	80	85					14																	77769260		2203	4300	6503	SO:0001583	missense	29954	exon5			GGATGTACTGGGA	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.574T>C	14.37:g.77769260A>G	ENSP00000261534:p.Tyr192His	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	96	7	NM_013382	0	0	5	5	0	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.782604	0.90282	.	.	ENSG00000009830	ENST00000261534;ENST00000554948	D;D	0.86865	-2.18;-2.18	5.54	5.54	0.83059	Glycosyl transferase, family 39 (1);	0.066257	0.64402	D	0.000006	D	0.93268	0.7855	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93930	0.7213	10	0.66056	D	0.02	-16.8283	15.6626	0.77199	1.0:0.0:0.0:0.0	.	192	Q9UKY4	POMT2_HUMAN	H	192;101	ENSP00000261534:Y192H;ENSP00000452060:Y101H	ENSP00000261534:Y192H	Y	-	1	0	POMT2	76839013	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.972000	0.93424	2.095000	0.63458	0.533000	0.62120	TAC	.		0.532	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		G	77769260	A	G	77769260	3	3	24	1	0	0	0	0	1	0	0	0	12272	391	14	3	1746	3	POMT2	14	77769260	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	55976224	77769260	29580280	39	2129											
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776827	38776827	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtggtggtggtggtggTggtggtggaggaggtggata	4	11	26	0	0	0	0	0	0	0	0	0	3	0	3	0	13	0	0	0	13	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr15:38776827T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G423G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gtggtggtggtggtggtggag	0.443																																					p.G423G		.											.	FAM98B-515	0			c.T1269A						.						19	18	18					15																	38776827		1515	3413	4928	SO:0001628	intergenic_variant	283742	exon8			TGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		15.37:g.38776827T>A		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	27	4	NM_173611	0	0	0	0	0	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	37	CCDS42015.1																																																																																			.		0.443	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38776827	T	A	38776827	1	1	24	0	1	0	0	0	0	0	0	0	5676	1683	59	5		5	FAM98B	15	38776827	IGR	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10		38776827	63754565	40	2130											
KIAA1199	57214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	81181040	81181040	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggtctcgtttctctgacAggacatcgaggctctgctgc	7	11	12	11	2	3	1	0	1	3	0	6	3	3	2	0	3	2	3	0	3	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr15:81181040A>T	ENST00000394685.3	+	9	1287		c.e9-1		KIAA1199_ENST00000220244.3_Splice_Site|KIAA1199_ENST00000356249.5_Splice_Site			Q8WUJ3	CEMIP_HUMAN							hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TTTCTCTGACAGGACATCGAG	0.498																																					.		.											.	KIAA1199-93	0			c.869-2A>T						.						101	99	100					15																	81181040		2203	4300	6503	SO:0001630	splice_region_variant	57214	exon8			TCTGACAGGACAT																												ENST00000394685.3:c.869-1A>T	15.37:g.81181040A>T		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	52	27	NM_018689	0	0	0	0	0	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Splice_Site	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.547385	0.27652	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6315	0.68660	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA1199	78968095	1.000000	0.71417	0.786000	0.31890	0.035000	0.12851	6.504000	0.73704	2.046000	0.60703	0.455000	0.32223	.	.		0.498	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		Intron	T	81181040	A	T	81181040	5	4	24	1	0	0	0	0	0	0	1	0	8234	202	7	5	893	5	KIAA1199	15	81181040	Splice_Site	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	42404213	81181040	21350352	41	2131											
SETD6	79918	broad.mit.edu	37	chr16	58549753	58549753	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctgcttcctgagctggtGccggcgggtggggctggagc	2	8	20	11	2	0	1	0	1	0	0	1	2	1	2	3	7	4	3	3	7	0	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr16:58549753G>T	ENST00000219315.4	+	2	136	c.86G>T	c.(85-87)tGc>tTc	p.C29F	SETD6_ENST00000310682.2_Missense_Mutation_p.C29F|SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000394266.4_Missense_Mutation_p.C29F			Q8TBK2	SETD6_HUMAN	SET domain containing 6	29					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CTGAGCTGGTGCCGGCGGGTG	0.736																																					p.C29F													.	SETD6-91	0			c.G86T						.						6	8	8					16																	58549753		2130	4188	6318	SO:0001583	missense	79918	exon2			GCTGGTGCCGGCG	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.86G>T	16.37:g.58549753G>T	ENSP00000219315:p.Cys29Phe	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	69	8	NM_024860	0	0	0	1	1	A8K380|B5ME38|Q9H787	Missense_Mutation	SNP	ENST00000219315.4	37	CCDS54013.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.651671	0.67472	.	.	ENSG00000103037	ENST00000310682;ENST00000394266;ENST00000219315;ENST00000447443;ENST00000458571	T;T;T;T	0.74632	2.52;2.52;2.52;-0.86	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.84786	0.5549	M	0.70275	2.135	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.996;0.999	D;P;D	0.73708	0.981;0.879;0.974	D	0.85594	0.1248	10	0.51188	T	0.08	6.0364	16.4587	0.84030	0.0:0.0:1.0:0.0	.	29;29;29	E9PC53;Q8TBK2;Q8TBK2-2	.;SETD6_HUMAN;.	F	29	ENSP00000310082:C29F;ENSP00000377809:C29F;ENSP00000219315:C29F;ENSP00000396437:C29F	ENSP00000219315:C29F	C	+	2	0	SETD6	57107254	1.000000	0.71417	0.979000	0.43373	0.135000	0.20990	4.541000	0.60670	2.437000	0.82529	0.555000	0.69702	TGC	.		0.736	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860		T	58549753	G	T	58549753	3	4	24	1	0	0	0	0	1	0	0	0	14167	1319	46	4	92	4	SETD6	16	58549753	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		58549753	31805000	42	2132											
GLTPD2	388323	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	4693110	4693110	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cactagggaggccttcaccaAggtgacagacctggaggctc	10	6	13	12	0	1	2	1	1	0	1	2	4	1	4	3	5	0	1	3	5	2	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr17:4693110A>G	ENST00000331264.7	+	4	448	c.395A>G	c.(394-396)aAg>aGg	p.K132R		NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	132						cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4						GCCTTCACCAAGGTGACAGAC	0.672																																					p.K132R		.											.	GLTPD2-68	0			c.A395G						.						16	17	16					17																	4693110		2178	4256	6434	SO:0001583	missense	388323	exon4			TCACCAAGGTGAC	BC029290	CCDS32534.1	17p13.2	2007-12-19				ENSG00000182327			33756	protein-coding gene	gene with protein product							Standard	NM_001014985		Approved		uc002fza.2	A6NH11		ENST00000331264.7:c.395A>G	17.37:g.4693110A>G	ENSP00000328070:p.Lys132Arg	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	157	88	NM_001014985	0	0	3	7	4	A7E2T2	Missense_Mutation	SNP	ENST00000331264.7	37	CCDS32534.1	.	.	.	.	.	.	.	.	.	.	A	32	5.182952	0.94885	.	.	ENSG00000182327	ENST00000331264	.	.	.	4.55	4.55	0.56014	Glycolipid transfer protein domain (3);	0.000000	0.85682	D	0.000000	T	0.81312	0.4796	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84725	0.0742	9	0.66056	D	0.02	-15.1395	11.95	0.52950	1.0:0.0:0.0:0.0	.	132	A6NH11	GLTD2_HUMAN	R	132	.	ENSP00000328070:K132R	K	+	2	0	GLTPD2	4639850	1.000000	0.71417	0.999000	0.59377	0.879000	0.50718	5.451000	0.66632	1.924000	0.55735	0.454000	0.30748	AAG	.		0.672	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985		G	4693110	A	G	4693110	3	3	24	1	0	0	0	0	1	0	0	0	6493	72	3	3	409	3	GLTPD2	17	4693110	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10		4693110	76502100	43	2133											
KDM6B	23135	broad.mit.edu	37	chr17	7751756	7751756	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaacagcaacaacacgaagCaggcgtggccccccaacccc	13	1	10	17	2	0	0	0	0	0	0	0	2	0	1	5	3	6	2	5	3	5	0			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr17:7751756C>T	ENST00000448097.2	+	11	2481	c.2150C>T	c.(2149-2151)gCa>gTa	p.A717V	KDM6B_ENST00000254846.5_Missense_Mutation_p.A717V			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	717	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CAACACGAAGCAGGCGTGGCC	0.587																																					p.A717V													.	KDM6B-205	0			c.C2150T						.						88	102	97					17																	7751756		2203	4300	6503	SO:0001583	missense	23135	exon11			ACGAAGCAGGCGT	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.2150C>T	17.37:g.7751756C>T	ENSP00000412513:p.Ala717Val	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	74	5	NM_001080424	0	0	11	11	0	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		.	.	.	.	.	.	.	.	.	.	C	13.19	2.162661	0.38217	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.12879	2.64;2.64	4.52	4.52	0.55395	.	0.954393	0.08691	N	0.907886	T	0.12263	0.0298	N	0.08118	0	0.29511	N	0.854171	P;P	0.50819	0.816;0.939	B;P	0.48524	0.115;0.58	T	0.13548	-1.0505	10	0.52906	T	0.07	-8.824	12.2604	0.54647	0.1706:0.8294:0.0:0.0	.	717;717	O15054;O15054-1	KDM6B_HUMAN;.	V	717	ENSP00000254846:A717V;ENSP00000412513:A717V	ENSP00000254846:A717V	A	+	2	0	KDM6B	7692481	0.702000	0.27816	0.999000	0.59377	0.929000	0.56500	1.157000	0.31724	2.523000	0.85059	0.491000	0.48974	GCA	.		0.587	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		T	7751756	C	T	7751756	3	4	24	1	0	0	0	0	1	0	0	0	8159	710	25	2	2180	2	KDM6B	17	7751756	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	3058646	7751756	73443454	44	2134											
TRIM25	7706	bcgsc.ca	37	chr17	54990934	54990934	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcagcgggtggtcctggaagGcggggctgtcgaagtgcggc	5	6	21	9	4	0	0	0	0	0	0	2	2	1	1	1	7	2	2	1	7	2	0			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr17:54990934G>A	ENST00000316881.4	-	1	465	c.416C>T	c.(415-417)gCc>gTc	p.A139V	TRIM25_ENST00000537230.1_Missense_Mutation_p.A139V	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	139					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					GTCCTGGAAGGCGGGGCTGTC	0.652																																					p.A139V													.	TRIM25-289	0			c.C416T						.						25	32	30					17																	54990934		2202	4297	6499	SO:0001583	missense	7706	exon1			TGGAAGGCGGGGC	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12932	protein-coding gene	gene with protein product		600453	"zinc finger protein 147 (estrogen-responsive finger protein)", "tripartite motif-containing 25"	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.416C>T	17.37:g.54990934G>A	ENSP00000323889:p.Ala139Val	Somatic	119	4		WXS	Illumina HiSeq	Phase_1	259	149	NM_005082	0	0	0	4	4		Missense_Mutation	SNP	ENST00000316881.4	37	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.094815	0.56075	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.69685	-0.42;-0.42	5.63	0.746	0.18365	.	0.274132	0.31809	N	0.007021	T	0.55033	0.1895	M	0.67625	2.065	0.09310	N	1	B	0.33379	0.41	B	0.25884	0.064	T	0.46289	-0.9202	10	0.35671	T	0.21	.	7.7359	0.28815	0.2116:0.1238:0.6646:0.0	.	139	Q14258	TRI25_HUMAN	V	139	ENSP00000323889:A139V;ENSP00000445961:A139V	ENSP00000323889:A139V	A	-	2	0	TRIM25	52345933	0.005000	0.15991	0.408000	0.26446	0.974000	0.67602	1.255000	0.32909	0.621000	0.30232	0.561000	0.74099	GCC	.		0.652	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		A	54990934	G	A	54990934	3	1	24	1	0	0	0	0	1	0	0	0	16532	1203	42	2	1512	2	TRIM25	17	54990934	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	47239178	54990934	26204276	45	2135											
SETBP1	26040	broad.mit.edu	37	chr18	42281356	42281356	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcccggcaaagagggggCgagtcagacttcctgccggt	8	6	15	12	3	1	2	1	0	0	2	3	3	3	2	3	4	2	2	3	4	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr18:42281356C>T	ENST00000282030.5	+	2	341	c.45C>T	c.(43-45)ggC>ggT	p.G15G	SETBP1_ENST00000426838.4_Silent_p.G15G	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	15						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AAAGAGGGGGCGAGTCAGACT	0.592									Schinzel-Giedion syndrome																												p.G15G													.	SETBP1-155	0			c.C45T						.						17	21	20					18																	42281356		692	1591	2283	SO:0001819	synonymous_variant	26040	exon2	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AGGGGGCGAGTCA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.45C>T	18.37:g.42281356C>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_001130110	0	0	2	2	0	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																			.		0.592	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		T	42281356	C	T	42281356	2	4	24	1	0	0	0	0	0	0	0	1	14161	755	27	1		1	SETBP1	18	42281356	Silent	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		42281356	35795892	46	2136											
CDC37	11140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10506875	10506875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgctccatgcgttccaccCgggcctgcgggcagggacgg	5	6	15	15	4	0	0	0	0	0	0	2	1	2	1	4	4	3	3	4	4	0	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr19:10506875C>T	ENST00000222005.2	-	2	160	c.107G>A	c.(106-108)cGg>cAg	p.R36Q		NM_007065.3	NP_008996.1	Q16543	CDC37_HUMAN	cell division cycle 37	36					protein targeting (GO:0006605)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	16			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		GCGTTCCACCCGGGCCTGCGG	0.632																																					p.R36Q		.											.	CDC37-522	0			c.G107A						.						39	42	41					19																	10506875		2203	4300	6503	SO:0001583	missense	11140	exon2			TCCACCCGGGCCT	U63131	CCDS12237.1	19p13.2	2013-01-17	2013-01-17		ENSG00000105401	ENSG00000105401			1735	protein-coding gene	gene with protein product	"CDC37 cell division cycle 37 homolog", "Hsp90 co-chaperone Cdc37", "CDC37 (cell division cycle 37, S. cerevisiae, homolog)"	605065	"CDC37 (cell division cycle 37, S. cerevisiae, homolog)", "CDC37 cell division cycle 37 homolog (S. cerevisiae)", "cell division cycle 37 homolog (S. cerevisiae)"			8703009, 8666233	Standard	NM_007065		Approved	P50CDC37	uc002mof.1	Q16543		ENST00000222005.2:c.107G>A	19.37:g.10506875C>T	ENSP00000222005:p.Arg36Gln	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	141	69	NM_007065	0	0	0	0	0	Q53YA2	Missense_Mutation	SNP	ENST00000222005.2	37	CCDS12237.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265565	0.95399	.	.	ENSG00000105401	ENST00000222005	T	0.57436	0.4	4.19	4.19	0.49359	Cdc37, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68568	0.3015	M	0.83852	2.665	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.56216	0.794;0.794	T	0.76130	-0.3072	10	0.87932	D	0	.	14.3942	0.67001	0.0:1.0:0.0:0.0	.	36;36	Q6FG59;Q16543	.;CDC37_HUMAN	Q	36	ENSP00000222005:R36Q	ENSP00000222005:R36Q	R	-	2	0	CDC37	10367875	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.268000	0.78473	2.058000	0.61347	0.555000	0.69702	CGG	.		0.632	CDC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451987.1	NM_007065		T	10506875	C	T	10506875	3	4	24	1	0	0	0	0	1	0	0	0	3074	652	23	1	1057	1	CDC37	19	10506875	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		10506875	48622108	47	2137											
GATA5	140628	hgsc.bcm.edu	37	chr20	61050059	61050059	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcccccgcactcaccgaaGgtgggcctgcggcctgggag	6	4	16	15	3	1	0	1	0	0	0	1	3	1	1	5	4	2	1	5	4	1	0			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr20:61050059G>T	ENST00000252997.2	-	2	580	c.519C>A	c.(517-519)acC>acA	p.T173T	RP13-379O24.3_ENST00000606283.1_lincRNA	NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	173					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			ACTCACCGAAGGTGGGCCTGC	0.721																																					p.T173T		.											.	GATA5-90	0			c.C519A						.						3	4	3					20																	61050059		1891	3784	5675	SO:0001819	synonymous_variant	140628	exon2			ACCGAAGGTGGGC	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"GATA zinc finger domain containing"	15802	protein-coding gene	gene with protein product		611496	"GATA-binding protein 5"			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.519C>A	20.37:g.61050059G>T		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	83	5	NM_080473	0	0	0	0	0	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			.		0.721	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473		T	61050059	G	T	61050059	2	4	24	1	0	0	0	0	0	0	0	1	6277	987	35	4		4	GATA5	20	61050059	Silent	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		61050059	1975461	48	2138											
COL20A1	57642	broad.mit.edu	37	chr20	61945126	61945126	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggagcccaccctccaacctGgccctggcctcggagacccc	7	4	10	20	1	0	1	0	0	0	1	2	3	1	2	8	4	2	0	8	4	1	0			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr20:61945126G>T	ENST00000358894.6	+	18	2341	c.2241G>T	c.(2239-2241)ctG>ctT	p.L747L	COL20A1_ENST00000422202.1_Silent_p.L754L|COL20A1_ENST00000435874.1_Silent_p.L754L|COL20A1_ENST00000326996.6_Silent_p.L747L	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	747	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CCTCCAACCTGGCCCTGGCCT	0.701																																					p.L747L													.	COL20A1-90	0			c.G2241T						.						17	23	21					20																	61945126		2027	4173	6200	SO:0001819	synonymous_variant	57642	exon18			CAACCTGGCCCTG	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2241G>T	20.37:g.61945126G>T		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	107	4	NM_020882	0	0	0	0	0	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	37	CCDS46628.1																																																																																			.		0.701	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61945126	G	T	61945126	2	4	24	1	0	0	0	0	0	0	0	1	3685	1335	47	4		4	COL20A1	20	61945126	Silent	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	895067	61945126	1080394	49	2139											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	162	12	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	24	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		29885562	21419004	50	2140											
ACO2	50	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	41911896	41911896	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtggaataccacgggccTggtgtagactccatctcctg	8	10	11	12	2	1	1	0	0	1	1	4	2	2	2	4	3	1	1	4	3	3	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr22:41911896T>C	ENST00000216254.4	+	6	832	c.810T>C	c.(808-810)ccT>ccC	p.P270P	ACO2_ENST00000466237.1_3'UTR|ACO2_ENST00000396512.3_Silent_p.P270P	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	270				P -> H (in Ref. 6; AAH26196). {ECO:0000305}.	cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						ACCACGGGCCTGGTGTAGACT	0.607																																					p.P270P		.											.	ACO2-290	0			c.T810C						.						63	48	53					22																	41911896		2203	4300	6503	SO:0001819	synonymous_variant	50	exon6			CGGGCCTGGTGTA	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"aconitate hydratase, mitochondrial"	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.810T>C	22.37:g.41911896T>C		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	124	69	NM_001098	0	0	26	50	24	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Silent	SNP	ENST00000216254.4	37	CCDS14017.1																																																																																			.		0.607	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098		C	41911896	T	C	41911896	2	2	24	1	0	0	0	0	0	0	0	1	147	1567	55	3		3	ACO2	22	41911896	Silent	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10	12026334	41911896	9392670	51	2141											
BRCC3	79184	broad.mit.edu;bcgsc.ca	37	chrX	154299904	154299904	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcacagagaaggaggaagtAatggggctgtgcatagggga	14	5	18	4	0	0	1	0	0	0	1	0	5	0	4	0	6	2	4	0	6	4	2	rs367616741		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chrX:154299904A>C	ENST00000369462.1	+	1	127	c.102A>C	c.(100-102)gtA>gtC	p.V34V	MTCP1_ENST00000369476.3_5'Flank|BRCC3_ENST00000330045.7_Silent_p.V34V|MTCP1_ENST00000362018.2_Intron|BRCC3_ENST00000340647.4_Silent_p.V34V|BRCC3_ENST00000369459.2_Silent_p.V34V|BRCC3_ENST00000399042.1_Silent_p.V34V|MTCP1_ENST00000482244.1_5'Flank|CMC4_ENST00000369484.3_5'Flank	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	34	MPN.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AGGAGGAAGTAATGGGGCTGT	0.612																																					p.V34V													.	BRCC3-706	0			c.A102C						.	A	,,	1,3664		0,1,1546,571	41	54	50		102,102,102	2.2	1	X		50	0,6585		0,0,2383,1819	no	coding-synonymous,coding-synonymous,coding-synonymous	BRCC3	NM_001018055.2,NM_001242640.1,NM_024332.3	,,	0,1,3929,2390	CC,CA,AA,A		0.0,0.0273,0.0098	,,	34/292,34/293,34/317	154299904	1,10249	2118	4202	6320	SO:0001819	synonymous_variant	79184	exon1			GGAAGTAATGGGG	X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515			24185	protein-coding gene	gene with protein product	"Lys-63-specific deubiquitinase"	300617	"chromosome X open reading frame 53"	CXorf53		1303175, 14636569	Standard	NM_024332		Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000369462.1:c.102A>C	X.37:g.154299904A>C		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	114	6	NM_024332	0	0	0	0	0	A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	Silent	SNP	ENST00000369462.1	37	CCDS56611.1																																																																																			.		0.612	BRCC3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058788.4	NM_024332		C	154299904	A	C	154299904	2	2	24	1	0	0	0	0	0	0	0	1	1503	349	13	5		5	BRCC3	23	154299904	Silent	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10		154299904	970656	52	2142											
PRKCZ	5590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	2066777	2066777	+	5'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcttccaagccaagcgCtttaacagggtgagtggccc	9	8	10	14	1	1	1	0	1	1	0	2	1	2	1	4	2	3	1	4	2	3	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:2066777C>T	ENST00000400921.2	+	0	545				PRKCZ_ENST00000400920.1_5'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta						actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	AAGCCAAGCGCTTTAACAGGG	0.552																																					p.R137R		.											.	PRKCZ-1465	0			c.C411T						.						48	48	48					1																	2066777		2203	4300	6503	SO:0001623	5_prime_UTR_variant	5590	exon5			CAAGCGCTTTAAC	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.-139C>T	1.37:g.2066777C>T		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	32	18	NM_002744	0	0	0	0	0	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	37	CCDS41229.1																																																																																			.		0.552	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2066777	C	T	2066777	1	4	25	0	1	0	0	0	0	0	0	0	12546	784	28	2		2	PRKCZ	1	2066777	5'UTR	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		2066777	247183844	1	2143											
CAP1	5538	bcgsc.ca	37	chr1	40535490	40535491	+	IGR	INS	-	-	G																															aaccagcccatcccccaaacINSgagccacaaagaaggagcca																								rs200369781|rs377554241|rs370362556	byFrequency	TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:40535490_40535491insG	ENST00000433473.3	-	0	2740				CAP1_ENST00000372797.3_Frame_Shift_Ins_p.R313fs|CAP1_ENST00000372798.1_Frame_Shift_Ins_p.R312fs|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000340450.3_Frame_Shift_Ins_p.R312fs|CAP1_ENST00000372802.1_Frame_Shift_Ins_p.R312fs|CAP1_ENST00000372805.3_Frame_Shift_Ins_p.R313fs|CAP1_ENST00000372792.2_Frame_Shift_Ins_p.R313fs	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ATCCCCCAAACGAGCCACAAAG	0.505																																					p.R313fs													.	CAP1-91	0			c.937_938insG						.																																			SO:0001628	intergenic_variant	10487	exon9			CCCAAACGAGCCA	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 1, infantile"	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40535491_40535491dupG		Somatic	215	1		WXS	Illumina HiSeq	Phase_1	197	22	NM_006367	0	0	0	0	0	B4DY24|Q6FGQ4	Frame_Shift_Ins	INS	ENST00000433473.3	37	CCDS447.1																																																																																			.		0.505	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		G	40535491	-	G	40535490	6	5	25	0	1	1	1	0	0	0	0	0	2625	528	19	0		0	CAP1	1	40535490	IGR	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10	38468713	40535490	208715131	2	2144											
LRRC8C	84230	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90180077	90180077	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgtggcataacagcatcAcctacatcccagagcatata	15	8	6	12	0	1	1	1	0	0	1	2	1	2	1	2	1	5	3	2	1	5	4	rs113075842		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:90180077A>G	ENST00000370454.4	+	3	2203	c.1948A>G	c.(1948-1950)Acc>Gcc	p.T650A	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	650					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		TAACAGCATCACCTACATCCC	0.418																																					p.T650A													.	LRRC8C-97	0			c.A1948G						.						60	56	57					1																	90180077		2203	4300	6503	SO:0001583	missense	84230	exon3			AGCATCACCTACA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1948A>G	1.37:g.90180077A>G	ENSP00000359483:p.Thr650Ala	Somatic	115	2		WXS	Illumina HiSeq	Phase_I	118	37	NM_032270	0	0	0	0	0	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	.	.	.	.	.	.	.	.	.	.	A	0.055	-1.238065	0.01493	.	.	ENSG00000171488	ENST00000370454	T	0.27104	1.69	5.86	-1.34	0.09143	.	0.278989	0.45126	N	0.000389	T	0.03739	0.0106	L	0.38175	1.15	0.32260	N	0.57027	B	0.06786	0.001	B	0.11329	0.006	T	0.44003	-0.9356	10	0.02654	T	1	.	5.6923	0.17837	0.5841:0.0:0.302:0.1139	.	650	Q8TDW0	LRC8C_HUMAN	A	650	ENSP00000359483:T650A	ENSP00000359483:T650A	T	+	1	0	LRRC8C	89952665	1.000000	0.71417	0.987000	0.45799	0.979000	0.70002	1.267000	0.33050	-0.390000	0.07774	0.528000	0.53228	ACC	A|0.500;G|0.500		0.418	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		G	90180077	A	G	90180077	3	3	25	1	0	0	0	0	1	0	0	0	9048	159	6	3	1954	3	LRRC8C	1	90180077	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	49644587	90180077	159070544	3	2145											
ZNF644	84146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	91403569	91403569	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggcctctaacatgatttGataatccaattttagtatca	13	15	6	7	0	2	2	1	2	1	0	3	2	3	2	2	1	1	1	2	1	5	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:91403569G>T	ENST00000370440.1	-	4	3378	c.3161C>A	c.(3160-3162)tCa>tAa	p.S1054*	ZNF644_ENST00000337393.5_Nonsense_Mutation_p.S1054*|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	1054					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(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		AACATGATTTGATAATCCAAT	0.363																																					p.S1054X		.											.	ZNF644-155	0			c.C3161A						.						81	80	81					1																	91403569		2203	4300	6503	SO:0001587	stop_gained	84146	exon4			TGATTTGATAATC	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.3161C>A	1.37:g.91403569G>T	ENSP00000359469:p.Ser1054*	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	16	NM_201269	0	0	4	5	1	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Nonsense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	G	41	9.121790	0.99073	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.694	20.1634	0.98142	0.0:0.0:1.0:0.0	.	.	.	.	X	1054;1054;626	.	ENSP00000337008:S1054X	S	-	2	0	ZNF644	91176157	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.294000	0.96088	2.773000	0.95371	0.655000	0.94253	TCA	.		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		T	91403569	G	T	91403569	4	4	25	1	0	0	0	0	0	1	0	0	18092	1294	45	4	834	4	ZNF644	1	91403569	Nonsense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	1223492	91403569	157847052	4	2146											
ADORA3	140	broad.mit.edu	37	chr1	112026372	112026372	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcgagaagggcttcaaagtGttgcctactttgttggggaa	9	11	14	7	2	1	1	1	0	0	1	1	3	1	2	1	3	2	3	1	3	4	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:112026372G>T	ENST00000369716.4	-	6	1114	c.981C>A	c.(979-981)aaC>aaA	p.N327K	ADORA3_ENST00000369717.4_Missense_Mutation_p.N246K	NM_020683.6	NP_065734.5	P33765	AA3R_HUMAN	adenosine A3 receptor	0					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	GCTTCAAAGTGTTGCCTACTT	0.418																																					p.N327K													.	ADORA3-156	0			c.C981A						.						79	72	74					1																	112026372		2203	4300	6503	SO:0001583	missense	140	exon6			CAAAGTGTTGCCT	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000369716.4:c.981C>A	1.37:g.112026372G>T	ENSP00000358730:p.Asn327Lys	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	110	5	NM_020683	0	0	1	1	0	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000369716.4	37	CCDS838.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.003|0.003	-2.506372|-2.506372	0.00155|0.00155	.|.	.|.	ENSG00000121933|ENSG00000121933	ENST00000369717;ENST00000369716;ENST00000355437;ENST00000443498|ENST00000414219	T;T|.	0.52526|.	2.44;0.66|.	4.6|4.6	2.62|2.62	0.31277|0.31277	.|.	0.961032|.	0.08574|.	N|.	0.925613|.	T|T	0.05318|0.05318	0.0141|0.0141	N|N	0.02916|0.02916	-0.46|-0.46	0.09310|0.09310	N|N	0.999998|0.999998	B;B|.	0.16396|.	0.017;0.001|.	B;B|.	0.15052|.	0.012;0.003|.	T|T	0.41342|0.41342	-0.9514|-0.9514	10|5	0.35671|.	T|.	0.21|.	-3.9086|-3.9086	11.1339|11.1339	0.48362|0.48362	0.0:0.3595:0.6405:0.0|0.0:0.3595:0.6405:0.0	.|.	246;327|.	Q5QNY7;P33765-2|.	.;.|.	K|K	246;327;158;152|187	ENSP00000358731:N246K;ENSP00000358730:N327K|.	ENSP00000347612:N158K|.	N|T	-|-	3|2	2|0	ADORA3|ADORA3	111827895|111827895	0.003000|0.003000	0.15002|0.15002	0.002000|0.002000	0.10522|0.10522	0.088000|0.088000	0.18126|0.18126	0.073000|0.073000	0.14640|0.14640	0.595000|0.595000	0.29777|0.29777	0.655000|0.655000	0.94253|0.94253	AAC|ACA	.		0.418	ADORA3-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157679.1	NM_000677, NM_020683		T	112026372	G	T	112026372	3	4	25	1	0	0	0	0	1	0	0	0	329	1368	48	4	66	4	ADORA3	1	112026372	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	20622803	112026372	137224249	5	2147											
ZC3H11A	9877	hgsc.bcm.edu	37	chr1	203787783	203787786	+	Frame_Shift_Del	DEL	GACA	GACA	-																															gcaagaagggcgctgttttcGacaggtgtgcaggtttcggc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	GACA	GACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:203787783_203787786delGACA	ENST00000545588.1	+	3	3967_3970	c.140_143delGACA	c.(139-144)cgacagfs	p.RQ47fs	ZC3H11A_ENST00000332127.4_Frame_Shift_Del_p.RQ47fs|ZC3H11A_ENST00000367210.1_Frame_Shift_Del_p.RQ47fs|ZC3H11A_ENST00000367212.3_Frame_Shift_Del_p.RQ47fs|ZC3H11A_ENST00000367214.1_Frame_Shift_Del_p.RQ47fs	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	47					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CGCTGTTTTCGACAGGTGTGCAGG	0.426																																					p.47_48del		.											.	ZC3H11A-515	0			c.140_143del						.																																			SO:0001589	frameshift_variant	9877	exon6			.		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"Zinc fingers, CCCH-type domain containing"	29093	protein-coding gene	gene with protein product		613513	"zinc finger CCCH-type domain containing 11A"	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.140_143delGACA	1.37:g.203787783_203787786delGACA	ENSP00000438527:p.Arg47fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	86	22	NM_014827	0	0	0	0	0	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Frame_Shift_Del	DEL	ENST00000545588.1	37	CCDS30978.1																																																																																			.		0.426	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827		-	203787786	GACA	-	203787783	7	5	25	1	0	1	0	1	0	0	0	0	17592	1058	37	0	146	0	ZC3H11A	1	203787783	Frame_Shift_Del	DEL	GACA	TCGA-A4-A5XZ-01A-11D-A31X-10	91761411	203787783	45462838	6	2148											
SUSD4	55061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223536686	223536686	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggatcacggccaagagtcTctggggggactgaggttgct	8	8	16	9	1	2	2	1	1	1	1	3	4	2	4	1	6	1	2	1	6	1	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:223536686T>C	ENST00000343846.3	-	1	715	c.82A>G	c.(82-84)Aga>Gga	p.R28G	SUSD4_ENST00000366878.4_Missense_Mutation_p.R28G|SUSD4_ENST00000366877.3_Missense_Mutation_p.R28G|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000484758.2_Missense_Mutation_p.R28G|SUSD4_ENST00000454695.2_5'UTR|SUSD4_ENST00000344029.6_Missense_Mutation_p.R28G|SUSD4_ENST00000494793.2_Missense_Mutation_p.R28G			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	28						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GCCAAGAGTCTCTGGGGGGAC	0.597																																					p.R28G		.											.	SUSD4-68	0			c.A82G						.						32	32	32					1																	223536686		2202	4299	6501	SO:0001583	missense	55061	exon2			AGAGTCTCTGGGG	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.82A>G	1.37:g.223536686T>C	ENSP00000344219:p.Arg28Gly	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	132	44	NM_017982	0	0	0	0	0	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	37	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722459	0.68959	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000271787;ENST00000344029;ENST00000342943;ENST00000366877	T;T;T	0.38560	1.18;1.18;1.13	4.86	4.86	0.63082	.	0.000000	0.46758	D	0.000278	T	0.43322	0.1242	N	0.14661	0.345	0.31376	N	0.679575	D;D;D	0.63880	0.987;0.992;0.993	D;D;P	0.71656	0.942;0.974;0.787	T	0.50939	-0.8768	10	0.66056	D	0.02	-11.375	8.8024	0.34916	0.0:0.0:0.1902:0.8098	.	28;28;28	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	G	28	ENSP00000344219:R28G;ENSP00000355843:R28G;ENSP00000339926:R28G	ENSP00000271787:R28G	R	-	1	2	SUSD4	221603309	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.992000	0.56980	1.800000	0.52685	0.459000	0.35465	AGA	.		0.597	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		C	223536686	T	C	223536686	3	2	25	1	0	0	0	0	1	0	0	0	15442	1559	54	3	1575	3	SUSD4	1	223536686	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	19748903	223536686	25713935	7	2149											
SNAP47	116841	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	227935595	227935595	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcttccccctctccagcaTagttgagatcaagaaggagg	11	8	10	12	0	2	2	1	1	1	2	4	4	3	3	3	2	2	3	3	2	3	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:227935595T>A	ENST00000366759.4	+	2	707	c.293T>A	c.(292-294)aTa>aAa	p.I98K	SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000315781.5_Missense_Mutation_p.I98K|SNAP47-AS1_ENST00000413347.2_RNA	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	98					long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						CTCTCCAGCATAGTTGAGATC	0.532																																					p.I98K													.	SNAP47-91	0			c.T293A						.						58	57	57					1																	227935595		2203	4300	6503	SO:0001583	missense	116841	exon2			CCAGCATAGTTGA	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 142"	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.293T>A	1.37:g.227935595T>A	ENSP00000355721:p.Ile98Lys	Somatic	98	1		WXS	Illumina HiSeq	Phase_I	86	37	NM_053052	0	0	10	19	9	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.94|14.94	2.684882|2.684882	0.47991|0.47991	.|.	.|.	ENSG00000143740|ENSG00000143740	ENST00000426344|ENST00000366759;ENST00000315781	.|T;T	.|0.22539	.|1.95;1.95	4.08|4.08	4.08|4.08	0.47627|0.47627	.|.	.|0.111196	.|0.64402	.|D	.|0.000014	T|T	0.43144|0.43144	0.1234|0.1234	M|M	0.77616|0.77616	2.38|2.38	0.42430|0.42430	D|D	0.99267|0.99267	.|D;D	.|0.67145	.|0.989;0.996	.|P;D	.|0.65010	.|0.885;0.931	T|T	0.47086|0.47086	-0.9144|-0.9144	5|10	.|0.87932	.|D	.|0	-1.6503|-1.6503	11.0526|11.0526	0.47898|0.47898	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|98;98	.|Q5SQN1;Q5SQN1-2	.|SNP47_HUMAN;.	Q|K	89|98	.|ENSP00000355721:I98K;ENSP00000314157:I98K	.|ENSP00000314157:I98K	H|I	+|+	3|2	2|0	SNAP47|SNAP47	226002218|226002218	0.999000|0.999000	0.42202|0.42202	0.004000|0.004000	0.12327|0.12327	0.004000|0.004000	0.04260|0.04260	7.222000|7.222000	0.78025|0.78025	1.716000|1.716000	0.51395|0.51395	0.482000|0.482000	0.46254|0.46254	CAT|ATA	.		0.532	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052		A	227935595	T	A	227935595	3	1	25	1	0	0	0	0	1	0	0	0	14864	1406	49	5	299	5	SNAP47	1	227935595	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	4398909	227935595	21315026	8	2150											
C2orf28	51374	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27436144	27436144	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgcccgttgctgcctgAatcagaagggcaccatcttg	8	10	11	12	1	2	2	1	1	1	1	2	2	2	2	3	1	4	4	3	1	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:27436144A>G	ENST00000606999.1	+	2	257	c.199A>G	c.(199-201)Aat>Gat	p.N67D	ATRAID_ENST00000405489.3_Missense_Mutation_p.N9D|SLC5A6_ENST00000310574.3_5'Flank|SLC5A6_ENST00000408041.1_5'Flank|ATRAID_ENST00000380171.3_Missense_Mutation_p.N122D	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor	67					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)											TTGCTGCCTGAATCAGAAGGG	0.468																																					p.N122D													.	.	0			c.A364G						.						84	82	82					2																	27436144		2203	4300	6503	SO:0001583	missense	51374	exon2			TGCCTGAATCAGA	BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"apoptosis-related protein 3"		"chromosome 2 open reading frame 28"	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405	ENST00000606999.1:c.199A>G	2.37:g.27436144A>G	ENSP00000476080:p.Asn67Asp	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	83	23	NM_080592	0	0	306	437	131	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Missense_Mutation	SNP	ENST00000606999.1	37		.	.	.	.	.	.	.	.	.	.	A	15.74	2.922795	0.52653	.	.	ENSG00000138085	ENST00000380171;ENST00000405489;ENST00000419744	T;T	0.43294	1.6;0.95	5.14	3.95	0.45737	.	0.376184	0.29791	N	0.011188	T	0.34861	0.0912	L	0.50333	1.59	0.25876	N	0.983648	B;P	0.43352	0.358;0.804	B;B	0.40066	0.116;0.318	T	0.17289	-1.0374	10	0.38643	T	0.18	1.3171	8.1132	0.30926	0.906:0.0:0.094:0.0	.	67;122	Q6UW56;Q6UW56-3	APR3_HUMAN;.	D	122;9;9	ENSP00000369518:N122D;ENSP00000384033:N9D	ENSP00000369518:N122D	N	+	1	0	C2orf28	27289648	0.851000	0.29673	1.000000	0.80357	0.993000	0.82548	1.004000	0.29822	0.869000	0.35703	0.459000	0.35465	AAT	.		0.468	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085		G	27436144	A	G	27436144	3	3	25	1	0	0	0	0	1	0	0	0	2166	246	9	3	370	3	C2orf28	2	27436144	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		27436144	215763229	9	2151											
FAM98A	25940	broad.mit.edu	37	chr2	33810281	33810281	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgcttatttcctcttccTccccctcggccaccatggtc	4	14	6	17	1	1	1	0	1	1	0	6	1	4	1	6	2	1	1	6	2	1	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:33810281T>C	ENST00000238823.8	-	8	1259	c.1119A>G	c.(1117-1119)ggA>ggG	p.G373G	FAM98A_ENST00000441530.2_Silent_p.G178G|FAM98A_ENST00000403368.1_3'UTR|FAM98A_ENST00000498340.1_5'Flank			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	374	Gly-rich.						poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					TTCCTCTTCCTCCCCCTCGGC	0.562																																					p.G373G													.	FAM98A-91	0			c.A1119G						.						228	186	200					2																	33810281		2203	4300	6503	SO:0001819	synonymous_variant	25940	exon8			TCTTCCTCCCCCT		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.1119A>G	2.37:g.33810281T>C		Somatic	73	4		WXS	Illumina HiSeq	Phase_I	124	7	NM_015475	0	0	49	49	0	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																			.		0.562	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		C	33810281	T	C	33810281	2	2	25	1	0	0	0	0	0	0	0	1	5675	1538	54	3		3	FAM98A	2	33810281	Silent	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	6374137	33810281	209389092	10	2152											
TMEM178	130733	broad.mit.edu	37	chr2	39934299	39934299	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagagcttgacccagcacGtggctggactcctgttcctc	7	9	12	13	1	0	2	0	1	0	1	3	4	2	3	3	3	2	4	3	3	0	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:39934299G>T	ENST00000281961.2	+	3	681	c.625G>T	c.(625-627)Gtg>Ttg	p.V209L	TMEM178A_ENST00000482239.1_3'UTR	NM_152390.2	NP_689603.2	Q8NBL3	T178A_HUMAN	transmembrane protein 178A	209						integral component of membrane (GO:0016021)											GACCCAGCACGTGGCTGGACT	0.602																																					p.V209L													.	.	0			c.G625T						.						63	54	57					2																	39934299		2203	4300	6503	SO:0001583	missense	130733	exon3			CAGCACGTGGCTG	BC029530	CCDS1804.1	2p22.1	2012-06-29	2012-06-29	2012-06-29	ENSG00000152154	ENSG00000152154			28517	protein-coding gene	gene with protein product			"transmembrane protein 178"	TMEM178		12975309	Standard	NM_001167959		Approved	MGC33926	uc002rrt.3	Q8NBL3	OTTHUMG00000128591	ENST00000281961.2:c.625G>T	2.37:g.39934299G>T	ENSP00000281961:p.Val209Leu	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	101	3	NM_152390	0	0	1	1	0	Q6UWI6|Q8N6N4	Missense_Mutation	SNP	ENST00000281961.2	37	CCDS1804.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.791631	0.90367	.	.	ENSG00000152154	ENST00000281961	T	0.64803	-0.12	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.57695	0.2071	L	0.41492	1.28	0.58432	D	0.999996	P	0.47677	0.899	P	0.44394	0.448	T	0.57093	-0.7870	9	.	.	.	-11.7503	16.2065	0.82133	0.0:0.0:1.0:0.0	.	209	Q8NBL3	TM178_HUMAN	L	209	ENSP00000281961:V209L	.	V	+	1	0	TMEM178	39787803	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.824000	0.69279	2.433000	0.82419	0.650000	0.86243	GTG	.		0.602	TMEM178A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250445.2	NM_152390		T	39934299	G	T	39934299	3	4	25	1	0	0	0	0	1	0	0	0	16127	1145	40	4	635	4	TMEM178	2	39934299	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	6124018	39934299	203265074	11	2153											
CLEC4F	165530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	71036918	71036918	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcccatctgtccagcgccaGgagccctctgtgcccctgtc	4	9	10	18	1	2	0	0	0	2	0	5	1	4	1	6	1	3	0	6	1	0	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:71036918G>A	ENST00000272367.2	-	6	1687	c.1611C>T	c.(1609-1611)tcC>tcT	p.S537S	CLEC4F_ENST00000426626.1_Silent_p.S537S	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	537	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						TCCAGCGCCAGGAGCCCTCTG	0.552																																					p.S537S	Colon(107;10 2157 6841 26035)	.											.	CLEC4F-95	0			c.C1611T						.						156	141	146					2																	71036918		2203	4300	6503	SO:0001819	synonymous_variant	165530	exon6			GCGCCAGGAGCCC	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.1611C>T	2.37:g.71036918G>A		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	88	25	NM_173535	0	0	0	0	0	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			.		0.552	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		A	71036918	G	A	71036918	2	1	25	1	0	0	0	0	0	0	0	1	3522	987	35	2		2	CLEC4F	2	71036918	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	31102619	71036918	172162455	12	2154											
RMND5A	64795	broad.mit.edu;bcgsc.ca	37	chr2	86947925	86947925	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcaagcacgagatcctgcaGagccacggtagggcggcccg	9	4	14	14	4	1	2	1	0	0	2	2	3	2	2	3	3	3	3	3	3	2	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:86947925G>A	ENST00000283632.4	+	1	630	c.135G>A	c.(133-135)caG>caA	p.Q45Q	RNF103-CHMP3_ENST00000604011.1_Intron|CHMP3_ENST00000439940.2_Intron	NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	45										kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						AGATCCTGCAGAGCCACGGTA	0.726																																					p.Q45Q													.	RMND5A-92	0			c.G135A						.						13	16	15					2																	86947925		2174	4283	6457	SO:0001819	synonymous_variant	64795	exon1			CCTGCAGAGCCAC	BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561			25850	protein-coding gene	gene with protein product	"GID complex subunit 2 homolog A"					12477932	Standard	NM_022780		Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.135G>A	2.37:g.86947925G>A		Somatic	94	1		WXS	Illumina HiSeq	Phase_I	52	22	NM_022780	0	0	0	0	0	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	Silent	SNP	ENST00000283632.4	37	CCDS1991.1																																																																																			.		0.726	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252591.2	NM_022780		A	86947925	G	A	86947925	2	1	25	1	0	0	0	0	0	0	0	1	13429	933	33	2		2	RMND5A	2	86947925	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	15911007	86947925	156251448	13	2155											
SCN3A	6328	ucsc.edu;bcgsc.ca	37	chr2	165948982	165948982	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgaggatcatgatgctgAtatcaaagacttgtctggtt	12	13	11	5	0	3	5	2	3	1	2	3	6	3	6	0	2	1	2	0	2	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:165948982A>G	ENST00000360093.3	-	27	5080	c.4589T>C	c.(4588-4590)aTc>aCc	p.I1530T	AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000409101.3_Missense_Mutation_p.I1481T|SCN3A_ENST00000540861.1_Missense_Mutation_p.I13T|SCN3A_ENST00000283254.7_Missense_Mutation_p.I1530T|SCN3A_ENST00000465043.1_5'UTR	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1530					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGATGCTGATATCAAAGAC	0.388																																					p.I1530T													.	SCN3A-141	0			c.T4589C						.						133	108	117					2																	165948982		2203	4300	6503	SO:0001583	missense	6328	exon27			ATGCTGATATCAA	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4589T>C	2.37:g.165948982A>G	ENSP00000353206:p.Ile1530Thr	Somatic	180	4		WXS	Illumina HiSeq		228	125	NM_006922	0	0	0	0	0	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	A	27.2	4.812464	0.90707	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.98776	0.9588	M	0.92738	3.34	0.58432	D	0.999999	D;D;D	0.71674	0.996;0.997;0.998	D;D;D	0.77557	0.99;0.963;0.948	D	0.99581	1.0973	10	0.59425	D	0.04	.	16.4053	0.83662	1.0:0.0:0.0:0.0	.	1481;1481;1530	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	T	1530;1530;1481;13	ENSP00000353206:I1530T;ENSP00000283254:I1530T;ENSP00000386726:I1481T;ENSP00000439920:I13T	ENSP00000283254:I1530T	I	-	2	0	SCN3A	165657228	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.287000	0.95975	2.333000	0.79357	0.482000	0.46254	ATC	.		0.388	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		G	165948982	A	G	165948982	3	3	25	1	0	0	0	0	1	0	0	0	13950	333	12	3	1421	3	SCN3A	2	165948982	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	79001057	165948982	77250391	14	2156											
SCN1A	6323	ucsc.edu;bcgsc.ca	37	chr2	166892799	166892799	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caatttctgctgtatgattgGacatacaactgtctttcttg	9	17	7	8	0	3	1	0	1	3	0	3	2	3	2	0	1	3	2	0	1	4	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:166892799G>A	ENST00000303395.4	-	16	3187	c.3188C>T	c.(3187-3189)tCc>tTc	p.S1063F	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.S1052F|SCN1A_ENST00000409050.1_Missense_Mutation_p.S1035F|SCN1A_ENST00000423058.2_Missense_Mutation_p.S1063F|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1063					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGTATGATTGGACATACAACT	0.313																																					p.S1063F													.	SCN1A-147	0			c.C3188T						.						131	122	125					2																	166892799		2203	4299	6502	SO:0001583	missense	6323	exon16			TGATTGGACATAC	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3188C>T	2.37:g.166892799G>A	ENSP00000303540:p.Ser1063Phe	Somatic	179	3		WXS	Illumina HiSeq		224	54	NM_001165963	0	0	0	0	0	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204104	0.58234	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85	5.44	5.44	0.79542	Sodium ion transport-associated (1);	0.261229	0.34245	N	0.004126	T	0.81278	0.4789	L	0.54323	1.7	0.44627	D	0.997601	P;B;B	0.41313	0.745;0.0;0.274	B;B;B	0.36719	0.231;0.001;0.179	D	0.83562	0.0107	10	0.72032	D	0.01	.	12.914	0.58195	0.0747:0.0:0.9253:0.0	.	1052;1035;1063	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	F	1063;1063;1052;1035	ENSP00000407030:S1063F;ENSP00000303540:S1063F;ENSP00000364554:S1052F;ENSP00000386312:S1035F	ENSP00000303540:S1063F	S	-	2	0	SCN1A	166601045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.520000	0.67080	2.709000	0.92574	0.655000	0.94253	TCC	.		0.313	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		A	166892799	G	A	166892799	3	1	25	1	0	0	0	0	1	0	0	0	13946	1174	41	2	2885	2	SCN1A	2	166892799	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	943817	166892799	76306574	15	2157											
SPEG	10290	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220342479	220342479	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggaaggagactcagcgacTtttatgacatccaccaggag	13	7	12	9	1	1	2	1	1	0	1	2	7	2	4	2	3	1	0	2	3	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:220342479T>C	ENST00000312358.7	+	21	4930	c.4798T>C	c.(4798-4800)Ttt>Ctt	p.F1600L	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1600					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACTCAGCGACTTTTATGACAT	0.612																																					p.F1600L													.	SPEG-383	0			c.T4798C						.						85	93	90					2																	220342479		2025	4169	6194	SO:0001583	missense	10290	exon21			AGCGACTTTTATG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4798T>C	2.37:g.220342479T>C	ENSP00000311684:p.Phe1600Leu	Somatic	68	1		WXS	Illumina HiSeq	Phase_I	85	46	NM_005876	0	0	0	0	0	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.167160	0.38217	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.38887	1.11	4.84	4.84	0.62591	Protein kinase-like domain (1);	0.182541	0.26453	N	0.024291	T	0.35219	0.0924	L	0.40543	1.245	0.80722	D	1	B	0.25904	0.137	B	0.28465	0.09	T	0.12091	-1.0561	10	0.26408	T	0.33	.	13.4398	0.61106	0.0:0.0:0.0:1.0	.	1600	Q15772	SPEG_HUMAN	L	1600	ENSP00000311684:F1600L	ENSP00000265327:F1600L	F	+	1	0	SPEG	220050723	0.996000	0.38824	0.989000	0.46669	0.935000	0.57460	1.911000	0.39937	2.148000	0.66965	0.533000	0.62120	TTT	.		0.612	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		C	220342479	T	C	220342479	3	2	25	1	0	0	0	0	1	0	0	0	15068	1609	56	3	4892	3	SPEG	2	220342479	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	53449680	220342479	22856894	16	2158											
PASK	23178	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242082279	242082279	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgtcctgctctggcagaGtctggaaagcccattccttc	6	11	10	14	1	2	1	0	0	2	1	5	2	4	2	3	2	2	3	3	2	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:242082279G>T	ENST00000405260.1	-	2	867	c.169C>A	c.(169-171)Ctc>Atc	p.L57I	PASK_ENST00000358649.4_Missense_Mutation_p.L57I|PASK_ENST00000539818.1_Intron|PASK_ENST00000403638.3_Missense_Mutation_p.L57I|PASK_ENST00000234040.4_Missense_Mutation_p.L57I|PASK_ENST00000544142.1_Missense_Mutation_p.D5E	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	57					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CTCTGGCAGAGTCTGGAAAGC	0.562																																					p.L57I													.	PASK-536	0			c.C169A						.						85	73	77					2																	242082279		2203	4300	6503	SO:0001583	missense	23178	exon2			GGCAGAGTCTGGA	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.169C>A	2.37:g.242082279G>T	ENSP00000384016:p.Leu57Ile	Somatic	53	2		WXS	Illumina HiSeq	Phase_I	56	30	NM_001252122	0	0	1	2	1	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.67|17.67	3.446805|3.446805	0.63178|0.63178	.|.	.|.	ENSG00000115687|ENSG00000115687	ENST00000544142|ENST00000234040;ENST00000405260;ENST00000358649;ENST00000403638;ENST00000452907	T|T;T;T;T	0.67523|0.75154	-0.27|-0.91;-0.91;-0.87;0.06	4.39|4.39	4.39|4.39	0.52855|0.52855	.|.	.|0.000000	.|0.41001	.|D	.|0.000973	D|D	0.83147|0.83147	0.5191|0.5191	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	B|D;D;D;D	0.27732|0.89917	0.187|0.999;0.999;1.0;0.999	B|D;D;D;D	0.27500|0.83275	0.08|0.994;0.996;0.996;0.994	D|D	0.84236|0.84236	0.0469|0.0469	9|10	0.87932|0.59425	D|D	0|0.04	.|.	13.1962|13.1962	0.59740|0.59740	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	5|57;57;57;57	F5GYW7|B7Z7R6;Q96RG2-2;G5E9F1;Q96RG2	.|.;.;.;PASK_HUMAN	E|I	5|57	ENSP00000441374:D5E|ENSP00000234040:L57I;ENSP00000384016:L57I;ENSP00000351475:L57I;ENSP00000384438:L57I	ENSP00000441374:D5E|ENSP00000234040:L57I	D|L	-|-	3|1	2|0	PASK|PASK	241730952|241730952	1.000000|1.000000	0.71417|0.71417	0.934000|0.934000	0.37439|0.37439	0.435000|0.435000	0.31806|0.31806	4.949000|4.949000	0.63596|0.63596	2.382000|2.382000	0.81193|0.81193	0.561000|0.561000	0.74099|0.74099	GAC|CTC	.		0.562	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		T	242082279	G	T	242082279	3	4	25	1	0	0	0	0	1	0	0	0	11498	1029	36	4	3870	4	PASK	2	242082279	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	21739800	242082279	1117094	17	2159											
HDLBP	3069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242196033	242196033	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctgctcggcagagatgagTaagacttcatggcgagcttt	10	10	12	9	2	1	3	1	1	0	2	2	5	1	3	1	2	2	4	1	2	1	3	rs200251201		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:242196033T>C	ENST00000391975.1	-	6	866	c.639A>G	c.(637-639)ttA>ttG	p.L213L	HDLBP_ENST00000427183.2_Silent_p.L249L|HDLBP_ENST00000310931.4_Silent_p.L213L|HDLBP_ENST00000391976.2_Silent_p.L213L	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	213	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CAGAGATGAGTAAGACTTCAT	0.567																																					p.L249L		.											.	HDLBP-290	0			c.A747G						.						176	156	163					2																	242196033		2203	4300	6503	SO:0001819	synonymous_variant	3069	exon7			GATGAGTAAGACT		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.639A>G	2.37:g.242196033T>C		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	131	35	NM_001243900	0	0	84	114	30	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	37	CCDS2547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.630|4.630	0.117115|0.117115	0.08881|0.08881	.|.	.|.	ENSG00000115677|ENSG00000115677	ENST00000373292|ENST00000453141	.|.	.|.	.|.	5.79|5.79	-0.967|-0.967	0.10316|0.10316	.|.	.|.	.|.	.|.	.|.	T|T	0.42223|0.42223	0.1193|0.1193	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29701|0.29701	-1.0003|-1.0003	4|4	.|.	.|.	.|.	-20.9924|-20.9924	2.4822|2.4822	0.04590|0.04590	0.1601:0.3764:0.3089:0.1546|0.1601:0.3764:0.3089:0.1546	.|.	.|.	.|.	.|.	A|C	91|114	.|.	.|.	T|Y	-|-	1|2	0|0	HDLBP|HDLBP	241844706|241844706	0.522000|0.522000	0.26266|0.26266	0.991000|0.991000	0.47740|0.47740	0.427000|0.427000	0.31564|0.31564	-0.124000|-0.124000	0.10595|0.10595	0.095000|0.095000	0.17434|0.17434	-0.326000|-0.326000	0.08463|0.08463	ACT|TAC	T|0.999;C|0.001		0.567	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		C	242196033	T	C	242196033	2	2	25	1	0	0	0	0	0	0	0	1	7046	1635	57	3		3	HDLBP	2	242196033	Silent	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	113754	242196033	1003340	18	2160											
CELSR3	1951	bcgsc.ca	37	chr3	48692763	48692763	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtagtatctcagatgcacTgtatgccattgcccgtcact	8	14	8	11	1	2	1	2	0	1	1	3	1	2	1	2	0	3	4	2	0	3	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:48692763T>A	ENST00000164024.4	-	5	5086	c.4806A>T	c.(4804-4806)acA>acT	p.T1602T	CELSR3_ENST00000544264.1_Silent_p.T1602T	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1602	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCAGATGCACTGTATGCCATT	0.577																																					p.T1602T													.	CELSR3-523	0			c.A4806T						.						137	126	130					3																	48692763		2203	4300	6503	SO:0001819	synonymous_variant	1951	exon5			ATGCACTGTATGC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.4806A>T	3.37:g.48692763T>A		Somatic	104	3		WXS	Illumina HiSeq	Phase_1	75	26	NM_001407	0	0	0	0	0	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			.		0.577	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48692763	T	A	48692763	2	1	25	1	0	0	0	0	0	0	0	1	3229	1567	55	5		5	CELSR3	3	48692763	Silent	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10		48692763	149329667	19	2161											
BSN	8927	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49689059	49689059	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctattcctctgacggcatCtctagctcccagagtgagat	8	11	10	12	1	2	3	0	2	2	2	5	4	4	3	2	2	1	3	2	2	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:49689059C>A	ENST00000296452.4	+	5	2184	c.2070C>A	c.(2068-2070)atC>atA	p.I690I		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	690					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CTGACGGCATCTCTAGCTCCC	0.602																																					p.I690I													.	BSN-97	0			c.C2070A						.						97	88	91					3																	49689059		2203	4300	6503	SO:0001819	synonymous_variant	8927	exon5			CGGCATCTCTAGC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.2070C>A	3.37:g.49689059C>A		Somatic	107	1		WXS	Illumina HiSeq	Phase_I	88	35	NM_003458	0	0	0	0	0	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			.		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49689059	C	A	49689059	2	1	25	1	0	0	0	0	0	0	0	1	1533	903	32	4		4	BSN	3	49689059	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	996296	49689059	148333371	20	2162											
ACOX2	8309	hgsc.bcm.edu;bcgsc.ca	37	chr3	58519841	58519842	+	Frame_Shift_Ins	INS	-	-	TATATTT																															gctctcacgaagactctgtgINStatatttaaggccacgtctc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:58519841_58519842insTATATTT	ENST00000302819.5	-	4	645_646	c.354_355insAAATATA	c.(352-357)atacacfs	p.H119fs	ACOX2_ENST00000459701.2_Frame_Shift_Ins_p.H119fs	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	119					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)		AAGACTCTGTGTATATTTAAGG	0.54																																					p.H119fs		.											.	ACOX2-90	0			c.355_356insAAATATA						.																																			SO:0001589	frameshift_variant	8309	exon4			.	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.348_354dupAAATATA	3.37:g.58519842_58519848dupTATATTT	ENSP00000307697:p.His119fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	65	12	NM_003500	0	0	0	0	0	A6NF16|B2R8U5	Frame_Shift_Ins	INS	ENST00000302819.5	37	CCDS33775.1																																																																																			.		0.54	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			TATATTT	58519842	-	TATATTT	58519841	7	5	25	1	0	1	1	0	0	0	0	0	159	1377	48	0	1738	0	ACOX2	3	58519841	Frame_Shift_Ins	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10	8830782	58519841	139502589	21	2163											
CADM2	253559	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	85851274	85851274	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caattttgacctgcagggttGatcaaaatgataacacctcc	13	11	7	10	0	1	3	1	3	0	0	2	3	2	3	3	1	2	2	3	1	4	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:85851274G>C	ENST00000407528.2	+	2	201	c.139G>C	c.(139-141)Gat>Cat	p.D47H	CADM2-AS2_ENST00000467225.1_RNA|CADM2_ENST00000383699.3_Missense_Mutation_p.D56H|CADM2_ENST00000405615.2_Missense_Mutation_p.D49H	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	47	Ig-like V-type.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTGCAGGGTTGATCAAAATGA	0.408																																					p.D56H		.											.	CADM2-228	0			c.G166C						.						90	75	80					3																	85851274		2203	4300	6503	SO:0001583	missense	253559	exon3			AGGGTTGATCAAA	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.139G>C	3.37:g.85851274G>C	ENSP00000384575:p.Asp47His	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	110	6	NM_001167675	0	0	0	0	0	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.343676	0.61073	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.64991	-0.13;-0.13;-0.13	5.27	5.27	0.74061	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.162021	0.53938	D	0.000054	T	0.64811	0.2632	L	0.35542	1.07	0.80722	D	1	P;P;P	0.50066	0.805;0.854;0.931	P;P;P	0.53689	0.591;0.517;0.732	T	0.59500	-0.7443	10	0.25751	T	0.34	.	19.2384	0.93871	0.0:0.0:1.0:0.0	.	49;56;47	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	H	56;47;49	ENSP00000373200:D56H;ENSP00000384575:D47H;ENSP00000384193:D49H	ENSP00000373200:D56H	D	+	1	0	CADM2	85933964	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.420000	0.97426	2.621000	0.88768	0.544000	0.68410	GAT	.		0.408	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		C	85851274	G	C	85851274	3	2	25	1	0	0	0	0	1	0	0	0	2573	1290	45	4	216	4	CADM2	3	85851274	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	27331433	85851274	112171156	22	2164											
PROS1	5627	broad.mit.edu	37	chr3	93646100	93646100	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccataaatgcttaccgtttcCgggtcattttcaaagacctc	10	13	6	12	2	2	1	2	0	0	1	4	1	3	1	4	1	2	2	4	1	4	5	rs6121		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:93646100C>T	ENST00000394236.3	-	2	544	c.228G>A	c.(226-228)ccG>ccA	p.P76P	PROS1_ENST00000407433.1_5'UTR	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	76	Gla. {ECO:0000255|PROSITE- ProRule:PRU00463}.		P -> L (in dbSNP:rs73846070). {ECO:0000269|PubMed:10613647, ECO:0000269|PubMed:15712227, ECO:0000269|PubMed:7803790}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	TTACCGTTTCCGGGTCATTTT	0.388																																					p.P76P													.	PROS1-153	0			c.G228A						.						102	100	101					3																	93646100		2203	4300	6503	SO:0001819	synonymous_variant	5627	exon2			CGTTTCCGGGTCA		CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.228G>A	3.37:g.93646100C>T		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	119	4	NM_000313	0	0	0	0	0	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Silent	SNP	ENST00000394236.3	37	CCDS2923.1																																																																																			C|0.999;A|0.001		0.388	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		T	93646100	C	T	93646100	2	4	25	1	0	0	0	0	0	0	0	1	12587	639	23	1		1	PROS1	3	93646100	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	7794826	93646100	104376330	23	2165											
CCDC52	152185	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113176133	113176133	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagtttaacgggcaactcttCctgtgggaattcagccactt	9	12	9	11	1	2	0	1	0	1	0	3	1	3	1	2	2	3	2	2	2	3	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:113176133C>T	ENST00000295872.4	-	13	1766	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	503					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						GGCAACTCTTCCTGTGGGAAT	0.448																																					p.E503K													.	SPICE1-70	0			c.G1507A						.						102	101	101					3																	113176133		2203	4300	6503	SO:0001583	missense	152185	exon13			ACTCTTCCTGTGG	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"spindle and centriole protein"	613447	"coiled-coil domain containing 52"	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1507G>A	3.37:g.113176133C>T	ENSP00000295872:p.Glu503Lys	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	116	46	NM_144718	0	0	3	9	6	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.006842	0.74932	.	.	ENSG00000163611	ENST00000295872	T	0.36878	1.23	5.63	4.75	0.60458	.	0.237434	0.37483	N	0.002065	T	0.39759	0.1090	M	0.65975	2.015	0.39240	D	0.963841	P;P	0.50156	0.932;0.872	P;P	0.45856	0.495;0.495	T	0.41645	-0.9497	10	0.54805	T	0.06	-13.2604	9.489	0.38948	0.0:0.9063:0.0:0.0937	.	399;503	B3KX77;Q8N0Z3	.;SPICE_HUMAN	K	503	ENSP00000295872:E503K	ENSP00000295872:E503K	E	-	1	0	SPICE1	114658823	1.000000	0.71417	1.000000	0.80357	0.535000	0.34838	2.750000	0.47500	2.659000	0.90383	0.561000	0.74099	GAA	.		0.448	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718		T	113176133	C	T	113176133	3	4	25	1	0	0	0	0	1	0	0	0	2828	864	30	2	1084	2	CCDC52	3	113176133	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	19530033	113176133	84846297	24	2166											
ALDH1L1	10840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	125826081	125826081	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgaaaacagttggctcaaAgaagaaccctgcaagagaga	17	6	11	7	0	1	5	1	1	0	4	1	6	1	5	1	1	3	3	1	1	6	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:125826081A>C	ENST00000393434.2	-	21	2705	c.2356T>G	c.(2356-2358)Ttt>Gtt	p.F786V	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.F786V|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.F796V|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.F685V	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	786	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	GTTGGCTCAAAGAAGAACCCT	0.557																																					p.F796V		.											.	ALDH1L1-156	0			c.T2386G						.						130	115	120					3																	125826081		2203	4300	6503	SO:0001583	missense	10840	exon21			GCTCAAAGAAGAA	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"Aldehyde dehydrogenases"	3978	protein-coding gene	gene with protein product	"cytosolic 10-formyltetrahydrofolate dehydrogenase"	600249	"formyltetrahydrofolate dehydrogenase"	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.2356T>G	3.37:g.125826081A>C	ENSP00000377083:p.Phe786Val	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	56	36	NM_001270364	0	0	0	0	0	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.660489	0.29515	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74	3.98	3.98	0.46160	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.56093	0.1962	N	0.00450	-1.49	0.80722	D	1	P;D;P	0.54772	0.755;0.968;0.501	P;D;P	0.63793	0.81;0.918;0.673	T	0.65203	-0.6225	10	0.27082	T	0.32	.	10.8723	0.46891	1.0:0.0:0.0:0.0	.	685;321;786	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	V	796;786;685;786	ENSP00000273450:F796V;ENSP00000420293:F786V;ENSP00000395881:F685V;ENSP00000377083:F786V	ENSP00000273450:F796V	F	-	1	0	ALDH1L1	127308771	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.579000	0.46059	1.677000	0.50941	0.260000	0.18958	TTT	.		0.557	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		C	125826081	A	C	125826081	3	2	25	1	0	0	0	0	1	0	0	0	494	72	3	5	364	5	ALDH1L1	3	125826081	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	12649948	125826081	72196349	25	2167											
PRKCI	5584	bcgsc.ca	37	chr3	170002334	170002334	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttgaaactggacaatgtaTtactggactctgaaggccac	13	11	9	8	0	1	2	0	2	1	0	1	4	1	4	1	3	2	1	1	3	5	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:170002334T>C	ENST00000295797.4	+	12	1458	c.1153T>C	c.(1153-1155)Tta>Cta	p.L385L		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	385	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	GGACAATGTATTACTGGACTC	0.338																																					p.L385L													.	PRKCI-1378	0			c.T1153C						.						61	61	61					3																	170002334		2203	4299	6502	SO:0001819	synonymous_variant	5584	exon12			AATGTATTACTGG		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1153T>C	3.37:g.170002334T>C		Somatic	553	9		WXS	Illumina HiSeq	Phase_1	800	449	NM_002740	0	0	5	17	12	D3DNQ4|Q8WW06	Silent	SNP	ENST00000295797.4	37	CCDS3212.2																																																																																			.		0.338	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		C	170002334	T	C	170002334	2	2	25	1	0	0	0	0	0	0	0	1	12543	1490	52	3		3	PRKCI	3	170002334	Silent	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	44176253	170002334	28020096	26	2168											
HTT	3064	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	3230734	3230734	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatcagtgaggtggtcagaTccgtaagtgagccttcccat	9	11	12	9	1	2	4	2	3	0	1	4	4	4	4	3	2	1	1	3	2	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr4:3230734T>C	ENST00000355072.5	+	59	8252	c.8107T>C	c.(8107-8109)Tcc>Ccc	p.S2703P	HTT_ENST00000513806.1_3'UTR	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2703					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GGTGGTCAGATCCGTAAGTGA	0.602																																					p.S2703P													.	HTT-281	0			c.T8107C						.						84	88	87					4																	3230734		2182	4272	6454	SO:0001583	missense	3064	exon59			GTCAGATCCGTAA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8107T>C	4.37:g.3230734T>C	ENSP00000347184:p.Ser2703Pro	Somatic	55	1		WXS	Illumina HiSeq	Phase_I	54	21	NM_002111	0	0	0	0	0	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901641	0.72754	.	.	ENSG00000197386	ENST00000355072	T	0.08458	3.09	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	M	0.73962	2.25	0.80722	D	1	D	0.58620	0.983	P	0.50590	0.645	T	0.01301	-1.1391	10	0.87932	D	0	.	14.7618	0.69612	0.0:0.0:0.0:1.0	.	2703	P42858	HD_HUMAN	P	2703	ENSP00000347184:S2703P	ENSP00000347184:S2703P	S	+	1	0	HTT	3200532	1.000000	0.71417	0.609000	0.28983	0.275000	0.26752	7.679000	0.84048	1.904000	0.55121	0.460000	0.39030	TCC	.		0.602	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		C	3230734	T	C	3230734	3	2	25	1	0	0	0	0	1	0	0	0	7478	1435	50	3	8341	3	HTT	4	3230734	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10		3230734	187923542	27	2169											
DDX60L	91351	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	169382991	169382991	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attaggaagttaaaaaggtaCgtttgtaaatcactcaggcc	15	11	9	6	1	2	0	2	0	0	0	2	1	2	1	1	3	1	4	1	3	8	5	rs17612630	byFrequency	TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr4:169382991C>T	ENST00000511577.1	-	5	712	c.465G>A	c.(463-465)acG>acA	p.T155T	DDX60L_ENST00000260184.7_Silent_p.T155T|DDX60L_ENST00000505890.1_Silent_p.T155T			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	155							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TAAAAAGGTACGTTTGTAAAT	0.368																																					p.T155T		.											.	DDX60L-69	0			c.G465A						.						59	53	55					4																	169382991		1850	4090	5940	SO:0001819	synonymous_variant	91351	exon5			AAGGTACGTTTGT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.465G>A	4.37:g.169382991C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	93	21	NM_001012967	0	0	2	5	3	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.904;A|0.096		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169382991	C	T	169382991	2	4	25	1	0	0	0	0	0	0	0	1	4385	523	19	1		1	DDX60L	4	169382991	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	166152257	169382991	21771285	28	2170											
SLC12A7	10723	broad.mit.edu	37	chr5	1087140	1087140	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcgatatcatgtagtaggAcccgccagctgcggagacaa	11	6	13	11	4	1	1	1	0	0	1	1	4	1	2	2	2	2	3	2	2	4	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:1087140A>C	ENST00000264930.5	-	6	596	c.553T>G	c.(553-555)Tcc>Gcc	p.S185A		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	185					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	ATGTAGTAGGACCCGCCAGCT	0.637																																					p.S185A													.	SLC12A7-138	0			c.T553G						.						21	22	22					5																	1087140		2197	4295	6492	SO:0001583	missense	10723	exon6			AGTAGGACCCGCC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.553T>G	5.37:g.1087140A>C	ENSP00000264930:p.Ser185Ala	Somatic	113	11		WXS	Illumina HiSeq	Phase_I	110	20	NM_006598	0	0	0	0	0	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	37	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.348266	0.24426	.	.	ENSG00000113504	ENST00000264930;ENST00000343658	D	0.98550	-4.99	3.93	3.93	0.45458	Amino acid permease domain (1);	0.067957	0.64402	N	0.000008	D	0.92916	0.7746	N	0.11106	0.095	0.53005	D	0.999961	B	0.15141	0.012	B	0.19946	0.027	D	0.89124	0.3505	10	0.07644	T	0.81	.	11.8847	0.52596	1.0:0.0:0.0:0.0	.	185	Q9Y666	S12A7_HUMAN	A	185	ENSP00000264930:S185A	ENSP00000264930:S185A	S	-	1	0	SLC12A7	1140140	1.000000	0.71417	0.996000	0.52242	0.228000	0.25075	6.424000	0.73366	1.562000	0.49601	0.459000	0.35465	TCC	.		0.637	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		C	1087140	A	C	1087140	3	2	25	1	0	0	0	0	1	0	0	0	14420	275	10	5	2774	5	SLC12A7	5	1087140	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		1087140	179828120	29	2171											
LIFR	3977	bcgsc.ca	37	chr5	38506175	38506175	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctaacatattttcctgaaaAactgttaattaacagaaaaa	19	13	3	6	0	1	2	0	1	1	1	2	2	2	2	1	0	3	1	1	0	8	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:38506175A>C	ENST00000263409.4	-	9	1285	c.1123T>G	c.(1123-1125)Ttt>Gtt	p.F375V	LIFR_ENST00000503088.1_5'UTR|LIFR_ENST00000453190.2_Splice_Site_p.F375V	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	375	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TTTCCTGAAAAACTGTTAATT	0.254			T	PLAG1	salivary adenoma																																p.F375V	Melanoma(13;4 730 6426 9861 34751)			Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR-1173	0			c.T1123G						.						35	37	37					5																	38506175		2200	4289	6489	SO:0001630	splice_region_variant	3977	exon9			CTGAAAAACTGTT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1122-1T>G	5.37:g.38506175A>C		Somatic	294	5		WXS	Illumina HiSeq	Phase_1	274	92	NM_002310	0	0	0	0	0	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.597226	0.46318	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.34472	1.36;1.36	5.45	2.84	0.33178	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.829009	0.11140	N	0.595326	T	0.37320	0.0999	M	0.78637	2.42	0.31000	N	0.720443	B	0.16802	0.019	B	0.17098	0.017	T	0.38757	-0.9646	10	0.21540	T	0.41	-21.4042	7.9903	0.30237	0.547:0.0:0.0:0.453	.	375	P42702	LIFR_HUMAN	V	375	ENSP00000263409:F375V;ENSP00000398368:F375V	ENSP00000263409:F375V	F	-	1	0	LIFR	38541932	1.000000	0.71417	0.996000	0.52242	0.972000	0.66771	2.188000	0.42612	0.856000	0.35383	0.533000	0.62120	TTT	.		0.254	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	Missense_Mutation	C	38506175	A	C	38506175	5	2	25	1	0	0	0	0	0	0	1	0	8802	28	1	5	2218	5	LIFR	5	38506175	Splice_Site	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	37419035	38506175	142409085	30	2172											
IK	3550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140034136	140034136	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccagcaaagagaaagaggaAgaggaactgatggaaaagcc	19	2	14	6	0	0	4	0	1	0	3	0	8	0	7	2	3	3	1	2	3	6	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:140034136A>C	ENST00000417647.2	+	7	694	c.555A>C	c.(553-555)gaA>gaC	p.E185D		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	185	Poly-Glu.				cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAAAGAGGAAGAGGAACTGA	0.388																																					p.E185D		.											.	IK-67	0			c.A555C						.						44	44	44					5																	140034136		1831	4083	5914	SO:0001583	missense	3550	exon7			AGAGGAAGAGGAA	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.555A>C	5.37:g.140034136A>C	ENSP00000396301:p.Glu185Asp	Somatic	516	1		WXS	Illumina HiSeq	Phase_I	467	155	NM_006083	0	0	48	75	27	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	37	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.326795	0.60743	.	.	ENSG00000113141	ENST00000417647;ENST00000508301;ENST00000261812;ENST00000502899	.	.	.	5.86	1.66	0.24008	RED-like, N-terminal (1);	0.042187	0.85682	D	0.000000	T	0.32255	0.0823	N	0.17674	0.51	0.48975	D	0.999737	B;B	0.24132	0.01;0.098	B;B	0.27500	0.026;0.08	T	0.04509	-1.0946	9	0.20519	T	0.43	.	7.8062	0.29204	0.5957:0.0:0.4043:0.0	.	185;185	Q9UK43;Q13123	.;RED_HUMAN	D	185	.	ENSP00000261812:E185D	E	+	3	2	IK	140014320	0.973000	0.33851	1.000000	0.80357	0.990000	0.78478	0.251000	0.18257	0.653000	0.30826	0.460000	0.39030	GAA	.		0.388	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083		C	140034136	A	C	140034136	3	2	25	1	0	0	0	0	1	0	0	0	7629	69	3	5	581	5	IK	5	140034136	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	101527961	140034136	40881124	31	2173											
PCDHA12	56137	broad.mit.edu	37	chr5	140256291	140256291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcgttggtgctggacagcGccctggaccgcgagagcgtg	6	7	16	12	5	0	1	0	0	0	1	1	4	0	3	2	3	3	2	2	3	0	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:140256291G>A	ENST00000398631.2	+	1	1234	c.1234G>A	c.(1234-1236)Gcc>Acc	p.A412T	PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	412	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGACAGCGCCCTGGACCG	0.607																																					p.A412T	Pancreas(113;759 1672 13322 24104 50104)												.	.	0			c.G1234A						.						196	189	192					5																	140256291		2203	4300	6503	SO:0001583	missense	56137	exon1			GACAGCGCCCTGG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1234G>A	5.37:g.140256291G>A	ENSP00000381628:p.Ala412Thr	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	174	8	NM_018903	0	0	0	0	0	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.438589	0.25900	.	.	ENSG00000251664	ENST00000398631	T	0.02682	4.2	4.81	-1.86	0.07760	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02304	0.0071	L	0.35593	1.075	0.09310	N	1	B;B	0.33528	0.056;0.416	B;B	0.37550	0.042;0.253	T	0.45071	-0.9286	9	0.33141	T	0.24	.	0.7087	0.00920	0.22:0.1806:0.3273:0.2721	.	412;412	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	412	ENSP00000381628:A412T	ENSP00000381628:A412T	A	+	1	0	PCDHA12	140236475	0.000000	0.05858	0.001000	0.08648	0.862000	0.49288	-1.193000	0.03049	-0.044000	0.13491	0.655000	0.94253	GCC	.		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256291	G	A	140256291	3	1	25	1	0	0	0	0	1	0	0	0	11548	1087	38	1	1236	1	PCDHA12	5	140256291	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	222155	140256291	40658969	32	2174											
PCDHGA11	56105	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140800833	140800833	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcggggaccgcagtcggctGctgctgctgctgtgcatttt	3	11	15	12	4	0	0	0	0	0	0	1	1	0	1	1	3	5	7	1	3	0	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:140800833G>A	ENST00000398587.2	+	1	72	c.39G>A	c.(37-39)ctG>ctA	p.L13L	PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Silent_p.L13L|PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	13					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGTCGGCTGCTGCTGCTGC	0.607																																					p.L13L													.	.	0			c.G39A						.						9	12	11					5																	140800833		1940	4125	6065	SO:0001819	synonymous_variant	56105	exon1			TCGGCTGCTGCTG	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.39G>A	5.37:g.140800833G>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	39	12	NM_032091	0	0	0	0	0	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																			.		0.607	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		A	140800833	G	A	140800833	2	1	25	1	0	0	0	0	0	0	0	1	11578	1306	46	2		2	PCDHGA11	5	140800833	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	544542	140800833	40114427	33	2175											
CDKAL1	54901	broad.mit.edu;bcgsc.ca	37	chr6	20739778	20739778	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagaggagaacaagaaaatcGtactggctggatgcgttcct	14	8	12	7	2	0	3	0	0	0	3	2	5	1	4	1	3	3	3	1	3	6	2	rs139954896		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr6:20739778G>C	ENST00000378610.1	+	4	410	c.400G>C	c.(400-402)Gta>Cta	p.V134L	CDKAL1_ENST00000274695.4_Missense_Mutation_p.V134L|CDKAL1_ENST00000378624.4_Missense_Mutation_p.V64L			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	134	MTTase N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00780}.				maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			CAAGAAAATCGTACTGGCTGG	0.433																																					p.V134L													.	CDKAL1-92	0			c.G400C						.						59	58	58					6																	20739778		2203	4300	6503	SO:0001583	missense	54901	exon6			AAAATCGTACTGG	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.400G>C	6.37:g.20739778G>C	ENSP00000367873:p.Val134Leu	Somatic	60	1		WXS	Illumina HiSeq	Phase_I	45	11	NM_017774	0	0	2	3	1	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	37	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	.	16.79	3.219539	0.58560	.	.	ENSG00000145996	ENST00000274695;ENST00000378624;ENST00000378610	T;T;T	0.50813	0.73;0.77;0.73	4.77	4.77	0.60923	Methylthiotransferase, N-terminal (2);	0.000000	0.64402	D	0.000001	T	0.56470	0.1987	M	0.80616	2.505	0.46749	D	0.999189	P;P	0.48998	0.918;0.592	P;P	0.54706	0.759;0.727	T	0.60301	-0.7290	10	0.42905	T	0.14	-13.099	16.602	0.84818	0.0:0.0:1.0:0.0	.	64;134	Q5VV42-2;Q5VV42	.;CDKAL_HUMAN	L	134;64;134	ENSP00000274695:V134L;ENSP00000367889:V64L;ENSP00000367873:V134L	ENSP00000274695:V134L	V	+	1	0	CDKAL1	20847757	1.000000	0.71417	0.625000	0.29200	0.147000	0.21601	8.674000	0.91191	2.192000	0.70111	0.557000	0.71058	GTA	G|1.000;A|0.000		0.433	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		C	20739778	G	C	20739778	3	2	25	1	0	0	0	0	1	0	0	0	3158	1145	40	4	414	4	CDKAL1	6	20739778	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		20739778	150375289	34	2176											
NFYA	4800	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	41059422	41059422	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaatgtggtcaattcaggaGggatggtcatggtaagaaaa	14	9	14	4	0	3	1	3	0	0	1	3	3	3	3	0	5	0	2	0	5	5	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr6:41059422G>A	ENST00000341376.6	+	7	904	c.703G>A	c.(703-705)Ggg>Agg	p.G235R	NFYA_ENST00000353205.5_Missense_Mutation_p.G206R|OARD1_ENST00000480585.1_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	235					cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					CAATTCAGGAGGGATGGTCAT	0.418																																					p.G235R		.											.	NFYA-226	0			c.G703A						.						229	209	216					6																	41059422		2203	4300	6503	SO:0001583	missense	4800	exon7			TCAGGAGGGATGG		CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167			7804	protein-coding gene	gene with protein product		189903				1774067, 9612081	Standard	NM_002505		Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.703G>A	6.37:g.41059422G>A	ENSP00000345702:p.Gly235Arg	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	55	21	NM_002505	0	0	0	0	0	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	37	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.975651	0.92919	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.71702	0.3371	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.72364	-0.4316	9	0.62326	D	0.03	-10.6151	18.9483	0.92630	0.0:0.0:1.0:0.0	.	206;235	P23511-2;P23511	.;NFYA_HUMAN	R	235;206	.	ENSP00000345702:G235R	G	+	1	0	NFYA	41167400	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.760000	0.98935	2.720000	0.93068	0.655000	0.94253	GGG	.		0.418	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			A	41059422	G	A	41059422	3	1	25	1	0	0	0	0	1	0	0	0	10415	1000	35	2	725	2	NFYA	6	41059422	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	20319644	41059422	130055645	35	2177											
YIPF3	25844	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43483379	43483379	+	Frame_Shift_Del	DEL	T	T	-																															atcaaagtagggtctgaggaTgtcgatgttggcgtacaagc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr6:43483379delT	ENST00000372422.2	-	3	531	c.349delA	c.(349-351)atcfs	p.I117fs	POLR1C_ENST00000304004.3_5'Flank|POLR1C_ENST00000372389.3_5'Flank|POLR1C_ENST00000372344.2_5'Flank|YIPF3_ENST00000506469.1_Frame_Shift_Del_p.I123fs	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	117					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			GGTCTGAGGATGTCGATGTTG	0.517																																					p.I117fs		.											.	YIPF3-90	0			c.349delA						.						129	120	123					6																	43483379		2203	4300	6503	SO:0001589	frameshift_variant	25844	exon3			.	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.349delA	6.37:g.43483379delT	ENSP00000361499:p.Ile117fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	81	32	NM_015388	0	0	0	0	0	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Frame_Shift_Del	DEL	ENST00000372422.2	37	CCDS4899.1																																																																																			.		0.517	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		-	43483379	T	-	43483379	7	5	25	1	0	1	0	1	0	0	0	0	17512	1464	51	0	731	0	YIPF3	6	43483379	Frame_Shift_Del	DEL	T	TCGA-A4-A5XZ-01A-11D-A31X-10	2423957	43483379	127631688	36	2178											
FTSJ2	8379	bcgsc.ca	37	chr7	2275155	2275155	+	5'Flank	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttccagggggaatatgtGaagaagatctaccccaagca	13	8	10	10	0	1	3	0	1	1	2	3	4	3	4	4	2	2	1	4	2	6	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:2275155G>T	ENST00000406869.1	-	0	0				FTSJ2_ENST00000242257.8_Missense_Mutation_p.H115N|FTSJ2_ENST00000407040.1_Missense_Mutation_p.H21N|MAD1L1_ENST00000265854.7_5'Flank|MAD1L1_ENST00000399654.2_5'Flank|MAD1L1_ENST00000402746.1_5'Flank|FTSJ2_ENST00000486040.1_5'UTR|FTSJ2_ENST00000440306.2_3'UTR			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)						mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GGGAATATGTGAAGAAGATCT	0.478																																					p.H115N													.	FTSJ2-91	0			c.C343A						.						59	58	59					7																	2275155		2203	4300	6503	SO:0001631	upstream_gene_variant	29960	exon3			ATATGTGAAGAAG	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493		7.37:g.2275155G>T	Exception_encountered	Somatic	29	1		WXS	Illumina HiSeq	Phase_1	74	27	NM_013393	0	0	14	23	9	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.840599	0.32513	.	.	ENSG00000122687	ENST00000242257;ENST00000407040	T;T	0.29397	1.57;1.57	5.47	5.47	0.80525	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.125817	0.52532	D	0.000064	T	0.21841	0.0526	N	0.16368	0.405	0.80722	D	1	B	0.12630	0.006	B	0.17722	0.019	T	0.03335	-1.1047	10	0.49607	T	0.09	13.2481	14.2064	0.65737	0.0:0.0:0.8506:0.1494	.	115	Q9UI43	RRMJ2_HUMAN	N	115;21	ENSP00000242257:H115N;ENSP00000384423:H21N	ENSP00000242257:H115N	H	-	1	0	FTSJ2	2241681	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.790000	0.55461	2.565000	0.86533	0.655000	0.94253	CAC	.		0.478	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		T	2275155	G	T	2275155	1	4	25	0	1	0	0	0	0	0	0	0	6107	1290	45	4		4	FTSJ2	7	2275155	5'Flank	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		2275155	156863508	37	2179											
NOD1	10392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	30492406	30492406	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccgctgtagcagcatGgacttgcccaccccagcatc	8	7	10	16	1	0	0	0	0	0	0	1	1	0	1	4	1	6	6	4	1	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:30492406G>A	ENST00000222823.4	-	6	1152	c.627C>T	c.(625-627)tcC>tcT	p.S209S	NOD1_ENST00000423334.2_Intron	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	209	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						GTAGCAGCATGGACTTGCCCA	0.612																																					p.S209S		.											.	NOD1-229	0			c.C627T						.						89	86	87					7																	30492406		2203	4300	6503	SO:0001819	synonymous_variant	10392	exon6			CAGCATGGACTTG	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"Nucleotide-binding domain and leucine rich repeat containing"	16390	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1", "NLR family, CARD domain containing 1"	605980	"caspase recruitment domain family, member 4"	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.627C>T	7.37:g.30492406G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	83	23	NM_006092	0	0	0	3	3	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			.		0.612	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			A	30492406	G	A	30492406	2	1	25	1	0	0	0	0	0	0	0	1	10542	1335	47	2		2	NOD1	7	30492406	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	28217251	30492406	128646257	38	2180											
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	44747231	44747232	+	Frame_Shift_Ins	INS	-	-	A																															aggaggtgcagaagtaccccINSaatgctgagctggcctggtg																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:44747231_44747232insA	ENST00000222673.5	+	22	2889_2890	c.2847_2848insA	c.(2848-2850)aatfs	p.N950fs	OGDH_ENST00000447398.1_Frame_Shift_Ins_p.N961fs|OGDH_ENST00000444676.1_Frame_Shift_Ins_p.N965fs|OGDH_ENST00000439616.2_Frame_Shift_Ins_p.N800fs|OGDH_ENST00000543843.1_Frame_Shift_Ins_p.N901fs|OGDH_ENST00000449767.1_Frame_Shift_Ins_p.N946fs	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	950					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	AGAAGTACCCCAATGCTGAGCT	0.574																																					p.P949fs		.											.	OGDH-228	0			c.2847_2848insA						.																																			SO:0001589	frameshift_variant	4967	exon22			.	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.2849dupA	7.37:g.44747233_44747233dupA	ENSP00000222673:p.Asn950fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	102	38	NM_002541	0	0	0	0	0	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Frame_Shift_Ins	INS	ENST00000222673.5	37	CCDS34627.1																																																																																			.		0.574	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			A	44747232	-	A	44747231	7	5	25	1	0	1	1	0	0	0	0	0	10865	581	21	0	3102	0	OGDH	7	44747231	Frame_Shift_Ins	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10	14254825	44747231	114391432	39	2181											
ZNF273	10793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	64388953	64388953	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcctttaaacggtccacaaCtcttactaaacataagagaa	17	9	5	10	1	1	1	0	0	1	1	2	2	2	1	2	1	5	0	2	1	8	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:64388953C>G	ENST00000476120.1	+	4	1318	c.1247C>G	c.(1246-1248)aCt>aGt	p.T416S	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.T351S	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	416					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(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				CGGTCCACAACTCTTACTAAA	0.348																																					p.T416S	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	.											.	ZNF273-90	0			c.C1247G						.						40	44	42					7																	64388953		2203	4298	6501	SO:0001583	missense	10793	exon4			CCACAACTCTTAC	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1247C>G	7.37:g.64388953C>G	ENSP00000418719:p.Thr416Ser	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	169	77	NM_021148	0	0	1	1	0	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	5.424	0.263316	0.10294	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.03358	3.96;3.96	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.11724	0.165	0.09310	N	1	B	0.19445	0.036	B	0.25405	0.06	T	0.50250	-0.8850	9	0.12103	T	0.63	.	7.3527	0.26700	0.0:1.0:0.0:0.0	.	416	Q14593	ZN273_HUMAN	S	416;351	ENSP00000418719:T416S;ENSP00000324518:T351S	ENSP00000324518:T351S	T	+	2	0	ZNF273	64026388	0.000000	0.05858	0.757000	0.31301	0.755000	0.42902	-6.036000	0.00084	0.202000	0.20498	0.205000	0.17691	ACT	.		0.348	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			G	64388953	C	G	64388953	3	3	25	1	0	0	0	0	1	0	0	0	17840	565	20	4	1261	4	ZNF273	7	64388953	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	19641722	64388953	94749710	40	2182											
ABCB4	5244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	87049331	87049331	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacctgtcttagcattgcttTaaaagccattgaccgcagtc	10	13	7	11	1	1	1	0	1	1	0	2	1	1	1	3	0	4	3	3	0	4	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:87049331T>C	ENST00000265723.4	-	19	2488	c.2377A>G	c.(2377-2379)Aaa>Gaa	p.K793E	ABCB4_ENST00000358400.3_Missense_Mutation_p.K793E|ABCB4_ENST00000359206.3_Missense_Mutation_p.K793E|ABCB4_ENST00000453593.1_Missense_Mutation_p.K793E|ABCB4_ENST00000545634.1_Missense_Mutation_p.K793E	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	793	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AGCATTGCTTTAAAAGCCATT	0.423																																					p.K793E		.											.	ABCB4-96	0			c.A2377G						.						183	167	173					7																	87049331		2203	4300	6503	SO:0001583	missense	5244	exon19			TTGCTTTAAAAGC	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2377A>G	7.37:g.87049331T>C	ENSP00000265723:p.Lys793Glu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	148	64	NM_018850	0	0	3	3	0	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299295	0.40694	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57	6.03	2.37	0.29283	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.390503	0.30003	N	0.010651	D	0.84543	0.5495	L	0.58101	1.795	0.31324	N	0.685702	B;B;B	0.10296	0.003;0.002;0.003	B;B;B	0.16722	0.016;0.007;0.012	T	0.80286	-0.1446	10	0.62326	D	0.03	-9.0118	6.8919	0.24234	0.0:0.1317:0.1275:0.7408	.	793;793;793	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	E	793	ENSP00000352135:K793E;ENSP00000351172:K793E;ENSP00000265723:K793E;ENSP00000392983:K793E;ENSP00000437465:K793E	ENSP00000265723:K793E	K	-	1	0	ABCB4	86887267	0.999000	0.42202	0.992000	0.48379	0.639000	0.38242	1.584000	0.36589	0.497000	0.27926	-0.256000	0.11100	AAA	.		0.423	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		C	87049331	T	C	87049331	3	2	25	1	0	0	0	0	1	0	0	0	43	1763	61	3	1523	3	ABCB4	7	87049331	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	22660378	87049331	72089332	41	2183											
GIGYF1	64599	bcgsc.ca	37	chr7	100279776	100279776	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaaattctttggcttccagCgtgtcccccaggcaggaacg	8	9	11	13	2	1	0	0	0	1	0	3	1	3	1	3	3	2	3	3	3	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:100279776C>T	ENST00000275732.5	-	22	4053	c.2844G>A	c.(2842-2844)acG>acA	p.T948T	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	948					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TGGCTTCCAGCGTGTCCCCCA	0.592																																					p.T948T													.	GIGYF1-136	0			c.G2844A						.						70	73	72					7																	100279776		2203	4300	6503	SO:0001819	synonymous_variant	64599	exon22			TTCCAGCGTGTCC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.2844G>A	7.37:g.100279776C>T		Somatic	36	0		WXS	Illumina HiSeq	Phase_1	58	4	NM_022574	0	0	32	32	0	Q6Y7W7|Q8WZ38	Silent	SNP	ENST00000275732.5	37	CCDS34708.1																																																																																			.		0.592	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		T	100279776	C	T	100279776	2	4	25	1	0	0	0	0	0	0	0	1	6397	755	27	1		1	GIGYF1	7	100279776	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	13230445	100279776	58858887	42	2184											
SRRT	51593	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100485329	100485329	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctctccacccagggtccTgagtttgtgcgcaaacatat	8	11	8	14	1	1	1	0	1	1	0	4	1	3	1	4	1	2	2	4	1	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:100485329T>C	ENST00000347433.4	+	17	2333	c.2175T>C	c.(2173-2175)ccT>ccC	p.P725P	SRRT_ENST00000457580.2_Silent_p.P725P|SRRT_ENST00000432932.1_Silent_p.P724P|SRRT_ENST00000388793.4_Silent_p.P724P			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	725					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCCAGGGTCCTGAGTTTGTGC	0.527																																					p.P725P													.	SRRT-92	0			c.T2175C						.						119	126	124					7																	100485329		2203	4300	6503	SO:0001819	synonymous_variant	51593	exon17			GGGTCCTGAGTTT		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2175T>C	7.37:g.100485329T>C		Somatic	123	2		WXS	Illumina HiSeq	Phase_I	189	62	NM_001128853	0	0	0	1	1	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Silent	SNP	ENST00000347433.4	37	CCDS34709.1																																																																																			.		0.527	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		C	100485329	T	C	100485329	2	2	25	1	0	0	0	0	0	0	0	1	15204	1567	55	3		3	SRRT	7	100485329	Silent	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	205553	100485329	58653334	43	2185											
PPP2CB	5516	bcgsc.ca	37	chr8	30651447	30651447	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acatacctccattacaagctGgtgggcacgagaaaccagtg	13	7	10	11	1	0	1	0	0	0	1	1	2	1	1	3	2	4	2	3	2	4	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr8:30651447G>C	ENST00000221138.4	-	5	1174	c.724C>G	c.(724-726)Cag>Gag	p.Q242E	PPP2CB_ENST00000518564.1_Intron	NM_001009552.1	NP_001009552.1	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta isozyme	242					apoptotic mitochondrial changes (GO:0008637)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of Ras protein signal transduction (GO:0046580)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|regulation of gene expression (GO:0010468)|response to antibiotic (GO:0046677)|response to endoplasmic reticulum stress (GO:0034976)|response to hydrogen peroxide (GO:0042542)	chromosome, centromeric region (GO:0000775)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	9				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	ATTACAAGCTGGTGGGCACGA	0.393																																					p.Q242E													.	PPP2CB-658	0			c.C724G						.						71	58	63					8																	30651447		2203	4300	6503	SO:0001583	missense	5516	exon5			CAAGCTGGTGGGC		CCDS6079.1	8p12	2011-05-24	2010-03-05		ENSG00000104695	ENSG00000104695	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9300	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, beta isoform"	176916	"protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform"			8383590	Standard	NM_001009552		Approved	PP2Abeta	uc003xik.3	P62714	OTTHUMG00000163949	ENST00000221138.4:c.724C>G	8.37:g.30651447G>C	ENSP00000221138:p.Gln242Glu	Somatic	380	5		WXS	Illumina HiSeq	Phase_1	350	122	NM_001009552	0	0	53	109	56	D3DSV4|P11082|Q6FHK5	Missense_Mutation	SNP	ENST00000221138.4	37	CCDS6079.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471144	0.63625	.	.	ENSG00000104695	ENST00000221138;ENST00000406655;ENST00000520334	T;T	0.56275	0.47;0.47	5.14	4.25	0.50352	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.70272	0.3205	M	0.76002	2.32	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	T	0.73978	-0.3812	10	0.87932	D	0	-12.013	13.0676	0.59043	0.0789:0.0:0.9211:0.0	.	242	P62714	PP2AB_HUMAN	E	242;242;80	ENSP00000221138:Q242E;ENSP00000430758:Q80E	ENSP00000221138:Q242E	Q	-	1	0	PPP2CB	30770989	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	7.647000	0.83462	2.536000	0.85505	0.655000	0.94253	CAG	.		0.393	PPP2CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376527.2	NM_001009552		C	30651447	G	C	30651447	3	2	25	1	0	0	0	0	1	0	0	0	12410	1357	47	4	217	4	PPP2CB	8	30651447	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		30651447	115712575	44	2186											
PRKDC	5591	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	48809814	48809814	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgagctaaaagccacttgaCcagatccaataaacacaatg	18	7	6	10	0	0	3	0	2	0	1	1	3	1	3	3	0	3	1	3	0	6	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr8:48809814C>G	ENST00000314191.2	-	30	3561	c.3505G>C	c.(3505-3507)Gtc>Ctc	p.V1169L	PRKDC_ENST00000338368.3_Missense_Mutation_p.V1169L|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	1169					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	AGCCACTTGACCAGATCCAAT	0.438								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)												.	PRKDC-1515	0			.						.						203	195	197					8																	48809814		1902	4137	6039	SO:0001583	missense	5591	.			ACTTGACCAGATC		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.3505G>C	8.37:g.48809814C>G	ENSP00000313420:p.Val1169Leu	Somatic	73	1		WXS	Illumina HiSeq	Phase_I	67	27	.	0	0	2	3	1	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	C	29.4	5.006298	0.93287	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.61742	0.08;0.08	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.79088	0.4387	.	.	.	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.83275	0.996;0.942	T	0.80717	-0.1258	9	0.72032	D	0.01	.	19.8316	0.96638	0.0:1.0:0.0:0.0	.	1169;1169	E7EUY0;P78527	.;PRKDC_HUMAN	L	1169	ENSP00000313420:V1169L;ENSP00000345182:V1169L	ENSP00000313420:V1169L	V	-	1	0	PRKDC	48972367	1.000000	0.71417	0.991000	0.47740	0.768000	0.43524	7.114000	0.77103	2.687000	0.91594	0.563000	0.77884	GTC	.		0.438	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		G	48809814	C	G	48809814	3	3	25	1	0	0	0	0	1	0	0	0	12550	507	18	4	9108	4	PRKDC	8	48809814	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	18158367	48809814	97554208	45	2187											
ST18	9705	broad.mit.edu	37	chr8	53077753	53077753	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcctgtgcatcccggcgtggGacacttgagcacattttcat	7	12	10	12	2	1	1	1	1	0	0	3	2	3	2	2	2	2	2	2	2	0	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr8:53077753G>T	ENST00000276480.7	-	12	1920	c.1237C>A	c.(1237-1239)Ccc>Acc	p.P413T		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	413					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CCCGGCGTGGGACACTTGAGC	0.403																																					p.P413T													.	ST18-95	0			c.C1237A						.						193	184	187					8																	53077753		2203	4300	6503	SO:0001583	missense	9705	exon12			GCGTGGGACACTT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.1237C>A	8.37:g.53077753G>T	ENSP00000276480:p.Pro413Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_014682	0	0	0	0	0	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.510803	0.85389	.	.	ENSG00000147488	ENST00000276480;ENST00000517580	T;T	0.70399	0.15;-0.48	5.92	5.92	0.95590	.	0.050397	0.85682	D	0.000000	D	0.85557	0.5724	M	0.77406	2.37	0.80722	D	1	D;D	0.89917	1.0;0.984	D;P	0.91635	0.999;0.841	D	0.85728	0.1329	10	0.66056	D	0.02	-20.0237	20.3081	0.98638	0.0:0.0:1.0:0.0	.	413;413	E5RHS3;O60284	.;ST18_HUMAN	T	413	ENSP00000276480:P413T;ENSP00000428521:P413T	ENSP00000276480:P413T	P	-	1	0	ST18	53240306	1.000000	0.71417	0.997000	0.53966	0.930000	0.56654	7.925000	0.87563	2.795000	0.96236	0.655000	0.94253	CCC	.		0.403	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53077753	G	T	53077753	3	4	25	1	0	0	0	0	1	0	0	0	15244	1174	41	4	1966	4	ST18	8	53077753	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	4267939	53077753	93286269	46	2188											
RB1CC1	9821	bcgsc.ca	37	chr8	53569322	53569322	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgtatttgattaattatttGttggttttccttttttaatt	7	27	5	2	0	0	1	0	1	0	0	1	1	1	1	1	1	0	3	1	1	4	13			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr8:53569322G>A	ENST00000025008.5	-	15	3590	c.3067C>T	c.(3067-3069)Caa>Taa	p.Q1023*	RB1CC1_ENST00000435644.2_Nonsense_Mutation_p.Q1023*|RB1CC1_ENST00000539297.1_Nonsense_Mutation_p.Q1023*|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1023					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTAATTATTTGTTGGTTTTCC	0.343																																					p.Q1023X	GBM(180;1701 2102 13475 42023 52570)												.	RB1CC1-170	0			c.C3067T						.						88	98	95					8																	53569322		2203	4300	6503	SO:0001587	stop_gained	9821	exon15			TTATTTGTTGGTT	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3067C>T	8.37:g.53569322G>A	ENSP00000025008:p.Gln1023*	Somatic	101	2		WXS	Illumina HiSeq	Phase_1	103	26	NM_001083617	0	0	7	7	0	Q86YR4|Q8WVU9|Q92601	Nonsense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	G	40	7.974633	0.98591	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	.	.	.	5.05	3.19	0.36642	.	0.462954	0.25408	N	0.030888	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-1.8988	15.3415	0.74300	0.0:0.2653:0.7347:0.0	.	.	.	.	X	1023	.	ENSP00000025008:Q1023X	Q	-	1	0	RB1CC1	53731875	0.868000	0.29978	0.034000	0.17996	0.142000	0.21351	3.458000	0.53014	0.607000	0.29982	-0.310000	0.09108	CAA	.		0.343	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		A	53569322	G	A	53569322	4	1	25	1	0	0	0	0	0	1	0	0	13131	1386	48	2	1757	2	RB1CC1	8	53569322	Nonsense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	491569	53569322	92794700	47	2189											
ARHGAP22	58504	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	49659052	49659052	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ttggctgtccctggtgacctCctcggagccccaccccactg	4	9	10	18	1	0	1	0	1	0	0	3	2	2	2	7	3	1	1	7	3	0	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr10:49659052C>G	ENST00000249601.4	-	9	1416	c.1120G>C	c.(1120-1122)Gag>Cag	p.E374Q	ARHGAP22_ENST00000374170.1_Missense_Mutation_p.E215Q|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.E207Q|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.E265Q|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.E380Q|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.E284Q|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.E390Q	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	374					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTGGTGACCTCCTCGGAGCCC	0.731																																					p.E390Q		.											.	ARHGAP22-228	0			c.G1168C						.						8	9	9					10																	49659052		2008	4065	6073	SO:0001583	missense	58504	exon9			TGACCTCCTCGGA	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1120G>C	10.37:g.49659052C>G	ENSP00000249601:p.Glu374Gln	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	60	25	NM_001256024	0	0	2	2	0	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.580505	0.65992	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.37915	2.7;2.36;1.17;1.51;2.34;2.66;2.7	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.62196	0.2408	M	0.81942	2.565	0.50039	D	0.999846	P;D;D;D;D;D	0.89917	0.621;1.0;0.972;1.0;0.959;1.0	B;D;P;D;P;D	0.74348	0.326;0.972;0.742;0.959;0.882;0.983	T	0.66352	-0.5945	10	0.59425	D	0.04	.	15.8862	0.79251	0.0:1.0:0.0:0.0	.	380;374;390;374;284;207	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	Q	374;265;215;207;284;380;390	ENSP00000249601:E374Q;ENSP00000363287:E265Q;ENSP00000363285:E215Q;ENSP00000422868:E207Q;ENSP00000410054:E284Q;ENSP00000416701:E380Q;ENSP00000412461:E390Q	ENSP00000249601:E374Q	E	-	1	0	ARHGAP22	49329058	1.000000	0.71417	0.573000	0.28510	0.349000	0.29174	6.759000	0.74934	2.440000	0.82611	0.313000	0.20887	GAG	.		0.731	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		G	49659052	C	G	49659052	3	3	25	1	0	0	0	0	1	0	0	0	872	864	30	4	984	4	ARHGAP22	10	49659052	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		49659052	85875695	48	2190											
DNA2	1763	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	70209856	70209856	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggcattatcttgtattttgTtttataccctcgatgtattt	7	21	6	7	2	1	0	0	0	1	0	2	1	1	0	1	1	1	4	1	1	5	10			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr10:70209856T>C	ENST00000358410.3	-	6	918	c.868A>G	c.(868-870)Aca>Gca	p.T290A	DNA2_ENST00000399179.2_Missense_Mutation_p.T290A|DNA2_ENST00000399180.2_Missense_Mutation_p.T376A	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	290	Nuclease activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TTGTATTTTGTTTTATACCCT	0.343																																					p.T290A													.	.	0			c.A868G						.						92	81	84					10																	70209856		1824	4080	5904	SO:0001583	missense	1763	exon6			ATTTTGTTTTATA	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.868A>G	10.37:g.70209856T>C	ENSP00000351185:p.Thr290Ala	Somatic	97	1		WXS	Illumina HiSeq	Phase_I	87	37	NM_001080449	0	0	0	0	0	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	T	3.741	-0.053473	0.07362	.	.	ENSG00000138346	ENST00000551118;ENST00000399180;ENST00000399179;ENST00000358410	D;D;D	0.93859	-2.79;-3.3;-2.78	5.1	0.0178	0.14113	.	0.664334	0.14826	N	0.296148	D	0.83096	0.5180	N	0.16790	0.44	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.67929	-0.5543	10	0.17369	T	0.5	.	6.2667	0.20930	0.1275:0.4247:0.0:0.4477	.	290;290	F8VR31;P51530	.;DNA2L_HUMAN	A	290;376;290;290	ENSP00000382133:T376A;ENSP00000382132:T290A;ENSP00000351185:T290A	ENSP00000351185:T290A	T	-	1	0	DNA2	69879862	0.024000	0.19004	0.024000	0.17045	0.954000	0.61252	0.114000	0.15520	0.021000	0.15133	0.533000	0.62120	ACA	.		0.343	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			C	70209856	T	C	70209856	3	2	25	1	0	0	0	0	1	0	0	0	4607	1725	60	3	2378	3	DNA2	10	70209856	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	20550804	70209856	65324891	49	2191											
ZNF408	79797	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46726233	46726233	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccccagagcctggagcccAgcagtctggcttccctacac	8	6	10	17	0	1	1	0	0	1	1	2	3	2	2	5	2	4	2	5	2	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr11:46726233A>C	ENST00000311764.2	+	5	1213	c.983A>C	c.(982-984)cAg>cCg	p.Q328P		NM_001184751.1|NM_024741.2	NP_001171680.1|NP_079017.1	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	328					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CCTGGAGCCCAGCAGTCTGGC	0.647																																					p.Q328P	Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)												.	ZNF408-90	0			c.A983C						.						66	63	64					11																	46726233		2201	4299	6500	SO:0001583	missense	79797	exon5			GAGCCCAGCAGTC	AF346626	CCDS7923.1	11p11.2	2008-02-05			ENSG00000175213	ENSG00000175213		"Zinc fingers, C2H2-type"	20041	protein-coding gene	gene with protein product						15231747	Standard	NM_024741		Approved	FLJ12827	uc010rgw.2	Q9H9D4	OTTHUMG00000166568	ENST00000311764.2:c.983A>C	11.37:g.46726233A>C	ENSP00000309606:p.Gln328Pro	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	49	17	NM_024741	0	0	5	12	7		Missense_Mutation	SNP	ENST00000311764.2	37	CCDS7923.1	.	.	.	.	.	.	.	.	.	.	A	13.66	2.304535	0.40795	.	.	ENSG00000175213	ENST00000311764	T	0.11385	2.78	5.7	0.326	0.15908	.	0.378186	0.19372	N	0.115863	T	0.05640	0.0148	L	0.34521	1.04	0.09310	N	1	B;B	0.31485	0.325;0.325	B;B	0.19391	0.025;0.025	T	0.30621	-0.9972	10	0.56958	D	0.05	-6.3858	1.7903	0.03050	0.3665:0.1419:0.0796:0.412	.	320;328	B4DXY4;Q9H9D4	.;ZN408_HUMAN	P	328	ENSP00000309606:Q328P	ENSP00000309606:Q328P	Q	+	2	0	ZNF408	46682809	0.001000	0.12720	0.076000	0.20297	0.071000	0.16799	0.395000	0.20850	0.372000	0.24591	0.383000	0.25322	CAG	.		0.647	ZNF408-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390485.2	NM_024741		C	46726233	A	C	46726233	3	2	25	1	0	0	0	0	1	0	0	0	17920	188	7	5	1033	5	ZNF408	11	46726233	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		46726233	88280283	50	2192											
PPP1CA	5499	ucsc.edu;bcgsc.ca	37	chr11	67168351	67168351	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggaaaccgccatactcaAatagtcgcagaaggtcgtag	14	6	12	9	3	1	1	1	0	0	1	3	3	1	2	2	2	2	2	2	2	6	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr11:67168351A>C	ENST00000376745.4	-	3	375	c.227T>G	c.(226-228)tTt>tGt	p.F76C	PPP1CA_ENST00000358239.4_Missense_Mutation_p.F32C|PPP1CA_ENST00000312989.7_Missense_Mutation_p.F87C|PPP1CA_ENST00000532446.1_5'UTR	NM_001008709.1|NM_002708.3	NP_001008709.1|NP_002699.1	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha isozyme	76					branching morphogenesis of an epithelial tube (GO:0048754)|cell cycle (GO:0007049)|cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|lung development (GO:0030324)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|MLL5-L complex (GO:0070688)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein phosphatase type 1 complex (GO:0000164)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)|ribonucleoprotein complex binding (GO:0043021)			breast(1)|lung(2)|pancreas(1)|urinary_tract(3)	7			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			GCCATACTCAAATAGTCGCAG	0.572																																					p.F87C													.	PPP1CA-659	0			c.T260G						.						103	100	101					11																	67168351		2200	4295	6495	SO:0001583	missense	5499	exon3			TACTCAAATAGTC		CCDS8160.1, CCDS8161.1, CCDS31618.1	11q13	2013-01-18	2010-03-05			ENSG00000172531	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9281	protein-coding gene	gene with protein product		176875	"protein phosphatase 1, catalytic subunit, alpha isoform"	PPP1A			Standard	NM_002708		Approved	PP1A, PP-1A, PP1alpha	uc001oku.1	P62136		ENST00000376745.4:c.227T>G	11.37:g.67168351A>C	ENSP00000365936:p.Phe76Cys	Somatic	109	2		WXS	Illumina HiSeq		76	22	NM_001008709	0	0	117	214	97	A6NNR3|B2R908|P08129|P20653|P22802|Q07161	Missense_Mutation	SNP	ENST00000376745.4	37	CCDS8160.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.406139	0.62288	.	.	ENSG00000172531	ENST00000312989;ENST00000451458;ENST00000376745;ENST00000358239;ENST00000527663;ENST00000546202;ENST00000542876	D;D;D;D;T;T	0.93076	-3.16;-3.16;-3.16;-3.16;3.2;3.2	5.08	5.08	0.68730	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.118294	0.56097	D	0.000028	D	0.98406	0.9470	H	0.99859	4.855	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.986;1.0;1.0	D;D;D;P;D;D	0.97110	1.0;1.0;0.999;0.865;0.999;0.998	D	0.99044	1.0825	10	0.87932	D	0	.	13.8572	0.63534	1.0:0.0:0.0:0.0	.	173;173;76;32;87;85	B3KXM2;E9PDP1;P62136;A6NNR3;Q07161;F8W0W8	.;.;PP1A_HUMAN;.;.;.	C	87;173;76;32;76;161;173	ENSP00000326031:F87C;ENSP00000365936:F76C;ENSP00000350974:F32C;ENSP00000431146:F76C;ENSP00000439568:F161C;ENSP00000438409:F173C	ENSP00000326031:F87C	F	-	2	0	PPP1CA	66924927	1.000000	0.71417	0.057000	0.19452	0.078000	0.17371	9.311000	0.96282	1.903000	0.55091	0.460000	0.39030	TTT	.		0.572	PPP1CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395487.1	NM_002708		C	67168351	A	C	67168351	3	2	25	1	0	0	0	0	1	0	0	0	12378	14	1	5	785	5	PPP1CA	11	67168351	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	20442118	67168351	67838165	51	2193											
CAPN5	726	broad.mit.edu	37	chr11	76823693	76823693	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaagcccaacgcctacgcggGcatcttccacttccacttct	9	9	6	17	3	2	0	0	0	2	0	4	0	4	0	4	1	3	1	4	1	3	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr11:76823693G>A	ENST00000278559.3	+	4	545	c.356G>A	c.(355-357)gGc>gAc	p.G119D	CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Missense_Mutation_p.G119D|CAPN5_ENST00000456580.2_Missense_Mutation_p.G159D	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	119	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GCCTACGCGGGCATCTTCCAC	0.607																																					p.G119D													.	CAPN5-90	0			c.G356A						.						115	95	102					11																	76823693		2200	4292	6492	SO:0001583	missense	726	exon4			ACGCGGGCATCTT		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.356G>A	11.37:g.76823693G>A	ENSP00000278559:p.Gly119Asp	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_004055	0	0	39	39	0	O00263	Missense_Mutation	SNP	ENST00000278559.3	37	CCDS8248.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.854437	0.91355	.	.	ENSG00000149260	ENST00000278559;ENST00000530987;ENST00000360841;ENST00000529629;ENST00000456580;ENST00000544318	T;T;T	0.58797	0.31;0.31;0.31	4.16	4.16	0.48862	Peptidase C2, calpain, catalytic domain (3);	0.056550	0.64402	D	0.000001	D	0.85860	0.5795	H	0.99347	4.525	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.92129	0.5710	10	0.87932	D	0	.	15.6119	0.76727	0.0:0.0:1.0:0.0	.	157;159;159;119	Q59GM2;E7EV01;Q6ZRM8;O15484	.;.;.;CAN5_HUMAN	D	119;88;159;119;159;159	ENSP00000278559:G119D;ENSP00000432332:G119D;ENSP00000409996:G159D	ENSP00000278559:G119D	G	+	2	0	CAPN5	76501341	1.000000	0.71417	0.972000	0.41901	0.978000	0.69477	9.543000	0.98089	2.139000	0.66308	0.561000	0.74099	GGC	.		0.607	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		A	76823693	G	A	76823693	3	1	25	1	0	0	0	0	1	0	0	0	2635	1203	42	2	366	2	CAPN5	11	76823693	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	9655342	76823693	58182823	52	2194											
MAML2	84441	broad.mit.edu	37	chr11	95825221	95825221	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttgctgctgctgctgctgCtgttgttgctgttgttgttg	0	20	14	7	0	0	0	0	0	0	0	0	0	0	0	0	0	7	13	0	0	0	6	rs571656416	byFrequency	TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr11:95825221C>T	ENST00000524717.1	-	2	3258	c.1974G>A	c.(1972-1974)caG>caA	p.Q658Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	658					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgttgttgct	0.527			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								C|||	4	0.000798722	0.0015	0	5008	,	,		17889	0.002		0	False		,,,				2504	0				p.Q658Q				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.G1974A						.																																			SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1974G>A	11.37:g.95825221C>T		Somatic	59	1		WXS	Illumina HiSeq	Phase_I	54	3	NM_032427	0	0	7	7	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.527	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825221	C	T	95825221	2	4	25	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825221	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	19001528	95825221	39181295	53	2195											
GRIA4	2893	bcgsc.ca	37	chr11	105623882	105623882	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccttcgttacgaggagcActcttgagtttgctggatca	9	12	11	9	2	2	2	1	1	1	1	3	5	2	4	1	2	3	4	1	2	1	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr11:105623882A>T	ENST00000530497.1	+	3	423	c.423A>T	c.(421-423)gcA>gcT	p.A141A	GRIA4_ENST00000282499.5_Silent_p.A141A|GRIA4_ENST00000525187.1_Silent_p.A141A|GRIA4_ENST00000393125.2_Silent_p.A141A|GRIA4_ENST00000428631.2_Silent_p.A141A|GRIA4_ENST00000393127.2_Silent_p.A141A			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	141					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		TACGAGGAGCACTCTTGAGTT	0.468																																					p.A141A													.	GRIA4-230	0			c.A423T						.						168	140	149					11																	105623882		2202	4299	6501	SO:0001819	synonymous_variant	2893	exon4			AGGAGCACTCTTG	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4574	protein-coding gene	gene with protein product		138246	"glutamate receptor, ionotrophic, AMPA 4"	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.423A>T	11.37:g.105623882A>T		Somatic	123	3		WXS	Illumina HiSeq	Phase_1	132	39	NM_001077244	0	0	0	0	0	Q86XE8	Silent	SNP	ENST00000530497.1	37	CCDS8333.1																																																																																			.		0.468	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1			T	105623882	A	T	105623882	2	4	25	1	0	0	0	0	0	0	0	1	6791	146	6	5		5	GRIA4	11	105623882	Silent	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	9798661	105623882	29382634	54	2196											
DDN	23109	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49390815	49390815	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggcggcggatacgggacAcggcttctcgcagggccccg	5	6	17	13	6	1	0	0	0	1	0	2	2	1	2	2	6	1	2	2	6	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr12:49390815A>T	ENST00000421952.2	-	2	1865	c.1844T>A	c.(1843-1845)gTg>gAg	p.V615E	RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	615	Interaction with CD2AP and NPHS1. {ECO:0000250}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						GATACGGGACACGGCTTCTCG	0.721																																					p.V615E		.											.	DDN-90	0			c.T1844A						.						5	5	5					12																	49390815		2080	4038	6118	SO:0001583	missense	23109	exon2			CGGGACACGGCTT	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.1844T>A	12.37:g.49390815A>T	ENSP00000390590:p.Val615Glu	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	28	13	NM_015086	0	0	0	0	0		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	A	24.9	4.581706	0.86748	.	.	ENSG00000181418	ENST00000421952	T	0.58940	0.3	4.12	4.12	0.48240	.	0.000000	0.41396	D	0.000887	T	0.63462	0.2513	L	0.32530	0.975	0.43936	D	0.99659	D	0.76494	0.999	D	0.71656	0.974	T	0.66783	-0.5836	10	0.87932	D	0	-0.1503	11.4668	0.50243	1.0:0.0:0.0:0.0	.	615	O94850	DEND_HUMAN	E	615	ENSP00000390590:V615E	ENSP00000390590:V615E	V	-	2	0	DDN	47677082	0.983000	0.35010	1.000000	0.80357	0.979000	0.70002	1.446000	0.35090	2.105000	0.64084	0.459000	0.35465	GTG	.		0.721	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			T	49390815	A	T	49390815	3	4	25	1	0	0	0	0	1	0	0	0	4339	159	6	5	295	5	DDN	12	49390815	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		49390815	84461080	55	2197											
LRIG3	121227	broad.mit.edu	37	chr12	59274493	59274493	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtatactccatcacctcGccaccttgggcccggaggtg	6	9	12	14	2	1	0	1	0	0	0	3	1	2	1	5	4	1	1	5	4	2	3	rs566187872		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr12:59274493G>A	ENST00000320743.3	-	13	1957	c.1671C>T	c.(1669-1671)ggC>ggT	p.G557G	LRIG3_ENST00000379141.4_Silent_p.G497G	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	557	Ig-like C2-type 1.				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)			CCATCACCTCGCCACCTTGGG	0.483			T	ROS1	NSCLC								G|||	1	0.000199681	0	0	5008	,	,		20461	0		0	False		,,,				2504	0.001				p.G557G				Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3-229	0			c.C1671T						.						123	104	111					12																	59274493		2203	4300	6503	SO:0001819	synonymous_variant	121227	exon13			CACCTCGCCACCT	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.1671C>T	12.37:g.59274493G>A		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	159	4	NM_153377	0	0	6	6	0	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																			.		0.483	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59274493	G	A	59274493	2	1	25	1	0	0	0	0	0	0	0	1	8971	1074	38	1		1	LRIG3	12	59274493	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	9883678	59274493	74577402	56	2198											
LYZ	4069	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	69743944	69743944	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacgagctacaaactacaatGctggagacagaagcactgat	16	6	9	10	1	0	3	0	1	0	2	0	5	0	3	0	1	6	3	0	1	5	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr12:69743944G>T	ENST00000261267.2	+	2	261	c.193G>T	c.(193-195)Gct>Tct	p.A65S	LYZ_ENST00000548839.1_Missense_Mutation_p.A65S|LYZ_ENST00000549690.1_Missense_Mutation_p.A65S	NM_000239.2	NP_000230.1	P61626	LYSC_HUMAN	lysozyme	65					cell wall macromolecule catabolic process (GO:0016998)|cytolysis (GO:0019835)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|lysozyme activity (GO:0003796)			endometrium(2)|lung(1)|upper_aerodigestive_tract(1)	4	all_epithelial(5;2.98e-35)|Lung NSC(4;9.93e-33)|all_lung(4;5.66e-31)|Breast(13;2.56e-06)|Esophageal squamous(21;0.187)		Epithelial(6;8.26e-19)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00503)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)		L-Aspartic Acid(DB00128)	AAACTACAATGCTGGAGACAG	0.408																																					p.A65S													.	LYZ-226	0			c.G193T						.						142	126	131					12																	69743944		2203	4300	6503	SO:0001583	missense	4069	exon2			TACAATGCTGGAG	X14008	CCDS8989.1	12q15	2014-09-17	2010-04-29			ENSG00000090382	3.2.1.17		6740	protein-coding gene	gene with protein product	"renal amyloidosis"	153450	"lysozyme (renal amyloidosis)"			8464497, 2546758	Standard	NM_000239		Approved		uc001suw.2	P61626	OTTHUMG00000169342	ENST00000261267.2:c.193G>T	12.37:g.69743944G>T	ENSP00000261267:p.Ala65Ser	Somatic	139	1		WXS	Illumina HiSeq	Phase_I	207	65	NM_000239	0	0	314	314	0	P00695|Q13170|Q9UCF8	Missense_Mutation	SNP	ENST00000261267.2	37	CCDS8989.1	.	.	.	.	.	.	.	.	.	.	G	3.494	-0.103183	0.06967	.	.	ENSG00000090382	ENST00000261267;ENST00000549690;ENST00000548839	T;T;T	0.74106	-0.81;-0.81;-0.81	5.94	2.04	0.26737	Lysozyme-like domain (1);	0.583053	0.18063	N	0.152887	T	0.45994	0.1370	N	0.04090	-0.28	0.18873	N	0.999986	B	0.02656	0.0	B	0.04013	0.001	T	0.25641	-1.0126	9	.	.	.	.	6.1029	0.20057	0.1274:0.4297:0.3725:0.0704	.	65	P61626	LYSC_HUMAN	S	65	ENSP00000261267:A65S;ENSP00000449898:A65S;ENSP00000449969:A65S	.	A	+	1	0	LYZ	68030211	0.000000	0.05858	0.049000	0.19019	0.034000	0.12701	-0.307000	0.08167	0.408000	0.25621	-0.855000	0.03028	GCT	.		0.408	LYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403624.2	NM_000239		T	69743944	G	T	69743944	3	4	25	1	0	0	0	0	1	0	0	0	9155	1319	46	4	199	4	LYZ	12	69743944	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	10469451	69743944	64107951	57	2199											
ATP2B1	490	hgsc.bcm.edu;bcgsc.ca	37	chr12	89992987	89992988	+	Frame_Shift_Ins	INS	-	-	AA																															tctcttcaacatcctctgctINSaattcctcctcaggtatttc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr12:89992987_89992988insAA	ENST00000428670.3	-	20	3713_3714	c.3257_3258insTT	c.(3256-3258)ttafs	p.L1086fs	ATP2B1_ENST00000393164.2_Frame_Shift_Ins_p.L829fs|ATP2B1_ENST00000261173.2_Frame_Shift_Ins_p.L1086fs|ATP2B1_ENST00000359142.3_Frame_Shift_Ins_p.L1086fs|ATP2B1_ENST00000348959.3_Frame_Shift_Ins_p.L1050fs			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	1086					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						CATCCTCTGCTAATTCCTCCTC	0.436																																					p.L1086fs		.											.	ATP2B1-516	0			c.3258_3259insTT						.																																			SO:0001589	frameshift_variant	490	exon19			.	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.3256_3257dupTT	12.37:g.89992988_89992989dupAA	ENSP00000392043:p.Leu1086fs	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	83	30	NM_001001323	0	0	0	0	0	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Frame_Shift_Ins	INS	ENST00000428670.3	37	CCDS9035.1																																																																																			.		0.436	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		AA	89992988	-	AA	89992987	7	5	25	1	0	1	1	0	0	0	0	0	1140	1519	53	0	570	0	ATP2B1	12	89992987	Frame_Shift_Ins	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10	20249043	89992987	43858908	58	2200											
THSD1	55901	hgsc.bcm.edu;bcgsc.ca	37	chr13	52971551	52971551	+	Frame_Shift_Del	DEL	G	G	-																															gtcctcttcccagggtatctGggggcctccttgaagacagt																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr13:52971551delG	ENST00000258613.4	-	3	1015	c.837delC	c.(835-837)cccfs	p.P279fs	RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron|THSD1_ENST00000349258.4_Frame_Shift_Del_p.P279fs	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	279					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CAGGGTATCTGGGGGCCTCCT	0.537																																					p.P279fs		.											.	THSD1-94	0			c.837delC						.						75	74	74					13																	52971551		2203	4300	6503	SO:0001589	frameshift_variant	55901	exon3			.	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.837delC	13.37:g.52971551delG	ENSP00000258613:p.Pro279fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	117	27	NM_018676	0	0	0	0	0	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Frame_Shift_Del	DEL	ENST00000258613.4	37	CCDS9432.1																																																																																			.		0.537	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			-	52971551	G	-	52971551	7	5	25	1	0	1	0	1	0	0	0	0	15909	1335	47	0	1733	0	THSD1	13	52971551	Frame_Shift_Del	DEL	G	TCGA-A4-A5XZ-01A-11D-A31X-10		52971551	62198327	59	2201											
ZIC2	7546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	100635322	100635322	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgagaaacccttcccctGccccttcccgggctgtggca	6	7	11	17	2	0	1	0	0	0	1	2	2	2	1	6	3	2	2	6	3	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr13:100635322G>A	ENST00000376335.3	+	1	1297	c.1004G>A	c.(1003-1005)tGc>tAc	p.C335Y		NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2	335			C -> F (in HPE5). {ECO:0000269|PubMed:19177455}.		brain development (GO:0007420)|developmental pigmentation (GO:0048066)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal ganglion cell axon guidance (GO:0031290)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCCTTCCCCTGCCCCTTCCCG	0.617																																					p.C335Y	Pancreas(97;119 1522 31925 44771 48764)	.											.	ZIC2-90	0			c.G1004A						.						81	89	86					13																	100635322		2203	4300	6503	SO:0001583	missense	7546	exon1			TCCCCTGCCCCTT	AF104902	CCDS9495.1	13q32	2013-01-08	2011-05-19		ENSG00000043355	ENSG00000043355		"Zinc fingers, C2H2-type"	12873	protein-coding gene	gene with protein product	"Zinc finger protein of the cerebellum 2"	603073	"Zic family member 2 (odd-paired Drosophila homolog)", "Zic family member 2 (odd-paired homolog, Drosophila)"			9771712	Standard	NM_007129		Approved	HPE5	uc001von.3	O95409	OTTHUMG00000017279	ENST00000376335.3:c.1004G>A	13.37:g.100635322G>A	ENSP00000365514:p.Cys335Tyr	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	87	26	NM_007129	0	0	0	0	0	Q5VYA9|Q9H309	Missense_Mutation	SNP	ENST00000376335.3	37	CCDS9495.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224811	0.79576	.	.	ENSG00000043355	ENST00000376335;ENST00000397444	D	0.85088	-1.94	4.69	4.69	0.59074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.93798	0.8017	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94910	0.8064	10	0.87932	D	0	.	18.1567	0.89693	0.0:0.0:1.0:0.0	.	335	O95409	ZIC2_HUMAN	Y	335;84	ENSP00000365514:C335Y	ENSP00000365514:C335Y	C	+	2	0	ZIC2	99433323	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.601000	0.98297	2.610000	0.88304	0.561000	0.74099	TGC	.		0.617	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	NM_007129		A	100635322	G	A	100635322	3	1	25	1	0	0	0	0	1	0	0	0	17711	1319	46	2	1006	2	ZIC2	13	100635322	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	47663771	100635322	14534556	60	2202											
SCFD1	23256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31175075	31175075	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggccagctatggcagcactAccactaaaccaatggggtaa	13	6	10	12	1	0	0	0	0	0	0	0	0	0	0	3	4	4	4	3	4	6	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:31175075A>T	ENST00000458591.2	+	18	1764	c.1537A>T	c.(1537-1539)Acc>Tcc	p.T513S	SCFD1_ENST00000554486.1_3'UTR|SCFD1_ENST00000544052.2_Missense_Mutation_p.T446S|SCFD1_ENST00000421551.3_Missense_Mutation_p.T454S|SCFD1_ENST00000541123.1_Missense_Mutation_p.T328S|SCFD1_ENST00000396629.2_Missense_Mutation_p.T421S	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	513					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		TGGCAGCACTACCACTAAACC	0.373																																					p.T513S		.											.	SCFD1-226	0			c.A1537T						.						84	87	86					14																	31175075		2203	4300	6503	SO:0001583	missense	23256	exon18			AGCACTACCACTA	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.1537A>T	14.37:g.31175075A>T	ENSP00000390783:p.Thr513Ser	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_016106	0	1	14	26	11	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	.	.	.	.	.	.	.	.	.	.	A	9.070	0.996695	0.19043	.	.	ENSG00000092108	ENST00000458591;ENST00000544052;ENST00000421551;ENST00000541123;ENST00000396629	T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96	5.71	4.58	0.56647	.	0.244841	0.38548	N	0.001656	T	0.38188	0.1031	N	0.00985	-1.075	0.33038	D	0.531027	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.12156	0.003;0.002;0.007;0.005	T	0.43589	-0.9382	10	0.15499	T	0.54	-35.8251	3.8893	0.09111	0.7124:0.0:0.2876:0.0	.	454;446;421;513	B7Z738;B7Z4U7;B7Z594;Q8WVM8	.;.;.;SCFD1_HUMAN	S	513;446;454;328;421	ENSP00000390783:T513S;ENSP00000443010:T446S;ENSP00000388078:T454S;ENSP00000443537:T328S;ENSP00000379870:T421S	ENSP00000309417:T521S	T	+	1	0	SCFD1	30244826	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.464000	0.53057	2.175000	0.68902	0.477000	0.44152	ACC	.		0.373	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		T	31175075	A	T	31175075	3	4	25	1	0	0	0	0	1	0	0	0	13921	391	14	5	1607	5	SCFD1	14	31175075	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		31175075	76174465	61	2203											
C14orf101	54916	broad.mit.edu;bcgsc.ca	37	chr14	57072352	57072352	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagcacacaataatactctAtgttttgtgcataatacctt	13	14	4	10	0	1	0	0	0	1	0	1	0	1	0	2	0	4	3	2	0	6	8			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:57072352A>C	ENST00000261556.6	+	5	709	c.587A>C	c.(586-588)tAt>tCt	p.Y196S	TMEM260_ENST00000538838.1_Missense_Mutation_p.Y196S|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	196						integral component of membrane (GO:0016021)											ATAATACTCTATGTTTTGTGC	0.264																																					p.Y196S													.	.	0			c.A587C						.						123	137	132					14																	57072352		2202	4297	6499	SO:0001583	missense	0	exon5			TACTCTATGTTTT	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.587A>C	14.37:g.57072352A>C	ENSP00000261556:p.Tyr196Ser	Somatic	105	2		WXS	Illumina HiSeq	Phase_I	112	42	NM_017799	0	0	3	7	4	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	37	CCDS9727.2	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517688	0.85495	.	.	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.44482	1.46;0.92	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.63486	0.2515	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.63171	-0.6697	10	0.39692	T	0.17	-13.4379	15.8297	0.78741	1.0:0.0:0.0:0.0	.	196	Q9NX78	CN101_HUMAN	S	196	ENSP00000261556:Y196S;ENSP00000441934:Y196S	ENSP00000261556:Y196S	Y	+	2	0	C14orf101	56142105	1.000000	0.71417	0.987000	0.45799	0.926000	0.56050	7.193000	0.77780	2.138000	0.66242	0.451000	0.29950	TAT	.		0.264	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		C	57072352	A	C	57072352	3	2	25	1	0	0	0	0	1	0	0	0	1738	449	16	5	605	5	C14orf101	14	57072352	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	25897277	57072352	50277188	62	2204											
ZFYVE26	23503	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	68252617	68252617	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagtgactgaaggacctgatCtagctgctgggagagggtgg	9	8	17	7	0	1	4	0	3	1	1	1	6	1	5	1	4	2	2	1	4	2	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:68252617C>T	ENST00000347230.4	-	18	3400	c.3262G>A	c.(3262-3264)Gat>Aat	p.D1088N	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.D1088N	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1088					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AGGACCTGATCTAGCTGCTGG	0.557																																					p.D1088N		.											.	ZFYVE26-162	0			c.G3262A						.						218	222	221					14																	68252617		2203	4300	6503	SO:0001583	missense	23503	exon18			CCTGATCTAGCTG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.3262G>A	14.37:g.68252617C>T	ENSP00000251119:p.Asp1088Asn	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	80	26	NM_015346	0	0	1	3	2	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817287	0.90790	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.30981	1.66;1.51	5.38	5.38	0.77491	.	0.530450	0.20377	N	0.093539	T	0.36908	0.0984	L	0.47716	1.5	0.40782	D	0.983189	P;P	0.39480	0.675;0.546	B;B	0.43658	0.426;0.164	T	0.21621	-1.0240	10	0.59425	D	0.04	0.0013	16.9198	0.86161	0.0:1.0:0.0:0.0	.	1088;1088	G3V2D8;Q68DK2	.;ZFY26_HUMAN	N	1088;1067;1088	ENSP00000251119:D1088N;ENSP00000450603:D1088N	ENSP00000251119:D1088N	D	-	1	0	ZFYVE26	67322370	0.998000	0.40836	0.480000	0.27341	0.939000	0.58152	3.840000	0.55843	2.512000	0.84698	0.655000	0.94253	GAT	.		0.557	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68252617	C	T	68252617	3	4	25	1	0	0	0	0	1	0	0	0	17700	913	32	2	4457	2	ZFYVE26	14	68252617	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	11180265	68252617	39096923	63	2205											
EXD2	55218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	69697234	69697234	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcctgaagtccctcgctgaGactgttttgaactttcccct	7	13	8	13	1	0	3	0	3	0	1	3	4	2	3	4	0	2	2	4	0	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:69697234G>C	ENST00000409018.3	+	4	764	c.636G>C	c.(634-636)gaG>gaC	p.E212D	EXD2_ENST00000409675.1_Missense_Mutation_p.E87D|EXD2_ENST00000409949.1_Missense_Mutation_p.E87D|EXD2_ENST00000449989.1_Missense_Mutation_p.E87D|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000312994.5_Missense_Mutation_p.E212D|EXD2_ENST00000409242.1_Missense_Mutation_p.E87D|EXD2_ENST00000409014.1_Missense_Mutation_p.E87D	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	212	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						CCCTCGCTGAGACTGTTTTGA	0.448																																					p.E212D		.											.	.	0			c.G636C						.						178	168	172					14																	69697234		2203	4300	6503	SO:0001583	missense	55218	exon4			CGCTGAGACTGTT	AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.636G>C	14.37:g.69697234G>C	ENSP00000387331:p.Glu212Asp	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	68	21	NM_001193361	0	0	6	18	12	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	37	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.507951	0.64410	.	.	ENSG00000081177	ENST00000409018;ENST00000193422;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000413191;ENST00000449989	T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	5.33	2.49	0.30216	-5&apos (1);Ribonuclease H-like (1); exonuclease (1);3&apos (1);	0.093871	0.64402	D	0.000001	T	0.70640	0.3247	M	0.75884	2.315	0.40602	D	0.981598	P;P	0.51057	0.941;0.908	P;P	0.58520	0.84;0.781	T	0.68637	-0.5356	10	0.33141	T	0.24	-25.4424	9.0491	0.36365	0.373:0.0:0.627:0.0	.	212;87	G5E947;Q9NVH0	.;EXD2_HUMAN	D	212;212;87;87;87;87;212;87;87	ENSP00000387331:E212D;ENSP00000386915:E87D;ENSP00000386762:E87D;ENSP00000386632:E87D;ENSP00000386839:E87D;ENSP00000313140:E212D;ENSP00000409089:E87D;ENSP00000392177:E87D	ENSP00000193422:E212D	E	+	3	2	EXD2	68766987	1.000000	0.71417	0.970000	0.41538	0.840000	0.47671	2.350000	0.44063	0.742000	0.32697	-0.136000	0.14681	GAG	.		0.448	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			C	69697234	G	C	69697234	3	2	25	1	0	0	0	0	1	0	0	0	5311	933	33	4	267	4	EXD2	14	69697234	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	1444617	69697234	37652306	64	2206											
ADAM20	8748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	70989617	70989617	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacacttcttacggatgcAgatcttttctggaccacata	10	12	8	11	1	3	1	0	0	3	1	3	3	3	3	1	3	2	2	1	3	2	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:70989617A>C	ENST00000256389.3	-	2	2252	c.2008T>G	c.(2008-2010)Tgc>Ggc	p.C670G	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	620					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TTACGGATGCAGATCTTTTCT	0.463																																					p.C670G		.											.	ADAM20-226	0			c.T2008G						.						416	313	348					14																	70989617		2203	4300	6503	SO:0001583	missense	8748	exon2			GGATGCAGATCTT	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.2008T>G	14.37:g.70989617A>C	ENSP00000256389:p.Cys670Gly	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	103	36	NM_003814	0	0	0	0	0	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.051177	0.55218	.	.	ENSG00000134007	ENST00000256389	T	0.02763	4.17	4.67	4.67	0.58626	ADAM, cysteine-rich (1);	0.000000	0.42682	D	0.000667	T	0.17066	0.0410	M	0.86805	2.84	0.20196	N	0.999929	D	0.89917	1.0	D	0.91635	0.999	T	0.03166	-1.1065	10	0.87932	D	0	.	12.6491	0.56751	1.0:0.0:0.0:0.0	.	620	O43506	ADA20_HUMAN	G	670	ENSP00000256389:C670G	ENSP00000256389:C670G	C	-	1	0	ADAM20	70059370	0.764000	0.28473	0.184000	0.23157	0.040000	0.13550	4.075000	0.57584	1.856000	0.53863	0.460000	0.39030	TGC	.		0.463	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			C	70989617	A	C	70989617	3	2	25	1	0	0	0	0	1	0	0	0	242	188	7	5	326	5	ADAM20	14	70989617	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	1292383	70989617	36359923	65	2207											
C14orf43	91748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	74206660	74206660	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctggttcctggcccccgaAgaggcaacgcttccgcttgt	6	9	12	14	3	0	1	0	0	0	1	2	2	2	1	4	3	2	5	4	3	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:74206660A>T	ENST00000286523.5	-	2	834	c.52T>A	c.(52-54)Ttc>Atc	p.F18I	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.F18I|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	18					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										TGGCCCCCGAAGAGGCAACGC	0.652																																					p.F18I		.											.	.	0			c.T52A						.						44	48	47					14																	74206660		2203	4300	6503	SO:0001583	missense	91748	exon2			CCCCGAAGAGGCA	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.52T>A	14.37:g.74206660A>T	ENSP00000286523:p.Phe18Ile	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	39	15	NM_194278	0	0	2	3	1	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824093	0.50739	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371;ENST00000421708	T;T;T;T	0.21734	2.0;2.0;2.0;1.99	4.96	4.96	0.65561	.	0.081627	0.51477	D	0.000084	T	0.15089	0.0364	N	0.24115	0.695	0.47737	D	0.999504	B;B	0.31318	0.319;0.319	B;B	0.27608	0.081;0.081	T	0.05666	-1.0871	10	0.72032	D	0.01	-4.5629	13.0167	0.58762	1.0:0.0:0.0:0.0	.	18;18	A0PJD3;Q6PJG2	.;CN043_HUMAN	I	18	ENSP00000377634:F18I;ENSP00000286523:F18I;ENSP00000407767:F18I;ENSP00000402380:F18I	ENSP00000286523:F18I	F	-	1	0	C14orf43	73276413	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	6.822000	0.75277	2.089000	0.63090	0.402000	0.26972	TTC	.		0.652	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		T	74206660	A	T	74206660	3	4	25	1	0	0	0	0	1	0	0	0	1778	72	3	5	3129	5	C14orf43	14	74206660	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	3217043	74206660	33142880	66	2208											
BCL2L10	10017	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	52404725	52404725	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcccggggtagccgaggtAggcggagaaaaaggaccggt	10	5	18	8	4	0	1	0	0	0	1	1	4	1	2	3	7	1	3	3	7	4	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr15:52404725A>T	ENST00000561198.1	-	1	240	c.199T>A	c.(199-201)Tac>Aac	p.Y67N	BCL2L10_ENST00000260442.3_Missense_Mutation_p.Y67N			Q9HD36	B2L10_HUMAN	BCL2-like 10 (apoptosis facilitator)	57					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|female gamete generation (GO:0007292)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2				all cancers(107;0.0148)		TAGCCGAGGTAGGCGGAGAAA	0.716																																					p.Y67N		.											.	BCL2L10-227	0			c.T199A						.						12	15	14					15																	52404725		2182	4283	6465	SO:0001583	missense	10017	exon1			CGAGGTAGGCGGA	AF285092	CCDS10148.1	15q21	2007-03-02			ENSG00000137875	ENSG00000137875			993	protein-coding gene	gene with protein product		606910				9829980, 9878060	Standard	NM_020396		Approved	Diva, Boo, BCL-B	uc002abq.3	Q9HD36	OTTHUMG00000131893	ENST00000561198.1:c.199T>A	15.37:g.52404725A>T	ENSP00000453562:p.Tyr67Asn	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	31	12	NM_020396	0	0	1	1	0	Q3SX80|Q52LQ9|Q8TCS9	Missense_Mutation	SNP	ENST00000561198.1	37		.	.	.	.	.	.	.	.	.	.	A	16.67	3.188072	0.57909	.	.	ENSG00000137875	ENST00000260442	T	0.11930	2.73	4.61	2.26	0.28386	Apoptosis regulator, Bcl-2, BH (2);	1.152810	0.06639	N	0.760739	T	0.27559	0.0677	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	D	0.65987	0.94	T	0.13229	-1.0517	10	0.66056	D	0.02	.	5.067	0.14587	0.7532:0.0:0.2468:0.0	.	57	Q9HD36	B2L10_HUMAN	N	67	ENSP00000260442:Y67N	ENSP00000260442:Y67N	Y	-	1	0	BCL2L10	50192017	0.000000	0.05858	0.003000	0.11579	0.015000	0.08874	0.370000	0.20433	0.800000	0.34041	0.533000	0.62120	TAC	.		0.716	BCL2L10-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000419386.1			T	52404725	A	T	52404725	3	4	25	1	0	0	0	0	1	0	0	0	1369	420	15	5	423	5	BCL2L10	15	52404725	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		52404725	50126667	67	2209											
ULK3	25989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75132623	75132623	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcttccagctccgagaacgaCctggaggcaaaggggggctg	9	6	15	11	2	1	1	0	0	1	1	3	4	3	2	3	5	2	3	3	5	2	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr15:75132623C>T	ENST00000440863.2	-	6	739	c.648G>A	c.(646-648)agG>agA	p.R216R	ULK3_ENST00000568667.1_Silent_p.R227R|ULK3_ENST00000569437.1_Silent_p.R216R	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						CCGAGAACGACCTGGAGGCAA	0.652																																					p.R216R		.											.	ULK3-290	0			c.G648A						.						25	27	26					15																	75132623		1915	4138	6053	SO:0001819	synonymous_variant	25989	exon6			GAACGACCTGGAG	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"unc-51-like kinase 3 (C. elegans)"				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.648G>A	15.37:g.75132623C>T		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	40	16	NM_001099436	0	0	11	14	3	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Silent	SNP	ENST00000440863.2	37	CCDS45305.1																																																																																			.		0.652	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518		T	75132623	C	T	75132623	2	4	25	1	0	0	0	0	0	0	0	1	17010	506	18	2		2	ULK3	15	75132623	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	22727898	75132623	27398769	68	2210											
CLDN9	9080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3063765	3063765	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccggcatcctggtgctcatCcctgtgtgctggacggcgca	4	9	14	14	3	1	0	1	0	0	0	3	1	3	1	3	4	2	4	3	4	0	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr16:3063765C>A	ENST00000445369.2	+	1	1309	c.402C>A	c.(400-402)atC>atA	p.I134I		NM_020982.3	NP_066192.1	O95484	CLD9_HUMAN	claudin 9	134					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(1)|lung(5)|prostate(2)	10						TGGTGCTCATCCCTGTGTGCT	0.662																																					p.I134I		.											.	CLDN9-90	0			c.C402A						.						82	80	81					16																	3063765		2198	4300	6498	SO:0001819	synonymous_variant	9080	exon1			GCTCATCCCTGTG	AJ130941	CCDS10487.1	16p13.3	2008-08-01			ENSG00000213937	ENSG00000213937		"Claudins"	2051	protein-coding gene	gene with protein product		615799				9441748, 18234789	Standard	NM_020982		Approved		uc010uwo.1	O95484	OTTHUMG00000129000	ENST00000445369.2:c.402C>A	16.37:g.3063765C>A		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	102	55	NM_020982	0	0	0	0	0		Silent	SNP	ENST00000445369.2	37	CCDS10487.1																																																																																			.		0.662	CLDN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250989.1	NM_020982		A	3063765	C	A	3063765	2	1	25	1	0	0	0	0	0	0	0	1	3498	845	30	4		4	CLDN9	16	3063765	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		3063765	87290988	69	2211											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	295	15		WXS	Illumina HiSeq		448	24	NM_145301	0	0	3	35	32	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		T	15457087	C	T	15457087	3	4	25	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		15457087	65738123	70	2212											
FOXN1	8456	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	26851949	26851949	+	Frame_Shift_Del	DEL	C	C	-																															gaggcctggtgtaacgggctCccctaccccagccaggagca																								rs548499213	byFrequency	TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:26851949delC	ENST00000226247.2	+	2	581	c.552delC	c.(550-552)ctcfs	p.L184fs	FOXN1_ENST00000579795.1_Frame_Shift_Del_p.L184fs	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	184					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					GTAACGGGCTCCCCTACCCCA	0.647																																					p.L184fs		.											.	FOXN1-226	0			c.552delC						.						25	27	26					17																	26851949		2202	4300	6502	SO:0001589	frameshift_variant	8456	exon2			.	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.552delC	17.37:g.26851949delC	ENSP00000226247:p.Leu184fs	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	62	21	NM_003593	0	0	0	0	0	B2R9Q7|O15352	Frame_Shift_Del	DEL	ENST00000226247.2	37	CCDS11232.1																																																																																			.		0.647	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			-	26851949	C	-	26851949	7	5	25	1	0	1	0	1	0	0	0	0	6038	842	30	0	558	0	FOXN1	17	26851949	Frame_Shift_Del	DEL	C	TCGA-A4-A5XZ-01A-11D-A31X-10	11394862	26851949	54343261	71	2213											
RPL19	6143	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37358657	37358657	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggctcgatgccggaaaaacaCcttggcccgccggaagggca	10	4	14	13	4	0	0	0	0	0	0	1	3	0	2	4	5	2	2	4	5	3	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:37358657C>T	ENST00000225430.4	+	3	262	c.200C>T	c.(199-201)aCc>aTc	p.T67I	RPL19_ENST00000582193.1_Missense_Mutation_p.T65I|RPL19_ENST00000579260.1_Missense_Mutation_p.T65I|RPL19_ENST00000579374.1_Missense_Mutation_p.T64I	NM_000981.3	NP_000972.1	P84098	RL19_HUMAN	ribosomal protein L19	67					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7						CGGAAAAACACCTTGGCCCGC	0.522																																					p.T67I													.	RPL19-90	0			c.C200T						.						62	62	62					17																	37358657		1915	4111	6026	SO:0001583	missense	6143	exon3			AAAACACCTTGGC		CCDS42312.1	17q12	2012-09-20			ENSG00000108298	ENSG00000108298		"L ribosomal proteins"	10312	protein-coding gene	gene with protein product	"60S ribosomal protein L19", "ribosomal protein L19, cytosolic, N-terminus truncated"	180466				1577483	Standard	XM_005257564		Approved	FLJ27452, MGC71997, DKFZp779D216, L19	uc002hrq.1	P84098	OTTHUMG00000178979	ENST00000225430.4:c.200C>T	17.37:g.37358657C>T	ENSP00000225430:p.Thr67Ile	Somatic	100	1		WXS	Illumina HiSeq	Phase_I	118	61	NM_000981	2	1	1108	2449	1338	B2R4K2|P14118|P22908|Q502Y6|Q7Z6E4	Missense_Mutation	SNP	ENST00000225430.4	37	CCDS42312.1	.	.	.	.	.	.	.	.	.	.	c	16.65	3.181855	0.57800	.	.	ENSG00000108298	ENST00000225430	.	.	.	5.44	5.44	0.79542	Ribosomal protein L19/L19e (2);	0.000000	0.85682	D	0.000000	T	0.64670	0.2619	L	0.46614	1.455	0.80722	D	1	B	0.15473	0.013	B	0.24848	0.056	T	0.59107	-0.7516	9	0.37606	T	0.19	.	19.2827	0.94058	0.0:1.0:0.0:0.0	.	67	P84098	RL19_HUMAN	I	67	.	ENSP00000225430:T67I	T	+	2	0	RPL19	34612183	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.870000	0.63035	2.545000	0.85829	0.655000	0.94253	ACC	.		0.522	RPL19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444190.1	NM_000981		T	37358657	C	T	37358657	3	4	25	1	0	0	0	0	1	0	0	0	13598	507	18	2	210	2	RPL19	17	37358657	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	10506708	37358657	43836553	72	2214											
KRT35	3886	bcgsc.ca	37	chr17	39636925	39636925	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaagtaggactggtagtcaGggcacatgtaggggacctgc	10	7	17	7	0	1	0	1	0	0	0	1	3	1	3	1	6	1	4	1	6	4	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:39636925G>T	ENST00000393989.1	-	1	467	c.425C>A	c.(424-426)cCt>cAt	p.P142H	KRT35_ENST00000246639.2_Missense_Mutation_p.P112H	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	142	Linker 1.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				CTGGTAGTCAGGGCACATGTA	0.582																																					p.P142H													.	KRT35-92	0			c.C425A						.						78	83	81					17																	39636925		2203	4300	6503	SO:0001583	missense	3886	exon1			TAGTCAGGGCACA	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"-", "Intermediate filaments type I, keratins (acidic)"	6453	protein-coding gene	gene with protein product	"hard keratin type I 5"	602764	"keratin, hair, acidic, 5"	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.425C>A	17.37:g.39636925G>T	ENSP00000377558:p.Pro142His	Somatic	54	0		WXS	Illumina HiSeq	Phase_1	43	4	NM_002280	0	0	0	0	0	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295516	0.40594	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.88896	-2.44;-2.44	5.18	5.18	0.71444	Filament (1);	0.000000	0.64402	D	0.000013	D	0.92648	0.7664	M	0.71296	2.17	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	D	0.85570	0.1233	10	0.36615	T	0.2	.	10.7023	0.45934	0.0:0.1414:0.7124:0.1462	.	142	Q92764	KRT35_HUMAN	H	112;142	ENSP00000246639:P112H;ENSP00000377558:P142H	ENSP00000246639:P112H	P	-	2	0	KRT35	36890451	0.000000	0.05858	0.879000	0.34478	0.801000	0.45260	0.314000	0.19432	2.689000	0.91719	0.511000	0.50034	CCT	.		0.582	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280		T	39636925	G	T	39636925	3	4	25	1	0	0	0	0	1	0	0	0	8493	1000	35	4	970	4	KRT35	17	39636925	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	2278268	39636925	41558285	73	2215											
TOB1	10140	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48941072	48941072	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactggtcccttttcaccaaTttggtaagaaacctcaaatg	12	12	6	11	0	2	1	2	0	0	1	3	1	3	1	3	2	1	1	3	2	4	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:48941072T>A	ENST00000268957.3	-	3	735	c.307A>T	c.(307-309)Att>Ttt	p.I103F	TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Missense_Mutation_p.I103F|TOB1-AS1_ENST00000416263.3_RNA	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	103					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			TTTTCACCAATTTGGTAAGAA	0.423											OREG0024576	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I103F	NSCLC(144;643 1919 24513 29423 40686)												.	TOB1-226	0			c.A307T						.						145	133	137					17																	48941072		2203	4300	6503	SO:0001583	missense	10140	exon2			CACCAATTTGGTA	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.307A>T	17.37:g.48941072T>A	ENSP00000268957:p.Ile103Phe	Somatic	134	1	958	WXS	Illumina HiSeq	Phase_I	182	45	NM_005749	0	1	73	105	31	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	37	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252047	0.59212	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.54279	0.58;0.58	5.69	5.69	0.88448	Anti-proliferative protein (4);	0.000000	0.85682	D	0.000000	T	0.51500	0.1678	L	0.58583	1.82	0.80722	D	1	P	0.43750	0.816	B	0.39027	0.288	T	0.58907	-0.7553	10	0.72032	D	0.01	.	15.942	0.79763	0.0:0.0:0.0:1.0	.	103	P50616	TOB1_HUMAN	F	103	ENSP00000427695:I103F;ENSP00000268957:I103F	ENSP00000268957:I103F	I	-	1	0	TOB1	46296071	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	7.698000	0.84413	2.162000	0.67917	0.533000	0.62120	ATT	.		0.423	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			A	48941072	T	A	48941072	3	1	25	1	0	0	0	0	1	0	0	0	16379	1493	52	5	734	5	TOB1	17	48941072	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	9304147	48941072	32254138	74	2216											
C17orf71	55181	hgsc.bcm.edu	37	chr17	57288259	57288259	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtagaacctcctcggaacCaagacccagctcatccagac	13	5	8	15	1	1	3	1	0	0	3	4	4	3	4	5	2	3	2	5	2	4	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:57288259C>A	ENST00000543872.2	+	2	1111	c.847C>A	c.(847-849)Caa>Aaa	p.Q283K	SMG8_ENST00000580498.1_Intron|CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.Q283K|SMG8_ENST00000578922.1_Missense_Mutation_p.Q283K			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	283					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						TCCTCGGAACCAAGACCCAGC	0.517																																					p.Q283K		.											.	SMG8-93	0			c.C847A						.						66	73	70					17																	57288259		2203	4300	6503	SO:0001583	missense	55181	exon1			CGGAACCAAGACC	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"chromosome 17 open reading frame 71", "smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.847C>A	17.37:g.57288259C>A	ENSP00000438748:p.Gln283Lys	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	74	5	NM_018149	0	0	4	4	0	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	C	8.062	0.768336	0.15983	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.41400	1.0;1.0	5.88	5.88	0.94601	.	0.345316	0.35179	N	0.003390	T	0.37732	0.1014	L	0.40543	1.245	0.43852	D	0.99644	B	0.19583	0.037	B	0.15052	0.012	T	0.09250	-1.0683	10	0.22706	T	0.39	-16.8779	19.2147	0.93772	0.0:1.0:0.0:0.0	.	283	Q8ND04	SMG8_HUMAN	K	283	ENSP00000300917:Q283K;ENSP00000438748:Q283K	ENSP00000300917:Q283K	Q	+	1	0	SMG8	54643041	0.999000	0.42202	1.000000	0.80357	0.961000	0.63080	3.993000	0.56987	2.769000	0.95229	0.655000	0.94253	CAA	.		0.517	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		A	57288259	C	A	57288259	3	1	25	1	0	0	0	0	1	0	0	0	1883	595	21	4	849	4	C17orf71	17	57288259	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	8347187	57288259	23906951	75	2217											
DDX5	1655	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62496852	62496852	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tataatcctctgaggagttaGggtagtcataattgatgaca	13	13	10	5	0	2	3	1	3	1	0	3	4	3	4	1	2	0	2	1	2	5	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:62496852G>C	ENST00000225792.5	-	12	1657	c.1256C>G	c.(1255-1257)cCt>cGt	p.P419R	DDX5_ENST00000578804.1_Missense_Mutation_p.P419R|DDX5_ENST00000450599.2_Missense_Mutation_p.P340R|MIR3064_ENST00000581130.1_RNA|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000580026.1_5'UTR	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	419	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TGAGGAGTTAGGGTAGTCATA	0.403			T	ETV4	prostate																																p.P419R	NSCLC(22;406 813 4871 19580 40307)			Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5-228	0			c.C1256G						.						140	124	129					17																	62496852		2203	4300	6503	SO:0001583	missense	1655	exon12			GAGTTAGGGTAGT	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"DEAD-boxes"	2746	protein-coding gene	gene with protein product		180630	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1256C>G	17.37:g.62496852G>C	ENSP00000225792:p.Pro419Arg	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	116	29	NM_004396	0	0	114	166	52	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	37	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.299147	0.23650	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.73	5.73	0.89815	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.91788	0.7402	H	0.99286	4.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.997	D	0.94552	0.7754	9	0.87932	D	0	-9.6298	20.2602	0.98440	0.0:0.0:1.0:0.0	.	340;419;419	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	R	419;349;408	.	ENSP00000225792:P408R	P	-	2	0	DDX5	59927314	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.175000	0.94831	2.861000	0.98227	0.655000	0.94253	CCT	.		0.403	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		C	62496852	G	C	62496852	3	2	25	1	0	0	0	0	1	0	0	0	4373	1000	35	4	596	4	DDX5	17	62496852	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	5208593	62496852	18698358	76	2218											
MGAT5B	146664	broad.mit.edu	37	chr17	74944059	74944059	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccccgcgcacgccctgcggGcctggctggccgtgcctggg	1	5	16	19	5	0	0	0	0	0	0	0	0	0	0	6	4	2	2	6	4	0	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:74944059G>T	ENST00000569840.2	+	17	2645	c.2071G>T	c.(2071-2073)Gcc>Tcc	p.A691S	MGAT5B_ENST00000301618.4_Missense_Mutation_p.A689S|RP11-87G24.3_ENST00000564292.1_RNA|MGAT5B_ENST00000428789.2_Missense_Mutation_p.A700S	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	691					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CGCCCTGCGGGCCTGGCTGGC	0.701																																					p.A700S													.	MGAT5B-93	0			c.G2098T						.						21	22	22					17																	74944059		2200	4298	6498	SO:0001583	missense	146664	exon15			CTGCGGGCCTGGC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	24140	protein-coding gene	gene with protein product		612441	"mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.2071G>T	17.37:g.74944059G>T	ENSP00000456037:p.Ala691Ser	Somatic	45	2		WXS	Illumina HiSeq	Phase_I	46	7	NM_198955	0	0	0	0	0	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	37	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.549882	0.45383	.	.	ENSG00000167889	ENST00000301618;ENST00000428789	T;T	0.43688	0.94;0.94	4.66	4.66	0.58398	.	0.238298	0.34411	N	0.003988	T	0.34600	0.0903	L	0.29908	0.895	0.33183	D	0.549746	P;P;P	0.41848	0.571;0.634;0.763	B;B;B	0.39119	0.163;0.085;0.291	T	0.54463	-0.8290	10	0.62326	D	0.03	-28.8763	16.5725	0.84622	0.0:0.0:1.0:0.0	.	96;700;689	Q3V5L5-4;Q3V5L5-2;Q3V5L5-5	.;.;.	S	689;700	ENSP00000301618:A689S;ENSP00000391227:A700S	ENSP00000301618:A689S	A	+	1	0	MGAT5B	72455654	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	4.928000	0.63447	2.129000	0.65627	0.557000	0.71058	GCC	.		0.701	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		T	74944059	G	T	74944059	3	4	25	1	0	0	0	0	1	0	0	0	9574	1203	42	4	2228	4	MGAT5B	17	74944059	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	12447207	74944059	6251151	77	2219											
DNAH17	8632	bcgsc.ca	37	chr17	76565539	76565539	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	catttacagccagggagatgCcactcaggacttcctcgatt	10	10	9	12	1	1	1	1	0	0	1	3	4	2	2	3	2	3	0	3	2	1	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:76565539C>T	ENST00000585328.1	-	8	1239	c.1115G>A	c.(1114-1116)gGc>gAc	p.G372D	DNAH17_ENST00000389840.5_Missense_Mutation_p.G372D	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	372	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CAGGGAGATGCCACTCAGGAC	0.522																																					p.G372D													.	DNAH17-142	0			c.G1115A						.						86	65	72					17																	76565539		2203	4300	6503	SO:0001583	missense	8632	exon8			GAGATGCCACTCA	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.1115G>A	17.37:g.76565539C>T	ENSP00000465516:p.Gly372Asp	Somatic	81	0		WXS	Illumina HiSeq	Phase_1	121	6	NM_173628	0	0	0	0	0	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	C	9.643	1.139584	0.21205	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.53857	0.6	4.65	2.59	0.31030	.	0.966446	0.08432	N	0.946763	T	0.50205	0.1602	L	0.51422	1.61	0.23168	N	0.998186	B	0.22276	0.067	B	0.29077	0.098	T	0.49744	-0.8907	10	0.87932	D	0	.	9.3745	0.38275	0.0:0.8257:0.0:0.1743	.	74	Q9UFH2-4	.	D	372	ENSP00000374490:G372D	ENSP00000300671:G372D	G	-	2	0	DNAH17	74077134	0.052000	0.20516	0.458000	0.27068	0.040000	0.13550	0.159000	0.16442	0.373000	0.24621	0.561000	0.74099	GGC	.		0.522	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76565539	C	T	76565539	3	4	25	1	0	0	0	0	1	0	0	0	4612	739	26	2	12569	2	DNAH17	17	76565539	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	1621480	76565539	4629671	78	2220											
RAB31	11031	broad.mit.edu	37	chr18	9815181	9815181	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtccagaaaacattgtaatGgccatcgctggaaacaagtg	14	8	11	8	1	0	1	0	0	0	1	2	2	1	2	2	3	2	2	2	3	5	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr18:9815181G>T	ENST00000578921.1	+	5	583	c.342G>T	c.(340-342)atG>atT	p.M114I		NM_006868.3	NP_006859.2	Q13636	RAB31_HUMAN	RAB31, member RAS oncogene family	113					cellular response to insulin stimulus (GO:0032869)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|phagosome maturation (GO:0090382)|receptor internalization (GO:0031623)|regulated secretory pathway (GO:0045055)|small GTPase mediated signal transduction (GO:0007264)	early endosome (GO:0005769)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(2)|large_intestine(2)|lung(3)|skin(1)	10						ACATTGTAATGGCCATCGCTG	0.403																																					p.M114I													.	RAB31-205	0			c.G342T						.						78	81	80					18																	9815181		1960	4133	6093	SO:0001583	missense	11031	exon5			TGTAATGGCCATC	U59877	CCDS45826.1	18p11.22	2014-03-18			ENSG00000168461	ENSG00000168461		"RAB, member RAS oncogene"	9771	protein-coding gene	gene with protein product		605694				8863739	Standard	NM_006868		Approved	Rab22B	uc002kog.2	Q13636	OTTHUMG00000178513	ENST00000578921.1:c.342G>T	18.37:g.9815181G>T	ENSP00000461945:p.Met114Ile	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	86	4	NM_006868	0	0	34	34	0	B2RBT7|Q15770|Q9HC00	Missense_Mutation	SNP	ENST00000578921.1	37	CCDS45826.1	.	.	.	.	.	.	.	.	.	.	G	5.185	0.219743	0.09863	.	.	ENSG00000168461	ENST00000306096;ENST00000435762	.	.	.	5.64	5.64	0.86602	Small GTP-binding protein domain (1);	0.045250	0.85682	D	0.000000	T	0.21921	0.0528	N	0.00408	-1.53	0.48341	D	0.999635	B	0.02656	0.0	B	0.11329	0.006	T	0.34079	-0.9843	8	.	.	.	-7.9846	18.8461	0.92208	0.0:0.0:1.0:0.0	.	113	Q13636	RAB31_HUMAN	I	114;105	.	.	M	+	3	0	RAB31	9805181	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.944000	0.49034	2.820000	0.97059	0.655000	0.94253	ATG	.		0.403	RAB31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442280.3			T	9815181	G	T	9815181	3	4	25	1	0	0	0	0	1	0	0	0	12952	1348	47	4	360	4	RAB31	18	9815181	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		9815181	68262067	79	2221											
POLRMT	5442	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	623528	623528	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccctgctggccagctccaTgtggagctgcttctcaaaga	8	9	10	14	0	1	1	1	0	1	1	3	2	2	2	3	2	4	4	3	2	1	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:623528T>C	ENST00000588649.2	-	6	1300	c.1216A>G	c.(1216-1218)Atg>Gtg	p.M406V	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	406					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCAGCTCCATGTGGAGCTGC	0.632																																					p.M406V		.											.	POLRMT-92	0			c.A1216G						.						54	50	51					19																	623528		2203	4300	6503	SO:0001583	missense	5442	exon6			GCTCCATGTGGAG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.1216A>G	19.37:g.623528T>C	ENSP00000465759:p.Met406Val	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	52	11	NM_005035	0	0	13	18	5	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.639596	0.00799	.	.	ENSG00000099821	ENST00000215591	T	0.39056	1.1	4.63	-4.26	0.03755	.	0.752409	0.12789	N	0.438968	T	0.08935	0.0221	N	0.01446	-0.86	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31280	-0.9949	10	0.02654	T	1	-12.8428	0.5899	0.00726	0.249:0.2907:0.1226:0.3377	.	406	O00411	RPOM_HUMAN	V	406	ENSP00000215591:M406V	ENSP00000215591:M406V	M	-	1	0	POLRMT	574528	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.196000	0.03041	-0.378000	0.07918	-2.005000	0.00442	ATG	.		0.632	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		C	623528	T	C	623528	3	2	25	1	0	0	0	0	1	0	0	0	12264	1464	51	3	2540	3	POLRMT	19	623528	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10		623528	58505455	80	2222											
KEAP1	9817	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10610566	10610566	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtagctgaaggtgcggttGccatgctgggagggcgtcac	6	9	18	8	2	1	1	1	1	0	0	1	2	1	2	1	4	4	4	1	4	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:10610566G>T	ENST00000171111.5	-	2	691	c.144C>A	c.(142-144)ggC>ggA	p.G48G	KEAP1_ENST00000393623.2_Silent_p.G48G|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	48					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	AGGTGCGGTTGCCATGCTGGG	0.627																																					p.G48G		.											.	KEAP1-637	0			c.C144A						.						136	108	118					19																	10610566		2203	4300	6503	SO:0001819	synonymous_variant	9817	exon2			GCGGTTGCCATGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.144C>A	19.37:g.10610566G>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	63	24	NM_012289	0	0	12	19	7	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	37	CCDS12239.1																																																																																			.		0.627	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		T	10610566	G	T	10610566	2	4	25	1	0	0	0	0	0	0	0	1	8162	1306	46	4		4	KEAP1	19	10610566	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	9987038	10610566	48518417	81	2223											
RFX1	5989	broad.mit.edu;ucsc.edu	37	chr19	14080923	14080923	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgcagtaagtagtggcagTagagggtgctccgtggcaga	10	8	17	6	1	0	2	0	0	0	2	1	2	1	2	1	3	2	7	1	3	3	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:14080923T>C	ENST00000254325.4	-	10	1613	c.1379A>G	c.(1378-1380)tAc>tGc	p.Y460C		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	460					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			GTAGTGGCAGTAGAGGGTGCT	0.627																																					p.Y460C													.	RFX1-92	0			c.A1379G						.						80	76	78					19																	14080923		2203	4300	6503	SO:0001583	missense	5989	exon10			TGGCAGTAGAGGG		CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"trans-acting regulatory factor 1", "enhancer factor C", "MHC class II regulatory factor RFX"	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.1379A>G	19.37:g.14080923T>C	ENSP00000254325:p.Tyr460Cys	Somatic	106	1		WXS	Illumina HiSeq	Phase_I	102	4	NM_002918	0	0	6	9	3		Missense_Mutation	SNP	ENST00000254325.4	37	CCDS12301.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.538770	0.85917	.	.	ENSG00000132005	ENST00000254325	D	0.91521	-2.86	5.41	5.41	0.78517	Winged helix-turn-helix transcription repressor DNA-binding (1);DNA-binding RFX (1);	0.000000	0.85682	D	0.000000	D	0.96552	0.8875	H	0.94345	3.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97588	1.0115	10	0.87932	D	0	-16.4954	14.4299	0.67243	0.0:0.0:0.0:1.0	.	460	P22670	RFX1_HUMAN	C	460	ENSP00000254325:Y460C	ENSP00000254325:Y460C	Y	-	2	0	RFX1	13941923	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.973000	0.88032	2.059000	0.61396	0.460000	0.39030	TAC	.		0.627	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918		C	14080923	T	C	14080923	3	2	25	1	0	0	0	0	1	0	0	0	13294	1638	57	3	1608	3	RFX1	19	14080923	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	3470357	14080923	45048060	82	2224											
MLL4	9757	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36229181	36229181	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccccacctcatccctgcAgggcatcgggtgctatatgt	6	11	9	15	1	2	0	1	0	1	0	5	0	3	0	4	2	2	3	4	2	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:36229181A>G	ENST00000222270.7	+	37	7872		c.e37-1		IGFLR1_ENST00000587101.1_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Splice_Site	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B						chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCATCCCTGCAGGGCATCGGG	0.602																																					.		.											.	MLL4-697	0			c.7873-2A>G						.						60	68	65					19																	36229181		2182	4290	6472	SO:0001630	splice_region_variant	8085	exon37			CCCTGCAGGGCAT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7873-1A>G	19.37:g.36229181A>G		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	36	15	NM_014727	0	0	0	3	3	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Splice_Site	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.890467	0.33348	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4398	0.67309	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AD000671.1	40921021	1.000000	0.71417	0.916000	0.36221	0.245000	0.25701	9.339000	0.96797	2.063000	0.61619	0.379000	0.24179	.	.		0.602	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Intron	G	36229181	A	G	36229181	5	3	25	1	0	0	0	0	0	0	1	0	9648	202	7	3	8017	3	MLL4	19	36229181	Splice_Site	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	22148258	36229181	22899802	83	2225											
CEACAM16	388551	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45211204	45211204	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggacgtaacactgaccGtgcagggctaccccaaggac	11	4	12	14	2	0	1	0	1	0	0	0	3	0	3	4	3	3	3	4	3	3	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:45211204G>A	ENST00000405314.2	+	5	1109	c.1012G>A	c.(1012-1014)Gtg>Atg	p.V338M	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM16_ENST00000587331.1_Missense_Mutation_p.V338M			Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16	338					sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)				endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				AACACTGACCGTGCAGGGCTA	0.672																																					p.V338M													.	CEACAM16-23	0			c.G1012A						.						15	17	16					19																	45211204		2147	4237	6384	SO:0001583	missense	388551	exon6			CTGACCGTGCAGG		CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31948	protein-coding gene	gene with protein product		614591				21368133	Standard	NM_001039213		Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000405314.2:c.1012G>A	19.37:g.45211204G>A	ENSP00000385576:p.Val338Met	Somatic	111	1		WXS	Illumina HiSeq	Phase_I	87	25	NM_001039213	0	0	0	0	0	A7LI12	Missense_Mutation	SNP	ENST00000405314.2	37	CCDS54278.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.098930	0.76870	.	.	ENSG00000213892	ENST00000396750;ENST00000405314	T	0.01902	4.57	5.87	5.87	0.94306	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.15046	0.0363	M	0.85099	2.735	0.34882	D	0.74467	D	0.89917	1.0	D	0.83275	0.996	T	0.01858	-1.1259	9	0.66056	D	0.02	-24.0687	15.7789	0.78243	0.0:0.0:1.0:0.0	.	397	Q2WEN9	CEA16_HUMAN	M	403;338	ENSP00000385576:V338M	ENSP00000379974:V403M	V	+	1	0	CEACAM16	49903044	0.992000	0.36948	0.599000	0.28851	0.752000	0.42762	4.967000	0.63722	2.788000	0.95919	0.650000	0.86243	GTG	.		0.672	CEACAM16-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		XM_371177		A	45211204	G	A	45211204	3	1	25	1	0	0	0	0	1	0	0	0	3194	1145	40	1	1030	1	CEACAM16	19	45211204	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	8982023	45211204	13917779	84	2226											
COL9A3	1299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	61467549	61467549	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctgcagtctggcagtcGaggggagctgggccccaaag	7	7	15	12	1	2	0	0	0	2	0	4	2	3	1	3	4	2	3	3	4	1	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr20:61467549G>T	ENST00000343916.3	+	28	1415	c.1412G>T	c.(1411-1413)cGa>cTa	p.R471L	COL9A3_ENST00000462700.1_3'UTR	NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	471	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					TCTGGCAGTCGAGGGGAGCTG	0.716																																					p.R471L		.											.	COL9A3-514	0			c.G1412T						.						18	24	22					20																	61467549		2201	4297	6498	SO:0001583	missense	1299	exon28			GCAGTCGAGGGGA	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1412G>T	20.37:g.61467549G>T	ENSP00000341640:p.Arg471Leu	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	81	22	NM_001853	0	0	0	0	0	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	37	CCDS13505.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448038	0.84101	.	.	ENSG00000092758	ENST00000343916	D	0.93712	-3.27	4.63	4.63	0.57726	.	0.283555	0.33127	N	0.005250	D	0.95367	0.8496	L	0.53729	1.69	0.46241	D	0.998947	D	0.89917	1.0	D	0.73380	0.98	D	0.94429	0.7648	10	0.32370	T	0.25	.	17.4821	0.87675	0.0:0.0:1.0:0.0	.	471	Q14050	CO9A3_HUMAN	L	471	ENSP00000341640:R471L	ENSP00000341640:R471L	R	+	2	0	COL9A3	60937994	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	7.254000	0.78329	2.117000	0.64856	0.561000	0.74099	CGA	.		0.716	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61467549	G	T	61467549	3	4	25	1	0	0	0	0	1	0	0	0	3715	1058	37	4	1522	4	COL9A3	20	61467549	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		61467549	1557971	85	2227											
GABPA	2551	bcgsc.ca	37	chr21	27130324	27130324	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aatatttttctttctagatcCcatacagtggtccacagacc	11	14	5	11	0	2	2	0	0	2	2	4	2	4	2	3	1	1	0	3	1	4	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr21:27130324C>A	ENST00000354828.3	+	6	1084	c.557C>A	c.(556-558)cCc>cAc	p.P186H	GABPA_ENST00000400075.3_Missense_Mutation_p.P186H	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	186	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|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 transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						TTTCTAGATCCCATACAGTGG	0.398																																					p.P186H													.	GABPA-227	0			c.C557A						.						64	64	64					21																	27130324		2203	4300	6503	SO:0001583	missense	2551	exon6			TAGATCCCATACA		CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"human nuclear respiratory factor-2 subunit alpha", "nuclear respiratory factor 2 alpha subunit"	600609	"GA-binding protein transcription factor, alpha subunit (60kD)"			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.557C>A	21.37:g.27130324C>A	ENSP00000346886:p.Pro186His	Somatic	212	6		WXS	Illumina HiSeq	Phase_1	245	85	NM_001197297	0	0	0	0	0	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.565778	0.86439	.	.	ENSG00000154727	ENST00000354828;ENST00000400075	T;T	0.68479	-0.33;-0.33	5.39	5.39	0.77823	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.000000	0.85682	D	0.000000	D	0.86585	0.5968	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89198	0.3555	10	0.87932	D	0	.	18.9426	0.92610	0.0:1.0:0.0:0.0	.	186	Q06546	GABPA_HUMAN	H	186	ENSP00000346886:P186H;ENSP00000382948:P186H	ENSP00000346886:P186H	P	+	2	0	GABPA	26052195	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.241000	0.78201	2.809000	0.96659	0.467000	0.42956	CCC	.		0.398	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040		A	27130324	C	A	27130324	3	1	25	1	0	0	0	0	1	0	0	0	6176	623	22	4	575	4	GABPA	21	27130324	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		27130324	20999571	86	2228											
DIP2A	23181	bcgsc.ca	37	chr21	47961748	47961748	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gttatggtgttatcagagtgGatactgaagaaaagttgtca	13	13	12	3	0	2	3	2	1	0	2	2	4	2	4	0	2	1	3	0	2	6	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr21:47961748G>T	ENST00000417564.2	+	18	2137	c.2116G>T	c.(2116-2118)Gat>Tat	p.D706Y	DIP2A_ENST00000435722.3_Missense_Mutation_p.D706Y|DIP2A_ENST00000466639.1_Missense_Mutation_p.D663Y|DIP2A_ENST00000318711.7_Missense_Mutation_p.D707Y|DIP2A_ENST00000400274.1_Missense_Mutation_p.D702Y|DIP2A_ENST00000427143.2_Missense_Mutation_p.D642Y|DIP2A_ENST00000457905.3_Missense_Mutation_p.D706Y			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	706					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TATCAGAGTGGATACTGAAGA	0.468																																					p.D706Y													.	DIP2A-24	0			c.G2116T						.						122	127	126					21																	47961748		1972	4176	6148	SO:0001583	missense	23181	exon18			AGAGTGGATACTG	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2116G>T	21.37:g.47961748G>T	ENSP00000392066:p.Asp706Tyr	Somatic	100	0		WXS	Illumina HiSeq	Phase_1	105	5	NM_206891	0	0	2	2	0	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.983767	0.74474	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000358985;ENST00000457905;ENST00000466639;ENST00000435722;ENST00000417564	T;T;T;T;T;T;T	0.26957	1.74;1.7;1.74;1.71;1.75;1.72;1.74	5.36	5.36	0.76844	AMP-dependent synthetase/ligase (1);	0.112204	0.64402	D	0.000018	T	0.58366	0.2117	M	0.87180	2.865	0.80722	D	1	P;P;D;P;P;P;P	0.89917	0.943;0.786;1.0;0.888;0.779;0.942;0.937	P;P;D;P;P;P;P	0.91635	0.776;0.75;0.999;0.898;0.776;0.819;0.69	T	0.63972	-0.6516	10	0.54805	T	0.06	-11.6569	18.1299	0.89598	0.0:0.0:1.0:0.0	.	707;642;663;642;706;706;706	E9PER1;E7EMA5;Q14689-3;B4E0F0;Q14689;Q14689-4;Q14689-2	.;.;.;.;DIP2A_HUMAN;.;.	Y	702;642;707;663;706;663;706;706	ENSP00000383133:D702Y;ENSP00000400528:D642Y;ENSP00000323633:D707Y;ENSP00000393434:D706Y;ENSP00000430249:D663Y;ENSP00000415089:D706Y;ENSP00000392066:D706Y	ENSP00000323633:D707Y	D	+	1	0	DIP2A	46786176	1.000000	0.71417	0.408000	0.26446	0.435000	0.31806	4.770000	0.62309	2.525000	0.85131	0.650000	0.86243	GAT	.		0.468	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		T	47961748	G	T	47961748	3	4	25	1	0	0	0	0	1	0	0	0	4538	1174	41	4	2186	4	DIP2A	21	47961748	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	20831424	47961748	168147	87	2229											
C22orf25	128989	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr22	20030918	20030918	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggatgaattctacagccgaCcctccaagttagctgacttc	10	10	9	12	1	1	2	0	2	1	0	3	4	2	3	3	1	3	2	3	1	4	4	rs551072560		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr22:20030918C>T	ENST00000327374.4	+	3	275	c.97C>T	c.(97-99)Ccc>Tcc	p.P33S	TANGO2_ENST00000420290.2_5'UTR|TANGO2_ENST00000447208.2_Missense_Mutation_p.P33S|TANGO2_ENST00000401886.1_Missense_Mutation_p.P33S|TANGO2_ENST00000456048.1_Missense_Mutation_p.P38S|TANGO2_ENST00000401833.1_Missense_Mutation_p.P74S|TANGO2_ENST00000479679.1_3'UTR|TANGO2_ENST00000434570.2_Missense_Mutation_p.P74S|TANGO2_ENST00000432883.1_Missense_Mutation_p.P33S|TANGO2_ENST00000398042.2_Missense_Mutation_p.P33S	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	33																	CTACAGCCGACCCTCCAAGTT	0.542													C|||	1	0.000199681	8e-04	0	5008	,	,		20269	0		0	False		,,,				2504	0				p.P33S		.											.	.	0			c.C97T						.						139	142	141					22																	20030918		2203	4300	6503	SO:0001583	missense	128989	exon3			AGCCGACCCTCCA		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 25"	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.97C>T	22.37:g.20030918C>T	ENSP00000332721:p.Pro33Ser	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	95	28	NM_152906	0	0	17	22	5	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	37	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320659	0.41096	.	.	ENSG00000183597	ENST00000401886;ENST00000432198;ENST00000447208;ENST00000398042;ENST00000450664;ENST00000327374;ENST00000432883;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000456048	T;T;T;T;T;T;T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8	4.89	3.87	0.44632	.	0.174725	0.50627	D	0.000101	T	0.57169	0.2035	M	0.92412	3.305	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.994;0.999;0.999;0.999;0.991	D;D;D;D;D;D;D	0.74674	0.984;0.984;0.932;0.984;0.984;0.975;0.933	T	0.66456	-0.5919	10	0.72032	D	0.01	-12.9932	11.3355	0.49500	0.0:0.9094:0.0:0.0906	.	33;74;33;74;33;33;33	B7Z9Q5;B7Z730;B7Z4A5;B7WNV6;Q6AHY1;Q6ICL3;Q6ICL3-2	.;.;.;.;.;CV025_HUMAN;.	S	33;33;33;33;33;33;33;74;33;74;38	ENSP00000385662:P33S;ENSP00000413850:P33S;ENSP00000389797:P33S;ENSP00000381122:P33S;ENSP00000415450:P33S;ENSP00000332721:P33S;ENSP00000402926:P33S;ENSP00000384827:P74S;ENSP00000411602:P33S;ENSP00000391262:P74S;ENSP00000403645:P38S	ENSP00000332721:P33S	P	+	1	0	C22orf25	18410918	1.000000	0.71417	0.061000	0.19648	0.149000	0.21700	4.652000	0.61454	1.197000	0.43143	-0.258000	0.10820	CCC	.		0.542	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906		T	20030918	C	T	20030918	3	4	25	1	0	0	0	0	1	0	0	0	2145	507	18	2	103	2	C22orf25	22	20030918	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		20030918	31273648	88	2230											
BCOR	54880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	39932148	39932148	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtttggacacgtttgtgtcAgttttagcatctggttcttc	5	18	11	7	1	3	0	1	0	2	0	4	1	3	1	0	3	1	5	0	3	1	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chrX:39932148A>G	ENST00000378444.4	-	4	2679	c.2451T>C	c.(2449-2451)acT>acC	p.T817T	BCOR_ENST00000397354.3_Silent_p.T817T|BCOR_ENST00000378455.4_Silent_p.T817T|BCOR_ENST00000342274.4_Silent_p.T817T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	817					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						CGTTTGTGTCAGTTTTAGCAT	0.547			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.T817T		.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR-229	0			c.T2451C						.						89	87	88					X																	39932148		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			TGTGTCAGTTTTA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.2451T>C	X.37:g.39932148A>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	72	36	NM_001123385	0	0	0	3	3	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			.		0.547	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		G	39932148	A	G	39932148	2	3	25	1	0	0	0	0	0	0	0	1	1387	175	7	3		3	BCOR	23	39932148	Silent	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		39932148	115338412	89	2231											
H6PD	9563	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	9305536	9305536	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccctttggccatgaccacttCtcagcccagcagctggccac	7	8	8	18	0	1	1	1	1	1	0	2	1	1	1	5	2	3	2	5	2	0	2	rs375431974		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:9305536C>T	ENST00000377403.2	+	2	845	c.543C>T	c.(541-543)ttC>ttT	p.F181F	H6PD_ENST00000602477.1_Silent_p.F192F	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	181	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		ATGACCACTTCTCAGCCCAGC	0.587																																					p.F181F		.											.	H6PD-90	0			c.C543T						.						47	52	50					1																	9305536		2203	4300	6503	SO:0001819	synonymous_variant	9563	exon2			CCACTTCTCAGCC	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"glucose dehyrogenase"	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.543C>T	1.37:g.9305536C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	101	39	NM_004285	0	0	5	10	5	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			.		0.587	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		T	9305536	C	T	9305536	2	4	26	1	0	0	0	0	0	0	0	1	6957	912	32	2		2	H6PD	1	9305536	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		9305536	239945085	1	2232											
C1orf130	400746	broad.mit.edu;bcgsc.ca	37	chr1	24921934	24921934	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcgagatgaccacagccAcccctctgggggataccacc	10	5	11	15	1	1	2	0	1	1	1	2	5	1	4	6	3	2	0	6	3	1	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:24921934A>T	ENST00000374392.2	+	2	79	c.13A>T	c.(13-15)Acc>Tcc	p.T5S	NCMAP_ENST00000486262.1_3'UTR	NM_001010980.4	NP_001010980.1	Q5T1S8	NCMAP_HUMAN	noncompact myelin associated protein	5					peripheral nervous system myelin formation (GO:0032290)|positive regulation of myelination (GO:0031643)	integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|Schmidt-Lanterman incisure (GO:0043220)	structural constituent of myelin sheath (GO:0019911)										GACCACAGCCACCCCTCTGGG	0.423																																					p.T5S													.	.	0			c.A13T						.						63	60	61					1																	24921934		2203	4300	6503	SO:0001583	missense	400746	exon2			ACAGCCACCCCTC	AK124519	CCDS30632.1	1p36.11	2012-07-31	2012-07-31	2012-07-31	ENSG00000184454	ENSG00000184454			29332	protein-coding gene	gene with protein product	"myelin protein of 11 kDa"		"chromosome 1 open reading frame 130"	C1orf130		18650334	Standard	NM_001010980		Approved	FLJ42528, MP11	uc001bjk.2	Q5T1S8	OTTHUMG00000003317	ENST00000374392.2:c.13A>T	1.37:g.24921934A>T	ENSP00000363513:p.Thr5Ser	Somatic	93	3		WXS	Illumina HiSeq	Phase_I	78	36	NM_001010980	0	0	1	1	0	A0PK04|B2RV34	Missense_Mutation	SNP	ENST00000374392.2	37	CCDS30632.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.815513	0.70912	.	.	ENSG00000184454	ENST00000374392	.	.	.	5.51	4.21	0.49690	.	0.249082	0.40385	N	0.001107	T	0.21631	0.0521	L	0.27053	0.805	0.28038	N	0.933887	P	0.40180	0.705	B	0.38264	0.269	T	0.07539	-1.0767	9	0.30854	T	0.27	-28.5482	5.6803	0.17771	0.8527:0.0:0.1473:0.0	.	5	Q5T1S8	CA130_HUMAN	S	5	.	ENSP00000363513:T5S	T	+	1	0	C1orf130	24794521	0.984000	0.35163	1.000000	0.80357	0.868000	0.49771	1.756000	0.38390	2.212000	0.71576	0.460000	0.39030	ACC	.		0.423	NCMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009288.2	NM_001010980		T	24921934	A	T	24921934	3	4	26	1	0	0	0	0	1	0	0	0	2003	159	6	5	15	5	C1orf130	1	24921934	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	15616398	24921934	224328687	2	2233											
KANK4	163782	bcgsc.ca	37	chr1	62740357	62740357	+	Frame_Shift_Del	DEL	A	A	-																															cctctggctcagcagcttccAactgtctggtggcctctgcc																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:62740357delA	ENST00000371153.4	-	3	797	c.419delT	c.(418-420)ttgfs	p.L140fs	KANK4_ENST00000371150.1_5'Flank|KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	140						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						AGCAGCTTCCAACTGTCTGGT	0.607																																					p.L140fs													.	KANK4-74	0			c.419delT						.						35	40	38					1																	62740357		2202	4300	6502	SO:0001589	frameshift_variant	163782	exon3			GCTTCCAACTGTC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.419delT	1.37:g.62740357delA	ENSP00000360195:p.Leu140fs	Somatic	50	1		WXS	Illumina HiSeq	Phase_1	61	24	NM_181712	0	0	0	0	0	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Frame_Shift_Del	DEL	ENST00000371153.4	37	CCDS620.1																																																																																			.		0.607	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		-	62740357	A	-	62740357	7	5	26	1	0	1	0	1	0	0	0	0	8000	131	5	0	2600	0	KANK4	1	62740357	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	37818423	62740357	186510264	3	2234	20	2									
KANK4	163782	bcgsc.ca	37	chr1	62740358	62740358	+	Missense_Mutation	SNP	A	A	T																															ctctggctcagcagcttccaActgtctggtggcctctgcca																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:62740358A>T	ENST00000371153.4	-	3	796	c.418T>A	c.(418-420)Ttg>Atg	p.L140M	KANK4_ENST00000371150.1_5'Flank|KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	140						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						GCAGCTTCCAACTGTCTGGTG	0.602																																					p.L140M													.	KANK4-74	0			c.T418A						.						35	40	38					1																	62740358		2202	4300	6502	SO:0001583	missense	163782	exon3			CTTCCAACTGTCT	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.418T>A	1.37:g.62740358A>T	ENSP00000360195:p.Leu140Met	Somatic	51	1		WXS	Illumina HiSeq	Phase_1	61	27	NM_181712	0	0	0	0	0	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.588891	0.46110	.	.	ENSG00000132854	ENST00000371153	T	0.78364	-1.17	4.99	-9.97	0.00440	.	2.125810	0.03072	N	0.157253	T	0.63570	0.2522	L	0.36672	1.1	0.09310	N	1	P	0.36438	0.553	B	0.33042	0.157	T	0.63024	-0.6729	10	0.40728	T	0.16	3.7777	9.5324	0.39202	0.1:0.429:0.4065:0.0645	.	140	Q5T7N3	KANK4_HUMAN	M	140	ENSP00000360195:L140M	ENSP00000360195:L140M	L	-	1	2	KANK4	62512946	0.000000	0.05858	0.000000	0.03702	0.492000	0.33523	-2.970000	0.00668	-3.647000	0.00127	-0.376000	0.06991	TTG	.		0.602	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		T	62740358	A	T	62740358	3	4	26	1	0	0	0	0	1	0	0	0	8000	40	2	5	2601	5	KANK4	1	62740358	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	1	62740358	186510263	4	2235	20	2									
RABGGTB	5876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	76253203	76253203	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcactccacagaaggatgttAttatcaagtcagatgcaccg	13	9	9	10	1	2	2	2	0	0	2	3	3	3	3	2	1	1	3	2	1	4	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:76253203A>G	ENST00000319942.3	+	2	96	c.25A>G	c.(25-27)Att>Gtt	p.I9V	SNORD45B_ENST00000364617.1_RNA|SNORD45C_ENST00000383893.1_RNA|RABGGTB_ENST00000535300.1_5'UTR|RABGGTB_ENST00000496055.1_3'UTR|RABGGTB_ENST00000370826.3_Missense_Mutation_p.I9V|SNORD45A_ENST00000384512.1_RNA	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	9					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						GAAGGATGTTATTATCAAGTC	0.368																																					p.I9V		.											.	RABGGTB-227	0			c.A25G						.						147	134	139					1																	76253203		2203	4300	6503	SO:0001583	missense	5876	exon2			GATGTTATTATCA	U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.25A>G	1.37:g.76253203A>G	ENSP00000317473:p.Ile9Val	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	162	72	NM_004582	0	0	56	113	57	Q92697	Missense_Mutation	SNP	ENST00000319942.3	37	CCDS669.1	.	.	.	.	.	.	.	.	.	.	A	9.952	1.220540	0.22457	.	.	ENSG00000137955	ENST00000319942;ENST00000370824;ENST00000370826	.	.	.	5.05	0.547	0.17202	.	0.830524	0.11309	N	0.577349	T	0.07683	0.0193	N	0.05199	-0.095	0.18873	N	0.999984	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	9	0.29301	T	0.29	-8.2035	10.2082	0.43126	0.5747:0.0:0.4253:0.0	.	9	P53611	PGTB2_HUMAN	V	9	.	ENSP00000317473:I9V	I	+	1	0	RABGGTB	76025791	0.001000	0.12720	0.210000	0.23637	0.847000	0.48162	0.335000	0.19806	0.044000	0.15775	0.533000	0.62120	ATT	.		0.368	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582		G	76253203	A	G	76253203	3	3	26	1	0	0	0	0	1	0	0	0	13000	449	16	3	31	3	RABGGTB	1	76253203	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	13512845	76253203	172997418	5	2236											
OVGP1	5016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	111957940	111957940	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacagcagatgacagccaaaAttgtggtaaagaagttgaac	17	7	10	7	0	0	4	0	2	0	2	0	4	0	4	1	1	3	3	1	1	6	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:111957940A>C	ENST00000369732.3	-	11	1238	c.1183T>G	c.(1183-1185)Ttt>Gtt	p.F395V	OVGP1_ENST00000540696.1_3'UTR	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	395					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		GACAGCCAAAATTGTGGTAAA	0.433																																					p.F395V		.											.	OVGP1-135	0			c.T1183G						.						48	46	47					1																	111957940		2203	4300	6503	SO:0001583	missense	5016	exon11			GCCAAAATTGTGG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"Mucins"	8524	protein-coding gene	gene with protein product	"oviductin"	603578	"mucin 9"	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1183T>G	1.37:g.111957940A>C	ENSP00000358747:p.Phe395Val	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	98	38	NM_002557	0	0	34	63	29	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791958	0.31685	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03860	3.78	4.43	0.705	0.18127	.	0.784649	0.10922	N	0.619328	T	0.00875	0.0029	L	0.36672	1.1	0.09310	N	1	B;P	0.39831	0.105;0.69	B;B	0.29598	0.014;0.104	T	0.47623	-0.9103	10	0.22109	T	0.4	-2.4013	3.3373	0.07106	0.5411:0.0:0.0994:0.3595	.	395;459	Q12889;Q59HH5	OVGP1_HUMAN;.	V	395;459;203	ENSP00000358747:F395V	ENSP00000358743:F459V	F	-	1	0	OVGP1	111759463	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	0.154000	0.16343	0.097000	0.17492	0.477000	0.44152	TTT	.		0.433	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		C	111957940	A	C	111957940	3	2	26	1	0	0	0	0	1	0	0	0	11351	101	4	5	857	5	OVGP1	1	111957940	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	35704737	111957940	137292681	6	2237											
NOTCH2	4853	bcgsc.ca	37	chr1	120506375	120506375	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcctgacactgaccatggtgGcaaggatcggggtcacagtt	9	9	13	10	1	1	2	1	2	0	0	3	3	2	3	2	5	0	2	2	5	1	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:120506375G>T	ENST00000256646.2	-	11	1956	c.1737C>A	c.(1735-1737)tgC>tgA	p.C579*		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	579	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GACCATGGTGGCAAGGATCGG	0.468			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.C579X				Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2-1441	0			c.C1737A						.						203	191	195					1																	120506375		2203	4300	6503	SO:0001587	stop_gained	4853	exon11	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	ATGGTGGCAAGGA	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.1737C>A	1.37:g.120506375G>T	ENSP00000256646:p.Cys579*	Somatic	74	0		WXS	Illumina HiSeq	Phase_1	93	5	NM_024408	0	0	14	14	0	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	40	8.141015	0.98672	.	.	ENSG00000134250	ENST00000256646;ENST00000539617	.	.	.	5.53	2.61	0.31194	.	0.000000	0.41194	U	0.000931	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.2182	0.37360	0.2947:0.0:0.7053:0.0	.	.	.	.	X	579;540	.	ENSP00000256646:C579X	C	-	3	2	NOTCH2	120307898	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.660000	0.37397	0.817000	0.34445	0.655000	0.94253	TGC	.		0.468	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120506375	G	T	120506375	4	4	26	1	0	0	0	0	0	1	0	0	10574	1195	42	4	5774	4	NOTCH2	1	120506375	Nonsense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	8548435	120506375	128744246	7	2238											
CCT3	7203	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156294858	156294858	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctccaggaagtgctcAgctacagacagcatttcccc	9	9	9	14	0	1	1	1	0	0	1	3	2	3	2	3	1	6	5	3	1	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:156294858A>G	ENST00000295688.3	-	6	607	c.327T>C	c.(325-327)gcT>gcC	p.A109A	CCT3_ENST00000368261.3_Silent_p.A64A|CCT3_ENST00000368259.2_Silent_p.A71A|CCT3_ENST00000472765.2_Silent_p.A64A	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	109					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GGAAGTGCTCAGCTACAGACA	0.413																																					p.A109A		.											.	CCT3-92	0			c.T327C						.						92	84	87					1																	156294858		2203	4300	6503	SO:0001819	synonymous_variant	7203	exon6			GTGCTCAGCTACA	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"Heat Shock Proteins / Chaperonins"	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.327T>C	1.37:g.156294858A>G		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_005998	0	0	88	172	84	A6NE14|Q5SZY1|Q9BR64	Silent	SNP	ENST00000295688.3	37	CCDS1140.2																																																																																			.		0.413	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		G	156294858	A	G	156294858	2	3	26	1	0	0	0	0	0	0	0	1	2960	175	7	3		3	CCT3	1	156294858	Silent	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	35788483	156294858	92955763	8	2239											
HHIPL2	79802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	222705394	222705394	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacgtggtgctgcccaggCaaagatcctgcttcttccat	8	10	11	12	1	1	1	0	0	1	1	3	2	3	2	3	3	3	3	3	3	1	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:222705394C>T	ENST00000343410.6	-	6	1695	c.1637G>A	c.(1636-1638)tGc>tAc	p.C546Y		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	546					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GCTGCCCAGGCAAAGATCCTG	0.428																																					p.C546Y		.											.	HHIPL2-69	0			c.G1637A						.						87	87	87					1																	222705394		2203	4300	6503	SO:0001583	missense	79802	exon6			CCCAGGCAAAGAT	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1637G>A	1.37:g.222705394C>T	ENSP00000342118:p.Cys546Tyr	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	65	31	NM_024746	0	0	0	0	0	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	22.9	4.343683	0.82022	.	.	ENSG00000143512	ENST00000343410	T	0.13307	2.6	5.0	5.0	0.66597	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.47600	0.1454	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58532	-0.7620	10	0.51188	T	0.08	-17.4954	17.9254	0.88982	0.0:1.0:0.0:0.0	.	546	Q6UWX4	HIPL2_HUMAN	Y	546	ENSP00000342118:C546Y	ENSP00000342118:C546Y	C	-	2	0	HHIPL2	220772017	1.000000	0.71417	0.980000	0.43619	0.936000	0.57629	5.693000	0.68264	2.304000	0.77564	0.591000	0.81541	TGC	.		0.428	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		T	222705394	C	T	222705394	3	4	26	1	0	0	0	0	1	0	0	0	7115	710	25	2	553	2	HHIPL2	1	222705394	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	66410536	222705394	26545227	9	2240											
C1orf95	375057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	226784625	226784625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaatcctcactgccatcGtcatggtgggctggatcatg	8	11	10	12	1	3	0	3	0	0	0	6	1	5	1	3	3	1	1	3	3	1	0	rs531129279		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:226784625G>A	ENST00000366788.3	+	2	430	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	C1orf95_ENST00000366789.4_Missense_Mutation_p.V109I	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95	109						integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		CACTGCCATCGTCATGGTGGG	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		22256	0		0	False		,,,				2504	0				p.V109I		.											.	C1orf95-91	0			c.G325A						.						167	143	151					1																	226784625		2203	4300	6503	SO:0001583	missense	375057	exon2			GCCATCGTCATGG	AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685			30491	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001003665		Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.325G>A	1.37:g.226784625G>A	ENSP00000355752:p.Val109Ile	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	91	38	NM_001003665	0	0	0	0	0	A6NGL2	Missense_Mutation	SNP	ENST00000366788.3	37	CCDS31044.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.469818	0.43839	.	.	ENSG00000203685	ENST00000366788;ENST00000366789	.	.	.	5.82	5.82	0.92795	.	0.154593	0.43919	D	0.000509	T	0.34658	0.0905	N	0.03324	-0.35	0.38912	D	0.957563	B	0.24368	0.102	B	0.17979	0.02	T	0.34825	-0.9813	9	0.08599	T	0.76	1.3905	19.6956	0.96023	0.0:0.0:1.0:0.0	.	109	Q69YW2	CA095_HUMAN	I	109	.	ENSP00000355752:V109I	V	+	1	0	C1orf95	224851248	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.144000	0.71762	2.756000	0.94617	0.561000	0.74099	GTC	.		0.612	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665		A	226784625	G	A	226784625	3	1	26	1	0	0	0	0	1	0	0	0	2078	1145	40	1	331	1	C1orf95	1	226784625	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	4079231	226784625	22465996	10	2241											
FANCL	55120	broad.mit.edu	37	chr2	58386912	58386912	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttatttcagtgtttcctTccagacatttttaaggtaat	9	20	5	7	0	2	1	1	0	1	1	4	1	4	1	2	1	0	2	2	1	3	9			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:58386912T>C	ENST00000233741.4	-	14	1152	c.1116A>G	c.(1114-1116)ggA>ggG	p.G372G	FANCL_ENST00000403295.3_Silent_p.G344G|VRK2_ENST00000412104.2_3'UTR|VRK2_ENST00000440705.2_3'UTR|VRK2_ENST00000340157.4_3'UTR|VRK2_ENST00000417641.2_3'UTR|VRK2_ENST00000435505.2_3'UTR|FANCL_ENST00000403676.1_Silent_p.G255G|FANCL_ENST00000402135.3_Silent_p.G377G	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	372					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						AGTGTTTCCTTCCAGACATTT	0.279								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G377G													.	FANCL-661	0			c.A1131G						.						88	91	90					2																	58386912		2203	4293	6496	SO:0001819	synonymous_variant	55120	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTTCCTTCCAGAC	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"Zinc fingers, PHD-type", "Fanconi anemia, complementation groups"	20748	protein-coding gene	gene with protein product		608111	"PHD finger protein 9"	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.1116A>G	2.37:g.58386912T>C		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	158	6	NM_001114636	0	0	11	11	0	Q6GU60	Silent	SNP	ENST00000233741.4	37	CCDS1860.1																																																																																			.		0.279	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062		C	58386912	T	C	58386912	2	2	26	1	0	0	0	0	0	0	0	1	5689	1770	62	3		3	FANCL	2	58386912	Silent	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10		58386912	184812461	11	2242											
DLX2	1746	broad.mit.edu	37	chr2	172967129	172967131	+	In_Frame_Del	DEL	GCT	GCT	-																															gactcctggggcttgtggagGctgctgctgctgctgctgtt																								rs376692475		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:172967129_172967131delGCT	ENST00000234198.4	-	1	497_499	c.136_138delAGC	c.(136-138)agcdel	p.S46del	DLX2_ENST00000466293.2_In_Frame_Del_p.S46del|AC104801.1_ENST00000448117.1_lincRNA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	46	Poly-Ser.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GCTTGTGGAGgctgctgctgctg	0.739																																					p.46_46del	GBM(188;775 2993 11256 23072)												.	DLX2-515	0			c.136_138del						.			19,76,3319		3,0,13,8,60,1623						4.5	1			15	96,156,6524		10,3,73,15,123,3164	no	codingComplex	DLX2	NM_004405.3		13,3,86,23,183,4787	A1A1,A1A2,A1R,A2A2,A2R,RR		3.719,2.7827,3.4053				115,232,9843				SO:0001651	inframe_deletion	1746	exon1			GTGGAGGCTGCTG	U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"Homeoboxes / ANTP class : NKL subclass"	2915	protein-coding gene	gene with protein product		126255	"distal-less homeo box 2"			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.136_138delAGC	2.37:g.172967138_172967140delGCT	ENSP00000234198:p.Ser46del	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	280	12	NM_004405	0	0	0	0	0	B4DMK4|B7ZA14	In_Frame_Del	DEL	ENST00000234198.4	37	CCDS2248.1																																																																																			.		0.739	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3			-	172967131	GCT	-	172967129	7	5	26	1	0	1	0	1	0	0	0	0	4582	1194	42	0	860	0	DLX2	2	172967129	In_Frame_Del	DEL	GCT	TCGA-A4-A5Y0-01A-11D-A31X-10	114580217	172967129	70232244	12	2243											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802216	185802216	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccactgtaaaaagaacacaaTacttttaaatggacaatcaa	20	9	4	8	0	1	1	1	0	0	1	1	2	1	2	1	1	2	1	1	1	10	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:185802216T>C	ENST00000302277.6	+	4	2687	c.2093T>C	c.(2092-2094)aTa>aCa	p.I698T		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	698							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AAGAACACAATACTTTTAAAT	0.294																																					p.I698T		.											.	ZNF804A-163	0			c.T2093C						.						73	67	69					2																	185802216		2194	4291	6485	SO:0001583	missense	91752	exon4			ACACAATACTTTT	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.2093T>C	2.37:g.185802216T>C	ENSP00000303252:p.Ile698Thr	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	569	30	NM_194250	0	0	0	0	0	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	T	3.795	-0.042847	0.07452	.	.	ENSG00000170396	ENST00000302277	T	0.05258	3.47	5.63	0.374	0.16183	.	1.826620	0.02817	N	0.125135	T	0.04227	0.0117	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40776	-0.9545	10	0.27082	T	0.32	-0.3078	8.4113	0.32644	0.0:0.5963:0.0:0.4037	.	698	Q7Z570	Z804A_HUMAN	T	698	ENSP00000303252:I698T	ENSP00000303252:I698T	I	+	2	0	ZNF804A	185510461	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.483000	0.22292	0.077000	0.16863	0.533000	0.62120	ATA	.		0.294	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185802216	T	C	185802216	3	2	26	1	0	0	0	0	1	0	0	0	18202	1406	49	3	2107	3	ZNF804A	2	185802216	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	12835087	185802216	57397157	13	2244											
TFPI	7035	broad.mit.edu	37	chr2	188332481	188332481	+	Splice_Site	DEL	T	T	-																															ggaagagtatcttctataccTtttttacatgccctcagaca																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:188332481delT	ENST00000233156.3	-	7	1101	c.807delA	c.(805-807)aaa>aa	p.K269fs	AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000392365.1_Splice_Site_p.K269fs	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	269					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	CTTCTATACCTTTTTTACATG	0.308																																					p.K269fs													.	TFPI-91	0			c.807delA						.						140	140	140					2																	188332481		2203	4300	6503	SO:0001630	splice_region_variant	7035	exon7			TATACCTTTTTTA		CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"extrinsic pathway inhibitor"	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.808+1A>-	2.37:g.188332481delT		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	615	9	NM_006287	0	0	0	0	0	O95103|Q53TS4	Frame_Shift_Del	DEL	ENST00000233156.3	37	CCDS2294.1																																																																																			.		0.308	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287	Frame_Shift_Del	-	188332481	T	-	188332481	8	5	26	1	0	1	0	1	0	0	1	0	15840	1623	56	0	115	0	TFPI	2	188332481	Splice_Site	DEL	T	TCGA-A4-A5Y0-01A-11D-A31X-10	2530265	188332481	54866892	14	2245											
WDR75	84128	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190306269	190306269	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgttgtggcggcagcgagttGaactttaggagagctgtgtt	7	12	16	6	3	0	2	0	1	0	1	0	4	0	2	0	3	3	5	0	3	2	5	rs201125667		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:190306269G>C	ENST00000314761.4	+	1	111	c.51G>C	c.(49-51)ttG>ttC	p.L17F		NM_032168.1	NP_115544.1	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	17						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			GCAGCGAGTTGAACTTTAGGA	0.587													G|||	1	0.000199681	0	0	5008	,	,		14558	0		0.001	False		,,,				2504	0				p.L17F													.	WDR75-92	0			c.G51C						.						89	73	79					2																	190306269		2197	4284	6481	SO:0001583	missense	84128	exon1			CGAGTTGAACTTT	AK091546	CCDS2298.1	2q32.2	2013-01-09			ENSG00000115368	ENSG00000115368		"WD repeat domain containing"	25725	protein-coding gene	gene with protein product	"UTP17, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_032168		Approved	FLJ12519, NET16, UTP17	uc002uql.1	Q8IWA0	OTTHUMG00000132660	ENST00000314761.4:c.51G>C	2.37:g.190306269G>C	ENSP00000314193:p.Leu17Phe	Somatic	173	1		WXS	Illumina HiSeq	Phase_I	406	80	NM_032168	0	0	13	20	7	Q96J10|Q9H8U8|Q9H9U5|Q9H9V8|Q9UIX2	Missense_Mutation	SNP	ENST00000314761.4	37	CCDS2298.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	19.74	3.884015	0.72410	.	.	ENSG00000115368	ENST00000314761	T	0.64438	-0.1	5.29	2.5	0.30297	.	0.212159	0.34046	N	0.004305	T	0.66992	0.2846	M	0.64404	1.975	0.48696	D	0.999699	D	0.67145	0.996	P	0.62649	0.905	T	0.64228	-0.6457	10	0.10111	T	0.7	-8.8137	8.5408	0.33390	0.0793:0.2906:0.6301:0.0	.	17	Q8IWA0	WDR75_HUMAN	F	17	ENSP00000314193:L17F	ENSP00000314193:L17F	L	+	3	2	WDR75	190014514	1.000000	0.71417	0.917000	0.36280	0.915000	0.54546	0.488000	0.22371	0.362000	0.24319	-0.262000	0.10625	TTG	G|0.999;C|0.001		0.587	WDR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255913.1	NM_032168		C	190306269	G	C	190306269	3	2	26	1	0	0	0	0	1	0	0	0	17358	1281	45	4	53	4	WDR75	2	190306269	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	1973788	190306269	52893104	15	2246											
FAM117B	150864	broad.mit.edu	37	chr2	203500041	203500043	+	In_Frame_Del	DEL	AGC	AGC	-																															gacggttccgttccagctgaAgcagcagcagcagcagcaac																								rs567562707	byFrequency	TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:203500041_203500043delAGC	ENST00000392238.2	+	1	131_133	c.131_133delAGC	c.(130-135)aagcag>aag	p.Q50del	FAM117B_ENST00000303116.6_5'UTR			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	50	Gly-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TTCCAGCTGAAGCAGCAGCAGCA	0.749																																					p.44_45del													.	FAM117B-91	0			c.131_133del						.																																			SO:0001651	inframe_deletion	150864	exon1			AGCTGAAGCAGCA	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.131_133delAGC	2.37:g.203500050_203500052delAGC	ENSP00000376071:p.Gln50del	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_173511	0	0	0	0	0	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	In_Frame_Del	DEL	ENST00000392238.2	37	CCDS33362.2																																																																																			.		0.749	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		-	203500043	AGC	-	203500041	7	5	26	1	0	1	0	1	0	0	0	0	5426	72	3	0	133	0	FAM117B	2	203500041	In_Frame_Del	DEL	AGC	TCGA-A4-A5Y0-01A-11D-A31X-10	13193772	203500041	39699332	16	2247											
CUL3	8452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	225362540	225362540	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gatgctggagtgtgagctgtCgaccactgtgtttggctaag	7	12	15	7	1	0	1	0	1	0	0	1	4	0	2	1	2	2	4	1	2	1	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:225362540C>G	ENST00000264414.4	-	12	1975	c.1637G>C	c.(1636-1638)cGa>cCa	p.R546P	CUL3_ENST00000409096.1_Missense_Mutation_p.R522P|CUL3_ENST00000409777.1_Missense_Mutation_p.R522P|CUL3_ENST00000344951.4_Missense_Mutation_p.R480P	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	546					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TGTGAGCTGTCGACCACTGTG	0.353																																					p.R552P		.											.	CUL3-229	0			c.G1655C						.						150	140	143					2																	225362540		2203	4300	6503	SO:0001583	missense	8452	exon12			AGCTGTCGACCAC	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1637G>C	2.37:g.225362540C>G	ENSP00000264414:p.Arg546Pro	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	52	48	NM_001257198	0	0	0	33	33	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	C	34	5.352209	0.95830	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	6.16	6.16	0.99307	Cullin, N-terminal (1);Cullin homology (3);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	H	0.98276	4.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97283	0.9919	10	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	480;524;546	Q13618-3;Q53S54;Q13618	.;.;CUL3_HUMAN	P	546;480;522;522	ENSP00000264414:R546P;ENSP00000343601:R480P;ENSP00000387200:R522P;ENSP00000386525:R522P	ENSP00000264414:R546P	R	-	2	0	CUL3	225070784	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.802000	0.85969	2.937000	0.99478	0.650000	0.86243	CGA	.		0.353	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			G	225362540	C	G	225362540	3	3	26	1	0	0	0	0	1	0	0	0	4062	884	31	4	689	4	CUL3	2	225362540	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	21862499	225362540	17836833	17	2248											
TRIP12	9320	bcgsc.ca	37	chr2	230675639	230675639	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagttggacagttggaacaCatcagagaaaacatgcgaac	18	6	10	7	1	1	1	1	0	0	1	1	5	1	3	0	2	4	2	0	2	5	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:230675639C>T	ENST00000283943.5	-	14	2212	c.2034G>A	c.(2032-2034)atG>atA	p.M678I	TRIP12_ENST00000389044.4_Missense_Mutation_p.M726I|TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389045.3_Missense_Mutation_p.M381I	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	678					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AGTTGGAACACATCAGAGAAA	0.363																																					p.M678I													.	TRIP12-572	0			c.G2034A						.						69	67	68					2																	230675639		2203	4300	6503	SO:0001583	missense	9320	exon14			GGAACACATCAGA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.2034G>A	2.37:g.230675639C>T	ENSP00000283943:p.Met678Ile	Somatic	262	4		WXS	Illumina HiSeq	Phase_1	167	149	NM_004238	0	0	0	7	7	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984619	0.74474	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.27890	1.64;1.64;1.64	5.56	5.56	0.83823	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.25827	0.0629	N	0.21508	0.67	0.80722	D	1	B;B;B;B	0.28933	0.068;0.127;0.228;0.127	B;B;B;B	0.33846	0.035;0.094;0.171;0.094	T	0.05209	-1.0899	10	0.14252	T	0.57	.	19.5388	0.95266	0.0:1.0:0.0:0.0	.	684;381;726;678	D4HL82;Q14CF1;Q14CA3;Q14669	.;.;.;TRIPC_HUMAN	I	678;381;726	ENSP00000283943:M678I;ENSP00000373697:M381I;ENSP00000373696:M726I	ENSP00000283943:M678I	M	-	3	0	TRIP12	230383883	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.741000	0.84997	2.622000	0.88805	0.650000	0.86243	ATG	.		0.363	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230675639	C	T	230675639	3	4	26	1	0	0	0	0	1	0	0	0	16589	478	17	2	4056	2	TRIP12	2	230675639	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	5313099	230675639	12523734	18	2249											
ULK4	54986	hgsc.bcm.edu;bcgsc.ca	37	chr3	41795965	41795965	+	Frame_Shift_Del	DEL	T	T	-																															gctgtcaagtaaacggataaTtgtggagacaaaaccctgta																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:41795965delT	ENST00000301831.4	-	22	2671	c.2209delA	c.(2209-2211)attfs	p.I738fs		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	738					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AAACGGATAATTGTGGAGACA	0.358																																					p.I737fs		.											.	ULK4-297	0			c.2209delA						.						82	79	80					3																	41795965		1820	4081	5901	SO:0001589	frameshift_variant	54986	exon22			.	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"unc-51-like kinase 4 (C. elegans)"			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2209delA	3.37:g.41795965delT	ENSP00000301831:p.Ile738fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	123	42	NM_017886	0	0	0	0	0	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Frame_Shift_Del	DEL	ENST00000301831.4	37	CCDS43071.1																																																																																			.		0.358	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		-	41795965	T	-	41795965	7	5	26	1	0	1	0	1	0	0	0	0	17011	1493	52	0	1682	0	ULK4	3	41795965	Frame_Shift_Del	DEL	T	TCGA-A4-A5Y0-01A-11D-A31X-10		41795965	156226465	19	2250											
CISH	1154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50645901	50645901	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtctgggctggggtaccCtctgccacctcctcgaggaa	5	10	12	14	1	3	0	0	0	3	0	5	2	4	1	4	4	2	2	4	4	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:50645901C>A	ENST00000348721.3	-	2	324	c.144G>T	c.(142-144)gaG>gaT	p.E48D	CISH_ENST00000443053.2_Missense_Mutation_p.E65D	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	48					intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CTGGGGTACCCTCTGCCACCT	0.642																																					p.E65D		.											.	CISH-710	0			c.G195T						.						54	49	51					3																	50645901		2203	4300	6503	SO:0001583	missense	1154	exon3			GGTACCCTCTGCC	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.144G>T	3.37:g.50645901C>A	ENSP00000294173:p.Glu48Asp	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	49	28	NM_013324	0	0	35	64	29	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	37	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	C	7.873	0.728634	0.15507	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	T;T	0.47177	0.85;0.87	6.03	2.26	0.28386	.	0.367420	0.28209	N	0.016181	T	0.35885	0.0947	L	0.57536	1.79	0.28436	N	0.917019	B;B	0.28082	0.2;0.048	B;B	0.23574	0.047;0.012	T	0.21690	-1.0238	10	0.14656	T	0.56	-8.0475	6.8677	0.24102	0.0:0.587:0.119:0.294	.	65;48	G5E9R1;Q9NSE2	.;CISH_HUMAN	D	65;48	ENSP00000409346:E65D;ENSP00000294173:E48D	ENSP00000294173:E48D	E	-	3	2	CISH	50620905	0.991000	0.36638	1.000000	0.80357	0.071000	0.16799	0.437000	0.21543	0.441000	0.26529	-0.150000	0.13652	GAG	.		0.642	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		A	50645901	C	A	50645901	3	1	26	1	0	0	0	0	1	0	0	0	3443	680	24	4	640	4	CISH	3	50645901	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	8849936	50645901	147376529	20	2251											
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52380547	52380547	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaggtggccatgcgcagcagCctgcgcgacatgagcaaggg	10	4	16	11	3	0	1	0	1	0	0	0	2	0	1	2	3	5	3	2	3	2	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:52380547C>A	ENST00000420323.2	+	11	1977	c.1716C>A	c.(1714-1716)agC>agA	p.S572R		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	572	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGCGCAGCAGCCTGCGCGACA	0.572																																					p.S572R		.											.	DNAH1-67	0			c.C1716A						.						55	57	56					3																	52380547		2141	4243	6384	SO:0001583	missense	25981	exon11			CAGCAGCCTGCGC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.1716C>A	3.37:g.52380547C>A	ENSP00000401514:p.Ser572Arg	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	42	11	NM_015512	0	0	1	1	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127059	0.56721	.	.	ENSG00000114841	ENST00000420323	T	0.24350	1.86	4.53	4.53	0.55603	.	0.443881	0.19011	N	0.125064	T	0.34513	0.0900	M	0.72894	2.215	0.39055	D	0.960409	P;P	0.45957	0.713;0.869	B;P	0.47981	0.434;0.563	T	0.15263	-1.0443	10	0.23302	T	0.38	.	11.8369	0.52330	0.0:0.9149:0.0:0.0851	.	572;572	C9JXH6;Q9P2D7-3	.;.	R	572	ENSP00000401514:S572R	ENSP00000401514:S572R	S	+	3	2	DNAH1	52355587	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	2.033000	0.41136	2.085000	0.62840	0.563000	0.77884	AGC	.		0.572	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52380547	C	A	52380547	3	1	26	1	0	0	0	0	1	0	0	0	4608	738	26	4	1754	4	DNAH1	3	52380547	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	1734646	52380547	145641883	21	2252											
IL17RB	55540	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	53886139	53886147	+	In_Frame_Del	DEL	CCCTCTGGT	CCCTCTGGT	-																															ccttccagactcagaccagaCcctctggtggtaaagtaagc																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	CCCTCTGGT	CCCTCTGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:53886139_53886147delCCCTCTGGT	ENST00000288167.3	+	4	349_357	c.340_348delCCCTCTGGT	c.(340-348)ccctctggtdel	p.PSG114del		NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	114					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		TCAGACCAGACCCTCTGGTGGTAAAGTAA	0.478																																					p.114_116del		.											.	IL17RB-229	0			c.340_348del						.																																			SO:0001651	inframe_deletion	55540	exon4			.	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"Interleukins and interleukin receptors"	18015	protein-coding gene	gene with protein product		605458	"interleukin 17B receptor"	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.340_348delCCCTCTGGT	3.37:g.53886139_53886147delCCCTCTGGT	ENSP00000288167:p.Pro114_Gly116del	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	103	35	NM_018725	0	0	0	0	0	Q9BPZ0|Q9NRL4|Q9NRM5	In_Frame_Del	DEL	ENST00000288167.3	37	CCDS2874.1																																																																																			.		0.478	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234		-	53886147	CCCTCTGGT	-	53886139	7	5	26	1	0	1	0	1	0	0	0	0	7661	507	18	0	354	0	IL17RB	3	53886139	In_Frame_Del	DEL	CCCTCTGGT	TCGA-A4-A5Y0-01A-11D-A31X-10	1505592	53886139	144136291	22	2253											
A4GNT	51146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	137849689	137849689	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaagtttccctaaacacttActtgattgtaccatgaaaac	14	14	4	9	0	0	2	0	2	0	0	1	2	1	2	2	0	4	2	2	0	7	7			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:137849689A>C	ENST00000236709.3	-	2	610		c.e2+1			NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase						carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						CTAAACACTTACTTGATTGTA	0.403																																					.		.											.	A4GNT-90	0			c.408+2T>G						.						65	65	65					3																	137849689		2202	4300	6502	SO:0001630	splice_region_variant	51146	exon3			ACACTTACTTGAT	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.408+1T>G	3.37:g.137849689A>C		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	195	96	NM_016161	0	0	0	0	0	Q0VDK1|Q0VDK2	Splice_Site	SNP	ENST00000236709.3	37	CCDS3097.1	.	.	.	.	.	.	.	.	.	.	A	13.58	2.279090	0.40294	.	.	ENSG00000118017	ENST00000236709	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4479	0.75248	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	A4GNT	139332379	1.000000	0.71417	0.995000	0.50966	0.387000	0.30353	6.414000	0.73318	2.046000	0.60703	0.454000	0.30748	.	.		0.403	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161	Intron	C	137849689	A	C	137849689	5	2	26	1	0	0	0	0	0	0	1	0	7	405	14	5	620	5	A4GNT	3	137849689	Splice_Site	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	83963550	137849689	60172741	23	2254											
PLS1	5357	ucsc.edu;bcgsc.ca	37	chr3	142403182	142403182	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgctgcgatgggtgaactAccatctgaccaatgcaggat	11	9	11	10	1	1	2	0	2	1	0	1	4	1	3	2	2	5	2	2	2	3	1	rs375726625		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:142403182A>G	ENST00000337777.3	+	8	1046	c.833A>G	c.(832-834)tAc>tGc	p.Y278C	PLS1_ENST00000457734.2_Missense_Mutation_p.Y278C|PLS1_ENST00000497002.1_Missense_Mutation_p.Y278C	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	278	Actin-binding 1.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						TGGGTGAACTACCATCTGACC	0.418																																					p.Y278C													.	PLS1-91	0			c.A833G						.	A	CYS/TYR,CYS/TYR,CYS/TYR	0,4406		0,0,2203	96	88	91		833,833,833	3.6	1	3		91	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PLS1	NM_001145319.1,NM_001172312.1,NM_002670.2	194,194,194	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	278/630,278/630,278/630	142403182	1,13005	2203	4300	6503	SO:0001583	missense	5357	exon8			TGAACTACCATCT	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.833A>G	3.37:g.142403182A>G	ENSP00000336831:p.Tyr278Cys	Somatic	212	2		WXS	Illumina HiSeq		230	112	NM_001172312	0	0	30	57	27	A8K2Q1|D3DNG3|Q8NEG6	Missense_Mutation	SNP	ENST00000337777.3	37	CCDS3125.1	.	.	.	.	.	.	.	.	.	.	A	18.47	3.631084	0.67015	0.0	1.16E-4	ENSG00000120756	ENST00000457734;ENST00000476044;ENST00000337777;ENST00000497002	D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64	4.83	3.59	0.41128	Calponin homology domain (5);	0.285780	0.40385	N	0.001105	D	0.96163	0.8749	M	0.91459	3.21	0.80722	D	1	P	0.50710	0.938	P	0.50791	0.65	D	0.96513	0.9380	10	0.87932	D	0	-13.5133	11.4387	0.50083	0.865:0.0:0.0:0.135	.	278	Q14651	PLSI_HUMAN	C	278;199;278;278	ENSP00000387890:Y278C;ENSP00000417481:Y199C;ENSP00000336831:Y278C;ENSP00000418700:Y278C	ENSP00000336831:Y278C	Y	+	2	0	PLS1	143885872	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	2.115000	0.41921	2.155000	0.67459	0.482000	0.46254	TAC	.		0.418	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		G	142403182	A	G	142403182	3	3	26	1	0	0	0	0	1	0	0	0	12133	391	14	3	859	3	PLS1	3	142403182	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	4553493	142403182	55619248	24	2255											
PRKCI	5584	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	170020905	170020905	+	Frame_Shift_Del	DEL	A	A	-																															tcttttgatgtctgcagaagAatgtgtctgatcctcatttt																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:170020905delA	ENST00000295797.4	+	18	2086	c.1781delA	c.(1780-1782)gaafs	p.E594fs		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	594	AGC-kinase C-terminal.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	TCTGCAGAAGAATGTGTCTGA	0.333																																					p.E594fs		.											.	PRKCI-1378	0			c.1781delA						.						154	140	145					3																	170020905		2203	4300	6503	SO:0001589	frameshift_variant	5584	exon18			.		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1781delA	3.37:g.170020905delA	ENSP00000295797:p.Glu594fs	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	86	36	NM_002740	0	0	0	0	0	D3DNQ4|Q8WW06	Frame_Shift_Del	DEL	ENST00000295797.4	37	CCDS3212.2																																																																																			.		0.333	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		-	170020905	A	-	170020905	7	5	26	1	0	1	0	1	0	0	0	0	12543	246	9	0	1851	0	PRKCI	3	170020905	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	27617723	170020905	28001525	25	2256											
ACTL6A	86	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179298770	179298770	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcggctaaagattccagaaGgattatttgacccttccaat	13	11	8	9	1	0	3	0	1	0	2	2	4	2	4	3	2	1	1	3	2	5	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:179298770G>T	ENST00000429709.2	+	10	1132	c.919G>T	c.(919-921)Gga>Tga	p.G307*	ACTL6A_ENST00000467615.1_3'UTR|ACTL6A_ENST00000392662.1_Nonsense_Mutation_p.G265*|ACTL6A_ENST00000450518.2_Nonsense_Mutation_p.G265*|RP11-15L13.4_ENST00000608818.1_RNA	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	307					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			GATTCCAGAAGGATTATTTGA	0.373																																					p.G307X													.	ACTL6A-91	0			c.G919T						.						105	109	107					3																	179298770		2203	4300	6503	SO:0001587	stop_gained	86	exon10			CCAGAAGGATTAT	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.919G>T	3.37:g.179298770G>T	ENSP00000397552:p.Gly307*	Somatic	306	2		WXS	Illumina HiSeq	Phase_I	304	158	NM_004301	0	0	17	17	0	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Nonsense_Mutation	SNP	ENST00000429709.2	37	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	G	40	7.977909	0.98591	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	.	.	.	5.41	5.41	0.78517	.	0.101413	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.1807	0.93622	0.0:0.0:1.0:0.0	.	.	.	.	X	307;265;265	.	ENSP00000376430:G265X	G	+	1	0	ACTL6A	180781464	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.476000	0.97823	2.542000	0.85734	0.467000	0.42956	GGA	.		0.373	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		T	179298770	G	T	179298770	4	4	26	1	0	0	0	0	0	1	0	0	198	1001	35	4	957	4	ACTL6A	3	179298770	Nonsense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	9277865	179298770	18723660	26	2257											
KLB	152831	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39435920	39435920	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttgggatctcattggatcGagccaaaccggtcggaaaac	11	8	12	10	4	1	0	1	0	1	0	4	4	1	3	2	4	3	1	2	4	3	2	rs369333502		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr4:39435920G>T	ENST00000257408.4	+	2	1013	c.916G>T	c.(916-918)Gag>Tag	p.E306*		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	306	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TCATTGGATCGAGCCAAACCG	0.463																																					p.E306X													.	KLB-69	0			c.G916T						.						113	97	103					4																	39435920		2203	4300	6503	SO:0001587	stop_gained	152831	exon2			TGGATCGAGCCAA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.916G>T	4.37:g.39435920G>T	ENSP00000257408:p.Glu306*	Somatic	175	1		WXS	Illumina HiSeq	Phase_I	185	76	NM_175737	0	0	0	0	0	Q2M3K8	Nonsense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.387429	0.82902	.	.	ENSG00000134962	ENST00000257408	.	.	.	6.17	6.17	0.99709	.	0.098850	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-32.149	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	.	.	.	X	306	.	ENSP00000257408:E306X	E	+	1	0	KLB	39112315	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	5.417000	0.66423	2.941000	0.99782	0.655000	0.94253	GAG	.		0.463	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		T	39435920	G	T	39435920	4	4	26	1	0	0	0	0	0	1	0	0	8353	1059	37	4	922	4	KLB	4	39435920	Nonsense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		39435920	151718356	27	2258											
WDFY3	23001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	85722839	85722839	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagcctgagaggctaatCgttcaaacatccgctgcagg	11	7	11	12	2	1	2	1	1	0	2	3	3	2	2	3	2	3	4	3	2	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr4:85722839C>A	ENST00000295888.4	-	17	3193	c.2786G>T	c.(2785-2787)cGa>cTa	p.R929L	WDFY3_ENST00000512267.1_5'Flank|WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000322366.6_Missense_Mutation_p.R929L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	929					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AGAGGCTAATCGTTCAAACAT	0.493																																					p.R929L		.											.	WDFY3-93	0			c.G2786T						.						109	112	111					4																	85722839		2203	4300	6503	SO:0001583	missense	23001	exon17			GCTAATCGTTCAA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.2786G>T	4.37:g.85722839C>A	ENSP00000295888:p.Arg929Leu	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	36	16	NM_014991	0	0	1	3	2	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890055	0.91889	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.57107	0.42;0.42	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.72475	-0.4282	10	0.54805	T	0.06	.	20.4024	0.99000	0.0:1.0:0.0:0.0	.	929	Q8IZQ1	WDFY3_HUMAN	L	929	ENSP00000318466:R929L;ENSP00000295888:R929L	ENSP00000295888:R929L	R	-	2	0	WDFY3	85941863	1.000000	0.71417	0.883000	0.34634	0.737000	0.42083	7.487000	0.81328	2.827000	0.97445	0.650000	0.86243	CGA	.		0.493	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85722839	C	A	85722839	3	1	26	1	0	0	0	0	1	0	0	0	17303	884	31	4	8002	4	WDFY3	4	85722839	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	46286919	85722839	105431437	28	2259											
ADAMTS12	81792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	33534943	33534943	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccattcacccaccggcaCttttcttgcaggcctgctgg	7	10	8	16	1	2	0	1	0	1	0	2	0	2	0	4	3	3	3	4	3	1	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr5:33534943C>A	ENST00000504830.1	-	23	4936	c.4601G>T	c.(4600-4602)aGt>aTt	p.S1534I	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.S1449I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1534					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CCCACCGGCACTTTTCTTGCA	0.433										HNSCC(64;0.19)																											p.S1534I		.											.	ADAMTS12-232	0			c.G4601T						.						130	124	126					5																	33534943		2203	4300	6503	SO:0001583	missense	81792	exon23			CCGGCACTTTTCT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4601G>T	5.37:g.33534943C>A	ENSP00000422554:p.Ser1534Ile	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	91	44	NM_030955	0	0	0	0	0	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.963656	0.34659	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.60548	0.19;0.18	4.98	0.386	0.16254	.	0.588898	0.19280	N	0.118200	T	0.43366	0.1244	L	0.52364	1.645	0.53005	D	0.999961	P;B	0.36837	0.571;0.435	B;B	0.36989	0.238;0.12	T	0.14392	-1.0474	10	0.30854	T	0.27	.	3.6087	0.08052	0.0:0.3846:0.2143:0.401	.	1449;1534	P58397-3;P58397	.;ATS12_HUMAN	I	1534;1449	ENSP00000422554:S1534I;ENSP00000344847:S1449I	ENSP00000344847:S1449I	S	-	2	0	ADAMTS12	33570700	0.000000	0.05858	0.922000	0.36590	0.973000	0.67179	0.033000	0.13754	0.202000	0.20498	0.563000	0.77884	AGT	.		0.433	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33534943	C	A	33534943	3	1	26	1	0	0	0	0	1	0	0	0	257	565	20	4	191	4	ADAMTS12	5	33534943	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		33534943	147380317	29	2260											
PCDHB14	56122	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140605127	140605127	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccccggcccaggcccaggccGactccctcaccgtctacctg	5	5	9	22	3	2	0	1	0	1	0	3	1	3	0	8	3	1	0	8	3	1	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr5:140605127G>A	ENST00000239449.4	+	1	2050	c.2050G>A	c.(2050-2052)Gac>Aac	p.D684N	PCDHB14_ENST00000515856.2_Missense_Mutation_p.D531N	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	684					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCCCAGGCCGACTCCCTCAC	0.701																																					p.D684N	Ovarian(141;50 1831 27899 33809 37648)	.											.	PCDHB14-91	0			c.G2050A						.						69	77	74					5																	140605127		2187	4284	6471	SO:0001583	missense	56122	exon1			CAGGCCGACTCCC	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2050G>A	5.37:g.140605127G>A	ENSP00000239449:p.Asp684Asn	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	73	5	NM_018934	0	0	3	3	0	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	-	11.91	1.778390	0.31502	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.52983	0.65;0.64	4.17	4.17	0.49024	.	.	.	.	.	T	0.47135	0.1429	M	0.83483	2.645	0.09310	N	1	P	0.35575	0.51	B	0.30572	0.117	T	0.52540	-0.8562	9	0.59425	D	0.04	.	6.9347	0.24461	0.0935:0.0:0.7321:0.1744	.	684	Q9Y5E9	PCDBE_HUMAN	N	531;684	ENSP00000444518:D531N;ENSP00000239449:D684N	ENSP00000239449:D684N	D	+	1	0	PCDHB14	140585311	0.747000	0.28283	0.039000	0.18376	0.064000	0.16182	2.451000	0.44952	2.022000	0.59522	0.650000	0.86243	GAC	.		0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		A	140605127	G	A	140605127	3	1	26	1	0	0	0	0	1	0	0	0	11565	1058	37	1	2052	1	PCDHB14	5	140605127	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	107070184	140605127	40310133	30	2261											
CD83	9308	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	14133946	14133946	+	Frame_Shift_Del	DEL	C	C	-																															ggagattgtcctgctgctggCtctggttattttctacttaa																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:14133946delC	ENST00000379153.3	+	4	620	c.449delC	c.(448-450)gctfs	p.A150fs		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	150					defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				CTGCTGCTGGCTCTGGTTATT	0.383																																					p.A150fs		.											.	CD83-90	0			c.449delC						.						132	132	132					6																	14133946		2203	4300	6503	SO:0001589	frameshift_variant	9308	exon4			.	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1703	protein-coding gene	gene with protein product		604534	"CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)", "CD83 molecule "			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.449delC	6.37:g.14133946delC	ENSP00000368450:p.Ala150fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	107	49	NM_004233	0	0	0	0	0	Q5THX9	Frame_Shift_Del	DEL	ENST00000379153.3	37	CCDS4532.1																																																																																			.		0.383	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			-	14133946	C	-	14133946	7	5	26	1	0	1	0	1	0	0	0	0	3047	797	28	0	463	0	CD83	6	14133946	Frame_Shift_Del	DEL	C	TCGA-A4-A5Y0-01A-11D-A31X-10		14133946	156981121	31	2262											
E2F3	1871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	20490451	20490451	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgctcagtttctatgggaaaCctttctcctctggcctcccc	5	14	7	15	0	4	0	1	0	3	0	6	1	5	1	5	2	2	2	5	2	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:20490451C>G	ENST00000346618.3	+	7	1254	c.1188C>G	c.(1186-1188)aaC>aaG	p.N396K	E2F3_ENST00000535432.1_Missense_Mutation_p.N265K	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	396	Transactivation. {ECO:0000255}.				mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			CTATGGGAAACCTTTCTCCTC	0.443																																					p.N396K		.											.	E2F3-414	0			c.C1188G						.						72	71	71					6																	20490451		2203	4300	6503	SO:0001583	missense	1871	exon7			GGGAAACCTTTCT	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.1188C>G	6.37:g.20490451C>G	ENSP00000262904:p.Asn396Lys	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	101	52	NM_001949	0	0	1	2	1	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	37	CCDS4545.1	.	.	.	.	.	.	.	.	.	.	C	0.070	-1.205397	0.01568	.	.	ENSG00000112242	ENST00000346618;ENST00000535432	T;T	0.06294	3.32;3.35	5.49	2.71	0.32032	.	0.637186	0.17731	N	0.163882	T	0.00637	0.0021	N	0.08118	0	0.20489	N	0.999892	B	0.15473	0.013	B	0.11329	0.006	T	0.46190	-0.9209	10	0.06236	T	0.91	.	3.2605	0.06846	0.2493:0.5042:0.1104:0.1361	.	396	O00716	E2F3_HUMAN	K	396;265	ENSP00000262904:N396K;ENSP00000443418:N265K	ENSP00000262904:N396K	N	+	3	2	E2F3	20598430	0.274000	0.24191	0.948000	0.38648	0.975000	0.68041	0.955000	0.29188	0.355000	0.24131	-0.224000	0.12420	AAC	.		0.443	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			G	20490451	C	G	20490451	3	3	26	1	0	0	0	0	1	0	0	0	4879	506	18	4	1214	4	E2F3	6	20490451	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	6356505	20490451	150624616	32	2263											
HLA-A	3105	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	29910554	29910554	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcccactccatgaggtatTtcttcacatccgtgtcccgg	6	12	8	15	2	2	1	1	1	1	0	6	1	6	1	4	2	0	2	4	2	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:29910554T>G	ENST00000396634.1	+	4	435	c.94T>G	c.(94-96)Ttc>Gtc	p.F32V	HLA-A_ENST00000376809.5_Missense_Mutation_p.F32V|HLA-A_ENST00000376806.5_Missense_Mutation_p.F32V|HLA-A_ENST00000376802.2_Missense_Mutation_p.F32V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	32	Alpha-1.				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)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CATGAGGTATTTCTTCACATC	0.726									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.F32V		.											.	HLA-A-92	0			c.T94G						.						15	15	15					6																	29910554		2179	4265	6444	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGTATTTCTTCA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.94T>G	6.37:g.29910554T>G	ENSP00000379873:p.Phe32Val	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	134	38	NM_001242758	0	0	958	958	0	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	10.84	1.463317	0.26248	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00932	5.53;5.53;5.53;5.53	3.72	2.53	0.30540	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.000000	0.35349	U	0.003271	T	0.03178	0.0093	H	0.96142	3.775	0.09310	N	1	D;D;D;D;D	0.76494	0.999;0.998;0.999;0.998;0.999	D;D;D;D;D	0.91635	0.999;0.998;0.999;0.998;0.999	T	0.29971	-0.9994	10	0.87932	D	0	.	5.839	0.18623	0.0:0.1258:0.0:0.8742	.	32;32;32;32;32	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	V	32	ENSP00000379873:F32V;ENSP00000366002:F32V;ENSP00000366005:F32V;ENSP00000365998:F32V	ENSP00000348012:F32V	F	+	1	0	HLA-A	30018533	0.004000	0.15560	0.034000	0.17996	0.201000	0.24016	0.452000	0.21795	0.620000	0.30215	0.391000	0.25812	TTC	.		0.726	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		G	29910554	T	G	29910554	3	3	26	1	0	0	0	0	1	0	0	0	7216	1841	64	5	100	5	HLA-A	6	29910554	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	9420103	29910554	141204513	33	2264											
BRD2	6046	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	32944714	32944714	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggacctcagcactgtcaagGtacccactgcatggggcaga	10	7	12	12	0	2	1	2	0	0	1	2	2	2	2	2	4	3	4	2	4	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:32944714G>A	ENST00000374825.4	+	7	2901		c.e7+1		BRD2_ENST00000395289.2_Splice_Site|BRD2_ENST00000395287.1_Splice_Site|BRD2_ENST00000374831.4_Splice_Site|BRD2_ENST00000443797.2_Splice_Site|BRD2_ENST00000449085.2_Splice_Site	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2						chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)	p.?(1)		central_nervous_system(3)|stomach(2)	5						CACTGTCAAGGTACCCACTGC	0.507																																					.		.											.	BRD2-398	1	Unknown(1)	upper_aerodigestive_tract(1)	c.1200+1G>A						.						60	64	63					6																	32944714		1472	2670	4142	SO:0001630	splice_region_variant	6046	exon7			GTCAAGGTACCCA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1200+1G>A	6.37:g.32944714G>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	42	21	NM_005104	0	0	1	21	20	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Splice_Site	SNP	ENST00000374825.4	37	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.493736	0.64186	.	.	ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449025;ENST00000449085	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8266	0.78711	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BRD2	33052692	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.592000	0.98245	2.679000	0.91253	0.637000	0.83480	.	.		0.507	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		Intron	A	32944714	G	A	32944714	5	1	26	1	0	0	0	0	0	0	1	0	1505	1275	44	2	1223	2	BRD2	6	32944714	Splice_Site	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	3034160	32944714	138170353	34	2265											
CAPN11	11131	broad.mit.edu	37	chr6	44148401	44148401	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagatagtggcaggagaggTgagcaggccacgagcggagg	12	4	19	6	2	0	3	0	1	0	2	0	6	0	4	1	6	2	2	1	6	2	2	rs200836901	byFrequency	TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:44148401T>G	ENST00000398776.1	+	16	1784		c.e16+2		CAPN11_ENST00000542245.1_Splice_Site	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GCAGGAGAGGTGAGCAGGCCA	0.607													t|||	28	0.00559105	0.0098	0.0014	5008	,	,		11389	0.003		0.003	False		,,,				2504	0.0082				.													.	CAPN11-136	0			c.1746+2T>G						.						32	36	35					6																	44148401		1912	4125	6037	SO:0001630	splice_region_variant	11131	exon16			GAGAGGTGAGCAG	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1746+2T>G	6.37:g.44148401T>G		Somatic	89	15		WXS	Illumina HiSeq	Phase_I	76	21	NM_007058	0	0	0	0	0	B2RA64|Q5T3G1|Q8N4R5	Splice_Site	SNP	ENST00000398776.1	37	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	t	26.6	4.751671	0.89753	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4973	0.61434	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CAPN11	44256379	1.000000	0.71417	0.988000	0.46212	0.751000	0.42716	5.666000	0.68059	2.045000	0.60652	0.404000	0.27445	.	T|0.999;A|0.000		0.607	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		Intron	G	44148401	T	G	44148401	5	3	26	1	0	0	0	0	0	0	1	0	2630	1710	59	5	1810	5	CAPN11	6	44148401	Splice_Site	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	11203687	44148401	126966666	35	2266											
MDN1	23195	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90392973	90392973	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtcaggctgttcttcctTgtcactctccaccagggatg	8	12	9	12	0	4	0	2	0	2	0	6	1	5	1	3	2	0	2	3	2	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:90392973T>G	ENST00000369393.3	-	73	12095	c.11980A>C	c.(11980-11982)Aag>Cag	p.K3994Q	MDN1_ENST00000428876.1_Missense_Mutation_p.K3994Q			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3994					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGTTCTTCCTTGTCACTCTCC	0.493																																					p.K3994Q													.	MDN1-100	0			c.A11980C						.						95	82	87					6																	90392973		2203	4300	6503	SO:0001583	missense	23195	exon73			CTTCCTTGTCACT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.11980A>C	6.37:g.90392973T>G	ENSP00000358400:p.Lys3994Gln	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	113	46	NM_014611	0	0	0	0	0	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	11.13	1.548514	0.27652	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03301	3.98;3.98	5.7	0.196	0.15159	.	0.418027	0.27802	N	0.017789	T	0.00784	0.0026	L	0.35793	1.09	0.24730	N	0.993092	B	0.14805	0.011	B	0.14023	0.01	T	0.47861	-0.9084	10	0.10902	T	0.67	.	6.7775	0.23628	0.0:0.2036:0.2011:0.5954	.	3994	Q9NU22	MDN1_HUMAN	Q	3994	ENSP00000358400:K3994Q;ENSP00000413970:K3994Q	ENSP00000358400:K3994Q	K	-	1	0	MDN1	90449694	1.000000	0.71417	0.988000	0.46212	0.877000	0.50540	1.992000	0.40737	0.122000	0.18314	0.459000	0.35465	AAG	.		0.493	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90392973	T	G	90392973	3	3	26	1	0	0	0	0	1	0	0	0	9440	1821	63	5	4930	5	MDN1	6	90392973	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	46244572	90392973	80722094	36	2267											
ASCC3	10973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	101075824	101075824	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgagataaaatttgttCgagatacaatgacctctaga	15	12	9	5	1	1	5	0	3	1	3	2	7	1	5	1	0	1	1	1	0	5	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:101075824C>A	ENST00000369162.2	-	28	4759	c.4415G>T	c.(4414-4416)cGa>cTa	p.R1472L		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1472	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AAAATTTGTTCGAGATACAAT	0.393																																					p.R1472L		.											.	ASCC3-96	0			c.G4415T						.						108	105	106					6																	101075824		2203	4300	6503	SO:0001583	missense	10973	exon28			TTTGTTCGAGATA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.4415G>T	6.37:g.101075824C>A	ENSP00000358159:p.Arg1472Leu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	69	30	NM_006828	0	0	1	10	9	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	32	5.124487	0.94429	.	.	ENSG00000112249	ENST00000369162	T	0.14640	2.49	6.17	6.17	0.99709	DEAD-like helicase (2);ATPase, AAA+ type, core (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.52224	0.1721	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68383	-0.5423	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1472	Q8N3C0	HELC1_HUMAN	L	1472	ENSP00000358159:R1472L	ENSP00000358159:R1472L	R	-	2	0	ASCC3	101182545	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CGA	.		0.393	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101075824	C	A	101075824	3	1	26	1	0	0	0	0	1	0	0	0	1034	884	31	4	2253	4	ASCC3	6	101075824	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	10682851	101075824	70039243	37	2268											
NRCAM	4897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107807453	107807453	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgtatgctgttcctggcaTtagaccctttaacccaaaga	10	14	7	10	0	0	2	0	0	0	2	1	2	1	2	3	1	2	4	3	1	4	6			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr7:107807453T>C	ENST00000425651.2	-	27	3378	c.3379A>G	c.(3379-3381)Atg>Gtg	p.M1127V	NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000379022.4_Missense_Mutation_p.M1127V|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379028.3_Missense_Mutation_p.M1127V	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1127	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GTTCCTGGCATTAGACCCTTT	0.433																																					p.M1127V		.											.	NRCAM-156	0			c.A3379G						.						76	81	79					7																	107807453		1972	4151	6123	SO:0001583	missense	4897	exon27			CTGGCATTAGACC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3379A>G	7.37:g.107807453T>C	ENSP00000401244:p.Met1127Val	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	133	50	NM_001037132	0	0	0	0	0	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	T	9.859	1.195856	0.22037	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022	T;T;T	0.55760	0.5;0.5;0.5	5.67	3.17	0.36434	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.360043	0.35838	N	0.002958	T	0.29945	0.0749	N	0.14661	0.345	0.27571	N	0.949892	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.14656	T	0.56	.	8.9597	0.35840	0.0:0.0674:0.126:0.8066	.	1127	Q92823	NRCAM_HUMAN	V	1127	ENSP00000368314:M1127V;ENSP00000401244:M1127V;ENSP00000368308:M1127V	ENSP00000368308:M1127V	M	-	1	0	NRCAM	107594689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.529000	0.60588	1.086000	0.41228	0.523000	0.50628	ATG	.		0.433	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		C	107807453	T	C	107807453	3	2	26	1	0	0	0	0	1	0	0	0	10670	1493	52	3	581	3	NRCAM	7	107807453	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10		107807453	51331210	38	2269											
OR6V1	346517	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142750247	142750247	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactctgtgcaagtcaggaaGgtcgtggccttggtgacttc	7	11	13	10	1	2	1	1	1	1	0	4	2	2	2	1	4	1	1	1	4	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr7:142750247G>C	ENST00000418316.1	+	1	831	c.810G>C	c.(808-810)aaG>aaC	p.K270N		NM_001001667.1	NP_001001667.1	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V, member 1	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	20	Melanoma(164;0.059)					AAGTCAGGAAGGTCGTGGCCT	0.507																																					p.K270N		.											.	OR6V1-23	0			c.G810C						.						104	112	110					7																	142750247		2053	4182	6235	SO:0001583	missense	346517	exon1			CAGGAAGGTCGTG		CCDS47728.1	7q34	2014-05-06			ENSG00000225781	ENSG00000225781		"GPCR / Class A : Olfactory receptors"	15090	protein-coding gene	gene with protein product						12732197	Standard	NM_001001667		Approved	GPR138	uc011ksv.2	Q8N148	OTTHUMG00000158385	ENST00000418316.1:c.810G>C	7.37:g.142750247G>C	ENSP00000396085:p.Lys270Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	80	41	NM_001001667	0	0	0	0	0	A4D2I0|B9EH48|Q6IF70	Missense_Mutation	SNP	ENST00000418316.1	37	CCDS47728.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109344	0.37242	.	.	ENSG00000225781	ENST00000418316	T	0.00207	8.55	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00666	0.0022	M	0.85041	2.73	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.48103	-0.9064	9	0.87932	D	0	.	14.772	0.69688	0.0:0.0:1.0:0.0	.	270	Q8N148	OR6V1_HUMAN	N	270	ENSP00000396085:K270N	ENSP00000396085:K270N	K	+	3	2	OR6V1	142460369	0.000000	0.05858	0.506000	0.27664	0.262000	0.26303	0.085000	0.14912	2.349000	0.79799	0.655000	0.94253	AAG	.		0.507	OR6V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350860.1			C	142750247	G	C	142750247	3	2	26	1	0	0	0	0	1	0	0	0	11237	991	35	4	812	4	OR6V1	7	142750247	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	34942794	142750247	16388416	39	2270											
DNAJB6	10049	broad.mit.edu;bcgsc.ca	37	chr7	157177601	157177601	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctaggtcacgggggcctcacTtcattctcttccacgtcatt	6	13	8	14	2	5	0	4	0	1	0	7	0	6	0	2	3	0	0	2	3	1	5	rs569868286		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr7:157177601T>C	ENST00000262177.4	+	7	724	c.519T>C	c.(517-519)acT>acC	p.T173T	DNAJB6_ENST00000452797.2_Silent_p.T124T|DNAJB6_ENST00000429029.2_Silent_p.T173T|DNAJB6_ENST00000443280.1_Intron	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	173	Interaction with KRT18.|Ser-rich.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGGGCCTCACTTCATTCTCTT	0.383													T|||	1	0.000199681	0	0	5008	,	,		19350	0		0	False		,,,				2504	0.001				p.T173T	Esophageal Squamous(46;195 967 1350 20350 43814)												.	DNAJB6-93	0			c.T519C						.						122	119	120					7																	157177601		2203	4298	6501	SO:0001819	synonymous_variant	10049	exon7			CCTCACTTCATTC	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.519T>C	7.37:g.157177601T>C		Somatic	78	1		WXS	Illumina HiSeq	Phase_I	95	37	NM_058246	0	0	31	31	0	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Silent	SNP	ENST00000262177.4	37	CCDS5946.1																																																																																			.		0.383	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			C	157177601	T	C	157177601	2	2	26	1	0	0	0	0	0	0	0	1	4635	1596	56	3		3	DNAJB6	7	157177601	Silent	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	14427354	157177601	1961062	40	2271			1	8		2	2	12	N	T_C	2.949234e-05
DNAJB6	10049	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	157177612	157177612	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gggcctcacttcattctcttCcacgtcatttggtggtagtg	5	15	10	11	1	4	0	3	0	1	0	6	0	5	0	2	3	0	1	2	3	1	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr7:157177612C>T	ENST00000262177.4	+	7	735	c.530C>T	c.(529-531)tCc>tTc	p.S177F	DNAJB6_ENST00000452797.2_Missense_Mutation_p.S128F|DNAJB6_ENST00000429029.2_Missense_Mutation_p.S177F|DNAJB6_ENST00000443280.1_Intron	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	177	Interaction with KRT18.|Ser-rich.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TCATTCTCTTCCACGTCATTT	0.393																																					p.S177F	Esophageal Squamous(46;195 967 1350 20350 43814)												.	DNAJB6-93	0			c.C530T						.						122	118	120					7																	157177612		2203	4300	6503	SO:0001583	missense	10049	exon7			TCTCTTCCACGTC	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.530C>T	7.37:g.157177612C>T	ENSP00000262177:p.Ser177Phe	Somatic	96	1		WXS	Illumina HiSeq	Phase_I	104	43	NM_058246	0	0	61	61	0	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	37	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673592	0.29693	.	.	ENSG00000105993	ENST00000429029;ENST00000262177;ENST00000417758;ENST00000452797;ENST00000421417	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	4.52	4.52	0.55395	.	0.233153	0.29021	N	0.013381	D	0.84669	0.5523	M	0.84156	2.68	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;0.999;0.999;0.983	D;D;D;P	0.76575	0.988;0.956;0.956;0.731	D	0.84838	0.0806	10	0.35671	T	0.21	.	17.5948	0.88009	0.0:1.0:0.0:0.0	.	128;177;177;177	B4DN73;A8KAG0;O75190;O75190-2	.;.;DNJB6_HUMAN;.	F	177;177;177;128;177	ENSP00000397556:S177F;ENSP00000262177:S177F;ENSP00000400665:S177F;ENSP00000402270:S128F	ENSP00000262177:S177F	S	+	2	0	DNAJB6	156870373	1.000000	0.71417	0.104000	0.21259	0.085000	0.17905	6.331000	0.72929	2.245000	0.73994	0.655000	0.94253	TCC	.		0.393	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			T	157177612	C	T	157177612	3	4	26	1	0	0	0	0	1	0	0	0	4635	855	30	2	552	2	DNAJB6	7	157177612	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	11	157177612	1961051	41	2272			1	8		2	2	12	N	T_C	2.949234e-05
SNAI2	6591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	49833817	49833817	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcttgaccaggaaggagCgcggcatcttgccagcgggt	7	8	15	11	3	2	1	0	1	2	0	2	3	2	3	2	4	3	2	2	4	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr8:49833817C>G	ENST00000396822.1	-	2	365	c.8G>C	c.(7-9)cGc>cCc	p.R3P	SNAI2_ENST00000020945.1_Missense_Mutation_p.R3P			O43623	SNAI2_HUMAN	snail family zinc finger 2	3	SNAG domain. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|cartilage morphogenesis (GO:0060536)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to ionizing radiation (GO:0071479)|desmosome disassembly (GO:0035921)|embryo development (GO:0009790)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|epithelium development (GO:0060429)|negative regulation of anoikis (GO:2000811)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter (GO:1900387)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|negative regulation of vitamin D receptor signaling pathway (GO:0070563)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone acetylation (GO:0035066)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of chemokine production (GO:0032642)|regulation of osteoblast differentiation (GO:0045667)|regulation of tight junction assembly (GO:2000810)|sensory perception of sound (GO:0007605)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)	18		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				CAGGAAGGAGCGCGGCATCTT	0.587																																					p.R3P		.											.	SNAI2-188	0			c.G8C						.						107	108	107					8																	49833817		2203	4300	6503	SO:0001583	missense	6591	exon1			AAGGAGCGCGGCA	U97060	CCDS6146.1	8q11.21	2013-05-23	2013-05-23	2002-02-28	ENSG00000019549	ENSG00000019549		"Snail homologs", "Zinc fingers, C2H2-type"	11094	protein-coding gene	gene with protein product		602150	"slug homolog, zinc finger protein (chicken)", "snail homolog 2 (Drosophila)"	SLUG		9337409, 9721220	Standard	NM_003068		Approved	SLUGH1, SNAIL2	uc003xqp.3	O43623	OTTHUMG00000149912	ENST00000396822.1:c.8G>C	8.37:g.49833817C>G	ENSP00000380034:p.Arg3Pro	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	38	22	NM_003068	0	0	0	0	0	B2R6P6|Q53FC1	Missense_Mutation	SNP	ENST00000396822.1	37	CCDS6146.1	.	.	.	.	.	.	.	.	.	.	C	32	5.143242	0.94560	.	.	ENSG00000019549	ENST00000020945;ENST00000396822	T;T	0.19938	2.11;2.11	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.52885	0.1762	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58808	-0.7571	9	.	.	.	-21.1684	18.5472	0.91052	0.0:1.0:0.0:0.0	.	3	O43623	SNAI2_HUMAN	P	3	ENSP00000020945:R3P;ENSP00000380034:R3P	.	R	-	2	0	SNAI2	49996370	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.380000	0.79704	2.377000	0.81083	0.313000	0.20887	CGC	.		0.587	SNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313873.2	NM_003068		G	49833817	C	G	49833817	3	3	26	1	0	0	0	0	1	0	0	0	14859	768	27	4	810	4	SNAI2	8	49833817	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		49833817	96530205	42	2273											
MTSS1	9788	hgsc.bcm.edu;bcgsc.ca	37	chr8	125570101	125570101	+	Frame_Shift_Del	DEL	A	A	-																															acttgataaactatagtgagAaaacccgttagacaactgga																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr8:125570101delA	ENST00000518547.1	-	11	1524	c.1051delT	c.(1051-1053)tctfs	p.S351fs	NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_Intron|MTSS1_ENST00000325064.5_Frame_Shift_Del_p.S355fs|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000524090.1_Frame_Shift_Del_p.S241fs|MTSS1_ENST00000395508.2_Frame_Shift_Del_p.S125fs|MTSS1_ENST00000378017.3_Intron|MTSS1_ENST00000431961.2_Intron	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	351	Ser-rich.				actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CTATAGTGAGAAAACCCGTTA	0.498																																					p.S351fs	Esophageal Squamous(160;622 1893 3862 8546 12509)	.											.	MTSS1-91	0			c.1051delT						.						22	23	23					8																	125570101		2196	4297	6493	SO:0001589	frameshift_variant	9788	exon11			.	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1051delT	8.37:g.125570101delA	ENSP00000429064:p.Ser351fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	56	17	NM_014751	0	0	0	0	0	J3KNK6|Q8TCA2|Q96RX2	Frame_Shift_Del	DEL	ENST00000518547.1	37	CCDS6353.1																																																																																			.		0.498	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		-	125570101	A	-	125570101	7	5	26	1	0	1	0	1	0	0	0	0	9987	246	9	0	1232	0	MTSS1	8	125570101	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	75736284	125570101	20793921	43	2274											
RFX3	5991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	3301560	3301560	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acttacatggctgttgagaaGagagcttctgtgagtggaca	11	11	13	6	0	1	3	0	2	1	2	1	6	1	4	0	2	2	3	0	2	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr9:3301560G>A	ENST00000382004.3	-	6	846	c.535C>T	c.(535-537)Ctt>Ttt	p.L179F	RFX3_ENST00000302303.1_Missense_Mutation_p.L179F|RFX3_ENST00000358730.2_Missense_Mutation_p.L179F	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	179					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		CTGTTGAGAAGAGAGCTTCTG	0.398																																					p.L179F		.											.	RFX3-93	0			c.C535T						.						157	135	143					9																	3301560		2203	4300	6503	SO:0001583	missense	5991	exon6			TGAGAAGAGAGCT	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.535C>T	9.37:g.3301560G>A	ENSP00000371434:p.Leu179Phe	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	87	44	NM_134428	0	0	0	0	0	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.832324	0.91036	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303;ENST00000451859	D;D;D;T	0.83075	-1.68;-1.68;-1.68;0.27	5.87	5.87	0.94306	.	0.137392	0.50627	D	0.000106	T	0.75110	0.3805	N	0.02011	-0.69	0.58432	D	0.999994	D;B;D	0.58620	0.983;0.037;0.965	P;B;P	0.55345	0.731;0.037;0.774	T	0.82536	-0.0408	10	0.56958	D	0.05	-9.8293	16.4906	0.84200	0.0:0.0:0.8686:0.1314	.	179;179;179	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	F	179	ENSP00000371434:L179F;ENSP00000351574:L179F;ENSP00000303847:L179F;ENSP00000411756:L179F	ENSP00000303847:L179F	L	-	1	0	RFX3	3291560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.781000	0.95711	0.655000	0.94253	CTT	.		0.398	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		A	3301560	G	A	3301560	3	1	26	1	0	0	0	0	1	0	0	0	13296	942	33	2	1922	2	RFX3	9	3301560	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		3301560	137911871	44	2275											
RASEF	158158	broad.mit.edu;bcgsc.ca	37	chr9	85637283	85637283	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttatgttctgcagcctgaaTcctctgatccatttcctctt	6	17	5	13	0	3	2	0	2	3	0	6	2	6	2	4	0	2	2	4	0	2	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr9:85637283T>G	ENST00000376447.3	-	3	897	c.637A>C	c.(637-639)Att>Ctt	p.I213L		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	213					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GCAGCCTGAATCCTCTGATCC	0.468																																					p.I213L													.	RASEF-280	0			c.A637C						.						276	237	250					9																	85637283		2203	4300	6503	SO:0001583	missense	158158	exon3			CCTGAATCCTCTG	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.637A>C	9.37:g.85637283T>G	ENSP00000365630:p.Ile213Leu	Somatic	95	2		WXS	Illumina HiSeq	Phase_I	69	27	NM_152573	0	0	4	7	3	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261658	0.59431	.	.	ENSG00000165105	ENST00000376447	T	0.61627	0.09	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.52757	0.1754	L	0.46947	1.48	0.80722	D	1	B	0.34329	0.449	B	0.35312	0.2	T	0.49322	-0.8952	10	0.25106	T	0.35	.	16.2792	0.82664	0.0:0.0:0.0:1.0	.	213	Q8IZ41	RASEF_HUMAN	L	213	ENSP00000365630:I213L	ENSP00000365630:I213L	I	-	1	0	RASEF	84827103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.504000	0.53347	2.243000	0.73865	0.533000	0.62120	ATT	.		0.468	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		G	85637283	T	G	85637283	3	3	26	1	0	0	0	0	1	0	0	0	13100	1435	50	5	1645	5	RASEF	9	85637283	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	82335723	85637283	55576148	45	2276											
EXOSC2	23404	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	133579154	133579154	+	Frame_Shift_Del	DEL	A	A	-																															ccagaggcttttggaacaggAgggataaggaggtgctccag																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr9:133579154delA	ENST00000372358.5	+	9	946	c.875delA	c.(874-876)gagfs	p.E292fs	EXOSC2_ENST00000372351.3_Frame_Shift_Del_p.E262fs|EXOSC2_ENST00000372352.3_Frame_Shift_Del_p.E284fs|EXOSC2_ENST00000546165.1_Frame_Shift_Del_p.E266fs|EXOSC2_ENST00000467138.1_3'UTR			Q13868	EXOS2_HUMAN	exosome component 2	292					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		TTGGAACAGGAGGGATAAGGA	0.478																																					p.E292fs	Pancreas(134;1683 1824 10118 27928 31640)	.											.	EXOSC2-91	0			c.875delA						.						118	127	124					9																	133579154		2203	4300	6503	SO:0001589	frameshift_variant	23404	exon9			.	AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.875delA	9.37:g.133579154delA	ENSP00000361433:p.Glu292fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	92	46	NM_014285	0	0	0	0	0	A3KFL3|B4DKK6|Q9NUY4	Frame_Shift_Del	DEL	ENST00000372358.5	37	CCDS6935.1																																																																																			.		0.478	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285		-	133579154	A	-	133579154	7	5	26	1	0	1	0	1	0	0	0	0	5328	304	11	0	909	0	EXOSC2	9	133579154	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	47941871	133579154	7634277	46	2277											
CYP26C1	340665	broad.mit.edu	37	chr10	94828244	94828244	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccattacatcccgttcggCggcggtgcgcgcagctgcct	4	10	12	15	6	0	0	0	0	0	0	3	0	2	0	3	3	4	3	3	3	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr10:94828244C>A	ENST00000285949.5	+	6	1359	c.1359C>A	c.(1357-1359)ggC>ggA	p.G453G		NM_183374.2	NP_899230.2	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C, polypeptide 1	453					anterior/posterior pattern specification (GO:0009952)|central nervous system development (GO:0007417)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|organelle fusion (GO:0048284)|oxidation-reduction process (GO:0055114)|retinoic acid catabolic process (GO:0034653)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			central_nervous_system(1)|lung(3)|ovary(1)	5		Colorectal(252;0.122)				TCCCGTTCGGCGGCGGTGCGC	0.697																																					p.G453G													.	CYP26C1-90	0			c.C1359A						.						8	10	9					10																	94828244		1922	3896	5818	SO:0001819	synonymous_variant	340665	exon6			GTTCGGCGGCGGT		CCDS7425.1	10q23.33	2003-11-20			ENSG00000187553	ENSG00000187553		"Cytochrome P450s"	20577	protein-coding gene	gene with protein product		608428					Standard	XR_246086		Approved		uc010qns.2	Q6V0L0	OTTHUMG00000018766	ENST00000285949.5:c.1359C>A	10.37:g.94828244C>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	54	4	NM_183374	0	0	0	0	0	Q5VXH6	Silent	SNP	ENST00000285949.5	37	CCDS7425.1																																																																																			.		0.697	CYP26C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049409.2	NM_183374		A	94828244	C	A	94828244	2	1	26	1	0	0	0	0	0	0	0	1	4163	755	27	4		4	CYP26C1	10	94828244	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		94828244	40706503	47	2278											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1276776	1276776	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgactggcgaggtgcaaccGgtggcctgtgcggtgagtgg	5	8	20	8	3	0	2	0	2	0	0	0	3	0	2	2	6	3	1	2	6	1	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:1276776G>T	ENST00000529681.1	+	37	16112	c.16054G>T	c.(16054-16056)Ggt>Tgt	p.G5352C	MUC5B_ENST00000447027.1_Missense_Mutation_p.G5355C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5352					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		AGGTGCAACCGGTGGCCTGTG	0.746																																					p.G5352C		.											.	.	0			c.G16054T						.						6	7	7					11																	1276776		1853	3899	5752	SO:0001583	missense	727897	exon37			GCAACCGGTGGCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16054G>T	11.37:g.1276776G>T	ENSP00000436812:p.Gly5352Cys	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	62	4	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	7.246	0.602241	0.13939	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.17054	2.3;2.47	4.01	-2.42	0.06542	.	.	.	.	.	T	0.34513	0.0900	M	0.79475	2.455	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.977	T	0.16012	-1.0417	9	0.87932	D	0	.	5.244	0.15487	0.4649:0.181:0.3541:0.0	.	5689;5355	A7Y9J9;E9PBJ0	.;.	C	5352;5355;5296;251;5064	ENSP00000436812:G5352C;ENSP00000415793:G5355C	ENSP00000343037:G5296C	G	+	1	0	MUC5B	1233352	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-3.094000	0.00607	-0.833000	0.04245	0.448000	0.29417	GGT	.		0.746	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1276776	G	T	1276776	3	4	26	1	0	0	0	0	1	0	0	0	10004	1116	39	4	16209	4	MUC5B	11	1276776	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		1276776	133729740	48	2279											
OSBPL5	114879	ucsc.edu	37	chr11	3143330	3143330	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagttctccttctgcgccTgggcccggggcacccgcggt	2	9	15	15	4	2	0	0	0	2	0	3	0	2	0	4	5	1	3	4	5	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:3143330T>C	ENST00000263650.7	-	5	460		c.e5-2		OSBPL5_ENST00000542243.1_Splice_Site|OSBPL5_ENST00000348039.5_Splice_Site|OSBPL5_ENST00000389989.3_Splice_Site|OSBPL5_ENST00000525498.1_Splice_Site	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5						cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CTTCTGCGCCTGGGCCCGGGG	0.692																																					.													.	OSBPL5-113	0			c.301-2A>G						.						37	30	32					11																	3143330		2189	4290	6479	SO:0001630	splice_region_variant	114879	exon6			TGCGCCTGGGCCC	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.301-2A>G	11.37:g.3143330T>C		Somatic	33	0		WXS	Illumina HiSeq		39	4	NM_001144063	0	0	0	0	0	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Splice_Site	SNP	ENST00000263650.7	37	CCDS31344.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.066069	0.36470	.	.	ENSG00000021762	ENST00000263650;ENST00000389989;ENST00000525498;ENST00000542243;ENST00000348039;ENST00000533234;ENST00000526122	.	.	.	4.17	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3464	0.60575	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	OSBPL5	3099906	1.000000	0.71417	0.973000	0.42090	0.193000	0.23685	7.255000	0.78338	1.760000	0.52011	0.459000	0.35465	.	.		0.692	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		Intron	C	3143330	T	C	3143330	5	2	26	1	0	0	0	0	0	0	1	0	11306	1594	55	3	2412	3	OSBPL5	11	3143330	Splice_Site	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	1866554	3143330	131863186	49	2280											
DTX4	23220	ucsc.edu;bcgsc.ca	37	chr11	58949824	58949824	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gacaaccatgggctctcctgCcagtcccccaggacccaaca	10	5	8	18	0	1	0	0	0	1	0	3	2	2	1	6	2	3	1	6	2	2	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:58949824C>T	ENST00000227451.3	+	2	928	c.824C>T	c.(823-825)gCc>gTc	p.A275V	DTX4_ENST00000532982.1_Missense_Mutation_p.A169V	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	275					innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				GGCTCTCCTGCCAGTCCCCCA	0.642																																					p.A275V													.	DTX4-501	0			c.C824T						.						26	37	33					11																	58949824		2040	4177	6217	SO:0001583	missense	23220	exon2			CTCCTGCCAGTCC	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"RING-type (C3HC4) zinc fingers"	29151	protein-coding gene	gene with protein product			"deltex 4 homolog (Drosophila)", "deltex homolog 4 (Drosophila)"			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.824C>T	11.37:g.58949824C>T	ENSP00000227451:p.Ala275Val	Somatic	30	0		WXS	Illumina HiSeq		32	4	NM_015177	0	0	2	2	0	Q0VF38	Missense_Mutation	SNP	ENST00000227451.3	37	CCDS44612.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.156869	0.38119	.	.	ENSG00000110042	ENST00000532982;ENST00000227451	T;T	0.11604	2.76;2.95	4.62	4.62	0.57501	.	0.565173	0.14508	U	0.315331	T	0.13114	0.0318	L	0.54323	1.7	0.36624	D	0.875918	P	0.37061	0.58	B	0.35114	0.196	T	0.15838	-1.0423	10	0.33940	T	0.23	.	14.4938	0.67670	0.0:1.0:0.0:0.0	.	275	Q9Y2E6	DTX4_HUMAN	V	169;275	ENSP00000434055:A169V;ENSP00000227451:A275V	ENSP00000227451:A275V	A	+	2	0	DTX4	58706400	0.999000	0.42202	0.997000	0.53966	0.943000	0.58893	3.118000	0.50414	2.410000	0.81850	0.655000	0.94253	GCC	.		0.642	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213		T	58949824	C	T	58949824	3	4	26	1	0	0	0	0	1	0	0	0	4808	739	26	2	830	2	DTX4	11	58949824	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	55806494	58949824	76056692	50	2281											
SF3B2	10992	broad.mit.edu;bcgsc.ca	37	chr11	65826742	65826742	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caaactggagaactctgcagCccccaagaagaagggatttg	14	6	11	10	0	1	3	0	0	1	3	1	5	1	4	2	2	4	1	2	2	5	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:65826742C>T	ENST00000322535.6	+	11	1302	c.1253C>T	c.(1252-1254)gCc>gTc	p.A418V	SF3B2_ENST00000528302.1_Missense_Mutation_p.A401V	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	418					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AACTCTGCAGCCCCCAAGAAG	0.532																																					p.A418V													.	SF3B2-92	0			c.C1253T						.						62	55	58					11																	65826742		2201	4295	6496	SO:0001583	missense	10992	exon11			CTGCAGCCCCCAA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1253C>T	11.37:g.65826742C>T	ENSP00000318861:p.Ala418Val	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	141	6	NM_006842	0	0	152	153	1	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	37	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315405	0.23908	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.06	-0.939	0.10408	.	0.379232	0.29073	N	0.013223	T	0.23289	0.0563	L	0.27053	0.805	0.19575	N	0.999966	B	0.02656	0.0	B	0.04013	0.001	T	0.20140	-1.0284	9	0.18276	T	0.48	0.0053	8.4596	0.32921	0.0:0.4852:0.0:0.5148	.	418	Q13435	SF3B2_HUMAN	V	401;418;322	.	ENSP00000318861:A418V	A	+	2	0	SF3B2	65583318	0.339000	0.24784	0.028000	0.17463	0.984000	0.73092	0.269000	0.18589	-0.516000	0.06470	0.555000	0.69702	GCC	.		0.532	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			T	65826742	C	T	65826742	3	4	26	1	0	0	0	0	1	0	0	0	14183	739	26	2	1295	2	SF3B2	11	65826742	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	6876918	65826742	69179774	51	2282											
VPS26B	112936	broad.mit.edu;bcgsc.ca	37	chr11	134095054	134095054	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcagagcgtggaggtggAaatccttctgaacgatgcag	10	7	16	8	3	1	2	0	1	1	1	2	5	2	4	1	4	3	2	1	4	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:134095054A>T	ENST00000281187.5	+	1	516	c.38A>T	c.(37-39)gAa>gTa	p.E13V	NCAPD3_ENST00000534548.2_5'Flank|NCAPD3_ENST00000526422.1_5'Flank|VPS26B_ENST00000525095.2_Missense_Mutation_p.E13V	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	13					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		GTGGAGGTGGAAATCCTTCTG	0.642																																					p.E13V	Colon(171;1263 1952 15904 45703 47982)												.	VPS26B-90	0			c.A38T						.						58	61	60					11																	134095054		2201	4297	6498	SO:0001583	missense	112936	exon1			AGGTGGAAATCCT		CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"vacuolar protein sorting 26 homolog B (yeast)"			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.38A>T	11.37:g.134095054A>T	ENSP00000281187:p.Glu13Val	Somatic	92	2		WXS	Illumina HiSeq	Phase_I	89	44	NM_052875	0	0	5	7	2	Q96A55	Missense_Mutation	SNP	ENST00000281187.5	37	CCDS8495.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.497538	0.85069	.	.	ENSG00000151502	ENST00000281187;ENST00000525095	.	.	.	4.82	4.82	0.62117	.	0.227351	0.44688	D	0.000426	T	0.76513	0.3998	M	0.86268	2.805	0.80722	D	1	B	0.27853	0.191	B	0.40329	0.326	T	0.78904	-0.2020	9	0.72032	D	0.01	0.1557	14.3603	0.66766	1.0:0.0:0.0:0.0	.	13	Q4G0F5	VP26B_HUMAN	V	13	.	ENSP00000281187:E13V	E	+	2	0	VPS26B	133600264	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.048000	0.93830	1.780000	0.52325	0.460000	0.39030	GAA	.		0.642	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393591.1	NM_052875		T	134095054	A	T	134095054	3	4	26	1	0	0	0	0	1	0	0	0	17231	246	9	5	40	5	VPS26B	11	134095054	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	68268312	134095054	911462	52	2283											
WNT10B	7480	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49362081	49362081	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagcagccagcatggagaagGaaaaagcactttctcggaaa	16	5	11	9	1	1	1	0	0	1	1	2	4	1	3	1	3	4	3	1	3	4	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr12:49362081G>T	ENST00000301061.4	-	4	707	c.359C>A	c.(358-360)tCc>tAc	p.S120Y	WNT10B_ENST00000407467.1_Missense_Mutation_p.S120Y|WNT10B_ENST00000403957.1_Missense_Mutation_p.S120Y	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	120					bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						CATGGAGAAGGAAAAAGCACT	0.572																																					p.S120Y													.	WNT10B-565	0			c.C359A						.						64	59	61					12																	49362081		2203	4300	6503	SO:0001583	missense	7480	exon4			GAGAAGGAAAAAG	X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"Wingless-type MMTV integration sites"	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.359C>A	12.37:g.49362081G>T	ENSP00000301061:p.Ser120Tyr	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	16	12	NM_003394	0	0	0	0	0	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Missense_Mutation	SNP	ENST00000301061.4	37	CCDS8775.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.82|10.82	1.457007|1.457007	0.26161|0.26161	.|.	.|.	ENSG00000169884|ENSG00000169884	ENST00000413630|ENST00000301061;ENST00000407467;ENST00000403957	T|T;T;T	0.79141|0.75938	-1.24|-0.98;-0.98;-0.98	5.01|5.01	4.12|4.12	0.48240|0.48240	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79452|0.79452	0.4448|0.4448	L|L	0.52573|0.52573	1.65|1.65	0.46586|0.46586	D|D	0.999111|0.999111	.|D;D	.|0.64830	.|0.994;0.973	.|D;P	.|0.64410	.|0.925;0.793	T|T	0.80111|0.80111	-0.1519|-0.1519	7|10	0.87932|0.87932	D|D	0|0	.|.	9.1429|9.1429	0.36914|0.36914	0.1709:0.0:0.8291:0.0|0.1709:0.0:0.8291:0.0	.|.	.|120;120	.|Q4VAJ4;O00744	.|.;WN10B_HUMAN	T|Y	132|120	ENSP00000398473:P132T|ENSP00000301061:S120Y;ENSP00000384691:S120Y;ENSP00000385980:S120Y	ENSP00000398473:P132T|ENSP00000301061:S120Y	P|S	-|-	1|2	0|0	WNT10B|WNT10B	47648348|47648348	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.797000|6.797000	0.75150|0.75150	1.256000|1.256000	0.44068|0.44068	0.491000|0.491000	0.48974|0.48974	CCT|TCC	.		0.572	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394		T	49362081	G	T	49362081	3	4	26	1	0	0	0	0	1	0	0	0	17416	1174	41	4	818	4	WNT10B	12	49362081	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		49362081	84489814	53	2284											
BAZ2A	11176	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57006901	57006901	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagactgaaggcagtagcatTattgagggaagggcaatcaa	15	7	14	5	0	1	3	1	2	0	1	1	5	1	4	0	3	1	4	0	3	6	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr12:57006901T>A	ENST00000551812.1	-	5	1232	c.1039A>T	c.(1039-1041)Aat>Tat	p.N347Y	BAZ2A_ENST00000179765.5_Missense_Mutation_p.N315Y|BAZ2A_ENST00000549884.1_Missense_Mutation_p.N345Y|BAZ2A_ENST00000379441.3_Missense_Mutation_p.N317Y	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	347					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						GCAGTAGCATTATTGAGGGAA	0.512																																					p.N347Y													.	BAZ2A-22	0			c.A1039T						.						126	128	127					12																	57006901		2020	4186	6206	SO:0001583	missense	11176	exon5			TAGCATTATTGAG	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.1039A>T	12.37:g.57006901T>A	ENSP00000446880:p.Asn347Tyr	Somatic	88	1		WXS	Illumina HiSeq	Phase_I	122	57	NM_013449	0	0	2	8	6	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663979	0.67700	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.14	5.14	0.70334	.	0.666605	0.15507	N	0.258746	T	0.40297	0.1111	N	0.14661	0.345	0.30496	N	0.77083	P;B	0.36837	0.571;0.435	B;B	0.35607	0.206;0.102	T	0.49606	-0.8922	10	0.87932	D	0	-27.8089	9.888	0.41272	0.0:0.0:0.279:0.721	.	345;347	F8VU39;Q9UIF9	.;BAZ2A_HUMAN	Y	317;315;347;345	ENSP00000368754:N317Y;ENSP00000179765:N315Y;ENSP00000446880:N347Y;ENSP00000447941:N345Y	ENSP00000179765:N315Y	N	-	1	0	BAZ2A	55293168	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.938000	0.40203	2.291000	0.77112	0.533000	0.62120	AAT	.		0.512	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	57006901	T	A	57006901	3	1	26	1	0	0	0	0	1	0	0	0	1332	1754	61	5	4778	5	BAZ2A	12	57006901	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	7644820	57006901	76844994	54	2285											
TMTC2	160335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	83251132	83251132	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgggacgagccgatgtcGgggccagtctcttctttctc	4	12	13	12	4	3	0	0	0	3	0	7	3	3	1	2	3	1	0	2	3	0	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr12:83251132G>T	ENST00000321196.3	+	2	1134	c.427G>T	c.(427-429)Ggg>Tgg	p.G143W	TMTC2_ENST00000548305.1_Missense_Mutation_p.G143W|TMTC2_ENST00000549919.1_Missense_Mutation_p.G137W	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	143					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						AGCCGATGTCGGGGCCAGTCT	0.547																																					p.G143W		.											.	TMTC2-92	0			c.G427T						.						115	95	102					12																	83251132		2203	4300	6503	SO:0001583	missense	160335	exon2			GATGTCGGGGCCA	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.427G>T	12.37:g.83251132G>T	ENSP00000322300:p.Gly143Trp	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	84	37	NM_152588	0	0	0	1	1	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146896	0.77888	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	T;T;T	0.60797	0.82;0.16;0.72	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.78342	0.4268	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.80171	-0.1493	10	0.72032	D	0.01	-15.2295	18.1624	0.89712	0.0:0.0:1.0:0.0	.	143;143	Q8N394;F8VSH2	TMTC2_HUMAN;.	W	143;143;137	ENSP00000322300:G143W;ENSP00000448292:G143W;ENSP00000447609:G137W	ENSP00000322300:G143W	G	+	1	0	TMTC2	81775263	1.000000	0.71417	0.941000	0.38009	0.945000	0.59286	9.174000	0.94824	2.788000	0.95919	0.650000	0.86243	GGG	.		0.547	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		T	83251132	G	T	83251132	3	4	26	1	0	0	0	0	1	0	0	0	16293	1116	39	4	433	4	TMTC2	12	83251132	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	26244231	83251132	50600763	55	2286											
FOXA1	3169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	38060788	38060788	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacatgaggttgttgatggAgaacgggtggttgaaggagt	10	10	19	2	1	0	4	0	3	0	1	0	7	0	6	0	6	1	3	0	6	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr14:38060788A>T	ENST00000250448.2	-	2	1262	c.1201T>A	c.(1201-1203)Tcc>Acc	p.S401T	FOXA1_ENST00000540786.1_Missense_Mutation_p.S368T|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	401					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		TTGTTGATGGAGAACGGGTGG	0.602																																					p.S401T		.											.	FOXA1-226	0			c.T1201A						.						109	78	89					14																	38060788		2203	4300	6503	SO:0001583	missense	3169	exon2			TGATGGAGAACGG	U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"Forkhead boxes"	5021	protein-coding gene	gene with protein product		602294	"hepatocyte nuclear factor 3, alpha"	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.1201T>A	14.37:g.38060788A>T	ENSP00000250448:p.Ser401Thr	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	116	63	NM_004496	0	0	1	1	0	B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	ENST00000250448.2	37	CCDS9665.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.861765	0.71949	.	.	ENSG00000129514	ENST00000250448;ENST00000540786	T;T	0.72051	-0.62;-0.62	4.29	4.29	0.51040	Forkhead box protein, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83727	0.5317	M	0.83384	2.64	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.86303	0.1681	10	0.87932	D	0	.	12.5253	0.56083	1.0:0.0:0.0:0.0	.	401	P55317	FOXA1_HUMAN	T	401;368	ENSP00000250448:S401T;ENSP00000440178:S368T	ENSP00000250448:S401T	S	-	1	0	FOXA1	37130539	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.050000	0.93843	1.798000	0.52647	0.329000	0.21502	TCC	.		0.602	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1			T	38060788	A	T	38060788	3	4	26	1	0	0	0	0	1	0	0	0	6008	304	11	5	221	5	FOXA1	14	38060788	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10		38060788	69288752	56	2287											
C14orf169	399671	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	73959009	73959009	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accagcgcaatacctggggtGacttcttagaggccatactg	10	9	11	11	1	1	2	0	1	1	1	1	2	1	2	3	3	3	1	3	3	4	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr14:73959009G>A	ENST00000553558.1	-	17	3166				C14orf169_ENST00000531973.1_RNA|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4											breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TACCTGGGGTGACTTCTTAGA	0.542																																					.													.	.	0			.						.						74	75	75					14																	73959009		2042	4191	6233	SO:0001627	intron_variant	79697	.			TGGGGTGACTTCT	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2844+760C>T	14.37:g.73959009G>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	53	24	.	0	0	8	13	5	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2																																																																																			.		0.542	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		A	73959009	G	A	73959009	1	1	26	0	1	0	0	0	0	0	0	0	1762	1277	45	2		2	C14orf169	14	73959009	Intron	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	35898221	73959009	33390531	57	2288											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493794	77493794	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgctgctgTtgctgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1	rs377151545|rs28718623|rs71125518	byFrequency	TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr14:77493794T>C	ENST00000238647.3	-	1	1240	c.342A>G	c.(340-342)caA>caG	p.Q114Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	114	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgttgctgctgct	0.697													T|||	1146	0.228834	0.1649	0.1758	5008	,	,		5976	0.2659		0.2614	False		,,,				2504	0.2812				p.Q114Q		.											.	IRF2BPL-90	0			c.A342G						.	-		160,2330		6,148,1091	2	2	2		342	0.6	0	14	dbSNP_125	2	324,4012		7,310,1851	no	coding-synonymous	IRF2BPL	NM_024496.2		13,458,2942	CC,CT,TT		7.4723,6.4257,7.0905		114/797	77493794	484,6342	1245	2168	3413	SO:0001819	synonymous_variant	64207	exon1			CTGCTGTTGCTGC	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.342A>G	14.37:g.77493794T>C		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	6	5	NM_024496	4	11	69	9962	9878	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			.		0.697	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		C	77493794	T	C	77493794	2	2	26	1	0	0	0	0	0	0	0	1	1777	1722	60	3		3	C14orf4	14	77493794	Silent	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	3534785	77493794	29855746	58	2289											
RAGE	5891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102718326	102718326	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttctgataatgggtatCttctccctgtacaatcaagg	9	17	7	8	0	4	1	1	1	3	0	5	1	4	1	1	2	1	2	1	2	5	7			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr14:102718326C>A	ENST00000361847.2	-	5	521	c.290G>T	c.(289-291)aGa>aTa	p.R97I	MOK_ENST00000524214.1_Missense_Mutation_p.R67I|MOK_ENST00000193029.6_5'UTR|MOK_ENST00000522874.1_Missense_Mutation_p.R97I	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	97	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TAATGGGTATCTTCTCCCTGT	0.333																																					p.R97I		.											.	.	0			c.G290T						.						73	80	78					14																	102718326		2203	4299	6502	SO:0001583	missense	5891	exon5			GGGTATCTTCTCC	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"renal tumor antigen"	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.290G>T	14.37:g.102718326C>A	ENSP00000355304:p.Arg97Ile	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	130	60	NM_014226	0	0	0	0	0	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703155	0.48412	.	.	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.45668	0.89;0.89;0.89	5.42	4.52	0.55395	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.177262	0.50627	D	0.000113	T	0.49762	0.1576	L	0.55481	1.735	0.80722	D	1	D;D	0.53151	0.958;0.958	P;P	0.55667	0.781;0.781	T	0.51395	-0.8711	10	0.72032	D	0.01	-8.7163	8.6721	0.34156	0.0:0.765:0.154:0.081	.	67;97	E7ERR8;Q9UQ07	.;MOK_HUMAN	I	97;97;67	ENSP00000429469:R97I;ENSP00000355304:R97I;ENSP00000428942:R67I	ENSP00000355304:R97I	R	-	2	0	RAGE	101788079	1.000000	0.71417	0.988000	0.46212	0.863000	0.49368	1.056000	0.30480	1.273000	0.44346	0.650000	0.86243	AGA	.		0.333	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3			A	102718326	C	A	102718326	3	1	26	1	0	0	0	0	1	0	0	0	13038	913	32	4	1001	4	RAGE	14	102718326	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	25224532	102718326	4631214	59	2290											
C15orf56	644809	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	40544920	40544920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccccggctgccccggaggttCgcggcgagaggacgggcctc	4	4	17	16	6	0	1	0	0	0	1	2	4	0	3	5	6	1	2	5	6	0	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr15:40544920C>T	ENST00000319503.3	-	1	191	c.170G>A	c.(169-171)cGa>cAa	p.R57Q	C15orf56_ENST00000559727.1_Missense_Mutation_p.R57Q|PAK6_ENST00000560346.1_Intron|PAK6_ENST00000260404.4_Intron|PAK6_ENST00000455577.2_Intron|RP11-133K1.2_ENST00000558658.1_Intron|PAK6_ENST00000453867.1_Intron|PAK6_ENST00000441369.1_Intron|PAK6_ENST00000542403.2_5'Flank	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	57										lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CCCGGAGGTTCGCGGCGAGAG	0.756																																					p.R57Q		.											.	C15orf56-68	0			c.G170A						.						4	5	5					15																	40544920		2008	3995	6003	SO:0001583	missense	644809	exon1			GAGGTTCGCGGCG		CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.170G>A	15.37:g.40544920C>T	ENSP00000315794:p.Arg57Gln	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	137	59	NM_001039905	0	0	1	1	0		Missense_Mutation	SNP	ENST00000319503.3	37	CCDS32197.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.440220	0.25900	.	.	ENSG00000176753	ENST00000319503	T	0.30714	1.52	2.0	-1.71	0.08133	.	.	.	.	.	T	0.10035	0.0246	N	0.08118	0	0.09310	N	0.999999	P	0.44241	0.829	B	0.29353	0.101	T	0.17868	-1.0355	9	0.87932	D	0	.	3.9423	0.09333	0.0:0.3247:0.4801:0.1952	.	57	Q8N910	CO056_HUMAN	Q	57	ENSP00000315794:R57Q	ENSP00000315794:R57Q	R	-	2	0	C15orf56	38332212	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.435000	0.07264	-1.253000	0.01494	CGA	.		0.756	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905		T	40544920	C	T	40544920	3	4	26	1	0	0	0	0	1	0	0	0	1808	884	31	1	323	1	C15orf56	15	40544920	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		40544920	61986472	60	2291											
CASC5	57082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	40914359	40914359	+	Frame_Shift_Del	DEL	A	A	-																															cagacataatagccaaaaacAgcttaaccgacacctggaac																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr15:40914359delA	ENST00000346991.5	+	11	2365	c.1975delA	c.(1975-1977)agcfs	p.S659fs	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Frame_Shift_Del_p.S633fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	659	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AGCCAAAAACAGCTTAACCGA	0.388																																					p.S659fs		.											.	CASC5-660	0			c.1975delA						.						82	79	80					15																	40914359		1881	4102	5983	SO:0001589	frameshift_variant	57082	exon11			.	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1975delA	15.37:g.40914359delA	ENSP00000335463:p.Ser659fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	111	45	NM_170589	0	0	0	0	0	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	37	CCDS42023.1																																																																																			.		0.388	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40914359	A	-	40914359	7	5	26	1	0	1	0	1	0	0	0	0	2669	188	7	0	2013	0	CASC5	15	40914359	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	369439	40914359	61617033	61	2292											
EME2	197342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1826070	1826070	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctttgcctgctcctaggCgctggaggcctgcagcacgg	4	9	14	14	2	0	0	0	0	0	0	1	1	1	1	4	4	5	4	4	4	1	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:1826070C>T	ENST00000568449.1	+	8	992	c.971C>T	c.(970-972)gCg>gTg	p.A324V	MRPS34_ENST00000177742.3_5'Flank|MRPS34_ENST00000397375.2_5'Flank|EME2_ENST00000307394.7_Splice_Site_p.A389V	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	324					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						TGCTCCTAGGCGCTGGAGGCC	0.726								Direct reversal of damage;Homologous recombination																													p.A324V		.											.	EME2-229	0			c.C971T						.						20	23	22					16																	1826070		2187	4278	6465	SO:0001630	splice_region_variant	197342	exon8			CCTAGGCGCTGGA	AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"	610886	"essential meiotic endonuclease 1 homolog 2 (S. pombe)"			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.970-1C>T	16.37:g.1826070C>T		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	62	22	NM_001257370	0	0	0	0	0	Q8TEP2|Q96RY3	Missense_Mutation	SNP	ENST00000568449.1	37	CCDS58404.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.716192	0.68844	.	.	ENSG00000197774	ENST00000307394;ENST00000454910	.	.	.	3.4	2.43	0.29744	ERCC4 domain (2);	0.097008	0.41396	D	0.000895	T	0.75664	0.3880	M	0.80847	2.515	0.53688	D	0.999978	D;D	0.89917	1.0;0.977	D;B	0.91635	0.999;0.425	T	0.74405	-0.3676	9	0.49607	T	0.09	-7.8093	8.3214	0.32132	0.0:0.883:0.0:0.117	.	338;190	A4GXA9;A4GXA9-2	EME2_HUMAN;.	V	389;345	.	ENSP00000303779:A389V	A	+	2	0	EME2	1766071	0.931000	0.31567	0.515000	0.27774	0.021000	0.10359	1.875000	0.39578	0.756000	0.33013	0.561000	0.74099	GCG	.		0.726	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865	Missense_Mutation	T	1826070	C	T	1826070	5	4	26	1	0	0	0	0	0	0	1	0	5102	782	27	1	1196	1	EME2	16	1826070	Splice_Site	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		1826070	88528683	62	2293											
ABCA3	21	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2369834	2369834	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acggccaggaagccttcccgGatgtaccctgggtgcgggag	7	6	16	12	3	0	0	0	0	0	0	1	3	1	3	4	5	3	1	4	5	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:2369834G>C	ENST00000301732.5	-	8	1321	c.621C>G	c.(619-621)atC>atG	p.I207M	ABCA3_ENST00000382381.3_Missense_Mutation_p.I207M	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	207					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	AGCCTTCCCGGATGTACCCTG	0.652																																					p.I207M		.											.	ABCA3-1015	0			c.C621G						.						71	62	65					16																	2369834		2198	4300	6498	SO:0001583	missense	21	exon8			TTCCCGGATGTAC	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"ATP binding cassette transporters / subfamily A"	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.621C>G	16.37:g.2369834G>C	ENSP00000301732:p.Ile207Met	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	33	10	NM_001089	0	0	0	0	0	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419127	0.25552	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.89939	-2.59	5.04	3.05	0.35203	.	0.339378	0.32314	N	0.006271	D	0.91858	0.7423	M	0.78637	2.42	0.80722	D	1	B;P;B	0.37370	0.302;0.592;0.287	B;P;B	0.54590	0.297;0.756;0.217	D	0.89048	0.3453	10	0.42905	T	0.14	.	6.8397	0.23955	0.148:0.1482:0.7038:0.0	.	207;269;207	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	M	207;269	ENSP00000301732:I207M	ENSP00000301732:I207M	I	-	3	3	ABCA3	2309835	1.000000	0.71417	0.843000	0.33291	0.138000	0.21146	3.628000	0.54259	0.688000	0.31529	0.655000	0.94253	ATC	.		0.652	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		C	2369834	G	C	2369834	3	2	26	1	0	0	0	0	1	0	0	0	33	1164	41	4	4597	4	ABCA3	16	2369834	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	543764	2369834	87984919	63	2294											
ADCY9	115	hgsc.bcm.edu;bcgsc.ca	37	chr16	4042307	4042307	+	Frame_Shift_Del	DEL	C	C	-																															ctgactgttggtgagcttctCctcttggggagggctgagga																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:4042307delC	ENST00000294016.3	-	5	2585	c.2047delG	c.(2047-2049)gagfs	p.E683fs	ADCY9_ENST00000571889.1_Intron	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	683					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GTGAGCTTCTCCTCTTGGGGA	0.582																																					p.E683fs		.											.	ADCY9-139	0			c.2047delG						.						72	67	69					16																	4042307		2197	4300	6497	SO:0001589	frameshift_variant	115	exon5			.	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2047delG	16.37:g.4042307delC	ENSP00000294016:p.Glu683fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	76	26	NM_001116	0	0	0	0	0	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Frame_Shift_Del	DEL	ENST00000294016.3	37	CCDS32382.1																																																																																			.		0.582	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			-	4042307	C	-	4042307	7	5	26	1	0	1	0	1	0	0	0	0	301	864	30	0	2042	0	ADCY9	16	4042307	Frame_Shift_Del	DEL	C	TCGA-A4-A5Y0-01A-11D-A31X-10	1672473	4042307	86312446	64	2295											
PRM3	5620	hgsc.bcm.edu	37	chr16	11367405	11367405	+	IGR	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgtgctgtggcctgggctGtggcctgggctctggcctgt	0	11	17	13	1	1	0	0	0	1	0	1	0	1	0	4	5	1	3	4	5	0	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:11367405G>C	ENST00000241808.4	-	0	680				PRM3_ENST00000327157.2_Missense_Mutation_p.H16Q|RMI2_ENST00000572173.1_Intron|SNORA48_ENST00000390926.1_RNA	NM_002762.2	NP_002753.2	P04554	PRM2_HUMAN	protamine 2						cell differentiation (GO:0030154)|chromosome condensation (GO:0030261)|DNA packaging (GO:0006323)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.0?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)	7						ggcctgggctgtggcctgggc	0.617																																					p.H16Q		.											.	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C48G						.						28	30	29					16																	11367405		1980	4149	6129	SO:0001628	intergenic_variant	58531	exon1			TGGGCTGTGGCCT		CCDS42118.1, CCDS66944.1	16p13.13	2013-10-17			ENSG00000122304	ENSG00000122304			9448	protein-coding gene	gene with protein product	"cancer/testis antigen family 94, member 2"	182890				16632464	Standard	NM_001286356		Approved	CT94.2	uc002dau.1	P04554	OTTHUMG00000172317		16.37:g.11367405G>C		Somatic	15	0		WXS	Illumina HiSeq	Phase_I	21	7	NM_021247	0	0	0	0	0	Q6ZMM0	Missense_Mutation	SNP	ENST00000241808.4	37	CCDS42118.1	.	.	.	.	.	.	.	.	.	.	G	2.311	-0.357977	0.05138	.	.	ENSG00000178257	ENST00000327157	T	0.53640	0.61	0.559	-1.12	0.09808	.	.	.	.	.	T	0.39963	0.1098	N	0.19112	0.55	0.09310	N	0.999999	P	0.47106	0.89	P	0.55055	0.767	T	0.31081	-0.9956	8	0.66056	D	0.02	.	.	.	.	.	16	Q9NNZ6	PRM3_HUMAN	Q	16	ENSP00000325638:H16Q	ENSP00000325638:H16Q	H	-	3	2	PRM3	11274906	0.193000	0.23313	0.002000	0.10522	0.005000	0.04900	-0.194000	0.09559	-1.041000	0.03266	-1.036000	0.02392	CAC	.		0.617	PRM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417808.1			C	11367405	G	C	11367405	1	2	26	0	1	0	0	0	0	0	0	0	12563	1368	48	4		4	PRM3	16	11367405	IGR	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	7325098	11367405	78987348	65	2296											
DCTPP1	79077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30435583	30435583	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctggcctgtggagtcacAgggaatgtccgcaggcccca	7	7	15	12	1	2	0	1	0	1	0	3	2	3	2	4	5	0	1	4	5	1	0	rs36092481		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:30435583A>T	ENST00000319285.4	-	3	578	c.484T>A	c.(484-486)Tgt>Agt	p.C162S	DCTPP1_ENST00000565758.1_Missense_Mutation_p.C41S|ZNF771_ENST00000566625.1_Intron|DCTPP1_ENST00000568973.1_Missense_Mutation_p.C41S|DCTPP1_ENST00000567983.1_Missense_Mutation_p.C63S|DCTPP1_ENST00000568434.1_Missense_Mutation_p.C41S	NM_024096.1	NP_077001.1	Q9H773	DCTP1_HUMAN	dCTP pyrophosphatase 1	162					nucleoside triphosphate catabolic process (GO:0009143)|protein homotetramerization (GO:0051289)	cytosol (GO:0005829)	dCTP diphosphatase activity (GO:0047840)|magnesium ion binding (GO:0000287)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|pyrimidine deoxyribonucleotide binding (GO:0032556)			kidney(1)|large_intestine(3)|upper_aerodigestive_tract(1)	5						GTGGAGTCACAGGGAATGTCC	0.597																																					p.C162S		.											.	DCTPP1-90	0			c.T484A						.						40	37	38					16																	30435583		2197	4300	6497	SO:0001583	missense	79077	exon3			AGTCACAGGGAAT	BC001344	CCDS10680.1	16p11.2	2009-02-11			ENSG00000179958	ENSG00000179958	3.6.1.12		28777	protein-coding gene	gene with protein product	"XTP3-transactivated protein A"	615840				15740738	Standard	NM_024096		Approved	MGC5627, RS21C6, CDA03, XTP3TPA	uc002dyf.3	Q9H773	OTTHUMG00000132416	ENST00000319285.4:c.484T>A	16.37:g.30435583A>T	ENSP00000322524:p.Cys162Ser	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	80	43	NM_024096	0	0	35	77	42		Missense_Mutation	SNP	ENST00000319285.4	37	CCDS10680.1	.	.	.	.	.	.	.	.	.	.	A	1.012	-0.687538	0.03328	.	.	ENSG00000179958	ENST00000319285	.	.	.	3.72	-0.855	0.10700	.	1.452180	0.04273	N	0.342559	T	0.23611	0.0571	N	0.20685	0.6	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.17531	-1.0366	9	0.05525	T	0.97	-32.526	6.9119	0.24340	0.5009:0.0:0.4991:0.0	.	162	Q9H773	DCTP1_HUMAN	S	162	.	ENSP00000322524:C162S	C	-	1	0	DCTPP1	30343084	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.017000	0.12590	-0.100000	0.12241	-0.353000	0.07706	TGT	.		0.597	DCTPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255553.2	NM_024096		T	30435583	A	T	30435583	3	4	26	1	0	0	0	0	1	0	0	0	4318	188	7	5	32	5	DCTPP1	16	30435583	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	19068178	30435583	59919170	66	2297											
DHX38	9785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72142801	72142801	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccccagattacatagtgtatCacgagttggtcatgaccacc	11	10	8	12	1	2	2	2	1	0	1	2	3	2	2	4	1	1	2	4	1	3	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:72142801C>T	ENST00000268482.3	+	24	3867	c.3358C>T	c.(3358-3360)Cac>Tac	p.H1120Y	DHX38_ENST00000536867.1_Missense_Mutation_p.H432Y	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	1120					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CATAGTGTATCACGAGTTGGT	0.542																																					p.H1120Y	Melanoma(97;711 1442 7855 13832 28836)	.											.	DHX38-227	0			c.C3358T						.						78	64	69					16																	72142801		2198	4300	6498	SO:0001583	missense	9785	exon24			GTGTATCACGAGT	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.3358C>T	16.37:g.72142801C>T	ENSP00000268482:p.His1120Tyr	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	62	23	NM_014003	0	0	14	26	12	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922424	0.92319	.	.	ENSG00000140829	ENST00000268482;ENST00000536867	T;T	0.02656	4.21;4.21	5.14	5.14	0.70334	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.22126	0.0533	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.02683	-1.1124	10	0.52906	T	0.07	.	18.8078	0.92045	0.0:1.0:0.0:0.0	.	432;1120	B4DVG8;Q92620	.;PRP16_HUMAN	Y	1120;432	ENSP00000268482:H1120Y;ENSP00000437898:H432Y	ENSP00000268482:H1120Y	H	+	1	0	DHX38	70700302	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	7.097000	0.76967	2.677000	0.91161	0.655000	0.94253	CAC	.		0.542	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		T	72142801	C	T	72142801	3	4	26	1	0	0	0	0	1	0	0	0	4522	826	29	2	3448	2	DHX38	16	72142801	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	41707218	72142801	18211952	67	2298											
MYH13	8735	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	10215392	10215392	+	Splice_Site	DEL	A	A	-																															tttgcttccactctgcaaggAcctgggagatgacaaaggga																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:10215392delA	ENST00000418404.3	-	31	4530	c.4367delT	c.(4366-4368)gtc>gc	p.V1456fs	MYH13_ENST00000252172.4_Splice_Site_p.V1456fs|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1456					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CTCTGCAAGGACCTGGGAGAT	0.517																																					p.V1456fs		.											.	MYH13-6	0			c.4367delT						.						56	54	55					17																	10215392		1981	4180	6161	SO:0001630	splice_region_variant	8735	exon32			.	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.4366-1T>-	17.37:g.10215392delA		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	93	30	NM_003802	0	0	0	0	0	O95252|Q9P0U8	Frame_Shift_Del	DEL	ENST00000418404.3	37	CCDS45613.1																																																																																			.		0.517	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	Frame_Shift_Del	-	10215392	A	-	10215392	8	5	26	1	0	1	0	1	0	0	1	0	10057	289	10	0	1489	0	MYH13	17	10215392	Splice_Site	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10		10215392	70979818	68	2299											
NCOR1	9611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	15971431	15971431	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagacttgttagaagaaatTgtaactggaaaaaaagagcc	18	9	10	4	0	0	4	0	0	0	4	0	5	0	5	1	1	2	3	1	1	8	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:15971431T>G	ENST00000268712.3	-	32	4775	c.4518A>C	c.(4516-4518)acA>acC	p.T1506T	NCOR1_ENST00000395857.3_Silent_p.T90T|NCOR1_ENST00000395851.1_Silent_p.T1522T	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1506	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TAGAAGAAATTGTAACTGGAA	0.403																																					p.T1522T		.											.	NCOR1-229	0			c.A4566C						.						33	33	33					17																	15971431		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon31			AGAAATTGTAACT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4518A>C	17.37:g.15971431T>G		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	117	32	NM_001190440	0	0	0	0	0	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.162182	0.38217	.	.	ENSG00000141027	ENST00000395849	.	.	.	5.76	-9.98	0.00438	.	.	.	.	.	.	.	.	.	.	.	0.36017	D	0.8385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3886	0.07281	0.1594:0.3155:0.0807:0.4444	.	.	.	.	.	-1	.	.	.	-	.	.	NCOR1	15912156	0.000000	0.05858	0.041000	0.18516	0.927000	0.56198	-0.918000	0.04021	-1.256000	0.02478	0.460000	0.39030	.	.		0.403	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15971431	T	G	15971431	2	3	26	1	0	0	0	0	0	0	0	1	10261	1799	63	5		5	NCOR1	17	15971431	Silent	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	5756039	15971431	65223779	69	2300											
CCR7	1236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38711306	38711306	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accccattgtagggcagctgGaagactatgaagaccacgac	13	6	11	11	1	0	3	0	1	0	2	0	5	0	4	3	2	1	3	3	2	4	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:38711306G>T	ENST00000246657.2	-	3	887	c.825C>A	c.(823-825)ttC>ttA	p.F275L	CCR7_ENST00000579344.1_Missense_Mutation_p.F269L	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	275					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				AGGGCAGCTGGAAGACTATGA	0.552																																					p.F275L		.											.	CCR7-659	0			c.C825A						.						209	173	185					17																	38711306		2203	4300	6503	SO:0001583	missense	1236	exon3			CAGCTGGAAGACT		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.825C>A	17.37:g.38711306G>T	ENSP00000246657:p.Phe275Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	129	41	NM_001838	0	0	0	0	0		Missense_Mutation	SNP	ENST00000246657.2	37	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286284	0.80803	.	.	ENSG00000126353	ENST00000246657	T	0.35973	1.28	5.83	5.83	0.93111	GPCR, rhodopsin-like superfamily (1);	0.225560	0.45867	D	0.000323	T	0.43033	0.1229	L	0.58669	1.825	0.80722	D	1	B	0.22541	0.071	B	0.30401	0.115	T	0.18023	-1.0350	10	0.35671	T	0.21	.	20.1082	0.97900	0.0:0.0:1.0:0.0	.	275	P32248	CCR7_HUMAN	L	275	ENSP00000246657:F275L	ENSP00000246657:F275L	F	-	3	2	CCR7	35964832	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.869000	0.99810	2.764000	0.94973	0.555000	0.69702	TTC	.		0.552	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			T	38711306	G	T	38711306	3	4	26	1	0	0	0	0	1	0	0	0	2952	1165	41	4	315	4	CCR7	17	38711306	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	22739875	38711306	42483904	70	2301											
SLC4A1	6521	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42335911	42335911	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatcggtgggaggcagcacTaggctgcagtccaggaagcc	9	5	16	11	1	0	0	0	0	0	0	2	2	1	2	2	5	3	5	2	5	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:42335911T>A	ENST00000262418.6	-	10	1112	c.957A>T	c.(955-957)ctA>ctT	p.L319L	SLC4A1_ENST00000471005.1_5'Flank|AC003043.1_ENST00000597382.1_Intron	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	319	Dimerization arm.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GAGGCAGCACTAGGCTGCAGT	0.632																																					p.L319L													.	SLC4A1-92	0			c.A957T						.						46	47	47					17																	42335911		2203	4300	6503	SO:0001819	synonymous_variant	6521	exon10			CAGCACTAGGCTG		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"CD molecules", "Blood group antigens", "Solute carriers"	11027	protein-coding gene	gene with protein product	"Froese blood group", "Swann blood group", "Wright blood group"	109270	"Waldner blood group", "erythrocyte membrane protein band 3", "Diego blood group", "solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)", "solute carrier family 4 (anion exchanger), member 1"	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.957A>T	17.37:g.42335911T>A		Somatic	118	1		WXS	Illumina HiSeq	Phase_I	189	56	NM_000342	0	0	0	0	0	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Silent	SNP	ENST00000262418.6	37	CCDS11481.1																																																																																			.		0.632	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		A	42335911	T	A	42335911	2	1	26	1	0	0	0	0	0	0	0	1	14682	1509	53	5		5	SLC4A1	17	42335911	Silent	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	3624605	42335911	38859299	71	2302											
PPP1R9B	84687	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48216644	48216644	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctttcttttcagctgcTggatctctgcctcagtgacc	5	16	7	13	0	4	1	2	1	2	0	5	2	4	2	3	1	4	2	3	1	1	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:48216644T>C	ENST00000316878.6	-	9	2053	c.2051A>G	c.(2050-2052)cAg>cGg	p.Q684R	PPP1R9B_ENST00000501501.2_5'UTR|AC002401.1_ENST00000451776.1_RNA	NM_032595.3	NP_115984.3	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	684	Interacts with TGN38. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to morphine (GO:0071315)|dendrite development (GO:0016358)|filopodium assembly (GO:0046847)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of cell proliferation (GO:0042127)|regulation of exit from mitosis (GO:0007096)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of protein phosphorylation (GO:0001932)|RNA splicing (GO:0008380)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|protein phosphatase type 1 complex (GO:0000164)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						TTTCAGCTGCTGGATCTCTGC	0.597																																					.													.	PPP1R9B-90	0			.						.						194	204	201					17																	48216644		2153	4255	6408	SO:0001583	missense	84687	.			AGCTGCTGGATCT	AJ401189	CCDS74102.1	17q21.33	2013-01-31	2011-10-04	2001-07-02	ENSG00000108819	ENSG00000108819		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9298	protein-coding gene	gene with protein product	"spinophilin", "Neurabin-2"	603325	"protein phosphatase 1, regulatory subunit 9B, spinophilin", "protein phosphatase 1, regulatory (inhibitor) subunit 9B"	PPP1R6, PPP1R9		9275233	Standard	NM_032595		Approved	Spn, SPINO	uc002iqh.4	Q96SB3	OTTHUMG00000162008	ENST00000316878.6:c.2051A>G	17.37:g.48216644T>C	ENSP00000475417:p.Gln684Arg	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	55	16	.	0	0	37	52	15	Q8TCR9	Missense_Mutation	SNP	ENST00000316878.6	37																																																																																				.		0.597	PPP1R9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032595		C	48216644	T	C	48216644	3	2	26	1	0	0	0	0	1	0	0	0	12408	1580	55	3	412	3	PPP1R9B	17	48216644	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	5880733	48216644	32978566	72	2303											
KIF2B	84643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	51901648	51901648	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acttccaggcaaacacctgtCaacgctcactcatccaggag	12	7	7	15	1	3	0	3	0	0	0	5	1	5	1	3	2	2	2	3	2	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:51901648C>T	ENST00000268919.4	+	1	1410	c.1254C>T	c.(1252-1254)gtC>gtT	p.V418V		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	418	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAACACCTGTCAACGCTCACT	0.512																																					p.V418V		.											.	KIF2B-98	0			c.C1254T						.						102	76	85					17																	51901648		2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			ACCTGTCAACGCT	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"Kinesins"	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1254C>T	17.37:g.51901648C>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	221	68	NM_032559	0	0	0	0	0	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	37	CCDS32685.1																																																																																			.		0.512	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901648	C	T	51901648	2	4	26	1	0	0	0	0	0	0	0	1	8319	813	29	2		2	KIF2B	17	51901648	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	3685004	51901648	29293562	73	2304											
KCNH6	81033	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61613115	61613115	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctggaccgctactctgagtAtggggcggctgtgctcttct	4	12	14	11	2	3	1	0	1	3	0	3	2	3	2	1	4	2	5	1	4	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:61613115A>G	ENST00000583023.1	+	6	1198	c.1187A>G	c.(1186-1188)tAt>tGt	p.Y396C	KCNH6_ENST00000580652.1_Missense_Mutation_p.Y396C|KCNH6_ENST00000456941.2_Missense_Mutation_p.Y396C|KCNH6_ENST00000314672.5_Missense_Mutation_p.Y396C|KCNH6_ENST00000581784.1_Missense_Mutation_p.Y396C	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	396					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TACTCTGAGTATGGGGCGGCT	0.622																																					p.Y396C													.	KCNH6-91	0			c.A1187G						.						88	78	81					17																	61613115		2203	4300	6503	SO:0001583	missense	81033	exon6			CTGAGTATGGGGC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1187A>G	17.37:g.61613115A>G	ENSP00000463533:p.Tyr396Cys	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	98	56	NM_030779	0	0	0	0	0	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	A	7.758	0.704715	0.15172	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.98493	-4.96;-4.96	4.36	4.36	0.52297	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99121	0.9697	M	0.94021	3.485	0.58432	D	0.999999	D;D;D;D;D	0.71674	0.998;0.971;0.998;0.971;0.987	D;D;D;D;D	0.81914	0.995;0.916;0.975;0.942;0.933	D	0.99278	1.0895	10	0.87932	D	0	.	13.7107	0.62667	1.0:0.0:0.0:0.0	.	273;396;396;396;396	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	C	396	ENSP00000318212:Y396C;ENSP00000396900:Y396C	ENSP00000318212:Y396C	Y	+	2	0	KCNH6	58966847	1.000000	0.71417	0.991000	0.47740	0.060000	0.15804	9.139000	0.94554	1.821000	0.53095	0.260000	0.18958	TAT	.		0.622	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		G	61613115	A	G	61613115	3	3	26	1	0	0	0	0	1	0	0	0	8057	449	16	3	1209	3	KCNH6	17	61613115	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	9711467	61613115	19582095	74	2305											
LAMA1	284217	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	6992669	6992669	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaagagtagaattgggtaGtaggaaatcttcatccaaag	15	10	11	5	0	2	3	1	1	1	2	3	4	3	4	1	2	0	3	1	2	7	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr18:6992669G>A	ENST00000389658.3	-	36	5152	c.5059C>T	c.(5059-5061)Cta>Tta	p.L1687L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1687	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GAATTGGGTAGTAGGAAATCT	0.358																																					p.L1687L													.	LAMA1-149	0			c.C5059T						.						148	143	145					18																	6992669		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon36			TGGGTAGTAGGAA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5059C>T	18.37:g.6992669G>A		Somatic	118	1		WXS	Illumina HiSeq	Phase_I	137	69	NM_005559	0	0	5	6	1		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			.		0.358	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		A	6992669	G	A	6992669	2	1	26	1	0	0	0	0	0	0	0	1	8626	1020	36	2		2	LAMA1	18	6992669	Silent	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		6992669	71084579	75	2306											
ANKRD12	23253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	9257703	9257703	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgccaggaaactcttgtgctCaggatccggcatcctttatg	8	12	10	11	1	2	0	1	0	1	0	4	2	4	2	3	3	3	2	3	3	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr18:9257703C>G	ENST00000262126.4	+	9	4678	c.4438C>G	c.(4438-4440)Cag>Gag	p.Q1480E	ANKRD12_ENST00000383440.2_Missense_Mutation_p.Q1457E|RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.Q1457E	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1480						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CTCTTGTGCTCAGGATCCGGC	0.418																																					p.Q1480E		.											.	ANKRD12-92	0			c.C4438G						.						49	52	51					18																	9257703		2200	4299	6499	SO:0001583	missense	23253	exon9			TGTGCTCAGGATC	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.4438C>G	18.37:g.9257703C>G	ENSP00000262126:p.Gln1480Glu	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	104	40	NM_015208	0	0	2	3	1	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234306	0.39498	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.68479	-0.33;-0.33	5.69	5.69	0.88448	.	0.303615	0.32444	N	0.006084	T	0.55768	0.1941	L	0.29908	0.895	0.44946	D	0.997969	P;P	0.38195	0.571;0.622	B;B	0.31101	0.124;0.097	T	0.58967	-0.7542	10	0.48119	T	0.1	-11.1383	19.8263	0.96618	0.0:1.0:0.0:0.0	.	1457;1480	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	E	1457;1480	ENSP00000372932:Q1457E;ENSP00000262126:Q1480E	ENSP00000262126:Q1480E	Q	+	1	0	ANKRD12	9247703	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	5.359000	0.66074	2.676000	0.91093	0.655000	0.94253	CAG	.		0.418	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9257703	C	G	9257703	3	3	26	1	0	0	0	0	1	0	0	0	640	827	29	4	4468	4	ANKRD12	18	9257703	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	2265034	9257703	68819545	76	2307											
MBP	4155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	74700845	74700845	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcttacctttccctgcgaCgggggtggtgtgcgaggcgt	3	11	17	10	4	1	0	0	0	1	0	2	2	2	0	2	5	3	0	2	5	1	2	rs112511603		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr18:74700845C>T	ENST00000397869.3	-	3	352	c.306G>A	c.(304-306)ccG>ccA	p.P102P	MBP_ENST00000359645.3_Silent_p.P128P|MBP_ENST00000578193.1_Silent_p.P102P|MBP_ENST00000382582.3_Silent_p.P128P|MBP_ENST00000354542.4_Intron|MBP_ENST00000579129.1_Silent_p.P235P|MBP_ENST00000526111.1_Silent_p.P80P|MBP_ENST00000397866.4_Silent_p.P102P|MBP_ENST00000355994.2_Silent_p.P235P|MBP_ENST00000580402.1_Silent_p.P235P|MBP_ENST00000397865.5_Silent_p.P102P|MBP_ENST00000528160.1_Intron|MBP_ENST00000397875.3_Silent_p.P112P|MBP_ENST00000527041.1_Intron			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	TTCCCTGCGACGGGGGTGGTG	0.527																																					p.P235P	NSCLC(17;72 1131 19392)	.											.	MBP-515	0			c.G705A						.						121	130	127					18																	74700845		2203	4300	6503	SO:0001819	synonymous_variant	4155	exon6			CTGCGACGGGGGT		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.306G>A	18.37:g.74700845C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	65	28	NM_001025101	0	0	0	0	0	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	37																																																																																				C|0.500;T|0.500		0.527	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081		T	74700845	C	T	74700845	2	4	26	1	0	0	0	0	0	0	0	1	9384	523	19	1		1	MBP	18	74700845	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	65443142	74700845	3376403	77	2308											
ZNF43	7594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	21990696	21990696	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggtttgaggatcggttaaAagctttgccacatttttcac	11	14	9	7	1	1	1	1	1	0	0	2	2	1	2	1	3	2	3	1	3	3	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr19:21990696A>T	ENST00000354959.4	-	4	2312	c.2143T>A	c.(2143-2145)Ttt>Att	p.F715I	ZNF43_ENST00000598381.1_Missense_Mutation_p.F709I|ZNF43_ENST00000595461.1_Missense_Mutation_p.F709I|ZNF43_ENST00000594012.1_Missense_Mutation_p.F709I	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	715					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)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		GATCGGTTAAAAGCTTTGCCA	0.363																																					p.F724I		.											.	ZNF43-154	0			c.T2170A						.						50	54	53					19																	21990696		2203	4299	6502	SO:0001583	missense	7594	exon4			GGTTAAAAGCTTT	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"Zinc fingers, C2H2-type", "-"	13109	protein-coding gene	gene with protein product		603972	"zinc finger protein 39-like 1 (KOX 27)", "zinc finger protein 43 (HTF6)"	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.2143T>A	19.37:g.21990696A>T	ENSP00000347045:p.Phe715Ile	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	37	20	NM_001256653	0	0	6	7	1	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	A	17.13	3.311136	0.60414	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.46451	0.87	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.66499	0.2795	M	0.91972	3.26	0.36120	D	0.845417	D	0.89917	1.0	D	0.81914	0.995	T	0.73953	-0.3820	9	0.87932	D	0	.	8.2856	0.31926	1.0:0.0:0.0:0.0	.	715	P17038	ZNF43_HUMAN	I	714;715	ENSP00000347045:F715I	ENSP00000347045:F715I	F	-	1	0	ZNF43	21782536	0.986000	0.35501	0.177000	0.23020	0.629000	0.37895	6.109000	0.71528	0.808000	0.34231	0.254000	0.18369	TTT	.		0.363	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		T	21990696	A	T	21990696	3	4	26	1	0	0	0	0	1	0	0	0	17935	14	1	5	290	5	ZNF43	19	21990696	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10		21990696	37138287	78	2309											
FBXO46	23403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46215847	46215847	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtataagtcacatgtgatctTgtccttggctcgggccccag	7	12	11	11	1	2	1	1	1	1	0	4	1	3	1	3	2	0	2	3	2	2	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr19:46215847T>C	ENST00000317683.3	-	2	1040	c.907A>G	c.(907-909)Aag>Gag	p.K303E		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	303										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CATGTGATCTTGTCCTTGGCT	0.682																																					p.K303E		.											.	FBXO46-159	0			c.A907G						.						31	36	34					19																	46215847		2004	4156	6160	SO:0001583	missense	23403	exon2			TGATCTTGTCCTT	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"F-boxes /  "other""	25069	protein-coding gene	gene with protein product		609117	"F-box only protein 34-like"	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.907A>G	19.37:g.46215847T>C	ENSP00000410007:p.Lys303Glu	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	101	47	NM_001080469	0	0	0	5	5		Missense_Mutation	SNP	ENST00000317683.3	37	CCDS46116.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.498092	0.26861	.	.	ENSG00000177051	ENST00000317683	.	.	.	4.39	3.37	0.38596	.	.	.	.	.	T	0.32194	0.0821	N	0.22421	0.69	0.38310	D	0.943215	B	0.31705	0.336	B	0.27796	0.083	T	0.12915	-1.0529	8	0.28530	T	0.3	-10.0116	6.4522	0.21910	0.0:0.1111:0.0:0.8889	.	303	Q6PJ61	FBX46_HUMAN	E	303	.	ENSP00000410007:K303E	K	-	1	0	FBXO46	50907687	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	3.177000	0.50871	0.737000	0.32582	-0.371000	0.07208	AAG	.		0.682	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179		C	46215847	T	C	46215847	3	2	26	1	0	0	0	0	1	0	0	0	5774	1821	63	3	908	3	FBXO46	19	46215847	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	24225151	46215847	12913136	79	2310											
EDN3	1908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	57876603	57876603	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtggctggccctggcgaggGgactgtggccccgacagcac	5	6	17	13	2	0	0	0	0	0	0	0	3	0	1	3	6	1	2	3	6	0	0	rs457651		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr20:57876603G>T	ENST00000337938.2	+	2	577	c.191G>T	c.(190-192)gGg>gTg	p.G64V	EDN3_ENST00000371028.2_Missense_Mutation_p.G64V|EDN3_ENST00000311585.7_Missense_Mutation_p.G64V|EDN3_ENST00000371025.3_Missense_Mutation_p.G64V|EDN3_ENST00000395654.3_Missense_Mutation_p.G64V	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	64					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					CCTGGCGAGGGGACTGTGGCC	0.716																																					p.G64V		.											.	EDN3-91	0			c.G191T						.						33	37	35					20																	57876603		2201	4300	6501	SO:0001583	missense	1908	exon2			GCGAGGGGACTGT	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.191G>T	20.37:g.57876603G>T	ENSP00000337128:p.Gly64Val	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	94	43	NM_207034	0	0	0	0	0	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	37	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720028	0.30503	.	.	ENSG00000124205	ENST00000337938;ENST00000311585;ENST00000371028;ENST00000371025;ENST00000395654	D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22	3.59	-7.18	0.01505	.	.	.	.	.	T	0.63105	0.2483	N	0.08118	0	0.09310	N	1	P;P;P;P	0.38110	0.618;0.543;0.483;0.51	B;B;B;B	0.33690	0.168;0.138;0.081;0.067	T	0.61053	-0.7140	9	0.36615	T	0.2	1.9985	0.3953	0.00417	0.2776:0.1274:0.2815:0.3135	.	64;64;64;64	P14138-2;Q7Z6D2;P14138;Q4FAT2	.;.;EDN3_HUMAN;.	V	64	ENSP00000337128:G64V;ENSP00000311854:G64V;ENSP00000360067:G64V;ENSP00000360064:G64V;ENSP00000379015:G64V	ENSP00000311854:G64V	G	+	2	0	EDN3	57309998	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-0.348000	0.07740	-1.885000	0.01118	0.313000	0.20887	GGG	G|1.000;A|0.000		0.716	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		T	57876603	G	T	57876603	3	4	26	1	0	0	0	0	1	0	0	0	4929	1232	43	4	197	4	EDN3	20	57876603	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		57876603	5148917	80	2311											
AR	367	hgsc.bcm.edu	37	chrX	66765207	66765208	+	Missense_Mutation	DNP	GC	GC	AG																															cagcagcagcagcagcagcaGcagcagcagcagcagcagca																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chrX:66765207_66765208GC>AG	ENST00000374690.3	+	1	743_744	c.219_220GC>AG	c.(217-222)caGCag>caAGag	p.Q74E	AR_ENST00000504326.1_Missense_Mutation_p.Q74E|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q74E	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	74	Gln-rich.|Modulating.|Poly-Gln.		Missing.		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcagcagcagcagca	0.668									Androgen Insensitivity Syndrome																												p.Q74E		.											.	AR-661	0			c.C220G						.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CAGCAGCAGCAGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	X.37:g.66765207_66765208delinsAG	ENSP00000363822:p.Gln74Glu	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	104	8	NM_000044	0	0	0	0	0	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	DNP	ENST00000374690.3	37	CCDS14387.1																																																																																			.		0.668	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		AG	66765208	GC	AG	66765207	3	1	26	1	0	0	0	0	1	0	0	0	836	962	34	2	221	2	AR	23	66765207	Missense_Mutation	DNP	GC	TCGA-A4-A5Y0-01A-11D-A31X-10		66765207	88505353	81	2312											
GLUD2	2747	ucsc.edu	37	chrX	120183026	120183026	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acggcagagttccaagacagTatatcgggtgcatctgagaa	13	8	12	8	2	1	3	0	1	1	3	3	4	2	3	1	2	1	4	1	2	4	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chrX:120183026T>G	ENST00000328078.1	+	1	1565	c.1488T>G	c.(1486-1488)agT>agG	p.S496R		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	496					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						TCCAAGACAGTATATCGGGTG	0.453																																					p.S496R													.	GLUD2-131	0			c.T1488G						.						163	129	141					X																	120183026		2203	4300	6503	SO:0001583	missense	2747	exon1			AGACAGTATATCG	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1488T>G	X.37:g.120183026T>G	ENSP00000327589:p.Ser496Arg	Somatic	145	0		WXS	Illumina HiSeq		176	2	NM_012084	1	0	5	157	151	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.467675	0.00011	.	.	ENSG00000182890	ENST00000328078	D	0.95918	-3.85	1.99	-3.98	0.04082	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.045906	0.85682	N	0.000000	T	0.72961	0.3526	N	0.00453	-1.485	0.19300	N	0.999976	B	0.02656	0.0	B	0.01281	0.0	T	0.76277	-0.3018	10	0.02654	T	1	.	4.3409	0.11110	0.6313:0.0:0.1881:0.1806	.	496	P49448	DHE4_HUMAN	R	496	ENSP00000327589:S496R	ENSP00000327589:S496R	S	+	3	2	GLUD2	120010707	1.000000	0.71417	0.043000	0.18650	0.080000	0.17528	0.344000	0.19962	-1.074000	0.03132	-1.405000	0.01134	AGT	.		0.453	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		G	120183026	T	G	120183026	3	3	26	1	0	0	0	0	1	0	0	0	6497	1635	57	5	1490	5	GLUD2	23	120183026	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	53417819	120183026	35087534	82	2313											
ATP11C	286410	broad.mit.edu;bcgsc.ca	37	chrX	138857091	138857091	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcatgcagagcttcaatggtCtctgcagcttgatcttgtag	8	13	11	9	0	3	2	1	1	2	1	4	2	3	2	0	1	4	6	0	1	2	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chrX:138857091C>G	ENST00000327569.3	-	19	2081	c.1983G>C	c.(1981-1983)gaG>gaC	p.E661D	ATP11C_ENST00000359686.2_Missense_Mutation_p.E661D|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000361648.2_Missense_Mutation_p.E661D|ATP11C_ENST00000370557.1_Missense_Mutation_p.E658D|ATP11C_ENST00000370543.1_Missense_Mutation_p.E661D	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	661					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					CTTCAATGGTCTCTGCAGCTT	0.463																																					p.E661D													.	ATP11C-198	0			c.G1983C						.						77	67	70					X																	138857091		2203	4300	6503	SO:0001583	missense	286410	exon19			AATGGTCTCTGCA	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1983G>C	X.37:g.138857091C>G	ENSP00000332756:p.Glu661Asp	Somatic	94	1		WXS	Illumina HiSeq	Phase_I	97	54	NM_001010986	0	0	2	2	0	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416378	0.42918	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22;-3.22	5.84	4.07	0.47477	HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.86381	0.5919	N	0.16368	0.405	0.50171	D	0.999855	B;B	0.23377	0.069;0.084	B;B	0.28139	0.051;0.086	T	0.80765	-0.1236	10	0.28530	T	0.3	.	10.299	0.43642	0.0:0.8396:0.0:0.1604	.	661;661	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	D	658;661;661;661;661	ENSP00000359588:E658D;ENSP00000355165:E661D;ENSP00000332756:E661D;ENSP00000359574:E661D;ENSP00000352715:E661D	ENSP00000332756:E661D	E	-	3	2	ATP11C	138684757	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.859000	0.27858	1.239000	0.43787	0.529000	0.55759	GAG	.		0.463	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		G	138857091	C	G	138857091	3	3	26	1	0	0	0	0	1	0	0	0	1122	912	32	4	1526	4	ATP11C	23	138857091	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	18674065	138857091	16413469	83	2314											
CNGA2	1260	bcgsc.ca	37	chrX	150912596	150912596	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgacgcacagctaatatcCgcagcctgggctactcagat	11	8	9	13	3	1	1	1	0	0	1	3	2	2	1	2	1	3	4	2	1	3	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chrX:150912596C>A	ENST00000329903.4	+	6	1654	c.1621C>A	c.(1621-1623)Cgc>Agc	p.R541S		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	541					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					AGCTAATATCCGCAGCCTGGG	0.498																																					p.R541S													.	CNGA2-193	0			c.C1621A						.						156	134	142					X																	150912596		2203	4300	6503	SO:0001583	missense	1260	exon7			AATATCCGCAGCC	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.1621C>A	X.37:g.150912596C>A	ENSP00000328478:p.Arg541Ser	Somatic	90	1		WXS	Illumina HiSeq	Phase_1	97	5	NM_005140	0	0	0	0	0	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307310	0.60305	.	.	ENSG00000183862	ENST00000329903	D	0.97114	-4.25	5.33	5.33	0.75918	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.98523	0.9507	M	0.90019	3.08	0.80722	D	1	D	0.62365	0.991	D	0.64595	0.927	D	0.99632	1.0986	10	0.87932	D	0	.	15.3498	0.74373	0.0:1.0:0.0:0.0	.	541	Q16280	CNGA2_HUMAN	S	541	ENSP00000328478:R541S	ENSP00000328478:R541S	R	+	1	0	CNGA2	150663252	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.561000	0.60809	2.216000	0.71823	0.529000	0.55759	CGC	.		0.498	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		A	150912596	C	A	150912596	3	1	26	1	0	0	0	0	1	0	0	0	3603	652	23	4	1643	4	CNGA2	23	150912596	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	12055505	150912596	4357964	84	2315											
KLHL17	339451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	898747	898748	+	Missense_Mutation	DNP	GG	GG	AA																															acctcagacctggctaccgtGgagtcctacgaccccgtgac																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:898747_898748GG>AA	ENST00000338591.3	+	8	1325_1326	c.1218_1219GG>AA	c.(1216-1221)gtGGag>gtAAag	p.E407K		NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	407	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGGCTACCGTGGAGTCCTACGA	0.624																																					p.E407K		.											.	KLHL17-90	0			c.G1219A						.																																			SO:0001583	missense	339451	exon8			ACCGTGGAGTCCT	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"Kelch-like", "BTB/POZ domain containing"	24023	protein-coding gene	gene with protein product	"actinfilin"		"kelch-like 17 (Drosophila)"			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	Exception_encountered	1.37:g.898747_898748delinsAA	ENSP00000343930:p.Glu407Lys	Somatic	166	1		WXS	Illumina HiSeq	Phase_I	177	124	NM_198317	0	0	0	0	0	Q5SV94	Missense_Mutation	DNP	ENST00000338591.3	37	CCDS30550.1																																																																																			.		0.624	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		AA	898748	GG	AA	898747	3	1	27	1	0	0	0	0	1	0	0	0	8393	1335	47	2	1248	2	KLHL17	1	898747	Missense_Mutation	DNP	GG	TCGA-A4-A5Y1-01A-11D-A28G-10		898747	248351874	1	2316											
TMEM51	55092	broad.mit.edu	37	chr1	15541888	15541888	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacctggcccatgtccagcAcccgacaggcgctgggcctc	6	5	13	17	2	0	0	0	0	0	0	2	2	1	1	5	4	1	2	5	4	0	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:15541888A>C	ENST00000428417.1	+	2	751	c.305A>C	c.(304-306)cAc>cCc	p.H102P	TMEM51_ENST00000400796.3_Missense_Mutation_p.H102P|TMEM51_ENST00000434578.2_Missense_Mutation_p.H102P|TMEM51_ENST00000376008.2_Missense_Mutation_p.H102P|TMEM51_ENST00000376014.3_Missense_Mutation_p.H102P	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	102						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CATGTCCAGCACCCGACAGGC	0.657																																					p.H102P													.	TMEM51-90	0			c.A305C						.						27	24	25					1																	15541888		2203	4300	6503	SO:0001583	missense	55092	exon2			TCCAGCACCCGAC	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.305A>C	1.37:g.15541888A>C	ENSP00000394899:p.His102Pro	Somatic	43	8		WXS	Illumina HiSeq	Phase_I	47	8	NM_018022	0	1	133	137	3	A8K819	Missense_Mutation	SNP	ENST00000428417.1	37	CCDS154.1	.	.	.	.	.	.	.	.	.	.	A	7.709	0.694835	0.15039	.	.	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	5.43	2.84	0.33178	.	0.849074	0.11191	N	0.589872	T	0.28300	0.0699	L	0.54323	1.7	0.29801	N	0.832443	B;B	0.11235	0.004;0.001	B;B	0.11329	0.006;0.004	T	0.27434	-1.0074	10	0.66056	D	0.02	-12.2869	6.0577	0.19820	0.74:0.1553:0.1047:0.0	.	102;102	Q9BSA0;Q9NW97	.;TMM51_HUMAN	P	102	ENSP00000394899:H102P;ENSP00000365182:H102P;ENSP00000412298:H102P;ENSP00000409665:H102P;ENSP00000383600:H102P;ENSP00000365176:H102P	ENSP00000303666:H102P	H	+	2	0	TMEM51	15414475	0.337000	0.24766	0.948000	0.38648	0.007000	0.05969	0.734000	0.26101	0.264000	0.21851	0.533000	0.62120	CAC	.		0.657	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		C	15541888	A	C	15541888	3	2	27	1	0	0	0	0	1	0	0	0	16209	159	6	5	307	5	TMEM51	1	15541888	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	14643141	15541888	233708733	2	2317											
FGGY	55277	hgsc.bcm.edu;bcgsc.ca	37	chr1	60019871	60019884	+	Frame_Shift_Del	DEL	TCTGTGGAACGTCT	TCTGTGGAACGTCT	-																															gacgtcacggctggctgtcaTctgtggaacgtcttcttgtc																								rs144977691|rs116481036|rs147926450	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	TCTGTGGAACGTCT	TCTGTGGAACGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:60019871_60019884delTCTGTGGAACGTCT	ENST00000303721.7	+	8	1049_1062	c.875_888delTCTGTGGAACGTCT	c.(874-888)atctgtggaacgtctfs	p.ICGTS292fs	FGGY_ENST00000371218.4_Frame_Shift_Del_p.ICGTS292fs|FGGY_ENST00000474476.1_3'UTR|FGGY_ENST00000371210.1_5'UTR|FGGY_ENST00000371212.1_Frame_Shift_Del_p.ICGTS204fs	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	292					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					CTGGCTGTCATCTGTGGAACGTCTTCTTGTCACA	0.561																																					p.292_296del		.											.	FGGY-69	0			c.875_888del						.																																			SO:0001589	frameshift_variant	55277	exon8			.		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.875_888delTCTGTGGAACGTCT	1.37:g.60019871_60019884delTCTGTGGAACGTCT	ENSP00000305922:p.Ile292fs	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	157	48	NM_001113411	0	0	0	0	0	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Frame_Shift_Del	DEL	ENST00000303721.7	37	CCDS611.2																																																																																			.		0.561	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		-	60019884	TCTGTGGAACGTCT	-	60019871	7	5	27	1	0	1	0	1	0	0	0	0	5890	1435	50	0	901	0	FGGY	1	60019871	Frame_Shift_Del	DEL	TCTGTGGAACGTCT	TCGA-A4-A5Y1-01A-11D-A28G-10	44477983	60019871	189230750	3	2318											
CD53	963	broad.mit.edu	37	chr1	111440473	111440473	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggtttcattccaatttcCtgtatatcggaatcatcacc	9	16	6	10	1	3	0	3	0	0	0	6	1	5	1	3	2	0	2	3	2	4	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:111440473C>A	ENST00000271324.5	+	7	659	c.547C>A	c.(547-549)Ctg>Atg	p.L183M	CD53_ENST00000429072.2_Missense_Mutation_p.L124M|CD53_ENST00000497404.1_Intron	NM_000560.3|NM_001040033.1	NP_000551.1|NP_001035122.1	P19397	CD53_HUMAN	CD53 molecule	183					positive regulation of myoblast fusion (GO:1901741)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	17		all_cancers(81;1.06e-05)|all_epithelial(167;1.95e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0264)|Colorectal(144;0.0375)|all cancers(265;0.11)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.141)|LUSC - Lung squamous cell carcinoma(189;0.144)		TTCCAATTTCCTGTATATCGG	0.378																																					p.L183M													.	CD53-90	0			c.C547A						.						223	205	211					1																	111440473		2203	4300	6503	SO:0001583	missense	963	exon7			AATTTCCTGTATA	BC040693	CCDS829.1	1p13	2013-02-14	2006-03-28		ENSG00000143119	ENSG00000143119		"CD molecules", "Tetraspanins"	1686	protein-coding gene	gene with protein product		151525	"CD53 antigen"	MOX44		8319976	Standard	XM_006711053		Approved	TSPAN25	uc001dzw.3	P19397	OTTHUMG00000048020	ENST00000271324.5:c.547C>A	1.37:g.111440473C>A	ENSP00000271324:p.Leu183Met	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	82	4	NM_000560	0	0	37	37	0	B2R905|Q5U0D6	Missense_Mutation	SNP	ENST00000271324.5	37	CCDS829.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225468	0.58668	.	.	ENSG00000143119	ENST00000429072;ENST00000271324	T;T	0.79653	2.99;-1.29	5.67	1.12	0.20585	.	0.000000	0.85682	D	0.000000	T	0.77844	0.4191	L	0.60012	1.86	0.23784	N	0.996851	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	T	0.69573	-0.5109	10	0.41790	T	0.15	.	8.6432	0.33989	0.0:0.5137:0.0:0.4863	.	124;183	B4DQB5;P19397	.;CD53_HUMAN	M	124;183	ENSP00000412250:L124M;ENSP00000271324:L183M	ENSP00000271324:L183M	L	+	1	2	CD53	111241996	0.999000	0.42202	0.999000	0.59377	0.711000	0.40976	0.421000	0.21280	0.153000	0.19213	0.557000	0.71058	CTG	.		0.378	CD53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032931.1	NM_000560		A	111440473	C	A	111440473	3	1	27	1	0	0	0	0	1	0	0	0	3029	680	24	4	569	4	CD53	1	111440473	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	51420602	111440473	137810148	4	2319											
CD1C	911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158261919	158261919	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gggctgtgagctgcattctgGaaagagcccagaaggcttct	9	9	14	9	0	2	3	0	1	2	2	2	4	2	4	1	3	3	4	1	3	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:158261919G>A	ENST00000368170.3	+	3	653	c.374G>A	c.(373-375)gGa>gAa	p.G125E		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	125					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					CTGCATTCTGGAAAGAGCCCA	0.448																																					p.G125E		.											.	CD1C-94	0			c.G374A						.						91	98	95					1																	158261919		2203	4300	6503	SO:0001583	missense	911	exon3			ATTCTGGAAAGAG	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1636	protein-coding gene	gene with protein product		188340	"CD1C antigen, c polypeptide", "CD1c antigen"	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.374G>A	1.37:g.158261919G>A	ENSP00000357152:p.Gly125Glu	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	192	89	NM_001765	0	0	1	1	0	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	ENST00000368170.3	37	CCDS1175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	13.26|13.26	2.185038|2.185038	0.38609|0.38609	.|.	.|.	ENSG00000158481|ENSG00000158481	ENST00000368169;ENST00000368170|ENST00000443761	T|.	0.06294|.	3.32|.	3.92|3.92	-0.561|-0.561	0.11785|0.11785	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2.458490|.	0.01726|.	N|.	0.028603|.	T|.	0.19805|.	0.0476|.	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	P|.	0.52577|.	0.954|.	B|.	0.44278|.	0.445|.	T|.	0.33803|.	-0.9854|.	10|.	0.87932|.	D|.	0|.	.|.	1.0278|1.0278	0.01531|0.01531	0.1994:0.1834:0.4297:0.1875|0.1994:0.1834:0.4297:0.1875	.|.	125|.	P29017|.	CD1C_HUMAN|.	E|X	125|59	ENSP00000357152:G125E|.	ENSP00000357151:G125E|.	G|W	+|+	2|3	0|0	CD1C|CD1C	156528543|156528543	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.020000|0.020000	0.10135|0.10135	-0.226000|-0.226000	0.09139|0.09139	0.093000|0.093000	0.17368|0.17368	0.644000|0.644000	0.83932|0.83932	GGA|TGG	.		0.448	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		A	158261919	G	A	158261919	3	1	27	1	0	0	0	0	1	0	0	0	2982	1174	41	2	384	2	CD1C	1	158261919	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	46821446	158261919	90988702	5	2320											
C1orf14	81626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	182898789	182898789	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtttatttcttaccatttcaGtagtcatcatttttgctaca	9	20	4	8	0	4	0	3	0	1	0	4	0	4	0	1	0	3	3	1	0	4	9			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:182898789G>T	ENST00000367547.3	-	6	1411	c.1175C>A	c.(1174-1176)aCt>aAt	p.T392N	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Missense_Mutation_p.T273N	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	464										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						TACCATTTCAGTAGTCATCAT	0.343																																					p.T392N		.											.	SHCBP1L-91	0			c.C1175A						.						97	94	95					1																	182898789		2202	4297	6499	SO:0001583	missense	81626	exon6			ATTTCAGTAGTCA	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.1175C>A	1.37:g.182898789G>T	ENSP00000356518:p.Thr392Asn	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	38	16	NM_030933	0	0	0	0	0	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	37	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470487	0.43942	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.47869	0.83;0.84	5.88	4.94	0.65067	Carbohydrate-binding/sugar hydrolysis domain (1);	0.212652	0.33092	N	0.005289	T	0.43277	0.1240	L	0.43152	1.355	0.25433	N	0.988169	B;B;B	0.26258	0.09;0.078;0.145	B;B;B	0.29785	0.024;0.034;0.107	T	0.38520	-0.9657	10	0.42905	T	0.14	-11.1083	14.1389	0.65306	0.0:0.1504:0.8496:0.0	.	464;273;392	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	N	392;461;273	ENSP00000356518:T392N;ENSP00000397308:T273N	ENSP00000287709:T461N	T	-	2	0	SHCBP1L	181165412	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.607000	0.67648	1.463000	0.47967	0.644000	0.83932	ACT	.		0.343	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182898789	G	T	182898789	3	4	27	1	0	0	0	0	1	0	0	0	2006	1029	36	4	806	4	C1orf14	1	182898789	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	24636870	182898789	66351832	6	2321											
TMEM9	252839	ucsc.edu;bcgsc.ca	37	chr1	201104800	201104800	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caccagcccatctagctgagCatcttgtgccgatcgaagac	10	8	9	14	2	2	2	0	1	2	1	3	4	2	2	3	0	4	2	3	0	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:201104800C>T	ENST00000367330.1	-	5	1059	c.543G>A	c.(541-543)atG>atA	p.M181I	TMEM9_ENST00000367333.2_Missense_Mutation_p.M181I|TMEM9_ENST00000485839.2_Missense_Mutation_p.M181I|TMEM9_ENST00000472411.1_5'UTR|TMEM9_ENST00000367332.1_Missense_Mutation_p.M184I|TMEM9_ENST00000367334.5_Missense_Mutation_p.M181I			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	181					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)				liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				TCTAGCTGAGCATCTTGTGCC	0.617																																					p.M181I													.	TMEM9-90	0			c.G543A						.						92	70	77					1																	201104800		2203	4300	6503	SO:0001583	missense	252839	exon6			GCTGAGCATCTTG		CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.543G>A	1.37:g.201104800C>T	ENSP00000356299:p.Met181Ile	Somatic	214	2		WXS	Illumina HiSeq		377	166	NM_016456	0	1	500	981	480	B1ALM6|Q96NQ9|Q9BQF5	Missense_Mutation	SNP	ENST00000367330.1	37	CCDS1408.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662422	0.47572	.	.	ENSG00000116857	ENST00000367334;ENST00000367332;ENST00000367330;ENST00000367329;ENST00000367333	.	.	.	4.55	4.55	0.56014	.	0.099091	0.64402	D	0.000003	T	0.59101	0.2169	L	0.53561	1.675	0.58432	D	0.999999	B;B;B	0.19200	0.034;0.011;0.004	B;B;B	0.21708	0.036;0.015;0.015	T	0.58640	-0.7601	9	0.42905	T	0.14	-36.8522	15.4854	0.75560	0.0:1.0:0.0:0.0	.	206;184;181	B4E1H4;B1ALM5;Q9P0T7	.;.;TMEM9_HUMAN	I	181;184;181;181;184	.	ENSP00000356298:M181I	M	-	3	0	TMEM9	199371423	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	5.672000	0.68102	2.066000	0.61787	0.313000	0.20887	ATG	.		0.617	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456		T	201104800	C	T	201104800	3	4	27	1	0	0	0	0	1	0	0	0	16249	710	25	2	12	2	TMEM9	1	201104800	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	18206011	201104800	48145821	7	2322											
NVL	4931	bcgsc.ca	37	chr1	224468833	224468833	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaataacttaccatgtttaGtaattcggggcccttgacag	11	13	8	9	1	1	1	1	1	0	0	2	1	1	1	2	2	2	2	2	2	5	7			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:224468833G>A	ENST00000281701.6	-	16	2213	c.1954C>T	c.(1954-1956)Cta>Tta	p.L652L	NVL_ENST00000391875.2_Silent_p.L546L|NVL_ENST00000361463.3_Silent_p.L546L|NVL_ENST00000482491.1_Silent_p.L376L|NVL_ENST00000340871.4_Silent_p.L463L|NVL_ENST00000469075.1_Silent_p.L561L	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	652						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ACCATGTTTAGTAATTCGGGG	0.353																																					p.L652L													.	NVL-92	0			c.C1954T						.						104	105	105					1																	224468833		2203	4300	6503	SO:0001819	synonymous_variant	4931	exon16			TGTTTAGTAATTC	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1954C>T	1.37:g.224468833G>A		Somatic	38	1		WXS	Illumina HiSeq	Phase_1	58	18	NM_002533	0	0	0	0	0	B4DMC4|B4DP98|Q96EM7	Silent	SNP	ENST00000281701.6	37	CCDS1541.1	.	.	.	.	.	.	.	.	.	.	g	7.644	0.681475	0.14907	.	.	ENSG00000143748	ENST00000469968	.	.	.	5.07	2.09	0.27110	.	.	.	.	.	T	0.58836	0.2150	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53865	-0.8378	4	.	.	.	-8.744	9.8868	0.41266	0.301:0.0:0.699:0.0	.	.	.	.	I	534	.	.	T	-	2	0	NVL	222535456	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.274000	0.33132	0.624000	0.30286	-0.436000	0.05848	ACT	.		0.353	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		A	224468833	G	A	224468833	2	1	27	1	0	0	0	0	0	0	0	1	10806	1020	36	2		2	NVL	1	224468833	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	23364033	224468833	24781788	8	2323											
SMC6	79677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	17847696	17847696	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaaagttacctcatgcttTgaggtgtgagcaagataaac	15	11	9	6	0	1	3	1	2	0	1	1	3	1	3	1	1	4	3	1	1	7	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:17847696T>G	ENST00000448223.2	-	27	3421	c.3152A>C	c.(3151-3153)cAa>cCa	p.Q1051P	SMC6_ENST00000381272.4_Missense_Mutation_p.Q1077P|SMC6_ENST00000402989.1_Missense_Mutation_p.Q1051P|SMC6_ENST00000351948.4_Missense_Mutation_p.Q1051P	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	1051					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCTCATGCTTTGAGGTGTGAG	0.308																																					p.Q1051P		.											.	SMC6-292	0			c.A3152C						.						76	72	74					2																	17847696		2203	4300	6503	SO:0001583	missense	79677	exon27			ATGCTTTGAGGTG	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.3152A>C	2.37:g.17847696T>G	ENSP00000404092:p.Gln1051Pro	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	43	22	NM_001142286	0	0	0	0	0	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.786888	0.70337	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	T;T;T;T	0.68181	-0.31;-0.31;2.02;-0.31	6.08	6.08	0.98989	RecF/RecN/SMC (1);	0.054551	0.85682	D	0.000000	T	0.79516	0.4459	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.81291	-0.0999	10	0.72032	D	0.01	.	12.8158	0.57665	0.1222:0.0:0.0:0.8778	.	1051	Q96SB8	SMC6_HUMAN	P	1051;1051;1077;1051	ENSP00000404092:Q1051P;ENSP00000323439:Q1051P;ENSP00000370672:Q1077P;ENSP00000384539:Q1051P	ENSP00000323439:Q1051P	Q	-	2	0	SMC6	17711177	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.920000	0.56446	2.333000	0.79357	0.482000	0.46254	CAA	.		0.308	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		G	17847696	T	G	17847696	3	3	27	1	0	0	0	0	1	0	0	0	14819	1812	63	5	131	5	SMC6	2	17847696	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		17847696	225351677	9	2324											
IFIH1	64135	ucsc.edu	37	chr2	163139080	163139080	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggaagagctgttcaactaGcagtaccttaaaaaaatgtg	15	9	10	7	1	1	1	1	0	0	1	1	2	1	2	1	1	4	4	1	1	8	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:163139080G>T	ENST00000263642.2	-	6	1497	c.1102C>A	c.(1102-1104)Cta>Ata	p.L368I		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	368	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TGTTCAACTAGCAGTACCTTA	0.373																																					p.L368I													.	IFIH1-91	0			c.C1102A						.						35	33	34					2																	163139080		2199	4299	6498	SO:0001583	missense	64135	exon6			CAACTAGCAGTAC	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"helicard"	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1102C>A	2.37:g.163139080G>T	ENSP00000263642:p.Leu368Ile	Somatic	28	0		WXS	Illumina HiSeq		39	4	NM_022168	0	0	0	0	0	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.045135	0.55110	.	.	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.19105	2.17	5.82	-1.96	0.07525	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.000000	0.64402	D	0.000001	T	0.45736	0.1357	M	0.87971	2.92	0.25815	N	0.984354	D	0.69078	0.997	D	0.85130	0.997	T	0.41538	-0.9503	10	0.49607	T	0.09	-10.6063	12.6349	0.56677	0.5567:0.0:0.4433:0.0	.	368	Q9BYX4	IFIH1_HUMAN	I	368	ENSP00000263642:L368I	ENSP00000263642:L368I	L	-	1	2	IFIH1	162847326	0.314000	0.24563	0.028000	0.17463	0.849000	0.48306	0.892000	0.28322	-0.312000	0.08741	-0.247000	0.11927	CTA	.		0.373	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		T	163139080	G	T	163139080	3	4	27	1	0	0	0	0	1	0	0	0	7541	962	34	4	2019	4	IFIH1	2	163139080	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	145291384	163139080	80060293	10	2325											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173352476	173352476	+	Frame_Shift_Del	DEL	A	A	-																															gtcactttttatttggttttAagtacaactgaagtcacctt																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:173352476delA	ENST00000264106.6	+	18	2585	c.2382delA	c.(2380-2382)ttafs	p.L794fs	ITGA6_ENST00000409532.1_Frame_Shift_Del_p.L636fs|ITGA6_ENST00000343713.4_Frame_Shift_Del_p.L750fs|ITGA6_ENST00000409080.1_Frame_Shift_Del_p.L755fs|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Frame_Shift_Del_p.L755fs|ITGA6_ENST00000375221.2_Frame_Shift_Del_p.L794fs			P23229	ITA6_HUMAN	integrin, alpha 6	794					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			ATTTGGTTTTAAGTACAACTG	0.333																																					p.L755fs		.											.	ITGA6-227	0			c.2265delA						.						123	118	120					2																	173352476		2203	4300	6503	SO:0001589	frameshift_variant	3655	exon17			.		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"CD molecules", "Integrins"	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2382delA	2.37:g.173352476delA	ENSP00000264106:p.Leu794fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	73	14	NM_000210	0	0	0	0	0	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Frame_Shift_Del	DEL	ENST00000264106.6	37																																																																																				.		0.333	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				-	173352476	A	-	173352476	7	5	27	1	0	1	0	1	0	0	0	0	7901	359	13	0	2331	0	ITGA6	2	173352476	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y1-01A-11D-A28G-10	10213396	173352476	69846897	11	2326											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179547441	179547441	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctgtgatgtattcttcaTgctcttcatatcgttcatac	8	18	5	10	1	5	1	3	1	2	0	6	1	5	1	1	0	3	3	1	0	4	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:179547441T>G	ENST00000591111.1	-	133	32350	c.32126A>C	c.(32125-32127)cAt>cCt	p.H10709P	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.H11026P|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.H9782P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATTCTTCATGCTCTTCATA	0.338																																					p.H11026P		.											.	TTN-636	0			c.A33077C						.						257	246	249					2																	179547441		1899	4119	6018	SO:0001583	missense	7273	exon135			TCTTCATGCTCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32126A>C	2.37:g.179547441T>G	ENSP00000465570:p.His10709Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	107	55	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	3.299	-0.143379	0.06669	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T;T	0.68331	-0.32;-0.1	4.98	2.59	0.31030	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.46889	0.1416	N	0.19112	0.55	0.58432	D	0.999996	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.35674	-0.9779	9	0.87932	D	0	.	5.0483	0.14496	0.0:0.1647:0.1536:0.6817	.	10709;10445	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	P	9782;640	ENSP00000343764:H9782P;ENSP00000401501:H640P	ENSP00000343764:H9782P	H	-	2	0	TTN	179255686	0.000000	0.05858	0.989000	0.46669	0.230000	0.25150	-0.913000	0.04042	0.338000	0.23692	-0.256000	0.11100	CAT	.		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179547441	T	G	179547441	3	3	27	1	0	0	0	0	1	0	0	0	16768	1464	51	5	71364	5	TTN	2	179547441	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	6194965	179547441	63651932	12	2327											
SSFA2	6744	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	182765617	182765618	+	Frame_Shift_Ins	INS	-	-	T																															atggaagtagaaaacccaaaINSttatgctttaacaagtaaga																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:182765617_182765618insT	ENST00000431877.2	+	7	877_878	c.698_699insT	c.(697-702)aattatfs	p.Y234fs	SSFA2_ENST00000428267.2_Frame_Shift_Ins_p.Y81fs|SSFA2_ENST00000409001.1_Frame_Shift_Ins_p.Y234fs|SSFA2_ENST00000320370.7_Frame_Shift_Ins_p.Y234fs	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	234						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			GAAAACCCAAATTATGCTTTAA	0.302																																					p.N233fs		.											.	SSFA2-153	0			c.698_699insT						.																																			SO:0001589	frameshift_variant	6744	exon7			.	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.700dupT	2.37:g.182765619_182765619dupT	ENSP00000388731:p.Tyr234fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	84	19	NM_001130445	0	0	0	0	0	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Frame_Shift_Ins	INS	ENST00000431877.2	37	CCDS46467.1																																																																																			.		0.302	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		T	182765618	-	T	182765617	7	5	27	1	0	1	1	0	0	0	0	0	15215	101	4	0	724	0	SSFA2	2	182765617	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	3218176	182765617	60433756	13	2328											
FSIP2	401024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	186671593	186671593	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaggccagataagggaaatCagttccctgggggtaaagtg	12	8	14	7	0	2	1	2	0	0	1	3	2	3	2	2	4	0	2	2	4	4	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:186671593C>T	ENST00000424728.1	+	17	17560	c.17560C>T	c.(17560-17562)Cag>Tag	p.Q5854*	FSIP2_ENST00000343098.5_Nonsense_Mutation_p.Q5943*			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5854										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TAAGGGAAATCAGTTCCCTGG	0.408																																					p.Q5943X		.											.	FSIP2-90	0			c.C17827T						.						87	79	82					2																	186671593		1841	4085	5926	SO:0001587	stop_gained	401024	exon17			GGAAATCAGTTCC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17560C>T	2.37:g.186671593C>T	ENSP00000401306:p.Gln5854*	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	90	23	NM_173651	0	0	0	0	0	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Nonsense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	C	55	24.779395	0.99962	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	.	.	.	4.87	1.8	0.24995	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	6.7948	0.23719	0.3174:0.4362:0.2464:0.0	.	.	.	.	X	5943;5854	.	ENSP00000344403:Q5943X	Q	+	1	0	FSIP2	186379838	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.056000	0.11787	0.131000	0.18576	0.591000	0.81541	CAG	.		0.408	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186671593	C	T	186671593	4	4	27	1	0	0	0	0	0	1	0	0	6094	827	29	2	17893	2	FSIP2	2	186671593	Nonsense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	3905976	186671593	56527780	14	2329											
TNP1	7141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	217724631	217724631	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcactcaccgtcatcgccccGtttcctacttttcaggttgc	5	14	6	16	3	4	0	4	0	0	0	6	0	5	0	4	1	2	2	4	1	1	5	rs561435538		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:217724631G>A	ENST00000236979.2	-	1	156	c.127C>T	c.(127-129)Cgg>Tgg	p.R43W	AC007563.5_ENST00000607591.1_RNA|AC007563.5_ENST00000447289.1_RNA	NM_003284.3	NP_003275.1	P09430	STP1_HUMAN	transition protein 1 (during histone to protamine replacement)	43					chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|fertilization, exchange of chromosomal proteins (GO:0035042)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|sexual reproduction (GO:0019953)|single strand break repair (GO:0000012)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|spermatid nucleus elongation (GO:0007290)	male germ cell nucleus (GO:0001673)|nucleosome (GO:0000786)	DNA binding (GO:0003677)			large_intestine(1)|lung(1)|stomach(1)	3		Renal(207;0.0822)		Epithelial(149;8.97e-07)|all cancers(144;2.46e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCGCCCCGTTTCCTACTT	0.552													G|||	1	0.000199681	0	0	5008	,	,		20388	0.001		0	False		,,,				2504	0				p.R43W		.											.	TNP1-90	0			c.C127T						.						217	195	203					2																	217724631		2203	4300	6503	SO:0001583	missense	7141	exon1			CGCCCCGTTTCCT		CCDS2406.1	2q35-q36	2008-06-03			ENSG00000118245	ENSG00000118245			11951	protein-coding gene	gene with protein product		190231				2249851	Standard	NM_003284		Approved		uc002vgk.3	P09430	OTTHUMG00000133057	ENST00000236979.2:c.127C>T	2.37:g.217724631G>A	ENSP00000236979:p.Arg43Trp	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	156	74	NM_003284	0	0	0	0	0		Missense_Mutation	SNP	ENST00000236979.2	37	CCDS2406.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957505	0.34565	.	.	ENSG00000118245	ENST00000236979	.	.	.	5.55	-1.5	0.08691	.	0.000000	0.52532	D	0.000080	T	0.64918	0.2642	.	.	.	0.21105	N	0.99979	D	0.89917	1.0	D	0.76071	0.987	T	0.64807	-0.6320	8	0.87932	D	0	-0.9614	15.5104	0.75776	0.0:0.0:0.2376:0.7624	.	43	P09430	STP1_HUMAN	W	43	.	ENSP00000236979:R43W	R	-	1	2	TNP1	217432876	0.771000	0.28555	0.434000	0.26772	0.816000	0.46133	0.173000	0.16724	-0.090000	0.12462	-0.182000	0.12963	CGG	.		0.552	TNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256673.1	NM_003284		A	217724631	G	A	217724631	3	1	27	1	0	0	0	0	1	0	0	0	16365	1144	40	1	48	1	TNP1	2	217724631	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	31053038	217724631	25474742	15	2330											
AGFG1	3267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	228399580	228399580	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtgatcagggaagtggCtttgggaccacaggtaaagc	10	8	17	6	0	1	1	1	1	0	0	1	3	1	3	1	6	1	2	1	6	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:228399580C>G	ENST00000310078.8	+	8	1304	c.1044C>G	c.(1042-1044)ggC>ggG	p.G348G	AGFG1_ENST00000409315.1_Intron|AGFG1_ENST00000409979.2_Silent_p.G372G|AGFG1_ENST00000409171.1_Silent_p.G348G|AGFG1_ENST00000373671.3_Silent_p.G308G	NM_001135188.1|NM_001135189.1|NM_004504.4	NP_001128660.1|NP_001128661.1|NP_004495.2	P52594	AGFG1_HUMAN	ArfGAP with FG repeats 1	348					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of ARF GTPase activity (GO:0032312)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)	ARF GTPase activator activity (GO:0008060)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(2)|ovary(1)|prostate(1)|skin(4)|stomach(1)	18						AGGGAAGTGGCTTTGGGACCA	0.433																																					p.G372G		.											.	AGFG1-228	0			c.C1116G						.						154	145	148					2																	228399580		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon9			AAGTGGCTTTGGG		CCDS2467.1, CCDS46533.1, CCDS46534.1, CCDS46535.1	2q36	2009-11-30	2008-09-22	2008-09-22	ENSG00000173744	ENSG00000173744		"ADP-ribosylation factor GTPase activating proteins"	5175	protein-coding gene	gene with protein product		600862	"HIV-1 Rev binding protein"	HRB		7637788	Standard	NM_004504		Approved	RIP, RAB	uc002vpd.2	P52594	OTTHUMG00000133186	ENST00000310078.8:c.1044C>G	2.37:g.228399580C>G		Somatic	186	1		WXS	Illumina HiSeq	Phase_I	218	130	NM_001135187	0	0	23	80	57	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	37	CCDS2467.1																																																																																			.		0.433	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		G	228399580	C	G	228399580	2	3	27	1	0	0	0	0	0	0	0	1	380	784	28	4		4	AGFG1	2	228399580	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	10674949	228399580	14799793	16	2331											
SH3BP4	23677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	235943690	235943690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaactccaatggcctccCtcgctgcaagtcagagggga	9	6	12	14	1	1	1	1	0	0	1	4	2	3	2	4	4	2	2	4	4	3	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:235943690C>T	ENST00000409212.1	+	3	551	c.44C>T	c.(43-45)cCt>cTt	p.P15L	SH3BP4_ENST00000392011.2_Missense_Mutation_p.P15L|SH3BP4_ENST00000344528.4_Missense_Mutation_p.P15L			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	15					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		AATGGCCTCCCTCGCTGCAAG	0.547																																					p.P15L		.											.	SH3BP4-94	0			c.C44T						.						51	53	52					2																	235943690		2203	4300	6503	SO:0001583	missense	23677	exon3			GCCTCCCTCGCTG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.44C>T	2.37:g.235943690C>T	ENSP00000386862:p.Pro15Leu	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	80	30	NM_014521	0	0	6	18	12	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496478	0.44352	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000444916;ENST00000446904;ENST00000454947	T;T;T;T;T	0.38560	2.49;1.18;2.49;2.49;1.13	4.91	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.32315	0.0825	L	0.34521	1.04	0.80722	D	1	B;B	0.13594	0.008;0.005	B;B	0.10450	0.005;0.005	T	0.11348	-1.0591	10	0.59425	D	0.04	-11.6851	11.1019	0.48179	0.0:0.9093:0.0:0.0907	.	15;15	A8K594;Q9P0V3	.;SH3B4_HUMAN	L	15	ENSP00000375867:P15L;ENSP00000403251:P15L;ENSP00000386862:P15L;ENSP00000340237:P15L;ENSP00000415391:P15L	ENSP00000340237:P15L	P	+	2	0	SH3BP4	235608429	0.999000	0.42202	0.870000	0.34147	0.360000	0.29518	4.311000	0.59147	1.064000	0.40671	0.655000	0.94253	CCT	.		0.547	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			T	235943690	C	T	235943690	3	4	27	1	0	0	0	0	1	0	0	0	14278	681	24	2	46	2	SH3BP4	2	235943690	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	7544110	235943690	7255683	17	2332											
IQSEC1	9922	broad.mit.edu	37	chr3	12949941	12949941	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccaggcaggcccggctcAgtgttccgttgcccgactcc	4	8	12	17	4	1	0	1	0	0	0	4	1	4	0	5	3	1	4	5	3	0	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:12949941A>T	ENST00000273221.4	-	12	2921	c.2705T>A	c.(2704-2706)cTg>cAg	p.L902Q		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	902					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGCCCGGCTCAGTGTTCCGTT	0.647																																					p.L902Q													.	IQSEC1-91	0			c.T2705A						.						52	55	54					3																	12949941		2203	4300	6503	SO:0001583	missense	9922	exon12			CGGCTCAGTGTTC	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2705T>A	3.37:g.12949941A>T	ENSP00000273221:p.Leu902Gln	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	110	4	NM_014869	0	0	6	6	0	O94863|Q96D85	Missense_Mutation	SNP	ENST00000273221.4	37	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.775009	0.49786	.	.	ENSG00000144711	ENST00000273221;ENST00000435445;ENST00000429247	T;T	0.61392	0.11;0.11	4.88	3.72	0.42706	.	0.136593	0.51477	D	0.000095	T	0.66973	0.2844	.	.	.	0.58432	D	0.999999	P;D;D	0.60575	0.955;0.988;0.988	P;P;P	0.62649	0.786;0.905;0.824	T	0.62784	-0.6781	9	0.28530	T	0.3	.	10.3171	0.43743	0.9214:0.0:0.0786:0.0	.	888;888;902	E9PG60;C9JMG9;Q6DN90	.;.;IQEC1_HUMAN	Q	902;888;888	ENSP00000273221:L902Q;ENSP00000402299:L888Q	ENSP00000273221:L902Q	L	-	2	0	IQSEC1	12924941	1.000000	0.71417	0.966000	0.40874	0.277000	0.26821	9.335000	0.96500	0.715000	0.32103	-0.250000	0.11733	CTG	.		0.647	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		T	12949941	A	T	12949941	3	4	27	1	0	0	0	0	1	0	0	0	7838	188	7	5	743	5	IQSEC1	3	12949941	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10		12949941	185072489	18	2333											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	47098859	47098859	+	Frame_Shift_Del	DEL	G	G	-																															tcccaggttctgcatctgttGctgttgtttctgagcctccc																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:47098859delG	ENST00000409792.3	-	15	6457	c.6415delC	c.(6415-6417)caafs	p.Q2140fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2140	Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGCATCTGTTGCTGTTGTTTC	0.478			"N, F, S, Mis"		clear cell renal carcinoma																																p.Q2139fs		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.6415delC						.						160	148	152					3																	47098859		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon15			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6415delC	3.37:g.47098859delG	ENSP00000386759:p.Gln2140fs	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	112	83	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.478	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47098859	G	-	47098859	7	5	27	1	0	1	0	1	0	0	0	0	14163	1328	46	0	1307	0	SETD2	3	47098859	Frame_Shift_Del	DEL	G	TCGA-A4-A5Y1-01A-11D-A28G-10	34148918	47098859	150923571	19	2334	21	2									
SETD2	29072	bcgsc.ca	37	chr3	47098860	47098860	+	Silent	SNP	C	C	T																															cccaggttctgcatctgttgCtgttgtttctgagcctcccg																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:47098860C>T	ENST00000409792.3	-	15	6456	c.6414G>A	c.(6412-6414)caG>caA	p.Q2138Q		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2138	Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCATCTGTTGCTGTTGTTTCT	0.473			"N, F, S, Mis"		clear cell renal carcinoma																																p.Q2138Q				Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.G6414A						.						160	148	152					3																	47098860		2203	4300	6503	SO:0001819	synonymous_variant	29072	exon15			CTGTTGCTGTTGT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6414G>A	3.37:g.47098860C>T		Somatic	159	0		WXS	Illumina HiSeq	Phase_1	109	83	NM_014159	0	0	3	3	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.473	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47098860	C	T	47098860	2	4	27	1	0	0	0	0	0	0	0	1	14163	796	28	2		2	SETD2	3	47098860	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	1	47098860	150923570	20	2335	21	2									
ARMC8	25852	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	137964017	137964040	+	Splice_Site	DEL	CGGAAGAAGGTGAGTCTGGGAGAG	CGGAAGAAGGTGAGTCTGGGAGAG	-																															gagcaaatgatgaagacatcCggaagaaggtgagtctggga																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CGGAAGAAGGTGAGTCTGGGAGAG	CGGAAGAAGGTGAGTCTGGGAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:137964017_137964040delCGGAAGAAGGTGAGTCTGGGAGAG	ENST00000469044.1	+	12	1397_1405	c.1126_1134delCGGAAGAAGGTGAGTCTGGGAGAG	c.(1126-1134)cggaagaagdel	p.RKK376del	ARMC8_ENST00000485396.1_Splice_Site_p.RKK303del|ARMC8_ENST00000358441.2_In_Frame_Del_p.RKKVSLGE362del|ARMC8_ENST00000470821.1_In_Frame_Del_p.RKKVSLGE376del|ARMC8_ENST00000471453.1_In_Frame_Del_p.RKKVSLGE362del|ARMC8_ENST00000491704.1_Splice_Site_p.RKK334del|ARMC8_ENST00000481646.1_Splice_Site_p.RKK362del|ARMC8_ENST00000393058.3_Splice_Site_p.RKK366del|ARMC8_ENST00000489213.1_In_Frame_Del_p.RKKVSLGE334del|ARMC8_ENST00000461822.1_Splice_Site_p.RKK309del|ARMC8_ENST00000538260.1_Splice_Site_p.RKK345del	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	376										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TGAAGACATCCGGAAGAAGGTGAGTCTGGGAGAGGGGCGTCCCC	0.491																																					p.362_369del		.											.	ARMC8-90	0			c.1084_1107del						.																																			SO:0001630	splice_region_variant	25852	exon13			.		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1134+1CGGAAGAAGGTGAGTCTGGGAGAG>-	3.37:g.137964017_137964040delCGGAAGAAGGTGAGTCTGGGAGAG		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	139	22	NM_213654	0	0	0	0	0	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	In_Frame_Del	DEL	ENST00000469044.1	37																																																																																				.		0.491	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	In_Frame_Del	-	137964040	CGGAAGAAGGTGAGTCTGGGAGAG	-	137964017	8	5	27	1	0	1	0	1	0	0	1	0	958	643	23	0	1130	0	ARMC8	3	137964017	Splice_Site	DEL	CGGAAGAAGGTGAGTCTGGGAGAG	TCGA-A4-A5Y1-01A-11D-A28G-10	90865157	137964017	60058413	21	2336											
ATP1B3	483	bcgsc.ca	37	chr3	141626058	141626058	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcattggaatatacattcagTaggtctgatccaacttcgta	12	13	8	8	1	2	1	1	1	1	0	4	2	3	2	1	2	2	3	1	2	6	7			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:141626058T>C	ENST00000286371.3	+	3	476	c.288T>C	c.(286-288)agT>agC	p.S96S	ATP1B3_ENST00000539728.1_Silent_p.S82S|ATP1B3_ENST00000462082.1_Intron	NM_001679.2	NP_001670.1	P54709	AT1B3_HUMAN	ATPase, Na+/K+ transporting, beta 3 polypeptide	96					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	caveola (GO:0005901)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)			cervix(1)|endometrium(1)|lung(2)	4						ATACATTCAGTAGGTCTGATC	0.358																																					p.S96S													.	ATP1B3-90	0			c.T288C						.						90	90	90					3																	141626058		2203	4300	6503	SO:0001819	synonymous_variant	483	exon3			ATTCAGTAGGTCT	BC011835	CCDS3121.1	3q23	2012-10-22			ENSG00000069849	ENSG00000069849		"CD molecules", "ATPases / P-type"	806	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-3", "sodium pump subunit beta-3", "sodium-potassium ATPase subunit beta 3 (non-catalytic)"	601867				8798450, 9457675	Standard	NM_001679		Approved	FLJ29027, CD298	uc003eug.1	P54709	OTTHUMG00000159081	ENST00000286371.3:c.288T>C	3.37:g.141626058T>C		Somatic	96	0		WXS	Illumina HiSeq	Phase_1	78	5	NM_001679	0	0	99	99	0	B7Z1N7	Silent	SNP	ENST00000286371.3	37	CCDS3121.1																																																																																			.		0.358	ATP1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353218.1	NM_001679		C	141626058	T	C	141626058	2	2	27	1	0	0	0	0	0	0	0	1	1135	1635	57	3		3	ATP1B3	3	141626058	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	3662041	141626058	56396372	22	2337											
GPR87	53836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151012432	151012432	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgactgccgtatgccatttgAcccccaaaggacttttaagt	10	12	8	11	1	0	2	0	2	0	0	0	3	0	3	4	1	2	1	4	1	3	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:151012432A>T	ENST00000260843.4	-	3	1066	c.602T>A	c.(601-603)gTc>gAc	p.V201D	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	201					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATGCCATTTGACCCCCAAAGG	0.453																																					p.V201D		.											.	GPR87-153	0			c.T602A						.						119	114	116					3																	151012432		2203	4300	6503	SO:0001583	missense	53836	exon3			CATTTGACCCCCA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"GPCR / Class A : Orphans"	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.602T>A	3.37:g.151012432A>T	ENSP00000260843:p.Val201Asp	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	178	36	NM_023915	0	0	0	0	0	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.721769	0.30503	.	.	ENSG00000138271	ENST00000260843	T	0.36699	1.24	5.45	1.74	0.24563	GPCR, rhodopsin-like superfamily (1);	0.457951	0.21222	N	0.078134	T	0.25082	0.0609	L	0.29908	0.895	0.20821	N	0.999843	B	0.31274	0.317	B	0.38842	0.283	T	0.29027	-1.0025	10	0.10902	T	0.67	-6.9007	8.0205	0.30406	0.6554:0.0:0.3446:0.0	.	201	Q9BY21	GPR87_HUMAN	D	201	ENSP00000260843:V201D	ENSP00000260843:V201D	V	-	2	0	GPR87	152495122	0.000000	0.05858	0.009000	0.14445	0.543000	0.35085	1.208000	0.32345	0.120000	0.18254	-0.408000	0.06270	GTC	.		0.453	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			T	151012432	A	T	151012432	3	4	27	1	0	0	0	0	1	0	0	0	6736	275	10	5	478	5	GPR87	3	151012432	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	9386374	151012432	47009998	23	2338											
SENP5	205564	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	196612951	196612952	+	Frame_Shift_Ins	INS	-	-	T																															ccagaacctaaagacccttcINSttgtcggcatcagccgtact																								rs148425489		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:196612951_196612952insT	ENST00000323460.5	+	2	1148_1149	c.899_900insT	c.(898-903)tcttgtfs	p.C301fs	SENP5_ENST00000445299.2_Frame_Shift_Ins_p.C301fs|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	301					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AAAGACCCTTCTTGTCGGCATC	0.53																																					p.S300fs	Ovarian(47;891 1095 11174 13858 51271)	.											.	SENP5-659	0			c.899_900insT						.																																			SO:0001589	frameshift_variant	205564	exon2			.	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"SUMO1/sentrin specific protease 5"			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.901dupT	3.37:g.196612953_196612953dupT	ENSP00000327197:p.Cys301fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	94	46	NM_152699	0	0	0	0	0	B4DY82|Q96SA5	Frame_Shift_Ins	INS	ENST00000323460.5	37	CCDS3322.1																																																																																			.		0.53	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		T	196612952	-	T	196612951	7	5	27	1	0	1	1	0	0	0	0	0	14081	913	32	0	901	0	SENP5	3	196612951	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	45600519	196612951	1409479	24	2339											
BOD1L	259282	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	13602646	13602646	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctttcctgagactgcacTggtcacactgctttctacaa	9	13	6	13	0	2	1	1	1	1	1	4	2	4	1	2	1	3	2	2	1	2	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:13602646T>G	ENST00000040738.5	-	10	6013	c.5878A>C	c.(5878-5880)Agt>Cgt	p.S1960R		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1960						nucleus (GO:0005634)	DNA binding (GO:0003677)										GAGACTGCACTGGTCACACTG	0.448																																					p.S1960R		.											.	.	0			c.A5878C						.						140	135	136					4																	13602646		2203	4300	6503	SO:0001583	missense	259282	exon10			CTGCACTGGTCAC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5878A>C	4.37:g.13602646T>G	ENSP00000040738:p.Ser1960Arg	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	152	14	NM_148894	0	0	20	21	1	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	17.39	3.376793	0.61735	.	.	ENSG00000038219	ENST00000040738	T	0.17691	2.26	5.55	4.35	0.52113	.	0.000000	0.64402	D	0.000002	T	0.13970	0.0338	L	0.34521	1.04	0.39358	D	0.96587	P	0.41673	0.759	B	0.38327	0.271	T	0.03315	-1.1049	10	0.72032	D	0.01	-6.7552	11.456	0.50183	0.0:0.0:0.1507:0.8493	.	1960	Q8NFC6	BOD1L_HUMAN	R	1960	ENSP00000040738:S1960R	ENSP00000040738:S1960R	S	-	1	0	BOD1L	13211744	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	4.808000	0.62583	0.904000	0.36572	0.459000	0.35465	AGT	.		0.448	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13602646	T	G	13602646	3	3	27	1	0	0	0	0	1	0	0	0	1484	1580	55	5	3345	5	BOD1L	4	13602646	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		13602646	177551630	25	2340											
PDS5A	23244	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	39851206	39851213	+	Frame_Shift_Del	DEL	CTTCATAA	CTTCATAA	-																															ttgatgttctctgccatcttCttcataaaggcatggctatt																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CTTCATAA	CTTCATAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:39851206_39851213delCTTCATAA	ENST00000303538.8	-	27	3685_3692	c.3146_3153delTTATGAAG	c.(3145-3153)tttatgaagfs	p.FMK1049fs		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						CTGCCATCTTCTTCATAAAGGCATGGCT	0.38																																					p.1049_1051del		.											.	.	0			c.3146_3153del						.																																			SO:0001589	frameshift_variant	23244	exon27			.	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.3146_3153delTTATGAAG	4.37:g.39851206_39851213delCTTCATAA	ENSP00000303427:p.Phe1049fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	82	23	NM_001100399	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000303538.8	37	CCDS47045.1																																																																																			.		0.38	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		-	39851213	CTTCATAA	-	39851206	7	5	27	1	0	1	0	1	0	0	0	0	11717	912	32	0	888	0	PDS5A	4	39851206	Frame_Shift_Del	DEL	CTTCATAA	TCGA-A4-A5Y1-01A-11D-A28G-10	26248560	39851206	151303070	26	2341	22	2									
PDS5A	23244	bcgsc.ca	37	chr4	39851214	39851214	+	Missense_Mutation	SNP	A	A	G																															ctctgccatcttcttcataaAggcatggctattgttttcat																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:39851214A>G	ENST00000303538.8	-	27	3684	c.3145T>C	c.(3145-3147)Ttt>Ctt	p.F1049L		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TTCTTCATAAAGGCATGGCTA	0.388																																					p.F1049L													.	.	0			c.T3145C						.						140	129	132					4																	39851214		1882	4129	6011	SO:0001583	missense	23244	exon27			TCATAAAGGCATG	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.3145T>C	4.37:g.39851214A>G	ENSP00000303427:p.Phe1049Leu	Somatic	90	0		WXS	Illumina HiSeq	Phase_1	76	23	NM_001100399	0	0	25	25	0		Missense_Mutation	SNP	ENST00000303538.8	37	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	A	34	5.366841	0.95900	.	.	ENSG00000121892	ENST00000303538	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.79269	0.4417	M	0.78637	2.42	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	T	0.80668	-0.1280	8	.	.	.	-15.3149	15.7677	0.78141	1.0:0.0:0.0:0.0	.	1049	Q29RF7	PDS5A_HUMAN	L	1049	.	.	F	-	1	0	PDS5A	39527609	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.224000	0.95209	2.112000	0.64535	0.533000	0.62120	TTT	.		0.388	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		G	39851214	A	G	39851214	3	3	27	1	0	0	0	0	1	0	0	0	11717	72	3	3	896	3	PDS5A	4	39851214	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	8	39851214	151303062	27	2342	22	2									
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48485850	48485850	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gttccctcggccctgggcgcCccacgcgctcccgttctggg	1	8	13	19	5	1	0	0	0	1	0	4	0	3	0	5	3	0	3	5	3	0	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:48485850C>G	ENST00000273861.4	+	1	491	c.272C>G	c.(271-273)cCc>cGc	p.P91R		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						CCCTGGGCGCCCCACGCGCTC	0.756																																					p.P91R		.											.	SLC10A4-90	0			c.C272G						.																																			SO:0001583	missense	201780	exon1			GGGCGCCCCACGC	BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"Solute carriers"	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.272C>G	4.37:g.48485850C>G	ENSP00000273861:p.Pro91Arg	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	34	10	NM_152679	0	0	0	0	0	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	37	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	c	14.82	2.648971	0.47362	.	.	ENSG00000145248	ENST00000273861	T	0.09255	3.0	4.58	3.74	0.42951	.	0.434744	0.26692	N	0.022981	T	0.08802	0.0218	L	0.40543	1.245	0.19575	N	0.999969	B	0.09022	0.002	B	0.06405	0.002	T	0.21690	-1.0238	10	0.45353	T	0.12	-26.3851	6.3555	0.21398	0.0:0.6733:0.1543:0.1724	.	91	Q96EP9	NTCP4_HUMAN	R	91	ENSP00000273861:P91R	ENSP00000273861:P91R	P	+	2	0	SLC10A4	48180607	0.004000	0.15560	0.599000	0.28851	0.923000	0.55619	1.782000	0.38654	1.159000	0.42565	-0.348000	0.07805	CCC	.		0.756	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		G	48485850	C	G	48485850	3	3	27	1	0	0	0	0	1	0	0	0	14408	623	22	4	274	4	SLC10A4	4	48485850	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	8634636	48485850	142668426	28	2343											
NMU	10874	hgsc.bcm.edu	37	chr4	56502304	56502304	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagcaggagcggggacGccgcggccacctgtccggcg	6	2	18	15	6	0	0	0	0	0	0	1	2	1	2	4	5	3	3	4	5	0	0	rs35771241	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:56502304G>T	ENST00000264218.3	-	1	161	c.56C>A	c.(55-57)gCg>gAg	p.A19E	NMU_ENST00000511469.1_Missense_Mutation_p.A19E|NMU_ENST00000515325.1_Intron|NMU_ENST00000505262.1_Missense_Mutation_p.A19E|NMU_ENST00000507338.1_Missense_Mutation_p.A19E	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	19					digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		gagcGGGGACGCCGCGGCCAC	0.761													G|||	88	0.0175719	0.0038	0.0245	5008	,	,		10083	0		0.0577	False		,,,				2504	0.0082				p.A19E		.											.	NMU-650	0			c.C56A	GRCh37	CM066152	NMU	M	rs35771241	.	G	GLU/ALA	34,3224		0,34,1595	5	7	6		56	1.1	0	4	dbSNP_126	6	262,5824		1,260,2782	no	missense	NMU	NM_006681.2	107	1,294,4377	TT,TG,GG		4.305,1.0436,3.1678	benign	19/175	56502304	296,9048	1629	3043	4672	SO:0001583	missense	10874	exon1			GGGGACGCCGCGG	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"Endogenous ligands"	7859	protein-coding gene	gene with protein product	"prepro-NMU"	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.56C>A	4.37:g.56502304G>T	ENSP00000264218:p.Ala19Glu	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	12	NM_006681	0	0	0	3	3		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	64	0.029304029304029304	6	0.012195121951219513	16	0.04419889502762431	0	0.0	42	0.055408970976253295	G	14.57	2.576146	0.45902	0.010436	0.04305	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.38887	1.11;1.25;1.19;1.18	2.89	1.06	0.20224	.	0.337479	0.19087	U	0.123078	T	0.03959	0.0111	L	0.44542	1.39	0.09310	N	1	D	0.54397	0.966	P	0.45195	0.473	T	0.03784	-1.1004	10	0.52906	T	0.07	-8.0688	3.8411	0.08914	0.1476:0.2562:0.5962:0.0	rs35771241	19	P48645	NMU_HUMAN	E	19	ENSP00000422399:A19E;ENSP00000264218:A19E;ENSP00000424246:A19E;ENSP00000422870:A19E	ENSP00000264218:A19E	A	-	2	0	NMU	56197061	0.000000	0.05858	0.001000	0.08648	0.273000	0.26683	-0.032000	0.12266	0.255000	0.21593	0.195000	0.17529	GCG	G|0.970;T|0.030		0.761	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2			T	56502304	G	T	56502304	3	4	27	1	0	0	0	0	1	0	0	0	10531	1087	38	4	504	4	NMU	4	56502304	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	8016454	56502304	134651972	29	2344											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123260393	123260393	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaatttagctgtttaccagTatcaagagtagaatgcatgt	14	13	8	6	0	1	2	1	0	0	2	1	2	1	2	1	0	3	5	1	0	7	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:123260393T>A	ENST00000264501.4	+	72	12555	c.12182T>A	c.(12181-12183)gTa>gAa	p.V4061E	KIAA1109_ENST00000388738.3_Missense_Mutation_p.V4061E			Q2LD37	K1109_HUMAN	KIAA1109	4061					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TGTTTACCAGTATCAAGAGTA	0.368																																					p.V4061E		.											.	KIAA1109-80	0			c.T12182A						.						134	120	124					4																	123260393		1830	4088	5918	SO:0001583	missense	84162	exon70			TACCAGTATCAAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12182T>A	4.37:g.123260393T>A	ENSP00000264501:p.Val4061Glu	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	121	66	NM_015312	0	0	18	41	23	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	28.3|28.3|28.3	4.907716|4.907716|4.907716	0.92107|0.92107|0.92107	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000442707|ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	.|T;T;T|.	.|0.35789|.	.|2.31;2.31;1.29|.	5.81|5.81|5.81	5.81|5.81|5.81	0.92471|0.92471|0.92471	.|.|.	.|0.067355|.	.|0.64402|.	.|D|.	.|0.000010|.	T|T|T	0.68540|0.68540|0.68540	0.3012|0.3012|0.3012	L|L|L	0.49126|0.49126|0.49126	1.545|1.545|1.545	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P;P|.	.|0.49961|.	.|0.899;0.93|.	.|P;P|.	.|0.45232|.	.|0.474;0.462|.	T|T|T	0.65853|0.65853|0.65853	-0.6067|-0.6067|-0.6067	5|10|5	.|0.66056|.	.|D|.	.|0.02|.	.|.|.	16.1637|16.1637|16.1637	0.81739|0.81739|0.81739	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|4060;4061|.	.|Q2LD37-4;Q2LD37|.	.|.;K1109_HUMAN|.	R|E|N	6|4061;4061;730|437	.|ENSP00000264501:V4061E;ENSP00000373390:V4061E;ENSP00000410874:V730E|.	.|ENSP00000264501:V4061E|.	S|V|Y	+|+|+	3|2|1	2|0|0	KIAA1109|KIAA1109|KIAA1109	123479843|123479843|123479843	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.963000|7.963000|7.963000	0.87922|0.87922|0.87922	2.216000|2.216000|2.216000	0.71823|0.71823|0.71823	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AGT|GTA|TAT	.		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123260393	T	A	123260393	3	1	27	1	0	0	0	0	1	0	0	0	8229	1638	57	5	12460	5	KIAA1109	4	123260393	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	66758089	123260393	67893883	30	2345											
ODZ3	55714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	183713663	183713663	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgggtacaagtcggagggtCttattcaaatacagaaggca	13	10	12	6	1	2	1	1	0	1	1	3	2	2	2	0	4	2	2	0	4	6	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:183713663C>T	ENST00000511685.1	+	26	5961	c.5838C>T	c.(5836-5838)gtC>gtT	p.V1946V	TENM3_ENST00000406950.2_Silent_p.V1946V			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1946					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTCGGAGGGTCTTATTCAAAT	0.448																																					p.V1946V		.											.	.	0			c.C5838T						.						63	63	63					4																	183713663		1880	4104	5984	SO:0001819	synonymous_variant	55714	exon25			GAGGGTCTTATTC	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5838C>T	4.37:g.183713663C>T		Somatic	149	0		WXS	Illumina HiSeq	Phase_I	206	69	NM_001080477	0	0	1	2	1	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			.		0.448	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183713663	C	T	183713663	2	4	27	1	0	0	0	0	0	0	0	1	10862	900	32	2		2	ODZ3	4	183713663	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	60453270	183713663	7440613	31	2346											
NKD2	85409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1033498	1033498	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccccctagtggcactccccGctgagaaagctgagggccgc	7	6	12	16	2	0	2	0	2	0	1	2	3	2	2	5	2	1	3	5	2	2	1	rs144426465		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:1033498G>A	ENST00000296849.5	+	5	443	c.214G>A	c.(214-216)Gct>Act	p.A72T	NKD2_ENST00000537972.1_Missense_Mutation_p.A72T|NKD2_ENST00000274150.4_Missense_Mutation_p.A72T	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	72	Targeting to the basolateral cell membrane.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GGCACTCCCCGCTGAGAAAGC	0.692																																					p.A72T		.											.	NKD2-226	0			c.G214A						.	C	THR/ALA	0,4370		0,0,2185	18	22	20		214	-0.3	0	5	dbSNP_134	20	6,8568		0,6,4281	yes	missense	NKD2	NM_033120.2	58	0,6,6466	AA,AG,GG		0.07,0.0,0.0464	benign	72/452	1033498	6,12938	2185	4287	6472	SO:0001583	missense	85409	exon5			CTCCCCGCTGAGA	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"EF-hand domain containing"	17046	protein-coding gene	gene with protein product	"naked cuticle-2", "Dvl-binding protein NKD2"	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.214G>A	5.37:g.1033498G>A	ENSP00000296849:p.Ala72Thr	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	226	51	NM_001271082	0	0	0	0	0	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	.	.	.	.	.	.	.	.	.	.	N	10.61	1.399838	0.25291	0.0	7.0E-4	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.00535	6.73;6.73;6.73	3.69	-0.271	0.12922	.	0.159534	0.41396	N	0.000898	T	0.00328	0.0010	N	0.22421	0.69	0.80722	D	1	B;B	0.33022	0.002;0.394	B;B	0.25506	0.002;0.061	T	0.72721	-0.4208	10	0.66056	D	0.02	-8.4045	2.08	0.03633	0.1396:0.4077:0.273:0.1798	.	72;72	Q969F2-2;Q969F2	.;NKD2_HUMAN	T	72	ENSP00000296849:A72T;ENSP00000274150:A72T;ENSP00000440925:A72T	ENSP00000274150:A72T	A	+	1	0	NKD2	1086498	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.116000	0.10724	-0.934000	0.03733	-5.484000	0.00000	GCT	G|1.000;A|0.000		0.692	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		A	1033498	G	A	1033498	3	1	27	1	0	0	0	0	1	0	0	0	10468	1087	38	1	232	1	NKD2	5	1033498	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1033498	179881762	32	2347											
DEPDC1B	55789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	59893587	59893587	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtggaagtattattacattCgaaaacttctagttctttga	12	17	7	5	1	2	1	0	1	2	0	3	3	2	2	0	1	2	2	0	1	7	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:59893587C>T	ENST00000265036.5	-	11	1650	c.1583G>A	c.(1582-1584)cGa>cAa	p.R528Q	DEPDC1B_ENST00000545085.1_Missense_Mutation_p.R439Q|DEPDC1B_ENST00000453022.2_Missense_Mutation_p.R466Q	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	528					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				TTATTACATTCGAAAACTTCT	0.418																																					p.R528Q		.											.	DEPDC1B-91	0			c.G1583A						.						174	167	170					5																	59893587		2203	4300	6503	SO:0001583	missense	55789	exon11			TACATTCGAAAAC	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1583G>A	5.37:g.59893587C>T	ENSP00000265036:p.Arg528Gln	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	77	21	NM_018369	0	0	10	12	2	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	37	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	C	34	5.383654	0.95967	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.49432	1.96;1.18;0.78	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.67767	0.2928	M	0.68593	2.085	0.53688	D	0.999979	D;D	0.89917	0.997;1.0	D;D	0.70227	0.968;0.941	T	0.64850	-0.6310	9	.	.	.	-9.0991	19.4868	0.95032	0.0:1.0:0.0:0.0	.	466;528	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	Q	528;466;439	ENSP00000265036:R528Q;ENSP00000389101:R466Q;ENSP00000438320:R439Q	.	R	-	2	0	DEPDC1B	59929344	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.694000	0.74587	2.838000	0.97847	0.591000	0.81541	CGA	.		0.418	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		T	59893587	C	T	59893587	3	4	27	1	0	0	0	0	1	0	0	0	4451	884	31	1	10	1	DEPDC1B	5	59893587	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	58860089	59893587	121021673	33	2348											
AP3B1	8546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	77521385	77521385	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtgcttttatctttcagaAgtttttcaattacttcaatt	9	21	4	7	0	4	1	3	0	1	1	4	1	4	1	0	0	2	2	0	0	5	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:77521385A>C	ENST00000255194.6	-	6	759	c.584T>G	c.(583-585)cTt>cGt	p.L195R	AP3B1_ENST00000519295.1_Missense_Mutation_p.L146R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	195					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		ATCTTTCAGAAGTTTTTCAAT	0.239									Hermansky-Pudlak syndrome																												p.L195R		.											.	AP3B1-90	0			c.T584G						.						55	55	55					5																	77521385		2193	4276	6469	SO:0001583	missense	8546	exon6	Familial Cancer Database	HPS, HPS1-8	TTCAGAAGTTTTT	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.584T>G	5.37:g.77521385A>C	ENSP00000255194:p.Leu195Arg	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	88	54	NM_003664	1	0	25	65	39	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	18.69	3.678934	0.68042	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.18502	2.21;2.21	5.59	4.44	0.53790	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54431	0.1858	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67023	-0.5775	10	0.87932	D	0	-1.7217	11.3981	0.49854	0.9293:0.0:0.0707:0.0	.	195	O00203	AP3B1_HUMAN	R	195;146;195;99	ENSP00000255194:L195R;ENSP00000430597:L146R	ENSP00000255194:L195R	L	-	2	0	AP3B1	77557141	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.245000	0.95431	0.959000	0.37980	-0.361000	0.07541	CTT	.		0.239	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77521385	A	C	77521385	3	2	27	1	0	0	0	0	1	0	0	0	744	72	3	5	2788	5	AP3B1	5	77521385	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	17627798	77521385	103393875	34	2349											
IK	3550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140037217	140037217	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catacctgaggcagggaaccCgtaacaagaagcttaagaag	16	5	11	9	1	0	3	0	1	0	2	0	4	0	4	2	2	4	3	2	2	7	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:140037217C>T	ENST00000417647.2	+	10	1019	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	294					cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGGAACCCGTAACAAGAA	0.473																																					p.R294C		.											.	IK-67	0			c.C880T						.						129	116	120					5																	140037217		1910	4122	6032	SO:0001583	missense	3550	exon10			GGAACCCGTAACA	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.880C>T	5.37:g.140037217C>T	ENSP00000396301:p.Arg294Cys	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	269	59	NM_006083	0	0	198	302	104	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	37	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584507	0.86748	.	.	ENSG00000113141	ENST00000417647	.	.	.	5.48	5.48	0.80851	RED-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80722	0.4677	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.83092	-0.0132	9	0.72032	D	0.01	.	14.198	0.65684	0.1496:0.8504:0.0:0.0	.	294;294	Q9UK43;Q13123	.;RED_HUMAN	C	294	.	ENSP00000396301:R294C	R	+	1	0	IK	140017401	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.692000	0.54727	2.730000	0.93505	0.655000	0.94253	CGT	.		0.473	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083		T	140037217	C	T	140037217	3	4	27	1	0	0	0	0	1	0	0	0	7629	652	23	1	918	1	IK	5	140037217	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	62515832	140037217	40878043	35	2350											
PCDHB6	56130	broad.mit.edu	37	chr5	140531290	140531290	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaggcatcaacgcccaggtCacctactcgctgctgccgcc	7	7	9	18	3	3	0	3	0	0	0	4	0	3	0	4	2	4	3	4	2	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:140531290C>T	ENST00000231136.1	+	1	1452	c.1452C>T	c.(1450-1452)gtC>gtT	p.V484V	PCDHB6_ENST00000543635.1_Silent_p.V348V	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGCCCAGGTCACCTACTCGC	0.647																																					p.V484V													.	PCDHB6-91	0			c.C1452T						.						100	108	105					5																	140531290		2203	4298	6501	SO:0001819	synonymous_variant	56130	exon1			CCAGGTCACCTAC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1452C>T	5.37:g.140531290C>T		Somatic	137	1		WXS	Illumina HiSeq	Phase_I	237	7	NM_018939	0	0	0	1	1	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			.		0.647	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140531290	C	T	140531290	2	4	27	1	0	0	0	0	0	0	0	1	11572	813	29	2		2	PCDHB6	5	140531290	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	494073	140531290	40383970	36	2351											
PCDHGB3	56102	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140751665	140751665	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgctgtacccagctctgggGcccgaaggctctgcgctctt	4	10	13	14	2	3	0	0	0	3	0	3	1	3	0	2	3	4	5	2	3	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:140751665G>A	ENST00000576222.1	+	1	1835	c.1704G>A	c.(1702-1704)ggG>ggA	p.G568G	PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	568					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCTCTGGGGCCCGAAGGCT	0.657																																					p.G568G													.	.	0			c.G1704A						.						41	51	48					5																	140751665		2199	4299	6498	SO:0001819	synonymous_variant	56102	exon1			TCTGGGGCCCGAA	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1704G>A	5.37:g.140751665G>A		Somatic	123	1		WXS	Illumina HiSeq	Phase_I	296	76	NM_018924	0	0	1	1	0	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			.		0.657	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140751665	G	A	140751665	2	1	27	1	0	0	0	0	0	0	0	1	11590	1190	42	2		2	PCDHGB3	5	140751665	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	220375	140751665	40163595	37	2352											
NMUR2	56923	broad.mit.edu	37	chr5	151775087	151775088	+	Missense_Mutation	DNP	GA	GA	AT																															cactcctccacaaagctgaaGaagagtcggtcaatgtggaa																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:151775087_151775088GA>AT	ENST00000255262.3	-	3	1034_1035	c.869_870TC>AT	c.(868-870)tTC>tAT	p.F290Y	NMUR2_ENST00000518933.1_5'UTR	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	290					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CAAAGCTGAAGAAGAGTCGGTC	0.485																																					p.F290Y													.	NMUR2-526	0			c.T869A						.																																			SO:0001583	missense	56923	exon3			CTGAAGAAGAGTC	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"GPCR / Class A : Neuromedin U receptors"	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.869_870delinsAT	5.37:g.151775087_151775088delinsAT	ENSP00000255262:p.Phe290Tyr	Somatic	372	0		WXS	Illumina HiSeq	Phase_I	459	9	NM_020167	0	0	0	0	0	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	DNP	ENST00000255262.3	37	CCDS4321.1																																																																																			.		0.485	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		AT	151775088	GA	AT	151775087	3	1	27	1	0	0	0	0	1	0	0	0	10533	933	33	2	385	2	NMUR2	5	151775087	Missense_Mutation	DNP	GA	TCGA-A4-A5Y1-01A-11D-A28G-10	11023422	151775087	29140173	38	2353											
FAM65B	9750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	24836059	24836059	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtgtcttcagtgagcgcttCactgagatgccccctggctt	5	13	11	12	1	3	2	2	2	1	1	3	3	3	2	2	1	2	2	2	1	0	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:24836059C>T	ENST00000259698.4	-	16	2318	c.2143G>A	c.(2143-2145)Gaa>Aaa	p.E715K	FAM65B_ENST00000538035.1_Missense_Mutation_p.E694K	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	715					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GTGAGCGCTTCACTGAGATGC	0.527																																					p.E715K		.											.	FAM65B-91	0			c.G2143A						.						105	90	94					6																	24836059		692	1591	2283	SO:0001583	missense	9750	exon16			GCGCTTCACTGAG	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.2143G>A	6.37:g.24836059C>T	ENSP00000259698:p.Glu715Lys	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	252	75	NM_014722	0	0	2	2	0	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966222	0.74131	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.35789	1.29;1.29	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	L	0.43152	1.355	0.80722	D	1	B;B	0.31548	0.264;0.328	B;B	0.30495	0.085;0.116	T	0.09640	-1.0665	10	0.66056	D	0.02	-10.1386	19.1916	0.93669	0.0:1.0:0.0:0.0	.	694;715	F5GX51;Q9Y4F9	.;FA65B_HUMAN	K	715;694	ENSP00000259698:E715K;ENSP00000441138:E694K	ENSP00000259698:E715K	E	-	1	0	FAM65B	24944038	1.000000	0.71417	0.595000	0.28798	0.748000	0.42578	7.452000	0.80683	2.541000	0.85698	0.655000	0.94253	GAA	.		0.527	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			T	24836059	C	T	24836059	3	4	27	1	0	0	0	0	1	0	0	0	5619	835	29	2	1095	2	FAM65B	6	24836059	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		24836059	146279008	39	2354											
HIST1H1C	3006	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	26056096	26056096	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcacagccttagcagcactTttggcagctttcttgggctt	6	15	9	11	0	2	0	1	0	1	0	2	0	2	0	1	2	4	5	1	2	1	7			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:26056096T>C	ENST00000343677.2	-	1	603	c.561A>G	c.(559-561)aaA>aaG	p.K187K		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	187					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TAGCAGCACTTTTGGCAGCTT	0.547																																					p.K187K		.											.	HIST1H1C-231	0			c.A561G						.						89	96	93					6																	26056096		2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			AGCACTTTTGGCA	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.561A>G	6.37:g.26056096T>C		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	143	12	NM_005319	0	0	33	47	14	A8K4I2	Silent	SNP	ENST00000343677.2	37	CCDS4577.1																																																																																			.		0.547	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		C	26056096	T	C	26056096	2	2	27	1	0	0	0	0	0	0	0	1	7145	1838	64	3		3	HIST1H1C	6	26056096	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	1220037	26056096	145058971	40	2355											
GRM4	2914	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	34059858	34059858	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtctggcgctgtggaggCgtagctgatctggggtatct	5	11	17	8	2	3	1	0	1	3	0	3	2	3	2	0	6	1	4	0	6	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:34059858C>T	ENST00000538487.2	-	3	981	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	GRM4_ENST00000374177.3_Missense_Mutation_p.A111T|GRM4_ENST00000374181.4_Missense_Mutation_p.A180T|GRM4_ENST00000455714.2_Missense_Mutation_p.A40T|GRM4_ENST00000535756.1_Missense_Mutation_p.A47T|GRM4_ENST00000609222.1_Missense_Mutation_p.A47T|GRM4_ENST00000544773.2_Missense_Mutation_p.A11T	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	180	Glutamate binding. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GCTGTGGAGGCGTAGCTGATC	0.647																																					p.A180T													.	GRM4-525	0			c.G538A						.						101	82	89					6																	34059858		2203	4300	6503	SO:0001583	missense	2914	exon3			TGGAGGCGTAGCT	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.538G>A	6.37:g.34059858C>T	ENSP00000440556:p.Ala180Thr	Somatic	128	2		WXS	Illumina HiSeq	Phase_I	182	83	NM_001256811	0	0	0	0	0	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.926278	0.92319	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	3.91	3.91	0.45181	GPCR, family 3, conserved site (1);Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000001	D	0.91157	0.7215	M	0.84082	2.675	0.80722	D	1	P;D;D;D;D;D	0.89917	0.897;0.994;1.0;0.998;0.998;1.0	P;D;D;D;D;D	0.79784	0.523;0.962;0.993;0.909;0.909;0.982	D	0.92178	0.5749	10	0.56958	D	0.05	.	16.069	0.80909	0.0:1.0:0.0:0.0	.	180;11;40;180;180;47	B7ZLU9;B7Z1T9;F5GXM5;A1L4F9;Q14833;B3KVL9	.;.;.;.;GRM4_HUMAN;.	T	180;111;47;11;180;40	ENSP00000363296:A180T;ENSP00000363292:A111T;ENSP00000437925:A47T;ENSP00000437730:A11T;ENSP00000440556:A180T;ENSP00000398456:A40T	ENSP00000363292:A111T	A	-	1	0	GRM4	34167836	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.647000	0.83462	2.001000	0.58596	0.561000	0.74099	GCC	.		0.647	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			T	34059858	C	T	34059858	3	4	27	1	0	0	0	0	1	0	0	0	6820	768	27	1	2236	1	GRM4	6	34059858	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	8003762	34059858	137055209	41	2356											
SLC26A5	375611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	103050896	103050896	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	caaacagatattttaacatgGaggtgaagacatgcacagct	16	9	9	7	0	0	3	0	1	0	2	0	4	0	4	0	2	4	2	0	2	4	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr7:103050896G>C	ENST00000306312.3	-	7	932	c.671C>G	c.(670-672)tCc>tGc	p.S224C	SLC26A5_ENST00000393723.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000393730.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000432958.2_Missense_Mutation_p.S224C|SLC26A5_ENST00000393735.2_Missense_Mutation_p.S224C|SLC26A5_ENST00000393729.1_Missense_Mutation_p.S187C|SLC26A5_ENST00000393727.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000356767.4_Missense_Mutation_p.S224C|SLC26A5_ENST00000339444.6_Missense_Mutation_p.S224C	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	224					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TTTTAACATGGAGGTGAAGAC	0.443																																					p.S224C		.											.	SLC26A5-91	0			c.C671G						.						73	71	71					7																	103050896		2203	4300	6503	SO:0001583	missense	375611	exon7			AACATGGAGGTGA	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.671C>G	7.37:g.103050896G>C	ENSP00000304783:p.Ser224Cys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_206883	0	0	0	0	0	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	37	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.816614	0.90790	.	.	ENSG00000170615	ENST00000339444;ENST00000356767;ENST00000393735;ENST00000306312;ENST00000393730;ENST00000432958;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	5.72	5.72	0.89469	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97898	0.9309	H	0.95365	3.66	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.998;0.999;0.997;0.999	D;D;D;D;D	0.73380	0.98;0.974;0.967;0.931;0.956	D	0.98561	1.0641	10	0.87932	D	0	.	19.885	0.96909	0.0:0.0:1.0:0.0	.	224;224;224;224;224	P58743;Q496J2;P58743-4;P58743-3;P58743-2	S26A5_HUMAN;.;.;.;.	C	224;224;224;224;224;224;187;224;224	ENSP00000342396:S224C;ENSP00000349210:S224C;ENSP00000377336:S224C;ENSP00000304783:S224C;ENSP00000377331:S224C;ENSP00000389733:S224C;ENSP00000377330:S187C;ENSP00000377328:S224C;ENSP00000377324:S224C	ENSP00000304783:S224C	S	-	2	0	SLC26A5	102838132	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.330000	0.96422	2.708000	0.92522	0.591000	0.81541	TCC	.		0.443	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		C	103050896	G	C	103050896	3	2	27	1	0	0	0	0	1	0	0	0	14552	1174	41	4	1660	4	SLC26A5	7	103050896	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		103050896	56087767	42	2357											
PLXNA4	91584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	131887415	131887415	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccggcttacctctgtgatgCgggggtttgtgcacttgctt	3	14	13	11	2	1	1	0	1	1	0	1	1	1	1	2	3	4	4	2	3	1	4	rs201337636	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr7:131887415C>T	ENST00000359827.3	-	12	3538	c.2576G>A	c.(2575-2577)cGc>cAc	p.R859H	PLXNA4_ENST00000321063.4_Missense_Mutation_p.R859H			Q9HCM2	PLXA4_HUMAN	plexin A4	859	IPT/TIG 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CTCTGTGATGCGGGGGTTTGT	0.662													C|||	2	0.000399361	8e-04	0	5008	,	,		16915	0.001		0	False		,,,				2504	0				p.R859H		.											.	PLXNA4-91	0			c.G2576A						.	C	HIS/ARG	0,3930		0,0,1965	40	42	42		2576	3.9	1	7		42	2,8298		0,2,4148	yes	missense	PLXNA4	NM_020911.1	29	0,2,6113	TT,TC,CC		0.0241,0.0,0.0164	possibly-damaging	859/1895	131887415	2,12228	1965	4150	6115	SO:0001583	missense	91584	exon12			GTGATGCGGGGGT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2576G>A	7.37:g.131887415C>T	ENSP00000352882:p.Arg859His	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	48	8	NM_020911	0	0	0	0	0	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	22.0	4.230340	0.79688	0.0	2.41E-4	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.76578	-1.03;-1.03	4.74	3.86	0.44501	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);	0.054169	0.64402	D	0.000003	D	0.82287	0.5004	M	0.76002	2.32	0.49915	D	0.999839	D	0.54772	0.968	P	0.55161	0.77	T	0.81955	-0.0696	10	0.46703	T	0.11	.	9.6194	0.39712	0.0:0.8177:0.0:0.1823	.	859	Q9HCM2	PLXA4_HUMAN	H	859	ENSP00000323194:R859H;ENSP00000352882:R859H	ENSP00000323194:R859H	R	-	2	0	PLXNA4	131537955	1.000000	0.71417	0.953000	0.39169	0.915000	0.54546	4.567000	0.60850	1.223000	0.43536	0.561000	0.74099	CGC	C|0.999;T|0.001		0.662	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131887415	C	T	131887415	3	4	27	1	0	0	0	0	1	0	0	0	12148	768	27	1	3192	1	PLXNA4	7	131887415	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	28836519	131887415	27251248	43	2358											
EIF4EBP1	1978	bcgsc.ca	37	chr8	37914734	37914734	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagccccccatggaagccaGccagagccacctgcgcaata	11	4	10	16	1	0	2	0	1	0	1	0	3	0	3	7	1	5	1	7	1	3	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr8:37914734G>A	ENST00000338825.4	+	2	514	c.281G>A	c.(280-282)aGc>aAc	p.S94N	EIF4EBP1_ENST00000520657.1_3'UTR	NM_004095.3	NP_004086.1	Q13541	4EBP1_HUMAN	eukaryotic translation initiation factor 4E binding protein 1	94					cellular protein metabolic process (GO:0044267)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translational initiation (GO:0045947)|positive regulation of mitotic cell cycle (GO:0045931)|response to ethanol (GO:0045471)|response to ischemia (GO:0002931)|TOR signaling (GO:0031929)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|protein complex (GO:0043234)	translation repressor activity (GO:0030371)			endometrium(1)|lung(1)|ovary(1)|urinary_tract(1)	4	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)				ATGGAAGCCAGCCAGAGCCAC	0.617																																					p.S94N	Melanoma(144;549 1821 15133 20335 46806)												.	EIF4EBP1-846	0			c.G281A						.						47	52	50					8																	37914734		2203	4300	6503	SO:0001583	missense	1978	exon2			AAGCCAGCCAGAG		CCDS6100.1	8p12	2008-10-08			ENSG00000187840	ENSG00000187840			3288	protein-coding gene	gene with protein product	"phosphorylated heat- and acid-stable protein regulated by insulin 1"	602223				7935836	Standard	NM_004095		Approved	PHAS-I, 4E-BP1	uc003xks.3	Q13541	OTTHUMG00000164012	ENST00000338825.4:c.281G>A	8.37:g.37914734G>A	ENSP00000340691:p.Ser94Asn	Somatic	52	0		WXS	Illumina HiSeq	Phase_1	56	4	NM_004095	0	0	43	43	0	B2R502|D3DSW8|Q6IBN3	Missense_Mutation	SNP	ENST00000338825.4	37	CCDS6100.1	.	.	.	.	.	.	.	.	.	.	G	0.964	-0.702275	0.03255	.	.	ENSG00000187840	ENST00000338825	.	.	.	4.58	2.61	0.31194	.	0.470791	0.21761	N	0.069502	T	0.15046	0.0363	N	0.05124	-0.11	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.22836	-1.0205	9	0.15066	T	0.55	-0.62	8.0013	0.30299	0.2188:0.0:0.7812:0.0	.	94	Q13541	4EBP1_HUMAN	N	94	.	ENSP00000340691:S94N	S	+	2	0	EIF4EBP1	38033891	0.867000	0.29959	0.808000	0.32385	0.251000	0.25915	1.072000	0.30678	1.150000	0.42419	0.455000	0.32223	AGC	.		0.617	EIF4EBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376743.1	NM_004095		A	37914734	G	A	37914734	3	1	27	1	0	0	0	0	1	0	0	0	5045	971	34	2	287	2	EIF4EBP1	8	37914734	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		37914734	108449288	44	2359											
STAU2	27067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	74464271	74464271	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagccttgaatccttgctaaAtattccagttgttttgaagg	11	15	8	7	0	0	2	0	2	0	0	2	2	2	2	3	1	2	3	3	1	6	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr8:74464271A>G	ENST00000521451.1	-	8	1222	c.846T>C	c.(844-846)taT>taC	p.Y282Y	STAU2_ENST00000521727.1_Silent_p.Y482Y|STAU2_ENST00000355780.5_Silent_p.Y470Y|STAU2_ENST00000519961.1_Silent_p.Y502Y|STAU2_ENST00000521210.1_Silent_p.Y398Y|STAU2_ENST00000524300.1_Silent_p.Y502Y|STAU2_ENST00000522695.1_Silent_p.Y470Y|STAU2_ENST00000517542.1_Silent_p.Y464Y|STAU2_ENST00000522509.1_Silent_p.Y470Y|STAU2_ENST00000523558.1_Silent_p.Y330Y			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	502					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TCCTTGCTAAATATTCCAGTT	0.363																																					p.Y502Y		.											.	STAU2-90	0			c.T1506C						.						56	61	59					8																	74464271		2203	4297	6500	SO:0001819	synonymous_variant	27067	exon13			TGCTAAATATTCC	Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"staufen (Drosophila, RNA-binding protein) homolog 2", "staufen, RNA binding protein, homolog 2 (Drosophila)"			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521451.1:c.846T>C	8.37:g.74464271A>G		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	143	61	NM_001164380	0	0	40	96	56	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	37																																																																																				.		0.363	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380		G	74464271	A	G	74464271	2	3	27	1	0	0	0	0	0	0	0	1	15305	108	4	3		3	STAU2	8	74464271	Silent	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	36549537	74464271	71899751	45	2360											
PSIP1	11168	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	15468982	15468982	+	Frame_Shift_Del	DEL	G	G	-																															agtgtagtaatcatctctgtGtgtttctgagcttgttgcat																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:15468982delG	ENST00000380733.4	-	13	1522	c.1179delC	c.(1177-1179)cacfs	p.H393fs	PSIP1_ENST00000380738.4_Frame_Shift_Del_p.H393fs			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	393					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TCATCTCTGTGTGTTTCTGAG	0.328																																					p.H393fs		.											.	PSIP1-658	0			c.1179delC						.						89	82	84					9																	15468982		2202	4300	6502	SO:0001589	frameshift_variant	11168	exon13			.	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.1179delC	9.37:g.15468982delG	ENSP00000370109:p.His393fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	51	28	NM_001128217	0	0	0	0	0	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Frame_Shift_Del	DEL	ENST00000380733.4	37	CCDS6479.1																																																																																			.		0.328	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		-	15468982	G	-	15468982	7	5	27	1	0	1	0	1	0	0	0	0	12692	1368	48	0	429	0	PSIP1	9	15468982	Frame_Shift_Del	DEL	G	TCGA-A4-A5Y1-01A-11D-A28G-10		15468982	125744449	46	2361											
OR13F1	138805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	107267461	107267461	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccttgaaaaaattgctgatTagaaatcattttaatactgc	15	14	6	6	0	1	3	1	2	0	1	1	3	1	3	1	0	3	1	1	0	7	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:107267461T>G	ENST00000334726.2	+	1	1007	c.918T>G	c.(916-918)atT>atG	p.I306M		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AATTGCTGATTAGAAATCATT	0.353																																					p.I306M		.											.	OR13F1-115	0			c.T918G						.						39	42	41					9																	107267461		2203	4300	6503	SO:0001583	missense	138805	exon1			GCTGATTAGAAAT		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"GPCR / Class A : Olfactory receptors"	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.918T>G	9.37:g.107267461T>G	ENSP00000334452:p.Ile306Met	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_001004485	0	0	0	0	0	Q6IF50	Missense_Mutation	SNP	ENST00000334726.2	37	CCDS35087.1	.	.	.	.	.	.	.	.	.	.	T	2.865	-0.235310	0.05983	.	.	ENSG00000186881	ENST00000334726	T	0.37411	1.2	4.3	-3.06	0.05379	.	0.941008	0.08732	N	0.901923	T	0.15262	0.0368	N	0.10972	0.075	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.20207	-1.0282	10	0.33141	T	0.24	.	3.0534	0.06176	0.1435:0.0881:0.443:0.3254	.	306	Q8NGS4	O13F1_HUMAN	M	306	ENSP00000334452:I306M	ENSP00000334452:I306M	I	+	3	3	OR13F1	106307282	0.000000	0.05858	0.004000	0.12327	0.446000	0.32137	-0.563000	0.05943	-0.521000	0.06426	-0.290000	0.09829	ATT	.		0.353	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1			G	107267461	T	G	107267461	3	3	27	1	0	0	0	0	1	0	0	0	10967	1742	61	5	920	5	OR13F1	9	107267461	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	91798479	107267461	33945970	47	2362											
SPTAN1	6709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131379924	131379924	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatctctcattcagggagaAgaagctgctggtgggctcag	9	9	13	10	0	4	2	3	0	1	2	5	3	4	2	1	3	2	3	1	3	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:131379924A>G	ENST00000372731.4	+	41	5458	c.5348A>G	c.(5347-5349)aAg>aGg	p.K1783R	SPTAN1_ENST00000358161.5_Missense_Mutation_p.K1788R|SPTAN1_ENST00000372739.3_Missense_Mutation_p.K1788R	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1783					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TTCAGGGAGAAGAAGCTGCTG	0.567																																					p.K1788R	NSCLC(120;833 1744 2558 35612 37579)	.											.	SPTAN1-158	0			c.A5363G						.						53	54	54					9																	131379924		2203	4300	6503	SO:0001583	missense	6709	exon42			GGGAGAAGAAGCT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.5348A>G	9.37:g.131379924A>G	ENSP00000361816:p.Lys1783Arg	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	143	50	NM_001130438	0	0	0	0	0	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628279	0.87560	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719;ENST00000372721	T;T;T	0.56444	0.46;0.46;0.46	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55103	1.725	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.97110	1.0;0.996;0.998	T	0.71101	-0.4690	10	0.66056	D	0.02	.	15.8191	0.78626	1.0:0.0:0.0:0.0	.	1763;1788;1783	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	R	1788;1783;1788;1763;32	ENSP00000350882:K1788R;ENSP00000361816:K1783R;ENSP00000361824:K1788R	ENSP00000350882:K1788R	K	+	2	0	SPTAN1	130419745	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	8.824000	0.92023	2.202000	0.70862	0.379000	0.24179	AAG	.		0.567	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		G	131379924	A	G	131379924	3	3	27	1	0	0	0	0	1	0	0	0	15149	72	3	3	5525	3	SPTAN1	9	131379924	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	24112463	131379924	9833507	48	2363											
EHMT1	79813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	140710514	140710514	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtcgtacagaatggtctcaGgtgagaggcagcttcctgcc	8	9	13	11	2	1	2	1	1	1	2	4	3	2	2	2	3	3	3	2	3	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:140710514G>A	ENST00000460843.1	+	23	3401	c.3374G>A	c.(3373-3375)aGg>aAg	p.R1125K		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1125					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AATGGTCTCAGGTGAGAGGCA	0.552																																					p.R1125K		.											.	EHMT1-154	0			c.G3374A						.						52	45	48					9																	140710514		2203	4300	6503	SO:0001630	splice_region_variant	79813	exon23			GTCTCAGGTGAGA	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	24650	protein-coding gene	gene with protein product		607001	"euchromatic histone methyltransferase 1"			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3374+1G>A	9.37:g.140710514G>A		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	67	35	NM_024757	0	0	0	16	16	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447711	0.26074	.	.	ENSG00000181090	ENST00000371400;ENST00000460843	D	0.88741	-2.42	5.11	5.11	0.69529	SET domain (1);	0.042517	0.85682	D	0.000000	T	0.73048	0.3537	N	0.04805	-0.155	0.80722	D	1	B	0.12013	0.005	B	0.08055	0.003	T	0.68379	-0.5424	10	0.02654	T	1	.	11.9694	0.53055	0.0798:0.0:0.9202:0.0	.	1125	Q9H9B1	EHMT1_HUMAN	K	1094;1125	ENSP00000417980:R1125K	ENSP00000360453:R1094K	R	+	2	0	EHMT1	139830335	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	7.876000	0.87215	2.357000	0.79964	0.591000	0.81541	AGG	.		0.552	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	Missense_Mutation	A	140710514	G	A	140710514	5	1	27	1	0	0	0	0	0	0	1	0	4994	1014	35	2	3513	2	EHMT1	9	140710514	Splice_Site	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	9330590	140710514	502917	49	2364											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	17169853	17169853	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattaagctgatagatttgaCtagatatattttgaggcaga	15	14	9	3	0	0	6	0	3	0	3	0	6	0	6	0	1	1	2	0	1	6	8	rs543983858		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:17169853C>A	ENST00000377833.4	-	3	388	c.323G>T	c.(322-324)aGt>aTt	p.S108I	CUBN_ENST00000377823.1_Missense_Mutation_p.S108I	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	108					cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATAGATTTGACTAGATATATT	0.338																																					p.S108I		.											.	CUBN-166	0			c.G323T						.						202	199	200					10																	17169853		2202	4300	6502	SO:0001583	missense	8029	exon3			ATTTGACTAGATA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.323G>T	10.37:g.17169853C>A	ENSP00000367064:p.Ser108Ile	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	39	19	NM_001081	0	0	0	0	0	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465566	0.43839	.	.	ENSG00000107611	ENST00000377833;ENST00000377823	T;D	0.89939	-1.04;-2.59	5.39	-1.65	0.08291	.	0.658141	0.14204	N	0.334504	T	0.77103	0.4081	N	0.19112	0.55	0.24501	N	0.994254	P	0.41265	0.744	B	0.36030	0.216	T	0.66991	-0.5783	10	0.33940	T	0.23	.	11.3077	0.49345	0.0:0.445:0.0:0.555	.	108	O60494	CUBN_HUMAN	I	108	ENSP00000367064:S108I;ENSP00000367054:S108I	ENSP00000367054:S108I	S	-	2	0	CUBN	17209859	0.964000	0.33143	0.979000	0.43373	0.946000	0.59487	-0.127000	0.10547	-0.237000	0.09739	0.650000	0.86243	AGT	.		0.338	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	17169853	C	A	17169853	3	1	27	1	0	0	0	0	1	0	0	0	4057	565	20	4	10808	4	CUBN	10	17169853	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		17169853	118364894	50	2365											
SLC25A28	81894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101370968	101370968	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgcaggaattcataggTcatgaagtgaatggcttgga	11	11	12	7	0	2	2	2	2	0	0	3	4	3	4	1	4	1	2	1	4	4	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:101370968T>A	ENST00000370495.4	-	4	761	c.733A>T	c.(733-735)Acc>Tcc	p.T245S	SLC25A28_ENST00000496035.1_5'UTR	NM_031212.3	NP_112489.3	Q96A46	MFRN2_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 28	245					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|stomach(1)	11		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)		AATTCATAGGTCATGAAGTGA	0.567																																					p.T245S		.											.	SLC25A28-90	0			c.A733T						.						66	69	68					10																	101370968		2005	4172	6177	SO:0001583	missense	81894	exon4			CATAGGTCATGAA	AF327402	CCDS41559.1	10q24.2	2013-05-22	2012-03-29		ENSG00000155287	ENSG00000155287		"Solute carriers"	23472	protein-coding gene	gene with protein product	"mitoferrin 2"	609767	"solute carrier family 25, member 28"			11297739	Standard	NM_031212		Approved	MRS3/4, MRS4L	uc001kpx.2	Q96A46	OTTHUMG00000018886	ENST00000370495.4:c.733A>T	10.37:g.101370968T>A	ENSP00000359526:p.Thr245Ser	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	137	44	NM_031212	0	0	24	42	18	Q4VBZ0|Q5T777|Q86VX5|Q969G8|Q9H2J3	Missense_Mutation	SNP	ENST00000370495.4	37	CCDS41559.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710038	0.68730	.	.	ENSG00000155287	ENST00000434701;ENST00000370495	T;T	0.80123	-1.34;-1.34	5.41	5.41	0.78517	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.76681	0.4021	L	0.49126	1.545	0.58432	D	0.999999	P	0.42456	0.78	B	0.42138	0.377	T	0.78175	-0.2306	10	0.52906	T	0.07	-32.8904	10.7365	0.46128	0.0:0.0735:0.0:0.9265	.	245	Q96A46	MFRN2_HUMAN	S	106;245	ENSP00000399102:T106S;ENSP00000359526:T245S	ENSP00000359526:T245S	T	-	1	0	SLC25A28	101360958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.678000	0.61641	2.271000	0.75665	0.459000	0.35465	ACC	.		0.567	SLC25A28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049801.1	NM_031212		A	101370968	T	A	101370968	3	1	27	1	0	0	0	0	1	0	0	0	14523	1667	58	5	365	5	SLC25A28	10	101370968	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	84201115	101370968	34163779	51	2366											
VAX1	11023	hgsc.bcm.edu	37	chr10	118893699	118893699	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgagcagcgagggcaccggCaggctgaagaggctgtggcc	8	3	18	12	3	0	2	0	1	0	1	0	4	0	2	3	5	2	5	3	5	1	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:118893699C>T	ENST00000369206.5	-	3	824	c.825G>A	c.(823-825)ctG>ctA	p.L275L	VAX1_ENST00000277905.2_Intron	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	275					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		AGGGCACCGGCAGGCTGAAGA	0.736																																					p.L275L		.											.	VAX1-92	0			c.G825A						.						18	20	19					10																	118893699		692	1591	2283	SO:0001819	synonymous_variant	11023	exon3			CACCGGCAGGCTG	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"Homeoboxes / ANTP class : NKL subclass"	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.825G>A	10.37:g.118893699C>T		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_001112704	0	0	0	0	0	B1AVW5|Q6ZSX0	Silent	SNP	ENST00000369206.5	37	CCDS44483.1																																																																																			.		0.736	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242		T	118893699	C	T	118893699	2	4	27	1	0	0	0	0	0	0	0	1	17167	697	25	2		2	VAX1	10	118893699	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	17522731	118893699	16641048	52	2367											
PDZD8	118987	broad.mit.edu	37	chr10	119044855	119044855	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaaaagttttcttccaactgGccaaagttatcttgcagcac	13	12	6	10	0	2	0	0	0	2	0	3	0	3	0	2	1	3	4	2	1	5	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:119044855G>A	ENST00000334464.5	-	5	1628	c.1389C>T	c.(1387-1389)ggC>ggT	p.G463G	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	463					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		CTTCCAACTGGCCAAAGTTAT	0.473																																					p.G463G													.	PDZD8-90	0			c.C1389T						.						98	99	99					10																	119044855		2203	4300	6503	SO:0001819	synonymous_variant	118987	exon5			CAACTGGCCAAAG	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1389C>T	10.37:g.119044855G>A		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	110	3	NM_173791	0	0	45	45	0	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	37	CCDS7600.1																																																																																			.		0.473	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119044855	G	A	119044855	2	1	27	1	0	0	0	0	0	0	0	1	11731	1190	42	2		2	PDZD8	10	119044855	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	151156	119044855	16489892	53	2368											
MUC2	4583	broad.mit.edu	37	chr11	1092950	1092950	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacccatcaccaccaccaCtacggtgaccccaaccccaa	13	3	4	21	1	1	1	1	1	0	0	1	2	1	1	8	1	2	0	8	1	3	1	rs199605832		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:1092950C>T	ENST00000441003.2	+	30	4796	c.4769C>T	c.(4768-4770)aCt>aTt	p.T1590I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1591I|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1591I(1)|p.T1590I(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccaccactacggtgacc	0.632																																					p.T1590I													.	MUC2-90	2	Substitution - Missense(2)	endometrium(2)	c.C4769T						.	C	ILE/THR	6,3646		0,6,1820	56	90	78		4766	-3.5	0	11		78	4,6702		0,4,3349	no	missense	MUC2	NM_002457.2	89	0,10,5169	TT,TC,CC		0.0596,0.1643,0.0965	possibly-damaging	1589/2813	1092950	10,10348	1826	3353	5179	SO:0001583	missense	4583	exon30			CCACCACTACGGT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4769C>T	11.37:g.1092950C>T	ENSP00000415183:p.Thr1590Ile	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	183	6	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	4.282	0.051491	0.08291	0.001643	5.96E-4	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15372	2.43;2.75	1.75	-3.51	0.04696	.	79.651400	0.00166	U	0.000017	T	0.09113	0.0225	.	.	.	0.09310	N	1	P	0.49090	0.919	B	0.31686	0.134	T	0.33954	-0.9848	9	0.51188	T	0.08	.	5.4287	0.16440	0.2102:0.3762:0.4136:0.0	.	1590	E7EUV1	.	I	1590;1591	ENSP00000415183:T1590I;ENSP00000351956:T1591I	ENSP00000351956:T1591I	T	+	2	0	MUC2	1082950	0.003000	0.15002	0.000000	0.03702	0.181000	0.23173	1.844000	0.39269	-1.047000	0.03242	0.121000	0.15741	ACT	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092950	C	T	1092950	3	4	27	1	0	0	0	0	1	0	0	0	10000	565	20	2	4887	2	MUC2	11	1092950	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		1092950	133913566	54	2369											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253980	1253980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggcgtacagctcagcgActggagggacggcgtctgca	9	5	16	11	4	2	0	1	0	1	0	2	3	2	2	0	4	4	3	0	4	2	1	rs202127660		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:1253980A>G	ENST00000529681.1	+	17	2103	c.2045A>G	c.(2044-2046)gAc>gGc	p.D682G	MUC5B_ENST00000447027.1_Missense_Mutation_p.D685G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	682					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGCTCAGCGACTGGAGGGAC	0.682																																					p.D682G		.											.	.	0			c.A2045G						.						21	24	23					11																	1253980		2116	4228	6344	SO:0001583	missense	727897	exon17			TCAGCGACTGGAG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2045A>G	11.37:g.1253980A>G	ENSP00000436812:p.Asp682Gly	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	153	12	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	A	7.541	0.660740	0.14645	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76060	-0.99;-0.99	4.6	2.72	0.32119	Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.50103	0.1596	N	0.02960	-0.455	0.24874	N	0.992269	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45920	-0.9228	9	0.87932	D	0	.	8.6635	0.34108	0.2416:0.0:0.7584:0.0	.	682;1341;685	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	682;685;683;718	ENSP00000436812:D682G;ENSP00000415793:D685G	ENSP00000343037:D683G	D	+	2	0	MUC5B	1210556	0.999000	0.42202	0.632000	0.29296	0.070000	0.16714	2.607000	0.46300	0.373000	0.24621	-1.983000	0.00453	GAC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1253980	A	G	1253980	3	3	27	1	0	0	0	0	1	0	0	0	10004	275	10	3	2120	3	MUC5B	11	1253980	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	161030	1253980	133752536	55	2370											
KCNQ1	3784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	2798240	2798240	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagtccattgggaagccCtcactgttcatctccgtctc	7	11	8	15	1	4	0	2	0	2	0	7	2	5	1	4	1	1	1	4	1	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:2798240C>G	ENST00000155840.5	+	14	1818	c.1710C>G	c.(1708-1710)ccC>ccG	p.P570P	KCNQ1_ENST00000335475.5_Silent_p.P443P	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	570					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	TTGGGAAGCCCTCACTGTTCA	0.602																																					p.P570P		.											.	KCNQ1-515	0			c.C1710G	GRCh37	CD057258	KCNQ1	D		.						249	175	200					11																	2798240		2202	4299	6501	SO:0001819	synonymous_variant	3784	exon14			GAAGCCCTCACTG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6294	protein-coding gene	gene with protein product	"Jervell and Lange-Nielsen syndrome 1"	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1710C>G	11.37:g.2798240C>G		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	185	53	NM_000218	0	0	21	22	1	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			.		0.602	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		G	2798240	C	G	2798240	2	3	27	1	0	0	0	0	0	0	0	1	8103	668	24	4		4	KCNQ1	11	2798240	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	1544260	2798240	132208276	56	2371											
SOX6	55553	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	16010773	16010773	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagagccattcattgctttaCttcctgtaatgtcagggcag	9	13	9	10	0	2	1	2	0	0	1	3	1	3	1	2	1	3	3	2	1	2	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:16010773C>A	ENST00000352083.6	-	14	1813	c.1736G>T	c.(1735-1737)aGt>aTt	p.S579I	SOX6_ENST00000528252.1_Missense_Mutation_p.S552I|SOX6_ENST00000528429.1_Missense_Mutation_p.S579I|SOX6_ENST00000527619.1_Missense_Mutation_p.S555I|SOX6_ENST00000316399.6_Intron|SOX6_ENST00000396356.3_Intron			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	579					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						CATTGCTTTACTTCCTGTAAT	0.507											OREG0020800	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S592I													.	SOX6-93	0			c.G1775T						.						87	85	85					11																	16010773		1327	2309	3636	SO:0001583	missense	55553	exon14			GCTTTACTTCCTG	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"SRY (sex determining region Y)-boxes"	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.1736G>T	11.37:g.16010773C>A	ENSP00000339876:p.Ser579Ile	Somatic	97	1	707	WXS	Illumina HiSeq	Phase_I	143	61	NM_001145819	0	0	0	0	0	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	C	14.32	2.500973	0.44455	.	.	ENSG00000110693	ENST00000352083;ENST00000528252;ENST00000527619;ENST00000528429	D;D;D;D	0.97959	-4.63;-4.63;-4.63;-4.63	5.71	4.8	0.61643	.	1.200610	0.05524	N	0.562644	D	0.94650	0.8275	N	0.14661	0.345	0.80722	D	1	B;B	0.26195	0.01;0.144	B;B	0.30179	0.014;0.112	T	0.80609	-0.1306	9	.	.	.	.	13.187	0.59686	0.0:0.9261:0.0:0.0739	.	579;555	P35712;P35712-2	SOX6_HUMAN;.	I	579;552;555;579	ENSP00000339876:S579I;ENSP00000432134:S552I;ENSP00000434455:S555I;ENSP00000433233:S579I	.	S	-	2	0	SOX6	15967349	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.486000	0.60286	1.421000	0.47157	-0.150000	0.13652	AGT	.		0.507	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326		A	16010773	C	A	16010773	3	1	27	1	0	0	0	0	1	0	0	0	14987	565	20	4	762	4	SOX6	11	16010773	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	13212533	16010773	118995743	57	2372											
KCNA4	3739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	30032894	30032894	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcggaccagacgaatgatTctgaggatggcaaaggacat	14	7	12	8	2	1	3	0	2	1	1	2	7	1	6	1	4	0	1	1	4	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:30032894T>C	ENST00000328224.6	-	2	2565	c.1332A>G	c.(1330-1332)agA>agG	p.R444R	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	444					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GACGAATGATTCTGAGGATGG	0.572																																					p.R444R		.											.	KCNA4-517	0			c.A1332G						.						70	68	69					11																	30032894		2059	4216	6275	SO:0001819	synonymous_variant	3739	exon2			AATGATTCTGAGG	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1332A>G	11.37:g.30032894T>C		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	104	30	NM_002233	0	0	0	0	0		Silent	SNP	ENST00000328224.6	37	CCDS41629.1																																																																																			.		0.572	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		C	30032894	T	C	30032894	2	2	27	1	0	0	0	0	0	0	0	1	8026	1780	62	3		3	KCNA4	11	30032894	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	14022121	30032894	104973622	58	2373											
TRIM44	54765	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	35684955	35684956	+	Frame_Shift_Ins	INS	-	-	T																															agcgaggcaggggaagagagINStgagtcggaggaagagagcg																								rs534573468	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:35684955_35684956insT	ENST00000299413.5	+	1	603_604	c.296_297insT	c.(295-300)agtgagfs	p.E100fs	RP1-276E15.1_ENST00000525573.2_lincRNA	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	100	Glu-rich.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				ggggaagagagtgagtcggagg	0.589																																					p.S99fs		.											.	TRIM44-227	0			c.296_297insT						.																																			SO:0001589	frameshift_variant	54765	exon1			.	BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19016	protein-coding gene	gene with protein product		612298	"tripartite motif-containing 44"				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.297dupT	11.37:g.35684956_35684956dupT	ENSP00000299413:p.Glu100fs	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	253	66	NM_017583	0	0	0	0	0	D3DR14|Q96QY2|Q9UGK0	Frame_Shift_Ins	INS	ENST00000299413.5	37	CCDS31461.1																																																																																			.		0.589	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389081.1	NM_017583		T	35684956	-	T	35684955	7	5	27	1	0	1	1	0	0	0	0	0	16552	1029	36	0	298	0	TRIM44	11	35684955	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	5652061	35684955	99321561	59	2374											
AMBRA1	55626	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46419222	46419222	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaagctgtccgggggcttagGcctcgctctgccagttgccc	4	9	14	14	2	1	0	0	0	1	0	3	1	2	0	4	3	3	4	4	3	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:46419222G>A	ENST00000458649.2	-	18	4093	c.3675C>T	c.(3673-3675)ggC>ggT	p.G1225G	AMBRA1_ENST00000426438.1_Silent_p.G1196G|AMBRA1_ENST00000528950.1_Silent_p.G1196G|AMBRA1_ENST00000298834.3_Silent_p.G1165G|AMBRA1_ENST00000314845.3_Silent_p.G1135G|AMBRA1_ENST00000533727.1_Silent_p.G1106G|AMBRA1_ENST00000534300.1_Silent_p.G1165G			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1225					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GGGGGCTTAGGCCTCGCTCTG	0.682																																					p.G1228G													.	AMBRA1-136	0			c.C3684T						.						55	58	57					11																	46419222		2202	4299	6501	SO:0001819	synonymous_variant	55626	exon20			GCTTAGGCCTCGC	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	25990	protein-coding gene	gene with protein product	"WD repeat domain 94", "DDB1 and CUL4 associated factor 3"	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.3675C>T	11.37:g.46419222G>A		Somatic	71	1		WXS	Illumina HiSeq	Phase_I	104	48	NM_001267782	0	0	20	52	32	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	37																																																																																				.		0.682	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		A	46419222	G	A	46419222	2	1	27	1	0	0	0	0	0	0	0	1	565	1190	42	2		2	AMBRA1	11	46419222	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	10734267	46419222	88587294	60	2375											
C12orf39	80763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	21680692	21680692	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttcatctccgaccagagccgGagaaaggacctctccgaccg	10	6	10	15	4	3	2	1	0	2	2	5	6	3	3	6	2	1	0	6	2	1	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:21680692G>C	ENST00000256969.2	+	4	343	c.177G>C	c.(175-177)cgG>cgC	p.R59R		NM_030572.2	NP_085049.1	Q9BT56	SPXN_HUMAN		59					long-chain fatty acid import (GO:0044539)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of renal sodium excretion (GO:0035814)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of sensory perception of pain (GO:0051930)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)	neuropeptide hormone activity (GO:0005184)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			endometrium(3)|large_intestine(1)|lung(2)|urinary_tract(1)	7						ACCAGAGCCGGAGAAAGGACC	0.647																																					p.R59R		.											.	C12orf39-90	0			c.G177C						.						20	21	21					12																	21680692		2195	4272	6467	SO:0001819	synonymous_variant	80763	exon4			GAGCCGGAGAAAG																												ENST00000256969.2:c.177G>C	12.37:g.21680692G>C		Somatic	203	1		WXS	Illumina HiSeq	Phase_I	215	158	NM_030572	0	0	0	154	154	B3KND6	Silent	SNP	ENST00000256969.2	37	CCDS31757.1																																																																																			.		0.647	C12orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402389.1			C	21680692	G	C	21680692	2	2	27	1	0	0	0	0	0	0	0	1	1688	1161	41	4		4	C12orf39	12	21680692	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		21680692	112171203	61	2376											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49436945	49436945	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcactgggcactggggatGccttcacgcccccatcctca	6	8	11	16	1	3	0	3	0	0	0	4	1	4	1	4	4	1	1	4	4	0	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:49436945G>A	ENST00000301067.7	-	25	5557	c.5558C>T	c.(5557-5559)gCa>gTa	p.A1853V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1853					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CACTGGGGATGCCTTCACGCC	0.587																																					p.A1853V		.											.	MLL2-612	0			c.C5558T						.						69	71	71					12																	49436945		2031	4183	6214	SO:0001583	missense	8085	exon25			GGGGATGCCTTCA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.5558C>T	12.37:g.49436945G>A	ENSP00000301067:p.Ala1853Val	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	104	8	NM_003482	0	0	4	4	0	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.980996	0.34942	.	.	ENSG00000167548	ENST00000301067	T	0.79554	-1.28	5.61	4.72	0.59763	.	0.000000	0.36303	N	0.002670	T	0.69504	0.3118	L	0.29908	0.895	0.30174	N	0.801069	B	0.26363	0.147	B	0.19391	0.025	T	0.69472	-0.5136	10	0.87932	D	0	.	10.4356	0.44433	0.0892:0.0:0.9108:0.0	.	1853	O14686	MLL2_HUMAN	V	1853	ENSP00000301067:A1853V	ENSP00000301067:A1853V	A	-	2	0	MLL2	47723212	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	2.943000	0.49026	1.371000	0.46172	0.655000	0.94253	GCA	.		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49436945	G	A	49436945	3	1	27	1	0	0	0	0	1	0	0	0	9646	1319	46	2	11175	2	MLL2	12	49436945	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	27756253	49436945	84414950	62	2377											
MDM1	56890	ucsc.edu;bcgsc.ca	37	chr12	68715135	68715135	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgtacactcacctgatttgGcatgtttccctttacatgtg	8	16	7	10	0	1	1	1	1	0	0	2	1	2	1	2	1	2	3	2	1	2	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:68715135G>A	ENST00000303145.7	-	7	1083	c.997C>T	c.(997-999)Cca>Tca	p.P333S	MDM1_ENST00000411698.2_Missense_Mutation_p.P288S|MDM1_ENST00000540418.1_Missense_Mutation_p.P53S	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	333					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		ACCTGATTTGGCATGTTTCCC	0.393																																					p.P333S													.	MDM1-95	0			c.C997T						.						103	92	96					12																	68715135		2203	4300	6503	SO:0001583	missense	56890	exon7			GATTTGGCATGTT	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.997C>T	12.37:g.68715135G>A	ENSP00000302537:p.Pro333Ser	Somatic	47	0		WXS	Illumina HiSeq		43	4	NM_017440	0	0	0	0	0	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	G	9.859	1.195883	0.22037	.	.	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.22743	1.94;1.94;1.94	4.79	2.76	0.32466	.	0.423727	0.23838	N	0.044062	T	0.12944	0.0314	L	0.28192	0.835	0.49582	D	0.999804	B;B	0.21147	0.041;0.052	B;B	0.16722	0.016;0.015	T	0.09509	-1.0671	9	.	.	.	-6.1724	9.5505	0.39306	0.0817:0.1438:0.7746:0.0	.	288;333	E7EPQ3;Q8TC05	.;MDM1_HUMAN	S	53;333;288	ENSP00000443815:P53S;ENSP00000302537:P333S;ENSP00000391006:P288S	.	P	-	1	0	MDM1	67001402	0.998000	0.40836	0.717000	0.30585	0.943000	0.58893	3.572000	0.53849	1.305000	0.44909	0.561000	0.74099	CCA	.		0.393	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		A	68715135	G	A	68715135	3	1	27	1	0	0	0	0	1	0	0	0	9437	1203	42	2	1179	2	MDM1	12	68715135	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	19278190	68715135	65136760	63	2378											
MYH7	4625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23886422	23886422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagggactcctcataggCgttcttgagtttgaagagct	8	13	11	9	1	2	3	1	2	1	1	4	4	4	4	2	2	1	3	2	2	2	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:23886422C>T	ENST00000355349.3	-	32	4621	c.4459G>A	c.(4459-4461)Gcc>Acc	p.A1487T	MIR208B_ENST00000401172.1_RNA|CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1487					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCATAGGCGTTCTTGAGT	0.597																																					p.A1487T		.											.	MYH7-94	0			c.G4459A						.						118	124	122					14																	23886422		2203	4300	6503	SO:0001583	missense	4625	exon32			CATAGGCGTTCTT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4459G>A	14.37:g.23886422C>T	ENSP00000347507:p.Ala1487Thr	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	83	34	NM_000257	0	0	0	0	0	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374149	0.82573	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.78364	-1.17	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.84000	0.5376	M	0.81942	2.565	0.39473	D	0.967754	P	0.43662	0.814	P	0.50440	0.641	D	0.86199	0.1617	9	0.59425	D	0.04	.	13.987	0.64341	0.1513:0.8487:0.0:0.0	.	1487	P12883	MYH7_HUMAN	T	1487;1492	ENSP00000347507:A1487T	ENSP00000347507:A1487T	A	-	1	0	MYH7	22956262	0.987000	0.35691	0.998000	0.56505	0.982000	0.71751	2.764000	0.47613	2.746000	0.94184	0.591000	0.81541	GCC	.		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23886422	C	T	23886422	3	4	27	1	0	0	0	0	1	0	0	0	10064	768	27	1	1384	1	MYH7	14	23886422	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		23886422	83463118	64	2379											
NFKBIA	4792	broad.mit.edu	37	chr14	35871853	35871853	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgaggtgaagggcagtcCggccattacagggctcctga	8	7	15	11	2	0	2	0	2	0	0	2	3	2	2	3	4	2	2	3	4	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:35871853C>T	ENST00000216797.5	-	5	754	c.653G>A	c.(652-654)cGg>cAg	p.R218Q	NFKBIA_ENST00000557100.1_5'UTR|NFKBIA_ENST00000557389.1_Missense_Mutation_p.R128Q|NFKBIA_ENST00000557140.1_Intron	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	218					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	AAGGGCAGTCCGGCCATTACA	0.507																																					p.R218Q													.	NFKBIA-721	0			c.G653A						.						73	71	71					14																	35871853		2203	4300	6503	SO:0001583	missense	4792	exon5			GCAGTCCGGCCAT		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"Ankyrin repeat domain containing"	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.653G>A	14.37:g.35871853C>T	ENSP00000216797:p.Arg218Gln	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	95	4	NM_020529	0	0	543	551	8	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	C	36	5.599390	0.96614	.	.	ENSG00000100906	ENST00000216797;ENST00000557389	T;T	0.65916	-0.18;-0.18	5.1	5.1	0.69264	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.68677	0.3027	N	0.20574	0.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72030	-0.4413	9	0.51188	T	0.08	-1.4444	18.8673	0.92298	0.0:1.0:0.0:0.0	.	218	P25963	IKBA_HUMAN	Q	218;128	ENSP00000216797:R218Q;ENSP00000450514:R128Q	ENSP00000216797:R218Q	R	-	2	0	NFKBIA	34941604	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.410000	0.80065	2.510000	0.84645	0.655000	0.94253	CGG	.		0.507	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		T	35871853	C	T	35871853	3	4	27	1	0	0	0	0	1	0	0	0	10403	652	23	1	308	1	NFKBIA	14	35871853	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	11985431	35871853	71477687	65	2380											
ABHD12B	145447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	51368558	51368558	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taaaaatagatttaccggaaCattccaggatttttacgtac	15	13	6	7	2	0	1	0	0	0	1	1	3	1	3	2	2	4	1	2	2	8	9			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:51368558C>T	ENST00000337334.2	+	10	807	c.792C>T	c.(790-792)aaC>aaT	p.N264N	PYGL_ENST00000532462.1_Intron|ABHD12B_ENST00000395752.1_Silent_p.N157N|ABHD12B_ENST00000353130.1_Silent_p.N187N	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	264							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					TTTACCGGAACATTCCAGGAT	0.308																																					p.N264N		.											.	ABHD12B-153	0			c.C792T						.						58	54	55					14																	51368558		2202	4297	6499	SO:0001819	synonymous_variant	145447	exon10			CCGGAACATTCCA	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"Abhydrolase domain containing"	19837	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 29"	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.792C>T	14.37:g.51368558C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	68	45	NM_001206673	0	0	0	0	0	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Silent	SNP	ENST00000337334.2	37	CCDS55916.1																																																																																			.		0.308	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1			T	51368558	C	T	51368558	2	4	27	1	0	0	0	0	0	0	0	1	77	477	17	2		2	ABHD12B	14	51368558	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	15496705	51368558	55980982	66	2381											
MPP5	64398	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	67787027	67787027	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataggaagagacctatcatcTtgattggtccacagaactgt	13	11	9	8	0	2	3	1	1	1	2	3	5	3	4	2	2	1	0	2	2	4	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:67787027T>C	ENST00000261681.4	+	12	2111	c.1450T>C	c.(1450-1452)Ttg>Ctg	p.L484L	ATP6V1D_ENST00000553974.1_Intron|MPP5_ENST00000555925.1_Silent_p.L450L	NM_022474.3	NP_071919.2	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	484	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|establishment of protein localization to plasma membrane (GO:0090002)|morphogenesis of an epithelial sheet (GO:0002011)|myelin assembly (GO:0032288)|peripheral nervous system myelin maintenance (GO:0032287)|protein localization to myelin sheath abaxonal region (GO:0035750)|tight junction assembly (GO:0070830)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lateral loop (GO:0043219)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	18				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		ACCTATCATCTTGATTGGTCC	0.408																																					p.L484L		.											.	MPP5-91	0			c.T1450C						.						111	104	107					14																	67787027		2203	4300	6503	SO:0001819	synonymous_variant	64398	exon12			ATCATCTTGATTG	AK022677	CCDS9779.1, CCDS58325.1	14q23.3	2008-08-11				ENSG00000072415			18669	protein-coding gene	gene with protein product	"stardust"	606958				11927608	Standard	NM_022474		Approved	PALS1, FLJ12615	uc001xjc.4	Q8N3R9		ENST00000261681.4:c.1450T>C	14.37:g.67787027T>C		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	40	30	NM_022474	0	0	2	27	25	A1L380|Q7Z631|Q86T98|Q8N7I5|Q9H9Q0	Silent	SNP	ENST00000261681.4	37	CCDS9779.1																																																																																			.		0.408	MPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412498.1	NM_022474		C	67787027	T	C	67787027	2	2	27	1	0	0	0	0	0	0	0	1	9762	1606	56	3		3	MPP5	14	67787027	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	16418469	67787027	39562513	67	2382											
YLPM1	56252	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	75248111	75248111	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caacatctttaccaagaatgGgagcgagagtttcagctatg	13	10	10	8	1	2	2	1	0	1	2	2	4	2	3	1	1	4	2	1	1	5	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:75248111G>A	ENST00000552421.1	+	4	1489	c.1365G>A	c.(1363-1365)tgG>tgA	p.W455*	YLPM1_ENST00000238571.3_Intron|YLPM1_ENST00000325680.7_Nonsense_Mutation_p.W455*			P49750	YLPM1_HUMAN	YLP motif containing 1	0					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ACCAAGAATGGGAGCGAGAGT	0.423																																					p.W455X		.											.	YLPM1-71	0			c.G1365A						.						40	37	38					14																	75248111		1917	4135	6052	SO:0001587	stop_gained	56252	exon4			AGAATGGGAGCGA	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1365G>A	14.37:g.75248111G>A	ENSP00000447921:p.Trp455*	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	166	124	NM_019589	0	0	0	1	1	P49752|Q96I64|Q9P1V7	Nonsense_Mutation	SNP	ENST00000552421.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.452918	0.96223	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000423680	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0557	0.97650	0.0:0.0:1.0:0.0	.	.	.	.	X	455;455;168	.	ENSP00000324463:W455X	W	+	3	0	YLPM1	74317864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.471000	0.97696	2.732000	0.93576	0.591000	0.81541	TGG	.		0.423	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		A	75248111	G	A	75248111	4	1	27	1	0	0	0	0	0	1	0	0	17519	1241	43	2	1379	2	YLPM1	14	75248111	Nonsense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	7461084	75248111	32101429	68	2383											
CATSPERB	79820	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	92195753	92195753	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgaaacttacctttattaTatactattcctgatgaaaat	14	17	3	7	0	1	3	0	3	1	0	2	3	2	3	2	0	3	0	2	0	9	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:92195753T>C	ENST00000256343.3	-	2	227	c.71A>G	c.(70-72)tAt>tGt	p.Y24C		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	24					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				ACCTTTATTATATACTATTCC	0.279																																					p.Y24C		.											.	CATSPERB-138	0			c.A71G						.						32	36	35					14																	92195753		2194	4276	6470	SO:0001583	missense	79820	exon2			TTATTATATACTA	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"chromosome 14 open reading frame 161", "cation channel, sperm-associated, beta"	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.71A>G	14.37:g.92195753T>C	ENSP00000256343:p.Tyr24Cys	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	152	68	NM_024764	0	0	0	0	0	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.150476	0.37923	.	.	ENSG00000133962	ENST00000256343;ENST00000553329;ENST00000554560;ENST00000556661;ENST00000553676	T	0.56941	0.43	5.22	4.05	0.47172	.	0.528936	0.15705	N	0.248736	T	0.58935	0.2157	L	0.47716	1.5	0.26423	N	0.976068	D	0.65815	0.995	P	0.58873	0.847	T	0.50550	-0.8815	10	0.66056	D	0.02	-4.0069	8.4676	0.32966	0.1734:0.0:0.0:0.8266	.	24	Q9H7T0	CTSRB_HUMAN	C	24	ENSP00000256343:Y24C	ENSP00000256343:Y24C	Y	-	2	0	CATSPERB	91265506	0.928000	0.31464	0.216000	0.23742	0.648000	0.38561	2.017000	0.40981	0.893000	0.36288	0.397000	0.26171	TAT	.		0.279	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		C	92195753	T	C	92195753	3	2	27	1	0	0	0	0	1	0	0	0	2697	1406	49	3	3383	3	CATSPERB	14	92195753	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	16947642	92195753	15153787	69	2384											
CASC5	57082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40913801	40913801	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaatgtctctcaaatatgAgagaggagaaaaatttgcta	17	10	8	6	0	2	3	1	1	1	2	3	5	2	3	1	1	1	1	1	1	6	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:40913801A>T	ENST00000346991.5	+	11	1807	c.1417A>T	c.(1417-1419)Aga>Tga	p.R473*	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Nonsense_Mutation_p.R447*			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	473	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		CTCAAATATGAGAGAGGAGAA	0.328																																					p.R473X		.											.	CASC5-660	0			c.A1417T						.						67	65	65					15																	40913801		1822	4080	5902	SO:0001587	stop_gained	57082	exon11			AATATGAGAGAGG	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1417A>T	15.37:g.40913801A>T	ENSP00000335463:p.Arg473*	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	146	57	NM_170589	0	0	3	3	0	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Nonsense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	A	38	7.205877	0.98136	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	.	.	.	5.94	2.3	0.28687	.	1.023320	0.07757	N	0.949536	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4785	0.16710	0.5262:0.2673:0.2064:0.0	.	.	.	.	X	473;447;447	.	ENSP00000260369:R447X	R	+	1	2	CASC5	38701093	0.001000	0.12720	0.969000	0.41365	0.966000	0.64601	0.013000	0.13310	0.490000	0.27771	0.455000	0.32223	AGA	.		0.328	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40913801	A	T	40913801	4	4	27	1	0	0	0	0	0	1	0	0	2669	296	11	5	1455	5	CASC5	15	40913801	Nonsense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10		40913801	61617591	70	2385											
RNF111	54778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	59344604	59344604	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaactgacagtgaagtggaGattgtaacagttggagaaag	15	9	13	4	0	1	4	1	2	0	2	1	6	1	4	0	2	2	2	0	2	4	3	rs137923008	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:59344604G>T	ENST00000557998.1	+	3	1268	c.981G>T	c.(979-981)gaG>gaT	p.E327D	RNF111_ENST00000559209.1_Missense_Mutation_p.E327D|RNF111_ENST00000561186.1_Missense_Mutation_p.E327D|RNF111_ENST00000434298.1_Missense_Mutation_p.E327D|RNF111_ENST00000348370.4_Missense_Mutation_p.E327D	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	327	Interaction with AXIN1.|Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		GTGAAGTGGAGATTGTAACAG	0.333																																					p.E327D	NSCLC(72;983 1365 10746 34387 47081)	.											.	RNF111-92	0			c.G981T						.						119	108	112					15																	59344604		2192	4291	6483	SO:0001583	missense	54778	exon3			AGTGGAGATTGTA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.981G>T	15.37:g.59344604G>T	ENSP00000452732:p.Glu327Asp	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	61	23	NM_017610	0	0	10	17	7	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	37	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972394	0.34848	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.39997	1.05;1.06	5.6	1.64	0.23874	.	0.000000	0.85682	D	0.000000	T	0.36082	0.0954	L	0.59436	1.845	0.51012	D	0.9999	B;B;B	0.27732	0.187;0.117;0.187	B;B;B	0.29267	0.1;0.046;0.1	T	0.15607	-1.0431	10	0.87932	D	0	-5.7934	6.825	0.23878	0.1993:0.0:0.6759:0.1248	.	327;327;327	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	D	327	ENSP00000288199:E327D;ENSP00000393641:E327D	ENSP00000288199:E327D	E	+	3	2	RNF111	57131896	1.000000	0.71417	0.997000	0.53966	0.284000	0.27059	4.092000	0.57707	0.051000	0.15978	-0.241000	0.12123	GAG	G|0.998;A|0.002		0.333	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		T	59344604	G	T	59344604	3	4	27	1	0	0	0	0	1	0	0	0	13457	933	33	4	987	4	RNF111	15	59344604	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	18430803	59344604	43186788	71	2386											
VPS13C	54832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	62155703	62155703	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtggtatcggtaagtctCtccttccaactttttgatat	9	16	7	9	1	1	1	0	1	1	0	5	1	3	1	2	2	1	2	2	2	4	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:62155703C>A	ENST00000261517.5	-	82	10961	c.10888G>T	c.(10888-10890)Gag>Tag	p.E3630*	VPS13C_ENST00000249837.3_Nonsense_Mutation_p.E3587*	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CGGTAAGTCTCTCCTTCCAAC	0.353																																					p.E3630X		.											.	VPS13C-92	0			c.G10888T						.						156	136	143					15																	62155703		2203	4300	6503	SO:0001587	stop_gained	54832	exon82			AAGTCTCTCCTTC	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10888G>T	15.37:g.62155703C>A	ENSP00000261517:p.Glu3630*	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	115	41	NM_020821	0	0	19	23	4		Nonsense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	53	21.012209	0.99936	.	.	ENSG00000129003	ENST00000249837;ENST00000261517	.	.	.	5.68	5.68	0.88126	.	0.055754	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	20.1554	0.98111	0.0:1.0:0.0:0.0	.	.	.	.	X	3587;3630	.	ENSP00000249837:E3587X	E	-	1	0	VPS13C	59942995	1.000000	0.71417	0.981000	0.43875	0.992000	0.81027	6.594000	0.74104	2.838000	0.97847	0.591000	0.81541	GAG	.		0.353	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62155703	C	A	62155703	4	1	27	1	0	0	0	0	0	1	0	0	17224	922	32	4	389	4	VPS13C	15	62155703	Nonsense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	2811099	62155703	40375689	72	2387											
PIAS1	8554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	68434644	68434644	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagggatatttctgggaccAaatgtgacttcacagtacag	12	11	10	8	0	2	1	1	1	1	0	2	3	2	3	1	2	1	1	1	2	4	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:68434644A>G	ENST00000249636.6	+	4	719	c.571A>G	c.(571-573)Aaa>Gaa	p.K191E	PIAS1_ENST00000545237.1_Missense_Mutation_p.K193E	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	191	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						TTCTGGGACCAAATGTGACTT	0.353																																					p.K191E		.											.	PIAS1-637	0			c.A571G						.						55	51	53					15																	68434644		1818	4073	5891	SO:0001583	missense	8554	exon4			GGGACCAAATGTG	AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"Zinc fingers, MIZ-type"	2752	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 3"	603566	"DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.571A>G	15.37:g.68434644A>G	ENSP00000249636:p.Lys191Glu	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	150	55	NM_016166	0	0	10	18	8	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	37	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.858688	0.91433	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.36340	1.26;1.26	5.39	5.39	0.77823	PINIT domain (1);	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.73217	2.22	0.80722	D	1	D;B	0.54047	0.964;0.107	D;P	0.65773	0.938;0.475	T	0.62793	-0.6779	10	0.72032	D	0.01	-13.0322	15.4074	0.74890	1.0:0.0:0.0:0.0	.	191;191	C5J4B4;O75925	.;PIAS1_HUMAN	E	191;193	ENSP00000249636:K191E;ENSP00000438574:K193E	ENSP00000249636:K191E	K	+	1	0	PIAS1	66221698	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.883000	0.92426	2.042000	0.60477	0.477000	0.44152	AAA	.		0.353	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2			G	68434644	A	G	68434644	3	3	27	1	0	0	0	0	1	0	0	0	11901	131	5	3	585	3	PIAS1	15	68434644	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	6278941	68434644	34096748	73	2388											
IL16	3603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	81517938	81517938	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgcagctggcagacacAtcggaggctgggcccagcag	8	6	15	12	1	1	1	0	0	1	1	2	2	1	2	1	4	3	5	1	4	0	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:81517938A>G	ENST00000302987.4	+	1	198	c.198A>G	c.(196-198)acA>acG	p.T66T	IL16_ENST00000394660.2_Silent_p.T66T			Q14005	IL16_HUMAN	interleukin 16	66					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TGGCAGACACATCGGAGGCTG	0.552																																					p.T66T		.											.	IL16-653	0			c.A198G						.						65	65	65					15																	81517938		2006	4190	6196	SO:0001819	synonymous_variant	3603	exon2			AGACACATCGGAG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.198A>G	15.37:g.81517938A>G		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	116	29	NM_001172128	0	0	1	1	0	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			.		0.552	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81517938	A	G	81517938	2	3	27	1	0	0	0	0	0	0	0	1	7654	204	8	3		3	IL16	15	81517938	Silent	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	13083294	81517938	21013454	74	2389											
FANCI	55215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	89856164	89856164	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagcctgaactatacgggAgagaaaaaggagaaacctgc	18	4	12	7	1	0	4	0	1	0	3	0	7	0	5	2	2	5	0	2	2	7	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:89856164A>T	ENST00000310775.7	+	35	3767	c.3681A>T	c.(3679-3681)ggA>ggT	p.G1227G	FANCI_ENST00000300027.8_Silent_p.G1167G|FANCI_ENST00000566615.1_3'UTR	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1227					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					ACTATACGGGAGAGAAAAAGG	0.423								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G1227G		.											.	FANCI-92	0			c.A3681T						.						77	76	76					15																	89856164		2200	4299	6499	SO:0001819	synonymous_variant	55215	exon35	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACGGGAGAGAAA	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.3681A>T	15.37:g.89856164A>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	51	21	NM_001113378	0	0	8	14	6	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	37	CCDS45346.1																																																																																			.		0.423	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		T	89856164	A	T	89856164	2	4	27	1	0	0	0	0	0	0	0	1	5688	291	11	5		5	FANCI	15	89856164	Silent	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	8338226	89856164	12675228	75	2390											
C16orf11	146325	hgsc.bcm.edu	37	chr16	614703	614703	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggctcctctgtgatgctgtGgcctgaggacggggatccag	5	9	16	11	2	1	2	0	2	1	0	3	4	3	4	3	5	1	2	3	5	0	0	rs199532631		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:614703G>C	ENST00000409413.3	+	3	1391	c.1112G>C	c.(1111-1113)tGg>tCg	p.W371S	NHLRC4_ENST00000540585.1_5'Flank|NHLRC4_ENST00000424439.2_5'Flank|PIGQ_ENST00000409527.2_5'Flank	NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		371	Pro-rich.									central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						GTGATGCTGTGGCCTGAGGAC	0.746																																					p.W371S		.											.	C16orf11-23	0			c.G1112C						.						2	3	2					16																	614703		1516	3313	4829	SO:0001583	missense	146325	exon3			TGCTGTGGCCTGA																												ENST00000409413.3:c.1112G>C	16.37:g.614703G>C	ENSP00000386499:p.Trp371Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	30	5	NM_145270	0	0	0	0	0	B8ZZ27|Q8N233|Q96AX3|Q96S23	Missense_Mutation	SNP	ENST00000409413.3	37	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	G	9.946	1.218820	0.22373	.	.	ENSG00000161992	ENST00000409413	T	0.07021	3.23	4.32	4.32	0.51571	.	0.000000	0.47455	D	0.000227	T	0.20941	0.0504	M	0.66939	2.045	0.47276	D	0.999376	D	0.56968	0.978	P	0.56343	0.796	T	0.00643	-1.1630	10	0.48119	T	0.1	.	14.3415	0.66630	0.0:0.0:1.0:0.0	.	371	P0CG20	CP011_HUMAN	S	371	ENSP00000386499:W371S	ENSP00000386499:W371S	W	+	2	0	C16orf11	554704	0.984000	0.35163	0.819000	0.32651	0.020000	0.10135	3.382000	0.52463	2.227000	0.72691	0.471000	0.43371	TGG	.		0.746	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1			C	614703	G	C	614703	3	2	27	1	0	0	0	0	1	0	0	0	1814	1357	47	4	1118	4	C16orf11	16	614703	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		614703	89740050	76	2391											
BAIAP3	8938	bcgsc.ca	37	chr16	1397801	1397801	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgctgcacgccgcggacCtgctccccctggacgccaac	6	5	12	18	4	0	0	0	0	0	0	1	2	1	2	5	3	4	3	5	3	1	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:1397801C>A	ENST00000324385.5	+	31	3267	c.3109C>A	c.(3109-3111)Ctg>Atg	p.L1037M	BAIAP3_ENST00000421665.2_Missense_Mutation_p.L966M|BAIAP3_ENST00000562208.1_Missense_Mutation_p.L979M|BAIAP3_ENST00000568887.1_Missense_Mutation_p.L974M|BAIAP3_ENST00000397488.2_Missense_Mutation_p.L1019M|BAIAP3_ENST00000397489.1_Missense_Mutation_p.L1019M|BAIAP3_ENST00000426824.3_Missense_Mutation_p.L1002M	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1037	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				CGCCGCGGACCTGCTCCCCCT	0.692																																					p.L1037M													.	BAIAP3-91	0			c.C3109A						.						16	20	18					16																	1397801		2181	4278	6459	SO:0001583	missense	8938	exon31			GCGGACCTGCTCC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.3109C>A	16.37:g.1397801C>A	ENSP00000324510:p.Leu1037Met	Somatic	23	1		WXS	Illumina HiSeq	Phase_1	169	112	NM_003933	0	0	1	5	4	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096317	0.56075	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67	5.22	2.87	0.33458	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.082361	0.48767	D	0.000177	D	0.90858	0.7128	M	0.88704	2.975	0.42401	D	0.992568	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.974;0.993;0.993;0.997	D	0.91254	0.5031	10	0.87932	D	0	-18.5947	9.7074	0.40225	0.0:0.7886:0.0:0.2114	.	966;979;1037;1019	E7EUB9;B4DIK3;O94812;A2A2B2	.;.;BAIP3_HUMAN;.	M	1002;1019;1037;1019;966	ENSP00000407242:L1002M;ENSP00000380625:L1019M;ENSP00000324510:L1037M;ENSP00000380626:L1019M;ENSP00000409533:L966M	ENSP00000324510:L1037M	L	+	1	2	BAIAP3	1337802	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	2.491000	0.45303	1.169000	0.42739	0.561000	0.74099	CTG	.		0.692	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			A	1397801	C	A	1397801	3	1	27	1	0	0	0	0	1	0	0	0	1305	680	24	4	3231	4	BAIAP3	16	1397801	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	783098	1397801	88956952	77	2392											
FAHD1	81889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1877593	1877593	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggggctgccctggactctGgcgaagagcttcacggcgtc	7	7	15	12	3	2	1	1	0	1	1	3	3	2	2	1	5	2	2	1	5	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:1877593G>T	ENST00000427358.2	+	1	369	c.363G>T	c.(361-363)ctG>ctT	p.L121L	FAHD1_ENST00000382668.4_Silent_p.L121L|FAHD1_ENST00000382666.4_Silent_p.L121L|HAGH_ENST00000397356.3_5'Flank|HAGH_ENST00000397353.2_5'Flank|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000455446.2_5'Flank	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	121						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						CCTGGACTCTGGCGAAGAGCT	0.642																																					p.L121L		.											.	FAHD1-90	0			c.G363T						.						38	34	36					16																	1877593		2199	4300	6499	SO:0001819	synonymous_variant	81889	exon1			GACTCTGGCGAAG	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 36"	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.363G>T	16.37:g.1877593G>T		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	273	39	NM_031208	0	0	220	277	57	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	37	CCDS10448.1																																																																																			.		0.642	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104		T	1877593	G	T	1877593	2	4	27	1	0	0	0	0	0	0	0	1	5388	1335	47	4		4	FAHD1	16	1877593	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	479792	1877593	88477160	78	2393											
PKD1	5310	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2153522	2153522	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccatcgaggccaccttggTggagacggtgtagttgctga	7	10	15	9	2	0	2	0	1	0	1	1	4	0	2	3	4	2	3	3	4	1	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:2153522T>C	ENST00000262304.4	-	23	8744	c.8536A>G	c.(8536-8538)Acc>Gcc	p.T2846A	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Missense_Mutation_p.T2846A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2846					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GCCACCTTGGTGGAGACGGTG	0.612																																					p.T2846A													.	PKD1-91	0			c.A8536G						.						28	30	30					16																	2153522		2160	4215	6375	SO:0001583	missense	5310	exon23			CCTTGGTGGAGAC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.8536A>G	16.37:g.2153522T>C	ENSP00000262304:p.Thr2846Ala	Somatic	28	1		WXS	Illumina HiSeq	Phase_I	91	68	NM_000296	0	0	283	298	15	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653296	0.47362	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.44881	0.91;0.91	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.60314	0.2259	M	0.78801	2.425	0.47183	D	0.999345	D;D	0.76494	0.996;0.999	D;D	0.67725	0.95;0.953	T	0.61471	-0.7056	10	0.40728	T	0.16	.	10.175	0.42933	0.1489:0.0:0.0:0.8511	.	2846;2846	P98161-3;P98161	.;PKD1_HUMAN	A	2846;2846;2181;1125	ENSP00000262304:T2846A;ENSP00000399501:T2846A	ENSP00000262304:T2846A	T	-	1	0	PKD1	2093523	1.000000	0.71417	1.000000	0.80357	0.071000	0.16799	5.623000	0.67757	1.940000	0.56252	0.454000	0.30748	ACC	.		0.612	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2153522	T	C	2153522	3	2	27	1	0	0	0	0	1	0	0	0	11989	1696	59	3	4471	3	PKD1	16	2153522	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	275929	2153522	88201231	79	2394											
PDXDC1	23042	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	15127164	15127164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ataagagcatgaagagctgcCtttatgtcggcatggcgagc	11	9	13	8	2	0	3	0	1	0	2	1	4	0	3	1	2	4	3	1	2	3	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:15127164C>T	ENST00000396410.4	+	19	1817	c.1720C>T	c.(1720-1722)Ctt>Ttt	p.L574F	PDXDC1_ENST00000450288.2_Missense_Mutation_p.L546F|PDXDC1_ENST00000563679.1_Missense_Mutation_p.L592F|PDXDC1_ENST00000325823.7_Missense_Mutation_p.L559F|PDXDC1_ENST00000447912.2_Missense_Mutation_p.L483F|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000569715.1_Missense_Mutation_p.L547F	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	574					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAAGAGCTGCCTTTATGTCGG	0.552																																					p.L574F													.	PDXDC1-91	0			c.C1720T						.						142	121	128					16																	15127164		2197	4300	6497	SO:0001583	missense	23042	exon19			AGCTGCCTTTATG	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.1720C>T	16.37:g.15127164C>T	ENSP00000379691:p.Leu574Phe	Somatic	98	2		WXS	Illumina HiSeq	Phase_I	206	143	NM_015027	0	0	64	282	218	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.503953	0.26949	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	T;T;T;T	0.28069	1.64;2.14;1.64;1.63	5.83	3.62	0.41486	.	0.182769	0.56097	D	0.000027	T	0.14313	0.0346	N	0.08118	0	0.27997	N	0.935443	B;B;B;B	0.28552	0.134;0.215;0.134;0.215	B;B;B;B	0.26969	0.051;0.075;0.051;0.051	T	0.12889	-1.0530	10	0.72032	D	0.01	-13.2868	5.6069	0.17385	0.6635:0.1687:0.1678:0.0	.	546;483;546;574	E7EPL4;E7EMH5;B4DR55;Q6P996	.;.;.;PDXD1_HUMAN	F	559;483;574;546	ENSP00000322807:L559F;ENSP00000400310:L483F;ENSP00000379691:L574F;ENSP00000391147:L546F	ENSP00000322807:L559F	L	+	1	0	PDXDC1	15034665	0.928000	0.31464	0.595000	0.28798	0.060000	0.15804	1.996000	0.40776	0.508000	0.28173	0.561000	0.74099	CTT	.		0.552	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		T	15127164	C	T	15127164	3	4	27	1	0	0	0	0	1	0	0	0	11722	681	24	2	1794	2	PDXDC1	16	15127164	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	12973642	15127164	75227589	80	2395											
CMTM4	146223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	66670440	66670440	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccttcacacggggagcaTgccatgatggtctctatgca	9	9	12	11	1	2	1	1	1	1	0	3	2	2	2	2	4	3	2	2	4	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:66670440T>A	ENST00000330687.4	-	2	412	c.231A>T	c.(229-231)gcA>gcT	p.A77A	CMTM4_ENST00000394106.2_Silent_p.A77A|CMTM4_ENST00000563952.1_Silent_p.A48A	NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	77	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		ACGGGGAGCATGCCATGATGG	0.443																																					p.A77A		.											.	CMTM4-227	0			c.A231T						.						117	103	108					16																	66670440		2201	4300	6501	SO:0001819	synonymous_variant	146223	exon2			GGAGCATGCCATG	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"chemokine-like factor super family 4", "chemokine-like factor superfamily 4"	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.231A>T	16.37:g.66670440T>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	95	5	NM_178818	0	0	9	9	0	Q52M40|Q8IZR4|Q8IZV1	Silent	SNP	ENST00000330687.4	37	CCDS10817.1																																																																																			.		0.443	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1			A	66670440	T	A	66670440	2	1	27	1	0	0	0	0	0	0	0	1	3591	1451	51	5		5	CMTM4	16	66670440	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	51543276	66670440	23684313	81	2396											
PRDM7	11105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	90127007	90127007	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccaggttctgctcttcAtcatcccgggcacagttcac	7	10	8	16	1	5	0	3	0	2	0	6	0	6	0	3	2	1	4	3	2	0	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:90127007A>T	ENST00000449207.2	-	9	994	c.975T>A	c.(973-975)gaT>gaA	p.D325E	PRDM7_ENST00000407825.1_Intron|PRDM7_ENST00000325921.6_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	325	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)			lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TCTGCTCTTCATCATCCCGGG	0.547																																					p.D325E		.											.	PRDM7-92	0			c.T975A						.						78	77	77					16																	90127007		1938	4120	6058	SO:0001583	missense	11105	exon9			CTCTTCATCATCC	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"Zinc fingers, C2H2-type", "-"	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.975T>A	16.37:g.90127007A>T	ENSP00000396732:p.Asp325Glu	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	210	119	NM_001098173	0	0	0	0	0	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.026388	0.00414	.	.	ENSG00000126856	ENST00000449207	T	0.41065	1.01	2.23	-4.45	0.03546	SET domain (2);	.	.	.	.	T	0.10594	0.0259	N	0.01297	-0.9	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.17137	-1.0379	8	.	.	.	-0.9636	1.139	0.01761	0.2061:0.3427:0.2807:0.1705	.	325	Q9NQW5	PRDM7_HUMAN	E	325	ENSP00000396732:D325E	.	D	-	3	2	PRDM7	88654508	0.000000	0.05858	0.092000	0.20876	0.342000	0.28953	-2.198000	0.01239	-1.546000	0.01717	0.397000	0.26171	GAT	.		0.547	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1			T	90127007	A	T	90127007	3	4	27	1	0	0	0	0	1	0	0	0	12490	214	8	5	511	5	PRDM7	16	90127007	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	23456567	90127007	227746	82	2397											
SHPK	23729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3514081	3514081	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggttctgaacaatgcctcGgcacagagcccgggtcacgt	9	7	12	13	3	2	2	1	1	1	1	3	2	2	2	2	3	3	2	2	3	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:3514081G>T	ENST00000225519.3	-	7	1312	c.1210C>A	c.(1210-1212)Cga>Aga	p.R404R	SHPK_ENST00000572705.1_5'Flank	NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase	404					carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		ACAATGCCTCGGCACAGAGCC	0.642																																					p.R404R		.											.	SHPK-69	0			c.C1210A						.						110	111	111					17																	3514081		2203	4300	6503	SO:0001819	synonymous_variant	23729	exon7			TGCCTCGGCACAG	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"carbohydrate kinase-like"	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694	ENST00000225519.3:c.1210C>A	17.37:g.3514081G>T		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	169	99	NM_013276	0	0	3	10	7	B2R640|Q8WUH3	Silent	SNP	ENST00000225519.3	37	CCDS11030.1																																																																																			.		0.642	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2			T	3514081	G	T	3514081	2	4	27	1	0	0	0	0	0	0	0	1	14322	1124	39	4		4	SHPK	17	3514081	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		3514081	77681129	83	2398											
P2RX1	5023	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3808622	3808622	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagacactgctgatgaggccGctcgaggtctggtagccctt	7	9	14	11	2	1	3	0	2	1	1	2	5	1	3	2	3	2	3	2	3	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:3808622G>C	ENST00000225538.3	-	2	451	c.177C>G	c.(175-177)agC>agG	p.S59R		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	59					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		TGATGAGGCCGCTCGAGGTCT	0.627																																					p.S59R		.											.	P2RX1-70	0			c.C177G						.						56	60	59					17																	3808622		2203	4300	6503	SO:0001583	missense	5023	exon2			GAGGCCGCTCGAG	X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.177C>G	17.37:g.3808622G>C	ENSP00000225538:p.Ser59Arg	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	117	31	NM_002558	0	0	0	0	0	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	37	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.773763	0.69992	.	.	ENSG00000108405	ENST00000225538	T	0.04551	3.6	5.84	-11.4	0.00090	.	0.368613	0.32671	N	0.005781	T	0.05273	0.0140	L	0.43152	1.355	0.09310	N	1	P	0.37122	0.583	P	0.46299	0.511	T	0.17167	-1.0378	10	0.87932	D	0	-16.9741	10.8476	0.46751	0.5956:0.089:0.3154:0.0	.	59	P51575	P2RX1_HUMAN	R	59	ENSP00000225538:S59R	ENSP00000225538:S59R	S	-	3	2	P2RX1	3755371	0.011000	0.17503	0.000000	0.03702	0.860000	0.49131	-0.937000	0.03942	-2.012000	0.00950	-0.291000	0.09656	AGC	.		0.627	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558		C	3808622	G	C	3808622	3	2	27	1	0	0	0	0	1	0	0	0	11365	1078	38	4	1066	4	P2RX1	17	3808622	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	294541	3808622	77386588	84	2399											
CAMTA2	23125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4873373	4873373	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caggcgacctcgctcaaaggGcagttcgctgtaggcggtag	8	7	15	11	4	1	0	1	0	0	0	3	1	1	0	1	4	0	6	1	4	3	3	rs189574616		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:4873373G>A	ENST00000348066.3	-	18	3136	c.3013C>T	c.(3013-3015)Ccc>Tcc	p.P1005S	CAMTA2_ENST00000572543.1_Missense_Mutation_p.P1010S|SPAG7_ENST00000571023.1_5'Flank|CAMTA2_ENST00000358183.4_Missense_Mutation_p.P1005S|SPAG7_ENST00000206020.3_5'Flank|SPAG7_ENST00000575142.1_5'Flank|SPAG7_ENST00000573366.1_5'Flank|RP5-1050D4.3_ENST00000576752.1_RNA|CAMTA2_ENST00000361571.5_Missense_Mutation_p.P1004S|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000381311.5_Missense_Mutation_p.P1007S|CAMTA2_ENST00000414043.3_Missense_Mutation_p.P1028S	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	1005					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CGCTCAAAGGGCAGTTCGCTG	0.557													G|||	1	0.000199681	8e-04	0	5008	,	,		21765	0		0	False		,,,				2504	0				p.P1028S		.											.	CAMTA2-91	0			c.C3082T						.						104	96	99					17																	4873373		2203	4300	6503	SO:0001583	missense	23125	exon18			CAAAGGGCAGTTC	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.3013C>T	17.37:g.4873373G>A	ENSP00000321813:p.Pro1005Ser	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	121	32	NM_001171167	0	0	0	1	1	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	37	CCDS11063.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	9.829	1.187845	0.21954	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.28255	2.86;1.85;1.62;1.85;1.63	4.74	2.76	0.32466	.	0.286130	0.33650	N	0.004688	T	0.19248	0.0462	N	0.25647	0.755	0.32120	N	0.588178	B;B;B;B	0.16396	0.002;0.001;0.001;0.017	B;B;B;B	0.12156	0.002;0.003;0.001;0.007	T	0.12451	-1.0547	10	0.33940	T	0.23	-7.2654	8.4723	0.32993	0.1889:0.0:0.8111:0.0	.	1028;1007;1005;1004	E7EWU5;O94983-3;O94983;O94983-4	.;.;CMTA2_HUMAN;.	S	1028;1007;1004;1005;1005	ENSP00000412886:P1028S;ENSP00000370712:P1007S;ENSP00000354828:P1004S;ENSP00000350910:P1005S;ENSP00000321813:P1005S	ENSP00000321813:P1005S	P	-	1	0	CAMTA2	4814097	0.198000	0.23374	0.985000	0.45067	0.764000	0.43329	0.468000	0.22051	0.625000	0.30304	0.555000	0.69702	CCC	G|0.999;A|0.000		0.557	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		A	4873373	G	A	4873373	3	1	27	1	0	0	0	0	1	0	0	0	2620	1203	42	2	669	2	CAMTA2	17	4873373	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	1064751	4873373	76321837	85	2400											
TP53I13	90313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27899239	27899239	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcaagggcccaggcagccctCttctagtggtgccaagaggc	8	7	13	13	0	3	1	1	0	2	1	3	1	3	1	3	4	2	1	3	4	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:27899239C>G	ENST00000301057.7	+	6	708	c.593C>G	c.(592-594)tCt>tGt	p.S198C	RP11-68I3.4_ENST00000579050.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	198						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		AGGCAGCCCTCTTCTAGTGGT	0.657																																					p.S198C		.											.	TP53I13-90	0			c.C593G						.						22	24	24					17																	27899239		1986	4140	6126	SO:0001583	missense	90313	exon6			AGCCCTCTTCTAG	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.593C>G	17.37:g.27899239C>G	ENSP00000301057:p.Ser198Cys	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	37	15	NM_138349	0	0	92	223	131	Q7L5U3	Missense_Mutation	SNP	ENST00000301057.7	37	CCDS42289.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.816310	0.50527	.	.	ENSG00000167543	ENST00000301057	.	.	.	3.94	1.89	0.25635	.	0.645758	0.14735	N	0.301505	T	0.51550	0.1681	M	0.63428	1.95	0.09310	N	1	D	0.69078	0.997	P	0.60345	0.873	T	0.36939	-0.9727	9	0.87932	D	0	-2.2609	5.6779	0.17759	0.0:0.7387:0.0:0.2613	.	198	Q8NBR0	P5I13_HUMAN	C	198	.	ENSP00000301057:S198C	S	+	2	0	TP53I13	24923365	0.000000	0.05858	0.002000	0.10522	0.018000	0.09664	-0.070000	0.11523	0.412000	0.25729	0.462000	0.41574	TCT	.		0.657	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349		G	27899239	C	G	27899239	3	3	27	1	0	0	0	0	1	0	0	0	16419	913	32	4	615	4	TP53I13	17	27899239	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	23025866	27899239	53295971	86	2401											
ATAD5	79915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	29220519	29220519	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatgaattgtcttgctaggAaacactctgaaagagaacag	15	10	10	6	0	2	3	0	2	2	1	2	5	2	4	0	1	3	2	0	1	6	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:29220519A>T	ENST00000321990.4	+	21	5026	c.4648A>T	c.(4648-4650)Aaa>Taa	p.K1550*		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1550					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TCTTGCTAGGAAACACTCTGA	0.358																																					p.K1550X		.											.	ATAD5-93	0			c.A4648T						.						42	50	47					17																	29220519		2201	4297	6498	SO:0001587	stop_gained	79915	exon21			GCTAGGAAACACT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4648A>T	17.37:g.29220519A>T	ENSP00000313171:p.Lys1550*	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	93	54	NM_024857	0	0	3	8	5	Q05DH0|Q69YR6|Q9H9I1	Nonsense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	42	9.739259	0.99252	.	.	ENSG00000176208	ENST00000321990	.	.	.	6.08	5.01	0.66863	.	0.805371	0.11834	N	0.524975	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.577	0.04808	0.6185:0.1452:0.0786:0.1577	.	.	.	.	X	1550	.	ENSP00000313171:K1550X	K	+	1	0	ATAD5	26244645	0.002000	0.14202	0.899000	0.35326	0.203000	0.24098	0.236000	0.17967	2.333000	0.79357	0.482000	0.46254	AAA	.		0.358	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29220519	A	T	29220519	4	4	27	1	0	0	0	0	0	1	0	0	1077	247	9	5	4730	5	ATAD5	17	29220519	Nonsense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	1321280	29220519	51974691	87	2402											
C17orf64	124773	broad.mit.edu	37	chr17	58499974	58499975	+	Frame_Shift_Ins	INS	-	-	G																															tggaggcctcagatgggcaaINSgggggtgaaggggacaagcc																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:58499974_58499975insG	ENST00000269127.4	+	1	105_106	c.21_22insG	c.(22-24)gggfs	p.G8fs		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	8										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CAGATGGGCAAGGGGGTGAAGG	0.614																																					p.Q7fs													.	C17orf64-271	0			c.21_22insG						.																																			SO:0001589	frameshift_variant	124773	exon1			TGGGCAAGGGGGT	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.26dupG	17.37:g.58499979_58499979dupG	ENSP00000269127:p.Gly8fs	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	196	6	NM_181707	0	0	0	0	0	Q8IY87	Frame_Shift_Ins	INS	ENST00000269127.4	37	CCDS32698.2																																																																																			.		0.614	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		G	58499975	-	G	58499974	7	5	27	1	0	1	1	0	0	0	0	0	1877	69	3	0	23	0	C17orf64	17	58499974	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	29279455	58499974	22695236	88	2403											
FAM38B	63895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	10691260	10691260	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgacgtaattgtagctctTggtgaggaagttccccagga	9	12	13	7	1	1	2	0	2	1	0	2	4	2	4	2	3	1	5	2	3	3	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr18:10691260T>A	ENST00000503781.3	-	44	6972	c.6973A>T	c.(6973-6975)Aag>Tag	p.K2325*	PIEZO2_ENST00000285141.4_Nonsense_Mutation_p.K180*|PIEZO2_ENST00000580640.1_Nonsense_Mutation_p.K2350*|PIEZO2_ENST00000538948.1_Nonsense_Mutation_p.K282*|PIEZO2_ENST00000302079.6_Nonsense_Mutation_p.K2325*	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2325					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TTGTAGCTCTTGGTGAGGAAG	0.493																																					p.K2325X		.											.	.	0			c.A6973T						.						128	112	118					18																	10691260		2203	4300	6503	SO:0001587	stop_gained	63895	exon44			AGCTCTTGGTGAG	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6973A>T	18.37:g.10691260T>A	ENSP00000421377:p.Lys2325*	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	272	76	NM_022068	0	0	8	8	0	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Nonsense_Mutation	SNP	ENST00000503781.3	37		.	.	.	.	.	.	.	.	.	.	T	43	9.868735	0.99284	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	.	.	.	5.62	5.62	0.85841	.	0.142737	0.47455	D	0.000228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1189	0.81329	0.0:0.0:0.0:1.0	.	.	.	.	X	282;2325;282;180	.	ENSP00000285141:K180X	K	-	1	0	FAM38B	10681260	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	8.005000	0.88553	2.263000	0.75096	0.533000	0.62120	AAG	.		0.493	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		A	10691260	T	A	10691260	4	1	27	1	0	0	0	0	0	1	0	0	5574	1821	63	5	1321	5	FAM38B	18	10691260	Nonsense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		10691260	67385988	89	2404											
RBBP8	5932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	20606136	20606136	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagatcttgatccttgtcCtcgtccaaaaagacgtcagc	11	10	9	11	2	2	3	1	1	1	2	6	4	5	4	3	1	1	0	3	1	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr18:20606136C>G	ENST00000399722.2	+	19	2978	c.2627C>G	c.(2626-2628)cCt>cGt	p.P876R	RBBP8_ENST00000327155.5_Missense_Mutation_p.P876R|RBBP8_ENST00000399725.2_Missense_Mutation_p.L844V|RBBP8_ENST00000360790.5_Missense_Mutation_p.P881R|RBBP8_ENST00000581687.1_Missense_Mutation_p.P54R|Y_RNA_ENST00000411091.1_RNA	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	876					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.P876L(1)|p.L844F(1)		central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GATCCTTGTCCTCGTCCAAAA	0.368								Homologous recombination																													p.P876R		.											.	RBBP8-659	2	Substitution - Missense(2)	prostate(2)	c.C2627G						.						128	114	119					18																	20606136		2203	4300	6503	SO:0001583	missense	5932	exon19			CTTGTCCTCGTCC	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.2627C>G	18.37:g.20606136C>G	ENSP00000382628:p.Pro876Arg	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	305	78	NM_002894	0	0	192	256	64	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	37	CCDS11875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.52|11.52	1.661903|1.661903	0.29515|0.29515	.|.	.|.	ENSG00000101773|ENSG00000101773	ENST00000399725;ENST00000399721|ENST00000327155;ENST00000399722;ENST00000360790	T|T;T;T	0.35048|0.30182	1.33|1.54;1.54;1.54	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|0.429012	.|0.25735	.|N	.|0.028643	T|T	0.24967|0.24967	0.0606|0.0606	N|N	0.14661|0.14661	0.345|0.345	0.30511|0.30511	N|N	0.769444|0.769444	P|D;D	0.42827|0.59767	0.791|0.986;0.986	B|P;P	0.38378|0.48873	0.272|0.593;0.593	T|T	0.07481|0.07481	-1.0770|-1.0770	9|10	0.87932|0.38643	D|T	0|0.18	-7.0083|-7.0083	12.5437|12.5437	0.56186|0.56186	0.2615:0.7385:0.0:0.0|0.2615:0.7385:0.0:0.0	.|.	844|881;876	A6NKN2|E7ETY1;Q99708	.|.;COM1_HUMAN	V|R	844|876;876;881	ENSP00000382630:L844V|ENSP00000323050:P876R;ENSP00000382628:P876R;ENSP00000354024:P881R	ENSP00000382627:L844V|ENSP00000323050:P876R	L|P	+|+	1|2	0|0	RBBP8|RBBP8	18860134|18860134	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	1.895000|1.895000	0.39778|0.39778	2.716000|2.716000	0.92895|0.92895	0.655000|0.655000	0.94253|0.94253	CTC|CCT	.		0.368	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		G	20606136	C	G	20606136	3	3	27	1	0	0	0	0	1	0	0	0	13137	681	24	4	2697	4	RBBP8	18	20606136	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	9914876	20606136	57471112	90	2405											
PCSK4	148223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1481811	1481811	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggggtggccctggcacGggagagccaggcgtatagtg	6	6	21	8	2	0	1	0	0	0	1	0	2	0	1	2	7	1	2	2	7	2	2	rs377189780		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:1481811G>A	ENST00000436106.2	-	0	0				C19orf25_ENST00000588849.1_5'Flank|C19orf25_ENST00000585675.1_5'Flank|C19orf25_ENST00000592872.1_5'Flank|C19orf25_ENST00000586564.1_5'Flank|C19orf25_ENST00000588427.1_5'Flank|CTB-25B13.6_ENST00000585643.1_RNA|PCSK4_ENST00000300954.5_Missense_Mutation_p.R739C|C19orf25_ENST00000588871.1_5'Flank|C19orf25_ENST00000591027.1_5'Flank|C19orf25_ENST00000427685.2_5'Flank			Q9UFG5	CS025_HUMAN	chromosome 19 open reading frame 25														Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCTGGCACGGGAGAGCCAG	0.672																																					p.R739C		.											.	PCSK4-90	0			c.C2215T						.						21	25	24					19																	1481811		2202	4296	6498	SO:0001631	upstream_gene_variant	54760	exon15			TGGCACGGGAGAG	AK075267	CCDS45898.1	19p13.3	2012-10-24			ENSG00000119559	ENSG00000119559			26711	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_152482		Approved	FLJ36666	uc010dsk.3	Q9UFG5	OTTHUMG00000180092		19.37:g.1481811G>A	Exception_encountered	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	104	12	NM_017573	0	1	18	23	4	B3KQN6|Q8N9R7|Q8WV94	Missense_Mutation	SNP	ENST00000436106.2	37	CCDS45898.1	.	.	.	.	.	.	.	.	.	.	g	8.277	0.814622	0.16607	.	.	ENSG00000115257	ENST00000300954	T	0.70749	-0.51	1.2	-2.4	0.06583	.	.	.	.	.	T	0.46268	0.1384	L	0.36672	1.1	0.09310	N	1	P	0.46457	0.878	B	0.26094	0.066	T	0.30880	-0.9963	9	0.52906	T	0.07	.	4.3765	0.11272	0.0:0.4776:0.2063:0.3161	.	739	Q6UW60	PCSK4_HUMAN	C	739	ENSP00000300954:R739C	ENSP00000300954:R739C	R	-	1	0	PCSK4	1432811	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-3.167000	0.00575	-2.042000	0.00914	-1.041000	0.02371	CGT	.		0.672	C19orf25-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449694.1	NM_152482		A	1481811	G	A	1481811	1	1	27	0	1	0	0	0	0	0	0	0	11628	1116	39	1		1	PCSK4	19	1481811	5'Flank	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1481811	57647172	91	2406											
NRTN	4902	hgsc.bcm.edu	37	chr19	5827909	5827909	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgcggccttgcgggctgcgcGagctggaggtgcgcgtgagc	3	6	20	12	7	0	1	0	1	0	0	0	3	0	2	1	4	5	2	1	4	0	1	rs375707068		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:5827909G>A	ENST00000303212.2	+	2	683	c.319G>A	c.(319-321)Gag>Aag	p.E107K		NM_004558.3	NP_004549.1	Q99748	NRTN_HUMAN	neurturin	107					axon guidance (GO:0007411)|MAPK cascade (GO:0000165)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|extracellular region (GO:0005576)	receptor binding (GO:0005102)			large_intestine(1)	1						CGGGCTGCGCGAGCTGGAGGT	0.806																																					p.E107K		.											.	NRTN-90	0			c.G319A						.	G	LYS/GLU	0,3794		0,0,1897	5	5	5		319	4.3	1	19		5	1,7493		0,1,3746	no	missense	NRTN	NM_004558.3	56	0,1,5643	AA,AG,GG		0.0133,0.0,0.0089	possibly-damaging	107/198	5827909	1,11287	1897	3747	5644	SO:0001583	missense	4902	exon2			CTGCGCGAGCTGG	U78110	CCDS12151.1	19p13.3	2014-01-30				ENSG00000171119		"Endogenous ligands"	8007	protein-coding gene	gene with protein product	"prepro-neurturin"	602018				8945474	Standard	NM_004558		Approved	NTN	uc002mde.3	Q99748		ENST00000303212.2:c.319G>A	19.37:g.5827909G>A	ENSP00000302648:p.Glu107Lys	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	9	8	NM_004558	0	0	0	0	0	B2RPE8	Missense_Mutation	SNP	ENST00000303212.2	37	CCDS12151.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650912	0.87958	0.0	1.33E-4	ENSG00000171119	ENST00000303212	D	0.84146	-1.81	4.33	4.33	0.51752	Transforming growth factor-beta, C-terminal (3);	0.128790	0.51477	D	0.000084	D	0.82513	0.5053	L	0.34521	1.04	0.39656	D	0.970533	D	0.63046	0.992	P	0.54856	0.762	T	0.81088	-0.1091	10	0.33940	T	0.23	-8.9466	8.5435	0.33406	0.1094:0.0:0.8906:0.0	.	107	Q99748	NRTN_HUMAN	K	107	ENSP00000302648:E107K	ENSP00000302648:E107K	E	+	1	0	NRTN	5778909	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.082000	0.50128	2.153000	0.67306	0.491000	0.48974	GAG	.		0.806	NRTN-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451882.2	NM_004558		A	5827909	G	A	5827909	3	1	27	1	0	0	0	0	1	0	0	0	10690	1059	37	1	325	1	NRTN	19	5827909	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	4346098	5827909	53301074	92	2407											
MED26	9441	bcgsc.ca	37	chr19	16688124	16688124	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggggatgagttggggaccaGggggtcgtggctagctttgg	5	9	22	5	1	0	1	0	1	0	0	1	3	0	3	1	8	1	3	1	8	1	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:16688124G>C	ENST00000263390.3	-	3	779	c.517C>G	c.(517-519)Ctg>Gtg	p.L173V	CTD-3222D19.2_ENST00000409035.1_Missense_Mutation_p.L181V|CTC-429P9.4_ENST00000593962.1_5'Flank	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	173					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						TTGGGGACCAGGGGGTCGTGG	0.697																																					p.L173V													.	MED26-70	0			c.C517G						.						35	42	40					19																	16688124		2191	4296	6487	SO:0001583	missense	9441	exon3			GGACCAGGGGGTC	AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.517C>G	19.37:g.16688124G>C	ENSP00000263390:p.Leu173Val	Somatic	44	1		WXS	Illumina HiSeq	Phase_1	88	41	NM_004831	0	0	3	6	3	A1A4S3|Q0VGB6	Missense_Mutation	SNP	ENST00000263390.3	37	CCDS12347.1	.	.	.	.	.	.	.	.	.	.	g	5.870	0.344609	0.11126	.	.	ENSG00000105085	ENST00000263390	.	.	.	4.96	3.93	0.45458	.	0.517604	0.18127	N	0.150847	T	0.16938	0.0407	N	0.17082	0.46	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.23655	-1.0182	9	0.09084	T	0.74	-12.4552	5.0117	0.14315	0.0835:0.1469:0.6179:0.1517	.	173	O95402	MED26_HUMAN	V	173	.	ENSP00000263390:L173V	L	-	1	2	MED26	16549124	0.996000	0.38824	0.897000	0.35233	0.439000	0.31926	1.533000	0.36040	2.322000	0.78497	0.645000	0.84053	CTG	.		0.697	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831		C	16688124	G	C	16688124	3	2	27	1	0	0	0	0	1	0	0	0	9469	991	35	4	1289	4	MED26	19	16688124	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	10860215	16688124	42440859	93	2408											
GAPDHS	26330	hgsc.bcm.edu	37	chr19	36033313	36033313	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccatacaggcagcttcggTaagctggggagaggtgccca	9	7	14	11	1	0	1	0	0	0	1	2	2	1	1	2	5	4	4	2	5	2	3	rs558746420	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:36033313T>C	ENST00000222286.4	+	5	656		c.e5+2		AD000090.2_ENST00000590125.1_RNA|AD000090.2_ENST00000589137.1_RNA|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000588286.1_RNA|AD000090.2_ENST00000590717.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic						carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCAGCTTCGGTAAGCTGGGGA	0.637																																					.		.											.	GAPDHS-226	0			c.540+2T>C						.						43	42	42					19																	36033313		2203	4300	6503	SO:0001630	splice_region_variant	26330	exon5			CTTCGGTAAGCTG	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.540+2T>C	19.37:g.36033313T>C		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	87	13	NM_014364	0	0	1	1	0	B2RC82|O60823|Q6JTT9|Q9HCU6	Splice_Site	SNP	ENST00000222286.4	37	CCDS12465.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.031348	0.75504	.	.	ENSG00000105679	ENST00000222286	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8058	0.52155	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAPDHS	40725153	1.000000	0.71417	0.798000	0.32154	0.842000	0.47809	7.479000	0.81095	2.115000	0.64714	0.379000	0.24179	.	.		0.637	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364	Intron	C	36033313	T	C	36033313	5	2	27	1	0	0	0	0	0	0	1	0	6257	1652	57	3	560	3	GAPDHS	19	36033313	Splice_Site	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	19345189	36033313	23095670	94	2409											
TBCB	1155	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	36606539	36606539	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacaccttccgctccgagaAgcgatacagccgcagcctca	11	5	8	17	4	1	1	1	0	0	1	3	3	3	1	5	0	5	2	5	0	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:36606539A>T	ENST00000221855.3	+	1	652	c.77A>T	c.(76-78)aAg>aTg	p.K26M	TBCB_ENST00000589996.1_Missense_Mutation_p.K26M|TBCB_ENST00000585746.1_5'Flank|TBCB_ENST00000392178.4_3'UTR|TBCB_ENST00000586868.1_5'Flank|POLR2I_ENST00000221859.4_5'Flank	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	26					'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGCTCCGAGAAGCGATACAGC	0.662																																					p.K26M		.											.	TBCB-90	0			c.A77T						.						34	23	27					19																	36606539		2202	4299	6501	SO:0001583	missense	1155	exon1			CCGAGAAGCGATA	AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"cytoskeleton-associated protein 1", "cytoskeleton associated protein 1"	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.77A>T	19.37:g.36606539A>T	ENSP00000221855:p.Lys26Met	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	159	72	NM_001281	0	0	44	67	23	O00111|O00674|O14728|Q6FGY5	Missense_Mutation	SNP	ENST00000221855.3	37	CCDS12488.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024046	0.75390	.	.	ENSG00000105254	ENST00000221855;ENST00000392178	D	0.92249	-3.0	5.33	4.31	0.51392	.	0.180969	0.47852	D	0.000214	D	0.90964	0.7159	M	0.76002	2.32	0.80722	D	1	P	0.44260	0.83	B	0.42422	0.387	D	0.89084	0.3478	10	0.54805	T	0.06	-27.6416	9.2292	0.37425	0.9131:0.0:0.0869:0.0	.	26	Q99426	TBCB_HUMAN	M	26	ENSP00000221855:K26M	ENSP00000221855:K26M	K	+	2	0	TBCB	41298379	1.000000	0.71417	0.979000	0.43373	0.871000	0.50021	2.209000	0.42806	0.863000	0.35553	0.397000	0.26171	AAG	.		0.662	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281		T	36606539	A	T	36606539	3	4	27	1	0	0	0	0	1	0	0	0	15662	72	3	5	79	5	TBCB	19	36606539	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	573226	36606539	22522444	95	2410											
FBL	2091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40330915	40330915	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccataaactgattccccaggGaccaggttcttggtgaccag	10	9	10	12	0	1	2	0	2	1	0	2	3	2	3	5	3	1	1	5	3	2	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:40330915G>A	ENST00000221801.3	-	4	449	c.336C>T	c.(334-336)gtC>gtT	p.V112V	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	112					histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		ATTCCCCAGGGACCAGGTTCT	0.577																																					p.V112V		.											.	FBL-91	0			c.C336T						.						103	91	95					19																	40330915		2203	4300	6503	SO:0001819	synonymous_variant	2091	exon4			CCCAGGGACCAGG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.336C>T	19.37:g.40330915G>A		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	93	26	NM_001436	0	0	88	150	62	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	37	CCDS12545.1																																																																																			.		0.577	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		A	40330915	G	A	40330915	2	1	27	1	0	0	0	0	0	0	0	1	5715	1161	41	2		2	FBL	19	40330915	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	3724376	40330915	18798068	96	2411											
KLK5	25818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	51451945	51451945	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgcagaacatggtgtcaTctatctgtctcgggtaagca	9	10	12	10	3	4	1	1	0	3	1	5	1	4	1	0	3	2	3	0	3	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:51451945T>G	ENST00000336334.3	-	5	1029	c.677A>C	c.(676-678)gAt>gCt	p.D226A	KLK5_ENST00000391809.2_Missense_Mutation_p.D226A|KLK5_ENST00000593428.1_Missense_Mutation_p.D226A|CTB-147C22.8_ENST00000601506.1_RNA|CTB-147C22.8_ENST00000594939.1_RNA	NM_012427.4	NP_036559	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5	226	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	epidermal lamellar body (GO:0097209)|extracellular space (GO:0005615)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		CATGGTGTCATCTATCTGTCT	0.507																																					p.D226A		.											.	KLK5-226	0			c.A677C						.						170	133	146					19																	51451945		2203	4300	6503	SO:0001583	missense	25818	exon5			GTGTCATCTATCT	AF135028	CCDS12810.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167754		"Kallikreins"	6366	protein-coding gene	gene with protein product		605643	"kallikrein 5"			10514489, 10608802, 1680072, 4, 16800723, 17012259	Standard	NM_012427		Approved	SCTE, KLK-L2	uc002puf.3	Q9Y337		ENST00000336334.3:c.677A>C	19.37:g.51451945T>G	ENSP00000337733:p.Asp226Ala	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	114	53	NM_012427	0	0	0	2	2	Q53ZR3|Q9HBG8	Missense_Mutation	SNP	ENST00000336334.3	37	CCDS12810.1	.	.	.	.	.	.	.	.	.	.	t	10.10	1.257295	0.22965	.	.	ENSG00000167754	ENST00000336334;ENST00000391809	D;D	0.88201	-2.35;-2.35	4.67	2.49	0.30216	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.34386	U	0.004020	T	0.79776	0.4504	N	0.16066	0.365	0.09310	N	1	P	0.40398	0.716	B	0.41036	0.346	T	0.71111	-0.4687	10	0.51188	T	0.08	.	10.2185	0.43184	0.0:0.0:0.5204:0.4796	.	226	Q9Y337	KLK5_HUMAN	A	226	ENSP00000337733:D226A;ENSP00000375685:D226A	ENSP00000337733:D226A	D	-	2	0	KLK5	56143757	1.000000	0.71417	0.006000	0.13384	0.020000	0.10135	5.146000	0.64845	0.262000	0.21774	-0.316000	0.08728	GAT	.		0.507	KLK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465057.1	NM_012427		G	51451945	T	G	51451945	3	3	27	1	0	0	0	0	1	0	0	0	8428	1435	50	5	212	5	KLK5	19	51451945	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	11121030	51451945	7677038	97	2412											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		.											.	.	0			c.G965A						.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	86	16	NM_001144989	0	0	3	3	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	27	1	0	0	0	0	1	0	0	0	18208	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	6933848	58385793	743190	98	2413	23	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385798	58385799	+	Missense_Mutation	DNP	CC	CC	TT																															ccacattcataaggtcttttCccagtgtgaactctctgatg																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:58385798_58385799CC>TT	ENST00000435989.2	-	3	1193_1194	c.959_960GG>AA	c.(958-960)gGG>gAA	p.G320E	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	320					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G320E(1)|p.G320G(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AAGGTCTTTTCCCAGTGTGAAC	0.356																																					p.G320E		.											.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	central_nervous_system(2)	c.G959A						.																																			SO:0001583	missense	730051	exon3			CTTTTCCCAGTGT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.959_960delinsTT	19.37:g.58385798_58385799delinsTT	ENSP00000410545:p.Gly320Glu	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	84	17	NM_001144989	0	0	0	0	0	A6NF35	Missense_Mutation	DNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.356	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		TT	58385799	CC	TT	58385798	3	4	27	1	0	0	0	0	1	0	0	0	18208	842	30	2	1611	2	ZNF814	19	58385798	Missense_Mutation	DNP	CC	TCGA-A4-A5Y1-01A-11D-A28G-10	5	58385798	743185	99	2414	23	2									
PCSK2	5126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	17417493	17417493	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtggatgggccccgggagCtcacgctgcaggccatggcc	6	5	16	14	2	1	0	1	0	0	0	1	2	1	2	4	5	2	3	4	5	0	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:17417493C>T	ENST00000262545.2	+	8	1165	c.850C>T	c.(850-852)Ctc>Ttc	p.L284F	PCSK2_ENST00000536609.1_Missense_Mutation_p.L249F|PCSK2_ENST00000377899.1_Missense_Mutation_p.L265F	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	284	Peptidase S8.			EL -> DV (in Ref. 1; AAA60032). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	GCCCCGGGAGCTCACGCTGCA	0.642																																					p.L284F		.											.	PCSK2-157	0			c.C850T						.						34	32	33					20																	17417493		2203	4300	6503	SO:0001583	missense	5126	exon8			CGGGAGCTCACGC	AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"neuroendocrine convertase 2", "KEX2-like endoprotease 2"	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.850C>T	20.37:g.17417493C>T	ENSP00000262545:p.Leu284Phe	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	174	65	NM_002594	0	0	0	0	0	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	37	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421696	0.83559	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	D;D;D	0.87887	-2.31;-2.31;-2.31	5.38	5.38	0.77491	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.92192	0.7524	M	0.79693	2.465	0.80722	D	1	B;D	0.53745	0.24;0.962	B;P	0.55391	0.146;0.775	D	0.92722	0.6192	10	0.56958	D	0.05	-19.6799	17.6879	0.88261	0.0:1.0:0.0:0.0	.	249;284	B4DFQ3;P16519	.;NEC2_HUMAN	F	265;284;249	ENSP00000367131:L265F;ENSP00000262545:L284F;ENSP00000437458:L249F	ENSP00000262545:L284F	L	+	1	0	PCSK2	17365493	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.647000	0.61418	2.519000	0.84933	0.655000	0.94253	CTC	.		0.642	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17417493	C	T	17417493	3	4	27	1	0	0	0	0	1	0	0	0	11627	797	28	2	880	2	PCSK2	20	17417493	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		17417493	45608027	100	2415											
CST3	1471	hgsc.bcm.edu	37	chr20	23618488	23618488	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggagcagcggggcgcgcagGggcccggccatggtcggcta	6	3	20	12	5	0	0	0	0	0	0	1	1	0	1	2	8	2	3	2	8	1	1	rs1055084	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:23618488G>A	ENST00000398411.1	-	1	94	c.12C>T	c.(10-12)ccC>ccT	p.P4P	CST3_ENST00000376925.3_Silent_p.P4P|CST3_ENST00000398409.1_Silent_p.P4P			P01034	CYTC_HUMAN	cystatin C	4					apoptotic process (GO:0006915)|brain development (GO:0007420)|cell activation (GO:0001775)|cellular response to hydrogen peroxide (GO:0070301)|circadian sleep/wake cycle, REM sleep (GO:0042747)|defense response (GO:0006952)|embryo implantation (GO:0007566)|extracellular fibril organization (GO:0043206)|eye development (GO:0001654)|negative regulation of blood vessel remodeling (GO:0060313)|negative regulation of cell death (GO:0060548)|negative regulation of collagen catabolic process (GO:0010711)|negative regulation of elastin catabolic process (GO:0060311)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|regulation of programmed cell death (GO:0043067)|regulation of tissue remodeling (GO:0034103)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|salivary gland development (GO:0007431)|Sertoli cell development (GO:0060009)	basement membrane (GO:0005604)|cell projection (GO:0042995)|contractile fiber (GO:0043292)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)			large_intestine(2)|lung(1)|ovary(1)	4	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					GGGCGCGCAGGGGCCCGGCCA	0.756													g|||	114	0.0227636	0.0015	0.0476	5008	,	,		7697	0		0.0696	False		,,,				2504	0.0092				p.P4P		.											.	CST3-91	0			c.C12T						.			35,2527		0,35,1246	2	2	2		12	-3	0	20	dbSNP_86	2	290,4772		2,286,2243	no	coding-synonymous	CST3	NM_000099.2		2,321,3489	AA,AG,GG		5.729,1.3661,4.2629		4/147	23618488	325,7299	1281	2531	3812	SO:0001819	synonymous_variant	1471	exon1			GCGCAGGGGCCCG		CCDS13158.1	20p11.2	2008-04-15	2008-04-15		ENSG00000101439	ENSG00000101439			2475	protein-coding gene	gene with protein product		604312	"cystatin C (amyloid angiopathy and cerebral hemorrhage)"			8486384	Standard	NM_000099		Approved		uc002wtn.1	P01034	OTTHUMG00000032080	ENST00000398411.1:c.12C>T	20.37:g.23618488G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	8	5	NM_000099	0	0	78	308	230	B2R5J9|D3DW42|Q6FGW9	Silent	SNP	ENST00000398411.1	37	CCDS13158.1																																																																																			T|0.037;C|0.962		0.756	CST3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256831.1	NM_000099		A	23618488	G	A	23618488	2	1	27	1	0	0	0	0	0	0	0	1	3979	1219	43	2		2	CST3	20	23618488	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	6200995	23618488	39407032	101	2416											
C20orf114	92747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31892698	31892698	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggattggctggttccaaGtaagtgttaacaggtggtgc	8	12	15	6	0	0	0	0	0	0	0	1	1	1	1	1	5	2	4	1	5	3	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:31892698G>A	ENST00000253354.1	+	13	1415		c.e13+1		BPIFB1_ENST00000464032.1_Splice_Site	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1						innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CTGGTTCCAAGTAAGTGTTAA	0.532																																					.		.											.	.	0			c.1254+1G>A						.						104	86	92					20																	31892698		2203	4300	6503	SO:0001630	splice_region_variant	92747	exon13			TTCCAAGTAAGTG	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"BPI fold containing"	16108	protein-coding gene	gene with protein product	"von Ebner minor salivary gland protein"		"chromosome 20 open reading frame 114"	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.1254+1G>A	20.37:g.31892698G>A		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	201	73	NM_033197	0	0	0	0	0	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Splice_Site	SNP	ENST00000253354.1	37	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043780	0.36085	.	.	ENSG00000125999	ENST00000253354	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.217	0.65800	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BPIFB1	31356359	0.999000	0.42202	0.998000	0.56505	0.266000	0.26442	4.225000	0.58600	2.740000	0.93945	0.561000	0.74099	.	.		0.532	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	Intron	A	31892698	G	A	31892698	5	1	27	1	0	0	0	0	0	0	1	0	2088	1043	36	2	1301	2	C20orf114	20	31892698	Splice_Site	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	8274210	31892698	31132822	102	2417											
MYT1	4661	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62859303	62859303	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcacccaccaaggacgacaAggaggaccccgagctgatga	13	2	13	13	2	0	2	0	2	0	0	0	7	0	5	4	4	1	2	4	4	2	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:62859303A>T	ENST00000328439.1	+	18	3018	c.2654A>T	c.(2653-2655)aAg>aTg	p.K885M	MYT1_ENST00000536311.1_Missense_Mutation_p.K912M|MYT1_ENST00000360149.4_Missense_Mutation_p.K564M	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AAGGACGACAAGGAGGACCCC	0.483																																					p.K885M	GBM(59;481 1041 20555 21139 33705)	.											.	MYT1-704	0			c.A2654T						.						89	88	88					20																	62859303		2203	4300	6503	SO:0001583	missense	4661	exon18			ACGACAAGGAGGA	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.2654A>T	20.37:g.62859303A>T	ENSP00000327465:p.Lys885Met	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	213	82	NM_004535	0	0	0	0	0	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279871	0.59758	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.54071	0.59;0.65;0.61	5.67	4.58	0.56647	.	0.115126	0.64402	D	0.000018	T	0.69251	0.3090	M	0.78637	2.42	0.53688	D	0.999978	D;D;D	0.67145	0.996;0.993;0.986	D;P;P	0.64144	0.922;0.886;0.621	T	0.72272	-0.4342	10	0.72032	D	0.01	-30.9363	11.5655	0.50802	0.9301:0.0:0.0699:0.0	.	912;885;564	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	M	564;885;912	ENSP00000353269:K564M;ENSP00000327465:K885M;ENSP00000442412:K912M	ENSP00000327465:K885M	K	+	2	0	MYT1	62329747	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.166000	0.71896	0.990000	0.38787	0.533000	0.62120	AAG	.		0.483	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62859303	A	T	62859303	3	4	27	1	0	0	0	0	1	0	0	0	10131	72	3	5	2716	5	MYT1	20	62859303	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	30966605	62859303	166217	103	2418											
KRTAP26-1	388818	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	31691828	31691828	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctgctggacacaacgtgaaGactttgaggacgataggcca	12	7	13	9	2	0	3	0	2	0	1	0	6	0	5	1	3	2	2	1	3	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr21:31691828G>C	ENST00000360542.3	-	1	779	c.526C>G	c.(526-528)Ctt>Gtt	p.L176V		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	176						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						ACAACGTGAAGACTTTGAGGA	0.557																																					p.L176V													.	KRTAP26-1-69	0			c.C526G						.						187	189	188					21																	31691828		2203	4300	6503	SO:0001583	missense	388818	exon1			CGTGAAGACTTTG	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"Keratin associated proteins"	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.526C>G	21.37:g.31691828G>C	ENSP00000353742:p.Leu176Val	Somatic	211	1		WXS	Illumina HiSeq	Phase_I	273	71	NM_203405	0	0	0	0	0	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	G	5.455	0.269066	0.10349	.	.	ENSG00000197683	ENST00000360542	T	0.16196	2.36	4.34	-3.92	0.04155	.	1.210090	0.06278	N	0.696883	T	0.11110	0.0271	L	0.51914	1.62	0.09310	N	1	B	0.21071	0.051	B	0.23150	0.044	T	0.39563	-0.9608	10	0.08837	T	0.75	-0.4306	1.1278	0.01739	0.1878:0.1582:0.2103:0.4437	.	176	Q6PEX3	KR261_HUMAN	V	176	ENSP00000353742:L176V	ENSP00000353742:L176V	L	-	1	0	KRTAP26-1	30613699	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.581000	0.05820	-0.855000	0.04125	0.650000	0.86243	CTT	.		0.557	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		C	31691828	G	C	31691828	3	2	27	1	0	0	0	0	1	0	0	0	8564	942	33	4	110	4	KRTAP26-1	21	31691828	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		31691828	16438067	104	2419											
ZNF280A	129025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	22869192	22869192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgacttgctagacttgaaaTgtctgtcattgccaggccag	9	13	10	9	0	2	3	1	2	1	1	2	3	2	3	2	1	2	1	2	1	2	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr22:22869192T>C	ENST00000302097.3	-	2	1015	c.763A>G	c.(763-765)Att>Gtt	p.I255V	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	255					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		AGACTTGAAATGTCTGTCATT	0.413																																					p.I255V		.											.	ZNF280A-69	0			c.A763G						.						126	115	119					22																	22869192		2203	4300	6503	SO:0001583	missense	129025	exon2			TTGAAATGTCTGT	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"zinc finger protein 280", "suppressor of hairy wing homolog 1 (Drosophila)"	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.763A>G	22.37:g.22869192T>C	ENSP00000302855:p.Ile255Val	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	121	100	NM_080740	0	0	0	0	0		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	.	.	.	.	.	.	.	.	.	.	T	2.685	-0.274412	0.05679	.	.	ENSG00000169548	ENST00000302097	T	0.01126	5.3	3.66	1.52	0.23074	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48163	-0.9059	9	0.20519	T	0.43	-0.1797	4.2473	0.10677	0.5866:0.2055:0.0:0.2079	.	255	P59817	Z280A_HUMAN	V	255	ENSP00000302855:I255V	ENSP00000302855:I255V	I	-	1	0	ZNF280A	21199192	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.195000	0.17155	0.264000	0.21851	-1.173000	0.01734	ATT	.		0.413	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740		C	22869192	T	C	22869192	3	2	27	1	0	0	0	0	1	0	0	0	17846	1464	51	3	869	3	ZNF280A	22	22869192	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		22869192	28435374	105	2420											
SELO	83642	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50649114	50649114	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacaccggccgctacgcgtaCagcaagcagcccgaggtgtg	10	4	13	14	5	0	0	0	0	0	0	0	1	0	0	3	2	6	4	3	2	4	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr22:50649114C>T	ENST00000380903.2	+	5	1183	c.1125C>T	c.(1123-1125)taC>taT	p.Y375Y	SELO_ENST00000492092.1_3'UTR|RP3-402G11.28_ENST00000608016.1_RNA	NM_031454.1	NP_113642.1	Q9BVL4	SELO_HUMAN		375													all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		GCTACGCGTACAGCAAGCAGC	0.682											OREG0026676	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	0			.						.						46	56	52					22																	50649114		2135	4228	6363	SO:0001819	synonymous_variant	0	.			CGCGTACAGCAAG																												ENST00000380903.2:c.1125C>T	22.37:g.50649114C>T		Somatic	128	1	971	WXS	Illumina HiSeq	Phase_I	149	104	.	0	0	2	24	22	Q2TAL2|Q5JZ81|Q8WUI0	Silent	SNP	ENST00000380903.2	37	CCDS43034.1																																																																																			.		0.682	SELO-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000075003.2			T	50649114	C	T	50649114	2	4	27	1	0	0	0	0	0	0	0	1	14050	489	17	2		2	SELO	22	50649114	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	27779922	50649114	655452	106	2421											
CSF2RA	1438	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	1407702	1407702	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgtttcatctacaatgcgGatttaatgaactgtacctgg	10	14	8	9	1	2	1	1	1	1	0	2	2	2	2	2	2	4	2	2	2	5	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:1407702G>T	ENST00000381524.3	+	6	580	c.394G>T	c.(394-396)Gat>Tat	p.D132Y	CSF2RA_ENST00000355805.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000361536.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000501036.2_5'UTR|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000381500.1_Missense_Mutation_p.D132Y|CSF2RA_ENST00000355432.3_Missense_Mutation_p.D132Y|BX649553.3_ENST00000581137.1_RNA|CSF2RA_ENST00000417535.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000432318.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381529.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381509.3_Missense_Mutation_p.D132Y			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	132					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	CTACAATGCGGATTTAATGAA	0.468																																					p.D132Y	Esophageal Squamous(131;723 1707 25334 40494 41806)	.											.	CSF2RA-42	0			c.G394T						.						173	182	179					X																	1407702		2203	4296	6499	SO:0001583	missense	1438	exon4			AATGCGGATTTAA	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"CD molecules", "Pseudoautosomal regions / PAR1"	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.394G>T	X.37:g.1407702G>T	ENSP00000370935:p.Asp132Tyr	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	389	127	NM_172247	0	0	35	68	33	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	3.532	-0.095615	0.07010	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;T;D;T;T;D;T;T;D;T	0.96104	-3.91;-3.91;0.5;-3.91;0.5;0.5;-3.91;0.5;0.5;-3.91;0.5	2.02	-0.156	0.13391	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.244990	0.06574	U	0.749174	D	0.95896	0.8664	.	.	.	0.18873	N	0.999989	P;P;P;D;B;P	0.57899	0.488;0.483;0.685;0.981;0.428;0.483	B;B;B;P;B;B	0.60012	0.092;0.239;0.269;0.867;0.154;0.157	D	0.86489	0.1796	9	0.66056	D	0.02	.	3.1267	0.06409	0.1944:0.2787:0.5269:0.0	.	132;132;132;132;132;132	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	Y	132	ENSP00000370940:D132Y;ENSP00000416437:D132Y;ENSP00000354836:D132Y;ENSP00000370935:D132Y;ENSP00000410667:D132Y;ENSP00000397452:D132Y;ENSP00000370920:D132Y;ENSP00000348058:D132Y;ENSP00000347606:D132Y;ENSP00000394227:D132Y;ENSP00000370911:D132Y	ENSP00000347606:D132Y	D	+	1	0	CSF2RA	1367702	0.006000	0.16342	0.001000	0.08648	0.041000	0.13682	-0.778000	0.04664	-0.259000	0.09432	0.280000	0.19369	GAT	.		0.468	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			T	1407702	G	T	1407702	3	4	27	1	0	0	0	0	1	0	0	0	3940	1174	41	4	408	4	CSF2RA	23	1407702	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1407702	153862858	107	2422											
FRMPD4	9758	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	12708337	12708337	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatcttaacccttcaagaGaagctctccatcaaaggcat	13	10	6	12	0	5	1	3	0	2	1	6	2	5	1	2	1	2	2	2	1	4	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:12708337G>T	ENST00000380682.1	+	8	1211	c.705G>T	c.(703-705)gaG>gaT	p.E235D		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	235	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						CCCTTCAAGAGAAGCTCTCCA	0.468																																					p.E235D													.	FRMPD4-263	0			c.G705T						.						162	126	139					X																	12708337		2203	4300	6503	SO:0001583	missense	9758	exon8			TCAAGAGAAGCTC	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"PDZ domain containing 10"	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.705G>T	X.37:g.12708337G>T	ENSP00000370057:p.Glu235Asp	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	118	99	NM_014728	0	0	0	0	0	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169935	0.38315	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.75704	-0.96	5.53	3.38	0.38709	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	N	0.11927	0.2	0.34600	D	0.716417	B;B	0.23735	0.09;0.049	B;B	0.32149	0.141;0.04	T	0.52290	-0.8595	10	0.23302	T	0.38	.	4.3093	0.10962	0.5191:0.0:0.4809:0.0	.	227;235	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	D	235;226;224	ENSP00000370057:E235D	ENSP00000304583:E224D	E	+	3	2	FRMPD4	12618258	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	2.167000	0.42415	1.230000	0.43646	0.600000	0.82982	GAG	.		0.468	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12708337	G	T	12708337	3	4	27	1	0	0	0	0	1	0	0	0	6078	933	33	4	735	4	FRMPD4	23	12708337	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	11300635	12708337	142562223	108	2423											
NAA10	8260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	153198018	153198018	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgatatgtccatggggcaCatcatctgggtcctcttccc	6	12	11	12	0	3	1	1	1	2	0	6	1	6	1	3	4	0	1	3	4	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:153198018C>T	ENST00000464845.1	-	4	517	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	NAA10_ENST00000393710.3_5'UTR|NAA10_ENST00000393712.3_Missense_Mutation_p.V67M|NAA10_ENST00000370015.4_Missense_Mutation_p.V67M|NAA10_ENST00000370009.1_Missense_Mutation_p.V67M	NM_001256120.1|NM_003491.3	NP_001243049.1|NP_003482.1	P41227	NAA10_HUMAN	N(alpha)-acetyltransferase 10, NatA catalytic subunit	67	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA packaging (GO:0006323)|internal protein amino acid acetylation (GO:0006475)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleolus (GO:0005730)|nucleus (GO:0005634)	N-acetyltransferase activity (GO:0008080)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(3)|kidney(1)|lung(3)|ovary(1)|prostate(1)	10						CCATGGGGCACATCATCTGGG	0.587																																					p.V67M	Ovarian(94;1099 1433 38814 45882 51063)	.											.	NAA10-159	0			c.G199A						.						68	49	55					X																	153198018		2202	4297	6499	SO:0001583	missense	8260	exon4			GGGGCACATCATC	BC000308	CCDS14737.1, CCDS59179.1	Xq28	2010-05-07	2010-01-14	2010-01-14	ENSG00000102030	ENSG00000102030	2.3.1.88	"N(alpha)-acetyltransferase subunits"	18704	protein-coding gene	gene with protein product		300013	"ARD1 homolog, N-acetyltransferase (S. cerevisiae)", "ARD1 homolog A, N-acetyltransferase (S. cerevisiae)"	ARD1, ARD1A		7981673, 19660095	Standard	NM_003491		Approved	DXS707, TE2	uc004fjm.2	P41227	OTTHUMG00000024225	ENST00000464845.1:c.199G>A	X.37:g.153198018C>T	ENSP00000417763:p.Val67Met	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	87	32	NM_001256119	1	0	89	152	62	A6NM98	Missense_Mutation	SNP	ENST00000464845.1	37	CCDS14737.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811472	0.50527	.	.	ENSG00000102030	ENST00000464845;ENST00000370015;ENST00000393712;ENST00000370009;ENST00000545734;ENST00000370011;ENST00000432089	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	5.04	3.25	0.37280	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.37892	0.1020	L	0.47016	1.485	0.54753	D	0.999981	B;P;P	0.44195	0.251;0.454;0.828	B;P;P	0.53954	0.375;0.738;0.738	T	0.08330	-1.0727	10	0.46703	T	0.11	-18.5174	9.0852	0.36577	0.0:0.8122:0.0:0.1878	.	67;67;67	B7Z9N2;A6NM98;P41227	.;.;NAA10_HUMAN	M	67;67;67;67;67;61;61	ENSP00000417763:V67M;ENSP00000359032:V67M;ENSP00000377315:V67M;ENSP00000359026:V67M;ENSP00000359028:V61M;ENSP00000413668:V61M	ENSP00000359026:V67M	V	-	1	0	NAA10	152851212	1.000000	0.71417	0.899000	0.35326	0.948000	0.59901	4.628000	0.61282	0.909000	0.36697	0.525000	0.51046	GTG	.		0.587	NAA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061108.2	NM_003491		T	153198018	C	T	153198018	3	4	27	1	0	0	0	0	1	0	0	0	10141	478	17	2	528	2	NAA10	23	153198018	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	140489681	153198018	2072542	109	2424											
PLXNA3	55558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	153700940	153700940	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctcccccagattctcaCggctctggaccgagatgcct	6	10	8	17	2	3	2	1	0	3	2	6	4	4	3	5	2	1	1	5	2	0	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:153700940C>T	ENST00000369682.3	+	33	5703	c.5528C>T	c.(5527-5529)aCg>aTg	p.T1843M		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1843					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)					CAGATTCTCACGGCTCTGGAC	0.607																																					p.T1843M		.											.	PLXNA3-132	0			c.C5528T						.						122	101	108					X																	153700940		2203	4300	6503	SO:0001583	missense	55558	exon33			TTCTCACGGCTCT	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.5528C>T	X.37:g.153700940C>T	ENSP00000358696:p.Thr1843Met	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	205	178	NM_017514	0	0	0	0	0	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807947	0.31961	.	.	ENSG00000130827	ENST00000369682	T	0.01015	5.44	5.32	0.143	0.14820	.	0.182827	0.46758	D	0.000265	T	0.01029	0.0034	L	0.52011	1.625	0.44295	D	0.997164	B	0.19583	0.037	B	0.14578	0.011	T	0.58880	-0.7558	10	0.46703	T	0.11	.	5.7954	0.18383	0.1253:0.3656:0.4303:0.0788	.	1843	P51805	PLXA3_HUMAN	M	1843	ENSP00000358696:T1843M	ENSP00000358696:T1843M	T	+	2	0	PLXNA3	153354134	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	0.251000	0.18257	-0.517000	0.06461	-0.191000	0.12829	ACG	.		0.607	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		T	153700940	C	T	153700940	3	4	27	1	0	0	0	0	1	0	0	0	12147	536	19	1	5654	1	PLXNA3	23	153700940	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	502922	153700940	1569620	110	2425											
AGRN	375790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	987003	987003	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgtgtcccgggggattCtcaggaccgcactgcgagaa	7	8	14	12	3	1	1	1	0	1	1	3	4	2	3	3	3	2	1	3	3	1	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:987003C>A	ENST00000379370.2	+	32	5591	c.5541C>A	c.(5539-5541)ttC>ttA	p.F1847L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1851	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		CCGGGGGATTCTCAGGACCGC	0.711																																					p.F1847L		.											.	AGRN-136	0			c.C5541A						.						24	25	25					1																	987003		2199	4296	6495	SO:0001583	missense	375790	exon32			GGGATTCTCAGGA	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"Proteoglycans / Extracellular Matrix : Other"	329	protein-coding gene	gene with protein product	"agrin proteoglycan"	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5541C>A	1.37:g.987003C>A	ENSP00000368678:p.Phe1847Leu	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	54	19	NM_198576	0	1	148	246	97	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.64|15.64	2.893312|2.893312	0.52121|0.52121	.|.	.|.	ENSG00000188157|ENSG00000188157	ENST00000379370;ENST00000379364|ENST00000419249	D|.	0.94000|.	-3.33|.	4.96|4.96	4.05|4.05	0.47172|0.47172	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.75177|0.75177	0.3814|0.3814	M|M	0.83118|0.83118	2.625|2.625	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.61080|.	0.989|.	P|.	0.62298|.	0.9|.	T|T	0.76782|0.76782	-0.2832|-0.2832	10|5	0.48119|.	T|.	0.1|.	-27.1498|-27.1498	12.382|12.382	0.55311|0.55311	0.0:0.9177:0.0:0.0823|0.0:0.9177:0.0:0.0823	.|.	1847|.	O00468|.	AGRIN_HUMAN|.	L|I	1847;190|150	ENSP00000368678:F1847L|.	ENSP00000368671:F190L|.	F|L	+|+	3|1	2|0	AGRN|AGRN	976866|976866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.032000|0.032000	0.12392|0.12392	2.087000|2.087000	0.41653|0.41653	1.112000|1.112000	0.41740|0.41740	0.555000|0.555000	0.69702|0.69702	TTC|CTC	.		0.711	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		A	987003	C	A	987003	3	1	28	1	0	0	0	0	1	0	0	0	397	912	32	4	5667	4	AGRN	1	987003	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10		987003	248263618	1	2426											
KLHL21	9903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6659179	6659179	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcgggagctggccgcagTccaccagcgaccacaggtcg	8	3	16	14	4	0	0	0	0	0	0	2	2	1	1	4	4	2	2	4	4	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:6659179T>C	ENST00000377658.4	-	2	1406	c.1355A>G	c.(1354-1356)gAc>gGc	p.D452G	KLHL21_ENST00000463043.1_Missense_Mutation_p.D85G|KLHL21_ENST00000467612.1_Missense_Mutation_p.D85G|KLHL21_ENST00000377663.3_Missense_Mutation_p.D452G	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	452					chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		CTGGCCGCAGTCCACCAGCGA	0.642																																					p.D452G		.											.	KLHL21-514	0			c.A1355G						.						47	45	46					1																	6659179		2203	4300	6503	SO:0001583	missense	9903	exon2			CCGCAGTCCACCA	AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413		"Kelch-like", "BTB/POZ domain containing"	29041	protein-coding gene	gene with protein product			"kelch-like 21 (Drosophila)"				Standard	XM_005263542		Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.1355A>G	1.37:g.6659179T>C	ENSP00000366886:p.Asp452Gly	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	170	56	NM_014851	0	0	3	5	2	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Missense_Mutation	SNP	ENST00000377658.4	37	CCDS30575.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.269130	0.40095	.	.	ENSG00000162413	ENST00000377658;ENST00000377663	T;T	0.74209	-0.72;-0.82	5.14	3.99	0.46301	Galactose oxidase, beta-propeller (1);	0.179251	0.64402	D	0.000019	T	0.54013	0.1832	N	0.08118	0	0.31114	N	0.70964	B;B	0.28933	0.02;0.228	B;B	0.30855	0.007;0.121	T	0.55036	-0.8203	10	0.27082	T	0.32	.	11.6365	0.51207	0.0:0.0:0.1489:0.851	.	452;452	Q9UJP4;Q9UJP4-2	KLH21_HUMAN;.	G	452	ENSP00000366886:D452G;ENSP00000366891:D452G	ENSP00000366886:D452G	D	-	2	0	KLHL21	6581766	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.336000	0.52113	0.877000	0.35895	0.533000	0.62120	GAC	.		0.642	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		C	6659179	T	C	6659179	3	2	28	1	0	0	0	0	1	0	0	0	8397	1667	58	3	450	3	KLHL21	1	6659179	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	5672176	6659179	242591442	2	2427											
INPP5B	3633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38343988	38343988	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccaggcaggagcacggcActtctcactgaaatgcaaag	14	5	10	12	1	1	1	1	1	1	0	2	2	1	2	1	3	2	4	1	3	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:38343988A>G	ENST00000373026.1	-	15	1789	c.1789T>C	c.(1789-1791)Tgc>Cgc	p.C597R	INPP5B_ENST00000458109.2_3'UTR|INPP5B_ENST00000373024.3_Missense_Mutation_p.C517R|INPP5B_ENST00000373023.2_Missense_Mutation_p.C597R|INPP5B_ENST00000373027.1_Missense_Mutation_p.C353R			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	597	5-phosphatase. {ECO:0000250}.|Substrate binding.			GSDDWDTSEKCRAPAWCDRI -> RALTTGIPVRSAVLLPG VIGF (in Ref. 5; AA sequence). {ECO:0000305}.	in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GGAGCACGGCACTTCTCACTG	0.547																																					p.C517R		.											.	INPP5B-227	0			c.T1549C						.						66	67	67					1																	38343988		2087	4203	6290	SO:0001583	missense	3633	exon16			CACGGCACTTCTC	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"inositol polyphosphate-5-phosphatase, 75kD"			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.1789T>C	1.37:g.38343988A>G	ENSP00000362117:p.Cys597Arg	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	80	19	NM_005540	0	0	0	0	0	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		.	.	.	.	.	.	.	.	.	.	A	19.27	3.796203	0.70567	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	5.43	5.43	0.79202	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.83473	0.5262	L	0.33624	1.015	0.80722	D	1	D;P	0.89917	1.0;0.861	D;B	0.68765	0.96;0.31	T	0.82133	-0.0608	10	0.30854	T	0.27	.	15.4883	0.75584	1.0:0.0:0.0:0.0	.	597;517	P32019;P32019-2	I5P2_HUMAN;.	R	353;597;597;597;517	ENSP00000362118:C353R;ENSP00000362114:C597R;ENSP00000362117:C597R;ENSP00000362115:C517R	ENSP00000362114:C597R	C	-	1	0	INPP5B	38116575	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.855000	0.92236	2.078000	0.62432	0.460000	0.39030	TGC	.		0.547	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		G	38343988	A	G	38343988	3	3	28	1	0	0	0	0	1	0	0	0	7776	159	6	3	1228	3	INPP5B	1	38343988	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	31684809	38343988	210906633	3	2428											
ACOT11	26027	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	55059680	55059687	+	Frame_Shift_Del	DEL	GCCACCTT	GCCACCTT	-																															ggaatgtgtgcaaggccttgGccaccttcgtggcccgccga																								rs35306628|rs370568235		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	GCCACCTT	GCCACCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:55059680_55059687delGCCACCTT	ENST00000371316.3	+	5	521_528	c.439_446delGCCACCTT	c.(439-447)gccaccttcfs	p.ATF147fs	ACOT11_ENST00000343744.2_Frame_Shift_Del_p.ATF147fs|ACOT11_ENST00000481208.1_3'UTR	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	147	Acyl coenzyme A hydrolase 1.				fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						CAAGGCCTTGGCCACCTTCGTGGCCCGC	0.625																																					p.147_149del	Ovarian(148;1440 1861 22015 32453 51933)	.											.	ACOT11-90	0			c.439_446del						.																																			SO:0001589	frameshift_variant	26027	exon5			.	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	18156	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 14"	606803	"thioesterase, adipose associated"	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.439_446delGCCACCTT	1.37:g.55059680_55059687delGCCACCTT	ENSP00000360366:p.Ala147fs	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	49	13	NM_147161	0	0	0	0	0	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Frame_Shift_Del	DEL	ENST00000371316.3	37	CCDS592.1																																																																																			.		0.625	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547		-	55059687	GCCACCTT	-	55059680	7	5	28	1	0	1	0	1	0	0	0	0	149	1203	42	0	457	0	ACOT11	1	55059680	Frame_Shift_Del	DEL	GCCACCTT	TCGA-A4-A6HP-01A-11D-A31X-10	16715692	55059680	194190941	4	2429											
PTGFR	5737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	78959108	78959108	+	Missense_Mutation	SNP	T	T	C																															tgcaatcacaggaattacacTtttaagagttaaatttaaaa																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:78959108T>C	ENST00000370757.3	+	2	917	c.680T>C	c.(679-681)cTt>cCt	p.L227P	PTGFR_ENST00000370758.1_Missense_Mutation_p.L227P|PTGFR_ENST00000370756.3_Missense_Mutation_p.L227P	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	227					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	GGAATTACACTTTTAAGAGTT	0.383																																					p.L227P		.											.	PTGFR-527	0			c.T680C						.						58	60	59					1																	78959108		2203	4300	6503	SO:0001583	missense	5737	exon2			TTACACTTTTAAG	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.680T>C	1.37:g.78959108T>C	ENSP00000359793:p.Leu227Pro	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	133	39	NM_000959	0	0	0	0	0	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	37	CCDS686.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901960	0.72754	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.52754	0.65;0.65;0.65	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.63954	0.2555	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.68685	-0.5343	10	0.87932	D	0	-21.0338	16.5479	0.84454	0.0:0.0:0.0:1.0	.	227;227	P43088;P43088-2	PF2R_HUMAN;.	P	227	ENSP00000359794:L227P;ENSP00000359793:L227P;ENSP00000359792:L227P	ENSP00000359792:L227P	L	+	2	0	PTGFR	78731696	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	CTT	.		0.383	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78959108	T	C	78959108	3	2	28	1	0	0	0	0	1	0	0	0	12779	1609	56	3	682	3	PTGFR	1	78959108	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	23899428	78959108	170291513	5	2430	24	2									
PTGFR	5737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	78959111	78959111	+	Missense_Mutation	SNP	T	T	C																															aatcacaggaattacactttTaagagttaaatttaaaagtc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:78959111T>C	ENST00000370757.3	+	2	920	c.683T>C	c.(682-684)tTa>tCa	p.L228S	PTGFR_ENST00000370758.1_Missense_Mutation_p.L228S|PTGFR_ENST00000370756.3_Missense_Mutation_p.L228S	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	228					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	ATTACACTTTTAAGAGTTAAA	0.388																																					p.L228S		.											.	PTGFR-527	0			c.T683C						.						57	59	58					1																	78959111		2203	4300	6503	SO:0001583	missense	5737	exon2			CACTTTTAAGAGT	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.683T>C	1.37:g.78959111T>C	ENSP00000359793:p.Leu228Ser	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	131	38	NM_000959	0	0	0	0	0	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	37	CCDS686.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.020614	0.75275	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.39997	1.05;1.05;1.05	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.074264	0.56097	D	0.000033	T	0.50514	0.1620	L	0.52573	1.65	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.989	T	0.45731	-0.9241	10	0.40728	T	0.16	-5.6031	16.5479	0.84454	0.0:0.0:0.0:1.0	.	228;228	P43088;P43088-2	PF2R_HUMAN;.	S	228	ENSP00000359794:L228S;ENSP00000359793:L228S;ENSP00000359792:L228S	ENSP00000359792:L228S	L	+	2	0	PTGFR	78731699	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	7.643000	0.83403	2.371000	0.80710	0.533000	0.62120	TTA	.		0.388	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78959111	T	C	78959111	3	2	28	1	0	0	0	0	1	0	0	0	12779	1764	61	3	685	3	PTGFR	1	78959111	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	3	78959111	170291510	6	2431	24	2									
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110740214	110740214	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggctacagcgcctggatcaAggaggaggtgaggggtgggg	8	5	22	6	1	1	1	1	1	0	0	1	4	1	4	1	9	2	1	1	9	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:110740214A>G	ENST00000331565.4	+	11	2293	c.1808A>G	c.(1807-1809)aAg>aGg	p.K603R		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	603					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GCCTGGATCAAGGAGGAGGTG	0.582											OREG0013652	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K603R		.											.	SLC6A17-92	0			c.A1808G						.						24	27	26					1																	110740214		2203	4300	6503	SO:0001583	missense	388662	exon11			GGATCAAGGAGGA		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1808A>G	1.37:g.110740214A>G	ENSP00000330199:p.Lys603Arg	Somatic	7	0	1429	WXS	Illumina HiSeq	Phase_I	22	11	NM_001010898	0	0	0	0	0	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.673675	0.29693	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74315	-0.83	5.03	2.63	0.31362	.	0.288442	0.37669	N	0.001989	T	0.23727	0.0574	N	0.04508	-0.205	0.26690	N	0.971361	B	0.02656	0.0	B	0.09377	0.004	T	0.29941	-0.9995	10	0.15066	T	0.55	.	7.503	0.27528	0.6046:0.0:0.3954:0.0	.	603	Q9H1V8	S6A17_HUMAN	R	603	ENSP00000330199:K603R	ENSP00000330199:K603R	K	+	2	0	SLC6A17	110541737	0.080000	0.21391	0.999000	0.59377	0.978000	0.69477	1.878000	0.39608	0.235000	0.21160	0.455000	0.32223	AAG	.		0.582	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		G	110740214	A	G	110740214	3	3	28	1	0	0	0	0	1	0	0	0	14712	72	3	3	1846	3	SLC6A17	1	110740214	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	31781103	110740214	138510407	7	2432											
PDE4DIP	9659	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	144874782	144874782	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catcagacaggaaagaggtgCtgctgggagagcggtgggag	11	5	19	6	1	1	3	1	0	0	3	1	6	1	5	0	5	3	2	0	5	1	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:144874782C>T	ENST00000369354.3	-	30	5015	c.4826G>A	c.(4825-4827)aGc>aAc	p.S1609N	RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.S1609N|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.S1565N|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.S1745N|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.S1745N|AL138796.1_ENST00000582173.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1609	NBPF. {ECO:0000255|PROSITE- ProRule:PRU00647}.				cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAAAGAGGTGCTGCTGGGAGA	0.537			T	PDGFRB	MPD																																p.S1609N		.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP-663	0			c.G4826A						.						253	241	245					1																	144874782		2203	4296	6499	SO:0001583	missense	9659	exon30			GAGGTGCTGCTGG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.4826G>A	1.37:g.144874782C>T	ENSP00000358360:p.Ser1609Asn	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	170	24	NM_014644	0	0	1	1	0	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058459	0.76074	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01767	4.65;4.76;4.76;4.73;4.78	5.91	2.8	0.32819	DUF1220 (2);	.	.	.	.	T	0.01558	0.0050	L	0.61218	1.895	0.80722	D	1	P;P	0.40970	0.634;0.734	B;B	0.43575	0.3;0.424	T	0.57046	-0.7878	9	0.56958	D	0.05	.	10.7557	0.46234	0.1347:0.622:0.2433:0.0	.	1565;1609	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	N	1565;1609;1609;1745;1745	ENSP00000327209:S1565N;ENSP00000358360:S1609N;ENSP00000358363:S1609N;ENSP00000435654:S1745N;ENSP00000358366:S1745N	ENSP00000327209:S1565N	S	-	2	0	PDE4DIP	143586139	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.387000	0.59626	0.794000	0.33899	0.650000	0.86243	AGC	.		0.537	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144874782	C	T	144874782	3	4	28	1	0	0	0	0	1	0	0	0	11669	797	28	2	2274	2	PDE4DIP	1	144874782	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	34134568	144874782	104375839	8	2433											
CELF3	11189	hgsc.bcm.edu	37	chr1	151678722	151678722	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctttgctgctgctgctgTtgctgctgctgctgctgctg	0	17	12	12	0	1	0	0	0	1	0	2	0	1	0	0	0	10	11	0	0	0	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:151678722T>C	ENST00000290583.4	-	10	1897	c.1104A>G	c.(1102-1104)caA>caG	p.Q368Q	RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000392706.3_Silent_p.Q163Q|CELF3_ENST00000470688.1_5'UTR|CELF3_ENST00000290585.4_Silent_p.Q318Q	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	368	Gln-rich.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						gctgctgctgttgctgctgct	0.657																																					p.Q368Q		.											.	CELF3-91	0			c.A1104G						.						19	20	20					1																	151678722		2200	4297	6497	SO:0001819	synonymous_variant	11189	exon10			CTGCTGTTGCTGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1104A>G	1.37:g.151678722T>C		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	34	4	NM_007185	0	0	3	105	102	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Silent	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	4.938	0.174339	0.09391	.	.	ENSG00000159409	ENST00000420342	.	.	.	3.25	1.39	0.22231	.	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19943	-1.0290	4	.	.	.	-0.0118	5.4728	0.16680	0.0:0.7409:0.0:0.2591	.	.	.	.	S	369	.	.	N	-	2	0	CELF3	149945346	0.076000	0.21285	1.000000	0.80357	0.644000	0.38419	-0.812000	0.04496	0.416000	0.25844	-0.389000	0.06534	AAC	.		0.657	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		C	151678722	T	C	151678722	2	2	28	1	0	0	0	0	0	0	0	1	3223	1722	60	3		3	CELF3	1	151678722	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	6803940	151678722	97571899	9	2434											
ASPM	259266	broad.mit.edu	37	chr1	197111690	197111690	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actgaagctgttgtcgaagaGggtgttacctcgtttttata	9	15	11	6	2	0	2	0	1	0	1	2	3	0	2	1	1	2	4	1	1	5	6			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:197111690G>T	ENST00000367409.4	-	3	1948	c.1692C>A	c.(1690-1692)ccC>ccA	p.P564P	ASPM_ENST00000294732.7_Silent_p.P564P	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	564					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGTCGAAGAGGGTGTTACCT	0.343																																					p.P564P													.	ASPM-615	0			c.C1692A						.						118	124	122					1																	197111690		2203	4300	6503	SO:0001819	synonymous_variant	259266	exon3			CGAAGAGGGTGTT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.1692C>A	1.37:g.197111690G>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	133	7	NM_001206846	0	0	0	0	0	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			.		0.343	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		T	197111690	G	T	197111690	2	4	28	1	0	0	0	0	0	0	0	1	1057	987	35	4		4	ASPM	1	197111690	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	45432968	197111690	52138931	10	2435											
RNPEP	6051	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	201958580	201958590	+	Frame_Shift_Del	DEL	TTCCAGATGTG	TTCCAGATGTG	-																															gaggtccaaataagttcttcTtccagatgtgtcagcccatc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	TTCCAGATGTG	TTCCAGATGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:201958580_201958590delTTCCAGATGTG	ENST00000295640.4	+	3	701_711	c.658_668delTTCCAGATGTG	c.(658-669)ttccagatgtgtfs	p.FQMC220fs	RNPEP_ENST00000471105.1_Intron|RNPEP_ENST00000367286.3_Frame_Shift_Del_p.FQMC220fs	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	220					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TAAGTTCTTCTTCCAGATGTGTCAGCCCATC	0.507																																					p.220_223del	GBM(19;39 479 7473 13131 19462)	.											.	RNPEP-91	0			c.658_668del						.																																			SO:0001589	frameshift_variant	6051	exon3			.	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.658_668delTTCCAGATGTG	1.37:g.201958580_201958590delTTCCAGATGTG	ENSP00000295640:p.Phe220fs	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	161	36	NM_020216	0	0	0	0	0	Q9BVM9|Q9H1D4|Q9NPT7	Frame_Shift_Del	DEL	ENST00000295640.4	37	CCDS1418.1																																																																																			.		0.507	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216		-	201958590	TTCCAGATGTG	-	201958580	7	5	28	1	0	1	0	1	0	0	0	0	13541	1609	56	0	668	0	RNPEP	1	201958580	Frame_Shift_Del	DEL	TTCCAGATGTG	TCGA-A4-A6HP-01A-11D-A31X-10	4846890	201958580	47292041	11	2436											
CR1L	1379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207881585	207881586	+	Missense_Mutation	DNP	GC	GC	TG																															gggcaatactgcccattggaGcatgaagccaccaatttgtc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:207881585_207881586GC>TG	ENST00000508064.2	+	10	1451_1452	c.1391_1392GC>TG	c.(1390-1392)aGC>aTG	p.S464M	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	464	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCCCATTGGAGCATGAAGCCAC	0.426																																					p.S464M		.											.	CR1L-46	0			c.C1392G						.																																			SO:0001583	missense	1379	exon10			TTGGAGCATGAAG	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	Exception_encountered	1.37:g.207881585_207881586delinsTG	ENSP00000421736:p.Ser464Met	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	267	72	NM_175710	0	0	0	0	0	Q32MC9|Q8NEU7	Missense_Mutation	DNP	ENST00000508064.2	37	CCDS44310.1																																																																																			.		0.426	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		TG	207881586	GC	TG	207881585	3	4	28	1	0	0	0	0	1	0	0	0	3847	971	34	4	1429	4	CR1L	1	207881585	Missense_Mutation	DNP	GC	TCGA-A4-A6HP-01A-11D-A31X-10	5923005	207881585	41369036	12	2437											
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228520936	228520936	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagagtccaccactgatgaGggccagctgccccaggtggt	9	6	13	13	0	0	3	0	2	0	1	1	3	1	3	5	3	2	1	5	3	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:228520936G>C	ENST00000422127.1	+	58	15812	c.15768G>C	c.(15766-15768)gaG>gaC	p.E5256D	OBSCN_ENST00000366707.4_Missense_Mutation_p.E2890D|OBSCN_ENST00000284548.11_Missense_Mutation_p.E5256D|OBSCN_ENST00000570156.2_Missense_Mutation_p.E6213D|OBSCN_ENST00000366709.4_Missense_Mutation_p.E2375D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5256					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCACTGATGAGGGCCAGCTGC	0.632																																					p.E6213D		.											.	OBSCN-403	0			c.G18639C						.						14	16	15					1																	228520936		1999	4165	6164	SO:0001583	missense	84033	exon69			TGATGAGGGCCAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15768G>C	1.37:g.228520936G>C	ENSP00000409493:p.Glu5256Asp	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	140	50	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475444	0.63737	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.65364	0.27;-0.15;-0.1;0.41	5.29	-2.78	0.05859	.	0.204869	0.40818	N	0.001014	T	0.30039	0.0752	N	0.04880	-0.145	0.34900	D	0.746403	B;B	0.16166	0.009;0.016	B;B	0.19148	0.011;0.024	T	0.01684	-1.1296	10	0.44086	T	0.13	.	2.9874	0.05972	0.3769:0.104:0.4128:0.1063	.	5256;5256	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	5256;5256;2890;2375	ENSP00000284548:E5256D;ENSP00000409493:E5256D;ENSP00000355668:E2890D;ENSP00000355670:E2375D	ENSP00000284548:E5256D	E	+	3	2	OBSCN	226587559	0.939000	0.31865	0.987000	0.45799	0.212000	0.24457	-0.019000	0.12546	-0.128000	0.11641	-0.254000	0.11334	GAG	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228520936	G	C	228520936	3	2	28	1	0	0	0	0	1	0	0	0	10838	991	35	4	15994	4	OBSCN	1	228520936	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	20639351	228520936	20729685	13	2438											
FMN2	56776	broad.mit.edu	37	chr1	240371139	240371139	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcccggagcgggcataccCcctcctccccctcttcccgg	3	8	8	22	3	1	0	0	0	1	0	5	1	5	1	7	3	2	1	7	3	1	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:240371139C>T	ENST00000319653.9	+	5	3257	c.3027C>T	c.(3025-3027)ccC>ccT	p.P1009P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1009	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCCCCTCCTCCCC	0.731																																					p.P1009P													.	FMN2-145	0			c.C3027T						.																																			SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3027C>T	1.37:g.240371139C>T		Somatic	59	1		WXS	Illumina HiSeq	Phase_I	104	8	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371139	C	T	240371139	2	4	28	1	0	0	0	0	0	0	0	1	5969	610	22	2		2	FMN2	1	240371139	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	11850203	240371139	8879482	14	2439											
OR2T29	343563	broad.mit.edu	37	chr1	248722428	248722429	+	Frame_Shift_Ins	INS	-	-	CG																															cacgtagcggtcataggccaINStggtggctagaaggaaaaat																								rs368626489|rs546109722		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:248722428_248722429insCG	ENST00000328570.3	-	1	368_369	c.364_365insCG	c.(364-366)atgfs	p.M122fs	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTCATAGGCCATGGTGGCTAGA	0.54																																					p.M122fs													.	.	0			c.365_366insCG						.			12,348		6,0,174						3	1			1	52,386		25,2,192	no	frameshift	OR2T29	NM_001004694.2		31,2,366	A1A1,A1R,RR		11.8721,3.3333,8.0201				64,734				SO:0001589	frameshift_variant	343563	exon1			TAGGCCATGGTGG		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"GPCR / Class A : Olfactory receptors"	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.364_365insCG	1.37:g.248722428_248722429insCG	ENSP00000331774:p.Met122fs	Somatic	454	25		WXS	Illumina HiSeq	Phase_I	889	44	NM_001004694	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000328570.3	37	CCDS55695.1																																																																																			.		0.54	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694		CG	248722429	-	CG	248722428	7	5	28	1	0	1	1	0	0	0	0	0	11048	217	8	0	586	0	OR2T29	1	248722428	Frame_Shift_Ins	INS	-	TCGA-A4-A6HP-01A-11D-A31X-10	8351289	248722428	528193	15	2440											
RTN4	57142	broad.mit.edu	37	chr2	55277140	55277140	+	Frame_Shift_Del	DEL	G	G	-																															ggctgccgctccggggcgacGgggggagcggccggcagggg																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:55277140delG	ENST00000337526.6	-	1	540	c.297delC	c.(295-297)cccfs	p.P99fs	RTN4_ENST00000357732.4_Frame_Shift_Del_p.P99fs|RTN4_ENST00000404909.1_Intron|RTN4_ENST00000354474.6_Intron|RTN4_ENST00000357376.3_5'Flank|RTN4_ENST00000394611.2_Intron|RTN4_ENST00000317610.7_Frame_Shift_Del_p.P99fs|RTN4_ENST00000402434.2_Frame_Shift_Del_p.P71fs	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	99					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						ccggggcgacggggggagcgg	0.771																																					p.P99fs													.	RTN4-155	0			c.297delC						.						2	3	3					2																	55277140		1205	2849	4054	SO:0001589	frameshift_variant	57142	exon1			GGCGACGGGGGGA	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.297delC	2.37:g.55277140delG	ENSP00000337838:p.Pro99fs	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_020532	0	0	0	0	0	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Frame_Shift_Del	DEL	ENST00000337526.6	37	CCDS42684.1																																																																																			.		0.771	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			-	55277140	G	-	55277140	7	5	28	1	0	1	0	1	0	0	0	0	13760	1103	39	0	3355	0	RTN4	2	55277140	Frame_Shift_Del	DEL	G	TCGA-A4-A6HP-01A-11D-A31X-10		55277140	187922233	16	2441											
ANXA4	307	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	70039804	70039804	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtgggagggatgaaggaaAttatctggacgatgctctcg	10	9	17	5	2	2	1	0	1	2	0	3	6	2	5	0	5	1	1	0	5	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:70039804A>T	ENST00000394295.4	+	8	745	c.497A>T	c.(496-498)aAt>aTt	p.N166I	ANXA4_ENST00000536030.1_Missense_Mutation_p.N82I|ANXA4_ENST00000409920.1_Missense_Mutation_p.N144I	NM_001153.3	NP_001144.1	P09525	ANXA4_HUMAN	annexin A4	164					epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						GATGAAGGAAATTATCTGGAC	0.443																																					p.N166I		.											.	ANXA4-90	0			c.A497T						.						113	101	105					2																	70039804		2203	4300	6503	SO:0001583	missense	307	exon8			AAGGAAATTATCT	M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"Annexins"	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000394295.4:c.497A>T	2.37:g.70039804A>T	ENSP00000377833:p.Asn166Ile	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	78	28	NM_001153	0	0	80	145	65	B4DDF9|Q96F33|Q9BWK1	Missense_Mutation	SNP	ENST00000394295.4	37	CCDS1894.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.083724	0.36758	.	.	ENSG00000196975	ENST00000409920;ENST00000394295;ENST00000536030	T;T;T	0.12147	2.71;2.71;2.71	5.67	3.15	0.36227	.	0.343196	0.34268	N	0.004120	T	0.13670	0.0331	M	0.64567	1.98	0.33200	D	0.551962	B;B;B	0.33135	0.155;0.399;0.155	B;B;B	0.35039	0.105;0.194;0.105	T	0.10497	-1.0627	9	.	.	.	.	5.8848	0.18876	0.635:0.2795:0.0855:0.0	.	164;144;166	P09525;Q6P452;Q6LES2	ANXA4_HUMAN;.;.	I	144;166;82	ENSP00000386756:N144I;ENSP00000377833:N166I;ENSP00000441931:N82I	.	N	+	2	0	ANXA4	69893308	0.145000	0.22656	0.915000	0.36163	0.808000	0.45660	1.316000	0.33620	0.982000	0.38575	0.533000	0.62120	AAT	.		0.443	ANXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251848.2	NM_001153		T	70039804	A	T	70039804	3	4	28	1	0	0	0	0	1	0	0	0	720	101	4	5	523	5	ANXA4	2	70039804	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	14762664	70039804	173159569	17	2442											
MPHOSPH10	10199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	71360588	71360588	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaggcctatttagaaaacaTagaaaaagaagaggaacgaa	21	5	11	4	1	0	4	0	0	0	4	0	7	0	6	1	3	2	0	1	3	10	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:71360588T>G	ENST00000244230.2	+	2	1002	c.650T>G	c.(649-651)aTa>aGa	p.I217R	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.I217R	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	217					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						TTAGAAAACATAGAAAAAGAA	0.353																																					p.I217R		.											.	MPHOSPH10-93	0			c.T650G						.						63	70	68					2																	71360588		2202	4300	6502	SO:0001583	missense	10199	exon2			AAAACATAGAAAA	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.650T>G	2.37:g.71360588T>G	ENSP00000244230:p.Ile217Arg	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	394	162	NM_005791	0	0	0	2	2	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.363316	0.41902	.	.	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.09817	2.94;2.94	5.04	5.04	0.67666	.	0.585812	0.20103	N	0.099190	T	0.09555	0.0235	N	0.19112	0.55	0.22389	N	0.999144	P;P	0.49696	0.927;0.655	P;B	0.46419	0.516;0.305	T	0.27434	-1.0074	10	0.17369	T	0.5	.	13.0251	0.58810	0.0:0.0:0.0:1.0	.	217;217	B3KPV5;O00566	.;MPP10_HUMAN	R	217;77	ENSP00000244230:I217R;ENSP00000393034:I77R	ENSP00000244230:I217R	I	+	2	0	MPHOSPH10	71214096	0.146000	0.22672	0.072000	0.20136	0.923000	0.55619	1.710000	0.37920	2.040000	0.60383	0.397000	0.26171	ATA	.		0.353	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		G	71360588	T	G	71360588	3	3	28	1	0	0	0	0	1	0	0	0	9750	1406	49	5	656	5	MPHOSPH10	2	71360588	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	1320784	71360588	171838785	18	2443											
IMMT	10989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	86371557	86371557	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacaaactttgctgctagcTccagatcaccatgctcaatg	11	11	7	12	0	2	2	2	1	0	1	3	2	3	2	2	0	5	4	2	0	3	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:86371557T>A	ENST00000410111.3	-	15	2498	c.2111A>T	c.(2110-2112)gAg>gTg	p.E704V	IMMT_ENST00000449247.2_Missense_Mutation_p.E693V|IMMT_ENST00000254636.5_Missense_Mutation_p.E605V|IMMT_ENST00000409051.2_Missense_Mutation_p.E657V|IMMT_ENST00000442664.2_Missense_Mutation_p.E703V	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	704					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TGCTGCTAGCTCCAGATCACC	0.488																																					p.E704V		.											.	IMMT-91	0			c.A2111T						.						102	97	98					2																	86371557		1969	4166	6135	SO:0001583	missense	10989	exon15			GCTAGCTCCAGAT	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.2111A>T	2.37:g.86371557T>A	ENSP00000387262:p.Glu704Val	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	146	43	NM_006839	0	1	62	113	50	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.501330	0.85176	.	.	ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.57431	0.2053	M	0.78049	2.395	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	T	0.59820	-0.7382	10	0.51188	T	0.08	-20.9731	15.8107	0.78561	0.0:0.0:0.0:1.0	.	657;692;693;672;704	B9A067;B4DKR1;Q16891-2;Q16891-3;Q16891	.;.;.;.;IMMT_HUMAN	V	605;693;704;703;657;693;672;318;605	ENSP00000254636:E605V;ENSP00000396899:E693V;ENSP00000387262:E704V;ENSP00000407788:E703V;ENSP00000387227:E657V	ENSP00000254636:E605V	E	-	2	0	IMMT	86225068	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.868000	0.87116	2.320000	0.78422	0.529000	0.55759	GAG	.		0.488	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		A	86371557	T	A	86371557	3	1	28	1	0	0	0	0	1	0	0	0	7739	1551	54	5	169	5	IMMT	2	86371557	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	15010969	86371557	156827816	19	2444											
SMPD4	55627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	130912744	130912744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caccatgagcgcgtgcttggGgctgaccaggtctgtgcgga	6	8	16	11	3	1	2	0	2	1	0	1	3	1	3	2	4	3	2	2	4	0	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:130912744G>A	ENST00000409031.1	-	15	2643	c.1495C>T	c.(1495-1497)Ccc>Tcc	p.P499S	SMPD4_ENST00000453750.1_Missense_Mutation_p.P248S|SMPD4_ENST00000452225.2_Missense_Mutation_p.P240S|SMPD4_ENST00000351288.6_Missense_Mutation_p.P470S|SMPD4_ENST00000339679.7_Missense_Mutation_p.P357S|SMPD4_ENST00000431183.2_Missense_Mutation_p.P397S|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000443958.2_Missense_Mutation_p.P163S|SMPD4_ENST00000426662.2_Missense_Mutation_p.P135S	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	460					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	GCGTGCTTGGGGCTGACCAGG	0.597																																					p.P499S		.											.	SMPD4-90	0			c.C1495T						.						89	85	86					2																	130912744		2203	4300	6503	SO:0001583	missense	55627	exon15			GCTTGGGGCTGAC	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1495C>T	2.37:g.130912744G>A	ENSP00000386531:p.Pro499Ser	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	83	20	NM_017951	0	0	4	6	2	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	18.79|18.79	3.698485|3.698485	0.68386|0.68386	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000430682|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159;ENST00000451542	.|.	.|.	.|.	4.24|4.24	4.24|4.24	0.50183|0.50183	.|.	0.182604|0.182604	0.47852|0.47852	D|D	0.000216|0.000216	T|T	0.76449|0.76449	0.3989|0.3989	M|M	0.74881|0.74881	2.28|2.28	0.42852|0.42852	D|D	0.994089|0.994089	.|D;D;D;D;P;D;P;D;D	.|0.71674	.|0.997;0.967;0.988;0.988;0.793;0.975;0.939;0.99;0.998	.|D;P;P;P;B;P;P;P;D	.|0.80764	.|0.931;0.595;0.896;0.896;0.258;0.644;0.745;0.878;0.994	T|T	0.75895|0.75895	-0.3156|-0.3156	6|9	.|0.29301	.|T	.|0.29	.|.	14.1436|14.1436	0.65336|0.65336	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|135;240;397;357;248;431;460;499;506	.|B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4	.|.;.;.;.;.;.;NSMA3_HUMAN;.;.	L|S	180|470;499;397;248;163;357;240;135;96;35;241	.|.	.|ENSP00000339721:P357S	P|P	-|-	2|1	0|0	SMPD4|SMPD4	130629214|130629214	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.637000|0.637000	0.38172|0.38172	5.392000|5.392000	0.66272|0.66272	1.886000|1.886000	0.54624|0.54624	0.305000|0.305000	0.20034|0.20034	CCC|CCC	.		0.597	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		A	130912744	G	A	130912744	3	1	28	1	0	0	0	0	1	0	0	0	14839	1232	43	2	1129	2	SMPD4	2	130912744	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	44541187	130912744	112286629	20	2445											
XIRP2	129446	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	168103277	168103277	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggtacaaaactgttacTgaagaaaaggcagtctctgg	15	9	11	6	0	1	3	0	2	1	1	2	3	1	3	0	3	3	3	0	3	8	2	rs200235198		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:168103277T>A	ENST00000409195.1	+	9	5464	c.5375T>A	c.(5374-5376)cTg>cAg	p.L1792Q	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.L1792Q|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.L1570Q|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1617					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAACTGTTACTGAAGAAAAGG	0.408																																					p.L1792Q													.	XIRP2-104	0			c.T5375A						.						180	172	174					2																	168103277		1930	4132	6062	SO:0001583	missense	129446	exon9			TGTTACTGAAGAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5375T>A	2.37:g.168103277T>A	ENSP00000386840:p.Leu1792Gln	Somatic	139	2		WXS	Illumina HiSeq	Phase_I	276	74	NM_152381	0	0	0	0	0	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.889248	0.52014	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04083	3.72;3.72;3.71	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000001	T	0.21590	0.0520	M	0.77103	2.36	0.58432	D	0.999999	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.72075	0.946;0.976;0.976	T	0.00322	-1.1818	10	0.52906	T	0.07	-10.6531	14.7546	0.69554	0.0:0.0:0.0:1.0	.	1617;1617;1570	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	1792;1792;1570	ENSP00000386840:L1792Q;ENSP00000295237:L1792Q;ENSP00000387255:L1570Q	ENSP00000295237:L1792Q	L	+	2	0	XIRP2	167811523	0.911000	0.30947	1.000000	0.80357	0.585000	0.36419	5.730000	0.68546	2.134000	0.65973	0.528000	0.53228	CTG	T|0.999;C|0.000		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168103277	T	A	168103277	3	1	28	1	0	0	0	0	1	0	0	0	17463	1580	55	5	5405	5	XIRP2	2	168103277	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	37190533	168103277	75096096	21	2446											
DNAJC10	54431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	183594619	183594619	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatcaaaggagagtttagtGagttttgcaatgcagcatgt	13	12	12	4	0	1	3	1	1	0	2	1	4	1	3	0	1	3	5	0	1	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:183594619G>T	ENST00000264065.7	+	8	1093	c.678G>T	c.(676-678)gtG>gtT	p.V226V	DNAJC10_ENST00000537515.1_Silent_p.V226V	NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	226	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			AGAGTTTAGTGAGTTTTGCAA	0.323																																					p.V226V	Pancreas(56;860 1183 25669 35822 48585)	.											.	DNAJC10-273	0			c.G678T						.						148	159	155					2																	183594619		2203	4300	6503	SO:0001819	synonymous_variant	54431	exon8			TTTAGTGAGTTTT		CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"Heat shock proteins / DNAJ (HSP40)", "Protein disulfide isomerases"	24637	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 19"	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.678G>T	2.37:g.183594619G>T		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	346	111	NM_001271581	0	0	0	0	0	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Silent	SNP	ENST00000264065.7	37	CCDS33345.1																																																																																			.		0.323	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981		T	183594619	G	T	183594619	2	4	28	1	0	0	0	0	0	0	0	1	4640	1277	45	4		4	DNAJC10	2	183594619	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	15491342	183594619	59604754	22	2447											
SF3B1	23451	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198285205	198285205	+	Missense_Mutation	SNP	T	T	A																															ttatcatggtccgcctatgcTttttgtattcatcttcccgg																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:198285205T>A	ENST00000335508.6	-	4	453	c.362A>T	c.(361-363)aAg>aTg	p.K121M	SF3B1_ENST00000487698.1_Missense_Mutation_p.K121M|SF3B1_ENST00000409915.4_Missense_Mutation_p.K121M|SF3B1_ENST00000414963.2_Missense_Mutation_p.K121M	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	121					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CCGCCTATGCTTTTTGTATTC	0.373			Mis		myelodysplastic syndrome																																p.K121M				Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.A362T						.						179	176	177					2																	198285205		2203	4300	6503	SO:0001583	missense	23451	exon4			CTATGCTTTTTGT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.362A>T	2.37:g.198285205T>A	ENSP00000335321:p.Lys121Met	Somatic	281	1		WXS	Illumina HiSeq	Phase_I	574	204	NM_012433	0	0	6	6	0	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	10.94	1.492662	0.26774	.	.	ENSG00000115524	ENST00000335508;ENST00000409915;ENST00000414963;ENST00000487698	.	.	.	5.93	5.93	0.95920	.	0.225047	0.45606	D	0.000347	T	0.55401	0.1918	L	0.49126	1.545	0.47407	D	0.999411	P;B;B	0.36249	0.545;0.002;0.132	B;B;B	0.36289	0.192;0.003;0.221	T	0.59857	-0.7375	9	0.72032	D	0.01	.	16.3764	0.83401	0.0:0.0:0.0:1.0	.	121;121;121	B4DGZ4;E9PCH3;O75533	.;.;SF3B1_HUMAN	M	121	.	ENSP00000335321:K121M	K	-	2	0	SF3B1	197993450	0.995000	0.38212	1.000000	0.80357	0.989000	0.77384	2.343000	0.44001	2.272000	0.75746	0.450000	0.29827	AAG	.		0.373	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198285205	T	A	198285205	3	1	28	1	0	0	0	0	1	0	0	0	14181	1609	56	5	3664	5	SF3B1	2	198285205	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	14690586	198285205	44914168	23	2448	25	2									
SF3B1	23451	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198285207	198285207	+	Silent	SNP	T	T	C																															atcatggtccgcctatgcttTttgtattcatcttcccggtc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:198285207T>C	ENST00000335508.6	-	4	451	c.360A>G	c.(358-360)aaA>aaG	p.K120K	SF3B1_ENST00000487698.1_Silent_p.K120K|SF3B1_ENST00000409915.4_Silent_p.K120K|SF3B1_ENST00000414963.2_Silent_p.K120K	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	120					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GCCTATGCTTTTTGTATTCAT	0.373			Mis		myelodysplastic syndrome																																p.K120K				Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.A360G						.						177	174	175					2																	198285207		2203	4300	6503	SO:0001819	synonymous_variant	23451	exon4			ATGCTTTTTGTAT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.360A>G	2.37:g.198285207T>C		Somatic	281	2		WXS	Illumina HiSeq	Phase_I	566	198	NM_012433	0	0	6	6	0	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			.		0.373	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198285207	T	C	198285207	2	2	28	1	0	0	0	0	0	0	0	1	14181	1838	64	3		3	SF3B1	2	198285207	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	2	198285207	44914166	24	2449	25	2									
HSPE1	3336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198365881	198365881	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaaactgtaaccaaaggAggcattatgcttccagaaaa	16	8	9	8	0	0	2	0	1	0	1	1	3	1	3	2	2	3	4	2	2	6	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:198365881A>G	ENST00000233893.5	+	2	530	c.87A>G	c.(85-87)ggA>ggG	p.G29G	HSPE1-MOB4_ENST00000604458.1_Silent_p.G29G|HSPE1_ENST00000465573.1_Intron|HSPD1_ENST00000544407.1_5'Flank|HSPD1_ENST00000345042.2_5'Flank|HSPD1_ENST00000388968.3_5'Flank|HSPE1_ENST00000409729.1_Intron|HSPE1_ENST00000409468.1_Silent_p.G29G	NM_002157.2	NP_002148.1	P61604	CH10_HUMAN	heat shock 10kDa protein 1	29					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|osteoblast differentiation (GO:0001649)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			lung(1)	1			Epithelial(96;0.225)			TAACCAAAGGAGGCATTATGC	0.438																																					p.G29G		.											.	HSPE1-226	0			c.A87G						.						59	60	60					2																	198365881		2203	4297	6500	SO:0001819	synonymous_variant	3336	exon2			CAAAGGAGGCATT	AF109872	CCDS2320.1	2q33.1	2013-10-17	2013-10-17		ENSG00000115541	ENSG00000115541		"Heat Shock Proteins / Chaperonins"	5269	protein-coding gene	gene with protein product	"chaperonin 10"	600141	"heat shock 10kD protein 1 (chaperonin 10)"			7914093, 7698325	Standard	NM_002157		Approved	CPN10, GROES		P61604	OTTHUMG00000132749	ENST00000233893.5:c.87A>G	2.37:g.198365881A>G		Somatic	187	0		WXS	Illumina HiSeq	Phase_I	367	141	NM_002157	0	0	422	825	403	O95421|Q04984|Q53X54|Q9UDH0	Silent	SNP	ENST00000233893.5	37	CCDS2320.1																																																																																			.		0.438	HSPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256112.1	NM_002157		G	198365881	A	G	198365881	2	3	28	1	0	0	0	0	0	0	0	1	7450	291	11	3		3	HSPE1	2	198365881	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	80674	198365881	44833492	25	2450											
NIF3L1	60491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	201768315	201768315	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgaggctttctttctgacCttcgagatatgctggattct	8	15	9	9	2	3	2	0	1	3	1	4	5	3	3	1	2	2	2	1	2	2	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:201768315C>A	ENST00000409020.1	+	7	1342	c.1048C>A	c.(1048-1050)Ctt>Att	p.L350I	NIF3L1_ENST00000359683.4_Missense_Mutation_p.L323I|NIF3L1_ENST00000409357.1_Missense_Mutation_p.L350I|NIF3L1_ENST00000416651.1_Missense_Mutation_p.L350I|NIF3L1_ENST00000409588.1_3'UTR			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	350					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						TCTTTCTGACCTTCGAGATAT	0.423																																					p.L350I		.											.	NIF3L1-91	0			c.C1048A						.						140	131	134					2																	201768315		1885	4113	5998	SO:0001583	missense	60491	exon7			TCTGACCTTCGAG	AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1", "NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.1048C>A	2.37:g.201768315C>A	ENSP00000386394:p.Leu350Ile	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	241	85	NM_001136039	0	0	20	32	12	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Missense_Mutation	SNP	ENST00000409020.1	37	CCDS46485.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.267008	0.80469	.	.	ENSG00000196290	ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.33	5.33	0.75918	.	0.052331	0.85682	D	0.000000	T	0.67618	0.2912	M	0.72624	2.21	0.46437	D	0.999043	D	0.69078	0.997	D	0.65573	0.936	T	0.65631	-0.6121	10	0.39692	T	0.17	-14.3245	19.3851	0.94553	0.0:1.0:0.0:0.0	.	350	Q9GZT8	NIF3L_HUMAN	I	350;350;323;350	ENSP00000400787:L350I;ENSP00000386394:L350I;ENSP00000352711:L323I;ENSP00000387315:L350I	ENSP00000352711:L323I	L	+	1	0	NIF3L1	201476560	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.771000	0.47670	2.656000	0.90262	0.557000	0.71058	CTT	.		0.423	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824		A	201768315	C	A	201768315	3	1	28	1	0	0	0	0	1	0	0	0	10442	681	24	4	1070	4	NIF3L1	2	201768315	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	3402434	201768315	41431058	26	2451											
RNF25	64320	broad.mit.edu	37	chr2	219529245	219529245	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctacagctgactcaggttccGcaggggcaggaggctagaaa	11	6	14	10	1	1	2	1	1	0	1	2	3	2	3	1	5	2	5	1	5	3	3	rs371228589		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:219529245G>A	ENST00000295704.2	-	10	1255	c.815C>T	c.(814-816)gCg>gTg	p.A272V		NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25	272					positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTCAGGTTCCGCAGGGGCAGG	0.552																																					p.A272V													.	RNF25-227	0			c.C815T						.	G	VAL/ALA	0,4406		0,0,2203	57	55	56		815	1.6	0	2		56	2,8596	2.2+/-6.3	0,2,4297	no	missense	RNF25	NM_022453.2	64	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign	272/460	219529245	2,13002	2203	4299	6502	SO:0001583	missense	64320	exon10			GGTTCCGCAGGGG		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"RING-type (C3HC4) zinc fingers"	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077	ENST00000295704.2:c.815C>T	2.37:g.219529245G>A	ENSP00000295704:p.Ala272Val	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	35	3	NM_022453	0	0	30	30	0	A8K0D6|Q53HQ5|Q9H874	Missense_Mutation	SNP	ENST00000295704.2	37	CCDS2420.1	.	.	.	.	.	.	.	.	.	.	G	0.524	-0.860994	0.02610	0.0	2.33E-4	ENSG00000163481	ENST00000295704	T	0.40225	1.04	5.41	1.59	0.23543	.	1.586980	0.03323	N	0.192235	T	0.16557	0.0398	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24476	-1.0159	10	0.09084	T	0.74	-5.7619	7.4443	0.27203	0.7535:0.0:0.2465:0.0	.	272	Q96BH1	RNF25_HUMAN	V	272	ENSP00000295704:A272V	ENSP00000295704:A272V	A	-	2	0	RNF25	219237489	0.010000	0.17322	0.038000	0.18304	0.862000	0.49288	0.329000	0.19698	0.165000	0.19558	-0.459000	0.05422	GCG	.		0.552	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453		A	219529245	G	A	219529245	3	1	28	1	0	0	0	0	1	0	0	0	13517	1087	38	1	568	1	RNF25	2	219529245	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	17760930	219529245	23670128	27	2452											
KIAA1486	57624	broad.mit.edu	37	chr2	226447157	226447157	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgctggtatttccccccGcccccgtgcattgctccccc	2	10	8	21	3	0	0	0	0	0	0	2	0	2	0	7	1	3	5	7	1	1	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:226447157G>A	ENST00000272907.6	+	4	1437	c.1024G>A	c.(1024-1026)Gcc>Acc	p.A342T	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	342	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												ATTTCCCCCCGCCCCCGTGCA	0.632																																					p.A342T													.	.	0			c.G1024A						.						20	22	21					2																	226447157		1864	4081	5945	SO:0001583	missense	57624	exon4			CCCCCCGCCCCCG	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1024G>A	2.37:g.226447157G>A	ENSP00000272907:p.Ala342Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	135	6	NM_020864	0	0	0	0	0	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	37	CCDS46529.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109563	0.37242	.	.	ENSG00000144460	ENST00000272907	T	0.47869	0.83	5.27	5.27	0.74061	.	0.186496	0.44483	D	0.000455	T	0.58438	0.2122	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.50206	-0.8855	10	0.05959	T	0.93	-28.7346	18.916	0.92506	0.0:0.0:1.0:0.0	.	342	Q9P242	K1486_HUMAN	T	342	ENSP00000272907:A342T	ENSP00000272907:A342T	A	+	1	0	KIAA1486	226155401	1.000000	0.71417	0.049000	0.19019	0.750000	0.42670	6.360000	0.73064	2.462000	0.83206	0.650000	0.86243	GCC	.		0.632	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		A	226447157	G	A	226447157	3	1	28	1	0	0	0	0	1	0	0	0	8258	1087	38	1	1034	1	KIAA1486	2	226447157	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	6917912	226447157	16752216	28	2453											
UGT1A9	54600	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	234580827	234580828	+	Frame_Shift_Ins	INS	-	-	T																															ttattcaacttcatatacccINStggaggatctggaccgggag																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:234580827_234580828insT	ENST00000354728.4	+	1	329_330	c.247_248insT	c.(247-249)ctgfs	p.L83fs	UGT1A1_ENST00000609637.1_Frame_Shift_Ins_p.L83fs|UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	83					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	TTCATATACCCTGGAGGATCTG	0.446																																					p.L83fs		.											.	UGT1A9-91	0			c.247_248insT						.																																			SO:0001589	frameshift_variant	54600	exon1			.	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.248dupT	2.37:g.234580828_234580828dupT	ENSP00000346768:p.Leu83fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	217	69	NM_021027	0	0	0	0	0	B8K285|P36509|Q9HAX0	Frame_Shift_Ins	INS	ENST00000354728.4	37	CCDS2505.1																																																																																			.		0.446	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		T	234580828	-	T	234580827	7	5	28	1	0	1	1	0	0	0	0	0	16985	680	24	0	249	0	UGT1A9	2	234580827	Frame_Shift_Ins	INS	-	TCGA-A4-A6HP-01A-11D-A31X-10	8133670	234580827	8618546	29	2454											
KLHL18	23276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47374712	47374713	+	Missense_Mutation	DNP	GC	GC	TA																															aggggtccctacctgcctgaGctgctgtccaatatccgcct																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:47374712_47374713GC>TA	ENST00000232766.5	+	5	686_687	c.666_667GC>TA	c.(664-669)gaGCtg>gaTAtg	p.222_223EL>DM	KLHL18_ENST00000455924.2_Missense_Mutation_p.110_111EL>DM	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	222	BACK.									endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		ACCTGCCTGAGCTGCTGTCCAA	0.569																																					p.EL222DM		.											.	KLHL18-90	0			c.C667A						.																																			SO:0001583	missense	23276	exon5			CCTGAGCTGCTGT	AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648		"Kelch-like", "BTB/POZ domain containing"	29120	protein-coding gene	gene with protein product			"kelch-like 18 (Drosophila)"			9872452	Standard	NM_025010		Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	Exception_encountered	3.37:g.47374712_47374713delinsTA	ENSP00000232766:p.E222_L223delinsDM	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	81	23	NM_025010	0	0	0	0	0	A8K612|Q7Z3E8|Q8N125	Missense_Mutation	DNP	ENST00000232766.5	37	CCDS33749.1																																																																																			.		0.569	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		TA	47374713	GC	TA	47374712	3	4	28	1	0	0	0	0	1	0	0	0	8394	962	34	4	684	4	KLHL18	3	47374712	Missense_Mutation	DNP	GC	TCGA-A4-A6HP-01A-11D-A31X-10		47374712	150647718	30	2455											
TMF1	7110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	69072460	69072460	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcagaatagtgttgtacctTtgatccaaatcctgaaaaat	14	13	7	7	0	0	3	0	2	0	1	2	3	2	3	3	0	2	3	3	0	6	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:69072460T>C	ENST00000398559.2	-	17	3366	c.3150A>G	c.(3148-3150)caA>caG	p.Q1050Q	CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000597366.1_RNA|TMF1_ENST00000489370.1_5'Flank|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Silent_p.Q1053Q|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	1050					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		TGTTGTACCTTTGATCCAAAT	0.299																																					p.Q1050Q		.											.	TMF1-90	0			c.A3150G						.						93	78	82					3																	69072460		1810	4067	5877	SO:0001819	synonymous_variant	7110	exon17			GTACCTTTGATCC		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.3150A>G	3.37:g.69072460T>C		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	196	61	NM_007114	0	0	0	3	3	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	37	CCDS43105.1																																																																																			.		0.299	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69072460	T	C	69072460	2	2	28	1	0	0	0	0	0	0	0	1	16260	1838	64	3		3	TMF1	3	69072460	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	21697748	69072460	128949970	31	2456											
BBX	56987	broad.mit.edu	37	chr3	107492048	107492048	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatataccattgaagccgtcGcaaaaggagactggggcata	14	8	11	8	2	0	2	0	1	0	1	1	3	0	2	2	3	2	2	2	3	7	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:107492048G>A	ENST00000325805.8	+	11	1767	c.1480G>A	c.(1480-1482)Gca>Aca	p.A494T	BBX_ENST00000416476.2_Intron|BBX_ENST00000402543.1_Missense_Mutation_p.A494T|BBX_ENST00000406780.1_Missense_Mutation_p.A494T|BBX_ENST00000415149.2_Missense_Mutation_p.A494T			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	494	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			TGAAGCCGTCGCAAAAGGAGA	0.483																																					p.A494T													.	BBX-94	0			c.G1480A						.						82	87	85					3																	107492048		2203	4300	6503	SO:0001583	missense	56987	exon11			GCCGTCGCAAAAG	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1480G>A	3.37:g.107492048G>A	ENSP00000319974:p.Ala494Thr	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	409	6	NM_001142568	0	0	0	0	0	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959348	0.74016	.	.	ENSG00000114439	ENST00000415149;ENST00000402543;ENST00000325805;ENST00000406780	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.94	5.94	0.96194	.	0.150283	0.64402	D	0.000014	T	0.65964	0.2742	L	0.32530	0.975	0.53005	D	0.999969	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.942;0.974;0.992	T	0.66917	-0.5802	10	0.87932	D	0	-12.6699	20.3523	0.98815	0.0:0.0:1.0:0.0	.	494;494;494	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	T	494	ENSP00000408358:A494T;ENSP00000385317:A494T;ENSP00000319974:A494T;ENSP00000385530:A494T	ENSP00000319974:A494T	A	+	1	0	BBX	108974738	1.000000	0.71417	0.974000	0.42286	0.199000	0.23934	9.107000	0.94261	2.821000	0.97095	0.484000	0.47621	GCA	.		0.483	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		A	107492048	G	A	107492048	3	1	28	1	0	0	0	0	1	0	0	0	1344	1087	38	1	1510	1	BBX	3	107492048	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	38419588	107492048	90530382	32	2457											
NDUFB4	4710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	120320001	120320001	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcctatgcaagaacaataaAtgtctatcctaatttcagac	15	11	6	9	0	2	2	1	0	1	2	3	2	3	2	2	1	2	1	2	1	8	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:120320001A>G	ENST00000184266.2	+	2	275	c.224A>G	c.(223-225)aAt>aGt	p.N75S	NDUFB4_ENST00000485064.1_Missense_Mutation_p.N75S|NDUFB4_ENST00000492739.1_Intron	NM_004547.5	NP_004538.2	O95168	NDUB4_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa	75					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|large_intestine(1)|lung(3)	5				GBM - Glioblastoma multiforme(114;0.14)		AGAACAATAAATGTCTATCCT	0.363																																					p.N75S		.											.	.	0			c.A224G						.						132	142	139					3																	120320001		2203	4296	6499	SO:0001583	missense	4710	exon2			CAATAAATGTCTA	AF044957	CCDS2999.1, CCDS54630.1	3q13.33	2011-07-04	2002-08-29		ENSG00000065518	ENSG00000065518		"Mitochondrial respiratory chain complex / Complex I"	7699	protein-coding gene	gene with protein product	"complex I B15 subunit"	603840	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4 (15kD, B15)"			9878551	Standard	NM_004547		Approved	B15	uc003edu.3	O95168	OTTHUMG00000159442	ENST00000184266.2:c.224A>G	3.37:g.120320001A>G	ENSP00000184266:p.Asn75Ser	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	179	71	NM_004547	0	0	128	295	167	B2RUY3|B9EJC7	Missense_Mutation	SNP	ENST00000184266.2	37	CCDS2999.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.635688	0.29068	.	.	ENSG00000065518	ENST00000184266;ENST00000485064	.	.	.	5.45	5.45	0.79879	.	0.052553	0.85682	D	0.000000	T	0.57562	0.2062	M	0.71581	2.175	0.80722	D	1	B;P	0.38129	0.103;0.619	B;B	0.38921	0.047;0.285	T	0.60929	-0.7165	9	0.45353	T	0.12	2.7254	11.8278	0.52278	1.0:0.0:0.0:0.0	.	75;75	O95168;B2RUY3	NDUB4_HUMAN;.	S	75	.	ENSP00000184266:N75S	N	+	2	0	NDUFB4	121802691	0.971000	0.33674	0.492000	0.27490	0.082000	0.17680	3.410000	0.52664	2.288000	0.76882	0.533000	0.62120	AAT	.		0.363	NDUFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355420.1	NM_004547		G	120320001	A	G	120320001	3	3	28	1	0	0	0	0	1	0	0	0	10309	101	4	3	230	3	NDUFB4	3	120320001	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	12827953	120320001	77702429	33	2458											
NMD3	51068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	160964158	160964158	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtctgggtacagaagacatCtgaaatgaatacagataaac	18	8	9	6	0	2	5	0	2	2	3	2	5	2	5	0	1	3	1	0	1	7	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:160964158C>T	ENST00000460469.1	+	11	1507	c.1052C>T	c.(1051-1053)tCt>tTt	p.S351F	NMD3_ENST00000472947.1_Missense_Mutation_p.S351F|NMD3_ENST00000351193.2_Missense_Mutation_p.S351F			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	351					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			CAGAAGACATCTGAAATGAAT	0.353																																					p.S351F		.											.	NMD3-91	0			c.C1052T						.						75	77	76					3																	160964158		2203	4300	6503	SO:0001583	missense	51068	exon12			AGACATCTGAAAT	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"NMD3 homolog (S. cerevisiae)"			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1052C>T	3.37:g.160964158C>T	ENSP00000419004:p.Ser351Phe	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	79	33	NM_015938	0	0	0	1	1	D3DNM7|Q9Y2Z6	Missense_Mutation	SNP	ENST00000460469.1	37	CCDS3194.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751897	0.89753	.	.	ENSG00000169251	ENST00000351193;ENST00000472947;ENST00000460469;ENST00000540137	T;T;T	0.24723	1.84;1.84;1.84	5.01	5.01	0.66863	.	0.055185	0.85682	D	0.000000	T	0.57388	0.2050	M	0.91354	3.2	0.80722	D	1	D;D;D	0.56968	0.972;0.978;0.976	P;P;P	0.59703	0.781;0.862;0.556	T	0.68213	-0.5468	10	0.87932	D	0	-30.719	18.1915	0.89808	0.0:1.0:0.0:0.0	.	351;351;351	B3KT11;C9JA08;Q96D46	.;.;NMD3_HUMAN	F	351;351;351;231	ENSP00000307525:S351F;ENSP00000417559:S351F;ENSP00000419004:S351F	ENSP00000307525:S351F	S	+	2	0	NMD3	162446852	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.963000	0.76055	2.709000	0.92574	0.655000	0.94253	TCT	.		0.353	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938		T	160964158	C	T	160964158	3	4	28	1	0	0	0	0	1	0	0	0	10514	913	32	2	1094	2	NMD3	3	160964158	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	40644157	160964158	37058272	34	2459											
PARL	55486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	183602604	183602604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgcctggccgcagccccAgcctctctgcgcccagcctc	4	5	9	23	3	1	0	0	0	1	0	3	0	1	0	8	1	4	1	8	1	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:183602604A>G	ENST00000317096.4	-	1	91	c.31T>C	c.(31-33)Tgg>Cgg	p.W11R	MIR4448_ENST00000584360.1_RNA|PARL_ENST00000435888.1_Missense_Mutation_p.W11R|PARL_ENST00000311101.5_Missense_Mutation_p.W11R|RP11-315J22.5_ENST00000445165.1_RNA	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	11					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CCGCAGCCCCAGCCTCTCTGC	0.697											OREG0015941	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W11R		.											.	PARL-90	0			c.T31C						.						10	11	11					3																	183602604		2174	4246	6420	SO:0001583	missense	55486	exon1			AGCCCCAGCCTCT	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"rhomboid 7 homolog 1 (Drosophila)"	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.31T>C	3.37:g.183602604A>G	ENSP00000325421:p.Trp11Arg	Somatic	17	0	1985	WXS	Illumina HiSeq	Phase_I	37	13	NM_018622	0	0	9	11	2	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	37	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650621	0.67472	.	.	ENSG00000175193	ENST00000317096;ENST00000311101;ENST00000435888	T;T;T	0.58652	0.42;0.32;0.33	4.72	4.72	0.59763	.	0.104022	0.38217	N	0.001779	T	0.51770	0.1694	L	0.40543	1.245	0.37352	D	0.910834	P;P	0.40107	0.703;0.664	B;B	0.42692	0.395;0.296	T	0.62959	-0.6743	10	0.87932	D	0	-25.2787	10.7723	0.46330	1.0:0.0:0.0:0.0	.	11;11	Q9H300-2;Q9H300	.;PARL_HUMAN	R	11	ENSP00000325421:W11R;ENSP00000310676:W11R;ENSP00000402137:W11R	ENSP00000310676:W11R	W	-	1	0	PARL	185085298	0.998000	0.40836	1.000000	0.80357	0.719000	0.41307	3.655000	0.54460	2.118000	0.64928	0.533000	0.62120	TGG	.		0.697	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		G	183602604	A	G	183602604	3	3	28	1	0	0	0	0	1	0	0	0	11477	188	7	3	1148	3	PARL	3	183602604	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	22638446	183602604	14419826	35	2460											
ZNF721	170960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	436719	436719	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttagtaagggttgtggAactagtaaacgctttaccac	12	13	10	6	1	0	0	0	0	0	0	0	1	0	1	1	2	3	5	1	2	7	8			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:436719A>G	ENST00000338977.5	-	2	1549	c.1501T>C	c.(1501-1503)Tcc>Ccc	p.S501P	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Missense_Mutation_p.S513P			Q8TF20	ZN721_HUMAN	zinc finger protein 721	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGGGTTGTGGAACTAGTAAAC	0.398																																					p.G513R		.											.	ZNF721-47	0			c.G1537C						.						84	92	89					4																	436719		2098	4242	6340	SO:0001583	missense	170960	exon3			TTGTGGAACTAGT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1501T>C	4.37:g.436719A>G	ENSP00000340524:p.Ser501Pro	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	126	41	NM_133474	0	0	0	0	0	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	A	3.452	-0.111794	0.06881	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.07908	3.15;3.15	0.419	-0.837	0.10766	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13927	0.0337	L	0.55743	1.74	0.09310	N	1	P;P;P	0.45348	0.856;0.669;0.777	P;P;P	0.55112	0.592;0.592;0.769	T	0.16217	-1.0410	9	0.42905	T	0.14	.	4.3636	0.11213	0.3506:0.0:0.6494:0.0	.	501;513;513	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	P	501;513	ENSP00000340524:S501P;ENSP00000428878:S513P	ENSP00000340524:S501P	S	-	1	0	ZNF721	426719	0.000000	0.05858	0.002000	0.10522	0.089000	0.18198	-1.976000	0.01497	-0.428000	0.07339	0.155000	0.16302	TCC	.		0.398	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	436719	A	G	436719	3	3	28	1	0	0	0	0	1	0	0	0	18154	246	9	3	1238	3	ZNF721	4	436719	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		436719	190717557	36	2461											
KIAA1530	57654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1369834	1369834	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctgtagcccctccagagcGttgccagagccacaggaggc	8	6	12	15	1	0	2	0	0	0	2	2	3	2	3	6	2	4	2	6	2	1	2	rs114098503	byFrequency	TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:1369834G>A	ENST00000389851.4	+	10	1893	c.1446G>A	c.(1444-1446)gcG>gcA	p.A482A	UVSSA_ENST00000511216.1_Silent_p.A482A|UVSSA_ENST00000511563.1_Silent_p.A33A|UVSSA_ENST00000512728.1_Silent_p.A33A|UVSSA_ENST00000507531.1_Silent_p.A482A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	482					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										CCTCCAGAGCGTTGCCAGAGC	0.697													g|||	2	0.000399361	0	0	5008	,	,		14914	0		0.001	False		,,,				2504	0.001				p.A482A		.											.	.	0			c.G1446A						.						14	16	15					4																	1369834		2182	4297	6479	SO:0001819	synonymous_variant	57654	exon10			CAGAGCGTTGCCA	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"KIAA1530"	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1446G>A	4.37:g.1369834G>A		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	84	33	NM_020894	0	0	0	0	0	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			G|0.999;A|0.001		0.697	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		A	1369834	G	A	1369834	2	1	28	1	0	0	0	0	0	0	0	1	8262	1132	40	1		1	KIAA1530	4	1369834	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	933115	1369834	189784442	37	2462											
RG9MTD2	93587	broad.mit.edu	37	chr4	100478514	100478514	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acacatacctgcacaggatgCagtgcccgtcggttttctgc	8	10	10	13	2	1	0	0	0	1	0	2	1	1	1	2	2	5	3	2	2	1	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:100478514C>T	ENST00000273962.3	-	4	720	c.408G>A	c.(406-408)ctG>ctA	p.L136L	TRMT10A_ENST00000394877.3_Silent_p.L136L|TRMT10A_ENST00000394876.2_Silent_p.L136L	NM_152292.4	NP_689505.1	Q8TBZ6	TM10A_HUMAN	tRNA methyltransferase 10 homolog A (S. cerevisiae)	136	SAM-dependent MTase TRM10-type. {ECO:0000255|PROSITE-ProRule:PRU01012}.				magnesium ion homeostasis (GO:0010960)	extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										GCACAGGATGCAGTGCCCGTC	0.343																																					p.L136L													.	.	0			c.G408A						.						103	97	99					4																	100478514		2203	4300	6503	SO:0001819	synonymous_variant	93587	exon4			AGGATGCAGTGCC	BC028373	CCDS3650.1	4q23	2012-06-28	2012-06-28	2012-06-28	ENSG00000145331	ENSG00000145331			28403	protein-coding gene	gene with protein product			"RNA (guanine-9-) methyltransferase domain containing 2"	RG9MTD2		12477932	Standard	NM_152292		Approved	MGC27034, TRM10	uc003hva.4	Q8TBZ6	OTTHUMG00000131025	ENST00000273962.3:c.408G>A	4.37:g.100478514C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	163	4	NM_001134666	0	0	0	0	0	B2R8X7|Q9Y2T9	Silent	SNP	ENST00000273962.3	37	CCDS3650.1																																																																																			.		0.343	TRMT10A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253668.1	NM_152292		T	100478514	C	T	100478514	2	4	28	1	0	0	0	0	0	0	0	1	13304	697	25	2		2	RG9MTD2	4	100478514	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	99108680	100478514	90675762	38	2463											
ALPK1	80216	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	113303701	113303701	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattggcgccgggttgcagcAgttactggtaggaagagcca	9	8	16	8	2	0	1	0	0	0	1	0	3	0	2	2	4	4	5	2	4	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:113303701A>T	ENST00000458497.1	+	4	548	c.269A>T	c.(268-270)cAg>cTg	p.Q90L	ALPK1_ENST00000504176.2_Intron|ALPK1_ENST00000177648.9_Missense_Mutation_p.Q90L	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	90							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GGGTTGCAGCAGTTACTGGTA	0.483																																					p.Q90L													.	ALPK1-337	0			c.A269T						.						82	68	73					4																	113303701		2203	4300	6503	SO:0001583	missense	80216	exon4			TGCAGCAGTTACT	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.269A>T	4.37:g.113303701A>T	ENSP00000398048:p.Gln90Leu	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	209	81	NM_001102406	0	0	0	0	0	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	A	14.96	2.691426	0.48097	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000309610	T;T	0.20200	2.09;2.09	5.63	1.82	0.25136	.	0.575913	0.18643	N	0.135223	T	0.21307	0.0513	L	0.50333	1.59	0.80722	D	1	B;B;B	0.32302	0.302;0.363;0.145	B;B;B	0.32289	0.05;0.143;0.075	T	0.05321	-1.0892	10	0.66056	D	0.02	-4.5503	13.5725	0.61856	0.5727:0.4273:0.0:0.0	.	65;90;90	E7EX13;Q96QP1;B3KUH8	.;ALPK1_HUMAN;.	L	90;90;65	ENSP00000398048:Q90L;ENSP00000177648:Q90L	ENSP00000177648:Q90L	Q	+	2	0	ALPK1	113523150	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.632000	0.54287	0.072000	0.16694	0.533000	0.62120	CAG	.		0.483	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		T	113303701	A	T	113303701	3	4	28	1	0	0	0	0	1	0	0	0	544	188	7	5	275	5	ALPK1	4	113303701	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	12825187	113303701	77850575	39	2464											
TMEM192	201931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	166000935	166000935	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttttcaacaatttcttctaGgcttgaaatagttctgcaag	11	16	6	8	0	4	1	1	1	3	0	4	1	4	1	0	1	2	3	0	1	6	8			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:166000935G>T	ENST00000306480.6	-	6	836	c.691C>A	c.(691-693)Cta>Ata	p.L231I	TMEM192_ENST00000506087.1_Missense_Mutation_p.L227I	NM_001100389.1	NP_001093859.1	Q8IY95	TM192_HUMAN	transmembrane protein 192	231						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0926)		ATTTCTTCTAGGCTTGAAATA	0.388																																					p.L231I		.											.	TMEM192-69	0			c.C691A						.						94	88	90					4																	166000935		1868	4109	5977	SO:0001583	missense	201931	exon6			CTTCTAGGCTTGA	BC036301	CCDS43279.1	4q32.3	2008-04-22			ENSG00000170088	ENSG00000170088			26775	protein-coding gene	gene with protein product						12477932	Standard	NM_001100389		Approved	FLJ38482	uc003iqz.4	Q8IY95	OTTHUMG00000161254	ENST00000306480.6:c.691C>A	4.37:g.166000935G>T	ENSP00000305069:p.Leu231Ile	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	76	27	NM_001100389	0	0	8	9	1	Q7Z3A1|Q8N928	Missense_Mutation	SNP	ENST00000306480.6	37	CCDS43279.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692853	0.30052	.	.	ENSG00000170088	ENST00000306480;ENST00000506087	.	.	.	5.97	3.32	0.38043	.	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	M	0.73962	2.25	0.41322	D	0.987189	B	0.27997	0.197	B	0.30716	0.119	T	0.60627	-0.7226	9	0.66056	D	0.02	-38.5919	6.9529	0.24556	0.3323:0.0:0.6677:0.0	.	231	Q8IY95	TM192_HUMAN	I	231;227	.	ENSP00000305069:L231I	L	-	1	2	TMEM192	166220385	1.000000	0.71417	0.172000	0.22920	0.509000	0.34042	2.379000	0.44318	0.868000	0.35678	0.591000	0.81541	CTA	.		0.388	TMEM192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364310.3	NM_152681		T	166000935	G	T	166000935	3	4	28	1	0	0	0	0	1	0	0	0	16147	991	35	4	128	4	TMEM192	4	166000935	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	52697234	166000935	25153341	40	2465											
PPARGC1B	133522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149213062	149213062	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagagctctgtgtgccccGtgcggcgttctcggagactg	4	10	16	11	4	2	2	0	0	2	2	3	4	2	2	2	3	3	2	2	3	0	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:149213062G>A	ENST00000309241.5	+	5	1458	c.1426G>A	c.(1426-1428)Gtg>Atg	p.V476M	PPARGC1B_ENST00000403750.1_Missense_Mutation_p.V412M|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.V476M|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.V437M	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	476					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TGTGTGCCCCGTGCGGCGTTC	0.637																																					p.V476M		.											.	PPARGC1B-186	0			c.G1426A						.						42	44	43					5																	149213062		2182	4277	6459	SO:0001583	missense	133522	exon5			TGCCCCGTGCGGC	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"RNA binding motif (RRM) containing"	30022	protein-coding gene	gene with protein product		608886	"peroxisome proliferative activated receptor, gamma, coactivator 1, beta"			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.1426G>A	5.37:g.149213062G>A	ENSP00000312649:p.Val476Met	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	82	27	NM_133263	0	0	0	0	0	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.80|18.80	3.700810|3.700810	0.68501|0.68501	.|.	.|.	ENSG00000155846|ENSG00000155846	ENST00000434684|ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	.|T;T;T;T	.|0.14266	.|2.53;2.52;2.54;2.52	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.29749|0.29749	0.0743|0.0743	L|L	0.36672|0.36672	1.1|1.1	0.43207|0.43207	D|D	0.995068|0.995068	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.999;0.999;0.999;0.999;0.999	T|T	0.01294|0.01294	-1.1393|-1.1393	5|10	.|0.66056	.|D	.|0.02	-15.2485|-15.2485	17.3201|17.3201	0.87233|0.87233	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|455;455;437;476;476	.|Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.|.;.;.;PRGC2_HUMAN;.	H|M	162|437;476;476;412	.|ENSP00000353638:V437M;ENSP00000377855:V476M;ENSP00000312649:V476M;ENSP00000384403:V412M	.|ENSP00000312649:V476M	R|V	+|+	2|1	0|0	PPARGC1B|PPARGC1B	149193255|149193255	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.758000|0.758000	0.43043|0.43043	4.727000|4.727000	0.61993|0.61993	2.521000|2.521000	0.84997|0.84997	0.462000|0.462000	0.41574|0.41574	CGT|GTG	.		0.637	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		A	149213062	G	A	149213062	3	1	28	1	0	0	0	0	1	0	0	0	12327	1145	40	1	1451	1	PPARGC1B	5	149213062	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		149213062	31702198	41	2466											
GALNT10	55568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	153755929	153755929	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaagggctgataaggaccCgaatgctgggggcctcagtg	9	6	18	8	1	1	1	1	1	0	0	1	4	1	3	2	5	1	2	2	5	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:153755929C>T	ENST00000297107.6	+	5	798	c.661C>T	c.(661-663)Cga>Tga	p.R221*	GALNT10_ENST00000377661.2_Intron|GALNT10_ENST00000519544.1_3'UTR|GALNT10_ENST00000425427.2_Nonsense_Mutation_p.R221*|SAP30L-AS1_ENST00000519727.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	221	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			GATAAGGACCCGAATGCTGGG	0.522																																					p.R221X		.											.	GALNT10-92	0			c.C661T						.						90	89	90					5																	153755929		2203	4300	6503	SO:0001587	stop_gained	55568	exon5			AGGACCCGAATGC	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19873	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 10"	608043	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.661C>T	5.37:g.153755929C>T	ENSP00000297107:p.Arg221*	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	159	61	NM_198321	0	0	0	0	0	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Nonsense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	C	38	7.017290	0.98006	.	.	ENSG00000164574	ENST00000425427;ENST00000297107	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	221	.	ENSP00000297107:R221X	R	+	1	2	GALNT10	153736122	0.997000	0.39634	1.000000	0.80357	0.936000	0.57629	3.644000	0.54381	2.884000	0.98904	0.655000	0.94253	CGA	.		0.522	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		T	153755929	C	T	153755929	4	4	28	1	0	0	0	0	0	1	0	0	6228	644	23	1	679	1	GALNT10	5	153755929	Nonsense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	4542867	153755929	27159331	42	2467											
CPEB4	80315	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	173317154	173317154	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaggatcgaatctccagtgTtgacagggtttgattatcaa	12	13	10	6	1	2	2	1	2	1	0	4	4	2	3	1	2	0	2	1	2	4	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:173317154T>G	ENST00000265085.5	+	1	1872	c.418T>G	c.(418-420)Ttg>Gtg	p.L140V	CPEB4_ENST00000334035.5_Missense_Mutation_p.L140V|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000520867.1_Missense_Mutation_p.L140V|CPEB4_ENST00000519835.1_Missense_Mutation_p.L140V|CPEB4_ENST00000522336.1_5'Flank	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	140					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			ATCTCCAGTGTTGACAGGGTT	0.448																																					p.L140V		.											.	CPEB4-90	0			c.T418G						.						103	105	105					5																	173317154		2203	4300	6503	SO:0001583	missense	80315	exon1			CCAGTGTTGACAG	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.418T>G	5.37:g.173317154T>G	ENSP00000265085:p.Leu140Val	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	111	8	NM_030627	0	0	0	0	0	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	37	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.525591	0.44969	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.96	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.59838	0.2223	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.71674	0.997;0.998;0.997;0.997	D;D;D;D	0.87578	0.996;0.998;0.996;0.996	T	0.61686	-0.7012	10	0.72032	D	0.01	-9.5609	9.6678	0.39994	0.0:0.1383:0.0:0.8617	.	140;140;140;140	B7ZLQ8;Q17RY0-2;E5RJM0;Q17RY0	.;.;.;CPEB4_HUMAN	V	140	ENSP00000265085:L140V;ENSP00000429092:L140V;ENSP00000334533:L140V;ENSP00000429048:L140V	ENSP00000265085:L140V	L	+	1	2	CPEB4	173249760	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.961000	0.40432	1.089000	0.41292	0.533000	0.62120	TTG	.		0.448	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		G	173317154	T	G	173317154	3	3	28	1	0	0	0	0	1	0	0	0	3809	1722	60	5	420	5	CPEB4	5	173317154	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	19561225	173317154	7598106	43	2468											
CDHR2	54825	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176018324	176018324	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taacatgtacaacactgagcGgtgagcaggggtcaaagggt	13	7	14	7	1	1	2	1	2	0	0	1	2	1	2	0	4	5	2	0	4	4	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:176018324G>A	ENST00000510636.1	+	29	3927	c.3653G>A	c.(3652-3654)cGa>cAa	p.R1218Q	CDHR2_ENST00000506348.1_Splice_Site_p.R1218Q|CDHR2_ENST00000261944.5_Splice_Site_p.R1218Q	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1218					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						AACACTGAGCGGTGAGCAGGG	0.597																																					p.R1218Q		.											.	CDHR2-70	0			c.G3653A						.						66	64	65					5																	176018324		2203	4300	6503	SO:0001630	splice_region_variant	54825	exon29			CTGAGCGGTGAGC	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"Cadherins / Cadherin-related"	18231	protein-coding gene	gene with protein product	"protocadherin LKC"		"protocadherin 24"	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.3653+1G>A	5.37:g.176018324G>A		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	122	44	NM_017675	0	0	0	1	1	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	g	12.10	1.836140	0.32421	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.56103	0.48;0.48;0.48	4.24	2.24	0.28232	.	.	.	.	.	T	0.45236	0.1332	M	0.70595	2.14	0.32458	N	0.544539	P	0.52061	0.95	B	0.38428	0.273	T	0.56378	-0.7989	9	0.25751	T	0.34	-7.212	9.1617	0.37028	0.203:0.0:0.797:0.0	.	1218	Q9BYE9	CDHR2_HUMAN	Q	1218	ENSP00000424565:R1218Q;ENSP00000261944:R1218Q;ENSP00000421078:R1218Q	ENSP00000261944:R1218Q	R	+	2	0	CDHR2	175950930	1.000000	0.71417	0.933000	0.37362	0.367000	0.29736	3.600000	0.54052	1.036000	0.39998	0.459000	0.35465	CGA	.		0.597	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	Missense_Mutation	A	176018324	G	A	176018324	5	1	28	1	0	0	0	0	0	0	1	0	3125	1130	39	1	3763	1	CDHR2	5	176018324	Splice_Site	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	2701170	176018324	4896936	44	2469											
DSP	1832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	7583589	7583589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctaaggaaaaatactctttgGtagaggccaagagaaagaaa	19	7	10	5	0	1	3	0	0	1	3	1	5	1	4	1	3	1	1	1	3	8	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:7583589G>A	ENST00000379802.3	+	24	6435	c.6094G>A	c.(6094-6096)Gta>Ata	p.V2032I	DSP_ENST00000418664.2_Missense_Mutation_p.V1433I	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2032	4.5 X 38 AA tandem repeats (Domain A).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		ATACTCTTTGGTAGAGGCCAA	0.478																																					p.V2032I		.											.	DSP-518	0			c.G6094A						.						49	54	52					6																	7583589		2203	4300	6503	SO:0001583	missense	1832	exon24			TCTTTGGTAGAGG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.6094G>A	6.37:g.7583589G>A	ENSP00000369129:p.Val2032Ile	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	114	32	NM_004415	0	0	2	2	0	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877522	0.51801	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.67523	-0.27;-0.27	4.98	4.98	0.66077	.	0.000000	0.52532	D	0.000074	T	0.44456	0.1294	L	0.36672	1.1	0.25902	N	0.983344	P;P	0.45078	0.85;0.779	B;B	0.41236	0.278;0.351	T	0.45131	-0.9282	10	0.22109	T	0.4	.	18.6091	0.91277	0.0:0.0:1.0:0.0	.	1480;2032	Q4LE79;P15924	.;DESP_HUMAN	I	2032;1433	ENSP00000369129:V2032I;ENSP00000396591:V1433I	ENSP00000369129:V2032I	V	+	1	0	DSP	7528588	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.384000	0.59607	2.459000	0.83118	0.655000	0.94253	GTA	.		0.478	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7583589	G	A	7583589	3	1	28	1	0	0	0	0	1	0	0	0	4792	1261	44	2	6188	2	DSP	6	7583589	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		7583589	163531478	45	2470											
TMEM170B	100113407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	11575733	11575733	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttggaagcgctggtatgggGcgttggacagactgtactga	8	11	16	6	2	0	2	0	1	0	1	0	4	0	4	0	5	2	4	0	5	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:11575733G>T	ENST00000379426.1	+	3	338	c.338G>T	c.(337-339)gGc>gTc	p.G113V	TMEM170B_ENST00000543875.1_Missense_Mutation_p.G113V	NM_001100829.1	NP_001094299.1	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	113						integral component of membrane (GO:0016021)				large_intestine(3)|lung(5)	8						CTGGTATGGGGCGTTGGACAG	0.473																																					p.G113V		.											.	TMEM170B-22	0			c.G338T						.						203	196	198					6																	11575733		1966	4141	6107	SO:0001583	missense	100113407	exon3			TATGGGGCGTTGG		CCDS43425.1	6p24.1	2008-08-08			ENSG00000205269	ENSG00000205269			34244	protein-coding gene	gene with protein product							Standard	NM_001100829		Approved		uc010jpa.4	Q5T4T1	OTTHUMG00000014259	ENST00000379426.1:c.338G>T	6.37:g.11575733G>T	ENSP00000368737:p.Gly113Val	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	134	36	NM_001100829	0	0	0	0	0		Missense_Mutation	SNP	ENST00000379426.1	37	CCDS43425.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.373246	0.82573	.	.	ENSG00000205269	ENST00000543875;ENST00000379426	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.72859	0.3513	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.75645	-0.3246	9	0.87932	D	0	-20.3795	19.0673	0.93116	0.0:0.0:1.0:0.0	.	113	Q5T4T1	T170B_HUMAN	V	113	.	ENSP00000368737:G113V	G	+	2	0	TMEM170B	11683719	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	9.466000	0.97665	2.502000	0.84385	0.579000	0.79373	GGC	.		0.473	TMEM170B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000039862.1	NM_001100829		T	11575733	G	T	11575733	3	4	28	1	0	0	0	0	1	0	0	0	16119	1203	42	4	348	4	TMEM170B	6	11575733	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	3992144	11575733	159539334	46	2471											
RIMS1	22999	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	73017054	73017055	+	Frame_Shift_Del	DEL	AT	AT	-																															tggttctagtcaagaacttgAtcgcgagcaatattccaagg																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:73017054_73017055delAT	ENST00000521978.1	+	27	3944_3945	c.3944_3945delAT	c.(3943-3945)gatfs	p.D1315fs	RIMS1_ENST00000520567.1_Intron|RIMS1_ENST00000401910.3_Frame_Shift_Del_p.D635fs|RIMS1_ENST00000538414.1_Frame_Shift_Del_p.D121fs|RIMS1_ENST00000518273.1_Intron|RIMS1_ENST00000517960.1_Frame_Shift_Del_p.D1107fs|RIMS1_ENST00000425662.2_Intron|RIMS1_ENST00000523963.1_Intron|RIMS1_ENST00000517827.1_Intron|RIMS1_ENST00000348717.5_Frame_Shift_Del_p.D1107fs|RIMS1_ENST00000264839.7_Frame_Shift_Del_p.D1164fs|RIMS1_ENST00000522291.1_Intron|RIMS1_ENST00000491071.2_Frame_Shift_Del_p.D1138fs	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1315					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CAAGAACTTGATCGCGAGCAAT	0.401																																					p.1315_1315del		.											.	RIMS1-144	0			c.3944_3945del						.																																			SO:0001589	frameshift_variant	22999	exon27			.	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.3944_3945delAT	6.37:g.73017054_73017055delAT	ENSP00000428417:p.Asp1315fs	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	118	34	NM_014989	0	0	0	0	0	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Frame_Shift_Del	DEL	ENST00000521978.1	37	CCDS47449.1																																																																																			.		0.401	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			-	73017055	AT	-	73017054	7	5	28	1	0	1	0	1	0	0	0	0	13399	333	12	0	4213	0	RIMS1	6	73017054	Frame_Shift_Del	DEL	AT	TCGA-A4-A6HP-01A-11D-A31X-10	61441321	73017054	98098013	47	2472											
ECT2L	345930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	139135653	139135653	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaggaaagagtggctcttaTaagtcattggtttgacctct	10	14	10	7	0	4	2	2	1	2	1	4	3	4	3	1	3	0	2	1	3	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:139135653T>C	ENST00000423192.1	+	3	253	c.92T>C	c.(91-93)aTa>aCa	p.I31T	ECT2L_ENST00000367682.2_Missense_Mutation_p.I31T|ECT2L_ENST00000541398.1_5'Flank			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	31							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						GTGGCTCTTATAAGTCATTGG	0.368			"N, Splice, Mis"		ETP ALL																																p.I31T		.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L-22	0			c.T92C						.						77	75	76					6																	139135653		1836	4092	5928	SO:0001583	missense	345930	exon3			CTCTTATAAGTCA		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"Rho guanine nucleotide exchange factors", "F-boxes /  "other""	21118	protein-coding gene	gene with protein product	"lung specific F-box and DH domain containing protein", "F-box protein 49"		"chromosome 6 open reading frame 91", "epithelial cell transforming sequence 2 oncogene-like"	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.92T>C	6.37:g.139135653T>C	ENSP00000387388:p.Ile31Thr	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	112	45	NM_001195037	0	0	0	0	0	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.809410	0.50421	.	.	ENSG00000203734	ENST00000423192;ENST00000401414;ENST00000367682	T;T;T	0.62498	0.02;0.65;0.02	5.43	5.43	0.79202	.	.	.	.	.	T	0.44477	0.1295	L	0.33485	1.01	0.80722	D	1	D	0.54047	0.964	P	0.45310	0.476	T	0.55347	-0.8155	9	0.87932	D	0	.	13.0191	0.58775	0.0:0.0:0.0:1.0	.	31	Q008S8	ECT2L_HUMAN	T	31	ENSP00000387388:I31T;ENSP00000385187:I31T;ENSP00000356655:I31T	ENSP00000356655:I31T	I	+	2	0	ECT2L	139177346	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.876000	0.63079	2.066000	0.61787	0.533000	0.62120	ATA	.		0.368	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		C	139135653	T	C	139135653	3	2	28	1	0	0	0	0	1	0	0	0	4913	1406	49	3	98	3	ECT2L	6	139135653	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	66118599	139135653	31979414	48	2473											
CITED2	10370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	139694869	139694869	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtccccggccccatcgcAtgcctgatgccgctcgtggc	5	7	11	18	4	0	1	0	1	0	0	3	1	1	1	6	2	2	2	6	2	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:139694869A>G	ENST00000367651.2	-	2	428	c.213T>C	c.(211-213)caT>caC	p.H71H	CITED2_ENST00000536159.1_Silent_p.H71H|CITED2_ENST00000537332.1_Silent_p.H71H	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	71					adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		GCCCCATCGCATGCCTGATGC	0.672																																					p.H76H	NSCLC(98;1219 1550 33720 43229 49330)	.											.	CITED2-90	0			c.T228C						.						34	34	34					6																	139694869		2203	4299	6502	SO:0001819	synonymous_variant	10370	exon2			CATCGCATGCCTG	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.213T>C	6.37:g.139694869A>G		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	33	11	NM_001168389	0	0	30	64	34	O95426|Q5VTF4	Silent	SNP	ENST00000367651.2	37	CCDS5195.1																																																																																			.		0.672	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			G	139694869	A	G	139694869	2	3	28	1	0	0	0	0	0	0	0	1	3446	214	8	3		3	CITED2	6	139694869	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	559216	139694869	31420198	49	2474											
RADIL	55698	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	4841357	4841357	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgcttttccacaggggccGccggactctggccagtcggg	5	7	15	14	4	1	0	0	0	1	0	3	1	2	1	4	5	1	1	4	5	0	2	rs369296363	byFrequency	TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:4841357G>A	ENST00000399583.3	-	12	2956	c.2769C>T	c.(2767-2769)ggC>ggT	p.G923G	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Silent_p.G683G	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	923	Pro-rich.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CACAGGGGCCGCCGGACTCTG	0.711													G|||	2	0.000399361	0.0015	0	5008	,	,		14081	0		0	False		,,,				2504	0				p.G923G		.											.	RADIL-994	0			c.C2769T						.	G		2,3724		0,2,1861	8	10	10		2769	-3.9	0	7		10	0,8120		0,0,4060	no	coding-synonymous	RADIL	NM_018059.4		0,2,5921	AA,AG,GG		0.0,0.0537,0.0169		923/1076	4841357	2,11844	1863	4060	5923	SO:0001819	synonymous_variant	55698	exon12			GGGGCCGCCGGAC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2769C>T	7.37:g.4841357G>A		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	300	118	NM_018059	0	0	4	5	1	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			.		0.711	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		A	4841357	G	A	4841357	2	1	28	1	0	0	0	0	0	0	0	1	13029	1074	38	1		1	RADIL	7	4841357	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		4841357	154297306	50	2475											
ZAN	7455	broad.mit.edu	37	chr7	100349675	100349675	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcagaaaaacccaccatTtccacagaaaaacccaccgt	16	5	3	17	1	1	2	1	0	0	2	2	2	2	2	6	0	2	0	6	0	4	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:100349675T>C	ENST00000348028.3	+	0	2112				ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000538115.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			AACCCACCATTTCCACAGAAA	0.517																																					.													.	ZAN-142	0			.						.						223	248	240					7																	100349675		1875	4109	5984			7455	.			CACCATTTCCACA	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100349675T>C		Somatic	103	1		WXS	Illumina HiSeq	Phase_I	525	11	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Silent	SNP	ENST00000348028.3	37																																																																																				.		0.517	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		C	100349675	T	C	100349675	1	2	28	0	1	0	0	0	0	0	0	0	17546	1829	64	3		3	ZAN	7	100349675	RNA	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	95508318	100349675	58788988	51	2476											
ZAN	7455	broad.mit.edu	37	chr7	100350033	100350033	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacagaaaaacccaccatcTccccagaaaaactcaccatc	17	4	2	18	0	2	2	1	0	1	2	4	2	2	2	6	0	2	0	6	0	4	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:100350033T>C	ENST00000348028.3	+	0	2470				ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000538115.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			ACCCACCATCTCCCCAGAAAA	0.522																																					.													.	ZAN-142	0			.						.						143	160	154					7																	100350033		1832	4071	5903			7455	.			ACCATCTCCCCAG	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100350033T>C		Somatic	176	9		WXS	Illumina HiSeq	Phase_I	659	35	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	t	4.272	0.049510	0.08243	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.62639	0.07;0.01;0.07	3.65	-0.219	0.13135	.	.	.	.	.	T	0.32376	0.0827	N	0.02315	-0.6	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19224	-1.0312	9	0.33141	T	0.24	.	8.1166	0.30946	0.0:0.5985:0.0:0.4015	.	769;769	F5H0T8;Q9Y493	.;ZAN_HUMAN	P	769	ENSP00000445943:S769P;ENSP00000445091:S769P;ENSP00000444427:S769P	ENSP00000423579:S769P	S	+	1	0	ZAN	100187969	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.302000	0.19192	-0.057000	0.13199	-0.859000	0.03014	TCC	.		0.522	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		C	100350033	T	C	100350033	1	2	28	0	1	0	0	0	0	0	0	0	17546	1551	54	3		3	ZAN	7	100350033	RNA	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	358	100350033	58788630	52	2477											
RINT1	60561	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	105189036	105189036	+	Frame_Shift_Del	DEL	A	A	-																															tgagccaaagcaactcccagAaaaatactctcttcctgcct																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:105189036delA	ENST00000257700.2	+	7	1106	c.875delA	c.(874-876)gaafs	p.E292fs		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	292	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CAACTCCCAGAAAAATACTCT	0.428																																					p.E292fs		.											.	RINT1-517	0			c.875delA						.						190	164	173					7																	105189036		2203	4300	6503	SO:0001589	frameshift_variant	60561	exon7			.	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.875delA	7.37:g.105189036delA	ENSP00000257700:p.Glu292fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	197	62	NM_021930	0	0	0	0	0	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Frame_Shift_Del	DEL	ENST00000257700.2	37	CCDS34726.1																																																																																			.		0.428	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		-	105189036	A	-	105189036	7	5	28	1	0	1	0	1	0	0	0	0	13408	246	9	0	901	0	RINT1	7	105189036	Frame_Shift_Del	DEL	A	TCGA-A4-A6HP-01A-11D-A31X-10	4839003	105189036	53949627	53	2478											
KEL	3792	broad.mit.edu	37	chr7	142640923	142640923	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acaattctagctcggagggaCcggacacagctcaggacaga	13	5	12	11	2	2	1	1	0	1	1	3	5	2	5	1	4	2	2	1	4	2	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:142640923C>T	ENST00000355265.2	-	14	2013	c.1539G>A	c.(1537-1539)cgG>cgA	p.R513R	KEL_ENST00000479768.2_5'Flank	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	513					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CTCGGAGGGACCGGACACAGC	0.562																																					p.R513R													.	KEL-93	0			c.G1539A						.						104	85	92					7																	142640923		2203	4300	6503	SO:0001819	synonymous_variant	3792	exon14			GAGGGACCGGACA	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1539G>A	7.37:g.142640923C>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	198	4	NM_000420	0	0	0	0	0	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	37	CCDS34766.1																																																																																			.		0.562	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		T	142640923	C	T	142640923	2	4	28	1	0	0	0	0	0	0	0	1	8163	494	18	2		2	KEL	7	142640923	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	37451887	142640923	16497740	54	2479											
SPAG11B	10407	bcgsc.ca	37	chr8	7308688	7308688	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccacacagatcctaaatGagggtcctcgagcctcccgg	10	7	10	14	2	0	2	0	1	0	1	5	3	4	2	5	2	1	0	5	2	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr8:7308688G>T	ENST00000297498.2	-	3	414	c.248C>A	c.(247-249)tCa>tAa	p.S83*	SPAG11B_ENST00000398462.2_Intron|SPAG11B_ENST00000528168.1_Nonsense_Mutation_p.S30*|SPAG11B_ENST00000361111.2_Intron|SPAG11B_ENST00000458665.1_Intron|SPAG11B_ENST00000359758.5_Intron	NM_016512.3	NP_057596.1	Q08648	SG11B_HUMAN	sperm associated antigen 11B	83					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				large_intestine(2)|lung(3)|urinary_tract(1)	6				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		GATCCTAAATGAGGGTCCTCG	0.458																																					p.S83X													.	SPAG11B-22	0			c.C248A						.						81	96	91					8																	7308688		2080	4190	6270	SO:0001587	stop_gained	10407	exon3			CTAAATGAGGGTC	AF168616	CCDS5964.1, CCDS5965.1, CCDS5966.1, CCDS5967.1, CCDS47774.1	8p23.1	2014-02-21	2007-03-15	2007-03-15	ENSG00000164871	ENSG00000164871			14534	protein-coding gene	gene with protein product	"epididymal protein 2B"	606560				8167223, 1693137	Standard	NM_058200		Approved	HE2, EP2, EP2C, EP2D, EDDM2B	uc003wrl.3	Q08648	OTTHUMG00000129219	ENST00000297498.2:c.248C>A	8.37:g.7308688G>T	ENSP00000297498:p.Ser83*	Somatic	317	2		WXS	Illumina HiSeq	Phase_1	623	19	NM_016512	0	0	0	0	0	E9PFH0|Q546A0|Q6ZYB2|Q9H4P8|Q9H4P9|Q9H4Q0|Q9H4Q1|Q9H4Q2|Q9NRT3|Q9NRV4|Q9NRV5|Q9NRV6|Q9NRV7|Q9NRV8	Nonsense_Mutation	SNP	ENST00000297498.2	37	CCDS5966.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195214	0.38806	.	.	ENSG00000164871	ENST00000297498;ENST00000528168	.	.	.	2.69	-0.306	0.12780	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	1.4268	0.02324	0.2199:0.4299:0.2162:0.134	.	.	.	.	X	83;30	.	ENSP00000297498:S83X	S	-	2	0	SPAG11B	7296098	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.109000	0.03309	-0.074000	0.12820	-1.314000	0.01303	TCA	.		0.458	SPAG11B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251390.2	NM_058202, NM_058200, NM_058201, NM_016512, NM_058203, NM_058206, NM_058207		T	7308688	G	T	7308688	4	4	28	1	0	0	0	0	0	1	0	0	15009	1294	45	4	276	4	SPAG11B	8	7308688	Nonsense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		7308688	139055334	55	2480											
TNKS	8658	broad.mit.edu	37	chr8	9605598	9605598	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgcaacagataagtgggCgtttactcccctccatgaag	13	9	9	10	1	0	2	0	1	0	1	2	2	2	2	3	1	3	2	3	1	5	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr8:9605598C>T	ENST00000310430.6	+	18	2734	c.2708C>T	c.(2707-2709)gCg>gTg	p.A903V	TNKS_ENST00000518281.1_Missense_Mutation_p.A666V	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	903					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		GATAAGTGGGCGTTTACTCCC	0.468																																					p.A903V													.	TNKS-660	0			c.C2708T						.						91	91	91					8																	9605598		2203	4300	6503	SO:0001583	missense	8658	exon18			AGTGGGCGTTTAC	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.2708C>T	8.37:g.9605598C>T	ENSP00000311579:p.Ala903Val	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	263	7	NM_003747	0	0	0	0	0	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	37	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	C	36	5.863179	0.97043	.	.	ENSG00000173273	ENST00000310430;ENST00000518281	T;T	0.70749	-0.51;2.38	5.88	5.88	0.94601	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.70701	0.3254	N	0.14661	0.345	0.80722	D	1	D	0.56968	0.978	P	0.55965	0.788	T	0.74968	-0.3483	10	0.66056	D	0.02	.	20.2381	0.98363	0.0:1.0:0.0:0.0	.	903	O95271	TNKS1_HUMAN	V	903;666	ENSP00000311579:A903V;ENSP00000429890:A666V	ENSP00000311579:A903V	A	+	2	0	TNKS	9643008	1.000000	0.71417	0.982000	0.44146	0.940000	0.58332	7.629000	0.83207	2.779000	0.95612	0.650000	0.86243	GCG	.		0.468	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		T	9605598	C	T	9605598	3	4	28	1	0	0	0	0	1	0	0	0	16351	768	27	1	2778	1	TNKS	8	9605598	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	2296910	9605598	136758424	56	2481											
SGK196	84197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	42977953	42977953	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgcccaggacgttctggAgacctaccagaaggtcttgg	9	8	12	12	1	2	2	0	0	2	2	2	4	2	3	3	4	2	1	3	4	2	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr8:42977953A>G	ENST00000331373.5	+	5	1241	c.986A>G	c.(985-987)gAg>gGg	p.E329G		NM_001277971.1|NM_032237.3	NP_001264900.1|NP_115613.1	Q9H5K3	SG196_HUMAN	protein-O-mannose kinase	329	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|carbohydrate phosphorylation (GO:0046835)|learning or memory (GO:0007611)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|protein O-linked glycosylation (GO:0006493)|sensory perception of pain (GO:0019233)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|carbohydrate kinase activity (GO:0019200)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|protein kinase activity (GO:0004672)										GACGTTCTGGAGACCTACCAG	0.478																																					p.E329G		.											.	.	0			c.A986G						.						87	94	91					8																	42977953		2203	4300	6503	SO:0001583	missense	0	exon5			TTCTGGAGACCTA		CCDS6141.1	8p11.21	2013-08-22			ENSG00000185900	ENSG00000185900			26267	protein-coding gene	gene with protein product		615247				16879967, 23519211	Standard	NM_001277971		Approved	FLJ23356, SgK196		Q9H5K3	OTTHUMG00000164100	ENST00000331373.5:c.986A>G	8.37:g.42977953A>G	ENSP00000331258:p.Glu329Gly	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	64	23	NM_032237	0	0	0	0	0		Missense_Mutation	SNP	ENST00000331373.5	37	CCDS6141.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.439110	0.25900	.	.	ENSG00000185900	ENST00000331373	T	0.23348	1.91	5.45	5.45	0.79879	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.258956	0.44483	D	0.000449	T	0.19446	0.0467	L	0.29908	0.895	0.26493	N	0.974911	B	0.22604	0.072	B	0.19391	0.025	T	0.12293	-1.0553	9	.	.	.	-20.8671	13.4611	0.61227	1.0:0.0:0.0:0.0	.	329	Q9H5K3	SG196_HUMAN	G	329	ENSP00000331258:E329G	.	E	+	2	0	AC113191.1	43097110	1.000000	0.71417	0.760000	0.31359	0.425000	0.31504	3.808000	0.55598	2.065000	0.61736	0.482000	0.46254	GAG	.		0.478	POMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377291.2	NM_032237		G	42977953	A	G	42977953	3	3	28	1	0	0	0	0	1	0	0	0	14240	304	11	3	992	3	SGK196	8	42977953	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	33372355	42977953	103386069	57	2482											
FER1L6	654463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	124992806	124992806	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aaatgaacgaaggctttgggGaaggtgtgtcattcaggggc	11	9	16	5	1	2	1	2	1	0	0	2	3	2	2	0	6	1	1	0	6	4	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr8:124992806G>A	ENST00000522917.1	+	11	1371	c.1165G>A	c.(1165-1167)Gaa>Aaa	p.E389K	FER1L6_ENST00000399018.1_Missense_Mutation_p.E389K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	389						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			AGGCTTTGGGGAAGGTGTGTC	0.512											OREG0018964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E389K		.											.	FER1L6-100	0			c.G1165A						.						161	159	160					8																	124992806		1882	4115	5997	SO:0001583	missense	654463	exon11			TTTGGGGAAGGTG	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.1165G>A	8.37:g.124992806G>A	ENSP00000428280:p.Glu389Lys	Somatic	115	0	1538	WXS	Illumina HiSeq	Phase_I	278	93	NM_001039112	0	0	0	0	0		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	35	5.527427	0.96431	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.83673	-1.75;-1.75	5.53	5.53	0.82687	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000003	D	0.91882	0.7430	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90993	0.4836	10	0.40728	T	0.16	.	19.466	0.94939	0.0:0.0:1.0:0.0	.	389	Q2WGJ9	FR1L6_HUMAN	K	389	ENSP00000428280:E389K;ENSP00000381982:E389K	ENSP00000381982:E389K	E	+	1	0	FER1L6	125061987	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.813000	0.99286	2.607000	0.88179	0.655000	0.94253	GAA	.		0.512	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	124992806	G	A	124992806	3	1	28	1	0	0	0	0	1	0	0	0	5834	1175	41	2	1203	2	FER1L6	8	124992806	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	82014853	124992806	21371216	58	2483											
AQP3	360	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	33443353	33443354	+	Frame_Shift_Ins	INS	-	-	A																															aaactattccagcacccaagINSaaggctcccagcgtctgtgc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:33443353_33443354insA	ENST00000297991.4	-	3	418_419	c.338_339insT	c.(337-339)ttcfs	p.F113fs	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	113					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		CAGCACCCAAGAAGGCTCCCAG	0.589																																					p.F113fs		.											.	AQP3-90	0			c.339_340insT						.																																			SO:0001589	frameshift_variant	360	exon3			.		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.339dupT	9.37:g.33443355_33443355dupA	ENSP00000297991:p.Phe113fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	148	49	NM_004925	0	0	0	0	0	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Frame_Shift_Ins	INS	ENST00000297991.4	37	CCDS6542.1																																																																																			.		0.589	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925		A	33443354	-	A	33443353	7	5	28	1	0	1	1	0	0	0	0	0	827	933	33	0	555	0	AQP3	9	33443353	Frame_Shift_Ins	INS	-	TCGA-A4-A6HP-01A-11D-A31X-10		33443353	107770078	59	2484											
ZBTB5	9925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	37441549	37441549	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgaggctcaggtgagctcaGgggctcagatttaaccacca	10	8	12	11	0	3	3	3	2	0	1	3	3	3	3	2	4	2	3	2	4	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:37441549G>T	ENST00000307750.4	-	2	1188	c.1000C>A	c.(1000-1002)Ctg>Atg	p.L334M		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	334					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		GGTGAGCTCAGGGGCTCAGAT	0.522																																					p.L334M		.											.	ZBTB5-92	0			c.C1000A						.						103	94	97					9																	37441549		2203	4300	6503	SO:0001583	missense	9925	exon2			AGCTCAGGGGCTC	AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.1000C>A	9.37:g.37441549G>T	ENSP00000307604:p.Leu334Met	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	45	12	NM_014872	0	0	0	1	1		Missense_Mutation	SNP	ENST00000307750.4	37	CCDS6610.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155723	0.38021	.	.	ENSG00000168795	ENST00000307750	T	0.16196	2.36	5.49	1.43	0.22495	.	0.167314	0.39985	N	0.001220	T	0.22360	0.0539	N	0.24115	0.695	0.48395	D	0.999648	D	0.71674	0.998	D	0.80764	0.994	T	0.01225	-1.1413	10	0.29301	T	0.29	.	10.2477	0.43352	0.3912:0.0:0.6088:0.0	.	334	O15062	ZBTB5_HUMAN	M	334	ENSP00000307604:L334M	ENSP00000307604:L334M	L	-	1	2	ZBTB5	37431549	0.995000	0.38212	0.998000	0.56505	0.932000	0.56968	1.979000	0.40608	0.457000	0.26962	-0.136000	0.14681	CTG	.		0.522	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		T	37441549	G	T	37441549	3	4	28	1	0	0	0	0	1	0	0	0	17583	991	35	4	1037	4	ZBTB5	9	37441549	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	3998196	37441549	103771882	60	2485											
ABCA1	19	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	107578436	107578436	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taacttacttcttccagggtCgtctctgagatgccataact	9	14	7	11	1	2	1	0	1	2	1	5	2	3	1	2	1	4	0	2	1	3	5	rs548468204	byFrequency	TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:107578436C>T	ENST00000374736.3	-	25	4120	c.3726G>A	c.(3724-3726)acG>acA	p.T1242T		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1242					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CTTCCAGGGTCGTCTCTGAGA	0.483													C|||	4	0.000798722	0	0	5008	,	,		19115	0		0	False		,,,				2504	0.0041				p.T1242T		.											.	ABCA1-1016	0			c.G3726A						.						166	178	174					9																	107578436		2203	4300	6503	SO:0001819	synonymous_variant	19	exon25			CAGGGTCGTCTCT	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.3726G>A	9.37:g.107578436C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	120	51	NM_005502	0	0	0	0	0	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			.		0.483	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107578436	C	T	107578436	2	4	28	1	0	0	0	0	0	0	0	1	28	871	31	1		1	ABCA1	9	107578436	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	70136887	107578436	33634995	61	2486											
PTPN3	5774	broad.mit.edu	37	chr9	112185015	112185015	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccagttgggagtaatgggAggggaacgagaaggcagact	13	6	17	5	1	0	2	0	0	0	2	0	6	0	5	1	5	2	3	1	5	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:112185015A>G	ENST00000374541.2	-	13	1223	c.1119T>C	c.(1117-1119)ccT>ccC	p.P373P	PTPN3_ENST00000262539.3_Intron|PTPN3_ENST00000446349.1_Intron|PTPN3_ENST00000412145.1_Silent_p.P242P	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	373					negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GAGTAATGGGAGGGGAACGAG	0.413																																					p.P373P													.	PTPN3-229	0			c.T1119C						.						160	146	151					9																	112185015		2203	4300	6503	SO:0001819	synonymous_variant	5774	exon13			AATGGGAGGGGAA		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.1119T>C	9.37:g.112185015A>G		Somatic	46	10		WXS	Illumina HiSeq	Phase_I	109	28	NM_002829	0	0	0	0	0	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			.		0.413	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			G	112185015	A	G	112185015	2	3	28	1	0	0	0	0	0	0	0	1	12821	291	11	3		3	PTPN3	9	112185015	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	4606579	112185015	29028416	62	2487											
COQ4	51117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131095205	131095205	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgggtgcattctttggaccGatccgacttggcgctcagta	6	12	12	11	3	2	0	1	0	1	0	3	3	3	1	2	3	1	3	2	3	1	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:131095205G>A	ENST00000300452.3	+	6	932	c.609G>A	c.(607-609)ccG>ccA	p.P203P	COQ4_ENST00000461102.1_3'UTR	NM_016035.3	NP_057119			coenzyme Q4											endometrium(4)|large_intestine(1)|lung(4)	9						TCTTTGGACCGATCCGACTTG	0.557																																					p.P203P		.											.	COQ4-90	0			c.G609A						.						194	158	171					9																	131095205		2203	4300	6503	SO:0001819	synonymous_variant	51117	exon6			TGGACCGATCCGA	AF151850	CCDS6898.1	9q34.2	2013-10-18	2013-10-18		ENSG00000167113	ENSG00000167113			19693	protein-coding gene	gene with protein product		612898	"coenzyme Q4 homolog (yeast)", "coenzyme Q4 homolog (S. cerevisiae)"			11469793, 18474229	Standard	NM_016035		Approved	CGI-92	uc004bur.4	Q9Y3A0	OTTHUMG00000020743	ENST00000300452.3:c.609G>A	9.37:g.131095205G>A		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	184	68	NM_016035	0	0	95	169	74		Silent	SNP	ENST00000300452.3	37	CCDS6898.1																																																																																			.		0.557	COQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054427.1	NM_016035		A	131095205	G	A	131095205	2	1	28	1	0	0	0	0	0	0	0	1	3753	1045	37	1		1	COQ4	9	131095205	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	18910190	131095205	10118226	63	2488											
SURF2	6835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	136227264	136227264	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaggccactgatgagagcaGgagagagacgaccgtgtacc	13	4	15	9	2	0	4	0	2	0	3	0	9	0	4	3	2	2	2	3	2	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:136227264G>T	ENST00000371964.4	+	5	682	c.641G>T	c.(640-642)aGg>aTg	p.R214M		NM_017503.3	NP_059973.4	Q15527	SURF2_HUMAN	surfeit 2	214						nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(145;4.87e-07)|Epithelial(140;4.02e-06)|all cancers(34;3.71e-05)		GATGAGAGCAGGAGAGAGACG	0.557																																					p.R214M		.											.	SURF2-226	0			c.G641T						.						131	111	118					9																	136227264		2203	4300	6503	SO:0001583	missense	6835	exon5			AGAGCAGGAGAGA		CCDS6967.1	9q33-q34	2008-07-21			ENSG00000148291	ENSG00000148291			11475	protein-coding gene	gene with protein product	"surfeit locus protein 2"	185630					Standard	NM_017503		Approved		uc004cdi.2	Q15527	OTTHUMG00000020867	ENST00000371964.4:c.641G>T	9.37:g.136227264G>T	ENSP00000361032:p.Arg214Met	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	52	19	NM_017503	0	0	8	72	64	Q6IBP9|Q96CD1	Missense_Mutation	SNP	ENST00000371964.4	37	CCDS6967.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.190148	0.38707	.	.	ENSG00000148291	ENST00000371964	T	0.33216	1.42	2.84	0.71	0.18157	.	0.792035	0.11077	N	0.602308	T	0.28566	0.0707	L	0.51422	1.61	0.09310	N	1	P	0.50710	0.938	P	0.45343	0.477	T	0.14227	-1.0480	10	0.54805	T	0.06	-4.7868	5.4059	0.16320	0.1238:0.2056:0.6706:0.0	.	214	Q15527	SURF2_HUMAN	M	214	ENSP00000361032:R214M	ENSP00000361032:R214M	R	+	2	0	SURF2	135217085	0.005000	0.15991	0.000000	0.03702	0.030000	0.12068	1.572000	0.36461	0.015000	0.14971	0.462000	0.41574	AGG	.		0.557	SURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054883.1	NM_017503		T	136227264	G	T	136227264	3	4	28	1	0	0	0	0	1	0	0	0	15436	1000	35	4	659	4	SURF2	9	136227264	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	5132059	136227264	4986167	64	2489											
NOTCH1	4851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139407915	139407915	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgccgccgttgacacaaGggttggattcacactcattg	9	10	12	10	2	2	1	2	1	0	0	2	2	2	2	2	3	1	2	2	3	1	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:139407915G>T	ENST00000277541.6	-	14	2357	c.2282C>A	c.(2281-2283)cCt>cAt	p.P761H		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	761	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTTGACACAAGGGTTGGATTC	0.587			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.P761H		.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1-5459	0			c.C2282A						.						104	118	113					9																	139407915		2187	4274	6461	SO:0001583	missense	4851	exon14			ACACAAGGGTTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2282C>A	9.37:g.139407915G>T	ENSP00000277541:p.Pro761His	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	68	20	NM_017617	0	0	0	0	0	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.497270	0.64186	.	.	ENSG00000148400	ENST00000277541	D	0.93189	-3.18	4.76	4.76	0.60689	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98725	1.0710	10	0.72032	D	0.01	.	16.7491	0.85480	0.0:0.0:1.0:0.0	.	761	P46531	NOTC1_HUMAN	H	761	ENSP00000277541:P761H	ENSP00000277541:P761H	P	-	2	0	NOTCH1	138527736	1.000000	0.71417	1.000000	0.80357	0.223000	0.24884	9.349000	0.97066	2.199000	0.70637	0.455000	0.32223	CCT	.		0.587	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		T	139407915	G	T	139407915	3	4	28	1	0	0	0	0	1	0	0	0	10573	1000	35	4	5469	4	NOTCH1	9	139407915	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	3180651	139407915	1805516	65	2490											
BMS1	9790	broad.mit.edu;bcgsc.ca	37	chr10	43294061	43294061	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtggaggccccccatgactgGgatttagaggaggtaagtct	9	9	15	8	0	1	2	0	1	1	1	1	5	1	5	3	5	0	1	3	5	2	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:43294061G>T	ENST00000374518.5	+	12	2298	c.2235G>T	c.(2233-2235)tgG>tgT	p.W745C		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	745					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CCCATGACTGGGATTTAGAGG	0.428																																					p.W745C													.	BMS1-93	0			c.G2235T						.						91	97	95					10																	43294061		2203	4300	6503	SO:0001583	missense	9790	exon12			TGACTGGGATTTA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2235G>T	10.37:g.43294061G>T	ENSP00000363642:p.Trp745Cys	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	173	7	NM_014753	0	0	0	0	0	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986911	0.74589	.	.	ENSG00000165733	ENST00000374518	T	0.53857	0.6	5.92	5.92	0.95590	.	0.060191	0.64402	D	0.000001	T	0.76314	0.3970	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77219	-0.2668	10	0.66056	D	0.02	.	20.3734	0.98896	0.0:0.0:1.0:0.0	.	745	Q14692	BMS1_HUMAN	C	745	ENSP00000363642:W745C	ENSP00000363642:W745C	W	+	3	0	BMS1	42614067	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	9.218000	0.95166	2.820000	0.97059	0.650000	0.86243	TGG	.		0.428	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		T	43294061	G	T	43294061	3	4	28	1	0	0	0	0	1	0	0	0	1473	1241	43	4	2277	4	BMS1	10	43294061	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		43294061	92240686	66	2491											
C10orf12	26148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	98741939	98741939	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctagcaaggaaatcacctcTcacgaggaaggaggtggaga	14	5	13	9	1	2	1	2	0	1	1	3	6	2	4	2	5	1	1	2	5	4	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:98741939T>G	ENST00000286067.2	+	1	899	c.792T>G	c.(790-792)tcT>tcG	p.S264S		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	264										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		AAATCACCTCTCACGAGGAAG	0.512																																					p.S264S		.											.	C10orf12-92	0			c.T792G						.						89	90	90					10																	98741939		2203	4300	6503	SO:0001819	synonymous_variant	26148	exon1			CACCTCTCACGAG	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.792T>G	10.37:g.98741939T>G		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	110	37	NM_015652	0	0	0	0	0	Q9H945|Q9Y457	Silent	SNP	ENST00000286067.2	37	CCDS7452.1																																																																																			.		0.512	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		G	98741939	T	G	98741939	2	3	28	1	0	0	0	0	0	0	0	1	1593	1538	54	5		5	C10orf12	10	98741939	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	55447878	98741939	36792808	67	2492											
PPRC1	23082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103906723	103906723	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccgatggaatgtcaagcGccatcaggacatcaccatca	12	7	8	14	2	4	0	4	0	0	0	5	3	5	2	3	2	1	0	3	2	2	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:103906723G>A	ENST00000278070.2	+	9	4013	c.3974G>A	c.(3973-3975)cGc>cAc	p.R1325H	PPRC1_ENST00000413464.2_Intron|PPRC1_ENST00000370012.1_Missense_Mutation_p.R292H|PPRC1_ENST00000489648.1_Intron	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1325					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		AATGTCAAGCGCCATCAGGAC	0.602																																					p.R1325H		.											.	PPRC1-227	0			c.G3974A						.						59	57	58					10																	103906723		2203	4300	6503	SO:0001583	missense	23082	exon9			TCAAGCGCCATCA	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.3974G>A	10.37:g.103906723G>A	ENSP00000278070:p.Arg1325His	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	79	22	NM_015062	0	0	6	7	1	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.057347	0.55325	.	.	ENSG00000148840	ENST00000278070;ENST00000370012	T;T	0.29655	1.92;1.56	5.76	4.85	0.62838	.	0.107026	0.64402	D	0.000005	T	0.14227	0.0344	L	0.27053	0.805	0.80722	D	1	P;B	0.37141	0.584;0.449	B;B	0.24541	0.054;0.024	T	0.05971	-1.0853	10	0.22109	T	0.4	.	5.5119	0.16886	0.2641:0.0:0.7359:0.0	.	1205;1325	Q5VV67-2;Q5VV67	.;PPRC1_HUMAN	H	1325;292	ENSP00000278070:R1325H;ENSP00000359029:R292H	ENSP00000278070:R1325H	R	+	2	0	PPRC1	103896713	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.757000	0.68766	2.724000	0.93272	0.462000	0.41574	CGC	.		0.602	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		A	103906723	G	A	103906723	3	1	28	1	0	0	0	0	1	0	0	0	12439	1087	38	1	4008	1	PPRC1	10	103906723	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	5164784	103906723	31628024	68	2493											
PDCD4	27250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	112655819	112655819	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggctggaataatttccaaAcaactcagagatctttgtcc	13	11	7	10	0	2	1	1	0	1	1	4	3	4	2	2	2	2	1	2	2	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:112655819A>G	ENST00000280154.7	+	11	1597	c.1323A>G	c.(1321-1323)aaA>aaG	p.K441K	MIR4680_ENST00000580906.1_RNA|PDCD4_ENST00000393104.2_Silent_p.K430K	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	441	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		TAATTTCCAAACAACTCAGAG	0.358																																					p.K441K	Ovarian(115;1498 1603 9363 40056 40885)	.											.	PDCD4-291	0			c.A1323G						.						78	78	78					10																	112655819		2202	4300	6502	SO:0001819	synonymous_variant	27250	exon11			TTCCAAACAACTC	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"nuclear antigen H731"	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.1323A>G	10.37:g.112655819A>G		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	205	64	NM_014456	0	0	13	26	13	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																			.		0.358	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		G	112655819	A	G	112655819	2	3	28	1	0	0	0	0	0	0	0	1	11647	40	2	3		3	PDCD4	10	112655819	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	8749096	112655819	22878928	69	2494											
SLC22A10	387775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63065116	63065116	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggacagataatcctgggAggcttggcttatgtcttccg	8	13	12	8	1	1	1	0	0	1	1	3	3	3	3	2	4	0	2	2	4	2	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:63065116A>T	ENST00000332793.6	+	4	749	c.747A>T	c.(745-747)ggA>ggT	p.G249G	SLC22A10_ENST00000525620.1_3'UTR|SLC22A10_ENST00000544661.1_Silent_p.G94G|SLC22A10_ENST00000535888.1_Silent_p.G39G|SLC22A10_ENST00000526800.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	249						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	TAATCCTGGGAGGCTTGGCTT	0.463																																					p.G249G		.											.	SLC22A10-92	0			c.A747T						.						159	149	152					11																	63065116		1933	4127	6060	SO:0001819	synonymous_variant	387775	exon4			CCTGGGAGGCTTG	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.747A>T	11.37:g.63065116A>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	156	64	NM_001039752	0	0	0	0	0	Q68CJ0	Silent	SNP	ENST00000332793.6	37	CCDS41661.1																																																																																			.		0.463	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		T	63065116	A	T	63065116	2	4	28	1	0	0	0	0	0	0	0	1	14473	291	11	5		5	SLC22A10	11	63065116	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		63065116	71941400	70	2495											
SLC22A10	387775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63071636	63071636	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcggctgttctgctgctActttttccagtgttgctgtt	4	18	10	9	1	1	0	0	0	1	0	3	1	2	0	1	1	4	7	1	1	2	6			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:63071636A>G	ENST00000332793.6	+	8	1344	c.1342A>G	c.(1342-1344)Act>Gct	p.T448A	SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000544661.1_Silent_p.L246L|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000526800.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	448						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	TTCTGCTGCTACTTTTTCCAG	0.483																																					p.T448A		.											.	SLC22A10-92	0			c.A1342G						.						212	217	215					11																	63071636		2073	4247	6320	SO:0001583	missense	387775	exon8			GCTGCTACTTTTT	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.1342A>G	11.37:g.63071636A>G	ENSP00000327569:p.Thr448Ala	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_001039752	0	0	0	0	0	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.853818	0.00066	.	.	ENSG00000184999	ENST00000332793	T	0.74526	-0.85	3.05	-6.11	0.02131	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.214933	0.39020	N	0.001483	T	0.27594	0.0678	N	0.00525	-1.395	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.33137	-0.9880	10	0.05351	T	0.99	.	5.742	0.18100	0.3421:0.0:0.1242:0.5336	.	448	Q63ZE4	S22AA_HUMAN	A	448	ENSP00000327569:T448A	ENSP00000327569:T448A	T	+	1	0	SLC22A10	62828212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.437000	0.01018	-3.799000	0.00105	-1.485000	0.00982	ACT	.		0.483	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		G	63071636	A	G	63071636	3	3	28	1	0	0	0	0	1	0	0	0	14473	391	14	3	1372	3	SLC22A10	11	63071636	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	6520	63071636	71934880	71	2496											
UNC93B1	81622	broad.mit.edu	37	chr11	67763107	67763107	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccagtcttgttcagggcActgcccacaccccaaagggc	9	7	10	15	0	2	0	1	0	1	0	3	0	3	0	4	2	1	2	4	2	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:67763107A>G	ENST00000227471.2	-	10	1414	c.1335T>C	c.(1333-1335)agT>agC	p.S445S	UNC93B1_ENST00000530331.1_5'UTR	NM_030930.2	NP_112192.2	Q9H1C4	UN93B_HUMAN	unc-93 homolog B1 (C. elegans)	446					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	early phagosome (GO:0032009)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)											TGTTCAGGGCACTGCCCACAC	0.617																																					.													.	.	0			.						.						10	10	10					11																	67763107		1758	3730	5488	SO:0001819	synonymous_variant	81622	.			CAGGGCACTGCCC	AJ271326	CCDS73334.1	11q13.2	2014-09-17	2001-11-28		ENSG00000110057	ENSG00000110057			13481	protein-coding gene	gene with protein product		608204	"unc93 (C. elegans) homolog B1"			11867227	Standard	NM_030930		Approved	UNC93	uc001omw.1	Q9H1C4	OTTHUMG00000167472	ENST00000227471.2:c.1335T>C	11.37:g.67763107A>G		Somatic	61	1		WXS	Illumina HiSeq	Phase_I	161	6	.	1	0	142	143	0	O95764|Q569H6|Q710D4	Silent	SNP	ENST00000227471.2	37																																																																																				.		0.617	UNC93B1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_030930		G	67763107	A	G	67763107	2	3	28	1	0	0	0	0	0	0	0	1	17030	156	6	3		3	UNC93B1	11	67763107	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	4691471	67763107	67243409	72	2497											
MAML2	84441	broad.mit.edu	37	chr11	95825254	95825254	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttgttgctgctgctgctgCtgttgttgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4	rs61749250		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:95825254C>T	ENST00000524717.1	-	2	3225	c.1941G>A	c.(1939-1941)caG>caA	p.Q647Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	647					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q647Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgttgttgct	0.512			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q647Q				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	1	Substitution - coding silent(1)	endometrium(1)	c.G1941A						.	C		0,4198		0,0,2099	35	40	38		1941	1.7	0.1	11	dbSNP_129	38	5,8237		0,5,4116	no	coding-synonymous	MAML2	NM_032427.1		0,5,6215	TT,TC,CC		0.0607,0.0,0.0402		647/1157	95825254	5,12435	2099	4121	6220	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1941G>A	11.37:g.95825254C>T		Somatic	40	1		WXS	Illumina HiSeq	Phase_I	76	4	NM_032427	0	0	1	1	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.512	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825254	C	T	95825254	2	4	28	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825254	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	28062147	95825254	39181262	73	2498											
NPAT	4863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	108043550	108043550	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttgctagaaggtttatcatCagtattttgggactcagggt	9	15	12	5	0	3	1	3	0	0	1	3	2	3	2	0	3	1	4	0	3	4	7			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:108043550C>T	ENST00000278612.8	-	13	2266	c.2161G>A	c.(2161-2163)Gat>Aat	p.D721N	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	721					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		GGTTTATCATCAGTATTTTGG	0.428																																					p.D721N		.											.	NPAT-117	0			c.G2161A						.						120	110	113					11																	108043550		1892	4120	6012	SO:0001583	missense	4863	exon13			TATCATCAGTATT	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.2161G>A	11.37:g.108043550C>T	ENSP00000278612:p.Asp721Asn	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	66	21	NM_002519	0	0	0	0	0	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	1.672	-0.508824	0.04231	.	.	ENSG00000149308	ENST00000278612	T	0.03982	3.74	5.55	-1.3	0.09259	.	1.001340	0.08051	N	0.996678	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.49204	-0.8964	10	0.18710	T	0.47	3.2313	6.8937	0.24245	0.1138:0.3772:0.0:0.509	.	721;721	B9EG70;Q14207	.;NPAT_HUMAN	N	721	ENSP00000278612:D721N	ENSP00000278612:D721N	D	-	1	0	NPAT	107548760	0.145000	0.22656	0.022000	0.16811	0.316000	0.28119	0.773000	0.26661	-0.127000	0.11661	-0.136000	0.14681	GAT	.		0.428	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		T	108043550	C	T	108043550	3	4	28	1	0	0	0	0	1	0	0	0	10592	826	29	2	2146	2	NPAT	11	108043550	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	12218296	108043550	26962966	74	2499											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118773516	118773516	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggggcactgccaggggcCgggggtggcggcggcggcag	3	2	25	11	5	0	0	0	0	0	0	0	0	0	0	2	11	1	2	2	11	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:118773516C>A	ENST00000334801.3	-	6	1900	c.936G>T	c.(934-936)ccG>ccT	p.P312P	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	312	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TGCCAGGGGCCGGGGGTGGCG	0.731																																					p.P312P		.											.	BCL9L-229	0			c.G936T						.						5	7	6					11																	118773516		2014	4005	6019	SO:0001819	synonymous_variant	283149	exon6			AGGGGCCGGGGGT	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.936G>T	11.37:g.118773516C>A		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	10	5	NM_182557	0	0	0	0	0	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			.		0.731	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118773516	C	A	118773516	2	1	28	1	0	0	0	0	0	0	0	1	1383	639	23	4		4	BCL9L	11	118773516	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	10729966	118773516	16233000	75	2500											
RECQL	5965	broad.mit.edu	37	chr12	21630777	21630777	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tattaaaagaagctgtaaaaGtaaaacacttttcaatgcac	19	11	5	6	0	1	1	1	0	0	1	1	1	1	1	0	0	3	4	0	0	9	6			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:21630777G>T	ENST00000444129.2	-	7	1295	c.827C>A	c.(826-828)aCt>aAt	p.T276N	RECQL_ENST00000421138.2_Missense_Mutation_p.T276N	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	276					DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						AGCTGTAAAAGTAAAACACTT	0.378								Other identified genes with known or suspected DNA repair function																													p.T276N													.	RECQL-228	0			c.C827A						.						64	63	63					12																	21630777		2203	4300	6503	SO:0001583	missense	5965	exon8			GTAAAAGTAAAAC	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"DNA helicase Q1-like"	600537	"RecQ protein-like (DNA helicase Q1-like)"			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.827C>A	12.37:g.21630777G>T	ENSP00000416739:p.Thr276Asn	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	219	4	NM_032941	0	0	4	4	0	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	37	CCDS31756.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.453790	0.84209	.	.	ENSG00000004700	ENST00000444129;ENST00000421138	T;T	0.57907	0.37;0.37	4.7	4.7	0.59300	DEAD-like helicase (1);	0.091999	0.85682	D	0.000000	T	0.60353	0.2262	M	0.70595	2.14	0.80722	D	1	P	0.51240	0.943	P	0.46850	0.529	T	0.65352	-0.6189	10	0.48119	T	0.1	-8.019	18.1964	0.89823	0.0:0.0:1.0:0.0	.	276	P46063	RECQ1_HUMAN	N	276	ENSP00000416739:T276N;ENSP00000395449:T276N	ENSP00000395449:T276N	T	-	2	0	RECQL	21522044	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.470000	0.80973	2.596000	0.87737	0.650000	0.86243	ACT	.		0.378	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		T	21630777	G	T	21630777	3	4	28	1	0	0	0	0	1	0	0	0	13233	1029	36	4	1158	4	RECQL	12	21630777	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		21630777	112221118	76	2501											
SOX5	6660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	23757377	23757377	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgaatgctggtaggagAtacagcagcaccaaggttgc	11	9	14	7	0	0	2	0	1	0	1	0	3	0	2	1	3	5	5	1	3	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:23757377A>G	ENST00000451604.2	-	9	1209	c.1108T>C	c.(1108-1110)Tct>Cct	p.S370P	SOX5_ENST00000309359.1_Missense_Mutation_p.S357P|SOX5_ENST00000537393.1_Missense_Mutation_p.S335P|SOX5_ENST00000381381.2_Missense_Mutation_p.S357P|SOX5_ENST00000545921.1_Missense_Mutation_p.S360P|SOX5_ENST00000541536.1_Missense_Mutation_p.S357P|SOX5_ENST00000546136.1_Missense_Mutation_p.S357P			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	370					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	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)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						CTGGTAGGAGATACAGCAGCA	0.502																																					p.S370P		.											.	SOX5-655	0			c.T1108C						.						164	133	144					12																	23757377		2203	4300	6503	SO:0001583	missense	6660	exon9			TAGGAGATACAGC	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.1108T>C	12.37:g.23757377A>G	ENSP00000398273:p.Ser370Pro	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	125	33	NM_006940	0	0	0	0	0	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520861	0.85495	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921	D;D;D;D;D;D;D	0.97831	-4.54;-4.54;-4.24;-4.55;-4.56;-4.24;-4.55	6.16	6.16	0.99307	.	0.171135	0.53938	D	0.000045	D	0.98251	0.9421	M	0.64567	1.98	0.53688	D	0.999975	D;P;D	0.60160	0.987;0.945;0.978	P;D;P	0.68621	0.907;0.959;0.809	D	0.98503	1.0615	10	0.41790	T	0.15	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	335;357;370	F5H0I3;P35711-4;P35711	.;.;SOX5_HUMAN	P	357;357;357;370;322;335;357;360	ENSP00000437487:S357P;ENSP00000308927:S357P;ENSP00000370788:S357P;ENSP00000398273:S370P;ENSP00000439832:S335P;ENSP00000441973:S357P;ENSP00000443520:S360P	ENSP00000308927:S357P	S	-	1	0	SOX5	23648644	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	5.618000	0.67722	2.367000	0.80283	0.528000	0.53228	TCT	.		0.502	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		G	23757377	A	G	23757377	3	3	28	1	0	0	0	0	1	0	0	0	14986	333	12	3	1221	3	SOX5	12	23757377	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	2126600	23757377	110094518	77	2502											
ADCY6	112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49168249	49168249	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaactgcggtgctatgtGcccgtgagcggacaatgctg	7	9	14	11	3	0	1	0	1	0	0	0	2	0	2	2	2	7	2	2	2	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:49168249G>A	ENST00000307885.4	-	13	2913	c.2219C>T	c.(2218-2220)gCa>gTa	p.A740V	ADCY6_ENST00000552090.1_5'UTR|MIR4701_ENST00000583094.1_RNA|ADCY6_ENST00000357869.3_Missense_Mutation_p.A740V|ADCY6_ENST00000550422.1_Missense_Mutation_p.A740V	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	740					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						GGTGCTATGTGCCCGTGAGCG	0.537																																					p.A740V		.											.	ADCY6-90	0			c.C2219T						.						134	112	119					12																	49168249		2203	4300	6503	SO:0001583	missense	112	exon14			CTATGTGCCCGTG		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"Adenylate cyclases"	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.2219C>T	12.37:g.49168249G>A	ENSP00000311405:p.Ala740Val	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	182	88	NM_020983	0	0	4	6	2	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	37	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.103172	0.37145	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.39787	1.06;1.06;1.06	4.42	3.51	0.40186	.	0.303154	0.30820	N	0.008801	T	0.28896	0.0717	L	0.36672	1.1	0.28148	N	0.929491	B;B	0.26041	0.14;0.004	B;B	0.28139	0.086;0.01	T	0.18618	-1.0331	10	0.13470	T	0.59	.	8.2466	0.31693	0.202:0.0:0.798:0.0	.	740;740	O43306-2;O43306	.;ADCY6_HUMAN	V	740	ENSP00000350536:A740V;ENSP00000446730:A740V;ENSP00000311405:A740V	ENSP00000311405:A740V	A	-	2	0	ADCY6	47454516	0.679000	0.27596	1.000000	0.80357	0.892000	0.51952	2.661000	0.46758	0.963000	0.38082	0.561000	0.74099	GCA	.		0.537	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		A	49168249	G	A	49168249	3	1	28	1	0	0	0	0	1	0	0	0	298	1319	46	2	1323	2	ADCY6	12	49168249	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	25410872	49168249	84683646	78	2503											
HOXC4	3221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54447788	54447788	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaatattcgcaaaatagcTacatccctgaacacagtccg	16	8	6	11	2	0	2	0	1	0	1	3	2	2	2	2	0	3	2	2	0	8	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:54447788T>A	ENST00000430889.2	+	1	128	c.82T>A	c.(82-84)Tac>Aac	p.Y28N	HOXC4_ENST00000609810.1_Missense_Mutation_p.Y28N|HOXC4_ENST00000303406.4_Missense_Mutation_p.Y28N	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	28					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						GCAAAATAGCTACATCCCTGA	0.493																																					p.Y28N		.											.	HOXC4-91	0			c.T82A						.						127	129	128					12																	54447788		2203	4300	6503	SO:0001583	missense	3221	exon3			AATAGCTACATCC		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.82T>A	12.37:g.54447788T>A	ENSP00000399808:p.Tyr28Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	205	40	NM_014620	0	0	1	2	1		Missense_Mutation	SNP	ENST00000430889.2	37	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710126	0.68730	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	D;D	0.83992	-1.79;-1.79	3.41	3.41	0.39046	.	0.152719	0.44902	D	0.000404	D	0.92014	0.7470	M	0.92317	3.295	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	D	0.93212	0.6601	10	0.72032	D	0.01	.	11.785	0.52037	0.0:0.0:0.0:1.0	.	28	P09017	HXC4_HUMAN	N	28	ENSP00000305973:Y28N;ENSP00000399808:Y28N	ENSP00000305973:Y28N	Y	+	1	0	HOXC4	52734055	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.592000	0.61027	1.775000	0.52247	0.379000	0.24179	TAC	.		0.493	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			A	54447788	T	A	54447788	3	1	28	1	0	0	0	0	1	0	0	0	7334	1522	53	5	84	5	HOXC4	12	54447788	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	5279539	54447788	79404107	79	2504											
NAB2	4665	broad.mit.edu	37	chr12	57485520	57485520	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcaggtgggactgggggTggtccagaccgactggagcc	7	5	19	10	1	0	1	0	0	0	1	1	4	1	3	3	6	2	2	3	6	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:57485520T>G	ENST00000300131.3	+	2	1074	c.696T>G	c.(694-696)ggT>ggG	p.G232G	NAB2_ENST00000357680.4_Silent_p.G232G|NAB2_ENST00000342556.6_Silent_p.G232G|NAB2_ENST00000554718.1_3'UTR	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	232					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GGACTGGGGGTGGTCCAGACC	0.667																																					p.G232G													.	NAB2-92	0			c.T696G						.						53	61	58					12																	57485520		2203	4300	6503	SO:0001819	synonymous_variant	4665	exon2			TGGGGGTGGTCCA	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.696T>G	12.37:g.57485520T>G		Somatic	63	7		WXS	Illumina HiSeq	Phase_I	166	16	NM_005967	0	0	11	11	0	B2RAK3|O76006|Q14797	Silent	SNP	ENST00000300131.3	37	CCDS8930.1																																																																																			.		0.667	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		G	57485520	T	G	57485520	2	3	28	1	0	0	0	0	0	0	0	1	10157	1683	59	5		5	NAB2	12	57485520	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	3037732	57485520	76366375	80	2505											
TPH2	121278	broad.mit.edu	37	chr12	72425407	72425407	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtattgaaaatgtggtgcagGaccttcgcagcgacttgaat	11	11	12	7	2	0	2	0	2	0	0	1	4	0	3	1	2	2	3	1	2	4	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:72425407G>A	ENST00000333850.3	+	11	1546	c.1405G>A	c.(1405-1407)Gac>Aac	p.D469N		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	469					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	TGTGGTGCAGGACCTTCGCAG	0.413																																					p.D469N													.	TPH2-93	0			c.G1405A						.						168	163	165					12																	72425407		2203	4300	6503	SO:0001583	missense	121278	exon11			GTGCAGGACCTTC	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.1405G>A	12.37:g.72425407G>A	ENSP00000329093:p.Asp469Asn	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	244	5	NM_173353	0	0	0	0	0	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	37	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835429	0.50951	.	.	ENSG00000139287	ENST00000333850	D	0.99507	-6.04	5.86	5.86	0.93980	Aromatic amino acid hydroxylase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.97114	0.9057	N	0.05510	-0.035	0.80722	D	1	B	0.19583	0.037	B	0.24006	0.05	D	0.95632	0.8690	10	0.12103	T	0.63	-30.7387	20.1858	0.98214	0.0:0.0:1.0:0.0	.	469	Q8IWU9	TPH2_HUMAN	N	469	ENSP00000329093:D469N	ENSP00000329093:D469N	D	+	1	0	TPH2	70711674	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.869000	0.99810	2.777000	0.95525	0.591000	0.81541	GAC	.		0.413	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		A	72425407	G	A	72425407	3	1	28	1	0	0	0	0	1	0	0	0	16435	1174	41	2	1447	2	TPH2	12	72425407	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	14939887	72425407	61426488	81	2506											
RNF10	9921	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120984362	120984362	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaaggggcggcggcagcagCaaactctttagctcttcttt	9	10	11	11	2	3	0	0	0	3	0	3	0	3	0	0	4	4	4	0	4	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:120984362C>A	ENST00000325954.4	+	2	773	c.312C>A	c.(310-312)agC>agA	p.S104R	RNF10_ENST00000413266.2_Missense_Mutation_p.S104R	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	104	Interaction with MEOX2.|Ser-rich.				negative regulation of Schwann cell proliferation (GO:0010626)|positive regulation of myelination (GO:0031643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autoubiquitination (GO:0051865)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	27	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGGCAGCAGCAAACTCTTTA	0.453																																					p.S104R													.	RNF10-227	0			c.C312A						.						60	62	61					12																	120984362		2203	4300	6503	SO:0001583	missense	9921	exon2			CAGCAGCAAACTC	AB027196	CCDS9201.1	12q23-q24	2013-01-09			ENSG00000022840	ENSG00000022840		"RING-type (C3HC4) zinc fingers"	10055	protein-coding gene	gene with protein product							Standard	NM_014868		Approved	KIAA0262, RIE2	uc001typ.4	Q8N5U6	OTTHUMG00000168999	ENST00000325954.4:c.312C>A	12.37:g.120984362C>A	ENSP00000322242:p.Ser104Arg	Somatic	46	2		WXS	Illumina HiSeq	Phase_I	165	40	NM_014868	0	0	8	10	2	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	37	CCDS9201.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669800	0.47677	.	.	ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000413266;ENST00000537997	D;D	0.88741	-2.42;-2.42	5.03	5.03	0.67393	.	0.200864	0.46758	D	0.000264	D	0.84483	0.5482	L	0.43152	1.355	0.36642	D	0.87688	B;B	0.26975	0.145;0.165	B;B	0.28784	0.029;0.094	T	0.82151	-0.0599	10	0.11182	T	0.66	.	16.9038	0.86120	0.0:1.0:0.0:0.0	.	104;104	Q8N5U6-2;Q8N5U6	.;RNF10_HUMAN	R	104;104;104;54	ENSP00000322242:S104R;ENSP00000415682:S104R	ENSP00000322242:S104R	S	+	3	2	RNF10	119468745	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.907000	0.48743	2.479000	0.83701	0.655000	0.94253	AGC	.		0.453	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4			A	120984362	C	A	120984362	3	1	28	1	0	0	0	0	1	0	0	0	13454	709	25	4	318	4	RNF10	12	120984362	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	48558955	120984362	12867533	82	2507											
GPR81	27198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123214112	123214112	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgagggttatgtgcagggCcccatggacagagggatcgc	8	7	17	9	1	0	2	0	1	0	1	1	4	0	4	2	4	1	3	2	4	1	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:123214112C>T	ENST00000436083.2	-	1	1278	c.775G>A	c.(775-777)Gcc>Acc	p.A259T	HCAR1_ENST00000432564.1_Missense_Mutation_p.A259T|HCAR1_ENST00000356987.2_Missense_Mutation_p.A259T			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	259					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						ATGTGCAGGGCCCCATGGACA	0.522																																					p.A259T		.											.	HCAR1-156	0			c.G775A						.						81	81	81					12																	123214112		2203	4300	6503	SO:0001583	missense	27198	exon1			GCAGGGCCCCATG	AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	4532	protein-coding gene	gene with protein product	"lactate receptor 1"	606923	"G protein-coupled receptor 104", "G protein-coupled receptor 81"	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.775G>A	12.37:g.123214112C>T	ENSP00000409980:p.Ala259Thr	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	213	92	NM_032554	0	0	0	0	0	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	CCDS9236.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.864791	0.51482	.	.	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.38401	1.14;1.14;1.14	5.62	4.72	0.59763	GPCR, rhodopsin-like superfamily (1);	0.162482	0.38272	N	0.001754	T	0.50292	0.1607	L	0.55481	1.735	0.37418	D	0.913513	D	0.61697	0.99	D	0.64877	0.93	T	0.49872	-0.8893	10	0.33141	T	0.24	-12.0983	12.8086	0.57628	0.0:0.9183:0.0:0.0817	.	259	Q9BXC0	HCAR1_HUMAN	T	259	ENSP00000349478:A259T;ENSP00000389255:A259T;ENSP00000409980:A259T	ENSP00000349478:A259T	A	-	1	0	HCAR1	121780065	0.985000	0.35326	0.946000	0.38457	0.043000	0.13939	2.721000	0.47260	2.653000	0.90120	0.655000	0.94253	GCC	.		0.522	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			T	123214112	C	T	123214112	3	4	28	1	0	0	0	0	1	0	0	0	6731	739	26	2	269	2	GPR81	12	123214112	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	2229750	123214112	10637783	83	2508											
GPR133	283383	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	131471648	131471648	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcttttccaggcccctatTggactcatgtcctatttaca	8	15	5	13	0	2	0	1	0	1	0	4	1	4	1	4	2	1	0	4	2	3	7			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:131471648T>G	ENST00000261654.5	+	6	1058	c.499T>G	c.(499-501)Tgg>Ggg	p.W167G	GPR133_ENST00000535015.1_Missense_Mutation_p.W199G	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	167					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(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		AGGCCCCTATTGGACTCATGT	0.493																																					p.W167G		.											.	GPR133-191	0			c.T499G						.						59	57	58					12																	131471648		2203	4300	6503	SO:0001583	missense	283383	exon6			CCCTATTGGACTC	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.499T>G	12.37:g.131471648T>G	ENSP00000261654:p.Trp167Gly	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	120	25	NM_198827	0	0	0	0	0	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.826517	0.50739	.	.	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015	D;D;D	0.86769	-2.17;-2.17;-2.17	4.55	4.55	0.56014	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.94679	0.8284	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.99	D	0.95634	0.8692	10	0.72032	D	0.01	.	13.1073	0.59253	0.0:0.0:0.0:1.0	.	199;167	B7ZLF7;Q6QNK2	.;GP133_HUMAN	G	167;107;199	ENSP00000261654:W167G;ENSP00000442501:W107G;ENSP00000444425:W199G	ENSP00000261654:W167G	W	+	1	0	GPR133	130037601	1.000000	0.71417	1.000000	0.80357	0.406000	0.30931	7.078000	0.76821	1.685000	0.51034	0.533000	0.62120	TGG	.		0.493	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		G	131471648	T	G	131471648	3	3	28	1	0	0	0	0	1	0	0	0	6663	1812	63	5	521	5	GPR133	12	131471648	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	8257536	131471648	2380247	84	2509											
COG6	57511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	40251678	40251678	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgacttctgatgaaatgAgtcttctccgaggtacaaga	13	11	9	8	1	3	5	0	4	3	1	4	6	3	5	1	1	2	1	1	1	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr13:40251678A>G	ENST00000455146.3	+	5	552	c.502A>G	c.(502-504)Agt>Ggt	p.S168G	COG6_ENST00000416691.1_Missense_Mutation_p.S168G	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	168					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		TGATGAAATGAGTCTTCTCCG	0.348																																					p.S168G		.											.	COG6-227	0			c.A502G						.						87	81	83					13																	40251678		2203	4300	6503	SO:0001583	missense	57511	exon5			GAAATGAGTCTTC	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.502A>G	13.37:g.40251678A>G	ENSP00000397441:p.Ser168Gly	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	113	36	NM_001145079	0	0	0	0	0	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.927586	0.34002	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.55588	0.51;0.51;0.51	5.78	-1.08	0.09936	.	0.333784	0.40640	N	0.001058	T	0.29321	0.0730	N	0.24115	0.695	0.28989	N	0.888159	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10989	-1.0606	10	0.22109	T	0.4	-11.1167	5.8826	0.18864	0.5582:0.1302:0.3116:0.0	.	189;168	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	G	168;199;168;168	ENSP00000403733:S168G;ENSP00000412877:S168G;ENSP00000397441:S168G	ENSP00000255468:S199G	S	+	1	0	COG6	39149678	1.000000	0.71417	0.941000	0.38009	0.875000	0.50365	2.795000	0.47861	-0.395000	0.07715	-0.334000	0.08254	AGT	.		0.348	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			G	40251678	A	G	40251678	3	3	28	1	0	0	0	0	1	0	0	0	3668	304	11	3	520	3	COG6	13	40251678	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		40251678	74918200	85	2510											
IPO5	3843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	98667795	98667795	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcattagtgcattgaagtAatgggagatggatgccttaa	12	12	11	6	0	1	2	1	1	0	1	1	4	1	3	2	2	2	2	2	2	4	4	rs61750357		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr13:98667795A>T	ENST00000490680.1	+	20	2402	c.2337A>T	c.(2335-2337)gtA>gtT	p.V779V	IPO5_ENST00000539640.1_Silent_p.V654V|IPO5_ENST00000261574.5_Silent_p.V797V			O00410	IPO5_HUMAN	importin 5	779					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GCATTGAAGTAATGGGAGATG	0.348																																					p.V797V		.											.	IPO5-228	0			c.A2391T						.						108	107	107					13																	98667795		2203	4300	6503	SO:0001819	synonymous_variant	3843	exon23			TGAAGTAATGGGA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.2337A>T	13.37:g.98667795A>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	167	61	NM_002271	0	0	0	0	0	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	37		.	.	.	.	.	.	.	.	.	.	A	10.56	1.383369	0.25031	.	.	ENSG00000065150	ENST00000469360	.	.	.	5.72	-3.39	0.04868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1611	7.7355	0.28812	0.295:0.5469:0.06:0.0981	.	.	.	.	L	781	.	.	X	+	2	2	IPO5	97465796	0.965000	0.33210	0.966000	0.40874	0.996000	0.88848	0.136000	0.15974	-0.832000	0.04251	0.533000	0.62120	TAA	.		0.348	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		T	98667795	A	T	98667795	2	4	28	1	0	0	0	0	0	0	0	1	7817	349	13	5		5	IPO5	13	98667795	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	58416117	98667795	16502083	86	2511											
ATP11A	23250	hgsc.bcm.edu;broad.mit.edu	37	chr13	113474213	113474213	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgtggcttttctgtcgccaGgttcgtgggtcgcatcaacg	5	12	13	11	5	2	0	1	0	1	0	5	0	2	0	1	3	1	3	1	3	1	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr13:113474213G>A	ENST00000487903.1	+	8	762		c.e8-1		ATP11A_ENST00000283558.8_Splice_Site|ATP11A_ENST00000375630.2_Splice_Site|ATP11A_ENST00000375645.3_Splice_Site			P98196	AT11A_HUMAN	ATPase, class VI, type 11A						phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				TCTGTCGCCAGGTTCGTGGGT	0.637																																					.		.											.	ATP11A-138	0			c.675-1G>A						.						125	89	101					13																	113474213		2203	4300	6503	SO:0001630	splice_region_variant	23250	exon8			TCGCCAGGTTCGT	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.675-1G>A	13.37:g.113474213G>A		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	57	18	NM_015205	0	0	0	0	0	Q5VXT2	Splice_Site	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927015	0.34002	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000418678	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8794	0.63674	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP11A	112522214	1.000000	0.71417	0.997000	0.53966	0.023000	0.10783	6.506000	0.73712	2.406000	0.81754	0.591000	0.81541	.	.		0.637	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	Intron	A	113474213	G	A	113474213	5	1	28	1	0	0	0	0	0	0	1	0	1120	1014	35	2	704	2	ATP11A	13	113474213	Splice_Site	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	14806418	113474213	1695665	87	2512											
LTBP2	4053	broad.mit.edu;ucsc.edu	37	chr14	74970233	74970233	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccagggtgagcggggggctGcagaagcagtggaaggagcc	9	4	20	8	1	0	2	0	1	0	1	1	4	1	4	2	6	4	3	2	6	2	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr14:74970233G>A	ENST00000261978.4	-	32	5045	c.4659C>T	c.(4657-4659)tgC>tgT	p.C1553C	LTBP2_ENST00000556690.1_Silent_p.C1509C	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1553	EGF-like 18; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GCGGGGGGCTGCAGAAGCAGT	0.652																																					p.C1553C													.	LTBP2-92	0			c.C4659T						.						57	41	47					14																	74970233		2203	4300	6503	SO:0001819	synonymous_variant	4053	exon32			GGGGCTGCAGAAG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.4659C>T	14.37:g.74970233G>A		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_000428	0	0	0	0	0	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																			.		0.652	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	74970233	G	A	74970233	2	1	28	1	0	0	0	0	0	0	0	1	9099	1311	46	2		2	LTBP2	14	74970233	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		74970233	32379307	88	2513											
ZSCAN29	146050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43653718	43653718	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtcaagacatttataaggTttctctccagtgtggattct	10	15	8	8	0	3	1	1	0	2	1	5	2	4	2	1	2	0	1	1	2	3	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr15:43653718T>C	ENST00000396976.2	-	5	2246	c.2112A>G	c.(2110-2112)aaA>aaG	p.K704K	ZSCAN29_ENST00000568898.1_Silent_p.K314K|ZSCAN29_ENST00000562072.1_3'UTR|ZSCAN29_ENST00000396972.1_Silent_p.K315K	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	704					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		ATTTATAAGGTTTCTCTCCAG	0.438																																					p.K704K		.											.	ZSCAN29-91	0			c.A2112G						.						60	57	58					15																	43653718		2201	4299	6500	SO:0001819	synonymous_variant	146050	exon5			ATAAGGTTTCTCT	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"-", "Zinc fingers, C2H2-type"	26673	protein-coding gene	gene with protein product			"zinc finger protein 690"	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.2112A>G	15.37:g.43653718T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	155	43	NM_152455	0	0	2	2	0	B3KVB9|Q32M75|Q32M76|Q8NA40	Silent	SNP	ENST00000396976.2	37	CCDS10095.2																																																																																			.		0.438	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		C	43653718	T	C	43653718	2	2	28	1	0	0	0	0	0	0	0	1	18268	1722	60	3		3	ZSCAN29	15	43653718	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10		43653718	58877674	89	2514											
FAM154B	283726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	82575198	82575198	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccacatgaattgatcccaaCagagagttgcaaacctttaa	15	9	7	10	0	0	3	0	2	0	1	1	4	1	3	3	0	3	2	3	0	4	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr15:82575198C>A	ENST00000339465.5	+	3	1061	c.992C>A	c.(991-993)aCa>aAa	p.T331K	FAM154B_ENST00000427381.2_Missense_Mutation_p.T316K|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	331										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						TTGATCCCAACAGAGAGTTGC	0.388																																					p.T331K		.											.	FAM154B-70	0			c.C992A						.						74	74	74					15																	82575198		2203	4300	6503	SO:0001583	missense	283726	exon3			TCCCAACAGAGAG	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.992C>A	15.37:g.82575198C>A	ENSP00000340445:p.Thr331Lys	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	402	132	NM_001008226	0	0	0	0	0	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.034412	0.35893	.	.	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.16743	2.32;2.32	4.22	3.28	0.37604	.	0.172782	0.36628	N	0.002496	T	0.36248	0.0960	M	0.82323	2.585	0.09310	N	0.999996	D;D	0.76494	0.999;0.984	D;P	0.68765	0.96;0.881	T	0.24693	-1.0153	10	0.14656	T	0.56	-8.4012	8.8098	0.34961	0.0:0.7627:0.1525:0.0849	.	316;331	B4E2M2;Q658L1	.;F154B_HUMAN	K	331;316	ENSP00000340445:T331K;ENSP00000403743:T316K	ENSP00000340445:T331K	T	+	2	0	FAM154B	80362253	0.114000	0.22134	0.015000	0.15790	0.341000	0.28922	0.879000	0.28146	0.867000	0.35654	0.404000	0.27445	ACA	.		0.388	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		A	82575198	C	A	82575198	3	1	28	1	0	0	0	0	1	0	0	0	5480	478	17	4	1002	4	FAM154B	15	82575198	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	38921480	82575198	19956194	90	2515											
ALPK3	57538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	85407685	85407685	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtttaggatcatcccactGtatctgatctaccggcctgc	8	13	8	12	1	3	1	1	1	2	0	4	2	4	2	3	2	2	2	3	2	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr15:85407685G>A	ENST00000258888.5	+	12	5285	c.5118G>A	c.(5116-5118)ctG>ctA	p.L1706L		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1706	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			TCATCCCACTGTATCTGATCT	0.512																																					p.L1706L		.											.	ALPK3-337	0			c.G5118A						.						94	84	87					15																	85407685		2203	4299	6502	SO:0001819	synonymous_variant	57538	exon12			CCCACTGTATCTG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.5118G>A	15.37:g.85407685G>A		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	122	47	NM_020778	0	0	0	0	0	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			.		0.512	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85407685	G	A	85407685	2	1	28	1	0	0	0	0	0	0	0	1	546	1364	48	2		2	ALPK3	15	85407685	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	2832487	85407685	17123707	91	2516											
NDUFB10	4716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2011289	2011289	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaatgcagtggaagagggActagtacgtgagccatgctg	12	7	15	7	2	0	2	0	1	0	1	0	5	0	4	1	2	4	3	1	2	4	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr16:2011289A>T	ENST00000268668.6	+	2	383	c.266A>T	c.(265-267)gAc>gTc	p.D89V	NDUFB10_ENST00000569148.1_Intron|SNORA64_ENST00000384674.1_RNA|SNORA10_ENST00000384084.1_RNA|NDUFB10_ENST00000543683.2_Missense_Mutation_p.D89V	NM_004548.2	NP_004539.1	O96000	NDUBA_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa	89					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			lung(1)|urinary_tract(1)	2						TGGAAGAGGGACTAGTACGTG	0.567																																					p.D89V		.											.	NDUFB10-90	0			c.A266T						.						194	142	160					16																	2011289		2199	4300	6499	SO:0001583	missense	4716	exon2			AGAGGGACTAGTA	AF044954	CCDS10451.1	16p13.3	2011-07-04	2002-08-29		ENSG00000140990	ENSG00000140990		"Mitochondrial respiratory chain complex / Complex I"	7696	protein-coding gene	gene with protein product	"complex I PDSW subunit"	603843	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22kD, PDSW)"			9763677, 9878551	Standard	NM_004548		Approved	PDSW	uc002cni.2	O96000	OTTHUMG00000128709	ENST00000268668.6:c.266A>T	16.37:g.2011289A>T	ENSP00000268668:p.Asp89Val	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	94	32	NM_004548	0	0	2	3	1	Q96II6	Missense_Mutation	SNP	ENST00000268668.6	37	CCDS10451.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.519366	0.64634	.	.	ENSG00000140990	ENST00000268668;ENST00000543683	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.81767	0.4892	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85631	0.1270	9	0.87932	D	0	-38.553	14.1338	0.65273	1.0:0.0:0.0:0.0	.	89;89	Q96II6;O96000	.;NDUBA_HUMAN	V	89	.	ENSP00000268668:D89V	D	+	2	0	NDUFB10	1951290	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	8.564000	0.90726	1.936000	0.56123	0.533000	0.62120	GAC	.		0.567	NDUFB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250614.2	NM_004548		T	2011289	A	T	2011289	3	4	28	1	0	0	0	0	1	0	0	0	10305	275	10	5	272	5	NDUFB10	16	2011289	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		2011289	88343464	92	2517											
TRAP1	10131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	3712967	3712967	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctctgataggcactcggcGgctgcggaagagcaggcgac	8	7	15	11	4	1	2	0	1	1	1	3	4	1	3	0	5	2	3	0	5	2	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr16:3712967G>A	ENST00000246957.5	-	15	1798	c.1710C>T	c.(1708-1710)gcC>gcT	p.A570A	TRAP1_ENST00000575671.1_Splice_Site_p.A361A|TRAP1_ENST00000538171.1_Splice_Site_p.A517A|DNASE1_ENST00000414110.2_Intron|DNASE1_ENST00000575152.1_3'UTR	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	570					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				GGCACTCGGCGGCTGCGGAAG	0.642																																					p.A570A		.											.	TRAP1-226	0			c.C1710T						.						60	46	51					16																	3712967		2197	4300	6497	SO:0001630	splice_region_variant	10131	exon15			CTCGGCGGCTGCG	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"Heat shock proteins / HSPC"	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1709-1C>T	16.37:g.3712967G>A		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	27	10	NM_016292	0	0	4	4	0	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	37	CCDS10508.1																																																																																			.		0.642	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	Silent	A	3712967	G	A	3712967	5	1	28	1	0	0	0	0	0	0	1	0	16488	1130	39	1	420	1	TRAP1	16	3712967	Splice_Site	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	1701678	3712967	86641786	93	2518											
ZZEF1	23140	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	3980188	3980189	+	Frame_Shift_Ins	INS	-	-	T																															cgagctgccattgaaaacacINStgagttacataatctttcta																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:3980188_3980189insT	ENST00000381638.2	-	20	3208_3209	c.3084_3085insA	c.(3082-3087)tcagtgfs	p.V1029fs	ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1029							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ATTGAAAACACTGAGTTACATA	0.47																																					p.V1029fs		.											.	ZZEF1-93	0			c.3085_3086insA						.																																			SO:0001589	frameshift_variant	23140	exon20			.	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.3085dupA	17.37:g.3980189_3980189dupT	ENSP00000371051:p.Val1029fs	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	222	121	NM_015113	0	0	0	0	0	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Frame_Shift_Ins	INS	ENST00000381638.2	37	CCDS11043.1																																																																																			.		0.47	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3980189	-	T	3980188	7	5	28	1	0	1	1	0	0	0	0	0	18287	565	20	0	5944	0	ZZEF1	17	3980188	Frame_Shift_Ins	INS	-	TCGA-A4-A6HP-01A-11D-A31X-10		3980188	77215022	94	2519											
KDM6B	23135	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	7748926	7748926	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcacgggaagcctttgcCcttgggggcctgagctgtgc	4	9	16	12	1	0	1	0	1	0	0	0	2	0	2	3	3	5	3	3	3	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:7748926C>A	ENST00000448097.2	+	4	385	c.54C>A	c.(52-54)gcC>gcA	p.A18A	KDM6B_ENST00000254846.5_Silent_p.A18A			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	18					cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						AAGCCTTTGCCCTTGGGGGCC	0.642																																					p.A18A		.											.	KDM6B-205	0			c.C54A						.						56	59	58					17																	7748926		2203	4300	6503	SO:0001819	synonymous_variant	23135	exon4			CTTTGCCCTTGGG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.54C>A	17.37:g.7748926C>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	184	40	NM_001080424	0	0	2	2	0	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				.		0.642	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		A	7748926	C	A	7748926	2	1	28	1	0	0	0	0	0	0	0	1	8159	610	22	4		4	KDM6B	17	7748926	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	3768738	7748926	73446284	95	2520											
ELAC2	60528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	12898190	12898190	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgcagtgccgcaccagAcaggtctgaaactgaaaggg	11	7	13	10	1	1	3	0	2	1	1	1	3	1	3	2	2	4	3	2	2	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:12898190A>G	ENST00000338034.4	-	21	2159	c.1920T>C	c.(1918-1920)tgT>tgC	p.C640C	ELAC2_ENST00000426905.3_Silent_p.C600C|ELAC2_ENST00000395962.2_Silent_p.C621C	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	640					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						GCCGCACCAGACAGGTCTGAA	0.622																																					p.C640C		.											.	ELAC2-90	0			c.T1920C						.						72	78	76					17																	12898190		2203	4300	6503	SO:0001819	synonymous_variant	60528	exon21			CACCAGACAGGTC	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1920T>C	17.37:g.12898190A>G		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	121	60	NM_018127	0	0	2	2	0	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																			.		0.622	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			G	12898190	A	G	12898190	2	3	28	1	0	0	0	0	0	0	0	1	5060	273	10	3		3	ELAC2	17	12898190	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	5149264	12898190	68297020	96	2521											
TBC1D28	254272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18541949	18541949	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttaccttcttggtgctcctAtattttgtccagtctgcaag	6	17	8	10	0	2	0	0	0	2	0	4	0	4	0	3	1	3	3	3	1	4	7			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:18541949A>G	ENST00000345096.4	-	6	963	c.264T>C	c.(262-264)taT>taC	p.Y88Y	TBC1D28_ENST00000405044.1_Silent_p.Y88Y			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	88							Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						TGGTGCTCCTATATTTTGTCC	0.542																																					p.Y88Y		.											.	TBC1D28-91	0			c.T264C						.						120	117	118					17																	18541949		1942	4126	6068	SO:0001819	synonymous_variant	254272	exon7			GCTCCTATATTTT		CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.264T>C	17.37:g.18541949A>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	142	60	NM_001039397	0	0	0	0	0	Q2M2E1	Silent	SNP	ENST00000345096.4	37	CCDS42273.1																																																																																			.		0.542	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397		G	18541949	A	G	18541949	2	3	28	1	0	0	0	0	0	0	0	1	15649	456	16	3		3	TBC1D28	17	18541949	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	5643759	18541949	62653261	97	2522											
MSL1	339287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38282491	38282491	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagctggtaaagaaggataAcgagaaagaaaggcacaagc	19	3	13	6	1	0	3	0	0	0	3	0	5	0	4	0	3	3	4	0	3	7	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:38282491A>G	ENST00000398532.4	+	2	1139	c.824A>G	c.(823-825)aAc>aGc	p.N275S	MSL1_ENST00000577454.1_Missense_Mutation_p.N275S|MSL1_ENST00000579565.1_Missense_Mutation_p.N12S|MSL1_ENST00000578648.1_Missense_Mutation_p.N275S	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	275					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						AAGAAGGATAACGAGAAAGAA	0.428																																					p.N12S		.											.	MSL1-68	0			c.A35G						.						98	98	98					17																	38282491		1949	4139	6088	SO:0001583	missense	339287	exon3			AGGATAACGAGAA		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.824A>G	17.37:g.38282491A>G	ENSP00000381543:p.Asn275Ser	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	231	110	NM_001012241	0	0	22	49	27	Q0VF46|Q69Z03	Missense_Mutation	SNP	ENST00000398532.4	37		.	.	.	.	.	.	.	.	.	.	A	11.43	1.637733	0.29157	.	.	ENSG00000188895	ENST00000339569;ENST00000398532	.	.	.	5.79	5.79	0.91817	.	0.270557	0.44688	D	0.000434	T	0.22820	0.0551	N	0.19112	0.55	0.26940	N	0.966276	B	0.16396	0.017	B	0.18263	0.021	T	0.28776	-1.0033	9	0.05436	T	0.98	-11.0278	8.4872	0.33078	0.8546:0.0:0.1454:0.0	.	275	Q68DK7	MSL1_HUMAN	S	12;275	.	ENSP00000341409:N12S	N	+	2	0	MSL1	35536017	0.994000	0.37717	1.000000	0.80357	0.965000	0.64279	2.451000	0.44952	2.208000	0.71279	0.533000	0.62120	AAC	.		0.428	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241		G	38282491	A	G	38282491	3	3	28	1	0	0	0	0	1	0	0	0	9902	43	2	3	37	3	MSL1	17	38282491	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	19740542	38282491	42912719	98	2523											
HOXB9	3219	broad.mit.edu	37	chr17	46703276	46703277	+	Missense_Mutation	DNP	TC	TC	CT																															caggcgcgcccagcagcggcTccgccttcaccgccgcctgg																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:46703276_46703277TC>CT	ENST00000311177.5	-	1	562_563	c.355_356GA>AG	c.(355-357)GAg>AGg	p.E119R	HOXB9_ENST00000550387.1_Intron|HOXB-AS4_ENST00000480386.1_RNA|HOXB7_ENST00000567101.2_Intron	NM_024017.4	NP_076922.1	P17482	HXB9_HUMAN	homeobox B9	119					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|embryonic skeletal system development (GO:0048706)|mammary gland development (GO:0030879)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(1)|large_intestine(1)|liver(1)|lung(6)|prostate(1)	12						CAGCAGCGGCTCCGCCTTCACC	0.728																																					p.E119R													.	HOXB9-90	0			c.G355A						.																																			SO:0001583	missense	3219	exon1			GCGGCTCCGCCTT		CCDS11534.1	17q21.32	2011-06-20	2005-12-22		ENSG00000170689	ENSG00000170689		"Homeoboxes / ANTP class : HOXL subclass"	5120	protein-coding gene	gene with protein product		142964	"homeo box B9"	HOX2E, HOX2		1973146, 1358459	Standard	NM_024017		Approved		uc002inx.3	P17482	OTTHUMG00000159907	ENST00000311177.5:c.355_356delinsCT	17.37:g.46703276_46703277delinsCT	ENSP00000309439:p.Glu119Arg	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	32	8	NM_024017	0	0	0	0	0	B2RDB7|Q9H1I1	Missense_Mutation	DNP	ENST00000311177.5	37	CCDS11534.1																																																																																			.		0.728	HOXB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358101.2			CT	46703277	TC	CT	46703276	3	2	28	1	0	0	0	0	1	0	0	0	7329	1551	54	3	404	3	HOXB9	17	46703276	Missense_Mutation	DNP	TC	TCGA-A4-A6HP-01A-11D-A31X-10	8420785	46703276	34491934	99	2524											
C17orf64	124773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58503225	58503225	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcgccatgccaagggcctgGatcaggacaccttcaaaact	11	7	10	13	1	2	0	2	0	0	0	2	2	2	2	4	3	3	0	4	3	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:58503225G>A	ENST00000269127.4	+	2	217	c.133G>A	c.(133-135)Gat>Aat	p.D45N		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	45										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CAAGGGCCTGGATCAGGACAC	0.587																																					p.D45N		.											.	C17orf64-271	0			c.G133A						.						49	50	50					17																	58503225		692	1591	2283	SO:0001583	missense	124773	exon2			GGCCTGGATCAGG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.133G>A	17.37:g.58503225G>A	ENSP00000269127:p.Asp45Asn	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	118	62	NM_181707	0	0	0	0	0	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	37	CCDS32698.2	.	.	.	.	.	.	.	.	.	.	G	8.915	0.959686	0.18507	.	.	ENSG00000141371	ENST00000428000;ENST00000269127	.	.	.	5.8	1.57	0.23409	.	1.190680	0.06014	N	0.650076	T	0.35422	0.0931	L	0.38838	1.175	0.09310	N	0.999999	B	0.22983	0.078	B	0.25614	0.062	T	0.35475	-0.9787	9	0.51188	T	0.08	0.2409	8.0582	0.30617	0.4133:0.0:0.5867:0.0	.	45	Q86WR6	CQ064_HUMAN	N	39;45	.	ENSP00000269127:D45N	D	+	1	0	C17orf64	55858007	0.078000	0.21339	0.143000	0.22291	0.070000	0.16714	0.157000	0.16402	0.087000	0.17167	-0.136000	0.14681	GAT	.		0.587	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		A	58503225	G	A	58503225	3	1	28	1	0	0	0	0	1	0	0	0	1877	1174	41	2	139	2	C17orf64	17	58503225	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	11799949	58503225	22691985	100	2525											
FHOD3	80206	broad.mit.edu	37	chr18	34261469	34261469	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggcagcagagagagagAggcggcggcaggagagagaa	14	1	19	7	2	0	5	0	0	0	5	0	9	0	5	0	5	1	3	0	5	1	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr18:34261469A>G	ENST00000359247.4	+	12	1381	c.1381A>G	c.(1381-1383)Agg>Ggg	p.R461G	FHOD3_ENST00000445677.1_Missense_Mutation_p.R423G|FHOD3_ENST00000590592.1_Missense_Mutation_p.R636G|FHOD3_ENST00000257209.4_Missense_Mutation_p.R461G|FHOD3_ENST00000591635.1_Intron	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	461					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				AGAGAGAGAGAGGCGGCGGCA	0.443																																					p.R461G													.	FHOD3-139	0			c.A1381G						.						88	96	94					18																	34261469		2203	4300	6503	SO:0001583	missense	80206	exon12			AGAGAGAGGCGGC	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1381A>G	18.37:g.34261469A>G	ENSP00000352186:p.Arg461Gly	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	301	8	NM_025135	0	0	1	1	0	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	A	19.55	3.848488	0.71603	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.39592	1.21;1.07;1.27	5.04	-0.736	0.11133	.	0.044666	0.85682	D	0.000000	T	0.54431	0.1858	M	0.66939	2.045	0.44976	D	0.997995	D;D;D;D	0.65815	0.991;0.995;0.986;0.988	P;P;P;P	0.59595	0.86;0.852;0.797;0.815	T	0.59161	-0.7506	10	0.87932	D	0	.	13.5796	0.61893	0.4531:0.5469:0.0:0.0	.	423;461;461;636	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	G	461;461;423	ENSP00000257209:R461G;ENSP00000352186:R461G;ENSP00000411430:R423G	ENSP00000257209:R461G	R	+	1	2	FHOD3	32515467	0.989000	0.36119	0.996000	0.52242	0.997000	0.91878	0.300000	0.19156	-0.274000	0.09232	0.533000	0.62120	AGG	.		0.443	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		G	34261469	A	G	34261469	3	3	28	1	0	0	0	0	1	0	0	0	5902	295	11	3	1427	3	FHOD3	18	34261469	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		34261469	43815779	101	2526											
PIAS2	9063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	44416377	44416377	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cacacacaggacaaatccagGtgggctttttctcattcatt	11	12	7	11	0	2	0	2	0	1	0	4	1	3	1	1	3	0	1	1	3	1	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr18:44416377G>A	ENST00000585916.1	-	9	1144	c.1145C>T	c.(1144-1146)aCc>aTc	p.T382I	PIAS2_ENST00000545673.1_Missense_Mutation_p.T92I|PIAS2_ENST00000324794.7_Missense_Mutation_p.T382I	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	382					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						ACAAATCCAGGTGGGCTTTTT	0.408																																					p.T382I		.											.	PIAS2-662	0			c.C1145T						.						118	114	115					18																	44416377		2203	4300	6503	SO:0001583	missense	9063	exon9			ATCCAGGTGGGCT	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1145C>T	18.37:g.44416377G>A	ENSP00000465676:p.Thr382Ile	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	329	44	NM_173206	0	0	3	3	0	O75927|Q96BT5|Q96KE3	Missense_Mutation	SNP	ENST00000585916.1	37	CCDS32824.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124311	0.94429	.	.	ENSG00000078043	ENST00000398654;ENST00000262161;ENST00000398651;ENST00000545673;ENST00000324794	T;T	0.53640	0.61;1.12	5.62	5.62	0.85841	Zinc finger, MIZ-type (2);	0.000000	0.85682	D	0.000000	T	0.74876	0.3774	M	0.87038	2.855	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;1.0	D;D;D;D;D	0.97110	0.996;1.0;0.994;0.992;1.0	T	0.78971	-0.1993	10	0.87932	D	0	-11.3089	19.6407	0.95757	0.0:0.0:1.0:0.0	.	92;386;382;382;382	B4DGW0;O75928-3;Q2TA77;O75928-2;O75928	.;.;.;.;PIAS2_HUMAN	I	382;382;378;92;382	ENSP00000443238:T92I;ENSP00000317163:T382I	ENSP00000262161:T382I	T	-	2	0	PIAS2	42670375	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.864000	0.99589	2.640000	0.89533	0.460000	0.39030	ACC	.		0.408	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		A	44416377	G	A	44416377	3	1	28	1	0	0	0	0	1	0	0	0	11902	1261	44	2	819	2	PIAS2	18	44416377	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	10154908	44416377	33660871	102	2527											
PRAM1	4670	ucsc.edu	37	chr19	8555985	8555985	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccctctgcccatggcaccTgagcgctgggtcttgtggtg	3	10	13	15	1	2	1	0	1	2	0	2	1	2	1	4	3	2	2	4	3	0	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:8555985T>C	ENST00000325495.4	+	0	2494				PRAM1_ENST00000255612.3_Splice_Site_p.R544G|PRAM1_ENST00000423345.4_Splice_Site_p.R545G	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						CCATGGCACCTGAGCGCTGGG	0.662																																					p.R545G													.	.	0			c.A1633G						.						32	37	35					19																	8555985		1999	4163	6162	SO:0001628	intergenic_variant	84106	exon5			GGCACCTGAGCGC	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383		19.37:g.8555985T>C		Somatic	13	1		WXS	Illumina HiSeq		42	4	NM_032152	0	0	3	3	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.577352	0.45902	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.16743	2.32;2.32	3.95	3.95	0.45737	.	0.000000	0.46145	D	0.000305	T	0.34366	0.0895	L	0.60455	1.87	0.34179	D	0.67073	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.48714	-0.9011	10	0.87932	D	0	.	9.5449	0.39275	0.0:0.0:0.0:1.0	.	545;593	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	G	544;545	ENSP00000255612:R544G;ENSP00000408342:R545G	ENSP00000255612:R544G	R	-	1	2	PRAM1	8461985	1.000000	0.71417	0.996000	0.52242	0.151000	0.21798	2.169000	0.42434	2.027000	0.59764	0.374000	0.22700	AGG	.		0.662	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			C	8555985	T	C	8555985	1	2	28	0	1	0	0	0	0	0	0	0	12452	1594	55	3		3	PRAM1	19	8555985	IGR	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10		8555985	50572998	103	2528											
ILVBL	10994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15226103	15226103	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcggaagtccgtcctcccaAtgaggatgttgaccacaacc	10	7	10	14	3	0	2	0	2	0	0	3	4	3	4	5	2	1	1	5	2	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:15226103A>G	ENST00000263383.3	-	16	1998	c.1859T>C	c.(1858-1860)aTt>aCt	p.I620T	ILVBL_ENST00000534378.1_Missense_Mutation_p.I513T	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	620						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CGTCCTCCCAATGAGGATGTT	0.607																																					p.I620T		.											.	ILVBL-92	0			c.T1859C						.						138	103	115					19																	15226103		2203	4300	6503	SO:0001583	missense	10994	exon16			CTCCCAATGAGGA	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1859T>C	19.37:g.15226103A>G	ENSP00000263383:p.Ile620Thr	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	76	24	NM_006844	0	1	179	341	161	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	37	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.905085	0.72868	.	.	ENSG00000105135	ENST00000263383	T	0.42900	0.96	5.37	5.37	0.77165	.	0.056671	0.64402	D	0.000002	T	0.58264	0.2110	M	0.68952	2.095	0.80722	D	1	D	0.71674	0.998	D	0.63877	0.919	T	0.59542	-0.7435	10	0.46703	T	0.11	-18.752	11.7697	0.51951	1.0:0.0:0.0:0.0	.	620	A1L0T0	ILVBL_HUMAN	T	620	ENSP00000263383:I620T	ENSP00000263383:I620T	I	-	2	0	ILVBL	15087103	1.000000	0.71417	0.998000	0.56505	0.840000	0.47671	6.822000	0.75277	2.044000	0.60594	0.533000	0.62120	ATT	.		0.607	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		G	15226103	A	G	15226103	3	3	28	1	0	0	0	0	1	0	0	0	7736	101	4	3	43	3	ILVBL	19	15226103	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	6670118	15226103	43902880	104	2529											
ZNF536	9745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	31040126	31040126	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtctgccctcagcaaagaCagcagcagcgatggcgggga	10	5	14	12	2	2	1	1	0	1	1	2	3	2	2	1	3	5	3	1	3	1	0	rs545401755		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:31040126C>G	ENST00000355537.3	+	4	3747	c.3600C>G	c.(3598-3600)gaC>gaG	p.D1200E		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1200					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					TCAGCAAAGACAGCAGCAGCG	0.592																																					p.D1200E		.											.	ZNF536-144	0			c.C3600G						.						62	63	63					19																	31040126		2203	4300	6503	SO:0001583	missense	9745	exon4			CAAAGACAGCAGC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3600C>G	19.37:g.31040126C>G	ENSP00000347730:p.Asp1200Glu	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	81	30	NM_014717	0	0	0	0	0	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	0.147	-1.095522	0.01858	.	.	ENSG00000198597	ENST00000355537	T	0.08546	3.08	5.59	3.11	0.35812	.	0.444542	0.25789	N	0.028284	T	0.03871	0.0109	N	0.12746	0.255	0.21675	N	0.999597	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44298	-0.9337	10	0.13108	T	0.6	-38.7005	6.6261	0.22830	0.2337:0.5954:0.0:0.1709	.	1200;1200	A7E228;O15090	.;ZN536_HUMAN	E	1200	ENSP00000347730:D1200E	ENSP00000347730:D1200E	D	+	3	2	ZNF536	35731966	0.207000	0.23482	0.966000	0.40874	0.051000	0.14879	0.146000	0.16180	1.319000	0.45190	0.655000	0.94253	GAC	.		0.592	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		G	31040126	C	G	31040126	3	3	28	1	0	0	0	0	1	0	0	0	18006	477	17	4	3610	4	ZNF536	19	31040126	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	15814023	31040126	28088857	105	2530											
ZNF146	7705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36727612	36727612	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggaaaacctccttacgcaCcagaaaattcacactggaga	17	6	7	11	1	1	2	1	0	0	2	2	4	2	3	3	2	2	1	3	2	6	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:36727612C>A	ENST00000443387.2	+	4	1262	c.270C>A	c.(268-270)caC>caA	p.H90Q	ZNF565_ENST00000355114.5_Intron|ZNF146_ENST00000456324.1_Missense_Mutation_p.H90Q	NM_007145.2	NP_009076.2	Q15072	OZF_HUMAN	zinc finger protein 146	90					regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11	Esophageal squamous(110;0.162)					TCCTTACGCACCAGAAAATTC	0.403																																					p.H90Q		.											.	ZNF146-90	0			c.C270A						.						67	72	70					19																	36727612		2203	4300	6503	SO:0001583	missense	7705	exon3			TACGCACCAGAAA	X70394	CCDS12492.1	19q13.1	2013-01-08				ENSG00000167635		"Zinc fingers, C2H2-type"	12931	protein-coding gene	gene with protein product		601505				10449921, 8641144	Standard	NM_001099639		Approved	OZF	uc010eeu.3	Q15072		ENST00000443387.2:c.270C>A	19.37:g.36727612C>A	ENSP00000392095:p.His90Gln	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	190	79	NM_001099638	0	0	6	8	2	Q2TB94	Missense_Mutation	SNP	ENST00000443387.2	37	CCDS12492.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870414	0.51588	.	.	ENSG00000167635	ENST00000443387;ENST00000456324	D;D	0.86865	-2.18;-2.18	4.46	3.34	0.38264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41396	D	0.000891	D	0.94135	0.8119	H	0.95402	3.665	0.33426	D	0.580462	D	0.62365	0.991	D	0.73708	0.981	D	0.94447	0.7664	10	0.87932	D	0	-10.1539	6.9293	0.24432	0.0:0.2248:0.0:0.7752	.	90	Q15072	OZF_HUMAN	Q	90	ENSP00000392095:H90Q;ENSP00000400391:H90Q	ENSP00000392095:H90Q	H	+	3	2	ZNF146	41419452	0.874000	0.30092	1.000000	0.80357	0.991000	0.79684	-0.067000	0.11579	0.946000	0.37632	-0.355000	0.07637	CAC	.		0.403	ZNF146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451706.1	NM_007145		A	36727612	C	A	36727612	3	1	28	1	0	0	0	0	1	0	0	0	17765	506	18	4	272	4	ZNF146	19	36727612	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	5687486	36727612	22401371	106	2531											
ZC3H4	23211	hgsc.bcm.edu;broad.mit.edu	37	chr19	47569625	47569625	+	Frame_Shift_Del	DEL	G	G	-																															gctggacactactggcaaaaGggggaggccgtggggtcgaa																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:47569625delG	ENST00000253048.5	-	15	3937	c.3900delC	c.(3898-3900)cccfs	p.P1300fs	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1300							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ACTGGCAAAAGGGGGAGGCCG	0.627																																					p.P1300fs		.											.	ZC3H4-74	0			c.3900delC						.						8	10	9					19																	47569625		1878	4043	5921	SO:0001589	frameshift_variant	23211	exon15			.	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"Zinc fingers, CCCH-type domain containing"	17808	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 7"	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.3900delC	19.37:g.47569625delG	ENSP00000253048:p.Pro1300fs	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	63	15	NM_015168	0	0	0	0	0	Q9Y420	Frame_Shift_Del	DEL	ENST00000253048.5	37	CCDS42582.1																																																																																			.		0.627	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			-	47569625	G	-	47569625	7	5	28	1	0	1	0	1	0	0	0	0	17602	987	35	0	15	0	ZC3H4	19	47569625	Frame_Shift_Del	DEL	G	TCGA-A4-A6HP-01A-11D-A31X-10	10842013	47569625	11559358	107	2532											
GYS1	2997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49485593	49485593	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactcatagcggccggcgatAaagaagtataaggtcttgtc	13	9	11	8	3	2	1	1	0	1	1	3	2	2	1	1	3	2	1	1	3	7	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:49485593A>G	ENST00000323798.3	-	7	1177	c.981T>C	c.(979-981)ttT>ttC	p.F327F	GYS1_ENST00000263276.6_Silent_p.F263F|GYS1_ENST00000541188.1_Silent_p.F247F|GYS1_ENST00000544287.1_5'UTR|GYS1_ENST00000540532.1_Missense_Mutation_p.L208S	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	327					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		GGCCGGCGATAAAGAAGTATA	0.542																																					p.F327F		.											.	GYS1-524	0			c.T981C						.						88	79	82					19																	49485593		2203	4300	6503	SO:0001819	synonymous_variant	2997	exon7			GGCGATAAAGAAG		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.981T>C	19.37:g.49485593A>G		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	171	62	NM_002103	0	0	1	2	1	Q9BTT9	Silent	SNP	ENST00000323798.3	37	CCDS12747.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.821993	0.50739	.	.	ENSG00000104812	ENST00000540532	T	0.27890	1.64	5.1	-3.84	0.04256	.	.	.	.	.	T	0.34366	0.0895	.	.	.	0.22754	N	0.998773	.	.	.	.	.	.	T	0.42965	-0.9420	6	0.41790	T	0.15	-14.4659	15.6467	0.77061	0.234:0.0:0.766:0.0	.	.	.	.	S	208	ENSP00000445197:L208S	ENSP00000445197:L208S	L	-	2	0	GYS1	54177405	1.000000	0.71417	0.849000	0.33467	0.997000	0.91878	1.654000	0.37334	-0.742000	0.04790	0.528000	0.53228	TTA	.		0.542	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		G	49485593	A	G	49485593	2	3	28	1	0	0	0	0	0	0	0	1	6933	359	13	3		3	GYS1	19	49485593	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	1915968	49485593	9643390	108	2533											
TMEM86B	255043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55740079	55740079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggctgagcagtgagtctTcagggtctgccccgctttgc	4	11	14	12	1	3	2	1	2	2	0	3	2	3	2	2	2	3	3	2	2	0	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:55740079T>C	ENST00000327042.4	-	1	553	c.31A>G	c.(31-33)Aag>Gag	p.K11E	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	11					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CAGTGAGTCTTCAGGGTCTGC	0.672																																					p.K11E		.											.	TMEM86B-90	0			c.A31G						.						25	26	26					19																	55740079		2203	4299	6502	SO:0001583	missense	255043	exon1			GAGTCTTCAGGGT	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.31A>G	19.37:g.55740079T>C	ENSP00000321038:p.Lys11Glu	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	107	40	NM_173804	0	0	5	10	5		Missense_Mutation	SNP	ENST00000327042.4	37	CCDS12920.1	.	.	.	.	.	.	.	.	.	.	T	8.776	0.926998	0.18056	.	.	ENSG00000180089	ENST00000327042	T	0.22743	1.94	4.76	-1.37	0.09056	.	2.056380	0.01961	N	0.043375	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31223	-0.9951	10	0.33940	T	0.23	.	11.2263	0.48886	0.0:0.5941:0.0:0.4059	.	11	Q8N661	TM86B_HUMAN	E	11	ENSP00000321038:K11E	ENSP00000321038:K11E	K	-	1	0	TMEM86B	60431891	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.228000	0.09114	-0.525000	0.06391	0.379000	0.24179	AAG	.		0.672	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804		C	55740079	T	C	55740079	3	2	28	1	0	0	0	0	1	0	0	0	16241	1792	62	3	661	3	TMEM86B	19	55740079	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	6254486	55740079	3388904	109	2534											
POLR3F	10621	broad.mit.edu	37	chr20	18448195	18448195	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagccgcctgacgcggatccGgtcgaaatagaaaacaggta	13	5	12	11	5	0	2	0	1	0	1	2	4	1	3	3	3	2	1	3	3	5	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:18448195G>A	ENST00000377603.4	+	1	425	c.45G>A	c.(43-45)ccG>ccA	p.P15P	DZANK1_ENST00000329494.5_5'Flank|POLR3F_ENST00000462997.1_3'UTR|DZANK1_ENST00000358866.6_5'Flank|DZANK1_ENST00000262547.5_5'Flank|DZANK1_ENST00000357236.4_5'Flank	NM_006466.2	NP_006457.2	Q9H1D9	RPC6_HUMAN	polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa	15					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)	2						ACGCGGATCCGGTCGAAATAG	0.622																																					p.P15P	GBM(69;898 1468 19907 52011)												.	POLR3F-90	0			c.G45A						.						51	53	52					20																	18448195		2203	4300	6503	SO:0001819	synonymous_variant	10621	exon1			GGATCCGGTCGAA	U93869	CCDS13135.1	20p11.23	2013-01-21	2002-08-29		ENSG00000132664	ENSG00000132664		"RNA polymerase subunits"	15763	protein-coding gene	gene with protein product	"RNA polymerase III C39 subunit"		"polymerase (RNA) III (DNA directed) polypeptide F (39 kDa)"			9171375	Standard	NM_006466		Approved	RPC39, RPC6	uc002wqv.3	Q9H1D9	OTTHUMG00000031971	ENST00000377603.4:c.45G>A	20.37:g.18448195G>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	242	6	NM_006466	0	0	1	1	0	A8K4C7|O15319	Silent	SNP	ENST00000377603.4	37	CCDS13135.1																																																																																			.		0.622	POLR3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078170.2	NM_006466		A	18448195	G	A	18448195	2	1	28	1	0	0	0	0	0	0	0	1	12259	1103	39	1		1	POLR3F	20	18448195	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		18448195	44577325	110	2535											
HM13	81502	ucsc.edu;bcgsc.ca	37	chr20	30156952	30156952	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaaatcctaaggatccagCggcagtgacagaatccaaag	15	6	10	10	1	1	2	1	1	0	1	4	3	4	3	3	2	1	1	3	2	4	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:30156952C>T	ENST00000340852.5	+	12	1188	c.1064C>T	c.(1063-1065)gCg>gTg	p.A355V	HM13_ENST00000398174.3_Missense_Mutation_p.A404V|HM13_ENST00000376127.3_Missense_Mutation_p.A313V|HM13_ENST00000492709.1_3'UTR|HM13_ENST00000335574.5_3'UTR|HM13-AS1_ENST00000412178.1_RNA	NM_030789.2	NP_110416.1	Q8TCT9	HM13_HUMAN	histocompatibility (minor) 13	355					membrane protein proteolysis (GO:0033619)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			AAGGATCCAGCGGCAGTGACA	0.473											OREG0025852	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A404V													.	HM13-153	0			c.C1211T						.						33	34	33					20																	30156952		2202	4297	6499	SO:0001583	missense	81502	exon13			ATCCAGCGGCAGT	AL110115	CCDS13182.1, CCDS13183.1, CCDS42861.1	20q11.21	2012-02-21			ENSG00000101294	ENSG00000101294			16435	protein-coding gene	gene with protein product	"signal peptide peptidase beta", "presenilin-like protein 3", "intramembrane protease", "signal peptide peptidase like 1"	607106				12077416, 14704149	Standard	NM_030789		Approved	H13, dJ324O17.1, SPP, PSL3, IMP1, IMPAS, PSENL3, SPPL1	uc002wwc.3	Q8TCT9	OTTHUMG00000032175	ENST00000340852.5:c.1064C>T	20.37:g.30156952C>T	ENSP00000343032:p.Ala355Val	Somatic	159	3	815	WXS	Illumina HiSeq		273	82	NM_178581	0	1	242	366	123	B2RAY5|E1P5L3|Q15K36|Q540H8|Q5JWP2|Q5JWP3|Q5JWP4|Q5JWP5|Q7Z4F2|Q86Y35|Q95H87|Q9H110|Q9H111	Missense_Mutation	SNP	ENST00000340852.5	37	CCDS13182.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.379383	0.42207	.	.	ENSG00000101294	ENST00000340852;ENST00000398174;ENST00000376127	T;T;T	0.27402	1.89;1.67;1.9	4.36	3.34	0.38264	.	.	.	.	.	T	0.14527	0.0351	N	0.08118	0	0.21802	N	0.999533	B;B	0.25609	0.0;0.13	B;B	0.23018	0.001;0.043	T	0.12811	-1.0533	9	0.18710	T	0.47	.	9.0093	0.36131	0.2202:0.7798:0.0:0.0	.	355;404	Q8TCT9;Q8TCT9-2	HM13_HUMAN;.	V	355;404;313	ENSP00000343032:A355V;ENSP00000381237:A404V;ENSP00000365296:A313V	ENSP00000343032:A355V	A	+	2	0	HM13	29620613	0.851000	0.29673	0.998000	0.56505	0.990000	0.78478	0.356000	0.20181	2.420000	0.82092	0.561000	0.74099	GCG	.		0.473	HM13-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078527.2	NM_178580		T	30156952	C	T	30156952	3	4	28	1	0	0	0	0	1	0	0	0	7238	768	27	1	1332	1	HM13	20	30156952	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	11708757	30156952	32868568	111	2536											
AHCY	191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	32878681	32878681	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttgccggcaatcatcacatCtgtggcccgcttgatgccat	7	11	9	14	2	3	1	2	1	1	0	3	1	3	1	3	2	2	2	3	2	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:32878681C>T	ENST00000217426.2	-	6	699	c.622G>A	c.(622-624)Gat>Aat	p.D208N	AHCY_ENST00000468908.1_5'Flank|AHCY_ENST00000538132.1_Missense_Mutation_p.D180N	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	208					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ATCATCACATCTGTGGCCCGC	0.587																																					p.D208N		.											.	AHCY-91	0			c.G622A						.						50	47	48					20																	32878681		2203	4300	6503	SO:0001583	missense	191	exon6			TCACATCTGTGGC	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.622G>A	20.37:g.32878681C>T	ENSP00000217426:p.Asp208Asn	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	112	42	NM_000687	0	1	44	69	24	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Missense_Mutation	SNP	ENST00000217426.2	37	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766291	0.90020	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	T;T	0.79352	-1.23;-1.26	4.74	3.78	0.43462	S-adenosyl-L-homocysteine hydrolase, NAD binding (1);	0.089011	0.85682	D	0.000000	D	0.86218	0.5880	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.88144	0.2846	10	0.87932	D	0	.	15.2705	0.73696	0.0:0.859:0.141:0.0	.	208	P23526	SAHH_HUMAN	N	208;180	ENSP00000217426:D208N;ENSP00000442820:D180N	ENSP00000217426:D208N	D	-	1	0	AHCY	32342342	1.000000	0.71417	0.977000	0.42913	0.981000	0.71138	7.529000	0.81952	1.333000	0.45449	0.561000	0.74099	GAT	.		0.587	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		T	32878681	C	T	32878681	3	4	28	1	0	0	0	0	1	0	0	0	409	913	32	2	696	2	AHCY	20	32878681	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	2721729	32878681	30146839	112	2537											
KIAA1755	85449	broad.mit.edu	37	chr20	36874404	36874404	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaaggaagctcagcccaTccccctggaagccagagtcc	11	4	10	16	0	1	2	1	0	0	2	3	4	3	4	6	2	3	1	6	2	3	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:36874404T>C	ENST00000279024.4	-	2	399	c.128A>G	c.(127-129)gAt>gGt	p.D43G		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	43										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCTCAGCCCATCCCCCTGGAA	0.602																																					p.D43G													.	KIAA1755-95	0			c.A128G						.						76	67	70					20																	36874404		2203	4300	6503	SO:0001583	missense	85449	exon2			AGCCCATCCCCCT	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.128A>G	20.37:g.36874404T>C	ENSP00000279024:p.Asp43Gly	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	84	4	NM_001029864	0	0	0	0	0	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.846553	0.91277	.	.	ENSG00000149633	ENST00000279024	T	0.39056	1.1	5.4	5.4	0.78164	.	0.000000	0.50627	D	0.000112	T	0.66607	0.2806	M	0.81942	2.565	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	T	0.71583	-0.4549	10	0.72032	D	0.01	.	14.9112	0.70758	0.0:0.0:0.0:1.0	.	43	Q5JYT7	K1755_HUMAN	G	43	ENSP00000279024:D43G	ENSP00000279024:D43G	D	-	2	0	KIAA1755	36307818	1.000000	0.71417	0.899000	0.35326	0.867000	0.49689	7.984000	0.88150	2.172000	0.68678	0.533000	0.62120	GAT	.		0.602	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		C	36874404	T	C	36874404	3	2	28	1	0	0	0	0	1	0	0	0	8278	1435	50	3	3526	3	KIAA1755	20	36874404	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	3995723	36874404	26151116	113	2538											
SLC13A3	64849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	45217868	45217868	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatcttctgcattggttcttAtctcagatttattcttcctc	6	21	4	10	0	5	1	1	0	5	1	8	1	6	1	1	1	1	2	1	1	3	9			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:45217868A>G	ENST00000279027.4	-	7	965	c.947T>C	c.(946-948)aTa>aCa	p.I316T	SLC13A3_ENST00000396360.1_Missense_Mutation_p.I269T|SLC13A3_ENST00000413164.2_Missense_Mutation_p.I266T|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000495082.1_Missense_Mutation_p.I269T|SLC13A3_ENST00000372121.1_Missense_Mutation_p.I266T|SLC13A3_ENST00000472148.1_Missense_Mutation_p.I269T|SLC13A3_ENST00000290317.5_Missense_Mutation_p.I269T|SLC13A3_ENST00000464518.1_5'Flank	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	316					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ATTGGTTCTTATCTCAGATTT	0.488																																					p.I316T		.											.	SLC13A3-91	0			c.T947C						.						115	114	114					20																	45217868		2203	4300	6503	SO:0001583	missense	64849	exon7			GTTCTTATCTCAG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.947T>C	20.37:g.45217868A>G	ENSP00000279027:p.Ile316Thr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	152	35	NM_022829	0	0	0	0	0	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	A	0.563	-0.844580	0.02671	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121	T;T;T;T;T;T;T;T;T	0.10099	3.84;3.75;4.1;3.75;3.57;3.84;3.26;2.92;2.91	5.84	4.74	0.60224	.	1.055960	0.07196	N	0.856503	T	0.10981	0.0268	L	0.27053	0.805	0.28449	N	0.916409	P;B;P;P	0.42161	0.772;0.128;0.515;0.571	B;B;B;B	0.43701	0.428;0.144;0.22;0.328	T	0.15178	-1.0446	10	0.13470	T	0.59	-3.1173	10.4316	0.44411	0.9264:0.0:0.0736:0.0	.	266;269;269;316	B4DIR8;Q8WWT9-3;F6WI18;Q8WWT9	.;.;.;S13A3_HUMAN	T	269;269;316;269;266;269;269;229;266	ENSP00000290317:I269T;ENSP00000379648:I269T;ENSP00000279027:I316T;ENSP00000420177:I269T;ENSP00000415852:I266T;ENSP00000419621:I269T;ENSP00000417784:I269T;ENSP00000395095:I229T;ENSP00000361193:I266T	ENSP00000279027:I316T	I	-	2	0	SLC13A3	44651275	0.575000	0.26692	0.001000	0.08648	0.055000	0.15305	3.364000	0.52328	1.044000	0.40200	0.529000	0.55759	ATA	.		0.488	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			G	45217868	A	G	45217868	3	3	28	1	0	0	0	0	1	0	0	0	14425	449	16	3	889	3	SLC13A3	20	45217868	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	8343464	45217868	17807652	114	2539											
C21orf33	8209	broad.mit.edu;bcgsc.ca	37	chr21	45563146	45563146	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggcgtcgaggtgactgTgggccacgagcaggaggaag	10	4	19	8	3	0	2	0	1	0	1	1	6	0	4	1	5	1	1	1	5	1	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr21:45563146T>G	ENST00000291577.6	+	6	674	c.581T>G	c.(580-582)gTg>gGg	p.V194G	C21orf33_ENST00000348499.5_Missense_Mutation_p.V163G	NM_004649.6	NP_004640	P30042	ES1_HUMAN	chromosome 21 open reading frame 33	194						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)		GAGGTGACTGTGGGCCACGAG	0.617																																					p.V194G													.	C21orf33-91	0			c.T581G						.						77	65	69					21																	45563146		2203	4300	6503	SO:0001583	missense	8209	exon6			TGACTGTGGGCCA	Y07572	CCDS33580.1, CCDS33581.1	21q22.3	2008-07-29			ENSG00000160221	ENSG00000160221			1273	protein-coding gene	gene with protein product		601659				9150728, 8975701	Standard	NM_004649		Approved	KNP-Ia, GT335, ES1, HES1, D21S2048E, KNPI, KNPH, KNP-I	uc002zec.4	P30042	OTTHUMG00000086916	ENST00000291577.6:c.581T>G	21.37:g.45563146T>G	ENSP00000291577:p.Val194Gly	Somatic	47	1		WXS	Illumina HiSeq	Phase_I	131	51	NM_004649	0	0	87	187	100	A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507	Missense_Mutation	SNP	ENST00000291577.6	37	CCDS33580.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	21.0|21.0|21.0	4.089390|4.089390|4.089390	0.76756|0.76756|0.76756	.|.|.	.|.|.	ENSG00000160221|ENSG00000248354;ENSG00000160221;ENSG00000160221|ENSG00000160221	ENST00000449622|ENST00000433711;ENST00000291577;ENST00000348499|ENST00000419699	.|T;T|.	.|0.78707|.	.|-1.2;1.63|.	4.69|4.69|4.69	4.69|4.69|4.69	0.59074|0.59074|0.59074	.|ThiJ/PfpI (1);|.	.|0.065935|.	.|0.64402|.	.|D|.	.|0.000006|.	T|T|T	0.62636|0.62636|0.62636	0.2444|0.2444|0.2444	L|L|L	0.49126|0.49126|0.49126	1.545|1.545|1.545	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.85130|.	.|0.991;0.997|.	T|T|T	0.61033|0.61033|0.61033	-0.7144|-0.7144|-0.7144	5|10|5	.|0.87932|.	.|D|.	.|0|.	-34.2275|-34.2275|-34.2275	14.4883|14.4883|14.4883	0.67631|0.67631|0.67631	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|163;194|.	.|P30042-2;P30042|.	.|.;ES1_HUMAN|.	W|G|G	182|173;194;163|110	.|ENSP00000291577:V194G;ENSP00000344901:V163G|.	.|ENSP00000415634:V173G|.	C|V|W	+|+|+	3|2|1	2|0|0	C21orf33|C21orf33;AP001055.7|C21orf33	44387574|44387574|44387574	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.448000|0.448000|0.448000	0.32197|0.32197|0.32197	7.555000|7.555000|7.555000	0.82223|0.82223|0.82223	1.891000|1.891000|1.891000	0.54761|0.54761|0.54761	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	TGT|GTG|TGG	.		0.617	C21orf33-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195824.1	NM_004649		G	45563146	T	G	45563146	3	3	28	1	0	0	0	0	1	0	0	0	2131	1696	59	5	603	5	C21orf33	21	45563146	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10		45563146	2566749	115	2540											
COL18A1	80781	broad.mit.edu	37	chr21	46911183	46911183	+	Frame_Shift_Del	DEL	C	C	-																															gggcagccgggcctccctggCccccccggacccccgggacc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr21:46911183delC	ENST00000359759.4	+	21	3378	c.3357delC	c.(3355-3357)ggcfs	p.G1119fs	COL18A1_ENST00000400337.2_Frame_Shift_Del_p.G704fs|COL18A1_ENST00000355480.5_Frame_Shift_Del_p.G884fs			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1119	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GCCTCCCTGGCCCCCCCGGAC	0.692																																					p.G884fs													.	COL18A1-90	0			c.2652delC						.						19	26	24					21																	46911183		1917	4091	6008	SO:0001589	frameshift_variant	80781	exon21			CCCTGGCCCCCCC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3357delC	21.37:g.46911183delC	ENSP00000352798:p.Gly1119fs	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	315	8	NM_030582	0	0	0	0	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Frame_Shift_Del	DEL	ENST00000359759.4	37																																																																																				.		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			-	46911183	C	-	46911183	7	5	28	1	0	1	0	1	0	0	0	0	3681	726	26	0	3553	0	COL18A1	21	46911183	Frame_Shift_Del	DEL	C	TCGA-A4-A6HP-01A-11D-A31X-10	1348037	46911183	1218712	116	2541											
MTMR3	8897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30403186	30403186	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaaatgcagatgatgagcAtctggtacagtcagtagcca	13	8	12	8	1	2	3	1	2	1	1	2	4	2	3	1	1	4	4	1	1	3	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr22:30403186A>C	ENST00000401950.2	+	10	1097	c.755A>C	c.(754-756)cAt>cCt	p.H252P	CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_Missense_Mutation_p.H252P|MTMR3_ENST00000351488.3_Missense_Mutation_p.H252P|MTMR3_ENST00000406629.1_Missense_Mutation_p.H252P|MTMR3_ENST00000323630.5_Missense_Mutation_p.H116P	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	252	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			GATGATGAGCATCTGGTACAG	0.547																																					p.H252P		.											.	MTMR3-292	0			c.A755C						.						94	87	89					22																	30403186		2203	4300	6503	SO:0001583	missense	8897	exon10			ATGAGCATCTGGT	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.755A>C	22.37:g.30403186A>C	ENSP00000384651:p.His252Pro	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	92	28	NM_153050	0	0	0	0	0	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	37	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872970	0.91664	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.87	5.87	0.94306	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.087453	0.85682	D	0.000000	D	0.95310	0.8478	M	0.69823	2.125	0.80722	D	1	D;P;D	0.69078	0.997;0.931;0.997	D;P;D	0.66847	0.947;0.781;0.947	D	0.95552	0.8621	10	0.66056	D	0.02	.	15.4554	0.75308	1.0:0.0:0.0:0.0	.	252;252;252	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	P	252;252;116;252;252	ENSP00000384651:H252P;ENSP00000331649:H252P;ENSP00000318070:H116P;ENSP00000307271:H252P;ENSP00000384077:H252P	ENSP00000318070:H116P	H	+	2	0	MTMR3	28733186	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	8.962000	0.93254	2.253000	0.74438	0.533000	0.62120	CAT	.		0.547	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		C	30403186	A	C	30403186	3	2	28	1	0	0	0	0	1	0	0	0	9970	217	8	5	785	5	MTMR3	22	30403186	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		30403186	20901380	117	2542											
CARD10	29775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37898635	37898635	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggaagtccaggccacagccCcgagccaggaggccttccgg	9	3	14	15	2	0	0	0	0	0	0	2	3	2	2	7	5	2	0	7	5	1	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr22:37898635C>G	ENST00000403299.1	-	12	1977	c.1761G>C	c.(1759-1761)cgG>cgC	p.R587R	CARD10_ENST00000406271.3_Silent_p.R301R|CARD10_ENST00000251973.5_Silent_p.R587R			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	587					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGCCACAGCCCCGAGCCAGGA	0.617																																					p.R587R		.											.	CARD10-662	0			c.G1761C						.						54	48	50					22																	37898635		2203	4300	6503	SO:0001819	synonymous_variant	29775	exon11			ACAGCCCCGAGCC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1761G>C	22.37:g.37898635C>G		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	63	21	NM_014550	0	0	10	15	5	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			.		0.617	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		G	37898635	C	G	37898635	2	3	28	1	0	0	0	0	0	0	0	1	2650	610	22	4		4	CARD10	22	37898635	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	7495449	37898635	13405931	118	2543											
PNPLA4	8228	broad.mit.edu	37	chrX	7868821	7868821	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcctcttgcttgggggaaaaAgggcttggttgagtctcacc	7	12	13	9	0	2	1	1	1	2	0	4	2	3	2	2	4	1	3	2	4	2	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chrX:7868821A>G	ENST00000381042.4	-	7	838	c.668T>C	c.(667-669)cTt>cCt	p.L223P	PNPLA4_ENST00000537427.1_Missense_Mutation_p.L136P|PNPLA4_ENST00000444736.1_Missense_Mutation_p.L223P	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	223					lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				TGGGGGAAAAAGGGCTTGGTT	0.353																																					p.L223P													.	PNPLA4-130	0			c.T668C						.						57	52	54					X																	7868821		2203	4299	6502	SO:0001583	missense	8228	exon7			GGAAAAAGGGCTT	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"Patatin-like phospholipase domain containing"	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.668T>C	X.37:g.7868821A>G	ENSP00000370430:p.Leu223Pro	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	379	5	NM_004650	0	0	46	46	0	A8K1H3|B4E362|Q8WW83	Missense_Mutation	SNP	ENST00000381042.4	37	CCDS14129.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.341460	0.41498	.	.	ENSG00000006757	ENST00000381042;ENST00000444736;ENST00000537427	T;T;T	0.81078	-1.45;-1.45;-1.45	4.38	4.38	0.52667	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.193685	0.33127	N	0.005243	D	0.89866	0.6839	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.90635	0.4570	10	0.87932	D	0	-22.634	9.3053	0.37872	1.0:0.0:0.0:0.0	.	223	P41247	PLPL4_HUMAN	P	223;223;136	ENSP00000370430:L223P;ENSP00000415245:L223P;ENSP00000443157:L136P	ENSP00000370430:L223P	L	-	2	0	PNPLA4	7828821	1.000000	0.71417	0.139000	0.22197	0.388000	0.30384	5.486000	0.66856	1.452000	0.47756	0.481000	0.45027	CTT	.		0.353	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650		G	7868821	A	G	7868821	3	3	28	1	0	0	0	0	1	0	0	0	12193	72	3	3	97	3	PNPLA4	23	7868821	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		7868821	147401739	119	2544											
FAM122C	159091	broad.mit.edu	37	chrX	133941690	133941690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gagttccactaccgcagacgGcaacattctgagaagagtca	13	7	10	11	2	2	3	1	1	1	3	3	5	3	3	2	1	2	3	2	1	3	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chrX:133941690G>A	ENST00000370784.4	+	1	468	c.62G>A	c.(61-63)gGc>gAc	p.G21D	FAM122C_ENST00000475361.1_3'UTR|FAM122C_ENST00000370785.3_Missense_Mutation_p.G21D|FAM122C_ENST00000445123.1_5'UTR|FAM122C_ENST00000414371.2_Missense_Mutation_p.G57D	NM_001170779.1	NP_001164250.1	Q6P4D5	F222C_HUMAN	family with sequence similarity 122C	21										endometrium(2)|kidney(1)|lung(2)	5	Acute lymphoblastic leukemia(192;0.000127)					ACCGCAGACGGCAACATTCTG	0.542																																					p.G57D													.	FAM122C-130	0			c.G170A						.						104	89	94					X																	133941690		2203	4300	6503	SO:0001583	missense	159091	exon4			CAGACGGCAACAT	BC017868	CCDS14644.1, CCDS55500.1, CCDS55501.1, CCDS76028.1	Xq26.3	2008-02-05	2006-07-11		ENSG00000156500	ENSG00000156500			25202	protein-coding gene	gene with protein product						12477932	Standard	NM_138819		Approved	RP3-473B4.1	uc004exz.2	Q6P4D5	OTTHUMG00000022716	ENST00000370784.4:c.62G>A	X.37:g.133941690G>A	ENSP00000359820:p.Gly21Asp	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	131	7	NM_001170780	0	0	0	0	0	F5H036|Q8WVK9	Missense_Mutation	SNP	ENST00000370784.4	37	CCDS55501.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.478893	0.26511	.	.	ENSG00000156500	ENST00000414371;ENST00000370784;ENST00000370785	T;T;T	0.56275	0.47;0.47;0.47	4.1	-0.0526	0.13821	.	0.656135	0.15470	N	0.260647	T	0.27349	0.0671	N	0.16266	0.395	0.19575	N	0.999963	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.09377	0.004;0.002;0.004;0.003	T	0.11131	-1.0600	10	0.39692	T	0.17	.	0.6124	0.00763	0.2476:0.1865:0.3719:0.194	.	57;21;21;21	F5H036;Q6P4D5;Q6P4D5-2;Q6P187	.;F222C_HUMAN;.;.	D	57;21;21	ENSP00000402477:G57D;ENSP00000359820:G21D;ENSP00000359821:G21D	ENSP00000359820:G21D	G	+	2	0	FAM122C	133769356	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.005000	0.12855	-0.275000	0.09219	0.594000	0.82650	GGC	.		0.542	FAM122C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_138819		A	133941690	G	A	133941690	3	1	28	1	0	0	0	0	1	0	0	0	5437	1203	42	2	176	2	FAM122C	23	133941690	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	126072869	133941690	21328870	120	2545											
SLC6A8	6535	broad.mit.edu	37	chrX	152958793	152958793	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcacagccctgggcagcTacaaccgcttcaacaacaac	12	5	6	18	1	2	0	2	0	0	0	2	0	2	0	3	1	7	3	3	1	5	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chrX:152958793T>C	ENST00000253122.5	+	6	1464	c.988T>C	c.(988-990)Tac>Cac	p.Y330H	SLC6A8_ENST00000430077.2_Missense_Mutation_p.Y215H|SLC6A8_ENST00000485324.1_3'UTR	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	330					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	CCTGGGCAGCTACAACCGCTT	0.632																																					p.Y330H													.	SLC6A8-131	0			c.T988C						.						45	49	48					X																	152958793		2203	4300	6503	SO:0001583	missense	6535	exon6			GGCAGCTACAACC		CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.988T>C	X.37:g.152958793T>C	ENSP00000253122:p.Tyr330His	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	114	5	NM_005629	0	0	43	43	0	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Missense_Mutation	SNP	ENST00000253122.5	37	CCDS14726.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	26.1|26.1	4.700265|4.700265	0.88924|0.88924	.|.	.|.	ENSG00000130821|ENSG00000130821	ENST00000413787|ENST00000253122;ENST00000430077;ENST00000328897	T|D;D	0.79653|0.84516	-1.29|-1.86;-1.86	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.64402	.|U	.|0.000003	D|D	0.92980|0.92980	0.7766|0.7766	M|M	0.89214|0.89214	3.015|3.015	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.993	D|D	0.94080|0.94080	0.7343|0.7343	7|10	0.87932|0.87932	D|D	0|0	.|.	12.9947|12.9947	0.58640|0.58640	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|349;330	.|Q59EV7;P48029	.|.;SC6A8_HUMAN	P|H	45|330;215;336	ENSP00000400463:L45P|ENSP00000253122:Y330H;ENSP00000403041:Y215H	ENSP00000400463:L45P|ENSP00000253122:Y330H	L|Y	+|+	2|1	0|0	SLC6A8|SLC6A8	152611987|152611987	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.753000|7.753000	0.85153|0.85153	1.914000|1.914000	0.55421|0.55421	0.430000|0.430000	0.28490|0.28490	CTA|TAC	.		0.632	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			C	152958793	T	C	152958793	3	2	28	1	0	0	0	0	1	0	0	0	14722	1522	53	3	1010	3	SLC6A8	23	152958793	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	19017103	152958793	2311767	121	2546											
PAFAH2	5051	hgsc.bcm.edu	37	chr1	26301009	26301009	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactgttcatgctgggcacaTatcttcttcatcaaattgac	10	14	7	10	0	5	1	3	1	2	0	5	2	5	1	0	1	1	3	0	1	2	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:26301009T>C	ENST00000374282.3	-	9	1070	c.891A>G	c.(889-891)atA>atG	p.I297M	PAFAH2_ENST00000374284.1_Missense_Mutation_p.I297M	NM_000437.3	NP_000428.2	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2, 40kDa	297					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|phospholipid binding (GO:0005543)			NS(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	9		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGGGCACATATCTTCTTCA	0.483																																					p.I297M		.											.	PAFAH2-70	0			c.A891G						.						122	111	115					1																	26301009		2203	4300	6503	SO:0001583	missense	5051	exon9			GGCACATATCTTC	D87845	CCDS270.1	1p34.3	2008-09-19	2002-08-29		ENSG00000158006	ENSG00000158006			8579	protein-coding gene	gene with protein product		602344	"platelet-activating factor acetylhydrolase 2 (40kD)"			8955149, 9494101	Standard	NM_000437		Approved	HSD-PLA2	uc001bld.4	Q99487	OTTHUMG00000007437	ENST00000374282.3:c.891A>G	1.37:g.26301009T>C	ENSP00000363400:p.Ile297Met	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_000437	0	0	3	3	0	D3DPK1|O15458|Q5SY02	Missense_Mutation	SNP	ENST00000374282.3	37	CCDS270.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.376158	0.42105	.	.	ENSG00000158006	ENST00000374282;ENST00000374284	T;T	0.55930	0.49;0.49	5.62	-7.94	0.01152	.	0.773311	0.11575	N	0.550395	T	0.29749	0.0743	L	0.31926	0.97	0.25838	N	0.984087	B	0.20052	0.041	B	0.24974	0.057	T	0.18555	-1.0333	10	0.31617	T	0.26	-0.4947	2.9217	0.05771	0.1873:0.1843:0.4707:0.1577	.	297	Q99487	PAFA2_HUMAN	M	297	ENSP00000363400:I297M;ENSP00000363402:I297M	ENSP00000363400:I297M	I	-	3	3	PAFAH2	26173596	0.145000	0.22656	0.777000	0.31699	0.998000	0.95712	-0.613000	0.05610	-1.073000	0.03137	0.529000	0.55759	ATA	.		0.483	PAFAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019544.1	NM_000437		C	26301009	T	C	26301009	3	2	29	1	0	0	0	0	1	0	0	0	11413	1396	49	3	299	3	PAFAH2	1	26301009	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		26301009	222949612	1	2547											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608825	26608825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggtccaggacagggacTggggccgggaccgggaccgg	7	3	20	11	3	0	0	0	0	0	0	1	4	1	4	4	8	0	0	4	8	0	0	rs66614970		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:26608825T>C	ENST00000374222.1	-	16	1992	c.1528A>G	c.(1528-1530)Agt>Ggt	p.S510G	UBXN11_ENST00000357089.4_Missense_Mutation_p.S477G|UBXN11_ENST00000374223.1_Missense_Mutation_p.S267G|UBXN11_ENST00000374217.2_Missense_Mutation_p.S477G|UBXN11_ENST00000374221.3_Missense_Mutation_p.S510G|UBXN11_ENST00000314675.7_Missense_Mutation_p.S390G			Q5T124	UBX11_HUMAN	UBX domain protein 11	510	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggacagggactggggccggga	0.716																																					p.S510G		.											.	UBXN11-91	1	Deletion - In frame(1)	ovary(1)	c.A1528G						.						15	18	17					1																	26608825		1744	3959	5703	SO:0001583	missense	91544	exon16			AGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1528A>G	1.37:g.26608825T>C	ENSP00000363339:p.Ser510Gly	Somatic	63	2		WXS	Illumina HiSeq	Phase_I	61	4	NM_183008	0	0	0	0	0	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	-	2.154	-0.393781	0.04899	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.18502	2.21;2.22;2.49;2.48;2.48;2.49	.	.	.	.	435.379000	0.00994	U	0.003579	T	0.07007	0.0178	N	0.02539	-0.55	0.18873	N	0.999985	.	.	.	.	.	.	T	0.21690	-1.0238	6	0.42905	T	0.14	.	.	.	.	.	477;390;510	Q5T124-2;Q5T124-3;Q5T124	.;.;UBX11_HUMAN	G	390;267;477;510;510;477	ENSP00000324721:S390G;ENSP00000363340:S267G;ENSP00000349601:S477G;ENSP00000363338:S510G;ENSP00000363339:S510G;ENSP00000363334:S477G	ENSP00000324721:S390G	S	-	1	0	UBXN11	26481412	0.000000	0.05858	0.130000	0.21974	0.142000	0.21351	-0.966000	0.03825	0.056000	0.16144	0.055000	0.15244	AGT	.		0.716	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		C	26608825	T	C	26608825	3	2	29	1	0	0	0	0	1	0	0	0	16946	1580	55	3	38	3	UBXN11	1	26608825	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	307816	26608825	222641796	2	2548											
BAI2	576	hgsc.bcm.edu	37	chr1	32210251	32210251	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgggcccgagttacctGtctgcgccatgtatagccca	7	8	13	13	3	1	0	0	0	1	0	1	2	1	0	4	2	3	2	4	2	3	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:32210251G>C	ENST00000373658.3	-	5	1261	c.920C>G	c.(919-921)aCa>aGa	p.T307R	BAI2_ENST00000398542.1_Missense_Mutation_p.T295R|BAI2_ENST00000527361.1_Missense_Mutation_p.T307R|BAI2_ENST00000257070.4_Missense_Mutation_p.T307R|BAI2_ENST00000398538.1_Missense_Mutation_p.T295R|BAI2_ENST00000373655.2_Missense_Mutation_p.T307R|BAI2_ENST00000440175.2_Missense_Mutation_p.T4R|BAI2_ENST00000398556.3_Missense_Mutation_p.T310R|BAI2_ENST00000398547.1_Missense_Mutation_p.T295R	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	307					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		CGAGTTACCTGTCTGCGCCAT	0.627																																					p.T307R		.											.	BAI2-526	0			c.C920G						.						86	73	77					1																	32210251		2203	4300	6503	SO:0001583	missense	576	exon5			TTACCTGTCTGCG	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.920C>G	1.37:g.32210251G>C	ENSP00000362762:p.Thr307Arg	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	40	3	NM_001703	0	0	0	0	0	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	G	15.01	2.705214	0.48412	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T;T	0.47177	1.48;1.68;0.89;0.88;1.86;0.85;0.85;1.6;0.92;1.46;1.34	4.4	4.4	0.53042	.	0.000000	0.35067	N	0.003474	T	0.56262	0.1973	L	0.29908	0.895	0.24426	N	0.994593	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.995;0.985;0.999;0.999;0.996	D;D;D;P;D;D;D	0.85130	0.997;0.986;0.974;0.72;0.979;0.991;0.943	T	0.51164	-0.8740	10	0.59425	D	0.04	.	14.2951	0.66308	0.0:0.0:1.0:0.0	.	295;307;295;4;295;307;307	A2A3C3;O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;.;BAI2_HUMAN	R	310;295;307;307;295;307;307;4;295;300;341	ENSP00000381564:T310R;ENSP00000381555:T295R;ENSP00000362762:T307R;ENSP00000362759:T307R;ENSP00000381550:T295R;ENSP00000257070:T307R;ENSP00000435397:T307R;ENSP00000391071:T4R;ENSP00000381548:T295R;ENSP00000410921:T300R;ENSP00000437219:T341R	ENSP00000257070:T307R	T	-	2	0	BAI2	31982838	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.540000	0.53611	2.172000	0.68678	0.313000	0.20887	ACA	.		0.627	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		C	32210251	G	C	32210251	3	2	29	1	0	0	0	0	1	0	0	0	1300	1377	48	4	3953	4	BAI2	1	32210251	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	5601426	32210251	217040370	3	2549											
ZMPSTE24	10269	broad.mit.edu	37	chr1	40733505	40733505	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatctctggagactttctggAcggttctgtggttatgctgg	5	16	13	7	1	3	1	0	0	3	1	4	3	3	2	0	5	1	3	0	5	2	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:40733505A>G	ENST00000372759.3	+	3	483	c.318A>G	c.(316-318)ggA>ggG	p.G106G		NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	106					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			GACTTTCTGGACGGTTCTGTG	0.383																																					p.G106G													.	ZMPSTE24-226	0			c.A318G						.						263	249	254					1																	40733505		2203	4300	6503	SO:0001819	synonymous_variant	10269	exon3			TTCTGGACGGTTC	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog"	606480	"zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)"			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.318A>G	1.37:g.40733505A>G		Somatic	419	0		WXS	Illumina HiSeq	Phase_I	569	5	NM_005857	0	0	2	2	0	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Silent	SNP	ENST00000372759.3	37	CCDS449.1																																																																																			.		0.383	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1			G	40733505	A	G	40733505	2	3	29	1	0	0	0	0	0	0	0	1	17730	262	10	3		3	ZMPSTE24	1	40733505	Silent	SNP	A	TCGA-AL-3466-01A-01D-1252-08	8523254	40733505	208517116	4	2550											
LRP8	7804	ucsc.edu	37	chr1	53723084	53723084	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggggctcttgtggtggcaggTactgtcctcgtcatggtaga	5	12	16	8	1	2	1	1	0	1	1	4	1	3	1	1	6	1	4	1	6	2	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:53723084T>G	ENST00000306052.6	-	15	2363	c.2262A>C	c.(2260-2262)gtA>gtC	p.V754V	LRP8_ENST00000354412.3_Intron|LRP8_ENST00000347547.2_Silent_p.V584V|LRP8_ENST00000465675.1_Silent_p.V307V|LRP8_ENST00000460214.1_5'UTR|LRP8_ENST00000371454.2_Silent_p.V754V	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	754	Clustered O-linked oligosaccharides.				ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						TGGTGGCAGGTACTGTCCTCG	0.542																																					p.V754V													.	LRP8-90	0			c.A2262C						.						275	223	240					1																	53723084		2203	4300	6503	SO:0001819	synonymous_variant	7804	exon15			GGCAGGTACTGTC	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"Low density lipoprotein receptors"	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2262A>C	1.37:g.53723084T>G		Somatic	109	12		WXS	Illumina HiSeq		188	32	NM_004631	0	0	19	26	7	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Silent	SNP	ENST00000306052.6	37	CCDS578.1																																																																																			.		0.542	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		G	53723084	T	G	53723084	2	3	29	1	0	0	0	0	0	0	0	1	8988	1625	57	5		5	LRP8	1	53723084	Silent	SNP	T	TCGA-AL-3466-01A-01D-1252-08	12989579	53723084	195527537	5	2551											
SASS6	163786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	100572938	100572938	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aatattaactacctcttgctCtttaattcgaagagactgtc	12	15	5	9	1	2	1	0	0	2	1	4	3	2	1	1	0	3	1	1	0	6	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:100572938C>G	ENST00000287482.5	-	11	1458	c.1318G>C	c.(1318-1320)Gag>Cag	p.E440Q	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.E273Q	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	440					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		ACCTCTTGCTCTTTAATTCGA	0.294																																					p.E440Q		.											.	SASS6-70	0			c.G1318C						.						57	53	54					1																	100572938		2201	4289	6490	SO:0001583	missense	163786	exon11			CTTGCTCTTTAAT	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1318G>C	1.37:g.100572938C>G	ENSP00000287482:p.Glu440Gln	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	88	13	NM_194292	0	0	0	0	0	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	37	CCDS764.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812823	0.32053	.	.	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.29397	1.57;1.57	5.38	5.38	0.77491	.	0.047861	0.85682	D	0.000000	T	0.23451	0.0567	L	0.60455	1.87	0.58432	D	0.999999	P	0.41546	0.754	B	0.39339	0.297	T	0.02743	-1.1116	10	0.35671	T	0.21	-9.3422	19.1244	0.93376	0.0:1.0:0.0:0.0	.	440	Q6UVJ0	SAS6_HUMAN	Q	440;413;273	ENSP00000287482:E440Q;ENSP00000440169:E273Q	ENSP00000287482:E440Q	E	-	1	0	SASS6	100345526	1.000000	0.71417	1.000000	0.80357	0.064000	0.16182	5.050000	0.64251	2.515000	0.84797	0.585000	0.79938	GAG	.		0.294	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		G	100572938	C	G	100572938	3	3	29	1	0	0	0	0	1	0	0	0	13882	922	32	4	683	4	SASS6	1	100572938	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	46849854	100572938	148677683	6	2552											
TARS2	80222	broad.mit.edu	37	chr1	150471422	150471422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttcctccgttccgtctatgCcgttcttggcttctccttcc	1	18	6	16	3	3	0	0	0	3	0	8	0	7	0	6	1	1	3	6	1	1	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:150471422C>T	ENST00000369064.3	+	12	1485	c.1451C>T	c.(1450-1452)gCc>gTc	p.A484V	TARS2_ENST00000369054.2_Missense_Mutation_p.A354V|TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000606933.1_Missense_Mutation_p.A402V	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	484					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	TCCGTCTATGCCGTTCTTGGC	0.587																																					p.A484V													.	TARS2-91	0			c.C1451T						.						163	136	145					1																	150471422		2203	4300	6503	SO:0001583	missense	80222	exon12			TCTATGCCGTTCT	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	30740	protein-coding gene	gene with protein product	"threonine tRNA ligase 2, mitochondrial"	612805	"threonyl-tRNA synthetase-like 1"	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1451C>T	1.37:g.150471422C>T	ENSP00000358060:p.Ala484Val	Somatic	348	1		WXS	Illumina HiSeq	Phase_I	699	7	NM_025150	0	0	31	31	0	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	37	CCDS952.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.119981	0.37436	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	T;T;T	0.68331	-0.32;-0.32;-0.32	4.81	2.86	0.33363	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.674200	0.15210	N	0.274517	T	0.49932	0.1586	M	0.63208	1.945	0.09310	N	0.999997	P;P;P	0.45634	0.863;0.849;0.629	B;B;B	0.43990	0.438;0.438;0.243	T	0.39272	-0.9622	10	0.56958	D	0.05	1.1321	10.2069	0.43118	0.154:0.6977:0.1484:0.0	.	354;209;484	Q9H9V2;E7EVR9;Q9BW92	.;.;SYTM_HUMAN	V	354;484;209;209	ENSP00000358050:A354V;ENSP00000358060:A484V;ENSP00000358047:A209V	ENSP00000358047:A209V	A	+	2	0	TARS2	148738046	0.042000	0.20092	0.001000	0.08648	0.220000	0.24768	2.457000	0.45005	0.583000	0.29574	0.655000	0.94253	GCC	.		0.587	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		T	150471422	C	T	150471422	3	4	29	1	0	0	0	0	1	0	0	0	15592	739	26	2	1497	2	TARS2	1	150471422	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	49898484	150471422	98779199	7	2553											
RPTN	126638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152127802	152127802	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtacttattttgcccttgTatttccccagtctgtgattg	7	18	7	9	0	1	1	0	1	1	0	2	1	2	1	3	0	2	2	3	0	4	8			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:152127802T>C	ENST00000316073.3	-	3	1837	c.1773A>G	c.(1771-1773)atA>atG	p.I591M		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	591	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TTTGCCCTTGTATTTCCCCAG	0.453																																					p.I591M		.											.	RPTN-68	0			c.A1773G						.						371	334	345					1																	152127802		1568	3582	5150	SO:0001583	missense	126638	exon3			CCCTTGTATTTCC	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1773A>G	1.37:g.152127802T>C	ENSP00000317895:p.Ile591Met	Somatic	594	0		WXS	Illumina HiSeq	Phase_I	769	224	NM_001122965	0	0	0	0	0	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	2.328	-0.353972	0.05173	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.13307	2.6	3.14	1.75	0.24633	.	.	.	.	.	T	0.01765	0.0056	N	0.08118	0	0.09310	N	1	P	0.41265	0.744	B	0.36608	0.229	T	0.42413	-0.9453	9	0.32370	T	0.25	0.0237	6.2084	0.20615	0.3116:0.0:0.0:0.6884	.	591	Q6XPR3	RPTN_HUMAN	M	591;246	ENSP00000317895:I591M	ENSP00000317895:I591M	I	-	3	3	RPTN	150394426	0.005000	0.15991	0.015000	0.15790	0.332000	0.28634	-0.725000	0.04942	0.119000	0.18210	0.450000	0.29827	ATA	.		0.453	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		C	152127802	T	C	152127802	3	2	29	1	0	0	0	0	1	0	0	0	13696	1628	57	3	585	3	RPTN	1	152127802	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	1656380	152127802	97122819	8	2554											
NUP210L	91181	broad.mit.edu	37	chr1	153991451	153991451	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggatgtcatgaaaaatCattgcagtccccggactcct	10	10	9	12	1	2	1	2	1	0	0	4	3	4	3	4	2	1	1	4	2	2	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:153991451C>A	ENST00000368559.3	-	33	4682	c.4611G>T	c.(4609-4611)atG>atT	p.M1537I	NUP210L_ENST00000368553.1_Missense_Mutation_p.M470I|NUP210L_ENST00000271854.3_Missense_Mutation_p.M1537I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1537					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CATGAAAAATCATTGCAGTCC	0.438																																					p.M1537I													.	NUP210L-77	0			c.G4611T						.						101	99	99					1																	153991451		1887	4112	5999	SO:0001583	missense	91181	exon33			AAAAATCATTGCA	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.4611G>T	1.37:g.153991451C>A	ENSP00000357547:p.Met1537Ile	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	183	6	NM_001159484	0	0	0	0	0	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.247010	0.39697	.	.	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.20738	3.66;2.05;3.37	5.61	-5.16	0.02857	.	0.431478	0.22335	N	0.061414	T	0.01523	0.0049	N	0.02539	-0.55	0.20196	N	0.99993	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.37009	-0.9724	10	0.49607	T	0.09	-32.0755	1.7189	0.02908	0.2068:0.3642:0.1855:0.2434	.	1537;1537	E7EP56;Q5VU65	.;P210L_HUMAN	I	1537;470;1537	ENSP00000357547:M1537I;ENSP00000357541:M470I;ENSP00000271854:M1537I	ENSP00000271854:M1537I	M	-	3	0	NUP210L	152258075	0.007000	0.16637	0.901000	0.35422	0.964000	0.63967	-0.837000	0.04377	-0.411000	0.07530	-0.302000	0.09304	ATG	.		0.438	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		A	153991451	C	A	153991451	3	1	29	1	0	0	0	0	1	0	0	0	10787	826	29	4	1087	4	NUP210L	1	153991451	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	1863649	153991451	95259170	9	2555											
GBA	2629	ucsc.edu	37	chr1	155206133	155206133	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacacaggcctctgaggcaAagagcatggtgttggggaac	11	6	14	10	0	1	2	0	1	1	1	1	3	1	3	2	5	2	3	2	5	2	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:155206133A>C	ENST00000327247.5	-	9	1359	c.1127T>G	c.(1126-1128)tTt>tGt	p.F376C	AL713999.1_ENST00000401290.1_RNA|GBA_ENST00000428024.3_Missense_Mutation_p.F289C|GBA_ENST00000368373.3_Missense_Mutation_p.F376C|GBA_ENST00000536770.1_Missense_Mutation_p.F263C|GBA_ENST00000427500.3_Missense_Mutation_p.F327C|GBA_ENST00000493842.1_5'Flank	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	376					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glucosylceramide catabolic process (GO:0006680)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of MAP kinase activity (GO:0043407)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of water loss via skin (GO:0033561)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to pH (GO:0009268)|response to testosterone (GO:0033574)|response to thyroid hormone (GO:0097066)|skin morphogenesis (GO:0043589)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)|termination of signal transduction (GO:0023021)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)	glucosylceramidase activity (GO:0004348)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	26	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Velaglucerase alfa(DB06720)	CTCTGAGGCAAAGAGCATGGT	0.567									Gaucher disease type I																												p.F376C													.	GBA-92	0			c.T1127G						.						78	69	72					1																	155206133		2203	4300	6503	SO:0001583	missense	2629	exon9	Familial Cancer Database	glucocerebrosidase insufficiency	GAGGCAAAGAGCA	M19285	CCDS1102.1, CCDS53373.1, CCDS53374.1	1q22	2010-01-19	2010-01-19		ENSG00000177628	ENSG00000177628	3.2.1.21		4177	protein-coding gene	gene with protein product		606463	"glucosylceramidase", "glucosidase, beta; acid (includes glucosylceramidase)"	GLUC		3359914	Standard	NM_001005742		Approved	GBA1	uc001fjl.3	P04062	OTTHUMG00000035841	ENST00000327247.5:c.1127T>G	1.37:g.155206133A>C	ENSP00000314508:p.Phe376Cys	Somatic	101	0		WXS	Illumina HiSeq		203	1	NM_001005742	0	0	29	37	8	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Missense_Mutation	SNP	ENST00000327247.5	37	CCDS1102.1	.	.	.	.	.	.	.	.	.	.	.	19.68	3.873368	0.72180	.	.	ENSG00000177628	ENST00000427500;ENST00000428024;ENST00000368373;ENST00000327247;ENST00000536770;ENST00000536555;ENST00000402928	D;D;D;D;D	0.99220	-5.58;-5.58;-5.58;-5.58;-5.58	3.67	3.67	0.42095	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000001	D	0.99108	0.9693	M	0.79926	2.475	0.50467	D	0.999875	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.984;0.988;0.993	D	0.99780	1.1027	10	0.87932	D	0	.	8.823	0.35039	1.0:0.0:0.0:0.0	.	327;263;376	B7Z5G2;F5H241;P04062	.;.;GLCM_HUMAN	C	327;289;376;376;263;333;361	ENSP00000402577:F327C;ENSP00000397986:F289C;ENSP00000357357:F376C;ENSP00000314508:F376C;ENSP00000445560:F263C	ENSP00000314508:F376C	F	-	2	0	GBA	153472757	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.259000	0.89855	1.650000	0.50662	0.397000	0.26171	TTT	.		0.567	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157		C	155206133	A	C	155206133	3	2	29	1	0	0	0	0	1	0	0	0	6286	14	1	5	499	5	GBA	1	155206133	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	1214682	155206133	94044488	10	2556											
FAM129A	116496	hgsc.bcm.edu;broad.mit.edu	37	chr1	184767228	184767228	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacctttcagagtttcatCaagcaggatctgatgtaaaa	13	13	7	8	0	4	2	3	1	1	1	4	3	4	3	1	1	2	3	1	1	4	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:184767228C>A	ENST00000367511.3	-	13	1844	c.1651G>T	c.(1651-1653)Gat>Tat	p.D551Y	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	551					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						AGAGTTTCATCAAGCAGGATC	0.453																																					p.D551Y		.											.	FAM129A-94	0			c.G1651T						.						87	78	81					1																	184767228		2203	4300	6503	SO:0001583	missense	116496	exon13			TTTCATCAAGCAG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.1651G>T	1.37:g.184767228C>A	ENSP00000356481:p.Asp551Tyr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	87	8	NM_052966	0	0	0	0	0	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.62|16.62	3.173955|3.173955	0.57692|0.57692	.|.	.|.	ENSG00000135842|ENSG00000135842	ENST00000367511|ENST00000417056	T|.	0.13307|.	2.6|.	5.37|5.37	4.44|4.44	0.53790|0.53790	.|.	0.408987|.	0.29225|.	N|.	0.012780|.	T|.	0.63189|.	0.2490|.	L|L	0.54323|0.54323	1.7|1.7	0.34170|0.34170	D|D	0.669652|0.669652	D;D|.	0.89917|.	0.986;1.0|.	P;D|.	0.73380|.	0.742;0.98|.	T|.	0.71794|.	-0.4485|.	10|.	0.72032|.	D|.	0.01|.	-7.0804|-7.0804	14.591|14.591	0.68365|0.68365	0.0:0.8548:0.1452:0.0|0.0:0.8548:0.1452:0.0	.|.	82;551|.	Q5TEY9;Q9BZQ8|.	.;NIBAN_HUMAN|.	Y|L	551|82	ENSP00000356481:D551Y|.	ENSP00000356481:D551Y|.	D|X	-|-	1|2	0|2	FAM129A|FAM129A	183033851|183033851	0.876000|0.876000	0.30132|0.30132	0.985000|0.985000	0.45067|0.45067	0.994000|0.994000	0.84299|0.84299	2.463000|2.463000	0.45058|0.45058	1.233000|1.233000	0.43693|0.43693	0.655000|0.655000	0.94253|0.94253	GAT|TGA	.		0.453	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			A	184767228	C	A	184767228	3	1	29	1	0	0	0	0	1	0	0	0	5452	826	29	4	1143	4	FAM129A	1	184767228	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	29561095	184767228	64483393	11	2557											
TPR	7175	broad.mit.edu	37	chr1	186327733	186327735	+	In_Frame_Del	DEL	GAT	GAT	-																															gattatctctctcaagtacaGatgattgcttgttggcttta																										TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:186327733_186327735delGAT	ENST00000367478.4	-	13	1733_1735	c.1437_1439delATC	c.(1435-1440)tcatct>tct	p.479_480SS>S	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	479	Necessary for association to the NPC.				carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTCAAGTACAGATGATTGCTTGT	0.32			T	NTRK1	papillary thyroid																																p.479_480del				Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR-228	0			c.1437_1439del						.																																			SO:0001651	inframe_deletion	7175	exon13			AGTACAGATGATT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.1437_1439delATC	1.37:g.186327736_186327738delGAT	ENSP00000356448:p.Ser480del	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	63	7	NM_003292	0	0	0	0	0	Q15655|Q5SWY0|Q99968	In_Frame_Del	DEL	ENST00000367478.4	37	CCDS41446.1																																																																																			.		0.32	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		-	186327735	GAT	-	186327733	7	5	29	1	0	1	0	1	0	0	0	0	16449	942	33	0	5808	0	TPR	1	186327733	In_Frame_Del	DEL	GAT	TCGA-AL-3466-01A-01D-1252-08	1560505	186327733	62922888	12	2558											
PTPN14	5784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214557259	214557259	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgccccgcaccatgctgtTcatcacctccaggctgtggc	6	9	9	17	1	2	0	2	0	0	0	3	0	3	0	5	2	2	4	5	2	0	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:214557259T>C	ENST00000366956.5	-	13	2133	c.1939A>G	c.(1939-1941)Aac>Gac	p.N647D	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	647					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		ACCATGCTGTTCATCACCTCC	0.662																																					p.N647D	Colon(92;557 1424 24372 34121 40073)	.											.	PTPN14-290	0			c.A1939G						.						50	42	45					1																	214557259		2203	4300	6503	SO:0001583	missense	5784	exon13			TGCTGTTCATCAC	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1939A>G	1.37:g.214557259T>C	ENSP00000355923:p.Asn647Asp	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	169	55	NM_005401	0	0	0	0	0	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.600155	0.46423	.	.	ENSG00000152104	ENST00000366956	T	0.66815	-0.23	5.66	4.43	0.53597	.	0.373344	0.33217	N	0.005146	T	0.45458	0.1343	N	0.08118	0	0.80722	D	1	B	0.12630	0.006	B	0.10450	0.005	T	0.35525	-0.9785	10	0.62326	D	0.03	.	9.7306	0.40359	0.0:0.1:0.0:0.9	.	647	Q15678	PTN14_HUMAN	D	647	ENSP00000355923:N647D	ENSP00000355923:N647D	N	-	1	0	PTPN14	212623882	1.000000	0.71417	0.970000	0.41538	0.991000	0.79684	3.785000	0.55424	0.847000	0.35167	0.455000	0.32223	AAC	.		0.662	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		C	214557259	T	C	214557259	3	2	29	1	0	0	0	0	1	0	0	0	12813	1783	62	3	1652	3	PTPN14	1	214557259	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	28229526	214557259	34693362	13	2559											
MOSC1	64757	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	220971317	220971317	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gttaaagcaaccaacttcagGcccaatattgtaatttcagg	14	11	7	9	0	2	0	2	0	0	0	2	0	2	0	2	2	3	3	2	2	7	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:220971317G>A	ENST00000366910.5	+	4	900	c.714G>A	c.(712-714)agG>agA	p.R238R	MARC1_ENST00000496110.1_3'UTR	NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	238	MOSC. {ECO:0000255|PROSITE- ProRule:PRU00670}.				detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										CCAACTTCAGGCCCAATATTG	0.443																																					p.R238R		.											.	.	0			c.G714A						.						168	167	167					1																	220971317		2203	4300	6503	SO:0001819	synonymous_variant	64757	exon4			CTTCAGGCCCAAT	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.714G>A	1.37:g.220971317G>A		Somatic	376	0		WXS	Illumina HiSeq	Phase_I	498	119	NM_022746	0	0	9	17	8	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Silent	SNP	ENST00000366910.5	37	CCDS1526.1	.	.	.	.	.	.	.	.	.	.	G	2.055	-0.416878	0.04766	.	.	ENSG00000186205	ENST00000407981	.	.	.	4.95	3.04	0.35103	.	.	.	.	.	T	0.47875	0.1469	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39057	-0.9632	4	.	.	.	-19.1717	4.6342	0.12516	0.2726:0.1776:0.5497:0.0	.	.	.	.	T	147	.	.	A	+	1	0	MOSC1	219037940	0.990000	0.36364	0.996000	0.52242	0.079000	0.17450	0.098000	0.15189	1.211000	0.43351	0.655000	0.94253	GCC	.		0.443	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		A	220971317	G	A	220971317	2	1	29	1	0	0	0	0	0	0	0	1	9738	1194	42	2		2	MOSC1	1	220971317	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08	6414058	220971317	28279304	14	2560											
SLC35F3	148641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	234458910	234458910	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagtgaggaagaaggaggAgcctgcagagggcgctgccg	12	3	18	8	2	0	3	0	1	0	2	0	6	0	6	2	4	3	2	2	4	3	0			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:234458910A>T	ENST00000366617.3	+	7	1415	c.1187A>T	c.(1186-1188)gAg>gTg	p.E396V	SLC35F3_ENST00000366618.3_Missense_Mutation_p.E465V			Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	396					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			AAGAAGGAGGAGCCTGCAGAG	0.587											OREG0014330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E465V		.											.	SLC35F3-92	0			c.A1394T						.						74	73	74					1																	234458910		2203	4300	6503	SO:0001583	missense	148641	exon8			AGGAGGAGCCTGC		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"Solute carriers"	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366617.3:c.1187A>T	1.37:g.234458910A>T	ENSP00000355576:p.Glu396Val	Somatic	160	0	2373	WXS	Illumina HiSeq	Phase_I	281	36	NM_173508	0	0	0	0	0	Q5TDD6|Q8N9C9	Missense_Mutation	SNP	ENST00000366617.3	37		.	.	.	.	.	.	.	.	.	.	A	25.5	4.643874	0.87859	.	.	ENSG00000183780	ENST00000366618;ENST00000366617	T;T	0.53857	0.6;0.62	5.62	5.62	0.85841	.	0.214041	0.48767	D	0.000163	T	0.58623	0.2135	L	0.50333	1.59	0.51482	D	0.999922	D;D	0.57571	0.966;0.98	P;P	0.51229	0.543;0.663	T	0.61983	-0.6950	10	0.59425	D	0.04	-20.2302	15.7908	0.78364	1.0:0.0:0.0:0.0	.	396;465	Q8IY50;Q8IY50-2	S35F3_HUMAN;.	V	465;396	ENSP00000355577:E465V;ENSP00000355576:E396V	ENSP00000355576:E396V	E	+	2	0	SLC35F3	232525533	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	8.954000	0.93051	2.132000	0.65825	0.402000	0.26972	GAG	.		0.587	SLC35F3-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000128322.1	NM_173508		T	234458910	A	T	234458910	3	4	29	1	0	0	0	0	1	0	0	0	14622	304	11	5	1424	5	SLC35F3	1	234458910	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	13487593	234458910	14791711	15	2561											
RAB11FIP5	26056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	73315269	73315269	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggatgagtgatgtggggaggCccccaggatgggacccccct	7	6	17	11	0	0	2	0	2	0	0	0	6	0	6	5	6	0	0	5	6	0	0			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:73315269C>T	ENST00000258098.6	-	3	1717	c.1477G>A	c.(1477-1479)Gcc>Acc	p.A493T	RAB11FIP5_ENST00000493523.2_5'UTR	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	493					cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)			biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						TGTGGGGAGGCCCCCAGGATG	0.607																																					p.A493T		.											.	RAB11FIP5-90	0			c.G1477A						.						69	74	72					2																	73315269		2203	4300	6503	SO:0001583	missense	26056	exon3			GGGAGGCCCCCAG	AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.1477G>A	2.37:g.73315269C>T	ENSP00000258098:p.Ala493Thr	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	484	55	NM_015470	0	0	0	0	0	O94939|Q9P0M1	Missense_Mutation	SNP	ENST00000258098.6	37	CCDS1923.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217658	0.58560	.	.	ENSG00000135631	ENST00000258098	T	0.50548	0.74	4.52	4.52	0.55395	.	0.334564	0.25935	N	0.027344	T	0.50905	0.1643	N	0.19112	0.55	0.34421	D	0.697508	D;D	0.63880	0.993;0.993	D;D	0.74674	0.971;0.984	T	0.55780	-0.8087	10	0.23891	T	0.37	-11.0892	14.4444	0.67340	0.0:1.0:0.0:0.0	.	493;493	Q9BXF6;Q2Z1P3	RFIP5_HUMAN;.	T	493	ENSP00000258098:A493T	ENSP00000258098:A493T	A	-	1	0	RAB11FIP5	73168777	0.002000	0.14202	0.992000	0.48379	0.966000	0.64601	-0.184000	0.09698	2.527000	0.85204	0.491000	0.48974	GCC	.		0.607	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470		T	73315269	C	T	73315269	3	4	29	1	0	0	0	0	1	0	0	0	12929	739	26	2	496	2	RAB11FIP5	2	73315269	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		73315269	169884104	16	2562											
LCT	3938	broad.mit.edu	37	chr2	136575259	136575259	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atccgggaccaggagatggaGaacttgtacacctgagcccg	11	6	13	11	2	0	3	0	1	0	2	1	6	1	4	4	3	3	1	4	3	2	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:136575259G>C	ENST00000264162.2	-	6	1369	c.1359C>G	c.(1357-1359)ttC>ttG	p.F453L	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	453	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AGGAGATGGAGAACTTGTACA	0.622																																					p.F453L													.	LCT-101	0			c.C1359G						.						63	60	61					2																	136575259		2203	4300	6503	SO:0001583	missense	3938	exon6			GATGGAGAACTTG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1359C>G	2.37:g.136575259G>C	ENSP00000264162:p.Phe453Leu	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	275	4	NM_002299	0	0	0	0	0	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252680	0.80135	.	.	ENSG00000115850	ENST00000264162	T	0.38887	1.11	5.77	1.76	0.24704	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.101961	0.64402	D	0.000002	T	0.61751	0.2372	M	0.82132	2.575	0.45946	D	0.998775	D	0.89917	1.0	D	0.91635	0.999	T	0.63070	-0.6719	10	0.87932	D	0	-31.2631	9.6032	0.39617	0.3854:0.0:0.6146:0.0	.	453	P09848	LPH_HUMAN	L	453	ENSP00000264162:F453L	ENSP00000264162:F453L	F	-	3	2	LCT	136291729	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.967000	0.40491	0.400000	0.25396	0.655000	0.94253	TTC	.		0.622	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		C	136575259	G	C	136575259	3	2	29	1	0	0	0	0	1	0	0	0	8714	933	33	4	4472	4	LCT	2	136575259	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	63259990	136575259	106624114	17	2563											
SCN3A	6328	broad.mit.edu	37	chr2	166010994	166010994	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgttgctttttaagctgttCgagcatctgctgaaattcgg	7	16	10	8	2	1	1	0	1	1	0	3	2	1	1	0	1	4	6	0	1	2	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:166010994C>T	ENST00000360093.3	-	11	1839	c.1348G>A	c.(1348-1350)Gaa>Aaa	p.E450K	SCN3A_ENST00000409101.3_Missense_Mutation_p.E450K|SCN3A_ENST00000283254.7_Missense_Mutation_p.E450K	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	450					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E450K(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTAAGCTGTTCGAGCATCTGC	0.403																																					p.E450K													.	SCN3A-141	1	Substitution - Missense(1)	large_intestine(1)	c.G1348A						.						117	113	114					2																	166010994		2203	4300	6503	SO:0001583	missense	6328	exon11			GCTGTTCGAGCAT	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1348G>A	2.37:g.166010994C>T	ENSP00000353206:p.Glu450Lys	Somatic	202	1		WXS	Illumina HiSeq	Phase_I	90	7	NM_001081676	0	0	0	0	0	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	C	21.2	4.109195	0.77096	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.96913	-4.17;-4.17;-4.15;-4.02	5.6	5.6	0.85130	.	0.100000	0.43579	D	0.000547	D	0.95214	0.8448	M	0.66439	2.03	0.80722	D	1	B;B;B;B;B	0.31837	0.342;0.342;0.198;0.198;0.198	B;B;B;B;B	0.23852	0.022;0.022;0.049;0.049;0.049	D	0.94142	0.7398	10	0.72032	D	0.01	.	19.6137	0.95619	0.0:1.0:0.0:0.0	.	450;450;450;450;450	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	K	450	ENSP00000353206:E450K;ENSP00000283254:E450K;ENSP00000386726:E450K;ENSP00000403348:E450K	ENSP00000283254:E450K	E	-	1	0	SCN3A	165719240	1.000000	0.71417	0.915000	0.36163	0.980000	0.70556	7.818000	0.86416	2.636000	0.89361	0.591000	0.81541	GAA	.		0.403	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		T	166010994	C	T	166010994	3	4	29	1	0	0	0	0	1	0	0	0	13950	893	31	1	4726	1	SCN3A	2	166010994	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	29435735	166010994	77188379	18	2564											
TTC30B	150737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178416990	178416990	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcatgcagcttcatactgtcCctccttgtagagcaaacaac	11	10	7	13	0	1	1	1	0	0	1	3	1	3	1	2	0	6	5	2	0	4	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:178416990C>T	ENST00000408939.3	-	1	752	c.502G>A	c.(502-504)Gga>Aga	p.G168R		NM_152517.2	NP_689730.2	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	168				Missing (in Ref. 1; BAB70953). {ECO:0000305}.	cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				cervix(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			TCATACTGTCCCTCCTTGTAG	0.567																																					p.G168R		.											.	.	0			c.G502A						.						161	177	172					2																	178416990		2203	4300	6503	SO:0001583	missense	150737	exon1			ACTGTCCCTCCTT	AK055552	CCDS42784.1	2q31.2	2014-02-21			ENSG00000196659	ENSG00000196659		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	26425	protein-coding gene	gene with protein product						12477932	Standard	NM_152517		Approved	FLJ30990, fleer, IFT70	uc002uln.3	Q8N4P2	OTTHUMG00000154166	ENST00000408939.3:c.502G>A	2.37:g.178416990C>T	ENSP00000386181:p.Gly168Arg	Somatic	459	1		WXS	Illumina HiSeq	Phase_I	828	103	NM_152517	0	0	0	0	0	Q63HQ1|Q96NE6	Missense_Mutation	SNP	ENST00000408939.3	37	CCDS42784.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.733709	0.48939	.	.	ENSG00000196659	ENST00000500357;ENST00000408939	T	0.65916	-0.18	4.51	4.51	0.55191	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77758	0.4178	M	0.78916	2.43	0.80722	D	1	D	0.53462	0.96	P	0.61070	0.883	T	0.80792	-0.1224	10	0.59425	D	0.04	.	17.7624	0.88468	0.0:1.0:0.0:0.0	.	168	Q8N4P2	TT30B_HUMAN	R	121;168	ENSP00000386181:G168R	ENSP00000386181:G168R	G	-	1	0	TTC30B	178125236	1.000000	0.71417	0.999000	0.59377	0.158000	0.22134	7.532000	0.81985	2.487000	0.83934	0.655000	0.94253	GGA	.		0.567	TTC30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334193.2	NM_152517		T	178416990	C	T	178416990	3	4	29	1	0	0	0	0	1	0	0	0	16732	632	22	2	1499	2	TTC30B	2	178416990	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	12405996	178416990	64782383	19	2565											
TTN	7273	broad.mit.edu	37	chr2	179415765	179415765	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagttccaacagcatttcttGcaattattctgaactcatag	12	15	5	9	0	3	1	1	1	2	0	4	1	4	1	1	0	4	3	1	0	6	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:179415765G>A	ENST00000591111.1	-	286	86794	c.86570C>T	c.(86569-86571)gCa>gTa	p.A28857V	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A21625V|TTN_ENST00000342992.6_Missense_Mutation_p.A27930V|TTN_ENST00000589042.1_Missense_Mutation_p.A30498V|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A21558V|TTN_ENST00000460472.2_Missense_Mutation_p.A21433V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28857	Fibronectin type-III 110. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGCATTTCTTGCAATTATTCT	0.418																																					p.A30498V													.	TTN-636	0			c.C91493T						.						80	76	77					2																	179415765		1885	4117	6002	SO:0001583	missense	7273	exon336			TTTCTTGCAATTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.86570C>T	2.37:g.179415765G>A	ENSP00000465570:p.Ala28857Val	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	36	3	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.467341	0.96257	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	5.9	5.9	0.94986	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.91408	0.7289	H	0.96301	3.8	0.80722	D	1	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	D	0.93227	0.6614	9	0.87932	D	0	.	20.2787	0.98501	0.0:0.0:1.0:0.0	.	21433;21558;21625;28857	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	27930;21433;21625;21558;21430	ENSP00000343764:A27930V;ENSP00000434586:A21433V;ENSP00000340554:A21625V;ENSP00000352154:A21558V	ENSP00000340554:A21625V	A	-	2	0	TTN	179124011	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.798000	0.96311	0.650000	0.86243	GCA	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179415765	G	A	179415765	3	1	29	1	0	0	0	0	1	0	0	0	16768	1319	46	2	16594	2	TTN	2	179415765	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	998775	179415765	63783608	20	2566											
TTLL4	9654	broad.mit.edu	37	chr2	219612347	219612347	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacaaaccctacctcatcagCggcagcaagtttgacctgcg	11	7	8	15	2	2	1	2	1	0	0	2	1	2	1	3	1	5	3	3	1	3	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:219612347C>T	ENST00000392102.1	+	11	2617	c.2277C>T	c.(2275-2277)agC>agT	p.S759S	TTLL4_ENST00000442769.1_Silent_p.S695S|TTLL4_ENST00000457313.1_Silent_p.S594S|TTLL4_ENST00000258398.4_Silent_p.S759S	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	759	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		ACCTCATCAGCGGCAGCAAGT	0.493																																					p.S759S	GBM(172;1818 2053 15407 20943 49753)												.	TTLL4-93	0			c.C2277T						.						153	140	145					2																	219612347		2203	4300	6503	SO:0001819	synonymous_variant	9654	exon11			CATCAGCGGCAGC		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.2277C>T	2.37:g.219612347C>T		Somatic	225	0		WXS	Illumina HiSeq	Phase_I	383	7	NM_014640	0	0	6	6	0	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	37	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	c	14.18	2.457214	0.43634	.	.	ENSG00000135912	ENST00000448224	.	.	.	5.28	-7.51	0.01346	.	.	.	.	.	T	0.64670	0.2619	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69461	-0.5139	4	.	.	.	.	17.4246	0.87522	0.0:0.3253:0.0:0.6747	.	.	.	.	V	91	.	.	A	+	2	0	TTLL4	219320591	0.000000	0.05858	0.683000	0.30040	0.987000	0.75469	-2.811000	0.00755	-1.636000	0.01533	-0.766000	0.03442	GCG	.		0.493	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		T	219612347	C	T	219612347	2	4	29	1	0	0	0	0	0	0	0	1	16762	767	27	1		1	TTLL4	2	219612347	Silent	SNP	C	TCGA-AL-3466-01A-01D-1252-08	40196582	219612347	23587026	21	2567											
FAM124B	79843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	225266233	225266233	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctggagagagtccaggaCgcgaaatagcctatcctctc	11	8	11	11	2	1	1	0	0	1	1	4	5	3	3	3	2	2	1	3	2	3	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:225266233C>T	ENST00000409685.3	-	1	518	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	FAM124B_ENST00000389874.3_Missense_Mutation_p.V85I|FAM124B_ENST00000243806.2_Missense_Mutation_p.V85I	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	85								p.V85I(2)		endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		GAGTCCAGGACGCGAAATAGC	0.552																																					p.V85I		.											.	FAM124B-92	2	Substitution - Missense(2)	endometrium(2)	c.G253A						.						59	57	58					2																	225266233		2203	4300	6503	SO:0001583	missense	79843	exon1			CCAGGACGCGAAA	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.253G>A	2.37:g.225266233C>T	ENSP00000386895:p.Val85Ile	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	145	20	NM_024785	0	0	0	0	0	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	C	4.854	0.158738	0.09236	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.46063	0.88;0.88;0.88	5.69	1.32	0.21799	.	0.311841	0.33691	N	0.004645	T	0.30510	0.0767	L	0.42686	1.345	0.09310	N	1	B;B	0.21452	0.056;0.004	B;B	0.17433	0.018;0.003	T	0.18871	-1.0323	10	0.44086	T	0.13	-7.8837	7.6061	0.28103	0.0:0.574:0.22:0.206	.	85;85	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	I	85	ENSP00000374524:V85I;ENSP00000386895:V85I;ENSP00000243806:V85I	ENSP00000243806:V85I	V	-	1	0	FAM124B	224974477	0.625000	0.27111	0.000000	0.03702	0.001000	0.01503	1.550000	0.36223	0.332000	0.23536	-0.137000	0.14449	GTC	.		0.552	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		T	225266233	C	T	225266233	3	4	29	1	0	0	0	0	1	0	0	0	5442	536	19	1	1213	1	FAM124B	2	225266233	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	5653886	225266233	17933140	22	2568											
COL6A3	1293	bcgsc.ca	37	chr2	238244962	238244962	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggggtctaacagtggcCatctttgtggccacaggctt	7	11	13	10	0	2	0	0	0	2	0	2	0	2	0	2	5	1	1	2	5	1	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:238244962C>G	ENST00000295550.4	-	40	9233	c.8781G>C	c.(8779-8781)atG>atC	p.M2927I	COL6A3_ENST00000472056.1_Missense_Mutation_p.M2320I|COL6A3_ENST00000347401.3_Missense_Mutation_p.M2726I|COL6A3_ENST00000353578.4_Missense_Mutation_p.M2721I|COL6A3_ENST00000346358.4_Missense_Mutation_p.M2727I|COL6A3_ENST00000409809.1_Missense_Mutation_p.M2721I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2927	Ala-rich.|Nonhelical region.		M -> T (in dbSNP:rs6728818). {ECO:0000269|PubMed:1689238}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TAACAGTGGCCATCTTTGTGG	0.592																																					p.M2927I													.	COL6A3-526	0			c.G8781C						.						62	75	71					2																	238244962		2203	4299	6502	SO:0001583	missense	1293	exon40			AGTGGCCATCTTT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.8781G>C	2.37:g.238244962C>G	ENSP00000295550:p.Met2927Ile	Somatic	190	0		WXS	Illumina HiSeq	Phase_1	376	17	NM_004369	0	0	0	0	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	9.410	1.080267	0.20309	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.87650	-2.28;-2.27;-2.25;-2.24;-2.25;-2.24	5.34	-6.48	0.01896	.	1.643600	0.03837	N	0.270051	T	0.74612	0.3739	N	0.22421	0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.59705	-0.7404	10	0.48119	T	0.1	.	3.8981	0.09149	0.1155:0.1768:0.1145:0.5932	.	2320;2721;2927	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	I	2927;2726;2721;2320;2721;2727	ENSP00000295550:M2927I;ENSP00000315609:M2726I;ENSP00000315873:M2721I;ENSP00000418285:M2320I;ENSP00000386844:M2721I;ENSP00000295546:M2727I	ENSP00000295550:M2927I	M	-	3	0	COL6A3	237909701	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-2.790000	0.00767	-1.377000	0.02123	-1.008000	0.02478	ATG	.		0.592	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238244962	C	G	238244962	3	3	29	1	0	0	0	0	1	0	0	0	3707	594	21	4	772	4	COL6A3	2	238244962	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	12978729	238244962	4954411	23	2569											
EXOSC7	23016	ucsc.edu	37	chr3	45049021	45049021	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgacgtgcatgaggaaagTggggaagggcagcctggacc	10	6	18	7	1	0	2	0	2	0	0	0	5	0	5	2	5	2	2	2	5	2	0			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:45049021T>G	ENST00000265564.7	+	7	773	c.725T>G	c.(724-726)gTg>gGg	p.V242G	CLEC3B_ENST00000490386.1_Intron|EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	242					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		ATGAGGAAAGTGGGGAAGGGC	0.612																																					p.V242G													.	EXOSC7-90	0			c.T725G						.						105	86	93					3																	45049021		2203	4300	6503	SO:0001583	missense	23016	exon7			GGAAAGTGGGGAA	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.725T>G	3.37:g.45049021T>G	ENSP00000265564:p.Val242Gly	Somatic	61	0		WXS	Illumina HiSeq		71	2	NM_015004	0	0	0	0	0	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	37	CCDS2725.1	.	.	.	.	.	.	.	.	.	.	T	13.38	2.218944	0.39201	.	.	ENSG00000075914	ENST00000265564	T	0.43294	0.95	5.77	5.77	0.91146	Exoribonuclease, phosphorolytic domain 2 (1);	0.185749	0.49305	D	0.000151	T	0.28665	0.0710	N	0.16368	0.405	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.08994	-1.0695	10	0.17832	T	0.49	-15.0992	16.0957	0.81123	0.0:0.0:0.0:1.0	.	242;242	B2RDZ9;Q15024	.;EXOS7_HUMAN	G	242	ENSP00000265564:V242G	ENSP00000265564:V242G	V	+	2	0	EXOSC7	45024025	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.289000	0.72696	2.199000	0.70637	0.533000	0.62120	GTG	.		0.612	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		G	45049021	T	G	45049021	3	3	29	1	0	0	0	0	1	0	0	0	5332	1696	59	5	751	5	EXOSC7	3	45049021	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		45049021	152973409	24	2570											
PFKFB4	5210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48577177	48577177	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagatggtcgctctccgttCtcgggtggtgtttgtggcat	5	14	14	8	3	2	1	0	0	2	1	5	1	2	1	1	4	0	4	1	4	1	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:48577177C>A	ENST00000232375.3	-	5	518	c.406G>T	c.(406-408)Gaa>Taa	p.E136*	PFKFB4_ENST00000416568.1_Nonsense_Mutation_p.E136*|PFKFB4_ENST00000541519.1_Nonsense_Mutation_p.E102*|PFKFB4_ENST00000536104.1_Nonsense_Mutation_p.E125*|PFKFB4_ENST00000545984.1_Missense_Mutation_p.E113D|PFKFB4_ENST00000383734.2_Nonsense_Mutation_p.E136*|PFKFB4_ENST00000490115.1_5'UTR	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	136	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		GCTCTCCGTTCTCGGGTGGTG	0.567																																					p.E136X		.											.	PFKFB4-153	0			c.G406T						.						114	107	109					3																	48577177		2203	4300	6503	SO:0001587	stop_gained	5210	exon5			TCCGTTCTCGGGT	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.406G>T	3.37:g.48577177C>A	ENSP00000232375:p.Glu136*	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	124	49	NM_004567	0	0	0	0	0	Q5S3G5|Q5XLC2|Q64EX5	Nonsense_Mutation	SNP	ENST00000232375.3	37	CCDS2771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.32|15.32	2.797337|2.797337	0.50208|0.50208	.|.	.|.	ENSG00000114268|ENSG00000114268	ENST00000545984|ENST00000232375;ENST00000536104;ENST00000416568;ENST00000383734;ENST00000541519;ENST00000452531;ENST00000412035	.|.	.|.	.|.	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.63307|.	0.2500|.	.|.	.|.	.|.	0.31708|0.31708	N|N	0.639831|0.639831	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71906|.	-0.4451|.	6|.	0.02654|0.87932	T|D	1|0	-15.7704|-15.7704	15.0132|15.0132	0.71565|0.71565	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|X	113|136;125;136;136;102;125;102	.|.	ENSP00000437844:E113D|ENSP00000232375:E136X	E|E	-|-	3|1	2|0	PFKFB4|PFKFB4	48552181|48552181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.769000|0.769000	0.43574|0.43574	7.645000|7.645000	0.83430|0.83430	2.419000|2.419000	0.82065|0.82065	0.467000|0.467000	0.42956|0.42956	GAG|GAA	.		0.567	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567		A	48577177	C	A	48577177	4	1	29	1	0	0	0	0	0	1	0	0	11789	922	32	4	1043	4	PFKFB4	3	48577177	Nonsense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	3528156	48577177	149445253	25	2571											
NPRL2	10641	ucsc.edu	37	chr3	50385070	50385070	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgatgatgttggggtcattTtcaagccgctcatccagctc	8	13	10	10	1	3	2	3	2	0	0	5	2	4	2	2	2	2	3	2	2	1	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:50385070T>A	ENST00000232501.3	-	11	1548	c.1110A>T	c.(1108-1110)gaA>gaT	p.E370D	ZMYND10-AS1_ENST00000440013.1_RNA|ZMYND10_ENST00000360165.3_5'Flank|NPRL2_ENST00000493465.1_5'UTR|ZMYND10_ENST00000231749.3_5'Flank	NM_006545.4	NP_006536.3	Q8WTW4	NPRL2_HUMAN	nitrogen permease regulator-like 2 (S. cerevisiae)	370					negative regulation of kinase activity (GO:0033673)|protein phosphorylation (GO:0006468)		GTPase activator activity (GO:0005096)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	11						TGGGGTCATTTTCAAGCCGCT	0.577																																					p.E370D													.	NPRL2-278	0			c.A1110T						.						148	116	127					3																	50385070		2203	4300	6503	SO:0001583	missense	10641	exon11			GTCATTTTCAAGC	AF040708	CCDS2826.1	3p21.3	2010-03-30	2010-03-30	2010-03-30	ENSG00000114388	ENSG00000114388			24969	protein-coding gene	gene with protein product		607072	"tumor suppressor candidate 4"	TUSC4		11085536	Standard	NM_006545		Approved	NPR2L, NPR2	uc003daj.1	Q8WTW4	OTTHUMG00000156864	ENST00000232501.3:c.1110A>T	3.37:g.50385070T>A	ENSP00000232501:p.Glu370Asp	Somatic	106	0		WXS	Illumina HiSeq		113	1	NM_006545	0	0	10	21	11	A8K831|Q6FGS2|Q9Y249|Q9Y497	Missense_Mutation	SNP	ENST00000232501.3	37	CCDS2826.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.090731	0.36855	.	.	ENSG00000114388	ENST00000232501	.	.	.	4.89	0.998	0.19857	.	0.050252	0.85682	D	0.000000	T	0.36635	0.0974	L	0.29908	0.895	0.53688	D	0.999977	B	0.06786	0.001	B	0.09377	0.004	T	0.07597	-1.0764	9	0.30854	T	0.27	-12.6028	4.0461	0.09773	0.0:0.3313:0.1858:0.4829	.	370	Q8WTW4	NPRL2_HUMAN	D	370	.	ENSP00000232501:E370D	E	-	3	2	NPRL2	50360074	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.528000	0.35985	0.455000	0.26910	0.459000	0.35465	GAA	.		0.577	NPRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346299.1	NM_006545		A	50385070	T	A	50385070	3	1	29	1	0	0	0	0	1	0	0	0	10623	1838	64	5	36	5	NPRL2	3	50385070	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	1807893	50385070	147637360	26	2572											
TKT	7086	hgsc.bcm.edu;broad.mit.edu	37	chr3	53264627	53264627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgcctgcccgtaggccttgCgggtggctatctgtgaggaa	5	10	16	10	2	1	1	0	1	1	0	1	2	1	2	3	4	3	2	3	4	3	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:53264627C>T	ENST00000462138.1	-	8	1041	c.953G>A	c.(952-954)cGc>cAc	p.R318H	TKT_ENST00000423525.2_Missense_Mutation_p.R318H|TKT_ENST00000461139.1_5'UTR|TKT_ENST00000296289.6_Missense_Mutation_p.R271H|TKT_ENST00000423516.1_Missense_Mutation_p.R326H			P29401	TKT_HUMAN	transketolase	318					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		GTAGGCCTTGCGGGTGGCTAT	0.587																																					p.R326H	Colon(133;1506 2347 35238 42177)	.											.	TKT-92	0			c.G977A						.						59	56	57					3																	53264627		2203	4300	6503	SO:0001583	missense	7086	exon9			GCCTTGCGGGTGG		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.953G>A	3.37:g.53264627C>T	ENSP00000417773:p.Arg318His	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	98	6	NM_001258028	0	0	1	1	0	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	37	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	C	35	5.563617	0.96527	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516;ENST00000296289;ENST00000414014	D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14	5.69	5.69	0.88448	Transketolase-like, pyrimidine-binding domain (2);	0.047547	0.85682	D	0.000000	D	0.97763	0.9266	H	0.97682	4.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.963;0.977;0.971	D	0.98701	1.0700	10	0.87932	D	0	-15.8701	19.8045	0.96525	0.0:1.0:0.0:0.0	.	326;235;318	E7EPA7;B3KSI4;P29401	.;.;TKT_HUMAN	H	318;318;326;271;152	ENSP00000417773:R318H;ENSP00000405455:R318H;ENSP00000391481:R326H;ENSP00000296289:R271H	ENSP00000296289:R271H	R	-	2	0	TKT	53239667	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.676000	0.91093	0.655000	0.94253	CGC	.		0.587	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			T	53264627	C	T	53264627	3	4	29	1	0	0	0	0	1	0	0	0	15966	768	27	1	946	1	TKT	3	53264627	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	2879557	53264627	144757803	27	2573											
PPP4R2	151987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	73110176	73110176	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatttttgttattgcagaaTgtgatggttgttagctgtgt	7	20	12	2	0	0	3	0	2	0	1	0	3	0	3	0	1	2	5	0	1	3	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:73110176T>A	ENST00000356692.5	+	5	637	c.384T>A	c.(382-384)aaT>aaA	p.N128K	PPP4R2_ENST00000394284.3_Missense_Mutation_p.N71K|PPP4R2_ENST00000295862.9_Missense_Mutation_p.N72K|EBLN2_ENST00000533473.1_5'Flank			Q9NY27	PP4R2_HUMAN	protein phosphatase 4, regulatory subunit 2	128					cellular protein modification process (GO:0006464)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA processing (GO:0006397)|regulation of catalytic activity (GO:0050790)|regulation of double-strand break repair via homologous recombination (GO:0010569)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)	protein binding, bridging (GO:0030674)|protein phosphatase type 4 regulator activity (GO:0030362)			breast(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)|urinary_tract(2)	12		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)		TATTGCAGAATGTGATGGTTG	0.259																																					p.N128K		.											.	PPP4R2-227	0			c.T384A						.						102	96	98					3																	73110176		2199	4292	6491	SO:0001583	missense	151987	exon5			GCAGAATGTGATG	AJ271448	CCDS2917.1	3q29	2010-06-18			ENSG00000163605	ENSG00000163605		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	18296	protein-coding gene	gene with protein product		613822				10769191	Standard	NM_174907		Approved		uc003dph.1	Q9NY27	OTTHUMG00000158816	ENST00000356692.5:c.384T>A	3.37:g.73110176T>A	ENSP00000349124:p.Asn128Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	34	8	NM_174907	0	0	0	0	0	A8K1I6|Q2TAJ9|Q498B8|Q8WXX6	Missense_Mutation	SNP	ENST00000356692.5	37	CCDS2917.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.417029	0.62511	.	.	ENSG00000163605	ENST00000356692;ENST00000488810;ENST00000394284;ENST00000295862	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	4.96	2.54	0.30619	.	0.000000	0.85682	D	0.000000	T	0.57036	0.2026	M	0.86178	2.8	0.80722	D	1	P;P	0.39903	0.694;0.505	B;B	0.41374	0.353;0.355	T	0.59467	-0.7449	10	0.72032	D	0.01	.	9.3514	0.38140	0.0:0.1471:0.0:0.8529	.	71;128	Q9NY27-2;Q9NY27	.;PP4R2_HUMAN	K	128;128;71;72	ENSP00000349124:N128K;ENSP00000418750:N128K;ENSP00000377825:N71K;ENSP00000295862:N72K	ENSP00000295862:N72K	N	+	3	2	PPP4R2	73192866	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	3.134000	0.50538	0.329000	0.23460	-0.297000	0.09499	AAT	.		0.259	PPP4R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352321.1	NM_174907		A	73110176	T	A	73110176	3	1	29	1	0	0	0	0	1	0	0	0	12433	1461	51	5	402	5	PPP4R2	3	73110176	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	19845549	73110176	124912254	28	2574											
MED12L	116931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151072983	151072983	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggagactgtgttcactaaaCtccagctcctttcatatttt	9	16	6	10	0	2	1	2	0	0	1	4	2	4	1	2	1	2	2	2	1	3	6	rs200848773		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:151072983C>T	ENST00000474524.1	+	16	2406	c.2368C>T	c.(2368-2370)Ctc>Ttc	p.L790F	MED12L_ENST00000273432.4_Missense_Mutation_p.L650F|MED12L_ENST00000491549.1_3'UTR|P2RY12_ENST00000302632.3_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	790						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GTTCACTAAACTCCAGCTCCT	0.358																																					p.L790F		.											.	MED12L-576	0			c.C2368T						.						103	104	103					3																	151072983		2203	4300	6503	SO:0001583	missense	116931	exon16			ACTAAACTCCAGC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2368C>T	3.37:g.151072983C>T	ENSP00000417235:p.Leu790Phe	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	61	17	NM_053002	0	0	0	0	0	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	3.897	-0.022893	0.07634	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.71341	-0.56;-0.56	5.35	5.35	0.76521	.	0.059800	0.64402	D	0.000002	T	0.31918	0.0812	N	0.00186	-1.895	0.80722	D	1	B;B	0.15141	0.006;0.012	B;B	0.17098	0.017;0.012	T	0.46830	-0.9163	10	0.11182	T	0.66	-18.4403	12.407	0.55445	0.0:0.922:0.0:0.078	.	650;790	F8WAE6;Q86YW9	.;MD12L_HUMAN	F	790;650	ENSP00000417235:L790F;ENSP00000273432:L650F	ENSP00000273432:L650F	L	+	1	0	MED12L	152555673	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	3.177000	0.50871	2.656000	0.90262	0.650000	0.86243	CTC	C|0.999;G|0.001		0.358	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	151072983	C	T	151072983	3	4	29	1	0	0	0	0	1	0	0	0	9454	565	20	2	2430	2	MED12L	3	151072983	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	77962807	151072983	46949447	29	2575											
SLC6A18	348932	broad.mit.edu	37	chr5	1244416	1244416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggagattttcgacaattttgCcgcttccccgaacctgctca	8	12	8	13	3	1	1	1	0	0	1	3	4	2	1	4	1	3	2	4	1	2	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr5:1244416C>T	ENST00000324642.3	+	10	1547	c.1424C>T	c.(1423-1425)gCc>gTc	p.A475V	SLC6A18_ENST00000296821.4_Missense_Mutation_p.A373V	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	475					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GACAATTTTGCCGCTTCCCCG	0.582																																					p.A475V													.	SLC6A18-91	0			c.C1424T						.						147	147	147					5																	1244416		2203	4300	6503	SO:0001583	missense	348932	exon10			ATTTTGCCGCTTC	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"Solute carriers"	26441	protein-coding gene	gene with protein product		610300	"solute carrier family 6 (neurotransmitter transporter), member 18", "solute carrier family 6, member 18"			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1424C>T	5.37:g.1244416C>T	ENSP00000323549:p.Ala475Val	Somatic	214	1		WXS	Illumina HiSeq	Phase_I	246	5	NM_182632	0	0	1	1	0		Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	C	12.56	1.975383	0.34848	.	.	ENSG00000164363	ENST00000324642;ENST00000296821	T;T	0.76578	-1.03;-1.03	4.87	-1.66	0.08265	.	0.373560	0.27126	N	0.020814	T	0.58177	0.2104	N	0.21617	0.685	0.09310	N	1	B	0.16802	0.019	B	0.15052	0.012	T	0.49341	-0.8950	10	0.87932	D	0	.	5.9492	0.19235	0.0:0.3423:0.141:0.5167	.	475	Q96N87	S6A18_HUMAN	V	475;373	ENSP00000323549:A475V;ENSP00000296821:A373V	ENSP00000296821:A373V	A	+	2	0	SLC6A18	1297416	0.226000	0.23696	0.000000	0.03702	0.001000	0.01503	0.643000	0.24750	-0.361000	0.08125	-1.036000	0.02392	GCC	.		0.582	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632		T	1244416	C	T	1244416	3	4	29	1	0	0	0	0	1	0	0	0	14713	739	26	2	1462	2	SLC6A18	5	1244416	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		1244416	179670844	30	2576											
HAVCR1	26762	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	156482352	156482362	+	Frame_Shift_Del	DEL	AATAGCTTATA	AATAGCTTATA	-																															cccttcttgaaaggtcccccAatagcttatagcgtgtgtcc																								rs111358310	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	AATAGCTTATA	AATAGCTTATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr5:156482352_156482362delAATAGCTTATA	ENST00000339252.3	-	2	761_771	c.229_239delTATAAGCTATT	c.(229-240)tataagctattgfs	p.YKLL77fs	HAVCR1_ENST00000523175.1_Frame_Shift_Del_p.YKLL77fs|HAVCR1_ENST00000522693.1_Frame_Shift_Del_p.YKLL77fs|HAVCR1_ENST00000544197.1_Frame_Shift_Del_p.YKLL77fs|HAVCR1_ENST00000425854.1_Frame_Shift_Del_p.YKLL77fs	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	Ig-like V-type.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AAGGTCCCCCAATAGCTTATAGCGTGTGTCC	0.479																																					p.77_80del		.											.	HAVCR1-92	0			c.229_239del						.																																			SO:0001589	frameshift_variant	26762	exon3			.	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.229_239delTATAAGCTATT	5.37:g.156482352_156482362delAATAGCTTATA	ENSP00000344844:p.Tyr77fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	271	52	NM_001099414	0	0	0	0	0	O43656	Frame_Shift_Del	DEL	ENST00000339252.3	37	CCDS43392.1																																																																																			.		0.479	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			-	156482362	AATAGCTTATA	-	156482352	7	5	29	1	0	1	0	1	0	0	0	0	6994	131	5	0	883	0	HAVCR1	5	156482352	Frame_Shift_Del	DEL	AATAGCTTATA	TCGA-AL-3466-01A-01D-1252-08	155237936	156482352	24432908	31	2577											
NSD1	64324	broad.mit.edu	37	chr5	176710903	176710903	+	Frame_Shift_Del	DEL	T	T	-																															tggagatacccgtgtaggccTttttgcactaagtgacatta																										TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr5:176710903delT	ENST00000439151.2	+	20	6170	c.6125delT	c.(6124-6126)cttfs	p.L2042fs	NSD1_ENST00000361032.4_Frame_Shift_Del_p.L1939fs|NSD1_ENST00000354179.4_Frame_Shift_Del_p.L1773fs|NSD1_ENST00000347982.4_Frame_Shift_Del_p.L1773fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2042	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CGTGTAGGCCTTTTTGCACTA	0.438			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.L2042fs				Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.6125delT						.						162	158	159					5																	176710903		2203	4300	6503	SO:0001589	frameshift_variant	64324	exon20	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TAGGCCTTTTTGC	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6125delT	5.37:g.176710903delT	ENSP00000395929:p.Leu2042fs	Somatic	371	0		WXS	Illumina HiSeq	Phase_I	1028	7	NM_022455	0	0	0	0	0	Q96PD8|Q96RN7	Frame_Shift_Del	DEL	ENST00000439151.2	37	CCDS4412.1																																																																																			.		0.438	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		-	176710903	T	-	176710903	7	5	29	1	0	1	0	1	0	0	0	0	10695	1609	56	0	6199	0	NSD1	5	176710903	Frame_Shift_Del	DEL	T	TCGA-AL-3466-01A-01D-1252-08	20228551	176710903	4204357	32	2578											
HIST1H2BL	8340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	27775403	27775403	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcgcacggcggtctggatCtccctggaggtgatggtcga	6	8	17	10	4	2	1	0	1	2	0	4	4	2	3	1	7	0	1	1	7	0	0	rs141648774		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:27775403C>T	ENST00000377401.2	-	1	306	c.282G>A	c.(280-282)gaG>gaA	p.E94E	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2AI_ENST00000358739.3_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	94					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						CGGTCTGGATCTCCCTGGAGG	0.617																																					p.E94E		.											.	HIST1H2BL-90	0			c.G282A						.						92	94	93					6																	27775403		2203	4300	6503	SO:0001819	synonymous_variant	8340	exon1			CTGGATCTCCCTG	Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"Histones / Replication-dependent"	4748	protein-coding gene	gene with protein product		602800	"H2B histone family, member C", "histone 1, H2bl"	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.282G>A	6.37:g.27775403C>T		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	197	143	NM_003519	0	0	0	6	6	B2R5A3|Q52LW9	Silent	SNP	ENST00000377401.2	37	CCDS4625.1																																																																																			C|1.000;A|0.000		0.617	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		T	27775403	C	T	27775403	2	4	29	1	0	0	0	0	0	0	0	1	7172	912	32	2		2	HIST1H2BL	6	27775403	Silent	SNP	C	TCGA-AL-3466-01A-01D-1252-08		27775403	143339664	33	2579											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239420	31239420	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgcaggttccgcaggctcActcggtcagcctgtgcctgg	4	8	14	15	4	2	0	2	0	0	0	4	0	3	0	3	4	2	4	3	4	0	1	rs41550619		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:31239420A>T	ENST00000376228.5	-	2	313	c.299T>A	c.(298-300)gTg>gAg	p.V100E	HLA-C_ENST00000383329.3_Missense_Mutation_p.V100E	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	100	Alpha-1.				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)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CCGCAGGCTCACTCGGTCAGC	0.706																																					p.V100E		.											.	HLA-C-90	0			c.T299A						.						43	44	43					6																	31239420		1511	2709	4220	SO:0001583	missense	3107	exon2			AGGCTCACTCGGT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.299T>A	6.37:g.31239420A>T	ENSP00000365402:p.Val100Glu	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	149	10	NM_002117	0	0	140	140	0	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	11.64|11.64	1.699559|1.699559	0.30142|0.30142	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00695	.|5.83;5.83	2.81|2.81	0.196|0.196	0.15159|0.15159	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.811394	.|0.09501	.|U	.|0.793662	T|T	0.00695|0.00695	0.0023|0.0023	L|L	0.59967|0.59967	1.855|1.855	0.09310|0.09310	N|N	1|1	.|D;B;D;B	.|0.71674	.|0.998;0.004;0.998;0.019	.|D;B;D;B	.|0.87578	.|0.998;0.047;0.998;0.078	T|T	0.42682|0.42682	-0.9437|-0.9437	5|10	.|0.09843	.|T	.|0.71	.|.	3.1169|3.1169	0.06377|0.06377	0.6065:0.2501:0.1435:0.0|0.6065:0.2501:0.1435:0.0	rs41550619|rs41550619	.|100;100;100;100	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	R|E	99|100;100;100;137	.|ENSP00000365402:V100E;ENSP00000372819:V100E	.|ENSP00000365402:V100E	S|V	-|-	3|2	2|0	HLA-C|HLA-C	31347399|31347399	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.015000|0.015000	0.08874|0.08874	-3.401000|-3.401000	0.00483|0.00483	0.042000|0.042000	0.15717|0.15717	0.254000|0.254000	0.18369|0.18369	AGT|GTG	.		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		T	31239420	A	T	31239420	3	4	29	1	0	0	0	0	1	0	0	0	7218	159	6	5	829	5	HLA-C	6	31239420	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	3464017	31239420	139875647	34	2580											
LY6G6F	259215	broad.mit.edu	37	chr6	31675742	31675742	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgcatggactctgtgacctgGcaggaagggaagggtcccgt	8	7	16	10	2	1	1	0	1	1	0	2	4	2	4	2	5	0	2	2	5	2	0			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:31675742G>A	ENST00000375832.4	+	3	499	c.477G>A	c.(475-477)tgG>tgA	p.W159*	MEGT1_ENST00000503322.1_Nonsense_Mutation_p.W159*|XXbac-BPG32J3.20_ENST00000461287.1_Intron|LY6G6F_ENST00000556581.1_Nonsense_Mutation_p.W159*	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						CTGTGACCTGGCAGGAAGGGA	0.617																																					p.W159X													.	LY6G6F-567	0			c.G477A						.						89	87	88					6																	31675742		1511	2709	4220	SO:0001587	stop_gained	259215	exon3			GACCTGGCAGGAA		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"Immunoglobulin superfamily / V-set domain containing"	13933	protein-coding gene	gene with protein product		611404	"chromosome 6 open reading frame 21"	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.477G>A	6.37:g.31675742G>A	ENSP00000364992:p.Trp159*	Somatic	173	1		WXS	Illumina HiSeq	Phase_I	228	6	NM_001003693	0	0	0	0	0	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Nonsense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.708008	0.89018	.	.	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	.	.	.	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5869	14.8659	0.70416	0.0:0.0:1.0:0.0	.	.	.	.	X	159	.	ENSP00000364992:W159X	W	+	3	0	XXbac-BPG32J3.19;LY6G6F	31783721	1.000000	0.71417	0.999000	0.59377	0.475000	0.33008	4.259000	0.58828	2.596000	0.87737	0.591000	0.81541	TGG	.		0.617	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693		A	31675742	G	A	31675742	4	1	29	1	0	0	0	0	0	1	0	0	9121	1212	42	2	487	2	LY6G6F	6	31675742	Nonsense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	436322	31675742	139439325	35	2581											
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32489853	32489853	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacgtcgctgtcgaagcgcaAgtcctcctcttggttataga	8	11	10	12	4	1	1	0	0	1	1	5	2	3	1	2	1	1	3	2	1	4	3	rs78961241	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:32489853A>G	ENST00000374975.3	-	2	261	c.199T>C	c.(199-201)Ttg>Ctg	p.L67L		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						TCGAAGCGCAAGTCCTCCTCT	0.577																																					p.L67L		.											.	HLA-DRB5-90	0			c.T199C						.						36	33	34					6																	32489853		1895	3648	5543	SO:0001819	synonymous_variant	3127	exon2			AGCGCAAGTCCTC		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.199T>C	6.37:g.32489853A>G		Somatic	5	2		WXS	Illumina HiSeq	Phase_I	8	8	NM_002125	0	0	0	0	0		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			A|0.266;C|0.734		0.577	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		G	32489853	A	G	32489853	2	3	29	1	0	0	0	0	0	0	0	1	7230	69	3	3		3	HLA-DRB5	6	32489853	Silent	SNP	A	TCGA-AL-3466-01A-01D-1252-08	814111	32489853	138625214	36	2582											
DEFB112	245915	hgsc.bcm.edu	37	chr6	50011485	50011485	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtacatgacttccacctacTaaaggtgatatggtgccctt	10	13	8	10	0	0	2	0	2	0	0	1	2	1	2	3	2	3	1	3	2	5	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:50011485T>C	ENST00000322246.4	-	2	144	c.145A>G	c.(145-147)Agt>Ggt	p.S49G		NM_001037498.1	NP_001032587.1	Q30KQ8	DB112_HUMAN	defensin, beta 112	49					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.042)					TTCCACCTACTAAAGGTGATA	0.408																																					p.S49G		.											.	DEFB112-90	0			c.A145G						.						157	127	137					6																	50011485		2203	4300	6503	SO:0001583	missense	245915	exon2			ACCTACTAAAGGT	DQ012016	CCDS34476.1	6p12.3	2010-03-30			ENSG00000180872	ENSG00000180872		"Defensins, beta"	18093	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037498		Approved	DEFB-12	uc011dws.2	Q30KQ8	OTTHUMG00000160215	ENST00000322246.4:c.145A>G	6.37:g.50011485T>C	ENSP00000319126:p.Ser49Gly	Somatic	265	1		WXS	Illumina HiSeq	Phase_I	34	2	NM_001037498	0	0	0	0	0	Q8NET0	Missense_Mutation	SNP	ENST00000322246.4	37	CCDS34476.1	.	.	.	.	.	.	.	.	.	.	T	8.550	0.875373	0.17395	.	.	ENSG00000180872	ENST00000322246	T	0.22539	1.95	3.43	-1.99	0.07457	.	1.179380	0.06513	N	0.738451	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44937	-0.9295	10	0.41790	T	0.15	-6.032	7.9034	0.29748	0.0:0.5629:0.0:0.4371	.	49	Q30KQ8	DB112_HUMAN	G	49	ENSP00000319126:S49G	ENSP00000319126:S49G	S	-	1	0	DEFB112	50119444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.890000	0.04140	-0.360000	0.08138	-0.384000	0.06662	AGT	.		0.408	DEFB112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359672.1	NM_001037498		C	50011485	T	C	50011485	3	2	29	1	0	0	0	0	1	0	0	0	4411	1522	53	3	199	3	DEFB112	6	50011485	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	17521632	50011485	121103582	37	2583											
C6orf142	90523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	53989447	53989447	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgaatatgtccttatTgtggactccgaaggggaaga	13	10	12	6	1	0	2	0	1	0	1	2	5	2	4	2	3	1	1	2	3	6	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:53989447T>C	ENST00000274897.5	+	3	509	c.396T>C	c.(394-396)atT>atC	p.I132I	MLIP_ENST00000511744.1_3'UTR|MLIP_ENST00000509997.1_Silent_p.I80I|MLIP_ENST00000502396.1_Silent_p.I143I|MLIP_ENST00000370877.2_Silent_p.I80I|MLIP_ENST00000514921.1_Silent_p.I132I|MLIP_ENST00000370876.2_Silent_p.I70I|MLIP_ENST00000358276.5_Silent_p.I126I	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	132						nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						ATGTCCTTATTGTGGACTCCG	0.502																																					p.I132I		.											.	MLIP-99	0			c.T396C						.						100	99	100					6																	53989447		2203	4300	6503	SO:0001819	synonymous_variant	90523	exon3			CCTTATTGTGGAC	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"muscle-enriched A-type lamin interacting protein"	614106	"chromosome 6 open reading frame 142"	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.396T>C	6.37:g.53989447T>C		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	166	127	NM_138569	0	0	0	0	0	B7Z2N0|D6RE05|Q96H08|Q96NF7	Silent	SNP	ENST00000274897.5	37	CCDS4954.1																																																																																			.		0.502	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569		C	53989447	T	C	53989447	2	2	29	1	0	0	0	0	0	0	0	1	2339	1800	63	3		3	C6orf142	6	53989447	Silent	SNP	T	TCGA-AL-3466-01A-01D-1252-08	3977962	53989447	117125620	38	2584											
NOS3	4846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	150698913	150698913	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcctctcccgcagcgccGtgaagatctccgcctcgctc	4	9	8	20	5	2	2	0	1	2	1	7	2	3	2	6	0	1	2	6	0	1	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr7:150698913G>A	ENST00000484524.1	+	12	1507	c.1507G>A	c.(1507-1509)Gtg>Atg	p.V503M	NOS3_ENST00000461406.1_Missense_Mutation_p.V297M|NOS3_ENST00000467517.1_Missense_Mutation_p.V503M|NOS3_ENST00000297494.3_Missense_Mutation_p.V503M	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGCAGCGCCGTGAAGATCTC	0.642																																					p.V503M		.											.	NOS3-1011	0			c.G1507A						.						53	51	52					7																	150698913		2203	4300	6503	SO:0001583	missense	4846	exon12			AGCGCCGTGAAGA		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1507G>A	7.37:g.150698913G>A	ENSP00000420215:p.Val503Met	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	174	53	NM_001160111	0	0	0	0	0	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	37	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907322	0.72868	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.17691	4.46;4.33;2.67;2.26	4.8	4.8	0.61643	.	0.000000	0.48767	D	0.000162	T	0.48660	0.1512	M	0.89414	3.03	0.58432	D	0.99999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.98;0.98;0.991;0.993;0.991	T	0.58869	-0.7560	10	0.87932	D	0	-4.5235	15.7394	0.77876	0.0:0.0:1.0:0.0	.	503;503;503;297;503	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	M	503;297;503;503	ENSP00000297494:V503M;ENSP00000417143:V297M;ENSP00000420215:V503M;ENSP00000420551:V503M	ENSP00000297494:V503M	V	+	1	0	NOS3	150329846	1.000000	0.71417	0.946000	0.38457	0.522000	0.34438	9.261000	0.95576	2.376000	0.81061	0.655000	0.94253	GTG	.		0.642	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		A	150698913	G	A	150698913	3	1	29	1	0	0	0	0	1	0	0	0	10570	1145	40	1	1553	1	NOS3	7	150698913	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08		150698913	8439750	39	2585											
OXR1	55074	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	107752622	107752622	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctatccatggactcttgttTatggtactggaaaacatggc	10	13	10	8	0	1	0	0	0	1	0	2	2	2	2	1	4	2	3	1	4	5	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr8:107752622T>A	ENST00000442977.2	+	13	2317	c.2218T>A	c.(2218-2220)Tat>Aat	p.Y740N	OXR1_ENST00000297447.6_Missense_Mutation_p.Y109N|OXR1_ENST00000449762.2_Missense_Mutation_p.Y82N|OXR1_ENST00000445937.1_Missense_Mutation_p.Y712N|OXR1_ENST00000521592.1_De_novo_Start_OutOfFrame|OXR1_ENST00000517566.2_Missense_Mutation_p.Y739N|OXR1_ENST00000312046.6_Missense_Mutation_p.Y705N|OXR1_ENST00000452423.2_Missense_Mutation_p.Y160N|OXR1_ENST00000531443.1_Missense_Mutation_p.Y712N	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	740	TLD.				adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			GACTCTTGTTTATGGTACTGG	0.383																																					p.Y740N		.											.	OXR1-68	0			c.T2218A						.						129	119	122					8																	107752622		2203	4300	6503	SO:0001583	missense	55074	exon13			CTTGTTTATGGTA	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.2218T>A	8.37:g.107752622T>A	ENSP00000405424:p.Tyr740Asn	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	75	11	NM_001198532	0	0	32	32	0	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	37	CCDS56548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.4|25.4	4.629261|4.629261	0.87560|0.87560	.|.	.|.	ENSG00000164830|ENSG00000164830	ENST00000519415|ENST00000445937;ENST00000531443;ENST00000517566;ENST00000452423;ENST00000442977;ENST00000312046;ENST00000449762;ENST00000297447	.|T;T;T;T;T;T;T;T	.|0.54279	.|0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.48|5.48	5.48|5.48	0.80851|0.80851	.|TLDc (2);	.|0.054965	.|0.85682	.|D	.|0.000000	T|T	0.82204|0.82204	0.4986|0.4986	H|H	0.97540|0.97540	4.025|4.025	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.999;1.0;0.999;0.992;0.998	.|D;D;D;D;D;D	.|0.81914	.|0.991;0.987;0.995;0.977;0.942;0.983	D|D	0.88810|0.88810	0.3291|0.3291	5|10	.|0.87932	.|D	.|0	-15.1603|-15.1603	15.5747|15.5747	0.76368|0.76368	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|705;740;739;82;109;712	.|Q8N573-2;Q8N573;D3HIS6;B7Z8N5;Q8N573-4;Q8N573-5	.|.;OXR1_HUMAN;.;.;.;.	L|N	383|712;712;739;160;740;705;82;109	.|ENSP00000402918:Y712N;ENSP00000431966:Y712N;ENSP00000429205:Y739N;ENSP00000395032:Y160N;ENSP00000405424:Y740N;ENSP00000311026:Y705N;ENSP00000408659:Y82N;ENSP00000297447:Y109N	.|ENSP00000297447:Y109N	F|Y	+|+	3|1	2|0	OXR1|OXR1	107821798|107821798	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	2.066000|2.066000	0.61787|0.61787	0.533000|0.533000	0.62120|0.62120	TTT|TAT	.		0.383	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		A	107752622	T	A	107752622	3	1	29	1	0	0	0	0	1	0	0	0	11360	1754	61	5	2383	5	OXR1	8	107752622	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		107752622	38611400	40	2586											
C9orf21	195827	hgsc.bcm.edu	37	chr9	99413724	99413724	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaatcttttataaatttcTctctcaggatcgacatagat	12	15	4	10	1	3	1	1	0	3	1	6	3	3	2	1	1	0	0	1	1	5	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr9:99413724T>C	ENST00000375234.3	-	4	368	c.369A>G	c.(367-369)agA>agG	p.R123R	AAED1_ENST00000464512.1_5'UTR	NM_153698.1	NP_714542.1	Q7RTV5	AAED1_HUMAN	AhpC/TSA antioxidant enzyme domain containing 1	123																	TATAAATTTCTCTCTCAGGAT	0.353																																					p.R123R		.											.	.	0			c.A369G						.						68	65	66					9																	99413724		2202	4300	6502	SO:0001819	synonymous_variant	195827	exon4			AATTTCTCTCTCA	BK000255	CCDS35073.1	9q22.32	2013-01-07	2012-03-06	2012-03-06	ENSG00000158122	ENSG00000158122			16881	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 21"	C9orf21			Standard	XM_005251783		Approved		uc004awm.3	Q7RTV5	OTTHUMG00000020299	ENST00000375234.3:c.369A>G	9.37:g.99413724T>C		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_153698	0	0	9	9	0	B2RMW4|Q5JU02	Silent	SNP	ENST00000375234.3	37	CCDS35073.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.35|10.35	1.325957|1.325957	0.24080|0.24080	.|.	.|.	ENSG00000158122|ENSG00000158122	ENST00000411939|ENST00000446045	.|T	.|0.43688	.|0.94	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.51584|0.51584	0.1683|0.1683	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49143|0.49143	-0.8970|-0.8970	4|6	.|.	.|.	.|.	-9.3239|-9.3239	13.3489|13.3489	0.60591|0.60591	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	G|G	51|77	.|ENSP00000398933:R77G	.|.	E|R	-|-	2|1	0|2	C9orf21|C9orf21	98453545|98453545	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.671000|1.671000	0.37513|0.37513	1.990000|1.990000	0.58119|0.58119	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.		0.353	AAED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053273.1	NM_153698		C	99413724	T	C	99413724	2	2	29	1	0	0	0	0	0	0	0	1	2479	1548	54	3		3	C9orf21	9	99413724	Silent	SNP	T	TCGA-AL-3466-01A-01D-1252-08		99413724	41799707	41	2587											
AKNA	80709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	117139726	117139726	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatctggctcctcttcagTcatgtccagctgacggccct	5	11	8	17	1	4	1	2	1	2	0	6	1	6	1	4	2	1	2	4	2	0	1	rs371041163		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr9:117139726T>C	ENST00000307564.4	-	3	522	c.361A>G	c.(361-363)Act>Gct	p.T121A	AKNA_ENST00000374075.5_Missense_Mutation_p.T40A|AKNA_ENST00000223791.3_5'Flank|AKNA_ENST00000312033.3_Missense_Mutation_p.T121A|AKNA_ENST00000374088.3_Missense_Mutation_p.T121A	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	121					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TCCTCTTCAGTCATGTCCAGC	0.602																																					p.T121A		.											.	AKNA-94	0			c.A361G						.						44	45	45					9																	117139726		2203	4300	6503	SO:0001583	missense	80709	exon3			CTTCAGTCATGTC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.361A>G	9.37:g.117139726T>C	ENSP00000303769:p.Thr121Ala	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	163	84	NM_030767	0	0	0	0	0	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.512748	0.64522	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	T;T;T;T	0.32272	2.69;2.69;2.7;1.46	4.58	0.597	0.17504	.	0.519095	0.16285	N	0.221162	T	0.18759	0.0450	L	0.27053	0.805	0.80722	D	1	B;B;B	0.33807	0.22;0.075;0.426	B;B;B	0.37692	0.208;0.035;0.256	T	0.06954	-1.0798	10	0.34782	T	0.22	-4.4222	3.703	0.08390	0.3391:0.1032:0.0:0.5577	.	121;121;40	Q7Z591-6;Q7Z591;Q7Z591-2	.;AKNA_HUMAN;.	A	121;121;40;121;121	ENSP00000303769:T121A;ENSP00000363201:T121A;ENSP00000363188:T40A;ENSP00000309222:T121A	ENSP00000303769:T121A	T	-	1	0	AKNA	116179547	0.975000	0.34042	0.174000	0.22961	0.155000	0.21991	0.491000	0.22419	0.172000	0.19760	0.379000	0.24179	ACT	.		0.602	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117139726	T	C	117139726	3	2	29	1	0	0	0	0	1	0	0	0	463	1667	58	3	4038	3	AKNA	9	117139726	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	17726002	117139726	24073705	42	2588											
DBC1	1620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	121930244	121930244	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaactgctcgctccgctcCgagtccacgttctgtggttc	5	12	10	14	4	1	1	0	1	1	0	6	2	4	1	3	1	2	5	3	1	1	2	rs370346617		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr9:121930244C>T	ENST00000265922.3	-	8	1865	c.1404G>A	c.(1402-1404)tcG>tcA	p.S468S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	468					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											CGCTCCGCTCCGAGTCCACGT	0.592																																					p.S468S		.											.	DBC1-582	0			c.G1404A						.	C		1,4405	2.1+/-5.4	0,1,2202	149	122	131		1404	0.4	1	9		131	0,8600		0,0,4300	no	coding-synonymous	DBC1	NM_014618.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		468/762	121930244	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1620	exon8			CCGCTCCGAGTCC	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"deleted in bladder cancer chromosome region candidate 1", "deleted in bladder cancer 1"	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1404G>A	9.37:g.121930244C>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	107	26	NM_014618	0	0	0	0	0	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			.		0.592	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121930244	C	T	121930244	2	4	29	1	0	0	0	0	0	0	0	1	4253	639	23	1		1	DBC1	9	121930244	Silent	SNP	C	TCGA-AL-3466-01A-01D-1252-08	4790518	121930244	19283187	43	2589											
GTPBP4	23560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	1043230	1043230	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtacccaaatgttgggaaGtccagcttcatcaacaaggt	12	9	11	9	0	2	0	2	0	0	0	3	1	3	1	2	3	3	3	2	3	5	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr10:1043230G>A	ENST00000360803.4	+	5	625	c.543G>A	c.(541-543)aaG>aaA	p.K181K	GTPBP4_ENST00000545048.1_Silent_p.K134K|GTPBP4_ENST00000491635.1_3'UTR|GTPBP4_ENST00000538293.1_Silent_p.K65K	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	181	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				GTP catabolic process (GO:0006184)|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 collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		ATGTTGGGAAGTCCAGCTTCA	0.443																																					p.K181K		.											.	GTPBP4-92	0			c.G543A						.						180	169	172					10																	1043230		2203	4300	6503	SO:0001819	synonymous_variant	23560	exon5			TGGGAAGTCCAGC	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"G protein-binding protein CRFG", " GTP-binding protein"					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.543G>A	10.37:g.1043230G>A		Somatic	390	1		WXS	Illumina HiSeq	Phase_I	456	204	NM_012341	0	0	11	20	9	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Silent	SNP	ENST00000360803.4	37	CCDS31132.1																																																																																			.		0.443	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341		A	1043230	G	A	1043230	2	1	29	1	0	0	0	0	0	0	0	1	6903	1020	36	2		2	GTPBP4	10	1043230	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08		1043230	134491517	44	2590											
PFKP	5214	ucsc.edu	37	chr10	3172124	3172124	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggggggctcgcggccggAgctgatgccgcatacatttt	6	9	16	10	4	0	1	0	1	0	0	1	2	0	2	2	5	3	3	2	5	1	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr10:3172124A>G	ENST00000381125.4	+	17	1873	c.1797A>G	c.(1795-1797)ggA>ggG	p.G599G	PFKP_ENST00000381075.2_Silent_p.G591G|PFKP_ENST00000381072.1_Silent_p.G17G	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	599	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TCGCGGCCGGAGCTGATGCCG	0.637																																					p.G599G													.	PFKP-253	0			c.A1797G						.						46	44	45					10																	3172124		2203	4300	6503	SO:0001819	synonymous_variant	5214	exon17			GGCCGGAGCTGAT	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"Phosphofructokinase, platelet type"	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1797A>G	10.37:g.3172124A>G		Somatic	98	4		WXS	Illumina HiSeq		125	4	NM_002627	0	0	0	0	0	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	a	0.412	-0.912933	0.02415	.	.	ENSG00000067057	ENST00000413079	.	.	.	4.49	-1.22	0.09494	.	.	.	.	.	T	0.39200	0.1069	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27434	-1.0074	4	.	.	.	.	0.901	0.01274	0.3028:0.2525:0.0973:0.3474	.	.	.	.	G	163	.	.	S	+	1	0	PFKP	3162124	0.000000	0.05858	0.287000	0.24848	0.008000	0.06430	-2.641000	0.00864	-0.159000	0.11021	-0.666000	0.03841	AGC	.		0.637	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		G	3172124	A	G	3172124	2	3	29	1	0	0	0	0	0	0	0	1	11792	291	11	3		3	PFKP	10	3172124	Silent	SNP	A	TCGA-AL-3466-01A-01D-1252-08	2128894	3172124	132362623	45	2591											
C10orf28	27291	hgsc.bcm.edu	37	chr10	99967975	99967975	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtactccttaagacaggtgAtgaagaagaaagctgtggtt	14	10	12	5	0	0	5	0	2	0	3	1	5	1	5	1	2	2	3	1	2	5	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr10:99967975A>G	ENST00000298999.3	+	5	407	c.104A>G	c.(103-105)gAt>gGt	p.D35G	R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.D35G|R3HCC1L_ENST00000370586.2_Intron	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	35							nucleotide binding (GO:0000166)										AAGACAGGTGATGAAGAAGAA	0.443																																					p.D35G		.											.	.	0			c.A104G						.						61	63	63					10																	99967975		2203	4300	6503	SO:0001583	missense	27291	exon4			CAGGTGATGAAGA	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.104A>G	10.37:g.99967975A>G	ENSP00000298999:p.Asp35Gly	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_001256620	0	0	5	5	0	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	A	2.186	-0.386501	0.04966	.	.	ENSG00000166024	ENST00000370584;ENST00000538495;ENST00000298999	T;T	0.13089	2.62;2.62	5.67	1.58	0.23477	.	0.627416	0.15583	N	0.254798	T	0.09555	0.0235	L	0.41824	1.3	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.35226	-0.9797	9	.	.	.	-0.1034	4.8076	0.13328	0.6597:0.1568:0.1834:0.0	.	35;35	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	G	35	ENSP00000359616:D35G;ENSP00000298999:D35G	.	D	+	2	0	C10orf28	99957965	0.382000	0.25148	0.002000	0.10522	0.018000	0.09664	1.329000	0.33770	0.027000	0.15297	0.454000	0.30748	GAT	.		0.443	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		G	99967975	A	G	99967975	3	3	29	1	0	0	0	0	1	0	0	0	1605	333	12	3	106	3	C10orf28	10	99967975	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	96795851	99967975	35566772	46	2592											
MUC5B	727897	broad.mit.edu	37	chr11	1258389	1258389	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccttcgccgcctgccgcTcccaggtggggctctggtct	2	9	12	18	3	2	0	0	0	2	0	4	0	3	0	6	4	1	2	6	4	0	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:1258389T>G	ENST00000529681.1	+	25	3350	c.3292T>G	c.(3292-3294)Tcc>Gcc	p.S1098A	MUC5B_ENST00000447027.1_Missense_Mutation_p.S1101A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1098	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGCCTGCCGCTCCCAGGTGGG	0.682																																					p.S1098A													.	.	0			c.T3292G						.						10	15	13					11																	1258389		1897	4084	5981	SO:0001583	missense	727897	exon25			TGCCGCTCCCAGG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3292T>G	11.37:g.1258389T>G	ENSP00000436812:p.Ser1098Ala	Somatic	36	1		WXS	Illumina HiSeq	Phase_I	30	3	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	5.715	0.316511	0.10845	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76839	-1.05;-1.05	4.38	-4.2	0.03823	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.59473	0.2196	N	0.10645	0.015	0.27479	N	0.952642	B;P;P	0.48089	0.026;0.905;0.905	B;P;P	0.47376	0.027;0.545;0.545	T	0.57613	-0.7781	9	0.87932	D	0	.	6.1245	0.20172	0.0:0.2029:0.3546:0.4425	.	1098;1791;1101	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	A	1098;1101;1099;1168	ENSP00000436812:S1098A;ENSP00000415793:S1101A	ENSP00000343037:S1099A	S	+	1	0	MUC5B	1214965	0.000000	0.05858	0.074000	0.20217	0.008000	0.06430	-0.169000	0.09911	-0.576000	0.05974	-0.648000	0.03929	TCC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1258389	T	G	1258389	3	3	29	1	0	0	0	0	1	0	0	0	10004	1551	54	5	3399	5	MUC5B	11	1258389	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		1258389	133748127	47	2593											
PIK3C2A	5286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	17190402	17190402	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatcctttgctagcaaacttGaaacatttttctcttcctca	10	16	4	11	0	2	1	1	1	1	0	5	2	4	1	2	0	4	2	2	0	3	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:17190402G>A	ENST00000265970.7	-	1	886	c.887C>T	c.(886-888)tCa>tTa	p.S296L	PIK3C2A_ENST00000540361.1_Intron|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	296					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TAGCAAACTTGAAACATTTTT	0.393																																					p.S296L		.											.	PIK3C2A-1310	0			c.C887T						.						176	170	172					11																	17190402		2200	4293	6493	SO:0001583	missense	5286	exon1			AAACTTGAAACAT	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.887C>T	11.37:g.17190402G>A	ENSP00000265970:p.Ser296Leu	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	278	59	NM_002645	0	0	9	9	0	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.239126	0.22711	.	.	ENSG00000011405	ENST00000265970;ENST00000544896	T	0.62639	0.01	5.49	5.49	0.81192	.	1.281530	0.04815	N	0.435973	T	0.54838	0.1883	N	0.19112	0.55	0.54753	D	0.999987	B;B	0.26258	0.145;0.0	B;B	0.21708	0.036;0.0	T	0.09422	-1.0675	10	0.51188	T	0.08	-3.6563	15.6995	0.77533	0.0:0.137:0.863:0.0	.	296;296	F5H5W9;O00443	.;P3C2A_HUMAN	L	296	ENSP00000265970:S296L	ENSP00000265970:S296L	S	-	2	0	PIK3C2A	17146978	0.228000	0.23718	0.359000	0.25824	0.485000	0.33311	1.793000	0.38764	2.570000	0.86706	0.563000	0.77884	TCA	.		0.393	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		A	17190402	G	A	17190402	3	1	29	1	0	0	0	0	1	0	0	0	11935	1294	45	2	4301	2	PIK3C2A	11	17190402	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	15932013	17190402	117816114	48	2594											
MS4A12	54860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	60268545	60268545	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agatcatggttggattgatgCacattggttttggaattgtt	9	17	12	3	0	1	2	1	1	0	1	1	4	1	4	0	4	1	4	0	4	1	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:60268545C>T	ENST00000016913.4	+	3	361	c.304C>T	c.(304-306)Cac>Tac	p.H102Y	MS4A12_ENST00000537076.1_Intron	NM_017716.2	NP_060186.2	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member 12	102						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)	17						TGGATTGATGCACATTGGTTT	0.373																																					p.H102Y		.											.	MS4A12-90	0			c.C304T						.						292	286	288					11																	60268545		2203	4300	6503	SO:0001583	missense	54860	exon3			TTGATGCACATTG	AK000224	CCDS7988.1, CCDS53638.1	11q12	2008-03-25				ENSG00000071203			13370	protein-coding gene	gene with protein product		606550				11401424, 11486273	Standard	NM_017716		Approved	Ms4a10, FLJ20217	uc001npr.3	Q9NXJ0		ENST00000016913.4:c.304C>T	11.37:g.60268545C>T	ENSP00000016913:p.His102Tyr	Somatic	591	0		WXS	Illumina HiSeq	Phase_I	298	44	NM_017716	0	0	0	0	0	F5GX98|Q8N6L4	Missense_Mutation	SNP	ENST00000016913.4	37	CCDS7988.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.277327	0.40294	.	.	ENSG00000071203	ENST00000016913;ENST00000530007	T;T	0.58506	4.27;0.33	5.14	5.14	0.70334	.	0.454353	0.25506	N	0.030212	T	0.66177	0.2763	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.62243	-0.6895	10	0.02654	T	1	.	14.0807	0.64919	0.0:1.0:0.0:0.0	.	102	Q9NXJ0	M4A12_HUMAN	Y	102	ENSP00000016913:H102Y;ENSP00000434783:H102Y	ENSP00000016913:H102Y	H	+	1	0	MS4A12	60025121	0.679000	0.27596	0.572000	0.28498	0.095000	0.18619	2.340000	0.43974	2.375000	0.81037	0.462000	0.41574	CAC	.		0.373	MS4A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383627.1			T	60268545	C	T	60268545	3	4	29	1	0	0	0	0	1	0	0	0	9881	710	25	2	310	2	MS4A12	11	60268545	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	43078143	60268545	74737971	49	2595											
VWCE	220001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	61026692	61026692	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctacagttgacaggggcctCagtgtctccatgcaggctcc	7	9	12	13	0	2	1	1	1	1	0	4	1	3	1	3	3	2	4	3	3	1	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:61026692C>A	ENST00000335613.5	-	20	2709	c.2323G>T	c.(2323-2325)Gag>Tag	p.E775*	VWCE_ENST00000535710.1_Nonsense_Mutation_p.E240*	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	775						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						ACAGGGGCCTCAGTGTCTCCA	0.567																																					p.E775X		.											.	VWCE-91	0			c.G2323T						.						40	42	41					11																	61026692		2203	4299	6502	SO:0001587	stop_gained	220001	exon20			GGGCCTCAGTGTC	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.2323G>T	11.37:g.61026692C>A	ENSP00000334186:p.Glu775*	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	112	22	NM_152718	0	0	0	0	0	A5PKV0|Q7Z7L6|Q86WK8	Nonsense_Mutation	SNP	ENST00000335613.5	37	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	C	37	6.304859	0.97458	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	.	.	.	4.63	-0.214	0.13161	.	0.840398	0.09913	N	0.739540	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	3.1614	0.06521	0.1831:0.4481:0.0:0.3689	.	.	.	.	X	775;240	.	ENSP00000334186:E775X	E	-	1	0	VWCE	60783268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.666000	0.05280	0.047000	0.15862	-0.982000	0.02568	GAG	.		0.567	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61026692	C	A	61026692	4	1	29	1	0	0	0	0	0	1	0	0	17278	835	29	4	548	4	VWCE	11	61026692	Nonsense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	758147	61026692	73979824	50	2596											
AHNAK	79026	ucsc.edu	37	chr11	62295728	62295728	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agccaggcatgctgaacttgGgcattttcatcttgggcatc	8	12	11	10	0	2	1	1	1	1	0	3	1	2	1	1	3	3	4	1	3	1	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:62295728G>A	ENST00000378024.4	-	5	6435	c.6161C>T	c.(6160-6162)cCc>cTc	p.P2054L	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2054					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GCTGAACTTGGGCATTTTCAT	0.507																																					p.P2054L													.	AHNAK-109	0			c.C6161T						.						280	285	283					11																	62295728		2202	4297	6499	SO:0001583	missense	79026	exon5			AACTTGGGCATTT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.6161C>T	11.37:g.62295728G>A	ENSP00000367263:p.Pro2054Leu	Somatic	615	1		WXS	Illumina HiSeq		802	2	NM_001620	0	0	39	46	7	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	g	19.32	3.805699	0.70682	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.03004	4.08	4.05	4.05	0.47172	.	0.000000	0.34555	U	0.003874	T	0.32734	0.0839	H	0.98507	4.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61397	-0.7071	10	0.87932	D	0	.	15.8511	0.78930	0.0:0.0:1.0:0.0	.	2054	Q09666	AHNK_HUMAN	L	143;2054	ENSP00000367263:P2054L	ENSP00000244934:P143L	P	-	2	0	AHNAK	62052304	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	6.174000	0.71943	1.803000	0.52742	0.298000	0.19748	CCC	.		0.507	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		A	62295728	G	A	62295728	3	1	29	1	0	0	0	0	1	0	0	0	414	1232	43	2	11631	2	AHNAK	11	62295728	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	1269036	62295728	72710788	51	2597											
PCSK7	9159	hgsc.bcm.edu	37	chr11	117079626	117079626	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacatacgagtccatgctgcGgggggcgccgatgagggaca	9	6	16	10	4	0	1	0	1	0	0	1	4	1	2	2	4	4	1	2	4	2	2	rs202038275		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:117079626G>C	ENST00000320934.3	-	13	2308	c.1678C>G	c.(1678-1680)Cgc>Ggc	p.R560G	PCSK7_ENST00000529458.1_5'Flank|PCSK7_ENST00000540028.1_Missense_Mutation_p.R201G	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	560					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		TCCATGCTGCGGGGGGCGCCG	0.597			T	IGH@	MLCLS																																p.R560G		.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7-658	0			c.C1678G						.						40	43	42					11																	117079626		2201	4296	6497	SO:0001583	missense	9159	exon13			TGCTGCGGGGGGC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1678C>G	11.37:g.117079626G>C	ENSP00000325917:p.Arg560Gly	Somatic	46	2		WXS	Illumina HiSeq	Phase_I	45	11	NM_004716	0	0	4	4	0	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	37	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082462	0.36758	.	.	ENSG00000160613	ENST00000320934;ENST00000540028;ENST00000543900	T;T	0.71222	-0.55;-0.55	4.68	3.77	0.43336	Proprotein convertase, P (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.82875	0.5132	M	0.85099	2.735	0.58432	D	0.999992	D	0.89917	1.0	D	0.83275	0.996	D	0.83562	0.0107	10	0.87932	D	0	-26.4093	7.8865	0.29653	0.0864:0.0:0.7545:0.1591	.	560	Q16549	PCSK7_HUMAN	G	560;201;560	ENSP00000325917:R560G;ENSP00000441944:R201G	ENSP00000325917:R560G	R	-	1	0	PCSK7	116584836	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	1.527000	0.35975	1.207000	0.43291	-0.362000	0.07510	CGC	G|0.875;C|0.125		0.597	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		C	117079626	G	C	117079626	3	2	29	1	0	0	0	0	1	0	0	0	11631	1116	39	4	699	4	PCSK7	11	117079626	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	54783898	117079626	17926890	52	2598											
ESAM	90952	broad.mit.edu	37	chr11	124624584	124624584	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgggcagtgcccacctcaTtgtgggccttgcagacatag	8	10	12	11	0	1	1	1	0	0	1	1	1	1	1	3	2	2	2	3	2	1	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:124624584T>C	ENST00000278927.5	-	5	812	c.683A>G	c.(682-684)aAt>aGt	p.N228S	ESAM_ENST00000442070.2_Missense_Mutation_p.N49S|VSIG2_ENST00000326621.5_5'Flank|VSIG2_ENST00000403470.1_5'Flank	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	228	Ig-like C2-type.				blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		GCCCACCTCATTGTGGGCCTT	0.522																																					p.N228S													.	ESAM-90	0			c.A683G						.						199	176	184					11																	124624584		2201	4299	6500	SO:0001583	missense	90952	exon5			ACCTCATTGTGGG	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.683A>G	11.37:g.124624584T>C	ENSP00000278927:p.Asn228Ser	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	304	4	NM_138961	0	0	0	0	0	B4DVN8|Q96T50	Missense_Mutation	SNP	ENST00000278927.5	37	CCDS8453.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846380	0.71603	.	.	ENSG00000149564	ENST00000442070;ENST00000444566;ENST00000278927;ENST00000435477	T;T;T;T	0.22743	3.53;3.53;1.94;1.94	5.83	5.83	0.93111	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	M	0.86864	2.845	0.54753	D	0.999988	P;D;D;D	0.76494	0.873;0.998;0.999;0.984	P;D;D;D	0.68039	0.707;0.955;0.936;0.93	T	0.54309	-0.8313	10	0.72032	D	0.01	.	8.7082	0.34367	0.0:0.0844:0.0:0.9156	.	49;228;228;101	B4DVN8;F8WDW9;Q96AP7;C9JIE7	.;.;ESAM_HUMAN;.	S	49;49;228;101	ENSP00000410351:N49S;ENSP00000406689:N49S;ENSP00000278927:N228S;ENSP00000415893:N101S	ENSP00000278927:N228S	N	-	2	0	ESAM	124129794	0.983000	0.35010	0.860000	0.33809	0.987000	0.75469	2.952000	0.49097	2.220000	0.72140	0.533000	0.62120	AAT	.		0.522	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961		C	124624584	T	C	124624584	3	2	29	1	0	0	0	0	1	0	0	0	5260	1493	52	3	501	3	ESAM	11	124624584	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	7544958	124624584	10381932	53	2599											
M6PR	4074	hgsc.bcm.edu;broad.mit.edu	37	chr12	9096395	9096395	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatacaacacagggtgcctcAccgctagggtgtgtcgattg	9	10	12	10	2	1	0	1	0	0	0	2	1	1	0	2	2	3	1	2	2	4	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr12:9096395A>G	ENST00000000412.3	-	4	922		c.e4+1			NM_002355.3	NP_002346.1	P20645	MPRD_HUMAN	mannose-6-phosphate receptor (cation dependent)						endosome to lysosome transport (GO:0008333)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	mannose binding (GO:0005537)|mannose transmembrane transporter activity (GO:0015578)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(1)	11		Hepatocellular(102;0.137)		BRCA - Breast invasive adenocarcinoma(232;0.0146)	Alglucosidase alfa(DB01272)	AGGGTGCCTCACCGCTAGGGT	0.527																																					.		.											.	M6PR-90	0			c.453+2T>C						.						79	64	69					12																	9096395		2203	4300	6503	SO:0001630	splice_region_variant	4074	exon5			TGCCTCACCGCTA		CCDS8598.1, CCDS73440.1	12p13.31	2013-09-20			ENSG00000003056	ENSG00000003056			6752	protein-coding gene	gene with protein product		154540					Standard	NM_002355		Approved		uc001qvf.3	P20645	OTTHUMG00000168276	ENST00000000412.3:c.453+1T>C	12.37:g.9096395A>G		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	100	18	NM_002355	0	0	0	0	0	A8K528|D3DUV5	Splice_Site	SNP	ENST00000000412.3	37	CCDS8598.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.111457	0.77210	.	.	ENSG00000003056	ENST00000000412;ENST00000537621	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6658	0.77227	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	M6PR	8987662	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.075000	0.76798	2.191000	0.70037	0.528000	0.53228	.	.		0.527	M6PR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399130.1		Intron	G	9096395	A	G	9096395	5	3	29	1	0	0	0	0	0	0	1	0	9165	173	6	3	394	3	M6PR	12	9096395	Splice_Site	SNP	A	TCGA-AL-3466-01A-01D-1252-08		9096395	124755500	54	2600											
HEATR5A	25938	ucsc.edu	37	chr14	31782236	31782236	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagagcaaaatcctgaagtGcagcaagccagagtctgctt	15	7	10	9	0	1	3	0	1	1	2	2	3	2	3	2	0	5	4	2	0	5	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr14:31782236G>A	ENST00000389961.3	-	27	4360	c.4361C>T	c.(4360-4362)gCa>gTa	p.A1454V	HEATR5A_ENST00000439348.1_Missense_Mutation_p.A1454V|HEATR5A_ENST00000439727.1_Missense_Mutation_p.A1167V|HEATR5A_ENST00000543095.2_Missense_Mutation_p.A1460V|AL136418.1_ENST00000582500.1_RNA			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1454										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		ATCCTGAAGTGCAGCAAGCCA	0.413																																					p.A1460V													.	HEATR5A-23	0			c.C4379T						.						151	145	147					14																	31782236		1987	4191	6178	SO:0001583	missense	25938	exon28			TGAAGTGCAGCAA	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.4361C>T	14.37:g.31782236G>A	ENSP00000374611:p.Ala1454Val	Somatic	176	0		WXS	Illumina HiSeq		116	1	NM_015473	0	0	0	0	0	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.9|20.9	4.073683|4.073683	0.76415|0.76415	.|.	.|.	ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095|ENST00000538864	T;T;T;T|.	0.53857|.	0.6;0.6;0.6;0.6|.	4.68|4.68	4.68|4.68	0.58851|0.58851	.|.	0.055107|.	0.64402|.	D|.	0.000001|.	T|T	0.69223|0.69223	0.3087|0.3087	L|L	0.52126|0.52126	1.63|1.63	0.80722|0.80722	D|D	1|1	P|.	0.34629|.	0.46|.	B|.	0.40375|.	0.327|.	T|T	0.67503|0.67503	-0.5654|-0.5654	10|5	0.40728|.	T|.	0.16|.	.|.	17.9551|17.9551	0.89065|0.89065	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1454|.	Q86XA9-2|.	.|.	V|Y	1454;1454;1167;1460|1088	ENSP00000374611:A1454V;ENSP00000405407:A1454V;ENSP00000408681:A1167V;ENSP00000437968:A1460V|.	ENSP00000374611:A1454V|.	A|H	-|-	2|1	0|0	HEATR5A|HEATR5A	30851987|30851987	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.996000|0.996000	0.88848|0.88848	5.153000|5.153000	0.64888|0.64888	2.310000|2.310000	0.77875|0.77875	0.561000|0.561000	0.74099|0.74099	GCA|CAC	.		0.413	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		A	31782236	G	A	31782236	3	1	29	1	0	0	0	0	1	0	0	0	7052	1319	46	2	1797	2	HEATR5A	14	31782236	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08		31782236	75567304	55	2601											
AHNAK2	113146	broad.mit.edu	37	chr14	105412623	105412623	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggtgccctttgaggccAgctccctcgggaacgtggcc	5	7	15	14	2	0	1	0	1	0	0	2	2	1	2	4	5	3	2	4	5	1	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr14:105412623A>G	ENST00000333244.5	-	7	9284	c.9165T>C	c.(9163-9165)gcT>gcC	p.A3055A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3055						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTTTGAGGCCAGCTCCCTCGG	0.607																																					p.A3055A													.	AHNAK2-47	0			c.T9165C						.						105	109	108					14																	105412623		1900	4099	5999	SO:0001819	synonymous_variant	113146	exon7			GAGGCCAGCTCCC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9165T>C	14.37:g.105412623A>G		Somatic	316	0		WXS	Illumina HiSeq	Phase_I	319	5	NM_138420	0	0	0	11	11	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105412623	A	G	105412623	2	3	29	1	0	0	0	0	0	0	0	1	415	175	7	3		3	AHNAK2	14	105412623	Silent	SNP	A	TCGA-AL-3466-01A-01D-1252-08	73630387	105412623	1936917	56	2602											
MEIS2	4212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	37184626	37184626	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcattcccataggaccaccCtgagaaacgtagtcccctgg	10	8	8	15	1	1	1	1	1	0	1	3	3	3	2	5	2	1	1	5	2	3	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr15:37184626C>A	ENST00000561208.1	-	12	1600	c.1182G>T	c.(1180-1182)caG>caT	p.Q394H	MEIS2_ENST00000557796.2_3'UTR|MEIS2_ENST00000424352.2_3'UTR|MEIS2_ENST00000340545.5_3'UTR|MEIS2_ENST00000397624.3_3'UTR|MEIS2_ENST00000338564.5_Missense_Mutation_p.Q387H|MEIS2_ENST00000559085.1_3'UTR|MEIS2_ENST00000219869.9_3'UTR|MEIS2_ENST00000444725.1_3'UTR|MEIS2_ENST00000397620.2_3'UTR|MEIS2_ENST00000559408.1_5'Flank|MEIS2_ENST00000382766.2_Missense_Mutation_p.Q387H			O14770	MEIS2_HUMAN	Meis homeobox 2	394	Transcriptional activation domain.				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TAGGACCACCCTGAGAAACGT	0.458																																					p.Q394H		.											.	MEIS2-92	0			c.G1182T						.						187	188	188					15																	37184626		2201	4297	6498	SO:0001583	missense	4212	exon12			ACCACCCTGAGAA	AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.1182G>T	15.37:g.37184626C>A	ENSP00000453793:p.Gln394His	Somatic	591	1		WXS	Illumina HiSeq	Phase_I	214	59	NM_170675	0	0	0	0	0	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.645203	0.29246	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766	D;D	0.86627	-2.15;-2.15	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.78046	0.4222	N	0.12182	0.205	0.80722	D	1	B;B;B;B	0.13145	0.001;0.002;0.001;0.007	B;B;B;B	0.13407	0.002;0.002;0.002;0.009	T	0.71087	-0.4694	10	0.22706	T	0.39	-1.914	18.9968	0.92817	0.0:1.0:0.0:0.0	.	387;394;374;90	O14770-4;O14770;B7Z6F6;Q6V703	.;MEIS2_HUMAN;.;.	H	394;387;387	ENSP00000341400:Q387H;ENSP00000372216:Q387H	ENSP00000326296:Q394H	Q	-	3	2	MEIS2	34971918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.801000	0.69115	2.705000	0.92388	0.655000	0.94253	CAG	.		0.458	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		A	37184626	C	A	37184626	3	1	29	1	0	0	0	0	1	0	0	0	9493	680	24	4	255	4	MEIS2	15	37184626	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		37184626	65346766	57	2603											
RHBDL1	9028	hgsc.bcm.edu	37	chr16	726121	726121	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gatgggtagggtggaagacgGgggaacaactgaggagctgg	11	5	21	4	1	0	2	0	1	0	1	0	6	0	5	0	7	3	2	0	7	4	1	rs200482219	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr16:726121G>C	ENST00000219551.2	+	1	47	c.20G>C	c.(19-21)gGg>gCg	p.G7A	LA16c-313D11.9_ENST00000571933.1_RNA|LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Intron			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	7					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				GTGGAAGACGGGGGAACAACT	0.682													G|||	4	0.000798722	0	0.0014	5008	,	,		10105	0		0.001	False		,,,				2504	0.002				p.G7A		.											.	RHBDL1-90	0			c.G20C						.	G	ALA/GLY	1,3923		0,1,1961	4	3	4		20	-0.9	0	16		4	2,7792		0,2,3895	yes	missense	RHBDL1	NM_003961.1	60	0,3,5856	CC,CG,GG		0.0257,0.0255,0.0256	benign	7/439	726121	3,11715	1962	3897	5859	SO:0001583	missense	9028	exon1			AAGACGGGGGAAC	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"rhomboid (veinlet, Drosophila)-like"	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.20G>C	16.37:g.726121G>C	ENSP00000219551:p.Gly7Ala	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	11	6	NM_003961	0	0	0	3	3	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	37	CCDS10418.1	4	0.0018315018315018315	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	10.26	1.301490	0.23736	2.55E-4	2.57E-4	ENSG00000103269	ENST00000219551	T	0.38722	1.12	3.59	-0.853	0.10709	.	.	.	.	.	T	0.19805	0.0476	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.20605	-1.0270	9	0.87932	D	0	.	4.0885	0.09958	0.3061:0.0:0.5279:0.1659	.	7	O75783	RHBL1_HUMAN	A	7	ENSP00000219551:G7A	ENSP00000219551:G7A	G	+	2	0	RHBDL1	666122	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.053000	0.11846	0.005000	0.14708	-0.521000	0.04368	GGG	G|0.998;C|0.002		0.682	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961		C	726121	G	C	726121	3	2	29	1	0	0	0	0	1	0	0	0	13353	1232	43	4	22	4	RHBDL1	16	726121	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08		726121	89628632	58	2604											
TNP2	7142	broad.mit.edu	37	chr16	11362955	11362955	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctccagttgggttgcggtgGctggccgggctctggctgga	2	10	19	10	2	1	0	0	0	1	0	2	1	2	1	2	7	1	6	2	7	0	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr16:11362955G>A	ENST00000312693.3	-	1	234	c.165C>T	c.(163-165)agC>agT	p.S55S	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	55					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S55R(1)|p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						GGTTGCGGTGGCTGGCCGGGC	0.617																																					p.S55S													.	.	2	Substitution - Missense(1)|Whole gene deletion(1)	upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	c.C165T						.						133	149	143					16																	11362955		2067	4203	6270	SO:0001819	synonymous_variant	7142	exon1			GCGGTGGCTGGCC		CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.165C>T	16.37:g.11362955G>A		Somatic	309	0		WXS	Illumina HiSeq	Phase_I	612	7	NM_005425	0	0	0	0	0	Q9NZB0	Silent	SNP	ENST00000312693.3	37	CCDS45410.1																																																																																			.		0.617	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425		A	11362955	G	A	11362955	2	1	29	1	0	0	0	0	0	0	0	1	16366	1194	42	2		2	TNP2	16	11362955	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08	10636834	11362955	78991798	59	2605											
B3GNT9	80262	hgsc.bcm.edu	37	chr16	67183948	67183948	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aacacgcggcgcaccagcgcCccctgcacgcgaccctccgc	7	2	10	22	7	0	0	0	0	0	0	1	1	1	0	5	1	3	2	5	1	1	0	rs146483793	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr16:67183948C>T	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.G147G	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GCACCAGCGCCCCCTGCACGC	0.746													c|||	3	0.000599042	0	0	5008	,	,		11171	0		0.003	False		,,,				2504	0				p.G147G		.											.	.	0			c.G441A						.			2,3338		0,2,1668	4	4	4		441	4.3	1	16	dbSNP_134	4	24,7148		0,24,3562	no	coding-synonymous	B3GNT9	NM_033309.2		0,26,5230	TT,TC,CC		0.3346,0.0599,0.2473		147/403	67183948	26,10486	1670	3586	5256	SO:0001628	intergenic_variant	84752	exon2			CAGCGCCCCCTGC	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		16.37:g.67183948C>T		Somatic	4	1		WXS	Illumina HiSeq	Phase_I	7	4	NM_033309	0	0	0	0	0	Q9HA86	Silent	SNP	ENST00000219139.3	37	CCDS10828.1																																																																																			C|0.998;T|0.002		0.746	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		T	67183948	C	T	67183948	1	4	29	0	1	0	0	0	0	0	0	0	1265	610	22	2		2	B3GNT9	16	67183948	IGR	SNP	C	TCGA-AL-3466-01A-01D-1252-08	55820993	67183948	23170805	60	2606											
CRISPLD2	83716	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	84940197	84940197	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttcttctttttttcagcctGgggactcctcgggatggaaa	6	16	10	9	1	3	0	1	0	2	0	5	3	4	3	2	4	1	0	2	4	1	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr16:84940197G>A	ENST00000262424.5	+	15	1667	c.1443G>A	c.(1441-1443)ctG>ctA	p.L481L	CRISPLD2_ENST00000567845.1_Silent_p.L480L	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	481	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						TTTTCAGCCTGGGGACTCCTC	0.597																																					p.L481L		.											.	CRISPLD2-90	0			c.G1443A						.						54	58	57					16																	84940197		2199	4300	6499	SO:0001819	synonymous_variant	83716	exon15			CAGCCTGGGGACT	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"LCCL domain containing cysteine-rich secretory protein 2"	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.1443G>A	16.37:g.84940197G>A		Somatic	256	0		WXS	Illumina HiSeq	Phase_I	282	59	NM_031476	0	0	0	0	0	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Silent	SNP	ENST00000262424.5	37	CCDS10949.1																																																																																			.		0.597	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		A	84940197	G	A	84940197	2	1	29	1	0	0	0	0	0	0	0	1	3889	1335	47	2		2	CRISPLD2	16	84940197	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08	17756249	84940197	5414556	61	2607											
ACACA	31	ucsc.edu	37	chr17	35487095	35487095	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccattgttgtgcataatcTggatgccccccagctggtta	7	12	9	13	0	1	0	0	0	1	0	1	1	1	1	5	2	3	4	5	2	2	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:35487095T>C	ENST00000394406.2	-	46	5808	c.5618A>G	c.(5617-5619)cAg>cGg	p.Q1873R	ACACA_ENST00000335166.5_Missense_Mutation_p.Q1795R|ACACA_ENST00000360679.3_Missense_Mutation_p.Q1815R|ACACA_ENST00000361253.5_5'UTR|ACACA_ENST00000353139.5_Missense_Mutation_p.Q1910R	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1873	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GTGCATAATCTGGATGCCCCC	0.493																																					p.Q1910R	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)												.	ACACA-154	0			c.A5729G						.						187	166	173					17																	35487095		2203	4300	6503	SO:0001583	missense	31	exon46			ATAATCTGGATGC	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.5618A>G	17.37:g.35487095T>C	ENSP00000377928:p.Gln1873Arg	Somatic	296	0		WXS	Illumina HiSeq		511	2	NM_198834	0	0	0	0	0	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	32	5.110753	0.94292	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330	D;D;D;D	0.97665	-4.48;-4.48;-4.48;-4.48	5.83	5.83	0.93111	Carboxyl transferase (1);Acetyl-coenzyme A carboxyltransferase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98188	0.9401	M	0.79475	2.455	0.80722	D	1	D;P;D;D	0.65815	0.995;0.956;0.989;0.986	P;P;D;P	0.66716	0.885;0.648;0.946;0.877	D	0.98678	1.0691	10	0.52906	T	0.07	-14.2837	16.1846	0.81942	0.0:0.0:0.0:1.0	.	572;1910;1873;1815	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	R	1910;1815;1873;1897;1795;572	ENSP00000344789:Q1910R;ENSP00000353898:Q1815R;ENSP00000377928:Q1873R;ENSP00000335323:Q1795R	ENSP00000335323:Q1795R	Q	-	2	0	ACACA	32561208	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.229000	0.72834	0.533000	0.62120	CAG	.		0.493	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		C	35487095	T	C	35487095	3	2	29	1	0	0	0	0	1	0	0	0	106	1580	55	3	1466	3	ACACA	17	35487095	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		35487095	45708115	62	2608											
PLEKHM1	9842	broad.mit.edu	37	chr17	43531102	43531102	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatttcagagcctccaaggAcagagaaaatatatagggca	17	7	9	8	0	1	2	1	0	0	2	2	4	2	3	2	2	1	1	2	2	6	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:43531102A>G	ENST00000430334.3	-	7	2249	c.2116T>C	c.(2116-2118)Tcc>Ccc	p.S706P	AC091132.1_ENST00000433601.1_RNA|PLEKHM1_ENST00000421073.2_Missense_Mutation_p.S617P	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	706	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GCCTCCAAGGACAGAGAAAAT	0.542																																					p.S706P													.	PLEKHM1-90	0			c.T2116C						.						47	44	45					17																	43531102		2203	4300	6503	SO:0001583	missense	9842	exon7			CCAAGGACAGAGA	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"Pleckstrin homology (PH) domain containing"	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.2116T>C	17.37:g.43531102A>G	ENSP00000389913:p.Ser706Pro	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	209	4	NM_014798	0	0	0	10	10	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	37	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	A	13.41	2.229476	0.39399	.	.	ENSG00000225190	ENST00000430334;ENST00000446609;ENST00000421073	T;T	0.64085	-0.08;-0.08	4.91	4.91	0.64330	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.063686	0.64402	D	0.000004	T	0.66386	0.2784	L	0.29908	0.895	0.46564	D	0.999104	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.994;0.996;0.991	T	0.68484	-0.5396	10	0.62326	D	0.03	.	9.0391	0.36307	0.8356:0.0:0.0:0.1644	.	617;655;706	F8W648;B4DRX1;Q9Y4G2	.;.;PKHM1_HUMAN	P	706;655;617	ENSP00000389913:S706P;ENSP00000414352:S617P	ENSP00000414352:S617P	S	-	1	0	PLEKHM1	40886885	1.000000	0.71417	1.000000	0.80357	0.062000	0.15995	6.744000	0.74854	2.079000	0.62486	0.477000	0.44152	TCC	.		0.542	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		G	43531102	A	G	43531102	3	3	29	1	0	0	0	0	1	0	0	0	12106	275	10	3	1078	3	PLEKHM1	17	43531102	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	8044007	43531102	37664108	63	2609											
NGFR	4804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	47588006	47588006	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtggttgtgggccttgtGgcctacatagccttcaagag	6	12	14	9	0	1	1	1	0	0	1	1	1	1	1	3	3	2	2	3	3	3	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:47588006G>T	ENST00000172229.3	+	4	926	c.801G>T	c.(799-801)gtG>gtT	p.V267V	NGFR_ENST00000504201.1_Silent_p.V173V|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	267					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					TGGGCCTTGTGGCCTACATAG	0.577																																					p.V267V		.											.	NGFR-947	0			c.G801T						.						112	101	105					17																	47588006		2203	4300	6503	SO:0001819	synonymous_variant	4804	exon4			CCTTGTGGCCTAC	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"Tumor necrosis factor receptor superfamily", "CD molecules"	7809	protein-coding gene	gene with protein product	"low affinity nerve growth factor receptor", "TNFR superfamily, member 16"	162010	"nerve growth factor receptor (TNFR superfamily, member 16)"			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.801G>T	17.37:g.47588006G>T		Somatic	205	0		WXS	Illumina HiSeq	Phase_I	333	56	NM_002507	0	0	0	0	0	B2R961|B4E096	Silent	SNP	ENST00000172229.3	37	CCDS11549.1																																																																																			.		0.577	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			T	47588006	G	T	47588006	2	4	29	1	0	0	0	0	0	0	0	1	10422	1335	47	4		4	NGFR	17	47588006	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08	4056904	47588006	33607204	64	2610											
CA10	56934	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	49710848	49710848	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaacccacctctatactgaAgcttctgggctcggttgttt	8	13	8	12	1	2	1	0	1	2	0	3	1	2	1	2	2	3	4	2	2	4	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:49710848A>C	ENST00000285273.4	-	9	2064	c.953T>G	c.(952-954)cTt>cGt	p.L318R	CA10_ENST00000340813.6_Missense_Mutation_p.L324R|CA10_ENST00000451037.2_Missense_Mutation_p.L318R|CA10_ENST00000442502.2_Missense_Mutation_p.L318R|CA10_ENST00000570565.1_Missense_Mutation_p.L243R|CA10_ENST00000571918.1_5'Flank	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	318					brain development (GO:0007420)					cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	TCTATACTGAAGCTTCTGGGC	0.502																																					p.L318R		.											.	CA10-516	0			c.T953G						.						123	112	116					17																	49710848		2203	4300	6503	SO:0001583	missense	56934	exon9			TACTGAAGCTTCT	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"Carbonic anhydrases"	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.953T>G	17.37:g.49710848A>C	ENSP00000285273:p.Leu318Arg	Somatic	197	1		WXS	Illumina HiSeq	Phase_I	156	23	NM_001082534	0	0	0	0	0	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.398967	0.62177	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.71341	-0.51;-0.51;-0.51;-0.56	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	T	0.61825	0.2378	N	0.19112	0.55	0.58432	D	0.999998	P;P;P	0.44578	0.838;0.838;0.835	B;B;B	0.44278	0.276;0.276;0.445	T	0.67325	-0.5699	10	0.59425	D	0.04	.	14.6889	0.69070	1.0:0.0:0.0:0.0	.	318;324;243	Q9NS85;Q68D28;B4DGL6	CAH10_HUMAN;.;.	R	318;318;318;324	ENSP00000390666:L318R;ENSP00000285273:L318R;ENSP00000405388:L318R;ENSP00000340363:L324R	ENSP00000285273:L318R	L	-	2	0	CA10	47065847	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.301000	0.78850	2.069000	0.61940	0.533000	0.62120	CTT	.		0.502	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		C	49710848	A	C	49710848	3	2	29	1	0	0	0	0	1	0	0	0	2517	72	3	5	41	5	CA10	17	49710848	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	2122842	49710848	31484362	65	2611											
OR4D1	26689	broad.mit.edu	37	chr17	56232804	56232804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacgatctcctaccagggctGcatggcccagatcttcttct	7	11	9	14	1	4	1	0	0	4	1	5	3	4	1	3	2	2	2	3	2	1	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:56232804G>A	ENST00000268912.5	+	1	311	c.290G>A	c.(289-291)tGc>tAc	p.C97Y		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	97					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						TACCAGGGCTGCATGGCCCAG	0.522																																					p.C97Y													.	OR4D1-91	0			c.G290A						.						116	120	119					17																	56232804		2177	4286	6463	SO:0001583	missense	26689	exon1			AGGGCTGCATGGC	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"GPCR / Class A : Olfactory receptors"	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.290G>A	17.37:g.56232804G>A	ENSP00000365451:p.Cys97Tyr	Somatic	227	1		WXS	Illumina HiSeq	Phase_I	583	7	NM_012374	0	0	0	0	0	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	g	22.3	4.276326	0.80580	.	.	ENSG00000141194	ENST00000268912	T	0.17054	2.3	5.63	5.63	0.86233	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.57344	0.2047	H	0.96365	3.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.71427	-0.4596	10	0.87932	D	0	-23.2293	17.178	0.86846	0.0:0.0:1.0:0.0	.	97	Q15615	OR4D1_HUMAN	Y	97	ENSP00000365451:C97Y	ENSP00000365451:C97Y	C	+	2	0	OR4D1	53587803	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.611000	0.67674	2.652000	0.90054	0.543000	0.68304	TGC	.		0.522	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1			A	56232804	G	A	56232804	3	1	29	1	0	0	0	0	1	0	0	0	11079	1319	46	2	292	2	OR4D1	17	56232804	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	6521956	56232804	24962406	66	2612											
RGS9	8787	broad.mit.edu	37	chr17	63156389	63156390	+	Frame_Shift_Ins	INS	-	-	A																															ctttattgtcaggtatggctINSacatttaccccctgcaagac																										TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:63156389_63156390insA	ENST00000262406.9	+	4	311_312	c.244_245insA	c.(244-246)tacfs	p.Y82fs	RGS9_ENST00000577186.1_3'UTR|RGS9_ENST00000443584.3_Frame_Shift_Ins_p.Y82fs|RGS9_ENST00000449996.3_Frame_Shift_Ins_p.Y82fs	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	82	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						CAGGTATGGCTACATTTACCCC	0.5																																					p.Y82_I83delinsX													.	RGS9-94	0			c.244_245insA						.																																			SO:0001589	frameshift_variant	8787	exon4			TATGGCTACATTT	AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"Regulators of G-protein signaling"	10004	protein-coding gene	gene with protein product	"regulator of G protein signalling 9", "regulator of G protein signalling 9L", "regulator of G-protein signaling 9L"	604067	"regulator of G-protein signalling 9"			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.245dupA	17.37:g.63156390_63156390dupA	ENSP00000262406:p.Tyr82fs	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	618	13	NM_001081955	0	0	0	0	0	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Nonsense_Mutation	INS	ENST00000262406.9	37	CCDS42373.1																																																																																			.		0.5	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835		A	63156390	-	A	63156389	7	5	29	1	0	1	1	0	0	0	0	0	13345	1522	53	0	258	0	RGS9	17	63156389	Frame_Shift_Ins	INS	-	TCGA-AL-3466-01A-01D-1252-08	6923585	63156389	18038821	67	2613											
COG1	9382	broad.mit.edu	37	chr17	71204538	71204538	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcagtgaagaagacaacaCgtctgcaccttcattattca	13	11	7	10	1	4	3	3	1	1	2	4	3	4	3	1	0	2	1	1	0	4	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:71204538C>T	ENST00000299886.4	+	14	2971	c.2891C>T	c.(2890-2892)aCg>aTg	p.T964M	FAM104A_ENST00000583178.1_5'Flank|FAM104A_ENST00000405159.3_3'UTR|FAM104A_ENST00000403627.3_3'UTR	NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	964					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GAAGACAACACGTCTGCACCT	0.473																																					p.T964M													.	COG1-91	0			c.C2891T						.						170	154	159					17																	71204538		2203	4300	6503	SO:0001583	missense	9382	exon14			ACAACACGTCTGC		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2891C>T	17.37:g.71204538C>T	ENSP00000299886:p.Thr964Met	Somatic	275	0		WXS	Illumina HiSeq	Phase_I	776	7	NM_018714	0	0	96	96	0	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.478672	0.63849	.	.	ENSG00000166685	ENST00000299886	T	0.24151	1.87	6.03	6.03	0.97812	.	0.449527	0.25951	N	0.027256	T	0.33265	0.0857	L	0.36672	1.1	0.80722	D	1	D	0.61080	0.989	P	0.49637	0.617	T	0.00615	-1.1643	10	0.41790	T	0.15	-12.1843	20.5666	0.99351	0.0:1.0:0.0:0.0	.	964	Q8WTW3	COG1_HUMAN	M	964	ENSP00000299886:T964M	ENSP00000299886:T964M	T	+	2	0	COG1	68716133	0.679000	0.27596	0.022000	0.16811	0.252000	0.25951	6.910000	0.75741	2.854000	0.98071	0.655000	0.94253	ACG	.		0.473	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			T	71204538	C	T	71204538	3	4	29	1	0	0	0	0	1	0	0	0	3663	536	19	1	2945	1	COG1	17	71204538	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	8048149	71204538	9990672	68	2614											
TMC8	147138	broad.mit.edu	37	chr17	76134728	76134757	+	In_Frame_Del	DEL	GCCCTTGGGCTCCCGCCCATTGGCCAGCGT	GCCCTTGGGCTCCCGCCCATTGGCCAGCGT	-																															aagtggtcccggagctggtgGcccttgggctcccgcccatt																								rs535003756|rs150356106|rs375895539		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	GCCCTTGGGCTCCCGCCCATTGGCCAGCGT	GCCCTTGGGCTCCCGCCCATTGGCCAGCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:76134728_76134757delGCCCTTGGGCTCCCGCCCATTGGCCAGCGT	ENST00000318430.5	+	14	2112_2141	c.1738_1767delGCCCTTGGGCTCCCGCCCATTGGCCAGCGT	c.(1738-1767)gcccttgggctcccgcccattggccagcgtdel	p.ALGLPPIGQR580del	TMC8_ENST00000589691.1_In_Frame_Del_p.ALGLPPIGQR357del|TMC8_ENST00000591144.1_3'UTR	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	580					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)	p.R589C(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			GGAGCTGGTGGCCCTTGGGCTCCCGCCCATTGGCCAGCGTGCCCTCCACT	0.67																																					p.580_589del													.	TMC8-90	1	Substitution - Missense(1)	prostate(1)	c.1738_1767del						.																																			SO:0001651	inframe_deletion	147138	exon14			CTGGTGGCCCTTG	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"epidermodysplasia verruciformis 2"	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.1738_1767delGCCCTTGGGCTCCCGCCCATTGGCCAGCGT	17.37:g.76134728_76134757delGCCCTTGGGCTCCCGCCCATTGGCCAGCGT	ENSP00000325561:p.Ala580_Arg589del	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	470	9	NM_152468	0	0	0	0	0	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	In_Frame_Del	DEL	ENST00000318430.5	37	CCDS32749.1																																																																																			.		0.67	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			-	76134757	GCCCTTGGGCTCCCGCCCATTGGCCAGCGT	-	76134728	7	5	29	1	0	1	0	1	0	0	0	0	16023	1203	42	0	1788	0	TMC8	17	76134728	In_Frame_Del	DEL	GCCCTTGGGCTCCCGCCCATTGGCCAGCGT	TCGA-AL-3466-01A-01D-1252-08	4930190	76134728	5060482	69	2615											
KIAA1632	57724	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	43514887	43514888	+	Frame_Shift_Ins	INS	-	-	A																															tccacagcatttgcacagacINSagagtcccaaagggcatctc																										TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr18:43514887_43514888insA	ENST00000282041.5	-	11	2178_2179	c.2144_2145insT	c.(2143-2145)ctgfs	p.L715fs		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	715					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TTTGCACAGACAGAGTCCCAAA	0.495																																					p.L715fs		.											.	EPG5-580	0			c.2145_2146insT						.																																			SO:0001589	frameshift_variant	57724	exon11			.	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.2145dupT	18.37:g.43514888_43514888dupA	ENSP00000282041:p.Leu715fs	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	151	34	NM_020964	0	0	0	0	0	A2BDF3|Q9H8C8	Frame_Shift_Ins	INS	ENST00000282041.5	37	CCDS11926.2																																																																																			.		0.495	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43514888	-	A	43514887	7	5	29	1	0	1	1	0	0	0	0	0	8270	465	17	0	5730	0	KIAA1632	18	43514887	Frame_Shift_Ins	INS	-	TCGA-AL-3466-01A-01D-1252-08		43514887	34562361	70	2616											
OLFM2	93145	ucsc.edu	37	chr19	9968019	9968019	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatacccgtaggcacccAtctcctcctgaatggccgcc	7	8	7	19	2	2	1	1	1	1	0	4	1	3	1	7	2	1	2	7	2	3	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr19:9968019A>G	ENST00000264833.4	-	4	685	c.500T>C	c.(499-501)aTg>aCg	p.M167T	OLFM2_ENST00000590841.1_Missense_Mutation_p.M89T	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	167					protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						GTAGGCACCCATCTCCTCCTG	0.642																																					p.M167T													.	OLFM2-132	0			c.T500C						.						96	77	83					19																	9968019		2203	4300	6503	SO:0001583	missense	93145	exon4			GCACCCATCTCCT	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"noelin 2"						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.500T>C	19.37:g.9968019A>G	ENSP00000264833:p.Met167Thr	Somatic	145	0		WXS	Illumina HiSeq		187	1	NM_058164	0	0	5	15	10	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	37	CCDS12221.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852880	0.51270	.	.	ENSG00000105088	ENST00000264833	D	0.87491	-2.26	3.84	3.84	0.44239	.	0.000000	0.85682	D	0.000000	T	0.80502	0.4635	L	0.43152	1.355	0.53688	D	0.999974	B	0.32051	0.354	B	0.30716	0.119	T	0.76591	-0.2903	9	.	.	.	.	10.6376	0.45573	1.0:0.0:0.0:0.0	.	167	O95897	NOE2_HUMAN	T	167	ENSP00000264833:M167T	.	M	-	2	0	OLFM2	9829019	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.225000	0.78051	1.619000	0.50296	0.379000	0.24179	ATG	.		0.642	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1			G	9968019	A	G	9968019	3	3	29	1	0	0	0	0	1	0	0	0	10879	217	8	3	876	3	OLFM2	19	9968019	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08		9968019	49160964	71	2617											
ZNF681	148213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	23926850	23926850	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atttgtaggatttctctccaGtatgaattctcttatgtgta	9	19	7	6	0	2	1	0	1	2	0	5	2	3	2	1	1	0	3	1	1	5	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr19:23926850G>A	ENST00000402377.3	-	4	1643	c.1502C>T	c.(1501-1503)aCt>aTt	p.T501I	ZNF681_ENST00000395385.3_Missense_Mutation_p.T432I	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	501					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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTCTCTCCAGTATGAATTCT	0.363																																					p.T501I		.											.	.	0			c.C1502T						.						49	54	52					19																	23926850		2190	4290	6480	SO:0001583	missense	148213	exon4			TCTCCAGTATGAA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1502C>T	19.37:g.23926850G>A	ENSP00000384000:p.Thr501Ile	Somatic	186	1		WXS	Illumina HiSeq	Phase_I	56	13	NM_138286	0	0	0	0	0	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	8.433	0.848964	0.17034	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.25749	1.78;1.78	1.51	0.0946	0.14481	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46151	0.1378	M	0.77406	2.37	0.24791	N	0.992756	D	0.76494	0.999	D	0.76575	0.988	T	0.26643	-1.0097	9	0.72032	D	0.01	.	6.9774	0.24683	0.0:0.2884:0.7116:0.0	.	501	Q96N22	ZN681_HUMAN	I	501;432	ENSP00000384000:T501I;ENSP00000378783:T432I	ENSP00000378783:T432I	T	-	2	0	ZNF681	23718690	0.453000	0.25721	0.248000	0.24265	0.199000	0.23934	1.070000	0.30653	-0.136000	0.11475	0.313000	0.20887	ACT	.		0.363	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		A	23926850	G	A	23926850	3	1	29	1	0	0	0	0	1	0	0	0	18120	1029	36	2	439	2	ZNF681	19	23926850	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	13958831	23926850	35202133	72	2618											
RYR1	6261	hgsc.bcm.edu	37	chr19	38943527	38943527	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacggcgctgcccatcgAgggcgttatcctgagcctgc	5	8	14	14	4	0	1	0	1	0	0	2	2	1	1	3	3	3	3	3	3	1	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr19:38943527A>G	ENST00000359596.3	+	13	1313	c.1313A>G	c.(1312-1314)gAg>gGg	p.E438G	RYR1_ENST00000355481.4_Missense_Mutation_p.E438G|RYR1_ENST00000360985.3_Missense_Mutation_p.E438G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	438					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGCCCATCGAGGGCGTTATC	0.662																																					p.E438G		.											.	RYR1-100	0			c.A1313G						.						38	27	31					19																	38943527		2201	4300	6501	SO:0001583	missense	6261	exon13			CCATCGAGGGCGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1313A>G	19.37:g.38943527A>G	ENSP00000352608:p.Glu438Gly	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001042723	0	0	3	3	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.686099	0.68157	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.89270	-2.49;-2.49;-2.49	4.47	4.47	0.54385	.	0.259510	0.29861	U	0.011004	D	0.89033	0.6600	L	0.52126	1.63	0.40231	D	0.977844	P;B	0.50943	0.94;0.402	P;B	0.50440	0.641;0.17	D	0.89761	0.3947	10	0.51188	T	0.08	.	13.6427	0.62260	1.0:0.0:0.0:0.0	.	438;438	P21817-2;P21817	.;RYR1_HUMAN	G	438	ENSP00000352608:E438G;ENSP00000347667:E438G;ENSP00000354254:E438G	ENSP00000347667:E438G	E	+	2	0	RYR1	43635367	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.701000	0.68325	1.892000	0.54788	0.456000	0.33151	GAG	.		0.662	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38943527	A	G	38943527	3	3	29	1	0	0	0	0	1	0	0	0	13800	304	11	3	1363	3	RYR1	19	38943527	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	15016677	38943527	20185456	73	2619											
ADCK4	79934	broad.mit.edu	37	chr19	41198098	41198098	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acaggccaggaaagcccctgCcagcttgcggtgcagggcat	9	5	14	13	1	0	0	0	0	0	0	0	1	0	1	4	4	5	3	4	4	1	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr19:41198098C>T	ENST00000324464.3	-	15	1778	c.1477G>A	c.(1477-1479)Gca>Aca	p.A493T	ADCK4_ENST00000450541.1_Missense_Mutation_p.A452T|NUMBL_ENST00000252891.4_5'Flank|ADCK4_ENST00000243583.6_Missense_Mutation_p.A452T|NUMBL_ENST00000599594.1_5'Flank|NUMBL_ENST00000540131.1_5'Flank|NUMBL_ENST00000598779.1_5'Flank	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	493						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			AAAGCCCCTGCCAGCTTGCGG	0.687																																					p.A493T													.	ADCK4-319	0			c.G1477A						.						28	28	28					19																	41198098		2194	4292	6486	SO:0001583	missense	79934	exon15			CCCCTGCCAGCTT	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.1477G>A	19.37:g.41198098C>T	ENSP00000315118:p.Ala493Thr	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_024876	0	0	9	9	0	Q8TAJ1|Q9HA52	Missense_Mutation	SNP	ENST00000324464.3	37	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	C	36	5.637838	0.96693	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	T;T;T	0.75154	-0.91;-0.44;-0.44	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	M	0.86268	2.805	0.58432	D	0.999998	P;D	0.54772	0.945;0.968	P;P	0.59171	0.647;0.853	D	0.88110	0.2825	10	0.66056	D	0.02	-10.2873	18.0164	0.89242	0.0:1.0:0.0:0.0	.	493;452	Q96D53;Q96D53-2	ADCK4_HUMAN;.	T	493;452;452	ENSP00000315118:A493T;ENSP00000412839:A452T;ENSP00000243583:A452T	ENSP00000243583:A452T	A	-	1	0	ADCK4	45889938	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	5.695000	0.68279	2.560000	0.86352	0.561000	0.74099	GCA	.		0.687	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		T	41198098	C	T	41198098	3	4	29	1	0	0	0	0	1	0	0	0	290	739	26	2	161	2	ADCK4	19	41198098	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	2254571	41198098	17930885	74	2620											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945880	48945880	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacagctgctgcagcgcTgaggccgccccaccgcccgc	6	5	12	18	4	0	1	0	1	0	0	0	1	0	1	5	1	5	5	5	1	1	1	rs62130268	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr19:48945880T>C	ENST00000263269.3	+	13	2785	c.2697T>C	c.(2695-2697)gcT>gcC	p.A899A		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	899					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTGCAGCGCTGAGGCCGCCC	0.781													c|||	3742	0.747204	0.6188	0.8545	5008	,	,		4716	0.6548		0.8887	False		,,,				2504	0.7945				p.A899A		.											.	GRIN2D-156	0			c.T2697C						.			1689,437		638,413,12	1	1	1		2697	-3.3	1	19	dbSNP_129	1	3712,202		1757,198,2	no	coding-synonymous	GRIN2D	NM_000836.2		2395,611,14	CC,CT,TT		5.161,20.555,10.5795		899/1337	48945880	5401,639	1063	1957	3020	SO:0001819	synonymous_variant	2906	exon13			CAGCGCTGAGGCC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2697T>C	19.37:g.48945880T>C		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	5	5	NM_000836	0	0	0	0	0		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			T|0.245;C|0.755		0.781	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			C	48945880	T	C	48945880	2	2	29	1	0	0	0	0	0	0	0	1	6803	1567	55	3		3	GRIN2D	19	48945880	Silent	SNP	T	TCGA-AL-3466-01A-01D-1252-08	7747782	48945880	10183103	75	2621											
GFRA4	64096	hgsc.bcm.edu	37	chr20	3641542	3641542	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggagggcggtgagccggagaGaggccccgtccccaccctcg	6	3	17	15	4	0	2	0	1	0	1	2	5	1	4	6	5	1	0	6	5	0	0	rs58634535	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr20:3641542G>A	ENST00000319242.3	-	2	440	c.441C>T	c.(439-441)ctC>ctT	p.L147L	GFRA4_ENST00000290417.2_Intron			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	147					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						GAGCCGGAGAGAGGCCCCGTC	0.761													G|||	1080	0.215655	0.2897	0.2075	5008	,	,		6888	0.2163		0.16	False		,,,				2504	0.1779				p.L147L		.											.	GFRA4-90	0			c.C441T						.	G	,	373,1901		10,353,774	1	2	2		,441	1	0	20	dbSNP_129	2	558,4460		15,528,1966	no	intron,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	25,881,2740	AA,AG,GG		11.12,16.4028,12.7674	,	,147/300	3641542	931,6361	1137	2509	3646	SO:0001819	synonymous_variant	64096	exon2			CGGAGAGAGGCCC	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"persephin receptor"					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.441C>T	20.37:g.3641542G>A		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_145762	0	0	0	0	0	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			G|0.788;A|0.212		0.761	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762		A	3641542	G	A	3641542	2	1	29	1	0	0	0	0	0	0	0	1	6370	929	33	2		2	GFRA4	20	3641542	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08		3641542	59383978	76	2622											
RNF160	26046	hgsc.bcm.edu	37	chr21	30339122	30339122	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttgttaattcccagcctTcaatcttctctccttctgaa	8	16	4	13	0	4	1	1	1	3	0	7	1	6	1	3	0	1	2	3	0	3	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr21:30339122T>C	ENST00000361371.5	-	10	1770	c.1691A>G	c.(1690-1692)gAa>gGa	p.E564G	LTN1_ENST00000389195.2_Missense_Mutation_p.E610G|LTN1_ENST00000389194.2_Missense_Mutation_p.E610G			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	564					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TTCCCAGCCTTCAATCTTCTC	0.348																																					p.E610G		.											.	LTN1-530	0			c.A1829G						.						59	55	56					21																	30339122		2203	4300	6503	SO:0001583	missense	26046	exon10			CAGCCTTCAATCT	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"RING-type (C3HC4) zinc fingers"	13082	protein-coding gene	gene with protein product	"listerin"	613083	"chromosome 21 open reading frame 98", "zinc finger protein 294", "ring finger protein 160"	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1691A>G	21.37:g.30339122T>C	ENSP00000354977:p.Glu564Gly	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_015565	0	0	0	0	0	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	T	3.601	-0.081617	0.07141	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000389195	T;T;T	0.26373	2.08;2.09;1.74	4.75	2.26	0.28386	.	0.523268	0.20481	N	0.091497	T	0.11153	0.0272	N	0.14661	0.345	0.09310	N	1	B	0.24258	0.1	B	0.19148	0.024	T	0.26155	-1.0111	10	0.20046	T	0.44	.	4.0986	0.10004	0.1787:0.0971:0.0:0.7242	.	564	O94822	LTN1_HUMAN	G	610;564;610	ENSP00000373846:E610G;ENSP00000354977:E564G;ENSP00000373847:E610G	ENSP00000354977:E564G	E	-	2	0	LTN1	29260993	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	0.551000	0.23361	0.357000	0.24183	0.528000	0.53228	GAA	.		0.348	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		C	30339122	T	C	30339122	3	2	29	1	0	0	0	0	1	0	0	0	13487	1783	62	3	3693	3	RNF160	21	30339122	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		30339122	17790773	77	2623											
SFRS15	57466	ucsc.edu	37	chr21	33044135	33044135	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcccggtcattttccaccctAtttccaaaagatcttcttcc	8	15	3	15	1	3	1	1	0	2	1	7	1	7	1	5	1	0	0	5	1	3	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr21:33044135A>G	ENST00000286835.7	-	20	3403	c.3021T>C	c.(3019-3021)aaT>aaC	p.N1007N	SCAF4_ENST00000434667.3_Silent_p.N992N|SCAF4_ENST00000399804.1_Silent_p.N985N	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	1007						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						TTTCCACCCTATTTCCAAAAG	0.478																																					p.N1007N													.	SCAF4-90	0			c.T3021C						.						145	144	144					21																	33044135		2203	4300	6503	SO:0001819	synonymous_variant	57466	exon20			CACCCTATTTCCA	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"RNA binding motif (RRM) containing"	19304	protein-coding gene	gene with protein product			"splicing factor, arginine/serine-rich 15"	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.3021T>C	21.37:g.33044135A>G		Somatic	296	0		WXS	Illumina HiSeq		372	1	NM_020706	0	0	10	10	0	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																			.		0.478	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889		G	33044135	A	G	33044135	2	3	29	1	0	0	0	0	0	0	0	1	14203	446	16	3		3	SFRS15	21	33044135	Silent	SNP	A	TCGA-AL-3466-01A-01D-1252-08	2705013	33044135	15085760	78	2624											
THOC5	8563	ucsc.edu	37	chr22	29924124	29924124	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcttcagcatctccttgcGtttgtcgtccaactgaaccc	6	13	6	16	2	3	1	1	1	2	0	6	1	4	1	4	0	4	2	4	0	2	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr22:29924124G>A	ENST00000490103.1	-	11	1131	c.1009C>T	c.(1009-1011)Cgc>Tgc	p.R337C	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.R337C|THOC5_ENST00000397873.2_Missense_Mutation_p.R337C|THOC5_ENST00000397872.1_Missense_Mutation_p.R337C	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	337					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATCTCCTTGCGTTTGTCGTCC	0.527																																					p.R337C													.	THOC5-585	0			c.C1009T						.						130	116	121					22																	29924124		2203	4300	6503	SO:0001583	missense	8563	exon12			CCTTGCGTTTGTC	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"THO complex subunits"	19074	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 79"	612733	"chromosome 22 open reading frame 19"	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1009C>T	22.37:g.29924124G>A	ENSP00000420306:p.Arg337Cys	Somatic	205	0		WXS	Illumina HiSeq		204	1	NM_001002878	0	0	2	7	5	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.7|21.7	4.188467|4.188467	0.78789|0.78789	.|.	.|.	ENSG00000100296|ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873|ENST00000443089	T;T;T;T|.	0.26373|.	1.74;1.74;1.74;1.74|.	4.99|4.99	3.95|3.95	0.45737|0.45737	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73102|0.73102	0.3544|0.3544	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.73380|.	0.98|.	T|T	0.74402|0.74402	-0.3677|-0.3677	10|5	0.72032|.	D|.	0.01|.	-14.3349|-14.3349	12.6222|12.6222	0.56610|0.56610	0.0:0.0:0.6985:0.3015|0.0:0.0:0.6985:0.3015	.|.	337|.	Q13769|.	THOC5_HUMAN|.	C|M	337|207	ENSP00000420306:R337C;ENSP00000380970:R337C;ENSP00000380969:R337C;ENSP00000380971:R337C|.	ENSP00000380969:R337C|.	R|T	-|-	1|2	0|0	THOC5|THOC5	28254124|28254124	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	3.368000|3.368000	0.52357|0.52357	1.310000|1.310000	0.45006|0.45006	0.552000|0.552000	0.68991|0.68991	CGC|ACG	.		0.527	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		A	29924124	G	A	29924124	3	1	29	1	0	0	0	0	1	0	0	0	15900	1145	40	1	1082	1	THOC5	22	29924124	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08		29924124	21380442	79	2625											
NLGN3	54413	broad.mit.edu	37	chrX	70387072	70387072	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctaccacgtggcctttggCcctgtgattgatggtgatgt	5	13	13	10	2	0	3	0	3	0	0	0	3	0	3	3	3	1	1	3	3	1	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chrX:70387072C>T	ENST00000358741.3	+	7	1428	c.1125C>T	c.(1123-1125)ggC>ggT	p.G375G	NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000374051.3_Silent_p.G355G|NLGN3_ENST00000536169.1_Silent_p.G335G	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	375					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					TGGCCTTTGGCCCTGTGATTG	0.557																																					p.G375G	Esophageal Squamous(103;760 1488 16849 22250 40351)												.	NLGN3-131	0			c.C1125T						.						126	87	100					X																	70387072		2203	4300	6503	SO:0001819	synonymous_variant	54413	exon7			CTTTGGCCCTGTG	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.1125C>T	X.37:g.70387072C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	145	4	NM_181303	0	0	0	0	0	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Silent	SNP	ENST00000358741.3	37	CCDS55441.1																																																																																			.		0.557	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		T	70387072	C	T	70387072	2	4	29	1	0	0	0	0	0	0	0	1	10489	726	26	2		2	NLGN3	23	70387072	Silent	SNP	C	TCGA-AL-3466-01A-01D-1252-08		70387072	84883488	80	2626											
HDAC8	55869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	71681922	71681922	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggtcaagtatgtccagcatcGagccgtgttggcaaggttat	9	11	13	8	2	1	0	1	0	0	0	3	1	2	0	2	3	2	5	2	3	4	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chrX:71681922G>C	ENST00000373573.3	-	9	1278	c.937C>G	c.(937-939)Cga>Gga	p.R313G	HDAC8_ENST00000373589.4_Missense_Mutation_p.R222G|HDAC8_ENST00000429103.2_Missense_Mutation_p.R118G|HDAC8_ENST00000373583.1_Intron	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	313	Histone deacetylase.				chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cohesin localization to chromatin (GO:0071922)|sister chromatid cohesion (GO:0007062)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(3)|cervix(1)|endometrium(1)|lung(4)|prostate(1)	10	Renal(35;0.156)				Vorinostat(DB02546)	GTCCAGCATCGAGCCGTGTTG	0.473																																					p.R313G		.											.	HDAC8-226	0			c.C937G						.						121	99	106					X																	71681922		2203	4300	6503	SO:0001583	missense	55869	exon9			AGCATCGAGCCGT	AF230097	CCDS14420.1, CCDS55448.1, CCDS55449.1, CCDS55450.1, CCDS55451.1, CCDS55452.1	Xq13	2014-01-29	2002-09-02	2002-09-06	ENSG00000147099	ENSG00000147099			13315	protein-coding gene	gene with protein product		300269	"histone deacetylase-like 1", "Wilson-Turner X-linked mental retardation syndrome"	HDACL1, WTS, MRXS6		10756090, 10922473, 22889856	Standard	NM_001166448		Approved	RPD3	uc004eau.3	Q9BY41	OTTHUMG00000021814	ENST00000373573.3:c.937C>G	X.37:g.71681922G>C	ENSP00000362674:p.Arg313Gly	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	35	10	NM_018486	0	0	8	8	0	A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	Missense_Mutation	SNP	ENST00000373573.3	37	CCDS14420.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.722648	0.68959	.	.	ENSG00000147099	ENST00000373573;ENST00000373589;ENST00000429103;ENST00000373568;ENST00000415409	T;T;T;T;T	0.75704	-0.57;-0.57;-0.57;-0.57;-0.96	5.3	5.3	0.74995	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.90758	0.7099	H	0.96748	3.875	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;0.993;1.0	D	0.93702	0.7016	10	0.87932	D	0	-8.4243	15.5432	0.76074	0.0:0.0:1.0:0.0	.	222;222;313	B4DKN0;A6NGJ7;Q9BY41	.;.;HDAC8_HUMAN	G	313;222;118;222;287	ENSP00000362674:R313G;ENSP00000362691:R222G;ENSP00000388459:R118G;ENSP00000362669:R222G;ENSP00000396424:R287G	ENSP00000362669:R222G	R	-	1	2	HDAC8	71598647	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.297000	0.96120	2.352000	0.79861	0.594000	0.82650	CGA	.		0.473	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057193.2	NM_018486		C	71681922	G	C	71681922	3	2	29	1	0	0	0	0	1	0	0	0	7034	1066	37	4	208	4	HDAC8	23	71681922	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08	1294850	71681922	83588638	81	2627											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10336447	10336447	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaactacgatgagactttgAgcactctgaggtactttctt	10	14	8	9	1	3	3	1	3	2	1	3	5	3	3	0	1	4	2	0	1	3	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr1:10336447A>G	ENST00000377086.1	+	12	1229	c.1027A>G	c.(1027-1029)Agc>Ggc	p.S343G	KIF1B_ENST00000263934.6_Missense_Mutation_p.S337G|KIF1B_ENST00000377083.1_Missense_Mutation_p.S337G|KIF1B_ENST00000377093.4_Missense_Mutation_p.S337G|KIF1B_ENST00000377081.1_Missense_Mutation_p.S343G			O60333	KIF1B_HUMAN	kinesin family member 1B	343	Interaction with KBP.|Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGAGACTTTGAGCACTCTGAG	0.418																																					p.S337G		.											.	KIF1B-93	0			c.A1009G						.						103	88	93					1																	10336447		2203	4300	6503	SO:0001583	missense	23095	exon11			ACTTTGAGCACTC	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.1027A>G	1.37:g.10336447A>G	ENSP00000366290:p.Ser343Gly	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_183416	0	0	0	0	0	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	A	34	5.364189	0.95877	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	D;D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55;-2.55	5.86	5.86	0.93980	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.94785	0.8316	M	0.87097	2.86	0.80722	D	1	D;P;D;P;D;D;P	0.64830	0.959;0.949;0.98;0.89;0.964;0.994;0.777	D;P;P;P;P;D;P	0.65010	0.929;0.508;0.85;0.477;0.484;0.931;0.55	D	0.95414	0.8501	10	0.72032	D	0.01	.	16.2652	0.82574	1.0:0.0:0.0:0.0	.	343;343;343;343;343;337;337	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	G	343;337;337;343;337;343	ENSP00000263934:S337G;ENSP00000366297:S337G;ENSP00000366290:S343G;ENSP00000366287:S337G;ENSP00000366284:S343G	ENSP00000263934:S337G	S	+	1	0	KIF1B	10259034	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.253000	0.95501	2.241000	0.73720	0.528000	0.53228	AGC	.		0.418	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			G	10336447	A	G	10336447	3	3	30	1	0	0	0	0	1	0	0	0	8305	304	11	3	1047	3	KIF1B	1	10336447	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08		10336447	238914174	1	2628											
MIER1	57708	hgsc.bcm.edu	37	chr1	67394625	67394625	+	5'Flank	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttacagactgtctgtggacTcttttcctgtcaaattacca	9	16	6	10	0	3	1	1	0	2	1	4	2	4	2	2	1	2	0	2	1	3	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr1:67394625T>C	ENST00000355356.3	+	0	0				MIER1_ENST00000371016.1_Silent_p.T13T|MIER1_ENST00000371018.3_Silent_p.T13T|MIER1_ENST00000401041.1_Intron|MIER1_ENST00000401042.3_5'Flank|MIER1_ENST00000371014.1_Intron|MIER1_ENST00000357692.2_Silent_p.T13T|MIER1_ENST00000371012.2_Silent_p.T13T|MIER1_ENST00000355977.6_Intron	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator						positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						GTCTGTGGACTCTTTTCCTGT	0.338																																					p.T13T		.											.	MIER1-91	0			c.T39C						.						122	108	113					1																	67394625		1849	4088	5937	SO:0001631	upstream_gene_variant	57708	exon3			GTGGACTCTTTTC		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194		1.37:g.67394625T>C	Exception_encountered	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_001146111	0	0	1	1	0	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Silent	SNP	ENST00000355356.3	37	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	T	9.694	1.152565	0.21371	.	.	ENSG00000198160	ENST00000371017	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	T	0.38054	0.1026	.	.	.	0.80722	D	1	P	0.51537	0.946	P	0.46825	0.528	T	0.22277	-1.0221	7	0.33141	T	0.24	.	11.1769	0.48606	0.0:0.0:0.0:1.0	.	20	Q6NXT7	.	P	17	.	ENSP00000360056:L17P	L	+	2	0	MIER1	67167213	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.367000	0.52350	2.073000	0.62155	0.454000	0.30748	CTC	.		0.338	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948		C	67394625	T	C	67394625	1	2	30	0	1	0	0	0	0	0	0	0	9605	1538	54	3		3	MIER1	1	67394625	5'Flank	SNP	T	TCGA-AL-3467-01A-01D-1252-08	57058178	67394625	181855996	2	2629											
ARHGAP29	9411	broad.mit.edu	37	chr1	94639430	94639431	+	Frame_Shift_Ins	INS	-	-	A																															gaaatttgacatccctacacINSaaattgtggaatttcacctt																										TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr1:94639430_94639431insA	ENST00000260526.6	-	23	3962_3963	c.3780_3781insT	c.(3778-3783)tttgtgfs	p.V1261fs	ARHGAP29_ENST00000482481.1_5'Flank	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	1261	Interaction with PTPN13/PTPL1.				positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CATCCCTACACAAATTGTGGAA	0.401																																					p.V1261fs													.	ARHGAP29-296	0			c.3781_3782insT						.																																			SO:0001589	frameshift_variant	9411	exon23			CCTACACAAATTG		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.3781dupT	1.37:g.94639433_94639433dupA	ENSP00000260526:p.Val1261fs	Somatic	335	0		WXS	Illumina HiSeq	Phase_I	340	17	NM_004815	0	0	0	0	0	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Frame_Shift_Ins	INS	ENST00000260526.6	37	CCDS748.1																																																																																			.		0.401	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		A	94639431	-	A	94639430	7	5	30	1	0	1	1	0	0	0	0	0	878	478	17	0	8	0	ARHGAP29	1	94639430	Frame_Shift_Ins	INS	-	TCGA-AL-3467-01A-01D-1252-08	27244805	94639430	154611191	3	2630											
BAT2L2	23215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171553162	171553162	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcctttctggtactgctattCacaactttccaactgtccaa	9	15	4	13	0	2	0	1	0	1	0	5	0	5	0	3	1	4	2	3	1	5	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr1:171553162C>T	ENST00000338920.4	+	29	7708	c.7471C>T	c.(7471-7473)Cac>Tac	p.H2491Y	PRRC2C_ENST00000426496.2_Missense_Mutation_p.H2426Y|PRRC2C_ENST00000367742.3_Missense_Mutation_p.H2493Y|PRRC2C_ENST00000392078.3_Missense_Mutation_p.H2493Y	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2491	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TACTGCTATTCACAACTTTCC	0.408																																					p.H2491Y		.											.	.	0			c.C7471T						.						140	131	134					1																	171553162		2203	4300	6503	SO:0001583	missense	23215	exon29			GCTATTCACAACT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.7471C>T	1.37:g.171553162C>T	ENSP00000343629:p.His2491Tyr	Somatic	232	1		WXS	Illumina HiSeq	Phase_I	213	75	NM_015172	0	0	44	68	24	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	19.93	3.918545	0.73098	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.02140	4.43;4.44;4.44;4.44	5.98	5.98	0.97165	.	0.000000	0.49305	D	0.000160	T	0.07052	0.0179	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	0.981;1.0	D;D	0.85130	0.954;0.997	T	0.30149	-0.9988	10	0.59425	D	0.04	.	20.4581	0.99154	0.0:1.0:0.0:0.0	.	2426;2491	B7WNZ6;Q9Y520-4	.;.	Y	2493;2445;2426;2493;2491;2248	ENSP00000375928:H2493Y;ENSP00000410219:H2426Y;ENSP00000356716:H2493Y;ENSP00000343629:H2491Y	ENSP00000343629:H2491Y	H	+	1	0	PRRC2C	169819786	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.487000	0.81328	2.835000	0.97688	0.650000	0.86243	CAC	.		0.408	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171553162	C	T	171553162	3	4	30	1	0	0	0	0	1	0	0	0	1322	826	29	2	7581	2	BAT2L2	1	171553162	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08	76913732	171553162	77697459	4	2631											
INTS7	25896	broad.mit.edu	37	chr1	212148638	212148638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaactccttcaaactatttAgccagaagtagaaatgttct	16	12	5	8	0	2	2	1	0	1	2	3	2	3	2	2	0	3	2	2	0	8	6			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr1:212148638A>G	ENST00000366994.3	-	13	1789	c.1685T>C	c.(1684-1686)cTa>cCa	p.L562P	INTS7_ENST00000366992.3_Missense_Mutation_p.L562P|INTS7_ENST00000440600.2_Missense_Mutation_p.L513P|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.L562P	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	562					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		CAAACTATTTAGCCAGAAGTA	0.368																																					p.L562P													.	INTS7-90	0			c.T1685C						.						89	96	94					1																	212148638		2203	4300	6503	SO:0001583	missense	25896	exon13			CTATTTAGCCAGA	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"chromosome 1 open reading frame 73"	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.1685T>C	1.37:g.212148638A>G	ENSP00000355961:p.Leu562Pro	Somatic	194	1		WXS	Illumina HiSeq	Phase_I	203	4	NM_015434	0	0	2	2	0	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.554880	0.86231	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.73575	-0.76;-0.69;-0.69;-0.17	6.06	6.06	0.98353	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85809	0.5783	M	0.73217	2.22	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.87097	0.2176	10	0.87932	D	0	-15.5011	16.6093	0.84858	1.0:0.0:0.0:0.0	.	513;562;562;562	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	P	562;562;562;513	ENSP00000355961:L562P;ENSP00000355960:L562P;ENSP00000355959:L562P;ENSP00000388908:L513P	ENSP00000355959:L562P	L	-	2	0	INTS7	210215261	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.999000	0.93557	2.324000	0.78689	0.533000	0.62120	CTA	.		0.368	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		G	212148638	A	G	212148638	3	3	30	1	0	0	0	0	1	0	0	0	7804	420	15	3	1235	3	INTS7	1	212148638	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08	40595476	212148638	37101983	5	2632											
THSD7B	80731	broad.mit.edu	37	chr2	138400116	138400116	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caaggagaaggacggccatgCcccacagagcttacccagga	13	3	12	13	1	0	2	0	0	0	2	0	5	0	4	4	4	3	1	4	4	3	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr2:138400116C>T	ENST00000409968.1	+	21	4036	c.3858C>T	c.(3856-3858)tgC>tgT	p.C1286C	THSD7B_ENST00000413152.2_Silent_p.C1258C|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Silent_p.C1289C			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	1288	TSP type-1 16. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		GACGGCCATGCCCCACAGAGC	0.507																																					.													.	THSD7B-75	0			.						.						112	113	113					2																	138400116		1903	4114	6017	SO:0001819	synonymous_variant	80731	.			GCCATGCCCCACA			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3858C>T	2.37:g.138400116C>T		Somatic	219	0		WXS	Illumina HiSeq	Phase_I	220	5	.	0	0	0	0	0		Silent	SNP	ENST00000409968.1	37																																																																																				.		0.507	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	138400116	C	T	138400116	2	4	30	1	0	0	0	0	0	0	0	1	15912	747	26	2		2	THSD7B	2	138400116	Silent	SNP	C	TCGA-AL-3467-01A-01D-1252-08		138400116	104799257	6	2633											
CACNB4	785	hgsc.bcm.edu	37	chr2	152727361	152727361	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaaacacaacttaccacttTttgcttctgttttgctaaaa	12	15	5	9	0	1	0	0	0	1	0	1	1	1	1	1	1	5	3	1	1	5	7			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr2:152727361T>C	ENST00000539935.1	-	7	680	c.613A>G	c.(613-615)Aaa>Gaa	p.K205E	CACNB4_ENST00000360283.6_Intron|CACNB4_ENST00000534999.1_Missense_Mutation_p.K171E|CACNB4_ENST00000397327.2_Missense_Mutation_p.K158E|CACNB4_ENST00000201943.5_Missense_Mutation_p.K205E|CACNB4_ENST00000427385.1_Missense_Mutation_p.K187E	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	205					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CTTACCACTTTTTGCTTCTGT	0.343																																					p.K205E		.											.	CACNB4-24	0			c.A613G						.						83	75	77					2																	152727361		1856	4097	5953	SO:0001583	missense	785	exon7			CCACTTTTTGCTT	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"Calcium channel subunits"	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.613A>G	2.37:g.152727361T>C	ENSP00000438949:p.Lys205Glu	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001145798	0	0	0	0	0	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	37	CCDS46426.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.452993	0.84209	.	.	ENSG00000182389	ENST00000539935;ENST00000543269;ENST00000439467;ENST00000534999;ENST00000397327;ENST00000427385;ENST00000201943	D;D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82;-1.82	5.92	5.92	0.95590	Src homology-3 domain (1);	.	.	.	.	D	0.93106	0.7805	M	0.89414	3.03	0.80722	D	1	D;B;B;B;B	0.58268	0.982;0.196;0.387;0.111;0.177	D;B;B;B;B	0.67548	0.952;0.077;0.106;0.067;0.142	D	0.94194	0.7444	9	0.87932	D	0	14.7567	15.1766	0.72916	0.0:0.0:0.0:1.0	.	205;171;205;187;171	A7BJ74;E7DBM8;O00305;B4DG40;O00305-2	.;.;CACB4_HUMAN;.;.	E	205;162;200;171;158;187;205	ENSP00000438949:K205E;ENSP00000390161:K200E;ENSP00000443893:K171E;ENSP00000380490:K158E;ENSP00000410978:K187E;ENSP00000201943:K205E	ENSP00000201943:K205E	K	-	1	0	CACNB4	152435607	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.791000	0.75120	2.255000	0.74692	0.533000	0.62120	AAA	.		0.343	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		C	152727361	T	C	152727361	3	2	30	1	0	0	0	0	1	0	0	0	2561	1850	64	3	981	3	CACNB4	2	152727361	Missense_Mutation	SNP	T	TCGA-AL-3467-01A-01D-1252-08	14327245	152727361	90472012	7	2634											
TMEFF2	23671	broad.mit.edu	37	chr2	193056717	193056717	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctctgtcatcataaccTcaaattcaaagagaacactc	14	13	3	11	0	5	1	4	0	1	1	7	2	5	1	1	0	2	0	1	0	4	4			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr2:193056717T>C	ENST00000272771.5	-	2	1357		c.e2-2		TMEFF2_ENST00000392314.1_Splice_Site|TMEFF2_ENST00000409056.3_Splice_Site	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2							extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			CATCATAACCTCAAATTCAAA	0.333																																					.	Pancreas(50;1277 1381 28487 47072)												.	TMEFF2-524	0			c.173-2A>G						.						73	70	71					2																	193056717		2203	4300	6503	SO:0001630	splice_region_variant	23671	exon3			ATAACCTCAAATT	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"transmembrane protein TENB2", "tomoregulin", "cancer/testis antigen family 120, member 2"	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.173-2A>G	2.37:g.193056717T>C		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	85	3	NM_016192	0	0	0	0	0	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Splice_Site	SNP	ENST00000272771.5	37	CCDS2314.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193835	0.78902	.	.	ENSG00000144339	ENST00000392314;ENST00000272771;ENST00000409056	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEFF2	192764962	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.698000	0.84413	2.302000	0.77476	0.533000	0.62120	.	.		0.333	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192	Intron	C	193056717	T	C	193056717	5	2	30	1	0	0	0	0	0	0	1	0	16046	1565	54	3	989	3	TMEFF2	2	193056717	Splice_Site	SNP	T	TCGA-AL-3467-01A-01D-1252-08	40329356	193056717	50142656	8	2635											
CCDC108	255101	ucsc.edu	37	chr2	219868976	219868976	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaccctggatagtgctcTggtctgtcttccttcggctg	4	13	10	14	1	3	0	0	0	3	0	5	1	4	1	3	3	2	2	3	3	2	3			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr2:219868976T>C	ENST00000341552.5	-	33	5336	c.5253A>G	c.(5251-5253)ccA>ccG	p.P1751P	CCDC108_ENST00000453220.1_Silent_p.P1751P|CCDC108_ENST00000441968.1_Silent_p.P1751P|AC097468.4_ENST00000441450.1_RNA|MIR375_ENST00000362103.2_RNA	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1751						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GATAGTGCTCTGGTCTGTCTT	0.537																																					p.P1751P													.	CCDC108-94	0			c.A5253G						.						167	157	161					2																	219868976		2203	4300	6503	SO:0001819	synonymous_variant	255101	exon33			GTGCTCTGGTCTG	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.5253A>G	2.37:g.219868976T>C		Somatic	315	0		WXS	Illumina HiSeq		332	2	NM_194302	0	0	4	4	0	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	37	CCDS2430.2																																																																																			.		0.537	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		C	219868976	T	C	219868976	2	2	30	1	0	0	0	0	0	0	0	1	2749	1567	55	3		3	CCDC108	2	219868976	Silent	SNP	T	TCGA-AL-3467-01A-01D-1252-08	26812259	219868976	23330397	9	2636											
AGAP1	116987	ucsc.edu	37	chr2	237028963	237028963	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgacgaggacctgcggacgGccatcctgctgctggcacac	7	5	13	16	4	0	0	0	0	0	0	1	4	1	2	4	4	3	3	4	4	0	0			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr2:237028963G>A	ENST00000304032.8	+	17	2822	c.2242G>A	c.(2242-2244)Gcc>Acc	p.A748T	AGAP1_ENST00000409538.1_Missense_Mutation_p.A960T|AGAP1_ENST00000336665.5_Missense_Mutation_p.A695T|AGAP1_ENST00000428334.2_Missense_Mutation_p.A587T	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	748					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						CCTGCGGACGGCCATCCTGCT	0.711																																					p.A748T													.	AGAP1-93	0			c.G2242A						.						35	37	36					2																	237028963		2201	4293	6494	SO:0001583	missense	116987	exon17			CGGACGGCCATCC	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16922	protein-coding gene	gene with protein product		608651	"centaurin, gamma 2"	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.2242G>A	2.37:g.237028963G>A	ENSP00000307634:p.Ala748Thr	Somatic	109	0		WXS	Illumina HiSeq		93	4	NM_001037131	0	0	7	7	0	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.6|23.6	4.430315|4.430315	0.83776|0.83776	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334|ENST00000453371	T;T;T;T|.	0.64991|.	-0.13;-0.13;-0.13;-0.13|.	4.47|4.47	4.47|4.47	0.54385|0.54385	Ankyrin repeat-containing domain (4);|.	0.202899|.	0.40728|.	N|.	0.001039|.	T|T	0.56232|0.56232	0.1971|0.1971	L|L	0.28694|0.28694	0.88|0.88	0.40528|0.40528	D|D	0.980901|0.980901	B;B|.	0.20052|.	0.001;0.041|.	B;B|.	0.30105|.	0.003;0.111|.	T|T	0.55010|0.55010	-0.8207|-0.8207	10|5	0.54805|.	T|.	0.06|.	.|.	17.1397|17.1397	0.86749|0.86749	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	695;748|.	Q9UPQ3-2;Q9UPQ3|.	.;AGAP1_HUMAN|.	T|D	748;695;960;587|149	ENSP00000307634:A748T;ENSP00000338378:A695T;ENSP00000386897:A960T;ENSP00000411824:A587T|.	ENSP00000307634:A748T|.	A|G	+|+	1|2	0|0	AGAP1|AGAP1	236693702|236693702	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.929000|0.929000	0.56500|0.56500	9.751000|9.751000	0.98889|0.98889	2.044000|2.044000	0.60594|0.60594	0.484000|0.484000	0.47621|0.47621	GCC|GGC	.		0.711	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		A	237028963	G	A	237028963	3	1	30	1	0	0	0	0	1	0	0	0	366	1203	42	2	2308	2	AGAP1	2	237028963	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08	17159987	237028963	6170410	10	2637											
PRRC1	133619	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	126860252	126860252	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttctttttcttctccaaatGtatcctccatggagtccttc	6	18	5	12	0	3	0	0	0	3	0	8	1	6	1	4	1	0	2	4	1	2	6			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr5:126860252G>T	ENST00000296666.8	+	3	321	c.133G>T	c.(133-135)Gta>Tta	p.V45L	PRRC1_ENST00000442138.2_Missense_Mutation_p.V45L|PRRC1_ENST00000512635.2_Missense_Mutation_p.V45L	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	45	Pro-rich.					Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		TTCTCCAAATGTATCCTCCAT	0.443																																					p.V45L		.											.	PRRC1-68	0			c.G133T						.						151	153	152					5																	126860252		2203	4300	6503	SO:0001583	missense	133619	exon3			CCAAATGTATCCT	AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244			28164	protein-coding gene	gene with protein product						15541471	Standard	NM_130809		Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.133G>T	5.37:g.126860252G>T	ENSP00000296666:p.Val45Leu	Somatic	429	1		WXS	Illumina HiSeq	Phase_I	408	28	NM_130809	0	0	50	50	0	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	Missense_Mutation	SNP	ENST00000296666.8	37	CCDS4143.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.576488	0.28092	.	.	ENSG00000164244	ENST00000296666;ENST00000442138;ENST00000330542;ENST00000414018;ENST00000512635;ENST00000512535	.	.	.	4.99	2.0	0.26442	.	1.090020	0.06908	N	0.807096	T	0.26231	0.0640	N	0.24115	0.695	0.09310	N	1	B;B	0.19073	0.003;0.033	B;B	0.18561	0.006;0.022	T	0.25187	-1.0139	9	0.27785	T	0.31	-3.6002	2.9579	0.05882	0.3558:0.0:0.4512:0.193	.	45;45	Q96M27;Q96M27-5	PRRC1_HUMAN;.	L	45	.	ENSP00000296666:V45L	V	+	1	0	PRRC1	126888151	0.006000	0.16342	0.001000	0.08648	0.002000	0.02628	1.215000	0.32431	0.683000	0.31428	-0.137000	0.14449	GTA	.		0.443	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250971.3	NM_130809		T	126860252	G	T	126860252	3	4	30	1	0	0	0	0	1	0	0	0	12633	1377	48	4	139	4	PRRC1	5	126860252	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08		126860252	54055008	11	2638											
BRD8	10902	broad.mit.edu	37	chr5	137506598	137506598	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agttctgcatctctctttagCcgtctataggaagaaagaga	12	12	9	8	1	4	2	0	0	4	2	5	4	4	3	1	1	2	2	1	1	5	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr5:137506598C>T	ENST00000254900.5	-	6	734	c.363G>A	c.(361-363)cgG>cgA	p.R121R	BRD8_ENST00000402931.1_Silent_p.R121R|BRD8_ENST00000411594.2_Silent_p.R121R|BRD8_ENST00000230901.5_Silent_p.R121R|BRD8_ENST00000455658.2_Silent_p.R80R	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	121					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CTCTCTTTAGCCGTCTATAGG	0.398																																					p.R121R													.	BRD8-91	0			c.G363A						.						138	135	136					5																	137506598		2203	4300	6503	SO:0001819	synonymous_variant	10902	exon6			CTTTAGCCGTCTA	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.363G>A	5.37:g.137506598C>T		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	193	4	NM_001164326	0	0	0	0	0	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Silent	SNP	ENST00000254900.5	37	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.276621	0.23307	.	.	ENSG00000112983	ENST00000441656	.	.	.	5.96	-7.56	0.01322	.	.	.	.	.	T	0.59142	0.2172	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63998	-0.6510	4	.	.	.	-9.1007	13.5918	0.61964	0.0976:0.1111:0.0:0.7913	.	.	.	.	D	115	.	.	G	-	2	0	BRD8	137534497	0.001000	0.12720	0.453000	0.27007	0.989000	0.77384	-1.551000	0.02178	-1.591000	0.01621	0.655000	0.94253	GGC	.		0.398	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		T	137506598	C	T	137506598	2	4	30	1	0	0	0	0	0	0	0	1	1509	726	26	2		2	BRD8	5	137506598	Silent	SNP	C	TCGA-AL-3467-01A-01D-1252-08	10646346	137506598	43408662	12	2639											
PCDHA4	56144	broad.mit.edu	37	chr5	140187880	140187880	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccactgggtacagtcatcGccctgatcagcgtgtccgac	7	9	10	15	3	2	1	2	1	0	0	5	2	4	1	3	1	2	1	3	1	1	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr5:140187880G>A	ENST00000530339.1	+	1	1108	c.1108G>A	c.(1108-1110)Gcc>Acc	p.A370T	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.A370T|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.A370T|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	370	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A370S(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACAGTCATCGCCCTGATCAG	0.493																																					p.A370T													.	PCDHA4-96	2	Substitution - Missense(2)	lung(2)	c.G1108A						.						97	94	95					5																	140187880		2203	4300	6503	SO:0001583	missense	56144	exon1			GTCATCGCCCTGA	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1108G>A	5.37:g.140187880G>A	ENSP00000435300:p.Ala370Thr	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	162	4	NM_031500	0	0	5	6	1	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	14.66	2.600395	0.46423	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.52754	0.65;0.65;0.65	4.72	4.72	0.59763	Cadherin (3);Cadherin-like (1);	0.000000	0.40302	U	0.001121	T	0.59810	0.2221	M	0.64567	1.98	0.29498	N	0.855113	P;D;D	0.57257	0.853;0.963;0.979	B;P;P	0.53518	0.322;0.728;0.728	T	0.61787	-0.6991	10	0.59425	D	0.04	.	18.0295	0.89278	0.0:0.0:1.0:0.0	.	370;370;370	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	T	370	ENSP00000423470:A370T;ENSP00000349344:A370T;ENSP00000435300:A370T	ENSP00000349344:A370T	A	+	1	0	PCDHA4	140168064	1.000000	0.71417	0.553000	0.28255	0.264000	0.26372	4.379000	0.59575	2.341000	0.79615	0.591000	0.81541	GCC	.		0.493	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140187880	G	A	140187880	3	1	30	1	0	0	0	0	1	0	0	0	11552	1087	38	1	1110	1	PCDHA4	5	140187880	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08	2681282	140187880	40727380	13	2640											
KIAA0141	9812	broad.mit.edu	37	chr5	141304998	141304998	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtccccatggcccaggcaCgagcgggggtccaaggtccc	7	4	15	15	2	0	0	0	0	0	0	3	1	3	0	5	6	1	1	5	6	1	0	rs148625091		TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr5:141304998C>T	ENST00000432126.2	+	3	304	c.170C>T	c.(169-171)aCg>aTg	p.T57M	KIAA0141_ENST00000194118.4_Missense_Mutation_p.T57M	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	57					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCCAGGCACGAGCGGGGGT	0.567																																					p.T57M													.	KIAA0141-91	0			c.C170T						.	C	MET/THR,MET/THR	0,4406		0,0,2203	116	90	99		170,170	0.2	0	5	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	57/516,57/516	141304998	1,13005	2203	4300	6503	SO:0001583	missense	9812	exon3			CAGGCACGAGCGG	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"death ligand signal enhancer"	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.170C>T	5.37:g.141304998C>T	ENSP00000396225:p.Thr57Met	Somatic	150	1		WXS	Illumina HiSeq	Phase_I	166	6	NM_001142603	0	0	37	37	0	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662032	0.29515	0.0	1.16E-4	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.18338	2.71;2.71;2.22	4.85	0.193	0.15139	.	0.865109	0.09867	N	0.745459	T	0.14570	0.0352	L	0.51422	1.61	0.09310	N	1	P	0.42337	0.776	B	0.36885	0.235	T	0.17018	-1.0383	10	0.49607	T	0.09	-0.1808	8.2847	0.31922	0.0:0.457:0.4427:0.1003	.	57	Q14154	DELE_HUMAN	M	57	ENSP00000396225:T57M;ENSP00000194118:T57M;ENSP00000422686:T57M	ENSP00000194118:T57M	T	+	2	0	KIAA0141	141285182	0.007000	0.16637	0.014000	0.15608	0.123000	0.20343	0.446000	0.21694	0.100000	0.17581	-0.564000	0.04169	ACG	C|1.000;T|0.000		0.567	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		T	141304998	C	T	141304998	3	4	30	1	0	0	0	0	1	0	0	0	8177	536	19	1	180	1	KIAA0141	5	141304998	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08	1117118	141304998	39610262	14	2641											
AMD1	262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	111208734	111208734	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggacatacttttgaaggAtgtgcaatgttcaatcataa	13	13	10	5	0	2	1	2	1	0	0	2	3	2	3	0	2	2	2	0	2	5	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr6:111208734A>G	ENST00000368885.3	+	2	473	c.137A>G	c.(136-138)gAt>gGt	p.D46G	AMD1_ENST00000368876.1_5'UTR|AMD1_ENST00000368882.3_Intron|AMD1_ENST00000368877.5_Intron|AMD1_ENST00000451850.2_Intron	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	46					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	CTTTTGAAGGATGTGCAATGT	0.353																																					p.D46G		.											.	AMD1-91	0			c.A137G						.						180	175	177					6																	111208734		2203	4300	6503	SO:0001583	missense	262	exon2			TGAAGGATGTGCA	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.137A>G	6.37:g.111208734A>G	ENSP00000357880:p.Asp46Gly	Somatic	271	0		WXS	Illumina HiSeq	Phase_I	305	53	NM_001634	0	0	24	30	6	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Missense_Mutation	SNP	ENST00000368885.3	37	CCDS5086.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020888	0.35606	.	.	ENSG00000123505	ENST00000368885	.	.	.	5.46	4.31	0.51392	S-adenosylmethionine decarboxylase, core (2);	0.184022	0.56097	N	0.000026	T	0.18002	0.0432	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.16722	0.016	T	0.06391	-1.0829	9	0.21014	T	0.42	.	11.2686	0.49124	0.9284:0.0:0.0716:0.0	.	46	P17707	DCAM_HUMAN	G	46	.	ENSP00000357880:D46G	D	+	2	0	AMD1	111315427	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.803000	0.91915	1.021000	0.39600	0.482000	0.46254	GAT	.		0.353	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			G	111208734	A	G	111208734	3	3	30	1	0	0	0	0	1	0	0	0	566	333	12	3	143	3	AMD1	6	111208734	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08		111208734	59906333	15	2642											
SNX13	23161	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	17836512	17836512	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcattcgaatacttttaTctctgcatggaacagcctct	9	16	5	11	1	3	0	1	0	3	0	6	2	3	1	1	1	4	1	1	1	4	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr7:17836512T>C	ENST00000409389.1	-	25	2769	c.2597A>G	c.(2596-2598)gAt>gGt	p.D866G	SNX13_ENST00000428135.3_Missense_Mutation_p.D855G|SNX13_ENST00000496855.1_5'UTR			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	866					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					AATACTTTTATCTCTGCATGG	0.318																																					p.D855G		.											.	SNX13-650	0			c.A2564G						.						186	172	176					7																	17836512		1832	4093	5925	SO:0001583	missense	23161	exon25			CTTTTATCTCTGC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"Sorting nexins"	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.2597A>G	7.37:g.17836512T>C	ENSP00000386705:p.Asp866Gly	Somatic	288	0		WXS	Illumina HiSeq	Phase_I	149	14	NM_015132	0	0	43	43	0	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	T	24.8	4.576015	0.86645	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.30714	1.52;1.52	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.52901	0.1763	M	0.65498	2.005	0.80722	D	1	D;P;D	0.67145	0.996;0.943;0.995	D;P;D	0.67548	0.952;0.867;0.94	T	0.55509	-0.8130	10	0.59425	D	0.04	-15.4175	15.4601	0.75349	0.0:0.0:0.0:1.0	.	652;866;855	B3KN60;B8ZZT9;Q9Y5W8-2	.;.;.	G	866;855;903	ENSP00000386705:D866G;ENSP00000398789:D855G	ENSP00000242044:D903G	D	-	2	0	SNX13	17803037	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.046000	0.60703	0.455000	0.32223	GAT	.		0.318	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		C	17836512	T	C	17836512	3	2	30	1	0	0	0	0	1	0	0	0	14916	1435	50	3	317	3	SNX13	7	17836512	Missense_Mutation	SNP	T	TCGA-AL-3467-01A-01D-1252-08		17836512	141302151	16	2643											
MUC17	140453	broad.mit.edu	37	chr7	100676555	100676555	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgctgaaggtaccagcatgCcaacctcaacttacagtgaa	13	8	8	12	0	1	2	1	2	0	0	1	2	1	2	3	1	7	3	3	1	6	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr7:100676555C>T	ENST00000306151.4	+	3	1922	c.1858C>T	c.(1858-1860)Cca>Tca	p.P620S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	620	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.P620A(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TACCAGCATGCCAACCTCAAC	0.478																																					p.P620S													.	MUC17-95	1	Substitution - Missense(1)	kidney(1)	c.C1858T						.						254	255	255					7																	100676555		2203	4300	6503	SO:0001583	missense	140453	exon3			AGCATGCCAACCT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.1858C>T	7.37:g.100676555C>T	ENSP00000302716:p.Pro620Ser	Somatic	449	0		WXS	Illumina HiSeq	Phase_I	524	8	NM_001040105	0	0	0	0	0	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	1.052	-0.675519	0.03378	.	.	ENSG00000169876	ENST00000306151	T	0.03152	4.03	0.926	-0.13	0.13498	.	.	.	.	.	T	0.01287	0.0042	N	0.03608	-0.345	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.46871	-0.9160	9	0.02654	T	1	.	3.2487	0.06806	0.0:0.6664:0.0:0.3336	.	620	Q685J3	MUC17_HUMAN	S	620	ENSP00000302716:P620S	ENSP00000302716:P620S	P	+	1	0	MUC17	100463275	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.977000	0.00164	-0.035000	0.13691	0.395000	0.25975	CCA	.		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100676555	C	T	100676555	3	4	30	1	0	0	0	0	1	0	0	0	9999	739	26	2	1868	2	MUC17	7	100676555	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08	82840043	100676555	58462108	17	2644											
BRAF	673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccactccatcgagatttcActgtagctagaccaaaatca	14	9	5	13	1	2	2	2	0	0	2	4	3	3	2	3	0	1	2	3	0	4	3	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.V600E	Colon(40;35 892 2973 5743 27438)	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF-92146	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A						.						112	104	107					7																	140453136		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	GATTTCACTGTAG	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	127	50	NM_004333	0	0	8	10	2	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA	.		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453136	A	T	140453136	3	4	30	1	0	0	0	0	1	0	0	0	1499	159	6	5	517	5	BRAF	7	140453136	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08	39776581	140453136	18685527	18	2645											
C10orf26	118980	broad.mit.edu	37	chr10	104503830	104503830	+	IGR	DEL	T	T	-																															gatggagaggagaaggctccTgggtggcatggcgctcctgc																										TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr10:104503830delT	ENST00000369893.5	+	0	6866				WBP1L_ENST00000448841.1_Frame_Shift_Del_p.L7fs	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2						iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		agaaggCTCCTGGGTGGCATG	0.692																																					p.L7fs													.	.	0			c.20delT						.						14	20	18					10																	104503830		2003	4117	6120	SO:0001628	intergenic_variant	54838	exon1			GGCTCCTGGGTGG	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"Sideroflexins"	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967		10.37:g.104503830delT		Somatic	9	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001083913	0	0	0	0	0	Q5JSM6	Frame_Shift_Del	DEL	ENST00000369893.5	37	CCDS7539.1																																																																																			.		0.692	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		-	104503830	T	-	104503830	6	5	30	0	1	1	0	1	0	0	0	0	1603	1580	55	0		0	C10orf26	10	104503830	IGR	DEL	T	TCGA-AL-3467-01A-01D-1252-08		104503830	31030917	19	2646											
GYLTL1B	120071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	45948105	45948105	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggaacctgctgcggagagAgctctttgtgtgccccagcc	6	9	14	12	1	1	1	0	0	1	1	1	4	1	3	4	2	6	2	4	2	1	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr11:45948105A>C	ENST00000531526.1	+	9	1232	c.1121A>C	c.(1120-1122)gAg>gCg	p.E374A	GYLTL1B_ENST00000325468.5_Missense_Mutation_p.E374A|GYLTL1B_ENST00000389968.3_Missense_Mutation_p.E101A|GYLTL1B_ENST00000536139.1_Missense_Mutation_p.E343A|GYLTL1B_ENST00000401752.1_Missense_Mutation_p.E374A|GYLTL1B_ENST00000529052.1_Missense_Mutation_p.E343A	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	374					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		CTGCGGAGAGAGCTCTTTGTG	0.567																																					p.E374A		.											.	GYLTL1B-92	0			c.A1121C						.						72	74	74					11																	45948105		2203	4299	6502	SO:0001583	missense	120071	exon9			GGAGAGAGCTCTT		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"Glycosyltransferase family 8 domain containing"	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1121A>C	11.37:g.45948105A>C	ENSP00000432869:p.Glu374Ala	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	104	35	NM_152312	0	0	17	46	29	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Missense_Mutation	SNP	ENST00000531526.1	37	CCDS31473.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.148701	0.57151	.	.	ENSG00000165905	ENST00000529052;ENST00000531526;ENST00000401752;ENST00000389968;ENST00000325468;ENST00000536139;ENST00000534410	T;T;T;D;T;T	0.83419	0.88;0.87;0.87;-1.72;0.87;0.88	5.45	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.80854	0.4703	M	0.66939	2.045	0.80722	D	1	P;B;B	0.36027	0.533;0.204;0.102	B;B;B	0.36418	0.224;0.099;0.068	T	0.79135	-0.1928	10	0.52906	T	0.07	-26.8748	11.3948	0.49836	0.9288:0.0:0.0712:0.0	.	343;343;374	B3KP69;E9PIZ2;Q8N3Y3	.;.;LARG2_HUMAN	A	343;374;374;101;374;343;35	ENSP00000431932:E343A;ENSP00000432869:E374A;ENSP00000385235:E374A;ENSP00000374618:E101A;ENSP00000324570:E374A;ENSP00000445044:E343A	ENSP00000324570:E374A	E	+	2	0	GYLTL1B	45904681	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.158000	0.77470	0.909000	0.36697	-0.411000	0.06167	GAG	.		0.567	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		C	45948105	A	C	45948105	3	2	30	1	0	0	0	0	1	0	0	0	6928	304	11	5	1151	5	GYLTL1B	11	45948105	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08		45948105	89058411	20	2647											
CORO1B	57175	broad.mit.edu	37	chr11	67206237	67206237	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggagcccggggccatggcggGccggctgtcagacaacacgt	7	4	17	13	4	1	1	1	0	0	1	1	2	1	2	3	6	2	1	3	6	1	0			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr11:67206237G>C	ENST00000341356.5	-	10	1359	c.1249C>G	c.(1249-1251)Ccc>Gcc	p.P417A	PTPRCAP_ENST00000326294.3_5'Flank|CORO1B_ENST00000393893.1_Missense_Mutation_p.P417A|CORO1B_ENST00000539724.1_5'UTR	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	417					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			GCCATGGCGGGCCGGCTGTCA	0.701																																					p.P417A													.	CORO1B-108	0			c.C1249G						.						6	7	6					11																	67206237		1982	4000	5982	SO:0001583	missense	57175	exon10			TGGCGGGCCGGCT	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"Coronins", "WD repeat domain containing"	2253	protein-coding gene	gene with protein product		609849	"coronin, actin-binding protein, 1B"			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.1249C>G	11.37:g.67206237G>C	ENSP00000340211:p.Pro417Ala	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	11	7	NM_020441	0	0	25	62	37	B2RD45	Missense_Mutation	SNP	ENST00000341356.5	37	CCDS8164.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859741	0.32884	.	.	ENSG00000172725	ENST00000393893;ENST00000341356	T;T	0.60797	0.16;0.16	4.58	3.62	0.41486	.	0.177538	0.27677	N	0.018318	T	0.44561	0.1299	L	0.34521	1.04	0.35506	D	0.800214	B	0.09022	0.002	B	0.10450	0.005	T	0.50541	-0.8816	10	0.28530	T	0.3	-8.2658	12.449	0.55667	0.0:0.1843:0.8157:0.0	.	417	Q9BR76	COR1B_HUMAN	A	417	ENSP00000377471:P417A;ENSP00000340211:P417A	ENSP00000340211:P417A	P	-	1	0	CORO1B	66962813	1.000000	0.71417	0.988000	0.46212	0.649000	0.38597	3.372000	0.52387	2.379000	0.81126	0.555000	0.69702	CCC	.		0.701	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441		C	67206237	G	C	67206237	3	2	30	1	0	0	0	0	1	0	0	0	3760	1203	42	4	228	4	CORO1B	11	67206237	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08	21258132	67206237	67800279	21	2648											
OR8D1	283159	hgsc.bcm.edu;broad.mit.edu	37	chr11	124180427	124180427	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggaagttcaccagcattttgGgagtaatgacagaggaatag	14	9	13	5	0	1	2	1	1	0	1	1	5	1	5	1	3	1	3	1	3	4	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr11:124180427G>A	ENST00000357821.2	-	1	306	c.236C>T	c.(235-237)cCc>cTc	p.P79L		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		CAGCATTTTGGGAGTAATGAC	0.458																																					p.P79L		.											.	OR8D1-71	0			c.C236T						.						69	65	66					11																	124180427		2201	4299	6500	SO:0001583	missense	283159	exon1			ATTTTGGGAGTAA	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.236C>T	11.37:g.124180427G>A	ENSP00000350474:p.Pro79Leu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	82	7	NM_001002917	0	0	0	0	0	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	37	CCDS31706.1	.	.	.	.	.	.	.	.	.	.	g	21.7	4.189733	0.78789	.	.	ENSG00000196341	ENST00000357821	T	0.01854	4.6	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36815	U	0.002395	T	0.22205	0.0535	H	0.97023	3.925	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	T	0.42832	-0.9428	10	0.87932	D	0	.	16.5818	0.84717	0.0:0.0:1.0:0.0	.	79	Q8WZ84	OR8D1_HUMAN	L	79	ENSP00000350474:P79L	ENSP00000350474:P79L	P	-	2	0	OR8D1	123685637	1.000000	0.71417	0.999000	0.59377	0.920000	0.55202	4.741000	0.62095	2.236000	0.73375	0.508000	0.49915	CCC	.		0.458	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		A	124180427	G	A	124180427	3	1	30	1	0	0	0	0	1	0	0	0	11257	1232	43	2	693	2	OR8D1	11	124180427	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08	56974190	124180427	10826089	22	2649											
KLRB1	3820	broad.mit.edu	37	chr12	9754098	9754098	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatggtgccccacttaccTgaaacactcaacccagtaac	13	8	6	14	0	1	2	1	2	0	0	1	2	1	2	4	1	5	1	4	1	4	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr12:9754098T>C	ENST00000229402.3	-	2	229	c.183A>G	c.(181-183)tcA>tcG	p.S61S		NM_002258.2	NP_002249.1	Q12918	KLRB1_HUMAN	killer cell lectin-like receptor subfamily B, member 1	61					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(6)|lung(4)	12						CCCACTTACCTGAAACACTCA	0.463																																					p.S61S													.	KLRB1-90	0			c.A183G						.						143	117	126					12																	9754098		2203	4300	6503	SO:0001630	splice_region_variant	3820	exon2			CTTACCTGAAACA	U11276	CCDS8601.1	12p13	2014-05-22			ENSG00000111796	ENSG00000111796		"Killer cell lectin-like receptors", "CD molecules", "C-type lectin domain containing"	6373	protein-coding gene	gene with protein product		602890		NKR		8077657	Standard	NM_002258		Approved	CD161, NKR-P1, NKR-P1A, hNKR-P1A, CLEC5B	uc010sgt.2	Q12918	OTTHUMG00000168581	ENST00000229402.3:c.184+1A>G	12.37:g.9754098T>C		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_002258	0	0	0	0	0	Q24K24	Silent	SNP	ENST00000229402.3	37	CCDS8601.1																																																																																			.		0.463	KLRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400280.1	NM_002258	Silent	C	9754098	T	C	9754098	5	2	30	1	0	0	0	0	0	0	1	0	8435	1594	55	3	513	3	KLRB1	12	9754098	Splice_Site	SNP	T	TCGA-AL-3467-01A-01D-1252-08		9754098	124097797	23	2650											
LDHB	3945	broad.mit.edu	37	chr12	21788543	21788543	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcttgagctgagcaaccTcatcatcctttagcttctgg	7	16	7	11	0	4	2	2	2	2	0	5	2	5	2	2	1	4	3	2	1	2	6			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr12:21788543T>C	ENST00000396076.1	-	8	1270	c.938A>G	c.(937-939)gAg>gGg	p.E313G	LDHB_ENST00000350669.1_Missense_Mutation_p.E313G	NM_001174097.1	NP_001167568.1	P07195	LDHB_HUMAN	lactate dehydrogenase B	313					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|lactate metabolic process (GO:0006089)|NAD metabolic process (GO:0019674)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	L-lactate dehydrogenase activity (GO:0004459)|NAD binding (GO:0051287)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	26						CTGAGCAACCTCATCATCCTT	0.458																																					p.E313G													.	LDHB-290	0			c.A938G						.						185	158	167					12																	21788543		2203	4300	6503	SO:0001583	missense	3945	exon8			GCAACCTCATCAT		CCDS8691.1	12p12.2-p12.1	2012-10-02			ENSG00000111716	ENSG00000111716	1.1.1.27		6541	protein-coding gene	gene with protein product		150100					Standard	NM_002300		Approved		uc001rfe.3	P07195	OTTHUMG00000133760	ENST00000396076.1:c.938A>G	12.37:g.21788543T>C	ENSP00000379386:p.Glu313Gly	Somatic	329	0		WXS	Illumina HiSeq	Phase_I	282	5	NM_002300	0	0	1953	1953	0		Missense_Mutation	SNP	ENST00000396076.1	37	CCDS8691.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.952417	0.92660	.	.	ENSG00000111716	ENST00000396076;ENST00000350669	T;T	0.73363	-0.74;-0.74	5.37	5.37	0.77165	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.90239	0.6948	H	0.97874	4.095	0.80722	D	1	D	0.63046	0.992	P	0.59948	0.866	D	0.93858	0.7151	10	0.87932	D	0	.	15.4488	0.75257	0.0:0.0:0.0:1.0	.	313	P07195	LDHB_HUMAN	G	313	ENSP00000379386:E313G;ENSP00000229319:E313G	ENSP00000229319:E313G	E	-	2	0	LDHB	21679810	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.965000	0.87945	2.039000	0.60335	0.529000	0.55759	GAG	.		0.458	LDHB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258220.2	NM_002300		C	21788543	T	C	21788543	3	2	30	1	0	0	0	0	1	0	0	0	8722	1551	54	3	70	3	LDHB	12	21788543	Missense_Mutation	SNP	T	TCGA-AL-3467-01A-01D-1252-08	12034445	21788543	112063352	24	2651											
CPNE6	9362	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	24544466	24544466	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggagatgcaggaagggaCggcaaaccctgggcaggagg	12	2	18	9	1	0	1	0	0	0	1	0	5	0	4	2	7	2	3	2	7	2	0			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr14:24544466C>A	ENST00000397016.2	+	9	1069	c.758C>A	c.(757-759)aCg>aAg	p.T253K	CPNE6_ENST00000216775.2_Missense_Mutation_p.T253K|CPNE6_ENST00000537691.1_Missense_Mutation_p.T308K	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	253					lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		CAGGAAGGGACGGCAAACCCT	0.567																																					p.T253K		.											.	CPNE6-93	0			c.C758A						.						111	106	107					14																	24544466		2203	4300	6503	SO:0001583	missense	9362	exon8			AAGGGACGGCAAA	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.758C>A	14.37:g.24544466C>A	ENSP00000380211:p.Thr253Lys	Somatic	250	1		WXS	Illumina HiSeq	Phase_I	271	121	NM_006032	0	0	0	0	0	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	37	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	3.945	-0.013372	0.07727	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.06294	3.32;3.34;3.34	5.13	5.13	0.70059	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000007	T	0.03783	0.0107	N	0.05487	-0.04	0.21020	N	0.999808	P;B	0.39326	0.668;0.192	B;B	0.40901	0.343;0.122	T	0.39165	-0.9627	10	0.05721	T	0.95	-31.3802	13.9546	0.64140	0.0:1.0:0.0:0.0	.	308;253	F5GXN1;O95741	.;CPNE6_HUMAN	K	308;253;253	ENSP00000440077:T308K;ENSP00000380211:T253K;ENSP00000216775:T253K	ENSP00000216775:T253K	T	+	2	0	CPNE6	23614306	0.908000	0.30866	0.997000	0.53966	0.900000	0.52787	0.035000	0.13797	2.676000	0.91093	0.467000	0.42956	ACG	.		0.567	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			A	24544466	C	A	24544466	3	1	30	1	0	0	0	0	1	0	0	0	3822	536	19	4	784	4	CPNE6	14	24544466	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08		24544466	82805074	25	2652											
NPAS3	64067	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	34263109	34263109	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttttttcgccagtgctgaAtaagggtcagtgtgtgacaa	9	15	11	6	1	1	2	1	2	0	0	2	2	1	2	1	1	1	1	1	1	3	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr14:34263109A>G	ENST00000356141.4	+	10	1160	c.1160A>G	c.(1159-1161)aAt>aGt	p.N387S	NPAS3_ENST00000346562.2_Missense_Mutation_p.N355S|NPAS3_ENST00000357798.5_Missense_Mutation_p.N374S|NPAS3_ENST00000548645.1_Missense_Mutation_p.N357S|NPAS3_ENST00000551492.1_Missense_Mutation_p.N392S			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	387	PAC.|PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CCAGTGCTGAATAAGGGTCAG	0.368																																					p.N387S		.											.	NPAS3-93	0			c.A1160G						.						107	102	103					14																	34263109		2203	4300	6503	SO:0001583	missense	64067	exon10			TGCTGAATAAGGG	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"Basic helix-loop-helix proteins"	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1160A>G	14.37:g.34263109A>G	ENSP00000348460:p.Asn387Ser	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	199	16	NM_001164749	0	0	2	2	0	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	37	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.085130	0.36758	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32;2.32	5.79	5.79	0.91817	PAS fold-3 (1);PAS (2);	0.000000	0.85682	D	0.000000	T	0.10766	0.0263	N	0.04297	-0.235	0.80722	D	1	P;B;P;P	0.35542	0.508;0.351;0.508;0.508	B;B;B;B	0.37304	0.234;0.246;0.234;0.234	T	0.31696	-0.9934	10	0.39692	T	0.17	.	16.1299	0.81422	1.0:0.0:0.0:0.0	.	357;387;355;374	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	S	364;392;355;357;387;374	ENSP00000448373:N364S;ENSP00000450392:N392S;ENSP00000319610:N355S;ENSP00000448916:N357S;ENSP00000348460:N387S;ENSP00000350446:N374S	ENSP00000319610:N355S	N	+	2	0	NPAS3	33332860	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.292000	0.72725	2.213000	0.71641	0.455000	0.32223	AAT	.		0.368	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			G	34263109	A	G	34263109	3	3	30	1	0	0	0	0	1	0	0	0	10590	101	4	3	1253	3	NPAS3	14	34263109	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08	9718643	34263109	73086431	26	2653											
C14orf142	84520	broad.mit.edu	37	chr14	93670051	93670051	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgttaagacggtgtttttggCcgttttgcagatggtccatc	6	16	12	7	2	0	2	0	0	0	2	2	2	1	2	2	3	1	4	2	3	1	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr14:93670051C>T	ENST00000306954.4	-	2	341	c.285G>A	c.(283-285)cgG>cgA	p.R95R	RP11-371E8.4_ENST00000557048.1_Intron|RP11-371E8.4_ENST00000557574.1_Intron	NM_032490.4	NP_115879.2	Q9BXV9	CN142_HUMAN	chromosome 14 open reading frame 142	95										endometrium(1)|skin(1)	2		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.177)|all cancers(159;0.198)|COAD - Colon adenocarcinoma(157;0.203)		GTGTTTTTGGCCGTTTTGCAG	0.338																																					p.R95R													.	C14orf142-90	0			c.G285A						.						261	242	248					14																	93670051		1921	4145	6066	SO:0001819	synonymous_variant	84520	exon2			TTTTGGCCGTTTT	AF277185	CCDS41981.1	14q32.12	2012-09-25			ENSG00000170270	ENSG00000170270			20356	protein-coding gene	gene with protein product							Standard	NM_032490		Approved		uc001ybl.1	Q9BXV9	OTTHUMG00000171267	ENST00000306954.4:c.285G>A	14.37:g.93670051C>T		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	204	6	NM_032490	0	0	31	31	0	Q0D2N1|Q0P6C4|Q3B7W5	Silent	SNP	ENST00000306954.4	37	CCDS41981.1																																																																																			.		0.338	C14orf142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412691.1	NM_032490		T	93670051	C	T	93670051	2	4	30	1	0	0	0	0	0	0	0	1	1751	726	26	2		2	C14orf142	14	93670051	Silent	SNP	C	TCGA-AL-3467-01A-01D-1252-08	59406942	93670051	13679489	27	2654											
PIGB	9488	hgsc.bcm.edu	37	chr15	55626159	55626159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcttcagacatttctgtcaaGaaccaagaaagcttgatctt	13	13	6	9	0	5	4	2	1	3	3	5	4	5	4	1	0	2	1	1	0	4	4			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr15:55626159G>A	ENST00000164305.5	+	6	1039	c.748G>A	c.(748-750)Gaa>Aaa	p.E250K	PIGB_ENST00000539642.1_Missense_Mutation_p.E55K	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	250					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		TTTCTGTCAAGAACCAAGAAA	0.388																																					p.E250K		.											.	PIGB-226	0			c.G748A						.						114	105	108					15																	55626159		1838	4108	5946	SO:0001583	missense	9488	exon6			TGTCAAGAACCAA	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	8959	protein-coding gene	gene with protein product	"GPI mannosyltransferase 3", "dol-P-Man dependent GPI mannosyltransferase"	604122	"phosphatidylinositol glycan, class B"			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.748G>A	15.37:g.55626159G>A	ENSP00000164305:p.Glu250Lys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_004855	0	0	10	10	0	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		.	.	.	.	.	.	.	.	.	.	G	25.4	4.638508	0.87760	.	.	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.63096	-0.02;-0.02	6.03	6.03	0.97812	.	0.143072	0.64402	D	0.000006	T	0.52354	0.1729	L	0.37630	1.12	0.58432	D	0.99999	B	0.16603	0.018	B	0.26310	0.068	T	0.47736	-0.9094	10	0.05620	T	0.96	-5.5916	17.7128	0.88326	0.0:0.0:1.0:0.0	.	250	Q92521	PIGB_HUMAN	K	250;55	ENSP00000164305:E250K;ENSP00000438963:E55K	ENSP00000164305:E250K	E	+	1	0	PIGB	53413451	1.000000	0.71417	0.958000	0.39756	0.988000	0.76386	9.087000	0.94110	2.861000	0.98227	0.655000	0.94253	GAA	.		0.388	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855		A	55626159	G	A	55626159	3	1	30	1	0	0	0	0	1	0	0	0	11911	943	33	2	770	2	PIGB	15	55626159	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08		55626159	46905233	28	2655											
GCOM1	100820829	broad.mit.edu	37	chr15	57922023	57922023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggcagttggaggtagcgCaagttgaaaaccagctgcta	13	7	14	7	1	0	2	0	1	0	1	0	3	0	3	1	3	4	7	1	3	5	4			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr15:57922023C>G	ENST00000267853.5	+	6	743	c.649C>G	c.(649-651)Caa>Gaa	p.Q217E	GCOM1_ENST00000574161.1_Missense_Mutation_p.Q217E|GCOM1_ENST00000380561.2_Missense_Mutation_p.Q186E|GCOM1_ENST00000572390.1_Missense_Mutation_p.Q217E|MYZAP_ENST00000380565.4_Missense_Mutation_p.Q217E|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380569.2_Missense_Mutation_p.Q217E|GCOM1_ENST00000380560.2_Missense_Mutation_p.Q148E|GCOM1_ENST00000396180.1_Missense_Mutation_p.Q186E|GCOM1_ENST00000380568.3_Missense_Mutation_p.Q217E|GCOM1_ENST00000587652.1_Missense_Mutation_p.Q217E			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	217					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											GGAGGTAGCGCAAGTTGAAAA	0.413																																					p.Q217E													.	GCOM1-91	0			c.C649G						.						95	90	92					15																	57922023		2192	4292	6484	SO:0001583	missense	145781	exon6			GTAGCGCAAGTTG	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"myocardium-enriched zonula adherens protein"	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.649C>G	15.37:g.57922023C>G	ENSP00000267853:p.Gln217Glu	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	106	5	NM_001018090	0	0	0	0	0	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	C	8.397	0.841141	0.16891	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01	5.43	3.54	0.40534	.	0.231577	0.44688	D	0.000424	T	0.37652	0.1011	L	0.56769	1.78	0.43326	D	0.995354	P;P;P;B	0.43024	0.544;0.798;0.544;0.402	B;B;B;B	0.44044	0.346;0.439;0.346;0.346	T	0.14172	-1.0482	10	0.13108	T	0.6	-7.7731	7.7864	0.29095	0.2881:0.6345:0.0:0.0774	.	217;217;217;217	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	E	217;186;186;148;217;217;217	ENSP00000369943:Q217E;ENSP00000369935:Q186E;ENSP00000379483:Q186E;ENSP00000369933:Q148E;ENSP00000267853:Q217E;ENSP00000369939:Q217E;ENSP00000369942:Q217E	ENSP00000267853:Q217E	Q	+	1	0	GCOM1	55709315	0.992000	0.36948	0.004000	0.12327	0.268000	0.26511	3.376000	0.52417	0.642000	0.30620	0.650000	0.86243	CAA	.		0.413	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		G	57922023	C	G	57922023	3	3	30	1	0	0	0	0	1	0	0	0	6324	711	25	4	671	4	GCOM1	15	57922023	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08	2295864	57922023	44609369	29	2656											
ZSCAN10	84891	hgsc.bcm.edu	37	chr16	3142579	3142579	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggctcccggtggatgccCtcgagcagcagcaccacctc	6	6	12	17	2	0	0	0	0	0	0	3	2	1	1	4	3	4	4	4	3	0	0			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr16:3142579C>T	ENST00000252463.2	-	1	282	c.195G>A	c.(193-195)gaG>gaA	p.E65E	ZSCAN10_ENST00000575108.1_Intron|ZSCAN10_ENST00000538082.2_Missense_Mutation_p.G73R|ZSCAN10_ENST00000572548.1_Intron	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	65	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(3)|endometrium(3)|kidney(1)|lung(8)|ovary(2)|prostate(1)|skin(4)|urinary_tract(1)	24						GGTGGATGCCCTCGAGCAGCA	0.701																																					p.E65E		.											.	ZSCAN10-227	0			c.G195A						.						8	8	8					16																	3142579		2158	4257	6415	SO:0001819	synonymous_variant	84891	exon1			GATGCCCTCGAGC	AA206569	CCDS10493.1, CCDS61813.1, CCDS61814.1	16p13.3	2013-01-08	2007-02-20	2007-02-20		ENSG00000130182		"-", "Zinc fingers, C2H2-type"	12997	protein-coding gene	gene with protein product			"zinc finger protein 206"	ZNF206		9653642	Standard	NM_032805		Approved		uc002ctv.1	Q96SZ4		ENST00000252463.2:c.195G>A	16.37:g.3142579C>T		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_032805	0	0	0	0	0	B3KQD3|H0YFS6|Q1WWM2	Silent	SNP	ENST00000252463.2	37	CCDS10493.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.761353	0.31228	.	.	ENSG00000130182	ENST00000538082	T	0.15372	2.43	5.4	4.45	0.53987	.	.	.	.	.	T	0.10852	0.0265	.	.	.	0.80722	D	1	B	0.22080	0.064	B	0.22880	0.042	T	0.13388	-1.0511	8	0.14252	T	0.57	-35.1187	10.1609	0.42851	0.0:0.9077:0.0:0.0923	.	88	Q1WWM2	.	R	88	ENSP00000440047:G88R	ENSP00000440047:G88R	G	-	1	0	ZSCAN10	3082580	0.002000	0.14202	0.999000	0.59377	0.059000	0.15707	0.052000	0.14163	1.286000	0.44565	0.561000	0.74099	GGG	.		0.701	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437124.2	NM_032805		T	3142579	C	T	3142579	2	4	30	1	0	0	0	0	0	0	0	1	18259	680	24	2		2	ZSCAN10	16	3142579	Silent	SNP	C	TCGA-AL-3467-01A-01D-1252-08		3142579	87212174	30	2657											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30745323	30745323	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacttcaccacagcctatttCaaacaggtactaagtaagat	16	10	5	10	0	2	1	2	0	0	1	2	1	2	1	2	1	4	2	2	1	6	6			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr16:30745323C>G	ENST00000262518.4	+	30	6988	c.6603C>G	c.(6601-6603)ttC>ttG	p.F2201L	SRCAP_ENST00000344771.4_Missense_Mutation_p.F2043L|SRCAP_ENST00000395059.2_Missense_Mutation_p.F2139L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2201					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CAGCCTATTTCAAACAGGTAC	0.453																																					p.F2201L		.											.	SRCAP-94	0			c.C6603G						.						67	60	63					16																	30745323		2197	4300	6497	SO:0001583	missense	10847	exon30			CTATTTCAAACAG	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.6603C>G	16.37:g.30745323C>G	ENSP00000262518:p.Phe2201Leu	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_006662	0	0	2	2	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744801	0.30865	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	T;T;T	0.07800	3.16;3.16;3.16	5.24	2.95	0.34219	.	0.380726	0.22784	N	0.055681	T	0.11367	0.0277	N	0.13003	0.285	0.31625	N	0.649832	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.11446	-1.0587	10	0.34782	T	0.22	-14.3882	7.2742	0.26275	0.0:0.329:0.0:0.671	.	2139;2201	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	L	2201;2139;2043	ENSP00000262518:F2201L;ENSP00000378499:F2139L;ENSP00000343042:F2043L	ENSP00000262518:F2201L	F	+	3	2	SRCAP	30652824	0.995000	0.38212	1.000000	0.80357	0.948000	0.59901	0.370000	0.20433	0.414000	0.25790	-0.414000	0.06135	TTC	.		0.453	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30745323	C	G	30745323	3	3	30	1	0	0	0	0	1	0	0	0	15167	825	29	4	6713	4	SRCAP	16	30745323	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08	27602744	30745323	59609430	31	2658											
CDH8	1006	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	61891030	61891031	+	Missense_Mutation	DNP	AG	AG	CT																															ttaggccacaaacctgtttcAggctcaatggaaaaataagg																										TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr16:61891030_61891031AG>CT	ENST00000577390.1	-	4	1613_1614	c.659_660CT>AG	c.(658-660)cCT>cAG	p.P220Q	CDH8_ENST00000299345.6_Missense_Mutation_p.P220Q|CDH8_ENST00000584337.1_Missense_Mutation_p.P220Q|CDH8_ENST00000577730.1_Missense_Mutation_p.P220Q	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	220	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		AACCTGTTTCAGGCTCAATGGA	0.391																																					p.P220Q		.											.	CDH8	0			c.C659A						.																																			SO:0001583	missense	1006	exon4			GTTTCAGGCTCAA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.659_660delinsCT	16.37:g.61891030_61891031delinsCT	ENSP00000462701:p.Pro220Gln	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	108	34		0	0	0	0	0	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	DNP	ENST00000577390.1	37	CCDS10802.1																																																																																			.		0.391	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		CT	61891031	AG	CT	61891030	3	2	30	1	0	0	0	0	1	0	0	0	3122	175	7	5	1775	5	CDH8	16	61891030	Missense_Mutation	DNP	AG	TCGA-AL-3467-01A-01D-1252-08	31145707	61891030	28463723	32	2659											
ZC3H18	124245	broad.mit.edu	37	chr16	88694029	88694029	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagatgtgcttgtgtgtccaGgtccctgagcgtgagcagcg	6	10	16	9	2	0	3	0	2	0	1	2	4	2	3	2	1	4	2	2	1	0	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr16:88694029G>C	ENST00000301011.5	+	14	2308		c.e14-1		ZC3H18_ENST00000452588.2_Splice_Site	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		TGTGTGTCCAGGTCCCTGAGC	0.602																																					.	Ovarian(121;375 2276 20373 38669)												.	ZC3H18-69	0			c.2109-1G>C						.						139	99	113					16																	88694029		2198	4300	6498	SO:0001630	splice_region_variant	124245	exon14			TGTCCAGGTCCCT	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.2109-1G>C	16.37:g.88694029G>C		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	192	4	NM_144604	0	0	1	1	0	Q96DG4|Q96MP7	Splice_Site	SNP	ENST00000301011.5	37	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990257	0.35131	.	.	ENSG00000158545	ENST00000301011;ENST00000452588	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9725	0.89117	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZC3H18	87221530	1.000000	0.71417	0.988000	0.46212	0.130000	0.20726	9.436000	0.97532	2.322000	0.78497	0.491000	0.48974	.	.		0.602	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	Intron	C	88694029	G	C	88694029	5	2	30	1	0	0	0	0	0	0	1	0	17600	1014	35	4	2158	4	ZC3H18	16	88694029	Splice_Site	SNP	G	TCGA-AL-3467-01A-01D-1252-08	26802999	88694029	1660724	33	2660											
HIC1	3090	hgsc.bcm.edu	37	chr17	1960939	1960939	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgaagcacgagccgggcCtgggtagctatggcgacgag	9	5	18	9	4	0	1	0	1	0	0	0	5	0	2	2	4	3	3	2	4	3	2	rs373870177		TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:1960939C>G	ENST00000322941.3	+	2	1012	c.1012C>G	c.(1012-1014)Ctg>Gtg	p.L338V	HIC1_ENST00000399849.3_Missense_Mutation_p.L319V|SMG6_ENST00000573166.1_5'Flank	NM_001098202.1	NP_001091672.1	Q14526	HIC1_HUMAN	hypermethylated in cancer 1	338					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(1)	3				READ - Rectum adenocarcinoma(1115;0.236)		CGAGCCGGGCCTGGGTAGCTA	0.766																																					p.L338V		.											.	HIC1-135	0			c.C1012G						.		VAL/LEU,VAL/LEU	0,2492		0,0,1246	3	3	3		1012,955	2.1	1	17		3	2,6230		0,2,3114	no	missense,missense	HIC1	NM_001098202.1,NM_006497.3	32,32	0,2,4360	GG,GC,CC		0.0321,0.0,0.0229	benign,benign	338/734,319/715	1960939	2,8722	1246	3116	4362	SO:0001583	missense	3090	exon2			CCGGGCCTGGGTA		CCDS42229.1, CCDS42230.1	17p13.3	2013-01-09				ENSG00000177374		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	4909	protein-coding gene	gene with protein product		603825					Standard	NM_006497		Approved	ZBTB29, ZNF901	uc010cjy.3	Q14526		ENST00000322941.3:c.1012C>G	17.37:g.1960939C>G	ENSP00000314080:p.Leu338Val	Somatic	8	2		WXS	Illumina HiSeq	Phase_I	10	6	NM_001098202	0	0	0	0	0	D3DTI4	Missense_Mutation	SNP	ENST00000322941.3	37	CCDS42229.1	.	.	.	.	.	.	.	.	.	.	c	11.22	1.575074	0.28092	0.0	3.21E-4	ENSG00000177374	ENST00000399849;ENST00000322941	T;T	0.06933	3.29;3.24	3.04	2.06	0.26882	.	.	.	.	.	T	0.04543	0.0124	L	0.29908	0.895	0.27607	N	0.948784	D	0.53885	0.963	B	0.34873	0.191	T	0.37888	-0.9686	9	0.19590	T	0.45	.	7.4577	0.27276	0.0:0.7749:0.0:0.2251	.	338	Q14526	HIC1_HUMAN	V	319;338	ENSP00000382742:L319V;ENSP00000314080:L338V	ENSP00000314080:L338V	L	+	1	2	HIC1	1907689	0.571000	0.26659	0.994000	0.49952	0.920000	0.55202	1.173000	0.31920	0.490000	0.27771	0.394000	0.25966	CTG	.		0.766	HIC1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438878.1	NM_006497		G	1960939	C	G	1960939	3	3	30	1	0	0	0	0	1	0	0	0	7122	680	24	4	1018	4	HIC1	17	1960939	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08		1960939	79234271	34	2661											
ZMYND15	84225	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	4645266	4645266	+	Frame_Shift_Del	DEL	G	G	-																															gttagccaaaaccccaatgcGgacatggggtccccggccag																								rs200238712		TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:4645266delG	ENST00000433935.1	+	4	941	c.884delG	c.(883-885)cggfs	p.R295fs	CXCL16_ENST00000293778.6_5'Flank|ZMYND15_ENST00000573751.2_Frame_Shift_Del_p.R295fs|ZMYND15_ENST00000592813.1_Frame_Shift_Del_p.R295fs|CXCL16_ENST00000574412.1_5'Flank|ZMYND15_ENST00000269289.6_Frame_Shift_Del_p.R295fs	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15	295					negative regulation of transcription, DNA-templated (GO:0045892)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)	18						ACCCCAATGCGGACATGGGGT	0.577																																					p.R295fs		.											.	ZMYND15-90	0			c.884delG						.						79	84	82					17																	4645266		2203	4300	6503	SO:0001589	frameshift_variant	84225	exon4			.	AL136893	CCDS11053.1, CCDS45584.1, CCDS58506.1	17p13.3	2008-05-02			ENSG00000141497	ENSG00000141497		"Zinc fingers, MYND-type"	20997	protein-coding gene	gene with protein product		614312				11230166	Standard	NM_001136046		Approved	DKFZp434N127	uc002fyu.3	Q9H091	OTTHUMG00000090760	ENST00000433935.1:c.884delG	17.37:g.4645266delG	ENSP00000391742:p.Arg295fs	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	224	83	NM_001136046	0	0	0	0	0	B4DXY5|I3L296	Frame_Shift_Del	DEL	ENST00000433935.1	37	CCDS45584.1																																																																																			.		0.577	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265		-	4645266	G	-	4645266	7	5	30	1	0	1	0	1	0	0	0	0	17740	1116	39	0	894	0	ZMYND15	17	4645266	Frame_Shift_Del	DEL	G	TCGA-AL-3467-01A-01D-1252-08	2684327	4645266	76549944	35	2662											
ACCN1	40	hgsc.bcm.edu	37	chr17	31618997	31618997	+	Intron	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctggcccctgcagcgccCgctcgccgcctctgccgccc	1	5	10	25	5	1	0	0	0	1	0	2	0	1	0	9	1	3	2	9	1	0	0	rs112647385	byFrequency	TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:31618997C>A	ENST00000359872.6	-	2	1317				ASIC2_ENST00000225823.2_Missense_Mutation_p.R46L|ASIC2_ENST00000448983.1_5'Flank	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CTGCAGCGCCCGCTCGCCGCC	0.806													C|||	1091	0.217851	0.112	0.1902	5008	,	,		5226	0.3194		0.2664	False		,,,				2504	0.226				p.R46L		.											.	.	0			c.G137T						.						1	2	2					17																	31618997		903	2226	3129	SO:0001627	intron_variant	40	exon1			AGCGCCCGCTCGC	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179912G>T	17.37:g.31618997C>A		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	7	5	NM_183377	0	0	0	0	0	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	37	CCDS42296.1	567	0.25961538461538464	84	0.17073170731707318	81	0.22375690607734808	197	0.34440559440559443	205	0.2704485488126649	C	13.69	2.313571	0.40996	.	.	ENSG00000108684	ENST00000225823	T	0.65178	-0.14	4.45	-0.0635	0.13776	.	1.386070	0.04769	N	0.427624	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.17038	0.02	B	0.10450	0.005	T	0.17715	-1.0360	9	0.29301	T	0.29	-24.8125	4.0823	0.09932	0.0:0.3667:0.3479:0.2854	.	46	E9PBX2	.	L	46	ENSP00000225823:R46L	ENSP00000225823:R46L	R	-	2	0	ACCN1	28643110	0.458000	0.25760	0.926000	0.36857	0.865000	0.49528	1.119000	0.31258	0.274000	0.22072	0.306000	0.20318	CGG	C|0.740;A|0.260		0.806	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		A	31618997	C	A	31618997	1	1	30	0	1	0	0	0	0	0	0	0	128	652	23	4		4	ACCN1	17	31618997	Intron	SNP	C	TCGA-AL-3467-01A-01D-1252-08	26973731	31618997	49576213	36	2663											
CDC27	996	hgsc.bcm.edu	37	chr17	45249350	45249350	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtagtacaactgtgtccttTcaagagtctatatgctttat	10	17	7	7	0	2	1	1	0	1	1	3	1	3	1	1	0	3	3	1	0	7	7			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:45249350T>C	ENST00000066544.3	-	3	277	c.184A>G	c.(184-186)Aaa>Gaa	p.K62E	CDC27_ENST00000527547.1_Missense_Mutation_p.K62E|CDC27_ENST00000531206.1_Missense_Mutation_p.K62E|CDC27_ENST00000528748.1_5'UTR|RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000446365.2_Intron	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	62					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTGTGTCCTTTCAAGAGTCTA	0.348																																					p.K62E		.											.	CDC27-291	0			c.A184G						.						42	41	41					17																	45249350		2202	4300	6502	SO:0001583	missense	996	exon3			GTCCTTTCAAGAG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.184A>G	17.37:g.45249350T>C	ENSP00000066544:p.Lys62Glu	Somatic	99	2		WXS	Illumina HiSeq	Phase_I	80	4	NM_001114091	0	0	12	12	0	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.820387	0.71028	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000527547;ENST00000526866	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	5.69	5.69	0.88448	Tetratricopeptide-like helical (1);	0.518646	0.23036	N	0.052667	T	0.70971	0.3285	L	0.39467	1.215	0.80722	D	1	B;P;P	0.46578	0.314;0.499;0.88	B;B;P	0.45099	0.082;0.112;0.469	T	0.74754	-0.3558	10	0.72032	D	0.01	-34.4674	13.8831	0.63693	0.0:0.0:0.0:1.0	.	62;62;62	G5EA36;G3V1C4;P30260	.;.;CDC27_HUMAN	E	62	ENSP00000066544:K62E;ENSP00000434614:K62E;ENSP00000437339:K62E;ENSP00000432105:K62E	ENSP00000066544:K62E	K	-	1	0	CDC27	42604349	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.803000	0.85983	2.173000	0.68751	0.482000	0.46254	AAA	.		0.348	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45249350	T	C	45249350	3	2	30	1	0	0	0	0	1	0	0	0	3072	1792	62	3	2376	3	CDC27	17	45249350	Missense_Mutation	SNP	T	TCGA-AL-3467-01A-01D-1252-08	13630353	45249350	35945860	37	2664											
TBX4	9496	hgsc.bcm.edu;broad.mit.edu	37	chr17	59560359	59560359	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccgttccccccctccctacGaccagcaaatgctgagcccc	7	7	6	21	2	0	1	0	1	0	0	3	2	3	1	8	0	4	3	8	0	2	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:59560359G>A	ENST00000240335.1	+	8	1165	c.1120G>A	c.(1120-1122)Gac>Aac	p.D374N	TBX4_ENST00000393853.4_Missense_Mutation_p.D375N|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	374					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCCTCCCTACGACCAGCAAAT	0.597																																					p.D374N		.											.	TBX4-227	0			c.G1120A						.						66	58	61					17																	59560359		2203	4300	6503	SO:0001583	missense	9496	exon8			CCCTACGACCAGC	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1120G>A	17.37:g.59560359G>A	ENSP00000240335:p.Asp374Asn	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	91	6	NM_018488	0	0	0	0	0	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	37	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231687	0.79688	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.85702	-2.02;-2.02	5.51	5.51	0.81932	.	0.377447	0.27455	N	0.019283	T	0.78805	0.4341	L	0.40543	1.245	0.58432	D	0.999997	P;P	0.47545	0.896;0.897	B;B	0.35971	0.215;0.212	T	0.79127	-0.1931	9	.	.	.	.	18.4116	0.90554	0.0:0.0:1.0:0.0	.	375;374	A5PKU7;P57082	.;TBX4_HUMAN	N	375;374	ENSP00000377435:D375N;ENSP00000240335:D374N	.	D	+	1	0	TBX4	56915141	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.574000	0.82434	2.590000	0.87494	0.655000	0.94253	GAC	.		0.597	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		A	59560359	G	A	59560359	3	1	30	1	0	0	0	0	1	0	0	0	15692	1058	37	1	1150	1	TBX4	17	59560359	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08	14311009	59560359	21634851	38	2665											
FBXO27	126433	broad.mit.edu	37	chr19	39521937	39521937	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagccgtccccaccgtgttGcaccatccactttcggaggc	6	8	9	18	3	0	0	0	0	0	0	3	1	2	1	7	2	2	2	7	2	0	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr19:39521937G>C	ENST00000292853.4	-	3	507	c.388C>G	c.(388-390)Caa>Gaa	p.Q130E	FBXO27_ENST00000600828.1_Missense_Mutation_p.Q129E|CTB-189B5.3_ENST00000597303.1_RNA|FBXO27_ENST00000509137.2_Missense_Mutation_p.Q130E	NM_178820.3	NP_849142.1	Q8NI29	FBX27_HUMAN	F-box protein 27	130	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|urinary_tract(2)	17	all_cancers(60;3.79e-07)|all_lung(34;1.26e-07)|Lung NSC(34;1.46e-07)|all_epithelial(25;4.69e-07)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCACCGTGTTGCACCATCCAC	0.587																																					p.Q130E													.	FBXO27-227	0			c.C388G						.						78	73	75					19																	39521937		2203	4300	6503	SO:0001583	missense	126433	exon3			CGTGTTGCACCAT	AF436061	CCDS12527.1	19q13.2	2008-02-05	2004-06-15			ENSG00000161243		"F-boxes /  "other""	18753	protein-coding gene	gene with protein product		609099	"F-box only protein 27"			126433	Standard	NM_178820		Approved	Fbg5, Fbx27	uc002okh.3	Q8NI29		ENST00000292853.4:c.388C>G	19.37:g.39521937G>C	ENSP00000292853:p.Gln130Glu	Somatic	122	9		WXS	Illumina HiSeq	Phase_I	142	20	NM_178820	0	0	1	1	0	Q96C87	Missense_Mutation	SNP	ENST00000292853.4	37	CCDS12527.1	.	.	.	.	.	.	.	.	.	.	G	5.303	0.241265	0.10077	.	.	ENSG00000161243	ENST00000292853;ENST00000509137	T;T	0.27256	1.68;1.68	3.66	-6.55	0.01854	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	2.361880	0.01889	N	0.038431	T	0.05823	0.0152	N	0.00595	-1.35	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45338	-0.9268	10	0.02654	T	1	-18.5204	8.9226	0.35621	0.0:0.4812:0.1868:0.3321	.	130	Q8NI29	FBX27_HUMAN	E	130	ENSP00000292853:Q130E;ENSP00000437662:Q130E	ENSP00000292853:Q130E	Q	-	1	0	FBXO27	44213777	0.000000	0.05858	0.000000	0.03702	0.526000	0.34562	-0.080000	0.11339	-0.660000	0.05352	0.479000	0.44913	CAA	.		0.587	FBXO27-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463281.1			C	39521937	G	C	39521937	3	2	30	1	0	0	0	0	1	0	0	0	5756	1328	46	4	479	4	FBXO27	19	39521937	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08		39521937	19607046	39	2666											
FBLN1	2192	hgsc.bcm.edu;broad.mit.edu	37	chr22	45929662	45929662	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgtcaatgaatgcatcacggGcagccacagctgccggcttg	9	8	12	12	2	2	1	2	1	0	0	2	1	2	1	2	2	4	4	2	2	2	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr22:45929662G>A	ENST00000327858.6	+	7	763	c.668G>A	c.(667-669)gGc>gAc	p.G223D	FBLN1_ENST00000262722.7_Missense_Mutation_p.G223D|FBLN1_ENST00000340923.5_Missense_Mutation_p.G223D|FBLN1_ENST00000442170.2_Missense_Mutation_p.G223D|FBLN1_ENST00000348697.2_Missense_Mutation_p.G223D|FBLN1_ENST00000402984.3_Missense_Mutation_p.G261D	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	223	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TGCATCACGGGCAGCCACAGC	0.567																																					p.G223D		.											.	FBLN1-515	0			c.G668A						.						75	79	78					22																	45929662		2203	4300	6503	SO:0001583	missense	2192	exon7			TCACGGGCAGCCA		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"Fibulins"	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.668G>A	22.37:g.45929662G>A	ENSP00000331544:p.Gly223Asp	Somatic	236	2		WXS	Illumina HiSeq	Phase_I	268	17	NM_006487	0	0	3	3	0	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652638	0.47362	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923;ENST00000451475	D;D;D;D;D;D;D	0.95588	-3.17;-3.75;-3.75;-3.75;-3.75;-3.75;-3.17	5.03	5.03	0.67393	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.146280	0.64402	D	0.000008	D	0.95714	0.8606	L	0.41632	1.29	0.40342	D	0.979041	D;D;D;D	0.76494	0.999;0.999;0.981;0.993	D;D;P;D	0.74023	0.971;0.982;0.902;0.917	D	0.94005	0.7279	10	0.18276	T	0.48	.	14.8128	0.70008	0.0:0.1447:0.8553:0.0	.	261;223;223;223	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	D	223;261;223;223;223;223;143	ENSP00000262723:G223D;ENSP00000385521:G261D;ENSP00000262722:G223D;ENSP00000331544:G223D;ENSP00000393812:G223D;ENSP00000342212:G223D;ENSP00000415160:G143D	ENSP00000262722:G223D	G	+	2	0	FBLN1	44308326	0.999000	0.42202	0.484000	0.27391	0.505000	0.33919	3.001000	0.49488	2.335000	0.79485	0.305000	0.20034	GGC	.		0.567	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		A	45929662	G	A	45929662	3	1	30	1	0	0	0	0	1	0	0	0	5717	1203	42	2	694	2	FBLN1	22	45929662	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08		45929662	5374904	40	2667											
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu	37	chr22	46785299	46785299	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcacgtcattgccaaagAgcgtgcccgtgtgctgtgta	7	10	13	11	4	1	1	1	0	0	1	1	1	1	1	2	0	5	3	2	0	2	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr22:46785299A>G	ENST00000262738.3	-	18	6442	c.6443T>C	c.(6442-6444)cTc>cCc	p.L2148P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2148					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ATTGCCAAAGAGCGTGCCCGT	0.667																																					p.L2148P		.											.	CELSR1-525	0			c.T6443C						.						48	41	43					22																	46785299		2203	4300	6503	SO:0001583	missense	9620	exon18			CCAAAGAGCGTGC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.6443T>C	22.37:g.46785299A>G	ENSP00000262738:p.Leu2148Pro	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	107	6	NM_014246	0	0	28	28	0	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	A	8.527	0.870135	0.17322	.	.	ENSG00000075275	ENST00000262738	T	0.14516	2.5	4.99	3.96	0.45880	Domain of unknown function DUF3497 (1);	0.304522	0.25386	N	0.031042	T	0.20373	0.0490	M	0.68952	2.095	0.38634	D	0.951442	B;B	0.29136	0.234;0.097	B;B	0.37451	0.25;0.16	T	0.03728	-1.1009	10	0.66056	D	0.02	.	10.2827	0.43550	0.9208:0.0:0.0792:0.0	.	469;2148	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	2148	ENSP00000262738:L2148P	ENSP00000262738:L2148P	L	-	2	0	CELSR1	45163963	1.000000	0.71417	0.594000	0.28785	0.090000	0.18270	2.630000	0.46494	0.763000	0.33175	0.533000	0.62120	CTC	.		0.667	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46785299	A	G	46785299	3	3	30	1	0	0	0	0	1	0	0	0	3227	304	11	3	2673	3	CELSR1	22	46785299	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08	855637	46785299	4519267	41	2668											
ARSF	416	broad.mit.edu;bcgsc.ca	37	chrX	3028196	3028196	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacggccgagacctcatgccCttgctgcagggcaacgtcag	8	6	13	14	3	2	1	2	0	0	1	2	3	2	1	3	2	4	3	3	2	1	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chrX:3028196C>T	ENST00000381127.1	+	10	1514	c.1293C>T	c.(1291-1293)ccC>ccT	p.P431P	ARSF_ENST00000359361.2_Silent_p.P431P|ARSF_ENST00000537104.1_Silent_p.P431P	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	431					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCTCATGCCCTTGCTGCAGG	0.567																																					p.P431P													.	ARSF-132	0			c.C1293T						.						114	82	93					X																	3028196		2203	4300	6503	SO:0001819	synonymous_variant	416	exon10			CATGCCCTTGCTG	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"Arylsulfatase family"	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1293C>T	X.37:g.3028196C>T		Somatic	220	1		WXS	Illumina HiSeq	Phase_I	252	9	NM_004042	0	0	0	0	0	Q8TCC5	Silent	SNP	ENST00000381127.1	37	CCDS14123.1																																																																																			.		0.567	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			T	3028196	C	T	3028196	2	4	30	1	0	0	0	0	0	0	0	1	992	668	24	2		2	ARSF	23	3028196	Silent	SNP	C	TCGA-AL-3467-01A-01D-1252-08		3028196	152242364	42	2669											
LUZP4	51213	broad.mit.edu	37	chrX	114541171	114541171	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtgatctcatagccacTcagagagatctcatagccac	13	8	8	12	0	3	4	3	1	2	3	5	5	3	4	2	0	2	0	2	0	2	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chrX:114541171T>A	ENST00000371920.3	+	4	751	c.744T>A	c.(742-744)acT>acA	p.T248T	LUZP4_ENST00000451986.2_Silent_p.T166T	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	248						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						TCATAGCCACTCAGAGAGATC	0.478																																					p.T248T													.	LUZP4-132	0			c.T744A						.						134	118	123					X																	114541171		2203	4300	6503	SO:0001819	synonymous_variant	51213	exon4			AGCCACTCAGAGA	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"cancer/testis antigen 28"	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.744T>A	X.37:g.114541171T>A		Somatic	293	0		WXS	Illumina HiSeq	Phase_I	201	7	NM_016383	0	0	0	0	0	B3KSD6	Silent	SNP	ENST00000371920.3	37	CCDS14567.1																																																																																			.		0.478	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383		A	114541171	T	A	114541171	2	1	30	1	0	0	0	0	0	0	0	1	9113	1538	54	5		5	LUZP4	23	114541171	Silent	SNP	T	TCGA-AL-3467-01A-01D-1252-08	111512975	114541171	40729389	43	2670											
GRIK3	2899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	37307384	37307384	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttccactggcccttgtcatCctgtgccccgtacttgccgt	3	13	9	16	2	1	0	1	0	0	0	3	0	3	0	6	1	3	2	6	1	1	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:37307384C>T	ENST00000373091.3	-	10	1499	c.1483G>A	c.(1483-1485)Gat>Aat	p.D495N	GRIK3_ENST00000373093.4_Missense_Mutation_p.D495N	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	495					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CCCTTGTCATCCTGTGCCCCG	0.597																																					p.D495N		.											.	GRIK3-158	0			c.G1483A						.						176	151	159					1																	37307384		2203	4300	6503	SO:0001583	missense	2899	exon10			TGTCATCCTGTGC	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1483G>A	1.37:g.37307384C>T	ENSP00000362183:p.Asp495Asn	Somatic	245	0		WXS	Illumina HiSeq	Phase_I	371	177	NM_000831	0	0	0	0	0	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	5.820	0.335627	0.11013	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.76060	-0.99;-0.99	4.86	4.86	0.63082	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	N	0.20881	0.62	0.54753	D	0.999986	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.57312	-0.7833	10	0.09338	T	0.73	.	18.3613	0.90375	0.0:1.0:0.0:0.0	.	495;495	A9Z1Z8;Q13003	.;GRIK3_HUMAN	N	495	ENSP00000362183:D495N;ENSP00000362185:D495N	ENSP00000362183:D495N	D	-	1	0	GRIK3	37079971	1.000000	0.71417	0.993000	0.49108	0.530000	0.34684	4.928000	0.63447	2.398000	0.81561	0.591000	0.81541	GAT	.		0.597	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37307384	C	T	37307384	3	4	31	1	0	0	0	0	1	0	0	0	6796	855	30	2	1304	2	GRIK3	1	37307384	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		37307384	211943237	1	2671											
FLG	2312	broad.mit.edu	37	chr1	152281871	152281871	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccagaactatctaccgattGctcatagtgggatccctgcc	9	11	8	13	1	2	1	1	0	1	1	4	3	4	2	4	1	4	1	4	1	4	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:152281871G>T	ENST00000368799.1	-	3	5526	c.5491C>A	c.(5491-5493)Caa>Aaa	p.Q1831K	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1831	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTACCGATTGCTCATAGTGG	0.572									Ichthyosis																												p.Q1831K													.	FLG-106	0			c.C5491A						.						364	357	359					1																	152281871		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCGATTGCTCATA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5491C>A	1.37:g.152281871G>T	ENSP00000357789:p.Gln1831Lys	Somatic	767	0		WXS	Illumina HiSeq	Phase_I	1352	17	NM_002016	0	0	0	0	0	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686907	0.29962	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03330	3.97	3.58	2.65	0.31530	.	.	.	.	.	T	0.06142	0.0159	M	0.81942	2.565	0.09310	N	1	P	0.40332	0.713	P	0.54815	0.761	T	0.26189	-1.0110	9	0.49607	T	0.09	-2.4962	6.2028	0.20585	0.1364:0.0:0.8636:0.0	.	1831	P20930	FILA_HUMAN	K	1831;66	ENSP00000357789:Q1831K	ENSP00000271820:Q66K	Q	-	1	0	FLG	150548495	0.432000	0.25554	0.025000	0.17156	0.004000	0.04260	1.937000	0.40193	2.004000	0.58718	0.586000	0.80456	CAA	.		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152281871	G	T	152281871	3	4	31	1	0	0	0	0	1	0	0	0	5941	1328	46	4	6698	4	FLG	1	152281871	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	114974487	152281871	96968750	2	2672											
CRTC2	200186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153924730	153924730	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcaggctggtcaggagatGgaaagatgctaggggaagga	12	6	19	4	0	1	2	1	0	0	2	1	6	1	5	0	8	1	3	0	8	3	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:153924730G>A	ENST00000368633.1	-	10	888	c.761C>T	c.(760-762)cCa>cTa	p.P254L	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Intron	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	254					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GTCAGGAGATGGAAAGATGCT	0.552																																					p.P254L		.											.	CRTC2-228	0			c.C761T						.						57	62	60					1																	153924730		2203	4300	6503	SO:0001583	missense	200186	exon10			GGAGATGGAAAGA	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.761C>T	1.37:g.153924730G>A	ENSP00000357622:p.Pro254Leu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	176	72	NM_181715	0	0	0	0	0	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966111	0.74131	.	.	ENSG00000160741	ENST00000368633	T	0.71817	-0.6	4.67	3.76	0.43208	Transducer of regulated CREB activity, middle domain (1);	0.213044	0.40554	N	0.001070	T	0.76385	0.3980	M	0.80332	2.49	0.51767	D	0.999939	D	0.58970	0.984	D	0.62955	0.909	T	0.80086	-0.1529	10	0.87932	D	0	-3.0813	10.3415	0.43882	0.0961:0.0:0.9039:0.0	.	254	Q53ET0	CRTC2_HUMAN	L	254	ENSP00000357622:P254L	ENSP00000357622:P254L	P	-	2	0	CRTC2	152191354	1.000000	0.71417	0.961000	0.40146	0.979000	0.70002	6.923000	0.75817	1.195000	0.43115	0.455000	0.32223	CCA	.		0.552	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153924730	G	A	153924730	3	1	31	1	0	0	0	0	1	0	0	0	3906	1348	47	2	1340	2	CRTC2	1	153924730	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	1642859	153924730	95325891	3	2673											
HAPLN2	60484	hgsc.bcm.edu;broad.mit.edu	37	chr1	156593855	156593855	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgactagacgcctccctggtCatcgcgggcgtgcgcctgga	5	7	14	15	6	1	1	1	0	0	1	3	3	2	2	3	3	1	0	3	3	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:156593855C>T	ENST00000255039.1	+	4	749	c.342C>T	c.(340-342)gtC>gtT	p.V114V		NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	114	Ig-like V-type.				cell adhesion (GO:0007155)|establishment of blood-nerve barrier (GO:0008065)|extracellular matrix assembly (GO:0085029)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	7	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTCCCTGGTCATCGCGGGCG	0.692																																					p.V114V		.											.	HAPLN2-90	0			c.C342T						.						30	29	30					1																	156593855		2191	4256	6447	SO:0001819	synonymous_variant	60484	exon4			CCTGGTCATCGCG	AB049054	CCDS1148.1	1q23.1	2013-01-11			ENSG00000132702	ENSG00000132702		"Immunoglobulin superfamily / V-set domain containing"	17410	protein-coding gene	gene with protein product	"brain link protein 1"					11027579, 11873941	Standard	NM_021817		Approved	BRAL1	uc001fpn.1	Q9GZV7	OTTHUMG00000033205	ENST00000255039.1:c.342C>T	1.37:g.156593855C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	76	45	NM_021817	0	0	0	0	0	Q5T3J0	Silent	SNP	ENST00000255039.1	37	CCDS1148.1																																																																																			.		0.692	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817		T	156593855	C	T	156593855	2	4	31	1	0	0	0	0	0	0	0	1	6976	813	29	2		2	HAPLN2	1	156593855	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	2669125	156593855	92656766	4	2674											
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	216073458	216073458	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatccaagaactatgtgcaCtgccaaatccattggaggca	14	8	9	10	0	0	1	0	0	0	1	2	3	2	2	3	2	3	2	3	2	5	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:216073458C>T	ENST00000307340.3	-	40	7939	c.7553G>A	c.(7552-7554)aGt>aAt	p.S2518N	RP5-1111A8.3_ENST00000414995.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.S2518N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2518	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTATGTGCACTGCCAAATCC	0.423										HNSCC(13;0.011)																											p.S2518N		.											.	USH2A-115	0			c.G7553A						.						146	120	129					1																	216073458		2203	4300	6503	SO:0001583	missense	7399	exon40			TGTGCACTGCCAA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7553G>A	1.37:g.216073458C>T	ENSP00000305941:p.Ser2518Asn	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	34	17	NM_206933	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.781126	0.49891	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54071	0.59;0.59	6.16	4.3	0.51218	Fibronectin, type III (5);Immunoglobulin-like fold (1);	0.558407	0.16087	N	0.230233	T	0.47783	0.1464	L	0.46157	1.445	0.09310	N	1	P	0.43231	0.801	P	0.46419	0.516	T	0.33727	-0.9857	10	0.32370	T	0.25	.	4.9527	0.14023	0.0:0.5906:0.1598:0.2496	.	2518	O75445	USH2A_HUMAN	N	2518	ENSP00000305941:S2518N;ENSP00000355910:S2518N	ENSP00000305941:S2518N	S	-	2	0	USH2A	214140081	0.558000	0.26554	0.182000	0.23118	0.991000	0.79684	1.002000	0.29796	0.923000	0.37045	0.650000	0.86243	AGT	.		0.423	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216073458	C	T	216073458	3	4	31	1	0	0	0	0	1	0	0	0	17069	565	20	2	8187	2	USH2A	1	216073458	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	59479603	216073458	33177163	5	2675											
OR2T35	403244	hgsc.bcm.edu	37	chr1	248801928	248801928	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggacacagagatgacagatAgagggataagcagcatcagc	17	4	13	7	0	1	4	1	1	0	3	1	7	1	6	0	2	3	2	0	2	2	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:248801928A>G	ENST00000317450.3	-	1	631	c.632T>C	c.(631-633)cTa>cCa	p.L211P		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GATGACAGATAGAGGGATAAG	0.542																																					p.L211P		.											.	OR2T35-46	0			c.T632C						.						100	78	85					1																	248801928		2051	4246	6297	SO:0001583	missense	403244	exon1			ACAGATAGAGGGA	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"GPCR / Class A : Olfactory receptors"	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.632T>C	1.37:g.248801928A>G	ENSP00000324369:p.Leu211Pro	Somatic	61	2		WXS	Illumina HiSeq	Phase_I	55	6	NM_001001827	0	0	0	0	0	Q6IEY7	Missense_Mutation	SNP	ENST00000317450.3	37	CCDS31123.1	.	.	.	.	.	.	.	.	.	.	.	7.882	0.730494	0.15507	.	.	ENSG00000177151	ENST00000317450	T	0.49432	0.78	2.88	2.88	0.33553	GPCR, rhodopsin-like superfamily (1);	0.402088	0.20997	N	0.081937	T	0.58878	0.2153	M	0.83384	2.64	0.09310	N	0.999997	P	0.46578	0.88	P	0.53102	0.718	T	0.53085	-0.8488	10	0.87932	D	0	.	6.3062	0.21139	0.8718:0.0:0.1282:0.0	.	211	Q8NGX2	O2T35_HUMAN	P	211	ENSP00000324369:L211P	ENSP00000324369:L211P	L	-	2	0	OR2T35	246868551	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.710000	0.25748	1.341000	0.45600	0.432000	0.28606	CTA	.		0.542	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827		G	248801928	A	G	248801928	3	3	31	1	0	0	0	0	1	0	0	0	11052	420	15	3	343	3	OR2T35	1	248801928	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	32728470	248801928	448693	6	2676											
KIDINS220	57498	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	8871568	8871568	+	Frame_Shift_Del	DEL	T	T	-																															catctttgagcagtggagtgTtatctgattcttctgtgcca																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:8871568delT	ENST00000256707.3	-	30	4779	c.4598delA	c.(4597-4599)aacfs	p.N1533fs	KIDINS220_ENST00000418530.1_Frame_Shift_Del_p.N1434fs|KIDINS220_ENST00000427284.1_Frame_Shift_Del_p.N1514fs|KIDINS220_ENST00000473731.1_Frame_Shift_Del_p.N1514fs	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1533					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CAGTGGAGTGTTATCTGATTC	0.478																																					p.N1533fs		.											.	KIDINS220-93	0			c.4598delA						.						82	83	82					2																	8871568		1930	4146	6076	SO:0001589	frameshift_variant	57498	exon30			.	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4598delA	2.37:g.8871568delT	ENSP00000256707:p.Asn1533fs	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	145	57	NM_020738	0	0	0	0	0	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Frame_Shift_Del	DEL	ENST00000256707.3	37	CCDS42650.1																																																																																			.		0.478	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		-	8871568	T	-	8871568	7	5	31	1	0	1	0	1	0	0	0	0	8292	1725	60	0	721	0	KIDINS220	2	8871568	Frame_Shift_Del	DEL	T	TCGA-AL-3472-01A-01D-1252-08		8871568	234327805	7	2677											
BIRC6	57448	broad.mit.edu	37	chr2	32660618	32660618	+	Frame_Shift_Del	DEL	A	A	-																															gtccctggttgatttgaatgAagaaatgcagcacatggatg																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:32660618delA	ENST00000421745.2	+	14	3598	c.3464delA	c.(3463-3465)gaafs	p.E1156fs		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1156					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GATTTGAATGAAGAAATGCAG	0.408																																					p.E1155fs	Pancreas(94;175 1509 16028 18060 45422)												.	BIRC6-233	0			c.3464delA						.						70	69	70					2																	32660618		2187	4256	6443	SO:0001589	frameshift_variant	57448	exon14			TGAATGAAGAAAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.3464delA	2.37:g.32660618delA	ENSP00000393596:p.Glu1156fs	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_016252	0	0	0	0	0	Q9ULD1	Frame_Shift_Del	DEL	ENST00000421745.2	37	CCDS33175.2																																																																																			.		0.408	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		-	32660618	A	-	32660618	7	5	31	1	0	1	0	1	0	0	0	0	1439	246	9	0	3518	0	BIRC6	2	32660618	Frame_Shift_Del	DEL	A	TCGA-AL-3472-01A-01D-1252-08	23789050	32660618	210538755	8	2678											
EMX1	2016	hgsc.bcm.edu	37	chr2	73145299	73145299	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgccgcggccgccgcgggCgcgggccgctcgctctacgg	1	4	17	19	10	1	0	0	0	1	0	2	0	1	0	5	4	2	2	5	4	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:73145299C>G	ENST00000258106.6	+	1	696	c.318C>G	c.(316-318)ggC>ggG	p.G106G	EMX1_ENST00000394111.5_Intron	NM_004097.2	NP_004088.2	Q04741	EMX1_HUMAN	empty spiracles homeobox 1	73					brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|in utero embryonic development (GO:0001701)|neuron projection extension (GO:1990138)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			cervix(1)|large_intestine(2)|lung(3)	6						ccgccgcgggcgcgggccgcT	0.761																																					p.G106G		.											.	EMX1-90	0			c.C318G						.						3	4	4					2																	73145299		1216	2944	4160	SO:0001819	synonymous_variant	2016	exon1			CGCGGGCGCGGGC	X68879	CCDS1921.2	2p13.2	2011-06-20	2007-02-15		ENSG00000135638	ENSG00000135638		"Homeoboxes / ANTP class : NKL subclass"	3340	protein-coding gene	gene with protein product		600034	"empty spiracles homolog 1 (Drosophila)"			7959790	Standard	XM_005264203		Approved		uc002sin.1	Q04741	OTTHUMG00000129778	ENST00000258106.6:c.318C>G	2.37:g.73145299C>G		Somatic	7	1		WXS	Illumina HiSeq	Phase_I	16	7	NM_004097	0	0	0	0	0	Q0D2P0|Q53T30|Q86XB0	Silent	SNP	ENST00000258106.6	37	CCDS1921.2																																																																																			.		0.761	EMX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251994.3			G	73145299	C	G	73145299	2	3	31	1	0	0	0	0	0	0	0	1	5120	755	27	4		4	EMX1	2	73145299	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	40484681	73145299	170054074	9	2679											
TSGA10	80705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	99689479	99689479	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttgttgcacgactgatttAccttgatgcctgttccatct	7	17	7	10	1	1	2	0	2	1	0	2	3	2	2	3	0	3	3	3	0	1	6			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:99689479A>C	ENST00000393483.3	-	13	1783		c.e13+1		TSGA10_ENST00000410001.1_Splice_Site|TSGA10_ENST00000539964.1_Splice_Site|TSGA10_ENST00000478090.1_Splice_Site|TSGA10_ENST00000542655.1_Intron|TSGA10_ENST00000355053.4_Splice_Site	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10						cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CGACTGATTTACCTTGATGCC	0.353																																					.		.											.	TSGA10-91	0			c.938+2T>G						.						158	136	144					2																	99689479		2203	4300	6503	SO:0001630	splice_region_variant	80705	exon14			TGATTTACCTTGA	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.938+1T>G	2.37:g.99689479A>C		Somatic	405	0		WXS	Illumina HiSeq	Phase_I	212	105	NM_025244	0	0	0	1	1	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Splice_Site	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398383	0.62177	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9136	0.47122	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TSGA10	99055911	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	5.076000	0.64413	2.092000	0.63282	0.477000	0.44152	.	.		0.353	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911	Intron	C	99689479	A	C	99689479	5	2	31	1	0	0	0	0	0	0	1	0	16650	405	14	5	1192	5	TSGA10	2	99689479	Splice_Site	SNP	A	TCGA-AL-3472-01A-01D-1252-08	26544180	99689479	143509894	10	2680											
SLC25A12	8604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	172647961	172647961	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaaaaaatttgtagttacCtgccatggctccagctgcaa	15	10	7	9	0	0	0	0	0	0	0	1	0	1	0	3	1	4	5	3	1	7	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:172647961C>G	ENST00000422440.2	-	15	1622	c.1585G>C	c.(1585-1587)Ggt>Cgt	p.G529R	SLC25A12_ENST00000392592.4_Splice_Site_p.G422R	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	529					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	TTGTAGTTACCTGCCATGGCT	0.353																																					p.G529R		.											.	SLC25A12-90	0			c.G1585C						.						68	70	69					2																	172647961		2203	4300	6503	SO:0001630	splice_region_variant	8604	exon15			AGTTACCTGCCAT	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1585+1G>C	2.37:g.172647961C>G		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	146	60	NM_003705	0	0	0	0	0	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952520	0.92660	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	D;D	0.85339	-1.97;-1.97	5.92	5.92	0.95590	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.95242	0.8457	H	0.95712	3.71	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.95808	0.8839	9	.	.	.	-13.0108	20.3206	0.98668	0.0:1.0:0.0:0.0	.	422;529	B3KR64;O75746	.;CMC1_HUMAN	R	529;422	ENSP00000388658:G529R;ENSP00000376371:G422R	.	G	-	1	0	SLC25A12	172356207	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.784000	0.85713	2.809000	0.96659	0.655000	0.94253	GGT	.		0.353	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	Missense_Mutation	G	172647961	C	G	172647961	5	3	31	1	0	0	0	0	0	0	1	0	14506	695	24	4	467	4	SLC25A12	2	172647961	Splice_Site	SNP	C	TCGA-AL-3472-01A-01D-1252-08	72958482	172647961	70551412	11	2681											
HOXD8	3234	hgsc.bcm.edu	37	chr2	176995295	176995295	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcccgcacgcgcccccgcaGgcgcacgcgcacccgcaccc	5	2	10	24	8	0	0	0	0	0	0	1	0	1	0	5	1	0	5	5	1	0	1	rs564911040	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:176995295G>C	ENST00000313173.4	+	1	828	c.201G>C	c.(199-201)caG>caC	p.Q67H	HOXD8_ENST00000548663.1_Intron|HOXD8_ENST00000544999.1_Missense_Mutation_p.Q67H|HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000450510.2_Missense_Mutation_p.Q67H|HOXD8_ENST00000429017.1_Intron	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8	67					anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		CGCCCCCGCAGGCGCACGCGC	0.786																																					p.Q67H		.											.	HOXD8-90	0			c.G201C						.						2	2	2					2																	176995295		839	1924	2763	SO:0001583	missense	3234	exon1			CCCGCAGGCGCAC		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"Homeoboxes / ANTP class : HOXL subclass"	5139	protein-coding gene	gene with protein product		142985	"homeo box D8"	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.201G>C	2.37:g.176995295G>C	ENSP00000315949:p.Gln67His	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_001199746	0	0	0	0	0	F8WBG7|Q5BL00|Q8IXZ1	Missense_Mutation	SNP	ENST00000313173.4	37	CCDS2268.1	.	.	.	.	.	.	.	.	.	.	G	7.325	0.617776	0.14129	.	.	ENSG00000175879	ENST00000313173;ENST00000544999;ENST00000450510	D;D;D	0.91237	-2.81;-2.71;-2.71	3.11	3.11	0.35812	.	1.271540	0.05917	N	0.632694	T	0.81240	0.4781	N	0.08118	0	0.21822	N	0.999524	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.66874	-0.5813	10	0.23891	T	0.37	.	10.1671	0.42886	0.0:0.0:1.0:0.0	.	67;67	Q8IXZ1;P13378	.;HXD8_HUMAN	H	67	ENSP00000315949:Q67H;ENSP00000437431:Q67H;ENSP00000409026:Q67H	ENSP00000315949:Q67H	Q	+	3	2	HOXD8	176703541	0.992000	0.36948	0.993000	0.49108	0.612000	0.37316	-0.177000	0.09796	1.473000	0.48159	0.442000	0.29010	CAG	.		0.786	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1			C	176995295	G	C	176995295	3	2	31	1	0	0	0	0	1	0	0	0	7346	991	35	4	203	4	HOXD8	2	176995295	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	4347334	176995295	66204078	12	2682											
SF3B1	23451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198260814	198260814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcttcaagtaacggtgttaCggcataaatgtagtcttttc	11	15	8	7	2	3	0	1	0	2	0	4	0	3	0	0	2	2	4	0	2	6	7			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:198260814C>T	ENST00000335508.6	-	23	3596	c.3505G>A	c.(3505-3507)Gta>Ata	p.V1169I		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	1169					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AACGGTGTTACGGCATAAATG	0.323			Mis		myelodysplastic syndrome																																p.V1169I		.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.G3505A						.						111	108	109					2																	198260814		2203	4300	6503	SO:0001583	missense	23451	exon23			GTGTTACGGCATA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.3505G>A	2.37:g.198260814C>T	ENSP00000335321:p.Val1169Ile	Somatic	322	0		WXS	Illumina HiSeq	Phase_I	105	43	NM_012433	0	0	218	390	172	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524051	0.44866	.	.	ENSG00000115524	ENST00000335508	T	0.63744	-0.06	5.11	5.11	0.69529	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58949	0.2158	L	0.50847	1.595	0.80722	D	1	D	0.56035	0.974	B	0.42361	0.385	T	0.57289	-0.7837	10	0.24483	T	0.36	.	19.0887	0.93217	0.0:1.0:0.0:0.0	.	1169	O75533	SF3B1_HUMAN	I	1169	ENSP00000335321:V1169I	ENSP00000335321:V1169I	V	-	1	0	SF3B1	197969059	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.534000	0.82004	2.826000	0.97356	0.655000	0.94253	GTA	.		0.323	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198260814	C	T	198260814	3	4	31	1	0	0	0	0	1	0	0	0	14181	536	19	1	421	1	SF3B1	2	198260814	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	21265519	198260814	44938559	13	2683											
PER2	8864	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	239176835	239176850	+	Splice_Site	DEL	GGACACTGCGGAGAAG	GGACACTGCGGAGAAG	-																															ttcattctcgtggcttttccGgacactgcggagaagagcca																								rs373179670|rs377264399|rs202102579|rs374332427		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	GGACACTGCGGAGAAG	GGACACTGCGGAGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:239176835_239176850delGGACACTGCGGAGAAG	ENST00000254657.3	-	8	1104_1108	c.825_829delCTTCTCCGCAGTGTCC	c.(823-831)agcttctcc>agcc	p.SFS275fs	PER2_ENST00000254658.3_Splice_Site_p.SFS275fs|PER2_ENST00000440245.1_Splice_Site_p.SFS275fs|PER2_ENST00000355768.2_Splice_Site_p.SFS275fs	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	275					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TGGCTTTTCCGGACACTGCGGAGAAGAGCCACGCTC	0.574																																					p.275_277del		.											.	PER2-154	0			c.825_829del						.																																			SO:0001630	splice_region_variant	8864	exon8			.	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.825-1CTTCTCCGCAGTGTCC>-	2.37:g.239176835_239176850delGGACACTGCGGAGAAG		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	129	35	NM_022817	0	0	0	0	0	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Frame_Shift_Del	DEL	ENST00000254657.3	37	CCDS2528.1																																																																																			.		0.574	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	Frame_Shift_Del	-	239176850	GGACACTGCGGAGAAG	-	239176835	8	5	31	1	0	1	0	1	0	0	1	0	11756	1115	39	0	3002	0	PER2	2	239176835	Splice_Site	DEL	GGACACTGCGGAGAAG	TCGA-AL-3472-01A-01D-1252-08	40916021	239176835	4022538	14	2684											
TRIM71	131405	hgsc.bcm.edu	37	chr3	32860208	32860208	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aacgcagcttcttcgcgctgCctcgactgccaggagcacct	7	8	10	16	4	1	0	0	0	1	0	3	2	1	1	3	1	5	4	3	1	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:32860208C>T	ENST00000383763.5	+	1	699	c.636C>T	c.(634-636)tgC>tgT	p.C212C		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	212					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTTCGCGCTGCCTCGACTGCC	0.726																																					p.C212C		.											.	TRIM71-92	0			c.C636T						.																																			SO:0001819	synonymous_variant	131405	exon1			GCGCTGCCTCGAC		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.636C>T	3.37:g.32860208C>T		Somatic	6	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_001039111	0	0	0	0	0		Silent	SNP	ENST00000383763.5	37	CCDS43060.1																																																																																			.		0.726	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		T	32860208	C	T	32860208	2	4	31	1	0	0	0	0	0	0	0	1	16577	747	26	2		2	TRIM71	3	32860208	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08		32860208	165162222	15	2685											
ITIH3	3699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52830615	52830615	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agacacggccaaggaggtttCctttgatgtggagctgccca	9	9	13	10	1	0	2	0	1	0	1	1	4	1	4	3	4	2	2	3	4	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:52830615C>T	ENST00000449956.2	+	3	239	c.233C>T	c.(232-234)tCc>tTc	p.S78F	ITIH3_ENST00000416872.2_Missense_Mutation_p.S78F	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	78	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		AAGGAGGTTTCCTTTGATGTG	0.562																																					p.S78F		.											.	ITIH3-93	0			c.C233T						.						76	82	80					3																	52830615		2122	4276	6398	SO:0001583	missense	3699	exon3			AGGTTTCCTTTGA		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"pre-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha-trypsin inhibitor heavy chain H3"	146650	"inter-alpha (globulin) inhibitor, H3 polypeptide", "inter-alpha (globulin) inhibitor H3"			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.233C>T	3.37:g.52830615C>T	ENSP00000415769:p.Ser78Phe	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	48	18	NM_002217	0	0	0	0	0	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	7.116	0.576936	0.13686	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	T;T	0.23552	1.9;1.9	4.43	2.45	0.29901	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.175288	0.50627	N	0.000112	T	0.10423	0.0255	N	0.10972	0.075	0.35532	D	0.802333	B;B	0.06786	0.001;0.001	B;B	0.13407	0.002;0.009	T	0.15694	-1.0428	10	0.17369	T	0.5	-12.815	4.7553	0.13080	0.0:0.6593:0.0:0.3407	.	78;78	E7ET33;Q06033	.;ITIH3_HUMAN	F	78;78;73;78;78	ENSP00000413922:S78F;ENSP00000415769:S78F	ENSP00000273291:S73F	S	+	2	0	ITIH3	52805655	0.000000	0.05858	0.973000	0.42090	0.946000	0.59487	-0.476000	0.06591	1.088000	0.41272	0.591000	0.81541	TCC	.		0.562	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52830615	C	T	52830615	3	4	31	1	0	0	0	0	1	0	0	0	7926	855	30	2	243	2	ITIH3	3	52830615	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	19970407	52830615	145191815	16	2686											
ZNF654	55279	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	88190087	88190087	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtataaaaaatcagtgaaaAgattaagatgtggcaaatgc	19	10	9	3	0	1	3	1	1	0	2	1	3	1	3	0	1	1	2	0	1	8	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:88190087A>T	ENST00000309495.5	+	1	1834	c.1627A>T	c.(1627-1629)Aga>Tga	p.R543*	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	543					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(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		ATCAGTGAAAAGATTAAGATG	0.383																																					p.R543X		.											.	ZNF654-69	0			c.A1627T						.						77	71	73					3																	88190087		1854	4098	5952	SO:0001587	stop_gained	55279	exon1			GTGAAAAGATTAA	AF543494	CCDS46874.1	3p11.1	2005-01-10			ENSG00000175105	ENSG00000175105			25612	protein-coding gene	gene with protein product							Standard	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	Q8IZM8	OTTHUMG00000159097	ENST00000309495.5:c.1627A>T	3.37:g.88190087A>T	ENSP00000312141:p.Arg543*	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	19	6	NM_018293	0	0	0	1	1	Q9H791|Q9NV14	Nonsense_Mutation	SNP	ENST00000309495.5	37	CCDS46874.1	.	.	.	.	.	.	.	.	.	.	a	39	7.456045	0.98296	.	.	ENSG00000175105	ENST00000309495	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7425	0.69467	1.0:0.0:0.0:0.0	.	.	.	.	X	543	.	ENSP00000312141:R543X	R	+	1	2	ZNF654	88272777	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.207000	0.72159	2.069000	0.61940	0.468000	0.43344	AGA	.		0.383	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2	NM_018293		T	88190087	A	T	88190087	4	4	31	1	0	0	0	0	0	1	0	0	18099	64	3	5	1629	5	ZNF654	3	88190087	Nonsense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	35359472	88190087	109832343	17	2687											
ASTE1	28990	hgsc.bcm.edu	37	chr3	130743394	130743394	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtcccaggattcggtggtGtctcctccctttagaactgg	7	12	11	11	1	1	1	0	0	1	1	5	2	3	2	3	4	1	0	3	4	3	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:130743394G>C	ENST00000264992.3	-	3	1198	c.757C>G	c.(757-759)Cac>Gac	p.H253D	ASTE1_ENST00000514044.1_Missense_Mutation_p.H253D|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000383366.4_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	253					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						ATTCGGTGGTGTCTCCTCCCT	0.448																																					p.H253D		.											.	ASTE1-90	0			c.C757G						.						70	66	67					3																	130743394		2203	4300	6503	SO:0001583	missense	28990	exon3			GGTGGTGTCTCCT	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.757C>G	3.37:g.130743394G>C	ENSP00000264992:p.His253Asp	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	44	3	NM_014065	0	0	4	4	0	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	37	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.403546	0.42613	.	.	ENSG00000034533	ENST00000514044;ENST00000264992;ENST00000446270	.	.	.	5.54	4.66	0.58398	.	0.361882	0.34906	N	0.003585	T	0.59810	0.2221	M	0.64997	1.995	0.35705	D	0.815896	P;P	0.38677	0.642;0.491	B;B	0.43225	0.412;0.322	T	0.69420	-0.5150	9	0.45353	T	0.12	-10.5342	13.084	0.59129	0.079:0.0:0.921:0.0	.	253;253	D6RG30;Q2TB18	.;ASTE1_HUMAN	D	253	.	ENSP00000264992:H253D	H	-	1	0	ASTE1	132226084	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.579000	0.46059	1.314000	0.45095	0.561000	0.74099	CAC	.		0.448	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		C	130743394	G	C	130743394	3	2	31	1	0	0	0	0	1	0	0	0	1063	1377	48	4	1298	4	ASTE1	3	130743394	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	42553307	130743394	67279036	18	2688											
SI	6476	hgsc.bcm.edu	37	chr3	164754251	164754251	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaatgcgactataagtcctAgaggattcttacggctgtta	11	13	9	8	2	1	1	0	0	1	1	2	3	2	2	1	2	2	2	1	2	6	7			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:164754251A>G	ENST00000264382.3	-	22	2503	c.2441T>C	c.(2440-2442)cTa>cCa	p.L814P		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	814	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TATAAGTCCTAGAGGATTCTT	0.343										HNSCC(35;0.089)																											p.L814P		.											.	SI-104	0			c.T2441C						.						92	94	93					3																	164754251		2203	4300	6503	SO:0001583	missense	6476	exon22			AGTCCTAGAGGAT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2441T>C	3.37:g.164754251A>G	ENSP00000264382:p.Leu814Pro	Somatic	227	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_001041	0	0	0	0	0	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.676143	0.47886	.	.	ENSG00000090402	ENST00000264382	D	0.90563	-2.69	4.52	4.52	0.55395	.	0.070268	0.64402	D	0.000018	D	0.95452	0.8523	M	0.87269	2.87	0.48632	D	0.999681	D	0.89917	1.0	D	0.97110	1.0	D	0.96051	0.9031	10	0.87932	D	0	.	13.2365	0.59972	1.0:0.0:0.0:0.0	.	814	P14410	SUIS_HUMAN	P	814	ENSP00000264382:L814P	ENSP00000264382:L814P	L	-	2	0	SI	166236945	0.998000	0.40836	0.325000	0.25375	0.453000	0.32348	7.680000	0.84062	2.010000	0.58986	0.528000	0.53228	CTA	.		0.343	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		G	164754251	A	G	164754251	3	3	31	1	0	0	0	0	1	0	0	0	14329	420	15	3	3150	3	SI	3	164754251	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	34010857	164754251	33268179	19	2689											
LYAR	55646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	4276342	4276342	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttttccttttcttctgcCgttcttcctttctttctctt	0	25	2	14	1	6	0	0	0	6	0	9	0	8	0	3	0	1	1	3	0	0	10			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:4276342C>T	ENST00000343470.4	-	7	824	c.584G>A	c.(583-585)cGg>cAg	p.R195Q	LYAR_ENST00000452476.1_Missense_Mutation_p.R195Q	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	195	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		tttcttctgccgttcttcctt	0.438																																					p.R195Q		.											.	LYAR-90	0			c.G584A						.						138	128	132					4																	4276342		2203	4300	6503	SO:0001583	missense	55646	exon7			TTCTGCCGTTCTT	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.584G>A	4.37:g.4276342C>T	ENSP00000345917:p.Arg195Gln	Somatic	256	0		WXS	Illumina HiSeq	Phase_I	301	137	NM_017816	0	0	2	5	3	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	37	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.089165	0.36855	.	.	ENSG00000145220	ENST00000343470;ENST00000452476	T;T	0.32753	1.44;1.44	5.19	5.19	0.71726	.	0.286976	0.36338	N	0.002645	T	0.30230	0.0758	M	0.72894	2.215	0.46222	D	0.998937	P	0.48503	0.911	B	0.31946	0.138	T	0.33523	-0.9865	10	0.44086	T	0.13	-12.7208	16.5728	0.84629	0.0:1.0:0.0:0.0	.	195	Q9NX58	LYAR_HUMAN	Q	195	ENSP00000345917:R195Q;ENSP00000397367:R195Q	ENSP00000345917:R195Q	R	-	2	0	LYAR	4327243	1.000000	0.71417	0.986000	0.45419	0.130000	0.20726	2.673000	0.46858	2.571000	0.86741	0.655000	0.94253	CGG	.		0.438	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		T	4276342	C	T	4276342	3	4	31	1	0	0	0	0	1	0	0	0	9128	652	23	1	571	1	LYAR	4	4276342	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		4276342	186877934	20	2690											
NSUN7	79730	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	40810405	40810405	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgctggatgggattgagttgGgtaaatcatcaaaacgggag	12	10	15	4	1	2	1	2	1	0	0	2	4	2	4	0	4	2	3	0	4	4	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:40810405G>C	ENST00000381782.2	+	12	2101	c.1606G>C	c.(1606-1608)Ggt>Cgt	p.G536R	NSUN7_ENST00000316607.5_3'UTR	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	536							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GATTGAGTTGGGTAAATCATC	0.428																																					p.G536R													.	NSUN7-90	0			c.G1606C						.						81	67	71					4																	40810405		692	1591	2283	SO:0001583	missense	79730	exon12			GAGTTGGGTAAAT	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.1606G>C	4.37:g.40810405G>C	ENSP00000371201:p.Gly536Arg	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	138	59	NM_024677	0	0	10	19	9	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	37	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783124	0.49891	.	.	ENSG00000179299	ENST00000381782	T	0.14640	2.49	5.6	3.87	0.44632	.	0.804730	0.11512	N	0.556627	T	0.11623	0.0283	L	0.47716	1.5	0.09310	N	0.999999	P	0.48089	0.905	B	0.39258	0.295	T	0.16837	-1.0389	10	0.31617	T	0.26	-7.9775	6.9881	0.24739	0.1529:0.1439:0.7032:0.0	.	536	Q8NE18	NSUN7_HUMAN	R	536	ENSP00000371201:G536R	ENSP00000371201:G536R	G	+	1	0	NSUN7	40505162	0.935000	0.31712	0.983000	0.44433	0.993000	0.82548	2.018000	0.40991	1.364000	0.46038	0.591000	0.81541	GGT	.		0.428	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		C	40810405	G	C	40810405	3	2	31	1	0	0	0	0	1	0	0	0	10709	1232	43	4	1648	4	NSUN7	4	40810405	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	36534063	40810405	150343871	21	2691											
GUF1	60558	ucsc.edu	37	chr4	44692823	44692823	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatttggagccagttgttttGggcactattatcacaccaga	10	14	9	8	0	1	1	1	0	0	1	1	2	1	2	2	2	1	3	2	2	3	7			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:44692823G>A	ENST00000281543.5	+	12	1619	c.1425G>A	c.(1423-1425)ttG>ttA	p.L475L	GUF1_ENST00000506793.1_3'UTR	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						CAGTTGTTTTGGGCACTATTA	0.308																																					p.L475L													.	GUF1-91	0			c.G1425A						.						79	82	81					4																	44692823		2203	4295	6498	SO:0001819	synonymous_variant	60558	exon12			TGTTTTGGGCACT		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.1425G>A	4.37:g.44692823G>A		Somatic	270	0		WXS	Illumina HiSeq		34	4	NM_021927	0	0	0	0	0		Silent	SNP	ENST00000281543.5	37	CCDS3468.1																																																																																			.		0.308	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		A	44692823	G	A	44692823	2	1	31	1	0	0	0	0	0	0	0	1	6920	1339	47	2		2	GUF1	4	44692823	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08	3882418	44692823	146461453	22	2692											
INTU	27152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	128564929	128564929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcaataaaaaaaatagcAatgacaatggaccagtatcc	19	7	7	8	0	0	1	0	1	0	0	1	2	1	2	2	1	2	4	2	1	9	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:128564929A>G	ENST00000335251.6	+	2	503	c.400A>G	c.(400-402)Aat>Gat	p.N134D	INTU_ENST00000296461.5_Missense_Mutation_p.N134D	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	134					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						AAAAAATAGCAATGACAATGG	0.358																																					p.N134D		.											.	INTU-91	0			c.A400G						.						69	71	71					4																	128564929		2203	4300	6503	SO:0001583	missense	27152	exon2			AATAGCAATGACA	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.400A>G	4.37:g.128564929A>G	ENSP00000334003:p.Asn134Asp	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_015693	0	0	0	1	1	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	A	1.750	-0.489422	0.04352	.	.	ENSG00000164066	ENST00000504491;ENST00000335251;ENST00000296461	T	0.44083	0.93	5.1	2.61	0.31194	.	0.890844	0.09986	N	0.730400	T	0.24736	0.0600	N	0.22421	0.69	0.22127	N	0.999348	B	0.06786	0.001	B	0.04013	0.001	T	0.25152	-1.0140	10	0.25751	T	0.34	-1.097	2.9593	0.05887	0.5157:0.2769:0.0738:0.1336	.	134	Q9ULD6	PDZD6_HUMAN	D	115;134;134	ENSP00000296461:N134D	ENSP00000296461:N134D	N	+	1	0	INTU	128784379	0.341000	0.24801	0.129000	0.21949	0.028000	0.11728	2.259000	0.43259	0.393000	0.25203	0.533000	0.62120	AAT	.		0.358	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		G	128564929	A	G	128564929	3	3	31	1	0	0	0	0	1	0	0	0	7807	130	5	3	406	3	INTU	4	128564929	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	83872106	128564929	62589347	23	2693											
CARD6	84674	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr5	40853728	40853728	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcagagcagaggcctaagtGgttccatcctttgccttttc	7	13	10	11	0	1	2	1	0	0	2	4	2	3	2	4	2	2	2	4	2	1	5			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr5:40853728G>T	ENST00000254691.5	+	3	2493	c.2294G>T	c.(2293-2295)tGg>tTg	p.W765L	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	765					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						AGGCCTAAGTGGTTCCATCCT	0.483																																					p.W765L		.											.	CARD6-230	0			c.G2294T						.						90	102	97					5																	40853728		2203	4300	6503	SO:0001583	missense	84674	exon3			CTAAGTGGTTCCA	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.2294G>T	5.37:g.40853728G>T	ENSP00000254691:p.Trp765Leu	Somatic	351	2		WXS	Illumina HiSeq	Phase_I	265	108	NM_032587	0	0	0	0	0	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	G	8.463	0.855682	0.17106	.	.	ENSG00000132357	ENST00000254691	T	0.12984	2.63	5.15	3.26	0.37387	.	0.373374	0.23666	N	0.045767	T	0.11239	0.0274	L	0.29908	0.895	0.80722	D	1	B	0.15141	0.012	B	0.13407	0.009	T	0.08472	-1.0720	10	0.72032	D	0.01	-0.0969	12.1755	0.54184	0.0:0.0:0.6929:0.3071	.	765	Q9BX69	CARD6_HUMAN	L	765	ENSP00000254691:W765L	ENSP00000254691:W765L	W	+	2	0	CARD6	40889485	0.972000	0.33761	0.945000	0.38365	0.313000	0.28021	1.591000	0.36665	1.369000	0.46134	0.561000	0.74099	TGG	.		0.483	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			T	40853728	G	T	40853728	3	4	31	1	0	0	0	0	1	0	0	0	2656	1357	47	4	2304	4	CARD6	5	40853728	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		40853728	140061532	24	2694											
PSD2	84249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	139193773	139193773	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaccccagcctgaaggaTggcctgtcagactcagactc	10	7	11	13	0	2	4	2	2	0	2	3	5	2	5	4	2	1	0	4	2	1	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr5:139193773T>C	ENST00000274710.3	+	4	1045	c.840T>C	c.(838-840)gaT>gaC	p.D280D		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	280	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTGAAGGATGGCCTGTCAG	0.632																																					p.D280D		.											.	PSD2-91	0			c.T840C						.						108	101	103					5																	139193773		2203	4300	6503	SO:0001819	synonymous_variant	84249	exon4			GAAGGATGGCCTG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.840T>C	5.37:g.139193773T>C		Somatic	329	0		WXS	Illumina HiSeq	Phase_I	577	261	NM_032289	0	0	0	0	0	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	37	CCDS4216.1																																																																																			.		0.632	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		C	139193773	T	C	139193773	2	2	31	1	0	0	0	0	0	0	0	1	12676	1461	51	3		3	PSD2	5	139193773	Silent	SNP	T	TCGA-AL-3472-01A-01D-1252-08	98340045	139193773	41721487	25	2695											
SLC25A2	83884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140683030	140683030	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccatttcatacatggtctGtagccggcacttcacaagct	9	12	7	13	1	3	0	2	0	1	0	4	0	4	0	2	2	3	3	2	2	3	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr5:140683030G>A	ENST00000239451.4	-	1	582	c.403C>T	c.(403-405)Cag>Tag	p.Q135*		NM_031947.2	NP_114153.1	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2	135					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)	TACATGGTCTGTAGCCGGCAC	0.522																																					p.Q135X		.											.	SLC25A2-91	0			c.C403T						.						100	108	105					5																	140683030		2203	4300	6503	SO:0001587	stop_gained	83884	exon1			TGGTCTGTAGCCG	AF332005	CCDS4258.1	5q31.3	2013-05-22			ENSG00000120329	ENSG00000120329		"Solute carriers"	22921	protein-coding gene	gene with protein product		608157				11004451	Standard	NM_031947		Approved	ORNT2	uc003ljf.3	Q9BXI2	OTTHUMG00000129604	ENST00000239451.4:c.403C>T	5.37:g.140683030G>A	ENSP00000239451:p.Gln135*	Somatic	353	1		WXS	Illumina HiSeq	Phase_I	503	204	NM_031947	0	0	0	1	1	Q496C1|Q6XUI0|Q8NFZ2	Nonsense_Mutation	SNP	ENST00000239451.4	37	CCDS4258.1	.	.	.	.	.	.	.	.	.	.	G	33	5.250551	0.95305	.	.	ENSG00000120329	ENST00000239451	.	.	.	3.78	3.78	0.43462	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-5.487	13.9383	0.64039	0.0:0.0:1.0:0.0	.	.	.	.	X	135	.	ENSP00000239451:Q135X	Q	-	1	0	SLC25A2	140663214	1.000000	0.71417	0.982000	0.44146	0.942000	0.58702	8.721000	0.91446	2.424000	0.82194	0.650000	0.86243	CAG	.		0.522	SLC25A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251799.2	NM_031947		A	140683030	G	A	140683030	4	1	31	1	0	0	0	0	0	1	0	0	14514	1386	48	2	506	2	SLC25A2	5	140683030	Nonsense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	1489257	140683030	40232230	26	2696											
C6orf195	154386	broad.mit.edu	37	chr6	2623877	2623877	+	Frame_Shift_Del	DEL	A	A	-																															ccgacaaggccggacccgggAggggagaggagcctgtagca																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:2623877delA	ENST00000296847.3	-	3	703	c.180delT	c.(178-180)cctfs	p.P61fs		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	61										cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				CGGACCCGGGAGGGGAGAGGA	0.622																																					p.P60fs													.	C6orf195-90	0			c.180delT						.						61	70	67					6																	2623877		2003	4159	6162	SO:0001589	frameshift_variant	154386	exon3			CCCGGGAGGGGAG	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.180delT	6.37:g.2623877delA	ENSP00000296847:p.Pro61fs	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	300	7	NM_152554	0	0	0	0	0	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Frame_Shift_Del	DEL	ENST00000296847.3	37	CCDS43416.1																																																																																			.		0.622	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554		-	2623877	A	-	2623877	7	5	31	1	0	1	0	1	0	0	0	0	2356	291	11	0	207	0	C6orf195	6	2623877	Frame_Shift_Del	DEL	A	TCGA-AL-3472-01A-01D-1252-08		2623877	168491190	27	2697											
SLC22A23	63027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	3410472	3410472	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcaaaatccttcaaagAacctgagtgtgctgaacatt	14	9	8	10	0	1	3	1	2	0	1	2	3	2	3	3	1	3	2	3	1	5	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:3410472A>T	ENST00000406686.3	-	3	862	c.863T>A	c.(862-864)tTc>tAc	p.F288Y	SLC22A23_ENST00000490273.1_Missense_Mutation_p.F7Y|SLC22A23_ENST00000380302.4_Missense_Mutation_p.F7Y|SLC22A23_ENST00000436008.2_Missense_Mutation_p.F288Y|SLC22A23_ENST00000380298.2_Missense_Mutation_p.F288Y	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	288					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				TCCTTCAAAGAACCTGAGTGT	0.448																																					p.F288Y		.											.	SLC22A23-23	0			c.T863A						.						112	96	101					6																	3410472		2203	4300	6503	SO:0001583	missense	63027	exon3			TCAAAGAACCTGA	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"Solute carriers"	21106	protein-coding gene	gene with protein product		611697	"chromosome 6 open reading frame 85"	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.863T>A	6.37:g.3410472A>T	ENSP00000385028:p.Phe288Tyr	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	64	61	NM_015482	0	0	0	0	0	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	37	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.980895	0.92982	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000380302;ENST00000490273;ENST00000485307;ENST00000467177;ENST00000380298	T;T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0;0.0	5.17	5.17	0.71159	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.71239	0.3316	M	0.64997	1.995	0.52501	D	0.999957	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.76110	-0.3079	10	0.87932	D	0	-30.1819	15.0144	0.71573	1.0:0.0:0.0:0.0	.	288;288	C9J4Z0;A1A5C7	.;S22AN_HUMAN	Y	288;288;7;7;116;114;288	ENSP00000410245:F288Y;ENSP00000385028:F288Y;ENSP00000369657:F7Y;ENSP00000419463:F7Y;ENSP00000418134:F116Y;ENSP00000418985:F114Y;ENSP00000369653:F288Y	ENSP00000369653:F288Y	F	-	2	0	SLC22A23	3355471	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.770000	0.91746	1.960000	0.56953	0.460000	0.39030	TTC	.		0.448	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		T	3410472	A	T	3410472	3	4	31	1	0	0	0	0	1	0	0	0	14484	246	9	5	1229	5	SLC22A23	6	3410472	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	786595	3410472	167704595	28	2698											
RREB1	6239	hgsc.bcm.edu	37	chr6	7246994	7246994	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcgacggcgaggcaggCgccgggggcgcggcctcgca	5	1	22	13	8	0	0	0	0	0	0	1	3	0	0	2	7	0	2	2	7	0	0	rs187908583	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:7246994C>T	ENST00000349384.6	+	11	4460	c.4146C>T	c.(4144-4146)ggC>ggT	p.G1382G	RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379938.2_Silent_p.G1437G|RREB1_ENST00000379933.3_Silent_p.G1382G	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1382					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GCGAGGCAGGCGCCGGGGGCG	0.692													C|||	33	0.00658946	0.025	0	5008	,	,		11874	0		0	False		,,,				2504	0				p.G1437G		.											.	RREB1-144	0			c.C4311T						.	C	,,,	60,4166		0,60,2053	11	13	13		4146,4311,,4146	-3.5	0	6		13	1,8303		0,1,4151	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	0,61,6204	TT,TC,CC		0.012,1.4198,0.4868	,,,	1382/1688,1437/1743,,1382/1688	7246994	61,12469	2113	4152	6265	SO:0001819	synonymous_variant	6239	exon12			GGCAGGCGCCGGG	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"Zinc fingers, C2H2-type"	10449	protein-coding gene	gene with protein product	"hindsight homolog (drosophila)"	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4146C>T	6.37:g.7246994C>T		Somatic	10	1		WXS	Illumina HiSeq	Phase_I	17	15	NM_001003699	0	0	0	3	3	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			C|0.993;T|0.007		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7246994	C	T	7246994	2	4	31	1	0	0	0	0	0	0	0	1	13711	755	27	1		1	RREB1	6	7246994	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	3836522	7246994	163868073	29	2699											
TRIM15	89870	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	30140094	30140094	+	Frame_Shift_Del	DEL	A	A	-																															tccctttctttgccgtctggAaaaaaggttcctgccttacg																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:30140094delA	ENST00000376694.4	+	7	1835	c.1366delA	c.(1366-1368)aaafs	p.K457fs	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	457	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						TGCCGTCTGGAAAAAAGGTTC	0.637																																					p.K456fs		.											.	TRIM15-90	0			c.1366delA						.						36	45	42					6																	30140094		1506	2707	4213	SO:0001589	frameshift_variant	89870	exon7			.	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16284	protein-coding gene	gene with protein product			"zinc finger protein 178", "tripartite motif-containing 15"	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.1366delA	6.37:g.30140094delA	ENSP00000365884:p.Lys457fs	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	184	81	NM_033229	0	0	0	0	0	A2BEC9|O95604|Q8IUX9|Q9C018	Frame_Shift_Del	DEL	ENST00000376694.4	37	CCDS4677.1																																																																																			.		0.637	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229		-	30140094	A	-	30140094	7	5	31	1	0	1	0	1	0	0	0	0	16523	247	9	0	1392	0	TRIM15	6	30140094	Frame_Shift_Del	DEL	A	TCGA-AL-3472-01A-01D-1252-08	22893100	30140094	140974973	30	2700											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51712728	51712728	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatctgtgtgcaccagcagtAggtaattaccaggagcaaag	14	8	11	8	0	1	0	0	0	1	0	1	1	1	1	2	2	4	5	2	2	5	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:51712728A>G	ENST00000371117.3	-	50	8227	c.7952T>C	c.(7951-7953)cTa>cCa	p.L2651P	PKHD1_ENST00000340994.4_Missense_Mutation_p.L2651P	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2651					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CACCAGCAGTAGGTAATTACC	0.458																																					p.L2651P		.											.	PKHD1-603	0			c.T7952C						.						127	126	127					6																	51712728		2203	4300	6503	SO:0001583	missense	5314	exon50			AGCAGTAGGTAAT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.7952T>C	6.37:g.51712728A>G	ENSP00000360158:p.Leu2651Pro	Somatic	267	0		WXS	Illumina HiSeq	Phase_I	81	72	NM_170724	0	0	0	26	26	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.784987	0.49997	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.89123	-2.28;-2.47	5.47	5.47	0.80525	.	0.128004	0.36409	N	0.002604	D	0.91606	0.7348	L	0.59436	1.845	0.58432	D	0.999997	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.73708	0.98;0.965;0.981	D	0.92508	0.6014	10	0.62326	D	0.03	.	15.0183	0.71605	1.0:0.0:0.0:0.0	.	2651;2651;2651	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	P	2651	ENSP00000360158:L2651P;ENSP00000341097:L2651P	ENSP00000341097:L2651P	L	-	2	0	PKHD1	51820687	1.000000	0.71417	0.992000	0.48379	0.153000	0.21895	6.098000	0.71458	2.196000	0.70406	0.528000	0.53228	CTA	.		0.458	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51712728	A	G	51712728	3	3	31	1	0	0	0	0	1	0	0	0	11997	420	15	3	4383	3	PKHD1	6	51712728	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	21572634	51712728	119402339	31	2701											
AHI1	54806	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	135732541	135732541	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcgttgaagaactttcaGtgtggacaaattcatcaatc	12	14	7	8	1	4	2	3	1	1	1	6	3	4	3	0	1	1	1	0	1	4	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:135732541G>C	ENST00000367800.4	-	19	3122	c.2906C>G	c.(2905-2907)aCt>aGt	p.T969S	AHI1_ENST00000327035.6_Missense_Mutation_p.T969S|AHI1_ENST00000417892.2_Missense_Mutation_p.T323S|AHI1_ENST00000457866.2_Missense_Mutation_p.T969S	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	969					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		AGAACTTTCAGTGTGGACAAA	0.373																																					p.T969S		.											.	AHI1-227	0			c.C2906G						.						143	137	139					6																	135732541		1847	4102	5949	SO:0001583	missense	54806	exon20			CTTTCAGTGTGGA	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.2906C>G	6.37:g.135732541G>C	ENSP00000356774:p.Thr969Ser	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	33	27	NM_001134832	0	0	2	5	3	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.95|12.95	2.090823|2.090823	0.36855|0.36855	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367799;ENST00000529865|ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602;ENST00000327035;ENST00000367801	.|T;T;T;T;T	.|0.37411	.|1.2;1.2;1.2;1.2;1.2	5.69|5.69	2.9|2.9	0.33743|0.33743	.|.	.|0.402955	.|0.30830	.|N	.|0.008787	T|T	0.13114|0.13114	0.0318|0.0318	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P;P;B	.|0.40431	.|0.717;0.595;0.451	.|B;B;B	.|0.41271	.|0.352;0.192;0.112	T|T	0.03662|0.03662	-1.1015|-1.1015	5|10	.|0.54805	.|T	.|0.06	-12.9903|-12.9903	9.4417|9.4417	0.38673|0.38673	0.0:0.2946:0.5522:0.1532|0.0:0.2946:0.5522:0.1532	.|.	.|969;969;969	.|Q8N157-2;Q8N157;Q4FD35	.|.;AHI1_HUMAN;.	V|S	469;36|969;969;323;969;969;969	.|ENSP00000356774:T969S;ENSP00000388650:T969S;ENSP00000416867:T323S;ENSP00000265602:T969S;ENSP00000322478:T969S	.|ENSP00000265602:T969S	L|T	-|-	1|2	2|0	AHI1|AHI1	135774234|135774234	0.951000|0.951000	0.32395|0.32395	0.977000|0.977000	0.42913|0.42913	0.960000|0.960000	0.62799|0.62799	0.749000|0.749000	0.26320|0.26320	0.311000|0.311000	0.23014|0.23014	-0.127000|-0.127000	0.14921|0.14921	CTG|ACT	.		0.373	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135732541	G	C	135732541	3	2	31	1	0	0	0	0	1	0	0	0	413	1029	36	4	777	4	AHI1	6	135732541	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	84019813	135732541	35382526	32	2702											
RADIL	55698	hgsc.bcm.edu;broad.mit.edu	37	chr7	4876021	4876021	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccctgcagaaggagcaGatgcggggactggtacagcg	10	5	17	9	2	0	2	0	0	0	2	0	4	0	4	1	4	6	4	1	4	3	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr7:4876021G>T	ENST00000399583.3	-	3	938	c.751C>A	c.(751-753)Ctg>Atg	p.L251M	RADIL_ENST00000536091.1_Missense_Mutation_p.L251M|RADIL_ENST00000538469.1_Missense_Mutation_p.L11M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	251					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		AGAAGGAGCAGATGCGGGGAC	0.701																																					p.L251M		.											.	RADIL-994	0			c.C751A						.						16	23	20					7																	4876021		2086	4206	6292	SO:0001583	missense	55698	exon3			GGAGCAGATGCGG	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.751C>A	7.37:g.4876021G>T	ENSP00000382492:p.Leu251Met	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	29	8	NM_018059	0	0	0	1	1	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.993465	0.35131	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000538469	T;T;T	0.06849	3.25;3.25;3.25	4.85	3.96	0.45880	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.000000	0.64402	D	0.000002	T	0.29914	0.0748	M	0.82630	2.6	0.35445	D	0.795246	D	0.89917	1.0	D	0.69307	0.963	T	0.43750	-0.9372	10	0.62326	D	0.03	-21.7944	13.6214	0.62138	0.0828:0.0:0.9172:0.0	.	251	Q96JH8	RADIL_HUMAN	M	251;225;251;11	ENSP00000382492:L251M;ENSP00000442533:L251M;ENSP00000442966:L11M	ENSP00000320946:L225M	L	-	1	2	RADIL	4842547	1.000000	0.71417	0.993000	0.49108	0.126000	0.20510	3.872000	0.56085	0.473000	0.27368	-1.598000	0.00824	CTG	.		0.701	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4876021	G	T	4876021	3	4	31	1	0	0	0	0	1	0	0	0	13029	933	33	4	2528	4	RADIL	7	4876021	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		4876021	154262642	33	2703											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116415115	116415115	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcagtgcagcatgtagTgattgggcccagtagcctga	9	8	14	10	0	0	2	0	2	0	0	0	2	0	2	3	2	3	5	3	2	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr7:116415115T>A	ENST00000318493.6	+	15	3450	c.3263T>A	c.(3262-3264)gTg>gAg	p.V1088E	MET_ENST00000397752.3_Missense_Mutation_p.V1070E|MET_ENST00000539704.1_5'Flank			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V1088E(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CAGCATGTAGTGATTGGGCCC	0.433			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1088E		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.T3263A						.						174	172	172					7																	116415115		2077	4220	6297	SO:0001583	missense	4233	exon15	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATGTAGTGATTGG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3263T>A	7.37:g.116415115T>A	ENSP00000317272:p.Val1088Glu	Somatic	316	2		WXS	Illumina HiSeq	Phase_I	283	165	NM_001127500	0	0	1	4	3	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.885631	0.91814	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000454623	T;T	0.73681	-0.77;-0.77	5.62	5.62	0.85841	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.84469	0.5479	M	0.62723	1.935	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.80764	0.994;0.989	D	0.86091	0.1550	10	0.87932	D	0	-15.0307	16.1067	0.81230	0.0:0.0:0.0:1.0	.	1088;1070	P08581-2;P08581	.;MET_HUMAN	E	1070;1088;155	ENSP00000380860:V1070E;ENSP00000317272:V1088E	ENSP00000317272:V1088E	V	+	2	0	MET	116202351	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.310000	0.78947	2.255000	0.74692	0.533000	0.62120	GTG	.		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116415115	T	A	116415115	3	1	31	1	0	0	0	0	1	0	0	0	9510	1696	59	5	3317	5	MET	7	116415115	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08	111539094	116415115	42723548	34	2704											
CALD1	800	hgsc.bcm.edu	37	chr7	134618593	134618593	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcagaggagaggcagaGgataaaagaggaagagaaaa	20	1	17	3	0	0	5	0	0	0	5	0	9	0	7	0	5	1	3	0	5	5	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr7:134618593G>C	ENST00000361675.2	+	5	1302	c.1073G>C	c.(1072-1074)aGg>aCg	p.R358T	CALD1_ENST00000361901.2_Intron|CALD1_ENST00000393118.2_Intron|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000361388.2_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000422748.1_Intron			Q05682	CALD1_HUMAN	caldesmon 1	358	3 X 14 AA tandem repeats of E-E-E-K-R-A- A-E-E-R-Q-R-I-K.				cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						gagaggcagaggataaaagag	0.527																																					p.R358T		.											.	CALD1-226	0			c.G1073C						.						135	153	147					7																	134618593		2200	4297	6497	SO:0001583	missense	800	exon5			GGCAGAGGATAAA	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1073G>C	7.37:g.134618593G>C	ENSP00000354826:p.Arg358Thr	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_033138	0	0	3	3	0	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	G	5.678	0.309637	0.10733	.	.	ENSG00000122786	ENST00000361675	T	0.42131	0.98	3.29	2.37	0.29283	.	0.752593	0.11286	U	0.579834	T	0.36138	0.0956	N	0.25647	0.755	0.80722	D	1	P	0.36010	0.532	P	0.45449	0.481	T	0.10543	-1.0625	9	.	.	.	-4.7522	8.5775	0.33607	0.1181:0.0:0.8819:0.0	.	358	Q05682	CALD1_HUMAN	T	358	ENSP00000354826:R358T	.	R	+	2	0	CALD1	134269133	0.231000	0.23751	0.011000	0.14972	0.046000	0.14306	0.262000	0.18460	1.390000	0.46547	0.457000	0.33378	AGG	.		0.527	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		C	134618593	G	C	134618593	3	2	31	1	0	0	0	0	1	0	0	0	2587	1000	35	4	1140	4	CALD1	7	134618593	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	18203478	134618593	24520070	35	2705											
FLJ43860	389690	broad.mit.edu	37	chr8	142480802	142480802	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttccagagtggggctccGtccgaatgggcctgggagag	6	8	17	10	2	0	2	0	0	0	2	3	4	3	2	4	4	0	2	4	4	1	1	rs372465445	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr8:142480802G>A	ENST00000430863.1	-	0	2147					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GTGGGGCTCCGTCCGAATGGG	0.632													G|||	2	0.000399361	8e-04	0	5008	,	,		16121	0		0	False		,,,				2504	0.001				.													.	.	0			.						.	G		0,3804		0,0,1902	30	33	32		2067	-4.5	0	8		32	1,8181		0,1,4090	no	coding-synonymous	FLJ43860	NM_207414.2		0,1,5992	AA,AG,GG		0.0122,0.0,0.0083		689/1319	142480802	1,11985	1902	4091	5993			389690	.			GGCTCCGTCCGAA			8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142480802G>A		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	9	4	.	0	0	0	0	0		Silent	SNP	ENST00000430863.1	37																																																																																				.		0.632	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		A	142480802	G	A	142480802	1	1	31	0	1	0	0	0	0	0	0	0	5949	1136	40	1		1	FLJ43860	8	142480802	RNA	SNP	G	TCGA-AL-3472-01A-01D-1252-08		142480802	3883220	36	2706											
DMRT2	10655	hgsc.bcm.edu	37	chr9	1051930	1051930	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtccccgagagcgctgcaCtcccgcgggcggcggcgcgg	3	3	18	17	9	0	1	0	0	0	1	2	2	2	1	3	5	2	2	3	5	0	0	rs112585712	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:1051930C>G	ENST00000358146.2	+	1	317	c.317C>G	c.(316-318)aCt>aGt	p.T106S	DMRT2_ENST00000302441.6_Missense_Mutation_p.T106S|DMRT2_ENST00000412350.2_Missense_Mutation_p.T106S|DMRT2_ENST00000382255.3_Missense_Mutation_p.T106S|DMRT2_ENST00000259622.6_Missense_Mutation_p.T106S|DMRT2_ENST00000382251.3_Missense_Mutation_p.T106S			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	106					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		GAGCGCTGCACTCCCGCGGGC	0.786													C|||	131	0.0261581	0.0015	0.0187	5008	,	,		9377	0.006		0.0537	False		,,,				2504	0.0573				p.T106S		.											.	DMRT2-514	0			c.C317G						.						1	1	1					9																	1051930		747	1711	2458	SO:0001583	missense	10655	exon2			GCTGCACTCCCGC	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"terra-like protein"	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.317C>G	9.37:g.1051930C>G	ENSP00000350865:p.Thr106Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_006557	0	0	0	0	0	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	52	0.023809523809523808	4	0.008130081300813009	8	0.022099447513812154	1	0.0017482517482517483	39	0.051451187335092345	C	8.378	0.836916	0.16891	.	.	ENSG00000173253	ENST00000382255;ENST00000382251;ENST00000412350;ENST00000302441;ENST00000358146;ENST00000259622	T;T;T;T;T;T	0.39997	1.05;2.04;1.05;2.04;2.04;1.05	3.82	0.583	0.17417	.	1.094080	0.07099	N	0.840084	T	0.03739	0.0106	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.14420	-1.0473	10	0.10636	T	0.68	0.1877	8.3816	0.32474	0.0:0.6844:0.1394:0.1761	.	106;106	Q05C20;Q9Y5R5	.;DMRT2_HUMAN	S	106	ENSP00000371690:T106S;ENSP00000371686:T106S;ENSP00000397494:T106S;ENSP00000305785:T106S;ENSP00000350865:T106S;ENSP00000259622:T106S	ENSP00000259622:T106S	T	+	2	0	DMRT2	1041930	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	-0.165000	0.09968	0.267000	0.21916	0.491000	0.48974	ACT	C|0.976;G|0.024		0.786	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		G	1051930	C	G	1051930	3	3	31	1	0	0	0	0	1	0	0	0	4597	565	20	4	319	4	DMRT2	9	1051930	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		1051930	140161501	37	2707											
KLHL9	55958	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	21334413	21334413	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacacagttatccaaagagActcctgatataagaaatact	18	9	5	9	0	0	3	0	1	0	2	2	4	2	3	2	0	2	1	2	0	7	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:21334413A>T	ENST00000359039.4	-	1	966	c.446T>A	c.(445-447)gTc>gAc	p.V149D	KLHL9_ENST00000537938.1_Missense_Mutation_p.V81D			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	149					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)				endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		ATCCAAAGAGACTCCTGATAT	0.338																																					p.V149D		.											.	KLHL9-94	0			c.T446A						.						39	43	42					9																	21334413		2203	4297	6500	SO:0001583	missense	55958	exon1			AAAGAGACTCCTG	AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.446T>A	9.37:g.21334413A>T	ENSP00000351933:p.Val149Asp	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	133	61	NM_018847	0	0	2	2	0	Q8TCQ2	Missense_Mutation	SNP	ENST00000359039.4	37	CCDS6503.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.455753	0.43634	.	.	ENSG00000198642	ENST00000359039;ENST00000537938	T;T	0.73152	-0.7;-0.72	5.21	5.21	0.72293	BTB/POZ-like (1);BTB/POZ fold (1);	0.136382	0.48286	D	0.000181	T	0.72236	0.3435	M	0.68317	2.08	0.80722	D	1	B	0.28933	0.228	B	0.36289	0.221	T	0.74423	-0.3670	10	0.87932	D	0	.	13.3494	0.60593	1.0:0.0:0.0:0.0	.	149	Q9P2J3	KLHL9_HUMAN	D	149;81	ENSP00000351933:V149D;ENSP00000437733:V81D	ENSP00000351933:V149D	V	-	2	0	KLHL9	21324413	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.891000	0.92485	2.111000	0.64477	0.528000	0.53228	GTC	.		0.338	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		T	21334413	A	T	21334413	3	4	31	1	0	0	0	0	1	0	0	0	8417	275	10	5	1411	5	KLHL9	9	21334413	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	20282483	21334413	119879018	38	2708											
PSAT1	29968	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	80942983	80942984	+	Frame_Shift_Ins	INS	-	-	A																															cagttgtccagtggagccccINSaaaatagaagcaagatgaat																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:80942983_80942984insA	ENST00000376588.3	+	8	954_955	c.886_887insA	c.(886-888)caafs	p.Q296fs	PSAT1_ENST00000347159.2_Intron	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	296					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						AGTGGAGCCCCAAAATAGAAGC	0.337																																					p.Q296fs	Colon(34;187 791 10662 18313 37609)	.											.	PSAT1-91	0			c.886_887insA						.																																			SO:0001589	frameshift_variant	29968	exon8			.	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.890dupA	9.37:g.80942987_80942987dupA	ENSP00000365773:p.Gln296fs	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	44	21	NM_058179	0	0	0	0	0	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Frame_Shift_Ins	INS	ENST00000376588.3	37	CCDS6660.1																																																																																			.		0.337	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		A	80942984	-	A	80942983	7	5	31	1	0	1	1	0	0	0	0	0	12673	595	21	0	916	0	PSAT1	9	80942983	Frame_Shift_Ins	INS	-	TCGA-AL-3472-01A-01D-1252-08	59608570	80942983	60270448	39	2709											
RPL12	6136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130213582	130213582	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actttgatctcgttggggtcGaacttcggcggcatggtgga	6	12	15	8	4	1	1	0	1	1	0	4	3	1	2	0	6	1	2	0	6	1	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:130213582G>A	ENST00000361436.5	-	1	102	c.15C>T	c.(13-15)ttC>ttT	p.F5F	LRSAM1_ENST00000373322.1_5'Flank|LRSAM1_ENST00000373324.4_5'Flank|LRSAM1_ENST00000300417.6_5'Flank|RPL12_ENST00000536368.1_Silent_p.F5F|RPL12_ENST00000497322.1_5'UTR|LRSAM1_ENST00000323301.4_5'Flank|SNORA65_ENST00000364432.1_RNA	NM_000976.3	NP_000967.1	P30050	RL12_HUMAN	ribosomal protein L12	5					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)	4						CGTTGGGGTCGAACTTCGGCG	0.652																																					p.F5F		.											.	RPL12-90	0			c.C15T						.						33	36	35					9																	130213582		2199	4296	6495	SO:0001819	synonymous_variant	6136	exon1			GGGGTCGAACTTC		CCDS6872.1	9q34	2011-04-06			ENSG00000197958	ENSG00000197958		"L ribosomal proteins"	10302	protein-coding gene	gene with protein product		180475				8441690	Standard	NM_000976		Approved	L12	uc004bqy.2	P30050	OTTHUMG00000020704	ENST00000361436.5:c.15C>T	9.37:g.130213582G>A		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	171	68	NM_000976	0	0	750	1364	614	Q5VVV2|Q6PB27	Silent	SNP	ENST00000361436.5	37	CCDS6872.1																																																																																			.		0.652	RPL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054189.1			A	130213582	G	A	130213582	2	1	31	1	0	0	0	0	0	0	0	1	13590	1049	37	1		1	RPL12	9	130213582	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08	49270599	130213582	10999849	40	2710											
AKR1E2	83592	hgsc.bcm.edu	37	chr10	4877871	4877871	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccttcttcgcagcctcCtcatccagaatggatcatga	8	12	6	15	1	4	2	2	1	2	1	8	3	6	3	4	1	1	1	4	1	1	2	rs149822509	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr10:4877871C>A	ENST00000298375.7	+	4	400	c.329C>A	c.(328-330)cCt>cAt	p.P110H	AKR1E2_ENST00000334019.4_Missense_Mutation_p.P110H|AKR1E2_ENST00000525281.1_3'UTR|AKR1E2_ENST00000345253.5_Missense_Mutation_p.P110H|AKR1E2_ENST00000532248.1_Missense_Mutation_p.P110H	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	110						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						TCGCAGCCTCCTCATCCAGAA	0.483																																					p.P110H	NSCLC(43;343 1097 20371 28813 45509)	.											.	AKR1E2-68	0			c.C329A						.						82	68	73					10																	4877871		2203	4300	6503	SO:0001583	missense	83592	exon4			AGCCTCCTCATCC	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"Aldo-keto reductases"	23437	protein-coding gene	gene with protein product			"aldo-keto reductase family 1, member C-like 2"	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.329C>A	10.37:g.4877871C>A	ENSP00000298375:p.Pro110His	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	73	26	NM_001271025	0	0	0	0	0	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Missense_Mutation	SNP	ENST00000298375.7	37	CCDS31134.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.940130	0.34283	.	.	ENSG00000165568	ENST00000462718;ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019;ENST00000345253	T;T;T;T;T	0.50277	0.75;2.3;2.3;2.3;1.87	3.39	2.47	0.30058	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.38268	0.1034	N	0.11201	0.11	0.09310	N	1	B;D;D;D;D	0.55385	0.007;0.965;0.965;0.971;0.965	B;P;P;P;P	0.54372	0.014;0.634;0.634;0.75;0.634	T	0.13764	-1.0497	9	0.72032	D	0.01	.	6.973	0.24658	0.0:0.8714:0.0:0.1286	.	71;110;110;110;110	B7Z7K2;Q96JD6-5;Q96JD6-2;Q96JD6;Q96JD6-3	.;.;.;AKCL2_HUMAN;.	H	6;114;110;110;110;110	ENSP00000435436:P114H;ENSP00000298375:P110H;ENSP00000432947:P110H;ENSP00000335034:P110H;ENSP00000335603:P110H	ENSP00000298375:P110H	P	+	2	0	AKR1E2	4867871	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	0.340000	0.19892	0.964000	0.38108	0.561000	0.74099	CCT	C|0.994;G|0.006		0.483	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436		A	4877871	C	A	4877871	3	1	31	1	0	0	0	0	1	0	0	0	474	681	24	4	343	4	AKR1E2	10	4877871	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		4877871	130656876	41	2711											
MINPP1	9562	hgsc.bcm.edu	37	chr10	89265100	89265100	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtacgcggactggatggAcgggcagctagtagagaagg	10	6	19	6	3	0	1	0	0	0	1	0	5	0	4	0	6	2	4	0	6	4	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr10:89265100A>G	ENST00000371996.4	+	1	469	c.428A>G	c.(427-429)gAc>gGc	p.D143G	MINPP1_ENST00000536010.1_5'Flank|MINPP1_ENST00000371994.4_Missense_Mutation_p.D143G	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	143					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		GACTGGATGGACGGGCAGCTA	0.677											OREG0020348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D143G		.											.	MINPP1-227	0			c.A428G						.						43	50	48					10																	89265100		2203	4300	6503	SO:0001583	missense	9562	exon1			GGATGGACGGGCA	AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"multiple inositol polyphosphate histidine phosphatase, 1"			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.428A>G	10.37:g.89265100A>G	ENSP00000361064:p.Asp143Gly	Somatic	58	1	1266	WXS	Illumina HiSeq	Phase_I	133	8	NM_004897	0	0	0	0	0	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Missense_Mutation	SNP	ENST00000371996.4	37	CCDS7384.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.709579	0.89018	.	.	ENSG00000107789	ENST00000371996;ENST00000371994;ENST00000546140	T;T	0.24151	1.87;1.87	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	M	0.66939	2.045	0.80722	D	1	D;D	0.71674	0.998;0.97	D;P	0.66084	0.941;0.869	T	0.40534	-0.9558	10	0.42905	T	0.14	-22.9462	14.034	0.64634	1.0:0.0:0.0:0.0	.	143;143	Q9UNW1-2;Q9UNW1	.;MINP1_HUMAN	G	143;143;2	ENSP00000361064:D143G;ENSP00000361062:D143G	ENSP00000361062:D143G	D	+	2	0	MINPP1	89255080	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.959000	0.70339	1.962000	0.57031	0.460000	0.39030	GAC	.		0.677	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1			G	89265100	A	G	89265100	3	3	31	1	0	0	0	0	1	0	0	0	9613	275	10	3	430	3	MINPP1	10	89265100	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	84387229	89265100	46269647	42	2712											
NAV2	89797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	19955397	19955397	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcccgagatgccaaaaaagtCctccaagattgccagcttca	13	7	8	13	1	1	2	1	0	0	2	3	3	3	2	5	0	3	1	5	0	4	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:19955397C>T	ENST00000396087.3	+	8	1775	c.1676C>T	c.(1675-1677)tCc>tTc	p.S559F	NAV2_ENST00000349880.4_Missense_Mutation_p.S536F|NAV2_ENST00000527559.2_Missense_Mutation_p.S488F|NAV2_ENST00000360655.4_Missense_Mutation_p.S472F|NAV2_ENST00000540292.1_Missense_Mutation_p.S490F|NAV2_ENST00000396085.1_Missense_Mutation_p.S536F	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	559					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCAAAAAAGTCCTCCAAGATT	0.562																																					p.S559F		.											.	NAV2-96	0			c.C1676T						.						87	98	94					11																	19955397		2198	4293	6491	SO:0001583	missense	89797	exon8			AAAAGTCCTCCAA	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.1676C>T	11.37:g.19955397C>T	ENSP00000379396:p.Ser559Phe	Somatic	162	1		WXS	Illumina HiSeq	Phase_I	316	133	NM_001244963	0	0	1	1	0	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	C	19.87	3.907427	0.72868	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000006	T	0.46347	0.1388	L	0.52573	1.65	0.80722	D	1	B;D	0.71674	0.365;0.998	B;D	0.63597	0.143;0.916	T	0.27434	-1.0074	9	.	.	.	.	14.2954	0.66308	0.0:0.8513:0.1487:0.0	.	536;472	Q8IVL1-3;Q8IVL1-4	.;.	F	472;536;536;559;488;490	ENSP00000353871:S472F;ENSP00000379394:S536F;ENSP00000309577:S536F;ENSP00000379396:S559F;ENSP00000435395:S488F;ENSP00000443489:S490F	.	S	+	2	0	NAV2	19911973	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.993000	0.70616	2.401000	0.81631	0.462000	0.41574	TCC	.		0.562	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	19955397	C	T	19955397	3	4	31	1	0	0	0	0	1	0	0	0	10209	855	30	2	1712	2	NAV2	11	19955397	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		19955397	115051119	43	2713											
FNBP4	23360	hgsc.bcm.edu	37	chr11	47788808	47788808	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagagttgcaggatgggcctAcggccgggtaccgcccggga	7	5	18	11	4	0	1	0	0	0	1	0	4	0	3	4	5	3	3	4	5	2	3	rs146921625	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:47788808A>G	ENST00000263773.5	-	1	45	c.33T>C	c.(31-33)cgT>cgC	p.R11R	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	11						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						GGATGGGCCTACGGCCGGGTA	0.751													A|||	59	0.0117812	0.0424	0.0043	5008	,	,		11665	0		0	False		,,,				2504	0				p.R11R		.											.	FNBP4-91	0			c.T33C						.	A		51,2841		0,51,1395	4	5	4		33	-0.8	1	11	dbSNP_134	4	0,6974		0,0,3487	no	coding-synonymous	FNBP4	NM_015308.2		0,51,4882	GG,GA,AA		0.0,1.7635,0.5169		11/1018	47788808	51,9815	1446	3487	4933	SO:0001819	synonymous_variant	23360	exon1			GGGCCTACGGCCG	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.33T>C	11.37:g.47788808A>G		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	12	7	NM_015308	0	0	0	0	0	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	37	CCDS41644.1																																																																																			A|0.986;G|0.014		0.751	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			G	47788808	A	G	47788808	2	3	31	1	0	0	0	0	0	0	0	1	5986	378	14	3		3	FNBP4	11	47788808	Silent	SNP	A	TCGA-AL-3472-01A-01D-1252-08	27833411	47788808	87217708	44	2714											
DLG2	1740	hgsc.bcm.edu	37	chr11	83770383	83770383	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggcctttgaacagtttgatTtccacaacggtctccaaaat	11	12	8	10	1	1	2	0	2	1	0	3	2	2	2	3	2	2	1	3	2	4	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:83770383T>C	ENST00000532653.1	-	6	881	c.579A>G	c.(577-579)gaA>gaG	p.E193E	DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000531015.1_Silent_p.E160E|DLG2_ENST00000524982.1_Silent_p.E193E|DLG2_ENST00000398309.2_Silent_p.E193E|DLG2_ENST00000537455.1_5'UTR|DLG2_ENST00000280241.8_Silent_p.E232E|DLG2_ENST00000543673.1_Silent_p.E298E|DLG2_ENST00000330014.6_Silent_p.E132E|DLG2_ENST00000418306.2_Silent_p.E142E|DLG2_ENST00000376104.2_Silent_p.E298E|DLG2_ENST00000398301.2_Silent_p.E232E			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ACAGTTTGATTTCCACAACGG	0.443																																					p.E298E		.											.	DLG2-96	0			c.A894G						.						144	133	136					11																	83770383		1891	4118	6009	SO:0001819	synonymous_variant	1740	exon11			TTTGATTTCCACA	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	2901	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 58"	603583	"discs, large homolog 2, chapsyn-110 (Drosophila)"			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.579A>G	11.37:g.83770383T>C		Somatic	247	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_001142699	0	0	0	0	0	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000532653.1	37																																																																																				.		0.443	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		C	83770383	T	C	83770383	2	2	31	1	0	0	0	0	0	0	0	1	4566	1838	64	3		3	DLG2	11	83770383	Silent	SNP	T	TCGA-AL-3472-01A-01D-1252-08	35981575	83770383	51236133	45	2715											
OR10G8	219869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	123900948	123900948	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgactgttggaatagtggccTcgggctgctttgtcctgata	6	14	13	8	1	0	2	0	2	0	0	2	3	1	3	2	3	1	3	2	3	3	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:123900948T>G	ENST00000431524.1	+	1	652	c.619T>G	c.(619-621)Tcg>Gcg	p.S207A		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AATAGTGGCCTCGGGCTGCTT	0.537																																					p.S207A		.											.	OR10G8-92	0			c.T619G						.						193	169	177					11																	123900948		2201	4299	6500	SO:0001583	missense	219869	exon1			GTGGCCTCGGGCT	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"GPCR / Class A : Olfactory receptors"	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.619T>G	11.37:g.123900948T>G	ENSP00000389072:p.Ser207Ala	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	173	71	NM_001004464	0	0	0	0	0	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	T	2.750	-0.260282	0.05791	.	.	ENSG00000234560	ENST00000431524	T	0.36157	1.27	2.91	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.953949	0.08599	N	0.921764	T	0.23330	0.0564	N	0.01482	-0.84	0.09310	N	1	B	0.30914	0.3	B	0.43194	0.411	T	0.46456	-0.9190	10	0.45353	T	0.12	.	11.0743	0.48021	0.0:0.0:0.0:1.0	.	207	Q8NGN5	O10G8_HUMAN	A	207	ENSP00000389072:S207A	ENSP00000389072:S207A	S	+	1	0	OR10G8	123406158	0.000000	0.05858	0.780000	0.31762	0.263000	0.26337	0.369000	0.20416	1.319000	0.45190	0.455000	0.32223	TCG	.		0.537	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		G	123900948	T	G	123900948	3	3	31	1	0	0	0	0	1	0	0	0	10929	1551	54	5	621	5	OR10G8	11	123900948	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08	40130565	123900948	11105568	46	2716											
ST14	6768	hgsc.bcm.edu;broad.mit.edu	37	chr11	130066334	130066334	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaggactacgtggagatcaAcggggagaagtgagtccccg	12	5	15	9	3	1	3	1	1	0	2	2	6	2	4	2	4	2	0	2	4	4	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:130066334A>G	ENST00000278742.5	+	10	1632	c.1214A>G	c.(1213-1215)aAc>aGc	p.N405S		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	405	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	GTGGAGATCAACGGGGAGAAG	0.677																																					p.N405S		.											.	ST14-94	0			c.A1214G						.						30	27	28					11																	130066334		2201	4296	6497	SO:0001583	missense	6768	exon10			AGATCAACGGGGA	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"Serine peptidases / Transmembrane"	11344	protein-coding gene	gene with protein product	"epithin", "matriptase"	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1214A>G	11.37:g.130066334A>G	ENSP00000278742:p.Asn405Ser	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	39	10	NM_021978	0	0	0	0	0	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.146950	0.77888	.	.	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.18960	2.18	4.62	4.62	0.57501	CUB (5);	0.000000	0.41097	D	0.000956	T	0.32102	0.0818	L	0.41710	1.295	0.58432	D	0.999999	D;D	0.67145	0.996;0.993	D;D	0.69654	0.936;0.965	T	0.03374	-1.1043	10	0.17832	T	0.49	.	12.2663	0.54681	1.0:0.0:0.0:0.0	.	215;405	B4DYI7;Q9Y5Y6	.;ST14_HUMAN	S	405;307	ENSP00000278742:N405S	ENSP00000278742:N405S	N	+	2	0	ST14	129571544	0.997000	0.39634	0.972000	0.41901	0.891000	0.51852	3.696000	0.54757	1.730000	0.51580	0.533000	0.62120	AAC	.		0.677	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			G	130066334	A	G	130066334	3	3	31	1	0	0	0	0	1	0	0	0	15243	43	2	3	1252	3	ST14	11	130066334	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	6165386	130066334	4940182	47	2717											
IQSEC3	440073	hgsc.bcm.edu	37	chr12	176334	176334	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gggcccaggaacctctccagGaccagggacagcgctcagca	10	3	13	15	1	2	0	1	0	1	0	3	3	2	3	4	4	3	2	4	4	1	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:176334G>C	ENST00000538872.1	+	1	404	c.286G>C	c.(286-288)Gac>Cac	p.D96H	IQSEC3_ENST00000326261.4_Missense_Mutation_p.D96H			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	96					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		ACCTCTCCAGGACCAGGGACA	0.791											OREG0006798	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=IQSEC3|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.D96H		.											.	IQSEC3-560	0			c.G286C						.						1	1	1					12																	176334		418	1472	1890	SO:0001583	missense	440073	exon1			CTCCAGGACCAGG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.286G>C	12.37:g.176334G>C	ENSP00000437554:p.Asp96His	Somatic	4	1	586	WXS	Illumina HiSeq	Phase_I	10	8	NM_001170738	0	0	0	0	0	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	37	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	g	13.67	2.306644	0.40795	.	.	ENSG00000120645	ENST00000538872;ENST00000326261	T;T	0.38722	1.12;1.12	3.92	0.307	0.15811	.	0.985349	0.08211	U	0.980809	T	0.33265	0.0857	L	0.36672	1.1	0.27393	N	0.955065	.	.	.	.	.	.	T	0.39742	-0.9599	8	0.72032	D	0.01	.	2.5389	0.04721	0.4107:0.0:0.37:0.2193	.	.	.	.	H	96	ENSP00000437554:D96H;ENSP00000315662:D96H	ENSP00000315662:D96H	D	+	1	0	IQSEC3	46595	1.000000	0.71417	0.933000	0.37362	0.334000	0.28698	1.225000	0.32551	-0.134000	0.11516	0.561000	0.74099	GAC	.		0.791	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		C	176334	G	C	176334	3	2	31	1	0	0	0	0	1	0	0	0	7840	1174	41	4	288	4	IQSEC3	12	176334	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		176334	133675561	48	2718											
FGF6	2251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	4554499	4554500	+	Missense_Mutation	DNP	CC	CC	AG																															ccgctgccgcttgatccccaCcaaatagccactttcccagt																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:4554499_4554500CC>AG	ENST00000228837.2	-	1	280_281	c.237_238GG>CT	c.(235-240)ttGGtg>ttCTtg	p.79_80LV>FL		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	79					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			TTGATCCCCACCAAATAGCCAC	0.653																																					p.LV79FL		.											.	FGF6	0			c.G237C						.																																			SO:0001583	missense	2251	exon1			CCCCACCAAATAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"Endogenous ligands"	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.237_238delinsAG	12.37:g.4554499_4554500delinsAG	ENSP00000228837:p.L79_V80delinsFL	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	241	116		0	0	0	0	0	Q0VAE1	Missense_Mutation	DNP	ENST00000228837.2	37	CCDS8527.1																																																																																			.		0.653	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		AG	4554500	CC	AG	4554499	3	1	31	1	0	0	0	0	1	0	0	0	5875	507	18	4	400	4	FGF6	12	4554499	Missense_Mutation	DNP	CC	TCGA-AL-3472-01A-01D-1252-08	4378165	4554499	129297396	49	2719											
LAG3	3902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6886462	6886462	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgggtcacctggatccCtggggaagctgctttgtgag	5	12	14	10	0	1	1	1	1	0	0	2	3	2	3	3	4	2	2	3	4	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:6886462C>A	ENST00000203629.2	+	6	1423	c.1090C>A	c.(1090-1092)Ctg>Atg	p.L364M		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	364	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						ACCTGGATCCCTGGGGAAGCT	0.512																																					p.L364M		.											.	LAG3-90	0			c.C1090A						.						113	112	112					12																	6886462		2203	4300	6503	SO:0001583	missense	3902	exon6			GGATCCCTGGGGA		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1090C>A	12.37:g.6886462C>A	ENSP00000203629:p.Leu364Met	Somatic	255	0		WXS	Illumina HiSeq	Phase_I	383	171	NM_002286	0	0	2	2	0	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.556120	0.45487	.	.	ENSG00000089692	ENST00000203629	T	0.11604	2.76	4.55	2.53	0.30540	.	1.747540	0.02897	N	0.134825	T	0.10937	0.0267	N	0.24115	0.695	0.09310	N	1	P	0.46277	0.875	P	0.44732	0.459	T	0.24584	-1.0156	10	0.33940	T	0.23	2.878	7.2879	0.26350	0.1917:0.6226:0.1858:0.0	.	364	P18627	LAG3_HUMAN	M	364	ENSP00000203629:L364M	ENSP00000203629:L364M	L	+	1	2	LAG3	6756723	0.025000	0.19082	0.471000	0.27229	0.889000	0.51656	-0.025000	0.12413	1.073000	0.40885	0.561000	0.74099	CTG	.		0.512	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			A	6886462	C	A	6886462	3	1	31	1	0	0	0	0	1	0	0	0	8621	680	24	4	1112	4	LAG3	12	6886462	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	2331963	6886462	126965433	50	2720											
LRP6	4040	hgsc.bcm.edu	37	chr12	12274105	12274105	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggcggtgggtagaggtgAtgagaatagctcctctctgt	7	11	17	6	1	1	3	0	2	1	2	3	4	2	3	1	5	1	2	1	5	3	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:12274105A>G	ENST00000261349.4	-	23	4873	c.4797T>C	c.(4795-4797)caT>caC	p.H1599H	BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Silent_p.H1554H	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1599					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				GGTAGAGGTGATGAGAATAGC	0.532																																					p.H1599H		.											.	LRP6-661	0			c.T4797C						.						123	100	108					12																	12274105		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon23			GAGGTGATGAGAA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4797T>C	12.37:g.12274105A>G		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_002336	0	0	3	3	0	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			.		0.532	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12274105	A	G	12274105	2	3	31	1	0	0	0	0	0	0	0	1	8987	330	12	3		3	LRP6	12	12274105	Silent	SNP	A	TCGA-AL-3472-01A-01D-1252-08	5387643	12274105	121577790	51	2721											
TMTC1	83857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	29670368	29670368	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcctactcaccagtgccaAgcggagctccctctgagaag	10	7	9	15	1	2	1	1	1	1	1	4	3	4	2	4	1	4	1	4	1	3	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:29670368A>G	ENST00000539277.1	-	14	2219	c.2161T>C	c.(2161-2163)Ttg>Ctg	p.L721L	TMTC1_ENST00000552618.1_Silent_p.L745L|TMTC1_ENST00000256062.5_Silent_p.L613L|RP11-310I24.1_ENST00000549070.1_RNA|TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000551659.1_Silent_p.L783L	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	721						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ACCAGTGCCAAGCGGAGCTCC	0.517																																					p.L721L		.											.	TMTC1-90	0			c.T2161C						.						117	114	115					12																	29670368		2203	4300	6503	SO:0001819	synonymous_variant	83857	exon14			GTGCCAAGCGGAG		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"Tetratricopeptide (TTC) repeat domain containing"	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2161T>C	12.37:g.29670368A>G		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	80	34	NM_001193451	0	0	0	0	0	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	ENST00000539277.1	37	CCDS53772.1																																																																																			.		0.517	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		G	29670368	A	G	29670368	2	3	31	1	0	0	0	0	0	0	0	1	16292	69	3	3		3	TMTC1	12	29670368	Silent	SNP	A	TCGA-AL-3472-01A-01D-1252-08	17396263	29670368	104181527	52	2722											
ALDH2	217	broad.mit.edu	37	chr12	112229114	112229114	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggctgtttgctcacaggctgGctttccccctggtgtggtca	3	13	13	12	0	2	0	2	0	0	0	3	0	3	0	2	5	1	5	2	5	0	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:112229114G>A	ENST00000261733.2	+	7	747	c.686G>A	c.(685-687)gGc>gAc	p.G229D	RP11-162P23.2_ENST00000546840.2_Missense_Mutation_p.A226T|ALDH2_ENST00000416293.3_Missense_Mutation_p.G182D	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	229					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	TCACAGGCTGGCTTTCCCCCT	0.582			T	HMGA2	leiomyoma																																p.G229D				Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	.	ALDH2-228	0			c.G686A						.						88	61	70					12																	112229114		2203	4300	6503	SO:0001583	missense	217	exon7			AGGCTGGCTTTCC	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.686G>A	12.37:g.112229114G>A	ENSP00000261733:p.Gly229Asp	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_000690	0	0	0	0	0	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	37	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316261	0.95655	.	.	ENSG00000257767;ENSG00000111275;ENSG00000111275;ENSG00000111275	ENST00000546840;ENST00000416293;ENST00000261733;ENST00000552234	T;T	0.31510	1.49;1.49	5.57	5.57	0.84162	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.63757	0.2538	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.69712	-0.5071	10	0.87932	D	0	.	19.1669	0.93561	0.0:0.0:1.0:0.0	.	182;229	E7EUE5;P05091	.;ALDH2_HUMAN	D	210;182;229;89	ENSP00000403349:G182D;ENSP00000261733:G229D	ENSP00000261733:G229D	G	+	2	0	ALDH2;RP11-162P23.2	110713497	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	9.476000	0.97823	2.614000	0.88457	0.563000	0.77884	GGC	.		0.582	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690		A	112229114	G	A	112229114	3	1	31	1	0	0	0	0	1	0	0	0	496	1203	42	2	712	2	ALDH2	12	112229114	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	82558746	112229114	21622781	53	2723											
RBM19	9904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	114397941	114397941	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcatgtttgctccaggCtctgggtttggccgggtccc	2	12	15	12	1	1	0	0	0	1	0	3	0	3	0	3	5	1	5	3	5	0	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:114397941C>T	ENST00000545145.2	-	3	340	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	RBM19_ENST00000261741.5_Missense_Mutation_p.A88T|RBM19_ENST00000392561.3_Missense_Mutation_p.A88T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	88					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TTGCTCCAGGCTCTGGGTTTG	0.532																																					p.A88T		.											.	RBM19-95	0			c.G262A						.						100	99	99					12																	114397941		2203	4300	6503	SO:0001583	missense	9904	exon3			TCCAGGCTCTGGG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.262G>A	12.37:g.114397941C>T	ENSP00000442053:p.Ala88Thr	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	144	54	NM_001146699	0	0	2	6	4	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102307	0.56183	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.74315	-0.83;-0.83;-0.83	4.86	4.86	0.63082	Nucleotide-binding, alpha-beta plait (1);	0.116689	0.56097	D	0.000023	T	0.76716	0.4026	M	0.79258	2.445	0.48288	D	0.999627	P	0.44478	0.836	B	0.41374	0.355	T	0.79381	-0.1827	10	0.40728	T	0.16	-26.8541	18.1761	0.89761	0.0:1.0:0.0:0.0	.	88	Q9Y4C8	RBM19_HUMAN	T	88	ENSP00000442053:A88T;ENSP00000376344:A88T;ENSP00000261741:A88T	ENSP00000261741:A88T	A	-	1	0	RBM19	112882324	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	3.397000	0.52572	2.513000	0.84729	0.557000	0.71058	GCC	.		0.532	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114397941	C	T	114397941	3	4	31	1	0	0	0	0	1	0	0	0	13153	797	28	2	2708	2	RBM19	12	114397941	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	2168827	114397941	19453954	54	2724											
ULK1	8408	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	132393457	132393457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcagctgacttcggcttcGcgcggtacctccagagcaac	7	7	11	16	5	0	2	0	1	0	1	3	2	1	2	3	2	4	5	3	2	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:132393457G>A	ENST00000321867.4	+	7	856	c.505G>A	c.(505-507)Gcg>Acg	p.A169T		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	169	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CTTCGGCTTCGCGCGGTACCT	0.711																																					p.A169T		.											.	ULK1-758	0			c.G505A						.						60	59	59					12																	132393457		2203	4300	6503	SO:0001583	missense	8408	exon7			GGCTTCGCGCGGT	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.505G>A	12.37:g.132393457G>A	ENSP00000324560:p.Ala169Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	139	60	NM_003565	0	0	3	5	2	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	G	36	5.828944	0.96996	.	.	ENSG00000177169	ENST00000321867;ENST00000537421;ENST00000542313	T;T;D	0.90133	0.97;0.97;-2.62	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96254	0.9185	10	0.87932	D	0	-34.7466	19.3607	0.94436	0.0:0.0:1.0:0.0	.	169	O75385	ULK1_HUMAN	T	169;86;63	ENSP00000324560:A169T;ENSP00000438953:A86T;ENSP00000444983:A63T	ENSP00000324560:A169T	A	+	1	0	ULK1	130959410	1.000000	0.71417	0.295000	0.24960	0.974000	0.67602	7.537000	0.82033	2.651000	0.90000	0.455000	0.32223	GCG	.		0.711	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			A	132393457	G	A	132393457	3	1	31	1	0	0	0	0	1	0	0	0	17008	1087	38	1	531	1	ULK1	12	132393457	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	17995516	132393457	1458438	55	2725											
C14orf126	112487	hgsc.bcm.edu	37	chr14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgggcctgaggaatccGgctaccctcagccatggctt	6	7	12	16	3	1	1	1	1	0	0	2	2	2	2	5	4	2	2	5	4	2	2	rs17097904	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	DTD2_ENST00000356180.4_Missense_Mutation_p.R6W|RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		.											.	.	1	Substitution - Missense(1)	skin(1)	c.C16T						.						12	12	12					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	15	2		WXS	Illumina HiSeq	Phase_I	20	6	NM_080664	0	0	6	13	7	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		A	31926584	G	A	31926584	3	1	31	1	0	0	0	0	1	0	0	0	1747	1115	39	1	502	1	C14orf126	14	31926584	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		31926584	75422956	56	2726											
ACYP1	97	hgsc.bcm.edu	37	chr14	75528414	75528414	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	actggtagcaaagctaactgGaacacagctcttgctgtgag	12	9	11	9	0	1	1	0	1	1	0	1	2	1	2	0	2	6	5	0	2	4	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr14:75528414G>C	ENST00000238618.3	-	2	188				ACYP1_ENST00000357971.3_Missense_Mutation_p.P46A|ACYP1_ENST00000555694.1_Intron|ACYP1_ENST00000555463.1_Intron|ACYP1_ENST00000555135.1_Missense_Mutation_p.P46A	NM_001107.3	NP_001098.1	P07311	ACYP1_HUMAN	acylphosphatase 1, erythrocyte (common) type						phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)	acylphosphatase activity (GO:0003998)			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.00646)		AAGCTAACTGGAACACAGCTC	0.358																																					p.P46A		.											.	ACYP1-226	0			c.C136G						.						69	67	68					14																	75528414		1872	4101	5973	SO:0001627	intron_variant	97	exon3			TAACTGGAACACA	X84194	CCDS9838.1, CCDS45137.1	14q24.3	2014-08-08			ENSG00000119640	ENSG00000119640	3.6.1.7		179	protein-coding gene	gene with protein product		600875				7796909, 9730610	Standard	NM_001107		Approved		uc001xrg.3	P07311	OTTHUMG00000171767	ENST00000238618.3:c.84+1758C>G	14.37:g.75528414G>C		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	53	18	NM_203488	0	0	1	1	0	A6NDV8|B2R590	Missense_Mutation	SNP	ENST00000238618.3	37	CCDS9838.1	.	.	.	.	.	.	.	.	.	.	G	9.868	1.198229	0.22037	.	.	ENSG00000119640	ENST00000357971;ENST00000555135	.	.	.	3.01	0.887	0.19200	.	.	.	.	.	T	0.36908	0.0984	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35450	-0.9788	7	0.87932	D	0	.	9.8551	0.41082	0.0:0.5438:0.4562:0.0	.	46	A6NDV8	.	A	46	.	ENSP00000350655:P46A	P	-	1	0	ACYP1	74598167	0.003000	0.15002	0.054000	0.19295	0.203000	0.24098	0.172000	0.16704	0.176000	0.19873	0.543000	0.68304	CCA	.		0.358	ACYP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415013.1			C	75528414	G	C	75528414	1	2	31	0	1	0	0	0	0	0	0	0	228	1174	41	4		4	ACYP1	14	75528414	Intron	SNP	G	TCGA-AL-3472-01A-01D-1252-08	43601830	75528414	31821126	57	2727											
CDC42BPB	9578	broad.mit.edu	37	chr14	103430982	103430982	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcggcgcaccttccacagCgggtccttgagacacggtca	7	7	12	15	4	1	1	1	1	0	1	3	2	3	1	3	3	2	1	3	3	0	2	rs142014338		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr14:103430982C>T	ENST00000361246.2	-	19	2871	c.2583G>A	c.(2581-2583)ccG>ccA	p.P861P		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CCTTCCACAGCGGGTCCTTGA	0.532																																					p.P861P													.	CDC42BPB-581	0			c.G2583A						.	C		0,4406		0,0,2203	32	31	31		2583	-7.2	0	14	dbSNP_134	31	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CDC42BPB	NM_006035.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		861/1712	103430982	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon19			CCACAGCGGGTCC	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.2583G>A	14.37:g.103430982C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	65	5	NM_006035	0	0	0	0	0		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			C|1.000;T|0.000		0.532	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		T	103430982	C	T	103430982	2	4	31	1	0	0	0	0	0	0	0	1	3079	755	27	1		1	CDC42BPB	14	103430982	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	27902568	103430982	3918558	58	2728											
NEDD4	4734	broad.mit.edu	37	chr15	56216867	56216868	+	Frame_Shift_Ins	INS	-	-	A																															cggttttcgtcaaacacttcINSaaaaagaagccggtgctgct																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr15:56216867_56216868insA	ENST00000435532.3	-	5	457_458	c.267_268insT	c.(265-270)tttgaafs	p.E90fs		NM_006154.2	NP_006145.2	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	1185	Ser-rich.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TCAAACACTTCAAAAAGAAGCC	0.371																																					p.E90_V91delinsX													.	NEDD4-723	0			c.268_269insT						.																																			SO:0001589	frameshift_variant	4734	exon5			ACACTTCAAAAAG	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"receptor-potentiating factor 1"	602278	"neural precursor cell expressed, developmentally down-regulated 4"			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000435532.3:c.268dupT	15.37:g.56216872_56216872dupA	ENSP00000410613:p.Glu90fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_006154	0	0	0	0	0	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Nonsense_Mutation	INS	ENST00000435532.3	37	CCDS45265.1																																																																																			.		0.371	NEDD4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359821.2	NM_198400		A	56216868	-	A	56216867	7	5	31	1	0	1	1	0	0	0	0	0	10336	835	29	0	4086	0	NEDD4	15	56216867	Frame_Shift_Ins	INS	-	TCGA-AL-3472-01A-01D-1252-08		56216867	46314525	59	2729											
LRRK1	79705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	101592098	101592098	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcatctcctgccccagaCacccggacctccccgtgccg	6	7	7	21	3	2	1	1	0	1	1	4	2	3	2	8	1	2	0	8	1	0	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr15:101592098C>A	ENST00000388948.3	+	24	3981	c.3622C>A	c.(3622-3624)Cac>Aac	p.H1208N	RP11-505E24.3_ENST00000558979.1_RNA|RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.H1205N	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTGCCCCAGACACCCGGACCT	0.617																																					p.H1208N		.											.	LRRK1-602	0			c.C3622A						.						53	62	59					15																	101592098		2037	4192	6229	SO:0001583	missense	79705	exon24			CCCAGACACCCGG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3622C>A	15.37:g.101592098C>A	ENSP00000373600:p.His1208Asn	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	125	55	NM_024652	0	0	0	0	0		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	C	33	5.194800	0.94960	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.73789	-0.76;-0.78	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	L	0.32530	0.975	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.83156	-0.0101	10	0.72032	D	0.01	.	19.2014	0.93713	0.0:1.0:0.0:0.0	.	1208	Q38SD2	LRRK1_HUMAN	N	1208;1205	ENSP00000373600:H1208N;ENSP00000284395:H1205N	ENSP00000284395:H1205N	H	+	1	0	LRRK1	99409621	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.669000	0.83911	2.541000	0.85698	0.655000	0.94253	CAC	.		0.617	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101592098	C	A	101592098	3	1	31	1	0	0	0	0	1	0	0	0	9057	478	17	4	3712	4	LRRK1	15	101592098	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	45375231	101592098	939294	60	2730											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	2814808	2814809	+	Frame_Shift_Ins	INS	-	-	T																															ttctgcatcttctcctgaaaINStgaaagatggtttacccaga																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:2814808_2814809insT	ENST00000301740.8	+	11	4828_4829	c.4279_4280insT	c.(4279-4281)atgfs	p.M1427fs		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1427	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TTCTCCTGAAATGAAAGATGGT	0.505																																					p.M1427fs		.											.	SRRM2-93	0			c.4279_4280insT						.																																			SO:0001589	frameshift_variant	23524	exon11			.	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.4280dupT	16.37:g.2814809_2814809dupT	ENSP00000301740:p.Met1427fs	Somatic	336	0		WXS	Illumina HiSeq	Phase_I	367	150	NM_016333	0	0	0	0	0	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Frame_Shift_Ins	INS	ENST00000301740.8	37	CCDS32373.1																																																																																			.		0.505	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2814809	-	T	2814808	7	5	31	1	0	1	1	0	0	0	0	0	15201	101	4	0	4317	0	SRRM2	16	2814808	Frame_Shift_Ins	INS	-	TCGA-AL-3472-01A-01D-1252-08		2814808	87539945	61	2731											
CLEC16A	23274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	11066855	11066855	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgctgttccttacttctccaAtttggtctggttcattggga	5	18	9	9	0	3	0	1	0	2	0	5	1	4	1	2	3	2	3	2	3	2	6			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:11066855A>C	ENST00000409790.1	+	7	895	c.665A>C	c.(664-666)aAt>aCt	p.N222T	CLEC16A_ENST00000409552.3_Missense_Mutation_p.N220T	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TACTTCTCCAATTTGGTCTGG	0.463																																					p.N222T		.											.	CLEC16A-92	0			c.A665C						.						86	83	84					16																	11066855		1967	4159	6126	SO:0001583	missense	23274	exon6			TCTCCAATTTGGT	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.665A>C	16.37:g.11066855A>C	ENSP00000387122:p.Asn222Thr	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	39	17	NM_015226	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575730	0.86645	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.50813	0.73	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.70595	2.14	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.78314	0.987;0.991	T	0.69161	-0.5218	10	0.51188	T	0.08	-24.4217	15.5133	0.75802	1.0:0.0:0.0:0.0	.	222;220	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	T	222;222;220	ENSP00000387122:N222T	ENSP00000386495:N220T	N	+	2	0	CLEC16A	10974356	1.000000	0.71417	0.937000	0.37676	0.978000	0.69477	9.228000	0.95250	2.251000	0.74343	0.528000	0.53228	AAT	.		0.463	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		C	11066855	A	C	11066855	3	2	31	1	0	0	0	0	1	0	0	0	3506	101	4	5	687	5	CLEC16A	16	11066855	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	8252047	11066855	79287898	62	2732											
ZNF423	23090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	49670867	49670867	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcacctggatggacacCttggagtcgaagacctcctg	9	8	13	11	1	0	1	0	0	0	1	2	5	1	4	4	4	1	1	4	4	1	1	rs373085653		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:49670867C>G	ENST00000561648.1	-	4	2249	c.2196G>C	c.(2194-2196)aaG>aaC	p.K732N	ZNF423_ENST00000562871.1_Missense_Mutation_p.K672N|ZNF423_ENST00000567169.1_Missense_Mutation_p.K615N|ZNF423_ENST00000262383.2_Missense_Mutation_p.K732N|ZNF423_ENST00000563137.2_Missense_Mutation_p.K672N|ZNF423_ENST00000535559.1_Missense_Mutation_p.K615N|ZNF423_ENST00000562520.1_Missense_Mutation_p.K672N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	732					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GGATGGACACCTTGGAGTCGA	0.567																																					p.K732N		.											.	ZNF423-228	0			c.G2196C						.						100	93	95					16																	49670867		2198	4300	6498	SO:0001583	missense	23090	exon4			GGACACCTTGGAG	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2196G>C	16.37:g.49670867C>G	ENSP00000455426:p.Lys732Asn	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	136	71	NM_015069	0	0	0	0	0	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872977	0.51695	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.30448	1.53;1.53	5.05	5.05	0.67936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.46946	0.1419	L	0.38531	1.155	0.53005	D	0.999969	D	0.89917	1.0	D	0.91635	0.999	T	0.31364	-0.9946	9	.	.	.	.	18.4141	0.90562	0.0:1.0:0.0:0.0	.	732	Q2M1K9	ZN423_HUMAN	N	732;615	ENSP00000262383:K732N;ENSP00000442321:K615N	.	K	-	3	2	ZNF423	48228368	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.361000	0.52306	2.352000	0.79861	0.561000	0.74099	AAG	.		0.567	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		G	49670867	C	G	49670867	3	3	31	1	0	0	0	0	1	0	0	0	17930	680	24	4	1678	4	ZNF423	16	49670867	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	38604012	49670867	40683886	63	2733											
KIAA0513	9764	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	85100829	85100829	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtgagaccactgagtctgCggacagtgagaatgacatgg	12	7	15	7	1	1	4	0	4	1	2	1	8	1	5	1	2	1	0	1	2	1	0	rs148950418		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:85100829C>T	ENST00000566428.1	+	2	783	c.152C>T	c.(151-153)gCg>gTg	p.A51V	KIAA0513_ENST00000258180.3_Missense_Mutation_p.A51V|KIAA0513_ENST00000538274.1_Missense_Mutation_p.A51V|KIAA0513_ENST00000567328.1_Missense_Mutation_p.A51V			O60268	K0513_HUMAN	KIAA0513	51						cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		ACTGAGTCTGCGGACAGTGAG	0.647																																					p.A51V		.											.	KIAA0513-135	0			c.C152T						.	C	VAL/ALA	1,4397	2.1+/-5.4	0,1,2198	72	58	63		152	4.5	0.2	16	dbSNP_134	63	0,8600		0,0,4300	no	missense	KIAA0513	NM_014732.2	64	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	51/412	85100829	1,12997	2199	4300	6499	SO:0001583	missense	9764	exon2			AGTCTGCGGACAG	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.152C>T	16.37:g.85100829C>T	ENSP00000457408:p.Ala51Val	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	113	34	NM_014732	0	0	0	1	1	B4DSS5|D3DUM2|Q8N6G0	Missense_Mutation	SNP	ENST00000566428.1	37	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700612	0.88924	2.27E-4	0.0	ENSG00000135709	ENST00000538274;ENST00000258180	T;T	0.38240	1.15;1.15	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	M	0.67953	2.075	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	T	0.58239	-0.7671	10	0.41790	T	0.15	-15.5029	16.2567	0.82522	0.0:1.0:0.0:0.0	.	51;51	B4DSS5;O60268	.;K0513_HUMAN	V	51	ENSP00000446439:A51V;ENSP00000258180:A51V	ENSP00000258180:A51V	A	+	2	0	KIAA0513	83658330	1.000000	0.71417	0.218000	0.23776	0.820000	0.46376	6.939000	0.75911	2.234000	0.73211	0.561000	0.74099	GCG	C|1.000;T|0.000		0.647	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732		T	85100829	C	T	85100829	3	4	31	1	0	0	0	0	1	0	0	0	8202	768	27	1	154	1	KIAA0513	16	85100829	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	35429962	85100829	5253924	64	2734											
MYH13	8735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10258306	10258306	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcactctggatttttctaaCagatctaaggtaacaaaaat	15	13	6	7	0	4	1	1	0	3	1	4	2	4	2	0	2	2	1	0	2	5	5			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr17:10258306C>G	ENST00000418404.3	-	9	970	c.807G>C	c.(805-807)ctG>ctC	p.L269L	MYH13_ENST00000252172.4_Silent_p.L269L			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	269	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						ATTTTTCTAACAGATCTAAGG	0.368																																					p.L269L		.											.	MYH13-6	0			c.G807C						.						71	70	71					17																	10258306		1848	4092	5940	SO:0001819	synonymous_variant	8735	exon10			TTCTAACAGATCT	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.807G>C	17.37:g.10258306C>G		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	91	16	NM_003802	0	0	0	0	0	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			.		0.368	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		G	10258306	C	G	10258306	2	3	31	1	0	0	0	0	0	0	0	1	10057	465	17	4		4	MYH13	17	10258306	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08		10258306	70936904	65	2735											
MPRIP	23164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17080727	17080727	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgccacggtgtccggatatgGtgcgtcctcgggtcatgccc	4	10	14	13	4	1	0	1	0	0	0	4	1	3	1	4	4	3	0	4	4	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr17:17080727G>A	ENST00000341712.4	+	21	2959		c.e21+1		MPRIP_ENST00000444976.1_Splice_Site|RN7SL775P_ENST00000498361.2_RNA|MPRIP_ENST00000395804.3_Splice_Site|RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000395811.5_Splice_Site			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TCCGGATATGGTGCGTCCTCG	0.582																																					.		.											.	MPRIP-90	0			c.2959+1G>A						.						64	57	59					17																	17080727		2203	4300	6503	SO:0001630	splice_region_variant	23164	exon21			GATATGGTGCGTC	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.2959+1G>A	17.37:g.17080727G>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	250	73	NM_015134	0	0	0	25	25	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Splice_Site	SNP	ENST00000341712.4	37	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.232815	0.39498	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712;ENST00000313485;ENST00000414263;ENST00000429184	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9433	0.92612	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MPRIP	17021452	1.000000	0.71417	0.960000	0.40013	0.094000	0.18550	9.358000	0.97109	2.539000	0.85634	0.563000	0.77884	.	.		0.582	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	Intron	A	17080727	G	A	17080727	5	1	31	1	0	0	0	0	0	0	1	0	9768	1275	44	2	3042	2	MPRIP	17	17080727	Splice_Site	SNP	G	TCGA-AL-3472-01A-01D-1252-08	6822421	17080727	64114483	66	2736											
NDUFS7	374291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1391140	1391140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacgaccagatgccggagcCgcgctacgtggtctccatgg	7	7	13	14	5	1	1	0	0	1	1	2	3	1	2	4	3	4	1	4	3	2	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:1391140C>T	ENST00000233627.9	+	6	727	c.431C>T	c.(430-432)cCg>cTg	p.P144L	NDUFS7_ENST00000414651.2_Missense_Mutation_p.P174L|NDUFS7_ENST00000546283.1_Missense_Mutation_p.P144L|NDUFS7_ENST00000539480.1_Missense_Mutation_p.P144L|AC005329.7_ENST00000585596.1_RNA|AC005329.7_ENST00000589734.1_RNA|NDUFS7_ENST00000313408.7_Missense_Mutation_p.P144L|NDUFS7_ENST00000540530.1_3'UTR|AC005329.7_ENST00000501448.1_RNA	NM_024407.4	NP_077718.3	O75251	NDUS7_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase)	144					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|synaptic membrane (GO:0097060)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|quinone binding (GO:0048038)			ovary(1)	1		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)|Breast(49;0.00186)|Lung NSC(49;0.00292)|all_lung(49;0.00419)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Doxorubicin(DB00997)	ATGCCGGAGCCGCGCTACGTG	0.687																																					p.P144L		.											.	NDUFS7-90	0			c.C431T						.						22	24	23					19																	1391140		2201	4298	6499	SO:0001583	missense	374291	exon6			CGGAGCCGCGCTA	AF115969	CCDS12063.1	19p13	2011-07-04	2002-08-29		ENSG00000115286	ENSG00000115286		"Mitochondrial respiratory chain complex / Complex I"	7714	protein-coding gene	gene with protein product	"complex I 20kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial"	601825	"NADH dehydrogenase (ubiquinone) Fe-S protein 7 (20kD) (NADH-coenzyme Q reductase)"			8938450	Standard	NM_024407		Approved	PSST, FLJ46880, FLJ45860, CI-20	uc002lse.4	O75251	OTTHUMG00000168077	ENST00000233627.9:c.431C>T	19.37:g.1391140C>T	ENSP00000233627:p.Pro144Leu	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	58	24	NM_024407	0	0	130	274	144	B3KRI2|Q2T9H7|Q9BV17	Missense_Mutation	SNP	ENST00000233627.9	37	CCDS12063.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298050	0.40694	.	.	ENSG00000115286	ENST00000546283;ENST00000233627;ENST00000539480;ENST00000313408;ENST00000414651;ENST00000538929;ENST00000538523;ENST00000540530;ENST00000535382	D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37	4.44	4.44	0.53790	NADH:ubiquinone oxidoreductase-like, 20kDa subunit (2);	.	.	.	.	D	0.96358	0.8812	H	0.97051	3.93	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;1.0;0.998;0.993	D	0.97936	1.0323	9	0.87932	D	0	.	15.6509	0.77091	0.0:1.0:0.0:0.0	.	144;151;144;144	F5H5N1;Q8NAS7;B3KRI2;O75251	.;.;.;NDUS7_HUMAN	L	144;144;144;144;174;63;63;63;63	ENSP00000440348:P144L;ENSP00000233627:P144L;ENSP00000443273:P144L;ENSP00000364262:P144L;ENSP00000406630:P174L	ENSP00000233627:P144L	P	+	2	0	NDUFS7	1342140	1.000000	0.71417	0.807000	0.32361	0.032000	0.12392	7.076000	0.76806	2.016000	0.59253	0.511000	0.50034	CCG	.		0.687	NDUFS7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397984.1	NM_024407		T	1391140	C	T	1391140	3	4	31	1	0	0	0	0	1	0	0	0	10323	652	23	1	453	1	NDUFS7	19	1391140	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		1391140	57737843	67	2737											
FAM108A1	81926	hgsc.bcm.edu	37	chr19	1881550	1881550	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcagcagagctcactcaGcgacagcccattcatggcgg	10	5	13	13	2	3	1	3	0	0	1	3	3	3	1	1	3	4	3	1	3	0	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:1881550G>A	ENST00000292577.7	-	2	449	c.16C>T	c.(16-18)Ctg>Ttg	p.L6L	ABHD17A_ENST00000250974.9_Silent_p.L6L|ABHD17A_ENST00000590661.1_Silent_p.L6L	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	6						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										AGCTCACTCAGCGACAGCCCA	0.761																																					p.L6L		.											.	FAM108A1-90	0			c.C16T						.																																			SO:0001819	synonymous_variant	81926	exon2			CACTCAGCGACAG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"Abhydrolase domain containing"	28756	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 27", "family with sequence similarity 108, member A1"	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.16C>T	19.37:g.1881550G>A		Somatic	29	2		WXS	Illumina HiSeq	Phase_I	74	8	NM_031213	0	0	11	11	0	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Silent	SNP	ENST00000292577.7	37	CCDS45902.1																																																																																			.		0.761	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		A	1881550	G	A	1881550	2	1	31	1	0	0	0	0	0	0	0	1	5407	962	34	2		2	FAM108A1	19	1881550	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08	490410	1881550	57247433	68	2738											
EEF2	1938	hgsc.bcm.edu;broad.mit.edu	37	chr19	3983291	3983293	+	Splice_Site	DEL	TGA	TGA	-																															gtagaagagggagatggcacTgatggagggagggactcgtc																								rs111408370		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:3983291_3983293delTGA	ENST00000309311.6	-	3	307		c.e3-2		EEF2_ENST00000600720.1_Splice_Site|SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2						cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGATGGCACTGATGGAGGGAGG	0.586																																					.	Colon(165;1804 1908 4071 6587 18799)	.											.	EEF2-90	0			.						.																																			SO:0001630	splice_region_variant	1938	.			.	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"polypeptidyl-tRNA translocase"	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.219-2TCA>-	19.37:g.3983291_3983293delTGA		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	64	19	.	0	0	0	0	0	B2RMP5|D6W618|Q58J86	Splice_Site	DEL	ENST00000309311.6	37	CCDS12117.1																																																																																			.		0.586	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	Intron	-	3983293	TGA	-	3983291	8	5	31	1	0	1	0	1	0	0	1	0	4940	1594	55	0	2411	0	EEF2	19	3983291	Splice_Site	DEL	TGA	TCGA-AL-3472-01A-01D-1252-08	2101741	3983291	55145692	69	2739											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9063328	9063328	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtggtgacttcagaggTggccagtatttcaactgagg	9	12	13	7	0	3	3	2	2	1	1	3	3	3	3	1	4	1	1	1	4	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:9063328T>C	ENST00000397910.4	-	3	24321	c.24118A>G	c.(24118-24120)Acc>Gcc	p.T8040A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8042	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ACTTCAGAGGTGGCCAGTATT	0.458																																					p.T8040A		.											.	MUC16-566	0			c.A24118G						.						130	120	124					19																	9063328		1946	4144	6090	SO:0001583	missense	94025	exon3			CAGAGGTGGCCAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.24118A>G	19.37:g.9063328T>C	ENSP00000381008:p.Thr8040Ala	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	79	40	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	8.827	0.938900	0.18281	.	.	ENSG00000181143	ENST00000397910	T	0.24908	1.83	2.66	-2.24	0.06909	.	.	.	.	.	T	0.28067	0.0692	L	0.35854	1.095	.	.	.	P	0.49961	0.93	P	0.54664	0.758	T	0.39313	-0.9620	8	0.87932	D	0	.	7.4725	0.27357	0.7363:0.0:0.0:0.2637	.	8040	B5ME49	.	A	8040	ENSP00000381008:T8040A	ENSP00000381008:T8040A	T	-	1	0	MUC16	8924328	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-1.059000	0.03479	-0.657000	0.05373	0.332000	0.21555	ACC	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9063328	T	C	9063328	3	2	31	1	0	0	0	0	1	0	0	0	9998	1696	59	3	19733	3	MUC16	19	9063328	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08	5080037	9063328	50065655	70	2740											
SFRS14	10147	broad.mit.edu	37	chr19	19120952	19120952	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccccggagcccttgagcacGgaggagcccccgccgctgcc	5	3	14	19	4	0	1	0	1	0	0	0	4	0	4	7	3	4	2	7	3	0	1	rs376121808		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:19120952G>A	ENST00000601879.1	-	5	2347	c.2050C>T	c.(2050-2052)Cgt>Tgt	p.R684C	SUGP2_ENST00000600377.1_Missense_Mutation_p.R698C|SUGP2_ENST00000456085.2_Missense_Mutation_p.R453C|SUGP2_ENST00000452918.2_Missense_Mutation_p.R684C|SUGP2_ENST00000337018.6_Missense_Mutation_p.R684C			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	684					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CCTTGAGCACGGAGGAGCCCC	0.672																																					p.R684C													.	SUGP2-91	0			c.C2050T						.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	60	63	62		2050,2050	3.1	0	19		62	0,8600		0,0,4300	no	missense,missense	SUGP2	NM_001017392.3,NM_014884.3	180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	684/1083,684/1083	19120952	1,13005	2203	4300	6503	SO:0001583	missense	10147	exon5			GAGCACGGAGGAG	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.2050C>T	19.37:g.19120952G>A	ENSP00000472286:p.Arg684Cys	Somatic	171	1		WXS	Illumina HiSeq	Phase_I	313	5	NM_014884	0	0	11	12	1	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	37	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255339	0.59321	2.27E-4	0.0	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918;ENST00000456085	T;T;T;T	0.14640	2.73;2.72;2.73;2.49	5.49	3.13	0.36017	.	0.391861	0.21398	N	0.075183	T	0.14141	0.0342	N	0.24115	0.695	0.09310	N	1	D;D;D	0.89917	1.0;1.0;0.993	P;P;P	0.54706	0.759;0.759;0.548	T	0.04454	-1.0950	10	0.87932	D	0	-13.4575	6.5426	0.22388	0.1447:0.1754:0.6799:0.0	.	453;684;684	E7ETX7;A8K5G0;Q8IX01	.;.;SUGP2_HUMAN	C	684;684;684;453	ENSP00000337926:R684C;ENSP00000332373:R684C;ENSP00000389380:R684C;ENSP00000409603:R453C	ENSP00000332373:R684C	R	-	1	0	SUGP2	18981952	0.002000	0.14202	0.026000	0.17262	0.697000	0.40408	0.810000	0.27183	2.590000	0.87494	0.655000	0.94253	CGT	.		0.672	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		A	19120952	G	A	19120952	3	1	31	1	0	0	0	0	1	0	0	0	14202	1116	39	1	1222	1	SFRS14	19	19120952	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	10057624	19120952	40008031	71	2741											
GGN	199720	hgsc.bcm.edu;broad.mit.edu	37	chr19	38876904	38876904	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtggcggcggtagggcccggGcttgggacgcaggcgccgag	4	4	22	11	6	0	0	0	0	0	0	0	2	0	1	2	7	0	3	2	7	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:38876904G>T	ENST00000334928.6	-	3	1130	c.998C>A	c.(997-999)gCc>gAc	p.A333D	SPRED3_ENST00000587013.1_5'Flank|AC005789.9_ENST00000585411.1_RNA|GGN_ENST00000591809.1_Intron	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	333	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TAGGGCCCGGGCTTGGGACGC	0.677																																					p.A333D		.											.	GGN-90	0			c.C998A						.						28	32	30					19																	38876904		2201	4299	6500	SO:0001583	missense	199720	exon3			GCCCGGGCTTGGG	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.998C>A	19.37:g.38876904G>T	ENSP00000334940:p.Ala333Asp	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	62	27	NM_152657	0	0	0	0	0	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	37	CCDS12516.1	.	.	.	.	.	.	.	.	.	.	G	6.337	0.430216	0.12045	.	.	ENSG00000179168	ENST00000334928	.	.	.	3.33	0.957	0.19613	.	1.070480	0.07455	N	0.899668	T	0.21227	0.0511	N	0.24115	0.695	0.09310	N	1	B;B	0.32829	0.386;0.386	B;B	0.25405	0.06;0.06	T	0.18650	-1.0330	9	0.45353	T	0.12	0.4297	5.4042	0.16312	0.0:0.2275:0.5387:0.2338	.	250;333	Q86UU5-2;Q86UU5	.;GGN_HUMAN	D	333	.	ENSP00000334940:A333D	A	-	2	0	GGN	43568744	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.059000	0.11731	0.082000	0.17018	0.462000	0.41574	GCC	.		0.677	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		T	38876904	G	T	38876904	3	4	31	1	0	0	0	0	1	0	0	0	6378	1203	42	4	968	4	GGN	19	38876904	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	19755952	38876904	20252079	72	2742											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41018832	41018832	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgagctgggcgggcggcgAgcgttgctgcagcaggccct	4	5	20	12	5	0	0	0	0	0	0	0	2	0	0	1	5	5	5	1	5	0	1	rs814533	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:41018832A>G	ENST00000352632.3	+	14	2222	c.2136A>G	c.(2134-2136)cgA>cgG	p.R712R	SPTBN4_ENST00000338932.3_Silent_p.R712R|SPTBN4_ENST00000595535.1_Silent_p.R712R|SPTBN4_ENST00000344104.3_Silent_p.R712R|SPTBN4_ENST00000598249.1_Silent_p.R712R			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	712					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGGGCGGCGAGCGTTGCTGC	0.751													G|||	1110	0.221645	0.4758	0.1239	5008	,	,		9743	0.1052		0.1372	False		,,,				2504	0.1544				p.R712R		.											.	SPTBN4-94	0			c.A2136G						.	G		502,1916		17,468,724	1	2	2		2136	3.2	1	19	dbSNP_86	2	282,4934		4,274,2330	no	coding-synonymous	SPTBN4	NM_020971.2		21,742,3054	GG,GA,AA		5.4064,20.761,10.2698		712/2565	41018832	784,6850	1209	2608	3817	SO:0001819	synonymous_variant	57731	exon14			GCGGCGAGCGTTG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.2136A>G	19.37:g.41018832A>G		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_020971	0	0	0	0	0	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			A|0.806;G|0.194		0.751	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			G	41018832	A	G	41018832	2	3	31	1	0	0	0	0	0	0	0	1	15153	291	11	3		3	SPTBN4	19	41018832	Silent	SNP	A	TCGA-AL-3472-01A-01D-1252-08	2141928	41018832	18110151	73	2743											
BCAM	4059	ucsc.edu	37	chr19	45322837	45322837	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctccatcctgtccctgcAgtgagcccccagacctccca	6	9	6	20	0	1	2	0	1	1	1	6	2	5	2	7	0	2	1	7	0	0	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:45322837A>C	ENST00000270233.6	+	13	1640		c.e13-1		BCAM_ENST00000589651.1_Splice_Site	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)						cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CTGTCCCTGCAGTGAGCCCCC	0.667																																					.													.	BCAM-91	0			c.1619-2A>C						.						37	37	37					19																	45322837		2203	4299	6502	SO:0001630	splice_region_variant	4059	exon13			CCCTGCAGTGAGC	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1619-1A>C	19.37:g.45322837A>C		Somatic	86	0		WXS	Illumina HiSeq		116	1	NM_005581	0	0	0	0	0	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Splice_Site	SNP	ENST00000270233.6	37	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	a	14.42	2.530172	0.45073	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	.	.	.	4.14	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9339	0.41539	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BCAM	50014677	1.000000	0.71417	0.986000	0.45419	0.611000	0.37282	4.357000	0.59436	1.669000	0.50854	0.434000	0.28630	.	.		0.667	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	Intron	C	45322837	A	C	45322837	5	2	31	1	0	0	0	0	0	0	1	0	1345	202	7	5	1667	5	BCAM	19	45322837	Splice_Site	SNP	A	TCGA-AL-3472-01A-01D-1252-08	4304005	45322837	13806146	74	2744											
CGB1	114335	hgsc.bcm.edu	37	chr19	49538974	49538974	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggtcaaggggtggtccttggGacccccgcagtcagtggtgc	5	8	17	11	1	2	0	2	0	0	0	3	1	3	1	3	6	1	1	3	6	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:49538974G>A	ENST00000301407.7	-	3	465	c.361C>T	c.(361-363)Ccc>Tcc	p.P121S	CGB1_ENST00000391869.3_Missense_Mutation_p.P121S|CTB-60B18.6_ENST00000591656.1_Intron	NM_033377.1	NP_203695.2	A6NKQ9	CGB1_HUMAN	chorionic gonadotropin, beta polypeptide 1	153						extracellular region (GO:0005576)				liver(1)|lung(1)	2		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		TGGTCCTTGGGACCCCCGCAG	0.677																																					p.P121S		.											.	CGB1-90	0			c.C361T						.						11	16	14					19																	49538974		2139	4235	6374	SO:0001583	missense	114335	exon3			CCTTGGGACCCCC	S80935	CCDS12751.2	19q13.32	2012-10-03				ENSG00000267631			16721	protein-coding gene	gene with protein product		608823				6194155	Standard	NM_033377		Approved		uc002plx.3	A6NKQ9	OTTHUMG00000150186	ENST00000301407.7:c.361C>T	19.37:g.49538974G>A	ENSP00000301407:p.Pro121Ser	Somatic	250	1		WXS	Illumina HiSeq	Phase_I	423	76	NM_033377	0	0	0	0	0	A4FVC8|A8MUK6	Missense_Mutation	SNP	ENST00000301407.7	37	CCDS12751.2	.	.	.	.	.	.	.	.	.	.	G	9.032	0.987577	0.18966	.	.	ENSG00000213030	ENST00000301407;ENST00000391869	D;D	0.90504	-2.68;-2.68	1.8	0.726	0.18248	.	0.327767	0.29376	N	0.012340	D	0.91009	0.7172	.	.	.	0.26016	N	0.981927	D	0.56287	0.975	P	0.59171	0.853	T	0.82577	-0.0388	9	0.51188	T	0.08	-17.962	4.3715	0.11249	0.2094:0.0:0.7906:0.0	.	121	A6NKQ9-2	.	S	121	ENSP00000301407:P121S;ENSP00000375742:P121S	ENSP00000301407:P121S	P	-	1	0	CGB1	54230786	1.000000	0.71417	0.354000	0.25760	0.178000	0.23041	2.506000	0.45433	0.322000	0.23283	0.194000	0.17425	CCC	.		0.677	CGB1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316746.4	NM_033377		A	49538974	G	A	49538974	3	1	31	1	0	0	0	0	1	0	0	0	3303	1174	41	2	110	2	CGB1	19	49538974	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	4216137	49538974	9590009	75	2745											
PRR12	57479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	50102854	50102854	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacccctgctgtgccacatcCcccaccttccggagcctttg	5	9	7	20	1	0	0	0	0	0	0	2	1	2	1	8	1	3	1	8	1	0	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:50102854C>T	ENST00000418929.2	+	5	4016	c.4004C>T	c.(4003-4005)cCc>cTc	p.P1335L		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							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)		GTGCCACATCCCCCACCTTCC	0.697																																					p.P1335L		.											.	PRR12-70	0			c.C4004T						.						12	15	14					19																	50102854		1955	4119	6074	SO:0001583	missense	57479	exon5			CACATCCCCCACC	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.4004C>T	19.37:g.50102854C>T	ENSP00000394510:p.Pro1335Leu	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	29	11	NM_020719	0	0	2	3	1	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	4.945	0.175637	0.09391	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	4.34	4.34	0.51931	.	0.157267	0.30338	N	0.009842	T	0.56949	0.2020	L	0.42245	1.32	0.48762	D	0.999702	B	0.20164	0.042	B	0.28709	0.093	T	0.58907	-0.7553	9	0.56958	D	0.05	-10.4584	14.2367	0.65932	0.0:1.0:0.0:0.0	.	1335	Q9ULL5-3	.	L	1335;515;515	.	ENSP00000246798:P515L	P	+	2	0	PRR12	54794666	0.029000	0.19370	0.156000	0.22583	0.027000	0.11550	3.359000	0.52292	2.424000	0.82194	0.563000	0.77884	CCC	.		0.697	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50102854	C	T	50102854	3	4	31	1	0	0	0	0	1	0	0	0	12613	623	22	2	4022	2	PRR12	19	50102854	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	563880	50102854	9026129	76	2746											
IL4I1	259307	hgsc.bcm.edu	37	chr19	50393285	50393285	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaaagccaccctggctgTgctggtcctccgcccaacgc	7	6	9	19	2	0	0	0	0	0	0	2	0	2	0	6	2	3	2	6	2	2	0	rs200284411	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:50393285T>C	ENST00000391826.2	-	8	1488	c.1346A>G	c.(1345-1347)cAc>cGc	p.H449R	IL4I1_ENST00000341114.3_Missense_Mutation_p.H471R|MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000595948.1_Missense_Mutation_p.H471R	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	449						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	ACCCTGGCTGTGCTGGTCCTC	0.662											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	6	0.00119808	0.0045	0	5008	,	,		15172	0		0	False		,,,				2504	0				p.H471R		.											.	IL4I1-523	0			c.A1412G						.	T	ARG/HIS,ARG/HIS	12,4176		0,12,2082	20	8	12		1346,1412	2.1	0.2	19		12	1,8227		0,1,4113	yes	missense,missense	IL4I1	NM_152899.1,NM_172374.1	29,29	0,13,6195	CC,CT,TT		0.0122,0.2865,0.1047	possibly-damaging,possibly-damaging	449/568,471/590	50393285	13,12403	2094	4114	6208	SO:0001583	missense	259307	exon10			TGGCTGTGCTGGT	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.1346A>G	19.37:g.50393285T>C	ENSP00000375702:p.His449Arg	Somatic	3	1	969	WXS	Illumina HiSeq	Phase_I	10	6	NM_172374	0	0	1	3	2	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Missense_Mutation	SNP	ENST00000391826.2	37	CCDS12787.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.369507	0.42003	0.002865	1.22E-4	ENSG00000104951	ENST00000341114;ENST00000391826	D;D	0.92446	-3.04;-3.04	5.39	2.1	0.27182	Amine oxidase (1);	0.420538	0.29328	N	0.012468	D	0.86932	0.6052	M	0.63843	1.955	0.27937	N	0.937667	B;B;B	0.30068	0.225;0.267;0.267	B;B;B	0.27380	0.047;0.079;0.079	T	0.80016	-0.1559	10	0.72032	D	0.01	-25.836	1.7906	0.03050	0.1686:0.0906:0.1762:0.5646	.	471;471;449	Q96RQ9-2;Q1WMJ3;Q96RQ9	.;.;OXLA_HUMAN	R	471;449	ENSP00000342557:H471R;ENSP00000375702:H449R	ENSP00000342557:H471R	H	-	2	0	IL4I1	55085097	1.000000	0.71417	0.167000	0.22817	0.002000	0.02628	4.187000	0.58344	0.322000	0.23283	-0.466000	0.05196	CAC	.		0.662	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			C	50393285	T	C	50393285	3	2	31	1	0	0	0	0	1	0	0	0	7718	1696	59	3	361	3	IL4I1	19	50393285	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08	290431	50393285	8735698	77	2747											
NUP62	23636	broad.mit.edu	37	chr19	50412018	50412018	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtggcctgctggaggaagtgCcgctcctggtcctctagctc	4	10	14	13	1	1	0	0	0	1	0	4	2	3	2	4	4	3	3	4	4	2	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:50412018C>T	ENST00000596217.1	-	2	2934	c.1047G>A	c.(1045-1047)cgG>cgA	p.R349R	IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000352066.3_Silent_p.R349R|NUP62_ENST00000413454.1_Silent_p.R349R|NUP62_ENST00000422090.2_Silent_p.R349R|NUP62_ENST00000597723.1_Intron|NUP62_ENST00000597029.1_Silent_p.R349R|NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000595948.1_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	349					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GGAGGAAGTGCCGCTCCTGGT	0.637																																					p.R349R													.	NUP62-615	0			c.G1047A						.						87	90	89					19																	50412018		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			GAAGTGCCGCTCC	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.1047G>A	19.37:g.50412018C>T		Somatic	301	1		WXS	Illumina HiSeq	Phase_I	469	6	NM_153719	0	0	7	7	0	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			.		0.637	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		T	50412018	C	T	50412018	2	4	31	1	0	0	0	0	0	0	0	1	10794	726	26	2		2	NUP62	19	50412018	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	18733	50412018	8716965	78	2748											
NLRP8	126205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56459468	56459468	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actgactgagctcagtactgGcaccatgcccatcacctggg	9	8	10	14	0	2	2	2	2	0	0	2	2	2	2	3	2	3	3	3	2	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:56459468G>A	ENST00000291971.3	+	1	271	c.200G>A	c.(199-201)gGc>gAc	p.G67D	NLRP8_ENST00000590542.1_Missense_Mutation_p.G67D	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	67	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CTCAGTACTGGCACCATGCCC	0.557																																					p.G67D		.											.	NLRP8-361	0			c.G200A						.						105	84	91					19																	56459468		2203	4300	6503	SO:0001583	missense	126205	exon1			GTACTGGCACCAT	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.200G>A	19.37:g.56459468G>A	ENSP00000291971:p.Gly67Asp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	50	24	NM_176811	0	0	0	0	0	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	5.435	0.265352	0.10294	.	.	ENSG00000179709	ENST00000291971	T	0.59083	0.29	1.98	-0.375	0.12509	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.45094	0.1325	L	0.47716	1.5	0.09310	N	1	B;B	0.24576	0.1;0.106	B;B	0.33295	0.056;0.161	T	0.38478	-0.9659	9	0.20046	T	0.44	.	2.9915	0.05984	0.1879:0.2955:0.5166:0.0	.	67;67	Q86W28-2;Q86W28	.;NALP8_HUMAN	D	67	ENSP00000291971:G67D	ENSP00000291971:G67D	G	+	2	0	NLRP8	61151280	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.665000	0.25083	-0.014000	0.14175	0.514000	0.50259	GGC	.		0.557	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56459468	G	A	56459468	3	1	31	1	0	0	0	0	1	0	0	0	10509	1203	42	2	202	2	NLRP8	19	56459468	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	6047450	56459468	2669515	79	2749											
ZNF583	147949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56934490	56934490	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatccttccagaagttcaaAataaagaatataacaaatct	21	10	3	7	0	2	2	1	0	1	2	4	2	4	2	2	0	1	1	2	0	10	5			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:56934490A>T	ENST00000333201.9	+	5	673	c.463A>T	c.(463-465)Aat>Tat	p.N155Y	ZNF583_ENST00000291598.7_Missense_Mutation_p.N155Y	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	155					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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		AGAAGTTCAAAATAAAGAATA	0.363																																					p.N155Y		.											.	ZNF583-91	0			c.A463T						.						71	78	76					19																	56934490		2202	4300	6502	SO:0001583	missense	147949	exon5			GTTCAAAATAAAG	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.463A>T	19.37:g.56934490A>T	ENSP00000388502:p.Asn155Tyr	Somatic	246	0		WXS	Illumina HiSeq	Phase_I	52	23	NM_001159861	0	0	1	3	2	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	37	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.236222	0.39498	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.01034	5.42;5.42	4.19	3.17	0.36434	.	0.536023	0.17228	N	0.182048	T	0.00468	0.0015	N	0.01464	-0.85	0.24096	N	0.995892	B	0.11235	0.004	B	0.06405	0.002	T	0.45731	-0.9241	9	.	.	.	.	7.714	0.28694	0.8962:0.0:0.1038:0.0	.	155	Q96ND8	ZN583_HUMAN	Y	155	ENSP00000291598:N155Y;ENSP00000388502:N155Y	.	N	+	1	0	ZNF583	61626302	0.000000	0.05858	0.416000	0.26546	0.379000	0.30106	0.567000	0.23608	0.776000	0.33473	0.379000	0.24179	AAT	.		0.363	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		T	56934490	A	T	56934490	3	4	31	1	0	0	0	0	1	0	0	0	18047	14	1	5	477	5	ZNF583	19	56934490	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	475022	56934490	2194493	80	2750											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	470423	470423	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aatgggtataacatatattaCctgatcataattgtcatgtc	14	15	6	6	0	2	1	2	1	0	0	3	1	2	1	1	1	2	1	1	1	7	7			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:470423C>A	ENST00000217244.3	-	10	1099		c.e10+1		CSNK2A1_ENST00000349736.5_Splice_Site|CSNK2A1_ENST00000400227.3_Splice_Site|CSNK2A1_ENST00000400217.2_Splice_Site	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide						axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			ACATATATTACCTGATCATAA	0.398																																					.		.											.	CSNK2A1-791	0			c.315+1G>T						.						74	63	67					20																	470423		2203	4300	6503	SO:0001630	splice_region_variant	1457	exon9			ATATTACCTGATC	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.723+1G>T	20.37:g.470423C>A		Somatic	71	1		WXS	Illumina HiSeq	Phase_I	54	3	NM_177560	0	0	0	0	0	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Splice_Site	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167561	0.78339	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0558	0.86533	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSNK2A1	418423	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.514000	0.81750	2.587000	0.87381	0.531000	0.56144	.	.		0.398	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895	Intron	A	470423	C	A	470423	5	1	31	1	0	0	0	0	0	0	1	0	3963	521	18	4	471	4	CSNK2A1	20	470423	Splice_Site	SNP	C	TCGA-AL-3472-01A-01D-1252-08		470423	62555097	81	2751											
PLTP	5360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44534919	44534919	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcacccggaagtccatGtccaggttgctggtggaagc	8	8	13	12	1	1	0	1	0	0	0	3	2	3	2	3	4	3	3	3	4	2	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:44534919G>A	ENST00000477313.1	-	7	1287	c.693C>T	c.(691-693)gaC>gaT	p.D231D	PLTP_ENST00000372431.3_Silent_p.D231D|PLTP_ENST00000354050.4_Silent_p.D179D|PLTP_ENST00000542937.1_Silent_p.D251D|PLTP_ENST00000372420.1_Silent_p.D143D|PLTP_ENST00000420868.2_Silent_p.D136D			P55058	PLTP_HUMAN	phospholipid transfer protein	231					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GGAAGTCCATGTCCAGGTTGC	0.507																																					p.D231D		.											.	PLTP-91	0			c.C693T						.						102	82	89					20																	44534919		2203	4300	6503	SO:0001819	synonymous_variant	5360	exon8			GTCCATGTCCAGG	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.693C>T	20.37:g.44534919G>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	82	34	NM_006227	0	0	0	0	0	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Silent	SNP	ENST00000477313.1	37	CCDS13386.1																																																																																			.		0.507	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		A	44534919	G	A	44534919	2	1	31	1	0	0	0	0	0	0	0	1	12140	1368	48	2		2	PLTP	20	44534919	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08	44064496	44534919	18490601	82	2752											
SLC12A5	57468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44670175	44670175	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtgctgccagtggcctcatCaaaggtctgcggagggacaa	9	7	15	10	1	3	0	2	0	1	0	3	2	3	2	2	5	3	1	2	5	2	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:44670175C>T	ENST00000454036.2	+	8	1180	c.1131C>T	c.(1129-1131)atC>atT	p.I377I	SLC12A5_ENST00000243964.3_Silent_p.I354I	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	377					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	GTGGCCTCATCAAAGGTCTGC	0.557																																					p.I377I		.											.	SLC12A5-156	0			c.C1131T						.						53	50	51					20																	44670175		2203	4300	6503	SO:0001819	synonymous_variant	57468	exon8			CCTCATCAAAGGT	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.1131C>T	20.37:g.44670175C>T		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	93	37	NM_001134771	0	0	0	0	0	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			.		0.557	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			T	44670175	C	T	44670175	2	4	31	1	0	0	0	0	0	0	0	1	14418	816	29	2		2	SLC12A5	20	44670175	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	135256	44670175	18355345	83	2753											
PCK1	5105	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	56140816	56140817	+	Frame_Shift_Del	DEL	GA	GA	-																															ccgacctcccctgtgaaatcGagagagagatccttgccttg																								rs17847705		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:56140816_56140817delGA	ENST00000319441.4	+	10	1989_1990	c.1825_1826delGA	c.(1825-1827)gagfs	p.E609fs	PCK1_ENST00000543666.1_Frame_Shift_Del_p.E292fs	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	609					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CTGTGAAATCGAGAGAGAGATC	0.47																																					p.609_609del		.											.	PCK1-227	0			c.1825_1826del						.																																			SO:0001589	frameshift_variant	5105	exon10			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1825_1826delGA	20.37:g.56140824_56140825delGA	ENSP00000319814:p.Glu609fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	102	32	NM_002591	0	0	0	0	0	A8K437|B4DT64|Q8TCA3|Q9UJD2	Frame_Shift_Del	DEL	ENST00000319441.4	37	CCDS13460.1																																																																																			.		0.47	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			-	56140817	GA	-	56140816	7	5	31	1	0	1	0	1	0	0	0	0	11607	1059	37	0	1859	0	PCK1	20	56140816	Frame_Shift_Del	DEL	GA	TCGA-AL-3472-01A-01D-1252-08	11470641	56140816	6884704	84	2754											
KRTAP13-3	337960	hgsc.bcm.edu	37	chr21	31797825	31797825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataactctgggaaggggaggTatggattctataattcagat	13	12	12	4	0	3	1	1	0	2	1	3	4	3	4	0	5	1	1	0	5	5	6			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr21:31797825T>C	ENST00000390690.2	-	1	461	c.406A>G	c.(406-408)Acc>Gcc	p.T136A		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	136						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						GAAGGGGAGGTATGGATTCTA	0.468																																					p.T136A		.											.	KRTAP13-3-92	0			c.A406G						.						48	50	49					21																	31797825		2019	4213	6232	SO:0001583	missense	337960	exon1			GGGAGGTATGGAT	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"Keratin associated proteins"	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.406A>G	21.37:g.31797825T>C	ENSP00000375109:p.Thr136Ala	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_181622	0	0	0	0	0	Q3LI78	Missense_Mutation	SNP	ENST00000390690.2	37	CCDS13591.1	.	.	.	.	.	.	.	.	.	.	t	8.990	0.977472	0.18812	.	.	ENSG00000240432	ENST00000390690;ENST00000448917	T	0.02974	4.09	4.78	-3.44	0.04796	.	0.372367	0.18614	U	0.136071	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42832	-0.9428	10	0.46703	T	0.11	0.8475	0.329	0.00315	0.2771:0.2364:0.1361:0.3504	.	136	Q3SY46	KR133_HUMAN	A	136;126	ENSP00000375109:T136A	ENSP00000375109:T136A	T	-	1	0	KRTAP13-3	30719696	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.855000	0.04295	-0.462000	0.06984	-0.214000	0.12660	ACC	.		0.468	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			C	31797825	T	C	31797825	3	2	31	1	0	0	0	0	1	0	0	0	8545	1638	57	3	116	3	KRTAP13-3	21	31797825	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08		31797825	16332070	85	2755											
PFKL	5211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr21	45743723	45743723	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgcatcgtcatgtgtgtcatCccagccaccatcagcaacaa	11	9	7	14	1	3	0	3	0	0	0	5	0	4	0	3	0	4	2	3	0	2	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr21:45743723C>T	ENST00000349048.4	+	16	1627	c.1572C>T	c.(1570-1572)atC>atT	p.I524I	PFKL_ENST00000403390.1_Silent_p.I571I	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	524	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		TGTGTGTCATCCCAGCCACCA	0.642																																					p.I524I		.											.	PFKL-251	0			c.C1572T						.						114	78	91					21																	45743723		2201	4300	6501	SO:0001819	synonymous_variant	5211	exon16			TGTCATCCCAGCC		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.1572C>T	21.37:g.45743723C>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	89	38	NM_002626	0	0	38	61	23	Q96A64|Q96IH4|Q9BR91	Silent	SNP	ENST00000349048.4	37	CCDS33582.1																																																																																			.		0.642	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1			T	45743723	C	T	45743723	2	4	31	1	0	0	0	0	0	0	0	1	11790	845	30	2		2	PFKL	21	45743723	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	13945898	45743723	2386172	86	2756											
INPP5J	27124	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	31523948	31523948	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaaacagcctcgtgttctGgttcggggacctgaacttcc	7	10	10	14	2	1	1	0	1	1	0	4	2	2	2	4	3	3	2	4	3	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr22:31523948G>C	ENST00000331075.5	+	7	1848	c.1799G>C	c.(1798-1800)tGg>tCg	p.W600S	INPP5J_ENST00000412277.2_Missense_Mutation_p.W533S|INPP5J_ENST00000401755.1_5'UTR|INPP5J_ENST00000400294.2_Missense_Mutation_p.W233S|INPP5J_ENST00000402238.1_5'UTR|INPP5J_ENST00000405300.1_Missense_Mutation_p.W233S|INPP5J_ENST00000404453.1_5'UTR|INPP5J_ENST00000404390.3_Missense_Mutation_p.W232S	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	600	Catalytic. {ECO:0000255}.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						CTCGTGTTCTGGTTCGGGGAC	0.577																																					p.W232S		.											.	INPP5J-205	0			c.G695C						.						47	45	45					22																	31523948		1913	4119	6032	SO:0001583	missense	27124	exon7			TGTTCTGGTTCGG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.1799G>C	22.37:g.31523948G>C	ENSP00000333262:p.Trp600Ser	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	110	46	NM_001002837	0	0	1	1	0	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Missense_Mutation	SNP	ENST00000331075.5	37		.	.	.	.	.	.	.	.	.	.	G	19.90	3.913228	0.72983	.	.	ENSG00000185133	ENST00000331075;ENST00000412277;ENST00000400294;ENST00000405300;ENST00000404390	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	4.76	4.76	0.60689	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.93792	0.8015	H	0.98068	4.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	D	0.96283	0.9208	10	0.87932	D	0	.	17.7408	0.88406	0.0:0.0:1.0:0.0	.	533;600;232	B4DF95;Q15735;Q15735-3	.;PI5PA_HUMAN;.	S	600;533;233;233;232	ENSP00000333262:W600S;ENSP00000392924:W533S;ENSP00000383150:W233S;ENSP00000384596:W233S;ENSP00000384534:W232S	ENSP00000333262:W600S	W	+	2	0	INPP5J	29853948	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	9.343000	0.97047	2.329000	0.79093	0.655000	0.94253	TGG	.		0.577	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837		C	31523948	G	C	31523948	3	2	31	1	0	0	0	0	1	0	0	0	7780	1357	47	4	721	4	INPP5J	22	31523948	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		31523948	19780618	87	2757											
MEI1	150365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42191444	42191444	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccggagtagcagtgtcctCtctcatgaagaggtgggtga	9	10	14	8	1	2	3	1	2	1	1	4	4	3	4	2	3	2	2	2	3	3	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr22:42191444C>A	ENST00000401548.3	+	29	3604	c.3564C>A	c.(3562-3564)ctC>ctA	p.L1188L	MEI1_ENST00000300398.4_Intron|MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000400107.1_Silent_p.L521L	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GCAGTGTCCTCTCTCATGAAG	0.542																																					p.L1188L		.											.	MEI1-70	0			c.C3564A						.						154	156	155					22																	42191444		2039	4204	6243	SO:0001819	synonymous_variant	150365	exon29			TGTCCTCTCTCAT	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3564C>A	22.37:g.42191444C>A		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	207	78	NM_152513	0	0	4	4	0		Silent	SNP	ENST00000401548.3	37	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	c	0.075	-1.194186	0.01594	.	.	ENSG00000167077	ENST00000423900	.	.	.	5.01	1.65	0.23941	.	0.552403	0.16357	N	0.217956	T	0.56108	0.1963	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54906	-0.8223	6	0.87932	D	0	-15.0087	2.2726	0.04095	0.1575:0.5189:0.1526:0.171	.	.	.	.	I	7	.	ENSP00000410973:L7I	L	+	1	0	MEI1	40521390	0.219000	0.23619	0.509000	0.27700	0.069000	0.16628	-0.099000	0.11007	0.139000	0.18822	-0.521000	0.04368	CTC	.		0.542	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		A	42191444	C	A	42191444	2	1	31	1	0	0	0	0	0	0	0	1	9490	900	32	4		4	MEI1	22	42191444	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	10667496	42191444	9113122	88	2758											
PJA1	64219	broad.mit.edu	37	chrX	68382203	68382203	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggccctcattgtcattggcGgtatccctccacctggaagt	6	12	10	13	1	2	0	2	0	0	0	4	1	4	1	4	4	0	1	4	4	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chrX:68382203G>A	ENST00000361478.1	-	2	1256	c.879C>T	c.(877-879)acC>acT	p.T293T	PJA1_ENST00000477231.1_5'UTR|PJA1_ENST00000374571.4_Silent_p.T238T|PJA1_ENST00000374583.1_Silent_p.T293T|PJA1_ENST00000374584.3_Silent_p.T105T	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	293					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						TGTCATTGGCGGTATCCCTCC	0.498																																					p.T293T													.	PJA1-130	0			c.C879T						.						86	69	75					X																	68382203		2203	4300	6503	SO:0001819	synonymous_variant	64219	exon2			ATTGGCGGTATCC	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"RING-type (C3HC4) zinc fingers"	16648	protein-coding gene	gene with protein product		300420	"praja 1", "praja ring finger 1"			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.879C>T	X.37:g.68382203G>A		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	108	3	NM_145119	0	0	1	1	0	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			.		0.498	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		A	68382203	G	A	68382203	2	1	31	1	0	0	0	0	0	0	0	1	11987	1103	39	1		1	PJA1	23	68382203	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08		68382203	86888357	89	2759											
CCDC27	148870	hgsc.bcm.edu	37	chr1	3679839	3679839	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggaagcgaggaggaggaAgaggaggaaggggacaggga	15	0	24	2	1	0	1	0	0	0	1	0	11	0	9	0	9	1	0	0	9	3	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:3679839A>G	ENST00000294600.2	+	7	1206	c.1122A>G	c.(1120-1122)gaA>gaG	p.E374E		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	374	Glu-rich.									breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		aggaggaggaagaggaggaag	0.647																																					p.E374E		.											.	CCDC27-91	0			c.A1122G						.						71	73	72					1																	3679839		2200	4299	6499	SO:0001819	synonymous_variant	148870	exon7			GGAGGAAGAGGAG		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1122A>G	1.37:g.3679839A>G		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_152492	0	0	0	0	0	Q5TBV3|Q96M50	Silent	SNP	ENST00000294600.2	37	CCDS50.1																																																																																			.		0.647	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492		G	3679839	A	G	3679839	2	3	32	1	0	0	0	0	0	0	0	1	2807	69	3	3		3	CCDC27	1	3679839	Silent	SNP	A	TCGA-AL-3473-01A-01D-1252-08		3679839	245570782	1	2760											
KIF1B	23095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10342493	10342493	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacttcatccccatcttccTgctcactcagtagtcaggtg	7	13	6	15	0	6	0	5	0	1	0	8	0	8	0	3	1	1	2	3	1	1	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:10342493T>A	ENST00000377086.1	+	15	1538	c.1336T>A	c.(1336-1338)Tgc>Agc	p.C446S	KIF1B_ENST00000263934.6_Missense_Mutation_p.C400S|KIF1B_ENST00000377083.1_Missense_Mutation_p.C400S|KIF1B_ENST00000377081.1_Missense_Mutation_p.C446S|KIF1B_ENST00000377093.4_Missense_Mutation_p.C400S			O60333	KIF1B_HUMAN	kinesin family member 1B	446					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCCATCTTCCTGCTCACTCAG	0.483																																					p.C400S		.											.	KIF1B-93	0			c.T1198A						.						145	132	137					1																	10342493		2203	4300	6503	SO:0001583	missense	23095	exon13			TCTTCCTGCTCAC	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.1336T>A	1.37:g.10342493T>A	ENSP00000366290:p.Cys446Ser	Somatic	183	1		WXS	Illumina HiSeq	Phase_I	144	24	NM_183416	0	0	0	0	0	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	T	9.981	1.228167	0.22542	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	T;T;T;T;T	0.71698	-0.41;-0.59;-0.44;-0.59;-0.44	5.38	5.38	0.77491	.	0.219298	0.48286	D	0.000184	T	0.42381	0.1200	N	0.01576	-0.805	0.50039	D	0.999845	B;B;B;B;B;B;B	0.19200	0.0;0.001;0.0;0.0;0.0;0.034;0.007	B;B;B;B;B;B;B	0.17098	0.001;0.0;0.001;0.001;0.0;0.017;0.004	T	0.47471	-0.9115	10	0.07990	T	0.79	.	15.7585	0.78058	0.0:0.0:0.0:1.0	.	432;406;446;420;446;400;400	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	S	446;400;400;446;400;446	ENSP00000263934:C400S;ENSP00000366297:C400S;ENSP00000366290:C446S;ENSP00000366287:C400S;ENSP00000366284:C446S	ENSP00000263934:C400S	C	+	1	0	KIF1B	10265080	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.373000	0.59537	2.191000	0.70037	0.529000	0.55759	TGC	.		0.483	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			A	10342493	T	A	10342493	3	1	32	1	0	0	0	0	1	0	0	0	8305	1580	55	5	1244	5	KIF1B	1	10342493	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	6662654	10342493	238908128	2	2761											
SCMH1	22955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	41503104	41503104	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caggatgaaagcaagggccgGtgcctttgggaggtgctgac	9	7	17	8	1	0	2	0	2	0	0	0	4	0	4	2	5	3	2	2	5	2	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:41503104G>A	ENST00000326197.7	-	12	1877	c.1578C>T	c.(1576-1578)caC>caT	p.H526H	SCMH1_ENST00000402904.2_Silent_p.H526H|SCMH1_ENST00000361191.5_Silent_p.H465H|SCMH1_ENST00000372596.1_Silent_p.H465H|SCMH1_ENST00000337495.5_Silent_p.H536H|SCMH1_ENST00000456518.2_Silent_p.H368H|SCMH1_ENST00000397171.2_Silent_p.H465H|SCMH1_ENST00000361705.3_Silent_p.H479H|SCMH1_ENST00000397174.2_Silent_p.H506H|SCMH1_ENST00000472037.1_5'UTR|SCMH1_ENST00000372595.1_Silent_p.H465H|SCMH1_ENST00000372597.1_Silent_p.H479H					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				GCAAGGGCCGGTGCCTTTGGG	0.587																																					p.H536H		.											.	SCMH1-90	0			c.C1608T						.						200	179	186					1																	41503104		2203	4300	6503	SO:0001819	synonymous_variant	22955	exon13			GGGCCGGTGCCTT	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.1578C>T	1.37:g.41503104G>A		Somatic	225	0		WXS	Illumina HiSeq	Phase_I	181	24	NM_001172219	0	0	37	64	27		Silent	SNP	ENST00000326197.7	37	CCDS30688.1																																																																																			.		0.587	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			A	41503104	G	A	41503104	2	1	32	1	0	0	0	0	0	0	0	1	13940	1252	44	2		2	SCMH1	1	41503104	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	31160611	41503104	207747517	3	2762											
INADL	10207	hgsc.bcm.edu	37	chr1	62516665	62516665	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggcaccgaacctattagtAgtgaggaagatggcagcgtc	11	7	14	9	3	0	2	0	1	0	1	1	4	0	3	2	3	2	3	2	3	5	3	rs375573695		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:62516665A>G	ENST00000371158.2	+	31	4174	c.4060A>G	c.(4060-4062)Agt>Ggt	p.S1354G	INADL_ENST00000545929.1_Missense_Mutation_p.S27G|INADL_ENST00000316485.6_Missense_Mutation_p.S1354G|INADL_ENST00000543708.1_Missense_Mutation_p.S138G	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1354					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						ACCTATTAGTAGTGAGGAAGA	0.403																																					p.S1354G		.											.	INADL-94	0			c.A4060G						.	A	GLY/SER	3,4403	6.2+/-15.9	0,3,2200	135	129	131		4060	-0.1	0.4	1		131	0,8600		0,0,4300	no	missense	INADL	NM_176877.2	56	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	benign	1354/1802	62516665	3,13003	2203	4300	6503	SO:0001583	missense	10207	exon31			ATTAGTAGTGAGG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4060A>G	1.37:g.62516665A>G	ENSP00000360200:p.Ser1354Gly	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_176877	0	0	13	13	0	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	7.721	0.697127	0.15106	6.81E-4	0.0	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708;ENST00000545929	T;T;T;T;T	0.34072	2.71;2.57;3.22;2.18;1.38	4.98	-0.0485	0.13838	.	0.641692	0.16310	N	0.220030	T	0.19446	0.0467	N	0.21282	0.65	0.19300	N	0.999977	B;B;B;B;B;B	0.10296	0.0;0.0;0.003;0.001;0.001;0.002	B;B;B;B;B;B	0.13407	0.0;0.001;0.006;0.003;0.002;0.009	T	0.13737	-1.0498	10	0.51188	T	0.08	.	3.256	0.06832	0.5452:0.0:0.2839:0.1709	.	27;138;813;1354;1354;1354	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	G	1354;1354;1354;1354;138;138;27	ENSP00000360200:S1354G;ENSP00000326199:S1354G;ENSP00000307496:S138G;ENSP00000445790:S138G;ENSP00000440094:S27G	ENSP00000307496:S138G	S	+	1	0	INADL	62289253	0.580000	0.26733	0.423000	0.26634	0.253000	0.25986	0.192000	0.17096	-0.097000	0.12307	0.533000	0.62120	AGT	.		0.403	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62516665	A	G	62516665	3	3	32	1	0	0	0	0	1	0	0	0	7752	420	15	3	4178	3	INADL	1	62516665	Missense_Mutation	SNP	A	TCGA-AL-3473-01A-01D-1252-08	21013561	62516665	186733956	4	2763											
PTGFR	5737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	78959187	78959187	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atggtaatccagctcctggcGataatgtgtgtctcctgtat	8	14	10	9	1	1	0	0	0	1	0	4	1	3	0	3	2	1	3	3	2	3	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:78959187G>A	ENST00000370757.3	+	2	996	c.759G>A	c.(757-759)gcG>gcA	p.A253A	PTGFR_ENST00000370758.1_Silent_p.A253A|PTGFR_ENST00000370756.3_Silent_p.A253A	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	253					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)	p.A253A(2)		breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	AGCTCCTGGCGATAATGTGTG	0.393																																					p.A253A		.											.	PTGFR-527	2	Substitution - coding silent(2)	skin(2)	c.G759A						.						52	49	50					1																	78959187		2203	4300	6503	SO:0001819	synonymous_variant	5737	exon2			CCTGGCGATAATG	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"GPCR / Class A : Prostanoid receptors"	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.759G>A	1.37:g.78959187G>A		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	127	17	NM_000959	0	0	0	0	0	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Silent	SNP	ENST00000370757.3	37	CCDS686.1																																																																																			.		0.393	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		A	78959187	G	A	78959187	2	1	32	1	0	0	0	0	0	0	0	1	12779	1045	37	1		1	PTGFR	1	78959187	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	16442522	78959187	170291434	5	2764											
AGL	178	broad.mit.edu	37	chr1	100346330	100346330	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtttatggatattacgcaTgataatgagtgtcctattgt	10	17	9	5	1	0	2	0	2	0	0	1	3	1	3	1	1	1	2	1	1	5	7			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:100346330T>A	ENST00000294724.4	+	14	2356	c.1878T>A	c.(1876-1878)caT>caA	p.H626Q	AGL_ENST00000370163.3_Missense_Mutation_p.H626Q|AGL_ENST00000370165.3_Missense_Mutation_p.H626Q|AGL_ENST00000370161.2_Missense_Mutation_p.H610Q|AGL_ENST00000361915.3_Missense_Mutation_p.H626Q|AGL_ENST00000361522.4_Missense_Mutation_p.H609Q|AGL_ENST00000361302.3_Missense_Mutation_p.H610Q	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	626					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATATTACGCATGATAATGAGT	0.388																																					p.H626Q													.	AGL-92	0			c.T1878A						.						321	284	296					1																	100346330		2203	4300	6503	SO:0001583	missense	178	exon14			TACGCATGATAAT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1878T>A	1.37:g.100346330T>A	ENSP00000294724:p.His626Gln	Somatic	377	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_000644	0	0	1	1	0	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.348979	0.61183	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42	6.08	-0.561	0.11785	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96074	0.8721	M	0.89353	3.025	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.95040	0.8177	10	0.87932	D	0	.	10.1565	0.42825	0.0:0.3802:0.0:0.6198	.	609;610;626	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	Q	626;626;626;626;610;610;609	ENSP00000355106:H626Q;ENSP00000359184:H626Q;ENSP00000359182:H626Q;ENSP00000294724:H626Q;ENSP00000354971:H610Q;ENSP00000359180:H610Q;ENSP00000354635:H609Q	ENSP00000294724:H626Q	H	+	3	2	AGL	100118918	1.000000	0.71417	0.992000	0.48379	0.734000	0.41952	0.657000	0.24963	-0.333000	0.08476	0.482000	0.46254	CAT	.		0.388	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		A	100346330	T	A	100346330	3	1	32	1	0	0	0	0	1	0	0	0	384	1461	51	5	1997	5	AGL	1	100346330	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	21387143	100346330	148904291	6	2765											
LRIG2	9860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	113657326	113657326	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tacctaaatgtcatttcatcCcccaattgtgactcttccca	10	14	3	14	0	3	1	2	1	1	0	5	1	5	1	4	0	1	0	4	0	4	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:113657326C>A	ENST00000361127.5	+	15	2556	c.2358C>A	c.(2356-2358)tcC>tcA	p.S786S	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	786					innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TCATTTCATCCCCCAATTGTG	0.468																																					p.S786S		.											.	LRIG2-229	0			c.C2358A						.						203	166	179					1																	113657326		2203	4300	6503	SO:0001819	synonymous_variant	9860	exon15			TTCATCCCCCAAT	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.2358C>A	1.37:g.113657326C>A		Somatic	298	1		WXS	Illumina HiSeq	Phase_I	111	15	NM_014813	0	0	2	3	1	Q9NSN2	Silent	SNP	ENST00000361127.5	37	CCDS30808.1																																																																																			.		0.468	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		A	113657326	C	A	113657326	2	1	32	1	0	0	0	0	0	0	0	1	8970	610	22	4		4	LRIG2	1	113657326	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	13310996	113657326	135593295	7	2766											
PEX19	5824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160253370	160253370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggccccgaagcatcaggggCcgtggtggtagaagggggtg	7	5	21	8	2	1	1	1	0	0	1	1	2	1	1	3	7	1	2	3	7	3	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:160253370C>T	ENST00000368072.5	-	2	151	c.130G>A	c.(130-132)Gcc>Acc	p.A44T	PEX19_ENST00000532508.1_5'UTR|DCAF8_ENST00000556710.1_Intron|PEX19_ENST00000440949.3_5'UTR|DCAF8_ENST00000608310.1_Intron	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	44	Docking to the peroxisome membrane and binding to PEX3.|Necessary for PEX19 function on peroxisome biogenesis.				chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|establishment of protein localization to peroxisome (GO:0072663)|negative regulation of lipid binding (GO:1900131)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	ATPase binding (GO:0051117)|peroxisome membrane class-1 targeting sequence binding (GO:0036105)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)	11	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCATCAGGGGCCGTGGTGGTA	0.562																																					p.A44T		.											.	PEX19-90	0			c.G130A						.						65	67	66					1																	160253370		2203	4300	6503	SO:0001583	missense	5824	exon2			CAGGGGCCGTGGT	Y09048	CCDS1201.1	1q22	2008-07-18	2004-03-17	2004-03-19	ENSG00000162735	ENSG00000162735			9713	protein-coding gene	gene with protein product	"housekeeping gene, 33kD"	600279	"peroxisomal farnesylated protein"	PXF		9339377, 10051604	Standard	NM_002857		Approved	HK33, D1S2223E, PMP1, PMPI, PXMP1		P40855	OTTHUMG00000033112	ENST00000368072.5:c.130G>A	1.37:g.160253370C>T	ENSP00000357051:p.Ala44Thr	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	200	27	NM_002857	0	0	30	70	40	D3DVE7|Q5QNY4|Q8NI97	Missense_Mutation	SNP	ENST00000368072.5	37	CCDS1201.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417114	0.62511	.	.	ENSG00000162735	ENST00000368072;ENST00000429425;ENST00000392220	.	.	.	4.61	0.66	0.17868	.	0.463549	0.23343	N	0.049217	T	0.12263	0.0298	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11792	-1.0573	9	0.13853	T	0.58	-0.5735	5.3692	0.16131	0.0:0.5415:0.1411:0.3175	.	44	P40855	PEX19_HUMAN	T	44;24;24	.	ENSP00000357051:A44T	A	-	1	0	PEX19	158519994	0.994000	0.37717	0.887000	0.34795	0.892000	0.51952	3.040000	0.49799	-0.022000	0.13986	-0.217000	0.12591	GCC	.		0.562	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857		T	160253370	C	T	160253370	3	4	32	1	0	0	0	0	1	0	0	0	11770	739	26	2	797	2	PEX19	1	160253370	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	46596044	160253370	88997251	8	2767											
FCGR2A	2212	broad.mit.edu	37	chr1	161475799	161475804	+	Splice_Site	DEL	TGAGTA	TGAGTA	-																															tctgcagacagtcaagctggTgagtatgccctttgcttcct																								rs573668650		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	TGAGTA	TGAGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:161475799_161475804delTGAGTA	ENST00000271450.6	+	2	144		c.e2+2		FCGR2A_ENST00000367972.4_Splice_Site	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GTCAAGCTGGTGAGTATGCCCTTTGC	0.471																																					.													.	FCGR2A-91	0			.						.																																			SO:0001630	splice_region_variant	2212	.			AGCTGGTGAGTAT	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3616	protein-coding gene	gene with protein product	"Immunoglobulin G Fc receptor II"	146790	"Fc fragment of IgG, low affinity IIa, receptor for (CD32)"	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.106+2TGAGTA>-	1.37:g.161475799_161475804delTGAGTA		Somatic	761	0		WXS	Illumina HiSeq	Phase_I	1172	0	.	0	0	0	0	0	Q8WUN1|Q8WW64	Splice_Site	DEL	ENST00000271450.6	37	CCDS44264.1																																																																																			.		0.471	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	Intron	-	161475804	TGAGTA	-	161475799	8	5	32	1	0	1	0	1	0	0	1	0	5800	1710	59	0	114	0	FCGR2A	1	161475799	Splice_Site	DEL	TGAGTA	TCGA-AL-3473-01A-01D-1252-08	1222429	161475799	87774822	9	2768											
TMEM183A	92703	hgsc.bcm.edu	37	chr1	202976622	202976622	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggcccggcccgctaggcaGgcctcgccccgatacggtcg	4	4	16	17	6	0	0	0	0	0	0	2	1	0	0	5	6	1	2	5	6	2	2	rs199910238	byFrequency	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:202976622G>T	ENST00000367242.3	+	1	109	c.29G>T	c.(28-30)aGg>aTg	p.R10M		NM_001079809.1|NM_138391.4	NP_001073277.1|NP_612400.3	Q8IXX5	T183A_HUMAN	transmembrane protein 183A	10			R -> M (in dbSNP:rs11558253). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|skin(3)	7			BRCA - Breast invasive adenocarcinoma(75;0.18)			CCGCTAGGCAGGCCTCGCCCC	0.766													G|||	27	0.00539137	0	0.013	5008	,	,		9878	0.001		0.0119	False		,,,				2504	0.0051				p.R10M		.											.	.	0			c.G29T						.						2	3	3					1																	202976622		1501	3310	4811	SO:0001583	missense	653659	exon1			TAGGCAGGCCTCG	BC013073	CCDS1432.1	1q31.1	2008-09-09	2006-12-18	2006-12-18	ENSG00000163444	ENSG00000163444			20173	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 37"	C1orf37			Standard	NM_138391		Approved		uc001gyu.1	Q8IXX5	OTTHUMG00000042051	ENST00000367242.3:c.29G>T	1.37:g.202976622G>T	ENSP00000356211:p.Arg10Met	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_001079809	0	0	3	14	11	A8K5W1|Q6NW15|Q96E06	Missense_Mutation	SNP	ENST00000367242.3	37	CCDS1432.1	13	0.005952380952380952	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	7	0.009234828496042216	G	15.26	2.779836	0.49891	.	.	ENSG00000163444	ENST00000367242	T	0.25414	1.8	4.82	3.91	0.45181	.	0.359030	0.24774	N	0.035707	T	0.13628	0.0330	N	0.22421	0.69	0.32624	N	0.522917	B;B;B;B	0.31351	0.32;0.32;0.284;0.284	B;B;B;B	0.34931	0.192;0.192;0.173;0.173	T	0.19224	-1.0312	10	0.49607	T	0.09	-1.6885	11.1122	0.48239	0.0865:0.0:0.9135:0.0	.	10;10;10;10	A8K5W1;Q8IXX5-2;Q1AE95;Q8IXX5	.;.;T183B_HUMAN;T183A_HUMAN	M	10	ENSP00000356211:R10M	ENSP00000356211:R10M	R	+	2	0	TMEM183A	201243245	0.084000	0.21492	0.950000	0.38849	0.370000	0.29829	0.669000	0.25142	1.253000	0.44018	0.557000	0.71058	AGG	.		0.766	TMEM183A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100129.1	NM_138391		T	202976622	G	T	202976622	3	4	32	1	0	0	0	0	1	0	0	0	16134	1000	35	4	31	4	TMEM183A	1	202976622	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	41500823	202976622	46273999	10	2769											
ESRRG	2104	hgsc.bcm.edu	37	chr1	216680501	216680501	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgaagcttctgaacggctTcaacatcttctatgtgcatg	9	13	8	11	1	4	2	1	2	3	0	4	2	4	2	1	1	4	3	1	1	4	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:216680501T>G	ENST00000408911.3	-	7	1310	c.1157A>C	c.(1156-1158)gAa>gCa	p.E386A	ESRRG_ENST00000463665.1_Missense_Mutation_p.E324A|ESRRG_ENST00000366937.1_Missense_Mutation_p.E398A|ESRRG_ENST00000487276.1_Missense_Mutation_p.E363A|ESRRG_ENST00000361395.2_Missense_Mutation_p.E363A|ESRRG_ENST00000359162.2_Missense_Mutation_p.E363A|ESRRG_ENST00000493748.1_Missense_Mutation_p.E363A|ESRRG_ENST00000361525.3_Missense_Mutation_p.E363A|ESRRG_ENST00000366938.2_Missense_Mutation_p.E363A|ESRRG_ENST00000391890.3_Missense_Mutation_p.E370A|ESRRG_ENST00000360012.3_Missense_Mutation_p.E363A|ESRRG_ENST00000366940.2_Missense_Mutation_p.E363A|ESRRG_ENST00000493603.1_Missense_Mutation_p.E363A	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	386					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|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)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CTGAACGGCTTCAACATCTTC	0.413																																					p.E398A		.											.	ESRRG-187	0			c.A1193C						.						91	84	86					1																	216680501		2203	4300	6503	SO:0001583	missense	2104	exon8			ACGGCTTCAACAT	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"Nuclear hormone receptors"	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.1157A>C	1.37:g.216680501T>G	ENSP00000386171:p.Glu386Ala	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_001243518	0	0	0	0	0	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	T	12.38	1.919936	0.33908	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748	D;D;D;D;D;D;D;D;D;D;D;D;D	0.98822	-5.16;-5.16;-5.16;-5.16;-5.16;-5.16;-5.16;-5.16;-5.16;-5.16;-4.08;-5.16;-5.16	5.61	5.61	0.85477	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.092649	0.64402	D	0.000001	D	0.97692	0.9243	M	0.61703	1.905	0.80722	D	1	B;B;B	0.27192	0.038;0.171;0.133	B;B;B	0.34536	0.185;0.097;0.102	D	0.97404	0.9998	10	0.32370	T	0.25	.	15.8204	0.78638	0.0:0.0:0.0:1.0	.	324;398;386	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	A	363;363;398;386;363;363;363;363;363;370;324;363;363;363	ENSP00000355225:E363A;ENSP00000355907:E363A;ENSP00000355904:E398A;ENSP00000386171:E386A;ENSP00000352077:E363A;ENSP00000354584:E363A;ENSP00000355905:E363A;ENSP00000353108:E363A;ENSP00000419594:E363A;ENSP00000375761:E370A;ENSP00000418629:E324A;ENSP00000419155:E363A;ENSP00000417374:E363A	ENSP00000346386:E363A	E	-	2	0	ESRRG	214747124	1.000000	0.71417	0.089000	0.20774	0.629000	0.37895	8.040000	0.89188	2.146000	0.66826	0.459000	0.35465	GAA	.		0.413	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		G	216680501	T	G	216680501	3	3	32	1	0	0	0	0	1	0	0	0	5275	1783	62	5	223	5	ESRRG	1	216680501	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	13703879	216680501	32570120	11	2770											
RYR2	6262	broad.mit.edu	37	chr1	237713899	237713899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctacactcttctggatgaccGaaccaagaaatccaacaagg	15	7	7	12	1	2	2	0	1	2	1	3	4	3	3	3	2	3	0	3	2	6	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:237713899G>A	ENST00000366574.2	+	27	3439	c.3122G>A	c.(3121-3123)cGa>cAa	p.R1041Q	RYR2_ENST00000360064.6_Missense_Mutation_p.R1039Q|RYR2_ENST00000542537.1_Missense_Mutation_p.R1025Q	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1041	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTGGATGACCGAACCAAGAAA	0.522																																					p.R1041Q													.	RYR2-158	0			c.G3122A						.						115	108	110					1																	237713899		1931	4146	6077	SO:0001583	missense	6262	exon27			ATGACCGAACCAA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3122G>A	1.37:g.237713899G>A	ENSP00000355533:p.Arg1041Gln	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	18	3	NM_001035	0	0	0	0	0	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.521739	0.85600	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91068	-2.78;-2.78;-2.78	5.14	5.14	0.70334	B30.2/SPRY domain (1);Ryanodine receptor Ryr (1);	0.000000	0.47852	U	0.000212	D	0.86481	0.5943	L	0.39566	1.225	0.80722	D	1	D	0.55605	0.972	B	0.43508	0.422	D	0.86298	0.1678	10	0.42905	T	0.14	.	12.0182	0.53326	0.0792:0.0:0.9208:0.0	.	1041	Q92736	RYR2_HUMAN	Q	1041;1039;1025	ENSP00000355533:R1041Q;ENSP00000353174:R1039Q;ENSP00000443798:R1025Q	ENSP00000353174:R1039Q	R	+	2	0	RYR2	235780522	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.929000	0.87595	2.393000	0.81446	0.563000	0.77884	CGA	.		0.522	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237713899	G	A	237713899	3	1	32	1	0	0	0	0	1	0	0	0	13801	1058	37	1	3228	1	RYR2	1	237713899	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	21033398	237713899	11536722	12	2771											
WDR35	57539	broad.mit.edu	37	chr2	20175308	20175308	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taccataaaatttccttgatTatcgtaaatgtgtatttccc	12	17	4	8	1	0	1	0	1	0	0	3	1	2	1	3	0	1	2	3	0	7	8			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:20175308T>A	ENST00000345530.3	-	6	668	c.553A>T	c.(553-555)Aat>Tat	p.N185Y	WDR35_ENST00000416055.2_5'UTR|WDR35_ENST00000281405.4_Missense_Mutation_p.N185Y	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	185					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTCCTTGATTATCGTAAATG	0.318																																					p.N185Y													.	WDR35-91	0			c.A553T						.						92	82	85					2																	20175308		2203	4300	6503	SO:0001583	missense	57539	exon6			CTTGATTATCGTA	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.553A>T	2.37:g.20175308T>A	ENSP00000314444:p.Asn185Tyr	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	24	4	NM_020779	0	0	0	0	0	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.858472	0.71834	.	.	ENSG00000118965	ENST00000345530;ENST00000281405	T;T	0.32023	1.47;1.47	5.24	5.24	0.73138	WD40/YVTN repeat-like-containing domain (1);	0.248299	0.46442	D	0.000290	T	0.50497	0.1619	M	0.75264	2.295	0.80722	D	1	P;B	0.46706	0.883;0.209	P;B	0.55785	0.784;0.322	T	0.53613	-0.8414	10	0.59425	D	0.04	-26.4985	14.6366	0.68694	0.0:0.0:0.0:1.0	.	185;185	Q9P2L0-2;Q9P2L0	.;WDR35_HUMAN	Y	185	ENSP00000314444:N185Y;ENSP00000281405:N185Y	ENSP00000281405:N185Y	N	-	1	0	WDR35	20038789	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	7.966000	0.87956	2.119000	0.64992	0.533000	0.62120	AAT	.		0.318	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		A	20175308	T	A	20175308	3	1	32	1	0	0	0	0	1	0	0	0	17322	1754	61	5	3084	5	WDR35	2	20175308	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08		20175308	223024065	13	2772											
PUM2	23369	hgsc.bcm.edu	37	chr2	20511256	20511256	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagaaagttaaaatcttactTaaaatctttgcaatcggcat	16	13	6	6	1	2	1	0	0	2	1	3	2	2	1	0	1	2	3	0	1	7	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:20511256T>C	ENST00000361078.2	-	4	539	c.517A>G	c.(517-519)Aat>Gat	p.N173D	PUM2_ENST00000319801.5_Splice_Site_p.N173D|PUM2_ENST00000420234.1_Intron|PUM2_ENST00000338086.5_Splice_Site_p.N173D|PUM2_ENST00000403432.1_Splice_Site_p.N173D|PUM2_ENST00000536417.1_Splice_Site_p.N117D			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	173	Interaction with SNAPIN.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAATCTTACTTAAAATCTTTG	0.323																																					p.N173D		.											.	PUM2-91	0			c.A517G						.						85	85	85					2																	20511256		2203	4300	6503	SO:0001630	splice_region_variant	23369	exon4			CTTACTTAAAATC	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.518+1A>G	2.37:g.20511256T>C		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_015317	0	0	0	0	0	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		.	.	.	.	.	.	.	.	.	.	T	18.22	3.576580	0.65878	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417;ENST00000442400	T;T;T;T;T;T	0.23552	1.9;2.17;2.17;2.1;1.9;1.97	5.84	5.84	0.93424	.	0.039993	0.85682	D	0.000000	T	0.32585	0.0834	M	0.65975	2.015	0.80722	D	1	B;B;P	0.35139	0.397;0.231;0.486	B;B;B	0.35607	0.206;0.037;0.149	T	0.10590	-1.0623	10	0.59425	D	0.04	-11.1657	16.2055	0.82126	0.0:0.0:0.0:1.0	.	117;173;173	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	D	173;173;173;64;173;117;173	ENSP00000338173:N173D;ENSP00000354370:N173D;ENSP00000326746:N173D;ENSP00000409905:N64D;ENSP00000385992:N173D;ENSP00000440093:N117D	ENSP00000326746:N173D	N	-	1	0	PUM2	20374737	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.929000	0.63455	2.220000	0.72140	0.533000	0.62120	AAT	.		0.323	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	Missense_Mutation	C	20511256	T	C	20511256	5	2	32	1	0	0	0	0	0	0	1	0	12858	1768	61	3	2745	3	PUM2	2	20511256	Splice_Site	SNP	T	TCGA-AL-3473-01A-01D-1252-08	335948	20511256	222688117	14	2773											
GDF7	151449	hgsc.bcm.edu	37	chr2	20870531	20870531	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccgcgcgttctgcctcttGctgcgcgcagtggcaggccc	2	8	13	18	5	2	0	0	0	2	0	2	0	2	0	4	2	3	4	4	2	0	2	rs192407174	byFrequency	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:20870531G>A	ENST00000272224.3	+	2	1275	c.699G>A	c.(697-699)ttG>ttA	p.L233L		NM_182828.2	NP_878248.2	Q7Z4P5	GDF7_HUMAN	growth differentiation factor 7	233					activin receptor signaling pathway (GO:0032924)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching morphogenesis of an epithelial tube (GO:0048754)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|forebrain morphogenesis (GO:0048853)|gland morphogenesis (GO:0022612)|growth (GO:0040007)|midbrain development (GO:0030901)|morphogenesis of an epithelial fold (GO:0060571)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of tendon cell differentiation (GO:2001051)|positive regulation of transcription, DNA-templated (GO:0045893)|reproductive structure development (GO:0048608)|roof plate formation (GO:0021509)|spinal cord association neuron differentiation (GO:0021527)	extracellular space (GO:0005615)				breast(1)|cervix(1)|endometrium(2)|lung(1)|prostate(1)|skin(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTGCCTCTTGCTGCGCGCAG	0.761													G|||	13	0.00259585	0.0015	0.0014	5008	,	,		9539	0		0.006	False		,,,				2504	0.0041				p.L233L		.											.	GDF7-226	0			c.G699A						.						2	2	2					2																	20870531		1206	2627	3833	SO:0001819	synonymous_variant	151449	exon2			CCTCTTGCTGCGC	AF522369	CCDS1701.1	2p24.1	2008-05-22			ENSG00000143869	ENSG00000143869			4222	protein-coding gene	gene with protein product		604651				10022976, 9808626	Standard	NM_182828		Approved	BMP12	uc002rdz.1	Q7Z4P5	OTTHUMG00000090781	ENST00000272224.3:c.699G>A	2.37:g.20870531G>A		Somatic	6	2		WXS	Illumina HiSeq	Phase_I	14	13	NM_182828	0	0	0	0	0		Silent	SNP	ENST00000272224.3	37	CCDS1701.1																																																																																			G|0.989;A|0.011		0.761	GDF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207563.2	NM_182828		A	20870531	G	A	20870531	2	1	32	1	0	0	0	0	0	0	0	1	6338	1310	46	2		2	GDF7	2	20870531	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	359275	20870531	222328842	15	2774											
PEX13	5194	broad.mit.edu	37	chr2	61275734	61275735	+	Frame_Shift_Ins	INS	-	-	G																															aaacggtggaatcaagtaaaINSgtttccaagcagcaacaatc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:61275734_61275735insG	ENST00000295030.5	+	4	1079_1080	c.1041_1042insG	c.(1042-1044)gttfs	p.V348fs		NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	348					cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			AATCAAGTAAAGTTTCCAAGCA	0.411																																					p.K347fs													.	PEX13-91	0			c.1041_1042insG						.																																			SO:0001589	frameshift_variant	5194	exon4			AAGTAAAGTTTCC	U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"peroxisome biogenesis factor 13"			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.1042dupG	2.37:g.61275735_61275735dupG	ENSP00000295030:p.Val348fs	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	79	8	NM_002618	0	0	0	0	0	B2RCS1	Frame_Shift_Ins	INS	ENST00000295030.5	37	CCDS1866.1																																																																																			.		0.411	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		G	61275735	-	G	61275734	7	5	32	1	0	1	1	0	0	0	0	0	11767	69	3	0	1055	0	PEX13	2	61275734	Frame_Shift_Ins	INS	-	TCGA-AL-3473-01A-01D-1252-08	40405203	61275734	181923639	16	2775											
ANKRD36B	0	hgsc.bcm.edu	37	chr2	98128421	98128421	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttttccaggttttggtttTttattgtgtctttttccagc	3	24	7	7	0	2	0	0	0	2	0	4	0	4	0	2	2	1	2	2	2	1	10	rs200637231		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:98128421T>C								AC159540.1 (37372 upstream) : ANKRD36B (35606 downstream)																							GTTTTGGTTTTTTATTGTGTC	0.368																																					p.K967R		.											.	.	0			c.A2900G						.						1	1	1					2																	98128421		294	676	970	SO:0001628	intergenic_variant	57730	exon39			TGGTTTTTTATTG																													2.37:g.98128421T>C		Somatic	143	2		WXS	Illumina HiSeq	Phase_I	26	4	NM_025190	0	0	5	5	0		Missense_Mutation	SNP		37																																																																																				T|0.250;C|0.750	0	0.368									C	98128421	T	C	98128421	1	2	32	0	1	0	0	0	0	0	0	0	666	1841	64	3		3	ANKRD36B	2	98128421	IGR	SNP	T	TCGA-AL-3473-01A-01D-1252-08	36852687	98128421	145070952	17	2776											
SCN3A	6328	hgsc.bcm.edu	37	chr2	165947167	165947167	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agatccatggcaataagctgGactttgttgggttttgctat	9	15	11	6	0	0	1	0	0	0	1	1	2	1	2	1	3	2	5	1	3	3	6			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:165947167G>C	ENST00000360093.3	-	28	5987	c.5496C>G	c.(5494-5496)gtC>gtG	p.V1832V	SCN3A_ENST00000465043.1_5'Flank|AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000283254.7_Silent_p.V1832V|SCN3A_ENST00000409101.3_Silent_p.V1783V|SCN3A_ENST00000540861.1_Silent_p.V315V	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1832					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAATAAGCTGGACTTTGTTGG	0.463																																					p.V1832V		.											.	SCN3A-141	0			c.C5496G						.						102	105	104					2																	165947167		2203	4300	6503	SO:0001819	synonymous_variant	6328	exon28			AAGCTGGACTTTG	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.5496C>G	2.37:g.165947167G>C		Somatic	238	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_006922	0	0	0	0	0	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				.		0.463	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	165947167	G	C	165947167	2	2	32	1	0	0	0	0	0	0	0	1	13950	1161	41	4		4	SCN3A	2	165947167	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	67818746	165947167	77252206	18	2777											
LRP2	4036	broad.mit.edu;ucsc.edu	37	chr2	170029726	170029726	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagttgtcacagagatgggCagagctcactgaaaagggag	14	6	15	6	0	2	3	2	1	0	2	2	6	2	4	0	2	1	3	0	2	3	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:170029726C>T	ENST00000263816.3	-	57	11308	c.11023G>A	c.(11023-11025)Gcc>Acc	p.A3675T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3675					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CAGAGATGGGCAGAGCTCACT	0.468																																					p.A3675T													.	LRP2-175	0			c.G11023A						.						83	81	82					2																	170029726		2203	4300	6503	SO:0001583	missense	4036	exon57			GATGGGCAGAGCT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11023G>A	2.37:g.170029726C>T	ENSP00000263816:p.Ala3675Thr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	69	6	NM_004525	0	0	0	1	1	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.765698	0.31228	.	.	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.89810	-2.57	5.61	3.79	0.43588	.	0.161611	0.53938	D	0.000050	T	0.80444	0.4624	L	0.28115	0.83	0.80722	D	1	P	0.40578	0.722	B	0.36719	0.231	T	0.74945	-0.3491	10	0.14656	T	0.56	.	14.6412	0.68726	0.3478:0.6522:0.0:0.0	.	3675	P98164	LRP2_HUMAN	T	3675;370	ENSP00000263816:A3675T	ENSP00000263816:A3675T	A	-	1	0	LRP2	169737972	1.000000	0.71417	0.092000	0.20876	0.755000	0.42902	2.239000	0.43079	0.703000	0.31848	0.655000	0.94253	GCC	.		0.468	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170029726	C	T	170029726	3	4	32	1	0	0	0	0	1	0	0	0	8981	710	25	2	3036	2	LRP2	2	170029726	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	4082559	170029726	73169647	19	2778											
SPHKAP	80309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	228882137	228882137	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atagtaatccagcagtaactCaaatcctctcccttcatttt	12	14	3	12	0	3	0	2	0	1	0	6	0	5	0	3	0	2	3	3	0	4	6			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:228882137C>T	ENST00000392056.3	-	7	3479	c.3433G>A	c.(3433-3435)Gag>Aag	p.E1145K	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E1145K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1145						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		AGCAGTAACTCAAATCCTCTC	0.527																																					p.E1145K		.											.	SPHKAP-167	0			c.G3433A						.						65	54	58					2																	228882137		2203	4300	6503	SO:0001583	missense	80309	exon7			GTAACTCAAATCC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.3433G>A	2.37:g.228882137C>T	ENSP00000375909:p.Glu1145Lys	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	157	25	NM_030623	0	0	0	0	0	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	30	5.054264	0.93793	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.62498	0.02;0.02	5.57	5.57	0.84162	.	0.089852	0.85682	D	0.000000	T	0.65842	0.2730	N	0.19112	0.55	0.58432	D	0.999995	P;D;D	0.65815	0.952;0.995;0.99	P;P;P	0.59487	0.601;0.82;0.858	T	0.69793	-0.5049	10	0.72032	D	0.01	.	18.8971	0.92427	0.0:1.0:0.0:0.0	.	176;1145;1145	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	K	1145	ENSP00000375909:E1145K;ENSP00000339886:E1145K	ENSP00000339886:E1145K	E	-	1	0	SPHKAP	228590381	1.000000	0.71417	0.983000	0.44433	0.989000	0.77384	7.152000	0.77419	2.785000	0.95823	0.655000	0.94253	GAG	.		0.527	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228882137	C	T	228882137	3	4	32	1	0	0	0	0	1	0	0	0	15080	835	29	2	1693	2	SPHKAP	2	228882137	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	58852411	228882137	14317236	20	2779											
VHL	7428	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	10188203	10188204	+	Frame_Shift_Ins	INS	-	-	T																															gcttgtcccgataggtcaccINStttggctcttcagagatgca																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:10188203_10188204insT	ENST00000256474.2	+	2	1186_1187	c.346_347insT	c.(346-348)cttfs	p.L116fs	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	116	Involved in binding to CCT complex.		L -> V (in VHLD). {ECO:0000269|PubMed:8730290}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(3)|p.L116fs*43(3)|p.W117fs*14(2)|p.L116V(1)|p.H115fs*15(1)|p.L116fs*16(1)|p.W117fs*42(1)|p.H115fs*41(1)|p.H115fs*42(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATAGGTCACCTTTGGCTCTTC	0.53		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																												p.L116fs		.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	.	VHL-6694	14	Deletion - Frameshift(9)|Unknown(3)|Substitution - Missense(1)|Insertion - Frameshift(1)	kidney(14)	c.346_347insT	GRCh37	CM961424	VHL	M		.																																			SO:0001589	frameshift_variant	7428	exon2	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	.	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.349dupT	3.37:g.10188206_10188206dupT	ENSP00000256474:p.Leu116fs	Somatic	308	0		WXS	Illumina HiSeq	Phase_I	443	81	NM_000551	0	0	0	0	0	B2RE45|Q13599|Q6PDA9	Frame_Shift_Ins	INS	ENST00000256474.2	37	CCDS2597.1																																																																																			.		0.53	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		T	10188204	-	T	10188203	7	5	32	1	0	1	1	0	0	0	0	0	17195	681	24	0	352	0	VHL	3	10188203	Frame_Shift_Ins	INS	-	TCGA-AL-3473-01A-01D-1252-08		10188203	187834227	21	2780											
OXSM	54995	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	25832524	25832524	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttaatcatgtccaactgcCtgcaaaatttcctgaaaatt	13	14	4	10	0	2	1	1	1	1	0	4	1	4	1	3	0	3	1	3	0	6	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:25832524C>A	ENST00000280701.3	+	2	112	c.13C>A	c.(13-15)Ctg>Atg	p.L5M	NGLY1_ENST00000417874.2_5'Flank|OXSM_ENST00000420173.2_Missense_Mutation_p.L5M|OXSM_ENST00000449808.1_3'UTR	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	5					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GTCCAACTGCCTGCAAAATTT	0.368																																					p.L5M		.											.	OXSM-132	0			c.C13A						.						83	88	86					3																	25832524		2203	4300	6503	SO:0001583	missense	54995	exon2			AACTGCCTGCAAA	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.13C>A	3.37:g.25832524C>A	ENSP00000280701:p.Leu5Met	Somatic	278	0		WXS	Illumina HiSeq	Phase_I	196	36	NM_017897	0	0	3	11	8		Missense_Mutation	SNP	ENST00000280701.3	37	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	C	7.760	0.705106	0.15172	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	4.84	3.7	0.42460	.	1.003210	0.08029	N	0.993289	T	0.24774	0.0601	N	0.08118	0	0.24531	N	0.994111	P;P	0.47677	0.899;0.838	P;B	0.51355	0.667;0.372	T	0.14117	-1.0484	9	0.52906	T	0.07	-10.4228	5.7793	0.18297	0.0:0.0885:0.1686:0.7429	.	5;5	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	M	5	.	ENSP00000280701:L5M	L	+	1	2	OXSM	25807528	0.036000	0.19791	0.572000	0.28498	0.418000	0.31294	0.834000	0.27518	0.992000	0.38840	-0.367000	0.07326	CTG	.		0.368	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		A	25832524	C	A	25832524	3	1	32	1	0	0	0	0	1	0	0	0	11361	680	24	4	15	4	OXSM	3	25832524	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	15644321	25832524	172189906	22	2781											
ZNF167	55888	broad.mit.edu	37	chr3	44612491	44612491	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcaccagagacttcacaCgggtgaaaagccctataaat	14	7	9	11	2	1	2	1	1	0	1	2	3	1	2	2	2	1	1	2	2	5	3	rs373307729		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:44612491C>T	ENST00000273320.3	+	6	2318	c.1889C>T	c.(1888-1890)aCg>aTg	p.T630M	ZKSCAN7_ENST00000431636.1_Intron|ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.T630M|RP11-944L7.4_ENST00000457331.1_RNA|RP11-944L7.5_ENST00000419137.1_Intron|ZKSCAN7_ENST00000341840.3_Intron	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	630					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T630M(1)									AGACTTCACACGGGTGAAAAG	0.408																																					p.T630M													.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1889T						.	C	MET/THR,	1,4405		0,1,2202	66	70	69		1889,	4.2	0.9	3		69	0,8600		0,0,4300	no	missense,intron	ZNF167	NM_018651.2,NM_025169.1	81,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,	630/755,	44612491	1,13005	2203	4300	6503	SO:0001583	missense	55888	exon6			TTCACACGGGTGA	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.1889C>T	3.37:g.44612491C>T	ENSP00000273320:p.Thr630Met	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_018651	0	0	1	1	0	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Missense_Mutation	SNP	ENST00000273320.3	37	CCDS2715.1	.	.	.	.	.	.	.	.	.	.	.	19.67	3.870147	0.72065	2.27E-4	0.0	ENSG00000196345	ENST00000426540;ENST00000273320;ENST00000315777	T;T	0.26373	1.74;1.74	4.2	4.2	0.49525	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.241708	0.21541	N	0.072899	T	0.52933	0.1765	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.60831	-0.7185	10	0.87932	D	0	-6.8142	15.5027	0.75713	0.0:1.0:0.0:0.0	.	630	Q9P0L1	ZN167_HUMAN	M	630;630;68	ENSP00000395524:T630M;ENSP00000273320:T630M	ENSP00000273320:T630M	T	+	2	0	ZNF167	44587495	0.125000	0.22332	0.913000	0.36048	0.946000	0.59487	1.167000	0.31847	2.179000	0.69175	0.655000	0.94253	ACG	.		0.408	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		T	44612491	C	T	44612491	3	4	32	1	0	0	0	0	1	0	0	0	17773	536	19	1	1907	1	ZNF167	3	44612491	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	18779967	44612491	153409939	23	2782											
LAMB2	3913	broad.mit.edu	37	chr3	49167097	49167098	+	Frame_Shift_Del	DEL	GG	GG	-																															cagtaacaggatccactgttGgggtcacaaggagtgctccc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:49167097_49167098delGG	ENST00000418109.1	-	12	1621_1622	c.1457_1458delCC	c.(1456-1458)cccfs	p.P486fs	LAMB2_ENST00000305544.4_Frame_Shift_Del_p.P486fs	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	486	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATCCACTGTTGGGGTCACAAGG	0.559																																					p.486_486del													.	LAMB2-93	0			c.1457_1458del						.																																			SO:0001589	frameshift_variant	3913	exon11			ACTGTTGGGGTCA		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1457_1458delCC	3.37:g.49167099_49167100delGG	ENSP00000388325:p.Pro486fs	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	125	0	NM_002292	0	0	0	0	0	Q16321	Frame_Shift_Del	DEL	ENST00000418109.1	37	CCDS2789.1																																																																																			.		0.559	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		-	49167098	GG	-	49167097	7	5	32	1	0	1	0	1	0	0	0	0	8632	1335	47	0	4026	0	LAMB2	3	49167097	Frame_Shift_Del	DEL	GG	TCGA-AL-3473-01A-01D-1252-08	4554606	49167097	148855333	24	2783											
BAP1	8314	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	52437889	52437889	+	Frame_Shift_Del	DEL	C	C	-																															ccgctcaatgcccctggcttCcctgttcccttccccttata																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:52437889delC	ENST00000460680.1	-	13	1743	c.1272delG	c.(1270-1272)gggfs	p.G424fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.G406fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K425fs*4(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCCCTGGCTTCCCTGTTCCCT	0.557			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.G424fs	GBM(101;493 1458 7992 21037 25532)	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1-1032	1	Deletion - Frameshift(1)	kidney(1)	c.1272delG						.						85	89	88					3																	52437889		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1272delG	3.37:g.52437889delC	ENSP00000417132:p.Gly424fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	333	62	NM_004656	0	0	0	0	0	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	37	CCDS2853.1																																																																																			.		0.557	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437889	C	-	52437889	7	5	32	1	0	1	0	1	0	0	0	0	1312	842	30	0	937	0	BAP1	3	52437889	Frame_Shift_Del	DEL	C	TCGA-AL-3473-01A-01D-1252-08	3270792	52437889	145584541	25	2784											
SPATA12	353324	hgsc.bcm.edu	37	chr3	57108279	57108279	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtatactccaacacacacaTacacacacatctgtaatcaa	18	8	2	13	0	2	0	1	0	1	0	3	0	3	0	1	0	3	2	1	0	6	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:57108279T>C	ENST00000334325.1	+	2	1232	c.557T>C	c.(556-558)aTa>aCa	p.I186T	ARHGEF3_ENST00000338458.4_Intron	NM_181727.1	NP_859078.1	Q7Z6I5	SPT12_HUMAN	spermatogenesis associated 12	186										large_intestine(2)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0111)|Kidney(284;0.0129)		AACACACACATACACACACAT	0.507																																					p.I186T		.											.	SPATA12-90	0			c.T557C						.						99	100	100					3																	57108279		2183	4253	6436	SO:0001583	missense	353324	exon2			CACACATACACAC	AY221117	CCDS2879.1	3p21.2	2012-09-19			ENSG00000186451	ENSG00000186451			23221	protein-coding gene	gene with protein product		609869				22981541, 17251597	Standard	NM_181727		Approved		uc003dij.1	Q7Z6I5	OTTHUMG00000158862	ENST00000334325.1:c.557T>C	3.37:g.57108279T>C	ENSP00000335392:p.Ile186Thr	Somatic	253	1		WXS	Illumina HiSeq	Phase_I	117	8	NM_181727	0	0	0	0	0	A0AVA8|B2RMW1	Missense_Mutation	SNP	ENST00000334325.1	37	CCDS2879.1	.	.	.	.	.	.	.	.	.	.	T	0.666	-0.803844	0.02819	.	.	ENSG00000186451	ENST00000334325	.	.	.	2.03	-2.63	0.06133	.	.	.	.	.	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17319	-1.0373	8	0.87932	D	0	.	2.9297	0.05795	0.2105:0.2753:0.0:0.5142	.	186	Q7Z6I5	SPT12_HUMAN	T	186	.	ENSP00000335392:I186T	I	+	2	0	SPATA12	57083319	0.001000	0.12720	0.000000	0.03702	0.085000	0.17905	-0.127000	0.10547	-0.825000	0.04290	-1.417000	0.01113	ATA	.		0.507	SPATA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352457.2	NM_181727		C	57108279	T	C	57108279	3	2	32	1	0	0	0	0	1	0	0	0	15031	1406	49	3	559	3	SPATA12	3	57108279	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	4670390	57108279	140914151	26	2785											
PROS1	5627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	93624723	93624723	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cacaaatttgactgcaacctCcatttatatttgagggatct	12	14	6	9	0	1	2	0	2	1	0	2	3	2	3	2	1	2	1	2	1	4	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:93624723C>G	ENST00000394236.3	-	6	822	c.506G>C	c.(505-507)gGa>gCa	p.G169A	PROS1_ENST00000407433.1_Missense_Mutation_p.G38A	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	169	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	ACTGCAACCTCCATTTATATT	0.299																																					p.G169A		.											.	PROS1-153	0			c.G506C						.						77	79	78					3																	93624723		2199	4296	6495	SO:0001583	missense	5627	exon6			CAACCTCCATTTA		CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.506G>C	3.37:g.93624723C>G	ENSP00000377783:p.Gly169Ala	Somatic	268	0		WXS	Illumina HiSeq	Phase_I	287	47	NM_000313	0	0	6	14	8	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	37	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.464378	0.63513	.	.	ENSG00000184500	ENST00000394236;ENST00000407433;ENST00000348974;ENST00000472684	D;D;D;D	0.98329	-4.87;-4.87;-4.87;-1.67	4.44	4.44	0.53790	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.125904	0.53938	D	0.000053	D	0.96334	0.8804	M	0.67397	2.05	0.40346	D	0.979083	P	0.46064	0.872	B	0.35655	0.207	D	0.96712	0.9526	10	0.62326	D	0.03	.	13.0646	0.59025	0.0:0.8385:0.1615:0.0	.	169	P07225	PROS_HUMAN	A	169;38;201;38	ENSP00000377783:G169A;ENSP00000385794:G38A;ENSP00000330021:G201A;ENSP00000419616:G38A	ENSP00000330021:G201A	G	-	2	0	PROS1	95107413	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.172000	0.42463	2.314000	0.78098	0.484000	0.47621	GGA	.		0.299	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		G	93624723	C	G	93624723	3	3	32	1	0	0	0	0	1	0	0	0	12587	855	30	4	1564	4	PROS1	3	93624723	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	36516444	93624723	104397707	27	2786											
FBXO40	51725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121341915	121341915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcaagacctttgccattaagCcggaggttgctccagagctg	9	10	11	11	1	1	2	1	0	0	2	2	3	2	3	4	2	4	3	4	2	2	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:121341915C>T	ENST00000338040.4	+	3	2053	c.1639C>T	c.(1639-1641)Ccg>Tcg	p.P547S		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	547					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		TGCCATTAAGCCGGAGGTTGC	0.493																																					p.P547S		.											.	FBXO40-273	0			c.C1639T						.						56	57	57					3																	121341915		2203	4300	6503	SO:0001583	missense	51725	exon3			ATTAAGCCGGAGG	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.1639C>T	3.37:g.121341915C>T	ENSP00000337510:p.Pro547Ser	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	133	24	NM_016298	0	0	0	0	0	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.475767	0.63737	.	.	ENSG00000163833	ENST00000338040	T	0.33865	1.39	5.96	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.60573	0.2279	M	0.77313	2.365	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.65685	-0.6108	10	0.87932	D	0	-6.694	12.9482	0.58384	0.0:0.9222:0.0:0.0778	.	547	Q9UH90	FBX40_HUMAN	S	547	ENSP00000337510:P547S	ENSP00000337510:P547S	P	+	1	0	FBXO40	122824605	1.000000	0.71417	0.997000	0.53966	0.957000	0.61999	7.818000	0.86416	1.541000	0.49316	-0.142000	0.14014	CCG	.		0.493	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		T	121341915	C	T	121341915	3	4	32	1	0	0	0	0	1	0	0	0	5768	739	26	2	1645	2	FBXO40	3	121341915	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	27717192	121341915	76680515	28	2787											
INTU	27152	hgsc.bcm.edu	37	chr4	128608920	128608920	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcagcctgcgaaactgcaTtccagcgccagtcccagtgc	8	8	9	16	2	1	0	1	0	0	0	3	1	3	0	4	0	6	1	4	0	1	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr4:128608920T>C	ENST00000335251.6	+	8	1450	c.1347T>C	c.(1345-1347)caT>caC	p.H449H		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	449					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						CGAAACTGCATTCCAGCGCCA	0.473																																					p.H449H		.											.	INTU-91	0			c.T1347C						.						131	124	126					4																	128608920		2203	4300	6503	SO:0001819	synonymous_variant	27152	exon8			ACTGCATTCCAGC	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.1347T>C	4.37:g.128608920T>C		Somatic	188	2		WXS	Illumina HiSeq	Phase_I	35	2	NM_015693	0	0	2	2	0	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Silent	SNP	ENST00000335251.6	37	CCDS34061.1																																																																																			.		0.473	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		C	128608920	T	C	128608920	2	2	32	1	0	0	0	0	0	0	0	1	7807	1490	52	3		3	INTU	4	128608920	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08		128608920	62545356	29	2788											
ITGA1	3672	hgsc.bcm.edu	37	chr5	52223476	52223476	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tgtaaagttggatatcccttCctgagaagaggagagatggt	12	11	13	5	0	0	3	0	1	0	3	2	7	2	5	2	3	0	2	2	3	4	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:52223476C>G	ENST00000282588.6	+	20	3134	c.2676C>G	c.(2674-2676)ttC>ttG	p.F892L		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	892					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				GATATCCCTTCCTGAGAAGAG	0.343																																					p.F892L		.											.	ITGA1-228	0			c.C2676G						.						127	123	124					5																	52223476		2203	4300	6503	SO:0001583	missense	3672	exon20			TCCCTTCCTGAGA	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.2676C>G	5.37:g.52223476C>G	ENSP00000282588:p.Phe892Leu	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_181501	0	0	7	7	0	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	37	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905631	0.52333	.	.	ENSG00000213949	ENST00000282588	T	0.44083	0.93	5.52	1.77	0.24775	Integrin alpha-2 (1);	0.048823	0.85682	D	0.000000	T	0.43055	0.1230	L	0.42245	1.32	0.53005	D	0.99996	P	0.46859	0.885	P	0.52031	0.688	T	0.23368	-1.0190	10	0.62326	D	0.03	.	8.4809	0.33043	0.0:0.6851:0.0:0.3149	.	892	P56199	ITA1_HUMAN	L	892	ENSP00000282588:F892L	ENSP00000282588:F892L	F	+	3	2	ITGA1	52259233	1.000000	0.71417	0.989000	0.46669	0.712000	0.41017	0.952000	0.29149	0.105000	0.17753	-0.157000	0.13467	TTC	.		0.343	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		G	52223476	C	G	52223476	3	3	32	1	0	0	0	0	1	0	0	0	7893	854	30	4	2754	4	ITGA1	5	52223476	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08		52223476	128691784	30	2789											
GPBP1	65056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	56542173	56542173	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctccaaggatgctggtcatTaagaaaggtaatacaaaaga	17	8	10	6	0	1	2	1	0	0	2	2	3	2	3	1	3	2	3	1	3	7	3	rs371740495		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:56542173T>A	ENST00000506184.2	+	7	1630	c.525T>A	c.(523-525)atT>atA	p.I175I	GPBP1_ENST00000264779.6_Silent_p.I182I|GPBP1_ENST00000454432.2_Silent_p.I195I|GPBP1_ENST00000538707.1_Silent_p.I182I|GPBP1_ENST00000424459.3_Silent_p.I195I|GPBP1_ENST00000511209.1_Silent_p.I182I|GPBP1_ENST00000514387.2_Silent_p.I4I			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	175					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		TGCTGGTCATTAAGAAAGGTA	0.383																																					p.I182I		.											.	GPBP1-135	0			c.T546A						.						84	86	85					5																	56542173		2203	4300	6503	SO:0001819	synonymous_variant	65056	exon6			GGTCATTAAGAAA		CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.525T>A	5.37:g.56542173T>A		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	68	10	NM_001127236	0	0	28	47	19	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Silent	SNP	ENST00000506184.2	37	CCDS34162.1																																																																																			.		0.383	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913		A	56542173	T	A	56542173	2	1	32	1	0	0	0	0	0	0	0	1	6615	1742	61	5		5	GPBP1	5	56542173	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08	4318697	56542173	124373087	31	2790											
MAST4	375449	hgsc.bcm.edu	37	chr5	66432458	66432458	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caggatctgattaccttactCctcaggcagaatcccctgga	10	10	8	13	0	2	2	1	1	1	1	4	4	4	4	4	3	2	1	4	3	3	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:66432458C>G	ENST00000403625.2	+	19	2755	c.2460C>G	c.(2458-2460)ctC>ctG	p.L820L	MAST4_ENST00000405643.1_Silent_p.L641L|MAST4_ENST00000403666.1_Silent_p.L631L|MAST4_ENST00000404260.3_Silent_p.L823L|MAST4_ENST00000261569.7_Silent_p.L626L	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	823	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TTACCTTACTCCTCAGGCAGA	0.443																																					p.L820L		.											.	MAST4-647	0			c.C2460G						.						51	51	51					5																	66432458		1871	4104	5975	SO:0001819	synonymous_variant	375449	exon19			CTTACTCCTCAGG	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2460C>G	5.37:g.66432458C>G		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	9	2	NM_001164664	0	0	1	1	0	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1																																																																																			.		0.443	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			G	66432458	C	G	66432458	2	3	32	1	0	0	0	0	0	0	0	1	9352	842	30	4		4	MAST4	5	66432458	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	9890285	66432458	114482802	32	2791											
PCDHA4	56144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140188710	140188710	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acggacgctccgcgccaccgCctactggtactggtgaagga	8	6	13	14	5	0	1	0	1	0	0	1	3	1	3	4	4	2	2	4	4	3	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:140188710C>T	ENST00000530339.1	+	1	1938	c.1938C>T	c.(1936-1938)cgC>cgT	p.R646R	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.R646R|PCDHA4_ENST00000356878.4_Silent_p.R646R	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	646	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGCCACCGCCTACTGGTAC	0.682																																					p.R646R		.											.	PCDHA4-96	0			c.C1938T						.						74	76	75					5																	140188710		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CCACCGCCTACTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1938C>T	5.37:g.140188710C>T		Somatic	156	0		WXS	Illumina HiSeq	Phase_I	345	50	NM_031500	0	0	0	0	0	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.		0.682	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140188710	C	T	140188710	2	4	32	1	0	0	0	0	0	0	0	1	11552	726	26	2		2	PCDHA4	5	140188710	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	73756252	140188710	40726550	33	2792											
LAMA2	3908	broad.mit.edu	37	chr6	129670492	129670492	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttgacgactaccgctgcacgGcttgtccacggggatatgaa	9	9	12	11	4	0	2	0	2	0	0	1	4	1	3	2	3	2	3	2	3	3	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr6:129670492G>A	ENST00000421865.2	+	31	4535	c.4486G>A	c.(4486-4488)Gct>Act	p.A1496T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1496	Laminin EGF-like 16. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCGCTGCACGGCTTGTCCACG	0.428																																					p.A1496T													.	LAMA2-162	0			c.G4486A						.						119	113	115					6																	129670492		2203	4300	6503	SO:0001583	missense	3908	exon31			TGCACGGCTTGTC	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.4486G>A	6.37:g.129670492G>A	ENSP00000400365:p.Ala1496Thr	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	27	4	NM_000426	0	0	0	0	0	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.491014	0.84962	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.63255	-0.03	5.98	5.98	0.97165	EGF-like, laminin (4);	0.057949	0.64402	D	0.000001	T	0.78635	0.4314	M	0.81239	2.535	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.91635	0.999;0.993	T	0.76424	-0.2964	10	0.45353	T	0.12	.	20.452	0.99131	0.0:0.0:1.0:0.0	.	1496;1496	A6NF00;P24043	.;LAMA2_HUMAN	T	1496	ENSP00000400365:A1496T	ENSP00000346769:A1496T	A	+	1	0	LAMA2	129712185	1.000000	0.71417	0.108000	0.21378	0.295000	0.27426	4.093000	0.57714	2.838000	0.97847	0.591000	0.81541	GCT	.		0.428	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129670492	G	A	129670492	3	1	32	1	0	0	0	0	1	0	0	0	8627	1203	42	2	4608	2	LAMA2	6	129670492	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		129670492	41444575	34	2793											
STXBP5	134957	broad.mit.edu	37	chr6	147637421	147637421	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggaaactccggagggtgaGcagccaccacctttgccaac	10	6	12	13	1	0	1	0	1	0	0	1	3	1	3	5	3	5	1	5	3	2	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr6:147637421G>A	ENST00000321680.6	+	16	1680	c.1680G>A	c.(1678-1680)gaG>gaA	p.E560E	STXBP5_ENST00000367481.3_Silent_p.E560E|STXBP5_ENST00000367480.3_Silent_p.E560E|STXBP5_ENST00000179882.6_Silent_p.E231E	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	560					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		CGGAGGGTGAGCAGCCACCAC	0.458																																					p.E560E													.	STXBP5-90	0			c.G1680A						.						87	87	87					6																	147637421		2203	4300	6503	SO:0001819	synonymous_variant	134957	exon16			GGGTGAGCAGCCA	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1680G>A	6.37:g.147637421G>A		Somatic	96	1		WXS	Illumina HiSeq	Phase_I	23	3	NM_139244	0	0	2	3	1	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Silent	SNP	ENST00000321680.6	37	CCDS47499.1																																																																																			.		0.458	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			A	147637421	G	A	147637421	2	1	32	1	0	0	0	0	0	0	0	1	15388	962	34	2		2	STXBP5	6	147637421	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	17966929	147637421	23477646	35	2794											
NOD1	10392	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	30472766	30472766	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgccaaactctctgccActtcatcgttgagttcattt	7	17	5	12	1	4	1	2	1	2	0	6	1	4	1	2	0	3	2	2	0	1	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:30472766A>G	ENST00000222823.4	-	12	3176	c.2651T>C	c.(2650-2652)gTg>gCg	p.V884A		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	884					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						ACTCTCTGCCACTTCATCGTT	0.393																																					p.V884A		.											.	NOD1-229	0			c.T2651C						.						133	117	123					7																	30472766		2203	4300	6503	SO:0001583	missense	10392	exon12			TCTGCCACTTCAT	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"Nucleotide-binding domain and leucine rich repeat containing"	16390	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1", "NLR family, CARD domain containing 1"	605980	"caspase recruitment domain family, member 4"	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.2651T>C	7.37:g.30472766A>G	ENSP00000222823:p.Val884Ala	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	44	8	NM_006092	0	0	23	25	2	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	.	.	.	.	.	.	.	.	.	.	A	3.545	-0.092917	0.07053	.	.	ENSG00000106100	ENST00000222823	T	0.51574	0.7	5.74	0.404	0.16355	.	0.399974	0.28544	N	0.014963	T	0.14013	0.0339	N	0.00815	-1.16	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09885	-1.0654	10	0.12103	T	0.63	.	8.3537	0.32318	0.5662:0.0:0.4338:0.0	.	884	Q9Y239	NOD1_HUMAN	A	884	ENSP00000222823:V884A	ENSP00000222823:V884A	V	-	2	0	NOD1	30439291	0.488000	0.25996	0.983000	0.44433	0.937000	0.57800	0.908000	0.28545	0.117000	0.18138	0.460000	0.39030	GTG	.		0.393	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			G	30472766	A	G	30472766	3	3	32	1	0	0	0	0	1	0	0	0	10542	159	6	3	222	3	NOD1	7	30472766	Missense_Mutation	SNP	A	TCGA-AL-3473-01A-01D-1252-08		30472766	128665897	36	2795											
HERPUD2	64224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	35674964	35674964	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggccactaggtttggagctGgtgggggttcttctccagga	5	11	17	8	0	2	0	0	0	2	0	3	2	2	2	2	7	1	3	2	7	1	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:35674964G>T	ENST00000396081.1	-	6	1526	c.722C>A	c.(721-723)cCa>cAa	p.P241Q	HERPUD2_ENST00000311350.3_Missense_Mutation_p.P241Q|HERPUD2_ENST00000426180.1_5'UTR	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	241					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						GTTTGGAGCTGGTGGGGGTTC	0.473																																					p.P241Q		.											.	HERPUD2-93	0			c.C722A						.						155	158	157					7																	35674964		2203	4300	6503	SO:0001583	missense	64224	exon7			GGAGCTGGTGGGG	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.722C>A	7.37:g.35674964G>T	ENSP00000379390:p.Pro241Gln	Somatic	358	1		WXS	Illumina HiSeq	Phase_I	120	17	NM_022373	0	0	44	55	11	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	37	CCDS5446.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.624185	0.46840	.	.	ENSG00000122557	ENST00000396081;ENST00000311350;ENST00000438224	T;T;T	0.32272	1.9;1.9;1.46	5.96	5.96	0.96718	.	0.264276	0.43579	D	0.000544	T	0.26774	0.0655	L	0.47190	1.495	0.44295	D	0.997168	B	0.16396	0.017	B	0.12837	0.008	T	0.06588	-1.0818	10	0.10636	T	0.68	-12.3571	14.5539	0.68086	0.0693:0.0:0.9307:0.0	.	241	Q9BSE4	HERP2_HUMAN	Q	241;241;177	ENSP00000379390:P241Q;ENSP00000310729:P241Q;ENSP00000415475:P177Q	ENSP00000310729:P241Q	P	-	2	0	HERPUD2	35641489	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	4.904000	0.63279	2.832000	0.97577	0.655000	0.94253	CCA	.		0.473	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		T	35674964	G	T	35674964	3	4	32	1	0	0	0	0	1	0	0	0	7085	1348	47	4	510	4	HERPUD2	7	35674964	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	5202198	35674964	123463699	37	2796											
NAPEPLD	222236	broad.mit.edu	37	chr7	102769017	102769017	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaggggtttttccatgttggCcacggattcacaaatctccc	8	12	10	11	1	2	0	1	0	1	0	4	2	3	1	3	4	0	2	3	4	1	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:102769017C>T	ENST00000417955.1	-	2	361	c.207G>A	c.(205-207)tgG>tgA	p.W69*	NAPEPLD_ENST00000465647.1_Nonsense_Mutation_p.W69*|NAPEPLD_ENST00000427257.1_Nonsense_Mutation_p.W69*|NAPEPLD_ENST00000455523.2_Nonsense_Mutation_p.W142*|NAPEPLD_ENST00000341533.4_Nonsense_Mutation_p.W69*			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	69					phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TCCATGTTGGCCACGGATTCA	0.403																																					p.W69X													.	NAPEPLD-227	0			c.G207A						.						127	116	119					7																	102769017		2203	4300	6503	SO:0001587	stop_gained	222236	exon2			TGTTGGCCACGGA	BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.207G>A	7.37:g.102769017C>T	ENSP00000407112:p.Trp69*	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	63	4	NM_001122838	0	0	3	3	0	Q5CZ87|Q769K1	Nonsense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.673876	0.88445	.	.	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523;ENST00000418294	.	.	.	6.16	6.16	0.99307	.	0.101764	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-13.6216	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	69;69;69;69;142;69	.	ENSP00000340093:W69X	W	-	3	0	NAPEPLD	102556253	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	7.150000	0.77403	2.937000	0.99478	0.650000	0.86243	TGG	.		0.403	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990		T	102769017	C	T	102769017	4	4	32	1	0	0	0	0	0	1	0	0	10188	740	26	2	990	2	NAPEPLD	7	102769017	Nonsense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	67094053	102769017	56369646	38	2797											
SSPO	23145	hgsc.bcm.edu	37	chr7	149487608	149487608	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgagggccccgacgcctgcgTtgaggctcccgcgcccccgg	3	4	15	19	7	0	1	0	1	0	0	1	3	1	1	6	3	1	2	6	3	0	1	rs1635798	byFrequency	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:149487608T>G	ENST00000378016.2	+	0	4921							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GACGCCTGCGTTGAGGCTCCC	0.776													G|||	1320	0.263578	0.6959	0.1095	5008	,	,		8211	0.1171		0.0885	False		,,,				2504	0.1196				.		.											.	.	0			c.4921+1T>G						.						1	1	1					7																	149487608		434	1167	1601			23145	exon32			CCTGCGTTGAGGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149487608T>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_198455	0	0	0	0	0	Q76B61	Splice_Site	SNP	ENST00000378016.2	37																																																																																				T|0.784;G|0.216		0.776	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149487608	T	G	149487608	1	3	32	0	1	0	0	0	0	0	0	0	15221	1739	60	5		5	SSPO	7	149487608	RNA	SNP	T	TCGA-AL-3473-01A-01D-1252-08	46718591	149487608	9651055	39	2798											
KIAA1967	57805	broad.mit.edu;bcgsc.ca	37	chr8	22474942	22474942	+	Frame_Shift_Del	DEL	G	G	-																															tgcctctgtagaaggaggatGggcttttgcccaaaccactc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr8:22474942delG	ENST00000308511.4	+	15	2104	c.1855delG	c.(1855-1857)gggfs	p.G619fs	CCAR2_ENST00000389279.3_Frame_Shift_Del_p.G619fs|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Frame_Shift_Del_p.G294fs			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	619					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GAAGGAGGATGGGCTTTTGCC	0.502																																					p.G619fs													.	KIAA1967-92	0			c.1855delG						.						101	113	109					8																	22474942		2203	4300	6503	SO:0001589	frameshift_variant	57805	exon15			GAGGATGGGCTTT	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1855delG	8.37:g.22474942delG	ENSP00000310670:p.Gly619fs	Somatic	322	0		WXS	Illumina HiSeq	Phase_I	669	97	NM_021174	0	0	0	0	0	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Frame_Shift_Del	DEL	ENST00000308511.4	37	CCDS34863.1																																																																																			.		0.502	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		-	22474942	G	-	22474942	7	5	32	1	0	1	0	1	0	0	0	0	8286	1348	47	0	1909	0	KIAA1967	8	22474942	Frame_Shift_Del	DEL	G	TCGA-AL-3473-01A-01D-1252-08		22474942	123889080	40	2799											
GAS1	2619	hgsc.bcm.edu	37	chr9	89560846	89560846	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgccgtcgtcgtcgtccagCggctgctcaccacccgcgcc	4	6	11	20	8	1	0	1	0	0	0	5	0	2	0	5	1	2	2	5	1	0	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr9:89560846C>G	ENST00000298743.7	-	1	1258	c.849G>C	c.(847-849)ccG>ccC	p.P283P	RP11-276H19.1_ENST00000415801.1_lincRNA	NM_002048.2	NP_002039.2	P54826	GAS1_HUMAN	growth arrest-specific 1	283					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cerebellum morphogenesis (GO:0021587)|developmental growth (GO:0048589)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|eye morphogenesis (GO:0048592)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein processing (GO:0010955)|negative regulation of smoothened signaling pathway (GO:0045879)|odontogenesis (GO:0042476)|outer ear morphogenesis (GO:0042473)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|programmed cell death (GO:0012501)|regulation of apoptotic process (GO:0042981)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|regulation of smoothened signaling pathway (GO:0008589)	anchored component of plasma membrane (GO:0046658)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|lung(2)|skin(1)	4						CGTCGTCCAGCGGCTGCTCAC	0.756																																					p.P283P		.											.	GAS1-226	0			c.G849C						.						4	6	5					9																	89560846		1831	3830	5661	SO:0001819	synonymous_variant	2619	exon1			GTCCAGCGGCTGC		CCDS6674.1	9q21.3-q22	2008-07-21			ENSG00000180447	ENSG00000180447			4165	protein-coding gene	gene with protein product	"Growth arrest-specific gene-1"	139185				8307588	Standard	NM_002048		Approved		uc004aox.4	P54826	OTTHUMG00000020141	ENST00000298743.7:c.849G>C	9.37:g.89560846C>G		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_002048	0	0	0	0	0	B9EGM4|Q6B086	Silent	SNP	ENST00000298743.7	37	CCDS6674.1																																																																																			.		0.756	GAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052928.1	NM_002048		G	89560846	C	G	89560846	2	3	32	1	0	0	0	0	0	0	0	1	6264	755	27	4		4	GAS1	9	89560846	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08		89560846	51652585	41	2800											
OR1L4	254973	hgsc.bcm.edu	37	chr9	125486286	125486286	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacatggagacaaagaattaTagcagcagcacctcaggctt	15	7	10	9	0	1	2	1	0	0	2	1	4	1	2	1	2	3	4	1	2	4	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr9:125486286T>C	ENST00000259466.1	+	1	18	c.18T>C	c.(16-18)taT>taC	p.Y6Y		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(3)|lung(13)|prostate(1)|skin(1)	20						CAAAGAATTATAGCAGCAGCA	0.488																																					p.Y6Y		.											.	OR1L4-68	0			c.T18C						.						151	146	148					9																	125486286		2203	4300	6503	SO:0001819	synonymous_variant	254973	exon1			GAATTATAGCAGC		CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"GPCR / Class A : Olfactory receptors"	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.18T>C	9.37:g.125486286T>C		Somatic	248	2		WXS	Illumina HiSeq	Phase_I	40	4	NM_001005235	0	0	0	0	0	Q6IFN0|Q96R81	Silent	SNP	ENST00000259466.1	37	CCDS35129.1																																																																																			.		0.488	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1			C	125486286	T	C	125486286	2	2	32	1	0	0	0	0	0	0	0	1	10991	1413	49	3		3	OR1L4	9	125486286	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08	35925440	125486286	15727145	42	2801											
PITRM1	10531	broad.mit.edu;bcgsc.ca	37	chr10	3199645	3199645	+	Frame_Shift_Del	DEL	A	A	-																															actgatgtcagcatcagcccAaagctggtagactgatgttt																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:3199645delA	ENST00000224949.4	-	12	1363	c.1329delT	c.(1327-1329)tttfs	p.F443fs	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Frame_Shift_Del_p.F411fs|PITRM1_ENST00000380994.1_5'UTR|PITRM1_ENST00000380989.2_Frame_Shift_Del_p.F443fs|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	443					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						GCATCAGCCCAAAGCTGGTAG	0.318																																					p.F443fs													.	PITRM1-91	0			c.1329delT						.						112	106	108					10																	3199645		1840	4105	5945	SO:0001589	frameshift_variant	10531	exon12			CAGCCCAAAGCTG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1329delT	10.37:g.3199645delA	ENSP00000224949:p.Phe443fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	34	8	NM_014889	0	0	0	0	0	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Frame_Shift_Del	DEL	ENST00000224949.4	37	CCDS59208.1																																																																																			.		0.318	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			-	3199645	A	-	3199645	7	5	32	1	0	1	0	1	0	0	0	0	11979	127	5	0	1848	0	PITRM1	10	3199645	Frame_Shift_Del	DEL	A	TCGA-AL-3473-01A-01D-1252-08		3199645	132335102	43	2802											
EPC1	80314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	32560793	32560793	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgccgttgatggacttgtAtgtacaagtgctgttggtgt	6	15	13	7	1	0	1	0	1	0	0	0	2	0	2	2	2	3	5	2	2	3	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:32560793A>G	ENST00000263062.8	-	14	2396	c.2127T>C	c.(2125-2127)caT>caC	p.H709H	RP11-166N17.1_ENST00000415731.2_RNA|EPC1_ENST00000375110.2_Silent_p.H636H|EPC1_ENST00000319778.6_Silent_p.H686H	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	709					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				ATGGACTTGTATGTACAAGTG	0.413																																					p.H709H		.											.	EPC1-93	0			c.T2127C						.						113	113	113					10																	32560793		2203	4300	6503	SO:0001819	synonymous_variant	80314	exon14			ACTTGTATGTACA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.2127T>C	10.37:g.32560793A>G		Somatic	179	1		WXS	Illumina HiSeq	Phase_I	53	5	NM_025209	0	0	18	25	7	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Silent	SNP	ENST00000263062.8	37	CCDS7172.1																																																																																			.		0.413	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			G	32560793	A	G	32560793	2	3	32	1	0	0	0	0	0	0	0	1	5173	446	16	3		3	EPC1	10	32560793	Silent	SNP	A	TCGA-AL-3473-01A-01D-1252-08	29361148	32560793	102973954	44	2803											
CUEDC2	79004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104184514	104184514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcccaggtcctccaggaccCcaagcacataggagaagatg	12	4	12	13	0	0	2	0	0	0	2	2	4	2	3	5	4	1	1	5	4	3	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:104184514C>T	ENST00000369937.4	-	3	255	c.110G>A	c.(109-111)gGg>gAg	p.G37E	CUEDC2_ENST00000465409.1_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	37						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTCCAGGACCCCAAGCACATA	0.592																																					p.G37E		.											.	CUEDC2-90	0			c.G110A						.						45	49	48					10																	104184514		1955	4136	6091	SO:0001583	missense	79004	exon3			AGGACCCCAAGCA	BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"chromosome 10 open reading frame 66"	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.110G>A	10.37:g.104184514C>T	ENSP00000358953:p.Gly37Glu	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	216	30	NM_024040	0	0	68	118	50	D3DR88|Q9BWG8	Missense_Mutation	SNP	ENST00000369937.4	37	CCDS41566.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.419316	0.83559	.	.	ENSG00000107874	ENST00000369937	D	0.85088	-1.94	5.36	5.36	0.76844	.	0.051192	0.85682	D	0.000000	D	0.89061	0.6608	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90111	0.4192	10	0.87932	D	0	-28.8879	18.4607	0.90737	0.0:1.0:0.0:0.0	.	37	Q9H467	CUED2_HUMAN	E	37	ENSP00000358953:G37E	ENSP00000358953:G37E	G	-	2	0	CUEDC2	104174504	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.245000	0.78237	2.688000	0.91661	0.561000	0.74099	GGG	.		0.592	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040		T	104184514	C	T	104184514	3	4	32	1	0	0	0	0	1	0	0	0	4059	623	22	2	781	2	CUEDC2	10	104184514	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	71623721	104184514	31350233	45	2804											
SORCS3	22986	hgsc.bcm.edu	37	chr10	107022222	107022222	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cggagcctgaggagctgctgGacaaagagctggacacgcgg	10	4	17	10	3	0	2	0	1	0	1	0	6	0	6	1	5	4	3	1	5	1	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:107022222G>C	ENST00000369701.3	+	26	3804	c.3577G>C	c.(3577-3579)Gac>Cac	p.D1193H		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1193					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GGAGCTGCTGGACAAAGAGCT	0.542																																					p.D1193H	NSCLC(116;1497 1690 7108 13108 14106)	.											.	SORCS3-99	0			c.G3577C						.						69	55	60					10																	107022222		2203	4300	6503	SO:0001583	missense	22986	exon26			CTGCTGGACAAAG	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3577G>C	10.37:g.107022222G>C	ENSP00000358715:p.Asp1193His	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_014978	0	0	10	10	0	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902493	0.92035	.	.	ENSG00000156395	ENST00000369701	T	0.19394	2.15	5.84	5.84	0.93424	.	0.105330	0.64402	D	0.000004	T	0.34106	0.0886	N	0.24115	0.695	0.58432	D	0.999998	D	0.76494	0.999	D	0.70935	0.971	T	0.02512	-1.1148	9	.	.	.	.	20.1579	0.98126	0.0:0.0:1.0:0.0	.	1193	Q9UPU3	SORC3_HUMAN	H	1193	ENSP00000358715:D1193H	.	D	+	1	0	SORCS3	107012212	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.767000	0.95098	0.555000	0.69702	GAC	.		0.542	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		C	107022222	G	C	107022222	3	2	32	1	0	0	0	0	1	0	0	0	14964	1174	41	4	3679	4	SORCS3	10	107022222	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	2837708	107022222	28512525	46	2805											
HTRA1	5654	broad.mit.edu	37	chr10	124273765	124273765	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggacagtccgtggtctccGccaatgatgtcagcgacgtc	8	9	12	12	4	2	1	1	1	1	0	5	3	3	2	3	2	1	0	3	2	1	0	rs371279115		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:124273765G>A	ENST00000368984.3	+	9	1461	c.1333G>A	c.(1333-1335)Gcc>Acc	p.A445T		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	445	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CGTGGTCTCCGCCAATGATGT	0.468													g|||	1	0.000199681	8e-04	0	5008	,	,		21134	0		0	False		,,,				2504	0				p.A445T													.	HTRA1-90	0			c.G1333A						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	283	250	262		1333	5.4	1	10		262	0,8600		0,0,4300	no	missense	HTRA1	NM_002775.4	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	445/481	124273765	1,13005	2203	4300	6503	SO:0001583	missense	5654	exon9			GTCTCCGCCAATG	AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"Serine peptidases / Serine peptidases"	9476	protein-coding gene	gene with protein product		602194	"protease, serine, 11 (IGF binding)"	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.1333G>A	10.37:g.124273765G>A	ENSP00000357980:p.Ala445Thr	Somatic	319	0		WXS	Illumina HiSeq	Phase_I	397	10	NM_002775	0	0	216	216	0	D3DRE4|Q9UNS5	Missense_Mutation	SNP	ENST00000368984.3	37	CCDS7630.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.953604	0.34471	2.27E-4	0.0	ENSG00000166033	ENST00000368984;ENST00000435263;ENST00000420892	T;T	0.27104	1.69;1.69	5.38	5.38	0.77491	PDZ/DHR/GLGF (4);	0.173330	0.50627	D	0.000107	T	0.17152	0.0412	N	0.26042	0.785	0.58432	D	0.999999	B	0.23990	0.095	B	0.22152	0.038	T	0.07790	-1.0754	10	0.13108	T	0.6	-11.7132	12.4957	0.55927	0.076:0.0:0.924:0.0	.	445	Q92743	HTRA1_HUMAN	T	445;412;186	ENSP00000357980:A445T;ENSP00000412676:A186T	ENSP00000357980:A445T	A	+	1	0	HTRA1	124263755	1.000000	0.71417	0.960000	0.40013	0.714000	0.41099	7.493000	0.81493	2.515000	0.84797	0.655000	0.94253	GCC	.		0.468	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775		A	124273765	G	A	124273765	3	1	32	1	0	0	0	0	1	0	0	0	7474	1087	38	1	1367	1	HTRA1	10	124273765	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	17251543	124273765	11260982	47	2806											
MUC2	4583	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	1104253	1104253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcgctcccctaggcatctggGgagcgggtgagcggggtggg	4	6	21	10	3	1	1	0	1	1	0	2	2	2	2	2	7	2	2	2	7	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:1104253G>A	ENST00000441003.2	+	49	8471	c.8444G>A	c.(8443-8445)gGg>gAg	p.G2815E		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5177					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	AGGCATCTGGGGAGCGGGTGA	0.692																																					p.G2811E		.											.	MUC2-90	0			c.G8432A						.						27	31	30					11																	1104253		1848	4082	5930	SO:0001583	missense	4583	exon50			ATCTGGGGAGCGG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8444G>A	11.37:g.1104253G>A	ENSP00000415183:p.Gly2815Glu	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	111	17	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	6.142	0.394436	0.11638	.	.	ENSG00000198788	ENST00000441003	T	0.14516	2.5	2.52	0.508	0.16972	.	.	.	.	.	T	0.10594	0.0259	L	0.44542	1.39	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.33471	-0.9867	9	0.87932	D	0	.	3.1167	0.06377	0.153:0.0:0.5868:0.2602	.	2815	E7EUV1	.	E	2815	ENSP00000415183:G2815E	ENSP00000415183:G2815E	G	+	2	0	MUC2	1094253	0.029000	0.19370	0.000000	0.03702	0.009000	0.06853	2.405000	0.44548	0.131000	0.18576	0.491000	0.48974	GGG	.		0.692	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1104253	G	A	1104253	3	1	32	1	0	0	0	0	1	0	0	0	10000	1232	43	2	8630	2	MUC2	11	1104253	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		1104253	133902263	48	2807											
MRGPRX3	117195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	18159638	18159638	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttctccagagggctctgcagGacacgcctgaggtggatgaa	9	8	14	10	1	2	3	0	2	2	1	3	5	2	5	2	4	1	2	2	4	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:18159638G>A	ENST00000396275.2	+	3	1250	c.889G>A	c.(889-891)Gac>Aac	p.D297N		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GGCTCTGCAGGACACGCCTGA	0.557																																					p.D297N		.											.	MRGPRX3-92	0			c.G889A						.						45	48	47					11																	18159638		2200	4292	6492	SO:0001583	missense	117195	exon3			CTGCAGGACACGC		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.889G>A	11.37:g.18159638G>A	ENSP00000379571:p.Asp297Asn	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	168	10	NM_054031	0	0	0	0	0	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.428032	0.62844	.	.	ENSG00000179826	ENST00000396275	T	0.25912	1.77	1.3	1.3	0.21679	.	0.429218	0.22048	N	0.065351	T	0.47469	0.1447	M	0.84433	2.695	0.24902	N	0.9921	D	0.89917	1.0	D	0.76575	0.988	T	0.18461	-1.0336	10	0.87932	D	0	.	5.9358	0.19165	0.0:0.0:1.0:0.0	.	297	Q96LB0	MRGX3_HUMAN	N	297	ENSP00000379571:D297N	ENSP00000379571:D297N	D	+	1	0	MRGPRX3	18116214	0.485000	0.25972	0.781000	0.31783	0.068000	0.16541	1.158000	0.31737	1.011000	0.39340	0.195000	0.17529	GAC	.		0.557	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		A	18159638	G	A	18159638	3	1	32	1	0	0	0	0	1	0	0	0	9793	1174	41	2	891	2	MRGPRX3	11	18159638	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	17055385	18159638	116846878	49	2808											
SNX15	29907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64802325	64802325	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgggggccgtaggccggtTtgaagcctcagtgatcgagg	6	8	17	10	3	1	2	1	2	0	0	2	3	1	2	4	5	1	2	4	5	2	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:64802325T>G	ENST00000377244.3	+	4	393	c.263T>G	c.(262-264)tTt>tGt	p.F88C	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Missense_Mutation_p.F88C	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	88	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						GTAGGCCGGTTTGAAGCCTCA	0.622																																					p.F88C	Esophageal Squamous(56;269 1304 3324 8253)	.											.	SNX15-227	0			c.T263G						.						55	54	54					11																	64802325		2201	4297	6498	SO:0001583	missense	29907	exon4			GCCGGTTTGAAGC	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"Sorting nexins"	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.263T>G	11.37:g.64802325T>G	ENSP00000366452:p.Phe88Cys	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	237	27	NM_147777	0	0	0	0	0	E5KQS6|Q9NRS5	Missense_Mutation	SNP	ENST00000377244.3	37	CCDS8089.1	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220623	0.22457	.	.	ENSG00000110025	ENST00000377244;ENST00000534637;ENST00000524831;ENST00000352068	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.24	5.24	0.73138	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.72922	0.3521	M	0.94142	3.5	0.80722	D	1	B;B;D	0.89917	0.002;0.032;1.0	B;B;D	0.91635	0.004;0.031;0.999	T	0.81028	-0.1118	10	0.87932	D	0	-11.7965	13.084	0.59129	0.0:0.0:0.0:1.0	.	88;88;88	E5KQS5;E5KQS6;Q9NRS6	.;.;SNX15_HUMAN	C	88;84;76;88	ENSP00000366452:F88C;ENSP00000437277:F84C;ENSP00000431690:F76C;ENSP00000316410:F88C	ENSP00000316410:F88C	F	+	2	0	SNX15	64558901	1.000000	0.71417	0.793000	0.32043	0.045000	0.14185	7.364000	0.79526	1.991000	0.58162	0.374000	0.22700	TTT	.		0.622	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3			G	64802325	T	G	64802325	3	3	32	1	0	0	0	0	1	0	0	0	14918	1841	64	5	277	5	SNX15	11	64802325	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	46642687	64802325	70204191	50	2809											
GDPD5	81544	broad.mit.edu	37	chr11	75146590	75146591	+	Frame_Shift_Ins	INS	-	-	G																															atgagggtcttggtgtggctINSgccaccccctcgggggccca																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:75146590_75146591insG	ENST00000336898.3	-	17	2616_2617	c.1779_1780insC	c.(1777-1782)ggcagcfs	p.S594fs	GDPD5_ENST00000376282.3_Frame_Shift_Ins_p.S475fs|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000526177.1_Frame_Shift_Ins_p.S456fs|GDPD5_ENST00000533784.1_Frame_Shift_Ins_p.S475fs|GDPD5_ENST00000533805.1_Frame_Shift_Ins_p.S349fs|GDPD5_ENST00000529721.1_Frame_Shift_Ins_p.S594fs	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	594					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						TTGGTGTGGCTGCCACCCCCTC	0.579																																					p.S594fs													.	GDPD5-91	0			c.1780_1781insC						.																																			SO:0001589	frameshift_variant	81544	exon17			TGTGGCTGCCACC	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1780dupC	11.37:g.75146591_75146591dupG	ENSP00000337972:p.Ser594fs	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	234	4	NM_030792	0	0	0	0	0	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Frame_Shift_Ins	INS	ENST00000336898.3	37	CCDS8238.1																																																																																			.		0.579	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		G	75146591	-	G	75146590	7	5	32	1	0	1	1	0	0	0	0	0	6347	1580	55	0	41	0	GDPD5	11	75146590	Frame_Shift_Ins	INS	-	TCGA-AL-3473-01A-01D-1252-08	10344265	75146590	59859926	51	2810											
BIRC3	330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102206814	102206814	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatgaacaagaacatgatgTtattaaacagaagacacaga	21	8	7	5	0	0	6	0	2	0	4	0	6	0	6	0	0	3	1	0	0	8	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:102206814T>G	ENST00000263464.3	+	7	4192	c.1442T>G	c.(1441-1443)gTt>gGt	p.V481G	BIRC3_ENST00000532808.1_Missense_Mutation_p.V481G	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	481	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GAACATGATGTTATTAAACAG	0.353			T	MALT1	MALT																																p.V481G		.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	BIRC3-662	0			c.T1442G						.						104	107	106					11																	102206814		2203	4298	6501	SO:0001583	missense	330	exon7			ATGATGTTATTAA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.1442T>G	11.37:g.102206814T>G	ENSP00000263464:p.Val481Gly	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	63	12	NM_001165	0	0	308	621	313	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	37	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	T	9.986	1.229473	0.22542	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	T;T	0.19532	2.14;2.14	4.98	1.35	0.21983	DEATH-like (2);Caspase Recruitment (3);	0.559991	0.21816	N	0.068695	T	0.16981	0.0408	L	0.58669	1.825	0.31062	N	0.71399	B	0.10296	0.003	B	0.15484	0.013	T	0.12915	-1.0529	10	0.27785	T	0.31	.	4.8847	0.13697	0.0:0.231:0.1477:0.6212	.	481	Q13489	BIRC3_HUMAN	G	481;481;249	ENSP00000263464:V481G;ENSP00000432907:V481G	ENSP00000263464:V481G	V	+	2	0	BIRC3	101712024	0.052000	0.20516	0.281000	0.24762	0.902000	0.53008	0.187000	0.16998	0.130000	0.18549	-0.316000	0.08728	GTT	.		0.353	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		G	102206814	T	G	102206814	3	3	32	1	0	0	0	0	1	0	0	0	1437	1725	60	5	1464	5	BIRC3	11	102206814	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	27060224	102206814	32799702	52	2811											
CASP1	834	broad.mit.edu;ucsc.edu	37	chr11	104903803	104903803	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattacctggaaaggaagAaagtactccttgagagtctt	14	10	10	7	0	1	2	0	1	1	2	2	5	2	4	2	2	3	2	2	2	5	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:104903803A>T	ENST00000533400.1	-	3	360	c.325T>A	c.(325-327)Tct>Act	p.S109T	CASP1_ENST00000415981.2_Intron|CASP1_ENST00000393136.4_Intron|CASP1_ENST00000534497.1_Intron|CASP1_ENST00000527979.1_Intron|CASP1_ENST00000526568.1_Intron|CASP1_ENST00000525825.1_Intron|CASP1_ENST00000598974.1_Missense_Mutation_p.S109T|CASP1_ENST00000593315.1_Intron|CASP1_ENST00000446369.1_Intron|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000436863.3_Missense_Mutation_p.S109T|CASP1_ENST00000528974.1_Missense_Mutation_p.S70T|CASP1_ENST00000594519.1_Intron	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	109					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	GGAAAGGAAGAAAGTACTCCT	0.358																																					p.S109T	NSCLC(41;1246 1743 4934)												.	CASP1-661	0			c.T325A						.						89	93	92					11																	104903803		2202	4299	6501	SO:0001583	missense	834	exon3			AGGAAGAAAGTAC	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"Caspases"	1499	protein-coding gene	gene with protein product	"caspase-1", "interleukin 1, beta, convertase"	147678	"caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)", "caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.325T>A	11.37:g.104903803A>T	ENSP00000433138:p.Ser109Thr	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_001257118	0	0	0	0	0	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Missense_Mutation	SNP	ENST00000533400.1	37	CCDS8330.1	.	.	.	.	.	.	.	.	.	.	.	1.034	-0.681045	0.03353	.	.	ENSG00000137752	ENST00000533400;ENST00000436863;ENST00000528974	T;T;T	0.02579	4.97;4.97;4.24	3.03	-1.43	0.08884	.	4.281240	0.00654	U	0.000568	T	0.02193	0.0068	L	0.29908	0.895	0.09310	N	1	B;B;B	0.32160	0.255;0.358;0.121	B;B;B	0.25987	0.049;0.065;0.047	T	0.41070	-0.9529	10	0.15066	T	0.55	.	2.6498	0.04995	0.3929:0.0:0.3944:0.2126	.	109;70;109	B4DKN4;B4DVD8;P29466	.;.;CASP1_HUMAN	T	109;109;70	ENSP00000433138:S109T;ENSP00000410076:S109T;ENSP00000434259:S70T	ENSP00000410076:S109T	S	-	1	0	CASP1	104409013	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.732000	0.04904	-0.249000	0.09569	-0.321000	0.08615	TCT	.		0.358	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292		T	104903803	A	T	104903803	3	4	32	1	0	0	0	0	1	0	0	0	2674	246	9	5	917	5	CASP1	11	104903803	Missense_Mutation	SNP	A	TCGA-AL-3473-01A-01D-1252-08	2696989	104903803	30102713	53	2812											
OR8G1	219865	hgsc.bcm.edu	37	chr11	124135727	124135727	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aataaagatgtccacgttgcCctgaagaaaacgctagggaa	16	7	10	8	2	0	3	0	1	0	2	1	4	1	4	2	1	2	2	2	1	8	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:124135727C>T	ENST00000524943.2	+	1	1005	c.1005C>T	c.(1003-1005)gcC>gcT	p.A335A	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	335						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		TCCACGTTGCCCTGAAGAAAA	0.403																																					p.A335A	Ovarian(169;523 1969 8640 31295 51256)	.											.	.	0			c.C1005T						.						54	52	53					11																	124135727		2018	4203	6221	SO:0001819	synonymous_variant	219865	exon1			CGTTGCCCTGAAG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"GPCR / Class A : Olfactory receptors"	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.1005C>T	11.37:g.124135727C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	46	11	NM_001005198	0	0	0	0	0	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	37																																																																																				.		0.403	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		T	124135727	C	T	124135727	2	4	32	1	0	0	0	0	0	0	0	1	11260	610	22	2		2	OR8G1	11	124135727	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	19231924	124135727	10870789	54	2813											
PKNOX2	63876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	125280693	125280693	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggagccttataccaacCggttaccatggtaacctccc	10	9	9	13	1	0	0	0	0	0	0	1	1	1	1	6	4	5	2	6	4	5	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:125280693C>T	ENST00000298282.9	+	9	1008	c.737C>T	c.(736-738)cCg>cTg	p.P246L	PKNOX2_ENST00000542175.1_Missense_Mutation_p.P182L|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	246					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TTATACCAACCGGTTACCATG	0.577																																					p.P246L		.											.	PKNOX2-93	0			c.C737T						.						94	91	92					11																	125280693		1947	4142	6089	SO:0001583	missense	63876	exon9			ACCAACCGGTTAC	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.737C>T	11.37:g.125280693C>T	ENSP00000298282:p.Pro246Leu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	137	27	NM_022062	0	0	0	0	0	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	37	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.066060	0.76187	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.25	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.93324	0.7872	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	D	0.93357	0.6723	10	0.59425	D	0.04	-12.9127	19.0405	0.92997	0.0:1.0:0.0:0.0	.	182;246	F5GZ15;Q96KN3	.;PKNX2_HUMAN	L	217;217;246;182;234	ENSP00000434732:P217L;ENSP00000433971:P217L;ENSP00000298282:P246L;ENSP00000441470:P182L	ENSP00000298282:P246L	P	+	2	0	PKNOX2	124785903	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.191000	0.77763	2.586000	0.87340	0.655000	0.94253	CCG	.		0.577	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			T	125280693	C	T	125280693	3	4	32	1	0	0	0	0	1	0	0	0	12009	652	23	1	759	1	PKNOX2	11	125280693	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	1144966	125280693	9725823	55	2814											
SNX19	399979	ucsc.edu	37	chr11	130785010	130785010	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcactggctgggcagggTgctggatctctggccttgga	4	9	19	9	0	1	0	0	0	1	0	2	2	1	2	1	8	1	4	1	8	0	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:130785010T>G	ENST00000265909.4	-	1	1394	c.825A>C	c.(823-825)gcA>gcC	p.A275A	SNX19_ENST00000528555.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000533214.1_Silent_p.A275A|SNX19_ENST00000533318.1_Intron|SNX19_ENST00000539184.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	275					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CTGGGCAGGGTGCTGGATCTC	0.547																																					p.A275A													.	SNX19-229	0			c.A825C						.						70	77	74					11																	130785010		2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			GCAGGGTGCTGGA	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.825A>C	11.37:g.130785010T>G		Somatic	193	21		WXS	Illumina HiSeq		287	18	NM_014758	0	0	9	10	1	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			.		0.547	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		G	130785010	T	G	130785010	2	3	32	1	0	0	0	0	0	0	0	1	14922	1683	59	5		5	SNX19	11	130785010	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08	5504317	130785010	4221506	56	2815											
WNK1	65125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	978188	978188	+	Intron	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttacaagaatccccactttTcttctgtttcccccaaggaa	10	13	5	13	0	2	1	0	0	2	1	4	2	4	2	4	1	1	2	4	1	5	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:978188T>A	ENST00000315939.6	+	9	2782				WNK1_ENST00000340908.4_Intron|WNK1_ENST00000574564.1_Missense_Mutation_p.F398Y|WNK1_ENST00000530271.2_Missense_Mutation_p.F1184Y|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000537687.1_Missense_Mutation_p.F1099Y	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TCCCCACTTTTCTTCTGTTTC	0.493																																					p.F1184Y	Colon(19;451 567 6672 12618 28860)	.											.	WNK1-916	0			c.T3551A						.						323	310	314					12																	978188		1914	4143	6057	SO:0001627	intron_variant	65125	exon10			CACTTTTCTTCTG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2140-2243T>A	12.37:g.978188T>A		Somatic	735	1		WXS	Illumina HiSeq	Phase_I	315	51	NM_213655	0	0	1	3	2	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440816	0.43326	.	.	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.16743	2.32;2.32	5.85	5.85	0.93711	.	.	.	.	.	T	0.23133	0.0559	.	.	.	0.80722	D	1	P	0.46656	0.882	B	0.44278	0.445	T	0.00842	-1.1544	8	0.52906	T	0.07	.	14.8154	0.70031	0.0:0.0:0.0:1.0	.	1184	F5H2M7	.	Y	1099;1184	ENSP00000444465:F1099Y;ENSP00000433548:F1184Y	ENSP00000433548:F1184Y	F	+	2	0	WNK1	848449	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.421000	0.52742	2.233000	0.73108	0.455000	0.32223	TTC	.		0.493	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	978188	T	A	978188	1	1	32	0	1	0	0	0	0	0	0	0	17410	1783	62	5		5	WNK1	12	978188	Intron	SNP	T	TCGA-AL-3473-01A-01D-1252-08		978188	132873707	57	2816											
CD27	939	hgsc.bcm.edu;broad.mit.edu	37	chr12	6554287	6554287	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggccacatccctggtggcTgtgcgttctggggaccctgg	4	9	15	13	2	1	0	0	0	1	0	2	1	2	1	3	6	1	2	3	6	0	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:6554287T>A	ENST00000266557.3	+	1	255	c.26T>A	c.(25-27)cTg>cAg	p.L9Q	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	9					cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						CCCTGGTGGCTGTGCGTTCTG	0.642																																					p.L9Q		.											.	CD27-659	0			c.T26A						.						18	24	22					12																	6554287		2202	4299	6501	SO:0001583	missense	939	exon1			GGTGGCTGTGCGT	M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"Tumor necrosis factor receptor superfamily", "CD molecules"	11922	protein-coding gene	gene with protein product		186711	"tumor necrosis factor receptor superfamily, member 7"	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.26T>A	12.37:g.6554287T>A	ENSP00000266557:p.Leu9Gln	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	41	6	NM_001242	0	0	140	140	0	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.473069	0.63737	.	.	ENSG00000139193	ENST00000266557	D	0.95788	-3.81	4.91	4.91	0.64330	.	0.254840	0.25922	N	0.027424	D	0.95726	0.8610	L	0.36672	1.1	0.41219	D	0.986497	D	0.89917	1.0	D	0.85130	0.997	D	0.95798	0.8830	10	0.72032	D	0.01	-12.3828	10.8657	0.46853	0.0:0.0:0.0:1.0	.	9	P26842	CD27_HUMAN	Q	9	ENSP00000266557:L9Q	ENSP00000266557:L9Q	L	+	2	0	CD27	6424548	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	3.432000	0.52824	2.064000	0.61679	0.455000	0.32223	CTG	.		0.642	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1			A	6554287	T	A	6554287	3	1	32	1	0	0	0	0	1	0	0	0	2996	1580	55	5	28	5	CD27	12	6554287	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	5576099	6554287	127297608	58	2817											
SOX5	6660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	24102509	24102509	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtactcacctttcaaactcCtgaggtaaatcagggtcagt	11	12	8	10	0	4	1	4	1	0	0	5	1	5	1	2	2	2	2	2	2	4	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:24102509C>G	ENST00000451604.2	-	1	128	c.27G>C	c.(25-27)caG>caC	p.Q9H	SOX5_ENST00000545921.1_Intron|SOX5_ENST00000441133.2_Missense_Mutation_p.Q9H|SOX5_ENST00000541847.1_Intron|SOX5_ENST00000536850.1_5'UTR|SOX5_ENST00000309359.1_5'UTR|SOX5_ENST00000381381.2_5'UTR|SOX5_ENST00000537393.1_Missense_Mutation_p.Q9H			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	9					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	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)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TTTCAAACTCCTGAGGTAAAT	0.433																																					p.Q9H		.											.	SOX5-655	0			c.G27C						.						112	102	106					12																	24102509		2203	4300	6503	SO:0001583	missense	6660	exon1			AAACTCCTGAGGT	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"SRY (sex determining region Y)-boxes"	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.27G>C	12.37:g.24102509C>G	ENSP00000398273:p.Gln9His	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	98	17	NM_006940	0	0	0	0	0	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	c	15.91	2.971147	0.53614	.	.	ENSG00000134532	ENST00000451604;ENST00000537393;ENST00000441133	D;D	0.97378	-4.34;-4.36	5.28	5.28	0.74379	.	0.154071	0.45126	D	0.000386	D	0.96222	0.8768	L	0.54323	1.7	0.80722	D	1	P;P	0.44309	0.832;0.826	P;B	0.44990	0.466;0.276	D	0.96291	0.9214	10	0.52906	T	0.07	.	17.0691	0.86568	0.0:1.0:0.0:0.0	.	9;9	G3V0H1;P35711	.;SOX5_HUMAN	H	9	ENSP00000398273:Q9H;ENSP00000439832:Q9H	ENSP00000393240:Q9H	Q	-	3	2	SOX5	23993776	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.509000	0.73725	2.631000	0.89168	0.645000	0.84053	CAG	.		0.433	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		G	24102509	C	G	24102509	3	3	32	1	0	0	0	0	1	0	0	0	14986	680	24	4	2334	4	SOX5	12	24102509	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	17548222	24102509	109749386	59	2818											
DDX11	1663	hgsc.bcm.edu	37	chr12	31242981	31242981	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcccttgggaaggaggccCgggcctgtccctattacggg	5	8	16	12	2	0	0	0	0	0	0	1	2	1	2	4	6	1	0	4	6	3	3	rs3892690		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:31242981C>A	ENST00000407793.2	+	9	1293	c.1042C>A	c.(1042-1044)Cgg>Agg	p.R348R	DDX11_ENST00000545668.1_Silent_p.R348R|DDX11_ENST00000228264.6_Silent_p.R322R|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Silent_p.R348R|DDX11_ENST00000542838.1_Silent_p.R348R	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	348	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GAAGGAGGCCCGGGCCTGTCC	0.647										Multiple Myeloma(12;0.14)																											p.R348R		.											.	DDX11-229	0			c.C1042A						.						1	2	2					12																	31242981		1322	2876	4198	SO:0001819	synonymous_variant	1663	exon9			GAGGCCCGGGCCT	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1042C>A	12.37:g.31242981C>A		Somatic	21	1		WXS	Illumina HiSeq	Phase_I	48	10	NM_030653	0	0	5	7	2	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			C|1.000;|0.000		0.647	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		A	31242981	C	A	31242981	2	1	32	1	0	0	0	0	0	0	0	1	4349	643	23	4		4	DDX11	12	31242981	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	7140472	31242981	102608914	60	2819											
SRGAP1	57522	hgsc.bcm.edu;broad.mit.edu	37	chr12	64377805	64377805	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcagcttctccaggatcTgcaagatttcttccgaaaaa	12	12	7	10	1	4	1	1	0	3	1	6	3	5	2	2	1	2	3	2	1	3	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:64377805T>A	ENST00000355086.3	+	2	670	c.146T>A	c.(145-147)cTg>cAg	p.L49Q	SRGAP1_ENST00000543397.1_Missense_Mutation_p.L9Q|SRGAP1_ENST00000357825.3_Missense_Mutation_p.L49Q	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	49	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTCCAGGATCTGCAAGATTTC	0.428																																					p.L49Q		.											.	SRGAP1-653	0			c.T146A						.						110	114	113					12																	64377805		2203	4300	6503	SO:0001583	missense	57522	exon2			AGGATCTGCAAGA	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.146T>A	12.37:g.64377805T>A	ENSP00000347198:p.Leu49Gln	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	86	12	NM_020762	0	0	0	0	0	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.690212	0.88735	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.56611	0.45;0.45;1.94	5.1	5.1	0.69264	Fps/Fes/Fer/CIP4 homology (3);	0.000000	0.28600	U	0.014776	T	0.74261	0.3693	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.987;0.987	T	0.77648	-0.2509	9	.	.	.	.	15.199	0.73120	0.0:0.0:0.0:1.0	.	49;9;49	Q7Z6B7;G5EA48;Q7Z6B7-2	SRGP1_HUMAN;.;.	Q	49;49;9	ENSP00000347198:L49Q;ENSP00000350480:L49Q;ENSP00000437948:L9Q	.	L	+	2	0	SRGAP1	62664072	1.000000	0.71417	0.997000	0.53966	0.933000	0.57130	7.975000	0.88055	2.060000	0.61445	0.477000	0.44152	CTG	.		0.428	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			A	64377805	T	A	64377805	3	1	32	1	0	0	0	0	1	0	0	0	15177	1580	55	5	152	5	SRGAP1	12	64377805	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	33134824	64377805	69474090	61	2820											
SLC35E3	55508	hgsc.bcm.edu	37	chr12	69140471	69140471	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccataggcacctatcagcTggccaaggccatgaccacgc	11	5	9	16	1	1	1	1	1	0	0	1	1	1	1	5	3	1	2	5	3	3	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:69140471T>C	ENST00000398004.2	+	1	586	c.314T>C	c.(313-315)cTg>cCg	p.L105P		NM_018656.2	NP_061126.2	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	105						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			ACCTATCAGCTGGCCAAGGCC	0.562																																					p.L105P		.											.	SLC35E3-514	0			c.T314C						.						126	135	132					12																	69140471		1995	4175	6170	SO:0001583	missense	55508	exon1			ATCAGCTGGCCAA	AF148713, AY358943	CCDS41808.1	12q15	2014-09-04			ENSG00000175782	ENSG00000175782		"Solute carriers"	20864	protein-coding gene	gene with protein product						12975309	Standard	XM_005269006		Approved	BLOV1	uc001suh.3	Q7Z769	OTTHUMG00000169282	ENST00000398004.2:c.314T>C	12.37:g.69140471T>C	ENSP00000381089:p.Leu105Pro	Somatic	249	2		WXS	Illumina HiSeq	Phase_I	505	36	NM_018656	0	0	5	10	5	A8K0T0|Q0P5Y5|Q9P0V1	Missense_Mutation	SNP	ENST00000398004.2	37	CCDS41808.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.685593	0.88639	.	.	ENSG00000175782	ENST00000398004	T	0.56941	0.43	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000001	T	0.72558	0.3475	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.75929	-0.3144	9	.	.	.	-9.0953	14.9804	0.71306	0.0:0.0:0.0:1.0	.	105	Q7Z769	S35E3_HUMAN	P	105	ENSP00000381089:L105P	.	L	+	2	0	SLC35E3	67426738	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.534000	0.82004	1.996000	0.58369	0.482000	0.46254	CTG	.		0.562	SLC35E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403241.1	NM_018656		C	69140471	T	C	69140471	3	2	32	1	0	0	0	0	1	0	0	0	14618	1580	55	3	316	3	SLC35E3	12	69140471	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	4762666	69140471	64711424	62	2821											
MYBPC1	4604	broad.mit.edu	37	chr12	102046970	102046970	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaaacaagcttcgtcttGagatccccatcagcggagaa	13	7	10	11	2	2	2	1	1	1	2	4	5	3	3	2	2	3	1	2	2	3	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:102046970G>T	ENST00000550270.1	+	16	1636	c.1636G>T	c.(1636-1638)Gag>Tag	p.E546*	MYBPC1_ENST00000549145.1_Nonsense_Mutation_p.E559*|MYBPC1_ENST00000547509.1_Nonsense_Mutation_p.E532*|MYBPC1_ENST00000541119.1_Nonsense_Mutation_p.E534*|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000452455.2_Nonsense_Mutation_p.E546*|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000551300.1_Nonsense_Mutation_p.E447*|MYBPC1_ENST00000441232.1_Nonsense_Mutation_p.E546*|MYBPC1_ENST00000545503.2_Nonsense_Mutation_p.E546*|MYBPC1_ENST00000360610.2_Nonsense_Mutation_p.E546*|MYBPC1_ENST00000361685.2_Nonsense_Mutation_p.E571*|MYBPC1_ENST00000536007.1_Nonsense_Mutation_p.E527*|MYBPC1_ENST00000547405.1_Nonsense_Mutation_p.E520*|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000361466.2_Nonsense_Mutation_p.E571*|MYBPC1_ENST00000553190.1_Nonsense_Mutation_p.E546*|MYBPC1_ENST00000392934.3_Nonsense_Mutation_p.E533*			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	546	Ig-like C2-type 5.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GCTTCGTCTTGAGATCCCCAT	0.458																																					p.E571X													.	MYBPC1-94	0			c.G1711T						.						145	139	141					12																	102046970		2203	4300	6503	SO:0001587	stop_gained	4604	exon18			CGTCTTGAGATCC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1636G>T	12.37:g.102046970G>T	ENSP00000449702:p.Glu546*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_206819	0	0	0	0	0	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Nonsense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	G	40	8.002340	0.98605	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	.	.	.	5.71	5.71	0.89125	.	0.000000	0.52532	D	0.000074	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.8505	0.96738	0.0:0.0:1.0:0.0	.	.	.	.	X	520;546;546;546;533;532;571;559;546;571;546;527;534;571;447;546	.	ENSP00000353822:E546X	E	+	1	0	MYBPC1	100571101	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.476000	0.97823	2.688000	0.91661	0.655000	0.94253	GAG	.		0.458	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102046970	G	T	102046970	4	4	32	1	0	0	0	0	0	1	0	0	10036	1291	45	4	1781	4	MYBPC1	12	102046970	Nonsense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	32906499	102046970	31804925	63	2822											
METT11D1	64745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21464718	21464719	+	Missense_Mutation	DNP	GG	GG	TT																															aaggaagaaaagttctctatGgtgatccttgctcgggggtc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:21464718_21464719GG>TT	ENST00000339374.6	+	13	1346_1347	c.1113_1114GG>TT	c.(1111-1116)atGGtg>atTTtg	p.371_372MV>IL	SLC39A2_ENST00000298681.4_5'Flank|SLC39A2_ENST00000554422.1_5'Flank|RP11-84C10.4_ENST00000557335.1_RNA|METTL17_ENST00000382985.4_Missense_Mutation_p.371_372MV>IL|METTL17_ENST00000556670.2_Missense_Mutation_p.371_372MV>IL	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	371					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						AGTTCTCTATGGTGATCCTTGC	0.465																																					p.MV371IL		.											.	METTL17	0			c.G1114T						.																																			SO:0001583	missense	64745	exon13			TCTATGGTGATCC	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"methyltransferase 11 domain containing 1"	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	Exception_encountered	14.37:g.21464718_21464719delinsTT	ENSP00000343041:p.M371_V372delinsIL	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	164	25		0	0	0	0	0	Q9BSH1|Q9BZH2|Q9BZH3	Missense_Mutation	DNP	ENST00000339374.6	37	CCDS9562.1																																																																																			.		0.465	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734		TT	21464719	GG	TT	21464718	3	4	32	1	0	0	0	0	1	0	0	0	9516	1348	47	4	1163	4	METT11D1	14	21464718	Missense_Mutation	DNP	GG	TCGA-AL-3473-01A-01D-1252-08		21464718	85884822	64	2823											
NID2	22795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	52485956	52485956	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgggccccagggtaggcatActgggcctgggcatggcgct	5	6	17	13	2	0	0	0	0	0	0	0	0	0	0	4	6	1	4	4	6	2	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:52485956A>C	ENST00000216286.5	-	14	2850	c.2851T>G	c.(2851-2853)Tat>Gat	p.Y951D	NID2_ENST00000541773.1_Missense_Mutation_p.Y850D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	951	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GGGTAGGCATACTGGGCCTGG	0.577																																					p.Y951D		.											.	NID2-158	0			c.T2851G						.						52	46	48					14																	52485956		2203	4300	6503	SO:0001583	missense	22795	exon14			AGGCATACTGGGC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2851T>G	14.37:g.52485956A>C	ENSP00000216286:p.Tyr951Asp	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	103	27	NM_007361	0	0	0	0	0	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.654|9.654	1.142329|1.142329	0.21205|0.21205	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	.|T;T	.|0.61742	.|0.08;0.08	5.32|5.32	0.0082|0.0082	0.14073|0.14073	.|Thyroglobulin type-1 (4);	.|1.030560	.|0.07634	.|N	.|0.929216	T|T	0.40473|0.40473	0.1118|0.1118	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.27997	.|0.0;0.021;0.197;0.117	.|B;B;B;B	.|0.29862	.|0.002;0.023;0.108;0.009	T|T	0.30387|0.30387	-0.9980|-0.9980	5|10	.|0.33940	.|T	.|0.23	.|.	5.3979|5.3979	0.16278|0.16278	0.0652:0.2279:0.4723:0.2346|0.0652:0.2279:0.4723:0.2346	.|.	.|545;850;953;951	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	G|D	219|951;545;850;953	.|ENSP00000216286:Y951D;ENSP00000443730:Y850D	.|ENSP00000216286:Y951D	V|Y	-|-	2|1	0|0	NID2|NID2	51555706|51555706	0.419000|0.419000	0.25449|0.25449	0.019000|0.019000	0.16419|0.16419	0.026000|0.026000	0.11368|0.11368	1.277000|1.277000	0.33167|0.33167	-0.092000|-0.092000	0.12417|0.12417	-0.242000|-0.242000	0.12053|0.12053	GTA|TAT	.		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			C	52485956	A	C	52485956	3	2	32	1	0	0	0	0	1	0	0	0	10441	391	14	5	1312	5	NID2	14	52485956	Missense_Mutation	SNP	A	TCGA-AL-3473-01A-01D-1252-08	31021238	52485956	54863584	65	2824											
C15orf23	90417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40685795	40685795	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggagcagctattagaaatGtaagaagaagcaagtggcca	17	7	12	5	0	0	3	0	0	0	3	0	4	0	4	1	2	3	4	1	2	7	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:40685795G>T	ENST00000249776.8	+	9	1063	c.948G>T	c.(946-948)atG>atT	p.M316I	KNSTRN_ENST00000416151.2_3'UTR|KNSTRN_ENST00000608100.1_Missense_Mutation_p.M238I|KNSTRN_ENST00000448395.2_3'UTR	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		TATTAGAAATGTAAGAAGaag	0.423																																					p.M316I		.											.	.	0			c.G948T						.						83	76	78					15																	40685795		1885	4111	5996	SO:0001583	missense	90417	exon9			AGAAATGTAAGAA	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.948G>T	15.37:g.40685795G>T	ENSP00000249776:p.Met316Ile	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	90	18	NM_033286	0	0	15	16	1		Missense_Mutation	SNP	ENST00000249776.8	37	CCDS42021.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.074155	0.36566	.	.	ENSG00000128944	ENST00000249776	T	0.27720	1.65	5.02	3.02	0.34903	.	0.171826	0.41938	D	0.000798	T	0.16128	0.0388	N	0.14661	0.345	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.06267	-1.0836	10	0.62326	D	0.03	-5.1946	5.8118	0.18469	0.0965:0.0:0.7133:0.1903	.	316	Q9Y448	T4AF1_HUMAN	I	316	ENSP00000249776:M316I	ENSP00000249776:M316I	M	+	3	0	C15orf23	38473087	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	1.826000	0.39092	1.491000	0.48482	0.650000	0.86243	ATG	.		0.423	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		T	40685795	G	T	40685795	3	4	32	1	0	0	0	0	1	0	0	0	1789	1377	48	4	1025	4	C15orf23	15	40685795	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		40685795	61845597	66	2825											
RAB27A	5873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	55516128	55516128	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggcttcctcctctttcacTactctctggtcctccagatc	5	15	5	16	0	3	1	1	0	2	1	9	1	7	1	4	2	1	1	4	2	1	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:55516128T>A	ENST00000396307.2	-	5	677	c.426A>T	c.(424-426)gtA>gtT	p.V142V	RAB27A_ENST00000569493.1_Silent_p.V142V|RAB27A_ENST00000336787.1_Silent_p.V142V|RAB27A_ENST00000564609.1_Silent_p.V142V	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	142					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CCTCTTTCACTACTCTCTGGT	0.398																																					p.V142V		.											.	RAB27A-228	0			c.A426T						.						167	168	167					15																	55516128		2193	4292	6485	SO:0001819	synonymous_variant	5873	exon6			TTTCACTACTCTC	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"RAB, member RAS oncogene"	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.426A>T	15.37:g.55516128T>A		Somatic	447	0		WXS	Illumina HiSeq	Phase_I	91	12	NM_183235	0	0	55	58	3	O00195|Q6FI40|Q9UIR9|Q9Y5U3	Silent	SNP	ENST00000396307.2	37	CCDS10153.1																																																																																			.		0.398	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236		A	55516128	T	A	55516128	2	1	32	1	0	0	0	0	0	0	0	1	12946	1509	53	5		5	RAB27A	15	55516128	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08	14830333	55516128	47015264	67	2826											
PIGQ	9091	broad.mit.edu	37	chr16	624651	624651	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggctgagccactggcagTcggagggcgtggaggccagc	6	5	19	11	3	0	1	0	1	0	0	1	3	0	3	2	6	3	2	2	6	0	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:624651T>G	ENST00000026218.5	+	2	665	c.577T>G	c.(577-579)Tcg>Gcg	p.S193A	PIGQ_ENST00000321878.5_Missense_Mutation_p.S193A|PIGQ_ENST00000470411.2_Missense_Mutation_p.S193A|PIGQ_ENST00000409527.2_Missense_Mutation_p.S193A	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	193					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				CCACTGGCAGTCGGAGGGCGT	0.682																																					p.S193A													.	PIGQ-226	0			c.T577G						.						10	12	11					16																	624651		2131	4203	6334	SO:0001583	missense	9091	exon2			TGGCAGTCGGAGG	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"Phosphatidylinositol glycan anchor biosynthesis"	14135	protein-coding gene	gene with protein product		605754	"phosphatidylinositol glycan, class Q"			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.577T>G	16.37:g.624651T>G	ENSP00000026218:p.Ser193Ala	Somatic	32	4		WXS	Illumina HiSeq	Phase_I	42	10	NM_148920	0	0	22	22	0	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206870	0.58343	.	.	ENSG00000007541	ENST00000409527;ENST00000409439;ENST00000422307;ENST00000321878;ENST00000026218;ENST00000470411	T;T;T;T;T;T	0.54479	0.63;0.61;0.62;0.63;1.84;0.57	5.45	5.45	0.79879	.	0.066299	0.64402	D	0.000008	T	0.67116	0.2859	M	0.66939	2.045	0.52501	D	0.999951	D;P;D;D	0.65815	0.984;0.956;0.981;0.995	P;P;P;P	0.61132	0.635;0.676;0.681;0.884	T	0.67998	-0.5525	9	.	.	.	-11.7834	14.6869	0.69055	0.0:0.0:0.0:1.0	.	207;193;193;193	E7ERP4;Q9BRB3;Q9BRB3-2;Q9BRB3-3	.;PIGQ_HUMAN;.;.	A	193	ENSP00000386760:S193A;ENSP00000386554:S193A;ENSP00000413753:S193A;ENSP00000326674:S193A;ENSP00000026218:S193A;ENSP00000439650:S193A	.	S	+	1	0	PIGQ	564652	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.958000	0.63660	2.077000	0.62373	0.459000	0.35465	TCG	.		0.682	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204		G	624651	T	G	624651	3	3	32	1	0	0	0	0	1	0	0	0	11922	1667	58	5	579	5	PIGQ	16	624651	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08		624651	89730102	68	2827											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_178167	0	0	0	0	0	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	32	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	1435023	2059674	88295079	69	2828											
RNPS1	10921	broad.mit.edu	37	chr16	2313224	2313224	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggatgctgaggaagagcTggagccactgcttgagccag	9	7	16	9	0	0	3	0	2	0	1	0	6	0	6	2	3	5	4	2	3	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:2313224T>G	ENST00000565678.1	-	4	837	c.292A>C	c.(292-294)Agc>Cgc	p.S98R	RNPS1_ENST00000561718.1_5'UTR|RNPS1_ENST00000566458.1_Missense_Mutation_p.S75R|RNPS1_ENST00000566397.1_5'UTR|RNPS1_ENST00000569598.2_Intron|RNPS1_ENST00000397086.2_Missense_Mutation_p.S98R|RNPS1_ENST00000568631.1_Missense_Mutation_p.S98R|RNPS1_ENST00000567147.1_Missense_Mutation_p.S75R|RNPS1_ENST00000301730.8_Missense_Mutation_p.S98R|RNPS1_ENST00000320225.5_Missense_Mutation_p.S98R			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	98	Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.|Necessary for interactions with UPF2 and UPF3B and UPF2-dependent NMD.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						gaggaagagctggagccactg	0.617																																					p.S98R													.	RNPS1-91	0			c.A292C						.						32	28	29					16																	2313224		2198	4300	6498	SO:0001583	missense	10921	exon4			AAGAGCTGGAGCC	AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"RNA binding motif (RRM) containing"	10080	protein-coding gene	gene with protein product		606447	"RNA-binding protein S1, serine-rich domain"			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.292A>C	16.37:g.2313224T>G	ENSP00000457723:p.Ser98Arg	Somatic	25	5		WXS	Illumina HiSeq	Phase_I	81	13	NM_006711	0	0	140	157	17	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Missense_Mutation	SNP	ENST00000565678.1	37	CCDS10465.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.015897	0.75161	.	.	ENSG00000205937	ENST00000320225;ENST00000397086;ENST00000301730	T;T;T	0.06933	3.24;3.24;3.24	6.06	6.06	0.98353	.	0.688144	0.15090	N	0.281144	T	0.23965	0.0580	L	0.59436	1.845	0.80722	D	1	D;D	0.64830	0.994;0.99	D;D	0.71870	0.975;0.944	T	0.01202	-1.1420	10	0.20046	T	0.44	-3.5075	14.5591	0.68123	0.0:0.0:0.0:1.0	.	75;98	Q15287-2;Q15287	.;RNPS1_HUMAN	R	98	ENSP00000315859:S98R;ENSP00000380275:S98R;ENSP00000301730:S98R	ENSP00000301730:S98R	S	-	1	0	RNPS1	2253225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.380000	0.79704	2.319000	0.78375	0.523000	0.50628	AGC	.		0.617	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594		G	2313224	T	G	2313224	3	3	32	1	0	0	0	0	1	0	0	0	13543	1580	55	5	645	5	RNPS1	16	2313224	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	253550	2313224	88041529	70	2829											
TMC7	79905	hgsc.bcm.edu;broad.mit.edu	37	chr16	19073098	19073098	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtgaacttattattttttAggaaagtcgtgacaagtgct	12	16	9	4	1	0	2	0	2	0	0	1	3	0	3	0	1	2	1	0	1	6	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:19073098A>T	ENST00000304381.5	+	16	2236		c.e16-1		RP11-626G11.5_ENST00000567047.1_RNA|RP11-626G11.5_ENST00000576433.1_RNA|RP11-626G11.5_ENST00000568971.1_RNA|RP11-626G11.5_ENST00000571934.1_RNA|TMC7_ENST00000421369.3_Splice_Site	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7						ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						ATTATTTTTTAGGAAAGTCGT	0.403																																					.		.											.	TMC7-93	0			c.2107-2A>T						.						87	80	82					16																	19073098		2197	4300	6497	SO:0001630	splice_region_variant	79905	exon16			TTTTTTAGGAAAG	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.2107-1A>T	16.37:g.19073098A>T		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	90	13	NM_024847	0	0	0	0	0	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Splice_Site	SNP	ENST00000304381.5	37	CCDS10573.1	.	.	.	.	.	.	.	.	.	.	A	14.61	2.586609	0.46110	.	.	ENSG00000170537	ENST00000304381;ENST00000421369	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2868	0.60247	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMC7	18980599	1.000000	0.71417	0.916000	0.36221	0.545000	0.35147	6.318000	0.72866	2.012000	0.59069	0.533000	0.62120	.	.		0.403	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	Intron	T	19073098	A	T	19073098	5	4	32	1	0	0	0	0	0	0	1	0	16022	434	15	5	2167	5	TMC7	16	19073098	Splice_Site	SNP	A	TCGA-AL-3473-01A-01D-1252-08	16759874	19073098	71281655	71	2830											
DNAH3	55567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21080893	21080893	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catccaaattgtcttgtatgCgaattagcttttcttcccat	9	17	5	10	1	2	0	0	0	2	0	4	1	4	0	2	0	2	2	2	0	4	7	rs577456196		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:21080893C>T	ENST00000261383.3	-	23	3223	c.3224G>A	c.(3223-3225)cGc>cAc	p.R1075H	DNAH3_ENST00000415178.1_Missense_Mutation_p.R1075H	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1075	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R1075P(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GTCTTGTATGCGAATTAGCTT	0.453													C|||	1	0.000199681	0	0	5008	,	,		19175	0.001		0	False		,,,				2504	0				p.R1075H		.											.	DNAH3-167	2	Substitution - Missense(2)	lung(2)	c.G3224A						.						173	130	144					16																	21080893		2201	4300	6501	SO:0001583	missense	55567	exon23			TGTATGCGAATTA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3224G>A	16.37:g.21080893C>T	ENSP00000261383:p.Arg1075His	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	96	14	NM_017539	0	0	0	0	0	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410395	0.25465	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.61859	0.07;0.07	5.4	4.22	0.49857	Dynein heavy chain, domain-2 (1);	0.726956	0.12981	N	0.423277	T	0.44519	0.1297	L	0.28192	0.835	0.09310	N	1	D	0.65815	0.995	P	0.49332	0.607	T	0.36625	-0.9740	10	0.26408	T	0.33	.	2.0715	0.03614	0.3159:0.4174:0.1475:0.1193	.	1075	Q8TD57	DYH3_HUMAN	H	1075	ENSP00000261383:R1075H;ENSP00000394245:R1075H	ENSP00000261383:R1075H	R	-	2	0	DNAH3	20988394	0.001000	0.12720	0.952000	0.39060	0.634000	0.38068	0.318000	0.19504	2.696000	0.92011	0.655000	0.94253	CGC	.		0.453	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21080893	C	T	21080893	3	4	32	1	0	0	0	0	1	0	0	0	4614	768	27	1	9285	1	DNAH3	16	21080893	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	2007795	21080893	69273860	72	2831											
TMEM107	84314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	8079579	8079579	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagcgtcaggaagcgagagGgcacaagccctgagacccgg	11	2	17	11	3	1	2	1	1	0	2	1	6	1	4	2	4	3	1	2	4	2	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:8079579G>T	ENST00000437139.2	-	1	113	c.26C>A	c.(25-27)cCc>cAc	p.P9H	TMEM107_ENST00000532998.1_Missense_Mutation_p.P9H|RP11-599B13.7_ENST00000581248.1_lincRNA|TMEM107_ENST00000431792.2_Missense_Mutation_p.P9H|TMEM107_ENST00000533070.1_Missense_Mutation_p.P9H|SNORD118_ENST00000363593.1_RNA|TMEM107_ENST00000316425.5_Missense_Mutation_p.P9H|TMEM107_ENST00000449985.2_Missense_Mutation_p.P9H	NM_183065.2	NP_898888.1	Q6UX40	TM107_HUMAN	transmembrane protein 107	9					cilium assembly (GO:0042384)|embryonic digit morphogenesis (GO:0042733)|neural tube patterning (GO:0021532)	integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(1)	6						GAAGCGAGAGGGCACAAGCCC	0.632																																					p.P9H		.											.	TMEM107-90	0			c.C26A						.						58	48	51					17																	8079579		2203	4300	6503	SO:0001583	missense	84314	exon1			CGAGAGGGCACAA	AF311338	CCDS11132.1, CCDS45607.1	17p13.1	2005-12-19				ENSG00000179029			28128	protein-coding gene	gene with protein product						12477932	Standard	NM_032354		Approved	MGC10744	uc002gkh.4	Q6UX40		ENST00000437139.2:c.26C>A	17.37:g.8079579G>T	ENSP00000402732:p.Pro9His	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	159	21	NM_183065	0	0	25	41	16	A0PJV7|Q6NSE3|Q6ZRX9|Q96T82	Missense_Mutation	SNP	ENST00000437139.2	37	CCDS45607.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431906	0.62844	.	.	ENSG00000179029	ENST00000449985;ENST00000532998;ENST00000437139;ENST00000533070;ENST00000316425;ENST00000431792;ENST00000415860	.	.	.	5.6	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.77465	0.4134	M	0.79475	2.455	0.49915	D	0.999835	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.982	T	0.79948	-0.1588	9	0.87932	D	0	-37.9001	10.8172	0.46583	0.0877:0.0:0.9123:0.0	.	9;9;9;9	B3KNL7;Q6UX40-3;Q6UX40-4;Q6UX40	.;.;.;TM107_HUMAN	H	9	.	ENSP00000314116:P9H	P	-	2	0	TMEM107	8020304	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	8.301000	0.89951	1.511000	0.48818	-0.158000	0.13435	CCC	.		0.632	TMEM107-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388844.1	NM_032354		T	8079579	G	T	8079579	3	4	32	1	0	0	0	0	1	0	0	0	16055	1232	43	4	434	4	TMEM107	17	8079579	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		8079579	73115631	73	2832											
ACCN1	40	hgsc.bcm.edu	37	chr17	31618997	31618997	+	Intron	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctggcccctgcagcgccCgctcgccgcctctgccgccc	1	5	10	25	5	1	0	0	0	1	0	2	0	1	0	9	1	3	2	9	1	0	0	rs112647385	byFrequency	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:31618997C>A	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Missense_Mutation_p.R46L	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CTGCAGCGCCCGCTCGCCGCC	0.806													C|||	1091	0.217851	0.112	0.1902	5008	,	,		5226	0.3194		0.2664	False		,,,				2504	0.226				p.R46L		.											.	.	0			c.G137T						.						1	2	2					17																	31618997		903	2226	3129	SO:0001627	intron_variant	40	exon1			AGCGCCCGCTCGC	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179912G>T	17.37:g.31618997C>A		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	7	7	NM_183377	0	0	0	0	0	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	37	CCDS42296.1	567	0.25961538461538464	84	0.17073170731707318	81	0.22375690607734808	197	0.34440559440559443	205	0.2704485488126649	C	13.69	2.313571	0.40996	.	.	ENSG00000108684	ENST00000225823	T	0.65178	-0.14	4.45	-0.0635	0.13776	.	1.386070	0.04769	N	0.427624	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.17038	0.02	B	0.10450	0.005	T	0.17715	-1.0360	9	0.29301	T	0.29	-24.8125	4.0823	0.09932	0.0:0.3667:0.3479:0.2854	.	46	E9PBX2	.	L	46	ENSP00000225823:R46L	ENSP00000225823:R46L	R	-	2	0	ACCN1	28643110	0.458000	0.25760	0.926000	0.36857	0.865000	0.49528	1.119000	0.31258	0.274000	0.22072	0.306000	0.20318	CGG	C|0.740;A|0.260		0.806	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		A	31618997	C	A	31618997	1	1	32	0	1	0	0	0	0	0	0	0	128	652	23	4		4	ACCN1	17	31618997	Intron	SNP	C	TCGA-AL-3473-01A-01D-1252-08	23539418	31618997	49576213	74	2833											
PSMC3IP	29893	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40726133	40726133	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctaccagcctccatgtagcgGcagctctgctgcaagctctg	7	9	10	15	1	2	0	0	0	2	0	3	0	3	0	3	1	7	6	3	1	3	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:40726133G>T	ENST00000393795.3	-	4	429	c.321C>A	c.(319-321)tgC>tgA	p.C107*	PSMC3IP_ENST00000587209.1_Nonsense_Mutation_p.C44*|PSMC3IP_ENST00000590760.1_Intron|PSMC3IP_ENST00000253789.5_Nonsense_Mutation_p.C107*	NM_001256015.1|NM_001256016.1|NM_016556.3	NP_001242944.1|NP_001242945.1|NP_057640.1	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein	107					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)|regulation of RNA biosynthetic process (GO:2001141)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(2)	7		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCATGTAGCGGCAGCTCTGCT	0.512																																					p.C107X													.	PSMC3IP-92	0			c.C321A						.						57	45	49					17																	40726133		2203	4300	6503	SO:0001587	stop_gained	29893	exon4			GTAGCGGCAGCTC	AB030304, NM_013290, BC008792	CCDS11431.1, CCDS45688.1, CCDS59289.1	17q21.2	2012-04-10				ENSG00000131470		"Proteasome (prosome, macropain) subunits"	17928	protein-coding gene	gene with protein product	"TBP-1 interacting protein"	608665				7490091, 10806355, 11739747	Standard	NM_016556		Approved	TBPIP, GT198, HUMGT198A	uc002iai.3	Q9P2W1		ENST00000393795.3:c.321C>A	17.37:g.40726133G>T	ENSP00000377384:p.Cys107*	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	64	15	NM_016556	0	0	3	5	2	C5ILB7|Q14458|Q8WXG2|Q96HA2	Nonsense_Mutation	SNP	ENST00000393795.3	37	CCDS45688.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354575	0.82243	.	.	ENSG00000131470	ENST00000393795;ENST00000253789	.	.	.	5.73	2.53	0.30540	.	0.092706	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-20.0948	9.5122	0.39085	0.297:0.0:0.703:0.0	.	.	.	.	X	107	.	ENSP00000253789:C107X	C	-	3	2	PSMC3IP	37979659	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.337000	0.52120	0.288000	0.22398	0.563000	0.77884	TGC	.		0.512	PSMC3IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450427.1	NM_013290		T	40726133	G	T	40726133	4	4	32	1	0	0	0	0	0	1	0	0	12717	1195	42	4	352	4	PSMC3IP	17	40726133	Nonsense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	9107136	40726133	40469077	75	2834											
TMEM106A	113277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41365849	41365849	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caccttctctctctctagagCtggagaagcagttggtggct	7	12	11	11	0	3	2	0	0	3	2	5	3	3	2	1	3	2	4	1	3	2	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:41365849C>T	ENST00000331615.3	+	4	451	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	TMEM106A_ENST00000592564.1_3'UTR|TMEM106A_ENST00000541594.1_Silent_p.L24L|TMEM106A_ENST00000588659.1_Silent_p.L72L|TMEM106A_ENST00000536052.1_Silent_p.L72L	NM_145041.1	NP_659478.1	Q96A25	T106A_HUMAN	transmembrane protein 106A	72						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		CTCTCTAGAGCTGGAGAAGCA	0.552																																					p.L72L		.											.	.	0			c.C214T						.						97	74	82					17																	41365849		2203	4296	6499	SO:0001819	synonymous_variant	113277	exon4			CTAGAGCTGGAGA	AK056132	CCDS11462.1, CCDS74073.1	17q21.31	2012-01-23			ENSG00000184988	ENSG00000184988			28288	protein-coding gene	gene with protein product							Standard	XM_006721658		Approved	MGC20235	uc002idn.1	Q96A25		ENST00000331615.3:c.214C>T	17.37:g.41365849C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	165	17	NM_145041	0	0	0	0	0	A8K2X2|B7Z698	Silent	SNP	ENST00000331615.3	37	CCDS11462.1																																																																																			.		0.552	TMEM106A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453470.2	NM_145041		T	41365849	C	T	41365849	2	4	32	1	0	0	0	0	0	0	0	1	16052	796	28	2		2	TMEM106A	17	41365849	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	639716	41365849	39829361	76	2835											
CDC27	996	hgsc.bcm.edu	37	chr17	45247409	45247409	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgttccccttctgcaagcCtttaaaatacaaatttaaag	13	15	4	9	0	1	0	0	0	1	0	2	0	2	0	3	0	3	2	3	0	7	8	rs78111769		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:45247409C>T	ENST00000066544.3	-	4	345		c.e4-1		CDC27_ENST00000531206.1_Splice_Site|RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000446365.2_Splice_Site|CDC27_ENST00000527547.1_Splice_Site|CDC27_ENST00000528748.1_Splice_Site	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTCTGCAAGCCTTTAAAATAC	0.318																																					.		.											.	CDC27-291	0			c.252-1G>A						.						51	59	56					17																	45247409		2203	4296	6499	SO:0001630	splice_region_variant	996	exon5			GCAAGCCTTTAAA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.252-1G>A	17.37:g.45247409C>T		Somatic	177	2		WXS	Illumina HiSeq	Phase_I	71	6	NM_001256	0	0	0	0	0	G3V1C4|Q16349|Q96F35	Splice_Site	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116295	0.77323	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000533415;ENST00000446365;ENST00000527547;ENST00000526866	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9253	0.86174	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDC27	42602408	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.687000	0.84139	2.663000	0.90544	0.655000	0.94253	.	.		0.318	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Intron	T	45247409	C	T	45247409	5	4	32	1	0	0	0	0	0	0	1	0	3072	695	24	2	2305	2	CDC27	17	45247409	Splice_Site	SNP	C	TCGA-AL-3473-01A-01D-1252-08	3881560	45247409	35947801	77	2836											
PHB	5245	broad.mit.edu	37	chr17	47486482	47486483	+	Frame_Shift_Del	DEL	CT	CT	-																															ctcacctgcctggagaccagCtctctctgggtgattagttc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:47486482_47486483delCT	ENST00000300408.3	-	5	503_504	c.431_432delAG	c.(430-432)gagfs	p.E144fs	RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000511832.1_Intron|PHB_ENST00000508009.1_5'UTR	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	144					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			TGGAGACCAGCTCTCTCTGGGT	0.554																																					p.144_144del													.	PHB-90	0			c.431_432del						.																																			SO:0001589	frameshift_variant	5245	exon5			GACCAGCTCTCTC		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.431_432delAG	17.37:g.47486488_47486489delCT	ENSP00000300408:p.Glu144fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	139	17	NM_002634	0	0	0	0	0	B4DY47|Q4VBQ0	Frame_Shift_Del	DEL	ENST00000300408.3	37	CCDS11548.1																																																																																			.		0.554	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634		-	47486483	CT	-	47486482	7	5	32	1	0	1	0	1	0	0	0	0	11840	796	28	0	398	0	PHB	17	47486482	Frame_Shift_Del	DEL	CT	TCGA-AL-3473-01A-01D-1252-08	2239073	47486482	33708728	78	2837											
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29444612	29444612	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaacagtggcatttcttctGtgattatgggatctaaacgt	10	14	9	8	1	3	1	0	1	3	0	3	2	3	2	1	2	2	1	1	2	4	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr18:29444612G>C	ENST00000283351.4	-	19	3058	c.2723C>G	c.(2722-2724)aCa>aGa	p.T908R	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.T854R	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	908					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CATTTCTTCTGTGATTATGGG	0.328																																					p.T908R		.											.	TRAPPC8-159	0			c.C2723G						.						117	112	114					18																	29444612		2203	4300	6503	SO:0001583	missense	22878	exon19			TCTTCTGTGATTA	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.2723C>G	18.37:g.29444612G>C	ENSP00000283351:p.Thr908Arg	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_014939	0	0	15	15	0	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.129354	0.37630	.	.	ENSG00000153339	ENST00000283351	T	0.09911	2.93	5.91	4.12	0.48240	.	0.093959	0.64402	D	0.000001	T	0.14917	0.0360	M	0.76328	2.33	0.80722	D	1	P	0.47910	0.902	B	0.41813	0.367	T	0.12319	-1.0552	10	0.20519	T	0.43	.	13.0419	0.58904	0.1324:0.0:0.8676:0.0	.	908	Q9Y2L5	TPPC8_HUMAN	R	908	ENSP00000283351:T908R	ENSP00000283351:T908R	T	-	2	0	TRAPPC8	27698610	1.000000	0.71417	0.989000	0.46669	0.994000	0.84299	6.119000	0.71590	1.513000	0.48852	0.555000	0.69702	ACA	.		0.328	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		C	29444612	G	C	29444612	3	2	32	1	0	0	0	0	1	0	0	0	8225	1377	48	4	1628	4	KIAA1012	18	29444612	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		29444612	48632636	79	2838											
ME2	4200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr18	48442562	48442562	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatttatttcgatctcagaCagaggtcatgttagatcaat	12	16	7	6	1	3	3	3	0	1	3	5	4	3	3	0	1	0	1	0	1	4	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr18:48442562C>G	ENST00000321341.5	+	5	689	c.417C>G	c.(415-417)gaC>gaG	p.D139E	ME2_ENST00000382927.3_Missense_Mutation_p.D139E	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	139					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		CGATCTCAGACAGAGGTCATG	0.333																																					p.D139E		.											.	ME2-90	0			c.C417G						.						186	177	180					18																	48442562		2203	4300	6503	SO:0001583	missense	4200	exon5			CTCAGACAGAGGT	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.417C>G	18.37:g.48442562C>G	ENSP00000321070:p.Asp139Glu	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	38	4	NM_001168335	0	0	10	20	10	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	37	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129308	0.77549	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.45668	0.89;0.89	5.8	5.8	0.92144	Malic enzyme, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.63698	0.2533	M	0.77712	2.385	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.61950	-0.6957	10	0.36615	T	0.2	-22.0057	12.879	0.58006	0.0:0.9218:0.0:0.0782	.	139;139	Q9BWL6;P23368	.;MAOM_HUMAN	E	139	ENSP00000321070:D139E;ENSP00000372384:D139E	ENSP00000321070:D139E	D	+	3	2	ME2	46696560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.392000	0.52537	2.741000	0.93983	0.650000	0.86243	GAC	.		0.333	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396		G	48442562	C	G	48442562	3	3	32	1	0	0	0	0	1	0	0	0	9443	477	17	4	431	4	ME2	18	48442562	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	18997950	48442562	29634686	80	2839											
MUC16	94025	broad.mit.edu	37	chr19	9067237	9067237	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaggaggacctgttcgagTgatgatggtcatatttgaag	12	11	14	4	1	1	4	1	3	0	1	2	7	1	6	1	3	0	1	1	3	3	3	rs201826382		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:9067237T>G	ENST00000397910.4	-	3	20412	c.20209A>C	c.(20209-20211)Act>Cct	p.T6737P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6739	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTGTTCGAGTGATGATGGTC	0.507																																					p.T6737P													.	MUC16-566	0			c.A20209C						.						277	272	274					19																	9067237		2188	4278	6466	SO:0001583	missense	94025	exon3			TTCGAGTGATGAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20209A>C	19.37:g.9067237T>G	ENSP00000381008:p.Thr6737Pro	Somatic	427	1		WXS	Illumina HiSeq	Phase_I	73	3	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	5.549	0.286102	0.10513	.	.	ENSG00000181143	ENST00000397910	T	0.02579	4.24	2.52	2.52	0.30459	.	.	.	.	.	T	0.02533	0.0077	N	0.12182	0.205	.	.	.	D	0.62365	0.991	P	0.47102	0.537	T	0.41448	-0.9508	8	0.87932	D	0	.	6.9393	0.24484	0.0:0.0:0.0:1.0	.	6737	B5ME49	.	P	6737	ENSP00000381008:T6737P	ENSP00000381008:T6737P	T	-	1	0	MUC16	8928237	0.000000	0.05858	0.006000	0.13384	0.009000	0.06853	-0.127000	0.10547	1.395000	0.46643	0.317000	0.21355	ACT	T|0.999;G|0.001		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9067237	T	G	9067237	3	3	32	1	0	0	0	0	1	0	0	0	9998	1696	59	5	23642	5	MUC16	19	9067237	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08		9067237	50061746	81	2840											
SLC25A42	284439	broad.mit.edu	37	chr19	19221630	19221630	+	Frame_Shift_Del	DEL	T	T	-																															gggtcccatcgccgtgggcaTcagcttcaccaccttcgacc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:19221630delT	ENST00000318596.7	+	8	1053	c.902delT	c.(901-903)atcfs	p.I301fs		NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	301					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			GCCGTGGGCATCAGCTTCACC	0.657																																					p.I301fs													.	SLC25A42-90	0			c.902delT						.						68	52	57					19																	19221630		2203	4300	6503	SO:0001589	frameshift_variant	284439	exon8			TGGGCATCAGCTT		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"Solute carriers"	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.902delT	19.37:g.19221630delT	ENSP00000326693:p.Ile301fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	192	24	NM_178526	0	0	0	0	0	D2T2J5|O14553|O43378	Frame_Shift_Del	DEL	ENST00000318596.7	37	CCDS32966.1																																																																																			.		0.657	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		-	19221630	T	-	19221630	7	5	32	1	0	1	0	1	0	0	0	0	14539	1435	50	0	928	0	SLC25A42	19	19221630	Frame_Shift_Del	DEL	T	TCGA-AL-3473-01A-01D-1252-08	10154393	19221630	39907353	82	2841											
APLP1	333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36362560	36362560	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacggctcgggcatgctctTaccctgtggctcggatcggt	4	10	14	13	4	1	0	0	0	1	0	4	1	1	1	1	5	2	5	1	5	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:36362560T>A	ENST00000221891.4	+	5	776	c.584T>A	c.(583-585)tTa>tAa	p.L195*	NPHS1_ENST00000591817.1_5'Flank|APLP1_ENST00000537454.2_Nonsense_Mutation_p.L156*|APLP1_ENST00000586861.1_Nonsense_Mutation_p.L189*	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	195					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGCATGCTCTTACCCTGTGGC	0.642																																					p.L195X		.											.	APLP1-92	0			c.T584A						.						111	105	107					19																	36362560		2203	4300	6503	SO:0001587	stop_gained	333	exon5			TGCTCTTACCCTG	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.584T>A	19.37:g.36362560T>A	ENSP00000221891:p.Leu195*	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	345	57	NM_005166	0	0	0	0	0	O00113|Q96A92	Nonsense_Mutation	SNP	ENST00000221891.4	37	CCDS32997.1	.	.	.	.	.	.	.	.	.	.	T	36	5.888940	0.97068	.	.	ENSG00000105290	ENST00000537454;ENST00000221891	.	.	.	4.41	4.41	0.53225	.	0.000000	0.33515	N	0.004832	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3771	11.5688	0.50822	0.0:0.0:0.0:1.0	.	.	.	.	X	156;195	.	ENSP00000221891:L195X	L	+	2	0	APLP1	41054400	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	7.189000	0.77747	1.630000	0.50440	0.379000	0.24179	TTA	.		0.642	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		A	36362560	T	A	36362560	4	1	32	1	0	0	0	0	0	1	0	0	778	1764	61	5	602	5	APLP1	19	36362560	Nonsense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	17140930	36362560	22766423	83	2842											
WDR62	284403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36582178	36582178	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcagtgattgacttttactCgggcgagtgcattgccaaga	9	12	11	9	2	1	3	1	2	0	1	2	4	1	3	1	1	3	1	1	1	2	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:36582178C>T	ENST00000270301.7	+	17	2111	c.2111C>T	c.(2110-2112)tCg>tTg	p.S704L	WDR62_ENST00000401500.2_Missense_Mutation_p.S704L			O43379	WDR62_HUMAN	WD repeat domain 62	704					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GACTTTTACTCGGGCGAGTGC	0.582																																					p.S704L		.											.	WDR62-90	0			c.C2111T						.						105	84	91					19																	36582178		2203	4300	6503	SO:0001583	missense	284403	exon17			TTTACTCGGGCGA	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"WD repeat domain containing"	24502	protein-coding gene	gene with protein product		613583	"chromosome 19 open reading frame 14", "microcephaly, primary autosomal recessive 2"	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2111C>T	19.37:g.36582178C>T	ENSP00000270301:p.Ser704Leu	Somatic	92	1		WXS	Illumina HiSeq	Phase_I	161	25	NM_173636	0	0	0	0	0	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	.	.	.	.	.	.	.	.	.	.	C	35	5.548778	0.96488	.	.	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.59906	0.87;0.23	5.35	5.35	0.76521	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.149243	0.46145	D	0.000308	T	0.80193	0.4578	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.964;0.973	D	0.83964	0.0323	10	0.87932	D	0	-12.0401	16.6023	0.84819	0.0:1.0:0.0:0.0	.	704;704	O43379-4;O43379	.;WDR62_HUMAN	L	704	ENSP00000384792:S704L;ENSP00000270301:S704L	ENSP00000270301:S704L	S	+	2	0	WDR62	41274018	1.000000	0.71417	0.968000	0.41197	0.999000	0.98932	7.278000	0.78587	2.780000	0.95670	0.655000	0.94253	TCG	.		0.582	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		T	36582178	C	T	36582178	3	4	32	1	0	0	0	0	1	0	0	0	17346	893	31	1	2177	1	WDR62	19	36582178	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	219618	36582178	22546805	84	2843											
ZNF585B	92285	hgsc.bcm.edu;broad.mit.edu	37	chr19	37678072	37678072	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggatttttccccagaataaaTtttttgatcttgagaggaag	12	15	9	5	0	1	3	0	2	1	2	2	6	2	5	2	2	0	0	2	2	4	7			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:37678072T>A	ENST00000532828.2	-	5	618	c.367A>T	c.(367-369)Att>Ttt	p.I123F	ZNF585B_ENST00000312908.5_5'Flank|ZNF585B_ENST00000531805.1_Missense_Mutation_p.I68F|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_Missense_Mutation_p.I123F	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCAGAATAAATTTTTTGATCT	0.373																																					p.I123F	Melanoma(93;882 1454 18863 28917 48427)	.											.	ZNF585B-91	0			c.A367T						.						59	64	62					19																	37678072		2202	4299	6501	SO:0001583	missense	92285	exon5			AATAAATTTTTTG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.367A>T	19.37:g.37678072T>A	ENSP00000433773:p.Ile123Phe	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	88	9	NM_152279	0	0	3	3	0	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	4.132	0.022795	0.08006	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000527838	T;T;T	0.08634	3.07;3.15;6.5	2.32	2.32	0.28847	.	0.230506	0.22120	U	0.064354	T	0.10551	0.0258	M	0.65498	2.005	0.80722	D	1	B	0.22909	0.077	B	0.20184	0.028	T	0.06427	-1.0827	10	0.72032	D	0.01	.	9.2461	0.37527	0.0:0.0:0.0:1.0	.	123	Q52M93	Z585B_HUMAN	F	68;123;123	ENSP00000436774:I68F;ENSP00000433773:I123F;ENSP00000435268:I123F	ENSP00000435268:I123F	I	-	1	0	ZNF585B	42369912	0.614000	0.27017	0.755000	0.31263	0.021000	0.10359	0.914000	0.28624	1.052000	0.40392	0.374000	0.22700	ATT	.		0.373	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		A	37678072	T	A	37678072	3	1	32	1	0	0	0	0	1	0	0	0	18050	1493	52	5	1946	5	ZNF585B	19	37678072	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	1095894	37678072	21450911	85	2844											
ZNF320	162967	broad.mit.edu	37	chr19	53385207	53385207	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccttgccctgttgatgacaAtgtattcatcatgcatttgg	8	15	9	9	0	2	2	2	2	0	0	2	2	2	2	2	1	2	3	2	1	2	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:53385207A>G	ENST00000595635.1	-	8	673	c.172T>C	c.(172-174)Ttg>Ctg	p.L58L	ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Silent_p.L58L	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		GTTGATGACAATGTATTCATC	0.358																																					p.L58L													.	ZNF320-91	0			c.T172C						.						138	136	137					19																	53385207		2203	4298	6501	SO:0001819	synonymous_variant	162967	exon4			ATGACAATGTATT	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.172T>C	19.37:g.53385207A>G		Somatic	310	0		WXS	Illumina HiSeq	Phase_I	187	5	NM_207333	0	0	16	16	0	Q8NDR6	Silent	SNP	ENST00000595635.1	37	CCDS33095.1																																																																																			.		0.358	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		G	53385207	A	G	53385207	2	3	32	1	0	0	0	0	0	0	0	1	17871	98	4	3		3	ZNF320	19	53385207	Silent	SNP	A	TCGA-AL-3473-01A-01D-1252-08	15707135	53385207	5743776	86	2845											
PLK1S1	101929591	broad.mit.edu;ucsc.edu	37	chr20	21143713	21143713	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgctgagcaagaaagagttgCcctatccactgaaaaaaatt	16	9	8	8	0	0	4	0	2	0	2	1	4	1	4	2	0	3	3	2	0	6	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:21143713C>T	ENST00000591761.1	-	0	5051				PLK1S1_ENST00000457464.1_RNA|RP5-872K7.7_ENST00000425746.2_RNA																							GAAAGAGTTGCCCTATCCACT	0.433																																					.													.	.	0			.						.						90	91	91					20																	21143713		1897	4110	6007			55857	.			GAGTTGCCCTATC																													20.37:g.21143713C>T		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	33	5	.	0	0	8	8	0		Missense_Mutation	SNP	ENST00000591761.1	37																																																																																				.		0.433	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			T	21143713	C	T	21143713	1	4	32	0	1	0	0	0	0	0	0	0	12121	739	26	2		2	PLK1S1	20	21143713	RNA	SNP	C	TCGA-AL-3473-01A-01D-1252-08		21143713	41881807	87	2846											
XRN2	22803	hgsc.bcm.edu	37	chr20	21367553	21367553	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atggaaccggatgctgcaaaCccagaatgcagccttccagc	12	6	10	13	1	0	1	0	0	0	1	1	3	1	3	4	2	7	3	4	2	3	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:21367553C>G	ENST00000377191.3	+	29	2791	c.2696C>G	c.(2695-2697)aCc>aGc	p.T899S	XRN2_ENST00000539513.1_Missense_Mutation_p.T845S|XRN2_ENST00000430571.2_Missense_Mutation_p.T823S	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	899					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						ATGCTGCAAACCCAGAATGCA	0.527																																					p.T899S		.											.	XRN2-515	0			c.C2696G						.						113	107	109					20																	21367553		2203	4300	6503	SO:0001583	missense	22803	exon29			TGCAAACCCAGAA	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2696C>G	20.37:g.21367553C>G	ENSP00000366396:p.Thr899Ser	Somatic	180	1		WXS	Illumina HiSeq	Phase_I	35	2	NM_012255	0	0	161	161	0	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	37	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	C	5.701	0.313921	0.10789	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.28666	1.6;1.6;1.6	6.17	1.63	0.23807	.	0.640269	0.17029	N	0.189797	T	0.10680	0.0261	N	0.03608	-0.345	0.19775	N	0.999951	B	0.02656	0.0	B	0.01281	0.0	T	0.36286	-0.9754	10	0.02654	T	1	0.091	9.5329	0.39205	0.5479:0.3867:0.0:0.0655	.	899	Q9H0D6	XRN2_HUMAN	S	899;823;845	ENSP00000366396:T899S;ENSP00000413548:T823S;ENSP00000441113:T845S	ENSP00000366396:T899S	T	+	2	0	XRN2	21315553	0.997000	0.39634	0.664000	0.29753	0.803000	0.45373	0.669000	0.25142	0.039000	0.15632	0.655000	0.94253	ACC	.		0.527	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		G	21367553	C	G	21367553	3	3	32	1	0	0	0	0	1	0	0	0	17493	507	18	4	2810	4	XRN2	20	21367553	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	223840	21367553	41657967	88	2847											
MYH7B	57644	broad.mit.edu;bcgsc.ca	37	chr20	33577862	33577862	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagaaaaacaaggatcccCtgaatgagaccgtggtcccc	13	6	11	11	1	0	3	0	2	0	2	2	6	2	4	5	3	1	0	5	3	4	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:33577862C>T	ENST00000262873.7	+	19	2031	c.1939C>T	c.(1939-1941)Ctg>Ttg	p.L647L	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	605	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CAAGGATCCCCTGAATGAGAC	0.572																																					p.L647L													.	MYH7B-136	0			c.C1939T						.						75	83	81					20																	33577862		2128	4269	6397	SO:0001819	synonymous_variant	57644	exon21			GATCCCCTGAATG	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1939C>T	20.37:g.33577862C>T		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	405	11	NM_020884	0	0	1	1	0	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			.		0.572	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33577862	C	T	33577862	2	4	32	1	0	0	0	0	0	0	0	1	10065	680	24	2		2	MYH7B	20	33577862	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	12210309	33577862	29447658	89	2848											
CSE1L	1434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47675025	47675025	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aactcagcgatgcaaatctgCaaacactaacagaatattta	18	9	5	9	1	2	1	1	0	1	1	2	2	2	1	0	0	6	2	0	0	7	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:47675025C>A	ENST00000262982.2	+	2	148	c.25C>A	c.(25-27)Caa>Aaa	p.Q9K	CSE1L_ENST00000542325.1_5'UTR|CSE1L_ENST00000396192.3_Missense_Mutation_p.Q9K	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	9					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TGCAAATCTGCAAACACTAAC	0.333																																					p.Q9K		.											.	CSE1L-290	0			c.C25A						.						100	109	106					20																	47675025		2203	4300	6503	SO:0001583	missense	1434	exon2			AATCTGCAAACAC	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.25C>A	20.37:g.47675025C>A	ENSP00000262982:p.Gln9Lys	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	234	24	NM_001256135	0	0	1	1	0	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Missense_Mutation	SNP	ENST00000262982.2	37	CCDS13412.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.561981	0.45590	.	.	ENSG00000124207	ENST00000262982;ENST00000396192	T;T	0.68624	-0.34;-0.34	5.3	4.36	0.52297	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58004	0.2092	L	0.59436	1.845	0.80722	D	1	B;P	0.36990	0.24;0.577	B;B	0.33042	0.157;0.13	T	0.55431	-0.8142	10	0.10902	T	0.67	-1.2095	14.1142	0.65142	0.0:0.927:0.0:0.073	.	9;9	F8W904;P55060	.;XPO2_HUMAN	K	9	ENSP00000262982:Q9K;ENSP00000379495:Q9K	ENSP00000262982:Q9K	Q	+	1	0	CSE1L	47108432	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.272000	0.78516	1.222000	0.43521	0.591000	0.81541	CAA	.		0.333	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		A	47675025	C	A	47675025	3	1	32	1	0	0	0	0	1	0	0	0	3936	711	25	4	27	4	CSE1L	20	47675025	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	14097163	47675025	15350495	90	2849											
ZNF512B	57473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62598869	62598870	+	Missense_Mutation	DNP	CG	CG	AA																															gtctgtccaccacggaccacCggcatccctgcagcacacaa																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:62598869_62598870CG>AA	ENST00000450537.1	-	3	188_189	c.128_129CG>TT	c.(127-129)cCG>cTT	p.P43L	ZNF512B_ENST00000217130.3_Missense_Mutation_p.P43L|ZNF512B_ENST00000369888.1_Missense_Mutation_p.P43L			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	43					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CACGGACCACCGGCATCCCTGC	0.639																																					p.P43L		.											.	ZNF512B	0			c.C128T						.																																			SO:0001583	missense	57473	exon3			ACCACCGGCATCC	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.128_129delinsAA	20.37:g.62598869_62598870delinsAA	ENSP00000393795:p.Pro43Leu	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	417	69		0	0	0	0	0	Q08AK9|Q9ULM4	Missense_Mutation	DNP	ENST00000450537.1	37	CCDS13548.1																																																																																			.		0.639	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		AA	62598870	CG	AA	62598869	3	1	32	1	0	0	0	0	1	0	0	0	17989	639	23	4	2609	4	ZNF512B	20	62598869	Missense_Mutation	DNP	CG	TCGA-AL-3473-01A-01D-1252-08	14923844	62598869	426651	91	2850											
DSCAM	1826	broad.mit.edu;bcgsc.ca	37	chr21	41447083	41447083	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagcatcttgagcccctcgTtggtcgtcagcccttcttcg	4	12	9	16	3	3	1	1	1	2	0	6	1	3	1	4	1	3	2	4	1	0	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr21:41447083T>C	ENST00000400454.1	-	27	5246	c.4769A>G	c.(4768-4770)aAc>aGc	p.N1590S		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1590					cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GAGCCCCTCGTTGGTCGTCAG	0.547																																					p.N1590S	Melanoma(134;970 1778 1785 21664 32388)												.	DSCAM-101	0			c.A4769G						.						124	128	127					21																	41447083		2066	4204	6270	SO:0001583	missense	1826	exon27			CCCTCGTTGGTCG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.4769A>G	21.37:g.41447083T>C	ENSP00000383303:p.Asn1590Ser	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	186	6	NM_001271534	0	0	0	0	0	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.148505	0.37923	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.57752	0.38;0.49	5.69	5.69	0.88448	.	0.113799	0.64402	D	0.000010	T	0.36744	0.0978	N	0.14661	0.345	0.34194	D	0.672378	B	0.10296	0.003	B	0.08055	0.003	T	0.42361	-0.9456	10	0.22109	T	0.4	.	15.9467	0.79799	0.0:0.0:0.0:1.0	.	1590	O60469	DSCAM_HUMAN	S	1590;1342	ENSP00000383303:N1590S;ENSP00000385342:N1342S	ENSP00000383303:N1590S	N	-	2	0	DSCAM	40368953	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.657000	0.67996	2.169000	0.68431	0.533000	0.62120	AAC	.		0.547	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41447083	T	C	41447083	3	2	32	1	0	0	0	0	1	0	0	0	4779	1725	60	3	1297	3	DSCAM	21	41447083	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08		41447083	6682812	92	2851											
TRIOBP	11078	broad.mit.edu	37	chr22	38129406	38129406	+	Frame_Shift_Del	DEL	C	C	-																															ccgaagacagtccagccctgCccccagcaggcaggtgagca																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr22:38129406delC	ENST00000406386.3	+	8	4304	c.4049delC	c.(4048-4050)gccfs	p.A1350fs		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1350					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCCAGCCCTGCCCCCAGCAGG	0.697																																					p.A1350fs													.	TRIOBP-136	0			c.4049delC						.						8	13	11					22																	38129406		1882	3870	5752	SO:0001589	frameshift_variant	11078	exon8			GCCCTGCCCCCAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.4049delC	22.37:g.38129406delC	ENSP00000384312:p.Ala1350fs	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_001039141	0	0	0	0	0	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Frame_Shift_Del	DEL	ENST00000406386.3	37	CCDS43015.1																																																																																			.		0.697	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			-	38129406	C	-	38129406	7	5	32	1	0	1	0	1	0	0	0	0	16586	739	26	0	4071	0	TRIOBP	22	38129406	Frame_Shift_Del	DEL	C	TCGA-AL-3473-01A-01D-1252-08		38129406	13175160	93	2852											
RLIM	51132	hgsc.bcm.edu	37	chrX	73811841	73811841	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgtgactctgccctttccaTatttcgatttgagactgagc	7	14	8	12	2	1	3	0	3	1	1	3	5	2	3	3	0	2	0	3	0	1	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chrX:73811841T>C	ENST00000332687.6	-	4	1527	c.1309A>G	c.(1309-1311)Atg>Gtg	p.M437V	RLIM_ENST00000349225.2_Missense_Mutation_p.M437V	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	437	Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCCTTTCCATATTTCGATTT	0.468																																					p.M437V	Esophageal Squamous(169;1899 1923 14997 18818 32118)	.											.	RLIM-228	0			c.A1309G						.						80	81	81					X																	73811841		2203	4300	6503	SO:0001583	missense	51132	exon5			TTTCCATATTTCG	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1309A>G	X.37:g.73811841T>C	ENSP00000328059:p.Met437Val	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_183353	0	0	11	11	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.045444	0.00039	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.07114	3.22;3.22	5.5	-5.67	0.02444	.	0.968910	0.08563	N	0.927213	T	0.02342	0.0072	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47249	-0.9132	10	0.17369	T	0.5	5.075	5.2448	0.15490	0.1268:0.5334:0.1263:0.2135	.	437	Q9NVW2	RNF12_HUMAN	V	437	ENSP00000328059:M437V;ENSP00000253571:M437V	ENSP00000328059:M437V	M	-	1	0	RLIM	73728566	0.000000	0.05858	0.023000	0.16930	0.160000	0.22226	-0.063000	0.11655	-0.764000	0.04651	0.486000	0.48141	ATG	.		0.468	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		C	73811841	T	C	73811841	3	2	32	1	0	0	0	0	1	0	0	0	13422	1406	49	3	569	3	RLIM	23	73811841	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08		73811841	81458719	94	2853											
COL4A6	1288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	107433650	107433650	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctttgaggcctaggtttccTtttggaccttgttctcctcg	3	17	9	12	1	1	1	0	1	1	0	4	2	2	2	5	3	0	2	5	3	1	7			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chrX:107433650T>G	ENST00000372216.4	-	20	1501	c.1401A>C	c.(1399-1401)aaA>aaC	p.K467N	COL4A6_ENST00000538570.1_Missense_Mutation_p.K466N|COL4A6_ENST00000545689.1_Missense_Mutation_p.K466N|COL4A6_ENST00000334504.7_Missense_Mutation_p.K466N|COL4A6_ENST00000394872.2_Missense_Mutation_p.K467N	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	467	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						CTAGGTTTCCTTTTGGACCTT	0.443									Alport syndrome with Diffuse Leiomyomatosis																												p.K467N	Melanoma(87;1895 1945 2589 7165)	.											.	COL4A6-199	0			c.A1401C						.						130	118	122					X																	107433650		2203	4300	6503	SO:0001583	missense	1288	exon20	Familial Cancer Database		GTTTCCTTTTGGA	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.1401A>C	X.37:g.107433650T>G	ENSP00000361290:p.Lys467Asn	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	99	38	NM_001847	0	0	0	0	0	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	37	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.915515	0.33815	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.25;-3.38	5.3	2.74	0.32292	.	0.000000	0.45361	D	0.000370	D	0.92506	0.7620	L	0.52206	1.635	0.33503	D	0.590155	D;D;D;D	0.61697	0.982;0.982;0.983;0.99	P;P;P;P	0.59487	0.764;0.764;0.725;0.858	D	0.91531	0.5242	10	0.59425	D	0.04	.	2.7178	0.05192	0.1932:0.2036:0.0:0.6032	.	466;466;467;466	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	N	467;466;467;466;466;466	ENSP00000361290:K467N;ENSP00000334733:K466N;ENSP00000378340:K467N;ENSP00000443707:K466N;ENSP00000445236:K466N	ENSP00000334733:K466N	K	-	3	2	COL4A6	107320306	0.993000	0.37304	0.998000	0.56505	0.987000	0.75469	0.944000	0.29043	0.886000	0.36113	0.486000	0.48141	AAA	.		0.443	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			G	107433650	T	G	107433650	3	3	32	1	0	0	0	0	1	0	0	0	3701	1606	56	5	3778	5	COL4A6	23	107433650	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	33621809	107433650	47836910	95	2854											
FLNA	2316	ucsc.edu	37	chrX	153588776	153588776	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgttgtagtccccgggctcGgtgggcacgtaggacacgga	7	8	16	10	4	0	0	0	0	0	0	2	2	1	2	2	5	0	5	2	5	2	3	rs372874251		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chrX:153588776G>A	ENST00000369850.3	-	22	3623	c.3387C>T	c.(3385-3387)acC>acT	p.T1129T	FLNA_ENST00000344736.4_Silent_p.T1129T|FLNA_ENST00000360319.4_Silent_p.T1129T|FLNA_ENST00000422373.1_Silent_p.T1129T|FLNA_ENST00000369856.3_5'Flank	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	1129					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)					CCCCGGGCTCGGTGGGCACGT	0.622											OREG0003593	type=REGULATORY REGION|Gene=FLNA|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T1129T													.	FLNA-599	0			c.C3387T						.		,	1,3732		0,1,1580,571	70	81	77		3387,3387	-9.8	0.5	X		77	0,6620		0,0,2402,1816	no	coding-synonymous,coding-synonymous	FLNA	NM_001110556.1,NM_001456.3	,	0,1,3982,2387	AA,AG,GG,G		0.0,0.0268,0.0097	,	1129/2648,1129/2640	153588776	1,10352	2152	4218	6370	SO:0001819	synonymous_variant	2316	exon22			GGGCTCGGTGGGC	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"actin binding protein 280"	300017	"filamin A, alpha (actin binding protein 280)"	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.3387C>T	X.37:g.153588776G>A		Somatic	68	0	1756	WXS	Illumina HiSeq		175	1	NM_001456	0	0	6	7	1	E9KL45|Q5HY53|Q5HY55|Q8NF52	Silent	SNP	ENST00000369850.3	37	CCDS48194.1																																																																																			.		0.622	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			A	153588776	G	A	153588776	2	1	32	1	0	0	0	0	0	0	0	1	5952	1103	39	1		1	FLNA	23	153588776	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	46155126	153588776	1681784	96	2855											
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	8415616	8415616	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctggtgggctgctgacatGgggggtgggatggccccagg	5	7	21	8	0	0	1	0	1	0	0	0	2	0	2	2	8	2	3	2	8	0	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr1:8415616G>T	ENST00000337907.3	-	23	5164	c.4530C>A	c.(4528-4530)ccC>ccA	p.P1510P	RERE_ENST00000400907.2_Silent_p.P528P|RERE_ENST00000476556.1_Silent_p.P956P|RERE_ENST00000400908.2_Silent_p.P1510P|RERE_ENST00000377464.1_Silent_p.P1242P	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1510	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		CTGCTGACATGGGGGGTGGGA	0.642																																					p.P1510P		.											.	RERE-515	0			c.C4530A						.						16	17	17					1																	8415616		2201	4295	6496	SO:0001819	synonymous_variant	473	exon23			TGACATGGGGGGT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.4530C>A	1.37:g.8415616G>T		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	36	9	NM_012102	0	0	6	11	5	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			.		0.642	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			T	8415616	G	T	8415616	2	4	33	1	0	0	0	0	0	0	0	1	13263	1335	47	4		4	RERE	1	8415616	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08		8415616	240835005	1	2856											
TSPAN2	10100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	115601516	115601516	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttactcactgttgagtggaaGgtgatgagtgtcccattgcc	8	13	12	8	0	1	3	1	3	0	0	2	4	2	4	2	2	2	1	2	2	2	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr1:115601516G>A	ENST00000369516.2	-	5	463	c.432C>T	c.(430-432)acC>acT	p.T144T	TSPAN2_ENST00000369515.2_Silent_p.T119T|TSPAN2_ENST00000491992.1_5'Flank|TSPAN2_ENST00000369514.2_Silent_p.T144T	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	144					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TTGAGTGGAAGGTGATGAGTG	0.398																																					p.T144T		.											.	TSPAN2-226	0			c.C432T						.						256	232	240					1																	115601516		2203	4300	6503	SO:0001819	synonymous_variant	10100	exon5			GTGGAAGGTGATG	AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"Tetraspanins"	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.432C>T	1.37:g.115601516G>A		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	167	40	NM_005725	0	0	0	0	0	D6PTH4|Q5TET2|Q8WU05	Silent	SNP	ENST00000369516.2	37	CCDS881.1																																																																																			.		0.398	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725		A	115601516	G	A	115601516	2	1	33	1	0	0	0	0	0	0	0	1	16677	987	35	2		2	TSPAN2	1	115601516	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	107185900	115601516	133649105	2	2857											
RGL1	23179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	183885638	183885638	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatggacacaaattcctcaGggatgtcttccttaatcaac	12	11	6	12	0	3	0	2	0	1	0	5	2	5	2	3	2	1	0	3	2	3	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr1:183885638G>C	ENST00000360851.3	+	16	1985	c.1807G>C	c.(1807-1809)Ggg>Cgg	p.G603R	RGL1_ENST00000304685.4_Missense_Mutation_p.G638R|RGL1_ENST00000536277.1_Missense_Mutation_p.G601R|RGL1_ENST00000539189.1_Missense_Mutation_p.G574R			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	603	Ser-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						AAATTCCTCAGGGATGTCTTC	0.502																																					p.G638R		.											.	RGL1-725	0			c.G1912C						.						186	182	183					1																	183885638		2203	4300	6503	SO:0001583	missense	23179	exon17			TCCTCAGGGATGT	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1807G>C	1.37:g.183885638G>C	ENSP00000354097:p.Gly603Arg	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	169	47	NM_015149	0	0	1	4	3	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	G	16.32	3.090748	0.55968	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.50548	0.76;0.76;0.79;0.78;0.74	5.05	5.05	0.67936	.	0.057165	0.64402	D	0.000001	T	0.48502	0.1503	L	0.40543	1.245	0.47245	D	0.999364	D;D;D;D	0.58268	0.982;0.969;0.969;0.969	P;P;B;P	0.51866	0.682;0.585;0.348;0.585	T	0.48670	-0.9015	10	0.54805	T	0.06	.	11.5322	0.50616	0.0831:0.0:0.9169:0.0	.	574;601;603;638	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	R	638;638;601;603;574	ENSP00000303192:G638R;ENSP00000356501:G638R;ENSP00000438662:G601R;ENSP00000354097:G603R;ENSP00000437355:G574R	ENSP00000303192:G638R	G	+	1	0	RGL1	182152261	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.475000	0.53136	2.345000	0.79718	0.650000	0.86243	GGG	.		0.502	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		C	183885638	G	C	183885638	3	2	33	1	0	0	0	0	1	0	0	0	13308	1000	35	4	1974	4	RGL1	1	183885638	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	68284122	183885638	65364983	3	2858											
TTC15	51112	hgsc.bcm.edu	37	chr2	3461447	3461447	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggcatgagcagcgtgaCtcaggagggcagacaaggtg	10	4	18	9	3	1	3	1	2	0	1	1	4	1	4	0	5	2	3	0	5	1	0	rs142960119		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:3461447C>G	ENST00000324266.5	+	7	1781	c.1586C>G	c.(1585-1587)aCt>aGt	p.T529S	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Missense_Mutation_p.T529S	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	529					vesicle-mediated transport (GO:0016192)												AGCAGCGTGACTCAGGAGGGC	0.527																																					p.T529S		.											.	.	0			c.C1586G						.						99	90	93					2																	3461447		2203	4300	6503	SO:0001583	missense	51112	exon7			GCGTGACTCAGGA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1586C>G	2.37:g.3461447C>G	ENSP00000324318:p.Thr529Ser	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_016030	0	0	25	25	0	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	5.619|5.619|5.619	0.298912|0.298912|0.298912	0.10622|0.10622|0.10622	.|.|.	.|.|.	ENSG00000171853|ENSG00000171853|ENSG00000171853	ENST00000433382|ENST00000441983|ENST00000382110;ENST00000304601;ENST00000324266;ENST00000415624	.|.|T;T	.|.|0.46451	.|.|0.87;0.87	5.1|5.1|5.1	5.1|5.1|5.1	0.69264|0.69264|0.69264	.|.|.	.|.|0.224065	.|.|0.45606	.|.|N	.|.|0.000346	T|T|T	0.24275|0.24275|0.24275	0.0588|0.0588|0.0588	N|N|N	0.04959|0.04959|0.04959	-0.14|-0.14|-0.14	0.35012|0.35012|0.35012	D|D|D	0.757003|0.757003|0.757003	.|.|B;B	.|.|0.15473	.|.|0.013;0.013	.|.|B;B	.|.|0.14023	.|.|0.01;0.007	T|T|T	0.16928|0.16928|0.16928	-1.0386|-1.0386|-1.0386	5|5|10	.|.|0.15952	.|.|T	.|.|0.53	.|.|.	17.6896|17.6896|17.6896	0.88266|0.88266|0.88266	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|512;529	.|.|E7ENL7;Q8WVT3	.|.|.;TPC12_HUMAN	E|V|S	74|209|529;512;529;27	.|.|ENSP00000371544:T529S;ENSP00000324318:T529S	.|.|ENSP00000303612:T512S	D|L|T	+|+|+	3|1|2	2|0|0	TTC15|TTC15|TTC15	3440454|3440454|3440454	0.239000|0.239000|0.239000	0.23836|0.23836|0.23836	0.007000|0.007000|0.007000	0.13788|0.13788|0.13788	0.188000|0.188000|0.188000	0.23474|0.23474|0.23474	3.898000|3.898000|3.898000	0.56281|0.56281|0.56281	2.650000|2.650000|2.650000	0.89964|0.89964|0.89964	0.467000|0.467000|0.467000	0.42956|0.42956|0.42956	GAC|CTC|ACT	C|1.000;T|0.000		0.527	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		G	3461447	C	G	3461447	3	3	33	1	0	0	0	0	1	0	0	0	16715	565	20	4	1608	4	TTC15	2	3461447	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		3461447	239737926	4	2859											
TTC15	51112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	3483103	3483103	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cactacctgcacgagagcgtGctcttcaacctgaccaccat	10	8	7	16	2	2	2	1	1	1	1	2	3	2	2	4	0	5	2	4	0	2	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:3483103G>A	ENST00000324266.5	+	12	2274	c.2079G>A	c.(2077-2079)gtG>gtA	p.V693V	TRAPPC12-AS1_ENST00000453806.1_RNA|TRAPPC12_ENST00000382110.2_Silent_p.V693V	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	693					vesicle-mediated transport (GO:0016192)												ACGAGAGCGTGCTCTTCAACC	0.632																																					p.V693V		.											.	.	0			c.G2079A						.						123	115	118					2																	3483103		2203	4300	6503	SO:0001819	synonymous_variant	51112	exon12			GAGCGTGCTCTTC	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.2079G>A	2.37:g.3483103G>A		Somatic	160	0		WXS	Illumina HiSeq	Phase_I	124	30	NM_016030	0	0	86	134	48	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	G	9.411	1.080605	0.20309	.	.	ENSG00000171853	ENST00000416918	.	.	.	4.55	-2.5	0.06384	.	.	.	.	.	T	0.50086	0.1595	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44436	-0.9328	4	.	.	.	.	6.1178	0.20136	0.0754:0.4917:0.1948:0.2381	.	.	.	.	T	80	.	.	A	+	1	0	TTC15	3462110	0.943000	0.32029	0.965000	0.40720	0.990000	0.78478	-0.009000	0.12765	-0.267000	0.09325	-0.150000	0.13652	GCT	.		0.632	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		A	3483103	G	A	3483103	2	1	33	1	0	0	0	0	0	0	0	1	16715	1306	46	2		2	TTC15	2	3483103	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	21656	3483103	239716270	5	2860											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32664736	32664736	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcacttgcttcacttttggcTaaagttgcagcaggcaaggt	9	13	10	9	0	2	0	2	0	0	0	2	0	2	0	0	3	3	6	0	3	3	6			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:32664736T>C	ENST00000421745.2	+	16	3926	c.3792T>C	c.(3790-3792)gcT>gcC	p.A1264A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1264					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CACTTTTGGCTAAAGTTGCAG	0.373																																					p.A1264A	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.T3792C						.						91	74	80					2																	32664736		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon16			TTTGGCTAAAGTT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.3792T>C	2.37:g.32664736T>C		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_016252	0	0	0	0	0	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			.		0.373	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32664736	T	C	32664736	2	2	33	1	0	0	0	0	0	0	0	1	1439	1509	53	3		3	BIRC6	2	32664736	Silent	SNP	T	TCGA-AL-7173-01A-11D-2136-08	29181633	32664736	210534637	6	2861											
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43451957	43451957	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtacagcagagcggccgcaGccgcggccgccgcggaggcg	6	1	18	16	9	0	1	0	0	0	1	0	2	0	2	4	4	4	3	4	4	1	1	rs149290349	byFrequency	TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:43451957G>A	ENST00000282388.3	-	2	1279	c.986C>T	c.(985-987)gCt>gTt	p.A329V	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	329	Poly-Ala.			AAAA -> LR (in Ref. 2; CAA55592). {ECO:0000305}.	cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				AGCGGCCGCAGCCGCGGCCGC	0.791													G|||	101	0.0201677	0.0015	0.0447	5008	,	,		7262	0		0.0586	False		,,,				2504	0.0092				p.A329V		.											.	ZFP36L2-226	0			c.C986T						.						2	5	4					2																	43451957		1011	2422	3433	SO:0001583	missense	678	exon2			GCCGCAGCCGCGG	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.986C>T	2.37:g.43451957G>A	ENSP00000282388:p.Ala329Val	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	11	6	NM_006887	0	0	0	0	0	Q53TB4|Q9BSJ3	Missense_Mutation	SNP	ENST00000282388.3	37	CCDS1811.1	80	0.03663003663003663	16	0.032520325203252036	22	0.06077348066298342	0	0.0	42	0.055408970976253295	G	10.73	1.433956	0.25813	.	.	ENSG00000152518	ENST00000282388	T	0.55234	0.53	3.24	3.24	0.37175	.	0.790844	0.11374	N	0.570585	T	0.04363	0.0120	N	0.14661	0.345	0.80722	D	1	P	0.38504	0.634	B	0.30646	0.118	T	0.04078	-1.0979	10	0.33141	T	0.24	-18.8132	14.2289	0.65877	0.0:0.0:1.0:0.0	.	329	P47974	TISD_HUMAN	V	329	ENSP00000282388:A329V	ENSP00000282388:A329V	A	-	2	0	ZFP36L2	43305461	0.980000	0.34600	0.099000	0.21106	0.025000	0.11179	0.000000	0.12993	1.626000	0.50381	0.491000	0.48974	GCT	G|0.963;A|0.037		0.791	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		A	43451957	G	A	43451957	3	1	33	1	0	0	0	0	1	0	0	0	17679	971	34	2	502	2	ZFP36L2	2	43451957	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	10787221	43451957	199747416	7	2862											
ANKRD36B	57730	hgsc.bcm.edu	37	chr2	98177298	98177298	+	RNA	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aatgagactttaattaccttCtcagctcgttgtttctgagg	9	16	8	8	1	2	2	1	2	2	1	4	3	2	2	1	1	2	3	1	1	3	6			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:98177298C>G	ENST00000443455.1	-	0	899							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TAATTACCTTCTCAGCTCGTT	0.303																																					p.E263D		.											.	.	0			c.G789C						.						21	17	18					2																	98177298		980	2031	3011			57730	exon7			TACCTTCTCAGCT	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98177298C>G		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_025190	0	0	0	0	0	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				.		0.303	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		G	98177298	C	G	98177298	1	3	33	0	1	0	0	0	0	0	0	0	666	912	32	4		4	ANKRD36B	2	98177298	RNA	SNP	C	TCGA-AL-7173-01A-11D-2136-08	54725341	98177298	145022075	8	2863											
SESTD1	91404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	180016091	180016091	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggttctatataacgagTcaatttgttggcggacacta	11	13	10	7	2	2	0	1	0	1	0	2	2	2	1	0	3	1	3	0	3	5	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:180016091T>A	ENST00000428443.3	-	6	713	c.397A>T	c.(397-399)Act>Tct	p.T133S		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	133	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			ATATAACGAGTCAATTTGTTG	0.353																																					p.T133S		.											.	SESTD1-228	0			c.A397T						.						71	70	70					2																	180016091		2203	4300	6503	SO:0001583	missense	91404	exon6			AACGAGTCAATTT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.397A>T	2.37:g.180016091T>A	ENSP00000415332:p.Thr133Ser	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	41	17	NM_178123	0	0	1	2	1	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.926704	0.52759	.	.	ENSG00000187231	ENST00000428443;ENST00000440010;ENST00000435047	T;T;T	0.21734	1.99;1.99;1.99	5.68	5.68	0.88126	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26412	0.0645	N	0.05383	-0.06	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.26710	-1.0095	9	.	.	.	-17.9645	16.2237	0.82280	0.0:0.0:0.0:1.0	.	133	Q86VW0	SESD1_HUMAN	S	133	ENSP00000415332:T133S;ENSP00000416164:T133S;ENSP00000410286:T133S	.	T	-	1	0	SESTD1	179724336	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.962000	0.87912	2.289000	0.77006	0.482000	0.46254	ACT	.		0.353	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	180016091	T	A	180016091	3	1	33	1	0	0	0	0	1	0	0	0	14159	1667	58	5	1745	5	SESTD1	2	180016091	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	81838793	180016091	63183282	9	2864											
CUL3	8452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	225422410	225422410	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcggtaacaacttctcttAgtccagtgtagagcttttct	8	16	8	9	1	2	1	0	0	2	1	5	1	3	1	1	1	3	4	1	1	4	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:225422410A>G	ENST00000264414.4	-	2	568	c.230T>C	c.(229-231)cTa>cCa	p.L77P	CUL3_ENST00000344951.4_Intron|CUL3_ENST00000409096.1_Missense_Mutation_p.L53P|CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409777.1_Missense_Mutation_p.L53P	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	77					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		AACTTCTCTTAGTCCAGTGTA	0.333																																					p.L83P		.											.	CUL3-229	0			c.T248C						.						84	86	85					2																	225422410		2202	4299	6501	SO:0001583	missense	8452	exon2			TCTCTTAGTCCAG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.230T>C	2.37:g.225422410A>G	ENSP00000264414:p.Leu77Pro	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_001257198	0	0	2	6	4	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.920164	0.73098	.	.	ENSG00000036257	ENST00000264414;ENST00000409096;ENST00000409777	T;T;T	0.79940	-1.32;-1.32;-1.32	5.61	5.61	0.85477	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	D	0.92857	0.7728	H	0.96239	3.79	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74348	0.983;0.983	D	0.95014	0.8154	10	0.87932	D	0	.	15.8142	0.78586	1.0:0.0:0.0:0.0	.	55;77	Q53S54;Q13618	.;CUL3_HUMAN	P	77;53;53	ENSP00000264414:L77P;ENSP00000387200:L53P;ENSP00000386525:L53P	ENSP00000264414:L77P	L	-	2	0	CUL3	225130654	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.194000	0.94962	2.143000	0.66587	0.533000	0.62120	CTA	.		0.333	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			G	225422410	A	G	225422410	3	3	33	1	0	0	0	0	1	0	0	0	4062	420	15	3	2136	3	CUL3	2	225422410	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	45406319	225422410	17776963	10	2865											
CUL3	8452	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	225449722	225449722	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgcctttgctcagattcGacatggtgctcgtcccctcc	4	12	9	16	3	1	1	1	0	0	1	5	2	3	1	5	1	3	2	5	1	0	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:225449722G>T	ENST00000264414.4	-	1	343	c.5C>A	c.(4-6)tCg>tAg	p.S2*	CUL3_ENST00000344951.4_Nonsense_Mutation_p.S2*	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	2					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GCTCAGATTCGACATGGTGCT	0.706																																					p.S2X		.											.	CUL3-229	0			c.C5A						.						34	31	32					2																	225449722		2199	4300	6499	SO:0001587	stop_gained	8452	exon1			AGATTCGACATGG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.5C>A	2.37:g.225449722G>T	ENSP00000264414:p.Ser2*	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	33	8	NM_003590	0	0	1	1	0	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Nonsense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	G	40	8.107774	0.98657	.	.	ENSG00000036257	ENST00000264414;ENST00000344951	.	.	.	3.18	0.952	0.19584	.	0.432093	0.18593	U	0.136664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6371	0.45571	0.0:0.375:0.625:0.0	.	.	.	.	X	2	.	ENSP00000264414:S2X	S	-	2	0	CUL3	225157966	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	2.063000	0.41423	0.257000	0.21650	0.305000	0.20034	TCG	.		0.706	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			T	225449722	G	T	225449722	4	4	33	1	0	0	0	0	0	1	0	0	4062	1059	37	4	2365	4	CUL3	2	225449722	Nonsense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	27312	225449722	17749651	11	2866											
CRBN	51185	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	3209360	3209360	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatatgaacattggtcttcTcttgagacaggttttgaagg	10	16	10	5	0	2	3	0	3	2	1	3	4	2	3	0	3	1	1	0	3	4	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:3209360T>C	ENST00000231948.4	-	5	667	c.645A>G	c.(643-645)agA>agG	p.R215R	CRBN_ENST00000432408.2_Silent_p.R214R	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	215	Lon.				negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)			endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	ATTGGTCTTCTCTTGAGACAG	0.363																																					p.R215R		.											.	CRBN-91	0			c.A645G						.						134	139	137					3																	3209360		2203	4300	6503	SO:0001819	synonymous_variant	51185	exon5			GTCTTCTCTTGAG	BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"mental retardation, non-syndromic, autosomal recessive, 2A"	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.645A>G	3.37:g.3209360T>C		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	155	13	NM_016302	0	0	7	7	0	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Silent	SNP	ENST00000231948.4	37	CCDS2562.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.290994	0.23564	.	.	ENSG00000113851	ENST00000424814;ENST00000450014	.	.	.	5.1	4.22	0.49857	.	.	.	.	.	T	0.57198	0.2037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52049	-0.8627	4	.	.	.	-0.4216	6.8828	0.24183	0.1419:0.7141:0.0:0.144	.	.	.	.	G	211	.	.	E	-	2	0	CRBN	3184360	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.276000	0.43408	0.666000	0.31087	-0.119000	0.15052	GAG	.		0.363	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302		C	3209360	T	C	3209360	2	2	33	1	0	0	0	0	0	0	0	1	3857	1548	54	3		3	CRBN	3	3209360	Silent	SNP	T	TCGA-AL-7173-01A-11D-2136-08		3209360	194813070	12	2867											
CAPN7	23473	hgsc.bcm.edu	37	chr3	15288291	15288291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattccttcaccatacacctTatcaaaacgggtgagaaaat	15	10	6	10	1	2	1	2	1	0	1	3	3	3	1	3	1	2	0	3	1	6	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:15288291T>C	ENST00000253693.2	+	18	2316	c.2063T>C	c.(2062-2064)tTa>tCa	p.L688S		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	688	Domain III.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCATACACCTTATCAAAACGG	0.284																																					p.L688S		.											.	CAPN7-91	0			c.T2063C						.						74	73	73					3																	15288291		2202	4300	6502	SO:0001583	missense	23473	exon18			ACACCTTATCAAA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.2063T>C	3.37:g.15288291T>C	ENSP00000253693:p.Leu688Ser	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_014296	0	0	0	0	0		Missense_Mutation	SNP	ENST00000253693.2	37	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.677192	0.29783	.	.	ENSG00000131375	ENST00000253693	D	0.86627	-2.15	5.48	5.48	0.80851	Peptidase C2, calpain, large subunit, domain III (1);Peptidase C2, calpain, domain III (1);	0.998190	0.08112	N	0.996014	D	0.82641	0.5081	L	0.29908	0.895	0.33618	D	0.604407	B	0.15141	0.012	B	0.15052	0.012	T	0.74097	-0.3775	10	0.25751	T	0.34	-1.9331	15.2344	0.73416	0.0:0.0:0.0:1.0	.	688	Q9Y6W3	CAN7_HUMAN	S	688	ENSP00000253693:L688S	ENSP00000253693:L688S	L	+	2	0	CAPN7	15263295	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	2.913000	0.48790	2.092000	0.63282	0.533000	0.62120	TTA	.		0.284	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		C	15288291	T	C	15288291	3	2	33	1	0	0	0	0	1	0	0	0	2637	1764	61	3	2133	3	CAPN7	3	15288291	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	12078931	15288291	182734139	13	2868											
ACAD9	28976	hgsc.bcm.edu	37	chr3	128612493	128612493	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgggctgcaagtcccagaaGaatatggtaagtcaagcaaa	15	8	11	7	0	1	2	1	0	0	2	2	2	2	2	1	2	2	4	1	2	7	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:128612493G>C	ENST00000308982.7	+	3	421	c.340G>C	c.(340-342)Gaa>Caa	p.E114Q		NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	114						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						AGTCCCAGAAGAATATGGTAA	0.448																																					p.E114Q		.											.	ACAD9-92	0			c.G340C						.						40	45	43					3																	128612493		2203	4300	6503	SO:0001583	missense	28976	exon3			CCAGAAGAATATG	AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"Mitochondrial respiratory chain complex assembly factors"	21497	protein-coding gene	gene with protein product		611103	"acyl-Coenzyme A dehydrogenase family, member 9"			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.340G>C	3.37:g.128612493G>C	ENSP00000312618:p.Glu114Gln	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_014049	0	0	0	0	0	D3DNB8|Q8WXX3	Missense_Mutation	SNP	ENST00000308982.7	37	CCDS3053.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723058	0.68959	.	.	ENSG00000177646	ENST00000308982;ENST00000514336	D;D	0.99809	-6.86;-6.86	5.94	5.94	0.96194	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	L	0.53249	1.67	0.80722	D	1	P	0.40970	0.734	B	0.37480	0.251	D	0.99909	1.1193	10	0.56958	D	0.05	.	17.8532	0.88754	0.0:0.0:1.0:0.0	.	114	Q9H845	ACAD9_HUMAN	Q	114;126	ENSP00000312618:E114Q;ENSP00000423758:E126Q	ENSP00000312618:E114Q	E	+	1	0	ACAD9	130095183	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	8.237000	0.89807	2.816000	0.96949	0.563000	0.77884	GAA	.		0.448	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049		C	128612493	G	C	128612493	3	2	33	1	0	0	0	0	1	0	0	0	111	943	33	4	350	4	ACAD9	3	128612493	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	113324202	128612493	69409937	14	2869											
COMMD2	51122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	149468478	149468478	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctatacctgtacatctagtCgccattcaaggttatgataa	12	13	7	9	1	2	1	1	1	1	0	3	1	2	1	2	1	2	3	2	1	7	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:149468478C>T	ENST00000473414.1	-	4	443	c.389G>A	c.(388-390)cGa>cAa	p.R130Q		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	130	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TACATCTAGTCGCCATTCAAG	0.333																																					p.R130Q		.											.	COMMD2-90	0			c.G389A						.						138	131	133					3																	149468478		2203	4300	6503	SO:0001583	missense	51122	exon4			TCTAGTCGCCATT	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.389G>A	3.37:g.149468478C>T	ENSP00000419475:p.Arg130Gln	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	123	25	NM_016094	0	0	0	0	0	Q561V4|Q9H3L5|Q9Y5V1	Missense_Mutation	SNP	ENST00000473414.1	37	CCDS3145.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480742	0.84747	.	.	ENSG00000114744	ENST00000473414	T	0.27104	1.69	5.36	4.49	0.54785	COMM domain (1);	0.000000	0.85682	D	0.000000	T	0.57858	0.2082	M	0.89715	3.055	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.68104	-0.5497	10	0.87932	D	0	-2.9867	13.9104	0.63864	0.0:0.9268:0.0:0.0732	.	130	Q86X83	COMD2_HUMAN	Q	130	ENSP00000419475:R130Q	ENSP00000419475:R130Q	R	-	2	0	COMMD2	150951168	1.000000	0.71417	0.996000	0.52242	0.823000	0.46562	6.402000	0.73260	1.397000	0.46682	0.650000	0.86243	CGA	.		0.333	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094		T	149468478	C	T	149468478	3	4	33	1	0	0	0	0	1	0	0	0	3722	884	31	1	218	1	COMMD2	3	149468478	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	20855985	149468478	48553952	15	2870											
FETUB	26998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186362554	186362554	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacagtttcaaaaaaaaagAtttacatgacgtgccctgac	17	9	6	9	1	1	3	1	2	0	1	1	3	1	3	1	0	3	1	1	0	6	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:186362554A>G	ENST00000265029.3	+	4	540	c.439A>G	c.(439-441)Att>Gtt	p.I147V	FETUB_ENST00000488561.1_3'UTR|FETUB_ENST00000539949.1_5'UTR|FETUB_ENST00000382136.3_Missense_Mutation_p.I110V|FETUB_ENST00000382134.3_Missense_Mutation_p.I82V|RP11-134F2.2_ENST00000428501.1_RNA|RP11-134F2.2_ENST00000455926.1_RNA|FETUB_ENST00000450521.1_Missense_Mutation_p.I147V	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	147					binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		AAAAAAAAAGATTTACATGAC	0.408																																					p.I147V		.											.	FETUB-92	0			c.A439G						.						102	96	98					3																	186362554		2203	4300	6503	SO:0001583	missense	26998	exon4			AAAAAGATTTACA	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.439A>G	3.37:g.186362554A>G	ENSP00000265029:p.Ile147Val	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	106	27	NM_014375	0	0	0	0	0	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	37	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	A	5.125	0.208699	0.09757	.	.	ENSG00000090512	ENST00000450521;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T	0.39406	3.17;3.17;1.08;3.14	5.29	-0.0385	0.13880	Proteinase inhibitor I25C, fetuin, conserved site (1);	0.418485	0.23250	N	0.050254	T	0.22085	0.0532	N	0.21583	0.68	0.19300	N	0.999976	B;B;B	0.13145	0.002;0.007;0.007	B;B;B	0.13407	0.004;0.009;0.004	T	0.11227	-1.0596	10	0.27785	T	0.31	-2.9015	4.6541	0.12610	0.592:0.1544:0.2537:0.0	.	110;82;147	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	V	147;147;82;110	ENSP00000404288:I147V;ENSP00000265029:I147V;ENSP00000371569:I82V;ENSP00000371571:I110V	ENSP00000265029:I147V	I	+	1	0	FETUB	187845248	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.250000	0.18235	-0.155000	0.11098	-0.274000	0.10170	ATT	.		0.408	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375		G	186362554	A	G	186362554	3	3	33	1	0	0	0	0	1	0	0	0	5840	333	12	3	453	3	FETUB	3	186362554	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	36894076	186362554	11659876	16	2871											
ST6GAL1	6480	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	186790685	186790685	+	Frame_Shift_Del	DEL	G	G	-																															aagacagtttgtacaatgaaGgaatcctaattgtatgggac																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:186790685delG	ENST00000169298.3	+	6	1428	c.754delG	c.(754-756)ggafs	p.G252fs	ST6GAL1_ENST00000448044.1_Frame_Shift_Del_p.G252fs|ST6GAL1_ENST00000457772.2_Frame_Shift_Del_p.G21fs	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	252					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GTACAATGAAGGAATCCTAAT	0.433																																					p.G252fs		.											.	ST6GAL1-650	0			c.754delG						.						142	139	140					3																	186790685		2203	4300	6503	SO:0001589	frameshift_variant	6480	exon5			.	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"ST6Gal I"	109675	"sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.754delG	3.37:g.186790685delG	ENSP00000169298:p.Gly252fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	142	29	NM_003032	0	0	0	0	0	A8KA14|B2R513|D3DNV3	Frame_Shift_Del	DEL	ENST00000169298.3	37	CCDS3285.1																																																																																			.		0.433	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		-	186790685	G	-	186790685	7	5	33	1	0	1	0	1	0	0	0	0	15253	1001	35	0	764	0	ST6GAL1	3	186790685	Frame_Shift_Del	DEL	G	TCGA-AL-7173-01A-11D-2136-08	428131	186790685	11231745	17	2872											
EGF	1950	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	110865158	110865158	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcagtacaacagagaaggaAgcaattctcttatttgctcc	13	12	7	9	0	2	1	1	0	1	1	4	3	3	2	1	1	4	3	1	1	6	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr4:110865158A>T	ENST00000265171.5	+	4	1115	c.670A>T	c.(670-672)Agc>Tgc	p.S224C	EGF_ENST00000509793.1_Missense_Mutation_p.S224C|EGF_ENST00000503392.1_Missense_Mutation_p.S224C	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	224					activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	CAGAGAAGGAAGCAATTCTCT	0.388																																					p.S224C		.											.	EGF-524	0			c.A670T						.						140	143	142					4																	110865158		2203	4300	6503	SO:0001583	missense	1950	exon4			GAAGGAAGCAATT	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"epidermal growth factor (beta-urogastrone)"				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.670A>T	4.37:g.110865158A>T	ENSP00000265171:p.Ser224Cys	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_001963	0	0	0	0	0	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	37	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.444933	0.63178	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.91464	-2.85;-2.85;-2.85	5.71	-0.638	0.11500	Six-bladed beta-propeller, TolB-like (1);	0.594017	0.19957	N	0.102292	D	0.91019	0.7175	L	0.57536	1.79	0.09310	N	1	D;D;D	0.64830	0.99;0.994;0.983	P;P;P	0.55999	0.619;0.789;0.619	D	0.85276	0.1059	10	0.72032	D	0.01	.	11.2107	0.48797	0.3476:0.0:0.6524:0.0	.	224;224;224	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	C	224	ENSP00000424316:S224C;ENSP00000265171:S224C;ENSP00000421384:S224C	ENSP00000265171:S224C	S	+	1	0	EGF	111084607	0.211000	0.23529	0.001000	0.08648	0.160000	0.22226	0.879000	0.28146	-0.085000	0.12573	0.533000	0.62120	AGC	.		0.388	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			T	110865158	A	T	110865158	3	4	33	1	0	0	0	0	1	0	0	0	4973	72	3	5	684	5	EGF	4	110865158	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08		110865158	80289118	18	2873											
INPP4B	8821	hgsc.bcm.edu	37	chr4	143159034	143159034	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacctgcacaaatcttctttAatgtgaagggaaatcaattc	14	13	6	8	0	3	1	1	1	2	0	4	2	3	2	1	1	2	1	1	1	6	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr4:143159034A>G	ENST00000513000.1	-	13	1252	c.819T>C	c.(817-819)atT>atC	p.I273I	INPP4B_ENST00000308502.4_Silent_p.I273I|INPP4B_ENST00000508116.1_Silent_p.I273I|INPP4B_ENST00000262992.4_Silent_p.I273I|INPP4B_ENST00000509777.1_Silent_p.I273I	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	273					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					AATCTTCTTTAATGTGAAGGG	0.294																																					p.I273I		.											.	INPP4B-228	0			c.T819C						.						39	39	39					4																	143159034		2202	4298	6500	SO:0001819	synonymous_variant	8821	exon13			TTCTTTAATGTGA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.819T>C	4.37:g.143159034A>G		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_003866	0	0	1	1	0	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			.		0.294	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		G	143159034	A	G	143159034	2	3	33	1	0	0	0	0	0	0	0	1	7774	358	13	3		3	INPP4B	4	143159034	Silent	SNP	A	TCGA-AL-7173-01A-11D-2136-08	32293876	143159034	47995242	19	2874											
C5orf42	65250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	37187887	37187887	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gatattgcctgcaactatagGataacttatcacggacatgc	13	11	8	9	1	1	0	1	0	0	0	1	3	1	2	1	2	5	1	1	2	6	6			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:37187887G>C	ENST00000508244.1	-	21	3962	c.3869C>G	c.(3868-3870)tCc>tGc	p.S1290C	C5orf42_ENST00000274258.7_Missense_Mutation_p.S171C|C5orf42_ENST00000425232.2_Missense_Mutation_p.S1290C			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1290						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GCAACTATAGGATAACTTATC	0.373																																					p.S1290C		.											.	C5orf42-94	0			c.C3869G						.						109	102	104					5																	37187887		2203	4300	6503	SO:0001583	missense	65250	exon22			CTATAGGATAACT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.3869C>G	5.37:g.37187887G>C	ENSP00000421690:p.Ser1290Cys	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	26	5	NM_023073	0	0	1	1	0	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867793	0.72065	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.49	5.49	0.81192	.	0.080123	0.49305	D	0.000159	T	0.75228	0.3821	L	0.29908	0.895	0.46701	D	0.999167	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.77525	-0.2555	10	0.87932	D	0	.	19.7365	0.96208	0.0:0.0:1.0:0.0	.	1290;171	E9PH94;Q9H799	.;CE042_HUMAN	C	1290;1290;171;338;171	ENSP00000421690:S1290C;ENSP00000389014:S1290C;ENSP00000274258:S171C;ENSP00000424223:S338C	ENSP00000274258:S171C	S	-	2	0	C5orf42	37223644	1.000000	0.71417	0.982000	0.44146	0.176000	0.22953	8.290000	0.89925	2.749000	0.94314	0.491000	0.48974	TCC	.		0.373	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37187887	G	C	37187887	3	2	33	1	0	0	0	0	1	0	0	0	2307	1174	41	4	5848	4	C5orf42	5	37187887	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08		37187887	143727373	20	2875											
C7	730	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	40964972	40964972	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgttggggaaatgcattgtCagagtgagtggcgtcagttg	8	13	16	4	1	2	2	2	1	0	1	2	3	2	3	0	3	1	3	0	3	1	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:40964972C>G	ENST00000313164.9	+	14	2238	c.1879C>G	c.(1879-1881)Cag>Gag	p.Q627E		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	627	CCP 2.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				AATGCATTGTCAGAGTGAGTG	0.403																																					p.Q627E		.											.	C7-22	0			c.C1879G						.						147	147	147					5																	40964972		1988	4163	6151	SO:0001583	missense	730	exon14			CATTGTCAGAGTG	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"Complement system"	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1879C>G	5.37:g.40964972C>G	ENSP00000322061:p.Gln627Glu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	159	8	NM_000587	0	0	0	0	0	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.296653	0.60086	.	.	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.44881	0.91	6.04	6.04	0.98038	Complement control module (2);Sushi/SCR/CCP (1);	0.184818	0.47455	D	0.000226	T	0.36276	0.0961	L	0.32530	0.975	0.49687	D	0.999811	P	0.46395	0.877	B	0.37480	0.251	T	0.21690	-1.0238	10	0.56958	D	0.05	-8.4484	20.5948	0.99439	0.0:1.0:0.0:0.0	.	627	P10643	CO7_HUMAN	E	627;467	ENSP00000322061:Q627E	ENSP00000322061:Q627E	Q	+	1	0	C7	41000729	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.443000	0.44881	2.873000	0.98535	0.563000	0.77884	CAG	.		0.403	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			G	40964972	C	G	40964972	3	3	33	1	0	0	0	0	1	0	0	0	2381	827	29	4	1933	4	C7	5	40964972	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3777085	40964972	139950288	21	2876											
ITGA1	3672	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	52204750	52204750	+	Frame_Shift_Del	DEL	T	T	-																															tggttcctactttggcagtaTtttaacaacaactgacattg																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:52204750delT	ENST00000282588.6	+	13	1936	c.1478delT	c.(1477-1479)attfs	p.I493fs		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	493					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTTGGCAGTATTTTAACAACA	0.383																																					p.I493fs		.											.	ITGA1-228	0			c.1478delT						.						154	149	151					5																	52204750		2203	4300	6503	SO:0001589	frameshift_variant	3672	exon13			.	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1478delT	5.37:g.52204750delT	ENSP00000282588:p.Ile493fs	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	145	31	NM_181501	0	0	0	0	0	B2RNU0	Frame_Shift_Del	DEL	ENST00000282588.6	37	CCDS3955.1																																																																																			.		0.383	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		-	52204750	T	-	52204750	7	5	33	1	0	1	0	1	0	0	0	0	7893	1493	52	0	1528	0	ITGA1	5	52204750	Frame_Shift_Del	DEL	T	TCGA-AL-7173-01A-11D-2136-08	11239778	52204750	128710510	22	2877											
LARS	51520	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	145552256	145552256	+	Frame_Shift_Del	DEL	T	T	-																															tagggaaacattacctcacaTttggataaagaaaacgtgtg																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:145552256delT	ENST00000394434.2	-	3	373	c.207delA	c.(205-207)aaafs	p.K69fs	LARS_ENST00000274562.9_Frame_Shift_Del_p.K69fs|LARS_ENST00000511505.1_5'UTR|LARS_ENST00000510191.1_Frame_Shift_Del_p.K15fs|LARS_ENST00000545646.1_Frame_Shift_Del_p.K69fs	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	69					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TTACCTCACATTTGGATAAAG	0.353																																					p.K69fs		.											.	LARS-90	0			c.207delA						.						94	87	90					5																	145552256		2203	4300	6503	SO:0001589	frameshift_variant	51520	exon3			.	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	6512	protein-coding gene	gene with protein product	"leucine tRNA ligase 1, cytoplasmic"	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.207delA	5.37:g.145552256delT	ENSP00000377954:p.Lys69fs	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	62	23	NM_020117	0	0	0	0	0	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Frame_Shift_Del	DEL	ENST00000394434.2	37	CCDS34265.1																																																																																			.		0.353	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		-	145552256	T	-	145552256	7	5	33	1	0	1	0	1	0	0	0	0	8655	1490	52	0	3443	0	LARS	5	145552256	Frame_Shift_Del	DEL	T	TCGA-AL-7173-01A-11D-2136-08	93347506	145552256	35363004	23	2878											
SPINK5	11005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	147510840	147510840	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggattctgagatgtgcaaaGactaccgagtattgcccagg	12	9	12	8	1	1	2	0	1	1	2	1	5	1	3	2	2	3	2	2	2	3	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:147510840G>C	ENST00000256084.7	+	31	3025	c.2983G>C	c.(2983-2985)Gac>Cac	p.D995H	SPINK5_ENST00000359874.3_Missense_Mutation_p.D1025H	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	995	Kazal-like 15. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGTGCAAAGACTACCGAGT	0.433																																					p.D1025H		.											.	SPINK5-138	0			c.G3073C						.						250	232	238					5																	147510840		1894	4123	6017	SO:0001583	missense	11005	exon32			TGCAAAGACTACC	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"Serine peptidase inhibitors, Kazal type"	15464	protein-coding gene	gene with protein product	"lymphoepithelial Kazal-type-related inhibitor"	605010	"serine protease inhibitor, Kazal type 5"			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.2983G>C	5.37:g.147510840G>C	ENSP00000256084:p.Asp995His	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	239	44	NM_001127698	0	0	0	0	0	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	4.580	0.107817	0.08780	.	.	ENSG00000133710	ENST00000359874;ENST00000256084	T;T	0.75367	-0.93;-0.93	4.69	0.694	0.18062	Proteinase inhibitor I1, Kazal (1);	0.707951	0.13366	N	0.393281	T	0.44180	0.1281	N	0.02539	-0.55	0.24542	N	0.994066	B;B	0.10296	0.003;0.0	B;B	0.09377	0.003;0.004	T	0.29274	-1.0017	10	0.22109	T	0.4	-0.8408	7.0127	0.24871	0.2944:0.3745:0.3311:0.0	.	1025;995	Q9NQ38-3;Q9NQ38	.;ISK5_HUMAN	H	1025;995	ENSP00000352936:D1025H;ENSP00000256084:D995H	ENSP00000256084:D995H	D	+	1	0	SPINK5	147491033	0.961000	0.32948	0.962000	0.40283	0.816000	0.46133	-0.005000	0.12855	-0.016000	0.14127	-0.136000	0.14681	GAC	.		0.433	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		C	147510840	G	C	147510840	3	2	33	1	0	0	0	0	1	0	0	0	15094	942	33	4	3211	4	SPINK5	5	147510840	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	1958584	147510840	33404420	24	2879											
PRIM2	5558	broad.mit.edu;bcgsc.ca	37	chr6	57246849	57246850	+	Missense_Mutation	DNP	GG	GG	TT																															atcccttttgctgatgctctGgatttgtttcgaggaaggaa																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr6:57246849_57246850GG>TT	ENST00000607273.1	+	7	663_664	c.576_577GG>TT	c.(574-579)ctGGat>ctTTat	p.D193Y	PRIM2_ENST00000389488.2_3'UTR	NM_000947.3	NP_000938.2	P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	193					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTGATGCTCTGGATTTGTTTCG	0.366																																					.													.	PRIM2-227	0			.						.																																			SO:0001583	missense	5558	.			GCTCTGGATTTGT		CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	Exception_encountered	6.37:g.57246849_57246850delinsTT	ENSP00000475738:p.Asp193Tyr	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	35	9	.	0	0	0	0	0	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Missense_Mutation	DNP	ENST00000607273.1	37																																																																																				.		0.366	PRIM2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000947		TT	57246850	GG	TT	57246849	3	4	33	1	0	0	0	0	1	0	0	0	12520	1335	47	4	598	4	PRIM2	6	57246849	Missense_Mutation	DNP	GG	TCGA-AL-7173-01A-11D-2136-08		57246849	113868218	25	2880											
HOXA1	3198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	27134334	27134334	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttgaagtggaactccttctCcagttccgtgagctgcttgg	6	13	12	10	1	1	2	0	2	1	0	4	3	3	3	3	2	3	4	3	2	2	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:27134334C>T	ENST00000343060.4	-	2	794	c.733G>A	c.(733-735)Gag>Aag	p.E245K	HOXA1_ENST00000355633.5_3'UTR|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOTAIRM1_ENST00000425358.2_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	245					abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AACTCCTTCTCCAGTTCCGTG	0.582																																					p.E245K		.											.	HOXA1-93	0			c.G733A						.						120	109	113					7																	27134334		2203	4300	6503	SO:0001583	missense	3198	exon2			CCTTCTCCAGTTC		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"Homeoboxes / ANTP class : HOXL subclass"	5099	protein-coding gene	gene with protein product		142955	"homeo box A1"	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.733G>A	7.37:g.27134334C>T	ENSP00000343246:p.Glu245Lys	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	205	46	NM_005522	0	0	3	4	1	A4D184|B2R8U7|O43363	Missense_Mutation	SNP	ENST00000343060.4	37	CCDS5401.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901126	0.92035	.	.	ENSG00000105991	ENST00000343060	D	0.97575	-4.44	5.31	5.31	0.75309	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.046170	0.85682	D	0.000000	D	0.98848	0.9611	M	0.92317	3.295	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.99686	1.1000	10	0.87932	D	0	.	18.98	0.92752	0.0:1.0:0.0:0.0	.	245	P49639	HXA1_HUMAN	K	245	ENSP00000343246:E245K	ENSP00000343246:E245K	E	-	1	0	HOXA1	27100859	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.770000	0.85390	2.495000	0.84180	0.655000	0.94253	GAG	.		0.582	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1			T	27134334	C	T	27134334	3	4	33	1	0	0	0	0	1	0	0	0	7309	864	30	2	278	2	HOXA1	7	27134334	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		27134334	132004329	26	2881											
GTF2I	2969	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	74146900	74146900	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgaagatctttatgtagaaGgacttcctgaaggaattcct	12	14	9	6	0	1	4	0	2	1	2	3	6	3	6	2	2	0	1	2	2	6	6			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:74146900G>C	ENST00000324896.4	+	15	1590	c.1201G>C	c.(1201-1203)Gga>Cga	p.G401R	GTF2I_ENST00000416070.1_Missense_Mutation_p.G360R|GTF2I_ENST00000353920.4_Missense_Mutation_p.G381R|GTF2I_ENST00000346152.4_Missense_Mutation_p.G380R	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	401					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						TTATGTAGAAGGACTTCCTGA	0.418																																					p.G401R		.											.	GTF2I-90	0			c.G1201C						.						47	48	48					7																	74146900		2201	4299	6500	SO:0001583	missense	2969	exon15			GTAGAAGGACTTC	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"General transcription factors"	4659	protein-coding gene	gene with protein product		601679	"general transcription factor II, i"	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1201G>C	7.37:g.74146900G>C	ENSP00000322542:p.Gly401Arg	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	125	36	NM_032999	0	0	12	18	6	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	ENST00000324896.4	37	CCDS5573.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.164966	0.57476	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	4.72	4.72	0.59763	.	0.000000	0.64402	D	0.000003	D	0.87289	0.6140	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.972;0.999;1.0;1.0	D	0.89083	0.3477	10	0.87932	D	0	-20.2102	16.6643	0.85248	0.0:0.0:1.0:0.0	.	379;360;381;380;401	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	R	401;396;381;380;360	ENSP00000322542:G401R;ENSP00000322671:G381R;ENSP00000322599:G380R;ENSP00000387651:G360R	ENSP00000322542:G401R	G	+	1	0	GTF2I	73784836	1.000000	0.71417	0.998000	0.56505	0.359000	0.29487	6.620000	0.74224	2.159000	0.67721	0.585000	0.79938	GGA	.		0.418	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999		C	74146900	G	C	74146900	3	2	33	1	0	0	0	0	1	0	0	0	6888	1001	35	4	1255	4	GTF2I	7	74146900	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	47012566	74146900	84991763	27	2882											
MAGI2	9863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	78131031	78131031	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcctcaggctgactgtaCactggtgcaggataaggctg	9	9	13	10	0	1	1	1	1	0	0	2	2	2	2	1	4	3	5	1	4	2	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:78131031C>A	ENST00000354212.4	-	5	1081	c.828G>T	c.(826-828)gtG>gtT	p.V276V	MAGI2_ENST00000419488.1_Silent_p.V276V|MAGI2_ENST00000522391.1_Silent_p.V276V|MAGI2_ENST00000536571.1_Silent_p.V108V|MAGI2_ENST00000535697.1_Silent_p.V113V	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	276	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GCTGACTGTACACTGGTGCAG	0.493																																					p.V276V		.											.	MAGI2-461	0			c.G828T						.						233	184	201					7																	78131031		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon5			ACTGTACACTGGT	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.828G>T	7.37:g.78131031C>A		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	105	22	NM_012301	0	0	1	1	0	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	37	CCDS5594.1																																																																																			.		0.493	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	78131031	C	A	78131031	2	1	33	1	0	0	0	0	0	0	0	1	9216	465	17	4		4	MAGI2	7	78131031	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3984131	78131031	81007632	28	2883											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	82763823	82763823	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttctttttactgttggagCttgttcagctttgggctcta	4	20	10	7	0	3	0	1	0	2	0	3	1	3	1	0	2	3	6	0	2	2	9			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:82763823C>G	ENST00000333891.9	-	3	3380	c.3043G>C	c.(3043-3045)Gct>Cct	p.A1015P	PCLO_ENST00000423517.2_Missense_Mutation_p.A1015P	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ACTGTTGGAGCTTGTTCAGCT	0.428																																					p.A1015P		.											.	PCLO-29	0			c.G3043C						.						87	84	85					7																	82763823		1833	4087	5920	SO:0001583	missense	27445	exon3			TTGGAGCTTGTTC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3043G>C	7.37:g.82763823C>G	ENSP00000334319:p.Ala1015Pro	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	57	16	NM_014510	0	0	0	0	0		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	7.239	0.600956	0.13939	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.76839	-1.05;-1.05	6.07	2.21	0.28008	.	.	.	.	.	T	0.66626	0.2808	L	0.36672	1.1	0.09310	N	0.999994	B;B	0.12630	0.006;0.006	B;B	0.10450	0.005;0.005	T	0.57659	-0.7773	9	0.87932	D	0	.	6.642	0.22914	0.1221:0.6245:0.0:0.2534	.	1015;1015	Q9Y6V0-5;Q9Y6V0-6	.;.	P	961;1015;1015	ENSP00000334319:A1015P;ENSP00000388393:A1015P	ENSP00000334319:A1015P	A	-	1	0	PCLO	82601759	0.000000	0.05858	0.011000	0.14972	0.864000	0.49448	0.079000	0.14782	0.126000	0.18424	-0.136000	0.14681	GCT	.		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82763823	C	G	82763823	3	3	33	1	0	0	0	0	1	0	0	0	11609	797	28	4	12494	4	PCLO	7	82763823	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	4632792	82763823	76374840	29	2884											
CYP3A7	1551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99328744	99328744	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccctggaattccaagctTcttaaaaagtccatgtgtac	11	11	9	10	0	1	0	0	0	1	0	3	1	3	1	3	2	2	2	3	2	6	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:99328744T>A	ENST00000336374.2	-	2	105	c.103A>T	c.(103-105)Aag>Tag	p.K35*		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	35					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	ATTCCAAGCTTCTTAAAAAGT	0.423																																					p.K35X		.											.	CYP3A7-91	0			c.A103T						.						105	98	100					7																	99328744		2203	4300	6503	SO:0001587	stop_gained	1551	exon2			CAAGCTTCTTAAA	AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"Cytochrome P450s"	2640	protein-coding gene	gene with protein product		605340	"cytochrome P450, subfamily IIIA, polypeptide 7"			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.103A>T	7.37:g.99328744T>A	ENSP00000337450:p.Lys35*	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	152	56	NM_000765	0	0	0	0	0	A4D288|Q9H241	Nonsense_Mutation	SNP	ENST00000336374.2	37	CCDS5673.1	.	.	.	.	.	.	.	.	.	.	T	11.23	1.576557	0.28092	.	.	ENSG00000160870	ENST00000292414;ENST00000336374	.	.	.	3.52	3.52	0.40303	.	0.100727	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5745	0.33590	0.0:0.0:0.0:1.0	.	.	.	.	X	35	.	ENSP00000292414:K35X	K	-	1	0	CYP3A7	99166680	1.000000	0.71417	0.974000	0.42286	0.205000	0.24178	4.328000	0.59253	1.598000	0.50083	0.418000	0.28097	AAG	.		0.423	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			A	99328744	T	A	99328744	4	1	33	1	0	0	0	0	0	1	0	0	4187	1792	62	5	1456	5	CYP3A7	7	99328744	Nonsense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	16564921	99328744	59809919	30	2885											
CUX1	1523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	101845410	101845410	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgtaccaggaggtggacAccatcgagctcacccggcag	11	5	12	13	2	1	0	1	0	0	0	2	3	1	2	3	4	2	3	3	4	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:101845410A>T	ENST00000292535.7	+	18	2871	c.2833A>T	c.(2833-2835)Acc>Tcc	p.T945S	CUX1_ENST00000550008.2_Missense_Mutation_p.T889S|CUX1_ENST00000546411.2_Missense_Mutation_p.T843S|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.T787S|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.T956S|CUX1_ENST00000549414.2_Missense_Mutation_p.T923S	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	945					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						GGAGGTGGACACCATCGAGCT	0.612																																					p.T956S		.											.	CUX1-160	0			c.A2866T						.						111	113	112					7																	101845410		2203	4300	6503	SO:0001583	missense	1523	exon18			GTGGACACCATCG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2833A>T	7.37:g.101845410A>T	ENSP00000292535:p.Thr945Ser	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	230	78	NM_001202543	0	0	1	3	2	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	37	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	33	5.209946	0.95069	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.79845	-1.28;-1.28;-1.3;-1.31;-1.22;-1.23	5.29	5.29	0.74685	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.132166	0.51477	D	0.000092	D	0.89511	0.6736	M	0.82056	2.57	0.80722	D	1	D;D	0.71674	0.992;0.998	D;D	0.80764	0.987;0.994	D	0.90018	0.4126	10	0.48119	T	0.1	-33.7771	15.2336	0.73411	1.0:0.0:0.0:0.0	.	945;956	P39880;P39880-3	CUX1_HUMAN;.	S	956;945;923;889;843;787	ENSP00000353401:T956S;ENSP00000292535:T945S;ENSP00000446630:T923S;ENSP00000447373:T889S;ENSP00000450125:T843S;ENSP00000451558:T787S	ENSP00000292535:T945S	T	+	1	0	CUX1	101632130	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.010000	0.58986	0.533000	0.62120	ACC	.		0.612	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		T	101845410	A	T	101845410	3	4	33	1	0	0	0	0	1	0	0	0	4070	159	6	5	2970	5	CUX1	7	101845410	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	2516666	101845410	57293253	31	2886											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116417463	116417463	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcattttggttgtgtatatCatgggactttgttggacaat	8	17	12	4	0	1	0	1	0	0	0	1	2	1	2	0	4	0	4	0	4	3	7	rs121913244		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:116417463C>T	ENST00000318493.6	+	16	3521	c.3334C>T	c.(3334-3336)Cat>Tat	p.H1112Y	MET_ENST00000397752.3_Missense_Mutation_p.H1094Y|MET_ENST00000539704.1_5'UTR			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.H1112Y(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTGTGTATATCATGGGACTTT	0.343			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.H1112Y		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.C3334T	GRCh37	CM993668	MET	M	rs121913244	.						188	175	179					7																	116417463		1832	4086	5918	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GTATATCATGGGA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3334C>T	7.37:g.116417463C>T	ENSP00000317272:p.His1112Tyr	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	181	62	NM_001127500	0	0	3	9	6	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615896	0.87359	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.33654	1.4;1.4	5.29	5.29	0.74685	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43919	0.1269	N	0.11364	0.135	0.80722	D	1	P;D	0.89917	0.937;1.0	P;D	0.91635	0.854;0.999	T	0.52711	-0.8539	10	0.51188	T	0.08	-16.8984	19.2953	0.94119	0.0:1.0:0.0:0.0	.	1112;1094	P08581-2;P08581	.;MET_HUMAN	Y	1094;1112	ENSP00000380860:H1094Y;ENSP00000317272:H1112Y	ENSP00000317272:H1112Y	H	+	1	0	MET	116204699	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.628000	0.89032	0.655000	0.94253	CAT	.		0.343	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116417463	C	T	116417463	3	4	33	1	0	0	0	0	1	0	0	0	9510	826	29	2	3392	2	MET	7	116417463	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	14572053	116417463	42721200	32	2887											
C7orf55	154791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	139030365	139030365	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatcaggaatttcatggcaAgggtgagcgctcggtggagg	10	8	16	7	2	2	1	2	1	0	0	3	3	2	3	0	6	1	2	0	6	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:139030365A>T	ENST00000297534.6	+	2	510	c.257A>T	c.(256-258)aAg>aTg	p.K86M	C7orf55_ENST00000481123.1_3'UTR|LUC7L2_ENST00000541515.3_Missense_Mutation_p.K86M|C7orf55-LUC7L2_ENST00000541170.3_Intron	NM_197964.4	NP_932068.2	Q96HJ9	CG055_HUMAN	chromosome 7 open reading frame 55	86						mitochondrion (GO:0005739)				breast(1)|lung(2)	3						TTTCATGGCAAGGGTGAGCGC	0.562																																					p.K86M		.											.	.	0			c.A257T						.						76	68	71					7																	139030365		2203	4300	6503	SO:0001583	missense	100996928	exon2			ATGGCAAGGGTGA	AF161386	CCDS5853.1	7q34	2009-01-22	2009-01-22	2009-01-22	ENSG00000164898	ENSG00000164898			26946	protein-coding gene	gene with protein product	"formation of mitochondrial complexes 1 homolog (S. cerevisiae)"					12477932	Standard	NM_197964		Approved	HSPC268, FMC1		Q96HJ9	OTTHUMG00000151719	ENST00000297534.6:c.257A>T	7.37:g.139030365A>T	ENSP00000297534:p.Lys86Met	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	81	16	NM_001244584	0	0	54	96	42	B7Z4Q3|Q75M90|Q9P0B3	Missense_Mutation	SNP	ENST00000297534.6	37	CCDS5853.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.963741	0.74016	.	.	ENSG00000164898;ENSG00000146963	ENST00000297534;ENST00000541515	T;T	0.53423	0.62;1.33	5.62	3.25	0.37280	.	.	.	.	.	T	0.44244	0.1284	M	0.71581	2.175	0.32737	N	0.508162	B;B	0.10296	0.003;0.003	B;B	0.14578	0.011;0.011	T	0.53968	-0.8363	9	0.87932	D	0	-0.2264	5.3084	0.15817	0.7154:0.0:0.1316:0.1531	.	86;86	B7Z4Q3;Q96HJ9	.;CG055_HUMAN	M	86	ENSP00000297534:K86M;ENSP00000440222:K86M	ENSP00000297534:K86M	K	+	2	0	LUC7L2;C7orf55	138680905	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.533000	0.36040	0.928000	0.37168	0.455000	0.32223	AAG	.		0.562	C7orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323626.1	NM_197964		T	139030365	A	T	139030365	3	4	33	1	0	0	0	0	1	0	0	0	2409	72	3	5	263	5	C7orf55	7	139030365	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	22612902	139030365	20108298	33	2888											
KEL	3792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142658089	142658089	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tattggtctctttggcccttCcacaggcaaagctgaagaag	10	11	10	10	0	1	2	0	1	1	1	3	2	2	2	2	3	1	2	2	3	4	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:142658089C>A	ENST00000355265.2	-	4	800	c.326G>T	c.(325-327)gGa>gTa	p.G109V	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	109					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					TTTGGCCCTTCCACAGGCAAA	0.512																																					p.G109V		.											.	KEL-93	0			c.G326T						.						133	133	133					7																	142658089		2203	4300	6503	SO:0001583	missense	3792	exon4			GCCCTTCCACAGG	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.326G>T	7.37:g.142658089C>A	ENSP00000347409:p.Gly109Val	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	208	40	NM_000420	0	0	0	0	0	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	CCDS34766.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.61|12.61	1.990455|1.990455	0.35131|0.35131	.|.	.|.	ENSG00000197993|ENSG00000197993	ENST00000355265;ENST00000476829;ENST00000467543|ENST00000460479	D;D;D|.	0.88741|.	-2.42;-2.42;-2.42|.	5.66|5.66	2.87|2.87	0.33458|0.33458	Peptidase M13 (1);|.	0.255042|.	0.27792|.	N|.	0.017836|.	T|T	0.71576|0.71576	0.3356|0.3356	M|M	0.83223|0.83223	2.63|2.63	0.45607|0.45607	D|D	0.998543|0.998543	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.68458|0.68458	-0.5403|-0.5403	10|5	0.87932|.	D|.	0|.	-14.3801|-14.3801	7.6264|7.6264	0.28214|0.28214	0.0:0.7371:0.0:0.2629|0.0:0.7371:0.0:0.2629	.|.	109|.	P23276|.	KELL_HUMAN|.	V|C	109;109;90|119	ENSP00000347409:G109V;ENSP00000419889:G109V;ENSP00000420011:G90V|.	ENSP00000347409:G109V|.	G|W	-|-	2|3	0|0	KEL|KEL	142368211|142368211	0.745000|0.745000	0.28261|0.28261	0.447000|0.447000	0.26932|0.26932	0.040000|0.040000	0.13550|0.13550	1.084000|1.084000	0.30828|0.30828	0.317000|0.317000	0.23160|0.23160	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.		0.512	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		A	142658089	C	A	142658089	3	1	33	1	0	0	0	0	1	0	0	0	8163	855	30	4	1936	4	KEL	7	142658089	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3627724	142658089	16480574	34	2889											
OR2A7	401427	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	143956670	143956670	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catctgaatccttgggccaaCgggaaatcccagtaggagga	12	7	12	10	1	1	1	0	1	1	0	3	4	3	4	3	4	1	1	3	4	4	2	rs531461622		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:143956670C>T	ENST00000493325.1	-	1	145	c.52G>A	c.(52-54)Gtt>Att	p.V18I	OR2A1-AS1_ENST00000487102.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|ARHGEF35_ENST00000543357.1_Intron|RP4-545C24.1_ENST00000460955.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA	NM_001005328.1	NP_001005328.1	Q96R45	OR2A7_HUMAN	olfactory receptor, family 2, subfamily A, member 7	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)	6	Melanoma(164;0.14)					CTTGGGCCAACGGGAAATCCC	0.498													c|||	1	0.000199681	8e-04	0	5008	,	,		31715	0		0	False		,,,				2504	0				p.V18I		.											.	OR2A7-23	0			c.G52A						.						100	128	118					7																	143956670		2201	4297	6498	SO:0001583	missense	401427	exon1			GGCCAACGGGAAA		CCDS55177.1	7q35	2013-09-20			ENSG00000243896	ENSG00000243896		"GPCR / Class A : Olfactory receptors"	8234	protein-coding gene	gene with protein product							Standard	NM_001005328		Approved	HSDJ0798C17	uc011kuc.2	Q96R45	OTTHUMG00000158002	ENST00000493325.1:c.52G>A	7.37:g.143956670C>T	ENSP00000420502:p.Val18Ile	Somatic	407	2		WXS	Illumina HiSeq	Phase_I	432	31	NM_001005328	0	0	3	3	0	B2RN57|Q6IFP4	Missense_Mutation	SNP	ENST00000493325.1	37	CCDS55177.1	.	.	.	.	.	.	.	.	.	.	c	0.608	-0.826223	0.02734	.	.	ENSG00000243896	ENST00000493325	T	0.00433	7.43	3.21	-3.87	0.04218	.	.	.	.	.	T	0.00178	0.0005	N	0.04245	-0.25	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.20273	-1.0280	9	0.39692	T	0.17	.	4.6601	0.12637	0.0891:0.4935:0.1752:0.2422	.	18	Q96R45	OR2A7_HUMAN	I	18	ENSP00000420502:V18I	ENSP00000420502:V18I	V	-	1	0	OR2A7	143587603	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.569000	0.00915	-0.991000	0.03476	-1.490000	0.00973	GTT	.		0.498	OR2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349979.1			T	143956670	C	T	143956670	3	4	33	1	0	0	0	0	1	0	0	0	11008	536	19	1	883	1	OR2A7	7	143956670	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	1298581	143956670	15181993	35	2890											
FBXO43	286151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	101152996	101152996	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ttttaattctgttaagatgtCcagtttttctatacccattt	9	21	4	7	0	2	1	0	0	2	1	3	1	3	1	2	0	1	2	2	0	4	9			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr8:101152996C>G	ENST00000428847.2	-	2	1802	c.1486G>C	c.(1486-1488)Gac>Cac	p.D496H		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	496	F-box.				meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			GTTAAGATGTCCAGTTTTTCT	0.388																																					p.D496H		.											.	FBXO43-226	0			c.G1486C						.						144	134	137					8																	101152996		1822	4082	5904	SO:0001583	missense	286151	exon2			AGATGTCCAGTTT	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1486G>C	8.37:g.101152996C>G	ENSP00000403293:p.Asp496His	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	160	36	NM_001029860	0	0	0	0	0		Missense_Mutation	SNP	ENST00000428847.2	37	CCDS47904.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070318	0.76301	.	.	ENSG00000156509	ENST00000428847	T	0.64618	-0.11	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.81394	0.4813	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84731	0.0745	10	0.87932	D	0	-12.012	18.3634	0.90383	0.0:1.0:0.0:0.0	.	462;496	C9J908;Q4G163	.;FBX43_HUMAN	H	496	ENSP00000403293:D496H	ENSP00000403293:D496H	D	-	1	0	FBXO43	101222172	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.034000	0.76511	2.398000	0.81561	0.655000	0.94253	GAC	.		0.388	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		G	101152996	C	G	101152996	3	3	33	1	0	0	0	0	1	0	0	0	5771	855	30	4	656	4	FBXO43	8	101152996	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		101152996	45211026	36	2891											
CPSF1	29894	hgsc.bcm.edu	37	chr8	145626922	145626922	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaagaaggagaaggaggCagcaagctcgagcttctccc	13	4	13	11	1	1	2	0	0	1	2	3	5	1	3	2	3	3	4	2	3	4	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr8:145626922C>G	ENST00000349769.3	-	4	302	c.208G>C	c.(208-210)Gcc>Ccc	p.A70P	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	70					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GAGAAGGAGGCAGCAAGCTCG	0.647																																					p.A70P	NSCLC(133;1088 1848 27708 34777 35269)	.											.	CPSF1-91	0			c.G208C						.						78	77	77					8																	145626922		2202	4300	6502	SO:0001583	missense	29894	exon4			AGGAGGCAGCAAG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"cleavage and polyadenylation specific factor 1, 160kD subunit"			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.208G>C	8.37:g.145626922C>G	ENSP00000339353:p.Ala70Pro	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_013291	0	0	10	10	0	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454700	0.43634	.	.	ENSG00000071894	ENST00000349769;ENST00000531042	T	0.51574	0.7	4.31	3.42	0.39159	.	0.000000	0.85682	D	0.000000	T	0.58595	0.2133	M	0.79926	2.475	0.58432	D	0.999997	P;P	0.40398	0.659;0.716	P;B	0.49140	0.601;0.372	T	0.59989	-0.7350	10	0.42905	T	0.14	-1.831	11.1686	0.48558	0.1853:0.8146:0.0:0.0	.	70;70	B4DEF4;Q10570	.;CPSF1_HUMAN	P	70	ENSP00000339353:A70P	ENSP00000339353:A70P	A	-	1	0	CPSF1	145597730	1.000000	0.71417	0.992000	0.48379	0.443000	0.32047	5.033000	0.64146	1.010000	0.39314	0.561000	0.74099	GCC	.		0.647	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		G	145626922	C	G	145626922	3	3	33	1	0	0	0	0	1	0	0	0	3830	710	25	4	4263	4	CPSF1	8	145626922	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	44473926	145626922	737100	37	2892											
FREM1	158326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	14801824	14801824	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggaatgtccaggtccaCagcgctgatgatggaagagt	10	8	15	8	1	0	3	0	2	0	1	2	5	2	5	2	4	1	1	2	4	2	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr9:14801824C>G	ENST00000380880.3	-	20	4303	c.3520G>C	c.(3520-3522)Gtg>Ctg	p.V1174L	FREM1_ENST00000380881.4_Missense_Mutation_p.V1175L|FREM1_ENST00000422223.2_Missense_Mutation_p.V1174L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1174					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TCCAGGTCCACAGCGCTGATG	0.493																																					p.V1174L		.											.	FREM1-138	0			c.G3520C						.						150	147	148					9																	14801824		2053	4219	6272	SO:0001583	missense	158326	exon21			GGTCCACAGCGCT	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.3520G>C	9.37:g.14801824C>G	ENSP00000370262:p.Val1174Leu	Somatic	227	0		WXS	Illumina HiSeq	Phase_I	160	36	NM_144966	0	0	0	0	0	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	8.474	0.858155	0.17178	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.49432	0.78;0.78;0.78	5.51	-0.193	0.13244	.	0.808695	0.12113	N	0.498353	T	0.32793	0.0841	L	0.33339	1.005	0.22017	N	0.999411	B	0.12013	0.005	B	0.09377	0.004	T	0.22556	-1.0213	10	0.21540	T	0.41	-0.3702	10.4355	0.44433	0.0:0.6222:0.0:0.3778	.	1174	Q5H8C1	FREM1_HUMAN	L	1175;1174;1174	ENSP00000370263:V1175L;ENSP00000412940:V1174L;ENSP00000370262:V1174L	ENSP00000370257:V1177L	V	-	1	0	FREM1	14791824	0.010000	0.17322	0.071000	0.20095	0.038000	0.13279	0.139000	0.16036	0.033000	0.15463	0.591000	0.81541	GTG	.		0.493	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14801824	C	G	14801824	3	3	33	1	0	0	0	0	1	0	0	0	6063	478	17	4	3141	4	FREM1	9	14801824	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		14801824	126411607	38	2893											
FCN1	2219	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	137801883	137801883	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttgttgttgtggcccgttaGagaattacctgctcacagaa	9	13	11	8	1	1	2	1	0	0	2	1	3	1	2	2	1	2	5	2	1	4	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr9:137801883G>C	ENST00000371806.3	-	9	833	c.742C>G	c.(742-744)Cta>Gta	p.L248V		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	248	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		TGGCCCGTTAGAGAATTACCT	0.507																																					p.L248V		.											.	FCN1-154	0			c.C742G						.						170	177	175					9																	137801883		2203	4300	6503	SO:0001583	missense	2219	exon9			CCGTTAGAGAATT	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.742C>G	9.37:g.137801883G>C	ENSP00000360871:p.Leu248Val	Somatic	283	0		WXS	Illumina HiSeq	Phase_I	253	53	NM_002003	0	0	0	0	0	Q5VYV5|Q92596	Missense_Mutation	SNP	ENST00000371806.3	37	CCDS6985.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.254797	0.39896	.	.	ENSG00000085265	ENST00000371806	T	0.78246	-1.16	3.29	1.19	0.21007	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	.	.	.	.	D	0.88742	0.6519	H	0.96833	3.89	0.33292	D	0.56369	D	0.67145	0.996	D	0.68765	0.96	D	0.85951	0.1464	9	0.87932	D	0	.	2.548	0.04742	0.2654:0.0:0.5025:0.2321	.	248	O00602	FCN1_HUMAN	V	248	ENSP00000360871:L248V	ENSP00000360871:L248V	L	-	1	2	FCN1	136941704	0.980000	0.34600	0.042000	0.18584	0.143000	0.21401	2.020000	0.41010	0.705000	0.31890	0.643000	0.83706	CTA	.		0.507	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		C	137801883	G	C	137801883	3	2	33	1	0	0	0	0	1	0	0	0	5810	933	33	4	242	4	FCN1	9	137801883	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	123000059	137801883	3411548	39	2894											
LHX3	8022	ucsc.edu	37	chr9	139091693	139091693	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgcgtgggcgggatgccCagctggcacgcggcgcactt	5	6	16	14	5	0	0	0	0	0	0	0	1	0	1	2	4	3	3	2	4	0	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr9:139091693C>T	ENST00000371748.5	-	3	381	c.285G>A	c.(283-285)ctG>ctA	p.L95L	LHX3_ENST00000371746.3_Silent_p.L100L	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	95	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		GCGGGATGCCCAGCTGGCACG	0.721																																					p.L100L													.	LHX3-91	0			c.G300A						.						13	12	12					9																	139091693		2185	4285	6470	SO:0001819	synonymous_variant	8022	exon3			GATGCCCAGCTGG	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"Homeoboxes / LIM class"	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.285G>A	9.37:g.139091693C>T		Somatic	18	0		WXS	Illumina HiSeq		23	4	NM_014564	0	0	0	0	0	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Silent	SNP	ENST00000371748.5	37	CCDS6994.1																																																																																			.		0.721	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3			T	139091693	C	T	139091693	2	4	33	1	0	0	0	0	0	0	0	1	8794	581	21	2		2	LHX3	9	139091693	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	1289810	139091693	2121738	40	2895											
PLAU	414236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	75672687	75672687	+	Intron	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtccccttgtagataagTcaaaaacctgctatgagggg	11	10	10	10	0	1	2	1	1	0	1	2	2	2	2	4	2	2	2	4	2	5	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr10:75672687T>A	ENST00000409178.1	-	3	301				PLAU_ENST00000372762.4_Missense_Mutation_p.S31T|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372764.3_Missense_Mutation_p.S67T|PLAU_ENST00000446342.1_Missense_Mutation_p.S50T|C10orf55_ENST00000412307.2_Intron	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					TGTAGATAAGTCAAAAACCTG	0.468																																					p.S67T		.											.	PLAU-118	0			c.T199A						.						50	49	49					10																	75672687		2203	4300	6503	SO:0001627	intron_variant	5328	exon5			GATAAGTCAAAAA		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.39+113A>T	10.37:g.75672687T>A		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	62	6	NM_002658	0	0	0	0	0	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	37	CCDS53541.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.440884	0.25900	.	.	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	T;T;T	0.62364	0.03;0.03;0.03	5.78	3.47	0.39725	Kringle-like fold (1);	0.659026	0.14635	N	0.307599	T	0.47875	0.1469	L	0.38692	1.165	0.09310	N	0.999999	B;B;B;B	0.24823	0.022;0.112;0.022;0.027	B;B;B;B	0.26864	0.026;0.074;0.014;0.018	T	0.34428	-0.9829	10	0.33141	T	0.24	.	5.3638	0.16103	0.0:0.0896:0.1988:0.7116	.	50;31;67;67	E7ET40;E7ESM2;B2R7F2;P00749	.;.;.;UROK_HUMAN	T	50;67;31;31	ENSP00000388474:S50T;ENSP00000361850:S67T;ENSP00000361848:S31T	ENSP00000361847:S31T	S	+	1	0	PLAU	75342693	0.000000	0.05858	0.022000	0.16811	0.143000	0.21401	0.117000	0.15583	1.009000	0.39289	-0.340000	0.08031	TCA	.		0.468	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		A	75672687	T	A	75672687	1	1	33	0	1	0	0	0	0	0	0	0	12048	1667	58	5		5	PLAU	10	75672687	Intron	SNP	T	TCGA-AL-7173-01A-11D-2136-08		75672687	59862060	41	2896											
RRP8	23378	ucsc.edu	37	chr11	6622569	6622569	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggccccatccagccgctgtgCcatgcgggctcgcaaagccc	6	5	12	18	3	0	0	0	0	0	0	2	0	1	0	6	2	4	3	6	2	1	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:6622569C>T	ENST00000254605.6	-	3	844	c.727G>A	c.(727-729)Gca>Aca	p.A243T	ILK_ENST00000396751.2_5'Flank|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000299421.4_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|RRP8_ENST00000534343.1_Intron|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000420936.2_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	243					cellular response to glucose starvation (GO:0042149)|chromatin modification (GO:0016568)|chromatin silencing at rDNA (GO:0000183)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription by glucose (GO:0046015)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rDNA heterochromatin (GO:0033553)	methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)	13						AGCCGCTGTGCCATGCGGGCT	0.632																																					p.A243T													.	RRP8-90	0			c.G727A						.						29	29	29					11																	6622569		2201	4296	6497	SO:0001583	missense	23378	exon3			GCTGTGCCATGCG	AB007869	CCDS31411.1	11p15.4	2009-02-23	2009-02-23	2009-02-23	ENSG00000132275	ENSG00000132275			29030	protein-coding gene	gene with protein product	RRP8 methyltransferase homolog (S. cerevisiae)	615818	"KIAA0409"	KIAA0409		9455477	Standard	NM_015324		Approved		uc001med.3	O43159		ENST00000254605.6:c.727G>A	11.37:g.6622569C>T	ENSP00000254605:p.Ala243Thr	Somatic	26	0		WXS	Illumina HiSeq		40	4	NM_015324	0	0	11	11	0	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674043	0.29693	.	.	ENSG00000132275	ENST00000254605;ENST00000533907	T;T	0.42131	0.98;0.98	5.85	0.654	0.17833	.	0.282817	0.38058	N	0.001840	T	0.20536	0.0494	N	0.12746	0.255	0.80722	D	1	B	0.17038	0.02	B	0.14578	0.011	T	0.07751	-1.0756	10	0.14252	T	0.57	-4.6887	10.3863	0.44143	0.0:0.6184:0.0:0.3816	.	243	O43159	RRP8_HUMAN	T	243	ENSP00000254605:A243T;ENSP00000436246:A243T	ENSP00000254605:A243T	A	-	1	0	RRP8	6579145	1.000000	0.71417	0.947000	0.38551	0.957000	0.61999	2.543000	0.45752	0.210000	0.20664	0.650000	0.86243	GCA	.		0.632	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		T	6622569	C	T	6622569	3	4	33	1	0	0	0	0	1	0	0	0	13722	739	26	2	663	2	RRP8	11	6622569	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		6622569	128383947	42	2897											
WDR74	54663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62606983	62606983	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgagcctgccacccacctttCaagatcccagtctcggtgcc	7	8	8	18	2	2	1	1	0	1	1	4	2	3	1	6	1	3	0	6	1	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:62606983C>G	ENST00000525239.1	-	2	597	c.60G>C	c.(58-60)ttG>ttC	p.L20F	WDR74_ENST00000311713.7_Missense_Mutation_p.L20F|WDR74_ENST00000278856.4_Missense_Mutation_p.L20F|RNU2-2P_ENST00000410396.1_RNA|WDR74_ENST00000525752.1_Intron|WDR74_ENST00000540620.1_5'UTR|WDR74_ENST00000529106.1_Missense_Mutation_p.L20F			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	20					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						ACCCACCTTTCAAGATCCCAG	0.632																																					p.L20F		.											.	WDR74-23	0			c.G60C						.						39	45	43					11																	62606983		2086	4226	6312	SO:0001583	missense	54663	exon2			ACCTTTCAAGATC		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"WD repeat domain containing"	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.60G>C	11.37:g.62606983C>G	ENSP00000432119:p.Leu20Phe	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	97	26	NM_018093	0	0	0	0	0	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Missense_Mutation	SNP	ENST00000525239.1	37	CCDS44630.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.49|18.49	3.634308|3.634308	0.67130|0.67130	.|.	.|.	ENSG00000133316|ENSG00000133316	ENST00000535048|ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000538098	.|T;T;T;T;T	.|0.39406	.|1.35;1.35;1.35;1.35;1.08	4.28|4.28	1.21|1.21	0.21127|0.21127	.|.	.|0.000000	.|0.64402	.|D	.|0.000007	T|T	0.48502|0.48502	0.1503|0.1503	L|L	0.43554|0.43554	1.36|1.36	0.48632|0.48632	D|D	0.999681|0.999681	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.97110	.|0.997;0.953;1.0	T|T	0.39057|0.39057	-0.9632|-0.9632	5|10	.|0.48119	.|T	.|0.1	-8.5329|-8.5329	5.8248|5.8248	0.18548|0.18548	0.0:0.6468:0.161:0.1922|0.0:0.6468:0.161:0.1922	.|.	.|20;20;20	.|B4E018;Q6RFH5;Q6RFH5-2	.|.;WDR74_HUMAN;.	Q|F	12|20	.|ENSP00000308931:L20F;ENSP00000435726:L20F;ENSP00000432119:L20F;ENSP00000278856:L20F;ENSP00000440612:L20F	.|ENSP00000278856:L20F	E|L	-|-	1|3	0|2	WDR74|WDR74	62363559|62363559	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.936000|0.936000	0.57629|0.57629	1.056000|1.056000	0.30480|0.30480	0.415000|0.415000	0.25817|0.25817	0.655000|0.655000	0.94253|0.94253	GAA|TTG	.		0.632	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093		G	62606983	C	G	62606983	3	3	33	1	0	0	0	0	1	0	0	0	17357	825	29	4	1141	4	WDR74	11	62606983	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	55984414	62606983	72399533	43	2898											
ESRRA	2101	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64074935	64074935	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctaccactatggtgtggcatCctgtgaggcctgcaaagcct	8	10	11	12	0	0	1	0	1	0	0	1	1	1	1	4	3	3	2	4	3	3	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:64074935C>A	ENST00000405666.1	+	2	518	c.284C>A	c.(283-285)tCc>tAc	p.S95Y	RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000000442.6_Missense_Mutation_p.S95Y|ESRRA_ENST00000406310.1_Missense_Mutation_p.S95Y	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	95					cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GGTGTGGCATCCTGTGAGGCC	0.657																																					p.S95Y													.	ESRRA-90	0			c.C284A						.						18	20	19					11																	64074935		2070	4214	6284	SO:0001583	missense	2101	exon2			TGGCATCCTGTGA	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"Nuclear hormone receptors"	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.284C>A	11.37:g.64074935C>A	ENSP00000384851:p.Ser95Tyr	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	45	6	NM_004451	0	0	15	25	10	Q14514	Missense_Mutation	SNP	ENST00000405666.1	37	CCDS41667.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.522137	0.85600	.	.	ENSG00000173153	ENST00000406310;ENST00000000442;ENST00000405666;ENST00000468670	D;D;D;D	0.97710	-4.5;-4.5;-4.5;-4.5	4.3	4.3	0.51218	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (6);	0.065007	0.64402	D	0.000005	D	0.99269	0.9745	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98316	1.0526	10	0.87932	D	0	.	14.6596	0.68861	0.0:1.0:0.0:0.0	.	95;95	P11474-2;P11474	.;ERR1_HUMAN	Y	95	ENSP00000385971:S95Y;ENSP00000000442:S95Y;ENSP00000384851:S95Y;ENSP00000441970:S95Y	ENSP00000000442:S95Y	S	+	2	0	ESRRA	63831511	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.329000	0.79170	2.399000	0.81585	0.462000	0.41574	TCC	.		0.657	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451		A	64074935	C	A	64074935	3	1	33	1	0	0	0	0	1	0	0	0	5273	855	30	4	286	4	ESRRA	11	64074935	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	1467952	64074935	70931581	44	2899											
SLCO2B1	11309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74915493	74915493	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaggttctgtgatctgcttCgccttagttttggctgtcct	4	17	10	10	1	2	1	0	1	2	0	4	1	3	1	2	2	1	4	2	2	1	5	rs192050675		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:74915493C>T	ENST00000289575.5	+	14	2393	c.1998C>T	c.(1996-1998)ttC>ttT	p.F666F	SLCO2B1_ENST00000428359.2_Silent_p.F644F|SLCO2B1_ENST00000525650.1_Silent_p.F522F|SLCO2B1_ENST00000341411.4_Silent_p.F439F|SLCO2B1_ENST00000532236.1_Silent_p.F550F|SLCO2B1_ENST00000454962.2_Silent_p.F439F	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	666					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	TGATCTGCTTCGCCTTAGTTT	0.552																																					p.F666F		.											.	SLCO2B1-154	0			c.C1998T						.	T	,,	1,4399	2.1+/-5.4	0,1,2199	139	119	126		1932,1566,1998	-3	0.1	11		126	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	SLCO2B1	NM_001145211.2,NM_001145212.2,NM_007256.4	,,	0,2,6491	TT,TC,CC		0.0116,0.0227,0.0154	,,	644/688,522/566,666/710	74915493	2,12984	2200	4293	6493	SO:0001819	synonymous_variant	11309	exon14			CTGCTTCGCCTTA	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.1998C>T	11.37:g.74915493C>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	130	27	NM_007256	0	0	5	5	0	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Silent	SNP	ENST00000289575.5	37	CCDS8235.1																																																																																			A|0.000;C|0.999		0.552	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		T	74915493	C	T	74915493	2	4	33	1	0	0	0	0	0	0	0	1	14759	883	31	1		1	SLCO2B1	11	74915493	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	10840558	74915493	60091023	45	2900											
MMP13	4322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102822873	102822873	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctaaggagtggccgaactCatgcgcagcaacaagaaaca	16	4	10	11	2	1	1	1	0	0	1	1	3	1	2	2	2	5	2	2	2	5	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:102822873C>G	ENST00000260302.3	-	5	695	c.667G>C	c.(667-669)Gag>Cag	p.E223Q	MMP13_ENST00000340273.4_Missense_Mutation_p.E223Q	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	223	Interaction with TIMP2.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E223K(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	TGGCCGAACTCATGCGCAGCA	0.433																																					p.E223Q		.											.	MMP13-229	1	Substitution - Missense(1)	NS(1)	c.G667C						.						160	152	154					11																	102822873		2202	4299	6501	SO:0001583	missense	4322	exon5			CGAACTCATGCGC	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"Endogenous ligands"	7159	protein-coding gene	gene with protein product	"collagenase 3"	600108	"matrix metalloproteinase 13 (collagenase 3)"			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.667G>C	11.37:g.102822873C>G	ENSP00000260302:p.Glu223Gln	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	179	32	NM_002427	0	0	0	0	0	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	34	5.305406	0.95601	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	D;D	0.83075	-1.68;-1.68	5.75	5.75	0.90469	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94355	0.8185	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95140	0.8263	10	0.87932	D	0	.	20.312	0.98644	0.0:1.0:0.0:0.0	.	223	P45452	MMP13_HUMAN	Q	223	ENSP00000260302:E223Q;ENSP00000339672:E223Q	ENSP00000260302:E223Q	E	-	1	0	MMP13	102328083	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.772000	0.85439	2.866000	0.98385	0.650000	0.86243	GAG	.		0.433	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		G	102822873	C	G	102822873	3	3	33	1	0	0	0	0	1	0	0	0	9677	835	29	4	772	4	MMP13	11	102822873	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	27907380	102822873	32183643	46	2901											
FKBP4	2288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2910328	2910328	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agaagggcctcttccgccggGgagaggcccacctggccgtg	6	5	16	14	3	1	2	0	0	1	2	2	3	2	2	6	5	0	0	6	5	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:2910328G>A	ENST00000001008.4	+	9	1265	c.1078G>A	c.(1078-1080)Gga>Aga	p.G360R	RP4-816N1.6_ENST00000547834.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	360	Interaction with tubulin. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			CTTCCGCCGGGGAGAGGCCCA	0.572																																					p.G360R		.											.	FKBP4-226	0			c.G1078A						.						56	61	59					12																	2910328		2203	4300	6503	SO:0001583	missense	2288	exon9			CGCCGGGGAGAGG	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.1078G>A	12.37:g.2910328G>A	ENSP00000001008:p.Gly360Arg	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	150	33	NM_002014	0	0	52	83	31	D3DUQ1|Q9UCP1|Q9UCV7	Missense_Mutation	SNP	ENST00000001008.4	37	CCDS8512.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.166076	0.78339	.	.	ENSG00000004478	ENST00000001008	T	0.66995	-0.24	5.57	4.68	0.58851	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.047223	0.85682	N	0.000000	D	0.87577	0.6212	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91165	0.4964	10	0.72032	D	0.01	-18.3148	13.2702	0.60155	0.0758:0.0:0.9242:0.0	.	360	Q02790	FKBP4_HUMAN	R	360	ENSP00000001008:G360R	ENSP00000001008:G360R	G	+	1	0	FKBP4	2780589	1.000000	0.71417	0.913000	0.36048	0.591000	0.36615	9.383000	0.97214	1.355000	0.45865	0.561000	0.74099	GGA	.		0.572	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			A	2910328	G	A	2910328	3	1	33	1	0	0	0	0	1	0	0	0	5929	1233	43	2	1112	2	FKBP4	12	2910328	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08		2910328	130941567	47	2902											
LRRC23	10233	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	7023220	7023220	+	3'UTR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgggcagtgtggggtgcAgaatggggtgcctaggcctg	5	9	19	8	0	1	1	0	0	1	1	1	1	1	1	2	6	2	2	2	6	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:7023220A>C	ENST00000007969.8	+	0	1442				ENO2_ENST00000544774.1_5'Flank|LRRC23_ENST00000429740.1_3'UTR|LRRC23_ENST00000323702.5_Silent_p.A308A|ENO2_ENST00000541477.1_5'Flank|ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000229277.1_5'Flank|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000538763.1_5'Flank|LRRC23_ENST00000443597.2_3'UTR	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23											NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						TGTGGGGTGCAGAATGGGGTG	0.657																																					p.A308A		.											.	LRRC23-23	0			c.A924C						.						94	90	92					12																	7023220		2203	4300	6503	SO:0001624	3_prime_UTR_variant	10233	exon7			GGGTGCAGAATGG	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.*190A>C	12.37:g.7023220A>C		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	170	65	NM_006992	0	0	15	62	47	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Silent	SNP	ENST00000007969.8	37	CCDS8569.1																																																																																			.		0.657	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992		C	7023220	A	C	7023220	1	2	33	0	1	0	0	0	0	0	0	0	9003	175	7	5		5	LRRC23	12	7023220	3'UTR	SNP	A	TCGA-AL-7173-01A-11D-2136-08	4112892	7023220	126828675	48	2903											
CD163	9332	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	7640255	7640255	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtcttgccattcaccaagcGaatttctgtgtatcctggaa	9	13	9	10	1	3	0	1	0	2	0	4	2	4	1	3	2	2	1	3	2	4	4	rs373039092		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:7640255G>A	ENST00000359156.4	-	8	1952	c.1750C>T	c.(1750-1752)Cgc>Tgc	p.R584C	CD163_ENST00000541972.1_Missense_Mutation_p.R572C|CD163_ENST00000396620.3_Missense_Mutation_p.R617C|CD163_ENST00000539632.1_5'Flank|CD163_ENST00000432237.2_Missense_Mutation_p.R584C	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	584	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.R584C(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	TTCACCAAGCGAATTTCTGTG	0.488																																					p.R584C		.											.	CD163-98	1	Substitution - Missense(1)	skin(1)	c.C1750T						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	70	71	71		1750,1750	5.2	0.9	12		71	1,8599		0,1,4299	no	missense,missense	CD163	NM_004244.5,NM_203416.3	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	584/1157,584/1122	7640255	1,13005	2203	4300	6503	SO:0001583	missense	9332	exon8			CCAAGCGAATTTC	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.1750C>T	12.37:g.7640255G>A	ENSP00000352071:p.Arg584Cys	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	166	9	NM_203416	0	0	0	0	0	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173313	0.57584	0.0	1.16E-4	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.21	5.21	0.72293	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	0.076247	0.51477	D	0.000083	T	0.79627	0.4478	M	0.93763	3.455	0.26882	N	0.967512	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.917;0.988	T	0.76509	-0.2933	10	0.87932	D	0	.	16.6253	0.84968	0.0:0.0:1.0:0.0	.	617;584;584	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	C	584;572;617;584	ENSP00000352071:R584C;ENSP00000444071:R572C;ENSP00000379863:R617C;ENSP00000403885:R584C	ENSP00000352071:R584C	R	-	1	0	CD163	7531522	0.513000	0.26194	0.917000	0.36280	0.574000	0.36063	1.594000	0.36697	2.592000	0.87571	0.655000	0.94253	CGC	.		0.488	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		A	7640255	G	A	7640255	3	1	33	1	0	0	0	0	1	0	0	0	2973	1058	37	1	1756	1	CD163	12	7640255	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	617035	7640255	126211640	49	2904											
MARCH9	92979	hgsc.bcm.edu	37	chr12	58149446	58149446	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgggcgcccttcgctggCtgctccacccgggacggcga	3	6	16	16	5	0	0	0	0	0	0	2	2	1	1	3	5	1	4	3	5	0	1	rs1689582	byFrequency	TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:58149446C>T	ENST00000266643.5	+	1	566	c.135C>T	c.(133-135)ggC>ggT	p.G45G	MARCH9_ENST00000548358.1_5'Flank	NM_138396.5	NP_612405.2	Q86YJ5	MARH9_HUMAN	membrane-associated ring finger (C3HC4) 9	45					protein ubiquitination (GO:0016567)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|large_intestine(2)|lung(1)	4	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			ccTTCGCTGGCTGCTCCACCC	0.801													C|||	4639	0.926318	0.789	0.9755	5008	,	,		3828	0.998		0.999	False		,,,				2504	0.9284				p.G45G		.											.	MARCH9-492	0			c.C135T						.						1	1	1					12																	58149446		343	936	1279	SO:0001819	synonymous_variant	92979	exon1			CGCTGGCTGCTCC	BC009489	CCDS31847.1	12q14.1	2013-01-09				ENSG00000139266		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	25139	protein-coding gene	gene with protein product		613336				14722266	Standard	NM_138396		Approved	RNF179, FLJ36578	uc001spx.2	Q86YJ5		ENST00000266643.5:c.135C>T	12.37:g.58149446C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	3	NM_138396	0	0	0	0	0	B2R9U9|Q86VN5|Q96GG2	Silent	SNP	ENST00000266643.5	37	CCDS31847.1																																																																																			T|0.004;G|0.064		0.801	MARCH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409244.1	NM_138396		T	58149446	C	T	58149446	2	4	33	1	0	0	0	0	0	0	0	1	9333	784	28	2		2	MARCH9	12	58149446	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	50509191	58149446	75702449	50	2905											
KERA	11081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	91449805	91449805	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caaatggcttttcaggaatgGtttctatcaggttgttttga	9	17	10	5	0	3	1	2	1	1	0	3	2	3	2	0	4	0	4	0	4	3	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:91449805G>C	ENST00000266719.3	-	2	501	c.254C>G	c.(253-255)aCc>aGc	p.T85S		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	85					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						TTCAGGAATGGTTTCTATCAG	0.353																																					p.T85S		.											.	KERA-91	0			c.C254G						.						119	112	115					12																	91449805		2202	4297	6499	SO:0001583	missense	11081	exon2			GGAATGGTTTCTA	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.254C>G	12.37:g.91449805G>C	ENSP00000266719:p.Thr85Ser	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	115	19	NM_007035	0	0	0	0	0		Missense_Mutation	SNP	ENST00000266719.3	37	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	G	8.585	0.883190	0.17467	.	.	ENSG00000139330	ENST00000266719	T	0.56444	0.46	6.04	6.04	0.98038	.	0.296558	0.42821	N	0.000642	T	0.28001	0.0690	N	0.02368	-0.58	0.25604	N	0.986567	B	0.10296	0.003	B	0.15870	0.014	T	0.04650	-1.0936	10	0.10111	T	0.7	-17.6051	16.8507	0.85993	0.0:0.0:0.8711:0.1289	.	85	O60938	KERA_HUMAN	S	85	ENSP00000266719:T85S	ENSP00000266719:T85S	T	-	2	0	KERA	89973936	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.631000	0.54280	2.890000	0.99128	0.650000	0.86243	ACC	.		0.353	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		C	91449805	G	C	91449805	3	2	33	1	0	0	0	0	1	0	0	0	8164	1261	44	4	812	4	KERA	12	91449805	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	33300359	91449805	42402090	51	2906											
SH2B3	10019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	111885276	111885276	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccctgatgctcatggagtGttcctggtgcggcagagcga	6	9	16	10	2	1	2	1	1	0	1	2	4	2	3	2	4	3	3	2	4	0	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:111885276G>A	ENST00000341259.2	+	6	1521	c.1164G>A	c.(1162-1164)gtG>gtA	p.V388V	SH2B3_ENST00000538307.1_Silent_p.V186V	NM_005475.2	NP_005466.1	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	388	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic hemopoiesis (GO:0035162)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)	phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	10					Pazopanib(DB06589)	CTCATGGAGTGTTCCTGGTGC	0.617																																					p.V388V		.											.	SH2B3-91	0			c.G1164A						.						65	70	69					12																	111885276		2203	4300	6503	SO:0001819	synonymous_variant	10019	exon6			TGGAGTGTTCCTG	AF055581	CCDS9153.1	12q24.12	2014-09-17				ENSG00000111252		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	29605	protein-coding gene	gene with protein product	"lymphocyte adaptor protein"	605093				10799879	Standard	NM_005475		Approved	LNK, IDDM20	uc001tse.3	Q9UQQ2		ENST00000341259.2:c.1164G>A	12.37:g.111885276G>A		Somatic	167	2		WXS	Illumina HiSeq	Phase_I	165	27	NM_005475	0	0	0	0	0	B9EGG5|O95184	Silent	SNP	ENST00000341259.2	37	CCDS9153.1																																																																																			.		0.617	SH2B3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404779.1	NM_005475		A	111885276	G	A	111885276	2	1	33	1	0	0	0	0	0	0	0	1	14261	1364	48	2		2	SH2B3	12	111885276	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	20435471	111885276	21966619	52	2907											
DDX54	79039	hgsc.bcm.edu	37	chr12	113596868	113596868	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcttggtcttgagttccggGcggactcggcctgcaggggt	3	11	17	10	3	1	1	0	1	1	0	3	2	2	2	2	6	2	3	2	6	0	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:113596868G>C	ENST00000306014.5	-	20	2487	c.2460C>G	c.(2458-2460)cgC>cgG	p.R820R	Y_RNA_ENST00000363029.1_RNA|CCDC42B_ENST00000335621.6_3'UTR|DDX54_ENST00000314045.7_Silent_p.R821R|DDX54_ENST00000549271.1_5'UTR	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	820					ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TGAGTTCCGGGCGGACTCGGC	0.667																																					p.R821R		.											.	DDX54-227	0			c.C2463G						.						17	19	18					12																	113596868		2203	4299	6502	SO:0001819	synonymous_variant	79039	exon20			TTCCGGGCGGACT	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2460C>G	12.37:g.113596868G>C		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_001111322	0	0	99	99	0	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	37	CCDS31907.1																																																																																			.		0.667	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		C	113596868	G	C	113596868	2	2	33	1	0	0	0	0	0	0	0	1	4378	1190	42	4		4	DDX54	12	113596868	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	1711592	113596868	20255027	53	2908											
DDX54	79039	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113610194	113610194	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagtttgcccttggcggggaAgctgtagttgatgacattgt	7	13	15	6	1	0	2	0	2	0	0	0	4	0	3	1	3	2	4	1	3	2	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:113610194A>G	ENST00000306014.5	-	11	1270	c.1243T>C	c.(1243-1245)Ttc>Ctc	p.F415L	DDX54_ENST00000314045.7_Missense_Mutation_p.F415L	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	415	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTGGCGGGGAAGCTGTAGTTG	0.637																																					p.F415L		.											.	DDX54-227	0			c.T1243C						.						80	65	70					12																	113610194		2203	4300	6503	SO:0001583	missense	79039	exon11			CGGGGAAGCTGTA	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1243T>C	12.37:g.113610194A>G	ENSP00000304072:p.Phe415Leu	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	51	21	NM_024072	0	0	12	36	24	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	.	.	.	.	.	.	.	.	.	.	A	32	5.178425	0.94846	.	.	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.72835	-0.69;-0.69	5.18	5.18	0.71444	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.75302	0.3831	L	0.28274	0.84	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.73380	0.966;0.98	T	0.79047	-0.1963	10	0.87932	D	0	.	14.7275	0.69354	1.0:0.0:0.0:0.0	.	415;415	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	L	415	ENSP00000323858:F415L;ENSP00000304072:F415L	ENSP00000304072:F415L	F	-	1	0	DDX54	112094577	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.294000	0.96088	1.966000	0.57179	0.528000	0.53228	TTC	.		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		G	113610194	A	G	113610194	3	3	33	1	0	0	0	0	1	0	0	0	4378	72	3	3	1445	3	DDX54	12	113610194	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	13326	113610194	20241701	54	2909											
CDK8	1024	broad.mit.edu;bcgsc.ca	37	chr13	26975735	26975736	+	Frame_Shift_Del	DEL	GG	GG	-																															ctcctaccactacctcaggtGgacttatcatgacctcagac																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr13:26975735_26975736delGG	ENST00000381527.3	+	12	1746_1747	c.1243_1244delGG	c.(1243-1245)ggafs	p.G415fs	CDK8_ENST00000536792.1_3'UTR|CDK8_ENST00000480323.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	415					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TACCTCAGGTGGACTTATCATG	0.446																																					p.415_415del													.	CDK8-1023	0			c.1243_1244del						.																																			SO:0001589	frameshift_variant	1024	exon12			TCAGGTGGACTTA	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.1243_1244delGG	13.37:g.26975735_26975736delGG	ENSP00000370938:p.Gly415fs	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	92	11	NM_001260	0	0	0	0	0	Q5VUF3|Q6ISB5	Frame_Shift_Del	DEL	ENST00000381527.3	37	CCDS9317.1																																																																																			.		0.446	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			-	26975736	GG	-	26975735	7	5	33	1	0	1	0	1	0	0	0	0	3156	1349	47	0	1289	0	CDK8	13	26975735	Frame_Shift_Del	DEL	GG	TCGA-AL-7173-01A-11D-2136-08		26975735	88194143	55	2910	26	2									
CDK8	1024	hgsc.bcm.edu;bcgsc.ca	37	chr13	26975738	26975738	+	Missense_Mutation	SNP	C	C	A																															ctaccactacctcaggtggaCttatcatgacctcagactat																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr13:26975738C>A	ENST00000381527.3	+	12	1749	c.1246C>A	c.(1246-1248)Ctt>Att	p.L416I	CDK8_ENST00000536792.1_3'UTR|CDK8_ENST00000480323.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	416					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		CTCAGGTGGACTTATCATGAC	0.438																																					p.L416I		.											.	CDK8-1023	0			c.C1246A						.						144	125	131					13																	26975738		2203	4300	6503	SO:0001583	missense	1024	exon12			GGTGGACTTATCA	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.1246C>A	13.37:g.26975738C>A	ENSP00000370938:p.Leu416Ile	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	97	12	NM_001260	0	0	1	1	0	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	37	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.903879	0.52333	.	.	ENSG00000132964	ENST00000381527	T	0.68025	-0.3	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.49490	0.1560	N	0.08118	0	0.80722	D	1	P;P	0.39282	0.666;0.586	B;B	0.37833	0.259;0.146	T	0.51957	-0.8639	10	0.28530	T	0.3	-6.9656	18.9814	0.92756	0.0:1.0:0.0:0.0	.	415;416	P49336-2;P49336	.;CDK8_HUMAN	I	416	ENSP00000370938:L416I	ENSP00000370938:L416I	L	+	1	0	CDK8	25873738	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	7.440000	0.80464	2.491000	0.84063	0.655000	0.94253	CTT	.		0.438	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			A	26975738	C	A	26975738	3	1	33	1	0	0	0	0	1	0	0	0	3156	565	20	4	1292	4	CDK8	13	26975738	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3	26975738	88194140	56	2911	26	2									
DIAPH3	81624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	60566699	60566699	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgtaaccagggcattgaTgagctgcatacaagctacct	13	9	10	9	0	0	3	0	2	0	1	0	3	0	3	2	1	6	5	2	1	4	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr13:60566699T>A	ENST00000400324.4	-	10	1253	c.1033A>T	c.(1033-1035)Atc>Ttc	p.I345F	DIAPH3_ENST00000377908.2_Missense_Mutation_p.I334F|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Missense_Mutation_p.I299F|DIAPH3_ENST00000267215.4_Missense_Mutation_p.I345F|DIAPH3_ENST00000400330.1_Missense_Mutation_p.I345F|DIAPH3_ENST00000400319.1_Missense_Mutation_p.I275F	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	345	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		AGGGCATTGATGAGCTGCATA	0.393																																					p.I345F		.											.	DIAPH3-516	0			c.A1033T						.						65	60	62					13																	60566699		1908	4138	6046	SO:0001583	missense	81624	exon10			CATTGATGAGCTG	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"diaphanous (Drosophila, homolog) 3", "auditory neuropathy, autosomal dominant 1", "diaphanous homolog 3 (Drosophila)"	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.1033A>T	13.37:g.60566699T>A	ENSP00000383178:p.Ile345Phe	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	52	8	NM_001042517	0	0	0	0	0	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.490483	0.84962	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	D;D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93;-2.93	5.77	5.77	0.91146	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.97334	0.9128	H	0.95114	3.625	0.54753	D	0.999989	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.996	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.98	D	0.98505	1.0616	10	0.87932	D	0	.	16.0865	0.81056	0.0:0.0:0.0:1.0	.	275;299;334;82;345	A8MYX0;C9JL55;C9JDG1;Q9NSV4-1;Q9NSV4	.;.;.;.;DIAP3_HUMAN	F	345;345;334;299;275;334;275;299;345;82;345	ENSP00000383178:I345F;ENSP00000383184:I345F;ENSP00000367141:I334F;ENSP00000383173:I275F;ENSP00000383174:I299F;ENSP00000267215:I345F	ENSP00000267214:I82F	I	-	1	0	DIAPH3	59464700	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.606000	0.82863	2.194000	0.70268	0.377000	0.23210	ATC	.		0.393	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60566699	T	A	60566699	3	1	33	1	0	0	0	0	1	0	0	0	4531	1464	51	5	2644	5	DIAPH3	13	60566699	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	33590961	60566699	54603179	57	2912											
CPNE6	9362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24545747	24545747	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgctatcaactttgacccGgaaaatcctgaatgtgaagg	12	12	9	8	1	1	3	1	3	0	0	2	4	2	4	2	2	2	1	2	2	6	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr14:24545747G>A	ENST00000397016.2	+	14	1457	c.1146G>A	c.(1144-1146)ccG>ccA	p.P382P	CPNE6_ENST00000216775.2_Silent_p.P382P|CPNE6_ENST00000537691.1_Silent_p.P437P	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	382	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		ACTTTGACCCGGAAAATCCTG	0.587																																					p.P382P		.											.	CPNE6-93	0			c.G1146A						.						100	103	102					14																	24545747		2203	4300	6503	SO:0001819	synonymous_variant	9362	exon13			TGACCCGGAAAAT	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.1146G>A	14.37:g.24545747G>A		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	94	30	NM_006032	0	0	0	0	0	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			.		0.587	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			A	24545747	G	A	24545747	2	1	33	1	0	0	0	0	0	0	0	1	3822	1103	39	1		1	CPNE6	14	24545747	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08		24545747	82803793	58	2913											
PAK6	56924	hgsc.bcm.edu	37	chr15	40557188	40557188	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgcagctccagcccatgAaggtaagaggggccggcagg	9	4	18	10	1	0	2	0	1	0	1	1	2	1	2	3	6	3	4	3	6	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:40557188A>G	ENST00000542403.2	+	2	313	c.202A>G	c.(202-204)Aag>Gag	p.K68E	PAK6_ENST00000453867.1_Missense_Mutation_p.K68E|PAK6_ENST00000455577.2_Missense_Mutation_p.K68E|PAK6_ENST00000260404.4_Missense_Mutation_p.K68E|PAK6_ENST00000441369.1_Missense_Mutation_p.K68E|RP11-133K1.2_ENST00000558658.1_Nonstop_Mutation_p.*161W|PAK6_ENST00000560346.1_Missense_Mutation_p.K68E	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	68	Linker.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		CCAGCCCATGAAGGTAAGAGG	0.622																																					p.K68E		.											.	PAK6-996	0			c.A202G						.						36	35	35					15																	40557188		2203	4300	6503	SO:0001583	missense	56924	exon3			CCCATGAAGGTAA	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"p21(CDKN1A)-activated kinase 6"			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.202A>G	15.37:g.40557188A>G	ENSP00000439597:p.Lys68Glu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001128629	0	0	0	0	0	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	37	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	A	34	5.371985	0.95923	.	.	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	D;D;D;D;D	0.86497	-1.97;-1.97;-2.13;-1.97;-1.97	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.86016	0.5832	M	0.63843	1.955	0.80722	D	1	B;B	0.33940	0.307;0.433	B;B	0.33454	0.079;0.164	D	0.86814	0.2000	10	0.87932	D	0	.	15.8022	0.78463	1.0:0.0:0.0:0.0	.	68;68	Q9NQU5;G5E9R2	PAK6_HUMAN;.	E	68	ENSP00000406873:K68E;ENSP00000401153:K68E;ENSP00000409465:K68E;ENSP00000260404:K68E;ENSP00000439597:K68E	ENSP00000260404:K68E	K	+	1	0	PAK6	38344480	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.309000	0.96252	2.202000	0.70862	0.533000	0.62120	AAG	.		0.622	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1			G	40557188	A	G	40557188	3	3	33	1	0	0	0	0	1	0	0	0	11430	247	9	3	204	3	PAK6	15	40557188	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08		40557188	61974204	59	2914											
ANKDD1A	348094	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	65214185	65214185	+	Frame_Shift_Del	DEL	A	A	-																															cgaatcctccagatcttggtAaactcaggggccaagatcca																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:65214185delA	ENST00000380230.3	+	4	362	c.333delA	c.(331-333)gtafs	p.V111fs	ANKDD1A_ENST00000395723.1_Frame_Shift_Del_p.V20fs|ANKDD1A_ENST00000496660.1_Frame_Shift_Del_p.V20fs|ANKDD1A_ENST00000319580.8_Frame_Shift_Del_p.K34fs|ANKDD1A_ENST00000357698.3_Frame_Shift_Del_p.V111fs|ANKDD1A_ENST00000395720.1_Frame_Shift_Del_p.V111fs|ANKDD1A_ENST00000491145.1_3'UTR|AC069368.3_ENST00000437723.1_Frame_Shift_Del_p.V183fs	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	111					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						AGATCTTGGTAAACTCAGGGG	0.577																																					p.V111fs		.											.	ANKDD1A-69	0			c.333delA						.						113	90	98					15																	65214185		2202	4299	6501	SO:0001589	frameshift_variant	348094	exon4			.		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.333delA	15.37:g.65214185delA	ENSP00000369579:p.Val111fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	80	17	NM_182703	0	0	0	0	0	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Frame_Shift_Del	DEL	ENST00000380230.3	37	CCDS10197.2																																																																																			.		0.577	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		-	65214185	A	-	65214185	7	5	33	1	0	1	0	1	0	0	0	0	624	349	13	0	347	0	ANKDD1A	15	65214185	Frame_Shift_Del	DEL	A	TCGA-AL-7173-01A-11D-2136-08	24656997	65214185	37317207	60	2915											
SEMA7A	8482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	74708932	74708932	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccctgcacaactgggccAcacgggacacattgagagga	12	5	11	13	1	1	1	1	1	0	1	1	4	1	3	2	3	2	1	2	3	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:74708932A>C	ENST00000261918.4	-	7	1333	c.785T>G	c.(784-786)gTg>gGg	p.V262G	SEMA7A_ENST00000543145.2_Missense_Mutation_p.V248G|SEMA7A_ENST00000542748.1_Missense_Mutation_p.V97G	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	262	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						CAACTGGGCCACACGGGACAC	0.552																																					p.V262G		.											.	SEMA7A-153	0			c.T785G						.						204	168	180					15																	74708932		2197	4296	6493	SO:0001583	missense	8482	exon7			TGGGCCACACGGG	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"Semaphorins", "CD molecules", "Blood group antigens", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10741	protein-coding gene	gene with protein product	"John Milton Hagen blood group", "H-Sema K1"	607961	"sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A", "sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.785T>G	15.37:g.74708932A>C	ENSP00000261918:p.Val262Gly	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	63	18	NM_003612	0	0	0	0	0	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	37	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.235032	0.58886	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.35789	1.29;1.29;1.29	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.065645	0.64402	D	0.000009	T	0.67316	0.2880	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.75622	-0.3254	10	0.87932	D	0	-18.6242	13.6573	0.62346	1.0:0.0:0.0:0.0	.	248;262	F5H1S0;O75326	.;SEM7A_HUMAN	G	262;248;97	ENSP00000261918:V262G;ENSP00000438966:V248G;ENSP00000441493:V97G	ENSP00000261918:V262G	V	-	2	0	SEMA7A	72495985	1.000000	0.71417	0.993000	0.49108	0.169000	0.22640	5.449000	0.66619	2.043000	0.60533	0.533000	0.62120	GTG	.		0.552	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		C	74708932	A	C	74708932	3	2	33	1	0	0	0	0	1	0	0	0	14075	159	6	5	1247	5	SEMA7A	15	74708932	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	9494747	74708932	27822460	61	2916											
SGK269	79834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	77406689	77406689	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagggtgttcctctgtactaGgctagggcaggcggtgaaag	8	9	16	8	1	1	1	0	1	1	0	2	1	2	1	1	5	1	4	1	5	4	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:77406689G>A	ENST00000560626.2	-	7	5525	c.5050C>T	c.(5050-5052)Cta>Tta	p.L1684L	PEAK1_ENST00000312493.4_Silent_p.L1684L			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1684					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTCTGTACTAGGCTAGGGCAG	0.542																																					p.L1684L		.											.	.	0			c.C5050T						.						93	96	95					15																	77406689		1943	4130	6073	SO:0001819	synonymous_variant	0	exon8			GTACTAGGCTAGG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.5050C>T	15.37:g.77406689G>A		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	137	34	NM_024776	0	0	1	1	0	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	37	CCDS42062.1																																																																																			.		0.542	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77406689	G	A	77406689	2	1	33	1	0	0	0	0	0	0	0	1	14243	991	35	2		2	SGK269	15	77406689	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	2697757	77406689	25124703	62	2917											
ZNF423	23090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	49670185	49670185	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccacagatgggacacaTgtagtgcttggcagggcccc	9	7	12	13	0	1	1	1	0	0	1	1	2	1	2	3	3	1	3	3	3	1	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr16:49670185T>C	ENST00000561648.1	-	4	2931	c.2878A>G	c.(2878-2880)Atg>Gtg	p.M960V	ZNF423_ENST00000562871.1_Missense_Mutation_p.M900V|ZNF423_ENST00000262383.2_Missense_Mutation_p.M960V|ZNF423_ENST00000562520.1_Missense_Mutation_p.M900V|ZNF423_ENST00000563137.2_Missense_Mutation_p.M900V|ZNF423_ENST00000567169.1_Missense_Mutation_p.M843V|ZNF423_ENST00000535559.1_Missense_Mutation_p.M843V	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	960					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ATGGGACACATGTAGTGCTTG	0.602																																					p.M960V		.											.	ZNF423-228	0			c.A2878G						.						72	54	60					16																	49670185		2198	4300	6498	SO:0001583	missense	23090	exon4			GACACATGTAGTG	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2878A>G	16.37:g.49670185T>C	ENSP00000455426:p.Met960Val	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	62	12	NM_015069	0	0	1	1	0	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766597	0.69878	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.16897	2.31;2.31	4.81	4.81	0.61882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.18551	0.0445	N	0.04043	-0.29	0.45648	D	0.998576	D	0.61697	0.99	D	0.67548	0.952	T	0.32375	-0.9909	9	.	.	.	-30.7346	14.3758	0.66874	0.0:0.0:0.0:1.0	.	960	Q2M1K9	ZN423_HUMAN	V	960;843	ENSP00000262383:M960V;ENSP00000442321:M843V	.	M	-	1	0	ZNF423	48227686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.289000	0.72696	1.814000	0.52955	0.459000	0.35465	ATG	.		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		C	49670185	T	C	49670185	3	2	33	1	0	0	0	0	1	0	0	0	17930	1464	51	3	996	3	ZNF423	16	49670185	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		49670185	40684568	63	2918											
PER1	5187	broad.mit.edu	37	chr17	8047060	8047060	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggggtgggccagggggTggagggtggcacgggtgagg	4	6	27	4	1	0	1	0	1	0	0	0	2	0	2	1	11	0	1	1	11	0	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:8047060T>G	ENST00000317276.4	-	19	2833	c.2596A>C	c.(2596-2598)Acc>Ccc	p.T866P	PER1_ENST00000581082.1_Missense_Mutation_p.T843P|PER1_ENST00000578089.1_5'UTR	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	866	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.T866P(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGCCAGGGGGTGGAGGGTGGC	0.667			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.T866P				Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1-723	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2596C						.																																			SO:0001583	missense	5187	exon19			AGGGGGTGGAGGG	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2596A>C	17.37:g.8047060T>G	ENSP00000314420:p.Thr866Pro	Somatic	23	7		WXS	Illumina HiSeq	Phase_I	28	6	NM_002616	0	0	12	12	0	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	T	7.008	0.556287	0.13436	.	.	ENSG00000179094	ENST00000317276	T	0.14893	2.47	5.42	1.94	0.25998	.	0.240541	0.41823	D	0.000811	T	0.12774	0.0310	L	0.58510	1.815	0.80722	D	1	B	0.21381	0.055	B	0.15052	0.012	T	0.19976	-1.0289	10	0.42905	T	0.14	-6.4874	0.9995	0.01474	0.1839:0.4226:0.1778:0.2157	.	866	O15534	PER1_HUMAN	P	866	ENSP00000314420:T866P	ENSP00000314420:T866P	T	-	1	0	PER1	7987785	0.361000	0.24972	1.000000	0.80357	0.452000	0.32318	-0.124000	0.10595	1.268000	0.44264	-0.468000	0.05107	ACC	.		0.667	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			G	8047060	T	G	8047060	3	3	33	1	0	0	0	0	1	0	0	0	11755	1696	59	5	1296	5	PER1	17	8047060	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		8047060	73148150	64	2919											
FLII	2314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18150655	18150655	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacatcgtcccaattcttgAacttggccttgaacacctgc	10	11	6	14	1	1	2	0	2	1	0	3	2	2	2	3	1	3	0	3	1	3	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:18150655A>C	ENST00000327031.4	-	21	2729	c.2504T>G	c.(2503-2505)tTc>tGc	p.F835C	FLII_ENST00000578558.1_Intron|FLII_ENST00000379450.4_Missense_Mutation_p.F749C|FLII_ENST00000579294.1_Missense_Mutation_p.F824C|FLII_ENST00000545457.2_Missense_Mutation_p.F780C	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	835					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CCAATTCTTGAACTTGGCCTT	0.602																																					p.F835C		.											.	FLII-91	0			c.T2504G						.						108	92	97					17																	18150655		2203	4300	6503	SO:0001583	missense	2314	exon21			TTCTTGAACTTGG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.2504T>G	17.37:g.18150655A>C	ENSP00000324573:p.Phe835Cys	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	109	18	NM_002018	0	0	20	37	17	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	A	19.68	3.872270	0.72180	.	.	ENSG00000177731	ENST00000327031;ENST00000379450	T;T	0.45276	0.9;0.9	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.67785	0.2930	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	0.996;0.996;1.0;0.993	T	0.73685	-0.3905	10	0.87932	D	0	-23.7587	15.4271	0.75061	1.0:0.0:0.0:0.0	.	749;749;835;804	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	C	835;749	ENSP00000324573:F835C;ENSP00000368763:F749C	ENSP00000324573:F835C	F	-	2	0	FLII	18091380	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	8.532000	0.90613	2.045000	0.60652	0.460000	0.39030	TTC	.		0.602	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		C	18150655	A	C	18150655	3	2	33	1	0	0	0	0	1	0	0	0	5944	246	9	5	1345	5	FLII	17	18150655	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	10103595	18150655	63044555	65	2920											
TAF15	8148	broad.mit.edu;bcgsc.ca	37	chr17	34149828	34149828	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagggaaaactacagccacCacacacaaggtaagatttac	19	5	7	10	0	0	1	0	0	0	1	0	2	0	2	2	2	4	1	2	2	7	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:34149828C>T	ENST00000588240.1	+	6	590	c.475C>T	c.(475-477)Cac>Tac	p.H159Y	TAF15_ENST00000592237.1_Missense_Mutation_p.H68Y|AC015849.19_ENST00000588415.1_RNA|AC015849.13_ENST00000589356.1_RNA|TAF15_ENST00000311979.3_Missense_Mutation_p.H156Y	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		CTACAGCCACCACACACAAGG	0.373			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.H159Y				Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15-723	0			c.C475T						.						108	100	102					17																	34149828		2203	4300	6503	SO:0001583	missense	8148	exon6			AGCCACCACACAC	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.475C>T	17.37:g.34149828C>T	ENSP00000466950:p.His159Tyr	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	90	6	NM_139215	0	0	1	1	0	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	37	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	C	12.56	1.973242	0.34848	.	.	ENSG00000172660	ENST00000311979	.	.	.	5.91	4.94	0.65067	.	.	.	.	.	T	0.36138	0.0956	L	0.38531	1.155	0.26742	N	0.970367	B;B	0.12013	0.003;0.005	B;B	0.08055	0.001;0.003	T	0.11060	-1.0603	8	0.15499	T	0.54	-9.2222	11.5059	0.50466	0.0:0.9153:0.0:0.0847	.	159;156	Q92804;Q92804-2	RBP56_HUMAN;.	Y	159	.	ENSP00000309558:H159Y	H	+	1	0	TAF15	31173941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.295000	0.43576	2.791000	0.96007	0.655000	0.94253	CAC	.		0.373	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		T	34149828	C	T	34149828	3	4	33	1	0	0	0	0	1	0	0	0	15550	594	21	2	497	2	TAF15	17	34149828	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	15999173	34149828	47045382	66	2921											
ZPBP2	124626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38027753	38027753	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataactgaaactggacagcTgatggtgaaagattttttgg	13	13	11	4	0	0	4	0	3	0	1	0	5	0	5	0	3	3	1	0	3	4	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:38027753T>C	ENST00000348931.4	+	4	472	c.281T>C	c.(280-282)cTg>cCg	p.L94P	ZPBP2_ENST00000584588.1_Missense_Mutation_p.L94P|ZPBP2_ENST00000377940.3_Missense_Mutation_p.L72P	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	94					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACTGGACAGCTGATGGTGAAA	0.294																																					p.L94P		.											.	ZPBP2-91	0			c.T281C						.						93	98	96					17																	38027753		2203	4298	6501	SO:0001583	missense	124626	exon4			GACAGCTGATGGT	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.281T>C	17.37:g.38027753T>C	ENSP00000335384:p.Leu94Pro	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	59	15	NM_199321	0	0	0	0	0	A8K8L8|Q6X783|Q86XL5	Missense_Mutation	SNP	ENST00000348931.4	37	CCDS11352.1	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855999	0.71834	.	.	ENSG00000186075	ENST00000348931;ENST00000377940	D;D	0.92397	-3.03;-3.03	5.46	5.46	0.80206	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49305	D	0.000158	D	0.95698	0.8601	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96132	0.9093	10	0.87932	D	0	-7.3583	13.7798	0.63077	0.0:0.0:0.0:1.0	.	72;94	Q6X784-2;Q6X784	.;ZPBP2_HUMAN	P	94;72	ENSP00000335384:L94P;ENSP00000367174:L72P	ENSP00000335384:L94P	L	+	2	0	ZPBP2	35281279	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	4.645000	0.61404	2.072000	0.62099	0.377000	0.23210	CTG	.		0.294	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844		C	38027753	T	C	38027753	3	2	33	1	0	0	0	0	1	0	0	0	18252	1580	55	3	295	3	ZPBP2	17	38027753	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	3877925	38027753	43167457	67	2922											
TIMP2	7077	broad.mit.edu;bcgsc.ca	37	chr17	76867041	76867047	+	Frame_Shift_Del	DEL	GGGGGCC	GGGGGCC	-																															accccacacactgccgaggaGggggccgtgtagataaactc																								rs372752139		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GGGGGCC	GGGGGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:76867041_76867047delGGGGGCC	ENST00000262768.7	-	3	571_577	c.273_279delGGCCCCC	c.(271-279)acggcccccfs	p.TAP91fs	TIMP2_ENST00000536189.2_Frame_Shift_Del_p.TAP14fs|TIMP2_ENST00000585421.1_Frame_Shift_Del_p.TAP14fs|TIMP2_ENST00000586057.1_Frame_Shift_Del_p.TAP14fs	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	91	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.A92V(1)|p.S94fs*43(1)		central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			CTGCCGAGGAGGGGGCCGTGTAGATAA	0.541																																					p.91_93del													.	TIMP2-650	2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|prostate(1)	c.273_279del						.																																			SO:0001589	frameshift_variant	7077	exon3			CGAGGAGGGGGCC		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"tissue inhibitor of metalloproteinase 2"			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.273_279delGGCCCCC	17.37:g.76867041_76867047delGGGGGCC	ENSP00000262768:p.Thr91fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	161	10	NM_003255	0	0	0	0	0	Q16121|Q93006|Q9UDF7	Frame_Shift_Del	DEL	ENST00000262768.7	37	CCDS11758.1																																																																																			.		0.541	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255		-	76867047	GGGGGCC	-	76867041	7	5	33	1	0	1	0	1	0	0	0	0	15950	987	35	0	395	0	TIMP2	17	76867041	Frame_Shift_Del	DEL	GGGGGCC	TCGA-AL-7173-01A-11D-2136-08	38839288	76867041	4328169	68	2923											
PLVAP	83483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17476968	17476968	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcttctcactcaagatgaTggcagccatgtacctctgat	9	13	8	11	0	3	3	2	2	2	1	4	3	3	3	2	1	3	3	2	1	2	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:17476968T>C	ENST00000252590.4	-	2	467	c.406A>G	c.(406-408)Atc>Gtc	p.I136V		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	136					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTCAAGATGATGGCAGCCATG	0.552																																					p.I136V		.											.	PLVAP-90	0			c.A406G						.						237	203	215					19																	17476968		2203	4300	6503	SO:0001583	missense	83483	exon2			AGATGATGGCAGC	AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.406A>G	19.37:g.17476968T>C	ENSP00000252590:p.Ile136Val	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	191	52	NM_031310	0	0	25	25	0	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Missense_Mutation	SNP	ENST00000252590.4	37	CCDS32952.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.551302	0.27739	.	.	ENSG00000130300	ENST00000252590	T	0.31247	1.5	4.07	3.05	0.35203	.	0.289259	0.35708	N	0.003037	T	0.33818	0.0876	L	0.34521	1.04	0.26494	N	0.974888	D	0.69078	0.997	D	0.80764	0.994	T	0.15178	-1.0446	10	0.10111	T	0.7	-51.4771	6.1733	0.20429	0.0:0.114:0.0:0.886	.	136	Q9BX97	PLVAP_HUMAN	V	136	ENSP00000252590:I136V	ENSP00000252590:I136V	I	-	1	0	PLVAP	17337968	1.000000	0.71417	0.994000	0.49952	0.058000	0.15608	2.845000	0.48254	0.915000	0.36847	0.459000	0.35465	ATC	.		0.552	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		C	17476968	T	C	17476968	3	2	33	1	0	0	0	0	1	0	0	0	12142	1464	51	3	942	3	PLVAP	19	17476968	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		17476968	41652015	69	2924											
APLP1	333	ucsc.edu	37	chr19	36361805	36361805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatccccccagatgtaccCggagctgcagattgcacgtg	8	8	11	14	2	0	3	0	1	0	2	1	4	1	4	4	1	4	4	4	1	1	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:36361805C>T	ENST00000221891.4	+	3	491	c.299C>T	c.(298-300)cCg>cTg	p.P100L	APLP1_ENST00000586861.1_Missense_Mutation_p.P94L|APLP1_ENST00000537454.2_Missense_Mutation_p.P61L|NPHS1_ENST00000591817.1_5'Flank	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	100					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CAGATGTACCCGGAGCTGCAG	0.662																																					p.P100L													.	APLP1-92	0			c.C299T						.						22	24	23					19																	36361805		2202	4299	6501	SO:0001583	missense	333	exon3			TGTACCCGGAGCT	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"amyloid-like protein 1", "amyloid precursor-like protein 1"	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.299C>T	19.37:g.36361805C>T	ENSP00000221891:p.Pro100Leu	Somatic	13	0		WXS	Illumina HiSeq		13	4	NM_005166	0	0	0	0	0	O00113|Q96A92	Missense_Mutation	SNP	ENST00000221891.4	37	CCDS32997.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.602174	0.87055	.	.	ENSG00000105290	ENST00000537454;ENST00000221891	D;D	0.95137	-3.49;-3.62	5.06	5.06	0.68205	Amyloidogenic glycoprotein, extracellular (1);Amyloidogenic glycoprotein, heparin-binding (3);	0.000000	0.48767	D	0.000170	D	0.96765	0.8944	M	0.75447	2.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.968;0.991;0.971	D	0.97163	0.9839	10	0.87932	D	0	-30.9183	13.913	0.63878	0.0:1.0:0.0:0.0	.	94;61;100;100	B7Z4G8;F5GZ08;P51693-2;P51693	.;.;.;APLP1_HUMAN	L	61;100	ENSP00000441501:P61L;ENSP00000221891:P100L	ENSP00000221891:P100L	P	+	2	0	APLP1	41053645	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	4.766000	0.62279	2.352000	0.79861	0.555000	0.69702	CCG	.		0.662	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		T	36361805	C	T	36361805	3	4	33	1	0	0	0	0	1	0	0	0	778	652	23	1	309	1	APLP1	19	36361805	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	18884837	36361805	22767178	70	2925											
ZNF780A	284323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40581903	40581903	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcatgaggagtatgagtaGgcagtttttcatagctgatc	12	12	12	5	0	1	3	1	3	0	0	2	4	1	4	0	2	2	6	0	2	4	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:40581903G>C	ENST00000595687.2	-	6	655	c.446C>G	c.(445-447)cCt>cGt	p.P149R	ZNF780A_ENST00000450241.2_Missense_Mutation_p.P115R|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000340963.5_Missense_Mutation_p.P149R|ZNF780A_ENST00000594395.1_Missense_Mutation_p.P150R|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000455521.1_Missense_Mutation_p.P150R	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	149					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(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AGTATGAGTAGGCAGTTTTTC	0.333																																					p.P150R		.											.	ZNF780A-22	0			c.C449G						.						198	170	179					19																	40581903		2203	4300	6503	SO:0001583	missense	284323	exon6			TGAGTAGGCAGTT	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.446C>G	19.37:g.40581903G>C	ENSP00000472189:p.Pro149Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	76	17	NM_001142577	0	0	0	0	0	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	G	0.101	-1.152082	0.01700	.	.	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	T;T	0.05447	3.44;3.46	0.928	0.928	0.19443	.	.	.	.	.	T	0.07413	0.0187	M	0.64404	1.975	0.09310	N	1	P;P	0.48162	0.51;0.906	B;B	0.44163	0.099;0.443	T	0.27872	-1.0061	9	0.15499	T	0.54	.	4.8476	0.13521	0.0:0.3981:0.6019:0.0	.	150;149	E9PB48;O75290	.;Z780A_HUMAN	R	149;150;149	ENSP00000400997:P150R;ENSP00000341507:P149R	ENSP00000341507:P149R	P	-	2	0	ZNF780A	45273743	0.000000	0.05858	0.009000	0.14445	0.048000	0.14542	-1.367000	0.02583	0.796000	0.33947	0.305000	0.20034	CCT	.		0.333	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		C	40581903	G	C	40581903	3	2	33	1	0	0	0	0	1	0	0	0	18184	1000	35	4	1610	4	ZNF780A	19	40581903	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	4220098	40581903	18547080	71	2926											
NLRP7	199713	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55449434	55449434	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactttctgcagatgacaggTgctacgggttacgtggtcac	8	11	12	10	2	2	2	1	1	1	1	2	2	2	2	0	3	4	3	0	3	2	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:55449434T>A	ENST00000590030.1	-	4	2147	c.2107A>T	c.(2107-2109)Acc>Tcc	p.T703S	NLRP7_ENST00000588756.1_Missense_Mutation_p.T703S|NLRP7_ENST00000448121.2_Missense_Mutation_p.T675S|NLRP7_ENST00000328092.5_Missense_Mutation_p.T675S|NLRP7_ENST00000340844.2_Missense_Mutation_p.T703S|NLRP7_ENST00000446217.1_Missense_Mutation_p.T731S|NLRP7_ENST00000592784.1_Missense_Mutation_p.T703S			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	703							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		AGATGACAGGTGCTACGGGTT	0.428																																					p.T703S		.											.	NLRP7-291	0			c.A2107T						.						243	252	249					19																	55449434		2203	4300	6503	SO:0001583	missense	199713	exon5			GACAGGTGCTACG	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.2107A>T	19.37:g.55449434T>A	ENSP00000465520:p.Thr703Ser	Somatic	421	0		WXS	Illumina HiSeq	Phase_I	418	101	NM_001127255	0	0	0	0	0	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	T	3.493	-0.103411	0.06967	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T	0.51325	0.71;0.71;0.71	2.19	-1.51	0.08664	.	0.529447	0.14299	N	0.328408	T	0.26159	0.0638	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.32203	0.264;0.151;0.151;0.36	B;B;B;B	0.26416	0.057;0.032;0.032;0.069	T	0.16041	-1.0416	10	0.16896	T	0.51	.	2.3	0.04160	0.4111:0.2735:0.0:0.3154	.	731;703;703;675	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	S	703;675;703;731;470	ENSP00000409137:T675S;ENSP00000339491:T703S;ENSP00000414273:T731S	ENSP00000329568:T703S	T	-	1	0	NLRP7	60141246	0.002000	0.14202	0.002000	0.10522	0.002000	0.02628	-0.473000	0.06615	-0.505000	0.06568	-1.288000	0.01363	ACC	.		0.428	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55449434	T	A	55449434	3	1	33	1	0	0	0	0	1	0	0	0	10508	1696	59	5	1034	5	NLRP7	19	55449434	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	14867531	55449434	3679549	72	2927											
NCOA5	57727	bcgsc.ca	37	chr20	44697260	44697260	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccattcgtaggtatcggTcataagagccttctctcctg	8	13	8	12	2	2	1	1	0	1	1	7	1	4	1	3	2	1	2	3	2	3	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr20:44697260T>C	ENST00000290231.6	-	4	547	c.383A>G	c.(382-384)gAc>gGc	p.D128G		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	128	Arg/Asp-rich (mixed charge).|Transcription repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				TAGGTATCGGTCATAAGAGCC	0.418																																					p.D128G													.	NCOA5-226	0			c.A383G						.						103	105	104					20																	44697260		2203	4300	6503	SO:0001583	missense	57727	exon4			TATCGGTCATAAG		CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"coactivator independent of AF-2"					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.383A>G	20.37:g.44697260T>C	ENSP00000290231:p.Asp128Gly	Somatic	123	1		WXS	Illumina HiSeq	Phase_1	101	4	NM_020967	0	0	0	0	0	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103262	0.76983	.	.	ENSG00000124160	ENST00000290231;ENST00000372291	T	0.55930	0.49	4.75	4.75	0.60458	.	0.044656	0.85682	D	0.000000	T	0.64349	0.2590	L	0.57536	1.79	0.58432	D	0.999998	D;D	0.64830	0.994;0.963	P;P	0.60886	0.88;0.797	T	0.65672	-0.6111	10	0.48119	T	0.1	-0.305	13.2648	0.60127	0.0:0.0:0.0:1.0	.	128;23	Q9HCD5;Q5JY17	NCOA5_HUMAN;.	G	128;23	ENSP00000290231:D128G	ENSP00000290231:D128G	D	-	2	0	NCOA5	44130667	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.739000	0.74827	2.005000	0.58758	0.528000	0.53228	GAC	.		0.418	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967		C	44697260	T	C	44697260	3	2	33	1	0	0	0	0	1	0	0	0	10258	1667	58	3	1376	3	NCOA5	20	44697260	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		44697260	18328260	73	2928											
CHRNA4	1137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	61982183	61982183	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtccacgcggctgtgcaTgttcaccaggtcgatcttgg	5	11	13	12	3	2	0	1	0	1	0	4	1	3	0	2	4	1	3	2	4	0	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr20:61982183T>C	ENST00000370263.4	-	5	801	c.580A>G	c.(580-582)Atg>Gtg	p.M194V	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	194					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	CGGCTGTGCATGTTCACCAGG	0.587																																					p.M194V		.											.	CHRNA4-91	0			c.A580G						.						138	114	122					20																	61982183		2203	4299	6502	SO:0001583	missense	1137	exon5			TGTGCATGTTCAC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.580A>G	20.37:g.61982183T>C	ENSP00000359285:p.Met194Val	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	96	25	NM_000744	0	0	0	0	0	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	37	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.814091	0.32053	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.78707	-1.2	4.87	2.6	0.31112	Neurotransmitter-gated ion-channel ligand-binding (3);	0.074711	0.85682	N	0.000000	T	0.61527	0.2354	N	0.16233	0.39	0.58432	D	0.999998	B;B	0.31125	0.309;0.017	B;B	0.31946	0.138;0.052	T	0.57382	-0.7821	10	0.72032	D	0.01	.	8.8251	0.35050	0.0:0.1556:0.0:0.8444	.	123;194	Q4VAQ5;P43681	.;ACHA4_HUMAN	V	100;194;123	ENSP00000359285:M194V	ENSP00000359280:M100V	M	-	1	0	CHRNA4	61452627	1.000000	0.71417	0.980000	0.43619	0.625000	0.37756	4.841000	0.62824	0.225000	0.20959	-0.379000	0.06801	ATG	.		0.587	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			C	61982183	T	C	61982183	3	2	33	1	0	0	0	0	1	0	0	0	3391	1464	51	3	1311	3	CHRNA4	20	61982183	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	17284923	61982183	1043337	74	2929											
ARFRP1	10139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62333531	62333531	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctctcctcgtcggtggaGtcaatgacgtagatgacgcc	8	9	12	12	4	2	3	1	2	1	1	5	4	2	4	3	2	1	1	3	2	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr20:62333531G>C	ENST00000359715.5	-	4	869	c.303C>G	c.(301-303)gaC>gaG	p.D101E	ARFRP1_ENST00000440854.1_Missense_Mutation_p.D101E|ARFRP1_ENST00000609142.1_Missense_Mutation_p.D101E|ARFRP1_ENST00000607873.1_Missense_Mutation_p.D54E|ARFRP1_ENST00000485858.1_5'Flank|ARFRP1_ENST00000324228.2_Missense_Mutation_p.D101E			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	101					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			CGTCGGTGGAGTCAATGACGT	0.632																																					p.D101E		.											.	ARFRP1-291	0			c.C303G						.						102	82	89					20																	62333531		2203	4297	6500	SO:0001583	missense	10139	exon5			GGTGGAGTCAATG	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"ADP-ribosylation factors"	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.303C>G	20.37:g.62333531G>C	ENSP00000352746:p.Asp101Glu	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	69	20	NM_001134758	0	0	29	53	24	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	37	CCDS13533.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178823	0.78564	.	.	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.79247	-1.25;-1.25;-1.25	5.53	-0.912	0.10504	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.91895	0.7434	H	0.99726	4.73	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90445	0.4434	10	0.87932	D	0	-27.1276	9.796	0.40735	0.4997:0.0:0.5003:0.0	.	101;101	B3KTR4;Q13795	.;ARFRP_HUMAN	E	101	ENSP00000403942:D101E;ENSP00000352746:D101E;ENSP00000326884:D101E	ENSP00000326884:D101E	D	-	3	2	ARFRP1	61803975	1.000000	0.71417	0.998000	0.56505	0.751000	0.42716	1.177000	0.31969	-0.026000	0.13895	0.462000	0.41574	GAC	.		0.632	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1			C	62333531	G	C	62333531	3	2	33	1	0	0	0	0	1	0	0	0	856	1020	36	4	322	4	ARFRP1	20	62333531	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	351348	62333531	691989	75	2930											
ZDHHC8	29801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	20130720	20130720	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgccacggcccctacccCgcagcttcagccccgtgctg	5	5	9	22	4	1	0	1	0	0	0	1	0	1	0	8	1	4	3	8	1	1	2	rs532240635		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:20130720C>T	ENST00000334554.7	+	10	1708	c.1567C>T	c.(1567-1569)Cgc>Tgc	p.R523C	ZDHHC8_ENST00000405930.3_Missense_Mutation_p.R523C|ZDHHC8_ENST00000320602.7_Missense_Mutation_p.R431C	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	523					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					GCCCCTACCCCGCAGCTTCAG	0.706																																					p.R523C		.											.	ZDHHC8-91	0			c.C1567T						.						17	21	19					22																	20130720		2173	4267	6440	SO:0001583	missense	29801	exon10			CTACCCCGCAGCT	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1567C>T	22.37:g.20130720C>T	ENSP00000334490:p.Arg523Cys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	56	14	NM_001185024	0	0	14	29	15	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Missense_Mutation	SNP	ENST00000334554.7	37	CCDS13776.1	.	.	.	.	.	.	.	.	.	.	.	16.52	3.147388	0.57151	.	.	ENSG00000099904	ENST00000334554;ENST00000320602;ENST00000405930	T;T;T	0.74002	1.22;-0.8;1.19	4.79	3.77	0.43336	.	1.375280	0.04372	N	0.359278	T	0.79411	0.4441	L	0.29908	0.895	0.49213	D	0.999762	D;D;D	0.69078	0.981;0.996;0.997	P;P;P	0.59703	0.635;0.862;0.642	T	0.65302	-0.6201	10	0.56958	D	0.05	.	12.8482	0.57842	0.0:0.9203:0.0:0.0797	.	431;523;523	Q9ULC8-2;Q9ULC8-3;Q9ULC8	.;.;ZDHC8_HUMAN	C	523;431;523	ENSP00000334490:R523C;ENSP00000317804:R431C;ENSP00000384716:R523C	ENSP00000317804:R431C	R	+	1	0	ZDHHC8	18510720	0.996000	0.38824	1.000000	0.80357	0.387000	0.30353	3.788000	0.55446	1.025000	0.39708	-0.339000	0.08088	CGC	.		0.706	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20130720	C	T	20130720	3	4	33	1	0	0	0	0	1	0	0	0	17653	652	23	1	1605	1	ZDHHC8	22	20130720	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		20130720	31173846	76	2931											
PPIL2	23759	hgsc.bcm.edu	37	chr22	22039049	22039049	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tactgttttgtagatgaagaGaaggccaaacaggacccgtc	13	9	11	8	1	0	3	0	1	0	2	1	5	0	4	2	2	2	2	2	2	5	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:22039049G>C	ENST00000335025.8	+	10	652	c.561G>C	c.(559-561)gaG>gaC	p.E187D	PPIL2_ENST00000456792.2_Missense_Mutation_p.E166D|PPIL2_ENST00000406385.1_Missense_Mutation_p.E187D|PPIL2_ENST00000398831.3_Missense_Mutation_p.E187D|PPIL2_ENST00000492445.2_Missense_Mutation_p.E187D|PPIL2_ENST00000412327.1_Missense_Mutation_p.E187D					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					TAGATGAAGAGAAGGCCAAAC	0.547																																					p.E187D		.											.	PPIL2-92	0			c.G561C						.						33	33	33					22																	22039049		2203	4300	6503	SO:0001583	missense	23759	exon10			TGAAGAGAAGGCC		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"U-box domain containing"	9261	protein-coding gene	gene with protein product	"U-box domain containing 7"	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.561G>C	22.37:g.22039049G>C	ENSP00000334553:p.Glu187Asp	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	39	7	NM_014337	0	0	0	0	0		Missense_Mutation	SNP	ENST00000335025.8	37	CCDS13793.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.898491	0.52227	.	.	ENSG00000100023	ENST00000412327;ENST00000335025;ENST00000398831;ENST00000492445;ENST00000406385;ENST00000456792	T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54	4.36	-1.8	0.07907	.	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	L	0.59436	1.845	0.51233	D	0.999914	P;P;P	0.51240	0.943;0.868;0.891	P;P;P	0.55508	0.698;0.494;0.777	T	0.19095	-1.0316	10	0.25106	T	0.35	.	11.6657	0.51372	0.4833:0.0:0.5167:0.0	.	166;187;187	E7EW80;Q13356-2;Q13356	.;.;PPIL2_HUMAN	D	187;187;187;187;187;166	ENSP00000390427:E187D;ENSP00000334553:E187D;ENSP00000381812:E187D;ENSP00000445312:E187D;ENSP00000384299:E187D;ENSP00000396228:E166D	ENSP00000334553:E187D	E	+	3	2	PPIL2	20369049	0.995000	0.38212	0.996000	0.52242	0.915000	0.54546	0.513000	0.22770	-0.235000	0.09767	0.591000	0.81541	GAG	.		0.547	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4			C	22039049	G	C	22039049	3	2	33	1	0	0	0	0	1	0	0	0	12356	933	33	4	599	4	PPIL2	22	22039049	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	1908329	22039049	29265517	77	2932											
MGAT3	4248	hgsc.bcm.edu;broad.mit.edu	37	chr22	39883780	39883780	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gcctgagggggccaacggctCctcggcccggcggccacccc	4	3	15	19	4	0	1	0	1	0	0	2	1	1	1	7	6	1	1	7	6	1	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:39883780C>G	ENST00000341184.6	+	2	643	c.428C>G	c.(427-429)tCc>tGc	p.S143C		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	143					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					GCCAACGGCTCCTCGGCCCGG	0.766																																					p.S143C		.											.	MGAT3-90	0			c.C428G						.						3	4	4					22																	39883780		1757	3560	5317	SO:0001583	missense	4248	exon2			ACGGCTCCTCGGC	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.428C>G	22.37:g.39883780C>G	ENSP00000345270:p.Ser143Cys	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_002409	0	0	0	0	0	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Missense_Mutation	SNP	ENST00000341184.6	37	CCDS13994.2	.	.	.	.	.	.	.	.	.	.	C	6.780	0.512956	0.12944	.	.	ENSG00000128268	ENST00000341184;ENST00000429402	.	.	.	5.03	4.02	0.46733	.	0.406546	0.20728	N	0.086767	T	0.32496	0.0831	N	0.24115	0.695	0.09310	N	1	B	0.26258	0.145	B	0.33196	0.159	T	0.29336	-1.0015	9	0.45353	T	0.12	.	11.7602	0.51898	0.0:0.9177:0.0:0.0823	.	143	Q09327	MGAT3_HUMAN	C	143	.	ENSP00000345270:S143C	S	+	2	0	MGAT3	38213726	0.245000	0.23899	0.011000	0.14972	0.179000	0.23085	2.329000	0.43876	1.126000	0.42016	0.467000	0.42956	TCC	.		0.766	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409		G	39883780	C	G	39883780	3	3	33	1	0	0	0	0	1	0	0	0	9569	855	30	4	430	4	MGAT3	22	39883780	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	17844731	39883780	11420786	78	2933											
ADSL	158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40745897	40745897	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatcaaacctggagaacaTcgacttcaagatggcagctg	15	7	10	9	1	2	2	2	0	0	2	3	5	2	2	1	2	3	2	1	2	4	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:40745897T>A	ENST00000216194.7	+	2	271	c.215T>A	c.(214-216)aTc>aAc	p.I72N	ADSL_ENST00000342312.6_Missense_Mutation_p.I72N|ADSL_ENST00000454266.2_Missense_Mutation_p.I72N	NM_000026.2	NP_000017.1	P30566	PUR8_HUMAN	adenylosuccinate lyase	72			I -> V (in ADSL deficiency; severe). {ECO:0000269|PubMed:10090474}.		'de novo' AMP biosynthetic process (GO:0044208)|'de novo' IMP biosynthetic process (GO:0006189)|aerobic respiration (GO:0009060)|AMP biosynthetic process (GO:0006167)|metabolic process (GO:0008152)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity (GO:0070626)|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity (GO:0004018)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(2)|ovary(1)|prostate(1)	19						CTGGAGAACATCGACTTCAAG	0.433																																					p.I72N	Colon(4;65 130 1097 1516)	.											.	ADSL-652	0			c.T215A						.						119	94	102					22																	40745897		2203	4300	6503	SO:0001583	missense	158	exon2			AGAACATCGACTT	X65867	CCDS14001.1, CCDS46714.1	22q13.1	2011-02-17			ENSG00000239900	ENSG00000239900	4.3.2.2		291	protein-coding gene	gene with protein product		608222				8404037	Standard	NM_000026		Approved		uc003ayp.4	P30566	OTTHUMG00000166425	ENST00000216194.7:c.215T>A	22.37:g.40745897T>A	ENSP00000216194:p.Ile72Asn	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	56	11	NM_001123378	0	0	9	18	9	B0QY76|O75495|Q5TI34	Missense_Mutation	SNP	ENST00000216194.7	37	CCDS14001.1	.	.	.	.	.	.	.	.	.	.	T	32	5.145835	0.94603	.	.	ENSG00000239900	ENST00000216194;ENST00000544206;ENST00000425605;ENST00000454266;ENST00000342312	D;D;D	0.95518	-3.73;-3.73;-3.64	5.59	5.59	0.84812	L-Aspartase-like (1);L-Aspartase-like, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98273	0.9428	M	0.93638	3.44	0.80722	D	1	D;D;D;D	0.71674	0.978;0.983;0.998;0.998	P;D;D;D	0.76575	0.822;0.929;0.988;0.988	D	0.99433	1.0936	10	0.72032	D	0.01	-8.6026	15.8537	0.78956	0.0:0.0:0.0:1.0	.	72;72;72;72	E7ERF4;P30566-2;Q71UA4;P30566	.;.;.;PUR8_HUMAN	N	72	ENSP00000216194:I72N;ENSP00000390107:I72N;ENSP00000341429:I72N	ENSP00000216194:I72N	I	+	2	0	ADSL	39075843	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.757000	0.85209	2.141000	0.66446	0.529000	0.55759	ATC	.		0.433	ADSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321386.1	NM_000026		A	40745897	T	A	40745897	3	1	33	1	0	0	0	0	1	0	0	0	346	1435	50	5	221	5	ADSL	22	40745897	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	862117	40745897	10558669	79	2934											
PARVG	64098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	44581694	44581694	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cactctgcttccaggaggaaAgaagaaatacctgccaccca	14	6	8	13	0	1	2	0	0	1	2	2	4	2	4	4	2	3	1	4	2	4	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:44581694A>T	ENST00000444313.3	+	4	570	c.86A>T	c.(85-87)aAg>aTg	p.K29M	PARVG_ENST00000422871.1_Missense_Mutation_p.K29M|PARVG_ENST00000415224.1_Missense_Mutation_p.K29M|PARVG_ENST00000453888.3_3'UTR	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	29					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				CCAGGAGGAAAGAAGAAATAC	0.577																																					p.K96M		.											.	PARVG-90	0			c.A287T						.						68	55	60					22																	44581694		2203	4300	6503	SO:0001583	missense	64098	exon3			GAGGAAAGAAGAA	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"Parvins"	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.86A>T	22.37:g.44581694A>T	ENSP00000391583:p.Lys29Met	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	46	11	NM_001254742	0	0	0	0	0	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Missense_Mutation	SNP	ENST00000444313.3	37	CCDS14057.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.083589	0.55861	.	.	ENSG00000138964	ENST00000422871;ENST00000453888;ENST00000444313;ENST00000415224	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.79	4.79	0.61399	Calponin homology domain (1);	0.161867	0.39985	N	0.001210	T	0.63733	0.2536	M	0.70595	2.14	0.42735	D	0.993721	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.944	T	0.66945	-0.5795	10	0.66056	D	0.02	3.0E-4	7.9054	0.29759	0.8163:0.0:0.0:0.1837	.	96;29	B4DDW5;Q9HBI0	.;PARVG_HUMAN	M	29;96;29;29	ENSP00000391453:K29M;ENSP00000416104:K96M;ENSP00000391583:K29M;ENSP00000416761:K29M	ENSP00000349378:K29M	K	+	2	0	PARVG	42913027	1.000000	0.71417	0.994000	0.49952	0.692000	0.40212	3.551000	0.53698	1.781000	0.52344	0.533000	0.62120	AAG	.		0.577	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141		T	44581694	A	T	44581694	3	4	33	1	0	0	0	0	1	0	0	0	11496	72	3	5	92	5	PARVG	22	44581694	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	3835797	44581694	6722872	80	2935											
HDAC10	83933	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	50684494	50684494	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggggcagcaccaagcccaAgatgcagctcaggaaaccac	14	2	11	14	0	1	1	1	0	0	1	1	2	1	2	3	3	5	4	3	3	3	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:50684494A>G	ENST00000216271.5	-	18	2030	c.1678T>C	c.(1678-1680)Ttg>Ctg	p.L560L	TUBGCP6_ENST00000248846.5_5'Flank|MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000498366.1_5'UTR|TUBGCP6_ENST00000439308.2_5'Flank|HDAC10_ENST00000349505.4_Silent_p.L540L|HDAC10_ENST00000448072.1_Silent_p.L510L	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	560					chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		ACCAAGCCCAAGATGCAGCTC	0.657																																					p.L560L		.											.	HDAC10-226	0			c.T1678C						.						41	44	43					22																	50684494		2201	4300	6501	SO:0001819	synonymous_variant	83933	exon18			AGCCCAAGATGCA	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1678T>C	22.37:g.50684494A>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	47	5	NM_032019	0	0	25	25	0	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Silent	SNP	ENST00000216271.5	37	CCDS14088.1																																																																																			.		0.657	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019		G	50684494	A	G	50684494	2	3	33	1	0	0	0	0	0	0	0	1	7026	69	3	3		3	HDAC10	22	50684494	Silent	SNP	A	TCGA-AL-7173-01A-11D-2136-08	6102800	50684494	620072	81	2936											
PRKX	5613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	3544550	3544550	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttgtcatcaaaaaacggaGgaaacctgttagaaaaacaa	19	7	9	6	1	2	1	2	0	0	1	2	3	2	3	1	3	3	2	1	3	8	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chrX:3544550G>C	ENST00000262848.5	-	5	1079	c.725C>G	c.(724-726)cCt>cGt	p.P242R	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				AAAAAACGGAGGAAACCTGTT	0.373																																					p.P242R		.											.	PRKX-540	0			c.C725G						.						108	93	98					X																	3544550		2203	4300	6503	SO:0001583	missense	5613	exon5			AACGGAGGAAACC		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.725C>G	X.37:g.3544550G>C	ENSP00000262848:p.Pro242Arg	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	25	7	NM_005044	0	0	0	0	0		Missense_Mutation	SNP	ENST00000262848.5	37	CCDS14125.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994637	0.35226	.	.	ENSG00000183943	ENST00000262848	T	0.09073	3.02	3.47	3.47	0.39725	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.19167	0.0460	L	0.39147	1.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00909	-1.1518	10	0.87932	D	0	-3.9448	12.0899	0.53719	0.0:0.0:1.0:0.0	.	242	P51817	PRKX_HUMAN	R	242	ENSP00000262848:P242R	ENSP00000262848:P242R	P	-	2	0	PRKX	3554550	1.000000	0.71417	0.936000	0.37596	0.310000	0.27922	6.948000	0.75965	1.374000	0.46228	0.529000	0.55759	CCT	.		0.373	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		C	3544550	G	C	3544550	3	2	33	1	0	0	0	0	1	0	0	0	12556	1000	35	4	367	4	PRKX	23	3544550	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08		3544550	151726010	82	2937											
KIAA2022	340533	broad.mit.edu	37	chrX	73961092	73961092	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaatggtcctgggacaccCtcttggaacccctttagtgt	7	12	9	13	0	1	0	0	0	1	0	3	2	3	2	5	3	1	0	5	3	3	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chrX:73961092C>T	ENST00000055682.6	-	3	3911	c.3300G>A	c.(3298-3300)gaG>gaA	p.E1100E		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1100					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGGGACACCCTCTTGGAACC	0.478																																					p.E1100E													.	KIAA2022-183	0			c.G3300A						.						75	70	72					X																	73961092		2203	4300	6503	SO:0001819	synonymous_variant	340533	exon3			GACACCCTCTTGG		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3300G>A	X.37:g.73961092C>T		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	83	4	NM_001008537	0	0	0	0	0	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	37	CCDS35337.1																																																																																			.		0.478	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		T	73961092	C	T	73961092	2	4	33	1	0	0	0	0	0	0	0	1	8290	680	24	2		2	KIAA2022	23	73961092	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	70416542	73961092	81309468	83	2938											
SYTL4	94121	hgsc.bcm.edu	37	chrX	99945081	99945081	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccagttacctgaaggccTgaggatttttctggtgttct	9	14	10	8	0	2	2	0	2	2	0	2	3	2	3	3	3	2	2	3	3	3	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chrX:99945081T>C	ENST00000372989.1	-	10	1130	c.799A>G	c.(799-801)Agg>Ggg	p.R267G	SYTL4_ENST00000372981.1_Missense_Mutation_p.R267G|SYTL4_ENST00000454200.2_Missense_Mutation_p.R268G|SYTL4_ENST00000276141.6_Missense_Mutation_p.R267G|SYTL4_ENST00000455616.1_Missense_Mutation_p.R267G|SYTL4_ENST00000263033.5_Missense_Mutation_p.R267G	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	267					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""Insulin(DB00071)|Insulin Regular(DB00030)"	CCTGAAGGCCTGAGGATTTTT	0.443																																					p.R267G		.											.	SYTL4-132	0			c.A799G						.						81	70	74					X																	99945081		2203	4300	6503	SO:0001583	missense	94121	exon9			AAGGCCTGAGGAT		CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"granuphilin-a", "exophilin-2"	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.799A>G	X.37:g.99945081T>C	ENSP00000362080:p.Arg267Gly	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	59	3	NM_001129896	0	0	0	0	0	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Missense_Mutation	SNP	ENST00000372989.1	37	CCDS14472.1	.	.	.	.	.	.	.	.	.	.	t	16.96	3.267176	0.59540	.	.	ENSG00000102362	ENST00000372989;ENST00000455616;ENST00000454200;ENST00000276141;ENST00000263033;ENST00000372981	T;T;T;T;T;T	0.68624	1.85;1.85;1.85;1.85;1.85;-0.34	5.7	5.7	0.88788	.	0.136293	0.64402	D	0.000002	T	0.63177	0.2489	L	0.53249	1.67	0.35835	D	0.825602	P;P	0.47762	0.9;0.893	P;B	0.45610	0.487;0.4	T	0.71321	-0.4628	9	.	.	.	-16.6096	8.1118	0.30920	0.1328:0.0:0.1353:0.7319	.	267;267	Q96C24-2;Q96C24	.;SYTL4_HUMAN	G	267;267;268;267;267;267	ENSP00000362080:R267G;ENSP00000390252:R267G;ENSP00000403556:R268G;ENSP00000276141:R267G;ENSP00000263033:R267G;ENSP00000362072:R267G	.	R	-	1	2	SYTL4	99831737	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.828000	0.62730	1.915000	0.55452	0.478000	0.44815	AGG	.		0.443	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1	NM_080737		C	99945081	T	C	99945081	3	2	33	1	0	0	0	0	1	0	0	0	15517	1579	55	3	1256	3	SYTL4	23	99945081	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	25983989	99945081	55325479	84	2939											
SPATA6	54558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	48918785	48918785	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctctttgtctttaagcaCgactcctgggcaagttacct	7	14	8	12	1	2	0	0	0	2	0	4	1	4	0	3	1	2	3	3	1	3	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:48918785C>T	ENST00000371847.3	-	2	234	c.70G>A	c.(70-72)Gtg>Atg	p.V24M	SPATA6_ENST00000396199.3_De_novo_Start_InFrame|SPATA6_ENST00000371843.3_Missense_Mutation_p.V24M|SPATA6_ENST00000463938.1_5'UTR	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	24					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TCTTTAAGCACGACTCCTGGG	0.373																																					p.V24M		.											.	SPATA6-91	0			c.G70A						.						124	118	120					1																	48918785		2203	4300	6503	SO:0001583	missense	54558	exon2			TAAGCACGACTCC	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"spermatogenesis-related factor-1"	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.70G>A	1.37:g.48918785C>T	ENSP00000360913:p.Val24Met	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	71	30	NM_019073	0	0	0	0	0	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.373114	0.24857	.	.	ENSG00000132122	ENST00000371847;ENST00000371843	T;T	0.12569	2.67;2.67	5.12	1.99	0.26369	.	0.662370	0.14247	N	0.331705	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B	0.33073	0.396;0.153	B;B	0.24394	0.053;0.053	T	0.41088	-0.9528	10	0.30854	T	0.27	.	3.3052	0.06997	0.1575:0.4045:0.3416:0.0963	.	24;24	Q9NWH7-2;Q9NWH7	.;SPAT6_HUMAN	M	24	ENSP00000360913:V24M;ENSP00000360909:V24M	ENSP00000360909:V24M	V	-	1	0	SPATA6	48691372	0.208000	0.23494	1.000000	0.80357	0.990000	0.78478	-0.170000	0.09897	1.163000	0.42636	0.555000	0.69702	GTG	.		0.373	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		T	48918785	C	T	48918785	3	4	34	1	0	0	0	0	1	0	0	0	15045	536	19	1	1444	1	SPATA6	1	48918785	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		48918785	200331836	1	2940											
GTF2B	2959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	89352944	89352944	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccataataacaactcacCtacaaccaagccacattcag	19	6	2	14	0	2	0	2	0	0	0	2	0	2	0	4	0	6	0	4	0	7	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:89352944C>G	ENST00000370500.5	-	2	242	c.124G>C	c.(124-126)Ggt>Cgt	p.G42R	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	42					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		AACAACTCACCTACAACCAAG	0.473																																					p.G42R		.											.	GTF2B-154	0			c.G124C						.						293	301	298					1																	89352944		2203	4300	6503	SO:0001630	splice_region_variant	2959	exon2			ACTCACCTACAAC	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.124+1G>C	1.37:g.89352944C>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	82	39	NM_001514	0	0	0	0	0	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	37	CCDS715.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.002123	0.74932	.	.	ENSG00000137947	ENST00000370500;ENST00000448623	T;T	0.43294	0.95;0.95	5.67	5.67	0.87782	Zinc finger, TFIIB-type (2);	0.000000	0.85682	D	0.000000	T	0.37156	0.0993	M	0.77103	2.36	0.80722	D	1	B	0.13145	0.007	B	0.23574	0.047	T	0.24977	-1.0145	9	.	.	.	-12.0703	19.7698	0.96359	0.0:1.0:0.0:0.0	.	42	Q00403	TF2B_HUMAN	R	42;41	ENSP00000359531:G42R;ENSP00000415741:G41R	.	G	-	1	0	GTF2B	89125532	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.125000	0.77193	2.659000	0.90383	0.655000	0.94253	GGT	.		0.473	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514	Missense_Mutation	G	89352944	C	G	89352944	5	3	34	1	0	0	0	0	0	0	1	0	6876	695	24	4	850	4	GTF2B	1	89352944	Splice_Site	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	40434159	89352944	159897677	2	2941											
C1orf146	388649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	92707844	92707844	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attcagtggaaaatggatcaAttatattttctctttctggt	11	18	7	5	0	4	0	2	0	2	0	5	2	4	2	0	3	0	0	0	3	5	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:92707844A>C	ENST00000370375.3	+	3	290	c.142A>C	c.(142-144)Att>Ctt	p.I48L	C1orf146_ENST00000370373.2_5'UTR	NM_001012425.1	NP_001012425.1	Q5VVC0	CA146_HUMAN	chromosome 1 open reading frame 146	48										breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		AAATGGATCAATTATATTTTC	0.308																																					p.I48L		.											.	C1orf146-91	0			c.A142C						.						111	112	112					1																	92707844		2203	4298	6501	SO:0001583	missense	388649	exon3			GGATCAATTATAT		CCDS30772.1	1p22.1	2008-02-05			ENSG00000203910	ENSG00000203910			24032	protein-coding gene	gene with protein product						15496913	Standard	NM_001012425		Approved		uc001doq.3	Q5VVC0	OTTHUMG00000010285	ENST00000370375.3:c.142A>C	1.37:g.92707844A>C	ENSP00000359401:p.Ile48Leu	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	20	10	NM_001012425	0	0	0	0	0	Q5VVC4	Missense_Mutation	SNP	ENST00000370375.3	37	CCDS30772.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.520239	0.44866	.	.	ENSG00000203910	ENST00000370375;ENST00000370373	.	.	.	5.15	2.85	0.33270	.	0.254660	0.34067	N	0.004296	T	0.11750	0.0286	N	0.24115	0.695	0.28249	N	0.92534	B	0.32507	0.373	B	0.30572	0.117	T	0.07986	-1.0744	9	0.59425	D	0.04	0.0214	8.2971	0.31993	0.7519:0.0:0.2481:0.0	.	48	Q5VVC0	CA146_HUMAN	L	48;27	.	ENSP00000359399:I27L	I	+	1	0	C1orf146	92480432	0.955000	0.32602	0.999000	0.59377	0.994000	0.84299	1.221000	0.32503	0.445000	0.26639	0.533000	0.62120	ATT	.		0.308	C1orf146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028364.1	NM_001012425		C	92707844	A	C	92707844	3	2	34	1	0	0	0	0	1	0	0	0	2009	101	4	5	148	5	C1orf146	1	92707844	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	3354900	92707844	156542777	3	2942											
AMPD2	271	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110170816	110170816	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgcacgtggagcagggcCgtgaacagacgctgcgggag	8	5	18	10	5	0	2	0	1	0	1	1	4	0	4	1	3	4	3	1	3	1	0	rs570605098		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:110170816C>G	ENST00000256578.3	+	10	1714	c.1354C>G	c.(1354-1356)Cgt>Ggt	p.R452G	AMPD2_ENST00000528454.1_Missense_Mutation_p.R334G|AMPD2_ENST00000342115.4_Missense_Mutation_p.R371G|AMPD2_ENST00000393688.3_Missense_Mutation_p.R333G|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000358729.4_Missense_Mutation_p.R377G|AMPD2_ENST00000528667.1_Missense_Mutation_p.R452G	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	452					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		GGAGCAGGGCCGTGAACAGAC	0.597																																					p.R452G													.	AMPD2-292	0			c.C1354G						.						74	73	73					1																	110170816		2203	4300	6503	SO:0001583	missense	271	exon10			CAGGGCCGTGAAC	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"AMPD isoform L"	102771	"adenosine monophosphate deaminase 2 (isoform L)"			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.1354C>G	1.37:g.110170816C>G	ENSP00000256578:p.Arg452Gly	Somatic	167	1		WXS	Illumina HiSeq	Phase_I	104	49	NM_004037	0	0	28	40	12	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Missense_Mutation	SNP	ENST00000256578.3	37	CCDS805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.57|15.57	2.873478|2.873478	0.51695|0.51695	.|.	.|.	ENSG00000116337|ENSG00000116337	ENST00000369840|ENST00000342115;ENST00000528667;ENST00000256578;ENST00000358729;ENST00000528454;ENST00000393688	.|D;D;D;D;D;D	.|0.83591	.|-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	5.04|5.04	4.13|4.13	0.48395|0.48395	.|Adenosine/AMP deaminase (1);	.|0.131267	.|0.50627	.|D	.|0.000110	T|T	0.61502|0.61502	0.2352|0.2352	L|L	0.32530|0.32530	0.975|0.975	0.39338|0.39338	D|D	0.965537|0.965537	.|B;B;B;B	.|0.29253	.|0.239;0.0;0.011;0.0	.|B;B;B;B	.|0.32211	.|0.142;0.004;0.026;0.002	T|T	0.66420|0.66420	-0.5928|-0.5928	5|10	.|0.72032	.|D	.|0.01	-18.7411|-18.7411	6.0763|6.0763	0.19917|0.19917	0.2887:0.6218:0.0:0.0894|0.2887:0.6218:0.0:0.0894	.|.	.|377;333;452;371	.|Q01433-4;Q01433-3;Q01433;Q01433-2	.|.;.;AMPD2_HUMAN;.	R|G	422|371;452;452;377;334;333	.|ENSP00000345498:R371G;ENSP00000436541:R452G;ENSP00000256578:R452G;ENSP00000351573:R377G;ENSP00000437164:R334G;ENSP00000377292:R333G	.|ENSP00000256578:R452G	P|R	+|+	2|1	0|0	AMPD2|AMPD2	109972339|109972339	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.962000|0.962000	0.63368|0.63368	2.423000|2.423000	0.44705|0.44705	1.367000|1.367000	0.46095|0.46095	0.561000|0.561000	0.74099|0.74099	CCG|CGT	.		0.597	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1			G	110170816	C	G	110170816	3	3	34	1	0	0	0	0	1	0	0	0	586	652	23	4	1433	4	AMPD2	1	110170816	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	17462972	110170816	139079805	4	2943											
ZNF697	90874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	120165395	120165395	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaagcctttgccgcagcccGcacacttgtgcggcttgttg	5	10	13	13	3	0	0	0	0	0	0	0	1	0	1	3	2	4	4	3	2	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:120165395G>A	ENST00000421812.2	-	3	1690	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	524					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		GCCGCAGCCCGCACACTTGTG	0.637																																					p.A524V		.											.	ZNF697-23	0			c.C1571T						.						13	17	16					1																	120165395		2127	4266	6393	SO:0001583	missense	90874	exon3			CAGCCCGCACACT	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"Zinc fingers, C2H2-type"	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.1571C>T	1.37:g.120165395G>A	ENSP00000396857:p.Ala524Val	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	86	36	NM_001080470	0	0	0	2	2	Q96IT2	Missense_Mutation	SNP	ENST00000421812.2	37	CCDS44202.1	.	.	.	.	.	.	.	.	.	.	G	2.237	-0.374694	0.05034	.	.	ENSG00000143067	ENST00000421812	T	0.17691	2.26	4.99	4.07	0.47477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.216152	0.23519	N	0.047302	T	0.03915	0.0110	N	0.20574	0.59	0.09310	N	1	B	0.23128	0.08	B	0.25291	0.059	T	0.32188	-0.9916	10	0.37606	T	0.19	-8.4913	8.9809	0.35964	0.0:0.1625:0.6694:0.1681	.	524	Q5TEC3	ZN697_HUMAN	V	524	ENSP00000396857:A524V	ENSP00000396857:A524V	A	-	2	0	ZNF697	119966918	0.000000	0.05858	0.026000	0.17262	0.005000	0.04900	0.294000	0.19047	1.414000	0.47017	-0.175000	0.13238	GCG	.		0.637	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		A	120165395	G	A	120165395	3	1	34	1	0	0	0	0	1	0	0	0	18132	1087	38	1	70	1	ZNF697	1	120165395	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	9994579	120165395	129085226	5	2944											
CREG1	8804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167515417	167515417	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggacccagatattggttaTattcaacttagcaaagaacc	15	10	7	9	0	1	2	1	0	0	2	1	3	1	3	2	2	3	2	2	2	7	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:167515417T>A	ENST00000370509.4	-	3	605	c.580A>T	c.(580-582)Ata>Tta	p.I194L	CREG1_ENST00000466652.1_5'UTR	NM_003851.2	NP_003842.1	O75629	CREG1_HUMAN	cellular repressor of E1A-stimulated genes 1	194					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|transcription factor complex (GO:0005667)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)|transcription corepressor activity (GO:0003714)										ATATTGGTTATATTCAACTTA	0.383																																					p.I194L		.											.	CREG1-186	0			c.A580T						.						73	75	74					1																	167515417		2203	4300	6503	SO:0001583	missense	8804	exon3			TGGTTATATTCAA	AF084523	CCDS1262.1	1q24	2008-02-05	2004-09-22	2004-09-22	ENSG00000143162	ENSG00000143162			2351	protein-coding gene	gene with protein product			"cellular repressor of E1A-stimulated genes"	CREG		9710587	Standard	NM_003851		Approved		uc001gel.3	O75629	OTTHUMG00000034682	ENST00000370509.4:c.580A>T	1.37:g.167515417T>A	ENSP00000359540:p.Ile194Leu	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	105	46	NM_003851	0	0	81	143	62	B2RDD4|Q8N9A3	Missense_Mutation	SNP	ENST00000370509.4	37	CCDS1262.1	.	.	.	.	.	.	.	.	.	.	T	33	5.194241	0.94960	.	.	ENSG00000143162	ENST00000370509	.	.	.	5.86	5.86	0.93980	FMN-binding split barrel-related (1);FMN-binding split barrel (1);	0.000000	0.85682	D	0.000000	T	0.76111	0.3942	M	0.82923	2.615	0.51012	D	0.999905	D	0.58620	0.983	D	0.68192	0.956	T	0.79102	-0.1941	8	0.52906	T	0.07	0.6411	16.2453	0.82441	0.0:0.0:0.0:1.0	.	194	O75629	CREG1_HUMAN	L	194	.	ENSP00000359540:I194L	I	-	1	0	CREG1	165782041	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	7.549000	0.82163	2.241000	0.73720	0.533000	0.62120	ATA	.		0.383	CREG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083911.1	NM_003851		A	167515417	T	A	167515417	3	1	34	1	0	0	0	0	1	0	0	0	3870	1406	49	5	90	5	CREG1	1	167515417	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	47350022	167515417	81735204	6	2945											
MOSC1	64757	hgsc.bcm.edu	37	chr1	220960439	220960439	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccacgcggcgccggcggctGctgcagcaggtgggcacagt	5	4	17	15	5	0	0	0	0	0	0	0	0	0	0	2	5	3	5	2	5	0	0	rs367900610		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:220960439G>T	ENST00000366910.5	+	1	339	c.153G>T	c.(151-153)ctG>ctT	p.L51L		NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	51					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										GCCGGCGGCTGCTGCAGCAGG	0.756																																					p.L51L		.											.	.	0			c.G153T						.	G		0,3888		0,0,1944	5	6	6		153	0.2	0.9	1		6	2,7704		0,2,3851	no	coding-synonymous	MOSC1	NM_022746.3		0,2,5795	TT,TG,GG		0.026,0.0,0.0173		51/338	220960439	2,11592	1944	3853	5797	SO:0001819	synonymous_variant	64757	exon1			GCGGCTGCTGCAG	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.153G>T	1.37:g.220960439G>T		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	25	10	NM_022746	0	0	0	0	0	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Silent	SNP	ENST00000366910.5	37	CCDS1526.1																																																																																			.		0.756	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		T	220960439	G	T	220960439	2	4	34	1	0	0	0	0	0	0	0	1	9738	1306	46	4		4	MOSC1	1	220960439	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	53445022	220960439	28290182	7	2946											
CEBPZ	10153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37455042	37455042	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgagctttggagctgatatTtgagcggaagagtagccttt	9	14	13	5	1	0	4	0	3	0	1	0	6	0	6	1	2	4	3	1	2	3	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:37455042T>A	ENST00000234170.5	-	2	1439	c.1294A>T	c.(1294-1296)Aat>Tat	p.N432Y		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	432					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				GAGCTGATATTTGAGCGGAAG	0.363																																					p.N432Y		.											.	CEBPZ-91	0			c.A1294T						.						102	104	103					2																	37455042		2203	4300	6503	SO:0001583	missense	10153	exon2			TGATATTTGAGCG	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1294A>T	2.37:g.37455042T>A	ENSP00000234170:p.Asn432Tyr	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	113	37	NM_005760	0	0	35	52	17	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.885601	0.72410	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.13420	2.59	5.31	5.31	0.75309	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46814	0.1412	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59289	-0.7482	10	0.87932	D	0	.	15.3016	0.73955	0.0:0.0:0.0:1.0	.	432	Q03701	CEBPZ_HUMAN	Y	432	ENSP00000234170:N432Y	ENSP00000234170:N432Y	N	-	1	0	CEBPZ	37308546	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.525000	0.81892	2.017000	0.59298	0.528000	0.53228	AAT	.		0.363	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37455042	T	A	37455042	3	1	34	1	0	0	0	0	1	0	0	0	3210	1841	64	5	1930	5	CEBPZ	2	37455042	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10		37455042	205744331	8	2947											
C2orf34	79823	hgsc.bcm.edu	37	chr2	44589184	44589184	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacgctgggaccggcgagaCcgcgcgagcagcgggcggga	7	1	21	12	8	0	1	0	0	0	1	0	6	0	4	2	5	2	2	2	5	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:44589184C>T	ENST00000378494.3	+	1	82	c.38C>T	c.(37-39)aCc>aTc	p.T13I	PREPL_ENST00000378520.3_5'Flank|CAMKMT_ENST00000407131.1_Missense_Mutation_p.T13I|PREPL_ENST00000409272.1_5'Flank|PREPL_ENST00000378511.3_5'Flank|PREPL_ENST00000409936.1_5'Flank|PREPL_ENST00000409411.1_5'Flank|CAMKMT_ENST00000402247.1_Missense_Mutation_p.T13I|PREPL_ENST00000409957.1_5'Flank|PREPL_ENST00000260648.6_5'Flank|PREPL_ENST00000540817.1_5'Flank|PREPL_ENST00000410081.1_5'Flank|CAMKMT_ENST00000403853.3_Missense_Mutation_p.T13I|PREPL_ENST00000541738.1_5'Flank	NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	13						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						ACCGGCGAGACCGCGCGAGCA	0.741																																					p.T13I		.											.	CAMKMT-90	0			c.C38T						.						4	7	6					2																	44589184		2073	4050	6123	SO:0001583	missense	79823	exon1			GCGAGACCGCGCG		CCDS1820.1	2p21	2011-06-22	2011-03-10	2011-03-10	ENSG00000143919	ENSG00000143919	2.1.1.60		26276	protein-coding gene	gene with protein product	"CaM KMT"	609559	"chromosome 2 open reading frame 34"	C2orf34		20975703	Standard	NM_024766		Approved	CLNMT	uc002rum.3	Q7Z624	OTTHUMG00000128761	ENST00000378494.3:c.38C>T	2.37:g.44589184C>T	ENSP00000367755:p.Thr13Ile	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	62	31	NM_024766	0	0	6	10	4	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	37	CCDS1820.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846091	0.51164	.	.	ENSG00000143919	ENST00000402247;ENST00000454848;ENST00000407131;ENST00000378494;ENST00000403853	.	.	.	4.91	4.91	0.64330	.	0.320112	0.26262	N	0.025387	T	0.41419	0.1158	L	0.40543	1.245	0.09310	N	0.999994	B;P	0.47762	0.079;0.9	B;P	0.47645	0.051;0.553	T	0.30765	-0.9967	9	0.39692	T	0.17	-0.7064	13.4872	0.61373	0.0:1.0:0.0:0.0	.	13;13	Q7Z624;Q7Z624-2	CMKMT_HUMAN;.	I	13	.	ENSP00000367755:T13I	T	+	2	0	CAMKMT	44442688	0.000000	0.05858	0.278000	0.24718	0.011000	0.07611	0.616000	0.24344	2.549000	0.85964	0.655000	0.94253	ACC	.		0.741	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766		T	44589184	C	T	44589184	3	4	34	1	0	0	0	0	1	0	0	0	2169	507	18	2	40	2	C2orf34	2	44589184	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	7134142	44589184	198610189	9	2948											
GCC2	9648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109087879	109087879	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggaaaacaataaactcagTtcagaaaaaaaacagttgag	22	6	8	5	0	2	2	2	1	0	1	2	4	2	3	0	1	3	2	0	1	9	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:109087879T>A	ENST00000309863.6	+	6	2808	c.2094T>A	c.(2092-2094)agT>agA	p.S698R		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	698					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						ATAAACTCAGTTCAGAAAAAA	0.308																																					p.S698R		.											.	GCC2-91	0			c.T2094A						.						114	143	133					2																	109087879		2203	4299	6502	SO:0001583	missense	9648	exon6			ACTCAGTTCAGAA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"GRIP and coiled-coil domain-containing 2"			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2094T>A	2.37:g.109087879T>A	ENSP00000307939:p.Ser698Arg	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	172	39	NM_181453	0	0	17	32	15	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.987|3.987	-0.005307|-0.005307	0.07773|0.07773	.|.	.|.	ENSG00000135968|ENSG00000135968	ENST00000309863;ENST00000409896|ENST00000393318	T|.	0.32023|.	1.47|.	5.5|5.5	4.27|4.27	0.50696|0.50696	.|.	0.676432|.	0.15756|.	N|.	0.246200|.	T|T	0.34019|0.34019	0.0883|0.0883	L|L	0.41236|0.41236	1.265|1.265	0.24442|0.24442	N|N	0.994523|0.994523	B|.	0.27625|.	0.183|.	B|.	0.22386|.	0.039|.	T|T	0.18840|0.18840	-1.0324|-1.0324	10|6	0.19590|0.12103	T|T	0.45|0.63	.|.	8.3633|8.3633	0.32372|0.32372	0.1299:0.0:0.1353:0.7349|0.1299:0.0:0.1353:0.7349	.|.	698|.	Q8IWJ2|.	GCC2_HUMAN|.	R|D	698;661|443	ENSP00000307939:S698R|.	ENSP00000307939:S698R|ENSP00000376993:V443D	S|V	+|+	3|2	2|0	GCC2|GCC2	108454311|108454311	0.010000|0.010000	0.17322|0.17322	0.942000|0.942000	0.38095|0.38095	0.386000|0.386000	0.30323|0.30323	0.472000|0.472000	0.22116|0.22116	2.213000|2.213000	0.71641|0.71641	0.528000|0.528000	0.53228|0.53228	AGT|GTT	.		0.308	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		A	109087879	T	A	109087879	3	1	34	1	0	0	0	0	1	0	0	0	6306	1722	60	5	2116	5	GCC2	2	109087879	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	64498695	109087879	134111494	10	2949											
ORC4L	5000	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	148695764	148695764	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacggaatgtgctttccttTgaacaaacttctgaaactct	13	13	6	9	1	2	2	0	2	2	0	3	3	3	3	1	1	5	1	1	1	5	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:148695764T>A	ENST00000392857.5	-	13	1180	c.1073A>T	c.(1072-1074)cAa>cTa	p.Q358L	ORC4_ENST00000535373.1_Missense_Mutation_p.Q358L|ORC4_ENST00000264169.2_Missense_Mutation_p.Q358L|ORC4_ENST00000536575.1_Missense_Mutation_p.Q274L|ORC4_ENST00000392858.1_Missense_Mutation_p.Q358L|ORC4_ENST00000540442.1_Missense_Mutation_p.Q284L|ORC4_ENST00000542387.1_Missense_Mutation_p.Q141L|AC009480.1_ENST00000584553.1_RNA|ORC4_ENST00000488761.1_5'Flank	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	358					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						TGCTTTCCTTTGAACAAACTT	0.328																																					p.Q358L		.											.	ORC4-207	0			c.A1073T						.						50	52	51					2																	148695764		2201	4299	6500	SO:0001583	missense	5000	exon13			TTCCTTTGAACAA	AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"ATPases / AAA-type"	8490	protein-coding gene	gene with protein product		603056	"origin recognition complex, subunit 4 (yeast homolog)-like", "origin recognition complex, subunit 4-like (yeast)", "origin recognition complex, subunit 4-like (S. cerevisiae)", "origin recognition complex, subunit 4 homolog (S. cerevisiae)"	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.1073A>T	2.37:g.148695764T>A	ENSP00000376597:p.Gln358Leu	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	156	8	NM_002552	0	0	52	58	6	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.162605	0.57368	.	.	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000540442;ENST00000536575;ENST00000392857;ENST00000542387	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.76478	0.3993	M	0.66939	2.045	0.80722	D	1	B	0.32573	0.376	B	0.30943	0.122	T	0.75445	-0.3315	10	0.41790	T	0.15	-17.6101	16.4116	0.83717	0.0:0.0:0.0:1.0	.	358	O43929	ORC4_HUMAN	L	358;358;358;284;274;358;141	ENSP00000264169:Q358L;ENSP00000441953:Q358L;ENSP00000376598:Q358L;ENSP00000438326:Q284L;ENSP00000441502:Q274L;ENSP00000376597:Q358L;ENSP00000437440:Q141L	ENSP00000264169:Q358L	Q	-	2	0	ORC4	148412234	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.684000	0.84104	2.276000	0.75962	0.528000	0.53228	CAA	.		0.328	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742		A	148695764	T	A	148695764	3	1	34	1	0	0	0	0	1	0	0	0	11290	1812	63	5	245	5	ORC4L	2	148695764	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	39607885	148695764	94503609	11	2950											
NEB	4703	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	152579988	152579989	+	Frame_Shift_Ins	INS	-	-	A																															ttgtctgcttcccagtcttcINSagtgtacagtttctaaatca																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:152579988_152579989insA	ENST00000172853.10	-	9	771_772	c.624_625insT	c.(622-627)actgaafs	p.E209fs	NEB_ENST00000604864.1_Frame_Shift_Ins_p.E209fs|NEB_ENST00000603639.1_Frame_Shift_Ins_p.E209fs|NEB_ENST00000397345.3_Frame_Shift_Ins_p.E209fs|NEB_ENST00000427231.2_Frame_Shift_Ins_p.E209fs|NEB_ENST00000409198.1_Frame_Shift_Ins_p.E209fs			P20929	NEBU_HUMAN	nebulin	209					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.E209*(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCCCAGTCTTCAGTGTACAGTT	0.391																																					p.E209_D210delinsX		.											.	NEB-145	1	Substitution - Nonsense(1)	autonomic_ganglia(1)	c.625_626insT						.																																			SO:0001589	frameshift_variant	4703	exon9			.	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.625dupT	2.37:g.152579989_152579989dupA	ENSP00000172853:p.Glu209fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	120	67	NM_004543	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Nonsense_Mutation	INS	ENST00000172853.10	37																																																																																				.		0.391	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152579989	-	A	152579988	7	5	34	1	0	1	1	0	0	0	0	0	10328	835	29	0	25757	0	NEB	2	152579988	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10	3884224	152579988	90619385	12	2951											
PKP4	8502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	159459582	159459582	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttctttctttttctttagCtcaactgagaagtcatttcc	7	21	4	9	0	5	1	2	1	3	1	6	2	6	1	1	0	2	1	1	0	3	8			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:159459582C>A	ENST00000389759.3	+	4	358	c.246C>A	c.(244-246)agC>agA	p.S82R	PKP4_ENST00000389757.3_Splice_Site_p.S82R	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	82					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TTTTCTTTAGCTCAACTGAGA	0.259										HNSCC(62;0.18)																											p.S82R		.											.	PKP4-97	0			c.C246A						.						39	47	45					2																	159459582		2180	4267	6447	SO:0001630	splice_region_variant	8502	exon4			CTTTAGCTCAACT	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.246-1C>A	2.37:g.159459582C>A		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	104	23	NM_001005476	0	0	0	0	0	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	37	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754453	0.49362	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.79653	-1.28;-1.29	5.48	5.48	0.80851	.	0.095284	0.64402	D	0.000001	T	0.75258	0.3825	L	0.59436	1.845	0.80722	D	1	B;P	0.42456	0.339;0.78	B;B	0.34779	0.189;0.18	T	0.76046	-0.3102	9	.	.	.	.	15.2074	0.73190	0.0:1.0:0.0:0.0	.	82;82	Q99569-2;Q99569	.;PKP4_HUMAN	R	82	ENSP00000374407:S82R;ENSP00000374409:S82R	.	S	+	3	2	PKP4	159167828	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	2.706000	0.47135	2.745000	0.94114	0.484000	0.47621	AGC	.		0.259	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		Missense_Mutation	A	159459582	C	A	159459582	5	1	34	1	0	0	0	0	0	0	1	0	12013	811	28	4	256	4	PKP4	2	159459582	Splice_Site	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	6879594	159459582	83739791	13	2952											
GPR155	151556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	175331330	175331330	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtttatatttcttactcAaaagaagaatagccagagac	15	12	7	7	0	2	3	1	0	1	3	2	4	2	3	1	0	2	2	1	0	8	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:175331330A>G	ENST00000392552.2	-	6	1446	c.1208T>C	c.(1207-1209)tTg>tCg	p.L403S	GPR155_ENST00000295500.4_Missense_Mutation_p.L403S|GPR155_ENST00000392551.2_Missense_Mutation_p.L403S	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	403					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						TTTCTTACTCAAAAGAAGAAT	0.274																																					p.L403S		.											.	GPR155-91	0			c.T1208C						.						78	87	84					2																	175331330		2202	4287	6489	SO:0001583	missense	151556	exon7			TTACTCAAAAGAA	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1208T>C	2.37:g.175331330A>G	ENSP00000376335:p.Leu403Ser	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	150	47	NM_001033045	0	0	4	5	1	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	37	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.485820	0.84854	.	.	ENSG00000163328	ENST00000392552;ENST00000392551;ENST00000295500	T;T;T	0.52983	0.64;0.64;0.64	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.67496	0.2899	M	0.71581	2.175	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	T	0.66881	-0.5811	10	0.38643	T	0.18	-8.6419	16.0125	0.80411	1.0:0.0:0.0:0.0	.	403	Q7Z3F1	GP155_HUMAN	S	403	ENSP00000376335:L403S;ENSP00000376334:L403S;ENSP00000295500:L403S	ENSP00000295500:L403S	L	-	2	0	GPR155	175039576	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.737000	0.91562	2.178000	0.69098	0.528000	0.53228	TTG	.		0.274	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		G	175331330	A	G	175331330	3	3	34	1	0	0	0	0	1	0	0	0	6680	131	5	3	1448	3	GPR155	2	175331330	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	15871748	175331330	67868043	14	2953											
NBEAL1	65065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	203972839	203972839	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccttttctttcagtgcttGgttttgcttagaccaggatc	5	18	9	9	0	2	1	1	0	1	1	3	2	2	2	2	2	3	3	2	2	1	7			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:203972839G>A	ENST00000449802.1	+	13	2123	c.1790G>A	c.(1789-1791)tGg>tAg	p.W597*		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	597										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TTCAGTGCTTGGTTTTGCTTA	0.408																																					p.W597X		.											.	NBEAL1-92	0			c.G1790A						.						60	50	53					2																	203972839		692	1591	2283	SO:0001587	stop_gained	65065	exon13			GTGCTTGGTTTTG	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.1790G>A	2.37:g.203972839G>A	ENSP00000399903:p.Trp597*	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	121	71	NM_001114132	0	0	0	1	1	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Nonsense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	41	8.993174	0.99029	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1076	0.93303	0.0:0.0:1.0:0.0	.	.	.	.	X	597	.	ENSP00000344985:W597X	W	+	2	0	NBEAL1	203681084	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.500000	0.84329	0.557000	0.71058	TGG	.		0.408	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			A	203972839	G	A	203972839	4	1	34	1	0	0	0	0	0	1	0	0	10213	1357	47	2	1836	2	NBEAL1	2	203972839	Nonsense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	28641509	203972839	39226534	15	2954											
C2orf62	375307	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219222408	219222408	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgcctcttcgtgcatgcCtctagccgaggcttcttgga	5	13	10	13	2	3	0	0	0	3	0	4	2	3	1	3	2	5	2	3	2	2	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:219222408C>T	ENST00000289388.3	+	3	299	c.270C>T	c.(268-270)gcC>gcT	p.A90A	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		90					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCGTGCATGCCTCTAGCCGAG	0.567																																					p.A90A		.											.	C2orf62-68	0			c.C270T						.						75	72	73					2																	219222408		2203	4300	6503	SO:0001819	synonymous_variant	375307	exon3			GCATGCCTCTAGC																												ENST00000289388.3:c.270C>T	2.37:g.219222408C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	73	37	NM_198559	0	0	11	45	34		Silent	SNP	ENST00000289388.3	37	CCDS2414.1																																																																																			.		0.567	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219222408	C	T	219222408	2	4	34	1	0	0	0	0	0	0	0	1	2187	668	24	2		2	C2orf62	2	219222408	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	15249569	219222408	23976965	16	2955											
LAMB2	3913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49161312	49161312	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgtctgttgcaactcctGcgcccgctgctctaggcgct	4	10	10	17	4	2	0	0	0	2	0	3	0	3	0	3	1	4	5	3	1	2	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr3:49161312G>C	ENST00000418109.1	-	25	3810	c.3646C>G	c.(3646-3648)Cag>Gag	p.Q1216E	USP19_ENST00000398888.2_5'Flank|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.Q1216E|USP19_ENST00000488993.1_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1216	Domain II.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGCAACTCCTGCGCCCGCTGC	0.612																																					p.Q1216E		.											.	LAMB2-93	0			c.C3646G						.						42	43	42					3																	49161312		2203	4300	6503	SO:0001583	missense	3913	exon24			ACTCCTGCGCCCG		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.3646C>G	3.37:g.49161312G>C	ENSP00000388325:p.Gln1216Glu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	84	57	NM_002292	0	0	102	300	198	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	0.910	-0.719263	0.03182	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34072	1.38;1.38	5.84	2.97	0.34412	.	0.513188	0.21549	N	0.072764	T	0.27933	0.0688	L	0.44542	1.39	0.21675	N	0.999593	B	0.17465	0.022	B	0.14023	0.01	T	0.26087	-1.0113	10	0.07175	T	0.84	.	14.3514	0.66705	0.0:0.0:0.4875:0.5125	.	1216	P55268	LAMB2_HUMAN	E	1216	ENSP00000388325:Q1216E;ENSP00000307156:Q1216E	ENSP00000307156:Q1216E	Q	-	1	0	LAMB2	49136316	0.007000	0.16637	0.323000	0.25347	0.532000	0.34746	0.332000	0.19751	0.326000	0.23384	0.561000	0.74099	CAG	.		0.612	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49161312	G	C	49161312	3	2	34	1	0	0	0	0	1	0	0	0	8632	1328	46	4	1786	4	LAMB2	3	49161312	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		49161312	148861118	17	2956											
MST1	327	broad.mit.edu	37	chr3	49723112	49723112	+	IGR	DEL	T	T	-																															catggctatccccatctgggTtccggcagaagttctcctcc																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr3:49723112delT	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Frame_Shift_Del_p.N435fs|MST1_ENST00000383728.3_3'UTR	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCCATCTGGGTTCCGGCAGAA	0.587																																					p.N435fs													.	MST1-278	0			c.1304delA						.						43	42	43					3																	49723112		2203	4300	6503	SO:0001628	intergenic_variant	4485	exon11			TCTGGGTTCCGGC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723112delT		Somatic	231	0		WXS	Illumina HiSeq	Phase_I	300	9	NM_020998	0	0	0	0	0	Q9BQ33|Q9P0Y2	Frame_Shift_Del	DEL	ENST00000296456.5	37	CCDS2801.1																																																																																			.		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			-	49723112	T	-	49723112	6	5	34	0	1	1	0	1	0	0	0	0	9915	1725	60	0		0	MST1	3	49723112	IGR	DEL	T	TCGA-AT-A5NU-01A-11D-A28G-10	561800	49723112	148299318	18	2957											
CRYBG3	131544	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	97595925	97595925	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataccacagtaagactagacAaaagaatgtctcttactgca	17	9	6	9	0	1	3	0	0	1	3	2	3	1	3	1	0	3	2	1	0	7	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr3:97595925A>T	ENST00000182096.4	+	1	107	c.43A>T	c.(43-45)Aaa>Taa	p.K15*		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	1963							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						AAGACTAGACAAAAGAATGTC	0.393																																					p.K1963X													.	CRYBG3-68	0			c.A5887T						.						61	57	58					3																	97595925		1837	4091	5928	SO:0001587	stop_gained	131544	exon4			CTAGACAAAAGAA			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.43A>T	3.37:g.97595925A>T	ENSP00000182096:p.Lys15*	Somatic	219	2		WXS	Illumina HiSeq	Phase_I	272	154	NM_153605	0	0	0	0	0	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Nonsense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	A	20.8	4.042531	0.75732	.	.	ENSG00000080200	ENST00000182096	.	.	.	5.6	1.79	0.24919	.	4.944570	0.00465	N	0.000108	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.082	0.25237	0.6464:0.2818:0.0718:0.0	.	.	.	.	X	15	.	ENSP00000182096:K15X	K	+	1	0	CRYBG3	99078615	0.001000	0.12720	0.000000	0.03702	0.022000	0.10575	0.754000	0.26390	0.074000	0.16767	-0.321000	0.08615	AAA	.		0.393	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		T	97595925	A	T	97595925	4	4	34	1	0	0	0	0	0	1	0	0	3919	131	5	5	45	5	CRYBG3	3	97595925	Nonsense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	47872813	97595925	100426505	19	2958											
PARP15	165631	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122354765	122354765	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaagcacatgtacgttgtgCgagtacttactggagtcttc	10	12	11	8	2	1	0	0	0	1	0	2	3	1	1	0	1	5	4	0	1	4	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr3:122354765C>T	ENST00000464300.2	+	12	1921	c.1855C>T	c.(1855-1857)Cga>Tga	p.R619*	PARP15_ENST00000483793.1_Nonsense_Mutation_p.R424*|PARP15_ENST00000310366.4_Nonsense_Mutation_p.R385*|PARP15_ENST00000493645.1_Nonsense_Mutation_p.R316*|PARP15_ENST00000465304.1_3'UTR	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	619	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		GTACGTTGTGCGAGTACTTAC	0.478																																					p.R619X													.	PARP15-524	0			c.C1855T						.						165	138	147					3																	122354765		2203	4300	6503	SO:0001587	stop_gained	165631	exon12			GTTGTGCGAGTAC	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"Poly (ADP-ribose) polymerases"	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1855C>T	3.37:g.122354765C>T	ENSP00000417214:p.Arg619*	Somatic	135	1		WXS	Illumina HiSeq	Phase_I	176	53	NM_001113523	0	0	4	4	0	J3KR47|Q8N1K3	Nonsense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.656138	0.47467	.	.	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	.	.	.	3.99	3.11	0.35812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.2151	0.43164	0.0:0.9003:0.0:0.0996	.	.	.	.	X	619;424;366;385;316	.	ENSP00000308436:R385X	R	+	1	2	PARP15	123837455	0.787000	0.28750	0.005000	0.12908	0.204000	0.24138	1.301000	0.33447	0.892000	0.36259	0.650000	0.86243	CGA	.		0.478	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615		T	122354765	C	T	122354765	4	4	34	1	0	0	0	0	0	1	0	0	11485	760	27	1	1970	1	PARP15	3	122354765	Nonsense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	24758840	122354765	75667665	20	2959											
EHHADH	1962	ucsc.edu	37	chr3	184935956	184935956	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcaaatctgattgcttctTcaaccgggtctgagtttaca	10	13	9	9	1	4	2	1	2	3	0	4	3	4	2	1	1	4	3	1	1	3	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr3:184935956T>A	ENST00000231887.3	-	5	611	c.536A>T	c.(535-537)gAa>gTa	p.E179V	EHHADH_ENST00000456310.1_Missense_Mutation_p.E83V|EHHADH_ENST00000475987.1_5'Flank	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	179	Enoyl-CoA hydratase / isomerase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			GATTGCTTCTTCAACCGGGTC	0.338																																					p.E179V													.	EHHADH-93	0			c.A536T						.						155	155	155					3																	184935956		2203	4300	6503	SO:0001583	missense	1962	exon5			GCTTCTTCAACCG	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.536A>T	3.37:g.184935956T>A	ENSP00000231887:p.Glu179Val	Somatic	28	0		WXS	Illumina HiSeq		39	4	NM_001966	0	0	25	25	0	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.293445	0.80914	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.74002	-0.8;-0.8	5.9	5.9	0.94986	.	0.367187	0.30658	N	0.009146	T	0.79323	0.4426	M	0.77820	2.39	0.80722	D	1	P	0.50369	0.934	P	0.47626	0.552	T	0.81913	-0.0715	10	0.56958	D	0.05	-26.7427	13.8388	0.63426	0.0:0.0:0.0:1.0	.	179	Q08426	ECHP_HUMAN	V	179;179;83	ENSP00000231887:E179V;ENSP00000387746:E83V	ENSP00000231887:E179V	E	-	2	0	EHHADH	186418650	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	4.409000	0.59768	2.260000	0.74910	0.528000	0.53228	GAA	.		0.338	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184935956	T	A	184935956	3	1	34	1	0	0	0	0	1	0	0	0	4993	1783	62	5	1647	5	EHHADH	3	184935956	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	62581191	184935956	13086474	21	2960											
MAEA	10296	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1316285	1316285	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaagtcccggctccggaaGatgaaggtgcacggactccc	11	5	12	13	3	0	2	0	1	0	1	3	4	3	4	3	4	2	2	3	4	4	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr4:1316285G>T	ENST00000303400.4	+	4	636	c.573G>T	c.(571-573)aaG>aaT	p.K191N	MAEA_ENST00000264750.6_Intron|MAEA_ENST00000505839.1_Missense_Mutation_p.K143N|MAEA_ENST00000510794.1_Missense_Mutation_p.K190N|MAEA_ENST00000514708.1_Intron|MAEA_ENST00000452175.2_Missense_Mutation_p.K112N|MAEA_ENST00000505177.2_Missense_Mutation_p.K191N	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	191	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	GGCTCCGGAAGATGAAGGTGC	0.662																																					p.K191N													.	MAEA-91	0			c.G573T						.						53	53	53					4																	1316285		2203	4300	6503	SO:0001583	missense	10296	exon4			CCGGAAGATGAAG	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"GID complex subunit 9, FYV10 homolog (S. cerevisiae)"	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.573G>T	4.37:g.1316285G>T	ENSP00000302830:p.Lys191Asn	Somatic	105	1		WXS	Illumina HiSeq	Phase_I	105	44	NM_001017405	0	0	0	0	0	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	37	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187358	0.78789	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000503653;ENST00000539495;ENST00000502558;ENST00000452175;ENST00000510794;ENST00000505839	T;T;T;T;T;T	0.70282	0.57;-0.07;-0.47;0.51;0.64;0.57	5.94	1.34	0.21922	CTLH, C-terminal LisH motif (2);	0.000000	0.85682	D	0.000000	T	0.82263	0.4999	M	0.85099	2.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.987	D;D;D	0.85130	0.997;0.996;0.95	T	0.80957	-0.1150	10	0.66056	D	0.02	-29.5845	8.5243	0.33296	0.5403:0.0:0.4597:0.0	.	190;191;191	B4DVN3;E7ESC7;Q7L5Y9	.;.;MAEA_HUMAN	N	191;191;191;170;123;112;190;143	ENSP00000302830:K191N;ENSP00000422215:K191N;ENSP00000421644:K191N;ENSP00000426903:K123N;ENSP00000411415:K112N;ENSP00000426807:K190N	ENSP00000302830:K191N	K	+	3	2	MAEA	1306285	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.400000	0.44504	0.317000	0.23160	0.655000	0.94253	AAG	.		0.662	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882		T	1316285	G	T	1316285	3	4	34	1	0	0	0	0	1	0	0	0	9178	933	33	4	587	4	MAEA	4	1316285	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		1316285	189837991	22	2961											
SLIT2	9353	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	20535255	20535255	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatttgaaggagcatctggTgtaaatgaaatacttcttac	13	13	9	6	0	2	2	0	2	2	0	2	3	2	3	0	2	3	3	0	2	6	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr4:20535255T>A	ENST00000504154.1	+	18	2001	c.1749T>A	c.(1747-1749)ggT>ggA	p.G583G	SLIT2_ENST00000273739.5_Silent_p.G587G|SLIT2_ENST00000503823.1_Silent_p.G575G|SLIT2_ENST00000503837.1_Silent_p.G579G	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	583					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GAGCATCTGGTGTAAATGAAA	0.328																																					p.G583G													.	SLIT2-521	0			c.T1749A						.						133	134	134					4																	20535255		2203	4300	6503	SO:0001819	synonymous_variant	9353	exon18			ATCTGGTGTAAAT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"slit (Drosophila) homolog 2"	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1749T>A	4.37:g.20535255T>A		Somatic	352	2		WXS	Illumina HiSeq	Phase_I	300	75	NM_004787	0	0	6	9	3	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			.		0.328	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20535255	T	A	20535255	2	1	34	1	0	0	0	0	0	0	0	1	14772	1683	59	5		5	SLIT2	4	20535255	Silent	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	19218970	20535255	170619021	23	2962											
CCDC149	91050	broad.mit.edu	37	chr4	24810216	24810216	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctcttctgacctcttccAgttctgcagctgcctgttcc	3	16	6	16	0	5	1	0	1	5	0	8	1	7	1	4	0	3	4	4	0	0	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr4:24810216A>C	ENST00000389609.4	-	13	1528	c.1385T>G	c.(1384-1386)cTg>cGg	p.L462R	CCDC149_ENST00000504487.1_Missense_Mutation_p.L462R|CCDC149_ENST00000502801.1_3'UTR|CCDC149_ENST00000428116.2_3'UTR	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	407										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				GACCTCTTCCAGTTCTGCAGC	0.527																																					p.L462R													.	CCDC149-68	0			c.T1385G						.						96	86	89					4																	24810216		692	1591	2283	SO:0001583	missense	91050	exon13			TCTTCCAGTTCTG		CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.1385T>G	4.37:g.24810216A>C	ENSP00000374260:p.Leu462Arg	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	67	3	NM_173463	0	0	11	11	0	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Missense_Mutation	SNP	ENST00000389609.4	37	CCDS33967.2	.	.	.	.	.	.	.	.	.	.	A	16.78	3.218696	0.58560	.	.	ENSG00000181982	ENST00000504487;ENST00000389609;ENST00000382116	.	.	.	5.38	-4.24	0.03777	.	1.262130	0.05375	N	0.536082	T	0.18383	0.0441	N	0.19112	0.55	0.09310	N	0.999999	P;P	0.40875	0.612;0.731	B;B	0.41764	0.143;0.366	T	0.16424	-1.0403	9	0.59425	D	0.04	3.0031	2.4486	0.04512	0.4465:0.1992:0.2548:0.0996	.	407;462	Q6ZUS6;G5EA04	CC149_HUMAN;.	R	462;462;386	.	ENSP00000371550:L386R	L	-	2	0	CCDC149	24419314	0.004000	0.15560	0.000000	0.03702	0.542000	0.35054	0.701000	0.25616	-0.755000	0.04709	-0.441000	0.05720	CTG	.		0.527	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463		C	24810216	A	C	24810216	3	2	34	1	0	0	0	0	1	0	0	0	2789	188	7	5	208	5	CCDC149	4	24810216	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	4274961	24810216	166344060	24	2963											
DSPP	1834	bcgsc.ca	37	chr4	88536614	88536614	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaatagtagtgacaacagcAatagcagtgacagcagcaac	17	6	10	8	0	0	2	0	2	0	0	0	2	0	2	0	0	6	6	0	0	7	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr4:88536614A>G	ENST00000282478.7	+	4	2833	c.2800A>G	c.(2800-2802)Aat>Gat	p.N934D	DSPP_ENST00000399271.1_Missense_Mutation_p.N934D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	934	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacaacagcaatagcagtga	0.478																																					p.N934D													.	DSPP-90	0			c.A2800G						.																																			SO:0001583	missense	1834	exon5			AACAGCAATAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2800A>G	4.37:g.88536614A>G	ENSP00000282478:p.Asn934Asp	Somatic	485	1		WXS	Illumina HiSeq	Phase_1	448	39	NM_014208	0	0	0	0	0	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	0.025	-1.380186	0.01204	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87334	-2.24;-2.24	1.73	0.826	0.18829	.	.	.	.	.	T	0.72374	0.3452	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54091	-0.8345	9	0.09843	T	0.71	.	4.3182	0.11003	0.2182:0.0:0.7818:0.0	.	934	Q9NZW4	DSPP_HUMAN	D	934	ENSP00000382213:N934D;ENSP00000282478:N934D	ENSP00000282478:N934D	N	+	1	0	DSPP	88755638	0.001000	0.12720	0.381000	0.26106	0.004000	0.04260	0.109000	0.15417	0.304000	0.22809	-1.256000	0.01477	AAT	.		0.478	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88536614	A	G	88536614	3	3	34	1	0	0	0	0	1	0	0	0	4793	130	5	3	2814	3	DSPP	4	88536614	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	63726398	88536614	102617662	25	2964											
ANAPC10	10393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	145916549	145916549	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttattgaacgatacatcatGaaatctatagttgtacatct	14	15	5	7	1	3	2	1	2	2	0	3	3	3	2	0	0	3	2	0	0	7	7			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr4:145916549G>T	ENST00000507656.1	-	5	627	c.534C>A	c.(532-534)ttC>ttA	p.F178L	ANAPC10_ENST00000309439.5_Missense_Mutation_p.F178L|ANAPC10_ENST00000451299.2_Missense_Mutation_p.F178L|ANAPC10_ENST00000510270.1_5'UTR	NM_001256706.1	NP_001243635.1	Q9UM13	APC10_HUMAN	anaphase promoting complex subunit 10	178	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(180;0.151)					GATACATCATGAAATCTATAG	0.303																																					p.F189L		.											.	ANAPC10-650	0			c.C567A						.						119	115	116					4																	145916549		1815	4079	5894	SO:0001583	missense	10393	exon7			CATCATGAAATCT	AF132794	CCDS43273.1	4q31	2011-06-15			ENSG00000164162	ENSG00000164162		"Anaphase promoting complex subunits"	24077	protein-coding gene	gene with protein product		613745				10318877, 11230166	Standard	NM_001256706		Approved	APC10, DOC1, DKFZP564L0562	uc031shk.1	Q9UM13	OTTHUMG00000161477	ENST00000507656.1:c.534C>A	4.37:g.145916549G>T	ENSP00000423995:p.Phe178Leu	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	51	27	NM_001256709	0	0	6	27	21	D3DNZ7|Q2V500|Q9UG51|Q9Y5R0	Missense_Mutation	SNP	ENST00000507656.1	37	CCDS43273.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607532	0.46527	.	.	ENSG00000164162	ENST00000507656;ENST00000309439;ENST00000451299	T;T;T	0.72615	-0.67;-0.67;-0.67	5.82	3.2	0.36748	Anaphase-promoting complex, subunit 10/DOC domain (2);	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	L	0.57536	1.79	0.80722	D	1	B	0.09022	0.002	B	0.20384	0.029	T	0.51687	-0.8674	10	0.19147	T	0.46	-9.7039	8.8754	0.35343	0.2784:0.0:0.7216:0.0	.	178	Q9UM13	APC10_HUMAN	L	178	ENSP00000423995:F178L;ENSP00000310071:F178L;ENSP00000403891:F178L	ENSP00000310071:F178L	F	-	3	2	ANAPC10	146135999	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.820000	0.48057	0.400000	0.25396	0.484000	0.47621	TTC	.		0.303	ANAPC10-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365090.1	NM_014885		T	145916549	G	T	145916549	3	4	34	1	0	0	0	0	1	0	0	0	599	1281	45	4	27	4	ANAPC10	4	145916549	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	57379935	145916549	45237727	26	2965											
ADAMTS12	81792	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	33658354	33658354	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcttcattgatgttacaActgcggtgaggctgacacat	11	12	10	8	1	2	3	1	3	1	0	2	4	2	3	0	2	3	2	0	2	3	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:33658354A>G	ENST00000504830.1	-	7	1460	c.1125T>C	c.(1123-1125)agT>agC	p.S375S	ADAMTS12_ENST00000352040.3_Silent_p.S375S|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	375	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TGATGTTACAACTGCGGTGAG	0.507										HNSCC(64;0.19)																											p.S375S		.											.	ADAMTS12-232	0			c.T1125C						.						145	145	145					5																	33658354		2203	4300	6503	SO:0001819	synonymous_variant	81792	exon7			GTTACAACTGCGG	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1125T>C	5.37:g.33658354A>G		Somatic	196	0		WXS	Illumina HiSeq	Phase_I	169	10	NM_030955	0	0	0	0	0	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																			.		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		G	33658354	A	G	33658354	2	3	34	1	0	0	0	0	0	0	0	1	257	40	2	3		3	ADAMTS12	5	33658354	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		33658354	147256906	27	2966											
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	90281309	90281309	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatctatcatcagagcatgtCacagatctatggactcattc	13	12	6	10	0	6	2	4	0	2	2	7	3	6	3	0	1	1	1	0	1	3	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:90281309C>T	ENST00000405460.2	+	85	18218	c.18122C>T	c.(18121-18123)tCa>tTa	p.S6041L	GPR98_ENST00000425867.2_Missense_Mutation_p.S1702L	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	6041					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CAGAGCATGTCACAGATCTAT	0.433																																					p.S6041L		.											.	GPR98-103	0			c.C18122T						.						181	166	171					5																	90281309		1920	4145	6065	SO:0001583	missense	84059	exon85			GCATGTCACAGAT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.18122C>T	5.37:g.90281309C>T	ENSP00000384582:p.Ser6041Leu	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	157	54	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352252	0.41700	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.29917	1.61;1.55	5.7	5.7	0.88788	GPCR, family 2-like (1);	0.379457	0.28989	N	0.013487	T	0.22399	0.0540	N	0.14661	0.345	0.22835	N	0.998674	B;B;B	0.24317	0.101;0.042;0.082	B;B;B	0.25506	0.061;0.061;0.036	T	0.10042	-1.0647	9	.	.	.	.	19.8221	0.96602	0.0:1.0:0.0:0.0	.	1702;6041;1702	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	L	6041;6041;1702	ENSP00000384582:S6041L;ENSP00000392618:S1702L	.	S	+	2	0	GPR98	90317065	0.993000	0.37304	0.750000	0.31169	0.347000	0.29111	4.029000	0.57253	2.690000	0.91761	0.557000	0.71058	TCA	.		0.433	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90281309	C	T	90281309	3	4	34	1	0	0	0	0	1	0	0	0	6742	838	29	2	18460	2	GPR98	5	90281309	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	56622955	90281309	90633951	28	2967											
PHF15	23338	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	133895661	133895661	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactggctggagctcatcaaCtcggagcttaaggagatggg	10	9	14	8	1	2	1	2	0	0	1	3	4	2	3	0	5	4	3	0	5	3	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:133895661C>A	ENST00000402835.1	+	5	708	c.453C>A	c.(451-453)aaC>aaA	p.N151K	PHF15_ENST00000395003.1_Missense_Mutation_p.N151K|PHF15_ENST00000361895.2_Missense_Mutation_p.N151K|PHF15_ENST00000282605.4_Missense_Mutation_p.N151K																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCTCATCAACTCGGAGCTTA	0.592																																					p.N151K													.	PHF15-90	0			c.C453A						.						77	67	70					5																	133895661		2203	4300	6503	SO:0001583	missense	23338	exon5			CATCAACTCGGAG																												ENST00000402835.1:c.453C>A	5.37:g.133895661C>A	ENSP00000384671:p.Asn151Lys	Somatic	202	1		WXS	Illumina HiSeq	Phase_I	130	58	NM_015288	0	0	9	16	7		Missense_Mutation	SNP	ENST00000402835.1	37		.	.	.	.	.	.	.	.	.	.	C	21.6	4.172913	0.78452	.	.	ENSG00000043143	ENST00000413974;ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000402835;ENST00000395003;ENST00000431355	T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31	5.67	3.89	0.44902	Enhancer of polycomb-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77391	0.4123	M	0.89095	3.005	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.80589	-0.1315	9	.	.	.	.	10.9336	0.47233	0.0:0.8496:0.0:0.1504	.	151;151;151;151;167	Q9NQC1;B5MBX1;D3DQA3;Q9NQC1-3;B3KPL2	JADE2_HUMAN;.;.;.;.	K	151;167;151;151;151;151;151;151	ENSP00000282605:N151K;ENSP00000354425:N151K;ENSP00000384671:N151K;ENSP00000378451:N151K;ENSP00000406189:N151K	.	N	+	3	2	PHF15	133923560	0.923000	0.31300	0.992000	0.48379	0.902000	0.53008	1.927000	0.40094	1.413000	0.46997	0.561000	0.74099	AAC	.		0.592	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			A	133895661	C	A	133895661	3	1	34	1	0	0	0	0	1	0	0	0	11852	564	20	4	467	4	PHF15	5	133895661	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	43614352	133895661	47019599	29	2968											
TRPC7	57113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	135561911	135561911	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagacagccagagttttgcTcgggcgaacttccattccac	10	10	9	12	2	0	2	0	0	0	2	3	3	2	2	3	1	3	2	3	1	2	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:135561911T>A	ENST00000513104.1	-	9	2355	c.2073A>T	c.(2071-2073)cgA>cgT	p.R691R	TRPC7_ENST00000355180.3_Silent_p.R630R|TRPC7_ENST00000426057.2_Silent_p.R575R	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	691					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGAGTTTTGCTCGGGCGAACT	0.443																																					p.R691R		.											.	.	0			c.A2073T						.						37	36	36					5																	135561911		1848	3950	5798	SO:0001819	synonymous_variant	57113	exon9			TTTTGCTCGGGCG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.2073A>T	5.37:g.135561911T>A		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	96	47	NM_020389	0	0	1	1	0	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	37	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	T	10.27	1.303877	0.23736	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	4.99	-2.08	0.07254	.	.	.	.	.	T	0.38161	0.1030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28073	-1.0055	4	.	.	.	-6.643	0.5481	0.00657	0.2789:0.2612:0.1187:0.3412	.	.	.	.	C	575;630;636	.	.	S	-	1	0	TRPC7	135589810	0.029000	0.19370	0.942000	0.38095	0.996000	0.88848	-0.795000	0.04580	-0.526000	0.06383	0.482000	0.46254	AGC	.		0.443	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135561911	T	A	135561911	2	1	34	1	0	0	0	0	0	0	0	1	16617	1538	54	5		5	TRPC7	5	135561911	Silent	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	1666250	135561911	45353349	30	2969											
HSPA9	3313	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	137903216	137903216	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattaatcacccgaagcacaTtcagtccagatatctggcca	13	9	6	13	1	3	1	2	0	1	1	4	2	4	1	3	1	1	1	3	1	3	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:137903216T>C	ENST00000297185.3	-	7	769	c.644A>G	c.(643-645)aAt>aGt	p.N215S	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	215					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCGAAGCACATTCAGTCCAGA	0.423																																					p.N215S		.											.	HSPA9-226	0			c.A644G						.						96	97	96					5																	137903216		2203	4300	6503	SO:0001583	missense	3313	exon7			AGCACATTCAGTC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.644A>G	5.37:g.137903216T>C	ENSP00000297185:p.Asn215Ser	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	69	7	NM_004134	0	0	149	154	5	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	37	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.699341	0.68501	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01203	5.18	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.04952	0.0133	H	0.95328	3.655	0.80722	D	1	B;B	0.24651	0.002;0.108	B;B	0.25884	0.006;0.064	T	0.01330	-1.1383	10	0.66056	D	0.02	-21.9951	15.0791	0.72099	0.0:0.0:0.0:1.0	.	146;215	B7Z1V7;P38646	.;GRP75_HUMAN	S	215;168;201	ENSP00000297185:N215S	ENSP00000297185:N215S	N	-	2	0	HSPA9	137931115	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.250000	0.72435	2.095000	0.63458	0.533000	0.62120	AAT	.		0.423	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		C	137903216	T	C	137903216	3	2	34	1	0	0	0	0	1	0	0	0	7438	1493	52	3	1439	3	HSPA9	5	137903216	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	2341305	137903216	43012044	31	2970											
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140176265	140176265	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcgcctagggctggcacCgctgctggcgcagtgagtga	5	8	17	11	3	0	2	0	2	0	0	0	2	0	2	2	4	1	5	2	4	1	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:140176265C>A	ENST00000526136.1	+	1	1716	c.1716C>A	c.(1714-1716)acC>acA	p.T572T	PCDHA2_ENST00000520672.2_Silent_p.T572T|PCDHA2_ENST00000378132.1_Silent_p.T572T|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	572					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCTGGCACCGCTGCTGGCG	0.682																																					p.T572T		.											.	PCDHA2-94	0			c.C1716A						.						97	92	93					5																	140176265		2203	4298	6501	SO:0001819	synonymous_variant	56146	exon1			TGGCACCGCTGCT	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"Cadherins / Protocadherins : Clustered"	8668	other	complex locus constituent	"KIAA0345-like 12"	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1716C>A	5.37:g.140176265C>A		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	177	13	NM_031495	0	0	2	3	1	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	CCDS54914.1																																																																																			.		0.682	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		A	140176265	C	A	140176265	2	1	34	1	0	0	0	0	0	0	0	1	11550	639	23	4		4	PCDHA2	5	140176265	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	2273049	140176265	40738995	32	2971											
DIAPH1	1729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140953451	140953451	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gccaacaccctcaggcaaagGagggggtggagggatggtag	11	4	18	8	0	1	0	1	0	0	0	1	3	1	3	2	7	1	2	2	7	3	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:140953451G>T	ENST00000398557.4	-	16	2106	c.1966C>A	c.(1966-1968)Cct>Act	p.P656T	DIAPH1_ENST00000389057.5_Missense_Mutation_p.P647T|DIAPH1_ENST00000520569.1_Missense_Mutation_p.P602T|DIAPH1_ENST00000398562.2_Missense_Mutation_p.P635T|DIAPH1_ENST00000389054.3_Missense_Mutation_p.P656T|DIAPH1_ENST00000398566.3_Missense_Mutation_p.P647T|DIAPH1_ENST00000253811.6_Missense_Mutation_p.P656T|DIAPH1_ENST00000518047.1_Missense_Mutation_p.P647T	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	656	FH1.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGGCAAAGGAGGGGGTGGA	0.592																																					p.P656T		.											.	DIAPH1-91	0			c.C1966A						.						9	9	9					5																	140953451		1969	4113	6082	SO:0001583	missense	1729	exon16			GCAAAGGAGGGGG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1966C>A	5.37:g.140953451G>T	ENSP00000381565:p.Pro656Thr	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	54	25	NM_005219	0	0	8	15	7	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	37	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	g	13.06	2.124083	0.37533	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047;ENST00000546094	T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.13;-0.15;-0.15;-0.15;-0.15;-0.15	4.73	4.73	0.59995	Formin Homology 1 (1);	0.242758	0.33875	N	0.004470	T	0.70430	0.3223	M	0.85373	2.75	0.48511	D	0.999665	P;P;P	0.43938	0.822;0.645;0.645	P;B;B	0.44477	0.451;0.41;0.41	T	0.73780	-0.3875	10	0.36615	T	0.2	.	16.9924	0.86357	0.0:0.0:1.0:0.0	.	602;647;656	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	T	656;602;635;647;647;656;656;647;95	ENSP00000373706:P656T;ENSP00000429282:P602T;ENSP00000381570:P635T;ENSP00000373709:P647T;ENSP00000381572:P647T;ENSP00000381565:P656T;ENSP00000253811:P656T;ENSP00000428268:P647T	ENSP00000253811:P656T	P	-	1	0	DIAPH1	140933635	0.998000	0.40836	1.000000	0.80357	0.566000	0.35808	3.542000	0.53625	2.629000	0.89072	0.472000	0.43445	CCT	.		0.592	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		T	140953451	G	T	140953451	3	4	34	1	0	0	0	0	1	0	0	0	4529	1174	41	4	1904	4	DIAPH1	5	140953451	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	777186	140953451	39961809	33	2972											
PCYOX1L	78991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	148747898	148747898	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccggcgaaagcagccccAggaggcagctgtttggcgag	8	6	15	12	3	0	0	0	0	0	0	1	3	1	1	3	4	3	4	3	4	1	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:148747898A>T	ENST00000274569.4	+	6	1228	c.1166A>T	c.(1165-1167)cAg>cTg	p.Q389L	PCYOX1L_ENST00000514349.1_Missense_Mutation_p.Q299L	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	389					prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)			breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGCAGCCCCAGGAGGCAGCT	0.557											OREG0016912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q389L	Ovarian(62;1136 1477 27277 27495)	.											.	PCYOX1L-91	0			c.A1166T						.						92	99	97					5																	148747898		2203	4300	6503	SO:0001583	missense	78991	exon6			AGCCCCAGGAGGC		CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.1166A>T	5.37:g.148747898A>T	ENSP00000274569:p.Gln389Leu	Somatic	125	0	1719	WXS	Illumina HiSeq	Phase_I	107	42	NM_024028	0	0	15	30	15	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	37	CCDS4296.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.122001	0.56613	.	.	ENSG00000145882	ENST00000274569;ENST00000514349	T;T	0.15718	2.4;2.4	5.51	5.51	0.81932	Prenylcysteine lyase (1);	0.000000	0.85682	D	0.000000	T	0.39759	0.1090	M	0.66939	2.045	0.80722	D	1	D;B;D	0.69078	0.997;0.216;0.993	D;B;P	0.80764	0.994;0.09;0.874	T	0.08994	-1.0695	10	0.32370	T	0.25	-22.8691	15.6328	0.76926	1.0:0.0:0.0:0.0	.	271;299;389	B3KXF9;E7EVZ5;Q8NBM8	.;.;PCYXL_HUMAN	L	389;299	ENSP00000274569:Q389L;ENSP00000428512:Q299L	ENSP00000274569:Q389L	Q	+	2	0	PCYOX1L	148728091	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	6.075000	0.71261	2.084000	0.62774	0.459000	0.35465	CAG	.		0.557	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028		T	148747898	A	T	148747898	3	4	34	1	0	0	0	0	1	0	0	0	11635	188	7	5	1188	5	PCYOX1L	5	148747898	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	7794447	148747898	32167362	34	2973											
RARS	5917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	167937680	167937680	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacaagttgaaggaaaaaGaaagagacaaggtaattcaa	21	6	11	3	0	1	3	1	1	0	2	1	6	1	5	0	3	0	2	0	3	8	3	rs148161788		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:167937680G>T	ENST00000231572.3	+	12	1495	c.1441G>T	c.(1441-1443)Gaa>Taa	p.E481*	RARS_ENST00000538719.1_Nonsense_Mutation_p.E275*	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	481					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.E481K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GAAGGAAAAAGAAAGAGACAA	0.373																																					p.E481X		.											.	RARS-93	1	Substitution - Missense(1)	skin(1)	c.G1441T						.						65	65	65					5																	167937680		2203	4300	6503	SO:0001587	stop_gained	5917	exon12			GAAAAAGAAAGAG	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1441G>T	5.37:g.167937680G>T	ENSP00000231572:p.Glu481*	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	128	51	NM_002887	0	0	0	0	0	B2RBS9|Q53GY4|Q9BWA1	Nonsense_Mutation	SNP	ENST00000231572.3	37	CCDS4367.1	.	.	.	.	.	.	.	.	.	.	G	38	6.721281	0.97788	.	.	ENSG00000113643	ENST00000231572;ENST00000538719	.	.	.	4.99	4.12	0.48240	.	0.150792	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-22.9725	15.7934	0.78384	0.0:0.1366:0.8634:0.0	.	.	.	.	X	481;275	.	ENSP00000231572:E481X	E	+	1	0	RARS	167870258	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.498000	0.81546	1.218000	0.43458	-0.150000	0.13652	GAA	.		0.373	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		T	167937680	G	T	167937680	4	4	34	1	0	0	0	0	0	1	0	0	13090	943	33	4	1487	4	RARS	5	167937680	Nonsense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	19189782	167937680	12977580	35	2974											
DDX41	51428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176943307	176943307	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttcagccttctctttaaGgtgctggtgctgatccagga	7	13	10	11	0	2	1	1	1	1	0	4	2	3	2	3	3	3	2	3	3	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:176943307G>C	ENST00000507955.1	-	3	803	c.280C>G	c.(280-282)Ctt>Gtt	p.L94V	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	94					apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TTCTCTTTAAGGTGCTGGTGC	0.582																																					p.L94V		.											.	DDX41-226	0			c.C280G						.						161	161	161					5																	176943307		2203	4300	6503	SO:0001583	missense	51428	exon3			CTTTAAGGTGCTG	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"DEAD-boxes"	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.280C>G	5.37:g.176943307G>C	ENSP00000422753:p.Leu94Val	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	84	36	NM_016222	0	0	75	147	72	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	37	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008160	0.75046	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.29142	1.58;1.59	5.38	4.5	0.54988	.	0.000000	0.64402	D	0.000003	T	0.48150	0.1484	L	0.56340	1.77	0.58432	D	0.999999	D	0.76494	0.999	D	0.68621	0.959	T	0.37244	-0.9714	10	0.42905	T	0.14	-23.2967	14.3294	0.66545	0.0725:0.0:0.9274:0.0	.	94	Q9UJV9	DDX41_HUMAN	V	112;94	ENSP00000330349:L112V;ENSP00000422753:L94V	ENSP00000330349:L112V	L	-	1	0	DDX41	176875913	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.218000	0.72224	2.513000	0.84729	0.491000	0.48974	CTT	.		0.582	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		C	176943307	G	C	176943307	3	2	34	1	0	0	0	0	1	0	0	0	4367	1000	35	4	1648	4	DDX41	5	176943307	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	9005627	176943307	3971953	36	2975											
DCDC2	51473	hgsc.bcm.edu	37	chr6	24357769	24357769	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttccggattcggtggccAgtccgcggggtgtagatgtt	5	11	16	9	4	0	1	0	0	0	1	3	2	2	2	3	5	1	3	3	5	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:24357769A>T	ENST00000378454.3	-	1	511	c.210T>A	c.(208-210)acT>acA	p.T70T	KAAG1_ENST00000274766.1_5'UTR	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	70	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TTCGGTGGCCAGTCCGCGGGG	0.597																																					p.T70T		.											.	DCDC2-91	0			c.T210A						.						39	38	38					6																	24357769		2203	4299	6502	SO:0001819	synonymous_variant	51473	exon2			GTGGCCAGTCCGC	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.210T>A	6.37:g.24357769A>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_001195610	0	0	88	88	0	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	37	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	A	4.106	0.017843	0.07959	.	.	ENSG00000146038	ENST00000436313	.	.	.	5.56	-4.43	0.03568	.	.	.	.	.	T	0.19248	0.0462	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41179	-0.9523	4	.	.	.	-10.2342	0.669	0.00856	0.2741:0.2931:0.2257:0.2071	.	.	.	.	Q	38	.	.	L	-	2	0	DCDC2	24465748	0.027000	0.19231	0.078000	0.20375	0.442000	0.32017	-0.787000	0.04618	-0.539000	0.06273	-1.491000	0.00971	CTG	.		0.597	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		T	24357769	A	T	24357769	2	4	34	1	0	0	0	0	0	0	0	1	4291	175	7	5		5	DCDC2	6	24357769	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		24357769	146757298	37	2976											
LRFN2	57497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	40399589	40399589	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacaagcacagcccgttccgGggggcttttgggaggctctc	6	8	14	13	2	1	0	0	0	1	0	3	1	2	1	2	5	2	4	2	5	1	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:40399589G>T	ENST00000338305.6	-	2	1806	c.1264C>A	c.(1264-1266)Ccg>Acg	p.P422T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	422	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCCCGTTCCGGGGGGCTTTTG	0.642																																					p.P422T		.											.	LRFN2-93	0			c.C1264A						.						44	48	47					6																	40399589		2203	4300	6503	SO:0001583	missense	57497	exon2			GTTCCGGGGGGCT	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	21226	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 2"	612808	"KIAA1246"	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1264C>A	6.37:g.40399589G>T	ENSP00000345985:p.Pro422Thr	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	56	23	NM_020737	0	0	0	0	0	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	37	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400939	0.25291	.	.	ENSG00000156564	ENST00000338305	T	0.72282	-0.64	5.38	5.38	0.77491	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.50718	0.1632	L	0.50333	1.59	0.80722	D	1	B	0.19445	0.036	B	0.20577	0.03	T	0.51309	-0.8722	10	0.13853	T	0.58	.	16.6167	0.84918	0.0:0.0:1.0:0.0	.	422	Q9ULH4	LRFN2_HUMAN	T	422	ENSP00000345985:P422T	ENSP00000345985:P422T	P	-	1	0	LRFN2	40507567	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	9.578000	0.98200	2.525000	0.85131	0.561000	0.74099	CCG	.		0.642	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40399589	G	T	40399589	3	4	34	1	0	0	0	0	1	0	0	0	8963	1232	43	4	1113	4	LRFN2	6	40399589	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	16041820	40399589	130715478	38	2977											
C6orf167	253714	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	97634560	97634560	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctgacacaattgttgatgCatactcctaaaaagaaataa	17	11	5	8	0	0	3	0	2	0	1	2	3	2	3	2	0	2	2	2	0	7	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:97634560C>T	ENST00000275053.4	-	15	2311	c.2046G>A	c.(2044-2046)atG>atA	p.M682I	MMS22L_ENST00000369251.2_Missense_Mutation_p.M642I	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	682					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ATTGTTGATGCATACTCCTAA	0.353																																					p.M682I													.	MMS22L-92	0			c.G2046A						.						68	61	64					6																	97634560		2203	4300	6503	SO:0001583	missense	253714	exon15			TTGATGCATACTC		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.2046G>A	6.37:g.97634560C>T	ENSP00000275053:p.Met682Ile	Somatic	125	1		WXS	Illumina HiSeq	Phase_I	124	44	NM_198468	0	0	0	0	0	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	C	6.612	0.481341	0.12581	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.27557	1.66;1.66	5.31	2.25	0.28309	.	0.490245	0.21528	N	0.073091	T	0.04048	0.0113	N	0.11427	0.14	0.23371	N	0.997812	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41197	-0.9522	10	0.27082	T	0.32	-3.7566	3.7368	0.08514	0.1899:0.4744:0.2506:0.0851	.	642;682	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	I	682;642	ENSP00000275053:M682I;ENSP00000358254:M642I	ENSP00000275053:M682I	M	-	3	0	MMS22L	97741281	0.994000	0.37717	0.998000	0.56505	0.995000	0.86356	0.280000	0.18790	0.190000	0.20209	0.585000	0.79938	ATG	.		0.353	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		T	97634560	C	T	97634560	3	4	34	1	0	0	0	0	1	0	0	0	2348	710	25	2	1729	2	C6orf167	6	97634560	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	57234971	97634560	73480507	39	2978											
BVES	11149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	105563684	105563684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgcagaggctgagctgatGttccagctttttggctttct	5	16	12	8	0	1	3	0	2	1	1	2	3	2	3	1	2	3	6	1	2	0	4	rs370149373		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:105563684G>A	ENST00000314641.5	-	7	1051	c.835C>T	c.(835-837)Cat>Tat	p.H279Y	BVES_ENST00000336775.5_Missense_Mutation_p.H279Y|BVES_ENST00000446408.2_Missense_Mutation_p.H279Y	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	279					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				CTGAGCTGATGTTCCAGCTTT	0.443																																					p.H279Y		.											.	BVES-90	0			c.C835T						.	G	TYR/HIS,TYR/HIS,TYR/HIS	0,4406		0,0,2203	145	121	129		835,835,835	4.8	1	6		129	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	BVES	NM_001199563.1,NM_007073.4,NM_147147.3	83,83,83	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	279/361,279/361,279/361	105563684	1,13005	2203	4300	6503	SO:0001583	missense	11149	exon7			GCTGATGTTCCAG	AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.835C>T	6.37:g.105563684G>A	ENSP00000313172:p.His279Tyr	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	97	32	NM_001199563	0	0	0	3	3	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	37	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.317534	0.23908	0.0	1.16E-4	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.17213	2.29;2.29;2.29	5.71	4.79	0.61399	.	0.279017	0.39544	N	0.001325	T	0.02688	0.0081	N	0.22421	0.69	0.27859	N	0.940468	P	0.40398	0.716	B	0.30495	0.116	T	0.34104	-0.9842	10	0.02654	T	1	-25.5861	13.3716	0.60717	0.0:0.0:0.7242:0.2758	.	279	Q8NE79	POPD1_HUMAN	Y	279	ENSP00000313172:H279Y;ENSP00000337259:H279Y;ENSP00000397310:H279Y	ENSP00000313172:H279Y	H	-	1	0	BVES	105670377	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	4.940000	0.63533	2.706000	0.92434	0.563000	0.77884	CAT	.		0.443	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		A	105563684	G	A	105563684	3	1	34	1	0	0	0	0	1	0	0	0	1578	1377	48	2	255	2	BVES	6	105563684	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	7929124	105563684	65551383	40	2979											
CITED2	10370	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	139694300	139694309	+	Frame_Shift_Del	DEL	CACACGAAGT	CACACGAAGT	-																															ctctgctgggctgctgtttgCacacgaagtccgtcataaaa																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	CACACGAAGT	CACACGAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:139694300_139694309delCACACGAAGT	ENST00000367651.2	-	2	988_997	c.773_782delACTTCGTGTG	c.(772-783)gacttcgtgtgcfs	p.DFVC258fs	CITED2_ENST00000537332.1_Frame_Shift_Del_p.DFVC258fs|CITED2_ENST00000536159.1_Frame_Shift_Del_p.DFVC258fs	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	258	Asp/Glu-rich (acidic).				adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		CTGCTGTTTGCACACGAAGTCCGTCATAAA	0.49																																					p.263_266del	NSCLC(98;1219 1550 33720 43229 49330)	.											.	CITED2-90	0			c.788_797del						.																																			SO:0001589	frameshift_variant	10370	exon2			.	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.773_782delACTTCGTGTG	6.37:g.139694300_139694309delCACACGAAGT	ENSP00000356623:p.Asp258fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	57	15	NM_001168389	0	0	0	0	0	O95426|Q5VTF4	Frame_Shift_Del	DEL	ENST00000367651.2	37	CCDS5195.1																																																																																			.		0.49	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			-	139694309	CACACGAAGT	-	139694300	7	5	34	1	0	1	0	1	0	0	0	0	3446	710	25	0	34	0	CITED2	6	139694300	Frame_Shift_Del	DEL	CACACGAAGT	TCGA-AT-A5NU-01A-11D-A28G-10	34130616	139694300	31420767	41	2980											
ARPC1B	10095	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	98988630	98988630	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcagtagctgcggctgggtAcatggcgtctgtttctcagc	6	11	14	10	2	2	0	1	0	2	0	3	0	2	0	0	3	5	6	0	3	2	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:98988630A>G	ENST00000451682.1	+	8	924	c.615A>G	c.(613-615)gtA>gtG	p.V205V	ARPC1B_ENST00000252725.5_Silent_p.V205V|PDAP1_ENST00000496335.1_5'Flank			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	205					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			GCGGCTGGGTACATGGCGTCT	0.627																																					p.V205V													.	ARPC1B-90	0			c.A615G						.						39	38	39					7																	98988630		2203	4300	6503	SO:0001819	synonymous_variant	10095	exon6			CTGGGTACATGGC	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.615A>G	7.37:g.98988630A>G		Somatic	93	1		WXS	Illumina HiSeq	Phase_I	98	56	NM_005720	1	1	333	927	592	Q9BU00	Silent	SNP	ENST00000451682.1	37	CCDS5661.1																																																																																			.		0.627	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		G	98988630	A	G	98988630	2	3	34	1	0	0	0	0	0	0	0	1	971	378	14	3		3	ARPC1B	7	98988630	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		98988630	60150033	42	2981											
FBXL13	222235	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	102553614	102553614	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tactgtaagcctttgtctgtGaaccgtctgcaataagccaa	11	12	8	10	1	2	1	0	1	2	0	2	1	2	1	3	0	5	2	3	0	6	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:102553614G>A	ENST00000313221.4	-	11	1353	c.927C>T	c.(925-927)ttC>ttT	p.F309F	FBXL13_ENST00000379305.3_Silent_p.F309F|FBXL13_ENST00000436908.1_Silent_p.F309F|FBXL13_ENST00000379306.3_Silent_p.F309F|FBXL13_ENST00000455112.2_Silent_p.F309F|FBXL13_ENST00000456695.1_Silent_p.F309F|FBXL13_ENST00000379308.3_Silent_p.F309F|LRRC17_ENST00000249377.4_Intron|LRRC17_ENST00000339431.4_Intron|FBXL13_ENST00000393772.2_Silent_p.F309F	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	309										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						CTTTGTCTGTGAACCGTCTGC	0.443																																					p.F309F		.											.	FBXL13-226	0			c.C927T						.						146	131	136					7																	102553614		2203	4300	6503	SO:0001819	synonymous_variant	222235	exon11			GTCTGTGAACCGT	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"F-boxes / Leucine-rich repeats"	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.927C>T	7.37:g.102553614G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	169	38	NM_001111038	0	0	0	3	3	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Silent	SNP	ENST00000313221.4	37	CCDS5726.1																																																																																			.		0.443	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032		A	102553614	G	A	102553614	2	1	34	1	0	0	0	0	0	0	0	1	5728	1281	45	2		2	FBXL13	7	102553614	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	3564984	102553614	56585049	43	2982											
LAMB1	3912	broad.mit.edu;bcgsc.ca	37	chr7	107599767	107599767	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgggtcgcagtcatcggCgtggccattgcactggcagg	6	8	15	12	3	1	0	1	0	0	0	3	0	1	0	1	5	1	3	1	5	0	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:107599767C>G	ENST00000222399.6	-	20	2847	c.2617G>C	c.(2617-2619)Gcc>Ccc	p.A873P	LAMB1_ENST00000393561.1_Missense_Mutation_p.A897P	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	873	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)	p.A873S(1)		NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						CAGTCATCGGCGTGGCCATTG	0.557																																					p.A873P													.	LAMB1-97	1	Substitution - Missense(1)	lung(1)	c.G2617C						.						129	118	122					7																	107599767		2203	4300	6503	SO:0001583	missense	3912	exon20			CATCGGCGTGGCC	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.2617G>C	7.37:g.107599767C>G	ENSP00000222399:p.Ala873Pro	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	227	9	NM_002291	0	0	187	207	20	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.899179	0.72754	.	.	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.62941	-0.01;-0.01	5.55	5.55	0.83447	EGF-like, laminin (3);	.	.	.	.	T	0.80259	0.4590	M	0.76727	2.345	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.95	T	0.81191	-0.1045	9	0.87932	D	0	.	19.6941	0.96016	0.0:1.0:0.0:0.0	.	873;897	P07942;G3XAI2	LAMB1_HUMAN;.	P	897;873	ENSP00000377191:A897P;ENSP00000222399:A873P	ENSP00000222399:A873P	A	-	1	0	LAMB1	107387003	0.877000	0.30153	0.815000	0.32552	0.459000	0.32528	1.734000	0.38166	2.885000	0.99019	0.655000	0.94253	GCC	.		0.557	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		G	107599767	C	G	107599767	3	3	34	1	0	0	0	0	1	0	0	0	8631	768	27	4	2803	4	LAMB1	7	107599767	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	5046153	107599767	51538896	44	2983											
LAMB1	3912	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107605061	107605061	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtggcaaagtagtaaccaGgttccacttcgttgcactga	10	10	12	9	1	0	1	0	1	0	0	2	1	1	1	2	3	2	6	2	3	3	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:107605061G>C	ENST00000222399.6	-	14	1864	c.1634C>G	c.(1633-1635)cCt>cGt	p.P545R	LAMB1_ENST00000393560.1_Missense_Mutation_p.P545R|LAMB1_ENST00000393561.1_Missense_Mutation_p.P569R	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	545					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GTAGTAACCAGGTTCCACTTC	0.567																																					p.P545R		.											.	LAMB1-97	0			c.C1634G						.						173	143	153					7																	107605061		2203	4300	6503	SO:0001583	missense	3912	exon14			TAACCAGGTTCCA	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1634C>G	7.37:g.107605061G>C	ENSP00000222399:p.Pro545Arg	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	202	73	NM_002291	0	0	196	284	88	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614445	0.66672	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.63096	-0.02;-0.02;0.91	4.64	4.64	0.57946	EGF-like, laminin (3);	.	.	.	.	T	0.72606	0.3481	M	0.69463	2.115	0.38209	D	0.940402	B;B;B	0.33777	0.213;0.425;0.321	B;P;B	0.47645	0.229;0.553;0.126	T	0.76737	-0.2849	9	0.49607	T	0.09	.	17.501	0.87732	0.0:0.0:1.0:0.0	.	545;545;569	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	R	569;545;545	ENSP00000377191:P569R;ENSP00000222399:P545R;ENSP00000377190:P545R	ENSP00000222399:P545R	P	-	2	0	LAMB1	107392297	1.000000	0.71417	0.631000	0.29282	0.798000	0.45092	9.435000	0.97529	2.129000	0.65627	0.563000	0.77884	CCT	.		0.567	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		C	107605061	G	C	107605061	3	2	34	1	0	0	0	0	1	0	0	0	8631	1000	35	4	3810	4	LAMB1	7	107605061	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	5294	107605061	51533602	45	2984											
KEL	3792	broad.mit.edu;bcgsc.ca	37	chr7	142640932	142640932	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcggagggaccggacacaGctcaggacagactgcaggaa	12	3	15	11	2	1	1	1	0	0	1	2	6	1	6	1	5	2	3	1	5	1	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:142640932G>T	ENST00000355265.2	-	14	2004	c.1530C>A	c.(1528-1530)agC>agA	p.S510R	KEL_ENST00000479768.2_5'Flank	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	510					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					ACCGGACACAGCTCAGGACAG	0.557																																					p.S510R													.	KEL-93	0			c.C1530A						.						95	78	84					7																	142640932		2203	4300	6503	SO:0001583	missense	3792	exon14			GACACAGCTCAGG	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"CD molecules", "Blood group antigens"	6308	protein-coding gene	gene with protein product		613883	"Kell blood group", "Kell blood group, metalloendopeptidase"			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1530C>A	7.37:g.142640932G>T	ENSP00000347409:p.Ser510Arg	Somatic	207	1		WXS	Illumina HiSeq	Phase_I	201	8	NM_000420	0	0	5	5	0	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624790	0.28889	.	.	ENSG00000197993	ENST00000355265	D	0.81499	-1.5	4.86	0.752	0.18398	.	0.373083	0.27227	N	0.020340	T	0.75664	0.3880	M	0.63843	1.955	0.28877	N	0.894608	D	0.60160	0.987	P	0.50708	0.648	T	0.69026	-0.5254	10	0.06891	T	0.86	-20.2736	6.581	0.22594	0.4159:0.0:0.5841:0.0	.	510	P23276	KELL_HUMAN	R	510	ENSP00000347409:S510R	ENSP00000347409:S510R	S	-	3	2	KEL	142351054	0.793000	0.28825	0.943000	0.38184	0.194000	0.23727	0.091000	0.15046	0.264000	0.21851	-0.122000	0.15005	AGC	.		0.557	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		T	142640932	G	T	142640932	3	4	34	1	0	0	0	0	1	0	0	0	8163	962	34	4	692	4	KEL	7	142640932	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	35035871	142640932	16497731	46	2985											
ASAH1	427	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	17916973	17916973	+	Splice_Site	DEL	T	T	-																															ctaccctgcttagcatcgagTctagatacaaaaggagagat																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr8:17916973delT	ENST00000262097.6	-	12	1229	c.918delA	c.(916-918)gaa>ga	p.E306fs	ASAH1_ENST00000381733.4_Splice_Site_p.E322fs|ASAH1_ENST00000417108.2_Splice_Site_p.E216fs|ASAH1_ENST00000520781.1_Splice_Site_p.E281fs|ASAH1_ENST00000314146.10_Splice_Site_p.E300fs	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	306					cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		TAGCATCGAGTCTAGATACAA	0.398																																					p.E322fs		.											.	ASAH1-90	0			c.966delA						.						185	167	173					8																	17916973		2203	4300	6503	SO:0001630	splice_region_variant	427	exon12			.	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"N-acylsphingosine amidohydrolase (acid ceramidase)"	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.918-1A>-	8.37:g.17916973delT		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	66	25	NM_004315	0	0	0	0	0	E9PDS0|Q6W898|Q96AS2	Frame_Shift_Del	DEL	ENST00000262097.6	37	CCDS6006.1																																																																																			.		0.398	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	Frame_Shift_Del	-	17916973	T	-	17916973	8	5	34	1	0	1	0	1	0	0	1	0	1007	1681	58	0	281	0	ASAH1	8	17916973	Splice_Site	DEL	T	TCGA-AT-A5NU-01A-11D-A28G-10		17916973	128447049	47	2986											
STMN4	81551	broad.mit.edu	37	chr8	27097616	27097616	+	Frame_Shift_Del	DEL	G	G	-																															gttttcctcaatggccttttGgatcacctctctctcatgtt																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr8:27097616delG	ENST00000265770.7	-	5	518	c.382delC	c.(382-384)caafs	p.Q128fs	STMN4_ENST00000519997.1_Frame_Shift_Del_p.Q119fs|STMN4_ENST00000350889.4_Frame_Shift_Del_p.Q155fs|STMN4_ENST00000519614.1_Frame_Shift_Del_p.Q128fs|STMN4_ENST00000522908.1_Frame_Shift_Del_p.Q155fs|STMN4_ENST00000523048.1_Frame_Shift_Del_p.Q155fs			Q9H169	STMN4_HUMAN	stathmin-like 4	128	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	ATGGCCTTTTGGATCACCTCT	0.512																																					p.Q155fs													.	STMN4-154	0			c.463delC						.						220	205	210					8																	27097616		2203	4300	6503	SO:0001589	frameshift_variant	81551	exon6			CCTTTTGGATCAC		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.382delC	8.37:g.27097616delG	ENSP00000265770:p.Gln128fs	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	131	10	NM_030795	0	0	0	0	0	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Frame_Shift_Del	DEL	ENST00000265770.7	37																																																																																				.		0.512	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		-	27097616	G	-	27097616	7	5	34	1	0	1	0	1	0	0	0	0	15343	1357	47	0	195	0	STMN4	8	27097616	Frame_Shift_Del	DEL	G	TCGA-AT-A5NU-01A-11D-A28G-10	9180643	27097616	119266406	48	2987											
CRH	1392	hgsc.bcm.edu	37	chr8	67089641	67089641	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accggcccgcggctcaggagCgccctgcatggcgggcaggg	5	3	18	15	5	1	0	1	0	0	0	1	1	1	1	3	6	2	3	3	6	0	0	rs560106713	byFrequency	TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr8:67089641C>T	ENST00000276571.3	-	2	518	c.72G>A	c.(70-72)gcG>gcA	p.A24A		NM_000756.2	NP_000747.1	P06850	CRF_HUMAN	corticotropin releasing hormone	24					adrenal gland development (GO:0030325)|associative learning (GO:0008306)|cellular response to cocaine (GO:0071314)|cellular response to dexamethasone stimulus (GO:0071549)|diterpenoid metabolic process (GO:0016101)|feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|ferulate metabolic process (GO:0033494)|glucocorticoid biosynthetic process (GO:0006704)|hormone-mediated apoptotic signaling pathway (GO:0008628)|hypothalamus development (GO:0021854)|inflammatory response (GO:0006954)|ion homeostasis (GO:0050801)|learning or memory (GO:0007611)|locomotory exploration behavior (GO:0035641)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|lung development (GO:0030324)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell death (GO:0060548)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gene expression (GO:0010629)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of luteinizing hormone secretion (GO:0033685)|negative regulation of norepinephrine secretion (GO:0010700)|parturition (GO:0007567)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of digestive system process (GO:0060456)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein phosphorylation (GO:0001934)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of serotonin secretion (GO:0014062)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to immobilization stress (GO:0035902)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|varicosity (GO:0043196)	hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|lung(2)|urinary_tract(1)	5		all_cancers(86;2.58e-06)|all_epithelial(80;6.27e-09)|all_lung(136;0.000414)|Lung NSC(129;0.0011)	Epithelial(68;0.0136)|all cancers(69;0.0507)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)		Corticotropin(DB01285)	GGCTCAGGAGCGCCCTGCATG	0.726											OREG0018805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	7	0.00139776	0.0053	0	5008	,	,		11538	0		0	False		,,,				2504	0				p.A24A		.											.	CRH-90	0			c.G72A						.						2	2	2					8																	67089641		1373	3133	4506	SO:0001819	synonymous_variant	1392	exon2			CAGGAGCGCCCTG		CCDS6188.1	8q13	2013-02-25				ENSG00000147571		"Endogenous ligands"	2355	protein-coding gene	gene with protein product	"corticotropin-releasing factor", "corticoliberin"	122560					Standard	NM_000756		Approved	CRF	uc003xvy.2	P06850		ENST00000276571.3:c.72G>A	8.37:g.67089641C>T		Somatic	0	0	1096	WXS	Illumina HiSeq	Phase_I	16	10	NM_000756	0	0	0	0	0	B3KQS4	Silent	SNP	ENST00000276571.3	37	CCDS6188.1																																																																																			.		0.726	CRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378926.1	NM_000756		T	67089641	C	T	67089641	2	4	34	1	0	0	0	0	0	0	0	1	3875	755	27	1		1	CRH	8	67089641	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	39992025	67089641	79274381	49	2988											
FAM83H	286077	broad.mit.edu	37	chr8	144808646	144808646	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacgccgcgggctctcgggTtggccgttctcctgcggcac	3	8	15	15	6	2	1	0	0	2	1	4	1	2	1	3	4	1	4	3	4	0	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr8:144808646T>C	ENST00000388913.3	-	5	3110	c.2985A>G	c.(2983-2985)caA>caG	p.Q995Q		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	995					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GGCTCTCGGGTTGGCCGTTCT	0.697																																					p.Q995Q													.	FAM83H-92	0			c.A2985G						.						10	13	12					8																	144808646		1983	4126	6109	SO:0001819	synonymous_variant	286077	exon5			CTCGGGTTGGCCG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2985A>G	8.37:g.144808646T>C		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	107	4	NM_198488	0	0	55	58	3	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	37	CCDS6410.2																																																																																			.		0.697	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		C	144808646	T	C	144808646	2	2	34	1	0	0	0	0	0	0	0	1	5659	1722	60	3		3	FAM83H	8	144808646	Silent	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	77719005	144808646	1555376	50	2989											
OPTN	10133	hgsc.bcm.edu;bcgsc.ca	37	chr10	13160980	13160981	+	Frame_Shift_Ins	INS	-	-	AAGGG																															agccagctcctgctgtgcctINSaagggaagggaatcagaagg																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:13160980_13160981insAAGGG	ENST00000378748.3	+	8	1081_1082	c.719_720insAAGGG	c.(718-723)ctaaggfs	p.-242fs	OPTN_ENST00000378747.3_Frame_Shift_Ins_p.-242fs|OPTN_ENST00000378752.3_Frame_Shift_Ins_p.-236fs|OPTN_ENST00000378764.2_Frame_Shift_Ins_p.-236fs|OPTN_ENST00000482140.1_3'UTR|OPTN_ENST00000378757.2_Frame_Shift_Ins_p.-242fs|OPTN_ENST00000263036.5_Frame_Shift_Ins_p.-242fs	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin						cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						CTGCTGTGCCTAAGGGAAGGGA	0.431																																					p.L240fs		.											.	OPTN-70	0			c.719_720insAAGGG						.																																			SO:0001589	frameshift_variant	10133	exon7			.	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"glaucoma 1, open angle, E (adult-onset)"	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.725_729dupAAGGG	10.37:g.13160986_13160990dupAAGGG	ENSP00000368022:p.Glu242fs	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	172	39	NM_001008212	0	0	0	0	0	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Frame_Shift_Ins	INS	ENST00000378748.3	37	CCDS7094.1																																																																																			.		0.431	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		AAGGG	13160981	-	AAGGG	13160980	7	5	34	1	0	1	1	0	0	0	0	0	10915	1522	53	0	737	0	OPTN	10	13160980	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10		13160980	122373767	51	2990											
FAM178A	55719	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102675796	102675796	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttcaaaccagcttcaaaaCaaggtatgtacactgttgat	14	12	6	9	0	3	1	2	1	1	0	3	1	3	1	1	1	4	4	1	1	6	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:102675796C>T	ENST00000238961.4	+	2	723	c.181C>T	c.(181-183)Caa>Taa	p.Q61*	FAM178A_ENST00000370271.3_Nonsense_Mutation_p.Q61*|FAM178A_ENST00000370269.3_Nonsense_Mutation_p.Q61*	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	61						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											AGCTTCAAAACAAGGTATGTA	0.333																																					p.Q61X		.											.	.	0			c.C181T						.						145	150	148					10																	102675796		2203	4300	6503	SO:0001587	stop_gained	55719	exon2			TCAAAACAAGGTA	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.181C>T	10.37:g.102675796C>T	ENSP00000238961:p.Gln61*	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	20	NM_001136123	0	0	0	0	0	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Nonsense_Mutation	SNP	ENST00000238961.4	37	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.510828	0.85389	.	.	ENSG00000119906	ENST00000370271;ENST00000238961;ENST00000370269	.	.	.	5.65	5.65	0.86999	.	0.136815	0.34386	N	0.004001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-7.1251	16.8133	0.85726	0.0:1.0:0.0:0.0	.	.	.	.	X	61	.	ENSP00000238961:Q61X	Q	+	1	0	FAM178A	102665786	1.000000	0.71417	1.000000	0.80357	0.448000	0.32197	4.535000	0.60629	2.819000	0.97034	0.650000	0.86243	CAA	.		0.333	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102675796	C	T	102675796	4	4	34	1	0	0	0	0	0	1	0	0	5519	479	17	2	187	2	FAM178A	10	102675796	Nonsense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	89514816	102675796	32858951	52	2991											
FBXL15	79176	broad.mit.edu	37	chr10	104182716	104182717	+	Frame_Shift_Ins	INS	-	-	G																															gtgctgctgcaggatatggcINSgggcttcgcaccttttgtca																								rs145311924		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:104182716_104182717insG	ENST00000224862.3	+	4	2185_2186	c.869_870insG	c.(868-873)gcgggcfs	p.AG290fs	PSD_ENST00000492902.2_5'Flank|CUEDC2_ENST00000465409.1_5'Flank|FBXL15_ENST00000369956.2_Frame_Shift_Ins_p.AG286fs	NM_024326.3	NP_077302.3	Q9H469	FXL15_HUMAN	F-box and leucine-rich repeat protein 15	290					bone mineralization (GO:0030282)|dorsal/ventral pattern formation (GO:0009953)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of BMP signaling pathway (GO:0030513)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)				kidney(1)	1		Colorectal(252;0.207)		Epithelial(162;1.19e-08)|all cancers(201;2.65e-07)		CAGGATATGGCGGGCTTCGCAC	0.649											OREG0020479	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A290fs													.	FBXL15-226	0			c.869_870insG						.																																			SO:0001589	frameshift_variant	79176	exon4			ATATGGCGGGCTT	BC036120	CCDS31273.1	10q24.32	2011-06-09	2004-06-15	2004-06-16	ENSG00000107872	ENSG00000107872		"F-boxes / Leucine-rich repeats"	28155	protein-coding gene	gene with protein product		610287	"F-box only protein 37"	FBXO37			Standard	NM_024326		Approved	MGC11279, Fbl15	uc001kvk.2	Q9H469	OTTHUMG00000018957	ENST00000224862.3:c.872dupG	10.37:g.104182719_104182719dupG	ENSP00000224862:p.Ala290fs	Somatic	53	0	1379	WXS	Illumina HiSeq	Phase_I	104	9	NM_024326	0	0	0	0	0	A1L4J8|B1AKX8|B1AKX9|B1AKY0|B1AKY1|C9JWA4|Q0D2Q3|Q49AL7|Q5JWA5	Frame_Shift_Ins	INS	ENST00000224862.3	37	CCDS31273.1																																																																																			.		0.649	FBXL15-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_370575		G	104182717	-	G	104182716	7	5	34	1	0	1	1	0	0	0	0	0	5730	768	27	0	883	0	FBXL15	10	104182716	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10	1506920	104182716	31352031	53	2992											
TDRD1	56165	broad.mit.edu;bcgsc.ca	37	chr10	115964520	115964520	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaatgttatcccagcagaaGggaattggagcagtgattgt	12	10	12	7	0	0	2	0	1	0	1	1	4	1	4	2	2	2	3	2	2	4	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:115964520G>A	ENST00000369280.1	+	10	1625	c.1165G>A	c.(1165-1167)Ggg>Agg	p.G389R	TDRD1_ENST00000251864.2_Missense_Mutation_p.G389R|TDRD1_ENST00000369282.1_Missense_Mutation_p.G389R|TDRD1_ENST00000422662.1_Missense_Mutation_p.G50R|TDRD1_ENST00000369281.2_Missense_Mutation_p.G389R			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	389					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		CCCAGCAGAAGGGAATTGGAG	0.363																																					p.G389R													.	TDRD1-90	0			c.G1165A						.						85	79	81					10																	115964520		2203	4300	6503	SO:0001583	missense	56165	exon10			GCAGAAGGGAATT	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.1165G>A	10.37:g.115964520G>A	ENSP00000358286:p.Gly389Arg	Somatic	87	2		WXS	Illumina HiSeq	Phase_I	79	36	NM_198795	0	0	0	0	0	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	37		.	.	.	.	.	.	.	.	.	.	G	24.8	4.573519	0.86542	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	T;T;T;T;T	0.24538	2.8;2.76;1.85;2.15;2.81	6.17	6.17	0.99709	.	0.173121	0.50627	D	0.000112	T	0.49406	0.1555	M	0.61703	1.905	0.42236	D	0.991914	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.996;0.997;0.999;0.999;0.989	T	0.14615	-1.0466	10	0.31617	T	0.26	-10.9572	17.7962	0.88572	0.0:0.0:1.0:0.0	.	50;389;389;389;389	Q9BXT4-4;Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	.;TDRD1_HUMAN;.;.;.	R	389;389;389;50;389	ENSP00000358288:G389R;ENSP00000251864:G389R;ENSP00000358287:G389R;ENSP00000402794:G50R;ENSP00000358286:G389R	ENSP00000251864:G389R	G	+	1	0	TDRD1	115954510	1.000000	0.71417	0.977000	0.42913	0.971000	0.66376	4.264000	0.58859	2.941000	0.99782	0.655000	0.94253	GGG	.		0.363	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			A	115964520	G	A	115964520	3	1	34	1	0	0	0	0	1	0	0	0	15762	1000	35	2	1199	2	TDRD1	10	115964520	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	11781804	115964520	19570227	54	2993											
WDR11	55717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	122665493	122665493	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctctcctggttctcctcTctctgggctgcttttttagc	2	17	9	13	0	4	0	0	0	4	0	7	0	4	0	2	3	2	4	2	3	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:122665493T>A	ENST00000263461.6	+	27	3643	c.3397T>A	c.(3397-3399)Tct>Act	p.S1133T	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						GGTTCTCCTCTCTCTGGGCTG	0.512																																					p.S1133T		.											.	WDR11-226	0			c.T3397A						.						117	106	110					10																	122665493		2203	4300	6503	SO:0001583	missense	55717	exon27			CTCCTCTCTCTGG	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3397T>A	10.37:g.122665493T>A	ENSP00000263461:p.Ser1133Thr	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	122	48	NM_018117	0	0	45	111	66	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.158729	0.57368	.	.	ENSG00000120008	ENST00000263461	D	0.91843	-2.92	5.63	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.94069	0.8099	L	0.58669	1.825	0.52501	D	0.999954	P;P;P;P	0.52842	0.956;0.956;0.911;0.682	D;D;P;B	0.65010	0.931;0.931;0.558;0.129	D	0.93073	0.6484	10	0.48119	T	0.1	-11.2569	11.9916	0.53178	0.1299:0.0:0.0:0.8701	.	1133;1133;424;662	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	T	1133	ENSP00000263461:S1133T	ENSP00000263461:S1133T	S	+	1	0	WDR11	122655483	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	5.888000	0.69758	0.923000	0.37045	0.455000	0.32223	TCT	.		0.512	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			A	122665493	T	A	122665493	3	1	34	1	0	0	0	0	1	0	0	0	17306	1551	54	5	3503	5	WDR11	10	122665493	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	6700973	122665493	12869254	55	2994											
OR5T2	219464	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	56000572	56000573	+	Frame_Shift_Del	DEL	AA	AA	-																															acaaacttgaagatatgcatAaagttacagttcatattatg																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:56000572_56000573delAA	ENST00000313264.4	-	1	164_165	c.89_90delTT	c.(88-90)tttfs	p.F30fs		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					AGATATGCATAAAGTTACAGTT	0.351																																					p.30_30del		.											.	OR5T2-70	0			c.89_90del						.																																			SO:0001589	frameshift_variant	219464	exon1			.	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.89_90delTT	11.37:g.56000572_56000573delAA	ENSP00000323688:p.Phe30fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	106	39	NM_001004746	0	0	0	0	0	B9EGX5|Q6IFC8	Frame_Shift_Del	DEL	ENST00000313264.4	37	CCDS31523.1																																																																																			.		0.351	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		-	56000573	AA	-	56000572	7	5	34	1	0	1	0	1	0	0	0	0	11208	359	13	0	988	0	OR5T2	11	56000572	Frame_Shift_Del	DEL	AA	TCGA-AT-A5NU-01A-11D-A28G-10		56000572	79005944	56	2995											
CDC42BPG	55561	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	64603951	64603963	+	Frame_Shift_Del	DEL	CCAGCTGGGGGCC	CCAGCTGGGGGCC	-																															cactgtcctgacctgggctaCcagctgggggcccatccgtc																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	CCAGCTGGGGGCC	CCAGCTGGGGGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:64603951_64603963delCCAGCTGGGGGCC	ENST00000342711.5	-	12	1423_1435	c.1424_1436delGGCCCCCAGCTGG	c.(1423-1437)gggcccccagctggtfs	p.GPPAG475fs		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						ACCTGGGCTACCAGCTGGGGGCCCATCCGTCTG	0.653											OREG0004017	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.475_479del		.											.	CDC42BPG-528	0			c.1424_1436del						.																																			SO:0001589	frameshift_variant	55561	exon12			.	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"Pleckstrin homology (PH) domain containing"	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.1424_1436delGGCCCCCAGCTGG	11.37:g.64603951_64603963delCCAGCTGGGGGCC	ENSP00000345133:p.Gly475fs	Somatic	99	0	1077	WXS	Illumina HiSeq	Phase_I	62	10	NM_017525	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000342711.5	37	CCDS31601.1																																																																																			.		0.653	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		-	64603963	CCAGCTGGGGGCC	-	64603951	7	5	34	1	0	1	0	1	0	0	0	0	3080	507	18	0	3323	0	CDC42BPG	11	64603951	Frame_Shift_Del	DEL	CCAGCTGGGGGCC	TCGA-AT-A5NU-01A-11D-A28G-10	8603379	64603951	70402565	57	2996											
TCIRG1	10312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67817430	67817430	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcctgctcatgccccaggAggaaaacaaggccgggttgc	9	6	13	13	1	1	0	1	0	0	0	1	2	1	2	4	4	5	2	4	4	3	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:67817430A>G	ENST00000265686.3	+	17	2123	c.2015A>G	c.(2014-2016)gAg>gGg	p.E672G	RP11-802E16.3_ENST00000534517.1_RNA|TCIRG1_ENST00000532635.1_Splice_Site_p.E456G|RP11-802E16.3_ENST00000526897.1_RNA|RP11-802E16.3_ENST00000529934.1_RNA	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	672					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						ATGCCCCAGGAGGAAAACAAG	0.637																																					p.E672G		.											.	TCIRG1-227	0			c.A2015G						.						38	39	39					11																	67817430		2199	4292	6491	SO:0001630	splice_region_variant	10312	exon17			CCCAGGAGGAAAA	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"ATPases / V-type"	11647	protein-coding gene	gene with protein product	"T-cell immune response cDNA 7"	604592	"T-cell, immune regulator 1", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.2014-1A>G	11.37:g.67817430A>G		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	72	38	NM_006019	0	0	0	0	0	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	.	.	.	.	.	.	.	.	.	.	A	8.644	0.896745	0.17686	.	.	ENSG00000110719	ENST00000265686;ENST00000532635;ENST00000546315	D;D	0.89123	-1.95;-2.47	4.21	1.83	0.25207	.	1.186560	0.05814	N	0.614544	T	0.78666	0.4319	N	0.17082	0.46	0.45194	D	0.998206	B	0.02656	0.0	B	0.06405	0.002	T	0.64024	-0.6504	10	0.15066	T	0.55	-4.3465	6.3839	0.21550	0.7598:0.0:0.2402:0.0	.	672	Q13488	VPP3_HUMAN	G	672;456;30	ENSP00000265686:E672G;ENSP00000434407:E456G	ENSP00000265686:E672G	E	+	2	0	TCIRG1	67574006	0.009000	0.17119	0.006000	0.13384	0.156000	0.22039	0.207000	0.17395	0.671000	0.31185	0.379000	0.24179	GAG	.		0.637	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	Missense_Mutation	G	67817430	A	G	67817430	5	3	34	1	0	0	0	0	0	0	1	0	15735	318	11	3	2077	3	TCIRG1	11	67817430	Splice_Site	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	3213479	67817430	67189086	58	2997											
NAALAD2	10003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	89868775	89868775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccacttctgtgcgctatcAtcaaagtatacggtggaaac	12	10	9	10	2	3	0	2	0	1	0	3	2	3	1	1	2	3	2	1	2	5	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:89868775A>G	ENST00000534061.1	+	2	361	c.131A>G	c.(130-132)cAt>cGt	p.H44R	NAALAD2_ENST00000525171.1_Missense_Mutation_p.H44R|NAALAD2_ENST00000321955.4_Missense_Mutation_p.H44R|NAALAD2_ENST00000375944.3_Missense_Mutation_p.H44R	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	44					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GTGCGCTATCATCAAAGTATA	0.343																																					p.H44R		.											.	NAALAD2-92	0			c.A131G						.						112	113	112					11																	89868775		2201	4299	6500	SO:0001583	missense	10003	exon2			GCTATCATCAAAG	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.131A>G	11.37:g.89868775A>G	ENSP00000432481:p.His44Arg	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	58	10	NM_005467	0	0	0	0	0	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	37	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	A	7.614	0.675410	0.14841	.	.	ENSG00000077616	ENST00000525497;ENST00000534061;ENST00000321955;ENST00000525171;ENST00000375944	T;T;T;T;T	0.42513	0.97;1.39;1.53;1.01;2.81	5.08	-0.0308	0.13912	.	0.762404	0.12673	N	0.448598	T	0.21674	0.0522	N	0.20986	0.625	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.0;0.003;0.001;0.001;0.0	T	0.18241	-1.0343	9	.	.	.	-1.591	2.7544	0.05289	0.5012:0.285:0.0769:0.1368	.	44;44;44;44;44	Q4KKV4;E9PJV2;Q9Y3Q0;E9PKX5;Q8IUX3	.;.;NALD2_HUMAN;.;.	R	44	ENSP00000431989:H44R;ENSP00000432481:H44R;ENSP00000320083:H44R;ENSP00000435249:H44R;ENSP00000365111:H44R	.	H	+	2	0	NAALAD2	89508423	0.776000	0.28616	0.094000	0.20943	0.701000	0.40568	0.409000	0.21082	-0.159000	0.11021	-0.305000	0.09177	CAT	.		0.343	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		G	89868775	A	G	89868775	3	3	34	1	0	0	0	0	1	0	0	0	10153	217	8	3	137	3	NAALAD2	11	89868775	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	22051345	89868775	45137741	59	2998											
MFSD5	84975	broad.mit.edu	37	chr12	53647798	53647798	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcactggcttgcctagggctCcttgtcctccatgacagtga	6	12	10	13	0	1	2	1	2	0	0	4	2	4	2	4	2	1	2	4	2	1	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr12:53647798C>T	ENST00000329548.4	+	2	1370	c.1179C>T	c.(1177-1179)ctC>ctT	p.L393L	MFSD5_ENST00000534842.1_Silent_p.L500L	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	393					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						GCCTAGGGCTCCTTGTCCTCC	0.542																																					p.L500L													.	MFSD5-93	0			c.C1500T						.						155	135	142					12																	53647798		2203	4300	6503	SO:0001819	synonymous_variant	84975	exon2			AGGGCTCCTTGTC	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.1179C>T	12.37:g.53647798C>T		Somatic	191	1		WXS	Illumina HiSeq	Phase_I	138	7	NM_001170790	0	0	83	83	0	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Silent	SNP	ENST00000329548.4	37	CCDS8851.1																																																																																			.		0.542	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889		T	53647798	C	T	53647798	2	4	34	1	0	0	0	0	0	0	0	1	9559	842	30	2		2	MFSD5	12	53647798	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		53647798	80204097	60	2999											
NT5DC3	51559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	104182695	104182695	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctcattcatctttcggaaaGgcctaacaacagaaatggga	14	10	8	9	1	3	1	2	0	2	1	5	3	3	3	1	3	2	0	1	3	4	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr12:104182695G>C	ENST00000392876.3	-	10	1062	c.1022C>G	c.(1021-1023)cCt>cGt	p.P341R		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	341						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						CTTTCGGAAAGGCCTAACAAC	0.423																																					p.P341R		.											.	NT5DC3-228	0			c.C1022G						.						192	183	186					12																	104182695		2203	4300	6503	SO:0001583	missense	51559	exon10			CGGAAAGGCCTAA	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.1022C>G	12.37:g.104182695G>C	ENSP00000376615:p.Pro341Arg	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	106	46	NM_001031701	0	0	2	2	0	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	37	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625073	0.87560	.	.	ENSG00000111696	ENST00000392876	T	0.26223	1.75	6.07	6.07	0.98685	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.60622	-0.7227	10	0.59425	D	0.04	-12.7708	20.6593	0.99626	0.0:0.0:1.0:0.0	.	341	Q86UY8	NT5D3_HUMAN	R	341	ENSP00000376615:P341R	ENSP00000376615:P341R	P	-	2	0	NT5DC3	102706825	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	9.515000	0.98015	2.885000	0.99019	0.655000	0.94253	CCT	.		0.423	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		C	104182695	G	C	104182695	3	2	34	1	0	0	0	0	1	0	0	0	10718	1000	35	4	644	4	NT5DC3	12	104182695	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	50534897	104182695	29669200	61	3000											
C13orf15	28984	hgsc.bcm.edu	37	chr13	42031876	42031876	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggcgcagggcagccccgcGgccgccgcggccgcaggtga	4	1	19	17	8	0	1	0	1	0	0	0	1	0	1	5	5	1	3	5	5	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr13:42031876G>A	ENST00000379359.3	+	1	182	c.33G>A	c.(31-33)gcG>gcA	p.A11A		NM_014059.2	NP_054778.2	Q9H4X1	RGCC_HUMAN	regulator of cell cycle	11	Ala-rich.				cellular response to hypoxia (GO:0071456)|complement activation (GO:0006956)|fibroblast activation (GO:0072537)|mitotic cell cycle arrest (GO:0071850)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of exit from mitosis (GO:0001100)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mitotic cell cycle phase transition (GO:1901991)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of mitosis (GO:0045840)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stress fiber assembly (GO:0051496)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)										gcagccccgcggccgccgcgg	0.741																																					p.A11A		.											.	.	0			c.G33A						.						1	1	1					13																	42031876		410	1255	1665	SO:0001819	synonymous_variant	28984	exon1			CCCCGCGGCCGCC	AF036549	CCDS41880.1	13q14.11	2012-02-20	2012-02-20	2012-02-20	ENSG00000102760	ENSG00000102760			20369	protein-coding gene	gene with protein product	"response gene to complement 32"	610077	"chromosome 13 open reading frame 15"	C13orf15		17146433, 19158077, 19652095	Standard	NM_014059		Approved	bA157L14.2, RGC-32, RGC32	uc001uyi.2	Q9H4X1	OTTHUMG00000016796	ENST00000379359.3:c.33G>A	13.37:g.42031876G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	25	14	NM_014059	0	0	0	0	0	Q6NZ48|Q9UL69	Silent	SNP	ENST00000379359.3	37	CCDS41880.1																																																																																			.		0.741	RGCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044684.1	NM_014059		A	42031876	G	A	42031876	2	1	34	1	0	0	0	0	0	0	0	1	1722	1103	39	1		1	C13orf15	13	42031876	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		42031876	73138002	62	3001											
NKX2-1	7080	hgsc.bcm.edu	37	chr14	36988288	36988288	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcggcagctcgctcatgttgCccaggttgccgttgcagtag	5	10	14	12	3	1	0	1	0	0	0	2	0	1	0	2	2	4	8	2	2	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr14:36988288C>A	ENST00000518149.1	-	2	880	c.275G>T	c.(274-276)gGc>gTc	p.G92V	NKX2-1_ENST00000498187.2_Missense_Mutation_p.G92V|NKX2-1_ENST00000522719.2_Missense_Mutation_p.G92V|RP11-896J10.3_ENST00000521945.1_RNA|NKX2-1_ENST00000354822.5_Missense_Mutation_p.G122V|NKX2-1-AS1_ENST00000521292.2_RNA			P43699	NKX21_HUMAN	NK2 homeobox 1	92					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|brain development (GO:0007420)|cerebral cortex cell migration (GO:0021795)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|Clara cell differentiation (GO:0060486)|developmental induction (GO:0031128)|endoderm development (GO:0007492)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|forebrain development (GO:0030900)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain neuron fate commitment (GO:0021877)|globus pallidus development (GO:0021759)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|locomotory behavior (GO:0007626)|lung development (GO:0030324)|lung saccule development (GO:0060430)|menarche (GO:0042696)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron migration (GO:0001764)|oligodendrocyte differentiation (GO:0048709)|phospholipid metabolic process (GO:0006644)|pituitary gland development (GO:0021983)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|rhythmic process (GO:0048511)|thyroid gland development (GO:0030878)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G92D(1)		large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	7	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)		GCTCATGTTGCCCAGGTTGCC	0.716			A		NSCLC																																p.G122V		.		Dom	yes		14	14q13	7080	NK2 homeobox 1		E	.	NKX2-1-658	1	Substitution - Missense(1)	skin(1)	c.G365T						.						10	14	13					14																	36988288		2088	4220	6308	SO:0001583	missense	7080	exon2			ATGTTGCCCAGGT		CCDS9659.1, CCDS41945.1	14q13.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000136352	ENSG00000136352		"Homeoboxes / ANTP class : NKL subclass"	11825	protein-coding gene	gene with protein product		600635	"benign chorea", "thyroid transcription factor 1"	NKX2A, BCH, TITF1		1976511	Standard	NM_001079668		Approved	TTF-1, TTF1	uc001wtu.3	P43699	OTTHUMG00000140225	ENST00000518149.1:c.275G>T	14.37:g.36988288C>A	ENSP00000428341:p.Gly92Val	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	26	13	NM_001079668	0	0	0	0	0	D3DSA3|O14954|O14955|Q7KZF6|Q9BRJ8	Missense_Mutation	SNP	ENST00000518149.1	37	CCDS9659.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357912	0.82243	.	.	ENSG00000136352	ENST00000354822;ENST00000498187;ENST00000518149;ENST00000522719	D;D;D;D	0.91521	-2.86;-2.82;-2.82;-2.82	4.7	4.7	0.59300	.	0.056339	0.64402	D	0.000001	D	0.94843	0.8334	M	0.84683	2.71	0.80722	D	1	D;P	0.57257	0.979;0.935	P;P	0.59546	0.859;0.544	D	0.94962	0.8109	10	0.49607	T	0.09	.	16.7821	0.85565	0.0:1.0:0.0:0.0	.	122;92	P43699-3;P43699	.;NKX21_HUMAN	V	122;92;92;92	ENSP00000346879:G122V;ENSP00000429607:G92V;ENSP00000428341:G92V;ENSP00000429519:G92V	ENSP00000346879:G122V	G	-	2	0	NKX2-1	36058039	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.934000	0.75880	2.442000	0.82660	0.455000	0.32223	GGC	.		0.716	NKX2-1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376225.2	NM_003317		A	36988288	C	A	36988288	3	1	34	1	0	0	0	0	1	0	0	0	10475	739	26	4	848	4	NKX2-1	14	36988288	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		36988288	70361252	63	3002											
ARID4A	5926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	58796735	58796735	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttagggcttcagaaagcaAgcatcttcttaaaaactaga	15	11	7	8	0	4	2	1	0	3	2	4	2	4	2	0	1	3	3	0	1	7	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr14:58796735A>C	ENST00000355431.3	+	11	1127	c.754A>C	c.(754-756)Agc>Cgc	p.S252R	ARID4A_ENST00000395168.3_Missense_Mutation_p.S252R|ARID4A_ENST00000348476.3_Missense_Mutation_p.S252R|ARID4A_ENST00000431317.2_Missense_Mutation_p.S252R	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	252					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TCAGAAAGCAAGCATCTTCTT	0.388																																					p.S252R		.											.	ARID4A-231	0			c.A754C						.						97	104	101					14																	58796735		2203	4300	6503	SO:0001583	missense	5926	exon11			AAAGCAAGCATCT	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.754A>C	14.37:g.58796735A>C	ENSP00000347602:p.Ser252Arg	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	151	66	NM_002892	0	0	1	3	2	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284422	0.59867	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000445108;ENST00000431317	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	6.07	4.94	0.65067	RBB1NT (1);	0.208574	0.64402	D	0.000015	T	0.24851	0.0603	L	0.57536	1.79	0.39498	D	0.96815	P;B;P	0.46277	0.875;0.139;0.702	P;B;P	0.52454	0.699;0.394;0.556	T	0.01420	-1.1359	10	0.42905	T	0.14	-12.6657	12.3445	0.55114	0.9343:0.0:0.0657:0.0	.	252;252;252	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	R	252;252;252;215;252	ENSP00000347602:S252R;ENSP00000344556:S252R;ENSP00000378597:S252R;ENSP00000397368:S252R	ENSP00000344556:S252R	S	+	1	0	ARID4A	57866488	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.593000	0.54001	1.112000	0.41740	-0.274000	0.10170	AGC	.		0.388	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58796735	A	C	58796735	3	2	34	1	0	0	0	0	1	0	0	0	919	72	3	5	792	5	ARID4A	14	58796735	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	21808447	58796735	48552805	64	3003											
TTC8	123016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	89338717	89338717	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcagtgcttcaggctggCtctggtcaacaacaacaacc	11	8	8	14	0	4	0	3	0	1	0	4	0	4	0	2	3	5	3	2	3	4	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr14:89338717C>T	ENST00000345383.5	+	12	1322	c.1238C>T	c.(1237-1239)gCt>gTt	p.A413V	TTC8_ENST00000380656.2_Missense_Mutation_p.A423V|TTC8_ENST00000358622.5_Missense_Mutation_p.A225V|TTC8_ENST00000346301.4_Missense_Mutation_p.A383V|TTC8_ENST00000338104.6_Missense_Mutation_p.A439V|TTC8_ENST00000354441.6_Missense_Mutation_p.A158V|TTC8_ENST00000536576.1_Missense_Mutation_p.A184V	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	449					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						TTCAGGCTGGCTCTGGTCAAC	0.532																																					p.A423V		.											.	TTC8-90	0			c.C1268T						.						123	105	111					14																	89338717		2203	4300	6503	SO:0001583	missense	123016	exon13			GGCTGGCTCTGGT	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"Tetratricopeptide (TTC) repeat domain containing"	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1238C>T	14.37:g.89338717C>T	ENSP00000339486:p.Ala413Val	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	122	58	NM_144596	0	0	19	33	14	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	37	CCDS9885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.900692|4.900692	0.92035|0.92035	.|.	.|.	ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	T;T;T;T;T;T;T|.	0.74106|.	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.101143|.	0.64402|.	D|.	0.000002|.	D|D	0.85733|0.85733	0.5765|0.5765	M|M	0.89904|0.89904	3.07|3.07	0.58432|0.58432	D|D	0.999999|0.999999	P;P;P;P;P|.	0.48089|.	0.905;0.604;0.885;0.55;0.685|.	P;B;P;B;B|.	0.47346|.	0.544;0.394;0.492;0.382;0.382|.	D|D	0.87391|0.87391	0.2363|0.2363	10|5	0.41790|.	T|.	0.15|.	-15.7808|-15.7808	19.96|19.96	0.97242|0.97242	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	158;184;449;393;423|.	Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.;.;TTC8_HUMAN;.;.|.	V|F	413;184;383;439;158;423;225|373	ENSP00000339486:A413V;ENSP00000445067:A184V;ENSP00000298324:A383V;ENSP00000337653:A439V;ENSP00000346427:A158V;ENSP00000370031:A423V;ENSP00000351439:A225V|.	ENSP00000337653:A439V|.	A|L	+|+	2|1	0|0	TTC8|TTC8	88408470|88408470	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	5.670000|5.670000	0.68088|0.68088	2.793000|2.793000	0.96121|0.96121	0.561000|0.561000	0.74099|0.74099	GCT|CTC	.		0.532	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		T	89338717	C	T	89338717	3	4	34	1	0	0	0	0	1	0	0	0	16747	797	28	2	1318	2	TTC8	14	89338717	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	30541982	89338717	18010823	65	3004											
TRPM1	4308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	31342655	31342655	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggtcagtttcttcctccActtcctctttcactttccct	3	17	6	15	0	4	0	2	0	2	0	8	0	8	0	4	2	0	1	4	2	0	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr15:31342655A>T	ENST00000256552.6	-	12	1541	c.1394T>A	c.(1393-1395)gTg>gAg	p.V465E	TRPM1_ENST00000397795.2_Missense_Mutation_p.V443E|TRPM1_ENST00000542188.1_Missense_Mutation_p.V482E	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		Ttcttcctccacttcctcttt	0.542																																					p.V482E		.											.	TRPM1-94	0			c.T1445A						.						208	217	214					15																	31342655		2000	4152	6152	SO:0001583	missense	4308	exon11			TCCTCCACTTCCT	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.1394T>A	15.37:g.31342655A>T	ENSP00000256552:p.Val465Glu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	100	38	NM_001252020	0	0	0	0	0		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	A	3.172	-0.169735	0.06461	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.72051	-0.62;-0.62;-0.62	4.8	-0.746	0.11095	.	0.495264	0.20727	N	0.086800	T	0.44074	0.1276	N	0.08118	0	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.12156	0.007;0.003	T	0.29822	-0.9999	10	0.66056	D	0.02	-6.1648	5.5491	0.17081	0.5174:0.0:0.3552:0.1273	.	437;443	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	E	443;482;465;443	ENSP00000380897:V443E;ENSP00000437849:V482E;ENSP00000256552:V465E	ENSP00000256552:V465E	V	-	2	0	TRPM1	29129947	0.010000	0.17322	0.812000	0.32479	0.123000	0.20343	0.172000	0.16704	-0.389000	0.07786	-1.843000	0.00578	GTG	.		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31342655	A	T	31342655	3	4	34	1	0	0	0	0	1	0	0	0	16618	159	6	5	3551	5	TRPM1	15	31342655	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		31342655	71188737	66	3005											
AQR	9716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	35189882	35189882	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttccttttcttccctttTccacttcttactggaaaagt	6	20	3	12	0	3	0	0	0	3	0	6	1	6	1	3	1	1	0	3	1	3	8			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr15:35189882T>G	ENST00000156471.5	-	21	2493	c.2268A>C	c.(2266-2268)ggA>ggC	p.G756G		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	756					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TCTTCCCTTTTCCACTTCTTA	0.393																																					p.G756G		.											.	AQR-135	0			c.A2268C						.						111	102	105					15																	35189882		1844	4108	5952	SO:0001819	synonymous_variant	9716	exon21			CCCTTTTCCACTT	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.2268A>C	15.37:g.35189882T>G		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	79	30	NM_014691	0	0	10	20	10	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	37	CCDS42013.1																																																																																			.		0.393	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35189882	T	G	35189882	2	3	34	1	0	0	0	0	0	0	0	1	835	1770	62	5		5	AQR	15	35189882	Silent	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	3847227	35189882	67341510	67	3006											
SMAD3	4088	broad.mit.edu	37	chr15	67473652	67473652	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tacgagctgaaccagcgcgtCggggagacattccacgcctc	9	6	12	14	5	0	2	0	1	0	1	3	4	1	2	3	2	4	1	3	2	2	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr15:67473652C>T	ENST00000327367.4	+	6	1042	c.732C>T	c.(730-732)gtC>gtT	p.V244V	SMAD3_ENST00000540846.2_Silent_p.V139V|SMAD3_ENST00000537194.2_Silent_p.V49V|SMAD3_ENST00000439724.3_Silent_p.V200V	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	244	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|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 wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		ACCAGCGCGTCGGGGAGACAT	0.607																																					p.V244V													.	SMAD3-904	0			c.C732T						.						77	62	67					15																	67473652		2201	4299	6500	SO:0001819	synonymous_variant	4088	exon6			GCGCGTCGGGGAG	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"SMADs"	6769	protein-coding gene	gene with protein product		603109	"MAD, mothers against decapentaplegic homolog 3 (Drosophila)", "SMAD, mothers against DPP homolog 3 (Drosophila)"	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.732C>T	15.37:g.67473652C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	92	3	NM_005902	0	0	20	20	0	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Silent	SNP	ENST00000327367.4	37	CCDS10222.1																																																																																			.		0.607	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902		T	67473652	C	T	67473652	2	4	34	1	0	0	0	0	0	0	0	1	14791	871	31	1		1	SMAD3	15	67473652	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	32283770	67473652	35057740	68	3007											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_178167	0	0	0	4	4	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	34	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10		2059674	88295079	69	3008											
PKD1	5310	ucsc.edu	37	chr16	2168072	2168072	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acctcggcggagccgtctccGaagtcccagcgtgtggcagt	6	7	14	14	5	1	0	0	0	1	0	4	2	2	1	4	3	2	1	4	3	1	0	rs554071267		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:2168072G>A	ENST00000262304.4	-	5	1129	c.921C>T	c.(919-921)ttC>ttT	p.F307F	PKD1_ENST00000423118.1_Silent_p.F307F|RP11-304L19.2_ENST00000562027.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	307	PKD 1. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGCCGTCTCCGAAGTCCCAGC	0.716													g|||	1	0.000199681	0	0	5008	,	,		14557	0		0	False		,,,				2504	0.001				p.F307F													.	PKD1-91	0			c.C921T						.						5	7	7					16																	2168072		2005	4072	6077	SO:0001819	synonymous_variant	5310	exon5			GTCTCCGAAGTCC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.921C>T	16.37:g.2168072G>A		Somatic	18	0		WXS	Illumina HiSeq		159	2	NM_000296	0	0	5	5	0	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.716	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2168072	G	A	2168072	2	1	34	1	0	0	0	0	0	0	0	1	11989	1049	37	1		1	PKD1	16	2168072	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	108398	2168072	88186681	70	3009											
TEKT5	146279	broad.mit.edu	37	chr16	10788448	10788448	+	Frame_Shift_Del	DEL	C	C	-																															ctgcagctggttggactggtCccagtcgtgggggctatagc																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:10788448delC	ENST00000283025.2	-	1	354	c.283delG	c.(283-285)gacfs	p.D95fs	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	95						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						TTGGACTGGTCCCAGTCGTGG	0.677																																					p.D95fs													.	TEKT5-92	0			c.283delG						.						65	76	72					16																	10788448		2197	4300	6497	SO:0001589	frameshift_variant	146279	exon1			ACTGGTCCCAGTC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.283delG	16.37:g.10788448delC	ENSP00000283025:p.Asp95fs	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	102	7	NM_144674	0	0	0	0	0	A1L3Z3	Frame_Shift_Del	DEL	ENST00000283025.2	37	CCDS10542.1																																																																																			.		0.677	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		-	10788448	C	-	10788448	7	5	34	1	0	1	0	1	0	0	0	0	15788	855	30	0	1202	0	TEKT5	16	10788448	Frame_Shift_Del	DEL	C	TCGA-AT-A5NU-01A-11D-A28G-10	8620376	10788448	79566305	71	3010											
CDH11	1009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	64981793	64981793	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcccaggtctaggcatgtActgatactcaggtttgatgt	9	12	12	8	0	2	2	1	2	1	0	2	3	2	2	1	3	3	3	1	3	3	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:64981793A>G	ENST00000268603.4	-	13	2719	c.2104T>C	c.(2104-2106)Tac>Cac	p.Y702H	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Missense_Mutation_p.Y576H	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	702					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y702H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CTAGGCATGTACTGATACTCA	0.522			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.Y702H		.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11-852	1	Substitution - Missense(1)	large_intestine(1)	c.T2104C						.						135	128	130					16																	64981793		2203	4300	6503	SO:0001583	missense	1009	exon13			GCATGTACTGATA	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"Cadherins / Major cadherins"	1750	protein-coding gene	gene with protein product	"OB-Cadherin"	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2104T>C	16.37:g.64981793A>G	ENSP00000268603:p.Tyr702His	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	223	117	NM_001797	0	0	15	15	0	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715271	0.48622	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	T	0.76060	-0.99	6.17	6.17	0.99709	Cadherin, cytoplasmic domain (1);	0.054697	0.85682	D	0.000000	T	0.76054	0.3934	L	0.31926	0.97	0.80722	D	1	D	0.55800	0.973	P	0.59115	0.852	T	0.71182	-0.4668	10	0.15499	T	0.54	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	702	P55287	CAD11_HUMAN	H	702;685	ENSP00000268603:Y702H	ENSP00000268603:Y702H	Y	-	1	0	CDH11	63539294	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	TAC	.		0.522	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		G	64981793	A	G	64981793	3	3	34	1	0	0	0	0	1	0	0	0	3103	391	14	3	290	3	CDH11	16	64981793	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	54193345	64981793	25372960	72	3011											
RLTPR	146206	ucsc.edu;bcgsc.ca	37	chr16	67690142	67690142	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gccttgcaggtgacattatgGacagttccacggaggcccct	8	9	12	12	1	0	1	0	1	0	0	1	3	1	3	4	4	1	2	4	4	1	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:67690142G>C	ENST00000334583.6	+	34	4082	c.3754G>C	c.(3754-3756)Gac>Cac	p.D1252H	RLTPR_ENST00000545661.1_Missense_Mutation_p.D1216H	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	1252					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TGACATTATGGACAGTTCCAC	0.602																																					p.D1252H													.	RLTPR-67	0			c.G3754C						.						140	138	139					16																	67690142		1996	4170	6166	SO:0001583	missense	146206	exon34			ATTATGGACAGTT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.3754G>C	16.37:g.67690142G>C	ENSP00000334958:p.Asp1252His	Somatic	255	3		WXS	Illumina HiSeq		341	162	NM_001013838	0	0	0	0	0	B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	37	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403657	0.62288	.	.	ENSG00000159753	ENST00000334583;ENST00000398282;ENST00000545661	T;T	0.34275	1.37;1.67	5.23	5.23	0.72850	.	0.000000	0.56097	D	0.000037	T	0.49695	0.1572	L	0.29908	0.895	0.43191	D	0.995023	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.51576	-0.8688	10	0.72032	D	0.01	-23.1754	16.9494	0.86240	0.0:0.0:1.0:0.0	.	1216;1252	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	H	1252;349;1216	ENSP00000334958:D1252H;ENSP00000441481:D1216H	ENSP00000334958:D1252H	D	+	1	0	RLTPR	66247643	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	5.707000	0.68370	2.596000	0.87737	0.591000	0.81541	GAC	.		0.602	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		C	67690142	G	C	67690142	3	2	34	1	0	0	0	0	1	0	0	0	13426	1174	41	4	3888	4	RLTPR	16	67690142	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	2708349	67690142	22664611	73	3012											
LCAT	3931	broad.mit.edu	37	chr16	67976298	67976298	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccagcatgggcttgatggagCcaccccagggagccccaaga	10	4	13	14	0	0	2	0	1	0	1	0	4	0	4	6	3	3	2	6	3	1	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:67976298C>A	ENST00000264005.5	-	5	745	c.716G>T	c.(715-717)gGc>gTc	p.G239V	CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	239					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		CTTGATGGAGCCACCCCAGGG	0.587																																					p.G239V													.	LCAT-44	0			c.G716T						.						51	56	55					16																	67976298		2198	4300	6498	SO:0001583	missense	3931	exon5			ATGGAGCCACCCC		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.716G>T	16.37:g.67976298C>A	ENSP00000264005:p.Gly239Val	Somatic	138	1		WXS	Illumina HiSeq	Phase_I	231	10	NM_000229	0	0	190	190	0	Q53XQ3	Missense_Mutation	SNP	ENST00000264005.5	37	CCDS10854.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.560286	0.86335	.	.	ENSG00000213398	ENST00000264005	D	0.99667	-6.34	4.99	4.99	0.66335	.	0.137403	0.47852	U	0.000220	D	0.99694	0.9884	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97487	1.0051	10	0.87932	D	0	-12.9043	15.8074	0.78524	0.0:1.0:0.0:0.0	.	239	P04180	LCAT_HUMAN	V	239	ENSP00000264005:G239V	ENSP00000264005:G239V	G	-	2	0	LCAT	66533799	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	7.651000	0.83577	2.590000	0.87494	0.561000	0.74099	GGC	.		0.587	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			A	67976298	C	A	67976298	3	1	34	1	0	0	0	0	1	0	0	0	8679	739	26	4	614	4	LCAT	16	67976298	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	286156	67976298	22378455	74	3013											
SERPINF1	5176	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	1679947	1679953	+	Frame_Shift_Del	DEL	GAGAACT	GAGAACT	-																															gttcattcatgacatagaccGagaactgaagaccgtgcagg																								rs146939364	byFrequency	TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	GAGAACT	GAGAACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:1679947_1679953delGAGAACT	ENST00000254722.4	+	7	1071_1077	c.908_914delGAGAACT	c.(907-915)cgagaactgfs	p.REL303fs		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	303					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L305V(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						GACATAGACCGAGAACTGAAGACCGTG	0.512																																					p.303_305del		.											.	SERPINF1-227	1	Substitution - Missense(1)	stomach(1)	c.908_914del						.																																			SO:0001589	frameshift_variant	5176	exon7			.	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.908_914delGAGAACT	17.37:g.1679947_1679953delGAGAACT	ENSP00000254722:p.Arg303fs	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	133	60	NM_002615	0	0	0	0	0	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Frame_Shift_Del	DEL	ENST00000254722.4	37	CCDS11012.1																																																																																			.		0.512	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		-	1679953	GAGAACT	-	1679947	7	5	34	1	0	1	0	1	0	0	0	0	14146	1058	37	0	930	0	SERPINF1	17	1679947	Frame_Shift_Del	DEL	GAGAACT	TCGA-AT-A5NU-01A-11D-A28G-10		1679947	79515263	75	3014											
WDR16	146845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	9501596	9501596	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcttccaaatagaaaaatCtggccaactgagtgccaaac	16	8	7	10	0	2	2	0	1	2	1	3	3	3	2	3	1	3	0	3	1	6	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:9501596C>A	ENST00000352665.5	+	5	651	c.582C>A	c.(580-582)atC>atA	p.I194I	WDR16_ENST00000396219.3_Silent_p.I126I|WDR16_ENST00000299764.5_Silent_p.I204I	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						ATAGAAAAATCTGGCCAACTG	0.328																																					p.I194I		.											.	WDR16-71	0			c.C582A						.						92	98	96					17																	9501596		2203	4300	6503	SO:0001819	synonymous_variant	146845	exon5			AAAAATCTGGCCA	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"WD repeat domain containing"	16053	protein-coding gene	gene with protein product	"WD40-repeat protein upregulated in HCC"	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.582C>A	17.37:g.9501596C>A		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	54	14	NM_145054	0	0	0	0	0		Silent	SNP	ENST00000352665.5	37	CCDS11149.2																																																																																			.		0.328	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		A	9501596	C	A	9501596	2	1	34	1	0	0	0	0	0	0	0	1	17309	903	32	4		4	WDR16	17	9501596	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	7821649	9501596	71693614	76	3015											
ACE	1636	broad.mit.edu	37	chr17	61566074	61566074	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgggcatgggagggctggCgagacaaggcggggagagcc	9	4	21	7	2	0	2	0	0	0	2	0	5	0	3	1	7	1	2	1	7	2	1	rs397514689		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:61566074C>T	ENST00000290866.4	+	16	2395	c.2371C>T	c.(2371-2373)Cga>Tga	p.R791*	ACE_ENST00000490216.2_Nonsense_Mutation_p.R217*|ACE_ENST00000428043.1_Nonsense_Mutation_p.R791*|ACE_ENST00000413513.3_Nonsense_Mutation_p.R217*|ACE_ENST00000577647.1_Nonsense_Mutation_p.R217*|ACE_ENST00000290863.6_Nonsense_Mutation_p.R217*|ACE_ENST00000421982.2_Nonsense_Mutation_p.R101*	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	791	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GGAGGGCTGGCGAGACAAGGC	0.562																																					p.R791X													.	ACE-94	0			c.C2371T						.						119	107	111					17																	61566074		2203	4300	6503	SO:0001587	stop_gained	1636	exon16			GGCTGGCGAGACA	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.2371C>T	17.37:g.61566074C>T	ENSP00000290866:p.Arg791*	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	112	4	NM_000789	0	0	6	6	0	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Nonsense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.192639	0.58017	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	.	.	.	5.93	2.45	0.29901	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-33.4471	15.4296	0.75081	0.354:0.646:0.0:0.0	.	.	.	.	X	791;791;217;217;101	.	ENSP00000290863:R217X	R	+	1	2	ACE	58919806	0.999000	0.42202	1.000000	0.80357	0.160000	0.22226	0.619000	0.24388	0.795000	0.33922	0.561000	0.74099	CGA	.		0.562	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			T	61566074	C	T	61566074	4	4	34	1	0	0	0	0	0	1	0	0	136	760	27	1	2636	1	ACE	17	61566074	Nonsense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	52064478	61566074	19629136	77	3016											
SAP30BP	29115	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73702116	73702116	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgtgacgggcaccaaaaaagGcaccacgaccaacgccacgt	14	3	10	14	4	0	1	0	1	0	0	0	2	0	1	4	2	1	2	4	2	4	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:73702116G>C	ENST00000584667.1	+	10	946	c.689G>C	c.(688-690)gGc>gCc	p.G230A	SAP30BP_ENST00000355423.3_Missense_Mutation_p.G214A	NM_013260.6	NP_037392.1			SAP30 binding protein											kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)	17	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACCAAAAAAGGcaccacgacc	0.567																																					p.G230A													.	SAP30BP-91	0			c.G689C						.						126	88	101					17																	73702116		2203	4300	6503	SO:0001583	missense	29115	exon10			AAAAAGGCACCAC	AY082382	CCDS11726.1	17q25.1	2006-01-05				ENSG00000161526			30785	protein-coding gene	gene with protein product		610218				15496587	Standard	NM_013260		Approved	HCNGP, HTRG, HTRP	uc002jpe.3	Q9UHR5		ENST00000584667.1:c.689G>C	17.37:g.73702116G>C	ENSP00000462116:p.Gly230Ala	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	60	24	NM_013260	0	0	166	238	72		Missense_Mutation	SNP	ENST00000584667.1	37	CCDS11726.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180200	0.78564	.	.	ENSG00000161526	ENST00000355423;ENST00000293208	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.55816	0.1944	L	0.47716	1.5	0.80722	D	1	P;P	0.41597	0.7;0.756	B;B	0.43783	0.431;0.351	T	0.49542	-0.8929	9	0.09338	T	0.73	-24.486	19.8045	0.96525	0.0:0.0:1.0:0.0	.	214;230	Q9UHR5-2;Q9UHR5	.;S30BP_HUMAN	A	230;214	.	ENSP00000293208:G214A	G	+	2	0	SAP30BP	71213711	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.925000	0.92832	2.676000	0.91093	0.655000	0.94253	GGC	.		0.567	SAP30BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448227.1	NM_013260		C	73702116	G	C	73702116	3	2	34	1	0	0	0	0	1	0	0	0	13866	1203	42	4	727	4	SAP30BP	17	73702116	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	12136042	73702116	7493094	78	3017											
MFSD11	79157	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	74738356	74738356	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgggcacttctgcagtctagGtaattatccttttgaggttc	7	16	10	8	0	2	1	0	1	2	0	4	1	3	1	1	3	1	4	1	3	3	7			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:74738356G>A	ENST00000588460.1	+	5	2479		c.e5+1		MFSD11_ENST00000590514.1_Splice_Site|MFSD11_ENST00000336509.4_Splice_Site|MFSD11_ENST00000593181.1_Intron|MFSD11_ENST00000355954.3_Intron|MFSD11_ENST00000586622.1_Splice_Site	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TGCAGTCTAGGTAATTATCCT	0.403																																					.		.											.	MFSD11-91	0			c.437+1G>A						.						140	140	140					17																	74738356		2203	4300	6503	SO:0001630	splice_region_variant	79157	exon6			GTCTAGGTAATTA	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.437+1G>A	17.37:g.74738356G>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	180	10	NM_001242534	0	0	0	0	0	O43442|Q9NXI5	Splice_Site	SNP	ENST00000588460.1	37	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.234688	0.79800	.	.	ENSG00000092931	ENST00000336509	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9326	0.97124	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MFSD11	72249951	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	9.471000	0.97696	2.720000	0.93068	0.650000	0.86243	.	.		0.403	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311	Intron	A	74738356	G	A	74738356	5	1	34	1	0	0	0	0	0	0	1	0	9554	1275	44	2	456	2	MFSD11	17	74738356	Splice_Site	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	1036240	74738356	6456854	79	3018											
CABLES1	91768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	20768825	20768825	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcgcctcatctcccagagatCttccttggagaccctggaag	8	9	10	14	1	3	2	1	0	2	2	5	5	4	3	4	2	0	0	4	2	1	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr18:20768825C>T	ENST00000256925.7	+	2	869	c.869C>T	c.(868-870)tCt>tTt	p.S290F	CABLES1_ENST00000420687.2_Missense_Mutation_p.S25F|CABLES1_ENST00000585061.1_3'UTR|CABLES1_ENST00000400473.2_5'UTR	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	290	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCCCAGAGATCTTCCTTGGAG	0.433																																					p.S290F		.											.	CABLES1-522	0			c.C869T						.						67	63	64					18																	20768825		1814	4069	5883	SO:0001583	missense	91768	exon2			AGAGATCTTCCTT	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.869C>T	18.37:g.20768825C>T	ENSP00000256925:p.Ser290Phe	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	24	7	NM_001100619	0	0	4	13	9	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	37	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817292	0.90790	.	.	ENSG00000134508	ENST00000256925;ENST00000420687	T;T	0.50548	0.74;0.78	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.83275	0.989;0.996	T	0.66705	-0.5856	10	0.87932	D	0	-11.7652	19.4124	0.94679	0.0:1.0:0.0:0.0	.	25;290	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	F	290;25	ENSP00000256925:S290F;ENSP00000413851:S25F	ENSP00000256925:S290F	S	+	2	0	CABLES1	19022823	1.000000	0.71417	0.958000	0.39756	0.852000	0.48524	7.345000	0.79337	2.595000	0.87683	0.556000	0.70494	TCT	.		0.433	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		T	20768825	C	T	20768825	3	4	34	1	0	0	0	0	1	0	0	0	2535	913	32	2	929	2	CABLES1	18	20768825	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		20768825	57308423	80	3019											
ABCA7	10347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1041554	1041554	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctctcttcctcttcttcAtcctggtggctgttcgccac	2	15	8	16	1	4	0	1	0	3	0	8	0	6	0	4	3	0	2	4	3	0	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:1041554A>T	ENST00000263094.6	+	3	343	c.112A>T	c.(112-114)Atc>Ttc	p.I38F	AC011558.5_ENST00000585757.1_RNA|ABCA7_ENST00000433129.1_Missense_Mutation_p.I38F|ABCA7_ENST00000435683.2_5'Flank	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	38					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCTTCTTCATCCTGGTGGC	0.637																																					p.I38F		.											.	ABCA7-98	0			c.A112T						.						103	107	106					19																	1041554		2203	4300	6503	SO:0001583	missense	10347	exon3			TTCTTCATCCTGG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.112A>T	19.37:g.1041554A>T	ENSP00000263094:p.Ile38Phe	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	25	9	NM_019112	0	0	3	11	8	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.986185	0.93044	.	.	ENSG00000064687	ENST00000263094;ENST00000524850;ENST00000531467;ENST00000433129	D;D;D;D	0.99194	-5.54;-5.54;-5.54;-5.54	4.78	4.78	0.61160	.	.	.	.	.	D	0.98839	0.9608	L	0.53729	1.69	0.47905	D	0.999542	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.997	D	0.99744	1.1016	9	0.87932	D	0	.	12.2354	0.54512	1.0:0.0:0.0:0.0	.	38;38	B4DVJ5;Q8IZY2	.;ABCA7_HUMAN	F	38;38;36;38	ENSP00000263094:I38F;ENSP00000431473:I38F;ENSP00000433545:I36F;ENSP00000414062:I38F	ENSP00000263094:I38F	I	+	1	0	ABCA7	992554	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	5.979000	0.70508	1.794000	0.52575	0.460000	0.39030	ATC	.		0.637	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1041554	A	T	1041554	3	4	34	1	0	0	0	0	1	0	0	0	37	217	8	5	118	5	ABCA7	19	1041554	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		1041554	58087429	81	3020											
ADAMTSL5	339366	hgsc.bcm.edu	37	chr19	1506086	1506086	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccagggccgggcgtagccGgcgtggggcagcagcagctg	5	4	19	13	4	0	0	0	0	0	0	1	0	1	0	3	5	4	5	3	5	1	1	rs186786015		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:1506086G>A	ENST00000413997.2	-	12	1373	c.1374C>T	c.(1372-1374)gcC>gcT	p.A458A	CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000395467.2_3'UTR|ADAMTSL5_ENST00000330475.4_Silent_p.A448A|ADAMTSL5_ENST00000590562.1_5'UTR			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	458	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.					extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGCGTAGCCGGCGTGGGGCA	0.721													G|||	1	0.000199681	0	0	5008	,	,		14339	0.001		0	False		,,,				2504	0				p.A448A		.											.	ADAMTSL5-90	0			c.C1344T						.	G		0,4384		0,0,2192	12	15	14		1344	-0.7	0.4	19		14	4,8564		0,4,4280	no	coding-synonymous	ADAMTSL5	NM_213604.2		0,4,6472	AA,AG,GG		0.0467,0.0,0.0309		448/472	1506086	4,12948	2192	4284	6476	SO:0001819	synonymous_variant	339366	exon12			GTAGCCGGCGTGG	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"thrombospondin, type I, domain containing 6"	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.1374C>T	19.37:g.1506086G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	42	20	NM_213604	1	0	17	36	18	B4DXK7|Q8IW95	Silent	SNP	ENST00000413997.2	37																																																																																				G|0.999;A|0.000		0.721	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919		A	1506086	G	A	1506086	2	1	34	1	0	0	0	0	0	0	0	1	278	1103	39	1		1	ADAMTSL5	19	1506086	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	464532	1506086	57622897	82	3021											
EVI5L	115704	hgsc.bcm.edu	37	chr19	7927064	7927064	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacggaagctggtcgtgggCgagctgcaggacgagctgat	8	6	17	10	4	0	1	0	1	0	0	1	5	0	3	1	4	4	4	1	4	1	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:7927064C>T	ENST00000270530.4	+	15	1864	c.1668C>T	c.(1666-1668)ggC>ggT	p.G556G	EVI5L_ENST00000538904.2_Silent_p.G567G	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	556					negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						TGGTCGTGGGCGAGCTGCAGG	0.731																																					p.G567G		.											.	EVI5L-91	0			c.C1701T						.						5	6	6					19																	7927064		2077	4154	6231	SO:0001819	synonymous_variant	115704	exon15			CGTGGGCGAGCTG	BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.1668C>T	19.37:g.7927064C>T		Somatic	4	0		WXS	Illumina HiSeq	Phase_I	15	10	NM_001159944	0	0	9	21	12	B9A6I9	Silent	SNP	ENST00000270530.4	37	CCDS12188.1																																																																																			.		0.731	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245		T	7927064	C	T	7927064	2	4	34	1	0	0	0	0	0	0	0	1	5303	755	27	1		1	EVI5L	19	7927064	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	6420978	7927064	51201919	83	3022											
TSHZ3	57616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	31768208	31768208	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgagtttgacatgaatgataCgacggcagatgtctttgccg	10	11	12	8	4	1	4	0	3	1	1	1	6	1	4	1	1	2	2	1	1	2	3	rs201694059		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:31768208C>T	ENST00000240587.4	-	2	2818	c.2491G>A	c.(2491-2493)Gta>Ata	p.V831I		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	831					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					ATGAATGATACGACGGCAGAT	0.527													C|||	1	0.000199681	0	0	5008	,	,		19141	0.001		0	False		,,,				2504	0				p.V831I		.											.	TSHZ3-232	0			c.G2491A						.						143	130	135					19																	31768208		2203	4300	6503	SO:0001583	missense	57616	exon2			ATGATACGACGGC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2491G>A	19.37:g.31768208C>T	ENSP00000240587:p.Val831Ile	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	199	81	NM_020856	0	0	0	0	0	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465152	0.43839	.	.	ENSG00000121297	ENST00000240587	T	0.11930	2.73	5.37	4.32	0.51571	.	0.118294	0.56097	D	0.000026	T	0.07593	0.0191	N	0.08118	0	0.48040	D	0.999571	B	0.21452	0.056	B	0.16722	0.016	T	0.33420	-0.9869	10	0.23302	T	0.38	-9.1996	14.4459	0.67349	0.0:0.9276:0.0:0.0723	.	831	Q63HK5	TSH3_HUMAN	I	831	ENSP00000240587:V831I	ENSP00000240587:V831I	V	-	1	0	TSHZ3	36460048	1.000000	0.71417	0.961000	0.40146	0.937000	0.57800	5.745000	0.68672	2.501000	0.84356	0.655000	0.94253	GTA	C|0.999;A|0.001		0.527	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31768208	C	T	31768208	3	4	34	1	0	0	0	0	1	0	0	0	16658	536	19	1	758	1	TSHZ3	19	31768208	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	23841144	31768208	27360775	84	3023											
ZNF181	339318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35231657	35231657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagaagaatttggaatataTagagaagttggaagggaagc	18	9	13	1	0	0	3	0	0	0	3	0	7	0	6	0	3	1	1	0	3	10	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:35231657T>C	ENST00000492450.1	+	4	460	c.371T>C	c.(370-372)aTa>aCa	p.I124T	ZNF181_ENST00000392232.3_Missense_Mutation_p.I168T|ZNF181_ENST00000459757.2_Missense_Mutation_p.I123T			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	124					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTGGAATATATAGAGAAGTTG	0.348																																					p.I124T		.											.	ZNF181-91	0			c.T371C						.						45	50	48					19																	35231657		2194	4294	6488	SO:0001583	missense	339318	exon4			AATATATAGAGAA	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"Zinc fingers, C2H2-type", "-"	12971	protein-coding gene	gene with protein product		606741	"zinc finger protein 181 (HHZ181)"				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.371T>C	19.37:g.35231657T>C	ENSP00000420727:p.Ile124Thr	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	107	29	NM_001029997	0	0	7	8	1	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.579817	0.00129	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	T;T;T	0.05717	3.4;3.49;3.46	2.89	-0.737	0.11129	.	.	.	.	.	T	0.04182	0.0116	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.46119	-0.9214	9	0.23302	T	0.38	.	1.2006	0.01884	0.1774:0.117:0.3517:0.3539	.	123;124	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	T	168;123;124;123	ENSP00000376065:I168T;ENSP00000420727:I124T;ENSP00000419435:I123T	ENSP00000376065:I168T	I	+	2	0	ZNF181	39923497	0.286000	0.24305	0.000000	0.03702	0.058000	0.15608	0.956000	0.29202	-0.238000	0.09724	-0.512000	0.04463	ATA	.		0.348	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		C	35231657	T	C	35231657	3	2	34	1	0	0	0	0	1	0	0	0	17781	1406	49	3	385	3	ZNF181	19	35231657	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	3463449	35231657	23897326	85	3024											
CATSPERG	57828	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38850108	38850108	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccatctctgtccctgcAgctctaacaaggaaaacttc	10	11	5	15	0	3	0	0	0	3	0	7	1	4	1	2	1	4	2	2	1	4	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:38850108A>T	ENST00000409235.3	+	14	1611		c.e14-1		CATSPERG_ENST00000215069.4_Intron|AC005625.1_ENST00000590304.1_RNA|CATSPERG_ENST00000410018.1_Splice_Site	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma						cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						CTGTCCCTGCAGCTCTAACAA	0.527																																					.		.											.	CATSPERG-92	0			c.1497-2A>T						.						75	61	66					19																	38850108		2203	4300	6503	SO:0001630	splice_region_variant	57828	exon14			CCCTGCAGCTCTA	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"chromosome 19 open reading frame 15", "cation channel, sperm-associated, gamma"	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.1497-1A>T	19.37:g.38850108A>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	69	33	NM_021185	0	0	0	0	0	A6NEG6|Q659E1	Splice_Site	SNP	ENST00000409235.3	37	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	A	14.07	2.426002	0.43020	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1118	0.53844	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CATSPERG	43541948	1.000000	0.71417	0.268000	0.24571	0.124000	0.20399	5.184000	0.65070	2.172000	0.68678	0.533000	0.62120	.	.		0.527	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	Intron	T	38850108	A	T	38850108	5	4	34	1	0	0	0	0	0	0	1	0	2698	202	7	5	1545	5	CATSPERG	19	38850108	Splice_Site	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	3618451	38850108	20278875	86	3025											
SUPT5H	6829	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	39966780	39966780	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttgtcagcatttccagtgaGcacctggagcctatcacccc	8	10	9	14	0	2	1	2	1	0	0	3	2	3	2	5	1	3	3	5	1	1	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:39966780G>C	ENST00000599117.1	+	30	3451	c.3084G>C	c.(3082-3084)gaG>gaC	p.E1028D	SUPT5H_ENST00000432763.2_Missense_Mutation_p.E1028D|SUPT5H_ENST00000359191.6_Missense_Mutation_p.E1024D|SUPT5H_ENST00000402194.2_Missense_Mutation_p.E1024D|SUPT5H_ENST00000598725.1_Missense_Mutation_p.E1028D			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	1028					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TTTCCAGTGAGCACCTGGAGC	0.577																																					p.E1028D		.											.	SUPT5H-94	0			c.G3084C						.						90	72	79					19																	39966780		2203	4300	6503	SO:0001583	missense	6829	exon28			CAGTGAGCACCTG	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.3084G>C	19.37:g.39966780G>C	ENSP00000470252:p.Glu1028Asp	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	86	10	NM_003169	0	0	292	306	14	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	G	9.397	1.076981	0.20227	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.42	-0.361	0.12564	.	0.102463	0.64402	D	0.000003	T	0.25901	0.0631	N	0.16201	0.385	0.51233	D	0.999916	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.03202	-1.1061	8	.	.	.	-29.1312	4.6807	0.12734	0.3392:0.0:0.5198:0.1409	.	1024;1028	O00267-2;O00267	.;SPT5H_HUMAN	D	1028;1024;1006;1028	.	.	E	+	3	2	SUPT5H	44658620	0.986000	0.35501	1.000000	0.80357	0.996000	0.88848	0.154000	0.16343	0.130000	0.18549	0.462000	0.41574	GAG	.		0.577	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		C	39966780	G	C	39966780	3	2	34	1	0	0	0	0	1	0	0	0	15431	962	34	4	3194	4	SUPT5H	19	39966780	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	1116672	39966780	19162203	87	3026											
PPM1N	147699	broad.mit.edu	37	chr19	46002036	46002036	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgggccttgtttgccgtcctCgacggccacggtggggctcg	2	10	16	13	5	0	0	0	0	0	0	3	1	1	0	4	5	1	2	4	5	0	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:46002036C>T	ENST00000451287.2	+	1	306	c.306C>T	c.(304-306)ctC>ctT	p.L102L	PPM1N_ENST00000396735.2_5'Flank|PPM1N_ENST00000396737.2_Intron|RTN2_ENST00000590526.1_5'Flank|PPM1N_ENST00000401705.1_Intron|PPM1N_ENST00000324688.4_Silent_p.L24L|RTN2_ENST00000589384.1_5'Flank|PPM1N_ENST00000396736.2_5'Flank|PPM1N_ENST00000456399.2_Intron|RTN2_ENST00000344680.4_5'Flank|PPM1N_ENST00000401593.1_5'Flank|RTN2_ENST00000245923.4_5'Flank	NM_001080401.1	NP_001073870.1	Q8N819	PPM1N_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	102	PP2C-like.						magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)	9						TTGCCGTCCTCGACGGCCACG	0.701																																					p.L102L													.	.	0			c.C306T						.						4	4	4					19																	46002036		1776	3705	5481	SO:0001819	synonymous_variant	147699	exon1			CGTCCTCGACGGC	AK097444	CCDS46115.1	19q13.32	2012-04-17			ENSG00000213889	ENSG00000213889		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	26845	protein-coding gene	gene with protein product							Standard	NM_001080401		Approved	FLJ40125	uc002pce.3	Q8N819	OTTHUMG00000140397	ENST00000451287.2:c.306C>T	19.37:g.46002036C>T		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	64	9	NM_001080401	0	0	0	2	2	Q6P662	Silent	SNP	ENST00000451287.2	37	CCDS46115.1																																																																																			.		0.701	PPM1N-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326517.2	NM_001080401		T	46002036	C	T	46002036	2	4	34	1	0	0	0	0	0	0	0	1	12375	871	31	1		1	PPM1N	19	46002036	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	6035256	46002036	13126947	88	3027											
CCDC9	26093	hgsc.bcm.edu	37	chr19	47763935	47763935	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggactcctccacagcagggaGgccgggccggcatgggccga	7	3	17	14	3	0	0	0	0	0	0	2	3	2	2	5	6	1	2	5	6	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:47763935G>A	ENST00000221922.6	+	5	523	c.301G>A	c.(301-303)Ggc>Agc	p.G101S		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	101	Gly-rich.						poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		ACAGCAGGGAGGCCGGGCCGG	0.756																																					p.G101S		.											.	CCDC9-90	0			c.G301A						.						13	15	14					19																	47763935		1920	4024	5944	SO:0001583	missense	26093	exon5			CAGGGAGGCCGGG	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.301G>A	19.37:g.47763935G>A	ENSP00000221922:p.Gly101Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	6	NM_015603	0	0	8	23	15		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	-	10.73	1.433672	0.25813	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.31769	1.48	3.32	2.26	0.28386	.	0.589357	0.16586	N	0.207978	T	0.26048	0.0635	L	0.54323	1.7	0.27250	N	0.958919	P	0.40180	0.705	B	0.40864	0.342	T	0.08046	-1.0741	10	0.25751	T	0.34	-10.5089	5.4967	0.16807	0.2634:0.0:0.7366:0.0	.	101	Q9Y3X0	CCDC9_HUMAN	S	101	ENSP00000221922:G101S	ENSP00000221922:G101S	G	+	1	0	CCDC9	52455775	0.926000	0.31397	0.964000	0.40570	0.633000	0.38033	1.380000	0.34351	0.731000	0.32448	0.431000	0.28591	GGC	.		0.756	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		A	47763935	G	A	47763935	3	1	34	1	0	0	0	0	1	0	0	0	2873	1000	35	2	315	2	CCDC9	19	47763935	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	1761899	47763935	11365048	89	3028											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48205552	48205552	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggccggacgcccgcgccCtcgtacccccacgctgcctc	3	4	10	24	7	0	0	0	0	0	0	2	1	0	1	7	2	2	2	7	2	1	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:48205552C>T	ENST00000396720.3	+	15	4757	c.4563C>T	c.(4561-4563)ccC>ccT	p.P1521P	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1521										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CGCCCGCGCCCTCGTACCCCC	0.741																																					p.P1521P		.											.	GLTSCR1-48	0			c.C4563T						.						11	13	12					19																	48205552		2094	4176	6270	SO:0001819	synonymous_variant	29998	exon15			CGCGCCCTCGTAC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.4563C>T	19.37:g.48205552C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	13	7	NM_015711	0	0	3	6	3	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			.		0.741	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48205552	C	T	48205552	2	4	34	1	0	0	0	0	0	0	0	1	6494	668	24	2		2	GLTSCR1	19	48205552	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	441617	48205552	10923431	90	3029											
OLIG1	116448	hgsc.bcm.edu	37	chr21	34442850	34442850	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gcgcccggccggacgccaagGaggagcagcagcagcagctg	9	1	17	14	4	0	0	0	0	0	0	0	3	0	3	3	4	5	5	3	4	1	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr21:34442850G>C	ENST00000382348.1	+	1	401	c.298G>C	c.(298-300)Gag>Cag	p.E100Q	AP000282.2_ENST00000454622.1_RNA|OLIG1_ENST00000333063.5_Missense_Mutation_p.E84Q|AP000282.2_ENST00000420356.1_RNA	NM_138983.2	NP_620450.2	Q8TAK6	OLIG1_HUMAN	oligodendrocyte transcription factor 1	100					neuron fate commitment (GO:0048663)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)	1						ggACGCCAAGGAGGAGCAGCA	0.746																																					p.E100Q		.											.	OLIG1-446	0			c.G298C						.						4	5	5					21																	34442850		1905	3895	5800	SO:0001583	missense	116448	exon1			GCCAAGGAGGAGC	AP000109	CCDS42920.1, CCDS42920.2	21q22.11	2013-05-21			ENSG00000184221	ENSG00000184221		"Basic helix-loop-helix proteins"	16983	protein-coding gene	gene with protein product	"oligodendrocyte-specific bHLH transcription factor 1", "oligodendrocyte lineage transcription factor 1", "basic domain, helix-loop-helix protein, class B, 6"	606385				11526205	Standard	NM_138983		Approved	BHLHB6, bHLHe21	uc002yqz.3	Q8TAK6	OTTHUMG00000065064	ENST00000382348.1:c.298G>C	21.37:g.34442850G>C	ENSP00000371785:p.Glu100Gln	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	22	13	NM_138983	0	0	0	0	0	Q7RTS0	Missense_Mutation	SNP	ENST00000382348.1	37	CCDS42920.2	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691676	0.48097	.	.	ENSG00000184221	ENST00000382348;ENST00000333063	D;D	0.98585	-5.01;-2.75	4.35	3.45	0.39498	.	0.466103	0.16859	U	0.196606	D	0.93802	0.8018	N	0.14661	0.345	0.29416	N	0.860923	P	0.38978	0.652	B	0.39027	0.288	D	0.90917	0.4780	10	0.33940	T	0.23	-11.8771	8.2305	0.31595	0.0932:0.1572:0.7496:0.0	.	100	Q8TAK6	OLIG1_HUMAN	Q	100;84	ENSP00000371785:E100Q;ENSP00000331066:E84Q	ENSP00000331066:E84Q	E	+	1	0	OLIG1	33364720	1.000000	0.71417	0.999000	0.59377	0.929000	0.56500	3.498000	0.53302	1.996000	0.58369	0.479000	0.44913	GAG	.		0.746	OLIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139730.1	NM_138983		C	34442850	G	C	34442850	3	2	34	1	0	0	0	0	1	0	0	0	10886	1175	41	4	300	4	OLIG1	21	34442850	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		34442850	13687045	91	3030											
KRTAP10-1	386677	hgsc.bcm.edu	37	chr21	45959197	45959197	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagaggcctcagcaggccggGcgggagcacgcggggcggca	7	1	20	13	5	1	1	1	0	0	1	1	2	1	2	2	7	2	3	2	7	0	0	rs200623181	byFrequency	TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr21:45959197G>A	ENST00000400375.1	-	1	881	c.837C>T	c.(835-837)cgC>cgT	p.R279R	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	279						keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						AGCAGGCCGGGCGGGAGCACG	0.716													G|||	12	0.00239617	0.0045	0.0014	5008	,	,		14843	0.001		0.003	False		,,,				2504	0.001				p.R279R		.											.	KRTAP10-1-91	0			c.C837T						.	G	,	19,4277		0,19,2129	16	21	19		,837	-2.5	0	21		19	3,8445		0,3,4221	no	intron,coding-synonymous	TSPEAR,KRTAP10-1	NM_144991.2,NM_198691.2	,	0,22,6350	AA,AG,GG		0.0355,0.4423,0.1726	,	,279/283	45959197	22,12722	2148	4224	6372	SO:0001819	synonymous_variant	386677	exon1			GGCCGGGCGGGAG	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"Keratin associated proteins"	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.837C>T	21.37:g.45959197G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	45	25	NM_198691	0	0	0	0	0	Q0VAR0|Q0VAR1	Silent	SNP	ENST00000400375.1	37	CCDS42954.1																																																																																			G|0.997;A|0.003		0.716	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1			A	45959197	G	A	45959197	2	1	34	1	0	0	0	0	0	0	0	1	8526	1190	42	2		2	KRTAP10-1	21	45959197	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	11516347	45959197	2170698	92	3031											
KRTAP10-3	386682	hgsc.bcm.edu;broad.mit.edu	37	chr21	45978023	45978023	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaggagggacacgcaggaGgccgggcggcagcagctggg	9	1	21	10	3	0	1	0	0	0	1	0	4	0	4	1	7	2	4	1	7	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr21:45978023G>A	ENST00000391620.1	-	1	620	c.576C>T	c.(574-576)gcC>gcT	p.A192A	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	192	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ACACGCAGGAGGCCGGGCGGC	0.721																																					p.A192A		.											.	KRTAP10-3-91	0			c.C576T						.						32	39	36					21																	45978023		2200	4298	6498	SO:0001819	synonymous_variant	386682	exon1			GCAGGAGGCCGGG	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"Keratin associated proteins"	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.576C>T	21.37:g.45978023G>A		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	165	9	NM_198696	0	0	0	0	0	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			.		0.721	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			A	45978023	G	A	45978023	2	1	34	1	0	0	0	0	0	0	0	1	8531	987	35	2		2	KRTAP10-3	21	45978023	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	18826	45978023	2151872	93	3032											
SEC14L2	23541	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	30818390	30818391	+	Frame_Shift_Ins	INS	-	-	A																															agctgggggcaggcaccccgINSaaataacaccttctcctata																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:30818390_30818391insA	ENST00000312932.9	+	12	1466_1467	c.1206_1207insA	c.(1207-1209)aaafs	p.K403fs	RNU6-564P_ENST00000410983.1_RNA|RP4-539M6.21_ENST00000608952.1_RNA|RP4-539M6.20_ENST00000608677.1_RNA|RP4-539M6.19_ENST00000439838.1_Intron|SEC14L2_ENST00000403484.1_Frame_Shift_Ins_p.K329fs|SEC14L2_ENST00000402592.3_Frame_Shift_Ins_p.K320fs	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)	403					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	CAGGCACCCCGAAATAACACCT	0.515																																					p.P402fs		.											.	SEC14L2-90	0			c.1206_1207insA						.																																			SO:0001589	frameshift_variant	23541	exon12			.	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"supernatant protein factor"	607558	"SEC14 (S. cerevisiae)-like 2"	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.1209dupA	22.37:g.30818393_30818393dupA	ENSP00000316203:p.Lys403fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	62	21	NM_012429	0	0	0	0	0	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Frame_Shift_Ins	INS	ENST00000312932.9	37	CCDS13876.1																																																																																			.		0.515	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429		A	30818391	-	A	30818390	7	5	34	1	0	1	1	0	0	0	0	0	14014	1045	37	0	1350	0	SEC14L2	22	30818390	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10		30818390	20486176	94	3033											
EIF3L	51386	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38273745	38273745	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcacgatgtaccccatgcGtattgatgagagcattcacc	10	10	8	13	2	2	2	2	2	0	1	2	4	2	2	4	0	3	3	4	0	2	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:38273745G>A	ENST00000412331.2	+	11	1724	c.1142G>A	c.(1141-1143)cGt>cAt	p.R381H	EIF3L_ENST00000406934.1_Missense_Mutation_p.R283H|EIF3L_ENST00000381683.6_Missense_Mutation_p.R333H	NM_016091.3	NP_057175.1			eukaryotic translation initiation factor 3, subunit L											kidney(2)|large_intestine(3)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TACCCCATGCGTATTGATGAG	0.507																																					p.R381H		.											.	EIF3L-69	0			c.G1142A						.						109	91	97					22																	38273745		2203	4300	6503	SO:0001583	missense	51386	exon11			CCATGCGTATTGA	AF083243	CCDS13960.1, CCDS56230.1	22q	2012-12-20	2009-01-07	2009-01-07	ENSG00000100129	ENSG00000100129			18138	protein-coding gene	gene with protein product			"eukaryotic translation initiation factor 3, subunit 6 interacting protein", "eukaryotic translation initiation factor 3, subunit E interacting protein"	EIF3S6IP, EIF3EIP		11042152, 11590142	Standard	NM_016091		Approved	HSPC021, HSPC025, EIF3S11	uc003auf.3	Q9Y262	OTTHUMG00000150671	ENST00000412331.2:c.1142G>A	22.37:g.38273745G>A	ENSP00000416892:p.Arg381His	Somatic	260	1		WXS	Illumina HiSeq	Phase_I	198	77	NM_016091	0	0	1	1	0		Missense_Mutation	SNP	ENST00000412331.2	37	CCDS13960.1	.	.	.	.	.	.	.	.	.	.	g	17.83	3.484330	0.63962	.	.	ENSG00000100129	ENST00000412331;ENST00000425539;ENST00000381683;ENST00000262832;ENST00000406934	T;T;T	0.47177	0.85;0.85;0.85	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.64170	1.965	0.80722	D	1	B;B;B;B	0.33755	0.424;0.205;0.241;0.391	B;B;B;B	0.34779	0.185;0.086;0.067;0.189	T	0.54912	-0.8222	10	0.52906	T	0.07	-11.4514	18.5732	0.91144	0.0:0.0:1.0:0.0	.	333;283;381;424	B4DYB2;B0QY90;Q9Y262;B0QY89	.;.;EIF3L_HUMAN;.	H	381;424;333;348;283	ENSP00000416892:R381H;ENSP00000371099:R333H;ENSP00000384634:R283H	ENSP00000262832:R348H	R	+	2	0	EIF3L	36603691	1.000000	0.71417	0.983000	0.44433	0.982000	0.71751	9.824000	0.99380	2.436000	0.82500	0.436000	0.28706	CGT	.		0.507	EIF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319551.2	NM_016091		A	38273745	G	A	38273745	3	1	34	1	0	0	0	0	1	0	0	0	5035	1145	40	1	1184	1	EIF3L	22	38273745	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	7455355	38273745	13030821	95	3034											
ENTHD1	150350	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40283710	40283710	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacttttatttcagcatctgAgtaatttttcacaaagtttt	11	19	5	6	0	3	1	2	1	1	0	3	2	3	1	0	0	1	3	0	0	3	8			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:40283710A>C	ENST00000325157.6	-	2	293	c.43T>G	c.(43-45)Tca>Gca	p.S15A		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	15	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.									breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					TCAGCATCTGAGTAATTTTTC	0.388																																					p.S15A		.											.	ENTHD1-93	0			c.T43G						.						79	77	78					22																	40283710		2203	4300	6503	SO:0001583	missense	150350	exon2			CATCTGAGTAATT	AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.43T>G	22.37:g.40283710A>C	ENSP00000317431:p.Ser15Ala	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	22	8	NM_152512	0	0	0	0	0	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	37	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.238534	0.79800	.	.	ENSG00000176177	ENST00000325157	T	0.51574	0.7	5.72	5.72	0.89469	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.000000	0.56097	D	0.000026	T	0.74336	0.3703	M	0.89968	3.075	0.46336	D	0.998993	P	0.45348	0.856	D	0.64687	0.928	T	0.79598	-0.1737	10	0.87932	D	0	-12.6774	15.6751	0.77311	1.0:0.0:0.0:0.0	.	15	Q8IYW4	ENTD1_HUMAN	A	15	ENSP00000317431:S15A	ENSP00000317431:S15A	S	-	1	0	ENTHD1	38613656	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.127000	0.64727	2.183000	0.69458	0.533000	0.62120	TCA	.		0.388	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		C	40283710	A	C	40283710	3	2	34	1	0	0	0	0	1	0	0	0	5150	304	11	5	1804	5	ENTHD1	22	40283710	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	2009965	40283710	11020856	96	3035											
CENPM	79019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42339699	42339699	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgctgcagtggctctccCgcccagctggaaagaagcca	10	6	12	13	1	1	1	0	0	1	1	2	3	1	2	3	2	4	4	3	2	3	0	rs138744954		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:42339699C>T	ENST00000215980.5	-	5	404	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	CENPM_ENST00000407253.3_Intron|CENPM_ENST00000404067.1_Intron|CENPM_ENST00000402338.1_Missense_Mutation_p.R72Q|CENPM_ENST00000402420.1_Silent_p.A100A	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	106					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						GTGGCTCTCCCGCCCAGCTGG	0.572																																					p.R106Q		.											.	CENPM-90	0			c.G317A						.	C	,GLN/ARG	0,4406		0,0,2203	78	59	65		,317	-4.7	1	22	dbSNP_134	65	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	CENPM	NM_001002876.1,NM_024053.3	,43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,benign	,106/181	42339699	2,13004	2203	4300	6503	SO:0001583	missense	79019	exon5			CTCTCCCGCCCAG	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"chromosome 22 open reading frame 18"	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.317G>A	22.37:g.42339699C>T	ENSP00000215980:p.Arg106Gln	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	94	37	NM_024053	0	0	0	0	0	A7LM22|B1AHQ9|Q6I9W3	Missense_Mutation	SNP	ENST00000215980.5	37	CCDS14025.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106900	0.37145	0.0	2.33E-4	ENSG00000100162	ENST00000215980;ENST00000402338	.	.	.	5.25	-4.72	0.03269	.	0.976709	0.08428	N	0.947321	T	0.26448	0.0646	N	0.16656	0.425	0.29767	N	0.83507	B	0.15930	0.015	B	0.10450	0.005	T	0.41070	-0.9529	9	0.11182	T	0.66	-34.5962	11.9913	0.53176	0.0:0.4651:0.0:0.5349	.	106	Q9NSP4	CENPM_HUMAN	Q	106;72	.	ENSP00000215980:R106Q	R	-	2	0	CENPM	40669645	0.002000	0.14202	0.956000	0.39512	0.972000	0.66771	-0.717000	0.04986	-0.651000	0.05415	-0.218000	0.12543	CGG	C|1.000;T|0.000		0.572	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053		T	42339699	C	T	42339699	3	4	34	1	0	0	0	0	1	0	0	0	3243	652	23	1	273	1	CENPM	22	42339699	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	2055989	42339699	8964867	97	3036											
MCAT	27349	hgsc.bcm.edu	37	chr22	43539309	43539309	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgccgcggcggtagctggCgcccaagcccctgacccacg	5	3	15	18	6	0	1	0	1	0	0	0	1	0	1	5	4	2	2	5	4	2	1	rs200527554	byFrequency	TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:43539309C>A	ENST00000290429.6	-	1	91	c.46G>T	c.(46-48)Gcc>Tcc	p.A16S	MCAT_ENST00000464244.1_5'Flank|MCAT_ENST00000327555.5_Missense_Mutation_p.A16S	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	16					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				CGGTAGCTGGCGCCCAAGCCC	0.761													C|||	44	0.00878594	8e-04	0.0014	5008	,	,		12066	0.001		0	False		,,,				2504	0.0419				p.A16S		.											.	MCAT-91	0			c.G46T						.	C	SER/ALA,SER/ALA	2,2788		0,2,1393	2	3	3		46,46	0.4	0	22		3	12,6196		0,12,3092	no	missense,missense	MCAT	NM_014507.3,NM_173467.4	99,99	0,14,4485	AA,AC,CC		0.1933,0.0717,0.1556	benign,benign	16/181,16/391	43539309	14,8984	1395	3104	4499	SO:0001583	missense	27349	exon1			AGCTGGCGCCCAA	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.46G>T	22.37:g.43539309C>A	ENSP00000290429:p.Ala16Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_014507	0	0	2	9	7	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	37	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005171	0.35415	7.17E-4	0.001933	ENSG00000100294	ENST00000327555;ENST00000290429	T	0.44482	0.92	5.13	0.374	0.16183	.	1.107710	0.06871	N	0.800769	T	0.19208	0.0461	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.006	T	0.24977	-1.0145	10	0.09590	T	0.72	-2.6285	4.8423	0.13496	0.1466:0.5099:0.2666:0.0768	.	16;16	B0QY72;Q8IVS2	.;FABD_HUMAN	S	16	ENSP00000290429:A16S	ENSP00000290429:A16S	A	-	1	0	MCAT	41869253	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.231000	0.09069	-0.090000	0.12462	-0.463000	0.05309	GCC	.		0.761	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467		A	43539309	C	A	43539309	3	1	34	1	0	0	0	0	1	0	0	0	9397	768	27	4	1142	4	MCAT	22	43539309	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	1199610	43539309	7765257	98	3037											
FAM47A	158724	bcgsc.ca	37	chrX	34148842	34148842	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagtcttgggaggctccgaGcggagactggacgtccgacg	7	6	17	11	6	1	1	0	0	1	1	3	7	3	3	2	4	1	1	2	4	0	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:34148842G>A	ENST00000346193.3	-	1	1605	c.1554C>T	c.(1552-1554)cgC>cgT	p.R518R		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	518										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GAGGCTCCGAGCGGAGACTGG	0.657																																					p.R518R													.	FAM47A-134	0			c.C1554T						.						27	27	27					X																	34148842		2185	4270	6455	SO:0001819	synonymous_variant	158724	exon1			CTCCGAGCGGAGA	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1554C>T	X.37:g.34148842G>A		Somatic	26	0		WXS	Illumina HiSeq	Phase_1	28	5	NM_203408	0	0	0	0	0	A8K8I9|Q8TAA0	Silent	SNP	ENST00000346193.3	37	CCDS43926.1																																																																																			.		0.657	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34148842	G	A	34148842	2	1	34	1	0	0	0	0	0	0	0	1	5588	958	34	2		2	FAM47A	23	34148842	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		34148842	121121718	99	3038											
HDAC6	10013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	48676773	48676773	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccgcatgggtgatgctgActacctagctgcctggcatc	6	9	12	14	1	0	2	0	2	0	0	1	2	0	2	4	2	4	4	4	2	2	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:48676773A>G	ENST00000334136.5	+	22	2319	c.2141A>G	c.(2140-2142)gAc>gGc	p.D714G	HDAC6_ENST00000444343.2_Missense_Mutation_p.D728G|HDAC6_ENST00000376619.2_Missense_Mutation_p.D714G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	714	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GGTGATGCTGACTACCTAGCT	0.637																																					p.D714G	Pancreas(112;205 1675 2305 8976 15959)	.											.	HDAC6-230	0			c.A2141G						.						53	42	45					X																	48676773		2203	4300	6503	SO:0001583	missense	10013	exon22			ATGCTGACTACCT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2141A>G	X.37:g.48676773A>G	ENSP00000334061:p.Asp714Gly	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	88	77	NM_006044	0	0	0	27	27	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.672707	0.88445	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813	T;T;T	0.71222	-0.55;-0.55;-0.55	5.35	5.35	0.76521	Histone deacetylase domain (2);	0.237016	0.41294	D	0.000917	T	0.76786	0.4036	L	0.43923	1.385	0.80722	D	1	P;D;P	0.57571	0.931;0.98;0.931	P;D;P	0.63703	0.848;0.917;0.848	T	0.79090	-0.1946	10	0.87932	D	0	-11.0343	12.2017	0.54331	1.0:0.0:0.0:0.0	.	704;362;714	B4DZN1;B3KVK5;Q9UBN7	.;.;HDAC6_HUMAN	G	728;714;714;714	ENSP00000398566:D728G;ENSP00000334061:D714G;ENSP00000365804:D714G	ENSP00000334061:D714G	D	+	2	0	HDAC6	48561717	1.000000	0.71417	0.932000	0.37286	0.989000	0.77384	8.533000	0.90617	1.785000	0.52413	0.486000	0.48141	GAC	.		0.637	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		G	48676773	A	G	48676773	3	3	34	1	0	0	0	0	1	0	0	0	7032	275	10	3	2223	3	HDAC6	23	48676773	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	14527931	48676773	106593787	100	3039											
SERPINA7	6906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	105280775	105280775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaccccaaggtctccacaAtctcagtttgggtgctgcag	9	10	10	12	0	2	1	1	1	2	0	4	1	2	1	3	2	3	3	3	2	3	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:105280775A>G	ENST00000327674.4	-	1	610	c.275T>C	c.(274-276)aTt>aCt	p.I92T	SERPINA7_ENST00000372563.1_Missense_Mutation_p.I92T|SERPINA7_ENST00000487487.1_5'Flank			P05543	THBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	92					aging (GO:0007568)|negative regulation of endopeptidase activity (GO:0010951)|post-embryonic development (GO:0009791)|regulation of proteolysis (GO:0030162)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to peptide hormone (GO:0043434)|response to prostaglandin E (GO:0034695)|response to vitamin A (GO:0033189)|thyroid hormone transport (GO:0070327)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone binding (GO:0042562)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|skin(3)	24					Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GGTCTCCACAATCTCAGTTTG	0.483																																					p.I92T		.											.	SERPINA7-226	0			c.T275C						.						82	75	78					X																	105280775		2203	4300	6503	SO:0001583	missense	6906	exon2			TCCACAATCTCAG	M14091	CCDS14518.1	Xq21-q22	2014-02-18	2005-08-18		ENSG00000123561	ENSG00000123561		"Serine (or cysteine) peptidase inhibitors"	11583	protein-coding gene	gene with protein product	"thyroxin-binding globulin", "thyroxine-binding globulin", "alpha-1 antiproteinase, antitrypsin"	314200	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7"	TBG		24172014	Standard	NM_000354		Approved		uc004eme.2	P05543	OTTHUMG00000022144	ENST00000327674.4:c.275T>C	X.37:g.105280775A>G	ENSP00000329374:p.Ile92Thr	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	46	6	NM_000354	0	0	0	0	0	D3DUX1	Missense_Mutation	SNP	ENST00000327674.4	37	CCDS14518.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.760784	0.31137	.	.	ENSG00000123561	ENST00000327674;ENST00000372563	D;D	0.85773	-2.03;-2.03	4.91	4.91	0.64330	Serpin domain (3);	0.073669	0.56097	D	0.000032	D	0.94298	0.8168	H	0.96175	3.78	0.40968	D	0.984676	D	0.89917	1.0	D	0.87578	0.998	D	0.95648	0.8704	10	0.87932	D	0	.	11.5511	0.50721	1.0:0.0:0.0:0.0	.	92	P05543	THBG_HUMAN	T	92	ENSP00000329374:I92T;ENSP00000361644:I92T	ENSP00000329374:I92T	I	-	2	0	SERPINA7	105167431	1.000000	0.71417	0.055000	0.19348	0.009000	0.06853	8.589000	0.90817	1.930000	0.55929	0.486000	0.48141	ATT	.		0.483	SERPINA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057790.1	NM_000354		G	105280775	A	G	105280775	3	3	34	1	0	0	0	0	1	0	0	0	14126	101	4	3	988	3	SERPINA7	23	105280775	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	56604002	105280775	49989785	101	3040											
ODZ1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123637524	123637524	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctcccagagaataaagtcagGgcacgtttcatattcatatc	13	11	7	10	1	3	1	3	0	0	1	5	2	4	1	1	1	0	2	1	1	5	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:123637524G>T	ENST00000371130.3	-	19	3394	c.3331C>A	c.(3331-3333)Cct>Act	p.P1111T	TENM1_ENST00000422452.2_Missense_Mutation_p.P1111T	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1111					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										ATAAAGTCAGGGCACGTTTCA	0.363																																					p.P1111T		.											.	.	0			c.C3331A						.						165	160	162					X																	123637524		2203	4300	6503	SO:0001583	missense	10178	exon19			AGTCAGGGCACGT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.3331C>A	X.37:g.123637524G>T	ENSP00000360171:p.Pro1111Thr	Somatic	134	1		WXS	Illumina HiSeq	Phase_I	155	132	NM_001163278	0	0	0	2	2	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.302140	0.40694	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85773	-2.03;-2.0	5.7	5.7	0.88788	.	0.060698	0.64402	D	0.000002	T	0.77955	0.4208	L	0.38953	1.18	0.51233	D	0.999913	B;B;B	0.17852	0.024;0.011;0.007	B;B;B	0.12156	0.007;0.005;0.004	T	0.71768	-0.4493	10	0.16420	T	0.52	.	13.7872	0.63117	0.0:0.0:0.8469:0.1531	.	1110;1111;1111	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	T	1111	ENSP00000360171:P1111T;ENSP00000403954:P1111T	ENSP00000360171:P1111T	P	-	1	0	ODZ1	123465205	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.633000	0.74286	2.402000	0.81655	0.600000	0.82982	CCT	.		0.363	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123637524	G	T	123637524	3	4	34	1	0	0	0	0	1	0	0	0	10860	1232	43	4	4923	4	ODZ1	23	123637524	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	18356749	123637524	31633036	102	3041											
RENBP	5973	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	153200984	153200985	+	Frame_Shift_Ins	INS	-	-	T																															gagagggccaccttgccctcINStcggctcaggtagccaaacc																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:153200984_153200985insT	ENST00000393700.3	-	10	1202_1203	c.1122_1123insA	c.(1120-1125)cgagagfs	p.E375fs	NAA10_ENST00000370009.1_5'Flank|NAA10_ENST00000464845.1_5'Flank|NAA10_ENST00000370015.4_5'Flank|RENBP_ENST00000369997.3_Frame_Shift_Ins_p.E361fs|NAA10_ENST00000393712.3_5'Flank|RENBP_ENST00000412763.1_3'UTR|NAA10_ENST00000393710.3_5'Flank	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	375					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	ACCTTGCCCTCTCGGCTCAGGT	0.644																																					p.E375fs		.											.	RENBP-132	0			c.1123_1124insA						.																																			SO:0001589	frameshift_variant	5973	exon10			.		CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"N-acylglucosamine 2-epimerase", "GlcNAc 2-epimerase", "N-acetyl-D-glucosamine 2-epimerase"	312420	"renin-binding protein"			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.1123dupA	X.37:g.153200985_153200985dupT	ENSP00000377303:p.Glu375fs	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	171	144	NM_002910	0	0	0	0	0	B4DNZ3|Q96BI6	Frame_Shift_Ins	INS	ENST00000393700.3	37	CCDS14738.2																																																																																			.		0.644	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910		T	153200985	-	T	153200984	7	5	34	1	0	1	1	0	0	0	0	0	13257	922	32	0	168	0	RENBP	23	153200984	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10	29563460	153200984	2069576	103	3042											
NBPF1	55672	broad.mit.edu	37	chr1	16907371	16907371	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctggttggagtcacaagggCcgtggctatttgaacaagtg	9	10	15	7	1	1	1	1	1	0	0	1	2	1	2	1	4	1	3	1	4	4	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:16907371C>T	ENST00000430580.2	-	16	2347	c.1460G>A	c.(1459-1461)gGc>gAc	p.G487D	NBPF1_ENST00000432949.1_5'Flank	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	487	NBPF 2. {ECO:0000255|PROSITE- ProRule:PRU00647}.			G -> S (in Ref. 2; BAB21784). {ECO:0000305}.		cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GTCACAAGGGCCGTGGCTATT	0.498																																					.													.	.	0			.						.						470	486	481					1																	16907371		2203	4298	6501	SO:0001583	missense	55672	.			CAAGGGCCGTGGC	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"neuroblastoma breakpoint family"	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.1460G>A	1.37:g.16907371C>T	ENSP00000474456:p.Gly487Asp	Somatic	2426	1		WXS	Illumina HiSeq	Phase_I	2347	68	.	0	0	90	94	4	Q8N4E8|Q9C0H0	Missense_Mutation	SNP	ENST00000430580.2	37																																																																																				.		0.498	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940		T	16907371	C	T	16907371	3	4	35	1	0	0	0	0	1	0	0	0	10217	739	26	2	2020	2	NBPF1	1	16907371	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08		16907371	232343250	1	3043											
UBXN11	91544	bcgsc.ca	37	chr1	26608825	26608825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggtccaggacagggacTggggccgggaccgggaccgg	7	3	20	11	3	0	0	0	0	0	0	1	4	1	4	4	8	0	0	4	8	0	0	rs66614970		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:26608825T>C	ENST00000374222.1	-	16	1992	c.1528A>G	c.(1528-1530)Agt>Ggt	p.S510G	UBXN11_ENST00000314675.7_Missense_Mutation_p.S390G|UBXN11_ENST00000374221.3_Missense_Mutation_p.S510G|UBXN11_ENST00000374223.1_Missense_Mutation_p.S267G|UBXN11_ENST00000357089.4_Missense_Mutation_p.S477G|UBXN11_ENST00000374217.2_Missense_Mutation_p.S477G			Q5T124	UBX11_HUMAN	UBX domain protein 11	510	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggacagggactggggccggga	0.716																																					p.S510G													.	UBXN11-91	1	Deletion - In frame(1)	ovary(1)	c.A1528G						.						15	18	17					1																	26608825		1744	3959	5703	SO:0001583	missense	91544	exon16			AGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1528A>G	1.37:g.26608825T>C	ENSP00000363339:p.Ser510Gly	Somatic	69	1		WXS	Illumina HiSeq	Phase_1	87	6	NM_183008	0	0	0	0	0	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	-	2.154	-0.393781	0.04899	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.18502	2.21;2.22;2.49;2.48;2.48;2.49	.	.	.	.	435.379000	0.00994	U	0.003579	T	0.07007	0.0178	N	0.02539	-0.55	0.18873	N	0.999985	.	.	.	.	.	.	T	0.21690	-1.0238	6	0.42905	T	0.14	.	.	.	.	.	477;390;510	Q5T124-2;Q5T124-3;Q5T124	.;.;UBX11_HUMAN	G	390;267;477;510;510;477	ENSP00000324721:S390G;ENSP00000363340:S267G;ENSP00000349601:S477G;ENSP00000363338:S510G;ENSP00000363339:S510G;ENSP00000363334:S477G	ENSP00000324721:S390G	S	-	1	0	UBXN11	26481412	0.000000	0.05858	0.130000	0.21974	0.142000	0.21351	-0.966000	0.03825	0.056000	0.16144	0.055000	0.15244	AGT	.		0.716	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		C	26608825	T	C	26608825	3	2	35	1	0	0	0	0	1	0	0	0	16946	1580	55	3	38	3	UBXN11	1	26608825	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	9701454	26608825	222641796	2	3044											
ANGPTL3	27329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	63066787	63066787	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattcaagaacccacagaaaTttctctatcttccaagccaa	15	11	3	12	0	3	2	1	0	2	2	5	2	4	2	3	0	2	0	3	0	7	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:63066787T>A	ENST00000371129.3	+	3	721	c.641T>A	c.(640-642)aTt>aAt	p.I214N	DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000251157.5_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	214					acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						CCCACAGAAATTTCTCTATCT	0.338																																					p.K214K		.											.	ANGPTL3-130	0			c.A641A						.						92	90	91					1																	63066787		2203	4298	6501	SO:0001583	missense	27329	exon3			CAGAAATTTCTCT	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.641T>A	1.37:g.63066787T>A	ENSP00000360170:p.Ile214Asn	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	128	18	NM_014495	0	0	1	6	5	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	37	CCDS622.1	.	.	.	.	.	.	.	.	.	.	T	6.726	0.502609	0.12822	.	.	ENSG00000132855	ENST00000371129	T	0.62498	0.02	5.36	-1.93	0.07594	.	1.409980	0.04232	N	0.335475	T	0.09555	0.0235	N	0.01576	-0.805	0.20764	N	0.999851	B	0.02656	0.0	B	0.01281	0.0	T	0.04413	-1.0953	10	0.17369	T	0.5	.	1.6612	0.02792	0.3425:0.1379:0.0856:0.4341	.	214	Q9Y5C1	ANGL3_HUMAN	N	214	ENSP00000360170:I214N	ENSP00000360170:I214N	I	+	2	0	ANGPTL3	62839375	0.740000	0.28207	0.994000	0.49952	0.801000	0.45260	0.181000	0.16880	-0.002000	0.14469	-0.649000	0.03915	ATT	.		0.338	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		A	63066787	T	A	63066787	3	1	35	1	0	0	0	0	1	0	0	0	615	1493	52	5	651	5	ANGPTL3	1	63066787	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	36457962	63066787	186183834	3	3045											
ANKRD35	148741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145562384	145562384	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggccacagagaagctgcGgaagctcctggcctcccaga	10	4	14	13	1	0	2	0	0	0	2	2	5	2	4	4	4	3	2	4	4	2	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:145562384G>C	ENST00000355594.4	+	10	2159	c.2072G>C	c.(2071-2073)cGg>cCg	p.R691P		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	691										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAGAAGCTGCGGAAGCTCCTG	0.632																																					p.R691P	Melanoma(9;127 754 22988 51047)	.											.	ANKRD35-95	0			c.G2072C						.						33	38	36					1																	145562384		2203	4300	6503	SO:0001583	missense	148741	exon10			AGCTGCGGAAGCT	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.2072G>C	1.37:g.145562384G>C	ENSP00000347802:p.Arg691Pro	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	49	7	NM_144698	0	0	0	0	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.376931	0.42105	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.57107	0.42	4.97	4.06	0.47325	.	0.000000	0.45361	D	0.000361	T	0.42675	0.1213	M	0.70595	2.14	0.80722	D	1	P	0.49862	0.929	P	0.46510	0.519	T	0.48186	-0.9057	10	0.52906	T	0.07	-21.9317	9.1164	0.36760	0.0988:0.0:0.9012:0.0	.	691	Q8N283	ANR35_HUMAN	P	600;691	ENSP00000347802:R691P	ENSP00000347802:R691P	R	+	2	0	ANKRD35	144273741	0.998000	0.40836	0.991000	0.47740	0.842000	0.47809	4.005000	0.57075	1.319000	0.45190	0.563000	0.77884	CGG	.		0.632	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		C	145562384	G	C	145562384	3	2	35	1	0	0	0	0	1	0	0	0	664	1116	39	4	2110	4	ANKRD35	1	145562384	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	82495597	145562384	103688237	4	3046											
ATP1B1	481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169094257	169094257	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcccagagggatgacaTgatttttgaagattgtggcg	10	12	13	6	1	1	5	1	3	0	2	1	6	1	6	1	2	1	0	1	2	1	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:169094257T>G	ENST00000367816.1	+	4	891	c.362T>G	c.(361-363)aTg>aGg	p.M121R	ATP1B1_ENST00000367815.4_Missense_Mutation_p.M121R|ATP1B1_ENST00000499679.3_Missense_Mutation_p.M65R|ATP1B1_ENST00000367813.3_Missense_Mutation_p.M113R			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	121					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					AGGGATGACATGATTTTTGAA	0.373																																					p.M121R		.											.	ATP1B1-540	0			c.T362G						.						170	167	168					1																	169094257		2203	4300	6503	SO:0001583	missense	481	exon3			ATGACATGATTTT	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.362T>G	1.37:g.169094257T>G	ENSP00000356790:p.Met121Arg	Somatic	302	0		WXS	Illumina HiSeq	Phase_I	320	60	NM_001677	1	0	266	602	335	Q5TGZ3	Missense_Mutation	SNP	ENST00000367816.1	37	CCDS1276.1	.	.	.	.	.	.	.	.	.	.	T	4.424	0.078374	0.08533	.	.	ENSG00000143153	ENST00000367816;ENST00000367815;ENST00000499679;ENST00000367813	T;T;T;T	0.28255	1.63;1.63;1.62;1.63	5.57	5.57	0.84162	.	0.083753	0.85682	D	0.000000	T	0.12732	0.0309	L	0.54323	1.7	0.43830	D	0.996406	B	0.28233	0.204	B	0.24269	0.052	T	0.09037	-1.0693	9	0.15952	T	0.53	-21.6982	10.9096	0.47101	0.14:0.0:0.0:0.86	.	121	P05026	AT1B1_HUMAN	R	121;121;65;113	ENSP00000356790:M121R;ENSP00000356789:M121R;ENSP00000423450:M65R;ENSP00000356787:M113R	ENSP00000356787:M113R	M	+	2	0	ATP1B1	167360881	0.023000	0.18921	1.000000	0.80357	0.432000	0.31715	1.328000	0.33758	2.114000	0.64651	0.533000	0.62120	ATG	.		0.373	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			G	169094257	T	G	169094257	3	3	35	1	0	0	0	0	1	0	0	0	1133	1464	51	5	372	5	ATP1B1	1	169094257	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	23531873	169094257	80156364	5	3047											
AGT	183	hgsc.bcm.edu;broad.mit.edu	37	chr1	230845905	230845905	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agcgtgggaggaccacagggGtatagagagccaggccctgc	10	4	17	10	1	0	1	0	0	0	1	0	4	0	3	3	5	3	1	3	5	2	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:230845905G>T	ENST00000366667.4	-	2	906	c.692C>A	c.(691-693)aCc>aAc	p.T231N	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	231					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GACCACAGGGGTATAGAGAGC	0.597																																					p.T231N		.											.	AGT-226	0			c.C692A						.						70	71	70					1																	230845905		2203	4300	6503	SO:0001583	missense	183	exon2			ACAGGGGTATAGA	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.692C>A	1.37:g.230845905G>T	ENSP00000355627:p.Thr231Asn	Somatic	119	2		WXS	Illumina HiSeq	Phase_I	95	11	NM_000029	0	0	3	6	3	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	G	6.198	0.404694	0.11754	.	.	ENSG00000135744	ENST00000366667	D	0.84370	-1.84	5.01	4.07	0.47477	Serpin domain (3);	0.366568	0.30401	N	0.009708	T	0.77765	0.4179	L	0.40543	1.245	0.09310	N	1	B;B;B	0.30664	0.289;0.111;0.289	B;B;B	0.29785	0.107;0.069;0.107	T	0.64833	-0.6314	10	0.27082	T	0.32	.	11.3331	0.49487	0.0:0.1372:0.7205:0.1423	.	231;231;231	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	N	231	ENSP00000355627:T231N	ENSP00000355627:T231N	T	-	2	0	AGT	228912528	0.716000	0.27956	0.008000	0.14137	0.017000	0.09413	4.528000	0.60580	1.191000	0.43056	0.591000	0.81541	ACC	.		0.597	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		T	230845905	G	T	230845905	3	4	35	1	0	0	0	0	1	0	0	0	399	1261	44	4	781	4	AGT	1	230845905	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	61751648	230845905	18404716	6	3048											
ARID4B	51742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	235386544	235386544	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagattcaaatttcgataTccaagtacaggtcgtttgtt	13	14	8	6	2	1	1	1	0	0	1	4	3	2	1	1	1	1	3	1	1	5	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:235386544T>C	ENST00000264183.3	-	13	1499	c.1002A>G	c.(1000-1002)ggA>ggG	p.G334G	ARID4B_ENST00000349213.3_Silent_p.G334G|ARID4B_ENST00000366603.2_Silent_p.G334G	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	334	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.|Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			AATTTCGATATCCAAGTACAG	0.299																																					p.G334G		.											.	ARID4B-228	0			c.A1002G						.						106	100	102					1																	235386544		2203	4298	6501	SO:0001819	synonymous_variant	51742	exon13			TCGATATCCAAGT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"-"	15550	protein-coding gene	gene with protein product		609696	"retinoblastoma binding protein 1-like 1", "AT rich interactive domain 4B (RBP1- like)"	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1002A>G	1.37:g.235386544T>C		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	42	6	NM_016374	0	0	2	2	0	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			.		0.299	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		C	235386544	T	C	235386544	2	2	35	1	0	0	0	0	0	0	0	1	920	1422	50	3		3	ARID4B	1	235386544	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	4540639	235386544	13864077	7	3049											
PSME4	23198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	54135515	54135515	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatcgggagtcaaattcaTgcttgtgagatccttggaat	10	13	10	8	1	2	1	2	1	0	1	5	4	4	3	2	2	1	1	2	2	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:54135515T>C	ENST00000404125.1	-	24	2781	c.2726A>G	c.(2725-2727)cAt>cGt	p.H909R	PSME4_ENST00000421748.2_Missense_Mutation_p.H53R	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	909					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)			GTCAAATTCATGCTTGTGAGA	0.338																																					p.H909R		.											.	PSME4-275	0			c.A2726G						.						57	57	57					2																	54135515		2203	4298	6501	SO:0001583	missense	23198	exon24			AATTCATGCTTGT	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.2726A>G	2.37:g.54135515T>C	ENSP00000384211:p.His909Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	46	8	NM_014614	0	0	20	29	9	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	10.65	1.409628	0.25465	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.10960	2.82;2.82	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.050889	0.85682	D	0.000000	T	0.09291	0.0229	L	0.29908	0.895	0.54753	D	0.999982	B;B;B	0.16603	0.007;0.001;0.018	B;B;B	0.12837	0.005;0.003;0.008	T	0.20706	-1.0267	10	0.16420	T	0.52	.	15.3474	0.74350	0.0:0.0:0.0:1.0	.	284;53;909	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	R	53;909	ENSP00000410830:H53R;ENSP00000384211:H909R	ENSP00000384211:H909R	H	-	2	0	PSME4	53989019	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.033000	0.64146	2.012000	0.59069	0.533000	0.62120	CAT	.		0.338	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54135515	T	C	54135515	3	2	35	1	0	0	0	0	1	0	0	0	12738	1464	51	3	2897	3	PSME4	2	54135515	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		54135515	189063858	8	3050											
PCBP1	5093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	70314950	70314950	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttatgcacggaaaggaagtAggaagcatcattgggaagaa	16	7	13	5	1	1	1	1	0	0	1	1	5	1	5	0	4	2	3	0	4	7	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:70314950A>G	ENST00000303577.5	+	1	366	c.75A>G	c.(73-75)gtA>gtG	p.V25V	PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000439670.2_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	25	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						GAAAGGAAGTAGGAAGCATCA	0.567																																					p.V25V	Colon(85;1146 1307 3484 18706 25380)	.											.	PCBP1-226	0			c.A75G						.						111	114	113					2																	70314950		2203	4300	6503	SO:0001819	synonymous_variant	5093	exon1			GGAAGTAGGAAGC		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.75A>G	2.37:g.70314950A>G		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	164	40	NM_006196	0	0	266	436	170	Q13157|Q14975	Silent	SNP	ENST00000303577.5	37	CCDS1898.1																																																																																			.		0.567	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		G	70314950	A	G	70314950	2	3	35	1	0	0	0	0	0	0	0	1	11526	407	15	3		3	PCBP1	2	70314950	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	16179435	70314950	172884423	9	3051											
SCN1A	6323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	166915109	166915109	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaatcttaatagctattttCctaagaggattgaagggagt	15	13	9	4	0	1	2	0	1	1	1	2	4	2	4	1	2	1	1	1	2	7	7	rs121917959		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:166915109C>T	ENST00000303395.4	-	2	353	c.354G>A	c.(352-354)agG>agA	p.R118R	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000409050.1_Silent_p.R118R|SCN1A_ENST00000375405.3_Silent_p.R118R|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Silent_p.R118R			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	118			R -> S (in EIEE6; dbSNP:rs121917959). {ECO:0000269|PubMed:18413471}.		adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAGCTATTTTCCTAAGAGGAT	0.338																																					p.R118R		.											.	SCN1A-147	0			c.G354A	GRCh37	CM081422	SCN1A	M	rs121917959	.						64	65	65					2																	166915109		2202	4298	6500	SO:0001819	synonymous_variant	6323	exon2			TATTTTCCTAAGA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.354G>A	2.37:g.166915109C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	95	13	NM_001165964	0	0	0	0	0	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166915109	C	T	166915109	2	4	35	1	0	0	0	0	0	0	0	1	13946	854	30	2		2	SCN1A	2	166915109	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	96600159	166915109	76284264	10	3052											
UBR3	130507	hgsc.bcm.edu;bcgsc.ca	37	chr2	170815017	170815017	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcacgacagaaaagctttatGgaaactgcaatggatgttgg	14	10	11	6	1	1	1	1	0	0	1	1	4	1	3	0	3	3	3	0	3	5	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:170815017G>A	ENST00000272793.5	+	24	3665	c.3615G>A	c.(3613-3615)atG>atA	p.M1205I	UBR3_ENST00000418381.1_Missense_Mutation_p.M1205I			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1205					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AAAGCTTTATGGAAACTGCAA	0.343																																					p.M1205I		.											.	UBR3-68	0			c.G3615A						.						95	101	99					2																	170815017		2203	4300	6503	SO:0001583	missense	130507	exon24			CTTTATGGAAACT	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3615G>A	2.37:g.170815017G>A	ENSP00000272793:p.Met1205Ile	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	134	26	NM_172070	0	0	4	6	2	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.648848|4.648848	0.87958|0.87958	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381|ENST00000392632	T;T|.	0.52983|.	0.64;0.64|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.75391|.	0.3843|.	M|M	0.64567|0.64567	1.98|1.98	0.80722|0.80722	D|D	1|1	P;P|.	0.50528|.	0.936;0.851|.	P;P|.	0.61201|.	0.885;0.838|.	T|.	0.70880|.	-0.4752|.	10|.	0.16420|.	T|.	0.52|.	.|.	20.5801|20.5801	0.99389|0.99389	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1205;1205|.	Q6ZT12;E7EVK3|.	UBR3_HUMAN;.|.	I|X	1205|263	ENSP00000272793:M1205I;ENSP00000396068:M1205I|.	ENSP00000272793:M1205I|.	M|W	+|+	3|2	0|0	UBR3|UBR3	170523263|170523263	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.828000|9.828000	0.99408|0.99408	2.873000|2.873000	0.98535|0.98535	0.643000|0.643000	0.83706|0.83706	ATG|TGG	.		0.343	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		A	170815017	G	A	170815017	3	1	35	1	0	0	0	0	1	0	0	0	16936	1348	47	2	3709	2	UBR3	2	170815017	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3899908	170815017	72384356	11	3053											
ZNF385B	151126	ucsc.edu;bcgsc.ca	37	chr2	180308133	180308133	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggctgccgccgctgcgagAggtgaggacaggaaggctgg	8	4	19	10	4	0	2	0	1	0	1	0	5	0	4	2	6	2	3	2	6	1	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:180308133A>G	ENST00000410066.1	-	10	1863	c.1260T>C	c.(1258-1260)ccT>ccC	p.P420P	ZNF385B_ENST00000336917.5_Silent_p.P318P|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409692.1_Silent_p.P318P|ZNF385B_ENST00000409343.1_Silent_p.P344P	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	420	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			CCGCTGCGAGAGGTGAGGACA	0.602																																					p.P420P	Colon(155;204 2491 32774 51842)												.	ZNF385B-23	0			c.T1260C						.						28	36	33					2																	180308133		2201	4299	6500	SO:0001819	synonymous_variant	151126	exon10			TGCGAGAGGTGAG	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.1260T>C	2.37:g.180308133A>G		Somatic	29	0		WXS	Illumina HiSeq		17	4	NM_152520	0	0	2	12	10	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Silent	SNP	ENST00000410066.1	37	CCDS33339.1																																																																																			.		0.602	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		G	180308133	A	G	180308133	2	3	35	1	0	0	0	0	0	0	0	1	17909	291	11	3		3	ZNF385B	2	180308133	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	9493116	180308133	62891240	12	3054											
SSFA2	6744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	182765433	182765433	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttttgtagtgtttcagaaTtgttggaactttatgaggaa	10	19	10	2	0	1	2	1	1	0	1	1	4	1	4	0	2	1	3	0	2	5	9			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:182765433T>C	ENST00000431877.2	+	7	693	c.514T>C	c.(514-516)Ttg>Ctg	p.L172L	SSFA2_ENST00000428267.2_Silent_p.L19L|SSFA2_ENST00000409001.1_Silent_p.L172L|SSFA2_ENST00000320370.7_Silent_p.L172L	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	172						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TGTTTCAGAATTGTTGGAACT	0.299																																					p.L172L		.											.	SSFA2-153	0			c.T514C						.						55	57	56					2																	182765433		2203	4299	6502	SO:0001819	synonymous_variant	6744	exon7			TCAGAATTGTTGG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.514T>C	2.37:g.182765433T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	103	18	NM_001130445	0	0	0	0	0	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Silent	SNP	ENST00000431877.2	37	CCDS46467.1																																																																																			.		0.299	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		C	182765433	T	C	182765433	2	2	35	1	0	0	0	0	0	0	0	1	15215	1490	52	3		3	SSFA2	2	182765433	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	2457300	182765433	60433940	13	3055											
AOX1	316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	201478584	201478584	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttattctgaatgaagtctcCcttttgggctcggcgccagg	6	13	11	11	2	2	2	0	2	2	0	4	2	2	2	2	3	0	1	2	3	3	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:201478584C>T	ENST00000374700.2	+	15	1747	c.1506C>T	c.(1504-1506)tcC>tcT	p.S502S	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	502					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ATGAAGTCTCCCTTTTGGGCT	0.478																																					p.S502S		.											.	AOX1-96	0			c.C1506T						.						91	87	88					2																	201478584		2203	4300	6503	SO:0001819	synonymous_variant	316	exon15			AGTCTCCCTTTTG	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1506C>T	2.37:g.201478584C>T		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	76	17	NM_001159	0	0	38	101	63	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																			.		0.478	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		T	201478584	C	T	201478584	2	4	35	1	0	0	0	0	0	0	0	1	729	610	22	2		2	AOX1	2	201478584	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	18713151	201478584	41720789	14	3056											
COL4A4	1286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	227872134	227872134	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgctggagcagaggaaaaCtgcaagtctgctttcaccgt	10	9	13	9	1	2	1	1	0	1	1	2	3	2	3	1	3	5	4	1	3	3	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:227872134C>T	ENST00000396625.3	-	48	5187	c.4980G>A	c.(4978-4980)caG>caA	p.Q1660Q	COL4A4_ENST00000329662.7_Silent_p.Q1657Q	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1660	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.			LQ -> FE (in Ref. 5; BAA04214). {ECO:0000305}.	axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CAGAGGAAAACTGCAAGTCTG	0.517																																					p.Q1660Q		.											.	COL4A4-142	0			c.G4980A						.						284	291	289					2																	227872134		1978	4170	6148	SO:0001819	synonymous_variant	1286	exon48			GGAAAACTGCAAG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"Collagens"	2206	protein-coding gene	gene with protein product	"collagen of basement membrane, alpha-4 chain"	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4980G>A	2.37:g.227872134C>T		Somatic	606	1		WXS	Illumina HiSeq	Phase_I	570	88	NM_000092	0	0	2	4	2	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			.		0.517	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	227872134	C	T	227872134	2	4	35	1	0	0	0	0	0	0	0	1	3699	564	20	2		2	COL4A4	2	227872134	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	26393550	227872134	15327239	15	3057											
DNAJB3	54578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234652351	234652351	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccgccctccgcccccGcctcgccatagcggtcatag	5	6	10	20	5	1	0	1	0	0	0	3	0	2	0	7	1	3	1	7	1	2	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:234652351G>A	ENST00000305139.6	+	2	1000				UGT1A3_ENST00000482026.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000480628.1_Intron|DNAJB3_ENST00000449667.1_RNA	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6						cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CTCCGCCCCCGCCTCGCCATA	0.627																																					p.A71V		.											.	.	0			c.C212T						.						97	108	105					2																	234652351		2007	4180	6187	SO:0001627	intron_variant	414061	exon1			GCCCCCGCCTCGC	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"UDP glucuronosyltransferases"	12538	other	complex locus constituent		606431	"UDP glycosyltransferase 1 family, polypeptide A6"			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.862-23329G>A	2.37:g.234652351G>A		Somatic	220	1		WXS	Illumina HiSeq	Phase_I	197	44	NM_001001394	0	0	0	0	0	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			.		0.627	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		A	234652351	G	A	234652351	1	1	35	0	1	0	0	0	0	0	0	0	4632	1087	38	1		1	DNAJB3	2	234652351	Intron	SNP	G	TCGA-B1-5398-01A-02D-1589-08	6780217	234652351	8547022	16	3058			1	9		2	2	22	N	G_A	9.293193e-05
DNAJB3	54578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234652372	234652372	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgccatagcggtcatagAtatcgcgtttcttggcgtcc	6	12	10	13	5	2	1	1	0	1	1	5	1	3	1	3	2	1	1	3	2	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:234652372A>G	ENST00000305139.6	+	2	1000				UGT1A3_ENST00000482026.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000480628.1_Intron|DNAJB3_ENST00000449667.1_RNA	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6						cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	GCGGTCATAGATATCGCGTTT	0.632																																					p.I64T		.											.	.	0			c.T191C						.						131	143	139					2																	234652372		2045	4204	6249	SO:0001627	intron_variant	414061	exon1			TCATAGATATCGC	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"UDP glucuronosyltransferases"	12538	other	complex locus constituent		606431	"UDP glycosyltransferase 1 family, polypeptide A6"			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.862-23308A>G	2.37:g.234652372A>G		Somatic	254	0		WXS	Illumina HiSeq	Phase_I	239	37	NM_001001394	0	0	1	1	0	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			.		0.632	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		G	234652372	A	G	234652372	1	3	35	0	1	0	0	0	0	0	0	0	4632	333	12	3		3	DNAJB3	2	234652372	Intron	SNP	A	TCGA-B1-5398-01A-02D-1589-08	21	234652372	8547001	17	3059			1	9		2	2	22	N	G_A	9.293193e-05
SH3BP4	23677	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	235962373	235962373	+	Frame_Shift_Del	DEL	C	C	-																															accaagcgctggaagcacctCactgggactctgatcttggt																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:235962373delC	ENST00000409212.1	+	6	3312	c.2805delC	c.(2803-2805)ctcfs	p.L935fs	SH3BP4_ENST00000344528.4_Frame_Shift_Del_p.L935fs|SH3BP4_ENST00000392011.2_Frame_Shift_Del_p.L935fs			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	935					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GGAAGCACCTCACTGGGACTC	0.592																																					p.L935fs		.											.	SH3BP4-94	0			c.2805delC						.						173	164	167					2																	235962373		2203	4300	6503	SO:0001589	frameshift_variant	23677	exon6			.	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.2805delC	2.37:g.235962373delC	ENSP00000386862:p.Leu935fs	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	163	34	NM_014521	0	0	0	0	0	O95082|Q309A3|Q53QD0|Q53TD1	Frame_Shift_Del	DEL	ENST00000409212.1	37	CCDS2513.1																																																																																			.		0.592	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			-	235962373	C	-	235962373	7	5	35	1	0	1	0	1	0	0	0	0	14278	813	29	0	2819	0	SH3BP4	2	235962373	Frame_Shift_Del	DEL	C	TCGA-B1-5398-01A-02D-1589-08	1310001	235962373	7237000	18	3060											
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238234213	238234213	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcacttaccaggagcgcaAaccttttcacattctttctg	11	13	5	12	1	4	0	2	0	2	0	4	1	4	1	2	1	3	1	2	1	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:238234213A>T	ENST00000295550.4	-	43	9935	c.9483T>A	c.(9481-9483)gtT>gtA	p.V3161V	COL6A3_ENST00000472056.1_Silent_p.V2554V|COL6A3_ENST00000347401.3_Silent_p.V2960V|COL6A3_ENST00000346358.4_Silent_p.V2961V|COL6A3_ENST00000409809.1_Silent_p.V2955V|COL6A3_ENST00000473258.1_5'UTR|COL6A3_ENST00000353578.4_Silent_p.V2955V	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3161	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGGAGCGCAAACCTTTTCAC	0.383																																					p.V3161V		.											.	COL6A3-526	0			c.T9483A						.						178	181	180					2																	238234213		2203	4300	6503	SO:0001819	synonymous_variant	1293	exon43			AGCGCAAACCTTT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.9483T>A	2.37:g.238234213A>T		Somatic	224	0		WXS	Illumina HiSeq	Phase_I	231	53	NM_004369	0	0	0	0	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			.		0.383	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238234213	A	T	238234213	2	4	35	1	0	0	0	0	0	0	0	1	3707	1	1	5		5	COL6A3	2	238234213	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	2271840	238234213	4965160	19	3061											
PER2	8864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	239184526	239184526	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtgtgtgtccactttcgaAgactggtcgctactgcagga	7	13	12	9	2	0	1	0	0	0	1	3	3	1	2	1	2	2	2	1	2	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:239184526A>C	ENST00000254657.3	-	4	585	c.306T>G	c.(304-306)tcT>tcG	p.S102S	PER2_ENST00000355768.2_Silent_p.S102S|PER2_ENST00000440245.1_Silent_p.S102S|PER2_ENST00000254658.3_Silent_p.S102S	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	102					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CCACTTTCGAAGACTGGTCGC	0.502																																					p.S102S		.											.	PER2-154	0			c.T306G						.						173	169	170					2																	239184526		2203	4300	6503	SO:0001819	synonymous_variant	8864	exon4			TTTCGAAGACTGG	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.306T>G	2.37:g.239184526A>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	116	19	NM_022817	0	0	2	4	2	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			.		0.502	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		C	239184526	A	C	239184526	2	2	35	1	0	0	0	0	0	0	0	1	11756	59	3	5		5	PER2	2	239184526	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	950313	239184526	4014847	20	3062											
NGLY1	55768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	25773885	25773885	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccccaagttctccaggtttAggggttttgggagatataaa	10	12	11	8	0	1	1	0	0	1	1	2	2	1	1	3	4	0	3	3	4	5	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr3:25773885A>T	ENST00000280700.5	-	9	1510	c.1350T>A	c.(1348-1350)ccT>ccA	p.P450P	NGLY1_ENST00000467224.1_Intron|NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000396649.3_Silent_p.P450P|NGLY1_ENST00000417874.2_Silent_p.P408P|NGLY1_ENST00000428257.1_Silent_p.P432P	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	450					glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						CTCCAGGTTTAGGGGTTTTGG	0.418																																					p.P450P		.											.	NGLY1-135	0			c.T1350A						.						102	108	106					3																	25773885		2203	4300	6503	SO:0001819	synonymous_variant	55768	exon9			AGGTTTAGGGGTT	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1350T>A	3.37:g.25773885A>T		Somatic	152	1		WXS	Illumina HiSeq	Phase_I	138	50	NM_018297	0	0	6	37	31	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Silent	SNP	ENST00000280700.5	37	CCDS33719.1																																																																																			.		0.418	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			T	25773885	A	T	25773885	2	4	35	1	0	0	0	0	0	0	0	1	10424	407	15	5		5	NGLY1	3	25773885	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08		25773885	172248545	21	3063											
SCN11A	11280	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	38891987	38891988	+	Frame_Shift_Del	DEL	GC	GC	-																															cttactaacaatggaaagaaGcacgaccacacagtcaaata																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr3:38891987_38891988delGC	ENST00000302328.3	-	25	4509_4510	c.4311_4312delGC	c.(4309-4314)gtgcttfs	p.L1439fs	SCN11A_ENST00000450244.1_Frame_Shift_Del_p.L1439fs|SCN11A_ENST00000456224.3_Frame_Shift_Del_p.L1401fs|SCN11A_ENST00000444237.2_Frame_Shift_Del_p.L1439fs	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1439					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGGAAAGAAGCACGACCACAC	0.347																																					p.1437_1438del		.											.	SCN11A-99	0			c.4311_4312del						.																																			SO:0001589	frameshift_variant	11280	exon25			.	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4311_4312delGC	3.37:g.38891987_38891988delGC	ENSP00000307599:p.Leu1439fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	136	39	NM_014139	0	0	0	0	0	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Frame_Shift_Del	DEL	ENST00000302328.3	37	CCDS33737.1																																																																																			.		0.347	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		-	38891988	GC	-	38891987	7	5	35	1	0	1	0	1	0	0	0	0	13945	971	34	0	1071	0	SCN11A	3	38891987	Frame_Shift_Del	DEL	GC	TCGA-B1-5398-01A-02D-1589-08	13118102	38891987	159130443	22	3064											
NDUFB5	4711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179334831	179334831	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaacactgggaatattataAggtttgtataggacattgac	15	12	10	4	0	0	2	0	1	0	1	0	4	0	4	0	3	1	2	0	3	7	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr3:179334831A>C	ENST00000259037.3	+	4	455	c.341A>C	c.(340-342)aAg>aCg	p.K114T	NDUFB5_ENST00000473500.1_3'UTR|NDUFB5_ENST00000472629.1_Splice_Site_p.K102T|NDUFB5_ENST00000493866.1_Splice_Site_p.K62T|snoU13_ENST00000459278.1_RNA	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	114					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			GAATATTATAAGGTTTGTATA	0.343																																					p.K114T		.											.	NDUFB5-91	0			c.A341C						.						79	78	78					3																	179334831		2203	4300	6503	SO:0001630	splice_region_variant	4711	exon4			ATTATAAGGTTTG	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"Mitochondrial respiratory chain complex / Complex I"	7700	protein-coding gene	gene with protein product	"complex I SGDH subunit"	603841	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.342+1A>C	3.37:g.179334831A>C		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	76	28	NM_002492	0	0	0	0	0	Q561V6	Missense_Mutation	SNP	ENST00000259037.3	37	CCDS3234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.66|15.66	2.899232|2.899232	0.52227|0.52227	.|.	.|.	ENSG00000136521|ENSG00000136521	ENST00000259037;ENST00000493866;ENST00000472629;ENST00000471112|ENST00000482604	T;T;T;T|.	0.55413|.	0.52;0.52;0.52;0.52|.	5.54|5.54	4.37|4.37	0.52481|0.52481	.|.	0.044583|.	0.85682|.	D|.	0.000000|.	T|T	0.74275|0.74275	0.3695|0.3695	M|M	0.86740|0.86740	2.835|2.835	0.80722|0.80722	D|D	1|1	D;P|.	0.63046|.	0.992;0.933|.	D;P|.	0.63703|.	0.917;0.827|.	T|T	0.74466|0.74466	-0.3656|-0.3656	10|5	0.87932|.	D|.	0|.	-13.9029|-13.9029	7.2091|7.2091	0.25923|0.25923	0.776:0.1461:0.0779:0.0|0.776:0.1461:0.0779:0.0	.|.	62;114|.	Q561V6;O43674|.	.;NDUB5_HUMAN|.	T|R	114;62;102;35|131	ENSP00000259037:K114T;ENSP00000419656:K62T;ENSP00000419248:K102T;ENSP00000419501:K35T|.	ENSP00000259037:K114T|.	K|S	+|+	2|1	0|0	NDUFB5|NDUFB5	180817525|180817525	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.531000|0.531000	0.34715|0.34715	6.924000|6.924000	0.75823|0.75823	0.923000|0.923000	0.37045|0.37045	-0.304000|-0.304000	0.09214|0.09214	AAG|AGC	.		0.343	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492	Missense_Mutation	C	179334831	A	C	179334831	5	2	35	1	0	0	0	0	0	0	1	0	10310	86	3	5	355	5	NDUFB5	3	179334831	Splice_Site	SNP	A	TCGA-B1-5398-01A-02D-1589-08	140442844	179334831	18687599	23	3065											
ABCC5	10057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183706444	183706444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccttcttgtgggccacaCgggccagagaagaaagccac	10	5	11	15	1	1	2	0	0	1	2	1	3	1	2	5	2	1	0	5	2	2	2	rs200810558		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr3:183706444C>T	ENST00000334444.6	-	4	599	c.359G>A	c.(358-360)cGt>cAt	p.R120H	ABCC5_ENST00000427120.2_Missense_Mutation_p.R120H|ABCC5_ENST00000382494.2_Missense_Mutation_p.R120H|ABCC5_ENST00000265586.6_Missense_Mutation_p.R120H|ABCC5_ENST00000392579.2_Missense_Mutation_p.R120H	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	120					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GTGGGCCACACGGGCCAGAGA	0.527																																					p.R120H		.											.	ABCC5-137	0			c.G359A						.						86	81	83					3																	183706444		2203	4300	6503	SO:0001583	missense	10057	exon4			GCCACACGGGCCA	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.359G>A	3.37:g.183706444C>T	ENSP00000333926:p.Arg120His	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	89	28	NM_005688	0	0	22	24	2	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.218	0.801935	0.16397	.	.	ENSG00000114770	ENST00000334444;ENST00000382495;ENST00000265586;ENST00000427120;ENST00000392579;ENST00000382494;ENST00000437341	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	5.75	1.45	0.22620	.	0.350255	0.30428	N	0.009657	T	0.81202	0.4773	M	0.62723	1.935	0.09310	N	1	B;B;B;B;B	0.16603	0.018;0.018;0.002;0.012;0.01	B;B;B;B;B	0.13407	0.007;0.007;0.003;0.004;0.009	T	0.62742	-0.6790	10	0.14656	T	0.56	-3.1865	8.6238	0.33877	0.1061:0.6423:0.0:0.2516	.	120;120;120;120;120	A5PKY6;Q29ZA9;Q86UX3;Q86W30;O15440	.;.;.;.;MRP5_HUMAN	H	120;56;120;120;120;120;120	ENSP00000333926:R120H;ENSP00000265586:R120H;ENSP00000404809:R120H;ENSP00000376358:R120H;ENSP00000371934:R120H;ENSP00000399726:R120H	ENSP00000265586:R120H	R	-	2	0	ABCC5	185189138	0.000000	0.05858	0.236000	0.24074	0.906000	0.53458	-0.323000	0.07997	0.349000	0.23975	0.655000	0.94253	CGT	C|0.999;T|0.000		0.527	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		T	183706444	C	T	183706444	3	4	35	1	0	0	0	0	1	0	0	0	56	536	19	1	4102	1	ABCC5	3	183706444	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	4371613	183706444	14315986	24	3066											
C4orf35	85438	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	71201158	71201158	+	Frame_Shift_Del	DEL	T	T	-																															actactgtttctttaatagaTttttccactgacatagcaaa																								rs367634444		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:71201158delT	ENST00000273936.5	+	1	476	c.402delT	c.(400-402)gatfs	p.D134fs		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	134					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CTTTAATAGATTTTTCCACTG	0.383																																					p.D134fs		.											.	CABS1-93	0			c.402delT						.						54	54	54					4																	71201158		2203	4298	6501	SO:0001589	frameshift_variant	85438	exon1			.	AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"casein-like phosphoprotein"		"chromosome 4 open reading frame 35"	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.402delT	4.37:g.71201158delT	ENSP00000273936:p.Asp134fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	116	23	NM_033122	0	0	0	0	0	B2RCB5|Q86UE0|Q96M17	Frame_Shift_Del	DEL	ENST00000273936.5	37	CCDS3539.1																																																																																			.		0.383	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122		-	71201158	T	-	71201158	7	5	35	1	0	1	0	1	0	0	0	0	2271	1490	52	0	404	0	C4orf35	4	71201158	Frame_Shift_Del	DEL	T	TCGA-B1-5398-01A-02D-1589-08		71201158	119953118	25	3067											
ANKRD17	26057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	74014608	74014608	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgtataaccttcatcatTgacctcttccaggctagctc	8	14	7	12	0	3	1	2	1	1	0	5	1	4	1	3	2	2	3	3	2	3	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:74014608T>A	ENST00000358602.4	-	8	1605	c.1489A>T	c.(1489-1491)Aat>Tat	p.N497Y	ANKRD17_ENST00000509867.2_Missense_Mutation_p.N384Y|ANKRD17_ENST00000330838.6_Missense_Mutation_p.N497Y|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	497					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCTTCATCATTGACCTCTTCC	0.443																																					p.N497Y		.											.	ANKRD17-234	0			c.A1489T						.						115	97	103					4																	74014608		2203	4300	6503	SO:0001583	missense	26057	exon8			CATCATTGACCTC	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"Ankyrin repeat domain containing"	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.1489A>T	4.37:g.74014608T>A	ENSP00000351416:p.Asn497Tyr	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	90	15	NM_198889	0	0	3	3	0	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.059277	0.76074	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.16897	2.31;2.31;2.31	5.43	4.25	0.50352	Ankyrin repeat-containing domain (5);	0.000000	0.64402	D	0.000002	T	0.37128	0.0992	M	0.61703	1.905	0.30866	N	0.732937	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;1.0;0.999	T	0.40478	-0.9561	10	0.72032	D	0.01	.	11.4205	0.49978	0.0:0.071:0.0:0.929	.	82;497;497;497;384	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	Y	497;497;497;384;497	ENSP00000351416:N497Y;ENSP00000332265:N497Y;ENSP00000427151:N384Y	ENSP00000332265:N497Y	N	-	1	0	ANKRD17	74233472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.885000	0.87282	1.002000	0.39104	0.482000	0.46254	AAT	.		0.443	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		A	74014608	T	A	74014608	3	1	35	1	0	0	0	0	1	0	0	0	646	1812	63	5	6430	5	ANKRD17	4	74014608	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	2813450	74014608	117139668	26	3068											
SCD5	79966	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	83719607	83719607	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccgggccgccgccgccCtcagagctttcgagcccggc	3	6	12	20	6	2	1	1	0	1	1	4	2	2	1	6	2	2	1	6	2	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:83719607C>G	ENST00000319540.4	-	1	403	c.84G>C	c.(82-84)gaG>gaC	p.E28D	SCD5_ENST00000282709.4_Missense_Mutation_p.E28D|SCD5_ENST00000273908.4_Missense_Mutation_p.E28D	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	28					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.E28D(2)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CGCCGCCGCCCTCAGAGCTTT	0.692																																					p.E28D		.											.	SCD5-91	2	Substitution - Missense(2)	lung(2)	c.G84C						.						21	23	22					4																	83719607		2200	4295	6495	SO:0001583	missense	79966	exon1			GCCGCCCTCAGAG	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.84G>C	4.37:g.83719607C>G	ENSP00000316329:p.Glu28Asp	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	39	5	NM_024906	0	0	2	6	4	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	37	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	C	9.274	1.046479	0.19748	.	.	ENSG00000145284	ENST00000319540;ENST00000273908;ENST00000282709	T	0.44083	0.93	4.24	2.39	0.29439	.	0.474937	0.20549	N	0.090143	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	B;B;B	0.24721	0.034;0.11;0.008	B;B;B	0.19946	0.027;0.027;0.003	T	0.11867	-1.0570	10	0.16896	T	0.51	-2.1795	2.9623	0.05896	0.1795:0.542:0.1749:0.1035	.	28;28;28	Q9BSN4;Q86SK9-2;Q86SK9	.;.;SCD5_HUMAN	D	28	ENSP00000316329:E28D	ENSP00000273908:E28D	E	-	3	2	SCD5	83938631	0.000000	0.05858	0.008000	0.14137	0.176000	0.22953	-0.141000	0.10327	0.973000	0.38340	0.471000	0.43371	GAG	.		0.692	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		G	83719607	C	G	83719607	3	3	35	1	0	0	0	0	1	0	0	0	13919	680	24	4	1134	4	SCD5	4	83719607	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	9704999	83719607	107434669	27	3069											
GUCY1B3	2983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	156725753	156725753	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttttttgcagataacaatAgggatacacactggagaggt	13	12	10	6	0	1	2	0	0	1	2	1	4	1	3	0	3	3	1	0	3	4	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:156725753A>G	ENST00000264424.8	+	12	1645	c.1563A>G	c.(1561-1563)atA>atG	p.I521M	GUCY1B3_ENST00000502959.1_Missense_Mutation_p.I543M|GUCY1B3_ENST00000513437.1_Missense_Mutation_p.I453M|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.I501M|GUCY1B3_ENST00000505154.1_Missense_Mutation_p.I453M|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.I488M|GUCY1B3_ENST00000507146.1_Missense_Mutation_p.I496M	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	521	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		AGATAACAATAGGGATACACA	0.373																																					p.I521M		.											.	.	0			c.A1563G						.						114	117	116					4																	156725753		1863	4098	5961	SO:0001583	missense	2983	exon12			AACAATAGGGATA	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1563A>G	4.37:g.156725753A>G	ENSP00000264424:p.Ile521Met	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	165	21	NM_000857	0	0	0	0	0	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	37	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181816	0.57800	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	D;D;D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05;-2.05	5.54	-0.268	0.12934	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.92912	0.7745	H	0.94264	3.515	0.52501	D	0.999953	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.996;0.998;0.991;0.995	D	0.91851	0.5491	10	0.87932	D	0	.	10.0789	0.42377	0.3827:0.5019:0.0:0.1153	.	501;543;496;488;521	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	M	453;543;501;496;521;488;453	ENSP00000427226:I453M;ENSP00000426786:I543M;ENSP00000426319:I501M;ENSP00000422313:I496M;ENSP00000264424:I521M;ENSP00000420842:I488M;ENSP00000425065:I453M	ENSP00000264424:I521M	I	+	3	3	GUCY1B3	156945203	0.972000	0.33761	0.998000	0.56505	0.987000	0.75469	0.228000	0.17814	0.045000	0.15804	-0.323000	0.08544	ATA	.		0.373	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			G	156725753	A	G	156725753	3	3	35	1	0	0	0	0	1	0	0	0	6916	410	15	3	1609	3	GUCY1B3	4	156725753	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	73006146	156725753	34428523	28	3070											
NEIL3	55247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	178243705	178243705	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaaactttggggaaggagctCtttatgtactttggaccaaa	12	12	11	6	0	1	0	0	0	1	0	1	4	1	3	1	4	3	2	1	4	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:178243705C>G	ENST00000264596.3	+	2	367	c.249C>G	c.(247-249)ctC>ctG	p.L83L		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	83					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		GGAAGGAGCTCTTTATGTACT	0.413								Base excision repair (BER), DNA glycosylases																													p.L83L		.											.	NEIL3-660	0			c.C249G						.						196	193	194					4																	178243705		2203	4300	6503	SO:0001819	synonymous_variant	55247	exon2			GGAGCTCTTTATG	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 3"	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.249C>G	4.37:g.178243705C>G		Somatic	194	1		WXS	Illumina HiSeq	Phase_I	243	32	NM_018248	0	0	1	2	1	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																			.		0.413	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		G	178243705	C	G	178243705	2	3	35	1	0	0	0	0	0	0	0	1	10346	900	32	4		4	NEIL3	4	178243705	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	21517952	178243705	12910571	29	3071											
CCDC110	256309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	186380443	186380443	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacagattcttttaggtaaTtctgtaagtactgaattttt	11	18	7	5	0	2	2	0	1	2	1	2	2	2	2	0	1	1	4	0	1	5	9			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:186380443T>A	ENST00000307588.3	-	6	1373	c.1298A>T	c.(1297-1299)aAt>aTt	p.N433I	CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.N396I|CCDC110_ENST00000510617.1_Missense_Mutation_p.N433I	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	433						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TTTTAGGTAATTCTGTAAGTA	0.318																																					p.N433I		.											.	CCDC110-90	0			c.A1298T						.						94	98	97					4																	186380443		2203	4297	6500	SO:0001583	missense	256309	exon6			AGGTAATTCTGTA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1298A>T	4.37:g.186380443T>A	ENSP00000306776:p.Asn433Ile	Somatic	285	0		WXS	Illumina HiSeq	Phase_I	261	51	NM_152775	0	0	0	0	0	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046799	0.55110	.	.	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.08807	3.06;3.05;3.05	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	T	0.24699	0.0599	M	0.66939	2.045	0.30797	N	0.740247	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.12167	-1.0558	10	0.51188	T	0.08	-18.2543	10.1029	0.42515	0.1493:0.0:0.0:0.8507	.	433;396;433	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	I	396;433;433	ENSP00000377172:N396I;ENSP00000306776:N433I;ENSP00000427246:N433I	ENSP00000306776:N433I	N	-	2	0	CCDC110	186617437	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.671000	0.54576	2.161000	0.67846	0.533000	0.62120	AAT	.		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		A	186380443	T	A	186380443	3	1	35	1	0	0	0	0	1	0	0	0	2753	1493	52	5	1211	5	CCDC110	4	186380443	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	8136738	186380443	4773833	30	3072											
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	31983432	31983432	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaaaaaggggaaacgaacCagaaagtttggggtcatctc	15	6	13	7	2	2	1	1	0	1	1	3	4	2	2	1	4	2	1	1	4	5	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:31983432C>G	ENST00000438447.1	+	3	1036	c.648C>G	c.(646-648)acC>acG	p.T216T	PDZD2_ENST00000282493.3_Silent_p.T216T			O15018	PDZD2_HUMAN	PDZ domain containing 2	216					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGAAACGAACCAGAAAGTTTG	0.557																																					p.T216T		.											.	PDZD2-563	0			c.C648G						.						87	85	85					5																	31983432		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon2			ACGAACCAGAAAG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.648C>G	5.37:g.31983432C>G		Somatic	149	0		WXS	Illumina HiSeq	Phase_I	138	30	NM_178140	0	0	0	0	0	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			.		0.557	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	31983432	C	G	31983432	2	3	35	1	0	0	0	0	0	0	0	1	11727	581	21	4		4	PDZD2	5	31983432	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08		31983432	148931828	31	3073											
AGXT2	64902	hgsc.bcm.edu;broad.mit.edu	37	chr5	35026613	35026613	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatctttagcttggcagcAgtctgcaaaaagcaaacaac	14	9	8	10	0	2	1	0	1	2	0	2	1	2	1	0	1	6	5	0	1	5	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:35026613A>C	ENST00000231420.6	-	8	972	c.772T>G	c.(772-774)Tgc>Ggc	p.C258G		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	258					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	GCTTGGCAGCAGTCTGCAAAA	0.368																																					p.C258G		.											.	AGXT2-94	0			c.T772G						.						90	79	83					5																	35026613		2203	4300	6503	SO:0001583	missense	64902	exon8			GGCAGCAGTCTGC	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"beta-alanine-pyruvate aminotransferase", "beta-ALAAT II"	612471	"alanine-glyoxylate aminotransferase 2"			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.772T>G	5.37:g.35026613A>C	ENSP00000231420:p.Cys258Gly	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	82	8	NM_031900	0	0	2	2	0	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	.	.	.	.	.	.	.	.	.	.	A	9.197	1.027582	0.19512	.	.	ENSG00000113492	ENST00000231420	D	0.81996	-1.56	5.7	3.21	0.36854	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.368655	0.34652	N	0.003790	T	0.64338	0.2589	N	0.10809	0.05	0.35502	D	0.799851	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.56866	-0.7908	10	0.21014	T	0.42	-4.9282	8.517	0.33253	0.6305:0.2497:0.0:0.1198	.	258;258	E9PDL7;Q9BYV1	.;AGT2_HUMAN	G	258	ENSP00000231420:C258G	ENSP00000231420:C258G	C	-	1	0	AGXT2	35062370	1.000000	0.71417	0.999000	0.59377	0.939000	0.58152	1.435000	0.34969	0.373000	0.24621	0.533000	0.62120	TGC	.		0.368	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900		C	35026613	A	C	35026613	3	2	35	1	0	0	0	0	1	0	0	0	405	188	7	5	800	5	AGXT2	5	35026613	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	3043181	35026613	145888647	32	3074											
ISL1	3670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	50683584	50683584	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcggccactgcaaatggcagGtactcctctgcccggctcgg	6	7	13	15	3	1	0	0	0	1	0	3	0	2	0	3	5	3	4	3	5	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:50683584G>T	ENST00000230658.7	+	3	1063		c.e3+1		ISL1_ENST00000505475.2_Splice_Site|ISL1_ENST00000511384.1_Splice_Site	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1						atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				CAAATGGCAGGTACTCCTCTG	0.637																																					.		.											.	ISL1-515	0			c.478+1G>T						.						23	25	24					5																	50683584		2037	4162	6199	SO:0001630	splice_region_variant	3670	exon3			TGGCAGGTACTCC	BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"Homeoboxes / LIM class"	6132	protein-coding gene	gene with protein product		600366	"ISL1 transcription factor, LIM/homeodomain, (islet-1)"			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.478+1G>T	5.37:g.50683584G>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_002202	0	0	0	0	0	P20663|P47894	Splice_Site	SNP	ENST00000230658.7	37	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.649867	0.87958	.	.	ENSG00000016082	ENST00000230658;ENST00000503187;ENST00000511384;ENST00000505475	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2404	0.93879	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ISL1	50719341	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.502000	0.81614	2.538000	0.85594	0.456000	0.33151	.	.		0.637	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202	Intron	T	50683584	G	T	50683584	5	4	35	1	0	0	0	0	0	0	1	0	7877	1275	44	4	489	4	ISL1	5	50683584	Splice_Site	SNP	G	TCGA-B1-5398-01A-02D-1589-08	15656971	50683584	130231676	33	3075											
ZNF366	167465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	71739940	71739940	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggctgtagggctccacctcGtagcagttatcctcctcttc	5	12	10	14	1	1	0	0	0	1	0	6	0	4	0	4	2	1	6	4	2	3	4	rs373642159		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:71739940G>C	ENST00000318442.5	-	5	2368	c.1878C>G	c.(1876-1878)taC>taG	p.Y626*	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	626	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		GCTCCACCTCGTAGCAGTTAT	0.667																																					p.Y626X		.											.	ZNF366-91	0			c.C1878G						.						94	108	103					5																	71739940		2203	4300	6503	SO:0001587	stop_gained	167465	exon5			CACCTCGTAGCAG	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.1878C>G	5.37:g.71739940G>C	ENSP00000313158:p.Tyr626*	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	372	65	NM_152625	0	0	1	1	0	Q5HYI9|Q7RTV4	Nonsense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	G	38	7.253100	0.98164	.	.	ENSG00000178175	ENST00000318442	.	.	.	5.78	-7.21	0.01490	.	0.868154	0.10255	N	0.696665	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.173	17.8813	0.88841	0.6695:0.0:0.3305:0.0	.	.	.	.	X	626	.	ENSP00000313158:Y626X	Y	-	3	2	ZNF366	71775696	0.385000	0.25172	0.000000	0.03702	0.206000	0.24218	-0.180000	0.09754	-1.491000	0.01840	-0.136000	0.14681	TAC	.		0.667	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			C	71739940	G	C	71739940	4	2	35	1	0	0	0	0	0	1	0	0	17902	1140	40	4	360	4	ZNF366	5	71739940	Nonsense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	21056356	71739940	109175320	34	3076											
MCC	4163	broad.mit.edu;bcgsc.ca	37	chr5	112458403	112458403	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtcagcagtaaccatggtAgactggttttcggggataga	11	11	13	6	1	1	2	1	0	0	2	2	3	1	3	1	4	2	4	1	4	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:112458403A>T	ENST00000302475.4	-	4	998	c.435T>A	c.(433-435)tcT>tcA	p.S145S	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000408903.3_Silent_p.S335S|MCC_ENST00000515367.2_Silent_p.S82S	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	145					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TAACCATGGTAGACTGGTTTT	0.502																																					p.S335S													.	MCC-69	0			c.T1005A						.						150	122	132					5																	112458403		2202	4300	6502	SO:0001819	synonymous_variant	4163	exon6			CATGGTAGACTGG		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"EF-hand domain containing"	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.435T>A	5.37:g.112458403A>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	68	6	NM_001085377	0	0	7	11	4	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			.		0.502	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		T	112458403	A	T	112458403	2	4	35	1	0	0	0	0	0	0	0	1	9398	407	15	5		5	MCC	5	112458403	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	40718463	112458403	68456857	35	3077											
PCDHA8	56140	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140222316	140222316	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaggagaacaacccgccGggctgccacatcttcacggt	10	6	12	13	3	2	2	1	1	1	1	2	3	2	2	3	3	3	1	3	3	3	1	rs202126810		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:140222316G>C	ENST00000531613.1	+	1	1410	c.1410G>C	c.(1408-1410)ccG>ccC	p.P470P	PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.P470P|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	470	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAACCCGCCGGGCTGCCACA	0.672																																					p.P470P		.											.	PCDHA8-92	0			c.G1410C						.						38	43	41					5																	140222316		2193	4252	6445	SO:0001819	synonymous_variant	56140	exon1			CCCGCCGGGCTGC	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1410G>C	5.37:g.140222316G>C		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	123	16	NM_031856	1	0	2	3	0	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																			G|0.999;T|0.001		0.672	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		C	140222316	G	C	140222316	2	2	35	1	0	0	0	0	0	0	0	1	11556	1103	39	4		4	PCDHA8	5	140222316	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	27763913	140222316	40692944	36	3078											
ARHGAP26	23092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	142513635	142513635	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctgcagcgagaggccccTgacgctcttccacaccgttc	6	8	10	17	3	1	2	0	1	1	1	4	3	3	2	5	1	2	3	5	1	0	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:142513635T>A	ENST00000274498.4	+	19	2180	c.1802T>A	c.(1801-1803)cTg>cAg	p.L601Q	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.L601Q	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	601	Ser-rich.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGAGGCCCCTGACGCTCTTC	0.582																																					p.L601Q		.											.	ARHGAP26-660	0			c.T1802A						.						129	110	116					5																	142513635		2203	4300	6503	SO:0001583	missense	23092	exon19			GGCCCCTGACGCT	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1802T>A	5.37:g.142513635T>A	ENSP00000274498:p.Leu601Gln	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	187	31	NM_015071	0	0	21	28	7	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	CCDS4277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.4|24.4	4.531454|4.531454	0.85706|0.85706	.|.	.|.	ENSG00000145819|ENSG00000145819	ENST00000274498;ENST00000378004;ENST00000418668|ENST00000443674;ENST00000418236	T;T|.	0.09630|.	2.96;2.97|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.55878|.	0.1948|.	L|L	0.29908|0.29908	0.895|0.895	0.51767|0.51767	D|D	0.99993|0.99993	D;D;D|.	0.76494|.	0.998;0.994;0.999|.	D;P;D|.	0.87578|.	0.995;0.852;0.998|.	T|.	0.52298|.	-0.8594|.	10|.	0.42905|.	T|.	0.14|.	.|.	15.3985|15.3985	0.74816|0.74816	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	601;174;601|.	Q9UNA1;B3KT96;Q9UNA1-2|.	RHG26_HUMAN;.;.|.	Q|R	601;601;174|220;173	ENSP00000274498:L601Q;ENSP00000367243:L601Q|.	ENSP00000274498:L601Q|.	L|X	+|+	2|1	0|0	ARHGAP26|ARHGAP26	142493828|142493828	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	5.763000|5.763000	0.68818|0.68818	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.		0.582	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		A	142513635	T	A	142513635	3	1	35	1	0	0	0	0	1	0	0	0	875	1580	55	5	1876	5	ARHGAP26	5	142513635	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	2291319	142513635	38401625	37	3079											
RBM27	54439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	145641187	145641187	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaccgattcattcgagtcTtgtggcatagggaaaataat	14	11	9	7	2	2	0	1	0	1	0	3	3	2	1	1	2	1	1	1	2	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:145641187T>G	ENST00000265271.5	+	13	2174	c.2008T>G	c.(2008-2010)Ttg>Gtg	p.L670V	RBM27_ENST00000506502.1_Missense_Mutation_p.L615V	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	670	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CATTCGAGTCTTGTGGCATAG	0.478																																					p.L670V		.											.	RBM27-70	0			c.T2008G						.						174	156	161					5																	145641187		1568	3582	5150	SO:0001583	missense	54439	exon13			CGAGTCTTGTGGC	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2008T>G	5.37:g.145641187T>G	ENSP00000265271:p.Leu670Val	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	229	34	NM_018989	0	0	10	10	0	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.473230	0.43942	.	.	ENSG00000091009	ENST00000265271	T	0.44083	0.93	5.5	-1.73	0.08081	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.106316	0.40222	N	0.001141	T	0.30634	0.0771	N	0.19112	0.55	0.09310	N	1	P;P	0.41748	0.568;0.761	B;P	0.45310	0.301;0.476	T	0.33701	-0.9858	10	0.66056	D	0.02	-6.6533	11.6531	0.51301	0.0:0.4781:0.0:0.5219	.	670;615	Q9P2N5;B3KY61	RBM27_HUMAN;.	V	670	ENSP00000265271:L670V	ENSP00000265271:L670V	L	+	1	2	RBM27	145621380	0.692000	0.27719	0.167000	0.22817	0.977000	0.68977	1.212000	0.32394	-0.779000	0.04560	-0.379000	0.06801	TTG	.		0.478	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		G	145641187	T	G	145641187	3	3	35	1	0	0	0	0	1	0	0	0	13159	1606	56	5	2058	5	RBM27	5	145641187	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	3127552	145641187	35274073	38	3080											
CPEB4	80315	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	173370039	173370039	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacatgcagcaaggacataTgggcgaaggagaggtaacat	15	6	14	6	1	0	2	0	1	0	1	0	5	0	3	0	4	3	3	0	4	4	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:173370039T>G	ENST00000265085.5	+	4	2723	c.1269T>G	c.(1267-1269)taT>taG	p.Y423*	CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000522336.1_Intron|CPEB4_ENST00000519835.1_Intron|CPEB4_ENST00000520867.1_Intron|CPEB4_ENST00000334035.5_Nonsense_Mutation_p.Y406*|CPEB4_ENST00000517880.1_Intron	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	423					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CAAGGACATATGGGCGAAGGA	0.348																																					p.Y423X		.											.	CPEB4-90	0			c.T1269G						.						187	195	192					5																	173370039		2203	4300	6503	SO:0001587	stop_gained	80315	exon4			GACATATGGGCGA	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.1269T>G	5.37:g.173370039T>G	ENSP00000265085:p.Tyr423*	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	328	44	NM_030627	0	0	0	0	0	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Nonsense_Mutation	SNP	ENST00000265085.5	37	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	T	41	8.729920	0.98931	.	.	ENSG00000113742	ENST00000265085;ENST00000334035	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6823	16.2484	0.82467	0.0:0.0:0.0:1.0	.	.	.	.	X	423;406	.	ENSP00000265085:Y423X	Y	+	3	2	CPEB4	173302645	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.965000	0.87945	2.291000	0.77112	0.533000	0.62120	TAT	.		0.348	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		G	173370039	T	G	173370039	4	3	35	1	0	0	0	0	0	1	0	0	3809	1471	51	5	1283	5	CPEB4	5	173370039	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	27728852	173370039	7545221	39	3081											
MAK	4117	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	10796389	10796389	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gggttgtccaacaacctgatCgattatatccggcagaggct	10	10	11	10	2	0	2	0	1	0	1	3	3	2	2	3	3	2	3	3	3	4	3	rs201812469	byFrequency	TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:10796389C>G	ENST00000313243.2	-	9	1367	c.985G>C	c.(985-987)Gat>Cat	p.D329H	MAK_ENST00000536370.1_3'UTR|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000354489.2_Missense_Mutation_p.D329H|MAK_ENST00000474039.1_Missense_Mutation_p.D329H|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000538030.1_Missense_Mutation_p.D329H			P20794	MAK_HUMAN	male germ cell-associated kinase	329	Glu/Pro-rich.		D -> E (in dbSNP:rs17579447).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				ACAACCTGATCGATTATATCC	0.483																																					p.D329H		.											.	MAK-335	0			c.G985C						.						120	124	123					6																	10796389		2203	4300	6503	SO:0001583	missense	4117	exon9			CCTGATCGATTAT		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.985G>C	6.37:g.10796389C>G	ENSP00000313021:p.Asp329His	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	130	26	NM_005906	0	0	0	0	0	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.380100	0.42207	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.72167	-0.63;-0.63;-0.63	4.96	4.09	0.47781	.	0.539095	0.20661	N	0.088033	T	0.51024	0.1650	L	0.32530	0.975	0.45108	D	0.998127	P	0.46512	0.879	P	0.47673	0.554	T	0.53878	-0.8376	10	0.42905	T	0.14	.	9.0292	0.36249	0.0:0.7735:0.1482:0.0784	.	329	P20794	MAK_HUMAN	H	329	ENSP00000313021:D329H;ENSP00000346484:D329H;ENSP00000442250:D329H	ENSP00000313021:D329H	D	-	1	0	MAK	10904375	0.415000	0.25416	0.068000	0.19968	0.049000	0.14656	1.369000	0.34227	1.220000	0.43490	0.448000	0.29417	GAT	C|0.999;T|0.000		0.483	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		G	10796389	C	G	10796389	3	3	35	1	0	0	0	0	1	0	0	0	9222	884	31	4	910	4	MAK	6	10796389	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08		10796389	160318678	40	3082											
MDC1	9656	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30679993	30679993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctctgcatctgtttcacagtCcccatgcagaggccaggctt	7	11	9	14	0	3	1	1	0	2	1	4	1	4	1	3	2	2	4	3	2	0	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:30679993C>T	ENST00000376406.3	-	5	2373	c.1726G>A	c.(1726-1728)Gac>Aac	p.D576N	MDC1_ENST00000376405.2_Missense_Mutation_p.D576N|MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000494654.1_5'Flank	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	576					DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GTTTCACAGTCCCCATGCAGA	0.542								Other conserved DNA damage response genes																													p.D576N		.											.	MDC1-273	0			c.G1726A						.						58	57	58					6																	30679993		1509	2709	4218	SO:0001583	missense	9656	exon5			CACAGTCCCCATG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.1726G>A	6.37:g.30679993C>T	ENSP00000365588:p.Asp576Asn	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	63	15	NM_014641	0	0	5	8	3	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	C	8.320	0.824001	0.16678	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.03553	3.97;3.89	4.32	1.5	0.22942	.	.	.	.	.	T	0.00875	0.0029	L	0.44542	1.39	0.09310	N	1	B;B;P;B	0.37466	0.037;0.054;0.596;0.003	B;B;B;B	0.35470	0.049;0.028;0.203;0.018	T	0.45906	-0.9229	9	0.15499	T	0.54	-2.5972	2.8168	0.05458	0.1874:0.5287:0.1815:0.1023	.	576;448;576;576	Q14676-2;B4DYH4;Q14676;Q14676-4	.;.;MDC1_HUMAN;.	N	576;576;576;448	ENSP00000365588:D576N;ENSP00000365587:D576N	ENSP00000365587:D576N	D	-	1	0	MDC1	30787972	0.031000	0.19500	0.001000	0.08648	0.006000	0.05464	1.511000	0.35801	0.106000	0.17784	-0.467000	0.05162	GAC	.		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		T	30679993	C	T	30679993	3	4	35	1	0	0	0	0	1	0	0	0	9428	855	30	2	4587	2	MDC1	6	30679993	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	19883604	30679993	140435074	41	3083											
HSPA1L	3305	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31778274	31778274	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgccggtgctcttgtccgtGgctgtgacattgagaatacc	6	13	12	10	2	1	2	0	2	1	1	2	3	2	2	3	2	3	2	3	2	2	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:31778274G>T	ENST00000375654.4	-	2	1665	c.1476C>A	c.(1474-1476)gcC>gcA	p.A492A	HSPA1L_ENST00000417199.3_Silent_p.A492A	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	492					binding of sperm to zona pellucida (GO:0007339)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|pleura(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TCTTGTCCGTGGCTGTGACAT	0.542																																					p.A492A		.											.	HSPA1L-230	0			c.C1476A						.						130	118	122					6																	31778274		2203	4300	6503	SO:0001819	synonymous_variant	3305	exon2			GTCCGTGGCTGTG	D85730	CCDS34413.1	6p21.3	2014-01-21	2002-08-29		ENSG00000204390	ENSG00000204390		"Heat shock proteins / HSP70"	5234	protein-coding gene	gene with protein product		140559	"heat shock 70kD protein-like 1"			9685725, 9349405	Standard	NM_005527		Approved	HSP70-HOM, hum70t	uc003nxh.3	P34931	OTTHUMG00000031208	ENST00000375654.4:c.1476C>A	6.37:g.31778274G>T		Somatic	217	1		WXS	Illumina HiSeq	Phase_I	197	35	NM_005527	0	0	0	0	0	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Silent	SNP	ENST00000375654.4	37	CCDS34413.1																																																																																			.		0.542	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			T	31778274	G	T	31778274	2	4	35	1	0	0	0	0	0	0	0	1	7431	1335	47	4		4	HSPA1L	6	31778274	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	1098281	31778274	139336793	42	3084											
SLC39A7	7922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33169242	33169242	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcacgagagcatctggcatGgacatacccacgatcacgac	12	6	9	14	3	3	1	2	0	1	1	3	5	3	2	1	2	2	2	1	2	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:33169242G>C	ENST00000374677.3	+	1	593	c.220G>C	c.(220-222)Gga>Cga	p.G74R	RXRB_ENST00000413614.2_5'Flank|RXRB_ENST00000374680.3_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.G74R|RXRB_ENST00000374685.4_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000544186.1_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	74	His-rich.				transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CATCTGGCATGGACATACCCA	0.552																																					p.G74R		.											.	SLC39A7-67	0			c.G220C						.						122	123	122					6																	33169242		2134	4244	6378	SO:0001583	missense	7922	exon1			TGGCATGGACATA	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.220G>C	6.37:g.33169242G>C	ENSP00000363809:p.Gly74Arg	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	100	21	NM_006979	0	0	102	189	87	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	37	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.840008	0.51057	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000374677	T;T	0.60920	0.15;0.15	4.75	4.75	0.60458	.	0.374050	0.27802	N	0.017796	T	0.30510	0.0767	L	0.27053	0.805	0.45946	D	0.99877	P	0.48162	0.906	B	0.44163	0.443	T	0.06643	-1.0815	10	0.13853	T	0.58	-11.1163	13.1907	0.59709	0.0:0.0:1.0:0.0	.	74	Q92504	S39A7_HUMAN	R	74;55;74	ENSP00000363807:G74R;ENSP00000363809:G74R	ENSP00000363807:G74R	G	+	1	0	SLC39A7	33277220	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.576000	0.53878	2.507000	0.84556	0.289000	0.19496	GGA	.		0.552	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		C	33169242	G	C	33169242	3	2	35	1	0	0	0	0	1	0	0	0	14655	1349	47	4	222	4	SLC39A7	6	33169242	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	1390968	33169242	137945825	43	3085											
MAPK14	1432	bcgsc.ca	37	chr6	36040750	36040750	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttatctaccaaattctcCgaggtctaaaggtacagata	13	12	6	10	1	3	1	0	0	3	1	5	2	4	1	3	2	2	1	3	2	7	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:36040750C>A	ENST00000229794.4	+	4	794	c.406C>A	c.(406-408)Cga>Aga	p.R136R	MAPK14_ENST00000468133.1_Silent_p.R59R|MAPK14_ENST00000229795.3_Silent_p.R136R|MAPK14_ENST00000310795.4_Silent_p.R136R	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						CCAAATTCTCCGAGGTCTAAA	0.373																																					p.R136R	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)												.	MAPK14-1444	0			c.C406A						.						83	79	80					6																	36040750		2203	4300	6503	SO:0001819	synonymous_variant	1432	exon4			ATTCTCCGAGGTC	L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.406C>A	6.37:g.36040750C>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_1	57	4	NM_139012	0	0	2	2	0	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Silent	SNP	ENST00000229794.4	37	CCDS4816.1																																																																																			.		0.373	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		A	36040750	C	A	36040750	2	1	35	1	0	0	0	0	0	0	0	1	9301	644	23	4		4	MAPK14	6	36040750	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	2871508	36040750	135074317	44	3086											
LMBRD1	55788	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	70451754	70451755	+	Frame_Shift_Ins	INS	-	-	AA																															ttttgttattgggaacattcINSaatggaacaaaggcactaca																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:70451754_70451755insAA	ENST00000370577.3	-	6	717_718	c.488_489insTT	c.(487-489)ttgfs	p.L163fs	LMBRD1_ENST00000370570.1_Frame_Shift_Ins_p.L90fs	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	163					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						TGGGAACATTCAATGGAACAAA	0.267																																					p.L163fs		.											.	LMBRD1-91	0			c.489_490insTT						.																																			SO:0001589	frameshift_variant	55788	exon6			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.487_488dupTT	6.37:g.70451755_70451756dupAA	ENSP00000359609:p.Leu163fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	90	14	NM_018368	0	0	0	0	0	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Ins	INS	ENST00000370577.3	37	CCDS4969.1																																																																																			.		0.267	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		AA	70451755	-	AA	70451754	7	5	35	1	0	1	1	0	0	0	0	0	8865	825	29	0	1177	0	LMBRD1	6	70451754	Frame_Shift_Ins	INS	-	TCGA-B1-5398-01A-02D-1589-08	34411004	70451754	100663313	45	3087											
TPBG	7162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	83075159	83075159	+	Frame_Shift_Del	DEL	G	G	-																															tggccgacctcagtcccttcGctttctcgggcagcaatgcc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:83075159delG	ENST00000369750.3	+	2	1098	c.481delG	c.(481-483)gctfs	p.A161fs	TPBG_ENST00000535040.1_Frame_Shift_Del_p.A161fs|TPBG_ENST00000543496.1_Frame_Shift_Del_p.A161fs			Q13641	TPBG_HUMAN	trophoblast glycoprotein	161					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		CAGTCCCTTCGCTTTCTCGGG	0.667																																					p.A161fs		.											.	TPBG-514	0			c.481delG						.						76	82	80					6																	83075159		2203	4300	6503	SO:0001589	frameshift_variant	7162	exon2			.	AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.481delG	6.37:g.83075159delG	ENSP00000358765:p.Ala161fs	Somatic	245	0		WXS	Illumina HiSeq	Phase_I	204	31	NM_001166392	0	0	0	0	0	A8K555	Frame_Shift_Del	DEL	ENST00000369750.3	37	CCDS4995.1																																																																																			.		0.667	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1			-	83075159	G	-	83075159	7	5	35	1	0	1	0	1	0	0	0	0	16427	1087	38	0	483	0	TPBG	6	83075159	Frame_Shift_Del	DEL	G	TCGA-B1-5398-01A-02D-1589-08	12623405	83075159	88039908	46	3088											
FIG4	9896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	110086287	110086287	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacagtttatggtgggaaaAtgtgctctggcctatcagct	9	12	12	8	0	2	0	1	0	1	0	2	1	2	1	1	3	2	4	1	3	4	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:110086287A>T	ENST00000230124.3	+	14	1630	c.1506A>T	c.(1504-1506)aaA>aaT	p.K502N	FIG4_ENST00000441478.2_Missense_Mutation_p.K225N	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	502	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TGGTGGGAAAATGTGCTCTGG	0.393																																					p.K502N		.											.	FIG4-69	0			c.A1506T						.						162	144	150					6																	110086287		2203	4300	6503	SO:0001583	missense	9896	exon14			GGGAAAATGTGCT	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1506A>T	6.37:g.110086287A>T	ENSP00000230124:p.Lys502Asn	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	135	25	NM_014845	0	0	21	32	11	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	37	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.709792	0.68730	.	.	ENSG00000112367	ENST00000441478;ENST00000230124	T;T	0.57436	1.65;0.4	5.22	-7.1	0.01547	Synaptojanin, N-terminal (1);	0.052794	0.64402	D	0.000001	T	0.57198	0.2037	M	0.85859	2.78	0.52501	D	0.999955	D;D	0.64830	0.994;0.973	P;P	0.59424	0.857;0.496	T	0.76130	-0.3072	10	0.59425	D	0.04	-25.2243	16.78	0.85561	0.4032:0.0:0.5968:0.0	.	225;502	F5H8L9;Q92562	.;FIG4_HUMAN	N	225;502	ENSP00000399443:K225N;ENSP00000230124:K502N	ENSP00000230124:K502N	K	+	3	2	FIG4	110192980	0.983000	0.35010	0.502000	0.27614	0.869000	0.49853	0.299000	0.19138	-1.402000	0.02056	-0.924000	0.02725	AAA	.		0.393	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		T	110086287	A	T	110086287	3	4	35	1	0	0	0	0	1	0	0	0	5907	98	4	5	1560	5	FIG4	6	110086287	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	27011128	110086287	61028780	47	3089											
AGR2	10551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	16837318	16837319	+	Splice_Site	DNP	AC	AC	GA																															gtgtttgtcagttgtttcatActaaaataaaaagaaaagca																								rs571596748		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:16837318_16837319AC>GA	ENST00000419304.2	-	6	483	c.331_331GT>TC	c.(331-333)GTta>TCtta	p.V111S	AGR2_ENST00000401412.1_Splice_Site_p.V111S|AGR2_ENST00000419572.2_Splice_Site_p.V131S	NM_006408.3	NP_006399.1	O95994	AGR2_HUMAN	anterior gradient 2	111					lung goblet cell differentiation (GO:0060480)|mucus secretion (GO:0070254)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	dystroglycan binding (GO:0002162)			endometrium(2)|lung(1)|prostate(1)|skin(2)	6	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		GTTGTTTCATACTAAAATAAAA	0.381																																					.		.											.	AGR2	0			c.331-1G>T						.																																			SO:0001630	splice_region_variant	10551	exon7			TTCATACTAAAAT	AF038451	CCDS5364.1	7p21.3	2013-07-31	2013-07-31		ENSG00000106541	ENSG00000106541		"Protein disulfide isomerases"	328	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 17"	606358	"anterior gradient 2 homolog (Xenopus laevis)"			9790916	Standard	NM_006408		Approved	XAG-2, HAG-2, AG2, PDIA17	uc003str.3	O95994	OTTHUMG00000023446	ENST00000419304.2:c.331_331delinsGA	7.37:g.16837318_16837319delinsGA		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	59	13		0	0	0	0	0		Splice_Site	DNP	ENST00000419304.2	37	CCDS5364.1																																																																																			.		0.381	AGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207594.2	NM_006408	Missense_Mutation	GA	16837319	AC	GA	16837318	5	3	35	1	0	0	0	0	0	0	1	0	395	405	14	3	208	3	AGR2	7	16837318	Splice_Site	DNP	AC	TCGA-B1-5398-01A-02D-1589-08		16837318	142301345	48	3090											
ABCB5	340273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	20778604	20778604	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaatgctttatcttttgatAgagtttttactgcaattgca	11	18	6	6	0	1	2	0	1	1	1	1	2	1	2	0	0	4	4	0	0	5	9			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:20778604A>G	ENST00000404938.2	+	24	3519		c.e24-1		ABCB5_ENST00000258738.6_Splice_Site	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5						antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						ATCTTTTGATAGAGTTTTTAC	0.393																																					.		.											.	ABCB5-158	0			c.2868-2A>G						.						59	57	58					7																	20778604		2203	4300	6503	SO:0001630	splice_region_variant	340273	exon24			TTTGATAGAGTTT	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"ATP binding cassette transporters / subfamily B"	46	protein-coding gene	gene with protein product	"P-glycoprotein ABCB5", "ATP-binding cassette protein"	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2868-1A>G	7.37:g.20778604A>G		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	48	7	NM_001163941	0	0	0	0	0	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Splice_Site	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.236102	0.39498	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9637	0.58472	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCB5	20745129	1.000000	0.71417	0.931000	0.37212	0.329000	0.28539	8.421000	0.90259	2.238000	0.73509	0.397000	0.26171	.	.		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	Intron	G	20778604	A	G	20778604	5	3	35	1	0	0	0	0	0	0	1	0	44	434	15	3	2997	3	ABCB5	7	20778604	Splice_Site	SNP	A	TCGA-B1-5398-01A-02D-1589-08	3941286	20778604	138360059	49	3091											
SBDS	51119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	66459200	66459200	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgcagctgttacccaccTgcttacagatttcagtttgg	7	14	9	11	0	1	1	1	0	0	1	1	1	1	1	2	1	6	6	2	1	2	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:66459200T>C	ENST00000246868.2	-	2	440	c.257A>G	c.(256-258)cAg>cGg	p.Q86R	TYW1_ENST00000359626.5_5'Flank	NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	86					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						GTTACCCACCTGCTTACAGAT	0.378			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.Q86R		.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS-523	0			c.A257G						.						153	133	139					7																	66459200		2203	4300	6503	SO:0001630	splice_region_variant	51119	exon2	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	CCCACCTGCTTAC	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.258+1A>G	7.37:g.66459200T>C		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	188	33	NM_016038	0	0	0	0	0	A8K0P4|Q96FX0|Q9NV53	Missense_Mutation	SNP	ENST00000246868.2	37	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209588	0.58343	.	.	ENSG00000126524	ENST00000246868	D	0.96011	-3.88	4.73	4.73	0.59995	Ribosome maturation protein SBDS, N-terminal (2);	0.104529	0.64402	D	0.000002	D	0.92886	0.7737	L	0.45422	1.42	0.58432	D	0.999999	B	0.15930	0.015	B	0.31016	0.123	D	0.89696	0.3901	10	0.32370	T	0.25	-14.8213	12.2034	0.54339	0.0:0.0:0.0:1.0	.	86	Q9Y3A5	SBDS_HUMAN	R	86	ENSP00000246868:Q86R	ENSP00000246868:Q86R	Q	-	2	0	SBDS	66096635	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.470000	0.53100	1.998000	0.58463	0.459000	0.35465	CAG	.		0.378	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038	Missense_Mutation	C	66459200	T	C	66459200	5	2	35	1	0	0	0	0	0	0	1	0	13889	1594	55	3	511	3	SBDS	7	66459200	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08	45680596	66459200	92679463	50	3092											
GPR22	2845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107115465	107115465	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtctttattgattatttcTacatttcttctctgctggac	7	21	5	8	0	4	1	0	1	4	0	5	2	4	2	0	1	2	1	0	1	3	8			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:107115465T>A	ENST00000304402.4	+	3	2303	c.960T>A	c.(958-960)tcT>tcA	p.S320S	COG5_ENST00000475638.2_Intron|COG5_ENST00000393603.2_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000297135.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	320					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						TGATTATTTCTACATTTCTTC	0.373																																					p.S320S		.											.	GPR22-92	0			c.T960A						.						112	115	114					7																	107115465		2203	4300	6503	SO:0001819	synonymous_variant	2845	exon3			TATTTCTACATTT	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.960T>A	7.37:g.107115465T>A		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	116	22	NM_005295	0	0	0	0	0	O14554	Silent	SNP	ENST00000304402.4	37	CCDS5744.1																																																																																			.		0.373	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			A	107115465	T	A	107115465	2	1	35	1	0	0	0	0	0	0	0	1	6702	1509	53	5		5	GPR22	7	107115465	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	40656265	107115465	52023198	51	3093											
IQUB	154865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	123136764	123136764	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttacattctaatgcattaTaaagaaattcaaaatcttca	18	14	2	7	0	4	1	2	0	2	1	4	1	4	1	0	0	2	1	0	0	8	7	rs567499713		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:123136764T>C	ENST00000466202.1	-	7	1796	c.1220A>G	c.(1219-1221)tAt>tGt	p.Y407C	IQUB_ENST00000324698.6_Missense_Mutation_p.Y407C|IQUB_ENST00000434450.1_Missense_Mutation_p.Y407C	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	407					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						TAATGCATTATAAAGAAATTC	0.308													T|||	1	0.000199681	8e-04	0	5008	,	,		16913	0		0	False		,,,				2504	0				p.Y407C		.											.	IQUB-156	0			c.A1220G						.						63	60	61					7																	123136764		2203	4298	6501	SO:0001583	missense	154865	exon7			GCATTATAAAGAA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.1220A>G	7.37:g.123136764T>C	ENSP00000417769:p.Tyr407Cys	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	84	17	NM_178827	0	0	0	0	0	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.680750	0.29872	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.58652	1.37;1.37;0.32	5.17	0.946	0.19549	.	0.119152	0.64402	D	0.000016	T	0.73705	0.3621	M	0.83692	2.655	0.45295	D	0.998293	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.969	T	0.75434	-0.3319	10	0.87932	D	0	.	10.8458	0.46743	0.3381:0.0:0.0:0.6619	.	407;407	Q8NA54-2;Q8NA54	.;IQUB_HUMAN	C	407	ENSP00000417769:Y407C;ENSP00000324882:Y407C;ENSP00000388498:Y407C	ENSP00000324882:Y407C	Y	-	2	0	IQUB	122924000	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.936000	0.40183	0.309000	0.22966	0.533000	0.62120	TAT	.		0.308	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		C	123136764	T	C	123136764	3	2	35	1	0	0	0	0	1	0	0	0	7841	1406	49	3	1183	3	IQUB	7	123136764	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	16021299	123136764	36001899	52	3094											
BRAF	673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	140453193	140453193	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcttcatgaagaaatataTctgaggtgtagtaagtaaag	15	12	11	3	0	3	3	1	2	2	1	3	3	3	3	0	2	0	3	0	2	8	6	rs121913370		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:140453193T>C	ENST00000288602.6	-	15	1802	c.1742A>G	c.(1741-1743)aAt>aGt	p.N581S		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	581	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> D (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262}.|N -> S (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N581S(9)|p.N581I(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AAGAAATATATCTGAGGTGTA	0.358		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.N581S	Colon(40;35 892 2973 5743 27438)	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF-92146	10	Substitution - Missense(10)	large_intestine(3)|lung(3)|skin(2)|ovary(1)|soft_tissue(1)	c.A1742G						.						86	83	84					7																	140453193		2203	4298	6501	SO:0001630	splice_region_variant	673	exon15	Familial Cancer Database	CFC, CFCS	AATATATCTGAGG	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1742-1A>G	7.37:g.140453193T>C		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	106	18	NM_004333	0	0	0	0	0	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.68|17.68	3.450518|3.450518	0.63290|0.63290	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.99803	.|-6.82	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99864|0.99864	0.9936|0.9936	H|H	0.96970|0.96970	3.915|3.915	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.96655|0.96655	0.9484|0.9484	5|10	.|0.59425	.|D	.|0.04	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|581	.|P15056	.|BRAF_HUMAN	V|S	189|581	.|ENSP00000288602:N581S	.|ENSP00000288602:N581S	I|N	-|-	1|2	0|0	BRAF|BRAF	140099662|140099662	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	ATA|AAT	.		0.358	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	Missense_Mutation	C	140453193	T	C	140453193	5	2	35	1	0	0	0	0	0	0	1	0	1499	1449	50	3	574	3	BRAF	7	140453193	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08	17316429	140453193	18685470	53	3095											
C9orf66	157983	bcgsc.ca	37	chr9	214551	214551	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgacctcgccagctttgtgGggctcccccgacttgcctac	4	9	10	18	3	0	0	0	0	0	0	2	2	1	0	6	2	3	2	6	2	1	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:214551G>T	ENST00000382387.2	-	1	1342	c.846C>A	c.(844-846)ccC>ccA	p.P282P	DOCK8_ENST00000453981.1_5'Flank|DOCK8_ENST00000432829.2_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	282										central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CAGCTTTGTGGGGCTCCCCCG	0.602																																					p.P282P													.	C9orf66-514	0			c.C846A						.						39	42	41					9																	214551		2203	4300	6503	SO:0001819	synonymous_variant	157983	exon1			TTTGTGGGGCTCC	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.846C>A	9.37:g.214551G>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_1	55	5	NM_152569	0	0	7	8	1	Q96NB0	Silent	SNP	ENST00000382387.2	37	CCDS6439.1																																																																																			.		0.602	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569		T	214551	G	T	214551	2	4	35	1	0	0	0	0	0	0	0	1	2496	1219	43	4		4	C9orf66	9	214551	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08		214551	140998880	54	3096											
KIF27	55582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	86485505	86485505	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatcaaggtcctcagcttTcggttttagaccttcttcct	6	16	7	12	1	3	1	2	0	1	1	6	1	5	1	3	2	2	3	3	2	2	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:86485505T>A	ENST00000297814.2	-	12	2829	c.2686A>T	c.(2686-2688)Aaa>Taa	p.K896*	RP11-575L7.4_ENST00000591217.1_RNA|KIF27_ENST00000413982.1_Nonsense_Mutation_p.K830*|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000586211.1_RNA|KIF27_ENST00000334204.2_Intron|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	896					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TCCTCAGCTTTCGGTTTTAGA	0.363																																					p.K896X		.											.	KIF27-523	0			c.A2686T						.						93	88	90					9																	86485505		2202	4300	6502	SO:0001587	stop_gained	55582	exon12			CAGCTTTCGGTTT	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"Kinesins"	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.2686A>T	9.37:g.86485505T>A	ENSP00000297814:p.Lys896*	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	143	18	NM_017576	0	0	1	1	0	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Nonsense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.962159	0.92791	.	.	ENSG00000165115	ENST00000297814;ENST00000413982	.	.	.	3.74	3.74	0.42951	.	0.000000	0.52532	U	0.000067	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9954	0.36050	0.0:0.0:0.0:1.0	.	.	.	.	X	896;830	.	ENSP00000297814:K896X	K	-	1	0	KIF27	85675325	0.392000	0.25229	0.385000	0.26158	0.016000	0.09150	0.777000	0.26718	1.682000	0.51000	0.240000	0.17902	AAA	.		0.363	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86485505	T	A	86485505	4	1	35	1	0	0	0	0	0	1	0	0	8317	1792	62	5	1547	5	KIF27	9	86485505	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	86270954	86485505	54727926	55	3097											
DAPK1	1612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	90254289	90254289	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgagaacataatgcttttGgatagaaatgtccccaaacc	14	10	7	10	0	0	2	0	1	0	2	1	4	1	3	4	1	3	1	4	1	5	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:90254289G>C	ENST00000408954.3	+	5	779	c.444G>C	c.(442-444)ttG>ttC	p.L148F	DAPK1_ENST00000472284.1_Missense_Mutation_p.L148F|DAPK1_ENST00000469640.2_Missense_Mutation_p.L148F|DAPK1_ENST00000358077.5_Missense_Mutation_p.L148F|DAPK1_ENST00000491893.1_Missense_Mutation_p.L148F	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TAATGCTTTTGGATAGAAATG	0.363									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.L148F		.											.	DAPK1-359	0			c.G444C						.						86	82	83					9																	90254289		1807	4078	5885	SO:0001583	missense	1612	exon5	Familial Cancer Database	Familial CLL	GCTTTTGGATAGA	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.444G>C	9.37:g.90254289G>C	ENSP00000386135:p.Leu148Phe	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	179	27	NM_004938	0	0	27	34	7	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.264980	0.59431	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.42	3.59	0.41128	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40728	N	0.001036	T	0.61714	0.2369	N	0.17800	0.525	0.58432	D	0.999993	P;P;D	0.76494	0.838;0.93;0.999	B;P;D	0.81914	0.41;0.51;0.995	T	0.62258	-0.6892	10	0.59425	D	0.04	.	7.0523	0.25079	0.1427:0.0:0.7183:0.139	.	148;148;148	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	F	148	ENSP00000350785:L148F;ENSP00000417076:L148F;ENSP00000418885:L148F;ENSP00000386135:L148F;ENSP00000419026:L148F	ENSP00000350785:L148F	L	+	3	2	DAPK1	89444109	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.692000	0.47018	0.850000	0.35239	-0.244000	0.11960	TTG	.		0.363	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		C	90254289	G	C	90254289	3	2	35	1	0	0	0	0	1	0	0	0	4241	1339	47	4	458	4	DAPK1	9	90254289	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3768784	90254289	50959142	56	3098											
PSMD5	5711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	123591454	123591454	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggtacagtagtttaaagaTtctggtgacacggaagaaat	14	11	12	4	1	1	3	0	1	1	2	1	4	1	4	0	3	1	3	0	3	6	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:123591454T>C	ENST00000210313.3	-	5	668	c.594A>G	c.(592-594)gaA>gaG	p.E198E	PSMD5_ENST00000373904.5_Silent_p.E155E|PSMD5-AS1_ENST00000589026.1_RNA	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	198					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)				endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						AGTTTAAAGATTCTGGTGACA	0.398																																					p.E198E		.											.	PSMD5-90	0			c.A594G						.						99	100	100					9																	123591454		2203	4300	6503	SO:0001819	synonymous_variant	5711	exon5			TAAAGATTCTGGT	AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"Proteasome (prosome, macropain) subunits"	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.594A>G	9.37:g.123591454T>C		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	110	17	NM_005047	0	0	7	12	5	B4DZM8|Q15045|Q4VXG8	Silent	SNP	ENST00000210313.3	37	CCDS6824.1																																																																																			.		0.398	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047		C	123591454	T	C	123591454	2	2	35	1	0	0	0	0	0	0	0	1	12730	1490	52	3		3	PSMD5	9	123591454	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	33337165	123591454	17621977	57	3099											
SPTAN1	6709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131339498	131339498	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctggcaagtgttcaggcTctgcttcggaagcacgaggg	8	8	15	10	2	2	0	1	0	1	0	3	3	2	1	1	4	2	5	1	4	2	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:131339498T>C	ENST00000372731.4	+	7	986	c.876T>C	c.(874-876)gcT>gcC	p.A292A	SPTAN1_ENST00000358161.5_Silent_p.A292A|SPTAN1_ENST00000372739.3_Silent_p.A292A	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	292					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GTGTTCAGGCTCTGCTTCGGA	0.473																																					p.A292A	NSCLC(120;833 1744 2558 35612 37579)	.											.	SPTAN1-158	0			c.T876C						.						134	136	135					9																	131339498		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon7			TCAGGCTCTGCTT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.876T>C	9.37:g.131339498T>C		Somatic	201	0		WXS	Illumina HiSeq	Phase_I	203	43	NM_003127	0	0	41	61	20	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			.		0.473	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		C	131339498	T	C	131339498	2	2	35	1	0	0	0	0	0	0	0	1	15149	1538	54	3		3	SPTAN1	9	131339498	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	7748044	131339498	9873933	58	3100											
KCNT1	57582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	138683918	138683918	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccgaccccctggctcacGtggccagcagctcccagagc	6	5	11	19	2	1	1	1	0	0	1	3	2	3	1	5	2	3	4	5	2	0	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:138683918G>A	ENST00000263604.3	+	31	3604	c.3604G>A	c.(3604-3606)Gtg>Atg	p.V1202M	KCNT1_ENST00000491806.2_Missense_Mutation_p.V1193M|KCNT1_ENST00000488444.2_Missense_Mutation_p.V1207M|KCNT1_ENST00000487664.1_Missense_Mutation_p.V1183M|KCNT1_ENST00000371757.2_Missense_Mutation_p.V1207M|KCNT1_ENST00000298480.5_Missense_Mutation_p.V1228M|KCNT1_ENST00000490355.2_Missense_Mutation_p.V1206M|KCNT1_ENST00000486577.2_Missense_Mutation_p.V1185M			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	1202					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CCTGGCTCACGTGGCCAGCAG	0.677																																					p.V1207M		.											.	KCNT1-137	0			c.G3619A						.						23	25	25					9																	138683918		2201	4299	6500	SO:0001583	missense	57582	exon31			GCTCACGTGGCCA	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.3604G>A	9.37:g.138683918G>A	ENSP00000263604:p.Val1202Met	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	42	7	NM_020822	0	0	0	0	0	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	37		.	.	.	.	.	.	.	.	.	.	G	13.10	2.136017	0.37728	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.25912	1.84;1.86;1.77;1.84	4.86	2.02	0.26589	.	0.135507	0.49305	N	0.000146	T	0.19565	0.0470	L	0.46157	1.445	0.43043	D	0.994636	B;B;B	0.32365	0.058;0.251;0.367	B;B;B	0.27500	0.027;0.037;0.08	T	0.03898	-1.0994	10	0.41790	T	0.15	-41.9415	9.4906	0.38958	0.2237:0.0:0.7763:0.0	.	1195;1207;1183	C9JYL2;B9EGP2;G5E9V0	.;.;.	M	1183;1228;1207;1187;1195;1209;1207;1202	ENSP00000417851:V1183M;ENSP00000298480:V1228M;ENSP00000360822:V1207M;ENSP00000263604:V1202M	ENSP00000263604:V1202M	V	+	1	0	KCNT1	137823739	1.000000	0.71417	0.999000	0.59377	0.475000	0.33008	2.313000	0.43735	0.132000	0.18615	0.561000	0.74099	GTG	.		0.677	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138683918	G	A	138683918	3	1	35	1	0	0	0	0	1	0	0	0	8112	1145	40	1	3741	1	KCNT1	9	138683918	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	7344420	138683918	2529513	59	3101											
RHOBTB1	9886	hgsc.bcm.edu;broad.mit.edu	37	chr10	62648933	62648934	+	Nonsense_Mutation	DNP	TC	TC	AG																															tgggggcaaaatatcccctcTctttatgggcctgaaataga																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr10:62648933_62648934TC>AG	ENST00000337910.5	-	6	829_830	c.492_493GA>CT	c.(490-495)aaGAga>aaCTga	p.164_165KR>N*	RHOBTB1_ENST00000357917.4_Nonsense_Mutation_p.164_165KR>N*	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	164	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					ATATCCCCTCTCTTTATGGGCC	0.391																																					p.KR164N*		.											.	RHOBTB1	0			c.G492C						.																																			SO:0001587	stop_gained	9886	exon6			CCCTCTCTTTATG	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.492_493delinsAG	10.37:g.62648933_62648934delinsAG	ENSP00000338671:p.K164_R165delinsN*	Somatic	107	1		WXS	Illumina HiSeq	Phase_I	119	13		0	0	0	0	0		Nonsense_Mutation	DNP	ENST00000337910.5	37	CCDS7261.1																																																																																			.		0.391	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			AG	62648934	TC	AG	62648933	4	1	35	1	0	0	0	0	0	1	0	0	13365	1559	54	5	1621	5	RHOBTB1	10	62648933	Nonsense_Mutation	DNP	TC	TCGA-B1-5398-01A-02D-1589-08		62648933	72885814	60	3102											
ENTPD7	57089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101458575	101458575	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agaggatgtgttgcgcattgGtggccgctaccatgggccaa	8	9	15	9	2	0	1	0	0	0	1	0	2	0	2	3	4	2	3	3	4	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr10:101458575G>C	ENST00000370489.4	+	10	1473	c.1295G>C	c.(1294-1296)gGt>gCt	p.G432A		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	432						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		TTGCGCATTGGTGGCCGCTAC	0.438																																					p.G432A		.											.	ENTPD7-91	0			c.G1295C						.						58	57	57					10																	101458575		2203	4300	6503	SO:0001583	missense	57089	exon10			GCATTGGTGGCCG	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.1295G>C	10.37:g.101458575G>C	ENSP00000359520:p.Gly432Ala	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	69	12	NM_020354	0	0	3	9	6	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310593	0.81358	.	.	ENSG00000198018	ENST00000370489	T	0.12879	2.64	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.37128	0.0992	M	0.71036	2.16	0.80722	D	1	D	0.60575	0.988	D	0.70935	0.971	T	0.03278	-1.1053	10	0.37606	T	0.19	-17.123	18.3825	0.90455	0.0:0.0:1.0:0.0	.	432	Q9NQZ7	ENTP7_HUMAN	A	432	ENSP00000359520:G432A	ENSP00000359520:G432A	G	+	2	0	ENTPD7	101448565	1.000000	0.71417	0.982000	0.44146	0.720000	0.41350	9.578000	0.98200	2.583000	0.87209	0.655000	0.94253	GGT	.		0.438	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		C	101458575	G	C	101458575	3	2	35	1	0	0	0	0	1	0	0	0	5157	1261	44	4	1329	4	ENTPD7	10	101458575	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	38809642	101458575	34076172	61	3103											
NFKB2	4791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104156717	104156717	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gacctggtaacacacagtgaCccacctcgtgctcatgccca	10	7	8	16	1	1	1	1	1	0	0	2	2	1	1	4	1	3	2	4	1	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr10:104156717C>T	ENST00000369966.3	+	6	550	c.300C>T	c.(298-300)gaC>gaT	p.D100D	NFKB2_ENST00000428099.1_Silent_p.D100D|NFKB2_ENST00000189444.6_Silent_p.D100D	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	100	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	CACACAGTGACCCACCTCGTG	0.597			T	IGH@	B-NHL																																p.D100D		.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2-522	0			c.C300T						.						78	84	82					10																	104156717		2080	4213	6293	SO:0001819	synonymous_variant	4791	exon6			CAGTGACCCACCT	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.300C>T	10.37:g.104156717C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	54	7	NM_001077494	0	0	19	35	16	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Silent	SNP	ENST00000369966.3	37	CCDS41564.1																																																																																			.		0.597	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			T	104156717	C	T	104156717	2	4	35	1	0	0	0	0	0	0	0	1	10402	506	18	2		2	NFKB2	10	104156717	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	2698142	104156717	31378030	62	3104											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092643	1092643	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaccactcccagccctccaAcaaccaccacaaccacccct	12	3	1	25	0	0	0	0	0	0	0	2	0	2	0	10	0	4	0	10	0	3	0	rs149562922		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:1092643A>C	ENST00000441003.2	+	30	4489	c.4462A>C	c.(4462-4464)Aca>Cca	p.T1488P	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1489P	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4223	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caGCCCTCCAACAaccaccac	0.627																																					p.T1488P		.											.	MUC2-90	0			c.A4462C						.						302	443	394					11																	1092643		1680	3118	4798	SO:0001583	missense	4583	exon30			CCTCCAACAACCA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4462A>C	11.37:g.1092643A>C	ENSP00000415183:p.Thr1488Pro	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	16	6	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	-	3.842	-0.033557	0.07543	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15952	2.41;2.38	1.28	1.28	0.21552	.	0.642730	0.11935	U	0.515356	T	0.27063	0.0663	.	.	.	0.09310	N	0.999998	D	0.64830	0.994	P	0.62885	0.908	T	0.12344	-1.0551	9	0.30078	T	0.28	.	6.6385	0.22897	1.0:0.0:0.0:0.0	.	1488	E7EUV1	.	P	1488;1489	ENSP00000415183:T1488P;ENSP00000351956:T1489P	ENSP00000351956:T1489P	T	+	1	0	MUC2	1082643	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-2.044000	0.01411	0.654000	0.30846	0.000000	0.15137	ACA	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1092643	A	C	1092643	3	2	35	1	0	0	0	0	1	0	0	0	10000	43	2	5	4580	5	MUC2	11	1092643	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08		1092643	133913873	63	3105											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092795	1092795	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctccaccaaccaccacTcccatcaccaccaccaccac	12	3	0	26	0	1	0	1	0	0	0	3	0	3	0	11	0	1	0	11	0	1	0	rs12786761		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:1092795T>A	ENST00000441003.2	+	30	4641	c.4614T>A	c.(4612-4614)acT>acA	p.T1538T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1539T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caaccaccactcccatcacca	0.627																																					p.T1538T		.											.	MUC2-90	0			c.T4614A						.						126	251	206					11																	1092795		1606	2836	4442	SO:0001819	synonymous_variant	4583	exon30			CACCACTCCCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4614T>A	11.37:g.1092795T>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092795	T	A	1092795	2	1	35	1	0	0	0	0	0	0	0	1	10000	1538	54	5		5	MUC2	11	1092795	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	152	1092795	133913721	64	3106											
OR51T1	401665	hgsc.bcm.edu;broad.mit.edu	37	chr11	4904096	4904096	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttttaatgtgaggggtcttAggggaagatgggattgaagg	10	12	18	1	0	1	3	0	2	1	1	1	5	1	5	0	6	0	1	0	6	4	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:4904096A>C	ENST00000322049.1	+	1	967	c.967A>C	c.(967-969)Agg>Cgg	p.R323R	OR51T1_ENST00000380378.1_Silent_p.R350R|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAGGGGTCTTAGGGGAAGATG	0.468																																					p.R350R		.											.	OR51T1-115	0			c.A1048C						.						56	56	56					11																	4904096		2201	4298	6499	SO:0001819	synonymous_variant	401665	exon1			GGTCTTAGGGGAA	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"GPCR / Class A : Olfactory receptors"	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.967A>C	11.37:g.4904096A>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	116	12	NM_001004759	0	0	0	0	0	Q6IFH9	Silent	SNP	ENST00000322049.1	37																																																																																				.		0.468	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		C	4904096	A	C	4904096	2	2	35	1	0	0	0	0	0	0	0	1	11132	411	15	5		5	OR51T1	11	4904096	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	3811301	4904096	130102420	65	3107											
CCKBR	887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6291417	6291417	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcacgagtgtggcagacgcGctcccacgcggctcgcgtga	6	5	16	14	7	0	2	0	1	0	1	2	3	1	2	1	3	0	4	1	3	0	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:6291417G>A	ENST00000334619.2	+	3	696	c.503G>A	c.(502-504)cGc>cAc	p.R168H	CCKBR_ENST00000525014.1_3'UTR|CCKBR_ENST00000532715.1_Missense_Mutation_p.R84H|CCKBR_ENST00000525462.1_Missense_Mutation_p.R168H	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	168					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	TGGCAGACGCGCTCCCACGCG	0.647																																					p.R168H		.											.	CCKBR-574	0			c.G503A						.						46	38	41					11																	6291417		2197	4290	6487	SO:0001583	missense	887	exon3			AGACGCGCTCCCA	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"GPCR / Class A : Cholecystokinin receptors"	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.503G>A	11.37:g.6291417G>A	ENSP00000335544:p.Arg168His	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	51	11	NM_176875	0	0	0	0	0	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	37	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.371373	0.82573	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.72725	-0.68;-0.68;-0.68	4.81	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84197	0.5419	M	0.88377	2.95	0.51012	D	0.999906	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.75020	0.937;0.975;0.985	D	0.85468	0.1171	10	0.52906	T	0.07	.	10.2312	0.43256	0.0916:0.0:0.9084:0.0	.	168;102;168	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	H	168;84;168	ENSP00000335544:R168H;ENSP00000432079:R84H;ENSP00000435534:R168H	ENSP00000335544:R168H	R	+	2	0	CCKBR	6247993	0.101000	0.21875	1.000000	0.80357	0.942000	0.58702	2.571000	0.45990	2.505000	0.84491	0.655000	0.94253	CGC	.		0.647	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		A	6291417	G	A	6291417	3	1	35	1	0	0	0	0	1	0	0	0	2887	1087	38	1	513	1	CCKBR	11	6291417	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	1387321	6291417	128715099	66	3108											
MAPK8IP1	9479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	45926284	45926284	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtagattgccaccacccgcCggctcaccgtgcactttaac	8	9	8	16	3	1	1	1	0	0	1	1	1	1	1	5	1	3	3	5	1	2	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:45926284C>T	ENST00000241014.2	+	9	1962	c.1792C>T	c.(1792-1794)Cgg>Tgg	p.R598W	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.R588W|RP11-618K13.2_ENST00000533218.1_RNA	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	598	Interaction with VRK2.|PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CACCACCCGCCGGCTCACCGT	0.612																																					p.R598W		.											.	MAPK8IP1-973	0			c.C1792T						.						77	80	79					11																	45926284		2203	4299	6502	SO:0001583	missense	9479	exon9			ACCCGCCGGCTCA		CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.1792C>T	11.37:g.45926284C>T	ENSP00000241014:p.Arg598Trp	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	116	21	NM_005456	0	0	7	14	7	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	37	CCDS7916.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.560899	0.86335	.	.	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.14766	2.48;2.48	5.84	4.87	0.63330	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.056704	0.64402	D	0.000002	T	0.35653	0.0939	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.03503	-1.1030	10	0.87932	D	0	-26.4988	16.4247	0.83810	0.0:0.8687:0.1313:0.0	.	598	Q9UQF2	JIP1_HUMAN	W	598;588	ENSP00000241014:R598W;ENSP00000378991:R588W	ENSP00000241014:R598W	R	+	1	2	MAPK8IP1	45882860	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.985000	0.29578	2.768000	0.95171	0.561000	0.74099	CGG	.		0.612	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456		T	45926284	C	T	45926284	3	4	35	1	0	0	0	0	1	0	0	0	9309	643	23	1	1826	1	MAPK8IP1	11	45926284	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	39634867	45926284	89080232	67	3109											
MADD	8567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47345285	47345285	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgtatgagcgctggtggtacGagaagctcatcaacatgacc	11	9	12	9	2	2	3	2	2	0	1	2	4	2	3	1	2	4	4	1	2	4	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:47345285G>C	ENST00000311027.5	+	31	4606	c.4441G>C	c.(4441-4443)Gag>Cag	p.E1481Q	MADD_ENST00000406482.1_Missense_Mutation_p.E1379Q|MADD_ENST00000402192.2_Missense_Mutation_p.E1421Q|MADD_ENST00000402799.1_Missense_Mutation_p.E1379Q|MADD_ENST00000405573.2_Missense_Mutation_p.E291Q|MADD_ENST00000342922.4_Missense_Mutation_p.E1422Q|MADD_ENST00000395336.3_Missense_Mutation_p.E1481Q|MADD_ENST00000395344.3_Missense_Mutation_p.E1375Q|MADD_ENST00000349238.3_Missense_Mutation_p.E1442Q|MADD_ENST00000407859.3_Missense_Mutation_p.E1399Q	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		CTGGTGGTACGAGAAGCTCAT	0.498																																					p.E1481Q		.											.	MADD-682	0			c.G4441C						.						223	167	186					11																	47345285		2201	4298	6499	SO:0001583	missense	8567	exon31			TGGTACGAGAAGC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4441G>C	11.37:g.47345285G>C	ENSP00000310933:p.Glu1481Gln	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	96	18	NM_130475	0	0	23	27	4		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	33	5.270702	0.95429	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192;ENST00000405573	T;T;T;T;T;T;T;T;T;T	0.57436	2.85;2.72;2.75;2.83;2.86;2.72;2.72;2.87;2.85;0.4	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.70762	0.3261	L	0.53561	1.675	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.998;0.998;0.999;0.999;0.999;0.999;0.999;0.998;0.997;0.998	T	0.71724	-0.4506	10	0.87932	D	0	-24.9261	19.903	0.96995	0.0:0.0:1.0:0.0	.	291;1375;1375;1481;1379;1379;1379;1442;1399;1481;1422	F8W8U2;B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;.;MADD_HUMAN;.	Q	1422;1379;1379;1379;1442;1481;1399;1375;1481;1421;291	ENSP00000343902:E1422Q;ENSP00000385585:E1379Q;ENSP00000384435:E1379Q;ENSP00000304505:E1442Q;ENSP00000310933:E1481Q;ENSP00000384204:E1399Q;ENSP00000378753:E1375Q;ENSP00000378745:E1481Q;ENSP00000384287:E1421Q;ENSP00000384483:E291Q	ENSP00000310933:E1481Q	E	+	1	0	MADD	47301861	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	8.947000	0.93000	2.705000	0.92388	0.549000	0.68633	GAG	.		0.498	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			C	47345285	G	C	47345285	3	2	35	1	0	0	0	0	1	0	0	0	9177	1059	37	4	4559	4	MADD	11	47345285	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	1419001	47345285	87661231	68	3110											
OR5D14	219436	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	55563325	55563326	+	Missense_Mutation	DNP	CT	CT	AA																															aaaagcatcttctactttagCtgcatgatgcagtacttcct																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:55563325_55563326CT>AA	ENST00000335605.1	+	1	294_295	c.294_295CT>AA	c.(292-297)agCTgc>agAAgc	p.98_99SC>RS		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TCTACTTTAGCTGCATGATGCA	0.455																																					p.SC98RS		.											.	OR5D14	0			c.T295A						.																																			SO:0001583	missense	219436	exon1			TTTAGCTGCATGA	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	Exception_encountered	11.37:g.55563325_55563326delinsAA	ENSP00000334456:p.S98_C99delinsRS	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	81	7		0	0	0	0	0	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	DNP	ENST00000335605.1	37	CCDS31508.1																																																																																			.		0.455	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		AA	55563326	CT	AA	55563325	3	1	35	1	0	0	0	0	1	0	0	0	11181	796	28	4	296	4	OR5D14	11	55563325	Missense_Mutation	DNP	CT	TCGA-B1-5398-01A-02D-1589-08	8218040	55563325	79443191	69	3111											
OR8I2	120586	broad.mit.edu	37	chr11	55861307	55861308	+	Frame_Shift_Ins	INS	-	-	T																															tgtgattccagcatcaatcaINSttttttttgtgacaccacag																								rs201548817|rs112181516|rs144690814	byFrequency	TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:55861307_55861308insT	ENST00000302124.2	+	1	555_556	c.524_525insT	c.(523-528)cattttfs	p.HF175fs		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H175fs*10(1)|p.C178fs*2(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					AGCATCAATCATTTTTTTTGTG	0.441																																					p.H175fs													.	OR8I2-113	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	ovary(1)|large_intestine(1)	c.524_525insT						.			0,4264		0,0,2132						3.2	1		dbSNP_132	145	1,8253		0,1,4126	no	frameshift	OR8I2	NM_001003750.1		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12517				SO:0001589	frameshift_variant	120586	exon1			TCAATCATTTTTT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.532dupT	11.37:g.55861315_55861315dupT	ENSP00000303864:p.His175fs	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	207	7	NM_001003750	0	0	0	0	0	B2RNN4|Q6IFC0|Q96RC5	Frame_Shift_Ins	INS	ENST00000302124.2	37	CCDS31517.1																																																																																			-|0.500;T|0.500		0.441	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		T	55861308	-	T	55861307	7	5	35	1	0	1	1	0	0	0	0	0	11266	217	8	0	526	0	OR8I2	11	55861307	Frame_Shift_Ins	INS	-	TCGA-B1-5398-01A-02D-1589-08	297982	55861307	79145209	70	3112											
SLC22A10	387775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63064875	63064875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccctgtttactgtgtactaCgcttcttggcaggtttttct	4	19	8	10	1	2	0	0	0	2	0	3	0	3	0	1	2	3	5	1	2	3	8	rs200183991		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:63064875C>T	ENST00000332793.6	+	3	609	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C	SLC22A10_ENST00000525620.1_3'UTR|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000544661.1_Missense_Mutation_p.R48C|SLC22A10_ENST00000535888.1_5'UTR	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	203						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	CTGTGTACTACGCTTCTTGGC	0.408																																					p.R203C		.											.	SLC22A10-92	0			c.C607T						.	C	CYS/ARG	2,4092		0,2,2045	170	169	169		607	2.3	0.3	11		169	0,8428		0,0,4214	yes	missense	SLC22A10	NM_001039752.3	180	0,2,6259	TT,TC,CC		0.0,0.0489,0.016	probably-damaging	203/542	63064875	2,12520	2047	4214	6261	SO:0001583	missense	387775	exon3			GTACTACGCTTCT	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.607C>T	11.37:g.63064875C>T	ENSP00000327569:p.Arg203Cys	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	232	31	NM_001039752	0	0	0	0	0	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306314	0.60305	4.89E-4	0.0	ENSG00000184999	ENST00000544661;ENST00000332793	D;D	0.90261	-2.64;-2.64	3.26	2.34	0.29019	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.066213	0.64402	N	0.000009	D	0.93341	0.7877	M	0.92077	3.27	0.80722	D	1	P	0.50819	0.939	P	0.50352	0.638	D	0.92539	0.6040	10	0.72032	D	0.01	.	8.4548	0.32893	0.0:0.8776:0.0:0.1224	.	203	Q63ZE4	S22AA_HUMAN	C	48;203	ENSP00000445667:R48C;ENSP00000327569:R203C	ENSP00000327569:R203C	R	+	1	0	SLC22A10	62821451	0.772000	0.28567	0.265000	0.24526	0.132000	0.20833	1.238000	0.32707	0.751000	0.32900	0.447000	0.29281	CGC	.		0.408	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		T	63064875	C	T	63064875	3	4	35	1	0	0	0	0	1	0	0	0	14473	536	19	1	617	1	SLC22A10	11	63064875	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	7203568	63064875	71941641	71	3113											
NUMA1	4926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	71724282	71724282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctgcccgcagctgctgagCtgttcgctcctgctctgcca	3	11	10	17	2	2	1	0	1	2	0	4	1	3	1	3	0	6	7	3	0	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:71724282C>T	ENST00000393695.3	-	15	4598	c.4267G>A	c.(4267-4269)Gct>Act	p.A1423T	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Missense_Mutation_p.A1423T|NUMA1_ENST00000351960.6_Intron	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						AGCTGCTGAGCTGTTCGCTCC	0.672			T	RARA	APL																																p.A1423T		.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1-633	0			c.G4267A						.						46	48	47					11																	71724282		2200	4293	6493	SO:0001583	missense	4926	exon15			GCTGAGCTGTTCG	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.4267G>A	11.37:g.71724282C>T	ENSP00000377298:p.Ala1423Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	123	25	NM_006185	0	0	60	107	47		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231361	0.39399	.	.	ENSG00000137497	ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T	0.13307	2.6;2.6	5.14	4.23	0.50019	.	0.000000	0.53938	D	0.000051	T	0.06645	0.0170	N	0.14661	0.345	0.20563	N	0.999885	P;B;B;P	0.39480	0.675;0.447;0.241;0.675	B;B;B;B	0.35550	0.205;0.148;0.148;0.205	T	0.25779	-1.0122	10	0.33940	T	0.23	.	5.9903	0.19456	0.1541:0.6873:0.0:0.1586	.	1429;907;1423;1423	Q4LE64;Q59HB8;Q14980-2;Q14980	.;.;.;NUMA1_HUMAN	T	1423;1423;986;392	ENSP00000351851:A1423T;ENSP00000377298:A1423T	ENSP00000351851:A1423T	A	-	1	0	NUMA1	71401930	0.000000	0.05858	0.838000	0.33150	0.876000	0.50452	-0.321000	0.08018	1.391000	0.46566	0.655000	0.94253	GCT	.		0.672	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			T	71724282	C	T	71724282	3	4	35	1	0	0	0	0	1	0	0	0	10776	797	28	2	2132	2	NUMA1	11	71724282	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	8659407	71724282	63282234	72	3114											
INPPL1	3636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	71948376	71948376	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccacagcttgggcaccacCggcaccctcgtgtgggagag	7	6	13	15	2	0	1	0	0	0	1	2	2	1	1	4	3	1	3	4	3	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:71948376C>T	ENST00000298229.2	+	26	3292	c.3088C>T	c.(3088-3090)Cgg>Tgg	p.R1030W	INPPL1_ENST00000541756.1_Missense_Mutation_p.R788W|PHOX2A_ENST00000544057.1_5'Flank|INPPL1_ENST00000538751.1_Missense_Mutation_p.R788W	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1030	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TGGGCACCACCGGCACCCTCG	0.642																																					p.R1030W		.											.	INPPL1-660	0			c.C3088T						.						70	76	74					11																	71948376		2200	4293	6493	SO:0001583	missense	3636	exon26			CACCACCGGCACC	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"Sterile alpha motif (SAM) domain containing", "SH2 domain containing"	6080	protein-coding gene	gene with protein product	"51C protein"	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.3088C>T	11.37:g.71948376C>T	ENSP00000298229:p.Arg1030Trp	Somatic	174	1		WXS	Illumina HiSeq	Phase_I	134	25	NM_001567	0	0	73	105	32	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	37	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	N	8.924	0.961831	0.18583	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751;ENST00000541752	D;D;D;T	0.96685	-2.99;-4.09;-4.09;1.34	5.22	2.26	0.28386	.	0.075539	0.52532	D	0.000068	D	0.89698	0.6790	N	0.14661	0.345	0.24350	N	0.994927	B	0.09022	0.002	B	0.01281	0.0	T	0.82568	-0.0392	10	0.66056	D	0.02	.	6.9513	0.24546	0.3121:0.6043:0.0:0.0835	.	1030	O15357	SHIP2_HUMAN	W	1030;788;788;43	ENSP00000298229:R1030W;ENSP00000446360:R788W;ENSP00000444619:R788W;ENSP00000441094:R43W	ENSP00000298229:R1030W	R	+	1	2	INPPL1	71626024	0.875000	0.30112	0.971000	0.41717	0.006000	0.05464	0.763000	0.26517	0.569000	0.29329	-0.217000	0.12591	CGG	.		0.642	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71948376	C	T	71948376	3	4	35	1	0	0	0	0	1	0	0	0	7782	643	23	1	3190	1	INPPL1	11	71948376	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	224094	71948376	63058140	73	3115											
ARHGEF17	9828	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	73021440	73021440	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggatccgctgcccctcaTcgtccaggaccaatatgtgc	8	8	11	14	2	1	0	1	0	0	0	4	3	3	3	5	3	2	1	5	3	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:73021440T>C	ENST00000263674.3	+	1	2107	c.1757T>C	c.(1756-1758)aTc>aCc	p.I586T	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	586					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CTGCCCCTCATCGTCCAGGAC	0.647																																					p.I586T		.											.	ARHGEF17-227	0			c.T1757C						.						48	50	49					11																	73021440		2200	4293	6493	SO:0001583	missense	9828	exon1			CCCTCATCGTCCA	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.1757T>C	11.37:g.73021440T>C	ENSP00000263674:p.Ile586Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	88	13	NM_014786	0	0	9	19	10	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	T	9.868	1.198064	0.22037	.	.	ENSG00000110237	ENST00000263674	T	0.55588	0.51	4.62	4.62	0.57501	.	1.144840	0.06515	N	0.738667	T	0.36608	0.0973	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.20974	-1.0259	10	0.87932	D	0	-9.7864	9.3506	0.38136	0.0:0.0:0.1804:0.8196	.	586	Q96PE2	ARHGH_HUMAN	T	586	ENSP00000263674:I586T	ENSP00000263674:I586T	I	+	2	0	ARHGEF17	72699088	0.963000	0.33076	0.006000	0.13384	0.872000	0.50106	3.475000	0.53136	1.931000	0.55961	0.459000	0.35465	ATC	.		0.647	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		C	73021440	T	C	73021440	3	2	35	1	0	0	0	0	1	0	0	0	900	1435	50	3	1759	3	ARHGEF17	11	73021440	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	1073064	73021440	61985076	74	3116											
GDPD4	220032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	76944148	76944148	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagttaatcctggagcaccaGgccagtgagaaaagccaagg	14	5	13	9	0	0	1	0	1	0	1	1	4	1	2	4	3	2	2	4	3	4	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:76944148G>C	ENST00000376217.2	-	13	1561	c.1311C>G	c.(1309-1311)gcC>gcG	p.A437A	GDPD4_ENST00000315938.4_Silent_p.A437A			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	437	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						TGGAGCACCAGGCCAGTGAGA	0.468																																					p.A437A		.											.	GDPD4-69	0			c.C1311G						.						168	146	153					11																	76944148		2200	4292	6492	SO:0001819	synonymous_variant	220032	exon13			GCACCAGGCCAGT	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1311C>G	11.37:g.76944148G>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	87	9	NM_182833	0	0	0	0	0	Q7Z5B0	Silent	SNP	ENST00000376217.2	37																																																																																				.		0.468	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833		C	76944148	G	C	76944148	2	2	35	1	0	0	0	0	0	0	0	1	6346	987	35	4		4	GDPD4	11	76944148	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3922708	76944148	58062368	75	3117											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877690	82877690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcactgaaccaaaggagaAtgtagaaaactggcaaagtt	18	6	11	6	0	0	3	0	1	0	2	0	4	0	3	1	3	2	4	1	3	7	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:82877690A>G	ENST00000298281.4	+	5	2203	c.1751A>G	c.(1750-1752)aAt>aGt	p.N584S		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	584					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CCAAAGGAGAATGTAGAAAAC	0.393																																					p.N584S		.											.	PCF11-23	0			c.A1751G						.						66	66	66					11																	82877690		1824	4044	5868	SO:0001583	missense	51585	exon5			AGGAGAATGTAGA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1751A>G	11.37:g.82877690A>G	ENSP00000298281:p.Asn584Ser	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	104	20	NM_015885	0	0	2	8	6	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172383	0.38315	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.50813	1.68;0.74;0.73	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.34483	0.0899	N	0.19112	0.55	0.29519	N	0.853609	P;P	0.43788	0.473;0.817	B;B	0.38500	0.091;0.275	T	0.25433	-1.0132	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	584;584	E9PQ01;O94913	.;PCF11_HUMAN	S	584	ENSP00000298281:N584S;ENSP00000434540:N584S;ENSP00000431567:N584S	.	N	+	2	0	PCF11	82555338	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	3.827000	0.55745	2.326000	0.78906	0.533000	0.62120	AAT	.		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877690	A	G	82877690	3	3	35	1	0	0	0	0	1	0	0	0	11599	101	4	3	1769	3	PCF11	11	82877690	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	5933542	82877690	52128826	76	3118											
CASP4	837	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	104825523	104825523	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaaaaaaggtttgaagaagCatttgtcctgccatacgttg	13	13	9	6	1	0	2	0	1	0	1	1	2	1	2	2	1	3	3	2	1	6	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:104825523C>T	ENST00000444739.2	-	2	1123	c.213G>A	c.(211-213)atG>atA	p.M71I	CASP4_ENST00000393150.3_Missense_Mutation_p.M15I|CASP4_ENST00000531333.1_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	71	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		TTTGAAGAAGCATTTGTCCTG	0.353																																					p.M71I		.											.	CASP4-660	0			c.G213A						.						187	177	181					11																	104825523		2202	4299	6501	SO:0001583	missense	837	exon2			AAGAAGCATTTGT	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"Caspases"	1505	protein-coding gene	gene with protein product		602664	"caspase 4, apoptosis-related cysteine protease"			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.213G>A	11.37:g.104825523C>T	ENSP00000388566:p.Met71Ile	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	224	37	NM_001225	0	0	33	50	17	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.174|0.174	-1.068340|-1.068340	0.01934|0.01934	.|.	.|.	ENSG00000196954|ENSG00000196954	ENST00000355546|ENST00000444739;ENST00000393150;ENST00000417440	.|T;T;T	.|0.18174	.|2.23;4.52;2.23	3.6|3.6	-1.75|-1.75	0.08031|0.08031	.|DEATH-like (2);Caspase Recruitment (3);	.|1.351520	.|0.05087	.|N	.|0.484541	T|T	0.06371|0.06371	0.0164|0.0164	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.11235	.|0.004;0.001;0.0	.|B;B;B	.|0.13407	.|0.009;0.004;0.002	T|T	0.26710|0.26710	-1.0095|-1.0095	6|10	0.02654|0.02654	T|T	1|1	.|.	0.1298|0.1298	0.00073|0.00073	0.3445:0.2198:0.1837:0.252|0.3445:0.2198:0.1837:0.252	.|.	.|71;71;71	.|B4DJH5;B4E2D2;P49662	.|.;.;CASP4_HUMAN	Y|I	25|71;15;71	.|ENSP00000388566:M71I;ENSP00000376857:M15I;ENSP00000401673:M71I	ENSP00000347741:C25Y|ENSP00000376857:M15I	C|M	-|-	2|3	0|0	CASP4|CASP4	104330733|104330733	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-2.136000|-2.136000	0.01305|0.01305	-0.231000|-0.231000	0.09825|0.09825	-0.150000|-0.150000	0.13652|0.13652	TGC|ATG	.		0.353	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		T	104825523	C	T	104825523	3	4	35	1	0	0	0	0	1	0	0	0	2679	710	25	2	948	2	CASP4	11	104825523	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	21947833	104825523	30180993	77	3119											
CLDN25	644672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113651037	113651037	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttgggctgggctgctggtAttttcctggctcttggtggg	2	15	16	8	0	1	0	0	0	1	0	2	0	2	0	1	6	1	5	1	6	1	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:113651037A>G	ENST00000453129.2	+	1	569	c.520A>G	c.(520-522)Att>Gtt	p.I174V		NM_001101389.1	NP_001094859.1	C9JDP6	CLD25_HUMAN	claudin 25	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			large_intestine(1)|lung(6)|ovary(1)|urinary_tract(2)	10						GGCTGCTGGTATTTTCCTGGC	0.557																																					p.I174V		.											.	.	0			c.A520G						.						88	93	92					11																	113651037		2014	4177	6191	SO:0001583	missense	644672	exon1			GCTGGTATTTTCC		CCDS44736.1	11q23.2	2009-09-22			ENSG00000228607	ENSG00000228607			37218	protein-coding gene	gene with protein product							Standard	NM_001101389		Approved		uc009yyw.1	C9JDP6	OTTHUMG00000168193	ENST00000453129.2:c.520A>G	11.37:g.113651037A>G	ENSP00000396304:p.Ile174Val	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	76	14	NM_001101389	0	0	0	0	0		Missense_Mutation	SNP	ENST00000453129.2	37	CCDS44736.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.253180	0.00268	.	.	ENSG00000228607	ENST00000453129	D	0.88896	-2.44	5.08	-10.2	0.00374	.	.	.	.	.	T	0.64427	0.2597	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.52442	-0.8575	9	0.06365	T	0.9	.	6.3055	0.21137	0.0807:0.1948:0.4667:0.2578	.	174	C9JDP6	CLD25_HUMAN	V	174	ENSP00000396304:I174V	ENSP00000396304:I174V	I	+	1	0	CLDN25	113156247	0.000000	0.05858	0.000000	0.03702	0.451000	0.32288	-1.048000	0.03517	-3.888000	0.00095	-0.925000	0.02716	ATT	.		0.557	CLDN25-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398706.1	NM_001101389		G	113651037	A	G	113651037	3	3	35	1	0	0	0	0	1	0	0	0	3491	449	16	3	522	3	CLDN25	11	113651037	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	8825514	113651037	21355479	78	3120											
FKBP4	2288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2909578	2909578	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaggtaaatacaagcaagcTttactacagtataagaagat	19	9	8	5	0	0	2	0	0	0	2	0	3	0	2	0	1	5	4	0	1	11	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:2909578T>G	ENST00000001008.4	+	8	1054	c.867T>G	c.(865-867)gcT>gcG	p.A289A	RP4-816N1.6_ENST00000547834.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	289	Interaction with tubulin. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			ACAAGCAAGCTTTACTACAGT	0.483																																					p.A289A		.											.	FKBP4-226	0			c.T867G						.						76	69	71					12																	2909578		2203	4300	6503	SO:0001819	synonymous_variant	2288	exon8			GCAAGCTTTACTA	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.867T>G	12.37:g.2909578T>G		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	58	10	NM_002014	0	0	76	135	59	D3DUQ1|Q9UCP1|Q9UCV7	Silent	SNP	ENST00000001008.4	37	CCDS8512.1																																																																																			.		0.483	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			G	2909578	T	G	2909578	2	3	35	1	0	0	0	0	0	0	0	1	5929	1596	56	5		5	FKBP4	12	2909578	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08		2909578	130942317	79	3121											
CHD4	1108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6707540	6707540	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggtgtgggagatggtggctGaccccacttccagattagga	8	10	15	8	0	0	3	0	1	0	2	1	5	1	4	3	5	0	1	3	5	1	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:6707540G>A	ENST00000357008.2	-	11	1697	c.1534C>T	c.(1534-1536)Cag>Tag	p.Q512*	CHD4_ENST00000544484.1_Nonsense_Mutation_p.Q509*|CHD4_ENST00000544040.1_Nonsense_Mutation_p.Q505*|CHD4_ENST00000309577.6_Nonsense_Mutation_p.Q512*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	512	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						GATGGTGGCTGACCCCACTTC	0.547																																					p.Q512X	Colon(32;586 792 4568 16848 45314)	.											.	CHD4-228	0			c.C1534T						.						137	140	139					12																	6707540		2203	4300	6503	SO:0001587	stop_gained	1108	exon11			GTGGCTGACCCCA	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.1534C>T	12.37:g.6707540G>A	ENSP00000349508:p.Gln512*	Somatic	285	0		WXS	Illumina HiSeq	Phase_I	278	43	NM_001273	0	0	71	72	1	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	39	7.490672	0.98316	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	3.86	3.86	0.44501	.	0.127870	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	9.8645	12.2938	0.54833	0.0:0.1709:0.8291:0.0	.	.	.	.	X	509;505;512;512;486	.	ENSP00000312419:Q512X	Q	-	1	0	CHD4	6577801	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.469000	0.60169	2.149000	0.67028	0.305000	0.20034	CAG	.		0.547	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6707540	G	A	6707540	4	1	35	1	0	0	0	0	0	1	0	0	3333	1299	45	2	4324	2	CHD4	12	6707540	Nonsense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3797962	6707540	127144355	80	3122											
RASSF8	11228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	26217472	26217472	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatagagaaatggagagatActgaaagacacttagcacct	17	9	9	6	0	0	4	0	1	0	3	0	7	0	5	1	1	2	1	1	1	6	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:26217472A>T	ENST00000405154.2	+	3	344	c.145A>T	c.(145-147)Act>Tct	p.T49S	RASSF8_ENST00000541490.1_Missense_Mutation_p.T49S|RASSF8_ENST00000381352.3_Missense_Mutation_p.T49S|RASSF8_ENST00000282884.9_Missense_Mutation_p.T49S|RASSF8_ENST00000542865.1_Missense_Mutation_p.T49S	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	49	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					ATGGAGAGATACTGAAAGACA	0.388																																					p.T49S		.											.	RASSF8-90	0			c.A145T						.						111	115	113					12																	26217472		2203	4300	6503	SO:0001583	missense	11228	exon4			AGAGATACTGAAA	U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"chromosome 12 open reading frame 2"	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.145A>T	12.37:g.26217472A>T	ENSP00000384491:p.Thr49Ser	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	179	32	NM_007211	0	0	1	1	0	A8K1Z0|O95647|Q5SCI2|Q76KB6	Missense_Mutation	SNP	ENST00000405154.2	37	CCDS53765.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826488	0.50739	.	.	ENSG00000123094	ENST00000381352;ENST00000535907;ENST00000405154;ENST00000542865;ENST00000541490;ENST00000542004;ENST00000542315;ENST00000541218;ENST00000282884;ENST00000545413;ENST00000541934	T;T;T;T;T;T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28	5.38	4.21	0.49690	Ras-association (3);	0.046729	0.85682	D	0.000000	T	0.21674	0.0522	N	0.17723	0.515	0.58432	D	0.999995	B;D	0.63046	0.383;0.992	B;D	0.64042	0.19;0.921	T	0.03008	-1.1083	10	0.21014	T	0.42	-11.7935	11.9163	0.52767	0.8541:0.1459:0.0:0.0	.	49;49	Q8NHQ8-2;Q8NHQ8	.;RASF8_HUMAN	S	49	ENSP00000370756:T49S;ENSP00000442036:T49S;ENSP00000384491:T49S;ENSP00000439839:T49S;ENSP00000443096:T49S;ENSP00000442485:T49S;ENSP00000441294:T49S;ENSP00000445970:T49S;ENSP00000282884:T49S;ENSP00000443696:T49S	ENSP00000282884:T49S	T	+	1	0	RASSF8	26108739	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.609000	0.61148	0.970000	0.38263	0.528000	0.53228	ACT	.		0.388	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211		T	26217472	A	T	26217472	3	4	35	1	0	0	0	0	1	0	0	0	13124	391	14	5	151	5	RASSF8	12	26217472	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	19509932	26217472	107634423	81	3123											
LRRK2	120892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	40681240	40681240	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcctcaggcagcgatggaaAtttttctgaagatgtgctgt	10	12	12	7	1	2	2	1	1	1	1	2	4	2	3	1	2	3	2	1	2	2	2	rs555679009		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:40681240A>T	ENST00000298910.7	+	20	2646	c.2588A>T	c.(2587-2589)aAt>aTt	p.N863I	LRRK2_ENST00000343742.2_Missense_Mutation_p.N863I	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	863					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGCGATGGAAATTTTTCTGAA	0.398																																					p.N863I		.											.	LRRK2-533	0			c.A2588T						.						123	118	119					12																	40681240		2202	4299	6501	SO:0001583	missense	120892	exon20			ATGGAAATTTTTC	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2588A>T	12.37:g.40681240A>T	ENSP00000298910:p.Asn863Ile	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	110	22	NM_198578	0	0	27	46	19	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	7.572	0.666963	0.14710	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.71579	2.25;-0.58	5.5	1.35	0.21983	.	0.449692	0.24999	N	0.033934	T	0.50309	0.1608	N	0.19112	0.55	0.09310	N	1	B;B	0.30455	0.28;0.121	B;B	0.30401	0.115;0.032	T	0.41016	-0.9532	10	0.46703	T	0.11	.	6.406	0.21664	0.6611:0.1269:0.212:0.0	.	863;863	E9PC85;Q5S007	.;LRRK2_HUMAN	I	863	ENSP00000341930:N863I;ENSP00000298910:N863I	ENSP00000298910:N863I	N	+	2	0	LRRK2	38967507	0.002000	0.14202	0.001000	0.08648	0.111000	0.19643	0.146000	0.16180	0.363000	0.24346	0.402000	0.26972	AAT	.		0.398	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40681240	A	T	40681240	3	4	35	1	0	0	0	0	1	0	0	0	9058	101	4	5	2666	5	LRRK2	12	40681240	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	14463768	40681240	93170655	82	3124											
PRICKLE1	144165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	42858293	42858293	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggaatcttcataccactGtgtttcatcatgattatacc	11	14	6	10	0	4	1	3	1	1	0	4	2	4	2	2	1	2	1	2	1	4	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:42858293G>A	ENST00000455697.1	-	7	1828	c.1543C>T	c.(1543-1545)Cag>Tag	p.Q515*	PRICKLE1_ENST00000552240.1_Nonsense_Mutation_p.Q515*|PRICKLE1_ENST00000345127.3_Nonsense_Mutation_p.Q515*|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Nonsense_Mutation_p.Q515*|PRICKLE1_ENST00000445766.2_Nonsense_Mutation_p.Q515*	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	515					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TCATACCACTGTGTTTCATCA	0.488																																					p.Q515X		.											.	PRICKLE1-518	0			c.C1543T						.						106	101	103					12																	42858293		2203	4300	6503	SO:0001587	stop_gained	144165	exon7			ACCACTGTGTTTC	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"prickle-like 1 (Drosophila)"			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1543C>T	12.37:g.42858293G>A	ENSP00000401060:p.Gln515*	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	157	29	NM_001144882	0	0	11	17	6	Q14C83|Q71QF8|Q96N00	Nonsense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	39	7.452020	0.98292	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	.	.	.	5.76	4.85	0.62838	.	0.319538	0.38959	N	0.001519	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-13.6227	16.3438	0.83116	0.0:0.0:0.8668:0.1332	.	.	.	.	X	515	.	ENSP00000345064:Q515X	Q	-	1	0	PRICKLE1	41144560	1.000000	0.71417	0.760000	0.31359	0.887000	0.51463	5.953000	0.70290	1.531000	0.49152	0.650000	0.86243	CAG	.		0.488	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			A	42858293	G	A	42858293	4	1	35	1	0	0	0	0	0	1	0	0	12515	1386	48	2	960	2	PRICKLE1	12	42858293	Nonsense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	2177053	42858293	90993602	83	3125											
ADAMTS20	80070	hgsc.bcm.edu;broad.mit.edu	37	chr12	43858498	43858498	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcagattatatatttcttCatctggtttgtcaagaagac	12	15	8	6	0	4	3	2	0	2	3	4	3	4	3	0	2	0	2	0	2	5	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:43858498C>T	ENST00000389420.3	-	10	1404	c.1405G>A	c.(1405-1407)Gaa>Aaa	p.E469K	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.E469K	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	469	Disintegrin.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TATATTTCTTCATCTGGTTTG	0.403																																					p.E469K		.											.	ADAMTS20-795	0			c.G1405A						.						93	85	88					12																	43858498		2203	4300	6503	SO:0001583	missense	80070	exon10			TTTCTTCATCTGG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1405G>A	12.37:g.43858498C>T	ENSP00000374071:p.Glu469Lys	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	100	9	NM_025003	0	0	0	0	0	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	5.358	0.251329	0.10130	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.03242	4.0;4.0	4.75	4.75	0.60458	Metallopeptidase, catalytic domain (1);	0.132902	0.33650	N	0.004689	T	0.04092	0.0114	L	0.29908	0.895	0.80722	D	1	B	0.09022	0.002	B	0.12837	0.008	T	0.49000	-0.8984	10	0.12766	T	0.61	.	18.6296	0.91355	0.0:1.0:0.0:0.0	.	469	P59510	ATS20_HUMAN	K	469	ENSP00000374071:E469K;ENSP00000448341:E469K	ENSP00000374068:E469K	E	-	1	0	ADAMTS20	42144765	0.952000	0.32445	0.750000	0.31169	0.068000	0.16541	2.779000	0.47734	2.563000	0.86464	0.591000	0.81541	GAA	.		0.403	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43858498	C	T	43858498	3	4	35	1	0	0	0	0	1	0	0	0	266	835	29	2	4446	2	ADAMTS20	12	43858498	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	1000205	43858498	89993397	84	3126											
SFRS2IP	9169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46318586	46318586	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggagggggtggtggtggTggtagtccctgagatacact	6	9	21	5	0	0	1	0	1	0	1	1	3	1	2	1	8	1	1	1	8	2	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:46318586T>A	ENST00000369367.3	-	12	4064	c.3831A>T	c.(3829-3831)ccA>ccT	p.P1277P	SCAF11_ENST00000549162.1_Silent_p.P1085P|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Silent_p.P1277P|SCAF11_ENST00000465950.1_Silent_p.P962P	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1277	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GTGGTGGTGGTGGTAGTCCCT	0.493																																					p.P1277P		.											.	SCAF11-93	0			c.A3831T						.						99	85	90					12																	46318586		2203	4300	6503	SO:0001819	synonymous_variant	9169	exon12			TGGTGGTGGTAGT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.3831A>T	12.37:g.46318586T>A		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	92	18	NM_004719	0	0	4	7	3	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			.		0.493	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		A	46318586	T	A	46318586	2	1	35	1	0	0	0	0	0	0	0	1	14209	1683	59	5		5	SFRS2IP	12	46318586	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	2460088	46318586	87533309	85	3127											
MBD6	114785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57922959	57922959	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaggcagctgtccctctgcCtccccgggcccgccctggcc	2	8	11	20	2	1	0	0	0	1	0	3	0	3	0	7	3	2	2	7	3	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:57922959C>T	ENST00000355673.3	+	13	3310	c.2954C>T	c.(2953-2955)cCt>cTt	p.P985L	MBD6_ENST00000431731.2_Missense_Mutation_p.P985L	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	985						chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						GTCCCTCTGCCTCCCCGGGCC	0.562																																					p.P985L		.											.	MBD6-516	0			c.C2954T						.						80	79	79					12																	57922959		2203	4300	6503	SO:0001583	missense	114785	exon13			CTCTGCCTCCCCG	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.2954C>T	12.37:g.57922959C>T	ENSP00000347896:p.Pro985Leu	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	93	23	NM_052897	0	0	39	57	18	Q8N3M0|Q8NA81|Q96Q00	Missense_Mutation	SNP	ENST00000355673.3	37	CCDS8944.1	.	.	.	.	.	.	.	.	.	.	c	15.34	2.804649	0.50315	.	.	ENSG00000166987	ENST00000355673;ENST00000431731	.	.	.	4.81	4.81	0.61882	.	0.000000	0.53938	D	0.000055	T	0.28532	0.0706	N	0.08118	0	0.49389	D	0.999785	P;P	0.46784	0.884;0.728	B;B	0.39562	0.303;0.199	T	0.28902	-1.0029	9	0.87932	D	0	-4.6123	13.5981	0.62002	0.0:1.0:0.0:0.0	.	985;985	Q6P0P0;Q96DN6	.;MBD6_HUMAN	L	985	.	ENSP00000347896:P985L	P	+	2	0	MBD6	56209226	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.576000	0.53878	2.683000	0.91414	0.558000	0.71614	CCT	.		0.562	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			T	57922959	C	T	57922959	3	4	35	1	0	0	0	0	1	0	0	0	9373	681	24	2	2996	2	MBD6	12	57922959	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	11604373	57922959	75928936	86	3128											
USP15	9958	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	62795034	62795034	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgacagtagtgtctccacTgcatctgaagaccaaattgt	12	11	9	9	0	2	3	0	2	2	1	3	4	2	3	2	0	1	2	2	0	3	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:62795034T>A	ENST00000280377.5	+	21	2800	c.2742T>A	c.(2740-2742)acT>acA	p.T914T	USP15_ENST00000393654.3_Silent_p.T889T|USP15_ENST00000353364.3_Silent_p.T885T	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	914	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		GTGTCTCCACTGCATCTGAAG	0.323																																					p.T914T	Melanoma(181;615 2041 39364 49691 50001)	.											.	USP15-1084	0			c.T2742A						.						69	68	68					12																	62795034		2203	4297	6500	SO:0001819	synonymous_variant	9958	exon21			CTCCACTGCATCT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2742T>A	12.37:g.62795034T>A		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	71	17	NM_001252078	0	0	3	5	2	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1																																																																																			.		0.323	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		A	62795034	T	A	62795034	2	1	35	1	0	0	0	0	0	0	0	1	17079	1567	55	5		5	USP15	12	62795034	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	4872075	62795034	71056861	87	3129											
GRIP1	23426	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	66838463	66838463	+	Frame_Shift_Del	DEL	T	T	-																															ggtgctgtcttctgttggaaTtccattgatggccatcactc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:66838463delT	ENST00000398016.3	-	12	1500	c.1432delA	c.(1432-1434)attfs	p.I478fs	GRIP1_ENST00000286445.7_Frame_Shift_Del_p.I530fs|GRIP1_ENST00000359742.4_Frame_Shift_Del_p.I530fs	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TCTGTTGGAATTCCATTGATG	0.458																																					p.I478fs		.											.	GRIP1-494	0			c.1432delA						.						136	131	133					12																	66838463		1962	4135	6097	SO:0001589	frameshift_variant	23426	exon12			.	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1432delA	12.37:g.66838463delT	ENSP00000381098:p.Ile478fs	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	106	22	NM_001178074	0	0	0	0	0	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Frame_Shift_Del	DEL	ENST00000398016.3	37	CCDS41807.1																																																																																			.		0.458	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			-	66838463	T	-	66838463	7	5	35	1	0	1	0	1	0	0	0	0	6808	1493	52	0	1850	0	GRIP1	12	66838463	Frame_Shift_Del	DEL	T	TCGA-B1-5398-01A-02D-1589-08	4043429	66838463	67013432	88	3130											
ALDH1L2	160428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	105433493	105433493	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acattttaaaaccaatacctCttcatgatctgtttgccaat	13	15	3	10	0	3	1	1	1	2	0	3	1	3	1	3	0	3	1	3	0	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:105433493C>T	ENST00000258494.9	-	17	2183	c.2043G>A	c.(2041-2043)aaG>aaA	p.K681K	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	681	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						ACCAATACCTCTTCATGATCT	0.388																																					p.K681K		.											.	ALDH1L2-91	0			c.G2043A						.						148	136	140					12																	105433493		2203	4300	6503	SO:0001819	synonymous_variant	160428	exon17			ATACCTCTTCATG	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2043G>A	12.37:g.105433493C>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	115	17	NM_001034173	0	0	0	0	0	Q3SY68|Q68D62|Q6AI55|Q8N922	Silent	SNP	ENST00000258494.9	37	CCDS31891.1																																																																																			.		0.388	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		T	105433493	C	T	105433493	2	4	35	1	0	0	0	0	0	0	0	1	495	912	32	2		2	ALDH1L2	12	105433493	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	38595030	105433493	28418402	89	3131											
PXN	5829	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	120653399	120653399	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccggggctgctccgcccGccgtcccgaggccagccggc	2	4	14	21	6	0	0	0	0	0	0	3	1	3	0	8	4	2	2	8	4	0	0	rs374919882	byFrequency	TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:120653399G>A	ENST00000228307.7	-	7	1038	c.897C>T	c.(895-897)ggC>ggT	p.G299G	PXN_ENST00000536957.1_Silent_p.G297G|PXN_ENST00000397506.3_Silent_p.G63G|PXN_ENST00000424649.2_Intron|PXN_ENST00000267257.7_Intron|PXN_ENST00000538144.1_Intron|PXN_ENST00000458477.2_Intron|PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542265.1_RNA	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	299					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGCTCCGCCCGCCGTCCCGAG	0.672													G|||	4	0.000798722	0	0	5008	,	,		11205	0		0	False		,,,				2504	0.0041				p.G299G		.											.	PXN-660	0			c.C897T						.	G	,,	1,3119		0,1,1559	27	35	32		897,,	3	0.7	12		32	0,7154		0,0,3577	no	coding-synonymous,intron,intron	PXN	NM_001080855.2,NM_002859.3,NM_025157.4	,,	0,1,5136	AA,AG,GG		0.0,0.0321,0.0097	,,	299/592,,	120653399	1,10273	1560	3577	5137	SO:0001819	synonymous_variant	5829	exon7			CCGCCCGCCGTCC	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.897C>T	12.37:g.120653399G>A		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	75	15	NM_001080855	0	0	9	9	0	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Silent	SNP	ENST00000228307.7	37	CCDS44997.1	.	.	.	.	.	.	.	.	.	.	G	0.728	-0.780857	0.02929	3.21E-4	0.0	ENSG00000089159	ENST00000550795	.	.	.	4.89	3.03	0.35002	.	.	.	.	.	T	0.35480	0.0933	.	.	.	0.24856	N	0.992376	.	.	.	.	.	.	T	0.19976	-1.0289	4	.	.	.	.	8.1293	0.31018	0.1991:0.0:0.8009:0.0	.	.	.	.	V	48	.	.	A	-	2	0	PXN	119137782	0.004000	0.15560	0.679000	0.29978	0.009000	0.06853	0.629000	0.24538	1.209000	0.43321	-0.148000	0.13756	GCG	.		0.672	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		A	120653399	G	A	120653399	2	1	35	1	0	0	0	0	0	0	0	1	12884	1074	38	1		1	PXN	12	120653399	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	15219906	120653399	13198496	90	3132											
DCLK1	9201	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	36382392	36382396	+	Frame_Shift_Del	DEL	GGAGA	GGAGA	-																															cggaaacattatcccagtatGgagaaggaaagtccacctgc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	GGAGA	GGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr13:36382392_36382396delGGAGA	ENST00000360631.3	-	14	2039_2043	c.1828_1832delTCTCC	c.(1828-1833)tctccafs	p.SP610fs	DCLK1_ENST00000379893.1_Frame_Shift_Del_p.SP303fs|DCLK1_ENST00000255448.4_Frame_Shift_Del_p.SP610fs			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.P611S(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		ATCCCAGTATGGAGAAGGAAAGTCC	0.424																																					p.610_611del		.											.	DCLK1-826	1	Substitution - Missense(1)	skin(1)	c.1828_1832del						.																																			SO:0001589	frameshift_variant	9201	exon14			.	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1828_1832delTCTCC	13.37:g.36382392_36382396delGGAGA	ENSP00000353846:p.Ser610fs	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	175	35	NM_004734	0	0	0	0	0	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Frame_Shift_Del	DEL	ENST00000360631.3	37																																																																																				.		0.424	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		-	36382396	GGAGA	-	36382392	7	5	35	1	0	1	0	1	0	0	0	0	4297	1348	47	0	377	0	DCLK1	13	36382392	Frame_Shift_Del	DEL	GGAGA	TCGA-B1-5398-01A-02D-1589-08		36382392	78787486	91	3133											
F10	2159	broad.mit.edu;bcgsc.ca	37	chr13	113803360	113803360	+	Frame_Shift_Del	DEL	C	C	-																															ctccggctcaagacccccatCaccttccgcatgaacgtggc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr13:113803360delC	ENST00000375559.3	+	8	1034	c.996delC	c.(994-996)atcfs	p.I332fs	F10_ENST00000375551.3_Frame_Shift_Del_p.S329fs|F10_ENST00000409306.1_Frame_Shift_Del_p.S331fs	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	332	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	AGACCCCCATCACCTTCCGCA	0.632																																					p.I332fs													.	F10-227	0			c.996delC						.						154	120	132					13																	113803360		2203	4300	6503	SO:0001589	frameshift_variant	2159	exon8			CCCCATCACCTTC		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.996delC	13.37:g.113803360delC	ENSP00000364709:p.Ile332fs	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	184	26	NM_000504	0	0	0	0	0	Q14340	Frame_Shift_Del	DEL	ENST00000375559.3	37	CCDS9530.1																																																																																			.		0.632	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			-	113803360	C	-	113803360	7	5	35	1	0	1	0	1	0	0	0	0	5349	816	29	0	1026	0	F10	13	113803360	Frame_Shift_Del	DEL	C	TCGA-B1-5398-01A-02D-1589-08	77420968	113803360	1366518	92	3134											
OR4N5	390437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20612708	20612708	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagctgacaaggtagttTctcttttccatactgtcatc	8	15	6	12	0	2	1	1	1	1	0	6	1	4	1	2	1	2	3	2	1	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:20612708T>G	ENST00000333629.1	+	1	814	c.814T>G	c.(814-816)Tct>Gct	p.S272A	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		CAAGGTAGTTTCTCTTTTCCA	0.418																																					p.S272A		.											.	OR4N5-69	0			c.T814G						.						165	167	167					14																	20612708		2203	4300	6503	SO:0001583	missense	390437	exon1			GTAGTTTCTCTTT		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.814T>G	14.37:g.20612708T>G	ENSP00000332110:p.Ser272Ala	Somatic	374	0		WXS	Illumina HiSeq	Phase_I	437	79	NM_001004724	0	0	0	0	0	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	37	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	T	1.597	-0.527459	0.04141	.	.	ENSG00000184394	ENST00000333629	T	0.00198	8.57	4.0	-2.2	0.06994	GPCR, rhodopsin-like superfamily (1);	0.172594	0.28198	N	0.016223	T	0.00109	0.0003	L	0.41492	1.28	0.09310	N	1	B	0.14012	0.009	B	0.21708	0.036	T	0.47586	-0.9106	10	0.02654	T	1	.	6.6619	0.23018	0.1429:0.0:0.4373:0.4197	.	272	Q8IXE1	OR4N5_HUMAN	A	272	ENSP00000332110:S272A	ENSP00000332110:S272A	S	+	1	0	OR4N5	19682548	0.000000	0.05858	0.534000	0.28014	0.087000	0.18053	-0.284000	0.08422	-0.115000	0.11915	-0.313000	0.08912	TCT	.		0.418	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			G	20612708	T	G	20612708	3	3	35	1	0	0	0	0	1	0	0	0	11105	1783	62	5	816	5	OR4N5	14	20612708	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		20612708	86736832	93	3135											
FANCM	57697	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	45667882	45667882	+	Frame_Shift_Del	DEL	T	T	-																															tgtttaggagaacaaagagcTatgacagcctgctgactacc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:45667882delT	ENST00000267430.5	+	22	5837	c.5752delT	c.(5752-5754)tatfs	p.Y1918fs	FANCM_ENST00000542564.2_Frame_Shift_Del_p.Y1892fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1918	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AACAAAGAGCTATGACAGCCT	0.363								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Y1918fs		.											.	FANCM-569	0			c.5752delT						.						84	83	83					14																	45667882		2203	4300	6503	SO:0001589	frameshift_variant	57697	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5752delT	14.37:g.45667882delT	ENSP00000267430:p.Tyr1918fs	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	107	22	NM_020937	0	0	0	0	0	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	37	CCDS32070.1																																																																																			.		0.363	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		-	45667882	T	-	45667882	7	5	35	1	0	1	0	1	0	0	0	0	5690	1522	53	0	5838	0	FANCM	14	45667882	Frame_Shift_Del	DEL	T	TCGA-B1-5398-01A-02D-1589-08	25055174	45667882	61681658	94	3136											
C14orf182	283551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	50472313	50472313	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttccacatggcacacggaccTtggaggcacagagggatggg	10	6	15	10	1	0	1	0	0	0	1	1	4	1	4	2	6	0	2	2	6	0	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:50472313T>C	ENST00000399206.1	-	1	1925	c.205A>G	c.(205-207)Agg>Ggg	p.R69G	C14orf182_ENST00000529902.1_5'UTR	NM_001012706.1	NP_001012724.1	A1A4T8	CN182_HUMAN	chromosome 14 open reading frame 182	69										large_intestine(2)|urinary_tract(1)	3						CACACGGACCTTGGAGGCACA	0.537																																					p.R69G		.											.	C14orf182-90	0			c.A205G						.						126	138	134					14																	50472313		2049	4187	6236	SO:0001630	splice_region_variant	283551	exon1			CGGACCTTGGAGG	AK090420	CCDS41949.1	14q22.1	2009-02-24			ENSG00000214900	ENSG00000214900			27503	protein-coding gene	gene with protein product							Standard	NM_001012706		Approved		uc001wxi.1	A1A4T8		ENST00000399206.1:c.206+1A>G	14.37:g.50472313T>C		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	160	24	NM_001012706	0	0	0	0	0	A8MYX4	Missense_Mutation	SNP	ENST00000399206.1	37	CCDS41949.1	.	.	.	.	.	.	.	.	.	.	T	4.441	0.081550	0.08533	.	.	ENSG00000214900	ENST00000399206	T	0.59906	0.23	3.15	0.664	0.17890	.	.	.	.	.	T	0.43986	0.1272	.	.	.	0.09310	N	1	B	0.24426	0.103	B	0.23419	0.046	T	0.40757	-0.9546	8	0.87932	D	0	.	5.9656	0.19322	0.6219:0.0:0.0:0.3781	.	69	A1A4T8-2	.	G	69	ENSP00000382157:R69G	ENSP00000382157:R69G	R	-	1	2	C14orf182	49542063	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.033000	0.13754	0.130000	0.18549	-0.509000	0.04479	AGG	.		0.537	C14orf182-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395717.1	NM_001012706	Missense_Mutation	C	50472313	T	C	50472313	5	2	35	1	0	0	0	0	0	0	1	0	1769	1623	56	3	130	3	C14orf182	14	50472313	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08	4804431	50472313	56877227	95	3137											
MLH3	27030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	75516130	75516130	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcctgtaccgagtggcattTactggtgaaataacgatttc	10	13	10	8	2	0	1	0	1	0	0	2	3	1	1	2	2	3	2	2	2	4	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:75516130T>A	ENST00000556740.1	-	1	264	c.229A>T	c.(229-231)Aaa>Taa	p.K77*	MLH3_ENST00000238662.7_Nonsense_Mutation_p.K77*|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Nonsense_Mutation_p.K77*|MLH3_ENST00000355774.2_Nonsense_Mutation_p.K77*			Q9UHC1	MLH3_HUMAN	mutL homolog 3	77					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GAGTGGCATTTACTGGTGAAA	0.448								Mismatch excision repair (MMR)																													p.K77X		.											.	MLH3-228	0			c.A229T						.						101	90	94					14																	75516130		2203	4300	6503	SO:0001587	stop_gained	27030	exon2			GGCATTTACTGGT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.229A>T	14.37:g.75516130T>A	ENSP00000452316:p.Lys77*	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	100	17	NM_014381	0	0	1	2	1	P49751|Q56DK9|Q9P292|Q9UHC0	Nonsense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646105	0.87958	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740;ENST00000553263;ENST00000557648	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.7094	15.6637	0.77209	0.0:0.0:0.0:1.0	.	.	.	.	X	77	.	ENSP00000238662:K77X	K	-	1	0	MLH3	74585883	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.036000	0.88901	2.095000	0.63458	0.533000	0.62120	AAA	.		0.448	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75516130	T	A	75516130	4	1	35	1	0	0	0	0	0	1	0	0	9643	1763	61	5	4180	5	MLH3	14	75516130	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	25043817	75516130	31833410	96	3138											
C14orf159	80017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	91642321	91642321	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaacctgcctacggggaTgccatggtgtgtcccccagg	7	8	12	14	1	0	0	0	0	0	0	2	1	2	1	6	4	4	0	6	4	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:91642321T>A	ENST00000523771.1	+	7	1239	c.636T>A	c.(634-636)gaT>gaA	p.D212E	C14orf159_ENST00000256324.10_Missense_Mutation_p.D217E|C14orf159_ENST00000521077.2_Missense_Mutation_p.D217E|C14orf159_ENST00000428926.2_Missense_Mutation_p.D212E|C14orf159_ENST00000523816.1_Missense_Mutation_p.D212E|C14orf159_ENST00000412671.2_Missense_Mutation_p.D217E|C14orf159_ENST00000518868.1_Missense_Mutation_p.D217E|C14orf159_ENST00000520328.1_Missense_Mutation_p.D200E|C14orf159_ENST00000525393.2_Missense_Mutation_p.D88E|C14orf159_ENST00000522322.1_Missense_Mutation_p.D212E			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	212						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCTACGGGGATGCCATGGTGT	0.527																																					p.D217E		.											.	C14orf159-92	0			c.T651A						.						102	90	94					14																	91642321		2203	4300	6503	SO:0001583	missense	80017	exon7			CGGGGATGCCATG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.636T>A	14.37:g.91642321T>A	ENSP00000429655:p.Asp212Glu	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	102	18	NM_001102368	0	0	32	50	18	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	T	3.538	-0.094274	0.07053	.	.	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000517518;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.06	-10.1	0.00402	.	0.938675	0.09028	N	0.859166	T	0.22166	0.0534	N	0.20807	0.61	0.09310	N	1	B;B;B;B;B;B	0.11235	0.003;0.004;0.003;0.0;0.001;0.003	B;B;B;B;B;B	0.16289	0.009;0.014;0.015;0.005;0.005;0.007	T	0.15378	-1.0439	10	0.39692	T	0.17	.	3.0379	0.06128	0.2001:0.225:0.4295:0.1454	.	212;88;217;200;217;217	Q7Z3D6;Q8NB88;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.;.	E	200;217;217;217;212;217;88;212;212;212;217	ENSP00000429453:D200E;ENSP00000256324:D217E;ENSP00000430137:D217E;ENSP00000428263:D217E;ENSP00000428974:D212E;ENSP00000428652:D217E;ENSP00000435459:D88E;ENSP00000404343:D212E;ENSP00000427953:D212E;ENSP00000429655:D212E;ENSP00000404196:D217E	ENSP00000256324:D217E	D	+	3	2	C14orf159	90712074	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.173000	0.03108	-3.740000	0.00113	0.459000	0.35465	GAT	.		0.527	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		A	91642321	T	A	91642321	3	1	35	1	0	0	0	0	1	0	0	0	1759	1461	51	5	669	5	C14orf159	14	91642321	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	16126191	91642321	15707219	97	3139											
PPP2R5C	5527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102323022	102323022	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actttgctttctgcttttcaGatgttcctcctgctgatcaa	6	18	6	11	0	3	2	2	1	1	1	5	2	5	2	2	0	3	4	2	0	1	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:102323022G>A	ENST00000334743.5	+	2	142		c.e2-1		PPP2R5C_ENST00000328724.5_Splice_Site|PPP2R5C_ENST00000422945.2_Splice_Site|PPP2R5C_ENST00000557095.1_Splice_Site|PPP2R5C_ENST00000445439.3_Splice_Site|PPP2R5C_ENST00000350249.3_Splice_Site	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CTGCTTTTCAGATGTTCCTCC	0.353																																					.		.											.	PPP2R5C-659	0			c.188-1G>A						.						177	165	169					14																	102323022		2203	4300	6503	SO:0001630	splice_region_variant	5527	exon4			TTTTCAGATGTTC	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.95-1G>A	14.37:g.102323022G>A		Somatic	353	0		WXS	Illumina HiSeq	Phase_I	311	56	NM_001161725	0	0	0	0	0	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Splice_Site	SNP	ENST00000334743.5	37	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633499	0.87660	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000557621;ENST00000445439;ENST00000334743;ENST00000557095	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3772	0.94517	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPP2R5C	101392775	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.813000	0.99286	2.573000	0.86826	0.511000	0.50034	.	.		0.353	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	Intron	A	102323022	G	A	102323022	5	1	35	1	0	0	0	0	0	0	1	0	12423	956	33	2	469	2	PPP2R5C	14	102323022	Splice_Site	SNP	G	TCGA-B1-5398-01A-02D-1589-08	10680701	102323022	5026518	98	3140											
BAG5	9529	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr14	104027517	104027517	+	5'UTR	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatacttttgttgtgttcAgtttcacaagcactaaaaga	12	15	6	8	0	2	1	2	0	0	1	3	1	3	1	1	0	2	4	1	0	4	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:104027517A>T	ENST00000445922.2	-	0	231				APOPT1_ENST00000556253.2_5'Flank|APOPT1_ENST00000409074.2_5'Flank|APOPT1_ENST00000247618.4_5'Flank|BAG5_ENST00000299204.4_5'UTR|BAG5_ENST00000337322.4_Silent_p.T36T|RP11-894P9.2_ENST00000556332.1_RNA|RP11-73M18.2_ENST00000472726.2_5'Flank	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5						negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			TGTTGTGTTCAGTTTCACAAG	0.353																																					p.T36T	NSCLC(171;1832 2055 18950 31566 41632)	.											.	BAG5-229	0			c.T108A						.						57	61	60					14																	104027517		2199	4285	6484	SO:0001623	5_prime_UTR_variant	9529	exon2			GTGTTCAGTTTCA	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.-16T>A	14.37:g.104027517A>T		Somatic	169	0		WXS	Illumina HiSeq	Phase_I	179	34	NM_001015049	0	0	0	0	0	O94950|Q86W59	Silent	SNP	ENST00000445922.2	37	CCDS9982.1																																																																																			.		0.353	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			T	104027517	A	T	104027517	1	4	35	0	1	0	0	0	0	0	0	0	1291	175	7	5		5	BAG5	14	104027517	5'UTR	SNP	A	TCGA-B1-5398-01A-02D-1589-08	1704495	104027517	3322023	99	3141											
AHNAK2	113146	broad.mit.edu	37	chr14	105409159	105409159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaggtgccctttgaggccgGctcccttgggcagggggccc	3	7	18	13	1	0	1	0	1	0	0	1	2	1	2	4	7	1	2	4	7	0	2	rs202233797	byFrequency	TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:105409159G>A	ENST00000333244.5	-	7	12748	c.12629C>T	c.(12628-12630)gCc>gTc	p.A4210V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4210						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.A4210V(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTTGAGGCCGGCTCCCTTGGG	0.642																																					p.A4210V													.	AHNAK2-47	1	Substitution - Missense(1)	lung(1)	c.C12629T						.						94	102	99					14																	105409159		1863	4091	5954	SO:0001583	missense	113146	exon7			AGGCCGGCTCCCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12629C>T	14.37:g.105409159G>A	ENSP00000353114:p.Ala4210Val	Somatic	262	0		WXS	Illumina HiSeq	Phase_I	223	4	NM_138420	0	0	10	10	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	14.25	2.480798	0.44044	.	.	ENSG00000185567	ENST00000333244	T	0.00768	5.72	3.61	-4.18	0.03846	.	0.514426	0.13911	N	0.354267	T	0.00998	0.0033	L	0.43923	1.385	0.09310	N	1	P	0.35894	0.526	P	0.48598	0.583	T	0.43426	-0.9392	10	0.26408	T	0.33	.	1.7885	0.03046	0.3986:0.2225:0.2669:0.112	.	4210	Q8IVF2	AHNK2_HUMAN	V	4210	ENSP00000353114:A4210V	ENSP00000353114:A4210V	A	-	2	0	AHNAK2	104480204	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-0.057000	0.11768	-0.718000	0.04949	0.306000	0.20318	GCC	.		0.642	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105409159	G	A	105409159	3	1	35	1	0	0	0	0	1	0	0	0	415	1203	42	2	4762	2	AHNAK2	14	105409159	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	1381642	105409159	1940381	100	3142											
AHNAK2	113146	broad.mit.edu	37	chr14	105413291	105413291	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacacatccaccgaggcctCgatggacttgcctggggccg	8	6	13	14	3	0	1	0	0	0	1	2	4	1	2	5	4	1	0	5	4	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:105413291C>A	ENST00000333244.5	-	7	8616	c.8497G>T	c.(8497-8499)Gag>Tag	p.E2833*	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2833						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACCGAGGCCTCGATGGACTTG	0.582																																					p.E2833X													.	AHNAK2-47	0			c.G8497T						.						207	226	220					14																	105413291		1969	4138	6107	SO:0001587	stop_gained	113146	exon7			AGGCCTCGATGGA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.8497G>T	14.37:g.105413291C>A	ENSP00000353114:p.Glu2833*	Somatic	427	0		WXS	Illumina HiSeq	Phase_I	400	7	NM_138420	12	0	45	57	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Nonsense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	49	14.983857	0.99818	.	.	ENSG00000185567	ENST00000333244	.	.	.	3.46	1.34	0.21922	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	7.3768	0.26833	0.1912:0.6238:0.185:0.0	.	.	.	.	X	2833	.	ENSP00000353114:E2833X	E	-	1	0	AHNAK2	104484336	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.660000	0.25009	0.394000	0.25230	0.306000	0.20318	GAG	.		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105413291	C	A	105413291	4	1	35	1	0	0	0	0	0	1	0	0	415	893	31	4	8894	4	AHNAK2	14	105413291	Nonsense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	4132	105413291	1936249	101	3143											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41854918	41854918	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttttaaatgtaacaggTgagcagcctcagaagggggc	11	10	13	7	0	2	2	1	1	1	1	2	2	2	2	1	3	3	3	1	3	4	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr15:41854918T>G	ENST00000263798.3	+	4	804		c.e4+2		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		ATGTAACAGGTGAGCAGCCTC	0.582																																					.		.											.	TYRO3-1388	0			c.580+2T>G						.						22	20	21					15																	41854918		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon4			AACAGGTGAGCAG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.580+2T>G	15.37:g.41854918T>G		Somatic	22	2		WXS	Illumina HiSeq	Phase_I	19	4	NM_006293	0	0	0	0	0	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.113398	0.77210	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5013	0.67724	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39642210	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.037000	0.70956	2.007000	0.58848	0.387000	0.25754	.	.		0.582	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron	G	41854918	T	G	41854918	5	3	35	1	0	0	0	0	0	0	1	0	16847	1710	59	5	596	5	TYRO3	15	41854918	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08		41854918	60676474	102	3144											
SCG3	29106	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51993377	51993377	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatggaaaaggaatatggAagcttgaaggattccacaaa	19	7	11	4	0	0	2	0	1	0	1	1	6	1	6	1	4	1	1	1	4	8	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr15:51993377A>G	ENST00000220478.3	+	10	1546	c.1143A>G	c.(1141-1143)ggA>ggG	p.G381G	SCG3_ENST00000542355.2_Silent_p.G149G	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III	381					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		AGGAATATGGAAGCTTGAAGG	0.413																																					p.G381G		.											.	SCG3-91	0			c.A1143G						.						185	171	176					15																	51993377		2195	4293	6488	SO:0001819	synonymous_variant	29106	exon10			ATATGGAAGCTTG	AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.1143A>G	15.37:g.51993377A>G		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	104	24	NM_013243	0	0	0	0	0	A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	Silent	SNP	ENST00000220478.3	37	CCDS10142.1																																																																																			.		0.413	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254670.2	NM_013243		G	51993377	A	G	51993377	2	3	35	1	0	0	0	0	0	0	0	1	13924	233	9	3		3	SCG3	15	51993377	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	10138459	51993377	50538015	103	3145											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2807812	2807812	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actcaccagttggcagaattAaatgagaagaagaatgaaag	19	7	10	5	0	1	5	1	2	0	4	1	6	1	5	1	1	0	2	1	1	7	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:2807812A>T	ENST00000301740.8	+	4	930	c.381A>T	c.(379-381)ttA>ttT	p.L127F		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	127					mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						tggcagaattaaatgagaaga	0.443																																					p.L127F		.											.	SRRM2-93	0			c.A381T						.						92	99	96					16																	2807812		2198	4300	6498	SO:0001583	missense	23524	exon4			AGAATTAAATGAG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.381A>T	16.37:g.2807812A>T	ENSP00000301740:p.Leu127Phe	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	207	32	NM_016333	0	0	57	74	17	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.997285	0.35226	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000396975;ENST00000426305	T	0.23348	1.91	4.96	1.41	0.22369	.	0.000000	0.40908	D	0.000991	T	0.25232	0.0613	N	0.14661	0.345	0.28270	N	0.924446	D	0.69078	0.997	D	0.63488	0.915	T	0.04900	-1.0919	10	0.51188	T	0.08	-4.0677	7.5072	0.27551	0.3974:0.0:0.6026:0.0	.	127	Q9UQ35	SRRM2_HUMAN	F	127;127;31;92	ENSP00000301740:L127F	ENSP00000301740:L127F	L	+	3	2	SRRM2	2747813	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.918000	0.28678	0.497000	0.27926	-0.414000	0.06135	TTA	.		0.443	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2807812	A	T	2807812	3	4	35	1	0	0	0	0	1	0	0	0	15201	359	13	5	391	5	SRRM2	16	2807812	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08		2807812	87546941	104	3146											
CLEC16A	23274	broad.mit.edu	37	chr16	11217780	11217780	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggccgcatccaggcaaggcGcatgaagatgcagagaatag	14	4	14	9	2	0	3	0	1	0	2	1	4	1	3	2	3	1	4	2	3	4	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:11217780G>A	ENST00000409790.1	+	21	2680	c.2450G>A	c.(2449-2451)cGc>cAc	p.R817H	CLEC16A_ENST00000381822.2_5'Flank|CLEC16A_ENST00000409552.3_Missense_Mutation_p.R799H	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CAGGCAAGGCGCATGAAGATG	0.587																																					p.R817H													.	CLEC16A-92	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2450A						.						28	30	29					16																	11217780		2076	4216	6292	SO:0001583	missense	23274	exon20			CAAGGCGCATGAA	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"C-type lectin domain containing"	29013	protein-coding gene	gene with protein product		611303	"KIAA0350"	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2450G>A	16.37:g.11217780G>A	ENSP00000387122:p.Arg817His	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	26	3	NM_015226	0	0	51	51	0		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.4|26.4	4.733694|4.733694	0.89482|0.89482	.|.	.|.	ENSG00000038532|ENSG00000038532	ENST00000428742|ENST00000409790;ENST00000542102;ENST00000409552;ENST00000436973	.|T	.|0.44083	.|0.93	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	.|0.047440	.|0.85682	.|D	.|0.000000	T|T	0.32496|0.32496	0.0831|0.0831	N|N	0.25647|0.25647	0.755|0.755	0.80722|0.80722	D|D	1|1	.|B;B	.|0.29805	.|0.017;0.257	.|B;B	.|0.22386	.|0.008;0.039	T|T	0.05971|0.05971	-1.0853|-1.0853	5|10	.|0.35671	.|T	.|0.21	-22.7297|-22.7297	18.5026|18.5026	0.90887|0.90887	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|817;799	.|Q2KHT3;Q2KHT3-2	.|CL16A_HUMAN;.	T|H	61|817;817;799;10	.|ENSP00000387122:R817H	.|ENSP00000386495:R799H	A|R	+|+	1|2	0|0	CLEC16A|CLEC16A	11125281|11125281	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.620000|6.620000	0.74224|0.74224	2.618000|2.618000	0.88619|0.88619	0.655000|0.655000	0.94253|0.94253	GCA|CGC	.		0.587	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11217780	G	A	11217780	3	1	35	1	0	0	0	0	1	0	0	0	3506	1087	38	1	2528	1	CLEC16A	16	11217780	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	8409968	11217780	79136973	105	3147											
XPO6	23214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	28157419	28157419	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttgaggagtttacctgtTgagaactgcttccttgtctc	6	17	10	8	0	1	2	0	2	1	1	3	4	2	3	2	1	3	4	2	1	2	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:28157419T>A	ENST00000304658.5	-	9	1830	c.1330A>T	c.(1330-1332)Aac>Tac	p.N444Y	XPO6_ENST00000565698.1_Missense_Mutation_p.N430Y	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	444					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						GTTTACCTGTTGAGAACTGCT	0.398																																					p.N444Y		.											.	XPO6-227	0			c.A1330T						.						209	195	199					16																	28157419		1880	4095	5975	SO:0001583	missense	23214	exon9			ACCTGTTGAGAAC	AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"Exportins"	19733	protein-coding gene	gene with protein product		608411	"RAN binding protein 20"	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.1330A>T	16.37:g.28157419T>A	ENSP00000302790:p.Asn444Tyr	Somatic	242	0		WXS	Illumina HiSeq	Phase_I	292	80	NM_015171	0	0	0	0	0	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	37	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.507676	0.44558	.	.	ENSG00000169180	ENST00000304658	T	0.47528	0.84	5.07	5.07	0.68467	Armadillo-like helical (1);Armadillo-type fold (1);	0.197221	0.52532	D	0.000061	T	0.33702	0.0872	L	0.29908	0.895	0.39270	D	0.964376	P;P	0.48162	0.906;0.79	B;B	0.41723	0.272;0.365	T	0.24012	-1.0172	10	0.42905	T	0.14	.	7.6658	0.28430	0.0:0.0948:0.0:0.9052	.	444;444	B7ZM10;Q96QU8	.;XPO6_HUMAN	Y	444	ENSP00000302790:N444Y	ENSP00000302790:N444Y	N	-	1	0	XPO6	28064920	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.790000	0.62453	1.925000	0.55765	0.524000	0.50904	AAC	.		0.398	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28157419	T	A	28157419	3	1	35	1	0	0	0	0	1	0	0	0	17481	1812	63	5	2111	5	XPO6	16	28157419	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	16939639	28157419	62197334	106	3148											
MVP	9961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	29848119	29848119	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcactggggaggagtggcTggtaacagtgcaggacacag	10	5	17	9	1	0	0	0	0	0	0	0	3	0	3	1	6	2	4	1	6	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:29848119T>G	ENST00000357402.5	+	7	887	c.749T>G	c.(748-750)cTg>cGg	p.L250R	MVP_ENST00000395353.1_Missense_Mutation_p.L250R|MVP_ENST00000452209.2_Silent_p.A64A	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	250					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						GAGGAGTGGCTGGTAACAGTG	0.642																																					p.L250R		.											.	MVP-93	0			c.T749G						.						49	48	48					16																	29848119		2196	4300	6496	SO:0001583	missense	9961	exon7			AGTGGCTGGTAAC	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"lung resistance-related protein"	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.749T>G	16.37:g.29848119T>G	ENSP00000349977:p.Leu250Arg	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	82	6	NM_017458	0	0	665	780	115	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.550045	0.86127	.	.	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.55930	0.49;0.49	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.77671	0.4165	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83011	-0.0172	10	0.87932	D	0	-19.7942	13.7862	0.63110	0.0:0.0:0.0:1.0	.	250	Q14764	MVP_HUMAN	R	250	ENSP00000349977:L250R;ENSP00000378760:L250R	ENSP00000349977:L250R	L	+	2	0	MVP	29755620	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	6.236000	0.72339	2.194000	0.70268	0.379000	0.24179	CTG	.		0.642	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		G	29848119	T	G	29848119	3	3	35	1	0	0	0	0	1	0	0	0	10021	1580	55	5	771	5	MVP	16	29848119	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	1690700	29848119	60506634	107	3149											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	30723210	30723210	+	Frame_Shift_Del	DEL	A	A	-																															tgaacattcagaggaggaagAaacaagtggaagttcagcat																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:30723210delA	ENST00000262518.4	+	12	1932	c.1547delA	c.(1546-1548)gaafs	p.E516fs	SNORA30_ENST00000384028.1_RNA|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.E516fs|SRCAP_ENST00000395059.2_Frame_Shift_Del_p.E516fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	516	Glu-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GAGGAGGAAGAAACAAGTGGA	0.473																																					p.E516fs		.											.	SRCAP-94	0			c.1547delA						.						74	71	72					16																	30723210		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon12			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.1547delA	16.37:g.30723210delA	ENSP00000262518:p.Glu516fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	78	13	NM_006662	0	0	0	0	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.473	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30723210	A	-	30723210	7	5	35	1	0	1	0	1	0	0	0	0	15167	246	9	0	1585	0	SRCAP	16	30723210	Frame_Shift_Del	DEL	A	TCGA-B1-5398-01A-02D-1589-08	875091	30723210	59631543	108	3150											
ZNF646	9726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31090723	31090723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagatgccaagtctcaagaGggagcaggcacccccttggg	10	5	15	11	0	1	2	1	0	1	2	2	4	1	3	3	4	2	2	3	4	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:31090723G>A	ENST00000394979.2	+	1	3501	c.3078G>A	c.(3076-3078)gaG>gaA	p.E1026E	ZNF646_ENST00000300850.5_Silent_p.E1026E			O15015	ZN646_HUMAN	zinc finger protein 646	1026					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						AGTCTCAAGAGGGAGCAGGCA	0.587																																					p.E1026E		.											.	ZNF646-153	0			c.G3078A						.						121	118	119					16																	31090723		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			TCAAGAGGGAGCA	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.3078G>A	16.37:g.31090723G>A		Somatic	252	0		WXS	Illumina HiSeq	Phase_I	232	34	NM_014699	0	0	10	12	2	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				.		0.587	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		A	31090723	G	A	31090723	2	1	35	1	0	0	0	0	0	0	0	1	18094	991	35	2		2	ZNF646	16	31090723	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	367513	31090723	59264030	109	3151											
CNOT1	23019	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	58633189	58633190	+	Frame_Shift_Ins	INS	-	-	CCAC																															atttttcttggttaaattgtINSccaccaggtagctgatttga																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:58633189_58633190insCCAC	ENST00000317147.5	-	2	384_385	c.52_53insGTGG	c.(52-54)gacfs	p.D18fs	CNOT1_ENST00000441024.2_Frame_Shift_Ins_p.D18fs|CNOT1_ENST00000569240.1_Frame_Shift_Ins_p.D18fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	18				D -> G (in Ref. 1; CAD97851). {ECO:0000305}.	gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GGTTAAATTGTCCACCAGGTAG	0.49																																					p.D18fs		.											.	CNOT1-95	0			c.53_54insGTGG						.																																			SO:0001589	frameshift_variant	23019	exon2			.	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.49_52dupGTGG	16.37:g.58633190_58633193dupCCAC	ENSP00000320949:p.Asp18fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	121	25	NM_016284	0	0	0	0	0	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Ins	INS	ENST00000317147.5	37	CCDS10799.1																																																																																			.		0.49	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		CCAC	58633190	-	CCAC	58633189	7	5	35	1	0	1	1	0	0	0	0	0	3623	1667	58	0	7491	0	CNOT1	16	58633189	Frame_Shift_Ins	INS	-	TCGA-B1-5398-01A-02D-1589-08	27542466	58633189	31721564	110	3152											
HAS3	3038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	69143465	69143465	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatcctgggcctgcaccTgctcattcagagcctttttg	5	12	9	15	1	2	1	2	0	0	1	3	1	3	1	5	1	3	2	5	1	0	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:69143465T>A	ENST00000306560.1	+	2	323	c.167T>A	c.(166-168)cTg>cAg	p.L56Q	HAS3_ENST00000219322.3_Missense_Mutation_p.L56Q|HAS3_ENST00000569188.1_Missense_Mutation_p.L56Q	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	56					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		GGCCTGCACCTGCTCATTCAG	0.657																																					p.L56Q		.											.	HAS3-90	0			c.T167A						.						93	79	84					16																	69143465		2198	4300	6498	SO:0001583	missense	3038	exon2			TGCACCTGCTCAT	BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.167T>A	16.37:g.69143465T>A	ENSP00000304440:p.Leu56Gln	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	100	13	NM_138612	0	0	1	1	0	A8K5T5|Q8WTZ0|Q9NYP0	Missense_Mutation	SNP	ENST00000306560.1	37	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.778165	0.90195	.	.	ENSG00000103044	ENST00000219322;ENST00000306560	T;T	0.55930	0.49;0.63	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.73393	0.3581	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.959;0.999	T	0.77370	-0.2613	10	0.87932	D	0	12.4482	15.438	0.75162	0.0:0.0:0.0:1.0	.	56;56	O00219;O00219-2	HAS3_HUMAN;.	Q	56	ENSP00000219322:L56Q;ENSP00000304440:L56Q	ENSP00000219322:L56Q	L	+	2	0	HAS3	67700966	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.924000	0.87555	2.143000	0.66587	0.459000	0.35465	CTG	.		0.657	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612		A	69143465	T	A	69143465	3	1	35	1	0	0	0	0	1	0	0	0	6984	1580	55	5	169	5	HAS3	16	69143465	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	10510276	69143465	21211288	111	3153											
SLC38A8	146167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	84063153	84063153	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacacagaggtccaggaggcAgggctgtaaacagacaagaa	17	3	13	8	0	0	3	0	0	0	3	1	4	1	4	1	4	2	3	1	4	5	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:84063153A>G	ENST00000299709.3	-	5	635	c.636T>C	c.(634-636)ccT>ccC	p.P212P		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	212					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TCCAGGAGGCAGGGCTGTAAA	0.493																																					p.P212P		.											.	SLC38A8-68	0			c.T636C						.						94	92	93					16																	84063153		2200	4300	6500	SO:0001819	synonymous_variant	146167	exon5			GGAGGCAGGGCTG		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"Solute carriers"	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.636T>C	16.37:g.84063153A>G		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	81	29	NM_001080442	0	0	0	0	0		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			.		0.493	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		G	84063153	A	G	84063153	2	3	35	1	0	0	0	0	0	0	0	1	14642	175	7	3		3	SLC38A8	16	84063153	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	14919688	84063153	6291600	112	3154											
TMEM220	388335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10626593	10626593	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agttgaatacttactttgagGaactgtggcacaggataatc	13	12	10	6	0	0	2	0	2	0	0	1	4	0	4	0	3	3	2	0	3	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:10626593G>C	ENST00000341871.3	-	5	805	c.341C>G	c.(340-342)tCc>tGc	p.S114C	TMEM220_ENST00000578345.1_Intron|TMEM220_ENST00000580186.1_5'UTR|TMEM220_ENST00000455996.2_Missense_Mutation_p.S104C	NM_001004313.1	NP_001004313.1	Q6QAJ8	TM220_HUMAN	transmembrane protein 220	114						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(1)|prostate(2)	5						TTACTTTGAGGAACTGTGGCA	0.468																																					p.S114C		.											.	TMEM220-90	0			c.C341G						.						163	145	151					17																	10626593		2203	4300	6503	SO:0001583	missense	388335	exon5			TTTGAGGAACTGT		CCDS32567.1	17p13.1	2008-08-08			ENSG00000187824	ENSG00000187824			33757	protein-coding gene	gene with protein product							Standard	NM_001004313		Approved		uc002gmx.3	Q6QAJ8		ENST00000341871.3:c.341C>G	17.37:g.10626593G>C	ENSP00000339830:p.Ser114Cys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	125	18	NM_001004313	0	0	0	0	0	A1YRJ4|B2RNE4|B4DJ52|B9EGW3	Missense_Mutation	SNP	ENST00000341871.3	37	CCDS32567.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.205169	0.58234	.	.	ENSG00000187824	ENST00000341871;ENST00000455996	.	.	.	5.63	4.66	0.58398	.	0.096587	0.41938	D	0.000796	T	0.77046	0.4073	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.948;0.998	T	0.79403	-0.1818	9	0.87932	D	0	-22.2883	11.3464	0.49563	0.0848:0.0:0.9152:0.0	.	104;114	Q6QAJ8-2;Q6QAJ8	.;TM220_HUMAN	C	114;104	.	ENSP00000339830:S114C	S	-	2	0	TMEM220	10567318	1.000000	0.71417	0.137000	0.22149	0.714000	0.41099	3.006000	0.49529	1.379000	0.46325	0.563000	0.77884	TCC	.		0.468	TMEM220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440333.1	NM_001004313		C	10626593	G	C	10626593	3	2	35	1	0	0	0	0	1	0	0	0	16176	1174	41	4	149	4	TMEM220	17	10626593	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08		10626593	70568617	113	3155											
FBXW10	10517	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	18653137	18653137	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacgatccctgcaatctatTggttgacctggatgacatca	10	12	9	10	1	2	2	1	2	1	0	3	4	3	3	2	2	2	3	2	2	3	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:18653137T>A	ENST00000395665.4	+	3	994	c.773T>A	c.(772-774)tTg>tAg	p.L258*	FBXW10_ENST00000308799.4_Nonsense_Mutation_p.L258*|FBXW10_ENST00000395667.1_Nonsense_Mutation_p.L258*|FBXW10_ENST00000301938.4_Nonsense_Mutation_p.L258*			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	258										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						TGCAATCTATTGGTTGACCTG	0.468																																					p.L258X		.											.	FBXW10-91	0			c.T773A						.						146	115	126					17																	18653137		2203	4300	6503	SO:0001587	stop_gained	10517	exon3			ATCTATTGGTTGA	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"F-boxes / WD-40 domains", "WD repeat domain containing"	1211	protein-coding gene	gene with protein product		611679	"chromosome 17 open reading frame 1A", "F-box and WD-40 domain protein 10"	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.773T>A	17.37:g.18653137T>A	ENSP00000379025:p.Leu258*	Somatic	302	0		WXS	Illumina HiSeq	Phase_I	314	49	NM_001267585	0	0	0	0	0	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Nonsense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	T	37	6.578584	0.97680	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	.	.	.	2.49	2.49	0.30216	.	0.395534	0.14928	U	0.290234	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5156	0.33244	0.0:0.0:0.0:1.0	.	.	.	.	X	258	.	ENSP00000306937:L258X	L	+	2	0	FBXW10	18593862	0.026000	0.19158	0.002000	0.10522	0.803000	0.45373	1.573000	0.36472	1.144000	0.42321	0.333000	0.21579	TTG	.		0.468	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		A	18653137	T	A	18653137	4	1	35	1	0	0	0	0	0	1	0	0	5782	1821	63	5	783	5	FBXW10	17	18653137	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	8026544	18653137	62542073	114	3156											
DHX58	79132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40262859	40262859	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtttaagttctaggtacTggctcatgatgacgttgtag	9	14	13	5	1	2	2	1	2	1	0	2	3	2	3	0	3	1	6	0	3	4	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:40262859T>A	ENST00000251642.3	-	5	665	c.443A>T	c.(442-444)cAg>cTg	p.Q148L		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	148	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TTCTAGGTACTGGCTCATGAT	0.612																																					p.Q148L		.											.	DHX58-90	0			c.A443T						.						189	163	172					17																	40262859		2203	4300	6503	SO:0001583	missense	79132	exon5			AGGTACTGGCTCA	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"RNA helicase LGP2"	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.443A>T	17.37:g.40262859T>A	ENSP00000251642:p.Gln148Leu	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	140	24	NM_024119	0	0	14	20	6	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653438	0.47362	.	.	ENSG00000108771	ENST00000251642;ENST00000423748;ENST00000413196;ENST00000430773	T;T;T	0.33438	3.64;1.41;1.94	4.93	-2.66	0.06077	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.568788	0.18403	N	0.142315	T	0.17874	0.0429	N	0.17800	0.525	0.19575	N	0.999962	B;B	0.22746	0.074;0.007	B;B	0.27500	0.08;0.015	T	0.22487	-1.0215	10	0.36615	T	0.2	.	11.295	0.49274	0.0:0.5209:0.0:0.4791	.	141;148	B7Z455;Q96C10	.;DHX58_HUMAN	L	148;111;148;148	ENSP00000251642:Q148L;ENSP00000416389:Q148L;ENSP00000404639:Q148L	ENSP00000251642:Q148L	Q	-	2	0	DHX58	37516385	0.000000	0.05858	0.973000	0.42090	0.876000	0.50452	-0.928000	0.03980	-0.318000	0.08665	-1.063000	0.02288	CAG	.		0.612	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119		A	40262859	T	A	40262859	3	1	35	1	0	0	0	0	1	0	0	0	4525	1580	55	5	1633	5	DHX58	17	40262859	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	21609722	40262859	40932351	115	3157											
NPEPPS	9520	hgsc.bcm.edu;broad.mit.edu	37	chr17	45699223	45699224	+	Nonsense_Mutation	DNP	GC	GC	TT																															ctgaatgctgcctggctaaaGcgagatgctgagagcatcca																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:45699223_45699224GC>TT	ENST00000322157.4	+	23	2934_2935	c.2697_2698GC>TT	c.(2695-2700)aaGCga>aaTTga	p.899_900KR>N*	RP11-580I16.2_ENST00000584391.1_RNA|RP11-580I16.2_ENST00000582066.1_RNA|NPEPPS_ENST00000544660.1_Nonsense_Mutation_p.819_820KR>N*|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000530173.1_Nonsense_Mutation_p.895_896KR>N*	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	899					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						CCTGGCTAAAGCGAGATGCTGA	0.54																																					p.KR899N*		.											.	NPEPPS	0			c.C2698T						.																																			SO:0001587	stop_gained	9520	exon23			CTAAAGCGAGATG	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	Exception_encountered	17.37:g.45699223_45699224delinsTT	ENSP00000320324:p.K899_R900delinsN*	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	54	4		0	0	0	0	0	B7Z463|Q6P145|Q9NP16|Q9UEM2	Nonsense_Mutation	DNP	ENST00000322157.4	37	CCDS45721.1																																																																																			.		0.54	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		TT	45699224	GC	TT	45699223	4	4	35	1	0	0	0	0	0	1	0	0	10601	962	34	4	2787	4	NPEPPS	17	45699223	Nonsense_Mutation	DNP	GC	TCGA-B1-5398-01A-02D-1589-08	5436364	45699223	35495987	116	3158											
COL1A1	1277	hgsc.bcm.edu;bcgsc.ca	37	chr17	48265470	48265470	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tacttacggcggggccacggGcgccaacagggccgacagga	9	3	16	13	5	0	0	0	0	0	0	0	2	0	1	3	6	3	0	3	6	3	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:48265470G>C	ENST00000225964.5	-	44	3366	c.3248C>G	c.(3247-3249)gCc>gGc	p.A1083G		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1083	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GGGGCCACGGGCGCCAACAGG	0.632			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.A1083G		.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1-986	0			c.C3248G						.						22	19	20					17																	48265470		2195	4297	6492	SO:0001583	missense	1277	exon44			CCACGGGCGCCAA	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.3248C>G	17.37:g.48265470G>C	ENSP00000225964:p.Ala1083Gly	Somatic	29	1		WXS	Illumina HiSeq	Phase_I	20	3	NM_000088	0	0	0	0	0	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	37	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.076520	0.36662	.	.	ENSG00000108821	ENST00000225964	D	0.93659	-3.26	5.26	4.29	0.51040	.	0.070349	0.56097	D	0.000026	D	0.91727	0.7384	L	0.45422	1.42	0.39212	D	0.963332	B	0.32302	0.363	B	0.42245	0.381	D	0.90605	0.4547	10	0.44086	T	0.13	.	11.9451	0.52924	0.085:0.0:0.915:0.0	.	1083	P02452	CO1A1_HUMAN	G	1083	ENSP00000225964:A1083G	ENSP00000225964:A1083G	A	-	2	0	COL1A1	45620469	1.000000	0.71417	1.000000	0.80357	0.366000	0.29705	3.598000	0.54038	1.216000	0.43427	0.462000	0.41574	GCC	.		0.632	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			C	48265470	G	C	48265470	3	2	35	1	0	0	0	0	1	0	0	0	3683	1203	42	4	1178	4	COL1A1	17	48265470	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	2566247	48265470	32929740	117	3159											
QRICH2	84074	hgsc.bcm.edu;broad.mit.edu	37	chr17	74303551	74303551	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtgcgtgctcaccctggCaaagctgagctcctcggcgg	5	8	14	14	4	1	1	1	1	0	0	3	1	2	1	2	3	4	4	2	3	1	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:74303551C>G	ENST00000262765.5	-	1	210	c.31G>C	c.(31-33)Gcc>Ccc	p.A11P		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	11										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTCACCCTGGCAAAGCTGAGC	0.701																																					p.A11P		.											.	QRICH2-94	0			c.G31C						.						57	51	53					17																	74303551		2203	4300	6503	SO:0001583	missense	84074	exon1			CCCTGGCAAAGCT	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.31G>C	17.37:g.74303551C>G	ENSP00000262765:p.Ala11Pro	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	49	4	NM_032134	0	0	0	0	0	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	C	9.811	1.183270	0.21870	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08984	3.03	4.13	-8.25	0.01025	.	.	.	.	.	T	0.03564	0.0102	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.36138	-0.9760	9	0.45353	T	0.12	11.3655	3.4716	0.07569	0.1651:0.1106:0.4721:0.2522	.	11	Q9H0J4	QRIC2_HUMAN	P	11	ENSP00000262765:A11P	ENSP00000262765:A11P	A	-	1	0	QRICH2	71815146	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.507000	0.02268	-3.600000	0.00134	0.411000	0.27672	GCC	.		0.701	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		G	74303551	C	G	74303551	3	3	35	1	0	0	0	0	1	0	0	0	12912	710	25	4	5036	4	QRICH2	17	74303551	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	26038081	74303551	6891659	118	3160											
MYO5B	4645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	47375980	47375980	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtaaatcttcagttgcttTttgagcttcctctcattctt	7	20	5	9	0	4	1	2	1	3	0	6	1	5	1	1	0	2	4	1	0	2	8			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr18:47375980T>A	ENST00000285039.7	-	32	4571	c.4272A>T	c.(4270-4272)aaA>aaT	p.K1424N	MYO5B_ENST00000592688.1_5'UTR|SCARNA17_ENST00000589499.1_RNA|MYO5B_ENST00000324581.6_Missense_Mutation_p.K539N	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1424					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCAGTTGCTTTTTGAGCTTCC	0.483																																					p.K1424N		.											.	MYO5B-72	0			c.A4272T						.						336	326	330					18																	47375980		1961	4155	6116	SO:0001583	missense	4645	exon32			TTGCTTTTTGAGC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.4272A>T	18.37:g.47375980T>A	ENSP00000285039:p.Lys1424Asn	Somatic	475	0		WXS	Illumina HiSeq	Phase_I	494	65	NM_001080467	0	0	48	85	37	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.929283	0.73327	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.27720	1.65;1.65	4.63	-8.81	0.00813	.	0.000000	0.85682	D	0.000000	T	0.48132	0.1483	M	0.75615	2.305	0.45914	D	0.998753	D;D	0.89917	0.999;1.0	D;D	0.85130	0.986;0.997	T	0.70737	-0.4790	10	0.42905	T	0.14	.	18.1767	0.89764	0.0:0.7032:0.0:0.2968	.	1424;539	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	N	1424;539	ENSP00000285039:K1424N;ENSP00000315531:K539N	ENSP00000285039:K1424N	K	-	3	2	MYO5B	45629978	0.939000	0.31865	0.188000	0.23233	0.960000	0.62799	0.054000	0.14205	-1.861000	0.01153	-0.441000	0.05720	AAA	.		0.483	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47375980	T	A	47375980	3	1	35	1	0	0	0	0	1	0	0	0	10104	1838	64	5	1310	5	MYO5B	18	47375980	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		47375980	30701268	119	3161											
FAM108A1	81926	broad.mit.edu	37	chr19	1880041	1880041	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgttgcagtggaggcgggAgcccaggccaatgtagaagc	10	6	17	8	1	0	1	0	0	0	1	0	4	0	3	2	4	3	3	2	4	3	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:1880041A>G	ENST00000292577.7	-	3	839	c.406T>C	c.(406-408)Tcc>Ccc	p.S136P	ABHD17A_ENST00000590661.1_Missense_Mutation_p.S118P|ABHD17A_ENST00000250974.9_Missense_Mutation_p.S187P	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	136						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										TGGAGGCGGGAGCCCAGGCCA	0.632																																					p.S187P													.	FAM108A1-90	0			c.T559C						.						34	36	35					19																	1880041		2200	4291	6491	SO:0001583	missense	81926	exon4			GGCGGGAGCCCAG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"Abhydrolase domain containing"	28756	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 27", "family with sequence similarity 108, member A1"	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.406T>C	19.37:g.1880041A>G	ENSP00000292577:p.Ser136Pro	Somatic	55	3		WXS	Illumina HiSeq	Phase_I	56	6	NM_031213	1	1	120	128	6	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Missense_Mutation	SNP	ENST00000292577.7	37	CCDS45902.1	.	.	.	.	.	.	.	.	.	.	a	15.06	2.720812	0.48728	.	.	ENSG00000129968	ENST00000250974;ENST00000292577	T;T	0.46063	0.88;0.88	4.41	-2.3	0.06785	.	0.201057	0.52532	D	0.000079	T	0.41949	0.1181	L	0.52266	1.64	0.26067	N	0.981275	B;P;B;P	0.43477	0.4;0.808;0.348;0.659	B;P;B;B	0.49799	0.427;0.622;0.301;0.301	T	0.43572	-0.9383	10	0.41790	T	0.15	-17.9715	11.1469	0.48436	0.6056:0.0:0.0:0.3944	.	136;187;136;136	Q96GS6;Q96GS6-2;Q96GS6-3;Q96GS6-4	F18A1_HUMAN;.;.;.	P	187;136	ENSP00000250974:S187P;ENSP00000292577:S136P	ENSP00000250974:S187P	S	-	1	0	FAM108A1	1831041	0.999000	0.42202	0.381000	0.26106	0.558000	0.35554	0.493000	0.22451	-0.942000	0.03695	-0.496000	0.04628	TCC	.		0.632	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		G	1880041	A	G	1880041	3	3	35	1	0	0	0	0	1	0	0	0	5407	304	11	3	538	3	FAM108A1	19	1880041	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08		1880041	57248942	120	3162											
ADAMTS10	81794	broad.mit.edu	37	chr19	8665858	8665858	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccacatcccggcgcccgTgataggccaccatcatcttg	7	8	9	17	3	2	1	1	1	1	0	4	1	4	1	5	2	0	1	5	2	1	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:8665858T>C	ENST00000597188.1	-	6	1034	c.764A>G	c.(763-765)cAc>cGc	p.H255R	ADAMTS10_ENST00000596709.1_5'UTR|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.H255R	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	255	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CCGGCGCCCGTGATAGGCCAC	0.612																																					p.H255R													.	ADAMTS10-229	0			c.A764G						.						107	92	97					19																	8665858		2203	4300	6503	SO:0001583	missense	81794	exon6			CGCCCGTGATAGG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.764A>G	19.37:g.8665858T>C	ENSP00000471851:p.His255Arg	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	117	3	NM_030957	0	0	6	6	0	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	37	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.306251	0.81247	.	.	ENSG00000142303	ENST00000270328	D	0.87179	-2.22	5.19	5.19	0.71726	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.90971	0.7161	M	0.83312	2.635	0.80722	D	1	P	0.34587	0.458	P	0.45195	0.473	D	0.91842	0.5484	10	0.87932	D	0	.	14.2288	0.65877	0.0:0.0:0.0:1.0	.	255	Q9H324	ATS10_HUMAN	R	255	ENSP00000270328:H255R	ENSP00000270328:H255R	H	-	2	0	ADAMTS10	8571858	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.539000	0.82063	1.962000	0.57031	0.374000	0.22700	CAC	.		0.612	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		C	8665858	T	C	8665858	3	2	35	1	0	0	0	0	1	0	0	0	256	1696	59	3	2631	3	ADAMTS10	19	8665858	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	6785817	8665858	50463125	121	3163											
EPOR	2057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11489162	11489162	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccggctccactgcctgcAtcgtcccccagcagcgctct	4	8	8	21	3	1	0	0	0	1	0	5	0	4	0	6	1	4	4	6	1	0	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:11489162A>G	ENST00000222139.6	-	8	1129	c.1025T>C	c.(1024-1026)aTg>aCg	p.M342T	EPOR_ENST00000592375.2_3'UTR	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	342					brain development (GO:0007420)|decidualization (GO:0046697)|erythropoietin-mediated signaling pathway (GO:0038162)|heart development (GO:0007507)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	erythropoietin receptor activity (GO:0004900)|identical protein binding (GO:0042802)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894)	CACTGCCTGCATCGTCCCCCA	0.627																																					p.M342T		.											.	EPOR-523	0			c.T1025C						.						39	39	39					19																	11489162		2203	4300	6503	SO:0001583	missense	2057	exon8			GCCTGCATCGTCC	M34986	CCDS12260.1	19p13.3-p13.2	2013-02-11				ENSG00000187266		"Fibronectin type III domain containing"	3416	protein-coding gene	gene with protein product		133171					Standard	NM_000121		Approved		uc002mrj.2	P19235		ENST00000222139.6:c.1025T>C	19.37:g.11489162A>G	ENSP00000222139:p.Met342Thr	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	66	16	NM_000121	0	0	23	24	1	B2RCG4|Q15443|Q2M205	Missense_Mutation	SNP	ENST00000222139.6	37	CCDS12260.1	.	.	.	.	.	.	.	.	.	.	A	0.131	-1.113064	0.01799	.	.	ENSG00000187266	ENST00000222139	T	0.79352	-1.26	4.83	2.68	0.31781	.	1.546610	0.03465	N	0.212798	T	0.42585	0.1209	N	0.00162	-1.95	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46541	-0.9184	10	0.11794	T	0.64	-27.943	8.2133	0.31496	0.196:0.0:0.804:0.0	.	342	P19235	EPOR_HUMAN	T	342	ENSP00000222139:M342T	ENSP00000222139:M342T	M	-	2	0	EPOR	11350162	0.004000	0.15560	0.008000	0.14137	0.543000	0.35085	0.974000	0.29436	0.531000	0.28639	-0.248000	0.11899	ATG	.		0.627	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1			G	11489162	A	G	11489162	3	3	35	1	0	0	0	0	1	0	0	0	5202	217	8	3	505	3	EPOR	19	11489162	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	2823304	11489162	47639821	122	3164											
ZNF254	9534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	24309780	24309780	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaccctacaagtgtgaagaAtgtggcaaagcatttatatg	16	10	9	6	0	0	2	0	1	0	1	0	2	0	2	1	1	3	2	1	1	8	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:24309780A>G	ENST00000357002.4	+	4	1093	c.978A>G	c.(976-978)gaA>gaG	p.E326E	ZNF254_ENST00000342944.6_Silent_p.E241E	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	326					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				AGTGTGAAGAATGTGGCAAAG	0.388																																					p.E326E		.											.	ZNF254-90	0			c.A978G						.						50	50	50					19																	24309780		2203	4300	6503	SO:0001819	synonymous_variant	9534	exon4			TGAAGAATGTGGC	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.978A>G	19.37:g.24309780A>G		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	94	12	NM_203282	0	0	1	2	1	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	37	CCDS32983.1																																																																																			.		0.388	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		G	24309780	A	G	24309780	2	3	35	1	0	0	0	0	0	0	0	1	17830	98	4	3		3	ZNF254	19	24309780	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	12820618	24309780	34819203	123	3165											
UBA2	10054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	34924279	34924279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctataatgtggaatttttccGacagtttatactggttatga	11	17	8	5	1	0	1	0	1	0	0	1	3	1	2	1	2	1	2	1	2	6	8	rs370848936		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:34924279G>A	ENST00000246548.4	+	4	390	c.320G>A	c.(319-321)cGa>cAa	p.R107Q	UBA2_ENST00000439527.2_Missense_Mutation_p.R11Q	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	107					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			GAATTTTTCCGACAGTTTATA	0.308																																					p.R107Q		.											.	UBA2-227	0			c.G320A						.	G	GLN/ARG	0,4404		0,0,2202	98	105	103		320	4.6	1	19		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	UBA2	NM_005499.2	43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign	107/641	34924279	1,13003	2202	4300	6502	SO:0001583	missense	10054	exon4			TTTTCCGACAGTT	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.320G>A	19.37:g.34924279G>A	ENSP00000246548:p.Arg107Gln	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	197	36	NM_005499	0	0	11	14	3	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Missense_Mutation	SNP	ENST00000246548.4	37	CCDS12439.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.582155	0.46006	0.0	1.16E-4	ENSG00000126261	ENST00000246548;ENST00000439527	T;T	0.29917	1.55;1.55	5.65	4.62	0.57501	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.111742	0.56097	D	0.000021	T	0.15132	0.0365	N	0.11000	0.08	0.47621	D	0.99947	B	0.20459	0.045	B	0.15484	0.013	T	0.09207	-1.0685	10	0.16896	T	0.51	-8.9388	9.9261	0.41494	0.1577:0.0:0.8423:0.0	.	107	Q9UBT2	SAE2_HUMAN	Q	107;11	ENSP00000246548:R107Q;ENSP00000437484:R11Q	ENSP00000246548:R107Q	R	+	2	0	UBA2	39616119	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.620000	0.67736	1.396000	0.46663	0.591000	0.81541	CGA	.		0.308	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499		A	34924279	G	A	34924279	3	1	35	1	0	0	0	0	1	0	0	0	16861	1058	37	1	334	1	UBA2	19	34924279	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	10614499	34924279	24204704	124	3166											
CEACAM6	4680	broad.mit.edu	37	chr19	42260723	42260723	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacaagctaccccagggcccGcatacagtggtcgagagaca	13	4	11	13	2	0	1	0	0	0	1	1	3	0	1	3	2	4	2	3	2	4	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:42260723G>A	ENST00000199764.6	+	2	498	c.280G>A	c.(280-282)Gca>Aca	p.A94T	AC011513.4_ENST00000601409.1_RNA|CEA_ENST00000598976.1_Intron	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	94	Ig-like V-type.				cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.A94T(1)		breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		CCCAGGGCCCGCATACAGTGG	0.463																																					p.A94T													.	CEACAM6-91	1	Substitution - Missense(1)	kidney(1)	c.G280A						.						279	265	270					19																	42260723		2203	4300	6503	SO:0001583	missense	4680	exon2			GGGCCCGCATACA	M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1818	protein-coding gene	gene with protein product		163980		NCA			Standard	NM_002483		Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.280G>A	19.37:g.42260723G>A	ENSP00000199764:p.Ala94Thr	Somatic	331	1		WXS	Illumina HiSeq	Phase_I	348	6	NM_002483	0	0	1	1	0	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	37	CCDS12585.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.322830	0.41096	.	.	ENSG00000086548	ENST00000199764	T	0.66280	-0.2	1.92	-3.78	0.04333	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70290	0.3207	M	0.79011	2.435	0.09310	N	1	D	0.60160	0.987	D	0.65140	0.932	T	0.61441	-0.7062	9	0.62326	D	0.03	.	4.0679	0.09869	0.1812:0.4767:0.3421:0.0	.	94	P40199	CEAM6_HUMAN	T	94	ENSP00000199764:A94T	ENSP00000199764:A94T	A	+	1	0	CEACAM6	46952563	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.016000	0.13377	-0.324000	0.08589	-0.680000	0.03767	GCA	.		0.463	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1			A	42260723	G	A	42260723	3	1	35	1	0	0	0	0	1	0	0	0	3202	1087	38	1	286	1	CEACAM6	19	42260723	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	7336444	42260723	16868260	125	3167											
LAIR1	3903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54872527	54872527	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgacgtcctcacctttCaccagcagctccaggtagtc	8	9	9	15	1	2	1	2	1	0	0	5	1	4	1	4	2	2	3	4	2	1	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:54872527C>A	ENST00000391742.2	-	3	512	c.360G>T	c.(358-360)gtG>gtT	p.V120V	LAIR1_ENST00000474878.1_Silent_p.V119V|LAIR1_ENST00000463489.1_Intron|LAIR1_ENST00000313038.6_Silent_p.V113V|LAIR1_ENST00000348231.4_Silent_p.V120V|LAIR1_ENST00000434277.2_Silent_p.V119V|LAIR1_ENST00000391743.3_Silent_p.V102V			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	120					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		CCTCACCTTTCACCAGCAGCT	0.582																																					p.V120V		.											.	LAIR1-94	0			c.G360T						.						105	100	102					19																	54872527		2203	4300	6503	SO:0001819	synonymous_variant	3903	exon3			ACCTTTCACCAGC	AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6477	protein-coding gene	gene with protein product		602992	"leukocyte-associated Ig-like receptor 1"			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.360G>T	19.37:g.54872527C>A		Somatic	226	0		WXS	Illumina HiSeq	Phase_I	197	37	NM_021706	0	0	0	0	0		Silent	SNP	ENST00000391742.2	37	CCDS12891.1																																																																																			.		0.582	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1			A	54872527	C	A	54872527	2	1	35	1	0	0	0	0	0	0	0	1	8623	813	29	4		4	LAIR1	19	54872527	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	12611804	54872527	4256456	126	3168											
ZNF773	374928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	58018029	58018029	+	Missense_Mutation	SNP	G	G	A																															ggcctttcatgctggaaaaaGgcattacaaatgcagtgaat																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:58018029G>A	ENST00000282292.4	+	4	706	c.566G>A	c.(565-567)aGg>aAg	p.R189K	ZNF773_ENST00000598770.1_Missense_Mutation_p.R188K|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	189					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(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		GCTGGAAAAAGGCATTACAAA	0.473																																					p.R189K		.											.	ZNF773-91	0			c.G566A						.						48	48	48					19																	58018029		2203	4297	6500	SO:0001583	missense	374928	exon4			GAAAAAGGCATTA	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.566G>A	19.37:g.58018029G>A	ENSP00000282292:p.Arg189Lys	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	56	5	NM_198542	0	0	13	13	0	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	1.360	-0.589074	0.03799	.	.	ENSG00000152439	ENST00000282292	T	0.21543	2.0	1.25	0.169	0.15017	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06962	0.0177	N	0.05259	-0.085	0.09310	N	1	B;B	0.28233	0.204;0.01	B;B	0.27076	0.076;0.003	T	0.36744	-0.9735	9	0.02654	T	1	.	4.9147	0.13840	0.3681:0.0:0.6319:0.0	.	188;189	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	K	189	ENSP00000282292:R189K	ENSP00000282292:R189K	R	+	2	0	ZNF773	62709841	0.000000	0.05858	0.006000	0.13384	0.429000	0.31625	-0.057000	0.11768	0.097000	0.17492	0.313000	0.20887	AGG	.		0.473	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		A	58018029	G	A	58018029	3	1	35	1	0	0	0	0	1	0	0	0	18178	1000	35	2	580	2	ZNF773	19	58018029	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3145502	58018029	1110954	127	3169	27	2									
ZNF773	374928	hgsc.bcm.edu;broad.mit.edu	37	chr19	58018032	58018032	+	Missense_Mutation	SNP	A	A	G																															ctttcatgctggaaaaaggcAttacaaatgcagtgaatgtg																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:58018032A>G	ENST00000282292.4	+	4	709	c.569A>G	c.(568-570)cAt>cGt	p.H190R	ZNF773_ENST00000598770.1_Missense_Mutation_p.H189R|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	190					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(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		GGAAAAAGGCATTACAAATGC	0.473																																					p.H190R		.											.	ZNF773-91	0			c.A569G						.						49	49	49					19																	58018032		2203	4297	6500	SO:0001583	missense	374928	exon4			AAAGGCATTACAA	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.569A>G	19.37:g.58018032A>G	ENSP00000282292:p.His190Arg	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	61	5	NM_198542	0	0	12	12	0	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	A	1.777	-0.482865	0.04383	.	.	ENSG00000152439	ENST00000282292	T	0.07327	3.2	1.25	0.141	0.14811	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04452	0.0122	N	0.13098	0.295	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.002	T	0.40098	-0.9581	9	0.66056	D	0.02	.	3.1074	0.06346	0.3454:0.4308:0.0:0.2238	.	189;190	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	R	190	ENSP00000282292:H190R	ENSP00000282292:H190R	H	+	2	0	ZNF773	62709844	0.000000	0.05858	0.002000	0.10522	0.468000	0.32798	-0.492000	0.06467	-0.023000	0.13963	0.260000	0.18958	CAT	.		0.473	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		G	58018032	A	G	58018032	3	3	35	1	0	0	0	0	1	0	0	0	18178	217	8	3	583	3	ZNF773	19	58018032	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	3	58018032	1110951	128	3170	27	2									
ASXL1	171023	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31015986	31015986	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggagggagaggagccagAggacacggctgatgtggaga	12	4	20	5	1	0	4	0	1	0	3	0	9	0	7	1	6	1	1	1	6	0	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr20:31015986A>G	ENST00000375687.4	+	5	732	c.308A>G	c.(307-309)gAg>gGg	p.E103G	ASXL1_ENST00000470145.1_3'UTR|ASXL1_ENST00000542461.1_3'UTR|ASXL1_ENST00000306058.5_Missense_Mutation_p.E98G	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	103					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GAGGAGCCAGAGGACACGGCT	0.532			"F, N, Mis"		"MDS, CMML"																																p.E103G		.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1-2057	0			c.A308G						.						128	121	123					20																	31015986		2203	4300	6503	SO:0001583	missense	171023	exon4			AGCCAGAGGACAC	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.308A>G	20.37:g.31015986A>G	ENSP00000364839:p.Glu103Gly	Somatic	130	1		WXS	Illumina HiSeq	Phase_I	132	14	NM_015338	0	0	6	9	3	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.627522	0.87560	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.17054	2.32;2.3	4.79	4.79	0.61399	.	0.541356	0.20252	N	0.096049	T	0.37812	0.1017	L	0.56769	1.78	0.53005	D	0.999964	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.10941	-1.0608	10	0.66056	D	0.02	-21.1422	13.9731	0.64255	1.0:0.0:0.0:0.0	.	98;103	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	G	103;103;103;93;98	ENSP00000364839:E103G;ENSP00000305119:E98G	ENSP00000305119:E98G	E	+	2	0	ASXL1	30479647	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.902000	0.63266	2.152000	0.67230	0.379000	0.24179	GAG	.		0.532	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		G	31015986	A	G	31015986	3	3	35	1	0	0	0	0	1	0	0	0	1067	304	11	3	332	3	ASXL1	20	31015986	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08		31015986	32009534	129	3171											
LBP	3929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	36989402	36989402	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtcctccgatctacagccTtatctccaaactctgccagg	8	11	7	15	1	3	0	0	0	3	0	6	1	5	0	5	1	4	0	5	1	3	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr20:36989402T>G	ENST00000217407.2	+	6	794	c.633T>G	c.(631-633)ccT>ccG	p.P211P		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	211					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				ATCTACAGCCTTATCTCCAAA	0.428																																					p.P211P		.											.	LBP-91	0			c.T633G						.						174	171	172					20																	36989402		2203	4300	6503	SO:0001819	synonymous_variant	3929	exon6			ACAGCCTTATCTC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"BPI fold containing"	6517	protein-coding gene	gene with protein product	"BPI fold containing family D, member 2"	151990	"lipopolysaccharide-binding protein"			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.633T>G	20.37:g.36989402T>G		Somatic	231	1		WXS	Illumina HiSeq	Phase_I	209	28	NM_004139	0	0	0	0	0	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			.		0.428	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		G	36989402	T	G	36989402	2	3	35	1	0	0	0	0	0	0	0	1	8672	1596	56	5		5	LBP	20	36989402	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	5973416	36989402	26036118	130	3172											
ZNF831	128611	broad.mit.edu	37	chr20	57769662	57769662	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcagtgtccctctgcccgcGgagcagaaggcaaaggcggc	8	4	15	14	4	1	1	0	0	1	1	2	2	2	2	2	4	2	3	2	4	2	0	rs548966248		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr20:57769662G>A	ENST00000371030.2	+	1	3588	c.3588G>A	c.(3586-3588)gcG>gcA	p.A1196A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1196							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CTCTGCCCGCGGAGCAGAAGG	0.637													G|||	1	0.000199681	8e-04	0	5008	,	,		19947	0		0	False		,,,				2504	0				p.A1196A													.	ZNF831-126	0			c.G3588A						.						35	41	39					20																	57769662		2075	4218	6293	SO:0001819	synonymous_variant	128611	exon1			GCCCGCGGAGCAG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3588G>A	20.37:g.57769662G>A		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_178457	0	0	1	1	0	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			.		0.637	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57769662	G	A	57769662	2	1	35	1	0	0	0	0	0	0	0	1	18217	1103	39	1		1	ZNF831	20	57769662	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	20780260	57769662	5255858	131	3173											
COL18A1	80781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46902710	46902710	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgctcttttccgtacaggGtgaagcaggcgccccaggac	7	8	12	14	2	1	1	0	1	1	0	2	2	2	2	4	3	3	3	4	3	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr21:46902710G>A	ENST00000359759.4	+	14	2942	c.2921G>A	c.(2920-2922)gGt>gAt	p.G974D	COL18A1_ENST00000355480.5_Splice_Site_p.G739D|COL18A1_ENST00000400337.2_Splice_Site_p.G559D			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	974	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TCCGTACAGGGTGAAGCAGGC	0.592																																					p.G739D		.											.	COL18A1-90	0			c.G2216A						.						116	125	122					21																	46902710		2050	4191	6241	SO:0001630	splice_region_variant	80781	exon14			TACAGGGTGAAGC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2920-1G>A	21.37:g.46902710G>A		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	98	16	NM_030582	0	0	0	0	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	G	14.50	2.553832	0.45487	.	.	ENSG00000182871	ENST00000400337;ENST00000355480;ENST00000359759	D;D;D	0.99532	-5.77;-6.1;-6.1	2.62	2.62	0.31277	.	.	.	.	.	D	0.99651	0.9871	H	0.95294	3.65	0.39801	D	0.972573	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98225	1.0480	9	0.87932	D	0	.	8.8912	0.35434	0.0:0.0:1.0:0.0	.	974;739;559	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	D	559;739;974	ENSP00000383191:G559D;ENSP00000347665:G739D;ENSP00000352798:G974D	ENSP00000347665:G739D	G	+	2	0	COL18A1	45727138	0.971000	0.33674	0.522000	0.27862	0.058000	0.15608	1.738000	0.38207	1.799000	0.52666	0.549000	0.68633	GGT	.		0.592	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		Missense_Mutation	A	46902710	G	A	46902710	5	1	35	1	0	0	0	0	0	0	1	0	3681	1275	44	2	3089	2	COL18A1	21	46902710	Splice_Site	SNP	G	TCGA-B1-5398-01A-02D-1589-08		46902710	1227185	132	3174											
SLC2A11	66035	hgsc.bcm.edu;broad.mit.edu	37	chr22	24226511	24226511	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtgacggggatcctggcCacagagctgtttgaccagat	9	8	15	9	1	0	4	0	2	0	2	1	6	1	6	3	4	1	2	3	4	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:24226511C>T	ENST00000345044.6	+	11	1453	c.1185C>T	c.(1183-1185)gcC>gcT	p.A395A	AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000316185.8_Silent_p.A398A|SLC2A11_ENST00000398356.2_Silent_p.A402A			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	395					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						GGATCCTGGCCACAGAGCTGT	0.652																																					p.A402A		.											.	SLC2A11-91	0			c.C1206T						.						52	50	51					22																	24226511		2203	4300	6503	SO:0001819	synonymous_variant	66035	exon12			CCTGGCCACAGAG	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"Solute carriers"	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.1185C>T	22.37:g.24226511C>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	75	12	NM_030807	0	0	7	13	6	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Silent	SNP	ENST00000345044.6	37	CCDS46673.1	.	.	.	.	.	.	.	.	.	.	C	9.191	1.025928	0.19512	.	.	ENSG00000251357	ENST00000502845	.	.	.	3.79	1.55	0.23275	.	.	.	.	.	T	0.46483	0.1395	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26744	-1.0094	4	.	.	.	.	4.1978	0.10452	0.0:0.5781:0.1966:0.2253	.	.	.	.	L	133	.	.	P	+	2	0	AP000350.10	22556511	0.411000	0.25384	0.996000	0.52242	0.855000	0.48748	0.053000	0.14184	0.331000	0.23511	0.505000	0.49811	CCA	.		0.652	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807		T	24226511	C	T	24226511	2	4	35	1	0	0	0	0	0	0	0	1	14572	581	21	2		2	SLC2A11	22	24226511	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08		24226511	27078055	133	3175											
NF2	4771	hgsc.bcm.edu;ucsc.edu	37	chr22	30069350	30069350	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagaaggccgcagaggcTgagcaggaaatgcagcgcat	12	3	15	11	2	0	3	0	1	0	2	0	4	0	4	2	3	3	5	2	3	2	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:30069350T>C	ENST00000338641.4	+	12	1656	c.1215T>C	c.(1213-1215)gcT>gcC	p.A405A	NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Silent_p.A363A|NF2_ENST00000353887.4_Silent_p.A322A|NF2_ENST00000397789.3_Silent_p.A405A|NF2_ENST00000403999.3_Silent_p.A405A|NF2_ENST00000347330.5_Intron|NF2_ENST00000334961.7_Silent_p.A322A|NF2_ENST00000403435.1_Silent_p.A376A|NF2_ENST00000361166.4_Silent_p.A405A|NF2_ENST00000361452.4_Silent_p.A364A	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	405	Glu-rich.				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.?(3)|p.M375fs*20(1)		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						CCGCAGAGGCTGAGCAGGAAA	0.607			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.A405A		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	4	Unknown(3)|Deletion - Frameshift(1)	large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	c.T1215C						.						54	46	49					22																	30069350		2203	4300	6503	SO:0001819	synonymous_variant	4771	exon12	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	AGAGGCTGAGCAG	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.1215T>C	22.37:g.30069350T>C		Somatic	15	0		WXS	Illumina HiSeq	Phase_I	10	3	NM_000268	0	0	23	40	17	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Silent	SNP	ENST00000338641.4	37	CCDS13861.1																																																																																			.		0.607	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		C	30069350	T	C	30069350	2	2	35	1	0	0	0	0	0	0	0	1	10383	1567	55	3		3	NF2	22	30069350	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	5842839	30069350	21235216	134	3176											
MCHR1	2847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	41076973	41076973	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcacctcctcgcacggggAgcatctcctacatcaacatc	10	8	7	16	2	3	0	2	0	1	0	7	2	4	1	3	2	3	2	3	2	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:41076973A>T	ENST00000249016.4	+	2	1006	c.310A>T	c.(310-312)Agc>Tgc	p.S104C	MCHR1_ENST00000381433.2_Missense_Mutation_p.S104C|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	104					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)			endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						TCGCACGGGGAGCATCTCCTA	0.567																																					p.S104C		.											.	MCHR1-90	0			c.A310T						.						139	105	117					22																	41076973		2203	4300	6503	SO:0001583	missense	2847	exon2			ACGGGGAGCATCT		CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"GPCR / Class A : MCH receptors"	4479	protein-coding gene	gene with protein product		601751	"G protein-coupled receptor 24"	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.310A>T	22.37:g.41076973A>T	ENSP00000249016:p.Ser104Cys	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	89	12	NM_005297	0	0	1	1	0	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	A	8.701	0.909808	0.17833	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.38077	1.16;1.16	4.87	3.77	0.43336	.	0.596448	0.17749	N	0.163281	T	0.21631	0.0521	N	0.14661	0.345	0.22866	N	0.998638	P	0.39576	0.679	B	0.37047	0.24	T	0.11421	-1.0588	10	0.59425	D	0.04	.	10.4074	0.44272	0.8375:0.1625:0.0:0.0	.	104	Q99705	MCHR1_HUMAN	C	104	ENSP00000249016:S104C;ENSP00000370841:S104C	ENSP00000249016:S104C	S	+	1	0	MCHR1	39406919	0.902000	0.30710	0.457000	0.27056	0.381000	0.30169	1.471000	0.35365	1.959000	0.56917	0.533000	0.62120	AGC	.		0.567	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297		T	41076973	A	T	41076973	3	4	35	1	0	0	0	0	1	0	0	0	9407	304	11	5	316	5	MCHR1	22	41076973	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	11007623	41076973	10227593	135	3177											
MEI1	150365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42149973	42149973	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactcagccctaaaccaggTgtgttccaatttcctctact	9	13	5	14	0	3	0	2	0	1	0	5	0	5	0	4	1	3	1	4	1	4	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:42149973T>G	ENST00000401548.3	+	17	1914	c.1874T>G	c.(1873-1875)gTg>gGg	p.V625G	MEI1_ENST00000300398.4_5'UTR|MEI1_ENST00000540833.1_Missense_Mutation_p.V365G|MEI1_ENST00000400107.1_5'UTR|MEI1_ENST00000540880.1_Intron	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTAAACCAGGTGTGTTCCAAT	0.458																																					p.V625G		.											.	MEI1-70	0			c.T1874G						.						194	171	178					22																	42149973		1926	4140	6066	SO:0001583	missense	150365	exon17			ACCAGGTGTGTTC	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.1874T>G	22.37:g.42149973T>G	ENSP00000384115:p.Val625Gly	Somatic	92	1		WXS	Illumina HiSeq	Phase_I	112	15	NM_152513	0	0	0	0	0		Missense_Mutation	SNP	ENST00000401548.3	37	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803218	0.31869	.	.	ENSG00000167077	ENST00000401548;ENST00000540833	T;T	0.05199	3.48;3.48	5.46	1.86	0.25419	.	0.350989	0.28016	N	0.016924	T	0.04770	0.0129	L	0.51422	1.61	0.80722	D	1	P	0.45827	0.867	B	0.35770	0.21	T	0.44081	-0.9351	10	0.72032	D	0.01	-8.4146	2.1403	0.03772	0.2341:0.3123:0.0:0.4536	.	625	Q5TIA1	MEI1_HUMAN	G	625;365	ENSP00000384115:V625G;ENSP00000444225:V365G	ENSP00000384115:V625G	V	+	2	0	MEI1	40479919	0.988000	0.35896	0.997000	0.53966	0.783000	0.44284	0.555000	0.23422	0.368000	0.24481	0.533000	0.62120	GTG	.		0.458	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		G	42149973	T	G	42149973	3	3	35	1	0	0	0	0	1	0	0	0	9490	1696	59	5	1940	5	MEI1	22	42149973	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	1073000	42149973	9154593	136	3178											
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46790151	46790151	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accagcctctggggcacggaAggtcgagtctgtggggaaaa	10	6	16	9	2	2	0	0	0	2	0	3	3	2	2	2	6	1	1	2	6	3	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:46790151A>T	ENST00000262738.3	-	14	5851	c.5852T>A	c.(5851-5853)cTt>cAt	p.L1951H		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1951	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GGGGCACGGAAGGTCGAGTCT	0.567																																					p.L1951H		.											.	CELSR1-525	0			c.T5852A						.						40	39	39					22																	46790151		2203	4300	6503	SO:0001583	missense	9620	exon14			CACGGAAGGTCGA	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5852T>A	22.37:g.46790151A>T	ENSP00000262738:p.Leu1951His	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	60	10	NM_014246	0	0	0	0	0	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	A	8.280	0.815341	0.16607	.	.	ENSG00000075275	ENST00000262738	D	0.92199	-2.99	3.47	3.47	0.39725	.	0.204155	0.30011	U	0.010631	D	0.92831	0.7720	L	0.40543	1.245	0.80722	D	1	D;B	0.76494	0.999;0.048	D;B	0.68765	0.96;0.025	D	0.92188	0.5757	10	0.48119	T	0.1	.	11.945	0.52924	1.0:0.0:0.0:0.0	.	272;1951	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	H	1951	ENSP00000262738:L1951H	ENSP00000262738:L1951H	L	-	2	0	CELSR1	45168815	0.967000	0.33354	0.996000	0.52242	0.436000	0.31835	2.258000	0.43249	1.360000	0.45960	0.379000	0.24179	CTT	.		0.567	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46790151	A	T	46790151	3	4	35	1	0	0	0	0	1	0	0	0	3227	72	3	5	3280	5	CELSR1	22	46790151	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	4640178	46790151	4514415	137	3179											
ARSD	414	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	2826885	2826885	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtggccatcaatcacccTgatttcatgaagagaacaca	13	9	8	11	0	3	3	3	2	0	1	3	4	3	3	2	1	1	1	2	1	3	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chrX:2826885T>C	ENST00000381154.1	-	9	1374		c.e9-2		ARSD-AS1_ENST00000414053.1_RNA	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D						cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCAATCACCCTGATTTCATGA	0.557																																					.													.	ARSD-130	0			c.1299-2A>G						.						88	60	69					X																	2826885		2203	4300	6503	SO:0001630	splice_region_variant	414	exon10			TCACCCTGATTTC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"Arylsulfatase family"	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.1299-2A>G	X.37:g.2826885T>C		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	25	7	NM_001669	0	0	0	0	0	Q9UHJ8	Splice_Site	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	T	4.507	0.094091	0.08632	.	.	ENSG00000006756	ENST00000381154;ENST00000458014	.	.	.	2.53	2.53	0.30540	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2604	0.43423	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARSD	2836885	1.000000	0.71417	0.407000	0.26434	0.177000	0.22998	5.771000	0.68881	0.883000	0.36040	0.233000	0.17823	.	.		0.557	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		Intron	C	2826885	T	C	2826885	5	2	35	1	0	0	0	0	0	0	1	0	990	1594	55	3	492	3	ARSD	23	2826885	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08		2826885	152443675	138	3180											
ERRFI1	54206	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	8074134	8074135	+	Frame_Shift_Del	DEL	AG	AG	-																															aggaagtctgtatctgagctAgttaggaattccacctcaca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:8074134_8074135delAG	ENST00000377482.5	-	4	747_748	c.524_525delCT	c.(523-525)actfs	p.T175fs	ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000467067.1_3'UTR	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	175					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TATCTGAGCTAGTTAGGAATTC	0.48																																					p.175_175del		.											.	ERRFI1-91	0			c.524_525del						.																																			SO:0001589	frameshift_variant	54206	exon4			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.524_525delCT	1.37:g.8074134_8074135delAG	ENSP00000366702:p.Thr175fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	99	41	NM_018948	0	0	0	0	0	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Del	DEL	ENST00000377482.5	37	CCDS94.1																																																																																			.		0.48	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		-	8074135	AG	-	8074134	7	5	36	1	0	1	0	1	0	0	0	0	5257	407	15	0	867	0	ERRFI1	1	8074134	Frame_Shift_Del	DEL	AG	TCGA-B1-A47M-01A-11D-A25F-10		8074134	241176487	1	3181											
KDM1A	23028	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	23383993	23383993	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaggatcgtgtgggtggacGagttgccacatttcgcaaag	10	9	14	8	3	0	0	0	0	0	0	2	3	0	2	1	3	1	2	1	3	1	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:23383993G>A	ENST00000356634.3	+	7	1096	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	KDM1A_ENST00000400181.4_Missense_Mutation_p.R336Q|MIR4419A_ENST00000583845.1_RNA|KDM1A_ENST00000542151.1_Missense_Mutation_p.R336Q|RP1-184J9.2_ENST00000427154.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	316	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						GTGGGTGGACGAGTTGCCACA	0.428																																					p.R336Q		.											.	KDM1A-206	0			c.G1007A						.						206	194	198					1																	23383993		2203	4300	6503	SO:0001583	missense	23028	exon8			GTGGACGAGTTGC	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.947G>A	1.37:g.23383993G>A	ENSP00000349049:p.Arg316Gln	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	113	6	NM_001009999	0	0	13	13	0	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	37	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	G	36	5.777153	0.96929	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	D;D;D	0.97710	-4.5;-4.5;-4.5	5.48	5.48	0.80851	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.99196	0.9721	H	0.96269	3.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.984;0.991	D	0.99113	1.0847	10	0.87932	D	0	-9.5301	18.3409	0.90304	0.0:0.0:1.0:0.0	.	336;316	O60341-2;O60341	.;KDM1A_HUMAN	Q	316;336;336	ENSP00000349049:R316Q;ENSP00000383042:R336Q;ENSP00000439072:R336Q	ENSP00000349049:R316Q	R	+	2	0	KDM1A	23256580	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.634000	0.98435	2.572000	0.86782	0.585000	0.79938	CGA	.		0.428	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23383993	G	A	23383993	3	1	36	1	0	0	0	0	1	0	0	0	8143	1058	37	1	1037	1	KDM1A	1	23383993	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	15309859	23383993	225866628	2	3182											
GNL2	29889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38042060	38042060	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcaatgggagccacgttgCaaactttcttagaacgcaat	12	10	9	10	2	1	1	0	0	1	1	1	2	1	2	1	1	5	4	1	1	5	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:38042060C>T	ENST00000373062.3	-	9	1105	c.1007G>A	c.(1006-1008)tGc>tAc	p.C336Y		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	336	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				AGCCACGTTGCAAACTTTCTT	0.423																																					p.C336Y		.											.	GNL2-91	0			c.G1007A						.						190	170	177					1																	38042060		2203	4300	6503	SO:0001583	missense	29889	exon9			ACGTTGCAAACTT	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.1007G>A	1.37:g.38042060C>T	ENSP00000362153:p.Cys336Tyr	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	69	24	NM_013285	0	0	4	12	8	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.162979|5.162979	0.94727|0.94727	.|.	.|.	ENSG00000134697|ENSG00000134697	ENST00000538069|ENST00000373062;ENST00000545489	.|T	.|0.13538	.|2.58	6.14|6.14	6.14|6.14	0.99180|0.99180	.|GTP-binding domain, HSR1-related (1);	.|0.041714	.|0.85682	.|D	.|0.000000	T|T	0.55657|0.55657	0.1934|0.1934	H|H	0.96996|0.96996	3.92|3.92	0.80722|0.80722	D|D	1|1	.|D	.|0.65815	.|0.995	.|D	.|0.70016	.|0.967	T|T	0.69045|0.69045	-0.5249|-0.5249	5|10	.|0.87932	.|D	.|0	-7.4933|-7.4933	20.8597|20.8597	0.99761|0.99761	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|336	.|Q13823	.|NOG2_HUMAN	T|Y	188|336;177	.|ENSP00000362153:C336Y	.|ENSP00000362153:C336Y	A|C	-|-	1|2	0|0	GNL2|GNL2	37814647|37814647	1.000000|1.000000	0.71417|0.71417	0.865000|0.865000	0.33974|0.33974	0.986000|0.986000	0.74619|0.74619	7.786000|7.786000	0.85741|0.85741	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCA|TGC	.		0.423	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		T	38042060	C	T	38042060	3	4	36	1	0	0	0	0	1	0	0	0	6556	710	25	2	1220	2	GNL2	1	38042060	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	14658067	38042060	211208561	3	3183											
GLIS1	148979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53995548	53995548	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccgggtgctggcacaggtaCggcttctcgcccgtgtggct	3	9	15	14	4	1	0	0	0	1	0	2	0	1	0	2	5	2	5	2	5	1	2	rs549794466		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:53995548C>T	ENST00000312233.2	-	4	1439	c.873G>A	c.(871-873)ccG>ccA	p.P291P		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						GGCACAGGTACGGCTTCTCGC	0.637																																					p.P291P		.											.	GLIS1-91	0			c.G873A						.						72	74	74					1																	53995548		2203	4300	6503	SO:0001819	synonymous_variant	148979	exon4			CAGGTACGGCTTC	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"Zinc fingers, C2H2-type"	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.873G>A	1.37:g.53995548C>T		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	52	27	NM_147193	0	0	0	9	9		Silent	SNP	ENST00000312233.2	37	CCDS582.1																																																																																			.		0.637	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		T	53995548	C	T	53995548	2	4	36	1	0	0	0	0	0	0	0	1	6465	523	19	1		1	GLIS1	1	53995548	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	15953488	53995548	195255073	4	3184											
SAMD13	148418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	84768963	84768963	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggaaaatggctctgtcggtGtaaaaaagtaagtgaagctg	15	9	13	4	1	1	1	0	1	1	0	2	2	1	2	0	3	1	4	0	3	7	2	rs556493054		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:84768963G>T	ENST00000370671.3	+	2	165	c.106G>T	c.(106-108)Gta>Tta	p.V36L	SAMD13_ENST00000370669.1_Missense_Mutation_p.V16L|SAMD13_ENST00000370670.2_Missense_Mutation_p.V16L|SAMD13_ENST00000394834.3_Missense_Mutation_p.V16L|SAMD13_ENST00000370668.3_Missense_Mutation_p.V16L|SAMD13_ENST00000370673.3_Missense_Mutation_p.V30L			Q5VXD3	SAM13_HUMAN	sterile alpha motif domain containing 13	36										lung(4)	4				all cancers(265;0.00667)|Epithelial(280;0.0219)|OV - Ovarian serous cystadenocarcinoma(397;0.136)		CTCTGTCGGTGTAAAAAAGTA	0.408																																					p.V30L		.											.	SAMD13-226	0			c.G88T						.						72	65	67					1																	84768963		2203	4300	6503	SO:0001583	missense	148418	exon2			GTCGGTGTAAAAA		CCDS30760.1, CCDS44166.1	1p31.1	2013-01-10			ENSG00000203943	ENSG00000203943		"Sterile alpha motif (SAM) domain containing"	24582	protein-coding gene	gene with protein product							Standard	NM_001010971		Approved		uc001djr.3	Q5VXD3	OTTHUMG00000009859	ENST00000370671.3:c.106G>T	1.37:g.84768963G>T	ENSP00000359705:p.Val36Leu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	53	22	NM_001010971	0	0	0	0	0	B3KPW8|D3DT11|Q53AI4|Q5VXD2|Q5VXD4	Missense_Mutation	SNP	ENST00000370671.3	37		.	.	.	.	.	.	.	.	.	.	G	10.75	1.439172	0.25900	.	.	ENSG00000203943	ENST00000370673;ENST00000370671;ENST00000394834;ENST00000370669;ENST00000370668;ENST00000370670	.	.	.	5.34	5.34	0.76211	.	0.391477	0.25631	N	0.029344	T	0.18130	0.0435	N	0.24115	0.695	0.80722	D	1	B;B	0.32101	0.032;0.356	B;B	0.27608	0.023;0.081	T	0.06516	-1.0822	9	0.13470	T	0.59	-11.7208	10.4571	0.44557	0.0893:0.0:0.9107:0.0	.	36;30	Q5VXD3;Q5VXD3-2	SAM13_HUMAN;.	L	30;36;16;16;16;16	.	ENSP00000359702:V16L	V	+	1	0	SAMD13	84541551	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.486000	0.60286	2.657000	0.90304	0.655000	0.94253	GTA	.		0.408	SAMD13-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027243.1	NM_001010971		T	84768963	G	T	84768963	3	4	36	1	0	0	0	0	1	0	0	0	13850	1377	48	4	94	4	SAMD13	1	84768963	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	30773415	84768963	164481658	5	3185											
CD58	965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	117078689	117078689	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaagatcattttccatctTaaaatatatactggttgagt	13	16	7	5	0	2	2	1	1	1	1	3	3	3	3	1	2	1	1	1	2	6	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:117078689T>C	ENST00000369489.5	-	3	592	c.526A>G	c.(526-528)Aag>Gag	p.K176E	CD58_ENST00000369487.3_Missense_Mutation_p.K176E|CD58_ENST00000457047.2_Missense_Mutation_p.K176E	NM_001779.2	NP_001770.1	P19256	LFA3_HUMAN	CD58 molecule	176					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interferon-gamma (GO:0071346)|cellular response to tumor necrosis factor (GO:0071356)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|positive regulation of interleukin-8 secretion (GO:2000484)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		TTTTCCATCTTAAAATATATA	0.353																																					p.K176E		.											.	CD58-90	0			c.A526G						.						115	111	112					1																	117078689		2203	4300	6503	SO:0001583	missense	965	exon3			CCATCTTAAAATA	BC005930	CCDS888.1, CCDS44199.1	1p13	2008-02-05	2006-03-28		ENSG00000116815	ENSG00000116815		"CD molecules"	1688	protein-coding gene	gene with protein product		153420	"CD58 antigen, (lymphocyte function-associated antigen 3)"	LFA3		9510189	Standard	NM_001144822		Approved		uc001egm.3	P19256	OTTHUMG00000022749	ENST00000369489.5:c.526A>G	1.37:g.117078689T>C	ENSP00000358501:p.Lys176Glu	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	48	16	NM_001144822	0	0	12	27	15	A8K7G5|Q5U053|Q6IB65|Q96KI9	Missense_Mutation	SNP	ENST00000369489.5	37	CCDS888.1	.	.	.	.	.	.	.	.	.	.	T	12.10	1.835666	0.32421	.	.	ENSG00000116815	ENST00000369489;ENST00000457047;ENST00000369487	T;T;T	0.41758	0.99;0.99;1.02	3.59	-6.97	0.01616	.	9.277070	0.00166	N	0.000001	T	0.07818	0.0196	L	0.29908	0.895	0.09310	N	1	P;B;P	0.50528	0.936;0.4;0.936	P;B;P	0.45167	0.472;0.118;0.472	T	0.41698	-0.9494	10	0.02654	T	1	.	2.2982	0.04155	0.1357:0.3744:0.2766:0.2133	.	176;176;176	P19256-3;B1AMW1;P19256	.;.;LFA3_HUMAN	E	176	ENSP00000358501:K176E;ENSP00000409080:K176E;ENSP00000358499:K176E	ENSP00000358499:K176E	K	-	1	0	CD58	116880212	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.440000	0.06888	-1.664000	0.01479	-0.290000	0.09829	AAG	.		0.353	CD58-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059036.1	NM_001779		C	117078689	T	C	117078689	3	2	36	1	0	0	0	0	1	0	0	0	3031	1763	61	3	246	3	CD58	1	117078689	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	32309726	117078689	132171932	6	3186											
POGZ	23126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151381040	151381040	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acagttcgtggctgccctcgGgaagcccggattgtcacctg	6	9	13	13	3	1	0	1	0	0	0	3	2	1	2	3	3	2	2	3	3	1	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:151381040G>A	ENST00000271715.2	-	14	2393	c.2079C>T	c.(2077-2079)tcC>tcT	p.S693S	POGZ_ENST00000368863.2_Silent_p.S598S|POGZ_ENST00000409503.1_Silent_p.S684S|POGZ_ENST00000361398.3_Silent_p.S640S|POGZ_ENST00000491586.1_Silent_p.S649S|POGZ_ENST00000540984.1_Silent_p.S55S|POGZ_ENST00000531094.1_Silent_p.S631S|POGZ_ENST00000392723.1_Silent_p.S640S	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	693					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCTGCCCTCGGGAAGCCCGGA	0.532																																					p.S693S		.											.	POGZ-93	0			c.C2079T						.						90	99	96					1																	151381040		2203	4300	6503	SO:0001819	synonymous_variant	23126	exon14			CCCTCGGGAAGCC	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.2079C>T	1.37:g.151381040G>A		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	48	17	NM_015100	0	0	3	3	0	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Silent	SNP	ENST00000271715.2	37	CCDS997.1																																																																																			.		0.532	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151381040	G	A	151381040	2	1	36	1	0	0	0	0	0	0	0	1	12212	1219	43	2		2	POGZ	1	151381040	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	34302351	151381040	97869581	7	3187											
VHLL	391104	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156268771	156268771	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcttgccatagtagttgagCcacacaggcagcacgattcg	11	8	11	11	2	0	1	0	1	0	0	1	2	0	1	2	1	4	5	2	1	2	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:156268771C>T	ENST00000339922.3	-	1	657	c.210G>A	c.(208-210)tgG>tgA	p.W70*		NM_001004319.2	NP_001004319.1	Q6RSH7	VHLL_HUMAN	von Hippel-Lindau tumor suppressor-like	70	Beta-domain.									endometrium(1)|lung(2)|ovary(1)	4	Hepatocellular(266;0.158)					AGTAGTTGAGCCACACAGGCA	0.597																																					p.W70X		.											.	VHLL-69	0			c.G210A						.						84	75	78					1																	156268771		2203	4300	6503	SO:0001587	stop_gained	391104	exon1			GTTGAGCCACACA			1q22	2013-09-24			ENSG00000189030	ENSG00000189030			30666	protein-coding gene	gene with protein product			"VHL pseudogene"	VHLP		14757845	Standard	NM_001004319		Approved	VLP	uc001fok.3	Q6RSH7	OTTHUMG00000024058	ENST00000339922.3:c.210G>A	1.37:g.156268771C>T	ENSP00000464258:p.Trp70*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	63	17	NM_001004319	0	0	0	0	0	A1L4M4	Nonsense_Mutation	SNP	ENST00000339922.3	37																																																																																				.		0.597	VHLL-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000060590.3	NM_001004319		T	156268771	C	T	156268771	4	4	36	1	0	0	0	0	0	1	0	0	17196	740	26	2	213	2	VHLL	1	156268771	Nonsense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	4887731	156268771	92981850	8	3188											
KLHL12	59349	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	202866048	202866048	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acatcaatgggagactgctgGcttccaaagcccccaaccac	12	6	8	15	0	1	1	1	0	0	1	2	2	2	1	4	2	3	2	4	2	3	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:202866048G>A	ENST00000367261.3	-	7	1091	c.873C>T	c.(871-873)agC>agT	p.S291S	KLHL12_ENST00000367259.1_Silent_p.S24S|KLHL12_ENST00000435533.3_Silent_p.S329S	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	291					COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			GAGACTGCTGGCTTCCAAAGC	0.473																																					p.S291S		.											.	KLHL12-522	0			c.C873T						.						201	210	207					1																	202866048		2203	4300	6503	SO:0001819	synonymous_variant	59349	exon7			CTGCTGGCTTCCA	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"Kelch-like", "BTB/POZ domain containing"	19360	protein-coding gene	gene with protein product		614522	"kelch-like 12 (Drosophila)"			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.873C>T	1.37:g.202866048G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	116	47	NM_021633	0	0	8	10	2	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			.		0.473	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633		A	202866048	G	A	202866048	2	1	36	1	0	0	0	0	0	0	0	1	8389	1194	42	2		2	KLHL12	1	202866048	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	46597277	202866048	46384573	9	3189											
C4BPB	725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207271520	207271520	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttagtgggcgtgcaggagCagcaatgcgttgatggggag	9	8	18	6	2	0	1	0	1	0	0	0	3	0	3	0	4	4	4	0	4	2	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:207271520C>A	ENST00000243611.5	+	5	823	c.529C>A	c.(529-531)Cag>Aag	p.Q177K	C4BPB_ENST00000367076.3_Missense_Mutation_p.Q176K|C4BPB_ENST00000367078.3_Missense_Mutation_p.Q177K|C4BPB_ENST00000470767.1_3'UTR|C4BPB_ENST00000391923.1_Missense_Mutation_p.Q177K	NM_000716.3	NP_000707.1	P20851	C4BPB_HUMAN	complement component 4 binding protein, beta	177	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)				breast(2)|lung(1)|ovary(1)	4						CGTGCAGGAGCAGCAATGCGT	0.478																																					p.Q177K		.											.	C4BPB-91	0			c.C529A						.						167	146	153					1																	207271520		2203	4300	6503	SO:0001583	missense	725	exon6			CAGGAGCAGCAAT	L11245	CCDS1476.1, CCDS31005.1	1q32	2008-07-18	2001-11-28		ENSG00000123843	ENSG00000123843			1328	protein-coding gene	gene with protein product	"complement component 4 binding protein, beta chain", "C4b binding protein, beta chain"	120831	"complement component 4-binding protein, beta"	C4BP		2300577, 8325877	Standard	XM_005273255		Approved		uc001hfj.3	P20851	OTTHUMG00000036035	ENST00000243611.5:c.529C>A	1.37:g.207271520C>A	ENSP00000243611:p.Gln177Lys	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	78	26	NM_001017365	0	0	0	0	0	A5JYP8|D3DT81|Q5VVR0|Q9BS25	Missense_Mutation	SNP	ENST00000243611.5	37	CCDS1476.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763769	0.31228	.	.	ENSG00000123843	ENST00000367078;ENST00000452902;ENST00000243611;ENST00000367076;ENST00000391923	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.0	3.07	0.35406	Complement control module (2);Sushi/SCR/CCP (3);	0.511839	0.16242	N	0.223086	T	0.60353	0.2262	M	0.62723	1.935	0.09310	N	0.999992	P;P	0.52170	0.951;0.939	P;P	0.52710	0.707;0.583	T	0.53788	-0.8389	10	0.02654	T	1	-3.3863	7.1729	0.25728	0.0:0.7347:0.1719:0.0935	.	177;176	P20851;P20851-2	C4BPB_HUMAN;.	K	177;177;177;176;177	ENSP00000356045:Q177K;ENSP00000392237:Q177K;ENSP00000243611:Q177K;ENSP00000356043:Q176K;ENSP00000375790:Q177K	ENSP00000243611:Q177K	Q	+	1	0	C4BPB	205338143	0.017000	0.18338	0.006000	0.13384	0.024000	0.10985	1.187000	0.32090	1.317000	0.45149	0.655000	0.94253	CAG	.		0.478	C4BPB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087847.2	NM_000716		A	207271520	C	A	207271520	3	1	36	1	0	0	0	0	1	0	0	0	2256	711	25	4	547	4	C4BPB	1	207271520	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	4405472	207271520	41979101	10	3190											
RPS6KC1	26750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	213251150	213251150	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctccatttgctaaaggaaTagtgtttggtaagtgattat	11	16	9	5	0	0	1	0	1	0	0	2	2	2	2	2	2	1	3	2	2	6	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:213251150T>C	ENST00000366960.3	+	3	404	c.254T>C	c.(253-255)aTa>aCa	p.I85T	RPS6KC1_ENST00000543354.1_5'UTR|RPS6KC1_ENST00000543470.1_5'UTR|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.I73T|RPS6KC1_ENST00000490299.1_3'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	85	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GCTAAAGGAATAGTGTTTGGT	0.279																																					p.I85T		.											.	RPS6KC1-417	0			c.T254C						.						77	74	75					1																	213251150		2202	4294	6496	SO:0001583	missense	26750	exon3			AAGGAATAGTGTT	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"ribosomal protein S6 kinase, 52kD, polypeptide 1"			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.254T>C	1.37:g.213251150T>C	ENSP00000355927:p.Ile85Thr	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	84	44	NM_012424	0	0	0	0	0	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	T	1.213	-0.629208	0.03610	.	.	ENSG00000136643	ENST00000366960;ENST00000366959	T;T	0.38887	1.11;1.11	5.4	0.0644	0.14353	Phox homologous domain (5);	0.247652	0.39909	N	0.001239	T	0.15349	0.0370	N	0.10760	0.04	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.16722	0.016;0.016	T	0.32929	-0.9888	10	0.02654	T	1	1.7807	5.8179	0.18506	0.5179:0.0738:0.0:0.4083	.	85;73	Q96S38;B1APS8	KS6C1_HUMAN;.	T	85;73	ENSP00000355927:I85T;ENSP00000355926:I73T	ENSP00000355926:I73T	I	+	2	0	RPS6KC1	211317773	1.000000	0.71417	0.979000	0.43373	0.998000	0.95712	1.559000	0.36320	-0.258000	0.09446	0.533000	0.62120	ATA	.		0.279	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		C	213251150	T	C	213251150	3	2	36	1	0	0	0	0	1	0	0	0	13690	1406	49	3	264	3	RPS6KC1	1	213251150	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	5979630	213251150	35999471	11	3191											
TLR5	7100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223286361	223286361	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactcctaggagaaggtccaGgtggtctcccatgatcctat	9	10	10	12	0	1	2	0	1	1	1	5	3	4	2	4	4	0	0	4	4	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:223286361G>A	ENST00000540964.1	-	4	474	c.13C>T	c.(13-15)Ctg>Ttg	p.L5L	TLR5_ENST00000342210.6_Silent_p.L5L			O60602	TLR5_HUMAN	toll-like receptor 5	5					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AGAAGGTCCAGGTGGTCTCCC	0.498																																					p.L5L		.											.	TLR5-525	0			c.C13T						.						37	38	38					1																	223286361		2203	4298	6501	SO:0001819	synonymous_variant	7100	exon6			GGTCCAGGTGGTC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.13C>T	1.37:g.223286361G>A		Somatic	210	0		WXS	Illumina HiSeq	Phase_I	154	57	NM_003268	0	0	3	3	0	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	37	CCDS31033.1																																																																																			.		0.498	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223286361	G	A	223286361	2	1	36	1	0	0	0	0	0	0	0	1	15986	991	35	2		2	TLR5	1	223286361	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	10035211	223286361	25964260	12	3192											
TRIB2	28951	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	12858616	12858616	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcattgcgtttcttgtatCgggaaatacttattgttgga	8	17	10	6	3	1	0	0	0	1	0	3	2	1	2	0	2	2	4	0	2	4	8			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:12858616C>A	ENST00000405331.3	+	1	253	c.183C>A	c.(181-183)atC>atA	p.I61I	RP11-333O1.1_ENST00000569860.1_lincRNA|TRIB2_ENST00000155926.4_Silent_p.I61I|TRIB2_ENST00000381465.2_Intron					tribbles pseudokinase 2											breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTTCTTGTATCGGGAAATACT	0.577											OREG0014450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I61I		.											.	TRIB2-333	0			c.C183A						.						74	78	76					2																	12858616		2203	4300	6503	SO:0001819	synonymous_variant	28951	exon1			TTGTATCGGGAAA	AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000405331.3:c.183C>A	2.37:g.12858616C>A		Somatic	97	0	683	WXS	Illumina HiSeq	Phase_I	73	29	NM_021643	0	0	3	4	1		Silent	SNP	ENST00000405331.3	37																																																																																				.		0.577	TRIB2-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000323585.1	NM_021643		A	12858616	C	A	12858616	2	1	36	1	0	0	0	0	0	0	0	1	16516	874	31	4		4	TRIB2	2	12858616	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		12858616	230340757	13	3193											
IL1RL2	8808	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	102805602	102805602	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagccttttgcttttaattGtacattccctcccataacat	9	16	3	13	0	0	0	0	0	0	0	2	0	2	0	4	0	4	2	4	0	3	8			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:102805602G>A	ENST00000264257.2	+	3	251	c.125G>A	c.(124-126)tGt>tAt	p.C42Y	IL1RL2_ENST00000441515.2_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.C42Y|IL1RL2_ENST00000481806.1_Intron	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	42	Ig-like C2-type 1.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						GCTTTTAATTGTACATTCCCT	0.358																																					p.C42Y		.											.	IL1RL2-92	0			c.G125A						.						90	89	89					2																	102805602		2203	4300	6503	SO:0001583	missense	8808	exon3			TTAATTGTACATT	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.125G>A	2.37:g.102805602G>A	ENSP00000264257:p.Cys42Tyr	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	49	18	NM_003854	0	0	0	0	0	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676325	0.67928	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	D;D;D	0.94537	-3.45;-3.45;-3.45	5.86	4.94	0.65067	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.274660	0.40908	D	0.000981	D	0.96448	0.8841	M	0.78637	2.42	0.45867	D	0.998726	D	0.55800	0.973	P	0.62560	0.904	D	0.95878	0.8896	10	0.59425	D	0.04	.	13.5643	0.61807	0.0:0.1562:0.8438:0.0	.	42	Q9HB29	ILRL2_HUMAN	Y	42	ENSP00000264257:C42Y;ENSP00000387611:C42Y;ENSP00000442184:C42Y	ENSP00000264257:C42Y	C	+	2	0	IL1RL2	102172034	0.992000	0.36948	0.966000	0.40874	0.967000	0.64934	3.468000	0.53086	2.937000	0.99478	0.650000	0.86243	TGT	.		0.358	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		A	102805602	G	A	102805602	3	1	36	1	0	0	0	0	1	0	0	0	7685	1377	48	2	131	2	IL1RL2	2	102805602	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	89946986	102805602	140393771	14	3194											
R3HDM1	23518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	136393707	136393707	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcaaatctatagaagaaaGagaagaagagtaccagagag	22	4	11	4	0	1	6	0	0	1	6	1	8	1	6	1	0	2	2	1	0	9	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:136393707G>T	ENST00000264160.4	+	11	1227	c.857G>T	c.(856-858)aGa>aTa	p.R286I	R3HDM1_ENST00000409606.1_Missense_Mutation_p.R286I|R3HDM1_ENST00000410054.1_Missense_Mutation_p.R230I|R3HDM1_ENST00000329971.3_Missense_Mutation_p.R242I|R3HDM1_ENST00000409478.1_Missense_Mutation_p.R242I	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	286	SUZ. {ECO:0000255|PROSITE- ProRule:PRU01009}.						poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		ATAGAAGAAAGAGAAGAAGAG	0.343																																					p.R286I		.											.	R3HDM1-91	0			c.G857T						.						150	164	159					2																	136393707		2203	4300	6503	SO:0001583	missense	23518	exon11			AAGAAAGAGAAGA	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing"	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.857G>T	2.37:g.136393707G>T	ENSP00000264160:p.Arg286Ile	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	84	26	NM_015361	0	0	0	0	0	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.2|24.2	4.500931|4.500931	0.85176|0.85176	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000456040|ENST00000422577;ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606	.|D;D;D;D;D	.|0.82526	.|-1.62;-1.62;-1.62;-1.62;-1.62	5.58|5.58	4.7|4.7	0.59300|0.59300	.|SUZ domain (1);	.|0.151795	.|0.64402	.|D	.|0.000020	.|D	.|0.90745	.|0.7095	M|M	0.79475|0.79475	2.455|2.455	0.48395|0.48395	D|D	0.999647|0.999647	.|D;D;D;D	.|0.89917	.|1.0;1.0;0.999;1.0	.|D;D;D;D	.|0.91635	.|0.997;0.999;0.998;0.999	.|D	.|0.92028	.|0.5631	.|10	.|0.87932	.|D	.|0	-12.4326|-12.4326	15.055|15.055	0.71908|0.71908	0.0685:0.0:0.9315:0.0|0.0685:0.0:0.9315:0.0	.|.	.|242;286;230;286	.|G5E9G8;E9PBB4;E9PG42;Q15032	.|.;.;.;R3HD1_HUMAN	X|I	269|242;242;286;242;230;286	.|ENSP00000386457:R242I;ENSP00000264160:R286I;ENSP00000331396:R242I;ENSP00000386877:R230I;ENSP00000387010:R286I	.|ENSP00000264160:R286I	E|R	+|+	1|2	0|0	R3HDM1|R3HDM1	136110177|136110177	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.821000|0.821000	0.46438|0.46438	7.981000|7.981000	0.88123|0.88123	1.501000|1.501000	0.48654|0.48654	-0.126000|-0.126000	0.14955|0.14955	GAG|AGA	.		0.343	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		T	136393707	G	T	136393707	3	4	36	1	0	0	0	0	1	0	0	0	12919	942	33	4	891	4	R3HDM1	2	136393707	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	33588105	136393707	106805666	15	3195											
SCN1A	6323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	166848746	166848746	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggcgtagatgaacatgActaggaagagtaggaggccg	14	6	16	5	2	0	5	0	2	0	3	0	7	0	7	1	4	1	2	1	4	5	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:166848746A>T	ENST00000303395.4	-	26	5038	c.5039T>A	c.(5038-5040)gTc>gAc	p.V1680D	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.V1669D|SCN1A_ENST00000409050.1_Missense_Mutation_p.V1652D|SCN1A_ENST00000423058.2_Missense_Mutation_p.V1680D			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1680					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GATGAACATGACTAGGAAGAG	0.478																																					p.V1680D		.											.	SCN1A-147	0			c.T5039A						.						178	164	169					2																	166848746		2203	4300	6503	SO:0001583	missense	6323	exon26			AACATGACTAGGA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.5039T>A	2.37:g.166848746A>T	ENSP00000303540:p.Val1680Asp	Somatic	314	0		WXS	Illumina HiSeq	Phase_I	268	89	NM_001165963	0	0	0	0	0	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331387	0.81690	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.98926	-5.24;-5.24;-5.24;-5.24	5.41	5.41	0.78517	.	0.000000	0.53938	D	0.000051	D	0.99423	0.9796	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98389	1.0562	10	0.87932	D	0	.	15.4593	0.75342	1.0:0.0:0.0:0.0	.	1669	P35498-2	.	D	1680;1680;1669;1652	ENSP00000407030:V1680D;ENSP00000303540:V1680D;ENSP00000364554:V1669D;ENSP00000386312:V1652D	ENSP00000303540:V1680D	V	-	2	0	SCN1A	166556992	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.106000	0.94253	2.049000	0.60858	0.528000	0.53228	GTC	.		0.478	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166848746	A	T	166848746	3	4	36	1	0	0	0	0	1	0	0	0	13946	275	10	5	994	5	SCN1A	2	166848746	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	30455039	166848746	76350627	16	3196											
NFE2L2	4780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178098806	178098806	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattgggagaaattcacctGtctcttcatctagttgtaac	11	14	8	8	0	4	1	2	0	2	1	5	3	4	1	1	1	1	2	1	1	4	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:178098806G>T	ENST00000397062.3	-	2	793	c.239C>A	c.(238-240)aCa>aAa	p.T80K	NFE2L2_ENST00000464747.1_Missense_Mutation_p.T64K|NFE2L2_ENST00000446151.2_Missense_Mutation_p.T64K|NFE2L2_ENST00000397063.4_Missense_Mutation_p.T64K|NFE2L2_ENST00000423513.1_Missense_Mutation_p.T64K	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	80					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T80K(3)|p.T80R(2)|p.T80I(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AAATTCACCTGTCTCTTCATC	0.443			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.T80K		.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2-90	6	Substitution - Missense(6)	lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|endometrium(1)	c.C239A						.						146	145	145					2																	178098806		1901	4109	6010	SO:0001583	missense	4780	exon2			TCACCTGTCTCTT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.239C>A	2.37:g.178098806G>T	ENSP00000380252:p.Thr80Lys	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	65	20	NM_006164	0	0	13	19	6	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.264788	0.80358	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.64327	0.2588	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.994;0.999;0.997	T	0.69087	-0.5238	10	0.87932	D	0	.	19.9976	0.97389	0.0:0.0:1.0:0.0	.	64;64;64;80	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	K	64;80;64;64;64;64;64	ENSP00000380253:T64K;ENSP00000380252:T80K;ENSP00000411575:T64K;ENSP00000391590:T64K;ENSP00000400073:T64K;ENSP00000412191:T64K;ENSP00000410015:T64K	ENSP00000380252:T80K	T	-	2	0	NFE2L2	177807052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.229000	0.95273	2.737000	0.93849	0.563000	0.77884	ACA	.		0.443	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		T	178098806	G	T	178098806	3	4	36	1	0	0	0	0	1	0	0	0	10394	1377	48	4	1594	4	NFE2L2	2	178098806	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	11250060	178098806	65100567	17	3197											
FAM117B	150864	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	203560690	203560690	+	Frame_Shift_Del	DEL	G	G	-																															ctcttgctgcaccgtatcttGctggacactggcctcgggat																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:203560690delG	ENST00000392238.2	+	2	688	c.688delG	c.(688-690)gctfs	p.A230fs	FAM117B_ENST00000303116.6_5'UTR			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	230										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						ACCGTATCTTGCTGGACACTG	0.483																																					p.A230fs		.											.	FAM117B-91	0			c.688delG						.						86	75	79					2																	203560690		2203	4300	6503	SO:0001589	frameshift_variant	150864	exon2			.	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.688delG	2.37:g.203560690delG	ENSP00000376071:p.Ala230fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	92	32	NM_173511	0	0	0	0	0	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	ENST00000392238.2	37	CCDS33362.2																																																																																			.		0.483	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		-	203560690	G	-	203560690	7	5	36	1	0	1	0	1	0	0	0	0	5426	1319	46	0	694	0	FAM117B	2	203560690	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	25461884	203560690	39638683	18	3198											
CHPF	79586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220404816	220404816	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagggtcagggctgccgcAgcatcaccaggctccagtgc	8	5	14	14	1	2	0	2	0	0	0	3	0	3	0	3	3	4	5	3	3	0	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:220404816A>T	ENST00000243776.6	-	4	1865	c.1617T>A	c.(1615-1617)gcT>gcA	p.A539A	CHPF_ENST00000535926.1_Silent_p.A377A	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	539	Ala-rich.				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GGGCTGCCGCAGCATCACCAG	0.657																																					p.A539A		.											.	CHPF-90	0			c.T1617A						.						15	15	15					2																	220404816		2197	4292	6489	SO:0001819	synonymous_variant	79586	exon4			TGCCGCAGCATCA	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1617T>A	2.37:g.220404816A>T		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	18	9	NM_024536	0	1	96	143	46	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			.		0.657	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		T	220404816	A	T	220404816	2	4	36	1	0	0	0	0	0	0	0	1	3374	175	7	5		5	CHPF	2	220404816	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	16844126	220404816	22794557	19	3199											
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238259816	238259816	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgcctcgttctccaggagcaCcagcggcacctccgcttccc	5	8	9	19	3	1	0	0	0	1	0	5	1	3	1	6	2	3	4	6	2	0	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:238259816C>G	ENST00000295550.4	-	27	7225	c.6773G>C	c.(6772-6774)gGt>gCt	p.G2258A	COL6A3_ENST00000346358.4_Missense_Mutation_p.G2058A|COL6A3_ENST00000347401.3_Missense_Mutation_p.G2057A|COL6A3_ENST00000409809.1_Missense_Mutation_p.G2052A|COL6A3_ENST00000472056.1_Missense_Mutation_p.G1651A|COL6A3_ENST00000353578.4_Missense_Mutation_p.G2052A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2258	Collagen-like 4.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TCCAGGAGCACCAGCGGCACC	0.572																																					p.G2258A		.											.	COL6A3-526	0			c.G6773C						.						102	83	89					2																	238259816		2203	4300	6503	SO:0001583	missense	1293	exon27			GGAGCACCAGCGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.6773G>C	2.37:g.238259816C>G	ENSP00000295550:p.Gly2258Ala	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	93	28	NM_004369	0	0	0	0	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.558422	0.27827	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.97850	-4.16;-4.16;-4.57;-4.16;-4.57;-4.16	5.42	5.42	0.78866	.	0.000000	0.56097	D	0.000040	D	0.99372	0.9779	H	0.99238	4.48	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.998	D	0.98306	1.0521	10	0.87932	D	0	.	17.4191	0.87510	0.0:1.0:0.0:0.0	.	1651;1651;2052;2258	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	A	2258;2057;2052;1651;2052;2058	ENSP00000295550:G2258A;ENSP00000315609:G2057A;ENSP00000315873:G2052A;ENSP00000418285:G1651A;ENSP00000386844:G2052A;ENSP00000295546:G2058A	ENSP00000295550:G2258A	G	-	2	0	COL6A3	237924555	0.999000	0.42202	0.110000	0.21437	0.435000	0.31806	5.960000	0.70348	2.543000	0.85770	0.650000	0.86243	GGT	.		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238259816	C	G	238259816	3	3	36	1	0	0	0	0	1	0	0	0	3707	507	18	4	2832	4	COL6A3	2	238259816	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	17855000	238259816	4939557	20	3200											
ILKAP	80895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	239093869	239093869	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgcaaattctgtgcagcaAattttgaggctcgaattcct	11	13	9	8	1	1	1	0	1	1	0	3	3	2	1	1	1	3	4	1	1	3	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:239093869A>G	ENST00000254654.3	-	6	660	c.485T>C	c.(484-486)tTt>tCt	p.F162S		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	162	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		CTGTGCAGCAAATTTTGAGGC	0.353																																					p.F162S		.											.	ILKAP-118	0			c.T485C						.						110	104	106					2																	239093869		2203	4300	6503	SO:0001583	missense	80895	exon6			GCAGCAAATTTTG	AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.485T>C	2.37:g.239093869A>G	ENSP00000254654:p.Phe162Ser	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	125	33	NM_030768	0	0	19	34	15	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	37	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082008	0.76528	.	.	ENSG00000132323	ENST00000254654;ENST00000457149	T;T	0.18810	2.19;2.19	5.86	5.86	0.93980	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	M	0.87617	2.895	0.80722	D	1	D	0.61080	0.989	D	0.67103	0.949	T	0.55425	-0.8143	10	0.66056	D	0.02	-4.2693	10.9192	0.47154	0.8595:0.0:0.0:0.1405	.	162	Q9H0C8	ILKAP_HUMAN	S	162;160	ENSP00000254654:F162S;ENSP00000395301:F160S	ENSP00000254654:F162S	F	-	2	0	ILKAP	238758608	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	3.341000	0.52151	2.241000	0.73720	0.528000	0.53228	TTT	.		0.353	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		G	239093869	A	G	239093869	3	3	36	1	0	0	0	0	1	0	0	0	7735	14	1	3	721	3	ILKAP	2	239093869	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	834053	239093869	4105504	21	3201											
ABHD5	51099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	43744053	43744053	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaggtggattcttggctgcTgcttactcgctgaagtaccc	6	13	11	11	1	1	1	0	1	1	0	2	2	1	2	1	3	4	5	1	3	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:43744053T>C	ENST00000458276.2	+	3	603	c.480T>C	c.(478-480)gcT>gcC	p.A160A		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	160					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)			kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		TCTTGGCTGCTGCTTACTCGC	0.468																																					p.A160A		.											.	ABHD5-91	0			c.T480C						.						205	195	198					3																	43744053		2203	4300	6503	SO:0001819	synonymous_variant	51099	exon3			GGCTGCTGCTTAC	AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"Abhydrolase domain containing"	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.480T>C	3.37:g.43744053T>C		Somatic	188	0		WXS	Illumina HiSeq	Phase_I	199	46	NM_016006	0	0	2	5	3	B2R9K0|Q9Y369	Silent	SNP	ENST00000458276.2	37	CCDS2711.1																																																																																			.		0.468	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006		C	43744053	T	C	43744053	2	2	36	1	0	0	0	0	0	0	0	1	85	1567	55	3		3	ABHD5	3	43744053	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10		43744053	154278377	22	3202											
LMOD3	56203	broad.mit.edu	37	chr3	69168646	69168646	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccacattggctaaactgAatgttttgatgtgcttgttt	9	16	8	8	0	0	2	0	2	0	0	0	2	0	2	1	1	2	4	1	1	3	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:69168646A>G	ENST00000420581.2	-	2	1039	c.860T>C	c.(859-861)tTc>tCc	p.F287S	LMOD3_ENST00000489031.1_Missense_Mutation_p.F287S|LMOD3_ENST00000475434.1_Missense_Mutation_p.F287S	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	287						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		GGCTAAACTGAATGTTTTGAT	0.398																																					p.F287S													.	LMOD3-23	0			c.T860C						.						199	180	186					3																	69168646		1979	4166	6145	SO:0001583	missense	56203	exon2			AAACTGAATGTTT	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.860T>C	3.37:g.69168646A>G	ENSP00000414670:p.Phe287Ser	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	81	3	NM_198271	0	0	0	0	0	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	37	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.948944	0.73787	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.19250	2.16;2.16;2.16	5.69	5.69	0.88448	.	0.091186	0.85682	D	0.000000	T	0.49474	0.1559	M	0.83483	2.645	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.56117	-0.8032	10	0.87932	D	0	-22.5676	15.9592	0.79914	1.0:0.0:0.0:0.0	.	287	Q0VAK6	LMOD3_HUMAN	S	287	ENSP00000414670:F287S;ENSP00000417210:F287S;ENSP00000418645:F287S	ENSP00000414670:F287S	F	-	2	0	LMOD3	69251336	1.000000	0.71417	0.997000	0.53966	0.887000	0.51463	9.339000	0.96797	2.180000	0.69256	0.482000	0.46254	TTC	.		0.398	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529		G	69168646	A	G	69168646	3	3	36	1	0	0	0	0	1	0	0	0	8881	246	9	3	830	3	LMOD3	3	69168646	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	25424593	69168646	128853784	23	3203											
RG9MTD1	54931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101284214	101284214	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caatgggctggaagggtgccCaggccatgcagtttggacaa	10	7	15	9	0	0	0	0	0	0	0	0	2	0	2	2	5	2	3	2	5	3	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:101284214C>T	ENST00000309922.6	+	2	743	c.589C>T	c.(589-591)Cag>Tag	p.Q197*		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	197	SAM-dependent MTase TRM10-type. {ECO:0000255|PROSITE-ProRule:PRU01012}.				mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										GAAGGGTGCCCAGGCCATGCA	0.398																																					p.Q197X		.											.	.	0			c.C589T						.						103	95	97					3																	101284214		1849	4094	5943	SO:0001587	stop_gained	54931	exon2			GGTGCCCAGGCCA	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.589C>T	3.37:g.101284214C>T	ENSP00000312356:p.Gln197*	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	50	16	NM_017819	0	0	15	22	7	Q9NRG5|Q9NX54|Q9Y596	Nonsense_Mutation	SNP	ENST00000309922.6	37	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956006	0.92726	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	.	.	.	5.96	5.96	0.96718	.	0.120526	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-25.6056	20.422	0.99049	0.0:1.0:0.0:0.0	.	.	.	.	X	197	.	ENSP00000312356:Q197X	Q	+	1	0	RG9MTD1	102766904	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.736000	0.68597	2.832000	0.97577	0.655000	0.94253	CAG	.		0.398	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		T	101284214	C	T	101284214	4	4	36	1	0	0	0	0	0	1	0	0	13303	595	21	2	591	2	RG9MTD1	3	101284214	Nonsense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	32115568	101284214	96738216	24	3204											
KIAA1407	57577	broad.mit.edu	37	chr3	113684200	113684200	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtccgaagggtgatccagagGatcctcctttaagaataaag	13	9	11	8	1	0	3	0	1	0	2	4	5	4	4	4	2	0	0	4	2	5	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:113684200G>A	ENST00000295878.3	-	17	2759	c.2613C>T	c.(2611-2613)atC>atT	p.I871I		NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	871										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TGATCCAGAGGATCCTCCTTT	0.343																																					p.I871I													.	KIAA1407-92	0			c.C2613T						.						60	65	63					3																	113684200		2203	4300	6503	SO:0001819	synonymous_variant	57577	exon17			CCAGAGGATCCTC	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2613C>T	3.37:g.113684200G>A		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	16	3	NM_020817	0	0	1	1	0	B4DYL1|Q9P2E0	Silent	SNP	ENST00000295878.3	37	CCDS2977.1																																																																																			.		0.343	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113684200	G	A	113684200	2	1	36	1	0	0	0	0	0	0	0	1	8250	1164	41	2		2	KIAA1407	3	113684200	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	12399986	113684200	84338230	25	3205											
LRCH3	84859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	197592302	197592302	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttctccacagagtgatgaCagacctaatgctctattaag	12	12	8	9	0	2	4	0	2	2	2	3	4	2	4	2	0	1	2	2	0	3	4	rs201375313		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:197592302C>G	ENST00000425562.2	+	16	1725	c.1725C>G	c.(1723-1725)gaC>gaG	p.D575E	LRCH3_ENST00000334859.4_Missense_Mutation_p.D575E|LRCH3_ENST00000414675.2_Missense_Mutation_p.D523E|LRCH3_ENST00000441090.2_Missense_Mutation_p.D421E|LRCH3_ENST00000438796.2_Missense_Mutation_p.D575E|LRCH3_ENST00000536618.1_Missense_Mutation_p.D170E			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	575						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AGAGTGATGACAGACCTAATG	0.274																																					p.D575E		.											.	LRCH3-91	0			c.C1725G						.						39	38	39					3																	197592302		2203	4300	6503	SO:0001583	missense	84859	exon16			TGATGACAGACCT	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1725C>G	3.37:g.197592302C>G	ENSP00000393579:p.Asp575Glu	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	154	41	NM_032773	0	0	0	0	0	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		.	.	.	.	.	.	.	.	.	.	C	4.270	0.049197	0.08243	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562;ENST00000536618;ENST00000452660;ENST00000433298	T;T;T;T;T;T;T;T	0.46451	2.09;1.5;2.1;2.36;2.11;0.89;0.87;0.97	4.97	2.98	0.34508	.	0.475028	0.22270	N	0.062279	T	0.26340	0.0643	L	0.29908	0.895	0.20563	N	0.999887	B;B;B;B;P	0.37663	0.102;0.058;0.056;0.033;0.604	B;B;B;B;B	0.33042	0.028;0.012;0.029;0.008;0.157	T	0.07539	-1.0767	10	0.31617	T	0.26	-1.0728	8.8539	0.35217	0.0:0.8043:0.0:0.1957	.	421;523;575;575;575	E9PD99;B4E0T7;Q96II8-2;Q96II8;Q96II8-3	.;.;.;LRCH3_HUMAN;.	E	575;421;523;575;575;170;86;48	ENSP00000399751:D575E;ENSP00000394609:D421E;ENSP00000394965:D523E;ENSP00000334375:D575E;ENSP00000393579:D575E;ENSP00000439083:D170E;ENSP00000395309:D86E;ENSP00000400164:D48E	ENSP00000334375:D575E	D	+	3	2	LRCH3	199076699	1.000000	0.71417	0.975000	0.42487	0.064000	0.16182	0.457000	0.21875	0.390000	0.25115	-0.480000	0.04831	GAC	C|0.999;T|0.001		0.274	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		G	197592302	C	G	197592302	3	3	36	1	0	0	0	0	1	0	0	0	8959	477	17	4	1787	4	LRCH3	3	197592302	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	83908102	197592302	430128	26	3206											
KCTD8	386617	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	44450334	44450334	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgagaacatgctggccaaAgtactgtccgggacgctgag	10	6	15	10	3	0	2	0	1	0	1	1	4	1	3	2	3	3	3	2	3	3	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:44450334A>T	ENST00000360029.3	-	1	490	c.207T>A	c.(205-207)acT>acA	p.T69T	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	69	BTB.				protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						TGCTGGCCAAAGTACTGTCCG	0.677										HNSCC(17;0.042)																											p.T69T		.											.	KCTD8-92	0			c.T207A						.						24	21	22					4																	44450334		2191	4278	6469	SO:0001819	synonymous_variant	386617	exon1			GGCCAAAGTACTG	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.207T>A	4.37:g.44450334A>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	33	16	NM_198353	0	0	0	0	0	A2RU39	Silent	SNP	ENST00000360029.3	37	CCDS3467.1																																																																																			.		0.677	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44450334	A	T	44450334	2	4	36	1	0	0	0	0	0	0	0	1	8136	59	3	5		5	KCTD8	4	44450334	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		44450334	146703942	27	3207											
AFF1	4299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	88053423	88053423	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttctgtctttgttcatagCatgcgttgccagtccatttt	6	18	7	10	1	3	0	1	0	2	0	4	0	4	0	2	0	3	3	2	0	1	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:88053423C>T	ENST00000307808.6	+	18	3573	c.3153C>T	c.(3151-3153)tgC>tgT	p.C1051C	AFF1_ENST00000544085.1_Splice_Site_p.C689C|AFF1_ENST00000395146.4_Splice_Site_p.C1058C	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1051					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TTGTTCATAGCATGCGTTGCC	0.393																																					p.C1058C		.											.	AFF1-289	0			c.C3174T						.						118	107	111					4																	88053423		2203	4300	6503	SO:0001630	splice_region_variant	4299	exon19			TCATAGCATGCGT	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.3153-1C>T	4.37:g.88053423C>T		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	118	34	NM_001166693	0	0	0	0	0	B4DTU1|E9PBM3	Silent	SNP	ENST00000307808.6	37	CCDS3616.1																																																																																			.		0.393	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	Silent	T	88053423	C	T	88053423	5	4	36	1	0	0	0	0	0	0	1	0	356	724	25	2	3265	2	AFF1	4	88053423	Splice_Site	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	43603089	88053423	103100853	28	3208											
ADH4	127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100057629	100057629	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttaccttggcattgttGattgcagccccatagccagt	8	13	8	12	0	0	1	0	1	0	0	0	1	0	1	5	1	4	3	5	1	2	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:100057629G>T	ENST00000265512.7	-	5	644	c.570C>A	c.(568-570)atC>atA	p.I190I	ADH4_ENST00000508393.1_Silent_p.I209I|ADH4_ENST00000423445.1_Silent_p.I209I|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000505590.1_Silent_p.I209I	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	190					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TGGCATTGTTGATTGCAGCCC	0.388																																					p.I190I		.											.	ADH4-228	0			c.C570A						.						162	144	150					4																	100057629		2203	4300	6503	SO:0001819	synonymous_variant	127	exon5			ATTGTTGATTGCA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.570C>A	4.37:g.100057629G>T		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	45	14	NM_000670	0	0	0	0	0	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	37	CCDS34032.1																																																																																			.		0.388	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		T	100057629	G	T	100057629	2	4	36	1	0	0	0	0	0	0	0	1	310	1280	45	4		4	ADH4	4	100057629	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	12004206	100057629	91096647	29	3209											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123109188	123109188	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtgaaaggaaagcttgaaAatgttcgagtcatgcttgtt	12	14	11	4	1	1	2	1	2	0	0	2	4	1	3	0	1	2	4	0	1	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:123109188A>T	ENST00000264501.4	+	9	1139	c.766A>T	c.(766-768)Aat>Tat	p.N256Y	KIAA1109_ENST00000455637.1_Missense_Mutation_p.N256Y|KIAA1109_ENST00000388738.3_Missense_Mutation_p.N256Y			Q2LD37	K1109_HUMAN	KIAA1109	256					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AAAGCTTGAAAATGTTCGAGT	0.313																																					p.N256Y		.											.	KIAA1109-80	0			c.A766T						.						103	94	97					4																	123109188		1842	4093	5935	SO:0001583	missense	84162	exon7			CTTGAAAATGTTC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.766A>T	4.37:g.123109188A>T	ENSP00000264501:p.Asn256Tyr	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	19	6	NM_015312	0	0	0	0	0	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.3|24.3	4.519360|4.519360	0.85495|0.85495	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|D;D;D	.|0.95272	.|-3.66;-3.66;-3.66	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|7739.210000	.|0.00604	.|U	.|0.000398	D|D	0.97204|0.97204	0.9086|0.9086	L|L	0.55213|0.55213	1.73|1.73	0.80722|0.80722	D|D	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.80764	.|0.994	D|D	0.87444|0.87444	0.2397|0.2397	5|10	.|0.87932	.|D	.|0	.|.	15.4917|15.4917	0.75611|0.75611	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|256	.|Q2LD37	.|K1109_HUMAN	I|Y	88|256	.|ENSP00000264501:N256Y;ENSP00000373390:N256Y;ENSP00000389925:N256Y	.|ENSP00000264501:N256Y	K|N	+|+	2|1	0|0	KIAA1109|KIAA1109	123328638|123328638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.232000|9.232000	0.95325|0.95325	2.065000|2.065000	0.61736|0.61736	0.459000|0.459000	0.35465|0.35465	AAA|AAT	.		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123109188	A	T	123109188	3	4	36	1	0	0	0	0	1	0	0	0	8229	14	1	5	792	5	KIAA1109	4	123109188	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	23051559	123109188	68045088	30	3210											
SMARCA5	8467	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	144457751	144457751	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcagaacctggtccaccttAtacaacagatatgcatctag	14	9	7	11	0	1	2	0	0	1	2	2	2	2	2	3	1	5	2	3	1	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:144457751A>C	ENST00000283131.3	+	11	1877	c.1415A>C	c.(1414-1416)tAt>tCt	p.Y472S		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	472					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GGTCCACCTTATACAACAGAT	0.398																																					p.Y472S		.											.	SMARCA5-227	0			c.A1415C						.						102	95	97					4																	144457751		2203	4300	6503	SO:0001583	missense	8467	exon11			CACCTTATACAAC	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.1415A>C	4.37:g.144457751A>C	ENSP00000283131:p.Tyr472Ser	Somatic	351	0		WXS	Illumina HiSeq	Phase_I	327	128	NM_003601	0	0	5	8	3		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.668376	0.88348	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	T	0.75050	-0.9	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.85720	0.5762	M	0.88906	2.99	0.80722	D	1	P	0.44380	0.834	P	0.53912	0.737	D	0.87814	0.2633	10	0.56958	D	0.05	-21.194	15.7551	0.78018	1.0:0.0:0.0:0.0	.	472	O60264	SMCA5_HUMAN	S	472;415;415	ENSP00000283131:Y472S	ENSP00000283131:Y472S	Y	+	2	0	SMARCA5	144677201	1.000000	0.71417	0.977000	0.42913	0.985000	0.73830	9.231000	0.95317	2.192000	0.70111	0.533000	0.62120	TAT	.		0.398	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			C	144457751	A	C	144457751	3	2	36	1	0	0	0	0	1	0	0	0	14803	449	16	5	1457	5	SMARCA5	4	144457751	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	21348563	144457751	46696525	31	3211											
FAM149A	25854	broad.mit.edu;bcgsc.ca	37	chr4	187093141	187093141	+	Nonstop_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattccaagtgacatcttgAaaccacctcaccagaaccat	15	8	5	13	0	2	4	1	2	1	2	3	4	3	4	5	0	2	0	5	0	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:187093141A>T	ENST00000356371.5	+	14	2322	c.2322A>T	c.(2320-2322)tgA>tgT	p.*774C	FAM149A_ENST00000389354.5_Nonstop_Mutation_p.*483C|FAM149A_ENST00000502970.1_Nonstop_Mutation_p.*483C|FAM149A_ENST00000227065.4_Nonstop_Mutation_p.*483C|FAM149A_ENST00000514153.1_Nonstop_Mutation_p.*483C|FAM149A_ENST00000503432.1_Nonstop_Mutation_p.*483C			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	0										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		TGACATCTTGAAACCACCTCA	0.423																																					p.X483C													.	FAM149A-90	0			c.A1449T						.						98	93	95					4																	187093141		2203	4300	6503	SO:0001578	stop_lost	25854	exon13			ATCTTGAAACCAC	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2322A>T	4.37:g.187093141A>T	ENSP00000348732:p.*774Cysext*33	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	63	6	NM_001006655	0	0	95	104	9	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		.	.	.	.	.	.	.	.	.	.	A	16.11	3.030830	0.54790	.	.	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354;ENST00000502894	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1839	0.65592	1.0:0.0:0.0:0.0	.	.	.	.	C	483;774;483;483;483;483;34	.	.	X	+	3	0	FAM149A	187330135	0.994000	0.37717	0.566000	0.28421	0.429000	0.31625	3.642000	0.54367	2.183000	0.69458	0.528000	0.53228	TGA	.		0.423	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		T	187093141	A	T	187093141	4	4	36	1	0	0	0	0	0	0	0	0	5471	259	9	5	1491	5	FAM149A	4	187093141	Nonstop_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	42635390	187093141	4061135	32	3212											
CDH6	1004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	31294229	31294229	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttacatccttcgagctcaagCtataaacagaaggacaggga	15	8	9	9	1	1	1	1	0	0	1	3	4	2	3	1	2	4	2	1	2	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:31294229C>A	ENST00000265071.2	+	3	654	c.389C>A	c.(388-390)gCt>gAt	p.A130D	CDH6_ENST00000514738.1_Missense_Mutation_p.A75D	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	130	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGAGCTCAAGCTATAAACAGA	0.458																																					p.A130D		.											.	CDH6-159	0			c.C389A						.						128	127	127					5																	31294229		2203	4300	6503	SO:0001583	missense	1004	exon3			CTCAAGCTATAAA	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.389C>A	5.37:g.31294229C>A	ENSP00000265071:p.Ala130Asp	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	68	21	NM_004932	0	0	7	16	9	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	37	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.436456	0.83885	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.71934	-0.61;-0.61	5.77	5.77	0.91146	Cadherin (4);Cadherin-like (1);	0.096902	0.64402	D	0.000001	D	0.90964	0.7159	H	0.98089	4.145	0.53688	D	0.999972	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93441	0.6794	10	0.87932	D	0	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	130;130	P55285;P55285-2	CADH6_HUMAN;.	D	75;130	ENSP00000424843:A75D;ENSP00000265071:A130D	ENSP00000265071:A130D	A	+	2	0	CDH6	31329986	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	3.261000	0.51530	2.885000	0.99019	0.655000	0.94253	GCT	.		0.458	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		A	31294229	C	A	31294229	3	1	36	1	0	0	0	0	1	0	0	0	3120	797	28	4	395	4	CDH6	5	31294229	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		31294229	149621031	33	3213											
DTWD2	285605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	118183873	118183873	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctattagtcggctgcatcCgaattacatactgactagaa	13	12	7	9	2	1	2	0	1	1	1	3	3	2	2	1	1	3	2	1	1	7	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:118183873C>T	ENST00000510708.1	-	5	671	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	DTWD2_ENST00000515439.3_Missense_Mutation_p.R117Q|DTWD2_ENST00000304058.4_Missense_Mutation_p.R147Q	NM_173666.2	NP_775937.1	Q8NBA8	DTWD2_HUMAN	DTW domain containing 2	213										breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)	13		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)		CGGCTGCATCCGAATTACATA	0.318																																					p.R213Q		.											.	DTWD2-90	0			c.G638A						.						67	64	65					5																	118183873		2202	4300	6502	SO:0001583	missense	285605	exon5			TGCATCCGAATTA		CCDS34216.1	5q23.1	2008-02-05			ENSG00000169570	ENSG00000169570			19334	protein-coding gene	gene with protein product							Standard	NM_173666		Approved	FLJ33977	uc003ksa.3	Q8NBA8	OTTHUMG00000162956	ENST00000510708.1:c.638G>A	5.37:g.118183873C>T	ENSP00000425048:p.Arg213Gln	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	136	41	NM_173666	0	0	1	1	0		Missense_Mutation	SNP	ENST00000510708.1	37	CCDS34216.1	.	.	.	.	.	.	.	.	.	.	C	33	5.223594	0.95139	.	.	ENSG00000169570	ENST00000304058;ENST00000510708;ENST00000515439	.	.	.	5.36	5.36	0.76844	DTW (1);	0.000000	0.85682	D	0.000000	D	0.86134	0.5860	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89151	0.3523	9	0.87932	D	0	-25.3975	18.6918	0.91586	0.0:1.0:0.0:0.0	.	213	Q8NBA8	DTWD2_HUMAN	Q	147;213;117	.	ENSP00000302892:R147Q	R	-	2	0	DTWD2	118211772	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.267000	0.78462	2.511000	0.84671	0.455000	0.32223	CGG	.		0.318	DTWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371167.2	NM_173666		T	118183873	C	T	118183873	3	4	36	1	0	0	0	0	1	0	0	0	4803	652	23	1	266	1	DTWD2	5	118183873	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	86889644	118183873	62731387	34	3214											
FAM13B	51306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	137346798	137346798	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagccattatcctgctcaCtatttcttgctctttcatgt	6	18	4	13	0	4	0	2	0	2	0	6	0	6	0	3	0	3	2	3	0	2	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:137346798C>G	ENST00000033079.3	-	6	1040	c.589G>C	c.(589-591)Gtg>Ctg	p.V197L	FAM13B_ENST00000420893.2_Missense_Mutation_p.V197L|FAM13B_ENST00000425075.2_Missense_Mutation_p.V79L	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	197	Glu-rich.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						ATCCTGCTCACTATTTCTTGC	0.338																																					p.V197L		.											.	.	0			c.G589C						.						155	147	150					5																	137346798		2203	4300	6503	SO:0001583	missense	51306	exon6			TGCTCACTATTTC	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.589G>C	5.37:g.137346798C>G	ENSP00000033079:p.Val197Leu	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	31	18	NM_001101800	0	0	0	0	0	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818248	0.90790	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.41400	1.0;2.01;1.0	5.59	5.59	0.84812	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.58495	0.2126	L	0.40543	1.245	0.80722	D	1	D;D;P	0.67145	0.996;0.996;0.461	D;D;B	0.77557	0.987;0.99;0.299	T	0.57476	-0.7805	10	0.54805	T	0.06	-6.8245	19.5907	0.95509	0.0:1.0:0.0:0.0	.	79;197;197	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	L	197;79;197	ENSP00000033079:V197L;ENSP00000394669:V79L;ENSP00000388521:V197L	ENSP00000033079:V197L	V	-	1	0	FAM13B	137374697	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.005000	0.63972	2.640000	0.89533	0.655000	0.94253	GTG	.		0.338	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			G	137346798	C	G	137346798	3	3	36	1	0	0	0	0	1	0	0	0	5469	565	20	4	2300	4	FAM13B	5	137346798	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	19162925	137346798	43568462	35	3215											
PCDHB10	56126	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140572491	140572494	+	Frame_Shift_Del	DEL	AGTC	AGTC	-																															atttaccgggctgagctgagAgtcagggatataaatgatca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	AGTC	AGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:140572491_140572494delAGTC	ENST00000239446.4	+	1	550_553	c.366_369delAGTC	c.(364-369)agagtcfs	p.RV122fs		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	122	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGAGCTGAGAGTCAGGGATATAA	0.422																																					p.122_123del		.											.	PCDHB10-92	0			c.366_369del						.																																			SO:0001589	frameshift_variant	56126	exon1			.	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.366_369delAGTC	5.37:g.140572491_140572494delAGTC	ENSP00000239446:p.Arg122fs	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	182	54	NM_018930	0	0	0	0	0	Q96T99	Frame_Shift_Del	DEL	ENST00000239446.4	37	CCDS4252.1																																																																																			.		0.422	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		-	140572494	AGTC	-	140572491	7	5	36	1	0	1	0	1	0	0	0	0	11561	301	11	0	368	0	PCDHB10	5	140572491	Frame_Shift_Del	DEL	AGTC	TCGA-B1-A47M-01A-11D-A25F-10	3225693	140572491	40342769	36	3216											
KIAA0141	9812	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141316790	141316790	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagcaggtaccaccttggaAtttgctatgagaaaggcctt	12	10	11	8	0	0	2	0	1	0	2	0	4	0	3	3	3	3	3	3	3	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:141316790A>C	ENST00000432126.2	+	11	1311	c.1177A>C	c.(1177-1179)Att>Ctt	p.I393L	KIAA0141_ENST00000194118.4_Missense_Mutation_p.I393L	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	393					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACCTTGGAATTTGCTATGA	0.517																																					p.I393L													.	KIAA0141-91	0			c.A1177C						.						169	162	165					5																	141316790		2203	4300	6503	SO:0001583	missense	9812	exon11			CTTGGAATTTGCT	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"death ligand signal enhancer"	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.1177A>C	5.37:g.141316790A>C	ENSP00000396225:p.Ile393Leu	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	88	30	NM_001142603	0	0	10	16	6	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.90|13.90	2.374638|2.374638	0.42105|0.42105	.|.	.|.	ENSG00000081791|ENSG00000081791	ENST00000507481|ENST00000432126;ENST00000194118	.|T;T	.|0.48836	.|0.8;0.8	5.6|5.6	4.45|4.45	0.53987|0.53987	.|Tetratricopeptide-like helical (1);	.|0.241061	.|0.39083	.|N	.|0.001473	T|T	0.42787|0.42787	0.1218|0.1218	N|N	0.24115|0.24115	0.695|0.695	0.29115|0.29115	N|N	0.880593|0.880593	.|D	.|0.61697	.|0.99	.|P	.|0.60886	.|0.88	T|T	0.26395|0.26395	-1.0104|-1.0104	5|10	.|0.10636	.|T	.|0.68	-10.6493|-10.6493	7.4726|7.4726	0.27357|0.27357	0.9061:0.0:0.0939:0.0|0.9061:0.0:0.0939:0.0	.|.	.|393	.|Q14154	.|DELE_HUMAN	D|L	94|393	.|ENSP00000396225:I393L;ENSP00000194118:I393L	.|ENSP00000194118:I393L	E|I	+|+	3|1	2|0	KIAA0141|KIAA0141	141296974|141296974	0.967000|0.967000	0.33354|0.33354	0.997000|0.997000	0.53966|0.53966	0.971000|0.971000	0.66376|0.66376	1.697000|1.697000	0.37784|0.37784	2.140000|2.140000	0.66376|0.66376	0.533000|0.533000	0.62120|0.62120	GAA|ATT	.		0.517	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		C	141316790	A	C	141316790	3	2	36	1	0	0	0	0	1	0	0	0	8177	101	4	5	1219	5	KIAA0141	5	141316790	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	744299	141316790	39598470	37	3217											
FAM71B	153745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156590131	156590131	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttctgctgcacacttgctgGtcgtaatactgcctgcaaac	8	13	8	12	1	1	0	0	0	1	0	2	0	1	0	1	1	7	5	1	1	3	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:156590131G>A	ENST00000302938.4	-	2	1240	c.1145C>T	c.(1144-1146)aCc>aTc	p.T382I		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	382						nucleus (GO:0005634)		p.T382N(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACACTTGCTGGTCGTAATACT	0.572																																					p.T382I		.											.	FAM71B-96	1	Substitution - Missense(1)	lung(1)	c.C1145T						.						47	49	48					5																	156590131		2203	4300	6503	SO:0001583	missense	153745	exon2			TTGCTGGTCGTAA		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1145C>T	5.37:g.156590131G>A	ENSP00000305596:p.Thr382Ile	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	51	11	NM_130899	0	0	0	0	0	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673011	0.47781	.	.	ENSG00000170613	ENST00000302938	T	0.18960	2.18	3.83	2.95	0.34219	.	0.314558	0.23165	N	0.051186	T	0.37598	0.1009	M	0.78801	2.425	0.09310	N	1	D	0.62365	0.991	P	0.57101	0.813	T	0.13548	-1.0505	10	0.72032	D	0.01	-18.4181	9.0093	0.36131	0.0:0.0:0.781:0.219	.	382	Q8TC56	FA71B_HUMAN	I	382	ENSP00000305596:T382I	ENSP00000305596:T382I	T	-	2	0	FAM71B	156522709	0.045000	0.20229	0.011000	0.14972	0.002000	0.02628	2.344000	0.44010	1.174000	0.42811	0.561000	0.74099	ACC	.		0.572	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156590131	G	A	156590131	3	1	36	1	0	0	0	0	1	0	0	0	5627	1261	44	2	676	2	FAM71B	5	156590131	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	15273341	156590131	24325129	38	3218											
CLK4	57396	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	178030682	178030683	+	Frame_Shift_Ins	INS	-	-	T																															atccaaggtaattctttgagINSttggatcatattctaacatt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:178030682_178030683insT	ENST00000316308.4	-	13	1549_1550	c.1381_1382insA	c.(1381-1383)actfs	p.T461fs		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	461	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		AATTCTTTGAGTTGGATCATAT	0.342																																					p.T461fs		.											.	CLK4-359	0			c.1382_1383insA						.																																			SO:0001589	frameshift_variant	57396	exon13			.	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1382dupA	5.37:g.178030684_178030684dupT	ENSP00000316948:p.Thr461fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	61	30	NM_020666	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000316308.4	37	CCDS4437.1																																																																																			.		0.342	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			T	178030683	-	T	178030682	7	5	36	1	0	1	1	0	0	0	0	0	3545	1029	36	0	67	0	CLK4	5	178030682	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10	21440551	178030682	2884578	39	3219											
JARID2	3720	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	15512476	15512476	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcaaagaggggatcaaggTgcacaggaccgtgcagcaga	13	4	16	8	1	1	2	1	0	0	2	1	4	1	4	1	4	4	4	1	4	2	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:15512476T>C	ENST00000341776.2	+	14	3234	c.2990T>C	c.(2989-2991)gTg>gCg	p.V997A	JARID2_ENST00000397311.3_Missense_Mutation_p.V825A	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	997	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GGGATCAAGGTGCACAGGACC	0.612																																					p.V997A													.	JARID2-228	0			c.T2990C						.						156	118	131					6																	15512476		2203	4300	6503	SO:0001583	missense	3720	exon14			TCAAGGTGCACAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2"	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.2990T>C	6.37:g.15512476T>C	ENSP00000341280:p.Val997Ala	Somatic	152	2		WXS	Illumina HiSeq	Phase_I	124	39	NM_004973	0	0	3	6	3	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.763511	0.89932	.	.	ENSG00000008083	ENST00000341776;ENST00000397311	T;T	0.75260	-0.92;-0.92	4.88	4.88	0.63580	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.82926	0.5143	M	0.76838	2.35	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.86039	0.1518	10	0.87932	D	0	-13.9821	14.7676	0.69651	0.0:0.0:0.0:1.0	.	997	Q92833	JARD2_HUMAN	A	997;825	ENSP00000341280:V997A;ENSP00000380478:V825A	ENSP00000341280:V997A	V	+	2	0	JARID2	15620455	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.983000	0.88140	1.945000	0.56424	0.413000	0.27773	GTG	.		0.612	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		C	15512476	T	C	15512476	3	2	36	1	0	0	0	0	1	0	0	0	7966	1696	59	3	3044	3	JARID2	6	15512476	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10		15512476	155602591	40	3220											
EHMT2	10919	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31852462	31852462	+	Frame_Shift_Del	DEL	G	G	-																															ctcccgagctgcgatgtgcaGgggggtgtccccatggtagt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:31852462delG	ENST00000375537.4	-	20	2569	c.2563delC	c.(2563-2565)ctgfs	p.L855fs	EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375530.4_Frame_Shift_Del_p.L821fs|EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000395728.3_Frame_Shift_Del_p.L912fs|EHMT2_ENST00000375528.4_Frame_Shift_Del_p.L878fs	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	855					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						GCGATGTGCAGGGGGGTGTCC	0.657																																					p.L855fs		.											.	EHMT2-91	0			c.2563delC						.						39	34	36					6																	31852462		1511	2708	4219	SO:0001589	frameshift_variant	10919	exon20			.	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.2563delC	6.37:g.31852462delG	ENSP00000364687:p.Leu855fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_006709	0	0	0	0	0	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Frame_Shift_Del	DEL	ENST00000375537.4	37	CCDS4725.1																																																																																			.		0.657	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		-	31852462	G	-	31852462	7	5	36	1	0	1	0	1	0	0	0	0	4995	991	35	0	1105	0	EHMT2	6	31852462	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	16339986	31852462	139262605	41	3221	28	2									
EHMT2	10919	hgsc.bcm.edu;bcgsc.ca	37	chr6	31852467	31852467	+	Missense_Mutation	SNP	G	G	A																															gagctgcgatgtgcagggggGtgtccccatggtagttgaca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:31852467G>A	ENST00000375537.4	-	20	2564	c.2558C>T	c.(2557-2559)aCc>aTc	p.T853I	EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375530.4_Missense_Mutation_p.T819I|EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000395728.3_Missense_Mutation_p.T910I|EHMT2_ENST00000375528.4_Missense_Mutation_p.T876I	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	853					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						GTGCAGGGGGGTGTCCCCATG	0.647																																					p.T853I		.											.	EHMT2-91	0			c.C2558T						.						39	33	36					6																	31852467		1511	2709	4220	SO:0001583	missense	10919	exon20			AGGGGGGTGTCCC	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.2558C>T	6.37:g.31852467G>A	ENSP00000364687:p.Thr853Ile	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	68	28	NM_006709	0	0	13	13	0	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175053	0.78564	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59	5.14	5.14	0.70334	Ankyrin repeat-containing domain (3);	0.055749	0.64402	D	0.000001	D	0.94245	0.8152	H	0.97829	4.085	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.81914	0.99;0.983;0.995;0.995	D	0.96314	0.9231	10	0.87932	D	0	.	17.3716	0.87380	0.0:0.0:1.0:0.0	.	876;819;853;674	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	I	910;876;819;853;674	ENSP00000379078:T910I;ENSP00000364678:T876I;ENSP00000364680:T819I;ENSP00000364687:T853I	ENSP00000364678:T876I	T	-	2	0	EHMT2	31960446	1.000000	0.71417	0.978000	0.43139	0.313000	0.28021	9.634000	0.98435	2.396000	0.81511	0.555000	0.69702	ACC	.		0.647	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		A	31852467	G	A	31852467	3	1	36	1	0	0	0	0	1	0	0	0	4995	1261	44	2	1110	2	EHMT2	6	31852467	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	5	31852467	139262600	42	3222	28	2									
TNXB	7148	broad.mit.edu	37	chr6	32029470	32029470	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctccatgctgggttctGtggggctgggggtctcttcc	1	12	17	11	0	2	0	0	0	2	0	5	0	4	0	3	6	1	3	3	6	0	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:32029470G>T	ENST00000375244.3	-	21	7397	c.7196C>A	c.(7195-7197)aCa>aAa	p.T2399K	TNXB_ENST00000375247.2_Missense_Mutation_p.T2399K			P22105	TENX_HUMAN	tenascin XB	2459	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCTGGGTTCTGTGGGGCTGGG	0.637																																					p.T2399K													.	TNXB-90	0			c.C7196A						.						46	56	53					6																	32029470		1184	2505	3689	SO:0001583	missense	7148	exon21			GGTTCTGTGGGGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7196C>A	6.37:g.32029470G>T	ENSP00000364393:p.Thr2399Lys	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_019105	0	0	2	2	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	G	6.173	0.400107	0.11696	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61392	0.24;0.11	3.69	2.81	0.32909	.	0.983616	0.08303	N	0.966524	T	0.35770	0.0943	M	0.84219	2.685	0.21553	N	0.999642	B	0.28419	0.211	B	0.30782	0.12	T	0.46652	-0.9176	10	0.10111	T	0.7	.	7.1853	0.25797	0.1256:0.0:0.8744:0.0	.	2399	P22105-3	.	K	2399	ENSP00000364393:T2399K;ENSP00000364396:T2399K	ENSP00000364393:T2399K	T	-	2	0	TNXB	32137448	0.001000	0.12720	0.643000	0.29450	0.077000	0.17291	0.359000	0.20233	0.877000	0.35895	0.585000	0.79938	ACA	.		0.637	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32029470	G	T	32029470	3	4	36	1	0	0	0	0	1	0	0	0	16378	1377	48	4	7613	4	TNXB	6	32029470	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	177003	32029470	139085597	43	3223											
C6orf222	389384	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	36294405	36294405	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccccctcttggcctcctcGgagccgtgtttcttggggtt	1	13	12	15	2	2	0	0	0	2	0	4	1	3	1	6	4	1	2	6	4	0	4	rs140796295		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:36294405G>C	ENST00000437635.2	-	5	1095	c.918C>G	c.(916-918)tcC>tcG	p.S306S		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	306										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						TGGCCTCCTCGGAGCCGTGTT	0.567																																					p.S306S													.	C6orf222-93	0			c.C918G						.						145	156	152					6																	36294405		2203	4300	6503	SO:0001819	synonymous_variant	389384	exon5			CTCCTCGGAGCCG		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.918C>G	6.37:g.36294405G>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	65	23	NM_001010903	0	0	0	0	0	B2RTY8	Silent	SNP	ENST00000437635.2	37	CCDS34439.1																																																																																			G|1.000;A|0.000		0.567	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		C	36294405	G	C	36294405	2	2	36	1	0	0	0	0	0	0	0	1	2362	1103	39	4		4	C6orf222	6	36294405	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	4264935	36294405	134820662	44	3224											
PTCRA	171558	broad.mit.edu	37	chr6	42893185	42893185	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cccggccacggagactggggGacgagaggccaccagctcac	9	2	15	15	3	1	2	1	0	0	2	1	5	1	3	4	5	1	1	4	5	0	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:42893185G>A	ENST00000304672.1	+	4	692	c.611G>A	c.(610-612)gGa>gAa	p.G204E	PTCRA_ENST00000441198.1_Missense_Mutation_p.G179E|PTCRA_ENST00000446507.1_Missense_Mutation_p.G97E	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	204					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			GAGACTGGGGGACGAGAGGCC	0.746																																					p.G219E													.	PTCRA-92	0			c.G656A						.						9	10	9					6																	42893185		2117	4116	6233	SO:0001583	missense	171558	exon4			CTGGGGGACGAGA	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.611G>A	6.37:g.42893185G>A	ENSP00000304447:p.Gly204Glu	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_001243168	0	0	0	0	0	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447346	0.25987	.	.	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507	T;T;T	0.58506	1.07;1.03;0.33	3.85	-0.363	0.12556	.	4.595490	0.00447	N	0.000093	T	0.18593	0.0446	N	0.24115	0.695	0.09310	N	1	P;B;B	0.37101	0.582;0.192;0.077	B;B;B	0.28709	0.093;0.029;0.017	T	0.14952	-1.0454	10	0.66056	D	0.02	.	4.8129	0.13353	0.211:0.3295:0.4595:0.0	.	97;179;204	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	E	204;179;97	ENSP00000304447:G204E;ENSP00000409550:G179E;ENSP00000392288:G97E	ENSP00000304447:G204E	G	+	2	0	PTCRA	43001163	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.075000	0.14686	-0.234000	0.09782	-0.140000	0.14226	GGA	.		0.746	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296		A	42893185	G	A	42893185	3	1	36	1	0	0	0	0	1	0	0	0	12764	1174	41	2	625	2	PTCRA	6	42893185	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	6598780	42893185	128221882	45	3225											
CUL9	23113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43184050	43184050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagcaccttttggctcatTcccactggggcgctgaacag	7	10	10	14	1	2	1	2	1	0	0	3	1	3	1	2	3	2	3	2	3	1	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:43184050T>C	ENST00000252050.4	+	31	6175	c.6091T>C	c.(6091-6093)Tcc>Ccc	p.S2031P	CUL9_ENST00000372647.2_Missense_Mutation_p.S2003P|CUL9_ENST00000354495.3_Missense_Mutation_p.S1921P|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2031					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TTTGGCTCATTCCCACTGGGG	0.602																																					p.S2031P		.											.	CUL9-529	0			c.T6091C						.						51	43	46					6																	43184050		2203	4300	6503	SO:0001583	missense	23113	exon31			GCTCATTCCCACT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.6091T>C	6.37:g.43184050T>C	ENSP00000252050:p.Ser2031Pro	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	58	18	NM_015089	0	0	5	16	11	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.563689	0.65651	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.04156	3.69;3.69;3.69	5.82	3.11	0.35812	.	0.282909	0.37809	N	0.001923	T	0.01835	0.0058	L	0.36672	1.1	0.28092	N	0.93174	P;P;P	0.38642	0.467;0.641;0.641	B;B;B	0.38562	0.26;0.276;0.276	T	0.41161	-0.9524	10	0.54805	T	0.06	-12.2048	9.9765	0.41786	0.1212:0.0:0.1122:0.7665	.	1921;2003;2031	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	P	2031;1921;2003	ENSP00000252050:S2031P;ENSP00000346490:S1921P;ENSP00000361730:S2003P	ENSP00000252050:S2031P	S	+	1	0	CUL9	43292028	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.643000	0.46604	1.001000	0.39076	0.533000	0.62120	TCC	.		0.602	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		C	43184050	T	C	43184050	3	2	36	1	0	0	0	0	1	0	0	0	4067	1783	62	3	6209	3	CUL9	6	43184050	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	290865	43184050	127931017	46	3226											
COL10A1	1300	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	116441541	116441541	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtccttgggtcataatgctGttgcctgttatacaaaattt	10	16	8	7	0	1	0	1	0	0	0	2	0	2	0	2	1	3	3	2	1	5	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:116441541G>T	ENST00000327673.4	-	2	2145	c.1738C>A	c.(1738-1740)Cag>Aag	p.Q580K	AL121963.1_ENST00000430695.1_5'Flank|COL10A1_ENST00000243222.4_Missense_Mutation_p.Q580K|NT5DC1_ENST00000319550.4_Intron			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	580	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		TCATAATGCTGTTGCCTGTTA	0.398																																					p.Q580K		.											.	COL10A1-90	0			c.C1738A						.						96	98	97					6																	116441541		2203	4300	6503	SO:0001583	missense	1300	exon3			AATGCTGTTGCCT		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"Collagens"	2185	protein-coding gene	gene with protein product	"Schmid metaphyseal chondrodysplasia"	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.1738C>A	6.37:g.116441541G>T	ENSP00000327368:p.Gln580Lys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	78	21	NM_000493	0	0	0	0	0	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	37	CCDS5105.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.829889	0.32329	.	.	ENSG00000123500	ENST00000243222;ENST00000327673	D;D	0.85556	-2.0;-2.0	4.74	2.88	0.33553	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.188788	0.47455	D	0.000223	T	0.56366	0.1980	L	0.41415	1.275	0.40364	D	0.97927	B	0.06786	0.001	B	0.08055	0.003	T	0.53767	-0.8392	10	0.02654	T	1	.	9.3923	0.38381	0.0:0.1413:0.5663:0.2925	.	580	Q03692	COAA1_HUMAN	K	580	ENSP00000243222:Q580K;ENSP00000327368:Q580K	ENSP00000243222:Q580K	Q	-	1	0	COL10A1	116548234	1.000000	0.71417	0.986000	0.45419	0.996000	0.88848	2.258000	0.43249	0.487000	0.27698	0.455000	0.32223	CAG	.		0.398	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1			T	116441541	G	T	116441541	3	4	36	1	0	0	0	0	1	0	0	0	3672	1386	48	4	308	4	COL10A1	6	116441541	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	73257491	116441541	54673526	47	3227											
RBM16	22828	bcgsc.ca	37	chr6	155143508	155143508	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agacagtggtcacaacccagGcagaggttttccctcctcct	9	9	9	14	0	1	2	1	0	0	2	4	2	4	2	4	3	1	2	4	3	1	2	rs372358045	byFrequency	TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:155143508G>T	ENST00000367178.3	+	16	2467	c.1891G>T	c.(1891-1893)Gca>Tca	p.A631S	SCAF8_ENST00000417268.1_Missense_Mutation_p.A631S|SCAF8_ENST00000367186.4_Missense_Mutation_p.A697S|RNU6-824P_ENST00000363724.1_RNA	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	631					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						CACAACCCAGGCAGAGGTTTT	0.428																																					p.A631S													.	SCAF8-91	0			c.G1891T						.						165	162	163					6																	155143508		2203	4300	6503	SO:0001583	missense	22828	exon16			ACCCAGGCAGAGG	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.1891G>T	6.37:g.155143508G>T	ENSP00000356146:p.Ala631Ser	Somatic	83	0		WXS	Illumina HiSeq	Phase_1	78	4	NM_014892	0	0	1	1	0	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.140142	0.37825	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.46451	0.89;0.89;0.87	5.68	2.91	0.33838	.	0.487974	0.19428	N	0.114517	T	0.07234	0.0183	N	0.21448	0.665	0.33934	D	0.642455	B;B;B;B	0.30824	0.141;0.296;0.141;0.172	B;B;B;B	0.19946	0.019;0.027;0.019;0.015	T	0.16364	-1.0405	10	0.18276	T	0.48	.	0.8618	0.01194	0.2464:0.1737:0.4012:0.1787	.	676;697;709;631	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	S	631;631;697	ENSP00000356146:A631S;ENSP00000413098:A631S;ENSP00000356154:A697S	ENSP00000356146:A631S	A	+	1	0	SCAF8	155185200	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.714000	0.25808	0.742000	0.32697	0.650000	0.86243	GCA	.		0.428	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		T	155143508	G	T	155143508	3	4	36	1	0	0	0	0	1	0	0	0	13150	1203	42	4	1953	4	RBM16	6	155143508	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	38701967	155143508	15971559	48	3228											
SBDS	51119	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr7	66456178	66456178	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgaccttgatcagtggcttGagcttttctttcagcttctt	6	18	8	9	0	4	3	2	3	2	0	4	3	4	3	1	1	2	3	1	1	0	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:66456178G>C	ENST00000246868.2	-	4	753	c.570C>G	c.(568-570)ctC>ctG	p.L190L		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	190					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						TCAGTGGCTTGAGCTTTTCTT	0.368			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.L190L		.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS-523	0			c.C570G						.						142	119	127					7																	66456178		2203	4300	6503	SO:0001819	synonymous_variant	51119	exon4	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	TGGCTTGAGCTTT	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.570C>G	7.37:g.66456178G>C		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	95	20	NM_016038	0	0	83	109	26	A8K0P4|Q96FX0|Q9NV53	Silent	SNP	ENST00000246868.2	37	CCDS5537.1																																																																																			.		0.368	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038		C	66456178	G	C	66456178	2	2	36	1	0	0	0	0	0	0	0	1	13889	1277	45	4		4	SBDS	7	66456178	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		66456178	92682485	49	3229											
CLDN12	9069	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	90042282	90042282	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcagcatgctgatcgccAtgggtgccctgctgctctgc	4	10	11	16	1	2	1	1	1	1	0	3	1	2	1	3	1	6	4	3	1	0	0	rs76988207	byFrequency	TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:90042282A>T	ENST00000287916.4	+	3	579	c.292A>T	c.(292-294)Atg>Ttg	p.M98L	CLDN12_ENST00000535571.1_Missense_Mutation_p.M98L|CLDN12_ENST00000394605.2_Missense_Mutation_p.M98L|CTB-13L3.1_ENST00000480135.1_RNA	NM_001185073.2|NM_012129.4	NP_001172002.1|NP_036261.1	P56749	CLD12_HUMAN	claudin 12	98					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)	15						GCTGATCGCCATGGGTGCCCT	0.557																																					p.M98L													.	CLDN12-90	0			c.A292T						.						185	160	168					7																	90042282		2203	4300	6503	SO:0001583	missense	9069	exon3			ATCGCCATGGGTG	AJ250713	CCDS5618.1	7q21	2008-07-18			ENSG00000157224	ENSG00000157224		"Claudins"	2034	protein-coding gene	gene with protein product		611232					Standard	NM_001185072		Approved		uc003ukr.3	P56749	OTTHUMG00000156612	ENST00000287916.4:c.292A>T	7.37:g.90042282A>T	ENSP00000287916:p.Met98Leu	Somatic	196	1		WXS	Illumina HiSeq	Phase_I	267	55	NM_012129	0	0	6	6	0	D6W5Q4|Q7LDZ0	Missense_Mutation	SNP	ENST00000287916.4	37	CCDS5618.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.335687	0.24253	.	.	ENSG00000157224	ENST00000422604;ENST00000416322;ENST00000496677;ENST00000287916;ENST00000535571;ENST00000394604;ENST00000394605;ENST00000427904	T;T;T;T;T;T;T	0.75260	-0.39;-0.63;-0.63;-0.63;-0.42;-0.63;-0.92	4.6	2.29	0.28610	.	0.396822	0.31963	N	0.006783	T	0.44414	0.1292	N	0.08118	0	0.25692	N	0.985671	B	0.02656	0.0	B	0.01281	0.0	T	0.24941	-1.0146	10	0.07030	T	0.85	-14.4012	4.7572	0.13090	0.5684:0.0:0.4316:0.0	.	98	P56749	CLD12_HUMAN	L	98	ENSP00000411399:M98L;ENSP00000419053:M98L;ENSP00000287916:M98L;ENSP00000443476:M98L;ENSP00000378102:M98L;ENSP00000378103:M98L;ENSP00000391062:M98L	ENSP00000287916:M98L	M	+	1	0	CLDN12	89880218	0.030000	0.19436	0.993000	0.49108	0.893000	0.52053	0.297000	0.19101	0.912000	0.36772	0.402000	0.26972	ATG	A|0.998;G|0.002		0.557	CLDN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059221.1	NM_012129		T	90042282	A	T	90042282	3	4	36	1	0	0	0	0	1	0	0	0	3480	217	8	5	294	5	CLDN12	7	90042282	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	23586104	90042282	69096381	50	3230											
ZNF498	221785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99219063	99219063	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgcttgggagccaggcaTccagctggggccagtggagg	7	5	19	10	1	0	0	0	0	0	0	1	2	1	2	3	7	2	3	3	7	0	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:99219063T>A	ENST00000394152.2	+	5	782	c.455T>A	c.(454-456)aTc>aAc	p.I152N	ZSCAN25_ENST00000334715.3_Missense_Mutation_p.I152N|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.I152N|ZSCAN25_ENST00000466948.1_Intron	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	152					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)										GAGCCAGGCATCCAGCTGGGG	0.592																																					p.I152N		.											.	.	0			c.T455A						.						73	71	72					7																	99219063		2203	4300	6503	SO:0001583	missense	221785	exon5			CAGGCATCCAGCT	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"-", "Zinc fingers, C2H2-type"	21961	protein-coding gene	gene with protein product			"zinc finger protein 498"	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.455T>A	7.37:g.99219063T>A	ENSP00000377708:p.Ile152Asn	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	169	66	NM_145115	0	0	9	11	2	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	T	13.88	2.370520	0.42003	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08896	3.1;3.1;3.04	5.08	5.08	0.68730	.	0.491076	0.17227	N	0.182081	T	0.06962	0.0177	N	0.24115	0.695	0.32243	N	0.572403	P;P	0.37276	0.589;0.454	B;B	0.37888	0.26;0.133	T	0.18053	-1.0349	10	0.26408	T	0.33	-10.0218	11.8202	0.52235	0.0:0.0:0.0:1.0	.	152;152	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	N	152	ENSP00000377708:I152N;ENSP00000334800:I152N;ENSP00000262941:I152N	ENSP00000262941:I152N	I	+	2	0	ZNF498	99056999	0.009000	0.17119	0.884000	0.34674	0.768000	0.43524	1.283000	0.33237	2.210000	0.71456	0.533000	0.62120	ATC	.		0.592	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		A	99219063	T	A	99219063	3	1	36	1	0	0	0	0	1	0	0	0	17979	1435	50	5	461	5	ZNF498	7	99219063	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	9176781	99219063	59919600	51	3231											
AASS	10157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121769482	121769482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttattgtgtgggagaaaaatGcataagtcttcctggacatt	12	14	10	5	0	1	1	0	0	1	1	2	3	2	2	1	2	1	1	1	2	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:121769482G>A	ENST00000393376.1	-	2	415	c.320C>T	c.(319-321)gCa>gTa	p.A107V	AASS_ENST00000417368.2_Missense_Mutation_p.A107V|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	107	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						GGAGAAAAATGCATAAGTCTT	0.348																																					p.A107V		.											.	AASS-92	0			c.C320T						.						59	61	60					7																	121769482		2202	4300	6502	SO:0001583	missense	10157	exon3			AAAAATGCATAAG	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.320C>T	7.37:g.121769482G>A	ENSP00000377040:p.Ala107Val	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	50	18	NM_005763	0	0	0	0	0	O95462	Missense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	13.69	2.312716	0.40895	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.74737	-0.87;-0.87	5.39	5.39	0.77823	Alanine dehydrogenase/PNT, N-terminal (1);	0.096191	0.64402	D	0.000001	T	0.63674	0.2531	N	0.20483	0.58	0.80722	D	1	B	0.32526	0.374	B	0.38225	0.268	T	0.59434	-0.7455	10	0.06365	T	0.9	-20.188	19.4914	0.95050	0.0:0.0:1.0:0.0	.	107	Q9UDR5	AASS_HUMAN	V	107	ENSP00000377040:A107V;ENSP00000403768:A107V	ENSP00000351834:A107V	A	-	2	0	AASS	121556718	1.000000	0.71417	0.929000	0.37066	0.990000	0.78478	9.799000	0.99117	2.681000	0.91329	0.655000	0.94253	GCA	.		0.348	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		A	121769482	G	A	121769482	3	1	36	1	0	0	0	0	1	0	0	0	24	1319	46	2	2548	2	AASS	7	121769482	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	22550419	121769482	37369181	52	3232											
VIPR2	7434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	158828654	158828654	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggactcacccggtgtcttcTaagtagagcctggccgcagt	7	10	12	12	2	3	1	1	0	2	1	3	2	3	2	3	3	1	2	3	3	2	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:158828654T>C	ENST00000262178.2	-	8	983	c.798A>G	c.(796-798)ttA>ttG	p.L266L	VIPR2_ENST00000377633.3_Silent_p.L250L|VIPR2_ENST00000402066.1_Silent_p.L407L	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	266					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CGGTGTCTTCTAAGTAGAGCC	0.597																																					p.L266L	Pancreas(154;1876 1931 2329 17914 20079)	.											.	VIPR2-91	0			c.A798G						.						81	60	67					7																	158828654		2203	4300	6503	SO:0001819	synonymous_variant	7434	exon8			GTCTTCTAAGTAG	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12695	protein-coding gene	gene with protein product	"VIP and PACAP receptor 2"	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.798A>G	7.37:g.158828654T>C		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	144	68	NM_003382	0	0	0	0	0	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1																																																																																			.		0.597	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		C	158828654	T	C	158828654	2	2	36	1	0	0	0	0	0	0	0	1	17203	1519	53	3		3	VIPR2	7	158828654	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	37059172	158828654	310009	53	3233											
MSR1	4481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	16021617	16021617	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggtctgagaatgttcccaAtctttcagtctgagatcatt	11	14	8	8	0	5	2	2	2	3	2	6	4	6	2	1	1	0	1	1	1	3	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr8:16021617A>G	ENST00000262101.5	-	5	895	c.774T>C	c.(772-774)gaT>gaC	p.D258D	MSR1_ENST00000536385.1_Silent_p.D32D|MSR1_ENST00000355282.2_Silent_p.D258D|MSR1_ENST00000445506.2_Silent_p.D276D|MSR1_ENST00000381998.4_Silent_p.D258D|MSR1_ENST00000350896.3_Silent_p.D258D			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	258					cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)			haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		AATGTTCCCAATCTTTCAGTC	0.303																																					p.D258D		.											.	MSR1-91	0			c.T774C						.						168	150	156					8																	16021617		2203	4299	6502	SO:0001819	synonymous_variant	4481	exon5			TTCCCAATCTTTC	D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"CD molecules"	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.774T>C	8.37:g.16021617A>G		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	55	13	NM_138715	0	0	0	0	0	D3DSP3|O60505|P21759|Q45F10	Silent	SNP	ENST00000262101.5	37	CCDS5995.1																																																																																			.		0.303	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			G	16021617	A	G	16021617	2	3	36	1	0	0	0	0	0	0	0	1	9911	98	4	3		3	MSR1	8	16021617	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		16021617	130342405	54	3234											
EYA1	2138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	72182014	72182014	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggacccagtaagcaaggaGtggaaaacaatgattgtctc	15	8	11	7	0	1	1	0	1	1	0	2	4	1	4	1	3	2	2	1	3	6	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr8:72182014G>A	ENST00000340726.3	-	11	1650	c.1011C>T	c.(1009-1011)caC>caT	p.H337H	EYA1_ENST00000388742.4_Silent_p.H337H|EYA1_ENST00000303824.7_Silent_p.H331H|EYA1_ENST00000419131.1_Silent_p.H332H|EYA1_ENST00000388740.3_Silent_p.H304H|EYA1_ENST00000388741.2_Silent_p.H303H|EYA1_ENST00000388743.2_Silent_p.H336H	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	337					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TAAGCAAGGAGTGGAAAACAA	0.403																																					p.H337H		.											.	EYA1-652	0			c.C1011T						.						172	156	161					8																	72182014		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon11			CAAGGAGTGGAAA	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1011C>T	8.37:g.72182014G>A		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	110	33	NM_000503	0	0	0	0	0	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	37	CCDS34906.1																																																																																			.		0.403	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		A	72182014	G	A	72182014	2	1	36	1	0	0	0	0	0	0	0	1	5341	1020	36	2		2	EYA1	8	72182014	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	56160397	72182014	74182008	55	3235											
FER1L6	654463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	124989660	124989660	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggctgtgtttttaggggCgaaccacagtgcagaagaac	10	9	13	9	1	0	2	0	0	0	2	0	3	0	2	2	3	3	3	2	3	4	3	rs535471573		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr8:124989660C>T	ENST00000522917.1	+	10	1080	c.874C>T	c.(874-876)Cga>Tga	p.R292*	FER1L6_ENST00000399018.1_Nonsense_Mutation_p.R292*	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	292	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TTTTTAGGGGCGAACCACAGT	0.478													C|||	1	0.000199681	0	0.0014	5008	,	,		21723	0		0	False		,,,				2504	0				p.R292X		.											.	FER1L6-100	0			c.C874T						.						128	126	127					8																	124989660		2043	4204	6247	SO:0001587	stop_gained	654463	exon10			TAGGGGCGAACCA	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.874C>T	8.37:g.124989660C>T	ENSP00000428280:p.Arg292*	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	124	46	NM_001039112	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	C	38	7.224901	0.98146	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	.	.	.	5.53	1.04	0.20106	.	0.091536	0.44688	U	0.000426	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	16.3285	0.82997	0.4563:0.5437:0.0:0.0	.	.	.	.	X	292	.	ENSP00000381982:R292X	R	+	1	2	FER1L6	125058841	0.002000	0.14202	0.996000	0.52242	0.952000	0.60782	0.481000	0.22260	0.264000	0.21851	-0.268000	0.10319	CGA	.		0.478	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	124989660	C	T	124989660	4	4	36	1	0	0	0	0	0	1	0	0	5834	760	27	1	908	1	FER1L6	8	124989660	Nonsense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	52807646	124989660	21374362	56	3236											
GLDC	2731	broad.mit.edu	37	chr9	6536187	6536187	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccgactcagtgggctcCaccatgagggtccctgccac	6	8	10	17	1	1	1	1	1	0	0	5	2	5	1	6	2	1	1	6	2	0	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:6536187C>A	ENST00000321612.6	-	23	2865	c.2715G>T	c.(2713-2715)gtG>gtT	p.V905V		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	905					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	CAGTGGGCTCCACCATGAGGG	0.577																																					p.V905V													.	GLDC-92	0			c.G2715T						.						40	33	36					9																	6536187		2203	4300	6503	SO:0001819	synonymous_variant	2731	exon23			GGGCTCCACCATG	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"glycine cleavage system protein P", "glycine decarboxylase"	238300	"glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.2715G>T	9.37:g.6536187C>A		Somatic	114	1		WXS	Illumina HiSeq	Phase_I	135	5	NM_000170	0	0	230	230	0	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			.		0.577	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		A	6536187	C	A	6536187	2	1	36	1	0	0	0	0	0	0	0	1	6453	581	21	4		4	GLDC	9	6536187	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		6536187	134677244	57	3237											
PRUNE2	158471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	79325026	79325026	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgctacccagttcaggctGaccaaattcagactcccagg	11	9	8	13	0	2	2	2	1	0	1	3	2	3	2	3	2	2	3	3	2	2	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:79325026G>A	ENST00000376718.3	-	8	2287	c.2164C>T	c.(2164-2166)Cag>Tag	p.Q722*	PRUNE2_ENST00000428286.1_Nonsense_Mutation_p.Q363*	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	722					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGTTCAGGCTGACCAAATTCA	0.458																																					p.Q722X		.											.	PRUNE2-157	0			c.C2164T						.						54	49	51					9																	79325026		1568	3582	5150	SO:0001587	stop_gained	158471	exon8			CAGGCTGACCAAA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.2164C>T	9.37:g.79325026G>A	ENSP00000365908:p.Gln722*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	69	36	NM_015225	0	0	0	0	0	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Nonsense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.95|13.95	2.388631|2.388631	0.42308|0.42308	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	.|.	.|.	.|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.000000|.	0.50627|.	D|.	0.000114|.	.|T	.|0.72128	.|0.3422	.|.	.|.	.|.	0.46149|0.46149	D|D	0.998894|0.998894	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69217	.|-0.5203	.|4	0.38643|.	T|.	0.18|.	-6.3717|-6.3717	15.6992|15.6992	0.77528|0.77528	0.0:0.1355:0.8645:0.0|0.0:0.1355:0.8645:0.0	.|.	.|.	.|.	.|.	X|L	722;363;721|43	.|.	ENSP00000365908:Q722X|.	Q|S	-|-	1|2	0|0	PRUNE2|PRUNE2	78514846|78514846	0.736000|0.736000	0.28164|0.28164	0.024000|0.024000	0.17045|0.17045	0.138000|0.138000	0.21146|0.21146	2.887000|2.887000	0.48586|0.48586	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.		0.458	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79325026	G	A	79325026	4	1	36	1	0	0	0	0	0	1	0	0	12670	1299	45	2	7150	2	PRUNE2	9	79325026	Nonsense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	72788839	79325026	61888405	58	3238											
WNK2	65268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	96079890	96079890	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcattcccggagccgcccCgaccctgtccgtgcccacac	5	6	10	20	4	1	0	1	0	0	0	3	2	3	1	7	2	2	0	7	2	0	1	rs377748076		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:96079890C>T	ENST00000297954.4	+	29	6716	c.6716C>T	c.(6715-6717)cCg>cTg	p.P2239L	WNK2_ENST00000349097.3_Missense_Mutation_p.P1851L|WNK2_ENST00000471076.1_3'UTR|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.P1814L|WNK2_ENST00000395477.2_Missense_Mutation_p.P2202L|WNK2_ENST00000356055.3_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2239					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GGAGCCGCCCCGACCCTGTCC	0.667																																					p.P2202L		.											.	WNK2-765	0			c.C6605T						.	A	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	52	44	47		6605	2.6	0	9		47	0,8596		0,0,4298	no	missense	WNK2	NM_006648.3	98	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign	2202/2218	96079890	1,13001	2203	4298	6501	SO:0001583	missense	65268	exon28			CCGCCCCGACCCT	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6716C>T	9.37:g.96079890C>T	ENSP00000297954:p.Pro2239Leu	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	18	5	NM_006648	0	0	4	15	11	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	6.441|6.441	0.449533|0.449533	0.12223|0.12223	2.27E-4|2.27E-4	0.0|0.0	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000432730;ENST00000448251	T;T;T;T|.	0.74842|.	-0.77;-0.88;-0.2;-0.01|.	5.73|5.73	2.64|2.64	0.31445|0.31445	.|.	0.398049|.	0.21391|.	N|.	0.075314|.	T|.	0.37073|.	0.0990|.	L|L	0.48642|0.48642	1.525|1.525	0.21967|0.21967	N|N	0.999449|0.999449	P;B;B;B|.	0.38195|.	0.622;0.066;0.108;0.255|.	B;B;B;B|.	0.32393|.	0.145;0.008;0.012;0.024|.	T|.	0.24977|.	-1.0145|.	10|.	0.87932|.	D|.	0|.	.|.	5.2308|5.2308	0.15420|0.15420	0.1562:0.6551:0.0:0.1887|0.1562:0.6551:0.0:0.1887	.|.	2202;1693;2202;2239|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	L|X	2239;2202;1851;1814|2198;999	ENSP00000297954:P2239L;ENSP00000378860:P2202L;ENSP00000297876:P1851L;ENSP00000411181:P1814L|.	ENSP00000297954:P2239L|.	P|R	+|+	2|1	0|2	WNK2|WNK2	95119711|95119711	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.006000|0.006000	0.05464|0.05464	0.676000|0.676000	0.25247|0.25247	0.229000|0.229000	0.21039|0.21039	-0.127000|-0.127000	0.14921|0.14921	CCG|CGA	.		0.667	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96079890	C	T	96079890	3	4	36	1	0	0	0	0	1	0	0	0	17411	652	23	1	6715	1	WNK2	9	96079890	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	16754864	96079890	45133541	59	3239											
TDRD7	23424	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	100227199	100227199	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatattacagtaagaatccTaagatcacaccagtccaggc	16	8	7	10	0	1	2	1	0	0	2	3	3	3	2	3	1	1	1	3	1	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:100227199T>G	ENST00000355295.4	+	8	1813	c.1518T>G	c.(1516-1518)ccT>ccG	p.P506P	TDRD7_ENST00000422139.2_Silent_p.P432P	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	506					germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				GTAAGAATCCTAAGATCACAC	0.458																																					p.P506P		.											.	TDRD7-93	0			c.T1518G						.						115	106	109					9																	100227199		2203	4300	6503	SO:0001819	synonymous_variant	23424	exon8			GAATCCTAAGATC	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.1518T>G	9.37:g.100227199T>G		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	126	27	NM_014290	0	0	7	8	1	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Silent	SNP	ENST00000355295.4	37	CCDS6725.1																																																																																			.		0.458	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		G	100227199	T	G	100227199	2	3	36	1	0	0	0	0	0	0	0	1	15767	1509	53	5		5	TDRD7	9	100227199	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	4147309	100227199	40986232	60	3240											
CTNNAL1	8727	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	111761412	111761413	+	Missense_Mutation	DNP	AT	AT	CC																															aatcccagttttcattggctAtagcttctcctactttaaca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:111761412_111761413AT>CC	ENST00000325551.4	-	2	351_352	c.265_266AT>GG	c.(265-267)ATa>GGa	p.I89G	CTNNAL1_ENST00000374593.4_Missense_Mutation_p.I89G|CTNNAL1_ENST00000374595.4_Missense_Mutation_p.I89G|CTNNAL1_ENST00000325580.6_Missense_Mutation_p.I89G	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	89					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TTCATTGGCTATAGCTTCTCCT	0.356																																					p.I89G		.											.	CTNNAL1-228	0			c.A265G						.																																			SO:0001583	missense	8727	exon2			TGGCTATAGCTTC	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.265_266delinsCC	9.37:g.111761412_111761413delinsCC	ENSP00000320434:p.Ile89Gly	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	55	14	NM_003798	0	0	0	0	0	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	DNP	ENST00000325551.4	37	CCDS6775.1																																																																																			.		0.356	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		CC	111761413	AT	CC	111761412	3	2	36	1	0	0	0	0	1	0	0	0	4021	449	16	5	2010	5	CTNNAL1	9	111761412	Missense_Mutation	DNP	AT	TCGA-B1-A47M-01A-11D-A25F-10	11534213	111761412	29452019	61	3241											
ZBTB6	10773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125673886	125673886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacagtctttatcagaatTttcatcttcattcttaacat	11	18	2	10	0	7	1	4	0	3	1	7	1	7	1	0	0	1	0	0	0	3	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:125673886T>C	ENST00000373659.3	-	2	554	c.466A>G	c.(466-468)Aat>Gat	p.N156D		NM_006626.5	NP_006617.1	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	156					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(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	11						TTATCAGAATTTTCATCTTCA	0.338																																					p.N156D		.											.	ZBTB6-90	0			c.A466G						.						57	57	57					9																	125673886		2203	4300	6503	SO:0001583	missense	10773	exon2			CAGAATTTTCATC	X82018	CCDS6846.1	9q33.1-q33.3	2013-01-08	2006-04-10	2006-04-10	ENSG00000186130	ENSG00000186130		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16764	protein-coding gene	gene with protein product		605976	"zinc finger protein 482"	ZNF482		7958847	Standard	NM_006626		Approved	ZID	uc004bnh.4	Q15916	OTTHUMG00000020628	ENST00000373659.3:c.466A>G	9.37:g.125673886T>C	ENSP00000362763:p.Asn156Asp	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	24	6	NM_006626	0	0	0	0	0	A8K8N6	Missense_Mutation	SNP	ENST00000373659.3	37	CCDS6846.1	.	.	.	.	.	.	.	.	.	.	T	1.533	-0.543782	0.04053	.	.	ENSG00000186130	ENST00000373659	T	0.09073	3.02	5.96	3.54	0.40534	.	1.010830	0.07908	N	0.973873	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.47129	-0.9141	10	0.10902	T	0.67	.	6.968	0.24632	0.0:0.0766:0.2858:0.6376	.	156	Q15916	ZBTB6_HUMAN	D	156	ENSP00000362763:N156D	ENSP00000362763:N156D	N	-	1	0	ZBTB6	124713707	0.001000	0.12720	0.992000	0.48379	0.995000	0.86356	0.967000	0.29344	0.460000	0.27045	0.533000	0.62120	AAT	.		0.338	ZBTB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053962.1	NM_006626		C	125673886	T	C	125673886	3	2	36	1	0	0	0	0	1	0	0	0	17584	1841	64	3	812	3	ZBTB6	9	125673886	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	13912474	125673886	15539545	62	3242											
ODF2	4957	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	131250301	131250301	+	Frame_Shift_Del	DEL	G	G	-																															aagctggagaatgagaggctGaaggttcgcagtgagagctg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:131250301delG	ENST00000434106.3	+	14	1896	c.1533delG	c.(1531-1533)ctgfs	p.L511fs	ODF2_ENST00000546203.1_Frame_Shift_Del_p.L492fs|ODF2_ENST00000372807.5_Frame_Shift_Del_p.L506fs|ODF2_ENST00000448249.3_Frame_Shift_Del_p.L430fs|ODF2_ENST00000393533.2_Frame_Shift_Del_p.L511fs|ODF2_ENST00000444119.2_Frame_Shift_Del_p.L487fs|ODF2_ENST00000393527.3_Frame_Shift_Del_p.L487fs|ODF2_ENST00000372814.3_Frame_Shift_Del_p.L555fs|ODF2_ENST00000604420.1_Frame_Shift_Del_p.L511fs|ODF2_ENST00000372791.3_Frame_Shift_Del_p.L492fs|ODF2_ENST00000351030.3_Frame_Shift_Del_p.L506fs	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	511					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						ATGAGAGGCTGAAGGTTCGCA	0.587																																					p.L575fs		.											.	ODF2-69	0			c.1725delG						.						72	63	66					9																	131250301		2203	4300	6503	SO:0001589	frameshift_variant	4957	exon14			.	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1533delG	9.37:g.131250301delG	ENSP00000403453:p.Leu511fs	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	46	16	NM_153435	0	0	0	0	0	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Frame_Shift_Del	DEL	ENST00000434106.3	37	CCDS56588.1																																																																																			.		0.587	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			-	131250301	G	-	131250301	7	5	36	1	0	1	0	1	0	0	0	0	10853	1277	45	0	1638	0	ODF2	9	131250301	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	5576415	131250301	9963130	63	3243											
NDOR1	27158	broad.mit.edu	37	chr9	140110791	140110791	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccaggaggagggtggaCtctgcagcccggacgcagcc	7	6	15	13	2	2	0	0	0	2	0	3	4	3	4	3	5	3	2	3	5	0	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:140110791C>G	ENST00000344894.5	+	14	1800	c.1717C>G	c.(1717-1719)Ctc>Gtc	p.L573V	NDOR1_ENST00000427047.2_3'UTR|NDOR1_ENST00000458322.2_Missense_Mutation_p.L566V|NDOR1_ENST00000371521.4_Missense_Mutation_p.L582V	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGAGGGTGGACTCTGCAGCCC	0.672																																					p.L582V													.	NDOR1-90	0			c.C1744G						.						53	57	56					9																	140110791		2203	4300	6503	SO:0001583	missense	27158	exon14			GGTGGACTCTGCA	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"NADPH dependent FMN and FAD containing oxidoreductase"	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.1717C>G	9.37:g.140110791C>G	ENSP00000343344:p.Leu573Val	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	25	5	NM_001144026	0	0	4	7	3		Missense_Mutation	SNP	ENST00000344894.5	37	CCDS7036.1	.	.	.	.	.	.	.	.	.	.	C	8.893	0.954486	0.18431	.	.	ENSG00000188566	ENST00000458322;ENST00000371521;ENST00000344894	T;T;T	0.78595	-1.19;-1.19;-1.19	4.06	4.06	0.47325	.	0.157147	0.45361	D	0.000369	T	0.74245	0.3691	L	0.58510	1.815	0.80722	D	1	B;B;B	0.27971	0.124;0.196;0.105	B;B;B	0.33799	0.082;0.17;0.055	T	0.70285	-0.4914	10	0.21540	T	0.41	0.2597	13.7542	0.62926	0.0:1.0:0.0:0.0	.	566;582;573	D3YTG6;Q9UHB4-2;Q9UHB4	.;.;NDOR1_HUMAN	V	566;582;573	ENSP00000389905:L566V;ENSP00000360576:L582V;ENSP00000343344:L573V	ENSP00000343344:L573V	L	+	1	0	NDOR1	139230612	0.822000	0.29219	0.970000	0.41538	0.122000	0.20287	1.362000	0.34148	2.109000	0.64355	0.561000	0.74099	CTC	.		0.672	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434		G	140110791	C	G	140110791	3	3	36	1	0	0	0	0	1	0	0	0	10275	565	20	4	1798	4	NDOR1	9	140110791	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	8860490	140110791	1102640	64	3244											
PARG	8505	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	51028288	51028288	+	Frame_Shift_Del	DEL	A	A	-																															attctgagtccccaaaggtgAaataaaccacatctcgctca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:51028288delA	ENST00000402038.3	-	13	1243	c.1244delT	c.(1243-1245)ttcfs	p.F415fs		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	900	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		CCCAAAGGTGAAATAAACCAC	0.423																																					p.F900fs		.											.	PARG-948	0			c.2699delT						.						139	114	122					10																	51028288		692	1591	2283	SO:0001589	frameshift_variant	8505	exon17			.	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1244delT	10.37:g.51028288delA	ENSP00000384408:p.Phe415fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	75	21	NM_003631	0	0	0	0	0	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Frame_Shift_Del	DEL	ENST00000402038.3	37																																																																																				.		0.423	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		-	51028288	A	-	51028288	7	5	36	1	0	1	0	1	0	0	0	0	11474	246	9	0	239	0	PARG	10	51028288	Frame_Shift_Del	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10		51028288	84506459	65	3245	29	2									
PARG	8505	hgsc.bcm.edu;bcgsc.ca	37	chr10	51028292	51028292	+	Missense_Mutation	SNP	A	A	T																															tgagtccccaaaggtgaaatAaaccacatctcgctcagctg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:51028292A>T	ENST00000402038.3	-	13	1239	c.1240T>A	c.(1240-1242)Tat>Aat	p.Y414N		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	899	A-domain.			F -> L (in Ref. 3; AAB61614). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		AAGGTGAAATAAACCACATCT	0.418																																					p.Y899N		.											.	PARG-948	0			c.T2695A						.						129	108	114					10																	51028292		692	1591	2283	SO:0001583	missense	8505	exon17			TGAAATAAACCAC	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1240T>A	10.37:g.51028292A>T	ENSP00000384408:p.Tyr414Asn	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	77	22	NM_003631	0	0	3	3	0	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.5|28.5	4.922052|4.922052	0.92319|0.92319	.|.	.|.	ENSG00000227345|ENSG00000227345	ENST00000432127|ENST00000402038	.|.	.|.	.|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|.	.|.	.|.	.|.	D|D	0.84447|0.84447	0.5474|0.5474	M|M	0.87971|0.87971	2.92|2.92	.|.	.|.	.|.	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D	.|0.97110	.|0.999;1.0;0.999;0.999;0.999;0.999;1.0	D|D	0.87072|0.87072	0.2160|0.2160	4|7	.|0.87932	.|D	.|0	-13.0842|-13.0842	16.5582|16.5582	0.84512|0.84512	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|817;899;450;167;414;439;899	.|Q86W56-2;Q86W56;A5YBK3;B4DHS4;Q5SQP4;B4DX76;Q0MQR4	.|.;PARG_HUMAN;.;.;.;.;.	L|N	114|414	.|.	.|ENSP00000384408:Y414N	F|Y	-|-	3|1	2|0	PARG|PARG	50698298|50698298	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.383000|8.383000	0.90157|0.90157	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	TTT|TAT	.		0.418	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		T	51028292	A	T	51028292	3	4	36	1	0	0	0	0	1	0	0	0	11474	362	13	5	243	5	PARG	10	51028292	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	4	51028292	84506455	66	3246	29	2									
TET1	80312	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	70446307	70446307	+	Frame_Shift_Del	DEL	G	G	-																															aaaagaacgtgtttcactcaGcctgttccccgttctggaaa																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:70446307delG	ENST00000373644.4	+	11	5456	c.5247delG	c.(5245-5247)cagfs	p.Q1749fs		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1749					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GTTTCACTCAGCCTGTTCCCC	0.507																																					p.Q1749fs		.											.	TET1-663	0			c.5247delG						.						104	105	105					10																	70446307		2203	4300	6503	SO:0001589	frameshift_variant	80312	exon11			.	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5247delG	10.37:g.70446307delG	ENSP00000362748:p.Gln1749fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	136	44	NM_030625	0	0	0	0	0	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Frame_Shift_Del	DEL	ENST00000373644.4	37	CCDS7281.1																																																																																			.		0.507	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		-	70446307	G	-	70446307	7	5	36	1	0	1	0	1	0	0	0	0	15801	962	34	0	5285	0	TET1	10	70446307	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	19418015	70446307	65088440	67	3247											
MGEA5	10724	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103552626	103552626	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaaataaggtctgatagtAtaaactttggaggtaggagt	15	11	13	2	0	1	1	0	1	1	0	1	4	1	4	0	5	1	2	0	5	8	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:103552626A>G	ENST00000361464.3	-	12	2540	c.2145T>C	c.(2143-2145)taT>taC	p.Y715Y	MGEA5_ENST00000357797.5_Silent_p.Y648Y|MGEA5_ENST00000482611.1_5'UTR|MGEA5_ENST00000439817.1_Silent_p.Y662Y	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	715					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		GTCTGATAGTATAAACTTTGG	0.413																																					p.Y715Y													.	MGEA5-93	0			c.T2145C						.						149	147	148					10																	103552626		2203	4300	6503	SO:0001819	synonymous_variant	10724	exon12			GATAGTATAAACT	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"nuclear cytoplasmic O-GlcNAcase and acetyltransferase"	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.2145T>C	10.37:g.103552626A>G		Somatic	56	1		WXS	Illumina HiSeq	Phase_I	76	31	NM_012215	0	0	7	10	3	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Silent	SNP	ENST00000361464.3	37	CCDS7520.1																																																																																			.		0.413	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		G	103552626	A	G	103552626	2	3	36	1	0	0	0	0	0	0	0	1	9580	456	16	3		3	MGEA5	10	103552626	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	33106319	103552626	31982121	68	3248											
SMC3	9126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	112361757	112361757	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgagcagtgcaacacagaaTtaaagaagtacagccatgtt	16	9	9	7	0	0	3	0	1	0	2	0	3	0	3	1	0	5	4	1	0	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:112361757T>A	ENST00000361804.4	+	25	3052	c.2926T>A	c.(2926-2928)Tta>Ata	p.L976I		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	976					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		CAACACAGAATTAAAGAAGTA	0.303																																					p.L976I		.											.	SMC3-92	0			c.T2926A						.						46	48	47					10																	112361757		2201	4300	6501	SO:0001583	missense	9126	exon25			ACAGAATTAAAGA	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.2926T>A	10.37:g.112361757T>A	ENSP00000354720:p.Leu976Ile	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	47	9	NM_005445	0	0	10	19	9	A8K156|O60464|Q5T482	Missense_Mutation	SNP	ENST00000361804.4	37	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669080	0.67814	.	.	ENSG00000108055	ENST00000361804	T	0.76839	-1.05	5.32	1.32	0.21799	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.80243	0.4587	M	0.75884	2.315	0.80722	D	1	D	0.62365	0.991	D	0.63283	0.913	T	0.78021	-0.2367	10	0.07175	T	0.84	.	6.5259	0.22301	0.0:0.5503:0.0:0.4497	.	976	Q9UQE7	SMC3_HUMAN	I	976	ENSP00000354720:L976I	ENSP00000354720:L976I	L	+	1	2	SMC3	112351747	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	3.542000	0.53625	0.427000	0.26145	0.477000	0.44152	TTA	.		0.303	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		A	112361757	T	A	112361757	3	1	36	1	0	0	0	0	1	0	0	0	14816	1490	52	5	3024	5	SMC3	10	112361757	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	8809131	112361757	23172990	69	3249											
RAB11FIP2	22841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	119798692	119798692	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctaactttctcccttttCtctcttttattttcttttct	4	24	2	11	0	5	0	0	0	5	0	7	0	5	0	1	1	1	1	1	1	2	10			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:119798692C>A	ENST00000355624.3	-	3	1495	c.1056G>T	c.(1054-1056)gaG>gaT	p.E352D	RP11-354M20.3_ENST00000451610.2_RNA|RP11-354M20.3_ENST00000417968.4_RNA|RAB11FIP2_ENST00000369199.3_Missense_Mutation_p.E352D	NM_014904.2	NP_055719.1	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2 (class I)	352					establishment of cell polarity (GO:0030010)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(8)	19		Colorectal(252;0.235)		all cancers(201;0.0238)		TCTCCCTTTTCTCTCTTTTAT	0.353																																					p.E352D		.											.	RAB11FIP2-90	0			c.G1056T						.						150	161	157					10																	119798692		2202	4300	6502	SO:0001583	missense	22841	exon3			CCTTTTCTCTCTT	AY037299	CCDS7602.1	10q26.12	2004-07-22			ENSG00000107560	ENSG00000107560			29152	protein-coding gene	gene with protein product		608599				11994279, 10231032	Standard	NM_014904		Approved	KIAA0941, nRip11, Rab11-FIP2	uc001ldj.2	Q7L804	OTTHUMG00000019128	ENST00000355624.3:c.1056G>T	10.37:g.119798692C>A	ENSP00000347839:p.Glu352Asp	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	57	17	NM_014904	0	0	1	2	1	A6NEI4|Q3I768|Q9Y2F0	Missense_Mutation	SNP	ENST00000355624.3	37	CCDS7602.1	.	.	.	.	.	.	.	.	.	.	C	9.205	1.029505	0.19512	.	.	ENSG00000107560	ENST00000355624;ENST00000369199	T;T	0.66638	-0.21;-0.22	5.76	0.259	0.15583	.	0.171402	0.53938	D	0.000046	T	0.51584	0.1683	L	0.50333	1.59	0.44627	D	0.997603	B;B	0.16166	0.016;0.007	B;B	0.13407	0.009;0.004	T	0.27157	-1.0082	10	0.17369	T	0.5	-21.6296	6.802	0.23756	0.0:0.5332:0.1101:0.3567	.	352;352	Q3I768;Q7L804	.;RFIP2_HUMAN	D	352	ENSP00000347839:E352D;ENSP00000358200:E352D	ENSP00000347839:E352D	E	-	3	2	RAB11FIP2	119788682	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.171000	0.31896	0.067000	0.16545	-0.355000	0.07637	GAG	.		0.353	RAB11FIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050583.1	NM_014904		A	119798692	C	A	119798692	3	1	36	1	0	0	0	0	1	0	0	0	12926	912	32	4	494	4	RAB11FIP2	10	119798692	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	7436935	119798692	15736055	70	3250											
OR51E1	143503	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4674486	4674486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaggcatttggcacttgcGtctctcatgtgtgtgctgtg	5	14	12	10	1	2	0	1	0	1	0	3	0	2	0	1	2	2	3	1	2	1	2	rs148787592		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:4674486G>A	ENST00000396952.5	+	2	1380	c.730G>A	c.(730-732)Gtc>Atc	p.V244I	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V243I(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCACTTGCGTCTCTCATGT	0.498																																					p.V244I		.											.	OR51E1-114	1	Substitution - Missense(1)	large_intestine(1)	c.G730A						.	G	ILE/VAL	0,4402		0,0,2201	243	229	234		730	4	1	11	dbSNP_134	234	3,8593	3.0+/-9.4	0,3,4295	yes	missense	OR51E1	NM_152430.3	29	0,3,6496	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging	244/319	4674486	3,12995	2201	4298	6499	SO:0001583	missense	143503	exon2			ACTTGCGTCTCTC	AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"GPCR / Class A : Olfactory receptors"	15194	protein-coding gene	gene with protein product		611267	"olfactory receptor, family 51, subfamily E, member 1 pseudogene"	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000396952.5:c.730G>A	11.37:g.4674486G>A	ENSP00000380155:p.Val244Ile	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	77	26	NM_152430	0	0	0	0	0	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	37	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	G	9.642	1.139187	0.21205	0.0	3.49E-4	ENSG00000180785	ENST00000396952	T	0.37584	1.19	4.89	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.255092	0.27563	N	0.018809	T	0.18551	0.0445	N	0.20881	0.62	0.80722	D	1	P	0.43826	0.818	B	0.37239	0.244	T	0.05007	-1.0912	10	0.07644	T	0.81	.	9.4332	0.38624	0.1719:0.0:0.8281:0.0	.	243	Q8TCB6	O51E1_HUMAN	I	244	ENSP00000380155:V244I	ENSP00000380155:V244I	V	+	1	0	OR51E1	4631062	0.000000	0.05858	1.000000	0.80357	0.830000	0.47004	0.514000	0.22786	1.435000	0.47434	0.655000	0.94253	GTC	G|1.000;A|0.000		0.498	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430		A	4674486	G	A	4674486	3	1	36	1	0	0	0	0	1	0	0	0	11120	1145	40	1	732	1	OR51E1	11	4674486	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		4674486	130332030	71	3251											
ZDHHC5	25921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57466844	57466844	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaaaagcccaacctggtGtctctgagacagaagaagtg	14	6	11	10	0	1	3	0	1	1	3	2	4	1	3	3	1	2	0	3	1	5	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:57466844G>A	ENST00000287169.3	+	11	3298	c.1936G>A	c.(1936-1938)Gtc>Atc	p.V646I	ZDHHC5_ENST00000527985.1_Missense_Mutation_p.V593I	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	646					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						CCAACCTGGTGTCTCTGAGAC	0.527																																					p.V646I		.											.	ZDHHC5-226	0			c.G1936A						.						60	62	61					11																	57466844		2201	4296	6497	SO:0001583	missense	25921	exon11			CCTGGTGTCTCTG	AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"Zinc fingers, DHHC-type"	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.1936G>A	11.37:g.57466844G>A	ENSP00000287169:p.Val646Ile	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	33	13	NM_015457	0	0	36	74	38	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Missense_Mutation	SNP	ENST00000287169.3	37	CCDS7965.1	.	.	.	.	.	.	.	.	.	.	G	8.863	0.947386	0.18356	.	.	ENSG00000156599	ENST00000527985;ENST00000287169	T;T	0.57436	0.4;1.41	5.83	5.83	0.93111	.	1.629370	0.03465	N	0.212746	T	0.55242	0.1908	N	0.11427	0.14	0.43043	D	0.994634	P	0.42584	0.784	P	0.55391	0.775	T	0.48525	-0.9028	10	0.08381	T	0.77	-21.3343	17.8915	0.88874	0.0:0.0:1.0:0.0	.	646	Q9C0B5	ZDHC5_HUMAN	I	593;646	ENSP00000432202:V593I;ENSP00000287169:V646I	ENSP00000287169:V646I	V	+	1	0	ZDHHC5	57223420	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.646000	0.46630	2.769000	0.95229	0.655000	0.94253	GTC	.		0.527	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457		A	57466844	G	A	57466844	3	1	36	1	0	0	0	0	1	0	0	0	17650	1377	48	2	1974	2	ZDHHC5	11	57466844	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	52792358	57466844	77539672	72	3252											
ARL2	402	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64789247	64789247	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcatccagggctgcagcGccgtcaccggggagaacctg	7	5	16	13	3	1	1	1	0	0	1	2	2	2	1	4	4	4	3	4	4	1	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:64789247G>A	ENST00000246747.4	+	5	570	c.475G>A	c.(475-477)Gcc>Acc	p.A159T	ARL2_ENST00000533729.1_Missense_Mutation_p.A132T|RP11-399J13.3_ENST00000301886.3_Intron|ARL2_ENST00000529384.1_Missense_Mutation_p.A159T	NM_001667.3	NP_001658.2	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	159					cell cycle (GO:0007049)|centrosome organization (GO:0051297)|GTP catabolic process (GO:0006184)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of GTPase activity (GO:0034260)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of microtubule polymerization (GO:0031116)|regulation of microtubule polymerization (GO:0031113)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)|tubulin complex assembly (GO:0007021)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|GTPase inhibitor activity (GO:0005095)	p.A159T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	5						GGGCTGCAGCGCCGTCACCGG	0.627																																					p.A159T		.											.	ARL2-181	1	Substitution - Missense(1)	lung(1)	c.G475A						.						56	49	51					11																	64789247		2201	4297	6498	SO:0001583	missense	402	exon5			TGCAGCGCCGTCA	AF493888	CCDS8088.1, CCDS55770.1	11q13	2014-05-09			ENSG00000213465	ENSG00000213465		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	693	protein-coding gene	gene with protein product		601175				8415637, 9253601	Standard	NM_001667		Approved	ARFL2	uc001och.4	P36404	OTTHUMG00000165728	ENST00000246747.4:c.475G>A	11.37:g.64789247G>A	ENSP00000246747:p.Ala159Thr	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	25	12	NM_001667	0	0	203	404	201	G3V184|Q9BUK8	Missense_Mutation	SNP	ENST00000246747.4	37	CCDS8088.1	.	.	.	.	.	.	.	.	.	.	G	32	5.153338	0.94645	.	.	ENSG00000213465	ENST00000246747;ENST00000529384;ENST00000533729	D;D;D	0.91351	-2.83;-2.83;-2.83	4.5	4.5	0.54988	.	0.000000	0.85682	U	0.000000	D	0.96222	0.8768	H	0.94385	3.53	0.80722	D	1	D	0.71674	0.998	D	0.66196	0.942	D	0.97253	0.9899	10	0.87932	D	0	-17.1644	14.7471	0.69496	0.0:0.0:1.0:0.0	.	159	P36404	ARL2_HUMAN	T	159;159;132	ENSP00000246747:A159T;ENSP00000436021:A159T;ENSP00000432971:A132T	ENSP00000246747:A159T	A	+	1	0	ARL2	64545823	1.000000	0.71417	0.984000	0.44739	0.890000	0.51754	8.981000	0.93465	2.343000	0.79666	0.484000	0.47621	GCC	.		0.627	ARL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385963.1	NM_001667		A	64789247	G	A	64789247	3	1	36	1	0	0	0	0	1	0	0	0	934	1087	38	1	493	1	ARL2	11	64789247	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	7322403	64789247	70217269	73	3253											
IL10RA	3587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117869943	117869943	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagaagacccagctgctgtgGcattccagggttacctgagg	10	8	13	10	0	0	3	0	1	0	2	1	3	1	3	3	3	3	4	3	3	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:117869943G>T	ENST00000227752.3	+	7	1444	c.1324G>T	c.(1324-1326)Gca>Tca	p.A442S	IL10RA_ENST00000545409.1_Missense_Mutation_p.A293S|IL10RA_ENST00000541785.1_Missense_Mutation_p.A422S|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	442					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		AGCTGCTGTGGCATTCCAGGG	0.637																																					p.A442S		.											.	IL10RA-91	0			c.G1324T						.						79	77	78					11																	117869943		2200	4296	6496	SO:0001583	missense	3587	exon7			GCTGTGGCATTCC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1324G>T	11.37:g.117869943G>T	ENSP00000227752:p.Ala442Ser	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	63	18	NM_001558	0	0	3	3	0	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.007738	0.35415	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.24723	1.84;1.84;1.84	5.83	2.69	0.31865	.	4.801410	0.00447	N	0.000099	T	0.28566	0.0707	L	0.60455	1.87	0.09310	N	1	B;B	0.26845	0.161;0.1	B;B	0.23852	0.049;0.024	T	0.20605	-1.0270	10	0.41790	T	0.15	-4.9837	6.4798	0.22057	0.1701:0.1494:0.6805:0.0	.	422;442	F5GYV8;Q13651	.;I10R1_HUMAN	S	442;422;293;422	ENSP00000227752:A442S;ENSP00000441397:A422S;ENSP00000443019:A293S	ENSP00000227752:A442S	A	+	1	0	IL10RA	117375153	0.268000	0.24133	0.043000	0.18650	0.009000	0.06853	0.801000	0.27055	1.438000	0.47492	0.563000	0.77884	GCA	.		0.637	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869943	G	T	117869943	3	4	36	1	0	0	0	0	1	0	0	0	7641	1203	42	4	1350	4	IL10RA	11	117869943	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	53080696	117869943	17136573	74	3254											
TAS2R14	50840	broad.mit.edu;bcgsc.ca	37	chr12	11091488	11091488	+	Frame_Shift_Del	DEL	A	A	-																															attggctatcttgagaaaatAaaaagtaccgaggcctgtag																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr12:11091488delA	ENST00000537503.1	-	1	374	c.319delT	c.(319-321)tatfs	p.Y107fs	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	107					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						TTGAGAAAATAAAAAGTACCG	0.368																																					p.Y107fs													.	TAS2R14-90	0			c.319delT						.						47	49	48					12																	11091488		2201	4300	6501	SO:0001589	frameshift_variant	50840	exon1			GAAAATAAAAAGT	AF227138	CCDS8637.1	12p13	2012-08-22			ENSG00000212127	ENSG00000212127		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14920	protein-coding gene	gene with protein product		604790				10761934, 10766242	Standard	NM_023922		Approved	T2R14, TRB1	uc010shi.2	Q9NYV8	OTTHUMG00000162720	ENST00000537503.1:c.319delT	12.37:g.11091488delA	ENSP00000441949:p.Tyr107fs	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	13	5	NM_023922	0	0	0	0	0	Q645X3	Frame_Shift_Del	DEL	ENST00000537503.1	37	CCDS8637.1																																																																																			.		0.368	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922		-	11091488	A	-	11091488	7	5	36	1	0	1	0	1	0	0	0	0	15600	362	13	0	637	0	TAS2R14	12	11091488	Frame_Shift_Del	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10		11091488	122760407	75	3255											
NAB2	4665	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	57486863	57486863	+	Frame_Shift_Del	DEL	C	C	-																															caggttggagaacagagtcaCcctgaaatccagcagcctcc																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr12:57486863delC	ENST00000300131.3	+	5	1539	c.1161delC	c.(1159-1161)cacfs	p.H387fs	NAB2_ENST00000342556.6_Frame_Shift_Del_p.H387fs|NAB2_ENST00000357680.4_3'UTR	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	387					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AACAGAGTCACCCTGAAATCC	0.622																																					p.H387fs		.											.	NAB2-92	0			c.1161delC						.						108	118	115					12																	57486863		2203	4300	6503	SO:0001589	frameshift_variant	4665	exon5			.	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.1161delC	12.37:g.57486863delC	ENSP00000300131:p.His387fs	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	54	19	NM_005967	0	0	0	0	0	B2RAK3|O76006|Q14797	Frame_Shift_Del	DEL	ENST00000300131.3	37	CCDS8930.1																																																																																			.		0.622	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		-	57486863	C	-	57486863	7	5	36	1	0	1	0	1	0	0	0	0	10157	506	18	0	1179	0	NAB2	12	57486863	Frame_Shift_Del	DEL	C	TCGA-B1-A47M-01A-11D-A25F-10	46395375	57486863	76365032	76	3256											
SLC25A15	10166	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	41381598	41381598	+	Splice_Site	DEL	A	A	-																															gggagatcaaaagatgaattAggtaaatgtgtttgcattga																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr13:41381598delA	ENST00000338625.4	+	5	857	c.621delA	c.(619-621)tta>tt	p.L207fs	SLC25A15_ENST00000478827.1_3'UTR	NM_014252.3	NP_055067.1	Q9Y619	ORNT1_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15	207					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|L-ornithine transmembrane transport (GO:1903352)|mitochondrial ornithine transport (GO:0000066)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	L-ornithine transmembrane transporter activity (GO:0000064)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|stomach(1)|urinary_tract(1)	14		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	AAGATGAATTAGGTAAATGTG	0.473																																					p.L207fs		.											.	SLC25A15-226	0			c.621delA						.						129	122	124					13																	41381598		2203	4300	6503	SO:0001630	splice_region_variant	10166	exon5			.	AF112968	CCDS9373.1	13q14	2013-05-22			ENSG00000102743	ENSG00000102743		"Solute carriers"	10985	protein-coding gene	gene with protein product	"ornithine transporter 1"	603861		ORNT1, HHH		10369256	Standard	NM_014252		Approved	ORC1, D13S327	uc001uxn.3	Q9Y619	OTTHUMG00000016776	ENST00000338625.4:c.622+1A>-	13.37:g.41381598delA		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	63	29	NM_014252	0	0	0	0	0	Q5VZD8|Q9HC45	Frame_Shift_Del	DEL	ENST00000338625.4	37	CCDS9373.1																																																																																			.		0.473	SLC25A15-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276149.2	NM_014252	Frame_Shift_Del	-	41381598	A	-	41381598	8	5	36	1	0	1	0	1	0	0	1	0	14509	434	15	0	635	0	SLC25A15	13	41381598	Splice_Site	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10		41381598	73788280	77	3257											
DOCK9	23348	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99481633	99481633	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcttcctgagctcgggcgtGctggcataggatttggccag	5	11	15	10	2	1	1	0	1	1	0	3	2	2	2	2	4	2	3	2	4	1	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr13:99481633G>A	ENST00000376460.1	-	43	4904	c.4824C>T	c.(4822-4824)agC>agT	p.S1608S	DOCK9-AS1_ENST00000439367.1_RNA|DOCK9_ENST00000339416.2_Silent_p.S1609S|DOCK9_ENST00000448493.2_3'UTR	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1609	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCTCGGGCGTGCTGGCATAGG	0.582																																					.													.	DOCK9-90	0			.						.						74	73	73					13																	99481633		2078	4229	6307	SO:0001819	synonymous_variant	23348	.			GGGCGTGCTGGCA	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.4824C>T	13.37:g.99481633G>A		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	110	35	.	0	0	0	4	4	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	37	CCDS45062.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.208|9.208	1.030269|1.030269	0.19512|0.19512	.|.	.|.	ENSG00000088387|ENSG00000088387	ENST00000419908|ENST00000400228	.|.	.|.	.|.	5.77|5.77	4.93|4.93	0.64822|0.64822	.|.	.|.	.|.	.|.	.|.	T|T	0.56906|0.56906	0.2017|0.2017	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.55872|0.55872	-0.8072|-0.8072	4|4	.|.	.|.	.|.	.|.	7.1809|7.1809	0.25772|0.25772	0.2836:0.0:0.7164:0.0|0.2836:0.0:0.7164:0.0	.|.	.|.	.|.	.|.	V|Y	26|196	.|.	.|.	A|H	-|-	2|1	0|0	DOCK9|DOCK9	98279634|98279634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.771000|0.771000	0.43674|0.43674	2.620000|2.620000	0.46410|0.46410	1.567000|1.567000	0.49668|0.49668	0.655000|0.655000	0.94253|0.94253	GCA|CAC	.		0.582	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		A	99481633	G	A	99481633	2	1	36	1	0	0	0	0	0	0	0	1	4705	1310	46	2		2	DOCK9	13	99481633	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	58100035	99481633	15688245	78	3258											
CLEC14A	161198	broad.mit.edu	37	chr14	38724899	38724899	+	Frame_Shift_Del	DEL	A	A	-																															acagccaggagaaaccccgcAaaggctcgttctccagggtg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:38724899delA	ENST00000342213.2	-	1	675	c.329delT	c.(328-330)ttgfs	p.L110fs		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	110	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		GAAACCCCGCAAAGGCTCGTT	0.692																																					p.L110fs													.	CLEC14A-94	0			c.329delT						.						19	25	23					14																	38724899		2191	4281	6472	SO:0001589	frameshift_variant	161198	exon1			CCCCGCAAAGGCT		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.329delT	14.37:g.38724899delA	ENSP00000353013:p.Leu110fs	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_175060	0	0	0	0	0	Q695G9|Q6PWT6|Q8N5V5	Frame_Shift_Del	DEL	ENST00000342213.2	37	CCDS9667.1																																																																																			.		0.692	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		-	38724899	A	-	38724899	7	5	36	1	0	1	0	1	0	0	0	0	3505	131	5	0	1147	0	CLEC14A	14	38724899	Frame_Shift_Del	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10		38724899	68624641	79	3259											
FBXO33	254170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	39871674	39871674	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaaacttccttgctgttgtAgaacacttatgtctccaaaa	13	13	5	10	0	1	1	0	0	1	1	3	1	2	1	2	0	3	3	2	0	6	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:39871674A>G	ENST00000298097.7	-	2	978	c.641T>C	c.(640-642)cTa>cCa	p.L214P	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	214					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		TTGCTGTTGTAGAACACTTAT	0.308																																					p.L214P		.											.	FBXO33-658	0			c.T641C						.						100	92	95					14																	39871674		2203	4298	6501	SO:0001583	missense	254170	exon2			TGTTGTAGAACAC	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"F-boxes /  "other""	19833	protein-coding gene	gene with protein product		609103	"F-box only protein 33"				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.641T>C	14.37:g.39871674A>G	ENSP00000298097:p.Leu214Pro	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	20	6	NM_203301	0	0	0	0	0	Q6PIR2|Q86TR2|Q86YE0	Missense_Mutation	SNP	ENST00000298097.7	37	CCDS9677.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.366608	0.41902	.	.	ENSG00000165355	ENST00000298097	T	0.01279	5.06	6.08	6.08	0.98989	.	0.072360	0.56097	D	0.000025	T	0.02929	0.0087	L	0.32530	0.975	0.80722	D	1	P	0.50272	0.933	P	0.50440	0.641	T	0.69232	-0.5199	9	.	.	.	-1.7988	16.6438	0.85155	1.0:0.0:0.0:0.0	.	214	Q7Z6M2	FBX33_HUMAN	P	214	ENSP00000298097:L214P	.	L	-	2	0	FBXO33	38941425	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	8.486000	0.90451	2.333000	0.79357	0.533000	0.62120	CTA	.		0.308	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			G	39871674	A	G	39871674	3	3	36	1	0	0	0	0	1	0	0	0	5762	420	15	3	1038	3	FBXO33	14	39871674	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	1146775	39871674	67477866	80	3260											
L2HGDH	79944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	50713788	50713788	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcattatttataattcaaaTctttgttgtacttcatctgc	10	21	3	7	0	5	0	3	0	2	0	5	0	5	0	0	0	2	2	0	0	5	10			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:50713788T>C	ENST00000267436.4	-	10	1777	c.1380A>G	c.(1378-1380)agA>agG	p.R460R	L2HGDH_ENST00000421284.3_Silent_p.R460R|L2HGDH_ENST00000261699.4_Intron			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	460					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					ATAATTCAAATCTTTGTTGTA	0.328																																					p.R460R		.											.	L2HGDH-92	0			c.A1380G						.						49	48	49					14																	50713788		2203	4300	6503	SO:0001819	synonymous_variant	79944	exon10			TTCAAATCTTTGT		CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"2-hydroxyglutarate dehydrogenase"	609584	"chromosome 14 open reading frame 160"	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.1380A>G	14.37:g.50713788T>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	103	38	NM_024884	0	0	1	1	0	Q9BRR1	Silent	SNP	ENST00000267436.4	37	CCDS9698.1																																																																																			.		0.328	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884		C	50713788	T	C	50713788	2	2	36	1	0	0	0	0	0	0	0	1	8611	1432	50	3		3	L2HGDH	14	50713788	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	10842114	50713788	56635752	81	3261											
ADAM20	8748	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	70990728	70990729	+	Frame_Shift_Del	DEL	CT	CT	-																															ccagtcaaaattacatcaacCtccaaaggatgatagaagga																								rs112672973		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:70990728_70990729delCT	ENST00000256389.3	-	2	1140_1141	c.896_897delAG	c.(895-897)gagfs	p.E299fs	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	249	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TTACATCAACCTCCAAAGGATG	0.347																																					p.299_299del		.											.	ADAM20-226	0			c.896_897del						.																																			SO:0001589	frameshift_variant	8748	exon2			.	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.896_897delAG	14.37:g.70990728_70990729delCT	ENSP00000256389:p.Glu299fs	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_003814	0	0	0	0	0	Q6GTZ1|Q9UKJ9	Frame_Shift_Del	DEL	ENST00000256389.3	37	CCDS32111.1																																																																																			.		0.347	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			-	70990729	CT	-	70990728	7	5	36	1	0	1	0	1	0	0	0	0	242	680	24	0	1437	0	ADAM20	14	70990728	Frame_Shift_Del	DEL	CT	TCGA-B1-A47M-01A-11D-A25F-10	20276940	70990728	36358812	82	3262											
MAP3K9	4293	broad.mit.edu	37	chr14	71199898	71199898	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttggcgtcagctgaggggTactcgtggccgagttgactg	5	10	18	8	3	1	2	1	2	0	0	2	3	1	2	1	5	2	4	1	5	1	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:71199898T>G	ENST00000554752.2	-	11	2187	c.2188A>C	c.(2188-2190)Acc>Ccc	p.T730P	MAP3K9_ENST00000381250.4_Missense_Mutation_p.T707P|MAP3K9_ENST00000555993.2_Missense_Mutation_p.T744P|MAP3K9_ENST00000554146.1_Missense_Mutation_p.T458P|MAP3K9_ENST00000553414.1_Missense_Mutation_p.T463P	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	730					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		AGCTGAGGGGTACTCGTGGCC	0.652																																					p.T744P	GBM(114;411 1587 13539 28235 50070)												.	MAP3K9-546	0			c.A2230C						.						58	62	61					14																	71199898		2203	4300	6503	SO:0001583	missense	4293	exon12			GAGGGGTACTCGT	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2188A>C	14.37:g.71199898T>G	ENSP00000451612:p.Thr730Pro	Somatic	43	3		WXS	Illumina HiSeq	Phase_I	18	5	NM_033141	0	0	0	0	0	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	37		.	.	.	.	.	.	.	.	.	.	T	17.53	3.412471	0.62511	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	4.77	4.77	0.60923	.	0.219310	0.47093	D	0.000260	T	0.50752	0.1634	L	0.46157	1.445	0.35984	D	0.836233	D;P;D;D	0.76494	0.998;0.583;0.999;0.999	D;B;D;D	0.78314	0.953;0.263;0.95;0.991	T	0.55515	-0.8129	10	0.26408	T	0.33	.	14.4699	0.67509	0.0:0.0:0.0:1.0	.	458;730;744;463	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	P	730;744;463;707;458;446	ENSP00000451612:T730P;ENSP00000451038:T463P;ENSP00000370649:T707P;ENSP00000451921:T458P	ENSP00000005198:T744P	T	-	1	0	MAP3K9	70269651	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.682000	0.37628	2.007000	0.58848	0.459000	0.35465	ACC	.		0.652	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			G	71199898	T	G	71199898	3	3	36	1	0	0	0	0	1	0	0	0	9282	1638	57	5	1134	5	MAP3K9	14	71199898	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	209170	71199898	36149642	83	3263											
C14orf115	55237	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	74824279	74824279	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagccctggccccactcTcatcgccggccaagaccctg	6	7	8	20	2	1	1	1	0	1	1	4	1	2	1	7	2	1	0	7	2	1	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:74824279T>A	ENST00000256362.4	+	2	1034	c.793T>A	c.(793-795)Tca>Aca	p.S265T		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	265					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GGCCCCACTCTCATCGCCGGC	0.637																																					p.S265T		.											.	VRTN-155	0			c.T793A						.						39	39	39					14																	74824279		2203	4300	6503	SO:0001583	missense	55237	exon2			CCACTCTCATCGC	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.793T>A	14.37:g.74824279T>A	ENSP00000256362:p.Ser265Thr	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	47	18	NM_018228	0	0	0	0	0	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	37	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.670536	0.00758	.	.	ENSG00000133980	ENST00000256362	T	0.42131	0.98	4.34	2.42	0.29668	.	0.896444	0.09544	N	0.787929	T	0.20047	0.0482	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.12837	0.008	T	0.27191	-1.0081	10	0.18276	T	0.48	0.001	5.0154	0.14333	0.0:0.5664:0.2316:0.202	.	265	Q9H8Y1	VRTN_HUMAN	T	265	ENSP00000256362:S265T	ENSP00000256362:S265T	S	+	1	0	VRTN	73894032	0.614000	0.27017	0.014000	0.15608	0.005000	0.04900	2.793000	0.47845	0.762000	0.33152	-0.337000	0.08149	TCA	.		0.637	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		A	74824279	T	A	74824279	3	1	36	1	0	0	0	0	1	0	0	0	1744	1551	54	5	795	5	C14orf115	14	74824279	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	3624381	74824279	32525261	84	3264											
GALC	2581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	88412007	88412007	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgctcgccagggtcttcAatatttgtaaaatattcaaa	13	14	7	7	1	3	1	2	1	1	0	4	1	3	1	1	1	1	2	1	1	6	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:88412007A>C	ENST00000261304.2	-	14	1666	c.1560T>G	c.(1558-1560)atT>atG	p.I520M	GALC_ENST00000393569.2_Missense_Mutation_p.I494M|GALC_ENST00000544807.2_Missense_Mutation_p.I464M|GALC_ENST00000393568.4_Missense_Mutation_p.I497M	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	520					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAGGGTCTTCAATATTTGTAA	0.398																																					p.I520M		.											.	GALC-90	0			c.T1560G						.						88	87	87					14																	88412007		1838	4079	5917	SO:0001583	missense	2581	exon14			GTCTTCAATATTT	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1560T>G	14.37:g.88412007A>C	ENSP00000261304:p.Ile520Met	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	39	10	NM_000153	0	0	4	4	0	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	37	CCDS9878.2	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.451307	0.01080	.	.	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	5.51	-11.0	0.00169	.	2.091110	0.01473	N	0.016351	D	0.85796	0.5780	N	0.12746	0.255	0.09310	N	1	B;B;B;B	0.11235	0.004;0.001;0.002;0.001	B;B;B;B	0.15052	0.007;0.012;0.012;0.012	T	0.76288	-0.3014	10	0.46703	T	0.11	4.0145	13.9406	0.64052	0.283:0.3027:0.4142:0.0	.	464;497;494;520	P54803-5;E7EPA4;P54803-4;P54803	.;.;.;GALC_HUMAN	M	520;464;494;309;497	ENSP00000261304:I520M;ENSP00000437513:I464M;ENSP00000377199:I494M;ENSP00000377198:I497M	ENSP00000261304:I520M	I	-	3	3	GALC	87481760	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.299000	0.01139	-6.093000	0.00006	-2.649000	0.00149	ATT	.		0.398	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2			C	88412007	A	C	88412007	3	2	36	1	0	0	0	0	1	0	0	0	6221	126	5	5	513	5	GALC	14	88412007	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	13587728	88412007	18937533	85	3265											
CALM1	801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	90870815	90870815	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagaagtagatgaaatgatCagagaagcagatattgatgg	18	8	13	2	0	1	7	1	3	0	4	1	9	1	7	0	1	1	2	0	1	6	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:90870815C>T	ENST00000356978.4	+	5	626	c.378C>T	c.(376-378)atC>atT	p.I126I	CALM1_ENST00000447653.3_Silent_p.I127I|CALM1_ENST00000553542.1_Silent_p.I90I|RP11-471B22.2_ENST00000555853.1_RNA|CALM1_ENST00000544280.2_Silent_p.I90I	NM_006888.4	NP_008819.1	P62158	CALM_HUMAN	calmodulin 1 (phosphorylase kinase, delta)	126	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|detection of calcium ion (GO:0005513)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide metabolic process (GO:0046209)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cyclic nucleotide metabolic process (GO:0030801)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cytokinesis (GO:0032465)|regulation of heart rate (GO:0002027)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcomere (GO:0030017)|spindle microtubule (GO:0005876)|spindle pole (GO:0000922)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|N-terminal myristoylation domain binding (GO:0031997)|nitric-oxide synthase regulator activity (GO:0030235)|phospholipase binding (GO:0043274)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|protein phosphatase activator activity (GO:0072542)|protein serine/threonine kinase activator activity (GO:0043539)|thioesterase binding (GO:0031996)|titin binding (GO:0031432)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	10		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.208)	Aprindine(DB01429)|Bepridil(DB01244)|Chlorpromazine(DB00477)|Cinchocaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Melatonin(DB01065)|Nicardipine(DB00622)|Nifedipine(DB01115)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)|Trifluoperazine(DB00831)	ATGAAATGATCAGAGAAGCAG	0.388																																					p.I126I		.											.	CALM1-90	0			c.C378T						.						135	127	130					14																	90870815		2203	4300	6503	SO:0001819	synonymous_variant	801	exon5			AATGATCAGAGAA		CCDS9892.1	14q32.11	2013-02-25			ENSG00000198668	ENSG00000198668	2.7.11.19	"EF-hand domain containing", "Endogenous ligands"	1442	protein-coding gene	gene with protein product	"prepro-calmodulin 1"	114180		CALML2		6385987	Standard	NM_006888		Approved	CAMI, PHKD, DD132	uc001xyl.2	P62158	OTTHUMG00000171044	ENST00000356978.4:c.378C>T	14.37:g.90870815C>T		Somatic	173	0		WXS	Illumina HiSeq	Phase_I	149	38	NM_006888	0	0	173	287	114	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000356978.4	37	CCDS9892.1																																																																																			.		0.388	CALM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411346.1			T	90870815	C	T	90870815	2	4	36	1	0	0	0	0	0	0	0	1	2590	816	29	2		2	CALM1	14	90870815	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	2458808	90870815	16478725	86	3266											
ATP10A	57194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	25981205	25981205	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagacacacgatactcacatGcagccgcgaaacctactcag	14	5	7	15	3	2	1	2	0	0	1	2	3	2	1	2	0	5	1	2	0	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr15:25981205G>A	ENST00000356865.6	-	3	849	c.738C>T	c.(736-738)tgC>tgT	p.C246C	RNA5SP390_ENST00000410191.1_RNA	NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	246					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ATACTCACATGCAGCCGCGAA	0.448																																					p.C246C		.											.	ATP10A-139	0			c.C738T						.						148	100	116					15																	25981205		2203	4300	6503	SO:0001819	synonymous_variant	57194	exon3			TCACATGCAGCCG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.738C>T	15.37:g.25981205G>A		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	99	38	NM_024490	0	0	0	0	0	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			.		0.448	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25981205	G	A	25981205	2	1	36	1	0	0	0	0	0	0	0	1	1117	1311	46	2		2	ATP10A	15	25981205	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		25981205	76550187	87	3267											
SECISBP2L	9728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	49293279	49293279	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcaatctctttacaaagAacctgattacaatacctgta	15	13	3	10	0	3	2	2	1	1	1	4	2	3	2	2	0	4	1	2	0	8	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr15:49293279A>C	ENST00000559471.1	-	15	2306	c.2043T>G	c.(2041-2043)gtT>gtG	p.V681V	SECISBP2L_ENST00000559122.1_5'UTR|SECISBP2L_ENST00000261847.3_Silent_p.V636V	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	681							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						CTTTACAAAGAACCTGATTAC	0.338																																					p.V681V		.											.	SECISBP2L-136	0			c.T2043G						.						60	54	56					15																	49293279		2197	4295	6492	SO:0001819	synonymous_variant	9728	exon15			ACAAAGAACCTGA	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2043T>G	15.37:g.49293279A>C		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	42	16	NM_001193489	0	0	1	1	0	Q8N767	Silent	SNP	ENST00000559471.1	37	CCDS53942.1																																																																																			.		0.338	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		C	49293279	A	C	49293279	2	2	36	1	0	0	0	0	0	0	0	1	14039	233	9	5		5	SECISBP2L	15	49293279	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	23312074	49293279	53238113	88	3268											
TEX9	374618	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	56686956	56686956	+	Frame_Shift_Del	DEL	A	A	-																															tatgcaacagtctcaagtagAaaaatacaaaactcttttcg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr15:56686956delA	ENST00000352903.2	+	9	776	c.752delA	c.(751-753)gaafs	p.E251fs	TEX9_ENST00000537232.1_Frame_Shift_Del_p.E176fs|RP11-48G14.2_ENST00000564401.1_lincRNA|TEX9_ENST00000561221.2_Frame_Shift_Del_p.E251fs|TEX9_ENST00000558083.2_Frame_Shift_Del_p.E176fs|TEX9_ENST00000560582.1_Frame_Shift_Del_p.E7fs	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	251										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TCTCAAGTAGAAAAATACAAA	0.303																																					p.E251fs		.											.	TEX9-90	0			c.752delA						.						46	50	49					15																	56686956		2191	4284	6475	SO:0001589	frameshift_variant	374618	exon9			.	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"testis expressed sequence 9"				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.752delA	15.37:g.56686956delA	ENSP00000342169:p.Glu251fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	85	29	NM_198524	0	0	0	0	0	B4DH73	Frame_Shift_Del	DEL	ENST00000352903.2	37	CCDS10157.1																																																																																			.		0.303	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		-	56686956	A	-	56686956	7	5	36	1	0	1	0	1	0	0	0	0	15816	246	9	0	786	0	TEX9	15	56686956	Frame_Shift_Del	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10	7393677	56686956	45844436	89	3269											
ARL2BP	23568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57283687	57283687	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccactgttgcagatttctttGgtagaaaaatacattgaaga	14	13	8	6	0	1	4	0	1	1	3	1	4	1	4	1	1	2	3	1	1	5	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr16:57283687G>T	ENST00000219204.3	+	4	486	c.216G>T	c.(214-216)ttG>ttT	p.L72F	RP11-407G23.4_ENST00000562409.1_RNA|RP11-407G23.3_ENST00000564376.1_RNA|ARL2BP_ENST00000562023.1_Intron	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	72					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						AGATTTCTTTGGTAGAAAAAT	0.423																																					p.L72F		.											.	ARL2BP-90	0			c.G216T						.						126	128	127					16																	57283687		2198	4300	6498	SO:0001583	missense	23568	exon4			TTCTTTGGTAGAA	AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"binder of Arl2"	615407	"retinitis pigmentosa 66 (autosomal recessive)"	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.216G>T	16.37:g.57283687G>T	ENSP00000219204:p.Leu72Phe	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	50	7	NM_012106	0	0	0	1	1	B3KQJ5|Q504R0	Missense_Mutation	SNP	ENST00000219204.3	37	CCDS10776.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.139821	0.56936	.	.	ENSG00000102931	ENST00000219204	T	0.54071	0.59	5.95	2.95	0.34219	ADP-ribosylation factor-like 2-binding protein, domain (2);	0.127524	0.37095	U	0.002259	T	0.70360	0.3215	M	0.88310	2.945	0.80722	D	1	D;D	0.71674	0.998;0.991	D;D	0.70716	0.97;0.934	T	0.68372	-0.5426	10	0.62326	D	0.03	-7.9781	5.1654	0.15082	0.2858:0.0:0.5774:0.1368	.	40;72	B4DQD8;Q9Y2Y0	.;AR2BP_HUMAN	F	72	ENSP00000219204:L72F	ENSP00000219204:L72F	L	+	3	2	ARL2BP	55841188	1.000000	0.71417	0.996000	0.52242	0.684000	0.39900	2.160000	0.42348	0.418000	0.25898	0.655000	0.94253	TTG	.		0.423	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106		T	57283687	G	T	57283687	3	4	36	1	0	0	0	0	1	0	0	0	935	1339	47	4	230	4	ARL2BP	16	57283687	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		57283687	33071066	90	3270											
KCTD11	147040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7256621	7256621	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagctccgtccaggtggaCaccttccgagccaacctttt	7	10	9	15	2	0	1	0	1	0	0	3	3	3	2	6	2	3	1	6	2	1	3	rs79616684		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:7256621C>T	ENST00000333751.3	+	1	1414	c.360C>T	c.(358-360)gaC>gaT	p.D120D	TMEM95_ENST00000330767.4_5'Flank|TMEM95_ENST00000576060.1_5'Flank|RP11-542C16.1_ENST00000572417.1_RNA|TMEM95_ENST00000389982.4_5'Flank	NM_001002914.2	NP_001002914.1	Q693B1	KCD11_HUMAN	potassium channel tetramerization domain containing 11	120					cell cycle (GO:0007049)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)				kidney(1)|large_intestine(2)|lung(1)	4		Prostate(122;0.157)				TCCAGGTGGACACCTTCCGAG	0.627																																					p.D120D		.											.	KCTD11-90	0			c.C360T						.						89	72	78					17																	7256621		2203	4300	6503	SO:0001819	synonymous_variant	147040	exon1			GGTGGACACCTTC	AK056227	CCDS32545.1	17p13.2	2013-06-20	2013-06-20	2003-11-26	ENSG00000213859	ENSG00000213859			21302	protein-coding gene	gene with protein product		609848	"chromosome 17 open reading frame 36", "potassium channel tetramerisation domain containing 11"	C17orf36		12186855, 21472142	Standard	NM_001002914		Approved	REN, KCASH1	uc002gge.4	Q693B1	OTTHUMG00000132061	ENST00000333751.3:c.360C>T	17.37:g.7256621C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	62	17	NM_001002914	0	0	34	42	8	B3KPE0	Silent	SNP	ENST00000333751.3	37	CCDS32545.1																																																																																			C|0.500;T|0.500		0.627	KCTD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255084.2	NM_001002914		T	7256621	C	T	7256621	2	4	36	1	0	0	0	0	0	0	0	1	8119	477	17	2		2	KCTD11	17	7256621	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		7256621	73938589	91	3271											
PEX12	5193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33904481	33904481	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattctctttaagccgtaaaAgttttcagaaaatgaggcac	15	12	7	7	1	2	2	1	1	1	1	3	2	2	2	1	1	1	3	1	1	6	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:33904481A>C	ENST00000225873.4	-	2	863	c.256T>G	c.(256-258)Ttt>Gtt	p.F86V	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	86					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAGCCGTAAAAGTTTTCAGAA	0.423																																					p.F86V		.											.	PEX12-90	0			c.T256G						.						149	167	161					17																	33904481		2203	4300	6503	SO:0001583	missense	5193	exon2			CGTAAAAGTTTTC	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.256T>G	17.37:g.33904481A>C	ENSP00000225873:p.Phe86Val	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	37	11	NM_000286	0	0	1	4	3	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	37	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.845090	0.91197	.	.	ENSG00000108733	ENST00000424525;ENST00000225873	D	0.85171	-1.95	5.63	5.63	0.86233	Pex, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93093	0.7801	M	0.86420	2.815	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94107	0.7367	10	0.72032	D	0.01	-21.3132	15.0234	0.71650	1.0:0.0:0.0:0.0	.	86	O00623	PEX12_HUMAN	V	86	ENSP00000225873:F86V	ENSP00000225873:F86V	F	-	1	0	PEX12	30928594	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.736000	0.74811	2.142000	0.66516	0.528000	0.53228	TTT	.		0.423	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		C	33904481	A	C	33904481	3	2	36	1	0	0	0	0	1	0	0	0	11766	72	3	5	831	5	PEX12	17	33904481	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	26647860	33904481	47290729	92	3272											
CDC6	990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38447445	38447445	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacaatcagctgacaattaAgtctcctagcaaaagagaac	17	8	7	9	0	2	3	1	2	1	1	3	4	2	3	1	0	3	2	1	0	7	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:38447445A>G	ENST00000209728.4	+	3	785	c.314A>G	c.(313-315)aAg>aGg	p.K105R		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	105					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						CTGACAATTAAGTCTCCTAGC	0.398																																					p.K105R		.											.	CDC6-662	0			c.A314G						.						121	110	114					17																	38447445		2203	4300	6503	SO:0001583	missense	990	exon3			CAATTAAGTCTCC	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"CDC6 (cell division cycle 6, S. cerevisiae) homolog", "CDC6 cell division cycle 6 homolog (S. cerevisiae)", "cell division cycle 6 homolog (S. cerevisiae)"	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.314A>G	17.37:g.38447445A>G	ENSP00000209728:p.Lys105Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	120	14	NM_001254	0	0	0	0	0	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.819366	0.32145	.	.	ENSG00000094804	ENST00000209728	T	0.51071	0.72	5.52	4.25	0.50352	.	0.245750	0.38959	N	0.001502	T	0.36166	0.0957	M	0.63428	1.95	0.22666	N	0.998871	B	0.14805	0.011	B	0.10450	0.005	T	0.24476	-1.0159	10	0.09338	T	0.73	-12.0983	4.517	0.11939	0.7131:0.0:0.1193:0.1676	.	105	Q99741	CDC6_HUMAN	R	105	ENSP00000209728:K105R	ENSP00000209728:K105R	K	+	2	0	CDC6	35700971	0.007000	0.16637	0.979000	0.43373	0.951000	0.60555	0.662000	0.25038	2.227000	0.72691	0.454000	0.30748	AAG	.		0.398	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			G	38447445	A	G	38447445	3	3	36	1	0	0	0	0	1	0	0	0	3089	72	3	3	320	3	CDC6	17	38447445	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	4542964	38447445	42747765	93	3273											
HDAC5	10014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42160014	42160014	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtaggagttttgcggtgatgGctacagagttgaagaagcag	11	10	16	4	1	0	4	0	2	0	2	0	5	0	5	0	3	3	5	0	3	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:42160014G>C	ENST00000393622.2	-	20	2877	c.2546C>G	c.(2545-2547)gCc>gGc	p.A849G	HDAC5_ENST00000336057.5_Missense_Mutation_p.A764G|HDAC5_ENST00000586802.1_Missense_Mutation_p.A849G|HDAC5_ENST00000225983.6_Missense_Mutation_p.A850G	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	849	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TGCGGTGATGGCTACAGAGTT	0.592																																					p.A850G		.											.	HDAC5-227	0			c.C2549G						.						104	91	95					17																	42160014		2203	4300	6503	SO:0001583	missense	10014	exon20			GTGATGGCTACAG	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2546C>G	17.37:g.42160014G>C	ENSP00000377244:p.Ala849Gly	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	176	51	NM_001015053	0	0	32	43	11	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	37	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	32	5.172286	0.94807	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.74737	-0.87;-0.87;-0.87	4.98	4.98	0.66077	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.89093	0.6617	M	0.91818	3.245	0.80722	D	1	D;D;P;B	0.69078	0.987;0.997;0.512;0.235	D;D;P;P	0.87578	0.976;0.998;0.511;0.744	D	0.91712	0.5382	10	0.87932	D	0	-14.2335	17.0238	0.86440	0.0:0.0:1.0:0.0	.	764;849;850;849	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	G	850;849;764	ENSP00000225983:A850G;ENSP00000377244:A849G;ENSP00000337290:A764G	ENSP00000225983:A850G	A	-	2	0	HDAC5	39515540	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.842000	0.99487	2.317000	0.78254	0.561000	0.74099	GCC	.		0.592	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		C	42160014	G	C	42160014	3	2	36	1	0	0	0	0	1	0	0	0	7031	1203	42	4	854	4	HDAC5	17	42160014	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	3712569	42160014	39035196	94	3274											
USP32	84669	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58288852	58288852	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcccagattgcttagacCtgtggctcccttttctgtgg	4	16	10	11	0	1	2	0	0	1	2	3	2	3	2	3	2	1	3	3	2	1	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:58288852C>A	ENST00000300896.4	-	20	2397	c.2203G>T	c.(2203-2205)Ggt>Tgt	p.G735C	USP32_ENST00000592339.1_Missense_Mutation_p.G405C	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	735	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			TTGCTTAGACCTGTGGCTCCC	0.413																																					p.G735C													.	USP32-704	0			c.G2203T						.						174	161	165					17																	58288852		2202	4300	6502	SO:0001583	missense	84669	exon20			TTAGACCTGTGGC	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.2203G>T	17.37:g.58288852C>A	ENSP00000300896:p.Gly735Cys	Somatic	189	1		WXS	Illumina HiSeq	Phase_I	221	70	NM_032582	0	0	1	1	0	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667058	0.88251	.	.	ENSG00000170832	ENST00000300896	D	0.88741	-2.42	5.39	5.39	0.77823	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.96321	0.8800	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97241	0.9891	10	0.87932	D	0	.	19.1546	0.93504	0.0:1.0:0.0:0.0	.	735	Q8NFA0	UBP32_HUMAN	C	735	ENSP00000300896:G735C	ENSP00000300896:G735C	G	-	1	0	USP32	55643634	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.770000	0.85390	2.537000	0.85549	0.655000	0.94253	GGT	.		0.413	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		A	58288852	C	A	58288852	3	1	36	1	0	0	0	0	1	0	0	0	17096	681	24	4	2671	4	USP32	17	58288852	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	16128838	58288852	22906358	95	3275											
NOL11	25926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65739904	65739904	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agattgaagtaagttttcggGagctacagaaattaaatcaa	17	11	9	4	1	1	3	1	1	0	2	2	4	1	4	0	1	2	3	0	1	7	6	rs370393293		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:65739904G>A	ENST00000253247.4	+	18	2204	c.2089G>A	c.(2089-2091)Gag>Aag	p.E697K	NOL11_ENST00000535137.1_Missense_Mutation_p.E515K|SNORA38B_ENST00000363524.1_RNA	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	697					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAGTTTTCGGGAGCTACAGAA	0.299																																					p.E697K		.											.	NOL11-90	0			c.G2089A						.	G	LYS/GLU	0,4404		0,0,2202	45	49	47		2089	4.2	1	17		47	1,8595	1.2+/-3.3	0,1,4297	no	missense	NOL11	NM_015462.3	56	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	697/720	65739904	1,12999	2202	4298	6500	SO:0001583	missense	25926	exon18			TTTCGGGAGCTAC	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.2089G>A	17.37:g.65739904G>A	ENSP00000253247:p.Glu697Lys	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	36	9	NM_015462	0	0	55	85	30	B7Z5V9|Q7L5S1|Q9UG18	Missense_Mutation	SNP	ENST00000253247.4	37	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.954162	0.73902	0.0	1.16E-4	ENSG00000130935	ENST00000253247;ENST00000535137	T	0.48836	0.8	5.27	4.25	0.50352	.	0.057766	0.64402	D	0.000002	T	0.51686	0.1689	M	0.74258	2.255	0.50813	D	0.999891	P	0.48294	0.908	B	0.44224	0.444	T	0.59994	-0.7349	10	0.56958	D	0.05	-20.9764	13.8316	0.63384	0.0:0.1531:0.8468:0.0	.	697	Q9H8H0	NOL11_HUMAN	K	697;515	ENSP00000253247:E697K	ENSP00000253247:E697K	E	+	1	0	NOL11	63170366	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.909000	0.63314	2.626000	0.88956	0.655000	0.94253	GAG	.		0.299	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		A	65739904	G	A	65739904	3	1	36	1	0	0	0	0	1	0	0	0	10547	1175	41	2	2159	2	NOL11	17	65739904	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	7451052	65739904	15455306	96	3276											
LGALS3BP	3959	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	76967786	76967786	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtccagggcactgggaaTcgcagccttccagccctcga	7	7	13	14	2	0	0	0	0	0	0	4	2	2	1	4	3	2	2	4	3	1	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:76967786T>C	ENST00000262776.3	-	6	1938	c.1630A>G	c.(1630-1632)Att>Gtt	p.I544V	LGALS3BP_ENST00000591778.1_3'UTR	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	544					cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GCACTGGGAATCGCAGCCTTC	0.612											OREG0024787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I544V	GBM(89;1105 1755 18102 21513)												.	LGALS3BP-515	0			c.A1630G						.						75	70	71					17																	76967786		2203	4300	6503	SO:0001583	missense	3959	exon6			TGGGAATCGCAGC	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"BTB/POZ domain containing", "Endogenous ligands"	6564	protein-coding gene	gene with protein product	"L3 antigen", "Mac-2-binding protein", "serum protein 90K", "transport and golgi organization 10 homolog B (Drosophila)"	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.1630A>G	17.37:g.76967786T>C	ENSP00000262776:p.Ile544Val	Somatic	88	1	1172	WXS	Illumina HiSeq	Phase_I	62	8	NM_005567	1	1	1545	2323	776	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	37	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	T	8.701	0.909734	0.17833	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.01455	4.87	3.52	-1.89	0.07689	.	0.725701	0.11232	N	0.585521	T	0.01730	0.0055	L	0.43152	1.355	0.21386	N	0.999705	B	0.09022	0.002	B	0.06405	0.002	T	0.43065	-0.9414	10	0.33141	T	0.24	-20.4235	5.8589	0.18734	0.0:0.1105:0.5287:0.3609	.	544	Q08380	LG3BP_HUMAN	V	544;532	ENSP00000262776:I544V	ENSP00000262776:I544V	I	-	1	0	LGALS3BP	74479381	0.000000	0.05858	0.003000	0.11579	0.045000	0.14185	-0.750000	0.04808	-0.411000	0.07530	0.459000	0.35465	ATT	.		0.612	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		C	76967786	T	C	76967786	3	2	36	1	0	0	0	0	1	0	0	0	8765	1435	50	3	131	3	LGALS3BP	17	76967786	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	11227882	76967786	4227424	97	3277											
THOC1	9984	bcgsc.ca	37	chr18	254346	254346	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagattaaactgactctgcAagttaagacctagtaaaaaa	18	9	6	8	0	1	3	0	1	1	2	1	3	1	3	2	0	2	3	2	0	8	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:254346A>G	ENST00000261600.6	-	8	537	c.530T>C	c.(529-531)tTg>tCg	p.L177S	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	177					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CTGACTCTGCAAGTTAAGACC	0.363																																					p.L177S													.	THOC1-91	0			c.T530C						.						73	63	66					18																	254346		1857	4074	5931	SO:0001583	missense	9984	exon8			CTCTGCAAGTTAA	AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"THO complex subunits"	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.530T>C	18.37:g.254346A>G	ENSP00000261600:p.Leu177Ser	Somatic	19	0		WXS	Illumina HiSeq	Phase_1	18	4	NM_005131	0	0	0	0	0	B2RBP6|Q15219|Q64I72|Q64I73	Missense_Mutation	SNP	ENST00000261600.6	37	CCDS45820.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.333686	0.81801	.	.	ENSG00000079134	ENST00000261600	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.80696	0.4672	M	0.79926	2.475	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.83306	-0.0025	9	0.87932	D	0	-9.0323	16.3947	0.83586	1.0:0.0:0.0:0.0	.	177;177	Q96FV9-2;Q96FV9	.;THOC1_HUMAN	S	177	.	ENSP00000261600:L177S	L	-	2	0	THOC1	244346	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.962000	0.93254	2.272000	0.75746	0.459000	0.35465	TTG	.		0.363	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		G	254346	A	G	254346	3	3	36	1	0	0	0	0	1	0	0	0	15896	131	5	3	1499	3	THOC1	18	254346	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		254346	77822902	98	3278											
TTR	7276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	29178601	29178601	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgctgagcccctactcctAttccaccacggctgtcgtca	6	10	7	18	2	1	1	1	1	0	0	4	1	3	1	6	1	3	2	6	1	2	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:29178601A>G	ENST00000237014.3	+	4	584	c.407A>G	c.(406-408)tAt>tGt	p.Y136C		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	136	Thyroid hormone binding.		Y -> S (in AMYL-TTR; amyloid polyneuropathy). {ECO:0000269|PubMed:10627135}.|Y -> V (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3675594}.		extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)			cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CCCTACTCCTATTCCACCACG	0.552																																					p.Y136C		.											.	TTR-91	0			c.A407G	GRCh37	CM971541	TTR	M		.						80	67	72					18																	29178601		2203	4300	6503	SO:0001583	missense	7276	exon4			ACTCCTATTCCAC	M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"prealbumin, amyloidosis type I", "carpal tunnel syndrome 1"	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.407A>G	18.37:g.29178601A>G	ENSP00000237014:p.Tyr136Cys	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	78	21	NM_000371	0	0	0	0	0	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Missense_Mutation	SNP	ENST00000237014.3	37	CCDS11899.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.089090	0.55968	.	.	ENSG00000118271	ENST00000237014;ENST00000432547;ENST00000541025	D	0.98120	-4.73	6.08	3.5	0.40072	Transthyretin, conserved site (1);Transthyretin/hydroxyisourate hydrolase, superfamily (4);	0.246709	0.42294	D	0.000722	D	0.98957	0.9645	H	0.96301	3.8	0.52501	D	0.999955	D	0.89917	1.0	D	0.87578	0.998	D	0.98496	1.0612	10	0.87932	D	0	-18.6558	10.7142	0.46002	0.7084:0.0:0.0:0.2916	.	136	P02766	TTHY_HUMAN	C	136;173;128	ENSP00000237014:Y136C	ENSP00000237014:Y136C	Y	+	2	0	TTR	27432599	0.995000	0.38212	0.908000	0.35775	0.474000	0.32979	3.175000	0.50855	2.333000	0.79357	0.482000	0.46254	TAT	.		0.552	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371		G	29178601	A	G	29178601	3	3	36	1	0	0	0	0	1	0	0	0	16771	449	16	3	421	3	TTR	18	29178601	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	28924255	29178601	48898647	99	3279											
C18orf21	83608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	33558958	33558958	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcttctctgaagggtggaCttttaaaataagaaatgcct	13	14	8	6	0	2	2	0	1	2	1	3	3	2	3	1	2	1	0	1	2	6	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:33558958C>G	ENST00000592875.1	+	5	1298	c.652C>G	c.(652-654)Ctt>Gtt	p.L218V	C18orf21_ENST00000333234.5_Missense_Mutation_p.L130V	NM_031446.4	NP_113634.3	Q32NC0	CR021_HUMAN	chromosome 18 open reading frame 21	218										endometrium(1)|kidney(1)|large_intestine(1)|skin(2)	5						GAAGGGTGGACTTTTAAAATA	0.308																																					p.L218V		.											.	C18orf21-90	0			c.C652G						.						50	54	53					18																	33558958		2202	4300	6502	SO:0001583	missense	83608	exon5			GGTGGACTTTTAA	BC025950	CCDS11916.2, CCDS56064.1, CCDS74212.1	18q12.2	2004-05-05			ENSG00000141428	ENSG00000141428			28802	protein-coding gene	gene with protein product						12477932	Standard	NM_031446		Approved	PNAS-131, PNAS-124, HsT3108	uc002kzc.3	Q32NC0	OTTHUMG00000128531	ENST00000592875.1:c.652C>G	18.37:g.33558958C>G	ENSP00000465517:p.Leu218Val	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	54	17	NM_031446	0	0	16	25	9	Q6GW03|Q9BXV6|Q9BXW2	Missense_Mutation	SNP	ENST00000592875.1	37	CCDS11916.2	.	.	.	.	.	.	.	.	.	.	C	14.98	2.697544	0.48307	.	.	ENSG00000141428	ENST00000333234;ENST00000269194	.	.	.	5.34	1.6	0.23607	.	.	.	.	.	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.18741	0.03	B	0.21151	0.033	T	0.20405	-1.0276	8	0.87932	D	0	.	3.9349	0.09301	0.1694:0.5002:0.0:0.3305	.	218	Q32NC0	CR021_HUMAN	V	218;130	.	ENSP00000269194:L130V	L	+	1	0	C18orf21	31812956	0.136000	0.22515	0.033000	0.17914	0.167000	0.22549	-0.006000	0.12833	0.641000	0.30601	0.655000	0.94253	CTT	.		0.308	C18orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250364.1	NM_031446		G	33558958	C	G	33558958	3	3	36	1	0	0	0	0	1	0	0	0	1903	565	20	4	670	4	C18orf21	18	33558958	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	4380357	33558958	44518290	100	3280											
MYO5B	4645	broad.mit.edu	37	chr18	47511190	47511190	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtatagaaaaagtcctctgCacttgctgtgggaggcgagg	10	10	14	7	1	1	1	0	0	1	1	2	3	2	2	1	3	2	3	1	3	4	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:47511190C>A	ENST00000285039.7	-	8	1143	c.844G>T	c.(844-846)Gca>Tca	p.A282S		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	282	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		AAGTCCTCTGCACTTGCTGTG	0.502																																					p.A282S													.	MYO5B-72	0			c.G844T						.						81	83	82					18																	47511190		1992	4174	6166	SO:0001583	missense	4645	exon8			CCTCTGCACTTGC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.844G>T	18.37:g.47511190C>A	ENSP00000285039:p.Ala282Ser	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	124	5	NM_001080467	0	0	0	0	0	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550068	0.86127	.	.	ENSG00000167306	ENST00000285039;ENST00000356732	D	0.95482	-3.72	5.51	4.62	0.57501	Myosin head, motor domain (2);	0.058279	0.64402	N	0.000002	D	0.96941	0.9001	M	0.84156	2.68	0.80722	D	1	B;P	0.37370	0.239;0.592	P;B	0.50537	0.643;0.304	D	0.96566	0.9419	10	0.48119	T	0.1	.	15.1015	0.72279	0.143:0.857:0.0:0.0	.	281;282	Q7Z7A5;Q9ULV0	.;MYO5B_HUMAN	S	282;281	ENSP00000285039:A282S	ENSP00000285039:A282S	A	-	1	0	MYO5B	45765188	1.000000	0.71417	0.033000	0.17914	0.216000	0.24613	5.990000	0.70595	1.278000	0.44430	0.561000	0.74099	GCA	.		0.502	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47511190	C	A	47511190	3	1	36	1	0	0	0	0	1	0	0	0	10104	710	25	4	4834	4	MYO5B	18	47511190	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	13952232	47511190	30566058	101	3281											
TSHZ1	10194	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	72999467	72999468	+	Frame_Shift_Ins	INS	-	-	A																															gaggccgagactgggaaggcINScaaaaaggagggaccgctgg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:72999467_72999468insA	ENST00000580243.1	+	2	2453_2454	c.2105_2106insA	c.(2104-2109)gccaaafs	p.K703fs	TSHZ1_ENST00000322038.5_Frame_Shift_Ins_p.K658fs			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	703					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		ACTGGGAAGGCCAAAAAGGAGG	0.55																																					p.A657fs		.											.	TSHZ1-90	0			c.1970_1971insA						.																																			SO:0001589	frameshift_variant	10194	exon2			.	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	Exception_encountered	18.37:g.72999467_72999468insA	ENSP00000464391:p.Lys703fs	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	103	31	NM_005786	0	0	0	0	0	O60534|Q4LE29|Q53EU4	Frame_Shift_Ins	INS	ENST00000580243.1	37																																																																																				.		0.55	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999468	-	A	72999467	7	5	36	1	0	1	1	0	0	0	0	0	16656	739	26	0	1972	0	TSHZ1	18	72999467	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10	25488277	72999467	5077781	102	3282	30	3									
TSHZ1	10194	hgsc.bcm.edu;bcgsc.ca	37	chr18	72999468	72999468	+	Silent	SNP	C	C	A																															gaggccgagactgggaaggcCaaaaaggagggaccgctgga																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:72999468C>A	ENST00000580243.1	+	2	2454	c.2106C>A	c.(2104-2106)gcC>gcA	p.A702A	TSHZ1_ENST00000322038.5_Silent_p.A657A			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	702					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CTGGGAAGGCCAAAAAGGAGG	0.547																																					p.A657A		.											.	TSHZ1-90	0			c.C1971A						.						99	88	92					18																	72999468		2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GAAGGCCAAAAAG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2106C>A	18.37:g.72999468C>A		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	102	35	NM_005786	0	0	2	2	0	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				.		0.547	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999468	C	A	72999468	2	1	36	1	0	0	0	0	0	0	0	1	16656	581	21	4		4	TSHZ1	18	72999468	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	1	72999468	5077780	103	3283	30	3									
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72999471	72999472	+	Frame_Shift_Ins	INS	-	-	A																															ccgagactgggaaggccaaaINSaaggagggaccgctggacgt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:72999471_72999472insA	ENST00000580243.1	+	2	2457_2458	c.2109_2110insA	c.(2110-2112)aagfs	p.K704fs	TSHZ1_ENST00000322038.5_Frame_Shift_Ins_p.K659fs			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	704					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GGAAGGCCAAAAAGGAGGGACC	0.545																																					p.K658fs		.											.	TSHZ1-90	0			c.1974_1975insA						.																																			SO:0001589	frameshift_variant	10194	exon2			.	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	10669	protein-coding gene	gene with protein product		614427	"serologically defined colon cancer antigen 33", "teashirt zinc finger 1", "teashirt family zinc finger 1"	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2111dupA	18.37:g.72999473_72999473dupA	ENSP00000464391:p.Lys704fs	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	103	25	NM_005786	0	0	0	0	0	O60534|Q4LE29|Q53EU4	Frame_Shift_Ins	INS	ENST00000580243.1	37																																																																																				.		0.545	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999472	-	A	72999471	7	5	36	1	0	1	1	0	0	0	0	0	16656	11	1	0	1976	0	TSHZ1	18	72999471	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10	3	72999471	5077777	104	3284	30	3									
SF4	57794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19427332	19427332	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgagcgatgagctcttcCtggtgaaggatgttcatgtt	7	15	12	7	1	3	3	1	3	2	0	4	5	4	4	1	2	2	3	1	2	1	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:19427332C>G	ENST00000247001.5	-	2	452	c.105G>C	c.(103-105)caG>caC	p.Q35H	SUGP1_ENST00000334782.5_Missense_Mutation_p.Q35H|SUGP1_ENST00000585763.1_5'UTR	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	35					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						TGAGCTCTTCCTGGTGAAGGA	0.517																																					p.Q35H		.											.	SUGP1-91	0			c.G105C						.						137	103	114					19																	19427332		2203	4300	6503	SO:0001583	missense	57794	exon2			CTCTTCCTGGTGA	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"G patch domain containing"	18643	protein-coding gene	gene with protein product		607992	"splicing factor 4"	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.105G>C	19.37:g.19427332C>G	ENSP00000247001:p.Gln35His	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	99	30	NM_172231	0	0	7	7	0	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.460953	0.63513	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	T	0.54279	0.58	4.88	-3.34	0.04943	.	0.000000	0.85682	D	0.000000	T	0.64832	0.2634	M	0.73962	2.25	0.50039	D	0.999841	D	0.71674	0.998	D	0.79784	0.993	T	0.67237	-0.5721	10	0.87932	D	0	.	10.2244	0.43216	0.0:0.2929:0.0:0.7071	.	35	Q8IWZ8	SUGP1_HUMAN	H	35	ENSP00000247001:Q35H	ENSP00000247001:Q35H	Q	-	3	2	SUGP1	19288332	0.067000	0.21026	0.993000	0.49108	0.968000	0.65278	-1.275000	0.02817	-0.260000	0.09418	-0.258000	0.10820	CAG	.		0.517	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		G	19427332	C	G	19427332	3	3	36	1	0	0	0	0	1	0	0	0	14187	680	24	4	1884	4	SF4	19	19427332	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		19427332	39701651	105	3285											
ZNF567	163081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	37210700	37210701	+	Missense_Mutation	DNP	TC	TC	AT																															ctcattcgtcatcagagaacTcacacgggagagaaaccata																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:37210700_37210701TC>AT	ENST00000536254.2	+	6	1296_1297	c.1074_1075TC>AT	c.(1072-1077)acTCac>acATac	p.H359Y	ZNF567_ENST00000360729.4_Missense_Mutation_p.H328Y|ZNF567_ENST00000392163.2_Missense_Mutation_p.H328Y|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Missense_Mutation_p.H328Y|ZNF567_ENST00000585696.1_Missense_Mutation_p.H328Y			Q8N184	ZN567_HUMAN	zinc finger protein 567	359					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATCAGAGAACTCACACGGGAGA	0.455																																					p.H359Y		.											.	ZNF567-90	0			c.C982T						.																																			SO:0001583	missense	163081	exon4			AGAACTCACACGG	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		Exception_encountered	19.37:g.37210700_37210701delinsAT	ENSP00000441838:p.His359Tyr	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	82	32	NM_152603	0	0	0	0	0	B3KX49|Q6N044	Missense_Mutation	DNP	ENST00000536254.2	37																																																																																				.		0.455	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		AT	37210701	TC	AT	37210700	3	1	36	1	0	0	0	0	1	0	0	0	18030	1538	54	5	991	5	ZNF567	19	37210700	Missense_Mutation	DNP	TC	TCGA-B1-A47M-01A-11D-A25F-10	17783368	37210700	21918283	106	3286											
ZNF569	148266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	37904781	37904781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagtatgaattctttgaTgtctaatgagatttgacatt	11	17	7	6	0	2	4	0	4	2	1	3	5	3	4	1	0	0	1	1	0	3	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:37904781T>C	ENST00000316950.6	-	6	1336	c.779A>G	c.(778-780)cAt>cGt	p.H260R	ZNF569_ENST00000392150.2_Missense_Mutation_p.H101R|ZNF569_ENST00000392149.2_Missense_Mutation_p.H260R	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	260					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(5)|endometrium(4)|large_intestine(16)|lung(11)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AATTCTTTGATGTCTAATGAG	0.313																																					p.H260R		.											.	ZNF569-154	0			c.A779G						.						74	81	79					19																	37904781		2203	4299	6502	SO:0001583	missense	148266	exon6			CTTTGATGTCTAA	AL833408	CCDS12503.1	19q13.12	2013-09-20			ENSG00000196437	ENSG00000196437		"Zinc fingers, C2H2-type", "-"	24737	protein-coding gene	gene with protein product		613904				12477932	Standard	NM_152484		Approved	FLJ32053, ZAP1	uc002ogi.3	Q5MCW4	OTTHUMG00000048172	ENST00000316950.6:c.779A>G	19.37:g.37904781T>C	ENSP00000325018:p.His260Arg	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_152484	0	0	0	2	2	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.145205	0.57044	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	D;D	0.86865	-2.18;-2.18	3.8	2.75	0.32379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38897	N	0.001523	D	0.93265	0.7854	M	0.92555	3.32	0.42876	D	0.994154	D;D	0.76494	0.999;0.999	D;D	0.62955	0.909;0.909	D	0.92892	0.6332	10	0.87932	D	0	.	9.5174	0.39113	0.0:0.0:0.1787:0.8213	.	101;260	Q17RR6;Q5MCW4	.;ZN569_HUMAN	R	260;101	ENSP00000325018:H260R;ENSP00000375993:H101R	ENSP00000325018:H260R	H	-	2	0	ZNF569	42596621	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.150000	0.50662	0.597000	0.29811	0.482000	0.46254	CAT	.		0.313	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		C	37904781	T	C	37904781	3	2	36	1	0	0	0	0	1	0	0	0	18032	1464	51	3	1285	3	ZNF569	19	37904781	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	694081	37904781	21224202	107	3287											
RABAC1	10567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42461228	42461228	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagaaggggaaggagatGcctccagccagagcatactg	14	4	14	9	0	0	4	0	0	0	4	1	6	1	5	3	3	4	1	3	3	4	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:42461228G>T	ENST00000222008.6	-	4	508	c.411C>A	c.(409-411)ggC>ggA	p.G137G	RABAC1_ENST00000601891.1_Intron|RABAC1_ENST00000601078.1_Silent_p.G43G	NM_006423.2	NP_006414.2	Q9UI14	PRAF1_HUMAN	Rab acceptor 1 (prenylated)	137						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	identical protein binding (GO:0042802)			central_nervous_system(1)|kidney(1)|prostate(1)	3						GGAAGGAGATGCCTCCAGCCA	0.642																																					p.G137G		.											.	RABAC1-90	0			c.C411A						.						77	75	76					19																	42461228		2203	4300	6503	SO:0001819	synonymous_variant	10567	exon4			GGAGATGCCTCCA	AJ133534	CCDS12593.1	19q13.2	2012-09-20			ENSG00000105404	ENSG00000105404			9794	protein-coding gene	gene with protein product	"PRA1 domain family 1", "prenylated Rab acceptor 1"	604925				10329441, 10751420	Standard	NM_006423		Approved	PRA1, PRAF1, YIP3	uc002osf.3	Q9UI14		ENST00000222008.6:c.411C>A	19.37:g.42461228G>T		Somatic	281	0		WXS	Illumina HiSeq	Phase_I	143	54	NM_006423	0	2	189	325	134	Q7Z4Y2|Q9Y3R1	Silent	SNP	ENST00000222008.6	37	CCDS12593.1																																																																																			.		0.642	RABAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463388.1	NM_006423		T	42461228	G	T	42461228	2	4	36	1	0	0	0	0	0	0	0	1	12992	1306	46	4		4	RABAC1	19	42461228	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	4556447	42461228	16667755	108	3288											
IRGQ	126298	broad.mit.edu	37	chr19	44099300	44099300	+	Frame_Shift_Del	DEL	G	G	-																															agggccccggcgctgcgggtGggcagctcagctcgcccaga																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:44099300delG	ENST00000602269.1	-	1	376	c.191delC	c.(190-192)ccafs	p.P65fs	ZNF576_ENST00000525771.1_5'Flank|IRGQ_ENST00000422989.1_Frame_Shift_Del_p.P65fs|ZNF576_ENST00000533118.1_5'Flank|ZNF576_ENST00000529930.1_5'Flank|IRGQ_ENST00000601520.1_5'Flank|SRRM5_ENST00000526798.1_5'Flank|ZNF576_ENST00000528387.1_5'Flank|ZNF576_ENST00000391965.2_5'Flank|ZNF576_ENST00000336564.4_5'Flank|L34079.2_ENST00000594374.1_5'Flank|SRRM5_ENST00000607544.1_5'Flank			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	65										endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				CGCTGCGGGTGGGCAGCTCAG	0.721																																					p.P64fs													.	IRGQ-92	0			c.191delC						.						6	7	7					19																	44099300		2116	4172	6288	SO:0001589	frameshift_variant	126298	exon2			GCGGGTGGGCAGC	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"immunity-related GTPase family, Q1"	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.191delC	19.37:g.44099300delG	ENSP00000472250:p.Pro65fs	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_001007561	0	0	0	0	0	B2RNP3	Frame_Shift_Del	DEL	ENST00000602269.1	37	CCDS33040.1																																																																																			.		0.721	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561		-	44099300	G	-	44099300	7	5	36	1	0	1	0	1	0	0	0	0	7860	1348	47	0	1688	0	IRGQ	19	44099300	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	1638072	44099300	15029683	109	3289											
CCDC155	147872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49920441	49920441	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcgggaactccagcaaGccctggtgcctgtgatgaaa	9	6	14	12	3	0	2	0	2	0	0	1	3	1	3	3	3	4	1	3	3	3	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:49920441G>A	ENST00000447857.3	+	19	1670	c.1465G>A	c.(1465-1467)Gcc>Acc	p.A489T		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	489						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						ACTCCAGCAAGCCCTGGTGCC	0.652																																					p.A489T		.											.	CCDC155-69	0			c.G1465A						.						23	26	25					19																	49920441		1938	4124	6062	SO:0001583	missense	147872	exon19			CAGCAAGCCCTGG		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1465G>A	19.37:g.49920441G>A	ENSP00000404220:p.Ala489Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	42	19	NM_144688	0	0	0	0	0	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	37	CCDS46140.1	.	.	.	.	.	.	.	.	.	.	g	16.07	3.019479	0.54576	.	.	ENSG00000161609	ENST00000447857	T	0.57595	0.39	3.88	3.88	0.44766	.	0.000000	0.46758	D	0.000279	T	0.68824	0.3043	M	0.72118	2.19	0.28879	N	0.89453	D;D	0.67145	0.996;0.996	D;D	0.79784	0.993;0.993	T	0.65179	-0.6231	10	0.87932	D	0	-7.7039	12.1446	0.54016	0.0:0.0:1.0:0.0	.	489;489	C9JGW3;Q8N6L0	.;CC155_HUMAN	T	489	ENSP00000404220:A489T	ENSP00000404220:A489T	A	+	1	0	CCDC155	54612253	0.984000	0.35163	0.893000	0.35052	0.131000	0.20780	4.606000	0.61126	2.123000	0.65237	0.444000	0.29173	GCC	.		0.652	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		A	49920441	G	A	49920441	3	1	36	1	0	0	0	0	1	0	0	0	2794	971	34	2	1535	2	CCDC155	19	49920441	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	5821141	49920441	9208542	110	3290											
AP2A1	160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50285918	50285918	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccctgcactgcatcgccaAcgtgggcagccgggagatgg	7	5	16	13	3	0	1	0	0	0	1	1	2	0	1	3	4	4	3	3	4	1	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:50285918A>G	ENST00000359032.5	+	4	410	c.410A>G	c.(409-411)aAc>aGc	p.N137S	AP2A1_ENST00000600199.1_3'UTR|AP2A1_ENST00000354293.5_Missense_Mutation_p.N137S	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	137					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		TGCATCGCCAACGTGGGCAGC	0.657																																					p.N137S		.											.	AP2A1-92	0			c.A410G						.						32	33	32					19																	50285918		2157	4257	6414	SO:0001583	missense	160	exon4			TCGCCAACGTGGG	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.410A>G	19.37:g.50285918A>G	ENSP00000351926:p.Asn137Ser	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	30	12	NM_130787	0	0	9	27	18	Q96CI7|Q96PP6|Q96PP7|Q9H070	Missense_Mutation	SNP	ENST00000359032.5	37	CCDS46148.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.527703	0.64860	.	.	ENSG00000196961	ENST00000354293;ENST00000359032	T;T	0.23950	1.88;1.88	5.54	5.54	0.83059	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.32133	0.0819	M	0.65975	2.015	0.80722	D	1	B;B	0.24533	0.025;0.105	B;B	0.28465	0.029;0.09	T	0.08617	-1.0713	10	0.52906	T	0.07	.	14.6526	0.68808	1.0:0.0:0.0:0.0	.	137;137	O95782-2;O95782	.;AP2A1_HUMAN	S	137	ENSP00000346246:N137S;ENSP00000351926:N137S	ENSP00000346246:N137S	N	+	2	0	AP2A1	54977730	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.309000	0.96252	2.103000	0.63969	0.455000	0.32223	AAC	.		0.657	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			G	50285918	A	G	50285918	3	3	36	1	0	0	0	0	1	0	0	0	739	43	2	3	424	3	AP2A1	19	50285918	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	365477	50285918	8843065	111	3291											
ZNF880	400713	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52887363	52887363	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctcccacaagaacaaaaagCacaaataagggaaaaaccgt	21	4	6	10	1	1	1	0	0	1	1	2	2	1	2	2	1	3	1	2	1	8	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:52887363C>T	ENST00000422689.2	+	4	545	c.530C>T	c.(529-531)gCa>gTa	p.A177V		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	177					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAACAAAAAGCACAAATAAGG	0.343																																					p.A177V													.	.	0			c.C530T						.						55	50	52					19																	52887363		692	1591	2283	SO:0001583	missense	400713	exon4			AAAAAGCACAAAT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"Zinc fingers, C2H2-type", "-"	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.530C>T	19.37:g.52887363C>T	ENSP00000406318:p.Ala177Val	Somatic	57	1		WXS	Illumina HiSeq	Phase_I	52	14	NM_001145434	0	0	0	0	0	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.692822	0.00731	.	.	ENSG00000221923	ENST00000422689	T	0.06142	3.34	1.46	-0.918	0.10482	.	.	.	.	.	T	0.02083	0.0065	N	0.02213	-0.635	0.09310	N	1	B	0.14805	0.011	B	0.15870	0.014	T	0.48658	-0.9016	8	.	.	.	.	4.5796	0.12252	0.0:0.3557:0.0:0.6443	.	177	Q6PDB4	ZN880_HUMAN	V	177	ENSP00000406318:A177V	.	A	+	2	0	ZNF880	57579175	0.032000	0.19561	0.010000	0.14722	0.007000	0.05969	-0.961000	0.03845	-0.035000	0.13691	-0.269000	0.10298	GCA	.		0.343	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434		T	52887363	C	T	52887363	3	4	36	1	0	0	0	0	1	0	0	0	18229	710	25	2	544	2	ZNF880	19	52887363	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	2601445	52887363	6241620	112	3292											
JAG1	182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	10639160	10639160	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccttccatgcaagttttgTtgccattctggtcacaggca	8	13	9	11	0	2	0	1	0	1	0	3	0	3	0	3	2	3	4	3	2	1	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:10639160T>G	ENST00000254958.5	-	4	1165	c.650A>C	c.(649-651)aAc>aCc	p.N217T	JAG1_ENST00000423891.2_Missense_Mutation_p.N58T	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	217	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GCAAGTTTTGTTGCCATTCTG	0.493									Alagille Syndrome																												p.N217T		.											.	JAG1-1273	0			c.A650C						.						126	119	121					20																	10639160		2203	4300	6503	SO:0001583	missense	182	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GTTTTGTTGCCAT	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.650A>C	20.37:g.10639160T>G	ENSP00000254958:p.Asn217Thr	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	58	25	NM_000214	0	0	1	2	1	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.463155	0.84425	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.96011	-3.88;-3.88	5.58	5.58	0.84498	Delta/Serrate/lag-2 (DSL) protein (3);	0.000000	0.85682	D	0.000000	D	0.95382	0.8501	L	0.50333	1.59	0.80722	D	1	D	0.52996	0.957	P	0.51833	0.681	D	0.95419	0.8505	10	0.54805	T	0.06	.	15.7475	0.77958	0.0:0.0:0.0:1.0	.	217	P78504	JAG1_HUMAN	T	217;58	ENSP00000254958:N217T;ENSP00000389519:N58T	ENSP00000254958:N217T	N	-	2	0	JAG1	10587160	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.124000	0.65301	0.460000	0.39030	AAC	.		0.493	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		G	10639160	T	G	10639160	3	3	36	1	0	0	0	0	1	0	0	0	7955	1725	60	5	3098	5	JAG1	20	10639160	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10		10639160	52386360	113	3293											
CTCFL	140690	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	56098141	56098141	+	Frame_Shift_Del	DEL	T	T	-																															taccctttgtctttctttgaTtttttgtagatttggccttt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:56098141delT	ENST00000608263.1	-	2	1398	c.737delA	c.(736-738)aatfs	p.N246fs	CTCFL_ENST00000433949.3_Frame_Shift_Del_p.N41fs|CTCFL_ENST00000481655.2_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000429804.3_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000422869.2_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000243914.3_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000423479.3_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000608440.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000539382.1_Frame_Shift_Del_p.N41fs|CTCFL_ENST00000432255.2_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000609232.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608158.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000608425.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000371196.2_Frame_Shift_Del_p.N246fs	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	246					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CTTTCTTTGATTTTTTGTAGA	0.398																																					p.N246fs		.											.	CTCFL-292	0			c.737delA						.						197	176	183					20																	56098141		2202	4300	6502	SO:0001589	frameshift_variant	140690	exon2			.		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.737delA	20.37:g.56098141delT	ENSP00000476783:p.Asn246fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	72	24	NM_001269044	0	0	0	0	0	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Frame_Shift_Del	DEL	ENST00000608263.1	37	CCDS13459.1																																																																																			.		0.398	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		-	56098141	T	-	56098141	7	5	36	1	0	1	0	1	0	0	0	0	4007	1493	52	0	1290	0	CTCFL	20	56098141	Frame_Shift_Del	DEL	T	TCGA-B1-A47M-01A-11D-A25F-10	45458981	56098141	6927379	114	3294											
LAMA5	3911	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	60908164	60908164	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acatcactgcccgtgcaggtGatcagtggcgggtgcgacgg	7	7	16	11	4	2	1	2	1	0	0	2	2	2	1	1	4	3	1	1	4	0	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:60908164G>A	ENST00000252999.3	-	26	3330	c.3264C>T	c.(3262-3264)atC>atT	p.I1088I	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1088	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CCGTGCAGGTGATCAGTGGCG	0.716																																					p.I1088I													.	LAMA5-93	0			c.C3264T						.						12	14	13					20																	60908164		2185	4270	6455	SO:0001819	synonymous_variant	3911	exon26			GCAGGTGATCAGT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.3264C>T	20.37:g.60908164G>A		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_005560	0	0	3	3	0	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			.		0.716	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60908164	G	A	60908164	2	1	36	1	0	0	0	0	0	0	0	1	8630	1280	45	2		2	LAMA5	20	60908164	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	4810023	60908164	2117356	115	3295											
MYT1	4661	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62851117	62851117	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggacttgagcatgcacAaacaccgcaaacgagaaaat	16	5	8	12	2	0	2	0	1	0	1	0	4	0	3	2	1	4	3	2	1	4	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:62851117A>G	ENST00000328439.1	+	13	2387	c.2023A>G	c.(2023-2025)Aaa>Gaa	p.K675E	MYT1_ENST00000360149.4_Missense_Mutation_p.K377E|MYT1_ENST00000536311.1_Missense_Mutation_p.K702E	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GAGCATGCACAAACACCGCAA	0.557																																					p.K675E	GBM(59;481 1041 20555 21139 33705)	.											.	MYT1-704	0			c.A2023G						.						107	99	102					20																	62851117		2203	4300	6503	SO:0001583	missense	4661	exon13			ATGCACAAACACC	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"Zinc fingers, C2HC-type containing"	7622	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 2"	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.2023A>G	20.37:g.62851117A>G	ENSP00000327465:p.Lys675Glu	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	174	67	NM_004535	0	0	0	0	0	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049072	0.75846	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.59083	0.29;0.29;0.29	5.75	5.75	0.90469	Myelin transcription factor 1 (1);	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.73598	2.24	0.58432	D	0.999999	D;D;P	0.55800	0.971;0.973;0.716	P;P;P	0.61874	0.641;0.895;0.487	T	0.77816	-0.2447	10	0.87932	D	0	-17.2533	16.0591	0.80826	1.0:0.0:0.0:0.0	.	702;675;377	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	E	377;675;702	ENSP00000353269:K377E;ENSP00000327465:K675E;ENSP00000442412:K702E	ENSP00000327465:K675E	K	+	1	0	MYT1	62321561	1.000000	0.71417	0.598000	0.28837	0.888000	0.51559	8.826000	0.92034	2.185000	0.69588	0.533000	0.62120	AAA	.		0.557	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		G	62851117	A	G	62851117	3	3	36	1	0	0	0	0	1	0	0	0	10131	131	5	3	2065	3	MYT1	20	62851117	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	1942953	62851117	174403	116	3296											
DYRK1A	1859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	38884349	38884349	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgcattgcatcatcaccatGgtaacagttcccatcaccat	12	11	5	13	0	3	0	3	0	0	0	4	0	4	0	3	1	3	4	3	1	1	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr21:38884349G>A	ENST00000398960.2	+	11	1882	c.1807G>A	c.(1807-1809)Ggt>Agt	p.G603S	DYRK1A_ENST00000455387.2_Missense_Mutation_p.G375S|DYRK1A_ENST00000339659.4_Missense_Mutation_p.G594S|DYRK1A_ENST00000338785.3_3'UTR	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	603					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCATCACCATGGTAACAGTTC	0.502																																					p.G603S	Melanoma(114;464 1602 31203 43785 45765)	.											.	DYRK1A-792	0			c.G1807A						.						115	98	104					21																	38884349		2203	4300	6503	SO:0001583	missense	1859	exon11			CACCATGGTAACA	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.1807G>A	21.37:g.38884349G>A	ENSP00000381932:p.Gly603Ser	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	129	45	NM_001396	0	0	1	5	4	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221682	0.58560	.	.	ENSG00000157540	ENST00000339659;ENST00000398960;ENST00000455387	T;T;T	0.55760	0.5;0.5;1.09	5.21	5.21	0.72293	.	0.298408	0.32459	N	0.006064	T	0.52725	0.1752	N	0.14661	0.345	0.53688	D	0.999979	D;D	0.60575	0.98;0.988	P;D	0.65010	0.855;0.931	T	0.44329	-0.9335	10	0.08599	T	0.76	.	18.785	0.91951	0.0:0.0:1.0:0.0	.	603;594	Q13627;Q13627-2	DYR1A_HUMAN;.	S	594;603;375	ENSP00000340373:G594S;ENSP00000381932:G603S;ENSP00000407854:G375S	ENSP00000340373:G594S	G	+	1	0	DYRK1A	37806219	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.746000	0.74866	2.434000	0.82447	0.655000	0.94253	GGT	.		0.502	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		A	38884349	G	A	38884349	3	1	36	1	0	0	0	0	1	0	0	0	4865	1348	47	2	1933	2	DYRK1A	21	38884349	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		38884349	9245546	117	3297											
SMARCB1	6598	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	24175838	24175839	+	Frame_Shift_Ins	INS	-	-	TT																															gtgcccactgctggagactcINStgacagacgctgagatggag																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr22:24175838_24175839insTT	ENST00000263121.7	+	8	1262_1263	c.1066_1067insTT	c.(1066-1068)ctgfs	p.L356fs	SMARCB1_ENST00000344921.6_Frame_Shift_Ins_p.L365fs|SMARCB1_ENST00000407422.3_Frame_Shift_Ins_p.L347fs|SMARCB1_ENST00000407082.3_Frame_Shift_Ins_p.L310fs|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	356					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GCTGGAGACTCTGACAGACGCT	0.629			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.L356fs		.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1-2699	3	Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)	c.1066_1067insTT						.																																			SO:0001589	frameshift_variant	6598	exon8			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	Exception_encountered	22.37:g.24175838_24175839insTT	ENSP00000263121:p.Leu356fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	90	24	NM_003073	0	0	0	0	0	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Ins	INS	ENST00000263121.7	37	CCDS13817.1																																																																																			.		0.629	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		TT	24175839	-	TT	24175838	7	5	36	1	0	1	1	0	0	0	0	0	14806	912	32	0	1096	0	SMARCB1	22	24175838	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10		24175838	27128728	118	3298											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30038228	30038229	+	Missense_Mutation	DNP	CT	CT	AC																															agatgaaaagatctactgccCtcctgaggcttctgtgctcc																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr22:30038228_30038229CT>AC	ENST00000338641.4	+	4	842_843	c.401_402CT>AC	c.(400-402)cCT>cAC	p.P134H	NF2_ENST00000413209.2_Missense_Mutation_p.P134H|NF2_ENST00000353887.4_Missense_Mutation_p.P51H|NF2_ENST00000397789.3_Missense_Mutation_p.P134H|NF2_ENST00000347330.5_Missense_Mutation_p.P51H|NF2_ENST00000403999.3_Missense_Mutation_p.P134H|NF2_ENST00000403435.1_Missense_Mutation_p.P134H|NF2_ENST00000334961.7_Missense_Mutation_p.P51H|NF2_ENST00000361676.4_Missense_Mutation_p.P92H|NF2_ENST00000361452.4_Missense_Mutation_p.P93H|NF2_ENST00000361166.4_Missense_Mutation_p.P134H	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	134	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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.V122_K149del(5)|p.?(3)|p.L127_P134del(1)|p.K123fs*2(1)		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						ATCTACTGCCCTCCTGAGGCTT	0.47			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.P134H		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	10	Deletion - In frame(6)|Unknown(3)|Deletion - Frameshift(1)	soft_tissue(8)|large_intestine(1)|stomach(1)	c.T402C						.																																			SO:0001583	missense	4771	exon4	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	CTGCCCTCCTGAG	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	Exception_encountered	22.37:g.30038228_30038229delinsAC	ENSP00000344666:p.Pro134His	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	49	20	NM_000268	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	DNP	ENST00000338641.4	37	CCDS13861.1																																																																																			.		0.47	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		AC	30038229	CT	AC	30038228	3	1	36	1	0	0	0	0	1	0	0	0	10383	681	24	4	415	4	NF2	22	30038228	Missense_Mutation	DNP	CT	TCGA-B1-A47M-01A-11D-A25F-10	5862390	30038228	21266338	119	3299											
SLC35A2	7355	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	48762075	48762075	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acggtgggaagacagctgcgGtggtggtggctgcccgggag	6	6	21	8	3	0	1	0	0	0	1	0	3	0	3	1	7	3	2	1	7	1	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chrX:48762075G>A	ENST00000247138.5	-	4	1114	c.1111C>T	c.(1111-1113)Ccg>Tcg	p.P371S	SLC35A2_ENST00000376515.3_Missense_Mutation_p.T150I|SLC35A2_ENST00000445167.2_Missense_Mutation_p.T174I|SLC35A2_ENST00000413561.2_Missense_Mutation_p.P310S|SLC35A2_ENST00000452555.2_Missense_Mutation_p.P399S|SLC35A2_ENST00000376521.1_Missense_Mutation_p.P371S|SLC35A2_ENST00000376529.3_Missense_Mutation_p.T174I	NM_005660.1	NP_005651.1	P78381	S35A2_HUMAN	solute carrier family 35 (UDP-galactose transporter), member A2	371					galactose metabolic process (GO:0006012)|transmembrane transport (GO:0055085)|UDP-galactose transport (GO:0015785)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	sugar:proton symporter activity (GO:0005351)|UDP-galactose transmembrane transporter activity (GO:0005459)			breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(2)	15						GACAGCTGCGGTGGTGGTGGC	0.652																																					p.P371S		.											.	SLC35A2-193	0			c.C1111T						.						40	34	36					X																	48762075		2203	4300	6503	SO:0001583	missense	7355	exon4			GCTGCGGTGGTGG	D88146	CCDS14311.1, CCDS35247.1, CCDS43937.1, CCDS65253.1, CCDS65254.1, CCDS75973.1, CCDS75974.1, CCDS75975.1	Xp11.23-p11.22	2013-05-22			ENSG00000102100	ENSG00000102100		"Solute carriers"	11022	protein-coding gene	gene with protein product		314375	"solute carrier family 35 (UDP-galactose transporter), member 2"	UGALT		8128316	Standard	NM_001042498		Approved	UGAT, UGT, UGT1, UGT2, UGTL	uc004dlo.1	P78381	OTTHUMG00000024129	ENST00000247138.5:c.1111C>T	X.37:g.48762075G>A	ENSP00000247138:p.Pro371Ser	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	23	13	NM_001042498	0	0	0	13	13	A8K2L9|A8K9V1|B4DE11|B4DPT2|E7EW45|Q8IV21|Q92553	Missense_Mutation	SNP	ENST00000247138.5	37	CCDS14311.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.494|7.494	0.651284|0.651284	0.14516|0.14516	.|.	.|.	ENSG00000102100|ENSG00000102100	ENST00000247138;ENST00000376521;ENST00000413561;ENST00000452555|ENST00000376529;ENST00000445167;ENST00000376515	T;T;T;T|.	0.42131|.	0.98;0.99;0.99;1.0|.	3.67|3.67	0.966|0.966	0.19667|0.19667	.|.	1.403590|.	0.04571|.	N|.	0.393258|.	T|T	0.16342|0.16342	0.0393|0.0393	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;D;B;B|B	0.54601|0.02656	0.003;0.0;0.967;0.002;0.001|0.0	B;B;P;B;B|B	0.62382|0.08055	0.003;0.0;0.901;0.001;0.001|0.003	T|T	0.29941|0.29941	-0.9995|-0.9995	10|8	0.32370|0.13470	T|T	0.25|0.59	-0.5438|-0.5438	3.4371|3.4371	0.07449|0.07449	0.3602:0.1976:0.4422:0.0|0.3602:0.1976:0.4422:0.0	.|.	310;399;384;371;371|174	B4DE11;E7EW45;B4DE15;P78381-2;P78381|P78381-3	.;.;.;.;S35A2_HUMAN|.	S|I	371;371;310;399|174;174;150	ENSP00000247138:P371S;ENSP00000365704:P371S;ENSP00000393233:P310S;ENSP00000416002:P399S|.	ENSP00000247138:P371S|ENSP00000365698:T150I	P|T	-|-	1|2	0|0	SLC35A2|SLC35A2	48647019|48647019	0.169000|0.169000	0.23002|0.23002	0.010000|0.010000	0.14722|0.14722	0.354000|0.354000	0.29330|0.29330	0.674000|0.674000	0.25218|0.25218	0.064000|0.064000	0.16427|0.16427	-0.881000|-0.881000	0.02953|0.02953	CCG|ACC	.		0.652	SLC35A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060790.1	NM_005660		A	48762075	G	A	48762075	3	1	36	1	0	0	0	0	1	0	0	0	14603	1261	44	2	243	2	SLC35A2	23	48762075	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		48762075	106508485	120	3300											
LPAR4	2846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	78011381	78011381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccctgtttaagactgaaacaCctttgaccacaaagccttcc	12	10	5	14	0	0	3	0	2	0	1	1	3	1	3	5	0	2	1	5	0	3	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chrX:78011381C>T	ENST00000435339.3	+	2	1401	c.1015C>T	c.(1015-1017)Cct>Tct	p.P339S		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	339					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						GACTGAAACACCTTTGACCAC	0.403																																					p.P339S		.											.	LPAR4-133	0			c.C1015T						.						151	134	140					X																	78011381		2203	4300	6503	SO:0001583	missense	2846	exon2			GAAACACCTTTGA	U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.1015C>T	X.37:g.78011381C>T	ENSP00000408205:p.Pro339Ser	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	66	47	NM_005296	0	0	0	0	0	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	37	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	C	8.708	0.911460	0.17833	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.70631	-0.5;-0.5	4.26	4.26	0.50523	.	0.407810	0.24314	N	0.039618	T	0.41259	0.1151	N	0.08118	0	0.38155	D	0.938872	B	0.34103	0.437	B	0.30401	0.115	T	0.50890	-0.8774	10	0.02654	T	1	.	8.4939	0.33117	0.0:0.8889:0.0:0.1111	.	339	Q99677	LPAR4_HUMAN	S	339	ENSP00000408205:P339S;ENSP00000362398:P339S	ENSP00000362398:P339S	P	+	1	0	LPAR4	77898037	0.970000	0.33590	1.000000	0.80357	0.927000	0.56198	1.463000	0.35277	1.961000	0.56991	0.422000	0.28245	CCT	.		0.403	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		T	78011381	C	T	78011381	3	4	36	1	0	0	0	0	1	0	0	0	8932	507	18	2	1017	2	LPAR4	23	78011381	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	29249306	78011381	77259179	121	3301											
DOCK7	85440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	63119731	63119731	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcaatatcatctggaggaaAttcaatcaaatcccgtaaag	16	11	6	8	1	5	0	4	0	1	0	6	2	6	2	1	2	0	1	1	2	7	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:63119731A>G	ENST00000340370.5	-	3	261	c.244T>C	c.(244-246)Ttt>Ctt	p.F82L	DOCK7_ENST00000404627.2_Missense_Mutation_p.F82L|DOCK7_ENST00000251157.5_Missense_Mutation_p.F82L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	82					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TCTGGAGGAAATTCAATCAAA	0.428																																					p.F82L		.											.	DOCK7-92	0			c.T244C						.						67	66	66					1																	63119731		2203	4300	6503	SO:0001583	missense	85440	exon3			GAGGAAATTCAAT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.244T>C	1.37:g.63119731A>G	ENSP00000340742:p.Phe82Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	85	27	NM_001272002	0	0	0	0	0	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	A	34	5.346120	0.95807	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.63580	-0.05;-0.05;-0.05	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.73799	0.3633	M	0.84156	2.68	0.80722	D	1	P;D;P	0.56521	0.911;0.976;0.861	P;P;P	0.62382	0.895;0.901;0.73	T	0.78314	-0.2252	10	0.59425	D	0.04	.	15.1374	0.72579	1.0:0.0:0.0:0.0	.	82;82;82	Q96NI0;Q96N67-2;Q96N67-5	.;.;.	L	82	ENSP00000251157:F82L;ENSP00000340742:F82L;ENSP00000384446:F82L	ENSP00000251157:F82L	F	-	1	0	DOCK7	62892319	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.683000	0.91236	2.162000	0.67917	0.533000	0.62120	TTT	.		0.428	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		G	63119731	A	G	63119731	3	3	37	1	0	0	0	0	1	0	0	0	4703	101	4	3	6273	3	DOCK7	1	63119731	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		63119731	186130890	1	3302											
HBXIP	10542	hgsc.bcm.edu;bcgsc.ca	37	chr1	110950347	110950347	+	5'Flank	DEL	C	C	-																															gggcgtggaccgtaacggcgCctccaaagggacaaaattga																								rs201420127		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:110950347delC	ENST00000602318.1	-	0	0				LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5_ENST00000474861.2_5'Flank|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5-AS1_ENST00000608067.1_RNA|LAMTOR5_ENST00000256644.4_Frame_Shift_Del_p.A48fs|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000610148.1_RNA			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											CGTAACGGCGCCTCCAAAGGG	0.617																																					p.A48fs		.											.	.	0			c.142delG						.						87	74	78					1																	110950347		2203	4300	6503	SO:0001631	upstream_gene_variant	10542	exon1			.	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"HBx-interacting protein", "hepatitis B virus x-interacting protein (9.6kD)"	608521	"hepatitis B virus x interacting protein"	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568		1.37:g.110950347delC	Exception_encountered	Somatic	297	0		WXS	Illumina HiSeq	Phase_I	216	42	NM_006402	0	0	0	0	0	Q6IBD8	Frame_Shift_Del	DEL	ENST00000602318.1	37																																																																																				.		0.617	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402		-	110950347	C	-	110950347	6	5	37	0	1	1	0	1	0	0	0	0	7009	739	26	0		0	HBXIP	1	110950347	5'Flank	DEL	C	TCGA-B1-A47N-01A-11D-A25F-10	47830616	110950347	138300274	2	3303											
PLEKHO1	51177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150131515	150131515	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaaggacccccctcggtctCcgccggattctgagtcagag	7	7	11	16	3	3	2	1	1	2	1	5	4	3	4	6	3	0	0	6	3	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:150131515C>A	ENST00000369124.4	+	6	1305	c.1027C>A	c.(1027-1029)Ccg>Acg	p.P343T	PLEKHO1_ENST00000369126.1_Missense_Mutation_p.P160T|PLEKHO1_ENST00000025469.6_Missense_Mutation_p.P309T	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	343	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCCTCGGTCTCCGCCGGATTC	0.607																																					p.P343T		.											.	PLEKHO1-226	0			c.C1027A						.						50	54	53					1																	150131515		2203	4300	6503	SO:0001583	missense	51177	exon6			CGGTCTCCGCCGG	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.1027C>A	1.37:g.150131515C>A	ENSP00000358120:p.Pro343Thr	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	127	19	NM_016274	0	0	101	101	0	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	37	CCDS945.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880995	0.51801	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124;ENST00000441340	T;T	0.41758	0.99;0.99	5.24	5.24	0.73138	.	0.515831	0.21943	N	0.066842	T	0.13329	0.0323	N	0.14661	0.345	0.35920	D	0.831769	B	0.34103	0.437	B	0.32090	0.14	T	0.07309	-1.0779	10	0.52906	T	0.07	-17.5791	8.9859	0.35994	0.0:0.899:0.0:0.101	.	343	Q53GL0	PKHO1_HUMAN	T	160;309;343;223	ENSP00000025469:P309T;ENSP00000358120:P343T	ENSP00000025469:P309T	P	+	1	0	PLEKHO1	148398139	0.278000	0.24230	1.000000	0.80357	0.732000	0.41865	1.272000	0.33109	2.726000	0.93360	0.655000	0.94253	CCG	.		0.607	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		A	150131515	C	A	150131515	3	1	37	1	0	0	0	0	1	0	0	0	12110	855	30	4	1049	4	PLEKHO1	1	150131515	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	39181168	150131515	99119106	3	3304											
C2orf61	285051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	47382353	47382353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacccaccaggtcttcccttAttgaggtggaagcggtggcg	7	9	13	12	2	1	1	0	1	1	0	2	2	2	2	3	5	1	0	3	5	2	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:47382353A>G	ENST00000445927.2	-	1	164	c.38T>C	c.(37-39)aTa>aCa	p.I13T	C2orf61_ENST00000294947.2_Missense_Mutation_p.I13T|RP11-761B3.1_ENST00000422269.1_Intron	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	13								p.0?(2)		endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GTCTTCCCTTATTGAGGTGGA	0.632																																					p.I13T		.											.	C2orf61-68	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T38C						.						103	86	91					2																	47382353		2203	4300	6503	SO:0001583	missense	285051	exon1			TCCCTTATTGAGG	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.38T>C	2.37:g.47382353A>G	ENSP00000408527:p.Ile13Thr	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	100	31	NM_173649	0	0	0	0	0	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	.	.	.	.	.	.	.	.	.	.	A	7.690	0.690952	0.15039	.	.	ENSG00000239605	ENST00000445927;ENST00000294947	T;T	0.32988	1.43;1.44	3.27	-2.91	0.05631	.	.	.	.	.	T	0.15219	0.0367	N	0.22421	0.69	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.27806	-1.0063	9	0.59425	D	0.04	-0.0687	0.6125	0.00764	0.3325:0.172:0.1132:0.3822	.	13	Q8N801	CB061_HUMAN	T	13	ENSP00000408527:I13T;ENSP00000294947:I13T	ENSP00000294947:I13T	I	-	2	0	C2orf61	47235857	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.157000	0.16402	-0.545000	0.06224	-0.527000	0.04329	ATA	.		0.632	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649		G	47382353	A	G	47382353	3	3	37	1	0	0	0	0	1	0	0	0	2186	449	16	3	751	3	C2orf61	2	47382353	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		47382353	195817020	4	3305											
ZNF2	7549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95847510	95847510	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	taatccacactggcaggaagCcttatgagtgtaacgagtgc	12	9	11	9	1	0	1	0	1	0	0	1	3	1	2	2	2	3	2	2	2	4	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:95847510C>G	ENST00000340539.5	+	5	1399	c.937C>G	c.(937-939)Cct>Gct	p.P313A	ZNF2_ENST00000295210.6_Missense_Mutation_p.P275A|ZNF2_ENST00000398107.2_Missense_Mutation_p.P271A|ZNF2_ENST00000453539.2_Missense_Mutation_p.P326A|ZNF2_ENST00000425369.1_Missense_Mutation_p.P233A	NM_021088.2	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	12		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		TGGCAGGAAGCCTTATGAGTG	0.468																																					p.P313A		.											.	ZNF2-90	0			c.C937G						.						72	78	76					2																	95847510		2117	4248	6365	SO:0001583	missense	7549	exon5			AGGAAGCCTTATG	X60152	CCDS42712.1, CCDS42713.1, CCDS62957.1	2q11.1	2013-09-24	2005-02-07		ENSG00000163067	ENSG00000275111		"Zinc fingers, C2H2-type", "-"	12991	protein-coding gene	gene with protein product		194500	"zinc finger protein 2 (A1-5)"			8183940, 1945843	Standard	NM_021088		Approved	A1-5, ZNF661, Zfp661	uc002suf.3	Q9BSG1	OTTHUMG00000155150	ENST00000340539.5:c.937C>G	2.37:g.95847510C>G	ENSP00000345392:p.Pro313Ala	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	153	53	NM_021088	0	0	0	0	0	A8MWV7|B4DIR4|Q4ZFY6|Q96G44|Q9UMC5	Missense_Mutation	SNP	ENST00000340539.5	37	CCDS42712.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197452	0.79015	.	.	ENSG00000163067	ENST00000398107;ENST00000340539;ENST00000425369;ENST00000295210;ENST00000453539	T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34	5.31	5.31	0.75309	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000154	T	0.43233	0.1238	M	0.77406	2.37	0.53688	D	0.999974	D;D;D	0.76494	0.986;0.999;0.962	P;D;P	0.66847	0.766;0.947;0.514	T	0.35051	-0.9804	10	0.87932	D	0	-19.4509	16.5178	0.84305	0.0:1.0:0.0:0.0	.	275;271;312	B4DIR4;A8MWV7;Q9BSG1	.;.;ZNF2_HUMAN	A	271;313;233;275;326	ENSP00000381178:P271A;ENSP00000345392:P313A;ENSP00000406017:P233A;ENSP00000295210:P275A;ENSP00000411051:P326A	ENSP00000295210:P275A	P	+	1	0	ZNF2	95211237	1.000000	0.71417	0.998000	0.56505	0.591000	0.36615	7.297000	0.78799	2.765000	0.95021	0.655000	0.94253	CCT	.		0.468	ZNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338595.2	NM_021088		G	95847510	C	G	95847510	3	3	37	1	0	0	0	0	1	0	0	0	17792	739	26	4	951	4	ZNF2	2	95847510	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	48465157	95847510	147351863	5	3306											
HOXD8	3234	hgsc.bcm.edu;bcgsc.ca	37	chr2	176996164	176996165	+	Frame_Shift_Ins	INS	-	-	CCCTAGCCCT																															aagaatcgaggtttcccacgINSccctagccctcaccgagaga																										TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:176996164_176996165insCCCTAGCCCT	ENST00000313173.4	+	2	1324_1325	c.697_698insCCCTAGCCCT	c.(697-699)gccfs	p.-236fs	HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000548663.1_Frame_Shift_Ins_p.-132fs|HOXD8_ENST00000544999.1_Frame_Shift_Ins_p.-235fs|HOXD8_ENST00000429017.1_Frame_Shift_Ins_p.-52fs|HOXD8_ENST00000450510.2_Frame_Shift_Ins_p.-235fs	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8						anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		GGTTTCCCACGCCCTAGCCCTC	0.446																																					p.A233fs		.											.	HOXD8-90	0			c.697_698insCCCTAGCCCT						.																																			SO:0001589	frameshift_variant	3234	exon2			.		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"Homeoboxes / ANTP class : HOXL subclass"	5139	protein-coding gene	gene with protein product		142985	"homeo box D8"	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.698_707dupCCCTAGCCCT	2.37:g.176996165_176996174dupCCCTAGCCCT	ENSP00000315949:p.Leu236fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	53	14	NM_019558	0	0	0	0	0	F8WBG7|Q5BL00|Q8IXZ1	Frame_Shift_Ins	INS	ENST00000313173.4	37	CCDS2268.1																																																																																			.		0.446	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1			CCCTAGCCCT	176996165	-	CCCTAGCCCT	176996164	7	5	37	1	0	1	1	0	0	0	0	0	7346	1087	38	0	703	0	HOXD8	2	176996164	Frame_Shift_Ins	INS	-	TCGA-B1-A47N-01A-11D-A25F-10	81148654	176996164	66203209	6	3307											
PGAP1	80055	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	197750195	197750195	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatgataaatcaaccccttGcaggctttgaaataaatatg	15	11	6	9	0	1	2	1	2	0	0	1	2	1	2	3	1	2	2	3	1	7	5			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:197750195G>T	ENST00000354764.4	-	12	1339	c.1225C>A	c.(1225-1227)Caa>Aaa	p.Q409K	PGAP1_ENST00000409475.1_Missense_Mutation_p.Q409K|PGAP1_ENST00000409188.1_3'UTR	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	409					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TCAACCCCTTGCAGGCTTTGA	0.284																																					p.Q409K		.											.	PGAP1-93	0			c.C1225A						.						52	59	57					2																	197750195		2191	4286	6477	SO:0001583	missense	80055	exon12			CCCCTTGCAGGCT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1225C>A	2.37:g.197750195G>T	ENSP00000346809:p.Gln409Lys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	71	5	NM_024989	0	0	0	0	0	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425404	0.43020	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475	.	.	.	5.26	5.26	0.73747	.	0.261976	0.38778	N	0.001561	T	0.56630	0.1998	N	0.24115	0.695	0.80722	D	1	B;P	0.49447	0.228;0.924	B;P	0.62298	0.083;0.9	T	0.46373	-0.9196	9	0.06891	T	0.86	-10.914	14.225	0.65853	0.0:0.0:1.0:0.0	.	409;409	Q75T13-3;Q75T13	.;PGAP1_HUMAN	K	189;409;409	.	ENSP00000346809:Q409K	Q	-	1	0	PGAP1	197458440	0.997000	0.39634	0.967000	0.41034	0.825000	0.46686	3.380000	0.52448	2.732000	0.93576	0.591000	0.81541	CAA	.		0.284	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		T	197750195	G	T	197750195	3	4	37	1	0	0	0	0	1	0	0	0	11803	1328	46	4	1607	4	PGAP1	2	197750195	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	20754031	197750195	45449178	7	3308											
STK11IP	114790	broad.mit.edu;bcgsc.ca	37	chr2	220465972	220465972	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcaggggatgtggtcctgtCtggctgtagcaccctgagcc	5	10	15	11	0	1	1	0	1	1	0	2	2	2	2	3	4	3	4	3	4	1	1	rs564151932		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:220465972C>T	ENST00000456909.1	+	3	167	c.77C>T	c.(76-78)tCt>tTt	p.S26F	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Missense_Mutation_p.S37F			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	37					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTGGTCCTGTCTGGCTGTAGC	0.517																																					p.S37F													.	STK11IP-91	0			c.C110T						.						55	58	57					2																	220465972		2166	4274	6440	SO:0001583	missense	114790	exon3			TCCTGTCTGGCTG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.77C>T	2.37:g.220465972C>T	ENSP00000389383:p.Ser26Phe	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	108	7	NM_052902	0	0	0	0	0	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		.	.	.	.	.	.	.	.	.	.	C	18.45	3.626530	0.66901	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.05996	3.36;3.36	4.93	4.93	0.64822	.	0.137054	0.45606	D	0.000355	T	0.19248	0.0462	M	0.62723	1.935	0.44000	D	0.996702	D;D;D;D;D	0.76494	0.999;0.996;0.999;0.999;0.999	D;P;D;D;D	0.71656	0.961;0.804;0.961;0.974;0.965	T	0.00057	-1.2174	10	0.49607	T	0.09	-16.0901	11.0821	0.48066	0.3078:0.6922:0.0:0.0	.	37;37;26;37;37	B4DUE4;B4DII2;E7ERV2;Q8N1F8-2;Q8N1F8	.;.;.;.;S11IP_HUMAN	F	26;37;37	ENSP00000389383:S26F;ENSP00000295641:S37F	ENSP00000295641:S37F	S	+	2	0	STK11IP	220174216	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	4.825000	0.62708	2.568000	0.86640	0.650000	0.86243	TCT	.		0.517	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220465972	C	T	220465972	3	4	37	1	0	0	0	0	1	0	0	0	15320	913	32	2	120	2	STK11IP	2	220465972	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	22715777	220465972	22733401	8	3309											
PFKFB4	5210	broad.mit.edu	37	chr3	48576038	48576038	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggttgacatagtcagggctGcccagtttcacttgctgccg	6	11	12	12	2	2	1	2	1	0	0	2	1	2	1	2	2	3	4	2	2	1	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:48576038G>T	ENST00000232375.3	-	7	637	c.525C>A	c.(523-525)ggC>ggA	p.G175G	PFKFB4_ENST00000541519.1_Silent_p.G141G|PFKFB4_ENST00000383734.2_Silent_p.G175G|PFKFB4_ENST00000416568.1_Silent_p.G175G|PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000545984.1_3'UTR|PFKFB4_ENST00000536104.1_Silent_p.G164G	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	175	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		AGTCAGGGCTGCCCAGTTTCA	0.592																																					p.G175G													.	PFKFB4-153	0			c.C525A						.						61	53	55					3																	48576038		2203	4300	6503	SO:0001819	synonymous_variant	5210	exon7			AGGGCTGCCCAGT	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.525C>A	3.37:g.48576038G>T		Somatic	136	1		WXS	Illumina HiSeq	Phase_I	105	6	NM_004567	0	0	1	1	0	Q5S3G5|Q5XLC2|Q64EX5	Silent	SNP	ENST00000232375.3	37	CCDS2771.1																																																																																			.		0.592	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567		T	48576038	G	T	48576038	2	4	37	1	0	0	0	0	0	0	0	1	11789	1306	46	4		4	PFKFB4	3	48576038	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		48576038	149446392	9	3310											
RRP9	9136	broad.mit.edu	37	chr3	51968675	51968675	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acaaggtctgtgttgaggagGgctgccaccgacgatatcca	10	8	13	10	2	1	1	0	1	1	0	2	4	2	2	3	3	1	2	3	3	2	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:51968675G>A	ENST00000232888.6	-	12	1225	c.1152C>T	c.(1150-1152)gcC>gcT	p.A384A		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	384					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		TGTTGAGGAGGGCTGCCACCG	0.662																																					p.A384A													.	RRP9-154	0			c.C1152T						.						50	53	52					3																	51968675		2203	4300	6503	SO:0001819	synonymous_variant	9136	exon12			GAGGAGGGCTGCC	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"WD repeat domain containing"	16829	protein-coding gene	gene with protein product			"RNA, U3 small nucleolar interacting protein 2"	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.1152C>T	3.37:g.51968675G>A		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	110	3	NM_004704	0	0	30	30	0	B2R996|Q8IZ30	Silent	SNP	ENST00000232888.6	37	CCDS2837.1																																																																																			.		0.662	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704		A	51968675	G	A	51968675	2	1	37	1	0	0	0	0	0	0	0	1	13723	1219	43	2		2	RRP9	3	51968675	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	3392637	51968675	146053755	10	3311											
MFSD1	64747	broad.mit.edu	37	chr3	158539426	158539426	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggattttcttcccaggcaGcaagtgcaattaacaggtat	11	13	9	8	0	1	0	0	0	1	0	2	1	2	1	1	3	3	4	1	3	4	6			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:158539426G>T	ENST00000264266.8	+	10	966	c.904G>T	c.(904-906)Gca>Tca	p.A302S	MFSD1_ENST00000415822.2_Missense_Mutation_p.A351S|MFSD1_ENST00000392813.4_Missense_Mutation_p.A312S			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	302					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTCCCAGGCAGCAAGTGCAAT	0.289																																					p.A351S	Pancreas(62;1186 1654 36636 37908)												.	MFSD1-90	0			c.G1051T						.						56	62	60					3																	158539426		2189	4298	6487	SO:0001583	missense	64747	exon10			CAGGCAGCAAGTG	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.904G>T	3.37:g.158539426G>T	ENSP00000264266:p.Ala302Ser	Somatic	68	1		WXS	Illumina HiSeq	Phase_I	102	4	NM_022736	0	0	1	1	0	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	37		.	.	.	.	.	.	.	.	.	.	G	26.8	4.776906	0.90195	.	.	ENSG00000118855	ENST00000415822;ENST00000392813;ENST00000264266;ENST00000361159	T;D;T	0.82433	0.06;-1.61;0.06	5.46	5.46	0.80206	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.217978	0.47093	D	0.000256	D	0.88514	0.6457	M	0.74258	2.255	0.80722	D	1	P;P	0.50272	0.933;0.809	P;P	0.53102	0.718;0.512	D	0.88012	0.2763	10	0.42905	T	0.14	.	18.9102	0.92481	0.0:0.0:1.0:0.0	.	312;302	C9JS94;Q9H3U5	.;MFSD1_HUMAN	S	351;312;302;226	ENSP00000403117:A351S;ENSP00000376560:A312S;ENSP00000264266:A302S	ENSP00000264266:A302S	A	+	1	0	MFSD1	160022120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.593000	0.67550	2.549000	0.85964	0.655000	0.94253	GCA	.		0.289	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		T	158539426	G	T	158539426	3	4	37	1	0	0	0	0	1	0	0	0	9552	971	34	4	1089	4	MFSD1	3	158539426	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	106570751	158539426	39483004	11	3312											
TPRG1	285386	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	188925189	188925189	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaatgtcaacaattgggAgttttgaaggattccaggct	14	11	11	5	0	1	2	1	1	0	1	2	4	2	4	1	3	1	2	1	3	5	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:188925189A>G	ENST00000345063.3	+	2	183	c.16A>G	c.(16-18)Agt>Ggt	p.S6G	TPRG1_ENST00000433971.1_Missense_Mutation_p.S6G	NM_198485.3	NP_940887.1	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	6						cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|skin(2)|urinary_tract(1)	16	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		AACAATTGGGAGTTTTGAAGG	0.458																																					p.S6G		.											.	TPRG1-90	0			c.A16G						.						97	95	96					3																	188925189		2203	4300	6503	SO:0001583	missense	285386	exon2			ATTGGGAGTTTTG	AK125682	CCDS3292.1	3q28	2008-02-04	2008-01-16	2008-01-16	ENSG00000188001	ENSG00000188001			24759	protein-coding gene	gene with protein product			"family with sequence similarity 79, member B"	FAM79B			Standard	NM_198485		Approved	FLJ41238, FLJ43694	uc003frw.2	Q6ZUI0	OTTHUMG00000156321	ENST00000345063.3:c.16A>G	3.37:g.188925189A>G	ENSP00000341031:p.Ser6Gly	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	149	23	NM_198485	0	0	0	0	0		Missense_Mutation	SNP	ENST00000345063.3	37	CCDS3292.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678779	0.47886	.	.	ENSG00000188001	ENST00000433971;ENST00000412373;ENST00000345063;ENST00000456832	.	.	.	5.83	5.83	0.93111	.	0.488214	0.25631	N	0.029360	T	0.39410	0.1077	L	0.34521	1.04	0.31374	N	0.679799	B	0.26363	0.147	B	0.29077	0.098	T	0.48681	-0.9014	9	0.45353	T	0.12	-5.1687	12.5927	0.56451	1.0:0.0:0.0:0.0	.	6	Q6ZUI0	TPRG1_HUMAN	G	6	.	ENSP00000341031:S6G	S	+	1	0	TPRG1	190407883	1.000000	0.71417	0.982000	0.44146	0.737000	0.42083	2.764000	0.47613	2.235000	0.73313	0.533000	0.62120	AGT	.		0.458	TPRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343931.1	NM_198485		G	188925189	A	G	188925189	3	3	37	1	0	0	0	0	1	0	0	0	16451	304	11	3	18	3	TPRG1	3	188925189	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10	30385763	188925189	9097241	12	3313											
MUC4	4585	broad.mit.edu;bcgsc.ca	37	chr3	195490958	195490958	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagcccacgtggggccGcctctgctggtacagggcac	7	5	14	15	2	1	0	0	0	1	0	1	0	1	0	3	4	4	4	3	4	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:195490958G>A	ENST00000346145.4	-	10	1333	c.1294C>T	c.(1294-1296)Cgg>Tgg	p.R432W	MUC4_ENST00000463781.3_Missense_Mutation_p.R4668W|MUC4_ENST00000475231.1_Missense_Mutation_p.R4616W|MUC4_ENST00000349607.4_Missense_Mutation_p.R381W	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1425					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACGTGGGGCCGCCTCTGCTGG	0.662																																					p.R4668W													.	MUC4-90	0			c.C14002T						.						18	16	16					3																	195490958		2200	4299	6499	SO:0001583	missense	4585	exon11			GGGGCCGCCTCTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.1294C>T	3.37:g.195490958G>A	ENSP00000304207:p.Arg432Trp	Somatic	330	0		WXS	Illumina HiSeq	Phase_I	210	10	NM_018406	0	0	0	0	0	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	9.013	0.982982	0.18889	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231	T;T;T;T	0.78126	-1.15;-0.44;-0.46;-0.33	5.25	-4.79	0.03200	AMOP (2);	0.750787	0.11391	N	0.568766	T	0.73814	0.3635	M	0.76002	2.32	0.25565	N	0.986958	P;P;P;P;B;B;D	0.53619	0.469;0.922;0.779;0.91;0.027;0.027;0.961	B;P;B;B;B;B;P	0.49451	0.107;0.611;0.199;0.303;0.019;0.019;0.466	T	0.65553	-0.6140	10	0.87932	D	0	-4.1234	1.1024	0.01687	0.3996:0.1018:0.1745:0.324	.	4540;1425;381;432;4668;4616;1373	E7ESK3;Q99102;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;MUC4_HUMAN;.;.;.;.;.	W	381;432;4668;4616	ENSP00000338109:R381W;ENSP00000304207:R432W;ENSP00000417498:R4668W;ENSP00000420243:R4616W	ENSP00000304207:R432W	R	-	1	2	MUC4	196976629	0.021000	0.18746	0.104000	0.21259	0.021000	0.10359	-0.327000	0.07955	-0.553000	0.06158	-0.187000	0.12897	CGG	.		0.662	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		A	195490958	G	A	195490958	3	1	37	1	0	0	0	0	1	0	0	0	10003	1086	38	1	2296	1	MUC4	3	195490958	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	6565769	195490958	2531472	13	3314											
UBA6	55236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	68534339	68534339	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaatgttaggaattgtccTgtctccagtttgtgaggatg	9	14	12	6	1	1	1	0	1	1	0	3	4	2	3	2	2	0	2	2	2	3	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr4:68534339T>C	ENST00000322244.5	-	9	782	c.723A>G	c.(721-723)acA>acG	p.T241T	UBA6_ENST00000420827.2_Silent_p.T241T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	241					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						GGAATTGTCCTGTCTCCAGTT	0.303																																					p.T241T		.											.	UBA6-90	0			c.A723G						.						123	120	121					4																	68534339		2203	4300	6503	SO:0001819	synonymous_variant	55236	exon9			TTGTCCTGTCTCC	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"Ubiquitin-like modifier activating enzymes"	25581	protein-coding gene	gene with protein product	"UBA6, ubiquitin-activating enzyme E1"	611361	"ubiquitin-activating enzyme E1-like 2"	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.723A>G	4.37:g.68534339T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	94	5	NM_018227	0	0	0	0	0	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1																																																																																			.		0.303	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		C	68534339	T	C	68534339	2	2	37	1	0	0	0	0	0	0	0	1	16865	1567	55	3		3	UBA6	4	68534339	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		68534339	122619937	14	3315											
ACCN5	51802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	156784757	156784757	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagaaccaccaccaaccagaGcaccctgcgaattttgctcc	12	6	6	17	1	0	2	0	0	0	2	1	3	1	2	6	0	5	2	6	0	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr4:156784757G>A	ENST00000537611.2	-	2	236	c.190C>T	c.(190-192)Ctc>Ttc	p.L64F	TDO2_ENST00000506181.1_Intron	NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	64					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										ACCAACCAGAGCACCCTGCGA	0.483																																					p.L64F		.											.	.	0			c.C190T						.						131	116	121					4																	156784757		2203	4300	6503	SO:0001583	missense	51802	exon2			ACCAGAGCACCCT	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.190C>T	4.37:g.156784757G>A	ENSP00000442477:p.Leu64Phe	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	149	56	NM_017419	0	0	0	0	0		Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	G	6.118	0.390031	0.11581	.	.	ENSG00000256394	ENST00000537611	T	0.65732	-0.17	4.24	1.65	0.23941	.	0.825563	0.10479	N	0.669867	T	0.38878	0.1057	N	0.11651	0.15	0.58432	D	0.999998	B	0.10296	0.003	B	0.17979	0.02	T	0.26744	-1.0094	10	0.02654	T	1	-0.483	12.6071	0.56529	0.0:0.0:0.5103:0.4896	.	64	Q9NY37	ACCN5_HUMAN	F	64	ENSP00000442477:L64F	ENSP00000264432:L64F	L	-	1	0	ACCN5	157004207	0.075000	0.21258	0.386000	0.26170	0.148000	0.21650	0.106000	0.15354	0.224000	0.20940	-0.271000	0.10264	CTC	.		0.483	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			A	156784757	G	A	156784757	3	1	37	1	0	0	0	0	1	0	0	0	132	971	34	2	1363	2	ACCN5	4	156784757	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	88250418	156784757	34369519	15	3316											
C6orf15	29113	broad.mit.edu	37	chr6	31079878	31079878	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacctcctgcaggtgggaaGccatctgatgcaggcacgct	9	7	13	12	1	1	1	0	1	1	0	2	3	2	2	3	3	4	4	3	3	2	0			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:31079878G>T	ENST00000259870.3	-	2	261	c.258C>A	c.(256-258)ggC>ggA	p.G86G	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	86					extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CAGGTGGGAAGCCATCTGATG	0.607																																					p.G86G													.	C6orf15-90	0			c.C258A						.						52	56	55					6																	31079878		2203	4300	6503	SO:0001819	synonymous_variant	29113	exon2			TGGGAAGCCATCT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.258C>A	6.37:g.31079878G>T		Somatic	156	1		WXS	Illumina HiSeq	Phase_I	117	7	NM_014070	0	0	0	0	0	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			.		0.607	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070		T	31079878	G	T	31079878	2	4	37	1	0	0	0	0	0	0	0	1	2342	958	34	4		4	C6orf15	6	31079878	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		31079878	140035189	16	3317											
SYNGAP1	8831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33400480	33400480	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaggcttcctgagccgaCggctaaaaagctccatcaaa	14	6	9	12	2	1	1	1	1	0	0	3	2	3	1	3	2	3	4	3	2	5	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:33400480C>T	ENST00000418600.2	+	5	507	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.R136W|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.R77W|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	136					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CCTGAGCCGACGGCTAAAAAG	0.577																																					p.R136W		.											.	SYNGAP1-48	0			c.C406T						.						56	49	51					6																	33400480		2203	4300	6503	SO:0001583	missense	8831	exon5			AGCCGACGGCTAA	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.406C>T	6.37:g.33400480C>T	ENSP00000403636:p.Arg136Trp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	54	16	NM_006772	0	0	2	2	0	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	15.30	2.792591	0.50102	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.28666	1.6;1.71;1.77	4.06	-1.15	0.09709	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	M	0.69358	2.11	0.58432	D	0.999996	D;D;D	0.71674	0.965;0.98;0.998	B;P;P	0.62382	0.416;0.621;0.901	T	0.43065	-0.9414	10	0.87932	D	0	.	11.9927	0.53184	0.6778:0.3221:0.0:0.0	.	136;136;136	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	W	136;136;136;77	ENSP00000293748:R136W;ENSP00000403636:R136W;ENSP00000412475:R77W	ENSP00000293748:R136W	R	+	1	2	SYNGAP1	33508458	0.994000	0.37717	0.996000	0.52242	0.938000	0.57974	1.265000	0.33027	0.002000	0.14630	0.467000	0.42956	CGG	.		0.577	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33400480	C	T	33400480	3	4	37	1	0	0	0	0	1	0	0	0	15479	527	19	1	424	1	SYNGAP1	6	33400480	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	2320602	33400480	137714587	17	3318											
C6orf153	88745	broad.mit.edu	37	chr6	42994982	42994982	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaaactgcagcaactgcttCagcgaatggtgagtgggtaa	13	8	13	7	1	1	2	1	1	0	1	1	3	1	2	0	2	6	4	0	2	4	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:42994982C>T	ENST00000244496.5	+	5	527	c.517C>T	c.(517-519)Cag>Tag	p.Q173*		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	173					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						GCAACTGCTTCAGCGAATGGT	0.438																																					p.Q173X													.	RRP36-90	0			c.C517T						.						132	122	125					6																	42994982		2203	4300	6503	SO:0001587	stop_gained	88745	exon5			CTGCTTCAGCGAA	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"chromosome 6 open reading frame 153"	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.517C>T	6.37:g.42994982C>T	ENSP00000244496:p.Gln173*	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_033112	0	0	0	0	0	Q9BRF6|Q9P0C8	Nonsense_Mutation	SNP	ENST00000244496.5	37	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.038361	0.35989	.	.	ENSG00000124541	ENST00000244496	.	.	.	5.81	4.89	0.63831	.	0.276138	0.29040	N	0.013327	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	11.6759	0.51430	0.2645:0.7355:0.0:0.0	.	.	.	.	X	173	.	ENSP00000244496:Q173X	Q	+	1	0	RRP36	43102960	0.922000	0.31269	1.000000	0.80357	0.087000	0.18053	1.686000	0.37669	2.741000	0.93983	0.650000	0.86243	CAG	.		0.438	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		T	42994982	C	T	42994982	4	4	37	1	0	0	0	0	0	1	0	0	2344	827	29	2	535	2	C6orf153	6	42994982	Nonsense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	9594502	42994982	128120085	18	3319											
HMGN3	9324	broad.mit.edu	37	chr6	79918284	79918284	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgacaatctggcagaccGtcttgtgggctacaaaggga	10	8	13	10	2	2	2	0	1	2	1	2	3	2	3	1	3	1	3	1	3	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:79918284G>T	ENST00000344726.5	-	3	204	c.76C>A	c.(76-78)Cgg>Agg	p.R26R	HMGN3_ENST00000275036.7_Silent_p.R26R	NM_001201362.1|NM_001201363.1|NM_004242.3	NP_001188291.1|NP_001188292.1|NP_004233.1	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3	26					chromatin modification (GO:0016568)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|thyroid hormone receptor binding (GO:0046966)			central_nervous_system(1)|kidney(2)|lung(1)	4		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)		CTGGCAGACCGTCTTGTGGGC	0.353																																					p.R26R													.	HMGN3-226	0			c.C76A						.						159	160	160					6																	79918284		2203	4300	6503	SO:0001819	synonymous_variant	9324	exon3			CAGACCGTCTTGT	L40357	CCDS4988.1, CCDS4989.1, CCDS75485.1	6q14.3	2011-07-01	2002-07-25	2002-07-26	ENSG00000118418	ENSG00000118418		"High-mobility group / Canonical"	12312	protein-coding gene	gene with protein product		604502	"thyroid hormone receptor interactor 7"	TRIP7		7776974, 11356838	Standard	NM_004242		Approved		uc021zbz.1	Q15651	OTTHUMG00000015073	ENST00000344726.5:c.76C>A	6.37:g.79918284G>T		Somatic	206	1		WXS	Illumina HiSeq	Phase_I	211	5	NM_001201362	0	0	2	2	0	B2RD37|Q5HYD3|Q7RTT0|Q969M5|Q9BZT7	Silent	SNP	ENST00000344726.5	37	CCDS4988.1																																																																																			.		0.353	HMGN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041300.1	NM_004242		T	79918284	G	T	79918284	2	4	37	1	0	0	0	0	0	0	0	1	7257	1144	40	4		4	HMGN3	6	79918284	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	36923302	79918284	91196783	19	3320											
LPA	4018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	161026202	161026202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actctgtccatttccgtggtAgcactcctgcaccccaggcc	6	10	8	17	1	1	0	0	0	1	0	4	0	4	0	6	2	2	3	6	2	1	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:161026202A>G	ENST00000316300.5	-	18	2865	c.2821T>C	c.(2821-2823)Tac>Cac	p.Y941H	LPA_ENST00000447678.1_Missense_Mutation_p.Y941H			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3449	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TTTCCGTGGTAGCACTCCTGC	0.458																																					p.Y941H		.											.	LPA-74	0			c.T2821C						.						269	278	275					6																	161026202		2200	4298	6498	SO:0001583	missense	4018	exon19			CGTGGTAGCACTC	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2821T>C	6.37:g.161026202A>G	ENSP00000321334:p.Tyr941His	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	32	NM_005577	0	0	0	0	0	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	a	10.16	1.275243	0.23307	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.65364	-0.15;-0.15	2.16	2.16	0.27623	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.72087	0.3417	H	0.95816	3.725	0.21782	N	0.999546	D	0.60160	0.987	D	0.70227	0.968	T	0.61004	-0.7150	9	0.26408	T	0.33	.	6.2159	0.20656	1.0:0.0:0.0:0.0	.	3449	P08519	APOA_HUMAN	H	941	ENSP00000321334:Y941H;ENSP00000395608:Y941H	ENSP00000321334:Y941H	Y	-	1	0	LPA	160946192	0.988000	0.35896	0.913000	0.36048	0.097000	0.18754	2.967000	0.49216	0.999000	0.39023	0.155000	0.16302	TAC	.		0.458	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		G	161026202	A	G	161026202	3	3	37	1	0	0	0	0	1	0	0	0	8928	420	15	3	3389	3	LPA	6	161026202	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10	81107918	161026202	10088865	20	3321											
TAX1BP1	8887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	27856559	27856559	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatacaaaggccacctgtcAgagtcccctcttggggactg	11	8	10	12	0	2	1	1	0	1	1	3	2	3	2	4	3	1	0	4	3	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:27856559A>T	ENST00000396319.2	+	15	2075	c.1987A>T	c.(1987-1989)Aga>Tga	p.R663*	TAX1BP1_ENST00000543117.1_Nonsense_Mutation_p.R621*|TAX1BP1_ENST00000409980.1_Nonsense_Mutation_p.R687*|TAX1BP1_ENST00000433216.2_Nonsense_Mutation_p.R464*|TAX1BP1_ENST00000265393.6_Nonsense_Mutation_p.R621*	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	663					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			GCCACCTGTCAGAGTCCCCTC	0.453																																					p.R663X		.											.	TAX1BP1-153	0			c.A1987T						.						63	65	65					7																	27856559		2203	4300	6503	SO:0001587	stop_gained	8887	exon15			CCTGTCAGAGTCC	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1987A>T	7.37:g.27856559A>T	ENSP00000379612:p.Arg663*	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	74	44	NM_006024	0	0	14	17	3	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Nonsense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.886755	0.91814	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	.	.	.	5.67	4.5	0.54988	.	0.000000	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	-17.6197	12.6545	0.56780	0.857:0.143:0.0:0.0	.	.	.	.	X	621;621;687;464;663;200	.	ENSP00000265393:R621X	R	+	1	2	TAX1BP1	27823084	1.000000	0.71417	0.999000	0.59377	0.808000	0.45660	2.947000	0.49058	0.975000	0.38392	0.533000	0.62120	AGA	.		0.453	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		T	27856559	A	T	27856559	4	4	37	1	0	0	0	0	0	1	0	0	15626	180	7	5	2041	5	TAX1BP1	7	27856559	Nonsense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		27856559	131282104	21	3322											
ZNF713	349075	bcgsc.ca	37	chr7	55991337	55991337	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagaggtaatcgcgcagttGgagctagaggaagaatgggt	12	7	16	6	2	0	3	0	0	0	3	1	5	0	5	1	4	1	4	1	4	4	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:55991337G>T	ENST00000429591.2	+	3	251	c.213G>T	c.(211-213)ttG>ttT	p.L71F	ZNF713_ENST00000482436.1_3'UTR|MRPS17_ENST00000426595.1_Missense_Mutation_p.L71F	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	71	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCGCGCAGTTGGAGCTAGAGG	0.453																																					p.L71F													.	ZNF713-92	0			c.G213T						.						93	77	83					7																	55991337		2203	4300	6503	SO:0001583	missense	349075	exon3			GCAGTTGGAGCTA	AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"Zinc fingers, C2H2-type", "-"	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.213G>T	7.37:g.55991337G>T	ENSP00000416662:p.Leu71Phe	Somatic	98	0		WXS	Illumina HiSeq	Phase_1	99	5	NM_182633	0	0	2	2	0		Missense_Mutation	SNP	ENST00000429591.2	37	CCDS34639.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640080	0.29157	.	.	ENSG00000249773;ENSG00000178665	ENST00000426595;ENST00000429591	T;T	0.01015	5.44;5.44	3.48	1.65	0.23941	Krueppel-associated box (3);	0.000000	0.31531	N	0.007495	T	0.03348	0.0097	M	0.73217	2.22	0.24694	N	0.993298	D	0.71674	0.998	D	0.80764	0.994	T	0.25047	-1.0143	10	0.87932	D	0	.	5.346	0.16010	0.2585:0.0:0.7415:0.0	.	71	Q8N859	ZN713_HUMAN	F	71	ENSP00000390331:L71F;ENSP00000416662:L71F	ENSP00000390331:L71F	L	+	3	2	RP11-15K19.2;ZNF713	55958831	1.000000	0.71417	0.958000	0.39756	0.229000	0.25112	1.556000	0.36288	0.460000	0.27045	0.655000	0.94253	TTG	.		0.453	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633		T	55991337	G	T	55991337	3	4	37	1	0	0	0	0	1	0	0	0	18149	1339	47	4	223	4	ZNF713	7	55991337	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	28134778	55991337	103147326	22	3323											
GIMAP8	155038	broad.mit.edu	37	chr7	150174500	150174500	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcactgaagaggacaaaacaGctgtggcgaaactggaggcc	14	5	13	9	1	1	2	1	1	0	1	1	5	1	4	1	4	3	1	1	4	4	0			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:150174500G>T	ENST00000307271.3	+	5	2204	c.1630G>T	c.(1630-1632)Gct>Tct	p.A544S		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	544	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		GGACAAAACAGCTGTGGCGAA	0.502																																					p.A544S													.	GIMAP8-95	0			c.G1630T						.						80	77	78					7																	150174500		2203	4300	6503	SO:0001583	missense	155038	exon5			AAAACAGCTGTGG	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1630G>T	7.37:g.150174500G>T	ENSP00000305107:p.Ala544Ser	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	100	6	NM_175571	0	0	5	5	0		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.633250	0.47049	.	.	ENSG00000171115	ENST00000307271	T	0.34859	1.34	4.44	1.39	0.22231	AIG1 (1);	3.096750	0.01386	N	0.013095	T	0.33673	0.0871	L	0.41236	1.265	0.09310	N	1	P	0.35793	0.521	B	0.38378	0.272	T	0.23833	-1.0177	10	0.45353	T	0.12	.	5.6382	0.17548	0.3651:0.0:0.6349:0.0	.	544	Q8ND71	GIMA8_HUMAN	S	544	ENSP00000305107:A544S	ENSP00000305107:A544S	A	+	1	0	GIMAP8	149805433	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.442000	0.21628	0.518000	0.28383	-0.150000	0.13652	GCT	.		0.502	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		T	150174500	G	T	150174500	3	4	37	1	0	0	0	0	1	0	0	0	6405	971	34	4	1644	4	GIMAP8	7	150174500	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	94183163	150174500	8964163	23	3324											
CHD7	55636	broad.mit.edu	37	chr8	61775123	61775123	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagatgggtggagctatggCgcctccaatgaaggatctac	10	8	13	10	1	1	2	0	1	1	1	2	4	2	4	3	4	2	1	3	4	4	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr8:61775123C>T	ENST00000423902.2	+	37	8467	c.7988C>T	c.(7987-7989)gCg>gTg	p.A2663V	CHD7_ENST00000524602.1_Missense_Mutation_p.A614V	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2663					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GGAGCTATGGCGCCTCCAATG	0.448																																					p.A2663V													.	CHD7-141	0			c.C7988T						.						48	52	51					8																	61775123		1869	4092	5961	SO:0001583	missense	55636	exon37			CTATGGCGCCTCC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.7988C>T	8.37:g.61775123C>T	ENSP00000392028:p.Ala2663Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	69	3	NM_017780	0	0	3	3	0	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	36	5.614620	0.96649	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602	T;T	0.71817	-0.6;-0.6	5.59	5.59	0.84812	BRK domain (2);	0.000000	0.64402	D	0.000007	D	0.84723	0.5535	M	0.76328	2.33	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.85891	0.1428	10	0.87932	D	0	-14.5932	19.592	0.95518	0.0:1.0:0.0:0.0	.	2663	Q9P2D1	CHD7_HUMAN	V	2663;2663;614	ENSP00000392028:A2663V;ENSP00000437061:A614V	ENSP00000307304:A2663V	A	+	2	0	CHD7	61937677	1.000000	0.71417	0.966000	0.40874	0.981000	0.71138	7.800000	0.85949	2.628000	0.89032	0.655000	0.94253	GCG	.		0.448	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		T	61775123	C	T	61775123	3	4	37	1	0	0	0	0	1	0	0	0	3336	768	27	1	8130	1	CHD7	8	61775123	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		61775123	84588899	24	3325											
LAMC3	10319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	133948708	133948708	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcccgtgccctcgccaggaGgtgagtcccaagacatggtg	7	6	15	13	2	0	2	0	1	0	1	2	3	1	3	4	4	1	0	4	4	1	0			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr9:133948708G>A	ENST00000361069.4	+	20	3627	c.3494G>A	c.(3493-3495)aGc>aAc	p.S1165N	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1165	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CTCGCCAGGAGGTGAGTCCCA	0.607																																					p.S1165N		.											.	LAMC3-93	0			c.G3494A						.						46	46	46					9																	133948708		2203	4300	6503	SO:0001630	splice_region_variant	10319	exon20			CCAGGAGGTGAGT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3494+1G>A	9.37:g.133948708G>A		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_006059	0	0	0	0	0	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450700	0.26074	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.29655	1.56	4.23	4.23	0.50019	.	0.177619	0.64402	D	0.000012	T	0.34221	0.0890	M	0.68317	2.08	0.39455	D	0.967477	P	0.36789	0.57	B	0.40038	0.317	T	0.15093	-1.0449	10	0.17832	T	0.49	.	14.3309	0.66556	0.0:0.0:1.0:0.0	.	1165	Q9Y6N6	LAMC3_HUMAN	N	1165	ENSP00000354360:S1165N	ENSP00000347156:S1165N	S	+	2	0	LAMC3	132938529	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.044000	0.71012	2.365000	0.80145	0.555000	0.69702	AGC	.		0.607	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation	A	133948708	G	A	133948708	5	1	37	1	0	0	0	0	0	0	1	0	8637	1014	35	2	3572	2	LAMC3	9	133948708	Splice_Site	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		133948708	7264723	25	3326											
ARHGAP21	57584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	24873803	24873803	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggtagcatctctgtgcccTcctagtgtatgtctgcgccg	4	13	11	13	3	2	0	0	0	2	0	5	0	3	0	3	1	3	3	3	1	3	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr10:24873803T>C	ENST00000396432.2	-	26	5901	c.5415A>G	c.(5413-5415)ggA>ggG	p.G1805G		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1804	Interaction with CTNNA1.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CTCTGTGCCCTCCTAGTGTAT	0.488																																					p.G1805G		.											.	ARHGAP21-235	0			c.A5415G						.						50	50	50					10																	24873803		2203	4300	6503	SO:0001819	synonymous_variant	57584	exon26			GTGCCCTCCTAGT	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.5415A>G	10.37:g.24873803T>C		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	86	32	NM_020824	0	0	14	23	9	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000396432.2	37	CCDS7144.2																																																																																			.		0.488	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24873803	T	C	24873803	2	2	37	1	0	0	0	0	0	0	0	1	871	1538	54	3		3	ARHGAP21	10	24873803	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		24873803	110660944	26	3327											
MUC5B	727897	broad.mit.edu	37	chr11	1281625	1281625	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctactcctgtgaggagggTaagtggaagccaccttccca	9	9	12	11	0	0	1	0	1	0	0	2	3	2	3	4	3	3	2	4	3	3	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:1281625T>G	ENST00000529681.1	+	47	17024		c.e47+2		MUC5B_ENST00000447027.1_Splice_Site	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming						cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GTGAGGAGGGTAAGTGGAAGC	0.667																																					.													.	.	0			c.16966+2T>G						.						25	30	28					11																	1281625		2116	4234	6350	SO:0001630	splice_region_variant	727897	exon47			GGAGGGTAAGTGG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16966+2T>G	11.37:g.1281625T>G		Somatic	175	10		WXS	Illumina HiSeq	Phase_I	116	11	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Splice_Site	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321366	0.41096	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	.	.	.	4.68	3.5	0.40072	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.177	0.25751	0.1985:0.0:0.0:0.8015	.	.	.	.	.	-1	.	.	.	+	.	.	MUC5B	1238201	1.000000	0.71417	0.187000	0.23214	0.732000	0.41865	2.167000	0.42415	0.773000	0.33404	0.533000	0.62120	.	.		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	Intron	G	1281625	T	G	1281625	5	3	37	1	0	0	0	0	0	0	1	0	10004	1652	57	5	17163	5	MUC5B	11	1281625	Splice_Site	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		1281625	133724891	27	3328											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643082	1643082	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaacccccacaagagccaTagccccccttggagccccca	10	4	8	19	0	0	1	0	0	0	1	0	3	0	3	8	2	4	0	8	2	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:1643082T>C	ENST00000399682.1	-	1	286	c.242A>G	c.(241-243)tAt>tGt	p.Y81C		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAAGAGCCATAGCCCCCCTT	0.657																																					p.Y81C		.											.	.	0			c.A242G						.						9	16	14					11																	1643082		684	1578	2262	SO:0001583	missense	387267	exon1			GAGCCATAGCCCC	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.242A>G	11.37:g.1643082T>C	ENSP00000382590:p.Tyr81Cys	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	29	4	NM_001012709	0	0	0	1	1		Missense_Mutation	SNP	ENST00000399682.1	37		.	.	.	.	.	.	.	.	.	.	C	0.053	-1.244643	0.01481	.	.	ENSG00000241598	ENST00000399682;ENST00000328953	T	0.00646	6.0	3.19	3.19	0.36642	.	.	.	.	.	T	0.00144	0.0004	N	0.00004	-3.39	0.20196	N	0.999929	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	.	5.8653	0.18771	0.0:0.738:0.0:0.262	rs59610171	81	Q6L8H1	KRA54_HUMAN	C	81	ENSP00000382590:Y81C	ENSP00000331603:Y81C	Y	-	2	0	KRTAP5-4	1599658	0.218000	0.23608	0.997000	0.53966	0.226000	0.24999	0.624000	0.24462	0.452000	0.26830	-0.254000	0.11334	TAT	.		0.657	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		C	1643082	T	C	1643082	3	2	37	1	0	0	0	0	1	0	0	0	8584	1406	49	3	448	3	KRTAP5-4	11	1643082	Missense_Mutation	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10	361457	1643082	133363434	28	3329											
ARHGAP1	392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46702650	46702650	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acatagaagatcttctgcccGaacttgaagctgttggtgga	11	11	11	8	1	2	3	0	1	2	2	2	5	2	4	1	2	3	2	1	2	4	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:46702650G>A	ENST00000311956.4	-	7	643	c.546C>T	c.(544-546)ttC>ttT	p.F182F		NM_004308.3	NP_004299.1	Q07960	RHG01_HUMAN	Rho GTPase activating protein 1	182	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	Rac GTPase activator activity (GO:0030675)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)		TCTTCTGCCCGAACTTGAAGC	0.602																																					p.F182F		.											.	ARHGAP1-227	0			c.C546T						.						84	90	88					11																	46702650		2201	4299	6500	SO:0001819	synonymous_variant	392	exon7			CTGCCCGAACTTG	BC018118	CCDS7922.1	11p11.2	2006-04-11			ENSG00000175220	ENSG00000175220		"Rho GTPase activating proteins"	673	protein-coding gene	gene with protein product		602732				8288572	Standard	NM_004308		Approved	RhoGAP, p50rhoGAP, CDC42GAP, Cdc42GAP	uc001ndd.4	Q07960	OTTHUMG00000166567	ENST00000311956.4:c.546C>T	11.37:g.46702650G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	58	5	NM_004308	0	0	0	0	0	D3DQQ6	Silent	SNP	ENST00000311956.4	37	CCDS7922.1	.	.	.	.	.	.	.	.	.	.	G	9.301	1.052993	0.19907	.	.	ENSG00000175220	ENST00000528837	.	.	.	5.28	1.37	0.22104	.	.	.	.	.	T	0.57770	0.2076	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51356	-0.8716	4	.	.	.	.	9.3727	0.38264	0.7873:0.0:0.2127:0.0	.	.	.	.	W	136	.	.	R	-	1	2	ARHGAP1	46659226	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.205000	0.32308	0.323000	0.23307	-0.459000	0.05422	CGG	.		0.602	ARHGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390472.1	NM_004308		A	46702650	G	A	46702650	2	1	37	1	0	0	0	0	0	0	0	1	861	1049	37	1		1	ARHGAP1	11	46702650	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	45059568	46702650	88303866	29	3330											
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	62296065	62296065	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaattttggcaccgacaCatccacatcccctttgactt	9	12	4	16	1	0	1	0	1	0	0	3	2	3	1	5	1	0	1	5	1	1	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:62296065C>T	ENST00000378024.4	-	5	6098	c.5824G>A	c.(5824-5826)Gtg>Atg	p.V1942M	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1942					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GGCACCGACACATCCACATCC	0.502																																					p.V1942M		.											.	AHNAK-109	0			c.G5824A						.						216	226	223					11																	62296065		2202	4299	6501	SO:0001583	missense	79026	exon5			CCGACACATCCAC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.5824G>A	11.37:g.62296065C>T	ENSP00000367263:p.Val1942Met	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	188	14	NM_001620	0	0	6	6	0	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	6.228	0.410192	0.11812	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.01272	5.07	2.29	1.33	0.21861	.	.	.	.	.	T	0.03608	0.0103	M	0.88105	2.93	0.27412	N	0.95455	P	0.41131	0.739	B	0.40602	0.334	T	0.14643	-1.0465	9	0.66056	D	0.02	.	7.0623	0.25133	0.0:0.8577:0.0:0.1423	.	1942	Q09666	AHNK_HUMAN	M	31;1942	ENSP00000367263:V1942M	ENSP00000244934:V31M	V	-	1	0	AHNAK	62052641	0.700000	0.27796	0.013000	0.15412	0.006000	0.05464	-0.172000	0.09868	0.317000	0.23160	0.186000	0.17326	GTG	.		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62296065	C	T	62296065	3	4	37	1	0	0	0	0	1	0	0	0	414	478	17	2	11968	2	AHNAK	11	62296065	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	15593415	62296065	72710451	30	3331											
PC	5091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66636384	66636384	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctcgatgaagtagtgctTgccgtgcctgtccaccagga	8	9	12	12	2	0	1	0	1	0	0	2	4	1	2	5	1	3	2	5	1	2	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:66636384T>C	ENST00000393958.2	-	9	1048	c.955A>G	c.(955-957)Aag>Gag	p.K319E	PC_ENST00000355677.3_Missense_Mutation_p.K319E|PC_ENST00000393955.2_Missense_Mutation_p.K319E|PC_ENST00000524491.1_Missense_Mutation_p.K279E|PC_ENST00000393960.1_Missense_Mutation_p.K319E	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	319	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	AAGTAGTGCTTGCCGTGCCTG	0.687																																					p.K319E		.											.	PC-228	0			c.A955G						.						92	81	84					11																	66636384		2200	4295	6495	SO:0001583	missense	5091	exon9			AGTGCTTGCCGTG	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.955A>G	11.37:g.66636384T>C	ENSP00000377530:p.Lys319Glu	Somatic	336	1		WXS	Illumina HiSeq	Phase_I	190	65	NM_000920	0	0	1	1	0	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.333430	0.41297	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31	4.65	4.65	0.58169	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.063886	0.64402	D	0.000015	D	0.91643	0.7359	N	0.13352	0.335	0.43226	D	0.995117	B	0.09022	0.002	B	0.21360	0.034	D	0.87584	0.2486	10	0.13108	T	0.6	-19.2405	12.029	0.53388	0.0:0.0:0.0:1.0	.	319	P11498	PYC_HUMAN	E	319;319;319;279;319	ENSP00000377527:K319E;ENSP00000377530:K319E;ENSP00000377532:K319E;ENSP00000434192:K279E;ENSP00000347900:K319E	ENSP00000347900:K319E	K	-	1	0	PC	66392960	0.994000	0.37717	1.000000	0.80357	0.938000	0.57974	1.707000	0.37888	1.730000	0.51580	0.459000	0.35465	AAG	.		0.687	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		C	66636384	T	C	66636384	3	2	37	1	0	0	0	0	1	0	0	0	11523	1821	63	3	2637	3	PC	11	66636384	Missense_Mutation	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10	4340319	66636384	68370132	31	3332											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825248	95825248	+	Silent	SNP	C	C	T																															tgctgttgttgttgctgctgCtgctgctgttgttgctgctg																										TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:95825248C>T	ENST00000524717.1	-	2	3231	c.1947G>A	c.(1945-1947)caG>caA	p.Q649Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	649					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gttgctgctgctgctgctgtt	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q649Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.G1947A						.						33	39	37					11																	95825248		2115	4166	6281	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1947G>A	11.37:g.95825248C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	139	25	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825248	C	T	95825248	2	4	37	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825248	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	29188864	95825248	39181268	32	3333	31	2									
MAML2	84441	ucsc.edu	37	chr11	95825254	95825254	+	Silent	SNP	C	C	T																															tgttgttgctgctgctgctgCtgttgttgctgctgctgctg																								rs61749250		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:95825254C>T	ENST00000524717.1	-	2	3225	c.1941G>A	c.(1939-1941)caG>caA	p.Q647Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	647					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q647Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgttgttgct	0.512			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q647Q				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	1	Substitution - coding silent(1)	endometrium(1)	c.G1941A						.	C		0,4198		0,0,2099	35	40	38		1941	1.7	0.1	11	dbSNP_129	38	5,8237		0,5,4116	no	coding-synonymous	MAML2	NM_032427.1		0,5,6215	TT,TC,CC		0.0607,0.0,0.0402		647/1157	95825254	5,12435	2099	4121	6220	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1941G>A	11.37:g.95825254C>T		Somatic	113	0		WXS	Illumina HiSeq		146	28	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.512	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825254	C	T	95825254	2	4	37	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825254	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	6	95825254	39181262	33	3334	31	2									
SLC6A12	6539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	306024	306024	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatagtcacagccttggggAaggcgatgaaggccagccca	11	6	13	11	1	2	1	2	1	0	0	2	3	2	2	3	4	2	0	3	4	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:306024A>G	ENST00000428720.1	-	11	1843	c.1100T>C	c.(1099-1101)tTc>tCc	p.F367S	SLC6A12_ENST00000397296.2_Missense_Mutation_p.F367S|SLC6A12_ENST00000538272.1_5'Flank|RP11-283I3.1_ENST00000544067.1_RNA|SLC6A12_ENST00000536824.1_Missense_Mutation_p.F367S|SLC6A12_ENST00000359674.4_Missense_Mutation_p.F367S|SLC6A12_ENST00000424061.2_Missense_Mutation_p.F367S	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	367					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AGCCTTGGGGAAGGCGATGAA	0.587																																					p.F367S		.											.	SLC6A12-91	0			c.T1100C						.						107	96	100					12																	306024		2203	4300	6503	SO:0001583	missense	6539	exon11			TTGGGGAAGGCGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1100T>C	12.37:g.306024A>G	ENSP00000388184:p.Phe367Ser	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	85	24	NM_001122848	0	0	5	7	2	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.780522	0.70222	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	4.26	4.26	0.50523	.	0.067703	0.64402	D	0.000013	D	0.86644	0.5982	M	0.85777	2.775	0.44261	D	0.997113	D	0.58268	0.982	D	0.70935	0.971	D	0.87360	0.2343	10	0.87932	D	0	.	7.5395	0.27729	0.6532:0.0:0.0:0.3468	.	367	P48065	S6A12_HUMAN	S	367	ENSP00000352702:F367S;ENSP00000380464:F367S;ENSP00000388184:F367S;ENSP00000399136:F367S;ENSP00000444268:F367S	ENSP00000352702:F367S	F	-	2	0	SLC6A12	176285	1.000000	0.71417	0.987000	0.45799	0.802000	0.45316	6.483000	0.73617	1.782000	0.52362	0.391000	0.25812	TTC	.		0.587	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		G	306024	A	G	306024	3	3	37	1	0	0	0	0	1	0	0	0	14707	246	9	3	768	3	SLC6A12	12	306024	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		306024	133545871	34	3335											
CACNA1C	775	bcgsc.ca	37	chr12	2794921	2794921	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctctcctaccaggatgacGaaaatcggcaactgacgctc	11	7	10	13	3	1	2	0	2	1	0	4	4	1	3	2	3	2	3	2	3	4	1	rs200231105	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:2794921G>A	ENST00000347598.4	+	46	5737	c.5737G>A	c.(5737-5739)Gaa>Aaa	p.E1913K	CACNA1C_ENST00000399649.1_Missense_Mutation_p.E1871K|CACNA1C_ENST00000399595.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000406454.3_Missense_Mutation_p.E1936K|CACNA1C_ENST00000399617.1_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399644.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000344100.3_Missense_Mutation_p.E1906K|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399634.1_Missense_Mutation_p.E1936K|CACNA1C_ENST00000399591.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000399603.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000327702.7_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399597.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399606.1_Missense_Mutation_p.E1885K|CACNA1C_ENST00000335762.5_Missense_Mutation_p.E1890K|CACNA1C_ENST00000399641.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399601.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000402845.3_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399638.1_Missense_Mutation_p.E1893K|CACNA1C_ENST00000399629.1_Missense_Mutation_p.E1882K|CACNA1C_ENST00000399637.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399621.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399655.1_Missense_Mutation_p.E1865K	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1948					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E1913K(2)|p.E1906K(2)|p.E1978K(2)|p.E1900K(2)|p.E1400K(2)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCAGGATGACGAAAATCGGCA	0.592																																					p.E1948K													.	CACNA1C-34	10	Substitution - Missense(10)	kidney(5)|endometrium(5)	c.G5842A						.						47	48	48					12																	2794921		2013	4164	6177	SO:0001583	missense	775	exon47			GATGACGAAAATC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5737G>A	12.37:g.2794921G>A	ENSP00000266376:p.Glu1913Lys	Somatic	139	7		WXS	Illumina HiSeq	Phase_1	175	20	NM_199460	0	0	0	0	0	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988512	0.53934	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39	4.26	3.35	0.38373	.	1.675690	0.03914	N	0.282339	T	0.64427	0.2597	L	0.39633	1.23	0.24214	N	0.99546	P;D;P;B;D;P;P;D;B;B;D;P;P;B;P;B;P;B;D;P;P;D;D;P;P	0.76494	0.801;0.999;0.941;0.097;0.999;0.921;0.953;0.961;0.11;0.33;0.978;0.941;0.757;0.432;0.902;0.306;0.757;0.062;0.978;0.588;0.769;0.961;0.961;0.882;0.941	B;P;B;B;D;B;B;P;B;B;P;B;B;B;B;B;B;B;P;B;B;P;P;B;B	0.78314	0.21;0.858;0.304;0.03;0.991;0.308;0.378;0.485;0.04;0.071;0.485;0.304;0.122;0.099;0.114;0.033;0.122;0.024;0.485;0.172;0.172;0.485;0.485;0.172;0.304	T	0.56056	-0.8042	10	0.07030	T	0.85	.	14.0749	0.64885	0.0:0.1521:0.8479:0.0	.	556;1906;1862;1948;1900;1884;1865;1882;1893;1865;1885;1865;1896;1913;1865;1900;1936;1873;1871;1873;1854;1884;1884;1865;1865	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	K	1890;1865;1865;1893;1865;1884;1884;1873;1865;1913;1885;1865;1906;1882;1900;1871;1884;1865;1936;1900;1936;1873;1766	ENSP00000336982:E1890K;ENSP00000382563:E1865K;ENSP00000382552:E1865K;ENSP00000382547:E1893K;ENSP00000382506:E1865K;ENSP00000382530:E1884K;ENSP00000382546:E1884K;ENSP00000382500:E1873K;ENSP00000382549:E1865K;ENSP00000266376:E1913K;ENSP00000382515:E1885K;ENSP00000382510:E1865K;ENSP00000341092:E1906K;ENSP00000382537:E1882K;ENSP00000329877:E1900K;ENSP00000382557:E1871K;ENSP00000385724:E1884K;ENSP00000382512:E1865K;ENSP00000382542:E1936K;ENSP00000382526:E1900K;ENSP00000385896:E1936K;ENSP00000382504:E1873K	ENSP00000323129:E1766K	E	+	1	0	CACNA1C	2665182	1.000000	0.71417	0.943000	0.38184	0.802000	0.45316	5.486000	0.66856	0.981000	0.38548	0.449000	0.29647	GAA	G|0.500;A|0.500		0.592	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2794921	G	A	2794921	3	1	37	1	0	0	0	0	1	0	0	0	2546	1059	37	1	6476	1	CACNA1C	12	2794921	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	2488897	2794921	131056974	35	3336											
R3HDM2	22864	broad.mit.edu	37	chr12	57648792	57648792	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctgagcatccttgagccActggatcttggcgccagaca	8	8	10	15	1	1	3	0	2	1	1	2	4	2	4	5	2	2	1	5	2	0	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:57648792A>C	ENST00000347140.3	-	24	3085	c.2695T>G	c.(2695-2697)Tgg>Ggg	p.W899G	R3HDM2_ENST00000403821.2_Missense_Mutation_p.W933G|R3HDM2_ENST00000402412.1_Missense_Mutation_p.W913G|R3HDM2_ENST00000358907.2_Missense_Mutation_p.W899G|R3HDM2_ENST00000413953.2_Intron|RP11-123K3.4_ENST00000548184.1_Intron|R3HDM2_ENST00000441731.2_Missense_Mutation_p.W594G			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	899						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TCCTTGAGCCACTGGATCTTG	0.637																																					p.W899G													.	R3HDM2-92	0			c.T2695G						.						63	60	61					12																	57648792		2203	4300	6503	SO:0001583	missense	22864	exon22			TGAGCCACTGGAT	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.2695T>G	12.37:g.57648792A>C	ENSP00000317903:p.Trp899Gly	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	82	5	NM_014925	0	0	3	3	0	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	A	18.09	3.545615	0.65198	.	.	ENSG00000179912	ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821	T;T;T;T;T;T;T	0.54279	0.58;1.53;1.55;1.53;0.58;1.18;1.53	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.66655	0.2811	L	0.52573	1.65	0.52099	D	0.999947	P;P;D;P	0.63880	0.487;0.487;0.993;0.578	B;B;D;B	0.72982	0.167;0.167;0.979;0.281	T	0.69409	-0.5153	10	0.87932	D	0	-4.49	14.5277	0.67900	1.0:0.0:0.0:0.0	.	933;913;899;626	B5MCG9;B5MCU0;Q9Y2K5;E9PAL1	.;.;R3HD2_HUMAN;.	G	626;899;913;899;594;664;933	ENSP00000377400:W626G;ENSP00000317903:W899G;ENSP00000385839:W913G;ENSP00000351784:W899G;ENSP00000408536:W594G;ENSP00000394676:W664G;ENSP00000385169:W933G	ENSP00000317903:W899G	W	-	1	0	R3HDM2	55935059	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.710000	0.91388	2.326000	0.78906	0.533000	0.62120	TGG	.		0.637	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		C	57648792	A	C	57648792	3	2	37	1	0	0	0	0	1	0	0	0	12920	159	6	5	239	5	R3HDM2	12	57648792	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10	54853871	57648792	76203103	36	3337											
ALX1	8092	broad.mit.edu;bcgsc.ca	37	chr12	85680745	85680745	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatcagttttgccaaggactGacagctacccacaggtatgc	11	10	9	11	0	1	1	1	1	0	0	1	2	1	2	2	2	4	3	2	2	4	5			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:85680745G>A	ENST00000316824.3	+	3	801	c.646G>A	c.(646-648)Gac>Aac	p.D216N		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	216					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		GCCAAGGACTGACAGCTACCC	0.378																																					p.D216N													.	ALX1-24	0			c.G646A						.						130	117	121					12																	85680745		2203	4300	6503	SO:0001583	missense	8092	exon3			AGGACTGACAGCT	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"Homeoboxes / PRD class"	1494	protein-coding gene	gene with protein product		601527	"cartilage paired-class homeoprotein 1"	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.646G>A	12.37:g.85680745G>A	ENSP00000315417:p.Asp216Asn	Somatic	52	1		WXS	Illumina HiSeq	Phase_I	69	6	NM_006982	0	0	0	0	0	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847661	0.71603	.	.	ENSG00000180318	ENST00000316824	D	0.92805	-3.11	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.91717	0.7381	L	0.61218	1.895	0.80722	D	1	B	0.15141	0.012	B	0.19946	0.027	D	0.87471	0.2414	10	0.54805	T	0.06	.	20.0044	0.97430	0.0:0.0:1.0:0.0	.	216	Q15699	ALX1_HUMAN	N	216	ENSP00000315417:D216N	ENSP00000315417:D216N	D	+	1	0	ALX1	84204876	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.864000	0.99589	2.714000	0.92807	0.650000	0.86243	GAC	.		0.378	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		A	85680745	G	A	85680745	3	1	37	1	0	0	0	0	1	0	0	0	556	1290	45	2	656	2	ALX1	12	85680745	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	28031953	85680745	48171150	37	3338											
GALNT9	50614	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132834320	132834320	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagttgtagccatgggcggcGttcgcatactgctgcacctc	6	10	12	13	3	0	0	0	0	0	0	2	0	0	0	2	2	4	6	2	2	2	4	rs554022886		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:132834320G>A	ENST00000328957.8	-	5	866	c.867C>T	c.(865-867)aaC>aaT	p.N289N	GALNT9_ENST00000535208.1_5'Flank|GALNT9_ENST00000535228.1_5'Flank	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	289					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		CATGGGCGGCGTTCGCATACT	0.632													g|||	1	0.000199681	8e-04	0	5008	,	,		12187	0		0	False		,,,				2504	0				p.N289N	Colon(186;2147 2752 13553 41466)	.											.	GALNT9-90	0			c.C867T						.						27	32	30					12																	132834320		692	1591	2283	SO:0001819	synonymous_variant	50614	exon5			GGCGGCGTTCGCA	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4131	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 9"	606251	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.867C>T	12.37:g.132834320G>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	72	18	NM_001122636	0	0	0	0	0	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37																																																																																				.		0.632	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		A	132834320	G	A	132834320	2	1	37	1	0	0	0	0	0	0	0	1	6240	1136	40	1		1	GALNT9	12	132834320	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	47153575	132834320	1017575	38	3339											
GJA3	2700	broad.mit.edu	37	chr13	20717168	20717168	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtagatgagggtgggcGtggacacgaagatgatctgc	10	7	17	7	2	1	4	0	2	1	2	1	6	1	5	1	4	1	1	1	4	2	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:20717168G>A	ENST00000241125.3	-	2	436	c.260C>T	c.(259-261)aCg>aTg	p.T87M		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	87			T -> M (in CTRCT14; pearl box cataract). {ECO:0000269|PubMed:17615540}.		cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		GAGGGTGGGCGTGGACACGAA	0.612																																					p.T87M													.	GJA3-69	0			c.C260T	GRCh37	CM071794	GJA3	M		.						85	75	78					13																	20717168		2203	4300	6503	SO:0001583	missense	2700	exon2			GTGGGCGTGGACA	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"Ion channels / Gap junction proteins (connexins)"	4277	protein-coding gene	gene with protein product	"connexin 46"	121015	"gap junction protein, alpha 3, 46kD (connexin 46)", "gap junction protein, alpha 3, 46kDa (connexin 46)"	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.260C>T	13.37:g.20717168G>A	ENSP00000241125:p.Thr87Met	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	145	5	NM_021954	0	0	0	0	0	Q0VAB7|Q9H537	Missense_Mutation	SNP	ENST00000241125.3	37	CCDS9289.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785307	0.90282	.	.	ENSG00000121743	ENST00000241125	D	0.99207	-5.56	5.36	5.36	0.76844	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99423	0.9796	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.99000	1.0811	10	0.72032	D	0.01	.	19.094	0.93242	0.0:0.0:1.0:0.0	.	87	Q9Y6H8	CXA3_HUMAN	M	87	ENSP00000241125:T87M	ENSP00000241125:T87M	T	-	2	0	GJA3	19615168	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.735000	0.98825	2.517000	0.84864	0.561000	0.74099	ACG	.		0.612	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954		A	20717168	G	A	20717168	3	1	37	1	0	0	0	0	1	0	0	0	6422	1145	40	1	1051	1	GJA3	13	20717168	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		20717168	94452710	39	3340											
GPR12	2835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	27332981	27332981	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacacatcactgggcgagcgCgctctctgggcgagactgga	8	7	14	12	4	2	1	1	0	1	1	3	4	2	2	0	3	2	1	0	3	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:27332981C>T	ENST00000381436.2	-	1	1446	c.984G>A	c.(982-984)gcG>gcA	p.A328A	GPR12_ENST00000405846.3_Silent_p.A328A			P47775	GPR12_HUMAN	G protein-coupled receptor 12	328					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		TGGGCGAGCGCGCTCTCTGGG	0.537																																					p.A328A		.											.	GPR12-90	0			c.G984A						.						65	67	66					13																	27332981		2203	4300	6503	SO:0001819	synonymous_variant	2835	exon2			CGAGCGCGCTCTC	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.984G>A	13.37:g.27332981C>T		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	127	56	NM_005288	0	0	0	0	0	Q5T8P3	Silent	SNP	ENST00000381436.2	37	CCDS9319.1																																																																																			.		0.537	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			T	27332981	C	T	27332981	2	4	37	1	0	0	0	0	0	0	0	1	6655	755	27	1		1	GPR12	13	27332981	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	6615813	27332981	87836897	40	3341											
FRY	10129	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	32823745	32823745	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagggccatggccgtcacccGgagcacatcttccacttcct	7	8	9	17	2	2	0	1	0	1	0	4	1	4	1	5	3	1	1	5	3	0	2	rs372186855		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:32823745G>T	ENST00000380250.3	+	49	7587	c.7091G>T	c.(7090-7092)cGg>cTg	p.R2364L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2364						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GCCGTCACCCGGAGCACATCT	0.542																																					p.R2364L		.											.	FRY-142	0			c.G7091T						.						73	76	75					13																	32823745		2015	4173	6188	SO:0001583	missense	10129	exon49			TCACCCGGAGCAC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.7091G>T	13.37:g.32823745G>T	ENSP00000369600:p.Arg2364Leu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_023037	0	0	6	6	0	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453660	0.96223	.	.	ENSG00000073910	ENST00000380250;ENST00000380257;ENST00000380235	T	0.25085	1.82	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	L	0.54323	1.7	0.80722	D	1	P	0.46784	0.884	B	0.42214	0.38	T	0.02821	-1.1106	10	0.54805	T	0.06	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	2364	Q5TBA9	FRY_HUMAN	L	2364;1174;5	ENSP00000369600:R2364L	ENSP00000369567:R5L	R	+	2	0	FRY	31721745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.894000	0.99253	0.655000	0.94253	CGG	.		0.542	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32823745	G	T	32823745	3	4	37	1	0	0	0	0	1	0	0	0	6082	1116	39	4	7285	4	FRY	13	32823745	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	5490764	32823745	82346133	41	3342											
C13orf23	80209	broad.mit.edu	37	chr13	39600511	39600511	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tagcatgaggagctttgcagCcccccttgaaagcctgtaat	10	10	10	11	0	0	2	0	2	0	0	0	3	0	3	4	1	5	4	4	1	3	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:39600511C>T	ENST00000352251.3	-	6	1216	c.383G>A	c.(382-384)gGc>gAc	p.G128D	PROSER1_ENST00000350125.3_Missense_Mutation_p.G106D|PROSER1_ENST00000484434.3_5'Flank	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	128																	AGCTTTGCAGCCCCCCTTGAA	0.393																																					p.G128D													.	.	0			c.G383A						.						87	92	90					13																	39600511		2203	4300	6503	SO:0001583	missense	80209	exon6			TTGCAGCCCCCCT	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.383G>A	13.37:g.39600511C>T	ENSP00000332034:p.Gly128Asp	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_025138	0	0	0	0	0	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.561329	0.86335	.	.	ENSG00000120685	ENST00000352251;ENST00000350125;ENST00000436678	T;T	0.70749	-0.51;-0.4	5.44	5.44	0.79542	.	.	.	.	.	T	0.74898	0.3777	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.72763	-0.4195	8	.	.	.	-2.7574	17.1251	0.86712	0.0:1.0:0.0:0.0	.	106;128	A6NJ97;Q86XN7	.;PRSR1_HUMAN	D	128;106;107	ENSP00000332034:G128D;ENSP00000339123:G106D	.	G	-	2	0	PROSER1	38498511	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	7.019000	0.76412	2.720000	0.93068	0.650000	0.86243	GGC	.		0.393	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		T	39600511	C	T	39600511	3	4	37	1	0	0	0	0	1	0	0	0	1725	739	26	2	2483	2	C13orf23	13	39600511	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	6776766	39600511	75569367	42	3343											
PRPF39	55015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	45564665	45564665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgacgctgacagaaacagaaGcaaatttccctccagaatat	16	8	7	10	1	0	5	0	2	0	3	2	5	2	5	2	0	2	2	2	0	5	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr14:45564665G>A	ENST00000355765.6	+	2	393	c.223G>A	c.(223-225)Gca>Aca	p.A75T		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	75					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AGAAACAGAAGCAAATTTCCC	0.403																																					p.A75T		.											.	PRPF39-70	0			c.G223A						.						46	47	46					14																	45564665		2031	4212	6243	SO:0001583	missense	55015	exon2			ACAGAAGCAAATT	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.223G>A	14.37:g.45564665G>A	ENSP00000348010:p.Ala75Thr	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	55	23	NM_017922	0	0	0	4	4	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927796	0.34002	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T	0.46819	0.86	5.72	4.83	0.62350	.	.	.	.	.	T	0.32675	0.0837	N	0.20986	0.625	0.26211	N	0.979309	B	0.19817	0.039	B	0.23018	0.043	T	0.20538	-1.0272	9	0.15499	T	0.54	-21.2955	10.525	0.44943	0.1491:0.0:0.8509:0.0	.	75	Q86UA1	PRP39_HUMAN	T	75	ENSP00000348010:A75T	ENSP00000348010:A75T	A	+	1	0	PRPF39	44634415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.367000	0.52350	1.429000	0.47314	0.591000	0.81541	GCA	.		0.403	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			A	45564665	G	A	45564665	3	1	37	1	0	0	0	0	1	0	0	0	12598	971	34	2	225	2	PRPF39	14	45564665	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		45564665	61784875	43	3344											
ARG2	384	broad.mit.edu	37	chr14	68117524	68117524	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctaacctggcagtagatGtgattgcttcaagctttggt	9	13	11	8	0	1	2	1	1	0	1	1	2	1	2	1	2	4	5	1	2	3	5	rs148319106	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr14:68117524G>T	ENST00000261783.3	+	8	1132	c.952G>T	c.(952-954)Gtg>Ttg	p.V318L	VTI1B_ENST00000554659.1_3'UTR	NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	318					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	GGCAGTAGATGTGATTGCTTC	0.473																																					p.V318L													.	ARG2-90	0			c.G952T						.						153	116	129					14																	68117524		2203	4300	6503	SO:0001583	missense	384	exon8			GTAGATGTGATTG	D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"arginase, type II"			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.952G>T	14.37:g.68117524G>T	ENSP00000261783:p.Val318Leu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	147	4	NM_001172	0	0	9	9	0	B2R690|Q6FHY8	Missense_Mutation	SNP	ENST00000261783.3	37	CCDS9785.1	.	.	.	.	.	.	.	.	.	.	G	8.265	0.812032	0.16537	.	.	ENSG00000081181	ENST00000261783	D	0.82167	-1.58	5.09	5.09	0.68999	Ureohydrolase domain (1);	0.252215	0.39544	N	0.001335	T	0.64080	0.2566	N	0.02751	-0.505	0.80722	D	1	B	0.16802	0.019	B	0.23716	0.048	T	0.63229	-0.6684	10	0.02654	T	1	.	18.6895	0.91578	0.0:0.0:1.0:0.0	.	318	P78540	ARGI2_HUMAN	L	318	ENSP00000261783:V318L	ENSP00000261783:V318L	V	+	1	0	ARG2	67187277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.586000	0.60984	2.661000	0.90470	0.655000	0.94253	GTG	G|0.999;A|0.001		0.473	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2	NM_001172		T	68117524	G	T	68117524	3	4	37	1	0	0	0	0	1	0	0	0	858	1377	48	4	982	4	ARG2	14	68117524	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	22552859	68117524	39232016	44	3345											
TGM7	116179	broad.mit.edu	37	chr15	43571977	43571977	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accctctggatacgcagcagCagctgcaggtcctggcccca	8	6	11	16	1	1	0	0	0	1	0	2	1	2	1	4	3	5	5	4	3	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:43571977C>A	ENST00000452443.2	-	10	1528	c.1524G>T	c.(1522-1524)ctG>ctT	p.L508L		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	508					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TACGCAGCAGCAGCTGCAGGT	0.657																																					p.L508L													.	TGM7-92	0			c.G1524T						.						38	44	42					15																	43571977		2201	4297	6498	SO:0001819	synonymous_variant	116179	exon10			CAGCAGCAGCTGC	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1524G>T	15.37:g.43571977C>A		Somatic	55	1		WXS	Illumina HiSeq	Phase_I	40	7	NM_052955	0	0	0	0	0		Silent	SNP	ENST00000452443.2	37	CCDS32213.1																																																																																			.		0.657	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		A	43571977	C	A	43571977	2	1	37	1	0	0	0	0	0	0	0	1	15867	697	25	4		4	TGM7	15	43571977	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		43571977	58959415	45	3346											
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75673957	75673957	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtacttgctcatacctcTgcttccacagggtcatccga	8	12	8	13	1	3	0	2	0	1	0	5	2	5	0	3	1	4	3	3	1	2	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:75673957T>A	ENST00000394947.3	-	18	3599	c.3285A>T	c.(3283-3285)gcA>gcT	p.A1095A	SIN3A_ENST00000360439.4_Silent_p.A1095A|SIN3A_ENST00000394949.4_Silent_p.A1095A	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						CTCATACCTCTGCTTCCACAG	0.527																																					p.A1095A		.											.	SIN3A-230	0			c.A3285T						.						227	191	203					15																	75673957		2197	4294	6491	SO:0001819	synonymous_variant	25942	exon18			TACCTCTGCTTCC	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3285A>T	15.37:g.75673957T>A		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	170	77	NM_001145358	0	0	0	0	0		Silent	SNP	ENST00000394947.3	37	CCDS10279.1																																																																																			.		0.527	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75673957	T	A	75673957	2	1	37	1	0	0	0	0	0	0	0	1	14357	1567	55	5		5	SIN3A	15	75673957	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10	32101980	75673957	26857435	46	3347			1	10		2	2	26	T		4.522337e-05
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75673982	75673982	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacagggtcatccgaattcTcctcttctgtgtccagaagc	8	11	8	14	1	4	1	1	0	3	1	7	2	6	1	4	1	1	0	4	1	2	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:75673982T>A	ENST00000394947.3	-	18	3574	c.3260A>T	c.(3259-3261)gAg>gTg	p.E1087V	SIN3A_ENST00000360439.4_Missense_Mutation_p.E1087V|SIN3A_ENST00000394949.4_Missense_Mutation_p.E1087V	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATCCGAATTCTCCTCTTCTGT	0.502																																					p.E1087V		.											.	SIN3A-230	0			c.A3260T						.						219	188	199					15																	75673982		2197	4294	6491	SO:0001583	missense	25942	exon18			GAATTCTCCTCTT	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3260A>T	15.37:g.75673982T>A	ENSP00000378402:p.Glu1087Val	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	173	75	NM_001145358	0	0	1	1	0		Missense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186474	0.78789	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.47528	0.84;0.84;0.84	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.47248	0.1435	L	0.61387	1.9	0.80722	D	1	B	0.28998	0.23	B	0.30716	0.119	T	0.41215	-0.9521	10	0.30078	T	0.28	-25.6466	14.6847	0.69042	0.0:0.0:0.0:1.0	.	1087	Q96ST3	SIN3A_HUMAN	V	1087	ENSP00000378402:E1087V;ENSP00000378403:E1087V;ENSP00000353622:E1087V	ENSP00000353622:E1087V	E	-	2	0	SIN3A	73461035	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.939000	0.87685	2.073000	0.62155	0.402000	0.26972	GAG	.		0.502	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75673982	T	A	75673982	3	1	37	1	0	0	0	0	1	0	0	0	14357	1551	54	5	577	5	SIN3A	15	75673982	Missense_Mutation	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10	25	75673982	26857410	47	3348			1	10		2	2	26	T		4.522337e-05
CARHSP1	23589	bcgsc.ca	37	chr16	8949067	8949067	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtctcatgcttggtgcctGgtgccaggtgagtgatgacg	6	11	16	8	1	1	3	1	3	1	0	2	3	1	3	2	4	3	1	2	4	0	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr16:8949067G>A	ENST00000396593.2	-	4	757	c.398C>T	c.(397-399)cCa>cTa	p.P133L	CARHSP1_ENST00000561530.1_Missense_Mutation_p.P133L|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000567554.1_Missense_Mutation_p.P133L|CARHSP1_ENST00000311052.5_Missense_Mutation_p.P133L|RP11-77H9.5_ENST00000564919.1_RNA	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	133					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						CTTGGTGCCTGGTGCCAGGTG	0.567																																					p.P133L													.	CARHSP1-90	0			c.C398T						.						188	135	153					16																	8949067		2197	4300	6497	SO:0001583	missense	23589	exon4			GTGCCTGGTGCCA	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"calcium regulated heat stable protein 1 (24kD)"			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.398C>T	16.37:g.8949067G>A	ENSP00000379838:p.Pro133Leu	Somatic	230	0		WXS	Illumina HiSeq	Phase_1	179	6	NM_001042476	0	0	273	273	0	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Missense_Mutation	SNP	ENST00000396593.2	37	CCDS10537.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142560	0.94560	.	.	ENSG00000153048	ENST00000396593;ENST00000311052	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.76154	0.3948	M	0.87269	2.87	0.80722	D	1	D	0.57257	0.979	P	0.49252	0.604	T	0.80594	-0.1313	9	0.87932	D	0	-2.1558	19.6321	0.95713	0.0:0.0:1.0:0.0	.	133	Q9Y2V2	CHSP1_HUMAN	L	133	.	ENSP00000311847:P133L	P	-	2	0	CARHSP1	8856568	1.000000	0.71417	0.701000	0.30321	0.760000	0.43138	9.751000	0.98889	2.884000	0.98904	0.655000	0.94253	CCA	.		0.567	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316		A	8949067	G	A	8949067	3	1	37	1	0	0	0	0	1	0	0	0	2659	1348	47	2	49	2	CARHSP1	16	8949067	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		8949067	81405686	48	3349											
FA2H	79152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	74750468	74750468	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agggaggctggcacagggggGaagaccaggcgggagccgtc	9	2	21	9	2	0	1	0	0	0	1	1	4	0	4	2	8	1	2	2	8	1	0			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr16:74750468G>C	ENST00000219368.3	-	6	885	c.816C>G	c.(814-816)ttC>ttG	p.F272L	FA2H_ENST00000544337.1_Missense_Mutation_p.F59L	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	272					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						GCACAGGGGGGAAGACCAGGC	0.677																																					p.F272L		.											.	FA2H-90	0			c.C816G						.						16	15	15					16																	74750468		2194	4297	6491	SO:0001583	missense	79152	exon6			AGGGGGGAAGACC	BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"Fatty acid hydroxylase domain containing"	21197	protein-coding gene	gene with protein product	"fatty acid hydroxylase"	611026	"fatty acid hydroxylase domain containing 1", "spastic paraplegia 35 (autosomal recessive)"	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.816C>G	16.37:g.74750468G>C	ENSP00000219368:p.Phe272Leu	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	39	16	NM_024306	0	0	0	0	0	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	37	CCDS10911.1	.	.	.	.	.	.	.	.	.	.	g	23.5	4.426263	0.83667	.	.	ENSG00000103089	ENST00000219368;ENST00000544337	D;D	0.83506	-1.73;-1.73	5.07	3.07	0.35406	Fatty acid hydroxylase (1);	0.000000	0.85682	D	0.000000	D	0.89203	0.6648	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87214	0.2249	10	0.40728	T	0.16	0.1308	11.6853	0.51483	0.1462:0.0:0.8538:0.0	.	272;180	Q7L5A8;B2RDE6	FA2H_HUMAN;.	L	272;59	ENSP00000219368:F272L;ENSP00000442334:F59L	ENSP00000219368:F272L	F	-	3	2	FA2H	73307969	1.000000	0.71417	0.997000	0.53966	0.948000	0.59901	2.233000	0.43027	0.524000	0.28502	0.651000	0.88453	TTC	.		0.677	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306		C	74750468	G	C	74750468	3	2	37	1	0	0	0	0	1	0	0	0	5368	1165	41	4	310	4	FA2H	16	74750468	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	65801401	74750468	15604285	49	3350											
WDR81	124997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	1630052	1630052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tggggctcctgcccttgcccCcgagcctcccctcatcccca	3	8	8	22	1	1	0	1	0	0	0	4	1	4	0	9	2	3	1	9	2	0	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:1630052C>T	ENST00000409644.1	+	1	1799	c.1799C>T	c.(1798-1800)cCc>cTc	p.P600L	WDR81_ENST00000446363.1_Intron|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	600	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GCCCTTGCCCCCGAGCCTCCC	0.657																																					p.P600L		.											.	WDR81-91	0			c.C1799T						.						14	18	17					17																	1630052		692	1589	2281	SO:0001583	missense	124997	exon1			TTGCCCCCGAGCC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.1799C>T	17.37:g.1630052C>T	ENSP00000386609:p.Pro600Leu	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	35	20	NM_001163809	0	0	0	0	0	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	5.306	0.241738	0.10077	.	.	ENSG00000167716	ENST00000409644	T	0.51574	0.7	5.43	5.43	0.79202	.	.	.	.	.	T	0.39545	0.1082	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12528	-1.0544	6	0.09590	T	0.72	.	12.5648	0.56304	0.0:0.9236:0.0:0.0764	.	.	.	.	L	600	ENSP00000386609:P600L	ENSP00000386609:P600L	P	+	2	0	WDR81	1576802	0.524000	0.26282	0.970000	0.41538	0.006000	0.05464	4.407000	0.59754	2.546000	0.85860	0.462000	0.41574	CCC	.		0.657	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1630052	C	T	1630052	3	4	37	1	0	0	0	0	1	0	0	0	17363	623	22	2	1863	2	WDR81	17	1630052	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		1630052	79565158	50	3351											
MYBBP1A	10514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4445767	4445767	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagtctctcacctgatgacGgggccgcaccgggcccgtga	7	6	14	14	4	2	3	1	3	1	0	3	4	2	3	4	3	0	1	4	3	1	0	rs200492249	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:4445767G>T	ENST00000254718.4	-	22	3385	c.3079C>A	c.(3079-3081)Cgt>Agt	p.R1027S	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.R1027S			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1027					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						ACCTGATGACGGGGCCGCACC	0.627																																					p.R1027S		.											.	MYBBP1A-92	0			c.C3079A						.						69	80	76					17																	4445767		2203	4300	6503	SO:0001583	missense	10514	exon22			GATGACGGGGCCG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3079C>A	17.37:g.4445767G>T	ENSP00000254718:p.Arg1027Ser	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	149	48	NM_014520	0	0	11	18	7	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195223	0.38806	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.67698	-0.28;-0.28	5.3	4.12	0.48240	Armadillo-type fold (1);	0.258408	0.43579	D	0.000546	T	0.68568	0.3015	M	0.65975	2.015	0.30663	N	0.754172	P;P	0.48407	0.854;0.91	B;P	0.49683	0.414;0.619	T	0.69591	-0.5104	10	0.38643	T	0.18	-19.6389	9.7224	0.40311	0.1107:0.0:0.8893:0.0	.	1027;1027	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	S	1027	ENSP00000370968:R1027S;ENSP00000254718:R1027S	ENSP00000254718:R1027S	R	-	1	0	MYBBP1A	4392516	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	2.897000	0.48664	2.473000	0.83533	0.561000	0.74099	CGT	G|0.999;A|0.001		0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4445767	G	T	4445767	3	4	37	1	0	0	0	0	1	0	0	0	10033	1116	39	4	967	4	MYBBP1A	17	4445767	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	2815715	4445767	76749443	51	3352											
NDC80	10403	bcgsc.ca	37	chr18	2585121	2585121	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtactaattagatacatactGccatgaaagaaagctcacct	16	10	6	9	0	1	3	1	1	0	2	1	3	1	3	2	0	5	2	2	0	7	5			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr18:2585121G>T	ENST00000261597.4	+	7	771	c.589G>T	c.(589-591)Gcc>Tcc	p.A197S		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	197	Interaction with RB1.|Interaction with the N-terminus of CDCA1.|Nuclear localization.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GATACATACTGCCATGAAAGA	0.333																																					p.A197S													.	NDC80-91	0			c.G589T						.						94	91	92					18																	2585121		2203	4300	6503	SO:0001583	missense	10403	exon7			CATACTGCCATGA	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.589G>T	18.37:g.2585121G>T	ENSP00000261597:p.Ala197Ser	Somatic	43	0		WXS	Illumina HiSeq	Phase_1	55	4	NM_006101	0	0	0	0	0	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	3.921	-0.018063	0.07681	.	.	ENSG00000080986	ENST00000261597;ENST00000543946	T	0.64438	-0.1	5.3	4.38	0.52667	.	0.163420	0.56097	D	0.000032	T	0.39462	0.1079	N	0.10874	0.06	0.37731	D	0.925259	B	0.06786	0.001	B	0.14578	0.011	T	0.32903	-0.9889	10	0.09843	T	0.71	-7.1468	13.3687	0.60701	0.0:0.0:0.8439:0.1561	.	197	O14777	NDC80_HUMAN	S	197	ENSP00000261597:A197S	ENSP00000261597:A197S	A	+	1	0	NDC80	2575121	1.000000	0.71417	0.977000	0.42913	0.981000	0.71138	3.611000	0.54132	2.625000	0.88918	0.650000	0.86243	GCC	.		0.333	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		T	2585121	G	T	2585121	3	4	37	1	0	0	0	0	1	0	0	0	10268	1319	46	4	611	4	NDC80	18	2585121	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		2585121	75492127	52	3353											
SHC2	25759	ucsc.edu;bcgsc.ca	37	chr19	422299	422299	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccggcggctcatccggccGtggtaccagggctcctgacg	4	6	15	16	5	1	1	1	1	0	0	3	1	3	1	5	5	1	3	5	5	1	1	rs375069437		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:422299G>T	ENST00000264554.6	-	11	1466	c.1467C>A	c.(1465-1467)caC>caA	p.H489Q		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	489	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCATCCGGCCGTGGTACCAGG	0.697																																					p.H489Q													.	SHC2-392	0			c.C1467A						.						12	15	14					19																	422299		2093	4207	6300	SO:0001583	missense	25759	exon11			CCGGCCGTGGTAC	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1467C>A	19.37:g.422299G>T	ENSP00000264554:p.His489Gln	Somatic	72	0		WXS	Illumina HiSeq		32	4	NM_012435	0	0	18	18	0	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.888479	0.52014	.	.	ENSG00000129946	ENST00000264554	T	0.68903	-0.36	4.75	-4.42	0.03579	SH2 motif (5);	0.048752	0.85682	D	0.000000	T	0.75982	0.3924	M	0.88031	2.925	0.50632	D	0.999882	D	0.64830	0.994	D	0.67900	0.954	T	0.73711	-0.3897	10	0.31617	T	0.26	-47.0739	7.0621	0.25131	0.5458:0.0:0.3369:0.1173	.	489	P98077	SHC2_HUMAN	Q	489	ENSP00000264554:H489Q	ENSP00000264554:H489Q	H	-	3	2	SHC2	373299	0.022000	0.18835	0.979000	0.43373	0.978000	0.69477	-0.881000	0.04179	-0.519000	0.06444	-0.130000	0.14895	CAC	.		0.697	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			T	422299	G	T	422299	3	4	37	1	0	0	0	0	1	0	0	0	14303	1136	40	4	289	4	SHC2	19	422299	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		422299	58706684	53	3354											
ZNF880	400713	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	52877551	52877551	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attctttctttttttaaataGgaatctgtcttcctgacctg	8	20	5	8	0	4	1	0	1	4	0	5	2	5	2	2	1	0	0	2	1	4	8			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:52877551G>A	ENST00000422689.2	+	3	154		c.e3-1		ZNF880_ENST00000597976.1_Splice_Site|ZNF880_ENST00000424032.2_Splice_Site|ZNF880_ENST00000600321.1_Splice_Site|ZNF880_ENST00000344085.5_Splice_Site	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880						regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						TTTTTAAATAGGAATCTGTCT	0.403																																					.		.											.	.	0			c.140-1G>A						.						52	43	46					19																	52877551		692	1591	2283	SO:0001630	splice_region_variant	400713	exon3			TAAATAGGAATCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"Zinc fingers, C2H2-type", "-"	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.140-1G>A	19.37:g.52877551G>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	78	11	NM_001145434	0	0	0	1	1	B4DNA6	Splice_Site	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	g	4.728	0.135350	0.09032	.	.	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	.	.	.	1.13	1.13	0.20643	.	.	.	.	.	.	.	.	.	.	.	0.23483	N	0.997585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6302	0.17506	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF880	57569363	0.003000	0.15002	0.027000	0.17364	0.231000	0.25187	0.510000	0.22723	0.920000	0.36970	0.448000	0.29417	.	.		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	Intron	A	52877551	G	A	52877551	5	1	37	1	0	0	0	0	0	0	1	0	18229	1014	35	2	149	2	ZNF880	19	52877551	Splice_Site	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	52455252	52877551	6251432	54	3355											
PCK1	5105	broad.mit.edu	37	chr20	56140434	56140434	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatgcatgacccctttgcCatgcggcccttctttggcta	6	13	8	14	1	2	1	1	1	1	0	2	1	2	1	4	2	3	2	4	2	1	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr20:56140434C>T	ENST00000319441.4	+	10	1607	c.1443C>T	c.(1441-1443)gcC>gcT	p.A481A	PCK1_ENST00000543666.1_Silent_p.A164A|PCK1_ENST00000535860.1_3'UTR	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	481					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			ACCCCTTTGCCATGCGGCCCT	0.507																																					p.A481A													.	PCK1-227	0			c.C1443T						.						94	93	93					20																	56140434		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon10			CTTTGCCATGCGG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1443C>T	20.37:g.56140434C>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	100	5	NM_002591	0	0	24	24	0	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			.		0.507	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			T	56140434	C	T	56140434	2	4	37	1	0	0	0	0	0	0	0	1	11607	581	21	2		2	PCK1	20	56140434	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		56140434	6885086	55	3356											
TSPYL2	64061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53114044	53114044	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggagttccagcgcaaccgCtcaggtaagtggcagtacca	12	6	12	11	2	1	0	1	0	0	0	2	1	2	1	3	3	3	6	3	3	4	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chrX:53114044C>A	ENST00000375442.4	+	3	1125	c.993C>A	c.(991-993)cgC>cgA	p.R331R		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	331					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|chromatin modification (GO:0016568)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA replication (GO:0008156)|nucleosome assembly (GO:0006334)|regulation of protein kinase activity (GO:0045859)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	rDNA binding (GO:0000182)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	19						AGCGCAACCGCTCAGGTAAGT	0.498																																					p.R331R		.											.	TSPYL2-130	0			c.C993A						.						105	85	92					X																	53114044		2203	4300	6503	SO:0001819	synonymous_variant	64061	exon3			CAACCGCTCAGGT	AF273046	CCDS14350.1	Xp11	2014-06-09			ENSG00000184205	ENSG00000184205			24358	protein-coding gene	gene with protein product		300564				11318608, 11395479	Standard	NM_022117		Approved	SE20-4, HRIHFB2216, CTCL, DENTT, CDA1, CINAP, TSPX	uc004drw.3	Q9H2G4	OTTHUMG00000021597	ENST00000375442.4:c.993C>A	X.37:g.53114044C>A		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	60	56	NM_022117	0	0	0	0	0	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	37	CCDS14350.1																																																																																			.		0.498	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		A	53114044	C	A	53114044	2	1	37	1	0	0	0	0	0	0	0	1	16693	784	28	4		4	TSPYL2	23	53114044	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		53114044	102156516	56	3357											
STAG2	10735	bcgsc.ca	37	chrX	123185066	123185066	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaactttttaccagtcggttCaaggttagtattacttaaga	12	15	8	6	1	1	1	1	0	0	1	2	2	1	1	1	2	3	3	1	2	7	8			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chrX:123185066C>T	ENST00000371160.1	+	12	1403	c.1113C>T	c.(1111-1113)ttC>ttT	p.F371F	STAG2_ENST00000371145.3_Silent_p.F371F|STAG2_ENST00000354548.5_Silent_p.F302F|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Silent_p.F371F|STAG2_ENST00000371157.3_Silent_p.F371F|STAG2_ENST00000371144.3_Silent_p.F371F	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	371	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CCAGTCGGTTCAAGGTTAGTA	0.303																																					p.F371F													.	STAG2-134	0			c.C1113T						.						31	32	32					X																	123185066		2203	4282	6485	SO:0001819	synonymous_variant	10735	exon12			TCGGTTCAAGGTT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1113C>T	X.37:g.123185066C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_1	50	4	NM_001042749	0	0	0	0	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	37	CCDS14607.1																																																																																			.		0.303	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123185066	C	T	123185066	2	4	37	1	0	0	0	0	0	0	0	1	15275	825	29	2		2	STAG2	23	123185066	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	70071022	123185066	32085494	57	3358											
SNIP1	79753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38005993	38005993	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttggtgtcctcaagaagtgCcccagaaagttcaaagcttg	11	10	11	9	0	2	2	2	0	0	2	3	2	3	2	3	1	2	3	3	1	4	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:38005993C>G	ENST00000296215.6	-	3	763	c.691G>C	c.(691-693)Gca>Cca	p.A231P	SNIP1_ENST00000468040.1_5'Flank	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	231					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				TCAAGAAGTGCCCCAGAAAGT	0.502																																					p.A231P		.											.	SNIP1-227	0			c.G691C						.						66	69	68					1																	38005993		2203	4300	6503	SO:0001583	missense	79753	exon3			GAAGTGCCCCAGA		CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.691G>C	1.37:g.38005993C>G	ENSP00000296215:p.Ala231Pro	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	118	63	NM_024700	0	0	1	2	1	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	37	CCDS419.1	.	.	.	.	.	.	.	.	.	.	C	32	5.162524	0.94727	.	.	ENSG00000163877	ENST00000296215;ENST00000436196	T	0.51071	0.72	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.73094	0.3543	M	0.87682	2.9	0.80722	D	1	D	0.69078	0.997	D	0.66602	0.945	T	0.72931	-0.4142	10	0.39692	T	0.17	-4.7851	20.1865	0.98220	0.0:1.0:0.0:0.0	.	231	Q8TAD8	SNIP1_HUMAN	P	231;215	ENSP00000296215:A231P	ENSP00000296215:A231P	A	-	1	0	SNIP1	37778580	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.440000	0.80464	2.775000	0.95449	0.655000	0.94253	GCA	.		0.502	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700		G	38005993	C	G	38005993	3	3	38	1	0	0	0	0	1	0	0	0	14880	739	26	4	507	4	SNIP1	1	38005993	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		38005993	211244628	1	3359											
DBT	1629	ucsc.edu;bcgsc.ca	37	chr1	100676255	100676255	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgcatagccaaccttatAtgttatattctggcagtttt	9	17	6	9	0	2	0	0	0	2	0	2	0	2	0	2	1	3	4	2	1	6	8			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:100676255A>G	ENST00000370132.4	-	8	1025	c.1012T>C	c.(1012-1014)Tat>Cat	p.Y338H	DBT_ENST00000370131.3_3'UTR	NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	338					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		CCAACCTTATATGTTATATTC	0.348																																					p.Y338H													.	DBT-91	0			c.T1012C						.						100	101	101					1																	100676255		2203	4300	6503	SO:0001583	missense	1629	exon8			CCTTATATGTTAT	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.1012T>C	1.37:g.100676255A>G	ENSP00000359151:p.Tyr338His	Somatic	353	3		WXS	Illumina HiSeq		351	166	NM_001918	0	0	0	0	0	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	37	CCDS767.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425349	0.62733	.	.	ENSG00000137992	ENST00000543138;ENST00000370132	T	0.46063	0.88	5.53	5.53	0.82687	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.44993	0.1320	M	0.79011	2.435	0.80722	D	1	B;P	0.41393	0.109;0.748	B;P	0.47827	0.206;0.558	T	0.43572	-0.9383	10	0.38643	T	0.18	-15.2965	15.9566	0.79891	1.0:0.0:0.0:0.0	.	157;338	F5H1F9;P11182	.;ODB2_HUMAN	H	157;338	ENSP00000359151:Y338H	ENSP00000359151:Y338H	Y	-	1	0	DBT	100448843	1.000000	0.71417	0.508000	0.27688	0.948000	0.59901	8.678000	0.91211	2.231000	0.72958	0.459000	0.35465	TAT	.		0.348	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918		G	100676255	A	G	100676255	3	3	38	1	0	0	0	0	1	0	0	0	4264	449	16	3	452	3	DBT	1	100676255	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	62670262	100676255	148574366	2	3360											
FCGR1B	2210	broad.mit.edu	37	chr1	120927211	120927212	+	Frame_Shift_Del	DEL	GC	GC	-																															tttttgttcctgacatttcaGctcttcttctaaatgtctgt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:120927211_120927212delGC	ENST00000369384.4	-	5	810_811	c.768_769delGC	c.(766-771)gagctgfs	p.EL256fs	RP11-439A17.9_ENST00000457996.1_RNA|RP11-439A17.10_ENST00000426275.1_RNA|FCGR1B_ENST00000369383.4_Frame_Shift_Del_p.EL164fs|FCGR1B_ENST00000472543.1_5'Flank	NM_001017986.3	NP_001017986.1	Q92637	FCGRB_HUMAN	Fc fragment of IgG, high affinity Ib, receptor (CD64)	256					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)|cytokine-mediated signaling pathway (GO:0019221)|Fc receptor signaling pathway (GO:0038093)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	immunoglobulin receptor activity (GO:0019763)			breast(1)|endometrium(1)|lung(2)	4	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)	Intravenous Immunoglobulin(DB00028)	TGACATTTCAGCTCTTCTTCTA	0.465																																					p.256_257del													.	.	0			c.768_769del						.																																			SO:0001589	frameshift_variant	2210	exon5			ATTTCAGCTCTTC		CCDS72844.1, CCDS72845.1, CCDS72846.1	1p11.2	2013-01-11	2005-02-02		ENSG00000198019	ENSG00000198019		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3614	protein-coding gene	gene with protein product		601502	"Fc fragment of IgG, high affinity Ib, receptor for (CD64)"			8697799, 9763663	Standard	NM_001017986		Approved	CD64b	uc001eip.3	Q92637	OTTHUMG00000040903	ENST00000369384.4:c.768_769delGC	1.37:g.120927211_120927212delGC	ENSP00000358391:p.Glu256fs	Somatic	618	0		WXS	Illumina HiSeq	Phase_I	511	66	NM_001017986	0	0	0	0	0	Q7KZ13|Q92638	Frame_Shift_Del	DEL	ENST00000369384.4	37	CCDS30821.1																																																																																			.		0.465	FCGR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098241.1			-	120927212	GC	-	120927211	7	5	38	1	0	1	0	1	0	0	0	0	5799	962	34	0	77	0	FCGR1B	1	120927211	Frame_Shift_Del	DEL	GC	TCGA-B1-A654-01A-11D-A31X-10	20250956	120927211	128323410	3	3361											
FCGR1A	2209	broad.mit.edu	37	chr1	149762998	149762999	+	Frame_Shift_Del	DEL	GC	GC	-																															gacagacatttagaagaagaGctgaaatgtcaggaacaaaa																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:149762998_149762999delGC	ENST00000369168.4	+	6	1104_1105	c.1050_1051delGC	c.(1048-1053)gagctgfs	p.EL350fs	RP11-196G18.21_ENST00000420462.1_RNA|RP11-196G18.3_ENST00000428289.1_RNA|HIST2H2BF_ENST00000545683.1_Intron	NM_000566.3	NP_000557.1	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor (CD64)	350					antibody-dependent cellular cytotoxicity (GO:0001788)|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)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intracellular signal transduction (GO:0035556)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of phagocytosis (GO:0050766)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG receptor activity (GO:0019770)|receptor signaling protein activity (GO:0005057)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)	10	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TAGAAGAAGAGCTGAAATGTCA	0.475																																					p.350_351del													.	FCGR1A-23	0			c.1050_1051del						.																																			SO:0001589	frameshift_variant	2209	exon6			AGAAGAGCTGAAA	BC032634	CCDS933.1	1q21.2-q21.3	2014-09-17	2005-02-02		ENSG00000150337	ENSG00000150337		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3613	protein-coding gene	gene with protein product		146760	"Fc fragment of IgG, high affinity Ia, receptor for (CD64)"			8697799, 9763663	Standard	NM_000566		Approved	CD64, CD64A	uc001esp.4	P12314	OTTHUMG00000012089	ENST00000369168.4:c.1050_1051delGC	1.37:g.149762998_149762999delGC	ENSP00000358165:p.Glu350fs	Somatic	433	0		WXS	Illumina HiSeq	Phase_I	420	26	NM_000566	0	0	0	0	0	P12315|Q5QNW7|Q92495|Q92663	Frame_Shift_Del	DEL	ENST00000369168.4	37	CCDS933.1																																																																																			.		0.475	FCGR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033446.1	NM_000566		-	149762999	GC	-	149762998	7	5	38	1	0	1	0	1	0	0	0	0	5798	962	34	0	1072	0	FCGR1A	1	149762998	Frame_Shift_Del	DEL	GC	TCGA-B1-A654-01A-11D-A31X-10	28835787	149762998	99487623	4	3362											
CRTC2	200186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153926765	153926765	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgggggaggagataagtAggcaggactatagggagagc	12	6	18	5	0	1	2	0	0	1	2	1	6	1	4	0	6	1	2	0	6	4	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:153926765A>G	ENST00000368633.1	-	4	527	c.400T>C	c.(400-402)Tac>Cac	p.Y134H	CRTC2_ENST00000476883.1_5'UTR|CRTC2_ENST00000368630.3_Intron	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	134					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGAGATAAGTAGGCAGGACTA	0.512																																					p.Y134H		.											.	CRTC2-228	0			c.T400C						.						61	54	56					1																	153926765		2203	4300	6503	SO:0001583	missense	200186	exon4			ATAAGTAGGCAGG	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.400T>C	1.37:g.153926765A>G	ENSP00000357622:p.Tyr134His	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	46	16	NM_181715	0	0	4	4	0	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253357	0.80135	.	.	ENSG00000160741	ENST00000368633	T	0.38240	1.15	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	T	0.26702	0.0653	M	0.66297	2.02	0.40914	D	0.984258	P	0.38020	0.615	B	0.40134	0.32	T	0.16453	-1.0402	10	0.54805	T	0.06	-12.6013	10.82	0.46599	1.0:0.0:0.0:0.0	.	134	Q53ET0	CRTC2_HUMAN	H	134	ENSP00000357622:Y134H	ENSP00000357622:Y134H	Y	-	1	0	CRTC2	152193389	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.516000	0.73755	2.065000	0.61736	0.397000	0.26171	TAC	.		0.512	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		G	153926765	A	G	153926765	3	3	38	1	0	0	0	0	1	0	0	0	3906	420	15	3	1725	3	CRTC2	1	153926765	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	4163767	153926765	95323856	5	3363											
C1orf27	54953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	186355194	186355194	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actttagaactggcaaatgaTtttcaaaatgccctgcgtag	13	12	8	8	1	1	2	1	1	0	1	1	2	1	2	1	1	3	2	1	1	6	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:186355194T>C	ENST00000287859.6	+	4	434	c.309T>C	c.(307-309)gaT>gaC	p.D103D	C1orf27_ENST00000419367.3_Intron|C1orf27_ENST00000367470.3_Silent_p.D103D|C1orf27_ENST00000432021.3_Silent_p.D103D	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	103						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						TGGCAAATGATTTTCAAAATG	0.289																																					p.D103D		.											.	C1orf27-23	0			c.T309C						.						46	44	44					1																	186355194		1786	4058	5844	SO:0001819	synonymous_variant	54953	exon4			AAATGATTTTCAA	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"transactivated by recombinant transforming growth factor beta"	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.309T>C	1.37:g.186355194T>C		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	84	37	NM_001164245	0	0	0	0	0	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Silent	SNP	ENST00000287859.6	37	CCDS53448.1																																																																																			.		0.289	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		C	186355194	T	C	186355194	2	2	38	1	0	0	0	0	0	0	0	1	2042	1490	52	3		3	C1orf27	1	186355194	Silent	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	32428429	186355194	62895427	6	3364											
DNAJC27	51277	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	25180723	25180723	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatattttccatgtttccatGaggtccaagctcttgcttca	9	16	6	10	0	2	1	1	1	1	0	5	1	5	1	3	1	2	3	3	1	3	6			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:25180723G>T	ENST00000264711.2	-	4	550	c.361C>A	c.(361-363)Cat>Aat	p.H121N	DNAJC27_ENST00000534855.1_Missense_Mutation_p.H50N|DNAJC27_ENST00000468467.1_5'UTR	NM_001198559.1|NM_016544.2	NP_001185488.1|NP_057628.1	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27	121					small GTPase mediated signal transduction (GO:0007264)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						ATGTTTCCATGAGGTCCAAGC	0.458																																					p.H121N													.	DNAJC27-228	0			c.C361A						.						121	116	118					2																	25180723		2203	4300	6503	SO:0001583	missense	51277	exon4			TTCCATGAGGTCC		CCDS1716.1, CCDS74493.1	2p23.3	2011-09-02	2008-08-20	2008-08-20	ENSG00000115137	ENSG00000115137		"Heat shock proteins / DNAJ (HSP40)"	30290	protein-coding gene	gene with protein product		613527	"rab and DnaJ domain containing"	RBJ		14980719	Standard	NM_016544		Approved	RabJS	uc002rft.2	Q9NZQ0	OTTHUMG00000125524	ENST00000264711.2:c.361C>A	2.37:g.25180723G>T	ENSP00000264711:p.His121Asn	Somatic	156	1		WXS	Illumina HiSeq	Phase_I	134	56	NM_016544	0	0	0	0	0	Q5JV88|Q86Y24	Missense_Mutation	SNP	ENST00000264711.2	37	CCDS1716.1	.	.	.	.	.	.	.	.	.	.	G	9.758	1.169198	0.21621	.	.	ENSG00000115137	ENST00000264711;ENST00000534855	T;T	0.76186	-0.5;-1.0	5.27	5.27	0.74061	Small GTP-binding protein domain (1);	0.105620	0.64402	D	0.000002	T	0.52933	0.1765	N	0.03194	-0.395	0.52501	D	0.999957	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.50171	-0.8859	10	0.16896	T	0.51	-24.3984	17.6166	0.88069	0.0:0.0:1.0:0.0	.	121;121	Q9NZQ0-3;Q9NZQ0	.;DJC27_HUMAN	N	121;50	ENSP00000264711:H121N;ENSP00000440086:H50N	ENSP00000264711:H121N	H	-	1	0	DNAJC27	25034227	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.524000	0.98036	2.750000	0.94351	0.563000	0.77884	CAT	.		0.458	DNAJC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246855.3	NM_016544		T	25180723	G	T	25180723	3	4	38	1	0	0	0	0	1	0	0	0	4656	1290	45	4	476	4	DNAJC27	2	25180723	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		25180723	218018650	7	3365											
SLC3A1	6519	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44547379	44547379	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcggctttgaagttatatcaAgatttaagtctacttcatgc	11	16	7	7	1	3	2	2	1	1	1	4	2	3	2	0	1	2	2	0	1	6	7			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:44547379A>G	ENST00000260649.6	+	10	1735	c.1659A>G	c.(1657-1659)caA>caG	p.Q553Q	PREPL_ENST00000409411.1_3'UTR|PREPL_ENST00000409936.1_3'UTR|SLC3A1_ENST00000409380.1_Silent_p.Q275Q|SLC3A1_ENST00000409740.3_Silent_p.Q184Q|PREPL_ENST00000541738.1_3'UTR|PREPL_ENST00000409957.1_3'UTR	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	553					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	AGTTATATCAAGATTTAAGTC	0.378																																					p.Q553Q													.	SLC3A1-90	0			c.A1659G						.						61	56	58					2																	44547379		2203	4300	6503	SO:0001819	synonymous_variant	6519	exon10			ATATCAAGATTTA		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1659A>G	2.37:g.44547379A>G		Somatic	117	1		WXS	Illumina HiSeq	Phase_I	112	38	NM_000341	0	0	182	348	166	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Silent	SNP	ENST00000260649.6	37	CCDS1819.1																																																																																			.		0.378	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		G	44547379	A	G	44547379	2	3	38	1	0	0	0	0	0	0	0	1	14658	69	3	3		3	SLC3A1	2	44547379	Silent	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	19366656	44547379	198651994	8	3366											
RGPD3	653489	broad.mit.edu	37	chr2	107049632	107049632	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgttttatttctgaatccGcatttcgcaaagaaccattt	12	16	5	8	2	1	2	0	1	1	1	3	2	2	2	2	0	1	3	2	0	5	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:107049632G>A	ENST00000409886.3	-	16	2402	c.2315C>T	c.(2314-2316)gCg>gTg	p.A772V	RGPD3_ENST00000304514.7_Missense_Mutation_p.A772V	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	772					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTCTGAATCCGCATTTCGCAA	0.373																																					p.A772V													.	RGPD3-23	0			c.C2315T						.						90	75	80					2																	107049632		692	1590	2282	SO:0001583	missense	653489	exon16			GAATCCGCATTTC		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"Tetratricopeptide (TTC) repeat domain containing"	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.2315C>T	2.37:g.107049632G>A	ENSP00000386588:p.Ala772Val	Somatic	725	1		WXS	Illumina HiSeq	Phase_I	656	7	NM_001144013	0	0	0	0	0	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	3.284	-0.146450	0.06627	.	.	ENSG00000153165	ENST00000409886;ENST00000452099;ENST00000304514	T;T	0.23348	1.91;1.91	2.34	1.42	0.22433	.	.	.	.	.	T	0.19127	0.0459	L	0.47716	1.5	0.22947	N	0.998528	B	0.15141	0.012	B	0.06405	0.002	T	0.16778	-1.0391	9	0.37606	T	0.19	-0.1623	4.3139	0.10984	0.2042:0.0:0.7958:0.0	.	772	A6NKT7	RGPD3_HUMAN	V	772;530;772	ENSP00000386588:A772V;ENSP00000303659:A772V	ENSP00000303659:A772V	A	-	2	0	RGPD3	106416064	0.918000	0.31147	0.919000	0.36401	0.028000	0.11728	0.415000	0.21181	1.308000	0.44962	0.173000	0.16961	GCG	.		0.373	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		A	107049632	G	A	107049632	3	1	38	1	0	0	0	0	1	0	0	0	13319	1087	38	1	2993	1	RGPD3	2	107049632	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	62502253	107049632	136149741	9	3367											
ERCC3	2071	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	128051097	128051097	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcatgcttaccacccagaGgggcctggaggtgtggtcgt	6	8	17	10	1	0	1	0	0	0	1	1	2	0	2	3	6	2	2	3	6	1	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:128051097G>T	ENST00000285398.2	-	2	320	c.226C>A	c.(226-228)Ctc>Atc	p.L76I	ERCC3_ENST00000493187.2_Missense_Mutation_p.L12I	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	76					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		ACCACCCAGAGGGGCCTGGAG	0.572			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.L76I		.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3-723	0			c.C226A						.						71	63	66					2																	128051097		2203	4300	6503	SO:0001583	missense	2071	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CCCAGAGGGGCCT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.226C>A	2.37:g.128051097G>T	ENSP00000285398:p.Leu76Ile	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_000122	0	0	1	1	0	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	37	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575903	0.86645	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.77877	-1.13;-1.13	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.76695	0.4023	L	0.39020	1.185	0.80722	D	1	B;P	0.36465	0.177;0.554	P;P	0.45946	0.498;0.498	T	0.75303	-0.3365	10	0.33141	T	0.24	-17.9364	17.1634	0.86809	0.0:0.0:1.0:0.0	.	76;76	A8K359;P19447	.;ERCC3_HUMAN	I	76;12	ENSP00000285398:L76I;ENSP00000444796:L12I	ENSP00000285398:L76I	L	-	1	0	ERCC3	127767567	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.997000	0.76270	2.277000	0.76020	0.563000	0.77884	CTC	.		0.572	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		T	128051097	G	T	128051097	3	4	38	1	0	0	0	0	1	0	0	0	5227	1000	35	4	2178	4	ERCC3	2	128051097	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	21001465	128051097	115148276	10	3368											
WDR33	55339	ucsc.edu;bcgsc.ca	37	chr2	128522273	128522273	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaaacaaagaaaaatattGtgtttatagggtgcagaaag	19	10	10	2	0	0	3	0	1	0	2	0	3	0	3	0	1	2	2	0	1	9	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:128522273G>A	ENST00000322313.4	-	6	785				WDR33_ENST00000393006.1_Intron|WDR33_ENST00000409658.3_Missense_Mutation_p.T252I	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GAAAAATATTGTGTTTATAGG	0.403																																					p.T252I													.	WDR33-90	0			c.C755T						.						39	44	42					2																	128522273		1327	2309	3636	SO:0001627	intron_variant	55339	exon6			AATATTGTGTTTA		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.626+128C>T	2.37:g.128522273G>A		Somatic	303	2		WXS	Illumina HiSeq		248	121	NM_001006622	0	0	2	6	4	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756277	0.49362	.	.	ENSG00000136709	ENST00000409658	T	0.36699	1.24	5.7	4.82	0.62117	.	.	.	.	.	T	0.59376	0.2189	.	.	.	0.25220	N	0.989915	D	0.62365	0.991	D	0.75484	0.986	T	0.54132	-0.8339	8	0.72032	D	0.01	.	13.4885	0.61379	0.0:0.0:0.8435:0.1565	.	252	Q9C0J8-2	.	I	252	ENSP00000387186:T252I	ENSP00000387186:T252I	T	-	2	0	WDR33	128238743	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.877000	0.63086	1.399000	0.46721	-0.181000	0.13052	ACA	.		0.403	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128522273	G	A	128522273	1	1	38	0	1	0	0	0	0	0	0	0	17320	1377	48	2		2	WDR33	2	128522273	Intron	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	471176	128522273	114677100	11	3369											
NEB	4703	broad.mit.edu	37	chr2	152359325	152359325	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accgagctaaagttctcttgAttgcgtttgactctctccat	8	15	7	11	2	2	2	0	2	2	0	5	3	3	2	2	0	2	3	2	0	2	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:152359325A>T	ENST00000172853.10	-	139	18954	c.18807T>A	c.(18805-18807)aaT>aaA	p.N6269K	NEB_ENST00000397345.3_Missense_Mutation_p.N7970K|NEB_ENST00000603639.1_Missense_Mutation_p.N7970K|NEB_ENST00000397336.2_Missense_Mutation_p.N7K|NEB_ENST00000427231.2_Missense_Mutation_p.N7970K|NEB_ENST00000509223.2_Intron|NEB_ENST00000409198.1_Missense_Mutation_p.N6269K|NEB_ENST00000604864.1_Missense_Mutation_p.N7970K|NEB_ENST00000498015.2_Intron			P20929	NEBU_HUMAN	nebulin	6269					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		AGTTCTCTTGATTGCGTTTGA	0.338																																					p.N8005K													.	NEB-145	0			c.T24015A						.						70	60	63					2																	152359325		1801	4066	5867	SO:0001583	missense	4703	exon168			CTCTTGATTGCGT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.18807T>A	2.37:g.152359325A>T	ENSP00000172853:p.Asn6269Lys	Somatic	94	2		WXS	Illumina HiSeq	Phase_I	82	6	NM_001271208	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	16.57|16.57|16.57	3.158885|3.158885|3.158885	0.57368|0.57368|0.57368	.|.|.	.|.|.	ENSG00000183091|ENSG00000183091|ENSG00000183091	ENST00000397337|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000397336;ENST00000424585|ENST00000421461	.|T;T;T;T;T;T|.	.|0.57107|.	.|0.42;0.42;0.42;0.42;4.06;0.42|.	5.57|5.57|5.57	5.57|5.57|5.57	0.84162|0.84162|0.84162	.|.|.	.|0.045524|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.73194|0.73194|0.73194	0.3556|0.3556|0.3556	M|M|M	0.91818|0.91818|0.91818	3.245|3.245|3.245	0.21652|0.21652|0.21652	N|N|N	0.999605|0.999605|0.999605	.|D;D|.	.|0.76494|.	.|0.999;0.996|.	.|D;D|.	.|0.91635|.	.|0.999;0.991|.	T|T|T	0.70142|0.70142|0.70142	-0.4953|-0.4953|-0.4953	5|10|5	.|0.42905|.	.|T|.	.|0.14|.	.|.|.	11.631|11.631|11.631	0.51175|0.51175|0.51175	0.9285:0.0:0.0715:0.0|0.9285:0.0:0.0715:0.0|0.9285:0.0:0.0715:0.0	.|.|.	.|6269;8032|.	.|P20929;F8WCL5|.	.|NEBU_HUMAN;.|.	N|K|T	166|6269;7970;7970;6269;7;197|147	.|ENSP00000386259:N6269K;ENSP00000380505:N7970K;ENSP00000416578:N7970K;ENSP00000172853:N6269K;ENSP00000380497:N7K;ENSP00000404876:N197K|.	.|ENSP00000172853:N6269K|.	I|N|S	-|-|-	2|3|1	0|2|0	NEB|NEB|NEB	152067571|152067571|152067571	0.997000|0.997000|0.997000	0.39634|0.39634|0.39634	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	0.638000|0.638000|0.638000	0.24674|0.24674|0.24674	2.113000|2.113000|2.113000	0.64589|0.64589|0.64589	0.528000|0.528000|0.528000	0.53228|0.53228|0.53228	ATC|AAT|TCA	.		0.338	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152359325	A	T	152359325	3	4	38	1	0	0	0	0	1	0	0	0	10328	330	12	5	1731	5	NEB	2	152359325	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	23837052	152359325	90840048	12	3370											
SSFA2	6744	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	182780851	182780851	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgccatcatggaaggacTcctacctgttcacggcttgc	9	10	10	12	1	2	0	2	0	0	0	3	3	3	2	3	3	3	2	3	3	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:182780851T>C	ENST00000431877.2	+	11	2663	c.2484T>C	c.(2482-2484)acT>acC	p.T828T	SSFA2_ENST00000409001.1_Silent_p.T828T|SSFA2_ENST00000428267.2_Silent_p.T675T|SSFA2_ENST00000320370.7_Silent_p.T828T|SSFA2_ENST00000409136.1_Silent_p.T337T	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	828						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			ATGGAAGGACTCCTACCTGTT	0.522																																					p.T828T													.	SSFA2-153	0			c.T2484C						.						108	120	116					2																	182780851		2203	4300	6503	SO:0001819	synonymous_variant	6744	exon11			AAGGACTCCTACC	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.2484T>C	2.37:g.182780851T>C		Somatic	81	1		WXS	Illumina HiSeq	Phase_I	100	44	NM_001130445	0	0	2	2	0	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Silent	SNP	ENST00000431877.2	37	CCDS46467.1																																																																																			.		0.522	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		C	182780851	T	C	182780851	2	2	38	1	0	0	0	0	0	0	0	1	15215	1538	54	3		3	SSFA2	2	182780851	Silent	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	30421526	182780851	60418522	13	3371											
BARD1	580	hgsc.bcm.edu;bcgsc.ca	37	chr2	215610468	215610468	+	Frame_Shift_Del	DEL	T	T	-																															gtactgtcaaactcagtataTtttttagccttaagaattac																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:215610468delT	ENST00000260947.4	-	8	1922	c.1788delA	c.(1786-1788)aaafs	p.K596fs	BARD1_ENST00000449967.2_Frame_Shift_Del_p.K452fs	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	596	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACTCAGTATATTTTTTAGCCT	0.398									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.K596fs		.											.	BARD1-415	0			c.1788delA						.						131	131	131					2																	215610468		2203	4300	6503	SO:0001589	frameshift_variant	580	exon8	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	.		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1788delA	2.37:g.215610468delT	ENSP00000260947:p.Lys596fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	75	23	NM_000465	0	0	0	0	0	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Frame_Shift_Del	DEL	ENST00000260947.4	37	CCDS2397.1																																																																																			.		0.398	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		-	215610468	T	-	215610468	7	5	38	1	0	1	0	1	0	0	0	0	1313	1490	52	0	561	0	BARD1	2	215610468	Frame_Shift_Del	DEL	T	TCGA-B1-A654-01A-11D-A31X-10	32829617	215610468	27588905	14	3372											
CHL1	10752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	383612	383612	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagaattagaacacatcgaaCaagatgaaagagtatacatg	20	7	8	6	1	0	5	0	1	0	4	1	6	0	5	0	0	3	1	0	0	8	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:383612C>A	ENST00000256509.2	+	7	1168	c.526C>A	c.(526-528)Caa>Aaa	p.Q176K	CHL1_ENST00000397491.2_Missense_Mutation_p.Q176K	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	578	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		ACACATCGAACAAGATGAAAG	0.378																																					p.Q176K		.											.	CHL1-583	0			c.C526A						.						70	64	66					3																	383612		2203	4300	6503	SO:0001583	missense	10752	exon5			ATCGAACAAGATG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.526C>A	3.37:g.383612C>A	ENSP00000256509:p.Gln176Lys	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	190	89	NM_001253388	0	0	0	0	0	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.654162	0.88056	.	.	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000435603	T;T;T	0.60672	1.1;1.1;0.17	5.43	5.43	0.79202	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.74566	0.3733	L	0.61387	1.9	0.80722	D	1	D;D;D	0.71674	0.989;0.98;0.998	P;P;D	0.91635	0.87;0.746;0.999	T	0.76337	-0.2996	10	0.87932	D	0	.	17.7511	0.88434	0.0:1.0:0.0:0.0	.	176;176;176	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	K	176	ENSP00000256509:Q176K;ENSP00000380628:Q176K;ENSP00000397445:Q176K	ENSP00000256509:Q176K	Q	+	1	0	CHL1	358612	1.000000	0.71417	0.957000	0.39632	0.774000	0.43823	6.928000	0.75846	2.696000	0.92011	0.591000	0.81541	CAA	.		0.378	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		A	383612	C	A	383612	3	1	38	1	0	0	0	0	1	0	0	0	3355	479	17	4	544	4	CHL1	3	383612	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		383612	197638818	15	3373											
FYCO1	79443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46000087	46000087	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acgtagttgttgcagcagtaGtaacagaagatgcggccaca	13	8	12	8	2	0	2	0	0	0	2	0	2	0	2	1	1	4	7	1	1	4	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:46000087G>C	ENST00000296137.2	-	13	3817	c.3612C>G	c.(3610-3612)taC>taG	p.Y1204*	FYCO1_ENST00000438446.1_5'UTR|FYCO1_ENST00000535325.1_Nonsense_Mutation_p.Y1204*	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1204					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TGCAGCAGTAGTAACAGAAGA	0.547																																					p.Y1204X		.											.	FYCO1-91	0			c.C3612G						.						72	70	71					3																	46000087		2203	4300	6503	SO:0001587	stop_gained	79443	exon13			GCAGTAGTAACAG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3612C>G	3.37:g.46000087G>C	ENSP00000296137:p.Tyr1204*	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	117	62	NM_024513	0	0	1	1	0	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Nonsense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	G	46	12.162409	0.99642	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	.	.	.	5.74	3.92	0.45320	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.7307	10.5363	0.45007	0.1343:0.0:0.8657:0.0	.	.	.	.	X	1204	.	.	Y	-	3	2	FYCO1	45975091	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.280000	0.51677	2.709000	0.92574	0.655000	0.94253	TAC	.		0.547	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		C	46000087	G	C	46000087	4	2	38	1	0	0	0	0	0	1	0	0	6144	1024	36	4	848	4	FYCO1	3	46000087	Nonsense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	45616475	46000087	152022343	16	3374											
CELSR3	1951	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	48699894	48699894	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaaagagctaaggctccGccaccgatatgcgcccttgg	10	6	12	13	3	0	1	0	0	0	1	1	3	1	2	4	3	2	2	4	3	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:48699894G>A	ENST00000164024.4	-	1	454	c.174C>T	c.(172-174)ggC>ggT	p.G58G	CELSR3_ENST00000544264.1_Silent_p.G58G|RP11-148G20.1_ENST00000421275.1_RNA	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	58					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTAAGGCTCCGCCACCGATAT	0.682																																					p.G58G		.											.	CELSR3-523	0			c.C174T						.						21	26	25					3																	48699894		2117	4162	6279	SO:0001819	synonymous_variant	1951	exon1			GGCTCCGCCACCG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.174C>T	3.37:g.48699894G>A		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_001407	0	0	0	0	0	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			.		0.682	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48699894	G	A	48699894	2	1	38	1	0	0	0	0	0	0	0	1	3229	1074	38	1		1	CELSR3	3	48699894	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	2699807	48699894	149322536	17	3375											
FRMD4B	23150	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	69230503	69230503	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatgtagtaactggaagacgGtggctcctgactctttgagt	10	12	12	7	1	1	3	0	2	1	1	2	4	2	4	1	3	1	3	1	3	4	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:69230503G>A	ENST00000398540.3	-	21	2481	c.2398C>T	c.(2398-2400)Ccg>Tcg	p.P800S	FRMD4B_ENST00000542259.1_Missense_Mutation_p.P746S|FRMD4B_ENST00000478263.1_Missense_Mutation_p.P452S	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	800					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CTGGAAGACGGTGGCTCCTGA	0.433																																					p.P800S		.											.	FRMD4B-72	0			c.C2398T						.						73	72	73					3																	69230503		1939	4143	6082	SO:0001583	missense	23150	exon21			AAGACGGTGGCTC	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.2398C>T	3.37:g.69230503G>A	ENSP00000381549:p.Pro800Ser	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	102	6	NM_015123	0	0	1	1	0	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152377	0.38021	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.86956	-2.19;-2.18	5.83	4.95	0.65309	.	0.224065	0.47455	D	0.000237	D	0.84813	0.5555	M	0.63843	1.955	0.09310	N	1	B;P	0.42203	0.058;0.773	B;B	0.35114	0.022;0.196	T	0.79351	-0.1839	10	0.72032	D	0.01	-1.8047	16.2232	0.82269	0.0:0.0:0.8659:0.1341	.	644;800	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	S	800;746;452	ENSP00000381549:P800S;ENSP00000437658:P746S	ENSP00000381549:P800S	P	-	1	0	FRMD4B	69313193	0.959000	0.32827	0.066000	0.19879	0.545000	0.35147	2.106000	0.41835	1.441000	0.47550	-0.293000	0.09583	CCG	.		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69230503	G	A	69230503	3	1	38	1	0	0	0	0	1	0	0	0	6071	1261	44	2	718	2	FRMD4B	3	69230503	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	20530609	69230503	128791927	18	3376											
SERPINI2	5276	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	167189524	167189526	+	In_Frame_Del	DEL	AAG	AAG	-																															gataaggaaacctcttgataAagatccactgcaaattcggt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:167189524_167189526delAAG	ENST00000476257.1	-	3	395_397	c.97_99delCTT	c.(97-99)cttdel	p.L33del	SERPINI2_ENST00000465031.1_5'UTR|SERPINI2_ENST00000471111.1_In_Frame_Del_p.L33del|SERPINI2_ENST00000461846.1_In_Frame_Del_p.L33del|SERPINI2_ENST00000264677.4_In_Frame_Del_p.L33del			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	33					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						CCTCTTGATAAAGATCCACTGCA	0.384																																					p.43_43del		.											.	SERPINI2-228	0			c.127_129del						.																																			SO:0001651	inframe_deletion	5276	exon3			.	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"Serine (or cysteine) peptidase inhibitors"	8945	protein-coding gene	gene with protein product		605587	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2", "serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.97_99delCTT	3.37:g.167189524_167189526delAAG	ENSP00000420621:p.Leu33del	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	75	35	NM_001012303	0	0	0	0	0		In_Frame_Del	DEL	ENST00000476257.1	37	CCDS3200.1																																																																																			.		0.384	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		-	167189526	AAG	-	167189524	7	5	38	1	0	1	0	1	0	0	0	0	14151	1	1	0	1150	0	SERPINI2	3	167189524	In_Frame_Del	DEL	AAG	TCGA-B1-A654-01A-11D-A31X-10	97959021	167189524	30832906	19	3377	32	2									
SERPINI2	5276	bcgsc.ca	37	chr3	167189527	167189527	+	Missense_Mutation	SNP	A	A	T																															aaggaaacctcttgataaagAtccactgcaaattcggtatt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:167189527A>T	ENST00000476257.1	-	3	394	c.96T>A	c.(94-96)gaT>gaA	p.D32E	SERPINI2_ENST00000465031.1_5'UTR|SERPINI2_ENST00000471111.1_Missense_Mutation_p.D32E|SERPINI2_ENST00000461846.1_Missense_Mutation_p.D32E|SERPINI2_ENST00000264677.4_Missense_Mutation_p.D32E			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	32					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						CTTGATAAAGATCCACTGCAA	0.383																																					p.D42E													.	SERPINI2-228	0			c.T126A						.						146	149	148					3																	167189527		2203	4300	6503	SO:0001583	missense	5276	exon3			ATAAAGATCCACT	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"Serine (or cysteine) peptidase inhibitors"	8945	protein-coding gene	gene with protein product		605587	"serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2", "serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.96T>A	3.37:g.167189527A>T	ENSP00000420621:p.Asp32Glu	Somatic	85	0		WXS	Illumina HiSeq	Phase_1	76	35	NM_001012303	0	0	0	0	0		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.826955	0.32329	.	.	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	5.7	3.0	0.34707	Serpin domain (3);	0.128799	0.56097	D	0.000029	D	0.87881	0.6289	L	0.50333	1.59	0.28074	N	0.932455	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.79550	-0.1757	10	0.37606	T	0.19	.	8.9818	0.35970	0.8227:0.0:0.1773:0.0	.	32;32	B4DDY9;O75830	.;SPI2_HUMAN	E	32	ENSP00000420621:D32E;ENSP00000417692:D32E;ENSP00000264677:D32E;ENSP00000419407:D32E;ENSP00000417752:D32E;ENSP00000419255:D32E	ENSP00000264677:D32E	D	-	3	2	SERPINI2	168672221	0.999000	0.42202	1.000000	0.80357	0.089000	0.18198	0.501000	0.22578	1.005000	0.39183	-0.262000	0.10625	GAT	.		0.383	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		T	167189527	A	T	167189527	3	4	38	1	0	0	0	0	1	0	0	0	14151	330	12	5	1153	5	SERPINI2	3	167189527	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	3	167189527	30832903	20	3378	32	2									
TP63	8626	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	189612036	189612036	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctgagcaatttcgacatgcGatctggaagggcatcctgga	10	9	12	10	2	1	1	0	1	1	0	3	5	2	3	2	3	2	2	2	3	2	1	rs148577576	byFrequency	TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:189612036G>C	ENST00000264731.3	+	14	1877	c.1788G>C	c.(1786-1788)gcG>gcC	p.A596A	TP63_ENST00000354600.5_Silent_p.A502A|TP63_ENST00000449992.1_Silent_p.A417A|TP63_ENST00000320472.5_3'UTR|TP63_ENST00000440651.2_Silent_p.A592A|TP63_ENST00000456148.1_Silent_p.A498A|TP63_ENST00000382063.4_Silent_p.A511A	NM_001114978.1|NM_003722.4	NP_001108450.1|NP_003713.3	Q9H3D4	P63_HUMAN	tumor protein p63	596	SAM.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TTCGACATGCGATCTGGAAGG	0.532										HNSCC(45;0.13)																											p.A596A													.	TP63-421	0			c.G1788C						.						83	81	81					3																	189612036		2203	4300	6503	SO:0001819	synonymous_variant	8626	exon14			ACATGCGATCTGG	AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282			15979	protein-coding gene	gene with protein product		603273	"tumor protein p73-like", "tumor protein p53-like", "tumor protein p53-competing protein"	TP73L, TP53L, TP53CP		9774969, 9662378, 11181441, 11181451	Standard	NM_003722		Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000264731.3:c.1788G>C	3.37:g.189612036G>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	75	30	NM_003722	0	0	0	0	0	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	Silent	SNP	ENST00000264731.3	37	CCDS3293.1																																																																																			G|0.998;A|0.002		0.532	TP63-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000343865.1	NM_003722		C	189612036	G	C	189612036	2	2	38	1	0	0	0	0	0	0	0	1	16425	1045	37	4		4	TP63	3	189612036	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	22422509	189612036	8410394	21	3379											
ADD1	118	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	2930230	2930232	+	In_Frame_Del	DEL	AAG	AAG	-																															cgtcctttctgaagaagagcAagaagaagagtgactcctga																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr4:2930230_2930232delAAG	ENST00000398129.1	+	14	2214_2216	c.2194_2196delAAG	c.(2194-2196)aagdel	p.K734del	ADD1_ENST00000355842.3_3'UTR|ADD1_ENST00000503455.2_3'UTR|ADD1_ENST00000398125.1_3'UTR|ADD1_ENST00000446856.1_In_Frame_Del_p.K734del|ADD1_ENST00000398123.2_3'UTR|ADD1_ENST00000264758.7_In_Frame_Del_p.K765del|ADD1_ENST00000513328.2_3'UTR			P35611	ADDA_HUMAN	adducin 1 (alpha)	734	Interaction with calmodulin. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GAAGAAGAGCAAGAAGAAGAGTG	0.616																																					p.763_763del	Esophageal Squamous(71;505 1201 20414 34538 37449)	.											.	ADD1-92	0			c.2287_2289del						.		,,,	2,4264		0,2,2131					,,,	5.2	1			63	0,8254		0,0,4127	no	utr-3,utr-3,coding,coding	ADD1	NM_176801.2,NM_014190.3,NM_014189.3,NM_001119.4	,,,	0,2,6258	A1A1,A1R,RR		0.0,0.0469,0.016	,,,	,,,		2,12518				SO:0001651	inframe_deletion	118	exon15			.	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.2194_2196delAAG	4.37:g.2930236_2930238delAAG	ENSP00000381197:p.Lys734del	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	117	50	NM_014189	0	0	0	0	0	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	In_Frame_Del	DEL	ENST00000398129.1	37	CCDS43205.1																																																																																			.		0.616	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		-	2930232	AAG	-	2930230	7	5	38	1	0	1	0	1	0	0	0	0	304	131	5	0	2379	0	ADD1	4	2930230	In_Frame_Del	DEL	AAG	TCGA-B1-A654-01A-11D-A31X-10		2930230	188224046	22	3380											
AFAP1	60312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	7783233	7783233	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagaggcctttctgtcagcaGgagagtagcgggcaaagatg	11	8	15	7	1	2	3	1	0	1	3	2	4	2	3	1	3	2	3	1	3	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr4:7783233G>T	ENST00000360265.4	-	12	1765				AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000382543.3_Missense_Mutation_p.P551H|AFAP1_ENST00000358461.2_Intron|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000420658.1_Missense_Mutation_p.P551H			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TCTGTCAGCAGGAGAGTAGCG	0.532																																					p.P551H		.											.	AFAP1-90	0			c.C1652A						.						123	119	120					4																	7783233		692	1591	2283	SO:0001627	intron_variant	60312	exon13			TCAGCAGGAGAGT	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2630C>A	4.37:g.7783233G>T		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	106	40	NM_001134647	0	0	0	0	0	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848151	0.91277	.	.	ENSG00000196526	ENST00000420658;ENST00000382543	T;T	0.16597	2.33;2.33	5.8	5.8	0.92144	.	.	.	.	.	T	0.21427	0.0516	L	0.36672	1.1	0.80722	D	1	D	0.61697	0.99	P	0.45946	0.498	T	0.00287	-1.1846	9	0.45353	T	0.12	.	20.0706	0.97721	0.0:0.0:1.0:0.0	.	551	E9PDT7	.	H	551	ENSP00000410689:P551H;ENSP00000371983:P551H	ENSP00000371983:P551H	P	-	2	0	AFAP1	7834133	1.000000	0.71417	0.588000	0.28705	0.985000	0.73830	7.463000	0.80869	2.744000	0.94065	0.655000	0.94253	CCT	.		0.532	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		T	7783233	G	T	7783233	1	4	38	0	1	0	0	0	0	0	0	0	353	1000	35	4		4	AFAP1	4	7783233	Intron	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	4853003	7783233	183371043	23	3381											
UGT2B15	7367	broad.mit.edu	37	chr4	69403575	69403575	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcgatccaggggcttcaccGgttgatcatgatgaattctt	8	13	10	10	2	3	3	2	3	1	0	5	4	4	3	2	3	0	2	2	3	1	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr4:69403575G>T	ENST00000317746.2	-	6	1403	c.1361C>A	c.(1360-1362)cCg>cAg	p.P454Q		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	454					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	GGGCTTCACCGGTTGATCATG	0.408																																					p.P454Q	Melanoma(18;649 833 28984 37818 38500)												.	UGT2B17-91	0			c.C1361A						.						96	95	96					4																	69403575		2092	3934	6026	SO:0001583	missense	7367	exon6			TTCACCGGTTGAT	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"UDP glucuronosyltransferases"	12547	protein-coding gene	gene with protein product		601903	"UDP glycosyltransferase 2 family, polypeptide B17"			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.1361C>A	4.37:g.69403575G>T	ENSP00000320401:p.Pro454Gln	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	135	5	NM_001077	0	0	0	0	0		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.029242	0.35797	.	.	ENSG00000197888	ENST00000317746	T	0.76186	-1.0	2.85	2.85	0.33270	.	0.000000	0.64402	U	0.000002	D	0.85106	0.5621	M	0.90019	3.08	0.34551	D	0.711274	.	.	.	.	.	.	D	0.90969	0.4818	8	0.87932	D	0	.	11.4257	0.50009	0.0:0.0:1.0:0.0	.	.	.	.	Q	454	ENSP00000320401:P454Q	ENSP00000320401:P454Q	P	-	2	0	UGT2B17	69086170	1.000000	0.71417	0.391000	0.26233	0.028000	0.11728	4.709000	0.61867	1.580000	0.49851	0.195000	0.17529	CCG	.		0.408	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		T	69403575	G	T	69403575	3	4	38	1	0	0	0	0	1	0	0	0	16991	1116	39	4	235	4	UGT2B15	4	69403575	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	61620342	69403575	121750701	24	3382											
ANXA10	11199	bcgsc.ca	37	chr4	169108558	169108558	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaagcactgcttgccatCtgtgctggtgatgctgagga	10	10	13	8	0	1	3	0	2	1	1	1	4	1	4	1	2	5	4	1	2	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr4:169108558C>A	ENST00000359299.3	+	12	1134	c.948C>A	c.(946-948)atC>atA	p.I316I		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	316						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		TGCTTGCCATCTGTGCTGGTG	0.338																																					p.I316I													.	ANXA10-90	0			c.C948A						.						109	103	105					4																	169108558		2203	4300	6503	SO:0001819	synonymous_variant	11199	exon12			TGCCATCTGTGCT	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"Annexins"	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.948C>A	4.37:g.169108558C>A		Somatic	435	4		WXS	Illumina HiSeq	Phase_1	360	148	NM_007193	0	0	0	0	0	Q96IQ5|Q9UJV4	Silent	SNP	ENST00000359299.3	37	CCDS34096.1																																																																																			.		0.338	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193		A	169108558	C	A	169108558	2	1	38	1	0	0	0	0	0	0	0	1	715	903	32	4		4	ANXA10	4	169108558	Silent	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	99704983	169108558	22045718	25	3383											
CTNND2	1501	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	10992734	10992734	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggagtagggcctttgcCggtccctctcgatggttgaa	7	10	15	9	2	1	1	0	1	1	0	3	4	2	3	3	5	1	2	3	5	2	3	rs367931998		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:10992734C>T	ENST00000304623.8	-	19	3329	c.3140G>A	c.(3139-3141)cGg>cAg	p.R1047Q	CTNND2_ENST00000503622.1_Missense_Mutation_p.R710Q|CTNND2_ENST00000511377.1_Missense_Mutation_p.R956Q|CTNND2_ENST00000359640.2_Missense_Mutation_p.R989Q|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000458100.2_Missense_Mutation_p.R614Q	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1047					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGGCCTTTGCCGGTCCCTCTC	0.587																																					p.R1047Q		.											.	CTNND2-293	0			c.G3140A						.						134	120	125					5																	10992734		2203	4300	6503	SO:0001583	missense	1501	exon19			CTTTGCCGGTCCC	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"Armadillo repeat containing"	2516	protein-coding gene	gene with protein product	"neural plakophilin-related arm-repeat protein"	604275	"catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.3140G>A	5.37:g.10992734C>T	ENSP00000307134:p.Arg1047Gln	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	49	25	NM_001332	0	0	0	1	1	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.691098	0.88735	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000538638;ENST00000458100;ENST00000503622	T;T;T;T;T	0.79554	-1.22;-1.28;-1.22;-1.25;-1.25	5.18	4.3	0.51218	.	0.063175	0.64402	D	0.000009	D	0.84497	0.5485	L	0.39245	1.2	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.993	D;D;P	0.70227	0.968;0.968;0.543	D	0.83914	0.0297	10	0.40728	T	0.16	-11.8165	14.9681	0.71210	0.1441:0.8559:0.0:0.0	.	710;639;1047	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	Q	1047;989;956;142;614;710	ENSP00000307134:R1047Q;ENSP00000352661:R989Q;ENSP00000426510:R956Q;ENSP00000391155:R614Q;ENSP00000426887:R710Q	ENSP00000307134:R1047Q	R	-	2	0	CTNND2	11045734	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.337000	0.79256	1.159000	0.42565	0.650000	0.86243	CGG	.		0.587	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	10992734	C	T	10992734	3	4	38	1	0	0	0	0	1	0	0	0	4026	652	23	1	553	1	CTNND2	5	10992734	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		10992734	169922526	26	3384											
ADAMTS12	81792	broad.mit.edu	37	chr5	33891915	33891915	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaaagttaaggagctgaGccaccacggaaaggtttgca	13	6	11	11	1	0	1	0	1	0	0	0	3	0	3	4	3	3	4	4	3	3	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:33891915G>T	ENST00000504830.1	-	1	382	c.47C>A	c.(46-48)gCt>gAt	p.A16D	ADAMTS12_ENST00000515401.1_Missense_Mutation_p.A16D|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.A16D	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	16					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						AAGGAGCTGAGCCACCACGGA	0.522										HNSCC(64;0.19)																											p.A16D													.	ADAMTS12-232	0			c.C47A						.						95	100	98					5																	33891915		2203	4300	6503	SO:0001583	missense	81792	exon1			AGCTGAGCCACCA	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.47C>A	5.37:g.33891915G>T	ENSP00000422554:p.Ala16Asp	Somatic	303	0		WXS	Illumina HiSeq	Phase_I	244	5	NM_030955	0	0	0	0	0	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.890371	0.72524	.	.	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.60424	0.19;0.19;3.31	5.61	2.48	0.30137	.	0.266944	0.30168	N	0.010257	T	0.49864	0.1582	L	0.27053	0.805	0.19775	N	0.999954	D;D;D	0.55385	0.969;0.971;0.971	P;P;P	0.53809	0.735;0.691;0.548	T	0.37197	-0.9716	10	0.66056	D	0.02	.	5.1183	0.14847	0.4699:0.0:0.5301:0.0	.	16;16;16	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	D	16	ENSP00000422554:A16D;ENSP00000344847:A16D;ENSP00000421638:A16D	ENSP00000344847:A16D	A	-	2	0	ADAMTS12	33927672	0.951000	0.32395	0.473000	0.27253	0.977000	0.68977	1.706000	0.37878	0.735000	0.32537	0.585000	0.79938	GCT	.		0.522	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33891915	G	T	33891915	3	4	38	1	0	0	0	0	1	0	0	0	257	971	34	4	4833	4	ADAMTS12	5	33891915	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	22899181	33891915	147023345	27	3385											
PCDHGC5	56097	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140870632	140870633	+	Frame_Shift_Ins	INS	-	-	T																															tgcgtggctctcctactcacINStgttgccacagtccacagcc																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:140870632_140870633insT	ENST00000252087.1	+	1	1825_1826	c.1825_1826insT	c.(1825-1827)ctgfs	p.L609fs	PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	609	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCTACTCACTGTTGCCACAG	0.619																																					p.L609fs		.											.	PCDHGC5-25	0			c.1825_1826insT						.																																			SO:0001589	frameshift_variant	56097	exon1			.	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1826dupT	5.37:g.140870633_140870633dupT	ENSP00000252087:p.Leu609fs	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	38	19	NM_018929	0	0	0	0	0	Q9Y5C2	Frame_Shift_Ins	INS	ENST00000252087.1	37	CCDS4263.1																																																																																			.		0.619	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		T	140870633	-	T	140870632	7	5	38	1	0	1	1	0	0	0	0	0	11597	564	20	0	1827	0	PCDHGC5	5	140870632	Frame_Shift_Ins	INS	-	TCGA-B1-A654-01A-11D-A31X-10	106978717	140870632	40044628	28	3386											
LARS	51520	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	145547749	145547751	+	In_Frame_Del	DEL	TCC	TCC	-																															ctgttttaacactggtttctTcctcttcctcttcttcatct																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:145547749_145547751delTCC	ENST00000394434.2	-	5	538_540	c.372_374delGGA	c.(370-375)gaggaa>gaa	p.124_125EE>E	LARS_ENST00000545646.1_Intron|LARS_ENST00000511505.1_Intron|LARS_ENST00000510191.1_In_Frame_Del_p.70_71EE>E|LARS_ENST00000274562.9_In_Frame_Del_p.97_98EE>E	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	124					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	ACTGGTTTCTTCCTCTTCCTCTT	0.33																																					p.124_125del		.											.	LARS-90	0			c.372_374del						.																																			SO:0001651	inframe_deletion	51520	exon5			.	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	6512	protein-coding gene	gene with protein product	"leucine tRNA ligase 1, cytoplasmic"	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.372_374delGGA	5.37:g.145547749_145547751delTCC	ENSP00000377954:p.Glu126del	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	88	28	NM_020117	0	0	0	0	0	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	In_Frame_Del	DEL	ENST00000394434.2	37	CCDS34265.1																																																																																			.		0.33	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		-	145547751	TCC	-	145547749	7	5	38	1	0	1	0	1	0	0	0	0	8655	1783	62	0	3268	0	LARS	5	145547749	In_Frame_Del	DEL	TCC	TCGA-B1-A654-01A-11D-A31X-10	4677117	145547749	35367511	29	3387											
BPHL	670	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	3137663	3137663	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccctctatgggtatgaCtactttgccagaacctgtga	10	11	10	10	0	1	3	0	2	1	1	1	4	1	3	3	1	4	1	3	1	5	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr6:3137663C>T	ENST00000380379.5	+	5	649	c.600C>T	c.(598-600)gaC>gaT	p.D200D	RP1-40E16.11_ENST00000447644.1_RNA|BPHL_ENST00000380368.2_Intron|BPHL_ENST00000380375.3_Silent_p.D183D|BPHL_ENST00000434640.1_Silent_p.D183D	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	200					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				ATGGGTATGACTACTTTGCCA	0.458																																					p.D200D													.	BPHL-90	0			c.C600T						.						131	134	133					6																	3137663		2203	4300	6503	SO:0001819	synonymous_variant	670	exon5			GTATGACTACTTT	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"breast epithelial mucin-associated antigen"	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.600C>T	6.37:g.3137663C>T		Somatic	178	1		WXS	Illumina HiSeq	Phase_I	132	54	NM_004332	0	0	10	13	3	Q00306|Q13855|Q3KP51	Silent	SNP	ENST00000380379.5	37	CCDS4483.2																																																																																			.		0.458	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5			T	3137663	C	T	3137663	2	4	38	1	0	0	0	0	0	0	0	1	1492	564	20	2		2	BPHL	6	3137663	Silent	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		3137663	167977404	30	3388											
PHACTR1	221692	bcgsc.ca	37	chr6	13228185	13228185	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgattgaatgtgatgacaAtaaagaaaatgtgcctcatg	15	12	10	4	0	1	5	1	4	0	1	1	5	1	5	1	0	1	0	1	0	6	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr6:13228185A>G	ENST00000379350.1	+	8	1253	c.1124A>G	c.(1123-1125)aAt>aGt	p.N375S	PHACTR1_ENST00000457702.2_Missense_Mutation_p.N230S|PHACTR1_ENST00000379345.2_Intron|PHACTR1_ENST00000332995.7_Missense_Mutation_p.N375S			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	375					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			TGTGATGACAATAAAGAAAAT	0.483																																					p.N375S													.	.	0			c.A1124G						.						170	174	172					6																	13228185		1986	4159	6145	SO:0001583	missense	221692	exon9			ATGACAATAAAGA	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.1124A>G	6.37:g.13228185A>G	ENSP00000368655:p.Asn375Ser	Somatic	94	2		WXS	Illumina HiSeq	Phase_1	80	38	NM_030948	0	0	0	1	1	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379350.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.41|18.41	3.617678|3.617678	0.66787|0.66787	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000415087|ENST00000379350;ENST00000332995;ENST00000432934;ENST00000457702	.|T;T;T	.|0.35789	.|1.29;1.36;1.41	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.142496	.|0.64402	.|D	.|0.000005	T|T	0.22475|0.22475	0.0542|0.0542	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.31817	.|0.208;0.231;0.341	.|B;B;B	.|0.33799	.|0.17;0.058;0.167	T|T	0.06588|0.06588	-1.0818|-1.0818	5|10	.|0.52906	.|T	.|0.07	-19.1766|-19.1766	15.5501|15.5501	0.76145|0.76145	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|444;375;375	.|E7ESR5;Q9C0D0;Q9C0D0-2	.|.;PHAR1_HUMAN;.	V|S	210|375;375;444;230	.|ENSP00000368655:N375S;ENSP00000329880:N375S;ENSP00000397669:N230S	.|ENSP00000329880:N375S	I|N	+|+	1|2	0|0	PHACTR1|PHACTR1	13336164|13336164	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.661000|8.661000	0.91125|0.91125	2.315000|2.315000	0.78130|0.78130	0.533000|0.533000	0.62120|0.62120	ATA|AAT	.		0.483	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		G	13228185	A	G	13228185	3	3	38	1	0	0	0	0	1	0	0	0	11835	101	4	3	1150	3	PHACTR1	6	13228185	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	10090522	13228185	157886882	31	3389											
SYNE1	23345	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152453307	152453307	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgtgggactcacagaccCtgaggtgtccagttcatcag	9	10	12	10	0	3	3	3	2	0	1	4	4	4	4	2	2	0	1	2	2	0	1	rs201664645	byFrequency	TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr6:152453307C>A	ENST00000367255.5	-	144	26645	c.26044G>T	c.(26044-26046)Ggg>Tgg	p.G8682W	SYNE1_ENST00000341594.5_Missense_Mutation_p.G8294W|SYNE1_ENST00000539504.1_Missense_Mutation_p.G837W|SYNE1_ENST00000265368.4_Missense_Mutation_p.G8682W|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.G8634W|SYNE1_ENST00000423061.1_Missense_Mutation_p.G8634W|SYNE1_ENST00000356820.4_Missense_Mutation_p.G3206W|SYNE1_ENST00000354674.4_Missense_Mutation_p.G860W	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8682	Ser-rich.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTCACAGACCCTGAGGTGTCC	0.512										HNSCC(10;0.0054)																											p.G8682W													.	SYNE1-607	0			c.G26044T						.						183	160	168					6																	152453307		2203	4300	6503	SO:0001583	missense	23345	exon144			CAGACCCTGAGGT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.26044G>T	6.37:g.152453307C>A	ENSP00000356224:p.Gly8682Trp	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	111	46	NM_182961	0	0	7	18	11	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.278156	0.80692	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.58506	0.42;4.53;1.26;0.44;0.33;0.44;0.57;2.48;1.44;4.55	5.75	5.75	0.90469	.	0.000000	0.50627	D	0.000116	T	0.74114	0.3674	M	0.75264	2.295	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.998;0.999;0.998;0.99	T	0.75944	-0.3139	10	0.87932	D	0	.	19.9447	0.97177	0.0:1.0:0.0:0.0	.	8682;8682;8634;8634;884	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	W	8682;837;1328;8634;8682;8634;8294;3206;867;862;1627;860	ENSP00000356224:G8682W;ENSP00000441052:G837W;ENSP00000356226:G1328W;ENSP00000396024:G8634W;ENSP00000265368:G8682W;ENSP00000390975:G8634W;ENSP00000341887:G8294W;ENSP00000349276:G3206W;ENSP00000356220:G1627W;ENSP00000346701:G860W	ENSP00000265368:G8682W	G	-	1	0	SYNE1	152495000	1.000000	0.71417	0.860000	0.33809	0.969000	0.65631	5.584000	0.67490	2.719000	0.93026	0.655000	0.94253	GGG	C|1.000;G|0.000		0.512	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152453307	C	A	152453307	3	1	38	1	0	0	0	0	1	0	0	0	15477	681	24	4	361	4	SYNE1	6	152453307	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	139225122	152453307	18661760	32	3390											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725800	15725800	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgctgatggtggtgatgGtggtggtggtggtggtggtg	2	14	23	2	0	0	2	0	2	0	0	0	2	0	2	0	9	2	2	0	9	0	0	rs113582077	byFrequency	TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:15725800G>A	ENST00000262041.5	-	1	637	c.228C>T	c.(226-228)caC>caT	p.H76H	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	76	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)	p.H80delH(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtgatggtggtggtggt	0.612																																					p.H76H	Esophageal Squamous(140;197 1769 16409 18257 29929)	.											.	MEOX2-515	1	Deletion - In frame(1)	stomach(1)	c.C228T						.						11	13	13					7																	15725800		2192	4293	6485	SO:0001819	synonymous_variant	4223	exon1			GTGATGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.228C>T	7.37:g.15725800G>A		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	35	9	NM_005924	0	0	0	0	0	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	37	CCDS34605.1																																																																																			.		0.612	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725800	G	A	15725800	2	1	38	1	0	0	0	0	0	0	0	1	9499	1252	44	2		2	MEOX2	7	15725800	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		15725800	143412863	33	3391											
DFNA5	1687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	24784199	24784199	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctcggcagagtctctgAtgagctgctgcaaatccacc	9	9	9	14	1	2	3	0	2	2	1	5	3	3	3	3	1	3	4	3	1	1	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:24784199A>T	ENST00000342947.3	-	3	811	c.386T>A	c.(385-387)aTc>aAc	p.I129N	DFNA5_ENST00000409970.1_5'UTR|DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000409775.3_Missense_Mutation_p.I129N	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	129					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						AGAGTCTCTGATGAGCTGCTG	0.507																																					p.I129N	GBM(78;184 1250 20134 20900 23600)	.											.	DFNA5-91	0			c.T386A						.						119	115	116					7																	24784199		2203	4300	6503	SO:0001583	missense	1687	exon3			TCTCTGATGAGCT	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.386T>A	7.37:g.24784199A>T	ENSP00000339587:p.Ile129Asn	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	66	12	NM_001127453	0	0	8	13	5	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.361849	0.61403	.	.	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.21932	1.98;1.98	5.59	5.59	0.84812	.	0.432748	0.26662	N	0.023150	T	0.42966	0.1226	M	0.67953	2.075	0.80722	D	1	D;D	0.61080	0.989;0.989	D;D	0.63283	0.913;0.913	T	0.22730	-1.0208	10	0.45353	T	0.12	-8.2661	15.7667	0.78131	1.0:0.0:0.0:0.0	.	129;129	A4FTY0;O60443	.;DFNA5_HUMAN	N	129	ENSP00000339587:I129N;ENSP00000386670:I129N	ENSP00000339587:I129N	I	-	2	0	DFNA5	24750724	1.000000	0.71417	0.742000	0.31022	0.252000	0.25951	5.678000	0.68153	2.138000	0.66242	0.528000	0.53228	ATC	.		0.507	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		T	24784199	A	T	24784199	3	4	38	1	0	0	0	0	1	0	0	0	4465	333	12	5	1136	5	DFNA5	7	24784199	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	9058399	24784199	134354464	34	3392											
HOXA9	3205	broad.mit.edu;bcgsc.ca	37	chr7	27203455	27203455	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgaagccagttggctgctgGgttatctgcggggaagagaa	10	9	16	6	1	1	2	0	1	1	1	1	4	1	3	1	4	3	4	1	4	4	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:27203455G>T	ENST00000343483.6	-	2	658	c.586C>A	c.(586-588)Cca>Aca	p.P196T	RP1-170O19.20_ENST00000470747.4_Missense_Mutation_p.P36T|RP1-170O19.20_ENST00000465941.1_5'UTR|HOXA9_ENST00000497089.1_5'UTR|HOXA9_ENST00000396345.1_3'UTR	NM_152739.3	NP_689952.1	P31269	HXA9_HUMAN	homeobox A9	196					endothelial cell activation (GO:0042118)|multicellular organismal development (GO:0007275)|negative regulation of myeloid cell differentiation (GO:0045638)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(1)|lung(5)|prostate(1)	8						TTGGCTGCTGGGTTATCTGCG	0.552			T	"NUP98, MSI2"	AML*																																p.P196T				Dom	yes		7	7p15-p14.2	3205	homeo box A9		L	.	HOXA9-1082	0			c.C586A						.						77	79	79					7																	27203455		2203	4300	6503	SO:0001583	missense	3205	exon2			CTGCTGGGTTATC		CCDS5409.1	7p15.2	2011-06-20	2005-12-22		ENSG00000078399	ENSG00000078399		"Homeoboxes / ANTP class : HOXL subclass"	5109	protein-coding gene	gene with protein product		142956	"homeo box A9"	HOX1G, HOX1		1973146, 1358459	Standard	NM_152739		Approved		uc003syt.3	P31269	OTTHUMG00000023220	ENST00000343483.6:c.586C>A	7.37:g.27203455G>T	ENSP00000343619:p.Pro196Thr	Somatic	43	1		WXS	Illumina HiSeq	Phase_I	76	19	NM_152739	0	0	1	1	0	O43369|O43429|Q99820	Missense_Mutation	SNP	ENST00000343483.6	37	CCDS5409.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205571	0.79127	.	.	ENSG00000078399;ENSG00000078399;ENSG00000078399;ENSG00000257184	ENST00000343483;ENST00000354032;ENST00000242050;ENST00000470747	D;D	0.95554	-3.74;-3.74	5.21	5.21	0.72293	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000011	D	0.96870	0.8978	M	0.64567	1.98	0.80722	D	1	D	0.61080	0.989	P	0.61477	0.889	D	0.97341	0.9957	10	0.87932	D	0	.	18.1322	0.89605	0.0:0.0:1.0:0.0	.	196	P31269	HXA9_HUMAN	T	196;120;187;36	ENSP00000343619:P196T;ENSP00000421799:P36T	ENSP00000242050:P187T	P	-	1	0	RP1-170O19.20;HOXA9	27169980	1.000000	0.71417	0.997000	0.53966	0.807000	0.45602	9.869000	0.99810	2.623000	0.88846	0.561000	0.74099	CCA	.		0.552	HOXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358706.2			T	27203455	G	T	27203455	3	4	38	1	0	0	0	0	1	0	0	0	7319	1232	43	4	236	4	HOXA9	7	27203455	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	2419256	27203455	131935208	35	3393											
HECW1	23072	broad.mit.edu;bcgsc.ca	37	chr7	43490498	43490498	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggcctgaacatcatcacTacccaacaatcgatgagcct	13	8	7	13	1	2	3	2	3	0	0	3	4	2	3	3	1	4	0	3	1	4	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:43490498T>C	ENST00000395891.2	+	12	3075	c.2470T>C	c.(2470-2472)Tac>Cac	p.Y824H	HECW1_ENST00000453890.1_Intron	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	824					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						ACATCATCACTACCCAACAAT	0.418																																					p.Y824H													.	HECW1-669	0			c.T2470C						.						140	138	139					7																	43490498		1944	4133	6077	SO:0001583	missense	23072	exon12			CATCACTACCCAA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2470T>C	7.37:g.43490498T>C	ENSP00000379228:p.Tyr824His	Somatic	46	1		WXS	Illumina HiSeq	Phase_I	67	37	NM_015052	0	0	0	0	0	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	T	29.3	4.997488	0.93227	.	.	ENSG00000002746	ENST00000395891;ENST00000265522	T	0.32515	1.45	5.97	5.97	0.96955	WW/Rsp5/WWP (1);	0.191964	0.46758	D	0.000271	T	0.39064	0.1064	L	0.34521	1.04	0.80722	D	1	D	0.59357	0.985	P	0.55667	0.781	T	0.06215	-1.0839	10	0.36615	T	0.2	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	824	Q76N89	HECW1_HUMAN	H	824	ENSP00000379228:Y824H	ENSP00000265522:Y824H	Y	+	1	0	HECW1	43457023	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.409000	0.80053	2.288000	0.76882	0.533000	0.62120	TAC	.		0.418	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		C	43490498	T	C	43490498	3	2	38	1	0	0	0	0	1	0	0	0	7063	1522	53	3	2508	3	HECW1	7	43490498	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	16287043	43490498	115648165	36	3394											
POR	5447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	75615290	75615290	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacggctgccgccgctcggaTgaggactacctgtaccggga	7	7	14	13	5	0	1	0	1	0	0	1	4	0	4	4	4	4	3	4	4	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:75615290T>C	ENST00000461988.1	+	14	1824	c.1719T>C	c.(1717-1719)gaT>gaC	p.D573D	POR_ENST00000545601.1_Silent_p.D381D|POR_ENST00000419840.1_Intron|POR_ENST00000394893.1_Silent_p.D573D|POR_ENST00000450476.1_Silent_p.D472D|TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA|POR_ENST00000439269.1_Silent_p.D311D	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	570					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCCGCTCGGATGAGGACTACC	0.692																																					p.D573D		.											.	POR-23	0			c.T1719C						.						11	17	15					7																	75615290		1973	4109	6082	SO:0001819	synonymous_variant	5447	exon14			CTCGGATGAGGAC	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1719T>C	7.37:g.75615290T>C		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	81	18	NM_000941	0	0	107	161	54	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1	.	.	.	.	.	.	.	.	.	.	T	6.335	0.429939	0.11987	.	.	ENSG00000127948	ENST00000447222	.	.	.	3.59	-1.16	0.09678	.	.	.	.	.	.	.	.	.	.	.	0.41802	D	0.989923	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.2896	4.2567	0.10721	0.1605:0.2767:0.0:0.5628	.	.	.	.	R	624	.	.	X	+	1	0	POR	75453226	0.000000	0.05858	0.885000	0.34714	0.753000	0.42808	-2.270000	0.01167	-0.213000	0.10094	-0.496000	0.04628	TGA	.		0.692	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		C	75615290	T	C	75615290	2	2	38	1	0	0	0	0	0	0	0	1	12283	1461	51	3		3	POR	7	75615290	Silent	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	32124792	75615290	83523373	37	3395											
PTCD1	26024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99022430	99022430	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccactcaccttcatgtctgtGagaagctgtagaccgtcctt	8	12	8	13	1	3	2	2	1	1	2	4	3	4	2	4	0	1	2	4	0	2	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:99022430G>A	ENST00000292478.4	-	6	1975	c.1725C>T	c.(1723-1725)ctC>ctT	p.L575L	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.L624L|PTCD1_ENST00000555673.1_Silent_p.L624L	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	575					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TCATGTCTGTGAGAAGCTGTA	0.612																																					p.L624L		.											.	.	0			c.C1872T						.						52	53	53					7																	99022430		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon7			GTCTGTGAGAAGC	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1725C>T	7.37:g.99022430G>A		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	30	9	NM_001198879	0	0	0	0	0	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	37	CCDS34691.1																																																																																			.		0.612	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99022430	G	A	99022430	2	1	38	1	0	0	0	0	0	0	0	1	12756	1277	45	2		2	PTCD1	7	99022430	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	23407140	99022430	60116233	38	3396											
MET	4233	ucsc.edu;bcgsc.ca	37	chr7	116423413	116423413	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggtcttgccagagacatgTatgataaagaatactatagt	14	13	9	5	0	1	3	0	1	1	2	1	4	1	3	1	1	2	1	1	1	7	7	rs121913247		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:116423413T>C	ENST00000318493.6	+	19	3929	c.3742T>C	c.(3742-3744)Tat>Cat	p.Y1248H	MET_ENST00000397752.3_Missense_Mutation_p.Y1230H|MET_ENST00000539704.1_Missense_Mutation_p.Y100H			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y1248H(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CAGAGACATGTATGATAAAGA	0.388			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.Y1248H				Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.T3742C	GRCh37	CM992180	MET	M	rs121913247	.						105	99	101					7																	116423413		1843	4095	5938	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GACATGTATGATA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3742T>C	7.37:g.116423413T>C	ENSP00000317272:p.Tyr1248His	Somatic	117	2		WXS	Illumina HiSeq		151	89	NM_001127500	0	0	1	4	3	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.622544	0.66787	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	D;D;D	0.83075	-1.68;-1.68;-1.68	5.46	5.46	0.80206	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90075	0.6900	M	0.68593	2.085	0.54753	D	0.999981	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91155	0.4956	10	0.87932	D	0	.	15.824	0.78683	0.0:0.0:0.0:1.0	.	1248;1230	P08581-2;P08581	.;MET_HUMAN	H	1230;1248;100	ENSP00000380860:Y1230H;ENSP00000317272:Y1248H;ENSP00000445020:Y100H	ENSP00000317272:Y1248H	Y	+	1	0	MET	116210649	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.145000	0.71769	2.197000	0.70478	0.460000	0.39030	TAT	.		0.388	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423413	T	C	116423413	3	2	38	1	0	0	0	0	1	0	0	0	9510	1638	57	3	3812	3	MET	7	116423413	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	17400983	116423413	42715250	39	3397											
POT1	25913	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	124503439	124503439	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctccgtccacttctgcttTgcccaagagctgacaagtca	8	11	8	14	1	2	2	1	1	1	1	4	2	4	2	3	0	4	3	3	0	2	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:124503439T>C	ENST00000357628.3	-	8	1109	c.511A>G	c.(511-513)Aaa>Gaa	p.K171E	POT1_ENST00000393329.1_Missense_Mutation_p.K40E	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	171					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						ACTTCTGCTTTGCCCAAGAGC	0.388																																					p.K171E	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)												.	POT1-227	0			c.A511G						.						114	107	110					7																	124503439		2203	4300	6503	SO:0001583	missense	25913	exon8			CTGCTTTGCCCAA	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"protection of telomeres 1 homolog (S. pombe)"			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.511A>G	7.37:g.124503439T>C	ENSP00000350249:p.Lys171Glu	Somatic	116	1		WXS	Illumina HiSeq	Phase_I	176	49	NM_015450	0	0	0	0	0	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	37	CCDS5793.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.613597	0.87359	.	.	ENSG00000128513	ENST00000357628;ENST00000393329;ENST00000451720;ENST00000440969;ENST00000393326;ENST00000265391	T;T	0.50548	0.8;0.74	5.47	5.47	0.80525	Nucleic acid-binding, OB-fold-like (1);	0.000000	0.85682	D	0.000000	T	0.67581	0.2908	M	0.75264	2.295	0.54753	D	0.999985	D	0.89917	1.0	D	0.87578	0.998	T	0.67177	-0.5736	10	0.34782	T	0.22	-9.8043	14.7435	0.69474	0.0:0.0:0.0:1.0	.	171	Q9NUX5	POTE1_HUMAN	E	171;40;171;171;171;170	ENSP00000350249:K171E;ENSP00000377002:K40E	ENSP00000265391:K170E	K	-	1	0	POT1	124290675	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.211000	0.72182	2.069000	0.61940	0.528000	0.53228	AAA	.		0.388	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			C	124503439	T	C	124503439	3	2	38	1	0	0	0	0	1	0	0	0	12286	1821	63	3	1441	3	POT1	7	124503439	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	8080026	124503439	34635224	40	3398											
MLL3	58508	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151884405	151884405	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtagagaactggggcaacAgttgccatttcacccagagc	11	8	12	10	0	1	2	1	0	0	2	1	3	1	2	2	2	4	3	2	2	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:151884405A>T	ENST00000262189.6	-	33	5168	c.4950T>A	c.(4948-4950)acT>acA	p.T1650T	KMT2C_ENST00000355193.2_Silent_p.T1650T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1650					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CTGGGGCAACAGTTGCCATTT	0.428																																					p.T1650T													.	MLL3-1398	0			c.T4950A						.						135	139	138					7																	151884405		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon33			GGCAACAGTTGCC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.4950T>A	7.37:g.151884405A>T		Somatic	102	1		WXS	Illumina HiSeq	Phase_I	138	38	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.428	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151884405	A	T	151884405	2	4	38	1	0	0	0	0	0	0	0	1	9647	175	7	5		5	MLL3	7	151884405	Silent	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	27380966	151884405	7254258	41	3399											
CTSB	1508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	11705226	11705226	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtaggtcgggctgtagccaGgctcacagatcttgctacac	8	10	12	11	1	2	1	1	0	1	1	3	1	2	1	1	3	3	5	1	3	3	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:11705226G>T	ENST00000353047.6	-	7	891	c.638C>A	c.(637-639)cCt>cAt	p.P213H	CTSB_ENST00000531089.1_Missense_Mutation_p.P213H|CTSB_ENST00000415599.2_3'UTR|CTSB_ENST00000434271.1_Missense_Mutation_p.P213H|CTSB_ENST00000345125.3_Missense_Mutation_p.P213H|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000530640.2_Missense_Mutation_p.P213H|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000533455.1_Missense_Mutation_p.P213H|CTSB_ENST00000453527.2_Missense_Mutation_p.P213H|CTSB_ENST00000534510.1_Missense_Mutation_p.P213H	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	213					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		GCTGTAGCCAGGCTCACAGAT	0.647																																					p.P213H		.											.	CTSB-90	0			c.C638A						.						109	104	105					8																	11705226		2203	4300	6503	SO:0001583	missense	1508	exon9			TAGCCAGGCTCAC	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.638C>A	8.37:g.11705226G>T	ENSP00000345672:p.Pro213His	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	53	24	NM_147780	0	0	96	186	90	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493396	0.44352	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328	D;D;D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	5.17	3.16	0.36331	Peptidase C1A, papain C-terminal (2);	0.662303	0.15592	N	0.254378	D	0.90765	0.7101	M	0.76838	2.35	0.45295	D	0.99829	D;P;P;D;D	0.60575	0.988;0.73;0.85;0.988;0.985	P;P;P;P;P	0.56163	0.752;0.512;0.512;0.723;0.793	D	0.90644	0.4577	10	0.52906	T	0.07	.	12.4013	0.55414	0.0:0.0:0.6427:0.3573	.	150;213;119;213;150	B3KUJ8;A8K2H4;B4DMY4;P07858;F5H2P9	.;.;.;CATB_HUMAN;.	H	213;150;213;213;213;213;213;213;213;119	ENSP00000415889:P213H;ENSP00000345672:P213H;ENSP00000435105:P213H;ENSP00000433215:P213H;ENSP00000409917:P213H;ENSP00000342070:P213H;ENSP00000432244:P213H;ENSP00000434217:P213H	ENSP00000342070:P213H	P	-	2	0	CTSB	11742635	0.137000	0.22531	0.501000	0.27601	0.244000	0.25665	2.483000	0.45233	2.397000	0.81536	0.561000	0.74099	CCT	.		0.647	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		T	11705226	G	T	11705226	3	4	38	1	0	0	0	0	1	0	0	0	4036	1000	35	4	397	4	CTSB	8	11705226	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		11705226	134658796	42	3400											
TRPA1	8989	ucsc.edu	37	chr8	72958841	72958841	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agatatttgaaattatactcGatctgtagaagacagaattt	16	14	7	4	1	1	5	0	1	1	4	2	6	1	5	0	0	1	1	0	0	7	6	rs367626209		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:72958841G>A	ENST00000262209.4	-	17	2175	c.1968C>T	c.(1966-1968)atC>atT	p.I656I	RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	656					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	AATTATACTCGATCTGTAGAA	0.294																																					p.I656I													.	TRPA1-230	0			c.C1968T						.	A		1,4405	824.0+/-416.5	0,1,2202	104	111	109		1968	-8.9	0.6	8		109	0,8600		0,0,4300	no	coding-synonymous	TRPA1	NM_007332.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		656/1120	72958841	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon17			ATACTCGATCTGT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1968C>T	8.37:g.72958841G>A		Somatic	66	0		WXS	Illumina HiSeq		39	4	NM_007332	0	0	0	0	0	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			.		0.294	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		A	72958841	G	A	72958841	2	1	38	1	0	0	0	0	0	0	0	1	16610	1048	37	1		1	TRPA1	8	72958841	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	61253615	72958841	73405181	43	3401											
LRRCC1	85444	ucsc.edu;bcgsc.ca	37	chr8	86027335	86027335	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgaatgatttgtttccaagGgtacagagcagttattctcc	10	15	9	7	0	1	3	0	2	1	1	3	3	2	3	2	1	2	4	2	1	4	6			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:86027335G>A	ENST00000360375.3	+	5	694	c.545G>A	c.(544-546)gGg>gAg	p.G182E	LRRCC1_ENST00000414626.2_Splice_Site_p.G162E	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	182	LRRCT.				mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						TGTTTCCAAGGGTACAGAGCA	0.318																																					p.G182E													.	LRRCC1-90	0			c.G545A						.						83	79	80					8																	86027335		1820	4089	5909	SO:0001630	splice_region_variant	85444	exon5			TCCAAGGGTACAG	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.545-1G>A	8.37:g.86027335G>A		Somatic	153	2		WXS	Illumina HiSeq		116	52	NM_033402	0	0	0	0	0	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.451934	0.84209	.	.	ENSG00000133739	ENST00000426019;ENST00000360375;ENST00000414626	T;T	0.23552	1.9;1.9	4.98	4.98	0.66077	U2A&apos (1);/phosphoprotein 32 family A, C-terminal (1);	0.000000	0.40554	N	0.001071	T	0.56262	0.1973	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.60687	-0.7214	9	.	.	.	.	18.599	0.91240	0.0:0.0:1.0:0.0	.	162;89;182	Q9C099-2;E9PE41;Q9C099	.;.;LRCC1_HUMAN	E	89;182;162	ENSP00000353538:G182E;ENSP00000394695:G162E	.	G	+	2	0	LRRCC1	86214587	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.393000	0.90182	2.468000	0.83385	0.460000	0.39030	GGG	.		0.318	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	Missense_Mutation	A	86027335	G	A	86027335	5	1	38	1	0	0	0	0	0	0	1	0	9051	1246	43	2	563	2	LRRCC1	8	86027335	Splice_Site	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	13068494	86027335	60336687	44	3402											
DCAF4L2	138009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	88885869	88885869	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtgcgggtatacccggagctCaggggtcgtcaggcctcgca	6	7	16	12	4	2	0	2	0	0	0	4	1	2	1	2	5	3	3	2	5	2	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:88885869C>G	ENST00000319675.3	-	1	427	c.331G>C	c.(331-333)Gag>Cag	p.E111Q		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	111										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						ACCCGGAGCTCAGGGGTCGTC	0.542																																					p.E111Q		.											.	DCAF4L2-91	0			c.G331C						.						138	133	135					8																	88885869		2203	4300	6503	SO:0001583	missense	138009	exon1			GGAGCTCAGGGGT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"WD repeat domain containing"	26657	protein-coding gene	gene with protein product			"WD repeat domain 21C"	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.331G>C	8.37:g.88885869C>G	ENSP00000316496:p.Glu111Gln	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	85	32	NM_152418	0	0	0	0	0		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247732	0.22880	.	.	ENSG00000176566	ENST00000319675	T	0.61510	0.1	1.39	0.34	0.15985	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.699660	0.15847	N	0.241732	T	0.38480	0.1042	L	0.29908	0.895	0.09310	N	1	P	0.37330	0.59	B	0.33846	0.171	T	0.22452	-1.0216	10	0.72032	D	0.01	.	6.1683	0.20402	0.3004:0.6996:0.0:0.0	.	111	Q8NA75	DC4L2_HUMAN	Q	111	ENSP00000316496:E111Q	ENSP00000316496:E111Q	E	-	1	0	DCAF4L2	88954985	0.999000	0.42202	0.001000	0.08648	0.010000	0.07245	1.840000	0.39230	-0.115000	0.11915	0.467000	0.42956	GAG	.		0.542	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		G	88885869	C	G	88885869	3	3	38	1	0	0	0	0	1	0	0	0	4278	835	29	4	860	4	DCAF4L2	8	88885869	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	2858534	88885869	57478153	45	3403											
PKHD1L1	93035	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	110488892	110488892	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacactagtactctatattaCttgggtatgtgtcattaggc	11	15	8	7	0	2	0	1	0	1	0	2	0	2	0	0	2	3	2	0	2	8	8			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:110488892C>G	ENST00000378402.5	+	52	9017	c.8913C>G	c.(8911-8913)taC>taG	p.Y2971*		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2971					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTCTATATTACTTGGGTATGT	0.343										HNSCC(38;0.096)																											p.Y2971X													.	PKHD1L1-145	0			c.C8913G						.						43	42	42					8																	110488892		1865	4100	5965	SO:0001587	stop_gained	93035	exon52			ATATTACTTGGGT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.8913C>G	8.37:g.110488892C>G	ENSP00000367655:p.Tyr2971*	Somatic	142	1		WXS	Illumina HiSeq	Phase_I	123	50	NM_177531	0	0	0	0	0	Q567P2|Q9UF27	Nonsense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	48	14.623838	0.99803	.	.	ENSG00000205038	ENST00000378402	.	.	.	5.69	-0.86	0.10680	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2209	0.54433	0.0:0.4969:0.0:0.5031	.	.	.	.	X	2971	.	ENSP00000367655:Y2971X	Y	+	3	2	PKHD1L1	110558068	0.445000	0.25657	0.710000	0.30468	0.416000	0.31233	0.485000	0.22324	-0.457000	0.07033	-1.128000	0.01989	TAC	.		0.343	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		G	110488892	C	G	110488892	4	3	38	1	0	0	0	0	0	1	0	0	11998	576	20	4	9119	4	PKHD1L1	8	110488892	Nonsense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	21603023	110488892	35875130	46	3404											
PHYHIPL	84457	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	60936661	60936661	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacagccccaccagcccCtgtgaggaggtgatcaaaaa	13	5	9	14	0	2	2	2	2	0	0	2	3	2	3	5	2	3	0	5	2	3	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr10:60936661C>A	ENST00000373880.4	+	1	312	c.48C>A	c.(46-48)ccC>ccA	p.P16P	PHYHIPL_ENST00000373878.3_5'Flank|PHYHIPL_ENST00000433653.1_Silent_p.P16P	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	16						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						CCACCAGCCCCTGTGAGGAGG	0.627																																					p.P16P		.											.	PHYHIPL-90	0			c.C48A						.						64	58	60					10																	60936661		2203	4300	6503	SO:0001819	synonymous_variant	84457	exon1			CAGCCCCTGTGAG	AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"Fibronectin type III domain containing"	29378	protein-coding gene	gene with protein product			"phytanoyl-CoA hydroxylase interacting protein-like"			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.48C>A	10.37:g.60936661C>A		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	46	17	NM_032439	0	0	2	3	1	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Silent	SNP	ENST00000373880.4	37	CCDS7254.1																																																																																			.		0.627	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		A	60936661	C	A	60936661	2	1	38	1	0	0	0	0	0	0	0	1	11893	668	24	4		4	PHYHIPL	10	60936661	Silent	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		60936661	74598086	47	3405											
KIAA1274	27143	ucsc.edu	37	chr10	72289809	72289809	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggtcctccagaaactccaGaaggacggacatagggtaag	13	5	13	10	2	0	2	0	0	0	2	3	4	3	4	3	4	1	1	3	4	4	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr10:72289809G>T	ENST00000263563.6	+	4	721	c.453G>T	c.(451-453)caG>caT	p.Q151H		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	151						cytosol (GO:0005829)											AGAAACTCCAGAAGGACGGAC	0.637																																					p.Q151H													.	.	0			c.G453T						.						45	44	44					10																	72289809		2203	4300	6503	SO:0001583	missense	27143	exon4			ACTCCAGAAGGAC	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"paladin", "KIAA1274"	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.453G>T	10.37:g.72289809G>T	ENSP00000263563:p.Gln151His	Somatic	35	0		WXS	Illumina HiSeq		38	4	NM_014431	0	0	0	0	0	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.073514	0.76415	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.29917	1.55	5.34	5.34	0.76211	.	0.055071	0.85682	D	0.000000	T	0.55940	0.1952	M	0.81239	2.535	0.58432	D	0.999997	D	0.56521	0.976	P	0.59012	0.85	T	0.58645	-0.7600	10	0.52906	T	0.07	-20.0085	19.0411	0.92999	0.0:0.0:1.0:0.0	.	151	Q9ULE6	PALD_HUMAN	H	151	ENSP00000263563:Q151H	ENSP00000263563:Q151H	Q	+	3	2	KIAA1274	71959815	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	5.250000	0.65432	2.673000	0.90976	0.557000	0.71058	CAG	.		0.637	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72289809	G	T	72289809	3	4	38	1	0	0	0	0	1	0	0	0	8241	933	33	4	463	4	KIAA1274	10	72289809	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	11353148	72289809	63244938	48	3406											
C10orf119	79892	broad.mit.edu	37	chr10	121591063	121591063	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctagctgctttgctctcaGccatcgttctcttgacagcg	5	14	8	14	2	3	1	1	1	3	0	6	1	3	1	1	0	5	4	1	0	1	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr10:121591063G>T	ENST00000360003.3	-	16	2021	c.1852C>A	c.(1852-1854)Ctg>Atg	p.L618M	MCMBP_ENST00000369077.3_Missense_Mutation_p.L616M|MCMBP_ENST00000466047.1_5'UTR	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	618					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TTTGCTCTCAGCCATCGTTCT	0.408																																					p.L618M													.	MCMBP-93	0			c.C1852A						.						87	80	83					10																	121591063		2203	4300	6503	SO:0001583	missense	79892	exon16			CTCTCAGCCATCG	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.1852C>A	10.37:g.121591063G>T	ENSP00000353098:p.Leu618Met	Somatic	81	1		WXS	Illumina HiSeq	Phase_I	81	4	NM_024834	0	0	27	27	0	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	37	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505668	0.44558	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	.	.	.	5.72	5.72	0.89469	.	0.064488	0.64402	D	0.000004	T	0.51466	0.1676	N	0.20685	0.6	0.53005	D	0.999961	B	0.20780	0.048	B	0.14023	0.01	T	0.43507	-0.9387	9	0.46703	T	0.11	-7.219	19.8722	0.96854	0.0:0.0:1.0:0.0	.	618	Q9BTE3	MCMBP_HUMAN	M	618;616	.	ENSP00000353098:L618M	L	-	1	2	MCMBP	121581053	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.215000	0.58534	2.700000	0.92200	0.585000	0.79938	CTG	.		0.408	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		T	121591063	G	T	121591063	3	4	38	1	0	0	0	0	1	0	0	0	1592	962	34	4	80	4	C10orf119	10	121591063	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	49301254	121591063	13943684	49	3407											
INSC	387755	broad.mit.edu;bcgsc.ca	37	chr11	15197495	15197495	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtcattagcacagagctgCgcaggatcgggcagaagctg	10	6	16	9	2	1	2	1	0	0	2	2	3	1	3	0	3	4	5	0	3	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr11:15197495C>A	ENST00000379554.3	+	3	452	c.406C>A	c.(406-408)Cgc>Agc	p.R136S	INSC_ENST00000528567.1_Missense_Mutation_p.R89S|INSC_ENST00000424273.1_Missense_Mutation_p.R89S|INSC_ENST00000379556.3_Missense_Mutation_p.R89S|INSC_ENST00000530161.1_Missense_Mutation_p.R89S|INSC_ENST00000525218.1_Missense_Mutation_p.R89S	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	136					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						CACAGAGCTGCGCAGGATCGG	0.652																																					p.R136S													.	INSC-94	0			c.C406A						.						28	31	30					11																	15197495		2047	4179	6226	SO:0001583	missense	387755	exon3			GAGCTGCGCAGGA	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"inscuteable spindle orientation adaptor protein"	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.406C>A	11.37:g.15197495C>A	ENSP00000368872:p.Arg136Ser	Somatic	53	2		WXS	Illumina HiSeq	Phase_I	47	22	NM_001031853	0	0	0	0	0	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	.	.	.	.	.	.	.	.	.	.	C	8.695	0.908328	0.17833	.	.	ENSG00000188487	ENST00000379554;ENST00000379556;ENST00000424273;ENST00000416761;ENST00000528567;ENST00000530161;ENST00000525218	T;T;T;T;T;T	0.28895	1.59;1.62;1.6;1.6;1.62;1.6	5.2	3.23	0.37069	.	0.249802	0.34628	N	0.003801	T	0.09818	0.0241	N	0.03608	-0.345	0.29192	N	0.875806	B;B;B;B	0.29531	0.188;0.017;0.077;0.247	B;B;B;B	0.28784	0.052;0.012;0.025;0.094	T	0.32428	-0.9907	10	0.02654	T	1	-21.7187	7.1996	0.25873	0.3943:0.4709:0.1348:0.0	.	89;89;89;136	Q1MX18-5;Q1MX18-4;A0PJX5;Q1MX18	.;.;.;INSC_HUMAN	S	136;89;89;89;89;89;89	ENSP00000368872:R136S;ENSP00000368874:R89S;ENSP00000389161:R89S;ENSP00000435022:R89S;ENSP00000436194:R89S;ENSP00000436113:R89S	ENSP00000368872:R136S	R	+	1	0	INSC	15154071	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.217000	0.58547	2.420000	0.82092	0.462000	0.41574	CGC	.		0.652	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		A	15197495	C	A	15197495	3	1	38	1	0	0	0	0	1	0	0	0	7785	768	27	4	416	4	INSC	11	15197495	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		15197495	119809021	50	3408											
MRPL11	65003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66204727	66204727	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtcaccaggcctgccacCtctttccctgggaggaagga	9	7	12	13	0	2	0	1	0	1	0	3	3	3	3	5	5	1	0	5	5	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr11:66204727C>G	ENST00000310999.7	-	4	414	c.321G>C	c.(319-321)gaG>gaC	p.E107D	MRPL11_ENST00000430466.2_Missense_Mutation_p.E81D|MRPL11_ENST00000329819.4_Missense_Mutation_p.E107D|MRPL11_ENST00000524576.1_5'UTR	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	107					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						GGCCTGCCACCTCTTTCCCTG	0.547																																					p.E107D		.											.	MRPL11-90	0			c.G321C						.						82	76	78					11																	66204727		2200	4295	6495	SO:0001583	missense	65003	exon4			TGCCACCTCTTTC	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"Mitochondrial ribosomal proteins / large subunits"	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.321G>C	11.37:g.66204727C>G	ENSP00000308897:p.Glu107Asp	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	41	22	NM_170739	0	0	0	0	0	A6NLT0|A8K219|Q32P46|Q96Q73	Missense_Mutation	SNP	ENST00000310999.7	37	CCDS8139.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399495	0.62177	.	.	ENSG00000174547	ENST00000310999;ENST00000430466;ENST00000329819	.	.	.	5.79	1.92	0.25849	Ribosomal protein L11, C-terminal (3);	0.099158	0.64402	D	0.000002	T	0.61123	0.2322	L	0.45352	1.415	0.58432	D	0.999993	D;D;D	0.71674	0.993;0.995;0.998	D;D;D	0.71184	0.953;0.962;0.972	T	0.54649	-0.8262	9	0.27785	T	0.31	-33.3697	7.3258	0.26555	0.0:0.5948:0.0:0.4052	.	81;107;107	Q9Y3B7-2;Q9Y3B7;A6NLT0	.;RM11_HUMAN;.	D	107;81;107	.	ENSP00000308897:E107D	E	-	3	2	MRPL11	65961303	0.998000	0.40836	1.000000	0.80357	0.858000	0.48976	0.534000	0.23098	0.384000	0.24942	-0.123000	0.14984	GAG	.		0.547	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050		G	66204727	C	G	66204727	3	3	38	1	0	0	0	0	1	0	0	0	9801	680	24	4	342	4	MRPL11	11	66204727	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	51007232	66204727	68801789	51	3409											
P2RY6	5031	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	73007583	73007583	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaatgggacaatggcaCaggccaggctctgggcttgc	9	7	15	10	0	1	0	0	0	1	0	1	2	1	2	1	6	1	3	1	6	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr11:73007583C>A	ENST00000393590.2	+	2	319	c.20C>A	c.(19-21)aCa>aAa	p.T7K	P2RY6_ENST00000542092.1_Missense_Mutation_p.T7K|P2RY6_ENST00000540342.1_Missense_Mutation_p.T7K|P2RY6_ENST00000393591.1_Missense_Mutation_p.T7K|P2RY6_ENST00000349767.2_Missense_Mutation_p.T7K|P2RY6_ENST00000393592.2_Missense_Mutation_p.T7K|P2RY6_ENST00000540124.1_Missense_Mutation_p.T7K|P2RY6_ENST00000538328.1_Missense_Mutation_p.T7K	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	7					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						GACAATGGCACAGGCCAGGCT	0.597																																					p.T7K													.	P2RY6-501	0			c.C20A						.						83	84	84					11																	73007583		2200	4293	6493	SO:0001583	missense	5031	exon4			ATGGCACAGGCCA		CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.20C>A	11.37:g.73007583C>A	ENSP00000377215:p.Thr7Lys	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	60	24	NM_176796	0	0	2	2	0	Q15754	Missense_Mutation	SNP	ENST00000393590.2	37	CCDS8220.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280371	0.80692	.	.	ENSG00000171631	ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000544437;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000536225;ENST00000535931;ENST00000538328	T;T;T;T;T;T;T;T;T;T;T	0.70986	-0.28;-0.28;-0.28;-0.28;1.3;-0.28;-0.28;-0.28;0.95;-0.53;-0.28	4.12	4.12	0.48240	.	0.795267	0.10928	N	0.618734	T	0.62696	0.2449	L	0.38175	1.15	0.19300	N	0.999978	P	0.37781	0.608	B	0.34824	0.19	T	0.59931	-0.7361	10	0.87932	D	0	.	14.2152	0.65788	0.0:1.0:0.0:0.0	.	7	Q15077	P2RY6_HUMAN	K	7	ENSP00000443427:T7K;ENSP00000445652:T7K;ENSP00000309771:T7K;ENSP00000377217:T7K;ENSP00000441079:T7K;ENSP00000377216:T7K;ENSP00000442551:T7K;ENSP00000377215:T7K;ENSP00000442509:T7K;ENSP00000440770:T7K;ENSP00000442990:T7K	ENSP00000309771:T7K	T	+	2	0	P2RY6	72685231	0.025000	0.19082	0.065000	0.19835	0.958000	0.62258	1.404000	0.34623	2.264000	0.75181	0.491000	0.48974	ACA	.		0.597	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			A	73007583	C	A	73007583	3	1	38	1	0	0	0	0	1	0	0	0	11380	478	17	4	22	4	P2RY6	11	73007583	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	6802856	73007583	61998933	52	3410											
MAML2	84441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	95825407	95825407	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgctgctgttgctgctgttg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs61901862		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q596Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.532			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q596Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	1	Substitution - coding silent(1)	kidney(1)	c.G1788A						.						28	35	33					11																	95825407		2119	4148	6267	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1788G>A	11.37:g.95825407C>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	88	10	NM_032427	0	0	904	913	9	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			C|0.250;T|0.750		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825407	C	T	95825407	2	4	38	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825407	Silent	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	22817824	95825407	39181109	53	3411											
SRGAP1	57522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64377795	64377795	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cggagatgcgagttcagcttCtccaggatctgcaagatttc	9	11	11	10	2	3	2	1	0	2	2	5	5	3	3	1	2	3	3	1	2	1	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:64377795C>T	ENST00000355086.3	+	2	660	c.136C>T	c.(136-138)Ctc>Ttc	p.L46F	SRGAP1_ENST00000357825.3_Missense_Mutation_p.L46F|SRGAP1_ENST00000543397.1_Missense_Mutation_p.L6F	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	46	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		AGTTCAGCTTCTCCAGGATCT	0.428																																					p.L46F		.											.	SRGAP1-653	0			c.C136T						.						105	110	108					12																	64377795		2203	4300	6503	SO:0001583	missense	57522	exon2			CAGCTTCTCCAGG	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.136C>T	12.37:g.64377795C>T	ENSP00000347198:p.Leu46Phe	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	59	24	NM_020762	0	0	0	0	0	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872961	0.91664	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.24151	1.87;1.87;1.87	5.1	5.1	0.69264	Fps/Fes/Fer/CIP4 homology (3);	0.000000	0.31760	U	0.007120	T	0.53190	0.1781	M	0.74389	2.26	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.996;0.994;0.997	T	0.52381	-0.8583	9	.	.	.	.	18.9008	0.92442	0.0:1.0:0.0:0.0	.	46;6;46	Q7Z6B7;G5EA48;Q7Z6B7-2	SRGP1_HUMAN;.;.	F	46;46;6	ENSP00000347198:L46F;ENSP00000350480:L46F;ENSP00000437948:L6F	.	L	+	1	0	SRGAP1	62664062	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	7.755000	0.85180	2.548000	0.85928	0.585000	0.79938	CTC	.		0.428	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64377795	C	T	64377795	3	4	38	1	0	0	0	0	1	0	0	0	15177	913	32	2	142	2	SRGAP1	12	64377795	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		64377795	69474100	54	3412											
SCYL2	55681	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	100731225	100731225	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacaagagcaggcacagaagCtgaaaagccagcagcctctt	16	4	10	11	0	1	3	0	1	1	2	1	3	1	3	2	1	6	4	2	1	5	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:100731225C>T	ENST00000360820.2	+	17	2523	c.2086C>T	c.(2086-2088)Ctg>Ttg	p.L696L		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	696					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						GGCACAGAAGCTGAAAAGCCA	0.373																																					p.L696L													.	SCYL2-336	0			c.C2086T						.						125	124	124					12																	100731225		2203	4300	6503	SO:0001819	synonymous_variant	55681	exon17			CAGAAGCTGAAAA	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2086C>T	12.37:g.100731225C>T		Somatic	60	1		WXS	Illumina HiSeq	Phase_I	50	26	NM_017988	0	0	0	0	0	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Silent	SNP	ENST00000360820.2	37	CCDS9076.1																																																																																			.		0.373	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		T	100731225	C	T	100731225	2	4	38	1	0	0	0	0	0	0	0	1	13980	796	28	2		2	SCYL2	12	100731225	Silent	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	36353430	100731225	33120670	55	3413											
ARL1	400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	101799660	101799660	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctcccacttgtaatctgTacaaaattgtggtttttcct	8	18	5	10	0	2	0	0	0	2	0	4	0	3	0	2	1	1	3	2	1	4	7			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:101799660T>C	ENST00000261636.8	-	2	278	c.104A>G	c.(103-105)tAc>tGc	p.Y35C	RP11-321F8.4_ENST00000547360.1_lincRNA|ARL1_ENST00000549302.1_5'UTR|ARL1_ENST00000536227.1_Missense_Mutation_p.Y18C|ARL1_ENST00000551828.1_Missense_Mutation_p.Y18C|ARL1_ENST00000551688.1_Intron|ARL1_ENST00000551671.1_Missense_Mutation_p.Y35C|ARL1_ENST00000539055.1_Intron	NM_001177.4	NP_001168.1	P40616	ARL1_HUMAN	ADP-ribosylation factor-like 1	35					activation of phospholipase D activity (GO:0031584)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)|toxin metabolic process (GO:0009404)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	enzyme activator activity (GO:0008047)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			central_nervous_system(1)|upper_aerodigestive_tract(1)	2		Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163)		GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125)		TTGTAATCTGTACAAAATTGT	0.368																																					p.Y35C		.											.	ARL1-205	0			c.A104G						.						82	73	76					12																	101799660		1850	4074	5924	SO:0001583	missense	400	exon2			AATCTGTACAAAA	BX537387	CCDS44958.1, CCDS73510.1	12q23.3	2014-05-09						"ADP-ribosylation factors-like", "ADP-ribosylation factors"	692	protein-coding gene	gene with protein product		603425					Standard	XM_005268869		Approved	ARFL1	uc001tib.3	P40616	OTTHUMG00000170271	ENST00000261636.8:c.104A>G	12.37:g.101799660T>C	ENSP00000261636:p.Tyr35Cys	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	83	39	NM_001177	0	0	19	31	12	B4DWW1|P80417|Q53XB1	Missense_Mutation	SNP	ENST00000261636.8	37	CCDS44958.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.691681	0.88735	.	.	ENSG00000120805	ENST00000261636;ENST00000536227;ENST00000551828;ENST00000551671	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.79	5.79	0.91817	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95069	0.8403	H	0.98818	4.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.97048	0.9762	10	0.72032	D	0.01	-8.9448	16.1803	0.81892	0.0:0.0:0.0:1.0	.	35;35	F8VYN9;P40616	.;ARL1_HUMAN	C	35;18;18;35	ENSP00000261636:Y35C;ENSP00000441808:Y18C;ENSP00000448850:Y18C;ENSP00000448912:Y35C	ENSP00000261636:Y35C	Y	-	2	0	ARL1	100323791	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.930000	0.87610	2.229000	0.72834	0.524000	0.50904	TAC	.		0.368	ARL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408246.1	NM_001177		C	101799660	T	C	101799660	3	2	38	1	0	0	0	0	1	0	0	0	925	1638	57	3	461	3	ARL1	12	101799660	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	1068435	101799660	32052235	56	3414											
USP30	84749	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	109490532	109490532	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccgcggccgacagggccAtccagcgcttcctgcggacc	6	5	13	17	5	0	1	0	1	0	0	2	3	2	2	6	3	2	1	6	3	0	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:109490532A>T	ENST00000257548.5	+	1	142	c.49A>T	c.(49-51)Atc>Ttc	p.I17F	USP30-AS1_ENST00000478808.2_RNA|USP30_ENST00000392784.2_Intron	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	17					mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						CGACAGGGCCATCCAGCGCTT	0.741																																					p.I17F		.											.	USP30-658	0			c.A49T						.						6	7	7					12																	109490532		1633	3539	5172	SO:0001583	missense	84749	exon1			AGGGCCATCCAGC	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.49A>T	12.37:g.109490532A>T	ENSP00000257548:p.Ile17Phe	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	55	26	NM_032663	0	0	0	0	0	Q8WTU7|Q96JX4|Q9BSS3	Missense_Mutation	SNP	ENST00000257548.5	37	CCDS9123.2	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071460	0.76301	.	.	ENSG00000135093	ENST00000257548;ENST00000536393	T	0.36699	1.24	4.83	-3.67	0.04476	.	0.525534	0.20286	N	0.095347	T	0.17746	0.0426	N	0.14661	0.345	0.36723	D	0.881283	B	0.02656	0.0	B	0.01281	0.0	T	0.03394	-1.1041	10	0.62326	D	0.03	-15.0275	9.4412	0.38670	0.2273:0.6458:0.0:0.1269	.	17	Q70CQ3	UBP30_HUMAN	F	17	ENSP00000257548:I17F	ENSP00000257548:I17F	I	+	1	0	USP30	107974915	0.830000	0.29337	0.983000	0.44433	0.992000	0.81027	-0.415000	0.07106	-0.293000	0.08986	0.482000	0.46254	ATC	.		0.741	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		T	109490532	A	T	109490532	3	4	38	1	0	0	0	0	1	0	0	0	17094	217	8	5	51	5	USP30	12	109490532	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	7690872	109490532	24361363	57	3415											
BRCA2	90634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	32972588	32972588	+	IGR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaatacgaaacacccataaAgaaaaaagaactgaattctc	22	6	4	9	1	1	3	0	1	1	2	2	4	1	3	1	0	3	0	1	0	10	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr13:32972588A>C	ENST00000380130.2	-	0	3046				BRCA2_ENST00000544455.1_Missense_Mutation_p.K3313T|BRCA2_ENST00000380152.3_Missense_Mutation_p.K3313T	NM_052818.2	NP_438169.2	Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1											large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		ACACCCATAAAGAAAAAAGAA	0.393																																					p.K3313T		.											.	BRCA2-3153	0			c.A9938C						.						69	72	71					13																	32972588		2203	4300	6503	SO:0001628	intergenic_variant	675	exon27			CCATAAAGAAAAA	U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697		13.37:g.32972588A>C		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	125	51	NM_000059	0	0	0	0	0	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380130.2	37	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	A	16.59	3.166079	0.57476	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00816	5.66;5.66	5.19	1.43	0.22495	.	0.585853	0.16656	N	0.205002	T	0.02688	0.0081	L	0.55834	1.745	0.29155	N	0.87815	D	0.71674	0.998	P	0.62560	0.904	T	0.30446	-0.9978	10	0.51188	T	0.08	.	8.9414	0.35731	0.7861:0.0:0.2139:0.0	.	3313	P51587	BRCA2_HUMAN	T	3313	ENSP00000369497:K3313T;ENSP00000439902:K3313T	ENSP00000369497:K3313T	K	+	2	0	BRCA2	31870588	0.216000	0.23585	0.108000	0.21378	0.601000	0.36947	2.044000	0.41241	0.111000	0.17947	0.383000	0.25322	AAG	.		0.393	N4BP2L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052818		C	32972588	A	C	32972588	1	2	38	0	1	0	0	0	0	0	0	0	1502	72	3	5		5	BRCA2	13	32972588	IGR	SNP	A	TCGA-B1-A654-01A-11D-A31X-10		32972588	82197290	58	3416											
SPRY2	10253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr13	80911824	80911824	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcgacccgttgccactcTgagctctggcctccatcagg	5	9	11	16	2	3	1	1	1	2	0	4	2	4	1	4	2	3	3	4	2	0	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr13:80911824T>C	ENST00000377102.1	-	2	994	c.17A>G	c.(16-18)cAg>cGg	p.Q6R	SPRY2_ENST00000540649.1_Missense_Mutation_p.Q6R|SPRY2_ENST00000377104.3_Missense_Mutation_p.Q6R			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	6					bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		GTTGCCACTCTGAGCTCTGGC	0.602																																					p.Q6R		.											.	SPRY2-659	0			c.A17G						.						36	39	38					13																	80911824		2203	4300	6503	SO:0001583	missense	10253	exon2			CCACTCTGAGCTC	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"sprouty (Drosophila) homolog 2"			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.17A>G	13.37:g.80911824T>C	ENSP00000366306:p.Gln6Arg	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	32	17	NM_005842	0	0	0	4	4	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	37	CCDS9463.1	.	.	.	.	.	.	.	.	.	.	T	18.75	3.690500	0.68271	.	.	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57273	0.41;0.41;0.41	5.2	5.2	0.72013	.	0.258022	0.39687	N	0.001300	T	0.58380	0.2118	M	0.70275	2.135	0.58432	D	0.999996	P	0.51791	0.948	P	0.45610	0.487	T	0.66408	-0.5931	10	0.87932	D	0	2.2461	15.1453	0.72647	0.0:0.0:0.0:1.0	.	6	O43597	SPY2_HUMAN	R	6	ENSP00000366308:Q6R;ENSP00000366306:Q6R;ENSP00000439027:Q6R	ENSP00000366306:Q6R	Q	-	2	0	SPRY2	79809825	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.437000	0.80417	1.989000	0.58080	0.529000	0.55759	CAG	.		0.602	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			C	80911824	T	C	80911824	3	2	38	1	0	0	0	0	1	0	0	0	15138	1580	55	3	934	3	SPRY2	13	80911824	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	47939236	80911824	34258054	59	3417											
ITPK1	3705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	93408247	93408247	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaactcgctcacgccctcgtAgcctgggggtgggagagaga	8	6	16	11	3	1	2	1	0	0	2	3	5	1	2	2	3	2	2	2	3	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr14:93408247A>T	ENST00000267615.6	-	11	1077	c.904T>A	c.(904-906)Tac>Aac	p.Y302N	ITPK1_ENST00000556603.2_Missense_Mutation_p.Y302N|ITPK1_ENST00000354313.3_Intron|ITPK1_ENST00000555495.1_Missense_Mutation_p.Y183N			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	302	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		ACGCCCTCGTAGCCTGGGGGT	0.652																																					p.Y302N		.											.	ITPK1-115	0			c.T904A						.						19	15	17					14																	93408247		2087	4121	6208	SO:0001583	missense	3705	exon11			CCTCGTAGCCTGG	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.904T>A	14.37:g.93408247A>T	ENSP00000267615:p.Tyr302Asn	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	31	18	NM_001142593	0	0	0	0	0	Q9BTL6|Q9H2E7	Missense_Mutation	SNP	ENST00000267615.6	37	CCDS9907.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.272145	0.80469	.	.	ENSG00000100605	ENST00000405174;ENST00000556603;ENST00000555495;ENST00000267615;ENST00000311458	.	.	.	4.59	4.59	0.56863	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.79764	0.4502	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.83445	0.0045	9	0.87932	D	0	-1.445	13.993	0.64378	1.0:0.0:0.0:0.0	.	302	Q13572	ITPK1_HUMAN	N	332;302;183;302;302	.	ENSP00000267615:Y302N	Y	-	1	0	ITPK1	92478000	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	8.912000	0.92726	1.717000	0.51406	0.460000	0.39030	TAC	.		0.652	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93408247	A	T	93408247	3	4	38	1	0	0	0	0	1	0	0	0	7937	420	15	5	392	5	ITPK1	14	93408247	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10		93408247	13941293	60	3418											
HSP90AA1	3320	broad.mit.edu;ucsc.edu	37	chr14	102548766	102548766	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcatggagatgtcaccaatcGgtttgacacaaccacctgta	12	9	9	11	1	1	2	1	1	0	1	2	3	1	2	3	2	1	3	3	2	3	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr14:102548766G>A	ENST00000216281.8	-	10	1976	c.1771C>T	c.(1771-1773)Cga>Tga	p.R591*	HSP90AA1_ENST00000334701.7_Nonsense_Mutation_p.R713*	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	591					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	GTCACCAATCGGTTTGACACA	0.393																																					p.R713X													.	HSP90AA1-949	0			c.C2137T						.						54	50	51					14																	102548766		2203	4300	6503	SO:0001587	stop_gained	3320	exon11			CCAATCGGTTTGA	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.1771C>T	14.37:g.102548766G>A	ENSP00000216281:p.Arg591*	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_001017963	0	1	110	113	2	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Nonsense_Mutation	SNP	ENST00000216281.8	37	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	g	40	8.219651	0.98712	.	.	ENSG00000080824	ENST00000216281;ENST00000334701	.	.	.	4.3	2.21	0.28008	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7696	11.5269	0.50584	0.0:0.0:0.5372:0.4628	.	.	.	.	X	591;713	.	ENSP00000216281:R591X	R	-	1	2	HSP90AA1	101618519	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.830000	0.48136	0.895000	0.36342	0.585000	0.79938	CGA	.		0.393	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		A	102548766	G	A	102548766	4	1	38	1	0	0	0	0	0	1	0	0	7422	1124	39	1	435	1	HSP90AA1	14	102548766	Nonsense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	9140519	102548766	4800774	61	3419											
WDR20	91833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102675840	102675840	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagtctcaaatgctggcAgcaaaagcagtgtcatggac	13	7	11	10	0	2	0	2	0	1	0	3	1	2	1	0	2	4	5	0	2	3	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr14:102675840A>G	ENST00000342702.3	+	3	1364	c.1333A>G	c.(1333-1335)Agc>Ggc	p.S445G	WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556511.2_Missense_Mutation_p.S384G|WDR20_ENST00000335263.5_Missense_Mutation_p.S445G|WDR20_ENST00000545563.1_Missense_Mutation_p.S272G|WDR20_ENST00000556807.1_Missense_Mutation_p.S384G|WDR20_ENST00000499851.2_Missense_Mutation_p.S188G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000454394.2_Missense_Mutation_p.S476G|WDR20_ENST00000424963.2_Missense_Mutation_p.S321G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	445										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AAATGCTGGCAGCAAAAGCAG	0.532											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S476G		.											.	WDR20-90	0			c.A1426G						.						101	103	102					14																	102675840		2203	4300	6503	SO:0001583	missense	91833	exon4			GCTGGCAGCAAAA	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1333A>G	14.37:g.102675840A>G	ENSP00000341037:p.Ser445Gly	Somatic	78	0	1368	WXS	Illumina HiSeq	Phase_I	73	31	NM_001242417	0	0	2	6	4	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	37	CCDS9969.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.709|6.709	0.499566|0.499566	0.12762|0.12762	.|.	.|.	ENSG00000140153|ENSG00000140153	ENST00000556511|ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	.|T;T;T;T;T;T;T	.|0.67698	.|-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.162599	.|0.64402	.|D	.|0.000002	T|T	0.56277|0.56277	0.1974|0.1974	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B;B;B	.|0.24882	.|0.001;0.113;0.001;0.0;0.0;0.043;0.0	.|B;B;B;B;B;B;B	.|0.24006	.|0.001;0.05;0.001;0.0;0.002;0.027;0.002	T|T	0.52087|0.52087	-0.8622|-0.8622	5|10	.|0.19590	.|T	.|0.45	.|.	16.0225|16.0225	0.80509|0.80509	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|476;457;384;445;384;321;445	.|E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.|.;.;.;.;.;.;WDR20_HUMAN	R|G	375|445;384;321;445;384;188;476;375;272	.|ENSP00000335434:S445G;ENSP00000395793:S321G;ENSP00000341037:S445G;ENSP00000450636:S384G;ENSP00000443641:S188G;ENSP00000406084:S476G;ENSP00000437927:S272G	.|ENSP00000299135:S384G	Q|S	+|+	2|1	0|0	WDR20|WDR20	101745593|101745593	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	7.099000|7.099000	0.76981|0.76981	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.		0.532	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		G	102675840	A	G	102675840	3	3	38	1	0	0	0	0	1	0	0	0	17313	188	7	3	1360	3	WDR20	14	102675840	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	127074	102675840	4673700	62	3420											
GLCE	26035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	69548696	69548696	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggctacaatgtggaagTccgagacagagtcaagtgca	14	7	13	7	1	1	3	1	1	0	2	2	5	2	4	1	2	2	2	1	2	5	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:69548696T>C	ENST00000261858.2	+	3	779	c.551T>C	c.(550-552)gTc>gCc	p.V184A	GLCE_ENST00000559420.2_Missense_Mutation_p.V120A	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	184					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						AATGTGGAAGTCCGAGACAGA	0.428																																					p.V184A		.											.	GLCE-92	0			c.T551C						.						101	101	101					15																	69548696		2200	4297	6497	SO:0001583	missense	26035	exon3			TGGAAGTCCGAGA	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.551T>C	15.37:g.69548696T>C	ENSP00000261858:p.Val184Ala	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	46	16	NM_015554	0	0	0	0	0	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	37	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246289	0.59103	.	.	ENSG00000138604	ENST00000261858	T	0.30714	1.52	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.36880	0.0983	M	0.79475	2.455	0.80722	D	1	B	0.22080	0.064	B	0.17722	0.019	T	0.20207	-1.0282	10	0.41790	T	0.15	-8.6789	14.1808	0.65574	0.0:0.0:0.0:1.0	.	184	O94923	GLCE_HUMAN	A	184	ENSP00000261858:V184A	ENSP00000261858:V184A	V	+	2	0	GLCE	67335750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.831000	0.86748	2.084000	0.62774	0.533000	0.62120	GTC	.		0.428	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69548696	T	C	69548696	3	2	38	1	0	0	0	0	1	0	0	0	6452	1667	58	3	553	3	GLCE	15	69548696	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10		69548696	32982696	63	3421											
MYO9A	4649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72190184	72190184	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagagaggatggcctctctaCtctttgctttgactgatagg	8	13	12	8	0	2	3	0	2	2	1	3	6	2	4	1	3	2	1	1	3	2	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:72190184C>G	ENST00000356056.5	-	25	5132	c.4660G>C	c.(4660-4662)Gta>Cta	p.V1554L	MYO9A_ENST00000566885.1_Missense_Mutation_p.V1174L|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Missense_Mutation_p.V1554L|MYO9A_ENST00000444904.1_Missense_Mutation_p.V1535L|MYO9A_ENST00000564571.1_Missense_Mutation_p.V1554L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1554	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GGCCTCTCTACTCTTTGCTTT	0.423																																					p.V1554L		.											.	MYO9A-93	0			c.G4660C						.						76	66	70					15																	72190184		2199	4297	6496	SO:0001583	missense	4649	exon25			TCTCTACTCTTTG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.4660G>C	15.37:g.72190184C>G	ENSP00000348349:p.Val1554Leu	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	93	42	NM_006901	0	0	0	1	1	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.285329	0.23478	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83992	-1.79;-1.79;-1.79	5.92	1.58	0.23477	.	.	.	.	.	T	0.66597	0.2805	L	0.27053	0.805	0.09310	N	1	B;B;B	0.12013	0.001;0.005;0.001	B;B;B	0.08055	0.002;0.003;0.001	T	0.50583	-0.8811	9	0.30078	T	0.28	.	0.594	0.00733	0.2435:0.3197:0.1226:0.3143	.	1535;1554;1554	B2RTY4-2;B2RTY4-4;B2RTY4	.;.;MYO9A_HUMAN	L	1554;1554;1535	ENSP00000348349:V1554L;ENSP00000399162:V1554L;ENSP00000398250:V1535L	ENSP00000348349:V1554L	V	-	1	0	MYO9A	69977238	0.001000	0.12720	0.003000	0.11579	0.983000	0.72400	0.281000	0.18810	0.024000	0.15214	0.650000	0.86243	GTA	.		0.423	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72190184	C	G	72190184	3	3	38	1	0	0	0	0	1	0	0	0	10109	565	20	4	3058	4	MYO9A	15	72190184	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	2641488	72190184	30341208	64	3422											
TMEM202	338949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72698982	72698982	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccttctttctcatctctgTctttaccatacttactggcc	5	17	5	14	0	4	0	1	0	4	0	6	0	4	0	3	2	3	0	3	2	3	6			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:72698982T>A	ENST00000341689.3	+	3	431	c.377T>A	c.(376-378)gTc>gAc	p.V126D	TMEM202_ENST00000567679.1_Missense_Mutation_p.S41T	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	126						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						CTCATCTCTGTCTTTACCATA	0.468																																					p.V126D		.											.	TMEM202-69	0			c.T377A						.						180	160	167					15																	72698982		2199	4297	6496	SO:0001583	missense	338949	exon3			TCTCTGTCTTTAC		CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.377T>A	15.37:g.72698982T>A	ENSP00000340212:p.Val126Asp	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	115	55	NM_001080462	0	0	0	0	0		Missense_Mutation	SNP	ENST00000341689.3	37	CCDS32287.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990387	0.35131	.	.	ENSG00000187806	ENST00000341689	T	0.66815	-0.23	5.42	1.84	0.25277	.	1.663070	0.03249	N	0.181492	T	0.71459	0.3342	L	0.53249	1.67	0.09310	N	1	P	0.47191	0.891	P	0.51355	0.667	T	0.54214	-0.8327	10	0.87932	D	0	-26.7102	6.0845	0.19960	0.0:0.3095:0.0:0.6905	.	126	A6NGA9	TM202_HUMAN	D	126	ENSP00000340212:V126D	ENSP00000340212:V126D	V	+	2	0	TMEM202	70486036	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.033000	0.13754	0.514000	0.28300	0.533000	0.62120	GTC	.		0.468	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462		A	72698982	T	A	72698982	3	1	38	1	0	0	0	0	1	0	0	0	16159	1667	58	5	387	5	TMEM202	15	72698982	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	508798	72698982	29832410	65	3423											
SCAMP5	192683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75309011	75309011	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgggggagccaccaactttGgcctcgcctttctctggctc	4	10	12	15	2	1	0	0	0	1	0	4	1	1	1	4	4	2	1	4	4	1	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:75309011G>T	ENST00000361900.6	+	5	421	c.214G>T	c.(214-216)Ggc>Tgc	p.G72C	SCAMP5_ENST00000545456.1_Intron|SCAMP5_ENST00000562212.1_Missense_Mutation_p.G72C|SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000568081.1_5'Flank|SCAMP5_ENST00000425597.3_Missense_Mutation_p.G72C	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	72					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						CACCAACTTTGGCCTCGCCTT	0.602																																					p.G72C		.											.	SCAMP5-23	0			c.G214T						.						138	140	139					15																	75309011		2150	4256	6406	SO:0001583	missense	192683	exon5			AACTTTGGCCTCG	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"Secretory carrier membrane proteins"	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.214G>T	15.37:g.75309011G>T	ENSP00000355387:p.Gly72Cys	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	39	17	NM_001178111	0	0	0	0	0	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Missense_Mutation	SNP	ENST00000361900.6	37	CCDS45306.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.024083	0.93462	.	.	ENSG00000198794	ENST00000361900;ENST00000425597	T;T	0.20332	2.08;2.08	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.56381	0.1981	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68194	-0.5473	10	0.87932	D	0	-0.2016	17.294	0.87164	0.0:0.0:1.0:0.0	.	72;72	Q8TAC9-2;Q8TAC9	.;SCAM5_HUMAN	C	72	ENSP00000355387:G72C;ENSP00000406547:G72C	ENSP00000355387:G72C	G	+	1	0	SCAMP5	73096064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.690000	0.98676	2.391000	0.81399	0.561000	0.74099	GGC	.		0.602	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967		T	75309011	G	T	75309011	3	4	38	1	0	0	0	0	1	0	0	0	13906	1348	47	4	224	4	SCAMP5	15	75309011	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	2610029	75309011	27222381	66	3424											
RPS2	6187	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	2014483	2014484	+	In_Frame_Ins	INS	-	-	CGGCCT																															ccttgcctccgcgagctccgINScggcctcggccccggccccg																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr16:2014483_2014484insCGGCCT	ENST00000343262.4	-	2	199_200	c.143_144insAGGCCG	c.(142-144)cgc>cgAGGCCGc	p.48_48R>RGR	RNF151_ENST00000569714.1_5'Flank|SNORA10_ENST00000384084.1_RNA|SNORA64_ENST00000384674.1_RNA|RPS2_ENST00000526522.1_In_Frame_Ins_p.48_48R>RGR|RNF151_ENST00000321392.3_5'Flank|RPS2_ENST00000529806.1_In_Frame_Ins_p.48_48R>RGR|SNHG9_ENST00000459373.1_lincRNA|RNF151_ENST00000569210.2_5'Flank|RPS2_ENST00000530225.1_In_Frame_Ins_p.48_48R>RGR	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2	48	Arg/Gly-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CGCGAGCTCCGCGGCCTCGGCC	0.757																																					p.R48delinsRGR		.											.	RPS2-90	0			c.144_145insAGGCCG						.																																			SO:0001652	inframe_insertion	6187	exon2			.	AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"S ribosomal proteins"	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.138_143dupAGGCCG	16.37:g.2014484_2014489dupCGGCCT	ENSP00000341885:p.GlyArg48dup	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_002952	0	0	0	0	0	B2R5G0|D3DU82|Q3MIB1	In_Frame_Ins	INS	ENST00000343262.4	37	CCDS10452.1																																																																																			.		0.757	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2	NM_002952		CGGCCT	2014484	-	CGGCCT	2014483	7	5	38	1	0	1	1	0	0	0	0	0	13663	1074	38	0	761	0	RPS2	16	2014483	In_Frame_Ins	INS	-	TCGA-B1-A654-01A-11D-A31X-10		2014483	88340270	67	3425											
SMG1	23049	broad.mit.edu	37	chr16	18864921	18864921	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacctgtagattcactctcGatccgaggatactcttcttc	8	14	6	13	2	4	1	1	0	3	1	7	4	5	2	2	1	2	1	2	1	3	6	rs188559863	byFrequency	TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr16:18864921G>T	ENST00000446231.2	-	31	5164	c.4752C>A	c.(4750-4752)atC>atA	p.I1584I	SMG1_ENST00000389467.3_Silent_p.I1584I			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1584	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ATTCACTCTCGATCCGAGGAT	0.328																																					p.I1584I													.	SMG1-1160	0			c.C4752A						.						78	68	71					16																	18864921		1820	4076	5896	SO:0001819	synonymous_variant	23049	exon31			ACTCTCGATCCGA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.4752C>A	16.37:g.18864921G>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	108	4	NM_015092	0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			G|0.999;A|0.001		0.328	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18864921	G	T	18864921	2	4	38	1	0	0	0	0	0	0	0	1	14827	1048	37	4		4	SMG1	16	18864921	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	16850438	18864921	71489832	68	3426											
ITGAD	3681	broad.mit.edu;bcgsc.ca	37	chr16	31414858	31414858	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaaacctcctgaagatccActtcaccttcacccaattcc	11	10	2	18	0	3	2	3	1	0	1	6	2	6	2	6	0	1	0	6	0	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr16:31414858A>C	ENST00000389202.2	+	7	645	c.596A>C	c.(595-597)cAc>cCc	p.H199P	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	199	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CTGAAGATCCACTTCACCTTC	0.542																																					p.H199P													.	ITGAD-226	0			c.A596C						.						116	93	101					16																	31414858		2197	4300	6497	SO:0001583	missense	3681	exon7			AGATCCACTTCAC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.596A>C	16.37:g.31414858A>C	ENSP00000373854:p.His199Pro	Somatic	51	1		WXS	Illumina HiSeq	Phase_I	64	32	NM_005353	0	0	0	0	0	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	A	17.08	3.298332	0.60195	.	.	ENSG00000156886	ENST00000316569;ENST00000444228;ENST00000389202	D	0.83250	-1.7	4.57	3.45	0.39498	von Willebrand factor, type A (3);	.	.	.	.	D	0.91436	0.7297	M	0.91300	3.195	0.37113	D	0.900445	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	D	0.92175	0.5747	9	0.72032	D	0.01	.	8.698	0.34307	0.8297:0.0:0.0:0.1703	.	199;215;199	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	P	63;215;199	ENSP00000373854:H199P	ENSP00000323325:H63P	H	+	2	0	ITGAD	31322359	0.992000	0.36948	0.920000	0.36463	0.687000	0.40016	5.957000	0.70323	0.756000	0.33013	0.328000	0.21473	CAC	.		0.542	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		C	31414858	A	C	31414858	3	2	38	1	0	0	0	0	1	0	0	0	7905	159	6	5	622	5	ITGAD	16	31414858	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	12549937	31414858	58939895	69	3427											
LCAT	3931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67976796	67976796	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtccaggtactccacaGagtaggtcttgccaaagcca	10	9	10	12	0	1	1	0	0	1	1	3	1	3	1	4	2	4	3	4	2	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr16:67976796G>T	ENST00000264005.5	-	3	424	c.395C>A	c.(394-396)tCt>tAt	p.S132Y	CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	132					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		GTACTCCACAGAGTAGGTCTT	0.662																																					p.S132Y		.											.	LCAT-44	0			c.C395A						.						62	68	66					16																	67976796		2198	4300	6498	SO:0001583	missense	3931	exon3			TCCACAGAGTAGG		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.395C>A	16.37:g.67976796G>T	ENSP00000264005:p.Ser132Tyr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_000229	0	0	8	10	2	Q53XQ3	Missense_Mutation	SNP	ENST00000264005.5	37	CCDS10854.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.685825	0.88639	.	.	ENSG00000213398	ENST00000264005	D	0.97161	-4.27	5.98	5.98	0.97165	.	0.138327	0.49916	U	0.000130	D	0.98573	0.9523	M	0.91920	3.255	0.46654	D	0.999148	D	0.52996	0.957	P	0.59171	0.853	D	0.99257	1.0889	10	0.87932	D	0	-13.366	18.0148	0.89236	0.0:0.0:1.0:0.0	.	132	P04180	LCAT_HUMAN	Y	132	ENSP00000264005:S132Y	ENSP00000264005:S132Y	S	-	2	0	LCAT	66534297	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.289000	0.96061	2.861000	0.98227	0.650000	0.86243	TCT	.		0.662	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			T	67976796	G	T	67976796	3	4	38	1	0	0	0	0	1	0	0	0	8679	942	33	4	943	4	LCAT	16	67976796	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	36561938	67976796	22377957	70	3428											
BCL6B	255877	hgsc.bcm.edu	37	chr17	6928020	6928031	+	In_Frame_Del	DEL	CAGCAGCAGCAG	CAGCAGCAGCAG	-																															cccagtggagacgaggcctcCagcagcagcagcagcagcag																								rs72254884|rs386385552		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	CAGCAGCAGCAG	CAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:6928020_6928031delCAGCAGCAGCAG	ENST00000293805.5	+	4	794_805	c.702_713delCAGCAGCAGCAG	c.(700-714)tccagcagcagcagc>tcc	p.234_238SSSSS>S		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	234	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						ACGAGGCCTCcagcagcagcagcagcagcagc	0.59																																					p.234_238del		.											.	BCL6B-227	0			c.702_713del						.																																			SO:0001651	inframe_deletion	255877	exon4			.	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1002	protein-coding gene	gene with protein product		608992	"zinc finger protein 62", "B-cell CLL/lymphoma 6, member B (zinc finger protein)"	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.702_713delCAGCAGCAGCAG	17.37:g.6928020_6928031delCAGCAGCAGCAG	ENSP00000293805:p.Ser238_Ser241del	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	67	23	NM_181844	0	0	0	0	0	Q6PCB4	In_Frame_Del	DEL	ENST00000293805.5	37	CCDS42248.1																																																																																			.		0.59	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844		-	6928031	CAGCAGCAGCAG	-	6928020	7	5	38	1	0	1	0	1	0	0	0	0	1378	581	21	0	712	0	BCL6B	17	6928020	In_Frame_Del	DEL	CAGCAGCAGCAG	TCGA-B1-A654-01A-11D-A31X-10		6928020	74267190	71	3429											
FAM134C	162427	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40734802	40734802	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtctgtgatggccaattccCtggcaacagtagaatcgtcc	10	10	10	11	1	1	2	0	1	1	1	4	2	3	2	3	2	1	2	3	2	4	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:40734802C>A	ENST00000309428.5	-	8	892	c.833G>T	c.(832-834)aGg>aTg	p.R278M	FAM134C_ENST00000585894.1_Missense_Mutation_p.R181M|FAM134C_ENST00000543197.1_Missense_Mutation_p.R83M	NM_178126.3	NP_835227.1	Q86VR2	F134C_HUMAN	family with sequence similarity 134, member C	278						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)		GGCCAATTCCCTGGCAACAGT	0.468																																					p.R278M													.	FAM134C-70	0			c.G833T						.						164	154	157					17																	40734802		2203	4300	6503	SO:0001583	missense	162427	exon8			AATTCCCTGGCAA	BC049370	CCDS11432.1	17q21.2	2007-05-01							27258	protein-coding gene	gene with protein product						12477932	Standard	NM_178126		Approved	DKFZp686B1036, FLJ33806	uc002ial.2	Q86VR2		ENST00000309428.5:c.833G>T	17.37:g.40734802C>A	ENSP00000309432:p.Arg278Met	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	101	34	NM_178126	0	0	4	7	3	B3KR75	Missense_Mutation	SNP	ENST00000309428.5	37	CCDS11432.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.396383	0.83011	.	.	ENSG00000141699	ENST00000309428;ENST00000543197	T;T	0.47528	0.84;0.87	6.17	5.21	0.72293	.	0.078533	0.85682	D	0.000000	T	0.52468	0.1736	L	0.36672	1.1	0.46654	D	0.999145	D	0.65815	0.995	D	0.63192	0.912	T	0.56238	-0.8012	10	0.87932	D	0	-17.1319	7.4263	0.27100	0.0:0.7314:0.0:0.2686	.	278	Q86VR2	F134C_HUMAN	M	278;83	ENSP00000309432:R278M;ENSP00000446235:R83M	ENSP00000309432:R278M	R	-	2	0	FAM134C	37988328	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.491000	0.45303	1.632000	0.50472	-0.140000	0.14226	AGG	.		0.468	FAM134C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450536.1	NM_178126		A	40734802	C	A	40734802	3	1	38	1	0	0	0	0	1	0	0	0	5463	681	24	4	575	4	FAM134C	17	40734802	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	33806782	40734802	40460408	72	3430											
HEXIM1	10614	broad.mit.edu	37	chr17	43226748	43226748	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtccggggccggagggggAagggagcctggaatcccaac	8	3	18	12	3	0	0	0	0	0	0	2	4	2	4	5	7	2	0	5	7	3	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:43226748A>G	ENST00000332499.2	+	1	2065	c.191A>G	c.(190-192)gAa>gGa	p.E64G	AC002117.1_ENST00000452741.1_RNA|AC002117.1_ENST00000589950.1_RNA	NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	64					heart development (GO:0007507)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			breast(1)|kidney(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCGGAGGGGGAAGGGAGCCTG	0.682											OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E64G													.	HEXIM1-23	0			c.A191G						.						31	33	33					17																	43226748		2202	4299	6501	SO:0001583	missense	10614	exon1			AGGGGGAAGGGAG	AB021179	CCDS11495.1	17q21.31	2006-03-28				ENSG00000186834			24953	protein-coding gene	gene with protein product		607328				12119119, 12832472	Standard	NM_006460		Approved	CLP-1, HIS1, MAQ1, EDG1	uc002iig.3	O94992		ENST00000332499.2:c.191A>G	17.37:g.43226748A>G	ENSP00000328773:p.Glu64Gly	Somatic	154	0	914	WXS	Illumina HiSeq	Phase_I	182	7	NM_006460	0	0	54	54	0	B2R8Y5	Missense_Mutation	SNP	ENST00000332499.2	37	CCDS11495.1	.	.	.	.	.	.	.	.	.	.	A	11.04	1.523233	0.27299	.	.	ENSG00000186834	ENST00000332499	.	.	.	4.36	0.691	0.18045	.	0.842697	0.10137	N	0.711287	T	0.21921	0.0528	N	0.16478	0.41	0.28652	N	0.906596	B	0.02656	0.0	B	0.04013	0.001	T	0.22661	-1.0210	9	0.28530	T	0.3	-3.5906	2.9745	0.05933	0.6069:0.0:0.21:0.183	.	64	O94992	HEXI1_HUMAN	G	64	.	ENSP00000328773:E64G	E	+	2	0	HEXIM1	40582531	0.992000	0.36948	0.921000	0.36526	0.880000	0.50808	1.340000	0.33896	0.205000	0.20568	0.459000	0.35465	GAA	.		0.682	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449821.2	NM_006460		G	43226748	A	G	43226748	3	3	38	1	0	0	0	0	1	0	0	0	7097	246	9	3	193	3	HEXIM1	17	43226748	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	2491946	43226748	37968462	73	3431											
PPP1R9B	84687	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48221032	48221032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacccagcttctccaggcccAtgtctgccccggcgcccatg	5	8	9	19	2	2	0	0	0	2	0	3	0	2	0	6	2	3	1	6	2	1	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:48221032A>G	ENST00000316878.6	-	5	1552	c.1550T>C	c.(1549-1551)aTg>aCg	p.M517T	AC002401.1_ENST00000451776.1_RNA|PPP1R9B_ENST00000501501.2_5'UTR	NM_032595.3	NP_115984.3	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	517	Interacts with RGS2. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to morphine (GO:0071315)|dendrite development (GO:0016358)|filopodium assembly (GO:0046847)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of cell proliferation (GO:0042127)|regulation of exit from mitosis (GO:0007096)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of protein phosphorylation (GO:0001932)|RNA splicing (GO:0008380)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|protein phosphatase type 1 complex (GO:0000164)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						CTCCAGGCCCATGTCTGCCCC	0.632																																					.													.	PPP1R9B-90	0			.						.						76	86	83					17																	48221032		2102	4218	6320	SO:0001583	missense	84687	.			AGGCCCATGTCTG	AJ401189	CCDS74102.1	17q21.33	2013-01-31	2011-10-04	2001-07-02	ENSG00000108819	ENSG00000108819		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9298	protein-coding gene	gene with protein product	"spinophilin", "Neurabin-2"	603325	"protein phosphatase 1, regulatory subunit 9B, spinophilin", "protein phosphatase 1, regulatory (inhibitor) subunit 9B"	PPP1R6, PPP1R9		9275233	Standard	NM_032595		Approved	Spn, SPINO	uc002iqh.4	Q96SB3	OTTHUMG00000162008	ENST00000316878.6:c.1550T>C	17.37:g.48221032A>G	ENSP00000475417:p.Met517Thr	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	58	35	.	0	0	11	18	7	Q8TCR9	Missense_Mutation	SNP	ENST00000316878.6	37																																																																																				.		0.632	PPP1R9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032595		G	48221032	A	G	48221032	3	3	38	1	0	0	0	0	1	0	0	0	12408	217	8	3	929	3	PPP1R9B	17	48221032	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	4994284	48221032	32974178	74	3432											
TMEM104	54868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72781730	72781730	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgtcctgctggtgttccTgggcttcatgaggtgagagg	4	12	15	10	1	1	2	1	2	0	1	4	3	3	2	3	4	1	3	3	4	0	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:72781730T>A	ENST00000335464.5	+	3	317	c.155T>A	c.(154-156)cTg>cAg	p.L52Q	TMEM104_ENST00000582773.1_Missense_Mutation_p.L52Q|TMEM104_ENST00000582330.1_Missense_Mutation_p.L52Q|TMEM104_ENST00000417024.2_Intron	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	52						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					CTGGTGTTCCTGGGCTTCATG	0.632																																					p.L52Q		.											.	TMEM104-90	0			c.T155A						.						76	56	63					17																	72781730		2203	4300	6503	SO:0001583	missense	54868	exon3			TGTTCCTGGGCTT	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.155T>A	17.37:g.72781730T>A	ENSP00000334849:p.Leu52Gln	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	60	34	NM_017728	0	0	0	0	0	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	37	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.482735	0.84747	.	.	ENSG00000109066	ENST00000335464	T	0.02498	4.27	4.98	4.98	0.66077	.	0.074254	0.53938	D	0.000043	T	0.16769	0.0403	M	0.84585	2.705	0.80722	D	1	D;D	0.76494	0.966;0.999	P;D	0.71656	0.869;0.974	T	0.00624	-1.1639	10	0.72032	D	0.01	-10.1576	14.642	0.68732	0.0:0.0:0.0:1.0	.	52;52	Q8NE00-2;Q8NE00	.;TM104_HUMAN	Q	52	ENSP00000334849:L52Q	ENSP00000334849:L52Q	L	+	2	0	TMEM104	70293325	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	7.568000	0.82369	1.872000	0.54250	0.260000	0.18958	CTG	.		0.632	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		A	72781730	T	A	72781730	3	1	38	1	0	0	0	0	1	0	0	0	16050	1580	55	5	161	5	TMEM104	17	72781730	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	24560698	72781730	8413480	75	3433											
ACSBG2	81616	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	6165945	6165945	+	Frame_Shift_Del	DEL	G	G	-																															gagcaggtcatcgagagccaGaaggcgaatcaatgcgcagt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:6165945delG	ENST00000586696.1	+	7	933	c.657delG	c.(655-657)cagfs	p.Q219fs	ACSBG2_ENST00000591403.1_Frame_Shift_Del_p.Q219fs|ACSBG2_ENST00000252669.5_Frame_Shift_Del_p.Q219fs|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000588304.1_Frame_Shift_Del_p.Q169fs|ACSBG2_ENST00000588485.1_Frame_Shift_Del_p.Q32fs			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	219					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCGAGAGCCAGAAGGCGAATC	0.517											OREG0025194	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q219fs		.											.	ACSBG2-23	0			c.657delG						.						163	130	141					19																	6165945		2203	4300	6503	SO:0001589	frameshift_variant	81616	exon7			.		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.657delG	19.37:g.6165945delG	ENSP00000465589:p.Gln219fs	Somatic	70	0	632	WXS	Illumina HiSeq	Phase_I	56	18	NM_030924	0	0	0	0	0	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Frame_Shift_Del	DEL	ENST00000586696.1	37	CCDS12159.1																																																																																			.		0.517	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		-	6165945	G	-	6165945	7	5	38	1	0	1	0	1	0	0	0	0	174	933	33	0	679	0	ACSBG2	19	6165945	Frame_Shift_Del	DEL	G	TCGA-B1-A654-01A-11D-A31X-10		6165945	52963038	76	3434											
ACER1	125981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6312214	6312214	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggggcatccatatgctatagCcactgcccaggagccacagg	10	6	12	13	0	0	0	0	0	0	0	1	1	1	1	4	4	4	2	4	4	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:6312214C>T	ENST00000301452.4	-	3	373	c.296G>A	c.(295-297)gGc>gAc	p.G99D		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	99					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						TATGCTATAGCCACTGCCCAG	0.607																																					p.G99D		.											.	ACER1-90	0			c.G296A						.						59	51	54					19																	6312214		2203	4300	6503	SO:0001583	missense	125981	exon3			CTATAGCCACTGC	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.296G>A	19.37:g.6312214C>T	ENSP00000301452:p.Gly99Asp	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	68	24	NM_133492	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301452.4	37	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	C	8.699	0.909265	0.17833	.	.	ENSG00000167769	ENST00000301452	T	0.42900	0.96	5.13	0.47	0.16747	.	0.527539	0.21637	N	0.071397	T	0.37210	0.0995	M	0.73598	2.24	0.22851	N	0.998658	P	0.42518	0.782	B	0.39503	0.301	T	0.32561	-0.9902	10	0.72032	D	0.01	-15.663	4.4791	0.11759	0.278:0.5108:0.1345:0.0768	.	99	Q8TDN7	ACER1_HUMAN	D	99	ENSP00000301452:G99D	ENSP00000301452:G99D	G	-	2	0	ACER1	6263214	0.936000	0.31750	0.029000	0.17559	0.086000	0.17979	1.990000	0.40717	-0.045000	0.13468	-1.740000	0.00687	GGC	.		0.607	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		T	6312214	C	T	6312214	3	4	38	1	0	0	0	0	1	0	0	0	138	739	26	2	514	2	ACER1	19	6312214	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	146269	6312214	52816769	77	3435											
SNRNP70	6625	ucsc.edu	37	chr19	49604725	49604725	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgaacacgagcgagacatgCactgtgagtacctcccgccg	11	5	11	14	5	0	2	0	1	0	1	1	5	1	2	3	0	4	2	3	0	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:49604725C>T	ENST00000598441.1	+	7	696	c.472C>T	c.(472-474)Cac>Tac	p.H158Y	SNRNP70_ENST00000221448.5_Missense_Mutation_p.H158Y			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	158	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						GCGAGACATGCACTGTGAGTA	0.622																																					p.H158Y													.	SNRNP70-90	0			c.C472T						.						118	82	94					19																	49604725		2203	4300	6503	SO:0001583	missense	6625	exon7			GACATGCACTGTG		CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"RNA binding motif (RRM) containing"	11150	protein-coding gene	gene with protein product		180740	"small nuclear ribonucleoprotein 70kDa (RNP antigen)"	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.472C>T	19.37:g.49604725C>T	ENSP00000472998:p.His158Tyr	Somatic	46	0		WXS	Illumina HiSeq		32	4	NM_003089	0	0	0	0	0	B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Missense_Mutation	SNP	ENST00000598441.1	37	CCDS12756.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.258592	0.80246	.	.	ENSG00000104852	ENST00000221448;ENST00000401730	T;T	0.16073	2.37;2.37	4.95	4.95	0.65309	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.16811	0.0404	L	0.43152	1.355	0.80722	D	1	P;P	0.42556	0.783;0.739	B;B	0.36289	0.221;0.167	T	0.02505	-1.1149	10	0.51188	T	0.08	-22.8404	17.358	0.87342	0.0:1.0:0.0:0.0	.	158;158	P08621;P08621-2	RU17_HUMAN;.	Y	158	ENSP00000221448:H158Y;ENSP00000385077:H158Y	ENSP00000221448:H158Y	H	+	1	0	SNRNP70	54296537	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.327000	0.79147	2.470000	0.83445	0.655000	0.94253	CAC	.		0.622	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089		T	49604725	C	T	49604725	3	4	38	1	0	0	0	0	1	0	0	0	14890	710	25	2	494	2	SNRNP70	19	49604725	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	43292511	49604725	9524258	78	3436											
UBE2S	27338	broad.mit.edu	37	chr19	55913035	55913035	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgagcagacgggcccgAgccgcatactcctcgtagtt	7	9	12	13	4	1	2	0	1	1	1	3	3	2	2	3	1	3	4	3	1	2	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:55913035A>G	ENST00000264552.9	-	4	625	c.438T>C	c.(436-438)gcT>gcC	p.A146A	CTD-2105E13.13_ENST00000589101.1_lincRNA|UBE2S_ENST00000592570.1_5'Flank|RPL28_ENST00000560055.1_Intron	NM_014501.2	NP_055316.2	Q16763	UBE2S_HUMAN	ubiquitin-conjugating enzyme E2S	146					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular protein modification process (GO:0006464)|exit from mitosis (GO:0010458)|free ubiquitin chain polymerization (GO:0010994)|protein K11-linked ubiquitination (GO:0070979)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)	anaphase-promoting complex (GO:0005680)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			lung(1)	1	Breast(117;0.155)		LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.11)		GACGGGCCCGAGCCGCATACT	0.677																																					p.A146A													.	UBE2S-226	0			c.T438C						.						9	12	11					19																	55913035		2142	4160	6302	SO:0001819	synonymous_variant	27338	exon4			GGCCCGAGCCGCA	BC004236	CCDS33114.1	19q13.43	2008-02-05				ENSG00000108106		"Ubiquitin-conjugating enzymes E2"	17895	protein-coding gene	gene with protein product	"ubiquitin carrier protein", "ubiquitin-conjugating enzyme E2-24 kD", "ubiquitin-protein ligase"	610309				1379239	Standard	NM_014501		Approved	E2-EPF	uc002qkx.1	Q16763		ENST00000264552.9:c.438T>C	19.37:g.55913035A>G		Somatic	92	3		WXS	Illumina HiSeq	Phase_I	103	17	NM_014501	0	0	85	85	0	Q9BTC1	Silent	SNP	ENST00000264552.9	37	CCDS33114.1																																																																																			.		0.677	UBE2S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453088.1	NM_014501		G	55913035	A	G	55913035	2	3	38	1	0	0	0	0	0	0	0	1	16905	291	11	3		3	UBE2S	19	55913035	Silent	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	6308310	55913035	3215948	79	3437											
ZNF71	58491	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57133380	57133380	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacacgggggagaagccctAcgcgtgcggggactgcggca	8	3	17	13	5	0	1	0	0	0	1	0	3	0	2	2	5	4	1	2	5	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:57133380A>T	ENST00000328070.6	+	3	959	c.725A>T	c.(724-726)tAc>tTc	p.Y242F		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	242					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)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GAGAAGCCCTACGCGTGCGGG	0.652																																					p.Y242F													.	ZNF71-91	0			c.A725T						.						52	49	50					19																	57133380		2203	4300	6503	SO:0001583	missense	58491	exon3			AGCCCTACGCGTG	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.725A>T	19.37:g.57133380A>T	ENSP00000328245:p.Tyr242Phe	Somatic	120	1		WXS	Illumina HiSeq	Phase_I	76	30	NM_021216	0	0	1	4	3	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	37	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.194552	0.38806	.	.	ENSG00000197951	ENST00000328070	T	0.18338	2.22	3.82	1.56	0.23342	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07999	0.0200	N	0.04132	-0.27	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.33979	-0.9847	9	0.49607	T	0.09	.	7.6854	0.28538	0.4953:0.0:0.0:0.5047	.	242	Q9NQZ8	ZNF71_HUMAN	F	242	ENSP00000328245:Y242F	ENSP00000328245:Y242F	Y	+	2	0	ZNF71	61825192	0.000000	0.05858	0.932000	0.37286	0.985000	0.73830	-0.089000	0.11180	0.050000	0.15949	0.459000	0.35465	TAC	.		0.652	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		T	57133380	A	T	57133380	3	4	38	1	0	0	0	0	1	0	0	0	18146	391	14	5	727	5	ZNF71	19	57133380	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	1220345	57133380	1995603	80	3438											
C21orf2	755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45750162	45750162	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgcacggcctccagcccCtctgcatccagctcccgcag	5	7	9	20	2	1	0	0	0	1	0	4	0	4	0	6	1	5	5	6	1	0	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr21:45750162C>A	ENST00000339818.4	-	7	897	c.690G>T	c.(688-690)gaG>gaT	p.E230D	C21orf2_ENST00000325223.7_Missense_Mutation_p.E229D|C21orf2_ENST00000397956.3_Missense_Mutation_p.E349D|C21orf2_ENST00000496321.1_5'UTR|AP001062.8_ENST00000422357.1_RNA|AP001062.7_ENST00000448927.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	230					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		CCTCCAGCCCCTCTGCATCCA	0.697																																					p.E349D		.											.	C21orf2-90	0			c.G1047T						.						15	15	15					21																	45750162		2189	4284	6473	SO:0001583	missense	755	exon7			CAGCCCCTCTGCA	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"nuclear encoded mitochondrial protein", "leucine rich repeat containing 76"	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.690G>T	21.37:g.45750162C>A	ENSP00000344566:p.Glu230Asp	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	55	23	NM_001271441	0	0	104	189	85	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589994	0.66105	.	.	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.50813	1.46;0.73;1.47	5.13	3.29	0.37713	.	0.111298	0.64402	D	0.000014	T	0.57242	0.2040	M	0.69823	2.125	0.34719	D	0.728514	D;D;D;D	0.67145	0.986;0.996;0.976;0.986	P;P;P;P	0.58266	0.737;0.836;0.551;0.737	T	0.65747	-0.6093	10	0.29301	T	0.29	-28.6583	9.0929	0.36621	0.0:0.8222:0.0:0.1778	.	229;349;230;189	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	D	230;349;229	ENSP00000344566:E230D;ENSP00000381047:E349D;ENSP00000317302:E229D	ENSP00000317302:E229D	E	-	3	2	C21orf2	44574590	1.000000	0.71417	0.986000	0.45419	0.343000	0.28985	2.457000	0.45005	1.153000	0.42468	0.655000	0.94253	GAG	.		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		A	45750162	C	A	45750162	3	1	38	1	0	0	0	0	1	0	0	0	2129	680	24	4	84	4	C21orf2	21	45750162	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		45750162	2379733	81	3439											
MN1	4330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	28192976	28192976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccctgaggccccgacggCgcactcacccttcttgccac	5	6	9	21	4	2	1	1	1	1	0	2	2	2	1	6	2	1	1	6	2	0	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr22:28192976C>T	ENST00000302326.4	-	1	4510	c.3556G>A	c.(3556-3558)Gcc>Acc	p.A1186T		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1186					intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						GCCCCGACGGCGCACTCACCC	0.647			T	ETV6	"AML, meningioma"																																p.A1186T		.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1-993	0			c.G3556A						.						18	20	19					22																	28192976		2099	4221	6320	SO:0001583	missense	4330	exon1			CGACGGCGCACTC	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"probable tumor suppressor protein MN1"	156100	"meningioma chromosome region"	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.3556G>A	22.37:g.28192976C>T	ENSP00000304956:p.Ala1186Thr	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	35	16	NM_002430	0	0	0	0	0	A9Z1V9	Missense_Mutation	SNP	ENST00000302326.4	37	CCDS42998.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.233669	0.58886	.	.	ENSG00000169184	ENST00000302326	T	0.47869	0.83	5.04	1.75	0.24633	.	0.148707	0.45361	D	0.000368	T	0.22126	0.0533	N	0.08118	0	0.24692	N	0.993302	B	0.02656	0.0	B	0.06405	0.002	T	0.10132	-1.0643	10	0.37606	T	0.19	-5.5453	4.928	0.13903	0.0:0.5962:0.1578:0.2459	.	1186	Q10571	MN1_HUMAN	T	1186	ENSP00000304956:A1186T	ENSP00000304956:A1186T	A	-	1	0	MN1	26522976	0.758000	0.28405	0.850000	0.33497	0.970000	0.65996	0.490000	0.22403	0.512000	0.28257	0.456000	0.33151	GCC	.		0.647	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		T	28192976	C	T	28192976	3	4	38	1	0	0	0	0	1	0	0	0	9698	768	27	1	414	1	MN1	22	28192976	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		28192976	23111590	82	3440											
CSNK1E	1454	ucsc.edu	37	chr22	38690182	38690182	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggaggagacgttggcgggcGcacccctgtgcagcctcata	8	6	15	12	3	1	1	1	0	0	1	1	3	1	2	3	4	2	3	3	4	1	2	rs200745813		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr22:38690182G>A	ENST00000396832.1	-	9	1411	c.1151C>T	c.(1150-1152)gCg>gTg	p.A384V	CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000400206.2_Missense_Mutation_p.A384V|CSNK1E_ENST00000359867.3_Missense_Mutation_p.A384V|CSNK1E_ENST00000403904.1_Missense_Mutation_p.A384V	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	384					cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GTTGGCGGGCGCACCCCTGTG	0.657													G|||	1	0.000199681	0	0	5008	,	,		14506	0		0.001	False		,,,				2504	0				p.A384V	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)												.	CSNK1E-1193	0			c.C1151T						.						36	37	36					22																	38690182		2203	4300	6503	SO:0001583	missense	1454	exon9			GCGGGCGCACCCC		CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.1151C>T	22.37:g.38690182G>A	ENSP00000380044:p.Ala384Val	Somatic	41	0		WXS	Illumina HiSeq		39	4	NM_001894	0	0	11	11	0		Missense_Mutation	SNP	ENST00000396832.1	37	CCDS13970.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	21.4|21.4	4.146633|4.146633	0.77888|0.77888	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904|ENST00000366216	T;T;T;T|.	0.56444|.	0.46;0.46;0.46;0.46|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	0.047888|.	0.85682|.	D|.	0.000000|.	T|T	0.56761|0.56761	0.2007|0.2007	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	B|.	0.15930|.	0.015|.	B|.	0.09377|.	0.004|.	T|T	0.49908|0.49908	-0.8889|-0.8889	10|5	0.42905|.	T|.	0.14|.	.|.	19.8045|19.8045	0.96525|0.96525	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	384|.	P49674|.	KC1E_HUMAN|.	V|C	384|87	ENSP00000352929:A384V;ENSP00000380044:A384V;ENSP00000383067:A384V;ENSP00000384074:A384V|.	ENSP00000352929:A384V|.	A|R	-|-	2|1	0|0	CSNK1E|CSNK1E	37020128|37020128	1.000000|1.000000	0.71417|0.71417	0.265000|0.265000	0.24526|0.24526	0.113000|0.113000	0.19764|0.19764	9.460000|9.460000	0.97641|0.97641	2.676000|2.676000	0.91093|0.91093	0.655000|0.655000	0.94253|0.94253	GCG|CGC	G|1.000;A|0.000		0.657	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		A	38690182	G	A	38690182	3	1	38	1	0	0	0	0	1	0	0	0	3959	1087	38	1	107	1	CSNK1E	22	38690182	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	10497206	38690182	12614384	83	3441											
OTC	5009	broad.mit.edu	37	chrX	38260574	38260574	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tattggctcgagtgtataaaCaatcagatttggacaccctg	12	12	9	8	1	1	1	1	0	0	1	2	3	1	2	1	2	1	2	1	2	5	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:38260574C>A	ENST00000039007.4	+	5	585	c.433C>A	c.(433-435)Caa>Aaa	p.Q145K	TM4SF2_ENST00000465127.1_Intron|OTC_ENST00000488812.1_3'UTR	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	145					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)	p.Q145K(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	AGTGTATAAACAATCAGATTT	0.403																																					p.Q145K													.	OTC-172	1	Substitution - Missense(1)	prostate(1)	c.C433A						.						108	81	90					X																	38260574		2202	4300	6502	SO:0001583	missense	5009	exon5			TATAAACAATCAG	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.433C>A	X.37:g.38260574C>A	ENSP00000039007:p.Gln145Lys	Somatic	125	8		WXS	Illumina HiSeq	Phase_I	88	12	NM_000531	0	0	0	0	0	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114759	0.77210	.	.	ENSG00000036473	ENST00000039007	D	0.98345	-4.88	5.97	5.97	0.96955	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding (1);	0.187966	0.64402	D	0.000019	D	0.97244	0.9099	M	0.72576	2.205	0.58432	D	0.999997	P	0.37525	0.598	B	0.32805	0.153	D	0.97447	1.0025	10	0.87932	D	0	-0.3779	19.371	0.94484	0.0:1.0:0.0:0.0	.	145	P00480	OTC_HUMAN	K	145	ENSP00000039007:Q145K	ENSP00000039007:Q145K	Q	+	1	0	OTC	38145518	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.440000	0.80464	2.527000	0.85204	0.600000	0.82982	CAA	.		0.403	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			A	38260574	C	A	38260574	3	1	38	1	0	0	0	0	1	0	0	0	11327	479	17	4	451	4	OTC	23	38260574	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		38260574	117009986	84	3442											
MID1IP1	58526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	38664368	38664368	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgatgttggcgtggaggtaGgcggcagtggcggctgcctg	5	8	20	8	4	0	0	0	0	0	0	0	2	0	1	1	7	1	4	1	7	1	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:38664368G>T	ENST00000336949.6	+	2	1114	c.169G>T	c.(169-171)Ggc>Tgc	p.G57C	MID1IP1_ENST00000378474.3_Missense_Mutation_p.G57C|MID1IP1-AS1_ENST00000436893.1_RNA|MID1IP1_ENST00000457894.1_Missense_Mutation_p.G57C	NM_021242.4	NP_067065.1	Q9NPA3	M1IP1_HUMAN	MID1 interacting protein 1	57					lipid metabolic process (GO:0006629)|negative regulation of microtubule depolymerization (GO:0007026)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of ligase activity (GO:0051351)|protein polymerization (GO:0051258)|regulation of lipid biosynthetic process (GO:0046890)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7						CGTGGAGGTAGGCGGCAGTGG	0.662																																					p.G57C		.											.	MID1IP1-130	0			c.G169T						.						42	33	37					X																	38664368		2202	4300	6502	SO:0001583	missense	58526	exon2			GAGGTAGGCGGCA		CCDS14249.1	Xp11.4	2012-02-23	2012-02-23		ENSG00000165175	ENSG00000165175			20715	protein-coding gene	gene with protein product	"gastrulation specific G12 homolog (zebrafish)"		"MID1 interacting protein 1 (gastrulation specific G12-like (zebrafish))"				Standard	NM_001098790		Approved	STRAIT11499, FLJ10386, MIG12, THRSPL, G12-like	uc010ngz.3	Q9NPA3	OTTHUMG00000024092	ENST00000336949.6:c.169G>T	X.37:g.38664368G>T	ENSP00000338706:p.Gly57Cys	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	151	74	NM_021242	0	0	2	53	51	D3DWB2	Missense_Mutation	SNP	ENST00000336949.6	37	CCDS14249.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964421	0.53507	.	.	ENSG00000165175	ENST00000457894;ENST00000378474;ENST00000336949	.	.	.	4.84	1.05	0.20165	.	0.159061	0.29286	N	0.012584	T	0.43277	0.1240	L	0.40543	1.245	0.33031	D	0.530214	D	0.58620	0.983	P	0.51297	0.665	T	0.54589	-0.8271	9	0.59425	D	0.04	-14.4554	6.8616	0.24069	0.4221:0.0:0.5779:0.0	.	57	Q9NPA3	M1IP1_HUMAN	C	57	.	ENSP00000338706:G57C	G	+	1	0	MID1IP1	38549312	0.735000	0.28153	0.940000	0.37924	0.993000	0.82548	0.654000	0.24918	0.136000	0.18733	0.529000	0.55759	GGC	.		0.662	MID1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060655.1			T	38664368	G	T	38664368	3	4	38	1	0	0	0	0	1	0	0	0	9602	1000	35	4	171	4	MID1IP1	23	38664368	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	403794	38664368	116606192	85	3443											
RPA4	29935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	96139635	96139635	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgaggcccgacagtggtttgGtagagagaaagtcaagcagg	12	6	16	7	2	1	2	1	0	0	2	1	5	1	2	1	4	1	3	1	4	3	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:96139635G>A	ENST00000373040.3	+	1	729	c.326G>A	c.(325-327)gGt>gAt	p.G109D	DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000324765.8_Intron|DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000373054.4_Intron	NM_013347.4	NP_037479.1	Q13156	RFA4_HUMAN	replication protein A4, 30kDa	109					DNA damage checkpoint (GO:0000077)|DNA recombination (GO:0006310)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	13						CAGTGGTTTGGTAGAGAGAAA	0.463								Other identified genes with known or suspected DNA repair function																													p.G109D		.											.	RPA4-227	0			c.G326A						.						101	87	92					X																	96139635		2203	4300	6503	SO:0001583	missense	29935	exon1			GGTTTGGTAGAGA	U24186	CCDS35345.1	Xq21	2010-04-09	2010-04-09		ENSG00000204086	ENSG00000204086			30305	protein-coding gene	gene with protein product		300767	"replication protein A4, 34kDa"			7760808	Standard	NM_013347		Approved	HSU24186	uc004efv.4	Q13156	OTTHUMG00000021987	ENST00000373040.3:c.326G>A	X.37:g.96139635G>A	ENSP00000362131:p.Gly109Asp	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	61	33	NM_013347	0	0	0	0	0	Q3SY03	Missense_Mutation	SNP	ENST00000373040.3	37	CCDS35345.1	.	.	.	.	.	.	.	.	.	.	G	0.245	-1.011087	0.02095	.	.	ENSG00000204086	ENST00000373040	T	0.37235	1.21	3.66	-0.387	0.12463	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);Nucleic acid binding, OB-fold, tRNA/helicase-type (1);	.	.	.	.	T	0.08313	0.0207	N	0.01086	-1.025	0.09310	N	1	B	0.25904	0.137	B	0.25759	0.063	T	0.29274	-1.0017	9	0.02654	T	1	-20.9474	2.3223	0.04214	0.1176:0.3079:0.405:0.1696	.	109	Q13156	RFA4_HUMAN	D	109	ENSP00000362131:G109D	ENSP00000362131:G109D	G	+	2	0	RPA4	96026291	0.001000	0.12720	0.000000	0.03702	0.019000	0.09904	0.691000	0.25467	-0.217000	0.10033	0.600000	0.82982	GGT	.		0.463	RPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057464.1	NM_013347		A	96139635	G	A	96139635	3	1	38	1	0	0	0	0	1	0	0	0	13571	1261	44	2	328	2	RPA4	23	96139635	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	57475267	96139635	59130925	86	3444											
RBMX2	51634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	129546641	129546641	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggaggcaagagaagaaaAgaccaggattagggacagag	18	2	17	4	0	0	4	0	0	0	4	0	9	0	7	1	4	0	1	1	4	5	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:129546641A>T	ENST00000305536.6	+	6	852	c.788A>T	c.(787-789)aAg>aTg	p.K263M		NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	263	Arg-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						AGAGAAGAAAAGACCAGGATT	0.527																																					p.K263M		.											.	RBMX2-134	0			c.A788T						.						69	67	68					X																	129546641		1931	4135	6066	SO:0001583	missense	51634	exon6			AAGAAAAGACCAG	AF078865	CCDS43993.1	Xq26.1	2013-02-12			ENSG00000134597	ENSG00000134597		"RNA binding motif (RRM) containing"	24282	protein-coding gene	gene with protein product						10810093	Standard	NM_016024		Approved	CGI-79	uc004evt.3	Q9Y388	OTTHUMG00000022395	ENST00000305536.6:c.788A>T	X.37:g.129546641A>T	ENSP00000339090:p.Lys263Met	Somatic	233	1		WXS	Illumina HiSeq	Phase_I	201	91	NM_016024	0	0	53	53	0	A8K9Z0|Q5JY82|Q9Y3I8	Missense_Mutation	SNP	ENST00000305536.6	37	CCDS43993.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804392	0.31869	.	.	ENSG00000134597	ENST00000305536;ENST00000538614	T	0.14516	2.5	4.9	-0.267	0.12938	.	0.462561	0.21532	N	0.073035	T	0.12987	0.0315	L	0.29908	0.895	0.18873	N	0.999989	P	0.50943	0.94	P	0.50231	0.635	T	0.13019	-1.0525	10	0.66056	D	0.02	.	7.4457	0.27209	0.5412:0.0:0.4588:0.0	.	263	Q9Y388	RBMX2_HUMAN	M	263	ENSP00000339090:K263M	ENSP00000339090:K263M	K	+	2	0	RBMX2	129374322	0.289000	0.24334	0.029000	0.17559	0.223000	0.24884	0.054000	0.14205	-0.329000	0.08527	0.417000	0.27973	AAG	.		0.527	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024		T	129546641	A	T	129546641	3	4	38	1	0	0	0	0	1	0	0	0	13184	72	3	5	810	5	RBMX2	23	129546641	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	33407006	129546641	25723919	87	3445											
ATP13A2	23400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	17318334	17318334	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcagccccaggaggctcaGgtctccttccacagtgtccc	7	7	10	17	0	2	0	1	0	1	0	5	1	4	1	5	3	2	2	5	3	0	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:17318334G>T	ENST00000326735.8	-	20	2179	c.2146C>A	c.(2146-2148)Ctg>Atg	p.L716M	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_Missense_Mutation_p.L711M|ATP13A2_ENST00000341676.5_Missense_Mutation_p.L711M			Q9NQ11	AT132_HUMAN	ATPase type 13A2	716					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGGAGGCTCAGGTCTCCTTCC	0.632																																					p.L716M		.											.	ATP13A2-93	0			c.C2146A						.						68	65	66					1																	17318334		2203	4300	6503	SO:0001583	missense	23400	exon20			GGCTCAGGTCTCC	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2146C>A	1.37:g.17318334G>T	ENSP00000327214:p.Leu716Met	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	64	18	NM_022089	0	0	24	45	21	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621251	0.28889	.	.	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000503552	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	4.7	2.82	0.32997	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.199920	0.45606	D	0.000358	T	0.81451	0.4825	L	0.47190	1.495	0.37079	D	0.898894	D;D;D	0.69078	0.995;0.966;0.997	D;P;D	0.75020	0.985;0.756;0.971	T	0.80919	-0.1167	10	0.39692	T	0.17	-15.6307	9.9597	0.41688	0.1542:0.0:0.8458:0.0	.	711;711;716	Q5JXY1;Q6S9Z9;Q9NQ11	.;.;AT132_HUMAN	M	716;711;711;186	ENSP00000327214:L716M;ENSP00000341115:L711M;ENSP00000413307:L711M;ENSP00000421126:L186M	ENSP00000327214:L716M	L	-	1	2	ATP13A2	17190921	0.553000	0.26513	0.638000	0.29380	0.383000	0.30230	0.854000	0.27791	0.590000	0.29694	0.491000	0.48974	CTG	.		0.632	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17318334	G	T	17318334	3	4	39	1	0	0	0	0	1	0	0	0	1125	991	35	4	1672	4	ATP13A2	1	17318334	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		17318334	231932287	1	3446											
RAP1GAP	5909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	21936724	21936724	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggagtgttctcatcctggaaGaccacagccacgatgtcgtt	9	10	11	11	2	1	1	1	0	1	1	4	4	2	3	3	2	1	2	3	2	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:21936724G>C	ENST00000374765.4	-	14	1088	c.888C>G	c.(886-888)gtC>gtG	p.V296V	RAP1GAP_ENST00000374761.2_Silent_p.V327V|RAP1GAP_ENST00000542643.2_Silent_p.V296V|RAP1GAP_ENST00000290101.4_Silent_p.V360V|RAP1GAP_ENST00000374763.2_Silent_p.V296V|RAP1GAP_ENST00000374757.3_5'Flank	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	296	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CATCCTGGAAGACCACAGCCA	0.637																																					p.V360V		.											.	RAP1GAP-245	0			c.C1080G						.						112	87	96					1																	21936724		2203	4300	6503	SO:0001819	synonymous_variant	5909	exon14			CTGGAAGACCACA	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.888C>G	1.37:g.21936724G>C		Somatic	156	0		WXS	Illumina HiSeq	Phase_I	191	52	NM_001145658	0	0	40	81	41	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			.		0.637	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		C	21936724	G	C	21936724	2	2	39	1	0	0	0	0	0	0	0	1	13069	929	33	4		4	RAP1GAP	1	21936724	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	4618390	21936724	227313897	2	3447											
CSF3R	1441	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	36939407	36939408	+	In_Frame_Ins	INS	-	-	GTC																															ggtgggtaggtgggtctcagINSgtcctggctcccactggcag																								rs145989033		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:36939407_36939408insGTC	ENST00000373106.1	-	5	989_990	c.442_443insGAC	c.(442-444)cct>cGACct	p.147_148insR	CSF3R_ENST00000418048.2_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000361632.4_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000487540.2_5'Flank|CSF3R_ENST00000331941.5_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000373103.1_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000338937.5_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000373104.1_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000440588.2_In_Frame_Ins_p.147_148insR	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	147	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GTGGGTCTCAGGTCCTGGCTCC	0.599																																					p.P148delinsRP		.											.	CSF3R-515	0			c.443_444insGAC						.																																			SO:0001652	inframe_insertion	1441	exon5			.	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"CD molecules", "Fibronectin type III domain containing"	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.440_442dupGAC	1.37:g.36939408_36939410dupGTC	ENSP00000362198:p.Gly147_Pro148insArg	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	76	25	NM_156039	0	0	0	0	0		In_Frame_Ins	INS	ENST00000373106.1	37	CCDS413.1																																																																																			.		0.599	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		GTC	36939408	-	GTC	36939407	7	5	39	1	0	1	1	0	0	0	0	0	3943	1000	35	0	2309	0	CSF3R	1	36939407	In_Frame_Ins	INS	-	TCGA-B1-A655-01A-11D-A31Z-10	15002683	36939407	212311214	3	3448											
RPS8	6202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45242407	45242407	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacaagaaataccgtgccCtgaggttggacgtggggaat	12	8	14	7	2	0	2	0	1	0	1	0	4	0	4	2	4	3	2	2	4	5	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:45242407C>G	ENST00000396651.3	+	3	332	c.172C>G	c.(172-174)Ctg>Gtg	p.L58V	RPS8_ENST00000485390.1_3'UTR|RP11-269F19.2_ENST00000428791.1_RNA|RPS8_ENST00000372209.3_Intron|SNORD38A_ENST00000365161.1_RNA|SNORD46_ENST00000364043.1_RNA|SNORD38B_ENST00000384690.1_RNA|SNORD55_ENST00000581525.1_RNA			P62241	RS8_HUMAN	ribosomal protein S8	58					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(2)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	10	Acute lymphoblastic leukemia(166;0.155)					ATACCGTGCCCTGAGGTTGGA	0.547																																					p.L58V		.											.	RPS8-91	0			c.C172G						.						73	64	67					1																	45242407		2203	4300	6503	SO:0001583	missense	6202	exon3			CGTGCCCTGAGGT	BC070875	CCDS513.1	1p34.1-p32	2011-04-05			ENSG00000142937	ENSG00000142937		"S ribosomal proteins"	10441	protein-coding gene	gene with protein product		600357				8432552	Standard	NM_001012		Approved	S8	uc001cmi.3	P62241	OTTHUMG00000008494	ENST00000396651.3:c.172C>G	1.37:g.45242407C>G	ENSP00000379888:p.Leu58Val	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	30	13	NM_001012	0	4	1158	2119	957	P09058|Q6IRL7	Missense_Mutation	SNP	ENST00000396651.3	37	CCDS513.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927456	0.52759	.	.	ENSG00000142937	ENST00000396651	T	0.37915	1.17	4.8	1.74	0.24563	.	0.000000	0.64402	D	0.000001	T	0.41003	0.1140	M	0.86953	2.85	0.80722	D	1	B	0.32101	0.356	B	0.31547	0.132	T	0.37619	-0.9698	10	0.87932	D	0	-24.8377	8.7594	0.34665	0.0:0.7558:0.0:0.2442	.	58	P62241	RS8_HUMAN	V	58	ENSP00000379888:L58V	ENSP00000379888:L58V	L	+	1	2	RPS8	45014994	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.400000	0.44504	0.166000	0.19597	0.655000	0.94253	CTG	.		0.547	RPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023439.1	NM_001012		G	45242407	C	G	45242407	3	3	39	1	0	0	0	0	1	0	0	0	13693	680	24	4	182	4	RPS8	1	45242407	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	8303000	45242407	204008214	4	3449											
CYP4X1	260293	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	47489659	47489659	+	Frame_Shift_Del	DEL	A	A	-																															cacccactggttccttgggcAccagaaggtagatgggaggg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:47489659delA	ENST00000371901.3	+	1	420	c.170delA	c.(169-171)cacfs	p.H57fs	CYP4X1_ENST00000538609.1_Intron	NM_178033.1	NP_828847.1	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X, polypeptide 1	57						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	17						TTCCTTGGGCACCagaaggta	0.682																																					p.H57fs		.											.	CYP4X1-92	0			c.170delA						.						13	15	14					1																	47489659		2197	4293	6490	SO:0001589	frameshift_variant	260293	exon1			.	AK091806	CCDS544.1	1p33	2008-02-05			ENSG00000186377	ENSG00000186377		"Cytochrome P450s"	20244	protein-coding gene	gene with protein product		614999				12176035	Standard	NM_178033		Approved	MGC40051	uc001cqt.3	Q8N118	OTTHUMG00000008017	ENST00000371901.3:c.170delA	1.37:g.47489659delA	ENSP00000360968:p.His57fs	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	79	25	NM_178033	0	0	0	0	0	G3V1U1|Q5VVE5|Q6ZN67|Q8NAZ3	Frame_Shift_Del	DEL	ENST00000371901.3	37	CCDS544.1																																																																																			.		0.682	CYP4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022017.1	NM_178033		-	47489659	A	-	47489659	7	5	39	1	0	1	0	1	0	0	0	0	4199	159	6	0	172	0	CYP4X1	1	47489659	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	2247252	47489659	201760962	5	3450											
SSBP3	23648	bcgsc.ca	37	chr1	54707864	54707864	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcactgttaggattgggccaGggtctgccagctcccgggcc	5	8	15	13	1	1	0	0	0	1	0	2	1	2	1	4	4	2	3	4	4	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:54707864G>T	ENST00000371320.3	-	11	1148	c.738C>A	c.(736-738)ccC>ccA	p.P246P	SSBP3_ENST00000371319.3_Silent_p.P219P|SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000417664.2_Silent_p.P136P|SSBP3_ENST00000357475.4_Silent_p.P226P	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	246	Gly-rich.|Pro-rich.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						GATTGGGCCAGGGTCTGCCAG	0.602																																					p.P246P													.	SSBP3-90	0			c.C738A						.						109	120	116					1																	54707864		2203	4300	6503	SO:0001819	synonymous_variant	23648	exon11			GGGCCAGGGTCTG		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"single-stranded DNA-binding protein 3"			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.738C>A	1.37:g.54707864G>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_1	49	4	NM_145716	0	0	17	17	0	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Silent	SNP	ENST00000371320.3	37	CCDS591.1																																																																																			.		0.602	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		T	54707864	G	T	54707864	2	4	39	1	0	0	0	0	0	0	0	1	15213	987	35	4		4	SSBP3	1	54707864	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	7218205	54707864	194542757	6	3451											
AMPD1	270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	115221050	115221050	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattcttctctttggtgctAtagaccactctgtcagcatc	8	15	7	11	0	4	2	1	0	3	2	6	2	4	2	1	1	2	2	1	1	2	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:115221050A>G	ENST00000520113.2	-	8	1110	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	AMPD1_ENST00000353928.6_Silent_p.Y332Y|AMPD1_ENST00000369538.3_Silent_p.Y361Y			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	365					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	CTTTGGTGCTATAGACCACTC	0.408																																					p.Y365Y		.											.	AMPD1-293	0			c.T1095C						.						160	155	157					1																	115221050		2203	4300	6503	SO:0001819	synonymous_variant	270	exon8			GGTGCTATAGACC	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1095T>C	1.37:g.115221050A>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	86	30	NM_000036	0	0	0	0	0	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Silent	SNP	ENST00000520113.2	37	CCDS876.2																																																																																			.		0.408	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			G	115221050	A	G	115221050	2	3	39	1	0	0	0	0	0	0	0	1	585	456	16	3		3	AMPD1	1	115221050	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	60513186	115221050	134029571	7	3452											
RPTN	126638	broad.mit.edu	37	chr1	152128065	152128065	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggaactttggccttgtcCgtctggctgaccataatgat	7	13	12	9	1	1	2	0	2	1	0	2	3	2	3	3	3	1	1	3	3	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:152128065C>T	ENST00000316073.3	-	3	1574	c.1510G>A	c.(1510-1512)Gga>Aga	p.G504R		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	504	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TGGCCTTGTCCGTCTGGCTGA	0.502																																					p.G504R													.	RPTN-68	0			c.G1510A						.						825	713	747					1																	152128065		1568	3582	5150	SO:0001583	missense	126638	exon3			CTTGTCCGTCTGG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1510G>A	1.37:g.152128065C>T	ENSP00000317895:p.Gly504Arg	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	90	5	NM_001122965	0	0	0	0	0	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	0.095	-1.161467	0.01673	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.10382	2.88	4.98	1.4	0.22301	.	0.464392	0.15779	N	0.245016	T	0.00524	0.0017	N	0.00227	-1.8	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.42447	-0.9451	10	0.13108	T	0.6	3.9809	4.2204	0.10554	0.1642:0.3864:0.0:0.4494	.	504	Q6XPR3	RPTN_HUMAN	R	504;159	ENSP00000317895:G504R	ENSP00000317895:G504R	G	-	1	0	RPTN	150394689	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.186000	0.16978	-0.024000	0.13941	-0.769000	0.03391	GGA	.		0.502	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		T	152128065	C	T	152128065	3	4	39	1	0	0	0	0	1	0	0	0	13696	661	23	1	848	1	RPTN	1	152128065	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	36907015	152128065	97122556	8	3453											
DDR2	4921	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	162724591	162724591	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcccccatgtacaagatcaaTtacagtcgggatggcactcg	11	8	10	12	2	1	1	1	0	0	1	3	2	1	2	2	2	2	2	2	2	4	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:162724591T>G	ENST00000367922.3	+	6	801	c.363T>G	c.(361-363)aaT>aaG	p.N121K	DDR2_ENST00000367921.3_Missense_Mutation_p.N121K	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	121	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	ACAAGATCAATTACAGTCGGG	0.522																																					p.N121K	NSCLC(161;314 2006 8283 19651 23192)												.	DDR2-1464	0			c.T363G						.						109	88	96					1																	162724591		2203	4300	6503	SO:0001583	missense	4921	exon6			GATCAATTACAGT	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.363T>G	1.37:g.162724591T>G	ENSP00000356899:p.Asn121Lys	Somatic	95	1		WXS	Illumina HiSeq	Phase_I	78	28	NM_001014796	0	0	1	1	0	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	37	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.244051	0.39697	.	.	ENSG00000162733	ENST00000446985;ENST00000415555;ENST00000542391;ENST00000367922;ENST00000367921	D;D;D;D	0.98135	-4.74;-4.74;-4.74;-4.74	5.68	-4.29	0.03721	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.091829	0.64402	D	0.000001	D	0.83751	0.5322	N	0.02129	-0.67	0.41489	D	0.988210	B	0.17667	0.023	B	0.14578	0.011	T	0.56956	-0.7893	9	0.41790	T	0.15	.	15.6753	0.77311	0.0:0.6384:0.0:0.3616	.	121	Q16832	DDR2_HUMAN	K	121	ENSP00000400309:N121K;ENSP00000391310:N121K;ENSP00000356899:N121K;ENSP00000356898:N121K	ENSP00000356898:N121K	N	+	3	2	DDR2	160991215	0.984000	0.35163	0.938000	0.37757	0.991000	0.79684	0.091000	0.15046	-0.872000	0.04037	-0.280000	0.10049	AAT	.		0.522	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		G	162724591	T	G	162724591	3	3	39	1	0	0	0	0	1	0	0	0	4343	1490	52	5	373	5	DDR2	1	162724591	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	10596526	162724591	86526030	9	3454											
HMCN1	83872	broad.mit.edu	37	chr1	185953350	185953350	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtgatgggagcctccataTtgaaagagttcagcttcagg	11	10	12	8	0	2	3	2	2	0	1	3	4	3	4	2	2	2	2	2	2	2	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:185953350T>G	ENST00000271588.4	+	19	3069	c.2840T>G	c.(2839-2841)aTt>aGt	p.I947S	HMCN1_ENST00000367492.2_Missense_Mutation_p.I947S|HMCN1_ENST00000485744.1_3'UTR	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	947	Ig-like C2-type 6.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGCCTCCATATTGAAAGAGTT	0.398																																					p.I947S													.	HMCN1-113	0			c.T2840G						.						172	170	171					1																	185953350		2203	4300	6503	SO:0001583	missense	83872	exon19			TCCATATTGAAAG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.2840T>G	1.37:g.185953350T>G	ENSP00000271588:p.Ile947Ser	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	67	3	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.530857	0.85706	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.79749	-1.3;-1.3	5.81	5.81	0.92471	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.162686	0.53938	D	0.000051	D	0.92270	0.7548	M	0.93763	3.455	0.54753	D	0.999987	D;D	0.67145	0.976;0.996	P;D	0.77004	0.908;0.989	D	0.94126	0.7384	10	0.87932	D	0	.	16.1501	0.81611	0.0:0.0:0.0:1.0	.	331;947	Q96RW7-3;Q96RW7	.;HMCN1_HUMAN	S	947	ENSP00000271588:I947S;ENSP00000356462:I947S	ENSP00000271588:I947S	I	+	2	0	HMCN1	184219973	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.083000	0.76859	2.219000	0.72066	0.533000	0.62120	ATT	.		0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	185953350	T	G	185953350	3	3	39	1	0	0	0	0	1	0	0	0	7241	1493	52	5	2914	5	HMCN1	1	185953350	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	23228759	185953350	63297271	10	3455											
MYT1L	23040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	1805513	1805513	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttccatctgggaattggaTtcatttagctccttgatttc	7	17	8	9	0	2	1	1	1	1	0	5	3	4	3	2	2	1	2	2	2	2	7			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:1805513T>C	ENST00000399161.2	-	23	3978	c.3231A>G	c.(3229-3231)gaA>gaG	p.E1077E	MYT1L_ENST00000407844.1_Silent_p.E73E|MYT1L_ENST00000428368.2_Silent_p.E1075E	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1077					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GGGAATTGGATTCATTTAGCT	0.333																																					p.E1075E		.											.	MYT1L-95	0			c.A3225G						.						232	228	229					2																	1805513		1805	4085	5890	SO:0001819	synonymous_variant	23040	exon23			ATTGGATTCATTT	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"Zinc fingers, C2HC-type containing"	7623	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 1"	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.3231A>G	2.37:g.1805513T>C		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	76	22	NM_015025	0	0	0	0	0	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				.		0.333	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		C	1805513	T	C	1805513	2	2	39	1	0	0	0	0	0	0	0	1	10132	1490	52	3		3	MYT1L	2	1805513	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		1805513	241393860	11	3456											
SMC6	79677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	17896324	17896324	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgggtcccgaagatgaaTgcaagctcctaaaagtgaga	13	9	11	8	1	1	3	0	2	1	2	3	5	3	3	2	1	2	2	2	1	5	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:17896324T>A	ENST00000448223.2	-	16	1803	c.1534A>T	c.(1534-1536)Att>Ttt	p.I512F	SMC6_ENST00000381272.4_Missense_Mutation_p.I538F|SMC6_ENST00000402989.1_Missense_Mutation_p.I512F|SMC6_ENST00000351948.4_Missense_Mutation_p.I512F	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	512	Flexible hinge.				cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CGAAGATGAATGCAAGCTCCT	0.368																																					p.I512F		.											.	SMC6-292	0			c.A1534T						.						71	74	73					2																	17896324		2203	4300	6503	SO:0001583	missense	79677	exon16			GATGAATGCAAGC	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1534A>T	2.37:g.17896324T>A	ENSP00000404092:p.Ile512Phe	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	66	28	NM_001142286	0	0	0	0	0	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349589	0.82132	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.31247	2.1;2.1;1.62;2.1;1.5	6.16	6.16	0.99307	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	M	0.74647	2.275	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.997	D;D;D	0.74674	0.961;0.984;0.977	T	0.57860	-0.7738	10	0.62326	D	0.03	.	13.2153	0.59856	0.0:0.0:0.1324:0.8676	.	538;538;512	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	F	512;512;538;512;538	ENSP00000404092:I512F;ENSP00000323439:I512F;ENSP00000370672:I538F;ENSP00000384539:I512F;ENSP00000408644:I538F	ENSP00000323439:I512F	I	-	1	0	SMC6	17759805	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.172000	0.65003	2.367000	0.80283	0.528000	0.53228	ATT	.		0.368	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17896324	T	A	17896324	3	1	39	1	0	0	0	0	1	0	0	0	14819	1464	51	5	1793	5	SMC6	2	17896324	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	16090811	17896324	225303049	12	3457											
RHOB	388	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	20647312	20647312	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcgtgttcagtaaggacgAgttccccgaggtgtacgtgc	8	10	14	9	4	1	0	1	0	0	0	3	4	2	1	2	2	2	4	2	2	2	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:20647312A>G	ENST00000272233.4	+	1	478	c.86A>G	c.(85-87)gAg>gGg	p.E29G		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	29					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|GTP catabolic process (GO:0006184)|negative regulation of cell cycle (GO:0045786)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|transformed cell apoptotic process (GO:0006927)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(2)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)	all_epithelial(98;4.19e-09)|Lung NSC(108;0.00452)|Ovarian(717;0.0164)		OV - Ovarian serous cystadenocarcinoma(76;1.14e-22)|Epithelial(75;7.84e-19)	Botulinum Toxin Type A(DB00083)	AGTAAGGACGAGTTCCCCGAG	0.662																																					p.E29G		.											.	RHOB-848	0			c.A86G						.						121	120	120					2																	20647312		2203	4300	6503	SO:0001583	missense	388	exon1			AGGACGAGTTCCC		CCDS1699.1	2p24	2012-02-27	2012-02-27	2004-03-24	ENSG00000143878	ENSG00000143878			668	protein-coding gene	gene with protein product	"oncogene RHO H6"	165370	"ras homolog gene family, member B"	ARH6, ARHB		3283705, 16278215	Standard	NM_004040		Approved	RhoB, RHOH6, MST081	uc002rdv.3	P62745	OTTHUMG00000090755	ENST00000272233.4:c.86A>G	2.37:g.20647312A>G	ENSP00000272233:p.Glu29Gly	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	85	26	NM_004040	0	0	92	135	43	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Missense_Mutation	SNP	ENST00000272233.4	37	CCDS1699.1	.	.	.	.	.	.	.	.	.	.	A	13.04	2.117942	0.37339	.	.	ENSG00000143878	ENST00000272233	T	0.78246	-1.16	5.74	4.56	0.56223	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	T	0.76471	0.3992	L	0.58810	1.83	0.53688	D	0.999978	B	0.29716	0.255	B	0.35727	0.209	T	0.74559	-0.3625	10	0.56958	D	0.05	-19.0458	12.9321	0.58292	0.8645:0.1355:0.0:0.0	.	29	P62745	RHOB_HUMAN	G	29	ENSP00000272233:E29G	ENSP00000272233:E29G	E	+	2	0	RHOB	20510793	1.000000	0.71417	1.000000	0.80357	0.018000	0.09664	9.156000	0.94705	0.963000	0.38082	0.533000	0.62120	GAG	.		0.662	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		G	20647312	A	G	20647312	3	3	39	1	0	0	0	0	1	0	0	0	13364	304	11	3	88	3	RHOB	2	20647312	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	2750988	20647312	222552061	13	3458											
SLC5A6	8884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27427730	27427730	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tggttcaccccgtataaggaGagcatcatgaagacaccccc	12	7	9	13	1	2	3	2	1	0	2	2	4	2	3	4	2	1	3	4	2	3	3	rs376306193		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:27427730G>C	ENST00000310574.3	-	8	1277	c.804C>G	c.(802-804)ctC>ctG	p.L268L	SLC5A6_ENST00000408041.1_Silent_p.L268L|SLC5A6_ENST00000461319.1_5'Flank	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	268					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CGTATAAGGAGAGCATCATGA	0.587																																					p.L268L		.											.	SLC5A6-92	0			c.C804G						.	G		0,4406		0,0,2203	103	95	98		804	-2.5	1	2		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC5A6	NM_021095.2		0,1,6502	CC,CG,GG		0.0116,0.0,0.0077		268/636	27427730	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8884	exon8			TAAGGAGAGCATC	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.804C>G	2.37:g.27427730G>C		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	30	10	NM_021095	0	0	19	25	6	B2RB85|D6W549|Q969Y5	Silent	SNP	ENST00000310574.3	37	CCDS1740.1																																																																																			.		0.587	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		C	27427730	G	C	27427730	2	2	39	1	0	0	0	0	0	0	0	1	14701	929	33	4		4	SLC5A6	2	27427730	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	6780418	27427730	215771643	14	3459											
SMEK2	57223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	55806886	55806886	+	Frame_Shift_Del	DEL	A	A	-																															catgcatacaatggttgtagAaaaaatttagaaattcactt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:55806886delA	ENST00000345102.5	-	9	1698	c.1397delT	c.(1396-1398)ttcfs	p.F466fs	SMEK2_ENST00000272313.5_Frame_Shift_Del_p.F466fs|SMEK2_ENST00000407823.3_Frame_Shift_Del_p.F466fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	466					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ATGGTTGTAGAAAAAATTTAG	0.303																																					p.F466fs		.											.	SMEK2-228	0			c.1397delT						.						76	80	79					2																	55806886		2203	4298	6501	SO:0001589	frameshift_variant	57223	exon9			.	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.1397delT	2.37:g.55806886delA	ENSP00000339769:p.Phe466fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	67	21	NM_001122964	0	0	0	0	0	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Del	DEL	ENST00000345102.5	37	CCDS46289.1																																																																																			.		0.303	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		-	55806886	A	-	55806886	7	5	39	1	0	1	0	1	0	0	0	0	14826	246	9	0	1188	0	SMEK2	2	55806886	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	28379156	55806886	187392487	15	3460											
INO80B	83444	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	74684908	74684908	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcacaggccaggcactcTgtagtcttcagtgctaccgc	7	8	10	16	2	3	0	1	0	2	0	3	0	3	0	3	2	2	4	3	2	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:74684908T>A	ENST00000233331.7	+	5	1082	c.988T>A	c.(988-990)Tgt>Agt	p.C330S	WBP1_ENST00000409737.1_5'Flank|WBP1_ENST00000233615.2_5'Flank|WBP1_ENST00000393972.3_5'Flank	NM_031288.3	NP_112578.2	Q9C086	IN80B_HUMAN	INO80 complex subunit B	330					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	13						CCAGGCACTCTGTAGTCTTCA	0.682																																					p.C330S		.											.	INO80B-226	0			c.T988A						.						18	20	19					2																	74684908		2117	4148	6265	SO:0001583	missense	83444	exon5			GCACTCTGTAGTC	AB054538	CCDS1942.2	2p13.1	2011-07-06	2008-08-07	2008-08-07	ENSG00000115274	ENSG00000115274		"Zinc fingers, HIT-type", "INO80 complex subunits"	13324	protein-coding gene	gene with protein product	"PAP-1 binding protein", "IES2 homolog (S. cerevisiae)"		"high mobility group AT-hook 1-like 4", "zinc finger, HIT type 4"	HMGA1L4, ZNHIT4		16230350	Standard	NM_031288		Approved	HMGIYL4, PAPA-1, hIes2, PAP-1BP, IES2	uc002slg.3	Q9C086	OTTHUMG00000129959	ENST00000233331.7:c.988T>A	2.37:g.74684908T>A	ENSP00000233331:p.Cys330Ser	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	25	8	NM_031288	0	0	6	10	4		Missense_Mutation	SNP	ENST00000233331.7	37	CCDS1942.2	.	.	.	.	.	.	.	.	.	.	T	27.9	4.869691	0.91587	.	.	ENSG00000115274	ENST00000233331	D	0.99042	-5.36	5.27	5.27	0.74061	Zinc finger, HIT-type (1);	0.000000	0.85682	D	0.000000	D	0.98927	0.9636	L	0.58354	1.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.995;0.995	D	0.99671	1.0996	10	0.87932	D	0	-20.6182	13.1927	0.59719	0.0:0.0:0.0:1.0	.	348;315;330	B4DJ31;B4DJ22;Q9C086	.;.;IN80B_HUMAN	S	330	ENSP00000233331:C330S	ENSP00000233331:C330S	C	+	1	0	INO80B	74538416	1.000000	0.71417	0.996000	0.52242	0.864000	0.49448	5.346000	0.65992	2.211000	0.71520	0.459000	0.35465	TGT	.		0.682	INO80B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252223.2	NM_031288		A	74684908	T	A	74684908	3	1	39	1	0	0	0	0	1	0	0	0	7768	1580	55	5	1006	5	INO80B	2	74684908	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	18878022	74684908	168514465	16	3461											
RPIA	22934	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	89037541	89037541	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttatcttggactggaagttTgaccgggtacacaaatggag	11	12	12	6	1	1	1	0	1	1	0	1	4	1	4	1	4	1	2	1	4	4	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:89037541T>G	ENST00000283646.4	+	8	841	c.786T>G	c.(784-786)ttT>ttG	p.F262L		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	262					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				ACTGGAAGTTTGACCGGGTAC	0.438																																					p.F262L		.											.	RPIA-91	0			c.T786G						.						154	143	146					2																	89037541		1889	4125	6014	SO:0001583	missense	22934	exon8			GAAGTTTGACCGG	L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"ribose 5-phosphate epimerase"	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.786T>G	2.37:g.89037541T>G	ENSP00000283646:p.Phe262Leu	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	114	9	NM_144563	0	0	19	21	2	Q541P9|Q96BJ6	Missense_Mutation	SNP	ENST00000283646.4	37	CCDS2004.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.473758	0.84640	.	.	ENSG00000153574	ENST00000283646;ENST00000543560	T	0.76186	-1.0	5.55	1.74	0.24563	.	0.000000	0.85682	D	0.000000	T	0.82144	0.4973	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78321	-0.2249	10	0.42905	T	0.14	-10.0604	9.4754	0.38869	0.0:0.2052:0.0:0.7948	.	262	P49247	RPIA_HUMAN	L	262;128	ENSP00000283646:F262L	ENSP00000283646:F262L	F	+	3	2	RPIA	88818656	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.082000	0.30803	0.056000	0.16144	0.383000	0.25322	TTT	.		0.438	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2			G	89037541	T	G	89037541	3	3	39	1	0	0	0	0	1	0	0	0	13585	1809	63	5	816	5	RPIA	2	89037541	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	14352633	89037541	154161832	17	3462											
FER1L5	90342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97368368	97368368	+	RNA	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctggagaaggacatgcagAagacagacatccactaccac	15	4	11	11	0	0	4	0	0	0	4	1	6	1	5	2	3	2	2	2	3	3	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:97368368A>C	ENST00000457909.1	+	0	4790							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						GGACATGCAGAAGACAGACAT	0.602																																					p.K1799Q		.											.	FER1L5-23	0			c.A5395C						.						39	45	43					2																	97368368		2131	4257	6388			90342	exon47			ATGCAGAAGACAG	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		2.37:g.97368368A>C		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	64	24	NM_001113382	0	0	0	0	0	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	37		.	.	.	.	.	.	.	.	.	.	A	12.29	1.894586	0.33442	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.29	4.14	0.48551	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.139522	0.32068	U	0.006626	T	0.71256	0.3318	M	0.72576	2.205	.	.	.	D;D;D	0.71674	0.981;0.998;0.989	P;D;P	0.69479	0.77;0.964;0.885	T	0.79436	-0.1804	8	0.87932	D	0	-9.4277	10.0645	0.42295	0.9196:0.0:0.0804:0.0	.	507;1799;508	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	Q	1799;1803;508	.	ENSP00000442027:K508Q	K	+	1	0	FER1L5	96732095	0.999000	0.42202	1.000000	0.80357	0.680000	0.39746	2.466000	0.45084	0.865000	0.35603	0.459000	0.35465	AAG	.		0.602	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		C	97368368	A	C	97368368	1	2	39	0	1	0	0	0	0	0	0	0	5833	247	9	5		5	FER1L5	2	97368368	RNA	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	8330827	97368368	145831005	18	3463											
LONRF2	164832	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	100903452	100903452	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgcgatcctggagagacGcgaaccaggaaacagactgt	13	6	12	10	3	1	2	1	0	0	2	2	7	2	4	2	2	3	0	2	2	2	0	rs182810197		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:100903452G>A	ENST00000393437.3	-	11	2633	c.1994C>T	c.(1993-1995)gCg>gTg	p.A665V	LONRF2_ENST00000409647.1_Missense_Mutation_p.A422V	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	665	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						CTGGAGAGACGCGAACCAGGA	0.488													G|||	1	0.000199681	0	0.0014	5008	,	,		21822	0		0	False		,,,				2504	0				p.A665V		.											.	LONRF2-154	0			c.C1994T						.						124	103	110					2																	100903452		2203	4300	6503	SO:0001583	missense	164832	exon11			AGAGACGCGAACC	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"RING-type (C3HC4) zinc fingers"	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1994C>T	2.37:g.100903452G>A	ENSP00000377086:p.Ala665Val	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	112	8	NM_198461	0	0	0	0	0	B9A006|Q6ZSR4	Missense_Mutation	SNP	ENST00000393437.3	37	CCDS2046.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	10.42	1.345572	0.24426	.	.	ENSG00000170500	ENST00000393437;ENST00000409647	T;T	0.43688	0.94;0.94	4.95	3.1	0.35709	Peptidase S16, lon N-terminal (1);PUA-like domain (1);	0.358147	0.30901	N	0.008647	T	0.17023	0.0409	N	0.02011	-0.69	0.18873	N	0.999981	B	0.21071	0.051	B	0.18561	0.022	T	0.18366	-1.0339	10	0.30078	T	0.28	-0.2116	10.2149	0.43162	0.0749:0.1365:0.7885:0.0	.	665	Q1L5Z9	LONF2_HUMAN	V	665;422	ENSP00000377086:A665V;ENSP00000386823:A422V	ENSP00000377086:A665V	A	-	2	0	LONRF2	100269884	1.000000	0.71417	0.001000	0.08648	0.826000	0.46750	5.277000	0.65586	0.462000	0.27095	0.655000	0.94253	GCG	G|0.999;A|0.000		0.488	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461		A	100903452	G	A	100903452	3	1	39	1	0	0	0	0	1	0	0	0	8920	1087	38	1	278	1	LONRF2	2	100903452	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	3535084	100903452	142295921	19	3464											
FAM123C	205147	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	131520234	131520234	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcagaccctggggggcggCgaagcaaagccttcctcccc	7	5	13	16	3	1	1	1	0	0	1	3	2	3	1	5	4	2	1	5	4	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:131520234C>T	ENST00000423981.1	+	2	699	c.589C>T	c.(589-591)Cga>Tga	p.R197*	AMER3_ENST00000321420.4_Nonsense_Mutation_p.R197*	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	197					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R197*(1)									TGGGGGGCGGCGAAGCAAAGC	0.667																																					p.R197X													.	.	1	Substitution - Nonsense(1)	prostate(1)	c.C589T						.						25	31	29					2																	131520234		2198	4286	6484	SO:0001587	stop_gained	205147	exon2			GGGCGGCGAAGCA	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.589C>T	2.37:g.131520234C>T	ENSP00000392700:p.Arg197*	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	34	4	NM_152698	0	0	0	0	0	B7ZLH6	Nonsense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.042473	0.55003	.	.	ENSG00000178171	ENST00000321420;ENST00000423981	.	.	.	5.1	3.13	0.36017	.	1.133320	0.06645	N	0.761843	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	7.8953	0.29702	0.1839:0.6383:0.1778:0.0	.	.	.	.	X	197	.	ENSP00000314914:R197X	R	+	1	2	FAM123C	131236704	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.129000	0.15830	1.247000	0.43917	0.561000	0.74099	CGA	.		0.667	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		T	131520234	C	T	131520234	4	4	39	1	0	0	0	0	0	1	0	0	5440	760	27	1	591	1	FAM123C	2	131520234	Nonsense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	30616782	131520234	111679139	20	3465											
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	168108259	168108259	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatctggctgtgacttcaagCatgccccaccaacctatgag	11	9	8	13	0	2	2	1	2	1	0	2	2	2	2	4	1	3	2	4	1	4	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:168108259C>T	ENST00000409195.1	+	9	10446	c.10357C>T	c.(10357-10359)Cat>Tat	p.H3453Y	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.H3231Y|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.H3453Y|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3278					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGACTTCAAGCATGCCCCACC	0.408																																					p.H3453Y		.											.	XIRP2-104	0			c.C10357T						.						61	61	61					2																	168108259		1916	4139	6055	SO:0001583	missense	129446	exon9			TTCAAGCATGCCC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10357C>T	2.37:g.168108259C>T	ENSP00000386840:p.His3453Tyr	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	148	59	NM_152381	0	0	0	0	0	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385682	0.61956	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02916	4.12;4.12;4.11	6.16	5.29	0.74685	.	0.224814	0.46145	N	0.000309	T	0.14141	0.0342	M	0.71581	2.175	0.49483	D	0.99979	D;D;B	0.76494	0.999;0.999;0.368	D;D;B	0.80764	0.986;0.994;0.15	T	0.00213	-1.1913	10	0.87932	D	0	-12.9779	14.5412	0.67997	0.0:0.9292:0.0:0.0708	.	3278;3278;3231	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Y	3453;3453;3231;867	ENSP00000386840:H3453Y;ENSP00000295237:H3453Y;ENSP00000387255:H3231Y	ENSP00000295237:H3453Y	H	+	1	0	XIRP2	167816505	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.228000	0.51270	1.628000	0.50416	-0.145000	0.13849	CAT	.		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168108259	C	T	168108259	3	4	39	1	0	0	0	0	1	0	0	0	17463	710	25	2	10387	2	XIRP2	2	168108259	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	36588025	168108259	75091114	21	3466											
SLC25A12	8604	broad.mit.edu;bcgsc.ca	37	chr2	172700922	172700937	+	Frame_Shift_Del	DEL	CGGTTATGCCCAAAAT	CGGTTATGCCCAAAAT	-																															tgtagttaagatgcttcttcCggttatgcccaaaatgcagt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	CGGTTATGCCCAAAAT	CGGTTATGCCCAAAAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:172700922_172700937delCGGTTATGCCCAAAAT	ENST00000422440.2	-	5	444_459	c.407_422delATTTTGGGCATAACCG	c.(406-423)cattttgggcataaccggfs	p.HFGHNR136fs	SLC25A12_ENST00000392592.4_Frame_Shift_Del_p.HFGHNR29fs|SLC25A12_ENST00000472748.1_5'UTR	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	136	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	ATGCTTCTTCCGGTTATGCCCAAAATGCAGTCGGAT	0.352																																					p.136_141del													.	SLC25A12-90	0			c.407_422del						.																																			SO:0001589	frameshift_variant	8604	exon5			TTCTTCCGGTTAT	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"Solute carriers", "EF-hand domain containing"	10982	protein-coding gene	gene with protein product		603667	"solute carrier family 25 (mitochondrial carrier, Aralar), member 12"			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.407_422delATTTTGGGCATAACCG	2.37:g.172700922_172700937delCGGTTATGCCCAAAAT	ENSP00000388658:p.His136fs	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	105	13	NM_003705	0	0	0	0	0	B3KR64|Q96AM8	Frame_Shift_Del	DEL	ENST00000422440.2	37	CCDS33327.1																																																																																			.		0.352	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		-	172700937	CGGTTATGCCCAAAAT	-	172700922	7	5	39	1	0	1	0	1	0	0	0	0	14506	652	23	0	1670	0	SLC25A12	2	172700922	Frame_Shift_Del	DEL	CGGTTATGCCCAAAAT	TCGA-B1-A655-01A-11D-A31Z-10	4592663	172700922	70498451	22	3467											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179577514	179577514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actttgtgatgtatctacatCgaacaactccagttcagcaa	13	12	6	10	1	2	1	1	1	1	0	4	2	3	1	1	0	4	3	1	0	5	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:179577514C>T	ENST00000591111.1	-	92	26511	c.26287G>A	c.(26287-26289)Gat>Aat	p.D8763N	TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D7836N|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.D9080N|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12916	Ig-like 70.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATCTACATCGAACAACTCC	0.418																																					p.D9080N		.											.	TTN-636	0			c.G27238A						.						88	84	85					2																	179577514		1928	4120	6048	SO:0001583	missense	7273	exon94			CTACATCGAACAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.26287G>A	2.37:g.179577514C>T	ENSP00000465570:p.Asp8763Asn	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	74	20	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	13.16	2.153386	0.38021	.	.	ENSG00000155657	ENST00000342992	T	0.38560	1.13	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23094	0.0558	N	0.03304	-0.355	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.08146	-1.0736	9	0.87932	D	0	.	12.9963	0.58648	0.0:0.9258:0.0:0.0742	.	8763	Q8WZ42	TITIN_HUMAN	N	7836	ENSP00000343764:D7836N	ENSP00000343764:D7836N	D	-	1	0	TTN	179285759	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	1.843000	0.39259	2.722000	0.93159	0.655000	0.94253	GAT	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179577514	C	T	179577514	3	4	39	1	0	0	0	0	1	0	0	0	16768	884	31	1	77367	1	TTN	2	179577514	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	6876592	179577514	63621859	23	3468											
FASTKD2	22868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	207655323	207655323	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctatgtgtttccagatcTgcttattgtttgggttcaag	6	18	11	6	0	2	1	1	0	1	1	3	1	3	1	1	1	2	5	1	1	3	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:207655323T>C	ENST00000236980.6	+	11	2274	c.1926T>C	c.(1924-1926)tcT>tcC	p.S642S	FASTKD2_ENST00000402774.3_Silent_p.S642S|FASTKD2_ENST00000403094.3_Silent_p.S642S	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	642	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TTTCCAGATCTGCTTATTGTT	0.363																																					p.S642S		.											.	FASTKD2-118	0			c.T1926C						.						159	159	159					2																	207655323		2203	4300	6503	SO:0001819	synonymous_variant	22868	exon11			CAGATCTGCTTAT	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"KIAA0971"	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1926T>C	2.37:g.207655323T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	43	14	NM_001136193	0	0	38	76	38	Q9NVX6|Q9Y2H7	Silent	SNP	ENST00000236980.6	37	CCDS2371.1																																																																																			.		0.363	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		C	207655323	T	C	207655323	2	2	39	1	0	0	0	0	0	0	0	1	5705	1567	55	3		3	FASTKD2	2	207655323	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	28077809	207655323	35544050	24	3469											
LRRFIP1	9208	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	238666100	238666100	+	Intron	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgttcctttcctcaggAaatccgacagctacagcaga	10	11	8	12	1	2	1	1	0	1	1	5	3	5	2	3	1	3	3	3	1	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:238666100A>T	ENST00000392000.4	+	9	864				LRRFIP1_ENST00000289175.6_Intron|LRRFIP1_ENST00000244815.5_Intron|LRRFIP1_ENST00000308482.9_Splice_Site_p.E378V	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TTTCCTCAGGAAATCCGACAG	0.473																																					p.E378V		.											.	LRRFIP1-153	0			c.A1133T						.						32	29	30					2																	238666100		1567	3579	5146	SO:0001627	intron_variant	9208	exon17			CTCAGGAAATCCG	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.747+1270A>T	2.37:g.238666100A>T		Somatic	270	0		WXS	Illumina HiSeq	Phase_I	221	66	NM_001137550	0	0	0	0	0	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.683862	0.68157	.	.	ENSG00000124831	ENST00000308482;ENST00000391999	T	0.53640	0.61	5.51	5.51	0.81932	.	.	.	.	.	T	0.51109	0.1655	M	0.75085	2.285	0.80722	D	1	B	0.32604	0.377	B	0.32465	0.146	T	0.57207	-0.7851	9	0.87932	D	0	.	14.8382	0.70201	1.0:0.0:0.0:0.0	.	378	E9PGZ2	.	V	378;368	ENSP00000310109:E378V	ENSP00000310109:E378V	E	+	2	0	LRRFIP1	238330839	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.546000	0.90661	2.097000	0.63578	0.533000	0.62120	GAA	.		0.473	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		T	238666100	A	T	238666100	1	4	39	0	1	0	0	0	0	0	0	0	9052	260	9	5		5	LRRFIP1	2	238666100	Intron	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	31010777	238666100	4533273	25	3470											
ZNF167	55888	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	44612087	44612087	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catactggggagaaaccttaTgaatgcaatgagtgtggaga	14	9	13	5	0	0	4	0	2	0	2	0	6	0	4	1	3	3	1	1	3	5	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:44612087T>C	ENST00000273320.3	+	6	1914	c.1485T>C	c.(1483-1485)taT>taC	p.Y495Y	ZKSCAN7_ENST00000341840.3_Intron|ZKSCAN7_ENST00000426540.1_Silent_p.Y495Y|RP11-944L7.5_ENST00000419137.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000431636.1_Intron	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	495					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)										AGAAACCTTATGAATGCAATG	0.448																																					p.Y495Y		.											.	.	0			c.T1485C						.						116	118	117					3																	44612087		2203	4300	6503	SO:0001819	synonymous_variant	55888	exon6			ACCTTATGAATGC	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"Zinc fingers, C2H2-type", "-", "-", "-"	12955	protein-coding gene	gene with protein product			"zinc finger protein 64", "zinc finger protein 448", "zinc finger protein 167"	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.1485T>C	3.37:g.44612087T>C		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	91	9	NM_018651	0	0	3	3	0	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Silent	SNP	ENST00000273320.3	37	CCDS2715.1																																																																																			.		0.448	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		C	44612087	T	C	44612087	2	2	39	1	0	0	0	0	0	0	0	1	17773	1471	51	3		3	ZNF167	3	44612087	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		44612087	153410343	26	3471											
VPRBP	9730	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	51452313	51452313	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtctgaatatcataaatcTttagagaagaagggatggga	16	10	11	4	0	3	3	1	1	2	2	3	6	3	5	0	2	0	0	0	2	7	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:51452313T>G	ENST00000335891.5	-	11	2266		c.e11-2					Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein						B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		ATCATAAATCTTTAGAGAAGA	0.373																																					.		.											.	VPRBP-92	0			c.3442-2A>C						.						58	51	53					3																	51452313		1852	4108	5960	SO:0001630	splice_region_variant	9730	exon18			TAAATCTTTAGAG	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.2257-2A>C	3.37:g.51452313T>G		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	70	6	NM_001171904	0	0	0	0	0	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Splice_Site	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	T	25.0	4.587425	0.86851	.	.	ENSG00000145041	ENST00000423656;ENST00000335891	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2997	0.82804	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	VPRBP	51427353	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.422000	0.80217	2.250000	0.74265	0.528000	0.53228	.	.		0.373	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	Intron	G	51452313	T	G	51452313	5	3	39	1	0	0	0	0	0	0	1	0	17218	1623	56	5	949	5	VPRBP	3	51452313	Splice_Site	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	6840226	51452313	146570117	27	3472											
FLNB	2317	broad.mit.edu	37	chr3	58121740	58121740	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccaaaagagccattgtccAtgacaataaagatggcacgt	16	7	8	10	1	0	3	0	1	0	2	1	3	1	3	3	1	1	1	3	1	5	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:58121740A>G	ENST00000295956.4	+	28	4871	c.4706A>G	c.(4705-4707)cAt>cGt	p.H1569R	FLNB_ENST00000490882.1_Missense_Mutation_p.H1600R|FLNB_ENST00000493452.1_Missense_Mutation_p.H1400R|FLNB_ENST00000357272.4_Missense_Mutation_p.H1569R|FLNB_ENST00000348383.5_Missense_Mutation_p.H1569R|FLNB_ENST00000358537.3_Missense_Mutation_p.H1569R|FLNB_ENST00000429972.2_Missense_Mutation_p.H1569R|FLNB_ENST00000419752.2_Missense_Mutation_p.H1400R	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1569					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.H1569R(1)		NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GCCATTGTCCATGACAATAAA	0.453																																					p.H1600R													.	FLNB-593	1	Substitution - Missense(1)	large_intestine(1)	c.A4799G						.						87	76	80					3																	58121740		2203	4300	6503	SO:0001583	missense	2317	exon29			TTGTCCATGACAA	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4706A>G	3.37:g.58121740A>G	ENSP00000295956:p.His1569Arg	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	139	4	NM_001164317	0	0	152	165	13	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	6.109	0.388346	0.11581	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.99	5.99	0.97316	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.437415	0.30168	N	0.010247	T	0.73164	0.3552	N	0.03967	-0.31	0.44880	D	0.997891	B;B;B;B;B;B	0.34061	0.382;0.002;0.272;0.0;0.436;0.436	B;B;B;B;B;B	0.43155	0.287;0.02;0.268;0.001;0.41;0.41	T	0.72070	-0.4401	10	0.02654	T	1	.	16.4791	0.84152	1.0:0.0:0.0:0.0	.	1569;1600;1400;1400;1569;1569	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	R	1569;1600;1569;1569;1569;1569;1400;1400	ENSP00000295956:H1569R;ENSP00000420213:H1600R;ENSP00000351339:H1569R;ENSP00000415599:H1569R;ENSP00000232447:H1569R;ENSP00000349819:H1569R;ENSP00000418510:H1400R;ENSP00000414532:H1400R	ENSP00000295956:H1569R	H	+	2	0	FLNB	58096780	0.998000	0.40836	0.824000	0.32777	0.986000	0.74619	4.078000	0.57606	2.284000	0.76573	0.528000	0.53228	CAT	.		0.453	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		G	58121740	A	G	58121740	3	3	39	1	0	0	0	0	1	0	0	0	5953	217	8	3	4913	3	FLNB	3	58121740	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	6669427	58121740	139900690	28	3473											
MME	4311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	154858036	154858036	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgtataacaagatgacAttggcccagatccaaaataa	16	10	6	9	0	1	3	0	1	1	2	2	3	2	3	2	1	1	1	2	1	6	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:154858036A>G	ENST00000460393.1	+	10	1032	c.912A>G	c.(910-912)acA>acG	p.T304T	MME_ENST00000360490.2_Silent_p.T304T|MME_ENST00000493237.1_Silent_p.T304T|MME_ENST00000492661.1_Silent_p.T304T|MME_ENST00000462745.1_Silent_p.T304T	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	304				T -> R (in Ref. 4; AAA51915). {ECO:0000305}.	angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	ACAAGATGACATTGGCCCAGA	0.323																																					p.T304T		.											.	MME-516	0			c.A912G						.						74	69	71					3																	154858036		2203	4298	6501	SO:0001819	synonymous_variant	4311	exon10			GATGACATTGGCC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"CD molecules"	7154	protein-coding gene	gene with protein product	"neutral endopeptidase", "enkephalinase", "neprilysin"	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.912A>G	3.37:g.154858036A>G		Somatic	293	0		WXS	Illumina HiSeq	Phase_I	324	109	NM_007287	0	0	10	20	10	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	37	CCDS3172.1																																																																																			.		0.323	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		G	154858036	A	G	154858036	2	3	39	1	0	0	0	0	0	0	0	1	9670	204	8	3		3	MME	3	154858036	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	96736296	154858036	43164394	29	3474											
AFAP1	60312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	7811366	7811366	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggaacatcttcctcagcTgaggaggtctgctcgtctgt	6	12	13	10	1	4	1	1	1	3	0	6	3	5	3	1	3	3	2	1	3	1	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:7811366T>C	ENST00000360265.4	-	8	1263	c.1029A>G	c.(1027-1029)tcA>tcG	p.S343S	AFAP1_ENST00000420658.1_Silent_p.S343S|AFAP1_ENST00000358461.2_Silent_p.S343S|AFAP1_ENST00000382543.3_Silent_p.S343S			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	343						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CTTCCTCAGCTGAGGAGGTCT	0.537																																					p.S343S		.											.	AFAP1-90	0			c.A1029G						.						145	115	125					4																	7811366		2203	4300	6503	SO:0001819	synonymous_variant	60312	exon9			CTCAGCTGAGGAG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1029A>G	4.37:g.7811366T>C		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	55	18	NM_001134647	0	0	10	24	14	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			.		0.537	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		C	7811366	T	C	7811366	2	2	39	1	0	0	0	0	0	0	0	1	353	1567	55	3		3	AFAP1	4	7811366	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		7811366	183342910	30	3475											
GUF1	60558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	44688034	44688034	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggcaattattgaaagaaTccccccgtgagtatttggtg	11	12	10	8	1	1	3	1	2	0	1	2	3	2	3	3	2	0	2	3	2	5	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:44688034T>C	ENST00000281543.5	+	7	922	c.728T>C	c.(727-729)aTc>aCc	p.I243T	GUF1_ENST00000506793.1_3'UTR	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						ATTGAAAGAATCCCCCCGTGA	0.318																																					p.I243T		.											.	GUF1-91	0			c.T728C						.						139	141	140					4																	44688034		2203	4298	6501	SO:0001583	missense	60558	exon7			AAAGAATCCCCCC		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.728T>C	4.37:g.44688034T>C	ENSP00000281543:p.Ile243Thr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	42	11	NM_021927	0	0	0	0	0		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.768731	0.69878	.	.	ENSG00000151806	ENST00000281543	T	0.72615	-0.67	5.72	5.72	0.89469	Protein synthesis factor, GTP-binding (1);	0.045776	0.85682	D	0.000000	T	0.79082	0.4386	M	0.73430	2.235	0.80722	D	1	P	0.48834	0.916	P	0.51701	0.677	T	0.82159	-0.0595	10	0.87932	D	0	-21.9459	15.1683	0.72846	0.0:0.0:0.0:1.0	.	243	Q8N442	GUF1_HUMAN	T	243	ENSP00000281543:I243T	ENSP00000281543:I243T	I	+	2	0	GUF1	44382791	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	7.594000	0.82698	2.169000	0.68431	0.460000	0.39030	ATC	.		0.318	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		C	44688034	T	C	44688034	3	2	39	1	0	0	0	0	1	0	0	0	6920	1435	50	3	754	3	GUF1	4	44688034	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	36876668	44688034	146466242	31	3476											
PKD2	5311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	88996109	88996109	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggctgttggatggggtggccGaggtcagtagtcatgagctg	6	10	19	6	1	2	1	2	1	0	0	2	3	2	2	1	6	1	4	1	6	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:88996109G>C	ENST00000508588.1	+	9	1317	c.922G>C	c.(922-924)Gag>Cag	p.E308Q	PKD2_ENST00000237596.2_Missense_Mutation_p.E890Q|PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Missense_Mutation_p.E308Q			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		TGGGGTGGCCGAGGTCAGTAG	0.468																																					p.E890Q		.											.	PKD2-91	0			c.G2668C						.						138	108	118					4																	88996109		2203	4300	6503	SO:0001583	missense	5311	exon14			GTGGCCGAGGTCA	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"Voltage-gated ion channels / Transient receptor potential cation channels", "EF-hand domain containing"	9009	protein-coding gene	gene with protein product	"transient receptor potential cation channel, subfamily P, member 2"	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.922G>C	4.37:g.88996109G>C	ENSP00000427131:p.Glu308Gln	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	87	18	NM_000297	0	0	0	0	0	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	G	23.9	4.473075	0.84640	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.92752	-0.39;-3.1;-3.1	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.95007	0.8384	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95429	0.8514	10	0.66056	D	0.02	-21.5133	18.3522	0.90342	0.0:0.0:1.0:0.0	.	890	Q13563	PKD2_HUMAN	Q	890;308;308	ENSP00000237596:E890Q;ENSP00000427131:E308Q;ENSP00000425289:E308Q	ENSP00000237596:E890Q	E	+	1	0	PKD2	89215133	1.000000	0.71417	0.985000	0.45067	0.635000	0.38103	9.576000	0.98192	2.318000	0.78349	0.650000	0.86243	GAG	.		0.468	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297		C	88996109	G	C	88996109	3	2	39	1	0	0	0	0	1	0	0	0	11992	1059	37	4	2722	4	PKD2	4	88996109	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	44308075	88996109	102158167	32	3477											
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	13839483	13839483	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgtctgtaagtggagttAttacaagcctgtcagtgcag	10	12	11	8	0	2	0	1	0	1	0	2	1	2	1	2	1	3	3	2	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:13839483A>C	ENST00000265104.4	-	35	5968	c.5864T>G	c.(5863-5865)aTa>aGa	p.I1955R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1955	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AAGTGGAGTTATTACAAGCCT	0.418									Kartagener syndrome																												p.I1955R		.											.	DNAH5-182	0			c.T5864G						.						126	129	128					5																	13839483		2203	4300	6503	SO:0001583	missense	1767	exon35	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAGTTATTACAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5864T>G	5.37:g.13839483A>C	ENSP00000265104:p.Ile1955Arg	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	55	19	NM_001369	0	0	1	2	1	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138855	0.77775	.	.	ENSG00000039139	ENST00000265104	T	0.14391	2.51	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.43678	0.1258	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53236	-0.8467	10	0.87932	D	0	.	13.8028	0.63212	1.0:0.0:0.0:0.0	.	1955	Q8TE73	DYH5_HUMAN	R	1955	ENSP00000265104:I1955R	ENSP00000265104:I1955R	I	-	2	0	DNAH5	13892483	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.307000	0.96226	1.870000	0.54199	0.533000	0.62120	ATA	.		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13839483	A	C	13839483	3	2	39	1	0	0	0	0	1	0	0	0	4615	449	16	5	8190	5	DNAH5	5	13839483	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10		13839483	167075777	33	3478											
AMACR	23600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	33998825	33998825	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgctgtcctgtaagtcgtAtagaaaggtgctccaccatc	9	12	9	11	1	1	1	0	0	1	1	5	1	3	1	3	1	2	4	3	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:33998825A>G	ENST00000335606.6	-	4	748	c.660T>C	c.(658-660)taT>taC	p.Y220Y	AMACR_ENST00000382072.2_Missense_Mutation_p.Y167H|AMACR_ENST00000382085.3_Silent_p.Y220Y|AMACR_ENST00000441713.2_Missense_Mutation_p.Y167H|AMACR_ENST00000512079.1_Silent_p.Y220Y|AMACR_ENST00000382068.3_Missense_Mutation_p.Y167H|AMACR_ENST00000426255.2_Silent_p.Y220Y|AMACR_ENST00000502637.1_Silent_p.Y205Y|RP11-1084J3.4_ENST00000382079.3_3'UTR|AMACR_ENST00000514195.1_5'UTR	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	220					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)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						TGTAAGTCGTATAGAAAGGTG	0.458																																					p.Y167H		.											.	AMACR-90	0			c.T499C						.						150	134	139					5																	33998825		2203	4300	6503	SO:0001819	synonymous_variant	23600	exon3			AGTCGTATAGAAA	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.660T>C	5.37:g.33998825A>G		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	106	34	NM_203382	0	0	147	331	184	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.568213	0.28003	.	.	ENSG00000242110	ENST00000382072;ENST00000441713	T;T	0.70164	-0.36;-0.46	5.34	0.947	0.19555	.	0.056699	0.64402	D	0.000001	T	0.45756	0.1358	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.14755	-1.0461	9	0.15499	T	0.54	-10.3866	8.1708	0.31254	0.5779:0.0:0.4221:0.0	.	167;167	Q6VRU4;Q9UHK6-4	.;.	H	167	ENSP00000371504:Y167H;ENSP00000403800:Y167H	ENSP00000371504:Y167H	Y	-	1	0	AMACR	34034582	0.996000	0.38824	0.997000	0.53966	0.411000	0.31082	0.457000	0.21875	0.241000	0.21283	-0.468000	0.05107	TAC	.		0.458	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		G	33998825	A	G	33998825	2	3	39	1	0	0	0	0	0	0	0	1	562	459	16	3		3	AMACR	5	33998825	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	20159342	33998825	146916435	34	3479											
ADAMTS6	11174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	64766709	64766709	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatgtttccactggggtcCatctttcccccaatattcta	8	15	5	13	0	3	0	1	0	2	0	6	0	6	0	4	2	0	1	4	2	3	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:64766709C>T	ENST00000536360.1	-	3	1171	c.358G>A	c.(358-360)Gga>Aga	p.G120R				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	120						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		CACTGGGGTCCATCTTTCCCC	0.373																																					p.G120R		.											.	ADAMTS6-226	0			c.G358A						.						110	109	109					5																	64766709		2203	4300	6503	SO:0001583	missense	11174	exon3			GGGGTCCATCTTT	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"ADAM metallopeptidases with thrombospondin type 1 motif"	222	protein-coding gene	gene with protein product	"a disintegrin and metalloproteinase with thrombospondin motifs 6"	605008	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.358G>A	5.37:g.64766709C>T	ENSP00000440995:p.Gly120Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	84	22	NM_197941	0	0	0	0	0	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Missense_Mutation	SNP	ENST00000536360.1	37		.	.	.	.	.	.	.	.	.	.	C	25.7	4.664354	0.88251	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	T;T;T	0.12039	2.72;2.72;2.72	5.78	5.78	0.91487	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.28830	0.0715	L	0.60455	1.87	0.80722	D	1	B	0.33857	0.429	P	0.47134	0.539	T	0.00599	-1.1651	10	0.28530	T	0.3	.	20.3754	0.98918	0.0:1.0:0.0:0.0	.	120	Q9UKP5	ATS6_HUMAN	R	120	ENSP00000370443:G120R;ENSP00000423551:G120R;ENSP00000440995:G120R	ENSP00000261306:G120R	G	-	1	0	ADAMTS6	64802465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.112000	0.77086	2.894000	0.99253	0.591000	0.81541	GGA	.		0.373	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941		T	64766709	C	T	64766709	3	4	39	1	0	0	0	0	1	0	0	0	270	603	21	2	3087	2	ADAMTS6	5	64766709	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	30767884	64766709	116148551	35	3480											
PCDHGA5	56110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140745640	140745640	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagctggcgcctcgctcCgcagaacctggctacctggt	5	8	14	14	3	0	1	0	0	0	1	2	2	1	2	4	4	3	4	4	4	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:140745640C>T	ENST00000518069.1	+	1	1743	c.1743C>T	c.(1741-1743)tcC>tcT	p.S581S	PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	581	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCTCGCTCCGCAGAACCTG	0.627																																					p.S581S		.											.	PCDHGA5-35	0			c.C1743T						.						97	108	105					5																	140745640		2203	4300	6503	SO:0001819	synonymous_variant	56110	exon1			TCGCTCCGCAGAA	AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"Cadherins / Protocadherins : Clustered"	8703	other	protocadherin	"cadherin ME3"	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.1743C>T	5.37:g.140745640C>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	104	35	NM_032054	0	0	0	0	0	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	37	CCDS54925.1																																																																																			.		0.627	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		T	140745640	C	T	140745640	2	4	39	1	0	0	0	0	0	0	0	1	11583	639	23	1		1	PCDHGA5	5	140745640	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	75978931	140745640	40169620	36	3481											
UBTD2	92181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	171661228	171661228	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttcaaggcatcccaaatctCtttccggccttcaaaagctg	10	11	6	14	1	3	0	2	0	1	0	6	0	5	0	3	2	1	2	3	2	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:171661228C>T	ENST00000393792.2	-	2	610	c.205G>A	c.(205-207)Gag>Aag	p.E69K		NM_152277.2	NP_689490.2	Q8WUN7	UBTD2_HUMAN	ubiquitin domain containing 2	69						cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCCAAATCTCTTTCCGGCCT	0.438																																					p.E69K		.											.	UBTD2-90	0			c.G205A						.						165	142	150					5																	171661228		2203	4300	6503	SO:0001583	missense	92181	exon2			AAATCTCTTTCCG	AF251700	CCDS4379.2	5q35.1	2008-10-30			ENSG00000168246	ENSG00000168246			24463	protein-coding gene	gene with protein product	"dendritic cell derived ubiquitin like protein"	610174				12507522	Standard	NM_152277		Approved	DC-UbP, MGC30022	uc003mbp.1	Q8WUN7	OTTHUMG00000130519	ENST00000393792.2:c.205G>A	5.37:g.171661228C>T	ENSP00000377381:p.Glu69Lys	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	93	32	NM_152277	0	0	12	24	12	Q8TDQ3	Missense_Mutation	SNP	ENST00000393792.2	37	CCDS4379.2	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035386	0.93630	.	.	ENSG00000168246	ENST00000393792	T	0.64260	-0.09	5.51	5.51	0.81932	.	0.047322	0.85682	D	0.000000	D	0.84014	0.5379	M	0.93328	3.405	0.80722	D	1	D	0.54772	0.968	D	0.66847	0.947	D	0.87994	0.2751	10	0.87932	D	0	.	16.9267	0.86178	0.0:1.0:0.0:0.0	.	69	Q8WUN7	UBTD2_HUMAN	K	69	ENSP00000377381:E69K	ENSP00000377381:E69K	E	-	1	0	UBTD2	171593833	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	7.640000	0.83355	2.584000	0.87258	0.563000	0.77884	GAG	.		0.438	UBTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252936.1	NM_152277		T	171661228	C	T	171661228	3	4	39	1	0	0	0	0	1	0	0	0	16941	922	32	2	507	2	UBTD2	5	171661228	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	30915588	171661228	9254032	37	3482											
RGS14	10636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176798989	176798989	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgcccgcccaagggccCagctccgaggagaccccacc	8	2	11	20	2	0	1	0	0	0	1	1	3	1	1	7	2	3	2	7	2	1	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:176798989C>T	ENST00000408923.3	+	15	1802	c.1614C>T	c.(1612-1614)ccC>ccT	p.P538P	RGS14_ENST00000506944.1_3'UTR	NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	538					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAAGGGCCCAGCTCCGAGG	0.627																																					p.P538P	NSCLC(47;353 1896 28036)	.											.	RGS14-226	0			c.C1614T						.						108	130	123					5																	176798989		2003	4169	6172	SO:0001819	synonymous_variant	10636	exon15			AGGGCCCAGCTCC	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"Regulators of G-protein signaling"	9996	protein-coding gene	gene with protein product		602513	"regulator of G-protein signalling 14"				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.1614C>T	5.37:g.176798989C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_006480	0	1	92	209	116	O43565|Q506M1|Q6ZWA4|Q8TD62	Silent	SNP	ENST00000408923.3	37	CCDS43405.1	.	.	.	.	.	.	.	.	.	.	C	2.400	-0.337801	0.05278	.	.	ENSG00000169220	ENST00000511890	T	0.45276	0.9	4.52	1.21	0.21127	.	0.378652	0.25866	N	0.027786	T	0.45975	0.1369	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.44922	-0.9296	7	0.87932	D	0	-6.9952	11.7553	0.51872	0.4686:0.5314:0.0:0.0	.	.	.	.	L	409	ENSP00000422329:P409L	ENSP00000422329:P409L	P	+	2	0	RGS14	176731595	0.000000	0.05858	0.363000	0.25875	0.442000	0.32017	-0.925000	0.03992	0.463000	0.27118	0.644000	0.83932	CCA	.		0.627	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		T	176798989	C	T	176798989	2	4	39	1	0	0	0	0	0	0	0	1	13329	581	21	2		2	RGS14	5	176798989	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	5137761	176798989	4116271	38	3483											
HIST1H2BJ	8970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	27100264	27100264	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggatctccctggaggtgatgGtcgagcgcttgttgtaatgc	6	12	15	8	2	1	1	0	1	1	0	3	4	1	3	1	4	2	3	1	4	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:27100264G>A	ENST00000607124.1	-	1	265	c.266C>T	c.(265-267)aCc>aTc	p.T89I	HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000541790.1_Missense_Mutation_p.T89I|HIST1H2BJ_ENST00000339812.2_Missense_Mutation_p.T89I			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	89					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(2)|lung(5)|ovary(1)|prostate(1)	10						GGAGGTGATGGTCGAGCGCTT	0.602																																					p.T89I		.											.	HIST1H2BJ-90	0			c.C266T						.						93	94	94					6																	27100264		2203	4297	6500	SO:0001583	missense	8970	exon1			GTGATGGTCGAGC	X00088	CCDS4618.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000124635	ENSG00000124635		"Histones / Replication-dependent"	4761	protein-coding gene	gene with protein product		615044	"H2B histone family, member R", "histone 1, H2bj"	H2BFR		6647026, 12408966	Standard	NM_021058		Approved	H2B/r	uc003niv.3	P06899	OTTHUMG00000014470	ENST00000607124.1:c.266C>T	6.37:g.27100264G>A	ENSP00000476136:p.Thr89Ile	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_021058	0	0	51	51	0	B2R4J4|O60816	Missense_Mutation	SNP	ENST00000607124.1	37	CCDS4618.1	.	.	.	.	.	.	.	.	.	.	G	31	5.078432	0.94000	.	.	ENSG00000124635	ENST00000541790;ENST00000339812	T;T	0.41758	0.99;0.99	4.16	4.16	0.48862	Histone-fold (2);Histone core (1);	0.000000	0.44097	U	0.000487	T	0.67590	0.2909	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77512	-0.2560	10	0.87932	D	0	.	14.7851	0.69796	0.0:0.0:1.0:0.0	.	89	P06899	H2B1J_HUMAN	I	89	ENSP00000445633:T89I;ENSP00000342886:T89I	ENSP00000342886:T89I	T	-	2	0	HIST1H2BJ	27208243	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.903000	0.92573	2.268000	0.75426	0.585000	0.79938	ACC	.		0.602	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		A	27100264	G	A	27100264	3	1	39	1	0	0	0	0	1	0	0	0	7170	1261	44	2	118	2	HIST1H2BJ	6	27100264	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		27100264	144014803	39	3484											
KCNK16	83795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	39285639	39285639	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtgcccaggtggttgaGgaagatcacgttaagcggga	9	8	15	9	2	1	2	1	1	0	1	1	4	1	4	2	4	2	2	2	4	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:39285639G>T	ENST00000373229.5	-	3	431	c.418C>A	c.(418-420)Ctc>Atc	p.L140I	KCNK16_ENST00000425054.2_Missense_Mutation_p.L140I|KCNK16_ENST00000437525.2_Missense_Mutation_p.L140I|KCNK16_ENST00000373227.4_Missense_Mutation_p.L140I|KCNK16_ENST00000507712.1_Missense_Mutation_p.L75I	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	140					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						AGGTGGTTGAGGAAGATCACG	0.592																																					p.L140I		.											.	KCNK16-229	0			c.C418A						.						63	52	56					6																	39285639		2203	4300	6503	SO:0001583	missense	83795	exon3			GGTTGAGGAAGAT	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.418C>A	6.37:g.39285639G>T	ENSP00000362326:p.Leu140Ile	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	60	7	NM_001135106	0	0	0	0	0	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Missense_Mutation	SNP	ENST00000373229.5	37	CCDS4843.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504087	0.85176	.	.	ENSG00000095981	ENST00000373229;ENST00000425054;ENST00000507712;ENST00000373227;ENST00000437525	T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99	5.65	4.78	0.61160	Ion transport 2 (1);	0.065126	0.64402	D	0.000007	T	0.26702	0.0653	L	0.41632	1.29	0.45979	D	0.998796	P;P;D;D	0.76494	0.939;0.707;0.986;0.999	P;P;P;D	0.77557	0.589;0.624;0.793;0.99	T	0.00599	-1.1651	10	0.39692	T	0.17	.	14.537	0.67969	0.0721:0.0:0.9279:0.0	.	140;140;140;140	B5TJL9;Q96T55-5;Q96T55-4;Q96T55	.;.;.;KCNKG_HUMAN	I	140;140;75;140;140	ENSP00000362326:L140I;ENSP00000391498:L140I;ENSP00000423842:L75I;ENSP00000362324:L140I;ENSP00000415375:L140I	ENSP00000362324:L140I	L	-	1	0	KCNK16	39393617	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.106000	0.64597	2.667000	0.90743	0.561000	0.74099	CTC	.		0.592	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		T	39285639	G	T	39285639	3	4	39	1	0	0	0	0	1	0	0	0	8084	1000	35	4	912	4	KCNK16	6	39285639	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	12185375	39285639	131829428	40	3485											
PRIM2	5558	broad.mit.edu;bcgsc.ca	37	chr6	57467163	57467163	+	3'UTR	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tatacacctttcagttgcctGaagattattctatccaatcc	11	15	4	11	0	2	2	1	1	1	1	4	2	4	2	4	0	2	1	4	0	6	7			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:57467163G>C	ENST00000389488.2	+	0	1191				PRIM2_ENST00000607273.1_3'UTR			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)						DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TCAGTTGCCTGAAGATTATTC	0.438																																					.													.	PRIM2-227	0			.						.						136	129	131					6																	57467163		1989	4189	6178	SO:0001624	3_prime_UTR_variant	5558	.			TTGCCTGAAGATT		CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.*1188G>C	6.37:g.57467163G>C		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	146	6	.	0	0	0	0	0	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Silent	SNP	ENST00000389488.2	37																																																																																				.		0.438	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000043468.3	NM_000947		C	57467163	G	C	57467163	1	2	39	0	1	0	0	0	0	0	0	0	12520	1277	45	4		4	PRIM2	6	57467163	3'UTR	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	18181524	57467163	113647904	41	3486											
PRSS35	167681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	84233613	84233613	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagctgtgaagctttcCacgggctgtagtggcattct	8	11	12	10	1	1	1	0	1	1	0	2	1	2	1	1	2	3	6	1	2	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:84233613C>T	ENST00000369700.3	+	2	630	c.453C>T	c.(451-453)tcC>tcT	p.S151S	PRSS35_ENST00000536636.1_Silent_p.S151S	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	151	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		TGAAGCTTTCCACGGGCTGTA	0.463																																					p.S151S		.											.	PRSS35-91	0			c.C453T						.						101	100	101					6																	84233613		2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			GCTTTCCACGGGC	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"Serine peptidases / Serine peptidases"	21387	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 158"	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.453C>T	6.37:g.84233613C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	115	40	NM_153362	0	0	0	0	0	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																			.		0.463	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		T	84233613	C	T	84233613	2	4	39	1	0	0	0	0	0	0	0	1	12653	581	21	2		2	PRSS35	6	84233613	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	26766450	84233613	86881454	42	3487											
ENPP3	5169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	132059234	132059234	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacagaaagaaatggagtaaAtgtggttagtggaccaatat	17	9	11	4	0	0	2	0	0	0	2	0	4	0	4	1	3	0	2	1	3	7	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:132059234A>C	ENST00000414305.1	+	24	2559	c.2231A>C	c.(2230-2232)aAt>aCt	p.N744T	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.N744T			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	744	Nuclease.		N -> H (in dbSNP:rs36094194).		immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		AATGGAGTAAATGTGGTTAGT	0.303																																					p.N744T		.											.	ENPP3-95	0			c.A2231C						.						114	125	121					6																	132059234		2203	4297	6500	SO:0001583	missense	5169	exon23			GAGTAAATGTGGT	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2231A>C	6.37:g.132059234A>C	ENSP00000406261:p.Asn744Thr	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	78	29	NM_005021	0	0	7	12	5	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	37	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286561	0.80803	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	T;T	0.69040	-0.37;-0.37	6.08	6.08	0.98989	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.196594	0.45867	D	0.000330	D	0.83036	0.5167	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86746	0.1957	10	0.87932	D	0	-31.3676	16.6512	0.85203	1.0:0.0:0.0:0.0	.	744	O14638	ENPP3_HUMAN	T	744	ENSP00000406261:N744T;ENSP00000350265:N744T	ENSP00000350265:N744T	N	+	2	0	ENPP3	132100927	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.974000	0.88039	2.333000	0.79357	0.482000	0.46254	AAT	.		0.303	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			C	132059234	A	C	132059234	3	2	39	1	0	0	0	0	1	0	0	0	5144	101	4	5	2321	5	ENPP3	6	132059234	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	47825621	132059234	39055833	43	3488											
SNX9	51429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	158358486	158358486	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaaagaaagatctccatttCctgatggaatgtaatcacga	15	10	7	9	1	2	3	1	1	1	2	4	5	3	4	3	1	0	1	3	1	4	2	rs532553158		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:158358486C>A	ENST00000392185.3	+	15	1635	c.1464C>A	c.(1462-1464)ttC>ttA	p.F488L		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	488	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)	p.F488F(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		ATCTCCATTTCCTGATGGAAT	0.378																																					p.F488L		.											.	SNX9-226	1	Substitution - coding silent(1)	skin(1)	c.C1464A						.						149	143	145					6																	158358486		2203	4300	6503	SO:0001583	missense	51429	exon15			CCATTTCCTGATG	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.1464C>A	6.37:g.158358486C>A	ENSP00000376024:p.Phe488Leu	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	80	20	NM_016224	0	1	54	101	46	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	37	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.528865	0.64860	.	.	ENSG00000130340	ENST00000539592;ENST00000392185;ENST00000252631	T	0.40476	1.03	5.39	2.61	0.31194	Sorting nexin protein, WASP-binding domain (1);	0.045544	0.85682	D	0.000000	T	0.20292	0.0488	L	0.43152	1.355	0.80722	D	1	P	0.52842	0.956	B	0.41619	0.361	T	0.03344	-1.1046	10	0.48119	T	0.1	-10.3916	8.3841	0.32491	0.0:0.6569:0.0:0.3431	.	488	Q9Y5X1	SNX9_HUMAN	L	488;488;288	ENSP00000376024:F488L	ENSP00000252631:F288L	F	+	3	2	SNX9	158278474	0.996000	0.38824	1.000000	0.80357	0.985000	0.73830	0.455000	0.21843	2.673000	0.90976	0.563000	0.77884	TTC	.		0.378	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1			A	158358486	C	A	158358486	3	1	39	1	0	0	0	0	1	0	0	0	14941	854	30	4	1522	4	SNX9	6	158358486	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	26299252	158358486	12756581	44	3489											
SCIN	85477	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	12680013	12680013	+	Frame_Shift_Del	DEL	T	T	-																															gagcctgttcacctactgagTttgttcaaagacaaaccgct																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:12680013delT	ENST00000297029.5	+	11	1553	c.1452delT	c.(1450-1452)agtfs	p.S484fs	SCIN_ENST00000519209.1_Frame_Shift_Del_p.S237fs|SCIN_ENST00000445618.2_Frame_Shift_Del_p.S237fs	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	484	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		ACCTACTGAGTTTGTTCAAAG	0.453																																					p.S484fs		.											.	SCIN-24	0			c.1452delT						.						58	56	57					7																	12680013		1863	4100	5963	SO:0001589	frameshift_variant	85477	exon11			.	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1452delT	7.37:g.12680013delT	ENSP00000297029:p.Ser484fs	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	51	17	NM_001112706	0	0	0	0	0	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Frame_Shift_Del	DEL	ENST00000297029.5	37	CCDS47545.1																																																																																			.		0.453	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		-	12680013	T	-	12680013	7	5	39	1	0	1	0	1	0	0	0	0	13937	1722	60	0	1494	0	SCIN	7	12680013	Frame_Shift_Del	DEL	T	TCGA-B1-A655-01A-11D-A31Z-10		12680013	146458650	45	3490											
POU6F2	11281	broad.mit.edu;bcgsc.ca	37	chr7	39504216	39504216	+	Frame_Shift_Del	DEL	A	A	-																															aagaacacaattaaacgcttAaaacagcacgagccggccac																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:39504216delA	ENST00000403058.1	+	11	2161	c.2007delA	c.(2005-2007)ttafs	p.L669fs	POU6F2_ENST00000559001.1_Frame_Shift_Del_p.L614fs|POU6F2_ENST00000518318.2_Frame_Shift_Del_p.L633fs	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	669					central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						TTAAACGCTTAAAACAGCACG	0.453																																					p.L669fs													.	POU6F2-90	0			c.2007delA						.						31	31	31					7																	39504216		2203	4300	6503	SO:0001589	frameshift_variant	11281	exon11			ACGCTTAAAACAG	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.2007delA	7.37:g.39504216delA	ENSP00000384004:p.Leu669fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	42	9	NM_007252	0	0	0	0	0	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Frame_Shift_Del	DEL	ENST00000403058.1	37	CCDS34620.2																																																																																			.		0.453	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		-	39504216	A	-	39504216	7	5	39	1	0	1	0	1	0	0	0	0	12311	359	13	0	2045	0	POU6F2	7	39504216	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	26824203	39504216	119634447	46	3491											
GCK	2645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44185276	44185276	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cgcagtcggtggtcgagggtCgcagccccagcgtgctcagg	5	6	17	13	5	1	0	1	0	0	0	4	1	1	0	2	4	3	3	2	4	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:44185276C>G	ENST00000403799.3	-	9	1542	c.1073G>C	c.(1072-1074)cGa>cCa	p.R358P	GCK_ENST00000395796.3_Missense_Mutation_p.R357P|GCK_ENST00000437084.1_Missense_Mutation_p.R341P|GCK_ENST00000345378.2_Missense_Mutation_p.R359P	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	358	Hexokinase type-2.				calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						GGTCGAGGGTCGCAGCCCCAG	0.697																																					p.R359P		.											.	GCK-416	0			c.G1076C						.						30	34	33					7																	44185276		2203	4299	6502	SO:0001583	missense	2645	exon9			GAGGGTCGCAGCC	AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.1073G>C	7.37:g.44185276C>G	ENSP00000384247:p.Arg358Pro	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	70	27	NM_033507	0	0	0	0	0	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	ENST00000403799.3	37	CCDS5479.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.547708	0.27652	.	.	ENSG00000106633	ENST00000336642;ENST00000403799;ENST00000395796;ENST00000345378;ENST00000437084	D;D;D;D;D	0.98044	-4.68;-4.68;-4.68;-4.68;-4.68	5.2	4.22	0.49857	Hexokinase, C-terminal (1);	0.488216	0.21760	N	0.069537	D	0.92961	0.7760	N	0.17248	0.465	0.36805	D	0.885564	B;B;B;B;B	0.32128	0.357;0.0;0.308;0.0;0.357	B;B;B;B;B	0.34536	0.094;0.001;0.185;0.003;0.094	D	0.91899	0.5530	10	0.34782	T	0.22	-12.1896	7.8212	0.29288	0.2196:0.6875:0.0:0.0928	.	358;359;357;341;358	P35557;P35557-2;P35557-3;C9JQD1;A7LFL1	HXK4_HUMAN;.;.;.;.	P	42;358;357;359;341	ENSP00000338009:R42P;ENSP00000384247:R358P;ENSP00000379142:R357P;ENSP00000223366:R359P;ENSP00000402840:R341P	ENSP00000338009:R42P	R	-	2	0	GCK	44151801	0.070000	0.21116	0.955000	0.39395	0.307000	0.27823	1.831000	0.39141	2.403000	0.81681	0.462000	0.41574	CGA	.		0.697	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			G	44185276	C	G	44185276	3	3	39	1	0	0	0	0	1	0	0	0	6313	884	31	4	332	4	GCK	7	44185276	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	4681060	44185276	114953387	47	3492											
POM121C	100101267	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	75070316	75070316	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctctttgagggcactcAgtacagtctcctttgcacat	7	15	7	12	0	4	1	1	1	3	0	6	1	4	1	1	1	2	3	1	1	1	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:75070316A>C	ENST00000257665.5	-	3	868	c.869T>G	c.(868-870)cTg>cGg	p.L290R	POM121C_ENST00000453279.2_Missense_Mutation_p.L48R			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	290	Pore side. {ECO:0000255}.|Required for targeting to the nucleus and nuclear pore complex.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						GAGGGCACTCAGTACAGTCTC	0.438																																					p.L48R		.											.	.	0			c.T143G						.						141	153	149					7																	75070316		2203	4298	6501	SO:0001583	missense	100101267	exon5			GCACTCAGTACAG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"POM121 membrane glycoprotein C"			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.869T>G	7.37:g.75070316A>C	ENSP00000257665:p.Leu290Arg	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	138	33	NM_001099415	0	0	30	46	16	O75115|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000257665.5	37		.	.	.	.	.	.	.	.	.	.	A	13.49	2.253891	0.39896	.	.	ENSG00000135213	ENST00000257665;ENST00000453279	T;T	0.39229	2.64;1.09	4.27	3.09	0.35607	.	0.499492	0.14888	N	0.292593	T	0.62233	0.2411	M	0.81497	2.545	0.44142	D	0.996934	D	0.89917	1.0	D	0.74674	0.984	T	0.60767	-0.7198	10	0.87932	D	0	.	8.0021	0.30304	0.8181:0.0:0.0:0.1819	.	290	A8CG34	P121C_HUMAN	R	290;48	ENSP00000257665:L290R;ENSP00000414208:L48R	ENSP00000257665:L290R	L	-	2	0	POM121C	74908252	1.000000	0.71417	0.998000	0.56505	0.211000	0.24417	6.656000	0.74396	0.601000	0.29879	-0.676000	0.03789	CTG	.		0.438	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415		C	75070316	A	C	75070316	3	2	39	1	0	0	0	0	1	0	0	0	12266	188	7	5	2864	5	POM121C	7	75070316	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	30885040	75070316	84068347	48	3493											
ZAN	7455	ucsc.edu	37	chr7	100349991	100349991	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacagaaaaacccaccatcTccccagaaaaacccaccacc	17	2	2	20	0	1	2	0	0	1	2	2	2	1	2	8	0	2	0	8	0	4	0	rs560599163	byFrequency	TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:100349991T>C	ENST00000348028.3	+	0	2428				ZAN_ENST00000546213.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000449052.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S755P(5)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			ACCCACCATCTCCCCAGAAAA	0.517													t|||	35	0.00698882	0.0038	0.0101	5008	,	,		14901	0.005		0.0129	False		,,,				2504	0.0051				.													.	ZAN-142	5	Substitution - Missense(5)	endometrium(4)|NS(1)	.						.						122	136	131					7																	100349991		1816	4060	5876			7455	.			ACCATCTCCCCAG	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100349991T>C		Somatic	149	27		WXS	Illumina HiSeq		142	34	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	t	5.435	0.265377	0.10294	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.63255	-0.03;0.11;-0.03	4.24	0.21	0.15231	.	.	.	.	.	T	0.29716	0.0742	N	0.01140	-0.99	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20571	-1.0271	9	0.33940	T	0.23	.	7.9077	0.29771	0.0:0.5221:0.0:0.4779	.	755;755	F5H0T8;Q9Y493	.;ZAN_HUMAN	P	755	ENSP00000445943:S755P;ENSP00000445091:S755P;ENSP00000444427:S755P	ENSP00000423579:S755P	S	+	1	0	ZAN	100187927	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.770000	0.00371	-0.086000	0.12550	-0.766000	0.03442	TCC	.		0.517	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		C	100349991	T	C	100349991	1	2	39	0	1	0	0	0	0	0	0	0	17546	1551	54	3		3	ZAN	7	100349991	RNA	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	25279675	100349991	58788672	49	3494											
ATP6V0A4	50617	broad.mit.edu	37	chr7	138394418	138394418	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagaggccctccatgatcaGaaggatggctactgtcagga	12	7	13	9	0	2	3	2	1	0	2	3	6	3	5	2	4	1	1	2	4	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:138394418G>T	ENST00000310018.2	-	21	2662	c.2380C>A	c.(2380-2382)Ctg>Atg	p.L794M	ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.L794M|ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.L794M	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	794					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						TCCATGATCAGAAGGATGGCT	0.537																																					p.L794M													.	ATP6V0A4-91	0			c.C2380A						.						176	173	174					7																	138394418		2203	4300	6503	SO:0001583	missense	50617	exon20			TGATCAGAAGGAT	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"ATPases / V-type"	866	protein-coding gene	gene with protein product		605239	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 4", "ATPase, H+ transporting, lysosomal V0 subunit A4"	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.2380C>A	7.37:g.138394418G>T	ENSP00000308122:p.Leu794Met	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	163	6	NM_130841	0	0	0	0	0	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301168	0.81136	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.87179	-2.22;-2.22;-2.22	5.71	4.82	0.62117	.	0.000000	0.64402	D	0.000009	D	0.91700	0.7376	L	0.57130	1.785	0.53005	D	0.999968	D	0.89917	1.0	D	0.87578	0.998	D	0.91877	0.5512	10	0.62326	D	0.03	-24.8445	14.9831	0.71327	0.0693:0.0:0.9307:0.0	.	794	Q9HBG4	VPP4_HUMAN	M	794	ENSP00000308122:L794M;ENSP00000376774:L794M;ENSP00000253856:L794M	ENSP00000308122:L794M	L	-	1	2	ATP6V0A4	138044958	1.000000	0.71417	0.344000	0.25628	0.995000	0.86356	6.461000	0.73522	2.694000	0.91930	0.655000	0.94253	CTG	.		0.537	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		T	138394418	G	T	138394418	3	4	39	1	0	0	0	0	1	0	0	0	1171	933	33	4	150	4	ATP6V0A4	7	138394418	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	38044427	138394418	20744245	50	3495											
DPP6	1804	broad.mit.edu	37	chr7	153750140	153750140	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggcgcggagcgatggtgacGaggaggacgtaagagcttct	10	6	18	7	5	1	2	0	1	1	1	1	7	1	5	0	5	2	2	0	5	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:153750140G>A	ENST00000377770.3	+	1	376	c.235G>A	c.(235-237)Gag>Aag	p.E79K	DPP6_ENST00000404039.1_Intron|DPP6_ENST00000406326.1_Missense_Mutation_p.E79K|AC006019.3_ENST00000425591.1_RNA			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	79					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CGATGGTGACGAGGAGGACGT	0.776																																					p.E79K	NSCLC(125;1384 1783 2490 7422 34254)												.	DPP6-652	0			c.G235A						.						1	2	2					7																	153750140		201	467	668	SO:0001583	missense	1804	exon1			GGTGACGAGGAGG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.235G>A	7.37:g.153750140G>A	ENSP00000367001:p.Glu79Lys	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_130797	0	0	0	0	0		Missense_Mutation	SNP	ENST00000377770.3	37		.	.	.	.	.	.	.	.	.	.	g	12.16	1.855547	0.32791	.	.	ENSG00000130226	ENST00000406326;ENST00000377770	T;T	0.41065	1.01;1.01	3.42	3.42	0.39159	.	4.209170	0.00883	N	0.002150	T	0.29321	0.0730	.	.	.	0.80722	D	1	B;P	0.38745	0.003;0.645	B;B	0.26614	0.001;0.071	T	0.26467	-1.0102	9	0.18710	T	0.47	-8.5179	14.2438	0.65975	0.0:0.0:1.0:0.0	.	79;79	P42658;Q8IYG9	DPP6_HUMAN;.	K	79	ENSP00000384393:E79K;ENSP00000367001:E79K	ENSP00000367001:E79K	E	+	1	0	DPP6	153381073	1.000000	0.71417	0.993000	0.49108	0.028000	0.11728	5.170000	0.64990	1.635000	0.50512	0.549000	0.68633	GAG	.		0.776	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	153750140	G	A	153750140	3	1	39	1	0	0	0	0	1	0	0	0	4741	1059	37	1	292	1	DPP6	7	153750140	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	15355722	153750140	5388523	51	3496											
MYOM2	9172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	2020508	2020508	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcaccttcaggagggaaggcGagacggtcactctcaagtgc	10	7	13	11	2	4	1	4	0	1	1	5	4	4	3	1	4	1	0	1	4	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:2020508G>C	ENST00000262113.4	+	9	1018	c.877G>C	c.(877-879)Gag>Cag	p.E293Q	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	293	Ig-like C2-type 2.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GAGGGAAGGCGAGACGGTCAC	0.602																																					p.E293Q		.											.	MYOM2-95	0			c.G877C						.						85	70	75					8																	2020508		2203	4300	6503	SO:0001583	missense	9172	exon9			GAAGGCGAGACGG		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.877G>C	8.37:g.2020508G>C	ENSP00000262113:p.Glu293Gln	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	29	9	NM_003970	0	0	0	0	0	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.485155	0.63962	.	.	ENSG00000036448	ENST00000262113	T	0.46063	0.88	5.13	4.25	0.50352	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.208574	0.40818	N	0.001006	T	0.46308	0.1386	M	0.63843	1.955	0.80722	D	1	B	0.29136	0.234	B	0.34180	0.177	T	0.50206	-0.8855	10	0.72032	D	0.01	.	15.6628	0.77203	0.0:0.1376:0.8624:0.0	.	293	P54296	MYOM2_HUMAN	Q	293	ENSP00000262113:E293Q	ENSP00000262113:E293Q	E	+	1	0	MYOM2	2007915	1.000000	0.71417	0.800000	0.32199	0.700000	0.40528	4.275000	0.58927	1.132000	0.42129	0.655000	0.94253	GAG	.		0.602	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		C	2020508	G	C	2020508	3	2	39	1	0	0	0	0	1	0	0	0	10117	1059	37	4	907	4	MYOM2	8	2020508	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		2020508	144343514	52	3497											
LOXL2	4017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	23198538	23198538	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tattgtatgtcctctccccaGggaagccaaacatgccgcag	10	9	9	13	1	1	0	0	0	1	0	3	1	2	1	5	1	3	2	5	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:23198538G>A	ENST00000389131.3	-	4	1079	c.710C>T	c.(709-711)cCt>cTt	p.P237L	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	237	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		CCTCTCCCCAGGGAAGCCAAA	0.537																																					p.P237L		.											.	LOXL2-272	0			c.C710T						.						163	132	142					8																	23198538		2203	4300	6503	SO:0001583	missense	4017	exon4			TCCCCAGGGAAGC	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.710C>T	8.37:g.23198538G>A	ENSP00000373783:p.Pro237Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	45	15	NM_002318	0	0	0	0	0	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Missense_Mutation	SNP	ENST00000389131.3	37	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920583	0.73213	.	.	ENSG00000134013	ENST00000389131	T	0.60424	0.19	5.83	5.83	0.93111	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.047123	0.85682	D	0.000000	T	0.78381	0.4274	M	0.83118	2.625	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.80636	-0.1294	10	0.72032	D	0.01	.	16.8345	0.85953	0.0:0.0:1.0:0.0	.	237	Q9Y4K0	LOXL2_HUMAN	L	237	ENSP00000373783:P237L	ENSP00000373783:P237L	P	-	2	0	LOXL2	23254483	1.000000	0.71417	0.975000	0.42487	0.192000	0.23643	9.751000	0.98889	2.750000	0.94351	0.655000	0.94253	CCT	.		0.537	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			A	23198538	G	A	23198538	3	1	39	1	0	0	0	0	1	0	0	0	8925	1000	35	2	1658	2	LOXL2	8	23198538	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	21178030	23198538	123165484	53	3498											
EXOSC4	54512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145134932	145134932	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttcagcacaggtgagcgCaagcgacggccacatgggga	11	4	14	12	3	1	1	1	1	0	0	1	3	1	2	2	4	3	2	2	4	1	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:145134932C>T	ENST00000316052.5	+	2	361	c.258C>T	c.(256-258)cgC>cgT	p.R86R	EXOSC4_ENST00000525936.1_Intron|GPAA1_ENST00000361036.6_5'Flank|GPAA1_ENST00000355091.4_5'Flank|CTD-3065J16.9_ENST00000524499.1_RNA	NM_019037.2	NP_061910.1	Q9NPD3	EXOS4_HUMAN	exosome component 4	86					defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)			lung(4)|prostate(1)|upper_aerodigestive_tract(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-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;3.48e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGGTGAGCGCAAGCGACGGC	0.627																																					p.R86R		.											.	EXOSC4-90	0			c.C258T						.						84	83	83					8																	145134932		2203	4300	6503	SO:0001819	synonymous_variant	54512	exon2			TGAGCGCAAGCGA	AF281133	CCDS6414.1	8q24.3	2004-03-26			ENSG00000178896	ENSG00000178896			18189	protein-coding gene	gene with protein product	"exosome component Rrp41"	606491				11110791	Standard	NM_019037		Approved	hRrp41p, FLJ20591, Rrp41p, RRP41, RRP41A, Ski6p, SKI6, p12A	uc003zau.3	Q9NPD3	OTTHUMG00000165437	ENST00000316052.5:c.258C>T	8.37:g.145134932C>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	118	40	NM_019037	0	0	17	33	16		Silent	SNP	ENST00000316052.5	37	CCDS6414.1																																																																																			.		0.627	EXOSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384065.1	NM_019037		T	145134932	C	T	145134932	2	4	39	1	0	0	0	0	0	0	0	1	5330	697	25	2		2	EXOSC4	8	145134932	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	121936394	145134932	1229090	54	3499											
SLC39A4	55630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145640398	145640398	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgttgctggagctgatgaggGgcacagggtcccagctgctg	6	9	17	9	0	0	2	0	2	0	0	1	3	1	3	1	4	4	6	1	4	0	1	rs200044971		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:145640398G>T	ENST00000301305.3	-	4	869	c.764C>A	c.(763-765)cCc>cAc	p.P255H	SLC39A4_ENST00000276833.5_Missense_Mutation_p.P230H|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	255					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GCTGATGAGGGGCACAGGGTC	0.672																																					p.P255H		.											.	SLC39A4-90	0			c.C764A						.						40	45	43					8																	145640398		2203	4300	6503	SO:0001583	missense	55630	exon4			ATGAGGGGCACAG	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"Solute carriers"	17129	protein-coding gene	gene with protein product		607059	"acrodermatitis enteropathica, zinc-deficiency type"	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.764C>A	8.37:g.145640398G>T	ENSP00000301305:p.Pro255His	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	38	15	NM_130849	0	0	0	0	0	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.850768	0.51270	.	.	ENSG00000147804	ENST00000276833;ENST00000301305;ENST00000526658	T;T;T	0.57436	0.4;0.4;0.4	5.0	-4.46	0.03536	.	3.799390	0.00575	N	0.000304	T	0.39989	0.1099	L	0.47716	1.5	0.09310	N	1	B;B	0.18461	0.028;0.028	B;B	0.16722	0.016;0.016	T	0.09662	-1.0664	10	0.38643	T	0.18	-5.3671	0.812	0.01095	0.3985:0.1207:0.2362:0.2446	.	255;230	Q6P5W5;A6NDY5	S39A4_HUMAN;.	H	230;255;161	ENSP00000276833:P230H;ENSP00000301305:P255H;ENSP00000434512:P161H	ENSP00000276833:P230H	P	-	2	0	SLC39A4	145611206	0.002000	0.14202	0.000000	0.03702	0.037000	0.13140	-0.570000	0.05895	-0.723000	0.04915	-0.320000	0.08662	CCC	G|0.998;A|0.002		0.672	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1			T	145640398	G	T	145640398	3	4	39	1	0	0	0	0	1	0	0	0	14652	1232	43	4	1215	4	SLC39A4	8	145640398	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	505466	145640398	723624	55	3500											
TTC39B	158219	broad.mit.edu	37	chr9	15190552	15190552	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caatctaatccagatcttacCaagtattagggagatgtaag	15	11	8	7	0	2	2	0	0	2	2	3	3	3	2	2	1	1	2	2	1	7	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:15190552C>G	ENST00000512701.2	-	11	1141	c.1105G>C	c.(1105-1107)Ggt>Cgt	p.G369R	TTC39B_ENST00000355694.2_Splice_Site_p.G303R|TTC39B_ENST00000507285.1_Splice_Site_p.G204R|TTC39B_ENST00000507993.1_Splice_Site_p.G204R|TTC39B_ENST00000297615.5_Splice_Site_p.G300R|TTC39B_ENST00000380850.4_Splice_Site_p.G369R|TTC39B_ENST00000541445.1_Intron			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	369										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						CAGATCTTACCAAGTATTAGG	0.453																																					p.G369R													.	TTC39B-187	0			c.G1105C						.						86	80	82					9																	15190552		2203	4300	6503	SO:0001630	splice_region_variant	158219	exon11			TCTTACCAAGTAT	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"Tetratricopeptide (TTC) repeat domain containing"	23704	protein-coding gene	gene with protein product		613574	"chromosome 9 open reading frame 52"	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1105+1G>C	9.37:g.15190552C>G		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	64	5	NM_001168340	0	0	0	0	0	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Missense_Mutation	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	C	33	5.210679	0.95069	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.74419	0.3714	M	0.86097	2.795	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.996;0.996	T	0.74850	-0.3524	9	.	.	.	-12.0584	20.5666	0.99351	0.0:1.0:0.0:0.0	.	300;369;369;301;303	F5H705;E9PAQ9;E9PE60;A5PLN1;Q5VTQ0	.;.;.;.;TT39B_HUMAN	R	369;300;303;369;204;204	ENSP00000370231:G369R;ENSP00000297615:G300R;ENSP00000347920:G303R;ENSP00000422496:G369R;ENSP00000426539:G204R;ENSP00000423392:G204R	.	G	-	1	0	TTC39B	15180552	1.000000	0.71417	0.997000	0.53966	0.841000	0.47740	7.359000	0.79477	2.854000	0.98071	0.655000	0.94253	GGT	.		0.453	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	Missense_Mutation	G	15190552	C	G	15190552	5	3	39	1	0	0	0	0	0	0	1	0	16741	608	21	4	1004	4	TTC39B	9	15190552	Splice_Site	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		15190552	126022879	56	3501											
C9orf93	203238	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	15729747	15729747	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacagacaaaagaaggaacTagagctgcagtattctgaac	17	6	10	8	0	1	4	0	1	1	3	1	5	1	5	0	1	4	4	0	1	7	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:15729747T>C	ENST00000380701.3	+	16	2328	c.2000T>C	c.(1999-2001)cTa>cCa	p.L667P	CCDC171_ENST00000297641.3_Missense_Mutation_p.L667P	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	667																	AAGAAGGAACTAGAGCTGCAG	0.463																																					p.L667P		.											.	.	0			c.T2000C						.						96	99	98					9																	15729747		2203	4299	6502	SO:0001583	missense	203238	exon16			AGGAACTAGAGCT	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.2000T>C	9.37:g.15729747T>C	ENSP00000370077:p.Leu667Pro	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	120	35	NM_173550	0	0	1	1	0	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.037598	0.54896	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.25912	1.77;1.77	5.61	5.61	0.85477	.	0.250009	0.33650	N	0.004693	T	0.39253	0.1071	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76575	0.988;0.982;0.982	T	0.30563	-0.9974	10	0.72032	D	0.01	-6.1701	15.7924	0.78376	0.0:0.0:0.0:1.0	.	675;667;667	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	P	667	ENSP00000297641:L667P;ENSP00000370077:L667P	ENSP00000297641:L667P	L	+	2	0	C9orf93	15719747	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.833000	0.69349	2.130000	0.65690	0.477000	0.44152	CTA	.		0.463	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15729747	T	C	15729747	3	2	39	1	0	0	0	0	1	0	0	0	2512	1522	53	3	2058	3	C9orf93	9	15729747	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	539195	15729747	125483684	57	3502											
TLN1	7094	broad.mit.edu;bcgsc.ca	37	chr9	35698339	35698339	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgaagtcgtttcattgccTccgagtcctggtcagccttg	5	13	10	13	2	2	1	2	1	0	0	5	2	4	1	5	1	2	1	5	1	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:35698339T>G	ENST00000314888.9	-	55	7705	c.7352A>C	c.(7351-7353)gAg>gCg	p.E2451A	TLN1_ENST00000540444.1_Missense_Mutation_p.E2339A	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2451	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTTCATTGCCTCCGAGTCCTG	0.542																																					p.E2451A													.	TLN1-609	0			c.A7352C						.						89	67	74					9																	35698339		2203	4300	6503	SO:0001583	missense	7094	exon55			ATTGCCTCCGAGT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.7352A>C	9.37:g.35698339T>G	ENSP00000316029:p.Glu2451Ala	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	48	4	NM_006289	0	0	162	174	12	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.673464	0.47781	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.44083	0.93;0.93	4.94	4.94	0.65067	I/LWEQ (4);	0.307466	0.35555	N	0.003124	T	0.37598	0.1009	L	0.42245	1.32	0.48341	D	0.999636	B	0.14805	0.011	B	0.22880	0.042	T	0.15263	-1.0443	10	0.34782	T	0.22	-25.864	14.4791	0.67567	0.0:0.0:0.0:1.0	.	2451	Q9Y490	TLN1_HUMAN	A	2451;2339	ENSP00000316029:E2451A;ENSP00000442981:E2339A	ENSP00000316029:E2451A	E	-	2	0	TLN1	35688339	1.000000	0.71417	0.996000	0.52242	0.930000	0.56654	7.802000	0.85969	2.087000	0.62958	0.529000	0.55759	GAG	.		0.542	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		G	35698339	T	G	35698339	3	3	39	1	0	0	0	0	1	0	0	0	15979	1551	54	5	285	5	TLN1	9	35698339	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	19968592	35698339	105515092	58	3503											
NPR2	4882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35792786	35792786	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcgggtgctgtggcctcTggtttttcggctaagaatga	6	13	14	8	2	1	2	0	1	1	1	2	2	1	2	1	4	2	3	1	4	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:35792786T>C	ENST00000342694.2	+	1	636	c.381T>C	c.(379-381)tcT>tcC	p.S127S		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	127					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	CTGTGGCCTCTGGTTTTTCGG	0.602																																					p.S127S		.											.	NPR2-335	0			c.T381C						.						125	106	112					9																	35792786		2203	4300	6503	SO:0001819	synonymous_variant	4882	exon1			GGCCTCTGGTTTT	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.381T>C	9.37:g.35792786T>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	70	14	NM_003995	0	0	8	13	5	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1																																																																																			.		0.602	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			C	35792786	T	C	35792786	2	2	39	1	0	0	0	0	0	0	0	1	10621	1567	55	3		3	NPR2	9	35792786	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	94447	35792786	105420645	59	3504											
NPR2	4882	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	35800822	35800822	+	Frame_Shift_Del	DEL	C	C	-																															tgtgcctttgacttggacgaCccatcctgtgataaaagtgg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:35800822delC	ENST00000342694.2	+	6	1590	c.1335delC	c.(1333-1335)gacfs	p.D445fs		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	445					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	ACTTGGACGACCCATCCTGTG	0.582																																					p.D445fs		.											.	NPR2-335	0			c.1335delC						.						126	103	111					9																	35800822		2203	4300	6503	SO:0001589	frameshift_variant	4882	exon6			.	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"guanylate cyclase B"	108961	"acromesomelic dysplasia, Maroteaux type", "atrionatriuretic peptide receptor B", "natriuretic peptide receptor B"	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.1335delC	9.37:g.35800822delC	ENSP00000341083:p.Asp445fs	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	82	21	NM_003995	0	0	0	0	0	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Frame_Shift_Del	DEL	ENST00000342694.2	37	CCDS6590.1																																																																																			.		0.582	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			-	35800822	C	-	35800822	7	5	39	1	0	1	0	1	0	0	0	0	10621	506	18	0	1357	0	NPR2	9	35800822	Frame_Shift_Del	DEL	C	TCGA-B1-A655-01A-11D-A31Z-10	8036	35800822	105412609	60	3505											
OR1N2	138882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125315955	125315955	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgtgctgggtgctaacCaactgtcctgccctgatgca	6	11	13	11	0	0	1	0	1	0	0	1	1	1	1	3	2	6	3	3	2	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:125315955C>T	ENST00000373688.2	+	1	565	c.507C>T	c.(505-507)acC>acT	p.T169T		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						GGGTGCTAACCAACTGTCCTG	0.532																																					p.T169T		.											.	OR1N2-72	0			c.C507T						.						141	123	129					9																	125315955		2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			GCTAACCAACTGT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.507C>T	9.37:g.125315955C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_001004457	0	0	0	0	0	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	37	CCDS35123.1																																																																																			.		0.532	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			T	125315955	C	T	125315955	2	4	39	1	0	0	0	0	0	0	0	1	10996	581	21	2		2	OR1N2	9	125315955	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	89515133	125315955	15897476	61	3506											
MED27	9442	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134889753	134889753	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacaagagttgtgggctgAgcctttggtctacgtttggc	7	12	15	7	1	1	2	0	1	1	1	1	3	1	3	1	4	2	3	1	4	2	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:134889753A>G	ENST00000292035.5	-	3	513	c.450T>C	c.(448-450)gcT>gcC	p.A150A	MED27_ENST00000357028.2_Silent_p.A150A	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	150					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		TTGTGGGCTGAGCCTTTGGTC	0.428																																					p.A150A	Colon(41;784 923 6932 42329 52483)	.											.	MED27-69	0			c.T450C						.						152	129	137					9																	134889753		2203	4300	6503	SO:0001819	synonymous_variant	9442	exon3			GGGCTGAGCCTTT	AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.450T>C	9.37:g.134889753A>G		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	80	12	NM_001253881	0	0	6	14	8	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Silent	SNP	ENST00000292035.5	37	CCDS6945.1																																																																																			.		0.428	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269		G	134889753	A	G	134889753	2	3	39	1	0	0	0	0	0	0	0	1	9470	291	11	3		3	MED27	9	134889753	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	9573798	134889753	6323678	62	3507											
GJD4	219770	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	35896876	35896876	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttttcggccggctacatcatCcacctcctcctccggaccct	5	11	6	19	3	1	0	1	0	0	0	6	1	5	1	7	3	1	1	7	3	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:35896876C>A	ENST00000321660.1	+	2	593	c.435C>A	c.(433-435)atC>atA	p.I145I	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	145					cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GCTACATCATCCACCTCCTCC	0.692																																					p.I145I		.											.	GJD4-155	0			c.C435A						.						17	18	18					10																	35896876		2196	4293	6489	SO:0001819	synonymous_variant	219770	exon2			CATCATCCACCTC	AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291		"Ion channels / Gap junction proteins (connexins)"	23296	protein-coding gene	gene with protein product	"connexin 40.1"	611922				12477932	Standard	NM_153368		Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.435C>A	10.37:g.35896876C>A		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	23	8	NM_153368	0	0	0	0	0	Q8N2R7	Silent	SNP	ENST00000321660.1	37	CCDS7191.1																																																																																			.		0.692	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368		A	35896876	C	A	35896876	2	1	39	1	0	0	0	0	0	0	0	1	6439	845	30	4		4	GJD4	10	35896876	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		35896876	99637871	63	3508											
ADAMTS14	140766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	72513573	72513573	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggtgggtgacggaggagtGgggtgcctgcagccggagct	6	6	21	8	2	0	1	0	1	0	0	0	4	0	4	2	7	4	2	2	7	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:72513573G>T	ENST00000373207.1	+	19	2747	c.2747G>T	c.(2746-2748)tGg>tTg	p.W916L	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.W919L	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	916	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						ACGGAGGAGTGGGGTGCCTGC	0.622																																					p.W919L		.											.	ADAMTS14-232	0			c.G2756T						.						16	12	14					10																	72513573		2194	4295	6489	SO:0001583	missense	140766	exon19			AGGAGTGGGGTGC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2747G>T	10.37:g.72513573G>T	ENSP00000362303:p.Trp916Leu	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	39	8	NM_139155	0	0	0	0	0	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.956346	0.73902	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.74315	-0.83;-0.83	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	D	0.92195	0.7525	H	0.99325	4.515	0.58432	D	0.999995	D;D	0.89917	0.967;1.0	P;D	0.80764	0.897;0.994	D	0.95625	0.8684	10	0.87932	D	0	.	17.1757	0.86841	0.0:0.0:1.0:0.0	.	916;919	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	L	919;916	ENSP00000362304:W919L;ENSP00000362303:W916L	ENSP00000362303:W916L	W	+	2	0	ADAMTS14	72183579	1.000000	0.71417	0.963000	0.40424	0.270000	0.26580	9.601000	0.98297	2.378000	0.81104	0.563000	0.77884	TGG	.		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72513573	G	T	72513573	3	4	39	1	0	0	0	0	1	0	0	0	259	1357	47	4	2830	4	ADAMTS14	10	72513573	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	36616697	72513573	63021174	64	3509											
C10orf11	83938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	77818509	77818509	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgagaggaggcgttggtcAgaggagtcttcatgaaggtg	11	8	17	5	2	3	3	2	1	1	2	3	6	3	5	0	5	1	1	0	5	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:77818509A>G	ENST00000372499.1	+	4	615	c.400A>G	c.(400-402)Aga>Gga	p.R134G	C10orf11_ENST00000593699.1_3'UTR	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	134	LRRCT.				melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GGCGTTGGTCAGAGGAGTCTT	0.488																																					p.R134G		.											.	C10orf11-90	0			c.A400G						.						148	136	140					10																	77818509		2203	4300	6503	SO:0001583	missense	83938	exon4			TTGGTCAGAGGAG	AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"oculocutaneous albinism 7, autosomal recessive"	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.400A>G	10.37:g.77818509A>G	ENSP00000361577:p.Arg134Gly	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	89	13	NM_032024	0	0	24	49	25	B1AVW6	Missense_Mutation	SNP	ENST00000372499.1	37	CCDS7351.1	.	.	.	.	.	.	.	.	.	.	A	18.82	3.704846	0.68615	.	.	ENSG00000148655	ENST00000354343;ENST00000372499	T	0.37235	1.21	5.66	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.51702	0.1690	M	0.83012	2.62	0.41798	D	0.989901	P	0.41313	0.745	P	0.49226	0.603	T	0.56974	-0.7890	10	0.46703	T	0.11	-22.7506	12.4457	0.55649	0.8601:0.1398:0.0:0.0	.	134	Q9H2I8	CJ011_HUMAN	G	162;134	ENSP00000361577:R134G	ENSP00000346310:R162G	R	+	1	2	C10orf11	77488515	0.984000	0.35163	1.000000	0.80357	0.977000	0.68977	2.280000	0.43443	2.164000	0.68074	0.533000	0.62120	AGA	.		0.488	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024		G	77818509	A	G	77818509	3	3	39	1	0	0	0	0	1	0	0	0	1586	180	7	3	414	3	C10orf11	10	77818509	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	5304936	77818509	57716238	65	3510											
C10orf12	26148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	98744160	98744160	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggattcttagaaaatattccAatattcgaggaaagctcaga	16	11	8	6	1	2	2	1	0	1	2	4	5	3	4	1	2	1	1	1	2	7	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:98744160A>C	ENST00000286067.2	+	1	3120	c.3013A>C	c.(3013-3015)Aat>Cat	p.N1005H		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	1005										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		AAAATATTCCAATATTCGAGG	0.453																																					p.N1005H		.											.	C10orf12-92	0			c.A3013C						.						50	56	54					10																	98744160		2203	4300	6503	SO:0001583	missense	26148	exon1			TATTCCAATATTC	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.3013A>C	10.37:g.98744160A>C	ENSP00000286067:p.Asn1005His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	60	21	NM_015652	0	0	1	3	2	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.409208	0.42715	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.11169	2.8	5.71	4.57	0.56435	.	0.273469	0.25106	U	0.033088	T	0.19005	0.0456	L	0.47716	1.5	0.34487	D	0.70458	D	0.55385	0.971	P	0.53224	0.721	T	0.18777	-1.0326	10	0.72032	D	0.01	-16.6286	12.7429	0.57264	0.7424:0.2576:0.0:0.0	.	1005	Q8N655	CJ012_HUMAN	H	1005;839	ENSP00000286067:N1005H	ENSP00000286067:N1005H	N	+	1	0	C10orf12	98734150	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	5.768000	0.68858	0.989000	0.38761	-0.313000	0.08912	AAT	.		0.453	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		C	98744160	A	C	98744160	3	2	39	1	0	0	0	0	1	0	0	0	1593	130	5	5	3015	5	C10orf12	10	98744160	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	20925651	98744160	36790587	66	3511											
ERLIN1	10613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101935785	101935785	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggattttattgaagattaagGtcttgtcataatctgcagta	12	16	9	4	0	3	2	1	1	2	1	3	3	3	3	0	2	1	2	0	2	5	7	rs369477049		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:101935785G>C	ENST00000421367.2	-	5	3054	c.347C>G	c.(346-348)aCc>aGc	p.T116S	ERLIN1_ENST00000407654.3_Missense_Mutation_p.T116S	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	114					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		GAAGATTAAGGTCTTGTCATA	0.393																																					p.T116S		.											.	.	0			c.C347G						.						161	145	150					10																	101935785		2203	4300	6503	SO:0001583	missense	10613	exon5			ATTAAGGTCTTGT	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"	611604	"chromosome 10 open reading frame 69", "SPFH domain family, member 1"	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.347C>G	10.37:g.101935785G>C	ENSP00000410964:p.Thr116Ser	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	97	35	NM_006459	0	0	13	26	13	B0QZ42|Q53HV0	Missense_Mutation	SNP	ENST00000421367.2	37	CCDS7487.2	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053929	0.55218	.	.	ENSG00000107566	ENST00000421367;ENST00000407654;ENST00000370410;ENST00000370408	D;D;D	0.94417	-3.42;-3.42;-3.42	4.96	4.96	0.65561	.	0.114986	0.64402	U	0.000019	D	0.95020	0.8388	M	0.78456	2.415	0.58432	D	0.999999	B;B	0.29270	0.24;0.24	B;B	0.42959	0.403;0.403	D	0.92339	0.5880	10	0.09590	T	0.72	-17.5613	16.0678	0.80897	0.0:0.0:1.0:0.0	.	114;116	O75477;D3DR65	ERLN1_HUMAN;.	S	116;116;32;116	ENSP00000410964:T116S;ENSP00000384900:T116S;ENSP00000359436:T116S	ENSP00000359436:T116S	T	-	2	0	ERLIN1	101925775	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.771000	0.98977	2.456000	0.83038	0.561000	0.74099	ACC	.		0.393	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459		C	101935785	G	C	101935785	3	2	39	1	0	0	0	0	1	0	0	0	5245	1261	44	4	727	4	ERLIN1	10	101935785	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	3191625	101935785	33598962	67	3512											
DOCK1	1793	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	128830577	128830577	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgctccaccaaactgacTcagaacggtgcgttcgagag	10	8	12	11	3	1	3	1	1	0	2	3	4	2	3	2	1	4	2	2	1	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:128830577T>A	ENST00000280333.6	+	18	1951	c.1842T>A	c.(1840-1842)acT>acA	p.T614T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	614					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CCAAACTGACTCAGAACGGTG	0.582																																					p.T614T													.	DOCK1-698	0			c.T1842A						.						20	20	20					10																	128830577		2118	4225	6343	SO:0001819	synonymous_variant	1793	exon18			ACTGACTCAGAAC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1842T>A	10.37:g.128830577T>A		Somatic	98	1		WXS	Illumina HiSeq	Phase_I	96	36	NM_001380	0	0	0	0	0	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				.		0.582	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	128830577	T	A	128830577	2	1	39	1	0	0	0	0	0	0	0	1	4695	1538	54	5		5	DOCK1	10	128830577	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	26894792	128830577	6704170	68	3513											
MUC2	4583	broad.mit.edu	37	chr11	1092973	1092973	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggtgaccccaaccccaacaCccaccggcacacagacccca	12	1	6	22	2	0	2	0	1	0	1	0	2	0	2	8	2	2	1	8	2	2	0	rs55847666		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:1092973C>T	ENST00000441003.2	+	30	4819	c.4792C>T	c.(4792-4794)Ccc>Tcc	p.P1598S	MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.P1598S(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aaccccaacacccaccggcac	0.637																																					p.P1598S													.	MUC2-90	1	Substitution - Missense(1)	endometrium(1)	c.C4792T						.						47	83	70					11																	1092973		1782	3238	5020	SO:0001583	missense	4583	exon30			CCAACACCCACCG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4792C>T	11.37:g.1092973C>T	ENSP00000415183:p.Pro1598Ser	Somatic	55	2		WXS	Illumina HiSeq	Phase_I	74	4	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.622	-0.077443	0.07184	.	.	ENSG00000198788	ENST00000441003	T	0.13778	2.56	1.75	-2.88	0.05682	.	.	.	.	.	T	0.04363	0.0120	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.43686	-0.9376	8	0.07482	T	0.82	.	3.4241	0.07403	0.4105:0.429:0.0:0.1605	rs55847666	1598	E7EUV1	.	S	1598	ENSP00000415183:P1598S	ENSP00000415183:P1598S	P	+	1	0	MUC2	1082973	0.007000	0.16637	0.000000	0.03702	0.120000	0.20174	0.230000	0.17852	-0.314000	0.08716	0.121000	0.15741	CCC	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092973	C	T	1092973	3	4	39	1	0	0	0	0	1	0	0	0	10000	507	18	2	4910	2	MUC2	11	1092973	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		1092973	133913543	69	3514											
KRTAP5-5	439915	bcgsc.ca	37	chr11	1651127	1651127	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtggaggccgtggctcCggctgtgggggctgtggctc	1	9	21	10	2	0	0	0	0	0	0	2	1	1	1	2	8	0	5	2	8	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:1651127C>T	ENST00000399676.2	+	1	95	c.57C>T	c.(55-57)tcC>tcT	p.S19S		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	19						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		gccgtggctccggctgtgggg	0.697																																					p.S19S													.	KRTAP5-5-23	0			c.C57T						.																																			SO:0001819	synonymous_variant	439915	exon1			TGGCTCCGGCTGT	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"Keratin associated proteins"	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.57C>T	11.37:g.1651127C>T		Somatic	172	3		WXS	Illumina HiSeq	Phase_1	217	14	NM_001001480	0	0	0	0	0	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			.		0.697	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			T	1651127	C	T	1651127	2	4	39	1	0	0	0	0	0	0	0	1	8585	639	23	1		1	KRTAP5-5	11	1651127	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	558154	1651127	133355389	70	3515											
HIPK3	10114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	33374883	33374883	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccacctgttagcctcTccgtgtacctcaagacctat	7	11	8	15	1	2	1	1	0	1	1	3	1	2	1	6	1	2	2	6	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:33374883T>C	ENST00000303296.4	+	17	3722	c.3417T>C	c.(3415-3417)tcT>tcC	p.S1139S	HIPK3_ENST00000379016.3_Silent_p.S1118S|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000456517.1_Silent_p.S1118S|HIPK3_ENST00000525975.1_Silent_p.S1118S	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	1139					apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TGTTAGCCTCTCCGTGTACCT	0.517																																					p.S1139S		.											.	HIPK3-336	0			c.T3417C						.						216	178	191					11																	33374883		2202	4298	6500	SO:0001819	synonymous_variant	10114	exon17			AGCCTCTCCGTGT	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"homeodomain-interacting protein kinase 3"			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.3417T>C	11.37:g.33374883T>C		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	112	31	NM_005734	0	0	34	66	32	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Silent	SNP	ENST00000303296.4	37	CCDS7884.1																																																																																			.		0.517	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33374883	T	C	33374883	2	2	39	1	0	0	0	0	0	0	0	1	7139	1538	54	3		3	HIPK3	11	33374883	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	31723756	33374883	101631633	71	3516											
KIAA0652	9776	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	46666907	46666907	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agactgtccaagtgattgtcCaggctcggcttggtgaaaag	10	10	13	8	1	0	3	0	2	0	1	3	3	2	3	2	3	0	2	2	3	3	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:46666907C>T	ENST00000434074.1	+	3	777	c.88C>T	c.(88-90)Cag>Tag	p.Q30*	ATG13_ENST00000451945.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000528494.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000359513.4_Nonsense_Mutation_p.Q30*|ATG13_ENST00000524625.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000529655.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000530500.1_5'UTR|ATG13_ENST00000526508.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000312040.4_Nonsense_Mutation_p.Q30*	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	30					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						AGTGATTGTCCAGGCTCGGCT	0.373																																					p.Q30X		.											.	ATG13-68	0			c.C88T						.						95	90	91					11																	46666907		2201	4299	6500	SO:0001587	stop_gained	9776	exon4			ATTGTCCAGGCTC	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"KIAA0652", "ATG13 autophagy related 13 homolog (S. cerevisiae)"	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.88C>T	11.37:g.46666907C>T	ENSP00000400642:p.Gln30*	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	91	5	NM_001142673	0	0	45	47	2	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Nonsense_Mutation	SNP	ENST00000434074.1	37	CCDS44582.1	.	.	.	.	.	.	.	.	.	.	C	37	6.442003	0.97568	.	.	ENSG00000175224	ENST00000395549;ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000533325;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000526078	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-10.2057	19.4568	0.94895	0.0:1.0:0.0:0.0	.	.	.	.	X	30	.	ENSP00000310321:Q30X	Q	+	1	0	ATG13	46623483	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.103000	0.77014	2.832000	0.97577	0.655000	0.94253	CAG	.		0.373	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		T	46666907	C	T	46666907	4	4	39	1	0	0	0	0	0	1	0	0	8209	595	21	2	94	2	KIAA0652	11	46666907	Nonsense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	13292024	46666907	88339609	72	3517											
PCNXL3	399909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65397996	65397996	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagtacgtgctggagggctAtagcattagtgacaataatg	13	10	12	6	1	0	1	0	1	0	0	0	2	0	2	0	2	3	4	0	2	7	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:65397996A>C	ENST00000355703.3	+	27	4930	c.4391A>C	c.(4390-4392)tAt>tCt	p.Y1464S	PCNXL3_ENST00000531280.1_3'UTR	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1464						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CTGGAGGGCTATAGCATTAGT	0.572																																					p.Y1464S		.											.	PCNXL3-46	0			c.A4391C						.						86	92	90					11																	65397996		2116	4217	6333	SO:0001583	missense	399909	exon27			AGGGCTATAGCAT	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.4391A>C	11.37:g.65397996A>C	ENSP00000347931:p.Tyr1464Ser	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	122	41	NM_032223	0	0	10	17	7	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559339	0.86335	.	.	ENSG00000197136	ENST00000355703	T	0.23552	1.9	5.02	5.02	0.67125	.	0.072055	0.56097	D	0.000021	T	0.55657	0.1934	M	0.88450	2.955	0.51767	D	0.999931	D;D	0.71674	0.982;0.998	D;D	0.73708	0.967;0.981	T	0.64516	-0.6389	10	0.87932	D	0	.	12.7937	0.57549	1.0:0.0:0.0:0.0	.	351;1464	Q9H6A9-3;Q9H6A9	.;PCX3_HUMAN	S	1464	ENSP00000347931:Y1464S	ENSP00000347931:Y1464S	Y	+	2	0	PCNXL3	65154572	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.753000	0.91637	2.131000	0.65755	0.529000	0.55759	TAT	.		0.572	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		C	65397996	A	C	65397996	3	2	39	1	0	0	0	0	1	0	0	0	11619	449	16	5	4497	5	PCNXL3	11	65397996	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	18731089	65397996	69608520	73	3518											
MRE11A	4361	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr11	94225958	94225958	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggtgcttacagtgcatctgCagtactcatttttatggtca	9	15	9	8	0	3	0	2	0	1	0	3	0	3	0	0	2	5	4	0	2	3	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:94225958C>A	ENST00000323929.3	-	2	232	c.10G>T	c.(10-12)Gca>Tca	p.A4S	MRE11A_ENST00000540013.1_Missense_Mutation_p.A4S|MRE11A_ENST00000393241.4_Missense_Mutation_p.A4S|ANKRD49_ENST00000540349.1_5'Flank|ANKRD49_ENST00000544612.1_5'Flank|ANKRD49_ENST00000544253.1_5'Flank|MRE11A_ENST00000323977.3_Missense_Mutation_p.A4S|MRE11A_ENST00000407439.3_5'UTR|MRE11A_ENST00000536144.1_5'UTR	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	4					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				AGTGCATCTGCAGTACTCATT	0.423								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																												p.A4S		.											.	MRE11A-722	0			c.G10T						.						113	103	107					11																	94225958		2201	4298	6499	SO:0001583	missense	4361	exon2	Familial Cancer Database	ATLD	CATCTGCAGTACT	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.10G>T	11.37:g.94225958C>A	ENSP00000325863:p.Ala4Ser	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	72	7	NM_005591	0	0	1	1	0	O43475	Missense_Mutation	SNP	ENST00000323929.3	37	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	C	7.672	0.687277	0.14973	.	.	ENSG00000020922	ENST00000323929;ENST00000323977;ENST00000393241;ENST00000540013;ENST00000536754;ENST00000538923	T;T;T;T;T	0.76709	-0.84;-0.82;-0.84;-1.03;-1.04	5.01	-0.599	0.11645	.	0.961041	0.08657	N	0.913092	T	0.51109	0.1655	N	0.11255	0.115	0.23572	N	0.997382	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.002	T	0.30416	-0.9979	10	0.09843	T	0.71	.	2.2535	0.04049	0.1419:0.4157:0.2764:0.1661	.	4;4	P49959-2;P49959	.;MRE11_HUMAN	S	4	ENSP00000325863:A4S;ENSP00000326094:A4S;ENSP00000376933:A4S;ENSP00000440986:A4S;ENSP00000439511:A4S	ENSP00000325863:A4S	A	-	1	0	MRE11A	93865606	0.867000	0.29959	0.427000	0.26684	0.159000	0.22180	-0.223000	0.09177	-0.420000	0.07427	0.561000	0.74099	GCA	.		0.423	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		A	94225958	C	A	94225958	3	1	39	1	0	0	0	0	1	0	0	0	9784	710	25	4	2192	4	MRE11A	11	94225958	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	28827962	94225958	40780558	74	3519											
PVRL1	5818	broad.mit.edu	37	chr11	119545966	119545968	+	In_Frame_Del	DEL	GAA	GAA	-																															ctgtagttgatgggtcccttGaagaagagggttctgttctg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:119545966_119545968delGAA	ENST00000264025.3	-	5	1434_1436	c.904_906delTTC	c.(904-906)ttcdel	p.F302del	PVRL1_ENST00000340882.2_In_Frame_Del_p.F302del|PVRL1_ENST00000341398.2_In_Frame_Del_p.F302del|PVRL1_ENST00000524510.1_5'Flank	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	302	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		TGGGTCCCTTGAAGAAGAGGGTT	0.567																																					p.302_302del													.	PVRL1-90	0			c.904_906del						.																																			SO:0001651	inframe_deletion	5818	exon5			TCCCTTGAAGAAG	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9706	protein-coding gene	gene with protein product	"nectin"	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.904_906delTTC	11.37:g.119545969_119545971delGAA	ENSP00000264025:p.Phe302del	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	113	7	NM_002855	0	0	0	0	0	O75465|Q2M3D3|Q9HBE6|Q9HBW2	In_Frame_Del	DEL	ENST00000264025.3	37	CCDS8426.1																																																																																			.		0.567	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			-	119545968	GAA	-	119545966	7	5	39	1	0	1	0	1	0	0	0	0	12871	1281	45	0	1101	0	PVRL1	11	119545966	In_Frame_Del	DEL	GAA	TCGA-B1-A655-01A-11D-A31Z-10	25320008	119545966	15460550	75	3520											
ASB8	140461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48543736	48543736	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaagcctcatctttctctgCtgcatagtggagggctgttc	7	13	10	11	0	3	0	1	0	2	0	5	1	3	1	1	2	3	4	1	2	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr12:48543736C>T	ENST00000317697.3	-	4	449	c.280G>A	c.(280-282)Gca>Aca	p.A94T	ASB8_ENST00000536953.1_3'UTR|ASB8_ENST00000536071.1_3'UTR|ASB8_ENST00000539528.1_3'UTR|ASB8_ENST00000535055.1_3'UTR|ASB8_ENST00000537754.1_5'UTR|ASB8_ENST00000536549.1_Missense_Mutation_p.A94T	NM_024095.3	NP_077000.1	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box containing 8	94					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|large_intestine(2)|lung(5)|soft_tissue(1)	11						TCTTTCTCTGCTGCATAGTGG	0.498																																					p.A94T		.											.	ASB8-226	0			c.G280A						.						67	62	64					12																	48543736		2203	4300	6503	SO:0001583	missense	140461	exon4			TCTCTGCTGCATA	AK024908	CCDS8761.1	12q13.12	2013-01-10	2011-01-25			ENSG00000177981		"Ankyrin repeat domain containing"	17183	protein-coding gene	gene with protein product		615053	"ankyrin repeat and SOCS box-containing 8"			12076535	Standard	NM_024095		Approved	MGC5540, FLJ21255	uc001rrh.3	Q9H765		ENST00000317697.3:c.280G>A	12.37:g.48543736C>T	ENSP00000320893:p.Ala94Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_024095	0	0	30	52	22	A8K1P2|Q547Q2	Missense_Mutation	SNP	ENST00000317697.3	37	CCDS8761.1	.	.	.	.	.	.	.	.	.	.	C	32	5.172801	0.94807	.	.	ENSG00000177981	ENST00000317697;ENST00000536549;ENST00000446549;ENST00000539503;ENST00000545791;ENST00000540212	T;T;T;T;T	0.71934	-0.61;-0.61;-0.6;-0.37;-0.37	5.3	5.3	0.74995	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.81269	0.4787	L	0.49126	1.545	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.81008	-0.1127	10	0.51188	T	0.08	-9.6125	18.938	0.92594	0.0:1.0:0.0:0.0	.	94	Q9H765	ASB8_HUMAN	T	94	ENSP00000320893:A94T;ENSP00000445622:A94T;ENSP00000444093:A94T;ENSP00000437769:A94T;ENSP00000442639:A94T	ENSP00000320893:A94T	A	-	1	0	ASB8	46830003	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.227000	0.78070	2.648000	0.89879	0.563000	0.77884	GCA	.		0.498	ASB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396497.1			T	48543736	C	T	48543736	3	4	39	1	0	0	0	0	1	0	0	0	1030	797	28	2	590	2	ASB8	12	48543736	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		48543736	85308159	76	3521											
GALNT6	11226	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	51758036	51758036	+	Frame_Shift_Del	DEL	A	A	-																															tggacgggcttggcgaactcAaaagtattaaggtcgatggt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr12:51758036delA	ENST00000543196.2	-	5	1123	c.918delT	c.(916-918)tttfs	p.F306fs	GALNT6_ENST00000356317.3_Frame_Shift_Del_p.F306fs			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	306					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TGGCGAACTCAAAAGTATTAA	0.577																																					p.F306fs		.											.	GALNT6-92	0			c.918delT						.						91	85	87					12																	51758036		2203	4300	6503	SO:0001589	frameshift_variant	11226	exon6			.	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.918delT	12.37:g.51758036delA	ENSP00000444171:p.Phe306fs	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	110	35	NM_007210	0	0	0	0	0	Q8IYH4|Q9H6G2|Q9UIV5	Frame_Shift_Del	DEL	ENST00000543196.2	37	CCDS8813.1																																																																																			.		0.577	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		-	51758036	A	-	51758036	7	5	39	1	0	1	0	1	0	0	0	0	6237	127	5	0	978	0	GALNT6	12	51758036	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	3214300	51758036	82093859	77	3522											
PARP4	143	ucsc.edu	37	chr13	25020900	25020900	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attagtgcacacagagttgcCtgaaatggggaaaaaaataa	18	8	10	5	0	0	2	0	1	0	1	0	3	0	3	1	2	2	2	1	2	6	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr13:25020900C>T	ENST00000381989.3	-	27	3391		c.e27-1			NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4						cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ACAGAGTTGCCTGAAATGGGG	0.373																																					.													.	PARP4-94	0			c.3286-1G>A						.						62	56	58					13																	25020900		2202	4300	6502	SO:0001630	splice_region_variant	143	exon28			AGTTGCCTGAAAT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3286-1G>A	13.37:g.25020900C>T		Somatic	170	0		WXS	Illumina HiSeq		133	1	NM_006437	0	0	0	0	0	O75903|Q14682|Q5QNZ9|Q9H1M6	Splice_Site	SNP	ENST00000381989.3	37	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660048	0.47572	.	.	ENSG00000102699	ENST00000381989	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.593	0.76554	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PARP4	23918900	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	6.055000	0.71103	2.615000	0.88500	0.644000	0.83932	.	.		0.373	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	Intron	T	25020900	C	T	25020900	5	4	39	1	0	0	0	0	0	0	1	0	11489	695	24	2	1921	2	PARP4	13	25020900	Splice_Site	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		25020900	90148978	78	3523											
ARHGAP5	394	hgsc.bcm.edu;bcgsc.ca	37	chr14	32560648	32560648	+	Frame_Shift_Del	DEL	A	A	-																															caagcctaaaattattccctAtttggatgcttataaaacac																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr14:32560648delA	ENST00000345122.3	+	2	1088	c.773delA	c.(772-774)tatfs	p.Y258fs	ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.Y258fs|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.Y258fs|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.Y258fs	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	258					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		ATTATTCCCTATTTGGATGCT	0.358																																					p.Y258fs	NSCLC(9;77 350 3443 29227 41353)	.											.	ARHGAP5-94	0			c.773delA						.						115	131	125					14																	32560648		2203	4299	6502	SO:0001589	frameshift_variant	394	exon2			.	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.773delA	14.37:g.32560648delA	ENSP00000371897:p.Tyr258fs	Somatic	279	0		WXS	Illumina HiSeq	Phase_I	167	85	NM_001173	0	0	0	0	0	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Frame_Shift_Del	DEL	ENST00000345122.3	37	CCDS32062.1																																																																																			.		0.358	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		-	32560648	A	-	32560648	7	5	39	1	0	1	0	1	0	0	0	0	886	449	16	0	775	0	ARHGAP5	14	32560648	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10		32560648	74788892	79	3524											
RGS6	9628	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	72939649	72939649	+	Frame_Shift_Del	DEL	C	C	-																															gaacgagccttttgggatgtCcacaggcctgtggtgagaaa																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr14:72939649delC	ENST00000553530.1	+	9	813	c.606delC	c.(604-606)gtcfs	p.V202fs	RGS6_ENST00000553525.1_Frame_Shift_Del_p.V202fs|RGS6_ENST00000434263.2_Frame_Shift_Del_p.V133fs|RGS6_ENST00000406236.4_Frame_Shift_Del_p.V202fs|RGS6_ENST00000404301.2_Frame_Shift_Del_p.V202fs|RGS6_ENST00000355512.6_Frame_Shift_Del_p.V202fs|RGS6_ENST00000554782.1_Frame_Shift_Del_p.V63fs|RGS6_ENST00000407322.4_Frame_Shift_Del_p.V202fs|RGS6_ENST00000402788.2_Frame_Shift_Del_p.V202fs|RGS6_ENST00000343854.6_Frame_Shift_Del_p.V202fs|RGS6_ENST00000553690.1_3'UTR|RGS6_ENST00000555571.1_Frame_Shift_Del_p.V202fs|RGS6_ENST00000556437.1_Frame_Shift_Del_p.V202fs	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	202					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		TTTGGGATGTCCACAGGCCTG	0.373																																					p.V202fs	Ovarian(143;1926 2468 21071 48641)	.											.	RGS6-227	0			c.606delC						.						137	153	148					14																	72939649		2203	4300	6503	SO:0001589	frameshift_variant	9628	exon9			.	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"Regulators of G-protein signaling"	10002	protein-coding gene	gene with protein product		603894	"regulator of G-protein signalling 6"			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.606delC	14.37:g.72939649delC	ENSP00000452331:p.Val202fs	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	150	70	NM_001204424	0	0	0	0	0	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Frame_Shift_Del	DEL	ENST00000553530.1	37	CCDS9808.1																																																																																			.		0.373	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			-	72939649	C	-	72939649	7	5	39	1	0	1	0	1	0	0	0	0	13341	842	30	0	636	0	RGS6	14	72939649	Frame_Shift_Del	DEL	C	TCGA-B1-A655-01A-11D-A31Z-10	40379001	72939649	34409891	80	3525											
SERPINA12	145264	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	94964196	94964196	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgggttttttgactgataAagtcattgatctgcttctga	9	17	9	6	0	3	4	1	4	2	0	3	4	3	4	0	1	1	2	0	1	2	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr14:94964196A>C	ENST00000341228.2	-	3	1334	c.539T>G	c.(538-540)tTt>tGt	p.F180C	SERPINA12_ENST00000556881.1_Missense_Mutation_p.F180C	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	180					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		TTGACTGATAAAGTCATTGAT	0.393																																					p.F180C		.											.	SERPINA12-310	0			c.T539G						.						93	91	92					14																	94964196		2203	4300	6503	SO:0001583	missense	145264	exon3			CTGATAAAGTCAT	AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.539T>G	14.37:g.94964196A>C	ENSP00000342109:p.Phe180Cys	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	82	39	NM_173850	0	0	0	0	0		Missense_Mutation	SNP	ENST00000341228.2	37	CCDS9926.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508445	0.27036	.	.	ENSG00000165953	ENST00000556881;ENST00000341228	D;D	0.84589	-1.87;-1.87	5.49	4.34	0.51931	Serpin domain (3);	0.119433	0.38111	N	0.001802	D	0.87692	0.6241	L	0.46819	1.47	0.20196	N	0.99993	D	0.71674	0.998	P	0.61275	0.886	T	0.80627	-0.1298	10	0.87932	D	0	.	11.607	0.51037	0.1385:0.0:0.0:0.8615	.	180	Q8IW75	SPA12_HUMAN	C	180	ENSP00000451738:F180C;ENSP00000342109:F180C	ENSP00000342109:F180C	F	-	2	0	SERPINA12	94033949	0.995000	0.38212	0.009000	0.14445	0.037000	0.13140	3.607000	0.54102	0.903000	0.36546	-0.339000	0.08088	TTT	.		0.393	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850		C	94964196	A	C	94964196	3	2	39	1	0	0	0	0	1	0	0	0	14121	14	1	5	721	5	SERPINA12	14	94964196	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	22024547	94964196	12385344	81	3526											
RASGRP1	10125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	38798102	38798102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catagatttcatcctcagtgTagtaaagatccagggataac	14	11	8	8	0	2	2	2	0	0	2	4	3	4	3	2	1	1	2	2	1	5	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:38798102T>C	ENST00000310803.5	-	10	1439	c.1262A>G	c.(1261-1263)tAc>tGc	p.Y421C	RP11-102L12.2_ENST00000560231.1_RNA|RASGRP1_ENST00000558164.1_Missense_Mutation_p.Y421C|RASGRP1_ENST00000450598.2_Missense_Mutation_p.Y421C|RASGRP1_ENST00000539159.1_Missense_Mutation_p.Y373C|RASGRP1_ENST00000561180.1_Missense_Mutation_p.Y472C|RASGRP1_ENST00000559830.1_Missense_Mutation_p.Y421C	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	421	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		ATCCTCAGTGTAGTAAAGATC	0.448																																					p.Y421C		.											.	RASGRP1-697	0			c.A1262G						.						75	74	74					15																	38798102		1892	4109	6001	SO:0001583	missense	10125	exon10			TCAGTGTAGTAAA	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1262A>G	15.37:g.38798102T>C	ENSP00000310244:p.Tyr421Cys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	68	25	NM_001128602	0	0	3	7	4	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	37	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.649116	0.67358	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.6	4.6	0.57074	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.69351	0.3101	M	0.79805	2.47	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;D	0.91635	0.999;0.976;0.989;0.995	T	0.74278	-0.3717	10	0.62326	D	0.03	-19.3572	14.1614	0.65450	0.0:0.0:0.0:1.0	.	421;421;421;421	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	C	421;421;421;421;373;421;421	ENSP00000310244:Y421C;ENSP00000388540:Y421C;ENSP00000444762:Y373C;ENSP00000413105:Y421C	ENSP00000310244:Y421C	Y	-	2	0	RASGRP1	36585394	1.000000	0.71417	0.998000	0.56505	0.724000	0.41520	7.525000	0.81892	1.909000	0.55274	0.533000	0.62120	TAC	.		0.448	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		C	38798102	T	C	38798102	3	2	39	1	0	0	0	0	1	0	0	0	13106	1638	57	3	1163	3	RASGRP1	15	38798102	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		38798102	63733290	82	3527											
DISP2	85455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40660678	40660678	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acactggcgaccctctggacCctcgtagcaacagcagcctg	9	6	10	16	2	1	0	0	0	1	0	2	2	1	1	3	2	4	3	3	2	2	1	rs375551948		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:40660678C>G	ENST00000267889.3	+	8	2452	c.2365C>G	c.(2365-2367)Cct>Gct	p.P789A	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	789					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CCCTCTGGACCCTCGTAGCAA	0.687																																					p.P789A		.											.	DISP2-92	0			c.C2365G						.						76	84	81					15																	40660678		2203	4300	6503	SO:0001583	missense	85455	exon8			CTGGACCCTCGTA	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2365C>G	15.37:g.40660678C>G	ENSP00000267889:p.Pro789Ala	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	66	19	NM_033510	0	0	0	0	0	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.158992	0.57368	.	.	ENSG00000140323	ENST00000267889	T	0.30981	1.51	5.14	4.2	0.49525	.	0.052280	0.85682	D	0.000000	T	0.58119	0.2100	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63651	-0.6589	10	0.48119	T	0.1	-12.1506	14.8747	0.70485	0.1445:0.8555:0.0:0.0	.	789	A7MBM2	DISP2_HUMAN	A	789	ENSP00000267889:P789A	ENSP00000267889:P789A	P	+	1	0	DISP2	38447970	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	7.645000	0.83430	1.343000	0.45638	0.561000	0.74099	CCT	.		0.687	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		G	40660678	C	G	40660678	3	3	39	1	0	0	0	0	1	0	0	0	4551	623	22	4	2395	4	DISP2	15	40660678	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	1862576	40660678	61870714	83	3528											
MGA	23269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42005518	42005518	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tggttgtacttgtttgaaaaGaaaagttgtacttgttaaag	13	16	10	2	0	0	2	0	1	0	1	0	2	0	2	0	1	2	6	0	1	8	8			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:42005518G>C	ENST00000570161.1	+	8	3254	c.3254G>C	c.(3253-3255)aGa>aCa	p.R1085T	MGA_ENST00000389936.4_Missense_Mutation_p.R1085T|MGA_ENST00000219905.7_Missense_Mutation_p.R1085T|MGA_ENST00000545763.1_Missense_Mutation_p.R1085T|MGA_ENST00000566586.1_Missense_Mutation_p.R1085T			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGTTTGAAAAGAAAAGTTGTA	0.458																																					p.R1085T		.											.	MGA-522	0			c.G3254C						.						98	94	96					15																	42005518		1937	4124	6061	SO:0001583	missense	23269	exon9			TGAAAAGAAAAGT	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.3254G>C	15.37:g.42005518G>C	ENSP00000457035:p.Arg1085Thr	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	80	24	NM_001080541	0	0	1	2	1	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245765	0.80024	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.17370	2.28;2.28;2.28	5.75	5.75	0.90469	.	0.177622	0.46758	D	0.000265	T	0.28433	0.0703	L	0.27053	0.805	0.35184	D	0.772759	D;D	0.76494	0.997;0.999	D;D	0.73708	0.981;0.931	T	0.25779	-1.0122	10	0.87932	D	0	.	13.1821	0.59660	0.0727:0.0:0.9273:0.0	.	1085;1085	F5H7K2;E7ENI0	.;.	T	1085	ENSP00000219905:R1085T;ENSP00000374586:R1085T;ENSP00000442467:R1085T	ENSP00000219905:R1085T	R	+	2	0	MGA	39792810	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.511000	0.53400	2.716000	0.92895	0.655000	0.94253	AGA	.		0.458	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	42005518	G	C	42005518	3	2	39	1	0	0	0	0	1	0	0	0	9565	942	33	4	3284	4	MGA	15	42005518	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	1344840	42005518	60525874	84	3529											
CEP152	22995	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	49074426	49074426	+	Splice_Site	DEL	C	C	-																															tgagccacctcttgtactgaCcctgcagaggaaagaaccat																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:49074426delC	ENST00000380950.2	-	11	1510	c.1323delG	c.(1321-1323)ggg>gg	p.G441fs	CEP152_ENST00000399334.3_Splice_Site_p.G441fs|CEP152_ENST00000325747.5_Splice_Site_p.G348fs|RP11-485O10.2_ENST00000558304.1_RNA	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	441					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		CTTGTACTGACCCTGCAGAGG	0.443																																					p.G441fs		.											.	CEP152-70	0			c.1323delG						.						86	82	83					15																	49074426		1973	4175	6148	SO:0001630	splice_region_variant	22995	exon11			.	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.1322-1G>-	15.37:g.49074426delC		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	30	10	NM_014985	0	0	0	0	0	E7ER66|Q17RV1|Q6NTA0	Frame_Shift_Del	DEL	ENST00000380950.2	37	CCDS58361.1																																																																																			.		0.443	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	Frame_Shift_Del	-	49074426	C	-	49074426	8	5	39	1	0	1	0	1	0	0	1	0	3254	521	18	0	3705	0	CEP152	15	49074426	Splice_Site	DEL	C	TCGA-B1-A655-01A-11D-A31Z-10	7068908	49074426	53456966	85	3530											
ALPK3	57538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	85400827	85400827	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggtccccggagctgtgAccctggcctcatagattccc	6	8	10	17	1	1	2	1	1	0	1	3	3	3	3	6	3	1	1	6	3	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:85400827A>T	ENST00000258888.5	+	6	3631	c.3464A>T	c.(3463-3465)gAc>gTc	p.D1155V		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1155					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CGGAGCTGTGACCCTGGCCTC	0.627																																					p.D1155V		.											.	ALPK3-337	0			c.A3464T						.						42	49	47					15																	85400827		2203	4299	6502	SO:0001583	missense	57538	exon6			GCTGTGACCCTGG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3464A>T	15.37:g.85400827A>T	ENSP00000258888:p.Asp1155Val	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_020778	0	0	26	49	23	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.792367	0.70452	.	.	ENSG00000136383	ENST00000258888	T	0.68624	-0.34	5.17	5.17	0.71159	.	0.513935	0.19872	N	0.104179	T	0.72590	0.3479	L	0.32530	0.975	0.54753	D	0.999988	D	0.89917	1.0	D	0.85130	0.997	T	0.74607	-0.3609	10	0.72032	D	0.01	-24.6636	11.4077	0.49908	1.0:0.0:0.0:0.0	.	1155	Q96L96	ALPK3_HUMAN	V	1155	ENSP00000258888:D1155V	ENSP00000258888:D1155V	D	+	2	0	ALPK3	83201831	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.636000	0.46545	1.958000	0.56883	0.460000	0.39030	GAC	.		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		T	85400827	A	T	85400827	3	4	39	1	0	0	0	0	1	0	0	0	546	275	10	5	3486	5	ALPK3	15	85400827	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	36326401	85400827	17130565	86	3531											
CACNA1H	8912	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	1268594	1268594	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgcctgcctcggcgcccCacccccgcccgctgcaggag	3	5	13	20	4	0	0	0	0	0	0	1	1	0	1	7	3	3	2	7	3	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr16:1268594C>A	ENST00000348261.5	+	33	6078	c.5830C>A	c.(5830-5832)Cac>Aac	p.H1944N	CACNA1H_ENST00000358590.4_Missense_Mutation_p.H1938N|CACNA1H_ENST00000565831.1_Missense_Mutation_p.H1938N	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1944					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CTCGGCGCCCCACCCCCGCCC	0.662																																					p.H1944N		.											.	CACNA1H-67	0			c.C5830A						.						14	17	16					16																	1268594		1988	4120	6108	SO:0001583	missense	8912	exon33			GCGCCCCACCCCC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5830C>A	16.37:g.1268594C>A	ENSP00000334198:p.His1944Asn	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	91	28	NM_021098	0	0	2	2	0	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	7.903	0.734914	0.15574	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-3.99	3.75	1.55	0.23275	.	3.133360	0.01371	N	0.012566	D	0.90823	0.7118	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.30973	0.034;0.029;0.0;0.302;0.039	B;B;B;B;B	0.24006	0.023;0.021;0.0;0.05;0.015	D	0.84424	0.0573	10	0.27082	T	0.32	.	2.7944	0.05397	0.2401:0.5032:0.0:0.2567	.	690;679;685;1938;1944	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	N	1944;1938	ENSP00000334198:H1944N;ENSP00000351401:H1938N	ENSP00000334198:H1944N	H	+	1	0	CACNA1H	1208595	0.947000	0.32204	0.001000	0.08648	0.001000	0.01503	0.399000	0.20916	0.806000	0.34183	0.563000	0.77884	CAC	.		0.662	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1268594	C	A	1268594	3	1	39	1	0	0	0	0	1	0	0	0	2551	594	21	4	5956	4	CACNA1H	16	1268594	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		1268594	89086159	87	3532											
BFAR	51283	broad.mit.edu	37	chr16	14738464	14738464	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccaaagtcagtattctcctCaggtaatgttcagcctatat	11	13	6	11	0	4	0	3	0	1	0	5	0	4	0	3	1	1	3	3	1	5	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr16:14738464C>T	ENST00000261658.2	+	2	538	c.261C>T	c.(259-261)ctC>ctT	p.L87L	RNU7-125P_ENST00000458760.1_RNA|BFAR_ENST00000563971.1_Silent_p.L87L|BFAR_ENST00000426842.2_Nonsense_Mutation_p.Q28*	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	87					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						GTATTCTCCTCAGGTAATGTT	0.408																																					p.L87L													.	BFAR-92	0			c.C261T						.						80	77	78					16																	14738464		2197	4300	6497	SO:0001819	synonymous_variant	51283	exon2			TCTCCTCAGGTAA	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"RING-type (C3HC4) zinc fingers", "Sterile alpha motif (SAM) domain containing"	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.261C>T	16.37:g.14738464C>T		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	32	10	NM_016561	0	0	0	0	0	A8K4Z9|B4DUT0|D3DUG8	Silent	SNP	ENST00000261658.2	37	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	C	37	6.614637	0.97705	.	.	ENSG00000103429	ENST00000426842	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	12.1377	0.53981	0.0:0.9215:0.0:0.0785	.	.	.	.	X	28	.	ENSP00000400634:Q28X	Q	+	1	0	BFAR	14645965	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.254000	0.32897	2.745000	0.94114	0.655000	0.94253	CAG	.		0.408	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		T	14738464	C	T	14738464	2	4	39	1	0	0	0	0	0	0	0	1	1415	813	29	2		2	BFAR	16	14738464	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	13469870	14738464	75616289	88	3533											
ZKSCAN2	342357	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	25266603	25266603	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtggaggcttccaggttcCtcccgagacaccgccctggg	6	7	14	14	2	0	1	0	0	0	1	3	4	3	2	5	4	0	2	5	4	0	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr16:25266603C>G	ENST00000328086.7	-	2	1313	c.510G>C	c.(508-510)gaG>gaC	p.E170D		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	170					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TTCCAGGTTCCTCCCGAGACA	0.622																																					p.E170D		.											.	ZKSCAN2-138	0			c.G510C						.						88	78	82					16																	25266603		2197	4300	6497	SO:0001583	missense	342357	exon2			AGGTTCCTCCCGA	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.510G>C	16.37:g.25266603C>G	ENSP00000331626:p.Glu170Asp	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_001012981	0	0	0	0	0	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660995	0.47572	.	.	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.14766	2.48	5.3	-2.75	0.05914	.	0.376195	0.25654	N	0.029181	T	0.11495	0.0280	L	0.55743	1.74	0.29398	N	0.862144	B;B	0.20550	0.046;0.003	B;B	0.27608	0.081;0.005	T	0.11251	-1.0595	10	0.52906	T	0.07	-11.4516	6.0464	0.19762	0.0:0.4411:0.1273:0.4316	.	170;170	Q63HK3-2;Q63HK3	.;ZKSC2_HUMAN	D	170	ENSP00000331626:E170D	ENSP00000331626:E170D	E	-	3	2	ZKSCAN2	25174104	0.027000	0.19231	0.445000	0.26908	0.501000	0.33797	-1.330000	0.02675	-0.703000	0.05049	0.555000	0.69702	GAG	.		0.622	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		G	25266603	C	G	25266603	3	3	39	1	0	0	0	0	1	0	0	0	17719	680	24	4	2417	4	ZKSCAN2	16	25266603	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	10528139	25266603	65088150	89	3534											
CHMP1A	5119	ucsc.edu	37	chr16	89713674	89713674	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatcactgaggagaccttCtgcaggtccatggtgctcag	8	10	11	12	0	3	2	2	1	1	1	5	3	5	2	3	3	2	2	3	3	0	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr16:89713674C>A	ENST00000397901.3	-	5	574	c.318G>T	c.(316-318)caG>caT	p.Q106H	CHMP1A_ENST00000535997.2_Missense_Mutation_p.Q42H|CHMP1A_ENST00000550102.1_Missense_Mutation_p.Q97H|CHMP1A_ENST00000253475.5_Nonsense_Mutation_p.E100*|CHMP1A_ENST00000547614.1_5'UTR	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	106					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)		AGGAGACCTTCTGCAGGTCCA	0.597																																					p.E100X													.	.	0			c.G298T						.						81	87	85					16																	89713674		2051	4196	6247	SO:0001583	missense	5119	exon4			GACCTTCTGCAGG	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.318G>T	16.37:g.89713674C>A	ENSP00000380998:p.Gln106His	Somatic	42	0		WXS	Illumina HiSeq		51	2	NM_001083314	0	0	120	138	18	A2RU09|Q14468|Q15779|Q96G31	Nonsense_Mutation	SNP	ENST00000397901.3	37	CCDS45552.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.7|29.7	5.028081|5.028081	0.93518|0.93518	.|.	.|.	ENSG00000131165|ENSG00000131165	ENST00000253475|ENST00000397901;ENST00000535997;ENST00000550102	.|T;T;T	.|0.72615	.|-0.67;-0.67;-0.67	5.58|5.58	4.64|4.64	0.57946|0.57946	.|.	0.000000|.	0.38720|.	N|.	0.001586|.	.|D	.|0.82513	.|0.5053	M|M	0.79258|0.79258	2.445|2.445	0.80722|0.80722	A|A	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.68943	.|0.961	.|D	.|0.87324	.|0.2320	.|8	0.87932|0.66056	D|D	0|0.02	-7.7945|-7.7945	12.6883|12.6883	0.56960|0.56960	0.0:0.8628:0.0:0.1372|0.0:0.8628:0.0:0.1372	.|.	.|106	.|Q9HD42	.|CHM1A_HUMAN	X|H	100|106;42;97	.|ENSP00000380998:Q106H;ENSP00000442120:Q42H;ENSP00000449243:Q97H	ENSP00000253475:E100X|ENSP00000380998:Q106H	E|Q	-|-	1|3	0|2	CHMP1A|CHMP1A	88241175|88241175	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.618000|0.618000	0.37518|0.37518	2.915000|2.915000	0.48805|0.48805	1.375000|1.375000	0.46248|0.46248	-0.119000|-0.119000	0.15052|0.15052	GAA|CAG	.		0.597	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		A	89713674	C	A	89713674	3	1	39	1	0	0	0	0	1	0	0	0	3358	922	32	4	436	4	CHMP1A	16	89713674	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	64447071	89713674	641079	90	3535											
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7578271	7578271	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttccactcggataagaTgctgaggaggggccagacct	9	9	12	11	1	0	3	0	1	0	2	3	5	2	5	4	4	1	1	4	4	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:7578271T>G	ENST00000269305.4	-	6	767	c.578A>C	c.(577-579)cAt>cCt	p.H193P	TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.H193P|TP53_ENST00000413465.2_Missense_Mutation_p.H193P|TP53_ENST00000420246.2_Missense_Mutation_p.H193P|TP53_ENST00000359597.4_Missense_Mutation_p.H193P|TP53_ENST00000445888.2_Missense_Mutation_p.H193P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193R(80)|p.H193L(42)|p.H193P(18)|p.0?(8)|p.?(6)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.H193fs*16(3)|p.P191fs*53(2)|p.H61P(2)|p.H100P(2)|p.A189fs*53(1)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P98_E105>Q(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGATAAGATGCTGAGGAGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.H193P	Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53-70225	193	Substitution - Missense(160)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	lung(36)|upper_aerodigestive_tract(26)|ovary(20)|breast(18)|oesophagus(14)|haematopoietic_and_lymphoid_tissue(12)|endometrium(12)|biliary_tract(10)|liver(9)|stomach(7)|central_nervous_system(6)|large_intestine(6)|urinary_tract(5)|skin(5)|bone(4)|pancreas(2)|prostate(1)	c.A578C	GRCh37	CM083194|CM951225	TP53	M		.						97	87	90					17																	7578271		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATAAGATGCTGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.578A>C	17.37:g.7578271T>G	ENSP00000269305:p.His193Pro	Somatic	120	1		WXS	Illumina HiSeq	Phase_I	123	29	NM_000546	0	1	8	18	9	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.377907	0.42105	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99855	-7.2;-7.2;-7.2;-7.2;-7.2;-7.2;-7.2;-7.2	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88906	2.99	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97320	0.9943	10	0.87932	D	0	-29.0766	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	P	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193P;ENSP00000352610:H193P;ENSP00000269305:H193P;ENSP00000398846:H193P;ENSP00000391127:H193P;ENSP00000391478:H193P;ENSP00000425104:H61P;ENSP00000423862:H100P	ENSP00000269305:H193P	H	-	2	0	TP53	7518996	1.000000	0.71417	0.814000	0.32528	0.023000	0.10783	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	CAT	.		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578271	T	G	7578271	3	3	39	1	0	0	0	0	1	0	0	0	16414	1464	51	5	716	5	TP53	17	7578271	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		7578271	73616939	91	3536											
STARD3	10948	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	37814678	37814685	+	Frame_Shift_Del	DEL	TGGCTACC	TGGCTACC	-																															ctgctcagcaaaggggcattTggctacctgctccccatcgt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	TGGCTACC	TGGCTACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:37814678_37814685delTGGCTACC	ENST00000336308.5	+	6	668_675	c.450_457delTGGCTACC	c.(448-459)tttggctacctgfs	p.GYL151fs	STARD3_ENST00000544210.2_Frame_Shift_Del_p.LAT146fs|STARD3_ENST00000394250.4_Frame_Shift_Del_p.GYL133fs|STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000580611.1_Frame_Shift_Del_p.GYL125fs	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	151	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AAGGGGCATTTGGCTACCTGCTCCCCAT	0.582																																					p.150_153del		.											.	STARD3-90	0			c.450_457del						.																																			SO:0001589	frameshift_variant	10948	exon6			.		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"StAR-related lipid transfer (START) domain containing"	17579	protein-coding gene	gene with protein product		607048	"START domain containing 3"				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.450_457delTGGCTACC	17.37:g.37814678_37814685delTGGCTACC	ENSP00000337446:p.Gly151fs	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	50	14	NM_006804	0	0	0	0	0	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Frame_Shift_Del	DEL	ENST00000336308.5	37	CCDS11341.1																																																																																			.		0.582	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1			-	37814685	TGGCTACC	-	37814678	7	5	39	1	0	1	0	1	0	0	0	0	15289	1821	63	0	468	0	STARD3	17	37814678	Frame_Shift_Del	DEL	TGGCTACC	TCGA-B1-A655-01A-11D-A31Z-10	30236407	37814678	43380532	92	3537											
BRCA1	672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41203099	41203099	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgggcatgttggtgaaGggcccatagcaacagatttc	9	10	13	9	0	0	2	0	1	0	1	1	2	0	2	2	3	2	3	2	3	3	3	rs273901762		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:41203099G>A	ENST00000357654.3	-	20	5431	c.5313C>T	c.(5311-5313)ccC>ccT	p.P1771P	BRCA1_ENST00000491747.2_Silent_p.P667P|BRCA1_ENST00000468300.1_Silent_p.P667P|BRCA1_ENST00000354071.3_Silent_p.P1506P|BRCA1_ENST00000591534.1_Silent_p.P262P|BRCA1_ENST00000471181.2_Silent_p.P1792P|BRCA1_ENST00000352993.3_Silent_p.P629P|BRCA1_ENST00000493795.1_Silent_p.P1724P|BRCA1_ENST00000351666.3_Silent_p.P588P|BRCA1_ENST00000309486.4_Silent_p.P1475P|BRCA1_ENST00000346315.3_Silent_p.P1532P|BRCA1_ENST00000586385.1_Silent_p.P81P|BRCA1_ENST00000591849.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1771	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGTTGGTGAAGGGCCCATAGC	0.478			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.P1792P		.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1-3415	0			c.C5376T						.						70	69	69					17																	41203099		2203	4300	6503	SO:0001819	synonymous_variant	672	exon21	Familial Cancer Database		GGTGAAGGGCCCA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5313C>T	17.37:g.41203099G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	63	24	NM_007300	0	0	2	4	2	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			.		0.478	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		A	41203099	G	A	41203099	2	1	39	1	0	0	0	0	0	0	0	1	1501	987	35	2		2	BRCA1	17	41203099	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	3388421	41203099	39992111	93	3538											
HEATR6	63897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58121036	58121036	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctggctgtgtctccagttGgtgcctggatgctgcccatg	3	14	13	11	0	2	0	0	0	2	0	3	1	2	1	3	3	3	3	3	3	0	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:58121036G>T	ENST00000184956.6	-	20	3450	c.3434C>A	c.(3433-3435)cCa>cAa	p.P1145Q	AC005702.3_ENST00000582298.1_RNA|AC005702.2_ENST00000577558.1_RNA|AC005702.1_ENST00000581326.1_RNA|MIR4737_ENST00000583979.1_RNA|AC005702.4_ENST00000583144.1_RNA|HEATR6_ENST00000585976.1_Missense_Mutation_p.P1033Q	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	1145							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GTCTCCAGTTGGTGCCTGGAT	0.542																																					p.P1145Q		.											.	HEATR6-227	0			c.C3434A						.						129	115	120					17																	58121036		2203	4300	6503	SO:0001583	missense	63897	exon20			CCAGTTGGTGCCT	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"amplified in breast cancer 1"					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.3434C>A	17.37:g.58121036G>T	ENSP00000184956:p.Pro1145Gln	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	207	49	NM_022070	0	0	15	18	3	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Missense_Mutation	SNP	ENST00000184956.6	37	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	G	0.083	-1.180886	0.01633	.	.	ENSG00000068097	ENST00000184956;ENST00000393017	T	0.64438	-0.1	4.96	0.0386	0.14201	Armadillo-type fold (1);	1.078860	0.07032	N	0.828585	T	0.32941	0.0846	N	0.03608	-0.345	0.09310	N	1	B;B	0.17268	0.021;0.0	B;B	0.13407	0.009;0.001	T	0.19451	-1.0305	10	0.20519	T	0.43	0.0678	3.9945	0.09551	0.5137:0.0:0.2773:0.209	.	880;1145	E7ESB9;Q6AI08	.;HEAT6_HUMAN	Q	1145;880	ENSP00000184956:P1145Q	ENSP00000184956:P1145Q	P	-	2	0	HEATR6	55475818	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.029000	0.12329	0.348000	0.23949	-0.312000	0.09012	CCA	.		0.542	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		T	58121036	G	T	58121036	3	4	39	1	0	0	0	0	1	0	0	0	7054	1348	47	4	115	4	HEATR6	17	58121036	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	16917937	58121036	23074174	94	3539											
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	65162707	65162707	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagaggggtaatcgatttaaTtgaaactgaagttcaacctg	14	11	10	6	1	1	3	1	2	0	1	2	4	1	3	1	2	2	2	1	2	5	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:65162707T>C	ENST00000358691.5	-	15	1948	c.1782A>G	c.(1780-1782)caA>caG	p.Q594Q	HELZ_ENST00000580168.1_Silent_p.Q594Q	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	594						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					ATCGATTTAATTGAAACTGAA	0.393																																					p.Q594Q		.											.	HELZ-92	0			c.A1782G						.						104	96	98					17																	65162707		1858	4110	5968	SO:0001819	synonymous_variant	9931	exon15			ATTTAATTGAAAC	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1782A>G	17.37:g.65162707T>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	117	9	NM_014877	0	0	9	12	3	I6L9H4	Silent	SNP	ENST00000358691.5	37	CCDS42374.1																																																																																			.		0.393	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		C	65162707	T	C	65162707	2	2	39	1	0	0	0	0	0	0	0	1	7070	1490	52	3		3	HELZ	17	65162707	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	7041671	65162707	16032503	95	3540											
FSCN2	25794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79496379	79496379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caccgctacgtctctgtgcgGcaaggtagggagggcacagg	8	6	16	11	3	1	0	0	0	1	0	2	1	1	1	1	5	2	4	1	5	3	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:79496379G>A	ENST00000417245.2	+	1	958	c.822G>A	c.(820-822)cgG>cgA	p.R274R	RP13-766D20.2_ENST00000442532.1_RNA|RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.R274R	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	274					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			TCTCTGTGCGGCAAGGTAGGG	0.647																																					p.R274R		.											.	.	0			c.G822A						.						9	10	10					17																	79496379		2169	4246	6415	SO:0001819	synonymous_variant	25794	exon1			TGTGCGGCAAGGT	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"Fascins"	3960	protein-coding gene	gene with protein product		607643	"fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)", "fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.822G>A	17.37:g.79496379G>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	123	73	NM_001077182	0	0	0	0	0	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	37	CCDS45811.1																																																																																			.		0.647	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		A	79496379	G	A	79496379	2	1	39	1	0	0	0	0	0	0	0	1	6087	1190	42	2		2	FSCN2	17	79496379	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	14333672	79496379	1698831	96	3541											
PCYT2	5833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79865647	79865647	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggattccgccgccgactcAcctggctgctgtgatgggct	4	9	15	13	3	1	1	1	1	0	0	2	3	2	2	4	4	1	3	4	4	0	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:79865647A>G	ENST00000538936.2	-	5	601		c.e5+1		PCYT2_ENST00000571105.1_Splice_Site|PCYT2_ENST00000538721.2_Splice_Site|PCYT2_ENST00000331285.3_Splice_Site|PCYT2_ENST00000570391.1_Splice_Site|PCYT2_ENST00000570388.1_Splice_Site	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	CCGCCGACTCACCTGGCTGCT	0.667																																					.		.											.	PCYT2-68	0			c.258+2T>C						.						55	45	49					17																	79865647		2203	4300	6503	SO:0001630	splice_region_variant	5833	exon6			CGACTCACCTGGC	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.492+1T>C	17.37:g.79865647A>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	52	14	NM_001256435	0	0	0	0	0	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Splice_Site	SNP	ENST00000538936.2	37	CCDS11791.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.829822	0.50845	.	.	ENSG00000185813	ENST00000538721;ENST00000538936;ENST00000331285	.	.	.	4.34	4.34	0.51931	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2492	0.54589	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PCYT2	77458939	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	8.242000	0.89818	1.812000	0.52913	0.459000	0.35465	.	.		0.667	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861	Intron	G	79865647	A	G	79865647	5	3	39	1	0	0	0	0	0	0	1	0	11638	173	6	3	769	3	PCYT2	17	79865647	Splice_Site	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	369268	79865647	1329563	97	3542											
TXNDC2	84203	broad.mit.edu	37	chr18	9887670	9887670	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctagaggaagccatcccAcccaaggagattgacatccc	12	6	8	15	0	0	3	0	1	0	2	3	5	3	4	5	2	1	0	5	2	3	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr18:9887670A>G	ENST00000306084.6	+	2	1393	c.1194A>G	c.(1192-1194)ccA>ccG	p.P398P	TXNDC2_ENST00000357775.5_Silent_p.P331P|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	398	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						AAGCCATCCCACCCAAGGAGA	0.562																																					p.P398P													.	TXNDC2-92	0			c.A1194G						.						118	106	110					18																	9887670		2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			CATCCCACCCAAG	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.1194A>G	18.37:g.9887670A>G		Somatic	122	4		WXS	Illumina HiSeq	Phase_I	128	9	NM_001098529	0	0	0	0	0	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			.		0.562	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			G	9887670	A	G	9887670	2	3	39	1	0	0	0	0	0	0	0	1	16830	146	6	3		3	TXNDC2	18	9887670	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10		9887670	68189578	98	3543			1	11		2	2	12	N	T_A	4.121799e-05
TXNDC2	84203	broad.mit.edu	37	chr18	9887681	9887681	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccatcccacccaaggagaTtgacatccccaagtccccag	12	5	7	17	0	0	2	0	1	0	1	3	3	3	2	7	1	1	0	7	1	2	1	rs553374563		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr18:9887681T>G	ENST00000306084.6	+	2	1404	c.1205T>G	c.(1204-1206)aTt>aGt	p.I402S	TXNDC2_ENST00000357775.5_Missense_Mutation_p.I335S|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	402	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CCCAAGGAGATTGACATCCCC	0.557																																					p.I402S													.	TXNDC2-92	0			c.T1205G						.						116	104	108					18																	9887681		2203	4300	6503	SO:0001583	missense	84203	exon2			AGGAGATTGACAT	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.1205T>G	18.37:g.9887681T>G	ENSP00000304908:p.Ile402Ser	Somatic	118	2		WXS	Illumina HiSeq	Phase_I	121	4	NM_001098529	0	0	0	0	0	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	t	0.023	-1.405408	0.01155	.	.	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.03772	3.81;3.81	3.43	-2.0	0.07433	.	7.730320	0.00481	N	0.000131	T	0.02888	0.0086	N	0.11427	0.14	0.09310	N	1	B	0.18741	0.03	B	0.21708	0.036	T	0.39375	-0.9617	9	.	.	.	.	3.3024	0.06988	0.2924:0.0:0.2459:0.4617	.	402	Q86VQ3	TXND2_HUMAN	S	200;335;402;387	ENSP00000350419:I335S;ENSP00000304908:I402S	.	I	+	2	0	TXNDC2	9877681	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.047000	0.03521	-0.479000	0.06813	-1.354000	0.01226	ATT	.		0.557	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			G	9887681	T	G	9887681	3	3	39	1	0	0	0	0	1	0	0	0	16830	1493	52	5	1211	5	TXNDC2	18	9887681	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	11	9887681	68189567	99	3544			1	11		2	2	12	N	T_A	4.121799e-05
KCNG2	26251	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	77659162	77659162	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgcgccttcctgcgcgcGccactcaacatcattgacat	9	9	8	15	4	2	1	2	1	0	0	3	1	3	1	3	0	3	0	3	0	2	2	rs140841838		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr18:77659162G>A	ENST00000316249.3	+	2	747	c.747G>A	c.(745-747)gcG>gcA	p.A249A	KCNG2_ENST00000590307.1_3'UTR	NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	249					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		TCCTGCGCGCGCCACTCAACA	0.677																																					p.A249A		.											.	KCNG2-90	0			c.G747A						.	G		0,4404		0,0,2202	43	39	40		747	-3.4	0	18	dbSNP_134	40	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KCNG2	NM_012283.1		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		249/467	77659162	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	26251	exon2			GCGCGCGCCACTC	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.747G>A	18.37:g.77659162G>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	26	6	NM_012283	0	0	0	0	0		Silent	SNP	ENST00000316249.3	37	CCDS12019.1																																																																																			G|1.000;A|0.000		0.677	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283		A	77659162	G	A	77659162	2	1	39	1	0	0	0	0	0	0	0	1	8049	1074	38	1		1	KCNG2	18	77659162	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	67771481	77659162	418086	100	3545											
ICAM1	3383	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10395839	10395839	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggtagcagccgcagtcaTaatgggcactgcaggcctca	9	8	13	11	1	2	0	2	0	0	0	2	0	2	0	2	3	3	5	2	3	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:10395839T>A	ENST00000264832.3	+	7	1800	c.1475T>A	c.(1474-1476)aTa>aAa	p.I492K	ICAM4_ENST00000340992.4_5'Flank|ICAM4_ENST00000393717.2_5'Flank|CTD-2369P2.5_ENST00000592893.1_RNA|CTD-2369P2.8_ENST00000589379.1_RNA|ICAM4_ENST00000380770.3_5'Flank|ICAM1_ENST00000423829.2_Missense_Mutation_p.I270K	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	492					adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GCCGCAGTCATAATGGGCACT	0.547																																					p.I492K		.											.	ICAM1-91	0			c.T1475A						.						103	105	104					19																	10395839		2203	4300	6503	SO:0001583	missense	3383	exon7			CAGTCATAATGGG		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	5344	protein-coding gene	gene with protein product	"human rhinovirus receptor"	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.1475T>A	19.37:g.10395839T>A	ENSP00000264832:p.Ile492Lys	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	83	29	NM_000201	0	0	59	108	49	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	.	.	.	.	.	.	.	.	.	.	T	12.45	1.941110	0.34283	.	.	ENSG00000090339	ENST00000264832;ENST00000423829	T;T	0.05199	4.24;3.48	5.22	3.07	0.35406	.	4.242400	0.00744	N	0.001020	T	0.05593	0.0147	N	0.19112	0.55	0.09310	N	0.999997	B;B	0.27286	0.142;0.174	B;B	0.22880	0.042;0.028	T	0.29305	-1.0016	10	0.42905	T	0.14	-14.6127	4.9491	0.14004	0.1651:0.0921:0.0:0.7428	.	270;492	E7ESS4;P05362	.;ICAM1_HUMAN	K	492;270	ENSP00000264832:I492K;ENSP00000413124:I270K	ENSP00000264832:I492K	I	+	2	0	ICAM1	10256839	0.000000	0.05858	0.006000	0.13384	0.011000	0.07611	0.007000	0.13174	0.909000	0.36697	0.459000	0.35465	ATA	.		0.547	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1			A	10395839	T	A	10395839	3	1	39	1	0	0	0	0	1	0	0	0	7500	1406	49	5	1501	5	ICAM1	19	10395839	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		10395839	48733144	101	3546											
CACNA1A	773	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	13418985	13418985	+	Frame_Shift_Del	DEL	A	A	-																															cgaagacgacaatgaacaggAaaaggagaaacaacaggctg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:13418985delA	ENST00000360228.5	-	14	1861	c.1862delT	c.(1861-1863)ttcfs	p.F621fs	CACNA1A_ENST00000573710.2_Frame_Shift_Del_p.F622fs	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	622					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	AATGAACAGGAAAAGGAGAAA	0.542																																					p.F622fs		.											.	CACNA1A-67	0			c.1865delT						.						95	98	97					19																	13418985		2088	4230	6318	SO:0001589	frameshift_variant	773	exon14			.	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.1862delT	19.37:g.13418985delA	ENSP00000353362:p.Phe621fs	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	126	42	NM_001127221	0	0	0	0	0	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Frame_Shift_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																			.		0.542	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		-	13418985	A	-	13418985	7	5	39	1	0	1	0	1	0	0	0	0	2544	246	9	0	5905	0	CACNA1A	19	13418985	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	3023146	13418985	45709998	102	3547											
PLEKHG2	64857	hgsc.bcm.edu;broad.mit.edu	37	chr19	39913652	39913652	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccgctgtgaaattcccgaagGttctcgccttcctagtctct	6	13	8	14	3	2	1	0	1	2	0	6	2	4	1	4	1	0	2	4	1	3	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:39913652G>A	ENST00000409794.3	+	18	2808	c.1958G>A	c.(1957-1959)gGt>gAt	p.G653D	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.G594D|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.G624D|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	653					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ATTCCCGAAGGTTCTCGCCTT	0.517																																					p.G653D		.											.	PLEKHG2-274	0			c.G1958A						.						95	100	98					19																	39913652		2203	4300	6503	SO:0001583	missense	64857	exon18			CCGAAGGTTCTCG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1958G>A	19.37:g.39913652G>A	ENSP00000386733:p.Gly653Asp	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	87	5	NM_022835	0	0	3	3	0	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.825|2.825	-0.243916|-0.243916	0.05906|0.05906	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508|ENST00000205135	T;T;T|.	0.69040|.	-0.25;-0.25;-0.37|.	3.44|3.44	0.133|0.133	0.14766|0.14766	.|.	1.062390|.	0.07458|.	N|.	0.900138|.	T|T	0.14830|0.14830	0.0358|0.0358	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B;B|.	0.30361|.	0.263;0.261;0.277|.	B;B;B|.	0.25987|.	0.065;0.044;0.043|.	T|T	0.26121|0.26121	-1.0112|-1.0112	10|5	0.46703|.	T|.	0.11|.	.|.	4.0591|4.0591	0.09831|0.09831	0.0:0.2305:0.195:0.5745|0.0:0.2305:0.195:0.5745	.|.	624;653;594|.	Q9H7P9-3;Q9H7P9;E7ESZ3|.	.;PKHG2_HUMAN;.|.	D|I	653;624;594|521	ENSP00000386733:G653D;ENSP00000392906:G624D;ENSP00000408857:G594D|.	ENSP00000386733:G653D|.	G|V	+|+	2|1	0|0	PLEKHG2|PLEKHG2	44605492|44605492	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.010000|0.010000	0.07245|0.07245	-0.226000|-0.226000	0.09139|0.09139	-0.034000|-0.034000	0.13713|0.13713	-0.467000|-0.467000	0.05162|0.05162	GGT|GTT	.		0.517	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		A	39913652	G	A	39913652	3	1	39	1	0	0	0	0	1	0	0	0	12095	1261	44	2	2024	2	PLEKHG2	19	39913652	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	26494667	39913652	19215331	103	3548											
SFRS16	11129	broad.mit.edu	37	chr19	45571284	45571284	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccacccaggaccgaacctgCcgctggtaaagagacaggag	12	3	12	14	2	0	1	0	0	0	1	0	5	0	3	5	3	2	2	5	3	3	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:45571284C>T	ENST00000221455.3	+	15	1777	c.1679C>T	c.(1678-1680)gCc>gTc	p.A560V	CLASRP_ENST00000391953.4_Missense_Mutation_p.A498V|CLASRP_ENST00000544944.2_Missense_Mutation_p.A560V	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	560	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						ACCGAACCTGCCGCTGGTAAA	0.632																																					p.A560V													.	CLASRP-154	0			c.C1679T						.						33	36	35					19																	45571284		2203	4300	6503	SO:0001583	missense	11129	exon15			AACCTGCCGCTGG	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.1679C>T	19.37:g.45571284C>T	ENSP00000221455:p.Ala560Val	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	193	4	NM_007056	0	0	0	0	0	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Missense_Mutation	SNP	ENST00000221455.3	37	CCDS12652.2	.	.	.	.	.	.	.	.	.	.	C	24.1	4.495983	0.85069	.	.	ENSG00000104859	ENST00000221455;ENST00000391952;ENST00000391953;ENST00000544944	T;T;T;T	0.34667	2.01;1.35;2.01;1.46	5.07	4.04	0.47022	.	0.000000	0.36002	U	0.002849	T	0.22166	0.0534	N	0.22421	0.69	0.43508	D	0.995761	P;P;P	0.41450	0.75;0.597;0.462	B;B;B	0.36335	0.222;0.133;0.063	T	0.03296	-1.1051	10	0.42905	T	0.14	-20.215	10.5428	0.45043	0.0:0.906:0.0:0.094	.	498;560;560	F8WAG9;F5H0Q6;Q8N2M8	.;.;CLASR_HUMAN	V	560;560;498;560	ENSP00000221455:A560V;ENSP00000375814:A560V;ENSP00000375815:A498V;ENSP00000438702:A560V	ENSP00000221455:A560V	A	+	2	0	CLASRP	50263124	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.030000	0.57260	2.370000	0.80446	0.313000	0.20887	GCC	.		0.632	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		T	45571284	C	T	45571284	3	4	39	1	0	0	0	0	1	0	0	0	14204	739	26	2	1733	2	SFRS16	19	45571284	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	5657632	45571284	13557699	104	3549											
TRPM4	54795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49674876	49674876	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctcagctcccatgtctcctCgtggctggctcagggggagc	4	9	14	14	1	3	0	2	0	1	0	6	1	4	1	2	4	2	4	2	4	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:49674876C>T	ENST00000252826.5	+	8	1026	c.900C>T	c.(898-900)ctC>ctT	p.L300L	TRPM4_ENST00000427978.2_Silent_p.L300L|TRPM4_ENST00000601347.1_3'UTR|TRPM4_ENST00000355712.5_Silent_p.L17L	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	300					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		CATGTCTCCTCGTGGCTGGCT	0.592																																					p.L300L		.											.	TRPM4-91	0			c.C900T						.						37	42	41					19																	49674876		2202	4300	6502	SO:0001819	synonymous_variant	54795	exon8			TCTCCTCGTGGCT	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.900C>T	19.37:g.49674876C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	72	23	NM_001195227	0	0	19	40	21	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	37	CCDS33073.1																																																																																			.		0.592	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49674876	C	T	49674876	2	4	39	1	0	0	0	0	0	0	0	1	16621	871	31	1		1	TRPM4	19	49674876	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	4103592	49674876	9454107	105	3550											
ZNF175	7728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52091298	52091298	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaagccttcacttctaagTctcaattcaaagagcatcag	14	10	7	10	0	5	1	4	0	2	1	6	2	5	2	1	1	2	1	1	1	4	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:52091298T>C	ENST00000262259.2	+	5	2072	c.1714T>C	c.(1714-1716)Tct>Cct	p.S572P	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	572					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		CACTTCTAAGTCTCAATTCAA	0.453																																					p.S572P		.											.	ZNF175-90	0			c.T1714C						.						87	85	86					19																	52091298		2203	4300	6503	SO:0001583	missense	7728	exon5			TCTAAGTCTCAAT	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.1714T>C	19.37:g.52091298T>C	ENSP00000262259:p.Ser572Pro	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	68	20	NM_007147	0	0	3	4	1	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.354614	0.41700	.	.	ENSG00000105497	ENST00000262259	T	0.18657	2.2	2.18	1.09	0.20402	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36963	0.0986	M	0.78344	2.41	0.09310	N	0.999999	D	0.65815	0.995	P	0.57911	0.829	T	0.13255	-1.0516	9	0.72032	D	0.01	.	6.4454	0.21873	0.0:0.0:0.2498:0.7502	.	572	Q9Y473	ZN175_HUMAN	P	572	ENSP00000262259:S572P	ENSP00000262259:S572P	S	+	1	0	ZNF175	56783110	0.000000	0.05858	0.703000	0.30354	0.992000	0.81027	-0.482000	0.06544	0.258000	0.21686	0.533000	0.62120	TCT	.		0.453	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		C	52091298	T	C	52091298	3	2	39	1	0	0	0	0	1	0	0	0	17777	1667	58	3	1728	3	ZNF175	19	52091298	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	2416422	52091298	7037685	106	3551											
NFATC2	4773	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	50051812	50051813	+	Frame_Shift_Del	DEL	GC	GC	-																															ttttacaggtgtgcggatatGcttgttccgatattcaggga																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr20:50051812_50051813delGC	ENST00000396009.3	-	8	2163_2164	c.1944_1945delGC	c.(1942-1947)aagcatfs	p.H649fs	NFATC2_ENST00000609507.1_Frame_Shift_Del_p.H430fs|NFATC2_ENST00000609943.1_Frame_Shift_Del_p.H629fs|NFATC2_ENST00000414705.1_Frame_Shift_Del_p.H629fs|NFATC2_ENST00000371564.3_Frame_Shift_Del_p.H649fs|NFATC2_ENST00000610033.1_Frame_Shift_Del_p.H430fs	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	649					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GTGCGGATATGCTTGTTCCGAT	0.436																																					p.648_649del		.											.	NFATC2-92	0			c.1944_1945del						.																																			SO:0001589	frameshift_variant	4773	exon8			.	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"Nuclear factor of activated T-cells"	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1944_1945delGC	20.37:g.50051812_50051813delGC	ENSP00000379330:p.His649fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	84	25	NM_012340	0	0	0	0	0	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Frame_Shift_Del	DEL	ENST00000396009.3	37	CCDS13437.1																																																																																			.		0.436	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		-	50051813	GC	-	50051812	7	5	39	1	0	1	0	1	0	0	0	0	10388	1319	46	0	892	0	NFATC2	20	50051812	Frame_Shift_Del	DEL	GC	TCGA-B1-A655-01A-11D-A31Z-10		50051812	12973708	107	3552											
BRWD1	54014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	40665927	40665927	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaagcggccattatgtgttGaccaaatctttaccaaacag	14	10	7	10	1	1	1	0	1	1	0	1	1	1	1	3	1	3	1	3	1	5	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr21:40665927G>T	ENST00000333229.2	-	8	968	c.641C>A	c.(640-642)tCa>tAa	p.S214*	BRWD1_ENST00000342449.3_Nonsense_Mutation_p.S214*|BRWD1_ENST00000380800.3_Nonsense_Mutation_p.S214*	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	214					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				ATTATGTGTTGACCAAATCTT	0.328																																					p.S214X	Melanoma(170;988 1986 4794 16843 39731)	.											.	BRWD1-94	0			c.C641A						.						82	77	79					21																	40665927		2203	4300	6503	SO:0001587	stop_gained	54014	exon8			TGTGTTGACCAAA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.641C>A	21.37:g.40665927G>T	ENSP00000330753:p.Ser214*	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	90	32	NM_018963	0	0	0	0	0	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Nonsense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	G	37	6.060061	0.97246	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	.	.	.	5.12	4.18	0.49190	.	0.110931	0.39985	N	0.001212	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.83	15.0594	0.71939	0.0:0.1423:0.8577:0.0	.	.	.	.	X	214	.	ENSP00000330753:S214X	S	-	2	0	BRWD1	39587797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.477000	0.73591	2.388000	0.81334	0.655000	0.94253	TCA	.		0.328	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40665927	G	T	40665927	4	4	39	1	0	0	0	0	0	1	0	0	1528	1294	45	4	6700	4	BRWD1	21	40665927	Nonsense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		40665927	7463968	108	3553											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46924434	46924434	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggcccccccggccccccAggccccccaggcccacgtgg	3	1	11	26	3	0	0	0	0	0	0	0	0	0	0	11	5	0	0	11	5	0	0	rs28696990|rs149296338|rs201180574|rs78227997	byFrequency	TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr21:46924434A>C	ENST00000359759.4	+	33	4098	c.4077A>C	c.(4075-4077)ccA>ccC	p.P1359P	COL18A1_ENST00000400337.2_Silent_p.P944P|COL18A1_ENST00000355480.5_Silent_p.P1124P|SLC19A1_ENST00000567670.1_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1359	Triple-helical region 9 (COL9).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		ccggccccccaggccccccag	0.706																																					.		.											.	COL18A1-90	0			c.2825-2A>C						.						1	2	2					21																	46924434		1040	2663	3703	SO:0001819	synonymous_variant	80781	exon35			CCCCCCAGGCCCC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4077A>C	21.37:g.46924434A>C		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_130445	0	0	0	0	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Splice_Site	SNP	ENST00000359759.4	37																																																																																				.		0.706	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			C	46924434	A	C	46924434	2	2	39	1	0	0	0	0	0	0	0	1	3681	202	7	5		5	COL18A1	21	46924434	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	6258507	46924434	1205461	109	3554											
RFPL3	10738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	32754194	32754195	+	Missense_Mutation	DNP	TA	TA	AT																															gctgtcccgtctgctcagacTatctggaaaaaccaatgtcc																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr22:32754194_32754195TA>AT	ENST00000249007.4	+	1	341_342	c.136_137TA>AT	c.(136-138)TAt>ATt	p.Y46I	RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Missense_Mutation_p.Y17I|RFPL3_ENST00000397468.1_Missense_Mutation_p.Y17I	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	46							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						CTGCTCAGACTATCTGGAAAAA	0.52																																					p.Y46I		.											.	RFPL3-91	0			c.A50T						.																																			SO:0001583	missense	10738	exon2			CAGACTATCTGGA	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	Exception_encountered	22.37:g.32754194_32754195delinsAT	ENSP00000249007:p.Tyr46Ile	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	150	40	NM_006604	0	0	0	0	0	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	DNP	ENST00000249007.4	37	CCDS43011.1																																																																																			.		0.52	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		AT	32754195	TA	AT	32754194	3	1	39	1	0	0	0	0	1	0	0	0	13287	1522	53	5	138	5	RFPL3	22	32754194	Missense_Mutation	DNP	TA	TCGA-B1-A655-01A-11D-A31Z-10		32754194	18550372	110	3555											
SSTR3	6753	broad.mit.edu	37	chr22	37602594	37602594	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttccccaggccctacaggtAgctgatgcgcatcgtgctgg	6	10	12	13	2	0	1	0	1	0	0	2	1	1	1	3	3	4	4	3	3	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr22:37602594A>G	ENST00000328544.3	-	2	1782	c.1249T>C	c.(1249-1251)Tac>Cac	p.Y417H	SSTR3_ENST00000402501.1_Missense_Mutation_p.Y417H	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	417					cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	CCCTACAGGTAGCTGATGCGC	0.652																																					p.Y417H													.	SSTR3-522	0			c.T1249C						.						46	50	49					22																	37602594		2202	4299	6501	SO:0001583	missense	6753	exon2			ACAGGTAGCTGAT		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"GPCR / Class A : Somatostatin receptors"	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1249T>C	22.37:g.37602594A>G	ENSP00000330138:p.Tyr417His	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	16	3	NM_001051	0	0	0	0	0	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	37	CCDS13944.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.775902	0.31411	.	.	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.72505	-0.66;-0.66	5.36	3.24	0.37175	.	2.384000	0.01954	U	0.042879	T	0.64080	0.2566	L	0.29908	0.895	0.25200	N	0.990069	B	0.09022	0.002	B	0.08055	0.003	T	0.52019	-0.8631	10	0.87932	D	0	.	9.3495	0.38129	0.8722:0.0:0.1278:0.0	.	417	P32745	SSR3_HUMAN	H	417	ENSP00000330138:Y417H;ENSP00000384904:Y417H	ENSP00000330138:Y417H	Y	-	1	0	SSTR3	35932540	0.997000	0.39634	0.983000	0.44433	0.131000	0.20780	2.509000	0.45459	0.373000	0.24621	0.402000	0.26972	TAC	.		0.652	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			G	37602594	A	G	37602594	3	3	39	1	0	0	0	0	1	0	0	0	15231	420	15	3	11	3	SSTR3	22	37602594	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	4848400	37602594	13701972	111	3556											
IL1RAPL1	11141	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	29973429	29973429	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggaggtggaggccctgaAgcacaccatcaagctcctga	11	5	12	13	0	1	2	1	2	0	0	2	4	2	4	4	4	2	2	4	4	2	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:29973429A>C	ENST00000378993.1	+	11	2256	c.1583A>C	c.(1582-1584)aAg>aCg	p.K528T	IL1RAPL1_ENST00000302196.4_Missense_Mutation_p.K528T	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	528	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						GAGGCCCTGAAGCACACCATC	0.413																																					p.K528T													.	IL1RAPL1-134	0			c.A1583C						.						61	57	59					X																	29973429		2202	4300	6502	SO:0001583	missense	11141	exon11			CCCTGAAGCACAC	AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5996	protein-coding gene	gene with protein product		300206	"mental retardation, X-linked 34", "mental retardation, X-linked 21", "mental retardation, X-linked 10"	IL1RAPL, MRX34, MRX21, MRX10		10471494, 10757639	Standard	NM_014271		Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.1583A>C	X.37:g.29973429A>C	ENSP00000368278:p.Lys528Thr	Somatic	192	1		WXS	Illumina HiSeq	Phase_I	127	61	NM_014271	0	0	0	0	0	A0AVG4|Q9UJ53	Missense_Mutation	SNP	ENST00000378993.1	37	CCDS14218.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.139991	0.56936	.	.	ENSG00000169306	ENST00000378993;ENST00000302196	T;T	0.09723	2.95;2.95	5.69	5.69	0.88448	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.85682	D	0.000000	T	0.37972	0.1023	M	0.86028	2.79	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.31392	-0.9945	9	.	.	.	.	14.9698	0.71223	1.0:0.0:0.0:0.0	.	528	Q9NZN1	IRPL1_HUMAN	T	528	ENSP00000368278:K528T;ENSP00000305200:K528T	.	K	+	2	0	IL1RAPL1	29883350	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.962000	0.93254	1.918000	0.55548	0.486000	0.48141	AAG	.		0.413	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056155.1	NM_014271		C	29973429	A	C	29973429	3	2	39	1	0	0	0	0	1	0	0	0	7682	72	3	5	1621	5	IL1RAPL1	23	29973429	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10		29973429	125297131	112	3557											
ERCC6L	54821	broad.mit.edu;bcgsc.ca	37	chrX	71427693	71427693	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagatattttaaatcccaaGgctttttctcctggggtagc	9	15	8	9	0	2	1	1	0	1	1	4	1	3	1	2	3	1	2	2	3	5	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:71427693G>T	ENST00000334463.3	-	2	1059	c.924C>A	c.(922-924)gcC>gcA	p.A308A	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Silent_p.A185A	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	308					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					TAAATCCCAAGGCTTTTTCTC	0.388																																					p.A308A													.	ERCC6L-93	0			c.C924A						.						80	82	81					X																	71427693		2203	4299	6502	SO:0001819	synonymous_variant	54821	exon2			TCCCAAGGCTTTT	AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.924C>A	X.37:g.71427693G>T		Somatic	222	0		WXS	Illumina HiSeq	Phase_I	149	6	NM_017669	0	0	0	0	0	Q8NCI1|Q96H93|Q9NXQ8	Silent	SNP	ENST00000334463.3	37	CCDS35329.1																																																																																			.		0.388	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71427693	G	T	71427693	2	4	39	1	0	0	0	0	0	0	0	1	5231	987	35	4		4	ERCC6L	23	71427693	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	41454264	71427693	83842867	113	3558											
TCEAL4	79921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	102841991	102841991	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggaaagccaaaagaaaaActaataaggggctggctcat	18	5	10	8	0	1	1	1	0	0	1	1	2	1	2	2	4	2	2	2	4	7	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:102841991A>G	ENST00000472745.1	+	3	940	c.388A>G	c.(388-390)Act>Gct	p.T130A	TCEAL4_ENST00000494801.1_Missense_Mutation_p.T130A|TCEAL4_ENST00000415568.2_Missense_Mutation_p.T130A|TCEAL4_ENST00000468024.1_Missense_Mutation_p.T130A|TCEAL4_ENST00000472484.1_Missense_Mutation_p.T130A|TCEAL4_ENST00000372629.4_Missense_Mutation_p.T273A			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						CAAAAGAAAAACTAATAAGGG	0.458																																					p.T130A		.											.	TCEAL4-130	0			c.A388G						.						103	105	104					X																	102841991		2203	4300	6503	SO:0001583	missense	79921	exon3			AGAAAAACTAATA	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.388A>G	X.37:g.102841991A>G	ENSP00000424314:p.Thr130Ala	Somatic	259	0		WXS	Illumina HiSeq	Phase_I	166	74	NM_001006935	0	0	18	163	145	Q8WY12|Q9H2H1|Q9H775	Missense_Mutation	SNP	ENST00000472745.1	37	CCDS14510.2	.	.	.	.	.	.	.	.	.	.	A	16.75	3.208774	0.58343	.	.	ENSG00000133142	ENST00000372629;ENST00000468024;ENST00000472484;ENST00000415568;ENST00000414064;ENST00000472745;ENST00000494801	T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89	3.99	2.8	0.32819	.	0.000000	0.48767	D	0.000161	T	0.24812	0.0602	M	0.74258	2.255	0.24242	N	0.995359	D	0.67145	0.996	P	0.62649	0.905	T	0.03296	-1.1051	10	0.56958	D	0.05	.	6.7545	0.23505	0.7622:0.2378:0.0:0.0	.	130	Q96EI5	TCAL4_HUMAN	A	273;130;130;130;101;130;130	ENSP00000361712:T273A;ENSP00000421857:T130A;ENSP00000421156:T130A;ENSP00000415564:T130A;ENSP00000424314:T130A;ENSP00000427494:T130A	ENSP00000361712:T273A	T	+	1	0	TCEAL4	102728647	1.000000	0.71417	0.931000	0.37212	0.715000	0.41141	1.685000	0.37659	0.692000	0.31613	0.352000	0.21897	ACT	.		0.458	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		G	102841991	A	G	102841991	3	3	39	1	0	0	0	0	1	0	0	0	15705	43	2	3	390	3	TCEAL4	23	102841991	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	31414298	102841991	52428569	114	3559											
DDX26B	203522	broad.mit.edu	37	chrX	134706893	134706893	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagaaatcacaggggaaactGcacttagactgacagaattg	17	7	10	7	0	1	4	1	1	0	3	1	5	1	5	0	2	2	1	0	2	5	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:134706893G>T	ENST00000370752.4	+	11	1775	c.1441G>T	c.(1441-1443)Gca>Tca	p.A481S	DDX26B_ENST00000481908.1_3'UTR	NM_182540.4	NP_872346.3	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B	481										large_intestine(1)|lung(8)	9	Acute lymphoblastic leukemia(192;6.56e-05)					AGGGGAAACTGCACTTAGACT	0.338																																					p.A481S													.	DDX26B-226	0			c.G1441T						.						72	74	74					X																	134706893		2203	4300	6503	SO:0001583	missense	203522	exon11			GAAACTGCACTTA	AK096544	CCDS35401.1	Xq26	2008-02-05			ENSG00000165359	ENSG00000165359		"DEAD-boxes"	27334	protein-coding gene	gene with protein product							Standard	NM_182540		Approved	FLJ41215	uc004eyw.4	Q5JSJ4	OTTHUMG00000022484	ENST00000370752.4:c.1441G>T	X.37:g.134706893G>T	ENSP00000359788:p.Ala481Ser	Somatic	354	0		WXS	Illumina HiSeq	Phase_I	218	4	NM_182540	0	0	8	8	0	Q5CZA2|Q6IPS3|Q6ZTU5|Q6ZWE4	Missense_Mutation	SNP	ENST00000370752.4	37	CCDS35401.1	.	.	.	.	.	.	.	.	.	.	G	5.243	0.230241	0.09969	.	.	ENSG00000165359	ENST00000370752	T	0.32023	1.47	5.35	2.23	0.28157	.	0.306915	0.40728	N	0.001032	T	0.07818	0.0196	N	0.02011	-0.69	0.30065	N	0.810556	B;B	0.11235	0.004;0.001	B;B	0.06405	0.002;0.001	T	0.22138	-1.0225	10	0.07482	T	0.82	-1.5046	1.9908	0.03446	0.1032:0.2478:0.364:0.2849	.	481;481	B9EIK3;Q5JSJ4	.;DX26B_HUMAN	S	481	ENSP00000359788:A481S	ENSP00000359788:A481S	A	+	1	0	DDX26B	134534559	1.000000	0.71417	0.529000	0.27951	0.164000	0.22412	1.954000	0.40362	0.507000	0.28148	-0.199000	0.12753	GCA	.		0.338	DDX26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058420.1	NM_182540		T	134706893	G	T	134706893	3	4	39	1	0	0	0	0	1	0	0	0	4359	1319	46	4	1483	4	DDX26B	23	134706893	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	31864902	134706893	20563667	115	3560											
F8	2157	broad.mit.edu	37	chrX	154159037	154159037	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagagatgctaactttgaAtaaggcattatctttagtca	15	13	7	6	0	2	2	1	1	1	1	2	3	2	2	0	1	2	2	0	1	6	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:154159037A>C	ENST00000360256.4	-	14	3228	c.3028T>G	c.(3028-3030)Ttc>Gtc	p.F1010V		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1010	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTAACTTTGAATAAGGCATTA	0.343																																					p.F1010V													.	F8-182	0			c.T3028G						.						78	75	76					X																	154159037		2203	4297	6500	SO:0001583	missense	2157	exon14			CTTTGAATAAGGC	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3028T>G	X.37:g.154159037A>C	ENSP00000353393:p.Phe1010Val	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	75	4	NM_000132	0	0	0	0	0	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	A	7.261	0.605220	0.14002	.	.	ENSG00000185010	ENST00000360256	D	0.99270	-5.66	5.33	2.89	0.33648	.	0.800309	0.11930	N	0.515829	D	0.97105	0.9054	M	0.62723	1.935	0.09310	N	1	P	0.39282	0.666	B	0.30179	0.112	D	0.93758	0.7064	10	0.33141	T	0.24	-1.944	4.1394	0.10186	0.6844:0.2081:0.1075:0.0	.	1010	P00451	FA8_HUMAN	V	1010	ENSP00000353393:F1010V	ENSP00000353393:F1010V	F	-	1	0	F8	153812231	0.371000	0.25056	0.045000	0.18777	0.247000	0.25773	1.497000	0.35649	0.646000	0.30693	0.451000	0.29950	TTC	.		0.343	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			C	154159037	A	C	154159037	3	2	39	1	0	0	0	0	1	0	0	0	5363	101	4	5	4107	5	F8	23	154159037	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	19452144	154159037	1111523	116	3561											
GABRD	2563	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1960690	1960690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagccaggcggcggtgcccGccagggtgtctctaggtacg	5	7	16	13	4	2	0	1	0	1	0	3	0	2	0	3	5	3	1	3	5	2	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:1960690G>A	ENST00000378585.4	+	7	915	c.832G>A	c.(832-834)Gcc>Acc	p.A278T		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	278					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	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)|Ketazolam(DB01587)|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)	GGCGGTGCCCGCCAGGGTGTC	0.682																																					p.A278T		.											.	GABRD-92	0			c.G832A						.						37	32	34					1																	1960690		2180	4269	6449	SO:0001583	missense	2563	exon7			GTGCCCGCCAGGG	BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4084	protein-coding gene	gene with protein product	"GABA(A) receptor, delta"	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.832G>A	1.37:g.1960690G>A	ENSP00000367848:p.Ala278Thr	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	56	9	NM_000815	0	0	2	2	0	Q8N4N9	Missense_Mutation	SNP	ENST00000378585.4	37	CCDS36.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624127	0.87560	.	.	ENSG00000187730	ENST00000378585	D	0.86164	-2.08	4.23	4.23	0.50019	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95198	0.8443	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96541	0.9400	10	0.87932	D	0	-18.1939	16.1634	0.81734	0.0:0.0:1.0:0.0	.	278	O14764	GBRD_HUMAN	T	278	ENSP00000367848:A278T	ENSP00000367848:A278T	A	+	1	0	GABRD	1950550	1.000000	0.71417	0.998000	0.56505	0.588000	0.36517	9.302000	0.96175	2.367000	0.80283	0.655000	0.94253	GCC	.		0.682	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098493.1	NM_000815		A	1960690	G	A	1960690	3	1	40	1	0	0	0	0	1	0	0	0	6188	1087	38	1	858	1	GABRD	1	1960690	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		1960690	247289931	1	3562											
ARID1A	8289	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27100918	27100918	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactgggcaggggcagccTcagcagcagcagttgccccc	8	4	14	15	0	1	0	1	0	0	0	1	0	1	0	3	3	6	7	3	3	0	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:27100918T>C	ENST00000324856.7	+	18	4571	c.4200T>C	c.(4198-4200)ccT>ccC	p.P1400P	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Silent_p.P1017P|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1400	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AGGGGCAGCCTCAGCAGCAGC	0.602			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.P1400P				Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.T4200C						.						43	42	42					1																	27100918		2203	4298	6501	SO:0001819	synonymous_variant	8289	exon18			GCAGCCTCAGCAG	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4200T>C	1.37:g.27100918T>C		Somatic	198	1		WXS	Illumina HiSeq	Phase_I	136	33	NM_006015	0	0	1	1	0	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	6.383	0.438690	0.12104	.	.	ENSG00000117713	ENST00000430799	.	.	.	5.84	-2.21	0.06973	.	.	.	.	.	T	0.42517	0.1206	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34875	-0.9811	4	.	.	.	-2.6103	3.654	0.08214	0.1906:0.2999:0.399:0.1105	.	.	.	.	P	297	.	.	S	+	1	0	ARID1A	26973505	0.996000	0.38824	0.991000	0.47740	0.939000	0.58152	0.430000	0.21428	-0.039000	0.13602	-0.313000	0.08912	TCA	.		0.602	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27100918	T	C	27100918	2	2	40	1	0	0	0	0	0	0	0	1	913	1538	54	3		3	ARID1A	1	27100918	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	25140228	27100918	222149703	2	3563											
NUDC	10726	broad.mit.edu	37	chr1	27268248	27268248	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgctctttgccccagaaaaAggatgcagagaatcatgagg	13	8	12	8	0	2	3	1	1	1	2	2	5	2	4	2	2	3	2	2	2	3	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:27268248A>G	ENST00000321265.5	+	4	491	c.368A>G	c.(367-369)aAg>aGg	p.K123R		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	123					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		CCCCAGAAAAAGGATGCAGAG	0.597																																					p.K123R													.	NUDC-91	0			c.A368G						.						63	59	60					1																	27268248		2203	4300	6503	SO:0001583	missense	10726	exon4			AGAAAAAGGATGC		CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"nuclear distribution gene C homolog (A. nidulans)", "nuclear distribution C homolog (A. nidulans)"				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.368A>G	1.37:g.27268248A>G	ENSP00000319664:p.Lys123Arg	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	162	4	NM_006600	0	0	0	0	0	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	37	CCDS292.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.286148	0.40394	.	.	ENSG00000090273	ENST00000435827;ENST00000321265;ENST00000452707	D	0.81908	-1.55	4.37	3.23	0.37069	.	0.090778	0.85682	D	0.000000	D	0.87414	0.6171	M	0.86502	2.82	0.43110	D	0.994819	D;B	0.58268	0.982;0.092	P;B	0.54664	0.758;0.086	D	0.85550	0.1221	10	0.40728	T	0.16	.	7.0842	0.25247	0.8125:0.0:0.1875:0.0	.	74;123	Q9H2R7;Q9Y266	.;NUDC_HUMAN	R	127;123;74	ENSP00000319664:K123R	ENSP00000319664:K123R	K	+	2	0	NUDC	27140835	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	3.248000	0.51430	0.847000	0.35167	0.533000	0.62120	AAG	.		0.597	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			G	27268248	A	G	27268248	3	3	40	1	0	0	0	0	1	0	0	0	10747	72	3	3	382	3	NUDC	1	27268248	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	167330	27268248	221982373	3	3564											
FGR	2268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27943445	27943445	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtagccgcccatgtccagtTtgcggatcttgtaatgcttc	7	13	10	11	2	1	0	0	0	1	0	3	1	2	1	3	1	3	4	3	1	2	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:27943445T>A	ENST00000374005.3	-	7	893	c.605A>T	c.(604-606)aAa>aTa	p.K202I	FGR_ENST00000399173.1_Missense_Mutation_p.K202I|FGR_ENST00000545953.1_Missense_Mutation_p.K136I|FGR_ENST00000374004.1_Missense_Mutation_p.K202I	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	202	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CATGTCCAGTTTGCGGATCTT	0.562																																					p.K202I		.											.	FGR-547	0			c.A605T						.						172	152	159					1																	27943445		2203	4300	6503	SO:0001583	missense	2268	exon7			TCCAGTTTGCGGA	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.605A>T	1.37:g.27943445T>A	ENSP00000363117:p.Lys202Ile	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	139	29	NM_001042729	0	0	21	21	0	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	37	CCDS305.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.098543	0.56183	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	4.38	4.38	0.52667	SH2 motif (5);	0.000000	0.56097	D	0.000024	D	0.90662	0.7071	M	0.81497	2.545	0.32422	N	0.549198	B	0.22080	0.064	B	0.36289	0.221	D	0.92358	0.5895	10	0.62326	D	0.03	.	13.1133	0.59285	0.0:0.0:0.0:1.0	.	202	P09769	FGR_HUMAN	I	202;136;202;202;202;202	ENSP00000363117:K202I;ENSP00000445302:K136I;ENSP00000382126:K202I;ENSP00000363116:K202I;ENSP00000363115:K202I;ENSP00000407670:K202I	ENSP00000363115:K202I	K	-	2	0	FGR	27816032	1.000000	0.71417	0.927000	0.36925	0.561000	0.35649	8.040000	0.89188	1.903000	0.55091	0.402000	0.26972	AAA	.		0.562	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		A	27943445	T	A	27943445	3	1	40	1	0	0	0	0	1	0	0	0	5893	1841	64	5	1012	5	FGR	1	27943445	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	675197	27943445	221307176	4	3565											
MRPS15	64960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36921882	36921882	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caattcccagcccccagcatAtcttctcaaagacatcatag	13	9	4	15	0	3	1	2	0	2	1	5	1	4	1	3	0	2	1	3	0	4	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:36921882A>G	ENST00000373116.5	-	7	703	c.542T>C	c.(541-543)aTa>aCa	p.I181T	MRPS15_ENST00000488606.1_5'UTR	NM_031280.3	NP_112570.2	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15	181					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCCCCAGCATATCTTCTCAAA	0.498																																					p.I181T		.											.	MRPS15-91	0			c.T542C						.						93	87	89					1																	36921882		2203	4300	6503	SO:0001583	missense	64960	exon7			CAGCATATCTTCT	AB049946	CCDS411.1	1p34.3	2012-09-13			ENSG00000116898	ENSG00000116898		"Mitochondrial ribosomal proteins / small subunits"	14504	protein-coding gene	gene with protein product		611979					Standard	NM_031280		Approved	FLJ11564	uc001cas.2	P82914	OTTHUMG00000008042	ENST00000373116.5:c.542T>C	1.37:g.36921882A>G	ENSP00000362208:p.Ile181Thr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	72	22	NM_031280	0	0	109	189	80	B2RD82|Q9H2K1	Missense_Mutation	SNP	ENST00000373116.5	37	CCDS411.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.615508	0.00828	.	.	ENSG00000116898	ENST00000373116	.	.	.	6.17	-2.05	0.07321	S15/NS1, RNA-binding (2);	0.501132	0.23960	N	0.042864	T	0.19846	0.0477	N	0.14661	0.345	0.09310	N	0.999999	B	0.09022	0.002	B	0.09377	0.004	T	0.29971	-0.9994	9	0.07813	T	0.8	-14.528	12.7078	0.57070	0.5586:0.0:0.4414:0.0	.	181	P82914	RT15_HUMAN	T	181	.	ENSP00000362208:I181T	I	-	2	0	MRPS15	36694469	0.606000	0.26949	0.007000	0.13788	0.015000	0.08874	1.243000	0.32767	-0.243000	0.09653	-0.899000	0.02877	ATA	.		0.498	MRPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022052.2	NM_031280		G	36921882	A	G	36921882	3	3	40	1	0	0	0	0	1	0	0	0	9850	449	16	3	239	3	MRPS15	1	36921882	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	8978437	36921882	212328739	5	3566											
BCAR3	8412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94033045	94033045	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgtttgggggaacacatgtgGactctgaagaataaggagta	13	10	14	4	0	1	2	0	1	1	1	1	5	1	5	0	4	1	2	0	4	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:94033045G>C	ENST00000370244.1	-	13	2378	c.2090C>G	c.(2089-2091)tCc>tGc	p.S697C	BCAR3_ENST00000539242.1_Missense_Mutation_p.S373C|BCAR3_ENST00000370247.3_Missense_Mutation_p.S606C|BCAR3_ENST00000260502.6_Missense_Mutation_p.S697C|BCAR3_ENST00000370243.1_Missense_Mutation_p.S697C	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	697	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		AACACATGTGGACTCTGAAGA	0.463																																					p.S697C		.											.	BCAR3-228	0			c.C2090G						.						103	107	105					1																	94033045		2203	4300	6503	SO:0001583	missense	8412	exon11			CATGTGGACTCTG	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"SH2 domain containing"	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.2090C>G	1.37:g.94033045G>C	ENSP00000359264:p.Ser697Cys	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	63	14	NM_001261409	0	0	0	0	0	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	37	CCDS745.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475298	0.63737	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243;ENST00000539242	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.85	4.92	0.64577	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.709965	0.14950	N	0.288969	T	0.26521	0.0648	L	0.53249	1.67	0.09310	N	1	P;P	0.52692	0.955;0.955	P;P	0.52598	0.703;0.703	T	0.12400	-1.0549	10	0.38643	T	0.18	-19.933	7.5531	0.27808	0.1189:0.0:0.7329:0.1482	.	697;606	O75815;Q5TEW3	BCAR3_HUMAN;.	C	606;697;697;697;373	ENSP00000359267:S606C;ENSP00000260502:S697C;ENSP00000359264:S697C;ENSP00000359263:S697C;ENSP00000441343:S373C	ENSP00000260502:S697C	S	-	2	0	BCAR3	93805633	1.000000	0.71417	0.201000	0.23476	0.452000	0.32318	3.862000	0.56009	1.434000	0.47414	0.655000	0.94253	TCC	.		0.463	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			C	94033045	G	C	94033045	3	2	40	1	0	0	0	0	1	0	0	0	1350	1174	41	4	395	4	BCAR3	1	94033045	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	57111163	94033045	155217576	6	3567											
DRAM2	128338	broad.mit.edu	37	chr1	111667502	111667502	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaacataaatggtagcaatGcctgggaaaagataatccaa	18	7	9	7	1	0	1	0	0	0	1	1	3	1	2	2	2	3	2	2	2	9	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:111667502G>T	ENST00000286692.4	-	5	818	c.201C>A	c.(199-201)tgC>tgA	p.C67*	DRAM2_ENST00000484310.1_5'UTR|DRAM2_ENST00000539140.1_Splice_Site_p.C67*			Q6UX65	DRAM2_HUMAN	DNA-damage regulated autophagy modulator 2	67					apoptotic process (GO:0006915)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|microtubule cytoskeleton (GO:0015630)				endometrium(1)|large_intestine(5)|lung(3)	9						TGGTAGCAATGCCTGGGAAAA	0.358																																					p.C67X													.	DRAM2-90	0			c.C201A						.						64	60	61					1																	111667502		2203	4300	6503	SO:0001630	splice_region_variant	128338	exon5			AGCAATGCCTGGG	AY336747	CCDS30801.1	1p13.3	2010-07-08	2009-06-12	2009-06-12	ENSG00000156171	ENSG00000156171			28769	protein-coding gene	gene with protein product		613360	"transmembrane protein 77"	TMEM77		12975309	Standard	NM_178454		Approved	MGC54289, PRO180, WWFQ154, RP5-1180E21.1	uc001ead.4	Q6UX65	OTTHUMG00000011911	ENST00000286692.4:c.200-1C>A	1.37:g.111667502G>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	63	4	NM_178454	0	0	0	0	0	B3SUG9|Q4VWF6|Q86VD3|Q8NBQ4	Nonsense_Mutation	SNP	ENST00000286692.4	37	CCDS30801.1	.	.	.	.	.	.	.	.	.	.	G	32	5.181425	0.94885	.	.	ENSG00000156171	ENST00000286692;ENST00000539140	.	.	.	6.17	-0.548	0.11833	.	0.205806	0.49916	D	0.000140	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	4.0975	0.09998	0.4393:0.0:0.4001:0.1606	.	.	.	.	X	67	.	ENSP00000286692:C67X	C	-	3	2	DRAM2	111469025	0.001000	0.12720	0.740000	0.30986	0.933000	0.57130	-0.417000	0.07088	0.197000	0.20387	-0.140000	0.14226	TGC	.		0.358	DRAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032930.3	NM_178454	Nonsense_Mutation	T	111667502	G	T	111667502	5	4	40	1	0	0	0	0	0	0	1	0	4765	1333	46	4	619	4	DRAM2	1	111667502	Splice_Site	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	17634457	111667502	137583119	7	3568											
FLG	2312	broad.mit.edu	37	chr1	152276113	152276113	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtcctgaccctcttgggacGctgagtgcctggagctgtct	4	12	13	12	1	2	2	0	2	2	0	3	4	3	4	3	2	2	2	3	2	0	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:152276113G>T	ENST00000368799.1	-	3	11284	c.11249C>A	c.(11248-11250)gCg>gAg	p.A3750E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3750	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTTGGGACGCTGAGTGCCT	0.602									Ichthyosis																												p.A3750E													.	FLG-106	0			c.C11249A						.						288	285	286					1																	152276113		2203	4297	6500	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGCTGAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11249C>A	1.37:g.152276113G>T	ENSP00000357789:p.Ala3750Glu	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	140	4	NM_002016	0	0	0	0	0	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	6.071	0.381482	0.11524	.	.	ENSG00000143631	ENST00000368799	T	0.01804	4.63	3.25	-6.5	0.01884	.	.	.	.	.	T	0.01029	0.0034	M	0.70595	2.14	0.09310	N	1	D	0.71674	0.998	D	0.67900	0.954	T	0.49360	-0.8948	9	0.07325	T	0.83	.	1.64	0.02750	0.1646:0.2649:0.4071:0.1633	.	3750	P20930	FILA_HUMAN	E	3750	ENSP00000357789:A3750E	ENSP00000357789:A3750E	A	-	2	0	FLG	150542737	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.206000	0.00274	-4.070000	0.00076	-1.430000	0.01095	GCG	.		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152276113	G	T	152276113	3	4	40	1	0	0	0	0	1	0	0	0	5941	1087	38	4	940	4	FLG	1	152276113	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	40608611	152276113	96974508	8	3569											
GON4L	54856	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	155734744	155734744	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatatcaataagtgatacAtattactgagtccacgaaat	16	11	7	7	1	1	2	1	2	0	0	2	3	2	2	1	1	2	1	1	1	7	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:155734744A>G	ENST00000368331.1	-	21	4522				GON4L_ENST00000437809.1_Intron|GON4L_ENST00000361040.5_Missense_Mutation_p.M1507T|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000271883.5_Intron	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TAAGTGATACATATTACTGAG	0.398																																					p.M1507T		.											.	GON4L-93	0			c.T4520C						.						84	76	78					1																	155734744		2203	4300	6503	SO:0001627	intron_variant	54856	exon21			TGATACATATTAC	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.4473+46T>C	1.37:g.155734744A>G		Somatic	299	0		WXS	Illumina HiSeq	Phase_I	303	86	NM_032292	0	0	6	9	3	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	A	10.67	1.416623	0.25552	.	.	ENSG00000116580	ENST00000361040	T	0.11277	2.79	4.47	-0.731	0.11151	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.46693	-0.9173	9	0.87932	D	0	.	4.9844	0.14182	0.5165:0.3159:0.1676:0.0	.	1507	Q3T8J9-2	.	T	1507	ENSP00000354322:M1507T	ENSP00000354322:M1507T	M	-	2	0	GON4L	154001368	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.744000	0.04839	-0.308000	0.08792	0.378000	0.23410	ATG	.		0.398	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		G	155734744	A	G	155734744	1	3	40	0	1	0	0	0	0	0	0	0	6592	217	8	3		3	GON4L	1	155734744	Intron	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	3458631	155734744	93515877	9	3570											
GORAB	92344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	170508438	170508438	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccttgtagagcaaagccaaaAacttgggcttcaagatggat	14	9	10	8	0	1	2	1	0	0	2	1	3	1	3	2	2	3	3	2	2	5	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:170508438A>C	ENST00000367763.3	+	2	244	c.224A>C	c.(223-225)aAa>aCa	p.K75T	GORAB_ENST00000367762.1_Missense_Mutation_p.K75T|GORAB_ENST00000465717.1_3'UTR	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	75						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						CAAAGCCAAAAACTTGGGCTT	0.443																																					p.K75T		.											.	GORAB-90	0			c.A224C						.						107	102	104					1																	170508438		2203	4300	6503	SO:0001583	missense	92344	exon2			GCCAAAAACTTGG	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"gerodermia osteodysplastica"	607983	"SCY1-like 1 binding protein 1"	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.224A>C	1.37:g.170508438A>C	ENSP00000356737:p.Lys75Thr	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	149	39	NM_152281	0	0	0	1	1	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	37	CCDS1289.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.186138	0.57909	.	.	ENSG00000120370	ENST00000367763;ENST00000367762	T;T	0.63580	-0.05;-0.05	5.49	4.37	0.52481	.	0.297450	0.41194	D	0.000932	T	0.62307	0.2417	M	0.70275	2.135	0.32365	N	0.556672	D	0.71674	0.998	D	0.66351	0.943	T	0.66268	-0.5966	10	0.56958	D	0.05	-12.6953	6.2817	0.21011	0.7838:0.0:0.0755:0.1408	.	75	Q5T7V8	GORAB_HUMAN	T	75	ENSP00000356737:K75T;ENSP00000356736:K75T	ENSP00000356736:K75T	K	+	2	0	GORAB	168775062	1.000000	0.71417	1.000000	0.80357	0.654000	0.38779	2.106000	0.41835	0.919000	0.36945	0.528000	0.53228	AAA	.		0.443	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281		C	170508438	A	C	170508438	3	2	40	1	0	0	0	0	1	0	0	0	6594	14	1	5	230	5	GORAB	1	170508438	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	14773694	170508438	78742183	10	3571											
PRDX6	9588	bcgsc.ca	37	chr1	173454533	173454534	+	Frame_Shift_Ins	INS	-	-	AAAAAAA																															caattgtgaagagcccacagINSaaaagttaccttttcccatc																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:173454533_173454534insAAAAAAA	ENST00000340385.5	+	3	418_419	c.286_287insAAAAAAA	c.(286-288)gaafs	p.-96fs	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6						hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)	p.E96*(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						AGAGCCCACAGAAAAGTTACCT	0.441																																					p.E96fs													.	PRDX6-186	1	Substitution - Nonsense(1)	urinary_tract(1)	c.286_287insAAAAAAA						.																																			SO:0001589	frameshift_variant	9588	exon3			CCCACAGAAAAGT	D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	Exception_encountered	1.37:g.173454533_173454534insAAAAAAA	ENSP00000342026:p.Glu96fs	Somatic	152	0		WXS	Illumina HiSeq	Phase_1	131	0	NM_004905	0	0	0	0	0	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Frame_Shift_Ins	INS	ENST00000340385.5	37	CCDS1307.1																																																																																			.		0.441	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		AAAAAAA	173454534	-	AAAAAAA	173454533	7	5	40	1	0	1	1	0	0	0	0	0	12498	943	33	0	296	0	PRDX6	1	173454533	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	2946095	173454533	75796088	11	3572											
TEDDM1	127670	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	182369011	182369011	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcattgatcatcacatgccAgcagaagaaggtggtgacaa	14	7	12	8	0	2	4	2	2	0	2	2	4	2	4	1	3	2	2	1	3	3	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:182369011A>G	ENST00000367565.1	-	1	740	c.610T>C	c.(610-612)Tgg>Cgg	p.W204R		NM_172000.3	NP_741997.3	Q5T9Z0	TEDM1_HUMAN	transmembrane epididymal protein 1	204						integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)	7						ATCACATGCCAGCAGAAGAAG	0.488																																					p.W204R													.	TEDDM1-92	0			c.T610C						.						96	87	90					1																	182369011		2203	4300	6503	SO:0001583	missense	127670	exon1			CATGCCAGCAGAA	AJ515384	CCDS30953.1	1q25.3	2009-09-17		2005-08-09	ENSG00000203730	ENSG00000203730			30233	protein-coding gene	gene with protein product	"putative membrane protein HE9", "transmembrane protein 45C", "epididymal protein 9"						Standard	NM_172000		Approved	HE9, Epdd1, TMEM45C, EDDM9	uc001gpe.3	Q5T9Z0	OTTHUMG00000037398	ENST00000367565.1:c.610T>C	1.37:g.182369011A>G	ENSP00000356536:p.Trp204Arg	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	114	29	NM_172000	0	0	0	0	0	Q8IVJ0	Missense_Mutation	SNP	ENST00000367565.1	37	CCDS30953.1	.	.	.	.	.	.	.	.	.	.	A	17.12	3.307925	0.60305	.	.	ENSG00000203730	ENST00000367565	T	0.53857	0.6	4.82	3.7	0.42460	.	0.000000	0.64402	D	0.000014	T	0.72252	0.3437	M	0.86864	2.845	0.33542	D	0.595044	D	0.89917	1.0	D	0.97110	1.0	T	0.80144	-0.1505	10	0.87932	D	0	-25.2564	8.2528	0.31737	0.9058:0.0:0.0942:0.0	.	204	Q5T9Z0	TEDM1_HUMAN	R	204	ENSP00000356536:W204R	ENSP00000356536:W204R	W	-	1	0	TEDDM1	180635634	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	2.946000	0.49050	0.880000	0.35969	0.460000	0.39030	TGG	.		0.488	TEDDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091029.1	NM_172000		G	182369011	A	G	182369011	3	3	40	1	0	0	0	0	1	0	0	0	15781	188	7	3	215	3	TEDDM1	1	182369011	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	8914478	182369011	66881610	12	3573											
LGTN	1939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	206767112	206767112	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgagtatgggtccagacCataggcctccaagttccgga	10	8	11	12	1	0	2	0	1	0	1	3	3	3	3	5	3	0	2	5	3	3	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:206767112C>T	ENST00000271764.2	-	14	1748	c.1540G>A	c.(1540-1542)Ggt>Agt	p.G514S	EIF2D_ENST00000367114.3_Missense_Mutation_p.G390S|EIF2D_ENST00000472709.2_Intron	NM_006893.2	NP_008824.2	P41214	EIF2D_HUMAN	eukaryotic translation initiation factor 2D	514	SUI1. {ECO:0000255|PROSITE- ProRule:PRU00200}.				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						GGGTCCAGACCATAGGCCTCC	0.622																																					p.G514S		.											.	EIF2D-92	0			c.G1540A						.						59	53	55					1																	206767112		2203	4300	6503	SO:0001583	missense	1939	exon14			CCAGACCATAGGC	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.1540G>A	1.37:g.206767112C>T	ENSP00000271764:p.Gly514Ser	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	37	8	NM_006893	0	0	82	122	40	Q5SY40|Q8IXV3|Q96DG3|Q96TG7|Q9NR27|Q9NSN0|Q9NV18|Q9NZ21	Missense_Mutation	SNP	ENST00000271764.2	37	CCDS1465.1	.	.	.	.	.	.	.	.	.	.	C	35	5.545011	0.96488	.	.	ENSG00000143486	ENST00000367114;ENST00000271764	T;T	0.31510	1.49;1.49	5.68	5.68	0.88126	Translation initiation factor SUI1 (3);	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.976	T	0.44050	-0.9353	10	0.21540	T	0.41	-19.8057	18.7742	0.91904	0.0:1.0:0.0:0.0	.	390;514	P41214-2;P41214	.;EIF2D_HUMAN	S	390;514	ENSP00000356081:G390S;ENSP00000271764:G514S	ENSP00000271764:G514S	G	-	1	0	EIF2D	204833735	1.000000	0.71417	0.991000	0.47740	0.995000	0.86356	7.586000	0.82596	2.676000	0.91093	0.563000	0.77884	GGT	.		0.622	EIF2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088475.1	NM_006893		T	206767112	C	T	206767112	3	4	40	1	0	0	0	0	1	0	0	0	8782	594	21	2	222	2	LGTN	1	206767112	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	24398101	206767112	42483509	13	3574											
PLXNA2	5362	broad.mit.edu	37	chr1	208257763	208257763	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgctggagctgttgaagcGcagagcggggacccggtgga	9	5	18	9	4	0	2	0	1	0	1	0	5	0	5	1	5	4	4	1	5	2	1	rs374437126		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:208257763G>A	ENST00000367033.3	-	10	3017	c.2260C>T	c.(2260-2262)Cgc>Tgc	p.R754C		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	754					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTGTTGAAGCGCAGAGCGGGG	0.622																																					p.R754C													.	PLXNA2-92	0			c.C2260T						.	G	CYS/ARG	0,4406		0,0,2203	64	70	68		2260	5.7	1	1		68	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLXNA2	NM_025179.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	754/1895	208257763	1,13005	2203	4300	6503	SO:0001583	missense	5362	exon10			TGAAGCGCAGAGC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2260C>T	1.37:g.208257763G>A	ENSP00000356000:p.Arg754Cys	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	66	3	NM_025179	0	0	0	0	0	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856472	0.91355	0.0	1.16E-4	ENSG00000076356	ENST00000367033	T	0.01025	5.43	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.08044	0.0201	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.65443	0.935	T	0.01087	-1.1456	10	0.56958	D	0.05	.	19.8253	0.96616	0.0:0.0:1.0:0.0	.	754	O75051	PLXA2_HUMAN	C	754	ENSP00000356000:R754C	ENSP00000356000:R754C	R	-	1	0	PLXNA2	206324386	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.527000	0.81931	2.676000	0.91093	0.650000	0.86243	CGC	.		0.622	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208257763	G	A	208257763	3	1	40	1	0	0	0	0	1	0	0	0	12146	1087	38	1	3516	1	PLXNA2	1	208257763	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	1490651	208257763	40992858	14	3575											
TP53BP2	7159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223983631	223983631	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggtatggagggtactcCtccaggtacacatcaagcac	10	8	13	10	0	1	0	1	0	0	0	3	1	3	1	2	5	3	4	2	5	4	3	rs376978247		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:223983631C>A	ENST00000343537.7	-	13	2901	c.2610G>T	c.(2608-2610)gaG>gaT	p.E870D	TP53BP2_ENST00000391879.2_Missense_Mutation_p.E103D|TP53BP2_ENST00000391878.2_Missense_Mutation_p.E741D|TP53BP2_ENST00000498843.1_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	864	Pro-rich.				cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GAGGGTACTCCTCCAGGTACA	0.572																																					p.E870D		.											.	TP53BP2-229	0			c.G2610T						.						104	105	105					1																	223983631		2203	4300	6503	SO:0001583	missense	7159	exon13			GTACTCCTCCAGG	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2610G>T	1.37:g.223983631C>A	ENSP00000341957:p.Glu870Asp	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	72	19	NM_001031685	0	0	3	8	5	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.85|16.85	3.235801|3.235801	0.58886|0.58886	.|.	.|.	ENSG00000143514|ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879|ENST00000494100	T;T;T|.	0.54279|.	0.68;0.85;0.58|.	5.55|5.55	3.32|3.32	0.38043|0.38043	Src homology-3 domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.60702|.	0.2289|.	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.997;0.997|.	D;D|.	0.72625|.	0.978;0.978|.	T|.	0.54938|.	-0.8218|.	10|.	0.34782|.	T|.	0.22|.	.|.	9.5862|9.5862	0.39517|0.39517	0.0:0.7192:0.0:0.2808|0.0:0.7192:0.0:0.2808	.|.	870;864|.	B4DG66;Q13625|.	.;ASPP2_HUMAN|.	D|X	741;870;103|204	ENSP00000375750:E741D;ENSP00000341957:E870D;ENSP00000375751:E103D|.	ENSP00000341957:E870D|.	E|G	-|-	3|1	2|0	TP53BP2|TP53BP2	222050254|222050254	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.740000|0.740000	0.42216|0.42216	1.205000|1.205000	0.32308|0.32308	0.441000|0.441000	0.26529|0.26529	0.563000|0.563000	0.77884|0.77884	GAG|GGA	.		0.572	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223983631	C	A	223983631	3	1	40	1	0	0	0	0	1	0	0	0	16417	680	24	4	818	4	TP53BP2	1	223983631	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	15725868	223983631	25266990	15	3576											
PARP1	142	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	226555997	226555999	+	In_Frame_Del	DEL	GAG	GAG	-																															ttgagagatccaggatctgaGagtcgctgctgccctgagac																								rs369734863		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:226555997_226555999delGAG	ENST00000366794.5	-	16	2321_2323	c.2178_2180delCTC	c.(2176-2181)gactct>gat	p.S727del	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	727	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CAGGATCTGAGAGTCGCTGCTGC	0.562								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.726_727del		.											.	PARP1-727	0			c.2178_2180del						.																																			SO:0001651	inframe_deletion	142	exon16			.	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2178_2180delCTC	1.37:g.226555997_226555999delGAG	ENSP00000355759:p.Ser727del	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	66	17	NM_001618	0	0	0	0	0	B1ANJ4|Q8IUZ9	In_Frame_Del	DEL	ENST00000366794.5	37	CCDS1554.1																																																																																			.		0.562	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		-	226555999	GAG	-	226555997	7	5	40	1	0	1	0	1	0	0	0	0	11480	942	33	0	896	0	PARP1	1	226555997	In_Frame_Del	DEL	GAG	TCGA-B1-A656-01A-11D-A31X-10	2572366	226555997	22694624	16	3577											
RPS7	6201	bcgsc.ca	37	chr2	3624203	3624205	+	In_Frame_Del	DEL	GTC	GTC	-																															aaaagttcagtgggaagcatGtcgtctttatcgctcaggta																								rs61730448	byFrequency	TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GTC	GTC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:3624203_3624205delGTC	ENST00000304921.5	+	4	438_440	c.274_276delGTC	c.(274-276)gtcdel	p.V93del	RPS7_ENST00000403564.1_In_Frame_Del_p.V93del|RPS7_ENST00000406376.1_In_Frame_Del_p.V93del|RPS7_ENST00000407445.3_In_Frame_Del_p.V93del	NM_001011.3	NP_001002.1	P62081	RS7_HUMAN	ribosomal protein S7	93					cellular protein metabolic process (GO:0044267)|cytoplasmic translation (GO:0002181)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ribosome (GO:0005840)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(2)|urinary_tract(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0963)|Epithelial(75;0.208)		TGGGAAGCATGTCGTCTTTATCG	0.409																																					p.92_92del													.	RPS7-90	0			c.274_276del						.																																			SO:0001651	inframe_deletion	6201	exon4			AAGCATGTCGTCT		CCDS1648.1	2p25	2011-04-05			ENSG00000171863	ENSG00000171863		"S ribosomal proteins"	10440	protein-coding gene	gene with protein product		603658				8522193, 10625621	Standard	NM_001011		Approved	S7	uc002qxw.3	P62081	OTTHUMG00000090305	ENST00000304921.5:c.274_276delGTC	2.37:g.3624206_3624208delGTC	ENSP00000339095:p.Val93del	Somatic	520	3		WXS	Illumina HiSeq	Phase_1	412	99	NM_001011	0	0	0	0	0	P23821|P24818|Q57Z92|Q6IPH1	In_Frame_Del	DEL	ENST00000304921.5	37	CCDS1648.1																																																																																			.		0.409	RPS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206667.1	NM_001011		-	3624205	GTC	-	3624203	7	5	40	1	0	1	0	1	0	0	0	0	13692	1377	48	0	284	0	RPS7	2	3624203	In_Frame_Del	DEL	GTC	TCGA-B1-A656-01A-11D-A31X-10		3624203	239575170	17	3578											
LPIN1	23175	broad.mit.edu	37	chr2	11925180	11925180	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccctctgcgggggcctcagCgaccaccgggagatcacgaa	8	5	13	15	4	3	1	2	0	1	1	4	4	4	1	4	3	2	0	4	3	1	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:11925180C>T	ENST00000256720.2	+	9	1512	c.1419C>T	c.(1417-1419)agC>agT	p.S473S	LPIN1_ENST00000404113.2_5'Flank|LPIN1_ENST00000425416.2_Silent_p.S479S|LPIN1_ENST00000449576.2_Silent_p.S558S|LPIN1_ENST00000396099.1_Silent_p.S515S|LPIN1_ENST00000396097.1_Silent_p.S203S	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	473					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		GGGGCCTCAGCGACCACCGGG	0.697											OREG0014445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S558S													.	LPIN1-156	0			c.C1674T						.						21	22	21					2																	11925180		2201	4296	6497	SO:0001819	synonymous_variant	23175	exon11			CCTCAGCGACCAC	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1419C>T	2.37:g.11925180C>T		Somatic	97	0	675	WXS	Illumina HiSeq	Phase_I	75	3	NM_001261428	0	0	0	0	0	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			.		0.697	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		T	11925180	C	T	11925180	2	4	40	1	0	0	0	0	0	0	0	1	8943	767	27	1		1	LPIN1	2	11925180	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	8300977	11925180	231274193	18	3579											
MYCN	4613	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	16082258	16082258	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacctcgagtttgactcgctAcagccctgcttctacccgga	7	10	9	15	3	1	1	0	1	1	0	3	4	1	2	3	1	4	3	3	1	2	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:16082258A>G	ENST00000281043.3	+	2	369	c.72A>G	c.(70-72)ctA>ctG	p.L24L	MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000453400.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	24					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TTGACTCGCTACAGCCCTGCT	0.642			A		neuroblastoma																																p.L24L		.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN-1271	0			c.A72G						.						54	56	56					2																	16082258		2203	4300	6503	SO:0001819	synonymous_variant	4613	exon2			CTCGCTACAGCCC	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.72A>G	2.37:g.16082258A>G		Somatic	264	0		WXS	Illumina HiSeq	Phase_I	216	58	NM_005378	0	0	0	0	0	Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	37	CCDS1687.1																																																																																			.		0.642	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		G	16082258	A	G	16082258	2	3	40	1	0	0	0	0	0	0	0	1	10046	378	14	3		3	MYCN	2	16082258	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	4157078	16082258	227117115	19	3580											
DPY30	84661	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32264491	32264491	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccacggcctcctgataccTgcgtttgtccctccagcatc	6	11	7	17	2	0	1	0	1	0	0	5	1	4	1	6	1	3	2	6	1	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:32264491T>A	ENST00000342166.5	-	2	150	c.35A>T	c.(34-36)cAg>cTg	p.Q12L	DPY30_ENST00000295066.3_Splice_Site_p.Q12L			Q9C005	DPY30_HUMAN	dpy-30 homolog (C. elegans)	12					endosomal transport (GO:0016197)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(2)	2	Acute lymphoblastic leukemia(172;0.155)					TCCTGATACCTGCGTTTGTCC	0.567																																					p.Q12L		.											.	DPY30-68	0			c.A35T						.						104	103	103					2																	32264491		2203	4300	6503	SO:0001630	splice_region_variant	84661	exon2			GATACCTGCGTTT		CCDS1777.1	2p22.3	2013-09-09			ENSG00000162961	ENSG00000162961			24590	protein-coding gene	gene with protein product		612032				12477932	Standard	XM_006712117		Approved	Saf19, HDPY-30, Cps25	uc002roa.1	Q9C005	OTTHUMG00000128457	ENST00000342166.5:c.36+1A>T	2.37:g.32264491T>A		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	103	29	NM_032574	0	0	0	0	0	D6W578	Missense_Mutation	SNP	ENST00000342166.5	37	CCDS1777.1	.	.	.	.	.	.	.	.	.	.	T	13.66	2.302365	0.40694	.	.	ENSG00000162961	ENST00000342166;ENST00000295066	.	.	.	5.92	3.54	0.40534	.	0.158879	0.56097	D	0.000023	T	0.44498	0.1296	.	.	.	0.41659	D	0.989174	B	0.14438	0.01	B	0.10450	0.005	T	0.45264	-0.9273	8	0.48119	T	0.1	-14.8864	9.1274	0.36824	0.0:0.0721:0.136:0.7919	.	12	Q9C005	DPY30_HUMAN	L	12	.	ENSP00000295066:Q12L	Q	-	2	0	DPY30	32117995	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	2.804000	0.47931	2.274000	0.75844	0.533000	0.62120	CAG	.		0.567	DPY30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250255.2	NM_032574	Missense_Mutation	A	32264491	T	A	32264491	5	1	40	1	0	0	0	0	0	0	1	0	4755	1594	55	5	280	5	DPY30	2	32264491	Splice_Site	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	16182233	32264491	210934882	20	3581											
EPAS1	2034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	46607787	46607787	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgtcggggatcagcgcaCagagttcttgggagcagcgc	7	6	17	11	4	2	1	1	0	1	1	3	3	2	3	1	4	3	3	1	4	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:46607787C>G	ENST00000263734.3	+	12	2486	c.1976C>G	c.(1975-1977)aCa>aGa	p.T659R		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	659					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			GATCAGCGCACAGAGTTCTTG	0.592																																					p.T659R		.											.	EPAS1-227	0			c.C1976G						.						71	83	79					2																	46607787		2199	4290	6489	SO:0001583	missense	2034	exon12			AGCGCACAGAGTT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1976C>G	2.37:g.46607787C>G	ENSP00000263734:p.Thr659Arg	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	76	17	NM_001430	0	0	5	6	1	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	37	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	C	9.602	1.128965	0.21041	.	.	ENSG00000116016	ENST00000263734	T	0.46451	0.87	4.89	3.08	0.35506	.	1.373260	0.04589	N	0.396496	T	0.30823	0.0777	N	0.22421	0.69	0.09310	N	1	B	0.23316	0.083	B	0.25405	0.06	T	0.26155	-1.0111	10	0.24483	T	0.36	.	6.4229	0.21754	0.1452:0.7017:0.0:0.1531	.	659	Q99814	EPAS1_HUMAN	R	659	ENSP00000263734:T659R	ENSP00000263734:T659R	T	+	2	0	EPAS1	46461291	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	1.108000	0.31123	0.480000	0.27534	-0.237000	0.12165	ACA	.		0.592	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		G	46607787	C	G	46607787	3	3	40	1	0	0	0	0	1	0	0	0	5163	478	17	4	2022	4	EPAS1	2	46607787	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	14343296	46607787	196591586	21	3582											
REV1	51455	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	100019396	100019397	+	Frame_Shift_Ins	INS	-	-	A																															tcatgttttagaaacccatcINSaattaacttctggggactgc																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:100019396_100019397insA	ENST00000258428.3	-	20	3567_3568	c.3339_3340insT	c.(3337-3342)attgatfs	p.D1114fs	REV1_ENST00000393445.3_Frame_Shift_Ins_p.D1113fs|REV1_ENST00000465835.1_5'Flank|RP11-527J8.1_ENST00000608144.1_RNA	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1114					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGAAACCCATCAATTAACTTCT	0.421								Direct reversal of damage																													p.D1114_G1115delinsX		.											.	REV1-92	0			c.3340_3341insT						.																																			SO:0001589	frameshift_variant	51455	exon20			.	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3340dupT	2.37:g.100019398_100019398dupA	ENSP00000258428:p.Asp1114fs	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	98	27	NM_016316	0	0	0	0	0	O95941|Q53SI7|Q9C0J4|Q9NUP2	Nonsense_Mutation	INS	ENST00000258428.3	37	CCDS2045.1																																																																																			.		0.421	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100019397	-	A	100019396	7	5	40	1	0	1	1	0	0	0	0	0	13271	826	29	0	431	0	REV1	2	100019396	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	53411609	100019396	143179977	22	3583											
CNTNAP5	129684	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	125175092	125175092	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcagtgagagcccgatttGttcgctttgtgcccctggaa	7	12	11	11	2	1	1	1	1	0	1	2	4	1	2	3	1	2	2	3	1	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:125175092G>A	ENST00000431078.1	+	4	818	c.454G>A	c.(454-456)Gtt>Att	p.V152I		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	152	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGCCCGATTTGTTCGCTTTGT	0.498																																					p.V152I													.	CNTNAP5-524	0			c.G454A						.						96	100	99					2																	125175092		1990	4172	6162	SO:0001583	missense	129684	exon4			CGATTTGTTCGCT	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.454G>A	2.37:g.125175092G>A	ENSP00000399013:p.Val152Ile	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	125	41	NM_130773	0	0	0	0	0	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974606	0.53720	.	.	ENSG00000155052	ENST00000431078	D	0.97642	-4.47	6.17	-6.25	0.02039	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.767069	0.11093	N	0.600490	D	0.90116	0.6912	N	0.16656	0.425	0.29732	N	0.837787	B	0.02656	0.0	B	0.10450	0.005	T	0.79266	-0.1874	10	0.20046	T	0.44	.	9.7379	0.40399	0.4913:0.3858:0.1229:0.0	.	152	Q8WYK1	CNTP5_HUMAN	I	152	ENSP00000399013:V152I	ENSP00000399013:V152I	V	+	1	0	CNTNAP5	124891562	0.005000	0.15991	0.001000	0.08648	0.952000	0.60782	0.076000	0.14712	-1.035000	0.03291	0.655000	0.94253	GTT	.		0.498	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125175092	G	A	125175092	3	1	40	1	0	0	0	0	1	0	0	0	3656	1377	48	2	468	2	CNTNAP5	2	125175092	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	25155696	125175092	118024281	23	3584											
HIBCH	26275	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	191069874	191069874	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatcactgcttcccaaagacTtaaagtgattattcaaatct	15	13	4	9	0	3	2	2	1	1	1	4	2	4	2	1	0	1	1	1	0	6	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:191069874T>C	ENST00000359678.5	-	14	1424	c.1130A>G	c.(1129-1131)aAg>aGg	p.K377R	HIBCH_ENST00000486981.1_5'UTR|HIBCH_ENST00000410045.1_Missense_Mutation_p.K154R|HIBCH_ENST00000392332.3_3'UTR	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	377					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			TCCCAAAGACTTAAAGTGATT	0.373																																					p.K377R													.	HIBCH-90	0			c.A1130G						.						85	80	82					2																	191069874		2202	4299	6501	SO:0001583	missense	26275	exon14			AAAGACTTAAAGT	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"3-hydroxyisobutyryl-Coenzyme A hydrolase"			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.1130A>G	2.37:g.191069874T>C	ENSP00000352706:p.Lys377Arg	Somatic	111	1		WXS	Illumina HiSeq	Phase_I	107	32	NM_014362	0	0	40	48	8	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Missense_Mutation	SNP	ENST00000359678.5	37	CCDS2304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.26|12.26	1.885753|1.885753	0.33255|0.33255	.|.	.|.	ENSG00000198130|ENSG00000198130	ENST00000359678;ENST00000410045|ENST00000399855	T|.	0.57907|.	0.37|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.226670|.	0.45606|.	D|.	0.000353|.	T|T	0.44477|0.44477	0.1295|0.1295	N|N	0.25825|0.25825	0.765|0.765	0.37023|0.37023	D|D	0.896302|0.896302	B|.	0.12630|.	0.006|.	B|.	0.16289|.	0.015|.	T|T	0.48614|0.48614	-0.9020|-0.9020	10|5	0.15066|.	T|.	0.55|.	-2.683|-2.683	9.365|9.365	0.38219|0.38219	0.0:0.0:0.18:0.82|0.0:0.0:0.18:0.82	.|.	377|.	Q6NVY1|.	HIBCH_HUMAN|.	R|G	377;154|29	ENSP00000352706:K377R|.	ENSP00000352706:K377R|.	K|S	-|-	2|1	0|0	HIBCH|HIBCH	190778119|190778119	0.976000|0.976000	0.34144|0.34144	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	1.768000|1.768000	0.38511|0.38511	2.243000|2.243000	0.73865|0.73865	0.533000|0.533000	0.62120|0.62120	AAG|AGT	.		0.373	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			C	191069874	T	C	191069874	3	2	40	1	0	0	0	0	1	0	0	0	7121	1609	56	3	34	3	HIBCH	2	191069874	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	65894782	191069874	52129499	24	3585											
ALS2	57679	broad.mit.edu	37	chr2	202572610	202572610	+	Frame_Shift_Del	DEL	G	G	-																															accctggctctggtgattcaGatcgggaatctgacttccca																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:202572610delG	ENST00000264276.6	-	28	4757	c.4385delC	c.(4384-4386)tctfs	p.S1462fs	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1462					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TGGTGATTCAGATCGGGAATC	0.488																																					p.S1462fs													.	ALS2-275	0			c.4385delC						.						75	72	73					2																	202572610		1869	4110	5979	SO:0001589	frameshift_variant	57679	exon28			GATTCAGATCGGG	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.4385delC	2.37:g.202572610delG	ENSP00000264276:p.Ser1462fs	Somatic	330	0		WXS	Illumina HiSeq	Phase_I	273	24	NM_020919	0	0	0	0	0	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Frame_Shift_Del	DEL	ENST00000264276.6	37	CCDS42800.1																																																																																			.		0.488	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		-	202572610	G	-	202572610	7	5	40	1	0	1	0	1	0	0	0	0	550	942	33	0	616	0	ALS2	2	202572610	Frame_Shift_Del	DEL	G	TCGA-B1-A656-01A-11D-A31X-10	11502736	202572610	40626763	25	3586	33	2									
ALS2	57679	broad.mit.edu;bcgsc.ca	37	chr2	202572613	202572623	+	Frame_Shift_Del	DEL	CGGGAATCTGA	CGGGAATCTGA	-																															ctggctctggtgattcagatCgggaatctgacttcccagtg																								rs374047961		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	CGGGAATCTGA	CGGGAATCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:202572613_202572623delCGGGAATCTGA	ENST00000264276.6	-	28	4744_4754	c.4372_4382delTCAGATTCCCG	c.(4372-4383)tcagattcccgafs	p.SDSR1458fs	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1458					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.R1461Q(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TGATTCAGATCGGGAATCTGACTTCCCAGTG	0.488																																					p.1458_1461del													.	ALS2-275	1	Substitution - Missense(1)	endometrium(1)	c.4372_4382del						.																																			SO:0001589	frameshift_variant	57679	exon28			TCAGATCGGGAAT	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.4372_4382delTCAGATTCCCG	2.37:g.202572613_202572623delCGGGAATCTGA	ENSP00000264276:p.Ser1458fs	Somatic	333	0		WXS	Illumina HiSeq	Phase_I	253	22	NM_020919	0	0	0	0	0	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Frame_Shift_Del	DEL	ENST00000264276.6	37	CCDS42800.1																																																																																			.		0.488	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		-	202572623	CGGGAATCTGA	-	202572613	7	5	40	1	0	1	0	1	0	0	0	0	550	884	31	0	619	0	ALS2	2	202572613	Frame_Shift_Del	DEL	CGGGAATCTGA	TCGA-B1-A656-01A-11D-A31X-10	3	202572613	40626760	26	3587	33	2									
NEU2	4759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233898967	233898967	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtcacggagcaacagcagCtgcagaccagggccaatgtg	13	4	13	11	1	1	1	1	0	0	1	1	2	1	2	2	2	5	4	2	2	3	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:233898967C>T	ENST00000233840.3	+	2	343	c.343C>T	c.(343-345)Ctg>Ttg	p.L115L		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	115					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	GCAACAGCAGCTGCAGACCAG	0.627																																					p.L115L		.											.	NEU2-90	0			c.C343T						.						89	72	78					2																	233898967		2203	4300	6503	SO:0001819	synonymous_variant	4759	exon2			CAGCAGCTGCAGA	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"N-acetyl-alpha-neuraminidase 2"	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.343C>T	2.37:g.233898967C>T		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	64	14	NM_005383	0	0	0	0	0	Q3KNW4|Q6NTB4	Silent	SNP	ENST00000233840.3	37	CCDS2501.1																																																																																			.		0.627	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		T	233898967	C	T	233898967	2	4	40	1	0	0	0	0	0	0	0	1	10368	796	28	2		2	NEU2	2	233898967	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	31326354	233898967	9300406	27	3588											
MTMR14	64419	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	9724894	9724896	+	In_Frame_Del	DEL	CCT	CCT	-																															gtgcaacaaacacaaaactaCctgaagctgctgctttcctt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:9724894_9724896delCCT	ENST00000296003.4	+	10	1052_1054	c.930_932delCCT	c.(928-933)tacctg>tag	p.310_311YL>*	MTMR14_ENST00000351233.5_In_Frame_Del_p.310_311YL>*|MTMR14_ENST00000420925.1_In_Frame_Del_p.64_65YL>*|MTMR14_ENST00000353332.5_In_Frame_Del_p.310_311YL>*	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	310					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					CACAAAACTACCTGAAGCTGCTG	0.429																																					p.310_311del		.											.	MTMR14-91	0			c.930_932del						.																																			SO:0001651	inframe_deletion	64419	exon10			.	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.930_932delCCT	3.37:g.9724894_9724896delCCT	ENSP00000296003:p.Tyr310_Leu311delins*	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	141	71	NM_022485	0	0	0	0	0	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	In_Frame_Del	DEL	ENST00000296003.4	37	CCDS43043.1																																																																																			.		0.429	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		-	9724896	CCT	-	9724894	7	5	40	1	0	1	0	1	0	0	0	0	9967	518	18	0	968	0	MTMR14	3	9724894	In_Frame_Del	DEL	CCT	TCGA-B1-A656-01A-11D-A31X-10		9724894	188297536	28	3589	34	2									
MTMR14	64419	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	9724897	9724898	+	Frame_Shift_Ins	INS	-	-	A																															aacaaacacaaaactacctgINSaagctgctgctttccttagt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:9724897_9724898insA	ENST00000296003.4	+	10	1055_1056	c.933_934insA	c.(934-936)aagfs	p.K312fs	MTMR14_ENST00000351233.5_Frame_Shift_Ins_p.K312fs|MTMR14_ENST00000420925.1_Frame_Shift_Ins_p.K66fs|MTMR14_ENST00000353332.5_Frame_Shift_Ins_p.K312fs	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	312					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					AAAACTACCTGAAGCTGCTGCT	0.431																																					p.L311fs		.											.	MTMR14-91	0			c.933_934insA						.																																			SO:0001589	frameshift_variant	64419	exon10			.	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.935dupA	3.37:g.9724899_9724899dupA	ENSP00000296003:p.Lys312fs	Somatic	291	0		WXS	Illumina HiSeq	Phase_I	143	67	NM_022485	0	0	0	0	0	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Frame_Shift_Ins	INS	ENST00000296003.4	37	CCDS43043.1																																																																																			.		0.431	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		A	9724898	-	A	9724897	7	5	40	1	0	1	1	0	0	0	0	0	9967	1277	45	0	971	0	MTMR14	3	9724897	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	3	9724897	188297533	29	3590	34	2									
HDAC11	79885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	13525052	13525052	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgcacacgaggcgctatctTaatgagctcaaggtacagga	12	8	12	9	2	2	1	1	1	1	0	2	3	2	2	0	3	3	4	0	3	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:13525052T>G	ENST00000295757.3	+	3	423	c.240T>G	c.(238-240)ctT>ctG	p.L80L	HDAC11_ENST00000404040.1_Silent_p.L80L|HDAC11_ENST00000402259.1_Intron|HDAC11_ENST00000437379.2_Silent_p.L52L|HDAC11_ENST00000402271.1_Silent_p.L80L|HDAC11_ENST00000405025.1_Silent_p.L52L|HDAC11_ENST00000446613.2_Intron|HDAC11_ENST00000404548.1_Silent_p.L80L|HDAC11_ENST00000433119.1_Silent_p.L52L|HDAC11_ENST00000522202.1_Silent_p.L52L	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	80	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						GGCGCTATCTTAATGAGCTCA	0.647																																					p.L80L		.											.	HDAC11-228	0			c.T240G						.						63	72	69					3																	13525052		2203	4300	6503	SO:0001819	synonymous_variant	79885	exon3			CTATCTTAATGAG	AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.240T>G	3.37:g.13525052T>G		Somatic	180	0		WXS	Illumina HiSeq	Phase_I	105	65	NM_024827	0	0	0	0	0	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Silent	SNP	ENST00000295757.3	37	CCDS2615.1																																																																																			.		0.647	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827		G	13525052	T	G	13525052	2	3	40	1	0	0	0	0	0	0	0	1	7027	1741	61	5		5	HDAC11	3	13525052	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	3800155	13525052	184497378	30	3591											
DAZL	1618	broad.mit.edu	37	chr3	16639640	16639640	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattatcttcacttctttcaCtgaaccatatctagcaaaga	13	14	4	10	0	5	2	2	1	3	1	5	3	5	2	1	0	2	1	1	0	5	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:16639640C>G	ENST00000399444.2	-	3	489	c.196G>C	c.(196-198)Gtg>Ctg	p.V66L	DAZL_ENST00000250863.8_Missense_Mutation_p.V86L	NM_001351.3	NP_001342.2	Q92904	DAZL_HUMAN	deleted in azoospermia-like	66	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)		RAF1/DAZL(2)	endometrium(1)|large_intestine(3)|lung(4)|prostate(3)	11						ACTTCTTTCACTGAACCATAT	0.333																																					p.V86L													.	DAZL-90	0			c.G256C						.						104	96	98					3																	16639640		1829	4090	5919	SO:0001583	missense	1618	exon3			CTTTCACTGAACC	BC027595	CCDS43059.1, CCDS54556.1	3p24	2013-02-12			ENSG00000092345	ENSG00000092345		"RNA binding motif (RRM) containing"	2685	protein-coding gene	gene with protein product		601486		DAZLA		8896558	Standard	NM_001351		Approved	DAZH, SPGYLA, MGC26406, DAZL1	uc003cbb.3	Q92904	OTTHUMG00000157050	ENST00000399444.2:c.196G>C	3.37:g.16639640C>G	ENSP00000382373:p.Val66Leu	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	176	5	NM_001190811	0	0	0	0	0	O15396|Q5HYB4|Q92909	Missense_Mutation	SNP	ENST00000399444.2	37	CCDS43059.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.920420	0.92249	.	.	ENSG00000092345	ENST00000250863;ENST00000399444;ENST00000454457	T;T;T	0.43294	0.95;0.95;0.95	5.55	5.55	0.83447	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.057203	0.64402	D	0.000001	T	0.66499	0.2795	M	0.69523	2.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68792	-0.5315	10	0.87932	D	0	-7.8288	19.5113	0.95142	0.0:1.0:0.0:0.0	.	66;86	Q92904;Q5HYB4	DAZL_HUMAN;.	L	86;66;104	ENSP00000250863:V86L;ENSP00000382373:V66L;ENSP00000398109:V104L	ENSP00000250863:V86L	V	-	1	0	DAZL	16614644	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.641000	0.74324	2.612000	0.88384	0.591000	0.81541	GTG	.		0.333	DAZL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347261.2	NM_001351		G	16639640	C	G	16639640	3	3	40	1	0	0	0	0	1	0	0	0	4252	565	20	4	727	4	DAZL	3	16639640	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	3114588	16639640	181382790	31	3592											
TRAK1	22906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	42218379	42218379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcactcggcttcttgaGgaggtaagtgctccagggga	7	10	15	9	1	2	1	1	1	1	0	4	3	3	3	1	5	1	4	1	5	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:42218379G>A	ENST00000327628.5	+	3	760	c.360G>A	c.(358-360)gaG>gaA	p.E120E	TRAK1_ENST00000449246.1_Silent_p.E46E|TRAK1_ENST00000396175.1_Silent_p.E62E|TRAK1_ENST00000341421.3_Silent_p.E62E|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	120	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GGCTTCTTGAGGAGGTAAGTG	0.388																																					p.E120E	GBM(44;195 884 22595 31865 41850)	.											.	TRAK1-91	0			c.G360A						.						157	164	162					3																	42218379		2203	4300	6503	SO:0001819	synonymous_variant	22906	exon3			TCTTGAGGAGGTA		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.360G>A	3.37:g.42218379G>A		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	82	39	NM_001265608	0	0	0	0	0	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	37	CCDS43072.1																																																																																			.		0.388	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		A	42218379	G	A	42218379	2	1	40	1	0	0	0	0	0	0	0	1	16482	991	35	2		2	TRAK1	3	42218379	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	25578739	42218379	155804051	32	3593											
SNRK	54861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	43388848	43388848	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggcagtcatggccaaccaAaattgatgtaccccaggacc	13	7	9	12	0	1	1	1	1	0	0	1	2	1	2	5	3	2	2	5	3	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:43388848A>T	ENST00000296088.7	+	7	1401	c.1097A>T	c.(1096-1098)aAa>aTa	p.K366I	SNRK_ENST00000454177.1_Missense_Mutation_p.K366I|SNRK_ENST00000429705.2_Missense_Mutation_p.K366I|SNRK-AS1_ENST00000422681.1_RNA|RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000437827.1_Missense_Mutation_p.K160I	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		TGGCCAACCAAAATTGATGTA	0.483																																					p.K366I		.											.	SNRK-815	0			c.A1097T						.						104	110	108					3																	43388848		1980	4155	6135	SO:0001583	missense	54861	exon7			CAACCAAAATTGA	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.1097A>T	3.37:g.43388848A>T	ENSP00000296088:p.Lys366Ile	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	27	16	NM_017719	0	0	0	1	1		Missense_Mutation	SNP	ENST00000296088.7	37	CCDS43075.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636679	0.47049	.	.	ENSG00000163788	ENST00000454177;ENST00000429705;ENST00000296088;ENST00000437827	T;T;T;T	0.66460	-0.21;-0.21;-0.21;2.71	5.07	3.91	0.45181	.	0.175030	0.49305	N	0.000150	T	0.48960	0.1529	N	0.19112	0.55	0.49687	D	0.999812	B	0.23735	0.09	B	0.21360	0.034	T	0.49244	-0.8960	10	0.42905	T	0.14	.	10.4529	0.44533	0.9229:0.0:0.0771:0.0	.	366	Q9NRH2	SNRK_HUMAN	I	366;366;366;160	ENSP00000401246:K366I;ENSP00000411375:K366I;ENSP00000296088:K366I;ENSP00000409516:K160I	ENSP00000296088:K366I	K	+	2	0	SNRK	43363852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.731000	0.68554	2.049000	0.60858	0.533000	0.62120	AAA	.		0.483	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		T	43388848	A	T	43388848	3	4	40	1	0	0	0	0	1	0	0	0	14883	14	1	5	1115	5	SNRK	3	43388848	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	1170469	43388848	154633582	33	3594											
NBEAL2	23218	broad.mit.edu	37	chr3	47030855	47030855	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgacccttaccaaacctggCggcgccagcgcagtgggtga	8	7	13	13	3	0	2	0	2	0	0	0	2	0	2	4	3	3	1	4	3	2	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:47030855C>T	ENST00000450053.3	+	5	636	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R153W	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	153					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCAAACCTGGCGGCGCCAGCG	0.667																																					p.R153W													.	NBEAL2-69	0			c.C457T						.						22	25	24					3																	47030855		2003	4141	6144	SO:0001583	missense	23218	exon5			ACCTGGCGGCGCC	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.457C>T	3.37:g.47030855C>T	ENSP00000415034:p.Arg153Trp	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_015175	0	0	0	0	0	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646968	0.67358	.	.	ENSG00000160796	ENST00000292309;ENST00000450053;ENST00000296147	T;T	0.73789	-0.78;-0.72	3.92	1.78	0.24846	.	.	.	.	.	D	0.83303	0.5225	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.964	D	0.83688	0.0175	9	0.87932	D	0	.	10.6426	0.45602	0.4823:0.5177:0.0:0.0	.	146;153	Q6ZNJ1-4;Q6ZNJ1	.;NBEL2_HUMAN	W	153;153;146	ENSP00000292309:R153W;ENSP00000415034:R153W	ENSP00000292309:R153W	R	+	1	2	NBEAL2	47005859	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.561000	0.23515	0.780000	0.33566	0.655000	0.94253	CGG	.		0.667	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47030855	C	T	47030855	3	4	40	1	0	0	0	0	1	0	0	0	10214	759	27	1	475	1	NBEAL2	3	47030855	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	3642007	47030855	150991575	34	3595											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	47165390	47165391	+	Frame_Shift_Ins	INS	-	-	A																															gcttctaaagattctggtacINSaattataattggtggttctt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:47165390_47165391insA	ENST00000409792.3	-	3	777_778	c.735_736insT	c.(733-738)attgtafs	p.V246fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	246	Pro-rich.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GATTCTGGTACAATTATAATTG	0.381			"N, F, S, Mis"		clear cell renal carcinoma																																p.V246fs		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.736_737insT						.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.736dupT	3.37:g.47165392_47165392dupA	ENSP00000386759:p.Val246fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	52	30	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.381	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47165391	-	A	47165390	7	5	40	1	0	1	1	0	0	0	0	0	14163	478	17	0	7034	0	SETD2	3	47165390	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	134535	47165390	150857040	35	3596											
PBRM1	55193	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52649430	52649430	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcccagctctttcctttTctccttgagtaacttctcca	5	16	6	14	0	3	1	0	1	3	0	6	1	4	1	4	1	2	2	4	1	1	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:52649430T>A	ENST00000296302.7	-	15	1862	c.1861A>T	c.(1861-1863)Aaa>Taa	p.K621*	PBRM1_ENST00000337303.4_Nonsense_Mutation_p.K621*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.K636*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.K621*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.K589*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.K621*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.K636*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.K621*			Q86U86	PB1_HUMAN	polybromo 1	621			K -> E (found in a case of clear cell renal carcinoma; somatic mutation). {ECO:0000269|PubMed:21248752}.		chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCTTTCCTTTTCTCCTTGAGT	0.363			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.K621X				Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.A1861T						.						116	105	109					3																	52649430		2203	4300	6503	SO:0001587	stop_gained	55193	exon16			TCCTTTTCTCCTT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1861A>T	3.37:g.52649430T>A	ENSP00000296302:p.Lys621*	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	63	35	NM_018313	0	0	0	0	0	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	T	41	8.750604	0.98939	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.69	5.69	0.88448	.	0.044753	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.8447	15.944	0.79779	0.0:0.0:0.0:1.0	.	.	.	.	X	589;621;621;621;621;621;636;636;621;580	.	ENSP00000296302:K621X	K	-	1	0	PBRM1	52624470	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	8.040000	0.89188	2.170000	0.68504	0.379000	0.24179	AAA	.		0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52649430	T	A	52649430	4	1	40	1	0	0	0	0	0	1	0	0	11517	1792	62	5	3103	5	PBRM1	3	52649430	Nonsense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	5484040	52649430	145373000	36	3597											
FAM116A	201627	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	57616537	57616537	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttctggaagaaactgtctTaattgaggtggactctagaa	12	13	10	6	0	4	3	0	1	4	2	4	5	4	5	0	3	1	0	0	3	5	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:57616537T>G	ENST00000311128.5	-	17	1492	c.1422A>C	c.(1420-1422)ttA>ttC	p.L474F	RP11-755B10.2_ENST00000470427.1_RNA	NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	474					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										GAAACTGTCTTAATTGAGGTG	0.353																																					p.L474F													.	.	0			c.A1422C						.						73	73	73					3																	57616537		2203	4300	6503	SO:0001583	missense	201627	exon17			CTGTCTTAATTGA	AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"DENN/MADD domain containing"	26635	protein-coding gene	gene with protein product			"family with sequence similarity 116, member A"	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.1422A>C	3.37:g.57616537T>G	ENSP00000311401:p.Leu474Phe	Somatic	125	1		WXS	Illumina HiSeq	Phase_I	116	39	NM_152678	0	0	1	1	0	Q7Z5T4|Q8N235|Q8TEG8	Missense_Mutation	SNP	ENST00000311128.5	37	CCDS33773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.83|18.83	3.706236|3.706236	0.68615|0.68615	.|.	.|.	ENSG00000174839|ENSG00000174839	ENST00000471531|ENST00000311128	.|.	.|.	.|.	5.94|5.94	3.59|3.59	0.41128|0.41128	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65015|0.65015	0.2651|0.2651	M|M	0.83118|0.83118	2.625|2.625	0.51482|0.51482	D|D	0.999927|0.999927	.|D	.|0.58620	.|0.983	.|P	.|0.54924	.|0.764	T|T	0.65121|0.65121	-0.6245|-0.6245	5|9	.|0.44086	.|T	.|0.13	-27.6308|-27.6308	2.8604|2.8604	0.05585|0.05585	0.0:0.3025:0.248:0.4495|0.0:0.3025:0.248:0.4495	.|.	.|474	.|Q8IWF6	.|F116A_HUMAN	Q|F	46|474	.|.	.|ENSP00000311401:L474F	K|L	-|-	1|3	0|2	FAM116A|FAM116A	57591577|57591577	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.953000|0.953000	0.61014|0.61014	1.091000|1.091000	0.30915|0.30915	1.070000|1.070000	0.40811|0.40811	0.455000|0.455000	0.32223|0.32223	AAG|TTA	.		0.353	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678		G	57616537	T	G	57616537	3	3	40	1	0	0	0	0	1	0	0	0	5423	1751	61	5	420	5	FAM116A	3	57616537	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	4967107	57616537	140405893	37	3598											
SH3TC1	54436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	8230146	8230146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggcagtggggctggccaacTtcggggccctgtgcctgcat	5	8	16	12	1	0	0	0	0	0	0	1	0	0	0	3	6	3	3	3	6	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:8230146T>C	ENST00000245105.3	+	12	2792	c.2725T>C	c.(2725-2727)Ttc>Ctc	p.F909L	SH3TC1_ENST00000539824.1_Missense_Mutation_p.F833L	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	909										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGGCCAACTTCGGGGCCCT	0.706																																					p.F909L	NSCLC(145;2298 2623 35616 37297)	.											.	SH3TC1-154	0			c.T2725C						.						32	39	37					4																	8230146		2202	4298	6500	SO:0001583	missense	54436	exon12			GCCAACTTCGGGG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2725T>C	4.37:g.8230146T>C	ENSP00000245105:p.Phe909Leu	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	82	24	NM_018986	0	0	7	10	3	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	T	3.669	-0.067891	0.07228	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.56103	0.48;0.48	4.63	0.869	0.19096	Tetratricopeptide-like helical (1);	0.456640	0.23165	N	0.051183	T	0.31765	0.0807	L	0.29908	0.895	0.32645	N	0.520198	B	0.21225	0.053	B	0.25759	0.063	T	0.40327	-0.9569	10	0.02654	T	1	-12.4248	8.0727	0.30699	0.0:0.2424:0.0:0.7576	.	909	Q8TE82	S3TC1_HUMAN	L	647;909;833;738	ENSP00000245105:F909L;ENSP00000441045:F833L	ENSP00000245105:F909L	F	+	1	0	SH3TC1	8281046	1.000000	0.71417	0.984000	0.44739	0.251000	0.25915	1.897000	0.39799	0.167000	0.19631	0.459000	0.35465	TTC	.		0.706	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		C	8230146	T	C	8230146	3	2	40	1	0	0	0	0	1	0	0	0	14293	1609	56	3	2767	3	SH3TC1	4	8230146	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10		8230146	182924130	38	3599											
NPFFR2	10886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	73012854	73012854	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	taccgagtgagactcaactcCcagaataaaaccagtccagt	15	7	7	12	1	1	2	1	1	0	2	3	4	3	2	4	0	3	0	4	0	5	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:73012854C>G	ENST00000308744.6	+	4	992	c.894C>G	c.(892-894)tcC>tcG	p.S298S	NPFFR2_ENST00000395999.1_Silent_p.S199S|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000358749.3_Silent_p.S196S|NPFFR2_ENST00000344413.5_3'UTR	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	298					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			GACTCAACTCCCAGAATAAAA	0.443																																					p.S298S		.											.	NPFFR2-92	0			c.C894G						.						121	117	119					4																	73012854		2203	4300	6503	SO:0001819	synonymous_variant	10886	exon4			CAACTCCCAGAAT	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.894C>G	4.37:g.73012854C>G		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	58	15	NM_004885	0	0	0	0	0	Q96RV1|Q9NR49	Silent	SNP	ENST00000308744.6	37	CCDS3551.1																																																																																			.		0.443	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		G	73012854	C	G	73012854	2	3	40	1	0	0	0	0	0	0	0	1	10604	610	22	4		4	NPFFR2	4	73012854	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	64782708	73012854	118141422	39	3600											
FAM13A	10144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	89658657	89658657	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggaagcagtttcgcccTcgataattggctgcagcaaa	13	8	11	9	2	0	1	0	0	0	1	2	3	0	2	1	2	3	5	1	2	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:89658657T>A	ENST00000264344.5	-	21	2819	c.2612A>T	c.(2611-2613)gAg>gTg	p.E871V	FAM13A_ENST00000513837.1_Missense_Mutation_p.E517V|FAM13A_ENST00000503556.1_Missense_Mutation_p.E531V|FAM13A_ENST00000395002.2_Intron|FAM13A_ENST00000511976.1_Missense_Mutation_p.E457V|FAM13A_ENST00000508369.1_Missense_Mutation_p.E545V	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	871					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						AGTTTCGCCCTCGATAATTGG	0.542																																					p.E871V		.											.	FAM13A-70	0			c.A2612T						.						103	100	101					4																	89658657		2203	4300	6503	SO:0001583	missense	10144	exon21			TCGCCCTCGATAA	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"Rho GTPase activating proteins"	19367	protein-coding gene	gene with protein product		613299	"family with sequence similarity 13, member A1"	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.2612A>T	4.37:g.89658657T>A	ENSP00000264344:p.Glu871Val	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	85	24	NM_014883	0	0	2	3	1	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640552	0.87859	.	.	ENSG00000138640	ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T	0.51817	1.33;0.69;0.77;0.7;0.71	4.84	4.84	0.62591	.	0.109676	0.64402	D	0.000010	T	0.66636	0.2809	M	0.71036	2.16	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999	D;D;D;D;D	0.71870	0.974;0.975;0.963;0.974;0.974	T	0.71377	-0.4611	10	0.87932	D	0	.	14.5853	0.68320	0.0:0.0:0.0:1.0	.	517;457;871;531;545	O94988-6;E9PGM7;O94988;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.	V	871;531;457;545;517	ENSP00000264344:E871V;ENSP00000427189:E531V;ENSP00000421914:E457V;ENSP00000421562:E545V;ENSP00000423252:E517V	ENSP00000264344:E871V	E	-	2	0	FAM13A	89877680	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.507000	0.81676	2.023000	0.59567	0.477000	0.44152	GAG	.		0.542	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			A	89658657	T	A	89658657	3	1	40	1	0	0	0	0	1	0	0	0	5468	1551	54	5	475	5	FAM13A	4	89658657	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	16645803	89658657	101495619	40	3601											
KIAA0922	23240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	154542029	154542029	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggggtgttgctccagtctCaaggtgcgtaattcttacta	9	13	11	8	1	2	0	1	0	2	0	4	0	3	0	1	3	3	3	1	3	5	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:154542029C>A	ENST00000409663.3	+	27	3738	c.3686C>A	c.(3685-3687)tCa>tAa	p.S1229*	KIAA0922_ENST00000409959.3_Nonsense_Mutation_p.S1230*|KIAA0922_ENST00000440693.1_Nonsense_Mutation_p.S1146*	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1229						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GCTCCAGTCTCAAGGTGCGTA	0.303																																					p.S1230X		.											.	KIAA0922-92	0			c.C3689A						.						94	112	106					4																	154542029		2203	4300	6503	SO:0001587	stop_gained	23240	exon27			CAGTCTCAAGGTG	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3686C>A	4.37:g.154542029C>A	ENSP00000386574:p.Ser1229*	Somatic	671	0		WXS	Illumina HiSeq	Phase_I	651	188	NM_001131007	0	0	0	0	0	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Nonsense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	40	7.923983	0.98563	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	.	.	.	5.5	3.61	0.41365	.	1.125250	0.06486	N	0.733676	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	0.0653	9.2055	0.37287	0.0:0.8085:0.0:0.1915	.	.	.	.	X	1229;1146;1230;1007	.	ENSP00000240487:S1007X	S	+	2	0	KIAA0922	154761479	0.021000	0.18746	0.003000	0.11579	0.003000	0.03518	1.282000	0.33226	0.532000	0.28657	0.563000	0.77884	TCA	.		0.303	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154542029	C	A	154542029	4	1	40	1	0	0	0	0	0	1	0	0	8222	838	29	4	3795	4	KIAA0922	4	154542029	Nonsense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	64883372	154542029	36612247	41	3602											
PALLD	23022	broad.mit.edu	37	chr4	169432701	169432701	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctatgactccctctcaGacatgcaggaagaaagcaag	13	8	8	12	0	2	3	1	1	2	2	4	4	3	4	2	1	2	2	2	1	4	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:169432701G>T	ENST00000505667.1	+	2	219	c.46G>T	c.(46-48)Gac>Tac	p.D16Y	PALLD_ENST00000261509.6_Missense_Mutation_p.D16Y|PALLD_ENST00000333488.4_5'Flank|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	16					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		CTCCCTCTCAGACATGCAGGA	0.512									Pancreatic Cancer, Familial Clustering of																												p.D16Y	Esophageal Squamous(109;1482 1532 18347 40239 51172)												.	PALLD-94	0			c.G46T						.						67	67	67					4																	169432701		2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CTCTCAGACATGC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.46G>T	4.37:g.169432701G>T	ENSP00000425556:p.Asp16Tyr	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	88	3	NM_001166108	0	0	0	0	0	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.988442	0.35036	.	.	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000511948	T;T	0.68479	-0.33;-0.07	5.56	5.56	0.83823	.	.	.	.	.	T	0.68265	0.2982	L	0.60455	1.87	0.80722	D	1	P;P	0.43169	0.8;0.8	B;B	0.41723	0.365;0.365	T	0.72821	-0.4177	9	0.72032	D	0.01	.	19.5035	0.95105	0.0:0.0:1.0:0.0	.	16;16	B7ZMM5;B2RTX2	.;.	Y	16	ENSP00000261509:D16Y;ENSP00000425556:D16Y	ENSP00000261509:D16Y	D	+	1	0	PALLD	169669276	1.000000	0.71417	0.244000	0.24202	0.032000	0.12392	6.761000	0.74945	2.616000	0.88540	0.655000	0.94253	GAC	.		0.512	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		T	169432701	G	T	169432701	3	4	40	1	0	0	0	0	1	0	0	0	11433	942	33	4	48	4	PALLD	4	169432701	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	14890672	169432701	21721575	42	3603											
C6	729	broad.mit.edu	37	chr5	41176588	41176588	+	Missense_Mutation	SNP	A	A	T																															gaaagttacctgagttctttAgttcctcactgctaaactga																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:41176588A>T	ENST00000263413.3	-	8	1421	c.1157T>A	c.(1156-1158)cTa>cAa	p.L386Q	C6_ENST00000337836.5_Missense_Mutation_p.L386Q|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	386	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGAGTTCTTTAGTTCCTCACT	0.393																																					p.L386Q													.	C6-95	0			c.T1157A						.						72	68	69					5																	41176588		2203	4300	6503	SO:0001583	missense	729	exon8			TTCTTTAGTTCCT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1157T>A	5.37:g.41176588A>T	ENSP00000263413:p.Leu386Gln	Somatic	147	1		WXS	Illumina HiSeq	Phase_I	181	4	NM_001115131	0	0	0	0	0		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	A	19.12	3.766774	0.69878	.	.	ENSG00000039537	ENST00000337836;ENST00000263413	D;D	0.85013	-1.93;-1.93	5.36	5.36	0.76844	Membrane attack complex component/perforin (MACPF) domain (3);	0.000000	0.64402	D	0.000001	D	0.93350	0.7880	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94523	0.7729	10	0.87932	D	0	-7.1975	15.5075	0.75753	1.0:0.0:0.0:0.0	.	386	P13671	CO6_HUMAN	Q	386	ENSP00000338861:L386Q;ENSP00000263413:L386Q	ENSP00000263413:L386Q	L	-	2	0	C6	41212345	1.000000	0.71417	0.407000	0.26434	0.621000	0.37620	8.172000	0.89677	2.250000	0.74265	0.482000	0.46254	CTA	.		0.393	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			T	41176588	A	T	41176588	3	4	40	1	0	0	0	0	1	0	0	0	2321	420	15	5	1691	5	C6	5	41176588	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		41176588	139738672	43	3604	35	2									
C6	729	broad.mit.edu	37	chr5	41176594	41176594	+	Missense_Mutation	SNP	T	T	G																															tacctgagttctttagttccTcactgctaaactgatagaga																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:41176594T>G	ENST00000263413.3	-	8	1415	c.1151A>C	c.(1150-1152)gAg>gCg	p.E384A	C6_ENST00000337836.5_Missense_Mutation_p.E384A|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	384	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CTTTAGTTCCTCACTGCTAAA	0.393																																					p.E384A													.	C6-95	0			c.A1151C						.						74	70	72					5																	41176594		2203	4300	6503	SO:0001583	missense	729	exon8			AGTTCCTCACTGC	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"Complement system"	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1151A>C	5.37:g.41176594T>G	ENSP00000263413:p.Glu384Ala	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	190	5	NM_001115131	0	0	3	3	0		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.527926	0.64860	.	.	ENSG00000039537	ENST00000337836;ENST00000263413	D;D	0.85629	-2.01;-2.01	5.36	5.36	0.76844	Membrane attack complex component/perforin (MACPF) domain (3);	0.103112	0.64402	D	0.000004	D	0.89853	0.6835	M	0.70275	2.135	0.58432	D	0.999998	D	0.59357	0.985	P	0.57679	0.825	D	0.89950	0.4079	10	0.46703	T	0.11	-18.8041	15.5075	0.75753	0.0:0.0:0.0:1.0	.	384	P13671	CO6_HUMAN	A	384	ENSP00000338861:E384A;ENSP00000263413:E384A	ENSP00000263413:E384A	E	-	2	0	C6	41212351	1.000000	0.71417	0.113000	0.21522	0.627000	0.37826	7.224000	0.78042	2.250000	0.74265	0.482000	0.46254	GAG	.		0.393	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			G	41176594	T	G	41176594	3	3	40	1	0	0	0	0	1	0	0	0	2321	1551	54	5	1697	5	C6	5	41176594	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	6	41176594	139738666	44	3605	35	2									
F2R	2149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	76029290	76029290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatggatacctgctctagtAacctgaataacagcatatac	16	10	6	9	0	1	1	0	1	1	0	1	2	1	2	2	1	6	3	2	1	8	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:76029290A>G	ENST00000319211.4	+	2	1505	c.1240A>G	c.(1240-1242)Aac>Gac	p.N414D		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	414					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260)	caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	CTGCTCTAGTAACCTGAATAA	0.388																																					p.N414D		.											.	F2R-93	0			c.A1240G						.						69	74	72					5																	76029290		2200	4300	6500	SO:0001583	missense	2149	exon2			TCTAGTAACCTGA	M62424	CCDS4032.1	5q13	2012-08-08			ENSG00000181104	ENSG00000181104		"GPCR / Class A : Protease activated receptors"	3537	protein-coding gene	gene with protein product		187930				8395910	Standard	NM_001992		Approved	TR, CF2R, PAR1, PAR-1	uc003ken.4	P25116	OTTHUMG00000131299	ENST00000319211.4:c.1240A>G	5.37:g.76029290A>G	ENSP00000321326:p.Asn414Asp	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	121	21	NM_001992	0	0	0	0	0	Q53XV0|Q96RF7|Q9BUN4	Missense_Mutation	SNP	ENST00000319211.4	37	CCDS4032.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610635	0.46527	.	.	ENSG00000181104	ENST00000319211	T	0.75938	-0.98	4.79	1.18	0.20946	.	0.606938	0.17367	N	0.176834	T	0.67477	0.2897	L	0.59436	1.845	0.29406	N	0.861551	P	0.35433	0.501	B	0.32864	0.154	T	0.59968	-0.7354	10	0.34782	T	0.22	-19.7943	13.2149	0.59854	0.7302:0.2698:0.0:0.0	.	414	P25116	PAR1_HUMAN	D	414	ENSP00000321326:N414D	ENSP00000321326:N414D	N	+	1	0	F2R	76065046	0.204000	0.23447	0.988000	0.46212	0.977000	0.68977	0.936000	0.28938	0.110000	0.17919	0.379000	0.24179	AAC	.		0.388	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2			G	76029290	A	G	76029290	3	3	40	1	0	0	0	0	1	0	0	0	5356	362	13	3	1246	3	F2R	5	76029290	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	34852696	76029290	104885970	45	3606											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950715	79950715	+	Missense_Mutation	SNP	G	G	C																															gcgctgcagcggctgcagcgGccgcagcggccgcagcgccc																								rs144776112|rs201874762		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:79950715G>C	ENST00000265081.6	+	1	249	c.169G>C	c.(169-171)Gcc>Ccc	p.A57P	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	57	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		ggctgcagcggccgcagcggc	0.692								Mismatch excision repair (MMR)																													p.A57P	Melanoma(88;1010 1399 13793 26548 36275)	.											.	MSH3-661	0			c.G169C						.						7	7	7					5																	79950715		2089	4077	6166	SO:0001583	missense	4437	exon1			GCAGCGGCCGCAG	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.169G>C	5.37:g.79950715G>C	ENSP00000265081:p.Ala57Pro	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	40	18	NM_002439	0	0	0	0	0	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	362	0.16575091575091574	115	0.23373983739837398	67	0.1850828729281768	32	0.055944055944055944	148	0.19525065963060687	-	0.222	-1.028222	0.02045	.	.	ENSG00000113318	ENST00000265081	D	0.87256	-2.23	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.02983	-1.1086	3	.	.	.	.	.	.	.	.	57	P20585	MSH3_HUMAN	P	57	ENSP00000265081:A57P	.	A	+	1	0	MSH3	79986471	0.041000	0.20044	0.049000	0.19019	0.152000	0.21847	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GCC	G|0.834;C|0.166		0.692	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		C	79950715	G	C	79950715	3	2	40	1	0	0	0	0	1	0	0	0	9896	1203	42	4	171	4	MSH3	5	79950715	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	3921425	79950715	100964545	46	3607	36	2									
MSH3	4437	hgsc.bcm.edu	37	chr5	79950718	79950718	+	Missense_Mutation	SNP	G	G	C																															ctgcagcggctgcagcggccGcagcggccgcagcgccccca																								rs148550291		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:79950718G>C	ENST00000265081.6	+	1	252	c.172G>C	c.(172-174)Gca>Cca	p.A58P	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	58	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		tgcagcggccgcagcggccgc	0.706								Mismatch excision repair (MMR)																													p.A58P	Melanoma(88;1010 1399 13793 26548 36275)	.											.	MSH3-661	0			c.G172C						.						6	7	6					5																	79950718		2077	4042	6119	SO:0001583	missense	4437	exon1			GCGGCCGCAGCGG	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.172G>C	5.37:g.79950718G>C	ENSP00000265081:p.Ala58Pro	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	38	8	NM_002439	0	0	0	0	0	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	355	0.16254578754578755	114	0.23170731707317074	67	0.1850828729281768	27	0.0472027972027972	147	0.19393139841688653	-	7.967	0.748328	0.15710	.	.	ENSG00000113318	ENST00000265081	D	0.87256	-2.23	.	.	.	.	.	.	.	.	T	0.00073	0.0002	N	0.19112	0.55	0.09310	N	1	B	0.22983	0.078	B	0.11329	0.006	T	0.00891	-1.1525	6	.	.	.	.	.	.	.	.	58	P20585	MSH3_HUMAN	P	58	ENSP00000265081:A58P	.	A	+	1	0	MSH3	79986474	0.036000	0.19791	0.017000	0.16124	0.213000	0.24496	0.000000	0.12993	-0.982000	0.03515	0.000000	0.15137	GCA	G|0.837;C|0.162		0.706	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		C	79950718	G	C	79950718	3	2	40	1	0	0	0	0	1	0	0	0	9896	1087	38	4	174	4	MSH3	5	79950718	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	3	79950718	100964542	47	3608	36	2									
AFF4	27125	broad.mit.edu;bcgsc.ca	37	chr5	132224787	132224791	+	Frame_Shift_Del	DEL	GCTTT	GCTTT	-																															tcacctgtcatcaaagacaaGctttgttctccgaggcttag																								rs370588988		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GCTTT	GCTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:132224787_132224791delGCTTT	ENST00000265343.5	-	14	3091_3095	c.2712_2716delAAAGC	c.(2710-2718)acaaagcttfs	p.KL905fs		NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	905					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCAAAGACAAGCTTTGTTCTCCGAG	0.351																																					p.904_906del	Ovarian(126;889 1733 2942 10745 11605)												.	AFF4-229	0			c.2712_2716del						.																																			SO:0001589	frameshift_variant	27125	exon14			AGACAAGCTTTGT	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2712_2716delAAAGC	5.37:g.132224787_132224791delGCTTT	ENSP00000265343:p.Lys905fs	Somatic	425	0		WXS	Illumina HiSeq	Phase_I	460	24	NM_014423	0	0	0	0	0	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Del	DEL	ENST00000265343.5	37	CCDS4164.1																																																																																			.		0.351	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		-	132224791	GCTTT	-	132224787	7	5	40	1	0	1	0	1	0	0	0	0	359	971	34	0	807	0	AFF4	5	132224787	Frame_Shift_Del	DEL	GCTTT	TCGA-B1-A656-01A-11D-A31X-10	52274069	132224787	48690473	48	3609											
TMEM173	340061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	138855862	138855862	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtctcaagagaaatccgtgCggagagggaggggcttttcc	9	8	16	8	2	1	2	1	0	1	2	4	5	3	3	2	5	1	1	2	5	2	2	rs117897081	byFrequency	TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:138855862C>T	ENST00000330794.4	-	8	1457	c.1124G>A	c.(1123-1125)cGc>cAc	p.R375H	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	375	C-terminal tail (CTT).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAAATCCGTGCGGAGAGGGAG	0.597																																					p.R375H		.											.	TMEM173-69	0			c.G1124A						.						44	44	44					5																	138855862		2203	4300	6503	SO:0001583	missense	340061	exon8			TCCGTGCGGAGAG		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.1124G>A	5.37:g.138855862C>T	ENSP00000331288:p.Arg375His	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	90	38	NM_198282	0	0	59	75	16	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.395533	0.42512	.	.	ENSG00000184584	ENST00000330794	T	0.30448	1.53	5.36	3.48	0.39840	.	0.070055	0.53938	N	0.000050	T	0.36744	0.0978	M	0.70595	2.14	0.35562	D	0.804743	D	0.60160	0.987	P	0.50537	0.643	T	0.49532	-0.8930	10	0.42905	T	0.14	-17.9707	5.749	0.18136	0.1568:0.6785:0.0:0.1647	.	375	Q86WV6	TM173_HUMAN	H	375	ENSP00000331288:R375H	ENSP00000331288:R375H	R	-	2	0	TMEM173	138836046	0.671000	0.27521	0.933000	0.37362	0.148000	0.21650	0.972000	0.29409	1.268000	0.44264	-0.369000	0.07265	CGC	C|0.995;A|0.005		0.597	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		T	138855862	C	T	138855862	3	4	40	1	0	0	0	0	1	0	0	0	16121	768	27	1	19	1	TMEM173	5	138855862	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	6631075	138855862	42059398	49	3610											
UNC5A	90249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176305475	176305475	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctctctgcatccccatcaGgagatccccttttatcacat	8	13	4	16	0	3	1	2	0	1	1	7	2	6	1	5	1	1	1	5	1	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:176305475G>A	ENST00000329542.4	+	13	2293		c.e13-1		UNC5A_ENST00000261961.3_Splice_Site	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)						anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.?(1)		endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCCCCATCAGGAGATCCCCT	0.612																																					.		.											.	UNC5A-91	1	Unknown(1)	kidney(1)	c.2020-1G>A						.						89	83	85					5																	176305475		2203	4300	6503	SO:0001630	splice_region_variant	90249	exon13			CCATCAGGAGATC	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.2020-1G>A	5.37:g.176305475G>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	110	24	NM_133369	0	0	0	0	0	B2RXE6|Q8TF26|Q96GP4	Splice_Site	SNP	ENST00000329542.4	37	CCDS34299.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275028	0.80580	.	.	ENSG00000113763	ENST00000329542;ENST00000261961	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.176	0.89761	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC5A	176238081	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.860000	0.99555	2.641000	0.89580	0.491000	0.48974	.	.		0.612	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300	Intron	A	176305475	G	A	176305475	5	1	40	1	0	0	0	0	0	0	1	0	17024	1014	35	2	2069	2	UNC5A	5	176305475	Splice_Site	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	37449613	176305475	4609785	50	3611											
UIMC1	51720	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176395662	176395662	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagtgccagtcagatgccCtagactcctgcctctcctct	6	12	8	15	0	3	3	1	1	2	2	5	3	4	3	5	0	3	0	5	0	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:176395662C>T	ENST00000377227.4	-	6	1226	c.1094G>A	c.(1093-1095)aGg>aAg	p.R365K	UIMC1_ENST00000377219.2_Missense_Mutation_p.R365K|UIMC1_ENST00000511320.1_Missense_Mutation_p.R365K|UIMC1_ENST00000506128.1_Intron|UIMC1_ENST00000503273.1_5'UTR			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	365	AIR.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTCAGATGCCCTAGACTCCTG	0.433																																					p.R365K													.	UIMC1-208	0			c.G1094A						.						169	160	163					5																	176395662		2203	4300	6503	SO:0001583	missense	51720	exon6			GATGCCCTAGACT	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1094G>A	5.37:g.176395662C>T	ENSP00000366434:p.Arg365Lys	Somatic	90	1		WXS	Illumina HiSeq	Phase_I	121	28	NM_016290	0	0	0	4	4	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.803874	0.31869	.	.	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000377220	T;T;T	0.26373	1.74;1.74;1.74	5.74	4.84	0.62591	.	0.370207	0.27600	N	0.018642	T	0.18215	0.0437	L	0.44542	1.39	0.30376	N	0.782434	P;P	0.41848	0.763;0.718	B;B	0.39027	0.288;0.215	T	0.06127	-1.0844	10	0.20519	T	0.43	.	5.9781	0.19391	0.1849:0.7:0.0:0.1152	.	365;287	Q96RL1;Q96RL1-3	UIMC1_HUMAN;.	K	365;365;365;287	ENSP00000366434:R365K;ENSP00000366425:R365K;ENSP00000421926:R365K	ENSP00000366425:R365K	R	-	2	0	UIMC1	176328268	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.690000	0.37711	2.716000	0.92895	0.555000	0.69702	AGG	.		0.433	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		T	176395662	C	T	176395662	3	4	40	1	0	0	0	0	1	0	0	0	17004	681	24	2	1105	2	UIMC1	5	176395662	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	90187	176395662	4519598	51	3612											
SQSTM1	8878	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179250983	179250983	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaacccgctacaagtgcAgcgtctgcccagactacgac	11	6	10	14	3	1	1	0	0	1	1	1	3	1	2	2	1	6	2	2	1	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:179250983A>T	ENST00000389805.4	+	3	605	c.427A>T	c.(427-429)Agc>Tgc	p.S143C	SQSTM1_ENST00000360718.5_Missense_Mutation_p.S59C|SQSTM1_ENST00000402874.3_Missense_Mutation_p.S59C|SQSTM1_ENST00000510187.1_Missense_Mutation_p.S143C|SQSTM1_ENST00000376929.3_Missense_Mutation_p.S59C	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	143	Interaction with GABRR3. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTACAAGTGCAGCGTCTGCCC	0.642																																					p.S143C													.	SQSTM1-92	0			c.A427T						.						81	75	77					5																	179250983		2203	4300	6503	SO:0001583	missense	8878	exon3			AAGTGCAGCGTCT	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"Paget disease of bone 3", "oxidative stress induced like"	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.427A>T	5.37:g.179250983A>T	ENSP00000374455:p.Ser143Cys	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	97	44	NM_003900	0	0	214	428	214	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Missense_Mutation	SNP	ENST00000389805.4	37	CCDS34317.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.090186	0.55968	.	.	ENSG00000161011	ENST00000376929;ENST00000514093;ENST00000422245;ENST00000389805;ENST00000504627;ENST00000402874;ENST00000510187;ENST00000360718	D;D;D;D;D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85	5.59	5.59	0.84812	Zinc finger, ZZ-type (4);	0.262605	0.44285	D	0.000467	D	0.93174	0.7826	L	0.58583	1.82	0.34038	D	0.654646	P;D	0.76494	0.498;0.999	B;D	0.66716	0.216;0.946	D	0.95449	0.8532	10	0.51188	T	0.08	-16.2832	11.7311	0.51737	0.8528:0.1472:0.0:0.0	.	143;143	Q13501;E7EMC7	SQSTM_HUMAN;.	C	59;59;59;143;166;59;143;59	ENSP00000366128:S59C;ENSP00000427308:S59C;ENSP00000394534:S59C;ENSP00000374455:S143C;ENSP00000425957:S166C;ENSP00000385553:S59C;ENSP00000424477:S143C;ENSP00000353944:S59C	ENSP00000353944:S59C	S	+	1	0	SQSTM1	179183589	1.000000	0.71417	0.997000	0.53966	0.390000	0.30446	3.781000	0.55394	2.120000	0.65058	0.459000	0.35465	AGC	.		0.642	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1			T	179250983	A	T	179250983	3	4	40	1	0	0	0	0	1	0	0	0	15162	188	7	5	437	5	SQSTM1	5	179250983	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	2855321	179250983	1664277	52	3613											
DHX16	8449	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30622528	30622528	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagacaagttcgtggtagagCagccagcgtggctgttgctc	9	9	14	9	2	0	2	0	0	0	2	2	2	0	2	1	2	4	6	1	2	3	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr6:30622528C>A	ENST00000376442.3	-	19	3147	c.2952G>T	c.(2950-2952)ctG>ctT	p.L984L	DHX16_ENST00000376437.5_Silent_p.L503L	NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	984					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CGTGGTAGAGCAGCCAGCGTG	0.542																																					p.L984L													.	DHX16-228	0			c.G2952T						.						142	115	125					6																	30622528		1511	2709	4220	SO:0001819	synonymous_variant	8449	exon19			GTAGAGCAGCCAG	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.2952G>T	6.37:g.30622528C>A		Somatic	117	2		WXS	Illumina HiSeq	Phase_I	75	22	NM_003587	0	0	46	67	21	O60322|Q5JP45|Q969X7|Q96QC1	Silent	SNP	ENST00000376442.3	37	CCDS4685.1																																																																																			.		0.542	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		A	30622528	C	A	30622528	2	1	40	1	0	0	0	0	0	0	0	1	4513	697	25	4		4	DHX16	6	30622528	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		30622528	140492539	53	3614											
TNFRSF21	27242	broad.mit.edu	37	chr6	47251781	47251781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggatcctgccggggccccTttttcagagtcctcgagctt	4	12	12	13	2	1	1	1	0	0	1	4	3	3	2	5	3	2	1	5	3	0	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr6:47251781T>C	ENST00000296861.2	-	3	1529	c.1136A>G	c.(1135-1137)aAg>aGg	p.K379R		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	379					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			CCGGGGCCCCTTTTTCAGAGT	0.512																																					p.K379R													.	TNFRSF21-227	0			c.A1136G						.						98	104	102					6																	47251781		2203	4300	6503	SO:0001583	missense	27242	exon3			GGCCCCTTTTTCA	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1136A>G	6.37:g.47251781T>C	ENSP00000296861:p.Lys379Arg	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	106	3	NM_014452	0	0	32	32	0	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.960173	0.92791	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.70631	-0.5	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.79753	0.4500	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82068	-0.0640	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	379	O75509	TNR21_HUMAN	R	379;68	ENSP00000296861:K379R	ENSP00000296861:K379R	K	-	2	0	TNFRSF21	47359740	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.708000	0.68377	2.371000	0.80710	0.533000	0.62120	AAG	.		0.512	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		C	47251781	T	C	47251781	3	2	40	1	0	0	0	0	1	0	0	0	16327	1609	56	3	847	3	TNFRSF21	6	47251781	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	16629253	47251781	123863286	54	3615											
COL19A1	1310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	70646796	70646796	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagtgccagtgcattccAaacaaggtatgctagtttta	12	11	9	9	0	0	0	0	0	0	0	1	1	1	0	3	1	4	4	3	1	5	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr6:70646796A>G	ENST00000322773.4	+	8	969	c.867A>G	c.(865-867)ccA>ccG	p.P289P		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	289					cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						AGTGCATTCCAAACAAGGTAT	0.448																																					p.P289P		.											.	COL19A1-156	0			c.A867G						.						145	136	139					6																	70646796		2203	4300	6503	SO:0001819	synonymous_variant	1310	exon8			CATTCCAAACAAG		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.867A>G	6.37:g.70646796A>G		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	102	28	NM_001858	0	0	0	0	0	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	37	CCDS4970.1																																																																																			.		0.448	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			G	70646796	A	G	70646796	2	3	40	1	0	0	0	0	0	0	0	1	3682	117	5	3		3	COL19A1	6	70646796	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	23395015	70646796	100468271	55	3616											
IMPG1	3617	broad.mit.edu	37	chr6	76640750	76640750	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctggttccagaccgtccagGctcccctggctgtcatatcc	5	10	9	17	1	1	1	1	0	0	1	5	1	5	1	7	3	0	3	7	3	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr6:76640750G>A	ENST00000369950.3	-	15	2352	c.2163C>T	c.(2161-2163)agC>agT	p.S721S	Y_RNA_ENST00000363170.1_RNA|IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GACCGTCCAGGCTCCCCTGGC	0.587																																					p.S721S	Pancreas(37;839 1141 2599 26037)												.	IMPG1-93	0			c.C2163T						.						123	103	109					6																	76640750		2203	4300	6503	SO:0001819	synonymous_variant	3617	exon15			GTCCAGGCTCCCC	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"sialoprotein associated with cones and rods"	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2163C>T	6.37:g.76640750G>A		Somatic	138	1		WXS	Illumina HiSeq	Phase_I	107	3	NM_001563	0	0	0	0	0		Silent	SNP	ENST00000369950.3	37	CCDS4985.1																																																																																			.		0.587	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76640750	G	A	76640750	2	1	40	1	0	0	0	0	0	0	0	1	7749	1194	42	2		2	IMPG1	6	76640750	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5993954	76640750	94474317	56	3617											
ABCA13	154664	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48319048	48319048	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttggaaaaacttaaagaaaGataattggaatgtttctaat	18	14	7	2	0	1	2	0	0	1	2	1	4	1	4	0	2	1	1	0	2	8	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:48319048G>A	ENST00000435803.1	+	18	8281	c.8257G>A	c.(8257-8259)Gat>Aat	p.D2753N		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2753					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTTAAAGAAAGATAATTGGAA	0.323																																					p.D2753N													.	ABCA13-521	0			c.G8257A						.						37	36	36					7																	48319048		1804	4066	5870	SO:0001583	missense	154664	exon18			AAGAAAGATAATT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.8257G>A	7.37:g.48319048G>A	ENSP00000411096:p.Asp2753Asn	Somatic	426	1		WXS	Illumina HiSeq	Phase_I	547	112	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189644	0.57909	.	.	ENSG00000179869	ENST00000435803	T	0.60548	0.18	5.31	3.5	0.40072	.	0.419222	0.20293	N	0.095183	T	0.49304	0.1549	L	0.29908	0.895	0.18873	N	0.999989	P	0.51057	0.941	P	0.48815	0.591	T	0.41070	-0.9529	10	0.87932	D	0	.	7.1966	0.25855	0.196:0.0:0.804:0.0	.	2753	Q86UQ4	ABCAD_HUMAN	N	2753	ENSP00000411096:D2753N	ENSP00000411096:D2753N	D	+	1	0	ABCA13	48289594	0.000000	0.05858	0.006000	0.13384	0.047000	0.14425	0.381000	0.20619	1.251000	0.43983	0.655000	0.94253	GAT	.		0.323	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48319048	G	A	48319048	3	1	40	1	0	0	0	0	1	0	0	0	31	942	33	2	8156	2	ABCA13	7	48319048	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		48319048	110819615	57	3618											
POM121L12	285877	broad.mit.edu	37	chr7	53103618	53103618	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggtgcggcccacccaggAccccgccaagccgcagcggg	7	1	15	18	5	0	0	0	0	0	0	0	2	0	1	6	4	3	1	6	4	1	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:53103618A>C	ENST00000408890.4	+	1	270	c.254A>C	c.(253-255)gAc>gCc	p.D85A		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	85										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CCCACCCAGGACCCCGCCAAG	0.711																																					p.D85A													.	.	0			c.A254C						.						13	17	16					7																	53103618		1875	4077	5952	SO:0001583	missense	285877	exon1			CCCAGGACCCCGC		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"POM121 membrane glycoprotein-like 12"				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.254A>C	7.37:g.53103618A>C	ENSP00000386133:p.Asp85Ala	Somatic	45	6		WXS	Illumina HiSeq	Phase_I	97	19	NM_182595	0	0	0	0	0	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.169558	0.38315	.	.	ENSG00000221900	ENST00000408890	T	0.24908	1.83	2.6	-1.55	0.08558	.	.	.	.	.	T	0.13200	0.0320	L	0.31926	0.97	0.09310	N	1	P	0.48694	0.914	B	0.37601	0.254	T	0.15954	-1.0419	9	0.40728	T	0.16	.	2.8435	0.05536	0.4096:0.26:0.3304:0.0	.	85	Q8N7R1	P1L12_HUMAN	A	85	ENSP00000386133:D85A	ENSP00000386133:D85A	D	+	2	0	POM121L12	53071112	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.256000	0.08757	-0.177000	0.10690	0.379000	0.24179	GAC	.		0.711	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		C	53103618	A	C	53103618	3	2	40	1	0	0	0	0	1	0	0	0	12267	275	10	5	256	5	POM121L12	7	53103618	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	4784570	53103618	106035045	58	3619											
LIMK1	3984	broad.mit.edu;bcgsc.ca	37	chr7	73535230	73535230	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtactggacagatcatcggGcgggtgaacgcagaccctga	10	7	14	10	3	1	4	1	2	0	2	2	5	1	5	1	3	2	2	1	3	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:73535230G>A	ENST00000336180.2	+	15	1683	c.1632G>A	c.(1630-1632)ggG>ggA	p.G544G	LIMK1_ENST00000418310.1_Silent_p.G574G|LIMK1_ENST00000538333.3_Silent_p.G510G	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	544	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	AGATCATCGGGCGGGTGAACG	0.647																																					p.G544G													.	LIMK1-523	0			c.G1632A						.						86	82	84					7																	73535230		2203	4300	6503	SO:0001819	synonymous_variant	3984	exon15			CATCGGGCGGGTG	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1632G>A	7.37:g.73535230G>A		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	126	6	NM_002314	0	0	0	0	0	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Silent	SNP	ENST00000336180.2	37	CCDS5563.1																																																																																			.		0.647	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		A	73535230	G	A	73535230	2	1	40	1	0	0	0	0	0	0	0	1	8823	1190	42	2		2	LIMK1	7	73535230	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	20431612	73535230	85603433	59	3620											
LMTK2	22853	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	97833339	97833339	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgctcagctccaagcctTctctccaaacatccaagtac	11	9	4	17	0	2	0	1	0	1	0	6	0	5	0	5	0	5	3	5	0	4	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:97833339T>G	ENST00000297293.5	+	13	4617	c.4324T>G	c.(4324-4326)Tct>Gct	p.S1442A		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1442					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CTCCAAGCCTTCTCTCCAAAC	0.527																																					p.S1442A													.	LMTK2-1381	0			c.T4324G						.						95	106	102					7																	97833339		2203	4300	6503	SO:0001583	missense	22853	exon13			AAGCCTTCTCTCC	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.4324T>G	7.37:g.97833339T>G	ENSP00000297293:p.Ser1442Ala	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	91	39	NM_014916	0	0	1	5	4	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.314063	0.23908	.	.	ENSG00000164715	ENST00000297293	T	0.78364	-1.17	5.84	-3.32	0.04973	.	0.326711	0.37623	N	0.002020	T	0.54143	0.1840	L	0.28274	0.84	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.32079	-0.9920	10	0.22706	T	0.39	.	3.7573	0.08591	0.1088:0.1347:0.448:0.3085	.	1442	Q8IWU2	LMTK2_HUMAN	A	1442	ENSP00000297293:S1442A	ENSP00000297293:S1442A	S	+	1	0	LMTK2	97671275	0.000000	0.05858	0.001000	0.08648	0.635000	0.38103	-0.076000	0.11412	-0.835000	0.04234	0.460000	0.39030	TCT	.		0.527	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		G	97833339	T	G	97833339	3	3	40	1	0	0	0	0	1	0	0	0	8882	1783	62	5	4374	5	LMTK2	7	97833339	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	24298109	97833339	61305324	60	3621											
SRRT	51593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100485704	100485704	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggactcccctacccacacCagactccccagggcctgatg	9	5	8	19	0	0	2	0	1	0	1	2	3	2	3	7	2	1	0	7	2	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:100485704C>A	ENST00000347433.4	+	18	2526	c.2368C>A	c.(2368-2370)Cag>Aag	p.Q790K	SRRT_ENST00000457580.2_Missense_Mutation_p.Q786K|SRRT_ENST00000388793.4_Missense_Mutation_p.Q789K|SRRT_ENST00000432932.1_Missense_Mutation_p.Q785K			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	790	Pro-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CTACCCACACCAGACTCCCCA	0.612																																					p.Q790K		.											.	SRRT-92	0			c.C2368A						.						52	56	55					7																	100485704		2203	4300	6503	SO:0001583	missense	51593	exon18			CCACACCAGACTC		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2368C>A	7.37:g.100485704C>A	ENSP00000314491:p.Gln790Lys	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	148	69	NM_015908	0	0	57	101	44	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217920	0.58560	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000342198;ENST00000432932;ENST00000347433;ENST00000448764;ENST00000445337	.	.	.	4.91	4.91	0.64330	Arsenite-resistance protein 2 (1);	0.000000	0.85682	D	0.000000	T	0.50446	0.1616	N	0.08118	0	0.51767	D	0.999935	B;P;P;D	0.53885	0.206;0.954;0.954;0.963	B;D;D;D	0.71414	0.058;0.954;0.954;0.973	T	0.46789	-0.9166	9	0.15952	T	0.53	.	15.6172	0.76775	0.0:1.0:0.0:0.0	.	789;785;786;790	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	K	786;789;155;785;790;420;67	.	ENSP00000344670:Q155K	Q	+	1	0	SRRT	100323640	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.964000	0.63701	2.545000	0.85829	0.484000	0.47621	CAG	.		0.612	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100485704	C	A	100485704	3	1	40	1	0	0	0	0	1	0	0	0	15204	595	21	4	2434	4	SRRT	7	100485704	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	2652365	100485704	58652959	61	3622											
CDHR3	222256	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	105673047	105673047	+	Frame_Shift_Del	DEL	G	G	-																															tgggctgaggatgctggtctGggttccagaaatgagggtgg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:105673047delG	ENST00000317716.9	+	19	2642	c.2562delG	c.(2560-2562)ctgfs	p.L854fs	CDHR3_ENST00000343407.5_3'UTR|CDHR3_ENST00000542731.1_Frame_Shift_Del_p.L854fs|CDHR3_ENST00000478080.1_Frame_Shift_Del_p.L766fs	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	854					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATGCTGGTCTGGGTTCCAGAA	0.552																																					p.L854fs		.											.	CDHR3-23	0			c.2562delG						.						68	76	73					7																	105673047		2097	4220	6317	SO:0001589	frameshift_variant	222256	exon19			.	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"Cadherins / Cadherin-related"	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.2562delG	7.37:g.105673047delG	ENSP00000325954:p.Leu854fs	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	170	37	NM_152750	0	0	0	0	0	Q8TCI7	Frame_Shift_Del	DEL	ENST00000317716.9	37	CCDS47684.1																																																																																			.		0.552	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		-	105673047	G	-	105673047	7	5	40	1	0	1	0	1	0	0	0	0	3126	1335	47	0	2636	0	CDHR3	7	105673047	Frame_Shift_Del	DEL	G	TCGA-B1-A656-01A-11D-A31X-10	5187343	105673047	53465616	62	3623											
DLD	1738	broad.mit.edu;bcgsc.ca	37	chr7	107556127	107556127	+	Frame_Shift_Del	DEL	A	A	-																															gctaccaagaagtcagatggAaaaattgatgtttcgtaagt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:107556127delA	ENST00000205402.5	+	9	1142	c.861delA	c.(859-861)ggafs	p.G287fs	DLD_ENST00000440410.1_Frame_Shift_Del_p.G264fs|DLD_ENST00000537148.1_Frame_Shift_Del_p.G188fs|DLD_ENST00000437604.2_Frame_Shift_Del_p.G239fs	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	287					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	AGTCAGATGGAAAAATTGATG	0.308																																					p.G287fs													.	DLD-226	0			c.861delA						.						52	54	54					7																	107556127		2203	4300	6503	SO:0001589	frameshift_variant	1738	exon9			AGATGGAAAAATT	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.861delA	7.37:g.107556127delA	ENSP00000205402:p.Gly287fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	126	14	NM_000108	0	0	0	0	0	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Frame_Shift_Del	DEL	ENST00000205402.5	37	CCDS5749.1																																																																																			.		0.308	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		-	107556127	A	-	107556127	7	5	40	1	0	1	0	1	0	0	0	0	4562	233	9	0	895	0	DLD	7	107556127	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	1883080	107556127	51582536	63	3624	37	2									
DLD	1738	bcgsc.ca	37	chr7	107556128	107556128	+	Nonsense_Mutation	SNP	A	A	T																															ctaccaagaagtcagatggaAaaattgatgtttcgtaagta																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:107556128A>T	ENST00000205402.5	+	9	1143	c.862A>T	c.(862-864)Aaa>Taa	p.K288*	DLD_ENST00000440410.1_Nonsense_Mutation_p.K265*|DLD_ENST00000537148.1_Nonsense_Mutation_p.K189*|DLD_ENST00000437604.2_Nonsense_Mutation_p.K240*	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	288					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	GTCAGATGGAAAAATTGATGT	0.313																																					p.K288X													.	DLD-226	0			c.A862T						.						52	54	54					7																	107556128		2203	4300	6503	SO:0001587	stop_gained	1738	exon9			GATGGAAAAATTG	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.862A>T	7.37:g.107556128A>T	ENSP00000205402:p.Lys288*	Somatic	124	0		WXS	Illumina HiSeq	Phase_1	125	14	NM_000108	0	0	0	0	0	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Nonsense_Mutation	SNP	ENST00000205402.5	37	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	A	37	6.003156	0.97189	.	.	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000537148;ENST00000440410;ENST00000437604;ENST00000539590	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0775	16.6512	0.85203	1.0:0.0:0.0:0.0	.	.	.	.	X	288;288;189;265;240;238	.	ENSP00000205402:K288X	K	+	1	0	DLD	107343364	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.359000	0.79477	2.333000	0.79357	0.482000	0.46254	AAA	.		0.313	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		T	107556128	A	T	107556128	4	4	40	1	0	0	0	0	0	1	0	0	4562	15	1	5	896	5	DLD	7	107556128	Nonsense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	1	107556128	51582535	64	3625	37	2									
CADPS2	93664	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	122081599	122081599	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagtgtagcttttagagcAccttcaggtcgtccaaaggg	11	10	12	8	1	1	1	1	0	0	1	3	2	2	1	2	2	2	3	2	2	4	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:122081599A>G	ENST00000449022.2	-	16	2338	c.2319T>C	c.(2317-2319)ggT>ggC	p.G773G	CADPS2_ENST00000412584.2_Silent_p.G770G|CADPS2_ENST00000334010.7_Silent_p.G774G|RP5-1101C3.1_ENST00000592542.1_RNA|CADPS2_ENST00000313070.7_Silent_p.G770G	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	773	Interaction with DRD2.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						CTTTTAGAGCACCTTCAGGTC	0.313																																					p.G773G													.	CADPS2-94	0			c.T2319C						.						41	38	39					7																	122081599		1742	3890	5632	SO:0001819	synonymous_variant	93664	exon16			TAGAGCACCTTCA		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.2319T>C	7.37:g.122081599A>G		Somatic	337	2		WXS	Illumina HiSeq	Phase_I	427	82	NM_001167940	0	0	1	1	0	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	37	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	A	9.548	1.115285	0.20795	.	.	ENSG00000081803	ENST00000397721	.	.	.	5.77	3.34	0.38264	.	.	.	.	.	T	0.61400	0.2344	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55761	-0.8090	4	.	.	.	-17.4989	10.8394	0.46706	0.5695:0.0:0.0:0.4305	.	.	.	.	R	419	.	.	C	-	1	0	CADPS2	121868835	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.814000	0.27239	0.425000	0.26087	-0.274000	0.10170	TGC	.		0.313	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		G	122081599	A	G	122081599	2	3	40	1	0	0	0	0	0	0	0	1	2577	146	6	3		3	CADPS2	7	122081599	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	14525471	122081599	37057064	65	3626											
TMEM176A	55365	broad.mit.edu;ucsc.edu	37	chr7	150501526	150501526	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcatctctgacccctctgtGgctgtactgctggagaatgt	6	12	12	11	0	2	2	0	1	2	1	3	3	2	2	2	3	2	4	2	3	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:150501526G>T	ENST00000484928.1	+	6	1213	c.632G>T	c.(631-633)tGg>tTg	p.W211L	TMEM176A_ENST00000461345.1_Missense_Mutation_p.W152L|TMEM176A_ENST00000004103.3_Missense_Mutation_p.W211L			Q96HP8	T176A_HUMAN	transmembrane protein 176A	211					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCCCTCTGTGGCTGTACTGC	0.557																																					p.W211L													.	TMEM176A-92	0			c.G632T						.						145	133	137					7																	150501526		2203	4300	6503	SO:0001583	missense	55365	exon6			CTCTGTGGCTGTA	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.632G>T	7.37:g.150501526G>T	ENSP00000417626:p.Trp211Leu	Somatic	73	1		WXS	Illumina HiSeq	Phase_I	83	14	NM_018487	1	0	1647	1652	4	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	.	.	.	.	.	.	.	.	.	.	G	2.416	-0.334160	0.05278	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536	T;T;T;T	0.01981	4.52;4.52;4.52;4.52	4.79	2.91	0.33838	.	1.300260	0.05601	N	0.576349	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.19445	0.036	B	0.19946	0.027	T	0.49476	-0.8936	10	0.41790	T	0.15	-19.4964	10.1706	0.42908	0.0:0.0:0.6371:0.3629	.	211	Q96HP8	T176A_HUMAN	L	211;211;152;163	ENSP00000417626:W211L;ENSP00000004103:W211L;ENSP00000420818:W152L;ENSP00000417834:W163L	ENSP00000004103:W211L	W	+	2	0	TMEM176A	150132459	0.009000	0.17119	0.376000	0.26042	0.857000	0.48899	0.314000	0.19432	0.503000	0.28060	0.655000	0.94253	TGG	.		0.557	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		T	150501526	G	T	150501526	3	4	40	1	0	0	0	0	1	0	0	0	16124	1357	47	4	650	4	TMEM176A	7	150501526	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	28419927	150501526	8637137	66	3627											
CHPF2	54480	broad.mit.edu	37	chr7	150935559	150935559	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctggaggggctggaggTgatggatgttttcctccggt	5	11	17	8	1	0	1	0	1	0	0	2	4	2	4	3	7	1	2	3	7	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:150935559T>G	ENST00000035307.2	+	4	3624	c.2111T>G	c.(2110-2112)gTg>gGg	p.V704G	MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.V696G	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	704					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						GGGCTGGAGGTGATGGATGTT	0.647																																					p.V704G													.	CHPF2-91	0			c.T2111G						.						46	42	43					7																	150935559		2197	4298	6495	SO:0001583	missense	54480	exon4			TGGAGGTGATGGA	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.2111T>G	7.37:g.150935559T>G	ENSP00000035307:p.Val704Gly	Somatic	112	17		WXS	Illumina HiSeq	Phase_I	128	22	NM_019015	0	1	79	83	3	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.946996	0.73672	.	.	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.19105	2.17;2.17	4.81	4.81	0.61882	.	0.059849	0.64402	D	0.000002	T	0.39279	0.1072	L	0.50333	1.59	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71184	0.972;0.917	T	0.18935	-1.0321	10	0.66056	D	0.02	-22.7599	13.7365	0.62821	0.0:0.0:0.0:1.0	.	704;696	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	G	696;704	ENSP00000418914:V696G;ENSP00000035307:V704G	ENSP00000035307:V704G	V	+	2	0	CHPF2	150566492	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.956000	0.70315	2.018000	0.59344	0.533000	0.62120	GTG	.		0.647	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		G	150935559	T	G	150935559	3	3	40	1	0	0	0	0	1	0	0	0	3375	1696	59	5	2125	5	CHPF2	7	150935559	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	434033	150935559	8203104	67	3628											
ANK1	286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	41551436	41551436	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatgacgctgcaaagcaggCgcaggctggtggtgtctccc	8	7	14	12	2	1	1	0	1	1	0	2	1	1	1	1	4	2	5	1	4	2	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr8:41551436C>T	ENST00000347528.4	-	29	3595	c.3512G>A	c.(3511-3513)cGc>cAc	p.R1171H	ANK1_ENST00000289734.7_Missense_Mutation_p.R1171H|ANK1_ENST00000379758.2_Missense_Mutation_p.R1171H|ANK1_ENST00000352337.4_Missense_Mutation_p.R1171H|ANK1_ENST00000396945.1_Missense_Mutation_p.R1171H|ANK1_ENST00000396942.1_Missense_Mutation_p.R1171H|ANK1_ENST00000265709.8_Missense_Mutation_p.R1212H	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1171	ZU5 2. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R1171H(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCAAAGCAGGCGCAGGCTGGT	0.647																																					p.R1212H		.											.	ANK1-716	1	Substitution - Missense(1)	large_intestine(1)	c.G3635A						.						31	28	29					8																	41551436		2203	4300	6503	SO:0001583	missense	286	exon30			AGCAGGCGCAGGC	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.3512G>A	8.37:g.41551436C>T	ENSP00000339620:p.Arg1171His	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	161	37	NM_001142446	0	0	0	0	0	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	35	5.421819	0.96111	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.73469	-0.72;-0.72;-0.69;-0.68;-0.69;-0.67;-0.75	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	M	0.80183	2.485	0.80722	D	1	D;D;D;P;D;D	0.89917	0.988;0.996;0.994;0.914;0.988;1.0	D;P;P;P;D;D	0.73708	0.91;0.821;0.677;0.498;0.91;0.981	D	0.88810	0.3291	10	0.87932	D	0	.	18.7318	0.91738	0.0:1.0:0.0:0.0	.	1212;1171;1171;1171;1171;487	P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.;.;ANK1_HUMAN;.;.;.	H	1171;1171;1171;1171;1171;1171;1212;1171	ENSP00000339620:R1171H;ENSP00000289734:R1171H;ENSP00000369082:R1171H;ENSP00000380149:R1171H;ENSP00000380147:R1171H;ENSP00000309131:R1171H;ENSP00000265709:R1212H	ENSP00000265709:R1212H	R	-	2	0	ANK1	41670593	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.794000	0.85869	2.493000	0.84123	0.313000	0.20887	CGC	.		0.647	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41551436	C	T	41551436	3	4	40	1	0	0	0	0	1	0	0	0	620	768	27	1	2515	1	ANK1	8	41551436	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		41551436	104812586	68	3629											
SLC20A2	6575	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	42302170	42302170	+	Frame_Shift_Del	DEL	T	T	-																															taaaaggcccatacctgttaTtttcctccgcatccacggac																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr8:42302170delT	ENST00000342228.3	-	6	1093	c.724delA	c.(724-726)atafs	p.I242fs	SLC20A2_ENST00000520262.1_Frame_Shift_Del_p.I242fs|SLC20A2_ENST00000520179.1_Frame_Shift_Del_p.I242fs	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	242					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)			breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ATACCTGTTATTTTCCTCCGC	0.463																																					p.I242X		.											.	SLC20A2-92	0			c.724delA						.						137	120	126					8																	42302170		2203	4300	6503	SO:0001589	frameshift_variant	6575	exon6			.		CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"Solute carriers"	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.724delA	8.37:g.42302170delT	ENSP00000340465:p.Ile242fs	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	126	42	NM_001257181	0	0	0	0	0		Nonsense_Mutation	DEL	ENST00000342228.3	37	CCDS6132.1																																																																																			.		0.463	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			-	42302170	T	-	42302170	7	5	40	1	0	1	0	1	0	0	0	0	14471	1493	52	0	1258	0	SLC20A2	8	42302170	Frame_Shift_Del	DEL	T	TCGA-B1-A656-01A-11D-A31X-10	750734	42302170	104061852	69	3630											
TRPA1	8989	bcgsc.ca	37	chr8	72964852	72964852	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttttgctcctgatgatcGtaagaacaacctccttcctc	9	13	5	14	1	0	3	0	2	0	1	5	3	3	3	5	0	3	2	5	0	3	4	rs147715599		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr8:72964852G>T	ENST00000262209.4	-	14	2000	c.1793C>A	c.(1792-1794)aCg>aAg	p.T598K	RP11-383H13.1_ENST00000537896.1_3'UTR|RP11-383H13.1_ENST00000457356.4_3'UTR|RP11-383H13.1_ENST00000524152.1_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	598					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CCTGATGATCGTAAGAACAAC	0.448																																					p.T598K													.	TRPA1-230	0			c.C1793A						.						141	122	129					8																	72964852		2203	4300	6503	SO:0001583	missense	8989	exon14			ATGATCGTAAGAA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1793C>A	8.37:g.72964852G>T	ENSP00000262209:p.Thr598Lys	Somatic	65	0		WXS	Illumina HiSeq	Phase_1	46	4	NM_007332	0	0	0	0	0	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.877413	0.33162	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.64438	-0.1;-0.1	4.98	2.19	0.27852	Ankyrin repeat-containing domain (3);	0.254047	0.47852	D	0.000208	T	0.56381	0.1981	M	0.64997	1.995	0.09310	N	1	P	0.45428	0.858	B	0.43225	0.412	T	0.47548	-0.9109	10	0.30078	T	0.28	-3.4347	8.5498	0.33444	0.3012:0.0:0.6988:0.0	.	598	O75762	TRPA1_HUMAN	K	450;598	ENSP00000428151:T450K;ENSP00000262209:T598K	ENSP00000262209:T598K	T	-	2	0	TRPA1	73127406	0.949000	0.32298	0.066000	0.19879	0.208000	0.24298	1.698000	0.37794	0.231000	0.21079	0.585000	0.79938	ACG	G|1.000;A|0.000		0.448	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		T	72964852	G	T	72964852	3	4	40	1	0	0	0	0	1	0	0	0	16610	1145	40	4	1622	4	TRPA1	8	72964852	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	30662682	72964852	73399170	70	3631											
RGS22	26166	broad.mit.edu	37	chr8	101054051	101054051	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctaggttcttctgtataagcGtatcttctatccagctgggg	7	15	10	9	1	4	0	0	0	4	0	5	0	5	0	1	3	2	4	1	3	5	8	rs200708091		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr8:101054051G>A	ENST00000360863.6	-	12	2111	c.1917C>T	c.(1915-1917)taC>taT	p.Y639Y	RGS22_ENST00000523437.1_Silent_p.Y627Y|RGS22_ENST00000523287.1_Silent_p.Y458Y	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	639					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CTGTATAAGCGTATCTTCTAT	0.358																																					p.Y639Y													.	RGS22-140	0			c.C1917T						.						117	106	110					8																	101054051		1834	4092	5926	SO:0001819	synonymous_variant	26166	exon12			ATAAGCGTATCTT	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"Regulators of G-protein signaling"	24499	protein-coding gene	gene with protein product		615650	"regulator of G-protein signalling 22"				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.1917C>T	8.37:g.101054051G>A		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	75	3	NM_015668	0	0	0	0	0	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																			G|0.999;A|0.001		0.358	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		A	101054051	G	A	101054051	2	1	40	1	0	0	0	0	0	0	0	1	13337	1140	40	1		1	RGS22	8	101054051	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	28089199	101054051	45309971	71	3632											
RFX3	5991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	3271084	3271084	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacaatttttctatcaggCtaaattgaagattcacaaca	15	12	5	9	0	3	2	2	1	1	1	3	2	3	2	1	1	1	1	1	1	6	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:3271084C>G	ENST00000382004.3	-	11	1432	c.1121G>C	c.(1120-1122)aGc>aCc	p.S374T	RFX3_ENST00000302303.1_Missense_Mutation_p.S374T|RFX3_ENST00000358730.2_Missense_Mutation_p.S374T	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	374					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		TTCTATCAGGCTAAATTGAAG	0.388																																					p.S374T		.											.	RFX3-93	0			c.G1121C						.						166	152	156					9																	3271084		2203	4300	6503	SO:0001583	missense	5991	exon11			ATCAGGCTAAATT	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1121G>C	9.37:g.3271084C>G	ENSP00000371434:p.Ser374Thr	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	122	35	NM_134428	0	0	0	0	0	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	c	5.417	0.262094	0.10239	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303	T;T;T	0.08102	3.13;3.13;3.13	5.76	4.85	0.62838	.	0.039316	0.85682	D	0.000000	T	0.03695	0.0105	N	0.04508	-0.205	0.48632	D	0.999686	B;B;B	0.09022	0.002;0.0;0.002	B;B;B	0.12156	0.007;0.007;0.004	T	0.43877	-0.9364	10	0.09338	T	0.73	-10.837	11.3803	0.49752	0.0:0.8614:0.0:0.1386	.	374;374;374	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	T	374	ENSP00000371434:S374T;ENSP00000351574:S374T;ENSP00000303847:S374T	ENSP00000303847:S374T	S	-	2	0	RFX3	3261084	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.760000	0.55235	2.738000	0.93877	0.645000	0.84053	AGC	.		0.388	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		G	3271084	C	G	3271084	3	3	40	1	0	0	0	0	1	0	0	0	13296	797	28	4	1316	4	RFX3	9	3271084	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		3271084	137942347	72	3633											
SLC24A2	25769	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	19516367	19516367	+	Frame_Shift_Del	DEL	A	A	-																															gccactggctggaatctgtgAatgacggtgtacaggagcca																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:19516367delA	ENST00000341998.2	-	10	1831	c.1770delT	c.(1768-1770)attfs	p.I590fs	SLC24A2_ENST00000286344.3_Frame_Shift_Del_p.I573fs	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	590					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		GGAATCTGTGAATGACGGTGT	0.547																																					p.I590fs		.											.	SLC24A2-517	0			c.1770delT						.						47	44	45					9																	19516367		2203	4300	6503	SO:0001589	frameshift_variant	25769	exon10			.	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1770delT	9.37:g.19516367delA	ENSP00000344801:p.Ile590fs	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	86	29	NM_020344	0	0	0	0	0	B7ZLL8|Q9NTN5|Q9NZQ4	Frame_Shift_Del	DEL	ENST00000341998.2	37	CCDS6493.1																																																																																			.		0.547	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		-	19516367	A	-	19516367	7	5	40	1	0	1	0	1	0	0	0	0	14498	242	9	0	219	0	SLC24A2	9	19516367	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	16245283	19516367	121697064	73	3634											
RASEF	158158	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	85624582	85624582	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtattcagactctgatcagcAtaatcacttttcaaagcatc	13	13	5	10	0	5	2	4	1	1	1	6	2	5	2	0	0	2	3	0	0	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:85624582A>T	ENST00000376447.3	-	6	1193	c.933T>A	c.(931-933)taT>taA	p.Y311*		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	311					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TCTGATCAGCATAATCACTTT	0.348																																					p.Y311X													.	RASEF-280	0			c.T933A						.						153	140	144					9																	85624582		2203	4300	6503	SO:0001587	stop_gained	158158	exon6			ATCAGCATAATCA	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.933T>A	9.37:g.85624582A>T	ENSP00000365630:p.Tyr311*	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	104	22	NM_152573	0	0	0	0	0	A6NC29|Q96N04	Nonsense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	A	39	7.753455	0.98471	.	.	ENSG00000165105	ENST00000376447	.	.	.	5.92	3.56	0.40772	.	0.142934	0.49916	D	0.000121	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.379	0.44099	0.8654:0.0:0.1346:0.0	.	.	.	.	X	311	.	ENSP00000365630:Y311X	Y	-	3	2	RASEF	84814402	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.535000	0.36061	0.483000	0.27608	0.383000	0.25322	TAT	.		0.348	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		T	85624582	A	T	85624582	4	4	40	1	0	0	0	0	0	1	0	0	13100	224	8	5	1337	5	RASEF	9	85624582	Nonsense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	66108215	85624582	55588849	74	3635											
STXBP1	6812	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130438137	130438137	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatcaaggaccctatgcgaGccatcgtccccattctgctg	9	9	9	14	2	2	1	1	0	1	1	4	3	3	2	4	1	3	1	4	1	2	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:130438137G>A	ENST00000373299.1	+	14	1280	c.1165G>A	c.(1165-1167)Gcc>Acc	p.A389T	STXBP1_ENST00000373302.3_Missense_Mutation_p.A389T|STXBP1_ENST00000481942.1_3'UTR	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	389					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						CCCTATGCGAGCCATCGTCCC	0.507																																					p.A389T		.											.	STXBP1-91	0			c.G1165A						.						157	112	127					9																	130438137		2203	4300	6503	SO:0001583	missense	6812	exon14			ATGCGAGCCATCG	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.1165G>A	9.37:g.130438137G>A	ENSP00000362396:p.Ala389Thr	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	92	22	NM_001032221	0	0	7	8	1	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	37	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.406455	0.42715	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000541198;ENST00000373299	T;T	0.80033	-1.33;-1.33	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.62913	0.2467	N	0.04203	-0.255	0.58432	D	0.999998	B;B	0.14012	0.009;0.008	B;B	0.18263	0.021;0.012	T	0.59369	-0.7467	10	0.13108	T	0.6	-12.1555	17.491	0.87703	0.0:0.0:1.0:0.0	.	389;389	P61764;P61764-2	STXB1_HUMAN;.	T	343;389;221;389	ENSP00000362399:A389T;ENSP00000362396:A389T	ENSP00000362396:A389T	A	+	1	0	STXBP1	129477958	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.669000	0.68081	2.793000	0.96121	0.655000	0.94253	GCC	.		0.507	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		A	130438137	G	A	130438137	3	1	40	1	0	0	0	0	1	0	0	0	15384	971	34	2	1219	2	STXBP1	9	130438137	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	44813555	130438137	10775294	75	3636											
ENG	2022	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130582297	130582297	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcccagaaggtcaggcccGtgatggtgcacttcaaatgc	9	8	13	11	1	2	2	2	1	0	1	3	2	3	2	2	4	2	1	2	4	2	1	rs199764615		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:130582297G>A	ENST00000373203.4	-	9	1554	c.1154C>T	c.(1153-1155)aCg>aTg	p.T385M	RP11-228B15.4_ENST00000439298.1_RNA|RP11-228B15.4_ENST00000425991.1_RNA|ENG_ENST00000480266.1_5'UTR|ENG_ENST00000344849.3_Missense_Mutation_p.T385M	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	385	Ser/Thr-rich.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						GGTCAGGCCCGTGATGGTGCA	0.607									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia				G|||	1	0.000199681	0	0	5008	,	,		18170	0		0.001	False		,,,				2504	0				p.T385M													.	ENG-90	0			c.C1154T						.						76	67	70					9																	130582297		2203	4300	6503	SO:0001583	missense	2022	exon9	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	AGGCCCGTGATGG	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"CD molecules"	3349	protein-coding gene	gene with protein product		131195	"Osler-Rendu-Weber syndrome 1"	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.1154C>T	9.37:g.130582297G>A	ENSP00000362299:p.Thr385Met	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	40	7	NM_001114753	0	0	57	58	1	Q14248|Q14926|Q5T9C0	Missense_Mutation	SNP	ENST00000373203.4	37	CCDS48029.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	2.178	-0.388283	0.04932	.	.	ENSG00000106991	ENST00000373203;ENST00000344849;ENST00000545345;ENST00000546301	D;D	0.82984	-1.67;-1.67	3.99	-7.97	0.01139	Zona pellucida sperm-binding protein (1);	2.913470	0.01331	N	0.011242	T	0.61123	0.2322	N	0.20685	0.6	0.09310	N	1	B;B	0.30511	0.282;0.282	B;B	0.21546	0.035;0.035	T	0.61008	-0.7149	10	0.13108	T	0.6	-8.77	0.8767	0.01226	0.364:0.2503:0.2057:0.1801	.	385;385	Q5T9B9;P17813	.;EGLN_HUMAN	M	385;385;385;203	ENSP00000362299:T385M;ENSP00000341917:T385M	ENSP00000341917:T385M	T	-	2	0	ENG	129622118	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.456000	0.01002	-3.548000	0.00143	-1.579000	0.00862	ACG	G|0.999;A|0.000		0.607	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1			A	130582297	G	A	130582297	3	1	40	1	0	0	0	0	1	0	0	0	5130	1145	40	1	876	1	ENG	9	130582297	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	144160	130582297	10631134	76	3637											
ASB6	140459	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	132400146	132400146	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgggcagaggcagggcttTgaccttcacatccacaggcc	8	7	13	13	1	1	2	1	1	0	1	3	2	2	2	3	4	0	3	3	4	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:132400146T>A	ENST00000277458.4	-	6	1354	c.1189A>T	c.(1189-1191)Aaa>Taa	p.K397*	RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000277459.4_3'UTR|ASB6_ENST00000450050.2_Nonsense_Mutation_p.K318*	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	397	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				GGCAGGGCTTTGACCTTCACA	0.607																																					p.K397X		.											.	ASB6-226	0			c.A1189T						.						66	63	64					9																	132400146		2203	4300	6503	SO:0001587	stop_gained	140459	exon6			GGGCTTTGACCTT		CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"Ankyrin repeat domain containing"	17181	protein-coding gene	gene with protein product		615051	"ankyrin repeat and SOCS box-containing 6"				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.1189A>T	9.37:g.132400146T>A	ENSP00000277458:p.Lys397*	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	29	9	NM_017873	0	0	13	27	14	Q5SZB7|Q9BV15	Nonsense_Mutation	SNP	ENST00000277458.4	37	CCDS6924.1	.	.	.	.	.	.	.	.	.	.	T	37	6.123362	0.97305	.	.	ENSG00000148331	ENST00000277458;ENST00000450050	.	.	.	4.95	0.937	0.19494	.	0.300887	0.39759	N	0.001264	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0669	11.7516	0.51852	0.0:0.0:0.4323:0.5677	.	.	.	.	X	397;318	.	ENSP00000277458:K397X	K	-	1	0	ASB6	131439967	0.998000	0.40836	0.854000	0.33618	0.993000	0.82548	1.584000	0.36589	-0.003000	0.14444	0.379000	0.24179	AAA	.		0.607	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873		A	132400146	T	A	132400146	4	1	40	1	0	0	0	0	0	1	0	0	1028	1821	63	5	80	5	ASB6	9	132400146	Nonsense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	1817849	132400146	8813285	77	3638											
ALOX5	240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	45936826	45936826	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgagattcaccattgcaaTcaacaccaaggcccgtgagc	12	7	9	13	2	2	2	2	2	0	1	2	3	2	2	3	1	3	1	3	1	3	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:45936826T>A	ENST00000374391.2	+	9	1273	c.1220T>A	c.(1219-1221)aTc>aAc	p.I407N	ALOX5_ENST00000542434.1_Missense_Mutation_p.I407N	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	407	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	ACCATTGCAATCAACACCAAG	0.627																																					p.I407N		.											.	ALOX5-228	0			c.T1220A						.						180	169	173					10																	45936826		2203	4300	6503	SO:0001583	missense	240	exon9			TTGCAATCAACAC	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.1220T>A	10.37:g.45936826T>A	ENSP00000363512:p.Ile407Asn	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	67	24	NM_000698	0	0	37	45	8	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	37	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185478	0.78677	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	D;D	0.94000	-3.33;-3.33	5.45	5.45	0.79879	Lipoxygenase, C-terminal (3);	0.047406	0.85682	D	0.000000	D	0.97399	0.9149	M	0.93197	3.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.989;0.995	D	0.98292	1.0514	10	0.87932	D	0	-34.9933	13.4602	0.61223	0.0:0.0:0.0:1.0	.	407;407;407	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	N	407	ENSP00000437634:I407N;ENSP00000363512:I407N	ENSP00000363512:I407N	I	+	2	0	ALOX5	45256832	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	7.996000	0.88334	2.054000	0.61138	0.533000	0.62120	ATC	.		0.627	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			A	45936826	T	A	45936826	3	1	40	1	0	0	0	0	1	0	0	0	540	1435	50	5	1254	5	ALOX5	10	45936826	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10		45936826	89597921	78	3639											
NCOA4	8031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	51585173	51585173	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgatgagaattgtgagaaGgaggctctgtataagtggct	11	12	15	3	0	1	3	0	3	1	2	1	6	1	4	0	3	0	3	0	3	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:51585173G>A	ENST00000443446.1	+	8	1501	c.1272G>A	c.(1270-1272)aaG>aaA	p.K424K	NCOA4_ENST00000374087.4_Silent_p.K424K|NCOA4_ENST00000374082.1_Silent_p.K424K|NCOA4_ENST00000438493.1_Silent_p.K440K|NCOA4_ENST00000414907.2_Silent_p.K258K|NCOA4_ENST00000452682.1_Silent_p.K440K|NCOA4_ENST00000430396.2_Silent_p.K324K|NCOA4_ENST00000344348.6_Silent_p.K424K	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	424					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						ATTGTGAGAAGGAGGCTCTGT	0.478			T	RET	papillary thyroid																																p.K440K		.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4-1042	0			c.G1320A						.						70	75	73					10																	51585173		2203	4300	6503	SO:0001819	synonymous_variant	8031	exon9			TGAGAAGGAGGCT	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1272G>A	10.37:g.51585173G>A		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	151	47	NM_001145261	0	0	7	8	1	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Silent	SNP	ENST00000443446.1	37	CCDS7237.1																																																																																			.		0.478	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		A	51585173	G	A	51585173	2	1	40	1	0	0	0	0	0	0	0	1	10257	991	35	2		2	NCOA4	10	51585173	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5648347	51585173	83949574	79	3640											
NUDT13	25961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74879906	74879906	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatacctggccccccggcacAgcctgttaggtaagtccaga	10	7	10	14	1	0	1	0	0	0	1	1	1	1	1	6	3	2	3	6	3	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:74879906A>C	ENST00000357321.4	+	3	332	c.214A>C	c.(214-216)Agc>Cgc	p.S72R	NUDT13_ENST00000349051.5_Missense_Mutation_p.S72R|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000372997.3_Missense_Mutation_p.S72R|NUDT13_ENST00000544879.1_5'UTR|NUDT13_ENST00000537969.1_5'UTR	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					CCCCCGGCACAGCCTGTTAGG	0.498																																					p.S72R		.											.	NUDT13-90	0			c.A214C						.						55	56	56					10																	74879906		2203	4300	6503	SO:0001583	missense	25961	exon3			CGGCACAGCCTGT	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.214A>C	10.37:g.74879906A>C	ENSP00000349874:p.Ser72Arg	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	52	17	NM_015901	0	0	0	0	0		Missense_Mutation	SNP	ENST00000357321.4	37	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887191	0.33348	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.32515	1.45;1.45;1.45	5.63	5.63	0.86233	NADH pyrophosphatase-like, N-terminal (1);	0.319618	0.40302	N	0.001140	T	0.25419	0.0618	L	0.38531	1.155	0.80722	D	1	B;B;B	0.33755	0.424;0.045;0.079	B;B;B	0.29942	0.109;0.102;0.092	T	0.03453	-1.1035	10	0.35671	T	0.21	.	15.0175	0.71597	1.0:0.0:0.0:0.0	.	72;72;72	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	R	72	ENSP00000349874:S72R;ENSP00000335326:S72R;ENSP00000362088:S72R	ENSP00000335326:S72R	S	+	1	0	NUDT13	74549912	0.996000	0.38824	0.776000	0.31678	0.176000	0.22953	3.633000	0.54295	2.148000	0.66965	0.533000	0.62120	AGC	.		0.498	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		C	74879906	A	C	74879906	3	2	40	1	0	0	0	0	1	0	0	0	10755	188	7	5	220	5	NUDT13	10	74879906	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	23294733	74879906	60654841	80	3641											
ZMIZ1	57178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	80968102	80968102	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcccacagcacttacagAatcctgccaacttccacaat	12	10	3	16	0	0	1	0	0	0	1	3	1	3	1	4	0	4	1	4	0	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:80968102A>T	ENST00000334512.5	+	6	642	c.70A>T	c.(70-72)Aat>Tat	p.N24Y		NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	24					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			GCACTTACAGAATCCTGCCAA	0.622																																					p.N24Y		.											.	ZMIZ1-292	0			c.A70T						.						68	56	60					10																	80968102		2203	4300	6503	SO:0001583	missense	57178	exon6			TTACAGAATCCTG	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.70A>T	10.37:g.80968102A>T	ENSP00000334474:p.Asn24Tyr	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	63	16	NM_020338	0	0	0	0	0	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	37	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.022073	0.75275	.	.	ENSG00000108175	ENST00000334512;ENST00000394592	T	0.34667	1.35	5.23	4.1	0.47936	.	.	.	.	.	T	0.52645	0.1747	L	0.60455	1.87	0.80722	D	1	D;D	0.65815	0.995;0.993	D;P	0.72982	0.979;0.885	T	0.52793	-0.8528	9	0.87932	D	0	-6.037	9.9202	0.41459	0.9182:0.0:0.0818:0.0	.	24;24	Q9ULJ6;A0JLS3	ZMIZ1_HUMAN;.	Y	24	ENSP00000334474:N24Y	ENSP00000334474:N24Y	N	+	1	0	ZMIZ1	80638108	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.717000	0.91425	0.846000	0.35142	0.379000	0.24179	AAT	.		0.622	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		T	80968102	A	T	80968102	3	4	40	1	0	0	0	0	1	0	0	0	17728	246	9	5	76	5	ZMIZ1	10	80968102	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	6088196	80968102	54566645	81	3642											
SORCS1	114815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	108371744	108371744	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccgggttgtagtcatccagGtttggagaaaaggacaagcg	11	9	14	7	2	1	1	1	0	0	1	3	3	3	2	2	4	1	3	2	4	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:108371744G>T	ENST00000263054.6	-	22	2965	c.2958C>A	c.(2956-2958)aaC>aaA	p.N986K	SORCS1_ENST00000369698.1_Missense_Mutation_p.N521K|SORCS1_ENST00000344440.6_Missense_Mutation_p.N986K|SORCS1_ENST00000478809.2_5'UTR	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	986					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGTCATCCAGGTTTGGAGAAA	0.463																																					p.N986K		.											.	SORCS1-153	0			c.C2958A						.						113	103	106					10																	108371744		2203	4300	6503	SO:0001583	missense	114815	exon22			ATCCAGGTTTGGA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2958C>A	10.37:g.108371744G>T	ENSP00000263054:p.Asn986Lys	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	158	44	NM_001206572	0	0	0	0	0	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.41|19.41	3.822407|3.822407	0.71028|0.71028	.|.	.|.	ENSG00000108018|ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440|ENST00000452214	T;T;T|.	0.24908|.	1.83;2.4;2.4|.	5.4|5.4	4.49|4.49	0.54785|0.54785	.|.	0.048600|.	0.85682|.	D|.	0.000000|.	T|T	0.73869|0.73869	0.3642|0.3642	M|M	0.80183|0.80183	2.485|2.485	0.44359|0.44359	D|D	0.997259|0.997259	D;D;D;D;D|.	0.58620|.	0.972;0.983;0.983;0.972;0.983|.	P;P;P;P;P|.	0.62298|.	0.797;0.9;0.9;0.797;0.9|.	T|T	0.75391|0.75391	-0.3334|-0.3334	9|5	.|.	.|.	.|.	-33.8428|-33.8428	11.7072|11.7072	0.51603|0.51603	0.1432:0.0:0.8568:0.0|0.1432:0.0:0.8568:0.0	.|.	986;986;986;986;986|.	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2|.	.;.;.;SORC1_HUMAN;.|.	K|N	521;986;986|1	ENSP00000358712:N521K;ENSP00000263054:N986K;ENSP00000345964:N986K|.	.|.	N|T	-|-	3|2	2|0	SORCS1|SORCS1	108361734|108361734	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.681000|1.681000	0.37618|0.37618	1.406000|1.406000	0.46857|0.46857	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.		0.463	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		T	108371744	G	T	108371744	3	4	40	1	0	0	0	0	1	0	0	0	14962	1252	44	4	802	4	SORCS1	10	108371744	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	27403642	108371744	27163003	82	3643											
OR5P2	120065	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr11	7818418	7818419	+	Missense_Mutation	DNP	TG	TG	AA																															aagaggatgactcgaaggatTggatcatctgttaagcccaa																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:7818418_7818419TG>AA	ENST00000329434.2	-	1	101_102	c.71_72CA>TT	c.(70-72)cCA>cTT	p.P24L	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CTCGAAGGATTGGATCATCTGT	0.426																																					p.P24L		.											.	OR5P2-496	0			c.C71T						.																																			SO:0001583	missense	120065	exon1			AGGATTGGATCAT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"GPCR / Class A : Olfactory receptors"	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.71_72delinsAA	11.37:g.7818418_7818419delinsAA	ENSP00000331823:p.Pro24Leu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	62	15	NM_153444	0	0	0	0	0	Q3MIS8	Missense_Mutation	DNP	ENST00000329434.2	37	CCDS7782.1																																																																																			.		0.426	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		AA	7818419	TG	AA	7818418	3	1	40	1	0	0	0	0	1	0	0	0	11204	1799	63	5	900	5	OR5P2	11	7818418	Missense_Mutation	DNP	TG	TCGA-B1-A656-01A-11D-A31X-10		7818418	127188098	83	3644	38	2									
OR5P2	120065	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr11	7818420	7818420	+	Missense_Mutation	SNP	G	G	T																															gaggatgactcgaaggattgGatcatctgttaagcccaata																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:7818420G>T	ENST00000329434.2	-	1	100	c.70C>A	c.(70-72)Cca>Aca	p.P24T	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CGAAGGATTGGATCATCTGTT	0.428																																					p.P24T		.											.	OR5P2-496	0			c.C70A						.						63	73	70					11																	7818420		2103	4292	6395	SO:0001583	missense	120065	exon1			GGATTGGATCATC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"GPCR / Class A : Olfactory receptors"	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.70C>A	11.37:g.7818420G>T	ENSP00000331823:p.Pro24Thr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	61	15	NM_153444	0	0	0	0	0	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710700	0.30322	.	.	ENSG00000183303	ENST00000329434	T	0.20200	2.09	5.5	4.59	0.56863	.	0.193570	0.37304	N	0.002145	T	0.32315	0.0825	M	0.74258	2.255	0.37509	D	0.917076	P	0.40376	0.715	P	0.45343	0.477	T	0.35101	-0.9802	10	0.52906	T	0.07	-10.9491	12.0929	0.53737	0.0821:0.0:0.9179:0.0	.	24	Q8WZ92	OR5P2_HUMAN	T	24	ENSP00000331823:P24T	ENSP00000331823:P24T	P	-	1	0	OR5P2	7774996	0.000000	0.05858	0.034000	0.17996	0.330000	0.28571	0.798000	0.27014	1.569000	0.49696	0.555000	0.69702	CCA	.		0.428	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		T	7818420	G	T	7818420	3	4	40	1	0	0	0	0	1	0	0	0	11204	1174	41	4	902	4	OR5P2	11	7818420	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	2	7818420	127188096	84	3645	38	2									
LGR4	55366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	27402259	27402259	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaggattatcatacaaatgtCtgtgaaaatatccaaaaaaa	20	10	6	5	0	2	1	1	1	1	0	3	3	3	2	1	1	1	0	1	1	9	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:27402259C>G	ENST00000379214.4	-	9	1274		c.e9-1		LGR4_ENST00000389858.4_Splice_Site	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4						bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						ATACAAATGTCTGTGAAAATA	0.299																																					.		.											.	LGR4-91	0			c.831-1G>C						.						49	52	51					11																	27402259		2201	4289	6490	SO:0001630	splice_region_variant	55366	exon10			AAATGTCTGTGAA	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.831-1G>C	11.37:g.27402259C>G		Somatic	232	0		WXS	Illumina HiSeq	Phase_I	223	73	NM_018490	0	0	0	0	0	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Splice_Site	SNP	ENST00000379214.4	37	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067334	0.76301	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7788	0.96409	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LGR4	27358835	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.487000	0.81328	2.749000	0.94314	0.460000	0.39030	.	.		0.299	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	Intron	G	27402259	C	G	27402259	5	3	40	1	0	0	0	0	0	0	1	0	8778	927	32	4	2065	4	LGR4	11	27402259	Splice_Site	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	19583839	27402259	107604257	85	3646											
PLCB3	5331	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64034708	64034708	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcttgtggctgggcagcagCaggtcctgcaacagctggca	7	8	15	11	0	1	0	0	0	1	0	2	0	2	0	1	4	5	7	1	4	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:64034708C>T	ENST00000540288.1	+	30	3569	c.3466C>T	c.(3466-3468)Cag>Tag	p.Q1156*	PLCB3_ENST00000325234.5_Nonsense_Mutation_p.Q1089*|PLCB3_ENST00000279230.6_Nonsense_Mutation_p.Q1156*	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1156					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TGGGCAGCAGCAGGTCCTGCA	0.672																																					p.Q1156X		.											.	PLCB3-228	0			c.C3466T						.						19	18	18					11																	64034708		1955	3784	5739	SO:0001587	stop_gained	5331	exon30			CAGCAGCAGGTCC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.3466C>T	11.37:g.64034708C>T	ENSP00000443631:p.Gln1156*	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	101	30	NM_000932	0	0	31	39	8	A5PKZ6|G5E960|Q8N1A4	Nonsense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	C	39	7.682014	0.98431	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	.	.	.	4.42	4.42	0.53409	.	0.339854	0.29830	N	0.011090	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	11.0366	0.47804	0.0:0.6842:0.3158:0.0	.	.	.	.	X	1156;1156;1089	.	ENSP00000279230:Q1156X	Q	+	1	0	PLCB3	63791284	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.151000	0.58105	2.297000	0.77311	0.561000	0.74099	CAG	.		0.672	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			T	64034708	C	T	64034708	4	4	40	1	0	0	0	0	0	1	0	0	12055	711	25	2	3584	2	PLCB3	11	64034708	Nonsense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	36632449	64034708	70971808	86	3647											
NRXN2	9379	broad.mit.edu	37	chr11	64453314	64453314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccgttgcgttgcagggtgCggaaggccagtgtgatctca	6	9	17	9	3	1	1	1	1	1	0	2	2	1	2	2	4	3	3	2	4	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:64453314C>T	ENST00000377551.1	-	5	1167	c.956G>A	c.(955-957)cGc>cAc	p.R319H	NRXN2_ENST00000409571.1_Missense_Mutation_p.R319H|NRXN2_ENST00000377559.3_Missense_Mutation_p.R295H|NRXN2_ENST00000265459.6_Missense_Mutation_p.R319H			Q9P2S2	NRX2A_HUMAN	neurexin 2	319	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TTGCAGGGTGCGGAAGGCCAG	0.562																																					p.R319H													.	NRXN2-232	0			c.G956A						.						358	285	310					11																	64453314		2201	4297	6498	SO:0001583	missense	9379	exon6			AGGGTGCGGAAGG		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.956G>A	11.37:g.64453314C>T	ENSP00000366774:p.Arg319His	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	191	5	NM_015080	0	0	0	0	0	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.1|23.1	4.374819|4.374819	0.82573|0.82573	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000417749|ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300	.|D;D;D;D;D	.|0.84370	.|-1.84;-1.79;-1.84;-1.84;-1.84	4.17|4.17	4.17|4.17	0.49024|0.49024	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.|0.000000	.|0.44097	.|U	.|0.000496	D|D	0.91637|0.91637	0.7357|0.7357	M|M	0.79475|0.79475	2.455|2.455	0.58432|0.58432	D|D	0.99999|0.99999	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.76575	.|0.988;0.973	D|D	0.92845|0.92845	0.6292|0.6292	5|10	.|0.87932	.|D	.|0	.|.	14.3646|14.3646	0.66799|0.66799	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|295;319	.|Q9P2S2-2;Q9P2S2	.|.;NRX2A_HUMAN	T|H	80|319;295;319;295;319;90	.|ENSP00000366774:R319H;ENSP00000366782:R295H;ENSP00000265459:R319H;ENSP00000386416:R319H;ENSP00000388971:R90H	.|ENSP00000265459:R319H	A|R	-|-	1|2	0|0	NRXN2|NRXN2	64209890|64209890	0.969000|0.969000	0.33509|0.33509	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	1.776000|1.776000	0.38594|0.38594	2.062000|2.062000	0.61559|0.61559	0.467000|0.467000	0.42956|0.42956	GCA|CGC	.		0.562	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64453314	C	T	64453314	3	4	40	1	0	0	0	0	1	0	0	0	10692	768	27	1	4523	1	NRXN2	11	64453314	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	418606	64453314	70553202	87	3648											
NAALADL1	10004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64813975	64813975	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaggctgtgtggtaggtgggGtagatcctggctgaagtctt	7	12	17	5	0	1	2	0	1	1	1	2	2	2	2	1	6	0	4	1	6	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:64813975G>A	ENST00000358658.3	-	14	1650	c.1623C>T	c.(1621-1623)taC>taT	p.Y541Y	NAALADL1_ENST00000528884.1_Intron|NAALADL1_ENST00000355721.3_Silent_p.Y500Y|NAALADL1_ENST00000340252.4_Silent_p.Y592Y|NAALADL1_ENST00000339885.2_Missense_Mutation_p.T511I|NAALADL1_ENST00000356632.3_Silent_p.Y506Y|NAALADL1_ENST00000355369.2_Intron|NAALADL1_ENST00000526799.1_5'UTR	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	541	NAALADase.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GGTAGGTGGGGTAGATCCTGG	0.552																																					p.Y541Y		.											.	NAALADL1-90	0			c.C1623T						.						130	109	116					11																	64813975		2201	4297	6498	SO:0001819	synonymous_variant	10004	exon14			GGTGGGGTAGATC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1623C>T	11.37:g.64813975G>A		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	138	31	NM_005468	0	0	0	0	0	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Silent	SNP	ENST00000358658.3	37	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.583064	0.65992	.	.	ENSG00000168060	ENST00000339885	T	0.48522	0.81	5.53	4.63	0.57726	.	.	.	.	.	T	0.49609	0.1567	.	.	.	0.26194	N	0.979542	.	.	.	.	.	.	T	0.48317	-0.9046	6	0.87932	D	0	-29.7051	8.5374	0.33371	0.1733:0.0:0.8267:0.0	.	.	.	.	I	511	ENSP00000340111:T511I	ENSP00000340111:T511I	T	-	2	0	NAALADL1	64570551	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.241000	0.51376	1.370000	0.46153	0.561000	0.74099	ACC	.		0.552	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		A	64813975	G	A	64813975	2	1	40	1	0	0	0	0	0	0	0	1	10154	1256	44	2		2	NAALADL1	11	64813975	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	360661	64813975	70192541	88	3649											
FAM86C	55199	broad.mit.edu	37	chr11	71507083	71507083	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtgctgtattgcccagaaGccatcgtgtcgctggtcggg	6	10	14	11	4	0	1	0	0	0	1	3	1	0	1	2	2	3	3	2	2	2	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:71507083G>A	ENST00000359244.4	+	4	305	c.282G>A	c.(280-282)aaG>aaA	p.K94K	FAM86C1_ENST00000426628.2_Silent_p.K87K|FAM86C1_ENST00000346333.6_Silent_p.K60K	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	94										lung(1)	1						TTGCCCAGAAGCCATCGTGTC	0.612																																					p.K94K													.	FAM86C1-90	0			c.G282A						.						44	48	46					11																	71507083		2199	4288	6487	SO:0001819	synonymous_variant	55199	exon4			CCAGAAGCCATCG	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"family with sequence similarity 86, member C"	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.282G>A	11.37:g.71507083G>A		Somatic	91	1		WXS	Illumina HiSeq	Phase_I	61	3	NM_018172	0	0	38	40	2	Q8N5D3	Silent	SNP	ENST00000359244.4	37	CCDS41686.1																																																																																			.		0.612	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563		A	71507083	G	A	71507083	2	1	40	1	0	0	0	0	0	0	0	1	5665	962	34	2		2	FAM86C	11	71507083	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	6693108	71507083	63499433	89	3650											
CLPB	81570	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	72145214	72145214	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaccccgttccagctgTcctgtcctgggagtgtttct	3	13	13	12	1	1	0	0	0	1	0	4	2	4	2	5	3	1	3	5	3	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:72145214T>A	ENST00000294053.3	-	1	478	c.305A>T	c.(304-306)gAc>gTc	p.D102V	CLPB_ENST00000437826.2_Silent_p.G21G|CLPB_ENST00000340729.5_Missense_Mutation_p.D102V|CLPB_ENST00000542555.1_5'Flank|CLPB_ENST00000445069.2_Intron|CLPB_ENST00000538039.1_Missense_Mutation_p.D102V|CLPB_ENST00000543042.1_5'UTR	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	102					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						GTTCCAGCTGTCCTGTCCTGG	0.662											OREG0021194	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D102V		.											.	CLPB-91	0			c.A305T						.						45	49	47					11																	72145214		2200	4292	6492	SO:0001583	missense	81570	exon1			CAGCTGTCCTGTC	BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"Ankyrin repeat domain containing"	30664	protein-coding gene	gene with protein product	"suppressor of potassium transport defect 3"					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.305A>T	11.37:g.72145214T>A	ENSP00000294053:p.Asp102Val	Somatic	96	0	1135	WXS	Illumina HiSeq	Phase_I	69	15	NM_001258392	0	0	3	3	0	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Missense_Mutation	SNP	ENST00000294053.3	37	CCDS8215.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964448	0.53507	.	.	ENSG00000162129	ENST00000294053;ENST00000538039;ENST00000340729	T;T;T	0.69175	1.9;1.08;-0.38	5.04	2.43	0.29744	.	0.289184	0.26286	N	0.025253	T	0.45856	0.1363	N	0.14661	0.345	0.80722	D	1	P;B;P	0.37955	0.514;0.437;0.612	B;B;B	0.38880	0.284;0.189;0.203	T	0.43637	-0.9379	10	0.72032	D	0.01	-12.7372	5.6906	0.17827	0.1674:0.0:0.1731:0.6594	.	102;102;102	F8W7P6;Q9H078-2;Q9H078	.;.;CLPB_HUMAN	V	102	ENSP00000294053:D102V;ENSP00000441518:D102V;ENSP00000340385:D102V	ENSP00000294053:D102V	D	-	2	0	CLPB	71822862	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	1.637000	0.37155	0.808000	0.34231	0.533000	0.62120	GAC	.		0.662	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1	NM_030813		A	72145214	T	A	72145214	3	1	40	1	0	0	0	0	1	0	0	0	3557	1667	58	5	1886	5	CLPB	11	72145214	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	638131	72145214	62861302	90	3651											
KCNE3	10008	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74168349	74168350	+	Missense_Mutation	DNP	TT	TT	AA																															catgataggggtcactacgcTtgtccactttgcgggagcgg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:74168349_74168350TT>AA	ENST00000310128.4	-	3	678_679	c.259_260AA>TT	c.(259-261)AAg>TTg	p.K87L	RP11-702H23.4_ENST00000533008.1_RNA|KCNE3_ENST00000525550.1_Missense_Mutation_p.K87L|RP11-702H23.6_ENST00000530510.1_RNA	NM_005472.4	NP_005463.1	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related family, member 3	87					regulation of potassium ion transport (GO:0043266)	integral component of membrane (GO:0016021)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			cervix(1)|large_intestine(1)|lung(1)|ovary(1)	4	Breast(11;2.86e-06)					GTCACTACGCTTGTCCACTTTG	0.495																																					p.K87L		.											.	KCNE3-69	0			c.A259T						.																																			SO:0001583	missense	10008	exon3			TACGCTTGTCCAC	AF076531	CCDS8232.1	11q13.4	2014-09-17				ENSG00000175538		"Potassium channels"	6243	protein-coding gene	gene with protein product		604433				10219239	Standard	NM_005472		Approved	MiRP2, HOKPP	uc001ovc.3	Q9Y6H6		ENST00000310128.4:c.259_260delinsAA	11.37:g.74168349_74168350delinsAA	ENSP00000310557:p.Lys87Leu	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	87	19	NM_005472	0	0	0	0	0		Missense_Mutation	DNP	ENST00000310128.4	37	CCDS8232.1																																																																																			.		0.495	KCNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385531.1	NM_005472		AA	74168350	TT	AA	74168349	3	1	40	1	0	0	0	0	1	0	0	0	8045	1609	56	5	55	5	KCNE3	11	74168349	Missense_Mutation	DNP	TT	TCGA-B1-A656-01A-11D-A31X-10	2023135	74168349	60838167	91	3652											
FZD4	8322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	86663362	86663362	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgtggtgggaatttgcTgcagttcagactctctggcc	5	14	13	9	0	3	1	1	0	2	1	4	2	3	2	1	3	2	4	1	3	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:86663362T>C	ENST00000531380.1	-	2	741	c.436A>G	c.(436-438)Agc>Ggc	p.S146G	PRSS23_ENST00000533902.2_3'UTR	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	146	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGGAATTTGCTGCAGTTCAGA	0.557																																					p.S146G		.											.	FZD4-1145	0			c.A436G						.						91	94	93					11																	86663362		2201	4299	6500	SO:0001583	missense	8322	exon2			ATTTGCTGCAGTT	AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"GPCR / Class F : Frizzled receptors", "CD molecules"	4042	protein-coding gene	gene with protein product		604579	"frizzled (Drosophila) homolog 4", "exudative vitreoretinopathy 1", "frizzled homolog 4 (Drosophila)", "frizzled 4, seven transmembrane spanning receptor", "frizzled family receptor 4"	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.436A>G	11.37:g.86663362T>C	ENSP00000434034:p.Ser146Gly	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	101	20	NM_012193	0	0	3	3	0	A8K9Q3|Q14C97|Q6S9E4	Missense_Mutation	SNP	ENST00000531380.1	37	CCDS8279.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915066	0.52546	.	.	ENSG00000174804	ENST00000531380	T	0.80393	-1.37	5.82	5.82	0.92795	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.82426	0.5034	M	0.77712	2.385	0.58432	D	0.999999	B	0.25441	0.126	B	0.32289	0.143	T	0.79037	-0.1967	9	.	.	.	.	16.1832	0.81925	0.0:0.0:0.0:1.0	.	146	Q9ULV1	FZD4_HUMAN	G	146	ENSP00000434034:S146G	.	S	-	1	0	FZD4	86341010	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.221000	0.58574	2.228000	0.72767	0.533000	0.62120	AGC	.		0.557	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193		C	86663362	T	C	86663362	3	2	40	1	0	0	0	0	1	0	0	0	6151	1580	55	3	1181	3	FZD4	11	86663362	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	12495013	86663362	48343154	92	3653											
DYNC2H1	79659	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	103091430	103091430	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaattcgctcactacgcatgCcacctgatgtaattagagat	13	11	7	10	2	1	2	1	1	0	1	2	3	1	2	2	0	2	3	2	0	4	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:103091430C>G	ENST00000375735.2	+	57	9169	c.9025C>G	c.(9025-9027)Cca>Gca	p.P3009A	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.P3009A|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3009	Stalk. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ACTACGCATGCCACCTGATGT	0.368																																					p.P3009A													.	DYNC2H1-68	0			c.C9025G						.						96	94	95					11																	103091430		1880	4118	5998	SO:0001583	missense	79659	exon57			CGCATGCCACCTG	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.9025C>G	11.37:g.103091430C>G	ENSP00000364887:p.Pro3009Ala	Somatic	119	1		WXS	Illumina HiSeq	Phase_I	106	14	NM_001377	0	0	0	0	0	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.814794	0.90790	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	D;D	0.81579	-1.51;-1.51	6.17	6.17	0.99709	Dynein heavy chain, coiled coil stalk (1);	0.113491	0.64402	D	0.000009	D	0.91713	0.7380	M	0.86573	2.825	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.976	D	0.91585	0.5282	10	0.72032	D	0.01	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	3009;3009	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	3009	ENSP00000364887:P3009A;ENSP00000381167:P3009A	ENSP00000364887:P3009A	P	+	1	0	DYNC2H1	102596640	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.794000	0.85869	2.941000	0.99782	0.655000	0.94253	CCA	.		0.368	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103091430	C	G	103091430	3	3	40	1	0	0	0	0	1	0	0	0	4857	739	26	4	9251	4	DYNC2H1	11	103091430	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	16428068	103091430	31915086	93	3654											
SLC35F2	54733	broad.mit.edu	37	chr11	107682461	107682461	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attagcttccacatctgctaGtcccagcaggatgtacttcc	9	12	7	13	0	1	0	0	0	1	0	4	1	4	1	3	1	4	4	3	1	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:107682461G>T	ENST00000525815.1	-	3	766	c.346C>A	c.(346-348)Cta>Ata	p.L116I	SLC35F2_ENST00000429869.1_Missense_Mutation_p.L116I|SLC35F2_ENST00000375682.4_Missense_Mutation_p.L69I|SLC35F2_ENST00000265836.7_5'UTR|SLC35F2_ENST00000525071.1_Missense_Mutation_p.L116I	NM_017515.4	NP_059985.2	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	116					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		ACATCTGCTAGTCCCAGCAGG	0.423																																					p.L116I													.	SLC35F2-90	0			c.C346A						.						219	203	208					11																	107682461		1884	4113	5997	SO:0001583	missense	54733	exon3			CTGCTAGTCCCAG		CCDS41709.1	11q22.3	2013-05-22			ENSG00000110660	ENSG00000110660		"Solute carriers"	23615	protein-coding gene	gene with protein product						9119394	Standard	NM_017515		Approved	FLJ13018	uc001pjq.3	Q8IXU6	OTTHUMG00000166366	ENST00000525815.1:c.346C>A	11.37:g.107682461G>T	ENSP00000436785:p.Leu116Ile	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	101	3	NM_017515	0	0	3	3	0	Q14963|Q5JPA8|Q6ZRQ3|Q9H947	Missense_Mutation	SNP	ENST00000525815.1	37	CCDS41709.1	.	.	.	.	.	.	.	.	.	.	G	8.640	0.895759	0.17686	.	.	ENSG00000110660	ENST00000525815;ENST00000525071;ENST00000375682;ENST00000429869	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.42	0.28	0.15682	.	0.161185	0.43260	D	0.000597	T	0.50990	0.1648	N	0.25094	0.71	0.58432	D	0.999999	B;B	0.28713	0.22;0.22	B;B	0.35114	0.196;0.163	T	0.12967	-1.0527	10	0.19147	T	0.46	.	5.5271	0.16964	0.4192:0.0:0.4572:0.1236	.	116;116	E9PJD1;Q8IXU6	.;S35F2_HUMAN	I	116;116;69;116	ENSP00000436785:L116I;ENSP00000434307:L116I;ENSP00000364834:L69I;ENSP00000393571:L116I	ENSP00000364834:L69I	L	-	1	2	SLC35F2	107187671	0.031000	0.19500	0.068000	0.19968	0.782000	0.44232	0.234000	0.17930	0.030000	0.15379	-0.266000	0.10368	CTA	.		0.423	SLC35F2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389417.1	NM_017515		T	107682461	G	T	107682461	3	4	40	1	0	0	0	0	1	0	0	0	14621	1020	36	4	802	4	SLC35F2	11	107682461	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	4591031	107682461	27324055	94	3655											
BACE1	23621	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117186300	117186300	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccacgtagtagccctgccccGacttgcccctcaggttgtcc	5	9	9	18	2	1	0	1	0	0	0	2	1	2	0	7	1	3	3	7	1	2	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:117186300G>A	ENST00000313005.6	-	1	672	c.212C>T	c.(211-213)tCg>tTg	p.S71L	AP000892.4_ENST00000504906.1_RNA|BACE1_ENST00000428381.2_Missense_Mutation_p.S71L|BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Missense_Mutation_p.S71L|BACE1_ENST00000445823.2_Missense_Mutation_p.S71L|BACE1_ENST00000513780.1_Missense_Mutation_p.S71L	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	71					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GCCCTGCCCCGACTTGCCCCT	0.697																																					p.S71L													.	BACE1-91	0			c.C212T						.						50	47	48					11																	117186300		2201	4296	6497	SO:0001583	missense	23621	exon1			TGCCCCGACTTGC	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"beta-site APP-cleaving enzyme"	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.212C>T	11.37:g.117186300G>A	ENSP00000318585:p.Ser71Leu	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	127	48	NM_138972	0	0	0	0	0	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Missense_Mutation	SNP	ENST00000313005.6	37	CCDS8383.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094932	0.94197	.	.	ENSG00000186318	ENST00000313005;ENST00000528053;ENST00000428381;ENST00000513780;ENST00000445823	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	4.99	4.99	0.66335	Peptidase aspartic (1);	0.000000	0.85682	D	0.000000	T	0.53206	0.1782	L	0.59436	1.845	0.80722	D	1	D;D;P;D;D	0.76494	0.999;0.998;0.878;0.993;0.995	P;D;B;P;P	0.64506	0.788;0.926;0.355;0.862;0.661	T	0.51395	-0.8711	10	0.02654	T	1	.	15.7488	0.77967	0.0:0.0:1.0:0.0	.	71;71;71;71;71	Q76KP0;P56817;P56817-3;P56817-4;P56817-2	.;BACE1_HUMAN;.;.;.	L	71	ENSP00000318585:S71L;ENSP00000431848:S71L;ENSP00000402228:S71L;ENSP00000424536:S71L;ENSP00000403685:S71L	ENSP00000318585:S71L	S	-	2	0	BACE1	116691510	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.645000	0.91049	2.302000	0.77476	0.655000	0.94253	TCG	.		0.697	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1			A	117186300	G	A	117186300	3	1	40	1	0	0	0	0	1	0	0	0	1282	1059	37	1	1329	1	BACE1	11	117186300	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	9503839	117186300	17820216	95	3656											
ADAMTS15	170689	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	130319535	130319535	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgcggtacgtggagacgCtggtggtcgcggacgagtca	6	7	17	11	7	1	1	1	0	0	1	3	4	2	2	1	5	1	2	1	5	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:130319535C>G	ENST00000299164.2	+	1	667	c.667C>G	c.(667-669)Ctg>Gtg	p.L223V		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	223	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		CGTGGAGACGCTGGTGGTCGC	0.667											OREG0021518	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L223V													.	ADAMTS15-291	0			c.C667G						.						35	31	32					11																	130319535		2195	4294	6489	SO:0001583	missense	170689	exon1			GAGACGCTGGTGG	AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"ADAM metallopeptidases with thrombospondin type 1 motif"	16305	protein-coding gene	gene with protein product		607509	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.667C>G	11.37:g.130319535C>G	ENSP00000299164:p.Leu223Val	Somatic	123	2	1579	WXS	Illumina HiSeq	Phase_I	99	11	NM_139055	0	0	0	0	0	Q32MI6	Missense_Mutation	SNP	ENST00000299164.2	37	CCDS8488.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.642991	0.67244	.	.	ENSG00000166106	ENST00000299164	D	0.87412	-2.25	5.21	3.35	0.38373	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	D	0.90428	0.7003	L	0.55743	1.74	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.89457	0.3734	9	0.66056	D	0.02	.	10.0356	0.42127	0.0:0.7626:0.0:0.2374	.	223	Q8TE58	ATS15_HUMAN	V	223	ENSP00000299164:L223V	ENSP00000299164:L223V	L	+	1	2	ADAMTS15	129824745	0.947000	0.32204	0.802000	0.32245	0.991000	0.79684	2.100000	0.41777	0.701000	0.31803	-0.137000	0.14449	CTG	.		0.667	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055		G	130319535	C	G	130319535	3	3	40	1	0	0	0	0	1	0	0	0	260	796	28	4	669	4	ADAMTS15	11	130319535	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	13133235	130319535	4686981	96	3657											
GUCY2C	2984	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	14839143	14839143	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agggccctatgaggacacagCccatccgttgtgcattctgt	8	10	11	12	1	1	1	0	1	1	0	2	2	2	2	3	2	2	2	3	2	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:14839143C>G	ENST00000261170.3	-	3	483	c.347G>C	c.(346-348)gGc>gCc	p.G116A	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	116					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	GAGGACACAGCCCATCCGTTG	0.428																																					p.G116A													.	GUCY2C-338	0			c.G347C						.						104	87	93					12																	14839143		2203	4300	6503	SO:0001583	missense	2984	exon3			ACACAGCCCATCC		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.347G>C	12.37:g.14839143C>G	ENSP00000261170:p.Gly116Ala	Somatic	85	1		WXS	Illumina HiSeq	Phase_I	73	27	NM_004963	0	0	0	0	0	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	37	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.855051	0.71719	.	.	ENSG00000070019	ENST00000261170	D	0.82255	-1.59	5.92	5.92	0.95590	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.88811	0.6538	M	0.74881	2.28	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.84414	0.0567	10	0.02654	T	1	.	15.8215	0.78648	0.0:1.0:0.0:0.0	.	116	P25092	GUC2C_HUMAN	A	116	ENSP00000261170:G116A	ENSP00000261170:G116A	G	-	2	0	GUCY2C	14730410	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	5.512000	0.67030	2.804000	0.96469	0.655000	0.94253	GGC	.		0.428	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			G	14839143	C	G	14839143	3	3	40	1	0	0	0	0	1	0	0	0	6917	739	26	4	2974	4	GUCY2C	12	14839143	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		14839143	119012752	97	3658											
PLCZ1	89869	hgsc.bcm.edu;bcgsc.ca	37	chr12	18876363	18876364	+	Frame_Shift_Ins	INS	-	-	T																															ttgctaaaagaattttccggINSttttcagaatatgtgttgaa																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:18876363_18876364insT	ENST00000266505.7	-	4	511_512	c.248_249insA	c.(247-249)aacfs	p.N83fs	PLCZ1_ENST00000447925.2_Frame_Shift_Ins_p.N81fs|PLCZ1_ENST00000435379.1_Intron|PLCZ1_ENST00000539875.1_Intron|RP11-361I14.2_ENST00000536931.1_RNA					phospholipase C, zeta 1											NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					GAATTTTCCGGTTTTCAGAATA	0.332																																					p.N83fs		.											.	PLCZ1-228	0			c.249_250insA						.																																			SO:0001589	frameshift_variant	89869	exon4			.	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.249dupA	12.37:g.18876367_18876367dupT	ENSP00000266505:p.Asn83fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	171	46	NM_033123	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000266505.7	37	CCDS8680.1																																																																																			.		0.332	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123		T	18876364	-	T	18876363	7	5	40	1	0	1	1	0	0	0	0	0	12070	1252	44	0	1625	0	PLCZ1	12	18876363	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	4037220	18876363	114975532	98	3659											
C12orf40	283461	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	40076521	40076521	+	Frame_Shift_Del	DEL	A	A	-																															tacattactgaaaaacactcAatacagcatatttgggggaa																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:40076521delA	ENST00000324616.5	+	8	949	c.795delA	c.(793-795)tcafs	p.S265fs	C12orf40_ENST00000405531.3_Frame_Shift_Del_p.S265fs|C12orf40_ENST00000398716.1_Frame_Shift_Del_p.S188fs	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	265										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						AAAAACACTCAATACAGCATA	0.353																																					p.S265fs		.											.	C12orf40-96	0			c.795delA						.						133	134	134					12																	40076521		1841	4086	5927	SO:0001589	frameshift_variant	283461	exon8			.	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.795delA	12.37:g.40076521delA	ENSP00000317671:p.Ser265fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	154	36	NM_001031748	0	0	0	0	0	B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	37	CCDS41770.1																																																																																			.		0.353	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		-	40076521	A	-	40076521	7	5	40	1	0	1	0	1	0	0	0	0	1690	117	5	0	825	0	C12orf40	12	40076521	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	21200158	40076521	93775374	99	3660											
FAM186B	84070	broad.mit.edu	37	chr12	49994268	49994268	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtggctggtgccctgcagcTatagcaccactgtcccgtat	7	10	11	13	1	0	0	0	0	0	0	1	0	1	0	3	2	4	5	3	2	3	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:49994268T>C	ENST00000257894.2	-	4	1316	c.1155A>G	c.(1153-1155)atA>atG	p.I385M	PRPF40B_ENST00000508736.1_3'UTR|FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.I295M	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	385						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCCCTGCAGCTATAGCACCAC	0.567																																					p.I385M													.	FAM186B-91	0			c.A1155G						.						86	68	74					12																	49994268		2203	4300	6503	SO:0001583	missense	84070	exon4			TGCAGCTATAGCA	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 25"	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1155A>G	12.37:g.49994268T>C	ENSP00000257894:p.Ile385Met	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_032130	0	0	0	0	0	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.276364	0.23307	.	.	ENSG00000135436	ENST00000544141;ENST00000257894	T;T	0.11821	2.74;2.94	5.11	-4.84	0.03151	.	1.605610	0.03763	N	0.258518	T	0.04452	0.0122	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38001	-0.9681	9	.	.	.	5.1651	6.7462	0.23462	0.268:0.55:0.0:0.1821	.	295;385	B4DZ15;Q8IYM0	.;F186B_HUMAN	M	295;385	ENSP00000438569:I295M;ENSP00000257894:I385M	.	I	-	3	3	FAM186B	48280535	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.673000	0.01951	-0.796000	0.04456	0.533000	0.62120	ATA	.		0.567	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130		C	49994268	T	C	49994268	3	2	40	1	0	0	0	0	1	0	0	0	5528	1512	53	3	1542	3	FAM186B	12	49994268	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	9917747	49994268	83857627	100	3661											
IGFBP6	3489	broad.mit.edu	37	chr12	53491528	53491530	+	In_Frame_Del	DEL	GCT	GCT	-																															ccccacaggctgctgccaccGctgctgctgctgctagctct																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:53491528_53491530delGCT	ENST00000301464.3	+	1	300_302	c.27_29delGCT	c.(25-30)ccgctg>ccg	p.L14del	IGFBP6_ENST00000548547.1_In_Frame_Del_p.L14del	NM_002178.2	NP_002169.1	P24592	IBP6_HUMAN	insulin-like growth factor binding protein 6	14					cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				large_intestine(1)|lung(3)|ovary(1)|pancreas(1)	6						tgctgccaccgctgctgctgctg	0.719																																					p.9_10del	Esophageal Squamous(83;1656 1718 30141 34380)												.	IGFBP6-523	0			c.27_29del						.			9,3135		2,5,1565						0.2	0.2			5	39,6279		7,25,3127	no	coding	IGFBP6	NM_002178.2		9,30,4692	A1A1,A1R,RR		0.6173,0.2863,0.5073				48,9414				SO:0001651	inframe_deletion	3489	exon1			GCCACCGCTGCTG		CCDS8846.1	12q13	2008-07-28				ENSG00000167779			5475	protein-coding gene	gene with protein product		146735				1850258, 10087296	Standard	NM_002178		Approved		uc001sbu.1	P24592	OTTHUMG00000169773	ENST00000301464.3:c.27_29delGCT	12.37:g.53491537_53491539delGCT	ENSP00000301464:p.Leu14del	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	102	7	NM_002178	0	0	0	0	0	Q14492	In_Frame_Del	DEL	ENST00000301464.3	37	CCDS8846.1																																																																																			.		0.719	IGFBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405813.1			-	53491530	GCT	-	53491528	7	5	40	1	0	1	0	1	0	0	0	0	7604	1074	38	0	29	0	IGFBP6	12	53491528	In_Frame_Del	DEL	GCT	TCGA-B1-A656-01A-11D-A31X-10	3497260	53491528	80360367	101	3662											
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	59268266	59268266	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacatttcccttcaaatacaTagggcctgtggatcccaaaa	13	10	6	12	0	1	0	1	0	0	0	3	1	3	1	3	2	1	0	3	2	5	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:59268266T>G	ENST00000320743.3	-	17	3071	c.2785A>C	c.(2785-2787)Atg>Ctg	p.M929L	LRIG3_ENST00000379141.4_Missense_Mutation_p.M869L	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	929					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)			TTCAAATACATAGGGCCTGTG	0.428			T	ROS1	NSCLC																																p.M929L		.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3-229	0			c.A2785C						.						148	135	139					12																	59268266		2203	4300	6503	SO:0001583	missense	121227	exon17			AATACATAGGGCC	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.2785A>C	12.37:g.59268266T>G	ENSP00000326759:p.Met929Leu	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	130	48	NM_153377	0	0	21	25	4	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.815|4.815	0.151595|0.151595	0.09185|0.09185	.|.	.|.	ENSG00000139263|ENSG00000139263	ENST00000379141;ENST00000320743|ENST00000550825	T;T|.	0.54479|.	0.62;0.57|.	6.03|6.03	5.14|5.14	0.70334|0.70334	.|.	0.517740|.	0.14462|.	N|.	0.318092|.	T|T	0.19366|0.19366	0.0465|0.0465	N|N	0.12182|0.12182	0.205|0.205	0.18873|0.18873	N|N	0.999984|0.999984	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.16453|0.16453	-1.0402|-1.0402	9|5	.|.	.|.	.|.	.|.	4.6325|4.6325	0.12509|0.12509	0.2843:0.5306:0.0:0.1851|0.2843:0.5306:0.0:0.1851	.|.	869;929|.	Q6UXM1-2;Q6UXM1|.	.;LRIG3_HUMAN|.	L|S	869;929|30	ENSP00000368436:M869L;ENSP00000326759:M929L|.	.|.	M|Y	-|-	1|2	0|0	LRIG3|LRIG3	57554533|57554533	0.449000|0.449000	0.25689|0.25689	0.998000|0.998000	0.56505|0.56505	0.018000|0.018000	0.09664|0.09664	0.724000|0.724000	0.25954|0.25954	1.568000|1.568000	0.49683|0.49683	-0.132000|-0.132000	0.14878|0.14878	ATG|TAT	.		0.428	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		G	59268266	T	G	59268266	3	3	40	1	0	0	0	0	1	0	0	0	8971	1406	49	5	586	5	LRIG3	12	59268266	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	5776738	59268266	74583629	102	3663											
GPN3	51184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	110902939	110902939	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggagtagttgaagtgttcTgctgctggatccaggtttac	8	13	13	7	1	1	1	0	1	1	0	2	3	2	3	1	3	3	6	1	3	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:110902939T>C	ENST00000228827.3	-	2	191	c.129A>G	c.(127-129)gcA>gcG	p.A43A	GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000537466.2_Silent_p.A53A|GPN3_ENST00000543199.1_Silent_p.A82A	NM_016301.3	NP_057385.3			GPN-loop GTPase 3											endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|urinary_tract(1)	8						TGAAGTGTTCTGCTGCTGGAT	0.547																																					p.A82A		.											.	GPN3-90	0			c.A246G						.						190	151	164					12																	110902939		2203	4300	6503	SO:0001819	synonymous_variant	51184	exon2			GTGTTCTGCTGCT	BC008416	CCDS9147.1, CCDS53830.1, CCDS53831.1	12q24.11	2012-12-18	2008-04-30	2008-04-30	ENSG00000111231	ENSG00000111231		"GPN-loop GTPases"	30186	protein-coding gene	gene with protein product			"ATP binding domain 1 family, member C"	ATPBD1C		12975309	Standard	NM_016301		Approved	MGC14560	uc021rdu.1	Q9UHW5	OTTHUMG00000169524	ENST00000228827.3:c.129A>G	12.37:g.110902939T>C		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	106	18	NM_001164372	0	0	13	18	5		Silent	SNP	ENST00000228827.3	37	CCDS9147.1																																																																																			.		0.547	GPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404607.1	NM_016301		C	110902939	T	C	110902939	2	2	40	1	0	0	0	0	0	0	0	1	6639	1567	55	3		3	GPN3	12	110902939	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	51634673	110902939	22948956	103	3664											
BRCA2	675	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	32912897	32912897	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaattctgaattacattctGacataagaaagaacaaaatg	20	11	5	5	0	2	4	0	2	2	2	2	4	2	4	0	0	2	0	0	0	9	5	rs397507331		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr13:32912897G>T	ENST00000380152.3	+	11	4638	c.4405G>T	c.(4405-4407)Gac>Tac	p.D1469Y	BRCA2_ENST00000544455.1_Missense_Mutation_p.D1469Y			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1469	Interaction with POLH.|Required for stimulation of POLH DNA polymerization activity.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATTACATTCTGACATAAGAAA	0.303			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.D1469Y	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2-3153	0			c.G4405T						.						53	62	59					13																	32912897		2201	4294	6495	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	CATTCTGACATAA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.4405G>T	13.37:g.32912897G>T	ENSP00000369497:p.Asp1469Tyr	Somatic	351	1		WXS	Illumina HiSeq	Phase_I	324	90	NM_000059	0	0	0	0	0	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321955	0.41096	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00691	5.84;5.84	5.95	3.25	0.37280	.	1.061550	0.07241	N	0.864150	T	0.00998	0.0033	N	0.22421	0.69	0.09310	N	1	P	0.51653	0.947	P	0.44561	0.453	T	0.58451	-0.7634	10	0.72032	D	0.01	.	9.2592	0.37601	0.2723:0.0:0.7277:0.0	.	1469	P51587	BRCA2_HUMAN	Y	1469	ENSP00000369497:D1469Y;ENSP00000439902:D1469Y	ENSP00000369497:D1469Y	D	+	1	0	BRCA2	31810897	0.000000	0.05858	0.761000	0.31378	0.872000	0.50106	0.402000	0.20965	1.512000	0.48834	0.563000	0.77884	GAC	.		0.303	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		T	32912897	G	T	32912897	3	4	40	1	0	0	0	0	1	0	0	0	1502	1290	45	4	4443	4	BRCA2	13	32912897	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		32912897	82256981	104	3665											
KLF5	688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	73636276	73636276	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaacgactgcccctcctcCggccccgacccaggccctcc	6	5	8	22	3	0	1	0	1	0	0	3	3	3	1	9	2	2	0	9	2	1	0	rs200707995	byFrequency	TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr13:73636276C>T	ENST00000377687.4	+	2	1075	c.539C>T	c.(538-540)cCg>cTg	p.P180L	KLF5_ENST00000539231.1_Missense_Mutation_p.P89L|KLF5_ENST00000477333.1_3'UTR	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	180					angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		GCCCCTCCTCCGGCCCCGACC	0.522													C|||	2	0.000399361	0	0	5008	,	,		18258	0.001		0	False		,,,				2504	0.001				p.P180L		.											.	KLF5-155	0			c.C539T						.						70	71	71					13																	73636276		2203	4300	6503	SO:0001583	missense	688	exon2			CTCCTCCGGCCCC	D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.539C>T	13.37:g.73636276C>T	ENSP00000366915:p.Pro180Leu	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	75	17	NM_001730	0	0	1	3	2	L0R3U5|L0R4T9|Q9UHP8	Missense_Mutation	SNP	ENST00000377687.4	37	CCDS9448.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	18.09	3.546448	0.65198	.	.	ENSG00000102554	ENST00000539231;ENST00000377687;ENST00000545883	T;T	0.07021	3.42;3.23	5.94	5.94	0.96194	.	0.132092	0.51477	D	0.000090	T	0.10337	0.0253	L	0.48642	1.525	0.80722	D	1	P	0.47545	0.897	B	0.35073	0.195	T	0.02232	-1.1191	10	0.72032	D	0.01	.	20.3591	0.98849	0.0:1.0:0.0:0.0	.	180	Q13887	KLF5_HUMAN	L	89;180;160	ENSP00000440407:P89L;ENSP00000366915:P180L	ENSP00000366915:P180L	P	+	2	0	KLF5	72534277	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.687000	0.37680	2.816000	0.96949	0.561000	0.74099	CCG	C|0.999;T|0.000		0.522	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1			T	73636276	C	T	73636276	3	4	40	1	0	0	0	0	1	0	0	0	8370	652	23	1	545	1	KLF5	13	73636276	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	40723379	73636276	41533602	105	3666											
FAM155A	728215	hgsc.bcm.edu	37	chr13	108518698	108518698	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgctgcctctgctgctgctGctgctgctgctgctgccgct	0	12	12	17	2	1	0	0	0	1	0	1	0	1	0	3	0	10	10	3	0	0	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr13:108518698G>T	ENST00000375915.2	-	1	385	c.247C>A	c.(247-249)Cag>Aag	p.Q83K		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	83	Poly-Gln.					integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						tgctgctgctgctgctgctgc	0.706																																					p.Q83K		.											.	FAM155A-23	0			c.C247A						.						16	22	20					13																	108518698		1929	3762	5691	SO:0001583	missense	728215	exon1			GCTGCTGCTGCTG	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.247C>A	13.37:g.108518698G>T	ENSP00000365080:p.Gln83Lys	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	28	5	NM_001080396	0	0	0	0	0	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	37	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487166	0.26686	.	.	ENSG00000204442	ENST00000375915	T	0.62364	0.03	4.45	4.45	0.53987	Armadillo-like helical (1);	0.715687	0.11618	N	0.546038	T	0.55146	0.1902	L	0.43923	1.385	0.25117	N	0.990675	B	0.13594	0.008	B	0.13407	0.009	T	0.45308	-0.9270	10	0.36615	T	0.2	.	12.5709	0.56337	0.0:0.0:1.0:0.0	.	83	B1AL88	F155A_HUMAN	K	83	ENSP00000365080:Q83K	ENSP00000365080:Q83K	Q	-	1	0	FAM155A	107316699	1.000000	0.71417	0.893000	0.35052	0.674000	0.39518	4.577000	0.60922	2.027000	0.59764	0.561000	0.74099	CAG	.		0.706	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		T	108518698	G	T	108518698	3	4	40	1	0	0	0	0	1	0	0	0	5481	1328	46	4	1141	4	FAM155A	13	108518698	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	34882422	108518698	6651180	106	3667											
MCF2L	23263	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	113719317	113719318	+	Frame_Shift_Ins	INS	-	-	G																															cagtccttcgggaccgagctINSggctgaaacagagctgccca																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr13:113719317_113719318insG	ENST00000375608.3	+	8	822_823	c.764_765insG	c.(763-768)ctggctfs	p.A256fs	MCF2L_ENST00000397030.1_Frame_Shift_Ins_p.A259fs|MCF2L_ENST00000375601.3_Frame_Shift_Ins_p.A230fs|MCF2L_ENST00000535094.2_Frame_Shift_Ins_p.A226fs|MCF2L_ENST00000375597.4_Frame_Shift_Ins_p.A224fs|MCF2L_ENST00000375604.2_Frame_Shift_Ins_p.A283fs|MCF2L_ENST00000442652.2_Frame_Shift_Ins_p.A256fs|MCF2L_ENST00000423482.2_Frame_Shift_Ins_p.A224fs|MCF2L_ENST00000434480.2_Frame_Shift_Ins_p.A232fs|MCF2L_ENST00000421756.1_Frame_Shift_Ins_p.A230fs			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	256					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GGGACCGAGCTGGCTGAAACAG	0.564																																					p.L225fs		.											.	MCF2L-228	0			c.674_675insG						.																																			SO:0001589	frameshift_variant	23263	exon7			.	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.766dupG	13.37:g.113719319_113719319dupG	ENSP00000364758:p.Ala256fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	76	16	NM_001112732	0	0	0	0	0	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Frame_Shift_Ins	INS	ENST00000375608.3	37																																																																																				.		0.564	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			G	113719318	-	G	113719317	7	5	40	1	0	1	1	0	0	0	0	0	9404	1580	55	0	966	0	MCF2L	13	113719317	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	5200619	113719317	1450561	107	3668											
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	39877738	39877738	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaatgccacagttcctgAtggagaatgctgtcctcgct	8	11	9	13	1	0	2	0	1	0	1	4	3	3	2	4	1	2	3	4	1	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:39877738A>G	ENST00000260356.5	+	7	1259	c.1094A>G	c.(1093-1095)gAt>gGt	p.D365G		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	365	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ACAGTTCCTGATGGAGAATGC	0.507																																					p.D365G		.											.	THBS1-653	0			c.A1094G						.						218	152	174					15																	39877738		2200	4297	6497	SO:0001583	missense	7057	exon7			TTCCTGATGGAGA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1094A>G	15.37:g.39877738A>G	ENSP00000260356:p.Asp365Gly	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	34	7	NM_003246	0	0	2	3	1	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	A	31	5.103828	0.94245	.	.	ENSG00000137801	ENST00000260356	T	0.65364	-0.15	5.86	5.86	0.93980	von Willebrand factor, type C (4);	0.000000	0.34676	N	0.003775	T	0.77751	0.4177	M	0.69463	2.115	0.58432	D	0.999998	D	0.76494	0.999	D	0.85130	0.997	T	0.79640	-0.1719	10	0.66056	D	0.02	-17.1145	15.4256	0.75048	1.0:0.0:0.0:0.0	.	365	P07996	TSP1_HUMAN	G	365	ENSP00000260356:D365G	ENSP00000260356:D365G	D	+	2	0	THBS1	37665030	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.339000	0.96797	2.237000	0.73441	0.533000	0.62120	GAT	.		0.507	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		G	39877738	A	G	39877738	3	3	40	1	0	0	0	0	1	0	0	0	15885	333	12	3	1116	3	THBS1	15	39877738	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		39877738	62653654	108	3669											
SPINT1	6692	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	41136856	41136856	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggcctccagggcacccaggCcgggccaccgcccgcgcccc	4	1	13	23	5	0	0	0	0	0	0	1	0	1	0	9	4	0	1	9	4	0	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:41136856C>A	ENST00000344051.4	+	2	338	c.104C>A	c.(103-105)gCc>gAc	p.A35D	RP11-532F12.5_ENST00000568419.1_RNA|RP11-532F12.5_ENST00000568525.1_RNA|SPINT1_ENST00000431806.1_Missense_Mutation_p.A35D|RP11-532F12.5_ENST00000564302.1_RNA|SPINT1_ENST00000562057.1_Missense_Mutation_p.A35D|RP11-532F12.5_ENST00000565315.1_RNA			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	35					branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GGCACCCAGGCCGGGCCACCG	0.761																																					p.A35D		.											.	SPINT1-91	0			c.C104A						.						6	8	8					15																	41136856		2067	4058	6125	SO:0001583	missense	6692	exon2			CCCAGGCCGGGCC		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.104C>A	15.37:g.41136856C>A	ENSP00000342098:p.Ala35Asp	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	77	23	NM_181642	0	0	0	0	0	Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	37	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.538187	0.65085	.	.	ENSG00000166145	ENST00000344051;ENST00000431806	D;D	0.95656	-3.76;-3.77	5.02	3.07	0.35406	.	0.452065	0.24688	N	0.036402	D	0.89591	0.6759	N	0.08118	0	0.09310	N	1	P;P;P	0.48162	0.906;0.9;0.906	B;P;P	0.49999	0.425;0.628;0.521	T	0.82341	-0.0505	10	0.29301	T	0.29	-21.5589	6.2982	0.21097	0.0:0.7099:0.1902:0.1	.	35;35;35	B2RBU9;O43278-2;O43278	.;.;SPIT1_HUMAN	D	35	ENSP00000342098:A35D;ENSP00000409935:A35D	ENSP00000342098:A35D	A	+	2	0	SPINT1	38924148	0.876000	0.30132	0.328000	0.25416	0.002000	0.02628	3.594000	0.54008	1.206000	0.43276	0.563000	0.77884	GCC	.		0.761	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		A	41136856	C	A	41136856	3	1	40	1	0	0	0	0	1	0	0	0	15100	739	26	4	106	4	SPINT1	15	41136856	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1259118	41136856	61394536	109	3670											
LRRC57	255252	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42837381	42837381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggatgctctggggaagcatgCtgagctcaagacaattctct	10	10	12	9	0	3	2	1	1	2	1	4	4	3	4	0	3	4	4	0	3	3	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:42837381C>T	ENST00000323443.2	-	4	939	c.572G>A	c.(571-573)aGc>aAc	p.S191N	LRRC57_ENST00000563454.1_Missense_Mutation_p.S191N|LRRC57_ENST00000397130.3_Missense_Mutation_p.S191N			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	191						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		GGGAAGCATGCTGAGCTCAAG	0.423																																					p.S191N		.											.	LRRC57-90	0			c.G572A						.						99	94	96					15																	42837381		2203	4299	6502	SO:0001583	missense	255252	exon5			AGCATGCTGAGCT	AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.572G>A	15.37:g.42837381C>T	ENSP00000326817:p.Ser191Asn	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	74	26	NM_153260	0	0	5	6	1	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	37	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243740	0.58995	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.46451	0.87;0.87	5.36	4.43	0.53597	.	0.131595	0.64402	D	0.000001	T	0.32763	0.0840	L	0.33339	1.005	0.54753	D	0.999984	B	0.11235	0.004	B	0.09377	0.004	T	0.08126	-1.0737	10	0.34782	T	0.22	.	14.3053	0.66380	0.0:0.9273:0.0:0.0727	.	191	Q8N9N7	LRC57_HUMAN	N	191	ENSP00000326817:S191N;ENSP00000380319:S191N	ENSP00000326817:S191N	S	-	2	0	LRRC57	40624673	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.969000	0.49232	2.520000	0.84964	0.557000	0.71058	AGC	.		0.423	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		T	42837381	C	T	42837381	3	4	40	1	0	0	0	0	1	0	0	0	9038	797	28	2	155	2	LRRC57	15	42837381	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1700525	42837381	59694011	110	3671											
SHC4	399694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	49148178	49148178	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acaacttttcacactgtatgGggcagtaagccatttgttcc	10	13	8	10	0	1	0	1	0	0	0	2	0	2	0	2	2	2	4	2	2	3	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:49148178G>T	ENST00000332408.4	-	8	1642	c.1214C>A	c.(1213-1215)cCc>cAc	p.P405H	SHC4_ENST00000396535.3_Missense_Mutation_p.P162H|SHC4_ENST00000537958.1_Missense_Mutation_p.P119H	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	405	CH1.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		ACACTGTATGGGGCAGTAAGC	0.408																																					p.P405H		.											.	SHC4-95	0			c.C1214A						.						140	128	132					15																	49148178		2197	4294	6491	SO:0001583	missense	399694	exon8			TGTATGGGGCAGT	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1214C>A	15.37:g.49148178G>T	ENSP00000329668:p.Pro405His	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	117	28	NM_203349	0	0	0	0	0	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	37	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.293981	0.60086	.	.	ENSG00000185634	ENST00000332408;ENST00000396535;ENST00000537958	T;T;T	0.31769	3.48;1.48;1.5	5.03	5.03	0.67393	.	0.200639	0.36134	N	0.002762	T	0.44435	0.1293	L	0.43923	1.385	0.46521	D	0.999085	P;D	0.69078	0.575;0.997	B;P	0.60886	0.211;0.88	T	0.31194	-0.9952	10	0.59425	D	0.04	-10.6953	15.38	0.74648	0.0:0.0:1.0:0.0	.	162;405	Q6S5L8-2;Q6S5L8	.;SHC4_HUMAN	H	405;162;119	ENSP00000329668:P405H;ENSP00000379786:P162H;ENSP00000443300:P119H	ENSP00000329668:P405H	P	-	2	0	SHC4	46935470	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.871000	0.69628	2.612000	0.88384	0.655000	0.94253	CCC	.		0.408	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		T	49148178	G	T	49148178	3	4	40	1	0	0	0	0	1	0	0	0	14305	1232	43	4	698	4	SHC4	15	49148178	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	6310797	49148178	53383214	111	3672											
FBXL22	283807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	63889797	63889797	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaacttcctcctgggccCggcactccgcagcctctcca	6	7	9	19	2	1	0	0	0	1	0	5	1	4	1	6	3	2	2	6	3	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:63889797C>T	ENST00000360587.2	+	1	246	c.206C>T	c.(205-207)cCg>cTg	p.P69L	USP3-AS1_ENST00000559861.1_RNA|USP3-AS1_ENST00000559737.1_RNA|FBXL22_ENST00000539570.3_Missense_Mutation_p.P63L|USP3-AS1_ENST00000560962.1_RNA|USP3-AS1_ENST00000560622.1_RNA|USP3-AS1_ENST00000558831.1_RNA|FBXL22_ENST00000534939.1_Missense_Mutation_p.P69L|USP3-AS1_ENST00000561191.1_RNA|USP3-AS1_ENST00000561256.1_RNA	NM_203373.2	NP_976307.2	Q6P050	FXL22_HUMAN	F-box and leucine-rich repeat protein 22	69					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(4)	4						CTCCTGGGCCCGGCACTCCGC	0.617																																					p.P69L		.											.	FBXL22-90	0			c.C206T						.						47	38	41					15																	63889797		2203	4300	6503	SO:0001583	missense	283807	exon1			TGGGCCCGGCACT	BC065833	CCDS10187.1, CCDS10187.2	15q22.1	2012-04-05			ENSG00000197361	ENSG00000197361		"F-boxes / Leucine-rich repeats"	27537	protein-coding gene	gene with protein product		609088				12477932	Standard	NM_203373		Approved	Fbl22, FLJ39626	uc002amn.4	Q6P050	OTTHUMG00000132905	ENST00000360587.2:c.206C>T	15.37:g.63889797C>T	ENSP00000353794:p.Pro69Leu	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	25	6	NM_203373	0	0	0	0	0		Missense_Mutation	SNP	ENST00000360587.2	37	CCDS10187.2	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799631	0.90538	.	.	ENSG00000197361	ENST00000360587;ENST00000539570	T;T	0.38722	1.12;1.12	5.72	5.72	0.89469	.	0.183522	0.48767	D	0.000162	T	0.58352	0.2116	L	0.48642	1.525	0.58432	D	0.999999	D	0.76494	0.999	D	0.63957	0.92	T	0.58940	-0.7547	10	0.87932	D	0	-2.5763	18.8613	0.92273	0.0:1.0:0.0:0.0	.	63	Q6P050	FXL22_HUMAN	L	69;63	ENSP00000353794:P69L;ENSP00000442112:P63L	ENSP00000353794:P69L	P	+	2	0	FBXL22	61676850	1.000000	0.71417	0.959000	0.39883	0.594000	0.36715	7.583000	0.82559	2.699000	0.92147	0.563000	0.77884	CCG	.		0.617	FBXL22-001	KNOWN	downstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256412.4	NM_203373		T	63889797	C	T	63889797	3	4	40	1	0	0	0	0	1	0	0	0	5738	652	23	1	190	1	FBXL22	15	63889797	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	14741619	63889797	38641595	112	3673											
LARP6	55323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	71128826	71128826	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcacgctcgttctcaccTccacttgcagtggtgccact	5	12	7	17	2	2	0	2	0	1	0	6	0	4	0	4	1	2	3	4	1	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:71128826T>C	ENST00000299213.8	-	2	289	c.219A>G	c.(217-219)ggA>ggG	p.G73G		NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	73					regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						CGTTCTCACCTCCACTTGCAG	0.522																																					p.G73G		.											.	LARP6-90	0			c.A219G						.						70	72	71					15																	71128826		2199	4297	6496	SO:0001819	synonymous_variant	55323	exon2			CTCACCTCCACTT	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"La ribonucleoprotein domain containing"	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.219A>G	15.37:g.71128826T>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	70	24	NM_018357	0	0	2	4	2	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			.		0.522	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		C	71128826	T	C	71128826	2	2	40	1	0	0	0	0	0	0	0	1	8653	1538	54	3		3	LARP6	15	71128826	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	7239029	71128826	31402566	113	3674											
NTRK3	4916	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	88680721	88680721	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggctgttgagcttggccTccccctgctcctgccagagc	3	11	11	16	0	1	2	0	1	1	1	3	2	3	2	5	2	4	4	5	2	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:88680721T>C	ENST00000360948.2	-	6	697	c.536A>G	c.(535-537)gAg>gGg	p.E179G	NTRK3_ENST00000540489.2_Missense_Mutation_p.E179G|NTRK3_ENST00000317501.3_Missense_Mutation_p.E179G|NTRK3_ENST00000355254.2_Missense_Mutation_p.E179G|NTRK3_ENST00000357724.2_Missense_Mutation_p.E179G|NTRK3_ENST00000557856.1_Missense_Mutation_p.E179G|NTRK3_ENST00000394480.2_Missense_Mutation_p.E179G|NTRK3_ENST00000542733.2_Missense_Mutation_p.E81G|NTRK3_ENST00000558676.1_Missense_Mutation_p.E179G	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	179	LRRCT.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GAGCTTGGCCTCCCCCTGCTC	0.567			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.E179G		.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3-3538	0			c.A536G						.						124	94	104					15																	88680721		2201	4299	6500	SO:0001583	missense	4916	exon7			TTGGCCTCCCCCT	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.536A>G	15.37:g.88680721T>C	ENSP00000354207:p.Glu179Gly	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	41	4	NM_001243101	0	0	0	0	0	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.219821	0.58560	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.71	5.71	0.89125	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92331	0.7567	L	0.51422	1.61	0.58432	D	0.999993	D;D;P;D;D;P	0.76494	0.999;0.999;0.47;0.999;0.998;0.47	D;D;B;D;D;B	0.81914	0.995;0.986;0.244;0.995;0.993;0.244	D	0.91792	0.5444	10	0.40728	T	0.16	.	15.1854	0.72996	0.0:0.0:0.0:1.0	.	81;179;179;179;179;179	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	G	179;179;179;179;81;179;179	ENSP00000377990:E179G;ENSP00000354207:E179G;ENSP00000350356:E179G;ENSP00000347397:E179G;ENSP00000437773:E81G;ENSP00000444673:E179G;ENSP00000318328:E179G	ENSP00000318328:E179G	E	-	2	0	NTRK3	86481725	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.723000	0.68492	2.171000	0.68590	0.528000	0.53228	GAG	.		0.567	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88680721	T	C	88680721	3	2	40	1	0	0	0	0	1	0	0	0	10734	1551	54	3	2301	3	NTRK3	15	88680721	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	17551895	88680721	13850671	114	3675											
PARN	5073	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	14678281	14678281	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgttgttaatgatatccTgcaaaccacgaagcaaagaa	16	10	8	7	1	0	2	0	1	0	1	1	3	1	2	2	0	3	4	2	0	6	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:14678281T>C	ENST00000437198.2	-	16	1147		c.e16-2		PARN_ENST00000539279.1_Splice_Site|PARN_ENST00000420015.2_Splice_Site|PARN_ENST00000341484.7_Splice_Site	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease						female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						AATGATATCCTGCAAACCACG	0.383																																					.		.											.	PARN-24	0			c.868-2A>G						.						52	50	51					16																	14678281		1825	4081	5906	SO:0001630	splice_region_variant	5073	exon16			ATATCCTGCAAAC	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"deadenylation nuclease"	604212	"poly(A)-specific ribonuclease (deadenylation nuclease)"			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.1006-2A>G	16.37:g.14678281T>C		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	60	22	NM_001242992	0	0	0	0	0	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Splice_Site	SNP	ENST00000437198.2	37	CCDS45419.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876641	0.72180	.	.	ENSG00000140694	ENST00000437198;ENST00000341484;ENST00000420015;ENST00000539279	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9377	0.70970	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PARN	14585782	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.627000	0.74258	2.198000	0.70561	0.456000	0.33151	.	.		0.383	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582	Intron	C	14678281	T	C	14678281	5	2	40	1	0	0	0	0	0	0	1	0	11479	1594	55	3	951	3	PARN	16	14678281	Splice_Site	SNP	T	TCGA-B1-A656-01A-11D-A31X-10		14678281	75676472	115	3676											
ACSM2A	123876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20489950	20489950	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggcacagaaggagacattgGcatcagggtcaaacccatca	14	5	11	11	1	3	2	3	0	0	2	3	3	3	2	1	4	1	2	1	4	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:20489950G>A	ENST00000573854.1	+	10	1346	c.1232G>A	c.(1231-1233)gGc>gAc	p.G411D	ACSM2A_ENST00000575690.1_Missense_Mutation_p.G411D|ACSM2A_ENST00000536134.1_Missense_Mutation_p.G183D|ACSM2A_ENST00000417235.2_Missense_Mutation_p.G332D|ACSM2A_ENST00000219054.6_Missense_Mutation_p.G411D|ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000396104.2_Missense_Mutation_p.G411D	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	411					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GGAGACATTGGCATCAGGGTC	0.527																																					p.G411D		.											.	ACSM2A-91	0			c.G1232A						.						103	87	92					16																	20489950		2203	4297	6500	SO:0001583	missense	123876	exon11			ACATTGGCATCAG	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1232G>A	16.37:g.20489950G>A	ENSP00000459451:p.Gly411Asp	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	67	24	NM_001010845	0	0	764	836	72	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	G	9.906	1.208165	0.22205	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	3.33	0.71	0.18157	AMP-dependent synthetase/ligase (1);	0.312022	0.23048	N	0.052540	T	0.57975	0.2090	M	0.68952	2.095	0.20638	N	0.99987	D;D	0.76494	0.999;0.999	D;D	0.74674	0.977;0.984	T	0.52313	-0.8592	10	0.87932	D	0	-4.1522	11.8873	0.52610	0.0:0.6828:0.3172:0.0	.	332;411	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	D	332;411;183;411	ENSP00000392169:G332D;ENSP00000219054:G411D;ENSP00000445082:G183D;ENSP00000379411:G411D	ENSP00000219054:G411D	G	+	2	0	ACSM2A	20397451	0.419000	0.25449	0.008000	0.14137	0.141000	0.21300	0.682000	0.25335	0.408000	0.25621	0.289000	0.19496	GGC	.		0.527	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		A	20489950	G	A	20489950	3	1	40	1	0	0	0	0	1	0	0	0	183	1203	42	2	1266	2	ACSM2A	16	20489950	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5811669	20489950	69864803	116	3677											
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	24801321	24801321	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taccactgaaatgactggacCaaataacactactaacttta	17	10	4	10	0	0	2	0	2	0	0	0	3	0	3	2	1	4	0	2	1	7	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:24801321C>G	ENST00000395799.3	+	6	1487	c.1358C>G	c.(1357-1359)cCa>cGa	p.P453R	TNRC6A_ENST00000315183.7_Missense_Mutation_p.P453R	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	453	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1, AGO3 and AGO4.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P453Q(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ATGACTGGACCAAATAACACT	0.438																																					p.P453R		.											.	TNRC6A-92	1	Substitution - Missense(1)	lung(1)	c.C1358G						.						58	56	57					16																	24801321		2197	4300	6497	SO:0001583	missense	27327	exon6			CTGGACCAAATAA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.1358C>G	16.37:g.24801321C>G	ENSP00000379144:p.Pro453Arg	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	102	25	NM_014494	0	0	0	0	0	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243926	0.58995	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.44881	0.91;1.02	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.67069	0.2854	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.989;0.999;0.998	T	0.67138	-0.5746	10	0.72032	D	0.01	-7.5051	20.3594	0.98849	0.0:1.0:0.0:0.0	.	200;453;453	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	R	453	ENSP00000326900:P453R;ENSP00000379144:P453R	ENSP00000326900:P453R	P	+	2	0	TNRC6A	24708822	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.247000	0.78257	2.816000	0.96949	0.563000	0.77884	CCA	.		0.438	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24801321	C	G	24801321	3	3	40	1	0	0	0	0	1	0	0	0	16372	594	21	4	1380	4	TNRC6A	16	24801321	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	4311371	24801321	65553432	117	3678											
ATP2A1	487	bcgsc.ca	37	chr16	28914659	28914659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagatgatcttcaagctcCgggccctggacctcacccag	8	7	9	17	1	3	2	2	1	1	1	4	3	4	3	5	2	1	1	5	2	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:28914659C>T	ENST00000357084.3	+	21	3145	c.2878C>T	c.(2878-2880)Cgg>Tgg	p.R960W	ATP2A1_ENST00000395503.4_Missense_Mutation_p.R960W|ATP2A1_ENST00000536376.1_Missense_Mutation_p.R835W	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	960					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						CTTCAAGCTCCGGGCCCTGGA	0.617																																					p.R960W													.	ATP2A1-93	0			c.C2878T						.						99	88	92					16																	28914659		2197	4300	6497	SO:0001583	missense	487	exon21			AAGCTCCGGGCCC		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"ATPases / P-type"	811	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 1", "calcium pump 1"	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.2878C>T	16.37:g.28914659C>T	ENSP00000349595:p.Arg960Trp	Somatic	86	0		WXS	Illumina HiSeq	Phase_1	70	4	NM_004320	0	0	3	3	0	A8K5J9|B3KY17|O14984	Missense_Mutation	SNP	ENST00000357084.3	37	CCDS10643.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473627	0.63737	.	.	ENSG00000196296	ENST00000357084;ENST00000395503;ENST00000536376	D;D;D	0.96073	-3.9;-3.9;-2.38	5.62	-0.253	0.12996	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.750250	0.12288	N	0.482260	D	0.93216	0.7839	L	0.29908	0.895	0.09310	N	1	P;P;P	0.41546	0.754;0.6;0.545	P;B;P	0.52957	0.714;0.195;0.54	D	0.86482	0.1792	10	0.87932	D	0	.	5.6958	0.17855	0.579:0.2428:0.1065:0.0717	.	835;960;960	B3KY17;O14983;O14983-2	.;AT2A1_HUMAN;.	W	960;960;835	ENSP00000349595:R960W;ENSP00000378879:R960W;ENSP00000443101:R835W	ENSP00000349595:R960W	R	+	1	2	ATP2A1	28822160	0.106000	0.21978	0.306000	0.25113	0.895000	0.52256	3.849000	0.55910	0.264000	0.21851	0.561000	0.74099	CGG	.		0.617	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		T	28914659	C	T	28914659	3	4	40	1	0	0	0	0	1	0	0	0	1137	643	23	1	2960	1	ATP2A1	16	28914659	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	4113338	28914659	61440094	118	3679											
ZNF764	92595	broad.mit.edu	37	chr16	30569338	30569338	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggtggccgtaggtctcccGcatcacgtcccggtacaggg	6	7	14	14	4	2	0	1	0	1	0	4	0	3	0	3	5	1	3	3	5	2	2	rs112425159		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:30569338G>T	ENST00000252797.2	-	1	246	c.166C>A	c.(166-168)Cgg>Agg	p.R56R	AC002310.13_ENST00000568114.1_Silent_p.R56R|ZNF764_ENST00000395091.2_Silent_p.R56R	NM_001172679.1|NM_033410.3	NP_001166150.1|NP_219363.2	Q96H86	ZN764_HUMAN	zinc finger protein 764	56	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7						TAGGTCTCCCGCATCACGTCC	0.731																																					p.R56R													.	ZNF764-91	0			c.C166A						.						22	24	23					16																	30569338		2195	4298	6493	SO:0001819	synonymous_variant	92595	exon1			TCTCCCGCATCAC	BC008821	CCDS10683.1, CCDS54001.1	16p11.2	2013-01-08			ENSG00000169951	ENSG00000169951		"Zinc fingers, C2H2-type", "-"	28200	protein-coding gene	gene with protein product						12477932	Standard	NM_033410		Approved	MGC13138	uc002dyq.3	Q96H86	OTTHUMG00000132406	ENST00000252797.2:c.166C>A	16.37:g.30569338G>T		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	144	5	NM_001172679	0	0	0	0	0	A8MZF4|B3KSN2|H9KV99|Q9BWS1	Silent	SNP	ENST00000252797.2	37	CCDS10683.1																																																																																			G|0.500;T|0.500		0.731	ZNF764-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255541.1	NM_033410		T	30569338	G	T	30569338	2	4	40	1	0	0	0	0	0	0	0	1	18170	1086	38	4		4	ZNF764	16	30569338	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	1654679	30569338	59785415	119	3680											
PYDC1	260434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31228204	31228204	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgtcggtgaggtccacgAtatctagctgcccgagcgcg	6	9	14	12	5	1	1	0	1	1	0	3	3	2	1	2	2	3	2	2	2	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:31228204A>G	ENST00000302964.3	-	1	476	c.146T>C	c.(145-147)aTc>aCc	p.I49T	PYDC1_ENST00000568383.1_5'Flank|TRIM72_ENST00000322122.3_Intron	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1	49	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						GAGGTCCACGATATCTAGCTG	0.652																																					p.I49T		.											.	PYDC1-68	0			c.T146C						.						68	61	63					16																	31228204		2197	4300	6497	SO:0001583	missense	260434	exon1			TCCACGATATCTA		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"pyrin domain containing 1"			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407	ENST00000302964.3:c.146T>C	16.37:g.31228204A>G	ENSP00000304336:p.Ile49Thr	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	98	23	NM_152901	0	0	0	0	0	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	37	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.362629	0.24684	.	.	ENSG00000169900	ENST00000302964	T	0.45276	0.9	4.3	0.865	0.19074	Pyrin (2);DEATH-like (2);	2.187950	0.03117	U	0.163273	T	0.29355	0.0731	.	.	.	0.09310	N	1	P	0.42296	0.775	B	0.40864	0.342	T	0.18209	-1.0344	9	0.18710	T	0.47	.	5.5097	0.16874	0.124:0.4356:0.4404:0.0	.	49	Q8WXC3	PYDC1_HUMAN	T	49	ENSP00000304336:I49T	ENSP00000304336:I49T	I	-	2	0	PYDC1	31135705	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-0.903000	0.04084	0.401000	0.25424	-0.415000	0.06103	ATC	.		0.652	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		G	31228204	A	G	31228204	3	3	40	1	0	0	0	0	1	0	0	0	12890	333	12	3	127	3	PYDC1	16	31228204	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	658866	31228204	59126549	120	3681											
N4BP1	9683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	48576974	48576974	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagatctctgagctggcatGggcaggttctgctggagact	8	10	15	8	0	2	3	0	1	2	2	3	5	2	3	0	4	2	5	0	4	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:48576974G>A	ENST00000262384.3	-	7	2768	c.2532C>T	c.(2530-2532)ccC>ccT	p.P844P	N4BP1_ENST00000565423.1_5'UTR	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	844					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GAGCTGGCATGGGCAGGTTCT	0.577																																					p.P844P		.											.	N4BP1-22	0			c.C2532T						.						53	52	53					16																	48576974		1974	4170	6144	SO:0001819	synonymous_variant	9683	exon7			TGGCATGGGCAGG	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.2532C>T	16.37:g.48576974G>A		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	68	9	NM_153029	0	0	24	25	1	A7MD49|Q2YDX1	Silent	SNP	ENST00000262384.3	37	CCDS45479.1																																																																																			.		0.577	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		A	48576974	G	A	48576974	2	1	40	1	0	0	0	0	0	0	0	1	10134	1335	47	2		2	N4BP1	16	48576974	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	17348770	48576974	41777779	121	3682											
ADCY7	113	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	50338447	50338447	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgagacccacgtccccaaCgggcggaggcctaaggtagg	9	4	16	12	3	0	1	0	1	0	1	1	3	1	2	4	6	1	1	4	6	3	2	rs144290211		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:50338447C>T	ENST00000394697.2	+	11	1885	c.1545C>T	c.(1543-1545)aaC>aaT	p.N515N	ADCY7_ENST00000566433.2_Silent_p.N515N|ADCY7_ENST00000537579.1_Intron|ADCY7_ENST00000254235.3_Silent_p.N515N|ADCY7_ENST00000538642.1_Silent_p.N515N			P51828	ADCY7_HUMAN	adenylate cyclase 7	515					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		ACGTCCCCAACGGGCGGAGGC	0.652													C|||	1	0.000199681	0	0	5008	,	,		18295	0		0	False		,,,				2504	0.001				p.N515N													.	ADCY7-91	0			c.C1545T						.	C		3,4393	6.2+/-15.9	0,3,2195	43	46	45		1545	-10	0	16	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous	ADCY7	NM_001114.3		0,3,6495	TT,TC,CC		0.0,0.0682,0.0231		515/1081	50338447	3,12993	2198	4300	6498	SO:0001819	synonymous_variant	113	exon10			CCCCAACGGGCGG	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"Adenylate cyclases"	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.1545C>T	16.37:g.50338447C>T		Somatic	107	2		WXS	Illumina HiSeq	Phase_I	112	26	NM_001114	0	0	4	5	1	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																			C|1.000;T|0.000		0.652	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			T	50338447	C	T	50338447	2	4	40	1	0	0	0	0	0	0	0	1	299	535	19	1		1	ADCY7	16	50338447	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1761473	50338447	40016306	122	3683											
BCAR1	9564	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	75276534	75276534	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtggccgggctgggaaacGggtgatggggtgtctgcttc	4	10	19	8	2	1	1	0	1	1	0	2	2	1	2	1	6	2	2	1	6	1	1	rs373232015		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:75276534G>C	ENST00000162330.5	-	2	593	c.467C>G	c.(466-468)cCg>cGg	p.P156R	BCAR1_ENST00000420641.3_Missense_Mutation_p.P174R|BCAR1_ENST00000546196.1_Missense_Mutation_p.P127R|BCAR1_ENST00000393422.2_Missense_Mutation_p.P174R|BCAR1_ENST00000393420.6_Missense_Mutation_p.P156R|BCAR1_ENST00000542031.2_Missense_Mutation_p.P154R|BCAR1_ENST00000538440.2_Missense_Mutation_p.P156R|BCAR1_ENST00000418647.3_Missense_Mutation_p.P202R|BCAR1_ENST00000535626.2_Intron	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	156	Substrate for kinases. {ECO:0000250}.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GCTGGGAAACGGGTGATGGGG	0.642																																					p.P202R													.	BCAR1-1145	0			c.C605G						.						100	99	99					16																	75276534		2198	4300	6498	SO:0001583	missense	9564	exon3			GGAAACGGGTGAT	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"Cas scaffolding proteins"	971	protein-coding gene	gene with protein product	"Crk-associated substrate", "Cas scaffolding protein family member 1"	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.467C>G	16.37:g.75276534G>C	ENSP00000162330:p.Pro156Arg	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	94	25	NM_001170714	0	0	5	8	3	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	.	.	.	.	.	.	.	.	.	.	G	5.268	0.234849	0.09969	.	.	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39	5.02	2.76	0.32466	.	1.250770	0.05591	N	0.574609	T	0.50735	0.1633	L	0.34521	1.04	0.09310	N	0.999999	B;P;P;B;B;P;B	0.46512	0.2;0.589;0.879;0.355;0.411;0.879;0.242	B;B;P;B;B;P;B	0.44518	0.09;0.174;0.452;0.186;0.229;0.452;0.052	T	0.50890	-0.8774	10	0.51188	T	0.08	-15.5833	13.9777	0.64284	0.0:0.0:0.687:0.313	.	174;202;154;156;174;156;156	B4DIW5;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945	.;.;.;.;.;.;BCAR1_HUMAN	R	156;174;174;156;202;156;154;127	ENSP00000162330:P156R;ENSP00000377074:P174R;ENSP00000392708:P174R;ENSP00000443841:P156R;ENSP00000391669:P202R;ENSP00000377072:P156R;ENSP00000440415:P154R;ENSP00000442161:P127R	ENSP00000162330:P156R	P	-	2	0	BCAR1	73834035	0.257000	0.24022	0.676000	0.29932	0.095000	0.18619	1.683000	0.37638	0.641000	0.30601	-0.824000	0.03097	CCG	.		0.642	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		C	75276534	G	C	75276534	3	2	40	1	0	0	0	0	1	0	0	0	1349	1116	39	4	2230	4	BCAR1	16	75276534	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	24938087	75276534	15078219	123	3684											
HS3ST3A1	9955	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	13504436	13504436	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagggcactggccgggcccGgaggggccatcctagccgga	7	3	18	13	3	0	1	0	0	0	1	1	3	1	3	5	7	1	1	5	7	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:13504436G>T	ENST00000284110.1	-	1	808	c.11C>A	c.(10-12)cCg>cAg	p.P4Q		NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	4					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGCCGGGCCCGGAGGGGCCAT	0.711																																					p.P4Q		.											.	HS3ST3A1-515	0			c.C11A						.						21	21	21					17																	13504436		2176	4264	6440	SO:0001583	missense	9955	exon1			GGGCCCGGAGGGG	AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"Sulfotransferases, membrane-bound"	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.11C>A	17.37:g.13504436G>T	ENSP00000284110:p.Pro4Gln	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	67	15	NM_006042	0	0	0	0	0	A8K7N2	Missense_Mutation	SNP	ENST00000284110.1	37	CCDS11165.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.778371	0.31502	.	.	ENSG00000153976	ENST00000284110	T	0.50548	0.74	2.79	-0.456	0.12190	.	0.327925	0.15205	U	0.274780	T	0.30854	0.0778	N	0.24115	0.695	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.05632	-1.0873	10	0.66056	D	0.02	.	9.3973	0.38410	0.3961:0.0:0.6039:0.0	.	4	Q9Y663	HS3SA_HUMAN	Q	4	ENSP00000284110:P4Q	ENSP00000284110:P4Q	P	-	2	0	HS3ST3A1	13445161	0.000000	0.05858	0.792000	0.32020	0.729000	0.41735	-0.271000	0.08572	-0.327000	0.08551	-1.119000	0.02030	CCG	.		0.711	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042		T	13504436	G	T	13504436	3	4	40	1	0	0	0	0	1	0	0	0	7386	1116	39	4	1217	4	HS3ST3A1	17	13504436	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		13504436	67690774	124	3685											
RAI1	10743	broad.mit.edu	37	chr17	17699993	17699995	+	In_Frame_Del	DEL	GCA	GCA	-																															gaacctggtcttgcggagccGcagcagcagcagcagcaacg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:17699993_17699995delGCA	ENST00000353383.1	+	3	4200_4202	c.3731_3733delGCA	c.(3730-3735)cgcagc>cgc	p.S1249del	RAI1_ENST00000261641.6_In_Frame_Del_p.S1249del	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1249	Poly-Ser.				circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		TTGCGGAGCCGCAGCAGCAGCAG	0.626																																					p.1244_1245del													.	RAI1-91	0			c.3731_3733del						.																																			SO:0001651	inframe_deletion	10743	exon3			GGAGCCGCAGCAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"Smith-Magenis syndrome chromosome region"	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.3731_3733delGCA	17.37:g.17700002_17700004delGCA	ENSP00000323074:p.Ser1249del	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	64	7	NM_030665	0	0	0	0	0	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	In_Frame_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			.		0.626	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		-	17699995	GCA	-	17699993	7	5	40	1	0	1	0	1	0	0	0	0	13039	1087	38	0	3733	0	RAI1	17	17699993	In_Frame_Del	DEL	GCA	TCGA-B1-A656-01A-11D-A31X-10	4195557	17699993	63495217	125	3686											
NF1	4763	broad.mit.edu	37	chr17	29533389	29533389	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagcaatacgaatggcaccGgtaagataaatcacgaattt	16	8	8	9	3	1	1	1	0	0	1	1	3	1	1	2	2	2	3	2	2	7	4	rs201604273		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:29533389G>A	ENST00000358273.4	+	12	1775	c.1392G>A	c.(1390-1392)ccG>ccA	p.P464P	NF1_ENST00000431387.4_Splice_Site_p.P464P|NF1_ENST00000356175.3_Splice_Site_p.P464P	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	464					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GAATGGCACCGGTAAGATAAA	0.383			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			G|||	1	0.000199681	0	0	5008	,	,		18347	0.001		0	False		,,,				2504	0				p.P464P			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1-3353	14	Whole gene deletion(8)|Unknown(6)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(3)|lung(1)	c.G1392A						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	147	135	139		1392,1392,1392	2.7	1	17		139	0,8600		0,0,4300	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	NF1	NM_000267.3,NM_001042492.2,NM_001128147.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	464/2819,464/2840,464/594	29533389	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	4763	exon12	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	GGCACCGGTAAGA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1392+1G>A	17.37:g.29533389G>A		Somatic	171	1		WXS	Illumina HiSeq	Phase_I	134	4	NM_001128147	0	0	0	0	0	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			G|0.999;A|0.000		0.383	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Silent	A	29533389	G	A	29533389	5	1	40	1	0	0	0	0	0	0	1	0	10382	1130	39	1	1438	1	NF1	17	29533389	Splice_Site	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	11833396	29533389	51661821	126	3687											
ZNF830	91603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33288777	33288777	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	actccggttaagagcgagctCctgtggcagactcacgtcct	8	9	11	13	3	1	2	1	0	0	2	4	3	4	2	3	2	2	3	3	2	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:33288777C>A	ENST00000361952.3	+	1	229	c.192C>A	c.(190-192)ctC>ctA	p.L64L	CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000436961.3_5'Flank|CCT6B_ENST00000421975.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	64					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				AGAGCGAGCTCCTGTGGCAGA	0.582																																					p.L64L		.											.	ZNF830-89	0			c.C192A						.						93	90	91					17																	33288777		2203	4300	6503	SO:0001819	synonymous_variant	91603	exon1			CGAGCTCCTGTGG	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.192C>A	17.37:g.33288777C>A		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	128	53	NM_052857	0	0	6	7	1	Q96F60|Q96GZ5|Q9BU38	Silent	SNP	ENST00000361952.3	37	CCDS32618.1																																																																																			.		0.582	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		A	33288777	C	A	33288777	2	1	40	1	0	0	0	0	0	0	0	1	18216	842	30	4		4	ZNF830	17	33288777	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	3755388	33288777	47906433	127	3688											
GGNBP2	79893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34934557	34934557	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaacgacacatacatgtttgCtgtgaaacagacttcattgc	13	11	8	9	1	1	2	1	1	0	1	1	4	1	2	0	0	5	2	0	0	3	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:34934557C>T	ENST00000304718.4	+	7	1102	c.786C>T	c.(784-786)tgC>tgT	p.C262C		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	262					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.C262C(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		TACATGTTTGCTGTGAAACAG	0.463																																					p.C262C		.											.	GGNBP2-70	1	Substitution - coding silent(1)	lung(1)	c.C786T						.						216	194	201					17																	34934557		2203	4300	6503	SO:0001819	synonymous_variant	79893	exon7			TGTTTGCTGTGAA	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"zinc finger protein 403"	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.786C>T	17.37:g.34934557C>T		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	108	24	NM_024835	0	0	6	6	0	B2RPK7|Q96T90|Q9GZR8|Q9H767	Silent	SNP	ENST00000304718.4	37	CCDS11314.1																																																																																			.		0.463	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34934557	C	T	34934557	2	4	40	1	0	0	0	0	0	0	0	1	6379	805	28	2		2	GGNBP2	17	34934557	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1645780	34934557	46260653	128	3689											
CNTNAP1	8506	broad.mit.edu	37	chr17	40849969	40849969	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttgccatacttttaggctGtgagtagcactgatcactaa	10	13	10	8	0	1	2	1	2	0	0	1	2	1	2	1	2	3	4	1	2	4	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:40849969G>T	ENST00000264638.4	+	23	4079		c.e23+1		CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1						axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		CTTTTAGGCTGTGAGTAGCAC	0.517																																					.													.	CNTNAP1-525	0			c.3862+1G>T						.						233	180	198					17																	40849969		2203	4300	6503	SO:0001630	splice_region_variant	8506	exon23			TAGGCTGTGAGTA	U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"neurexin 4"	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.3862+1G>T	17.37:g.40849969G>T		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	74	3	NM_003632	0	0	0	0	0		Splice_Site	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.414119	0.83449	.	.	ENSG00000108797	ENST00000264638	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8389	0.85963	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTNAP1	38103495	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.784000	0.68990	2.716000	0.92895	0.650000	0.86243	.	.		0.517	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	Intron	T	40849969	G	T	40849969	5	4	40	1	0	0	0	0	0	0	1	0	3652	1391	48	4	3953	4	CNTNAP1	17	40849969	Splice_Site	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5915412	40849969	40345241	129	3690											
NBR1	4077	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41343439	41343439	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaagcagaaaagcaaaggtTgcgagctgagaagaaacaac	20	4	11	6	1	0	3	0	1	0	3	0	5	0	3	0	1	6	4	0	1	8	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:41343439T>C	ENST00000422280.1	+	10	1373	c.914T>C	c.(913-915)tTg>tCg	p.L305S	NBR1_ENST00000389312.4_Missense_Mutation_p.L305S|NBR1_ENST00000589872.1_Missense_Mutation_p.L305S|NBR1_ENST00000542611.1_Missense_Mutation_p.L284S|NBR1_ENST00000341165.6_Missense_Mutation_p.L305S|NBR1_ENST00000590996.1_Missense_Mutation_p.L305S	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	305					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		AAGCAAAGGTTGCGAGCTGAG	0.373																																					p.L305S													.	NBR1-130	0			c.T914C						.						46	46	46					17																	41343439		1855	4107	5962	SO:0001583	missense	4077	exon10			AAAGGTTGCGAGC	X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.914T>C	17.37:g.41343439T>C	ENSP00000411250:p.Leu305Ser	Somatic	383	1		WXS	Illumina HiSeq	Phase_I	324	83	NM_031862	0	0	6	9	3	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	37	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.489318	0.84962	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.54479	1.18;0.57;1.18;1.18	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	T	0.59046	0.2165	N	0.24115	0.695	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	T	0.61540	-0.7042	10	0.48119	T	0.1	-5.3106	13.949	0.64104	0.0:0.0:0.0:1.0	.	305;284;305;305	A8K1U0;B7Z5R6;Q14596-2;Q14596	.;.;.;NBR1_HUMAN	S	305;284;305;305;305	ENSP00000411250:L305S;ENSP00000437545:L284S;ENSP00000343479:L305S;ENSP00000373963:L305S	ENSP00000343479:L305S	L	+	2	0	NBR1	38596965	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.175000	0.77632	2.044000	0.60594	0.533000	0.62120	TTG	.		0.373	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		C	41343439	T	C	41343439	3	2	40	1	0	0	0	0	1	0	0	0	10226	1821	63	3	948	3	NBR1	17	41343439	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	493470	41343439	39851771	130	3691											
RPRML	388394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45056083	45056083	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcaccagaaagttgatcatGctctcggacttgatgagcag	11	10	11	9	1	2	4	1	3	1	1	3	5	2	5	1	1	3	4	1	1	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:45056083G>T	ENST00000322329.3	-	1	531	c.291C>A	c.(289-291)agC>agA	p.S97R	LRRC37A17P_ENST00000570478.1_RNA|RP11-156P1.2_ENST00000571841.1_Intron|GOSR2_ENST00000439730.2_Intron	NM_203400.4	NP_981945.1	Q8N4K4	RPRML_HUMAN	reprimo-like	97						integral component of membrane (GO:0016021)				lung(1)	1						AGTTGATCATGCTCTCGGACT	0.652																																					p.S97R		.											.	RPRML-68	0			c.C291A						.						34	32	33					17																	45056083		2201	4300	6501	SO:0001583	missense	388394	exon1			GATCATGCTCTCG	BC033942	CCDS11508.1	17q21.32	2006-09-26				ENSG00000179673			32422	protein-coding gene	gene with protein product							Standard	NM_203400		Approved	MGC43894	uc002ilb.3	Q8N4K4		ENST00000322329.3:c.291C>A	17.37:g.45056083G>T	ENSP00000318032:p.Ser97Arg	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	102	28	NM_203400	0	0	1	1	0		Missense_Mutation	SNP	ENST00000322329.3	37	CCDS11508.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444031	0.63067	.	.	ENSG00000179673	ENST00000322329	.	.	.	3.72	2.72	0.32119	.	0.000000	0.85682	D	0.000000	T	0.66655	0.2811	L	0.52573	1.65	0.58432	D	0.999997	D	0.76494	0.999	D	0.72075	0.976	T	0.65561	-0.6138	9	0.52906	T	0.07	-8.687	10.3405	0.43875	0.103:0.0:0.897:0.0	.	97	Q8N4K4	RPRML_HUMAN	R	97	.	ENSP00000318032:S97R	S	-	3	2	RPRML	42411082	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.546000	0.45778	0.727000	0.32360	0.313000	0.20887	AGC	.		0.652	RPRML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440919.1	NM_203400		T	45056083	G	T	45056083	3	4	40	1	0	0	0	0	1	0	0	0	13651	1310	46	4	75	4	RPRML	17	45056083	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	3712644	45056083	36139127	131	3692											
HOXB4	3214	hgsc.bcm.edu;bcgsc.ca	37	chr17	46655633	46655634	+	In_Frame_Ins	INS	-	-	CTT																															tattcctcgcatggagggaaINScttggggtcgacatagtttg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:46655633_46655634insCTT	ENST00000332503.5	-	1	1839_1840	c.48_49insAAG	c.(46-51)aagttc>aagAAGttc	p.16_17insK	HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000489475.1_Intron|HOXB3_ENST00000465120.3_Intron|MIR10A_ENST00000385043.1_RNA|HOXB3_ENST00000476342.1_Intron|HOXB3_ENST00000472863.1_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	16	Pro-rich (part of the transcriptional activation domain).				anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						CATGGAGGGAACTTGGGGTCGA	0.5																																					p.F17delinsKF		.											.	HOXB4-515	0			c.49_50insAAG						.																																			SO:0001652	inframe_insertion	3214	exon1			.		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.46_48dupAAG	17.37:g.46655634_46655636dupCTT	ENSP00000328928:p.Lys16_Lys16dup	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	188	36	NM_024015	0	0	0	0	0	Q9NTA0	In_Frame_Ins	INS	ENST00000332503.5	37	CCDS11529.1																																																																																			.		0.5	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			CTT	46655634	-	CTT	46655633	7	5	40	1	0	1	1	0	0	0	0	0	7324	43	2	0	714	0	HOXB4	17	46655633	In_Frame_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	1599550	46655633	34539577	132	3693											
ABCA10	10349	broad.mit.edu	37	chr17	67189985	67189985	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttcctttggctgaatcccTtttattttagcaaataccct	9	17	4	11	0	0	1	0	1	0	0	2	1	2	1	3	1	2	2	3	1	5	7			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:67189985T>C	ENST00000269081.4	-	14	2400	c.1491A>G	c.(1489-1491)aaA>aaG	p.K497K	ABCA10_ENST00000416101.2_Intron	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	497	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					GCTGAATCCCTTTTATTTTAG	0.328																																					p.K497K													.	ABCA10-93	0			c.A1491G						.						142	142	142					17																	67189985		2203	4300	6503	SO:0001819	synonymous_variant	10349	exon14			AATCCCTTTTATT	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.1491A>G	17.37:g.67189985T>C		Somatic	167	0		WXS	Illumina HiSeq	Phase_I	157	4	NM_080282	0	0	0	0	0	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																			.		0.328	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		C	67189985	T	C	67189985	2	2	40	1	0	0	0	0	0	0	0	1	29	1606	56	3		3	ABCA10	17	67189985	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	20534352	67189985	14005225	133	3694											
FDXR	2232	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72862364	72862364	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgatggtcctctgccccgtaGctctgatgaaagatggcagg	8	9	13	11	2	2	3	0	2	2	1	3	4	3	3	3	3	2	3	3	3	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:72862364G>A	ENST00000293195.5	-	5	474	c.396C>T	c.(394-396)agC>agT	p.S132S	FDXR_ENST00000583917.1_Silent_p.S133S|FDXR_ENST00000413947.2_Silent_p.S163S|FDXR_ENST00000582944.1_Silent_p.S124S|FDXR_ENST00000420580.2_Silent_p.S92S|FDXR_ENST00000442102.2_Silent_p.S175S|FDXR_ENST00000455107.2_Silent_p.S88S|FDXR_ENST00000581530.1_Silent_p.S132S|FDXR_ENST00000544854.1_Silent_p.S80S|FDXR_ENST00000581969.1_5'UTR	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	132					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	CTGCCCCGTAGCTCTGATGAA	0.657																																					p.S175S													.	FDXR-226	0			c.C525T						.						30	35	34					17																	72862364		2203	4300	6503	SO:0001819	synonymous_variant	2232	exon5			CCCGTAGCTCTGA	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.396C>T	17.37:g.72862364G>A		Somatic	103	1		WXS	Illumina HiSeq	Phase_I	74	12	NM_001258012	0	0	0	0	0	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Silent	SNP	ENST00000293195.5	37	CCDS58593.1																																																																																			.		0.657	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		A	72862364	G	A	72862364	2	1	40	1	0	0	0	0	0	0	0	1	5826	962	34	2		2	FDXR	17	72862364	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5672379	72862364	8332846	134	3695											
FBF1	85302	broad.mit.edu	37	chr17	73916511	73916511	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggactctgggagcaggggCtggaggagaggaagagaggt	11	4	22	4	0	1	2	0	0	1	2	1	8	1	6	0	8	1	2	0	8	1	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:73916511C>A	ENST00000586717.1	-	17	1906		c.e17-1		FBF1_ENST00000319129.5_Splice_Site|FBF1_ENST00000389570.4_Splice_Site			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1						apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						GGAGCAGGGGCTGGAGGAGAG	0.632																																					.													.	FBF1-205	0			c.1630-1G>T						.						19	23	22					17																	73916511		1975	4158	6133	SO:0001630	splice_region_variant	85302	exon18			CAGGGGCTGGAGG	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"albatross"					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.1633-1G>T	17.37:g.73916511C>A		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	103	3	NM_001080542	0	0	0	0	0	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Splice_Site	SNP	ENST00000586717.1	37		.	.	.	.	.	.	.	.	.	.	C	6.970	0.548988	0.13312	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.49051	D	0.999741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5633	0.50790	0.2254:0.7746:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FBF1	71428106	0.990000	0.36364	0.155000	0.22561	0.037000	0.13140	4.709000	0.61867	2.445000	0.82738	0.655000	0.94253	.	.		0.632	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	Intron	A	73916511	C	A	73916511	5	1	40	1	0	0	0	0	0	0	1	0	5714	811	28	4	1824	4	FBF1	17	73916511	Splice_Site	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1054147	73916511	7278699	135	3696											
CEP192	55125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	13055803	13055803	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atatcaccagcgagttgagtAccacaattattcaaggcagt	14	10	8	9	1	2	1	2	1	0	0	2	2	2	1	2	1	2	3	2	1	5	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr18:13055803A>T	ENST00000325971.8	+	17	3019	c.1426A>T	c.(1426-1428)Acc>Tcc	p.T476S	CEP192_ENST00000430049.2_Missense_Mutation_p.T597S|CEP192_ENST00000506447.1_Missense_Mutation_p.T1072S			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	476					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGAGTTGAGTACCACAATTAT	0.368																																					p.T1072S		.											.	CEP192-27	0			c.A3214T						.						57	57	57					18																	13055803		2203	4300	6503	SO:0001583	missense	55125	exon19			TTGAGTACCACAA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1426A>T	18.37:g.13055803A>T	ENSP00000317156:p.Thr476Ser	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	42	14	NM_032142	0	0	0	0	0	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	A	19.71	3.878317	0.72294	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.21031	2.03;2.03;2.03	4.5	4.5	0.54988	.	0.111905	0.39687	N	0.001284	T	0.22704	0.0548	L	0.39397	1.21	0.42538	D	0.993064	B;B;P	0.43973	0.291;0.291;0.823	B;B;P	0.44477	0.214;0.214;0.451	T	0.02307	-1.1179	10	0.44086	T	0.13	-5.7927	14.1063	0.65091	1.0:0.0:0.0:0.0	.	597;1072;476	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	S	1072;476;476;597	ENSP00000427550:T1072S;ENSP00000317156:T476S;ENSP00000389190:T597S	ENSP00000317156:T476S	T	+	1	0	CEP192	13045803	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	6.760000	0.74939	1.790000	0.52503	0.460000	0.39030	ACC	.		0.368	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13055803	A	T	13055803	3	4	40	1	0	0	0	0	1	0	0	0	3257	391	14	5	3284	5	CEP192	18	13055803	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		13055803	65021445	136	3697											
CABLES1	91768	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	20814665	20814665	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtggagctgggtgctgatggGaaggtaaggctgccaggctg	7	8	20	6	0	0	1	0	1	0	0	0	3	0	3	1	6	3	5	1	6	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr18:20814665G>A	ENST00000256925.7	+	5	1182	c.1182G>A	c.(1180-1182)ggG>ggA	p.G394G	CABLES1_ENST00000585061.1_Intron|CABLES1_ENST00000400473.2_Silent_p.G67G|CABLES1_ENST00000420687.2_Silent_p.G129G|TMEM241_ENST00000450466.2_Intron	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	394	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GTGCTGATGGGAAGGTAAGGC	0.562																																					p.G394G													.	CABLES1-522	0			c.G1182A						.						59	64	62					18																	20814665		2034	4195	6229	SO:0001819	synonymous_variant	91768	exon5			TGATGGGAAGGTA	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1182G>A	18.37:g.20814665G>A		Somatic	136	1		WXS	Illumina HiSeq	Phase_I	73	24	NM_001100619	0	0	0	0	0	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Silent	SNP	ENST00000256925.7	37	CCDS42417.1																																																																																			.		0.562	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		A	20814665	G	A	20814665	2	1	40	1	0	0	0	0	0	0	0	1	2535	1161	41	2		2	CABLES1	18	20814665	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	7758862	20814665	57262583	137	3698											
PHLPP1	23239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	60384475	60384475	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcggagattggctgccTcatccgcttctatgcaggta	7	11	12	11	2	2	1	1	0	1	1	4	3	3	2	2	4	2	4	2	4	2	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr18:60384475T>A	ENST00000262719.5	+	1	1793	c.1559T>A	c.(1558-1560)cTc>cAc	p.L520H	PHLPP1_ENST00000400316.4_Missense_Mutation_p.L8H			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	520					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						ATTGGCTGCCTCATCCGCTTC	0.537																																					p.L520H		.											.	.	0			c.T1559A						.						76	88	84					18																	60384475		2032	4181	6213	SO:0001583	missense	23239	exon1			GCTGCCTCATCCG	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.1559T>A	18.37:g.60384475T>A	ENSP00000262719:p.Leu520His	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	46	16	NM_194449	0	0	0	0	0	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	37	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	T	21.9	4.221833	0.79464	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.35605	1.52;1.3	3.91	3.91	0.45181	.	.	.	.	.	T	0.49932	0.1586	L	0.43923	1.385	0.45272	D	0.998273	D	0.89917	1.0	D	0.87578	0.998	T	0.51498	-0.8698	9	0.66056	D	0.02	-10.6803	11.9254	0.52817	0.0:0.0:0.0:1.0	.	520	O60346	PHLP1_HUMAN	H	8;520	ENSP00000383170:L8H;ENSP00000262719:L520H	ENSP00000262719:L520H	L	+	2	0	PHLPP1	58535455	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.650000	0.74368	1.653000	0.50694	0.454000	0.30748	CTC	.		0.537	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		A	60384475	T	A	60384475	3	1	40	1	0	0	0	0	1	0	0	0	11880	1551	54	5	1561	5	PHLPP1	18	60384475	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	39569810	60384475	17692773	138	3699											
FSD1	79187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4306032	4306032	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaaacagatgctgctgaaCgtggaggtgaaggcggtggg	10	7	18	6	2	0	4	0	3	0	1	0	5	0	5	0	5	4	2	0	5	3	0	rs143212819	byFrequency	TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:4306032C>T	ENST00000221856.6	+	2	252	c.105C>T	c.(103-105)aaC>aaT	p.N35N	FSD1_ENST00000597590.1_Silent_p.N35N	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	35					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGCTGAACGTGGAGGTGA	0.547													C|||	2	0.000399361	0	0.0014	5008	,	,		18860	0		0.001	False		,,,				2504	0				p.N35N		.											.	FSD1-91	0			c.C105T						.	C		0,4406		0,0,2203	107	112	110		105	-2	1	19	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FSD1	NM_024333.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		35/497	4306032	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	79187	exon2			GCTGAACGTGGAG	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.105C>T	19.37:g.4306032C>T		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	79	28	NM_024333	0	0	0	0	0	B2RDT0|Q9BXN0|Q9HAG4	Silent	SNP	ENST00000221856.6	37	CCDS12127.1																																																																																			C|1.000;T|0.000		0.547	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		T	4306032	C	T	4306032	2	4	40	1	0	0	0	0	0	0	0	1	6089	535	19	1		1	FSD1	19	4306032	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		4306032	54822951	139	3700											
FEM1A	55527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4792820	4792820	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaacgagatctgcttggggcCcttaaacactggaggcgggc	10	7	14	10	2	1	1	0	0	1	1	1	3	1	2	1	5	3	1	1	5	3	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:4792820C>A	ENST00000269856.3	+	1	1093	c.954C>A	c.(952-954)gcC>gcA	p.A318A	AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	318					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		TGCTTGGGGCCCTTAAACACT	0.597																																					p.A318A		.											.	FEM1A-90	0			c.C954A						.						47	51	50					19																	4792820		2203	4299	6502	SO:0001819	synonymous_variant	55527	exon1			TGGGGCCCTTAAA	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"Ankyrin repeat domain containing"	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.954C>A	19.37:g.4792820C>A		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	108	32	NM_018708	0	0	1	2	1	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	37	CCDS12135.1																																																																																			.		0.597	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			A	4792820	C	A	4792820	2	1	40	1	0	0	0	0	0	0	0	1	5828	610	22	4		4	FEM1A	19	4792820	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	486788	4792820	54336163	140	3701											
ZNF558	148156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8922694	8922694	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcgtgctgaagactttaaAacactgattacattcattga	13	15	6	7	1	1	4	1	3	0	1	2	4	1	4	0	0	3	1	0	0	4	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:8922694A>G	ENST00000601372.1	-	10	1183	c.472T>C	c.(472-474)Ttt>Ctt	p.F158L	ZNF558_ENST00000301475.1_Missense_Mutation_p.F158L|ZNF558_ENST00000444186.2_Missense_Mutation_p.F87L			Q96NG5	ZN558_HUMAN	zinc finger protein 558	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15						AAGACTTTAAAACACTGATTA	0.338																																					p.F158L		.											.	ZNF558-90	0			c.T472C						.						42	38	40					19																	8922694		2203	4300	6503	SO:0001583	missense	148156	exon6			CTTTAAAACACTG	AK055494	CCDS12208.1	19p13.2	2013-09-20			ENSG00000167785	ENSG00000167785		"Zinc fingers, C2H2-type", "-"	26422	protein-coding gene	gene with protein product							Standard	NM_144693		Approved	FLJ30932	uc002mkn.1	Q96NG5	OTTHUMG00000182196	ENST00000601372.1:c.472T>C	19.37:g.8922694A>G	ENSP00000471277:p.Phe158Leu	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	72	9	NM_144693	0	0	0	0	0	A8K5F0|B7Z798	Missense_Mutation	SNP	ENST00000601372.1	37	CCDS12208.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492197	0.84962	.	.	ENSG00000167785	ENST00000301475;ENST00000444186	T;T	0.07216	3.21;3.21	5.07	4.0	0.46444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44688	D	0.000434	T	0.04137	0.0115	N	0.12182	0.205	0.34332	D	0.687801	P	0.39250	0.665	B	0.30716	0.119	T	0.30208	-0.9986	10	0.72032	D	0.01	-19.1944	8.9778	0.35946	0.7058:0.2942:0.0:0.0	.	158	Q96NG5	ZN558_HUMAN	L	158;87	ENSP00000301475:F158L;ENSP00000410703:F87L	ENSP00000301475:F158L	F	-	1	0	ZNF558	8783694	0.975000	0.34042	0.999000	0.59377	0.988000	0.76386	1.844000	0.39269	2.128000	0.65567	0.482000	0.46254	TTT	.		0.338	ZNF558-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459955.2	NM_144693		G	8922694	A	G	8922694	3	3	40	1	0	0	0	0	1	0	0	0	18021	14	1	3	740	3	ZNF558	19	8922694	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	4129874	8922694	50206289	141	3702											
ZNF426	79088	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9639297	9639297	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacattgtttacactcatagGgtttttctccagtgtggatt	8	17	8	8	0	2	0	1	0	1	0	3	1	2	1	1	2	1	2	1	2	2	7			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:9639297G>A	ENST00000535489.1	-	6	1760	c.1424C>T	c.(1423-1425)cCc>cTc	p.P475L	ZNF426_ENST00000593003.1_Missense_Mutation_p.P437L|ZNF426_ENST00000253115.2_Missense_Mutation_p.P475L			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	475					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(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						ACACTCATAGGGTTTTTCTCC	0.428																																					p.P475L		.											.	ZNF426-91	0			c.C1424T						.						95	93	94					19																	9639297		2203	4300	6503	SO:0001583	missense	79088	exon8			TCATAGGGTTTTT	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"Zinc fingers, C2H2-type", "-"	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.1424C>T	19.37:g.9639297G>A	ENSP00000439017:p.Pro475Leu	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	114	29	NM_024106	0	0	0	0	0	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.326242	0.60743	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.17054	2.3;2.3	1.52	1.52	0.23074	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36717	0.0977	M	0.74546	2.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.99	T	0.24012	-1.0172	9	0.72032	D	0.01	.	8.9649	0.35869	0.0:0.0:1.0:0.0	.	462;475	Q59EH4;Q9BUY5	.;ZN426_HUMAN	L	462;475;475	ENSP00000253115:P475L;ENSP00000439017:P475L	ENSP00000253115:P475L	P	-	2	0	ZNF426	9500297	0.426000	0.25506	0.005000	0.12908	0.100000	0.18952	1.495000	0.35627	1.133000	0.42147	0.563000	0.77884	CCC	.		0.428	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		A	9639297	G	A	9639297	3	1	40	1	0	0	0	0	1	0	0	0	17932	1232	43	2	244	2	ZNF426	19	9639297	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	716603	9639297	49489686	142	3703											
ICAM3	3385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10444569	10444569	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcttcccccattgcttcTgtcggctgcatagacgtgag	5	13	11	12	2	2	2	0	1	2	1	4	2	3	2	2	2	2	4	2	2	1	5	rs369252388		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:10444569T>A	ENST00000160262.5	-	7	1816	c.1608A>T	c.(1606-1608)acA>acT	p.T536T	RAVER1_ENST00000293677.6_5'Flank|ICAM3_ENST00000589261.1_Silent_p.T459T	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	536					extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			CCATTGCTTCTGTCGGCTGCA	0.567																																					p.T536T		.											.	ICAM3-131	0			c.A1608T						.	T		0,4406		0,0,2203	180	166	171		1608	-8.7	0	19		171	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ICAM3	NM_002162.3		0,1,6502	AA,AT,TT		0.0116,0.0,0.0077		536/548	10444569	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon7			TGCTTCTGTCGGC		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.1608A>T	19.37:g.10444569T>A		Somatic	162	0		WXS	Illumina HiSeq	Phase_I	121	24	NM_002162	0	0	56	70	14	Q6PD68	Silent	SNP	ENST00000160262.5	37	CCDS12235.1																																																																																			.		0.567	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1			A	10444569	T	A	10444569	2	1	40	1	0	0	0	0	0	0	0	1	7502	1567	55	5		5	ICAM3	19	10444569	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	805272	10444569	48684414	143	3704											
CYP4F3	4051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15752256	15752256	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcctgtcctcgctgggcCtttggccaatggcagcatcc	5	10	12	14	1	0	1	0	1	0	0	3	1	2	1	5	3	2	3	5	3	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:15752256C>G	ENST00000221307.8	+	2	78	c.31C>G	c.(31-33)Ctt>Gtt	p.L11V	CYP4F3_ENST00000585846.1_Missense_Mutation_p.L11V|CYP4F3_ENST00000591058.1_Missense_Mutation_p.L11V|CYP4F3_ENST00000586182.2_Missense_Mutation_p.L11V	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	11					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						CTCGCTGGGCCTTTGGCCAAT	0.652																																					p.L11V		.											.	CYP4F3-93	0			c.C31G						.						56	56	56					19																	15752256		2203	4300	6503	SO:0001583	missense	4051	exon2			CTGGGCCTTTGGC	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"Cytochrome P450s"	2646	protein-coding gene	gene with protein product		601270	"cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.31C>G	19.37:g.15752256C>G	ENSP00000221307:p.Leu11Val	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	64	16	NM_001199209	0	0	0	0	0	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	37	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	12.16	1.854157	0.32791	.	.	ENSG00000186529	ENST00000221307	D	0.93426	-3.22	3.73	2.65	0.31530	.	0.298234	0.22742	U	0.056184	D	0.92450	0.7603	M	0.73598	2.24	0.09310	N	1	P;P	0.38420	0.63;0.63	B;B	0.43082	0.317;0.407	D	0.85130	0.0974	10	0.42905	T	0.14	.	8.5276	0.33315	0.2301:0.7698:0.0:0.0	.	11;11	B7Z8Z3;Q08477	.;CP4F3_HUMAN	V	11	ENSP00000221307:L11V	ENSP00000221307:L11V	L	+	1	0	CYP4F3	15613256	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-0.157000	0.10085	0.504000	0.28082	0.411000	0.27672	CTT	.		0.652	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		G	15752256	C	G	15752256	3	3	40	1	0	0	0	0	1	0	0	0	4196	681	24	4	33	4	CYP4F3	19	15752256	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	5307687	15752256	43376727	144	3705											
CPAMD8	27151	broad.mit.edu	37	chr19	17056401	17056401	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acgtgatccaccccgatgggGaccctcctgtcggcgtgatt	6	9	12	14	4	0	2	0	2	0	0	3	4	2	3	5	3	0	0	5	3	0	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:17056401G>T	ENST00000443236.1	-	22	2923	c.2892C>A	c.(2890-2892)gtC>gtA	p.V964V		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	917						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCCCGATGGGGACCCTCCTGT	0.567																																					p.V964V													.	CPAMD8-141	0			c.C2892A						.						97	105	103					19																	17056401		2029	4159	6188	SO:0001819	synonymous_variant	27151	exon22			GATGGGGACCCTC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2892C>A	19.37:g.17056401G>T		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	63	3	NM_015692	0	0	0	0	0	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	G	4.981	0.182145	0.09495	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.49	-0.451	0.12214	.	.	.	.	.	T	0.32645	0.0836	.	.	.	0.26785	N	0.969518	.	.	.	.	.	.	T	0.32534	-0.9903	4	.	.	.	.	8.8157	0.34993	0.3659:0.0:0.6341:0.0	.	.	.	.	Y	975	.	.	S	-	2	0	CPAMD8	16917401	1.000000	0.71417	0.005000	0.12908	0.047000	0.14425	1.514000	0.35834	0.057000	0.16193	0.591000	0.81541	TCC	.		0.567	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17056401	G	T	17056401	2	4	40	1	0	0	0	0	0	0	0	1	3801	1161	41	4		4	CPAMD8	19	17056401	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	1304145	17056401	42072582	145	3706											
ZNF506	440515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19905760	19905760	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccacattcctcacatttgtaGggtttctctccagtatgaat	9	15	6	11	0	2	1	1	1	1	0	5	1	4	1	3	1	0	3	3	1	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:19905760G>C	ENST00000540806.2	-	4	1024	c.936C>G	c.(934-936)ccC>ccG	p.P312P	ZNF506_ENST00000450683.2_Silent_p.P280P|CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000443905.2_Silent_p.P312P|CTC-559E9.6_ENST00000589657.1_RNA|ZNF506_ENST00000587461.1_Intron			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						CACATTTGTAGGGTTTCTCTC	0.373																																					p.P312P		.											.	ZNF506-68	0			c.C936G						.						55	59	57					19																	19905760		2197	4300	6497	SO:0001819	synonymous_variant	440515	exon4			TTTGTAGGGTTTC	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"Zinc fingers, C2H2-type", "-"	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.936C>G	19.37:g.19905760G>C		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	39	10	NM_001099269	3	0	1	4	0	B3KTH6	Silent	SNP	ENST00000540806.2	37	CCDS42531.1																																																																																			.		0.373	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		C	19905760	G	C	19905760	2	2	40	1	0	0	0	0	0	0	0	1	17984	987	35	4		4	ZNF506	19	19905760	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	2849359	19905760	39223223	146	3707											
LTBP4	8425	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41129532	41129532	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacgaatgtcagctcttcCgagaccaggtgtgcaagagt	10	9	13	9	2	2	2	1	0	1	2	3	5	3	3	2	2	2	2	2	2	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:41129532C>T	ENST00000308370.7	+	29	3778	c.3778C>T	c.(3778-3780)Cga>Tga	p.R1260*	LTBP4_ENST00000204005.9_Nonsense_Mutation_p.R1223*|LTBP4_ENST00000602240.1_3'UTR|LTBP4_ENST00000545697.1_Nonsense_Mutation_p.R628*|LTBP4_ENST00000243562.9_3'UTR|LTBP4_ENST00000396819.3_Nonsense_Mutation_p.R1193*	NM_001042544.1	NP_001036009.1	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4	1261	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|growth hormone secretion (GO:0030252)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|regulation of cell differentiation (GO:0045595)|regulation of cell growth (GO:0001558)|regulation of proteolysis (GO:0030162)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|integrin binding (GO:0005178)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TCAGCTCTTCCGAGACCAGGT	0.587																																					.													.	LTBP4-93	0			.						.						78	81	80					19																	41129532		2099	4233	6332	SO:0001587	stop_gained	8425	.			CTCTTCCGAGACC	Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006		"Latent transforming growth factor, beta binding proteins"	6717	protein-coding gene	gene with protein product		604710				9660815, 9271198	Standard	NM_003573		Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000308370.7:c.3778C>T	19.37:g.41129532C>T	ENSP00000311905:p.Arg1260*	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	45	12	.	0	0	27	30	3	O00508|O75412|O75413	Nonsense_Mutation	SNP	ENST00000308370.7	37		.	.	.	.	.	.	.	.	.	.	C	42	9.163582	0.99085	.	.	ENSG00000090006	ENST00000204005;ENST00000545697;ENST00000308370;ENST00000396819;ENST00000318809	.	.	.	3.84	2.72	0.32119	.	0.966303	0.08373	U	0.955762	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	6.3251	0.21239	0.1718:0.4914:0.3368:0.0	.	.	.	.	X	1223;628;1260;1193;21	.	ENSP00000204005:R1223X	R	+	1	2	LTBP4	45821372	0.156000	0.22821	1.000000	0.80357	0.911000	0.54048	0.335000	0.19806	1.972000	0.57404	0.313000	0.20887	CGA	.		0.587	LTBP4-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003573		T	41129532	C	T	41129532	4	4	40	1	0	0	0	0	0	1	0	0	9101	644	23	1	4183	1	LTBP4	19	41129532	Nonsense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	21223772	41129532	17999451	147	3708											
CYP2F1	1572	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	41627458	41627458	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcgactatgatgatgagCgtctgctcaccattatccgc	8	12	9	12	3	2	3	1	3	1	0	4	4	3	3	2	0	2	2	2	0	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:41627458C>T	ENST00000331105.2	+	5	652	c.580C>T	c.(580-582)Cgt>Tgt	p.R194C		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	194					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						TGATGATGAGCGTCTGCTCAC	0.562																																					p.R194C		.											.	CYP2F1-90	0			c.C580T						.						113	115	115					19																	41627458		2181	4299	6480	SO:0001583	missense	1572	exon5			GATGAGCGTCTGC	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"Cytochrome P450s"	2632	protein-coding gene	gene with protein product		124070	"cytochrome P450, subfamily IIF, polypeptide 1"	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.580C>T	19.37:g.41627458C>T	ENSP00000333534:p.Arg194Cys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	43	13	NM_000774	0	0	1	1	0	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	.	.	.	.	.	.	.	.	.	.	c	10.84	1.464169	0.26335	.	.	ENSG00000197446	ENST00000331105	T	0.69435	-0.4	2.87	2.87	0.33458	.	0.714608	0.13306	U	0.397870	T	0.79052	0.4381	M	0.79475	2.455	0.34749	D	0.731557	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.983	T	0.82147	-0.0601	10	0.72032	D	0.01	.	7.7914	0.29123	0.0:0.7393:0.2607:0.0	.	194;194	Q32MN5;P24903	.;CP2F1_HUMAN	C	194	ENSP00000333534:R194C	ENSP00000333534:R194C	R	+	1	0	CYP2F1	46319298	0.000000	0.05858	0.113000	0.21522	0.208000	0.24298	-0.348000	0.07740	1.461000	0.47929	0.064000	0.15345	CGT	.		0.562	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2			T	41627458	C	T	41627458	3	4	40	1	0	0	0	0	1	0	0	0	4177	768	27	1	594	1	CYP2F1	19	41627458	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	497926	41627458	17501525	148	3709											
PSG9	5678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	43772079	43772079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatactgtttctcttccaCtgtatgcaggcccatatata	11	15	5	10	0	1	0	0	0	1	0	3	0	2	0	2	1	2	3	2	1	7	8			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:43772079C>T	ENST00000270077.3	-	2	383	c.287G>A	c.(286-288)aGt>aAt	p.S96N	PSG9_ENST00000418820.2_Missense_Mutation_p.S96N|PSG9_ENST00000443718.3_Missense_Mutation_p.S96N|PSG9_ENST00000291752.5_Missense_Mutation_p.S96N|PSG9_ENST00000593948.1_Missense_Mutation_p.S96N|PSG9_ENST00000244293.7_Missense_Mutation_p.S96N|PSG9_ENST00000596730.1_Missense_Mutation_p.S96N	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	96	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				TTCTCTTCCACTGTATGCAGG	0.428																																					p.S96N		.											.	PSG9-92	0			c.G287A						.						250	239	243					19																	43772079		2203	4300	6503	SO:0001583	missense	5678	exon2			CTTCCACTGTATG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.287G>A	19.37:g.43772079C>T	ENSP00000270077:p.Ser96Asn	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	149	44	NM_002784	0	0	0	0	0	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	10.79|10.79	1.448341|1.448341	0.26074|0.26074	.|.	.|.	ENSG00000183668|ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293|ENST00000418820	T;T;T;T|.	0.69175|.	-0.38;-0.38;-0.38;-0.38|.	1.56|1.56	-1.3|-1.3	0.09259|0.09259	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.65249|0.65249	0.2673|0.2673	M|M	0.93507|0.93507	3.425|3.425	0.09310|0.09310	N|N	1|1	P;P;D;P;B;B|.	0.53885|.	0.729;0.904;0.963;0.872;0.056;0.184|.	P;D;D;P;B;B|.	0.67231|.	0.826;0.921;0.95;0.686;0.272;0.393|.	T|T	0.59873|0.59873	-0.7372|-0.7372	9|5	0.54805|.	T|.	0.06|.	.|.	7.098|7.098	0.25321|0.25321	0.0:0.4456:0.5544:0.0|0.0:0.4456:0.5544:0.0	.|.	96;45;96;96;96;96|.	E7EW65;Q15225;Q15227;G3XAA7;Q6LEU7;Q00887|.	.;.;.;.;.;PSG9_HUMAN|.	N|M	96;96;96;57;96|83	ENSP00000270077:S96N;ENSP00000291752:S96N;ENSP00000396753:S96N;ENSP00000244293:S96N|.	ENSP00000244293:S96N|.	S|V	-|-	2|1	0|0	PSG9|PSG9	48463919|48463919	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.052000|0.052000	0.14988|0.14988	-0.107000|-0.107000	0.10873|0.10873	-0.216000|-0.216000	0.10048|0.10048	-0.876000|-0.876000	0.02978|0.02978	AGT|GTG	.		0.428	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		T	43772079	C	T	43772079	3	4	40	1	0	0	0	0	1	0	0	0	12691	565	20	2	1013	2	PSG9	19	43772079	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	2144621	43772079	15356904	149	3710											
SFRS16	11129	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45561034	45561034	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agagaagaaggcttccatcgGttatacctacgaggacagca	14	7	11	9	2	0	2	0	0	0	2	2	5	1	3	2	3	3	3	2	3	5	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:45561034G>A	ENST00000221455.3	+	7	589	c.491G>A	c.(490-492)gGt>gAt	p.G164D	CLASRP_ENST00000544944.2_Missense_Mutation_p.G164D|CLASRP_ENST00000391953.4_Missense_Mutation_p.G102D	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	164					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						GCTTCCATCGGTTATACCTAC	0.617																																					p.G164D													.	CLASRP-154	0			c.G491A						.						132	111	118					19																	45561034		2203	4300	6503	SO:0001583	missense	11129	exon7			CCATCGGTTATAC	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.491G>A	19.37:g.45561034G>A	ENSP00000221455:p.Gly164Asp	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	106	28	NM_007056	0	0	16	29	13	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Missense_Mutation	SNP	ENST00000221455.3	37	CCDS12652.2	.	.	.	.	.	.	.	.	.	.	G	26.0	4.690578	0.88735	.	.	ENSG00000104859	ENST00000221455;ENST00000391952;ENST00000391953;ENST00000544944	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	4.7	4.7	0.59300	Splicing factor, suppressor of white apricot (1);	0.000000	0.36932	U	0.002335	T	0.61274	0.2334	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.997	T	0.66548	-0.5896	10	0.87932	D	0	-30.767	15.1769	0.72920	0.0:0.0:1.0:0.0	.	102;164;164	F8WAG9;F5H0Q6;Q8N2M8	.;.;CLASR_HUMAN	D	164;164;102;164	ENSP00000221455:G164D;ENSP00000375814:G164D;ENSP00000375815:G102D;ENSP00000438702:G164D	ENSP00000221455:G164D	G	+	2	0	CLASRP	50252874	1.000000	0.71417	0.996000	0.52242	0.916000	0.54674	9.208000	0.95075	2.434000	0.82447	0.563000	0.77884	GGT	.		0.617	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		A	45561034	G	A	45561034	3	1	40	1	0	0	0	0	1	0	0	0	14204	1261	44	2	513	2	SFRS16	19	45561034	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	1788955	45561034	13567949	150	3711											
DMWD	1762	broad.mit.edu	37	chr19	46289396	46289396	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgcgggccaggggggggTgcgggtagagcacgtcttca	5	6	22	8	3	2	1	1	0	1	1	2	1	2	1	1	7	3	2	1	7	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:46289396T>G	ENST00000270223.6	-	3	1403	c.1358A>C	c.(1357-1359)cAc>cCc	p.H453P	DMWD_ENST00000601370.1_5'Flank|AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000377735.3_Missense_Mutation_p.H453P	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	453										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		CAGGGGGGGGTGCGGGTAGAG	0.711																																					p.H453P													.	DMWD-90	0			c.A1358C						.						5	6	6					19																	46289396		2081	4094	6175	SO:0001583	missense	1762	exon3			GGGGGGTGCGGGT	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"WD repeat domain containing"	2936	protein-coding gene	gene with protein product		609857	"dystrophia myotonica-containing WD repeat motif"			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1358A>C	19.37:g.46289396T>G	ENSP00000270223:p.His453Pro	Somatic	66	12		WXS	Illumina HiSeq	Phase_I	96	28	NM_004943	0	0	1	1	0		Missense_Mutation	SNP	ENST00000270223.6	37	CCDS33054.1	.	.	.	.	.	.	.	.	.	.	T	11.77	1.738941	0.30774	.	.	ENSG00000185800	ENST00000377735;ENST00000270223	T;T	0.58506	0.33;0.33	4.12	2.02	0.26589	.	0.136335	0.49916	D	0.000126	T	0.42944	0.1225	L	0.42245	1.32	0.40057	D	0.975844	B;B;B	0.09022	0.0;0.002;0.001	B;B;B	0.09377	0.001;0.004;0.002	T	0.30238	-0.9985	10	0.39692	T	0.17	-34.1134	5.3843	0.16211	0.0:0.1001:0.1807:0.7191	.	138;453;453	Q8WUW6;G5E9A7;Q09019	.;.;DMWD_HUMAN	P	453	ENSP00000366964:H453P;ENSP00000270223:H453P	ENSP00000270223:H453P	H	-	2	0	DMWD	50981236	1.000000	0.71417	0.824000	0.32777	0.083000	0.17756	0.976000	0.29462	0.745000	0.32763	-0.527000	0.04329	CAC	.		0.711	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943		G	46289396	T	G	46289396	3	3	40	1	0	0	0	0	1	0	0	0	4604	1696	59	5	678	5	DMWD	19	46289396	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	728362	46289396	12839587	151	3712											
ZNF836	162962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52660313	52660313	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctaatgtgtgttttctcaAgttgggtgggtaatgacagc	8	14	12	7	0	1	1	1	1	1	0	2	1	1	1	1	2	1	3	1	2	3	5	rs186568049		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:52660313A>T	ENST00000322146.8	-	5	1144	c.623T>A	c.(622-624)cTt>cAt	p.L208H	ZNF836_ENST00000597252.1_Missense_Mutation_p.L208H|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	208					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)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TGTTTTCTCAAGTTGGGTGGG	0.373																																					p.L208H		.											.	ZNF836-46	0			c.T623A						.						66	64	65					19																	52660313		1911	4155	6066	SO:0001583	missense	162962	exon5			TTCTCAAGTTGGG	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.623T>A	19.37:g.52660313A>T	ENSP00000325038:p.Leu208His	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	177	48	NM_001102657	0	0	0	0	0		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	A	0.030	-1.337491	0.01287	.	.	ENSG00000196267	ENST00000322146;ENST00000396443	T	0.06371	3.31	1.8	-0.761	0.11038	.	.	.	.	.	T	0.02380	0.0073	N	0.08118	0	0.09310	N	1	P	0.50943	0.94	B	0.43783	0.431	T	0.13737	-1.0498	9	0.02654	T	1	.	2.5139	0.04663	0.2469:0.1649:0.0:0.5882	.	208	Q6ZNA1	ZN836_HUMAN	H	208;6	ENSP00000325038:L208H	ENSP00000325038:L208H	L	-	2	0	ZNF836	57352125	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.440000	0.21592	-0.496000	0.06650	-1.328000	0.01277	CTT	A|0.999;C|0.000		0.373	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		T	52660313	A	T	52660313	3	4	40	1	0	0	0	0	1	0	0	0	18219	72	3	5	2189	5	ZNF836	19	52660313	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	6370917	52660313	6468670	152	3713											
PTPRH	5794	broad.mit.edu	37	chr19	55697891	55697891	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcatggatgggcttcagggGcacccgggaccagtcatcta	8	8	13	12	1	4	0	3	0	1	0	4	2	4	2	2	5	0	2	2	5	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:55697891G>A	ENST00000376350.3	-	15	2606	c.2584C>T	c.(2584-2586)Ccc>Tcc	p.P862S	PTPRH_ENST00000263434.5_Missense_Mutation_p.P684S	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	862	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GGCTTCAGGGGCACCCGGGAC	0.587																																					p.P862S													.	PTPRH-138	0			c.C2584T						.						67	68	68					19																	55697891		2203	4300	6503	SO:0001583	missense	5794	exon15			TCAGGGGCACCCG		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2584C>T	19.37:g.55697891G>A	ENSP00000365528:p.Pro862Ser	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_002842	0	0	1	1	0	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.220909	0.39201	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	D;D	0.83075	-1.68;-1.68	5.25	3.06	0.35304	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.416142	0.17903	N	0.158107	T	0.67896	0.2942	N	0.16790	0.44	0.27804	N	0.942366	B;B	0.28419	0.211;0.211	B;B	0.29862	0.062;0.108	T	0.59101	-0.7517	10	0.41790	T	0.15	.	5.8507	0.18691	0.1711:0.0:0.6776:0.1513	.	684;862	C9JCH2;Q9HD43	.;PTPRH_HUMAN	S	862;684	ENSP00000365528:P862S;ENSP00000263434:P684S	ENSP00000263434:P684S	P	-	1	0	PTPRH	60389703	0.250000	0.23951	0.985000	0.45067	0.951000	0.60555	0.209000	0.17435	0.677000	0.31305	-0.156000	0.13503	CCC	.		0.587	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55697891	G	A	55697891	3	1	40	1	0	0	0	0	1	0	0	0	12835	1203	42	2	787	2	PTPRH	19	55697891	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	3037578	55697891	3431092	153	3714											
ZIM2	23619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57286732	57286732	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgccttcctggggatcctttCctagaggatcctttgattgt	5	16	10	10	0	0	2	0	1	0	1	4	4	4	4	5	3	1	0	5	3	1	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:57286732C>T	ENST00000391708.3	-	12	1450	c.908G>A	c.(907-909)gGa>gAa	p.G303E	ZIM2_ENST00000221722.5_Missense_Mutation_p.G303E|ZIM2_ENST00000599935.1_Missense_Mutation_p.G303E|AC006115.3_ENST00000597946.1_RNA|AC006115.3_ENST00000595954.1_RNA|ZIM2_ENST00000593711.1_Missense_Mutation_p.G303E|ZIM2_ENST00000601070.1_Missense_Mutation_p.G303E|AC006115.3_ENST00000594400.1_RNA	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		GGGATCCTTTCCTAGAGGATC	0.453																																					p.G303E		.											.	ZIM2-28	0			c.G908A						.						119	114	116					19																	57286732		2203	4300	6503	SO:0001583	missense	23619	exon11			TCCTTTCCTAGAG	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"Zinc fingers, C2H2-type"	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.908G>A	19.37:g.57286732C>T	ENSP00000375589:p.Gly303Glu	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	88	21	NM_015363	0	0	0	0	0	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720643	0.48728	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.04317	3.65;3.65	3.89	0.45	0.16624	.	.	.	.	.	T	0.03220	0.0094	N	0.24115	0.695	.	.	.	B	0.21606	0.058	B	0.20184	0.028	T	0.37911	-0.9685	8	0.49607	T	0.09	.	2.8917	0.05678	0.3745:0.3962:0.0:0.2293	.	303	Q9NZV7	ZIM2_HUMAN	E	303	ENSP00000375589:G303E;ENSP00000221722:G303E	ENSP00000221722:G303E	G	-	2	0	ZIM2	61978544	0.000000	0.05858	0.131000	0.22000	0.731000	0.41821	-0.337000	0.07852	0.176000	0.19873	0.655000	0.94253	GGA	.		0.453	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			T	57286732	C	T	57286732	3	4	40	1	0	0	0	0	1	0	0	0	17716	855	30	2	679	2	ZIM2	19	57286732	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1588841	57286732	1842251	154	3715											
ATRN	8455	broad.mit.edu;bcgsc.ca	37	chr20	3452154	3452154	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agcaatgccagcactgcgggGgccgcttcaggtgagtggcg	7	6	17	11	3	1	1	1	1	0	0	1	1	1	1	2	4	4	3	2	4	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr20:3452154G>C	ENST00000262919.5	+	1	468	c.400G>C	c.(400-402)Ggc>Cgc	p.G134R	ATRN_ENST00000446916.2_Missense_Mutation_p.G134R	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	134	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						GCACTGCGGGGGCCGCTTCAG	0.701																																					p.G134R													.	ATRN-154	0			c.G400C						.						3	4	4					20																	3452154		1855	3869	5724	SO:0001583	missense	8455	exon1			TGCGGGGGCCGCT	AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"mahogany protein"	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.400G>C	20.37:g.3452154G>C	ENSP00000262919:p.Gly134Arg	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	23	4	NM_139321	0	0	0	0	0	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	37	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	G	35	5.490406	0.96339	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.63913	-0.07;-0.07	5.32	5.32	0.75619	EGF-like, laminin (1);CUB (5);	0.113928	0.64402	N	0.000014	D	0.84374	0.5458	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.975	D	0.88025	0.2771	10	0.87932	D	0	-14.9415	18.1397	0.89636	0.0:0.0:1.0:0.0	.	134;134	O75882;O75882-2	ATRN_HUMAN;.	R	134;134;60	ENSP00000262919:G134R;ENSP00000416587:G134R	ENSP00000262919:G134R	G	+	1	0	ATRN	3400154	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.035000	0.93752	2.632000	0.89209	0.555000	0.69702	GGC	.		0.701	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321		C	3452154	G	C	3452154	3	2	40	1	0	0	0	0	1	0	0	0	1207	1232	43	4	402	4	ATRN	20	3452154	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		3452154	59573366	155	3716											
SSTR4	6754	broad.mit.edu	37	chr20	23016957	23016957	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgcctttctacgtggtgcaGctgctgaacctcttcgtgac	6	13	10	12	2	2	2	0	2	2	0	3	2	2	2	2	1	6	3	2	1	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr20:23016957G>T	ENST00000255008.3	+	1	901	c.837G>T	c.(835-837)caG>caT	p.Q279H	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	279					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					ACGTGGTGCAGCTGCTGAACC	0.572																																					p.Q279H	Esophageal Squamous(15;850 1104 16640)												.	SSTR4-522	0			c.G837T						.						199	205	203					20																	23016957		2203	4300	6503	SO:0001583	missense	6754	exon1			GGTGCAGCTGCTG		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.837G>T	20.37:g.23016957G>T	ENSP00000255008:p.Gln279His	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	67	3	NM_001052	0	0	0	0	0	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648929	0.47362	.	.	ENSG00000132671	ENST00000255008	T	0.37411	1.2	3.36	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000012	T	0.50480	0.1618	L	0.58810	1.83	0.44388	D	0.997296	D	0.76494	0.999	D	0.79108	0.992	T	0.51585	-0.8687	10	0.72032	D	0.01	.	7.6455	0.28318	0.1218:0.0:0.8782:0.0	.	279	P31391	SSR4_HUMAN	H	279	ENSP00000255008:Q279H	ENSP00000255008:Q279H	Q	+	3	2	SSTR4	22964957	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.821000	0.39041	1.694000	0.51137	0.655000	0.94253	CAG	.		0.572	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			T	23016957	G	T	23016957	3	4	40	1	0	0	0	0	1	0	0	0	15232	962	34	4	839	4	SSTR4	20	23016957	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	19564803	23016957	40008563	156	3717											
TIAM1	7074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	32639267	32639267	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ataaaactcgtgctctacatGttgactttctgcgtttccca	9	15	6	11	2	2	1	0	1	2	0	4	1	3	1	1	0	4	3	1	0	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr21:32639267G>A	ENST00000286827.3	-	5	493	c.22C>T	c.(22-24)Cat>Tat	p.H8Y	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.H8Y	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	8					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						TGCTCTACATGTTGACTTTCT	0.527																																					p.H8Y		.											.	TIAM1-724	0			c.C22T						.						54	56	55					21																	32639267		2203	4300	6503	SO:0001583	missense	7074	exon5			CTACATGTTGACT		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.22C>T	21.37:g.32639267G>A	ENSP00000286827:p.His8Tyr	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	24	7	NM_003253	0	0	0	0	0	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.358038	0.41801	.	.	ENSG00000156299	ENST00000286827;ENST00000541036;ENST00000455508	T;T	0.39056	1.1;1.1	5.08	2.64	0.31445	.	0.211502	0.47852	D	0.000203	T	0.23611	0.0571	N	0.08118	0	0.21147	N	0.999772	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.22521	-1.0214	10	0.87932	D	0	.	11.7355	0.51763	0.0:0.0:0.3141:0.6859	.	8;8;8	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	Y	8	ENSP00000286827:H8Y;ENSP00000441570:H8Y	ENSP00000286827:H8Y	H	-	1	0	TIAM1	31561138	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	5.772000	0.68889	0.251000	0.21505	0.460000	0.39030	CAT	.		0.527	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32639267	G	A	32639267	3	1	40	1	0	0	0	0	1	0	0	0	15922	1377	48	2	4853	2	TIAM1	21	32639267	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		32639267	15490628	157	3718											
ASMTL	8623	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	1540611	1540611	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgctggtttgttccctctcgGatggcaaactccaggtatgt	6	14	11	10	1	1	0	0	0	1	0	4	1	3	1	2	4	2	5	2	4	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:1540611G>C	ENST00000381317.3	-	9	1217	c.1185C>G	c.(1183-1185)atC>atG	p.I395M	ASMTL_ENST00000381333.4_Missense_Mutation_p.I379M|ASMTL_ENST00000534940.1_Missense_Mutation_p.I337M|ASMTL_ENST00000416733.2_Missense_Mutation_p.I319M	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	395	ASMT-like.					cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TTCCCTCTCGGATGGCAAACT	0.537																																					p.I395M		.											.	ASMTL-62	0			c.C1185G						.						267	279	275					X																	1540611		2010	4172	6182	SO:0001583	missense	8623	exon9			CTCTCGGATGGCA	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"Pseudoautosomal regions / PAR1"	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1185C>G	X.37:g.1540611G>C	ENSP00000370718:p.Ile395Met	Somatic	561	1		WXS	Illumina HiSeq	Phase_I	288	119	NM_004192	0	0	6	28	22	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	.	.	.	.	.	.	.	.	.	.	g	11.19	1.566957	0.28003	.	.	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	1.58	-3.16	0.05217	O-methyltransferase, family 2 (1);	0.083070	0.47093	U	0.000252	T	0.24275	0.0588	L	0.38175	1.15	0.09310	N	1	D;D;D	0.60575	0.979;0.988;0.979	P;P;P	0.55713	0.782;0.666;0.582	T	0.14643	-1.0465	10	0.87932	D	0	.	5.5218	0.16938	0.2398:0.184:0.5763:0.0	.	319;379;395	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	M	319;337;379;395	ENSP00000410578:I319M;ENSP00000446410:I337M;ENSP00000370734:I379M;ENSP00000370718:I395M	ENSP00000370718:I395M	I	-	3	3	ASMTL	1500611	0.986000	0.35501	0.006000	0.13384	0.132000	0.20833	-0.099000	0.11007	-0.451000	0.07097	0.100000	0.15512	ATC	.		0.537	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		C	1540611	G	C	1540611	3	2	40	1	0	0	0	0	1	0	0	0	1047	1164	41	4	700	4	ASMTL	23	1540611	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		1540611	153729949	158	3719											
PIR	8544	broad.mit.edu;bcgsc.ca	37	chrX	15403223	15403224	+	In_Frame_Ins	INS	-	-	TCA																															agaaatctcttcattggtgtINStcatcacaaatggacctagg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:15403223_15403224insTCA	ENST00000380421.3	-	10	1235_1236	c.775_776insTGA	c.(775-777)aac>aTGAac	p.258_259insM	PIR_ENST00000380420.5_In_Frame_Ins_p.258_259insM|FIGF_ENST00000297904.3_5'Flank	NM_001018109.2|NM_003662.3	NP_001018119.1|NP_003653.1	O00625	PIR_HUMAN	pirin (iron-binding nuclear protein)	258					monocyte differentiation (GO:0030224)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|quercetin 2,3-dioxygenase activity (GO:0008127)|transcription cofactor activity (GO:0003712)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9	Hepatocellular(33;0.183)					TTCATTGGTGTTCATCACAAAT	0.376																																					p.N259delinsMN	Ovarian(180;1587 2015 10555 34192 51653)												.	PIR-131	0			c.776_777insTGA						.																																			SO:0001652	inframe_insertion	8544	exon10			TTGGTGTTCATCA	Y07868	CCDS14167.1	Xp22.31	2008-02-05			ENSG00000087842	ENSG00000087842			30048	protein-coding gene	gene with protein product		300931				9079676	Standard	NM_003662		Approved		uc004cwv.3	O00625	OTTHUMG00000021176	ENST00000380421.3:c.773_775dupTGA	X.37:g.15403227_15403229dupTCA	ENSP00000369786:p.Met258_Met258dup	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	28	9	NM_001018109	0	0	0	0	0	Q5U0G0|Q6FHD2	In_Frame_Ins	INS	ENST00000380421.3	37	CCDS14167.1																																																																																			.		0.376	PIR-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055863.1	NM_003662		TCA	15403224	-	TCA	15403223	7	5	40	1	0	1	1	0	0	0	0	0	11970	1725	60	0	100	0	PIR	23	15403223	In_Frame_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	13862612	15403223	139867337	159	3720											
ACOT9	23597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	23723161	23723161	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaacaggtttctgaaacatGatgtcatctactgctaccac	12	12	6	11	0	4	2	2	2	2	0	4	2	4	2	1	1	5	2	1	1	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:23723161G>A	ENST00000336430.7	-	13	1160	c.1029C>T	c.(1027-1029)atC>atT	p.I343I	ACOT9_ENST00000379303.5_Silent_p.I352I|ACOT9_ENST00000379295.1_Silent_p.I283I	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	343					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)			breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						TCTGAAACATGATGTCATCTA	0.403																																					p.I352I		.											.	ACOT9-133	0			c.C1056T						.						120	109	113					X																	23723161		2203	4300	6503	SO:0001819	synonymous_variant	23597	exon14			AAACATGATGTCA	AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"Acyl CoA thioesterases"	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.1029C>T	X.37:g.23723161G>A		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	161	100	NM_001037171	0	0	18	33	15	B3KNC9|B7ZM94	Silent	SNP	ENST00000336430.7	37	CCDS35216.1																																																																																			.		0.403	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332		A	23723161	G	A	23723161	2	1	40	1	0	0	0	0	0	0	0	1	157	1280	45	2		2	ACOT9	23	23723161	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	8319938	23723161	131547399	160	3721											
AR	367	hgsc.bcm.edu	37	chrX	66765167	66765167	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgctgctgctgcagcagcAgcagcagcagcagcagcagc	9	6	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	0	0	0	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:66765167A>T	ENST00000374690.3	+	1	703	c.179A>T	c.(178-180)cAg>cTg	p.Q60L	AR_ENST00000504326.1_Missense_Mutation_p.Q60L|AR_ENST00000396044.3_Missense_Mutation_p.Q60L|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	60	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTgcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q60L		.											.	AR-661	0			c.A179T	GRCh37	CI994028	AR	I		.						6	9	8					X																	66765167		1971	3901	5872	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.179A>T	X.37:g.66765167A>T	ENSP00000363822:p.Gln60Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	77	7	NM_000044	0	0	4	4	0	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.27	1.588228	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.57436	0.4;0.4;0.4	.	.	.	.	1.241110	0.06210	N	0.684797	T	0.29288	0.0729	N	0.19112	0.55	0.09310	N	0.999999	P;P;.	0.36048	0.534;0.534;.	B;B;.	0.29862	0.08;0.108;.	T	0.11494	-1.0585	8	0.12103	T	0.63	.	.	.	.	.	60;60;58	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	60	ENSP00000363822:Q60L;ENSP00000421155:Q60L;ENSP00000379359:Q60L	ENSP00000363822:Q60L	Q	+	2	0	AR	66681892	0.997000	0.39634	0.860000	0.33809	0.513000	0.34164	1.220000	0.32491	0.000000	0.14550	0.000000	0.15137	CAG	.		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765167	A	T	66765167	3	4	40	1	0	0	0	0	1	0	0	0	836	188	7	5	181	5	AR	23	66765167	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	43042006	66765167	88505393	161	3722											
ZMAT1	84460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	101152941	101152941	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacatagtgagactgagcAataagtggagagctaaacat	16	7	10	8	0	0	3	0	2	0	2	0	5	0	3	1	1	3	2	1	1	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:101152941A>T	ENST00000372782.3	-	5	452	c.405T>A	c.(403-405)atT>atA	p.I135I	ZMAT1_ENST00000458570.1_5'UTR|ZMAT1_ENST00000540921.1_Silent_p.I135I	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	135						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GAGACTGAGCAATAAGTGGAG	0.403																																					p.I135I		.											.	ZMAT1-131	0			c.T405A						.						157	124	135					X																	101152941		2203	4300	6503	SO:0001819	synonymous_variant	84460	exon5			CTGAGCAATAAGT	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.405T>A	X.37:g.101152941A>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	76	36	NM_001011657	0	0	0	0	0	Q8NDS3|Q96JN6	Silent	SNP	ENST00000372782.3	37	CCDS35348.1																																																																																			.		0.403	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			T	101152941	A	T	101152941	2	4	40	1	0	0	0	0	0	0	0	1	17723	126	5	5		5	ZMAT1	23	101152941	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	34387774	101152941	54117619	162	3723											
PNCK	139728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	152937048	152937048	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtgcctagcatgttcccaGcctggattttggagagtcca	7	11	12	11	1	0	1	0	0	0	1	2	3	2	2	4	3	3	2	4	3	1	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:152937048G>C	ENST00000370150.1	-	6	672	c.494C>G	c.(493-495)gCt>gGt	p.A165G	PNCK_ENST00000370145.4_Missense_Mutation_p.A182G|PNCK_ENST00000447676.2_Missense_Mutation_p.A248G|PNCK_ENST00000340888.3_Missense_Mutation_p.A165G|PNCK_ENST00000370142.1_Missense_Mutation_p.A165G|PNCK_ENST00000393831.2_Missense_Mutation_p.A165G|PNCK_ENST00000475172.1_5'UTR			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CATGTTCCCAGCCTGGATTTT	0.602																																					p.A248G		.											.	PNCK-207	0			c.C743G						.						121	112	115					X																	152937048		2203	4300	6503	SO:0001583	missense	139728	exon6			TTCCCAGCCTGGA	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.494C>G	X.37:g.152937048G>C	ENSP00000359169:p.Ala165Gly	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	66	39	NM_001039582	0	0	0	1	1	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Missense_Mutation	SNP	ENST00000370150.1	37		.	.	.	.	.	.	.	.	.	.	g	7.308	0.614372	0.14129	.	.	ENSG00000130822	ENST00000340888;ENST00000370150;ENST00000393831;ENST00000370142;ENST00000370145;ENST00000447676;ENST00000439087;ENST00000422811	T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	4.91	3.95	0.45737	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.215813	0.29579	N	0.011742	T	0.32734	0.0839	N	0.01789	-0.72	0.28784	N	0.899677	B;B;B;B	0.28350	0.001;0.208;0.026;0.026	B;B;B;B	0.22152	0.01;0.038;0.022;0.022	T	0.31586	-0.9938	10	0.49607	T	0.09	-9.2523	10.6054	0.45392	0.0:0.0:0.689:0.311	.	192;248;182;165	B4DJG4;Q6P2M8-5;B4E1A6;Q6P2M8	.;.;.;KCC1B_HUMAN	G	165;165;165;165;182;248;165;165	ENSP00000340586:A165G;ENSP00000359169:A165G;ENSP00000377417:A165G;ENSP00000359161:A165G;ENSP00000359164:A182G;ENSP00000405950:A248G;ENSP00000415770:A165G;ENSP00000391772:A165G	ENSP00000340586:A165G	A	-	2	0	PNCK	152590242	0.291000	0.24352	0.998000	0.56505	0.864000	0.49448	3.237000	0.51344	2.005000	0.58758	0.529000	0.55759	GCT	.		0.602	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		C	152937048	G	C	152937048	3	2	40	1	0	0	0	0	1	0	0	0	12171	971	34	4	561	4	PNCK	23	152937048	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	51784107	152937048	2333512	163	3724											
SLC2A1	6513	ucsc.edu;bcgsc.ca	37	chr1	43394677	43394677	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctatgaggtgcagggtccGccggcctgctcgctccacca	5	7	13	16	3	0	1	0	1	0	0	3	1	2	1	6	3	2	3	6	3	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:43394677G>T	ENST00000426263.3	-	8	1178	c.1000C>A	c.(1000-1002)Cgg>Agg	p.R334R	SLC2A1_ENST00000475162.1_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	334					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	TGCAGGGTCCGCCGGCCTGCT	0.622																																					p.R334R													.	SLC2A1-94	0			c.C1000A						.						97	92	94					1																	43394677		2203	4300	6503	SO:0001819	synonymous_variant	6513	exon8			GGGTCCGCCGGCC	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"Solute carriers"	11005	protein-coding gene	gene with protein product		138140	"human T-cell leukemia virus (I and II) receptor"	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.1000C>A	1.37:g.43394677G>T		Somatic	31	0		WXS	Illumina HiSeq		41	4	NM_006516	0	0	19	19	0	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	37	CCDS477.1																																																																																			.		0.622	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516		T	43394677	G	T	43394677	2	4	41	1	0	0	0	0	0	0	0	1	14570	1086	38	4		4	SLC2A1	1	43394677	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		43394677	205855944	1	3725											
HIPK1	204851	broad.mit.edu	37	chr1	114483094	114483094	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actgaaaatagagccctctgGctgggatgtttcaggacaga	12	9	12	8	0	2	3	1	1	1	2	2	5	2	5	1	3	1	2	1	3	3	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:114483094G>T	ENST00000369558.1	+	2	321	c.89G>T	c.(88-90)gGc>gTc	p.G30V	HIPK1_ENST00000369561.4_Missense_Mutation_p.G30V|HIPK1_ENST00000369555.2_Missense_Mutation_p.G30V|HIPK1_ENST00000369559.4_Missense_Mutation_p.G30V|HIPK1_ENST00000426820.2_Missense_Mutation_p.G30V|HIPK1_ENST00000369554.2_Missense_Mutation_p.G30V			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	30					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGCCCTCTGGCTGGGATGTT	0.507																																					p.G30V													.	HIPK1-361	0			c.G89T						.						208	227	220					1																	114483094		2203	4300	6503	SO:0001583	missense	204851	exon2			CCTCTGGCTGGGA	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.89G>T	1.37:g.114483094G>T	ENSP00000358571:p.Gly30Val	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	93	4	NM_152696	0	0	4	4	0	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.364752	0.24684	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000514621;ENST00000503968	T;T;T;T;T;T;T;T;T	0.46063	0.89;0.9;0.93;0.88;0.88;0.93;0.89;1.0;1.0	4.92	4.92	0.64577	.	0.171901	0.39407	N	0.001364	T	0.16769	0.0403	N	0.24115	0.695	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.03739	-1.1008	10	0.36615	T	0.2	.	14.0344	0.64636	0.0:0.0:0.8392:0.1608	.	30;30	Q86Z02;Q86Z02-2	HIPK1_HUMAN;.	V	101;30;30;30;30;30;30;30;30	ENSP00000407442:G101V;ENSP00000358572:G30V;ENSP00000409673:G30V;ENSP00000358567:G30V;ENSP00000358568:G30V;ENSP00000358571:G30V;ENSP00000358574:G30V;ENSP00000422322:G30V;ENSP00000426695:G30V	ENSP00000358567:G30V	G	+	2	0	HIPK1	114284617	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.683000	0.37638	2.271000	0.75665	0.650000	0.86243	GGC	.		0.507	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		T	114483094	G	T	114483094	3	4	41	1	0	0	0	0	1	0	0	0	7137	1203	42	4	91	4	HIPK1	1	114483094	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	71088417	114483094	134767527	2	3726											
DENND4B	9909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153916546	153916546	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacacaccccagctcaacgAgggggggcttgtcacggccc	8	4	13	16	2	2	0	2	0	0	0	2	1	2	0	3	4	2	3	3	4	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:153916546A>G	ENST00000361217.4	-	2	723	c.305T>C	c.(304-306)cTc>cCc	p.L102P		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	102	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGCTCAACGAGGGGGGGCTT	0.632																																					p.L102P		.											.	DENND4B-69	0			c.T305C						.						28	32	31					1																	153916546		1905	4105	6010	SO:0001583	missense	9909	exon2			TCAACGAGGGGGG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.305T>C	1.37:g.153916546A>G	ENSP00000354597:p.Leu102Pro	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	72	17	NM_014856	0	0	0	0	0	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314898	0.81358	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.29655	1.56;1.56	4.7	4.7	0.59300	MABP domain (1);	.	.	.	.	T	0.34164	0.0888	L	0.52126	1.63	0.80722	D	1	D	0.64830	0.994	P	0.59288	0.855	T	0.19451	-1.0305	9	0.87932	D	0	-8.3452	13.2712	0.60161	1.0:0.0:0.0:0.0	.	102	O75064	DEN4B_HUMAN	P	102;113	ENSP00000354597:L102P;ENSP00000357635:L113P	ENSP00000354597:L102P	L	-	2	0	DENND4B	152183170	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.903000	0.92573	1.964000	0.57103	0.379000	0.24179	CTC	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		G	153916546	A	G	153916546	3	3	41	1	0	0	0	0	1	0	0	0	4445	304	11	3	4293	3	DENND4B	1	153916546	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	39433452	153916546	95334075	3	3727											
THBS3	7059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155175049	155175049	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgcccatcagccaggccCgcttgctgtaggttcacggc	5	8	13	15	3	2	0	2	0	0	0	2	0	2	0	3	3	3	4	3	3	1	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:155175049C>T	ENST00000368378.3	-	3	365	c.345G>A	c.(343-345)gcG>gcA	p.A115A	RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000430312.1_RNA|THBS3_ENST00000457183.2_Intron|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000486260.1_5'UTR|THBS3_ENST00000541990.1_5'UTR	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	115	Laminin G-like.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.A115A(1)		breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CAGCCAGGCCCGCTTGCTGTA	0.627																																					p.A115A		.											.	THBS3-222	1	Substitution - coding silent(1)	lung(1)	c.G345A						.						100	82	88					1																	155175049		2203	4300	6503	SO:0001819	synonymous_variant	7059	exon3			CAGGCCCGCTTGC	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.345G>A	1.37:g.155175049C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	13	NM_007112	0	0	10	15	5	B1AVR8|B4DQ20|Q8WV34	Silent	SNP	ENST00000368378.3	37	CCDS1099.1																																																																																			.		0.627	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		T	155175049	C	T	155175049	2	4	41	1	0	0	0	0	0	0	0	1	15887	639	23	1		1	THBS3	1	155175049	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	1258503	155175049	94075572	4	3728											
CADM3	57863	broad.mit.edu	37	chr1	159166790	159166790	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagtgacagtggcacctacGgctgcacagccaccagcaac	12	4	11	14	1	0	2	0	1	0	1	0	2	0	2	3	2	5	4	3	2	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:159166790G>T	ENST00000368125.4	+	7	1049	c.892G>T	c.(892-894)Ggc>Tgc	p.G298C	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000497636.1_3'UTR|CADM3_ENST00000368124.4_Missense_Mutation_p.G332C	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	298	Ig-like C2-type 2.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					TGGCACCTACGGCTGCACAGC	0.542																																					p.G332C													.	CADM3-92	0			c.G994T						.						124	104	110					1																	159166790		2203	4300	6503	SO:0001583	missense	57863	exon8			ACCTACGGCTGCA	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.892G>T	1.37:g.159166790G>T	ENSP00000357107:p.Gly298Cys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	107	4	NM_021189	0	0	1	1	0	Q8IZQ9|Q9NVJ5|Q9UJP1	Missense_Mutation	SNP	ENST00000368125.4	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220537	0.58560	.	.	ENSG00000162706	ENST00000368124;ENST00000368125	T;T	0.12361	2.69;2.69	5.07	4.12	0.48240	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.542570	0.19235	N	0.119301	T	0.10208	0.0250	N	0.24115	0.695	0.34409	D	0.696165	P;D;D	0.69078	0.943;0.989;0.997	P;D;P	0.63488	0.861;0.915;0.826	T	0.02991	-1.1085	10	0.52906	T	0.07	.	6.4405	0.21847	0.099:0.1987:0.7022:0.0	.	252;298;332	Q8N126-3;Q8N126;Q8N126-2	.;CADM3_HUMAN;.	C	332;298	ENSP00000357106:G332C;ENSP00000357107:G298C	ENSP00000357106:G332C	G	+	1	0	CADM3	157433414	0.003000	0.15002	0.995000	0.50966	0.951000	0.60555	0.144000	0.16135	2.629000	0.89072	0.591000	0.81541	GGC	.		0.542	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		T	159166790	G	T	159166790	3	4	41	1	0	0	0	0	1	0	0	0	2574	1116	39	4	1024	4	CADM3	1	159166790	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	3991741	159166790	90083831	5	3729											
C1orf112	55732	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169798424	169798424	+	Frame_Shift_Del	DEL	T	T	-																															gatatctctactcaaagccgTtttctacagttttgagcagt																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:169798424delT	ENST00000286031.6	+	13	1848	c.1148delT	c.(1147-1149)gttfs	p.V383fs	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000413811.2_Frame_Shift_Del_p.F311fs|C1orf112_ENST00000359326.4_Frame_Shift_Del_p.V383fs	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	383										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CTCAAAGCCGTTTTCTACAGT	0.368																																					p.V383fs		.											.	C1orf112-90	0			c.1148delT						.						133	130	131					1																	169798424		2203	4300	6503	SO:0001589	frameshift_variant	55732	exon13			.	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1148delT	1.37:g.169798424delT	ENSP00000286031:p.Val383fs	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	111	29	NM_018186	0	0	0	0	0	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Frame_Shift_Del	DEL	ENST00000286031.6	37	CCDS1285.1																																																																																			.		0.368	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		-	169798424	T	-	169798424	7	5	41	1	0	1	0	1	0	0	0	0	1991	1725	60	0	1190	0	C1orf112	1	169798424	Frame_Shift_Del	DEL	T	TCGA-B1-A657-01A-11D-A31X-10	10631634	169798424	79452197	6	3730											
C1orf14	81626	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	182922005	182922005	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcaggggctcctccgcCgccgccgccgccgcctctcc	2	4	13	22	6	1	0	0	0	1	0	4	0	3	0	9	3	1	3	9	3	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:182922005C>G	ENST00000367547.3	-	1	500	c.264G>C	c.(262-264)gcG>gcC	p.A88A	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_5'Flank	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	160										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						GCTCCTccgccgccgccgccg	0.746																																					p.A88A		.											.	SHCBP1L-91	0			c.G264C						.						5	6	6					1																	182922005		2140	4210	6350	SO:0001819	synonymous_variant	81626	exon1			CTCCGCCGCCGCC	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.264G>C	1.37:g.182922005C>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	43	18	NM_030933	0	0	0	0	0	Q4G195|Q9BZQ3|Q9H2B6	Silent	SNP	ENST00000367547.3	37	CCDS30955.1																																																																																			.		0.746	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		G	182922005	C	G	182922005	2	3	41	1	0	0	0	0	0	0	0	1	2006	639	23	4		4	C1orf14	1	182922005	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	13123581	182922005	66328616	7	3731											
F13B	2165	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	197020002	197020002	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaggagatgtgcacattccTttagattctgcaaaaataag	14	11	10	6	0	1	2	0	0	1	2	2	4	2	3	1	2	2	2	1	2	4	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:197020002T>C	ENST00000367412.1	-	10	1606	c.1563A>G	c.(1561-1563)aaA>aaG	p.K521K	F13B_ENST00000490002.1_5'Flank	NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	521					blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						TGCACATTCCTTTAGATTCTG	0.348																																					p.K521K		.											.	F13B-92	0			c.A1563G						.						85	85	85					1																	197020002		2203	4300	6503	SO:0001819	synonymous_variant	2165	exon10			CATTCCTTTAGAT	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.1563A>G	1.37:g.197020002T>C		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	68	27	NM_001994	0	0	0	0	0	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	37	CCDS1388.1																																																																																			.		0.348	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		C	197020002	T	C	197020002	2	2	41	1	0	0	0	0	0	0	0	1	5354	1606	56	3		3	F13B	1	197020002	Silent	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	14097997	197020002	52230619	8	3732											
PPP1R15B	84919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204379052	204379052	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaattctggcagcagtctgAattgttgctgtaaagttctg	10	14	10	7	0	3	1	0	1	3	0	3	1	3	1	0	1	2	6	0	1	4	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:204379052A>G	ENST00000367188.4	-	1	1867	c.1488T>C	c.(1486-1488)atT>atC	p.I496I	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	496					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			CAGCAGTCTGAATTGTTGCTG	0.458																																					p.I496I		.											.	PPP1R15B-652	0			c.T1488C						.						73	78	76					1																	204379052		2203	4300	6503	SO:0001819	synonymous_variant	84919	exon1			AGTCTGAATTGTT	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1488T>C	1.37:g.204379052A>G		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	72	23	NM_032833	0	0	7	16	9	Q53GQ4|Q658M2|Q6P156|Q96SN1	Silent	SNP	ENST00000367188.4	37	CCDS1445.1																																																																																			.		0.458	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		G	204379052	A	G	204379052	2	3	41	1	0	0	0	0	0	0	0	1	12393	242	9	3		3	PPP1R15B	1	204379052	Silent	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	7359050	204379052	44871569	9	3733											
PARP1	142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	226570817	226570817	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccacggaggcgctggttTctggggggaatatacggtcc	6	8	16	11	4	1	0	0	0	1	0	2	2	2	2	3	7	1	2	3	7	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:226570817T>A	ENST00000366794.5	-	8	1222	c.1079A>T	c.(1078-1080)gAa>gTa	p.E360V		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	360					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		GGCGCTGGTTTCTGGGGGGAA	0.507								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.E360V		.											.	PARP1-727	0			c.A1079T						.						111	139	129					1																	226570817		2203	4300	6503	SO:0001583	missense	142	exon8			CTGGTTTCTGGGG	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"Poly (ADP-ribose) polymerases"	270	protein-coding gene	gene with protein product		173870	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)", "poly (ADP-ribose) polymerase family, member 1"	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.1079A>T	1.37:g.226570817T>A	ENSP00000355759:p.Glu360Val	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	96	40	NM_001618	0	0	7	14	7	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.525131	0.27299	.	.	ENSG00000143799	ENST00000366794	T	0.09723	2.95	5.26	5.26	0.73747	.	0.049169	0.85682	D	0.000000	T	0.05731	0.0150	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.38090	-0.9677	10	0.32370	T	0.25	.	9.4103	0.38487	0.0:0.0804:0.0:0.9196	.	360	P09874	PARP1_HUMAN	V	360	ENSP00000355759:E360V	ENSP00000355759:E360V	E	-	2	0	PARP1	224637440	0.994000	0.37717	0.177000	0.23020	0.267000	0.26476	3.623000	0.54224	1.977000	0.57605	0.454000	0.30748	GAA	.		0.507	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		A	226570817	T	A	226570817	3	1	41	1	0	0	0	0	1	0	0	0	11480	1783	62	5	2029	5	PARP1	1	226570817	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	22191765	226570817	22679804	10	3734											
C1orf96	126731	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	229461075	229461076	+	Frame_Shift_Del	DEL	AG	AG	-																															ctgttcttctccacatccacAgagtgagctcgctgcctttg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:229461075_229461076delAG	ENST00000366687.1	-	3	770_771	c.719_720delCT	c.(718-720)tctfs	p.S240fs	CCSAP_ENST00000366686.1_Frame_Shift_Del_p.S126fs|RP4-803J11.2_ENST00000418348.1_RNA|CCSAP_ENST00000284617.2_Frame_Shift_Del_p.S240fs|CCSAP_ENST00000483092.1_5'UTR			Q6IQ19	CCSAP_HUMAN	centriole, cilia and spindle-associated protein	240					multicellular organismal development (GO:0007275)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of embryonic development (GO:0045995)	axon (GO:0030424)|axoneme (GO:0005930)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cilium (GO:0005929)|spindle (GO:0005819)											CCACATCCACAGAGTGAGCTCG	0.441																																					p.240_240del		.											.	.	0			c.719_720del						.																																			SO:0001589	frameshift_variant	126731	exon4			.	BC071609	CCDS1577.1	1q42.13	2012-06-19	2012-06-19	2012-06-19	ENSG00000154429	ENSG00000154429			29578	protein-coding gene	gene with protein product	"centriole and spindle-associated protein"		"chromosome 1 open reading frame 96"	C1orf96		22493317	Standard	NM_145257		Approved	FLJ41471, CSAP	uc001htl.4	Q6IQ19	OTTHUMG00000037663	ENST00000366687.1:c.719_720delCT	1.37:g.229461077_229461078delAG	ENSP00000355648:p.Ser240fs	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	101	28	NM_145257	0	0	0	0	0	A8K5X2|Q6P9G2|Q6ZW85|Q8IXU1|Q96BM2	Frame_Shift_Del	DEL	ENST00000366687.1	37	CCDS1577.1																																																																																			.		0.441	CCSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091839.1	NM_145257		-	229461076	AG	-	229461075	7	5	41	1	0	1	0	1	0	0	0	0	2079	175	7	0	96	0	C1orf96	1	229461075	Frame_Shift_Del	DEL	AG	TCGA-B1-A657-01A-11D-A31X-10	2890258	229461075	19789546	11	3735											
ARID4B	51742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	235345203	235345203	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attactgccactacttggaaAttctgcttttctgtcattga	9	17	6	9	0	3	1	1	1	2	0	3	2	3	2	1	1	4	1	1	1	3	7			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:235345203A>T	ENST00000264183.3	-	20	3528	c.3031T>A	c.(3031-3033)Ttt>Att	p.F1011I	ARID4B_ENST00000366603.2_Missense_Mutation_p.F1011I|ARID4B_ENST00000494543.1_5'Flank|ARID4B_ENST00000349213.3_Missense_Mutation_p.F925I	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	1011					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			CTACTTGGAAATTCTGCTTTT	0.438																																					p.F1011I		.											.	ARID4B-228	0			c.T3031A						.						116	121	119					1																	235345203		2203	4300	6503	SO:0001583	missense	51742	exon20			TTGGAAATTCTGC	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"-"	15550	protein-coding gene	gene with protein product		609696	"retinoblastoma binding protein 1-like 1", "AT rich interactive domain 4B (RBP1- like)"	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.3031T>A	1.37:g.235345203A>T	ENSP00000264183:p.Phe1011Ile	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	77	24	NM_016374	0	0	3	12	9	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.17|18.17	3.563590|3.563590	0.65651|0.65651	.|.	.|.	ENSG00000054267|ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183|ENST00000444620	T;T;T|.	0.23552|.	1.9;1.95;1.95|.	5.18|5.18	4.03|4.03	0.46877|0.46877	.|.	0.359358|.	0.32785|.	N|.	0.005655|.	T|T	0.47303|0.47303	0.1438|0.1438	N|N	0.19112|0.19112	0.55|0.55	0.53688|0.53688	D|D	0.999971|0.999971	D;D;D;D|.	0.67145|.	0.996;0.992;0.996;0.987|.	D;D;D;D|.	0.77557|.	0.99;0.974;0.99;0.942|.	T|T	0.33085|0.33085	-0.9882|-0.9882	10|5	0.25751|.	T|.	0.34|.	-11.9576|-11.9576	12.1739|12.1739	0.54173|0.54173	0.8568:0.1432:0.0:0.0|0.8568:0.1432:0.0:0.0	.|.	692;1011;925;1011|.	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39|.	.;.;.;ARI4B_HUMAN|.	I|K	1011;925;1011;1011|410	ENSP00000264184:F925I;ENSP00000355562:F1011I;ENSP00000264183:F1011I|.	ENSP00000264183:F1011I|.	F|N	-|-	1|3	0|2	ARID4B|ARID4B	233411826|233411826	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.991000|0.991000	0.79684|0.79684	5.361000|5.361000	0.66092|0.66092	0.956000|0.956000	0.37904|0.37904	0.477000|0.477000	0.44152|0.44152	TTT|AAT	.		0.438	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		T	235345203	A	T	235345203	3	4	41	1	0	0	0	0	1	0	0	0	920	101	4	5	927	5	ARID4B	1	235345203	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	5884128	235345203	13905418	12	3736											
FMN2	56776	hgsc.bcm.edu	37	chr1	240371139	240371139	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcccggagcgggcataccCcctcctccccctcttcccgg	3	8	8	22	3	1	0	0	0	1	0	5	1	5	1	7	3	2	1	7	3	1	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:240371139C>T	ENST00000319653.9	+	5	3257	c.3027C>T	c.(3025-3027)ccC>ccT	p.P1009P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1009	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCCCCTCCTCCCC	0.731																																					p.P1009P		.											.	FMN2-145	0			c.C3027T						.																																			SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3027C>T	1.37:g.240371139C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	81	5	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371139	C	T	240371139	2	4	41	1	0	0	0	0	0	0	0	1	5969	610	22	2		2	FMN2	1	240371139	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	5025936	240371139	8879482	13	3737											
ARID5A	10865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97215160	97215160	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcatgaaggagcgacacacgCccatcgagagggtgccccat	11	5	12	13	3	1	2	1	1	0	1	2	5	1	3	3	2	2	0	3	2	1	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:97215160C>A	ENST00000357485.3	+	3	301	c.223C>A	c.(223-225)Ccc>Acc	p.P75T	ARID5A_ENST00000454558.2_Missense_Mutation_p.P7T	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	75	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						GCGACACACGCCCATCGAGAG	0.697																																					p.P75T		.											.	ARID5A-226	0			c.C223A						.						97	90	92					2																	97215160		2203	4300	6503	SO:0001583	missense	10865	exon3			CACACGCCCATCG	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"-"	17361	protein-coding gene	gene with protein product	"modulator recognition factor 1"	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.223C>A	2.37:g.97215160C>A	ENSP00000350078:p.Pro75Thr	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	127	72	NM_212481	0	0	4	5	1	Q6NX37	Missense_Mutation	SNP	ENST00000357485.3	37	CCDS33251.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586158	0.86851	.	.	ENSG00000196843	ENST00000357485;ENST00000359765;ENST00000454558	T;T	0.64085	-0.08;-0.08	5.07	5.07	0.68467	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.64402	D	0.000002	T	0.77274	0.4106	M	0.75777	2.31	0.51233	D	0.999918	D	0.58970	0.984	D	0.69307	0.963	T	0.79401	-0.1819	10	0.72032	D	0.01	-21.3112	13.8159	0.63292	0.0:1.0:0.0:0.0	.	75	Q03989	ARI5A_HUMAN	T	75;75;7	ENSP00000350078:P75T;ENSP00000400785:P7T	ENSP00000350078:P75T	P	+	1	0	ARID5A	96578887	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.160000	0.58164	2.653000	0.90120	0.561000	0.74099	CCC	.		0.697	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481		A	97215160	C	A	97215160	3	1	41	1	0	0	0	0	1	0	0	0	921	739	26	4	233	4	ARID5A	2	97215160	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		97215160	145984213	14	3738											
IL1R2	7850	broad.mit.edu	37	chr2	102638648	102638649	+	Splice_Site	INS	-	-	A																															tttccttacatctttctcagINSaaaaaaaagaagagaccatt																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:102638648_102638649insA	ENST00000332549.3	+	6	917_918		c.e6-1		IL1R2_ENST00000441002.1_Splice_Site|IL1R2_ENST00000393414.2_Splice_Site	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II						cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						ATCTTTCTCAGAAAAAAAAGAA	0.441																																					.	Pancreas(106;189 1628 2302 5133 12295)												.	IL1R2-522	0			c.689-1->A						.																																			SO:0001630	splice_region_variant	7850	exon6			TTCTCAGAAAAAA	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.689-1->A	2.37:g.102638656_102638656dupA		Somatic	262	0		WXS	Illumina HiSeq	Phase_I	355	8	NM_004633	0	0	0	0	0	D3DVJ5|Q6LCE6|Q9UE68	Splice_Site	INS	ENST00000332549.3	37	CCDS2054.1																																																																																			.		0.441	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	Intron	A	102638649	-	A	102638648	8	5	41	1	0	1	1	0	0	0	1	0	7680	956	33	0	706	0	IL1R2	2	102638648	Splice_Site	INS	-	TCGA-B1-A657-01A-11D-A31X-10	5423488	102638648	140560725	15	3739											
KBTBD10	10324	broad.mit.edu;bcgsc.ca	37	chr2	170382094	170382096	+	Splice_Site	DEL	GGT	GGT	-																															actttttttttcctccatcaGgtatgaagatgataaaaaag																								rs112795676		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	GGT	GGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:170382094_170382096delGGT	ENST00000284669.1	+	6	1786_1788	c.1709_1711delGGT	c.(1708-1713)aggtat>aat	p.570_571RY>N	RP11-724O16.1_ENST00000513963.1_Splice_Site_p.508_509RY>N|BBS5_ENST00000554017.1_Splice_Site_p.508_509RY>N	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	570					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)											TCCTCCATCAGGTATGAAGATGA	0.379																																					p.570_571del													.	.	0			c.1710_1711del						.																																			SO:0001630	splice_region_variant	10324	exon6			CCATCAGGTATGA	AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1710-1GGT>-	2.37:g.170382094_170382096delGGT		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	68	8	NM_006063	0	0	0	0	0	Q53R42	Frame_Shift_Del	DEL	ENST00000284669.1	37	CCDS2234.1																																																																																			.		0.379	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063	In_Frame_Del	-	170382096	GGT	-	170382094	8	5	41	1	0	1	0	1	0	0	1	0	8011	1014	35	0	1731	0	KBTBD10	2	170382094	Splice_Site	DEL	GGT	TCGA-B1-A657-01A-11D-A31X-10	67743446	170382094	72817279	16	3740	39	2									
KBTBD10	10324	broad.mit.edu;bcgsc.ca	37	chr2	170382098	170382107	+	Frame_Shift_Del	DEL	TGAAGATGAT	TGAAGATGAT	-																															tttttttcctccatcaggtaTgaagatgataaaaaagaatg																								rs144510735		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	TGAAGATGAT	TGAAGATGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:170382098_170382107delTGAAGATGAT	ENST00000284669.1	+	6	1790_1799	c.1713_1722delTGAAGATGAT	c.(1711-1722)tatgaagatgatfs	p.YEDD571fs	RP11-724O16.1_ENST00000513963.1_Frame_Shift_Del_p.YEDD509fs|BBS5_ENST00000554017.1_Frame_Shift_Del_p.YEDD509fs	NM_006063.2	NP_006054.2	O60662	KLH41_HUMAN	kelch-like family member 41	571					myofibril assembly (GO:0030239)|protein ubiquitination (GO:0016567)|regulation of lateral pseudopodium assembly (GO:0031275)|regulation of myoblast differentiation (GO:0045661)|regulation of myoblast proliferation (GO:2000291)|regulation of skeletal muscle cell differentiation (GO:2001014)|skeletal muscle cell differentiation (GO:0035914)|striated muscle contraction (GO:0006941)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|M band (GO:0031430)|pseudopodium (GO:0031143)											CCATCAGGTATGAAGATGATAAAAAAGAAT	0.367																																					p.571_574del													.	.	0			c.1713_1722del						.																																			SO:0001589	frameshift_variant	10324	exon6			CAGGTATGAAGAT	AF056929	CCDS2234.1	2q31.1	2013-02-22	2013-02-22	2013-01-08	ENSG00000239474	ENSG00000239474		"Kelch-like", "BTB/POZ domain containing"	16905	protein-coding gene	gene with protein product	"sarcomeric muscle protein"	607701	"kelch repeat and BTB (POZ) domain containing 10", "kelch-like 41 (Drosophila)"	KBTBD10		9655184	Standard	NM_006063		Approved	SARCOSIN, Krp1	uc002ueu.1	O60662	OTTHUMG00000132205	ENST00000284669.1:c.1713_1722delTGAAGATGAT	2.37:g.170382098_170382107delTGAAGATGAT	ENSP00000284669:p.Tyr571fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	68	8	NM_006063	0	0	0	0	0	Q53R42	Frame_Shift_Del	DEL	ENST00000284669.1	37	CCDS2234.1																																																																																			.		0.367	KLHL41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255263.1	NM_006063		-	170382107	TGAAGATGAT	-	170382098	7	5	41	1	0	1	0	1	0	0	0	0	8011	1471	51	0	1735	0	KBTBD10	2	170382098	Frame_Shift_Del	DEL	TGAAGATGAT	TCGA-B1-A657-01A-11D-A31X-10	4	170382098	72817275	17	3741	39	2									
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179431535	179431535	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactcttagacgcaaatctgTaatgcggcgtttattacatt	11	14	7	9	3	2	1	0	0	2	1	2	1	2	1	0	1	2	3	0	1	5	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:179431535T>C	ENST00000591111.1	-	276	74625	c.74401A>G	c.(74401-74403)Aca>Gca	p.T24801A	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T17569A|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T17502A|TTN_ENST00000460472.2_Missense_Mutation_p.T17377A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T26442A|TTN_ENST00000342992.6_Missense_Mutation_p.T23874A			Q8WZ42	TITIN_HUMAN	titin	24801	Fibronectin type-III 80. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CGCAAATCTGTAATGCGGCGT	0.428																																					p.T26442A		.											.	TTN-636	0			c.A79324G						.						71	70	70					2																	179431535		1854	4108	5962	SO:0001583	missense	7273	exon326			AATCTGTAATGCG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74401A>G	2.37:g.179431535T>C	ENSP00000465570:p.Thr24801Ala	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	60	42	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.10	1.835271	0.32421	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.75	4.57	0.56435	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56543	0.1992	L	0.41415	1.275	0.58432	D	0.999992	D;D;D;D	0.56746	0.977;0.977;0.977;0.958	P;P;P;P	0.49192	0.602;0.602;0.602;0.506	T	0.60073	-0.7334	9	0.87932	D	0	.	13.2067	0.59800	0.0:0.0:0.1326:0.8674	.	17377;17502;17569;24801	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	23874;17377;17569;17502;17375	ENSP00000343764:T23874A;ENSP00000434586:T17377A;ENSP00000340554:T17569A;ENSP00000352154:T17502A	ENSP00000340554:T17569A	T	-	1	0	TTN	179139781	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	0.965000	0.38133	0.459000	0.35465	ACA	.		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179431535	T	C	179431535	3	2	41	1	0	0	0	0	1	0	0	0	16768	1638	57	3	28803	3	TTN	2	179431535	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	9049437	179431535	63767838	18	3742											
PPARG	5468	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	12447397	12447397	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	atagccatcaggtttgggcgGatgccacaggccgagaagga	11	6	15	9	2	1	1	1	0	0	1	1	4	1	3	3	5	2	1	3	5	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:12447397G>C	ENST00000287820.6	+	5	757	c.636G>C	c.(634-636)cgG>cgC	p.R212R	PPARG_ENST00000397015.2_Silent_p.R184R|PPARG_ENST00000539812.1_Silent_p.R182R|PPARG_ENST00000397026.2_Silent_p.R190R|PPARG_ENST00000397012.2_Silent_p.R184R|PPARG_ENST00000397000.1_Silent_p.R184R|PPARG_ENST00000309576.6_Silent_p.R184R|PPARG_ENST00000397010.2_Silent_p.R184R	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	212	Interaction with FAM120B. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|brown fat cell differentiation (GO:0050873)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|cellular response to lithium ion (GO:0071285)|epithelial cell differentiation (GO:0030855)|fatty acid oxidation (GO:0019395)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|innate immune response (GO:0045087)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|lipoprotein transport (GO:0042953)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle receptor biosynthetic process (GO:0045713)|monocyte differentiation (GO:0030224)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of cell growth (GO:0030308)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ regeneration (GO:0031100)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|placenta development (GO:0001890)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood pressure (GO:0008217)|regulation of cholesterol transporter activity (GO:0060694)|regulation of transcription involved in cell fate commitment (GO:0060850)|response to caffeine (GO:0031000)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to lipid (GO:0033993)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|arachidonic acid binding (GO:0050544)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|prostaglandin receptor activity (GO:0004955)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region DNA binding (GO:0001012)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		PAX8/PPARG(117)	breast(2)|endometrium(4)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20					Balsalazide(DB01014)|Bezafibrate(DB01393)|Glipizide(DB01067)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Mesalazine(DB00244)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rosiglitazone(DB00412)|Sulfasalazine(DB00795)|Telmisartan(DB00966)	GGTTTGGGCGGATGCCACAGG	0.542			T	PAX8	follicular thyroid		"Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"																														p.R212R		.		Dom	yes		3	3p25	5468	"peroxisome proliferative activated receptor, gamma"	yes	E	.	PPARG-1043	0			c.G636C						.						66	65	65					3																	12447397		2203	4300	6503	SO:0001819	synonymous_variant	5468	exon5			TGGGCGGATGCCA	X90563	CCDS2609.1, CCDS2610.2	3p25	2013-01-16	2006-10-17		ENSG00000132170	ENSG00000132170		"Nuclear hormone receptors"	9236	protein-coding gene	gene with protein product		601487	"peroxisome proliferative activated receptor, gamma"			7862171, 9750197	Standard	NM_005037		Approved	PPARG1, PPARG2, NR1C3, PPARgamma	uc003bwx.3	P37231	OTTHUMG00000129764	ENST00000287820.6:c.636G>C	3.37:g.12447397G>C		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	83	5	NM_015869	0	0	46	49	3	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Silent	SNP	ENST00000287820.6	37	CCDS2609.1																																																																																			.		0.542	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037		C	12447397	G	C	12447397	2	2	41	1	0	0	0	0	0	0	0	1	12325	1161	41	4		4	PPARG	3	12447397	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		12447397	185575033	19	3743											
DLEC1	9940	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	38101279	38101280	+	In_Frame_Ins	INS	-	-	CAT																															acagcgagttgctacggaaaINScatcatttgatctccccaga																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:38101279_38101280insCAT	ENST00000308059.6	+	3	630_631	c.609_610insCAT	c.(610-612)cat>CATcat	p.204_204H>HH	DLEC1_ENST00000346219.3_In_Frame_Ins_p.204_204H>HH|DLEC1_ENST00000452631.2_In_Frame_Ins_p.204_204H>HH					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TGCTACGGAAACATCATTTGAT	0.465																																					p.K203delinsKH		.											.	DLEC1-161	0			c.609_610insCAT						.																																			SO:0001652	inframe_insertion	9940	exon3			.	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"cilia and flagella associated protein 81"	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.613_615dupCAT	3.37:g.38101283_38101285dupCAT	ENSP00000308597:p.His205dup	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	91	39	NM_007337	0	0	0	0	0		In_Frame_Ins	INS	ENST00000308059.6	37	CCDS2672.2																																																																																			.		0.465	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		CAT	38101280	-	CAT	38101279	7	5	41	1	0	1	1	0	0	0	0	0	4563	40	2	0	619	0	DLEC1	3	38101279	In_Frame_Ins	INS	-	TCGA-B1-A657-01A-11D-A31X-10	25653882	38101279	159921151	20	3744											
LIMD1	8994	hgsc.bcm.edu;broad.mit.edu	37	chr3	45714309	45714327	+	Splice_Site	DEL	ACAAGTAAGAAGGGATGGG	ACAAGTAAGAAGGGATGGG	-																															ctactgtgtccgagattaccAcaagtaagaagggatgggag																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	ACAAGTAAGAAGGGATGGG	ACAAGTAAGAAGGGATGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:45714309_45714327delACAAGTAAGAAGGGATGGG	ENST00000273317.4	+	5	1790_1793	c.1769_1772delACAAGTAAGAAGGGATGGG	c.(1768-1773)cacaag>cg	p.HK590fs	LIMD1_ENST00000440097.1_Splice_Site_p.HK590fs|LIMD1_ENST00000465039.1_3'UTR	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	590	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.|Necessary for nuclear localization.				cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		CGAGATTACCACAAGTAAGAAGGGATGGGAGCAGACAGG	0.53																																					p.590_591del		.											.	LIMD1-279	0			c.1769_1772del						.																																			SO:0001630	splice_region_variant	8994	exon5			.	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.1772+1ACAAGTAAGAAGGGATGGG>-	3.37:g.45714309_45714327delACAAGTAAGAAGGGATGGG		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	59	10	NM_014240	0	0	0	0	0	Q17RQ1|Q9BQQ9|Q9NQ47	Frame_Shift_Del	DEL	ENST00000273317.4	37	CCDS2729.1																																																																																			.		0.53	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	Frame_Shift_Del	-	45714327	ACAAGTAAGAAGGGATGGG	-	45714309	8	5	41	1	0	1	0	1	0	0	1	0	8820	159	6	0	1787	0	LIMD1	3	45714309	Splice_Site	DEL	ACAAGTAAGAAGGGATGGG	TCGA-B1-A657-01A-11D-A31X-10	7613030	45714309	152308121	21	3745											
DAG1	1605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49547996	49547996	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgtgggcctctcgctgcTgctgcccctctcggggagga	2	10	15	14	2	3	0	0	0	3	0	5	2	3	2	3	4	3	3	3	4	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:49547996T>C	ENST00000539901.1	+	2	587	c.29T>C	c.(28-30)cTg>cCg	p.L10P	DAG1_ENST00000479935.1_3'UTR|DAG1_ENST00000308775.2_Missense_Mutation_p.L10P|DAG1_ENST00000541308.1_Missense_Mutation_p.L10P|DAG1_ENST00000515359.2_Missense_Mutation_p.L10P|DAG1_ENST00000538711.1_Missense_Mutation_p.L10P|DAG1_ENST00000545947.1_Missense_Mutation_p.L10P	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	10					basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CTCTCGCTGCTGCTGCCCCTC	0.577																																					p.L10P		.											.	DAG1-92	0			c.T29C						.						85	84	84					3																	49547996		2203	4300	6503	SO:0001583	missense	1605	exon3			CGCTGCTGCTGCC	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.29T>C	3.37:g.49547996T>C	ENSP00000439334:p.Leu10Pro	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	60	13	NM_001177642	0	0	0	0	0	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	37	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	T	8.905	0.957260	0.18507	.	.	ENSG00000173402	ENST00000515359;ENST00000421560;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711;ENST00000418588;ENST00000431960;ENST00000452317;ENST00000435508;ENST00000452060;ENST00000428779;ENST00000419218	T;T;T;T;T;T;T;T;T;T;T;T;T	0.60797	0.78;0.77;0.78;0.78;0.78;0.78;0.78;0.75;0.76;0.16;0.64;0.74;0.76	5.85	4.7	0.59300	.	0.080454	0.51477	N	0.000097	T	0.42086	0.1187	L	0.29908	0.895	0.53688	D	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.31138	-0.9954	10	0.52906	T	0.07	-6.6126	6.3137	0.21178	0.1406:0.0754:0.0:0.784	.	10	Q14118	DAG1_HUMAN	P	10	ENSP00000440705:L10P;ENSP00000412067:L10P;ENSP00000312435:L10P;ENSP00000442600:L10P;ENSP00000440590:L10P;ENSP00000439334:L10P;ENSP00000438421:L10P;ENSP00000405859:L10P;ENSP00000388833:L10P;ENSP00000387859:L10P;ENSP00000415321:L10P;ENSP00000410145:L10P;ENSP00000401382:L10P	ENSP00000312435:L10P	L	+	2	0	DAG1	49523000	0.990000	0.36364	1.000000	0.80357	0.095000	0.18619	1.145000	0.31577	1.044000	0.40200	0.455000	0.32223	CTG	.		0.577	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			C	49547996	T	C	49547996	3	2	41	1	0	0	0	0	1	0	0	0	4231	1580	55	3	31	3	DAG1	3	49547996	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	3833687	49547996	148474434	22	3746											
DNAH1	25981	broad.mit.edu;bcgsc.ca	37	chr3	52361913	52361913	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tccaggtatttgacaatgagGactttgactgccggactccc	9	11	10	11	1	0	3	0	3	0	0	2	5	2	5	3	3	1	1	3	3	2	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:52361913G>A	ENST00000420323.2	+	6	1015	c.754G>A	c.(754-756)Gac>Aac	p.D252N		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	252	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGACAATGAGGACTTTGACTG	0.572																																					p.D252N													.	DNAH1-67	0			c.G754A						.						76	76	76					3																	52361913		1969	4139	6108	SO:0001583	missense	25981	exon6			AATGAGGACTTTG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.754G>A	3.37:g.52361913G>A	ENSP00000401514:p.Asp252Asn	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	161	6	NM_015512	0	0	3	3	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.558493	0.65538	.	.	ENSG00000114841	ENST00000420323	T	0.23552	1.9	5.55	5.55	0.83447	.	0.420477	0.19607	N	0.110248	T	0.21718	0.0523	N	0.19112	0.55	0.36079	D	0.842653	B;B	0.14805	0.011;0.01	B;B	0.25614	0.011;0.062	T	0.12451	-1.0547	10	0.38643	T	0.18	.	17.6919	0.88270	0.0:0.0:1.0:0.0	.	252;252	C9JXH6;Q9P2D7-3	.;.	N	252	ENSP00000401514:D252N	ENSP00000401514:D252N	D	+	1	0	DNAH1	52336953	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.316000	0.89985	2.620000	0.88729	0.563000	0.77884	GAC	.		0.572	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52361913	G	A	52361913	3	1	41	1	0	0	0	0	1	0	0	0	4608	1174	41	2	772	2	DNAH1	3	52361913	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	2813917	52361913	145660517	23	3747											
MBNL1	4154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	152163262	152163262	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcacatttgcaagccaagatCaaggctgcccaataccaggt	13	7	9	12	0	1	1	1	0	0	1	1	1	1	1	3	2	4	3	3	2	5	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:152163262C>T	ENST00000463374.1	+	4	1252	c.741C>T	c.(739-741)atC>atT	p.I247I	MBNL1_ENST00000485509.1_Silent_p.I247I|MBNL1_ENST00000545754.1_Silent_p.I179I|MBNL1_ENST00000324196.5_Silent_p.I247I|MBNL1_ENST00000485910.1_Silent_p.I179I|MBNL1_ENST00000324210.5_Silent_p.I247I|MBNL1_ENST00000357472.3_Silent_p.I247I|MBNL1_ENST00000493459.1_Silent_p.I190I|MBNL1_ENST00000282488.7_Silent_p.I179I|MBNL1_ENST00000498502.1_Silent_p.I247I|MBNL1_ENST00000355460.2_Silent_p.I247I|MBNL1_ENST00000282486.6_Silent_p.I247I|MBNL1_ENST00000492948.1_Silent_p.I247I	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	247					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AAGCCAAGATCAAGGCTGCCC	0.507																																					p.I247I		.											.	MBNL1-91	0			c.C741T						.						101	100	101					3																	152163262		2203	4300	6503	SO:0001819	synonymous_variant	4154	exon5			CAAGATCAAGGCT	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.741C>T	3.37:g.152163262C>T		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	145	37	NM_207292	0	0	3	10	7	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Silent	SNP	ENST00000463374.1	37	CCDS3165.1	.	.	.	.	.	.	.	.	.	.	C	9.846	1.192282	0.21954	.	.	ENSG00000152601	ENST00000464596	.	.	.	5.42	4.54	0.55810	.	.	.	.	.	T	0.69762	0.3147	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68727	-0.5332	4	.	.	.	-15.5766	13.8836	0.63696	0.0:0.927:0.0:0.073	.	.	.	.	L	246	.	.	S	+	2	0	MBNL1	153645952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.700000	0.37815	1.284000	0.44531	0.655000	0.94253	TCA	.		0.507	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		T	152163262	C	T	152163262	2	4	41	1	0	0	0	0	0	0	0	1	9378	816	29	2		2	MBNL1	3	152163262	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	99801349	152163262	45859168	24	3748											
USP13	8975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179462840	179462840	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcacccagatgaactgaTcgcttatgaactaacgagaa	14	10	7	10	2	1	5	1	3	0	2	2	6	1	5	1	0	3	1	1	0	5	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:179462840T>A	ENST00000263966.3	+	13	2015	c.1544T>A	c.(1543-1545)aTc>aAc	p.I515N	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Missense_Mutation_p.I450N	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	515	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			GATGAACTGATCGCTTATGAA	0.478																																					p.I515N		.											.	USP13-659	0			c.T1544A						.						120	113	115					3																	179462840		2203	4300	6503	SO:0001583	missense	8975	exon13			AACTGATCGCTTA	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"Ubiquitin-specific peptidases"	12611	protein-coding gene	gene with protein product		603591	"ubiquitin specific protease 13 (isopeptidase T-3)"			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.1544T>A	3.37:g.179462840T>A	ENSP00000263966:p.Ile515Asn	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	158	65	NM_003940	0	0	0	0	0	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	T	11.23	1.576799	0.28092	.	.	ENSG00000058056	ENST00000263966;ENST00000496897;ENST00000497155	T;T	0.13778	2.56;2.57	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.145148	0.48286	D	0.000197	T	0.14056	0.0340	N	0.26042	0.785	0.58432	D	0.999993	P;B	0.38335	0.627;0.244	P;B	0.44422	0.449;0.281	T	0.16247	-1.0409	10	0.17832	T	0.49	-17.5512	15.1067	0.72326	0.0:0.0:0.0:1.0	.	515;515	Q92995;A8K2S3	UBP13_HUMAN;.	N	515;450;161	ENSP00000263966:I515N;ENSP00000417146:I450N	ENSP00000263966:I515N	I	+	2	0	USP13	180945534	1.000000	0.71417	0.955000	0.39395	0.938000	0.57974	6.035000	0.70940	1.966000	0.57179	0.533000	0.62120	ATC	.		0.478	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179462840	T	A	179462840	3	1	41	1	0	0	0	0	1	0	0	0	17077	1435	50	5	1594	5	USP13	3	179462840	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	27299578	179462840	18559590	25	3749											
DLG1	1739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	196888577	196888577	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacagggatcacagggacAgtgggaggagagggaagaac	15	2	19	5	0	1	2	1	0	0	2	1	8	1	7	0	6	1	0	0	6	2	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:196888577A>T	ENST00000419354.1	-	6	802	c.516T>A	c.(514-516)acT>acA	p.T172T	DLG1_ENST00000450955.1_Intron|DLG1_ENST00000448528.2_Silent_p.T172T|DLG1_ENST00000422288.1_Intron|DLG1_ENST00000357674.4_Intron|DLG1_ENST00000452595.1_Intron|DLG1_ENST00000443183.1_Intron|DLG1_ENST00000392382.2_Intron|DLG1_ENST00000346964.2_Silent_p.T172T|DLG1_ENST00000314062.3_Intron			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	172	Interaction with SH3 domains.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TCACAGGGACAGTGGGAGGAG	0.388																																					p.T172T		.											.	DLG1-118	0			c.T516A						.						71	75	74					3																	196888577		2203	4300	6503	SO:0001819	synonymous_variant	1739	exon6			AGGGACAGTGGGA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.516T>A	3.37:g.196888577A>T		Somatic	381	0		WXS	Illumina HiSeq	Phase_I	398	99	NM_001098424	0	0	17	20	3	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	37	CCDS43194.1																																																																																			.		0.388	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		T	196888577	A	T	196888577	2	4	41	1	0	0	0	0	0	0	0	1	4565	175	7	5		5	DLG1	3	196888577	Silent	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	17425737	196888577	1133853	26	3750											
CLNK	116449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	10522421	10522421	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaagtgctcttacctctgtTttgcacactgtggttgcttg	6	16	10	9	0	2	0	0	0	2	0	2	1	2	0	1	1	4	5	1	1	2	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:10522421T>G	ENST00000226951.6	-	15	1005	c.766A>C	c.(766-768)Aac>Cac	p.N256H		NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	256					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						TTACCTCTGTTTTGCACACTG	0.373																																					p.N256H	GBM(87;402 1286 6949 13902 35851)	.											.	CLNK-23	0			c.A766C						.						140	125	129					4																	10522421		1858	4107	5965	SO:0001583	missense	116449	exon15			CTCTGTTTTGCAC	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"SH2 domain containing"	17438	protein-coding gene	gene with protein product	"mast cell immunoreceptor signal transducer"	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.766A>C	4.37:g.10522421T>G	ENSP00000226951:p.Asn256His	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	104	35	NM_052964	0	0	0	0	0	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	T	8.569	0.879522	0.17467	.	.	ENSG00000109684	ENST00000226951;ENST00000429087	T	0.23552	1.9	3.58	2.44	0.29823	.	1.529250	0.03878	N	0.276734	T	0.19565	0.0470	N	0.24115	0.695	0.34150	D	0.667466	B	0.26876	0.162	B	0.30855	0.121	T	0.34179	-0.9839	10	0.46703	T	0.11	-4.8736	3.7403	0.08527	0.0:0.2405:0.0:0.7595	.	256	Q7Z7G1	CLNK_HUMAN	H	256;220	ENSP00000226951:N256H	ENSP00000226951:N256H	N	-	1	0	CLNK	10131519	0.030000	0.19436	0.584000	0.28653	0.521000	0.34408	0.593000	0.23999	0.761000	0.33130	0.379000	0.24179	AAC	.		0.373	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		G	10522421	T	G	10522421	3	3	41	1	0	0	0	0	1	0	0	0	3553	1841	64	5	540	5	CLNK	4	10522421	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		10522421	180631855	27	3751											
USP46	64854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	53492228	53492228	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcattggtaagcgttcccTgaaaaatctcatggacccag	11	12	8	10	1	2	1	2	1	1	0	4	2	3	2	2	2	1	2	2	2	3	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:53492228T>C	ENST00000441222.3	-	4	702	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	USP46_ENST00000508499.1_Missense_Mutation_p.Q166R|USP46_ENST00000451218.2_Missense_Mutation_p.Q146R	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	173	USP.				adult feeding behavior (GO:0008343)|behavioral fear response (GO:0001662)|behavioral response to ethanol (GO:0048149)|protein deubiquitination (GO:0016579)|regulation of synaptic transmission, GABAergic (GO:0032228)|righting reflex (GO:0060013)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)	12			LUSC - Lung squamous cell carcinoma(32;0.0295)			AAGCGTTCCCTGAAAAATCTC	0.383																																					p.Q173R		.											.	USP46-637	0			c.A518G						.						123	117	119					4																	53492228		1869	4137	6006	SO:0001583	missense	64854	exon4			GTTCCCTGAAAAA	AK022614	CCDS47053.1, CCDS47054.1	4q12	2008-02-05	2005-08-08		ENSG00000109189	ENSG00000109189		"Ubiquitin-specific peptidases"	20075	protein-coding gene	gene with protein product		612849	"ubiquitin specific protease 46"			12838346	Standard	NM_022832		Approved	FLJ12552	uc003gzn.3	P62068	OTTHUMG00000160640	ENST00000441222.3:c.518A>G	4.37:g.53492228T>C	ENSP00000407818:p.Gln173Arg	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	202	64	NM_022832	0	0	1	4	3	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Missense_Mutation	SNP	ENST00000441222.3	37	CCDS47053.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.958840	0.53400	.	.	ENSG00000109189	ENST00000441222;ENST00000451218;ENST00000508499	T;T;T	0.31247	1.5;1.5;1.5	5.08	5.08	0.68730	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000018	T	0.33818	0.0876	M	0.67953	2.075	0.80722	D	1	B;B;B;B	0.18610	0.02;0.011;0.029;0.01	B;B;B;B	0.29077	0.059;0.059;0.098;0.025	T	0.13872	-1.0493	10	0.12430	T	0.62	-17.1457	14.345	0.66654	0.0:0.0:0.0:1.0	.	57;161;173;166	P62068-2;P62068-4;P62068;P62068-3	.;.;UBP46_HUMAN;.	R	173;146;166	ENSP00000407818:Q173R;ENSP00000390102:Q146R;ENSP00000423244:Q166R	ENSP00000407818:Q173R	Q	-	2	0	USP46	53186985	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	6.263000	0.72521	2.046000	0.60703	0.528000	0.53228	CAG	.		0.383	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832		C	53492228	T	C	53492228	3	2	41	1	0	0	0	0	1	0	0	0	17110	1580	55	3	606	3	USP46	4	53492228	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	42969807	53492228	137662048	28	3752											
EXOC1	55763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	56759888	56759888	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggaccctgcttctttccTaagtactacattgggaaatg	9	14	9	9	0	1	0	0	0	1	0	2	2	2	2	2	2	3	2	2	2	4	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:56759888T>C	ENST00000381295.2	+	15	2243	c.1895T>C	c.(1894-1896)cTa>cCa	p.L632P	EXOC1_ENST00000346134.7_Missense_Mutation_p.L632P|EXOC1_ENST00000349598.6_Missense_Mutation_p.L617P	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	632					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					GCTTCTTTCCTAAGTACTACA	0.343																																					p.L632P		.											.	EXOC1-950	0			c.T1895C						.						95	89	91					4																	56759888		2203	4300	6503	SO:0001583	missense	55763	exon15			CTTTCCTAAGTAC	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1895T>C	4.37:g.56759888T>C	ENSP00000370695:p.Leu632Pro	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	121	40	NM_018261	0	0	18	29	11	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.097917	0.76870	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.80529	0.4640	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.952;0.997	T	0.83349	-0.0004	9	0.87932	D	0	.	16.0821	0.81012	0.0:0.0:0.0:1.0	.	617;632	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	P	632;632;617	.	ENSP00000326514:L632P	L	+	2	0	EXOC1	56454645	1.000000	0.71417	0.150000	0.22450	0.970000	0.65996	7.698000	0.84413	2.200000	0.70718	0.460000	0.39030	CTA	.		0.343	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56759888	T	C	56759888	3	2	41	1	0	0	0	0	1	0	0	0	5314	1522	53	3	1949	3	EXOC1	4	56759888	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	3267660	56759888	134394388	29	3753											
CXCL1	2919	broad.mit.edu	37	chr4	74735703	74735704	+	Frame_Shift_Ins	INS	-	-	C																															atcatcgaaaagatgctgaaINScaggtgagttatggtttcca																								rs549189473		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:74735703_74735704insC	ENST00000395761.3	+	3	372_373	c.305_306insC	c.(304-309)aacagtfs	p.S103fs	CXCL1_ENST00000509101.1_3'UTR	NM_001511.3	NP_001502.1	P09341	GROA_HUMAN	chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)	103					actin cytoskeleton organization (GO:0030036)|cell chemotaxis (GO:0060326)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|enzyme activator activity (GO:0008047)|receptor binding (GO:0005102)			lung(2)	2	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			AAGATGCTGAACAGGTGAGTTA	0.475																																					p.N102fs													.	CXCL1-204	0			c.305_306insC						.																																			SO:0001589	frameshift_variant	2919	exon3			TGCTGAACAGGTG	J03561	CCDS47074.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163739		"Endogenous ligands"	4602	protein-coding gene	gene with protein product		155730	"GRO1 oncogene (melanoma growth stimulating activity, alpha)", "fibroblast secretory protein"	MGSA, GRO1, FSP		2217207	Standard	NM_001511		Approved	SCYB1, GROa, MGSA-a, NAP-3	uc003hhh.3	P09341		ENST00000395761.3:c.306dupC	4.37:g.74735704_74735704dupC	ENSP00000379110:p.Ser103fs	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	170	9	NM_001511	0	0	0	0	0	Q9UCR7	Frame_Shift_Ins	INS	ENST00000395761.3	37	CCDS47074.1																																																																																			.		0.475	CXCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362734.1			C	74735704	-	C	74735703	7	5	41	1	0	1	1	0	0	0	0	0	4083	43	2	0	315	0	CXCL1	4	74735703	Frame_Shift_Ins	INS	-	TCGA-B1-A657-01A-11D-A31X-10	17975815	74735703	116418573	30	3754											
CDKL2	8999	bcgsc.ca	37	chr4	76521462	76521462	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattaatgttataaatgcctGatggggaatgtctgttcggt	10	15	11	5	1	1	1	0	1	1	0	2	2	1	2	1	3	1	2	1	3	5	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:76521462G>T	ENST00000429927.2	-	10	2088	c.1385C>A	c.(1384-1386)tCa>tAa	p.S462*	CDKL2_ENST00000307465.4_Nonsense_Mutation_p.S462*	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	462					sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ATAAATGCCTGATGGGGAATG	0.328																																					p.S462X													.	CDKL2-454	0			c.C1385A						.						175	163	167					4																	76521462		2203	4300	6503	SO:0001587	stop_gained	8999	exon10			ATGCCTGATGGGG	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.1385C>A	4.37:g.76521462G>T	ENSP00000412365:p.Ser462*	Somatic	132	0		WXS	Illumina HiSeq	Phase_1	101	5	NM_003948	0	0	14	14	0	B2R695	Nonsense_Mutation	SNP	ENST00000429927.2	37	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	G	42	9.585214	0.99211	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3084	11.0954	0.48141	0.0:0.0:0.8156:0.1844	.	.	.	.	X	462	.	ENSP00000306340:S462X	S	-	2	0	CDKL2	76740486	1.000000	0.71417	0.996000	0.52242	0.796000	0.44982	2.209000	0.42806	2.738000	0.93877	0.655000	0.94253	TCA	.		0.328	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		T	76521462	G	T	76521462	4	4	41	1	0	0	0	0	0	1	0	0	3160	1294	45	4	104	4	CDKL2	4	76521462	Nonsense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	1785759	76521462	114632814	31	3755											
ANTXR2	118429	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	80976344	80976344	+	Frame_Shift_Del	DEL	C	C	-																															ggacaccaacacaataaacaCtagccccaagtgacctggat																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:80976344delC	ENST00000307333.7	-	6	517	c.515delG	c.(514-516)agtfs	p.S172fs	ANTXR2_ENST00000404191.1_Frame_Shift_Del_p.S95fs|ANTXR2_ENST00000403729.2_Frame_Shift_Del_p.S172fs|ANTXR2_ENST00000346652.6_Frame_Shift_Del_p.S172fs|ANTXR2_ENST00000295465.4_Frame_Shift_Del_p.S172fs	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	172	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						ACAATAAACACTAGCCCCAAG	0.383									Juvenile Hyaline Fibromatosis																												p.S172fs		.											.	ANTXR2-23	0			c.515delG						.						75	67	69					4																	80976344		1845	4088	5933	SO:0001589	frameshift_variant	118429	exon6	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	.	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.515delG	4.37:g.80976344delC	ENSP00000306185:p.Ser172fs	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	127	42	NM_001145794	0	0	0	0	0	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Frame_Shift_Del	DEL	ENST00000307333.7	37	CCDS47086.1																																																																																			.		0.383	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		-	80976344	C	-	80976344	7	5	41	1	0	1	0	1	0	0	0	0	712	565	20	0	1041	0	ANTXR2	4	80976344	Frame_Shift_Del	DEL	C	TCGA-B1-A657-01A-11D-A31X-10	4454882	80976344	110177932	32	3756											
FAT1	2195	broad.mit.edu	37	chr4	187541450	187541450	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgacatagcgaatgacatggCccacctcagtgtccacttta	11	10	8	12	1	1	2	1	2	0	0	2	3	2	2	3	1	1	0	3	1	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:187541450C>A	ENST00000441802.2	-	10	6499	c.6290G>T	c.(6289-6291)gGc>gTc	p.G2097V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2097	Cadherin 19. {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						AATGACATGGCCCACCTCAGT	0.468										HNSCC(5;0.00058)																											p.G2097V	Colon(197;1040 2055 4143 4984 49344)												.	FAT1-34	0			c.G6290T						.						172	164	167					4																	187541450		1989	4161	6150	SO:0001583	missense	2195	exon10			ACATGGCCCACCT	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.6290G>T	4.37:g.187541450C>A	ENSP00000406229:p.Gly2097Val	Somatic	131	2		WXS	Illumina HiSeq	Phase_I	134	5	NM_005245	0	0	12	12	0		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	13.41	2.227440	0.39399	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.70399	-0.48	5.1	5.1	0.69264	Cadherin (3);Cadherin-like (1);	0.049638	0.85682	D	0.000000	D	0.89822	0.6826	H	0.96662	3.86	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.93050	0.6465	10	0.87932	D	0	.	18.7073	0.91643	0.0:1.0:0.0:0.0	.	2097	Q14517	FAT1_HUMAN	V	2097;2099	ENSP00000406229:G2097V	ENSP00000260147:G2099V	G	-	2	0	FAT1	187778444	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	4.797000	0.62503	2.653000	0.90120	0.563000	0.77884	GGC	.		0.468	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187541450	C	A	187541450	3	1	41	1	0	0	0	0	1	0	0	0	5708	739	26	4	7548	4	FAT1	4	187541450	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	106565106	187541450	3612826	33	3757											
ZNF474	133923	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	121487756	121487756	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccattctaaagaacccaCtttccttatcaaccaagctg	13	11	3	14	0	3	1	2	0	1	1	4	1	4	1	4	0	3	1	4	0	6	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:121487756C>A	ENST00000296600.4	+	2	454	c.71C>A	c.(70-72)aCt>aAt	p.T24N	CTC-441N14.1_ENST00000505209.1_RNA|CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	24							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		AAAGAACCCACTTTCCTTATC	0.378																																					p.T24N		.											.	ZNF474-90	0			c.C71A						.						84	89	88					5																	121487756		2203	4300	6503	SO:0001583	missense	133923	exon2			AACCCACTTTCCT	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"Zinc fingers, C2H2-type"	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.71C>A	5.37:g.121487756C>A	ENSP00000296600:p.Thr24Asn	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	98	25	NM_207317	0	0	0	0	0	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091741	0.36952	.	.	ENSG00000164185	ENST00000296600;ENST00000504912;ENST00000505843	T	0.52526	0.66	5.05	5.05	0.67936	.	0.714933	0.11261	U	0.582526	T	0.47985	0.1475	L	0.32530	0.975	0.30368	N	0.783168	D	0.54601	0.967	P	0.52823	0.71	T	0.35051	-0.9804	10	0.31617	T	0.26	-19.2224	10.871	0.46883	0.0:0.9131:0.0:0.0869	.	24	Q6S9Z5	ZN474_HUMAN	N	24	ENSP00000296600:T24N	ENSP00000296600:T24N	T	+	2	0	ZNF474	121515655	0.887000	0.30362	1.000000	0.80357	0.931000	0.56810	1.121000	0.31283	2.624000	0.88883	0.655000	0.94253	ACT	.		0.378	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		A	121487756	C	A	121487756	3	1	41	1	0	0	0	0	1	0	0	0	17964	565	20	4	73	4	ZNF474	5	121487756	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		121487756	59427504	34	3758											
NKX2-5	1482	broad.mit.edu	37	chr5	172659726	172659726	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggggaaggcccggcggggTaagcggcagtgcagctgtag	7	5	20	9	3	0	0	0	0	0	0	0	1	0	1	1	7	3	5	1	7	3	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:172659726T>G	ENST00000329198.4	-	2	1094	c.821A>C	c.(820-822)tAc>tCc	p.Y274S		NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	274	Ala/Pro-rich.				adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCCGGCGGGGTAAGCGGCAGT	0.677																																					p.Y274S	Esophageal Squamous(72;810 1219 2387 13420 44943)												.	NKX2-5-90	0			c.A821C						.						11	14	13					5																	172659726		2197	4288	6485	SO:0001583	missense	1482	exon2			GCGGGGTAAGCGG	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.821A>C	5.37:g.172659726T>G	ENSP00000327758:p.Tyr274Ser	Somatic	136	21		WXS	Illumina HiSeq	Phase_I	181	40	NM_004387	0	0	0	0	0	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	.	.	.	.	.	.	.	.	.	.	T	11.46	1.646353	0.29246	.	.	ENSG00000183072	ENST00000329198	D	0.90620	-2.7	4.15	4.15	0.48705	.	.	.	.	.	D	0.88872	0.6555	M	0.78456	2.415	0.80722	D	1	P	0.37330	0.59	B	0.34180	0.177	D	0.87077	0.2163	9	0.23891	T	0.37	.	13.3587	0.60644	0.0:0.0:0.0:1.0	.	274	P52952	NKX25_HUMAN	S	274	ENSP00000327758:Y274S	ENSP00000327758:Y274S	Y	-	2	0	NKX2-5	172592332	1.000000	0.71417	0.988000	0.46212	0.087000	0.18053	1.799000	0.38824	1.735000	0.51646	0.443000	0.29094	TAC	.		0.677	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			G	172659726	T	G	172659726	3	3	41	1	0	0	0	0	1	0	0	0	10479	1638	57	5	157	5	NKX2-5	5	172659726	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	51171970	172659726	8255534	35	3759											
NKX2-5	1482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	172660100	172660100	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgctccagctcatagacCtgcgcctgcgagaagagcac	9	5	11	16	4	1	3	1	0	0	3	2	4	2	3	4	0	4	3	4	0	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:172660100C>A	ENST00000329198.4	-	2	720	c.447G>T	c.(445-447)caG>caT	p.Q149H	NKX2-5_ENST00000424406.2_3'UTR|NKX2-5_ENST00000521848.1_3'UTR	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	149					adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCTCATAGACCTGCGCCTGCG	0.687																																					p.Q149H	Esophageal Squamous(72;810 1219 2387 13420 44943)	.											.	NKX2-5-90	0			c.G447T						.						14	12	13					5																	172660100		2202	4297	6499	SO:0001583	missense	1482	exon2			ATAGACCTGCGCC	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.447G>T	5.37:g.172660100C>A	ENSP00000327758:p.Gln149His	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	74	22	NM_004387	0	0	0	0	0	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.825180	0.71143	.	.	ENSG00000183072	ENST00000329198	D	0.98044	-4.68	4.21	0.675	0.17952	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.49916	D	0.000124	D	0.98950	0.9643	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98290	1.0513	10	0.87932	D	0	.	9.3001	0.37840	0.0:0.6233:0.0:0.3767	.	149	P52952	NKX25_HUMAN	H	149	ENSP00000327758:Q149H	ENSP00000327758:Q149H	Q	-	3	2	NKX2-5	172592706	0.997000	0.39634	0.999000	0.59377	0.962000	0.63368	0.536000	0.23129	0.002000	0.14630	0.462000	0.41574	CAG	.		0.687	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			A	172660100	C	A	172660100	3	1	41	1	0	0	0	0	1	0	0	0	10479	680	24	4	531	4	NKX2-5	5	172660100	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	374	172660100	8255160	36	3760											
FGFR4	2264	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr5	176520385	176520385	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgactccagcaggcagAaccaagtctcccactttgca	11	7	8	15	0	1	2	0	1	1	1	3	2	2	2	4	1	4	3	4	1	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:176520385A>G	ENST00000292408.4	+	10	1496				FGFR4_ENST00000393637.1_Silent_p.R370R|FGFR4_ENST00000393648.2_Intron|FGFR4_ENST00000502906.1_Intron|FGFR4_ENST00000292410.3_Silent_p.R370R	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4						alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CAGCAGGCAGAACCAAGTCTC	0.642										TSP Lung(9;0.080)																											p.R370R		.											.	FGFR4-1460	0			c.A1110G						.						77	80	79					5																	176520385		2203	4300	6503	SO:0001627	intron_variant	2264	exon8			AGGCAGAACCAAG	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1252-22A>G	5.37:g.176520385A>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	87	37	NM_022963	0	0	2	11	9	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Silent	SNP	ENST00000292408.4	37	CCDS4410.1																																																																																			.		0.642	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			G	176520385	A	G	176520385	1	3	41	0	1	0	0	0	0	0	0	0	5887	243	9	3		3	FGFR4	5	176520385	Intron	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	3860285	176520385	4394875	37	3761											
MUC21	394263	broad.mit.edu	37	chr6	30954813	30954813	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggatcagcacagtcaccaaTtctgagtccagcacaccctc	11	7	8	15	0	3	1	2	1	1	0	5	2	4	2	3	1	2	2	3	1	1	1	rs9262371		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:30954813T>C	ENST00000376296.3	+	2	1102	c.861T>C	c.(859-861)aaT>aaC	p.N287N	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	287	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTCACCAATTCTGAGTCCA	0.602																																					p.N287N													.	MUC21-92	0			c.T861C						.						206	198	201					6																	30954813		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CACCAATTCTGAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.861T>C	6.37:g.30954813T>C		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	152	8	NM_001010909	0	0	0	0	0	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			T|0.967;C|0.033		0.602	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30954813	T	C	30954813	2	2	41	1	0	0	0	0	0	0	0	1	10002	1490	52	3		3	MUC21	6	30954813	Silent	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		30954813	140160254	38	3762											
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	38863980	38863980	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgaagactctgtgtttgaAgtacccaaaatatatgaatt	14	13	7	7	0	1	4	0	3	1	1	1	4	1	4	2	0	1	2	2	0	8	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:38863980A>C	ENST00000359357.3	+	58	8522	c.8268A>C	c.(8266-8268)gaA>gaC	p.E2756D	DNAH8_ENST00000449981.2_Missense_Mutation_p.E2973D|DNAH8_ENST00000441566.1_Missense_Mutation_p.E2720D			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2756					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CTGTGTTTGAAGTACCCAAAA	0.408																																					p.E2973D		.											.	DNAH8-615	0			c.A8919C						.						111	103	105					6																	38863980		2203	4300	6503	SO:0001583	missense	1769	exon60			GTTTGAAGTACCC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.8268A>C	6.37:g.38863980A>C	ENSP00000352312:p.Glu2756Asp	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	100	23	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	11.73	1.726071	0.30593	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T;T	0.29142	1.58;1.75;1.75;1.72	5.36	4.19	0.49359	.	0.050135	0.85682	D	0.000000	T	0.09730	0.0239	L	0.41710	1.295	0.53688	D	0.99997	B	0.11235	0.004	B	0.15052	0.012	T	0.07849	-1.0751	10	0.34782	T	0.22	.	4.8304	0.13437	0.7142:0.0:0.1479:0.1378	.	2756	Q96JB1	DYH8_HUMAN	D	2961;2961;2756;2720	ENSP00000415331:E2961D;ENSP00000333363:E2961D;ENSP00000352312:E2756D;ENSP00000402294:E2720D	ENSP00000333363:E2961D	E	+	3	2	DNAH8	38971958	0.986000	0.35501	0.985000	0.45067	0.950000	0.60333	0.446000	0.21694	0.975000	0.38392	0.482000	0.46254	GAA	.		0.408	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38863980	A	C	38863980	3	2	41	1	0	0	0	0	1	0	0	0	4618	69	3	5	8490	5	DNAH8	6	38863980	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	7909167	38863980	132251087	39	3763											
GCLC	2729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	53380907	53380907	+	Splice_Site	SNP	C	C	T																															caacacaaagccatactcacCtgaagcgagggtgcttgttt																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:53380907C>T	ENST00000229416.6	-	4	1043	c.560G>A	c.(559-561)aGt>aAt	p.S187N	GCLC_ENST00000514004.1_Splice_Site_p.S187N	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	187					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	CCATACTCACCTGAAGCGAGG	0.468																																					p.S187N		.											.	GCLC-515	0			c.G560A						.						125	118	120					6																	53380907		2203	4300	6503	SO:0001630	splice_region_variant	2729	exon4			ACTCACCTGAAGC	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.560+1G>A	6.37:g.53380907C>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	65	15	NM_001498	0	0	0	0	0	Q14399	Missense_Mutation	SNP	ENST00000229416.6	37	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532099	0.85812	.	.	ENSG00000001084	ENST00000229416;ENST00000514004;ENST00000514933	T;T;T	0.54479	0.57;0.57;0.57	5.26	5.26	0.73747	.	0.072360	0.85682	D	0.000000	T	0.43322	0.1242	M	0.68593	2.085	0.80722	D	1	P	0.45531	0.86	B	0.39503	0.301	T	0.47983	-0.9074	9	.	.	.	-14.2666	19.2221	0.93801	0.0:1.0:0.0:0.0	.	187	P48506	GSH1_HUMAN	N	187;187;134	ENSP00000229416:S187N;ENSP00000421908:S187N;ENSP00000423615:S134N	.	S	-	2	0	GCLC	53488866	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.776000	0.85560	2.622000	0.88805	0.561000	0.74099	AGT	.		0.468	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		Missense_Mutation	T	53380907	C	T	53380907	5	4	41	1	0	0	0	0	0	0	1	0	6315	695	24	2	1405	2	GCLC	6	53380907	Splice_Site	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	14516927	53380907	117734160	40	3764	40	2									
GCLC	2729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	53380911	53380911	+	Missense_Mutation	SNP	A	A	G																															acaaagccatactcacctgaAgcgagggtgcttgtttattg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:53380911A>G	ENST00000229416.6	-	4	1039	c.556T>C	c.(556-558)Ttc>Ctc	p.F186L	GCLC_ENST00000514004.1_Missense_Mutation_p.F186L	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	186					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	ACTCACCTGAAGCGAGGGTGC	0.473																																					p.F186L		.											.	GCLC-515	0			c.T556C						.						125	118	121					6																	53380911		2203	4300	6503	SO:0001583	missense	2729	exon4			ACCTGAAGCGAGG	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.556T>C	6.37:g.53380911A>G	ENSP00000229416:p.Phe186Leu	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	67	16	NM_001498	0	0	0	0	0	Q14399	Missense_Mutation	SNP	ENST00000229416.6	37	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	A	34	5.408603	0.96051	.	.	ENSG00000001084	ENST00000229416;ENST00000514004;ENST00000514933	T;T;T	0.76578	-1.03;0.25;-1.03	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.90642	0.7065	H	0.96080	3.765	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.93595	0.6925	10	0.87932	D	0	.	15.6543	0.77121	1.0:0.0:0.0:0.0	.	186	P48506	GSH1_HUMAN	L	186;186;133	ENSP00000229416:F186L;ENSP00000421908:F186L;ENSP00000423615:F133L	ENSP00000229416:F186L	F	-	1	0	GCLC	53488870	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.164000	0.68074	0.459000	0.35465	TTC	.		0.473	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			G	53380911	A	G	53380911	3	3	41	1	0	0	0	0	1	0	0	0	6315	72	3	3	1409	3	GCLC	6	53380911	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	4	53380911	117734156	41	3765	40	2									
FAM135A	57579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	71236101	71236101	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtactatgaagaaacagattAttcagctttggatggaacaa	16	11	9	5	0	1	3	1	1	0	2	1	5	1	5	0	2	4	2	0	2	7	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:71236101A>G	ENST00000418814.2	+	15	3928	c.3314A>G	c.(3313-3315)tAt>tGt	p.Y1105C	FAM135A_ENST00000370479.3_Missense_Mutation_p.Y892C|FAM135A_ENST00000361499.3_Missense_Mutation_p.Y909C|FAM135A_ENST00000505769.1_Missense_Mutation_p.Y685C|FAM135A_ENST00000457062.2_Missense_Mutation_p.Y892C|FAM135A_ENST00000505868.1_Missense_Mutation_p.Y1105C	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1105										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						GAAACAGATTATTCAGCTTTG	0.348																																					p.Y1105C		.											.	FAM135A-90	0			c.A3314G						.						84	91	88					6																	71236101		2203	4300	6503	SO:0001583	missense	57579	exon13			CAGATTATTCAGC	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.3314A>G	6.37:g.71236101A>G	ENSP00000410768:p.Tyr1105Cys	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	159	48	NM_001162529	0	0	4	9	5	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	A	3.081	-0.188920	0.06299	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.23552	2.22;2.22;1.9;2.22;2.22;2.2	5.9	2.09	0.27110	.	0.582275	0.19653	N	0.109143	T	0.06050	0.0157	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.09022	0.0;0.0;0.0;0.002	B;B;B;B	0.06405	0.002;0.001;0.001;0.002	T	0.35773	-0.9775	10	0.38643	T	0.18	.	3.5522	0.07851	0.6563:0.1354:0.0711:0.1372	.	1105;1105;909;892	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	C	1105;892;685;892;909;1105	ENSP00000410768:Y1105C;ENSP00000359510:Y892C;ENSP00000423785:Y685C;ENSP00000409201:Y892C;ENSP00000354913:Y909C;ENSP00000423307:Y1105C	ENSP00000354913:Y909C	Y	+	2	0	FAM135A	71292822	0.798000	0.28890	0.004000	0.12327	0.251000	0.25915	1.664000	0.37439	0.115000	0.18071	0.533000	0.62120	TAT	.		0.348	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71236101	A	G	71236101	3	3	41	1	0	0	0	0	1	0	0	0	5464	449	16	3	3442	3	FAM135A	6	71236101	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	17855190	71236101	99878966	42	3766											
PSMB1	5689	broad.mit.edu	37	chr6	170852793	170852793	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caattgcccccgtagtcatgGccttattattggaatgctta	9	14	8	10	1	1	0	1	0	0	0	1	1	1	1	3	2	2	2	3	2	6	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:170852793G>T	ENST00000262193.6	-	4	427	c.329C>A	c.(328-330)gCc>gAc	p.A110D	PSMB1_ENST00000462957.1_5'UTR	NM_002793.3	NP_002784.1	P20618	PSB1_HUMAN	proteasome (prosome, macropain) subunit, beta type, 1	110					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)|Carfilzomib(DB08889)	CGTAGTCATGGCCTTATTATT	0.398																																					p.A110D													.	PSMB1-91	0			c.C329A						.						133	116	122					6																	170852793		2203	4300	6503	SO:0001583	missense	5689	exon4			GTCATGGCCTTAT	D00761	CCDS34577.1	6q27	2008-02-05			ENSG00000008018	ENSG00000008018		"Proteasome (prosome, macropain) subunits"	9537	protein-coding gene	gene with protein product		602017				2025653	Standard	NM_002793		Approved	PMSB1, HC5	uc011ehe.2	P20618	OTTHUMG00000016087	ENST00000262193.6:c.329C>A	6.37:g.170852793G>T	ENSP00000262193:p.Ala110Asp	Somatic	94	2		WXS	Illumina HiSeq	Phase_I	75	7	NM_002793	0	2	337	341	2	B5BU76|Q9BWA8	Missense_Mutation	SNP	ENST00000262193.6	37	CCDS34577.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073855	0.36566	.	.	ENSG00000008018	ENST00000262193;ENST00000392093	T	0.21031	2.03	5.08	4.21	0.49690	.	0.106709	0.64402	D	0.000006	T	0.04092	0.0114	N	0.12961	0.28	0.37161	D	0.9026	B	0.28713	0.22	B	0.25614	0.062	T	0.28681	-1.0036	10	0.14252	T	0.57	-16.9599	11.2538	0.49041	0.1478:0.0:0.8522:0.0	.	110	P20618	PSB1_HUMAN	D	110;115	ENSP00000262193:A110D	ENSP00000262193:A110D	A	-	2	0	PSMB1	170694718	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.782000	0.62396	1.284000	0.44531	0.650000	0.86243	GCC	.		0.398	PSMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043278.2	NM_002793		T	170852793	G	T	170852793	3	4	41	1	0	0	0	0	1	0	0	0	12703	1203	42	4	408	4	PSMB1	6	170852793	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	99616692	170852793	262274	43	3767											
FAM20C	56975	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	193541	193541	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaactgccgcccgcggcCgagccggccgagcgcgcctt	6	3	15	17	8	0	1	0	0	0	1	0	4	0	1	6	2	4	0	6	2	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:193541C>T	ENST00000313766.5	+	1	573	c.342C>T	c.(340-342)gcC>gcT	p.A114A	AC093627.12_ENST00000467050.1_RNA	NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C	114					dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		CGCCCGCGGCCGAGCCGGCCG	0.741																																					p.A114A		.											.	.	0			c.C342T						.						1	1	1					7																	193541		632	1547	2179	SO:0001819	synonymous_variant	56975	exon1			CGCGGCCGAGCCG	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.342C>T	7.37:g.193541C>T		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	40	23	NM_020223	0	0	2	3	1	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Silent	SNP	ENST00000313766.5	37	CCDS47522.1																																																																																			.		0.741	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223		T	193541	C	T	193541	2	4	41	1	0	0	0	0	0	0	0	1	5555	639	23	1		1	FAM20C	7	193541	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		193541	158945122	44	3768			1	12		2	2	21	N	T_C	6.848036e-05
FAM20C	56975	hgsc.bcm.edu;broad.mit.edu	37	chr7	193561	193561	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagccggccgagcgcgcctTgcgggggcgggatcccggcg	3	3	20	15	9	0	0	0	0	0	0	1	3	1	1	4	5	3	0	4	5	0	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:193561T>A	ENST00000313766.5	+	1	593	c.362T>A	c.(361-363)tTg>tAg	p.L121*	AC093627.12_ENST00000467050.1_RNA	NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C	121					dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		GAGCGCGCCTTGCGGGGGCGG	0.766																																					p.L121X		.											.	.	0			c.T362A						.						1	1	1					7																	193561		742	1670	2412	SO:0001587	stop_gained	56975	exon1			GCGCCTTGCGGGG	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.362T>A	7.37:g.193561T>A	ENSP00000322323:p.Leu121*	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	26	14	NM_020223	0	0	2	5	3	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Nonsense_Mutation	SNP	ENST00000313766.5	37	CCDS47522.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.498085	0.85069	.	.	ENSG00000177706	ENST00000313766	.	.	.	4.45	-5.01	0.02991	.	3.462960	0.02171	U	0.059669	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	5.991	0.19460	0.0:0.2449:0.3819:0.3732	.	.	.	.	X	121	.	ENSP00000322323:L121X	L	+	2	0	FAM20C	288644	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.083000	0.11286	-0.496000	0.06650	0.459000	0.35465	TTG	.		0.766	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223		A	193561	T	A	193561	4	1	41	1	0	0	0	0	0	1	0	0	5555	1821	63	5	364	5	FAM20C	7	193561	Nonsense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	20	193561	158945102	45	3769			1	12		2	2	21	N	T_C	6.848036e-05
THSD7A	221981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	11582721	11582721	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggataggtccagtgcataAttttaagtccattggctttg	10	14	11	6	0	0	0	0	0	0	0	2	1	2	1	2	3	1	2	2	3	3	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:11582721A>C	ENST00000423059.4	-	5	1728	c.1477T>G	c.(1477-1479)Tta>Gta	p.L493V		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	493	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CCAGTGCATAATTTTAAGTCC	0.383										HNSCC(18;0.044)																											p.L493V		.											.	THSD7A-71	0			c.T1477G						.						127	122	124					7																	11582721		1872	4098	5970	SO:0001583	missense	221981	exon5			TGCATAATTTTAA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1477T>G	7.37:g.11582721A>C	ENSP00000406482:p.Leu493Val	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	166	75	NM_015204	0	0	1	1	0		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921725	0.52653	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.60920	0.15	5.78	4.61	0.57282	.	0.197404	0.43110	D	0.000620	T	0.64735	0.2625	M	0.76574	2.34	0.45307	D	0.998302	P	0.45594	0.862	P	0.52109	0.69	T	0.61613	-0.7027	10	0.21540	T	0.41	.	10.5833	0.45267	0.8816:0.0:0.1184:0.0	.	493	Q9UPZ6	THS7A_HUMAN	V	493	ENSP00000406482:L493V	ENSP00000262042:L493V	L	-	1	2	THSD7A	11549246	0.998000	0.40836	0.998000	0.56505	0.944000	0.59088	3.710000	0.54860	2.333000	0.79357	0.482000	0.46254	TTA	.		0.383	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		C	11582721	A	C	11582721	3	2	41	1	0	0	0	0	1	0	0	0	15911	98	4	5	3588	5	THSD7A	7	11582721	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	11389160	11582721	147555942	46	3770											
TMED4	222068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44621390	44621390	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagggcaggaagacctcctTctgcttatcccacatctggg	8	9	11	13	1	2	1	0	0	2	1	4	3	4	2	3	3	1	2	3	3	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:44621390T>G	ENST00000457408.2	-	2	245	c.193A>C	c.(193-195)Aag>Cag	p.K65Q	TMED4_ENST00000289577.5_Missense_Mutation_p.K65Q|TMED4_ENST00000444131.2_5'UTR|TMED4_ENST00000481238.1_Missense_Mutation_p.K65Q	NM_182547.2	NP_872353.2	Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain containing 4	65	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						AAGACCTCCTTCTGCTTATCC	0.657																																					p.K65Q		.											.	TMED4-90	0			c.A193C						.						99	100	100					7																	44621390		2203	4300	6503	SO:0001583	missense	222068	exon2			CCTCCTTCTGCTT	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.193A>C	7.37:g.44621390T>G	ENSP00000404042:p.Lys65Gln	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	115	49	NM_182547	0	0	31	68	37	A4D2K8|B4DFJ4|Q56VW3|Q7Z432|Q8N2P6	Missense_Mutation	SNP	ENST00000457408.2	37	CCDS5493.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812640	0.50527	.	.	ENSG00000158604	ENST00000457408;ENST00000289577;ENST00000481238	T;T;T	0.46819	2.22;0.86;1.46	5.36	5.36	0.76844	GOLD (2);	0.227073	0.44285	D	0.000478	T	0.24353	0.0590	N	0.04018	-0.295	0.31797	N	0.628865	B;B	0.14438	0.01;0.007	B;B	0.19666	0.022;0.026	T	0.19192	-1.0313	10	0.27785	T	0.31	-9.1229	8.6427	0.33987	0.17:0.0:0.0:0.83	.	65;65	Q7Z7H5-3;Q7Z7H5	.;TMED4_HUMAN	Q	65	ENSP00000404042:K65Q;ENSP00000289577:K65Q;ENSP00000417443:K65Q	ENSP00000289577:K65Q	K	-	1	0	TMED4	44587915	0.974000	0.33945	1.000000	0.80357	0.998000	0.95712	1.146000	0.31589	2.246000	0.74042	0.533000	0.62120	AAG	.		0.657	TMED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251290.1	NM_182547		G	44621390	T	G	44621390	3	3	41	1	0	0	0	0	1	0	0	0	16038	1792	62	5	506	5	TMED4	7	44621390	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	33038669	44621390	114517273	47	3771											
PNPLA8	50640	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	108154603	108154603	+	Frame_Shift_Del	DEL	T	T	-																															attaccttgacagccactccTtttccttcaggaaattctag																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:108154603delT	ENST00000422087.1	-	5	1597	c.1191delA	c.(1189-1191)aaafs	p.K397fs	PNPLA8_ENST00000436062.1_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000483879.1_Intron|PNPLA8_ENST00000257694.8_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000426128.2_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000388728.5_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000453144.1_Frame_Shift_Del_p.K297fs	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	397					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						CAGCCACTCCTTTTCCTTCAG	0.353																																					p.K397fs		.											.	PNPLA8-135	0			c.1191delA						.						189	210	203					7																	108154603		2203	4300	6503	SO:0001589	frameshift_variant	50640	exon3			.	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.1191delA	7.37:g.108154603delT	ENSP00000410804:p.Lys397fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	106	23	NM_001256008	0	0	0	0	0	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Frame_Shift_Del	DEL	ENST00000422087.1	37	CCDS34733.1																																																																																			.		0.353	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		-	108154603	T	-	108154603	7	5	41	1	0	1	0	1	0	0	0	0	12197	1606	56	0	1189	0	PNPLA8	7	108154603	Frame_Shift_Del	DEL	T	TCGA-B1-A657-01A-11D-A31X-10	63533213	108154603	50984060	48	3772											
FLNC	2318	broad.mit.edu	37	chr7	128489441	128489441	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacggtgatcacggtggatGccaaggcagccggtgagggg	9	5	19	8	3	1	3	1	2	0	1	1	4	1	4	2	7	2	1	2	7	1	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:128489441G>T	ENST00000325888.8	+	30	5269	c.5008G>T	c.(5008-5010)Gcc>Tcc	p.A1670S	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.A1670S	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1670					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CACGGTGGATGCCAAGGCAGC	0.627																																					p.A1670S													.	FLNC-141	0			c.G5008T						.						73	83	80					7																	128489441		2166	4264	6430	SO:0001583	missense	2318	exon30			GTGGATGCCAAGG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.5008G>T	7.37:g.128489441G>T	ENSP00000327145:p.Ala1670Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	100	3	NM_001127487	0	0	23	23	0	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	36	5.630736	0.96682	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85484	-1.99;-1.99	5.65	5.65	0.86999	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92283	0.7552	M	0.71296	2.17	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.87578	0.998;0.909	D	0.92346	0.5885	10	0.66056	D	0.02	.	19.7405	0.96228	0.0:0.0:1.0:0.0	.	1670;1670	Q14315-2;Q14315	.;FLNC_HUMAN	S	1670	ENSP00000327145:A1670S;ENSP00000344002:A1670S	ENSP00000327145:A1670S	A	+	1	0	FLNC	128276677	1.000000	0.71417	0.976000	0.42696	0.993000	0.82548	9.869000	0.99810	2.655000	0.90218	0.655000	0.94253	GCC	.		0.627	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128489441	G	T	128489441	3	4	41	1	0	0	0	0	1	0	0	0	5954	1319	46	4	5126	4	FLNC	7	128489441	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	20334838	128489441	30649222	49	3773											
CHCHD3	54927	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	132570441	132570442	+	Frame_Shift_Ins	INS	-	-	G																															cctctcctccagtctagccaINSgctgttctttgtagaatgca																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:132570441_132570442insG	ENST00000262570.5	-	5	577_578	c.433_434insC	c.(433-435)ctgfs	p.L145fs	CHCHD3_ENST00000448878.1_Frame_Shift_Ins_p.L150fs|CHCHD3_ENST00000476546.1_5'UTR	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	145					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						CAGTCTAGCCAGCTGTTCTTTG	0.332																																					p.L145fs		.											.	CHCHD3-90	0			c.434_435insC						.																																			SO:0001589	frameshift_variant	54927	exon5			.	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21906	protein-coding gene	gene with protein product	"mitochondrial inner membrane organizing system 3", "protein phosphatase 1, regulatory subunit 22"	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.434dupC	7.37:g.132570442_132570442dupG	ENSP00000262570:p.Leu145fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	65	15	NM_017812	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000262570.5	37	CCDS5828.1																																																																																			.		0.332	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		G	132570442	-	G	132570441	7	5	41	1	0	1	1	0	0	0	0	0	3323	188	7	0	265	0	CHCHD3	7	132570441	Frame_Shift_Ins	INS	-	TCGA-B1-A657-01A-11D-A31X-10	4081000	132570441	26568222	50	3774											
XRCC2	7516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	152345944	152345944	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcgtcgagaggcatgagaaGgttcttctgatgagctcgag	9	10	15	7	3	2	4	0	3	2	2	5	7	2	4	0	2	1	3	0	2	1	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:152345944G>T	ENST00000359321.1	-	3	711	c.626C>A	c.(625-627)cCt>cAt	p.P209H	XRCC2_ENST00000495707.1_5'UTR	NM_005431.1	NP_005422.1	O43543	XRCC2_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 2	209					centrosome organization (GO:0051297)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of neurogenesis (GO:0050769)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|strand invasion (GO:0042148)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			NS(1)|breast(1)|large_intestine(5)|liver(1)|lung(1)|prostate(2)	11		all_hematologic(28;0.0592)|Prostate(32;0.081)	OV - Ovarian serous cystadenocarcinoma(82;0.0423)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0429)		GGCATGAGAAGGTTCTTCTGA	0.453								Homologous recombination																													p.P209H		.											.	XRCC2-1084	0			c.C626A						.						180	179	180					7																	152345944		2203	4300	6503	SO:0001583	missense	7516	exon3			TGAGAAGGTTCTT	Y08837	CCDS5933.1	7q36	2006-05-04			ENSG00000196584	ENSG00000196584			12829	protein-coding gene	gene with protein product	"RAD51-like"	600375				7607692, 10422536	Standard	NM_005431		Approved		uc003wld.3	O43543	OTTHUMG00000151470	ENST00000359321.1:c.626C>A	7.37:g.152345944G>T	ENSP00000352271:p.Pro209His	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	90	17	NM_005431	0	0	0	0	0	B2R925	Missense_Mutation	SNP	ENST00000359321.1	37	CCDS5933.1	.	.	.	.	.	.	.	.	.	.	G	3.744	-0.053028	0.07362	.	.	ENSG00000196584	ENST00000359321	T	0.59364	0.27	5.06	5.06	0.68205	.	0.796894	0.11753	N	0.532874	T	0.49098	0.1537	L	0.36672	1.1	0.09310	N	1	B	0.19331	0.035	B	0.21708	0.036	T	0.38134	-0.9675	10	0.45353	T	0.12	-11.3151	10.9302	0.47213	0.0958:0.0:0.9042:0.0	.	209	O43543	XRCC2_HUMAN	H	209	ENSP00000352271:P209H	ENSP00000352271:P209H	P	-	2	0	XRCC2	151976877	0.216000	0.23585	0.036000	0.18154	0.024000	0.10985	2.673000	0.46858	2.353000	0.79882	0.467000	0.42956	CCT	.		0.453	XRCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322783.1	NM_005431		T	152345944	G	T	152345944	3	4	41	1	0	0	0	0	1	0	0	0	17486	1000	35	4	220	4	XRCC2	7	152345944	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	19775503	152345944	6792719	51	3775											
WDR67	93594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	124154514	124154514	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcctaggtgattaaagaaAatttggcaaaggctgaacaa	16	11	9	5	0	0	3	0	2	0	1	1	3	1	3	1	3	1	2	1	3	8	4	rs144810574	byFrequency	TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:124154514A>T	ENST00000287380.1	+	19	2743	c.2653A>T	c.(2653-2655)Aat>Tat	p.N885Y	TBC1D31_ENST00000521676.1_Missense_Mutation_p.N762Y|TBC1D31_ENST00000378080.2_Intron|TBC1D31_ENST00000518805.1_Missense_Mutation_p.N439Y|TBC1D31_ENST00000309336.3_Intron|TBC1D31_ENST00000327098.5_Intron|TBC1D31_ENST00000522420.1_Missense_Mutation_p.N780Y	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	885						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										GATTAAAGAAAATTTGGCAAA	0.338																																					p.N885Y		.											.	WDR67-226	0			c.A2653T						.						51	48	49					8																	124154514		2203	4300	6503	SO:0001583	missense	93594	exon19			AAAGAAAATTTGG	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"WD repeat domain containing"	30888	protein-coding gene	gene with protein product			"WD repeat domain 67"	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2653A>T	8.37:g.124154514A>T	ENSP00000287380:p.Asn885Tyr	Somatic	405	1		WXS	Illumina HiSeq	Phase_I	349	107	NM_145647	0	0	1	1	0	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Missense_Mutation	SNP	ENST00000287380.1	37	CCDS6338.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474411	0.26423	.	.	ENSG00000156787	ENST00000287380;ENST00000522420;ENST00000521676;ENST00000518805	D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09	5.36	4.15	0.48705	.	0.359706	0.32120	N	0.006559	T	0.80199	0.4579	L	0.29908	0.895	0.58432	D	0.999994	P;B	0.42785	0.79;0.0	B;B	0.41723	0.365;0.001	T	0.81892	-0.0724	10	0.72032	D	0.01	-12.8896	9.5604	0.39366	0.7375:0.0:0.0:0.2625	.	780;885	E7ERK7;Q96DN5	.;WDR67_HUMAN	Y	885;780;762;439	ENSP00000287380:N885Y;ENSP00000429334:N780Y;ENSP00000430628:N762Y;ENSP00000429494:N439Y	ENSP00000287380:N885Y	N	+	1	0	WDR67	124223695	0.899000	0.30636	0.992000	0.48379	0.716000	0.41182	1.826000	0.39092	2.046000	0.60703	0.386000	0.25728	AAT	A|0.999;C|0.001		0.338	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647		T	124154514	A	T	124154514	3	4	41	1	0	0	0	0	1	0	0	0	17351	14	1	5	2727	5	WDR67	8	124154514	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		124154514	22209508	52	3776											
FAM49B	51571	broad.mit.edu;bcgsc.ca	37	chr8	130866576	130866576	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agctgaaatcattctgtatgGcaggatttgtcatctgaaga	12	13	10	6	0	4	3	2	2	2	1	4	4	4	4	0	2	1	3	0	2	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:130866576G>T	ENST00000519824.2	-	7	725	c.452C>A	c.(451-453)gCc>gAc	p.A151D	FAM49B_ENST00000522941.1_Missense_Mutation_p.A5D|FAM49B_ENST00000517654.1_Missense_Mutation_p.A151D|FAM49B_ENST00000522746.1_Missense_Mutation_p.A151D|FAM49B_ENST00000401979.2_Missense_Mutation_p.A151D|FAM49B_ENST00000523509.1_Missense_Mutation_p.A151D|FAM49B_ENST00000522250.1_Missense_Mutation_p.A5D|FAM49B_ENST00000519540.1_Missense_Mutation_p.A151D|FAM49B_ENST00000518879.1_5'Flank|FAM49B_ENST00000519110.1_Missense_Mutation_p.A151D	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	151						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			ATTCTGTATGGCAGGATTTGT	0.308																																					p.A151D													.	FAM49B-90	0			c.C452A						.						114	104	108					8																	130866576		2203	4299	6502	SO:0001583	missense	51571	exon7			TGTATGGCAGGAT	AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.452C>A	8.37:g.130866576G>T	ENSP00000429150:p.Ala151Asp	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	92	5	NM_016623	0	0	49	49	0	Q96AZ5|Q9NW21|Q9NZE7	Missense_Mutation	SNP	ENST00000519824.2	37	CCDS6361.1	.	.	.	.	.	.	.	.	.	.	G	33	5.252236	0.95336	.	.	ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000522250;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000522941;ENST00000311292	T;T;T;T;T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57;0.57	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.73418	0.3584	M	0.85299	2.745	0.80722	D	1	D	0.53462	0.96	P	0.58130	0.833	T	0.76567	-0.2912	10	0.62326	D	0.03	-6.4013	18.6274	0.91346	0.0:0.0:1.0:0.0	.	151	Q9NUQ9	FA49B_HUMAN	D	151;151;151;151;5;151;151;151;5;105	ENSP00000428117:A151D;ENSP00000429802:A151D;ENSP00000384880:A151D;ENSP00000429078:A151D;ENSP00000429978:A5D;ENSP00000429150:A151D;ENSP00000430674:A151D;ENSP00000429499:A151D;ENSP00000430433:A5D	ENSP00000311651:A105D	A	-	2	0	FAM49B	130935758	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.586000	0.98226	2.745000	0.94114	0.491000	0.48974	GCC	.		0.308	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623		T	130866576	G	T	130866576	3	4	41	1	0	0	0	0	1	0	0	0	5595	1203	42	4	546	4	FAM49B	8	130866576	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	6712062	130866576	15497446	53	3777											
COL22A1	169044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	139707081	139707081	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactcaccggttccccaggCaggcctggatcgcccttctc	6	8	10	17	2	2	1	1	0	1	1	5	2	3	2	5	4	0	2	5	4	0	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:139707081C>A	ENST00000303045.6	-	33	3080	c.2634G>T	c.(2632-2634)ctG>ctT	p.L878L	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Silent_p.L878L	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	878	Collagen-like 7.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTTCCCCAGGCAGGCCTGGAT	0.607										HNSCC(7;0.00092)																											p.L878L		.											.	COL22A1-103	0			c.G2634T						.						104	98	100					8																	139707081		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon33			CCCAGGCAGGCCT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2634G>T	8.37:g.139707081C>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	54	16	NM_152888	0	0	0	0	0	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			.		0.607	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139707081	C	A	139707081	2	1	41	1	0	0	0	0	0	0	0	1	3687	697	25	4		4	COL22A1	8	139707081	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	8840505	139707081	6656941	54	3778											
SCRIB	23513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144892982	144892982	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctcccctgctgcccagcAtcctctgcagcaggtgagcg	6	7	12	16	1	1	1	0	1	1	0	3	1	3	1	4	2	6	5	4	2	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:144892982A>T	ENST00000320476.3	-	12	1284	c.1278T>A	c.(1276-1278)gaT>gaA	p.D426E	SCRIB_ENST00000377533.3_Missense_Mutation_p.D345E|SCRIB_ENST00000356994.2_Missense_Mutation_p.D426E|MIR937_ENST00000401271.1_RNA	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	426	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCTGCCCAGCATCCTCTGCAG	0.662																																					p.D426E	Pancreas(51;966 1133 10533 14576 29674)	.											.	SCRIB-228	0			c.T1278A						.						24	25	25					8																	144892982		2202	4298	6500	SO:0001583	missense	23513	exon12			CCCAGCATCCTCT	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"scribbled homolog (Drosophila)"			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1278T>A	8.37:g.144892982A>T	ENSP00000322938:p.Asp426Glu	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	21	6	NM_015356	0	0	0	0	0	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951040	0.53186	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.76448	-1.02;-1.02;-1.02	3.91	-5.87	0.02297	.	.	.	.	.	T	0.37972	0.1023	N	0.02011	-0.69	0.19775	N	0.999951	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.40683	-0.9550	9	0.06365	T	0.9	.	0.624	0.00783	0.3145:0.12:0.3208:0.2448	.	426;426	Q14160;Q14160-3	SCRIB_HUMAN;.	E	426;426;345	ENSP00000349486:D426E;ENSP00000322938:D426E;ENSP00000366756:D345E	ENSP00000322938:D426E	D	-	3	2	SCRIB	144964970	0.000000	0.05858	0.001000	0.08648	0.733000	0.41908	-0.296000	0.08287	-1.858000	0.01158	-0.464000	0.05259	GAT	.		0.662	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		T	144892982	A	T	144892982	3	4	41	1	0	0	0	0	1	0	0	0	13969	214	8	5	3793	5	SCRIB	8	144892982	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	5185901	144892982	1471040	55	3779											
KIAA2026	158358	broad.mit.edu;bcgsc.ca	37	chr9	6007447	6007447	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcggcccttccgccaccTcctcctccgcggtggcaacg	3	7	11	20	6	0	0	0	0	0	0	4	0	4	0	7	3	2	1	7	3	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr9:6007447T>C	ENST00000399933.3	-	1	340	c.341A>G	c.(340-342)gAg>gGg	p.E114G	KIAA2026_ENST00000381461.2_Missense_Mutation_p.E114G|MIR4665_ENST00000581132.1_RNA	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	114										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TTCCGCCACCTCCTCCTCCGC	0.716																																					p.E114G													.	KIAA2026-92	0			c.A341G						.						11	14	13					9																	6007447		1846	4079	5925	SO:0001583	missense	158358	exon1			GCCACCTCCTCCT	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.341A>G	9.37:g.6007447T>C	ENSP00000382815:p.Glu114Gly	Somatic	38	2		WXS	Illumina HiSeq	Phase_I	54	19	NM_001017969	0	0	0	0	0	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	37		.	.	.	.	.	.	.	.	.	.	T	12.00	1.806818	0.31961	.	.	ENSG00000183354	ENST00000399933;ENST00000381461;ENST00000513355	.	.	.	4.34	1.7	0.24286	Bromodomain (1);	.	.	.	.	T	0.17492	0.0420	N	0.08118	0	0.23994	N	0.996238	B	0.06786	0.001	B	0.09377	0.004	T	0.18085	-1.0348	8	0.62326	D	0.03	.	4.8866	0.13706	0.0:0.1904:0.2208:0.5888	.	114	Q5HYC2	K2026_HUMAN	G	114	.	ENSP00000370870:E114G	E	-	2	0	KIAA2026	5997447	0.000000	0.05858	1.000000	0.80357	0.483000	0.33249	0.084000	0.14891	0.653000	0.30826	0.402000	0.26972	GAG	.		0.716	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		C	6007447	T	C	6007447	3	2	41	1	0	0	0	0	1	0	0	0	8291	1551	54	3	6002	3	KIAA2026	9	6007447	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		6007447	135205984	56	3780											
SHB	6461	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	37919918	37919918	+	Frame_Shift_Del	DEL	C	C	-																															agtggatgacttccgggacaCtgtcgaacggagggctgttc																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr9:37919918delC	ENST00000377707.3	-	6	1995	c.1430delG	c.(1429-1431)agtfs	p.S477fs	RP11-613M10.9_ENST00000540557.1_Intron	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	477	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		TTCCGGGACACTGTCGAACGG	0.517																																					p.S477fs		.											.	SHB-92	0			c.1430delG						.						145	154	151					9																	37919918		2044	4183	6227	SO:0001589	frameshift_variant	6461	exon6			.		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"SH2 domain containing"	10838	protein-coding gene	gene with protein product		600314	"SHB adaptor protein (a Src homology 2 protein)", "SHB (Src homology 2 domain containing) adaptor protein B"			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.1430delG	9.37:g.37919918delC	ENSP00000366936:p.Ser477fs	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	140	35	NM_003028	0	0	0	0	0	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Frame_Shift_Del	DEL	ENST00000377707.3	37	CCDS43806.1																																																																																			.		0.517	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1			-	37919918	C	-	37919918	7	5	41	1	0	1	0	1	0	0	0	0	14300	565	20	0	103	0	SHB	9	37919918	Frame_Shift_Del	DEL	C	TCGA-B1-A657-01A-11D-A31X-10	31912471	37919918	103293513	57	3781											
PBX3	5090	ucsc.edu;bcgsc.ca	37	chr9	128723051	128723051	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctctatgctgcaaagaCggccgtgacagctgcacacg	11	6	10	14	3	1	2	0	1	1	1	1	2	1	2	2	1	5	4	2	1	3	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr9:128723051C>T	ENST00000373489.5	+	6	948	c.932C>T	c.(931-933)aCg>aTg	p.T311M	PBX3_ENST00000373483.2_Missense_Mutation_p.T130M|PBX3_ENST00000342287.5_Missense_Mutation_p.T311M|PBX3_ENST00000538998.1_3'UTR|PBX3_ENST00000447726.2_Missense_Mutation_p.T236M|PBX3_ENST00000373487.4_Missense_Mutation_p.T332M	NM_006195.5	NP_006186.1	P40426	PBX3_HUMAN	pre-B-cell leukemia homeobox 3	311					adult locomotory behavior (GO:0008344)|anterior compartment pattern formation (GO:0007387)|dorsal spinal cord development (GO:0021516)|neuron development (GO:0048666)|posterior compartment specification (GO:0007388)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)	24						GCTGCAAAGACGGCCGTGACA	0.517																																					p.T311M													.	PBX3-91	0			c.C932T						.						69	59	62					9																	128723051		2203	4300	6503	SO:0001583	missense	5090	exon6			CAAAGACGGCCGT		CCDS6865.1, CCDS48021.1	9q33.3	2011-06-20	2007-01-30		ENSG00000167081	ENSG00000167081		"Homeoboxes / TALE class"	8634	protein-coding gene	gene with protein product		176312	"pre-B-cell leukemia transcription factor 3"			1682799	Standard	NM_006195		Approved		uc004bqb.3	P40426	OTTHUMG00000020684	ENST00000373489.5:c.932C>T	9.37:g.128723051C>T	ENSP00000362588:p.Thr311Met	Somatic	182	2		WXS	Illumina HiSeq		164	39	NM_006195	0	0	6	7	1	E9PB27|Q5JSA0|Q5JSA1|Q5VXL3|Q96PF9|Q96PG0	Missense_Mutation	SNP	ENST00000373489.5	37	CCDS6865.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.806995	0.90623	.	.	ENSG00000167081	ENST00000373492;ENST00000373489;ENST00000342287;ENST00000373487;ENST00000373483;ENST00000373482;ENST00000447726;ENST00000538998	D;D;T;D;D;D	0.89617	-2.33;-2.28;1.69;-2.5;-2.54;-2.41	5.87	5.87	0.94306	.	0.090349	0.85682	D	0.000000	D	0.94420	0.8205	M	0.76574	2.34	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;P;P	0.75020	0.985;0.846;0.828	D	0.93532	0.6870	10	0.49607	T	0.09	.	20.2192	0.98319	0.0:1.0:0.0:0.0	.	222;332;311	B7Z5Q0;Q5JS98;P40426	.;.;PBX3_HUMAN	M	130;311;311;332;130;130;236;222	ENSP00000362588:T311M;ENSP00000341990:T311M;ENSP00000362586:T332M;ENSP00000362582:T130M;ENSP00000387456:T236M;ENSP00000444005:T222M	ENSP00000341990:T311M	T	+	2	0	PBX3	127762872	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.487000	0.81328	2.780000	0.95670	0.655000	0.94253	ACG	.		0.517	PBX3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417765.1			T	128723051	C	T	128723051	3	4	41	1	0	0	0	0	1	0	0	0	11520	536	19	1	954	1	PBX3	9	128723051	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	90803133	128723051	12490380	58	3782											
C9orf86	55684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139734263	139734263	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcagactgaagaatgactcgGacctcttcgggctggggctg	8	9	14	10	2	2	4	1	2	1	2	4	5	2	5	1	4	0	2	1	4	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr9:139734263G>A	ENST00000311502.7	+	13	2112	c.1876G>A	c.(1876-1878)Gac>Aac	p.D626N	RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371675.3_Missense_Mutation_p.D511N|RABL6_ENST00000371663.4_Missense_Mutation_p.D627N|RABL6_ENST00000432842.2_3'UTR			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	626					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										GAATGACTCGGACCTCTTCGG	0.657																																					p.D627N		.											.	.	0			c.G1879A						.						29	35	33					9																	139734263		1894	4100	5994	SO:0001583	missense	55684	exon13			GACTCGGACCTCT	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1876G>A	9.37:g.139734263G>A	ENSP00000311134:p.Asp626Asn	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	49	18	NM_001173988	0	0	36	59	23	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	37	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	19.33	3.807620	0.70797	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.80909	-1.11;-1.14;-1.13;-1.43	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.88930	0.6571	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.996	D	0.90196	0.4253	10	0.66056	D	0.02	-24.3311	15.167	0.72837	0.0:0.0:1.0:0.0	.	420;627;626	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	N	627;626;511;420	ENSP00000360727:D627N;ENSP00000311134:D626N;ENSP00000360740:D511N;ENSP00000408442:D420N	ENSP00000311134:D626N	D	+	1	0	C9orf86	138854084	1.000000	0.71417	0.511000	0.27724	0.034000	0.12701	7.931000	0.87625	2.162000	0.67917	0.561000	0.74099	GAC	.		0.657	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		A	139734263	G	A	139734263	3	1	41	1	0	0	0	0	1	0	0	0	2508	1174	41	2	2173	2	C9orf86	9	139734263	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	11011212	139734263	1479168	59	3783											
RHOBTB1	9886	broad.mit.edu;bcgsc.ca	37	chr10	62637691	62637691	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtgcaaccaagtgtggcagGcaaaatctgtttgccaaggc	12	8	12	9	0	1	0	0	0	1	0	1	0	1	0	2	3	3	4	2	3	5	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr10:62637691G>A	ENST00000337910.5	-	8	2038	c.1701C>T	c.(1699-1701)tgC>tgT	p.C567C	RHOBTB1_ENST00000490827.1_5'Flank|RHOBTB1_ENST00000357917.4_Silent_p.C567C	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	567					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					AGTGTGGCAGGCAAAATCTGT	0.403																																					p.C567C													.	RHOBTB1-228	0			c.C1701T						.						95	90	92					10																	62637691		2203	4300	6503	SO:0001819	synonymous_variant	9886	exon8			TGGCAGGCAAAAT	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"BTB/POZ domain containing"	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1701C>T	10.37:g.62637691G>A		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	153	6	NM_014836	0	0	53	53	0		Silent	SNP	ENST00000337910.5	37	CCDS7261.1																																																																																			.		0.403	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			A	62637691	G	A	62637691	2	1	41	1	0	0	0	0	0	0	0	1	13365	1195	42	2		2	RHOBTB1	10	62637691	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		62637691	72897056	60	3784											
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	89692845	89692845	+	Frame_Shift_Del	DEL	A	A	-																															cttttgtgaagatcttgaccAatggctaagtgaagatgaca																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr10:89692845delA	ENST00000371953.3	+	5	1686	c.329delA	c.(328-330)caafs	p.Q110fs		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	110	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(5)|p.Y27fs*1(2)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GATCTTGACCAATGGCTAAGT	0.398		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.Q110fs		.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN-17735	50	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	c.329delA						.						127	117	121					10																	89692845		2203	4297	6500	SO:0001589	frameshift_variant	5728	exon5	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.329delA	10.37:g.89692845delA	ENSP00000361021:p.Gln110fs	Somatic	229	0		WXS	Illumina HiSeq	Phase_I	224	59	NM_000314	0	0	0	0	0	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	37	CCDS31238.1																																																																																			.		0.398	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89692845	A	-	89692845	7	5	41	1	0	1	0	1	0	0	0	0	12767	130	5	0	347	0	PTEN	10	89692845	Frame_Shift_Del	DEL	A	TCGA-B1-A657-01A-11D-A31X-10	27055154	89692845	45841902	61	3785											
SYCE1	93426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	135372389	135372390	+	Missense_Mutation	DNP	AG	AG	TT																															cggctctcttacgcgagtccAgttccttctgcagggcctca																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr10:135372389_135372390AG>TT	ENST00000343131.5	-	4	366_367	c.262_263CT>AA	c.(262-264)CTg>AAg	p.L88K	SYCE1_ENST00000432597.2_Missense_Mutation_p.L52K|SPRN_ENST00000541506.1_Intron|SYCE1_ENST00000368517.3_Missense_Mutation_p.L52K	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	88					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACGCGAGTCCAGTTCCTTCTGC	0.53																																					p.L88K		.											.	SYCE1-91	0			c.C262A						.																																			SO:0001583	missense	93426	exon4			AGTCCAGTTCCTT	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"cancer/testis antigen 76"	611486	"chromosome 10 open reading frame 94"	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.262_263delinsTT	10.37:g.135372389_135372390delinsTT	ENSP00000341282:p.Leu88Lys	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	72	22	NM_001143764	0	0	0	0	0	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	DNP	ENST00000343131.5	37	CCDS44501.1																																																																																			.		0.53	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564		TT	135372390	AG	TT	135372389	3	4	41	1	0	0	0	0	1	0	0	0	15460	188	7	5	875	5	SYCE1	10	135372389	Missense_Mutation	DNP	AG	TCGA-B1-A657-01A-11D-A31X-10	45679544	135372389	162358	62	3786											
DAK	26007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	61111339	61111339	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccttagatgctgaaaccActgcagcagcctggcctaac	10	8	9	14	0	0	2	0	1	0	1	0	2	0	2	4	1	7	3	4	1	3	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:61111339A>G	ENST00000394900.3	+	12	1223	c.994A>G	c.(994-996)Act>Gct	p.T332A		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	332	DhaK. {ECO:0000255|PROSITE- ProRule:PRU00814}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						TGCTGAAACCACTGCAGCAGC	0.627																																					p.T332A		.											.	DAK-115	0			c.A994G						.						88	95	93					11																	61111339		2203	4299	6502	SO:0001583	missense	26007	exon12			GAAACCACTGCAG		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.994A>G	11.37:g.61111339A>G	ENSP00000378360:p.Thr332Ala	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_015533	0	0	0	0	0	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	37	CCDS8003.1	.	.	.	.	.	.	.	.	.	.	A	9.592	1.126311	0.20959	.	.	ENSG00000149476	ENST00000394900;ENST00000529479	T;T	0.29142	1.58;1.58	5.84	3.45	0.39498	Dak kinase (2);	0.410578	0.28219	N	0.016157	T	0.18045	0.0433	N	0.25957	0.775	0.19575	N	0.999969	B;B	0.11235	0.004;0.0	B;B	0.16289	0.015;0.005	T	0.21280	-1.0250	10	0.25106	T	0.35	-6.7353	5.6557	0.17640	0.6665:0.0:0.0707:0.2628	.	332;332	Q2L9C1;Q3LXA3	.;DHAK_HUMAN	A	332;331	ENSP00000378360:T332A;ENSP00000432539:T331A	ENSP00000378360:T332A	T	+	1	0	DAK	60867915	0.984000	0.35163	0.040000	0.18447	0.922000	0.55478	3.052000	0.49893	0.443000	0.26582	0.533000	0.62120	ACT	.		0.627	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		G	61111339	A	G	61111339	3	3	41	1	0	0	0	0	1	0	0	0	4234	159	6	3	1036	3	DAK	11	61111339	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		61111339	73895177	63	3787											
CCDC87	55231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66359427	66359427	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caactgcttcagatcctcagCcacgatgagcccagtcagct	10	8	8	15	1	3	2	3	1	0	1	4	3	4	2	3	0	5	2	3	0	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:66359427C>T	ENST00000333861.3	-	1	1127	c.1060G>A	c.(1060-1062)Gct>Act	p.A354T	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	354					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						AGATCCTCAGCCACGATGAGC	0.587																																					p.A354T		.											.	CCDC87-92	0			c.G1060A						.						49	55	53					11																	66359427		2200	4295	6495	SO:0001583	missense	55231	exon1			CCTCAGCCACGAT	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.1060G>A	11.37:g.66359427C>T	ENSP00000328487:p.Ala354Thr	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	69	29	NM_018219	0	0	0	0	0	Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	37	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390249	0.42410	.	.	ENSG00000182791	ENST00000333861	T	0.32753	1.44	5.3	1.08	0.20341	.	0.256314	0.25159	N	0.032698	T	0.24353	0.0590	M	0.67953	2.075	0.31044	N	0.715953	B	0.27882	0.192	B	0.21151	0.033	T	0.13150	-1.0520	10	0.44086	T	0.13	.	3.6025	0.08030	0.1848:0.5359:0.0:0.2793	.	354	Q9NVE4	CCD87_HUMAN	T	354	ENSP00000328487:A354T	ENSP00000328487:A354T	A	-	1	0	CCDC87	66116003	0.993000	0.37304	0.982000	0.44146	0.282000	0.26991	0.720000	0.25896	0.395000	0.25257	-0.251000	0.11542	GCT	.		0.587	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		T	66359427	C	T	66359427	3	4	41	1	0	0	0	0	1	0	0	0	2868	739	26	2	1493	2	CCDC87	11	66359427	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	5248088	66359427	68647089	64	3788											
ANKRD13D	338692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67058950	67058950	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctctggtttctcttaggccCccgatttctacgttgagatg	5	15	10	11	2	3	1	0	1	3	1	4	3	3	1	2	2	1	3	2	2	2	5	rs373999660		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:67058950C>A	ENST00000447274.2	+	4	1269	c.94C>A	c.(94-96)Ccc>Acc	p.P32T	ANKRD13D_ENST00000514166.1_Missense_Mutation_p.P32T|ANKRD13D_ENST00000511455.2_Missense_Mutation_p.P119T|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.P32T			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	32						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CTCTTAGGCCCCCGATTTCTA	0.627																																					p.P119T		.											.	ANKRD13D-91	0			c.C355A						.						58	61	60					11																	67058950		2200	4295	6495	SO:0001583	missense	338692	exon4			TAGGCCCCCGATT	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.94C>A	11.37:g.67058950C>A	ENSP00000402616:p.Pro32Thr	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	36	10	NM_207354	0	0	2	2	0	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	37		.	.	.	.	.	.	.	.	.	.	C	14.41	2.526001	0.44969	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.35048	1.33;1.49;1.33;1.33	3.95	3.02	0.34903	.	0.093915	0.45361	D	0.000371	T	0.45538	0.1347	M	0.67397	2.05	0.45108	D	0.998126	P;D	0.59357	0.887;0.985	B;P	0.53809	0.441;0.735	T	0.44862	-0.9300	10	0.66056	D	0.02	-20.8257	8.6108	0.33801	0.0:0.7549:0.157:0.0882	.	119;32	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	T	32;119;32;32	ENSP00000402616:P32T;ENSP00000427130:P119T;ENSP00000310874:P32T;ENSP00000444404:P32T	ENSP00000310874:P32T	P	+	1	0	ANKRD13D	66815526	0.007000	0.16637	0.972000	0.41901	0.271000	0.26615	1.546000	0.36179	1.014000	0.39417	0.561000	0.74099	CCC	.		0.627	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		A	67058950	C	A	67058950	3	1	41	1	0	0	0	0	1	0	0	0	644	623	22	4	369	4	ANKRD13D	11	67058950	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	699523	67058950	67947566	65	3789											
PITPNM1	9600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	67267651	67267651	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggggaggcatctgggcctggGggggcctcaggcccatcggg	4	5	21	11	1	2	0	1	0	1	0	3	1	2	1	3	9	0	1	3	9	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:67267651G>A	ENST00000534749.1	-	5	1070	c.882C>T	c.(880-882)ccC>ccT	p.P294P	PITPNM1_ENST00000436757.2_Silent_p.P294P|PITPNM1_ENST00000356404.3_Silent_p.P294P			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	294					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CTGGGCCTGGGGGGGCCTCAG	0.692																																					p.P294P	GBM(28;144 709 4607 5525)	.											.	PITPNM1-227	0			c.C882T						.						25	31	29					11																	67267651		2171	4250	6421	SO:0001819	synonymous_variant	9600	exon6			GCCTGGGGGGGCC	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.882C>T	11.37:g.67267651G>A		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	23	11	NM_001130848	0	0	14	23	9	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	37	CCDS31620.1																																																																																			.		0.692	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		A	67267651	G	A	67267651	2	1	41	1	0	0	0	0	0	0	0	1	11976	1219	43	2		2	PITPNM1	11	67267651	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	208701	67267651	67738865	66	3790											
LRP6	4040	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12303827	12303827	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtcgtgagtcaatccaataGagttgcttgtccagtgggtc	8	13	12	8	1	1	2	1	1	0	1	5	2	3	2	2	1	1	2	2	1	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:12303827G>C	ENST00000261349.4	-	13	3013	c.2937C>G	c.(2935-2937)ctC>ctG	p.L979L	LRP6_ENST00000543091.1_Silent_p.L979L	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	979	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CAATCCAATAGAGTTGCTTGT	0.468																																					p.L979L													.	LRP6-661	0			c.C2937G						.						234	209	218					12																	12303827		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon13			CCAATAGAGTTGC	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.2937C>G	12.37:g.12303827G>C		Somatic	154	2		WXS	Illumina HiSeq	Phase_I	126	35	NM_002336	0	0	0	0	0	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			.		0.468	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12303827	G	C	12303827	2	2	41	1	0	0	0	0	0	0	0	1	8987	929	33	4		4	LRP6	12	12303827	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		12303827	121548068	67	3791											
LASS5	91012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	50529605	50529605	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccgctgatacttggcataaTtggccagtttggctgcctgg	6	12	13	10	1	0	1	0	1	0	0	0	1	0	1	3	4	2	4	3	4	2	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:50529605T>C	ENST00000317551.6	-	8	906	c.782A>G	c.(781-783)aAt>aGt	p.N261S	CERS5_ENST00000422340.2_Missense_Mutation_p.N203S	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	261	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CTTGGCATAATTGGCCAGTTT	0.428																																					p.N261S		.											.	.	0			c.A782G						.						92	88	89					12																	50529605		2203	4300	6503	SO:0001583	missense	91012	exon8			GCATAATTGGCCA		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.782A>G	12.37:g.50529605T>C	ENSP00000325485:p.Asn261Ser	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	87	20	NM_147190	0	0	10	20	10	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	37	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.79|15.79	2.936979|2.936979	0.52972|0.52972	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000550547;ENST00000547800|ENST00000551005;ENST00000317551;ENST00000422340	.|D;D;D	.|0.84660	.|-1.88;-1.88;-1.88	4.7|4.7	4.7|4.7	0.59300|0.59300	.|TRAM/LAG1/CLN8 homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.86239|0.86239	0.5885|0.5885	L|L	0.58101|0.58101	1.795|1.795	0.58432|0.58432	D|D	0.999999|0.999999	.|P;B;P	.|0.40794	.|0.688;0.198;0.729	.|P;B;P	.|0.47346	.|0.491;0.14;0.544	D|D	0.86223|0.86223	0.1632|0.1632	5|10	.|0.42905	.|T	.|0.14	-12.9936|-12.9936	14.6573|14.6573	0.68844|0.68844	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|203;261;180	.|B4DV54;Q8N5B7;F8W0U5	.|.;CERS5_HUMAN;.	V|S	63;165|180;261;203	.|ENSP00000447556:N180S;ENSP00000325485:N261S;ENSP00000389050:N203S	.|ENSP00000325485:N261S	I|N	-|-	1|2	0|0	CERS5|CERS5	48815872|48815872	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.868000|7.868000	0.87116|0.87116	2.099000|2.099000	0.63709|0.63709	0.533000|0.533000	0.62120|0.62120	ATT|AAT	.		0.428	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		C	50529605	T	C	50529605	3	2	41	1	0	0	0	0	1	0	0	0	8663	1493	52	3	408	3	LASS5	12	50529605	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	38225778	50529605	83322290	68	3792											
PTPRR	5801	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	71139777	71139777	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctcggacagtgctggctgTaatgtgatgggcgataggtg	7	10	17	7	2	0	1	0	1	0	0	1	3	0	2	1	4	1	3	1	4	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:71139777T>A	ENST00000283228.2	-	6	1280	c.828A>T	c.(826-828)ttA>ttT	p.L276F	PTPRR_ENST00000549308.1_Missense_Mutation_p.L31F|PTPRR_ENST00000440835.2_Missense_Mutation_p.L31F|PTPRR_ENST00000378778.1_Missense_Mutation_p.L70F|PTPRR_ENST00000342084.4_Missense_Mutation_p.L164F	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	276					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		GTGCTGGCTGTAATGTGATGG	0.473																																					p.L276F													.	PTPRR-652	0			c.A828T						.						207	168	181					12																	71139777		2203	4300	6503	SO:0001583	missense	5801	exon6			TGGCTGTAATGTG	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.828A>T	12.37:g.71139777T>A	ENSP00000283228:p.Leu276Phe	Somatic	144	1		WXS	Illumina HiSeq	Phase_I	128	36	NM_002849	0	0	0	1	1	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.066317	0.36470	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308;ENST00000550661	T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33	5.0	2.61	0.31194	.	0.177186	0.25997	N	0.026967	T	0.23094	0.0558	L	0.44542	1.39	0.24575	N	0.993907	P;P;P;P	0.49961	0.93;0.731;0.731;0.612	B;B;B;B	0.44224	0.36;0.444;0.241;0.347	T	0.09314	-1.0680	10	0.12766	T	0.61	-2.501	0.2888	0.00255	0.2828:0.1721:0.1493:0.3959	.	125;164;70;276	B7Z998;F5GXR7;Q15256-4;Q15256	.;.;.;PTPRR_HUMAN	F	31;276;70;164;31;31	ENSP00000391750:L31F;ENSP00000283228:L276F;ENSP00000368054:L70F;ENSP00000339605:L164F;ENSP00000446943:L31F;ENSP00000449616:L31F	ENSP00000283228:L276F	L	-	3	2	PTPRR	69426044	0.939000	0.31865	0.664000	0.29753	0.391000	0.30476	0.029000	0.13666	0.247000	0.21414	0.533000	0.62120	TTA	.		0.473	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71139777	T	A	71139777	3	1	41	1	0	0	0	0	1	0	0	0	12842	1635	57	5	1181	5	PTPRR	12	71139777	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	20610172	71139777	62712118	69	3793											
SIRT4	23409	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	120750516	120750517	+	Frame_Shift_Del	DEL	AA	AA	-																															tgtgcacaagcgtgtaaaagAagccgactccctcttggtgg																								rs16950058|rs201277474	byFrequency	TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:120750516_120750517delAA	ENST00000202967.4	+	3	814_815	c.755_756delAA	c.(754-756)gaafs	p.E252fs	RNU6-1088P_ENST00000516850.1_RNA|SIRT4_ENST00000537892.1_3'UTR	NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGTGTAAAAGAAGCCGACTCCC	0.525																																					p.252_252del		.											.	SIRT4-226	0			c.755_756del						.																																			SO:0001589	frameshift_variant	23409	exon3			.	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4", "sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.755_756delAA	12.37:g.120750516_120750517delAA	ENSP00000202967:p.Glu252fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	104	29	NM_012240	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000202967.4	37	CCDS9194.1																																																																																			.		0.525	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		-	120750517	AA	-	120750516	7	5	41	1	0	1	0	1	0	0	0	0	14372	246	9	0	761	0	SIRT4	12	120750516	Frame_Shift_Del	DEL	AA	TCGA-B1-A657-01A-11D-A31X-10	49610739	120750516	13101379	70	3794	41	2									
SIRT4	23409	bcgsc.ca	37	chr12	120750518	120750518	+	Missense_Mutation	SNP	G	G	C																															tgcacaagcgtgtaaaagaaGccgactccctcttggtggtg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:120750518G>C	ENST00000202967.4	+	3	816	c.757G>C	c.(757-759)Gcc>Ccc	p.A253P	RNU6-1088P_ENST00000516850.1_RNA|SIRT4_ENST00000537892.1_3'UTR	NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGTAAAAGAAGCCGACTCCCT	0.527																																					p.A253P													.	SIRT4-226	0			c.G757C						.						67	64	65					12																	120750518		2203	4300	6503	SO:0001583	missense	23409	exon3			AAAGAAGCCGACT	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4", "sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.757G>C	12.37:g.120750518G>C	ENSP00000202967:p.Ala253Pro	Somatic	146	0		WXS	Illumina HiSeq	Phase_1	104	28	NM_012240	0	0	1	1	0		Missense_Mutation	SNP	ENST00000202967.4	37	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994165	0.74703	.	.	ENSG00000089163	ENST00000202967	T	0.50548	0.74	4.59	4.59	0.56863	.	0.109676	0.64402	D	0.000007	T	0.75102	0.3804	H	0.95504	3.68	0.50467	D	0.999878	D	0.57257	0.979	P	0.62649	0.905	T	0.82727	-0.0314	10	0.66056	D	0.02	-23.7192	14.265	0.66110	0.0:0.0:0.8416:0.1584	.	253	Q9Y6E7	SIRT4_HUMAN	P	253	ENSP00000202967:A253P	ENSP00000202967:A253P	A	+	1	0	SIRT4	119234901	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	3.260000	0.51523	2.490000	0.84030	0.650000	0.86243	GCC	.		0.527	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		C	120750518	G	C	120750518	3	2	41	1	0	0	0	0	1	0	0	0	14372	971	34	4	763	4	SIRT4	12	120750518	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	2	120750518	13101377	71	3795	41	2									
GSX1	219409	hgsc.bcm.edu	37	chr13	28367053	28367053	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccccccgggccgcccgcgCtgcctctactcaaggcttcc	3	6	11	21	4	2	0	1	0	1	0	3	0	3	0	7	3	2	2	7	3	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr13:28367053C>T	ENST00000302945.2	+	1	274	c.226C>T	c.(226-228)Ctg>Ttg	p.L76L		NM_145657.1	NP_663632.1	Q9H4S2	GSX1_HUMAN	GS homeobox 1	76					adenohypophysis development (GO:0021984)|hypothalamus development (GO:0021854)|neuron fate commitment (GO:0048663)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		gccgcccgcgcTGCCTCTACT	0.741																																					p.L76L		.											.	GSX1-69	0			c.C226T						.						2	3	3					13																	28367053		1552	3186	4738	SO:0001819	synonymous_variant	219409	exon1			CCCGCGCTGCCTC	AB044157	CCDS9326.1	13q12.2	2012-03-09		2007-07-26	ENSG00000169840	ENSG00000169840		"Homeoboxes / ANTP class : HOXL subclass"	20374	protein-coding gene	gene with protein product				GSH1			Standard	NM_145657		Approved	Gsh-1	uc001urr.1	Q9H4S2	OTTHUMG00000016637	ENST00000302945.2:c.226C>T	13.37:g.28367053C>T		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	16	4	NM_145657	0	0	0	0	0	Q9UD62	Silent	SNP	ENST00000302945.2	37	CCDS9326.1																																																																																			.		0.741	GSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044309.2	NM_145657		T	28367053	C	T	28367053	2	4	41	1	0	0	0	0	0	0	0	1	6870	796	28	2		2	GSX1	13	28367053	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		28367053	86802825	72	3796											
NBEA	26960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	35758158	35758158	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaagtttgaaccatggatTccttgccaagttaattcctg	10	14	7	10	0	0	1	0	1	0	0	3	2	3	2	5	1	2	2	5	1	4	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr13:35758158T>G	ENST00000400445.3	+	30	5411	c.4877T>G	c.(4876-4878)tTc>tGc	p.F1626C	NBEA_ENST00000540320.1_Missense_Mutation_p.F1626C|NBEA_ENST00000379939.2_Missense_Mutation_p.F1623C|NBEA_ENST00000310336.4_Missense_Mutation_p.F1626C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1626					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AACCATGGATTCCTTGCCAAG	0.413																																					p.F1626C		.											.	NBEA-144	0			c.T4877G						.						122	110	113					13																	35758158		1890	4124	6014	SO:0001583	missense	26960	exon30			ATGGATTCCTTGC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.4877T>G	13.37:g.35758158T>G	ENSP00000383295:p.Phe1626Cys	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	102	32	NM_015678	0	0	1	1	0	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497854	0.44455	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.50277	0.76;0.75;0.75;0.76	5.82	5.82	0.92795	.	0.290400	0.35291	N	0.003313	T	0.31796	0.0808	N	0.08118	0	0.80722	D	1	B	0.27732	0.187	B	0.30855	0.121	T	0.19745	-1.0296	10	0.45353	T	0.12	.	14.7488	0.69508	0.0:0.0:0.0:1.0	.	1623	Q5T321	.	C	1626;1626;1623;1626	ENSP00000440951:F1626C;ENSP00000383295:F1626C;ENSP00000369271:F1623C;ENSP00000308534:F1626C	ENSP00000308534:F1626C	F	+	2	0	NBEA	34656158	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.896000	0.63222	2.222000	0.72286	0.383000	0.25322	TTC	.		0.413	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35758158	T	G	35758158	3	3	41	1	0	0	0	0	1	0	0	0	10212	1783	62	5	4995	5	NBEA	13	35758158	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	7391105	35758158	79411720	73	3797											
GPR137C	283554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	53099007	53099007	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtccatttaattatggcTgggataatctttcagataag	14	14	8	5	0	2	1	1	0	1	1	3	2	3	2	1	2	0	1	1	2	5	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr14:53099007T>A	ENST00000321662.6	+	4	847	c.847T>A	c.(847-849)Tgg>Agg	p.W283R		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	283						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					TAATTATGGCTGGGATAATCT	0.378																																					p.W283R		.											.	GPR137C-68	0			c.T847A						.						125	122	123					14																	53099007		1858	4099	5957	SO:0001583	missense	283554	exon4			TATGGCTGGGATA	BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.847T>A	14.37:g.53099007T>A	ENSP00000315106:p.Trp283Arg	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	126	24	NM_001099652	0	0	0	0	0	Q86SM2	Missense_Mutation	SNP	ENST00000321662.6	37	CCDS45106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.1|25.1	4.606362|4.606362	0.87157|0.87157	.|.	.|.	ENSG00000180998|ENSG00000180998	ENST00000542169|ENST00000321662	.|T	.|0.62498	.|0.02	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77942|0.77942	0.4206|0.4206	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	T|T	0.80360|0.80360	-0.1415|-0.1415	5|10	.|0.87932	.|D	.|0	-12.2616|-12.2616	16.0439|16.0439	0.80704|0.80704	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|283;112	.|Q8N3F9;B3KW22	.|G137C_HUMAN;.	Q|R	252|283	.|ENSP00000315106:W283R	.|ENSP00000315106:W283R	L|W	+|+	2|1	0|0	GPR137C|GPR137C	52168757|52168757	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.499000|7.499000	0.81566|0.81566	2.250000|2.250000	0.74265|0.74265	0.482000|0.482000	0.46254|0.46254	CTG|TGG	.		0.378	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615		A	53099007	T	A	53099007	3	1	41	1	0	0	0	0	1	0	0	0	6667	1580	55	5	861	5	GPR137C	14	53099007	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		53099007	54250533	74	3798											
DNAJC17	55192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41099608	41099608	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatgcctagcagcgcgtAcaggtccatctgtaagagct	10	9	10	12	2	2	1	1	0	1	1	3	1	3	1	2	1	5	4	2	1	4	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:41099608A>G	ENST00000220496.4	-	1	67	c.37T>C	c.(37-39)Tac>Cac	p.Y13H	ZFYVE19_ENST00000564258.1_5'UTR|ZFYVE19_ENST00000299173.10_5'Flank|ZFYVE19_ENST00000355341.4_5'UTR|ZFYVE19_ENST00000336455.5_Missense_Mutation_p.Y41C|ZFYVE19_ENST00000570108.1_Missense_Mutation_p.Y41C	NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	13	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		AGCAGCGCGTACAGGTCCATC	0.577																																					p.Y41C		.											.	ZFYVE19-91	0			c.A122G						.						180	134	150					15																	41099608		2203	4300	6503	SO:0001583	missense	84936	exon1			GCGCGTACAGGTC	AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"Heat shock proteins / DNAJ (HSP40)", "RNA binding motif (RRM) containing"	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.37T>C	15.37:g.41099608A>G	ENSP00000220496:p.Tyr13His	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	155	43	NM_032850	0	0	14	20	6		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.8|27.8	4.859778|4.859778	0.91433|0.91433	.|.	.|.	ENSG00000166140|ENSG00000104129	ENST00000336455|ENST00000220496	T|T	0.27402|0.58940	1.67|0.3	5.35|5.35	5.35|5.35	0.76521|0.76521	.|Heat shock protein DnaJ, N-terminal (5);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.81730|0.81730	0.4884|0.4884	M|M	0.94063|0.94063	3.49|3.49	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.86513|0.86513	0.1811|0.1811	8|10	0.87932|0.87932	D|D	0|0	.|.	14.7373|14.7373	0.69424|0.69424	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|13	.|Q9NVM6	.|DJC17_HUMAN	C|H	41|13	ENSP00000337824:Y41C|ENSP00000220496:Y13H	ENSP00000337824:Y41C|ENSP00000220496:Y13H	Y|Y	+|-	2|1	0|0	ZFYVE19|DNAJC17	38886900|38886900	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.383000|5.383000	0.66219|0.66219	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TAC|TAC	.		0.577	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163		G	41099608	A	G	41099608	3	3	41	1	0	0	0	0	1	0	0	0	4647	391	14	3	921	3	DNAJC17	15	41099608	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		41099608	61431784	75	3799											
MFAP1	4236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	44105507	44105507	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcttcctgctccagctccttCtgtttcaatgcttcggcttc	3	16	7	15	1	2	0	1	0	1	0	7	0	5	0	3	1	3	6	3	1	1	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:44105507C>T	ENST00000267812.3	-	5	898	c.666G>A	c.(664-666)caG>caA	p.Q222Q		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	222					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		CCAGCTCCTTCTGTTTCAATG	0.488																																					p.Q222Q		.											.	MFAP1-226	0			c.G666A						.						350	297	315					15																	44105507		2198	4298	6496	SO:0001819	synonymous_variant	4236	exon5			CTCCTTCTGTTTC		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.666G>A	15.37:g.44105507C>T		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	74	23	NM_005926	0	0	31	55	24	Q86TG6	Silent	SNP	ENST00000267812.3	37	CCDS10105.1																																																																																			.		0.488	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		T	44105507	C	T	44105507	2	4	41	1	0	0	0	0	0	0	0	1	9538	912	32	2		2	MFAP1	15	44105507	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	3005899	44105507	58425885	76	3800											
SECISBP2L	9728	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	49304926	49304926	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagaagaagcaatgtccacAgaattaaaggatgtcaaaca	19	8	8	6	0	1	3	1	0	0	3	2	4	2	4	1	1	2	1	1	1	8	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:49304926A>T	ENST00000559471.1	-	12	1913	c.1650T>A	c.(1648-1650)tcT>tcA	p.S550S	SECISBP2L_ENST00000261847.3_Silent_p.S505S	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	550							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						CAATGTCCACAGAATTAAAGG	0.358																																					p.S550S													.	SECISBP2L-136	0			c.T1650A						.						116	123	121					15																	49304926		2197	4295	6492	SO:0001819	synonymous_variant	9728	exon12			GTCCACAGAATTA	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1650T>A	15.37:g.49304926A>T		Somatic	205	1		WXS	Illumina HiSeq	Phase_I	146	34	NM_001193489	0	0	4	7	3	Q8N767	Silent	SNP	ENST00000559471.1	37	CCDS53942.1																																																																																			.		0.358	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		T	49304926	A	T	49304926	2	4	41	1	0	0	0	0	0	0	0	1	14039	175	7	5		5	SECISBP2L	15	49304926	Silent	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	5199419	49304926	53226466	77	3801											
PIF1	80119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65114469	65114469	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggttcctacttacctgcAaaggcatggagggtggtgcc	8	9	15	9	0	0	0	0	0	0	0	1	1	1	1	3	6	4	3	3	6	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:65114469A>T	ENST00000268043.4	-	4	907	c.813T>A	c.(811-813)ttT>ttA	p.F271L	PIF1_ENST00000333425.6_Missense_Mutation_p.F271L|PIF1_ENST00000559239.1_Missense_Mutation_p.F271L					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						ACTTACCTGCAAAGGCATGGA	0.612																																					p.F271L		.											.	PIF1-227	0			c.T813A						.						60	64	63					15																	65114469		2202	4299	6501	SO:0001583	missense	80119	exon4			ACCTGCAAAGGCA	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"chromosome 15 open reading frame 20", "PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.813T>A	15.37:g.65114469A>T	ENSP00000268043:p.Phe271Leu	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	45	10	NM_025049	0	0	0	0	0		Missense_Mutation	SNP	ENST00000268043.4	37	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	A	24.6	4.553832	0.86231	.	.	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.52295	0.67;0.67	4.98	2.66	0.31614	.	0.100402	0.64402	D	0.000001	T	0.54711	0.1875	L	0.48174	1.505	0.80722	D	1	D	0.58970	0.984	D	0.64877	0.93	T	0.50725	-0.8794	10	0.54805	T	0.06	-11.173	7.9896	0.30233	0.8322:0.0:0.1678:0.0	.	271	Q9H611	PIF1_HUMAN	L	271	ENSP00000268043:F271L;ENSP00000328174:F271L	ENSP00000268043:F271L	F	-	3	2	PIF1	62901522	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.558000	0.36309	0.336000	0.23639	0.533000	0.62120	TTT	.		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		T	65114469	A	T	65114469	3	4	41	1	0	0	0	0	1	0	0	0	11909	127	5	5	1152	5	PIF1	15	65114469	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	15809543	65114469	37416923	78	3802											
NEO1	4756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	73581573	73581573	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccctttgactcccagccaCcccagcgtaagtagaagcat	10	8	8	15	1	0	2	0	1	0	1	1	2	1	2	5	0	4	3	5	0	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:73581573C>A	ENST00000339362.5	+	26	4183	c.3736C>A	c.(3736-3738)Ccc>Acc	p.P1246T	NEO1_ENST00000261908.6_Missense_Mutation_p.P1246T|NEO1_ENST00000558964.1_Missense_Mutation_p.P1235T|NEO1_ENST00000560262.1_Missense_Mutation_p.P1246T			Q92859	NEO1_HUMAN	neogenin 1	1246					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						CTCCCAGCCACCCCAGCGTAA	0.458																																					p.P1246T		.											.	NEO1-116	0			c.C3736A						.						154	102	119					15																	73581573		2198	4297	6495	SO:0001583	missense	4756	exon25			CAGCCACCCCAGC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.3736C>A	15.37:g.73581573C>A	ENSP00000341198:p.Pro1246Thr	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	73	32	NM_001172623	0	0	0	0	0	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.713733	0.89112	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.45276	0.9;0.9	5.48	5.48	0.80851	Neogenin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.61640	0.2363	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.999	D;D;D;D	0.75484	0.986;0.968;0.98;0.98	T	0.53627	-0.8412	10	0.17832	T	0.49	-12.2116	19.387	0.94560	0.0:1.0:0.0:0.0	.	1246;1235;957;1246	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	T	1246;957;1246	ENSP00000341198:P1246T;ENSP00000261908:P1246T	ENSP00000261908:P1246T	P	+	1	0	NEO1	71368626	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.463000	0.80869	2.572000	0.86782	0.655000	0.94253	CCC	.		0.458	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		A	73581573	C	A	73581573	3	1	41	1	0	0	0	0	1	0	0	0	10362	507	18	4	3834	4	NEO1	15	73581573	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	8467104	73581573	28949819	79	3803											
PML	5371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	74325643	74325643	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaggcccagcacctccaaGgcagtctcaccaccccacct	9	4	6	22	0	1	0	1	0	1	0	3	0	2	0	8	2	1	2	8	2	1	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:74325643G>A	ENST00000268058.3	+	6	1641	c.1545G>A	c.(1543-1545)aaG>aaA	p.K515K	PML_ENST00000565898.1_Silent_p.K467K|PML_ENST00000436891.3_Silent_p.K515K|PML_ENST00000567543.1_Intron|PML_ENST00000569965.1_Silent_p.K515K|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Silent_p.K467K|PML_ENST00000563500.1_Silent_p.K467K|PML_ENST00000359928.4_Intron|PML_ENST00000564428.1_Silent_p.K467K|PML_ENST00000569477.1_Silent_p.K515K|PML_ENST00000435786.2_Silent_p.K515K|PML_ENST00000395135.3_Silent_p.K515K|PML_ENST00000268059.6_Silent_p.K515K	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	515	Interaction with PER2.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GCACCTCCAAGGCAGTCTCAC	0.652			T	"RARA, PAX5"	"APL, ALL"																																p.K515K		.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML-1083	0			c.G1545A						.						62	58	60					15																	74325643		2198	4297	6495	SO:0001819	synonymous_variant	5371	exon6			CTCCAAGGCAGTC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1545G>A	15.37:g.74325643G>A		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	85	21	NM_033244	0	0	28	46	18	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	37	CCDS10255.1																																																																																			.		0.652	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		A	74325643	G	A	74325643	2	1	41	1	0	0	0	0	0	0	0	1	12161	991	35	2		2	PML	15	74325643	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	744070	74325643	28205749	80	3804											
SLC28A1	9154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	85476453	85476453	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctccaagctggtctacccGgaggtggaggagtccaagtt	8	9	13	11	1	2	0	0	0	2	0	4	3	3	3	3	5	2	2	3	5	3	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:85476453G>A	ENST00000286749.3	+	12	1251	c.1161G>A	c.(1159-1161)ccG>ccA	p.P387P	SLC28A1_ENST00000537216.1_Silent_p.P387P|SLC28A1_ENST00000394573.1_Silent_p.P387P|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537624.1_Silent_p.P387P			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	387					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TGGTCTACCCGGAGGTGGAGG	0.572																																					p.P387P		.											.	SLC28A1-93	0			c.G1161A						.						132	113	119					15																	85476453		2203	4299	6502	SO:0001819	synonymous_variant	9154	exon13			CTACCCGGAGGTG	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"Solute carriers"	11001	protein-coding gene	gene with protein product		606207	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1161G>A	15.37:g.85476453G>A		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	56	17	NM_004213	0	0	12	19	7	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			.		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			A	85476453	G	A	85476453	2	1	41	1	0	0	0	0	0	0	0	1	14563	1103	39	1		1	SLC28A1	15	85476453	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	11150810	85476453	17054939	81	3805											
ZNF597	146434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3487293	3487293	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaagtgtgttggttcctaAatattcagagagttctacta	13	14	9	5	0	2	2	1	0	1	2	3	3	3	2	1	1	1	3	1	1	6	8			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:3487293A>T	ENST00000301744.4	-	4	641	c.406T>A	c.(406-408)Tta>Ata	p.L136I		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						TTGGTTCCTAAATATTCAGAG	0.403																																					p.L136I		.											.	ZNF597-90	0			c.T406A						.						133	137	136					16																	3487293		2197	4300	6497	SO:0001583	missense	146434	exon4			TTCCTAAATATTC	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"Zinc fingers, C2H2-type", "-"	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.406T>A	16.37:g.3487293A>T	ENSP00000301744:p.Leu136Ile	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	208	123	NM_152457	0	0	0	3	3		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	A	5.442	0.266748	0.10294	.	.	ENSG00000167981	ENST00000301744	T	0.06849	3.25	4.91	2.52	0.30459	.	0.000000	0.36101	N	0.002790	T	0.05593	0.0147	L	0.41236	1.265	0.09310	N	1	P	0.47350	0.894	B	0.39935	0.314	T	0.31251	-0.9950	10	0.22706	T	0.39	-1.0026	3.965	0.09428	0.7202:0.0:0.0973:0.1825	.	136	Q96LX8	ZN597_HUMAN	I	136	ENSP00000301744:L136I	ENSP00000301744:L136I	L	-	1	2	ZNF597	3427294	0.067000	0.21026	0.811000	0.32455	0.229000	0.25112	0.918000	0.28678	0.994000	0.38892	0.533000	0.62120	TTA	.		0.403	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		T	3487293	A	T	3487293	3	4	41	1	0	0	0	0	1	0	0	0	18059	11	1	5	872	5	ZNF597	16	3487293	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		3487293	86867460	82	3806											
ZNF646	9726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31092685	31092685	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagcggcccttccgctgcacCcagtgcgggcgctcctaccg	4	6	13	18	5	0	0	0	0	0	0	2	1	2	0	5	2	4	3	5	2	1	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:31092685C>T	ENST00000394979.2	+	1	5463	c.5040C>T	c.(5038-5040)acC>acT	p.T1680T	ZNF646_ENST00000300850.5_Silent_p.T1680T			O15015	ZN646_HUMAN	zinc finger protein 646	1680					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						TCCGCTGCACCCAGTGCGGGC	0.652																																					p.T1680T		.											.	ZNF646-153	0			c.C5040T						.						68	80	76					16																	31092685		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			CTGCACCCAGTGC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.5040C>T	16.37:g.31092685C>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	112	19	NM_014699	0	0	8	12	4	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				.		0.652	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		T	31092685	C	T	31092685	2	4	41	1	0	0	0	0	0	0	0	1	18094	610	22	2		2	ZNF646	16	31092685	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	27605392	31092685	59262068	83	3807											
PRSS36	146547	broad.mit.edu	37	chr16	31154780	31154780	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gccaggcccctggccgcgggGccttcccgcactctgagggg	3	5	16	17	3	1	1	0	1	1	0	2	1	2	1	6	6	0	1	6	6	0	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:31154780G>T	ENST00000268281.4	-	8	1041	c.983C>A	c.(982-984)gCc>gAc	p.A328D	PRSS36_ENST00000418068.2_Missense_Mutation_p.A328D|PRSS36_ENST00000569305.1_Missense_Mutation_p.A328D	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	328	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						TGGCCGCGGGGCCTTCCCGCA	0.667																																					p.A328D													.	PRSS36-91	0			c.C983A						.						27	33	31					16																	31154780		2197	4300	6497	SO:0001583	missense	146547	exon8			CGCGGGGCCTTCC	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"Serine peptidases / Serine peptidases"	26906	protein-coding gene	gene with protein product	"polyserase 2"	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.983C>A	16.37:g.31154780G>T	ENSP00000268281:p.Ala328Asp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	79	8	NM_001258291	0	0	0	0	0	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	37	CCDS32436.1	.	.	.	.	.	.	.	.	.	.	G	8.398	0.841279	0.16891	.	.	ENSG00000178226	ENST00000268281;ENST00000418068	D;D	0.88509	-2.39;-2.39	4.11	3.12	0.35913	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.85318	0.5669	N	0.13327	0.33	0.09310	N	0.999997	D;D;D	0.71674	0.986;0.998;0.998	P;D;D	0.69824	0.823;0.966;0.966	T	0.73145	-0.4075	9	0.02654	T	1	.	9.4339	0.38626	0.0:0.2171:0.7829:0.0	.	328;328;328	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	D	328	ENSP00000268281:A328D;ENSP00000407160:A328D	ENSP00000268281:A328D	A	-	2	0	PRSS36	31062281	0.181000	0.23161	0.573000	0.28510	0.893000	0.52053	1.534000	0.36051	0.901000	0.36495	0.491000	0.48974	GCC	.		0.667	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		T	31154780	G	T	31154780	3	4	41	1	0	0	0	0	1	0	0	0	12654	1203	42	4	1616	4	PRSS36	16	31154780	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	62095	31154780	59199973	84	3808											
ITGAM	3684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31335987	31335987	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttagaattgcatcgaggacCcagtgagccccattgtgctg	9	10	11	11	1	0	2	0	1	0	1	1	4	0	3	3	1	3	2	3	1	2	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:31335987C>A	ENST00000287497.8	+	18	2248	c.2173C>A	c.(2173-2175)Cca>Aca	p.P725T	ITGAM_ENST00000544665.3_Missense_Mutation_p.P726T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	725					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CATCGAGGACCCAGTGAGCCC	0.602																																					p.P726T		.											.	ITGAM-226	0			c.C2176A						.						49	51	50					16																	31335987		1980	4148	6128	SO:0001583	missense	3684	exon18			GAGGACCCAGTGA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2173C>A	16.37:g.31335987C>A	ENSP00000287497:p.Pro725Thr	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	140	17	NM_001145808	0	0	5	5	0	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	C	5.122	0.208084	0.09704	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.42513	0.97;0.97	4.64	-0.352	0.12598	Integrin alpha-2 (1);	.	.	.	.	T	0.16599	0.0399	N	0.11427	0.14	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12156	0.007;0.004;0.004	T	0.28586	-1.0039	9	0.07030	T	0.85	.	3.2574	0.06836	0.4401:0.1772:0.0:0.3826	.	131;725;725	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	T	726;725	ENSP00000441691:P726T;ENSP00000287497:P725T	ENSP00000287497:P725T	P	+	1	0	ITGAM	31243488	0.534000	0.26362	0.001000	0.08648	0.001000	0.01503	0.014000	0.13333	-0.004000	0.14419	-1.364000	0.01208	CCA	.		0.602	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31335987	C	A	31335987	3	1	41	1	0	0	0	0	1	0	0	0	7908	623	22	4	2246	4	ITGAM	16	31335987	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	181207	31335987	59018766	85	3809											
CLEC18A	348174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	69988283	69988283	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcaagccagggcagcccTctgtggaaccccaaccccga	9	4	11	17	1	2	0	1	0	1	0	2	2	2	1	6	3	4	2	6	3	3	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:69988283T>C	ENST00000288040.6	+	3	450	c.263T>C	c.(262-264)cTc>cCc	p.L88P	CLEC18A_ENST00000568461.1_Missense_Mutation_p.L88P|CLEC18A_ENST00000449317.2_Missense_Mutation_p.L88P|CLEC18A_ENST00000393701.2_Missense_Mutation_p.L88P	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	88	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						AGGGCAGCCCTCTGTGGAACC	0.662																																					p.L88P		.											.	CLEC18A-68	0			c.T263C						.						54	49	51					16																	69988283		2198	4300	6498	SO:0001583	missense	348174	exon4			CAGCCCTCTGTGG	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"C-type lectin domain containing"	30388	protein-coding gene	gene with protein product	"mannose receptor-like"					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.263T>C	16.37:g.69988283T>C	ENSP00000288040:p.Leu88Pro	Somatic	309	1		WXS	Illumina HiSeq	Phase_I	396	181	NM_001271197	0	0	0	3	3	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	9.120	1.008658	0.19199	.	.	ENSG00000157322	ENST00000393701;ENST00000539957;ENST00000449317;ENST00000288040	T;T;T	0.07908	3.15;3.15;3.15	1.97	1.97	0.26223	CAP domain (3);	0.922111	0.09270	N	0.825284	T	0.07999	0.0200	L	0.47190	1.495	0.52501	D	0.999956	B;B;B	0.19331	0.035;0.004;0.003	B;B;B	0.17098	0.017;0.007;0.006	T	0.17137	-1.0379	9	.	.	.	.	5.9927	0.19476	0.0:0.0:0.0:1.0	.	88;88;88	B4DPF2;A5D8T8;F8W692	.;CL18A_HUMAN;.	P	88	ENSP00000377304:L88P;ENSP00000413990:L88P;ENSP00000288040:L88P	.	L	+	2	0	CLEC18A	68545784	0.004000	0.15560	0.898000	0.35279	0.442000	0.32017	0.109000	0.15417	1.168000	0.42723	0.155000	0.16302	CTC	.		0.662	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619		C	69988283	T	C	69988283	3	2	41	1	0	0	0	0	1	0	0	0	3508	1551	54	3	273	3	CLEC18A	16	69988283	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	38652296	69988283	20366470	86	3810											
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72984405	72984405	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctcgtgcctggagttgAccgtgtgcagccgcagcttc	4	10	14	13	3	0	1	0	1	0	0	2	2	0	2	4	2	4	4	4	2	0	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:72984405A>C	ENST00000268489.5	-	3	3851	c.3179T>G	c.(3178-3180)gTc>gGc	p.V1060G	ZFHX3_ENST00000397992.5_Missense_Mutation_p.V146G	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1060					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCTGGAGTTGACCGTGTGCAG	0.602																																					p.V1060G		.											.	ZFHX3-72	0			c.T3179G						.						70	59	63					16																	72984405		2198	4300	6498	SO:0001583	missense	463	exon3			GAGTTGACCGTGT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.3179T>G	16.37:g.72984405A>C	ENSP00000268489:p.Val1060Gly	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	72	37	NM_006885	0	0	0	2	2	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	A	15.80	2.939889	0.52972	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.49432	0.78;0.78	5.31	4.22	0.49857	Zinc finger, C2H2-like (1);	0.148255	0.30464	N	0.009580	T	0.42449	0.1203	N	0.19112	0.55	0.80722	D	1	P	0.48640	0.913	P	0.51918	0.684	T	0.25606	-1.0127	10	0.41790	T	0.15	.	11.0251	0.47741	0.927:0.0:0.073:0.0	.	1060	Q15911	ZFHX3_HUMAN	G	1060;146	ENSP00000268489:V1060G;ENSP00000438926:V146G	ENSP00000268489:V1060G	V	-	2	0	ZFHX3	71541906	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	5.860000	0.69546	0.859000	0.35456	0.528000	0.53228	GTC	.		0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72984405	A	C	72984405	3	2	41	1	0	0	0	0	1	0	0	0	17666	275	10	5	7964	5	ZFHX3	16	72984405	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	2996122	72984405	17370348	87	3811											
JPH3	57338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	87678517	87678517	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcagaacatcctcgtcggcGgcaagcgcaagaacctcatc	12	5	10	14	4	1	2	1	0	0	2	5	2	2	2	2	2	4	3	2	2	4	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:87678517G>A	ENST00000284262.2	+	2	1278	c.1036G>A	c.(1036-1038)Ggc>Agc	p.G346S		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	346					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		CCTCGTCGGCGGCAAGCGCAA	0.677																																					p.G346S		.											.	JPH3-92	0			c.G1036A						.						45	54	51					16																	87678517		2197	4300	6497	SO:0001583	missense	57338	exon2			GTCGGCGGCAAGC	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"trinucleotide repeat containing 22"	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1036G>A	16.37:g.87678517G>A	ENSP00000284262:p.Gly346Ser	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	71	29	NM_020655	0	0	0	0	0	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531280	0.85706	.	.	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.45668	0.89	4.56	4.56	0.56223	.	0.050973	0.85682	D	0.000000	T	0.37919	0.1021	L	0.46157	1.445	0.80722	D	1	P	0.42941	0.794	B	0.38562	0.276	T	0.29088	-1.0023	10	0.37606	T	0.19	.	16.3368	0.83067	0.0:0.0:1.0:0.0	.	346	Q8WXH2	JPH3_HUMAN	S	209;346	ENSP00000284262:G346S	ENSP00000284262:G346S	G	+	1	0	JPH3	86236018	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	9.580000	0.98207	2.098000	0.63641	0.561000	0.74099	GGC	.		0.677	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			A	87678517	G	A	87678517	3	1	41	1	0	0	0	0	1	0	0	0	7983	1116	39	1	1042	1	JPH3	16	87678517	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	14694112	87678517	2676236	88	3812											
KLHL11	55175	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40010765	40010766	+	Missense_Mutation	DNP	TG	TG	CT																															aatgctatagagcttcccttTgacttctgttagtccaaaag																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr17:40010765_40010766TG>CT	ENST00000319121.3	-	2	1413_1414	c.1353_1354CA>AG	c.(1351-1356)gtCAaa>gtAGaa	p.K452E		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	452										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				AGCTTCCCTTTGACTTCTGTTA	0.376																																					p.K452E													.	KLHL11-90	0			c.C1353A						.																																			SO:0001583	missense	55175	exon2			CCCTTTGACTTCT		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.1353_1354delinsCT	17.37:g.40010765_40010766delinsCT	ENSP00000314608:p.Lys452Glu	Somatic	206	1		WXS	Illumina HiSeq	Phase_I	214	97	NM_018143	0	0	0	0	0		Missense_Mutation	DNP	ENST00000319121.3	37	CCDS11411.1																																																																																			.		0.376	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		CT	40010766	TG	CT	40010765	3	2	41	1	0	0	0	0	1	0	0	0	8388	1821	63	3	776	3	KLHL11	17	40010765	Missense_Mutation	DNP	TG	TCGA-B1-A657-01A-11D-A31X-10		40010765	41184445	89	3813											
KIF18B	146909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	43009571	43009571	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagctctggggtgcagggCtggctgggagggtggggtgg	3	7	26	5	0	1	0	0	0	1	0	1	2	1	2	0	10	2	4	0	10	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr17:43009571C>T	ENST00000593135.1	-	10	1339	c.1242G>A	c.(1240-1242)caG>caA	p.Q414Q	KIF18B_ENST00000339151.4_Silent_p.Q426Q|KIF18B_ENST00000587309.1_Silent_p.Q426Q|KIF18B_ENST00000438933.2_Silent_p.Q426Q|KIF18B_ENST00000590129.1_Silent_p.Q435Q	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	435	Pro-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GGGTGCAGGGCTGGCTGGGAG	0.657																																					p.Q426Q		.											.	KIF18B-70	0			c.G1278A						.						18	21	20					17																	43009571		1898	4102	6000	SO:0001819	synonymous_variant	146909	exon10			GCAGGGCTGGCTG		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"Kinesins"	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.1242G>A	17.37:g.43009571C>T		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	51	8	NM_001264573	0	0	0	0	0	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Silent	SNP	ENST00000593135.1	37	CCDS45709.2																																																																																			.		0.657	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443		T	43009571	C	T	43009571	2	4	41	1	0	0	0	0	0	0	0	1	8302	796	28	2		2	KIF18B	17	43009571	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	2998806	43009571	38185639	90	3814											
TLK2	11011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	60663585	60663585	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaaaaggagaattaccaCaagtaagtgatacttgagtg	18	8	11	4	0	0	4	0	2	0	2	0	6	0	4	1	1	2	1	1	1	7	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr17:60663585C>A	ENST00000326270.9	+	17	1792	c.1524C>A	c.(1522-1524)caC>caA	p.H508Q	TLK2_ENST00000346027.5_Missense_Mutation_p.H486Q|TLK2_ENST00000582809.1_Missense_Mutation_p.H337Q|TLK2_ENST00000343388.7_Missense_Mutation_p.H454Q|TLK2_ENST00000542523.1_Missense_Mutation_p.H454Q	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	508	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						AGAATTACCACAAGTAAGTGA	0.328																																					p.H486Q		.											.	TLK2-464	0			c.C1458A						.						33	34	33					17																	60663585		2202	4297	6499	SO:0001583	missense	11011	exon16			TTACCACAAGTAA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1524C>A	17.37:g.60663585C>A	ENSP00000316512:p.His508Gln	Somatic	737	1		WXS	Illumina HiSeq	Phase_I	639	311	NM_006852	0	0	0	0	0	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	C	8.052	0.766147	0.15983	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.45	3.48	0.39840	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62841	0.2461	N	0.26042	0.785	0.80722	D	1	D;B;B;B	0.69078	0.997;0.005;0.028;0.157	D;B;B;B	0.66351	0.943;0.037;0.064;0.166	T	0.62044	-0.6937	10	0.54805	T	0.06	-0.8054	8.4022	0.32592	0.0:0.7596:0.0:0.2404	.	508;454;486;486	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	Q	486;454;508;454	ENSP00000275780:H486Q;ENSP00000340800:H454Q;ENSP00000316512:H508Q;ENSP00000442311:H454Q	ENSP00000316512:H508Q	H	+	3	2	TLK2	58017317	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	5.818000	0.69236	0.688000	0.31529	-0.251000	0.11542	CAC	.		0.328	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		A	60663585	C	A	60663585	3	1	41	1	0	0	0	0	1	0	0	0	15976	477	17	4	1516	4	TLK2	17	60663585	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	17654014	60663585	20531625	91	3815											
LPIN2	9663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2939488	2939488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctagtaccttggtggacTctgggaatccgccccacgtc	7	9	10	15	2	1	0	0	0	1	0	3	2	2	2	5	3	1	1	5	3	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr18:2939488T>C	ENST00000261596.4	-	6	1050	c.812A>G	c.(811-813)gAg>gGg	p.E271G		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	271					cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		CTTGGTGGACTCTGGGAATCC	0.493																																					p.E271G		.											.	LPIN2-227	0			c.A812G						.						125	117	120					18																	2939488		2203	4300	6503	SO:0001583	missense	9663	exon6			GTGGACTCTGGGA	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.812A>G	18.37:g.2939488T>C	ENSP00000261596:p.Glu271Gly	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	42	16	NM_014646	0	0	0	0	0	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103696	0.76983	.	.	ENSG00000101577	ENST00000261596	T	0.81247	-1.47	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.87337	0.6152	M	0.70595	2.14	0.80722	D	1	D	0.62365	0.991	P	0.60012	0.867	D	0.86664	0.1906	10	0.38643	T	0.18	-35.667	16.2194	0.82247	0.0:0.0:0.0:1.0	.	271	Q92539	LPIN2_HUMAN	G	271	ENSP00000261596:E271G	ENSP00000261596:E271G	E	-	2	0	LPIN2	2929488	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	7.649000	0.83500	2.234000	0.73211	0.528000	0.53228	GAG	.		0.493	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		C	2939488	T	C	2939488	3	2	41	1	0	0	0	0	1	0	0	0	8944	1551	54	3	1938	3	LPIN2	18	2939488	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		2939488	75137760	92	3816											
C18orf34	374864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	30992013	30992013	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acctatattggtttgatcatCtctagtggaagaagaggaaa	14	12	10	5	0	2	3	1	1	1	2	3	5	2	5	1	3	0	1	1	3	6	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr18:30992013C>T	ENST00000383096.3	-	3	222	c.40G>A	c.(40-42)Gat>Aat	p.D14N	CCDC178_ENST00000406524.2_Missense_Mutation_p.D14N|CCDC178_ENST00000403303.1_Missense_Mutation_p.D14N|CCDC178_ENST00000579916.1_Missense_Mutation_p.D14N|CCDC178_ENST00000300227.8_Missense_Mutation_p.D14N|CCDC178_ENST00000402325.1_Missense_Mutation_p.D14N|CCDC178_ENST00000579947.1_Missense_Mutation_p.D14N|CCDC178_ENST00000583930.1_Missense_Mutation_p.D14N			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	14																	GTTTGATCATCTCTAGTGGAA	0.274																																					p.D14N		.											.	.	0			c.G40A						.						43	45	44					18																	30992013		2201	4293	6494	SO:0001583	missense	374864	exon2			GATCATCTCTAGT	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 34"	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.40G>A	18.37:g.30992013C>T	ENSP00000372576:p.Asp14Asn	Somatic	552	1		WXS	Illumina HiSeq	Phase_I	432	150	NM_001105528	0	0	0	0	0	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	C	4.876	0.162801	0.09287	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.49432	2.37;2.37;2.37;2.35;2.36;0.78	3.45	1.65	0.23941	.	.	.	.	.	T	0.30262	0.0759	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.25609	0.13;0.13;0.13;0.13;0.13	B;B;B;B;B	0.24269	0.052;0.032;0.052;0.052;0.052	T	0.20605	-1.0270	9	0.48119	T	0.1	0.1645	5.6192	0.17448	0.0:0.7486:0.0:0.2514	.	14;14;14;14;14	F8W7A7;A1L4G8;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;CR034_HUMAN	N	14	ENSP00000385591:D14N;ENSP00000372576:D14N;ENSP00000300227:D14N;ENSP00000385867:D14N;ENSP00000385234:D14N;ENSP00000382130:D14N	ENSP00000300227:D14N	D	-	1	0	C18orf34	29246011	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.323000	0.07997	0.464000	0.27142	0.655000	0.94253	GAT	.		0.274	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		T	30992013	C	T	30992013	3	4	41	1	0	0	0	0	1	0	0	0	1908	913	32	2	2647	2	C18orf34	18	30992013	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	28052525	30992013	47085235	93	3817											
PTPRS	5802	bcgsc.ca	37	chr19	5214700	5214700	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgtacgcgttctgacaccGgtagccgtccacgtagttgg	8	10	12	11	5	1	1	0	1	1	0	2	1	2	1	3	2	2	5	3	2	4	5	rs373940938		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:5214700G>T	ENST00000587303.1	-	28	4465	c.4366C>A	c.(4366-4368)Cgg>Agg	p.R1456R	PTPRS_ENST00000588012.1_Silent_p.R1418R|PTPRS_ENST00000592099.1_Silent_p.R1009R|PTPRS_ENST00000372412.4_Silent_p.R1457R|PTPRS_ENST00000357368.4_Silent_p.R1456R|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000353284.2_Silent_p.R1009R|PTPRS_ENST00000262963.6_Silent_p.R1436R|PTPRS_ENST00000348075.2_Silent_p.R1418R			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1456	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	TTCTGACACCGGTAGCCGTCC	0.607																																					p.R1456R													.	PTPRS-357	0			c.C4366A						.						55	42	46					19																	5214700		2203	4300	6503	SO:0001819	synonymous_variant	5802	exon29			GACACCGGTAGCC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.4366C>A	19.37:g.5214700G>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_1	59	4	NM_002850	0	0	0	0	0	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			.		0.607	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			T	5214700	G	T	5214700	2	4	41	1	0	0	0	0	0	0	0	1	12843	1115	39	4		4	PTPRS	19	5214700	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		5214700	53914283	94	3818											
FBN3	84467	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8183905	8183905	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccttgcacactcgtccacGtctgaaggtttgtgtggaaa	8	12	10	11	2	1	1	0	1	1	0	4	2	3	2	2	2	1	2	2	2	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:8183905G>A	ENST00000600128.1	-	26	3627	c.3213C>T	c.(3211-3213)gaC>gaT	p.D1071D	FBN3_ENST00000601739.1_Splice_Site_p.D1071D|FBN3_ENST00000270509.2_Splice_Site_p.D1071D			Q75N90	FBN3_HUMAN	fibrillin 3	1071	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACTCGTCCACGTCTGAAGGTT	0.617																																					p.D1071D		.											.	FBN3-100	0			c.C3213T						.						66	52	57					19																	8183905		2203	4300	6503	SO:0001630	splice_region_variant	84467	exon25			GTCCACGTCTGAA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3212-1C>T	19.37:g.8183905G>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	28	12	NM_032447	0	0	0	0	0	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			.		0.617	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	Silent	A	8183905	G	A	8183905	5	1	41	1	0	0	0	0	0	0	1	0	5723	1159	40	1	5372	1	FBN3	19	8183905	Splice_Site	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	2969205	8183905	50945078	95	3819											
PRDX2	7001	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	12911694	12911694	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggacctgagggtgtgagcTtagctgcaacctccctcttt	7	12	11	11	0	1	2	0	2	1	0	2	3	2	3	3	2	4	3	3	2	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:12911694T>C	ENST00000301522.2	-	3	386				PRDX2_ENST00000334482.5_Intron|PRDX2_ENST00000435703.1_Missense_Mutation_p.K98R|CTD-2659N19.10_ENST00000585496.1_RNA	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2						cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						gggtgtgagcttagctgcaac	0.572																																					p.K98R		.											.	PRDX2-90	0			c.A293G						.						48	45	46					19																	12911694		2197	4296	6493	SO:0001627	intron_variant	7001	exon3			GTGAGCTTAGCTG		CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"thioredoxin-dependent peroxide reductase 1", "thiol-specific antioxidant 1", "natural killer-enhancing factor B", "thioredoxin peroxidase 1", "torin"	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.257+35A>G	19.37:g.12911694T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	76	22	NM_181738	0	0	0	0	0	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Missense_Mutation	SNP	ENST00000301522.2	37	CCDS12281.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.649424	0.29336	.	.	ENSG00000167815	ENST00000435703	T	0.45668	0.89	3.3	-6.61	0.01818	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.30001	-0.9993	8	0.87932	D	0	.	5.1763	0.15137	0.0:0.3936:0.2769:0.3294	.	98	A8K0C0	.	R	98	ENSP00000408905:K98R	ENSP00000408905:K98R	K	-	2	0	PRDX2	12772694	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.583000	0.05807	-1.609000	0.01585	0.379000	0.24179	AAG	.		0.572	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809		C	12911694	T	C	12911694	1	2	41	0	1	0	0	0	0	0	0	0	12494	1609	56	3		3	PRDX2	19	12911694	Intron	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	4727789	12911694	46217289	96	3820											
LSM14A	26065	broad.mit.edu	37	chr19	34710315	34710315	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccaggtgctccttcagcTccaaggagagggcgtggggg	6	7	17	11	1	1	1	1	0	0	1	4	2	4	1	3	5	2	3	3	5	1	1	rs201741862		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:34710315T>G	ENST00000433627.5	+	7	876	c.801T>G	c.(799-801)gcT>gcG	p.A267A	LSM14A_ENST00000544216.3_Silent_p.A267A|LSM14A_ENST00000540746.2_Silent_p.A226A	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	267					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.A267A(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					CTCCTTCAGCTCCAAGGAGAG	0.438																																					p.A267A													.	LSM14A-91	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.T801G						.						64	74	71					19																	34710315		2203	4300	6503	SO:0001819	synonymous_variant	26065	exon7			TTCAGCTCCAAGG	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.801T>G	19.37:g.34710315T>G		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	112	4	NM_001114093	0	0	20	20	0	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Silent	SNP	ENST00000433627.5	37	CCDS46040.1																																																																																			T|0.999;G|0.001		0.438	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		G	34710315	T	G	34710315	2	3	41	1	0	0	0	0	0	0	0	1	9079	1538	54	5		5	LSM14A	19	34710315	Silent	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	21798621	34710315	24418668	97	3821											
ZNF576	79177	broad.mit.edu	37	chr19	44103092	44103092	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggacttcgtggcccagaaGctgcagggggtcctcttcat	6	9	14	12	2	2	1	1	0	1	1	4	2	3	2	2	4	2	2	2	4	1	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:44103092G>T	ENST00000336564.4	+	3	349	c.195G>T	c.(193-195)aaG>aaT	p.K65N	SRRM5_ENST00000526798.1_Intron|IRGQ_ENST00000422989.1_5'Flank|ZNF576_ENST00000533118.1_Missense_Mutation_p.K65N|ZNF576_ENST00000391965.2_Missense_Mutation_p.K65N|ZNF576_ENST00000525771.1_Missense_Mutation_p.K65N|ZNF576_ENST00000529930.1_Missense_Mutation_p.K65N|ZNF576_ENST00000528387.1_Missense_Mutation_p.K65N|SRRM5_ENST00000607544.1_Intron	NM_001145347.1	NP_001138819.1	Q9H609	ZN576_HUMAN	zinc finger protein 576	65					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(1)|prostate(1)	2		Prostate(69;0.0199)				TGGCCCAGAAGCTGCAGGGGG	0.647																																					p.K65N													.	ZNF576-90	0			c.G195T						.						87	102	97					19																	44103092		2203	4300	6503	SO:0001583	missense	79177	exon3			CCAGAAGCTGCAG	AK026353	CCDS12625.1	19q13.31	2013-09-20			ENSG00000124444	ENSG00000124444		"Zinc fingers, C2H2-type"	28357	protein-coding gene	gene with protein product						12477932	Standard	NM_024327		Approved	MGC2508	uc002owz.2	Q9H609	OTTHUMG00000165479	ENST00000336564.4:c.195G>T	19.37:g.44103092G>T	ENSP00000337852:p.Lys65Asn	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_001145347	0	0	10	10	0	Q9BU03	Missense_Mutation	SNP	ENST00000336564.4	37	CCDS12625.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374618	0.61735	.	.	ENSG00000124444	ENST00000391965;ENST00000525771;ENST00000533118;ENST00000528387;ENST00000529930;ENST00000336564	T;T;T;T;T;T	0.01359	4.98;4.98;4.98;4.98;4.98;4.98	3.93	2.89	0.33648	.	0.204121	0.35772	N	0.002997	T	0.00906	0.0030	N	0.08118	0	0.80722	D	1	B	0.34290	0.447	B	0.32393	0.145	T	0.69308	-0.5179	10	0.59425	D	0.04	-16.2701	7.5611	0.27851	0.115:0.0:0.885:0.0	.	65	Q9H609	ZN576_HUMAN	N	65	ENSP00000375827:K65N;ENSP00000436182:K65N;ENSP00000435899:K65N;ENSP00000435934:K65N;ENSP00000435463:K65N;ENSP00000337852:K65N	ENSP00000337852:K65N	K	+	3	2	ZNF576	48794932	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.823000	0.27366	1.260000	0.44134	0.591000	0.81541	AAG	.		0.647	ZNF576-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384397.1	NM_024327		T	44103092	G	T	44103092	3	4	41	1	0	0	0	0	1	0	0	0	18040	962	34	4	201	4	ZNF576	19	44103092	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	9392777	44103092	15025891	98	3822											
PVR	5817	broad.mit.edu;bcgsc.ca	37	chr19	45162149	45162149	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgtgaggtcctttggcaCtgtcatctgtgtccctcgag	4	13	11	13	2	2	1	1	1	1	0	6	2	5	1	3	2	0	1	3	2	0	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:45162149C>T	ENST00000425690.3	+	6	1430	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	PVR_ENST00000344956.4_Intron|PVR_ENST00000403059.4_Intron|PVR_ENST00000406449.4_Silent_p.H377H|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	377					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		TCCTTTGGCACTGTCATCTGT	0.512																																					p.H377H													.	PVR-90	0			c.C1131T						.						150	139	143					19																	45162149		2203	4300	6503	SO:0001819	synonymous_variant	5817	exon6			TTGGCACTGTCAT	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9705	protein-coding gene	gene with protein product	"nectin-like 5"	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.1131C>T	19.37:g.45162149C>T		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	79	6	NM_006505	0	0	28	30	2	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Silent	SNP	ENST00000425690.3	37	CCDS12640.1																																																																																			.		0.512	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		T	45162149	C	T	45162149	2	4	41	1	0	0	0	0	0	0	0	1	12869	564	20	2		2	PVR	19	45162149	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	1059057	45162149	13966834	99	3823											
FBXO46	23403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46215777	46215777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatccgccctggccagcAggaactccacgttgctgggg	6	7	12	16	2	1	0	1	0	0	0	3	1	3	1	5	4	3	3	5	4	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:46215777A>G	ENST00000317683.3	-	2	1110	c.977T>C	c.(976-978)cTg>cCg	p.L326P		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	326										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CCTGGCCAGCAGGAACTCCAC	0.697																																					p.L326P		.											.	FBXO46-159	0			c.T977C						.						24	27	26					19																	46215777		1982	4149	6131	SO:0001583	missense	23403	exon2			GCCAGCAGGAACT	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"F-boxes /  "other""	25069	protein-coding gene	gene with protein product		609117	"F-box only protein 34-like"	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.977T>C	19.37:g.46215777A>G	ENSP00000410007:p.Leu326Pro	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	96	27	NM_001080469	0	0	6	8	2		Missense_Mutation	SNP	ENST00000317683.3	37	CCDS46116.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643535	0.47258	.	.	ENSG00000177051	ENST00000317683	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	T	0.52789	0.1756	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51204	-0.8735	8	0.30078	T	0.28	-6.761	11.5914	0.50947	1.0:0.0:0.0:0.0	.	326	Q6PJ61	FBX46_HUMAN	P	326	.	ENSP00000410007:L326P	L	-	2	0	FBXO46	50907617	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	5.008000	0.63991	1.851000	0.53745	0.460000	0.39030	CTG	.		0.697	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179		G	46215777	A	G	46215777	3	3	41	1	0	0	0	0	1	0	0	0	5774	188	7	3	838	3	FBXO46	19	46215777	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	1053628	46215777	12913206	100	3824											
DEFB118	117285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	29960794	29960794	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaatgaagaccacaggcgaGttcctgcgacatctcccaca	12	6	8	15	2	1	2	0	1	1	1	3	4	2	2	4	1	1	1	4	1	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr20:29960794G>T	ENST00000253381.2	+	2	226	c.193G>T	c.(193-195)Gtt>Ttt	p.V65F		NM_054112.2	NP_473453.1	Q96PH6	DB118_HUMAN	defensin, beta 118	65					cell-matrix adhesion (GO:0007160)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(1)|lung(7)|ovary(3)|pancreas(1)|prostate(1)	14	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CCACAGGCGAGTTCCTGCGAC	0.443																																					p.V65F		.											.	DEFB118-94	0			c.G193T						.						155	137	143					20																	29960794		2203	4300	6503	SO:0001583	missense	117285	exon2			AGGCGAGTTCCTG	AF347073	CCDS13177.1	20q11.21	2008-02-01	2002-05-09	2002-05-10	ENSG00000131068	ENSG00000131068		"Defensins, beta"	16196	protein-coding gene	gene with protein product		607650	"chromosome 20 open reading frame 63"	C20orf63		11564719, 15033915	Standard	NM_054112		Approved	dJ1018D12.3, DEFB-18, ESC42	uc002wvr.3	Q96PH6	OTTHUMG00000032161	ENST00000253381.2:c.193G>T	20.37:g.29960794G>T	ENSP00000253381:p.Val65Phe	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	109	30	NM_054112	0	0	0	0	0	Q17RC4|Q8N691|Q9NUH0	Missense_Mutation	SNP	ENST00000253381.2	37	CCDS13177.1	.	.	.	.	.	.	.	.	.	.	G	2.822	-0.244584	0.05906	.	.	ENSG00000131068	ENST00000253381	T	0.07908	3.15	3.19	-6.39	0.01951	.	7.214320	0.00397	N	0.000047	T	0.04588	0.0125	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.35201	-0.9798	10	0.15066	T	0.55	-0.7743	3.7626	0.08610	0.1823:0.2329:0.4708:0.114	.	65	Q96PH6	DB118_HUMAN	F	65	ENSP00000253381:V65F	ENSP00000253381:V65F	V	+	1	0	DEFB118	29424455	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.760000	0.00786	-2.810000	0.00348	-2.435000	0.00213	GTT	.		0.443	DEFB118-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078501.2	NM_054112		T	29960794	G	T	29960794	3	4	41	1	0	0	0	0	1	0	0	0	4416	1029	36	4	199	4	DEFB118	20	29960794	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		29960794	33064726	101	3825											
TPX2	22974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	30388879	30388879	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attctccactcgattccactGctaaactcagctgtgagctg	9	12	7	13	1	2	1	1	1	1	0	5	2	3	1	2	0	4	3	2	0	2	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr20:30388879G>T	ENST00000300403.6	+	18	2768	c.2240G>T	c.(2239-2241)tGc>tTc	p.C747F	TPX2_ENST00000340513.4_Missense_Mutation_p.C783F	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	747					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			CGATTCCACTGCTAAACTCAG	0.512																																					p.C747F		.											.	TPX2-290	0			c.G2240T						.						123	105	111					20																	30388879		2203	4300	6503	SO:0001583	missense	22974	exon18			TCCACTGCTAAAC	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"chromosome 20 open reading frame 1", "TPX2, microtubule-associated, homolog (Xenopus laevis)"	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.2240G>T	20.37:g.30388879G>T	ENSP00000300403:p.Cys747Phe	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	67	23	NM_012112	0	0	0	1	1	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492479	0.64074	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.37058	1.22	5.28	5.28	0.74379	.	0.110708	0.64402	D	0.000005	T	0.59169	0.2174	M	0.63428	1.95	0.43021	D	0.994579	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.61307	-0.7089	10	0.87932	D	0	.	18.0758	0.89426	0.0:0.0:1.0:0.0	.	783;747	Q96RR5;Q9ULW0	.;TPX2_HUMAN	F	747;783	ENSP00000341145:C783F	ENSP00000300403:C747F	C	+	2	0	TPX2	29852540	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	3.773000	0.55333	2.745000	0.94114	0.655000	0.94253	TGC	.		0.512	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30388879	G	T	30388879	3	4	41	1	0	0	0	0	1	0	0	0	16465	1319	46	4	2302	4	TPX2	20	30388879	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	428085	30388879	32636641	102	3826											
SUSD2	56241	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24579518	24579518	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctccgggcaagtgcacTgtgtgtcacctctgctctat	6	12	9	14	1	3	0	1	0	2	0	5	0	5	0	3	1	2	3	3	1	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr22:24579518T>A	ENST00000358321.3	+	3	604	c.343T>A	c.(343-345)Tgt>Agt	p.C115S		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	115					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						GCAAGTGCACTGTGTGTCACC	0.632																																					p.C115S		.											.	SUSD2-91	0			c.T343A						.						130	114	119					22																	24579518		2203	4300	6503	SO:0001583	missense	56241	exon3			GTGCACTGTGTGT	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.343T>A	22.37:g.24579518T>A	ENSP00000351075:p.Cys115Ser	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	46	19	NM_019601	0	0	0	0	0	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	37	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185964	0.78789	.	.	ENSG00000099994	ENST00000358321	D	0.84873	-1.91	3.5	3.5	0.40072	.	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	M	0.78637	2.42	0.50467	D	0.999877	D	0.71674	0.998	D	0.78314	0.991	D	0.90662	0.4591	10	0.87932	D	0	-25.3814	8.8392	0.35131	0.0:0.0:0.0:1.0	.	115	Q9UGT4	SUSD2_HUMAN	S	115	ENSP00000351075:C115S	ENSP00000351075:C115S	C	+	1	0	SUSD2	22909518	1.000000	0.71417	0.993000	0.49108	0.923000	0.55619	6.119000	0.71590	1.859000	0.53934	0.369000	0.22263	TGT	.		0.632	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24579518	T	A	24579518	3	1	41	1	0	0	0	0	1	0	0	0	15440	1580	55	5	353	5	SUSD2	22	24579518	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		24579518	26725048	103	3827											
PIM3	415116	broad.mit.edu	37	chr22	50355280	50355280	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgccctggacgagccgcTggcgcgccgcttcttcgcgc	2	6	15	18	9	1	0	0	0	1	0	2	2	1	1	3	3	1	2	3	3	0	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr22:50355280T>C	ENST00000360612.4	+	4	872	c.437T>C	c.(436-438)cTg>cCg	p.L146P		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	146	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		GACGAGCCGCTGGCGCGCCGC	0.692																																					p.L146P													.	PIM3-521	0			c.T437C						.						7	7	7					22																	50355280		2114	4127	6241	SO:0001583	missense	415116	exon4			AGCCGCTGGCGCG	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"pim-3 oncogene"			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.437T>C	22.37:g.50355280T>C	ENSP00000353824:p.Leu146Pro	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	35	11	NM_001001852	0	0	2	3	1	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Missense_Mutation	SNP	ENST00000360612.4	37	CCDS33678.1	.	.	.	.	.	.	.	.	.	.	t	12.38	1.920821	0.33908	.	.	ENSG00000198355	ENST00000360612	T	0.66280	-0.2	3.46	1.26	0.21427	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.211787	0.37623	N	0.002018	T	0.67477	0.2897	M	0.71036	2.16	0.47862	D	0.999536	D	0.57257	0.979	P	0.57425	0.82	T	0.64516	-0.6389	10	0.54805	T	0.06	.	5.5868	0.17279	0.0:0.5218:0.0:0.4782	.	146	Q86V86	PIM3_HUMAN	P	146	ENSP00000353824:L146P	ENSP00000353824:L146P	L	+	2	0	PIM3	48741284	0.994000	0.37717	0.009000	0.14445	0.001000	0.01503	2.493000	0.45320	0.251000	0.21505	-0.332000	0.08345	CTG	.		0.692	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852		C	50355280	T	C	50355280	3	2	41	1	0	0	0	0	1	0	0	0	11955	1580	55	3	451	3	PIM3	22	50355280	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	25775762	50355280	949286	104	3828											
RAI2	10742	broad.mit.edu	37	chrX	17819166	17819166	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttgagccagggcactgacTtcatggagagatccagggcc	9	7	13	12	0	1	3	1	2	0	1	2	5	2	4	4	3	1	1	4	3	0	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chrX:17819166T>G	ENST00000545871.1	-	3	1425	c.965A>C	c.(964-966)aAg>aCg	p.K322T	RAI2_ENST00000415486.3_Missense_Mutation_p.K272T|RAI2_ENST00000331511.1_Missense_Mutation_p.K322T|RAI2_ENST00000360011.1_Missense_Mutation_p.K322T|RAI2_ENST00000451717.1_Missense_Mutation_p.K322T	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	322					embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					GGGCACTGACTTCATGGAGAG	0.567																																					p.K322T													.	RAI2-131	0			c.A965C						.						104	98	100					X																	17819166		2203	4300	6503	SO:0001583	missense	10742	exon3			ACTGACTTCATGG	Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.965A>C	X.37:g.17819166T>G	ENSP00000444210:p.Lys322Thr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_001172739	0	0	51	55	4	B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	37	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	t	15.67	2.900999	0.52227	.	.	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.39056	1.13;1.13;1.13;1.13;1.1	5.29	5.29	0.74685	.	0.160590	0.42420	D	0.000711	T	0.58694	0.2140	L	0.55481	1.735	0.49582	D	0.999808	D;D	0.89917	1.0;1.0	D;D	0.71870	0.975;0.975	T	0.61554	-0.7039	10	0.66056	D	0.02	-27.0086	14.0079	0.64475	0.0:0.0:0.0:1.0	.	272;322	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	T	322;322;322;322;272	ENSP00000333456:K322T;ENSP00000353106:K322T;ENSP00000444210:K322T;ENSP00000401323:K322T;ENSP00000392578:K272T	ENSP00000333456:K322T	K	-	2	0	RAI2	17729087	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.282000	0.58971	1.963000	0.57068	0.483000	0.47432	AAG	.		0.567	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785		G	17819166	T	G	17819166	3	3	41	1	0	0	0	0	1	0	0	0	13041	1609	56	5	631	5	RAI2	23	17819166	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		17819166	137451394	105	3829											
SNX12	29934	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70280928	70280928	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcttgcaggaacatgtGtaggcagcgttcattctgag	8	12	11	10	1	3	1	1	1	2	0	4	2	4	2	1	2	3	4	1	2	2	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chrX:70280928G>T	ENST00000374274.3	-	4	543	c.427C>A	c.(427-429)Cac>Aac	p.H143N	SNX12_ENST00000465030.1_5'UTR|SNX12_ENST00000276105.3_Missense_Mutation_p.H139N	NM_001256185.1|NM_001256188.1|NM_013346.3	NP_001243114.1|NP_001243117.1|NP_037478.2	Q9UMY4	SNX12_HUMAN	sorting nexin 12	143	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of protein transport (GO:0051224)|regulation of endocytosis (GO:0030100)	early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)	p.H143Y(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	Renal(35;0.156)					AGGAACATGTGTAGGCAGCGT	0.517																																					p.H143N		.											.	SNX12-226	1	Substitution - Missense(1)	lung(1)	c.C427A						.						104	78	87					X																	70280928		2203	4300	6503	SO:0001583	missense	29934	exon5			ACATGTGTAGGCA	AF171229	CCDS14405.1, CCDS59169.1	Xq13.1	2008-03-11			ENSG00000147164	ENSG00000147164		"Sorting nexins"	14976	protein-coding gene	gene with protein product		300883					Standard	NM_013346		Approved		uc004dyr.2	Q9UMY4	OTTHUMG00000021786	ENST00000374274.3:c.427C>A	X.37:g.70280928G>T	ENSP00000363392:p.His143Asn	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	47	32	NM_001256185	0	0	7	61	54	F8W8K5|Q8WUG9	Missense_Mutation	SNP	ENST00000374274.3	37	CCDS14405.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.698895	0.48307	.	.	ENSG00000147164	ENST00000374274;ENST00000276105	T;T	0.39787	1.06;1.06	5.25	5.25	0.73442	.	0.208471	0.50627	D	0.000112	T	0.66557	0.2801	M	0.79926	2.475	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.66964	-0.5790	10	0.38643	T	0.18	-19.7041	16.8073	0.85709	0.0:0.0:1.0:0.0	.	143	Q3SYF1	.	N	143;139	ENSP00000363392:H143N;ENSP00000276105:H139N	ENSP00000276105:H139N	H	-	1	0	SNX12	70197653	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.653000	0.98506	2.434000	0.82447	0.594000	0.82650	CAC	.		0.517	SNX12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057094.1	NM_013346		T	70280928	G	T	70280928	3	4	41	1	0	0	0	0	1	0	0	0	14915	1377	48	4	65	4	SNX12	23	70280928	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	52461762	70280928	84989632	106	3830											
BRWD3	254065	bcgsc.ca	37	chrX	79932816	79932816	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tttctcttgattcctgtccgGggctctctgccatcaccatt	4	16	7	14	1	3	1	1	1	2	0	7	1	5	1	4	2	1	1	4	2	0	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chrX:79932816G>T	ENST00000373275.4	-	41	4917	c.4701C>A	c.(4699-4701)ccC>ccA	p.P1567P	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1567					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TTCCTGTCCGGGGCTCTCTGC	0.358																																					p.P1567P													.	BRWD3-134	0			c.C4701A						.						43	41	42					X																	79932816		2203	4299	6502	SO:0001819	synonymous_variant	254065	exon41			TGTCCGGGGCTCT		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.4701C>A	X.37:g.79932816G>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_1	45	4	NM_153252	0	0	5	5	0	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	37	CCDS14447.1																																																																																			.		0.358	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		T	79932816	G	T	79932816	2	4	41	1	0	0	0	0	0	0	0	1	1529	1219	43	4		4	BRWD3	23	79932816	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	9651888	79932816	75337744	107	3831											
ODZ1	10178	bcgsc.ca	37	chrX	123515037	123515037	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaccttggttgcttcccTccttcaaggcaccgtccatc	7	11	7	16	1	1	0	1	0	0	0	5	0	4	0	5	2	2	4	5	2	2	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chrX:123515037T>G	ENST00000371130.3	-	31	7590	c.7527A>C	c.(7525-7527)ggA>ggC	p.G2509G	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.G2516G	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2509					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTTGCTTCCCTCCTTCAAGGC	0.448																																					p.G2516G													.	.	0			c.A7548C						.						126	120	122					X																	123515037		2202	4298	6500	SO:0001819	synonymous_variant	10178	exon32			CTTCCCTCCTTCA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7527A>C	X.37:g.123515037T>G		Somatic	31	1		WXS	Illumina HiSeq	Phase_1	27	22	NM_001163278	0	0	0	4	4	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			.		0.448	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		G	123515037	T	G	123515037	2	3	41	1	0	0	0	0	0	0	0	1	10860	1538	54	5		5	ODZ1	23	123515037	Silent	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	43582221	123515037	31755523	108	3832											
SLC9A6	10479	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	135098843	135098843	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttggcagagaatttcatcTtctcctacatggggctgaca	9	13	9	10	0	4	2	1	1	3	1	5	3	4	2	1	3	1	2	1	3	2	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chrX:135098843T>A	ENST00000370698.3	+	10	1215	c.1180T>A	c.(1180-1182)Ttc>Atc	p.F394I	SLC9A6_ENST00000370695.4_Missense_Mutation_p.F426I|SLC9A6_ENST00000370701.1_Missense_Mutation_p.F374I	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	394					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GAATTTCATCTTCTCCTACAT	0.348																																					p.F426I													.	SLC9A6-131	0			c.T1276A						.						141	119	126					X																	135098843		2203	4300	6503	SO:0001583	missense	10479	exon10			TTCATCTTCTCCT	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"Solute carriers"	11079	protein-coding gene	gene with protein product		300231	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 6", "solute carrier family 9 (sodium/hydrogen exchanger), member 6"			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.1180T>A	X.37:g.135098843T>A	ENSP00000359732:p.Phe394Ile	Somatic	93	1		WXS	Illumina HiSeq	Phase_I	70	41	NM_001042537	0	0	0	7	7	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Missense_Mutation	SNP	ENST00000370698.3	37	CCDS14654.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.035859	0.93630	.	.	ENSG00000198689	ENST00000370701;ENST00000370698;ENST00000370695	T;T;T	0.60171	0.21;0.21;0.21	5.67	5.67	0.87782	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	D	0.84624	0.5513	H	0.97940	4.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.90110	0.4191	10	0.87932	D	0	.	14.0301	0.64610	0.0:0.0:0.0:1.0	.	426;394	Q92581-2;Q92581	.;SL9A6_HUMAN	I	374;394;426	ENSP00000359735:F374I;ENSP00000359732:F394I;ENSP00000359729:F426I	ENSP00000359729:F426I	F	+	1	0	SLC9A6	134926509	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	1.911000	0.55334	0.486000	0.48141	TTC	.		0.348	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359		A	135098843	T	A	135098843	3	1	41	1	0	0	0	0	1	0	0	0	14750	1609	56	5	1314	5	SLC9A6	23	135098843	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	11583806	135098843	20171717	109	3833											
ELTD1	64123	hgsc.bcm.edu;broad.mit.edu	37	chr1	79402059	79402059	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatatgaggatgaatatgTttcatgttatatgaatcaaa	15	16	7	3	0	3	3	3	3	0	0	3	4	3	4	0	1	0	2	0	1	7	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:79402059T>C	ENST00000370742.3	-	7	861	c.798A>G	c.(796-798)aaA>aaG	p.K266K		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	266					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		GATGAATATGTTTCATGTTAT	0.259																																					p.K266K		.											.	ELTD1-24	0			c.A798G						.						61	63	62					1																	79402059		1789	4015	5804	SO:0001819	synonymous_variant	64123	exon7			AATATGTTTCATG	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.798A>G	1.37:g.79402059T>C		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	164	23	NM_022159	0	0	3	3	0	B1AR71|Q5KU34	Silent	SNP	ENST00000370742.3	37	CCDS41352.1																																																																																			.		0.259	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		C	79402059	T	C	79402059	2	2	42	1	0	0	0	0	0	0	0	1	5097	1722	60	3		3	ELTD1	1	79402059	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08		79402059	169848562	1	3834											
AMY2B	280	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	104122036	104122036	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacaggcattaaaatctacGtttctgacgatggcaaagct	13	10	9	9	2	2	1	0	1	2	0	2	2	2	1	0	2	2	5	0	2	4	3	rs143243690	byFrequency	TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:104122036G>A	ENST00000361355.4	+	12	2066	c.1450G>A	c.(1450-1452)Gtt>Att	p.V484I	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	484					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TAAAATCTACGTTTCTGACGA	0.323													.|||	2	0.000399361	0	0	5008	,	,		17291	0		0.001	False		,,,				2504	0.001				p.V484I		.											.	AMY2B-90	0			c.G1450A						.	G	ILE/VAL	0,4406		0,0,2203	227	235	232		1450	2.2	0.2	1	dbSNP_134	232	1,8599	1.2+/-3.3	0,1,4299	no	missense	AMY2B	NM_020978.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	484/512	104122036	1,13005	2203	4300	6503	SO:0001583	missense	280	exon12			ATCTACGTTTCTG	M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"amylase, alpha 2B; pancreatic"	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.1450G>A	1.37:g.104122036G>A	ENSP00000354610:p.Val484Ile	Somatic	735	1		WXS	Illumina HiSeq	Phase_I	1115	198	NM_020978	0	0	10	15	5	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	.	.	.	.	.	.	.	.	.	.	G	8.662	0.900711	0.17686	0.0	1.16E-4	ENSG00000240038	ENST00000361355	T	0.78595	-1.19	4.14	2.25	0.28309	Alpha-amylase, C-terminal all beta (2);Glycosyl hydrolase, family 13, all-beta (1);	0.067775	0.64402	N	0.000017	T	0.74168	0.3681	H	0.95884	3.735	0.48040	D	0.999579	B	0.22346	0.068	B	0.20184	0.028	T	0.72577	-0.4251	10	0.56958	D	0.05	.	8.6944	0.34287	0.2605:0.0:0.7395:0.0	.	484	P19961	AMY2B_HUMAN	I	484	ENSP00000354610:V484I	ENSP00000354610:V484I	V	+	1	0	AMY2B	103923559	1.000000	0.71417	0.165000	0.22776	0.168000	0.22595	4.103000	0.57783	0.339000	0.23719	-0.224000	0.12420	GTT	G|1.000;A|0.000		0.323	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		A	104122036	G	A	104122036	3	1	42	1	0	0	0	0	1	0	0	0	595	1145	40	1	1488	1	AMY2B	1	104122036	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	24719977	104122036	145128585	2	3835											
LRIG2	9860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	113616063	113616063	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctaggcgtcccggaggagcAgttgctggggtgtcgatcta	6	9	16	10	3	1	0	0	0	1	0	3	3	2	2	2	5	2	3	2	5	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:113616063A>T	ENST00000361127.5	+	1	233	c.35A>T	c.(34-36)cAg>cTg	p.Q12L	RP11-31F15.2_ENST00000421157.1_lincRNA	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	12					innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		CCGGAGGAGCAGTTGCTGGGG	0.642											OREG0013684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q12L		.											.	LRIG2-229	0			c.A35T						.						109	125	120					1																	113616063		2203	4300	6503	SO:0001583	missense	9860	exon1			AGGAGCAGTTGCT	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.35A>T	1.37:g.113616063A>T	ENSP00000355396:p.Gln12Leu	Somatic	320	0	1451	WXS	Illumina HiSeq	Phase_I	352	123	NM_014813	0	0	0	0	0	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	9.612	1.131598	0.21041	.	.	ENSG00000198799	ENST00000361127	T	0.60920	0.15	4.86	-2.01	0.07410	.	0.866104	0.09769	N	0.758205	T	0.10637	0.0260	N	0.08118	0	0.21220	N	0.99976	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	10	0.35671	T	0.21	.	0.3463	0.00342	0.1887:0.2563:0.2382:0.3168	.	12	O94898	LRIG2_HUMAN	L	12	ENSP00000355396:Q12L	ENSP00000355396:Q12L	Q	+	2	0	LRIG2	113417586	0.910000	0.30920	0.987000	0.45799	0.031000	0.12232	-0.515000	0.06290	-0.294000	0.08973	-0.290000	0.09829	CAG	.		0.642	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		T	113616063	A	T	113616063	3	4	42	1	0	0	0	0	1	0	0	0	8970	188	7	5	37	5	LRIG2	1	113616063	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	9494027	113616063	135634558	3	3836											
LASS2	29956	ucsc.edu	37	chr1	150940937	150940937	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcgttgggaggtgcccgcagCcgagttttctcctttatgtt	4	14	13	10	3	1	0	0	0	1	0	2	2	1	1	3	2	2	4	3	2	1	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:150940937C>T	ENST00000271688.6	-	3	611	c.225G>A	c.(223-225)cgG>cgA	p.R75R	RP11-316M1.12_ENST00000561111.1_RNA|CERS2_ENST00000368954.5_Silent_p.R75R|CERS2_ENST00000561294.1_Silent_p.R75R|RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000345896.4_5'UTR	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	75					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GTGCCCGCAGCCGAGTTTTCT	0.557																																					p.R75R													.	.	0			c.G225A						.						79	76	77					1																	150940937		2203	4300	6503	SO:0001819	synonymous_variant	29956	exon3			CCGCAGCCGAGTT	AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"Homeoboxes / CERS class"	14076	protein-coding gene	gene with protein product		606920	"longevity assurance (LAG1, S. cerevisiae) homolog 2", "LAG1 longevity assurance homolog 2 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 2"	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.225G>A	1.37:g.150940937C>T		Somatic	53	0		WXS	Illumina HiSeq		71	4	NM_022075	0	0	281	375	94	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Silent	SNP	ENST00000271688.6	37	CCDS973.1																																																																																			.		0.557	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2	NM_022075		T	150940937	C	T	150940937	2	4	42	1	0	0	0	0	0	0	0	1	8660	726	26	2		2	LASS2	1	150940937	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	37324874	150940937	98309684	4	3837											
KIAA0907	22889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155899153	155899153	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttgatactgcagccccaCtaagtcggctgatctaaaaa	13	9	9	10	1	1	2	0	2	1	0	2	3	1	2	2	1	3	3	2	1	5	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:155899153C>G	ENST00000368321.3	-	4	421	c.398G>C	c.(397-399)aGt>aCt	p.S133T	KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368319.3_Missense_Mutation_p.S133T|KIAA0907_ENST00000368320.3_Missense_Mutation_p.S133T	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	133							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			TGCAGCCCCACTAAGTCGGCT	0.408																																					p.S133T		.											.	KIAA0907-90	0			c.G398C						.						126	119	122					1																	155899153		2203	4300	6503	SO:0001583	missense	22889	exon4			GCCCCACTAAGTC	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.398G>C	1.37:g.155899153C>G	ENSP00000357304:p.Ser133Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	139	52	NM_014949	0	0	22	49	27	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	37	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524402	0.64747	.	.	ENSG00000132680	ENST00000368321;ENST00000368320;ENST00000368319	T;T;T	0.34859	1.34;1.34;1.34	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	N	0.16790	0.44	0.80722	D	1	P;P;P;P;P;B	0.50819	0.873;0.939;0.873;0.884;0.682;0.336	P;P;B;P;B;B	0.52646	0.541;0.699;0.439;0.705;0.303;0.395	T	0.01720	-1.1288	10	0.08179	T	0.78	-11.4646	17.2104	0.86929	0.0:1.0:0.0:0.0	.	133;133;133;133;133;133	D3DVA4;Q7Z7F0-4;A8K1I7;Q7Z7F0-3;Q7Z7F0-2;Q7Z7F0	.;.;.;.;.;K0907_HUMAN	T	133	ENSP00000357304:S133T;ENSP00000357303:S133T;ENSP00000357302:S133T	ENSP00000357302:S133T	S	-	2	0	KIAA0907	154165777	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.105000	0.77031	2.831000	0.97527	0.650000	0.86243	AGT	.		0.408	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		G	155899153	C	G	155899153	3	3	42	1	0	0	0	0	1	0	0	0	8220	565	20	4	1490	4	KIAA0907	1	155899153	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	4958216	155899153	93351468	5	3838											
USF1	7391	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161011569	161011569	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggggaagtaagtatagTgcgtctcagcagctgtcccc	8	10	13	10	1	1	0	1	0	1	0	3	1	2	1	2	2	4	5	2	2	4	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:161011569T>C	ENST00000368021.3	-	6	548	c.344A>G	c.(343-345)cAc>cGc	p.H115R	USF1_ENST00000368019.1_Missense_Mutation_p.H115R|F11R_ENST00000289779.3_5'Flank|USF1_ENST00000368020.1_Missense_Mutation_p.H115R|TSTD1_ENST00000368023.3_5'Flank|TSTD1_ENST00000423014.2_5'Flank|USF1_ENST00000435396.1_Missense_Mutation_p.H56R|TSTD1_ENST00000318289.10_5'Flank|TSTD1_ENST00000368024.1_5'Flank	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	115					carbon catabolite regulation of transcription (GO:0045990)|cellular response to insulin stimulus (GO:0032869)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|negative regulation of fibrinolysis (GO:0051918)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GTAAGTATAGTGCGTCTCAGC	0.572											OREG0013936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H115R		.											.	USF1-516	0			c.A344G						.						95	87	90					1																	161011569		2203	4300	6503	SO:0001583	missense	7391	exon6			GTATAGTGCGTCT	BC035505	CCDS1214.1	1q22-q23	2013-05-21			ENSG00000158773	ENSG00000158773		"Basic helix-loop-helix proteins"	12593	protein-coding gene	gene with protein product		191523				8486371	Standard	NM_007122		Approved	UEF, MLTFI, bHLHb11	uc031pqv.1	P22415	OTTHUMG00000031472	ENST00000368021.3:c.344A>G	1.37:g.161011569T>C	ENSP00000357000:p.His115Arg	Somatic	123	0	1813	WXS	Illumina HiSeq	Phase_I	141	13	NM_001276373	0	0	33	39	6	B2RBZ4|Q5SY46|Q7Z5Y1	Missense_Mutation	SNP	ENST00000368021.3	37	CCDS1214.1	.	.	.	.	.	.	.	.	.	.	T	5.051	0.195050	0.09599	.	.	ENSG00000158773	ENST00000368020;ENST00000368021;ENST00000435396;ENST00000368019;ENST00000534633	D;D;D;D	0.91740	-2.9;-2.9;-2.85;-2.89	5.23	5.23	0.72850	.	0.048337	0.85682	D	0.000000	T	0.72614	0.3482	N	0.19112	0.55	0.42447	D	0.992738	B	0.11235	0.004	B	0.09377	0.004	T	0.67480	-0.5660	10	0.02654	T	1	-18.6648	13.1223	0.59334	0.0:0.0:0.0:1.0	.	115	P22415	USF1_HUMAN	R	115;115;56;115;56	ENSP00000356999:H115R;ENSP00000357000:H115R;ENSP00000390109:H56R;ENSP00000356998:H115R	ENSP00000356998:H115R	H	-	2	0	USF1	159278193	0.992000	0.36948	0.993000	0.49108	0.996000	0.88848	1.041000	0.30291	2.194000	0.70268	0.533000	0.62120	CAC	.		0.572	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122		C	161011569	T	C	161011569	3	2	42	1	0	0	0	0	1	0	0	0	17065	1696	59	3	612	3	USF1	1	161011569	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	5112416	161011569	88239052	6	3839											
TMCC2	9911	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	205238546	205238546	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcggcgtggtggagggcGtcaagggcagcctctctggc	4	6	21	10	3	2	0	1	0	1	0	3	1	2	1	1	8	1	1	1	8	1	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:205238546G>T	ENST00000358024.3	+	3	1605	c.1216G>T	c.(1216-1218)Gtc>Ttc	p.V406F	TMCC2_ENST00000329800.7_Missense_Mutation_p.V166F|TMCC2_ENST00000545499.1_Missense_Mutation_p.V328F|TMCC2_ENST00000330675.7_Missense_Mutation_p.V181F|TMCC2_ENST00000495538.1_3'UTR	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	406						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GGTGGAGGGCGTCAAGGGCAG	0.682																																					p.V406F		.											.	TMCC2-91	0			c.G1216T						.						32	35	34					1																	205238546		2202	4299	6501	SO:0001583	missense	9911	exon3			GAGGGCGTCAAGG	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"Transmembrane and coiled-coil domain containing"	24239	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 2"			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.1216G>T	1.37:g.205238546G>T	ENSP00000350718:p.Val406Phe	Somatic	92	2		WXS	Illumina HiSeq	Phase_I	114	36	NM_014858	0	0	0	0	0	A2RRH3|B7Z1P7|Q6ZN09	Missense_Mutation	SNP	ENST00000358024.3	37	CCDS30984.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035722	0.75617	.	.	ENSG00000133069	ENST00000358024;ENST00000545499;ENST00000367159;ENST00000330675;ENST00000329800	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.75148	0.3810	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.97110	1.0;1.0;1.0;0.974	T	0.75841	-0.3175	10	0.59425	D	0.04	.	19.6803	0.95960	0.0:0.0:1.0:0.0	.	202;166;181;406	Q8IW47;G5E963;B2RAX5;O75069	.;.;.;TMCC2_HUMAN	F	406;328;210;181;166	ENSP00000350718:V406F;ENSP00000437943:V328F;ENSP00000356127:V210F;ENSP00000331842:V181F;ENSP00000329436:V166F	ENSP00000329436:V166F	V	+	1	0	TMCC2	203505169	1.000000	0.71417	0.998000	0.56505	0.361000	0.29550	8.004000	0.88535	2.756000	0.94617	0.561000	0.74099	GTC	.		0.682	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		T	205238546	G	T	205238546	3	4	42	1	0	0	0	0	1	0	0	0	16025	1145	40	4	1226	4	TMCC2	1	205238546	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	44226977	205238546	44012075	7	3840											
FBXO11	80204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	48050458	48050458	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggcttttacttcaaagccTgctatcctatttctgtgtat	8	18	6	9	0	2	0	1	0	1	0	3	0	3	0	2	1	3	3	2	1	6	8			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:48050458T>G	ENST00000403359.3	-	12	1512	c.1440A>C	c.(1438-1440)gcA>gcC	p.A480A	FBXO11_ENST00000316377.4_Silent_p.A396A|FBXO11_ENST00000402508.1_Silent_p.A396A|FBXO11_ENST00000434523.2_5'UTR	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	480					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTTCAAAGCCTGCTATCCTAT	0.373			"Mis, F, D"		DLBCL																																p.A480A		.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11-659	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.A1440C						.						82	77	78					2																	48050458		2203	4300	6503	SO:0001819	synonymous_variant	80204	exon12			AAAGCCTGCTATC	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.1440A>C	2.37:g.48050458T>G		Somatic	71	1		WXS	Illumina HiSeq	Phase_I	89	30	NM_001190274	0	0	13	26	13	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Silent	SNP	ENST00000403359.3	37	CCDS54357.1																																																																																			.		0.373	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		G	48050458	T	G	48050458	2	3	42	1	0	0	0	0	0	0	0	1	5746	1567	55	5		5	FBXO11	2	48050458	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08		48050458	195148915	8	3841											
STON1	11037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	48808956	48808956	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttctgactactgtggaggAggagctgatgaagttgccag	9	11	14	7	0	1	3	0	3	1	0	1	6	1	6	1	3	3	2	1	3	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:48808956A>G	ENST00000406226.1	+	3	1379	c.1184A>G	c.(1183-1185)gAg>gGg	p.E395G	STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.E395G|STON1_ENST00000404752.1_Missense_Mutation_p.E395G|STON1_ENST00000309835.3_Missense_Mutation_p.E395G|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.E395G|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.E395G|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.E395G|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.E395G	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	395	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACTGTGGAGGAGGAGCTGATG	0.433																																					p.E395G		.											.	STON1-91	0			c.A1184G						.						75	74	74					2																	48808956		2203	4300	6503	SO:0001583	missense	11037	exon3			TGGAGGAGGAGCT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1184A>G	2.37:g.48808956A>G	ENSP00000384615:p.Glu395Gly	Somatic	96	1		WXS	Illumina HiSeq	Phase_I	134	40	NM_001198595	0	0	3	4	1	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.961262	0.74016	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.14893	2.52;2.52;2.52;2.49;2.47;2.49;2.49;2.67	5.27	5.27	0.74061	Stonin homology (1);	0.000000	0.85682	D	0.000000	T	0.43233	0.1238	M	0.75264	2.295	0.58432	D	0.99999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.963;0.998	T	0.41305	-0.9516	10	0.87932	D	0	.	15.3726	0.74577	1.0:0.0:0.0:0.0	.	395;395;395	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	G	395	ENSP00000385273:E395G;ENSP00000384615:E395G;ENSP00000310969:E395G;ENSP00000385499:E395G;ENSP00000385701:E395G;ENSP00000378236:E395G;ENSP00000311493:E395G;ENSP00000378234:E395G	ENSP00000310969:E395G	E	+	2	0	STON1-GTF2A1L;STON1	48662460	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.128000	0.94424	2.209000	0.71365	0.533000	0.62120	GAG	.		0.433	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		G	48808956	A	G	48808956	3	3	42	1	0	0	0	0	1	0	0	0	15348	304	11	3	1186	3	STON1	2	48808956	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	758498	48808956	194390417	9	3842											
IMMT	10989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	86371415	86371415	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggctgcacctgagtggtTcctattcctacggcgctggc	4	12	12	13	2	1	1	0	1	1	0	3	1	3	1	3	4	2	4	3	4	2	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:86371415T>G	ENST00000410111.3	-	15	2640	c.2253A>C	c.(2251-2253)ggA>ggC	p.G751G	IMMT_ENST00000449247.2_Silent_p.G740G|IMMT_ENST00000409051.2_Silent_p.G704G|IMMT_ENST00000254636.5_Silent_p.G652G|IMMT_ENST00000442664.2_Silent_p.G750G	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	751					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCTGAGTGGTTCCTATTCCTA	0.478																																					p.G751G		.											.	IMMT-91	0			c.A2253C						.						68	66	67					2																	86371415		1922	4128	6050	SO:0001819	synonymous_variant	10989	exon15			AGTGGTTCCTATT	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.2253A>C	2.37:g.86371415T>G		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	101	40	NM_006839	0	0	52	115	63	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	7.004	0.555382	0.13436	.	.	ENSG00000132305	ENST00000419070	.	.	.	5.3	-1.19	0.09585	.	.	.	.	.	T	0.52058	0.1711	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44329	-0.9335	4	.	.	.	-22.8427	7.6657	0.28430	0.0:0.4268:0.1243:0.4489	.	.	.	.	H	606	.	.	N	-	1	0	IMMT	86224926	0.864000	0.29904	0.998000	0.56505	0.905000	0.53344	-0.251000	0.08818	-0.076000	0.12775	-0.256000	0.11100	AAC	.		0.478	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		G	86371415	T	G	86371415	2	3	42	1	0	0	0	0	0	0	0	1	7739	1770	62	5		5	IMMT	2	86371415	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	37562459	86371415	156827958	10	3843											
VWC2L	402117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	215440518	215440518	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcagtgttcgaaacgtGaatgccaaggcaagcagact	12	8	11	10	2	1	2	1	1	0	1	2	3	1	2	1	1	4	4	1	1	4	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:215440518G>T	ENST00000312504.5	+	4	1445	c.643G>T	c.(643-645)Gaa>Taa	p.E215*	AC107218.3_ENST00000412896.1_RNA|VWC2L_ENST00000427124.1_3'UTR|AC107218.3_ENST00000437883.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	215					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						TTCGAAACGTGAATGCCAAGG	0.458																																					p.E215X		.											.	.	0			c.G643T						.						225	220	221					2																	215440518		2026	4199	6225	SO:0001587	stop_gained	402117	exon4			AAACGTGAATGCC	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.643G>T	2.37:g.215440518G>T	ENSP00000308976:p.Glu215*	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	305	93	NM_001080500	0	0	0	0	0	A6NC69|B2RUW7|B7X8X1	Nonsense_Mutation	SNP	ENST00000312504.5	37	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	G	44	10.583132	0.99432	.	.	ENSG00000174453	ENST00000312504	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-3.3711	19.5796	0.95461	0.0:0.0:1.0:0.0	.	.	.	.	X	215	.	ENSP00000308976:E215X	E	+	1	0	VWC2L	215148763	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	9.476000	0.97823	2.624000	0.88883	0.655000	0.94253	GAA	.		0.458	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		T	215440518	G	T	215440518	4	4	42	1	0	0	0	0	0	1	0	0	17277	1291	45	4	653	4	VWC2L	2	215440518	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	129069103	215440518	27758855	11	3844											
GIGYF2	26058	broad.mit.edu;bcgsc.ca	37	chr2	233681733	233681734	+	Frame_Shift_Ins	INS	-	-	AGGAAAC																															aggaagaagaacttgcccgaINSaggaaacaggtatgtatctg																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:233681733_233681734insAGGAAAC	ENST00000409547.1	+	22	2672_2673	c.2361_2362insAGGAAAC	c.(2362-2364)aggfs	p.-790fs	GIGYF2_ENST00000373563.4_Frame_Shift_Ins_p.-790fs|GIGYF2_ENST00000373566.3_Frame_Shift_Ins_p.-812fs|GIGYF2_ENST00000452341.2_Frame_Shift_Ins_p.-621fs|GIGYF2_ENST00000409480.1_Frame_Shift_Ins_p.-812fs|GIGYF2_ENST00000409451.3_Frame_Shift_Ins_p.-811fs|GIGYF2_ENST00000409196.3_Frame_Shift_Ins_p.-784fs	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2						adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AACTTGCCCGAAGGAAACAGGT	0.47																																					p.R808fs													.	GIGYF2-28	0			c.2424_2425insAGGAAAC						.																																			SO:0001589	frameshift_variant	26058	exon22			TGCCCGAAGGAAA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2362_2368dupAGGAAAC	2.37:g.233681734_233681740dupAGGAAAC	ENSP00000386537:p.Gln790fs	Somatic	246	0		WXS	Illumina HiSeq	Phase_I	300	45	NM_001103147	0	0	0	0	0	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Frame_Shift_Ins	INS	ENST00000409547.1	37	CCDS33401.1																																																																																			.		0.47	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		AGGAAAC	233681734	-	AGGAAAC	233681733	7	5	42	1	0	1	1	0	0	0	0	0	6398	233	9	0	2501	0	GIGYF2	2	233681733	Frame_Shift_Ins	INS	-	TCGA-B3-3925-01A-01D-1458-08	18241215	233681733	9517640	12	3845			1	13		2	2	12	N	T_-	3.091364e-05
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233681744	233681744	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttgcccgaaggaaacaggTatgtatctgggaactctgac	12	9	11	9	1	2	1	0	1	2	0	2	4	2	3	1	3	3	2	1	3	5	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:233681744T>A	ENST00000409547.1	+	22	2681		c.e22+2		GIGYF2_ENST00000373563.4_Splice_Site|GIGYF2_ENST00000373566.3_Splice_Site|GIGYF2_ENST00000452341.2_Splice_Site|GIGYF2_ENST00000409480.1_Splice_Site|GIGYF2_ENST00000409451.3_Splice_Site|GIGYF2_ENST00000409196.3_Splice_Site	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2						adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AGGAAACAGGTATGTATCTGG	0.468																																					.		.											.	GIGYF2-28	0			c.2352+2T>A						.						239	230	233					2																	233681744		2203	4300	6503	SO:0001630	splice_region_variant	26058	exon19			AACAGGTATGTAT	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2370+2T>A	2.37:g.233681744T>A		Somatic	278	1		WXS	Illumina HiSeq	Phase_I	344	93	NM_001103148	0	0	0	0	0	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Splice_Site	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085687	0.36758	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	.	.	.	3.76	3.76	0.43208	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9462	0.58373	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GIGYF2	233389988	1.000000	0.71417	0.938000	0.37757	0.311000	0.27955	5.934000	0.70138	1.709000	0.51313	0.379000	0.24179	.	.		0.468	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	Intron	A	233681744	T	A	233681744	5	1	42	1	0	0	0	0	0	0	1	0	6398	1652	57	5	2512	5	GIGYF2	2	233681744	Splice_Site	SNP	T	TCGA-B3-3925-01A-01D-1458-08	11	233681744	9517629	13	3846			1	13		2	2	12	N	T_-	3.091364e-05
OGG1	4968	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	9798226	9798227	+	Frame_Shift_Ins	INS	-	-	AA																															tggatgtccatatgtggcacINSattgcccaacgtgactacag																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:9798226_9798227insAA	ENST00000344629.7	+	5	1162_1163	c.819_820insAA	c.(820-822)attfs	p.I274fs	OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000339511.5_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000302003.7_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000302008.8_Frame_Shift_Ins_p.I274fs			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	274					acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					ATATGTGGCACATTGCCCAACG	0.599								Base excision repair (BER), DNA glycosylases																													p.H273fs		.											.	OGG1-660	0			c.819_820insAA						.																																			SO:0001589	frameshift_variant	4968	exon5			.	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"8-hydroxyguanine DNA glycosylase", "OGG1 type 1e", "OGG1 type 1d", "OGG1 type 1g", "OGG1 type 1h"	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	Exception_encountered	3.37:g.9798226_9798227insAA	ENSP00000342851:p.Ile274fs	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	86	28	NM_016819	0	0	0	0	0	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Frame_Shift_Ins	INS	ENST00000344629.7	37	CCDS2581.1																																																																																			.		0.599	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		AA	9798227	-	AA	9798226	7	5	42	1	0	1	1	0	0	0	0	0	10871	477	17	0	837	0	OGG1	3	9798226	Frame_Shift_Ins	INS	-	TCGA-B3-3925-01A-01D-1458-08		9798226	188224204	14	3847	42	2									
OGG1	4968	hgsc.bcm.edu;bcgsc.ca	37	chr3	9798228	9798228	+	Missense_Mutation	SNP	T	T	A																															ggatgtccatatgtggcacaTtgcccaacgtgactacagct																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:9798228T>A	ENST00000344629.7	+	5	1164	c.821T>A	c.(820-822)aTt>aAt	p.I274N	OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Missense_Mutation_p.I274N|OGG1_ENST00000339511.5_Missense_Mutation_p.I274N|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Missense_Mutation_p.I274N|OGG1_ENST00000302003.7_Missense_Mutation_p.I274N|OGG1_ENST00000302008.8_Missense_Mutation_p.I274N			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	274					acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					ATGTGGCACATTGCCCAACGT	0.602								Base excision repair (BER), DNA glycosylases																													p.I274N		.											.	OGG1-660	0			c.T821A						.						81	78	79					3																	9798228		2203	4300	6503	SO:0001583	missense	4968	exon5			GGCACATTGCCCA	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"8-hydroxyguanine DNA glycosylase", "OGG1 type 1e", "OGG1 type 1d", "OGG1 type 1g", "OGG1 type 1h"	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.821T>A	3.37:g.9798228T>A	ENSP00000342851:p.Ile274Asn	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	79	31	NM_016819	0	0	13	13	0	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.74|17.74	3.464569|3.464569	0.63513|0.63513	.|.	.|.	ENSG00000114026|ENSG00000114026	ENST00000302003;ENST00000344629;ENST00000302036;ENST00000339511;ENST00000449570;ENST00000302008|ENST00000441094;ENST00000416333	D;D;D;D;D;D|.	0.88046|.	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33|.	5.43|5.43	5.43|5.43	0.79202|0.79202	HhH-GPD domain (2);DNA glycosylase (1);Helix-turn-helix, base-excision DNA repair, C-terminal (1);|.	0.044994|.	0.85682|.	D|.	0.000000|.	D|D	0.87124|0.87124	0.6099|0.6099	H|H	0.95745|0.95745	3.715|3.715	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D|D	0.91042|0.91042	0.4872|0.4872	10|5	0.87932|.	D|.	0|.	-15.1918|-15.1918	15.7624|15.7624	0.78096|0.78096	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	274;274;274;274;274;274;274;274|.	E5KPN1;O15527-3;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2|.	.;.;.;.;.;.;OGG1_HUMAN;.|.	N|M	274|172;41	ENSP00000305584:I274N;ENSP00000342851:I274N;ENSP00000306561:I274N;ENSP00000345520:I274N;ENSP00000403598:I274N;ENSP00000305527:I274N|.	ENSP00000305584:I274N|.	I|L	+|+	2|1	0|2	OGG1|OGG1	9773228|9773228	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.135000|0.135000	0.20990|0.20990	7.054000|7.054000	0.76649|0.76649	2.176000|2.176000	0.68965|0.68965	0.533000|0.533000	0.62120|0.62120	ATT|TTG	.		0.602	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		A	9798228	T	A	9798228	3	1	42	1	0	0	0	0	1	0	0	0	10871	1493	52	5	839	5	OGG1	3	9798228	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	2	9798228	188224202	15	3848	42	2									
RAF1	5894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	12633229	12633229	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaacagccacctcattccTgaaggcctggaattgctctg	10	9	9	13	0	2	2	1	1	1	1	3	3	3	3	4	2	3	1	4	2	3	2	rs368807126		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:12633229T>A	ENST00000251849.4	-	11	1610	c.1171A>T	c.(1171-1173)Agg>Tgg	p.R391W	RAF1_ENST00000534997.1_Missense_Mutation_p.R176W|RAF1_ENST00000542177.1_Missense_Mutation_p.R310W|RAF1_ENST00000442415.2_Missense_Mutation_p.R411W	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	391	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	ACCTCATTCCTGAAGGCCTGG	0.507			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.R391W		.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1-1404	0			c.A1171T						.	T	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	110	99	103		1171	4	1	3		103	0,8600		0,0,4300	no	missense	RAF1	NM_002880.3	101	0,1,6502	AA,AT,TT		0.0,0.0227,0.0077	probably-damaging	391/649	12633229	1,13005	2203	4300	6503	SO:0001583	missense	5894	exon11	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CATTCCTGAAGGC	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.1171A>T	3.37:g.12633229T>A	ENSP00000251849:p.Arg391Trp	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	102	31	NM_002880	0	0	57	92	35	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.216060	0.79352	2.27E-4	0.0	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66	5.15	3.96	0.45880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84419	0.5468	L	0.28192	0.835	0.80722	D	1	D;D;D	0.71674	0.994;0.994;0.998	D;D;D	0.77557	0.99;0.985;0.99	D	0.85467	0.1170	10	0.87932	D	0	.	11.796	0.52100	0.0:0.0:0.2774:0.7226	.	310;176;391	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	W	391;411;270;176;310	ENSP00000251849:R391W;ENSP00000401888:R411W;ENSP00000398591:R270W;ENSP00000441186:R176W;ENSP00000443567:R310W	ENSP00000251849:R391W	R	-	1	2	RAF1	12608229	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.865000	0.56033	1.047000	0.40274	0.533000	0.62120	AGG	.		0.507	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		A	12633229	T	A	12633229	3	1	42	1	0	0	0	0	1	0	0	0	13034	1579	55	5	803	5	RAF1	3	12633229	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	2835001	12633229	185389201	16	3849											
TOP2B	7155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	25646332	25646332	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaaaaacagaagcagaatCttcttcattactgtcaaatt	17	12	5	7	0	4	3	2	1	2	2	4	3	4	3	0	0	3	1	0	0	7	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:25646332C>A	ENST00000264331.4	-	33	4407	c.4408G>T	c.(4408-4410)Gat>Tat	p.D1470Y	TOP2B_ENST00000542520.1_Missense_Mutation_p.D322Y|TOP2B_ENST00000540199.1_Missense_Mutation_p.D322Y|TOP2B_ENST00000435706.2_Missense_Mutation_p.D1465Y	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1470					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)	p.D1465Y(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GAAGCAGAATCTTCTTCATTA	0.313																																					p.D1465Y		.											.	TOP2B-273	1	Substitution - Missense(1)	large_intestine(1)	c.G4393T						.						118	110	112					3																	25646332		1811	4068	5879	SO:0001583	missense	7155	exon33			CAGAATCTTCTTC	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.4408G>T	3.37:g.25646332C>A	ENSP00000264331:p.Asp1470Tyr	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	142	54	NM_001068	0	0	54	74	20	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	C	19.71	3.878740	0.72294	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.49720	0.77;0.85;0.85;0.77	5.48	5.48	0.80851	.	0.262894	0.42964	D	0.000636	T	0.51261	0.1664	N	0.08118	0	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.995;0.996	T	0.61744	-0.7000	10	0.66056	D	0.02	-20.2424	17.9046	0.88914	0.0:1.0:0.0:0.0	.	1470;1465	Q02880;Q02880-2	TOP2B_HUMAN;.	Y	322;1465;1470;322	ENSP00000446023:D322Y;ENSP00000396704:D1465Y;ENSP00000264331:D1470Y;ENSP00000437352:D322Y	ENSP00000264331:D1470Y	D	-	1	0	TOP2B	25621336	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.225000	0.65294	2.722000	0.93159	0.563000	0.77884	GAT	.		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				A	25646332	C	A	25646332	3	1	42	1	0	0	0	0	1	0	0	0	16399	913	32	4	488	4	TOP2B	3	25646332	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	13013103	25646332	172376098	17	3850											
SCN10A	6336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38835251	38835251	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccggtgtgtgctgtagaacGgatctagatcctccaggggc	7	9	14	11	2	1	2	0	0	1	2	3	3	3	3	3	4	2	2	3	4	3	2	rs140609990		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:38835251G>A	ENST00000449082.2	-	1	250	c.251C>T	c.(250-252)cCg>cTg	p.P84L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	84					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GCTGTAGAACGGATCTAGATC	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		12896	0		0	False		,,,				2504	0				p.P84L		.											.	SCN10A-99	0			c.C251T						.	G	LEU/PRO	6,4400	9.9+/-24.2	0,6,2197	154	158	157		251	5.2	1	3	dbSNP_134	157	0,8600		0,0,4300	yes	missense	SCN10A	NM_006514.2	98	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	possibly-damaging	84/1957	38835251	6,13000	2203	4300	6503	SO:0001583	missense	6336	exon1			TAGAACGGATCTA	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.251C>T	3.37:g.38835251G>A	ENSP00000390600:p.Pro84Leu	Somatic	212	0		WXS	Illumina HiSeq	Phase_I	316	94	NM_006514	0	0	0	0	0	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689442	0.48097	0.001362	0.0	ENSG00000185313	ENST00000449082	D	0.96856	-4.15	5.19	5.19	0.71726	.	0.170309	0.52532	D	0.000066	D	0.96842	0.8969	M	0.91612	3.225	0.52501	D	0.999956	D	0.54601	0.967	B	0.41135	0.348	D	0.98036	1.0379	10	0.87932	D	0	.	18.9136	0.92496	0.0:0.0:1.0:0.0	.	84	Q9Y5Y9	SCNAA_HUMAN	L	84	ENSP00000390600:P84L	ENSP00000390600:P84L	P	-	2	0	SCN10A	38810255	1.000000	0.71417	0.997000	0.53966	0.163000	0.22366	9.575000	0.98187	2.704000	0.92352	0.563000	0.77884	CCG	G|1.000;A|0.000		0.572	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38835251	G	A	38835251	3	1	42	1	0	0	0	0	1	0	0	0	13944	1116	39	1	5727	1	SCN10A	3	38835251	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	13188919	38835251	159187179	18	3851											
MST1	63891	hgsc.bcm.edu	37	chr3	49725253	49725253	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatcctcctgccaaggccCgggcaccaccgcatgtagca	9	5	9	18	2	0	0	0	0	0	0	2	0	2	0	6	2	2	4	6	2	2	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:49725253C>T	ENST00000327697.6	+	0	0				MST1_ENST00000449682.2_Missense_Mutation_p.G58R|RNF123_ENST00000432042.1_5'Flank|MST1_ENST00000494828.2_Intron|MST1_ENST00000383728.3_Intron|MST1_ENST00000545762.1_Missense_Mutation_p.G44R|AC099668.5_ENST00000563780.1_RNA	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		TGCCAAGGCCCGGGCACCACC	0.607																																					p.G58R		.											.	MST1-278	0			c.G172A						.						28	27	27					3																	49725253		2203	4295	6498	SO:0001631	upstream_gene_variant	4485	exon2			AAGGCCCGGGCAC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891		3.37:g.49725253C>T	Exception_encountered	Somatic	95	1		WXS	Illumina HiSeq	Phase_I	96	5	NM_020998	0	0	16	16	0	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	2.518	-0.311453	0.05422	.	.	ENSG00000173531	ENST00000449682;ENST00000545762	T;T	0.63580	-0.05;-0.05	5.3	-5.56	0.02529	.	1.093190	0.07160	N	0.850623	T	0.40932	0.1137	L	0.36672	1.1	0.09310	N	1	P;B	0.38642	0.641;0.067	B;B	0.33521	0.165;0.037	T	0.31558	-0.9939	10	0.10902	T	0.67	.	8.1541	0.31158	0.104:0.3551:0.0:0.5409	.	44;58	B7Z538;G3XAK1	.;.	R	58;44	ENSP00000414287:G58R;ENSP00000437535:G44R	ENSP00000411117:G58R	G	-	1	0	MST1	49700257	0.000000	0.05858	0.001000	0.08648	0.396000	0.30629	-0.844000	0.04345	-0.784000	0.04528	-0.218000	0.12543	GGG	.		0.607	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49725253	C	T	49725253	1	4	42	0	1	0	0	0	0	0	0	0	9915	652	23	1		1	MST1	3	49725253	5'Flank	SNP	C	TCGA-B3-3925-01A-01D-1458-08	10890002	49725253	148297177	19	3852											
ATP6V1A	523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113503595	113503595	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tggaattgtcagtgagaactCgcttatcaaacacaaaatca	16	10	7	8	1	3	1	3	1	0	1	4	3	3	2	0	1	2	1	0	1	6	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:113503595C>G	ENST00000273398.3	+	5	587	c.479C>G	c.(478-480)tCg>tGg	p.S160W	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.S127W	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	160					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	AGTGAGAACTCGCTTATCAAA	0.368																																					p.S160W		.											.	ATP6V1A-93	0			c.C479G						.						121	116	118					3																	113503595		2203	4300	6503	SO:0001583	missense	523	exon5			AGAACTCGCTTAT	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.479C>G	3.37:g.113503595C>G	ENSP00000273398:p.Ser160Trp	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	171	58	NM_001690	0	0	27	46	19	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	37	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	C	18.49	3.634753	0.67130	.	.	ENSG00000114573	ENST00000273398;ENST00000538620;ENST00000496747;ENST00000475322	D;T	0.86956	-2.19;-1.41	6.07	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.92502	0.7619	M	0.78916	2.43	0.80722	D	1	D	0.64830	0.994	P	0.61397	0.888	D	0.93432	0.6786	10	0.87932	D	0	-10.5657	15.5979	0.76602	0.0:0.9341:0.0:0.0659	.	160	P38606	VATA_HUMAN	W	160;127;127;160	ENSP00000273398:S160W;ENSP00000439874:S127W	ENSP00000273398:S160W	S	+	2	0	ATP6V1A	114986285	1.000000	0.71417	0.905000	0.35620	0.616000	0.37450	7.253000	0.78320	1.578000	0.49821	0.655000	0.94253	TCG	.		0.368	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		G	113503595	C	G	113503595	3	3	42	1	0	0	0	0	1	0	0	0	1178	893	31	4	493	4	ATP6V1A	3	113503595	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	63778342	113503595	84518835	20	3853											
RUFY3	22902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	71659564	71659564	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccggctcttcaaacaggActttggagacaagatcaaca	15	7	8	11	1	3	2	2	0	1	2	3	4	3	3	1	3	3	1	1	3	4	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:71659564A>G	ENST00000226328.4	+	0	4233				RUFY3_ENST00000502653.1_Missense_Mutation_p.D414G|RUFY3_ENST00000381006.3_Missense_Mutation_p.D467G	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3						negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TTCAAACAGGACTTTGGAGAC	0.527																																					p.D467G		.											.	RUFY3-90	0			c.A1400G						.						52	48	50					4																	71659564		2203	4300	6503	SO:0001628	intergenic_variant	22902	exon13			AACAGGACTTTGG	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910		4.37:g.71659564A>G		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	99	34	NM_001037442	0	0	5	11	6	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.597113	0.66332	.	.	ENSG00000018189	ENST00000381006;ENST00000502653	T;T	0.08720	3.06;3.06	5.87	5.87	0.94306	.	0.237818	0.42294	D	0.000726	T	0.10508	0.0257	.	.	.	0.80722	D	1	B	0.31548	0.328	B	0.31101	0.124	T	0.04900	-1.0919	9	0.51188	T	0.08	-8.0298	16.2631	0.82557	1.0:0.0:0.0:0.0	.	467	Q7L099-3	.	G	467;414	ENSP00000370394:D467G;ENSP00000425400:D414G	ENSP00000370394:D467G	D	+	2	0	RUFY3	71878428	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.930000	0.92872	2.239000	0.73571	0.528000	0.53228	GAC	.		0.527	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		G	71659564	A	G	71659564	1	3	42	0	1	0	0	0	0	0	0	0	13772	275	10	3		3	RUFY3	4	71659564	IGR	SNP	A	TCGA-B3-3925-01A-01D-1458-08		71659564	119494712	21	3854											
CDKL2	8999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76532405	76532405	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaccaatagttctggagcTctgtaccatcgggttgccac	9	10	9	13	1	2	0	0	0	2	0	3	1	2	1	4	2	4	4	4	2	4	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:76532405T>C	ENST00000429927.2	-	4	1207	c.504A>G	c.(502-504)agA>agG	p.R168R	CDKL2_ENST00000307465.4_Silent_p.R168R	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	168	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GTTCTGGAGCTCTGTACCATC	0.453																																					p.R168R		.											.	CDKL2-454	0			c.A504G						.						98	93	95					4																	76532405		2203	4300	6503	SO:0001819	synonymous_variant	8999	exon4			TGGAGCTCTGTAC	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.504A>G	4.37:g.76532405T>C		Somatic	98	1		WXS	Illumina HiSeq	Phase_I	124	44	NM_003948	0	0	2	3	1	B2R695	Silent	SNP	ENST00000429927.2	37	CCDS3570.1																																																																																			.		0.453	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		C	76532405	T	C	76532405	2	2	42	1	0	0	0	0	0	0	0	1	3160	1548	54	3		3	CDKL2	4	76532405	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	4872841	76532405	114621871	22	3855											
TIGD2	166815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	90035227	90035227	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgttggatgcaatttatGaagtgtcaagagcttggaac	12	12	12	5	0	1	2	1	1	0	1	1	4	1	4	0	2	3	3	0	2	5	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:90035227G>T	ENST00000317005.2	+	1	1260	c.1102G>T	c.(1102-1104)Gaa>Taa	p.E368*	FAM13A_ENST00000502459.1_5'Flank|RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	368	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		TGCAATTTATGAAGTGTCAAG	0.363																																					p.E368X		.											.	TIGD2-90	0			c.G1102T						.						81	80	80					4																	90035227		2203	4300	6503	SO:0001587	stop_gained	166815	exon1			ATTTATGAAGTGT	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1102G>T	4.37:g.90035227G>T	ENSP00000317170:p.Glu368*	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	103	31	NM_145715	0	0	9	11	2		Nonsense_Mutation	SNP	ENST00000317005.2	37	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	G	35	5.519555	0.96416	.	.	ENSG00000180346	ENST00000317005	.	.	.	4.36	3.47	0.39725	.	0.000000	0.43110	D	0.000607	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-9.209	6.0713	0.19891	0.1044:0.193:0.7026:0.0	.	.	.	.	X	368	.	ENSP00000317170:E368X	E	+	1	0	TIGD2	90254250	1.000000	0.71417	0.996000	0.52242	0.956000	0.61745	2.543000	0.45752	2.264000	0.75181	0.460000	0.39030	GAA	.		0.363	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715		T	90035227	G	T	90035227	4	4	42	1	0	0	0	0	0	1	0	0	15928	1291	45	4	1104	4	TIGD2	4	90035227	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	13502822	90035227	101119049	23	3856											
PCDH18	54510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	138450855	138450855	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagtgactggtgactgttGtgactctgccggctgcccat	5	13	13	10	1	1	4	0	4	1	0	1	4	1	4	2	2	2	2	2	2	0	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:138450855G>A	ENST00000344876.4	-	1	2774	c.2388C>T	c.(2386-2388)caC>caT	p.H796H	PCDH18_ENST00000412923.2_Silent_p.H796H|PCDH18_ENST00000507846.1_Silent_p.H576H|PCDH18_ENST00000510305.1_Silent_p.H7H|PCDH18_ENST00000511115.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	796					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GGTGACTGTTGTGACTCTGCC	0.498																																					p.H796H		.											.	PCDH18-185	0			c.C2388T						.						125	109	114					4																	138450855		2203	4300	6503	SO:0001819	synonymous_variant	54510	exon1			ACTGTTGTGACTC	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"Cadherins / Protocadherins : Non-clustered"	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2388C>T	4.37:g.138450855G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	97	44	NM_019035	0	0	1	1	0	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																			.		0.498	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		A	138450855	G	A	138450855	2	1	42	1	0	0	0	0	0	0	0	1	11539	1368	48	2		2	PCDH18	4	138450855	Silent	SNP	G	TCGA-B3-3925-01A-01D-1458-08	48415628	138450855	52703421	24	3857											
ABCE1	6059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	146041306	146041306	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggtgatgctgggggaaaatgGtaagttttctgttttgtgat	8	16	15	2	0	1	2	0	2	1	0	1	3	1	3	0	4	1	4	0	4	3	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:146041306G>A	ENST00000296577.4	+	11	1659		c.e11+1		OTUD4_ENST00000455611.2_Intron|ABCE1_ENST00000502803.1_Splice_Site	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1						negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					GGGGAAAATGGTAAGTTTTCT	0.313																																					.		.											.	ABCE1-91	0			c.1144+1G>A						.						66	72	70					4																	146041306		2203	4296	6499	SO:0001630	splice_region_variant	6059	exon11			AAAATGGTAAGTT	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"ATP binding cassette transporters / subfamily E"	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.1144+1G>A	4.37:g.146041306G>A		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	95	33	NM_002940	0	0	0	2	2	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Splice_Site	SNP	ENST00000296577.4	37	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.276838	0.80580	.	.	ENSG00000164163	ENST00000296577	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3284	0.94273	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCE1	146260756	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.869000	0.99810	2.623000	0.88846	0.555000	0.69702	.	.		0.313	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	Intron	A	146041306	G	A	146041306	5	1	42	1	0	0	0	0	0	0	1	0	64	1275	44	2	1183	2	ABCE1	4	146041306	Splice_Site	SNP	G	TCGA-B3-3925-01A-01D-1458-08	7590451	146041306	45112970	25	3858											
DDR1	780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30857025	30857025	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctggtgccccgcagggtcgGtgtttcccaaggaggaggag	6	7	17	11	2	0	0	0	0	0	0	2	3	1	3	4	6	1	2	4	6	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:30857025G>A	ENST00000324771.8	+	6	783	c.235G>A	c.(235-237)Gtg>Atg	p.V79M	DDR1_ENST00000454612.2_Missense_Mutation_p.V79M|DDR1_ENST00000508312.1_Missense_Mutation_p.V97M|DDR1_ENST00000376567.2_Missense_Mutation_p.V79M|DDR1_ENST00000376570.4_Missense_Mutation_p.V79M|DDR1_ENST00000361741.4_5'Flank|DDR1_ENST00000376569.3_Missense_Mutation_p.V79M|DDR1_ENST00000513240.1_Missense_Mutation_p.V79M|DDR1_ENST00000376575.3_Missense_Mutation_p.V79M|DDR1_ENST00000418800.2_Missense_Mutation_p.V79M|DDR1_ENST00000376568.3_Missense_Mutation_p.V79M|DDR1_ENST00000446312.1_Missense_Mutation_p.V79M|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000452441.1_Missense_Mutation_p.V79M			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	79	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CGCAGGGTCGGTGTTTCCCAA	0.647																																					p.V97M		.											.	DDR1-1403	0			c.G289A						.						174	186	181					6																	30857025		1511	2709	4220	SO:0001583	missense	780	exon4			GGGTCGGTGTTTC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"CD molecules"	2730	protein-coding gene	gene with protein product		600408	"discoidin domain receptor family, member 1"	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.235G>A	6.37:g.30857025G>A	ENSP00000318217:p.Val79Met	Somatic	384	0		WXS	Illumina HiSeq	Phase_I	482	150	NM_001202523	0	0	124	270	146	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.45|16.45	3.125934|3.125934	0.56721|0.56721	.|.	.|.	ENSG00000204580|ENSG00000204580	ENST00000424544|ENST00000505066;ENST00000460944;ENST00000324771;ENST00000505534;ENST00000508317;ENST00000418800;ENST00000509639;ENST00000454612;ENST00000437124;ENST00000396342;ENST00000512694;ENST00000515233;ENST00000515881;ENST00000376569;ENST00000511510;ENST00000376575;ENST00000376570;ENST00000446312;ENST00000504927;ENST00000428153;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000512336;ENST00000421124;ENST00000512725;ENST00000504679;ENST00000503495;ENST00000376567;ENST00000513240	.|D;D;D;D;D;D;D;D;D;D;D;D;T;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.98987	.|-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;0.66;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3	4.84|4.84	4.84|4.84	0.62591|0.62591	.|Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	.|0.156961	.|0.41396	.|D	.|0.000884	D|D	0.98729|0.98729	0.9573|0.9573	M|M	0.67517|0.67517	2.055|2.055	0.20563|0.20563	N|N	0.99989|0.99989	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.973;0.984;0.998;0.976;1.0	D|D	0.95690|0.95690	0.8739|0.8739	5|10	.|0.87932	.|D	.|0	.|.	11.2046|11.2046	0.48762|0.48762	0.0:0.1855:0.8145:0.0|0.0:0.1855:0.8145:0.0	.|.	.|79;105;97;79;79	.|Q08345-4;B7Z3A2;B7Z2K0;Q08345-5;Q08345	.|.;.;.;.;DDR1_HUMAN	D|M	62|79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;97;79;79;79;79;105;79;79	.|ENSP00000421189:V79M;ENSP00000426420:V79M;ENSP00000318217:V79M;ENSP00000420833:V79M;ENSP00000427369:V79M;ENSP00000407699:V79M;ENSP00000422331:V79M;ENSP00000406091:V79M;ENSP00000394273:V79M;ENSP00000379631:V79M;ENSP00000426229:V79M;ENSP00000422467:V79M;ENSP00000423492:V79M;ENSP00000365753:V79M;ENSP00000425113:V79M;ENSP00000365759:V79M;ENSP00000365754:V79M;ENSP00000405998:V79M;ENSP00000427597:V79M;ENSP00000390593:V79M;ENSP00000365752:V79M;ENSP00000405039:V79M;ENSP00000422442:V97M;ENSP00000421719:V79M;ENSP00000409682:V79M;ENSP00000422108:V79M;ENSP00000423906:V79M;ENSP00000423749:V105M;ENSP00000365751:V79M;ENSP00000427552:V79M	.|ENSP00000318217:V79M	G|V	+|+	2|1	0|0	DDR1|DDR1	30965004|30965004	1.000000|1.000000	0.71417|0.71417	0.415000|0.415000	0.26534|0.26534	0.938000|0.938000	0.57974|0.57974	4.107000|4.107000	0.57811|0.57811	2.509000|2.509000	0.84616|0.84616	0.305000|0.305000	0.20034|0.20034	GGT|GTG	.		0.647	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		A	30857025	G	A	30857025	3	1	42	1	0	0	0	0	1	0	0	0	4342	1261	44	2	245	2	DDR1	6	30857025	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		30857025	140258042	26	3859											
CD2AP	23607	bcgsc.ca	37	chr6	47591945	47591953	+	In_Frame_Del	DEL	AGCTGTCCT	AGCTGTCCT	-																															gaaatagagaagctgaaaaaAgctgtcctgtcttcttgagt																								rs201892753		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	AGCTGTCCT	AGCTGTCCT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:47591945_47591953delAGCTGTCCT	ENST00000359314.5	+	18	2358_2366	c.1902_1910delAGCTGTCCT	c.(1900-1911)aaagctgtcctg>aag	p.AVL635del		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	635					mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			AGCTGAAAAAAGCTGTCCTGTCTTCTTGA	0.335																																					p.634_637del													.	CD2AP-92	0			c.1902_1910del						.																																			SO:0001651	inframe_deletion	23607	exon18			GAAAAAAGCTGTC	AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1902_1910delAGCTGTCCT	6.37:g.47591945_47591953delAGCTGTCCT	ENSP00000352264:p.Ala635_Leu637del	Somatic	73	0		WXS	Illumina HiSeq	Phase_1	74	6	NM_012120	0	0	0	0	0	A6NL34|Q5VYA3|Q9UG97	In_Frame_Del	DEL	ENST00000359314.5	37	CCDS34472.1																																																																																			.		0.335	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			-	47591953	AGCTGTCCT	-	47591945	7	5	42	1	0	1	0	1	0	0	0	0	3000	69	3	0	1972	0	CD2AP	6	47591945	In_Frame_Del	DEL	AGCTGTCCT	TCGA-B3-3925-01A-01D-1458-08	16734920	47591945	123523122	27	3860											
PREP	5550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	105825364	105825364	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactgctcaagaaatggcaCagtaatcttattctgggcct	12	11	8	10	0	3	1	1	0	2	1	3	1	3	1	1	2	1	3	1	2	4	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:105825364C>G	ENST00000369110.3	-	3	343	c.151G>C	c.(151-153)Gtg>Ctg	p.V51L		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	51					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.V51L(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AGAAATGGCACAGTAATCTTA	0.353																																					p.V51L		.											.	PREP-93	1	Substitution - Missense(1)	lung(1)	c.G151C						.						95	93	94					6																	105825364		2203	4300	6503	SO:0001583	missense	5550	exon3			ATGGCACAGTAAT		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.151G>C	6.37:g.105825364C>G	ENSP00000358106:p.Val51Leu	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	173	62	NM_002726	0	0	9	15	6	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812019	0.32053	.	.	ENSG00000085377	ENST00000369110	T	0.44881	0.91	5.76	4.89	0.63831	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.241940	0.41823	D	0.000804	T	0.07098	0.0180	N	0.01352	-0.895	0.39317	D	0.965174	B	0.02656	0.0	B	0.01281	0.0	T	0.15065	-1.0450	10	0.25751	T	0.34	-16.8555	10.4377	0.44445	0.0:0.8553:0.0:0.1447	.	51	P48147	PPCE_HUMAN	L	51	ENSP00000358106:V51L	ENSP00000358106:V51L	V	-	1	0	PREP	105932057	0.730000	0.28100	0.982000	0.44146	0.979000	0.70002	1.374000	0.34283	2.700000	0.92200	0.650000	0.86243	GTG	.		0.353	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1			G	105825364	C	G	105825364	3	3	42	1	0	0	0	0	1	0	0	0	12503	478	17	4	2033	4	PREP	6	105825364	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	58233419	105825364	65289703	28	3861											
ROS1	6098	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	117622147	117622147	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaacttaccttcaaagctTtcatttatgactccactgtt	11	16	3	11	0	3	1	3	1	0	0	4	1	4	1	2	0	3	2	2	0	4	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:117622147T>G	ENST00000368508.3	-	42	6921	c.6723A>C	c.(6721-6723)gaA>gaC	p.E2241D	RN7SKP51_ENST00000410781.1_RNA|ROS1_ENST00000368507.3_Missense_Mutation_p.E2235D|RN7SKP18_ENST00000516005.1_RNA	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2241					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CTTCAAAGCTTTCATTTATGA	0.333			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.E2241D		.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1-1353	0			c.A6723C						.						77	74	75					6																	117622147		2203	4300	6503	SO:0001583	missense	6098	exon42			AAAGCTTTCATTT	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.6723A>C	6.37:g.117622147T>G	ENSP00000357494:p.Glu2241Asp	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	109	38	NM_002944	0	0	0	0	0	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.713310	0.30413	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.71341	-0.56;-0.56	4.98	1.37	0.22104	.	0.267889	0.32190	N	0.006450	T	0.30823	0.0777	L	0.27053	0.805	0.23174	N	0.998172	B	0.24963	0.115	B	0.20577	0.03	T	0.18871	-1.0323	10	0.30854	T	0.27	.	7.4549	0.27261	0.0:0.2549:0.0:0.7451	.	2241	P08922	ROS1_HUMAN	D	2241;2235	ENSP00000357494:E2241D;ENSP00000357493:E2235D	ENSP00000357493:E2235D	E	-	3	2	ROS1	117728840	0.999000	0.42202	0.996000	0.52242	0.448000	0.32197	0.295000	0.19065	0.439000	0.26476	0.459000	0.35465	GAA	.		0.333	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117622147	T	G	117622147	3	3	42	1	0	0	0	0	1	0	0	0	13563	1838	64	5	328	5	ROS1	6	117622147	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	11796783	117622147	53492920	29	3862											
RAET1L	154064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	150342042	150342042	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctttttctcctgttaccTcctgcacttggctccagggt	3	18	7	13	0	2	0	0	0	2	0	5	0	4	0	4	2	2	3	4	2	1	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:150342042T>A	ENST00000367341.1	-	3	629	c.630A>T	c.(628-630)ggA>ggT	p.G210G	RAET1L_ENST00000286380.2_Splice_Site_p.G210G			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	210	MHC class I alpha-2 like. {ECO:0000250}.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		TCCTGTTACCTCCTGCACTTG	0.468																																					p.G210G		.											.	RAET1L-90	0			c.A630T						.						129	129	129					6																	150342042		2203	4300	6503	SO:0001630	splice_region_variant	154064	exon3			GTTACCTCCTGCA	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.631+1A>T	6.37:g.150342042T>A		Somatic	182	1		WXS	Illumina HiSeq	Phase_I	235	84	NM_130900	0	0	0	0	0	A3KME4|Q8TE74	Silent	SNP	ENST00000367341.1	37	CCDS5224.1																																																																																			.		0.468	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	Silent	A	150342042	T	A	150342042	5	1	42	1	0	0	0	0	0	0	1	0	13033	1565	54	5	117	5	RAET1L	6	150342042	Splice_Site	SNP	T	TCGA-B3-3925-01A-01D-1458-08	32719895	150342042	20773025	30	3863											
ZAN	7455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100383746	100383746	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacttccgacaacagcaacaGcaattgtgtctcagacagta	14	8	7	12	1	1	1	1	0	1	1	3	2	2	1	1	0	4	3	1	0	4	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:100383746G>T	ENST00000348028.3	+	0	7126				ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000427578.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			AACAGCAACAGCAATTGTGTC	0.632																																					.													.	ZAN-142	0			.						.						102	105	104					7																	100383746		1978	4178	6156			7455	.			GCAACAGCAATTG	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100383746G>T		Somatic	202	1		WXS	Illumina HiSeq	Phase_I	282	138	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	G	10.27	1.303037	0.23736	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585;ENST00000546213	T;T;T;T	0.05925	3.37;3.37;3.37;3.37	4.59	0.255	0.15561	von Willebrand factor, type C (1);von Willebrand factor, type D domain (1);	1.390360	0.04747	N	0.423915	T	0.11239	0.0274	.	.	.	0.09310	N	1	D;D;D	0.61697	0.987;0.987;0.99	P;P;P	0.62298	0.838;0.838;0.9	T	0.35101	-0.9802	9	0.16896	T	0.51	.	3.5726	0.07922	0.3486:0.1924:0.459:0.0	.	794;2320;2321	F5GX59;F5H0T8;Q9Y493	.;.;ZAN_HUMAN	I	2320;2320;2320;794	ENSP00000445943:S2320I;ENSP00000445091:S2320I;ENSP00000444427:S2320I;ENSP00000441117:S794I	ENSP00000445091:S2320I	S	+	2	0	ZAN	100221682	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.036000	0.12185	0.212000	0.20703	0.655000	0.94253	AGC	.		0.632	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100383746	G	T	100383746	1	4	42	0	1	0	0	0	0	0	0	0	17546	971	34	4		4	ZAN	7	100383746	RNA	SNP	G	TCGA-B3-3925-01A-01D-1458-08		100383746	58754917	31	3864											
MUC17	140453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100692247	100692247	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagttcaaacagacattcacGgaacaggtaagtctgggaga	15	7	12	7	1	3	2	2	0	1	2	3	5	3	3	0	3	2	2	0	3	3	3	rs200175178		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:100692247G>A	ENST00000306151.4	+	5	12721	c.12657G>A	c.(12655-12657)acG>acA	p.T4219T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4219	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGACATTCACGGAACAGGTAA	0.507													G|||	1	0.000199681	0	0	5008	,	,		18356	0.001		0	False		,,,				2504	0				p.T4219T		.											.	MUC17-95	0			c.G12657A						.	G		1,4405	2.1+/-5.4	0,1,2202	74	66	68		12657	-8.8	0	7		68	0,8600		0,0,4300	no	coding-synonymous	MUC17	NM_001040105.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		4219/4494	100692247	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon5			ATTCACGGAACAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.12657G>A	7.37:g.100692247G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	135	47	NM_001040105	0	0	0	0	0	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.999;A|0.000		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100692247	G	A	100692247	2	1	42	1	0	0	0	0	0	0	0	1	9999	1103	39	1		1	MUC17	7	100692247	Silent	SNP	G	TCGA-B3-3925-01A-01D-1458-08	308501	100692247	58446416	32	3865											
ASB15	142685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	123264837	123264837	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgctgccgagtatggtcaCtgtgacgtgttagaacatct	8	12	12	9	3	2	2	1	1	1	1	3	3	2	2	1	1	2	3	1	1	3	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:123264837C>A	ENST00000451558.1	+	10	1187	c.666C>A	c.(664-666)caC>caA	p.H222Q	ASB15_ENST00000451215.1_Missense_Mutation_p.H222Q|RP11-390E23.3_ENST00000418409.1_RNA|RP11-390E23.3_ENST00000422401.1_RNA|ASB15_ENST00000275699.3_Missense_Mutation_p.H222Q|ASB15_ENST00000434204.1_Missense_Mutation_p.H222Q|RP11-390E23.3_ENST00000451016.1_RNA|RP11-390E23.3_ENST00000440504.1_RNA|RP11-390E23.3_ENST00000429396.1_RNA|ASB15_ENST00000540573.1_Missense_Mutation_p.H222Q			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	222					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						AGTATGGTCACTGTGACGTGT	0.468											OREG0018282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H222Q		.											.	ASB15-228	0			c.C666A						.						132	95	107					7																	123264837		2203	4300	6503	SO:0001583	missense	142685	exon6			TGGTCACTGTGAC	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"Ankyrin repeat domain containing"	19767	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 15"			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.666C>A	7.37:g.123264837C>A	ENSP00000397655:p.His222Gln	Somatic	61	0	1525	WXS	Illumina HiSeq	Phase_I	83	35	NM_080928	0	0	0	0	0	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.811718	0.32053	.	.	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000447789;ENST00000275699	T;T;T;T;T;T	0.65549	-0.1;-0.1;-0.1;-0.1;-0.16;-0.1	5.36	5.36	0.76844	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.67154	0.2863	L	0.33792	1.035	0.58432	D	0.999999	D	0.54601	0.967	P	0.58391	0.838	T	0.60924	-0.7166	10	0.22706	T	0.39	-7.5108	19.4438	0.94838	0.0:1.0:0.0:0.0	.	222	Q8WXK1	ASB15_HUMAN	Q	222;222;222;222;11;222;222	ENSP00000397655:H222Q;ENSP00000390963:H222Q;ENSP00000416433:H222Q;ENSP00000438643:H222Q;ENSP00000401166:H222Q;ENSP00000275699:H222Q	ENSP00000275699:H222Q	H	+	3	2	ASB15	123052073	0.988000	0.35896	1.000000	0.80357	0.235000	0.25334	1.161000	0.31773	2.674000	0.91012	0.491000	0.48974	CAC	.		0.468	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			A	123264837	C	A	123264837	3	1	42	1	0	0	0	0	1	0	0	0	1020	564	20	4	684	4	ASB15	7	123264837	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	22572590	123264837	35873826	33	3866											
MGAM	8972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	141800677	141800677	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctggctcttctgggatgaTgggcaaagcattggtgagta	8	11	16	6	0	2	2	0	2	2	0	2	3	2	3	0	5	1	5	0	5	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:141800677T>G	ENST00000549489.2	+	45	5357	c.5262T>G	c.(5260-5262)gaT>gaG	p.D1754E	MGAM_ENST00000475668.2_Missense_Mutation_p.D2650E	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1754	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCTGGGATGATGGGCAAAGCA	0.502																																					p.D1754E		.											.	MGAM-70	0			c.T5262G						.						86	86	86					7																	141800677		1981	4153	6134	SO:0001583	missense	8972	exon45			GGATGATGGGCAA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.5262T>G	7.37:g.141800677T>G	ENSP00000447378:p.Asp1754Glu	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	52	26	NM_004668	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.550375	0.65311	.	.	ENSG00000257335	ENST00000549489;ENST00000475668	D	0.96265	-3.96	4.83	1.2	0.21068	.	.	.	.	.	D	0.97343	0.9131	M	0.89414	3.03	0.24431	N	0.994574	D	0.55172	0.97	P	0.56823	0.807	D	0.92205	0.5771	9	0.87932	D	0	.	7.7862	0.29093	0.0:0.3312:0.0:0.6688	.	1754	O43451	MGA_HUMAN	E	1754;2651	ENSP00000447378:D1754E	ENSP00000373973:D1754E	D	+	3	2	MGAM	141447146	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	0.614000	0.24314	0.058000	0.16222	-0.269000	0.10298	GAT	.		0.502	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141800677	T	G	141800677	3	3	42	1	0	0	0	0	1	0	0	0	9566	1461	51	5	5436	5	MGAM	7	141800677	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	18535840	141800677	17337986	34	3867											
BMP1	649	broad.mit.edu;bcgsc.ca	37	chr8	22022973	22022973	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggctgctgctgctcccgcgtCccggccggccgctggacttg	1	8	15	17	5	0	0	0	0	0	0	2	1	2	1	4	4	3	5	4	4	0	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr8:22022973C>A	ENST00000306385.5	+	1	725	c.55C>A	c.(55-57)Ccc>Acc	p.P19T	BMP1_ENST00000306349.8_Missense_Mutation_p.P19T|BMP1_ENST00000354870.5_Missense_Mutation_p.P19T|BMP1_ENST00000397816.3_Missense_Mutation_p.P19T|BMP1_ENST00000397814.3_Missense_Mutation_p.P19T	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	19					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GCTCCCGCGTCCCGGCCGGCC	0.736																																					p.P19T													.	BMP1-155	0			c.C55A						.						10	12	12					8																	22022973		2117	4160	6277	SO:0001583	missense	649	exon1			CCGCGTCCCGGCC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.55C>A	8.37:g.22022973C>A	ENSP00000305714:p.Pro19Thr	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	27	7	NM_001199	0	0	3	7	4	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.048783	0.55110	.	.	ENSG00000168487	ENST00000306385;ENST00000354870;ENST00000397816;ENST00000306349;ENST00000397814	T;T;T;T;T	0.81247	0.17;-1.47;-0.11;0.03;1.11	3.84	2.92	0.33932	.	.	.	.	.	T	0.66694	0.2815	N	0.14661	0.345	0.22479	N	0.999063	B;B;B	0.24092	0.001;0.001;0.097	B;B;B	0.28709	0.005;0.01;0.093	T	0.57602	-0.7783	9	0.49607	T	0.09	.	8.9784	0.35950	0.0:0.7582:0.2418:0.0	.	19;19;19	P13497;P13497-2;P13497-6	BMP1_HUMAN;.;.	T	19	ENSP00000305714:P19T;ENSP00000346941:P19T;ENSP00000380917:P19T;ENSP00000306121:P19T;ENSP00000380915:P19T	ENSP00000306121:P19T	P	+	1	0	BMP1	22078918	0.998000	0.40836	0.998000	0.56505	0.989000	0.77384	2.517000	0.45529	0.551000	0.29008	0.561000	0.74099	CCC	.		0.736	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		A	22022973	C	A	22022973	3	1	42	1	0	0	0	0	1	0	0	0	1457	855	30	4	57	4	BMP1	8	22022973	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		22022973	124341049	35	3868											
SNTB1	6641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	121587444	121587444	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaccagggctggtttccactGtttcttgctctcccctggca	5	13	9	14	0	2	0	0	0	2	0	4	0	3	0	4	3	2	5	4	3	1	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr8:121587444G>A	ENST00000395601.3	-	5	1432	c.1018C>T	c.(1018-1020)Cag>Tag	p.Q340*	SNTB1_ENST00000517992.1_Nonsense_Mutation_p.Q340*|SNTB1_ENST00000519177.1_5'UTR	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	340	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GGTTTCCACTGTTTCTTGCTC	0.483																																					p.Q340X		.											.	SNTB1-228	0			c.C1018T						.						149	139	142					8																	121587444		2203	4300	6503	SO:0001587	stop_gained	6641	exon4			TCCACTGTTTCTT	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.1018C>T	8.37:g.121587444G>A	ENSP00000378965:p.Gln340*	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	219	62	NM_021021	0	0	6	6	0	A8K9E0|O14912|Q4KMG8	Nonsense_Mutation	SNP	ENST00000395601.3	37	CCDS6334.1	.	.	.	.	.	.	.	.	.	.	G	40	8.420009	0.98803	.	.	ENSG00000172164	ENST00000395601;ENST00000517992	.	.	.	6.01	5.11	0.69529	.	0.476872	0.25380	N	0.031082	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7345	0.85444	0.0:0.0:0.8703:0.1297	.	.	.	.	X	340	.	ENSP00000378965:Q340X	Q	-	1	0	SNTB1	121656625	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	6.995000	0.76257	2.861000	0.98227	0.650000	0.86243	CAG	.		0.483	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		A	121587444	G	A	121587444	4	1	42	1	0	0	0	0	0	1	0	0	14904	1386	48	2	614	2	SNTB1	8	121587444	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	99564471	121587444	24776578	36	3869											
ZFP41	286128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144332048	144332048	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcagaaaaaagaagacgcCgaccccaagggaggaggcag	17	0	15	9	2	0	3	0	0	0	3	0	6	0	5	3	4	0	2	3	4	5	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr8:144332048C>T	ENST00000330701.4	+	2	404	c.35C>T	c.(34-36)cCg>cTg	p.P12L	ZFP41_ENST00000522452.1_Missense_Mutation_p.P12L|ZFP41_ENST00000520584.1_Missense_Mutation_p.P12L	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	12					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			AAGAAGACGCCGACCCCAAGG	0.592																																					p.P12L		.											.	ZFP41-91	0			c.C35T						.						26	30	29					8																	144332048		2200	4299	6499	SO:0001583	missense	286128	exon2			AGACGCCGACCCC		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"Zinc fingers, C2H2-type"	26786	protein-coding gene	gene with protein product			"zinc finger protein 41 homolog (mouse)"			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.35C>T	8.37:g.144332048C>T	ENSP00000327427:p.Pro12Leu	Somatic	40	1		WXS	Illumina HiSeq	Phase_I	44	12	NM_173832	0	0	2	2	0	D3DWJ5	Missense_Mutation	SNP	ENST00000330701.4	37	CCDS6397.1	.	.	.	.	.	.	.	.	.	.	C	9.918	1.211334	0.22289	.	.	ENSG00000181638	ENST00000520584;ENST00000330701;ENST00000522452	T;T;T	0.05855	3.38;3.38;3.38	2.5	0.0503	0.14293	.	.	.	.	.	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.27971	0.196	B	0.17433	0.018	T	0.42189	-0.9466	9	0.66056	D	0.02	-3.2814	3.4146	0.07371	0.4823:0.3537:0.164:0.0	.	12	Q8N8Y5	ZFP41_HUMAN	L	12	ENSP00000430465:P12L;ENSP00000327427:P12L;ENSP00000428966:P12L	ENSP00000327427:P12L	P	+	2	0	ZFP41	144403423	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.038000	0.12144	-0.010000	0.14271	0.491000	0.48974	CCG	.		0.592	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832		T	144332048	C	T	144332048	3	4	42	1	0	0	0	0	1	0	0	0	17681	652	23	1	37	1	ZFP41	8	144332048	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	22744604	144332048	2031974	37	3870											
FLJ46321	389763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	84608132	84608132	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttccgtatgaggatgctgtGgggccttcccctcaaggtcc	5	12	12	12	1	1	1	1	1	0	0	4	2	4	2	5	4	1	2	5	4	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr9:84608132G>A	ENST00000344803.2	+	4	2794	c.2747G>A	c.(2746-2748)tGg>tAg	p.W916*		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	916					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGGATGCTGTGGGGCCTTCCC	0.463																																					p.W916X		.											.	.	0			c.G2747A						.						53	49	50					9																	84608132		1870	4093	5963	SO:0001587	stop_gained	389763	exon4			TGCTGTGGGGCCT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2747G>A	9.37:g.84608132G>A	ENSP00000341988:p.Trp916*	Somatic	71	1		WXS	Illumina HiSeq	Phase_I	89	34	NM_001001670	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	31	5.080052	0.94050	.	.	ENSG00000214929	ENST00000344803	.	.	.	3.09	-0.249	0.13011	.	1.642750	0.03466	N	0.213012	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	6.5839	5.1689	0.15099	0.1287:0.4109:0.4603:0.0	.	.	.	.	X	916	.	ENSP00000341988:W916X	W	+	2	0	FAM75D1	83797952	0.969000	0.33509	0.000000	0.03702	0.018000	0.09664	1.347000	0.33975	-0.147000	0.11254	0.558000	0.71614	TGG	.		0.463	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84608132	G	A	84608132	4	1	42	1	0	0	0	0	0	1	0	0	5951	1357	47	2	2761	2	FLJ46321	9	84608132	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		84608132	56605299	38	3871											
C10orf12	26148	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	98741324	98741326	+	In_Frame_Del	DEL	TTT	TTT	-																															actgctgacaaagagaatacTttacagtgtccaaaaacacc																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:98741324_98741326delTTT	ENST00000286067.2	+	1	284_286	c.177_179delTTT	c.(175-180)acttta>aca	p.L60del		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	60										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		AAGAGAATACTTTACAGTGTCCA	0.404																																					p.59_60del		.											.	C10orf12-92	0			c.177_179del						.																																			SO:0001651	inframe_deletion	26148	exon1			.	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.177_179delTTT	10.37:g.98741324_98741326delTTT	ENSP00000286067:p.Leu60del	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	108	37	NM_015652	0	0	0	0	0	Q9H945|Q9Y457	In_Frame_Del	DEL	ENST00000286067.2	37	CCDS7452.1																																																																																			.		0.404	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		-	98741326	TTT	-	98741324	7	5	42	1	0	1	0	1	0	0	0	0	1593	1596	56	0	179	0	C10orf12	10	98741324	In_Frame_Del	DEL	TTT	TCGA-B3-3925-01A-01D-1458-08		98741324	36793423	39	3872											
PYROXD2	84795	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	100167696	100167696	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgacagctgcacccccgAtcacatggcgcctctcgaag	9	6	10	16	3	2	1	1	1	1	0	3	3	2	1	3	1	2	2	3	1	1	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:100167696A>G	ENST00000370575.4	-	3	254	c.206T>C	c.(205-207)aTc>aCc	p.I69T	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	69							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						TGCACCCCCGATCACATGGCG	0.627																																					p.I69T													.	PYROXD2-90	0			c.T206C						.						77	56	63					10																	100167696		2203	4300	6503	SO:0001583	missense	84795	exon3			CCCCCGATCACAT	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.206T>C	10.37:g.100167696A>G	ENSP00000359607:p.Ile69Thr	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	17	4	NM_032709	0	0	6	7	1	D3DR61|Q5TAA9|Q9BRQ1	Missense_Mutation	SNP	ENST00000370575.4	37	CCDS7474.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.558944	0.45590	.	.	ENSG00000119943	ENST00000370575	D	0.82433	-1.61	5.18	4.04	0.47022	.	0.244484	0.41938	N	0.000785	T	0.78438	0.4283	L	0.55103	1.725	0.47905	D	0.999546	B	0.09022	0.002	B	0.17979	0.02	T	0.72243	-0.4350	10	0.42905	T	0.14	-17.704	10.6458	0.45619	0.9233:0.0:0.0767:0.0	.	69	Q8N2H3	PYRD2_HUMAN	T	69	ENSP00000359607:I69T	ENSP00000359607:I69T	I	-	2	0	PYROXD2	100157686	1.000000	0.71417	0.955000	0.39395	0.932000	0.56968	7.281000	0.78621	0.816000	0.34421	0.460000	0.39030	ATC	.		0.627	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		G	100167696	A	G	100167696	3	3	42	1	0	0	0	0	1	0	0	0	12899	333	12	3	1595	3	PYROXD2	10	100167696	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	1426372	100167696	35367051	40	3873											
COL17A1	1308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105793764	105793764	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagatctccagcaaagtcAgctcccaatagtccgccatt	11	9	6	15	1	2	1	1	0	1	1	6	1	5	1	5	0	2	2	5	0	3	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:105793764A>G	ENST00000353479.5	-	52	4385	c.4095T>C	c.(4093-4095)gcT>gcC	p.A1365A	COL17A1_ENST00000369733.3_Silent_p.A1283A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1365	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CAGCAAAGTCAGCTCCCAATA	0.587																																					p.A1365A		.											.	COL17A1-95	0			c.T4095C						.						109	106	107					10																	105793764		2203	4300	6503	SO:0001819	synonymous_variant	1308	exon52			AAAGTCAGCTCCC	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.4095T>C	10.37:g.105793764A>G		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	140	42	NM_000494	0	0	0	1	1	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			.		0.587	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		G	105793764	A	G	105793764	2	3	42	1	0	0	0	0	0	0	0	1	3680	175	7	3		3	COL17A1	10	105793764	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08	5626068	105793764	29740983	41	3874											
PTPRE	5791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	129859261	129859261	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccctgttcagactacatCaatgcttcctacatagatgt	11	14	5	11	0	2	2	2	0	0	2	4	2	4	2	2	0	3	2	2	0	4	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:129859261C>A	ENST00000254667.3	+	8	849	c.570C>A	c.(568-570)atC>atA	p.I190I	PTPRE_ENST00000430713.2_3'UTR|PTPRE_ENST00000419012.2_Silent_p.I190I|PTPRE_ENST00000306042.5_Silent_p.I132I	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	190	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	CAGACTACATCAATGCTTCCT	0.483																																					p.I190I	Colon(52;977 1184 20575 41685)	.											.	PTPRE-227	0			c.C570A						.						175	160	165					10																	129859261		2203	4300	6503	SO:0001819	synonymous_variant	5791	exon8			CTACATCAATGCT	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.570C>A	10.37:g.129859261C>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	109	38	NM_006504	0	0	4	8	4	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	37	CCDS7657.1																																																																																			.		0.483	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			A	129859261	C	A	129859261	2	1	42	1	0	0	0	0	0	0	0	1	12832	816	29	4		4	PTPRE	10	129859261	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	24065497	129859261	5675486	42	3875											
PAOX	196743	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	135193909	135193909	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaatgctgtgtgagcggCacccacagcatggacctggt	8	8	14	11	1	0	1	0	1	0	0	0	3	0	3	2	4	3	3	2	4	1	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:135193909C>T	ENST00000278060.5	+	2	671	c.588C>T	c.(586-588)ggC>ggT	p.G196G	PAOX_ENST00000357296.3_Silent_p.G196G|PAOX_ENST00000480071.2_Silent_p.G196G|PAOX_ENST00000368539.4_Intron|PAOX_ENST00000368535.2_3'UTR|AL360181.1_ENST00000597657.1_5'Flank	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN	polyamine oxidase (exo-N4-amino)	334					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|positive regulation of spermidine biosynthetic process (GO:1901307)|putrescine biosynthetic process (GO:0009446)|putrescine catabolic process (GO:0009447)|small molecule metabolic process (GO:0044281)|spermidine catabolic process (GO:0046203)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	peroxisomal matrix (GO:0005782)	N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)|N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052904)|N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052903)|polyamine oxidase activity (GO:0046592)|receptor binding (GO:0005102)|spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23		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;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		GTGTGAGCGGCACCCACAGCA	0.622																																					p.G196G		.											.	PAOX-131	0			c.C588T						.						33	36	35					10																	135193909		2202	4299	6501	SO:0001819	synonymous_variant	196743	exon2			GAGCGGCACCCAC	BC032778	CCDS7682.1, CCDS7683.1, CCDS7684.1	10q26.3	2003-11-13			ENSG00000148832	ENSG00000148832			20837	protein-coding gene	gene with protein product		615853				12660232	Standard	NM_207127		Approved	PAO	uc001lmv.3	Q6QHF9	OTTHUMG00000019318	ENST00000278060.5:c.588C>T	10.37:g.135193909C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	83	7	NM_207128	0	0	12	13	1	D3DXI6|Q5VWY0|Q6QHF5|Q6QHF6|Q6QHF7|Q6QHF8|Q6QHG0|Q6QHG1|Q6QHG2|Q6QHG3|Q6QHG4|Q6QHG5|Q6QHG6|Q86WP9|Q8N555|Q8NCX3	Silent	SNP	ENST00000278060.5	37	CCDS7683.1																																																																																			.		0.622	PAOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051146.2	NM_152911		T	135193909	C	T	135193909	2	4	42	1	0	0	0	0	0	0	0	1	11449	697	25	2		2	PAOX	10	135193909	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	5334648	135193909	340838	43	3876											
HPX	3263	ucsc.edu;bcgsc.ca	37	chr11	6453151	6453151	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtttttcttcccaggaaaagGcagcatccactgctgaagga	11	10	10	10	0	1	1	0	1	1	0	3	3	3	3	2	3	2	4	2	3	3	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr11:6453151G>C	ENST00000265983.3	-	8	1032	c.932C>G	c.(931-933)gCc>gGc	p.A311G		NM_000613.2	NP_000604.1	P02790	HEMO_HUMAN	hemopexin	311					cellular iron ion homeostasis (GO:0006879)|heme metabolic process (GO:0042168)|heme transport (GO:0015886)|hemoglobin metabolic process (GO:0020027)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|viral process (GO:0016032)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme transporter activity (GO:0015232)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(11)|prostate(1)	15		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		CCAGGAAAAGGCAGCATCCAC	0.542																																					p.A311G													.	HPX-90	0			c.C932G						.						138	142	140					11																	6453151		2201	4296	6497	SO:0001583	missense	3263	exon8			GAAAAGGCAGCAT	J03048	CCDS7763.1	11p15.5-p15.4	2012-10-02			ENSG00000110169	ENSG00000110169			5171	protein-coding gene	gene with protein product		142290				2989777, 2842511	Standard	NM_000613		Approved		uc001mdg.2	P02790	OTTHUMG00000133399	ENST00000265983.3:c.932C>G	11.37:g.6453151G>C	ENSP00000265983:p.Ala311Gly	Somatic	224	6		WXS	Illumina HiSeq		295	100	NM_000613	0	0	0	0	0	B2R957	Missense_Mutation	SNP	ENST00000265983.3	37	CCDS7763.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.375067	0.82682	.	.	ENSG00000110169	ENST00000265983	T	0.06687	3.27	5.72	5.72	0.89469	Hemopexin/matrixin, conserved site (1);Hemopexin/matrixin (2);	0.047287	0.85682	D	0.000000	T	0.27454	0.0674	M	0.64404	1.975	0.54753	D	0.99998	D	0.76494	0.999	D	0.70487	0.969	T	0.00113	-1.2042	10	0.87932	D	0	-20.1039	17.3732	0.87384	0.0:0.0:1.0:0.0	.	311	P02790	HEMO_HUMAN	G	311	ENSP00000265983:A311G	ENSP00000265983:A311G	A	-	2	0	HPX	6409727	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.858000	0.62947	2.715000	0.92844	0.561000	0.74099	GCC	.		0.542	HPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257256.1	NM_000613		C	6453151	G	C	6453151	3	2	42	1	0	0	0	0	1	0	0	0	7367	1203	42	4	468	4	HPX	11	6453151	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		6453151	128553365	44	3877											
ARHGAP32	9743	hgsc.bcm.edu;bcgsc.ca	37	chr11	128839901	128839901	+	Frame_Shift_Del	DEL	T	T	-																															tgctgactacattatggtcgTtgggagagaaatagccagtc																								rs141030632	byFrequency	TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr11:128839901delT	ENST00000310343.9	-	22	5164	c.5165delA	c.(5164-5166)aacfs	p.N1722fs	ARHGAP32_ENST00000527272.1_Frame_Shift_Del_p.N1373fs|ARHGAP32_ENST00000392657.3_Frame_Shift_Del_p.N1373fs|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1722	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						ATTATGGTCGTTGGGAGAGAA	0.507																																					p.N1722fs		.											.	ARHGAP32-231	0			c.5165delA						.						95	85	89					11																	128839901		2201	4297	6498	SO:0001589	frameshift_variant	9743	exon22			.	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.5165delA	11.37:g.128839901delT	ENSP00000310561:p.Asn1722fs	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	198	44	NM_001142685	0	0	0	0	0	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Frame_Shift_Del	DEL	ENST00000310343.9	37	CCDS44769.1																																																																																			.		0.507	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		-	128839901	T	-	128839901	7	5	42	1	0	1	0	1	0	0	0	0	881	1725	60	0	1102	0	ARHGAP32	11	128839901	Frame_Shift_Del	DEL	T	TCGA-B3-3925-01A-01D-1458-08	122386750	128839901	6166615	45	3878											
GYS2	2998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	21757442	21757442	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaagcaacttcaaagagcaGtaactcctccacaggaagtt	15	7	7	12	0	1	1	1	0	0	1	3	2	3	2	3	1	4	4	3	1	5	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:21757442G>T	ENST00000261195.2	-	1	339	c.85C>A	c.(85-87)Ctg>Atg	p.L29M		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	29					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TCAAAGAGCAGTAACTCCTCC	0.493																																					p.L29M	Colon(149;9 1820 3690 10544 50424)	.											.	GYS2-523	0			c.C85A						.						117	114	115					12																	21757442		2203	4299	6502	SO:0001583	missense	2998	exon1			AGAGCAGTAACTC		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.85C>A	12.37:g.21757442G>T	ENSP00000261195:p.Leu29Met	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	346	175	NM_021957	0	0	0	0	0	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864428	0.51482	.	.	ENSG00000111713	ENST00000261195	T	0.66638	-0.22	5.28	2.44	0.29823	.	0.076400	0.53938	D	0.000050	T	0.52964	0.1767	N	0.19112	0.55	0.34049	D	0.655926	P	0.52577	0.954	P	0.48166	0.569	T	0.61584	-0.7033	10	0.46703	T	0.11	-15.2558	7.1986	0.25868	0.35:0.0:0.65:0.0	.	29	P54840	GYS2_HUMAN	M	29	ENSP00000261195:L29M	ENSP00000261195:L29M	L	-	1	2	GYS2	21648709	0.646000	0.27295	0.229000	0.23960	0.989000	0.77384	0.796000	0.26986	0.361000	0.24292	0.655000	0.94253	CTG	.		0.493	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		T	21757442	G	T	21757442	3	4	42	1	0	0	0	0	1	0	0	0	6934	1020	36	4	2090	4	GYS2	12	21757442	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		21757442	112094453	46	3879											
ALG10	84920	ucsc.edu	37	chr12	34179835	34179835	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaaatagtcaggacattcaAaggtttatgtggtaatatca	15	12	8	6	0	3	0	3	0	0	0	3	1	3	1	1	3	0	2	1	3	6	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:34179835A>G	ENST00000266483.2	+	3	1726	c.1407A>G	c.(1405-1407)caA>caG	p.Q469Q	AC046130.1_ENST00000401300.2_RNA|ALG10_ENST00000538927.1_Intron|RP11-847H18.2_ENST00000501954.2_RNA	NM_032834.3	NP_116223.3	Q5BKT4	AG10A_HUMAN	ALG10, alpha-1,2-glucosyltransferase	469					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)				AGGACATTCAAAGGTTTATGT	0.338																																					p.Q469Q													.	ALG10-91	0			c.A1407G						.						120	125	123					12																	34179835		2203	4295	6498	SO:0001819	synonymous_variant	84920	exon3			CATTCAAAGGTTT	AJ312278	CCDS41769.1	12p11.21	2013-03-04	2013-03-04		ENSG00000139133	ENSG00000139133	2.4.1.256		23162	protein-coding gene	gene with protein product	"derepression of ITR1 expression 2 homolog (S. cerevisiae)", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"	603313	"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (yeast)", "asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (S. pombe)"				Standard	NM_032834		Approved	FLJ14751, DIE2, ALG10A	uc001rlm.3	Q5BKT4	OTTHUMG00000169285	ENST00000266483.2:c.1407A>G	12.37:g.34179835A>G		Somatic	248	0		WXS	Illumina HiSeq		506	2	NM_032834	0	0	10	14	4	Q6NS98|Q96DU0|Q96SM6	Silent	SNP	ENST00000266483.2	37	CCDS41769.1																																																																																			.		0.338	ALG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403309.1	NM_032834		G	34179835	A	G	34179835	2	3	42	1	0	0	0	0	0	0	0	1	511	11	1	3		3	ALG10	12	34179835	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08	12422393	34179835	99672060	47	3880											
TSFM	25895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	58177005	58177005	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgaagctgcggcggaaaaCaggctactcctttgtaaatt	12	10	10	9	2	0	1	0	1	0	0	1	2	1	2	1	3	4	3	1	3	6	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:58177005C>T	ENST00000300209.8	+	0	2563				TSFM_ENST00000454289.3_Missense_Mutation_p.T57I|RP11-571M6.15_ENST00000471530.1_Nonsense_Mutation_p.Q72*|TSFM_ENST00000350762.5_5'UTR|TSFM_ENST00000550559.1_Missense_Mutation_p.T57I|TSFM_ENST00000548851.1_Missense_Mutation_p.T57I|TSFM_ENST00000540550.1_Missense_Mutation_p.T57I|TSFM_ENST00000323833.8_Missense_Mutation_p.T57I|TSFM_ENST00000543727.1_Missense_Mutation_p.T57I|TSFM_ENST00000497617.1_3'UTR|RP11-571M6.15_ENST00000553083.1_3'UTR	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						CGGCGGAAAACAGGCTACTCC	0.582											OREG0021954	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T57I		.											.	TSFM-492	0			c.C170T						.						100	110	107					12																	58177005		2203	4300	6503	SO:0001628	intergenic_variant	10102	exon2			GGAAAACAGGCTA	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		12.37:g.58177005C>T		Somatic	215	0	1028	WXS	Illumina HiSeq	Phase_I	337	96	NM_005726	0	0	26	28	2	Q9H749|Q9Y3W2	Missense_Mutation	SNP	ENST00000300209.8	37	CCDS8957.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599184	0.87055	.	.	ENSG00000123297	ENST00000454289;ENST00000543727;ENST00000540550;ENST00000323833;ENST00000550559;ENST00000548851;ENST00000434359;ENST00000457189	.	.	.	5.29	5.29	0.74685	Translation elongation factor Ts, conserved site (1);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	D	0.89784	0.6815	H	0.97103	3.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.92805	0.6259	9	0.87932	D	0	.	17.8551	0.88760	0.0:1.0:0.0:0.0	.	57;57;57	B4E391;P43897;P43897-2	.;EFTS_HUMAN;.	I	57;57;57;57;57;57;7;7	.	ENSP00000313877:T57I	T	+	2	0	TSFM	56463272	1.000000	0.71417	0.991000	0.47740	0.509000	0.34042	6.612000	0.74187	2.753000	0.94483	0.462000	0.41574	ACA	.		0.582	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		T	58177005	C	T	58177005	1	4	42	0	1	0	0	0	0	0	0	0	16648	478	17	2		2	TSFM	12	58177005	IGR	SNP	C	TCGA-B3-3925-01A-01D-1458-08	23997170	58177005	75674890	48	3881											
CCDC63	160762	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	111321841	111321841	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttcctttcctagctctcaaGgcaaagaagcatgtcaagaa	13	11	7	10	0	2	2	2	0	1	2	5	2	4	2	2	1	2	3	2	1	6	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:111321841G>C	ENST00000308208.5	+	8	1103	c.861G>C	c.(859-861)aaG>aaC	p.K287N	CCDC63_ENST00000545036.1_Missense_Mutation_p.K247N|CCDC63_ENST00000552694.1_Missense_Mutation_p.K208N	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	287										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						TAGCTCTCAAGGCAAAGAAGC	0.502																																					p.K287N		.											.	CCDC63-134	0			c.G861C						.						129	129	129					12																	111321841		2203	4300	6503	SO:0001583	missense	160762	exon8			TCTCAAGGCAAAG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"outer row dynein assembly 5 homolog (Chlamydomonas)"						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.861G>C	12.37:g.111321841G>C	ENSP00000312399:p.Lys287Asn	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	296	144	NM_152591	0	0	0	0	0	B4DY03|Q0P603|Q6P2E1	Missense_Mutation	SNP	ENST00000308208.5	37	CCDS9151.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177145	0.38413	.	.	ENSG00000173093	ENST00000545036;ENST00000308208;ENST00000552694	T;T;T	0.21734	1.99;1.99;1.99	5.68	4.78	0.61160	.	0.332758	0.32357	N	0.006214	T	0.45836	0.1362	M	0.83012	2.62	0.33081	D	0.536687	D	0.71674	0.998	D	0.66351	0.943	T	0.64296	-0.6441	10	0.66056	D	0.02	.	10.8325	0.46669	0.089:0.0:0.911:0.0	.	287	Q8NA47	CCD63_HUMAN	N	247;287;208	ENSP00000445881:K247N;ENSP00000312399:K287N;ENSP00000450217:K208N	ENSP00000312399:K287N	K	+	3	2	CCDC63	109806224	0.905000	0.30787	0.841000	0.33234	0.034000	0.12701	1.260000	0.32968	1.383000	0.46405	0.655000	0.94253	AAG	.		0.502	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		C	111321841	G	C	111321841	3	2	42	1	0	0	0	0	1	0	0	0	2840	991	35	4	887	4	CCDC63	12	111321841	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	53144836	111321841	22530054	49	3882											
ANAPC5	51433	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	121746455	121746458	+	Frame_Shift_Del	DEL	TTCT	TTCT	-																															agtcaacctttgcaaaatagTtcttggcttcattgaggttc																								rs146935401		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:121746455_121746458delTTCT	ENST00000261819.3	-	17	2214_2217	c.2093_2096delAGAA	c.(2092-2097)aagaacfs	p.KN698fs	ANAPC5_ENST00000541887.1_Frame_Shift_Del_p.KN685fs|ANAPC5_ENST00000535482.1_Frame_Shift_Del_p.KN364fs|ANAPC5_ENST00000344395.4_Frame_Shift_Del_p.KN586fs|ANAPC5_ENST00000441917.2_Frame_Shift_Del_p.KN586fs|ANAPC5_ENST00000544314.1_5'UTR	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	698					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGCAAAATAGTTCTTGGCTTCATT	0.49																																					p.698_699del		.											.	ANAPC5-290	0			c.2093_2096del						.																																			SO:0001589	frameshift_variant	51433	exon17			.	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.2093_2096delAGAA	12.37:g.121746455_121746458delTTCT	ENSP00000261819:p.Lys698fs	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	299	132	NM_016237	0	0	0	0	0	E9PFB2|Q8N4H7|Q9BQD4	Frame_Shift_Del	DEL	ENST00000261819.3	37	CCDS9220.1																																																																																			.		0.49	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			-	121746458	TTCT	-	121746455	7	5	42	1	0	1	0	1	0	0	0	0	605	1725	60	0	175	0	ANAPC5	12	121746455	Frame_Shift_Del	DEL	TTCT	TCGA-B3-3925-01A-01D-1458-08	10424614	121746455	12105440	50	3883											
KDM2B	84678	broad.mit.edu	37	chr12	121880611	121880611	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgttggccagcgccatgCggtcctcggcgttcttccag	3	11	13	14	4	1	0	0	0	1	0	4	0	3	0	4	3	2	3	4	3	0	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:121880611C>T	ENST00000377071.4	-	19	2705	c.2633G>A	c.(2632-2634)cGc>cAc	p.R878H	KDM2B_ENST00000542973.1_Missense_Mutation_p.R246H|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Missense_Mutation_p.R809H	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	878					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CAGCGCCATGCGGTCCTCGGC	0.731																																					p.R878H													.	KDM2B-638	0			c.G2633A						.						8	10	9					12																	121880611		1880	4090	5970	SO:0001583	missense	84678	exon19			GCCATGCGGTCCT	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2633G>A	12.37:g.121880611C>T	ENSP00000366271:p.Arg878His	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	37	3	NM_032590	0	0	21	21	0	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	32	5.183689	0.94885	.	.	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043;ENST00000261824	T;T;T	0.25579	2.14;2.49;1.79	5.73	5.73	0.89815	.	0.272823	0.26556	N	0.023710	T	0.39545	0.1082	L	0.53249	1.67	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.991;0.996	P;P;P;P	0.51806	0.586;0.68;0.511;0.68	T	0.03739	-1.1008	10	0.41790	T	0.15	-19.7174	19.8984	0.96975	0.0:1.0:0.0:0.0	.	318;878;809;321	B7ZB05;Q8NHM5;A8MRS1;B4DSN4	.;KDM2B_HUMAN;.;.	H	866;246;809;878;321;881	ENSP00000437821:R246H;ENSP00000366269:R809H;ENSP00000366271:R878H	ENSP00000261824:R881H	R	-	2	0	KDM2B	120364994	0.998000	0.40836	0.671000	0.29857	0.953000	0.61014	4.082000	0.57635	2.713000	0.92767	0.655000	0.94253	CGC	.		0.731	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121880611	C	T	121880611	3	4	42	1	0	0	0	0	1	0	0	0	8146	768	27	1	1449	1	KDM2B	12	121880611	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	134156	121880611	11971284	51	3884											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123073262	123073262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttcttttctaaaagttaTttggagagactacattagtt	11	19	6	5	0	3	1	0	0	3	1	3	3	3	2	0	1	1	2	0	1	5	10			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:123073262T>C	ENST00000333479.7	+	40	4075	c.3898T>C	c.(3898-3900)Ttt>Ctt	p.F1300L	KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1300					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		CTAAAAGTTATTTGGAGAGAC	0.269																																					p.F1300L		.											.	KNTC1-543	0			c.T3898C						.						23	22	22					12																	123073262		1781	4037	5818	SO:0001583	missense	9735	exon40			AAGTTATTTGGAG		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.3898T>C	12.37:g.123073262T>C	ENSP00000328236:p.Phe1300Leu	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	7	4	NM_014708	0	0	0	0	0	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.650570	0.29336	.	.	ENSG00000184445	ENST00000333479	T	0.13196	2.61	5.55	3.18	0.36537	.	0.329620	0.32719	N	0.005728	T	0.06781	0.0173	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32107	-0.9919	10	0.12430	T	0.62	-6.5911	4.9227	0.13878	0.0:0.1133:0.1847:0.7019	.	1300	P50748	KNTC1_HUMAN	L	1300	ENSP00000328236:F1300L	ENSP00000328236:F1300L	F	+	1	0	KNTC1	121639215	1.000000	0.71417	0.861000	0.33841	0.748000	0.42578	1.230000	0.32612	0.386000	0.24997	0.383000	0.25322	TTT	.		0.269	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			C	123073262	T	C	123073262	3	2	42	1	0	0	0	0	1	0	0	0	8449	1493	52	3	4052	3	KNTC1	12	123073262	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	1192651	123073262	10778633	52	3885											
POSTN	10631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	38154716	38154716	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctaaagcgcttatcttgtTttaacttttcatggagggat	10	16	8	7	1	2	0	1	0	1	0	2	2	2	2	1	2	2	2	1	2	4	7			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr13:38154716T>G	ENST00000379747.4	-	11	1628	c.1511A>C	c.(1510-1512)aAa>aCa	p.K504T	POSTN_ENST00000379742.4_Missense_Mutation_p.K504T|POSTN_ENST00000541481.1_Missense_Mutation_p.K504T|POSTN_ENST00000379743.4_Missense_Mutation_p.K504T|POSTN_ENST00000541179.1_Missense_Mutation_p.K504T|POSTN_ENST00000379749.4_Missense_Mutation_p.K504T	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	504	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		CTTATCTTGTTTTAACTTTTC	0.438																																					p.K504T		.											.	POSTN-516	0			c.A1511C						.						285	273	277					13																	38154716		2203	4300	6503	SO:0001583	missense	10631	exon11			TCTTGTTTTAACT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1511A>C	13.37:g.38154716T>G	ENSP00000369071:p.Lys504Thr	Somatic	262	2		WXS	Illumina HiSeq	Phase_I	411	141	NM_006475	0	0	2	2	0	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	T	9.783	1.175925	0.21704	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.91521	-2.86;-2.86;-2.86;-2.86;-2.86;-2.86	5.02	2.15	0.27550	FAS1 domain (3);	0.424660	0.27971	N	0.017111	T	0.77618	0.4157	N	0.12443	0.215	0.09310	N	1	B;B;B;B;B;B;B	0.31054	0.306;0.141;0.002;0.231;0.043;0.01;0.002	B;B;B;B;B;B;B	0.26310	0.05;0.068;0.002;0.068;0.049;0.006;0.002	T	0.64702	-0.6345	10	0.25751	T	0.34	-14.9201	8.1022	0.30863	0.0:0.4967:0.0:0.5033	.	504;504;504;504;504;504;504	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	T	504	ENSP00000437959:K504T;ENSP00000369073:K504T;ENSP00000369071:K504T;ENSP00000369067:K504T;ENSP00000369066:K504T;ENSP00000437953:K504T	ENSP00000369066:K504T	K	-	2	0	POSTN	37052716	0.009000	0.17119	0.326000	0.25389	0.966000	0.64601	0.133000	0.15912	0.196000	0.20367	-0.410000	0.06199	AAA	.		0.438	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		G	38154716	T	G	38154716	3	3	42	1	0	0	0	0	1	0	0	0	12285	1841	64	5	1051	5	POSTN	13	38154716	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08		38154716	77015162	53	3886											
PCDH20	64881	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	61987658	61987658	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgatcttcaccttcacaaAcctgaagtattcctgaggca	11	10	8	12	1	3	2	2	2	1	0	4	3	4	2	3	2	1	2	3	2	3	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr13:61987658A>G	ENST00000409186.1	-	5	2679	c.574T>C	c.(574-576)Ttt>Ctt	p.F192L	PCDH20_ENST00000409204.4_Missense_Mutation_p.F192L			Q8N6Y1	PCD20_HUMAN	protocadherin 20	192	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		ACCTTCACAAACCTGAAGTAT	0.532																																					p.F192L		.											.	PCDH20-581	0			c.T574C						.						98	83	89					13																	61987658		2203	4300	6503	SO:0001583	missense	64881	exon2			TCACAAACCTGAA	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.574T>C	13.37:g.61987658A>G	ENSP00000386653:p.Phe192Leu	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	193	20	NM_022843	0	0	4	5	1	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	a	8.597	0.886017	0.17540	.	.	ENSG00000197991	ENST00000409204;ENST00000409186	T;T	0.49432	0.78;0.78	5.65	5.65	0.86999	.	0.091594	0.48286	D	0.000189	T	0.17662	0.0424	N	0.02842	-0.48	0.38070	D	0.936352	B	0.02656	0.0	B	0.01281	0.0	T	0.26430	-1.0103	10	0.02654	T	1	.	6.0665	0.19866	0.8001:0.0:0.1999:0.0	.	192	A8K1K9	.	L	192	ENSP00000387250:F192L;ENSP00000386653:F192L	ENSP00000386653:F192L	F	-	1	0	PCDH20	60885659	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	6.222000	0.72249	2.152000	0.67230	0.529000	0.55759	TTT	.		0.532	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		G	61987658	A	G	61987658	3	3	42	1	0	0	0	0	1	0	0	0	11541	43	2	3	2285	3	PCDH20	13	61987658	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	23832942	61987658	53182220	54	3887											
MYH7	4625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23886422	23886422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagggactcctcataggCgttcttgagtttgaagagct	8	13	11	9	1	2	3	1	2	1	1	4	4	4	4	2	2	1	3	2	2	2	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr14:23886422C>T	ENST00000355349.3	-	32	4621	c.4459G>A	c.(4459-4461)Gcc>Acc	p.A1487T	MIR208B_ENST00000401172.1_RNA|CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1487					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCATAGGCGTTCTTGAGT	0.597																																					p.A1487T		.											.	MYH7-94	0			c.G4459A						.						118	124	122					14																	23886422		2203	4300	6503	SO:0001583	missense	4625	exon32			CATAGGCGTTCTT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4459G>A	14.37:g.23886422C>T	ENSP00000347507:p.Ala1487Thr	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	257	77	NM_000257	0	0	0	0	0	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374149	0.82573	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.78364	-1.17	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.84000	0.5376	M	0.81942	2.565	0.39473	D	0.967754	P	0.43662	0.814	P	0.50440	0.641	D	0.86199	0.1617	9	0.59425	D	0.04	.	13.987	0.64341	0.1513:0.8487:0.0:0.0	.	1487	P12883	MYH7_HUMAN	T	1487;1492	ENSP00000347507:A1487T	ENSP00000347507:A1487T	A	-	1	0	MYH7	22956262	0.987000	0.35691	0.998000	0.56505	0.982000	0.71751	2.764000	0.47613	2.746000	0.94184	0.591000	0.81541	GCC	.		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23886422	C	T	23886422	3	4	42	1	0	0	0	0	1	0	0	0	10064	768	27	1	1384	1	MYH7	14	23886422	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		23886422	83463118	55	3888											
PLCB2	5330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40594160	40594160	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgcagatccactcacttTgcctttggggaggtggcagg	6	10	16	9	0	1	1	1	0	0	1	2	2	2	2	2	6	2	2	2	6	0	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:40594160T>A	ENST00000260402.3	-	7	829	c.580A>T	c.(580-582)Aaa>Taa	p.K194*	PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000456256.2_Nonsense_Mutation_p.K194*|PLCB2_ENST00000557821.1_Nonsense_Mutation_p.K194*|PLCB2_ENST00000543785.2_Nonsense_Mutation_p.K194*	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	194					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CCACTCACTTTGCCTTTGGGG	0.582																																					p.K194X		.											.	PLCB2-275	0			c.A580T						.						43	46	45					15																	40594160		2018	4185	6203	SO:0001587	stop_gained	5330	exon7			TCACTTTGCCTTT		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.580A>T	15.37:g.40594160T>A	ENSP00000260402:p.Lys194*	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	72	21	NM_004573	0	0	0	0	0	A8K6J2|B9EGH5	Nonsense_Mutation	SNP	ENST00000260402.3	37	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	T	37	6.183272	0.97357	.	.	ENSG00000137841	ENST00000260402;ENST00000456256;ENST00000543785	.	.	.	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9216	0.70843	0.0:0.0:0.0:1.0	.	.	.	.	X	194	.	ENSP00000260402:K194X	K	-	1	0	PLCB2	38381452	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	4.795000	0.62489	2.185000	0.69588	0.454000	0.30748	AAA	.		0.582	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40594160	T	A	40594160	4	1	42	1	0	0	0	0	0	1	0	0	12054	1821	63	5	3081	5	PLCB2	15	40594160	Nonsense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08		40594160	61937232	56	3889											
C15orf52	388115	broad.mit.edu	37	chr15	40633079	40633079	+	Frame_Shift_Del	DEL	A	A	-																															tggggagccagagtgggaggAaagctggagccaccggagcc																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:40633079delA	ENST00000559313.1	-	1	89	c.74delT	c.(73-75)ttcfs	p.F25fs	C15orf52_ENST00000557973.1_5'UTR|C15orf52_ENST00000397536.2_5'Flank	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	25							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GAGTGGGAGGAAAGCTGGAGC	0.642																																					p.F25fs													.	C15orf52-153	0			c.74delT						.						11	17	15					15																	40633079		1859	4102	5961	SO:0001589	frameshift_variant	388115	exon1			GGGAGGAAAGCTG	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.74delT	15.37:g.40633079delA	ENSP00000453969:p.Phe25fs	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	28	9	NM_207380	0	0	0	0	0	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Frame_Shift_Del	DEL	ENST00000559313.1	37	CCDS10055.2																																																																																			.		0.642	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380		-	40633079	A	-	40633079	7	5	42	1	0	1	0	1	0	0	0	0	1804	246	9	0	1574	0	C15orf52	15	40633079	Frame_Shift_Del	DEL	A	TCGA-B3-3925-01A-01D-1458-08	38919	40633079	61898313	57	3890											
GLDN	342035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51693835	51693835	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagccctcacttctgaatgGcagttacacgttcatccacc	9	11	6	15	1	4	1	3	1	1	0	5	1	5	1	3	1	2	3	3	1	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:51693835G>A	ENST00000335449.6	+	9	1129	c.1073G>A	c.(1072-1074)gGc>gAc	p.G358D	GLDN_ENST00000396399.2_Missense_Mutation_p.G234D	NM_181789.2	NP_861454.2	Q6ZMI3	GLDN_HUMAN	gliomedin	358	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|microvillus organization (GO:0032528)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		CTTCTGAATGGCAGTTACACG	0.483											OREG0023125	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G358D		.											.	GLDN-92	0			c.G1073A						.						267	204	226					15																	51693835		2196	4293	6489	SO:0001583	missense	342035	exon9			TGAATGGCAGTTA	AY358144	CCDS10140.2	15q15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000186417	ENSG00000186417			29514	protein-coding gene	gene with protein product		608603	"collomin"	COLM		16039564, 12642876	Standard	XM_005254338		Approved	CRG-L2, CLOM, colmedin, UNC-112	uc002aba.3	Q6ZMI3	OTTHUMG00000131746	ENST00000335449.6:c.1073G>A	15.37:g.51693835G>A	ENSP00000335196:p.Gly358Asp	Somatic	176	0	979	WXS	Illumina HiSeq	Phase_I	197	76	NM_181789	0	0	3	3	0	Q6UXZ7|Q7Z359	Missense_Mutation	SNP	ENST00000335449.6	37	CCDS10140.2	.	.	.	.	.	.	.	.	.	.	G	4.101	0.016804	0.07959	.	.	ENSG00000186417	ENST00000335449;ENST00000396399;ENST00000537339	D;D	0.88431	-2.38;-2.38	5.71	3.4	0.38934	Olfactomedin-like (3);	0.890672	0.09441	N	0.801780	T	0.77274	0.4106	N	0.14661	0.345	0.20638	N	0.999872	B	0.13594	0.008	B	0.16289	0.015	T	0.61855	-0.6977	10	0.12103	T	0.63	.	7.3269	0.26560	0.359:0.0:0.641:0.0	.	358	Q6ZMI3	GLDN_HUMAN	D	358;234;234	ENSP00000335196:G358D;ENSP00000379681:G234D	ENSP00000335196:G358D	G	+	2	0	GLDN	49481127	0.992000	0.36948	0.561000	0.28357	0.921000	0.55340	1.691000	0.37721	1.316000	0.45131	0.655000	0.94253	GGC	.		0.483	GLDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254667.2	NM_181789		A	51693835	G	A	51693835	3	1	42	1	0	0	0	0	1	0	0	0	6454	1203	42	2	1107	2	GLDN	15	51693835	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	11060756	51693835	50837557	58	3891											
VPS13C	54832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	62221845	62221845	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acactggcacatacatacagCttgtcaagaacagcatcaat	16	8	6	11	0	2	1	2	0	0	1	2	1	2	1	0	1	5	3	0	1	5	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:62221845C>G	ENST00000261517.5	-	51	6214	c.6141G>C	c.(6139-6141)aaG>aaC	p.K2047N	VPS13C_ENST00000249837.3_Missense_Mutation_p.K2004N|VPS13C_ENST00000395898.3_Missense_Mutation_p.K2004N|VPS13C_ENST00000395896.4_Missense_Mutation_p.K2047N	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATACATACAGCTTGTCAAGAA	0.368																																					p.K2047N		.											.	VPS13C-92	0			c.G6141C						.						192	162	172					15																	62221845		2203	4300	6503	SO:0001583	missense	54832	exon51			ATACAGCTTGTCA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6141G>C	15.37:g.62221845C>G	ENSP00000261517:p.Lys2047Asn	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	82	30	NM_020821	0	0	11	16	5		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069131	0.76301	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T;T	0.46451	0.87;0.87;1.04;1.03	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.51449	0.1675	M	0.71581	2.175	0.80722	D	1	P;P;P;B	0.40794	0.544;0.729;0.544;0.409	B;B;B;B	0.44044	0.176;0.439;0.34;0.336	T	0.51601	-0.8685	10	0.37606	T	0.19	.	18.867	0.92296	0.0:1.0:0.0:0.0	.	2004;2047;2004;2047	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	N	2004;2047;2047;2047	ENSP00000249837:K2004N;ENSP00000261517:K2047N;ENSP00000379233:K2047N;ENSP00000379235:K2047N	ENSP00000249837:K2004N	K	-	3	2	VPS13C	60009137	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.197000	0.42696	2.442000	0.82660	0.655000	0.94253	AAG	.		0.368	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		G	62221845	C	G	62221845	3	3	42	1	0	0	0	0	1	0	0	0	17224	796	28	4	5288	4	VPS13C	15	62221845	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	10528010	62221845	40309547	59	3892											
CALML4	91860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	68497600	68497600	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccattctggggcctcggcTgctacccgtgggcttgctgc	3	10	13	15	2	1	0	0	0	1	0	2	0	1	0	3	4	4	4	3	4	1	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:68497600T>G	ENST00000467889.1	-	1	299	c.115A>C	c.(115-117)Agc>Cgc	p.S39R	CALML4_ENST00000448060.2_Missense_Mutation_p.S39R|CALML4_ENST00000540479.1_5'UTR|CALML4_ENST00000395465.3_Missense_Mutation_p.S39R|RP11-315D16.2_ENST00000562767.1_Intron	NM_033429.2	NP_219501.2	Q96GE6	CALL4_HUMAN	calmodulin-like 4	39							calcium ion binding (GO:0005509)			large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4						GGGCCTCGGCTGCTACCCGTG	0.612																																					p.S39R		.											.	CALML4-90	0			c.A115C						.						69	66	67					15																	68497600		2200	4298	6498	SO:0001583	missense	91860	exon1			CTCGGCTGCTACC	AF308287	CCDS10226.2, CCDS42052.1, CCDS66808.1	15q22.31	2013-01-10			ENSG00000129007	ENSG00000129007		"EF-hand domain containing"	18445	protein-coding gene	gene with protein product							Standard	NM_033429		Approved	MGC4809, NY-BR-20	uc002arb.3	Q96GE6	OTTHUMG00000133287	ENST00000467889.1:c.115A>C	15.37:g.68497600T>G	ENSP00000419081:p.Ser39Arg	Somatic	106	1		WXS	Illumina HiSeq	Phase_I	121	41	NM_033429	0	0	16	26	10	B4DL15|F8W6Y4|Q6MZY3|Q6N048|Q9H286	Missense_Mutation	SNP	ENST00000467889.1	37	CCDS10226.2	.	.	.	.	.	.	.	.	.	.	T	10.48	1.362660	0.24684	.	.	ENSG00000129007	ENST00000395465;ENST00000448060;ENST00000467889	T;T;T	0.71934	1.94;-0.44;-0.61	3.41	1.98	0.26296	.	.	.	.	.	T	0.67627	0.2913	N	0.19112	0.55	0.19300	N	0.99998	D;B	0.69078	0.997;0.02	D;B	0.75484	0.986;0.012	T	0.54866	-0.8229	9	0.72032	D	0.01	2.9936	2.4394	0.04490	0.0:0.2172:0.2897:0.4931	.	39;39	F8W6Y4;Q96GE6	.;CALL4_HUMAN	R	39	ENSP00000378848:S39R;ENSP00000400755:S39R;ENSP00000419081:S39R	ENSP00000378848:S39R	S	-	1	0	CALML4	66284654	0.001000	0.12720	0.013000	0.15412	0.013000	0.08279	0.068000	0.14531	1.306000	0.44926	0.459000	0.35465	AGC	.		0.612	CALML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257067.3	NM_033429		G	68497600	T	G	68497600	3	3	42	1	0	0	0	0	1	0	0	0	2594	1580	55	5	495	5	CALML4	15	68497600	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	6275755	68497600	34033792	60	3893											
MYO9A	4649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72192125	72192125	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttccctgtaggctttccatcTtgcttgtatgcaaatagcag	8	15	8	10	0	1	0	0	0	1	0	3	0	3	0	2	1	3	6	2	1	4	7			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:72192125T>G	ENST00000356056.5	-	24	3845	c.3373A>C	c.(3373-3375)Aga>Cga	p.R1125R	MYO9A_ENST00000424560.1_Silent_p.R1125R|MYO9A_ENST00000444904.1_Silent_p.R1106R|MYO9A_ENST00000564571.1_Silent_p.R1125R|MYO9A_ENST00000566885.1_Silent_p.R745R|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1125	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GCTTTCCATCTTGCTTGTATG	0.438																																					p.R1125R		.											.	MYO9A-93	0			c.A3373C						.						85	81	82					15																	72192125		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon24			TCCATCTTGCTTG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.3373A>C	15.37:g.72192125T>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	123	46	NM_006901	0	0	10	26	16	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	37	CCDS10239.1																																																																																			.		0.438	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72192125	T	G	72192125	2	3	42	1	0	0	0	0	0	0	0	1	10109	1617	56	5		5	MYO9A	15	72192125	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	3694525	72192125	30339267	61	3894											
ADAMTSL3	57188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	84581896	84581896	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccacgtgtgggccgggtgtgCaggtccgtgaggtgaagtgc	5	8	19	9	3	0	2	0	2	0	0	1	2	1	2	3	4	2	1	3	4	1	0	rs202011681	byFrequency	TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:84581896C>T	ENST00000286744.5	+	16	1977	c.1753C>T	c.(1753-1755)Cag>Tag	p.Q585*	ADAMTSL3_ENST00000567476.1_Nonsense_Mutation_p.Q585*	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	585	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GCCGGGTGTGCAGGTCCGTGA	0.582																																					p.Q585X		.											.	ADAMTSL3-1153	0			c.C1753T						.						89	81	84					15																	84581896		2203	4300	6503	SO:0001587	stop_gained	57188	exon16			GGTGTGCAGGTCC	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1753C>T	15.37:g.84581896C>T	ENSP00000286744:p.Gln585*	Somatic	176	1		WXS	Illumina HiSeq	Phase_I	198	52	NM_207517	0	0	0	0	0	A1A566|A1A567|Q9ULI7	Nonsense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	38	7.094589	0.98059	.	.	ENSG00000156218	ENST00000286744	.	.	.	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.1118	0.89538	0.0:1.0:0.0:0.0	.	.	.	.	X	585	.	ENSP00000286744:Q585X	Q	+	1	0	ADAMTSL3	82372900	1.000000	0.71417	0.186000	0.23195	0.277000	0.26821	7.180000	0.77674	2.246000	0.74042	0.563000	0.77884	CAG	C|0.999;G|0.001		0.582	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84581896	C	T	84581896	4	4	42	1	0	0	0	0	0	1	0	0	276	711	25	2	1811	2	ADAMTSL3	15	84581896	Nonsense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	12389771	84581896	17949496	62	3895											
BTBD12	84464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3641173	3641173	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcttcatctgcccaCattgacctcaagagttcctg	7	13	5	16	0	4	2	2	1	2	1	7	2	7	2	5	0	1	1	5	0	1	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr16:3641173C>G	ENST00000294008.3	-	12	3106	c.2466G>C	c.(2464-2466)atG>atC	p.M822I		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	822	Glu-rich.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CATCTGCCCACATTGACCTCA	0.468								Direct reversal of damage																													p.M822I		.											.	SLX4-94	0			c.G2466C						.						165	176	172					16																	3641173		2197	4300	6497	SO:0001583	missense	84464	exon12			TGCCCACATTGAC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2466G>C	16.37:g.3641173C>G	ENSP00000294008:p.Met822Ile	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	291	79	NM_032444	0	0	6	9	3	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727924	0.69074	.	.	ENSG00000188827	ENST00000294008	T	0.01347	4.99	5.57	5.57	0.84162	.	0.430257	0.24894	N	0.034741	T	0.02304	0.0071	L	0.47190	1.495	0.28137	N	0.92995	B	0.30406	0.278	B	0.24155	0.051	T	0.37267	-0.9713	10	0.45353	T	0.12	.	18.5351	0.91008	0.0:1.0:0.0:0.0	.	822	Q8IY92	SLX4_HUMAN	I	822	ENSP00000294008:M822I	ENSP00000294008:M822I	M	-	3	0	SLX4	3581174	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	3.184000	0.50926	2.619000	0.88677	0.561000	0.74099	ATG	.		0.468	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		G	3641173	C	G	3641173	3	3	42	1	0	0	0	0	1	0	0	0	1543	478	17	4	3054	4	BTBD12	16	3641173	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		3641173	86713580	63	3896											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu	37	chr16	18844471	18844471	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tctggaaatatgatttgccgGaaattcgaattcaattccta	13	14	7	7	2	2	1	1	1	1	0	4	4	3	3	2	2	1	0	2	2	6	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr16:18844471G>A	ENST00000446231.2	-	51	8995	c.8583C>T	c.(8581-8583)ttC>ttT	p.F2861F	SMG1_ENST00000389467.3_Silent_p.F2861F			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2861					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGATTTGCCGGAAATTCGAAT	0.338																																					p.F2861F		.											.	SMG1-1160	0			c.C8583T						.						57	54	55					16																	18844471		1826	4082	5908	SO:0001819	synonymous_variant	23049	exon51			TTGCCGGAAATTC	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.8583C>T	16.37:g.18844471G>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	97	28	NM_015092	0	0	14	31	17	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			.		0.338	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18844471	G	A	18844471	2	1	42	1	0	0	0	0	0	0	0	1	14827	1165	41	2		2	SMG1	16	18844471	Silent	SNP	G	TCGA-B3-3925-01A-01D-1458-08	15203298	18844471	71510282	64	3897											
CORO1A	11151	ucsc.edu	37	chr16	30198806	30198806	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcatgagtgagcggcaggTggcgctgtgggacacagtga	8	6	18	9	3	0	3	0	3	0	0	0	4	0	4	1	4	1	3	1	4	0	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr16:30198806T>G	ENST00000219150.5	+	6	1045	c.740T>G	c.(739-741)gTg>gGg	p.V247G	RP11-455F5.5_ENST00000568506.1_RNA|CORO1A_ENST00000570045.1_Missense_Mutation_p.V247G|RP11-455F5.5_ENST00000567153.1_RNA|CORO1A_ENST00000565497.1_Missense_Mutation_p.V247G|RP11-455F5.5_ENST00000566144.1_RNA	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	247					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						GAGCGGCAGGTGGCGCTGTGG	0.672																																					p.V247G													.	CORO1A-226	0			c.T740G						.						23	24	24					16																	30198806		2196	4299	6495	SO:0001583	missense	11151	exon7			GGCAGGTGGCGCT	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"Coronins", "WD repeat domain containing"	2252	protein-coding gene	gene with protein product	"Clabp TACO"	605000	"coronin, actin-binding protein, 1A"			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.740T>G	16.37:g.30198806T>G	ENSP00000219150:p.Val247Gly	Somatic	60	5		WXS	Illumina HiSeq		37	3	NM_001193333	0	0	30	41	11	B2RBL1|Q2YD73	Missense_Mutation	SNP	ENST00000219150.5	37	CCDS10673.1	.	.	.	.	.	.	.	.	.	.	.	17.74	3.464028	0.63513	.	.	ENSG00000102879	ENST00000219150	T	0.01838	4.61	5.44	5.44	0.79542	WD40/YVTN repeat-like-containing domain (1);	0.058879	0.64402	D	0.000002	T	0.07548	0.0190	M	0.85630	2.765	0.80722	D	1	P;B	0.50710	0.938;0.077	P;B	0.45474	0.482;0.069	T	0.01914	-1.1248	10	0.87932	D	0	-15.8268	14.4786	0.67564	0.0:0.0:0.0:1.0	.	303;247	Q59G88;P31146	.;COR1A_HUMAN	G	247	ENSP00000219150:V247G	ENSP00000219150:V247G	V	+	2	0	CORO1A	30106307	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.943000	0.87716	2.082000	0.62665	0.459000	0.35465	GTG	.		0.672	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074		G	30198806	T	G	30198806	3	3	42	1	0	0	0	0	1	0	0	0	3759	1696	59	5	758	5	CORO1A	16	30198806	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	11354335	30198806	60155947	65	3898											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30732089	30732089	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagtggtggtggtgaacaacCcacgggcgcccctgggccct	6	6	15	14	2	0	1	0	1	0	0	0	1	0	1	4	5	2	0	4	5	2	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr16:30732089C>A	ENST00000262518.4	+	20	3428	c.3043C>A	c.(3043-3045)Cca>Aca	p.P1015T	SRCAP_ENST00000395059.2_Missense_Mutation_p.P1015T|SRCAP_ENST00000344771.4_Missense_Mutation_p.P1015T	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1015	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GGTGAACAACCCACGGGCGCC	0.602																																					p.P1015T		.											.	SRCAP-94	0			c.C3043A						.						65	74	71					16																	30732089		2197	4300	6497	SO:0001583	missense	10847	exon20			AACAACCCACGGG	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3043C>A	16.37:g.30732089C>A	ENSP00000262518:p.Pro1015Thr	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	275	93	NM_006662	0	0	11	14	3	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	15.07	2.724931	0.48833	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91631	-2.88;-2.81;-2.85	5.25	5.25	0.73442	.	0.000000	0.50627	D	0.000110	D	0.90219	0.6942	N	0.14661	0.345	0.41912	D	0.990471	D;D;D	0.76494	0.999;0.999;0.997	D;D;P	0.67382	0.934;0.951;0.895	D	0.87595	0.2493	10	0.25106	T	0.35	-10.7491	11.2203	0.48851	0.0:0.9156:0.0:0.0844	.	1015;1015;1015	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	T	1015	ENSP00000262518:P1015T;ENSP00000378499:P1015T;ENSP00000343042:P1015T	ENSP00000262518:P1015T	P	+	1	0	SRCAP	30639590	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	4.640000	0.61368	2.729000	0.93468	0.557000	0.71058	CCA	.		0.602	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30732089	C	A	30732089	3	1	42	1	0	0	0	0	1	0	0	0	15167	623	22	4	3113	4	SRCAP	16	30732089	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	533283	30732089	59622664	66	3899											
ZZEF1	23140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3953114	3953114	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gatcttctaggctcgagtccCcatctggcaatacacccagc	9	9	8	15	1	3	0	0	0	3	0	5	2	4	0	3	2	2	2	3	2	3	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:3953114C>T	ENST00000381638.2	-	37	6027	c.5903G>A	c.(5902-5904)gGg>gAg	p.G1968E		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1968							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GCTCGAGTCCCCATCTGGCAA	0.498																																					p.G1968E		.											.	ZZEF1-93	0			c.G5903A						.						97	92	94					17																	3953114		2203	4300	6503	SO:0001583	missense	23140	exon37			GAGTCCCCATCTG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.5903G>A	17.37:g.3953114C>T	ENSP00000371051:p.Gly1968Glu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	170	54	NM_015113	0	0	8	8	0	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222545	0.58668	.	.	ENSG00000074755	ENST00000381638	T	0.20881	2.04	5.33	4.35	0.52113	.	0.334072	0.36555	N	0.002540	T	0.21427	0.0516	N	0.19112	0.55	0.40921	D	0.984313	D;D	0.59767	0.962;0.986	P;P	0.54174	0.744;0.738	T	0.00888	-1.1526	10	0.49607	T	0.09	-17.7018	10.7443	0.46170	0.0:0.9108:0.0:0.0892	.	1968;1968	O43149-2;O43149	.;ZZEF1_HUMAN	E	1968	ENSP00000371051:G1968E	ENSP00000371051:G1968E	G	-	2	0	ZZEF1	3899863	0.864000	0.29904	0.970000	0.41538	0.425000	0.31504	1.732000	0.38146	2.672000	0.90937	0.508000	0.49915	GGG	.		0.498	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3953114	C	T	3953114	3	4	42	1	0	0	0	0	1	0	0	0	18287	623	22	2	3058	2	ZZEF1	17	3953114	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		3953114	77242096	67	3900											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y	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	265	268					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	362	19		WXS	Illumina HiSeq		787	74	NM_145301	0	0	4	30	26	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		T	15457087	C	T	15457087	3	4	42	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	11503973	15457087	65738123	68	3901											
RAB34	83871	broad.mit.edu	37	chr17	27045260	27045260	+	5'UTR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcggcgcttccctcctcAactccaggcctgggaggtga	6	7	14	14	2	1	1	1	1	0	0	4	3	4	2	4	5	1	1	4	5	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:27045260A>C	ENST00000301043.6	-	0	173				RPL23A_ENST00000496182.1_5'Flank|RPL23A_ENST00000422514.2_5'Flank|RAB34_ENST00000453384.3_Missense_Mutation_p.L9W|RAB34_ENST00000395243.3_5'Flank|RPL23A_ENST00000394938.4_5'Flank|RAB34_ENST00000415040.2_5'Flank|RAB34_ENST00000395242.2_5'Flank|RPL23A_ENST00000472628.1_5'Flank|RAB34_ENST00000395245.3_5'Flank|SNORD42B_ENST00000458893.1_RNA|RAB34_ENST00000450529.1_5'Flank|RAB34_ENST00000436730.3_5'Flank|RAB34_ENST00000447716.1_Missense_Mutation_p.L9W	NM_001256277.1	NP_001243206.1	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family						antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					TTCCCTCCTCAACTCCAGGCC	0.662																																					p.L9W	Pancreas(175;216 2049 29940 32498 41589)												.	RAB34-227	0			c.T26G						.						35	46	43					17																	27045260		692	1591	2283	SO:0001623	5_prime_UTR_variant	83871	exon1			CTCCTCAACTCCA	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"RAB, member RAS oncogene"	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000301043.6:c.-280T>G	17.37:g.27045260A>C		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	23	6	NM_001142624	0	0	0	0	0	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000301043.6	37	CCDS11240.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.083287	0.36758	.	.	ENSG00000109113	ENST00000453384;ENST00000447716;ENST00000430132	T;T;T	0.72835	-0.69;-0.4;-0.2	5.53	-0.792	0.10925	.	.	.	.	.	T	0.45438	0.1342	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	8	0.87932	D	0	.	4.8613	0.13585	0.477:0.3112:0.2119:0.0	.	9	E7ES60	.	W	9	ENSP00000413156:L9W;ENSP00000410403:L9W;ENSP00000407953:L9W	ENSP00000407953:L9W	L	-	2	0	RAB34	24069387	0.101000	0.21875	0.983000	0.44433	0.894000	0.52154	-0.002000	0.12924	-0.072000	0.12864	-0.468000	0.05107	TTG	.		0.662	RAB34-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255959.4	NM_031934		C	27045260	A	C	27045260	1	2	42	0	1	0	0	0	0	0	0	0	12956	131	5	5		5	RAB34	17	27045260	5'UTR	SNP	A	TCGA-B3-3925-01A-01D-1458-08	11588173	27045260	54149950	69	3902											
QRICH2	84074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74283337	74283337	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagccttgcccctgtctTggctctccctcaactcggcc	3	11	9	18	1	3	0	1	0	2	0	5	0	3	0	5	3	3	2	5	3	1	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:74283337T>A	ENST00000262765.5	-	7	3628	c.3449A>T	c.(3448-3450)cAa>cTa	p.Q1150L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1150										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GCCCCTGTCTTGGCTCTCCCT	0.567																																					p.Q1150L		.											.	QRICH2-94	0			c.A3449T						.						128	104	112					17																	74283337		2203	4300	6503	SO:0001583	missense	84074	exon7			CTGTCTTGGCTCT	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.3449A>T	17.37:g.74283337T>A	ENSP00000262765:p.Gln1150Leu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	118	31	NM_032134	0	0	1	1	0	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420700	0.83559	.	.	ENSG00000129646	ENST00000262765;ENST00000447564;ENST00000301613	T;T	0.63580	1.79;-0.05	4.89	4.89	0.63831	.	.	.	.	.	T	0.67906	0.2943	L	0.34521	1.04	0.32374	N	0.555436	D;D	0.71674	0.998;0.998	D;D	0.66351	0.943;0.943	T	0.73704	-0.3899	9	0.52906	T	0.07	-7.7869	12.7966	0.57562	0.0:0.0:0.0:1.0	.	1150;1150	B5MD94;Q9H0J4	.;QRIC2_HUMAN	L	1150;158;1150	ENSP00000262765:Q1150L;ENSP00000394461:Q158L	ENSP00000262765:Q1150L	Q	-	2	0	QRICH2	71794932	1.000000	0.71417	0.985000	0.45067	0.931000	0.56810	4.519000	0.60517	1.836000	0.53414	0.454000	0.30748	CAA	.		0.567	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74283337	T	A	74283337	3	1	42	1	0	0	0	0	1	0	0	0	12912	1812	63	5	1594	5	QRICH2	17	74283337	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	47238077	74283337	6911873	70	3903											
TBCD	6904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80888515	80888515	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgaggacaaccttctgaatGagaggtgagtggtgtctctt	9	13	13	6	0	2	4	0	4	2	1	3	6	2	5	1	3	1	0	1	3	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:80888515G>C	ENST00000355528.4	+	33	3239	c.3109G>C	c.(3109-3111)Gag>Cag	p.E1037Q	TBCD_ENST00000539345.2_Missense_Mutation_p.E1037Q	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1037					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CCTTCTGAATGAGAGGTGAGT	0.597																																					p.E1037Q		.											.	TBCD-22	0			c.G3109C						.						92	89	90					17																	80888515		2024	4185	6209	SO:0001583	missense	6904	exon33			CTGAATGAGAGGT	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"tubulin-specific chaperone d"				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3109G>C	17.37:g.80888515G>C	ENSP00000347719:p.Glu1037Gln	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	106	27	NM_005993	0	0	0	0	0	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.751852	0.31046	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000539345	T	0.35236	1.32	4.63	2.48	0.30137	Armadillo-like helical (1);Armadillo-type fold (1);Tubulin-specific chaperone D, C-terminal (1);	0.128907	0.50627	D	0.000107	T	0.27731	0.0682	L	0.42245	1.32	0.80722	D	1	P;P;P	0.41313	0.745;0.601;0.709	B;B;B	0.41946	0.27;0.307;0.371	T	0.02632	-1.1131	9	.	.	.	.	5.3369	0.15963	0.113:0.2093:0.6777:0.0	.	814;1037;1037	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	Q	1037;788;29	ENSP00000347719:E1037Q	.	E	+	1	0	TBCD	78481804	1.000000	0.71417	0.852000	0.33557	0.360000	0.29518	3.799000	0.55529	0.939000	0.37446	0.591000	0.81541	GAG	.		0.597	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		C	80888515	G	C	80888515	3	2	42	1	0	0	0	0	1	0	0	0	15665	1291	45	4	3239	4	TBCD	17	80888515	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	6605178	80888515	306695	71	3904											
HDHD2	84064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	44662721	44662721	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagcttgccttttaagagcTtcctgtgcgcctggcacagc	7	12	10	12	1	0	1	0	0	0	1	1	1	1	1	3	1	5	3	3	1	2	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr18:44662721T>C	ENST00000300605.6	-	2	242	c.90A>G	c.(88-90)gaA>gaG	p.E30E	HDHD2_ENST00000587841.1_Intron|IER3IP1_ENST00000588705.1_3'UTR	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	30						extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						TTTTAAGAGCTTCCTGTGCGC	0.463																																					p.E30E		.											.	HDHD2-90	0			c.A90G						.						99	82	88					18																	44662721		2203	4300	6503	SO:0001819	synonymous_variant	84064	exon2			AAGAGCTTCCTGT	AL136681	CCDS32829.1	18q21.1	2008-02-05				ENSG00000167220			25364	protein-coding gene	gene with protein product						11230166	Standard	NM_032124		Approved	DKFZP564D1378	uc002lcs.3	Q9H0R4		ENST00000300605.6:c.90A>G	18.37:g.44662721T>C		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	221	83	NM_032124	0	0	4	7	3	A8K7T3|Q96NV4	Silent	SNP	ENST00000300605.6	37	CCDS32829.1																																																																																			.		0.463	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124		C	44662721	T	C	44662721	2	2	42	1	0	0	0	0	0	0	0	1	7044	1606	56	3		3	HDHD2	18	44662721	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08		44662721	33414527	72	3905											
MYO5B	4645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	47500737	47500737	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tacccatagatgtccaggacCccgatgaaggagtgctgctt	10	9	11	11	1	0	2	0	1	0	1	1	5	1	4	4	2	3	2	4	2	3	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr18:47500737C>T	ENST00000285039.7	-	10	1604	c.1305G>A	c.(1303-1305)ggG>ggA	p.G435G		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	435	Myosin motor.		G -> R (in DIAR2). {ECO:0000269|PubMed:20186687}.		endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TGTCCAGGACCCCGATGAAGG	0.582																																					p.G435G		.											.	MYO5B-72	0			c.G1305A						.						98	108	104					18																	47500737		2136	4239	6375	SO:0001819	synonymous_variant	4645	exon10			CAGGACCCCGATG	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"Myosins / Myosin superfamily : Class V"	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.1305G>A	18.37:g.47500737C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	92	35	NM_001080467	0	0	34	89	55	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			.		0.582	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47500737	C	T	47500737	2	4	42	1	0	0	0	0	0	0	0	1	10104	610	22	2		2	MYO5B	18	47500737	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	2838016	47500737	30576511	73	3906											
RAB27B	5874	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	52555227	52555230	+	Splice_Site	DEL	CCAA	CCAA	-																															catctgctttcttttcaaggCcaactgcaagcaaatgctta																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	CCAA	CCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr18:52555227_52555230delCCAA	ENST00000262094.5	+	5	866_869	c.345_348delCCAA	c.(343-348)agccaa>ag	p.SQ115fs	RAB27B_ENST00000586594.1_3'UTR|RP11-839G9.1_ENST00000588466.1_RNA	NM_004163.4	NP_004154.2	O00194	RB27B_HUMAN	RAB27B, member RAS oncogene family	115					multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|multivesicular body membrane (GO:0032585)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein domain specific binding (GO:0019904)			large_intestine(3)|lung(3)|skin(1)	7				Colorectal(16;0.0273)|READ - Rectum adenocarcinoma(59;0.219)		CTTTTCAAGGCCAACTGCAAGCAA	0.402																																					p.115_116del		.											.	RAB27B-227	0			c.345_348del						.																																			SO:0001630	splice_region_variant	5874	exon5			.	U57093	CCDS11958.1	18q21.2	2006-12-18			ENSG00000041353	ENSG00000041353		"RAB, member RAS oncogene"	9767	protein-coding gene	gene with protein product		603869				9066979	Standard	NM_004163		Approved		uc002lfr.3	O00194	OTTHUMG00000132710	ENST00000262094.5:c.344-1CCAA>-	18.37:g.52555227_52555230delCCAA		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	199	39	NM_004163	0	0	0	0	0	B2RAB0|Q9BZB6	Frame_Shift_Del	DEL	ENST00000262094.5	37	CCDS11958.1																																																																																			.		0.402	RAB27B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256008.3	NM_004163	Frame_Shift_Del	-	52555230	CCAA	-	52555227	8	5	42	1	0	1	0	1	0	0	1	0	12947	753	26	0	359	0	RAB27B	18	52555227	Splice_Site	DEL	CCAA	TCGA-B3-3925-01A-01D-1458-08	5054490	52555227	25522021	74	3907											
RFX2	5990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6013026	6013026	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgcatgggctgctgccgCatggccatgtactgcgtgtc	4	11	15	11	2	0	0	0	0	0	0	1	0	0	0	2	3	5	5	2	3	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:6013026C>T	ENST00000303657.5	-	8	1019	c.870G>A	c.(868-870)atG>atA	p.M290I	CTC-232P5.1_ENST00000587836.1_RNA|RFX2_ENST00000592546.1_Missense_Mutation_p.M265I|RFX2_ENST00000359161.3_Missense_Mutation_p.M290I	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GCTGCTGCCGCATGGCCATGT	0.617																																					p.M290I	Colon(38;171 817 19800 47433 48051)	.											.	RFX2-156	0			c.G870A						.						104	104	104					19																	6013026		2203	4300	6503	SO:0001583	missense	5990	exon8			CTGCCGCATGGCC		CCDS12157.1, CCDS12158.1	19p13.3	2011-11-23			ENSG00000087903	ENSG00000087903			9983	protein-coding gene	gene with protein product	"trans-acting regulatory factor 2", "DNA binding protein RFX2", "HLA class II regulatory factor RFX2"	142765				1505960	Standard	NM_000635		Approved	FLJ14226	uc002meb.3	P48378		ENST00000303657.5:c.870G>A	19.37:g.6013026C>T	ENSP00000306335:p.Met290Ile	Somatic	279	0		WXS	Illumina HiSeq	Phase_I	320	119	NM_000635	0	0	4	9	5	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414320	0.62511	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T	0.65364	-0.15	4.99	4.99	0.66335	.	0.038993	0.85682	D	0.000000	T	0.57359	0.2048	L	0.60845	1.875	0.80722	D	1	B;B	0.13594	0.008;0.005	B;B	0.17722	0.019;0.013	T	0.57341	-0.7828	10	0.51188	T	0.08	-34.5934	10.8416	0.46720	0.0:0.9125:0.0:0.0875	.	265;290	P48378-2;P48378	.;RFX2_HUMAN	I	290;265;77	ENSP00000306335:M290I	ENSP00000306335:M290I	M	-	3	0	RFX2	5964026	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.796000	0.62496	2.473000	0.83533	0.557000	0.71058	ATG	.		0.617	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635		T	6013026	C	T	6013026	3	4	42	1	0	0	0	0	1	0	0	0	13295	710	25	2	1345	2	RFX2	19	6013026	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		6013026	53115957	75	3908											
PSMC4	5704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40486339	40486339	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actagcaagatgaacctctcTgaggaggttgacttggaaga	13	9	12	7	0	1	5	0	3	1	2	2	7	1	7	1	3	2	2	1	3	4	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:40486339T>C	ENST00000157812.2	+	9	1263	c.1065T>C	c.(1063-1065)tcT>tcC	p.S355S	PSMC4_ENST00000455878.2_Silent_p.S324S	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	355					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)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TGAACCTCTCTGAGGAGGTTG	0.517																																					p.S355S	Colon(105;1478 1543 4034 6132 38638)	.											.	PSMC4-91	0			c.T1065C						.						115	120	118					19																	40486339		2203	4300	6503	SO:0001819	synonymous_variant	5704	exon9			CCTCTCTGAGGAG	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.1065T>C	19.37:g.40486339T>C		Somatic	251	2		WXS	Illumina HiSeq	Phase_I	299	103	NM_006503	0	0	36	73	37	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																			.		0.517	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		C	40486339	T	C	40486339	2	2	42	1	0	0	0	0	0	0	0	1	12718	1567	55	3		3	PSMC4	19	40486339	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	34473313	40486339	18642644	76	3909											
GIPR	2696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46184876	46184876	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcagggcttcctggtcagCgtcctctactgcttcatcaa	6	11	11	13	1	4	0	3	0	1	0	6	0	6	0	2	3	3	3	2	3	2	3	rs529800464		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:46184876C>G	ENST00000590918.1	+	13	1266	c.1167C>G	c.(1165-1167)agC>agG	p.S389R	GIPR_ENST00000263281.3_Missense_Mutation_p.S389R|GIPR_ENST00000304207.8_Missense_Mutation_p.S353R	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	389					activation of adenylate cyclase activity (GO:0007190)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|endocrine pancreas development (GO:0031018)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|response to axon injury (GO:0048678)|response to calcium ion (GO:0051592)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gastric inhibitory peptide receptor activity (GO:0016519)|peptide hormone binding (GO:0017046)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|kidney(2)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	12		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		TCCTGGTCAGCGTCCTCTACT	0.677																																					p.S389R		.											.	GIPR-523	0			c.C1167G						.						35	40	38					19																	46184876		2203	4300	6503	SO:0001583	missense	2696	exon13			GGTCAGCGTCCTC		CCDS12671.1	19q13.2-q13.3	2012-08-10				ENSG00000010310		"GPCR / Class B : Glucagon receptors"	4271	protein-coding gene	gene with protein product		137241				7490109	Standard	NM_000164		Approved		uc002pcu.1	P48546		ENST00000590918.1:c.1167C>G	19.37:g.46184876C>G	ENSP00000467494:p.Ser389Arg	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	99	30	NM_000164	0	0	1	1	0	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Missense_Mutation	SNP	ENST00000590918.1	37	CCDS12671.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160957	0.78226	.	.	ENSG00000010310	ENST00000263281;ENST00000304207	T;T	0.58940	0.3;1.18	4.81	2.65	0.31530	GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1);	0.209202	0.33959	N	0.004388	T	0.68842	0.3045	M	0.65677	2.01	0.35843	D	0.826177	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.73380	0.98;0.953;0.971	T	0.73898	-0.3837	10	0.87932	D	0	.	7.5841	0.27982	0.0:0.8105:0.0:0.1895	.	353;389;389	B7WP14;P48546;P48546-2	.;GIPR_HUMAN;.	R	389;353	ENSP00000263281:S389R;ENSP00000305321:S353R	ENSP00000263281:S389R	S	+	3	2	GIPR	50876716	0.911000	0.30947	0.991000	0.47740	0.988000	0.76386	0.947000	0.29082	0.609000	0.30018	0.561000	0.74099	AGC	.		0.677	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1			G	46184876	C	G	46184876	3	3	42	1	0	0	0	0	1	0	0	0	6415	767	27	4	1213	4	GIPR	19	46184876	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	5698537	46184876	12944107	77	3910											
FGF21	26291	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	49261265	49261265	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttaccagtccgaagccCacggcctcccgctgcacctg	7	8	9	17	3	0	0	0	0	0	0	2	1	2	0	6	1	3	3	6	1	2	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:49261265C>A	ENST00000593756.1	+	4	990	c.418C>A	c.(418-420)Cac>Aac	p.H140N	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Missense_Mutation_p.H140N			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	140					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		GTCCGAAGCCCACGGCCTCCC	0.632																																					p.H140N		.											.	FGF21-522	0			c.C418A						.						81	88	86					19																	49261265		2203	4299	6502	SO:0001583	missense	26291	exon3			GAAGCCCACGGCC	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.418C>A	19.37:g.49261265C>A	ENSP00000471477:p.His140Asn	Somatic	241	1		WXS	Illumina HiSeq	Phase_I	218	78	NM_019113	0	0	0	0	0	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	37	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.647950	0.29336	.	.	ENSG00000105550	ENST00000222157	D	0.86497	-2.13	4.44	3.35	0.38373	.	1.000120	0.08080	N	1.000000	D	0.84293	0.5440	L	0.54908	1.71	0.09310	N	1	B	0.17268	0.021	B	0.19391	0.025	T	0.73905	-0.3835	10	0.66056	D	0.02	2.4195	7.726	0.28761	0.0:0.8737:0.0:0.1263	.	140	Q9NSA1	FGF21_HUMAN	N	140	ENSP00000222157:H140N	ENSP00000222157:H140N	H	+	1	0	FGF21	53953077	0.000000	0.05858	0.010000	0.14722	0.013000	0.08279	0.607000	0.24209	1.123000	0.41961	-0.424000	0.05967	CAC	.		0.632	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1			A	49261265	C	A	49261265	3	1	42	1	0	0	0	0	1	0	0	0	5869	594	21	4	428	4	FGF21	19	49261265	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	3076389	49261265	9867718	78	3911											
SIGLEC9	27180	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	51633170	51633170	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctgactgaaccttgggCagaagacagtcccccagacc	10	5	10	16	0	0	5	0	2	0	3	1	5	1	5	6	1	1	1	6	1	2	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:51633170C>G	ENST00000250360.3	+	7	1293	c.1226C>G	c.(1225-1227)gCa>gGa	p.A409G	SIGLEC9_ENST00000440804.3_Intron	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	409					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GAACCTTGGGCAGAAGACAGT	0.602																																					p.A409G		.											.	SIGLEC9-91	0			c.C1226G						.						72	77	75					19																	51633170		2203	4300	6503	SO:0001583	missense	27180	exon7			CTTGGGCAGAAGA	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.1226C>G	19.37:g.51633170C>G	ENSP00000250360:p.Ala409Gly	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	142	38	NM_014441	0	0	7	7	0	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	2.098	-0.406818	0.04832	.	.	ENSG00000129450	ENST00000250360	T	0.11277	2.79	1.96	-1.87	0.07737	.	.	.	.	.	T	0.08403	0.0209	M	0.63843	1.955	0.09310	N	1	P	0.35174	0.488	B	0.32211	0.142	T	0.31916	-0.9926	9	0.22109	T	0.4	.	2.1117	0.03704	0.2511:0.4132:0.0:0.3357	.	409	Q9Y336	SIGL9_HUMAN	G	409	ENSP00000250360:A409G	ENSP00000250360:A409G	A	+	2	0	SIGLEC9	56324982	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.824000	0.01708	-0.341000	0.08376	-0.346000	0.07831	GCA	.		0.602	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		G	51633170	C	G	51633170	3	3	42	1	0	0	0	0	1	0	0	0	14347	710	25	4	1252	4	SIGLEC9	19	51633170	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	2371905	51633170	7495813	79	3912											
C20orf12	55184	hgsc.bcm.edu;broad.mit.edu	37	chr20	18433281	18433281	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggactggcgggtgggtggtCtagaacctgatcctccacca	7	8	15	11	1	1	2	0	1	1	1	3	3	3	3	4	5	1	0	4	5	2	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr20:18433281C>G	ENST00000358866.6	-	5	543	c.521G>C	c.(520-522)aGa>aCa	p.R174T	DZANK1_ENST00000329494.5_Missense_Mutation_p.R176T|DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000262547.5_Missense_Mutation_p.R174T|DZANK1_ENST00000357236.4_Missense_Mutation_p.D24H			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	174							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						GGTGGGTGGTCTAGAACCTGA	0.423																																					p.R174T		.											.	.	0			c.G521C						.						49	50	50					20																	18433281		1839	4074	5913	SO:0001583	missense	55184	exon6			GGTGGTCTAGAAC	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.521G>C	20.37:g.18433281C>G	ENSP00000351734:p.Arg174Thr	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	35	8	NM_001099407	0	0	1	2	1	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	37	CCDS46582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.147|9.147	1.015323|1.015323	0.19355|0.19355	.|.	.|.	ENSG00000089091|ENSG00000089091	ENST00000357236|ENST00000262547;ENST00000329494	D|T;T	0.85556|0.63913	-2.0|-0.07;0.61	5.3|5.3	4.33|4.33	0.51752|0.51752	.|.	.|3.465350	.|0.00919	.|U	.|0.002568	T|T	0.57257|0.57257	0.2041|0.2041	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	1|1	B|B;B	0.11235|0.21606	0.004|0.005;0.058	B|B;B	0.15052|0.17979	0.012|0.003;0.02	T|T	0.41324|0.41324	-0.9515|-0.9515	9|10	0.87932|0.14656	D|T	0|0.56	-0.0767|-0.0767	11.2055|11.2055	0.48767|0.48767	0.0:0.6648:0.3352:0.0|0.0:0.6648:0.3352:0.0	.|.	24|193;174	Q9NVP4-4|B7Z631;Q9NVP4	.|.;DZAN1_HUMAN	H|T	24|174;176	ENSP00000349774:D24H|ENSP00000262547:R174T;ENSP00000328866:R176T	ENSP00000349774:D24H|ENSP00000262547:R174T	D|R	-|-	1|2	0|0	C20orf12|C20orf12	18381281|18381281	0.008000|0.008000	0.16893|0.16893	0.007000|0.007000	0.13788|0.13788	0.202000|0.202000	0.24057|0.24057	2.031000|2.031000	0.41117|0.41117	2.498000|2.498000	0.84270|0.84270	0.455000|0.455000	0.32223|0.32223	GAC|AGA	.		0.423	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		G	18433281	C	G	18433281	3	3	42	1	0	0	0	0	1	0	0	0	2091	913	32	4	1801	4	C20orf12	20	18433281	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		18433281	44592239	80	3913											
CD40	958	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44757638	44757638	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gccaaccggtcacccaggagGatggcaaagagagtcgcatc	12	4	13	12	2	1	1	1	0	0	1	3	4	1	3	3	4	1	2	3	4	2	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr20:44757638G>C	ENST00000372285.3	+	9	865	c.793G>C	c.(793-795)Gat>Cat	p.D265H	CD40_ENST00000372276.3_3'UTR|CD40_ENST00000489304.1_3'UTR	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	265					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				CACCCAGGAGGATGGCAAAGA	0.582									Immune Deficiency with Hyper-IgM																												p.D265H		.											.	CD40-659	0			c.G793C						.						94	86	89					20																	44757638		2203	4300	6503	SO:0001583	missense	958	exon9	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	CAGGAGGATGGCA	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"Tumor necrosis factor receptor superfamily", "CD molecules"	11919	protein-coding gene	gene with protein product		109535	"tumor necrosis factor receptor superfamily, member 5"	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.793G>C	20.37:g.44757638G>C	ENSP00000361359:p.Asp265His	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	208	43	NM_001250	0	0	34	42	8	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Missense_Mutation	SNP	ENST00000372285.3	37	CCDS13393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.14|19.14	3.769455|3.769455	0.69992|0.69992	.|.	.|.	ENSG00000101017|ENSG00000101017	ENST00000372285|ENST00000372278	T|.	0.75050|.	-0.9|.	4.61|4.61	4.61|4.61	0.57282|0.57282	.|.	2.083250|.	0.02069|.	N|.	0.051393|.	T|T	0.72078|0.72078	0.3416|0.3416	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.75792|0.75792	-0.3193|-0.3193	10|6	0.48119|0.87932	T|D	0.1|0	-17.99|-17.99	14.7536|14.7536	0.69546|0.69546	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	265|.	P25942|.	TNR5_HUMAN|.	H|S	265|214	ENSP00000361359:D265H|.	ENSP00000361359:D265H|ENSP00000361352:R214S	D|R	+|+	1|3	0|2	CD40|CD40	44191045|44191045	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.759000|0.759000	0.43091|0.43091	5.327000|5.327000	0.65881|0.65881	2.375000|2.375000	0.81037|0.81037	0.491000|0.491000	0.48974|0.48974	GAT|AGG	.		0.582	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		C	44757638	G	C	44757638	3	2	42	1	0	0	0	0	1	0	0	0	3021	1174	41	4	827	4	CD40	20	44757638	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	26324357	44757638	18267882	81	3914											
ZNFX1	57169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47887763	47887763	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggcgatccattttggagcTacaagccttccgaagaacct	10	10	9	12	2	0	1	0	0	0	1	2	4	2	2	4	2	4	1	4	2	4	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr20:47887763T>C	ENST00000396105.1	-	3	832	c.586A>G	c.(586-588)Agc>Ggc	p.S196G	ZNFX1_ENST00000371752.1_Missense_Mutation_p.S196G|ZNFX1_ENST00000371754.4_Missense_Mutation_p.S196G	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	196							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ATTTTGGAGCTACAAGCCTTC	0.448																																					p.S196G		.											.	ZNFX1-24	0			c.A586G						.						122	125	124					20																	47887763		2203	4300	6503	SO:0001583	missense	57169	exon3			TGGAGCTACAAGC	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.586A>G	20.37:g.47887763T>C	ENSP00000379412:p.Ser196Gly	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	306	151	NM_021035	0	0	17	37	20	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	T	9.975	1.226419	0.22542	.	.	ENSG00000124201	ENST00000396106;ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744	D;D;D;T	0.86865	-1.89;-2.18;-2.18;-0.82	5.86	5.86	0.93980	.	0.260907	0.49916	D	0.000128	T	0.81564	0.4849	L	0.45581	1.43	0.25150	N	0.990437	B	0.13145	0.007	B	0.10450	0.005	T	0.66590	-0.5885	10	0.21540	T	0.41	-21.586	10.261	0.43427	0.0:0.0774:0.0:0.9226	.	196	Q9P2E3	ZNFX1_HUMAN	G	196	ENSP00000360819:S196G;ENSP00000360817:S196G;ENSP00000379412:S196G;ENSP00000360809:S196G	ENSP00000360809:S196G	S	-	1	0	ZNFX1	47321170	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	1.608000	0.36847	2.241000	0.73720	0.533000	0.62120	AGC	.		0.448	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		C	47887763	T	C	47887763	3	2	42	1	0	0	0	0	1	0	0	0	18237	1522	53	3	5218	3	ZNFX1	20	47887763	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	3130125	47887763	15137757	82	3915											
GNAZ	2781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	23438484	23438484	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaccttcaagatggtggAcgtgggggggcagaggtcag	8	7	18	8	1	3	2	3	0	0	2	3	3	3	3	1	6	0	2	1	6	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:23438484A>G	ENST00000248996.4	+	2	1268	c.602A>G	c.(601-603)gAc>gGc	p.D201G	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	201					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		AAGATGGTGGACGTGGGGGGG	0.567																																					p.D201G		.											.	GNAZ-963	0			c.A602G						.						131	136	135					22																	23438484		2203	4300	6503	SO:0001583	missense	2781	exon2			TGGTGGACGTGGG		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.602A>G	22.37:g.23438484A>G	ENSP00000248996:p.Asp201Gly	Somatic	247	1		WXS	Illumina HiSeq	Phase_I	228	69	NM_002073	0	0	3	7	4	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	37	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.367786	0.42003	.	.	ENSG00000128266	ENST00000248996;ENST00000456059	D	0.95656	-3.77	4.7	2.53	0.30540	.	0.000000	0.85682	D	0.000000	D	0.96386	0.8821	H	0.98577	4.27	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	D	0.92468	0.5983	10	0.87932	D	0	.	6.794	0.23715	0.7665:0.1527:0.0808:0.0	.	201	P19086	GNAZ_HUMAN	G	201;149	ENSP00000248996:D201G	ENSP00000248996:D201G	D	+	2	0	GNAZ	21768484	1.000000	0.71417	0.650000	0.29550	0.158000	0.22134	9.084000	0.94076	0.268000	0.21939	-0.313000	0.08912	GAC	.		0.567	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		G	23438484	A	G	23438484	3	3	42	1	0	0	0	0	1	0	0	0	6534	275	10	3	604	3	GNAZ	22	23438484	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08		23438484	27866082	83	3916											
CABIN1	23523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24447425	24447425	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaacttgtgcagcccatTcctttcttcacgtaggttgt	7	15	8	11	1	2	1	1	1	1	0	3	1	3	1	2	1	3	3	2	1	2	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:24447425T>A	ENST00000398319.2	+	8	1180	c.795T>A	c.(793-795)atT>atA	p.I265I	CABIN1_ENST00000405822.2_Intron|CABIN1_ENST00000263119.5_Silent_p.I265I	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	265					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TGCAGCCCATTCCTTTCTTCA	0.577																																					p.I265I		.											.	CABIN1-94	0			c.T795A						.						100	85	90					22																	24447425		2203	4300	6503	SO:0001819	synonymous_variant	23523	exon8			GCCCATTCCTTTC	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.795T>A	22.37:g.24447425T>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	56	24	NM_001199281	0	0	0	0	0	G5E9F3|Q6PHY0|Q9Y460	Silent	SNP	ENST00000398319.2	37	CCDS13823.1																																																																																			.		0.577	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24447425	T	A	24447425	2	1	42	1	0	0	0	0	0	0	0	1	2534	1771	62	5		5	CABIN1	22	24447425	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	1008941	24447425	26857141	84	3917											
DEPDC5	9681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	32193641	32193641	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttcacttctcgtaaccattAaaaaactcttcatccagtat	13	14	2	12	1	4	0	2	0	2	0	6	0	5	0	2	0	2	2	2	0	5	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:32193641A>T	ENST00000382112.3	+	12	893	c.823A>T	c.(823-825)Aaa>Taa	p.K275*	DEPDC5_ENST00000400246.1_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000400242.3_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000535622.1_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000536766.1_Nonsense_Mutation_p.K247*|DEPDC5_ENST00000382111.2_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000400248.2_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000400249.2_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000266091.3_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000382105.2_Nonsense_Mutation_p.K275*	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	275					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CGTAACCATTAAAAAACTCTT	0.438																																					p.K275X		.											.	DEPDC5-519	0			c.A823T						.						83	84	84					22																	32193641		1902	4127	6029	SO:0001587	stop_gained	9681	exon13			ACCATTAAAAAAC	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.823A>T	22.37:g.32193641A>T	ENSP00000371546:p.Lys275*	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	69	28	NM_001242897	0	0	0	0	0	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Nonsense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	38	6.793795	0.97841	.	.	ENSG00000100150	ENST00000535622;ENST00000536766;ENST00000400242;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9647	0.64202	1.0:0.0:0.0:0.0	.	.	.	.	X	275;247;275;275;275;275;275;275;275;275;275	.	ENSP00000266091:K275X	K	+	1	0	DEPDC5	30523641	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.097000	0.94193	1.921000	0.55644	0.443000	0.29094	AAA	.		0.438	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32193641	A	T	32193641	4	4	42	1	0	0	0	0	0	1	0	0	4453	363	13	5	869	5	DEPDC5	22	32193641	Nonsense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	7746216	32193641	19110925	85	3918											
SOX10	6663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38374016	38374016	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggcactccgcctcgccCtgggcggccttcccgttctt	1	9	12	19	5	1	0	0	0	1	0	4	0	3	0	6	4	0	2	6	4	0	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:38374016C>T	ENST00000396884.2	-	3	837	c.555G>A	c.(553-555)caG>caA	p.Q185Q	SOX10_ENST00000470555.1_5'Flank|POLR2F_ENST00000405557.1_Intron|SOX10_ENST00000360880.2_Silent_p.Q185Q|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	185					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)			NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					CCGCCTCGCCCTGGGCGGCCT	0.682																																					p.Q185Q	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	.											.	SOX10-650	0			c.G555A						.						30	30	30					22																	38374016		2202	4300	6502	SO:0001819	synonymous_variant	6663	exon3			CTCGCCCTGGGCG		CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"SRY (sex determining region Y)-boxes"	11190	protein-coding gene	gene with protein product	"dominant megacolon, mouse, human homolog of"	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.555G>A	22.37:g.38374016C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	67	19	NM_006941	0	0	0	0	0	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	37	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.215656	0.01542	.	.	ENSG00000100146	ENST00000446929	.	.	.	4.24	0.707	0.18139	.	.	.	.	.	T	0.50531	0.1621	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34329	-0.9833	4	.	.	.	.	4.6565	0.12620	0.1228:0.6075:0.12:0.1497	.	.	.	.	K	62	.	.	R	-	2	0	SOX10	36703962	1.000000	0.71417	0.997000	0.53966	0.009000	0.06853	2.108000	0.41854	-0.014000	0.14175	-1.644000	0.00765	AGG	.		0.682	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941		T	38374016	C	T	38374016	2	4	42	1	0	0	0	0	0	0	0	1	14973	680	24	2		2	SOX10	22	38374016	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	6180375	38374016	12930550	86	3919											
MXRA5	25878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	3238719	3238719	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatgggagaggaattgttgtActtgataatcttggagttgt	11	15	13	2	0	1	2	0	1	1	1	1	5	1	4	0	3	1	3	0	3	4	7			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chrX:3238719A>G	ENST00000217939.6	-	5	5161	c.5007T>C	c.(5005-5007)agT>agC	p.S1669S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1669						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GAATTGTTGTACTTGATAATC	0.438																																					p.S1669S		.											.	MXRA5-136	0			c.T5007C						.						171	162	165					X																	3238719		2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			TGTTGTACTTGAT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7539	protein-coding gene	gene with protein product	"adlican"					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5007T>C	X.37:g.3238719A>G		Somatic	221	0		WXS	Illumina HiSeq	Phase_I	292	220	NM_015419	0	0	1	13	12	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			.		0.438	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		G	3238719	A	G	3238719	2	3	42	1	0	0	0	0	0	0	0	1	10028	388	14	3		3	MXRA5	23	3238719	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08		3238719	152031841	87	3920											
CTPS2	56474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	16685795	16685795	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgaacttacctttcaagttAaggcagtttcttgcaaactc	11	14	6	10	1	2	0	1	0	1	0	4	1	2	0	1	1	4	4	1	1	5	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chrX:16685795A>C	ENST00000443824.1	-	12	1985	c.1242T>G	c.(1240-1242)ctT>ctG	p.L414L	CTPS2_ENST00000380241.3_Silent_p.L414L|CTPS2_ENST00000359276.4_Silent_p.L414L	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	414	Glutamine amidotransferase type-1. {ECO:0000255|PROSITE-ProRule:PRU00605}.				'de novo' CTP biosynthetic process (GO:0044210)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP synthase activity (GO:0003883)			breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Hepatocellular(33;0.0997)					CTTTCAAGTTAAGGCAGTTTC	0.323																																					p.L414L		.											.	CTPS2-228	0			c.T1242G						.						104	95	98					X																	16685795		2203	4300	6503	SO:0001819	synonymous_variant	56474	exon12			CAAGTTAAGGCAG	AF086422	CCDS14175.1	Xp22	2012-05-02	2012-05-02		ENSG00000047230	ENSG00000047230	6.3.4.2		2520	protein-coding gene	gene with protein product		300380	"CTP synthase II"			10899599	Standard	NM_001144002		Approved		uc004cxm.3	Q9NRF8	OTTHUMG00000021193	ENST00000443824.1:c.1242T>G	X.37:g.16685795A>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	85	58	NM_001144002	0	0	0	0	0	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	Silent	SNP	ENST00000443824.1	37	CCDS14175.1	.	.	.	.	.	.	.	.	.	.	A	8.285	0.816447	0.16607	.	.	ENSG00000047230	ENST00000455276	.	.	.	5.47	-4.64	0.03349	.	0.000000	0.64402	D	0.000015	.	.	.	.	.	.	0.44862	D	0.997874	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.4425	9.4054	0.38457	0.1945:0.5966:0.0:0.2089	.	.	.	.	X	36	.	ENSP00000400431:L36X	L	-	2	0	CTPS2	16595716	0.000000	0.05858	0.699000	0.30290	0.941000	0.58515	-1.673000	0.01951	-0.843000	0.04189	0.486000	0.48141	TTA	.		0.323	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055906.1	NM_019857		C	16685795	A	C	16685795	2	2	42	1	0	0	0	0	0	0	0	1	4029	349	13	5		5	CTPS2	23	16685795	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08	13447076	16685795	138584765	88	3921											
VCAM1	7412	hgsc.bcm.edu	37	chr1	101186217	101186217	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	catctacgctgacaatgaatCctgttagttttgggaacgaa	12	12	9	8	2	1	2	0	2	1	0	2	4	2	3	1	1	2	3	1	1	6	4			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr1:101186217C>G	ENST00000294728.2	+	2	351	c.250C>G	c.(250-252)Cct>Gct	p.P84A	VCAM1_ENST00000370115.1_Missense_Mutation_p.P84A|VCAM1_ENST00000370119.4_Intron|VCAM1_ENST00000347652.2_Missense_Mutation_p.P84A	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	84	Ig-like C2-type 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	GACAATGAATCCTGTTAGTTT	0.458																																					p.P84A		.											.	VCAM1-90	0			c.C250G						.						108	94	99					1																	101186217		2203	4300	6503	SO:0001583	missense	7412	exon2			ATGAATCCTGTTA	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.250C>G	1.37:g.101186217C>G	ENSP00000294728:p.Pro84Ala	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	14	2	NM_001078	1	1	2720	2722	0	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486427	0.44147	.	.	ENSG00000162692	ENST00000347652;ENST00000294728;ENST00000370115	T;T;T	0.08720	3.06;3.06;3.06	5.82	4.91	0.64330	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.156736	0.64402	D	0.000017	T	0.09069	0.0224	M	0.76002	2.32	0.45046	D	0.998063	P;P	0.45078	0.836;0.85	P;P	0.48227	0.455;0.571	T	0.02933	-1.1092	9	.	.	.	-13.1447	10.2074	0.43120	0.0:0.8461:0.0:0.1539	.	84;84	P19320-2;P19320	.;VCAM1_HUMAN	A	84	ENSP00000304611:P84A;ENSP00000294728:P84A;ENSP00000359133:P84A	.	P	+	1	0	VCAM1	100958805	0.909000	0.30893	0.809000	0.32408	0.400000	0.30750	1.327000	0.33746	1.462000	0.47948	0.655000	0.94253	CCT	.		0.458	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		G	101186217	C	G	101186217	3	3	43	1	0	0	0	0	1	0	0	0	17170	855	30	4	256	4	VCAM1	1	101186217	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		101186217	148064404	1	3922											
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186916022	186916022	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tgtctggggcagtgccttttCcatattgttcaacagagttt	7	16	10	8	0	2	1	1	0	1	1	3	1	3	1	2	2	2	3	2	2	2	6			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr1:186916022C>G	ENST00000367466.3	+	12	1345	c.1193C>G	c.(1192-1194)tCc>tGc	p.S398C	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.S338C	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	398	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	AGTGCCTTTTCCATATTGTTC	0.358																																					p.S398C		.											.	PLA2G4A-721	0			c.C1193G						.						152	148	150					1																	186916022		2203	4300	6503	SO:0001583	missense	5321	exon12			CCTTTTCCATATT	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.1193C>G	1.37:g.186916022C>G	ENSP00000356436:p.Ser398Cys	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_024420	0	0	0	0	0	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.465195	0.84425	.	.	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.23348	1.91;1.91	5.71	5.71	0.89125	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.000000	0.85682	D	0.000000	T	0.43255	0.1239	L	0.37561	1.115	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.69307	0.963;0.949	T	0.26155	-1.0111	10	0.87932	D	0	-23.1063	18.8397	0.92177	0.0:1.0:0.0:0.0	.	338;398	E7EU42;P47712	.;PA24A_HUMAN	C	398;338	ENSP00000356436:S398C;ENSP00000406892:S338C	ENSP00000356436:S398C	S	+	2	0	PLA2G4A	185182645	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.518000	0.81795	2.685000	0.91497	0.585000	0.79938	TCC	.		0.358	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		G	186916022	C	G	186916022	3	3	43	1	0	0	0	0	1	0	0	0	12027	855	30	4	1235	4	PLA2G4A	1	186916022	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08	85729805	186916022	62334599	2	3923											
ALK	238	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	29432730	29432730	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacaggtcaagaggcagtttCtggcagcaatgtctctggga	10	9	14	8	0	3	1	1	0	2	1	4	3	3	2	0	4	1	4	0	4	2	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr2:29432730C>G	ENST00000389048.3	-	25	4664	c.3758G>C	c.(3757-3759)aGa>aCa	p.R1253T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GAGGCAGTTTCTGGCAGCAAT	0.493			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R1253T		.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK-3833	0			c.G3758C						.						105	107	106					2																	29432730		2203	4300	6503	SO:0001583	missense	238	exon25	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGTTTCTGGCAG	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.3758G>C	2.37:g.29432730C>G	ENSP00000373700:p.Arg1253Thr	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	105	16	NM_004304	0	0	0	0	0	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.983743	0.93044	.	.	ENSG00000171094	ENST00000389048	D	0.87571	-2.27	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000057	D	0.95468	0.8528	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96698	0.9516	9	.	.	.	.	17.5154	0.87771	0.0:1.0:0.0:0.0	.	1253	Q9UM73	ALK_HUMAN	T	1253	ENSP00000373700:R1253T	.	R	-	2	0	ALK	29286234	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.462000	0.80851	2.418000	0.82041	0.655000	0.94253	AGA	.		0.493	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29432730	C	G	29432730	3	3	43	1	0	0	0	0	1	0	0	0	525	913	32	4	1124	4	ALK	2	29432730	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		29432730	213766643	3	3924											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141032014	141032014	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaaaatatatcttcactgTctttatttataatgcagtgc	12	17	5	7	0	3	0	1	0	2	0	3	0	3	0	0	0	3	2	0	0	7	8			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr2:141032014T>C	ENST00000389484.3	-	85	14092	c.13121A>G	c.(13120-13122)gAc>gGc	p.D4374G		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4374	EGF-like 21. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATCTTCACTGTCTTTATTTAT	0.393										TSP Lung(27;0.18)																											p.D4374G	Colon(99;50 2074 2507 20106)	.											.	LRP1B-311	0			c.A13121G						.						116	106	110					2																	141032014		2203	4300	6503	SO:0001583	missense	53353	exon85			TCACTGTCTTTAT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.13121A>G	2.37:g.141032014T>C	ENSP00000374135:p.Asp4374Gly	Somatic	214	1		WXS	Illumina HiSeq	Phase_I	36	2	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.22|16.22	3.061483|3.061483	0.55432|0.55432	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484;ENST00000544579|ENST00000437977;ENST00000442974	D|.	0.90069|.	-2.61|.	5.32|5.32	2.95|2.95	0.34219|0.34219	.|.	0.076891|.	0.53938|.	U|.	0.000043|.	T|T	0.18383|0.18383	0.0441|0.0441	N|N	0.01522|0.01522	-0.82|-0.82	0.40380|0.40380	D|D	0.979439|0.979439	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.05451|0.05451	-1.0884|-1.0884	10|5	0.25751|.	T|.	0.34|.	.|.	7.8801|7.8801	0.29616|0.29616	0.0:0.163:0.0:0.837|0.0:0.163:0.0:0.837	.|.	4374|.	Q9NZR2|.	LRP1B_HUMAN|.	G|A	4374;4312|606;106	ENSP00000374135:D4374G|.	ENSP00000374135:D4374G|.	D|T	-|-	2|1	0|0	LRP1B|LRP1B	140748484|140748484	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.990000|0.990000	0.78478|0.78478	2.892000|2.892000	0.48625|0.48625	0.853000|0.853000	0.35312|0.35312	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.		0.393	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141032014	T	C	141032014	3	2	43	1	0	0	0	0	1	0	0	0	8980	1667	58	3	706	3	LRP1B	2	141032014	Missense_Mutation	SNP	T	TCGA-B3-3926-01A-01D-1252-08	111599284	141032014	102167359	4	3925											
TTN	7273	ucsc.edu;bcgsc.ca	37	chr2	179476553	179476553	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactccagcttcattttcaGcccgaacctgaaactggacc	11	9	6	15	1	2	1	2	1	0	0	3	3	3	2	4	1	5	1	4	1	3	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr2:179476553G>T	ENST00000591111.1	-	218	45784	c.45560C>A	c.(45559-45561)gCt>gAt	p.A15187D	TTN_ENST00000359218.5_Missense_Mutation_p.A7888D|TTN_ENST00000460472.2_Missense_Mutation_p.A7763D|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A16828D|TTN_ENST00000342992.6_Missense_Mutation_p.A14260D|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A7955D|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15187	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCATTTTCAGCCCGAACCTG	0.458																																					p.A16828D													.	TTN-636	0			c.C50483A						.						134	128	130					2																	179476553		1927	4145	6072	SO:0001583	missense	7273	exon268			TTTTCAGCCCGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.45560C>A	2.37:g.179476553G>T	ENSP00000465570:p.Ala15187Asp	Somatic	311	3		WXS	Illumina HiSeq		42	14	NM_001267550	0	0	6	9	3	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	12.70	2.015567	0.35511	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.97	5.08	0.68730	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87637	0.6227	H	0.97940	4.11	0.80722	D	1	D;D;D;D	0.62365	0.991;0.991;0.991;0.991	D;D;D;D	0.64776	0.929;0.929;0.929;0.929	D	0.91566	0.5268	9	0.87932	D	0	.	15.4698	0.75432	0.0673:0.0:0.9327:0.0	.	7763;7888;7955;15187	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	14260;7763;7955;7888;7763	ENSP00000343764:A14260D;ENSP00000434586:A7763D;ENSP00000340554:A7955D;ENSP00000352154:A7888D	ENSP00000340554:A7955D	A	-	2	0	TTN	179184798	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	7.952000	0.87827	2.828000	0.97474	0.650000	0.86243	GCT	.		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179476553	G	T	179476553	3	4	43	1	0	0	0	0	1	0	0	0	16768	971	34	4	57590	4	TTN	2	179476553	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08	38444539	179476553	63722820	5	3926											
SLC9A10	285335	broad.mit.edu	37	chr3	111958847	111958847	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttgttgatgtggcatcaCgaagacctttgatacaaaca	13	13	8	7	1	1	3	1	2	0	1	1	4	1	3	1	1	2	2	1	1	3	5	rs374694708		TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr3:111958847C>G	ENST00000305815.5	-	12	1538	c.1286G>C	c.(1285-1287)cGt>cCt	p.R429P	SLC9C1_ENST00000487372.1_Missense_Mutation_p.R381P	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	429					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TGTGGCATCACGAAGACCTTT	0.338																																					p.R429P													.	.	0			c.G1286C						.						97	86	90					3																	111958847		2203	4300	6503	SO:0001583	missense	285335	exon12			GCATCACGAAGAC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1286G>C	3.37:g.111958847C>G	ENSP00000306627:p.Arg429Pro	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	111	3	NM_183061	0	0	0	0	0	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.185129	0.38609	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.78364	-1.17;-1.15	5.48	0.43	0.16515	.	0.206543	0.34853	N	0.003623	T	0.74619	0.3740	L	0.32530	0.975	0.31989	N	0.604902	D;D	0.76494	0.993;0.999	D;D	0.65773	0.938;0.937	T	0.71708	-0.4511	10	0.30854	T	0.27	-7.2332	4.8798	0.13674	0.1386:0.5768:0.0:0.2846	.	381;429	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	P	429;381	ENSP00000306627:R429P;ENSP00000420688:R381P	ENSP00000306627:R429P	R	-	2	0	SLC9A10	113441537	0.480000	0.25933	0.845000	0.33349	0.751000	0.42716	-0.612000	0.05616	-0.225000	0.09913	0.511000	0.50034	CGT	.		0.338	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		G	111958847	C	G	111958847	3	3	43	1	0	0	0	0	1	0	0	0	14742	536	19	4	2319	4	SLC9A10	3	111958847	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		111958847	86063583	6	3927											
PLXND1	23129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	129284750	129284750	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcgcgcaccgcaaagtcCttctgctgctccagcgcgtg	5	9	11	16	5	1	0	0	0	1	0	4	0	3	0	3	0	3	4	3	0	1	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr3:129284750C>A	ENST00000324093.4	-	24	4480	c.4302G>T	c.(4300-4302)aaG>aaT	p.K1434N	PLXND1_ENST00000393239.1_Missense_Mutation_p.K1434N	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1434					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CCGCAAAGTCCTTCTGCTGCT	0.587																																					p.K1434N	Ovarian(97;366 1484 3738 22084 39045)	.											.	PLXND1-90	0			c.G4302T						.						107	90	96					3																	129284750		2203	4300	6503	SO:0001583	missense	23129	exon24			AAAGTCCTTCTGC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4302G>T	3.37:g.129284750C>A	ENSP00000317128:p.Lys1434Asn	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	117	15	NM_015103	0	0	18	18	0	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069256	0.55539	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.12879	2.64;2.64	4.86	2.99	0.34606	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.106561	0.64402	D	0.000006	T	0.28400	0.0702	L	0.59436	1.845	0.53005	D	0.999968	P;D	0.76494	0.643;0.999	B;D	0.71184	0.315;0.972	T	0.01448	-1.1352	10	0.87932	D	0	.	8.6019	0.33749	0.0:0.7443:0.0:0.2557	.	29;1434	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	N	1434	ENSP00000317128:K1434N;ENSP00000376931:K1434N	ENSP00000317128:K1434N	K	-	3	2	PLXND1	130767440	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	0.849000	0.27723	0.973000	0.38340	0.563000	0.77884	AAG	.		0.587	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		A	129284750	C	A	129284750	3	1	43	1	0	0	0	0	1	0	0	0	12153	680	24	4	1527	4	PLXND1	3	129284750	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08	17325903	129284750	68737680	7	3928											
SLC2A2	6514	broad.mit.edu	37	chr3	170727776	170727776	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctgatatgcttcttccaGcaattataagtatatgagat	12	15	7	7	0	1	2	0	2	1	1	3	3	3	2	2	0	2	3	2	0	6	7			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr3:170727776G>T	ENST00000314251.3	-	4	546	c.467C>A	c.(466-468)gCt>gAt	p.A156D	SLC2A2_ENST00000382808.4_Missense_Mutation_p.A37D	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	156					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	GCTTCTTCCAGCAATTATAAG	0.393																																					p.A156D													.	SLC2A2-515	0			c.C467A						.						68	67	67					3																	170727776		2202	4300	6502	SO:0001583	missense	6514	exon4			CTTCCAGCAATTA	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.467C>A	3.37:g.170727776G>T	ENSP00000323568:p.Ala156Asp	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	19	3	NM_000340	0	1	24	44	19	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.299157	0.60195	.	.	ENSG00000163581	ENST00000314251;ENST00000382808	D;D	0.82526	-1.62;-1.62	5.52	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.571600	0.18420	N	0.141799	D	0.85915	0.5808	M	0.89353	3.025	0.18873	N	0.999986	P	0.36144	0.539	B	0.38921	0.285	T	0.80870	-0.1189	10	0.87932	D	0	.	11.222	0.48860	0.1495:0.0:0.8505:0.0	.	156	P11168	GTR2_HUMAN	D	156;37	ENSP00000323568:A156D;ENSP00000372258:A37D	ENSP00000323568:A156D	A	-	2	0	SLC2A2	172210470	0.812000	0.29077	0.981000	0.43875	0.466000	0.32739	4.427000	0.59888	1.334000	0.45468	-0.140000	0.14226	GCT	.		0.393	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		T	170727776	G	T	170727776	3	4	43	1	0	0	0	0	1	0	0	0	14576	971	34	4	1139	4	SLC2A2	3	170727776	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08	41443026	170727776	27294654	8	3929											
ELF2	1998	hgsc.bcm.edu	37	chr4	139980523	139980523	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttgacactgtgcaagctGtgtagctgggatggtaataa	11	11	13	6	0	0	1	0	1	0	0	0	2	0	2	0	2	3	6	0	2	4	4			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr4:139980523G>C	ENST00000394235.2	-	10	1862	c.1360C>G	c.(1360-1362)Cag>Gag	p.Q454E	ELF2_ENST00000358635.3_Missense_Mutation_p.Q406E|ELF2_ENST00000379549.2_Missense_Mutation_p.Q377E|ELF2_ENST00000510408.1_Missense_Mutation_p.Q394E|ELF2_ENST00000265495.4_Missense_Mutation_p.Q454E|ELF2_ENST00000515489.1_Intron|ELF2_ENST00000379550.1_Missense_Mutation_p.Q466E	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					TGTGCAAGCTGTGTAGCTGGG	0.458																																					p.T454A		.											.	ELF2-228	0			c.A1360G						.						81	74	77					4																	139980523		2203	4300	6503	SO:0001583	missense	1998	exon9			CAAGCTGTGTAGC	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.1360C>G	4.37:g.139980523G>C	ENSP00000377782:p.Gln454Glu	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_201999	0	0	14	14	0		Missense_Mutation	SNP	ENST00000394235.2	37	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951130	0.53186	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000540754;ENST00000510408	T;T;T;T;T;T	0.12774	2.65;2.86;2.84;2.86;2.85;2.65	5.8	4.95	0.65309	.	0.048024	0.85682	N	0.000000	T	0.26919	0.0659	L	0.34521	1.04	0.51767	D	0.999939	D;D;D;B;D	0.69078	0.997;0.99;0.997;0.006;0.99	P;D;P;B;P	0.72982	0.81;0.979;0.779;0.007;0.848	T	0.01814	-1.1268	9	.	.	.	.	16.8692	0.86037	0.0:0.1284:0.8716:0.0	.	269;454;377;394;406	B7Z8R4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	E	406;454;466;454;377;269;394	ENSP00000351458:Q406E;ENSP00000377782:Q454E;ENSP00000368868:Q466E;ENSP00000265495:Q454E;ENSP00000368867:Q377E;ENSP00000426997:Q394E	.	Q	-	1	0	ELF2	140199973	1.000000	0.71417	0.483000	0.27378	0.992000	0.81027	9.206000	0.95056	1.441000	0.47550	0.650000	0.86243	CAG	.		0.458	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		C	139980523	G	C	139980523	3	2	43	1	0	0	0	0	1	0	0	0	5067	1386	48	4	389	4	ELF2	4	139980523	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08		139980523	51173753	9	3930											
POU4F3	5459	broad.mit.edu	37	chr5	145719656	145719656	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagatccccggcgtgggctcGctgagccaaagcaccatctg	9	6	12	14	3	1	2	0	1	1	1	3	2	2	2	4	2	2	3	4	2	2	0			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr5:145719656G>T	ENST00000230732.4	+	2	755	c.666G>T	c.(664-666)tcG>tcT	p.S222S	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	222	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGTGGGCTCGCTGAGCCAAA	0.642																																					p.S222S													.	POU4F3-90	0			c.G666T						.						47	50	49					5																	145719656		2203	4300	6503	SO:0001819	synonymous_variant	5459	exon2			GGGCTCGCTGAGC	U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"Homeoboxes / POU class"	9220	protein-coding gene	gene with protein product		602460	"POU domain class 4, transcription factor 3"	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.666G>T	5.37:g.145719656G>T		Somatic	141	1		WXS	Illumina HiSeq	Phase_I	225	6	NM_002700	0	0	0	0	0	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	37	CCDS4281.1																																																																																			.		0.642	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		T	145719656	G	T	145719656	2	4	43	1	0	0	0	0	0	0	0	1	12306	1074	38	4		4	POU4F3	5	145719656	Silent	SNP	G	TCGA-B3-3926-01A-01D-1252-08		145719656	35195604	10	3931											
RBAK	57786	hgsc.bcm.edu;ucsc.edu	37	chr7	5105227	5105227	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acgtacttgatgtggaaaatCtctgaagtcagatctcaatt	13	13	8	7	1	3	3	2	2	2	1	5	4	3	4	0	1	1	1	0	1	5	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr7:5105227C>T	ENST00000353796.3	+	6	2464	c.2140C>T	c.(2140-2142)Ctc>Ttc	p.L714F	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.L714F|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	714	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L714I(1)		NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGTGGAAAATCTCTGAAGTCA	0.373																																					p.L714F		.											.	RBAK-653	1	Substitution - Missense(1)	large_intestine(1)	c.C2140T						.						38	41	40					7																	5105227		2116	4249	6365	SO:0001583	missense	57786	exon6			GAAAATCTCTGAA	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.2140C>T	7.37:g.5105227C>T	ENSP00000275423:p.Leu714Phe	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	56	15	NM_001204456	0	0	8	10	2	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	37	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.428124	0.25726	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.07688	3.17;3.17	3.63	2.74	0.32292	.	0.328508	0.22348	N	0.061256	T	0.06188	0.0160	N	0.08118	0	0.30907	N	0.729093	P	0.51240	0.943	P	0.49799	0.622	T	0.35076	-0.9803	8	.	.	.	.	9.2279	0.37418	0.0:0.8873:0.0:0.1127	.	714	Q9NYW8	RBAK_HUMAN	F	714	ENSP00000275423:L714F;ENSP00000380120:L714F	.	L	+	1	0	RBAK	5071753	0.000000	0.05858	0.637000	0.29366	0.480000	0.33159	0.225000	0.17757	1.089000	0.41292	0.455000	0.32223	CTC	.		0.373	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		T	5105227	C	T	5105227	3	4	43	1	0	0	0	0	1	0	0	0	13132	913	32	2	2154	2	RBAK	7	5105227	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		5105227	154033436	11	3932											
EPDR1	54749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	37960767	37960767	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgacgggctcaaccagcgcGtgcgggtgctggacgagagg	8	4	18	11	6	1	1	1	0	0	1	1	4	1	2	1	4	4	2	1	4	1	0			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr7:37960767G>T	ENST00000199448.4	+	1	605	c.226G>T	c.(226-228)Gtg>Ttg	p.V76L	EPDR1_ENST00000559325.1_Missense_Mutation_p.V196L|EPDR1_ENST00000423717.1_Missense_Mutation_p.V76L|EPDR1_ENST00000476620.1_Intron|EPDR1_ENST00000425345.1_5'Flank	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	76					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						CAACCAGCGCGTGCGGGTGCT	0.706																																					p.V76L		.											.	EPDR1-91	0			c.G226T						.						15	16	16					7																	37960767		2107	4126	6233	SO:0001583	missense	54749	exon1			CAGCGCGTGCGGG	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.226G>T	7.37:g.37960767G>T	ENSP00000199448:p.Val76Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	135	18	NM_001242946	0	0	29	32	3	A8K4C0|C9JYS3|Q06BL0|Q99M77	Missense_Mutation	SNP	ENST00000199448.4	37	CCDS5454.2	.	.	.	.	.	.	.	.	.	.	G	11.76	1.733873	0.30684	.	.	ENSG00000086289	ENST00000199448;ENST00000423717	.	.	.	4.04	1.93	0.25924	.	0.478080	0.21214	N	0.078255	T	0.40473	0.1118	L	0.42686	1.345	0.80722	D	1	B	0.16603	0.018	B	0.09377	0.004	T	0.14392	-1.0474	9	0.21014	T	0.42	-17.3655	3.9195	0.09237	0.2427:0.1958:0.5615:0.0	.	196	A4D1W8	.	L	196;170	.	ENSP00000199448:V196L	V	+	1	0	EPDR1	37927292	0.988000	0.35896	1.000000	0.80357	0.959000	0.62525	0.596000	0.24044	0.866000	0.35629	0.313000	0.20887	GTG	.		0.706	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		T	37960767	G	T	37960767	3	4	43	1	0	0	0	0	1	0	0	0	5176	1145	40	4	588	4	EPDR1	7	37960767	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08	32855540	37960767	121177896	12	3933											
SRRT	51593	broad.mit.edu	37	chr7	100485034	100485034	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaggcccagaagatggggcGcaaagacccagagcaggaag	15	1	16	9	1	0	5	0	0	0	5	0	6	0	6	2	4	1	2	2	4	3	0			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr7:100485034G>A	ENST00000347433.4	+	16	2227	c.2069G>A	c.(2068-2070)cGc>cAc	p.R690H	SRRT_ENST00000388793.4_Missense_Mutation_p.R689H|SRRT_ENST00000432932.1_Missense_Mutation_p.R689H|SRRT_ENST00000457580.2_Missense_Mutation_p.R690H			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	690					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						AAGATGGGGCGCAAAGACCCA	0.552																																					p.R690H													.	SRRT-92	0			c.G2069A						.						111	106	108					7																	100485034		2203	4300	6503	SO:0001583	missense	51593	exon16			TGGGGCGCAAAGA		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2069G>A	7.37:g.100485034G>A	ENSP00000314491:p.Arg690His	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	343	6	NM_001128853	0	0	31	31	0	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647866	0.67358	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000342198;ENST00000432932;ENST00000347433;ENST00000448764	.	.	.	4.83	4.83	0.62350	Arsenite-resistance protein 2 (1);	0.057795	0.64402	D	0.000004	T	0.67078	0.2855	L	0.59436	1.845	0.51767	D	0.999938	D;D;D;D	0.89917	0.994;0.999;0.999;1.0	P;P;D;D	0.70935	0.579;0.871;0.95;0.971	T	0.63765	-0.6563	9	0.30078	T	0.28	.	8.9298	0.35663	0.1002:0.0:0.8998:0.0	.	689;689;690;690	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	H	690;689;55;689;690;320	.	ENSP00000344670:R55H	R	+	2	0	SRRT	100322970	0.410000	0.25376	0.915000	0.36163	0.575000	0.36095	3.229000	0.51278	2.500000	0.84329	0.297000	0.19635	CGC	.		0.552	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100485034	G	A	100485034	3	1	43	1	0	0	0	0	1	0	0	0	15204	1087	38	1	2127	1	SRRT	7	100485034	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08	62524267	100485034	58653629	13	3934											
UBAP2	55833	hgsc.bcm.edu	37	chr9	33960823	33960823	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catctgacagcaaacacttaCatcttcagtccagtcttctg	11	12	5	13	0	5	1	1	1	4	0	6	1	6	1	1	0	3	1	1	0	2	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr9:33960823C>G	ENST00000379238.1	-	10	916		c.e10+1		UBAP2_ENST00000360802.1_Splice_Site|UBAP2_ENST00000418786.2_Splice_Site|UBAP2_ENST00000379239.4_Splice_Site|UBAP2_ENST00000449054.1_Splice_Site|UBAP2_ENST00000539807.1_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CAAACACTTACATCTTCAGTC	0.398																																					.		.											.	UBAP2-94	0			c.798+1G>C						.						124	118	120					9																	33960823		2203	4300	6503	SO:0001630	splice_region_variant	55833	exon11			CACTTACATCTTC	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.798+1G>C	9.37:g.33960823C>G		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_018449	0	0	0	0	0		Splice_Site	SNP	ENST00000379238.1	37	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061796	0.76187	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379260;ENST00000379239;ENST00000418786;ENST00000412543;ENST00000421278	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.786	0.96437	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBAP2	33950823	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.966000	0.70395	2.676000	0.91093	0.563000	0.77884	.	.		0.398	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	Intron	G	33960823	C	G	33960823	5	3	43	1	0	0	0	0	0	0	1	0	16870	492	17	4	2640	4	UBAP2	9	33960823	Splice_Site	SNP	C	TCGA-B3-3926-01A-01D-1252-08		33960823	107252608	14	3935											
ITPRIP	85450	ucsc.edu	37	chr10	106075205	106075205	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacagcagtggcctgtccAcctgccagttctcgtacatg	7	9	11	14	1	1	0	0	0	1	0	3	0	2	0	4	2	3	4	4	2	1	2			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr10:106075205A>C	ENST00000337478.1	-	2	776	c.605T>G	c.(604-606)gTg>gGg	p.V202G	ITPRIP_ENST00000358187.2_Missense_Mutation_p.V202G|ITPRIP_ENST00000278071.2_Missense_Mutation_p.V202G|RP11-127L20.5_ENST00000472915.2_RNA	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	202						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						TGGCCTGTCCACCTGCCAGTT	0.632																																					p.V202G													.	ITPRIP-90	0			c.T605G						.																																			SO:0001583	missense	85450	exon2			CTGTCCACCTGCC	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.605T>G	10.37:g.106075205A>C	ENSP00000337178:p.Val202Gly	Somatic	123	27		WXS	Illumina HiSeq		269	78	NM_001272013	0	0	5	6	1	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Missense_Mutation	SNP	ENST00000337478.1	37	CCDS7557.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.721146	0.30503	.	.	ENSG00000148841	ENST00000337478;ENST00000278071;ENST00000358187	T;T;T	0.26067	1.76;1.76;1.76	5.37	1.76	0.24704	.	0.251839	0.38837	N	0.001552	T	0.27967	0.0689	M	0.74881	2.28	0.58432	D	0.999997	P	0.48589	0.912	B	0.41412	0.356	T	0.07712	-1.0758	10	0.87932	D	0	-16.2086	8.9471	0.35764	0.7067:0.0:0.2933:0.0	.	202	Q8IWB1	IPRI_HUMAN	G	202	ENSP00000337178:V202G;ENSP00000278071:V202G;ENSP00000350915:V202G	ENSP00000278071:V202G	V	-	2	0	ITPRIP	106065195	0.997000	0.39634	0.993000	0.49108	0.899000	0.52679	2.937000	0.48979	0.111000	0.17947	-0.385000	0.06624	GTG	.		0.632	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		C	106075205	A	C	106075205	3	2	43	1	0	0	0	0	1	0	0	0	7944	159	6	5	1042	5	ITPRIP	10	106075205	Missense_Mutation	SNP	A	TCGA-B3-3926-01A-01D-1252-08		106075205	29459542	15	3936											
MRGPRX4	117196	ucsc.edu;bcgsc.ca	37	chr11	18195248	18195248	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgtcctgctctggggcCtgtccctgctgtttagtatg	2	16	13	10	0	1	0	0	0	1	0	3	0	3	0	3	2	2	4	3	2	2	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr11:18195248C>T	ENST00000314254.3	+	1	865	c.445C>T	c.(445-447)Ctg>Ttg	p.L149L	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GCTCTGGGGCCTGTCCCTGCT	0.577																																					p.L149L													.	MRGPRX4-91	0			c.C445T						.						240	229	233					11																	18195248		2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			TGGGGCCTGTCCC	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.445C>T	11.37:g.18195248C>T		Somatic	483	4		WXS	Illumina HiSeq		767	131	NM_054032	0	0	0	0	0	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			.		0.577	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		T	18195248	C	T	18195248	2	4	43	1	0	0	0	0	0	0	0	1	9794	680	24	2		2	MRGPRX4	11	18195248	Silent	SNP	C	TCGA-B3-3926-01A-01D-1252-08		18195248	116811268	16	3937											
C1QTNF4	114900	hgsc.bcm.edu	37	chr11	47611940	47611940	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgggcgcgcctagcgcgtaCtgcggggcgccatgcagccg	4	4	17	16	8	0	0	0	0	0	0	0	0	0	0	4	3	5	2	4	3	2	2	rs142453721	byFrequency	TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr11:47611940C>G	ENST00000302514.3	-	2	939	c.423G>C	c.(421-423)caG>caC	p.Q141H		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	141	C1q 1. {ECO:0000255|PROSITE- ProRule:PRU00368}.			Q -> H (in Ref. 1; AAK17962). {ECO:0000305}.		extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						CTAGCGCGTACTGCGGGGCGC	0.771													C|||	86	0.0171725	0.0023	0.0303	5008	,	,		2805	0.002		0.0537	False		,,,				2504	0.0061				p.Q141H		.											.	C1QTNF4-90	0			c.G423C						.						1	1	1					11																	47611940		1018	2050	3068	SO:0001583	missense	114900	exon2			CGCGTACTGCGGG	AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247			14346	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 4"	614911				16094384	Standard	NM_031909		Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.423G>C	11.37:g.47611940C>G	ENSP00000302274:p.Gln141His	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_031909	0	0	0	0	0	Q8IV25	Missense_Mutation	SNP	ENST00000302514.3	37	CCDS7942.1	41	0.018772893772893772	2	0.0040650406504065045	9	0.024861878453038673	3	0.005244755244755245	27	0.03562005277044855	C	16.01	3.000217	0.54147	.	.	ENSG00000172247	ENST00000302514	T	0.74947	-0.89	4.5	3.57	0.40892	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.708561	0.13520	U	0.381762	T	0.37571	0.1008	L	0.29908	0.895	0.37167	D	0.902841	P	0.48998	0.918	P	0.52267	0.694	T	0.54296	-0.8315	10	0.22706	T	0.39	.	8.4836	0.33059	0.0:0.7611:0.1559:0.0829	.	141	Q9BXJ3	C1QT4_HUMAN	H	141	ENSP00000302274:Q141H	ENSP00000302274:Q141H	Q	-	3	2	C1QTNF4	47568516	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	0.739000	0.26173	0.981000	0.38548	0.462000	0.41574	CAG	C|0.981;G|0.019		0.771	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391772.1	NM_031909		G	47611940	C	G	47611940	3	3	43	1	0	0	0	0	1	0	0	0	1971	564	20	4	570	4	C1QTNF4	11	47611940	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08	29416692	47611940	87394576	17	3938											
NAALAD2	10003	broad.mit.edu	37	chr11	89911214	89911214	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatgcagaagctttgaaaaActatgcagcaagtatctata	16	11	7	7	0	1	2	0	1	1	1	1	2	1	2	0	0	5	5	0	0	9	6			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr11:89911214A>T	ENST00000534061.1	+	16	2017	c.1787A>T	c.(1786-1788)aAc>aTc	p.N596I	NAALAD2_ENST00000321955.4_Missense_Mutation_p.N563I|NAALAD2_ENST00000375944.3_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	596					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GCTTTGAAAAACTATGCAGCA	0.343																																					p.N596I													.	NAALAD2-92	0			c.A1787T						.						76	81	79					11																	89911214		2201	4299	6500	SO:0001583	missense	10003	exon16			TGAAAAACTATGC	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1787A>T	11.37:g.89911214A>T	ENSP00000432481:p.Asn596Ile	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	234	5	NM_005467	0	0	0	0	0	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	37	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	a	10.98	1.504470	0.26949	.	.	ENSG00000077616	ENST00000534061;ENST00000321955	T;T	0.31510	1.49;1.49	5.63	3.29	0.37713	Transferrin receptor-like, dimerisation domain (2);	0.216956	0.40640	N	0.001045	T	0.16385	0.0394	L	0.28458	0.855	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13469	-1.0508	9	.	.	.	-7.9053	1.5294	0.02532	0.4262:0.301:0.1284:0.1444	.	596	Q9Y3Q0	NALD2_HUMAN	I	596;563	ENSP00000432481:N596I;ENSP00000320083:N563I	.	N	+	2	0	NAALAD2	89550862	0.543000	0.26434	1.000000	0.80357	0.813000	0.45954	0.092000	0.15066	0.415000	0.25817	-0.270000	0.10280	AAC	.		0.343	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		T	89911214	A	T	89911214	3	4	43	1	0	0	0	0	1	0	0	0	10153	43	2	5	1849	5	NAALAD2	11	89911214	Missense_Mutation	SNP	A	TCGA-B3-3926-01A-01D-1252-08	42299274	89911214	45095302	18	3939											
MLL2	8085	broad.mit.edu	37	chr12	49445198	49445198	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagataggtgtggctcctcAggccggggggacaggtgcgg	6	6	21	8	2	1	1	1	0	0	1	2	3	2	2	2	9	1	1	2	9	1	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr12:49445198A>G	ENST00000301067.7	-	10	2267	c.2268T>C	c.(2266-2268)ccT>ccC	p.P756P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	756	Pro-rich.			Missing (in Ref. 1; AAC51734). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GTGGCTCCTCAGGCCGGGGGG	0.692																																					p.P756P													.	MLL2-612	0			c.T2268C						.						20	23	22					12																	49445198		1725	3776	5501	SO:0001819	synonymous_variant	8085	exon10			CTCCTCAGGCCGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.2268T>C	12.37:g.49445198A>G		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	137	3	NM_003482	0	0	1	1	0	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.692	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49445198	A	G	49445198	2	3	43	1	0	0	0	0	0	0	0	1	9646	175	7	3		3	MLL2	12	49445198	Silent	SNP	A	TCGA-B3-3926-01A-01D-1252-08		49445198	84406697	19	3940											
SLC46A3	283537	hgsc.bcm.edu	37	chr13	29278214	29278214	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctccaagtgtttctaagaaAgcaatacaagcaaacagggt	16	8	8	9	0	1	1	0	0	1	1	2	1	2	1	2	1	4	3	2	1	7	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr13:29278214A>G	ENST00000266943.6	-	5	1536	c.1167T>C	c.(1165-1167)gcT>gcC	p.A389A	SLC46A3_ENST00000475385.1_5'UTR|RNU6-53P_ENST00000365367.1_RNA|SLC46A3_ENST00000380814.4_Silent_p.A389A	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	389					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		TTTCTAAGAAAGCAATACAAG	0.408																																					p.A389A		.											.	SLC46A3-69	0			c.T1167C						.						69	74	72					13																	29278214		2203	4300	6503	SO:0001819	synonymous_variant	283537	exon5			TAAGAAAGCAATA		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.1167T>C	13.37:g.29278214A>G		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_181785	0	0	39	39	0	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Silent	SNP	ENST00000266943.6	37	CCDS9332.1																																																																																			.		0.408	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		G	29278214	A	G	29278214	2	3	43	1	0	0	0	0	0	0	0	1	14678	59	3	3		3	SLC46A3	13	29278214	Silent	SNP	A	TCGA-B3-3926-01A-01D-1252-08		29278214	85891664	20	3941											
REC8	79711	ucsc.edu;bcgsc.ca	37	chr14	24646579	24646579	+	IGR	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcccgcggctcccacctccaGctcctgcagagtaagggcaa	8	6	10	17	2	0	1	0	0	0	1	4	1	4	1	5	2	2	5	5	2	2	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr14:24646579G>C	ENST00000354464.6	-	0	3646				REC8_ENST00000311457.3_Missense_Mutation_p.A242P|REC8_ENST00000559919.1_Missense_Mutation_p.A242P	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4						DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CCCACCTCCAGCTCCTGCAGA	0.567																																					p.A242P													.	REC8-90	0			c.G724C						.						81	84	83					14																	24646579		1932	4124	6056	SO:0001628	intergenic_variant	9985	exon9			CCTCCAGCTCCTG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801		14.37:g.24646579G>C		Somatic	173	3		WXS	Illumina HiSeq		158	80	NM_001048205	0	0	0	2	2	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.298998	0.40694	.	.	ENSG00000100918	ENST00000311457;ENST00000447460	T	0.24151	1.87	5.04	4.11	0.48088	.	0.320873	0.29389	N	0.012292	T	0.22975	0.0555	L	0.51422	1.61	0.09310	N	1	B;B	0.19073	0.033;0.02	B;B	0.17433	0.018;0.008	T	0.06972	-1.0797	10	0.29301	T	0.29	-0.117	11.5558	0.50748	0.0:0.1793:0.8207:0.0	.	243;243	O95072-2;O95072	.;REC8_HUMAN	P	242	ENSP00000308699:A242P	ENSP00000308699:A242P	A	+	1	0	REC8	23716419	0.449000	0.25689	0.573000	0.28510	0.428000	0.31595	1.284000	0.33249	2.630000	0.89119	0.561000	0.74099	GCT	.		0.567	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		C	24646579	G	C	24646579	1	2	43	0	1	0	0	0	0	0	0	0	13231	971	34	4		4	REC8	14	24646579	IGR	SNP	G	TCGA-B3-3926-01A-01D-1252-08		24646579	82702961	21	3942											
C14orf126	112487	hgsc.bcm.edu	37	chr14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgggcctgaggaatccGgctaccctcagccatggctt	6	7	12	16	3	1	1	1	1	0	0	2	2	2	2	5	4	2	2	5	4	2	2	rs17097904	byFrequency	TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	DTD2_ENST00000356180.4_Missense_Mutation_p.R6W|RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		.											.	.	1	Substitution - Missense(1)	skin(1)	c.C16T						.						12	12	12					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	11	1		WXS	Illumina HiSeq	Phase_I	17	7	NM_080664	0	0	21	30	9	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		A	31926584	G	A	31926584	3	1	43	1	0	0	0	0	1	0	0	0	1747	1115	39	1	502	1	C14orf126	14	31926584	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08	7280005	31926584	75422956	22	3943											
SAV1	60485	hgsc.bcm.edu;broad.mit.edu	37	chr14	51132122	51132129	+	Frame_Shift_Del	DEL	CTAGACTT	CTAGACTT	-																															atactctctagggacatctgCtagacttctggcaagataag																										TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	CTAGACTT	CTAGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr14:51132122_51132129delCTAGACTT	ENST00000324679.4	-	2	666_673	c.303_310delAAGTCTAG	c.(301-312)agaagtctagcafs	p.RSLA101fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	101					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					GGGACATCTGCTAGACTTCTGGCAAGAT	0.385																																					p.101_104del		.											.	SAV1-658	0			c.303_310del						.																																			SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.303_310delAAGTCTAG	14.37:g.51132122_51132129delCTAGACTT	ENSP00000324729:p.Arg101fs	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	50	13	NM_021818	0	0	0	0	0	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Frame_Shift_Del	DEL	ENST00000324679.4	37	CCDS9701.1																																																																																			.		0.385	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			-	51132129	CTAGACTT	-	51132122	7	5	43	1	0	1	0	1	0	0	0	0	13888	797	28	0	857	0	SAV1	14	51132122	Frame_Shift_Del	DEL	CTAGACTT	TCGA-B3-3926-01A-01D-1252-08	19205538	51132122	56217418	23	3944											
CBFA2T3	863	hgsc.bcm.edu	37	chr16	88943542	88943542	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcaccgggtcggccaccaCggctgtggggccctgcaggc	5	4	17	15	3	0	0	0	0	0	0	1	0	0	0	4	7	1	3	4	7	0	0	rs200760802	byFrequency	TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr16:88943542C>T	ENST00000268679.4	-	12	2200	c.1804G>A	c.(1804-1806)Gtg>Atg	p.V602M	CBFA2T3_ENST00000436887.2_Missense_Mutation_p.V564M|CBFA2T3_ENST00000360302.2_Missense_Mutation_p.V516M|CBFA2T3_ENST00000327483.5_Missense_Mutation_p.V516M|CBFA2T3_ENST00000448839.1_Missense_Mutation_p.V526M	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	602					cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		TCGGCCACCACGGCTGTGGGG	0.726			T	RUNX1	AML								c|||	11	0.00219649	0.0015	0	5008	,	,		14091	0		0.004	False		,,,				2504	0.0051				p.V602M		.		Dom	yes		16	16q24	863	"core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"		L	.	CBFA2T3-722	0			c.G1804A						.	C	MET/VAL,MET/VAL	8,4120		0,8,2056	7	7	7		1804,1546	1.4	0	16		7	49,7995		0,49,3973	yes	missense,missense	CBFA2T3	NM_005187.5,NM_175931.2	21,21	0,57,6029	TT,TC,CC		0.6091,0.1938,0.4683	benign,benign	602/654,516/568	88943542	57,12115	2064	4022	6086	SO:0001583	missense	863	exon12			CCACCACGGCTGT	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"Zinc fingers, MYND-type", "A-kinase anchor proteins"	1537	protein-coding gene	gene with protein product	"myeloid translocation gene 8 and 16b"	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.1804G>A	16.37:g.88943542C>T	ENSP00000268679:p.Val602Met	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	7	6	NM_005187	0	0	0	0	0	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	37	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	C	8.769	0.925438	0.18056	0.001938	0.006091	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000448839;ENST00000360302	T;T;T;T;T	0.45668	1.47;0.89;0.89;1.48;1.47	4.07	1.36	0.22044	.	2.039650	0.03219	U	0.177234	T	0.20251	0.0487	N	0.22421	0.69	0.09310	N	1	B;B	0.26318	0.146;0.03	B;B	0.19946	0.012;0.027	T	0.15723	-1.0427	10	0.42905	T	0.14	0.553	1.7885	0.03046	0.176:0.4794:0.2008:0.1438	.	602;516	O75081;O75081-2	MTG16_HUMAN;.	M	516;602;564;526;516	ENSP00000332122:V516M;ENSP00000268679:V602M;ENSP00000395739:V564M;ENSP00000401254:V526M;ENSP00000353449:V516M	ENSP00000268679:V602M	V	-	1	0	CBFA2T3	87471043	0.163000	0.22920	0.000000	0.03702	0.006000	0.05464	1.796000	0.38794	0.254000	0.21573	0.485000	0.47835	GTG	.		0.726	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187		T	88943542	C	T	88943542	3	4	43	1	0	0	0	0	1	0	0	0	2704	536	19	1	161	1	CBFA2T3	16	88943542	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		88943542	1411211	24	3945											
VPS53	55275	broad.mit.edu	37	chr17	465803	465803	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaggtacttctggaaaatgGtggtcagggcgatcatgggc	9	9	17	6	1	3	0	2	0	1	0	3	3	3	2	0	7	1	1	0	7	3	2			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr17:465803G>A	ENST00000571805.1	-	14	1632	c.1496C>T	c.(1495-1497)aCc>aTc	p.T499I	VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000291074.5_Missense_Mutation_p.T470I|VPS53_ENST00000437048.2_Missense_Mutation_p.T499I|VPS53_ENST00000401468.3_Missense_Mutation_p.T222I|VPS53_ENST00000446250.2_Missense_Mutation_p.T301I|VPS53_ENST00000574029.1_Intron			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	499					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		CTGGAAAATGGTGGTCAGGGC	0.537																																					p.T499I													.	VPS53-90	0			c.C1496T						.						85	78	80					17																	465803		2203	4300	6503	SO:0001583	missense	55275	exon14			AAAATGGTGGTCA		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"vacuolar protein sorting 53 (yeast)"			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.1496C>T	17.37:g.465803G>A	ENSP00000459312:p.Thr499Ile	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	149	4	NM_001128159	0	0	20	20	0	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		.	.	.	.	.	.	.	.	.	.	G	15.51	2.854197	0.51270	.	.	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000401468;ENST00000389040	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	6.07	5.1	0.69264	.	0.042101	0.85682	D	0.000000	T	0.22975	0.0555	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B	0.15141	0.012;0.001;0.0;0.0;0.001	B;B;B;B;B	0.21546	0.035;0.002;0.005;0.002;0.005	T	0.02781	-1.1111	10	0.36615	T	0.2	-26.6231	13.8962	0.63773	0.0721:0.0:0.9279:0.0	.	222;499;301;499;470	E7EVT8;Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;.;VPS53_HUMAN;.	I	499;301;470;222;451	ENSP00000401435:T499I;ENSP00000394386:T301I;ENSP00000291074:T470I;ENSP00000384294:T222I;ENSP00000373692:T451I	ENSP00000291074:T470I	T	-	2	0	VPS53	412553	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.575000	0.82447	2.884000	0.98904	0.655000	0.94253	ACC	.		0.537	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		A	465803	G	A	465803	3	1	43	1	0	0	0	0	1	0	0	0	17248	1261	44	2	1053	2	VPS53	17	465803	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08		465803	80729407	25	3946											
KRTAP1-5	83895	hgsc.bcm.edu	37	chr17	39183062	39183062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgggcggcaccacctgaTacgggtgctcacagctccac	7	7	12	15	2	2	1	1	1	1	0	3	1	3	1	3	3	3	3	3	3	1	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr17:39183062T>C	ENST00000361883.5	-	1	392	c.346A>G	c.(346-348)Atc>Gtc	p.I116V		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	116	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			CACCACCTGATACGGGTGCTC	0.642																																					p.I116V		.											.	.	0			c.A346G						.						24	30	28					17																	39183062		2127	4246	6373	SO:0001583	missense	83895	exon1			ACCTGATACGGGT	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"Keratin associated proteins"	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.346A>G	17.37:g.39183062T>C	ENSP00000355302:p.Ile116Val	Somatic	46	2		WXS	Illumina HiSeq	Phase_I	98	5	NM_031957	0	0	0	0	0	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Missense_Mutation	SNP	ENST00000361883.5	37	CCDS42321.1	.	.	.	.	.	.	.	.	.	.	T	6.541	0.468074	0.12461	.	.	ENSG00000221852	ENST00000361883;ENST00000543389	T	0.29655	1.56	5.49	-0.0728	0.13738	.	.	.	.	.	T	0.14399	0.0348	N	0.04768	-0.165	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.26360	-1.0105	9	0.36615	T	0.2	.	8.8456	0.35168	0.0:0.5303:0.0:0.4697	.	116	Q9BYS1	KRA15_HUMAN	V	116;106	ENSP00000355302:I116V	ENSP00000355302:I116V	I	-	1	0	KRTAP1-5	36436588	0.006000	0.16342	0.012000	0.15200	0.491000	0.33493	-0.214000	0.09292	-0.197000	0.10350	0.459000	0.35465	ATC	.		0.642	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1			C	39183062	T	C	39183062	3	2	43	1	0	0	0	0	1	0	0	0	8525	1406	49	3	182	3	KRTAP1-5	17	39183062	Missense_Mutation	SNP	T	TCGA-B3-3926-01A-01D-1252-08	38717259	39183062	42012148	26	3947											
MRC2	9902	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	60766323	60766323	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctgccagaagggcacgggTatgtgtcaccagtcacctgg	9	8	13	11	1	3	1	2	0	1	1	3	1	3	1	3	3	1	2	3	3	2	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr17:60766323T>C	ENST00000303375.5	+	23	3736		c.e23+2		MRC2_ENST00000580916.1_Splice_Site|MRC2_ENST00000446119.2_Splice_Site	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2						collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						AGGGCACGGGTATGTGTCACC	0.642																																					.		.											.	MRC2-117	0			c.3334+2T>C						.						42	35	37					17																	60766323		2203	4300	6503	SO:0001630	splice_region_variant	9902	exon23			CACGGGTATGTGT	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3334+2T>C	17.37:g.60766323T>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	81	14	NM_006039	0	0	0	0	0	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Splice_Site	SNP	ENST00000303375.5	37	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.155893	0.78114	.	.	ENSG00000011028	ENST00000303375;ENST00000446119	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3771	0.66886	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MRC2	58120055	1.000000	0.71417	0.863000	0.33907	0.565000	0.35776	5.032000	0.64140	1.978000	0.57642	0.459000	0.35465	.	.		0.642	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		Intron	C	60766323	T	C	60766323	5	2	43	1	0	0	0	0	0	0	1	0	9783	1652	57	3	3426	3	MRC2	17	60766323	Splice_Site	SNP	T	TCGA-B3-3926-01A-01D-1252-08	21583261	60766323	20428887	27	3948											
NOL4	8715	hgsc.bcm.edu	37	chr18	31709939	31709939	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaaagaaatcttcaaccaCagctacccgtcgtaaagata	16	8	6	11	2	3	2	2	0	1	2	4	2	3	2	2	0	3	2	2	0	7	4			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr18:31709939C>G	ENST00000261592.5	-	2	607	c.310G>C	c.(310-312)Gtg>Ctg	p.V104L	NOL4_ENST00000269185.4_5'UTR|NOL4_ENST00000538587.1_Missense_Mutation_p.V30L|NOL4_ENST00000589544.1_Missense_Mutation_p.V104L|NOL4_ENST00000535475.1_5'UTR	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	104						nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						TCTTCAACCACAGCTACCCGT	0.388																																					p.V104L		.											.	NOL4-93	0			c.G310C						.						109	97	101					18																	31709939		2203	4300	6503	SO:0001583	missense	8715	exon2			CAACCACAGCTAC	AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746			7870	protein-coding gene	gene with protein product	"cancer/testis antigen 125"	603577				9813152	Standard	NM_003787		Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.310G>C	18.37:g.31709939C>G	ENSP00000261592:p.Val104Leu	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_003787	0	0	0	0	0	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	Missense_Mutation	SNP	ENST00000261592.5	37	CCDS11907.2	.	.	.	.	.	.	.	.	.	.	C	30	5.049814	0.93740	.	.	ENSG00000101746	ENST00000261592;ENST00000538587	D	0.83755	-1.76	5.61	5.61	0.85477	.	.	.	.	.	D	0.89708	0.6793	L	0.58810	1.83	0.80722	D	1	P;P;D	0.61697	0.902;0.902;0.99	D;P;D	0.70935	0.927;0.893;0.971	D	0.90122	0.4200	9	0.72032	D	0.01	-8.97	18.6148	0.91299	0.0:1.0:0.0:0.0	.	30;104;104	B4DSQ0;O94818;O94818-2	.;NOL4_HUMAN;.	L	104;30	ENSP00000261592:V104L	ENSP00000261592:V104L	V	-	1	0	NOL4	29963937	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.329000	0.79170	2.639000	0.89480	0.585000	0.79938	GTG	.		0.388	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255386.1	NM_003787		G	31709939	C	G	31709939	3	3	43	1	0	0	0	0	1	0	0	0	10550	478	17	4	1646	4	NOL4	18	31709939	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		31709939	46367309	28	3949											
AMH	268	hgsc.bcm.edu	37	chr19	2251512	2251512	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcgcgctctgcccaggTggccccggcggcctcggcga	2	6	15	18	6	1	0	0	0	1	0	3	1	1	0	4	5	2	2	4	5	0	0	rs7252789	byFrequency	TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr19:2251512T>A	ENST00000221496.4	+	5	1261	c.1239T>A	c.(1237-1239)ggT>ggA	p.G413G	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	413					aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCTGCCCAGGTGGCCCCGGCG	0.776									Persistant Mullerian Duct Syndrome (type I and II)				T|||	4602	0.91893	0.9259	0.951	5008	,	,		7149	0.9683		0.9354	False		,,,				2504	0.819				p.G413G		.											.	AMH-130	0			c.T1239A						.						1	1	1					19																	2251512		452	789	1241	SO:0001819	synonymous_variant	268	exon5	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	CCCAGGTGGCCCC	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"Endogenous ligands"	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.1239T>A	19.37:g.2251512T>A		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_000479	0	0	0	0	0	O75246|Q6GTN3	Silent	SNP	ENST00000221496.4	37	CCDS12085.1																																																																																			T|0.069;A|0.931		0.776	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479		A	2251512	T	A	2251512	2	1	43	1	0	0	0	0	0	0	0	1	572	1683	59	5		5	AMH	19	2251512	Silent	SNP	T	TCGA-B3-3926-01A-01D-1252-08		2251512	56877471	29	3950											
UBA52	7311	hgsc.bcm.edu;broad.mit.edu	37	chr19	18685757	18685757	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagcttgcccagaaatacAactgcgacaagatgatctgc	13	7	9	12	1	1	3	0	1	1	2	1	4	1	3	2	0	6	1	2	0	4	2			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr19:18685757A>T	ENST00000442744.2	+	4	326	c.268A>T	c.(268-270)Aac>Tac	p.N90Y	UBA52_ENST00000599551.1_Missense_Mutation_p.N90Y|UBA52_ENST00000596273.1_Missense_Mutation_p.N90Y|UBA52_ENST00000598780.1_Missense_Mutation_p.N90Y|UBA52_ENST00000597451.1_Missense_Mutation_p.N90Y|UBA52_ENST00000595158.1_Missense_Mutation_p.N90Y|UBA52_ENST00000599595.1_Missense_Mutation_p.N90Y|UBA52_ENST00000596304.1_Missense_Mutation_p.N90Y|UBA52_ENST00000595683.1_Missense_Mutation_p.N90Y|CRLF1_ENST00000594325.1_Intron|UBA52_ENST00000430157.2_Missense_Mutation_p.N90Y	NM_001033930.1	NP_001029102.1	P62987	RL40_HUMAN	ubiquitin A-52 residue ribosomal protein fusion product 1	90					activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|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 type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(2)	3						CCAGAAATACAACTGCGACAA	0.612																																					p.N90Y		.											.	UBA52-90	0			c.A268T						.						46	42	43					19																	18685757		2203	4300	6503	SO:0001583	missense	7311	exon4			AAATACAACTGCG		CCDS12382.1	19p13.1-p12	2011-04-06			ENSG00000221983	ENSG00000221983		"L ribosomal proteins"	12458	protein-coding gene	gene with protein product	"ribosomal protein L40", "ubiquitin-52 amino acid fusion protein", "ubiquitin carboxyl extension protein 52", "60S ribosomal protein L40", "ubiquitin-CEP52"	191321				8188300	Standard	XM_005260051		Approved	RPL40, CEP52, HUBCEP52, MGC57125, MGC126879, MGC126881, L40	uc002njs.3	P62987		ENST00000442744.2:c.268A>T	19.37:g.18685757A>T	ENSP00000388107:p.Asn90Tyr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	128	13	NM_001033930	0	0	756	775	19	P02248|P02249|P02250|P14793|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000442744.2	37	CCDS12382.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273436	0.80580	.	.	ENSG00000221983	ENST00000442744;ENST00000430157	T;T	0.45668	0.89;0.89	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.67822	0.2934	M	0.93197	3.39	0.58432	D	0.99999	D	0.59767	0.986	P	0.59424	0.857	T	0.76822	-0.2817	10	0.87932	D	0	-2.438	11.7658	0.51930	1.0:0.0:0.0:0.0	.	90	P62987	RL40_HUMAN	Y	90	ENSP00000388107:N90Y;ENSP00000396910:N90Y	ENSP00000396910:N90Y	N	+	1	0	UBA52	18546757	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.564000	0.60830	1.667000	0.50832	0.379000	0.24179	AAC	.		0.612	UBA52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465117.2	NM_003333		T	18685757	A	T	18685757	3	4	43	1	0	0	0	0	1	0	0	0	16864	130	5	5	278	5	UBA52	19	18685757	Missense_Mutation	SNP	A	TCGA-B3-3926-01A-01D-1252-08	16434245	18685757	40443226	30	3951											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945880	48945880	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacagctgctgcagcgcTgaggccgccccaccgcccgc	6	5	12	18	4	0	1	0	1	0	0	0	1	0	1	5	1	5	5	5	1	1	1	rs62130268	byFrequency	TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr19:48945880T>C	ENST00000263269.3	+	13	2785	c.2697T>C	c.(2695-2697)gcT>gcC	p.A899A		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	899					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTGCAGCGCTGAGGCCGCCC	0.781													c|||	3742	0.747204	0.6188	0.8545	5008	,	,		4716	0.6548		0.8887	False		,,,				2504	0.7945				p.A899A		.											.	GRIN2D-156	0			c.T2697C						.			1689,437		638,413,12	1	1	1		2697	-3.3	1	19	dbSNP_129	1	3712,202		1757,198,2	no	coding-synonymous	GRIN2D	NM_000836.2		2395,611,14	CC,CT,TT		5.161,20.555,10.5795		899/1337	48945880	5401,639	1063	1957	3020	SO:0001819	synonymous_variant	2906	exon13			CAGCGCTGAGGCC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2697T>C	19.37:g.48945880T>C		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_000836	0	0	0	1	1		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			T|0.245;C|0.755		0.781	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			C	48945880	T	C	48945880	2	2	43	1	0	0	0	0	0	0	0	1	6803	1567	55	3		3	GRIN2D	19	48945880	Silent	SNP	T	TCGA-B3-3926-01A-01D-1252-08	30260123	48945880	10183103	31	3952											
THBD	7056	broad.mit.edu	37	chr20	23029807	23029807	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agctggtgttgttgtctcccGtaacccactggaagccgcgc	6	10	12	13	3	1	0	0	0	1	0	2	1	1	1	3	2	3	4	3	2	2	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr20:23029807G>A	ENST00000377103.2	-	1	571	c.335C>T	c.(334-336)aCg>aTg	p.T112M		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	112	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	GTTGTCTCCCGTAACCCACTG	0.716																																					p.T112M													.	THBD-90	0			c.C335T						.						15	10	12					20																	23029807		2174	4264	6438	SO:0001583	missense	7056	exon1			TCTCCCGTAACCC		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"CD molecules"	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.335C>T	20.37:g.23029807G>A	ENSP00000366307:p.Thr112Met	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	16	5	NM_000361	0	0	0	0	0	Q8IV29|Q9UC32	Missense_Mutation	SNP	ENST00000377103.2	37	CCDS13148.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095410	0.56075	.	.	ENSG00000178726	ENST00000377103;ENST00000503590	T	0.56611	0.45	5.71	5.71	0.89125	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.162218	0.40640	U	0.001050	T	0.74604	0.3738	M	0.79258	2.445	0.30209	N	0.797945	D	0.89917	1.0	D	0.76071	0.987	T	0.74383	-0.3683	10	0.87932	D	0	-19.0767	18.836	0.92162	0.0:0.0:1.0:0.0	.	112	P07204	TRBM_HUMAN	M	112;94	ENSP00000366307:T112M	ENSP00000366307:T112M	T	-	2	0	THBD	22977807	1.000000	0.71417	0.309000	0.25155	0.229000	0.25112	6.436000	0.73417	2.703000	0.92315	0.549000	0.68633	ACG	.		0.716	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2			A	23029807	G	A	23029807	3	1	43	1	0	0	0	0	1	0	0	0	15884	1145	40	1	1396	1	THBD	20	23029807	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08		23029807	39995713	32	3953											
CDC42EP1	11135	broad.mit.edu	37	chr22	37962631	37962631	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagctggtgcggagggTgggggcgcccccccggagga	4	4	21	12	3	0	0	0	0	0	0	0	3	0	3	3	7	3	3	3	7	0	0			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr22:37962631T>G	ENST00000249014.4	+	2	695	c.275T>G	c.(274-276)gTg>gGg	p.V92G		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	92					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GTGCGGAGGGTGGGGGCGCCC	0.697																																					p.V92G													.	CDC42EP1-90	0			c.T275G						.						27	29	28					22																	37962631		2201	4293	6494	SO:0001583	missense	11135	exon2			GGAGGGTGGGGGC	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"55 kDa bone marrow stromal/endothelial cell protein", "serum constituent protein"	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.275T>G	22.37:g.37962631T>G	ENSP00000249014:p.Val92Gly	Somatic	71	15		WXS	Illumina HiSeq	Phase_I	66	28	NM_152243	0	0	11	12	1	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	37	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	T	8.072	0.770536	0.15983	.	.	ENSG00000128283	ENST00000249014	T	0.31247	1.5	5.22	3.03	0.35002	.	0.247549	0.30036	N	0.010569	T	0.20495	0.0493	L	0.39898	1.24	0.22728	N	0.99881	B	0.12630	0.006	B	0.13407	0.009	T	0.18023	-1.0350	10	0.20046	T	0.44	-20.0019	6.2589	0.20889	0.0:0.1809:0.2291:0.59	.	92	Q00587	BORG5_HUMAN	G	92	ENSP00000249014:V92G	ENSP00000249014:V92G	V	+	2	0	CDC42EP1	36292577	0.001000	0.12720	0.742000	0.31022	0.794000	0.44872	-0.110000	0.10824	0.841000	0.35020	0.460000	0.39030	GTG	.		0.697	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243		G	37962631	T	G	37962631	3	3	43	1	0	0	0	0	1	0	0	0	3081	1696	59	5	277	5	CDC42EP1	22	37962631	Missense_Mutation	SNP	T	TCGA-B3-3926-01A-01D-1252-08		37962631	13341935	33	3954											
EGFL6	25975	broad.mit.edu	37	chrX	13635856	13635856	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatttgttttagctatcccTgaaaattctgtgaaggaagt	11	17	8	5	0	1	2	0	2	1	0	2	3	2	3	1	1	1	2	1	1	7	6			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chrX:13635856T>C	ENST00000361306.1	+	8	1043	c.786T>C	c.(784-786)ccT>ccC	p.P262P	EGFL6_ENST00000380602.3_Silent_p.P262P	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	262					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						TAGCTATCCCTGAAAATTCTG	0.343																																					p.P262P													.	EGFL6-193	0			c.T786C						.						108	112	110					X																	13635856		2203	4300	6503	SO:0001819	synonymous_variant	25975	exon8			TATCCCTGAAAAT	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"MAM and EGF domain containing"	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.786T>C	X.37:g.13635856T>C		Somatic	399	0		WXS	Illumina HiSeq	Phase_I	529	4	NM_001167890	0	0	0	0	0	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	37	CCDS14155.1																																																																																			.		0.343	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		C	13635856	T	C	13635856	2	2	43	1	0	0	0	0	0	0	0	1	4974	1567	55	3		3	EGFL6	23	13635856	Silent	SNP	T	TCGA-B3-3926-01A-01D-1252-08		13635856	141634704	34	3955											
PLS3	5358	broad.mit.edu	37	chrX	114874764	114874764	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatcaaatcgcaccaaaAggacaaaaggaaggtgaacc	19	4	8	10	1	2	1	2	1	0	0	3	3	2	3	2	3	1	1	2	3	8	0			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chrX:114874764A>G	ENST00000420625.2	+	9	1070	c.936A>G	c.(934-936)aaA>aaG	p.K312K	PLS3_ENST00000537301.1_Silent_p.K299K|PLS3_ENST00000543070.1_5'UTR|PLS3_ENST00000289290.3_Silent_p.K276K|PLS3_ENST00000539310.1_Silent_p.K267K|PLS3_ENST00000355899.3_Silent_p.K312K	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	312	Actin-binding 1.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						TCGCACCAAAAGGACAAAAGG	0.348																																					p.K312K	Colon(160;1047 1864 8490 12969 29601)												.	PLS3-193	0			c.A936G						.						172	148	156					X																	114874764		2203	4300	6503	SO:0001819	synonymous_variant	5358	exon9			ACCAAAAGGACAA	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.936A>G	X.37:g.114874764A>G		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	154	3	NM_005032	0	0	133	133	0	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Silent	SNP	ENST00000420625.2	37	CCDS14568.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.303651	0.23736	.	.	ENSG00000102024	ENST00000497870	.	.	.	5.67	3.33	0.38152	.	.	.	.	.	T	0.57475	0.2056	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52079	-0.8623	4	.	.	.	-23.4399	7.8255	0.29313	0.8273:0.0:0.1727:0.0	.	.	.	.	G	33	.	.	R	+	1	2	PLS3	114781020	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.820000	0.55693	0.797000	0.33971	0.486000	0.48141	AGG	.		0.348	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			G	114874764	A	G	114874764	2	3	43	1	0	0	0	0	0	0	0	1	12134	69	3	3		3	PLS3	23	114874764	Silent	SNP	A	TCGA-B3-3926-01A-01D-1252-08	101238908	114874764	40395796	35	3956											
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16952767	16952767	+	3'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcctcaacatcttagcCtttgcggcgctgtactacaa	8	13	6	14	2	3	0	1	0	2	0	4	0	4	0	2	1	5	2	2	1	5	5	rs373089425		TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chrY:16952767C>T	ENST00000476359.1	+	0	2621							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.A692A(1)		large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						ACATCTTAGCCTTTGCGGCGC	0.502																																					p.A692A		.											.	.	1	Substitution - coding silent(1)	prostate(1)	c.C2076T						.	C	,	0,571		0,571	53	72	66		1572,2076	-3.8	0	Y		66	1,1871		1,1871	no	coding-synonymous,coding-synonymous	NLGN4Y	NM_001206850.1,NM_014893.4	,	1,2442	T,C		0.0534,0.0,0.0409	,	524/649,692/817	16952767	1,2442	974	2291	3265	SO:0001624	3_prime_UTR_variant	22829	exon6			CTTAGCCTTTGCG		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*2618C>T	Y.37:g.16952767C>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_014893	0	0	0	2	2	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Silent	SNP	ENST00000476359.1	37																																																																																				.		0.502	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		T	16952767	C	T	16952767	1	4	43	0	1	0	0	0	0	0	0	0	10491	668	24	2		2	NLGN4Y	24	16952767	3'UTR	SNP	C	TCGA-B3-3926-01A-01D-1252-08		16952767	42420799	36	3957											
LRIG2	9860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	113616165	113616165	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcaggtctctgccccgcgcCctgctcctgccgcattcctc	3	9	9	20	3	1	0	0	0	1	0	5	0	3	0	6	1	4	3	6	1	0	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:113616165C>A	ENST00000361127.5	+	1	335	c.137C>A	c.(136-138)cCc>cAc	p.P46H	RP11-31F15.2_ENST00000421157.1_lincRNA	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	46	LRRNT.				innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TGCCCCGCGCCCTGCTCCTGC	0.652											OREG0013684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P46H		.											.	LRIG2-229	0			c.C137A						.						86	99	95					1																	113616165		2203	4299	6502	SO:0001583	missense	9860	exon1			CCGCGCCCTGCTC	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"Immunoglobulin superfamily / I-set domain containing"	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.137C>A	1.37:g.113616165C>A	ENSP00000355396:p.Pro46His	Somatic	354	1	1451	WXS	Illumina HiSeq	Phase_I	360	69	NM_014813	0	0	1	2	1	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858502	0.32791	.	.	ENSG00000198799	ENST00000361127	T	0.61859	0.07	5.05	-1.12	0.09808	.	0.293082	0.31760	N	0.007115	T	0.24547	0.0595	L	0.52573	1.65	0.36317	D	0.857988	B	0.02656	0.0	B	0.01281	0.0	T	0.02885	-1.1098	10	0.45353	T	0.12	.	4.1545	0.10254	0.159:0.3987:0.0:0.4423	.	46	O94898	LRIG2_HUMAN	H	46	ENSP00000355396:P46H	ENSP00000355396:P46H	P	+	2	0	LRIG2	113417688	0.631000	0.27164	0.487000	0.27428	0.620000	0.37586	-0.116000	0.10724	-0.400000	0.07656	-0.137000	0.14449	CCC	.		0.652	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		A	113616165	C	A	113616165	3	1	44	1	0	0	0	0	1	0	0	0	8970	623	22	4	139	4	LRIG2	1	113616165	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08		113616165	135634456	1	3958											
ATP1A1	476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	116941400	116941400	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctttgcctcaattgtgactgGagtagaggaaggtgagagct	10	11	14	6	0	1	3	1	2	0	2	1	6	1	5	1	3	2	2	1	3	3	3	rs11540954		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:116941400G>C	ENST00000295598.5	+	16	2534	c.2282G>C	c.(2281-2283)gGa>gCa	p.G761A	ATP1A1_ENST00000369496.4_Missense_Mutation_p.G730A|ATP1A1_ENST00000537345.1_Missense_Mutation_p.G761A	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	761					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	ATTGTGACTGGAGTAGAGGAA	0.438																																					p.G761A		.											.	ATP1A1-91	0			c.G2282C						.						138	136	136					1																	116941400		2203	4300	6503	SO:0001583	missense	476	exon16			TGACTGGAGTAGA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2282G>C	1.37:g.116941400G>C	ENSP00000295598:p.Gly761Ala	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	178	56	NM_000701	0	0	0	0	0	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988230	0.93106	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000369496	D;D;D	0.91577	-2.87;-2.87;-2.86	5.23	5.23	0.72850	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.88937	0.6573	N	0.11106	0.095	0.80722	D	1	D;D	0.65815	0.995;0.992	D;D	0.70227	0.968;0.929	D	0.91640	0.5326	10	0.66056	D	0.02	.	19.0012	0.92834	0.0:0.0:1.0:0.0	rs11540954	761;761	F5H3A1;P05023	.;AT1A1_HUMAN	A	761;761;730	ENSP00000295598:G761A;ENSP00000445306:G761A;ENSP00000358508:G730A	ENSP00000295598:G761A	G	+	2	0	ATP1A1	116742923	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.657000	0.98554	2.718000	0.92993	0.655000	0.94253	GGA	.		0.438	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116941400	G	C	116941400	3	2	44	1	0	0	0	0	1	0	0	0	1129	1174	41	4	2360	4	ATP1A1	1	116941400	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	3325235	116941400	132309221	2	3959											
ATP1B1	481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169096584	169096584	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaatgatgaaacttatggcTacaaagagggcaaaccgtgc	16	8	10	7	1	0	3	0	2	0	1	0	3	0	3	1	2	4	2	1	2	7	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:169096584T>C	ENST00000367816.1	+	5	1034	c.505T>C	c.(505-507)Tac>Cac	p.Y169H	ATP1B1_ENST00000367815.4_Missense_Mutation_p.Y169H|ATP1B1_ENST00000367813.3_Missense_Mutation_p.Y161H|ATP1B1_ENST00000499679.3_Missense_Mutation_p.Y113H			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	169					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					AACTTATGGCTACAAAGAGGG	0.388																																					p.Y169H		.											.	ATP1B1-540	0			c.T505C						.						104	101	102					1																	169096584		2203	4300	6503	SO:0001583	missense	481	exon4			TATGGCTACAAAG	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.505T>C	1.37:g.169096584T>C	ENSP00000356790:p.Tyr169His	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	188	58	NM_001677	0	0	339	912	573	Q5TGZ3	Missense_Mutation	SNP	ENST00000367816.1	37	CCDS1276.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.574319	0.86542	.	.	ENSG00000143153	ENST00000367816;ENST00000367815;ENST00000499679;ENST00000367813	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	6.02	6.02	0.97574	.	0.049448	0.85682	D	0.000000	T	0.72087	0.3417	M	0.92738	3.34	0.42584	D	0.993227	D	0.76494	0.999	D	0.76071	0.987	T	0.80130	-0.1511	9	0.87932	D	0	-19.3541	16.5446	0.84426	0.0:0.0:0.0:1.0	.	169	P05026	AT1B1_HUMAN	H	169;169;113;161	ENSP00000356790:Y169H;ENSP00000356789:Y169H;ENSP00000423450:Y113H;ENSP00000356787:Y161H	ENSP00000356787:Y161H	Y	+	1	0	ATP1B1	167363208	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	7.388000	0.79795	2.311000	0.77944	0.533000	0.62120	TAC	.		0.388	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			C	169096584	T	C	169096584	3	2	44	1	0	0	0	0	1	0	0	0	1133	1522	53	3	519	3	ATP1B1	1	169096584	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	52155184	169096584	80154037	3	3960											
SELE	6401	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169698749	169698749	+	Frame_Shift_Del	DEL	T	T	-																															ggttgtgttccatgggaagcTtccagggttttggaaacatt																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:169698749delT	ENST00000333360.7	-	6	920	c.781delA	c.(781-783)agcfs	p.S261fs	SELE_ENST00000367781.4_Frame_Shift_Del_p.S261fs|SELE_ENST00000367776.1_Frame_Shift_Del_p.S261fs|SELE_ENST00000367777.1_Frame_Shift_Del_p.S261fs|SELE_ENST00000367779.4_Frame_Shift_Del_p.S261fs|SELE_ENST00000367782.4_Frame_Shift_Del_p.S261fs|SELE_ENST00000367775.1_Frame_Shift_Del_p.S199fs|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367780.4_Frame_Shift_Del_p.S199fs|SELE_ENST00000367774.1_Frame_Shift_Del_p.S261fs	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	261	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.S261G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	CATGGGAAGCTTCCAGGGTTT	0.448																																					p.S261fs		.											.	SELE-95	1	Substitution - Missense(1)	lung(1)	c.781delA						.						137	130	132					1																	169698749		2203	4300	6503	SO:0001589	frameshift_variant	6401	exon6			.	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"CD molecules"	10718	protein-coding gene	gene with protein product		131210	"endothelial adhesion molecule 1"	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.781delA	1.37:g.169698749delT	ENSP00000331736:p.Ser261fs	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	250	97	NM_000450	0	0	0	0	0	A2RRD6|P16111	Frame_Shift_Del	DEL	ENST00000333360.7	37	CCDS1283.1																																																																																			.		0.448	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		-	169698749	T	-	169698749	7	5	44	1	0	1	0	1	0	0	0	0	14045	1609	56	0	1083	0	SELE	1	169698749	Frame_Shift_Del	DEL	T	TCGA-B3-4103-01A-01D-1458-08	602165	169698749	79551872	4	3961											
CEP350	9857	hgsc.bcm.edu;broad.mit.edu	37	chr1	179965912	179965912	+	Frame_Shift_Del	DEL	A	A	-																															accagcaattgatgcattgcAaaattctgaatgtttgatta																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:179965912delA	ENST00000367607.3	+	6	1038	c.620delA	c.(619-621)caafs	p.Q207fs		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	207					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						GATGCATTGCAAAATTCTGAA	0.378																																					p.Q207fs		.											.	CEP350-26	0			c.620delA						.						78	73	75					1																	179965912		2203	4300	6503	SO:0001589	frameshift_variant	9857	exon6			.	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.620delA	1.37:g.179965912delA	ENSP00000356579:p.Gln207fs	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	55	12	NM_014810	0	0	0	0	0	O75068|Q8TDK3|Q8WY20	Frame_Shift_Del	DEL	ENST00000367607.3	37	CCDS1336.1																																																																																			.		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		-	179965912	A	-	179965912	7	5	44	1	0	1	0	1	0	0	0	0	3260	130	5	0	638	0	CEP350	1	179965912	Frame_Shift_Del	DEL	A	TCGA-B3-4103-01A-01D-1458-08	10267163	179965912	69284709	5	3962											
ELF3	1999	broad.mit.edu;bcgsc.ca	37	chr1	201981806	201981814	+	In_Frame_Del	DEL	GGTCAGCAA	GGTCAGCAA	-																															cccaggagctgctggacgacGgtcagcaagccagcccctac																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	GGTCAGCAA	GGTCAGCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:201981806_201981814delGGTCAGCAA	ENST00000359651.3	+	4	3709_3717	c.517_525delGGTCAGCAA	c.(517-525)ggtcagcaadel	p.GQQ173del	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367284.5_In_Frame_Del_p.GQQ173del|ELF3_ENST00000367283.3_In_Frame_Del_p.GQQ173del|RP11-465N4.4_ENST00000419190.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						GCTGGACGACGGTCAGCAAGCCAGCCCCT	0.66																																					p.173_175del													.	ELF3-226	0			c.517_525del						.																																			SO:0001651	inframe_deletion	1999	exon5			GACGACGGTCAGC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.517_525delGGTCAGCAA	1.37:g.201981806_201981814delGGTCAGCAA	ENSP00000352673:p.Gly173_Gln175del	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	72	9	NM_001114309	0	0	0	0	0		In_Frame_Del	DEL	ENST00000359651.3	37	CCDS1419.1																																																																																			.		0.66	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		-	201981814	GGTCAGCAA	-	201981806	7	5	44	1	0	1	0	1	0	0	0	0	5068	1116	39	0	531	0	ELF3	1	201981806	In_Frame_Del	DEL	GGTCAGCAA	TCGA-B3-4103-01A-01D-1458-08	22015894	201981806	47268815	6	3963											
GOLT1A	127845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204183026	204183026	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttactctgccattcggtgatGgagatcatgccgcactcagc	8	11	10	12	2	3	2	2	1	1	1	4	3	3	2	2	2	4	1	2	2	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:204183026G>T	ENST00000308302.3	-	1	194	c.9C>A	c.(7-9)tcC>tcA	p.S3S		NM_198447.1	NP_940849.1			golgi transport 1A											kidney(1)|lung(2)|urinary_tract(1)	4	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)			ATTCGGTGATGGAGATCATGC	0.642																																					p.S3S		.											.	GOLT1A-514	0			c.C9A						.						68	53	58					1																	204183026		2203	4300	6503	SO:0001819	synonymous_variant	127845	exon1			GGTGATGGAGATC	BC058832	CCDS1443.1	1q32.1	2010-06-24	2010-06-24		ENSG00000174567	ENSG00000174567			24766	protein-coding gene	gene with protein product			"golgi transport 1 homolog A (S. cerevisiae)"			12477932	Standard	NM_198447		Approved	FLJ42654, CGI-141, YMR292W, GOT1, MGC62027	uc001has.1	Q6ZVE7	OTTHUMG00000036056	ENST00000308302.3:c.9C>A	1.37:g.204183026G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	50	11	NM_198447	0	0	0	2	2		Silent	SNP	ENST00000308302.3	37	CCDS1443.1																																																																																			.		0.642	GOLT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087887.1	NM_198447		T	204183026	G	T	204183026	2	4	44	1	0	0	0	0	0	0	0	1	6590	1335	47	4		4	GOLT1A	1	204183026	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08	2201220	204183026	45067595	7	3964											
GRHL1	29841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	10101557	10101557	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagagaccttcaaggaaggcGttcaggaggtaaggaaacaa	16	5	13	7	1	2	1	2	0	0	1	2	5	2	4	1	5	1	2	1	5	5	3	rs140278187		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:10101557G>A	ENST00000324907.9	+	4	797	c.661G>A	c.(661-663)Gtt>Att	p.V221I	GRHL1_ENST00000405379.2_Missense_Mutation_p.V221I|GRHL1_ENST00000324883.5_Silent_p.A57A	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	221					cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		CAAGGAAGGCGTTCAGGAGGT	0.463													G|||	1	0.000199681	0	0	5008	,	,		19940	0		0.001	False		,,,				2504	0				p.V221I		.											.	GRHL1-92	0			c.G661A						.	G	ILE/VAL	0,4406		0,0,2203	77	76	76		661	4.6	1	2	dbSNP_134	76	6,8594	5.0+/-18.6	0,6,4294	yes	missense	GRHL1	NM_198182.2	29	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	221/619	10101557	6,13000	2203	4300	6503	SO:0001583	missense	29841	exon4			GAAGGCGTTCAGG	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"transcription factor CP2-like 2"	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.661G>A	2.37:g.10101557G>A	ENSP00000324693:p.Val221Ile	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	170	54	NM_198182	0	0	0	0	0	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	37	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	G	13.48	2.248540	0.39797	0.0	6.98E-4	ENSG00000134317	ENST00000405379;ENST00000324907	T;T	0.11604	2.76;2.76	5.5	4.63	0.57726	.	0.205183	0.45361	D	0.000378	T	0.07369	0.0186	N	0.08118	0	0.80722	D	1	P	0.39520	0.676	B	0.41666	0.363	T	0.47394	-0.9121	10	0.23302	T	0.38	.	14.5094	0.67774	0.0707:0.0:0.9293:0.0	.	221	Q9NZI5	GRHL1_HUMAN	I	221	ENSP00000384209:V221I;ENSP00000324693:V221I	ENSP00000324693:V221I	V	+	1	0	GRHL1	10019008	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.852000	0.55934	1.337000	0.45525	-0.244000	0.11960	GTT	G|1.000;A|0.000		0.463	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		A	10101557	G	A	10101557	3	1	44	1	0	0	0	0	1	0	0	0	6784	1145	40	1	675	1	GRHL1	2	10101557	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		10101557	233097816	8	3965											
BRE	9577	broad.mit.edu	37	chr2	28550286	28550286	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagggcctcagagggagagAgaactgctcagtaattttga	12	8	15	6	0	2	4	2	1	0	3	2	7	2	5	1	3	2	2	1	3	2	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:28550286A>G	ENST00000344773.2	+	12	1372	c.1234A>G	c.(1234-1236)Aga>Gga	p.R412G	BRE_ENST00000361704.2_Intron|BRE_ENST00000379632.2_Intron|BRE_ENST00000342045.2_Intron|BRE_ENST00000379624.1_Intron	NM_004899.4	NP_004890.2			brain and reproductive organ-expressed (TNFRSF1A modulator)											NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					AGAGGGAGAGAGAACTGCTCA	0.478																																					p.R412G													.	BRE-228	0			c.A1234G						.						68	79	75					2																	28550286		2203	4300	6503	SO:0001583	missense	9577	exon12			GGAGAGAGAACTG	AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 4"	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000344773.2:c.1234A>G	2.37:g.28550286A>G	ENSP00000343412:p.Arg412Gly	Somatic	301	0		WXS	Illumina HiSeq	Phase_I	307	7	NM_004899	0	0	15	15	0		Missense_Mutation	SNP	ENST00000344773.2	37	CCDS1764.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.893537	0.33442	.	.	ENSG00000158019	ENST00000344773	.	.	.	3.24	0.643	0.17770	.	.	.	.	.	T	0.40347	0.1113	.	.	.	0.33502	D	0.590076	B	0.20780	0.048	B	0.18263	0.021	T	0.45249	-0.9274	7	0.87932	D	0	0.1143	7.4919	0.27466	0.537:0.463:0.0:0.0	.	412	Q9NXR7-1	.	G	412	.	ENSP00000343412:R412G	R	+	1	2	BRE	28403790	0.042000	0.20092	0.519000	0.27824	0.987000	0.75469	0.226000	0.17776	0.125000	0.18397	0.379000	0.24179	AGA	.		0.478	BRE-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215111.1			G	28550286	A	G	28550286	3	3	44	1	0	0	0	0	1	0	0	0	1512	296	11	3	1323	3	BRE	2	28550286	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	18448729	28550286	214649087	9	3966											
TMEM37	6344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	120194829	120194829	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtgggtcatgggttccaTcctcctcctggtgtctttcg	4	14	11	12	1	2	0	1	0	1	0	7	0	6	0	4	3	0	1	4	3	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:120194829T>C	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_Missense_Mutation_p.I129T|TMEM37_ENST00000409826.1_Missense_Mutation_p.I141T	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	ATGGGTTCCATCCTCCTCCTG	0.567																																					p.I129T		.											.	TMEM37-135	0			c.T386C						.						178	170	172					2																	120194829		2203	4300	6503	SO:0001628	intergenic_variant	140738	exon2			GTTCCATCCTCCT		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"GPCR / Class B : Glucagon receptors"	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194829T>C		Somatic	464	0		WXS	Illumina HiSeq	Phase_I	471	126	NM_183240	0	0	31	58	27	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	T	0.231	-1.020958	0.02061	.	.	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.97	-0.356	0.12583	.	1.570890	0.03832	N	0.269166	T	0.20129	0.0484	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.11542	-1.0583	9	0.28530	T	0.3	-15.3671	1.4103	0.02290	0.1454:0.1645:0.1419:0.5481	.	129	Q8WXS4	CCGL_HUMAN	T	141;129	.	ENSP00000303148:I129T	I	+	2	0	TMEM37	119911299	0.156000	0.22821	0.071000	0.20095	0.017000	0.09413	0.523000	0.22925	-0.194000	0.10399	0.533000	0.62120	ATC	.		0.567	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			C	120194829	T	C	120194829	1	2	44	0	1	0	0	0	0	0	0	0	16190	1435	50	3		3	TMEM37	2	120194829	IGR	SNP	T	TCGA-B3-4103-01A-01D-1458-08	91644543	120194829	123004544	10	3967											
NEB	4703	broad.mit.edu	37	chr2	152484285	152484285	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacatcatcttggggtcatCttcaatgttccgggctccaa	8	12	8	13	1	5	0	3	0	2	0	7	0	7	0	3	3	0	2	3	3	2	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:152484285C>A	ENST00000172853.10	-	65	9313	c.9166G>T	c.(9166-9168)Gat>Tat	p.D3056Y	NEB_ENST00000397345.3_Missense_Mutation_p.D3299Y|NEB_ENST00000409198.1_Missense_Mutation_p.D3056Y|NEB_ENST00000604864.1_Missense_Mutation_p.D3299Y|NEB_ENST00000427231.2_Missense_Mutation_p.D3299Y|NEB_ENST00000603639.1_Missense_Mutation_p.D3299Y			P20929	NEBU_HUMAN	nebulin	3056					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTGGGGTCATCTTCAATGTTC	0.453																																					p.D3299Y													.	NEB-145	0			c.G9895T						.						263	247	252					2																	152484285		1915	4130	6045	SO:0001583	missense	4703	exon69			GGTCATCTTCAAT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.9166G>T	2.37:g.152484285C>A	ENSP00000172853:p.Asp3056Tyr	Somatic	538	3		WXS	Illumina HiSeq	Phase_I	517	7	NM_001271208	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	26.9	4.780183	0.90195	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.85106	0.5621	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87186	0.2231	10	0.87932	D	0	.	19.5796	0.95461	0.0:1.0:0.0:0.0	.	3056	P20929	NEBU_HUMAN	Y	3056;3299;3299;3056	ENSP00000386259:D3056Y;ENSP00000380505:D3299Y;ENSP00000416578:D3299Y;ENSP00000172853:D3056Y	ENSP00000172853:D3056Y	D	-	1	0	NEB	152192531	1.000000	0.71417	0.948000	0.38648	0.941000	0.58515	7.683000	0.84093	2.624000	0.88883	0.655000	0.94253	GAT	.		0.453	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152484285	C	A	152484285	3	1	44	1	0	0	0	0	1	0	0	0	10328	913	32	4	16247	4	NEB	2	152484285	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	32289456	152484285	90715088	11	3968											
KCNH7	90134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	163241347	163241347	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcatcatcaatggaggagAtgaaagatgaggatctgctt	13	11	12	5	0	4	4	3	2	1	2	4	7	4	6	0	3	1	2	0	3	2	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:163241347A>G	ENST00000332142.5	-	13	2912	c.2813T>C	c.(2812-2814)aTc>aCc	p.I938T		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	938					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AATGGAGGAGATGAAAGATGA	0.408																																					p.I938T	GBM(196;1492 2208 17507 24132 45496)	.											.	KCNH7-95	0			c.T2813C						.						242	233	236					2																	163241347		2203	4300	6503	SO:0001583	missense	90134	exon13			GAGGAGATGAAAG	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2813T>C	2.37:g.163241347A>G	ENSP00000331727:p.Ile938Thr	Somatic	459	1		WXS	Illumina HiSeq	Phase_I	437	141	NM_033272	0	0	0	0	0	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	37	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	A	8.070	0.770061	0.15983	.	.	ENSG00000184611	ENST00000332142	D	0.98474	-4.95	5.6	4.45	0.53987	.	0.526834	0.21408	N	0.075025	D	0.92446	0.7602	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	D	0.88732	0.3237	10	0.10636	T	0.68	.	9.6489	0.39886	0.9219:0.0:0.0781:0.0	.	938	Q9NS40	KCNH7_HUMAN	T	938	ENSP00000331727:I938T	ENSP00000331727:I938T	I	-	2	0	KCNH7	162949593	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.587000	0.53957	2.141000	0.66446	0.533000	0.62120	ATC	.		0.408	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		G	163241347	A	G	163241347	3	3	44	1	0	0	0	0	1	0	0	0	8058	333	12	3	793	3	KCNH7	2	163241347	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	10757062	163241347	79958026	12	3969											
GRM2	2912	broad.mit.edu	37	chr3	51746862	51746862	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttcacccgttctgaggatgCccgggagctgcttgctgcca	5	10	13	13	2	2	1	1	1	1	0	2	3	2	3	3	2	5	5	3	2	0	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:51746862C>T	ENST00000395052.3	+	3	1058	c.824C>T	c.(823-825)gCc>gTc	p.A275V	GRM2_ENST00000475478.1_Intron|GRM2_ENST00000442933.2_Missense_Mutation_p.A275V	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	275					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TCTGAGGATGCCCGGGAGCTG	0.677																																					p.A275V													.	GRM2-522	0			c.C824T						.						27	28	28					3																	51746862		2202	4295	6497	SO:0001583	missense	2912	exon3			AGGATGCCCGGGA	L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.824C>T	3.37:g.51746862C>T	ENSP00000378492:p.Ala275Val	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	116	4	NM_000839	0	0	0	0	0	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	c	15.79	2.937342	0.52972	.	.	ENSG00000164082	ENST00000395052;ENST00000442933	D;D	0.83506	-1.73;-1.73	5.23	5.23	0.72850	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.74535	0.3729	N	0.26042	0.785	0.80722	D	1	P	0.36438	0.553	B	0.37692	0.256	T	0.71307	-0.4632	10	0.07813	T	0.8	.	19.2131	0.93765	0.0:1.0:0.0:0.0	.	275	Q14416	GRM2_HUMAN	V	275	ENSP00000378492:A275V;ENSP00000408906:A275V	ENSP00000296479:A275V	A	+	2	0	GRM2	51721902	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.804000	0.85993	2.633000	0.89246	0.645000	0.84053	GCC	.		0.677	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51746862	C	T	51746862	3	4	44	1	0	0	0	0	1	0	0	0	6818	739	26	2	830	2	GRM2	3	51746862	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08		51746862	146275568	13	3970											
ITGB5	3693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	124515613	124515614	+	Nonsense_Mutation	DNP	CC	CC	AT																															ccgcagggcaaacacatgctCcgtgtgtctgctgggacagc																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:124515613_124515614CC>AT	ENST00000296181.4	-	10	1610_1611	c.1314_1315GG>AT	c.(1312-1317)acGGag>acATag	p.E439*		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	439					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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AACACATGCTCCGTGTGTCTGC	0.609																																					p.E439*		.											.	ITGB5	0			c.G1314A						.																																			SO:0001587	stop_gained	3693	exon10			ATGCTCCGTGTGT	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1314_1315delinsAT	3.37:g.124515613_124515614delinsAT	ENSP00000296181:p.Glu439*	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	91	24		0	0	0	0	0	B0LPF8|B2RD70	Nonsense_Mutation	DNP	ENST00000296181.4	37	CCDS3030.1																																																																																			.		0.609	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		AT	124515614	CC	AT	124515613	4	1	44	1	0	0	0	0	0	1	0	0	7919	864	30	4	1108	4	ITGB5	3	124515613	Nonsense_Mutation	DNP	CC	TCGA-B3-4103-01A-01D-1458-08	72768751	124515613	73506817	14	3971											
MFN1	55669	ucsc.edu	37	chr3	179094914	179094914	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaccttttaacactggatgtTaagaaaaaaatcaaggaggt	18	10	8	5	0	1	1	1	0	0	1	1	3	1	3	1	3	2	1	1	3	7	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:179094914T>G	ENST00000471841.1	+	11	1308	c.1182T>G	c.(1180-1182)gtT>gtG	p.V394V	MFN1_ENST00000263969.5_Silent_p.V394V|MFN1_ENST00000280653.7_Silent_p.V394V	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	394					mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			CACTGGATGTTAAGAAAAAAA	0.358																																					p.V394V													.	MFN1-155	0			c.T1182G						.						66	65	65					3																	179094914		2203	4300	6503	SO:0001819	synonymous_variant	55669	exon11			GGATGTTAAGAAA	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.1182T>G	3.37:g.179094914T>G		Somatic	99	0		WXS	Illumina HiSeq		151	1	NM_033540	0	0	69	81	12	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Silent	SNP	ENST00000471841.1	37	CCDS3228.1																																																																																			.		0.358	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		G	179094914	T	G	179094914	2	3	44	1	0	0	0	0	0	0	0	1	9548	1741	61	5		5	MFN1	3	179094914	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08	54579301	179094914	18927516	15	3972											
PCYT1A	5130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	195974373	195974373	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagcctttgaagttgtgtgtGagctcatcactgcaaactgg	10	12	11	8	0	2	2	2	2	0	0	2	2	2	2	1	1	4	3	1	1	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:195974373G>A	ENST00000292823.2	-	6	523	c.351C>T	c.(349-351)ctC>ctT	p.L117L	PCYT1A_ENST00000491544.1_5'UTR|PCYT1A_ENST00000419333.1_Silent_p.L117L|PCYT1A_ENST00000431016.1_Silent_p.L117L	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	117					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	AGTTGTGTGTGAGCTCATCAC	0.527																																					p.L117L		.											.	PCYT1A-90	0			c.C351T						.						171	138	149					3																	195974373		2203	4300	6503	SO:0001819	synonymous_variant	5130	exon6			GTGTGTGAGCTCA	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.351C>T	3.37:g.195974373G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	245	63	NM_005017	0	0	27	37	10	A9LYK9|D3DXB1|Q86Y88	Silent	SNP	ENST00000292823.2	37	CCDS3315.1																																																																																			.		0.527	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		A	195974373	G	A	195974373	2	1	44	1	0	0	0	0	0	0	0	1	11636	1277	45	2		2	PCYT1A	3	195974373	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08	16879459	195974373	2048057	16	3973											
LRRC33	375387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	196387840	196387840	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aatcagatctcactttgtccCctgccagctgcctcggaccg	7	10	8	16	2	2	1	2	0	1	1	5	2	3	2	5	1	3	1	5	1	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:196387840C>T	ENST00000328557.4	+	3	1529	c.1326C>T	c.(1324-1326)ccC>ccT	p.P442P		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	442					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CACTTTGTCCCCTGCCAGCTG	0.592																																					p.P442P		.											.	LRRC33-92	0			c.C1326T						.						144	148	147					3																	196387840		2203	4300	6503	SO:0001819	synonymous_variant	375387	exon3			TTGTCCCCTGCCA	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1326C>T	3.37:g.196387840C>T		Somatic	439	1		WXS	Illumina HiSeq	Phase_I	489	202	NM_198565	0	0	9	9	0		Silent	SNP	ENST00000328557.4	37	CCDS3319.1																																																																																			.		0.592	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		T	196387840	C	T	196387840	2	4	44	1	0	0	0	0	0	0	0	1	9013	610	22	2		2	LRRC33	3	196387840	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08	413467	196387840	1634590	17	3974											
CLOCK	9575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	56301654	56301654	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagttgctgctgttgctgAgactgatgttgctggtgatg	5	15	15	6	0	0	4	0	4	0	1	0	5	0	4	0	1	4	7	0	1	0	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:56301654A>T	ENST00000309964.4	-	22	2719	c.2469T>A	c.(2467-2469)tcT>tcA	p.S823S	CLOCK_ENST00000381322.1_Silent_p.S823S|CLOCK_ENST00000513440.1_Silent_p.S823S	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	823	Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.|Poly-Gln.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			GCTGTTGCTGAGACTGATGTT	0.527																																					p.S823S		.											.	CLOCK-515	0			c.T2469A						.						273	230	244					4																	56301654		2203	4300	6503	SO:0001819	synonymous_variant	9575	exon23			TTGCTGAGACTGA	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.2469T>A	4.37:g.56301654A>T		Somatic	205	0		WXS	Illumina HiSeq	Phase_I	195	62	NM_004898	0	0	5	11	6	A0AV01|A2I2N9|O14516|Q9UIT8	Silent	SNP	ENST00000309964.4	37	CCDS3500.1																																																																																			.		0.527	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		T	56301654	A	T	56301654	2	4	44	1	0	0	0	0	0	0	0	1	3555	291	11	5		5	CLOCK	4	56301654	Silent	SNP	A	TCGA-B3-4103-01A-01D-1458-08		56301654	134852622	18	3975											
UGT2B7	7364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	69978199	69978199	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagagaatgttatgaaattAtcaagaattcaacatgatca	20	11	6	4	0	3	4	3	2	0	2	3	5	3	4	0	0	1	1	0	0	8	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:69978199A>G	ENST00000305231.7	+	6	1381	c.1335A>G	c.(1333-1335)ttA>ttG	p.L445L	UGT2B7_ENST00000509763.1_3'UTR|UGT2B7_ENST00000508661.1_3'UTR	NM_001074.2	NP_001065.2	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	445					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TTATGAAATTATCAAGAATTC	0.393																																					p.L445L		.											.	UGT2B7-92	0			c.A1335G						.						66	70	69					4																	69978199		2203	4300	6503	SO:0001819	synonymous_variant	7364	exon6			GAAATTATCAAGA	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000305231.7:c.1335A>G	4.37:g.69978199A>G		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	252	66	NM_001074	0	0	8	40	32	B2R810|Q6GTW0	Silent	SNP	ENST00000305231.7	37	CCDS3526.1																																																																																			.		0.393	UGT2B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251560.1	NM_001074		G	69978199	A	G	69978199	2	3	44	1	0	0	0	0	0	0	0	1	16995	446	16	3		3	UGT2B7	4	69978199	Silent	SNP	A	TCGA-B3-4103-01A-01D-1458-08	13676545	69978199	121176077	19	3976											
ARHGAP24	83478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	86921691	86921691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcctccatgatgaactggAtcaggagaggaaaaagttca	15	7	12	7	0	2	3	2	2	0	1	3	7	3	5	2	3	2	1	2	3	3	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:86921691A>G	ENST00000395184.1	+	10	2529	c.2063A>G	c.(2062-2064)gAt>gGt	p.D688G	RP13-514E23.2_ENST00000610225.1_RNA|ARHGAP24_ENST00000395183.2_Missense_Mutation_p.D593G|ARHGAP24_ENST00000264343.4_Missense_Mutation_p.D595G	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	688					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GATGAACTGGATCAGGAGAGG	0.448																																					p.D688G		.											.	ARHGAP24-227	0			c.A2063G						.						71	73	72					4																	86921691		2203	4300	6503	SO:0001583	missense	83478	exon10			AACTGGATCAGGA	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.2063A>G	4.37:g.86921691A>G	ENSP00000378611:p.Asp688Gly	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	129	53	NM_001025616	0	0	23	34	11	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	37	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.865537	0.91511	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.57095	0.2030	L	0.54323	1.7	0.80722	D	1	D;D;P	0.69078	0.959;0.997;0.877	P;P;B	0.60117	0.637;0.869;0.339	T	0.60439	-0.7263	10	0.87932	D	0	.	16.002	0.80301	1.0:0.0:0.0:0.0	.	593;595;688	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	G	688;593;603;595	ENSP00000378611:D688G;ENSP00000378610:D593G;ENSP00000425589:D603G;ENSP00000264343:D595G	ENSP00000264343:D595G	D	+	2	0	ARHGAP24	87140715	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.248000	0.95456	2.241000	0.73720	0.533000	0.62120	GAT	.		0.448	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		G	86921691	A	G	86921691	3	3	44	1	0	0	0	0	1	0	0	0	873	333	12	3	2213	3	ARHGAP24	4	86921691	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	16943492	86921691	104232585	20	3977											
BMPR1B	658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	96025660	96025660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccccaccccccgtccaaagGtcttgcgttgtaaatgccac	8	8	7	18	2	1	0	0	0	1	0	2	0	2	0	7	1	2	2	7	1	3	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:96025660G>A	ENST00000515059.1	+	4	368	c.85G>A	c.(85-87)Gtc>Atc	p.V29I	BMPR1B_ENST00000394931.1_Missense_Mutation_p.V29I|BMPR1B_ENST00000264568.4_Missense_Mutation_p.V29I|BMPR1B_ENST00000502683.1_Missense_Mutation_p.V29I|BMPR1B_ENST00000440890.2_Missense_Mutation_p.V59I	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	29					BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		CCGTCCAAAGGTCTTGCGTTG	0.423																																					p.V59I		.											.	BMPR1B-1378	0			c.G175A						.						118	113	115					4																	96025660		2203	4300	6503	SO:0001583	missense	658	exon2			CCAAAGGTCTTGC	D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"CD molecules"	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.85G>A	4.37:g.96025660G>A	ENSP00000426617:p.Val29Ile	Somatic	140	1		WXS	Illumina HiSeq	Phase_I	171	54	NM_001256793	0	0	2	2	0	B2R953|B4DSV1|P78366	Missense_Mutation	SNP	ENST00000515059.1	37	CCDS3642.1	.	.	.	.	.	.	.	.	.	.	G	8.620	0.891209	0.17613	.	.	ENSG00000138696	ENST00000515059;ENST00000506363;ENST00000512312;ENST00000509540;ENST00000440890;ENST00000502683;ENST00000264568;ENST00000394931	D;D;D;D;D;D;D;D	0.93426	-1.56;-3.22;-1.56;-1.56;-1.53;-2.65;-1.56;-1.56	5.68	-1.03	0.10102	.	0.948531	0.08708	N	0.905412	D	0.84982	0.5593	N	0.14661	0.345	0.20196	N	0.999927	B	0.02656	0.0	B	0.01281	0.0	T	0.69072	-0.5242	10	0.21540	T	0.41	.	10.8392	0.46704	0.5928:0.0:0.4072:0.0	.	29	O00238	BMR1B_HUMAN	I	29;29;29;29;59;29;29;29	ENSP00000426617:V29I;ENSP00000421144:V29I;ENSP00000425444:V29I;ENSP00000421671:V29I;ENSP00000401907:V59I;ENSP00000424693:V29I;ENSP00000264568:V29I;ENSP00000378389:V29I	ENSP00000264568:V29I	V	+	1	0	BMPR1B	96244683	0.981000	0.34729	0.995000	0.50966	0.773000	0.43773	0.118000	0.15605	-0.111000	0.12001	-0.312000	0.09012	GTC	.		0.423	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203		A	96025660	G	A	96025660	3	1	44	1	0	0	0	0	1	0	0	0	1471	1261	44	2	87	2	BMPR1B	4	96025660	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	9103969	96025660	95128616	21	3978											
SEMA5A	9037	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	9226981	9226981	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacaaaaagaagccatacCgagcggttggtgcagacagg	14	4	14	9	2	0	2	0	0	0	2	0	3	0	2	2	4	4	3	2	4	4	2	rs141767878		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr5:9226981C>T	ENST00000382496.5	-	7	1097	c.432G>A	c.(430-432)tcG>tcA	p.S144S		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	144	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GAAGCCATACCGAGCGGTTGG	0.438																																					p.S144S		.											.	SEMA5A-91	0			c.G432A						.	C		0,4406		0,0,2203	56	60	58		432	4.1	1	5	dbSNP_134	58	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	SEMA5A	NM_003966.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		144/1075	9226981	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	9037	exon7			CCATACCGAGCGG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.432+1G>A	5.37:g.9226981C>T		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	117	6	NM_003966	0	0	0	0	0	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352056	0.41700	0.0	1.16E-4	ENSG00000112902	ENST00000514923	.	.	.	4.93	4.05	0.47172	.	.	.	.	.	T	0.62708	0.2450	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60826	-0.7186	4	.	.	.	.	11.7678	0.51941	0.0:0.823:0.177:0.0	.	.	.	.	I	92	.	.	V	-	1	0	SEMA5A	9279981	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.490000	0.53245	1.185000	0.42971	0.655000	0.94253	GTT	C|1.000;T|0.000		0.438	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		Silent	T	9226981	C	T	9226981	5	4	44	1	0	0	0	0	0	0	1	0	14069	666	23	1	2860	1	SEMA5A	5	9226981	Splice_Site	SNP	C	TCGA-B3-4103-01A-01D-1458-08		9226981	171688279	22	3979											
ADAMTS19	171019	broad.mit.edu;bcgsc.ca	37	chr5	128956361	128956361	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtgtgctgatggtcttcAtatcatgtctggtgaatgga	8	15	12	6	1	4	2	2	2	2	0	5	3	4	3	0	3	1	1	0	3	2	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr5:128956361A>G	ENST00000274487.4	+	9	1656	c.1511A>G	c.(1510-1512)cAt>cGt	p.H504R	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	504	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GATGGTCTTCATATCATGTCT	0.373																																					p.H504R													.	ADAMTS19-295	0			c.A1511G						.						167	153	157					5																	128956361		2203	4300	6503	SO:0001583	missense	171019	exon9			GTCTTCATATCAT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1511A>G	5.37:g.128956361A>G	ENSP00000274487:p.His504Arg	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	276	11	NM_133638	0	0	0	0	0		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893486	0.72639	.	.	ENSG00000145808	ENST00000274487	T	0.62639	0.01	4.51	4.51	0.55191	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	T	0.73140	0.3549	L	0.49126	1.545	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.72459	-0.4287	9	.	.	.	.	14.8814	0.70537	1.0:0.0:0.0:0.0	.	504	Q8TE59	ATS19_HUMAN	R	504	ENSP00000274487:H504R	.	H	+	2	0	ADAMTS19	128984260	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.916000	0.87491	2.246000	0.74042	0.533000	0.62120	CAT	.		0.373	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	128956361	A	G	128956361	3	3	44	1	0	0	0	0	1	0	0	0	264	217	8	3	1545	3	ADAMTS19	5	128956361	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	119729380	128956361	51958899	23	3980											
GABRG2	2566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	161576298	161576298	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggaaaccaagcaaggacaaAgataaaaagaagaaaaaccc	24	1	8	8	1	0	3	0	0	0	3	0	5	0	5	2	2	3	1	2	2	10	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr5:161576298A>T	ENST00000361925.4	+	8	1327	c.1107A>T	c.(1105-1107)aaA>aaT	p.K369N	GABRG2_ENST00000414552.2_Missense_Mutation_p.K409N|GABRG2_ENST00000356592.3_Missense_Mutation_p.K369N|GABRG2_ENST00000393933.4_Missense_Mutation_p.K274N			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	369					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	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)|Ginkgo biloba(DB01381)|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)	GCAAGGACAAAGATAAAAAGA	0.373																																					p.K409N		.											.	GABRG2-95	0			c.A1227T						.						118	102	107					5																	161576298		2203	4300	6503	SO:0001583	missense	2566	exon9			GGACAAAGATAAA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1107A>T	5.37:g.161576298A>T	ENSP00000354651:p.Lys369Asn	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	178	57	NM_198903	0	0	0	0	0	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	37	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.633505	0.47049	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.86865	-2.18;-2.18;-2.15;-2.15	5.61	0.527	0.17084	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.305790	0.04797	N	0.432698	D	0.85535	0.5719	M	0.68317	2.08	0.48511	D	0.999667	B;B;B	0.14438	0.01;0.007;0.01	B;B;B	0.23852	0.02;0.049;0.049	T	0.70916	-0.4742	10	0.56958	D	0.05	.	5.4602	0.16612	0.5861:0.1356:0.2784:0.0	.	409;369;369	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	N	369;409;369;274	ENSP00000349000:K369N;ENSP00000410732:K409N;ENSP00000354651:K369N;ENSP00000377510:K274N	ENSP00000349000:K369N	K	+	3	2	GABRG2	161508876	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	3.143000	0.50608	-0.128000	0.11641	-0.263000	0.10527	AAA	.		0.373	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			T	161576298	A	T	161576298	3	4	44	1	0	0	0	0	1	0	0	0	6191	69	3	5	1261	5	GABRG2	5	161576298	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	32619937	161576298	19338962	24	3981											
VARS	7407	broad.mit.edu	37	chr6	31753451	31753451	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctccaccaccacctgggtgGcaatacctgcatggtcacag	9	8	9	15	0	2	0	1	0	1	0	3	0	2	0	5	3	2	2	5	3	2	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr6:31753451G>A	ENST00000375663.3	-	9	1600	c.1160C>T	c.(1159-1161)gCc>gTc	p.A387V	VARS_ENST00000444930.2_Missense_Mutation_p.A92V	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	387					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CACCTGGGTGGCAATACCTGC	0.632																																					p.A387V													.	VARS-93	0			c.C1160T						.						79	71	74					6																	31753451		1510	2708	4218	SO:0001583	missense	7407	exon9			TGGGTGGCAATAC	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.1160C>T	6.37:g.31753451G>A	ENSP00000364815:p.Ala387Val	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	142	4	NM_006295	0	0	10	10	0	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408749	0.96072	.	.	ENSG00000204394	ENST00000375663;ENST00000444930	T;T	0.25085	1.82;1.82	5.29	5.29	0.74685	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.126292	0.53938	D	0.000054	T	0.67618	0.2912	H	0.99689	4.705	0.54753	D	0.999984	D	0.89917	1.0	D	0.80764	0.994	D	0.83482	0.0065	10	0.87932	D	0	-8.9805	16.4619	0.84059	0.0:0.0:1.0:0.0	.	387	P26640	SYVC_HUMAN	V	387;92	ENSP00000364815:A387V;ENSP00000398317:A92V	ENSP00000364815:A387V	A	-	2	0	VARS	31861430	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	8.678000	0.91211	2.489000	0.83994	0.655000	0.94253	GCC	.		0.632	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		A	31753451	G	A	31753451	3	1	44	1	0	0	0	0	1	0	0	0	17156	1203	42	2	2722	2	VARS	6	31753451	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		31753451	139361616	25	3982											
DST	667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	56499603	56499603	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggagttacaagtacctcaAtttgtctgtagtcacagata	13	13	8	7	0	3	1	2	0	1	1	3	2	3	2	1	1	2	3	1	1	7	6	rs374149298		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr6:56499603A>C	ENST00000361203.3	-	21	2709	c.2702T>G	c.(2701-2703)aTt>aGt	p.I901S	DST_ENST00000446842.2_Missense_Mutation_p.I575S|DST_ENST00000370788.2_Missense_Mutation_p.I901S|DST_ENST00000518935.1_Missense_Mutation_p.I575S|DST_ENST00000370754.5_Missense_Mutation_p.I1079S|DST_ENST00000421834.2_Missense_Mutation_p.I901S|DST_ENST00000312431.6_Missense_Mutation_p.I901S|DST_ENST00000244364.6_Missense_Mutation_p.I575S|DST_ENST00000370769.4_Missense_Mutation_p.I901S|DST_ENST00000370765.6_Missense_Mutation_p.I575S			Q03001	DYST_HUMAN	dystonin	901	SH3.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGTACCTCAATTTGTCTGTA	0.358																																					p.I575S		.											.	DST-523	0			c.T1724G						.						192	193	192					6																	56499603		2203	4300	6503	SO:0001583	missense	667	exon11			ACCTCAATTTGTC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.2702T>G	6.37:g.56499603A>C	ENSP00000354508:p.Ile901Ser	Somatic	316	2		WXS	Illumina HiSeq	Phase_I	332	105	NM_001723	0	0	0	0	0	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	A	23.5	4.426398	0.83667	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;T;T;T;T;T;T;T	0.80033	-0.13;-0.13;-0.13;-0.13;-0.13;-1.33;-0.13;-0.13;-1.33;-1.33;-0.13;-1.33	5.28	5.28	0.74379	.	0.000000	0.49305	D	0.000147	D	0.84156	0.5410	M	0.63428	1.95	0.37034	D	0.896819	D;D;D;D;D;P;D;D	0.89917	0.999;0.998;0.999;0.991;1.0;0.839;0.999;1.0	D;D;D;D;D;P;D;D	0.87578	0.915;0.986;0.915;0.955;0.998;0.872;0.915;0.996	T	0.82149	-0.0600	9	0.25751	T	0.34	.	15.3783	0.74630	1.0:0.0:0.0:0.0	.	901;901;1079;575;575;575;901;575	Q5TBT1;E7ERU2;E9PEB9;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;DYST_HUMAN;.	S	575;1079;901;901;575;901;901;901;575;941;575;575	ENSP00000244364:I575S;ENSP00000359790:I1079S;ENSP00000359805:I901S;ENSP00000400883:I901S;ENSP00000393645:I575S;ENSP00000307959:I901S;ENSP00000359824:I901S;ENSP00000354508:I901S;ENSP00000404924:I575S;ENSP00000431030:I941S;ENSP00000359801:I575S;ENSP00000431003:I575S	ENSP00000244364:I575S	I	-	2	0	DST	56607562	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.139000	0.94554	2.227000	0.72691	0.460000	0.39030	ATT	.		0.358	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56499603	A	C	56499603	3	2	44	1	0	0	0	0	1	0	0	0	4794	101	4	5	18727	5	DST	6	56499603	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	24746152	56499603	114615464	26	3983											
FAM135A	57579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	71234676	71234676	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatagtgaaattacacaaaTggaacacaatctggcatcca	17	8	7	9	1	1	1	0	1	1	0	2	3	2	2	1	2	2	1	1	2	6	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr6:71234676T>A	ENST00000418814.2	+	15	2503	c.1889T>A	c.(1888-1890)aTg>aAg	p.M630K	FAM135A_ENST00000505868.1_Missense_Mutation_p.M630K|FAM135A_ENST00000370479.3_Missense_Mutation_p.M417K|FAM135A_ENST00000505769.1_Missense_Mutation_p.M434K|FAM135A_ENST00000361499.3_Missense_Mutation_p.M434K|FAM135A_ENST00000457062.2_Missense_Mutation_p.M417K	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	630										breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						ATTACACAAATGGAACACAAT	0.393																																					p.M630K		.											.	FAM135A-90	0			c.T1889A						.						70	64	66					6																	71234676		2203	4299	6502	SO:0001583	missense	57579	exon13			CACAAATGGAACA	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"KIAA1411"	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.1889T>A	6.37:g.71234676T>A	ENSP00000410768:p.Met630Lys	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	127	52	NM_001162529	0	0	7	10	3	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	T	10.84	1.464055	0.26335	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.87	3.5	0.40072	.	0.419502	0.28453	N	0.015293	T	0.28928	0.0718	N	0.08118	0	0.27751	N	0.944159	B;B;B;B	0.15473	0.013;0.008;0.011;0.013	B;B;B;B	0.20577	0.03;0.008;0.019;0.03	T	0.27571	-1.0070	10	0.06494	T	0.89	.	8.0899	0.30795	0.0:0.2862:0.0:0.7138	.	630;630;434;417	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	K	630;417;434;417;434;630	ENSP00000410768:M630K;ENSP00000359510:M417K;ENSP00000423785:M434K;ENSP00000409201:M417K;ENSP00000354913:M434K;ENSP00000423307:M630K	ENSP00000354913:M434K	M	+	2	0	FAM135A	71291397	0.983000	0.35010	0.999000	0.59377	0.962000	0.63368	0.518000	0.22847	0.576000	0.29452	0.533000	0.62120	ATG	.		0.393	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		A	71234676	T	A	71234676	3	1	44	1	0	0	0	0	1	0	0	0	5464	1464	51	5	2017	5	FAM135A	6	71234676	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	14735073	71234676	99880391	27	3984											
CCDC132	55610	broad.mit.edu	37	chr7	92882045	92882045	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatagtattgaacaagtatAtttttctgtggattcatttg	12	19	7	3	0	2	1	1	1	1	0	2	2	2	2	0	1	1	2	0	1	7	10			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:92882045A>G	ENST00000305866.5	+	3	310	c.182A>G	c.(181-183)tAt>tGt	p.Y61C	CCDC132_ENST00000317751.6_5'UTR|CCDC132_ENST00000544910.1_Missense_Mutation_p.Y31C|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000251739.5_Missense_Mutation_p.Y61C|CCDC132_ENST00000541136.1_Intron	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	61						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GAACAAGTATATTTTTCTGTG	0.323																																					p.Y61C													.	CCDC132-90	0			c.A182G						.						90	98	95					7																	92882045		2203	4300	6503	SO:0001583	missense	55610	exon3			AAGTATATTTTTC	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.182A>G	7.37:g.92882045A>G	ENSP00000307666:p.Tyr61Cys	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	219	4	NM_024553	0	0	4	4	0	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331798	0.81801	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000458530	.	.	.	5.42	5.42	0.78866	Vacuolar protein sorting-associated protein 54 (1);	0.000000	0.85682	D	0.000000	T	0.78426	0.4281	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.995;0.997;0.996	T	0.81104	-0.1084	9	0.87932	D	0	-33.2209	15.7673	0.78138	1.0:0.0:0.0:0.0	.	31;61;61	F5H5U7;Q96JG6;Q96JG6-2	.;CC132_HUMAN;.	C	61;61;31;61	.	ENSP00000251739:Y61C	Y	+	2	0	CCDC132	92719981	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.400000	0.90200	2.198000	0.70561	0.482000	0.46254	TAT	.		0.323	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92882045	A	G	92882045	3	3	44	1	0	0	0	0	1	0	0	0	2773	449	16	3	192	3	CCDC132	7	92882045	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08		92882045	66256618	28	3985											
AP4M1	9179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99700326	99700326	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccgtcatttcattcacaTcagacacagcggcctctatt	9	12	7	13	2	5	1	4	0	1	1	5	1	5	1	2	2	1	0	2	2	1	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:99700326T>C	ENST00000359593.4	+	3	334	c.176T>C	c.(175-177)aTc>aCc	p.I59T	MCM7_ENST00000303887.5_5'Flank|AP4M1_ENST00000422582.1_5'UTR|AP4M1_ENST00000478501.1_3'UTR|MCM7_ENST00000343023.6_5'Flank|AP4M1_ENST00000429084.1_Missense_Mutation_p.I66T|AP4M1_ENST00000421755.1_Missense_Mutation_p.I59T|MCM7_ENST00000354230.3_5'Flank	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	59					Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTCATTCACATCAGACACAGC	0.527																																					p.I59T	Pancreas(174;1182 2812 29595 49511)	.											.	AP4M1-90	0			c.T176C						.						142	129	134					7																	99700326		2203	4300	6503	SO:0001583	missense	9179	exon3			TTCACATCAGACA	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"mu-adaptin-related protein-2", "mu subunit of AP-4", "AP-4 adapter complex mu subunit", "adaptor-related protein complex AP-4 mu4 subunit"	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.176T>C	7.37:g.99700326T>C	ENSP00000352603:p.Ile59Thr	Somatic	186	1		WXS	Illumina HiSeq	Phase_I	266	56	NM_004722	0	0	15	19	4	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	37	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.075789	0.55646	.	.	ENSG00000221838	ENST00000429084;ENST00000359593;ENST00000439416;ENST00000421755	T;T;D;T	0.81579	-1.36;-1.36;-1.51;-1.36	5.48	5.48	0.80851	Longin-like (1);AP complex, mu/sigma subunit (1);	0.294221	0.37623	N	0.002007	D	0.84732	0.5537	L	0.56769	1.78	0.80722	D	1	P;B;P;P	0.51449	0.816;0.049;0.905;0.945	B;B;P;P	0.57468	0.177;0.084;0.637;0.821	D	0.85571	0.1234	10	0.56958	D	0.05	-5.926	11.9735	0.53078	0.0:0.0:0.0:1.0	.	59;11;66;59	C9JMG3;B4DKN7;C9JC87;O00189	.;.;.;AP4M1_HUMAN	T	66;59;59;59	ENSP00000403663:I66T;ENSP00000352603:I59T;ENSP00000414286:I59T;ENSP00000412185:I59T	ENSP00000352603:I59T	I	+	2	0	AP4M1	99538262	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	6.448000	0.73469	2.068000	0.61886	0.459000	0.35465	ATC	.		0.527	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		C	99700326	T	C	99700326	3	2	44	1	0	0	0	0	1	0	0	0	753	1435	50	3	186	3	AP4M1	7	99700326	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	6818281	99700326	59438337	29	3986											
CTTNBP2	83992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	117364734	117364734	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagtgttataactggaaacTatggataaagggaaacttcc	16	10	9	6	0	0	0	0	0	0	0	1	3	1	3	1	3	3	1	1	3	8	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:117364734T>A	ENST00000160373.3	-	19	4405	c.4314A>T	c.(4312-4314)atA>atT	p.I1438I		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1438					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AACTGGAAACTATGGATAAAG	0.438																																					p.I1438I		.											.	CTTNBP2-94	0			c.A4314T						.						106	96	100					7																	117364734		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon19			GGAAACTATGGAT		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4314A>T	7.37:g.117364734T>A		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	187	53	NM_033427	0	0	7	8	1	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	2.995	-0.207314	0.06180	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.45	-4.08	0.03963	.	.	.	.	.	T	0.38532	0.1044	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37934	-0.9684	4	.	.	.	-1.618	1.9951	0.03455	0.2862:0.4031:0.1445:0.1662	.	.	.	.	C	926	.	.	S	-	1	0	CTTNBP2	117151970	0.378000	0.25114	0.285000	0.24819	0.253000	0.25986	-0.307000	0.08167	-0.488000	0.06726	-0.408000	0.06270	AGT	.		0.438	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117364734	T	A	117364734	2	1	44	1	0	0	0	0	0	0	0	1	4051	1512	53	5		5	CTTNBP2	7	117364734	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08	17664408	117364734	41773929	30	3987											
CTTNBP2	83992	broad.mit.edu;bcgsc.ca	37	chr7	117396642	117396642	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttctgcatcatctggagaggGatcatggaggcataagtcac	11	10	12	8	0	5	1	3	0	2	1	5	4	5	3	0	4	1	2	0	4	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:117396642G>A	ENST00000160373.3	-	12	3406	c.3315C>T	c.(3313-3315)atC>atT	p.I1105I		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1105					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TCTGGAGAGGGATCATGGAGG	0.498																																					p.I1105I													.	CTTNBP2-94	0			c.C3315T						.						199	168	179					7																	117396642		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon12			GAGAGGGATCATG		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.3315C>T	7.37:g.117396642G>A		Somatic	192	0		WXS	Illumina HiSeq	Phase_I	236	9	NM_033427	0	0	21	21	0	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.822|9.822	1.185943|1.185943	0.21870|0.21870	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000435233;ENST00000416239	.|.	.|.	.|.	5.43|5.43	1.59|1.59	0.23543|0.23543	.|.	.|.	.|.	.|.	.|.	T|T	0.57710|0.57710	0.2072|0.2072	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49418|0.49418	-0.8942|-0.8942	4|4	.|.	.|.	.|.	-5.5934|-5.5934	9.2734|9.2734	0.37686|0.37686	0.2853:0.0:0.7147:0.0|0.2853:0.0:0.7147:0.0	.|.	.|.	.|.	.|.	S|F	593|119;101	.|.	.|.	P|S	-|-	1|2	0|0	CTTNBP2|CTTNBP2	117183878|117183878	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.980000|0.980000	0.70556|0.70556	1.199000|1.199000	0.32235|0.32235	0.075000|0.075000	0.16796|0.16796	0.591000|0.591000	0.81541|0.81541	CCC|TCC	.		0.498	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117396642	G	A	117396642	2	1	44	1	0	0	0	0	0	0	0	1	4051	1164	41	2		2	CTTNBP2	7	117396642	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08	31908	117396642	41742021	31	3988											
ARF5	381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	127229193	127229193	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaactgaagttgggggagAttgtcaccaccatcccaacc	13	7	9	12	0	1	2	1	1	0	1	2	3	2	2	4	2	2	1	4	2	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:127229193A>G	ENST00000000233.5	+	2	278	c.124A>G	c.(124-126)Att>Gtt	p.I42V	ARF5_ENST00000467281.1_3'UTR|GCC1_ENST00000497650.1_Intron	NM_001662.3	NP_001653.1	P84085	ARF5_HUMAN	ADP-ribosylation factor 5	42					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			cervix(2)|kidney(1)|lung(10)|ovary(1)	14						GTTGGGGGAGATTGTCACCAC	0.632											OREG0018287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I42V		.											.	ARF5-228	0			c.A124G						.						84	77	79					7																	127229193		2203	4300	6503	SO:0001583	missense	381	exon2			GGGGAGATTGTCA		CCDS34745.1	7q31.3	2008-07-18			ENSG00000004059	ENSG00000004059		"ADP-ribosylation factors"	658	protein-coding gene	gene with protein product		103188				1993656	Standard	NM_001662		Approved		uc003vmb.2	P84085	OTTHUMG00000023246	ENST00000000233.5:c.124A>G	7.37:g.127229193A>G	ENSP00000000233:p.Ile42Val	Somatic	99	0	1555	WXS	Illumina HiSeq	Phase_I	117	46	NM_001662	0	0	92	240	148	P26437	Missense_Mutation	SNP	ENST00000000233.5	37	CCDS34745.1	.	.	.	.	.	.	.	.	.	.	a	17.35	3.367076	0.61513	.	.	ENSG00000004059	ENST00000000233;ENST00000415666	D;D	0.81821	-1.54;-1.54	5.19	3.96	0.45880	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	N	0.03050	-0.425	0.44635	D	0.997619	B;B	0.10296	0.003;0.003	B;B	0.16289	0.015;0.015	T	0.53746	-0.8395	10	0.29301	T	0.29	-8.2547	9.1237	0.36801	0.8363:0.0:0.0:0.1636	.	42;42	A4D0Z3;P84085	.;ARF5_HUMAN	V	42	ENSP00000000233:I42V;ENSP00000412701:I42V	ENSP00000000233:I42V	I	+	1	0	ARF5	127016429	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.106000	0.77039	1.962000	0.57031	0.444000	0.29173	ATT	.		0.632	ARF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059567.2	NM_001662		G	127229193	A	G	127229193	3	3	44	1	0	0	0	0	1	0	0	0	847	333	12	3	130	3	ARF5	7	127229193	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	9832551	127229193	31909470	32	3989											
KRBA1	84626	broad.mit.edu	37	chr7	149422542	149422542	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccaggagactctaggtctcaGaagcctgaactgcaacccca	12	6	9	14	0	2	3	1	1	2	2	3	4	2	3	4	2	4	1	4	2	4	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:149422542G>C	ENST00000485033.2	+	9	1263	c.1263G>C	c.(1261-1263)caG>caC	p.Q421H	KRBA1_ENST00000479560.1_3'UTR|KRBA1_ENST00000319551.8_Missense_Mutation_p.Q421H|KRBA1_ENST00000255992.10_Missense_Mutation_p.Q421H			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	433										breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTAGGTCTCAGAAGCCTGAAC	0.597																																					.													.	KRBA1-91	0			.						.						36	39	38					7																	149422542		2050	4209	6259	SO:0001583	missense	84626	.			GTCTCAGAAGCCT	AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.1263G>C	7.37:g.149422542G>C	ENSP00000420112:p.Gln421His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	45	4	.	0	0	5	5	0	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Missense_Mutation	SNP	ENST00000485033.2	37		.	.	.	.	.	.	.	.	.	.	G	13.83	2.354201	0.41700	.	.	ENSG00000133619	ENST00000255992;ENST00000319551;ENST00000485033	T;T;T	0.35421	1.31;1.31;1.31	4.65	-0.91	0.10511	.	1.054700	0.07500	N	0.907072	T	0.25568	0.0622	L	0.34521	1.04	0.09310	N	1	B;B	0.23249	0.037;0.082	B;B	0.19946	0.012;0.027	T	0.31586	-0.9938	10	0.52906	T	0.07	-1.5465	6.0403	0.19730	0.1922:0.4524:0.3554:0.0	.	421;421	E7ENE9;A5PL33	.;KRBA1_HUMAN	H	421	ENSP00000255992:Q421H;ENSP00000317165:Q421H;ENSP00000420112:Q421H	ENSP00000255992:Q421H	Q	+	3	2	KRBA1	149053475	0.001000	0.12720	0.002000	0.10522	0.022000	0.10575	0.008000	0.13197	-0.094000	0.12374	0.655000	0.94253	CAG	.		0.597	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534		C	149422542	G	C	149422542	3	2	44	1	0	0	0	0	1	0	0	0	8460	933	33	4	1297	4	KRBA1	7	149422542	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	22193349	149422542	9716121	33	3990											
SLC26A7	115111	broad.mit.edu	37	chr8	92330447	92330447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcccttctcctcttaggtgGccatgtttgtgctgcaactg	4	15	9	13	0	2	0	0	0	2	0	4	0	3	0	3	2	3	3	3	2	2	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:92330447G>A	ENST00000276609.3	+	5	720	c.481G>A	c.(481-483)Gcc>Acc	p.A161T	SLC26A7_ENST00000523719.1_Missense_Mutation_p.A161T|SLC26A7_ENST00000309536.2_Missense_Mutation_p.A161T	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			CTCTTAGGTGGCCATGTTTGT	0.478																																					p.A161T													.	SLC26A7-92	0			c.G481A						.						104	95	98					8																	92330447		2203	4300	6503	SO:0001583	missense	115111	exon5			TAGGTGGCCATGT	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"Solute carriers"	14467	protein-coding gene	gene with protein product		608479	"solute carrier family 26, member 7"			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.481G>A	8.37:g.92330447G>A	ENSP00000276609:p.Ala161Thr	Somatic	254	1		WXS	Illumina HiSeq	Phase_I	278	4	NM_134266	0	0	0	0	0		Missense_Mutation	SNP	ENST00000276609.3	37	CCDS6254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.35|14.35	2.510420|2.510420	0.44660|0.44660	.|.	.|.	ENSG00000147606|ENSG00000147606	ENST00000522862;ENST00000523719;ENST00000276609;ENST00000309536|ENST00000520818	D;D;D;D|.	0.93366|.	-2.96;-3.21;-3.21;-3.21|.	5.95|5.95	4.17|4.17	0.49024|0.49024	.|.	0.566027|.	0.18096|.	N|.	0.151846|.	T|.	0.46073|.	0.1374|.	M|M	0.62723|0.62723	1.935|1.935	0.26123|0.26123	N|N	0.980525|0.980525	B;B|.	0.09022|.	0.001;0.002|.	B;B|.	0.09377|.	0.004;0.002|.	T|.	0.36648|.	-0.9739|.	10|.	0.26408|.	T|.	0.33|.	.|.	7.5583|7.5583	0.27837|0.27837	0.1364:0.0:0.7295:0.134|0.1364:0.0:0.7295:0.134	.|.	161;161|.	Q8TE54-2;Q8TE54|.	.;S26A7_HUMAN|.	T|X	161|28	ENSP00000428881:A161T;ENSP00000428849:A161T;ENSP00000276609:A161T;ENSP00000309504:A161T|.	ENSP00000276609:A161T|.	A|W	+|+	1|3	0|0	SLC26A7|SLC26A7	92399623|92399623	0.997000|0.997000	0.39634|0.39634	0.998000|0.998000	0.56505|0.56505	0.572000|0.572000	0.35998|0.35998	2.809000|2.809000	0.47971|0.47971	0.858000|0.858000	0.35431|0.35431	0.650000|0.650000	0.86243|0.86243	GCC|TGG	.		0.478	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			A	92330447	G	A	92330447	3	1	44	1	0	0	0	0	1	0	0	0	14554	1203	42	2	495	2	SLC26A7	8	92330447	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		92330447	54033575	34	3991											
RBM12B	389677	broad.mit.edu	37	chr8	94746263	94746263	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggagcgcctgaaatgctcCtgaggcggccgcctgaaatg	8	6	15	12	4	0	3	0	3	0	0	1	4	1	4	4	3	2	1	4	3	2	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:94746263C>A	ENST00000399300.2	-	3	2589	c.2376G>T	c.(2374-2376)caG>caT	p.Q792H	RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Missense_Mutation_p.Q672H|RBM12B_ENST00000520961.1_Intron	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	792							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TGAAATGCTCCTGAGGCGGCC	0.637																																					p.Q792H													.	RBM12B-90	0			c.G2376T						.						43	46	45					8																	94746263		1808	4066	5874	SO:0001583	missense	389677	exon3			ATGCTCCTGAGGC		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.2376G>T	8.37:g.94746263C>A	ENSP00000382239:p.Gln792His	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	136	4	NM_203390	0	0	9	9	0	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.322943	0.41096	.	.	ENSG00000183808	ENST00000399300;ENST00000517700	T;T	0.07688	3.17;3.25	4.17	-3.89	0.04193	.	1.818140	0.03196	N	0.174075	T	0.05090	0.0136	N	0.12182	0.205	0.09310	N	0.999993	B	0.23442	0.085	B	0.17098	0.017	T	0.41161	-0.9524	10	0.72032	D	0.01	-0.1022	6.4362	0.21825	0.1265:0.3175:0.0:0.556	.	792	Q8IXT5	RB12B_HUMAN	H	792;672	ENSP00000382239:Q792H;ENSP00000427729:Q672H	ENSP00000382239:Q792H	Q	-	3	2	RBM12B	94815439	0.005000	0.15991	0.014000	0.15608	0.432000	0.31715	-0.419000	0.07071	-0.985000	0.03503	-0.251000	0.11542	CAG	.		0.637	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		A	94746263	C	A	94746263	3	1	44	1	0	0	0	0	1	0	0	0	13146	680	24	4	633	4	RBM12B	8	94746263	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	2415816	94746263	51617759	35	3992											
KIAA1429	25962	broad.mit.edu	37	chr8	95507107	95507107	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaaatccagatctgtatctAtctcttcagcctgaaatgga	12	12	6	11	0	4	2	1	1	3	1	6	3	5	3	3	1	1	1	3	1	4	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:95507107A>G	ENST00000297591.5	-	20	4697	c.4622T>C	c.(4621-4623)aTa>aCa	p.I1541T	KIAA1429_ENST00000437199.1_3'UTR	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1541					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ATCTGTATCTATCTCTTCAGC	0.318																																					p.I1541T													.	KIAA1429-92	0			c.T4622C						.						131	141	137					8																	95507107		2203	4300	6503	SO:0001583	missense	25962	exon20			GTATCTATCTCTT	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.4622T>C	8.37:g.95507107A>G	ENSP00000297591:p.Ile1541Thr	Somatic	341	0		WXS	Illumina HiSeq	Phase_I	365	6	NM_015496	0	0	13	13	0	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.758289	0.49468	.	.	ENSG00000164944	ENST00000297591	T	0.47177	0.85	5.16	5.16	0.70880	.	0.156815	0.53938	N	0.000043	T	0.29389	0.0732	L	0.27053	0.805	0.80722	D	1	P	0.36535	0.557	B	0.33750	0.169	T	0.08994	-1.0695	10	0.11182	T	0.66	-15.6722	9.7797	0.40640	0.9225:0.0:0.0775:0.0	.	1541	Q69YN4	VIR_HUMAN	T	1541	ENSP00000297591:I1541T	ENSP00000297591:I1541T	I	-	2	0	KIAA1429	95576283	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.939000	0.75911	2.085000	0.62840	0.528000	0.53228	ATA	.		0.318	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		G	95507107	A	G	95507107	3	3	44	1	0	0	0	0	1	0	0	0	8252	449	16	3	836	3	KIAA1429	8	95507107	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	760844	95507107	50856915	36	3993											
ABRA	137735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	107782408	107782408	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctccccgctttccttttcgCccggagccatgctgcccacc	3	10	7	21	3	0	0	0	0	0	0	3	1	2	1	8	1	3	2	8	1	0	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:107782408C>A	ENST00000311955.3	-	1	65	c.11G>T	c.(10-12)gGc>gTc	p.G4V		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			TTCCTTTTCGCCCGGAGCCAT	0.597																																					p.G4V		.											.	ABRA-92	0			c.G11T						.						33	37	35					8																	107782408		2202	4295	6497	SO:0001583	missense	137735	exon1			TTTTCGCCCGGAG	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.11G>T	8.37:g.107782408C>A	ENSP00000311436:p.Gly4Val	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	125	27	NM_139166	0	0	0	0	0		Missense_Mutation	SNP	ENST00000311955.3	37	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	C	13.23	2.174542	0.38413	.	.	ENSG00000174429	ENST00000311955	.	.	.	5.66	3.63	0.41609	.	0.510379	0.22113	N	0.064446	T	0.45796	0.1360	L	0.44542	1.39	0.53005	D	0.999964	P	0.42203	0.773	P	0.45712	0.491	T	0.45948	-0.9226	9	0.59425	D	0.04	-3.5289	4.2762	0.10809	0.0:0.5455:0.0:0.4545	.	4	Q8N0Z2	ABRA_HUMAN	V	4	.	ENSP00000311436:G4V	G	-	2	0	ABRA	107851584	1.000000	0.71417	0.870000	0.34147	0.314000	0.28054	1.867000	0.39499	1.377000	0.46286	0.655000	0.94253	GGC	.		0.597	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		A	107782408	C	A	107782408	3	1	44	1	0	0	0	0	1	0	0	0	100	739	26	4	1142	4	ABRA	8	107782408	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	12275301	107782408	38581614	37	3994											
MRPL13	28998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	121455496	121455496	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagcagcaagtttgccaggtGgctgcattttcccatctaag	9	12	10	10	0	1	0	0	0	1	0	2	0	2	0	2	2	4	5	2	2	3	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:121455496G>A	ENST00000306185.3	-	2	371	c.80C>T	c.(79-81)cCa>cTa	p.P27L	MTBP_ENST00000305949.1_5'Flank	NM_014078.5	NP_054797.2	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13	27					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	6	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TTTGCCAGGTGGCTGCATTTT	0.373																																					p.P27L		.											.	MRPL13-226	0			c.C80T						.						123	118	120					8																	121455496		2203	4300	6503	SO:0001583	missense	28998	exon2			CCAGGTGGCTGCA	AB049640	CCDS6332.1	8q22.1-q22.3	2012-09-13			ENSG00000172172	ENSG00000172172		"Mitochondrial ribosomal proteins / large subunits"	14278	protein-coding gene	gene with protein product		610200				11543634	Standard	NM_014078		Approved	L13, RPL13, L13mt, RPML13, L13A	uc003ypa.3	Q9BYD1	OTTHUMG00000165039	ENST00000306185.3:c.80C>T	8.37:g.121455496G>A	ENSP00000306548:p.Pro27Leu	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	194	62	NM_014078	0	0	31	46	15	B2R4R8|Q9UI04	Missense_Mutation	SNP	ENST00000306185.3	37	CCDS6332.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.607489	0.87157	.	.	ENSG00000172172	ENST00000306185;ENST00000518918	.	.	.	5.65	5.65	0.86999	Ribosomal protein L13 domain (2);	0.000000	0.85682	D	0.000000	D	0.83280	0.5220	M	0.80508	2.5	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82942	-0.0207	9	0.45353	T	0.12	-0.4573	19.3324	0.94297	0.0:0.0:1.0:0.0	.	27	Q9BYD1	RM13_HUMAN	L	27;3	.	ENSP00000306548:P27L	P	-	2	0	MRPL13	121524677	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	9.102000	0.94226	2.663000	0.90544	0.542000	0.68232	CCA	.		0.373	MRPL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381523.1	NM_014078		A	121455496	G	A	121455496	3	1	44	1	0	0	0	0	1	0	0	0	9803	1348	47	2	480	2	MRPL13	8	121455496	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	13673088	121455496	24908526	38	3995											
CYHR1	50626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145690192	145690192	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagccccagtgtactcacCtcggctgtgctcacggctgc	5	9	10	17	2	3	0	3	0	0	0	4	0	3	0	3	2	4	4	3	2	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:145690192C>G	ENST00000438911.2	-	1	226	c.93G>C	c.(91-93)gaG>gaC	p.E31D	CTD-2517M22.16_ENST00000525461.1_RNA|CYHR1_ENST00000403000.2_Splice_Site_p.E31D|CYHR1_ENST00000424149.2_Splice_Site_p.E31D|KIFC2_ENST00000301332.2_5'Flank|CYHR1_ENST00000306145.5_Splice_Site_p.E31D|KIFC2_ENST00000301331.5_5'Flank|CYHR1_ENST00000530374.1_5'Flank	NM_138496.1	NP_612505.1	Q6ZMK1	CYHR1_HUMAN	cysteine/histidine-rich 1	31						cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(3)|ovary(2)	7	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GTGTACTCACCTCGGCTGTGC	0.627																																					p.E31D		.											.	CYHR1-90	0			c.G93C						.						37	38	38					8																	145690192		2197	4298	6495	SO:0001630	splice_region_variant	50626	exon2			ACTCACCTCGGCT	AB007965	CCDS6426.1, CCDS47943.1	8q24	2004-12-07	2005-07-24		ENSG00000187954	ENSG00000187954			17806	protein-coding gene	gene with protein product			"cysteine and histidine rich 1"			10745073	Standard	NM_138496		Approved	CHRP, KIAA0496, MGC13010	uc003zcv.2	Q6ZMK1	OTTHUMG00000165171	ENST00000438911.2:c.93+1G>C	8.37:g.145690192C>G		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_032687	0	0	0	4	4	B3KSX0|D3DWM3|Q9BSF6|Q9BSU6	Missense_Mutation	SNP	ENST00000438911.2	37	CCDS47943.1	.	.	.	.	.	.	.	.	.	.	c	17.42	3.385251	0.61956	.	.	ENSG00000187954	ENST00000438911;ENST00000526887;ENST00000403000;ENST00000424149;ENST00000306145;ENST00000533764;ENST00000530637	T;T;T;T;T;T;T	0.43688	0.94;1.65;0.94;0.94;0.94;0.94;0.94	4.22	4.22	0.49857	.	0.251507	0.25386	U	0.031059	T	0.24736	0.0600	N	0.08118	0	0.09310	N	0.999991	B;B	0.21606	0.058;0.0	B;B	0.19391	0.025;0.001	T	0.27297	-1.0078	10	0.72032	D	0.01	.	12.4423	0.55631	0.0:1.0:0.0:0.0	.	31;31	Q6ZMK1-3;Q6ZMK1	.;CYHR1_HUMAN	D	31	ENSP00000387426:E31D;ENSP00000434470:E31D;ENSP00000385962:E31D;ENSP00000414647:E31D;ENSP00000304826:E31D;ENSP00000432902:E31D;ENSP00000434642:E31D	ENSP00000304826:E31D	E	-	3	2	CYHR1	145661000	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	2.359000	0.44142	2.074000	0.62210	0.556000	0.70494	GAG	.		0.627	CYHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382438.1	NM_032687	Missense_Mutation	G	145690192	C	G	145690192	5	3	44	1	0	0	0	0	0	0	1	0	4146	695	24	4	1348	4	CYHR1	8	145690192	Splice_Site	SNP	C	TCGA-B3-4103-01A-01D-1458-08	24234696	145690192	673830	39	3996											
FREM1	158326	hgsc.bcm.edu;broad.mit.edu	37	chr9	14824065	14824065	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggccgtaggattcttaacTacttttggtatgctgtccac	8	14	10	9	1	1	0	0	0	1	0	2	1	2	1	2	3	3	3	2	3	4	7	rs200760404		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr9:14824065T>G	ENST00000380880.3	-	12	2910	c.2127A>C	c.(2125-2127)gtA>gtC	p.V709V	FREM1_ENST00000380881.4_Silent_p.V710V|FREM1_ENST00000422223.2_Silent_p.V709V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	709					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GATTCTTAACTACTTTTGGTA	0.408																																					p.V709V		.											.	FREM1-138	0			c.A2127C						.						70	69	69					9																	14824065		1929	4143	6072	SO:0001819	synonymous_variant	158326	exon13			CTTAACTACTTTT	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2127A>C	9.37:g.14824065T>G		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	25	5	NM_144966	0	0	2	2	0	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			T|1.000;C|0.000		0.408	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14824065	T	G	14824065	2	3	44	1	0	0	0	0	0	0	0	1	6063	1509	53	5		5	FREM1	9	14824065	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08		14824065	126389366	40	3997											
TNFSF8	944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	117666220	117666220	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagaaactgttcagtctgaAttactgtataagaagatgga	16	11	10	4	0	2	4	1	1	1	3	2	6	2	5	0	1	2	2	0	1	6	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr9:117666220A>C	ENST00000223795.2	-	4	809	c.696T>G	c.(694-696)aaT>aaG	p.N232K	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	232					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						TTCAGTCTGAATTACTGTATA	0.408																																					p.N232K		.											.	TNFSF8-655	0			c.T696G						.						165	157	159					9																	117666220		2203	4300	6503	SO:0001583	missense	944	exon4			GTCTGAATTACTG	L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.696T>G	9.37:g.117666220A>C	ENSP00000223795:p.Asn232Lys	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	273	82	NM_001244	0	0	0	0	0	O43404	Missense_Mutation	SNP	ENST00000223795.2	37	CCDS6810.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.255547	0.22965	.	.	ENSG00000106952	ENST00000223795	.	.	.	5.78	2.21	0.28008	.	0.916415	0.09426	N	0.803692	T	0.18130	0.0435	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.23048	-1.0199	9	0.48119	T	0.1	-0.0101	4.7061	0.12849	0.6059:0.1526:0.2415:0.0	.	232	P32971	TNFL8_HUMAN	K	232	.	ENSP00000223795:N232K	N	-	3	2	TNFSF8	116706041	0.167000	0.22975	0.531000	0.27976	0.664000	0.39144	0.394000	0.20834	0.135000	0.18707	-0.256000	0.11100	AAT	.		0.408	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			C	117666220	A	C	117666220	3	2	44	1	0	0	0	0	1	0	0	0	16343	98	4	5	12	5	TNFSF8	9	117666220	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	102842155	117666220	23547211	41	3998											
TOR1A	1861	broad.mit.edu	37	chr9	132584984	132584984	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttgctgacgaaatttttgCcggtgcctgtccacccgtgc	5	13	10	13	3	1	1	0	1	1	0	2	2	2	1	4	1	4	1	4	1	1	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr9:132584984C>T	ENST00000351698.4	-	2	368	c.320G>A	c.(319-321)gGc>gAc	p.G107D	TOR1A_ENST00000473084.1_5'UTR	NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	107	Interaction with SNAPIN.				ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.G107D(4)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				GAAATTTTTGCCGGTGCCTGT	0.468																																					p.G107D													.	TOR1A-90	4	Substitution - Missense(4)	kidney(3)|lung(1)	c.G320A						.						226	200	209					9																	132584984		2203	4300	6503	SO:0001583	missense	1861	exon2			TTTTTGCCGGTGC	AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"dystonia 1, torsion (autosomal dominant; torsin A)"	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.320G>A	9.37:g.132584984C>T	ENSP00000345719:p.Gly107Asp	Somatic	459	0		WXS	Illumina HiSeq	Phase_I	420	7	NM_000113	0	0	54	54	0	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.838232	0.71373	.	.	ENSG00000136827	ENST00000351698	D	0.92099	-2.97	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.97281	0.9111	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98397	1.0566	10	0.87932	D	0	-8.4354	17.7332	0.88384	0.0:1.0:0.0:0.0	.	107;107	O14656-2;O14656	.;TOR1A_HUMAN	D	107	ENSP00000345719:G107D	ENSP00000345719:G107D	G	-	2	0	TOR1A	131624805	1.000000	0.71417	0.995000	0.50966	0.072000	0.16883	7.484000	0.81180	2.439000	0.82584	0.561000	0.74099	GGC	.		0.468	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113		T	132584984	C	T	132584984	3	4	44	1	0	0	0	0	1	0	0	0	16404	739	26	2	694	2	TOR1A	9	132584984	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	14918764	132584984	8628447	42	3999											
FAM188A	80013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	15879212	15879212	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttgaacacacctttgtcagTaatacagaatacagaaaaag	18	9	6	8	0	1	3	1	1	0	2	1	3	1	3	1	0	3	1	1	0	7	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr10:15879212T>A	ENST00000277632.3	-	6	787	c.567A>T	c.(565-567)ttA>ttT	p.L189F	FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	189					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						CCTTTGTCAGTAATACAGAAT	0.353																																					p.L189F	Pancreas(159;946 1953 2111 4475 22008)	.											.	FAM188A-228	0			c.A567T						.						131	131	131					10																	15879212		2203	4296	6499	SO:0001583	missense	80013	exon6			TGTCAGTAATACA	AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"caspase recruitment domain containing pro-apoptotic protein", "CARD-containing protein"	611649	"chromosome 10 open reading frame 97"	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.567A>T	10.37:g.15879212T>A	ENSP00000277632:p.Leu189Phe	Somatic	228	1		WXS	Illumina HiSeq	Phase_I	278	79	NM_024948	0	0	0	0	0	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Missense_Mutation	SNP	ENST00000277632.3	37	CCDS7110.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.995741	0.35226	.	.	ENSG00000148481	ENST00000277632;ENST00000418767;ENST00000436829	T;T;T	0.35973	1.28;1.28;1.28	5.82	4.62	0.57501	.	0.100055	0.64402	D	0.000004	T	0.25082	0.0609	N	0.17379	0.485	0.80722	D	1	P	0.37101	0.582	B	0.40444	0.329	T	0.05468	-1.0883	10	0.39692	T	0.17	-10.9766	10.0517	0.42219	0.2595:0.0:0.0:0.7405	.	189	Q9H8M7	F188A_HUMAN	F	189;29;42	ENSP00000277632:L189F;ENSP00000388661:L29F;ENSP00000389883:L42F	ENSP00000277632:L189F	L	-	3	2	FAM188A	15919218	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.047000	0.41269	2.217000	0.71921	0.482000	0.46254	TTA	.		0.353	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948		A	15879212	T	A	15879212	3	1	44	1	0	0	0	0	1	0	0	0	5530	1635	57	5	810	5	FAM188A	10	15879212	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08		15879212	119655535	43	4000											
TNKS2	80351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	93593686	93593686	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatctacaaacctgccgccTactcctgagctatgggtgtg	8	11	9	13	1	2	1	1	1	1	0	3	1	3	1	4	1	5	1	4	1	4	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr10:93593686T>C	ENST00000371627.4	+	12	1731	c.1352T>C	c.(1351-1353)cTa>cCa	p.L451P		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	451					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				ACCTGCCGCCTACTCCTGAGC	0.413																																					p.L451P		.											.	TNKS2-541	0			c.T1352C						.						148	131	137					10																	93593686		2203	4300	6503	SO:0001583	missense	80351	exon12			GCCGCCTACTCCT	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1352T>C	10.37:g.93593686T>C	ENSP00000360689:p.Leu451Pro	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	240	79	NM_025235	0	0	8	11	3	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	37	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715685	0.89112	.	.	ENSG00000107854	ENST00000371627	T	0.70164	-0.46	5.83	5.83	0.93111	Ankyrin repeat-containing domain (3);	0.000000	0.47093	D	0.000247	D	0.86489	0.5945	M	0.94142	3.5	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.89940	0.4072	10	0.62326	D	0.03	.	16.1968	0.82036	0.0:0.0:0.0:1.0	.	451	Q9H2K2	TNKS2_HUMAN	P	451	ENSP00000360689:L451P	ENSP00000360689:L451P	L	+	2	0	TNKS2	93583666	1.000000	0.71417	0.975000	0.42487	0.983000	0.72400	8.040000	0.89188	2.225000	0.72522	0.533000	0.62120	CTA	.		0.413	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		C	93593686	T	C	93593686	3	2	44	1	0	0	0	0	1	0	0	0	16353	1522	53	3	1398	3	TNKS2	10	93593686	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	77714474	93593686	41941061	44	4001											
ITPRIP	85450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	106075425	106075425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaggccctgcaagggggCgccccccagcccaggcagct	6	3	16	16	1	0	1	0	1	0	0	0	1	0	1	5	5	3	3	5	5	1	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr10:106075425C>T	ENST00000337478.1	-	2	556	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	RP11-127L20.5_ENST00000472915.2_RNA|ITPRIP_ENST00000358187.2_Missense_Mutation_p.A129T|ITPRIP_ENST00000278071.2_Missense_Mutation_p.A129T	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	129						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						TGCAAGGGGGCGCCCCCCAGC	0.692																																					p.A129T		.											.	ITPRIP-90	0			c.G385A						.						35	41	39					10																	106075425		2203	4298	6501	SO:0001583	missense	85450	exon2			AGGGGGCGCCCCC	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.385G>A	10.37:g.106075425C>T	ENSP00000337178:p.Ala129Thr	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	179	76	NM_001272013	0	0	6	9	3	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Missense_Mutation	SNP	ENST00000337478.1	37	CCDS7557.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.730767	0.00687	.	.	ENSG00000148841	ENST00000337478;ENST00000278071;ENST00000358187	T;T;T	0.22134	1.97;1.97;1.97	5.68	-5.02	0.02982	.	1.189030	0.05773	N	0.607175	T	0.10551	0.0258	N	0.13043	0.29	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.39563	-0.9608	10	0.12430	T	0.62	-5.7595	10.1192	0.42609	0.0857:0.426:0.0:0.4883	.	129	Q8IWB1	IPRI_HUMAN	T	129	ENSP00000337178:A129T;ENSP00000278071:A129T;ENSP00000350915:A129T	ENSP00000278071:A129T	A	-	1	0	ITPRIP	106065415	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.312000	0.08113	-1.181000	0.02730	-1.119000	0.02030	GCC	.		0.692	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		T	106075425	C	T	106075425	3	4	44	1	0	0	0	0	1	0	0	0	7944	768	27	1	1262	1	ITPRIP	10	106075425	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	12481739	106075425	29459322	45	4002											
WDR11	55717	ucsc.edu	37	chr10	122622314	122622314	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagcctccctcaggccctggGaaaaaagtttacatatccag	13	8	8	12	0	1	0	1	0	0	0	3	1	3	1	4	2	2	1	4	2	6	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr10:122622314G>A	ENST00000263461.6	+	5	840	c.594G>A	c.(592-594)ggG>ggA	p.G198G		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CAGGCCCTGGGAAAAAAGTTT	0.433																																					p.G198G													.	WDR11-226	0			c.G594A						.						122	136	131					10																	122622314		2203	4300	6503	SO:0001819	synonymous_variant	55717	exon5			CCCTGGGAAAAAA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.594G>A	10.37:g.122622314G>A		Somatic	346	0		WXS	Illumina HiSeq		357	3	NM_018117	0	0	39	43	4	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			.		0.433	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			A	122622314	G	A	122622314	2	1	44	1	0	0	0	0	0	0	0	1	17306	1161	41	2		2	WDR11	10	122622314	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08	16546889	122622314	12912433	46	4003											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093502	1093502	+	Missense_Mutation	SNP	C	C	G																															ggtactcatcaccaccaccaCtacgatgaccccaaccccaa																								rs529542452		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:1093502C>G	ENST00000441003.2	+	30	5348	c.5321C>G	c.(5320-5322)aCt>aGt	p.T1774S	MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.T62S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccaccactacgatgacc	0.617													N|||	1	0.000199681	0	0	5008	,	,		28151	0		0.001	False		,,,				2504	0				p.T1774S		.											.	MUC2-90	0			c.C5321G						.																																			SO:0001583	missense	4583	exon30			CCACCACTACGAT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5321C>G	11.37:g.1093502C>G	ENSP00000415183:p.Thr1774Ser	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	13	6	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.027	-1.361543	0.01235	.	.	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.10668	2.85;2.86	1.82	-1.79	0.07932	.	.	.	.	.	T	0.06234	0.0161	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.39563	-0.9608	8	0.33940	T	0.23	.	5.1534	0.15021	0.0:0.449:0.4024:0.1486	.	1774	E7EUV1	.	S	1774;62	ENSP00000415183:T1774S;ENSP00000331373:T62S	ENSP00000331373:T62S	T	+	2	0	MUC2	1083502	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.389000	0.07342	-0.316000	0.08690	-1.112000	0.02068	ACT	.		0.617	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093502	C	G	1093502	3	3	44	1	0	0	0	0	1	0	0	0	10000	565	20	4	5439	4	MUC2	11	1093502	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08		1093502	133913014	47	4004	43	2									
MUC2	4583	hgsc.bcm.edu	37	chr11	1093507	1093507	+	Missense_Mutation	SNP	A	A	G																															tcatcaccaccaccactacgAtgaccccaaccccaacaccc																								rs56189540		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:1093507A>G	ENST00000441003.2	+	30	5353	c.5326A>G	c.(5326-5328)Atg>Gtg	p.M1776V	MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.M64V	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caccactacgatgaccccaac	0.607																																					p.M1776V		.											.	MUC2-90	0			c.A5326G						.						94	120	111					11																	1093507		2159	4225	6384	SO:0001583	missense	4583	exon30			ACTACGATGACCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5326A>G	11.37:g.1093507A>G	ENSP00000415183:p.Met1776Val	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	14	10	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	4.089	0.014464	0.07959	.	.	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.06687	3.27;3.89	1.82	0.848	0.18966	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44726	-0.9309	8	0.24483	T	0.36	.	4.4625	0.11673	0.5672:0.0:0.4328:0.0	rs56189540	1776	E7EUV1	.	V	1776;64	ENSP00000415183:M1776V;ENSP00000331373:M64V	ENSP00000331373:M64V	M	+	1	0	MUC2	1083507	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.412000	0.07132	0.113000	0.18004	-1.063000	0.02288	ATG	.		0.607	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093507	A	G	1093507	3	3	44	1	0	0	0	0	1	0	0	0	10000	333	12	3	5444	3	MUC2	11	1093507	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	5	1093507	133913009	48	4005	43	2									
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411941	6411941	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggatgggcctggtgctggCgctggcgctggcgctggcgc	1	9	20	11	4	0	0	0	0	0	0	0	1	0	1	1	7	1	4	1	7	0	1	rs550365194|rs550067660|rs71467507|rs78250081|rs558809956|rs3838786	byFrequency	TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:6411941C>T	ENST00000342245.4	+	1	281	c.113C>T	c.(112-114)gCg>gTg	p.A38V	SMPD1_ENST00000299397.3_Missense_Mutation_p.A38V|SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.A38V|SMPD1_ENST00000527275.1_Missense_Mutation_p.A38V	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggtgctggcgctggcgctg	0.711																																					p.A38V		.											.	SMPD1-90	0			c.C113T						.						11	14	13					11																	6411941		2185	4258	6443	SO:0001583	missense	6609	exon1			TGCTGGCGCTGGC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.113C>T	11.37:g.6411941C>T	ENSP00000340409:p.Ala38Val	Somatic	33	1		WXS	Illumina HiSeq	Phase_I	53	7	NM_000543	0	0	21	21	0	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	37	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234305	0.39498	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	4.54	-1.08	0.09936	.	.	.	.	.	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.002;0.013	B;B	0.10450	0.002;0.005	T	0.47275	-0.9130	9	0.12103	T	0.63	.	6.8659	0.24093	0.0:0.5614:0.262:0.1766	.	38;38	E9PKS3;G3XAB5	.;.	V	38	ENSP00000299397:A38V;ENSP00000349203:A38V;ENSP00000340409:A38V;ENSP00000435350:A38V	ENSP00000299397:A38V	A	+	2	0	SMPD1	6368517	0.000000	0.05858	0.130000	0.21974	0.033000	0.12548	-2.110000	0.01334	-0.479000	0.06813	-1.305000	0.01319	GCG	.		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411941	C	T	6411941	3	4	44	1	0	0	0	0	1	0	0	0	14836	768	27	1	115	1	SMPD1	11	6411941	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	5318434	6411941	128594575	49	4006											
MRGPRX1	259249	broad.mit.edu;bcgsc.ca	37	chr11	18955994	18955994	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcggtgctcacggcactcAgaaagctcaggcctgcaaag	10	6	12	13	2	3	1	3	0	0	1	4	1	3	1	1	3	3	5	1	3	2	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:18955994A>T	ENST00000302797.3	-	1	562	c.338T>A	c.(337-339)cTg>cAg	p.L113Q	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	113					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CACGGCACTCAGAAAGCTCAG	0.542																																					p.L113Q													.	MRGPRX1-92	0			c.T338A						.						100	96	98					11																	18955994		2194	4286	6480	SO:0001583	missense	259249	exon1			GCACTCAGAAAGC		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"GPCR / Class A : Orphans"	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.338T>A	11.37:g.18955994A>T	ENSP00000305766:p.Leu113Gln	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	141	6	NM_147199	0	0	0	0	0	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	16.41	3.114997	0.56505	.	.	ENSG00000170255	ENST00000302797	D	0.81579	-1.51	2.28	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000078	D	0.91199	0.7227	H	0.95982	3.75	0.29298	N	0.868908	D	0.89917	1.0	D	0.91635	0.999	D	0.85057	0.0932	10	0.87932	D	0	.	8.4333	0.32771	1.0:0.0:0.0:0.0	.	113	Q96LB2	MRGX1_HUMAN	Q	113	ENSP00000305766:L113Q	ENSP00000305766:L113Q	L	-	2	0	MRGPRX1	18912570	0.996000	0.38824	0.008000	0.14137	0.026000	0.11368	7.327000	0.79147	1.292000	0.44672	0.402000	0.26972	CTG	.		0.542	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		T	18955994	A	T	18955994	3	4	44	1	0	0	0	0	1	0	0	0	9791	188	7	5	634	5	MRGPRX1	11	18955994	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	12544053	18955994	116050522	50	4007											
ABCG4	64137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119027678	119027678	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggctgagaagaagagcaGccctgagaagaacgaggtcc	14	5	14	8	1	0	5	0	2	0	5	1	8	1	5	2	2	3	2	2	2	5	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:119027678G>T	ENST00000449422.2	+	9	1210	c.1022G>T	c.(1021-1023)aGc>aTc	p.S341I	AP002956.1_ENST00000599663.1_Intron|ABCG4_ENST00000307417.3_Missense_Mutation_p.S341I|ABCG4_ENST00000531739.1_Missense_Mutation_p.S341I	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	341					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		AAGAAGAGCAGCCCTGAGAAG	0.607																																					p.S341I		.											.	ABCG4-92	0			c.G1022T						.						180	164	170					11																	119027678		2200	4295	6495	SO:0001583	missense	64137	exon9			AGAGCAGCCCTGA	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"ATP binding cassette transporters / subfamily G"	13884	protein-coding gene	gene with protein product	"putative ABC transporter", "ATP-binding cassette, subfamily G, member 4"	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1022G>T	11.37:g.119027678G>T	ENSP00000406874:p.Ser341Ile	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	220	75	NM_022169	0	0	0	0	0	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.998773	0.54147	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.87412	-2.25;-2.25;-2.25;0.85	5.65	3.69	0.42338	.	0.573919	0.21547	N	0.072794	T	0.78660	0.4318	L	0.35854	1.095	0.36220	D	0.851913	B	0.13594	0.008	B	0.13407	0.009	T	0.75360	-0.3345	10	0.38643	T	0.18	-8.3485	6.2254	0.20706	0.071:0.1345:0.6546:0.1398	.	341	Q9H172	ABCG4_HUMAN	I	341;341;341;19	ENSP00000304111:S341I;ENSP00000406874:S341I;ENSP00000434318:S341I;ENSP00000434571:S19I	ENSP00000304111:S341I	S	+	2	0	ABCG4	118532888	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.327000	0.43858	1.359000	0.45940	0.655000	0.94253	AGC	.		0.607	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119027678	G	T	119027678	3	4	44	1	0	0	0	0	1	0	0	0	70	971	34	4	1052	4	ABCG4	11	119027678	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	100071684	119027678	15978838	51	4008											
TXNRD1	7296	bcgsc.ca	37	chr12	104705164	104705164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttatcatcattggaggtGgctcaggaggtctggcagct	8	11	13	9	0	4	0	3	0	1	0	4	2	4	2	1	6	1	3	1	6	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr12:104705164G>A	ENST00000525566.1	+	5	535	c.511G>A	c.(511-513)Ggc>Agc	p.G171S	TXNRD1_ENST00000354940.6_Missense_Mutation_p.G21S|TXNRD1_ENST00000524698.1_Missense_Mutation_p.G21S|TXNRD1_ENST00000378070.4_Missense_Mutation_p.G120S|TXNRD1_ENST00000388854.3_Missense_Mutation_p.G73S|TXNRD1_ENST00000542918.1_Missense_Mutation_p.G71S|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000503506.2_Missense_Mutation_p.G21S|TXNRD1_ENST00000429002.2_Missense_Mutation_p.G171S|TXNRD1_ENST00000526691.1_Missense_Mutation_p.G73S|TXNRD1_ENST00000397736.2_Missense_Mutation_p.G65S|TXNRD1_ENST00000526390.1_Missense_Mutation_p.G65S|TXNRD1_ENST00000529546.1_Intron|TXNRD1_ENST00000526950.1_Missense_Mutation_p.G90S|TXNRD1_ENST00000427956.1_Missense_Mutation_p.G136S	NM_001093771.2	NP_001087240.1	Q16881	TRXR1_HUMAN	thioredoxin reductase 1	171					cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cellular lipid metabolic process (GO:0044255)|mesoderm formation (GO:0001707)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	16					Arsenic trioxide(DB01169)|Flavin adenine dinucleotide(DB03147)	CATTGGAGGTGGCTCAGGAGG	0.468																																					.	Ovarian(139;555 1836 9186 9946 10884)												.	TXNRD1-90	0			.						.						107	99	102					12																	104705164		1967	4147	6114	SO:0001583	missense	7296	.			GGAGGTGGCTCAG		CCDS53820.1, CCDS53821.1, CCDS53823.1, CCDS58274.1	12q23-q24.1	2012-03-01							12437	protein-coding gene	gene with protein product		601112				7589432	Standard	NM_001093771		Approved	TXNR, GRIM-12, Trxr1	uc021rcx.2	Q16881		ENST00000525566.1:c.511G>A	12.37:g.104705164G>A	ENSP00000434516:p.Gly171Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_1	77	5	.	0	0	48	48	0	B7Z1F4|B7Z3Y8|B7Z904|E9PMY9|F5H780|Q6FI31|Q6VB40|Q6VB41|Q6VB42|Q6VBP2|Q6VBP3|Q6VBP4|Q6VBP5|Q6VBP9|Q6VBQ0|Q6YNQ1|Q76P53|Q7LA96|Q8WVC8|Q99475|Q9UES8|Q9UH79	Missense_Mutation	SNP	ENST00000525566.1	37	CCDS53820.1	.	.	.	.	.	.	.	.	.	.	G	35	5.445208	0.96187	.	.	ENSG00000198431	ENST00000525566;ENST00000429002;ENST00000526266;ENST00000503506;ENST00000526691;ENST00000531691;ENST00000388854;ENST00000354940;ENST00000526390;ENST00000531689;ENST00000528079;ENST00000526580;ENST00000529784;ENST00000524698;ENST00000542918;ENST00000378070;ENST00000527335;ENST00000397736;ENST00000427956;ENST00000526950	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;T;D;D;D	0.99060	-5.38;-5.38;-2.29;-5.38;-5.38;-2.29;-5.38;-5.38;-5.38;-2.29;-2.29;-4.7;-5.38;-5.38;-5.38;-1.08;-5.38;-5.38;-5.38	5.75	5.75	0.90469	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99750	0.9900	H	0.99900	4.915	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.996;0.997;0.998;0.996;0.997;0.998;0.998	D	0.96754	0.9556	10	0.87932	D	0	-18.1178	19.9889	0.97359	0.0:0.0:1.0:0.0	.	71;65;171;73;21;171;136	B7Z2S5;E2QRB9;B7Z904;Q16881-4;B2R5P6;Q16881;E7EW10	.;.;.;.;.;TRXR1_HUMAN;.	S	171;171;21;21;73;65;73;21;65;21;90;21;21;21;71;120;21;65;136;90	ENSP00000434516:G171S;ENSP00000412045:G171S;ENSP00000431294:G21S;ENSP00000421934:G21S;ENSP00000435929:G73S;ENSP00000431925:G65S;ENSP00000373506:G73S;ENSP00000347020:G21S;ENSP00000435123:G65S;ENSP00000433507:G21S;ENSP00000433887:G21S;ENSP00000436229:G21S;ENSP00000433425:G21S;ENSP00000440978:G71S;ENSP00000367310:G120S;ENSP00000433599:G21S;ENSP00000380844:G65S;ENSP00000393328:G136S;ENSP00000432812:G90S	ENSP00000347020:G21S	G	+	1	0	TXNRD1	103229294	1.000000	0.71417	0.960000	0.40013	0.770000	0.43624	9.015000	0.93640	2.727000	0.93392	0.650000	0.86243	GGC	.		0.468	TXNRD1-001	KNOWN	basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000389960.1	NM_003330		A	104705164	G	A	104705164	3	1	44	1	0	0	0	0	1	0	0	0	16840	1348	47	2	543	2	TXNRD1	12	104705164	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		104705164	29146731	52	4009											
WDR66	144406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	122413567	122413567	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttttgtcatgagagcaatTggcttttacccatctgaaga	10	14	8	9	0	2	3	1	2	1	2	2	4	2	3	2	1	2	2	2	1	3	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr12:122413567T>C	ENST00000288912.4	+	19	3836	c.2982T>C	c.(2980-2982)atT>atC	p.I994I		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	994							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TGAGAGCAATTGGCTTTTACC	0.438																																					p.I994I	Esophageal Squamous(85;849 1794 49757 52143)	.											.	WDR66-92	0			c.T2982C						.						119	111	113					12																	122413567		1915	4145	6060	SO:0001819	synonymous_variant	144406	exon19			AGCAATTGGCTTT	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2982T>C	12.37:g.122413567T>C		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	141	49	NM_144668	0	0	2	2	0	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			.		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		C	122413567	T	C	122413567	2	2	44	1	0	0	0	0	0	0	0	1	17350	1800	63	3		3	WDR66	12	122413567	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08	17708403	122413567	11438328	53	4010											
RDH12	145226	broad.mit.edu	37	chr14	68191259	68191259	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtagtggtgatcactggCgccaacacgggcattggcaa	11	7	14	9	2	1	1	1	1	0	0	1	1	1	1	1	5	1	3	1	5	4	2	rs140371232	byFrequency	TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr14:68191259C>T	ENST00000551171.1	+	4	462	c.138C>T	c.(136-138)ggC>ggT	p.G46G	RDH12_ENST00000539142.1_Silent_p.G46G|RDH12_ENST00000267502.3_Silent_p.G46G	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	46					photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)	p.G46G(1)		large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	TGATCACTGGCGCCAACACGG	0.542													C|||	3	0.000599042	0	0	5008	,	,		18362	0		0	False		,,,				2504	0.0031				p.G46G													.	RDH12-91	1	Substitution - coding silent(1)	prostate(1)	c.C138T						.	C		0,4406		0,0,2203	252	206	222		138	-2.8	1	14	dbSNP_134	222	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RDH12	NM_152443.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		46/317	68191259	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	145226	exon4			CACTGGCGCCAAC	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19977	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 2"	608830	"retinol dehydrogenase 12 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.138C>T	14.37:g.68191259C>T		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	170	6	NM_152443	0	0	3	3	0	B2RDA2|Q8TAW6	Silent	SNP	ENST00000551171.1	37	CCDS9787.1																																																																																			C|1.000;T|0.000		0.542	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1			T	68191259	C	T	68191259	2	4	44	1	0	0	0	0	0	0	0	1	13223	755	27	1		1	RDH12	14	68191259	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08		68191259	39158281	54	4011											
ANGEL1	23357	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	77274402	77274411	+	Frame_Shift_Del	DEL	GAGTGAACTG	GAGTGAACTG	-																															caggatgttataagacatcaGagtgaactggaactgagggc																								rs138394702	byFrequency	TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	GAGTGAACTG	GAGTGAACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr14:77274402_77274411delGAGTGAACTG	ENST00000251089.2	-	3	842_851	c.730_739delCAGTTCACTC	c.(730-741)cagttcactctgfs	p.QFTL244fs	ANGEL1_ENST00000554941.1_5'Flank	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	244										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		TAAGACATCAGAGTGAACTGGAACTGAGGG	0.505																																					p.244_247del		.											.	ANGEL1-93	0			c.730_739del						.																																			SO:0001589	frameshift_variant	23357	exon3			.	AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.730_739delCAGTTCACTC	14.37:g.77274402_77274411delGAGTGAACTG	ENSP00000251089:p.Gln244fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	121	26	NM_015305	0	0	0	0	0	B4DWL7|O94859|Q8NCS9	Frame_Shift_Del	DEL	ENST00000251089.2	37	CCDS9852.1																																																																																			.		0.505	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305		-	77274411	GAGTGAACTG	-	77274402	7	5	44	1	0	1	0	1	0	0	0	0	608	933	33	0	1305	0	ANGEL1	14	77274402	Frame_Shift_Del	DEL	GAGTGAACTG	TCGA-B3-4103-01A-01D-1458-08	9083143	77274402	30075138	55	4012											
JAG2	3714	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	105622266	105622266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccgctgaagtgcaggctcTtccagcggtcctccgggttg	4	9	15	13	3	1	1	0	1	1	0	4	1	4	1	4	4	2	4	4	4	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr14:105622266T>C	ENST00000331782.3	-	4	939	c.536A>G	c.(535-537)aAg>aGg	p.K179R	JAG2_ENST00000347004.2_Missense_Mutation_p.K179R|RP11-44N21.4_ENST00000548203.1_RNA	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	179					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		GTGCAGGCTCTTCCAGCGGTC	0.632																																					p.K179R		.											.	JAG2-846	0			c.A536G						.						44	36	39					14																	105622266		2199	4294	6493	SO:0001583	missense	3714	exon4			AGGCTCTTCCAGC	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.536A>G	14.37:g.105622266T>C	ENSP00000328169:p.Lys179Arg	Somatic	51	1		WXS	Illumina HiSeq	Phase_I	55	14	NM_145159	0	0	1	3	2	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	.	.	.	.	.	.	.	.	.	.	T	17.54	3.415310	0.62511	.	.	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.96168	-3.93;-3.93	4.48	4.48	0.54585	Delta/Serrate/lag-2 (DSL) protein (2);	0.067676	0.64402	U	0.000011	D	0.94417	0.8204	L	0.49126	1.545	0.38795	D	0.95507	D;P	0.54772	0.968;0.947	P;P	0.51615	0.625;0.675	D	0.93846	0.7141	10	0.45353	T	0.12	.	9.3373	0.38058	0.0:0.0:0.1806:0.8194	.	179;179	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	R	179	ENSP00000328169:K179R;ENSP00000328566:K179R	ENSP00000328169:K179R	K	-	2	0	JAG2	104693311	1.000000	0.71417	1.000000	0.80357	0.542000	0.35054	5.935000	0.70145	1.649000	0.50652	0.460000	0.39030	AAG	.		0.632	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			C	105622266	T	C	105622266	3	2	44	1	0	0	0	0	1	0	0	0	7956	1609	56	3	3272	3	JAG2	14	105622266	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	28347864	105622266	1727274	56	4013											
TMC3	342125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	81648105	81648105	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctcctgttcttccaatataGcttcctttaagaaaaataca	13	15	3	10	0	2	1	0	0	2	1	5	1	4	1	3	0	2	2	3	0	7	8			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr15:81648105G>A	ENST00000359440.5	-	9	1031	c.896C>T	c.(895-897)gCt>gTt	p.A299V	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.A299V|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TTCCAATATAGCTTCCTTTAA	0.284																																					p.A299V		.											.	TMC3-70	0			c.C896T						.						120	114	116					15																	81648105		1789	4056	5845	SO:0001583	missense	342125	exon9			AATATAGCTTCCT	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.896C>T	15.37:g.81648105G>A	ENSP00000352413:p.Ala299Val	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	112	35	NM_001080532	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.901887	0.52227	.	.	ENSG00000188869	ENST00000359440	T	0.21191	2.02	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.37183	0.0994	L	0.54965	1.715	0.58432	D	0.999997	D;D	0.58970	0.984;0.973	P;P	0.56514	0.785;0.8	T	0.15037	-1.0451	10	0.72032	D	0.01	-13.4261	16.9402	0.86216	0.0:0.0:1.0:0.0	.	299;299	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	V	299	ENSP00000352413:A299V	ENSP00000352413:A299V	A	-	2	0	TMC3	79435160	1.000000	0.71417	0.925000	0.36789	0.111000	0.19643	6.165000	0.71891	2.408000	0.81797	0.555000	0.69702	GCT	.		0.284	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		A	81648105	G	A	81648105	3	1	44	1	0	0	0	0	1	0	0	0	16018	971	34	2	2462	2	TMC3	15	81648105	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		81648105	20883287	57	4014											
ADAMTS17	170691	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	100657190	100657190	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcatgttctacactggcacCcgggcagtgtgtgcctccag	6	9	12	14	2	1	0	0	0	1	0	2	0	2	0	3	2	2	4	3	2	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr15:100657190C>T	ENST00000268070.4	-	13	1855	c.1750G>A	c.(1750-1752)Ggt>Agt	p.G584S		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	584	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		ACACTGGCACCCGGGCAGTGT	0.632																																					p.G584S		.											.	ADAMTS17-228	0			c.G1750A						.						39	33	35					15																	100657190		2203	4300	6503	SO:0001583	missense	170691	exon13			TGGCACCCGGGCA	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1750G>A	15.37:g.100657190C>T	ENSP00000268070:p.Gly584Ser	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	50	20	NM_139057	0	0	0	0	0	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259132	0.80246	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	T	0.60672	0.17	5.18	5.18	0.71444	.	0.141210	0.47852	D	0.000203	T	0.69459	0.3113	M	0.88450	2.955	0.54753	D	0.999987	P;B	0.38473	0.633;0.251	B;B	0.40375	0.327;0.108	T	0.77120	-0.2705	10	0.87932	D	0	.	18.7048	0.91633	0.0:1.0:0.0:0.0	.	341;584	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	S	584;341	ENSP00000268070:G584S	ENSP00000268070:G584S	G	-	1	0	ADAMTS17	98474713	0.870000	0.30015	0.451000	0.26982	0.858000	0.48976	2.708000	0.47152	2.419000	0.82065	0.655000	0.94253	GGT	.		0.632	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		T	100657190	C	T	100657190	3	4	44	1	0	0	0	0	1	0	0	0	262	623	22	2	1577	2	ADAMTS17	15	100657190	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	19009085	100657190	1874202	58	4015											
IFT140	9742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1608090	1608090	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggacaccatctgagggatgtGgtggcacccaggctccacct	8	7	13	13	0	1	1	0	1	1	0	2	3	2	3	4	5	0	2	4	5	0	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr16:1608090G>T	ENST00000426508.2	-	19	2608	c.2245C>A	c.(2245-2247)Cac>Aac	p.H749N	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	749					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				TGAGGGATGTGGTGGCACCCA	0.552																																					p.H749N		.											.	IFT140-95	0			c.C2245A						.						149	145	146					16																	1608090		2199	4300	6499	SO:0001583	missense	9742	exon19			GGATGTGGTGGCA	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2245C>A	16.37:g.1608090G>T	ENSP00000406012:p.His749Asn	Somatic	421	1		WXS	Illumina HiSeq	Phase_I	568	163	NM_014714	0	0	17	24	7	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	9.526	1.109524	0.20714	.	.	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.41400	1.0	5.0	-3.73	0.04398	.	0.869820	0.10298	N	0.691510	T	0.15912	0.0383	N	0.08118	0	0.09310	N	1	B;B	0.23735	0.017;0.09	B;B	0.26416	0.021;0.069	T	0.23048	-1.0199	10	0.17832	T	0.49	.	1.4862	0.02447	0.393:0.097:0.2946:0.2155	.	749;474	Q96RY7;B4DR58	IF140_HUMAN;.	N	749	ENSP00000406012:H749N	ENSP00000380562:H749N	H	-	1	0	IFT140	1548091	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-0.055000	0.11807	-1.123000	0.02940	0.563000	0.77884	CAC	.		0.552	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1608090	G	T	1608090	3	4	44	1	0	0	0	0	1	0	0	0	7577	1348	47	4	2195	4	IFT140	16	1608090	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		1608090	88746663	59	4016											
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2230812	2230812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agccgtcggcacgggtggggGcgcaggccccggggcagccg	4	2	21	14	6	0	0	0	0	0	0	1	0	0	0	4	7	2	3	4	7	0	0	rs185628064	byFrequency	TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr16:2230812G>A	ENST00000343516.6	-	18	2649	c.2557C>T	c.(2557-2559)Ccc>Tcc	p.P853S	CASKIN1_ENST00000564289.1_5'Flank	NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	853	Pro-rich.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						ACGGGTGGGGGCGCAGGCCCC	0.756													G|||	36	0.0071885	0	0.0187	5008	,	,		9211	0		0.0229	False		,,,				2504	0				p.P853S		.											.	CASKIN1-92	0			c.C2557T						.	G	SER/PRO	8,2372		0,8,1182	2	3	3		2557	1	0	16		3	100,5436		0,100,2668	no	missense	CASKIN1	NM_020764.3	74	0,108,3850	AA,AG,GG		1.8064,0.3361,1.3643	possibly-damaging	853/1432	2230812	108,7808	1190	2768	3958	SO:0001583	missense	57524	exon18			GTGGGGGCGCAGG	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.2557C>T	16.37:g.2230812G>A	ENSP00000345436:p.Pro853Ser	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	13	10	NM_020764	0	0	0	0	0	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	37	CCDS42103.1	33	0.01510989010989011	6	0.012195121951219513	8	0.022099447513812154	0	0.0	19	0.025065963060686015	G	2.762	-0.257580	0.05791	0.003361	0.018064	ENSG00000167971	ENST00000343516	T	0.65916	-0.18	3.14	0.956	0.19608	.	.	.	.	.	T	0.19208	0.0461	L	0.29908	0.895	0.09310	N	1	P	0.42827	0.791	B	0.35413	0.202	T	0.13872	-1.0493	9	0.46703	T	0.11	-12.2106	5.9751	0.19373	0.0:0.4472:0.3781:0.1747	.	853	Q8WXD9	CSKI1_HUMAN	S	853	ENSP00000345436:P853S	ENSP00000345436:P853S	P	-	1	0	CASKIN1	2170813	0.022000	0.18835	0.037000	0.18230	0.056000	0.15407	0.672000	0.25187	1.568000	0.49683	0.407000	0.27541	CCC	G|0.985;A|0.015		0.756	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		A	2230812	G	A	2230812	3	1	44	1	0	0	0	0	1	0	0	0	2672	1203	42	2	1750	2	CASKIN1	16	2230812	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	622722	2230812	88123941	60	4017											
HCFC1R1	54985	broad.mit.edu;bcgsc.ca	37	chr16	3073346	3073346	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttctcctcagacagaaactGcttgcgcagaggctccctgg	8	9	11	13	1	2	3	1	0	1	3	4	3	3	3	2	2	3	4	2	2	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr16:3073346G>C	ENST00000248089.3	-	3	473	c.169C>G	c.(169-171)Cag>Gag	p.Q57E	HCFC1R1_ENST00000574151.1_Missense_Mutation_p.Q38E|HCFC1R1_ENST00000572355.1_Missense_Mutation_p.Q17E|HCFC1R1_ENST00000354679.3_Missense_Mutation_p.Q55E|THOC6_ENST00000326266.8_5'Flank|THOC6_ENST00000575576.1_5'Flank|HCFC1R1_ENST00000574980.1_Missense_Mutation_p.Q57E|THOC6_ENST00000574549.1_5'Flank|HCFC1R1_ENST00000396916.1_Missense_Mutation_p.Q57E|THOC6_ENST00000253952.9_5'Flank	NM_017885.2	NP_060355.1	Q9NWW0	HPIP_HUMAN	host cell factor C1 regulator 1 (XPO1 dependent)	57						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(1)|upper_aerodigestive_tract(1)	3						GACAGAAACTGCTTGCGCAGA	0.592																																					p.Q57E													.	HCFC1R1-90	0			c.C169G						.						99	105	103					16																	3073346		2198	4300	6498	SO:0001583	missense	54985	exon3			GAAACTGCTTGCG	AK000575	CCDS10490.1, CCDS32375.1, CCDS73815.1	16p13.3	2008-02-05	2005-12-01			ENSG00000103145			21198	protein-coding gene	gene with protein product			"host cell factor C1 regulator 1 (XPO1 dependant)"			12235138	Standard	NM_001002018		Approved	HPIP, FLJ20568	uc002csy.1	Q9NWW0		ENST00000248089.3:c.169C>G	16.37:g.3073346G>C	ENSP00000248089:p.Gln57Glu	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	284	9	NM_017885	0	1	380	388	7	D3DUA7|Q68EN7	Missense_Mutation	SNP	ENST00000248089.3	37	CCDS10490.1	.	.	.	.	.	.	.	.	.	.	G	9.580	1.123400	0.20959	.	.	ENSG00000103145	ENST00000248089;ENST00000354679;ENST00000396916	T;T	0.46819	0.86;0.86	5.69	4.74	0.60224	.	0.869784	0.09802	N	0.753977	T	0.34919	0.0914	N	0.19112	0.55	0.33679	D	0.611854	B;B	0.31817	0.341;0.049	B;B	0.31101	0.124;0.018	T	0.43877	-0.9364	10	0.51188	T	0.08	-8.8739	10.4168	0.44327	0.0893:0.0:0.9107:0.0	.	38;57	Q9NWW0-2;Q9NWW0	.;HPIP_HUMAN	E	57;38;57	ENSP00000248089:Q57E;ENSP00000380123:Q57E	ENSP00000248089:Q57E	Q	-	1	0	HCFC1R1	3013347	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	3.551000	0.53698	1.421000	0.47157	0.655000	0.94253	CAG	.		0.592	HCFC1R1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436969.1	NM_017885		C	3073346	G	C	3073346	3	2	44	1	0	0	0	0	1	0	0	0	7013	1328	46	4	255	4	HCFC1R1	16	3073346	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	842534	3073346	87281407	61	4018											
RBBP6	5930	broad.mit.edu	37	chr16	24551952	24551952	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ggaatcccttggcaccatgtCctgtgtgcattataaatttt	9	15	8	9	0	0	0	0	0	0	0	2	1	2	1	3	2	1	2	3	2	4	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr16:24551952C>G	ENST00000319715.4	+	1	437	c.5C>G	c.(4-6)tCc>tGc	p.S2C	RBBP6_ENST00000381039.3_Missense_Mutation_p.S2C|RBBP6_ENST00000452655.2_Missense_Mutation_p.S2C|RBBP6_ENST00000348022.2_Missense_Mutation_p.S2C	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	2					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		GGCACCATGTCCTGTGTGCAT	0.408																																					p.S2C													.	RBBP6-230	0			c.C5G						.						114	101	106					16																	24551952		2197	4300	6497	SO:0001583	missense	5930	exon1			CCATGTCCTGTGT		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5C>G	16.37:g.24551952C>G	ENSP00000317872:p.Ser2Cys	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	213	6	NM_018703	0	0	10	12	2	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.578787	0.86645	.	.	ENSG00000122257	ENST00000381039;ENST00000452655;ENST00000319715;ENST00000348022	T;T;T;T	0.64085	0.85;-0.08;0.97;1.08	5.26	5.26	0.73747	.	0.060916	0.64402	D	0.000002	T	0.81795	0.4898	M	0.86651	2.83	0.58432	D	0.999998	D;P;P;D	0.89917	0.999;0.956;0.927;1.0	D;P;P;D	0.80764	0.994;0.74;0.554;0.971	D	0.83673	0.0167	10	0.48119	T	0.1	-8.0E-4	17.4217	0.87517	0.0:1.0:0.0:0.0	.	2;2;2;2	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-3	.;.;RBBP6_HUMAN;.	C	2	ENSP00000370427:S2C;ENSP00000390537:S2C;ENSP00000317872:S2C;ENSP00000316291:S2C	ENSP00000317872:S2C	S	+	2	0	RBBP6	24459453	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.190000	0.77755	2.449000	0.82847	0.655000	0.94253	TCC	.		0.408	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		G	24551952	C	G	24551952	3	3	44	1	0	0	0	0	1	0	0	0	13135	855	30	4	7	4	RBBP6	16	24551952	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	21478606	24551952	65802801	62	4019											
KIAA0664	23277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	2604434	2604434	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggggacaaaggcactacCttttcttctgcagcacagcg	10	8	12	11	1	2	0	0	0	2	0	2	2	2	2	1	4	4	3	1	4	2	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:2604434C>T	ENST00000570628.2	-	7	1016	c.911G>A	c.(910-912)aGg>aAg	p.R304K	CLUH_ENST00000435359.1_Splice_Site_p.R304K|CLUH_ENST00000538975.1_Splice_Site_p.R304K			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	304					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											AAGGCACTACCTTTTCTTCTG	0.602																																					p.R304K		.											.	.	0			c.G911A						.						37	38	38					17																	2604434		2030	4170	6200	SO:0001630	splice_region_variant	23277	exon7			CACTACCTTTTCT	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.911+1G>A	17.37:g.2604434C>T		Somatic	63	1		WXS	Illumina HiSeq	Phase_I	73	39	NM_015229	0	0	1	7	6	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490254	0.84962	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	T;T	0.80909	-1.43;-1.43	5.18	5.18	0.71444	GSKIP/TIF31 domain (1);	0.000000	0.85682	D	0.000000	T	0.76919	0.4055	L	0.43598	1.365	0.80722	D	1	P;B	0.36412	0.552;0.35	B;B	0.38500	0.275;0.188	T	0.74842	-0.3527	9	.	.	.	.	17.6956	0.88281	0.0:1.0:0.0:0.0	.	304;304	O75153;C9J6D7	K0664_HUMAN;.	K	304	ENSP00000388872:R304K;ENSP00000439628:R304K	.	R	-	2	0	KIAA0664	2551184	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	5.780000	0.68956	2.409000	0.81822	0.655000	0.94253	AGG	.		0.602	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	Missense_Mutation	T	2604434	C	T	2604434	5	4	44	1	0	0	0	0	0	0	1	0	8210	695	24	2	3098	2	KIAA0664	17	2604434	Splice_Site	SNP	C	TCGA-B3-4103-01A-01D-1458-08		2604434	78590776	63	4020											
ANKFY1	51479	broad.mit.edu;bcgsc.ca	37	chr17	4084580	4084580	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagcaggcggtgggctcgtTgttttcatcaatggctctgt	7	13	13	8	2	3	0	2	0	1	0	4	0	3	0	0	4	1	5	0	4	2	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:4084580T>C	ENST00000341657.4	-	16	2244	c.2209A>G	c.(2209-2211)Aac>Gac	p.N737D	CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000570535.1_Missense_Mutation_p.N779D|ANKFY1_ENST00000574367.1_Missense_Mutation_p.N738D	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	737	Interaction with RHOD and RAB5A. {ECO:0000269|PubMed:24102721}.				endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GTGGGCTCGTTGTTTTCATCA	0.522																																					p.N779D													.	ANKFY1-93	0			c.A2335G						.						60	60	60					17																	4084580		1933	4142	6075	SO:0001583	missense	51479	exon16			GCTCGTTGTTTTC	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"Zinc fingers, FYVE domain containing", "BTB/POZ domain containing", "Ankyrin repeat domain containing"	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2209A>G	17.37:g.4084580T>C	ENSP00000343362:p.Asn737Asp	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	212	7	NM_001257999	0	0	31	31	0	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	T	10.77	1.445290	0.25987	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	5.43	3.05	0.35203	Ankyrin repeat-containing domain (4);	0.153953	0.56097	D	0.000024	T	0.41673	0.1169	L	0.31294	0.92	0.80722	D	1	B;B;B;B	0.15473	0.001;0.006;0.005;0.013	B;B;B;B	0.15052	0.003;0.011;0.007;0.012	T	0.28364	-1.0046	9	0.49607	T	0.09	-14.4722	7.4956	0.27487	0.0:0.0754:0.1418:0.7828	.	679;737;738;779	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	D	738;679	.	ENSP00000343362:N738D	N	-	1	0	ANKFY1	4031329	1.000000	0.71417	0.953000	0.39169	0.282000	0.26991	5.095000	0.64529	0.870000	0.35726	0.459000	0.35465	AAC	.		0.522	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		C	4084580	T	C	4084580	3	2	44	1	0	0	0	0	1	0	0	0	626	1812	63	3	1340	3	ANKFY1	17	4084580	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	1480146	4084580	77110630	64	4021											
ASGR1	432	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7081872	7081872	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgctgaaggtcttgatacTccttggtcatgatagggctg	8	13	13	7	0	2	3	1	3	1	0	3	4	3	3	1	3	2	2	1	3	3	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:7081872T>G	ENST00000269299.3	-	2	410	c.11A>C	c.(10-12)gAg>gCg	p.E4A	ASGR1_ENST00000380920.4_5'Flank|ASGR1_ENST00000572879.1_5'Flank|ASGR1_ENST00000574388.1_Missense_Mutation_p.E4A	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	4					cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						GTCTTGATACTCCTTGGTCAT	0.577																																					p.E4A		.											.	ASGR1-153	0			c.A11C						.						129	90	103					17																	7081872		2203	4300	6503	SO:0001583	missense	432	exon2			TGATACTCCTTGG		CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"C-type lectin domain containing"	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.11A>C	17.37:g.7081872T>G	ENSP00000269299:p.Glu4Ala	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	124	60	NM_001671	0	0	0	0	0	I3L1X1	Missense_Mutation	SNP	ENST00000269299.3	37	CCDS11089.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533519	0.45073	.	.	ENSG00000141505	ENST00000269299;ENST00000380920	T	0.01015	5.44	4.43	4.43	0.53597	.	0.332135	0.21660	N	0.071026	T	0.00724	0.0024	N	0.14661	0.345	0.80722	D	1	B	0.30741	0.293	B	0.22386	0.039	T	0.73212	-0.4054	10	0.32370	T	0.25	.	10.0445	0.42177	0.0:0.0:0.0:1.0	.	4	P07306	ASGR1_HUMAN	A	4	ENSP00000269299:E4A	ENSP00000269299:E4A	E	-	2	0	ASGR1	7022596	0.996000	0.38824	0.991000	0.47740	0.852000	0.48524	3.429000	0.52800	1.875000	0.54330	0.449000	0.29647	GAG	.		0.577	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671		G	7081872	T	G	7081872	3	3	44	1	0	0	0	0	1	0	0	0	1040	1551	54	5	896	5	ASGR1	17	7081872	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	2997292	7081872	74113338	65	4022											
PFAS	5198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	8170542	8170542	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctttcccaaagcctccgtgcCccgtgagcctggtgagggag	6	8	13	14	2	0	2	0	2	0	0	2	3	2	3	6	2	3	0	6	2	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:8170542C>T	ENST00000314666.6	+	24	3297	c.3164C>T	c.(3163-3165)cCc>cTc	p.P1055L	PFAS_ENST00000545834.1_Missense_Mutation_p.P631L	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1055					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	GCCTCCGTGCCCCGTGAGCCT	0.677																																					p.P1055L		.											.	PFAS-94	0			c.C3164T						.						18	17	17					17																	8170542		2201	4299	6500	SO:0001583	missense	5198	exon24			CCGTGCCCCGTGA	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"FGAR amidotransferase"	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3164C>T	17.37:g.8170542C>T	ENSP00000313490:p.Pro1055Leu	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_012393	0	0	1	1	0	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	.	.	.	.	.	.	.	.	.	.	C	6.971	0.549059	0.13312	.	.	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.33216	1.42;2.17	5.57	4.6	0.57074	AIR synthase-related protein, C-terminal (1);	0.289920	0.33959	N	0.004381	T	0.20495	0.0493	N	0.22421	0.69	0.48452	D	0.999654	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.04509	-1.0946	10	0.87932	D	0	-5.7605	8.6639	0.34110	0.0:0.8278:0.0:0.1722	.	1055;1055	A8K8N7;O15067	.;PUR4_HUMAN	L	631;1055;464	ENSP00000441706:P631L;ENSP00000313490:P1055L	ENSP00000313490:P1055L	P	+	2	0	PFAS	8111267	0.561000	0.26578	0.827000	0.32855	0.173000	0.22820	1.670000	0.37502	1.368000	0.46115	0.655000	0.94253	CCC	.		0.677	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			T	8170542	C	T	8170542	3	4	44	1	0	0	0	0	1	0	0	0	11780	623	22	2	3254	2	PFAS	17	8170542	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	1088670	8170542	73024668	66	4023											
PIPOX	51268	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	27370356	27370357	+	Splice_Site	INS	-	-	G																															aggatcctcctgctggagcaINSggtactgtgtcccttctgca																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:27370356_27370357insG	ENST00000323372.4	+	1	439_440	c.113_114insG	c.(112-117)cagttc>caGgttc	p.F39fs	PIPOX_ENST00000583215.1_Intron	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	39					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)			endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	CTGCTGGAGCAGGTACTGTGTC	0.584																																					p.Q38fs		.											.	PIPOX-90	0			c.113_114insG						.																																			SO:0001630	splice_region_variant	51268	exon1			.	AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"L-pipecolic acid oxidase"					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.114+1->G	17.37:g.27370358_27370358dupG		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	156	78	NM_016518	0	0	0	0	0	B3KNH0|Q96H28|Q9C070	Frame_Shift_Ins	INS	ENST00000323372.4	37	CCDS11248.1																																																																																			.		0.584	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518	Frame_Shift_Ins	G	27370357	-	G	27370356	8	5	44	1	0	1	1	0	0	0	1	0	11969	202	7	0	115	0	PIPOX	17	27370356	Splice_Site	INS	-	TCGA-B3-4103-01A-01D-1458-08	19199814	27370356	53824854	67	4024											
MAP3K14	9020	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	43364549	43364549	+	RNA	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatggtgcagctctcctgctCaggggtcctggggaggggtt	4	10	18	9	0	2	0	1	0	1	0	4	2	3	1	2	7	3	4	2	7	0	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:43364549C>T	ENST00000344686.2	-	0	616							Q99558	M3K14_HUMAN	mitogen-activated protein kinase kinase kinase 14						cellular response to mechanical stimulus (GO:0071260)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|T cell costimulation (GO:0031295)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|NF-kappaB-inducing kinase activity (GO:0004704)|protein kinase activity (GO:0004672)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CTCTCCTGCTCAGGGGTCCTG	0.617																																					.													.	MAP3K14-1453	0			.						.						43	44	44					17																	43364549		1988	4161	6149			9020	.			CCTGCTCAGGGGT	Y10256	CCDS74079.1	17q21.31	2014-06-16			ENSG00000006062	ENSG00000006062	2.7.11.25	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6853	protein-coding gene	gene with protein product	"serine/threonine protein-kinase"	604655				9020361	Standard	NM_003954		Approved	NIK, HSNIK, FTDCR1B, HS	uc002iiw.1	Q99558	OTTHUMG00000180364		17.37:g.43364549C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	87	20	.	0	0	2	5	3	A8K2D8|D3DX67|Q8IYN1	Missense_Mutation	SNP	ENST00000344686.2	37		.	.	.	.	.	.	.	.	.	.	C	25.5	4.647380	0.87958	.	.	ENSG00000006062	ENST00000344686	.	.	.	5.26	5.26	0.73747	.	0.000000	0.64402	D	0.000005	T	0.79347	0.4430	.	.	.	0.34884	D	0.744823	D	0.63880	0.993	D	0.72625	0.978	T	0.82985	-0.0185	7	0.87932	D	0	.	16.0168	0.80445	0.0:1.0:0.0:0.0	.	170	Q99558	M3K14_HUMAN	K	170	.	ENSP00000342059:E170K	E	-	1	0	MAP3K14	40720332	0.997000	0.39634	0.983000	0.44433	0.963000	0.63663	4.708000	0.61859	2.451000	0.82905	0.563000	0.77884	GAG	.		0.617	MAP3K14-201	KNOWN	basic	processed_transcript	processed_transcript		NM_003954		T	43364549	C	T	43364549	1	4	44	0	1	0	0	0	0	0	0	0	9273	835	29	2		2	MAP3K14	17	43364549	RNA	SNP	C	TCGA-B3-4103-01A-01D-1458-08	15994193	43364549	37830661	68	4025											
ACE	1636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61562641	61562641	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagcaagtttgtggaggaaTatgaccggacatcccaggtg	11	8	13	9	1	0	1	0	1	0	0	1	4	1	4	3	4	1	2	3	4	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:61562641T>C	ENST00000290866.4	+	13	1990	c.1966T>C	c.(1966-1968)Tat>Cat	p.Y656H	ACE_ENST00000421982.2_5'UTR|ACE_ENST00000490216.2_Missense_Mutation_p.Y82H|ACE_ENST00000577647.1_Missense_Mutation_p.Y82H|ACE_ENST00000428043.1_Missense_Mutation_p.Y656H|ACE_ENST00000290863.6_Missense_Mutation_p.Y82H|ACE_ENST00000413513.3_Missense_Mutation_p.Y82H	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	656	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	TGTGGAGGAATATGACCGGAC	0.552																																					p.Y656H		.											.	ACE-94	0			c.T1966C						.						165	123	137					17																	61562641		2203	4300	6503	SO:0001583	missense	1636	exon13			GAGGAATATGACC	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1966T>C	17.37:g.61562641T>C	ENSP00000290866:p.Tyr656His	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	111	52	NM_000789	0	0	4	14	10	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.460662	0.43736	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.09	5.09	0.68999	.	0.060975	0.64402	D	0.000002	T	0.71031	0.3292	M	0.86864	2.845	0.80722	D	1	D;D;P;D	0.76494	0.971;0.998;0.881;0.999	P;D;P;D	0.85130	0.887;0.997;0.843;0.994	T	0.75584	-0.3267	10	0.54805	T	0.06	-20.9481	12.3936	0.55373	0.0:0.0:0.0:1.0	.	82;656;82;656	B4DXI3;P12821-2;P12821-3;P12821	.;.;.;ACE_HUMAN	H	656;656;82;82	ENSP00000290866:Y656H;ENSP00000397593:Y656H;ENSP00000290863:Y82H;ENSP00000392247:Y82H	ENSP00000290863:Y82H	Y	+	1	0	ACE	58916373	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	4.885000	0.63142	1.919000	0.55581	0.379000	0.24179	TAT	.		0.552	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			C	61562641	T	C	61562641	3	2	44	1	0	0	0	0	1	0	0	0	136	1406	49	3	2219	3	ACE	17	61562641	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	18198092	61562641	19632569	69	4026											
MYOM1	8736	broad.mit.edu	37	chr18	3188900	3188900	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctggatgccgtggactgcTtggatgctgtggactgcttg	4	12	16	9	1	0	0	0	0	0	0	0	4	0	4	2	4	4	3	2	4	0	2	rs548278691		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr18:3188900T>C	ENST00000356443.4	-	4	950	c.617A>G	c.(616-618)aAg>aGg	p.K206R	RP13-270P17.2_ENST00000580139.1_RNA|MYOM1_ENST00000400569.3_Missense_Mutation_p.K206R|MYOM1_ENST00000261606.7_Missense_Mutation_p.K206R	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	206	6 X 6 AA tandem repeats.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.K206R(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGTGGACTGCTTGGATGCTGT	0.532													T|||	1	0.000199681	0	0.0014	5008	,	,		15575	0		0	False		,,,				2504	0				p.K206R													.	MYOM1-94	1	Substitution - Missense(1)	endometrium(1)	c.A617G						.						289	273	279					18																	3188900		2064	4189	6253	SO:0001583	missense	8736	exon4			GACTGCTTGGATG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7613	protein-coding gene	gene with protein product	"skelemin"	603508	"myomesin 1 (skelemin) (185kD)", "myomesin 1 (skelemin) 185kDa", "myomesin 1, 185kDa"			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.617A>G	18.37:g.3188900T>C	ENSP00000348821:p.Lys206Arg	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	237	4	NM_003803	0	0	3	3	0	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	1.883	-0.457460	0.04508	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.48522	0.97;0.97;0.81	3.06	0.613	0.17597	.	1.261730	0.06568	N	0.747992	T	0.24851	0.0603	N	0.08118	0	0.09310	N	1	B;B	0.26195	0.144;0.089	B;B	0.19391	0.025;0.011	T	0.19582	-1.0301	10	0.20519	T	0.43	.	6.672	0.23074	0.0:0.167:0.0:0.833	.	206;206	P52179-2;P52179	.;MYOM1_HUMAN	R	206	ENSP00000348821:K206R;ENSP00000383413:K206R;ENSP00000261606:K206R	ENSP00000261606:K206R	K	-	2	0	MYOM1	3178900	0.978000	0.34361	0.001000	0.08648	0.000000	0.00434	1.274000	0.33132	0.017000	0.15025	-1.273000	0.01405	AAG	.		0.532	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		C	3188900	T	C	3188900	3	2	44	1	0	0	0	0	1	0	0	0	10116	1609	56	3	4580	3	MYOM1	18	3188900	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08		3188900	74888348	70	4027											
VPS4B	9525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	61058289	61058289	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actgtaggttttgtgttagaTagtgaccgcaacatatccga	11	13	10	7	2	0	2	0	1	0	1	1	3	1	2	2	1	1	4	2	1	5	6	rs200045966		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr18:61058289T>C	ENST00000238497.5	-	11	1457	c.1254A>G	c.(1252-1254)ctA>ctG	p.L418L		NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	418					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						TTGTGTTAGATAGTGACCGCA	0.348													T|||	1	0.000199681	0	0	5008	,	,		17931	0.001		0	False		,,,				2504	0				p.L418L		.											.	VPS4B-91	0			c.A1254G						.						121	112	115					18																	61058289		2203	4300	6503	SO:0001819	synonymous_variant	9525	exon11			GTTAGATAGTGAC	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"ATPases / AAA-type"	10895	protein-coding gene	gene with protein product		609983	"suppressor of K+ transport defect 1", "vacuolar protein sorting 4B (yeast)"	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.1254A>G	18.37:g.61058289T>C		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	136	17	NM_004869	0	0	37	44	7	Q69HW4|Q9GZS7	Silent	SNP	ENST00000238497.5	37	CCDS11983.1																																																																																			T|0.999;C|0.000		0.348	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		C	61058289	T	C	61058289	2	2	44	1	0	0	0	0	0	0	0	1	17246	1393	49	3		3	VPS4B	18	61058289	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08	57869389	61058289	17018959	71	4028											
DAZAP1	26528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1428875	1428875	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctgagcctcgggacagcaAgagccaagcgccgggacagc	11	2	15	13	3	0	2	0	1	0	1	1	4	0	4	3	2	6	2	3	2	2	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:1428875A>G	ENST00000233078.4	+	8	742	c.581A>G	c.(580-582)aAg>aGg	p.K194R	DAZAP1_ENST00000336761.6_Missense_Mutation_p.K194R|DAZAP1_ENST00000586579.1_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	194					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|maternal placenta development (GO:0001893)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGGACAGCAAGAGCCAAGCG	0.657																																					p.K194R		.											.	DAZAP1-153	0			c.A581G						.						37	46	43					19																	1428875		2203	4300	6503	SO:0001583	missense	26528	exon8			ACAGCAAGAGCCA		CCDS12065.1, CCDS12066.1	19p13.3	2013-07-16			ENSG00000071626	ENSG00000071626		"RNA binding motif (RRM) containing"	2683	protein-coding gene	gene with protein product	"deleted in azoospermia associated protein 1"	607430				10857750, 23658607	Standard	XM_005259530		Approved	MGC19907	uc002lsn.3	Q96EP5		ENST00000233078.4:c.581A>G	19.37:g.1428875A>G	ENSP00000233078:p.Lys194Arg	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	87	26	NM_018959	0	0	61	134	73	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	37	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711305	0.48517	.	.	ENSG00000071626	ENST00000233078;ENST00000336761	T;T	0.73363	-0.74;-0.74	5.03	5.03	0.67393	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.74891	0.3776	N	0.24115	0.695	0.80722	D	1	P;B;B	0.46578	0.88;0.073;0.119	P;B;B	0.62184	0.899;0.014;0.031	T	0.71573	-0.4552	10	0.22109	T	0.4	.	13.948	0.64099	1.0:0.0:0.0:0.0	.	261;194;194	Q5IRN4;Q96EP5;Q96EP5-2	.;DAZP1_HUMAN;.	R	194	ENSP00000233078:K194R;ENSP00000337132:K194R	ENSP00000233078:K194R	K	+	2	0	DAZAP1	1379875	1.000000	0.71417	0.983000	0.44433	0.941000	0.58515	6.547000	0.73892	1.906000	0.55180	0.459000	0.35465	AAG	.		0.657	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		G	1428875	A	G	1428875	3	3	44	1	0	0	0	0	1	0	0	0	4250	72	3	3	611	3	DAZAP1	19	1428875	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08		1428875	57700108	72	4029											
EEF2	1938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	3979985	3979985	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cgtcttcaccaggaactggtCcacgcccacgaggcccacaa	10	5	9	17	3	2	0	1	0	1	0	3	2	3	1	4	3	1	0	4	3	2	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:3979985C>T	ENST00000309311.6	-	10	1514	c.1426G>A	c.(1426-1428)Gac>Aac	p.D476N	SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	476					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGAACTGGTCCACGCCCACG	0.592																																					p.D476N	Colon(165;1804 1908 4071 6587 18799)	.											.	EEF2-90	0			c.G1426A						.						69	57	61					19																	3979985		2203	4300	6503	SO:0001583	missense	1938	exon10			ACTGGTCCACGCC	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"polypeptidyl-tRNA translocase"	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.1426G>A	19.37:g.3979985C>T	ENSP00000307940:p.Asp476Asn	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	76	23	NM_001961	1	1	765	1429	662	B2RMP5|D6W618|Q58J86	Missense_Mutation	SNP	ENST00000309311.6	37	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	C	35	5.492373	0.96339	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	D	0.82255	-1.59	5.45	5.45	0.79879	Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	D	0.95239	0.8456	H	0.98965	4.385	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.97201	0.9864	10	0.87932	D	0	-55.7781	18.2479	0.89993	0.0:1.0:0.0:0.0	.	476	P13639	EF2_HUMAN	N	476	ENSP00000307940:D476N	ENSP00000307940:D476N	D	-	1	0	EEF2	3930985	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	7.773000	0.85462	2.555000	0.86185	0.561000	0.74099	GAC	.		0.592	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961		T	3979985	C	T	3979985	3	4	44	1	0	0	0	0	1	0	0	0	4940	855	30	2	1174	2	EEF2	19	3979985	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	2551110	3979985	55148998	73	4030											
FBN3	84467	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	8182139	8182139	+	Frame_Shift_Del	DEL	T	T	-																															cagtgttaatacagtgcacgTcacacccaccattctggacc																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:8182139delT	ENST00000600128.1	-	28	3914	c.3500delA	c.(3499-3501)gacfs	p.D1167fs	FBN3_ENST00000270509.2_Frame_Shift_Del_p.D1167fs|FBN3_ENST00000601739.1_Frame_Shift_Del_p.D1167fs			Q75N90	FBN3_HUMAN	fibrillin 3	1167	EGF-like 16; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACAGTGCACGTCACACCCACC	0.637																																					p.D1167fs		.											.	FBN3-100	0			c.3500delA						.						82	67	72					19																	8182139		2203	4300	6503	SO:0001589	frameshift_variant	84467	exon27			.		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3500delA	19.37:g.8182139delT	ENSP00000470498:p.Asp1167fs	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	62	14	NM_032447	0	0	0	0	0	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Frame_Shift_Del	DEL	ENST00000600128.1	37	CCDS12196.1																																																																																			.		0.637	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		-	8182139	T	-	8182139	7	5	44	1	0	1	0	1	0	0	0	0	5723	1667	58	0	5077	0	FBN3	19	8182139	Frame_Shift_Del	DEL	T	TCGA-B3-4103-01A-01D-1458-08	4202154	8182139	50946844	74	4031											
EIF3G	8666	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10230530	10230530	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actcactcaaagtctccagtAggcatcgcaaaaagtattct	14	10	6	11	1	4	0	2	0	2	0	6	0	4	0	1	1	0	4	1	1	5	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:10230530A>G	ENST00000253108.4	-	1	48	c.6T>C	c.(4-6)ccT>ccC	p.P2P	EIF3G_ENST00000587168.1_5'Flank	NM_003755.3	NP_003746.2			eukaryotic translation initiation factor 3, subunit G											central_nervous_system(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			AGTCTCCAGTAGGCATCGCAA	0.642											OREG0025231	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P2P	Colon(124;1100 1638 3822 4510 4876)	.											.	EIF3G-68	0			c.T6C						.						57	60	59					19																	10230530		2203	4300	6503	SO:0001819	synonymous_variant	8666	exon1			TCCAGTAGGCATC	U96074	CCDS12227.1	19p13.2	2013-02-12	2007-07-27	2007-07-27		ENSG00000130811		"RNA binding motif (RRM) containing"	3274	protein-coding gene	gene with protein product		603913	"eukaryotic translation initiation factor 3, subunit 4 delta, 44kDa"	EIF3S4		9822659	Standard	NM_003755		Approved	eIF3-delta, eIF3-p44, eIF3g	uc002mnd.3	O75821		ENST00000253108.4:c.6T>C	19.37:g.10230530A>G		Somatic	120	0	663	WXS	Illumina HiSeq	Phase_I	114	27	NM_003755	0	0	0	0	0		Silent	SNP	ENST00000253108.4	37	CCDS12227.1																																																																																			.		0.642	EIF3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451144.1			G	10230530	A	G	10230530	2	3	44	1	0	0	0	0	0	0	0	1	5030	407	15	3		3	EIF3G	19	10230530	Silent	SNP	A	TCGA-B3-4103-01A-01D-1458-08	2048391	10230530	48898453	75	4032											
ZNF627	199692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11728624	11728624	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgatccacttactttcgaGtacatgaaaaaattcatact	14	13	5	9	2	1	1	1	1	0	0	4	3	2	1	1	0	3	1	1	0	6	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:11728624G>T	ENST00000361113.5	+	4	1514	c.1306G>T	c.(1306-1308)Gta>Tta	p.V436L	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	436					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)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						TTACTTTCGAGTACATGAAAA	0.423																																					p.V436L	Melanoma(112;173 1614 10731 17751 23322)	.											.	ZNF627-91	0			c.G1306T						.						55	59	57					19																	11728624		2198	4297	6495	SO:0001583	missense	199692	exon4			TTTCGAGTACATG	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.1306G>T	19.37:g.11728624G>T	ENSP00000354414:p.Val436Leu	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	149	38	NM_145295	0	0	12	21	9	O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	ENST00000361113.5	37	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	g	3.954	-0.011756	0.07727	.	.	ENSG00000198551	ENST00000361113	T	0.07908	3.15	1.43	-2.1	0.07210	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04588	0.0125	N	0.25825	0.765	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44345	-0.9334	9	0.23302	T	0.38	.	3.0288	0.06099	0.5661:0.2481:0.1857:0.0	.	436	Q7L945	ZN627_HUMAN	L	436	ENSP00000354414:V436L	ENSP00000354414:V436L	V	+	1	0	ZNF627	11589624	0.000000	0.05858	0.000000	0.03702	0.781000	0.44180	-2.946000	0.00680	-0.450000	0.07107	-0.670000	0.03821	GTA	.		0.423	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		T	11728624	G	T	11728624	3	4	44	1	0	0	0	0	1	0	0	0	18083	1029	36	4	1320	4	ZNF627	19	11728624	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	1498094	11728624	47400359	76	4033											
NXNL1	115861	broad.mit.edu	37	chr19	17571478	17571478	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccagctgagccgcccgcagTacatagaactcatctgtgag	10	7	11	13	2	2	3	1	2	1	1	2	3	2	3	3	0	4	3	3	0	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:17571478T>G	ENST00000301944.2	-	1	285	c.201A>C	c.(199-201)gtA>gtC	p.V67V	CTD-2521M24.10_ENST00000594663.1_5'UTR	NM_138454.1	NP_612463.1	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1	67	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				photoreceptor cell maintenance (GO:0045494)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	6						CCGCCCGCAGTACATAGAACT	0.582																																					p.V67V													.	NXNL1-46	0			c.A201C						.						76	71	73					19																	17571478		2203	4300	6503	SO:0001819	synonymous_variant	115861	exon1			CCGCAGTACATAG	BC014127	CCDS12360.1	19p13.11	2014-05-21	2007-08-16	2007-08-16	ENSG00000171773	ENSG00000171773			25179	protein-coding gene	gene with protein product		608791	"thioredoxin-like 6"	TXNL6		12477932	Standard	NM_138454		Approved	RDCVF	uc002ngs.3	Q96CM4	OTTHUMG00000182798	ENST00000301944.2:c.201A>C	19.37:g.17571478T>G		Somatic	156	0		WXS	Illumina HiSeq	Phase_I	154	4	NM_138454	0	0	0	0	0	Q0QD37	Silent	SNP	ENST00000301944.2	37	CCDS12360.1																																																																																			.		0.582	NXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463803.1	NM_138454		G	17571478	T	G	17571478	2	3	44	1	0	0	0	0	0	0	0	1	10814	1625	57	5		5	NXNL1	19	17571478	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08	5842854	17571478	41557505	77	4034											
BCKDHA	593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41928188	41928188	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcaacttcgctgccacaCttgagtgccccatcatcttc	7	12	6	16	1	3	1	2	1	1	0	5	1	3	1	3	0	3	2	3	0	1	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:41928188C>G	ENST00000269980.2	+	6	1134	c.766C>G	c.(766-768)Ctt>Gtt	p.L256V	BCKDHA_ENST00000595085.1_Missense_Mutation_p.L290V|BCKDHA_ENST00000535632.1_3'UTR|BCKDHA_ENST00000457836.2_Missense_Mutation_p.L234V|CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.L290V	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	256					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						CGCTGCCACACTTGAGTGCCC	0.612																																					p.L256V		.											.	BCKDHA-90	0			c.C766G						.						114	100	104					19																	41928188		2203	4300	6503	SO:0001583	missense	593	exon6			GCCACACTTGAGT	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"maple syrup urine disease"	608348	"branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)", "2-oxoisovalerate dehydrogenase (lipoamide)"	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.766C>G	19.37:g.41928188C>G	ENSP00000269980:p.Leu256Val	Somatic	200	1		WXS	Illumina HiSeq	Phase_I	173	38	NM_000709	0	0	25	50	25	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.256185	0.59321	.	.	ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	D;D;D;D	0.95756	-3.8;-3.8;-3.8;-3.8	4.77	2.48	0.30137	Dehydrogenase, E1 component (1);	0.072118	0.53938	D	0.000049	D	0.96543	0.8872	M	0.81802	2.56	0.54753	D	0.999983	D;B;P;B	0.59767	0.986;0.407;0.88;0.193	P;B;P;B	0.59012	0.85;0.219;0.71;0.132	D	0.95960	0.8961	10	0.59425	D	0.04	-34.1699	10.718	0.46023	0.0:0.812:0.0:0.188	.	234;256;256;290	B4DP47;Q59EI3;P12694;F5H5P2	.;.;ODBA_HUMAN;.	V	290;256;227;234;256	ENSP00000443246:L290V;ENSP00000269980:L256V;ENSP00000440345:L227V;ENSP00000416000:L234V	ENSP00000269980:L256V	L	+	1	0	BCKDHA;CTC-435M10.3	46620028	0.863000	0.29885	0.621000	0.29145	0.908000	0.53690	1.593000	0.36686	1.209000	0.43321	0.563000	0.77884	CTT	.		0.612	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709		G	41928188	C	G	41928188	3	3	44	1	0	0	0	0	1	0	0	0	1360	565	20	4	788	4	BCKDHA	19	41928188	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	24356710	41928188	17200795	78	4035											
SLC5A3	6526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	35467607	35467607	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctaatagaagcaccgtgaGtggatacttcctggcggggc	10	9	13	9	2	1	2	0	1	1	1	2	3	2	3	2	4	2	1	2	4	4	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr21:35467607G>A	ENST00000381151.3	+	2	622	c.110G>A	c.(109-111)aGt>aAt	p.S37N	AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron|SLC5A3_ENST00000608209.1_Missense_Mutation_p.S37N			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	37					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						AGCACCGTGAGTGGATACTTC	0.488																																					p.S37N		.											.	SLC5A3-92	0			c.G110A						.						169	168	169					21																	35467607		2203	4300	6503	SO:0001583	missense	6526	exon2			CCGTGAGTGGATA		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.110G>A	21.37:g.35467607G>A	ENSP00000370543:p.Ser37Asn	Somatic	265	0		WXS	Illumina HiSeq	Phase_I	308	107	NM_006933	0	0	2	5	3	O43489	Missense_Mutation	SNP	ENST00000381151.3	37	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502590	0.44455	.	.	ENSG00000198743	ENST00000381151	D	0.86497	-2.13	6.09	6.09	0.99107	.	0.000000	0.85682	D	0.000000	D	0.84252	0.5431	L	0.42487	1.325	0.52099	D	0.999947	B	0.27286	0.174	B	0.20767	0.031	T	0.80355	-0.1417	10	0.56958	D	0.05	.	19.2541	0.93938	0.0:0.0:1.0:0.0	.	37	P53794	SC5A3_HUMAN	N	37	ENSP00000370543:S37N	ENSP00000370543:S37N	S	+	2	0	SLC5A3	34389477	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.594000	0.98254	2.898000	0.99336	0.596000	0.82720	AGT	.		0.488	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			A	35467607	G	A	35467607	3	1	44	1	0	0	0	0	1	0	0	0	14698	1029	36	2	112	2	SLC5A3	21	35467607	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		35467607	12662288	79	4036											
SUSD2	56241	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24581140	24581140	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgagaggaccctgtggcCtgggcacgaactcagtgcca	8	7	13	13	2	1	1	1	0	0	1	2	4	2	2	4	3	2	1	4	3	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:24581140C>A	ENST00000358321.3	+	6	1122	c.861C>A	c.(859-861)gcC>gcA	p.A287A		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	287	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						ACCCTGTGGCCTGGGCACGAA	0.662																																					p.A287A		.											.	SUSD2-91	0			c.C861A						.						29	30	30					22																	24581140		2203	4299	6502	SO:0001819	synonymous_variant	56241	exon6			TGTGGCCTGGGCA	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.861C>A	22.37:g.24581140C>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	69	21	NM_019601	0	0	15	17	2	Q9H5Y6	Silent	SNP	ENST00000358321.3	37	CCDS13824.1																																																																																			.		0.662	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24581140	C	A	24581140	2	1	44	1	0	0	0	0	0	0	0	1	15440	668	24	4		4	SUSD2	22	24581140	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08		24581140	26723426	80	4037											
BAIAP2L2	80115	ucsc.edu	37	chr22	38483204	38483204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaggtcatgggggtcaCgggggtcatgggattcacgg	7	8	19	7	2	4	0	4	0	0	0	4	2	4	2	0	8	0	0	0	8	0	1	rs201090429	byFrequency	TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:38483204C>T	ENST00000381669.3	-	11	1330	c.1186G>A	c.(1186-1188)Gtg>Atg	p.V396M	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	396					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					atgggggtcacgggggtcatg	0.627													C|||	25	0.00499201	0.0068	0	5008	,	,		13610	0.003		0.005	False		,,,				2504	0.0082				p.V396M													.	BAIAP2L2-91	0			c.G1186A						.						37	45	42					22																	38483204		1928	4122	6050	SO:0001583	missense	80115	exon11			GGGTCACGGGGGT	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1186G>A	22.37:g.38483204C>T	ENSP00000371085:p.Val396Met	Somatic	60	2		WXS	Illumina HiSeq		90	4	NM_025045	0	0	17	17	0	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	.	.	.	.	.	.	.	.	.	.	C	7.609	0.674489	0.14841	.	.	ENSG00000128298	ENST00000381669;ENST00000402500;ENST00000428572	T;T	0.21932	1.98;1.98	3.32	-3.36	0.04913	.	1.502590	0.04754	N	0.425150	T	0.11110	0.0271	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33240	-0.9876	10	0.45353	T	0.12	-10.8299	4.4703	0.11708	0.2523:0.4451:0.0:0.3026	.	396	Q6UXY1	BI2L2_HUMAN	M	396;396;87	ENSP00000371085:V396M;ENSP00000410074:V87M	ENSP00000371085:V396M	V	-	1	0	BAIAP2L2	36813150	.	.	0.275000	0.24674	0.069000	0.16628	.	.	-0.339000	0.08401	-1.449000	0.01048	GTG	C|0.997;T|0.003		0.627	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		T	38483204	C	T	38483204	3	4	44	1	0	0	0	0	1	0	0	0	1304	536	19	1	419	1	BAIAP2L2	22	38483204	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	13902064	38483204	12821362	81	4038											
EP300	2033	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	41574679	41574681	+	In_Frame_Del	DEL	CCC	CCC	-																															ctccacggccacagtcccagCccccccactccagtccttcc																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:41574679_41574681delCCC	ENST00000263253.7	+	31	8183_8185	c.6964_6966delCCC	c.(6964-6966)cccdel	p.P2323del	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2323					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACAGTCCCAGCCCCCCCACTCCA	0.616			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.2322_2322del		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300-2011	0			c.6964_6966del						.																																			SO:0001651	inframe_deletion	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6964_6966delCCC	22.37:g.41574682_41574684delCCC	ENSP00000263253:p.Pro2323del	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	146	38	NM_001429	0	0	0	0	0	B1AKC2	In_Frame_Del	DEL	ENST00000263253.7	37	CCDS14010.1																																																																																			.		0.616	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41574681	CCC	-	41574679	7	5	44	1	0	1	0	1	0	0	0	0	5161	739	26	0	7086	0	EP300	22	41574679	In_Frame_Del	DEL	CCC	TCGA-B3-4103-01A-01D-1458-08	3091475	41574679	9729887	82	4039											
TTLL1	25809	broad.mit.edu;bcgsc.ca	37	chr22	43442517	43442517	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgttgagggtgtcattaatCaggttgtacttgaggattcg	9	15	13	4	1	2	2	2	2	0	0	3	3	2	3	0	3	1	3	0	3	2	6			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:43442517C>G	ENST00000266254.7	-	10	1281	c.1041G>C	c.(1039-1041)ctG>ctC	p.L347L	TTLL1_ENST00000331018.7_Silent_p.L318L|AL022476.2_ENST00000443063.1_RNA	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	347	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		TGTCATTAATCAGGTTGTACT	0.512																																					p.L347L													.	TTLL1-92	0			c.G1041C						.						365	313	331					22																	43442517		2203	4300	6503	SO:0001819	synonymous_variant	25809	exon10			ATTAATCAGGTTG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"Tubulin tyrosine ligase-like family"	1312	protein-coding gene	gene with protein product		608955	"tubulin tyrosine ligase-like 1"	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.1041G>C	22.37:g.43442517C>G		Somatic	305	0		WXS	Illumina HiSeq	Phase_I	290	13	NM_012263	0	0	19	19	0	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	C	3.860	-0.030135	0.07543	.	.	ENSG00000100271	ENST00000495814	.	.	.	5.41	0.463	0.16700	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2216	0.15371	0.1717:0.307:0.4416:0.0796	.	.	.	.	S	273	.	.	X	-	2	2	TTLL1	41772461	0.997000	0.39634	0.466000	0.27168	0.403000	0.30841	0.331000	0.19733	0.219000	0.20840	0.555000	0.69702	TGA	.		0.512	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		G	43442517	C	G	43442517	2	3	44	1	0	0	0	0	0	0	0	1	16755	813	29	4		4	TTLL1	22	43442517	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08	1867838	43442517	7862049	83	4040											
CCNL2	81669	hgsc.bcm.edu;broad.mit.edu	37	chr1	1334456	1334456	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agctcgcagcccaccacgcgGaggtcggtctctgtgtcggt	5	8	14	14	5	1	0	0	0	1	0	5	1	1	1	2	4	2	2	2	4	0	0	rs374243154		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:1334456G>A	ENST00000400809.3	-	1	236	c.231C>T	c.(229-231)ctC>ctT	p.L77L	CCNL2_ENST00000408952.5_5'Flank|RP4-758J18.2_ENST00000576232.1_5'Flank|RP4-758J18.2_ENST00000444362.1_5'Flank|CCNL2_ENST00000408918.4_Silent_p.L77L|MRPL20_ENST00000493287.1_5'Flank|RP4-758J18.2_ENST00000448629.2_5'Flank	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	77					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		CCACCACGCGGAGGTCGGTCT	0.692																																					p.L77L		.											.	CCNL2-70	0			c.C231T						.	G	,	0,4404		0,0,2202	52	43	46		231,231	0.9	0.1	1		46	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	CCNL2	NM_001039577.3,NM_030937.4	,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,	77/227,77/521	1334456	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	81669	exon1			CACGCGGAGGTCG	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.231C>T	1.37:g.1334456G>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	47	16	NM_030937	0	0	28	63	35	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Silent	SNP	ENST00000400809.3	37	CCDS30557.1																																																																																			.		0.692	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		A	1334456	G	A	1334456	2	1	45	1	0	0	0	0	0	0	0	1	2938	1161	41	2		2	CCNL2	1	1334456	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08		1334456	247916165	1	4041											
CCNL2	81669	hgsc.bcm.edu;broad.mit.edu	37	chr1	1334592	1334592	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccccgatcagcaccccctgcGaccctgagggtgcgccccca	6	4	10	21	3	1	1	1	1	0	0	1	3	1	1	7	1	3	1	7	1	0	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:1334592G>A	ENST00000400809.3	-	1	100	c.95C>T	c.(94-96)tCg>tTg	p.S32L	CCNL2_ENST00000408952.5_5'Flank|RP4-758J18.2_ENST00000576232.1_5'Flank|RP4-758J18.2_ENST00000444362.1_5'Flank|CCNL2_ENST00000408918.4_Missense_Mutation_p.S32L|MRPL20_ENST00000493287.1_5'Flank|RP4-758J18.2_ENST00000448629.2_5'Flank	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	32					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		CACCCCCTGCGACCCTGAGGG	0.711																																					p.S32L		.											.	CCNL2-70	0			c.C95T						.						39	35	36					1																	1334592		2202	4300	6502	SO:0001583	missense	81669	exon1			CCCTGCGACCCTG	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.95C>T	1.37:g.1334592G>A	ENSP00000383611:p.Ser32Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	63	28	NM_030937	0	0	16	31	15	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Missense_Mutation	SNP	ENST00000400809.3	37	CCDS30557.1	.	.	.	.	.	.	.	.	.	.	G	9.593	1.126618	0.20959	.	.	ENSG00000221978	ENST00000400809;ENST00000408918	T;T	0.45668	1.45;0.89	2.66	1.69	0.24217	.	0.620701	0.13809	N	0.361266	T	0.34571	0.0902	L	0.50333	1.59	0.45762	D	0.998651	B;B;B;B	0.25390	0.076;0.038;0.076;0.125	B;B;B;B	0.16722	0.012;0.016;0.007;0.016	T	0.18461	-1.0336	10	0.48119	T	0.1	.	9.3386	0.38065	0.0:0.2214:0.7786:0.0	.	32;32;32;32	F2Z3J5;C9J148;Q96S94;Q96S94-2	.;.;CCNL2_HUMAN;.	L	32	ENSP00000383611:S32L;ENSP00000386158:S32L	ENSP00000383611:S32L	S	-	2	0	CCNL2	1324455	0.139000	0.22563	0.041000	0.18516	0.007000	0.05969	3.167000	0.50793	0.644000	0.30656	0.591000	0.81541	TCG	.		0.711	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		A	1334592	G	A	1334592	3	1	45	1	0	0	0	0	1	0	0	0	2938	1059	37	1	1537	1	CCNL2	1	1334592	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	136	1334592	247916029	2	4042											
PLEKHG5	57449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	6528353	6528353	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agggtggaggggaaggaactCgtggggactctggggcccga	8	5	21	7	2	1	0	0	0	1	0	2	5	1	4	1	9	1	0	1	9	2	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:6528353C>T	ENST00000400915.3	-	21	2777	c.2711G>A	c.(2710-2712)cGa>cAa	p.R904Q	TNFRSF25_ENST00000356876.3_5'Flank|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.R927Q|PLEKHG5_ENST00000400913.1_Missense_Mutation_p.R848Q|PLEKHG5_ENST00000377728.3_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000377782.3_5'Flank|PLEKHG5_ENST00000377740.3_Intron|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.R917Q|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.R885Q|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.R848Q|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000351959.5_5'Flank|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.R925Q|TNFRSF25_ENST00000461703.2_5'Flank|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000348333.3_5'Flank|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000351748.3_5'Flank	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	904					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GGAAGGAACTCGTGGGGACTC	0.662																																					p.R927Q		.											.	PLEKHG5-652	0			c.G2780A						.						13	15	14					1																	6528353		2184	4290	6474	SO:0001583	missense	57449	exon21			GGAACTCGTGGGG	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2711G>A	1.37:g.6528353C>T	ENSP00000383706:p.Arg904Gln	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	18	8	NM_001265592	0	0	13	28	15	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	37	CCDS41241.1	.	.	.	.	.	.	.	.	.	.	C	0.669	-0.802826	0.02841	.	.	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000535966;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1	4.88	-8.23	0.01033	.	0.885603	0.10069	N	0.719935	T	0.21921	0.0528	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.13594	0.008;0.0;0.008;0.002	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.25984	-1.0116	10	0.11182	T	0.66	-0.2459	2.6352	0.04956	0.1692:0.3187:0.354:0.158	.	917;848;925;904	F5GZ21;O94827-4;O94827-2;O94827	.;.;.;PKHG5_HUMAN	Q	925;848;848;904;885;848;848;917;848;754;927;848	ENSP00000366977:R925Q;ENSP00000344570:R848Q;ENSP00000383704:R848Q;ENSP00000383706:R904Q;ENSP00000366961:R885Q;ENSP00000366957:R848Q;ENSP00000366954:R848Q;ENSP00000441445:R917Q;ENSP00000366966:R848Q;ENSP00000439625:R927Q;ENSP00000437710:R848Q	ENSP00000344570:R848Q	R	-	2	0	PLEKHG5	6450940	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.455000	0.02379	-1.208000	0.02634	-2.049000	0.00408	CGA	.		0.662	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		T	6528353	C	T	6528353	3	4	45	1	0	0	0	0	1	0	0	0	12099	884	31	1	485	1	PLEKHG5	1	6528353	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	5193761	6528353	242722268	3	4043											
PRAMEF1	65121	hgsc.bcm.edu;broad.mit.edu	37	chr1	12854436	12854436	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacatgtcctggccacgtctGataagaaagcttcgttgtta	11	12	9	9	2	1	2	0	1	1	1	3	2	2	2	2	1	2	3	2	1	4	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:12854436G>C	ENST00000332296.7	+	3	763	c.660G>C	c.(658-660)ctG>ctC	p.L220L	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	220					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCACGTCTGATAAGAAAGC	0.393																																					p.L220L		.											.	PRAMEF1-22	0			c.G660C						.						271	250	257					1																	12854436		2203	4300	6503	SO:0001819	synonymous_variant	65121	exon3			ACGTCTGATAAGA	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"-"	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.660G>C	1.37:g.12854436G>C		Somatic	789	1		WXS	Illumina HiSeq	Phase_I	1313	504	NM_023013	0	0	0	0	0	Q9UQP2	Silent	SNP	ENST00000332296.7	37	CCDS148.1																																																																																			.		0.393	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013		C	12854436	G	C	12854436	2	2	45	1	0	0	0	0	0	0	0	1	12454	1277	45	4		4	PRAMEF1	1	12854436	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	6326083	12854436	236396185	4	4044											
THRAP3	9967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	36748232	36748232	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagatctgcatcaagatctcGttctcgttcattttcgaagt	10	15	7	9	3	5	2	2	0	3	2	8	3	5	2	0	0	1	3	0	0	3	4	rs148045717		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:36748232G>A	ENST00000354618.5	+	3	292	c.68G>A	c.(67-69)cGt>cAt	p.R23H	THRAP3_ENST00000469141.2_Missense_Mutation_p.R23H	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	23	Arg-rich.|Required for mRNA splicing activation.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TCAAGATCTCGTTCTCGTTCA	0.453			T	USP6	aneurysmal bone cysts																																p.R23H	Pancreas(129;785 1795 20938 23278 32581)	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3-663	0			c.G68A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	124	110	114		68	5.8	1	1	dbSNP_134	114	0,8600		0,0,4300	no	missense	THRAP3	NM_005119.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	23/956	36748232	1,13005	2203	4300	6503	SO:0001583	missense	9967	exon3			GATCTCGTTCTCG	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.68G>A	1.37:g.36748232G>A	ENSP00000346634:p.Arg23His	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	182	82	NM_005119	0	0	30	48	18	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	37	CCDS405.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031760	0.93575	2.27E-4	0.0	ENSG00000054118	ENST00000354618;ENST00000469141;ENST00000478853	T;T	0.14766	2.48;2.48	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.36082	0.0954	L	0.55481	1.735	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.00986	-1.1490	10	0.72032	D	0.01	-8.0853	19.3309	0.94288	0.0:0.0:1.0:0.0	.	23	Q9Y2W1	TR150_HUMAN	H	23	ENSP00000346634:R23H;ENSP00000433825:R23H	ENSP00000346634:R23H	R	+	2	0	THRAP3	36520819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.473000	0.60196	2.880000	0.98712	0.650000	0.86243	CGT	G|1.000;A|0.000		0.453	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		A	36748232	G	A	36748232	3	1	45	1	0	0	0	0	1	0	0	0	15906	1145	40	1	70	1	THRAP3	1	36748232	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	23893796	36748232	212502389	5	4045											
MACF1	23499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	39910503	39910503	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagcagtaagatggaagaaaGaaaggtacagtgtatgatcc	17	7	12	5	0	0	4	0	1	0	3	1	5	1	5	1	2	2	4	1	2	6	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:39910503G>C	ENST00000372915.3	+	79	19385	c.19298G>C	c.(19297-19299)aGa>aCa	p.R6433T	MACF1_ENST00000289893.4_Missense_Mutation_p.R4977T|MACF1_ENST00000539005.1_Missense_Mutation_p.R4345T|MACF1_ENST00000564288.1_Missense_Mutation_p.R6534T|MACF1_ENST00000361689.2_Missense_Mutation_p.R4475T|MACF1_ENST00000567887.1_Missense_Mutation_p.R6571T|MACF1_ENST00000317713.7_Missense_Mutation_p.R4475T|MACF1_ENST00000545844.1_Missense_Mutation_p.R4475T			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6433					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ATGGAAGAAAGAAAGGTACAG	0.418																																					p.R4475T		.											.	MACF1-165	0			c.G13424C						.						105	96	99					1																	39910503		2203	4300	6503	SO:0001583	missense	23499	exon77			AAGAAAGAAAGGT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.19298G>C	1.37:g.39910503G>C	ENSP00000362006:p.Arg6433Thr	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	109	49	NM_012090	0	0	0	0	0	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.305218|5.305218	0.95601|0.95601	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.60920	.|0.15;0.15;0.15;0.15;0.15;0.15	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.80824|0.80824	0.4697|0.4697	M|M	0.85299|0.85299	2.745|2.745	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.85130	.|0.997;0.997	T|T	0.81662|0.81662	-0.0831|-0.0831	5|10	.|0.87932	.|D	.|0	.|.	20.8598|20.8598	0.99761|0.99761	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|6433;4475	.|Q9UPN3;F8W8Q1	.|MACF1_HUMAN;.	N|T	3478|4475;6433;4475;4475;4345;4977	.|ENSP00000439537:R4475T;ENSP00000362006:R6433T;ENSP00000354573:R4475T;ENSP00000313438:R4475T;ENSP00000444364:R4345T;ENSP00000289893:R4977T	.|ENSP00000289893:R4977T	K|R	+|+	3|2	2|0	MACF1|MACF1	39683090|39683090	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.831000|7.831000	0.86748|0.86748	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	AAG|AGA	.		0.418	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39910503	G	C	39910503	3	2	45	1	0	0	0	0	1	0	0	0	9169	942	33	4	19877	4	MACF1	1	39910503	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	3162271	39910503	209340118	6	4046											
ST7L	54879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	113126670	113126670	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgtttctcctgccttgagTgcctgtttaaataacctttc	7	18	6	10	0	1	1	0	1	1	0	3	1	1	1	4	0	3	2	4	0	3	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:113126670T>C	ENST00000358039.4	-	7	1084	c.780A>G	c.(778-780)gcA>gcG	p.A260A	ST7L_ENST00000543570.1_Silent_p.A243A|ST7L_ENST00000343210.7_Silent_p.A260A|ST7L_ENST00000369666.1_Silent_p.A243A|ST7L_ENST00000490067.1_Silent_p.A243A|ST7L_ENST00000369669.1_Silent_p.A77A|ST7L_ENST00000538187.1_Silent_p.A204A|ST7L_ENST00000360743.4_Silent_p.A260A|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000369668.2_Silent_p.A260A|ST7L_ENST00000544629.1_Silent_p.A195A	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	260					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTGCCTTGAGTGCCTGTTTAA	0.433																																					p.A260A		.											.	ST7L-90	0			c.A780G						.						168	148	155					1																	113126670		2203	4300	6503	SO:0001819	synonymous_variant	54879	exon7			CTTGAGTGCCTGT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.780A>G	1.37:g.113126670T>C		Somatic	144	1		WXS	Illumina HiSeq	Phase_I	223	105	NM_138728	0	0	0	0	0	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Silent	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.446176	0.25987	.	.	ENSG00000007341	ENST00000418497	.	.	.	5.66	-2.14	0.07123	.	.	.	.	.	T	0.24005	0.0581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31110	-0.9955	4	.	.	.	-15.1242	2.6912	0.05121	0.222:0.0684:0.286:0.4236	.	.	.	.	R	132	.	.	H	-	2	0	ST7L	112928193	0.441000	0.25626	0.997000	0.53966	0.998000	0.95712	-0.396000	0.07278	-0.182000	0.10602	0.460000	0.39030	CAC	.		0.433	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			C	113126670	T	C	113126670	2	2	45	1	0	0	0	0	0	0	0	1	15262	1683	59	3		3	ST7L	1	113126670	Silent	SNP	T	TCGA-B3-4104-01A-01D-1458-08	73216167	113126670	136123951	7	4047											
ATP1A1	476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	116931284	116931284	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccttgtgattcgaaatggtGagaaaatgagcataaatgcg	14	10	11	6	2	0	3	0	3	0	1	1	5	0	3	1	1	2	1	1	1	5	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:116931284G>A	ENST00000295598.5	+	6	778	c.526G>A	c.(526-528)Gag>Aag	p.E176K	ATP1A1_ENST00000369496.4_Missense_Mutation_p.E145K|ATP1A1_ENST00000537345.1_Missense_Mutation_p.E176K	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	176					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	TCGAAATGGTGAGAAAATGAG	0.398																																					p.E176K		.											.	ATP1A1-91	0			c.G526A						.						99	104	102					1																	116931284		2203	4300	6503	SO:0001583	missense	476	exon6			AATGGTGAGAAAA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.526G>A	1.37:g.116931284G>A	ENSP00000295598:p.Glu176Lys	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	251	98	NM_000701	0	0	59	101	42	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.528363	0.85706	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	D;D;D	0.90069	-2.61;-2.61;-2.61	5.17	5.17	0.71159	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.048596	0.85682	D	0.000000	T	0.77671	0.4165	N	0.05351	-0.065	0.80722	D	1	B;B	0.25904	0.044;0.137	B;B	0.38803	0.124;0.282	T	0.75300	-0.3366	10	0.33940	T	0.23	.	18.8482	0.92215	0.0:0.0:1.0:0.0	.	176;176	F5H3A1;P05023	.;AT1A1_HUMAN	K	176;176;175;145	ENSP00000295598:E176K;ENSP00000445306:E176K;ENSP00000358508:E145K	ENSP00000295598:E176K	E	+	1	0	ATP1A1	116732807	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	9.657000	0.98554	2.676000	0.91093	0.655000	0.94253	GAG	.		0.398	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		A	116931284	G	A	116931284	3	1	45	1	0	0	0	0	1	0	0	0	1129	1291	45	2	564	2	ATP1A1	1	116931284	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	3804614	116931284	132319337	8	4048											
NBPF14	25832	hgsc.bcm.edu	37	chr1	148025786	148025786	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcagcttgcttgagctGctctgcaagcttctcctcct	4	14	7	16	0	3	1	1	1	2	0	6	1	5	1	3	0	6	6	3	0	1	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:148025786G>A	ENST00000369219.1	-	1	62	c.46C>T	c.(46-48)Cag>Tag	p.Q16*				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	16						cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					TGCTTGAGCTGCTCTGCAAGC	0.527																																					p.Q16X		.											.	NBPF14-91	0			c.C46T						.						45	62	56					1																	148025786		988	2174	3162	SO:0001587	stop_gained	25832	exon1			TGAGCTGCTCTGC	AK092351		1q21.1	2013-01-17			ENSG00000122497			"neuroblastoma breakpoint family"	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.46C>T	1.37:g.148025786G>A	ENSP00000358221:p.Gln16*	Somatic	1065	0		WXS	Illumina HiSeq	Phase_I	1187	144	NM_015383	0	0	84	87	3	Q5TI23|Q8IX76|Q9UJI9	Nonsense_Mutation	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	g	10.94	1.492532	0.26774	.	.	ENSG00000122497	ENST00000369219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	.	.	.	.	.	.	.	.	X	16	.	ENSP00000358221:Q16X	Q	-	1	0	NBPF14	146492410	0.000000	0.05858	0.005000	0.12908	0.154000	0.21943	-1.767000	0.01795	-0.921000	0.03794	0.064000	0.15345	CAG	.		0.527	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		A	148025786	G	A	148025786	4	1	45	1	0	0	0	0	0	1	0	0	10220	1328	46	2	2807	2	NBPF14	1	148025786	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	31094502	148025786	101224835	9	4049											
SHE	126669	hgsc.bcm.edu	37	chr1	154474217	154474217	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggctgtccttggggccgaCgccggccctgccgctcccca	2	6	13	20	5	0	0	0	0	0	0	2	1	2	0	8	4	1	2	8	4	0	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:154474217C>T	ENST00000304760.2	-	1	372	c.286G>A	c.(286-288)Gtc>Atc	p.V96I	TDRD10_ENST00000368482.4_5'Flank|TDRD10_ENST00000368480.3_5'Flank	NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	96										breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTGGGGCCGACGCCGGCCCTG	0.731																																					p.V96I		.											.	SHE-95	0			c.G286A						.						4	5	4					1																	154474217		1898	3852	5750	SO:0001583	missense	126669	exon1			GGCCGACGCCGGC	AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"SH2 domain containing"	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.286G>A	1.37:g.154474217C>T	ENSP00000307369:p.Val96Ile	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	21	8	NM_001010846	0	0	0	0	0	Q8TEQ5	Missense_Mutation	SNP	ENST00000304760.2	37	CCDS30877.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.028934	0.35797	.	.	ENSG00000169291	ENST00000304760	T	0.29655	1.56	4.34	3.41	0.39046	.	7739.210000	0.00166	N	0.000002	T	0.08891	0.0220	N	0.14661	0.345	0.09310	N	1	B	0.20988	0.05	B	0.08055	0.003	T	0.16217	-1.0410	10	0.51188	T	0.08	-10.482	10.0975	0.42484	0.0:0.7964:0.2036:0.0	.	96	Q5VZ18	SHE_HUMAN	I	96	ENSP00000307369:V96I	ENSP00000307369:V96I	V	-	1	0	SHE	152740841	0.000000	0.05858	0.001000	0.08648	0.756000	0.42949	-0.544000	0.06077	1.011000	0.39340	0.561000	0.74099	GTC	.		0.731	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846		T	154474217	C	T	154474217	3	4	45	1	0	0	0	0	1	0	0	0	14308	536	19	1	1225	1	SHE	1	154474217	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	6448431	154474217	94776404	10	4050											
TDRD10	126668	hgsc.bcm.edu;broad.mit.edu	37	chr1	154493835	154493835	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgggctccatgcagaaagtGacacttgcaatccaggagct	11	8	11	11	0	0	2	0	1	0	1	2	3	2	3	2	2	3	4	2	2	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:154493835G>A	ENST00000368480.3	+	6	334	c.249G>A	c.(247-249)gtG>gtA	p.V83V	TDRD10_ENST00000368482.4_Silent_p.V83V			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	83	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGCAGAAAGTGACACTTGCAA	0.502																																					p.V83V		.											.	TDRD10-91	0			c.G249A						.						139	147	144					1																	154493835		2203	4300	6503	SO:0001819	synonymous_variant	126668	exon6			GAAAGTGACACTT	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.249G>A	1.37:g.154493835G>A		Somatic	311	0		WXS	Illumina HiSeq	Phase_I	368	35	NM_182499	0	0	1	1	0	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Silent	SNP	ENST00000368480.3	37	CCDS41406.1																																																																																			.		0.502	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		A	154493835	G	A	154493835	2	1	45	1	0	0	0	0	0	0	0	1	15763	1277	45	2		2	TDRD10	1	154493835	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	19618	154493835	94756786	11	4051											
NDUFS2	4720	broad.mit.edu	37	chr1	161183707	161183707	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcagatgtcgttgccatCataggtacgaggcctattgt	8	13	12	8	2	1	1	1	0	0	1	2	2	1	1	2	3	2	3	2	3	3	6			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:161183707C>A	ENST00000367993.3	+	14	1798	c.1350C>A	c.(1348-1350)atC>atA	p.I450I	NDUFS2_ENST00000465923.1_3'UTR|FCER1G_ENST00000367992.3_5'Flank|NDUFS2_ENST00000392179.4_Silent_p.I450I|FCER1G_ENST00000289902.1_5'Flank	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	450					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	TCGTTGCCATCATAGGTACGA	0.493																																					p.I450I													.	NDUFS2-91	0			c.C1350A						.						201	172	182					1																	161183707		2203	4300	6503	SO:0001819	synonymous_variant	4720	exon13			TGCCATCATAGGT	BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7708	protein-coding gene	gene with protein product	"complex I 49kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"	602985	"NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.1350C>A	1.37:g.161183707C>A		Somatic	267	0		WXS	Illumina HiSeq	Phase_I	329	5	NM_001166159	0	0	21	21	0	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Silent	SNP	ENST00000367993.3	37	CCDS1224.1																																																																																			.		0.493	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550		A	161183707	C	A	161183707	2	1	45	1	0	0	0	0	0	0	0	1	10318	816	29	4		4	NDUFS2	1	161183707	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	6689872	161183707	88066914	12	4052											
F5	2153	broad.mit.edu	37	chr1	169525999	169525999	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atggctgagaccttatgatgGttctgctccaggacctggcc	7	11	12	11	0	1	2	0	2	1	1	2	4	2	3	4	4	1	3	4	4	1	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:169525999G>C	ENST00000367797.3	-	6	1038	c.837C>G	c.(835-837)aaC>aaG	p.N279K	F5_ENST00000367796.3_Missense_Mutation_p.N279K|F5_ENST00000546081.1_Missense_Mutation_p.N142K	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	279	F5/8 type A 1.|Plastocyanin-like 2.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CCTTATGATGGTTCTGCTCCA	0.517																																					p.N279K													.	F5-157	0			c.C837G						.						166	132	144					1																	169525999		2203	4300	6503	SO:0001583	missense	2153	exon6			ATGATGGTTCTGC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.837C>G	1.37:g.169525999G>C	ENSP00000356771:p.Asn279Lys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	120	4	NM_000130	0	0	1	1	0	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.091117	0.55968	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98777	-5.13;-5.13;-5.13	6.07	5.13	0.70059	Cupredoxin (2);	0.647124	0.17395	N	0.175782	D	0.91112	0.7202	L	0.37630	1.12	0.33636	D	0.606619	B	0.29988	0.264	B	0.26693	0.072	D	0.84453	0.0589	9	0.05436	T	0.98	-19.8836	7.2531	0.26160	0.1508:0.0:0.7031:0.1461	.	279	P12259	FA5_HUMAN	K	279;279;142	ENSP00000356771:N279K;ENSP00000356770:N279K;ENSP00000439664:N142K	ENSP00000356770:N279K	N	-	3	2	F5	167792623	0.990000	0.36364	0.964000	0.40570	0.993000	0.82548	0.914000	0.28624	1.516000	0.48900	0.650000	0.86243	AAC	.		0.517	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		C	169525999	G	C	169525999	3	2	45	1	0	0	0	0	1	0	0	0	5361	1252	44	4	5917	4	F5	1	169525999	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	8342292	169525999	79724622	13	4053											
XPR1	9213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	180849312	180849312	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgtggcccccctgaacgcaGatgatcagactctcctagaa	10	8	9	14	1	2	5	1	2	1	3	3	5	2	5	4	1	1	1	4	1	3	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:180849312G>C	ENST00000367590.4	+	14	2107	c.1909G>C	c.(1909-1911)Gat>Cat	p.D637H	XPR1_ENST00000367589.3_Missense_Mutation_p.D572H	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	637	EXS. {ECO:0000255|PROSITE- ProRule:PRU00712}.				G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CCTGAACGCAGATGATCAGAC	0.517																																					p.D637H		.											.	XPR1-90	0			c.G1909C						.						132	126	128					1																	180849312		2203	4300	6503	SO:0001583	missense	9213	exon14			AACGCAGATGATC	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"xenotropic and polytropic retrovirus receptor"			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1909G>C	1.37:g.180849312G>C	ENSP00000356562:p.Asp637His	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	185	90	NM_004736	0	0	24	36	12	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	G	32	5.157082	0.94686	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.48522	0.81	5.75	5.75	0.90469	EXS, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70430	0.3223	M	0.82823	2.61	0.58432	D	0.999994	D;D	0.61080	0.989;0.982	P;P	0.60949	0.881;0.839	T	0.73206	-0.4056	10	0.59425	D	0.04	-16.0548	19.5298	0.95223	0.0:0.0:1.0:0.0	.	572;637	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	H	637;572	ENSP00000356562:D637H	ENSP00000356561:D572H	D	+	1	0	XPR1	179115935	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.726000	0.98782	2.707000	0.92482	0.591000	0.81541	GAT	.		0.517	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		C	180849312	G	C	180849312	3	2	45	1	0	0	0	0	1	0	0	0	17484	942	33	4	1963	4	XPR1	1	180849312	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	11323313	180849312	68401309	14	4054											
LRRN2	10446	hgsc.bcm.edu;broad.mit.edu	37	chr1	204587907	204587907	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctcacggaccgggaggCgctggaggtccggaggctcc	6	4	17	14	4	1	0	1	0	0	0	3	4	3	4	4	7	0	3	4	7	0	0	rs371946869		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:204587907C>T	ENST00000367175.1	-	1	3426	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.R405H|LRRN2_ENST00000367176.3_Missense_Mutation_p.R405H			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	405	LRRCT.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GACCGGGAGGCGCTGGAGGTC	0.662													C|||	1	0.000199681	0	0	5008	,	,		16007	0		0	False		,,,				2504	0.001				p.R405H		.											.	LRRN2-514	0			c.G1214A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	41	46	44		1214,1214	4.6	1	1		44	2,8598	1.2+/-3.3	0,2,4298	no	missense,missense	LRRN2	NM_006338.2,NM_201630.1	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	405/714,405/714	204587907	2,13004	2203	4300	6503	SO:0001583	missense	10446	exon3			GGGAGGCGCTGGA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1214G>A	1.37:g.204587907C>T	ENSP00000356143:p.Arg405His	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	116	8	NM_006338	0	0	0	0	0	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070520	0.36566	0.0	2.33E-4	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.59502	0.26;0.26;0.26	5.69	4.59	0.56863	Cysteine-rich flanking region, C-terminal (1);	0.159801	0.29767	N	0.011250	T	0.36580	0.0972	N	0.08118	0	0.37294	D	0.90841	B	0.17465	0.022	B	0.09377	0.004	T	0.40059	-0.9583	10	0.66056	D	0.02	.	11.5883	0.50931	0.0:0.7898:0.1305:0.0797	.	405	O75325	LRRN2_HUMAN	H	405	ENSP00000356144:R405H;ENSP00000356145:R405H;ENSP00000356143:R405H	ENSP00000356143:R405H	R	-	2	0	LRRN2	202854530	0.939000	0.31865	1.000000	0.80357	0.940000	0.58332	1.848000	0.39309	2.684000	0.91462	0.557000	0.71058	CGC	.		0.662	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		T	204587907	C	T	204587907	3	4	45	1	0	0	0	0	1	0	0	0	9060	768	27	1	931	1	LRRN2	1	204587907	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	23738595	204587907	44662714	15	4055											
SLC26A9	115019	hgsc.bcm.edu;ucsc.edu	37	chr1	205888030	205888030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgggcaaagaggactgcgtCatgtatgctgggaaagacgt	11	8	15	7	2	1	2	1	0	0	2	1	4	1	4	0	3	2	3	0	3	3	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:205888030C>T	ENST00000367135.3	-	19	2307	c.2194G>A	c.(2194-2196)Gac>Aac	p.D732N	SLC26A9_ENST00000340781.4_Missense_Mutation_p.D732N|SLC26A9_ENST00000367134.2_Missense_Mutation_p.D732N	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	732	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			AGGACTGCGTCATGTATGCTG	0.517											OREG0014164	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D732N		.											.	SLC26A9-92	0			c.G2194A						.						310	292	298					1																	205888030		2203	4300	6503	SO:0001583	missense	115019	exon19			CTGCGTCATGTAT	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"Solute carriers"	14469	protein-coding gene	gene with protein product	"anion transporter/exchanger-9"	608481	"solute carrier family 26, member 9"			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.2194G>A	1.37:g.205888030C>T	ENSP00000356103:p.Asp732Asn	Somatic	502	2	2155	WXS	Illumina HiSeq	Phase_I	646	307	NM_134325	0	0	0	0	0	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484381	0.63962	.	.	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.90069	-2.61;-2.61;-2.61	5.2	5.2	0.72013	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.000000	0.85682	D	0.000000	D	0.95137	0.8424	M	0.84948	2.725	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95535	0.8607	10	0.72032	D	0.01	.	18.7233	0.91704	0.0:1.0:0.0:0.0	.	732;732	Q7LBE3;B1AVM8	S26A9_HUMAN;.	N	732	ENSP00000341682:D732N;ENSP00000356103:D732N;ENSP00000356102:D732N	ENSP00000341682:D732N	D	-	1	0	SLC26A9	204154653	1.000000	0.71417	0.271000	0.24616	0.102000	0.19082	6.298000	0.72763	2.584000	0.87258	0.563000	0.77884	GAC	.		0.517	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		T	205888030	C	T	205888030	3	4	45	1	0	0	0	0	1	0	0	0	14556	826	29	2	489	2	SLC26A9	1	205888030	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	1300123	205888030	43362591	16	4056											
ADCY3	109	broad.mit.edu	37	chr2	25057766	25057766	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcagccaggtcctgcaggcGcagcctccggcgtgggttgg	4	7	17	13	3	1	0	1	0	0	0	3	0	3	0	4	5	3	3	4	5	0	1	rs142082596		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:25057766G>A	ENST00000260600.5	-	9	2553	c.1702C>T	c.(1702-1704)Cgc>Tgc	p.R568C	ADCY3_ENST00000405392.1_Missense_Mutation_p.R201C|ADCY3_ENST00000450524.1_5'Flank	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	568					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TCCTGCAGGCGCAGCCTCCGG	0.652													G|||	1	0.000199681	0	0	5008	,	,		16963	0		0.001	False		,,,				2504	0				p.R568C													.	ADCY3-94	0			c.C1702T						.	G	CYS/ARG	0,4404		0,0,2202	29	29	29		1702	5.1	1	2	dbSNP_134	29	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADCY3	NM_004036.3	180	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign	568/1145	25057766	1,13003	2202	4300	6502	SO:0001583	missense	109	exon9			GCAGGCGCAGCCT	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1702C>T	2.37:g.25057766G>A	ENSP00000260600:p.Arg568Cys	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_004036	0	0	21	21	0	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.34	3.364062	0.61513	0.0	1.16E-4	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879	T;T	0.46819	0.86;0.86	5.05	5.05	0.67936	.	0.062472	0.64402	D	0.000003	T	0.40645	0.1125	N	0.24115	0.695	0.51012	D	0.9999	B;P;D	0.63046	0.002;0.844;0.992	B;B;P	0.46339	0.001;0.28;0.513	T	0.24512	-1.0158	10	0.33940	T	0.23	.	16.979	0.86322	0.0:0.0:1.0:0.0	.	568;568;201	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	C	568;201;543	ENSP00000260600:R568C;ENSP00000384484:R201C	ENSP00000260600:R568C	R	-	1	0	ADCY3	24911270	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.613000	0.67688	2.344000	0.79699	0.563000	0.77884	CGC	G|1.000;A|0.000		0.652	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			A	25057766	G	A	25057766	3	1	45	1	0	0	0	0	1	0	0	0	295	1087	38	1	1784	1	ADCY3	2	25057766	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		25057766	218141607	17	4057											
ETAA1	54465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	67631299	67631299	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttattcaagacgaaattcaAaattgtatagttacatctaa	17	14	5	5	1	3	1	2	0	1	1	3	2	3	1	0	0	1	3	0	0	9	8			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:67631299A>G	ENST00000272342.5	+	5	1615	c.1485A>G	c.(1483-1485)caA>caG	p.Q495Q	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	495						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						ACGAAATTCAAAATTGTATAG	0.279																																					p.Q495Q		.											.	ETAA1-156	0			c.A1485G						.						20	22	22					2																	67631299		2126	4252	6378	SO:0001819	synonymous_variant	54465	exon5			AATTCAAAATTGT	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"Ewing's tumor-associated antigen 1"			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1485A>G	2.37:g.67631299A>G		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	89	44	NM_019002	0	0	5	5	0	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	37	CCDS1882.1																																																																																			.		0.279	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		G	67631299	A	G	67631299	2	3	45	1	0	0	0	0	0	0	0	1	5280	11	1	3		3	ETAA1	2	67631299	Silent	SNP	A	TCGA-B3-4104-01A-01D-1458-08	42573533	67631299	175568074	18	4058											
AFF3	3899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	100623250	100623250	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggggcctgatcttggccGtccattggcctcacatacgc	6	10	11	14	2	3	1	2	1	1	0	4	1	4	1	4	4	1	0	4	4	1	3	rs138844530		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:100623250G>A	ENST00000409236.2	-	5	829	c.717C>T	c.(715-717)gaC>gaT	p.D239D	AFF3_ENST00000409579.1_Silent_p.D264D|AFF3_ENST00000356421.2_Silent_p.D264D|AFF3_ENST00000317233.4_Silent_p.D239D			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	239					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GATCTTGGCCGTCCATTGGCC	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		18592	0		0	False		,,,				2504	0				p.D264D		.											.	AFF3-230	0			c.C792T						.	G	,	1,4405	2.1+/-5.4	0,1,2202	83	76	79		792,717	-7.5	0.9	2	dbSNP_134	79	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	AFF3	NM_001025108.1,NM_002285.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	264/1252,239/1227	100623250	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3899	exon6			TTGGCCGTCCATT	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.717C>T	2.37:g.100623250G>A		Somatic	100	1		WXS	Illumina HiSeq	Phase_I	102	43	NM_001025108	0	0	0	0	0	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																			G|1.000;A|0.000		0.572	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		A	100623250	G	A	100623250	2	1	45	1	0	0	0	0	0	0	0	1	358	1136	40	1		1	AFF3	2	100623250	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	32991951	100623250	142576123	19	4059											
SH3RF3	344558	broad.mit.edu	37	chr2	110065844	110065844	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctcccaacgtcagtgccGcaaacctcaacggggaggct	10	5	10	16	3	2	0	2	0	0	0	3	1	3	1	4	3	4	2	4	3	3	0	rs369331698		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:110065844G>A	ENST00000309415.6	+	8	2047	c.2047G>A	c.(2047-2049)Gca>Aca	p.A683T		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	683							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						CGTCAGTGCCGCAAACCTCAA	0.622																																					p.A683T													.	SH3RF3-24	0			c.G2047A						.	G	THR/ALA	1,4173		0,1,2086	32	39	37		2047	4	0.8	2		37	0,8446		0,0,4223	no	missense	SH3RF3	NM_001099289.1	58	0,1,6309	AA,AG,GG		0.0,0.024,0.0079	possibly-damaging	683/883	110065844	1,12619	2087	4223	6310	SO:0001583	missense	344558	exon8			AGTGCCGCAAACC	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"RING-type (C3HC4) zinc fingers"	24699	protein-coding gene	gene with protein product			"SH3 multiple domains 4"	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.2047G>A	2.37:g.110065844G>A	ENSP00000309186:p.Ala683Thr	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	42	3	NM_001099289	0	0	3	3	0	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	G	12.40	1.926213	0.34002	2.4E-4	0.0	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.59906	0.23;2.07	4.9	4.03	0.46877	.	0.238285	0.41712	N	0.000823	T	0.46464	0.1394	.	.	.	0.38387	D	0.945298	P	0.35656	0.514	B	0.28139	0.086	T	0.53837	-0.8382	9	0.51188	T	0.08	-22.8632	13.0862	0.59142	0.0771:0.0:0.9229:0.0	.	683	Q8TEJ3	SH3R3_HUMAN	T	683	ENSP00000414997:A683T;ENSP00000309186:A683T	ENSP00000309186:A683T	A	+	1	0	SH3RF3	109432276	1.000000	0.71417	0.790000	0.31976	0.245000	0.25701	3.980000	0.56895	1.300000	0.44818	0.655000	0.94253	GCA	.		0.622	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		A	110065844	G	A	110065844	3	1	45	1	0	0	0	0	1	0	0	0	14292	1087	38	1	2077	1	SH3RF3	2	110065844	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	9442594	110065844	133133529	20	4060											
POTEF	728378	hgsc.bcm.edu	37	chr2	130868165	130868165	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctggccgtctgtccagataGatcttgagaagatacatcaa	12	11	9	9	1	4	4	1	1	3	4	5	5	5	4	2	1	1	0	2	1	4	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:130868165G>C	ENST00000409914.2	-	7	1405	c.1006C>G	c.(1006-1008)Cta>Gta	p.L336V	RNU6-1049P_ENST00000516414.1_RNA|POTEF_ENST00000357462.5_Missense_Mutation_p.L336V|POTEF_ENST00000360967.5_Missense_Mutation_p.L336V|POTEF_ENST00000361163.4_Missense_Mutation_p.L346V|AC018804.3_ENST00000433507.1_RNA	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	336					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TGTCCAGATAGATCTTGAGAA	0.368																																					p.L336V		.											.	POTEF-27	0			c.C1006G						.						14	14	14					2																	130868165		1694	3647	5341	SO:0001583	missense	728378	exon7			CAGATAGATCTTG	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.1006C>G	2.37:g.130868165G>C	ENSP00000386786:p.Leu336Val	Somatic	341	0		WXS	Illumina HiSeq	Phase_I	503	26	NM_001099771	0	0	3	3	0	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	1.850	-0.465204	0.04476	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.64085	-0.08;-0.08;-0.08;0.63	0.887	-1.77	0.07982	Ankyrin repeat-containing domain (4);	3.437520	0.02566	U	0.097359	T	0.33294	0.0858	N	0.02539	-0.55	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.10776	-1.0615	10	0.38643	T	0.18	.	2.5236	0.04686	0.0:0.4188:0.3215:0.2597	.	336	A5A3E0	POTEF_HUMAN	V	336;336;336;346	ENSP00000350052:L336V;ENSP00000386786:L336V;ENSP00000354232:L336V;ENSP00000355012:L346V	ENSP00000350052:L336V	L	-	1	2	POTEF	130584635	0.001000	0.12720	0.006000	0.13384	0.255000	0.26057	-2.256000	0.01181	-0.731000	0.04862	0.162000	0.16502	CTA	.		0.368	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		C	130868165	G	C	130868165	3	2	45	1	0	0	0	0	1	0	0	0	12291	933	33	4	2265	4	POTEF	2	130868165	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	20802321	130868165	112331208	21	4061											
POTEE	445582	hgsc.bcm.edu	37	chr2	131985905	131985905	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgatgtatcttctcaagatCtatctggacagacggccaga	11	12	9	9	1	4	4	1	1	4	3	5	5	4	5	1	2	0	1	1	2	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:131985905C>G	ENST00000356920.5	+	5	1100	c.1006C>G	c.(1006-1008)Cta>Gta	p.L336V	PLEKHB2_ENST00000303908.3_Intron|RNU6-127P_ENST00000390897.1_RNA|POTEE_ENST00000358087.5_Missense_Mutation_p.L346V|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	336					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TTCTCAAGATCTATCTGGACA	0.373																																					p.L336V		.											.	.	0			c.C1006G						.						2	3	2					2																	131985905		1105	2580	3685	SO:0001583	missense	445582	exon5			CAAGATCTATCTG	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.1006C>G	2.37:g.131985905C>G	ENSP00000439189:p.Leu336Val	Somatic	393	0		WXS	Illumina HiSeq	Phase_I	646	33	NM_001083538	0	0	3	3	0	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	10.40	1.339185	0.24253	.	.	ENSG00000188219	ENST00000356920;ENST00000358087	T;T	0.64085	-0.08;0.63	0.887	-1.77	0.07982	Ankyrin repeat-containing domain (3);	3.437520	0.02566	U	0.097359	T	0.36441	0.0967	N	0.04132	-0.27	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.11792	-1.0573	10	0.40728	T	0.16	.	2.5236	0.04686	0.2597:0.3215:0.4188:0.0	.	336	Q6S8J3	POTEE_HUMAN	V	336;346	ENSP00000439189:L336V;ENSP00000443049:L346V	ENSP00000439189:L336V	L	+	1	2	AC131180.1	131702375	0.000000	0.05858	0.006000	0.13384	0.317000	0.28152	-1.726000	0.01861	-0.731000	0.04862	0.162000	0.16502	CTA	.		0.373	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		G	131985905	C	G	131985905	3	3	45	1	0	0	0	0	1	0	0	0	12290	912	32	4	1024	4	POTEE	2	131985905	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	1117740	131985905	111213468	22	4062											
NEB	4703	broad.mit.edu	37	chr2	152397247	152397247	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcacgtctttagcatgcttCaaggctgtggtctggtttcc	5	16	10	10	1	4	0	2	0	2	0	5	0	5	0	1	3	2	4	1	3	2	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:152397247C>T	ENST00000172853.10	-	109	15795	c.15648G>A	c.(15646-15648)ttG>ttA	p.L5216L	NEB_ENST00000427231.2_Silent_p.L6917L|NEB_ENST00000603639.1_Silent_p.L6917L|NEB_ENST00000604864.1_Silent_p.L6917L|NEB_ENST00000397345.3_Silent_p.L6917L|NEB_ENST00000409198.1_Silent_p.L5216L			P20929	NEBU_HUMAN	nebulin	5216					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TAGCATGCTTCAAGGCTGTGG	0.433																																					p.L6917L													.	NEB-145	0			c.G20751A						.						155	151	152					2																	152397247		2037	4208	6245	SO:0001819	synonymous_variant	4703	exon137			ATGCTTCAAGGCT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.15648G>A	2.37:g.152397247C>T		Somatic	139	1		WXS	Illumina HiSeq	Phase_I	186	10	NM_001271208	0	0	1	1	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.		0.433	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152397247	C	T	152397247	2	4	45	1	0	0	0	0	0	0	0	1	10328	825	29	2		2	NEB	2	152397247	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	20411342	152397247	90802126	23	4063											
CCDC108	255101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	219886640	219886640	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cacattcccaaaggccagctCcttttcctttgcctggaggc	7	11	8	15	0	0	0	0	0	0	0	3	1	3	1	5	3	2	1	5	3	1	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:219886640C>T	ENST00000341552.5	-	18	3075	c.2992G>A	c.(2992-2994)Gag>Aag	p.E998K	CCDC108_ENST00000453220.1_Missense_Mutation_p.E998K|CCDC108_ENST00000441968.1_Missense_Mutation_p.E998K	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	998						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAGGCCAGCTCCTTTTCCTTT	0.597																																					p.E998K		.											.	CCDC108-94	0			c.G2992A						.						103	108	106					2																	219886640		2203	4300	6503	SO:0001583	missense	255101	exon18			CCAGCTCCTTTTC	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2992G>A	2.37:g.219886640C>T	ENSP00000340776:p.Glu998Lys	Somatic	279	0		WXS	Illumina HiSeq	Phase_I	159	90	NM_194302	0	0	0	0	0	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	9.157	1.017735	0.19355	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.05199	3.48;3.48;3.48	4.89	3.11	0.35812	.	0.308243	0.23081	N	0.052148	T	0.08626	0.0214	M	0.67953	2.075	0.27209	N	0.959953	P	0.35656	0.514	B	0.37650	0.255	T	0.20107	-1.0285	10	0.12103	T	0.63	-17.3902	10.4801	0.44689	0.0:0.5718:0.3504:0.0778	.	998	Q6ZU64	CC108_HUMAN	K	998	ENSP00000340776:E998K;ENSP00000413377:E998K;ENSP00000409117:E998K	ENSP00000340776:E998K	E	-	1	0	CCDC108	219594884	0.378000	0.25114	0.953000	0.39169	0.255000	0.26057	0.327000	0.19663	0.289000	0.22422	-1.886000	0.00541	GAG	.		0.597	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219886640	C	T	219886640	3	4	45	1	0	0	0	0	1	0	0	0	2749	864	30	2	2857	2	CCDC108	2	219886640	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	67489393	219886640	23312733	24	4064											
TUBA4A	7277	broad.mit.edu	37	chr2	220115274	220115274	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccaggcctcggcgatggCggtcgtgttgctcagcatgc	4	8	16	13	4	1	0	1	0	0	0	3	1	1	0	2	5	3	3	2	5	0	1	rs368743618		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:220115274C>T	ENST00000248437.4	-	4	1320	c.1147G>A	c.(1147-1149)Gcc>Acc	p.A383T	TUBA4A_ENST00000498660.1_5'Flank|TUBA4A_ENST00000392088.2_Missense_Mutation_p.A368T|TUBA4B_ENST00000490341.1_RNA	NM_006000.2	NP_005991.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	383					'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	TCGGCGATGGCGGTCGTGTTG	0.622																																					p.A383T													.	TUBA4A-93	0			c.G1147A						.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	86	72	77		1147	5.1	1	2		77	0,8600		0,0,4300	no	missense	TUBA4A	NM_006000.1	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	383/449	220115274	1,13005	2203	4300	6503	SO:0001583	missense	7277	exon4			CGATGGCGGTCGT	AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824		"Tubulins"	12407	protein-coding gene	gene with protein product		191110	"tubulin, alpha 1 (testis specific)", "tubulin, alpha 1"	TUBA1		3785200	Standard	NM_006000		Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000248437.4:c.1147G>A	2.37:g.220115274C>T	ENSP00000248437:p.Ala383Thr	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	81	4	NM_006000	0	0	9	9	0	A8MUB1|B3KNQ6|P05215	Missense_Mutation	SNP	ENST00000248437.4	37	CCDS2438.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.340976	0.60963	2.27E-4	0.0	ENSG00000127824	ENST00000248437;ENST00000392088	D;D	0.84298	-1.83;-1.83	5.05	5.05	0.67936	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.64402	D	0.000002	D	0.96093	0.8727	H	0.99705	4.715	0.80722	D	1	D	0.65815	0.995	D	0.65233	0.933	D	0.98196	1.0465	10	0.87932	D	0	.	18.5797	0.91166	0.0:1.0:0.0:0.0	.	383	P68366	TBA4A_HUMAN	T	383;368	ENSP00000248437:A383T;ENSP00000375938:A368T	ENSP00000248437:A383T	A	-	1	0	TUBA4A	219823518	1.000000	0.71417	0.989000	0.46669	0.796000	0.44982	7.622000	0.83099	2.608000	0.88229	0.650000	0.86243	GCC	.		0.622	TUBA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256816.3	NM_006000		T	220115274	C	T	220115274	3	4	45	1	0	0	0	0	1	0	0	0	16782	768	27	1	203	1	TUBA4A	2	220115274	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	228634	220115274	23084099	25	4065											
OBSL1	23363	hgsc.bcm.edu;broad.mit.edu	37	chr2	220420911	220420911	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccacctcgcacccagcgcacGgcccccgctgcacccactcg	6	3	8	24	5	0	0	0	0	0	0	2	0	0	0	6	1	2	4	6	1	0	0	rs200341414		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:220420911G>A	ENST00000404537.1	-	14	4496	c.4440C>T	c.(4438-4440)gcC>gcT	p.A1480A	OBSL1_ENST00000603926.1_Silent_p.A1480A|OBSL1_ENST00000265317.5_Silent_p.A379A|RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000265318.4_Missense_Mutation_p.P1347L|OBSL1_ENST00000373876.1_Silent_p.A1388A	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1480	Ig-like 12.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CCCAGCGCACGGCCCCCGCTG	0.657													G|||	1	0.000199681	0	0	5008	,	,		14964	0		0.001	False		,,,				2504	0				p.A1480A		.											.	OBSL1-71	0			c.C4440T						.	G	,	0,4222		0,0,2111	20	26	24		4440,4440	-5.8	0.9	2		24	1,8429		0,1,4214	no	coding-synonymous,coding-synonymous	OBSL1	NM_001173431.1,NM_015311.2	,	0,1,6325	AA,AG,GG		0.0119,0.0,0.0079	,	1480/1544,1480/1897	220420911	1,12651	2111	4215	6326	SO:0001819	synonymous_variant	23363	exon14			GCGCACGGCCCCC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4440C>T	2.37:g.220420911G>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	22	8	NM_001173431	0	0	1	1	0	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	0.022	-1.408515	0.01155	0.0	1.19E-4	ENSG00000124006	ENST00000265318;ENST00000456147	T	0.56611	0.45	4.67	-5.8	0.02347	.	.	.	.	.	T	0.36524	0.0970	.	.	.	0.33297	D	0.564277	.	.	.	.	.	.	T	0.44952	-0.9294	6	0.23891	T	0.37	.	6.0534	0.19799	0.4558:0.0:0.2936:0.2506	.	.	.	.	L	1347;382	ENSP00000265318:P1347L	ENSP00000265318:P1347L	P	-	2	0	OBSL1	220129155	0.001000	0.12720	0.892000	0.35008	0.055000	0.15305	-1.760000	0.01806	-0.994000	0.03463	-1.174000	0.01732	CCG	G|0.999;A|0.001		0.657	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			A	220420911	G	A	220420911	2	1	45	1	0	0	0	0	0	0	0	1	10839	1103	39	1		1	OBSL1	2	220420911	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	305637	220420911	22778462	26	4066											
LHFPL4	375323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	9547649	9547649	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcccacagcacactcGcctttgttctccggcttgag	6	9	8	18	2	1	1	0	1	1	0	3	1	1	1	5	1	2	3	5	1	0	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:9547649G>A	ENST00000287585.6	-	3	929		c.e3+1			NM_198560.2	NP_940962.1	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 4							integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(3)|skin(1)	10	Medulloblastoma(99;0.227)					CAGCACACTCGCCTTTGTTCT	0.592																																					.		.											.	LHFPL4-71	0			c.643+2C>T						.						92	94	93					3																	9547649		2203	4300	6503	SO:0001630	splice_region_variant	375323	exon4			ACACTCGCCTTTG	AY278320	CCDS33691.1	3p25.3	2006-06-13			ENSG00000156959	ENSG00000156959			29568	protein-coding gene	gene with protein product		610240				15905332	Standard	NM_198560		Approved		uc003bry.3	Q7Z7J7	OTTHUMG00000155066	ENST00000287585.6:c.643+1C>T	3.37:g.9547649G>A		Somatic	372	2		WXS	Illumina HiSeq	Phase_I	390	176	NM_198560	0	0	0	0	0	A1L383|A4D0Q5	Splice_Site	SNP	ENST00000287585.6	37	CCDS33691.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.152833	0.57259	.	.	ENSG00000156959	ENST00000287585	.	.	.	5.49	1.02	0.19986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.1995	0.25873	0.6562:0.0:0.3438:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LHFPL4	9522649	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	3.006000	0.49529	0.261000	0.21753	0.655000	0.94253	.	.		0.592	LHFPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338298.1	NM_198560	Intron	A	9547649	G	A	9547649	5	1	45	1	0	0	0	0	0	0	1	0	8789	1101	38	1	106	1	LHFPL4	3	9547649	Splice_Site	SNP	G	TCGA-B3-4104-01A-01D-1458-08		9547649	188474781	27	4067											
EFHB	151651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	19925989	19925989	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cttggtctcagaagtgtccgGagagtcttttctgtgcttcc	5	15	11	10	1	3	2	1	0	3	2	6	3	5	2	2	2	1	1	2	2	1	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:19925989G>C	ENST00000295824.9	-	11	2213	c.2052C>G	c.(2050-2052)ctC>ctG	p.L684L	EFHB_ENST00000344838.4_Silent_p.L554L	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	684							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						GAAGTGTCCGGAGAGTCTTTT	0.393																																					p.L684L		.											.	EFHB-22	0			c.C2052G						.						126	130	128					3																	19925989		2203	4300	6503	SO:0001819	synonymous_variant	151651	exon11			TGTCCGGAGAGTC	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"EF-hand domain containing"	26330	protein-coding gene	gene with protein product	"cilia and flagella associated protein 21"					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2052C>G	3.37:g.19925989G>C		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	190	85	NM_144715	0	0	0	0	0	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	37	CCDS33715.2																																																																																			.		0.393	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		C	19925989	G	C	19925989	2	2	45	1	0	0	0	0	0	0	0	1	4956	1161	41	4		4	EFHB	3	19925989	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	10378340	19925989	178096441	28	4068											
RAD54L2	23132	broad.mit.edu	37	chr3	51667682	51667682	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggctgtattctggcccaCagcatgggtctggggaaaac	8	11	13	9	0	2	0	0	0	2	0	2	1	2	1	1	5	2	3	1	5	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:51667682C>T	ENST00000409535.2	+	7	1040	c.915C>T	c.(913-915)caC>caT	p.H305H	RAD54L2_ENST00000296477.3_5'UTR	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	305	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TTCTGGCCCACAGCATGGGTC	0.527																																					p.H305H													.	RAD54L2-93	0			c.C915T						.						105	111	109					3																	51667682		2203	4300	6503	SO:0001819	synonymous_variant	23132	exon7			GGCCCACAGCATG	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.915C>T	3.37:g.51667682C>T		Somatic	182	0		WXS	Illumina HiSeq	Phase_I	219	6	NM_015106	0	0	5	5	0	Q8TB57|Q9BV54	Silent	SNP	ENST00000409535.2	37	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	C	8.949	0.967608	0.18659	.	.	ENSG00000164080	ENST00000432863	.	.	.	5.55	2.41	0.29592	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.0289	8.2154	0.31507	0.0:0.593:0.0:0.407	.	.	.	.	X	134	.	.	Q	+	1	0	RAD54L2	51642722	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.322000	0.33689	0.152000	0.19188	0.655000	0.94253	CAG	.		0.527	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		T	51667682	C	T	51667682	2	4	45	1	0	0	0	0	0	0	0	1	13026	477	17	2		2	RAD54L2	3	51667682	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	31741693	51667682	146354748	29	4069											
PARP3	10039	broad.mit.edu	37	chr3	51979556	51979556	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggccctgcaggcagtctctGagcaggagaagacggtggag	10	5	17	9	1	1	3	0	1	1	2	2	5	1	4	1	5	2	3	1	5	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:51979556G>C	ENST00000417220.2	+	8	1395	c.907G>C	c.(907-909)Gag>Cag	p.E303Q	PARP3_ENST00000431474.1_Missense_Mutation_p.E303Q|PARP3_ENST00000398755.3_Missense_Mutation_p.E310Q			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	303					DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGCAGTCTCTGAGCAGGAGAA	0.622																																					p.E310Q													.	PARP3-660	0			c.G928C						.						42	48	46					3																	51979556		2085	4206	6291	SO:0001583	missense	10039	exon7			GTCTCTGAGCAGG	AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"Poly (ADP-ribose) polymerases"	273	protein-coding gene	gene with protein product	"poly(ADP-ribose) synthetase-3", "NAD+ ADP-ribosyltransferase 3", "poly(ADP-ribose) polymerase 3"	607726	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	ENST00000417220.2:c.907G>C	3.37:g.51979556G>C	ENSP00000395951:p.Glu303Gln	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	107	3	NM_001003931	0	0	14	14	0	Q8NER9|Q96CG2|Q9UG81	Missense_Mutation	SNP	ENST00000417220.2	37	CCDS43097.1	.	.	.	.	.	.	.	.	.	.	G	9.374	1.071180	0.20147	.	.	ENSG00000041880	ENST00000417220;ENST00000431474;ENST00000398755;ENST00000498510	T;T;T;T	0.11821	2.74;2.74;2.74;2.74	4.74	1.99	0.26369	Poly(ADP-ribose) polymerase, regulatory domain (3);	0.185088	0.47852	D	0.000218	T	0.13927	0.0337	L	0.61387	1.9	0.25613	N	0.986488	B;B	0.32010	0.312;0.351	B;B	0.33750	0.054;0.169	T	0.13629	-1.0502	10	0.49607	T	0.09	-17.5701	6.3533	0.21387	0.2469:0.172:0.5812:0.0	.	310;303	Q9Y6F1-2;Q9Y6F1	.;PARP3_HUMAN	Q	303;303;310;303	ENSP00000395951:E303Q;ENSP00000401511:E303Q;ENSP00000381740:E310Q;ENSP00000417625:E303Q	ENSP00000381740:E310Q	E	+	1	0	PARP3	51954596	0.545000	0.26449	0.005000	0.12908	0.385000	0.30292	1.575000	0.36493	0.241000	0.21283	0.561000	0.74099	GAG	.		0.622	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4		C	51979556	G	C	51979556	3	2	45	1	0	0	0	0	1	0	0	0	11488	1291	45	4	954	4	PARP3	3	51979556	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	311874	51979556	146042874	30	4070											
FLNB	2317	broad.mit.edu	37	chr3	58089735	58089735	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gactttctggatggggtctaCgcattcgagtattaccccag	8	12	11	10	2	2	0	0	0	2	0	3	3	2	1	2	3	2	2	2	3	3	5	rs371251819		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:58089735C>T	ENST00000295956.4	+	10	1698	c.1533C>T	c.(1531-1533)taC>taT	p.Y511Y	FLNB_ENST00000493452.1_Silent_p.Y342Y|FLNB_ENST00000358537.3_Silent_p.Y511Y|FLNB_ENST00000357272.4_Silent_p.Y511Y|FLNB_ENST00000429972.2_Silent_p.Y511Y|FLNB_ENST00000419752.2_Silent_p.Y342Y|FLNB_ENST00000348383.5_Silent_p.Y511Y|FLNB_ENST00000490882.1_Silent_p.Y511Y	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	511					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		ATGGGGTCTACGCATTCGAGT	0.542																																					p.Y511Y													.	FLNB-593	0			c.C1533T						.	C	,,,	0,4406		0,0,2203	87	86	86		1533,1533,1533,1533	-5.2	0.4	3		86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	511/2634,511/2592,511/2579,511/2603	58089735	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon10			GGTCTACGCATTC	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"actin binding protein 278"	603381	"filamin B, beta (actin binding protein 278)", "Larsen syndrome 1 (autosomal dominant)"	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.1533C>T	3.37:g.58089735C>T		Somatic	188	0		WXS	Illumina HiSeq	Phase_I	173	4	NM_001457	0	0	10	10	0	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			.		0.542	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		T	58089735	C	T	58089735	2	4	45	1	0	0	0	0	0	0	0	1	5953	547	19	1		1	FLNB	3	58089735	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	6110179	58089735	139932695	31	4071											
GOLGB1	2804	broad.mit.edu	37	chr3	121386444	121386444	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtgttgcatagctgctgctGagcttcagaaaagctttagg	9	12	13	7	0	1	2	1	1	0	1	1	2	1	2	0	2	6	7	0	2	4	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:121386444G>A	ENST00000340645.5	-	20	9543	c.9418C>T	c.(9418-9420)Cag>Tag	p.Q3140*	GOLGB1_ENST00000393667.3_Nonsense_Mutation_p.Q3150*	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	3140					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AGCTGCTGCTGAGCTTCAGAA	0.423																																					p.Q3150X													.	GOLGB1-161	0			c.C9448T						.						71	64	67					3																	121386444		2203	4300	6503	SO:0001587	stop_gained	2804	exon20			GCTGCTGAGCTTC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.9418C>T	3.37:g.121386444G>A	ENSP00000341848:p.Gln3140*	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	136	5	NM_001256486	0	0	90	90	0	B2ZZ91|D3DN92|E7EP74|Q14398	Nonsense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	G	51	17.699545	0.99891	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	.	.	.	5.33	5.33	0.75918	.	0.107337	0.42053	D	0.000765	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	14.3897	0.66970	0.0:0.0:1.0:0.0	.	.	.	.	X	3140;3150	.	ENSP00000341848:Q3140X	Q	-	1	0	GOLGB1	122869134	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.018000	0.40991	2.775000	0.95449	0.650000	0.86243	CAG	.		0.423	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121386444	G	A	121386444	4	1	45	1	0	0	0	0	0	1	0	0	6585	1299	45	2	373	2	GOLGB1	3	121386444	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	63296709	121386444	76635986	32	4072											
COL6A6	131873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	130287049	130287049	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttggtgtagtccagttcagcGacatcaataaggaagagttt	12	12	11	6	1	2	1	2	0	0	1	3	3	3	2	1	2	1	3	1	2	4	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:130287049G>A	ENST00000358511.6	+	5	2033	c.2002G>A	c.(2002-2004)Gac>Aac	p.D668N	COL6A6_ENST00000453409.2_Missense_Mutation_p.D668N	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	668	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		p.D668N(1)		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						CCAGTTCAGCGACATCAATAA	0.423																																					p.D668N		.											.	COL6A6-76	1	Substitution - Missense(1)	large_intestine(1)	c.G2002A						.						178	173	175					3																	130287049		1922	4127	6049	SO:0001583	missense	131873	exon5			TTCAGCGACATCA	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.2002G>A	3.37:g.130287049G>A	ENSP00000351310:p.Asp668Asn	Somatic	239	0		WXS	Illumina HiSeq	Phase_I	330	152	NM_001102608	0	0	0	0	0	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	4.358	0.066002	0.08388	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.79749	-1.3;-1.3	5.53	-3.41	0.04839	von Willebrand factor, type A (3);	0.427722	0.21922	N	0.067159	T	0.71307	0.3324	L	0.50993	1.605	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.58335	-0.7654	10	0.38643	T	0.18	.	13.4535	0.61184	0.0599:0.6662:0.1805:0.0934	.	668	A6NMZ7	CO6A6_HUMAN	N	668	ENSP00000351310:D668N;ENSP00000399236:D668N	ENSP00000351310:D668N	D	+	1	0	COL6A6	131769739	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.129000	0.10515	-0.601000	0.05783	0.655000	0.94253	GAC	.		0.423	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130287049	G	A	130287049	3	1	45	1	0	0	0	0	1	0	0	0	3709	1058	37	1	2020	1	COL6A6	3	130287049	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	8900605	130287049	67735381	33	4073											
DLG1	1739	broad.mit.edu	37	chr3	196771534	196771534	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaacccagatgtaagaaccaGattgttcttctatgatctgt	12	13	8	8	0	3	4	0	1	3	3	3	5	3	4	2	0	2	2	2	0	4	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:196771534G>C	ENST00000419354.1	-	26	2961	c.2675C>G	c.(2674-2676)tCt>tGt	p.S892C	DLG1_ENST00000357674.4_Missense_Mutation_p.S881C|DLG1_ENST00000346964.2_Missense_Mutation_p.S914C|DLG1_ENST00000450955.1_Missense_Mutation_p.S881C|DLG1_ENST00000392382.2_Missense_Mutation_p.S859C|DLG1_ENST00000314062.3_Missense_Mutation_p.S841C|DLG1_ENST00000452595.1_Missense_Mutation_p.S776C|DLG1_ENST00000448528.2_Missense_Mutation_p.S892C|DLG1_ENST00000443183.1_Missense_Mutation_p.S788C|DLG1_ENST00000422288.1_Missense_Mutation_p.S841C			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	892					actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		GTAAGAACCAGATTGTTCTTC	0.378																																					p.S914C													.	DLG1-118	0			c.C2741G						.						158	151	153					3																	196771534		2203	4300	6503	SO:0001583	missense	1739	exon26			GAACCAGATTGTT	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"discs large homolog 1", "presynaptic protein SAP97", "synapse-associated protein 97"	601014	"discs, large (Drosophila) homolog 1"			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.2675C>G	3.37:g.196771534G>C	ENSP00000407531:p.Ser892Cys	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	245	7	NM_004087	0	0	41	43	2	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	37	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645743	0.67358	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955	T;T;T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.26	5.26	0.73747	Guanylate kinase/L-type calcium channel (1);	0.000000	0.85682	D	0.000000	T	0.47021	0.1423	M	0.88906	2.99	0.80722	D	1	D;D;D;D;D	0.76494	0.984;0.973;0.984;0.981;0.999	P;P;P;P;D	0.63113	0.772;0.841;0.735;0.779;0.911	T	0.52200	-0.8607	10	0.41790	T	0.15	.	17.8536	0.88755	0.0:0.0:1.0:0.0	.	881;776;788;892;914	Q12959-4;E9PG21;E7EWL7;Q12959;Q12959-2	.;.;.;DLG1_HUMAN;.	C	914;905;881;879;841;892;776;841;892;788;859;881	ENSP00000345731:S914C;ENSP00000350303:S881C;ENSP00000321087:S841C;ENSP00000407531:S892C;ENSP00000398939:S776C;ENSP00000413238:S841C;ENSP00000391732:S892C;ENSP00000396658:S788C;ENSP00000376187:S859C;ENSP00000411278:S881C	ENSP00000321087:S841C	S	-	2	0	DLG1	198255931	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.469000	0.83416	0.655000	0.94253	TCT	.		0.378	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		C	196771534	G	C	196771534	3	2	45	1	0	0	0	0	1	0	0	0	4565	942	33	4	43	4	DLG1	3	196771534	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	66484485	196771534	1250896	34	4074											
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu	37	chr4	1803568	1803568	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atctgcccccacagagcgctCcccgcaccggcccatcctgc	6	5	8	22	3	1	1	0	0	1	1	3	1	3	1	7	1	3	2	7	1	0	0	rs121913483		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:1803568C>G	ENST00000260795.2	+	6	848	c.746C>G	c.(745-747)tCc>tGc	p.S249C	FGFR3_ENST00000412135.2_Missense_Mutation_p.S249C|FGFR3_ENST00000440486.2_Missense_Mutation_p.S249C|FGFR3_ENST00000340107.4_Missense_Mutation_p.S249C|FGFR3_ENST00000352904.1_Missense_Mutation_p.S249C|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Missense_Mutation_p.S249C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	249			S -> C (in KERSEB, bladder cancer, cervical cancer and TD1). {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:8589699, ECO:0000269|PubMed:8845844}.		alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.S249C(1204)|p.R248_S249del(1)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	ACAGAGCGCTCCCCGCACCGG	0.736		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.S249C		.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	1205	Substitution - Missense(1204)|Deletion - In frame(1)	urinary_tract(1168)|skin(27)|cervix(5)|lung(4)|upper_aerodigestive_tract(1)	c.C746G	GRCh37	CM950470	FGFR3	M	rs121913483	.						13	16	15					4																	1803568		2180	4267	6447	SO:0001583	missense	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	AGCGCTCCCCGCA	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.746C>G	4.37:g.1803568C>G	ENSP00000260795:p.Ser249Cys	Somatic	44	1		WXS	Illumina HiSeq	Phase_I	32	14	NM_001163213	0	0	3	9	6	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	c	18.75	3.690127	0.68271	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904;ENST00000507588	D;T;T;T;T;T;T	0.82081	-1.57;-1.35;-1.33;-1.33;-1.33;-1.33;-1.32	3.94	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.92808	0.7713	M	0.92412	3.305	0.30597	A	0.239052	D;D;D;D;D;D	0.89917	0.998;0.997;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.80764	0.906;0.978;0.983;0.994;0.968;0.993	D	0.94822	0.7988	9	0.72032	D	0.01	.	16.2883	0.82736	0.0:1.0:0.0:0.0	.	212;249;249;249;249;249	Q8NI15;P22607-2;P22607-4;P22607-3;P22607;F8W9L4	.;.;.;.;FGFR3_HUMAN;.	C	249;249;249;249;249;249;69	ENSP00000420533:S249C;ENSP00000339824:S249C;ENSP00000414914:S249C;ENSP00000412903:S249C;ENSP00000260795:S249C;ENSP00000231803:S249C;ENSP00000427289:S69C	ENSP00000260795:S249C	S	+	2	0	FGFR3	1773366	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	7.424000	0.80242	1.903000	0.55091	0.436000	0.28706	TCC	.		0.736	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1803568	C	G	1803568	3	3	45	1	0	0	0	0	1	0	0	0	5886	855	30	4	768	4	FGFR3	4	1803568	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		1803568	189350708	35	4075			1	14		3	3	182	C		2.36579e-07
FGFR3	2261	broad.mit.edu	37	chr4	1803584	1803584	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctccccgcaccggcccatCctgcaggcggggctgccggc	3	4	14	20	5	0	0	0	0	0	0	2	0	2	0	6	5	2	4	6	5	0	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:1803584C>A	ENST00000260795.2	+	6	864	c.762C>A	c.(760-762)atC>atA	p.I254I	FGFR3_ENST00000412135.2_Silent_p.I254I|FGFR3_ENST00000440486.2_Silent_p.I254I|FGFR3_ENST00000340107.4_Silent_p.I254I|FGFR3_ENST00000352904.1_Silent_p.I254I|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Silent_p.I254I			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	254	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	ACCGGCCCATCCTGCAGGCGG	0.731		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.I254I				Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	0			c.C762A						.						15	18	17					4																	1803584		2167	4251	6418	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GCCCATCCTGCAG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.762C>A	4.37:g.1803584C>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_001163213	0	0	114	262	148	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			.		0.731	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		A	1803584	C	A	1803584	2	1	45	1	0	0	0	0	0	0	0	1	5886	845	30	4		4	FGFR3	4	1803584	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	16	1803584	189350692	36	4076			1	14		3	3	182	C		2.36579e-07
FGFR3	2261	ucsc.edu	37	chr4	1803749	1803749	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaccctacgttaccgtgctCaaggtgggccaccgtgtgca	8	8	11	14	3	1	0	1	0	0	0	1	0	1	0	4	2	4	3	4	2	3	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:1803749C>T	ENST00000260795.2	+	6	1029	c.927C>T	c.(925-927)ctC>ctT	p.L309L	FGFR3_ENST00000412135.2_Silent_p.L309L|FGFR3_ENST00000440486.2_Silent_p.L309L|FGFR3_ENST00000340107.4_Silent_p.L309L|FGFR3_ENST00000352904.1_Silent_p.L309L|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Silent_p.L309L			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	309	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TTACCGTGCTCAAGGTGGGCC	0.662		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.L309L				Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	0			c.C927T						.						34	30	31					4																	1803749		2200	4298	6498	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CGTGCTCAAGGTG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.927C>T	4.37:g.1803749C>T		Somatic	28	0		WXS	Illumina HiSeq		20	6	NM_001163213	0	0	22	60	38	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			.		0.662	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		T	1803749	C	T	1803749	2	4	45	1	0	0	0	0	0	0	0	1	5886	813	29	2		2	FGFR3	4	1803749	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	165	1803749	189350527	37	4077			1	14		3	3	182	C		2.36579e-07
UNC5C	8633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr4	96127913	96127913	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggcccacagctcaccacagGggtcaaaagtgtctgagagt	11	6	13	11	0	3	1	2	1	1	1	3	2	3	1	2	3	1	1	2	3	2	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:96127913G>T	ENST00000453304.1	-	11	2116	c.1768C>A	c.(1768-1770)Cct>Act	p.P590T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	590	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)	p.P590T(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CTCACCACAGGGGTCAAAAGT	0.537																																					p.P590T		.											.	UNC5C-94	1	Substitution - Missense(1)	lung(1)	c.C1768A						.						50	49	50					4																	96127913		2203	4300	6503	SO:0001583	missense	8633	exon11			CCACAGGGGTCAA	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"Immunoglobulin superfamily / I-set domain containing"	12569	protein-coding gene	gene with protein product		603610	"unc5 (C.elegans homolog) c"			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1768C>A	4.37:g.96127913G>T	ENSP00000406022:p.Pro590Thr	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	106	20	NM_003728	0	0	1	1	0	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471684	0.63737	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.56103	0.48;0.48	5.28	5.28	0.74379	ZU5 (3);	0.000000	0.85682	D	0.000000	T	0.71804	0.3383	M	0.90977	3.165	0.80722	D	1	P;B	0.49559	0.925;0.055	P;B	0.49561	0.615;0.021	T	0.80127	-0.1512	10	0.87932	D	0	.	19.2637	0.93979	0.0:0.0:1.0:0.0	.	590;590	A8K385;O95185	.;UNC5C_HUMAN	T	590;549;609	ENSP00000406022:P590T;ENSP00000426924:P609T	ENSP00000328673:P549T	P	-	1	0	UNC5C	96346936	1.000000	0.71417	0.971000	0.41717	0.843000	0.47879	7.884000	0.87274	2.611000	0.88343	0.563000	0.77884	CCT	.		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96127913	G	T	96127913	3	4	45	1	0	0	0	0	1	0	0	0	17026	1232	43	4	1051	4	UNC5C	4	96127913	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	94324164	96127913	95026363	38	4078											
TRIML1	339976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr4	189068521	189068521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctcactgaacagccacGtctgaggggcgtgccctgag	7	8	13	13	2	3	3	1	3	2	0	3	3	3	3	2	2	4	1	2	2	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:189068521G>A	ENST00000332517.3	+	6	1542	c.1402G>A	c.(1402-1404)Gtc>Atc	p.V468I	TRIML1_ENST00000507581.1_3'UTR	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	468	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GAACAGCCACGTCTGAGGGGC	0.542																																					p.V468I	Melanoma(31;213 1036 16579 23968 32372)	.											.	TRIML1-156	0			c.G1402A						.						38	40	39					4																	189068521		2199	4297	6496	SO:0001583	missense	339976	exon6			AGCCACGTCTGAG	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"RING-type (C3HC4) zinc fingers"	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.1402G>A	4.37:g.189068521G>A	ENSP00000327738:p.Val468Ile	Somatic	127	1		WXS	Illumina HiSeq	Phase_I	133	67	NM_178556	0	0	0	0	0	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	.	.	.	.	.	.	.	.	.	.	g	11.82	1.751945	0.31046	.	.	ENSG00000184108	ENST00000332517	T	0.61158	0.13	4.79	0.492	0.16872	B30.2/SPRY domain (1);	1.487680	0.04495	N	0.380167	T	0.31734	0.0806	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.15150	-1.0447	10	0.13108	T	0.6	-2.5793	2.7703	0.05332	0.4061:0.0:0.3903:0.2036	.	468	Q8N9V2	TRIML_HUMAN	I	468	ENSP00000327738:V468I	ENSP00000327738:V468I	V	+	1	0	TRIML1	189305515	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.020000	0.13466	0.267000	0.21916	-0.142000	0.14014	GTC	.		0.542	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		A	189068521	G	A	189068521	3	1	45	1	0	0	0	0	1	0	0	0	16583	1145	40	1	1424	1	TRIML1	4	189068521	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	92940608	189068521	2085755	39	4079											
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr5	140725009	140725009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaacaaccccagaggagcctCcatcttctcagtgacagccc	12	6	7	16	0	2	2	1	1	2	1	4	3	3	3	5	1	4	0	5	1	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr5:140725009C>T	ENST00000253812.6	+	1	1409	c.1409C>T	c.(1408-1410)tCc>tTc	p.S470F	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	470	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGGAGCCTCCATCTTCTCA	0.547																																					p.S470F		.											.	PCDHGA3-68	0			c.C1409T						.						116	132	127					5																	140725009		2135	4271	6406	SO:0001583	missense	56112	exon1			GAGCCTCCATCTT	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1409C>T	5.37:g.140725009C>T	ENSP00000253812:p.Ser470Phe	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	308	143	NM_032011	0	0	0	0	0	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	15.45	2.838553	0.51057	.	.	ENSG00000254245	ENST00000253812	T	0.02709	4.19	5.36	4.5	0.54988	Cadherin (3);Cadherin-like (1);	0.000000	0.33199	U	0.005170	T	0.09468	0.0233	M	0.64997	1.995	0.27060	N	0.963586	P;P	0.49358	0.734;0.923	P;P	0.56648	0.485;0.803	T	0.01566	-1.1323	10	0.72032	D	0.01	.	11.5922	0.50951	0.0:0.8506:0.0:0.1494	.	470;470	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	F	470	ENSP00000253812:S470F	ENSP00000253812:S470F	S	+	2	0	PCDHGA3	140705193	0.021000	0.18746	1.000000	0.80357	0.953000	0.61014	1.432000	0.34936	1.399000	0.46721	0.563000	0.77884	TCC	.		0.547	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140725009	C	T	140725009	3	4	45	1	0	0	0	0	1	0	0	0	11581	855	30	2	1411	2	PCDHGA3	5	140725009	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		140725009	40190251	40	4080											
PCDHGA12	26025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr5	140811015	140811015	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcaccgcgcgcatccgcgTgatggttctggatgcgaacg	7	7	15	12	7	1	1	0	1	1	0	2	3	2	2	2	3	2	3	2	3	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr5:140811015T>C	ENST00000252085.3	+	1	831	c.689T>C	c.(688-690)gTg>gCg	p.V230A	PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	230	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCATCCGCGTGATGGTTCTG	0.657																																					p.V230A		.											.	PCDHGA12-27	0			c.T689C						.						52	53	53					5																	140811015		2203	4300	6503	SO:0001583	missense	26025	exon1			TCCGCGTGATGGT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.689T>C	5.37:g.140811015T>C	ENSP00000252085:p.Val230Ala	Somatic	191	1		WXS	Illumina HiSeq	Phase_I	162	70	NM_032094	0	0	3	3	0	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	t	19.24	3.789729	0.70337	.	.	ENSG00000253159	ENST00000252085	T	0.72505	-0.66	4.89	4.89	0.63831	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.89378	0.6698	H	0.99404	4.55	0.21064	N	0.999791	P;P	0.50156	0.791;0.932	P;P	0.55508	0.668;0.777	D	0.84959	0.0876	9	0.87932	D	0	.	14.3394	0.66614	0.0:0.0:0.0:1.0	.	230;230	O60330-2;O60330	.;PCDGC_HUMAN	A	230	ENSP00000252085:V230A	ENSP00000252085:V230A	V	+	2	0	PCDHGA12	140791199	1.000000	0.71417	0.751000	0.31187	0.627000	0.37826	7.868000	0.87116	2.064000	0.61679	0.533000	0.62120	GTG	.		0.657	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		C	140811015	T	C	140811015	3	2	45	1	0	0	0	0	1	0	0	0	11579	1696	59	3	691	3	PCDHGA12	5	140811015	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	86006	140811015	40104245	41	4081											
CLINT1	9685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr5	157240138	157240138	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctttgttcttctttgctttCtttcgctcttcacgaagcct	3	21	5	12	2	6	0	1	0	5	0	7	1	6	0	1	0	2	3	1	0	1	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr5:157240138C>G	ENST00000411809.2	-	5	654	c.450G>C	c.(448-450)aaG>aaC	p.K150N	CLINT1_ENST00000523908.1_Missense_Mutation_p.K150N|CLINT1_ENST00000523094.1_Missense_Mutation_p.K132N|CLINT1_ENST00000296951.5_Missense_Mutation_p.K132N|CLINT1_ENST00000530742.1_Missense_Mutation_p.K132N	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	150					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCTTTGCTTTCTTTCGCTCTT	0.423																																					p.K150N	Colon(22;427 587 2170 6147 14291)	.											.	CLINT1-48	0			c.G450C						.						217	207	210					5																	157240138		1913	4128	6041	SO:0001583	missense	9685	exon5			TGCTTTCTTTCGC	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.450G>C	5.37:g.157240138C>G	ENSP00000388340:p.Lys150Asn	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	168	83	NM_014666	0	0	36	68	32	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Missense_Mutation	SNP	ENST00000411809.2	37	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275997	0.59649	.	.	ENSG00000113282	ENST00000523094;ENST00000530742;ENST00000411809;ENST00000296951;ENST00000523908	T;T;T;T;T	0.54279	0.6;0.6;0.6;0.6;0.58	5.88	4.05	0.47172	ENTH/VHS (1);	0.085100	0.85682	D	0.000000	T	0.67608	0.2911	M	0.75884	2.315	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.989	T	0.64689	-0.6348	10	0.33141	T	0.24	-15.7865	9.2432	0.37509	0.0:0.7587:0.0:0.2413	.	150;150	B7Z6F8;Q14677	.;EPN4_HUMAN	N	132;132;150;132;150	ENSP00000429345:K132N;ENSP00000433419:K132N;ENSP00000388340:K150N;ENSP00000296951:K132N;ENSP00000429824:K150N	ENSP00000296951:K132N	K	-	3	2	CLINT1	157172716	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.312000	0.33574	0.753000	0.32945	0.655000	0.94253	AAG	.		0.423	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666		G	157240138	C	G	157240138	3	3	45	1	0	0	0	0	1	0	0	0	3537	912	32	4	1459	4	CLINT1	5	157240138	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	16429123	157240138	23675122	42	4082											
FLT4	2324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr5	180048230	180048230	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaggtcggtcaagttctgCgtgagccgaggggcttccag	7	8	17	9	3	2	1	1	1	1	0	4	3	3	2	2	5	2	2	2	5	1	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr5:180048230C>T	ENST00000261937.6	-	14	2121	c.2043G>A	c.(2041-2043)acG>acA	p.T681T	FLT4_ENST00000393347.3_Silent_p.T681T|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.T681T	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	681	Ig-like C2-type 7.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAAGTTCTGCGTGAGCCGAG	0.637																																					p.T681T	Colon(97;1075 1466 27033 27547 35871)	.											.	FLT4-1490	0			c.G2043A						.						26	30	29					5																	180048230		2201	4293	6494	SO:0001819	synonymous_variant	2324	exon14			GTTCTGCGTGAGC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2043G>A	5.37:g.180048230C>T		Somatic	91	1		WXS	Illumina HiSeq	Phase_I	64	30	NM_182925	0	0	5	6	1	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			.		0.637	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			T	180048230	C	T	180048230	2	4	45	1	0	0	0	0	0	0	0	1	5963	755	27	1		1	FLT4	5	180048230	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	22808092	180048230	867030	43	4083											
OR14J1	442191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr6	29274483	29274483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gactatggtcaatttgacttCaatgagtggattccttctta	10	16	8	7	0	3	2	2	2	1	0	4	4	4	3	1	2	0	0	1	2	4	6			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:29274483C>T	ENST00000377160.2	+	1	81	c.17C>T	c.(16-18)tCa>tTa	p.S6L		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						AATTTGACTTCAATGAGTGGA	0.403																																					p.S6L		.											.	OR14J1-1	0			c.C17T						.						178	185	182					6																	29274483		1511	2709	4220	SO:0001583	missense	442191	exon1			TGACTTCAATGAG		CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"GPCR / Class A : Olfactory receptors"	13971	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily U, member 1"	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.17C>T	6.37:g.29274483C>T	ENSP00000366365:p.Ser6Leu	Somatic	258	0		WXS	Illumina HiSeq	Phase_I	408	159	NM_030946	0	0	0	0	0	A2BEC2|B0V078|Q5ST27	Missense_Mutation	SNP	ENST00000377160.2	37	CCDS34362.1	.	.	.	.	.	.	.	.	.	.	C	7.344	0.621483	0.14193	.	.	ENSG00000204695	ENST00000377160	T	0.00522	6.84	4.73	1.88	0.25563	.	0.481890	0.15328	N	0.268184	T	0.00073	0.0002	N	0.05414	-0.055	0.09310	N	1	B	0.25441	0.126	B	0.24701	0.055	T	0.08911	-1.0699	10	0.27785	T	0.31	.	4.4271	0.11509	0.1483:0.4819:0.288:0.0819	.	6	Q9UGF5	O14J1_HUMAN	L	6	ENSP00000366365:S6L	ENSP00000366365:S6L	S	+	2	0	OR14J1	29382462	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.295000	0.01143	0.263000	0.21812	0.655000	0.94253	TCA	.		0.403	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2			T	29274483	C	T	29274483	3	4	45	1	0	0	0	0	1	0	0	0	10974	838	29	2	19	2	OR14J1	6	29274483	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		29274483	141840584	44	4084											
BRD2	6046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr6	32945959	32945959	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtccaatatccaagccCaagaggaaaagagagaaaaa	20	3	10	8	0	0	3	0	0	0	3	2	5	2	4	3	2	1	0	3	2	8	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:32945959C>G	ENST00000374825.4	+	10	3336	c.1635C>G	c.(1633-1635)ccC>ccG	p.P545P	BRD2_ENST00000395287.1_Silent_p.P545P|BRD2_ENST00000395289.2_Silent_p.P545P|BRD2_ENST00000443797.2_Silent_p.P425P|BRD2_ENST00000449085.2_Silent_p.P498P|BRD2_ENST00000374831.4_Silent_p.P545P	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	545	Arg/Lys-rich (highly basic).				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TATCCAAGCCCAAGAGGAAAA	0.463																																					p.P545P		.											.	BRD2-398	0			c.C1635G						.						38	46	43					6																	32945959		1508	2708	4216	SO:0001819	synonymous_variant	6046	exon10			CAAGCCCAAGAGG	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1635C>G	6.37:g.32945959C>G		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	91	36	NM_005104	0	0	46	87	41	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	C	10.41	1.342233	0.24339	.	.	ENSG00000204256	ENST00000449025	T	0.31247	1.5	5.35	-3.94	0.04130	.	0.000000	0.49916	D	0.000124	T	0.08403	0.0209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14924	-1.0455	7	0.18710	T	0.47	-14.208	4.8892	0.13719	0.4611:0.1625:0.0:0.3764	.	.	.	.	R	551	ENSP00000409613:P551R	ENSP00000409613:P551R	P	+	2	0	BRD2	33053937	0.103000	0.21917	0.943000	0.38184	0.899000	0.52679	-0.561000	0.05957	-0.702000	0.05056	-0.272000	0.10252	CCA	.		0.463	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			G	32945959	C	G	32945959	2	3	45	1	0	0	0	0	0	0	0	1	1505	581	21	4		4	BRD2	6	32945959	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3671476	32945959	138169108	45	4085											
BRD2	6046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr6	32947799	32947799	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggagccctctttacgtgattCaaacccagaagagattgaga	13	9	10	9	1	2	4	1	2	1	3	2	7	2	5	2	1	3	0	2	1	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:32947799C>G	ENST00000374825.4	+	11	3737	c.2036C>G	c.(2035-2037)tCa>tGa	p.S679*	BRD2_ENST00000395287.1_Nonsense_Mutation_p.S714*|BRD2_ENST00000395289.2_Nonsense_Mutation_p.S714*|BRD2_ENST00000443797.2_Nonsense_Mutation_p.S559*|BRD2_ENST00000449085.2_Nonsense_Mutation_p.S632*|BRD2_ENST00000374831.4_Nonsense_Mutation_p.S679*	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	679	NET. {ECO:0000255|PROSITE- ProRule:PRU00857}.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TTACGTGATTCAAACCCAGAA	0.498																																					p.S714X		.											.	BRD2-398	0			c.C2141G						.						65	64	64					6																	32947799		1511	2709	4220	SO:0001587	stop_gained	6046	exon11			GTGATTCAAACCC	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.2036C>G	6.37:g.32947799C>G	ENSP00000363958:p.Ser679*	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	105	44	NM_001199455	0	0	77	116	39	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Nonsense_Mutation	SNP	ENST00000374825.4	37	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	52|52	19.743137|19.743137	0.99923|0.99923	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.000000	.|0.41605	.|D	.|0.000858	T|.	0.70055|.	0.3180|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.70457|.	-0.4866|.	3|.	.|0.52906	.|T	.|0.07	-14.2571|-14.2571	16.9633|16.9633	0.86278|0.86278	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	E|X	685|679;679;714;559;714;632	.|.	.|ENSP00000363958:S679X	Q|S	+|+	1|2	0|0	BRD2|BRD2	33055777|33055777	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.637000|7.637000	0.83313|0.83313	2.873000|2.873000	0.98535|0.98535	0.643000|0.643000	0.83706|0.83706	CAA|TCA	.		0.498	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			G	32947799	C	G	32947799	4	3	45	1	0	0	0	0	0	1	0	0	1505	838	29	4	2074	4	BRD2	6	32947799	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	1840	32947799	138167268	46	4086											
SMPD2	6610	hgsc.bcm.edu;broad.mit.edu	37	chr6	109763791	109763791	+	Frame_Shift_Del	DEL	C	C	-																															aggacatctacctagcacatCgtgtggcccaagcttgggaa																								rs534167199		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:109763791delC	ENST00000258052.3	+	6	813	c.454delC	c.(454-456)cgtfs	p.R152fs	PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	152					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)	p.R152C(1)		endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		CCTAGCACATCGTGTGGCCCA	0.537																																					p.R152fs		.											.	SMPD2-90	1	Substitution - Missense(1)	endometrium(1)	c.454delC						.						169	147	154					6																	109763791		2203	4300	6503	SO:0001589	frameshift_variant	6610	exon6			.	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.454delC	6.37:g.109763791delC	ENSP00000258052:p.Arg152fs	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	259	117	NM_003080	0	0	0	0	0	Q5TED1|Q9BWR3	Frame_Shift_Del	DEL	ENST00000258052.3	37	CCDS5075.1																																																																																			.		0.537	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			-	109763791	C	-	109763791	7	5	45	1	0	1	0	1	0	0	0	0	14837	884	31	0	476	0	SMPD2	6	109763791	Frame_Shift_Del	DEL	C	TCGA-B3-4104-01A-01D-1458-08	76815992	109763791	61351276	47	4087											
HECW1	23072	broad.mit.edu	37	chr7	43519234	43519234	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tttcgtggaccacaacagtcGagctaccactttcattgacc	10	11	7	13	2	1	1	1	1	0	0	3	3	1	2	3	1	3	1	3	1	2	4	rs531623127		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:43519234G>C	ENST00000395891.2	+	17	3730	c.3125G>C	c.(3124-3126)cGa>cCa	p.R1042P	HECW1_ENST00000453890.1_Missense_Mutation_p.R1008P	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1042	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CACAACAGTCGAGCTACCACT	0.493																																					p.R1042P													.	HECW1-669	0			c.G3125C						.						160	151	154					7																	43519234		1940	4154	6094	SO:0001583	missense	23072	exon17			ACAGTCGAGCTAC	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3125G>C	7.37:g.43519234G>C	ENSP00000379228:p.Arg1042Pro	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	283	8	NM_015052	0	0	0	0	0	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	G	32	5.133939	0.94517	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	D;D	0.85702	-2.02;-2.02	5.53	5.53	0.82687	WW/Rsp5/WWP (6);	0.056927	0.64402	D	0.000001	D	0.94265	0.8158	M	0.90922	3.16	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.976	D	0.95065	0.8199	10	0.87932	D	0	.	19.4697	0.94958	0.0:0.0:1.0:0.0	.	1008;1042	B4DH42;Q76N89	.;HECW1_HUMAN	P	1042;1008;1042	ENSP00000379228:R1042P;ENSP00000407774:R1008P	ENSP00000265522:R1042P	R	+	2	0	HECW1	43485759	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.840000	0.99478	2.611000	0.88343	0.462000	0.41574	CGA	.		0.493	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		C	43519234	G	C	43519234	3	2	45	1	0	0	0	0	1	0	0	0	7063	1058	37	4	3183	4	HECW1	7	43519234	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		43519234	115619429	48	4088											
CTTNBP2	83992	broad.mit.edu	37	chr7	117407188	117407188	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attgcacttgtctctcctttCtggctcaagccctccgtgcc	4	14	7	16	1	3	0	1	0	2	0	6	0	5	0	4	1	3	2	4	1	1	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:117407188C>G	ENST00000160373.3	-	9	2912	c.2821G>C	c.(2821-2823)Gaa>Caa	p.E941Q		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	941					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TCTCTCCTTTCTGGCTCAAGC	0.433																																					p.E941Q													.	CTTNBP2-94	0			c.G2821C						.						173	145	154					7																	117407188		2203	4300	6503	SO:0001583	missense	83992	exon9			TCCTTTCTGGCTC		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2821G>C	7.37:g.117407188C>G	ENSP00000160373:p.Glu941Gln	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	210	5	NM_033427	0	0	1	1	0	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.970686|3.970686	0.74246|0.74246	.|.	.|.	ENSG00000077063|ENSG00000077063	ENST00000160373|ENST00000446636	T|.	0.53857|.	0.6|.	5.64|5.64	5.64|5.64	0.86602|0.86602	Ankyrin repeat-containing domain (2);|.	0.278035|.	0.44483|.	D|.	0.000453|.	T|T	0.67785|0.67785	0.2930|0.2930	L|L	0.40543|0.40543	1.245|1.245	0.46981|0.46981	D|D	0.999274|0.999274	D|.	0.58620|.	0.983|.	P|.	0.52386|.	0.697|.	T|T	0.61402|0.61402	-0.7070|-0.7070	10|5	0.54805|.	T|.	0.06|.	-10.6121|-10.6121	20.0666|20.0666	0.97706|0.97706	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	941|.	Q8WZ74|.	CTTB2_HUMAN|.	Q|T	941|428	ENSP00000160373:E941Q|.	ENSP00000160373:E941Q|.	E|R	-|-	1|2	0|0	CTTNBP2|CTTNBP2	117194424|117194424	1.000000|1.000000	0.71417|0.71417	0.294000|0.294000	0.24946|0.24946	0.588000|0.588000	0.36517|0.36517	5.568000|5.568000	0.67385|0.67385	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	GAA|AGA	.		0.433	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117407188	C	G	117407188	3	3	45	1	0	0	0	0	1	0	0	0	4051	922	32	4	2230	4	CTTNBP2	7	117407188	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	73887954	117407188	41731475	49	4089											
CHRM2	1129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	136700056	136700056	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgatgattgcagctgcctgGgtcctctctttcatcctctg	5	15	9	12	0	3	2	1	2	2	0	6	2	5	2	3	1	3	2	3	1	0	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:136700056G>T	ENST00000445907.2	+	3	972	c.444G>T	c.(442-444)tgG>tgT	p.W148C	CHRM2_ENST00000397608.3_Missense_Mutation_p.W148C|CHRM2_ENST00000402486.3_Missense_Mutation_p.W148C|CHRM2_ENST00000401861.1_Missense_Mutation_p.W148C|CHRM2_ENST00000453373.1_Missense_Mutation_p.W148C|CHRM2_ENST00000320658.5_Missense_Mutation_p.W148C|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000425981.2_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	148					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAGCTGCCTGGGTCCTCTCTT	0.488																																					p.W148C		.											.	CHRM2-94	0			c.G444T						.						66	68	68					7																	136700056		2203	4300	6503	SO:0001583	missense	1129	exon3			TGCCTGGGTCCTC		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.444G>T	7.37:g.136700056G>T	ENSP00000399745:p.Trp148Cys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	145	26	NM_001006632	0	0	0	0	0	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.567740	0.65651	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97340	0.9130	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98748	1.0719	10	0.87932	D	0	-1.0967	19.7244	0.96157	0.0:0.0:1.0:0.0	.	148	P08172	ACM2_HUMAN	C	148	ENSP00000399745:W148C;ENSP00000415386:W148C;ENSP00000319984:W148C;ENSP00000380733:W148C;ENSP00000384937:W148C;ENSP00000384401:W148C	ENSP00000319984:W148C	W	+	3	0	CHRM2	136350596	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.807000	0.99171	2.659000	0.90383	0.655000	0.94253	TGG	.		0.488	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			T	136700056	G	T	136700056	3	4	45	1	0	0	0	0	1	0	0	0	3383	1241	43	4	446	4	CHRM2	7	136700056	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	19292868	136700056	22438607	50	4090											
PRKAG2	51422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	151372582	151372582	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaggaagacgggcagaacCtctgccctgtgtccgggggg	8	5	18	10	2	1	2	0	0	1	2	2	4	2	4	3	6	2	1	3	6	3	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:151372582C>G	ENST00000287878.4	-	4	1112	c.608G>C	c.(607-609)aGg>aCg	p.R203T	PRKAG2_ENST00000461529.1_5'Flank|PRKAG2_ENST00000492843.1_Missense_Mutation_p.R79T|PRKAG2_ENST00000392801.2_Missense_Mutation_p.R159T|PRKAG2_ENST00000433631.2_Missense_Mutation_p.R79T	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	203					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	CGGGCAGAACCTCTGCCCTGT	0.587																																					p.R203T		.											.	PRKAG2-658	0			c.G608C						.						82	75	77					7																	151372582		2203	4300	6503	SO:0001583	missense	51422	exon4			CAGAACCTCTGCC	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.608G>C	7.37:g.151372582C>G	ENSP00000287878:p.Arg203Thr	Somatic	113	1		WXS	Illumina HiSeq	Phase_I	118	49	NM_016203	0	0	0	0	0	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Missense_Mutation	SNP	ENST00000287878.4	37	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.264778	0.59431	.	.	ENSG00000106617	ENST00000287878;ENST00000492843;ENST00000433631;ENST00000392801	D;D;D;D	0.90385	-2.25;-2.66;-2.66;-2.63	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.94255	0.8155	L	0.60455	1.87	0.47245	D	0.999369	P;D;D	0.67145	0.704;0.996;0.976	B;D;P	0.77557	0.15;0.99;0.703	D	0.94164	0.7417	10	0.52906	T	0.07	.	18.022	0.89258	0.0:1.0:0.0:0.0	.	79;203;203	B7Z6X8;Q8NCK6;Q9UGJ0	.;.;AAKG2_HUMAN	T	203;79;79;159	ENSP00000287878:R203T;ENSP00000419577:R79T;ENSP00000406544:R79T;ENSP00000376549:R159T	ENSP00000287878:R203T	R	-	2	0	PRKAG2	151003515	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	5.317000	0.65822	2.489000	0.83994	0.456000	0.33151	AGG	.		0.587	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		G	151372582	C	G	151372582	3	3	45	1	0	0	0	0	1	0	0	0	12530	681	24	4	1153	4	PRKAG2	7	151372582	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	14672526	151372582	7766081	51	4091											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	151879016	151879016	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcccaaggatttgggaaattGatctgtcatcacaggcctag	11	10	11	9	0	3	1	2	1	1	0	3	3	3	3	2	3	0	0	2	3	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:151879016G>A	ENST00000262189.6	-	36	6147	c.5929C>T	c.(5929-5931)Caa>Taa	p.Q1977*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.Q1977*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1977	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTGGGAAATTGATCTGTCATC	0.458																																					p.Q1977X		.											.	MLL3-1398	0			c.C5929T						.						215	223	220					7																	151879016		2203	4300	6503	SO:0001587	stop_gained	58508	exon36			GAAATTGATCTGT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5929C>T	7.37:g.151879016G>A	ENSP00000262189:p.Gln1977*	Somatic	536	0		WXS	Illumina HiSeq	Phase_I	722	115	NM_170606	0	0	5	5	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	47	13.696566	0.99758	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.37	4.49	0.54785	.	0.000000	0.42420	U	0.000717	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3796	0.44104	0.1499:0.0:0.8501:0.0	.	.	.	.	X	1977	.	ENSP00000262189:Q1977X	Q	-	1	0	MLL3	151509949	1.000000	0.71417	0.139000	0.22197	0.959000	0.62525	6.683000	0.74533	1.289000	0.44618	0.558000	0.71614	CAA	.		0.458	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151879016	G	A	151879016	4	1	45	1	0	0	0	0	0	1	0	0	9647	1299	45	2	8902	2	MLL3	7	151879016	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	506434	151879016	7259647	52	4092											
ERLIN2	11160	broad.mit.edu	37	chr8	37597912	37597912	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgctgacttcgaccagcgGccctggtttccatctcatgc	5	11	9	16	2	1	1	1	1	1	0	4	2	2	1	4	2	3	2	4	2	0	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr8:37597912G>A	ENST00000276461.5	+	3	204	c.137G>A	c.(136-138)gGc>gAc	p.G46D	ERLIN2_ENST00000518586.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000335171.6_Missense_Mutation_p.G46D|RP11-863K10.7_ENST00000330539.1_5'Flank|ERLIN2_ENST00000523107.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000523887.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000519638.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000397228.2_Missense_Mutation_p.G46D	NM_007175.6	NP_009106.1	O94905	ERLN2_HUMAN	ER lipid raft associated 2	46					cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|lung(5)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			TCGACCAGCGGCCCTGGTTTC	0.537																																					p.G46D													.	ERLIN2-90	0			c.G137A						.						228	199	208					8																	37597912		2203	4300	6503	SO:0001583	missense	11160	exon3			CCAGCGGCCCTGG	AY358108	CCDS6095.1, CCDS34879.1	8p11.2	2012-11-23	2007-01-26	2007-01-26	ENSG00000147475	ENSG00000147475			1356	protein-coding gene	gene with protein product		611605	"chromosome 8 open reading frame 2", "SPFH domain family, member 2"	C8orf2, SPFH2, Erlin-2		10449903, 15897872, 16835267	Standard	NM_007175		Approved	NET32, SPG18	uc003xke.4	O94905	OTTHUMG00000164005	ENST00000276461.5:c.137G>A	8.37:g.37597912G>A	ENSP00000276461:p.Gly46Asp	Somatic	390	0		WXS	Illumina HiSeq	Phase_I	498	25	NM_001003791	0	0	22	22	0	A0JLQ1|A8K5S9|B4DM38|D3DSW0|Q6NW21|Q86VS6|Q86W49	Missense_Mutation	SNP	ENST00000276461.5	37	CCDS6095.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263471	0.80358	.	.	ENSG00000147475	ENST00000397228;ENST00000523887;ENST00000276461;ENST00000518586;ENST00000335171;ENST00000521644;ENST00000519638	D;D;D;D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43;-3.43;-3.43;-3.43	5.91	5.91	0.95273	.	0.088984	0.85682	D	0.000000	D	0.95204	0.8445	L	0.45137	1.4	0.80722	D	1	D;B;B	0.58620	0.983;0.257;0.009	P;B;B	0.57502	0.822;0.162;0.029	D	0.94048	0.7315	10	0.37606	T	0.19	-17.7147	19.29	0.94095	0.0:0.0:1.0:0.0	.	46;46;46	O94905;O94905-3;O94905-2	ERLN2_HUMAN;.;.	D	46	ENSP00000380405:G46D;ENSP00000429903:G46D;ENSP00000276461:G46D;ENSP00000427847:G46D;ENSP00000335220:G46D;ENSP00000429621:G46D;ENSP00000428112:G46D	ENSP00000276461:G46D	G	+	2	0	ERLIN2	37717070	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.379000	0.97198	2.799000	0.96334	0.650000	0.86243	GGC	.		0.537	ERLIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376712.2	NM_007175		A	37597912	G	A	37597912	3	1	45	1	0	0	0	0	1	0	0	0	5246	1203	42	2	143	2	ERLIN2	8	37597912	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		37597912	108766110	53	4093											
ST18	9705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr8	53028901	53028901	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttagacctgccagctctttCagcagactttcattgttctg	7	15	7	12	0	4	2	2	0	2	2	4	2	4	2	2	0	3	3	2	0	1	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr8:53028901C>T	ENST00000276480.7	-	25	3620	c.2937G>A	c.(2935-2937)ctG>ctA	p.L979L		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	979					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CCAGCTCTTTCAGCAGACTTT	0.433																																					p.L979L		.											.	ST18-95	0			c.G2937A						.						232	167	189					8																	53028901		2203	4300	6503	SO:0001819	synonymous_variant	9705	exon25			CTCTTTCAGCAGA	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2937G>A	8.37:g.53028901C>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	175	69	NM_014682	0	0	0	0	0	Q17RY1	Silent	SNP	ENST00000276480.7	37	CCDS6149.1																																																																																			.		0.433	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53028901	C	T	53028901	2	4	45	1	0	0	0	0	0	0	0	1	15244	813	29	2		2	ST18	8	53028901	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	15430989	53028901	93335121	54	4094			2	15		2	2	12	C		4.192863e-05
ST18	9705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr8	53028912	53028912	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagctctttcagcagactttCattgttctgttctatgagtt	7	18	7	9	0	5	2	2	1	3	1	5	2	5	2	0	0	2	5	0	0	1	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr8:53028912C>T	ENST00000276480.7	-	25	3609	c.2926G>A	c.(2926-2928)Gaa>Aaa	p.E976K		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	976					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				AGCAGACTTTCATTGTTCTGT	0.438																																					p.E976K		.											.	ST18-95	0			c.G2926A						.						238	170	193					8																	53028912		2203	4300	6503	SO:0001583	missense	9705	exon25			GACTTTCATTGTT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2926G>A	8.37:g.53028912C>T	ENSP00000276480:p.Glu976Lys	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	160	60	NM_014682	0	0	0	0	0	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	C	36	5.702512	0.96812	.	.	ENSG00000147488	ENST00000276480	T	0.49139	0.79	5.63	5.63	0.86233	.	0.048484	0.85682	D	0.000000	T	0.60779	0.2295	L	0.49778	1.585	0.80722	D	1	D	0.62365	0.991	P	0.57204	0.815	T	0.61063	-0.7138	10	0.59425	D	0.04	-24.3803	19.6718	0.95914	0.0:1.0:0.0:0.0	.	976	O60284	ST18_HUMAN	K	976	ENSP00000276480:E976K	ENSP00000276480:E976K	E	-	1	0	ST18	53191465	1.000000	0.71417	0.869000	0.34112	0.805000	0.45488	4.884000	0.63135	2.643000	0.89663	0.655000	0.94253	GAA	.		0.438	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53028912	C	T	53028912	3	4	45	1	0	0	0	0	1	0	0	0	15244	835	29	2	225	2	ST18	8	53028912	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	11	53028912	93335110	55	4095			2	15		2	2	12	C		4.192863e-05
GRHL2	79977	broad.mit.edu	37	chr8	102631907	102631907	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	catagagcttattgccagatCaaggtcttctgtgacaaagt	12	12	9	8	0	3	3	1	1	2	2	3	3	3	3	1	1	2	1	1	1	4	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr8:102631907C>G	ENST00000251808.3	+	9	1577	c.1239C>G	c.(1237-1239)atC>atG	p.I413M	GRHL2_ENST00000395927.1_Missense_Mutation_p.I397M	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	413					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			ATTGCCAGATCAAGGTCTTCT	0.338																																					p.I413M													.	GRHL2-93	0			c.C1239G						.						97	96	96					8																	102631907		2203	4300	6503	SO:0001583	missense	79977	exon9			CCAGATCAAGGTC	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"deafness, autosomal dominant 28", "transcription factor CP2-like 3"	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.1239C>G	8.37:g.102631907C>G	ENSP00000251808:p.Ile413Met	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	264	8	NM_024915	0	0	30	30	0	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	37	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.981703	0.74474	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	T;T	0.24538	1.85;1.85	5.85	5.85	0.93711	CP2 transcription factor (1);	0.046113	0.85682	D	0.000000	T	0.52075	0.1712	M	0.72353	2.195	0.80722	D	1	D	0.61080	0.989	D	0.64877	0.93	T	0.49753	-0.8906	10	0.66056	D	0.02	-36.8225	20.1634	0.98142	0.0:1.0:0.0:0.0	.	413	Q6ISB3	GRHL2_HUMAN	M	413;397;413	ENSP00000251808:I413M;ENSP00000379260:I397M	ENSP00000251808:I413M	I	+	3	3	GRHL2	102701083	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.929000	0.63455	2.773000	0.95371	0.655000	0.94253	ATC	.		0.338	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		G	102631907	C	G	102631907	3	3	45	1	0	0	0	0	1	0	0	0	6785	816	29	4	1273	4	GRHL2	8	102631907	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	49602995	102631907	43732115	56	4096											
VLDLR	7436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr9	2651933	2651933	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccaaaagggacttctgccGcatgggccattcttcctctc	7	10	8	16	1	3	0	0	0	3	0	5	1	4	1	5	2	1	1	5	2	2	3	rs183359461		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:2651933G>A	ENST00000382100.3	+	17	2751	c.2395G>A	c.(2395-2397)Gca>Aca	p.A799T	VLDLR_ENST00000382099.2_Missense_Mutation_p.A771T	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	799					cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.A799T(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		GACTTCTGCCGCATGGGCCAT	0.433																																					p.A799T		.											.	VLDLR-516	1	Substitution - Missense(1)	pancreas(1)	c.G2395A						.	G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	108	98	101		2311,2395	5.1	1	9		101	0,8600		0,0,4300	no	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	771/846,799/874	2651933	1,13005	2203	4300	6503	SO:0001583	missense	7436	exon17			TCTGCCGCATGGG		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.2395G>A	9.37:g.2651933G>A	ENSP00000371532:p.Ala799Thr	Somatic	123	2		WXS	Illumina HiSeq	Phase_I	177	50	NM_003383	0	0	4	5	1	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.791586	0.50102	2.27E-4	0.0	ENSG00000147852	ENST00000382100;ENST00000382099;ENST00000382092	T;T	0.72942	-0.7;-0.7	5.11	5.11	0.69529	.	0.303026	0.23627	N	0.046179	T	0.68220	0.2977	L	0.31752	0.955	0.58432	D	0.999999	D;D;P	0.62365	0.991;0.984;0.946	P;B;B	0.50490	0.642;0.439;0.306	T	0.64659	-0.6355	10	0.22706	T	0.39	.	18.8988	0.92434	0.0:0.0:1.0:0.0	.	771;771;799	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	T	799;771;678	ENSP00000371532:A799T;ENSP00000371531:A771T	ENSP00000371524:A678T	A	+	1	0	VLDLR	2641933	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	8.532000	0.90613	2.526000	0.85167	0.591000	0.81541	GCA	G|0.999;T|0.000		0.433	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		A	2651933	G	A	2651933	3	1	45	1	0	0	0	0	1	0	0	0	17207	1087	38	1	2461	1	VLDLR	9	2651933	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		2651933	138561498	57	4097											
TYRP1	7306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr9	12704628	12704628	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacaaacccatttgtctcCaaatgatcctatttttgtcc	10	14	6	11	0	1	1	0	1	1	0	4	2	3	2	4	1	1	0	4	1	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:12704628C>A	ENST00000388918.5	+	6	1313	c.1184C>A	c.(1183-1185)cCa>cAa	p.P395Q	RP11-3L8.3_ENST00000417638.1_RNA|TYRP1_ENST00000381136.2_Missense_Mutation_p.P105Q|TYRP1_ENST00000381137.2_Missense_Mutation_p.P104Q	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	395				PN -> SQ (in Ref. 7; CAA35820). {ECO:0000305}.	acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		CATTTGTCTCCAAATGATCCT	0.443									Oculocutaneous Albinism																												p.P395Q		.											.	TYRP1-226	0			c.C1184A						.						122	105	111					9																	12704628		2203	4300	6503	SO:0001583	missense	7306	exon6	Familial Cancer Database		TGTCTCCAAATGA	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.1184C>A	9.37:g.12704628C>A	ENSP00000373570:p.Pro395Gln	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	380	111	NM_000550	0	0	0	0	0	P78468|P78469|Q13721|Q15679	Missense_Mutation	SNP	ENST00000388918.5	37	CCDS34990.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173865	0.78452	.	.	ENSG00000107165	ENST00000381137;ENST00000388918;ENST00000381136	D;D;D	0.99089	-5.41;-5.41;-5.41	5.5	5.5	0.81552	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.000000	0.85682	D	0.000000	D	0.99468	0.9811	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98693	1.0697	10	0.72032	D	0.01	-20.7972	19.7537	0.96281	0.0:1.0:0.0:0.0	.	395	P17643	TYRP1_HUMAN	Q	104;395;105	ENSP00000370529:P104Q;ENSP00000373570:P395Q;ENSP00000370528:P105Q	ENSP00000370528:P105Q	P	+	2	0	TYRP1	12694628	1.000000	0.71417	0.999000	0.59377	0.634000	0.38068	7.370000	0.79589	2.736000	0.93811	0.591000	0.81541	CCA	.		0.443	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		A	12704628	C	A	12704628	3	1	45	1	0	0	0	0	1	0	0	0	16849	594	21	4	1202	4	TYRP1	9	12704628	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	10052695	12704628	128508803	58	4098											
C9orf24	84688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr9	34397497	34397497	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaccaatctcccacttacCggagtcagaaacttgttggc	10	9	7	15	1	2	1	1	0	1	1	3	2	2	2	4	2	2	1	4	2	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:34397497C>T	ENST00000297623.2	-	1	333	c.135G>A	c.(133-135)ccG>ccA	p.P45P		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	45					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		TCCCACTTACCGGAGTCAGAA	0.522																																					p.P45P		.											.	C9orf24-91	0			c.G135A						.						125	117	120					9																	34397497		2203	4300	6503	SO:0001630	splice_region_variant	84688	exon1			ACTTACCGGAGTC	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"ciliated bronchial epithelium 1", "spermatid-specific manchette-related protein 1"					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.135+1G>A	9.37:g.34397497C>T		Somatic	215	0		WXS	Illumina HiSeq	Phase_I	308	87	NM_032596	0	0	2	2	0	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	37	CCDS6554.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.408871	0.42715	.	.	ENSG00000164972	ENST00000444429	.	.	.	5.44	4.53	0.55603	.	.	.	.	.	T	0.61739	0.2371	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59721	-0.7401	4	.	.	.	-0.9559	10.3744	0.44073	0.0:0.9067:0.0:0.0933	.	.	.	.	R	11	.	.	G	-	1	0	C9orf24	34387497	0.988000	0.35896	0.992000	0.48379	0.887000	0.51463	2.922000	0.48860	1.271000	0.44313	0.467000	0.42956	GGG	.		0.522	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	Silent	T	34397497	C	T	34397497	5	4	45	1	0	0	0	0	0	0	1	0	2481	666	23	1	787	1	C9orf24	9	34397497	Splice_Site	SNP	C	TCGA-B3-4104-01A-01D-1458-08	21692869	34397497	106815934	59	4099											
ALDH1B1	219	hgsc.bcm.edu;broad.mit.edu	37	chr9	38396007	38396007	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagcccgggaagccttcCgcctggggtccccatggcgc	6	5	14	16	3	0	0	0	0	0	0	2	1	2	1	6	4	3	1	6	4	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:38396007C>T	ENST00000377698.3	+	2	415	c.262C>T	c.(262-264)Cgc>Tgc	p.R88C		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	88					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		GGAAGCCTTCCGCCTGGGGTC	0.677																																					p.R88C		.											.	ALDH1B1-227	0			c.C262T						.						62	67	65					9																	38396007		2203	4300	6503	SO:0001583	missense	219	exon2			GCCTTCCGCCTGG	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.262C>T	9.37:g.38396007C>T	ENSP00000366927:p.Arg88Cys	Somatic	221	0		WXS	Illumina HiSeq	Phase_I	313	22	NM_000692	0	0	5	5	0	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121727	0.37436	.	.	ENSG00000137124	ENST00000377698	T	0.77358	-1.09	5.61	2.7	0.31948	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.373330	0.22798	N	0.055518	T	0.71443	0.3340	M	0.67625	2.065	0.43377	D	0.995473	B	0.14012	0.009	B	0.18561	0.022	T	0.68349	-0.5432	10	0.87932	D	0	.	4.9629	0.14076	0.2807:0.5588:0.0:0.1605	.	88	P30837	AL1B1_HUMAN	C	88	ENSP00000366927:R88C	ENSP00000366927:R88C	R	+	1	0	ALDH1B1	38386007	0.002000	0.14202	0.982000	0.44146	0.995000	0.86356	-0.376000	0.07465	0.750000	0.32877	0.655000	0.94253	CGC	.		0.677	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			T	38396007	C	T	38396007	3	4	45	1	0	0	0	0	1	0	0	0	493	652	23	1	264	1	ALDH1B1	9	38396007	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3998510	38396007	102817424	60	4100											
CAMSAP1	157922	ucsc.edu	37	chr9	138713398	138713398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgagagattttcaggatggCctgctgcagcgtactgatgg	8	11	14	8	1	1	3	1	2	0	1	1	5	1	4	1	3	4	3	1	3	1	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:138713398C>T	ENST00000389532.4	-	11	3173	c.3109G>A	c.(3109-3111)Gcc>Acc	p.A1037T	CAMSAP1_ENST00000312405.6_Missense_Mutation_p.A759T|CAMSAP1_ENST00000483991.1_5'UTR|CAMSAP1_ENST00000409386.3_Missense_Mutation_p.A1048T	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	1037					cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		TTCAGGATGGCCTGCTGCAGC	0.527																																					p.A1037T													.	CAMSAP1-92	0			c.G3109A						.						74	69	71					9																	138713398		2203	4300	6503	SO:0001583	missense	157922	exon11			GGATGGCCTGCTG	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.3109G>A	9.37:g.138713398C>T	ENSP00000374183:p.Ala1037Thr	Somatic	103	1		WXS	Illumina HiSeq		57	3	NM_015447	0	0	6	9	3	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Missense_Mutation	SNP	ENST00000389532.4	37	CCDS35176.2	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220917	0.58560	.	.	ENSG00000130559	ENST00000389532;ENST00000312405;ENST00000409386	T;T;T	0.14893	2.47;2.47;2.47	4.91	4.91	0.64330	.	0.114253	0.64402	D	0.000010	T	0.43590	0.1254	M	0.73598	2.24	0.44462	D	0.997399	D;D	0.89917	1.0;0.97	D;P	0.69142	0.962;0.839	T	0.45249	-0.9274	10	0.87932	D	0	-2.6208	18.4729	0.90781	0.0:1.0:0.0:0.0	.	1037;1048	Q5T5Y3;Q5T5Y3-3	CAMP1_HUMAN;.	T	1037;759;1048	ENSP00000374183:A1037T;ENSP00000312463:A759T;ENSP00000386420:A1048T	ENSP00000312463:A759T	A	-	1	0	CAMSAP1	137853219	1.000000	0.71417	1.000000	0.80357	0.019000	0.09904	4.748000	0.62148	2.413000	0.81919	0.655000	0.94253	GCC	.		0.527	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		T	138713398	C	T	138713398	3	4	45	1	0	0	0	0	1	0	0	0	2617	739	26	2	1727	2	CAMSAP1	9	138713398	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	100317391	138713398	2500033	61	4101											
NEBL	10529	hgsc.bcm.edu;broad.mit.edu	37	chr10	21309109	21309109	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtgtatctgccaccgtggtGaaggactgcttcgggtagtg	6	11	16	8	2	1	1	0	1	1	0	2	2	1	2	2	4	2	3	2	4	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr10:21309109G>A	ENST00000417816.2	-	3	539	c.186C>T	c.(184-186)ttC>ttT	p.F62F	NEBL_ENST00000377159.4_Silent_p.F28F	NM_001173484.1|NM_213569.2	NP_001166955.1|NP_998734.1	O76041	NEBL_HUMAN	nebulette	107					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CCACCGTGGTGAAGGACTGCT	0.413																																					p.F62F		.											.	NEBL-92	0			c.C186T						.						103	97	99					10																	21309109		2203	4300	6503	SO:0001819	synonymous_variant	10529	exon3			CGTGGTGAAGGAC	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000417816.2:c.186C>T	10.37:g.21309109G>A		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	193	11	NM_001173484	0	0	6	6	0	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000417816.2	37	CCDS7133.1																																																																																			.		0.413	NEBL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047112.1	NM_006393		A	21309109	G	A	21309109	2	1	45	1	0	0	0	0	0	0	0	1	10329	1281	45	2		2	NEBL	10	21309109	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08		21309109	114225638	62	4102											
SGMS1	259230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	52071078	52071078	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgtgtggccgctgtacagaTagtccccacacatgttgtga	8	10	11	12	2	0	2	0	1	0	1	1	2	1	2	4	1	1	3	4	1	2	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr10:52071078T>C	ENST00000361781.2	-	9	1798	c.839A>G	c.(838-840)tAt>tGt	p.Y280C	SGMS1_ENST00000429490.1_Missense_Mutation_p.Y111C	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	286					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCTGTACAGATAGTCCCCACA	0.453																																					p.Y280C		.											.	SGMS1-227	0			c.A839G						.						141	105	117					10																	52071078		2203	4300	6503	SO:0001583	missense	259230	exon9			TACAGATAGTCCC	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.839A>G	10.37:g.52071078T>C	ENSP00000354829:p.Tyr280Cys	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	129	57	NM_147156	0	0	11	25	14	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	37	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.171766	0.78452	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T	0.53206	0.63	5.87	4.68	0.58851	.	0.056539	0.64402	D	0.000001	T	0.65974	0.2743	M	0.73430	2.235	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.76575	0.968;0.988	T	0.69548	-0.5116	10	0.87932	D	0	-23.9233	11.1732	0.48584	0.1378:0.0:0.0:0.8622	.	111;286	B4DJU2;Q86VZ5	.;SMS1_HUMAN	C	80;280;111	ENSP00000354829:Y280C	ENSP00000354829:Y280C	Y	-	2	0	SGMS1	51741084	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.058000	0.64300	2.371000	0.80710	0.533000	0.62120	TAT	.		0.453	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		C	52071078	T	C	52071078	3	2	45	1	0	0	0	0	1	0	0	0	14246	1406	49	3	414	3	SGMS1	10	52071078	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	30761969	52071078	83463669	63	4103											
IDE	3416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	94297234	94297234	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	atattctcgcttgtcttcagGagacttggtaatgtgatttc	8	17	9	7	1	3	2	1	1	2	1	5	3	3	2	0	2	0	2	0	2	2	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr10:94297234G>C	ENST00000265986.6	-	2	228	c.172C>G	c.(172-174)Cct>Gct	p.P58A		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	58					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TTGTCTTCAGGAGACTTGGTA	0.388																																					p.P58A		.											.	IDE-92	0			c.C172G						.						216	192	200					10																	94297234		2203	4300	6503	SO:0001583	missense	3416	exon2			CTTCAGGAGACTT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.172C>G	10.37:g.94297234G>C	ENSP00000265986:p.Pro58Ala	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	210	85	NM_004969	0	0	4	9	5	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	37	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.430602	0.25726	.	.	ENSG00000119912	ENST00000265986;ENST00000436178	T;T	0.30448	1.53;1.53	5.58	5.58	0.84498	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.056903	0.64402	D	0.000001	T	0.20659	0.0497	N	0.14661	0.345	0.80722	D	1	B	0.13145	0.007	B	0.14578	0.011	T	0.09228	-1.0684	10	0.10902	T	0.67	-4.7075	19.5704	0.95409	0.0:0.0:1.0:0.0	.	58	P14735	IDE_HUMAN	A	58;44	ENSP00000265986:P58A;ENSP00000408850:P44A	ENSP00000265986:P58A	P	-	1	0	IDE	94287214	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.325000	0.96381	2.624000	0.88883	0.655000	0.94253	CCT	.		0.388	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94297234	G	C	94297234	3	2	45	1	0	0	0	0	1	0	0	0	7514	1174	41	4	2983	4	IDE	10	94297234	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	42226156	94297234	41237513	64	4104											
RIC8A	60626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	209483	209483	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcatctggctgcagagtgTccgaatcctgtcccgggacc	6	10	12	13	2	2	1	1	0	1	1	5	3	5	2	4	2	1	2	4	2	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:209483T>A	ENST00000526104.1	+	3	1553	c.209T>A	c.(208-210)gTc>gAc	p.V70D	RIC8A_ENST00000527696.1_Missense_Mutation_p.V64D|BET1L_ENST00000410108.1_5'Flank|BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000325147.9_5'Flank|RIC8A_ENST00000325207.5_Missense_Mutation_p.V70D|BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000332865.6_5'Flank|BET1L_ENST00000382762.3_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	70					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTGCAGAGTGTCCGAATCCTG	0.642																																					p.V70D		.											.	RIC8A-514	0			c.T209A						.						83	79	80					11																	209483		2203	4300	6503	SO:0001583	missense	60626	exon3			AGAGTGTCCGAAT	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.209T>A	11.37:g.209483T>A	ENSP00000432008:p.Val70Asp	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	107	23	NM_021932	0	0	50	54	4	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	37		.	.	.	.	.	.	.	.	.	.	T	31	5.086235	0.94100	.	.	ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000531209;ENST00000528357;ENST00000530889;ENST00000527696	T;T;T;T	0.53423	0.7;0.7;0.62;0.7	4.32	4.32	0.51571	Armadillo-type fold (1);	0.242015	0.40302	N	0.001130	T	0.54983	0.1892	L	0.39898	1.24	0.53688	D	0.999973	D;P;P	0.58620	0.983;0.904;0.951	P;P;P	0.59761	0.807;0.863;0.784	T	0.59621	-0.7420	10	0.87932	D	0	-12.0203	13.3635	0.60669	0.0:0.0:0.0:1.0	.	64;70;70	Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3	.;RIC8A_HUMAN;.	D	70;70;70;46;74;64	ENSP00000432008:V70D;ENSP00000325941:V70D;ENSP00000433968:V74D;ENSP00000434833:V64D	ENSP00000325941:V70D	V	+	2	0	RIC8A	199483	1.000000	0.71417	0.975000	0.42487	0.986000	0.74619	7.525000	0.81892	1.906000	0.55180	0.459000	0.35465	GTC	.		0.642	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		A	209483	T	A	209483	3	1	45	1	0	0	0	0	1	0	0	0	13387	1667	58	5	219	5	RIC8A	11	209483	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08		209483	134797033	65	4105											
OR4S2	219431	broad.mit.edu	37	chr11	55418712	55418712	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttggttgcactgagatcttCatccttactgtaatggccta	8	16	8	9	0	2	1	1	1	1	1	3	2	3	1	2	2	2	3	2	2	3	6			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:55418712C>T	ENST00000312422.2	+	1	333	c.333C>T	c.(331-333)ttC>ttT	p.F111F		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				CTGAGATCTTCATCCTTACTG	0.403																																					p.F111F													.	OR4S2-71	0			c.C333T						.						213	178	190					11																	55418712		2183	4039	6222	SO:0001819	synonymous_variant	219431	exon1			GATCTTCATCCTT	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"GPCR / Class A : Olfactory receptors"	15183	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily S, member 2 pseudogene"	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.333C>T	11.37:g.55418712C>T		Somatic	447	1		WXS	Illumina HiSeq	Phase_I	591	20	NM_001004059	0	0	0	0	0	Q6IF72	Silent	SNP	ENST00000312422.2	37	CCDS31505.1																																																																																			.		0.403	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		T	55418712	C	T	55418712	2	4	45	1	0	0	0	0	0	0	0	1	11109	825	29	2		2	OR4S2	11	55418712	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	55209229	55418712	79587804	66	4106											
APLNR	187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	57004337	57004337	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaacacggtccagagcaccaGaccgttgcccgtggtgccca	10	5	11	15	3	0	2	0	0	0	2	1	2	1	2	5	2	4	2	5	2	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:57004337G>C	ENST00000606794.1	-	1	338	c.142C>G	c.(142-144)Ctg>Gtg	p.L48V		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	48					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CAGAGCACCAGACCGTTGCCC	0.592																																					p.L48V		.											.	APLNR-573	0			c.C142G						.						75	72	73					11																	57004337		2201	4296	6497	SO:0001583	missense	187	exon1			GCACCAGACCGTT	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"APJ (apelin) receptor"	600052	"angiotensin II receptor-like 1"	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.142C>G	11.37:g.57004337G>C	ENSP00000475344:p.Leu48Val	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	149	70	NM_005161	0	0	2	2	0		Missense_Mutation	SNP	ENST00000606794.1	37	CCDS7950.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034103	0.35893	.	.	ENSG00000134817	ENST00000257254;ENST00000444275	T	0.77098	-1.07	5.25	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.088434	0.47455	D	0.000235	T	0.71417	0.3337	L	0.35593	1.075	0.37382	D	0.912064	P	0.43231	0.801	P	0.45610	0.487	T	0.74506	-0.3643	10	0.36615	T	0.2	-13.9545	12.6969	0.57010	0.0931:0.0:0.9069:0.0	.	48	P35414	APJ_HUMAN	V	48;13	ENSP00000257254:L48V	ENSP00000257254:L48V	L	-	1	2	APLNR	56760913	0.027000	0.19231	1.000000	0.80357	0.995000	0.86356	0.324000	0.19610	2.460000	0.83146	0.561000	0.74099	CTG	.		0.592	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161		C	57004337	G	C	57004337	3	2	45	1	0	0	0	0	1	0	0	0	777	933	33	4	1004	4	APLNR	11	57004337	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	1585625	57004337	78002179	67	4107											
MS4A15	219995	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	60540926	60540926	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcctttgctgggacagccaTtctgctcatggattttggtg	5	14	13	9	0	2	0	1	0	1	0	2	2	2	2	2	4	3	2	2	4	0	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:60540926T>A	ENST00000405633.3	+	5	546	c.467T>A	c.(466-468)aTt>aAt	p.I156N	MS4A15_ENST00000528170.1_Missense_Mutation_p.I115N|MS4A15_ENST00000337911.4_Missense_Mutation_p.I63N	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	156						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						GGGACAGCCATTCTGCTCATG	0.572																																					p.I156N		.											.	MS4A15-69	0			c.T467A						.						101	82	89					11																	60540926		2203	4300	6503	SO:0001583	missense	219995	exon5			CAGCCATTCTGCT	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.467T>A	11.37:g.60540926T>A	ENSP00000386022:p.Ile156Asn	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	70	39	NM_001098835	0	0	0	0	0	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	37	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159477	0.78226	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.02763	4.17;4.17;4.17	4.73	4.73	0.59995	.	0.564419	0.18877	N	0.128670	T	0.12433	0.0302	M	0.82132	2.575	0.32907	D	0.514004	D;D	0.61080	0.98;0.989	P;P	0.60345	0.873;0.837	T	0.06006	-1.0851	10	0.87932	D	0	-4.8067	10.6302	0.45532	0.0:0.0:0.0:1.0	.	115;156	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	N	115;63;156	ENSP00000434165:I115N;ENSP00000338692:I63N;ENSP00000386022:I156N	ENSP00000338692:I63N	I	+	2	0	MS4A15	60297502	0.968000	0.33430	0.979000	0.43373	0.987000	0.75469	2.143000	0.42187	1.772000	0.52199	0.454000	0.30748	ATT	.		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1			A	60540926	T	A	60540926	3	1	45	1	0	0	0	0	1	0	0	0	9884	1493	52	5	481	5	MS4A15	11	60540926	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	3536589	60540926	74465590	68	4108											
VWCE	220001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	61026184	61026184	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccccgagaagcccccactGggggctgctgggggccaggg	5	3	17	16	1	0	1	0	0	0	1	0	2	0	1	6	5	2	2	6	5	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:61026184G>A	ENST00000335613.5	-	20	3217	c.2831C>T	c.(2830-2832)cCa>cTa	p.P944L	VWCE_ENST00000535710.1_Missense_Mutation_p.P409L	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	944						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						AGCCCCCACTGGGGGCTGCTG	0.662																																					p.P944L		.											.	VWCE-91	0			c.C2831T						.						32	41	38					11																	61026184		2181	4260	6441	SO:0001583	missense	220001	exon20			CCCACTGGGGGCT	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.2831C>T	11.37:g.61026184G>A	ENSP00000334186:p.Pro944Leu	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	178	55	NM_152718	0	0	4	4	0	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	37	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	G	7.159	0.585335	0.13749	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	T;T	0.68025	-0.3;3.56	4.57	2.7	0.31948	.	1.078380	0.07367	N	0.885042	T	0.43545	0.1252	N	0.03115	-0.41	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33007	-0.9885	10	0.48119	T	0.1	.	7.595	0.28044	0.2008:0.0:0.7992:0.0	.	944	Q96DN2	VWCE_HUMAN	L	944;409	ENSP00000334186:P944L;ENSP00000442570:P409L	ENSP00000334186:P944L	P	-	2	0	VWCE	60782760	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.128000	0.31369	0.478000	0.27488	-0.254000	0.11334	CCA	.		0.662	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61026184	G	A	61026184	3	1	45	1	0	0	0	0	1	0	0	0	17278	1348	47	2	40	2	VWCE	11	61026184	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	485258	61026184	73980332	69	4109											
CORO1B	57175	hgsc.bcm.edu;broad.mit.edu	37	chr11	67207603	67207603	+	Frame_Shift_Del	DEL	C	C	-																															tcttaccgggcgatctcgcaCttgctgacctccaggccccg																										TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:67207603delC	ENST00000341356.5	-	8	1103	c.993delG	c.(991-993)aagfs	p.K331fs	CORO1B_ENST00000539724.1_Intron|PTPRCAP_ENST00000326294.3_5'Flank|CORO1B_ENST00000393893.1_Frame_Shift_Del_p.K331fs	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	331					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CGATCTCGCACTTGCTGACCT	0.622																																					p.K331fs		.											.	CORO1B-108	0			c.993delG						.						65	67	66					11																	67207603		2200	4295	6495	SO:0001589	frameshift_variant	57175	exon8			.	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"Coronins", "WD repeat domain containing"	2253	protein-coding gene	gene with protein product		609849	"coronin, actin-binding protein, 1B"			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.993delG	11.37:g.67207603delC	ENSP00000340211:p.Lys331fs	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	139	65	NM_020441	0	0	0	0	0	B2RD45	Frame_Shift_Del	DEL	ENST00000341356.5	37	CCDS8164.1																																																																																			.		0.622	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441		-	67207603	C	-	67207603	7	5	45	1	0	1	0	1	0	0	0	0	3760	564	20	0	492	0	CORO1B	11	67207603	Frame_Shift_Del	DEL	C	TCGA-B3-4104-01A-01D-1458-08	6181419	67207603	67798913	70	4110											
STARD10	10809	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	72470333	72470333	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcgggcgatgtcaaaagtctCaatgacgttgctgtcccatt	9	11	11	10	3	2	1	2	1	1	0	4	2	3	1	1	1	1	2	1	1	3	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:72470333C>G	ENST00000334805.6	-	3	1220	c.301G>C	c.(301-303)Gag>Cag	p.E101Q	STARD10_ENST00000538536.1_Missense_Mutation_p.E55Q|STARD10_ENST00000545082.1_Missense_Mutation_p.E72Q|ARAP1_ENST00000359373.5_Intron|STARD10_ENST00000538437.1_5'UTR|STARD10_ENST00000543304.1_Missense_Mutation_p.E101Q	NM_006645.2	NP_006636.2	Q9Y365	PCTL_HUMAN	StAR-related lipid transfer (START) domain containing 10	101	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				bile acid secretion (GO:0032782)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)	cytosol (GO:0005829)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|microvillus (GO:0005902)	lipid binding (GO:0008289)			endometrium(4)|large_intestine(1)|lung(2)|prostate(1)	8			BRCA - Breast invasive adenocarcinoma(5;7.08e-07)			TCAAAAGTCTCAATGACGTTG	0.562																																					p.E101Q		.											.	STARD10-90	0			c.G301C						.						138	143	141					11																	72470333		2184	4279	6463	SO:0001583	missense	10809	exon3			AAGTCTCAATGAC	AF039696	CCDS41688.1	11q13	2011-09-12	2007-08-16	2003-02-07		ENSG00000214530		"StAR-related lipid transfer (START) domain containing"	10666	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 28", "START domain containing 10"	SDCCAG28		9610721	Standard	NM_006645		Approved	NY-CO-28, CGI-52, PCTP2	uc001otb.3	Q9Y365		ENST00000334805.6:c.301G>C	11.37:g.72470333C>G	ENSP00000335247:p.Glu101Gln	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	127	64	NM_006645	0	0	38	68	30	O60532	Missense_Mutation	SNP	ENST00000334805.6	37	CCDS41688.1	.	.	.	.	.	.	.	.	.	.	C	36	5.751817	0.96890	.	.	ENSG00000214530	ENST00000537351;ENST00000543304;ENST00000334805;ENST00000538536;ENST00000545082;ENST00000544767;ENST00000537947;ENST00000536728;ENST00000542989;ENST00000546314;ENST00000539138;ENST00000535054	T;T;T;T;T;T;T;T;T;T;D;T	0.85088	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;-1.94;0.81	5.95	5.95	0.96441	Lipid-binding START (3);START-like domain (1);	0.062950	0.64402	U	0.000008	D	0.91126	0.7206	M	0.79805	2.47	0.58432	D	0.999995	P;P	0.52316	0.94;0.952	P;P	0.57720	0.591;0.826	D	0.88905	0.3355	10	0.28530	T	0.3	-28.7367	17.8792	0.88835	0.0:1.0:0.0:0.0	.	55;101	F5GY11;Q9Y365	.;PCTL_HUMAN	Q	8;101;101;55;72;32;101;32;101;101;72;55	ENSP00000445708:E8Q;ENSP00000438792:E101Q;ENSP00000335247:E101Q;ENSP00000440016:E55Q;ENSP00000443548:E72Q;ENSP00000438357:E32Q;ENSP00000445657:E101Q;ENSP00000442414:E32Q;ENSP00000443597:E101Q;ENSP00000445886:E101Q;ENSP00000441589:E72Q;ENSP00000440924:E55Q	ENSP00000335247:E101Q	E	-	1	0	STARD10	72147981	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.825000	0.97269	0.655000	0.94253	GAG	.		0.562	STARD10-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397254.1			G	72470333	C	G	72470333	3	3	45	1	0	0	0	0	1	0	0	0	15287	835	29	4	594	4	STARD10	11	72470333	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	5262730	72470333	62536183	71	4111											
ARRB1	408	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	74985127	74985127	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caggtcctcacagggtgctaGaggccaagttcgtgtcttcg	7	10	13	11	2	2	1	1	0	1	1	5	1	3	1	2	3	1	2	2	3	2	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:74985127G>C	ENST00000420843.2	-	11	1002	c.905C>G	c.(904-906)tCt>tGt	p.S302C	ARRB1_ENST00000393505.4_Missense_Mutation_p.S302C|ARRB1_ENST00000360025.3_Missense_Mutation_p.S302C	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	302					activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						CAGGGTGCTAGAGGCCAAGTT	0.602																																					p.S302C		.											.	ARRB1-567	0			c.C905G						.						263	213	230					11																	74985127		2200	4293	6493	SO:0001583	missense	408	exon11			GTGCTAGAGGCCA	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"arrestin 2"	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.905C>G	11.37:g.74985127G>C	ENSP00000409581:p.Ser302Cys	Somatic	382	0		WXS	Illumina HiSeq	Phase_I	366	162	NM_020251	0	0	0	0	0	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Missense_Mutation	SNP	ENST00000420843.2	37	CCDS44684.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125072	0.77436	.	.	ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025	T;T;T	0.19250	2.16;2.16;2.16	4.51	4.51	0.55191	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.50633	0.1627	M	0.87827	2.91	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.71870	0.933;0.975	T	0.60712	-0.7209	10	0.72032	D	0.01	-10.6596	14.7321	0.69388	0.0:0.0:1.0:0.0	.	302;302	P49407-2;P49407	.;ARRB1_HUMAN	C	302	ENSP00000409581:S302C;ENSP00000377141:S302C;ENSP00000353124:S302C	ENSP00000353124:S302C	S	-	2	0	ARRB1	74662775	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.770000	0.98971	2.058000	0.61347	0.462000	0.41574	TCT	.		0.602	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041		C	74985127	G	C	74985127	3	2	45	1	0	0	0	0	1	0	0	0	981	942	33	4	375	4	ARRB1	11	74985127	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	2514794	74985127	60021389	72	4112											
RAPGEF3	10411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	48142257	48142257	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgttgggtcatgagcactgGaatctggtcccatggcctcc	6	11	12	12	0	2	1	1	1	1	0	4	2	4	2	3	4	1	2	3	4	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:48142257G>A	ENST00000449771.2	-	12	1311	c.1223C>T	c.(1222-1224)tCc>tTc	p.S408F	RAPGEF3_ENST00000171000.4_Missense_Mutation_p.S366F|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.S366F|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.S408F|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.S408F|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.S366F|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.S366F			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	408	Interaction with PDE3B.|N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		ATGAGCACTGGAATCTGGTCC	0.547																																					p.S408F		.											.	RAPGEF3-660	0			c.C1223T						.						131	109	117					12																	48142257		2203	4300	6503	SO:0001583	missense	10411	exon12			GCACTGGAATCTG	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"exchange protein directly activated by cAMP 1"	606057	"RAP guanine-nucleotide-exchange factor (GEF) 3"			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1223C>T	12.37:g.48142257G>A	ENSP00000395708:p.Ser408Phe	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	82	30	NM_001098531	0	0	2	4	2	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512216	0.85389	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	T;T;T;T;T;T;T	0.71579	-0.39;-0.4;-0.39;-0.39;-0.4;-0.58;-0.49	5.16	5.16	0.70880	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.662303	0.13744	N	0.365734	T	0.80210	0.4581	L	0.44542	1.39	0.58432	D	0.999999	D;D	0.89917	0.992;1.0	D;D	0.77557	0.937;0.99	T	0.79320	-0.1852	10	0.59425	D	0.04	.	16.511	0.84284	0.0:0.0:1.0:0.0	.	420;408	B7Z5J6;O95398	.;RPGF3_HUMAN	F	366;408;55;366;366;366;408;420;366;408	ENSP00000384521:S366F;ENSP00000395708:S408F;ENSP00000448619:S366F;ENSP00000171000:S366F;ENSP00000373864:S408F;ENSP00000448480:S366F;ENSP00000378764:S408F	ENSP00000171000:S366F	S	-	2	0	RAPGEF3	46428524	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.309000	0.78937	2.588000	0.87417	0.650000	0.86243	TCC	.		0.547	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		A	48142257	G	A	48142257	3	1	45	1	0	0	0	0	1	0	0	0	13077	1174	41	2	1616	2	RAPGEF3	12	48142257	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		48142257	85709638	73	4113											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	49425839	49425839	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtagctgctgctgctgctGaggacttaagtgccgcagct	6	11	13	11	1	0	1	0	1	0	0	0	2	0	2	1	1	7	8	1	1	2	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:49425839G>A	ENST00000301067.7	-	39	12648	c.12649C>T	c.(12649-12651)Cag>Tag	p.Q4217*		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4217	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TGCTGCTGCTGAGGACTTAAG	0.622																																					p.Q4217X		.											.	MLL2-612	0			c.C12649T						.						29	33	32					12																	49425839		2083	4219	6302	SO:0001587	stop_gained	8085	exon39			GCTGCTGAGGACT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.12649C>T	12.37:g.49425839G>A	ENSP00000301067:p.Gln4217*	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	81	36	NM_003482	0	0	12	18	6	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	53	20.787619	0.99934	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.89	4.89	0.63831	.	0.000000	0.34531	N	0.003897	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.7009	0.88294	0.0:0.0:1.0:0.0	.	.	.	.	X	4217	.	ENSP00000301067:Q4217X	Q	-	1	0	MLL2	47712106	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	6.491000	0.73649	2.662000	0.90505	0.655000	0.94253	CAG	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49425839	G	A	49425839	4	1	45	1	0	0	0	0	0	1	0	0	9646	1299	45	2	4028	2	MLL2	12	49425839	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	1283582	49425839	84426056	74	4114											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu	37	chr12	49426526	49426526	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgctgctgctgttgttgctGaggagacagtaaagttcgac	8	13	13	7	1	0	2	0	1	0	1	1	4	0	2	0	1	4	8	0	1	2	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:49426526G>A	ENST00000301067.7	-	39	11961	c.11962C>T	c.(11962-11964)Cag>Tag	p.Q3988*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3988	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3718*(1)									TGTTGTTGCTGAGGAGACAGT	0.532																																					p.Q3988X		.											.	MLL2-612	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C11962T						.						64	70	68					12																	49426526		2196	4296	6492	SO:0001587	stop_gained	8085	exon39			GTTGCTGAGGAGA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11962C>T	12.37:g.49426526G>A	ENSP00000301067:p.Gln3988*	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	31	13	NM_003482	0	0	2	7	5	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	50	17.079656	0.99878	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.88	4.88	0.63580	.	0.000000	0.34652	N	0.003786	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.6695	0.88212	0.0:0.0:1.0:0.0	.	.	.	.	X	3988	.	ENSP00000301067:Q3988X	Q	-	1	0	MLL2	47712793	0.997000	0.39634	1.000000	0.80357	0.099000	0.18886	3.213000	0.51153	2.643000	0.89663	0.655000	0.94253	CAG	.		0.532	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49426526	G	A	49426526	4	1	45	1	0	0	0	0	0	1	0	0	9646	1299	45	2	4715	2	MLL2	12	49426526	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	687	49426526	84425369	75	4115											
HSP90B1	7184	broad.mit.edu	37	chr12	104327895	104327895	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggccagtcaacttctgaattGattggccagtttggtgtcgg	7	13	13	8	1	2	2	1	2	1	0	3	2	2	2	2	4	1	1	2	4	2	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:104327895G>C	ENST00000299767.5	+	5	755	c.573G>C	c.(571-573)ttG>ttC	p.L191F		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	191					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CTTCTGAATTGATTGGCCAGT	0.428																																					p.L191F													.	HSP90B1-93	0			c.G573C						.						117	113	115					12																	104327895		2203	4300	6503	SO:0001583	missense	7184	exon5			TGAATTGATTGGC	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.573G>C	12.37:g.104327895G>C	ENSP00000299767:p.Leu191Phe	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	261	6	NM_003299	0	0	284	290	6	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.631800	0.67015	.	.	ENSG00000166598	ENST00000299767;ENST00000537375	T	0.23147	1.92	5.92	5.01	0.66863	ATPase-like, ATP-binding domain (4);	0.000000	0.64402	D	0.000001	T	0.57021	0.2025	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.983	T	0.63998	-0.6510	10	0.87932	D	0	.	7.1278	0.25482	0.1456:0.1887:0.6657:0.0	.	217;191	Q59FC6;P14625	.;ENPL_HUMAN	F	191	ENSP00000299767:L191F	ENSP00000299767:L191F	L	+	3	2	HSP90B1	102852025	1.000000	0.71417	0.990000	0.47175	0.996000	0.88848	2.147000	0.42226	1.416000	0.47057	0.650000	0.86243	TTG	.		0.428	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		C	104327895	G	C	104327895	3	2	45	1	0	0	0	0	1	0	0	0	7424	1281	45	4	591	4	HSP90B1	12	104327895	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	54901369	104327895	29524000	76	4116											
INSM2	84684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	36005048	36005048	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	attttctcgtgcaagcactgCccgtccactttttttagctc	6	16	6	13	2	1	0	0	0	1	0	4	0	2	0	2	0	4	3	2	0	2	6			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:36005048C>T	ENST00000307169.3	+	1	1801	c.1590C>T	c.(1588-1590)tgC>tgT	p.C530C		NM_032594.3	NP_115983.3	Q96T92	INSM2_HUMAN	insulinoma-associated 2	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	10	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)		GCAAGCACTGCCCGTCCACTT	0.627																																					p.C530C		.											.	INSM2-226	0			c.C1590T						.						31	34	33					14																	36005048		2200	4297	6497	SO:0001819	synonymous_variant	84684	exon1			GCACTGCCCGTCC	AF260323	CCDS9657.1	14q13.1	2013-01-08			ENSG00000168348	ENSG00000168348		"Zinc fingers, C2H2-type"	17539	protein-coding gene	gene with protein product	"mlt 1"	614027					Standard	NM_032594		Approved	IA-6	uc001wth.1	Q96T92	OTTHUMG00000140223	ENST00000307169.3:c.1590C>T	14.37:g.36005048C>T		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	116	23	NM_032594	0	0	0	0	0	A1L432|J9Y024|Q8N8K7|Q96Q84	Silent	SNP	ENST00000307169.3	37	CCDS9657.1																																																																																			.		0.627	INSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276686.1			T	36005048	C	T	36005048	2	4	45	1	0	0	0	0	0	0	0	1	7793	747	26	2		2	INSM2	14	36005048	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08		36005048	71344492	77	4117											
MIA2	117153	hgsc.bcm.edu	37	chr14	39717145	39717145	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaatctgatactataccatAtttgaaaaagttcttgtata	15	15	5	6	1	2	2	0	2	2	0	2	3	2	2	1	0	2	2	1	0	9	9			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:39717145A>G	ENST00000280082.3	+	4	1566	c.1367A>G	c.(1366-1368)tAt>tGt	p.Y456C	MIA2_ENST00000556784.1_Missense_Mutation_p.Y455C|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.Y456C	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	456					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		ACTATACCATATTTGAAAAAG	0.313																																					p.Y456C		.											.	MIA2-154	0			c.A1367G						.						54	60	58					14																	39717145		2202	4298	6500	SO:0001583	missense	117153	exon4			TACCATATTTGAA	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.1367A>G	14.37:g.39717145A>G	ENSP00000280082:p.Tyr456Cys	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	102	6	NM_054024	0	0	0	0	0	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.185016	0.38609	.	.	ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000556784;ENST00000553728	T;T;T	0.51325	0.71;0.73;3.13	5.49	5.49	0.81192	.	0.192329	0.25878	N	0.027707	T	0.63022	0.2476	M	0.71581	2.175	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.986;0.994	T	0.59343	-0.7472	9	.	.	.	-8.4686	6.8201	0.23852	0.7925:0.0:0.0729:0.1346	.	456;456	Q96PC5;Q96PC5-2	MIA2_HUMAN;.	C	456;455;456	ENSP00000280082:Y456C;ENSP00000451934:Y455C;ENSP00000452252:Y456C	.	Y	+	2	0	MIA2;RP11-407N17.3	38786896	0.979000	0.34478	0.736000	0.30914	0.664000	0.39144	1.014000	0.29950	2.103000	0.63969	0.529000	0.55759	TAT	.		0.313	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		G	39717145	A	G	39717145	3	3	45	1	0	0	0	0	1	0	0	0	9589	449	16	3	1381	3	MIA2	14	39717145	Missense_Mutation	SNP	A	TCGA-B3-4104-01A-01D-1458-08	3712097	39717145	67632395	78	4118											
FKBP3	2287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	45603575	45603575	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atctgaaccgtgttcctgcaGaaacttgataatgtccttct	10	14	7	10	1	2	3	0	2	2	1	4	3	4	3	3	0	3	2	3	0	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:45603575G>A	ENST00000216330.3	-	2	495	c.85C>T	c.(85-87)Ctg>Ttg	p.L29L	FKBP3_ENST00000396062.3_Silent_p.L29L|FANCM_ENST00000542564.2_5'Flank|FANCM_ENST00000556036.1_5'Flank|FANCM_ENST00000267430.5_5'Flank			Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	29					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			NS(1)|biliary_tract(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	12						TGTTCCTGCAGAAACTTGATA	0.652																																					p.L29L		.											.	FKBP3-226	0			c.C85T						.						85	76	79					14																	45603575		2203	4300	6503	SO:0001819	synonymous_variant	2287	exon1			CCTGCAGAAACTT	M96256	CCDS9683.1	14q21.2	2008-08-11	2002-08-29		ENSG00000100442	ENSG00000100442			3719	protein-coding gene	gene with protein product		186947	"FK506-binding protein 3 (25kD)"			1374240, 1532945	Standard	NM_002013		Approved	FKBP-25, PPIase	uc010tqf.2	Q00688	OTTHUMG00000140267	ENST00000216330.3:c.85C>T	14.37:g.45603575G>A		Somatic	215	0		WXS	Illumina HiSeq	Phase_I	161	59	NM_002013	0	0	13	20	7	B2R4Q9|Q14317	Silent	SNP	ENST00000216330.3	37	CCDS9683.1																																																																																			.		0.652	FKBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276796.1	NM_002013		A	45603575	G	A	45603575	2	1	45	1	0	0	0	0	0	0	0	1	5928	933	33	2		2	FKBP3	14	45603575	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	5886430	45603575	61745965	79	4119											
ZFP36L1	677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	69256349	69256349	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tggctgctgctggagctgctCaggtagccctcctggtccga	4	10	14	13	1	1	0	1	0	0	0	3	2	3	1	3	4	5	6	3	4	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:69256349C>G	ENST00000439696.2	-	2	1219	c.918G>C	c.(916-918)ctG>ctC	p.L306L	ZFP36L1_ENST00000336440.3_Silent_p.L306L|ZFP36L1_ENST00000555997.1_3'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	306					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TGGAGCTGCTCAGGTAGCCCT	0.597											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L375L		.											.	ZFP36L1-91	0			c.G1125C						.						71	79	76					14																	69256349		2203	4300	6503	SO:0001819	synonymous_variant	677	exon3			GCTGCTCAGGTAG	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"RING-type (C3HC4) zinc fingers"	1107	protein-coding gene	gene with protein product		601064	"zinc finger protein, C3H type, 36-like 1", "zinc finger protein 36, C3H type-like 1"	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.918G>C	14.37:g.69256349C>G		Somatic	229	0	1113	WXS	Illumina HiSeq	Phase_I	196	81	NM_001244701	1	0	90	169	78	Q13851	Silent	SNP	ENST00000439696.2	37	CCDS9791.1																																																																																			.		0.597	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			G	69256349	C	G	69256349	2	3	45	1	0	0	0	0	0	0	0	1	17678	813	29	4		4	ZFP36L1	14	69256349	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	23652774	69256349	38093191	80	4120											
MLH3	27030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	75514890	75514890	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagagctatgttccaggaaaGattttttatgtttctcattt	11	18	7	5	0	1	2	1	0	1	2	3	3	2	3	1	1	1	3	1	1	4	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:75514890G>C	ENST00000556740.1	-	1	1504	c.1469C>G	c.(1468-1470)tCt>tGt	p.S490C	MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000355774.2_Missense_Mutation_p.S490C|MLH3_ENST00000238662.7_Missense_Mutation_p.S490C|MLH3_ENST00000380968.2_De_novo_Start_OutOfFrame|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Missense_Mutation_p.S490C			Q9UHC1	MLH3_HUMAN	mutL homolog 3	490					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.S490Y(2)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TTCCAGGAAAGATTTTTTATG	0.378								Mismatch excision repair (MMR)																													p.S490C		.											.	MLH3-228	2	Substitution - Missense(2)	lung(2)	c.C1469G						.						90	97	95					14																	75514890		2203	4299	6502	SO:0001583	missense	27030	exon2			AGGAAAGATTTTT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1469C>G	14.37:g.75514890G>C	ENSP00000452316:p.Ser490Cys	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	358	134	NM_014381	0	0	1	4	3	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	6.646	0.487760	0.12641	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	D;D;D;D	0.83506	-1.63;-1.67;-1.73;-1.63	5.34	-0.28	0.12886	.	1.749140	0.02828	N	0.126415	T	0.81786	0.4896	L	0.56769	1.78	0.09310	N	0.999996	P;P	0.48503	0.911;0.761	P;B	0.47162	0.54;0.24	T	0.65705	-0.6103	10	0.54805	T	0.06	0.3633	2.4863	0.04600	0.2139:0.342:0.3276:0.1165	.	490;490	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	C	490	ENSP00000348020:S490C;ENSP00000238662:S490C;ENSP00000451540:S490C;ENSP00000452316:S490C	ENSP00000238662:S490C	S	-	2	0	MLH3	74584643	0.000000	0.05858	0.121000	0.21740	0.448000	0.32197	0.167000	0.16602	-0.075000	0.12798	-0.291000	0.09656	TCT	.		0.378	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		C	75514890	G	C	75514890	3	2	45	1	0	0	0	0	1	0	0	0	9643	942	33	4	2940	4	MLH3	14	75514890	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	6258541	75514890	31834650	81	4121											
PPP2R5C	5527	broad.mit.edu	37	chr14	102391505	102391505	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aagatccgaagaaggaccgtCctcttgcacgccgcaagtcc	11	6	10	14	4	1	2	0	0	1	2	4	4	4	3	5	1	1	2	5	1	4	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:102391505C>G	ENST00000334743.5	+	14	1519	c.1471C>G	c.(1471-1473)Cct>Gct	p.P491A	PPP2R5C_ENST00000350249.3_Missense_Mutation_p.P452A|PPP2R5C_ENST00000328724.5_Missense_Mutation_p.P507A|PPP2R5C_ENST00000422945.2_Missense_Mutation_p.P522A	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	491					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GAAGGACCGTCCTCTTGCACG	0.552																																					p.P522A													.	PPP2R5C-659	0			c.C1564G						.						147	159	155					14																	102391505		2203	4300	6503	SO:0001583	missense	5527	exon16			GACCGTCCTCTTG	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.1471C>G	14.37:g.102391505C>G	ENSP00000333905:p.Pro491Ala	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	427	7	NM_001161725	0	0	19	20	1	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000334743.5	37	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.028934	0.35797	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334743	T;T;T;T;T	0.48522	0.96;0.82;0.96;0.81;0.96	6.17	2.25	0.28309	.	0.200176	0.53938	N	0.000050	T	0.50633	0.1627	M	0.74881	2.28	0.47441	D	0.999424	B;B;B;B	0.16396	0.002;0.0;0.0;0.017	B;B;B;B	0.12837	0.008;0.003;0.001;0.006	T	0.51411	-0.8709	10	0.36615	T	0.2	-2.3351	18.9747	0.92731	0.0:0.5569:0.4431:0.0	.	522;452;491;507	F5GWP3;Q13362-3;Q13362;Q6ZN33	.;.;2A5G_HUMAN;.	A	522;507;520;452;491	ENSP00000412324:P522A;ENSP00000329009:P507A;ENSP00000450931:P520A;ENSP00000262239:P452A;ENSP00000333905:P491A	ENSP00000329009:P507A	P	+	1	0	PPP2R5C	101461258	1.000000	0.71417	0.294000	0.24946	0.986000	0.74619	2.801000	0.47908	0.146000	0.19002	0.655000	0.94253	CCT	.		0.552	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		G	102391505	C	G	102391505	3	3	45	1	0	0	0	0	1	0	0	0	12423	855	30	4	1918	4	PPP2R5C	14	102391505	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	26876615	102391505	4958035	82	4122											
GABRB3	2562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	26793190	26793190	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agttgtcaaaggatattgctGaattcctggtatcgccaatg	11	13	10	7	1	1	1	1	1	0	0	3	2	2	2	2	2	1	3	2	2	5	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr15:26793190G>C	ENST00000311550.5	-	9	1283	c.1172C>G	c.(1171-1173)tCa>tGa	p.S391*	GABRB3_ENST00000400188.3_Nonsense_Mutation_p.S320*|GABRB3_ENST00000541819.2_Nonsense_Mutation_p.S447*|GABRB3_ENST00000299267.4_Nonsense_Mutation_p.S391*|GABRB3_ENST00000545868.1_Nonsense_Mutation_p.S306*	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	391					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|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)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	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)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGATATTGCTGAATTCCTGGT	0.493																																					p.S391X		.											.	GABRB3-518	0			c.C1172G						.						123	114	117					15																	26793190		2203	4300	6503	SO:0001587	stop_gained	2562	exon9			ATTGCTGAATTCC		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4083	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 3"	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1172C>G	15.37:g.26793190G>C	ENSP00000308725:p.Ser391*	Somatic	245	0		WXS	Illumina HiSeq	Phase_I	273	125	NM_021912	0	0	8	8	0	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Nonsense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	G	32	5.176507	0.94846	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	.	.	.	5.82	4.9	0.64082	.	0.597023	0.16989	N	0.191371	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	13.4207	0.60996	0.0746:0.0:0.9254:0.0	.	.	.	.	X	391;447;391;320;306	.	ENSP00000299267:S391X	S	-	2	0	GABRB3	24344283	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.681000	0.61663	2.752000	0.94435	0.655000	0.94253	TCA	.		0.493	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			C	26793190	G	C	26793190	4	2	45	1	0	0	0	0	0	1	0	0	6187	1294	45	4	253	4	GABRB3	15	26793190	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		26793190	75738202	83	4123											
APBA2	321	broad.mit.edu	37	chr15	29368274	29368274	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagacaaagaaggtggcatCatttccaagttttgtggctg	12	11	11	7	0	1	2	1	0	0	2	2	2	2	2	1	3	0	3	1	3	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr15:29368274C>A	ENST00000558402.1	+	7	1648	c.1049C>A	c.(1048-1050)tCa>tAa	p.S350*	APBA2_ENST00000411764.1_Nonsense_Mutation_p.S350*|APBA2_ENST00000561069.1_Nonsense_Mutation_p.S350*|APBA2_ENST00000558259.1_Nonsense_Mutation_p.S350*|APBA2_ENST00000558330.1_Nonsense_Mutation_p.S350*			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	350					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		AAGGTGGCATCATTTCCAAGT	0.373																																					p.S350X													.	APBA2-90	0			c.C1049A						.						181	182	181					15																	29368274		2203	4300	6503	SO:0001587	stop_gained	321	exon5			TGGCATCATTTCC	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1049C>A	15.37:g.29368274C>A	ENSP00000453293:p.Ser350*	Somatic	311	0		WXS	Illumina HiSeq	Phase_I	423	8	NM_005503	0	0	0	0	0	E9PGI4|O60571|Q5XKC0	Nonsense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	40	8.254019	0.98727	.	.	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	.	.	.	4.85	4.85	0.62838	.	0.168736	0.39407	N	0.001363	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4725	0.75449	0.0:1.0:0.0:0.0	.	.	.	.	X	350;350;54	.	ENSP00000219865:S350X	S	+	2	0	APBA2	27155566	0.995000	0.38212	0.736000	0.30914	0.984000	0.73092	5.880000	0.69698	2.243000	0.73865	0.655000	0.94253	TCA	.		0.373	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		A	29368274	C	A	29368274	4	1	45	1	0	0	0	0	0	1	0	0	757	838	29	4	1059	4	APBA2	15	29368274	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	2575084	29368274	73163118	84	4124											
DMXL2	23312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	51857284	51857284	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttaaatacaattgctaaataCcttgaggatcccatgctaag	15	12	6	8	0	0	1	0	1	0	0	1	2	1	2	2	1	4	2	2	1	8	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr15:51857284C>A	ENST00000251076.5	-	4	652		c.e4+1		DMXL2_ENST00000449909.3_Splice_Site|DMXL2_ENST00000543779.2_Splice_Site|DMXL2_ENST00000560421.1_Splice_Site	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2							cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTGCTAAATACCTTGAGGATC	0.294																																					.		.											.	DMXL2-99	0			c.364+1G>T						.						26	26	26					15																	51857284		2194	4290	6484	SO:0001630	splice_region_variant	23312	exon5			TAAATACCTTGAG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.364+1G>T	15.37:g.51857284C>A		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	55	24	NM_015263	0	0	0	0	0	B2RTR3|B7ZMH3|F5GWF1|O94938	Splice_Site	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052647	0.75960	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4422	0.90670	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DMXL2	49644576	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	6.430000	0.73391	2.419000	0.82065	0.655000	0.94253	.	.		0.294	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	Intron	A	51857284	C	A	51857284	5	1	45	1	0	0	0	0	0	0	1	0	4606	521	18	4	8908	4	DMXL2	15	51857284	Splice_Site	SNP	C	TCGA-B3-4104-01A-01D-1458-08	22489010	51857284	50674108	85	4125											
NTN3	4917	broad.mit.edu	37	chr16	2522390	2522390	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgctcacaaggcctagcacgGcaggtgaccccagggacatg	10	5	13	13	1	1	1	1	1	0	0	1	2	1	2	3	4	2	3	3	4	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:2522390G>C	ENST00000293973.1	+	1	891	c.688G>C	c.(688-690)Gca>Cca	p.A230P	TBC1D24_ENST00000293970.5_5'Flank|TBC1D24_ENST00000567020.1_5'Flank	NM_006181.2	NP_006172.1	O00634	NET3_HUMAN	netrin 3	230	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(2)|lung(3)|prostate(1)	7						GCCTAGCACGGCAGGTGACCC	0.667																																					p.A230P													.	NTN3-90	0			c.G688C						.						45	42	43					16																	2522390		2197	4295	6492	SO:0001583	missense	4917	exon1			AGCACGGCAGGTG	U86759	CCDS10469.1	16p13.3	2013-03-01	2008-10-29	2008-10-29	ENSG00000162068	ENSG00000162068		"Netrins"	8030	protein-coding gene	gene with protein product	"Netrin-3"	602349	"netrin 2 (chicken)-like", "netrin 2-like (chicken)"	NTN2L		9143507, 10366627	Standard	NM_006181		Approved		uc002cqj.3	O00634	OTTHUMG00000128867	ENST00000293973.1:c.688G>C	16.37:g.2522390G>C	ENSP00000293973:p.Ala230Pro	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	91	3	NM_006181	0	0	0	0	0		Missense_Mutation	SNP	ENST00000293973.1	37	CCDS10469.1	.	.	.	.	.	.	.	.	.	.	G	5.453	0.268715	0.10349	.	.	ENSG00000162068	ENST00000293973	T	0.75367	-0.93	3.94	2.98	0.34508	Laminin, N-terminal (3);	0.832194	0.10240	N	0.698483	T	0.55737	0.1939	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43032	-0.9416	10	0.33141	T	0.24	.	12.0483	0.53493	0.0:0.8149:0.1851:0.0	.	230	O00634	NET3_HUMAN	P	230	ENSP00000293973:A230P	ENSP00000293973:A230P	A	+	1	0	NTN3	2462391	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	0.200000	0.17257	0.876000	0.35872	0.305000	0.20034	GCA	.		0.667	NTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250812.1	NM_006181		C	2522390	G	C	2522390	3	2	45	1	0	0	0	0	1	0	0	0	10727	1203	42	4	690	4	NTN3	16	2522390	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		2522390	87832363	86	4126											
GGA2	23062	broad.mit.edu	37	chr16	23503028	23503028	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cagcatctgataagcgtctcGaatcttgatgtcttccggaa	10	12	9	10	3	4	2	0	2	4	0	6	4	5	3	1	1	2	1	1	1	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:23503028G>C	ENST00000309859.4	-	5	527	c.445C>G	c.(445-447)Cga>Gga	p.R149G	GGA2_ENST00000567468.1_Missense_Mutation_p.R149G	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	149	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)	p.R149*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		TAAGCGTCTCGAATCTTGATG	0.443																																					p.R149G													.	GGA2-91	1	Substitution - Nonsense(1)	large_intestine(1)	c.C445G						.						182	160	167					16																	23503028		2197	4300	6497	SO:0001583	missense	23062	exon5			CGTCTCGAATCTT	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.445C>G	16.37:g.23503028G>C	ENSP00000311962:p.Arg149Gly	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	407	9	NM_015044	0	0	46	47	1	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.214586	0.39102	.	.	ENSG00000103365	ENST00000309859	T	0.22945	1.93	5.48	4.49	0.54785	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.141960	0.49305	D	0.000151	T	0.42630	0.1211	L	0.59436	1.845	0.37997	D	0.934095	D	0.71674	0.998	D	0.68039	0.955	T	0.34775	-0.9815	10	0.42905	T	0.14	-12.57	11.491	0.50381	0.0:0.0:0.689:0.311	.	149	Q9UJY4	GGA2_HUMAN	G	149	ENSP00000311962:R149G	ENSP00000311962:R149G	R	-	1	2	GGA2	23410529	0.999000	0.42202	1.000000	0.80357	0.802000	0.45316	1.149000	0.31626	2.568000	0.86640	0.643000	0.83706	CGA	.		0.443	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			C	23503028	G	C	23503028	3	2	45	1	0	0	0	0	1	0	0	0	6373	1066	37	4	1448	4	GGA2	16	23503028	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	20980638	23503028	66851725	87	4127											
SEZ6L2	26470	broad.mit.edu	37	chr16	29884594	29884594	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctggctggtccactgggAggggtggccgggcacacagg	5	5	21	10	1	0	0	0	0	0	0	1	1	1	1	2	9	0	3	2	9	0	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:29884594A>G	ENST00000308713.5	-	14	2982	c.2455T>C	c.(2455-2457)Tcc>Ccc	p.S819P	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.S775P|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.S705P|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.S749P	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	819	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTCCACTGGGAGGGGTGGCCG	0.642																																					p.S819P													.	SEZ6L2-92	0			c.T2455C						.						45	48	47					16																	29884594		2197	4300	6497	SO:0001583	missense	26470	exon14			ACTGGGAGGGGTG	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.2455T>C	16.37:g.29884594A>G	ENSP00000312550:p.Ser819Pro	Somatic	88	7		WXS	Illumina HiSeq	Phase_I	82	13	NM_001243332	0	0	4	4	0	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.229317	0.79688	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	4.39	4.39	0.52855	Complement control module (2);Sushi/SCR/CCP (3);	0.220176	0.26244	N	0.025488	T	0.77356	0.4118	M	0.62088	1.915	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.986;0.971;0.983;0.986;0.983	D;P;P;P;P;P	0.75484	0.986;0.825;0.773;0.731;0.825;0.731	T	0.76170	-0.3057	10	0.35671	T	0.21	.	12.7207	0.57140	1.0:0.0:0.0:0.0	.	775;819;705;749;819;749	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	P	749;819;705;775	ENSP00000310206:S749P;ENSP00000312550:S819P;ENSP00000319215:S705P;ENSP00000439412:S775P	ENSP00000312550:S819P	S	-	1	0	SEZ6L2	29792095	1.000000	0.71417	0.989000	0.46669	0.984000	0.73092	6.921000	0.75805	1.831000	0.53308	0.533000	0.62120	TCC	.		0.642	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		G	29884594	A	G	29884594	3	3	45	1	0	0	0	0	1	0	0	0	14176	304	11	3	336	3	SEZ6L2	16	29884594	Missense_Mutation	SNP	A	TCGA-B3-4104-01A-01D-1458-08	6381566	29884594	60470159	88	4128											
CX3CL1	6376	hgsc.bcm.edu;broad.mit.edu	37	chr16	57413597	57413597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacgtgcagcaagatgacatCaaagatacctgtagctttgc	13	9	9	10	1	1	3	1	1	0	2	1	3	1	3	1	0	5	4	1	0	4	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:57413597C>T	ENST00000006053.6	+	2	233	c.122C>T	c.(121-123)tCa>tTa	p.S41L	CX3CL1_ENST00000564948.1_Intron|CX3CL1_ENST00000563383.1_Missense_Mutation_p.S47L|CX3CL1_ENST00000565912.1_Missense_Mutation_p.S3L	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	41	Chemokine.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AAGATGACATCAAAGATACCT	0.517																																					p.S41L		.											.	CX3CL1-226	0			c.C122T						.						180	130	147					16																	57413597		2198	4300	6498	SO:0001583	missense	6376	exon2			TGACATCAAAGAT	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"Endogenous ligands"	10647	protein-coding gene	gene with protein product		601880	"small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.122C>T	16.37:g.57413597C>T	ENSP00000006053:p.Ser41Leu	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	109	6	NM_002996	0	0	9	9	0	O00672	Missense_Mutation	SNP	ENST00000006053.6	37	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	C	10.24	1.296655	0.23650	.	.	ENSG00000006210	ENST00000006053	T	0.05199	3.48	3.0	0.929	0.19449	Chemokine interleukin-8-like domain (3);	2.900500	0.01491	N	0.017077	T	0.10551	0.0258	L	0.55103	1.725	0.09310	N	1	B	0.29862	0.259	B	0.35114	0.196	T	0.36744	-0.9735	10	0.87932	D	0	-27.7552	5.6639	0.17684	0.2253:0.5558:0.2189:0.0	.	41	P78423	X3CL1_HUMAN	L	41	ENSP00000006053:S41L	ENSP00000006053:S41L	S	+	2	0	CX3CL1	55971098	0.000000	0.05858	0.004000	0.12327	0.044000	0.14063	-1.476000	0.02333	0.302000	0.22762	0.460000	0.39030	TCA	.		0.517	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		T	57413597	C	T	57413597	3	4	45	1	0	0	0	0	1	0	0	0	4080	838	29	2	128	2	CX3CL1	16	57413597	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	27529003	57413597	32941156	89	4129											
WDR59	79726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	74990405	74990405	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atagtgtgcaaagctgtcatGaggattccactgcacagctc	11	10	10	10	0	1	1	1	1	0	0	3	2	2	2	1	1	4	4	1	1	2	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:74990405G>A	ENST00000262144.6	-	3	338	c.208C>T	c.(208-210)Cat>Tat	p.H70Y	WDR59_ENST00000562331.1_5'UTR	NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	70										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						AAGCTGTCATGAGGATTCCAC	0.468																																					p.H70Y		.											.	WDR59-92	0			c.C208T						.						106	94	98					16																	74990405		2198	4300	6498	SO:0001583	missense	79726	exon3			TGTCATGAGGATT	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"WD repeat domain containing"	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.208C>T	16.37:g.74990405G>A	ENSP00000262144:p.His70Tyr	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	123	42	NM_030581	0	0	3	10	7	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	CCDS32488.1	.	.	.	.	.	.	.	.	.	.	G	35	5.427353	0.96131	.	.	ENSG00000103091	ENST00000262144;ENST00000536050	T	0.70282	-0.47	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83119	0.5185	M	0.78049	2.395	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.968	T	0.76072	-0.3093	10	0.06236	T	0.91	-22.0166	20.8794	0.99867	0.0:0.0:1.0:0.0	.	70;70	Q6PJI9-2;Q6PJI9	.;WDR59_HUMAN	Y	70;49	ENSP00000262144:H70Y	ENSP00000262144:H70Y	H	-	1	0	WDR59	73547906	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.410000	0.97335	2.941000	0.99782	0.655000	0.94253	CAT	.		0.468	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		A	74990405	G	A	74990405	3	1	45	1	0	0	0	0	1	0	0	0	17341	1290	45	2	2812	2	WDR59	16	74990405	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	17576808	74990405	15364348	90	4130											
ZDHHC7	55625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	85010706	85010706	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagaacaaagcttaccgtctCgtcgttgcatatggagtgga	11	10	12	8	3	1	1	0	0	1	1	3	4	1	3	1	2	4	3	1	2	4	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:85010706C>T	ENST00000313732.4	-	7	1097	c.745G>A	c.(745-747)Gag>Aag	p.E249K	ZDHHC7_ENST00000564466.1_Missense_Mutation_p.E286K|ZDHHC7_ENST00000569488.1_5'Flank	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	249					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						CTTACCGTCTCGTCGTTGCAT	0.448																																					p.E286K		.											.	ZDHHC7-289	0			c.G856A						.						162	149	153					16																	85010706		2199	4300	6499	SO:0001583	missense	55625	exon8			CCGTCTCGTCGTT	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"Zinc fingers, DHHC-type"	18459	protein-coding gene	gene with protein product	"Sertoli cell gene with zinc finger domain-&#946;"	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.745G>A	16.37:g.85010706C>T	ENSP00000315604:p.Glu249Lys	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	285	130	NM_001145548	0	0	0	1	1	D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	37	CCDS10950.1	.	.	.	.	.	.	.	.	.	.	C	36	5.726803	0.96847	.	.	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.23552	1.9;1.9	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.47395	0.1443	L	0.57130	1.785	0.80722	D	1	P;D	0.71674	0.943;0.998	P;P	0.62184	0.674;0.899	T	0.26677	-1.0096	10	0.54805	T	0.06	-14.3722	19.2167	0.93781	0.0:1.0:0.0:0.0	.	286;249	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	K	249;286	ENSP00000315604:E249K;ENSP00000341681:E286K	ENSP00000315604:E249K	E	-	1	0	ZDHHC7	83568207	1.000000	0.71417	0.981000	0.43875	0.844000	0.47949	7.666000	0.83877	2.784000	0.95788	0.655000	0.94253	GAG	.		0.448	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		T	85010706	C	T	85010706	3	4	45	1	0	0	0	0	1	0	0	0	17652	893	31	1	189	1	ZDHHC7	16	85010706	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	10020301	85010706	5344047	91	4131											
ITGAE	3682	hgsc.bcm.edu;broad.mit.edu	37	chr17	3659152	3659152	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatctgagcactgaagccaAtctgtgccagctggtagtga	10	9	13	9	0	2	3	0	3	2	0	2	4	2	4	2	2	4	3	2	2	3	1	rs376670383		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:3659152A>T	ENST00000263087.4	-	11	1309	c.1211T>A	c.(1210-1212)aTt>aAt	p.I404N		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	404					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		ACTGAAGCCAATCTGTGCCAG	0.592																																					p.I404N	NSCLC(182;635 2928 8995 38788)	.											.	ITGAE-161	0			c.T1211A						.						93	58	70					17																	3659152		2203	4300	6503	SO:0001583	missense	3682	exon11			AAGCCAATCTGTG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"CD molecules", "Integrins"	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.1211T>A	17.37:g.3659152A>T	ENSP00000263087:p.Ile404Asn	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_002208	0	0	0	0	0	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	A	9.577	1.122528	0.20877	.	.	ENSG00000083457	ENST00000263087	T	0.58358	0.34	4.49	2.07	0.26955	.	.	.	.	.	T	0.41143	0.1146	L	0.51422	1.61	0.22571	N	0.998974	P	0.34462	0.454	B	0.29785	0.107	T	0.28744	-1.0034	9	0.51188	T	0.08	.	5.4982	0.16815	0.6409:0.0:0.3591:0.0	.	404	P38570	ITAE_HUMAN	N	404	ENSP00000263087:I404N	ENSP00000263087:I404N	I	-	2	0	ITGAE	3605901	0.002000	0.14202	0.605000	0.28930	0.320000	0.28249	0.698000	0.25571	0.284000	0.22305	0.421000	0.28195	ATT	.		0.592	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		T	3659152	A	T	3659152	3	4	45	1	0	0	0	0	1	0	0	0	7906	101	4	5	2412	5	ITGAE	17	3659152	Missense_Mutation	SNP	A	TCGA-B3-4104-01A-01D-1458-08		3659152	77536058	92	4132											
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	7579415	7579415	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagaagatgacaggggcCaggagggggctggtgcaggg	10	3	22	6	0	0	3	0	1	0	2	0	5	0	5	1	8	1	2	1	8	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:7579415C>T	ENST00000269305.4	-	4	461	c.272G>A	c.(271-273)tGg>tAg	p.W91*	TP53_ENST00000359597.4_Nonsense_Mutation_p.W91*|TP53_ENST00000455263.2_Nonsense_Mutation_p.W91*|TP53_ENST00000413465.2_Nonsense_Mutation_p.W91*|TP53_ENST00000445888.2_Nonsense_Mutation_p.W91*|TP53_ENST00000420246.2_Nonsense_Mutation_p.W91*|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	91	Interaction with WWOX.		W -> C (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.W91*(7)|p.G59fs*23(3)|p.V73fs*9(1)|p.D48fs*55(1)|p.A88fs*52(1)|p.W91fs*13(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGACAGGGGCCAGGAGGGGGC	0.632		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.W91X	Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53-70225	25	Deletion - Frameshift(10)|Whole gene deletion(8)|Substitution - Nonsense(7)	lung(7)|upper_aerodigestive_tract(4)|bone(4)|central_nervous_system(3)|breast(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|prostate(1)|liver(1)	c.G272A						.						44	50	48					17																	7579415		2202	4299	6501	SO:0001587	stop_gained	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGGGGCCAGGAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.272G>A	17.37:g.7579415C>T	ENSP00000269305:p.Trp91*	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	143	23	NM_000546	0	0	58	60	2	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911071	0.72983	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	4.08	4.08	0.47627	.	0.425160	0.22616	N	0.057766	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-8.1711	14.5887	0.68347	0.0:1.0:0.0:0.0	.	.	.	.	X	91	.	ENSP00000269305:W91X	W	-	2	0	TP53	7520140	0.997000	0.39634	0.998000	0.56505	0.633000	0.38033	-0.143000	0.10296	2.561000	0.86390	0.561000	0.74099	TGG	.		0.632	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7579415	C	T	7579415	4	4	45	1	0	0	0	0	0	1	0	0	16414	595	21	2	1030	2	TP53	17	7579415	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3920263	7579415	73615795	93	4133											
MLLT6	4302	hgsc.bcm.edu	37	chr17	36881009	36881009	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctccaccccgctgctgtctgCgggtacccctggcctgctgc	2	9	11	19	2	1	0	0	0	1	0	2	0	2	0	6	2	5	4	6	2	1	1	rs150198262	byFrequency	TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:36881009C>A	ENST00000325718.7	+	19	3111	c.3020C>A	c.(3019-3021)gCg>gAg	p.A1007E		NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	1007					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					CTGCTGTCTGCGGGTACCCCT	0.677			T	MLL	AL																																p.A1007E		.		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	.	MLLT6-659	0			c.C3020A						.						13	16	15					17																	36881009		2196	4297	6493	SO:0001583	missense	4302	exon19			TGTCTGCGGGTAC		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"Zinc fingers, PHD-type"	7138	protein-coding gene	gene with protein product	"Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6", "trithorax homolog"	600328	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.3020C>A	17.37:g.36881009C>A	ENSP00000316426:p.Ala1007Glu	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_005937	0	0	49	49	0	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Missense_Mutation	SNP	ENST00000325718.7	37	CCDS11327.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.725015	0.68959	.	.	ENSG00000108292	ENST00000325718	T	0.46451	0.87	5.19	5.19	0.71726	.	0.696318	0.14064	N	0.343867	T	0.34890	0.0913	L	0.29908	0.895	0.36941	D	0.892365	B	0.27498	0.18	B	0.23275	0.045	T	0.36625	-0.9740	10	0.72032	D	0.01	.	15.9024	0.79392	0.0:1.0:0.0:0.0	.	1007	P55198	AF17_HUMAN	E	1007	ENSP00000316426:A1007E	ENSP00000316426:A1007E	A	+	2	0	MLLT6	34134535	0.994000	0.37717	0.541000	0.28102	0.960000	0.62799	5.959000	0.70339	2.860000	0.98153	0.655000	0.94253	GCG	C|0.999;T|0.001		0.677	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		A	36881009	C	A	36881009	3	1	45	1	0	0	0	0	1	0	0	0	9655	768	27	4	3094	4	MLLT6	17	36881009	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	29301594	36881009	44314201	94	4134											
KRT13	3860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	39659037	39659037	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgaatcatggcagtgttggTagacacctccttgttcagct	8	13	10	10	0	2	2	2	1	0	1	3	2	3	2	2	2	1	5	2	2	2	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:39659037T>A	ENST00000246635.3	-	5	971	c.925A>T	c.(925-927)Acc>Tcc	p.T309S	KRT13_ENST00000336861.3_Missense_Mutation_p.T309S|KRT13_ENST00000587544.1_Missense_Mutation_p.T309S|KRT13_ENST00000587118.1_5'Flank|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	309	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				GCAGTGTTGGTAGACACCTCC	0.577																																					p.T309S		.											.	KRT13-95	0			c.A925T						.						216	195	202					17																	39659037		2203	4300	6503	SO:0001583	missense	3860	exon5			TGTTGGTAGACAC		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.925A>T	17.37:g.39659037T>A	ENSP00000246635:p.Thr309Ser	Somatic	456	0		WXS	Illumina HiSeq	Phase_I	447	195	NM_002274	0	0	15	39	24	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	37	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	T	0.668	-0.803036	0.02841	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	T;T	0.76968	-1.06;-1.06	4.45	-3.03	0.05429	Filament (1);	0.306290	0.23211	N	0.050674	T	0.51058	0.1652	N	0.05124	-0.11	0.09310	N	1	B;B;B;B	0.15719	0.014;0.008;0.006;0.008	B;B;B;B	0.28305	0.053;0.088;0.03;0.088	T	0.47446	-0.9117	10	0.02654	T	1	.	12.9134	0.58192	0.301:0.0:0.0:0.699	.	297;309;309;309	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	S	309;309;297	ENSP00000246635:T309S;ENSP00000336604:T309S	ENSP00000157775:T297S	T	-	1	0	KRT13	36912563	0.000000	0.05858	0.056000	0.19401	0.751000	0.42716	-0.832000	0.04400	-0.336000	0.08438	0.391000	0.25812	ACC	.		0.577	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39659037	T	A	39659037	3	1	45	1	0	0	0	0	1	0	0	0	8471	1638	57	5	467	5	KRT13	17	39659037	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	2778028	39659037	41536173	95	4135											
DBF4B	80174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	42828063	42828063	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtgtgagtgccacaaccctCctgccggccttgcccaaggg	6	8	12	15	1	0	1	0	1	0	0	1	1	1	1	6	2	4	0	6	2	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:42828063C>T	ENST00000315005.3	+	14	1428	c.1290C>T	c.(1288-1290)ctC>ctT	p.L430L	DBF4B_ENST00000393547.2_Intron	NM_145663.2	NP_663696.1	Q8NFT6	DBF4B_HUMAN	DBF4 zinc finger B	430					cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of protein kinase activity (GO:0045860)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)	7		Prostate(33;0.0322)				CCACAACCCTCCTGCCGGCCT	0.617																																					p.L430L		.											.	DBF4B-227	0			c.C1290T						.						56	52	53					17																	42828063		2203	4300	6503	SO:0001819	synonymous_variant	80174	exon14			AACCCTCCTGCCG	AF465820	CCDS11485.1, CCDS45706.1, CCDS45706.2	17q21.31	2014-02-17	2014-02-17		ENSG00000161692	ENSG00000161692		"Zinc fingers, DBF-type"	17883	protein-coding gene	gene with protein product	"chiffon homolog B (Drosophila)", "zinc finger, DBF-type containing 1B"	611661	"DBF4 homolog B (S. cerevisiae)"			15668232	Standard	NM_145663		Approved	FLJ13087, DRF1, ASKL1, chifb, ZDBF1B	uc002ihf.3	Q8NFT6	OTTHUMG00000165717	ENST00000315005.3:c.1290C>T	17.37:g.42828063C>T		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	131	59	NM_145663	0	0	0	1	1	D3DX56|Q8TEX0|Q96B19|Q9H912	Silent	SNP	ENST00000315005.3	37	CCDS11485.1																																																																																			.		0.617	DBF4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385930.1	NM_025104		T	42828063	C	T	42828063	2	4	45	1	0	0	0	0	0	0	0	1	4255	842	30	2		2	DBF4B	17	42828063	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3169026	42828063	38367147	96	4136											
EPN3	55040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	48615544	48615544	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggccctcgccatgagccgtGaggaggcagagaaggtgagg	9	5	18	9	2	0	4	0	3	0	1	1	6	0	5	3	5	1	1	3	5	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48615544G>A	ENST00000268933.3	+	3	1246	c.667G>A	c.(667-669)Gag>Aag	p.E223K	RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_Missense_Mutation_p.E167K|EPN3_ENST00000537145.1_Missense_Mutation_p.E278K	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	223						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CATGAGCCGTGAGGAGGCAGA	0.667																																					p.E223K		.											.	EPN3-91	0			c.G667A						.						47	38	41					17																	48615544		2203	4300	6503	SO:0001583	missense	55040	exon3			AGCCGTGAGGAGG	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.667G>A	17.37:g.48615544G>A	ENSP00000268933:p.Glu223Lys	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	43	29	NM_017957	0	0	3	7	4	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.925509	0.92319	.	.	ENSG00000049283	ENST00000268933;ENST00000442715;ENST00000537145;ENST00000541226;ENST00000411703	T;T;T	0.58060	2.08;1.24;0.36	4.54	4.54	0.55810	Ubiquitin interacting motif (3);	0.062476	0.64402	D	0.000007	T	0.73434	0.3586	M	0.79805	2.47	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.997;0.998;0.992	T	0.74408	-0.3675	10	0.35671	T	0.21	-20.981	17.345	0.87308	0.0:0.0:1.0:0.0	.	278;278;223	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	K	223;278;278;167;223	ENSP00000268933:E223K;ENSP00000439512:E278K;ENSP00000440540:E167K	ENSP00000268933:E223K	E	+	1	0	EPN3	45970543	1.000000	0.71417	0.861000	0.33841	0.595000	0.36748	9.783000	0.99037	2.247000	0.74100	0.456000	0.33151	GAG	.		0.667	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		A	48615544	G	A	48615544	3	1	45	1	0	0	0	0	1	0	0	0	5200	1291	45	2	673	2	EPN3	17	48615544	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	5787481	48615544	32579666	97	4137											
EPN3	55040	hgsc.bcm.edu;ucsc.edu	37	chr17	48616322	48616322	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgagccggcaggagcacgaGaaggtagtgggccgagcccg	9	3	18	11	4	0	2	0	1	0	1	0	5	0	3	3	4	3	3	3	4	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48616322G>C	ENST00000268933.3	+	4	1338	c.759G>C	c.(757-759)gaG>gaC	p.E253D	RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_Intron|EPN3_ENST00000537145.1_Intron	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	253						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			AGGAGCACGAGAAGGTAGTGG	0.687																																					p.E253D		.											.	EPN3-91	0			c.G759C						.						24	24	24					17																	48616322		2201	4299	6500	SO:0001583	missense	55040	exon4			GCACGAGAAGGTA	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.759G>C	17.37:g.48616322G>C	ENSP00000268933:p.Glu253Asp	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	24	11	NM_017957	0	0	2	2	0	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204206	0.38905	.	.	ENSG00000049283	ENST00000268933;ENST00000411703	T	0.15256	2.44	4.5	3.51	0.40186	Ubiquitin interacting motif (2);	0.319926	0.29668	N	0.011504	T	0.12944	0.0314	L	0.42245	1.32	0.80722	D	1	B	0.12630	0.006	B	0.13407	0.009	T	0.07309	-1.0779	10	0.11794	T	0.64	.	9.5827	0.39497	0.0:0.1552:0.684:0.1609	.	253	Q9H201	EPN3_HUMAN	D	253	ENSP00000268933:E253D	ENSP00000268933:E253D	E	+	3	2	EPN3	45971321	1.000000	0.71417	0.999000	0.59377	0.801000	0.45260	4.211000	0.58507	1.001000	0.39076	0.313000	0.20887	GAG	.		0.687	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		C	48616322	G	C	48616322	3	2	45	1	0	0	0	0	1	0	0	0	5200	933	33	4	769	4	EPN3	17	48616322	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	778	48616322	32578888	98	4138											
SPATA20	64847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	48628090	48628090	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccggaggcttctatagcgcaGaagatgcagactcgccccca	10	6	11	14	3	1	3	0	0	1	3	2	4	1	4	3	2	2	3	3	2	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48628090G>A	ENST00000356488.4	+	10	1230	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	SPATA20_ENST00000006658.6_Missense_Mutation_p.E399K|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000393244.3_Missense_Mutation_p.E339K	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	383					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CTATAGCGCAGAAGATGCAGA	0.672											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E399K		.											.	SPATA20-90	0			c.G1195A						.						47	58	54					17																	48628090		2203	4299	6502	SO:0001583	missense	64847	exon11			AGCGCAGAAGATG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1147G>A	17.37:g.48628090G>A	ENSP00000348878:p.Glu383Lys	Somatic	323	1	119	WXS	Illumina HiSeq	Phase_I	450	205	NM_022827	0	0	28	28	0	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393663	0.83011	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.30981	1.51;1.51;1.51	5.64	5.64	0.86602	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.000000	0.85682	D	0.000000	T	0.68137	0.2968	H	0.95187	3.635	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.77557	0.99;0.964	T	0.77907	-0.2412	10	0.72032	D	0.01	-3.9451	16.6877	0.85314	0.0:0.1292:0.8708:0.0	.	383;399	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	K	399;383;339	ENSP00000006658:E399K;ENSP00000348878:E383K;ENSP00000376935:E339K	ENSP00000006658:E399K	E	+	1	0	SPATA20	45983089	1.000000	0.71417	0.953000	0.39169	0.342000	0.28953	7.988000	0.88194	2.664000	0.90586	0.655000	0.94253	GAA	.		0.672	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48628090	G	A	48628090	3	1	45	1	0	0	0	0	1	0	0	0	15038	943	33	2	1237	2	SPATA20	17	48628090	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	11768	48628090	32567120	99	4139											
SPATA20	64847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	48628385	48628385	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagggggagctgcagggccaGaatgtgctgaccgtccggta	9	6	17	9	2	0	2	0	1	0	1	1	3	1	3	3	4	3	4	3	4	3	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48628385G>A	ENST00000356488.4	+	11	1445	c.1362G>A	c.(1360-1362)caG>caA	p.Q454Q	SPATA20_ENST00000006658.6_Silent_p.Q470Q|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000393244.3_Silent_p.Q410Q	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	454					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TGCAGGGCCAGAATGTGCTGA	0.637											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q470Q		.											.	SPATA20-90	0			c.G1410A						.						37	42	40					17																	48628385		2203	4300	6503	SO:0001819	synonymous_variant	64847	exon12			GGGCCAGAATGTG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1362G>A	17.37:g.48628385G>A		Somatic	100	0	119	WXS	Illumina HiSeq	Phase_I	145	67	NM_022827	0	0	27	27	0	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	37	CCDS58563.1																																																																																			.		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48628385	G	A	48628385	2	1	45	1	0	0	0	0	0	0	0	1	15038	933	33	2		2	SPATA20	17	48628385	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	295	48628385	32566825	100	4140											
TEX2	55852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	62238165	62238165	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atatatagccccttacccttCtttgccaatttctccaacct	9	15	2	15	0	2	0	0	0	2	0	3	0	2	0	6	0	4	0	6	0	6	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:62238165C>G	ENST00000583097.1	-	8	2972	c.2800G>C	c.(2800-2802)Gaa>Caa	p.E934Q	TEX2_ENST00000258991.3_Missense_Mutation_p.E941Q|TEX2_ENST00000584379.1_Missense_Mutation_p.E934Q			Q8IWB9	TEX2_HUMAN	testis expressed 2	934					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		CCTTACCCTTCTTTGCCAATT	0.463																																					p.E941Q		.											.	TEX2-91	0			c.G2821C						.						176	187	183					17																	62238165		2203	4300	6503	SO:0001583	missense	55852	exon8			ACCCTTCTTTGCC	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.2800G>C	17.37:g.62238165C>G	ENSP00000462665:p.Glu934Gln	Somatic	408	0		WXS	Illumina HiSeq	Phase_I	1011	701	NM_018469	0	0	0	0	0	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	37		.	.	.	.	.	.	.	.	.	.	C	16.25	3.069164	0.55539	.	.	ENSG00000136478	ENST00000258991	T	0.50548	0.74	5.84	5.84	0.93424	.	0.096119	0.64402	D	0.000001	T	0.67711	0.2922	M	0.68952	2.095	0.80722	D	1	D;D	0.69078	0.997;0.962	D;P	0.65010	0.931;0.756	T	0.66464	-0.5917	10	0.52906	T	0.07	.	20.1386	0.98045	0.0:1.0:0.0:0.0	.	941;934	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	Q	941	ENSP00000258991:E941Q	ENSP00000258991:E941Q	E	-	1	0	TEX2	59591897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.767000	0.95098	0.561000	0.74099	GAA	.		0.463	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		G	62238165	C	G	62238165	3	3	45	1	0	0	0	0	1	0	0	0	15813	922	32	4	603	4	TEX2	17	62238165	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	13609780	62238165	18957045	101	4141											
CACNG4	27092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	65026963	65026963	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccatgggggagctgtccaTgtacacgctgtccagggagc	7	7	14	13	1	0	0	0	0	0	0	2	2	2	2	4	3	3	3	4	3	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:65026963T>C	ENST00000262138.3	+	4	829	c.827T>C	c.(826-828)aTg>aCg	p.M276T	AC005544.1_ENST00000375684.1_5'Flank|RP11-74H8.1_ENST00000579138.1_RNA	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	276					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			GAGCTGTCCATGTACACGCTG	0.647																																					p.M276T		.											.	CACNG4-90	0			c.T827C						.						38	35	36					17																	65026963		2203	4300	6503	SO:0001583	missense	27092	exon4			TGTCCATGTACAC	AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"Calcium channel subunits"	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.827T>C	17.37:g.65026963T>C	ENSP00000262138:p.Met276Thr	Somatic	102	1		WXS	Illumina HiSeq	Phase_I	163	33	NM_014405	0	0	2	2	0	B2RCK0	Missense_Mutation	SNP	ENST00000262138.3	37	CCDS11667.1	.	.	.	.	.	.	.	.	.	.	T	15.02	2.709441	0.48517	.	.	ENSG00000075461	ENST00000262138	T	0.57436	0.4	5.15	5.15	0.70609	.	0.039332	0.85682	D	0.000000	T	0.53562	0.1804	M	0.77313	2.365	0.80722	D	1	P	0.42827	0.791	B	0.35859	0.212	T	0.64483	-0.6397	10	0.87932	D	0	-22.375	15.0541	0.71897	0.0:0.0:0.0:1.0	.	276	Q9UBN1	CCG4_HUMAN	T	276	ENSP00000262138:M276T	ENSP00000262138:M276T	M	+	2	0	CACNG4	62457425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.578000	0.82498	1.967000	0.57214	0.529000	0.55759	ATG	.		0.647	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405		C	65026963	T	C	65026963	3	2	45	1	0	0	0	0	1	0	0	0	2565	1464	51	3	841	3	CACNG4	17	65026963	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	2788798	65026963	16168247	102	4142											
SLC38A10	124565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	79249777	79249777	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgagggtcttacctgctgctCacacagcagcgtgctcaggg	7	8	13	13	2	3	0	2	0	1	0	3	1	3	0	1	2	6	4	1	2	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:79249777C>T	ENST00000374759.3	-	8	1287	c.904G>A	c.(904-906)Gag>Aag	p.E302K	SLC38A10_ENST00000288439.5_Missense_Mutation_p.E302K|SLC38A10_ENST00000546352.1_5'UTR	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	302					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			ACCTGCTGCTCACACAGCAGC	0.597																																					p.E302K		.											.	SLC38A10-70	0			c.G904A						.						91	87	88					17																	79249777		2203	4300	6503	SO:0001583	missense	124565	exon8			GCTGCTCACACAG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.904G>A	17.37:g.79249777C>T	ENSP00000363891:p.Glu302Lys	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	361	77	NM_001037984	0	0	0	0	0	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	37	CCDS42397.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.510735	0.85389	.	.	ENSG00000157637	ENST00000374759;ENST00000288439	T;T	0.02216	4.39;4.39	4.88	4.88	0.63580	.	0.239727	0.41396	D	0.000893	T	0.05456	0.0144	N	0.16567	0.415	0.58432	D	0.999998	B;D	0.89917	0.178;1.0	B;D	0.85130	0.054;0.997	T	0.65307	-0.6200	10	0.16420	T	0.52	-37.9351	17.6417	0.88138	0.0:1.0:0.0:0.0	.	302;302	Q9HBR0-2;Q9HBR0	.;S38AA_HUMAN	K	302	ENSP00000363891:E302K;ENSP00000288439:E302K	ENSP00000288439:E302K	E	-	1	0	SLC38A10	76864372	1.000000	0.71417	0.929000	0.37066	0.845000	0.48019	7.379000	0.79691	2.244000	0.73946	0.655000	0.94253	GAG	.		0.597	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79249777	C	T	79249777	3	4	45	1	0	0	0	0	1	0	0	0	14634	835	29	2	2769	2	SLC38A10	17	79249777	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	14222814	79249777	1945433	103	4143											
DSC2	1824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr18	28660162	28660162	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	catgcgaacagtctgtattgGagggttacactcagggccct	9	10	12	10	1	2	0	1	0	1	0	2	2	2	1	1	3	3	2	1	3	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr18:28660162G>C	ENST00000280904.6	-	10	1863	c.1420C>G	c.(1420-1422)Cca>Gca	p.P474A	DSC2_ENST00000251081.6_Missense_Mutation_p.P474A	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	474	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			GTCTGTATTGGAGGGTTACAC	0.443																																					p.P474A		.											.	DSC2-517	0			c.C1420G						.						195	167	177					18																	28660162		2203	4300	6503	SO:0001583	missense	1824	exon10			GTATTGGAGGGTT	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"Cadherins / Major cadherins"	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.1420C>G	18.37:g.28660162G>C	ENSP00000280904:p.Pro474Ala	Somatic	265	0		WXS	Illumina HiSeq	Phase_I	427	225	NM_024422	0	0	2	2	0		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	G	5.668	0.307878	0.10733	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.60548	0.18;0.18	5.92	-2.13	0.07144	Cadherin (3);Cadherin-like (1);	2.202610	0.03087	N	0.159213	T	0.31199	0.0789	N	0.11673	0.155	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.15052	0.005;0.012	T	0.20672	-1.0268	10	0.06365	T	0.9	.	4.1607	0.10282	0.1425:0.4668:0.1934:0.1973	.	474;474	Q02487;Q02487-2	DSC2_HUMAN;.	A	474;474;240;487	ENSP00000251081:P474A;ENSP00000280904:P474A	ENSP00000251081:P474A	P	-	1	0	DSC2	26914160	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-0.336000	0.07863	-0.382000	0.07870	-0.150000	0.13652	CCA	.		0.443	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28660162	G	C	28660162	3	2	45	1	0	0	0	0	1	0	0	0	4777	1174	41	4	1353	4	DSC2	18	28660162	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		28660162	49417086	104	4144											
C19orf21	126353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	757669	757669	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacaagccccacctggccaaCgggcacgtggttcccatcaa	11	5	9	16	2	1	0	1	0	0	0	2	0	2	0	5	3	3	2	5	3	4	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr19:757669C>T	ENST00000215582.6	+	2	826	c.723C>T	c.(721-723)aaC>aaT	p.N241N		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	241					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											ACCTGGCCAACGGGCACGTGG	0.672																																					p.N241N		.											.	C19orf21-91	0			c.C723T						.						24	27	26					19																	757669		2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			GGCCAACGGGCAC	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.723C>T	19.37:g.757669C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	59	29	NM_173481	0	0	2	13	11		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			.		0.672	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	757669	C	T	757669	2	4	45	1	0	0	0	0	0	0	0	1	1919	535	19	1		1	C19orf21	19	757669	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08		757669	58371314	105	4145											
PIK3R2	5296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	18279617	18279617	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgggcaagatcaaccgcacGcaggcagaggagatgctgag	12	4	16	9	2	1	4	1	1	0	3	1	5	1	4	1	3	2	5	1	3	2	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr19:18279617G>A	ENST00000593731.1	+	15	2450	c.1890G>A	c.(1888-1890)acG>acA	p.T630T	PIK3R2_ENST00000222254.8_Silent_p.T630T			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	630	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	TCAACCGCACGCAGGCAGAGG	0.657											OREG0025359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T630T		.											.	PIK3R2-1311	0			c.G1890A						.						75	48	57					19																	18279617		2203	4300	6503	SO:0001819	synonymous_variant	5296	exon15			CCGCACGCAGGCA		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1890G>A	19.37:g.18279617G>A		Somatic	65	0	724	WXS	Illumina HiSeq	Phase_I	48	21	NM_005027	0	0	19	40	21	Q5EAT5|Q9UPH9	Silent	SNP	ENST00000593731.1	37	CCDS12371.1																																																																																			.		0.657	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		A	18279617	G	A	18279617	2	1	45	1	0	0	0	0	0	0	0	1	11945	1074	38	1		1	PIK3R2	19	18279617	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	17521948	18279617	40849366	106	4146											
PRR12	57479	hgsc.bcm.edu;broad.mit.edu	37	chr19	50099849	50099849	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtccactacggggcaggcGccaaggagctgggggccttc	6	7	16	12	2	0	0	0	0	0	0	2	1	1	1	3	6	2	2	3	6	2	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr19:50099849G>A	ENST00000418929.2	+	4	2269	c.2257G>A	c.(2257-2259)Gcc>Acc	p.A753T		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							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)		CGGGGCAGGCGCCAAGGAGCT	0.692																																					p.A753T		.											.	PRR12-70	0			c.G2257A						.						9	11	10					19																	50099849		1883	4040	5923	SO:0001583	missense	57479	exon4			GCAGGCGCCAAGG	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.2257G>A	19.37:g.50099849G>A	ENSP00000394510:p.Ala753Thr	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	18	6	NM_020719	0	0	8	10	2	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	7.112	0.576277	0.13686	.	.	ENSG00000126464	ENST00000418929	.	.	.	3.56	3.56	0.40772	.	.	.	.	.	T	0.33177	0.0854	.	.	.	0.26879	N	0.967589	D	0.61080	0.989	P	0.48552	0.581	T	0.06516	-1.0822	7	0.23891	T	0.37	.	10.6184	0.45465	0.0:0.197:0.803:0.0	.	753	Q9ULL5-3	.	T	753	.	ENSP00000394510:A753T	A	+	1	0	PRR12	54791661	0.998000	0.40836	1.000000	0.80357	0.271000	0.26615	1.743000	0.38258	2.001000	0.58596	0.313000	0.20887	GCC	.		0.692	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		A	50099849	G	A	50099849	3	1	45	1	0	0	0	0	1	0	0	0	12613	1087	38	1	2271	1	PRR12	19	50099849	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	31820232	50099849	9029134	107	4147											
CPXM1	56265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	2775058	2775058	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcccctggggtcagcagacgCcaataatccccgccccacgc	8	5	9	19	3	1	1	1	0	0	1	3	1	3	1	7	2	1	1	7	2	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr20:2775058C>A	ENST00000380605.2	-	14	2047	c.1983G>T	c.(1981-1983)tgG>tgT	p.W661C		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	661					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TCAGCAGACGCCAATAATCCC	0.597																																					p.W661C		.											.	CPXM1-94	0			c.G1983T						.						56	55	55					20																	2775058		2203	4300	6503	SO:0001583	missense	56265	exon14			CAGACGCCAATAA	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.1983G>T	20.37:g.2775058C>A	ENSP00000369979:p.Trp661Cys	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	106	24	NM_019609	0	0	10	12	2	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	c	21.1	4.099189	0.76983	.	.	ENSG00000088882	ENST00000380605;ENST00000421947	T	0.41758	0.99	5.12	5.12	0.69794	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.000000	0.85682	D	0.000000	T	0.76399	0.3982	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84208	0.0454	10	0.87932	D	0	-16.2562	16.4323	0.83853	0.0:1.0:0.0:0.0	.	661	Q96SM3	CPXM1_HUMAN	C	661;357	ENSP00000369979:W661C	ENSP00000369979:W661C	W	-	3	0	CPXM1	2723058	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.560000	0.82277	2.821000	0.97095	0.651000	0.88453	TGG	.		0.597	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		A	2775058	C	A	2775058	3	1	45	1	0	0	0	0	1	0	0	0	3843	740	26	4	225	4	CPXM1	20	2775058	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		2775058	60250462	108	4148											
CTCFL	140690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	56090811	56090811	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtttcagcttgtaggtatctCtgctggcatagctgcactgg	6	14	12	9	0	2	0	1	0	1	0	3	0	2	0	0	3	4	8	0	3	3	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr20:56090811C>G	ENST00000608263.1	-	5	1800	c.1139G>C	c.(1138-1140)aGa>aCa	p.R380T	CTCFL_ENST00000539382.1_Missense_Mutation_p.R175T|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000609232.1_Missense_Mutation_p.R380T|CTCFL_ENST00000422869.2_Missense_Mutation_p.R380T|CTCFL_ENST00000608425.1_Missense_Mutation_p.R380T|CTCFL_ENST00000608903.1_Missense_Mutation_p.R118T|CTCFL_ENST00000502686.2_Missense_Mutation_p.R118T|CTCFL_ENST00000608440.1_Missense_Mutation_p.R380T|CTCFL_ENST00000371196.2_Missense_Mutation_p.R380T|CTCFL_ENST00000433949.3_Missense_Mutation_p.R175T|CTCFL_ENST00000429804.3_Missense_Mutation_p.R380T|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Missense_Mutation_p.R380T|CTCFL_ENST00000423479.3_Missense_Mutation_p.R380T	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	380					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GTAGGTATCTCTGCTGGCATA	0.483																																					p.R380T		.											.	CTCFL-292	0			c.G1139C						.						175	165	169					20																	56090811		2203	4300	6503	SO:0001583	missense	140690	exon5			GTATCTCTGCTGG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1139G>C	20.37:g.56090811C>G	ENSP00000476783:p.Arg380Thr	Somatic	338	0		WXS	Illumina HiSeq	Phase_I	573	253	NM_001269044	0	0	0	0	0	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.933464	0.34096	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.27557	2.51;2.51;2.51;1.66;2.51;2.51;1.66;2.51;2.51;2.51	5.24	0.214	0.15249	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.465807	0.17788	N	0.161995	T	0.20700	0.0498	N	0.16016	0.355	0.35738	D	0.818477	B;P;B;P;P	0.43231	0.016;0.801;0.056;0.801;0.801	B;B;B;P;P	0.49012	0.038;0.412;0.088;0.598;0.598	T	0.18398	-1.0338	10	0.12103	T	0.63	-30.8232	9.21	0.37313	0.0:0.5082:0.0:0.4918	.	380;380;380;380;380	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	T	380;380;380;380;380;118;380;380;175;380	ENSP00000415579:R380T;ENSP00000243914:R380T;ENSP00000360239:R380T;ENSP00000415329:R380T;ENSP00000392034:R380T;ENSP00000437999:R118T;ENSP00000413713:R380T;ENSP00000403369:R380T;ENSP00000439998:R175T;ENSP00000399061:R380T	ENSP00000243914:R380T	R	-	2	0	CTCFL	55524217	0.986000	0.35501	0.791000	0.31998	0.533000	0.34776	0.574000	0.23714	0.045000	0.15804	-0.312000	0.09012	AGA	.		0.483	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		G	56090811	C	G	56090811	3	3	45	1	0	0	0	0	1	0	0	0	4007	913	32	4	876	4	CTCFL	20	56090811	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	53315753	56090811	6934709	109	4149											
ZBTB46	140685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	62407208	62407208	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggggtgaggggagggcccaGatagctggcttctcctccca	6	8	16	11	0	1	2	0	1	1	1	3	3	2	3	3	6	1	2	3	6	1	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr20:62407208G>A	ENST00000245663.4	-	3	1195	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	ZBTB46_ENST00000395104.1_Silent_p.L349L|ZBTB46_ENST00000302995.2_Silent_p.L349L	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	349					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GGAGGGCCCAGATAGCTGGCT	0.662																																					p.L349L		.											.	ZBTB46-154	0			c.C1045T						.						56	58	57					20																	62407208		2203	4300	6503	SO:0001819	synonymous_variant	140685	exon3			GGCCCAGATAGCT	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1045C>T	20.37:g.62407208G>A		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	208	99	NM_025224	0	0	5	5	0	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			.		0.662	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		A	62407208	G	A	62407208	2	1	45	1	0	0	0	0	0	0	0	1	17579	933	33	2		2	ZBTB46	20	62407208	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	6316397	62407208	618312	110	4150											
SLC25A1	6576	broad.mit.edu	37	chr22	19164390	19164390	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgcgcagggaggtcatgacGaagaagcggatggcctggtt	9	8	17	7	3	1	2	1	1	0	1	1	5	1	4	1	5	2	2	1	5	2	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:19164390G>A	ENST00000215882.5	-	6	756	c.600C>T	c.(598-600)ttC>ttT	p.F200F	SLC25A1_ENST00000451283.1_Silent_p.F97F|SLC25A1_ENST00000461267.1_5'UTR|CLTCL1_ENST00000442042.2_5'Flank	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	200					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		AGGTCATGACGAAGAAGCGGA	0.642																																					p.F207F													.	SLC25A1-90	0			c.C621T						.						92	82	85					22																	19164390		2203	4300	6503	SO:0001819	synonymous_variant	6576	exon5			CATGACGAAGAAG	U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"Solute carriers"	10979	protein-coding gene	gene with protein product		190315	"solute carrier family 20 (mitochondrial citrate transporter), member 3"	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.600C>T	22.37:g.19164390G>A		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	154	6	NM_001256534	0	0	123	123	0	A8K8E8|Q9BSK6	Silent	SNP	ENST00000215882.5	37	CCDS13758.1																																																																																			.		0.642	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984		A	19164390	G	A	19164390	2	1	45	1	0	0	0	0	0	0	0	1	14503	1049	37	1		1	SLC25A1	22	19164390	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08		19164390	32140176	111	4151											
PICK1	9463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr22	38470965	38470965	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctgcgggatgccgacgtcttCcccatcgaggtagacctggc	6	8	13	14	4	1	1	0	0	1	1	3	4	2	2	4	3	2	1	4	3	1	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:38470965C>G	ENST00000404072.3	+	13	1421	c.1074C>G	c.(1072-1074)ttC>ttG	p.F358L	PICK1_ENST00000356976.3_Missense_Mutation_p.F358L|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	358					ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					CCGACGTCTTCCCCATCGAGG	0.607																																					p.F358L		.											.	PICK1-226	0			c.C1074G						.						106	74	85					22																	38470965		2203	4300	6503	SO:0001583	missense	9463	exon13			CGTCTTCCCCATC	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.1074C>G	22.37:g.38470965C>G	ENSP00000385205:p.Phe358Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	66	25	NM_012407	0	0	22	30	8	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	37	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273750	0.80580	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	T;T	0.37411	1.2;1.2	4.33	3.21	0.36854	.	0.047493	0.85682	N	0.000000	T	0.55800	0.1943	M	0.81497	2.545	0.58432	D	0.999998	D	0.63880	0.993	D	0.68192	0.956	T	0.59726	-0.7400	10	0.72032	D	0.01	-17.1105	8.2306	0.31595	0.0:0.7398:0.162:0.0982	.	358	Q9NRD5	PICK1_HUMAN	L	358	ENSP00000385205:F358L;ENSP00000349465:F358L	ENSP00000349465:F358L	F	+	3	2	PICK1	36800911	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.142000	0.42177	2.124000	0.65301	0.561000	0.74099	TTC	.		0.607	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		G	38470965	C	G	38470965	3	3	45	1	0	0	0	0	1	0	0	0	11907	854	30	4	1120	4	PICK1	22	38470965	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	19306575	38470965	12833601	112	4152											
MKL1	57591	hgsc.bcm.edu;broad.mit.edu	37	chr22	40814967	40814967	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcacgaggatctgcagtggcGaggcctgcagggtcagctgc	7	7	16	11	2	3	0	2	0	1	0	3	3	3	1	1	4	4	3	1	4	0	0	rs199908950		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:40814967G>A	ENST00000355630.3	-	12	2065	c.1475C>T	c.(1474-1476)tCg>tTg	p.S492L	MKL1_ENST00000402042.1_Missense_Mutation_p.S442L|MKL1_ENST00000396617.3_Missense_Mutation_p.S492L|MKL1_ENST00000407029.1_Missense_Mutation_p.S492L	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	492					negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						CTGCAGTGGCGAGGCCTGCAG	0.677			T	RBM15	acute megakaryocytic leukemia																																p.S492L		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	0			c.C1475T						.						29	30	30					22																	40814967		2200	4299	6499	SO:0001583	missense	57591	exon12			AGTGGCGAGGCCT	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1475C>T	22.37:g.40814967G>A	ENSP00000347847:p.Ser492Leu	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	68	11	NM_020831	0	0	6	6	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.036393	0.75617	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.69040	-0.29;-0.37;-0.36;-0.29	5.15	5.15	0.70609	.	0.061993	0.64402	D	0.000003	D	0.86163	0.5867	M	0.92367	3.3	0.52099	D	0.999946	B;D;D	0.76494	0.255;0.999;0.999	B;D;D	0.72625	0.024;0.978;0.978	D	0.88893	0.3347	10	0.62326	D	0.03	-16.568	18.819	0.92089	0.0:0.0:1.0:0.0	.	442;492;492	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	L	492;492;442;492	ENSP00000347847:S492L;ENSP00000379861:S492L;ENSP00000385584:S442L;ENSP00000385835:S492L	ENSP00000347847:S492L	S	-	2	0	MKL1	39144913	1.000000	0.71417	0.515000	0.27774	0.937000	0.57800	6.783000	0.75078	2.676000	0.91093	0.591000	0.81541	TCG	G|0.999;A|0.001		0.677	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		A	40814967	G	A	40814967	3	1	45	1	0	0	0	0	1	0	0	0	9626	1059	37	1	1336	1	MKL1	22	40814967	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	2344002	40814967	10489599	113	4153											
PARVB	29780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr22	44564537	44564537	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctttacaacctgttcacCaagtacaagaacgtggagtg	12	11	9	9	1	2	1	1	0	1	1	2	2	2	2	2	1	4	3	2	1	6	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:44564537C>T	ENST00000338758.7	+	13	1137	c.1074C>T	c.(1072-1074)acC>acT	p.T358T	PARVB_ENST00000406477.3_Silent_p.T391T|PARVB_ENST00000404989.1_Silent_p.T321T	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	358	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				ACCTGTTCACCAAGTACAAGA	0.552																																					p.T391T		.											.	PARVB-226	0			c.C1173T						.						99	92	94					22																	44564537		2203	4300	6503	SO:0001819	synonymous_variant	29780	exon14			GTTCACCAAGTAC	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"Parvins"	14653	protein-coding gene	gene with protein product	"affixin"	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.1074C>T	22.37:g.44564537C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	117	13	NM_001003828	0	0	8	8	0	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	37	CCDS14056.1																																																																																			.		0.552	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		T	44564537	C	T	44564537	2	4	45	1	0	0	0	0	0	0	0	1	11495	581	21	2		2	PARVB	22	44564537	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3749570	44564537	6740029	114	4154											
GTSE1	51512	broad.mit.edu	37	chr22	46712115	46712115	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcggagcagctcacggcacCcccctcagcatcccccaccc	8	3	8	22	2	2	0	2	0	0	0	3	1	3	1	6	2	4	4	6	2	0	0	rs542415397		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:46712115C>T	ENST00000454366.1	+	7	1450	c.1238C>T	c.(1237-1239)cCc>cTc	p.P413L		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	394					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CTCACGGCACCCCCCTCAGCA	0.627																																					p.P413L	GBM(153;542 1915 12487 29016 50495)												.	GTSE1-187	0			c.C1238T						.						28	34	32					22																	46712115		2203	4299	6502	SO:0001583	missense	51512	exon7			CGGCACCCCCCTC	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1238C>T	22.37:g.46712115C>T	ENSP00000415430:p.Pro413Leu	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	133	5	NM_016426	0	0	7	7	0	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	C	12.37	1.918468	0.33908	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07567	3.18	5.03	1.63	0.23807	.	0.747054	0.13230	N	0.403722	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.32101	0.053;0.356	B;B	0.34346	0.032;0.18	T	0.41502	-0.9505	10	0.44086	T	0.13	-7.8341	5.8869	0.18886	0.2662:0.5811:0.0:0.1527	.	394;373	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	L	413;373	ENSP00000415430:P413L	ENSP00000354634:P373L	P	+	2	0	GTSE1	45090779	0.001000	0.12720	0.014000	0.15608	0.004000	0.04260	0.808000	0.27154	0.211000	0.20683	0.650000	0.86243	CCC	.		0.627	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		T	46712115	C	T	46712115	3	4	45	1	0	0	0	0	1	0	0	0	6906	623	22	2	1260	2	GTSE1	22	46712115	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	2147578	46712115	4592451	115	4155											
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr22	46930992	46930992	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctcattcagacgaagctcGtaggtgggctgcgtgaacac	9	9	12	11	3	2	2	2	1	0	1	4	3	3	2	1	2	3	3	1	2	3	2	rs529594359		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:46930992G>A	ENST00000262738.3	-	1	2075	c.2076C>T	c.(2074-2076)taC>taT	p.Y692Y	CELSR1_ENST00000395964.1_Silent_p.Y692Y|CELSR1_ENST00000497509.1_5'Flank	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	692	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GACGAAGCTCGTAGGTGGGCT	0.642													G|||	1	0.000199681	8e-04	0	5008	,	,		18477	0		0	False		,,,				2504	0				p.Y692Y		.											.	CELSR1-525	0			c.C2076T						.						44	28	34					22																	46930992		2201	4298	6499	SO:0001819	synonymous_variant	9620	exon1			AAGCTCGTAGGTG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.2076C>T	22.37:g.46930992G>A		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	48	13	NM_014246	0	0	1	3	2	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	3.230	-0.157692	0.06544	.	.	ENSG00000075275	ENST00000454637	.	.	.	4.51	1.53	0.23141	.	.	.	.	.	T	0.55689	0.1936	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48479	-0.9032	4	.	.	.	.	8.3078	0.32053	0.4017:0.0:0.5983:0.0	.	.	.	.	M	67	.	.	T	-	2	0	CELSR1	45309656	0.873000	0.30073	0.986000	0.45419	0.599000	0.36880	-0.092000	0.11129	0.459000	0.27016	0.305000	0.20034	ACG	.		0.642	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46930992	G	A	46930992	2	1	45	1	0	0	0	0	0	0	0	1	3227	1140	40	1		1	CELSR1	22	46930992	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	218877	46930992	4373574	116	4156											
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chrX	123176469	123176469	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcagaactctgagataattCgaaaaatgactgaagaattc	17	10	8	6	1	1	5	0	3	1	3	3	7	1	5	0	0	2	1	0	0	6	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chrX:123176469C>T	ENST00000371160.1	+	7	726	c.436C>T	c.(436-438)Cga>Tga	p.R146*	STAG2_ENST00000371145.3_Nonsense_Mutation_p.R146*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.R77*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.R146*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.R146*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.R146*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	146					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TGAGATAATTCGAAAAATGAC	0.284																																					p.R146X		.											.	STAG2-134	0			c.C436T						.						79	75	76					X																	123176469		2203	4300	6503	SO:0001587	stop_gained	10735	exon7			ATAATTCGAAAAA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.436C>T	X.37:g.123176469C>T	ENSP00000360202:p.Arg146*	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	98	85	NM_001042749	0	0	1	8	7	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.683809	0.88639	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000435103;ENST00000371157;ENST00000371145;ENST00000371144;ENST00000428941;ENST00000435215	.	.	.	5.74	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.2847	12.9796	0.58555	0.2934:0.7066:0.0:0.0	.	.	.	.	X	146;146;77;146;146;146;146;146;146;146	.	ENSP00000218089:R146X	R	+	1	2	STAG2	123004150	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.312000	0.33574	1.156000	0.42514	0.522000	0.50473	CGA	.		0.284	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123176469	C	T	123176469	4	4	45	1	0	0	0	0	0	1	0	0	15275	876	31	1	454	1	STAG2	23	123176469	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		123176469	32094091	117	4157											
IL9R	3581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chrX	155232601	155232601	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggagagtgaggccctgaggcGagacatgggcacctggctcc	8	5	17	11	1	0	4	0	2	0	2	1	6	1	4	3	5	0	2	3	5	0	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chrX:155232601G>A	ENST00000244174.5	+	2	238	c.59G>A	c.(58-60)cGa>cAa	p.R20Q	IL9R_ENST00000424344.3_5'UTR|IL9R_ENST00000540897.1_Missense_Mutation_p.R57Q|IL9R_ENST00000369423.2_Missense_Mutation_p.R67Q	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	20					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCCCTGAGGCGAGACATGGGC	0.612																																					p.R67Q		.											.	IL9R-40	0			c.G200A						.	G	GLN/ARG	1,4405		0,1,2202	164	163	163		59	-2.3	0	X		163	0,8592		0,0,4296	no	missense	IL9R	NM_002186.2	43	0,1,6498	AA,AG,GG		0.0,0.0227,0.0077	benign	20/522	155232601	1,12997	2203	4296	6499	SO:0001583	missense	3581	exon3			TGAGGCGAGACAT	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.59G>A	X.37:g.155232601G>A	ENSP00000244174:p.Arg20Gln	Somatic	282	1		WXS	Illumina HiSeq	Phase_I	236	84	NM_176786	0	0	0	0	0	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	37	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	g	5.676	0.309355	0.10733	2.27E-4	0.0	ENSG00000124334	ENST00000244174;ENST00000369423;ENST00000540897	T;T;T	0.22743	2.98;1.94;1.94	1.18	-2.35	0.06684	.	4.396220	0.00735	N	0.000961	T	0.09512	0.0234	.	.	.	0.09310	N	1	B;B	0.28419	0.021;0.211	B;B	0.10450	0.002;0.005	T	0.11324	-1.0592	9	0.13108	T	0.6	-13.6917	3.8243	0.08848	0.2084:0.4817:0.3099:0.0	.	20;67	Q01113;B9ZVT0	IL9R_HUMAN;.	Q	20;67;57	ENSP00000244174:R20Q;ENSP00000358431:R67Q;ENSP00000438112:R57Q	ENSP00000244174:R20Q	R	+	2	0	IL9R	154885795	0.000000	0.05858	0.000000	0.03702	0.739000	0.42172	-0.677000	0.05215	-1.521000	0.01771	-0.733000	0.03571	CGA	.		0.612	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		A	155232601	G	A	155232601	3	1	45	1	0	0	0	0	1	0	0	0	7729	1058	37	1	65	1	IL9R	23	155232601	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	32056132	155232601	37959	118	4158											
S100PBP	64766	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	33292114	33292114	+	Frame_Shift_Del	DEL	A	A	-																															ccattaaacagacgctctgtActagaaaagaatcttataaa																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:33292114delA	ENST00000373475.5	+	3	668	c.414delA	c.(412-414)gtafs	p.V138fs	S100PBP_ENST00000398243.3_Frame_Shift_Del_p.V138fs|S100PBP_ENST00000373476.1_Frame_Shift_Del_p.V138fs|S100PBP_ENST00000356689.3_3'UTR	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GACGCTCTGTACTAGAAAAGA	0.413																																					p.V138fs		.											.	S100PBP-90	0			c.414delA						.						55	56	56					1																	33292114		2203	4300	6503	SO:0001589	frameshift_variant	64766	exon3			.	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"S100P binding protein 1"	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.414delA	1.37:g.33292114delA	ENSP00000362574:p.Val138fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	70	16	NM_001256121	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000373475.5	37	CCDS30666.1																																																																																			.		0.413	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753		-	33292114	A	-	33292114	7	5	46	1	0	1	0	1	0	0	0	0	13823	378	14	0	416	0	S100PBP	1	33292114	Frame_Shift_Del	DEL	A	TCGA-B3-8121-01A-21D-2396-08		33292114	215958507	1	4159											
ATP5F1	515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	112002161	112002161	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaaagaatcgcctggactAtcatatatctgtgcagaaca	15	10	8	8	1	2	2	1	0	1	2	3	3	2	3	1	1	2	2	1	1	7	4	rs201457142		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:112002161A>G	ENST00000369722.3	+	6	1202	c.596A>G	c.(595-597)tAt>tGt	p.Y199C	ATP5F1_ENST00000369721.4_3'UTR|ATP5F1_ENST00000483994.1_Missense_Mutation_p.Y138C	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1	199					ATP catabolic process (GO:0006200)|ATP synthesis coupled proton transport (GO:0015986)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		CGCCTGGACTATCATATATCT	0.418													A|||	1	0.000199681	8e-04	0	5008	,	,		19484	0		0	False		,,,				2504	0				p.Y199C		.											.	ATP5F1-90	0			c.A596G						.	A	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	79	85	83		596	4.8	1	1		83	1,8599		0,1,4299	no	missense	ATP5F1	NM_001688.4	194	0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154	probably-damaging	199/257	112002161	2,13004	2203	4300	6503	SO:0001583	missense	515	exon6			TGGACTATCATAT	X60221	CCDS836.1	1p13.2	2012-10-12	2010-06-11		ENSG00000116459	ENSG00000116459		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	840	protein-coding gene	gene with protein product		603270	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1"			1831354	Standard	XM_005270929		Approved		uc001ebc.3	P24539	OTTHUMG00000011745	ENST00000369722.3:c.596A>G	1.37:g.112002161A>G	ENSP00000358737:p.Tyr199Cys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	50	7	NM_001688	0	0	171	276	105	Q9BQ68|Q9BRU8	Missense_Mutation	SNP	ENST00000369722.3	37	CCDS836.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.189998	0.58017	2.27E-4	1.16E-4	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.38887	1.11;1.11	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71178	-0.4669	10	0.59425	D	0.04	.	14.394	0.66999	1.0:0.0:0.0:0.0	.	199;199	Q08ET0;P24539	.;AT5F1_HUMAN	C	199;138	ENSP00000358737:Y199C;ENSP00000420366:Y138C	ENSP00000358737:Y199C	Y	+	2	0	ATP5F1	111803684	1.000000	0.71417	0.998000	0.56505	0.208000	0.24298	8.489000	0.90461	1.956000	0.56807	0.383000	0.25322	TAT	A|0.999;G|0.001		0.418	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	NM_001688		G	112002161	A	G	112002161	3	3	46	1	0	0	0	0	1	0	0	0	1153	449	16	3	618	3	ATP5F1	1	112002161	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	78710047	112002161	137248460	2	4160											
SLC16A1	6566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	113460277	113460277	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tagggttaagtccaggaactGattaattgtttggaagactg	12	13	12	4	0	0	2	0	1	0	1	1	4	1	4	1	3	1	2	1	3	5	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:113460277G>A	ENST00000538576.1	-	4	1582	c.751C>T	c.(751-753)Cag>Tag	p.Q251*	SLC16A1_ENST00000369626.3_Nonsense_Mutation_p.Q251*|SLC16A1_ENST00000433570.4_Nonsense_Mutation_p.Q251*	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	251					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	TCCAGGAACTGATTAATTGTT	0.388																																					p.Q251X		.											.	SLC16A1-514	0			c.C751T						.						101	103	103					1																	113460277		2203	4300	6503	SO:0001587	stop_gained	6566	exon4			GGAACTGATTAAT	BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.751C>T	1.37:g.113460277G>A	ENSP00000441065:p.Gln251*	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	86	17	NM_001166496	0	0	9	14	5	Q49A45|Q5T8R6|Q9NSJ9	Nonsense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639199	0.67244	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570;ENST00000443580	.	.	.	5.74	-3.2	0.05156	.	0.477590	0.27223	N	0.020353	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6817	0.91548	0.0:0.0:0.6596:0.3404	.	.	.	.	X	251	.	ENSP00000358640:Q251X	Q	-	1	0	SLC16A1	113261800	0.997000	0.39634	0.183000	0.23137	0.253000	0.25986	1.851000	0.39338	-0.739000	0.04809	-0.457000	0.05445	CAG	.		0.388	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		A	113460277	G	A	113460277	4	1	46	1	0	0	0	0	0	1	0	0	14434	1299	45	2	759	2	SLC16A1	1	113460277	Nonsense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	1458116	113460277	135790344	3	4161											
SNAPIN	23557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153631989	153631989	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccctatgttaagaagctaCttaatgcccggcgacgcgtt	10	10	9	12	4	0	1	0	0	0	1	0	2	0	1	3	1	3	3	3	1	5	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:153631989C>G	ENST00000368685.5	+	3	346	c.256C>G	c.(256-258)Ctt>Gtt	p.L86V	SNAPIN_ENST00000478558.1_3'UTR|ILF2_ENST00000480213.1_5'Flank	NM_012437.5	NP_036569.1	O95295	SNAPN_HUMAN	SNAP-associated protein	86	Interaction with TOR1A.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|negative regulation of neuron projection development (GO:0010977)|neuron projection development (GO:0031175)|neurotransmitter secretion (GO:0007269)|positive regulation of late endosome to lysosome transport (GO:1902824)|regulation of protein binding (GO:0043393)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle fusion to presynaptic membrane (GO:0031629)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle transport (GO:0048489)|terminal button organization (GO:0072553)|viral process (GO:0016032)	BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			lung(3)	3	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TAAGAAGCTACTTAATGCCCG	0.443																																					p.L86V		.											.	SNAPIN-68	0			c.C256G						.						147	146	146					1																	153631989		2203	4300	6503	SO:0001583	missense	23557	exon3			AAGCTACTTAATG	AF086837	CCDS1049.1	1q22	2013-09-27		2007-11-14	ENSG00000143553	ENSG00000143553		"Biogenesis of lysosomal organelles complex-1 subunits"	17145	protein-coding gene	gene with protein product	"snapin", "SNAP-25-binding protein", "biogenesis of lysosomal organelles complex-1, subunit 7"	607007		SNAPAP		10195194, 12659861	Standard	NM_012437		Approved	BLOC1S7	uc001fcq.4	O95295	OTTHUMG00000037086	ENST00000368685.5:c.256C>G	1.37:g.153631989C>G	ENSP00000357674:p.Leu86Val	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	95	14	NM_012437	0	0	36	51	15	D3DV56|Q5SXU8	Missense_Mutation	SNP	ENST00000368685.5	37	CCDS1049.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734669	0.48939	.	.	ENSG00000143553	ENST00000368685	T	0.46451	0.87	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.19685	0.0473	L	0.39245	1.2	0.49582	D	0.999803	B	0.28998	0.23	B	0.20955	0.032	T	0.03364	-1.1044	10	0.15066	T	0.55	-16.4091	17.2626	0.87075	0.0:1.0:0.0:0.0	.	86	O95295	SNAPN_HUMAN	V	86	ENSP00000357674:L86V	ENSP00000357674:L86V	L	+	1	0	SNAPIN	151898613	0.999000	0.42202	0.961000	0.40146	0.986000	0.74619	4.168000	0.58216	2.941000	0.99782	0.655000	0.94253	CTT	.		0.443	SNAPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090036.1	NM_012437		G	153631989	C	G	153631989	3	3	46	1	0	0	0	0	1	0	0	0	14871	565	20	4	266	4	SNAPIN	1	153631989	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	40171712	153631989	95618632	4	4162											
NLRC4	58484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32475306	32475307	+	Missense_Mutation	DNP	GC	GC	CT																															tatggctttcagaatttcttGctcagtggtgtttttcacac																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:32475306_32475307GC>CT	ENST00000404025.2	-	5	2114_2115	c.1626_1627GC>AG	c.(1624-1629)gaGCaa>gaAGaa	p.Q543E	NLRC4_ENST00000360906.5_Missense_Mutation_p.Q543E|NLRC4_ENST00000402280.1_Missense_Mutation_p.Q543E|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	543					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					AGAATTTCTTGCTCAGTGGTGT	0.446																																					p.Q543E		.											.	NLRC4	0			c.G1626A						.																																			SO:0001583	missense	58484	exon4			TTCTTGCTCAGTG	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"Nucleotide-binding domain and leucine rich repeat containing"	16412	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4"	606831	"caspase recruitment domain family, member 12"	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1626_1627delinsCT	2.37:g.32475306_32475307delinsCT	ENSP00000385090:p.Gln543Glu	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	106	21		0	0	0	0	0	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	DNP	ENST00000404025.2	37	CCDS33174.1																																																																																			.		0.446	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		CT	32475307	GC	CT	32475306	3	2	46	1	0	0	0	0	1	0	0	0	10495	1328	46	4	1471	4	NLRC4	2	32475306	Missense_Mutation	DNP	GC	TCGA-B3-8121-01A-21D-2396-08		32475306	210724067	5	4163											
TLX2	3196	hgsc.bcm.edu	37	chr2	74742182	74742182	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ccaggcggcgtgatccgcgtCcctgcgcaccgcccgctgcc	3	5	13	20	7	0	1	0	1	0	0	2	1	2	1	6	2	2	2	6	2	0	0	rs115897631	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:74742182C>G	ENST00000233638.7	+	1	572	c.249C>G	c.(247-249)gtC>gtG	p.V83V	TLX2_ENST00000497238.1_3'UTR	NM_016170.4	NP_057254.1	O43763	TLX2_HUMAN	T-cell leukemia homeobox 2	83	Gly-rich.				enteric nervous system development (GO:0048484)|mesoderm formation (GO:0001707)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|ovary(1)	2						TGATCCGCGTCCCTGCGCACC	0.771													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		10293	0		0	False		,,,				2504	0				p.V83V	Esophageal Squamous(7;240 533 18610 24312)	.											.	TLX2-90	0			c.C249G						.	C		90,3398		0,90,1654	5	4	4		249	3.3	1	2	dbSNP_132	4	1,6837		0,1,3418	no	coding-synonymous	TLX2	NM_016170.4		0,91,5072	GG,GC,CC		0.0146,2.5803,0.8813		83/285	74742182	91,10235	1744	3419	5163	SO:0001819	synonymous_variant	3196	exon1			CCGCGTCCCTGCG	AJ002607	CCDS1947.1	2p13.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000115297	ENSG00000115297		"Homeoboxes / ANTP class : NKL subclass"	5057	protein-coding gene	gene with protein product		604240	"homeo box 11-like 1", "T-cell leukemia, homeobox 2"	HOX11L1		10343123	Standard	NM_016170		Approved	Enx, Tlx2, NCX	uc002sma.2	O43763	OTTHUMG00000129960	ENST00000233638.7:c.249C>G	2.37:g.74742182C>G		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	6	5	NM_016170	0	0	0	0	0	Q9UD56|Q9UQ48	Silent	SNP	ENST00000233638.7	37	CCDS1947.1																																																																																			C|0.992;G|0.008		0.771	TLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252224.3			G	74742182	C	G	74742182	2	3	46	1	0	0	0	0	0	0	0	1	15993	842	30	4		4	TLX2	2	74742182	Silent	SNP	C	TCGA-B3-8121-01A-21D-2396-08	42266876	74742182	168457191	6	4164											
SLC20A1	6574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	113418129	113418129	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaccatggggaaggatctGacaccgatcacaccctctag	12	6	10	13	1	3	2	1	1	2	1	3	5	3	4	3	3	0	0	3	3	2	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:113418129G>A	ENST00000272542.3	+	9	2312	c.1773G>A	c.(1771-1773)ctG>ctA	p.L591L		NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	591					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						GGAAGGATCTGACACCGATCA	0.448																																					p.L591L		.											.	SLC20A1-92	0			c.G1773A						.						114	103	107					2																	113418129		2203	4300	6503	SO:0001819	synonymous_variant	6574	exon9			GGATCTGACACCG		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.1773G>A	2.37:g.113418129G>A		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	66	16	NM_005415	0	0	12	17	5	Q08344|Q6DHX8|Q9UQ82	Silent	SNP	ENST00000272542.3	37	CCDS2099.1																																																																																			.		0.448	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		A	113418129	G	A	113418129	2	1	46	1	0	0	0	0	0	0	0	1	14470	1277	45	2		2	SLC20A1	2	113418129	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	38675947	113418129	129781244	7	4165											
HAT1	8520	hgsc.bcm.edu	37	chr2	172848182	172848182	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgaaccaaatagaaataagCatgcaacatgaacagctgga	20	6	8	7	0	0	3	0	2	0	1	0	4	0	4	1	1	6	3	1	1	7	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:172848182C>A	ENST00000264108.4	+	11	1212	c.1176C>A	c.(1174-1176)agC>agA	p.S392R	SLC25A12_ENST00000472748.1_Intron|HAT1_ENST00000392584.1_Missense_Mutation_p.S307R	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	392					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)			breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TAGAAATAAGCATGCAACATG	0.388																																					p.S392R		.											.	HAT1-290	0			c.C1176A						.						112	112	112					2																	172848182		2203	4300	6503	SO:0001583	missense	8520	exon11			AATAAGCATGCAA	AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases"	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.1176C>A	2.37:g.172848182C>A	ENSP00000264108:p.Ser392Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_003642	0	0	34	34	0	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Missense_Mutation	SNP	ENST00000264108.4	37	CCDS2245.1	.	.	.	.	.	.	.	.	.	.	C	3.309	-0.141123	0.06669	.	.	ENSG00000128708	ENST00000392584;ENST00000264108	.	.	.	5.94	3.11	0.35812	.	0.224777	0.53938	D	0.000049	T	0.40423	0.1116	L	0.38175	1.15	0.32521	N	0.536232	B	0.02656	0.0	B	0.04013	0.001	T	0.45220	-0.9276	9	0.87932	D	0	-6.6111	8.5772	0.33605	0.0:0.7345:0.127:0.1386	.	392	O14929	HAT1_HUMAN	R	307;392	.	ENSP00000264108:S392R	S	+	3	2	HAT1	172556428	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.923000	0.28757	0.370000	0.24538	0.591000	0.81541	AGC	.		0.388	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642		A	172848182	C	A	172848182	3	1	46	1	0	0	0	0	1	0	0	0	6985	709	25	4	1218	4	HAT1	2	172848182	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	59430053	172848182	70351191	8	4166											
ZNF142	7701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219510938	219510938	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgtgcacacggaggtagtgCttccacttggtgacatagcc	9	10	12	10	1	0	1	0	1	0	0	1	2	1	2	2	3	3	3	2	3	2	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:219510938C>A	ENST00000449707.1	-	7	1828	c.1407G>T	c.(1405-1407)aaG>aaT	p.K469N	ZNF142_ENST00000411696.2_Missense_Mutation_p.K469N	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	469					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(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGGTAGTGCTTCCACTTGG	0.517																																					p.K469N	Colon(170;867 1942 8995 15834 18053)	.											.	ZNF142-137	0			c.G1407T						.						226	220	222					2																	219510938		2153	4245	6398	SO:0001583	missense	7701	exon7			GTAGTGCTTCCAC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1407G>T	2.37:g.219510938C>A	ENSP00000408643:p.Lys469Asn	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	139	32	NM_001105537	0	0	0	1	1	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188772	0.78789	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.54071	0.59;0.59	5.19	5.19	0.71726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.62684	0.2448	L	0.41906	1.305	0.42919	D	0.994282	D;D	0.89917	1.0;0.999	D;D	0.85130	0.996;0.997	T	0.62978	-0.6739	10	0.54805	T	0.06	-14.9575	12.26	0.54645	0.0:0.9228:0.0:0.0772	.	469;306	P52746;A8MWU9	ZN142_HUMAN;.	N	469	ENSP00000408643:K469N;ENSP00000398798:K469N	ENSP00000398798:K469N	K	-	3	2	ZNF142	219219182	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.173000	0.50839	2.709000	0.92574	0.561000	0.74099	AAG	.		0.517	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		A	219510938	C	A	219510938	3	1	46	1	0	0	0	0	1	0	0	0	17763	796	28	4	3672	4	ZNF142	2	219510938	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	46662756	219510938	23688435	9	4167											
AP1S3	130340	hgsc.bcm.edu	37	chr2	224640715	224640715	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctattgcacagcaaaaatatAaactagcataccttgaaatg	18	10	5	8	0	0	1	0	1	0	0	0	1	0	1	1	0	5	3	1	0	9	7			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:224640715A>G	ENST00000446015.2	-	3	227	c.194T>C	c.(193-195)tTa>tCa	p.L65S	AP1S3_ENST00000409375.1_Missense_Mutation_p.L65S|AP1S3_ENST00000443700.1_Missense_Mutation_p.L65S|AP1S3_ENST00000423110.1_Missense_Mutation_p.L65S|AP1S3_ENST00000396654.2_Missense_Mutation_p.L65S|AP1S3_ENST00000396653.2_Intron			Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3 subunit	65					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane coat (GO:0030117)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			NS(1)|breast(1)|lung(2)	4		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GCAAAAATATAAACTAGCATA	0.373																																					p.L65S		.											.	AP1S3-90	0			c.T194C						.						71	63	65					2																	224640715		1873	4111	5984	SO:0001583	missense	130340	exon3			AAATATAAACTAG	AF393369	CCDS42827.1	2q36.3	2008-02-05			ENSG00000152056	ENSG00000152056			18971	protein-coding gene	gene with protein product		615781					Standard	NR_110905		Approved		uc002vnn.3	Q96PC3	OTTHUMG00000133165	ENST00000446015.2:c.194T>C	2.37:g.224640715A>G	ENSP00000388738:p.Leu65Ser	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_001039569	0	0	0	0	0	B4DQZ1|Q8WTY1|Q96DD1	Missense_Mutation	SNP	ENST00000446015.2	37		.	.	.	.	.	.	.	.	.	.	A	26.4	4.730571	0.89390	.	.	ENSG00000152056	ENST00000443700;ENST00000396654;ENST00000446015;ENST00000409375;ENST00000423110	.	.	.	6.17	6.17	0.99709	Clathrin adaptor complex, small chain (1);Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.91054	0.7185	H	0.98849	4.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94471	0.7685	9	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	65;65	Q96PC3;Q96PC3-4	AP1S3_HUMAN;.	S	65	.	ENSP00000379891:L65S	L	-	2	0	AP1S3	224348959	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.890000	0.92477	2.371000	0.80710	0.533000	0.62120	TTA	.		0.373	AP1S3-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383293.1			G	224640715	A	G	224640715	3	3	46	1	0	0	0	0	1	0	0	0	738	372	13	3	282	3	AP1S3	2	224640715	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	5129777	224640715	18558658	10	4168											
USP40	55230	hgsc.bcm.edu	37	chr2	234399860	234399860	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atcttctgagatctctatgtCtcccaagtagaggagagaaa	13	11	9	8	0	4	3	0	1	4	3	6	6	4	4	1	1	0	1	1	1	4	3			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:234399860C>G	ENST00000427112.2	-	25	2997	c.2962G>C	c.(2962-2964)Gac>Cac	p.D988H	USP40_ENST00000251722.6_Missense_Mutation_p.D988H|USP40_ENST00000450966.1_Missense_Mutation_p.D1000H|USP40_ENST00000496298.1_5'Flank			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	988					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		ATCTCTATGTCTCCCAAGTAG	0.483																																					p.D1000H		.											.	USP40-455	0			c.G2998C						.						46	46	46					2																	234399860		1900	4127	6027	SO:0001583	missense	55230	exon25			CTATGTCTCCCAA	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2962G>C	2.37:g.234399860C>G	ENSP00000387898:p.Asp988His	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_018218	0	0	27	27	0	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.69|12.69	2.014480|2.014480	0.35511|0.35511	.|.	.|.	ENSG00000085982|ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112|ENST00000430158	T;T;T|.	0.05580|.	3.42;3.42;3.42|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	2.234570|.	0.01674|.	N|.	0.025743|.	T|T	0.54481|0.54481	0.1861|0.1861	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	D;P|.	0.65815|.	0.995;0.942|.	P;P|.	0.60609|.	0.877;0.573|.	T|T	0.50423|0.50423	-0.8830|-0.8830	10|5	0.59425|.	D|.	0.04|.	.|.	10.9828|10.9828	0.47506|0.47506	0.0:0.9073:0.0:0.0927|0.0:0.9073:0.0:0.0927	.|.	1000;648|.	Q9NVE5-3;B4DN96|.	.;.|.	H|D	1000;988;988|163	ENSP00000415434:D1000H;ENSP00000251722:D988H;ENSP00000387898:D988H|.	ENSP00000251722:D988H|.	D|E	-|-	1|3	0|2	USP40|USP40	234064599|234064599	0.816000|0.816000	0.29132|0.29132	0.546000|0.546000	0.28166|0.28166	0.175000|0.175000	0.22909|0.22909	1.821000|1.821000	0.39041|0.39041	2.455000|2.455000	0.83008|0.83008	0.655000|0.655000	0.94253|0.94253	GAC|GAG	.		0.483	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		G	234399860	C	G	234399860	3	3	46	1	0	0	0	0	1	0	0	0	17105	913	32	4	773	4	USP40	2	234399860	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	9759145	234399860	8799513	11	4169											
PTH1R	5745	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	46944260	46944260	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattttttgtcgcaatcataTactgtttctgcaatggcgag	9	16	9	7	2	2	0	1	0	1	0	3	2	2	0	0	1	2	3	0	1	4	6			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr3:46944260T>C	ENST00000313049.5	+	13	1578	c.1375T>C	c.(1375-1377)Tac>Cac	p.Y459H	PTH1R_ENST00000418619.1_Missense_Mutation_p.Y459H|PTH1R_ENST00000430002.2_Missense_Mutation_p.Y459H|PTH1R_ENST00000449590.1_Missense_Mutation_p.Y459H			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	459					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	CGCAATCATATACTGTTTCTG	0.582																																					p.Y459H		.											.	PTH1R-522	0			c.T1375C						.						111	119	116					3																	46944260		2203	4300	6503	SO:0001583	missense	5745	exon14			ATCATATACTGTT		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"GPCR / Class B : Parathyroid hormone receptors"	9608	protein-coding gene	gene with protein product		168468	"parathyroid hormone receptor 1"	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.1375T>C	3.37:g.46944260T>C	ENSP00000321999:p.Tyr459His	Somatic	162	1		WXS	Illumina HiSeq	Phase_I	165	14	NM_001184744	0	0	0	0	0	Q2M1U3	Missense_Mutation	SNP	ENST00000313049.5	37	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.558192	0.86231	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049;ENST00000313063;ENST00000422115	T;T;T;T;T;T	0.75050	0.07;0.07;0.07;0.07;0.07;-0.9	4.86	4.86	0.63082	GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1);	.	.	.	.	D	0.85168	0.5635	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87180	0.2227	9	0.87932	D	0	.	13.9612	0.64180	0.0:0.0:0.0:1.0	.	459	Q03431	PTH1R_HUMAN	H	459;459;459;459;459;764;31	ENSP00000402723:Y459H;ENSP00000411424:Y459H;ENSP00000400977:Y459H;ENSP00000413774:Y459H;ENSP00000321999:Y459H;ENSP00000396176:Y31H	ENSP00000321999:Y459H	Y	+	1	0	PTH1R	46919264	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.294000	0.72738	1.941000	0.56285	0.533000	0.62120	TAC	.		0.582	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316		C	46944260	T	C	46944260	3	2	46	1	0	0	0	0	1	0	0	0	12788	1406	49	3	1425	3	PTH1R	3	46944260	Missense_Mutation	SNP	T	TCGA-B3-8121-01A-21D-2396-08		46944260	151078170	12	4170											
CCDC66	285331	hgsc.bcm.edu	37	chr3	56627106	56627106	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgaccgtcaaagaaaaataGaggaaaaaattatatattca	22	9	6	4	1	2	3	2	1	0	2	2	4	2	4	1	1	0	0	1	1	10	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr3:56627106G>C	ENST00000394672.3	+	8	1115	c.1045G>C	c.(1045-1047)Gag>Cag	p.E349Q	CCDC66_ENST00000436465.2_Missense_Mutation_p.E349Q|CCDC66_ENST00000326595.7_Missense_Mutation_p.E315Q	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	349					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		AAGAAAAATAGAGGAAAAAAT	0.303																																					p.E349Q		.											.	CCDC66-135	0			c.G1045C						.						43	48	46					3																	56627106		2197	4299	6496	SO:0001583	missense	285331	exon8			AAAATAGAGGAAA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1045G>C	3.37:g.56627106G>C	ENSP00000378167:p.Glu349Gln	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_001141947	0	0	4	4	0	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.088605	0.55968	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.24350	1.87;1.86;1.87	5.82	3.95	0.45737	.	0.207425	0.42420	D	0.000714	T	0.33933	0.0880	M	0.67953	2.075	0.80722	D	1	D	0.56521	0.976	P	0.50049	0.629	T	0.03240	-1.1057	10	0.44086	T	0.13	-7.3571	10.5988	0.45354	0.0742:0.1342:0.7916:0.0	.	349	A2RUB6	CCD66_HUMAN	Q	349;315;349	ENSP00000378167:E349Q;ENSP00000326050:E315Q;ENSP00000404320:E349Q	ENSP00000326050:E315Q	E	+	1	0	CCDC66	56602146	0.974000	0.33945	0.674000	0.29902	0.712000	0.41017	1.726000	0.38085	2.745000	0.94114	0.655000	0.94253	GAG	.		0.303	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		C	56627106	G	C	56627106	3	2	46	1	0	0	0	0	1	0	0	0	2844	943	33	4	1075	4	CCDC66	3	56627106	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	9682846	56627106	141395324	13	4171											
CCDC66	285331	hgsc.bcm.edu	37	chr3	56651517	56651517	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcagatggaattgcttcatTtggtagaaaaaaataatcct	15	12	9	5	0	1	2	1	0	0	2	2	3	2	3	1	3	1	3	1	3	6	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr3:56651517T>G	ENST00000394672.3	+	14	2291	c.2221T>G	c.(2221-2223)Ttg>Gtg	p.L741V	CCDC66_ENST00000436465.2_Missense_Mutation_p.L741V|CCDC66_ENST00000326595.7_Missense_Mutation_p.L707V	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	741					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		ATTGCTTCATTTGGTAGAAAA	0.388																																					p.L741V		.											.	CCDC66-135	0			c.T2221G						.						51	53	52					3																	56651517		2203	4299	6502	SO:0001583	missense	285331	exon14			CTTCATTTGGTAG	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.2221T>G	3.37:g.56651517T>G	ENSP00000378167:p.Leu741Val	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_001141947	0	0	1	1	0	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.474208	0.63737	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.35048	1.33;1.34;1.33	5.68	2.95	0.34219	.	0.091880	0.44688	N	0.000436	T	0.54838	0.1883	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.56517	-0.7966	10	0.72032	D	0.01	-6.3152	9.4116	0.38496	0.0:0.2208:0.0:0.7792	.	741	A2RUB6	CCD66_HUMAN	V	741;707;741	ENSP00000378167:L741V;ENSP00000326050:L707V;ENSP00000404320:L741V	ENSP00000326050:L707V	L	+	1	2	CCDC66	56626557	0.099000	0.21834	0.996000	0.52242	0.982000	0.71751	-0.033000	0.12246	0.971000	0.38288	0.460000	0.39030	TTG	.		0.388	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		G	56651517	T	G	56651517	3	3	46	1	0	0	0	0	1	0	0	0	2844	1838	64	5	2275	5	CCDC66	3	56651517	Missense_Mutation	SNP	T	TCGA-B3-8121-01A-21D-2396-08	24411	56651517	141370913	14	4172											
MINA	84864	hgsc.bcm.edu	37	chr3	97673274	97673274	+	Silent	SNP	G	G	T																															atggtcacgtgagtagagtgGgccagccccgcaggagtgtc																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr3:97673274G>T	ENST00000333396.7	-	5	1329	c.747C>A	c.(745-747)gcC>gcA	p.A249A	MINA_ENST00000394198.2_Silent_p.A249A|MINA_ENST00000360258.4_Silent_p.A249A|MINA_ENST00000330299.2_Silent_p.A249A	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						GAGTAGAGTGGGCCAGCCCCG	0.532																																					p.A249A		.											.	MINA-91	0			c.C747A						.						118	103	108					3																	97673274		2203	4300	6503	SO:0001819	synonymous_variant	84864	exon5			AGAGTGGGCCAGC	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.747C>A	3.37:g.97673274G>T		Somatic	50	1		WXS	Illumina HiSeq	Phase_I	68	8	NM_001261829	0	0	0	0	0		Silent	SNP	ENST00000333396.7	37	CCDS43114.1																																																																																			.		0.532	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778		T	97673274	G	T	97673274	2	4	46	1	0	0	0	0	0	0	0	1	9611	1219	43	4		4	MINA	3	97673274	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	41021757	97673274	100349156	15	4173	44	2									
MINA	84864	broad.mit.edu	37	chr3	97673276	97673276	+	Frame_Shift_Del	DEL	C	C	-																															ggtcacgtgagtagagtgggCcagccccgcaggagtgtccg																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr3:97673276delC	ENST00000333396.7	-	5	1327	c.745delG	c.(745-747)gccfs	p.A249fs	MINA_ENST00000394198.2_Frame_Shift_Del_p.A249fs|MINA_ENST00000360258.4_Frame_Shift_Del_p.A249fs|MINA_ENST00000330299.2_Frame_Shift_Del_p.A249fs	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						GTAGAGTGGGCCAGCCCCGCA	0.527																																					p.A249fs													.	MINA-91	0			c.745delG						.						117	102	107					3																	97673276		2203	4300	6503	SO:0001589	frameshift_variant	84864	exon5			AGTGGGCCAGCCC	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.745delG	3.37:g.97673276delC	ENSP00000328251:p.Ala249fs	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	64	8	NM_001261829	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000333396.7	37	CCDS43114.1																																																																																			.		0.527	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778		-	97673276	C	-	97673276	7	5	46	1	0	1	0	1	0	0	0	0	9611	739	26	0	676	0	MINA	3	97673276	Frame_Shift_Del	DEL	C	TCGA-B3-8121-01A-21D-2396-08	2	97673276	100349154	16	4174	44	2									
RNF13	11342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	149678840	149678840	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aatgaacatgatgtcgtggtCcagttgcagcctaatggtga	11	11	12	7	1	0	3	0	3	0	0	2	3	1	3	2	2	3	2	2	2	3	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr3:149678840C>T	ENST00000344229.3	+	11	1797	c.1095C>T	c.(1093-1095)gtC>gtT	p.V365V	RNF13_ENST00000392894.3_Silent_p.V365V|RNF13_ENST00000361785.6_Silent_p.V246V	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	365					protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ATGTCGTGGTCCAGTTGCAGC	0.358																																					p.V365V		.											.	RNF13-227	0			c.C1095T						.						104	101	102					3																	149678840		2203	4300	6503	SO:0001819	synonymous_variant	11342	exon11			CGTGGTCCAGTTG	AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"RING-type (C3HC4) zinc fingers"	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.1095C>T	3.37:g.149678840C>T		Somatic	122	1		WXS	Illumina HiSeq	Phase_I	90	19	NM_007282	0	0	51	76	25	A6NC87|B3KR12|Q05D66|Q6IBJ9	Silent	SNP	ENST00000344229.3	37	CCDS3146.1	.	.	.	.	.	.	.	.	.	.	C	3.702	-0.061365	0.07317	.	.	ENSG00000082996	ENST00000468289	.	.	.	5.83	4.94	0.65067	.	.	.	.	.	T	0.59155	0.2173	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57505	-0.7800	4	.	.	.	-22.4106	8.2513	0.31724	0.0:0.7328:0.132:0.1353	.	.	.	.	S	167	.	.	P	+	1	0	RNF13	151161530	0.987000	0.35691	1.000000	0.80357	0.648000	0.38561	0.188000	0.17018	1.419000	0.47118	0.655000	0.94253	CCA	.		0.358	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384		T	149678840	C	T	149678840	2	4	46	1	0	0	0	0	0	0	0	1	13469	842	30	2		2	RNF13	3	149678840	Silent	SNP	C	TCGA-B3-8121-01A-21D-2396-08	52005564	149678840	48343590	17	4175											
EXOC1	55763	hgsc.bcm.edu	37	chr4	56765984	56765984	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaaaaaaagaagccaaacaAaaatacacagatcaccttca	24	4	4	9	0	2	2	2	0	0	2	2	3	2	2	2	0	3	0	2	0	9	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr4:56765984A>G	ENST00000381295.2	+	17	2619	c.2271A>G	c.(2269-2271)caA>caG	p.Q757Q	EXOC1_ENST00000349598.6_Silent_p.Q742Q|EXOC1_ENST00000346134.7_Silent_p.Q757Q	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	757					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					AAGCCAAACAAAAATACACAG	0.318																																					p.Q757Q		.											.	EXOC1-950	0			c.A2271G						.						79	88	85					4																	56765984		2203	4300	6503	SO:0001819	synonymous_variant	55763	exon17			CAAACAAAAATAC	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.2271A>G	4.37:g.56765984A>G		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	50	5	NM_018261	0	0	36	36	0	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Silent	SNP	ENST00000381295.2	37	CCDS3502.1																																																																																			.		0.318	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		G	56765984	A	G	56765984	2	3	46	1	0	0	0	0	0	0	0	1	5314	11	1	3		3	EXOC1	4	56765984	Silent	SNP	A	TCGA-B3-8121-01A-21D-2396-08		56765984	134388292	18	4176											
INPP4B	8821	hgsc.bcm.edu	37	chr4	143044565	143044565	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaccacaaaccaatccagCaagctgaaaaaaaaatattg	23	5	4	9	0	0	1	0	1	0	0	1	1	1	1	3	0	4	2	3	0	10	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr4:143044565C>A	ENST00000513000.1	-	21	2330	c.1897G>T	c.(1897-1899)Gct>Tct	p.A633S	INPP4B_ENST00000508116.1_Missense_Mutation_p.A633S|INPP4B_ENST00000308502.4_Missense_Mutation_p.A633S|INPP4B_ENST00000509777.1_Missense_Mutation_p.A633S|INPP4B_ENST00000262992.4_Missense_Mutation_p.A633S	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	633					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					ACCAATCCAGCAAGCTGAAAA	0.353																																					p.A633S		.											.	INPP4B-228	0			c.G1897T						.						68	66	67					4																	143044565		2203	4300	6503	SO:0001583	missense	8821	exon21			ATCCAGCAAGCTG	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.1897G>T	4.37:g.143044565C>A	ENSP00000425487:p.Ala633Ser	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_003866	0	0	0	0	0	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.144850	0.37825	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12;1.12;1.12;1.12	6.03	5.19	0.71726	.	0.111768	0.64402	D	0.000012	T	0.22205	0.0535	N	0.05467	-0.045	0.47584	D	0.999464	B;B	0.26195	0.141;0.144	B;B	0.26614	0.034;0.071	T	0.09662	-1.0664	10	0.22706	T	0.39	.	10.3798	0.44104	0.1324:0.7999:0.0:0.0677	.	504;633	B7Z6T2;O15327	.;INP4B_HUMAN	S	633;633;633;504;633;633;448;448;633;504	ENSP00000425487:A633S;ENSP00000262992:A633S;ENSP00000308441:A633S;ENSP00000423954:A633S;ENSP00000422793:A633S;ENSP00000426207:A448S;ENSP00000427250:A633S;ENSP00000421065:A504S	ENSP00000262992:A633S	A	-	1	0	INPP4B	143264015	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	2.615000	0.46368	2.868000	0.98415	0.557000	0.71058	GCT	.		0.353	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		A	143044565	C	A	143044565	3	1	46	1	0	0	0	0	1	0	0	0	7774	710	25	4	905	4	INPP4B	4	143044565	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	86278581	143044565	48109711	19	4177											
ZDHHC11	79844	hgsc.bcm.edu;broad.mit.edu	37	chr5	837562	837562	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcttctttgcggttattaAtgagatactcaaaggtggtc	9	16	9	7	1	3	1	1	1	2	1	5	2	3	1	0	3	2	1	0	3	4	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr5:837562A>C	ENST00000283441.8	-	6	1201	c.818T>G	c.(817-819)aTt>aGt	p.I273S	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.I273S|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	273						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCGGTTATTAATGAGATACTC	0.493																																					p.I273S		.											.	ZDHHC11-92	0			c.T818G						.						174	202	192					5																	837562		2203	4300	6503	SO:0001583	missense	79844	exon6			TTATTAATGAGAT	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"Zinc fingers, DHHC-type"	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.818T>G	5.37:g.837562A>C	ENSP00000283441:p.Ile273Ser	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	109	12	NM_024786	0	0	0	0	0	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	a	9.260	1.043028	0.19748	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193	T;T;T	0.50813	1.93;1.93;0.73	1.51	-3.03	0.05429	.	.	.	.	.	T	0.30070	0.0753	N	0.17379	0.485	0.09310	N	1	P	0.39624	0.681	B	0.43052	0.406	T	0.21008	-1.0258	9	0.54805	T	0.06	-23.2267	4.2626	0.10747	0.3762:0.1778:0.4459:0.0	.	273	Q9H8X9	ZDH11_HUMAN	S	273;273;48	ENSP00000397719:I273S;ENSP00000283441:I273S;ENSP00000426873:I48S	ENSP00000283441:I273S	I	-	2	0	ZDHHC11	890562	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.756000	0.01813	-1.924000	0.01064	0.315000	0.21342	ATT	.		0.493	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786		C	837562	A	C	837562	3	2	46	1	0	0	0	0	1	0	0	0	17633	101	4	5	448	5	ZDHHC11	5	837562	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08		837562	180077698	20	4178											
ADAMTS16	170690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	5235247	5235247	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtgtgccgagcacaacagCagacgattcagagggcggca	12	4	14	11	3	1	2	1	0	0	2	1	4	1	2	1	2	4	3	1	2	1	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr5:5235247C>G	ENST00000274181.7	+	13	2109	c.1971C>G	c.(1969-1971)agC>agG	p.S657R	ADAMTS16_ENST00000513709.1_3'UTR	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	657	Cys-rich.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AGCACAACAGCAGACGATTCA	0.512																																					p.S657R		.											.	ADAMTS16-275	0			c.C1971G						.						76	80	79					5																	5235247		1950	4152	6102	SO:0001583	missense	170690	exon13			CAACAGCAGACGA	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1971C>G	5.37:g.5235247C>G	ENSP00000274181:p.Ser657Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	124	16	NM_139056	0	0	3	4	1	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.302320	0.23736	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.63580	-0.05	4.57	3.68	0.42216	.	0.198340	0.50627	D	0.000116	T	0.56702	0.2003	M	0.62016	1.91	0.80722	D	1	P;B	0.50710	0.938;0.296	B;B	0.41860	0.368;0.292	T	0.58825	-0.7568	10	0.33940	T	0.23	.	11.2853	0.49218	0.0:0.908:0.0:0.092	.	657;657	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	R	657	ENSP00000274181:S657R	ENSP00000274181:S657R	S	+	3	2	ADAMTS16	5288247	1.000000	0.71417	0.100000	0.21137	0.015000	0.08874	2.587000	0.46128	2.270000	0.75569	0.655000	0.94253	AGC	.		0.512	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		G	5235247	C	G	5235247	3	3	46	1	0	0	0	0	1	0	0	0	261	709	25	4	2021	4	ADAMTS16	5	5235247	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	4397685	5235247	175680013	21	4179											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82850838	82850838	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtttgagcatgacttccgttGgactgatggcagcacactgg	8	11	13	9	1	0	3	0	3	0	0	1	4	1	4	1	3	2	5	1	3	0	3			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr5:82850838G>A	ENST00000265077.3	+	12	10281	c.9716G>A	c.(9715-9717)tGg>tAg	p.W3239*	VCAN_ENST00000343200.5_Nonsense_Mutation_p.W2252*|VCAN_ENST00000512590.2_Nonsense_Mutation_p.W1437*|VCAN_ENST00000502527.2_Nonsense_Mutation_p.W498*|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Nonsense_Mutation_p.W1485*	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3239	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.W3239S(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GACTTCCGTTGGACTGATGGC	0.443																																					p.W3239X		.											.	VCAN-238	1	Substitution - Missense(1)	lung(1)	c.G9716A						.						236	192	207					5																	82850838		2203	4300	6503	SO:0001587	stop_gained	1462	exon12			TCCGTTGGACTGA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9716G>A	5.37:g.82850838G>A	ENSP00000265077:p.Trp3239*	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	79	13	NM_004385	0	0	170	187	17	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Nonsense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	48	13.927085	0.99770	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	.	.	.	5.81	5.81	0.92471	.	0.000000	0.56097	D	0.000028	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.089	0.97809	0.0:0.0:1.0:0.0	.	.	.	.	X	3239;2252;1485;1437;498	.	ENSP00000265077:W3239X	W	+	2	0	VCAN	82886594	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.756000	0.98918	2.752000	0.94435	0.557000	0.71058	TGG	.		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82850838	G	A	82850838	4	1	46	1	0	0	0	0	0	1	0	0	17171	1357	47	2	9758	2	VCAN	5	82850838	Nonsense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	77615591	82850838	98064422	22	4180											
HIST1H4B	8366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	26027471	26027471	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	acctttaccgcctttgccgcGaccagacatgtctaaccagc	9	9	7	16	3	1	1	0	0	1	1	1	2	1	1	6	0	4	0	6	0	2	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:26027471G>C	ENST00000377364.3	-	1	9	c.10C>G	c.(10-12)Cgc>Ggc	p.R4G		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	4					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(4)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	13						CCTTTGCCGCGACCAGACATG	0.512																																					p.R4G		.											.	HIST1H4B-70	0			c.C10G						.						49	47	47					6																	26027471		2203	4300	6503	SO:0001583	missense	8366	exon1			TGCCGCGACCAGA	X67081	CCDS4572.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124529	ENSG00000278705		"Histones / Replication-dependent"	4789	protein-coding gene	gene with protein product		602829	"H4 histone family, member I", "histone 1, H4b"	H4FI		9119399, 12408966	Standard	NM_003544		Approved	H4/I	uc003nfr.3	P62805	OTTHUMG00000014417	ENST00000377364.3:c.10C>G	6.37:g.26027471G>C	ENSP00000366581:p.Arg4Gly	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	104	16	NM_003544	0	0	0	0	0	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377364.3	37	CCDS4572.1	.	.	.	.	.	.	.	.	.	.	g	12.98	2.099423	0.37048	.	.	ENSG00000124529	ENST00000377364	.	.	.	4.56	3.6	0.41247	.	0.000000	0.47852	U	0.000206	T	0.42988	0.1227	.	.	.	0.29320	N	0.867408	.	.	.	.	.	.	T	0.30592	-0.9973	6	0.72032	D	0.01	.	13.1415	0.59438	0.0:0.0:0.7636:0.2364	.	.	.	.	G	4	.	ENSP00000366581:R4G	R	-	1	0	HIST1H4B	26135450	0.573000	0.26676	0.167000	0.22817	0.033000	0.12548	0.731000	0.26058	2.454000	0.82982	0.563000	0.77884	CGC	.		0.512	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544		C	26027471	G	C	26027471	3	2	46	1	0	0	0	0	1	0	0	0	7187	1058	37	4	305	4	HIST1H4B	6	26027471	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08		26027471	145087596	23	4181											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51924820	51924820	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatttgtctctggagccacaAagaacccactgagccgtgct	10	10	9	12	1	1	2	0	1	1	1	2	3	1	3	3	1	4	1	3	1	3	2	rs143341567		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:51924820A>C	ENST00000371117.3	-	15	1414	c.1139T>G	c.(1138-1140)tTt>tGt	p.F380C	PKHD1_ENST00000340994.4_Missense_Mutation_p.F380C|AL590391.1_ENST00000408630.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	380					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TGGAGCCACAAAGAACCCACT	0.443																																					p.F380C		.											.	PKHD1-603	0			c.T1139G						.						85	77	80					6																	51924820		2203	4300	6503	SO:0001583	missense	5314	exon15			GCCACAAAGAACC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1139T>G	6.37:g.51924820A>C	ENSP00000360158:p.Phe380Cys	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	67	18	NM_170724	0	0	1	1	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110642	0.77210	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.76968	-1.06;-1.06	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000001	D	0.85617	0.5738	M	0.78049	2.395	0.38168	D	0.939231	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.88299	0.2948	10	0.87932	D	0	.	15.0065	0.71516	1.0:0.0:0.0:0.0	.	380;380	P08F94-2;P08F94	.;PKHD1_HUMAN	C	380	ENSP00000360158:F380C;ENSP00000341097:F380C	ENSP00000341097:F380C	F	-	2	0	PKHD1	52032779	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.103000	0.71492	2.195000	0.70347	0.528000	0.53228	TTT	A|1.000;G|0.000		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51924820	A	C	51924820	3	2	46	1	0	0	0	0	1	0	0	0	11997	14	1	5	11336	5	PKHD1	6	51924820	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	25897349	51924820	119190247	24	4182											
KCNQ5	56479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	73905126	73905126	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcagcttgcctcatgtcAaactgaaataagttcttcat	11	13	5	12	0	5	1	4	1	1	0	5	1	5	1	2	0	3	2	2	0	3	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:73905126A>G	ENST00000370398.1	+	14	2897	c.2788A>G	c.(2788-2790)Aaa>Gaa	p.K930E	KCNQ5_ENST00000355194.4_Missense_Mutation_p.K930E|KCNQ5_ENST00000355635.3_Missense_Mutation_p.K931E|KCNQ5_ENST00000342056.2_Missense_Mutation_p.K949E|KCNQ5_ENST00000402622.2_Missense_Mutation_p.K940E|KCNQ5_ENST00000403813.2_Missense_Mutation_p.K921E|KCNQ5_ENST00000414165.2_Missense_Mutation_p.K820E	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	930					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GCCTCATGTCAAACTGAAATA	0.408																																					p.K949E	GBM(142;1375 1859 14391 23261 44706)	.											.	KCNQ5-158	0			c.A2845G						.						64	65	65					6																	73905126		2203	4300	6503	SO:0001583	missense	56479	exon15			CATGTCAAACTGA	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2788A>G	6.37:g.73905126A>G	ENSP00000359425:p.Lys930Glu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	112	17	NM_001160133	0	0	0	0	0	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	37	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	A	14.61	2.587561	0.46110	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D	0.99429	-5.66;-5.66;-5.66;-5.66;-5.67;-5.7;-5.89	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.98698	0.9563	N	0.24115	0.695	0.24539	N	0.994073	D;P;B;P;B	0.61697	0.99;0.792;0.017;0.525;0.435	D;B;B;B;B	0.72982	0.979;0.254;0.021;0.117;0.078	D	0.96550	0.9407	10	0.62326	D	0.03	.	16.4622	0.84064	1.0:0.0:0.0:0.0	.	820;940;949;921;930	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;.;KCNQ5_HUMAN	E	949;949;930;930;940;931;921;820	ENSP00000345055:K949E;ENSP00000347326:K930E;ENSP00000359425:K930E;ENSP00000385501:K940E;ENSP00000347853:K931E;ENSP00000384453:K921E;ENSP00000409861:K820E	ENSP00000345055:K949E	K	+	1	0	KCNQ5	73961847	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.654000	0.67974	2.289000	0.77006	0.533000	0.62120	AAA	.		0.408	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		G	73905126	A	G	73905126	3	3	46	1	0	0	0	0	1	0	0	0	8107	131	5	3	2903	3	KCNQ5	6	73905126	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	21980306	73905126	97209941	25	4183											
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461775	82461775	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccgccgaagtcgccgccGccgaagtcgccgcctagggg	5	3	15	18	9	0	0	0	0	0	0	2	2	0	0	8	2	0	0	8	2	3	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:82461775G>T	ENST00000320172.6	-	2	398	c.84C>A	c.(82-84)ggC>ggA	p.G28G	FAM46A_ENST00000369754.3_Silent_p.G47G|FAM46A_ENST00000369756.3_Silent_p.G109G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	28					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		agtcgccgccgccgaagtcgc	0.692																																					p.G28G		.											.	FAM46A-90	0			c.C84A						.						3	5	4					6																	82461775		1351	3152	4503	SO:0001819	synonymous_variant	55603	exon2			GCCGCCGCCGAAG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.84C>A	6.37:g.82461775G>T		Somatic	22	1		WXS	Illumina HiSeq	Phase_I	35	2	NM_017633	0	0	1	1	0	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	37	CCDS34489.1																																																																																			.		0.692	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			T	82461775	G	T	82461775	2	4	46	1	0	0	0	0	0	0	0	1	5584	1074	38	4		4	FAM46A	6	82461775	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	8556649	82461775	88653292	26	4184											
RARS2	57038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	88231239	88231239	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatctatagcagctgcaagAtctctgaaacaaagtggcca	14	8	9	10	1	2	2	0	1	2	1	3	3	2	2	1	1	4	3	1	1	5	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:88231239A>T	ENST00000369536.5	-	12	1023	c.978T>A	c.(976-978)gaT>gaA	p.D326E	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	326					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		CAGCTGCAAGATCTCTGAAAC	0.323																																					p.D326E		.											.	RARS2-92	0			c.T978A						.						83	83	83					6																	88231239		2203	4300	6503	SO:0001583	missense	57038	exon12			TGCAAGATCTCTG	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.978T>A	6.37:g.88231239A>T	ENSP00000358549:p.Asp326Glu	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	33	8	NM_020320	0	0	0	0	0	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219539	0.79464	.	.	ENSG00000146282	ENST00000369536	D	0.82081	-1.57	5.83	-1.0	0.10196	Arginyl-tRNA synthetase, class Ia, core (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.90335	0.6976	H	0.95712	3.71	0.58432	D	0.999996	D	0.71674	0.998	D	0.80764	0.994	D	0.90743	0.4651	10	0.87932	D	0	.	11.7636	0.51918	0.557:0.0:0.443:0.0	.	326	Q5T160	SYRM_HUMAN	E	326	ENSP00000358549:D326E	ENSP00000358549:D326E	D	-	3	2	RARS2	88287958	0.984000	0.35163	0.987000	0.45799	0.993000	0.82548	0.740000	0.26188	-0.395000	0.07715	0.533000	0.62120	GAT	.		0.323	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		T	88231239	A	T	88231239	3	4	46	1	0	0	0	0	1	0	0	0	13091	330	12	5	794	5	RARS2	6	88231239	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	5769464	88231239	82883828	27	4185											
SEC63	11231	hgsc.bcm.edu	37	chr6	108227977	108227977	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctccagccaaaaccatgatAagacctaacaaaacaaaaga	21	4	5	11	0	0	3	0	1	0	2	1	3	1	3	4	0	4	1	4	0	8	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:108227977A>G	ENST00000369002.4	-	9	917	c.738T>C	c.(736-738)ctT>ctC	p.L246L		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	246	SEC63 1.				liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		AAACCATGATAAGACCTAACA	0.348																																					p.L246L		.											.	SEC63-227	0			c.T738C						.						95	95	95					6																	108227977		2203	4300	6503	SO:0001819	synonymous_variant	11231	exon9			CATGATAAGACCT	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"Heat shock proteins / DNAJ (HSP40)"	21082	protein-coding gene	gene with protein product		608648	"SEC63-like (S. cerevisiae)"			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.738T>C	6.37:g.108227977A>G		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_007214	0	0	0	0	0	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Silent	SNP	ENST00000369002.4	37	CCDS5061.1																																																																																			.		0.348	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214		G	108227977	A	G	108227977	2	3	46	1	0	0	0	0	0	0	0	1	14037	349	13	3		3	SEC63	6	108227977	Silent	SNP	A	TCGA-B3-8121-01A-21D-2396-08	19996738	108227977	62887090	28	4186											
IGFBP1	3484	broad.mit.edu	37	chr7	45932569	45932569	+	Frame_Shift_Del	DEL	C	C	-																															gtctttgcagtgtgagacatCcatggatggagaggcgggac																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:45932569delC	ENST00000275525.3	+	4	955	c.659delC	c.(658-660)tccfs	p.S220fs	IGFBP1_ENST00000457280.1_Frame_Shift_Del_p.S218fs|IGFBP1_ENST00000468955.1_Frame_Shift_Del_p.S177fs	NM_000596.2	NP_000587.1	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	220	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)|tissue regeneration (GO:0042246)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	insulin-like growth factor binding (GO:0005520)			large_intestine(2)|lung(4)	6						TGTGAGACATCCATGGATGGA	0.547																																					p.S220fs													.	IGFBP1-946	0			c.659delC						.						84	79	81					7																	45932569		2203	4300	6503	SO:0001589	frameshift_variant	3484	exon4			AGACATCCATGGA		CCDS5504.1	7p12.3	2014-09-16			ENSG00000146678	ENSG00000146678			5469	protein-coding gene	gene with protein product	"placental protein 12", "amniotic fluid binding protein", "alpha-pregnancy-associated endometrial globulin", "growth hormone independent-binding protein", "binding protein-28", "binding protein-26", "binding protein-25", "IGF-binding protein 1"	146730		IBP1		2461294	Standard	NM_000596		Approved	IGF-BP25, AFBP, hIGFBP-1, PP12	uc003tnp.3	P08833	OTTHUMG00000152343	ENST00000275525.3:c.659delC	7.37:g.45932569delC	ENSP00000275525:p.Ser220fs	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	115	9	NM_000596	0	0	0	0	0	A4D2F4|D3DVL9|Q8IYP5	Frame_Shift_Del	DEL	ENST00000275525.3	37	CCDS5504.1																																																																																			.		0.547	IGFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251355.2	NM_000596		-	45932569	C	-	45932569	7	5	46	1	0	1	0	1	0	0	0	0	7599	855	30	0	673	0	IGFBP1	7	45932569	Frame_Shift_Del	DEL	C	TCGA-B3-8121-01A-21D-2396-08		45932569	113206094	29	4187											
CYP51A1	1595	broad.mit.edu;bcgsc.ca	37	chr7	91753101	91753107	+	Frame_Shift_Del	DEL	CTGTCTG	CTGTCTG	-																															tcatcaattttttcttgagaCtgtctgcgtttctggattgc																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	CTGTCTG	CTGTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:91753101_91753107delCTGTCTG	ENST00000003100.8	-	6	996_1002	c.831_837delCAGACAG	c.(829-837)cgcagacagfs	p.RRQ277fs	LRRD1_ENST00000422722.1_5'UTR|CYP51A1_ENST00000450723.1_Frame_Shift_Del_p.RRQ172fs	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	271					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	TTTCTTGAGACTGTCTGCGTTTCTGGA	0.338																																					p.277_279del	GBM(70;1100 1190 11592 25836 51397)												.	CYP51A1-90	0			c.831_837del						.																																			SO:0001589	frameshift_variant	1595	exon6			TTGAGACTGTCTG	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"Cytochrome P450s"	2649	protein-coding gene	gene with protein product		601637	"cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.831_837delCAGACAG	7.37:g.91753101_91753107delCTGTCTG	ENSP00000003100:p.Arg277fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	35	9	NM_000786	0	0	0	0	0	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Frame_Shift_Del	DEL	ENST00000003100.8	37	CCDS5623.1																																																																																			.		0.338	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4			-	91753107	CTGTCTG	-	91753101	7	5	46	1	0	1	0	1	0	0	0	0	4201	564	20	0	712	0	CYP51A1	7	91753101	Frame_Shift_Del	DEL	CTGTCTG	TCGA-B3-8121-01A-21D-2396-08	45820532	91753101	67385562	30	4188	45	2									
CYP51A1	1595	bcgsc.ca	37	chr7	91753108	91753108	+	Missense_Mutation	SNP	C	C	A																															ttttttcttgagactgtctgCgtttctggattgccttatag																								rs140702410		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:91753108C>A	ENST00000003100.8	-	6	995	c.830G>T	c.(829-831)cGc>cTc	p.R277L	LRRD1_ENST00000422722.1_5'UTR|CYP51A1_ENST00000450723.1_Missense_Mutation_p.R172L	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	271					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	AGACTGTCTGCGTTTCTGGAT	0.338													C|||	1	0.000199681	0	0	5008	,	,		18889	0.001		0	False		,,,				2504	0				p.R277L	GBM(70;1100 1190 11592 25836 51397)												.	CYP51A1-90	0			c.G830T						.						114	109	111					7																	91753108		2203	4299	6502	SO:0001583	missense	1595	exon6			TGTCTGCGTTTCT	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"Cytochrome P450s"	2649	protein-coding gene	gene with protein product		601637	"cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.830G>T	7.37:g.91753108C>A	ENSP00000003100:p.Arg277Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_1	33	9	NM_000786	0	0	5	5	0	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Missense_Mutation	SNP	ENST00000003100.8	37	CCDS5623.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	36	5.825382	0.96996	.	.	ENSG00000001630	ENST00000003100;ENST00000496998;ENST00000450723	D;D	0.87571	-2.27;-2.27	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.95389	0.8503	M	0.93763	3.455	0.80722	D	1	D;D	0.76494	0.996;0.999	P;D	0.68621	0.904;0.959	D	0.95988	0.8983	10	0.87932	D	0	.	19.8632	0.96793	0.0:1.0:0.0:0.0	.	217;271	B3KRC6;Q16850	.;CP51A_HUMAN	L	277;217;172	ENSP00000003100:R277L;ENSP00000406757:R172L	ENSP00000003100:R277L	R	-	2	0	CYP51A1	91591044	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.906000	0.69900	2.699000	0.92147	0.655000	0.94253	CGC	C|0.999;A|0.000		0.338	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4			A	91753108	C	A	91753108	3	1	46	1	0	0	0	0	1	0	0	0	4201	768	27	4	719	4	CYP51A1	7	91753108	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	7	91753108	67385555	31	4189	45	2									
C7orf47	221908	hgsc.bcm.edu	37	chr7	100033305	100033305	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggagagccaatttctccctGagcgcggcattcagaacctg	10	8	11	12	2	2	3	1	1	1	2	3	4	2	3	3	2	3	1	3	2	2	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:100033305G>C	ENST00000292330.2	-	3	727	c.537C>G	c.(535-537)ctC>ctG	p.L179L	RP11-758P17.3_ENST00000475250.1_RNA|PPP1R35_ENST00000476185.1_Intron|RP11-758P17.2_ENST00000492523.1_RNA	NM_145030.2	NP_659467.1	Q8TAP8	PPR35_HUMAN	protein phosphatase 1, regulatory subunit 35	179					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										ATTTCTCCCTGAGCGCGGCAT	0.667																																					p.L179L		.											.	.	0			c.C537G						.						22	24	23					7																	100033305		2203	4298	6501	SO:0001819	synonymous_variant	221908	exon3			CTCCCTGAGCGCG	BC026269	CCDS5694.1	7q22.1	2012-04-17	2011-10-11	2011-10-11	ENSG00000160813	ENSG00000160813		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	28320	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 47"	C7orf47		12477932	Standard	NM_145030		Approved	MGC22793	uc003uuy.1	Q8TAP8	OTTHUMG00000159540	ENST00000292330.2:c.537C>G	7.37:g.100033305G>C		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_145030	0	0	15	15	0	A4D2C5	Silent	SNP	ENST00000292330.2	37	CCDS5694.1																																																																																			.		0.667	PPP1R35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356095.2	NM_145030		C	100033305	G	C	100033305	2	2	46	1	0	0	0	0	0	0	0	1	2403	1277	45	4		4	C7orf47	7	100033305	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	8280197	100033305	59105358	32	4190											
TRIP6	7205	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	100465513	100465514	+	Frame_Shift_Ins	INS	-	-	C																															caccccagggtcaatttttgINScccccttccatctgagcagt																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:100465513_100465514insC	ENST00000200457.4	+	2	500_501	c.140_141insC	c.(139-144)tgccccfs	p.CP47fs		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	47					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					GTCAATTTTTGCCCCCTTCCAT	0.624																																					p.C47fs		.											.	TRIP6-514	0			c.140_141insC						.																																			SO:0001589	frameshift_variant	7205	exon2			.	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.145dupC	7.37:g.100465518_100465518dupC	ENSP00000200457:p.Cys47fs	Somatic	265	0		WXS	Illumina HiSeq	Phase_I	335	81	NM_003302	0	0	0	0	0	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Frame_Shift_Ins	INS	ENST00000200457.4	37	CCDS5708.1																																																																																			.		0.624	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		C	100465514	-	C	100465513	7	5	46	1	0	1	1	0	0	0	0	0	16592	1319	46	0	146	0	TRIP6	7	100465513	Frame_Shift_Ins	INS	-	TCGA-B3-8121-01A-21D-2396-08	432208	100465513	58673150	33	4191											
MTBP	27085	hgsc.bcm.edu	37	chr8	121528430	121528430	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgcctttatcccagaaaaAggtgatatattacatgcaca	15	12	6	8	0	0	2	0	1	0	1	1	2	1	2	2	1	3	1	2	1	6	6			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr8:121528430A>G	ENST00000305949.1	+	18	2290	c.2245A>G	c.(2245-2247)Aga>Gga	p.R749G		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	749	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TCCCAGAAAAAGGTGATATAT	0.313																																					p.R749G		.											.	MTBP-228	0			c.A2245G						.						28	28	28					8																	121528430		2202	4299	6501	SO:0001630	splice_region_variant	27085	exon18			AGAAAAAGGTGAT		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.2246+1A>G	8.37:g.121528430A>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_022045	0	0	0	0	0	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	37	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313636	0.81358	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.78953	0.4365	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81066	-0.1101	9	0.87932	D	0	-29.3945	16.4534	0.84003	1.0:0.0:0.0:0.0	.	749	Q96DY7	MTBP_HUMAN	G	749	.	ENSP00000303398:R749G	R	+	1	2	MTBP	121597611	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	8.045000	0.89436	2.285000	0.76669	0.477000	0.44152	AGA	.		0.313	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	Missense_Mutation	G	121528430	A	G	121528430	5	3	46	1	0	0	0	0	0	0	1	0	9937	86	3	3	2315	3	MTBP	8	121528430	Splice_Site	SNP	A	TCGA-B3-8121-01A-21D-2396-08		121528430	24835592	34	4192											
CEP78	84131	broad.mit.edu	37	chr9	80866948	80866948	+	Frame_Shift_Del	DEL	A	A	-																															tggcgtactgcagaacgtgcAaaaagacacaggtagggtat																								rs138501486		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr9:80866948delA	ENST00000424347.2	+	9	1483	c.1194delA	c.(1192-1194)gcafs	p.A398fs	CEP78_ENST00000277082.5_Frame_Shift_Del_p.A398fs|CEP78_ENST00000376598.2_Frame_Shift_Del_p.A398fs|CEP78_ENST00000376597.4_Frame_Shift_Del_p.A399fs|CEP78_ENST00000415759.2_Frame_Shift_Del_p.A399fs			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	398					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						CAGAACGTGCAAAAAGACACA	0.418																																					p.A399fs													.	CEP78-69	0			c.1197delA						.						33	32	33					9																	80866948		1842	4087	5929	SO:0001589	frameshift_variant	84131	exon9			ACGTGCAAAAAGA	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 81"	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.1194delA	9.37:g.80866948delA	ENSP00000411284:p.Ala398fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	29	7	NM_001098802	0	0	0	0	0	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Frame_Shift_Del	DEL	ENST00000424347.2	37																																																																																				.		0.418	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991		-	80866948	A	-	80866948	7	5	46	1	0	1	0	1	0	0	0	0	3268	117	5	0	1231	0	CEP78	9	80866948	Frame_Shift_Del	DEL	A	TCGA-B3-8121-01A-21D-2396-08		80866948	60346483	35	4193											
EGFL7	51162	hgsc.bcm.edu	37	chr9	139566442	139566442	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcactggagcatgggctccCggaccccggcagcctcctgg	5	5	15	16	2	0	0	0	0	0	0	2	2	2	2	5	6	2	4	5	6	0	0	rs200483435		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr9:139566442C>T	ENST00000371699.1	+	9	1612	c.701C>T	c.(700-702)cCg>cTg	p.P234L	EGFL7_ENST00000406555.3_Missense_Mutation_p.P234L|EGFL7_ENST00000371698.3_Missense_Mutation_p.P234L|EGFL7_ENST00000308874.7_Missense_Mutation_p.P234L|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000492002.1_3'UTR			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	234					angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CATGGGCTCCCGGACCCCGGC	0.682											OREG0019619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	1	0.000199681	0	0	5008	,	,		14601	0.001		0	False		,,,				2504	0				p.P234L		.											.	EGFL7-523	0			c.C701T						.	C	LEU/PRO,LEU/PRO	5,3897		0,5,1946	7	8	8		701,701	2.1	0.2	9		8	2,7586		0,2,3792	no	missense,missense	EGFL7	NM_016215.4,NM_201446.2	98,98	0,7,5738	TT,TC,CC		0.0264,0.1281,0.0609	benign,benign	234/274,234/274	139566442	7,11483	1951	3794	5745	SO:0001583	missense	51162	exon10			GGCTCCCGGACCC	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.701C>T	9.37:g.139566442C>T	ENSP00000360764:p.Pro234Leu	Somatic	2	0	1649	WXS	Illumina HiSeq	Phase_I	5	2	NM_016215	0	0	4	9	5	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	37	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.357701	0.24598	0.001281	2.64E-4	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	4.15	2.14	0.27477	.	0.785119	0.11711	N	0.536941	T	0.77805	0.4185	L	0.53249	1.67	0.09310	N	1	P	0.39094	0.659	B	0.22386	0.039	T	0.63148	-0.6702	10	0.59425	D	0.04	-10.7703	10.945	0.47296	0.4098:0.5902:0.0:0.0	.	234	Q9UHF1	EGFL7_HUMAN	L	234	ENSP00000360764:P234L;ENSP00000307843:P234L;ENSP00000385639:P234L;ENSP00000360763:P234L	ENSP00000307843:P234L	P	+	2	0	EGFL7	138686263	0.693000	0.27728	0.150000	0.22450	0.048000	0.14542	1.407000	0.34657	0.138000	0.18790	0.561000	0.74099	CCG	.		0.682	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		T	139566442	C	T	139566442	3	4	46	1	0	0	0	0	1	0	0	0	4975	652	23	1	727	1	EGFL7	9	139566442	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	58699494	139566442	1646989	36	4194											
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49365382	49365382	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcagaaaatatctgtcgAaagtctggttagaggagatg	13	11	12	5	1	3	3	1	0	2	3	4	5	3	3	0	2	1	2	0	2	5	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr10:49365382A>G	ENST00000374201.3	-	29	4215	c.3913T>C	c.(3913-3915)Tcg>Ccg	p.S1305P	FRMPD2_ENST00000463706.1_5'Flank|RP11-13E1.5_ENST00000429307.1_RNA|FRMPD2_ENST00000305531.3_Missense_Mutation_p.S1280P|FRMPD2_ENST00000474573.1_Missense_Mutation_p.S257P|FRMPD2_ENST00000407470.4_Missense_Mutation_p.S1273P	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	1305					tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		ATATCTGTCGAAAGTCTGGTT	0.433																																					p.S1305P		.											.	FRMPD2-153	0			c.T3913C						.						1	1	1					10																	49365382		249	629	878	SO:0001583	missense	143162	exon29			CTGTCGAAAGTCT	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"PDZ domain containing 5C"	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.3913T>C	10.37:g.49365382A>G	ENSP00000363317:p.Ser1305Pro	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	180	23	NM_001018071	0	0	0	1	1	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.780390	0.31502	.	.	ENSG00000170324	ENST00000474573;ENST00000374201;ENST00000305531;ENST00000407470	T;T;T;T	0.67345	3.3;-0.23;-0.26;-0.26	4.25	-3.06	0.05379	.	.	.	.	.	T	0.46678	0.1405	N	0.24115	0.695	0.09310	N	1	B;B;B;P	0.40476	0.002;0.001;0.002;0.718	B;B;B;B	0.41036	0.004;0.002;0.004;0.346	T	0.41538	-0.9503	9	0.72032	D	0.01	.	2.4491	0.04514	0.1971:0.3749:0.3097:0.1183	.	1280;1305;1273;316	Q68DX3-2;Q68DX3;F8WCT2;Q68DX3-4	.;FRPD2_HUMAN;.;.	P	257;1305;1280;1273	ENSP00000422446:S257P;ENSP00000363317:S1305P;ENSP00000307079:S1280P;ENSP00000384339:S1273P	ENSP00000307079:S1280P	S	-	1	0	FRMPD2	49035388	0.021000	0.18746	0.000000	0.03702	0.873000	0.50193	-0.185000	0.09684	-0.595000	0.05828	0.529000	0.55759	TCG	.		0.433	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		G	49365382	A	G	49365382	3	3	46	1	0	0	0	0	1	0	0	0	6077	246	9	3	20	3	FRMPD2	10	49365382	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08		49365382	86169365	37	4195											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50532033	50532033	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctaaacggataccaagagaaGgagcccagtgaatgtcagtc	15	6	11	9	1	1	2	1	1	0	1	2	5	1	4	2	2	3	0	2	2	6	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr10:50532033G>A	ENST00000374144.3	+	3	1731	c.1443G>A	c.(1441-1443)aaG>aaA	p.K481K	C10orf71_ENST00000323868.4_Silent_p.K481K			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	481										endometrium(1)	1						ACCAAGAGAAGGAGCCCAGTG	0.562																																					p.K481K		.											.	C10orf71-90	0			c.G1443A						.						32	35	34					10																	50532033		2071	4207	6278	SO:0001819	synonymous_variant	118461	exon3			AGAGAAGGAGCCC	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1443G>A	10.37:g.50532033G>A		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_001135196	0	0	0	0	0	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			.		0.562	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		A	50532033	G	A	50532033	2	1	46	1	0	0	0	0	0	0	0	1	1618	991	35	2		2	C10orf71	10	50532033	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	1166651	50532033	85002714	38	4196											
CCAR1	55749	hgsc.bcm.edu	37	chr10	70547739	70547739	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcttgcttttaccggaaatTaacagacacctcaaaagatg	15	11	6	9	1	2	2	1	0	1	2	2	3	2	3	2	1	3	1	2	1	5	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr10:70547739T>G	ENST00000265872.6	+	22	3055	c.2936T>G	c.(2935-2937)tTa>tGa	p.L979*	CCAR1_ENST00000535016.1_Nonsense_Mutation_p.L964*|CCAR1_ENST00000543719.1_Nonsense_Mutation_p.L964*	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	979					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TACCGGAAATTAACAGACACC	0.333																																					p.L979X		.											.	CCAR1-159	0			c.T2936G						.						74	77	76					10																	70547739		2203	4300	6503	SO:0001587	stop_gained	55749	exon22			GGAAATTAACAGA	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.2936T>G	10.37:g.70547739T>G	ENSP00000265872:p.Leu979*	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_018237	0	0	50	50	0	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Nonsense_Mutation	SNP	ENST00000265872.6	37	CCDS7282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	41|41	8.925078|8.925078	0.99004|0.99004	.|.	.|.	ENSG00000060339|ENSG00000060339	ENST00000543706|ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	T|.	0.37652|.	0.1011|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35151|.	-0.9800|.	3|.	.|0.02654	.|T	.|1	-7.0371|-7.0371	15.4296|15.4296	0.75081|0.75081	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	M|X	268|979;964;964;964	.|.	.|ENSP00000265872:L979X	I|L	+|+	3|2	3|0	CCAR1|CCAR1	70217745|70217745	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.668000|7.668000	0.83897|0.83897	2.035000|2.035000	0.60131|0.60131	0.460000|0.460000	0.39030|0.39030	ATT|TTA	.		0.333	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		G	70547739	T	G	70547739	4	3	46	1	0	0	0	0	0	1	0	0	2736	1764	61	5	3018	5	CCAR1	10	70547739	Nonsense_Mutation	SNP	T	TCGA-B3-8121-01A-21D-2396-08	20015706	70547739	64987008	39	4197											
PAPSS2	9060	bcgsc.ca	37	chr10	89474790	89474790	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atatccacgaactctttgtgCcggaaaacaaacttgaccac	14	9	6	12	2	1	1	0	1	1	0	2	3	2	2	3	1	4	0	3	1	5	3			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr10:89474790C>T	ENST00000361175.4	+	6	1057	c.688C>T	c.(688-690)Ccg>Tcg	p.P230S	PAPSS2_ENST00000456849.1_Missense_Mutation_p.P230S|PAPSS2_ENST00000427144.2_Missense_Mutation_p.P234S	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	230					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		ACTCTTTGTGCCGGAAAACAA	0.383																																					p.P230S													.	PAPSS2-493	0			c.C688T						.						85	79	81					10																	89474790		2203	4300	6503	SO:0001583	missense	9060	exon6			TTTGTGCCGGAAA	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.688C>T	10.37:g.89474790C>T	ENSP00000354436:p.Pro230Ser	Somatic	81	0		WXS	Illumina HiSeq	Phase_1	70	5	NM_001015880	0	0	26	26	0	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	37	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.626170	0.28978	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.21543	2.0;2.0;2.0	6.06	6.06	0.98353	Sulphate adenylyltransferase (1);PUA-like domain (1);	0.147545	0.64402	D	0.000008	T	0.27559	0.0677	L	0.56396	1.775	0.51767	D	0.999933	B;B	0.15141	0.005;0.012	B;B	0.16722	0.011;0.016	T	0.02450	-1.1157	10	0.31617	T	0.26	-14.4668	20.6208	0.99490	0.0:1.0:0.0:0.0	.	230;230	O95340;O95340-2	PAPS2_HUMAN;.	S	230;230;234;229	ENSP00000354436:P230S;ENSP00000406157:P230S;ENSP00000397123:P234S	ENSP00000354436:P230S	P	+	1	0	PAPSS2	89464770	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	2.986000	0.49370	2.882000	0.98803	0.655000	0.94253	CCG	.		0.383	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			T	89474790	C	T	89474790	3	4	46	1	0	0	0	0	1	0	0	0	11461	739	26	2	710	2	PAPSS2	10	89474790	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	18927051	89474790	46059957	40	4198											
HELLS	3070	hgsc.bcm.edu	37	chr10	96356840	96356840	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attagtgataaagatctagaGttgttgttagatcgaagtga	14	14	11	2	1	1	5	0	2	1	3	2	6	1	5	0	0	0	3	0	0	6	6			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr10:96356840G>T	ENST00000348459.5	+	21	2499	c.2394G>T	c.(2392-2394)gaG>gaT	p.E798D	RP11-119K6.6_ENST00000432120.1_RNA|HELLS_ENST00000394036.1_3'UTR|HELLS_ENST00000394045.1_Missense_Mutation_p.E700D|HELLS_ENST00000371332.4_Missense_Mutation_p.E844D|HELLS_ENST00000239026.6_3'UTR	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		AAGATCTAGAGTTGTTGTTAG	0.294																																					p.E798D		.											.	HELLS-92	0			c.G2394T						.						139	137	138					10																	96356840		2203	4299	6502	SO:0001583	missense	3070	exon21			TCTAGAGTTGTTG	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.2394G>T	10.37:g.96356840G>T	ENSP00000239027:p.Glu798Asp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_018063	0	0	0	0	0		Missense_Mutation	SNP	ENST00000348459.5	37	CCDS7434.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.083952	0.36758	.	.	ENSG00000119969	ENST00000348459;ENST00000394045;ENST00000371332;ENST00000371327	D;D;D;D	0.89343	-2.35;-1.98;-2.5;-1.65	6.02	-3.23	0.05109	.	0.203022	0.51477	D	0.000090	T	0.73329	0.3573	N	0.12182	0.205	0.80722	D	1	B;B;B;B;B	0.31241	0.012;0.011;0.041;0.2;0.315	B;B;B;B;B	0.24155	0.023;0.013;0.032;0.051;0.029	T	0.57195	-0.7853	10	0.27785	T	0.31	-16.0318	13.003	0.58687	0.5469:0.0:0.4531:0.0	.	782;769;668;700;798	Q9NRZ9-2;Q6I7N8;Q9NRZ9-6;Q9NRZ9-5;Q9NRZ9	.;.;.;.;HELLS_HUMAN	D	798;700;844;235	ENSP00000239027:E798D;ENSP00000377609:E700D;ENSP00000360383:E844D;ENSP00000360378:E235D	ENSP00000239027:E798D	E	+	3	2	HELLS	96346830	0.794000	0.28838	0.958000	0.39756	0.963000	0.63663	-0.100000	0.10990	-0.481000	0.06792	-0.982000	0.02568	GAG	.		0.294	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		T	96356840	G	T	96356840	3	4	46	1	0	0	0	0	1	0	0	0	7067	1020	36	4	2476	4	HELLS	10	96356840	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	6882050	96356840	39177907	41	4199											
CAPRIN2	65981	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	30888129	30888129	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttctctgggccttcttttgCgcttttagtagctgttaaaa	6	18	8	9	1	2	0	0	0	2	0	3	0	2	0	1	1	2	4	1	1	4	8	rs145888176		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:30888129C>T	ENST00000395805.2	-	4	1129	c.582G>A	c.(580-582)gcG>gcA	p.A194A	CAPRIN2_ENST00000538387.1_5'Flank|CAPRIN2_ENST00000417045.1_Silent_p.A194A|CAPRIN2_ENST00000298892.5_Silent_p.A194A|CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000251071.5_Silent_p.A194A	NM_001206856.1	NP_001193785.1			caprin family member 2									p.A194A(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					CCTTCTTTTGCGCTTTTAGTA	0.378																																					p.A194A		.											.	CAPRIN2-92	1	Substitution - coding silent(1)	lung(1)	c.G582A						.	C	,,,	0,4406		0,0,2203	127	123	125		582,582,582,582	-5.3	1	12	dbSNP_134	125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAPRIN2	NM_001002259.1,NM_001206856.1,NM_023925.3,NM_032156.3	,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,	194/1128,194/906,194/1078,194/961	30888129	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65981	exon4			CTTTTGCGCTTTT	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.582G>A	12.37:g.30888129C>T		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	91	5	NM_023925	0	0	0	0	0		Silent	SNP	ENST00000395805.2	37	CCDS55816.1																																																																																			C|1.000;T|0.000		0.378	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		T	30888129	C	T	30888129	2	4	46	1	0	0	0	0	0	0	0	1	2642	755	27	1		1	CAPRIN2	12	30888129	Silent	SNP	C	TCGA-B3-8121-01A-21D-2396-08		30888129	102963766	42	4200											
EEA1	8411	hgsc.bcm.edu	37	chr12	93196321	93196322	+	Missense_Mutation	DNP	TT	TT	AG																															gcttctttctccattttcacTttttgtagttctgttactgt																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:93196321_93196322TT>AG	ENST00000322349.8	-	19	2792_2793	c.2528_2529AA>CT	c.(2527-2529)aAA>aCT	p.K843T		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	843					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						CCATTTTCACTTTTTGTAGTTC	0.297																																					p.K843T		.											.	EEA1	0			c.A2528C						.																																			SO:0001583	missense	8411	exon19			TTCACTTTTTGTA	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"Zinc fingers, FYVE domain containing"	3185	protein-coding gene	gene with protein product		605070	"early endosome antigen 1, 162kD"			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.2528_2529delinsAG	12.37:g.93196321_93196322delinsAG	ENSP00000317955:p.Lys843Thr	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	16	2		0	0	0	0	0	Q14221	Missense_Mutation	DNP	ENST00000322349.8	37	CCDS31874.1																																																																																			.		0.297	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		AG	93196322	TT	AG	93196321	3	1	46	1	0	0	0	0	1	0	0	0	4932	1606	56	5	1750	5	EEA1	12	93196321	Missense_Mutation	DNP	TT	TCGA-B3-8121-01A-21D-2396-08	62308192	93196321	40655574	43	4201											
GIT2	9815	broad.mit.edu;bcgsc.ca	37	chr12	110385121	110385127	+	Frame_Shift_Del	DEL	TGGGAGA	TGGGAGA	-																															gggcggctcgcttctcccatTgggagatatggtttctgacc																								rs185965842	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	TGGGAGA	TGGGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:110385121_110385127delTGGGAGA	ENST00000355312.3	-	15	1574_1580	c.1575_1581delTCTCCCA	c.(1573-1581)tatctcccafs	p.YLP525fs	GIT2_ENST00000361006.5_Frame_Shift_Del_p.YLP525fs|GIT2_ENST00000338373.5_Intron|GIT2_ENST00000356259.4_Intron|GIT2_ENST00000360185.4_Frame_Shift_Del_p.YLP475fs|GIT2_ENST00000551209.1_Frame_Shift_Del_p.YLP474fs|GIT2_ENST00000547815.1_3'UTR|GIT2_ENST00000354574.4_Frame_Shift_Del_p.YLP477fs|GIT2_ENST00000457474.2_Frame_Shift_Del_p.YLP477fs|GIT2_ENST00000343646.5_Frame_Shift_Del_p.YLP445fs|GIT2_ENST00000553118.1_Intron|TCHP_ENST00000550780.1_Intron	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	525					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.L526I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						CTTCTCCCATTGGGAGATATGGTTTCT	0.57																																					p.525_527del													.	GIT2-226	1	Substitution - Missense(1)	large_intestine(1)	c.1575_1581del						.																																			SO:0001589	frameshift_variant	9815	exon15			TCCCATTGGGAGA	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1575_1581delTCTCCCA	12.37:g.110385121_110385127delTGGGAGA	ENSP00000347464:p.Tyr525fs	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	107	13	NM_001135214	0	0	0	0	0	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Frame_Shift_Del	DEL	ENST00000355312.3	37	CCDS9138.1																																																																																			.		0.57	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		-	110385127	TGGGAGA	-	110385121	7	5	46	1	0	1	0	1	0	0	0	0	6417	1799	63	0	722	0	GIT2	12	110385121	Frame_Shift_Del	DEL	TGGGAGA	TCGA-B3-8121-01A-21D-2396-08	17188800	110385121	23466774	44	4202											
RAN	5901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	131359114	131359114	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtgtgccatcataatgtttGatgtaacatcgagagttact	12	14	9	6	1	1	2	1	1	0	1	2	3	1	2	1	0	3	3	1	0	3	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:131359114G>A	ENST00000543796.1	+	5	529	c.271G>A	c.(271-273)Gat>Aat	p.D91N	RAN_ENST00000541630.1_Missense_Mutation_p.D3N|RAN_ENST00000254675.3_Missense_Mutation_p.D3N|RAN_ENST00000392367.3_Missense_Mutation_p.D108N|RAN_ENST00000392369.2_Missense_Mutation_p.D91N			P62826	RAN_HUMAN	RAN, member RAS oncogene family	91					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		CATAATGTTTGATGTAACATC	0.413																																					p.D91N		.											.	RAN-847	0			c.G271A						.						122	103	109					12																	131359114		2203	4300	6503	SO:0001583	missense	5901	exon5			ATGTTTGATGTAA	M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341			9846	protein-coding gene	gene with protein product		601179				8421051	Standard	XM_005253592		Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.271G>A	12.37:g.131359114G>A	ENSP00000446215:p.Asp91Asn	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	50	9	NM_006325	0	0	95	140	45	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	37	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769269	0.90020	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000541630;ENST00000392369;ENST00000254675;ENST00000535090;ENST00000392367	D;D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	3.93	3.93	0.45458	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95465	0.8527	H	0.96720	3.87	0.80722	D	1	D;D	0.55800	0.973;0.973	D;D	0.68192	0.956;0.956	D	0.97181	0.9851	10	0.87932	D	0	-17.8637	15.3182	0.74099	0.0:0.0:1.0:0.0	.	91;91	A8K3Z8;P62826	.;RAN_HUMAN	N	91;109;3;91;3;87;108	ENSP00000446215:D91N;ENSP00000396127:D109N;ENSP00000441210:D3N;ENSP00000376176:D91N;ENSP00000254675:D3N;ENSP00000444042:D87N;ENSP00000376174:D108N	ENSP00000254675:D3N	D	+	1	0	RAN	129925067	1.000000	0.71417	0.974000	0.42286	0.827000	0.46813	9.335000	0.96500	1.906000	0.55180	0.561000	0.74099	GAT	.		0.413	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		A	131359114	G	A	131359114	3	1	46	1	0	0	0	0	1	0	0	0	13056	1290	45	2	285	2	RAN	12	131359114	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	20973993	131359114	2492781	45	4203											
EP400	57634	hgsc.bcm.edu	37	chr12	132547147	132547147	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcagcagcaacagcagcaGcagcaacagacgacgacgac	16	0	11	14	3	0	1	0	0	0	1	0	4	0	1	0	0	9	7	0	0	2	0			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:132547147G>A	ENST00000333577.4	+	48	8452	c.8343G>A	c.(8341-8343)caG>caA	p.Q2781Q	EP400_ENST00000330386.6_Silent_p.Q2664Q|EP400_ENST00000389561.2_Silent_p.Q2745Q|EP400_ENST00000332482.4_Silent_p.Q2708Q|EP400_ENST00000389562.2_Silent_p.Q2744Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2781	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		aacagcagcagcagcaacagA	0.612																																					p.Q2745Q		.											.	EP400-520	0			c.G8235A						.						61	48	52					12																	132547147		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8343G>A	12.37:g.132547147G>A		Somatic	90	1		WXS	Illumina HiSeq	Phase_I	132	7	NM_015409	0	0	9	9	0	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.		0.612	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547147	G	A	132547147	2	1	46	1	0	0	0	0	0	0	0	1	5162	962	34	2		2	EP400	12	132547147	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	1188033	132547147	1304748	46	4204											
PCNX	22990	broad.mit.edu	37	chr14	71476434	71476434	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagcaagaagagcatccAatatctggtatgtgtgaagt	14	9	11	7	0	1	3	0	1	1	2	2	3	2	3	1	1	3	4	1	1	6	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr14:71476434A>G	ENST00000304743.2	+	9	3159	c.2713A>G	c.(2713-2715)Aat>Gat	p.N905D	PCNX_ENST00000238570.5_Missense_Mutation_p.N905D|PCNX_ENST00000439984.3_Missense_Mutation_p.N799D	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	905						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AAGAGCATCCAATATCTGGTA	0.338																																					p.N905D													.	PCNX-91	0			c.A2713G						.						115	94	101					14																	71476434		2203	4300	6503	SO:0001583	missense	22990	exon9			GCATCCAATATCT	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.2713A>G	14.37:g.71476434A>G	ENSP00000304192:p.Asn905Asp	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_014982	0	0	0	0	0	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.465591	0.63513	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.21361	2.01;2.01;2.86	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.38295	0.1035	L	0.53249	1.67	0.45995	D	0.998805	B;D	0.63880	0.039;0.993	B;D	0.70935	0.016;0.971	T	0.07849	-1.0751	10	0.20046	T	0.44	.	14.5438	0.68015	1.0:0.0:0.0:0.0	.	799;905	B2RTR6;Q96RV3	.;PCX1_HUMAN	D	905;905;799	ENSP00000304192:N905D;ENSP00000238570:N905D;ENSP00000396617:N799D	ENSP00000238570:N905D	N	+	1	0	PCNX	70546187	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.084000	0.89516	1.904000	0.55121	0.477000	0.44152	AAT	.		0.338	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71476434	A	G	71476434	3	3	46	1	0	0	0	0	1	0	0	0	11617	130	5	3	2747	3	PCNX	14	71476434	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08		71476434	35873106	47	4205											
POMT2	29954	hgsc.bcm.edu;broad.mit.edu	37	chr14	77765102	77765102	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcagaactgaagaaaccGtcaccagggccactgtgggg	13	4	14	10	1	1	3	1	1	0	2	1	3	1	3	3	4	2	1	3	4	4	0	rs186690580	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr14:77765102G>A	ENST00000261534.4	-	8	1138	c.936C>T	c.(934-936)gaC>gaT	p.D312D		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	312						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		TGAAGAAACCGTCACCAGGGC	0.532													G|||	2	0.000399361	0	0	5008	,	,		20776	0.001		0	False		,,,				2504	0.001				p.D312D		.											.	POMT2-91	0			c.C936T						.	G		0,4406		0,0,2203	65	59	61		936	1.6	1	14		61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	POMT2	NM_013382.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		312/751	77765102	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	29954	exon8			GAAACCGTCACCA	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.936C>T	14.37:g.77765102G>A		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_013382	0	0	0	0	0	Q9NSG6|Q9P1W0|Q9P1W2	Silent	SNP	ENST00000261534.4	37	CCDS9857.1																																																																																			G|0.999;A|0.000		0.532	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		A	77765102	G	A	77765102	2	1	46	1	0	0	0	0	0	0	0	1	12272	1136	40	1		1	POMT2	14	77765102	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	6288668	77765102	29584438	48	4206											
TJP1	7082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	30008820	30008820	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgaaatagcttactttgaAgaataactagaaaaatttga	18	12	8	3	0	0	5	0	3	0	2	0	5	0	5	0	1	3	1	0	1	9	6			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr15:30008820A>G	ENST00000346128.6	-	23	4671	c.4197T>C	c.(4195-4197)tcT>tcC	p.S1399S	TJP1_ENST00000400011.2_Silent_p.S1323S|TJP1_ENST00000356107.6_Silent_p.S1399S|TJP1_ENST00000545208.2_Silent_p.S1319S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1399					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		CTTACTTTGAAGAATAACTAG	0.368																																					p.S1399S	Melanoma(77;681 1843 6309 6570)	.											.	TJP1-95	0			c.T4197C						.						60	61	61					15																	30008820		1812	4085	5897	SO:0001819	synonymous_variant	7082	exon23			CTTTGAAGAATAA		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.4197T>C	15.37:g.30008820A>G		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	54	7	NM_003257	0	0	0	0	0	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																			.		0.368	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		G	30008820	A	G	30008820	2	3	46	1	0	0	0	0	0	0	0	1	15961	59	3	3		3	TJP1	15	30008820	Silent	SNP	A	TCGA-B3-8121-01A-21D-2396-08		30008820	72522572	49	4207											
TJP1	7082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	30065529	30065529	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggattatctcgtccaccaGatattgcaattccaaatcca	13	11	6	11	1	1	1	0	0	1	1	5	3	4	2	4	1	1	1	4	1	4	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr15:30065529G>T	ENST00000346128.6	-	3	590	c.116C>A	c.(115-117)tCt>tAt	p.S39Y	TJP1_ENST00000400011.2_Missense_Mutation_p.S43Y|TJP1_ENST00000356107.6_Missense_Mutation_p.S39Y|TJP1_ENST00000495972.2_Missense_Mutation_p.S39Y|TJP1_ENST00000545208.2_Missense_Mutation_p.S39Y	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	39	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TCGTCCACCAGATATTGCAAT	0.363																																					p.S39Y	Melanoma(77;681 1843 6309 6570)	.											.	TJP1-95	0			c.C116A						.						136	121	126					15																	30065529		1874	4102	5976	SO:0001583	missense	7082	exon3			CCACCAGATATTG		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.116C>A	15.37:g.30065529G>T	ENSP00000281537:p.Ser39Tyr	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	108	19	NM_175610	0	0	0	2	2	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.859179	0.71834	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.5	5.5	0.81552	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.66509	0.2796	M	0.92026	3.265	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.998	T	0.73291	-0.4029	9	.	.	.	.	19.7625	0.96325	0.0:0.0:1.0:0.0	.	32;39;39;43	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	Y	39;43;39;39;39	ENSP00000281537:S39Y;ENSP00000382890:S43Y;ENSP00000441202:S39Y;ENSP00000348416:S39Y	.	S	-	2	0	TJP1	27852821	1.000000	0.71417	0.999000	0.59377	0.256000	0.26092	9.715000	0.98748	2.749000	0.94314	0.585000	0.79938	TCT	.		0.363	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		T	30065529	G	T	30065529	3	4	46	1	0	0	0	0	1	0	0	0	15961	942	33	4	5234	4	TJP1	15	30065529	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	56709	30065529	72465863	50	4208											
PRTG	283659	broad.mit.edu	37	chr15	55931963	55931963	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcaggaagatggaagatgagGtgttagccttcgcatagaga	13	8	15	5	1	0	4	0	1	0	3	1	7	0	6	1	3	1	3	1	3	4	3	rs373584731		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr15:55931963G>A	ENST00000389286.4	-	13	2248	c.2201C>T	c.(2200-2202)aCc>aTc	p.T734I		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		GGAAGATGAGGTGTTAGCCTT	0.488													G|||	1	0.000199681	8e-04	0	5008	,	,		20157	0		0	False		,,,				2504	0				p.T734I													.	PRTG-92	0			c.C2201T						.	G	ILE/THR	2,4126		0,2,2062	165	181	176		2201	1.6	1	15		176	0,8394		0,0,4197	no	missense	PRTG	NM_173814.4	89	0,2,6259	AA,AG,GG		0.0,0.0484,0.016	possibly-damaging	734/1151	55931963	2,12520	2064	4197	6261	SO:0001583	missense	283659	exon13			GATGAGGTGTTAG	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26373	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 5"	613261	"protogenin homolog (Gallus gallus)"				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2201C>T	15.37:g.55931963G>A	ENSP00000373937:p.Thr734Ile	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	157	5	NM_173814	0	0	0	0	0		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038427	0.55003	4.84E-4	0.0	ENSG00000166450	ENST00000389286	T	0.60920	0.15	5.81	1.56	0.23342	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.490245	0.22272	N	0.062255	T	0.58438	0.2122	L	0.52011	1.625	0.80722	D	1	B	0.27316	0.175	B	0.35770	0.21	T	0.61108	-0.7129	10	0.72032	D	0.01	-4.8253	18.3429	0.90312	0.0:0.6101:0.3899:0.0	.	734	Q2VWP7	PRTG_HUMAN	I	734	ENSP00000373937:T734I	ENSP00000373937:T734I	T	-	2	0	PRTG	53719255	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	1.843000	0.39259	0.036000	0.15547	0.655000	0.94253	ACC	.		0.488	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		A	55931963	G	A	55931963	3	1	46	1	0	0	0	0	1	0	0	0	12667	1261	44	2	1283	2	PRTG	15	55931963	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	25866434	55931963	46599429	51	4209											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79058944	79058944	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctacccgtggagggcgcAgcaggatggctgtgtggtgg	5	7	21	8	2	0	0	0	0	0	0	0	2	0	2	1	7	2	4	1	7	1	1	rs529497330	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr15:79058944A>T	ENST00000388820.4	-	19	3519	c.3309T>A	c.(3307-3309)gcT>gcA	p.A1103A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1103					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						TGGAGGGCGCAGCAGGATGGC	0.672													a|||	254	0.0507188	0.1619	0.0231	5008	,	,		10839	0.0169		0.005	False		,,,				2504	0.002				p.A1103A		.											.	ADAMTS7-226	0			c.T3309A						.						11	18	16					15																	79058944		2079	4266	6345	SO:0001819	synonymous_variant	11173	exon19			GGGCGCAGCAGGA	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3309T>A	15.37:g.79058944A>T		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_014272	0	0	2	2	0	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			A|1.000;T|0.000		0.672	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79058944	A	T	79058944	2	4	46	1	0	0	0	0	0	0	0	1	271	175	7	5		5	ADAMTS7	15	79058944	Silent	SNP	A	TCGA-B3-8121-01A-21D-2396-08	23126981	79058944	23472448	52	4210											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_178167	0	0	0	1	1	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	46	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-B3-8121-01A-21D-2396-08		2059674	88295079	53	4211											
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085361	5085361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcttcaagtttctctccagCatgcagtctctgatgtttga	7	17	7	10	0	4	2	1	2	3	0	7	2	5	2	1	0	2	4	1	0	1	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr17:5085361C>T	ENST00000399604.4	-	1	2331	c.2191G>A	c.(2191-2193)Gct>Act	p.A731T	ZNF594_ENST00000575779.1_Missense_Mutation_p.A731T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	731					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TTCTCTCCAGCATGCAGTCTC	0.428																																					p.A731T		.											.	ZNF594-71	0			c.G2191A						.						168	177	174					17																	5085361		2125	4259	6384	SO:0001583	missense	84622	exon2			CTCCAGCATGCAG	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2191G>A	17.37:g.5085361C>T	ENSP00000382513:p.Ala731Thr	Somatic	168	2		WXS	Illumina HiSeq	Phase_I	160	8	NM_032530	0	0	13	13	0	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.773005	0.00640	.	.	ENSG00000180626	ENST00000399604;ENST00000389222	T	0.08720	3.06	1.17	-1.83	0.07833	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02012	0.0063	N	0.01446	-0.86	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44065	-0.9352	9	0.02654	T	1	.	5.162	0.15066	0.0:0.4347:0.0:0.5653	.	731	Q96JF6	ZN594_HUMAN	T	731;298	ENSP00000382513:A731T	ENSP00000373874:A298T	A	-	1	0	ZNF594	5026085	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-0.382000	0.07408	-0.478000	0.06823	-0.396000	0.06452	GCT	.		0.428	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		T	5085361	C	T	5085361	3	4	46	1	0	0	0	0	1	0	0	0	18056	710	25	2	236	2	ZNF594	17	5085361	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08		5085361	76109849	54	4212											
EFCAB3	146779	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	60484528	60484528	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaataaaggagcctttgcaTttctttgaggattatttttt	11	18	8	4	0	1	2	0	1	1	1	1	4	1	4	1	2	2	1	1	2	4	8			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr17:60484528T>C	ENST00000305286.3	+	8	900	c.822T>C	c.(820-822)caT>caC	p.H274H	EFCAB3_ENST00000450662.2_Silent_p.H326H	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	274							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			AGCCTTTGCATTTCTTTGAGG	0.358																																					p.H326H		.											.	EFCAB3-227	0			c.T978C						.						80	82	81					17																	60484528		2203	4300	6503	SO:0001819	synonymous_variant	146779	exon10			TTTGCATTTCTTT	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.822T>C	17.37:g.60484528T>C		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	74	7	NM_001144933	0	0	0	0	0	J3KQM8	Silent	SNP	ENST00000305286.3	37	CCDS11632.1																																																																																			.		0.358	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503		C	60484528	T	C	60484528	2	2	46	1	0	0	0	0	0	0	0	1	4946	1490	52	3		3	EFCAB3	17	60484528	Silent	SNP	T	TCGA-B3-8121-01A-21D-2396-08	55399167	60484528	20710682	55	4213											
C17orf80	55028	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	71231747	71231747	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctactgatcaaaaagtttaTcagtccaagccagctacact	14	10	5	12	0	2	1	2	1	0	0	3	1	3	1	3	0	4	2	3	0	6	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr17:71231747T>G	ENST00000535032.2	+	2	239	c.126T>G	c.(124-126)taT>taG	p.Y42*	C17orf80_ENST00000359042.2_Nonsense_Mutation_p.Y42*|C17orf80_ENST00000268942.8_Nonsense_Mutation_p.Y42*|C17orf80_ENST00000426147.2_Nonsense_Mutation_p.Y42*|C17orf80_ENST00000582793.1_Intron|C17orf80_ENST00000255557.4_Nonsense_Mutation_p.Y42*|C17orf80_ENST00000577615.1_Nonsense_Mutation_p.Y42*|FAM104A_ENST00000583178.1_Intron			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	42						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			AAAAAGTTTATCAGTCCAAGC	0.378																																					p.Y42X													.	C17orf80-91	0			c.T126G						.						64	56	59					17																	71231747		2203	4300	6503	SO:0001587	stop_gained	55028	exon3			AGTTTATCAGTCC	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"sperm-expressed protein 1", "migration-inducing protein 3"					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.126T>G	17.37:g.71231747T>G	ENSP00000440551:p.Tyr42*	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	47	7	NM_001100621	0	0	12	16	4	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Nonsense_Mutation	SNP	ENST00000535032.2	37	CCDS11694.1	.	.	.	.	.	.	.	.	.	.	T	34	5.308460	0.95629	.	.	ENSG00000141219	ENST00000255557;ENST00000359042;ENST00000268942;ENST00000426147;ENST00000535032	.	.	.	5.55	3.32	0.38043	.	1.540210	0.03731	N	0.253448	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0107	5.6005	0.17351	0.0:0.0906:0.1918:0.7176	.	.	.	.	X	42	.	ENSP00000255557:Y42X	Y	+	3	2	C17orf80	68743342	0.003000	0.15002	0.001000	0.08648	0.079000	0.17450	1.233000	0.32648	0.398000	0.25338	0.459000	0.35465	TAT	.		0.378	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941		G	71231747	T	G	71231747	4	3	46	1	0	0	0	0	0	1	0	0	1890	1442	50	5	128	5	C17orf80	17	71231747	Nonsense_Mutation	SNP	T	TCGA-B3-8121-01A-21D-2396-08	10747219	71231747	9963463	56	4214											
KLHL14	57565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	30350134	30350134	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacgttggccgtgtagaggtActcgagcaccaggcgcagcc	8	6	14	13	4	0	1	0	0	0	1	1	2	0	1	3	3	3	5	3	3	2	3			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr18:30350134A>C	ENST00000359358.4	-	2	859	c.421T>G	c.(421-423)Tac>Gac	p.Y141D	AC012123.1_ENST00000426194.1_Intron|KLHL14_ENST00000358095.4_Missense_Mutation_p.Y141D	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	141	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						GTGTAGAGGTACTCGAGCACC	0.642																																					p.Y141D		.											.	KLHL14-91	0			c.T421G						.						99	99	99					18																	30350134		2203	4300	6503	SO:0001583	missense	57565	exon2			AGAGGTACTCGAG	AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"Kelch-like", "BTB/POZ domain containing"	29266	protein-coding gene	gene with protein product	"printor"	613772	"kelch-like 14 (Drosophila)"			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.421T>G	18.37:g.30350134A>C	ENSP00000352314:p.Tyr141Asp	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	268	50	NM_020805	0	0	0	0	0	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	A	9.978	1.227338	0.22542	.	.	ENSG00000197705	ENST00000359358;ENST00000358095	T;T	0.71222	-0.55;-0.55	4.34	4.34	0.51931	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.134366	0.51477	D	0.000081	T	0.78660	0.4318	L	0.48362	1.52	0.80722	D	1	D	0.63880	0.993	D	0.81914	0.995	T	0.80876	-0.1186	10	0.87932	D	0	.	13.0081	0.58717	1.0:0.0:0.0:0.0	.	141	Q9P2G3	KLH14_HUMAN	D	141	ENSP00000352314:Y141D;ENSP00000350808:Y141D	ENSP00000350808:Y141D	Y	-	1	0	KLHL14	28604132	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.006000	0.70724	1.738000	0.51689	0.377000	0.23210	TAC	.		0.642	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			C	30350134	A	C	30350134	3	2	46	1	0	0	0	0	1	0	0	0	8391	391	14	5	1497	5	KLHL14	18	30350134	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08		30350134	47727114	57	4215											
ATP5A1	498	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	43671697	43671697	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgcttgaacattcctcAgcccatgtacgcgggcaata	9	11	8	13	2	2	1	1	1	1	0	3	1	3	1	2	1	4	3	2	1	4	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr18:43671697A>G	ENST00000398752.6	-	3	381	c.260T>C	c.(259-261)cTg>cCg	p.L87P	ATP5A1_ENST00000591267.1_5'Flank|ATP5A1_ENST00000590665.1_Missense_Mutation_p.L87P|ATP5A1_ENST00000282050.2_Missense_Mutation_p.L87P|ATP5A1_ENST00000593152.2_Missense_Mutation_p.L37P	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	87					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						AACATTCCTCAGCCCATGTAC	0.388																																					p.L87P		.											.	ATP5A1-90	0			c.T260C						.						100	98	98					18																	43671697		2203	4300	6503	SO:0001583	missense	498	exon3			TTCCTCAGCCCAT	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.260T>C	18.37:g.43671697A>G	ENSP00000381736:p.Leu87Pro	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	103	25	NM_004046	0	0	124	243	119	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	37	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527021	0.85706	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.88354	-2.37;-2.37	5.24	5.24	0.73138	ATPase, F1/A1 complex, alpha subunit, N-terminal (1);ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal (1);ATPase, F1/A1 complex, alpha/beta subunit, N-terminal (1);	0.147149	0.47852	D	0.000217	D	0.96873	0.8979	H	0.98996	4.395	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.98545	1.0634	10	0.87932	D	0	-17.4309	15.1468	0.72662	1.0:0.0:0.0:0.0	.	87	P25705	ATPA_HUMAN	P	87;87;37	ENSP00000282050:L87P;ENSP00000381736:L87P	ENSP00000282050:L87P	L	-	2	0	ATP5A1	41925695	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.176000	0.94839	1.975000	0.57531	0.533000	0.62120	CTG	.		0.388	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		G	43671697	A	G	43671697	3	3	46	1	0	0	0	0	1	0	0	0	1148	188	7	3	1441	3	ATP5A1	18	43671697	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	13321563	43671697	34405551	58	4216											
EPOR	2057	hgsc.bcm.edu	37	chr19	11491644	11491644	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtcaggatgagggggtccAggtctaagaggcggggagga	9	5	21	6	2	2	2	1	1	1	1	3	5	3	5	1	8	0	0	1	8	1	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:11491644A>C	ENST00000222139.6	-	6	847	c.743T>G	c.(742-744)cTg>cGg	p.L248R	EPOR_ENST00000592375.2_Missense_Mutation_p.L248R	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	248					brain development (GO:0007420)|decidualization (GO:0046697)|erythropoietin-mediated signaling pathway (GO:0038162)|heart development (GO:0007507)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	erythropoietin receptor activity (GO:0004900)|identical protein binding (GO:0042802)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894)	GAGGGGGTCCAGGTCTAAGAG	0.682											OREG0025255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L248R		.											.	EPOR-523	0			c.T743G						.						43	30	35					19																	11491644		2129	4182	6311	SO:0001583	missense	2057	exon6			GGGTCCAGGTCTA	M34986	CCDS12260.1	19p13.3-p13.2	2013-02-11				ENSG00000187266		"Fibronectin type III domain containing"	3416	protein-coding gene	gene with protein product		133171					Standard	NM_000121		Approved		uc002mrj.2	P19235		ENST00000222139.6:c.743T>G	19.37:g.11491644A>C	ENSP00000222139:p.Leu248Arg	Somatic	7	1	672	WXS	Illumina HiSeq	Phase_I	8	5	NM_000121	0	0	2	3	1	B2RCG4|Q15443|Q2M205	Missense_Mutation	SNP	ENST00000222139.6	37	CCDS12260.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684759	0.88639	.	.	ENSG00000187266	ENST00000222139	D	0.82526	-1.62	5.76	5.76	0.90799	.	0.172266	0.39544	N	0.001323	D	0.89167	0.6638	M	0.66939	2.045	0.49483	D	0.999798	D	0.89917	1.0	D	0.85130	0.997	D	0.87554	0.2467	10	0.30078	T	0.28	-15.7654	13.6048	0.62041	1.0:0.0:0.0:0.0	.	248	P19235	EPOR_HUMAN	R	248	ENSP00000222139:L248R	ENSP00000222139:L248R	L	-	2	0	EPOR	11352644	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.997000	0.70646	2.211000	0.71520	0.454000	0.30748	CTG	.		0.682	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1			C	11491644	A	C	11491644	3	2	46	1	0	0	0	0	1	0	0	0	5202	188	7	5	795	5	EPOR	19	11491644	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08		11491644	47637339	59	4217											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31770237	31770237	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacagctgctgctgctgctActgctgctgctgctgctgcc	3	11	11	16	0	0	0	0	0	0	0	0	0	0	0	2	0	12	10	2	0	1	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:31770237A>G	ENST00000240587.4	-	2	789	c.462T>C	c.(460-462)agT>agC	p.S154S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	154	Ser-rich.				in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					tgctgctgctactgctgctgc	0.607																																					p.S154S		.											.	TSHZ3-232	0			c.T462C						.						39	44	42					19																	31770237		2184	4294	6478	SO:0001819	synonymous_variant	57616	exon2			GCTGCTACTGCTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.462T>C	19.37:g.31770237A>G		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_020856	2	3	14	2020	2001	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			.		0.607	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31770237	A	G	31770237	2	3	46	1	0	0	0	0	0	0	0	1	16658	388	14	3		3	TSHZ3	19	31770237	Silent	SNP	A	TCGA-B3-8121-01A-21D-2396-08	20278593	31770237	27358746	60	4218											
ANKRD27	84079	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	33132944	33132944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaaacctctctggcttggaGactgtgtaatgagctgcacc	10	10	10	11	0	1	2	0	1	1	1	2	3	1	2	2	2	3	4	2	2	2	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:33132944G>A	ENST00000306065.4	-	10	1048	c.890C>T	c.(889-891)tCt>tTt	p.S297F	ANKRD27_ENST00000587352.1_Missense_Mutation_p.S297F	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	297	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CTGGCTTGGAGACTGTGTAAT	0.493																																					p.S297F		.											.	ANKRD27-95	0			c.C890T						.						149	138	142					19																	33132944		2203	4300	6503	SO:0001583	missense	84079	exon10			CTTGGAGACTGTG	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"Ankyrin repeat domain containing"	25310	protein-coding gene	gene with protein product	"Vps9 domain and ankyrin-repeat-containing protein"					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.890C>T	19.37:g.33132944G>A	ENSP00000304292:p.Ser297Phe	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	199	53	NM_032139	0	0	0	0	0	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	37	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	G	9.152	1.016485	0.19355	.	.	ENSG00000105186	ENST00000306065	T	0.31247	1.5	5.43	5.43	0.79202	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.000000	0.64402	D	0.000017	T	0.40222	0.1108	M	0.72118	2.19	0.53005	D	0.999961	B	0.23058	0.079	B	0.28638	0.092	T	0.23904	-1.0175	10	0.44086	T	0.13	-22.3055	19.253	0.93933	0.0:0.0:1.0:0.0	.	297	Q96NW4	ANR27_HUMAN	F	297	ENSP00000304292:S297F	ENSP00000304292:S297F	S	-	2	0	ANKRD27	37824784	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	5.388000	0.66249	2.551000	0.86045	0.563000	0.77884	TCT	.		0.493	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33132944	G	A	33132944	3	1	46	1	0	0	0	0	1	0	0	0	655	942	33	2	2342	2	ANKRD27	19	33132944	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	1362707	33132944	25996039	61	4219											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39226899	39226899	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgaggggcgagcggtcGgcgcgcagcagccggggcag	5	2	22	12	7	0	1	0	1	0	0	1	2	0	1	1	6	3	4	1	6	0	0	rs574197181	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:39226899G>A	ENST00000328867.4	-	12	1742	c.1434C>T	c.(1432-1434)gcC>gcT	p.A478A	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.A329A	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	478	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GCGAGCGGTCGGCGCGCAGCA	0.771													g|||	54	0.0107827	0.0408	0	5008	,	,		3282	0		0	False		,,,				2504	0				p.A478A		.											.	CAPN12-91	0			c.C1434T						.						2	3	3					19																	39226899		1176	2318	3494	SO:0001819	synonymous_variant	147968	exon12			GCGGTCGGCGCGC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"EF-hand domain containing"	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1434C>T	19.37:g.39226899G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_144691	0	0	0	3	3		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			.		0.771	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			A	39226899	G	A	39226899	2	1	46	1	0	0	0	0	0	0	0	1	2631	1103	39	1		1	CAPN12	19	39226899	Silent	SNP	G	TCGA-B3-8121-01A-21D-2396-08	6093955	39226899	19902084	62	4220											
LILRB3	11025	hgsc.bcm.edu	37	chr19	54725773	54725773	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtataatagtaatagcaTgtgaacctccacctgtggct	11	14	8	8	0	0	1	0	1	0	0	1	1	1	1	3	1	2	4	3	1	6	6	rs559292350	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:54725773T>C	ENST00000391750.1	-	5	721	c.585A>G	c.(583-585)acA>acG	p.T195T	LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000346401.6_Silent_p.T195T|LILRA6_ENST00000440558.2_Intron|LILRB3_ENST00000424807.1_Silent_p.T195T|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000407860.2_Silent_p.T195T|LILRB3_ENST00000245620.9_Silent_p.T195T|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	195	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGTAATAGCATGTGAACCTCC	0.622													.|||	121	0.0241613	0.0893	0.0043	5008	,	,		7962	0		0	False		,,,				2504	0				p.T195T		.											.	LILRB3-93	0			c.A585G						.						15	30	25					19																	54725773		1380	3348	4728	SO:0001819	synonymous_variant	11025	exon4			ATAGCATGTGAAC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.585A>G	19.37:g.54725773T>C		Somatic	12	2		WXS	Illumina HiSeq	Phase_I	20	7	NM_006864	0	0	2	4	2	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			.		0.622	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		C	54725773	T	C	54725773	2	2	46	1	0	0	0	0	0	0	0	1	8814	1451	51	3		3	LILRB3	19	54725773	Silent	SNP	T	TCGA-B3-8121-01A-21D-2396-08	15498874	54725773	4403210	63	4221											
LILRA5	353514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54819027	54819027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgacggactgaggttatcaGctgctcctgaaaatcaaaac	13	9	10	9	1	2	3	2	3	0	0	3	4	3	4	1	2	3	3	1	2	5	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:54819027G>A	ENST00000301219.3	-	6	838	c.719C>T	c.(718-720)gCt>gTt	p.A240V	LILRA5_ENST00000346508.3_Missense_Mutation_p.A228V|AC008984.2_ENST00000507363.1_RNA	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	240					innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAGGTTATCAGCTGCTCCTGA	0.517																																					p.A240V		.											.	LILRA5-91	0			c.C719T						.						83	76	78					19																	54819027		2203	4300	6503	SO:0001583	missense	353514	exon6			TTATCAGCTGCTC	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.719C>T	19.37:g.54819027G>A	ENSP00000301219:p.Ala240Val	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	66	13	NM_021250	0	0	0	0	0	A6NHI3	Missense_Mutation	SNP	ENST00000301219.3	37	CCDS12888.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383828	0.25031	.	.	ENSG00000187116	ENST00000301219;ENST00000346508	T;T	0.00502	7.02;6.95	2.31	2.31	0.28768	.	.	.	.	.	T	0.00608	0.0020	M	0.62154	1.92	0.21386	N	0.999702	B;B	0.25048	0.117;0.014	B;B	0.31946	0.138;0.01	T	0.37103	-0.9720	9	0.38643	T	0.18	.	8.1667	0.31230	0.0:0.0:1.0:0.0	.	228;240	A6NI73-2;A6NI73	.;LIRA5_HUMAN	V	240;228	ENSP00000301219:A240V;ENSP00000302948:A228V	ENSP00000301219:A240V	A	-	2	0	LILRA5	59510839	0.000000	0.05858	0.004000	0.12327	0.073000	0.16967	0.233000	0.17911	1.603000	0.50134	0.536000	0.68110	GCT	.		0.517	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		A	54819027	G	A	54819027	3	1	46	1	0	0	0	0	1	0	0	0	8810	971	34	2	188	2	LILRA5	19	54819027	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	93254	54819027	4309956	64	4222											
ZNF341	84905	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	32345059	32345060	+	Frame_Shift_Ins	INS	-	-	C																															aaaccccgccgcccccatgaINSccagcgccaccgggggcacg																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr20:32345059_32345060insC	ENST00000375200.1	+	6	1212_1213	c.847_848insC	c.(847-849)accfs	p.T283fs	ZNF341_ENST00000342427.2_Frame_Shift_Ins_p.T283fs	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	283					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						CGCCCCCATGACCAGCGCCACC	0.629																																					p.T283fs		.											.	ZNF341-92	0			c.847_848insC						.																																			SO:0001589	frameshift_variant	84905	exon6			.	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"Zinc fingers, C2H2-type"	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.849dupC	20.37:g.32345061_32345061dupC	ENSP00000364346:p.Thr283fs	Somatic	318	0		WXS	Illumina HiSeq	Phase_I	414	128	NM_032819	0	0	0	0	0	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Frame_Shift_Ins	INS	ENST00000375200.1	37																																																																																				.		0.629	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				C	32345060	-	C	32345059	7	5	46	1	0	1	1	0	0	0	0	0	17889	275	10	0	869	0	ZNF341	20	32345059	Frame_Shift_Ins	INS	-	TCGA-B3-8121-01A-21D-2396-08		32345059	30680461	65	4223											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43940524	43940524	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cacggtctgcggttacatggGactggacagcgcgtccggca	7	7	15	12	5	1	0	0	0	1	0	2	2	2	2	1	5	3	2	1	5	1	1	rs35472429	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr20:43940524G>T	ENST00000343694.3	+	5	446	c.374G>T	c.(373-375)gGa>gTa	p.G125V	RBPJL_ENST00000372743.1_Missense_Mutation_p.G125V|RBPJL_ENST00000372741.3_Missense_Mutation_p.G125V	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	125					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GGTTACATGGGACTGGACAGC	0.662											OREG0025979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	20	0.00399361	0.0136	0.0029	5008	,	,		17313	0		0	False		,,,				2504	0				p.G125V		.											.	RBPJL-227	0			c.G374T						.	G	VAL/GLY	17,4097		0,17,2040	10	8	8		374	5.4	1	20	dbSNP_126	8	0,8032		0,0,4016	yes	missense	RBPJL	NM_014276.2	109	0,17,6056	TT,TG,GG		0.0,0.4132,0.14	probably-damaging	125/518	43940524	17,12129	2057	4016	6073	SO:0001583	missense	11317	exon5			ACATGGGACTGGA	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.374G>T	20.37:g.43940524G>T	ENSP00000341243:p.Gly125Val	Somatic	1	1	920	WXS	Illumina HiSeq	Phase_I	9	4	NM_014276	0	0	0	0	0	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	31	5.088237	0.94100	0.004132	0.0	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	D;D;D	0.87412	-2.25;-2.25;-2.25	5.38	5.38	0.77491	LAG1, DNA binding (2);p53-like transcription factor, DNA-binding (1);	0.143198	0.48767	D	0.000172	D	0.88683	0.6503	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.90545	0.4505	10	0.87932	D	0	-13.1573	16.2671	0.82593	0.0:0.0:1.0:0.0	rs35472429	125;125	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	V	125	ENSP00000361828:G125V;ENSP00000361826:G125V;ENSP00000341243:G125V	ENSP00000341243:G125V	G	+	2	0	RBPJL	43373938	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.904000	0.87408	2.512000	0.84698	0.561000	0.74099	GGA	G|0.996;T|0.004		0.662	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		T	43940524	G	T	43940524	3	4	46	1	0	0	0	0	1	0	0	0	13194	1174	41	4	392	4	RBPJL	20	43940524	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	11595465	43940524	19084996	66	4224											
NUP50	10762	broad.mit.edu;bcgsc.ca	37	chr22	45574449	45574449	+	Frame_Shift_Del	DEL	T	T	-																															tgaaacacagtctccttcccTttttggctcaacaaaattac																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr22:45574449delT	ENST00000347635.4	+	5	1137	c.671delT	c.(670-672)cttfs	p.L224fs	NUP50_ENST00000425733.2_5'UTR|CTA-268H5.12_ENST00000610217.1_RNA|NUP50_ENST00000396096.2_Frame_Shift_Del_p.L196fs|NUP50_ENST00000407019.2_Frame_Shift_Del_p.L196fs	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	224	5 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TCTCCTTCCCTTTTTGGCTCA	0.408																																					p.L224fs													.	NUP50-68	0			c.671delT						.						40	41	40					22																	45574449		2203	4300	6503	SO:0001589	frameshift_variant	10762	exon5			CTTCCCTTTTTGG	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"nucleoporin 50kD"	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.671delT	22.37:g.45574449delT	ENSP00000345895:p.Leu224fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	81	11	NM_007172	0	0	0	0	0	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Frame_Shift_Del	DEL	ENST00000347635.4	37	CCDS14062.1																																																																																			.		0.408	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2			-	45574449	T	-	45574449	7	5	46	1	0	1	0	1	0	0	0	0	10792	1609	56	0	685	0	NUP50	22	45574449	Frame_Shift_Del	DEL	T	TCGA-B3-8121-01A-21D-2396-08		45574449	5730117	67	4225											
HUWE1	10075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53589174	53589174	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctgagtgtgctcctcCtcatcctcagggtccaggat	5	13	9	14	0	3	1	2	1	1	0	8	2	8	2	5	2	1	1	5	2	0	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chrX:53589174C>T	ENST00000342160.3	-	53	7693	c.7236G>A	c.(7234-7236)gaG>gaA	p.E2412E	HUWE1_ENST00000262854.6_Silent_p.E2412E			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2412	Glu-rich.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.E2275D(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TGTGCTCCTCCTCATCCTCAG	0.498																																					p.E2412E		.											.	HUWE1-280	1	Substitution - Missense(1)	breast(1)	c.G7236A						.						138	86	104					X																	53589174		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon54			CTCCTCCTCATCC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.7236G>A	X.37:g.53589174C>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	57	16	NM_031407	0	0	8	32	24	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	2.473	-0.321458	0.05386	.	.	ENSG00000086758	ENST00000427052	.	.	.	4.93	4.05	0.47172	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55082	-0.8196	4	.	.	.	.	8.1437	0.31100	0.0:0.8128:0.0:0.1872	.	.	.	.	R	1446	.	.	G	-	1	0	HUWE1	53605899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.451000	0.35145	2.164000	0.68074	0.513000	0.50165	GGA	.		0.498	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53589174	C	T	53589174	2	4	46	1	0	0	0	0	0	0	0	1	7482	680	24	2		2	HUWE1	23	53589174	Silent	SNP	C	TCGA-B3-8121-01A-21D-2396-08		53589174	101681386	68	4226											
NAP1L3	4675	ucsc.edu	37	chrX	92927724	92927724	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggttttctttagggttttCttcttcctcaccctctaagg	4	19	8	10	0	5	0	1	0	4	0	6	0	6	0	2	3	0	2	2	3	2	9			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chrX:92927724C>T	ENST00000373079.3	-	1	843	c.580G>A	c.(580-582)Gaa>Aaa	p.E194K	FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.E187K	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	194	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TTAGGGTTTTCTTCTTCCTCA	0.433																																					p.E194K													.	NAP1L3-131	0			c.G580A						.						82	81	81					X																	92927724		2203	4300	6503	SO:0001583	missense	4675	exon1			GGTTTTCTTCTTC		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.580G>A	X.37:g.92927724C>T	ENSP00000362171:p.Glu194Lys	Somatic	151	1		WXS	Illumina HiSeq		72	3	NM_004538	0	0	9	12	3	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.644848	0.29246	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.27890	1.64	3.78	2.87	0.33458	.	0.747635	0.11017	N	0.608855	T	0.21307	0.0513	L	0.31294	0.92	0.29536	N	0.852442	P	0.38711	0.643	B	0.37346	0.247	T	0.10382	-1.0632	10	0.27082	T	0.32	.	8.0903	0.30797	0.0:0.8654:0.0:0.1346	.	194	Q99457	NP1L3_HUMAN	K	194;187	ENSP00000362171:E194K	ENSP00000362171:E194K	E	-	1	0	NAP1L3	92814380	0.993000	0.37304	0.602000	0.28890	0.428000	0.31595	1.911000	0.39937	0.910000	0.36722	0.529000	0.55759	GAA	.		0.433	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		T	92927724	C	T	92927724	3	4	46	1	0	0	0	0	1	0	0	0	10183	922	32	2	944	2	NAP1L3	23	92927724	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	39338550	92927724	62342836	69	4227											
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16952767	16952767	+	3'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcctcaacatcttagcCtttgcggcgctgtactacaa	8	13	6	14	2	3	0	1	0	2	0	4	0	4	0	2	1	5	2	2	1	5	5	rs373089425		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chrY:16952767C>T	ENST00000476359.1	+	0	2621							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.A692A(1)		large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						ACATCTTAGCCTTTGCGGCGC	0.502																																					p.A692A		.											.	.	1	Substitution - coding silent(1)	prostate(1)	c.C2076T						.	C	,	0,571		0,571	53	72	66		1572,2076	-3.8	0	Y		66	1,1871		1,1871	no	coding-synonymous,coding-synonymous	NLGN4Y	NM_001206850.1,NM_014893.4	,	1,2442	T,C		0.0534,0.0,0.0409	,	524/649,692/817	16952767	1,2442	974	2291	3265	SO:0001624	3_prime_UTR_variant	22829	exon6			CTTAGCCTTTGCG		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*2618C>T	Y.37:g.16952767C>T		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	5	5	NM_014893	0	0	0	1	1	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Silent	SNP	ENST00000476359.1	37																																																																																				.		0.502	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		T	16952767	C	T	16952767	1	4	46	0	1	0	0	0	0	0	0	0	10491	668	24	2		2	NLGN4Y	24	16952767	3'UTR	SNP	C	TCGA-B3-8121-01A-21D-2396-08		16952767	42420799	70	4228											
MTOR	2475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11273603	11273603	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgatcgtgctctgaattgaGgtgttcatgacccagaattc	10	13	10	8	1	2	5	1	4	1	1	4	5	2	5	1	1	1	2	1	1	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:11273603G>C	ENST00000361445.4	-	21	3214	c.3138C>G	c.(3136-3138)acC>acG	p.T1046T		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1046					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCTGAATTGAGGTGTTCATGA	0.458																																					p.T1046T		.											.	MTOR-1439	0			c.C3138G						.						97	98	98					1																	11273603		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon21			AATTGAGGTGTTC	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3138C>G	1.37:g.11273603G>C		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	187	71	NM_004958	0	0	2	4	2	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			.		0.458	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		C	11273603	G	C	11273603	2	2	47	1	0	0	0	0	0	0	0	1	9979	987	35	4		4	MTOR	1	11273603	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08		11273603	237977018	1	4229											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	19490300	19490300	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcagtttttcaactacattCttctgtgacaggtatttctt	8	20	5	8	0	5	1	2	1	3	0	5	1	5	1	0	1	2	2	0	1	3	9			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:19490300C>G	ENST00000375254.3	-	34	4749	c.4722G>C	c.(4720-4722)aaG>aaC	p.K1574N	UBR4_ENST00000375226.2_Missense_Mutation_p.K1574N|UBR4_ENST00000375217.2_Missense_Mutation_p.K1574N|UBR4_ENST00000375267.2_Missense_Mutation_p.K1574N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1574					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAACTACATTCTTCTGTGACA	0.403																																					p.K1574N		.											.	UBR4-612	0			c.G4722C						.						191	172	178					1																	19490300		2203	4300	6503	SO:0001583	missense	23352	exon34			TACATTCTTCTGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.4722G>C	1.37:g.19490300C>G	ENSP00000364403:p.Lys1574Asn	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	175	70	NM_020765	0	0	0	0	0	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698108	0.68386	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.15	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73273	0.3566	L	0.39898	1.24	0.80722	D	1	D	0.57899	0.981	D	0.67231	0.95	T	0.73040	-0.4108	10	0.49607	T	0.09	.	12.9635	0.58472	0.0:0.9263:0.0:0.0737	.	1574	Q5T4S7	UBR4_HUMAN	N	1574;1574;1574;1574;284;790	ENSP00000364403:K1574N;ENSP00000364416:K1574N;ENSP00000364365:K1574N;ENSP00000364374:K1574N;ENSP00000404897:K284N	ENSP00000364365:K1574N	K	-	3	2	UBR4	19362887	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.411000	0.59781	2.674000	0.91012	0.655000	0.94253	AAG	.		0.403	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		G	19490300	C	G	19490300	3	3	47	1	0	0	0	0	1	0	0	0	16937	912	32	4	11121	4	UBR4	1	19490300	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	8216697	19490300	229760321	2	4230											
EPHA8	2046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22927186	22927186	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatccgctggacggccccAgaggccatcgccttccgcac	6	5	10	20	4	0	1	0	0	0	1	3	2	2	2	7	3	0	2	7	3	0	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:22927186A>T	ENST00000166244.3	+	14	2493	c.2421A>T	c.(2419-2421)ccA>ccT	p.P807P		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	807	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGACGGCCCCAGAGGCCATCG	0.682																																					p.P807P		.											.	EPHA8-1380	0			c.A2421T						.						58	61	60					1																	22927186		2203	4299	6502	SO:0001819	synonymous_variant	2046	exon14			GGCCCCAGAGGCC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2421A>T	1.37:g.22927186A>T		Somatic	249	0		WXS	Illumina HiSeq	Phase_I	225	82	NM_020526	0	0	0	0	0	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			.		0.682	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22927186	A	T	22927186	2	4	47	1	0	0	0	0	0	0	0	1	5186	175	7	5		5	EPHA8	1	22927186	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	3436886	22927186	226323435	3	4231											
ZMYM6	9204	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	35457962	35457962	+	Frame_Shift_Del	DEL	T	T	-																															gaagattgggaagatggaaaTttcatagcatcttcctgtgt																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:35457962delT	ENST00000357182.4	-	15	2246	c.2019delA	c.(2017-2019)aaafs	p.K673fs	ZMYM6_ENST00000373340.2_Frame_Shift_Del_p.K673fs|ZMYM6_ENST00000487874.1_Frame_Shift_Del_p.K673fs|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	673					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				AAGATGGAAATTTCATAGCAT	0.383																																					p.K673fs		.											.	ZMYM6-93	0			c.2019delA						.						150	142	145					1																	35457962		2203	4300	6503	SO:0001589	frameshift_variant	9204	exon15			.	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"Zinc fingers, MYM type", "Zinc fingers, BED-type"	13050	protein-coding gene	gene with protein product	"zinc finger, BED-type containing 7"	613567	"zinc finger protein 258", "zinc finger, MYM-type containing 6"	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.2019delA	1.37:g.35457962delT	ENSP00000349708:p.Lys673fs	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	165	54	NM_007167	0	0	0	0	0	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Frame_Shift_Del	DEL	ENST00000357182.4	37	CCDS387.2																																																																																			.		0.383	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		-	35457962	T	-	35457962	7	5	47	1	0	1	0	1	0	0	0	0	17736	1490	52	0	1966	0	ZMYM6	1	35457962	Frame_Shift_Del	DEL	T	TCGA-B9-4113-01A-01D-1252-08	12530776	35457962	213792659	4	4232											
MCOLN3	55283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	85487988	85487988	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggaattccttacgttgtaCtttgcaaagaaaccgaggta	12	12	10	7	2	0	1	0	0	0	1	1	3	1	2	2	2	4	4	2	2	6	6	rs375444573		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:85487988C>A	ENST00000370589.2	-	10	1243	c.1191G>T	c.(1189-1191)aaG>aaT	p.K397N	MCOLN3_ENST00000341115.4_Missense_Mutation_p.K341N|MCOLN3_ENST00000474447.1_5'UTR|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	397					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TTACGTTGTACTTTGCAAAGA	0.433																																					p.K397N		.											.	MCOLN3-91	0			c.G1191T						.						85	78	81					1																	85487988		2203	4300	6503	SO:0001583	missense	55283	exon10			GTTGTACTTTGCA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1191G>T	1.37:g.85487988C>A	ENSP00000359621:p.Lys397Asn	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	52	19	NM_018298	0	0	0	0	0	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	37	CCDS701.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319843	0.41096	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115	T;T	0.69926	-0.44;-0.44	5.74	4.78	0.61160	Polycystin cation channel, PKD1/PKD2 (1);	0.088648	0.85682	D	0.000000	T	0.40645	0.1125	L	0.41710	1.295	0.48830	D	0.999718	B;B	0.27625	0.076;0.183	B;B	0.29077	0.043;0.098	T	0.42949	-0.9421	10	0.41790	T	0.15	-17.9811	9.0071	0.36117	0.0:0.7676:0.0:0.2324	.	341;397	Q8TDD5-2;Q8TDD5	.;MCLN3_HUMAN	N	397;397;341;341	ENSP00000359621:K397N;ENSP00000342698:K341N	ENSP00000304843:K397N	K	-	3	2	MCOLN3	85260576	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	1.405000	0.34635	1.307000	0.44944	0.655000	0.94253	AAG	.		0.433	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		A	85487988	C	A	85487988	3	1	47	1	0	0	0	0	1	0	0	0	9422	564	20	4	486	4	MCOLN3	1	85487988	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	50030026	85487988	163762633	5	4233											
GBP1	2633	broad.mit.edu	37	chr1	89528891	89528891	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttctcaatgaggcacattggGcctgtcatgtggatctctga	8	13	11	9	0	3	2	2	2	2	0	5	3	3	3	1	3	0	1	1	3	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:89528891G>T	ENST00000370473.4	-	2	246	c.27C>A	c.(25-27)ggC>ggA	p.G9G		NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	9	GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.G9G(1)		endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		GGCACATTGGGCCTGTCATGT	0.468																																					p.G9G													.	GBP1-92	1	Substitution - coding silent(1)	endometrium(1)	c.C27A						.						119	110	113					1																	89528891		2203	4300	6503	SO:0001819	synonymous_variant	2633	exon2			CATTGGGCCTGTC	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"guanylate binding protein 1, interferon-inducible, 67kDa"			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.27C>A	1.37:g.89528891G>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	193	9	NM_002053	0	0	34	34	0	D3DT26|Q5T8M1	Silent	SNP	ENST00000370473.4	37	CCDS718.1																																																																																			.		0.468	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053		T	89528891	G	T	89528891	2	4	47	1	0	0	0	0	0	0	0	1	6293	1190	42	4		4	GBP1	1	89528891	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	4040903	89528891	159721730	6	4234											
PIGR	5284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207105906	207105906	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagcgctctggagcttcCaccttgttcctcagagctgg	6	10	11	14	1	2	1	1	0	1	1	4	3	4	2	4	2	3	4	4	2	0	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:207105906C>A	ENST00000356495.4	-	8	2086	c.1903G>T	c.(1903-1905)Gga>Tga	p.G635*	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	635					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CTGGAGCTTCCACCTTGTTCC	0.617																																					p.G635X		.											.	PIGR-92	0			c.G1903T						.						46	47	47					1																	207105906		2203	4300	6503	SO:0001587	stop_gained	5284	exon8			AGCTTCCACCTTG		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1903G>T	1.37:g.207105906C>A	ENSP00000348888:p.Gly635*	Somatic	149	1		WXS	Illumina HiSeq	Phase_I	158	66	NM_002644	0	0	321	342	21	Q68D81|Q8IZY7	Nonsense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.695601	0.88830	.	.	ENSG00000162896	ENST00000356495	.	.	.	4.98	0.946	0.19549	.	0.594424	0.16002	N	0.234264	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-7.615	1.477	0.02428	0.1369:0.415:0.1336:0.3145	.	.	.	.	X	635	.	ENSP00000348888:G635X	G	-	1	0	PIGR	205172529	0.000000	0.05858	0.020000	0.16555	0.025000	0.11179	-0.769000	0.04710	0.019000	0.15079	0.561000	0.74099	GGA	.		0.617	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		A	207105906	C	A	207105906	4	1	47	1	0	0	0	0	0	1	0	0	11923	603	21	4	407	4	PIGR	1	207105906	Nonsense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	117577015	207105906	42144715	7	4235											
CD46	4179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207940508	207940508	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtctgtgacagtaacagtaCttgggatcccccagttccaa	10	11	9	11	0	1	1	0	1	1	0	3	2	3	2	3	1	2	3	3	1	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:207940508C>A	ENST00000358170.2	+	6	980	c.824C>A	c.(823-825)aCt>aAt	p.T275N	CD46_ENST00000357714.1_Missense_Mutation_p.T275N|CD46_ENST00000441839.2_Missense_Mutation_p.T275N|CD46_ENST00000367041.1_Missense_Mutation_p.T275N|CD46_ENST00000360212.2_Missense_Mutation_p.T275N|CD46_ENST00000322875.4_Missense_Mutation_p.T275N|CD46_ENST00000367042.1_Missense_Mutation_p.T275N|CD46_ENST00000322918.5_Missense_Mutation_p.T275N|CD46_ENST00000361067.1_Missense_Mutation_p.T275N|CD46_ENST00000354848.1_Missense_Mutation_p.T275N|CD46_ENST00000480003.1_Missense_Mutation_p.T275N|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000367047.1_Missense_Mutation_p.T212N	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	275	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						AGTAACAGTACTTGGGATCCC	0.358																																					p.T275N		.											.	CD46-963	0			c.C824A						.						110	105	107					1																	207940508		2203	4300	6503	SO:0001583	missense	4179	exon6			ACAGTACTTGGGA	BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.824C>A	1.37:g.207940508C>A	ENSP00000350893:p.Thr275Asn	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	60	23	NM_172352	0	0	127	216	89	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	ENST00000358170.2	37	CCDS1485.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142222	0.57044	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000322918;ENST00000367042;ENST00000367041;ENST00000357714;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000360212;ENST00000480003	T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.05	-4.14	0.03892	Complement control module (2);Sushi/SCR/CCP (3);	1.003600	0.08033	N	0.993895	T	0.68815	0.3042	M	0.69463	2.115	0.09310	N	1	P;B;D;P;B;D;B;D;P;P;P;D;D;D	0.63880	0.582;0.253;0.993;0.582;0.253;0.969;0.395;0.979;0.582;0.836;0.582;0.961;0.961;0.975	B;B;P;B;B;D;B;P;B;B;B;D;D;D	0.75020	0.2;0.141;0.869;0.2;0.141;0.974;0.227;0.831;0.2;0.32;0.2;0.961;0.961;0.985	T	0.60647	-0.7222	10	0.72032	D	0.01	.	1.9531	0.03370	0.4968:0.2102:0.1229:0.1701	.	275;275;275;275;275;275;275;275;275;275;275;275;275;275	P15529-4;P15529-5;P15529-14;P15529-3;P15529-12;P15529-13;P15529-2;P15529-11;P15529-7;P15529-9;P15529-15;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;.;.;.;.;.;MCP_HUMAN	N	275;275;275;275;275;275;275;212;275;275;275;275	ENSP00000350893:T275N;ENSP00000346912:T275N;ENSP00000314664:T275N;ENSP00000356009:T275N;ENSP00000356008:T275N;ENSP00000350346:T275N;ENSP00000313875:T275N;ENSP00000356014:T212N;ENSP00000413543:T275N;ENSP00000354358:T275N;ENSP00000353342:T275N;ENSP00000418471:T275N	ENSP00000313875:T275N	T	+	2	0	CD46	206007131	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-0.614000	0.05604	-0.469000	0.06911	0.655000	0.94253	ACT	.		0.358	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		A	207940508	C	A	207940508	3	1	47	1	0	0	0	0	1	0	0	0	3024	565	20	4	846	4	CD46	1	207940508	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	834602	207940508	41310113	8	4236											
RBM34	23029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	235318245	235318245	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caacaaacacagttctctcaTtctttaatctctcttcttct	10	17	1	13	0	7	0	1	0	6	0	9	0	7	0	0	0	2	1	0	0	3	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:235318245T>A	ENST00000408888.3	-	4	778	c.548A>T	c.(547-549)aAt>aTt	p.N183I	RBM34_ENST00000366606.3_Missense_Mutation_p.N178I			P42696	RBM34_HUMAN	RNA binding motif protein 34	183						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			AGTTCTCTCATTCTTTAATCT	0.328																																					p.N183I		.											.	RBM34-46	0			c.A548T						.						159	139	145					1																	235318245		1826	4086	5912	SO:0001583	missense	23029	exon4			CTCTCATTCTTTA		CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"RNA binding motif (RRM) containing"	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.548A>T	1.37:g.235318245T>A	ENSP00000386226:p.Asn183Ile	Somatic	288	0		WXS	Illumina HiSeq	Phase_I	266	90	NM_001161533	0	0	7	20	13	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	37	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643590	0.67244	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000447801	T;T;T	0.75154	-0.91;-0.91;0.96	5.87	5.87	0.94306	Nucleotide-binding, alpha-beta plait (1);	0.236119	0.48767	D	0.000162	D	0.85225	0.5648	M	0.76328	2.33	0.80722	D	1	D;B	0.89917	1.0;0.431	D;B	0.81914	0.995;0.186	D	0.85305	0.1075	10	0.45353	T	0.12	-17.2719	14.8054	0.69952	0.0:0.0:0.0:1.0	.	183;183	P42696-2;P42696	.;RBM34_HUMAN	I	183;178;181	ENSP00000386226:N183I;ENSP00000355565:N178I;ENSP00000400000:N181I	ENSP00000355565:N178I	N	-	2	0	RBM34	233384868	0.999000	0.42202	0.998000	0.56505	0.918000	0.54935	4.345000	0.59360	2.371000	0.80710	0.533000	0.62120	AAT	.		0.328	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014		A	235318245	T	A	235318245	3	1	47	1	0	0	0	0	1	0	0	0	13163	1493	52	5	797	5	RBM34	1	235318245	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	27377737	235318245	13932376	9	4237											
FMN2	56776	hgsc.bcm.edu	37	chr1	240371661	240371661	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccctctacctggagtgggAatacctcctccgccccctct	5	9	7	20	1	2	0	0	0	2	0	4	2	4	2	8	2	2	0	8	2	3	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:240371661A>C	ENST00000319653.9	+	5	3779	c.3549A>C	c.(3547-3549)ggA>ggC	p.G1183G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1183	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTGGAGTGGGAATACCTCCTC	0.682																																					p.G1183G		.											.	FMN2-145	0			c.A3549C						.						15	16	16					1																	240371661		2200	4294	6494	SO:0001819	synonymous_variant	56776	exon5			AGTGGGAATACCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3549A>C	1.37:g.240371661A>C		Somatic	44	1		WXS	Illumina HiSeq	Phase_I	32	3	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.		0.682	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240371661	A	C	240371661	2	2	47	1	0	0	0	0	0	0	0	1	5969	233	9	5		5	FMN2	1	240371661	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	5053416	240371661	8878960	10	4238											
HADHA	3030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	26459821	26459821	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atttcattcataacttctgaGaactctgaatgtagctcttt	11	17	5	8	0	5	2	2	2	3	1	5	3	5	2	0	0	3	2	0	0	4	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:26459821G>C	ENST00000380649.3	-	4	345	c.216C>G	c.(214-216)ttC>ttG	p.F72L	HADHA_ENST00000457468.2_Intron|HADHA_ENST00000461025.1_5'Flank	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	72					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAACTTCTGAGAACTCTGAAT	0.403																																					p.F72L		.											.	HADHA-91	0			c.C216G						.						102	99	100					2																	26459821		2203	4300	6503	SO:0001583	missense	3030	exon4			TTCTGAGAACTCT	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.216C>G	2.37:g.26459821G>C	ENSP00000370023:p.Phe72Leu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	246	82	NM_000182	0	0	61	118	57	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	37	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	G	5.697	0.313101	0.10789	.	.	ENSG00000084754	ENST00000380649	T	0.57907	0.37	5.78	1.36	0.22044	Crotonase, core (1);	0.277100	0.45126	N	0.000390	T	0.26011	0.0634	N	0.12831	0.26	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.07790	-1.0754	10	0.07990	T	0.79	-24.6945	7.1425	0.25564	0.2509:0.1413:0.6078:0.0	.	72	P40939	ECHA_HUMAN	L	72	ENSP00000370023:F72L	ENSP00000370023:F72L	F	-	3	2	HADHA	26313325	0.026000	0.19158	0.266000	0.24541	0.047000	0.14425	0.239000	0.18023	0.351000	0.24027	0.591000	0.81541	TTC	.		0.403	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26459821	G	C	26459821	3	2	47	1	0	0	0	0	1	0	0	0	6964	933	33	4	2143	4	HADHA	2	26459821	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		26459821	216739552	11	4239											
GTF3C2	2976	broad.mit.edu;bcgsc.ca	37	chr2	27565919	27565920	+	Frame_Shift_Ins	INS	-	-	TGGCCTTT																															gatggaggattaggctgttgINSgggccttttggggccttttc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565919_27565920insTGGCCTTT	ENST00000359541.2	-	3	771_772	c.342_343insAAAGGCCA	c.(340-345)ccccaafs	p.Q115fs	AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000589853.1_RNA|GTF3C2_ENST00000264720.3_Frame_Shift_Ins_p.Q115fs			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	115					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTAGGCTGTTGGGGCCTTTTGG	0.535																																					p.P115fs													.	GTF3C2-92	0			c.343_344insAAAGGCCA						.																																			SO:0001589	frameshift_variant	2976	exon3			GCTGTTGGGGCCT	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.342_343insAAAGGCCA	2.37:g.27565919_27565920insTGGCCTTT	ENSP00000352536:p.Gln115fs	Somatic	315	0		WXS	Illumina HiSeq	Phase_I	219	28	NM_001035521	0	0	0	0	0	D6W557|Q16632|Q9BWI7	Frame_Shift_Ins	INS	ENST00000359541.2	37	CCDS1749.1																																																																																			.		0.535	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			TGGCCTTT	27565920	-	TGGCCTTT	27565919	7	5	47	1	0	1	1	0	0	0	0	0	6894	1357	47	0	2460	0	GTF3C2	2	27565919	Frame_Shift_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08	1106098	27565919	215633454	12	4240	46	2									
GTF3C2	2976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27565920	27565920	+	Silent	SNP	G	G	T																															gatggaggattaggctgttgGggccttttggggccttttcg																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565920G>T	ENST00000359541.2	-	3	771	c.342C>A	c.(340-342)ccC>ccA	p.P114P	AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000589853.1_RNA|GTF3C2_ENST00000264720.3_Silent_p.P114P			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	114					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGGCTGTTGGGGCCTTTTGG	0.537																																					p.V114V		.											.	GTF3C2-92	0			c.T342A						.						94	89	91					2																	27565920		2203	4300	6503	SO:0001819	synonymous_variant	2976	exon4			CTGTTGGGGCCTT	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.342C>A	2.37:g.27565920G>T		Somatic	331	1		WXS	Illumina HiSeq	Phase_I	227	78	NM_001521	0	0	31	31	0	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	37	CCDS1749.1																																																																																			.		0.537	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			T	27565920	G	T	27565920	2	4	47	1	0	0	0	0	0	0	0	1	6894	1219	43	4		4	GTF3C2	2	27565920	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	1	27565920	215633453	13	4241	46	2									
EML4	27436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	42488420	42488420	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actccagaaagcaagaatgcTactcccaccaaaaggtttta	16	8	6	11	0	0	2	0	0	0	2	2	2	2	2	3	1	3	3	3	1	7	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:42488420T>C	ENST00000318522.5	+	4	760	c.498T>C	c.(496-498)gcT>gcC	p.A166A	EML4_ENST00000402711.2_Intron|EML4_ENST00000401738.3_Silent_p.A166A	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	166					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						GCAAGAATGCTACTCCCACCA	0.423			T	ALK	NSCLC																																p.A166A		.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4-3734	0			c.T498C						.						166	164	165					2																	42488420		2203	4300	6503	SO:0001819	synonymous_variant	27436	exon4			GAATGCTACTCCC	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"WD repeat domain containing"	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.498T>C	2.37:g.42488420T>C		Somatic	165	1		WXS	Illumina HiSeq	Phase_I	115	31	NM_019063	0	0	0	0	0	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Silent	SNP	ENST00000318522.5	37	CCDS1807.1																																																																																			.		0.423	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063		C	42488420	T	C	42488420	2	2	47	1	0	0	0	0	0	0	0	1	5112	1509	53	3		3	EML4	2	42488420	Silent	SNP	T	TCGA-B9-4113-01A-01D-1252-08	14922500	42488420	200710953	14	4242											
HAAO	23498	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	42994588	42994588	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcaagagggtcaccccagggGcttcttgcaggcagggtcct	7	7	15	12	0	2	1	1	0	1	1	3	1	3	1	3	5	1	4	3	5	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:42994588G>C	ENST00000294973.6	-	10	905	c.850C>G	c.(850-852)Ccc>Gcc	p.P284A		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase											breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						CACCCCAGGGGCTTCTTGCAG	0.617																																					p.P284A		.											.	HAAO-91	0			c.C850G						.						38	38	38					2																	42994588		2203	4300	6503	SO:0001583	missense	23498	exon10			CCAGGGGCTTCTT	Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.850C>G	2.37:g.42994588G>C	ENSP00000294973:p.Pro284Ala	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	67	11	NM_012205	0	0	27	43	16		Missense_Mutation	SNP	ENST00000294973.6	37	CCDS33187.1	.	.	.	.	.	.	.	.	.	.	g	10.57	1.385999	0.25031	.	.	ENSG00000162882	ENST00000294973	T	0.30182	1.54	4.83	1.94	0.25998	.	0.156970	0.42682	N	0.000678	T	0.24275	0.0588	L	0.55743	1.74	0.45791	D	0.998671	B	0.06786	0.001	B	0.01281	0.0	T	0.06320	-1.0833	10	0.44086	T	0.13	.	5.3274	0.15915	0.1974:0.1834:0.6193:0.0	.	284	P46952	3HAO_HUMAN	A	284	ENSP00000294973:P284A	ENSP00000294973:P284A	P	-	1	0	HAAO	42848092	0.924000	0.31332	0.996000	0.52242	0.700000	0.40528	1.053000	0.30442	0.449000	0.26747	0.550000	0.68814	CCC	.		0.617	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2			C	42994588	G	C	42994588	3	2	47	1	0	0	0	0	1	0	0	0	6958	1203	42	4	14	4	HAAO	2	42994588	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	506168	42994588	200204785	15	4243											
ANTXR1	84168	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	69472576	69472579	+	Frame_Shift_Del	DEL	GCAC	GCAC	-																															aggctccacctcccaacaggGcacctcctccctcccgccct																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	GCAC	GCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:69472576_69472579delGCAC	ENST00000303714.4	+	18	1976_1979	c.1654_1657delGCAC	c.(1654-1659)gcacctfs	p.AP552fs		NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	552	Pro-rich.				actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						tcccaacagggcacctcctccctc	0.647									Familial Infantile Hemangioma																												p.552_553del		.											.	ANTXR1-94	0			c.1654_1657del						.																																			SO:0001589	frameshift_variant	84168	exon18	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	.	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.1654_1657delGCAC	2.37:g.69472576_69472579delGCAC	ENSP00000301945:p.Ala552fs	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	106	22	NM_032208	0	0	0	0	0	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Frame_Shift_Del	DEL	ENST00000303714.4	37	CCDS1892.1																																																																																			.		0.647	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		-	69472579	GCAC	-	69472576	7	5	47	1	0	1	0	1	0	0	0	0	711	1203	42	0	1801	0	ANTXR1	2	69472576	Frame_Shift_Del	DEL	GCAC	TCGA-B9-4113-01A-01D-1252-08	26477988	69472576	173726797	16	4244											
EDAR	10913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109527287	109527287	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcctccacgctcttcccCgggtggctggtgcaacaggc	4	8	14	15	2	1	0	0	0	1	0	3	0	3	0	4	5	2	3	4	5	1	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:109527287C>T	ENST00000258443.2	-	8	1105	c.675G>A	c.(673-675)ccG>ccA	p.P225P	EDAR_ENST00000409271.1_Silent_p.P257P|EDAR_ENST00000376651.1_Silent_p.P257P	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	225					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						CGCTCTTCCCCGGGTGGCTGG	0.647																																					p.P225P		.											.	EDAR-92	0			c.G675A						.						59	58	58					2																	109527287		2203	4300	6503	SO:0001819	synonymous_variant	10913	exon8			CTTCCCCGGGTGG	AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"Tumor necrosis factor receptor superfamily"	2895	protein-coding gene	gene with protein product		604095	"ectodysplasin 1, anhidrotic receptor"	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.675G>A	2.37:g.109527287C>T		Somatic	207	1		WXS	Illumina HiSeq	Phase_I	150	48	NM_022336	0	0	1	5	4	B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Silent	SNP	ENST00000258443.2	37	CCDS2081.1																																																																																			.		0.647	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1			T	109527287	C	T	109527287	2	4	47	1	0	0	0	0	0	0	0	1	4916	639	23	1		1	EDAR	2	109527287	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	40054711	109527287	133672086	17	4245											
BIN1	274	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	127818193	127818193	+	Intron	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcttctttctgcgcagcCgcgaaaacagtttacttttc	7	16	7	11	3	3	0	0	0	3	0	4	1	3	0	1	0	4	3	1	0	3	7	rs117721706	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:127818193C>G	ENST00000316724.5	-	11	1269				BIN1_ENST00000351659.3_Intron|BIN1_ENST00000352848.3_Missense_Mutation_p.R263P|BIN1_ENST00000409400.1_Intron|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000259238.4_Missense_Mutation_p.R263P|BIN1_ENST00000376113.2_Missense_Mutation_p.R263P|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000346226.3_Intron|BIN1_ENST00000393041.3_Intron|BIN1_ENST00000357970.3_Intron	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1						cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		TCTGCGCAGCCGCGAAAACAG	0.632																																					p.R263P		.											.	BIN1-655	0			c.G788C						.						120	112	114					2																	127818193		2203	4300	6503	SO:0001627	intron_variant	274	exon10			CGCAGCCGCGAAA	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.858-1462G>C	2.37:g.127818193C>G		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	143	47	NM_139346	0	0	0	0	0	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387780	0.61956	.	.	ENSG00000136717	ENST00000376113;ENST00000259238;ENST00000352848	T;T;T	0.56611	0.45;0.47;0.53	4.72	4.72	0.59763	.	.	.	.	.	T	0.68559	0.3014	.	.	.	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.75484	0.986;0.986;0.986	T	0.66031	-0.6024	8	0.29301	T	0.29	.	14.976	0.71273	0.0:1.0:0.0:0.0	.	263;263;263	O00499-8;O00499-11;O00499-10	.;.;.	P	263	ENSP00000365281:R263P;ENSP00000259238:R263P;ENSP00000315284:R263P	ENSP00000259238:R263P	R	-	2	0	BIN1	127534663	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.415000	0.52700	2.337000	0.79520	0.561000	0.74099	CGG	C|0.992;T|0.008		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		G	127818193	C	G	127818193	1	3	47	0	1	0	0	0	0	0	0	0	1433	652	23	4		4	BIN1	2	127818193	Intron	SNP	C	TCGA-B9-4113-01A-01D-1252-08	18290906	127818193	115381180	18	4246											
ORC2L	4999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	201790595	201790595	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tactatccagtctagctgatCcagtatactgcggaaagtac	12	11	8	10	1	1	1	0	1	1	0	3	2	3	2	2	1	5	3	2	1	7	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:201790595C>A	ENST00000234296.2	-	13	1360	c.1111G>T	c.(1111-1113)Gat>Tat	p.D371Y	RN7SL694P_ENST00000584245.1_RNA	NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	371					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						TCTAGCTGATCCAGTATACTG	0.348																																					p.D371Y		.											.	ORC2-209	0			c.G1111T						.						154	148	150					2																	201790595		2203	4300	6503	SO:0001583	missense	4999	exon13			GCTGATCCAGTAT		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1111G>T	2.37:g.201790595C>A	ENSP00000234296:p.Asp371Tyr	Somatic	213	1		WXS	Illumina HiSeq	Phase_I	218	79	NM_006190	0	0	3	3	0	Q13204|Q53TX5	Missense_Mutation	SNP	ENST00000234296.2	37	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273726	0.80580	.	.	ENSG00000115942	ENST00000234296	T	0.45276	0.9	5.34	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.68329	0.2989	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.75178	-0.3409	10	0.72032	D	0.01	-18.2187	14.1557	0.65417	0.0:0.9274:0.0:0.0726	.	371;371	B4DYU9;Q13416	.;ORC2_HUMAN	Y	371	ENSP00000234296:D371Y	ENSP00000234296:D371Y	D	-	1	0	ORC2	201498840	1.000000	0.71417	0.995000	0.50966	0.963000	0.63663	7.050000	0.76620	1.396000	0.46663	0.585000	0.79938	GAT	.		0.348	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		A	201790595	C	A	201790595	3	1	47	1	0	0	0	0	1	0	0	0	11288	855	30	4	646	4	ORC2L	2	201790595	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	73972402	201790595	41408778	19	4247											
XRCC5	7520	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	216981563	216981564	+	Frame_Shift_Ins	INS	-	-	C																															ccaggttctcaacaggctgaINSctgtatcctttttctgccag																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:216981563_216981564insC	ENST00000392133.3	+	5	778_779	c.317_318insC	c.(316-321)gacttcfs	p.F107fs	XRCC5_ENST00000392132.2_Frame_Shift_Ins_p.F107fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	107					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		CAACAGGCTGACTGTATCCTTT	0.421								Non-homologous end-joining																													p.D106fs		.											.	XRCC5-970	0			c.317_318insC						.																																			SO:0001589	frameshift_variant	7520	exon3			.	AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246			12833	protein-coding gene	gene with protein product	"Ku autoantigen, 80kDa"	194364	"X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)"			9636207, 9214634	Standard	NM_021141		Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.318dupC	2.37:g.216981564_216981564dupC	ENSP00000375978:p.Phe107fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	75	24	NM_021141	0	0	0	0	0	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Frame_Shift_Ins	INS	ENST00000392133.3	37	CCDS2402.1																																																																																			.		0.421	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		C	216981564	-	C	216981563	7	5	47	1	0	1	1	0	0	0	0	0	17489	275	10	0	327	0	XRCC5	2	216981563	Frame_Shift_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08	15190968	216981563	26217810	20	4248											
TRNT1	51095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	3189651	3189651	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtaccaaggagagcactGtctcctaaaggaaatgcagc	15	6	11	9	0	1	1	0	0	1	1	2	4	1	2	2	2	4	3	2	2	6	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:3189651G>C	ENST00000251607.6	+	8	1220	c.1118G>C	c.(1117-1119)tGt>tCt	p.C373S	TRNT1_ENST00000280591.6_Missense_Mutation_p.C353S	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	373					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)			breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		GGAGAGCACTGTCTCCTAAAG	0.438																																					p.C373S		.											.	TRNT1-90	0			c.G1118C						.						118	110	113					3																	3189651		2203	4300	6503	SO:0001583	missense	51095	exon8			AGCACTGTCTCCT	AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.1118G>C	3.37:g.3189651G>C	ENSP00000251607:p.Cys373Ser	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	20	8	NM_182916	0	0	14	20	6	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Missense_Mutation	SNP	ENST00000251607.6	37	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	G	9.399	1.077394	0.20227	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	T;T	0.39229	1.09;1.11	5.24	2.0	0.26442	.	1.262890	0.05220	N	0.508422	T	0.22085	0.0532	N	0.08118	0	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19910	-1.0291	10	0.17832	T	0.49	-3.7877	5.7122	0.17941	0.1687:0.3466:0.4847:0.0	.	353;373	Q96Q11-2;Q96Q11	.;TRNT1_HUMAN	S	373;353	ENSP00000251607:C373S;ENSP00000280591:C353S	ENSP00000251607:C373S	C	+	2	0	TRNT1	3164651	0.026000	0.19158	0.010000	0.14722	0.971000	0.66376	2.269000	0.43346	1.168000	0.42723	0.655000	0.94253	TGT	.		0.438	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			C	3189651	G	C	3189651	3	2	47	1	0	0	0	0	1	0	0	0	16606	1377	48	4	1144	4	TRNT1	3	3189651	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		3189651	194832779	21	4249											
OSBPL10	114884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	31774841	31774841	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgatggcaaagagccaaGtgtcccatttttcagctgct	9	11	11	10	0	1	2	1	1	0	1	2	2	2	2	2	2	3	4	2	2	2	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:31774841G>A	ENST00000396556.2	-	6	1125	c.1003C>T	c.(1003-1005)Ctt>Ttt	p.L335F	OSBPL10_ENST00000438237.2_Missense_Mutation_p.L271F|OSBPL10_ENST00000467647.1_5'UTR	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	335					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		AAAGAGCCAAGTGTCCCATTT	0.473																																					p.L335F		.											.	OSBPL10-69	0			c.C1003T						.						166	156	159					3																	31774841		2203	4300	6503	SO:0001583	missense	114884	exon6			AGCCAAGTGTCCC	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1003C>T	3.37:g.31774841G>A	ENSP00000379804:p.Leu335Phe	Somatic	318	0		WXS	Illumina HiSeq	Phase_I	285	80	NM_017784	0	0	5	16	11	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.285363	0.40394	.	.	ENSG00000144645	ENST00000396556;ENST00000438237;ENST00000428241	T;T;T	0.52983	1.87;2.22;0.64	5.66	2.21	0.28008	.	0.326770	0.33075	N	0.005319	T	0.41328	0.1154	M	0.68952	2.095	0.45076	D	0.998091	B;B;B	0.19445	0.036;0.005;0.001	B;B;B	0.15870	0.014;0.005;0.005	T	0.30621	-0.9972	10	0.52906	T	0.07	-1.9596	6.3688	0.21469	0.2078:0.138:0.6542:0.0	.	271;335;103	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	F	335;271;143	ENSP00000379804:L335F;ENSP00000406124:L271F;ENSP00000399200:L143F	ENSP00000379804:L335F	L	-	1	0	OSBPL10	31749845	0.602000	0.26916	0.675000	0.29917	0.982000	0.71751	0.776000	0.26704	0.470000	0.27294	0.555000	0.69702	CTT	.		0.473	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	31774841	G	A	31774841	3	1	47	1	0	0	0	0	1	0	0	0	11301	1029	36	2	1319	2	OSBPL10	3	31774841	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	28585190	31774841	166247589	22	4250											
ATR	545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142274792	142274792	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacagaagcttttagttgAgaagatgaacattcatgttg	14	12	10	5	0	1	5	1	2	0	4	1	6	1	5	0	0	2	3	0	0	4	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:142274792A>T	ENST00000350721.4	-	10	2389	c.2268T>A	c.(2266-2268)tcT>tcA	p.S756S	ATR_ENST00000383101.3_Silent_p.S692S	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	756					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CTTTTAGTTGAGAAGATGAAC	0.368								Other conserved DNA damage response genes																													p.S756S		.											.	ATR-1139	0			c.T2268A						.						118	119	119					3																	142274792		2203	4300	6503	SO:0001819	synonymous_variant	545	exon10			TAGTTGAGAAGAT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2268T>A	3.37:g.142274792A>T		Somatic	178	0		WXS	Illumina HiSeq	Phase_I	128	42	NM_001184	0	0	2	2	0	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			.		0.368	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142274792	A	T	142274792	2	4	47	1	0	0	0	0	0	0	0	1	1205	291	11	5		5	ATR	3	142274792	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	110499951	142274792	55747638	23	4251											
CRYGS	1427	broad.mit.edu	37	chr3	186256498	186256498	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgtcattactccacaatgCggcggaaagactggacagct	12	8	10	11	2	1	1	1	0	0	1	2	3	2	3	1	3	3	1	1	3	3	1	rs201717880		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:186256498C>T	ENST00000392499.2	-	4	863	c.524G>A	c.(523-525)cGc>cAc	p.R175H	CRYGS_ENST00000307944.5_Missense_Mutation_p.R175H	NM_017541.2	NP_060011.1	P22914	CRBS_HUMAN	crystallin, gamma S	175	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|morphogenesis of an epithelium (GO:0002009)		structural constituent of eye lens (GO:0005212)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	11	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		CTCCACAATGCGGCGGAAAGA	0.547																																					p.R175H													.	CRYGS-90	0			c.G524A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	67	64	65		524	5.8	1	3		65	0,8600		0,0,4300	no	missense	CRYGS	NM_017541.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	175/179	186256498	1,13005	2203	4300	6503	SO:0001583	missense	1427	exon3			ACAATGCGGCGGA		CCDS3275.1	3q27.3	2013-02-14			ENSG00000213139	ENSG00000213139			2417	protein-coding gene	gene with protein product	"crystallin, gamma 8"	123730		CRYG8			Standard	NM_017541		Approved		uc003fqe.3	P22914	OTTHUMG00000156615	ENST00000392499.2:c.524G>A	3.37:g.186256498C>T	ENSP00000376287:p.Arg175His	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	217	4	NM_017541	0	0	6	6	0	B2RAF8	Missense_Mutation	SNP	ENST00000392499.2	37	CCDS3275.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913335	0.92178	2.27E-4	0.0	ENSG00000213139	ENST00000392499;ENST00000307944	T;T	0.78364	-1.17;-1.17	5.76	5.76	0.90799	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.081544	0.49916	U	0.000130	D	0.88948	0.6576	M	0.88775	2.98	0.52099	D	0.999945	D	0.63880	0.993	D	0.64144	0.922	D	0.90435	0.4427	10	0.72032	D	0.01	.	15.4519	0.75279	0.0:1.0:0.0:0.0	.	175	P22914	CRBS_HUMAN	H	175	ENSP00000376287:R175H;ENSP00000312099:R175H	ENSP00000312099:R175H	R	-	2	0	CRYGS	187739192	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.626000	0.67777	2.721000	0.93114	0.563000	0.77884	CGC	C|0.999;T|0.001		0.547	CRYGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344784.1	NM_017541		T	186256498	C	T	186256498	3	4	47	1	0	0	0	0	1	0	0	0	3925	768	27	1	16	1	CRYGS	3	186256498	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	43981706	186256498	11765932	24	4252											
SLC26A1	10861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	985220	985220	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgcagcccggccagcaatGagtaggcgatggcctgcggc	7	5	16	13	3	0	1	0	1	0	0	0	2	0	1	3	4	4	4	3	4	2	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:985220G>A	ENST00000361661.2	-	3	649	c.272C>T	c.(271-273)tCa>tTa	p.S91L	IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Missense_Mutation_p.S91L|IDUA_ENST00000453894.1_Intron|SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398520.2_Missense_Mutation_p.S91L	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	91					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCAGCAATGAGTAGGCGAT	0.632																																					p.S91L		.											.	SLC26A1-91	0			c.C272T						.						105	99	101					4																	985220		2203	4300	6503	SO:0001583	missense	10861	exon2			AGCAATGAGTAGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.272C>T	4.37:g.985220G>A	ENSP00000354721:p.Ser91Leu	Somatic	257	0		WXS	Illumina HiSeq	Phase_I	228	82	NM_022042	0	0	0	0	0	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	37	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559905	0.65538	.	.	ENSG00000145217	ENST00000398520;ENST00000361661;ENST00000398516	D;D;D	0.92495	-3.05;-3.05;-3.05	5.18	5.18	0.71444	.	0.226096	0.46758	D	0.000276	D	0.96993	0.9018	M	0.93763	3.455	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.72338	0.977;0.969	D	0.98001	1.0360	10	0.87932	D	0	.	16.1549	0.81657	0.0:0.0:1.0:0.0	.	91;91	Q9H2B4;Q96BK0	S26A1_HUMAN;.	L	91	ENSP00000381532:S91L;ENSP00000354721:S91L;ENSP00000381528:S91L	ENSP00000354721:S91L	S	-	2	0	SLC26A1	975220	0.998000	0.40836	0.985000	0.45067	0.336000	0.28762	2.673000	0.46858	2.402000	0.81655	0.313000	0.20887	TCA	.		0.632	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		A	985220	G	A	985220	3	1	47	1	0	0	0	0	1	0	0	0	14546	1294	45	2	1944	2	SLC26A1	4	985220	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		985220	190169056	25	4253											
ACOX3	8310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	8417674	8417674	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tctccaaggacagatcggctCcaggggaacgagcgaaaaga	14	4	13	10	3	1	2	0	0	1	2	4	6	2	4	2	4	2	1	2	4	4	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:8417674C>T	ENST00000356406.5	-	3	274	c.197G>A	c.(196-198)gGa>gAa	p.G66E	ACOX3_ENST00000413009.2_Missense_Mutation_p.G66E|ACOX3_ENST00000503233.1_Missense_Mutation_p.G66E	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	66					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CAGATCGGCTCCAGGGGAACG	0.483																																					p.G66E		.											.	ACOX3-90	0			c.G197A						.						71	67	68					4																	8417674		2203	4300	6503	SO:0001583	missense	8310	exon3			TCGGCTCCAGGGG	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.197G>A	4.37:g.8417674C>T	ENSP00000348775:p.Gly66Glu	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	197	74	NM_001101667	0	0	3	7	4	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	9.453	1.091143	0.20471	.	.	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	T;T;T	0.41758	0.99;0.99;0.99	5.39	-0.535	0.11879	Acyl-CoA dehydrogenase/oxidase (1);	0.611319	0.16430	N	0.214753	T	0.21509	0.0518	L	0.31664	0.95	0.38700	D	0.952962	B;B	0.16166	0.016;0.01	B;B	0.17433	0.018;0.005	T	0.33007	-0.9885	10	0.02654	T	1	-6.3195	6.2369	0.20768	0.0:0.5193:0.1203:0.3604	.	66;66	O15254-2;O15254	.;ACOX3_HUMAN	E	66	ENSP00000413994:G66E;ENSP00000348775:G66E;ENSP00000421625:G66E	ENSP00000348775:G66E	G	-	2	0	ACOX3	8468574	0.730000	0.28100	0.000000	0.03702	0.001000	0.01503	1.878000	0.39608	-0.212000	0.10109	-0.145000	0.13849	GGA	.		0.483	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			T	8417674	C	T	8417674	3	4	47	1	0	0	0	0	1	0	0	0	160	855	30	2	1969	2	ACOX3	4	8417674	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	7432454	8417674	182736602	26	4254											
GPR125	166647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	22390249	22390249	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtaatacaaagaaacagcCaaagccccaaacatccacag	19	3	7	12	0	0	1	0	0	0	1	1	1	1	1	4	1	5	1	4	1	6	2	rs76872619	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:22390249C>G	ENST00000334304.5	-	19	3314	c.3045G>C	c.(3043-3045)ttG>ttC	p.L1015F	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	1015					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				AAGAAACAGCCAAAGCCCCAA	0.443																																					p.L1015F		.											.	GPR125-91	0			c.G3045C						.						99	100	99					4																	22390249		2203	4300	6503	SO:0001583	missense	166647	exon19			AACAGCCAAAGCC	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing"	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.3045G>C	4.37:g.22390249C>G	ENSP00000334952:p.Leu1015Phe	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	144	57	NM_145290	0	0	68	125	57	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.184403	0.38609	.	.	ENSG00000152990	ENST00000334304	T	0.57107	0.42	5.94	5.94	0.96194	GPCR, family 2-like (1);	0.113047	0.64402	D	0.000011	T	0.52256	0.1723	L	0.58428	1.81	0.80722	D	1	B;B	0.12013	0.005;0.001	B;B	0.22753	0.041;0.007	T	0.43972	-0.9358	10	0.40728	T	0.16	-0.1446	15.9022	0.79387	0.1359:0.8641:0.0:0.0	.	872;1015	Q8IWK6-3;Q8IWK6	.;GP125_HUMAN	F	1015	ENSP00000334952:L1015F	ENSP00000334952:L1015F	L	-	3	2	GPR125	21999347	1.000000	0.71417	0.987000	0.45799	0.924000	0.55760	3.534000	0.53568	2.807000	0.96579	0.650000	0.86243	TTG	C|1.000;T|0.000		0.443	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			G	22390249	C	G	22390249	3	3	47	1	0	0	0	0	1	0	0	0	6659	593	21	4	924	4	GPR125	4	22390249	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	13972575	22390249	168764027	27	4255											
AASDH	132949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57248668	57248668	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgttttttttcaacaaggAtatactttagattacatttt	11	22	4	4	0	1	1	1	0	0	1	1	2	1	2	0	1	3	1	0	1	6	12			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:57248668A>T	ENST00000205214.6	-	3	506	c.326T>A	c.(325-327)aTc>aAc	p.I109N	AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000513376.1_Missense_Mutation_p.I9N|AASDH_ENST00000602986.1_Intron|AASDH_ENST00000451613.1_Missense_Mutation_p.I109N|AASDH_ENST00000502617.1_Missense_Mutation_p.I109N|AASDH_ENST00000510762.1_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	109					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TTCAACAAGGATATACTTTAG	0.323																																					p.I109N		.											.	AASDH-94	0			c.T326A						.						47	48	48					4																	57248668		2203	4300	6503	SO:0001583	missense	132949	exon3			ACAAGGATATACT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.326T>A	4.37:g.57248668A>T	ENSP00000205214:p.Ile109Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	45	16	NM_181806	0	0	1	1	0	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.611899	0.87258	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000502617	T;T;T;T	0.66638	0.83;-0.22;0.83;0.83	5.88	5.88	0.94601	AMP-dependent synthetase/ligase (1);	0.289492	0.43919	D	0.000514	T	0.81093	0.4751	M	0.78049	2.395	0.25673	N	0.985874	D;D;D;D	0.65815	0.989;0.991;0.995;0.991	P;D;P;P	0.63957	0.87;0.92;0.902;0.873	T	0.76408	-0.2970	10	0.87932	D	0	-4.2072	15.9439	0.79779	1.0:0.0:0.0:0.0	.	109;109;109;109	Q4L235-4;B4E2K0;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	N	109;9;109;109	ENSP00000205214:I109N;ENSP00000423760:I9N;ENSP00000409656:I109N;ENSP00000421171:I109N	ENSP00000205214:I109N	I	-	2	0	AASDH	56943425	1.000000	0.71417	0.864000	0.33941	0.979000	0.70002	6.594000	0.74104	2.250000	0.74265	0.533000	0.62120	ATC	.		0.323	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		T	57248668	A	T	57248668	3	4	47	1	0	0	0	0	1	0	0	0	22	333	12	5	3022	5	AASDH	4	57248668	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	34858419	57248668	133905608	28	4256											
ABCG2	9429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	89039327	89039327	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cataagtcttcctgaggccaAtaaggtgaggctatcaaaca	14	9	9	9	0	2	2	1	2	1	0	3	2	3	2	2	3	1	1	2	3	5	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:89039327A>G	ENST00000237612.3	-	7	1320	c.775T>C	c.(775-777)Ttg>Ctg	p.L259L	ABCG2_ENST00000515655.1_Silent_p.L259L	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	259	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CCTGAGGCCAATAAGGTGAGG	0.433																																					p.L259L		.											.	ABCG2-90	0			c.T775C						.						127	115	119					4																	89039327		2203	4300	6503	SO:0001819	synonymous_variant	9429	exon7			AGGCCAATAAGGT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.775T>C	4.37:g.89039327A>G		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	86	32	NM_004827	0	0	3	3	0	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Silent	SNP	ENST00000237612.3	37	CCDS3628.1																																																																																			.		0.433	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		G	89039327	A	G	89039327	2	3	47	1	0	0	0	0	0	0	0	1	69	98	4	3		3	ABCG2	4	89039327	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	31790659	89039327	102114949	29	4257											
NDST4	64579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	115767018	115767018	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgtctgaggggtcaatgagGatggtgatgatcttggcttt	7	14	15	5	0	3	4	1	4	2	0	3	5	3	5	0	5	0	1	0	5	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:115767018G>A	ENST00000264363.2	-	10	2754	c.2076C>T	c.(2074-2076)atC>atT	p.I692I		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	692	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GGTCAATGAGGATGGTGATGA	0.433																																					p.I692I		.											.	NDST4-94	0			c.C2076T						.						135	126	129					4																	115767018		2203	4300	6503	SO:0001819	synonymous_variant	64579	exon10			AATGAGGATGGTG	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2076C>T	4.37:g.115767018G>A		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	128	51	NM_022569	0	0	0	0	0	Q2KHM8	Silent	SNP	ENST00000264363.2	37	CCDS3706.1																																																																																			.		0.433	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		A	115767018	G	A	115767018	2	1	47	1	0	0	0	0	0	0	0	1	10284	1164	41	2		2	NDST4	4	115767018	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	26727691	115767018	75387258	30	4258											
ASB5	140458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	177136796	177136796	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtaacgttggcagctggagTtgtgggataaggtgcaatct	10	11	15	5	1	1	0	0	0	1	0	1	2	1	2	0	4	3	6	0	4	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:177136796T>C	ENST00000296525.3	-	7	1058	c.945A>G	c.(943-945)caA>caG	p.Q315Q	ASB5_ENST00000512254.1_Silent_p.Q262Q	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	315	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GCAGCTGGAGTTGTGGGATAA	0.368																																					p.Q315Q		.											.	ASB5-228	0			c.A945G						.						119	109	113					4																	177136796		2203	4300	6503	SO:0001819	synonymous_variant	140458	exon7			CTGGAGTTGTGGG	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"Ankyrin repeat domain containing"	17180	protein-coding gene	gene with protein product		615050	"ankyrin repeat and SOCS box-containing 5"				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.945A>G	4.37:g.177136796T>C		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	56	16	NM_080874	0	0	0	0	0	Q8N7B5	Silent	SNP	ENST00000296525.3	37	CCDS3827.1																																																																																			.		0.368	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1			C	177136796	T	C	177136796	2	2	47	1	0	0	0	0	0	0	0	1	1027	1722	60	3		3	ASB5	4	177136796	Silent	SNP	T	TCGA-B9-4113-01A-01D-1252-08	61369778	177136796	14017480	31	4259											
FAM149A	25854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187077186	187077186	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgaacaaaaaccagctcAgcccggtaggaaatggcgca	14	6	10	11	2	2	1	1	1	1	0	2	2	2	2	2	3	4	3	2	3	5	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:187077186A>G	ENST00000356371.5	+	7	1289	c.1289A>G	c.(1288-1290)cAg>cGg	p.Q430R	FAM149A_ENST00000502970.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000389354.5_Missense_Mutation_p.Q139R|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000514153.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000503432.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000227065.4_Missense_Mutation_p.Q139R			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	430										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		AAACCAGCTCAGCCCGGTAGG	0.433																																					p.Q139R		.											.	FAM149A-90	0			c.A416G						.						103	96	98					4																	187077186		2203	4300	6503	SO:0001583	missense	25854	exon6			CAGCTCAGCCCGG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1289A>G	4.37:g.187077186A>G	ENSP00000348732:p.Gln430Arg	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	114	41	NM_001006655	0	0	50	89	39	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		.	.	.	.	.	.	.	.	.	.	A	8.579	0.881917	0.17467	.	.	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.11169	2.81;2.8;2.81;2.81;2.81;2.81	5.46	-10.9	0.00192	.	1.583490	0.03252	N	0.182041	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.08055	0.002;0.003;0.001	T	0.34004	-0.9846	10	0.12766	T	0.61	0.1667	2.1131	0.03708	0.3:0.2092:0.3344:0.1565	.	430;430;139	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	R	139;430;139;139;139;139	ENSP00000426835:Q139R;ENSP00000348732:Q430R;ENSP00000227065:Q139R;ENSP00000427155:Q139R;ENSP00000424380:Q139R;ENSP00000374005:Q139R	ENSP00000227065:Q139R	Q	+	2	0	FAM149A	187314180	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.206000	0.03011	-1.534000	0.01743	-0.343000	0.07986	CAG	.		0.433	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		G	187077186	A	G	187077186	3	3	47	1	0	0	0	0	1	0	0	0	5471	188	7	3	430	3	FAM149A	4	187077186	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	9940390	187077186	4077090	32	4260											
LIFR	3977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	38504185	38504185	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttaacagctgttgaattaaTatccttcactttgaatgaag	13	16	6	6	0	1	3	1	3	0	0	2	3	2	3	1	0	2	2	1	0	6	7			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:38504185T>C	ENST00000263409.4	-	10	1492	c.1330A>G	c.(1330-1332)Att>Gtt	p.I444V	LIFR_ENST00000453190.2_Missense_Mutation_p.I444V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	444	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GTTGAATTAATATCCTTCACT	0.269			T	PLAG1	salivary adenoma																																p.I444V	Melanoma(13;4 730 6426 9861 34751)	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR-1173	0			c.A1330G						.						54	59	58					5																	38504185		2201	4295	6496	SO:0001583	missense	3977	exon10			AATTAATATCCTT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1330A>G	5.37:g.38504185T>C	ENSP00000263409:p.Ile444Val	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	57	18	NM_002310	0	0	0	0	0	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	T	3.712	-0.059335	0.07317	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.56103	0.48;0.48	5.65	-2.44	0.06502	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.807977	0.11218	N	0.587055	T	0.34164	0.0888	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30534	-0.9975	10	0.11794	T	0.64	-5.8891	11.1796	0.48620	0.0:0.4564:0.0:0.5436	.	444	P42702	LIFR_HUMAN	V	444	ENSP00000263409:I444V;ENSP00000398368:I444V	ENSP00000263409:I444V	I	-	1	0	LIFR	38539942	0.638000	0.27225	0.525000	0.27900	0.996000	0.88848	0.083000	0.14871	-0.426000	0.07360	0.528000	0.53228	ATT	.		0.269	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		C	38504185	T	C	38504185	3	2	47	1	0	0	0	0	1	0	0	0	8802	1406	49	3	2007	3	LIFR	5	38504185	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		38504185	142411075	33	4261											
RICTOR	253260	broad.mit.edu	37	chr5	38953603	38953603	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagttttttaatttcttccCacttatccaaatctggtgta	9	19	4	9	0	3	0	1	0	2	0	5	0	5	0	2	1	0	2	2	1	4	7			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:38953603C>G	ENST00000357387.3	-	28	2780	c.2750G>C	c.(2749-2751)tGg>tCg	p.W917S	RICTOR_ENST00000296782.5_Missense_Mutation_p.W917S|RICTOR_ENST00000503698.1_5'Flank	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2									p.W917L(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					AATTTCTTCCCACTTATCCAA	0.284																																					p.W917S													.	RICTOR-849	1	Substitution - Missense(1)	lung(1)	c.G2750C						.						108	118	115					5																	38953603		2201	4292	6493	SO:0001583	missense	253260	exon28			TCTTCCCACTTAT		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.2750G>C	5.37:g.38953603C>G	ENSP00000349959:p.Trp917Ser	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_152756	0	0	3	4	1		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.144587	0.37825	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.62105	0.05;0.05	5.38	5.38	0.77491	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.71221	0.3314	L	0.39633	1.23	0.80722	D	1	B;D	0.76494	0.019;0.999	B;D	0.83275	0.06;0.996	T	0.73132	-0.4079	10	0.87932	D	0	-6.6249	13.2617	0.60108	0.0:0.9169:0.0:0.0831	.	917;917	Q6R327;Q6R327-3	RICTR_HUMAN;.	S	917	ENSP00000349959:W917S;ENSP00000296782:W917S	ENSP00000296782:W917S	W	-	2	0	RICTOR	38989360	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.058000	0.57463	2.668000	0.90789	0.591000	0.81541	TGG	.		0.284	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		G	38953603	C	G	38953603	3	3	47	1	0	0	0	0	1	0	0	0	13390	595	21	4	2420	4	RICTOR	5	38953603	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	449418	38953603	141961657	34	4262											
C5orf34	375444	ucsc.edu	37	chr5	43490825	43490825	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatgatgttactgttgtCacatatctaaagtgaataca	14	13	6	8	0	2	2	1	2	1	0	2	2	2	2	1	0	2	2	1	0	6	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:43490825C>A	ENST00000306862.2	-	11	1962	c.1587G>T	c.(1585-1587)gtG>gtT	p.V529V	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	529										breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					TTACTGTTGTCACATATCTAA	0.318																																					p.V529V													.	C5orf34-153	0			c.G1587T						.						77	73	75					5																	43490825		2203	4300	6503	SO:0001819	synonymous_variant	375444	exon11			TGTTGTCACATAT	AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.1587G>T	5.37:g.43490825C>A		Somatic	41	0		WXS	Illumina HiSeq		35	4	NM_198566	0	0	0	0	0		Silent	SNP	ENST00000306862.2	37	CCDS3946.1																																																																																			.		0.318	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566		A	43490825	C	A	43490825	2	1	47	1	0	0	0	0	0	0	0	1	2299	813	29	4		4	C5orf34	5	43490825	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	4537222	43490825	137424435	35	4263											
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735215	140735218	+	Frame_Shift_Del	DEL	GCAA	GCAA	-																															ctgaaaatgaaaatcctgggGcaagatttcctcttcctgaa																								rs11575949	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	GCAA	GCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:140735215_140735218delGCAA	ENST00000571252.1	+	1	448_451	c.448_451delGCAA	c.(448-453)gcaagafs	p.AR150fs	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	150	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in dbSNP:rs11575949).		homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATCCTGGGGCAAGATTTCCTCT	0.446																																					p.150_151del		.											.	.	0			c.448_451del						.																																			SO:0001589	frameshift_variant	56111	exon1			.	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.448_451delGCAA	5.37:g.140735215_140735218delGCAA	ENSP00000458570:p.Ala150fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	81	19	NM_018917	0	0	0	0	0	Q9Y5D3	Frame_Shift_Del	DEL	ENST00000571252.1	37	CCDS58979.1																																																																																			.		0.446	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		-	140735218	GCAA	-	140735215	7	5	47	1	0	1	0	1	0	0	0	0	11582	1203	42	0	450	0	PCDHGA4	5	140735215	Frame_Shift_Del	DEL	GCAA	TCGA-B9-4113-01A-01D-1252-08	97244390	140735215	40180045	36	4264	47	3									
PCDHGA4	56111	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140735217	140735218	+	Frame_Shift_Ins	INS	-	-	G																															aaaatgaaaatcctggggcaINSagatttcctcttcctgaagc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:140735217_140735218insG	ENST00000571252.1	+	1	450_451	c.450_451insG	c.(451-453)agafs	p.R151fs	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	151	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCTGGGGCAAGATTTCCTCT	0.45																																					p.A150fs		.											.	.	0			c.450_451insG						.																																			SO:0001589	frameshift_variant	56111	exon1			.	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		Exception_encountered	5.37:g.140735217_140735218insG	ENSP00000458570:p.Arg151fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	77	22	NM_018917	0	0	0	0	0	Q9Y5D3	Frame_Shift_Ins	INS	ENST00000571252.1	37	CCDS58979.1																																																																																			.		0.45	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		G	140735218	-	G	140735217	7	5	47	1	0	1	1	0	0	0	0	0	11582	117	5	0	452	0	PCDHGA4	5	140735217	Frame_Shift_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08	2	140735217	40180043	37	4265	47	3									
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735218	140735218	+	Missense_Mutation	SNP	A	A	G																															aaaatgaaaatcctggggcaAgatttcctcttcctgaagct																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:140735218A>G	ENST00000571252.1	+	1	451	c.451A>G	c.(451-453)Aga>Gga	p.R151G	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	151	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTGGGGCAAGATTTCCTCT	0.453																																					p.R151G		.											.	.	0			c.A451G						.						68	70	70					5																	140735218		1883	4114	5997	SO:0001583	missense	56111	exon1			GGGGCAAGATTTC	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.451A>G	5.37:g.140735218A>G	ENSP00000458570:p.Arg151Gly	Somatic	110	2		WXS	Illumina HiSeq	Phase_I	79	22	NM_018917	0	0	0	0	0	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.		0.453	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		G	140735218	A	G	140735218	3	3	47	1	0	0	0	0	1	0	0	0	11582	64	3	3	453	3	PCDHGA4	5	140735218	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	1	140735218	40180042	38	4266	47	3									
SLC36A3	285641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	150660717	150660717	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgaagaagatgccgatagaGtacatcagcttgactgactg	13	9	12	7	1	1	6	1	3	0	3	1	7	1	6	1	0	3	2	1	0	4	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:150660717G>T	ENST00000335230.3	-	9	1413	c.1002C>A	c.(1000-1002)taC>taA	p.Y334*	SLC36A3_ENST00000377713.3_Nonsense_Mutation_p.Y375*	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	334						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCCGATAGAGTACATCAGCT	0.522																																					p.Y375X		.											.	SLC36A3-93	0			c.C1125A						.						222	171	188					5																	150660717		2203	4300	6503	SO:0001587	stop_gained	285641	exon10			GATAGAGTACATC	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1002C>A	5.37:g.150660717G>T	ENSP00000334750:p.Tyr334*	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	198	75	NM_001145017	0	0	0	0	0	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Nonsense_Mutation	SNP	ENST00000335230.3	37	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	G	39	7.569738	0.98365	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	.	.	.	4.06	1.12	0.20585	.	0.196500	0.45361	D	0.000367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.071	7.6369	0.28272	0.4739:0.0:0.5261:0.0	.	.	.	.	X	334;375	.	ENSP00000334750:Y334X	Y	-	3	2	SLC36A3	150640910	1.000000	0.71417	0.967000	0.41034	0.964000	0.63967	1.720000	0.38022	0.092000	0.17331	0.561000	0.74099	TAC	.		0.522	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150660717	G	T	150660717	4	4	47	1	0	0	0	0	0	1	0	0	14627	1024	36	4	418	4	SLC36A3	5	150660717	Nonsense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	9925499	150660717	30254543	39	4267											
RGS14	10636	hgsc.bcm.edu;broad.mit.edu	37	chr5	176797996	176797996	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcagcccattctggagaaGcacggcttgagcccgctaga	9	7	12	13	2	1	3	0	1	1	2	1	4	1	3	2	2	4	4	2	2	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:176797996G>T	ENST00000408923.3	+	11	1406	c.1218G>T	c.(1216-1218)aaG>aaT	p.K406N		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	406	Necessary for interaction with RABGEF1. {ECO:0000250}.|RBD 2. {ECO:0000255|PROSITE- ProRule:PRU00262}.				cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCTGGAGAAGCACGGCTTGA	0.751																																					p.K406N	NSCLC(47;353 1896 28036)	.											.	RGS14-226	0			c.G1218T						.						10	12	11					5																	176797996		1750	3841	5591	SO:0001583	missense	10636	exon11			GGAGAAGCACGGC	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"Regulators of G-protein signaling"	9996	protein-coding gene	gene with protein product		602513	"regulator of G-protein signalling 14"				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.1218G>T	5.37:g.176797996G>T	ENSP00000386229:p.Lys406Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	49	16	NM_006480	0	0	6	7	1	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.43|13.43	2.234827|2.234827	0.39498|0.39498	.|.	.|.	ENSG00000169220|ENSG00000169220	ENST00000408923;ENST00000336477|ENST00000511890	T|.	0.63417|.	-0.04|.	4.96|4.96	2.0|2.0	0.26442|0.26442	Raf-like Ras-binding (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61060|0.61060	0.2317|0.2317	M|M	0.71206|0.71206	2.165|2.165	0.42256|0.42256	D|D	0.991993|0.991993	D;D;D|.	0.89917|.	1.0;1.0;0.995|.	D;D;D|.	0.97110|.	1.0;0.999;0.951|.	T|T	0.57940|0.57940	-0.7724|-0.7724	10|5	0.87932|.	D|.	0|.	-28.6256|-28.6256	5.8726|5.8726	0.18812|0.18812	0.3015:0.0:0.5635:0.135|0.3015:0.0:0.5635:0.135	.|.	177;254;406|.	B3KUX0;O43566-5;O43566|.	.;.;RGS14_HUMAN|.	N|I	406;187|277	ENSP00000386229:K406N|.	ENSP00000336864:K187N|.	K|S	+|+	3|2	2|0	RGS14|RGS14	176730602|176730602	1.000000|1.000000	0.71417|0.71417	0.972000|0.972000	0.41901|0.41901	0.033000|0.033000	0.12548|0.12548	1.059000|1.059000	0.30517|0.30517	0.704000|0.704000	0.31869|0.31869	-0.225000|-0.225000	0.12378|0.12378	AAG|AGC	.		0.751	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		T	176797996	G	T	176797996	3	4	47	1	0	0	0	0	1	0	0	0	13329	962	34	4	1260	4	RGS14	5	176797996	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	26137279	176797996	4117264	40	4268											
SQSTM1	8878	hgsc.bcm.edu	37	chr5	179248068	179248068	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcggcgggtccgggaccctgCgagcggctgctgagccgggt	3	5	20	13	6	0	1	0	1	0	0	1	3	1	2	3	5	4	2	3	5	0	0	rs11548639		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:179248068C>T	ENST00000389805.4	+	1	310	c.132C>T	c.(130-132)tgC>tgT	p.C44C	SQSTM1_ENST00000376929.3_Intron|SQSTM1_ENST00000360718.5_5'Flank|SQSTM1_ENST00000510187.1_Silent_p.C44C|SQSTM1_ENST00000402874.3_5'UTR	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	44	Interaction with LCK.|Interaction with PRKCZ and dimerization. {ECO:0000250}.|OPR.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGGGACCCTGCGAGCGGCTGC	0.771																																					p.C44C		.											.	SQSTM1-92	0			c.C132T						.						3	4	3					5																	179248068		1580	3507	5087	SO:0001819	synonymous_variant	8878	exon1			ACCCTGCGAGCGG	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"Paget disease of bone 3", "oxidative stress induced like"	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.132C>T	5.37:g.179248068C>T		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	15	7	NM_003900	0	0	12	20	8	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1																																																																																			.		0.771	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1			T	179248068	C	T	179248068	2	4	47	1	0	0	0	0	0	0	0	1	15162	776	27	1		1	SQSTM1	5	179248068	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	2450072	179248068	1667192	41	4269											
OR11A1	26531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	29395381	29395381	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccaaggaggacaaatTcagtaatagtttcgtttcct	14	11	9	7	1	1	1	1	0	0	1	3	3	2	3	2	2	1	3	2	2	5	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:29395381T>G	ENST00000377149.1	-	5	510	c.38A>C	c.(37-39)gAa>gCa	p.E13A	OR11A1_ENST00000377148.1_Missense_Mutation_p.E13A|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.E13A			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						GAGGACAAATTCAGTAATAGT	0.398																																					p.E13A		.											.	OR11A1-23	0			c.A38C						.						67	65	66					6																	29395381		1509	2709	4218	SO:0001583	missense	26531	exon1			ACAAATTCAGTAA		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"GPCR / Class A : Olfactory receptors"	8176	protein-coding gene	gene with protein product			"olfactory receptor, family 11, subfamily A, member 2"	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.38A>C	6.37:g.29395381T>G	ENSP00000366354:p.Glu13Ala	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	98	34	NM_013937	0	0	0	0	0	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.118839	0.56505	.	.	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.01119	5.31;5.31;5.31	3.66	2.48	0.30137	.	0.000000	0.33290	U	0.005076	T	0.00998	0.0033	M	0.88512	2.96	0.09310	N	1	P	0.34977	0.478	B	0.38327	0.271	T	0.41928	-0.9481	10	0.54805	T	0.06	-0.4728	5.5487	0.17079	0.0:0.2499:0.0:0.7501	.	13	Q9GZK7	O11A1_HUMAN	A	13	ENSP00000366353:E13A;ENSP00000366354:E13A;ENSP00000366352:E13A	ENSP00000366352:E13A	E	-	2	0	OR11A1	29503360	0.004000	0.15560	0.093000	0.20910	0.716000	0.41182	0.571000	0.23669	0.465000	0.27167	0.327000	0.21459	GAA	.		0.398	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			G	29395381	T	G	29395381	3	3	47	1	0	0	0	0	1	0	0	0	10950	1783	62	5	913	5	OR11A1	6	29395381	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		29395381	141719686	42	4270											
PNPLA1	285848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	36269817	36269817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aggagtgggttcccaaagggGatggaaggggcagccatggt	10	6	19	6	0	0	0	0	0	0	0	1	3	1	3	2	8	1	2	2	8	2	1	rs182227800		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:36269817G>A	ENST00000394571.2	+	6	955	c.955G>A	c.(955-957)Gat>Aat	p.D319N	PNPLA1_ENST00000388715.3_Missense_Mutation_p.D224N|PNPLA1_ENST00000312917.5_Missense_Mutation_p.D233N	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	319					lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						TCCCAAAGGGGATGGAAGGGG	0.572											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0	0	5008	,	,		19080	0.001		0	False		,,,				2504	0				p.D319N		.											.	PNPLA1-137	0			c.G955A						.						94	95	95					6																	36269817		2203	4300	6503	SO:0001583	missense	285848	exon6			AAAGGGGATGGAA		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"Patatin-like phospholipase domain containing"	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.955G>A	6.37:g.36269817G>A	ENSP00000378072:p.Asp319Asn	Somatic	217	0	861	WXS	Illumina HiSeq	Phase_I	169	61	NM_001145717	0	0	0	0	0	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.08	1.829459	0.32329	.	.	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.29917	1.82;1.82;1.55;1.55	5.54	2.28	0.28536	.	51.883400	0.00166	N	0.000000	T	0.07324	0.0185	N	0.24115	0.695	0.09310	N	1	B;B	0.12013	0.002;0.005	B;B	0.10450	0.004;0.005	T	0.16424	-1.0403	10	0.30078	T	0.28	-1.3164	3.422	0.07397	0.26:0.2173:0.5227:0.0	.	319;233	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	N	224;233;320;319	ENSP00000373367:D224N;ENSP00000321116:D233N;ENSP00000391868:D320N;ENSP00000378072:D319N	ENSP00000321116:D233N	D	+	1	0	PNPLA1	36377795	0.000000	0.05858	0.001000	0.08648	0.112000	0.19704	0.380000	0.20602	0.680000	0.31366	0.650000	0.86243	GAT	G|0.999;A|0.000		0.572	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		A	36269817	G	A	36269817	3	1	47	1	0	0	0	0	1	0	0	0	12190	1174	41	2	1004	2	PNPLA1	6	36269817	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	6874436	36269817	134845250	43	4271											
HECA	51696	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	139495590	139495590	+	Frame_Shift_Del	DEL	A	A	-																															ttcacaagatcatctgcatcAagtgtaagtcacggtgggat																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:139495590delA	ENST00000367658.2	+	3	1666	c.1381delA	c.(1381-1383)aagfs	p.K461fs	RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000590219.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	461					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		CATCTGCATCAAGTGTAAGTC	0.547																																					p.K461fs		.											.	HECA-90	0			c.1381delA						.						234	198	210					6																	139495590		2203	4300	6503	SO:0001589	frameshift_variant	51696	exon3			.	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.1381delA	6.37:g.139495590delA	ENSP00000356630:p.Lys461fs	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	180	59	NM_016217	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000367658.2	37	CCDS5194.1																																																																																			.		0.547	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		-	139495590	A	-	139495590	7	5	47	1	0	1	0	1	0	0	0	0	7059	131	5	0	1391	0	HECA	6	139495590	Frame_Shift_Del	DEL	A	TCGA-B9-4113-01A-01D-1252-08	103225773	139495590	31619477	44	4272											
SEPT7	989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	35912377	35912377	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcagtggataatagtaattgGtaagaagggtttgtcctcac	12	12	12	5	0	1	1	1	0	0	1	2	2	2	2	1	3	0	4	1	3	5	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:35912377G>A	ENST00000435235.1	+	4	650		c.e4+1		SEPT7_ENST00000399035.3_Splice_Site|SEPT7_ENST00000494488.2_Splice_Site|SEPT7_ENST00000469679.2_Splice_Site|SEPT7_ENST00000475109.1_Splice_Site|SEPT7_ENST00000399034.2_Splice_Site|SEPT7_ENST00000350320.6_Splice_Site			Q16181	SEPT7_HUMAN	septin 7						cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						ATAGTAATTGGTAAGAAGGGT	0.388																																					.		.											.	.	0			c.374+1G>A						.						134	127	129					7																	35912377		1851	4091	5942	SO:0001630	splice_region_variant	989	exon4			TAATTGGTAAGAA	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.218+1G>A	7.37:g.35912377G>A		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	35	13	NM_001011553	0	0	0	12	12	Q52M76|Q6NX50	Splice_Site	SNP	ENST00000435235.1	37		.	.	.	.	.	.	.	.	.	.	g	24.0	4.477060	0.84640	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000469679;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0851	0.89455	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEPT7	35878902	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.695000	0.98691	2.338000	0.79540	0.574000	0.79327	.	.		0.388	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788	Intron	A	35912377	G	A	35912377	5	1	47	1	0	0	0	0	0	0	1	0	14101	1275	44	2	390	2	SEPT7	7	35912377	Splice_Site	SNP	G	TCGA-B9-4113-01A-01D-1252-08		35912377	123226286	45	4273											
PRKRIP1	79706	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	102040095	102040096	+	Splice_Site	DNP	GG	GG	AA																															atggatgccatggctgagaaGgtcagtgagccagaaggctg																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:102040095_102040096GG>AA	ENST00000496391.1	+	7	1616	c.306_306GG>AA	c.(304-306)aaGG>aaAAg	p.K102K	PRKRIP1_ENST00000462601.1_Splice_Site_p.K45K|PRKRIP1_ENST00000397912.3_Splice_Site_p.K102K|PRKRIP1_ENST00000482465.1_3'UTR|PRKRIP1_ENST00000354783.4_Splice_Site_p.K64K			Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)	102	Required for RNA-binding. {ECO:0000250}.				negative regulation of phosphorylation (GO:0042326)|negative regulation of protein kinase activity (GO:0006469)|renal system process (GO:0003014)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|lung(4)|ovary(1)	6						TGGCTGAGAAGGTCAGTGAGCC	0.554																																					.		.											.	PRKRIP1	0			c.306+1G>A						.																																			SO:0001630	splice_region_variant	79706	exon3			GAGAAGGTCAGTG	AK023964	CCDS34714.1	7q22.1	2013-01-09			ENSG00000128563	ENSG00000128563		"Zinc fingers, C2H2-type", "-"	21894	protein-coding gene	gene with protein product	"likely ortholog of mouse C114 dsRNA-binding protein", "KRAB box domain containing 3"					12679338	Standard	NM_024653		Approved	C114, FLJ13902, KRBOX3	uc003uzh.2	Q9H875	OTTHUMG00000157717	Exception_encountered	7.37:g.102040095_102040096delinsAA		Somatic	223	0		WXS	Illumina HiSeq	Phase_I	360	147		0	0	0	0	0	B4DGM2|Q8NDM6|Q96CF8	Splice_Site	DNP	ENST00000496391.1	37	CCDS34714.1																																																																																			.		0.554	PRKRIP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349489.1	NM_024653	Silent	AA	102040096	GG	AA	102040095	5	1	47	1	0	0	0	0	0	0	1	0	12554	1014	35	2	316	2	PRKRIP1	7	102040095	Splice_Site	DNP	GG	TCGA-B9-4113-01A-01D-1252-08	66127718	102040095	57098568	46	4274											
ZNF777	27153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	149129443	149129443	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgaagctgctgtcgcaCtcggggcacttgtagggctt	5	11	15	10	2	0	1	0	1	0	0	2	1	0	1	0	4	2	7	0	4	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:149129443C>T	ENST00000247930.4	-	6	2243	c.1920G>A	c.(1918-1920)gaG>gaA	p.E640E		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	640					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TGCTGTCGCACTCGGGGCACT	0.652																																					p.E640E		.											.	ZNF777-136	0			c.G1920A						.						90	106	100					7																	149129443		2182	4272	6454	SO:0001819	synonymous_variant	27153	exon6			GTCGCACTCGGGG	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1920G>A	7.37:g.149129443C>T		Somatic	366	1		WXS	Illumina HiSeq	Phase_I	515	202	NM_015694	0	0	15	20	5	Q8N2R2|Q8N659	Silent	SNP	ENST00000247930.4	37	CCDS43675.1																																																																																			.		0.652	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		T	149129443	C	T	149129443	2	4	47	1	0	0	0	0	0	0	0	1	18182	564	20	2		2	ZNF777	7	149129443	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	47089348	149129443	10009220	47	4275											
AGTPBP1	23287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	88201776	88201776	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcttcactgcagccaagtaTtgcaacagccccttagcatg	10	9	8	14	1	1	0	1	0	0	0	1	0	1	0	3	0	6	5	3	0	4	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr9:88201776T>A	ENST00000357081.3	-	22	3147	c.3003A>T	c.(3001-3003)caA>caT	p.Q1001H	AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.Q961H|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.Q1013H			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	1001					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						CAGCCAAGTATTGCAACAGCC	0.388																																					p.Q961H		.											.	AGTPBP1-158	0			c.A2883T						.						135	122	126					9																	88201776		2203	4300	6503	SO:0001583	missense	23287	exon22			CAAGTATTGCAAC	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.3003A>T	9.37:g.88201776T>A	ENSP00000349592:p.Gln1001His	Somatic	163	1		WXS	Illumina HiSeq	Phase_I	110	38	NM_015239	0	0	10	16	6	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	T	15.79	2.937535	0.52972	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109	T;T;T	0.11604	2.76;2.76;2.76	5.24	-1.34	0.09143	Peptidase M14, carboxypeptidase A (1);	0.055490	0.64402	D	0.000001	T	0.18800	0.0451	L	0.44542	1.39	0.80722	D	1	P;D;P	0.89917	0.616;1.0;0.485	B;D;B	0.81914	0.236;0.995;0.43	T	0.00242	-1.1885	10	0.23891	T	0.37	-11.4782	11.3569	0.49621	0.0:0.4688:0.0:0.5312	.	1013;1001;961	Q9UPW5-3;Q9UPW5;Q9UPW5-2	.;CBPC1_HUMAN;.	H	1001;961;1013	ENSP00000349592:Q1001H;ENSP00000365251:Q961H;ENSP00000365277:Q1013H	ENSP00000349592:Q1001H	Q	-	3	2	AGTPBP1	87391596	0.850000	0.29656	0.595000	0.28798	0.714000	0.41099	0.041000	0.13927	-0.637000	0.05516	-0.242000	0.12053	CAA	.		0.388	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		A	88201776	T	A	88201776	3	1	47	1	0	0	0	0	1	0	0	0	400	1490	52	5	697	5	AGTPBP1	9	88201776	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		88201776	53011655	48	4276											
COL5A1	1289	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	137593045	137593045	+	Frame_Shift_Del	DEL	A	A	-																															gaattgctctcagcgtccacAagaaaaatgtcaccttgatc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr9:137593045delA	ENST00000371817.3	+	4	934	c.520delA	c.(520-522)aagfs	p.K175fs	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	175	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CAGCGTCCACAAGAAAAATGT	0.478																																					p.K174fs		.											.	COL5A1-524	0			c.520delA						.						132	100	111					9																	137593045		2203	4298	6501	SO:0001589	frameshift_variant	1289	exon4			.	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.520delA	9.37:g.137593045delA	ENSP00000360882:p.Lys175fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	78	28	NM_000093	0	0	0	0	0	Q15094|Q5SUX4	Frame_Shift_Del	DEL	ENST00000371817.3	37	CCDS6982.1																																																																																			.		0.478	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		-	137593045	A	-	137593045	7	5	47	1	0	1	0	1	0	0	0	0	3702	131	5	0	534	0	COL5A1	9	137593045	Frame_Shift_Del	DEL	A	TCGA-B9-4113-01A-01D-1252-08	49391269	137593045	3620386	49	4277											
ECD	11319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74896486	74896486	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggttcctagtggtgaaactTttgctgatgcaggtgtgtgc	6	15	14	6	0	0	2	0	2	0	0	1	2	1	2	1	3	4	3	1	3	2	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr10:74896486T>G	ENST00000372979.4	-	13	1886	c.1680A>C	c.(1678-1680)aaA>aaC	p.K560N	ECD_ENST00000454759.2_Missense_Mutation_p.K517N|ECD_ENST00000430082.2_Missense_Mutation_p.K593N	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	560					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TGGTGAAACTTTTGCTGATGC	0.418																																					p.K593N		.											.	ECD-91	0			c.A1779C						.						221	194	203					10																	74896486		2203	4300	6503	SO:0001583	missense	11319	exon14			GAAACTTTTGCTG	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1680A>C	10.37:g.74896486T>G	ENSP00000362070:p.Lys560Asn	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	179	75	NM_001135752	0	0	32	48	16	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.034517	0.75617	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19669	2.13;2.13;2.13	5.66	3.37	0.38596	.	0.091325	0.85682	D	0.000000	T	0.34048	0.0884	M	0.64997	1.995	0.47037	D	0.999297	D;D;P	0.60575	0.978;0.988;0.51	P;P;P	0.60286	0.872;0.872;0.493	T	0.03597	-1.1021	10	0.40728	T	0.16	-2.9522	7.962	0.30076	0.0:0.1669:0.0:0.8331	.	517;593;560	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	N	560;593;517	ENSP00000362070:K560N;ENSP00000401566:K593N;ENSP00000395786:K517N	ENSP00000362070:K560N	K	-	3	2	ECD	74566492	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.537000	0.36083	0.981000	0.38548	0.533000	0.62120	AAA	.		0.418	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		G	74896486	T	G	74896486	3	3	47	1	0	0	0	0	1	0	0	0	4899	1838	64	5	262	5	ECD	10	74896486	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		74896486	60638261	50	4278											
COX15	1355	hgsc.bcm.edu	37	chr10	101491791	101491791	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaggccctcaacggcggaaAgagcaatcgctgcatactga	13	5	11	12	3	1	2	1	1	0	1	2	3	1	3	1	3	4	3	1	3	5	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr10:101491791A>C	ENST00000016171.5	-	1	66	c.16T>G	c.(16-18)Ttt>Gtt	p.F6V	CUTC_ENST00000493385.1_Intron|CUTC_ENST00000370476.5_5'Flank|COX15_ENST00000370483.5_Missense_Mutation_p.F6V			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	6					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		AACGGCGGAAAGAGCAATCGC	0.607																																					p.F6V		.											.	COX15-227	0			c.T16G						.						48	36	40					10																	101491791		2203	4300	6503	SO:0001583	missense	1355	exon1			GCGGAAAGAGCAA	AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.16T>G	10.37:g.101491791A>C	ENSP00000016171:p.Phe6Val	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	56	18	NM_078470	0	0	9	11	2	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	37	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	A	6.792	0.515219	0.12944	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	.	.	.	4.58	0.265	0.15612	.	0.865040	0.09787	N	0.755882	T	0.23054	0.0557	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21621	-1.0240	9	0.27785	T	0.31	1.4857	3.7279	0.08481	0.4456:0.2267:0.3277:0.0	.	6;6	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	V	6	.	ENSP00000016171:F6V	F	-	1	0	COX15	101481781	0.005000	0.15991	0.002000	0.10522	0.186000	0.23388	-0.083000	0.11286	-0.100000	0.12241	0.454000	0.30748	TTT	.		0.607	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		C	101491791	A	C	101491791	3	2	47	1	0	0	0	0	1	0	0	0	3770	72	3	5	1322	5	COX15	10	101491791	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	26595305	101491791	34042956	51	4279											
E2F8	79733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	19251275	19251275	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgcacaccgttgggctcAggccttggggtggcgtcaca	5	9	16	11	2	2	0	2	0	0	0	2	0	2	0	2	6	1	3	2	6	0	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:19251275A>T	ENST00000527884.1	-	10	1851	c.1619T>A	c.(1618-1620)cTg>cAg	p.L540Q	E2F8_ENST00000250024.4_Missense_Mutation_p.L540Q|RP11-428C19.4_ENST00000527978.1_RNA	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	540					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CGTTGGGCTCAGGCCTTGGGG	0.582																																					p.L540Q		.											.	E2F8-91	0			c.T1619A						.						116	110	112					11																	19251275		2199	4293	6492	SO:0001583	missense	79733	exon10			GGGCTCAGGCCTT		CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1619T>A	11.37:g.19251275A>T	ENSP00000434199:p.Leu540Gln	Somatic	448	0		WXS	Illumina HiSeq	Phase_I	410	146	NM_001256372	0	0	0	0	0	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Missense_Mutation	SNP	ENST00000527884.1	37	CCDS7849.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.208327	0.39003	.	.	ENSG00000129173	ENST00000527884;ENST00000396159;ENST00000250024	T;T	0.19669	2.13;2.13	5.63	3.22	0.36961	.	0.443233	0.22737	N	0.056245	T	0.17323	0.0416	M	0.62723	1.935	0.38602	D	0.950684	P	0.37955	0.612	B	0.34722	0.188	T	0.13737	-1.0498	10	0.66056	D	0.02	-1.4647	1.4873	0.02450	0.4262:0.2981:0.1324:0.1433	.	540	A0AVK6	E2F8_HUMAN	Q	540	ENSP00000434199:L540Q;ENSP00000250024:L540Q	ENSP00000250024:L540Q	L	-	2	0	E2F8	19207851	0.981000	0.34729	1.000000	0.80357	0.949000	0.60115	1.281000	0.33214	0.376000	0.24707	0.533000	0.62120	CTG	.		0.582	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680		T	19251275	A	T	19251275	3	4	47	1	0	0	0	0	1	0	0	0	4884	188	7	5	1000	5	E2F8	11	19251275	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08		19251275	115755241	52	4280											
QSER1	79832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	32954930	32954930	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacaagcatctcttgagtCatcaacccaaaggctatctg	12	9	7	13	0	4	1	2	1	2	0	5	1	4	1	2	1	2	2	2	1	4	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:32954930C>A	ENST00000399302.2	+	4	2074	c.1739C>A	c.(1738-1740)tCa>tAa	p.S580*	QSER1_ENST00000527788.1_Nonsense_Mutation_p.S341*	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	580										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TCTCTTGAGTCATCAACCCAA	0.398																																					p.S580X		.											.	QSER1-95	0			c.C1739A						.						82	77	79					11																	32954930		1869	4115	5984	SO:0001587	stop_gained	79832	exon4			TTGAGTCATCAAC	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.1739C>A	11.37:g.32954930C>A	ENSP00000382241:p.Ser580*	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	48	14	NM_001076786	0	0	0	0	0	Q6ZU30|Q6ZUR5	Nonsense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281137	0.80692	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	.	.	.	5.01	5.01	0.66863	.	0.480260	0.19152	N	0.121422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6645	0.91485	0.0:1.0:0.0:0.0	.	.	.	.	X	580;341;341	.	ENSP00000078652:S341X	S	+	2	0	QSER1	32911506	0.999000	0.42202	0.049000	0.19019	0.007000	0.05969	5.597000	0.67577	2.496000	0.84212	0.591000	0.81541	TCA	.		0.398	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		A	32954930	C	A	32954930	4	1	47	1	0	0	0	0	0	1	0	0	12914	838	29	4	1745	4	QSER1	11	32954930	Nonsense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	13703655	32954930	102051586	53	4281											
MADD	8567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47304129	47304129	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtactttggggaatggatccTtaaccccaccaactatgcct	10	11	8	12	0	0	0	0	0	0	0	1	2	1	2	5	3	4	1	5	3	5	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:47304129T>G	ENST00000311027.5	+	9	1832	c.1667T>G	c.(1666-1668)cTt>cGt	p.L556R	MADD_ENST00000395344.3_Missense_Mutation_p.L556R|MADD_ENST00000402192.2_Missense_Mutation_p.L556R|MADD_ENST00000395336.3_Missense_Mutation_p.L556R|MADD_ENST00000406482.1_Missense_Mutation_p.L556R|MADD_ENST00000342922.4_Missense_Mutation_p.L556R|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000407859.3_Missense_Mutation_p.L556R|MADD_ENST00000402799.1_Missense_Mutation_p.L556R|MADD_ENST00000349238.3_Missense_Mutation_p.L556R	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GAATGGATCCTTAACCCCACC	0.537																																					p.L556R		.											.	MADD-682	0			c.T1667G						.						69	53	58					11																	47304129		2201	4298	6499	SO:0001583	missense	8567	exon9			GGATCCTTAACCC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1667T>G	11.37:g.47304129T>G	ENSP00000310933:p.Leu556Arg	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	137	50	NM_130474	0	0	3	11	8		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.010292	0.93346	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.08896	3.16;3.05;3.05;3.14;3.15;3.04;3.06;3.15;3.16	5.77	5.77	0.91146	dDENN (1);	0.000000	0.85682	D	0.000000	T	0.28797	0.0714	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.997;0.998;0.991;0.991;0.991;0.997;0.999;0.999;0.999	T	0.00686	-1.1610	10	0.87932	D	0	-13.2301	16.383	0.83481	0.0:0.0:0.0:1.0	.	556;556;556;556;556;556;556;556;556;556	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	R	556	ENSP00000343902:L556R;ENSP00000385585:L556R;ENSP00000384435:L556R;ENSP00000304505:L556R;ENSP00000310933:L556R;ENSP00000384204:L556R;ENSP00000378753:L556R;ENSP00000378745:L556R;ENSP00000384287:L556R	ENSP00000310933:L556R	L	+	2	0	MADD	47260705	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	7.628000	0.83189	2.326000	0.78906	0.533000	0.62120	CTT	.		0.537	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			G	47304129	T	G	47304129	3	3	47	1	0	0	0	0	1	0	0	0	9177	1609	56	5	1697	5	MADD	11	47304129	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	14349199	47304129	87702387	54	4282											
A2ML1	144568	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	9006738	9006738	+	Frame_Shift_Del	DEL	A	A	-																															tctcaggtcacattaactttActattagtacaaagattctg																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:9006738delA	ENST00000299698.7	+	21	2785	c.2605delA	c.(2605-2607)actfs	p.T869fs	A2ML1_ENST00000539547.1_Frame_Shift_Del_p.T378fs	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CATTAACTTTACTATTAGTAC	0.468																																					p.T869fs		.											.	A2ML1-93	0			c.2605delA						.						55	56	56					12																	9006738		1864	4095	5959	SO:0001589	frameshift_variant	144568	exon21			.	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2605delA	12.37:g.9006738delA	ENSP00000299698:p.Thr869fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	134	72	NM_144670	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000299698.7	37	CCDS8596.2																																																																																			.		0.468	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		-	9006738	A	-	9006738	7	5	47	1	0	1	0	1	0	0	0	0	5	391	14	0	2687	0	A2ML1	12	9006738	Frame_Shift_Del	DEL	A	TCGA-B9-4113-01A-01D-1252-08		9006738	124845157	55	4283											
PIK3C2G	5288	hgsc.bcm.edu;broad.mit.edu	37	chr12	18658292	18658292	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattcatcctgggagtatgtGaccgtcacaatgataatatc	12	12	8	9	1	2	2	2	2	0	0	4	3	3	3	2	1	0	1	2	1	4	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:18658292G>A	ENST00000266497.5	+	22	3135	c.3097G>A	c.(3097-3099)Gac>Aac	p.D1033N	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.D1074N|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.D1033N			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1033	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				GGGAGTATGTGACCGTCACAA	0.393																																					p.D1033N		.											.	PIK3C2G-1312	0			c.G3097A						.						129	112	117					12																	18658292		1934	4151	6085	SO:0001583	missense	5288	exon23			GTATGTGACCGTC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"phosphoinositide-3-kinase, class 2, gamma polypeptide"			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3097G>A	12.37:g.18658292G>A	ENSP00000266497:p.Asp1033Asn	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	11	7	NM_004570	0	0	0	0	0	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018323	0.93404	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.94897	-3.55;-3.55;-3.55	4.47	4.47	0.54385	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.127925	0.51477	D	0.000089	D	0.98105	0.9375	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98863	1.0763	10	0.87932	D	0	-20.5375	17.403	0.87465	0.0:0.0:1.0:0.0	.	1073;1074;1033	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	N	1033;1033;1074	ENSP00000404845:D1033N;ENSP00000266497:D1033N;ENSP00000445381:D1074N	ENSP00000266497:D1033N	D	+	1	0	PIK3C2G	18549559	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.524000	0.98036	2.771000	0.95319	0.650000	0.86243	GAC	.		0.393	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18658292	G	A	18658292	3	1	47	1	0	0	0	0	1	0	0	0	11937	1290	45	2	3183	2	PIK3C2G	12	18658292	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	9651554	18658292	115193603	56	4284											
PDZRN4	29951	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	41585335	41585335	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gattcaatattataggaggtCgaccaaatcaggtaaaacac	17	9	8	7	1	2	0	2	0	0	0	3	3	2	1	1	3	1	1	1	3	7	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:41585335C>T	ENST00000402685.2	+	2	732	c.724C>T	c.(724-726)Cga>Tga	p.R242*		NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	242	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TATAGGAGGTCGACCAAATCA	0.303																																					p.R242X		.											.	PDZRN4-296	0			c.C724T						.						97	90	92					12																	41585335		1568	3576	5144	SO:0001587	stop_gained	29951	exon2			GGAGGTCGACCAA	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.724C>T	12.37:g.41585335C>T	ENSP00000384197:p.Arg242*	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	105	34	NM_001164595	0	0	0	0	0	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	C	37	6.538183	0.97646	.	.	ENSG00000165966	ENST00000402685	.	.	.	4.48	2.64	0.31445	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.2118	0.37322	0.0:0.8273:0.0:0.1727	.	.	.	.	X	242	.	ENSP00000384197:R242X	R	+	1	2	PDZRN4	39871602	0.791000	0.28800	0.992000	0.48379	0.995000	0.86356	1.196000	0.32198	0.591000	0.29711	0.563000	0.77884	CGA	.		0.303	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41585335	C	T	41585335	4	4	47	1	0	0	0	0	0	1	0	0	11736	876	31	1	730	1	PDZRN4	12	41585335	Nonsense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	22927043	41585335	92266560	57	4285											
ACAD10	80724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112184083	112184083	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggcacgtccctgtatgccCccgaggtaccttctttaaag	7	11	10	13	2	1	0	0	0	1	0	2	1	2	0	4	2	2	3	4	2	4	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:112184083C>A	ENST00000313698.4	+	14	2406	c.2251C>A	c.(2251-2253)Ccc>Acc	p.P751T	ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000392636.2_Missense_Mutation_p.P353T|ACAD10_ENST00000455480.2_Missense_Mutation_p.P782T	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	751						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						CCTGTATGCCCCCGAGGTACC	0.473																																					p.P782T		.											.	ACAD10-92	0			c.C2344A						.						106	103	104					12																	112184083		2203	4300	6503	SO:0001583	missense	80724	exon15			TATGCCCCCGAGG	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"acyl-Coenzyme A dehydrogenase family, member 10"			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.2251C>A	12.37:g.112184083C>A	ENSP00000325137:p.Pro751Thr	Somatic	265	0		WXS	Illumina HiSeq	Phase_I	339	89	NM_001136538	0	0	0	2	2	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	37	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.408994	0.62399	.	.	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000455480;ENST00000515283;ENST00000313698	D;D;D	0.99660	-6.32;-6.32;-6.32	5.29	3.43	0.39272	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.378699	0.25436	N	0.030684	D	0.99629	0.9864	H	0.97732	4.065	0.80722	D	1	D;B;B	0.53462	0.96;0.209;0.298	P;B;B	0.57057	0.812;0.396;0.141	D	0.98657	1.0682	10	0.87932	D	0	.	9.228	0.37418	0.1463:0.776:0.0:0.0777	.	782;751;751	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	T	353;751;782;144;751	ENSP00000376411:P353T;ENSP00000389813:P782T;ENSP00000325137:P751T	ENSP00000325137:P751T	P	+	1	0	ACAD10	110668466	0.071000	0.21146	0.012000	0.15200	0.965000	0.64279	1.166000	0.31834	0.708000	0.31955	0.561000	0.74099	CCC	.		0.473	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		A	112184083	C	A	112184083	3	1	47	1	0	0	0	0	1	0	0	0	108	623	22	4	2398	4	ACAD10	12	112184083	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	70598748	112184083	21667812	58	4286											
TMEM132D	121256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	130184819	130184819	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctcggaaagcaaagaccctCaggcacggcagcttctcccc	10	6	9	16	2	3	1	1	0	2	1	5	2	3	2	3	3	2	4	3	3	2	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:130184819C>G	ENST00000422113.2	-	2	830	c.504G>C	c.(502-504)ctG>ctC	p.L168L	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	168					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CAAAGACCCTCAGGCACGGCA	0.662																																					p.L168L		.											.	TMEM132D-106	0			c.G504C						.						18	20	20					12																	130184819		2203	4299	6502	SO:0001819	synonymous_variant	121256	exon2			GACCCTCAGGCAC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 153"	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.504G>C	12.37:g.130184819C>G		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	103	57	NM_133448	0	0	0	0	0	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			.		0.662	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		G	130184819	C	G	130184819	2	3	47	1	0	0	0	0	0	0	0	1	16079	813	29	4		4	TMEM132D	12	130184819	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	18000736	130184819	3667076	59	4287											
SLC46A3	283537	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	29287510	29287510	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggaatggaaaggcaaaatAgcaaagcaaacagagccaaa	21	3	10	7	0	0	1	0	0	0	1	0	3	0	3	1	3	4	3	1	3	8	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:29287510A>G	ENST00000266943.6	-	3	736	c.367T>C	c.(367-369)Tat>Cat	p.Y123H	SLC46A3_ENST00000380814.4_Missense_Mutation_p.Y123H	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	123					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		AAGGCAAAATAGCAAAGCAAA	0.408																																					p.Y123H		.											.	SLC46A3-69	0			c.T367C						.						74	67	69					13																	29287510		2203	4300	6503	SO:0001583	missense	283537	exon3			CAAAATAGCAAAG		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.367T>C	13.37:g.29287510A>G	ENSP00000266943:p.Tyr123His	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	54	13	NM_181785	0	0	36	57	21	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	37	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.182467	0.78677	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.80994	-1.44;-1.44	6.17	5.0	0.66597	Major facilitator superfamily domain, general substrate transporter (1);	0.059964	0.64402	D	0.000002	D	0.88123	0.6352	M	0.74881	2.28	0.42496	D	0.992918	D;B;B	0.89917	1.0;0.36;0.413	D;B;B	0.79784	0.993;0.139;0.219	D	0.87590	0.2490	10	0.42905	T	0.14	-22.8055	12.1889	0.54257	0.9341:0.0:0.0659:0.0	.	48;123;123	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	H	123	ENSP00000266943:Y123H;ENSP00000370192:Y123H	ENSP00000266943:Y123H	Y	-	1	0	SLC46A3	28185510	1.000000	0.71417	0.981000	0.43875	0.958000	0.62258	6.725000	0.74752	1.160000	0.42584	0.533000	0.62120	TAT	.		0.408	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		G	29287510	A	G	29287510	3	3	47	1	0	0	0	0	1	0	0	0	14678	420	15	3	1048	3	SLC46A3	13	29287510	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08		29287510	85882368	60	4288											
BRCA2	675	hgsc.bcm.edu	37	chr13	32913098	32913098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaaaaagttaaaattgcaAaggaatctttggacaaagtg	19	9	10	3	0	1	0	0	0	1	0	1	3	1	3	0	3	1	2	0	3	8	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:32913098A>G	ENST00000380152.3	+	11	4839	c.4606A>G	c.(4606-4608)Aag>Gag	p.K1536E	BRCA2_ENST00000544455.1_Missense_Mutation_p.K1536E			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1536	Interaction with POLH.|Required for stimulation of POLH DNA polymerization activity.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAAAATTGCAAAGGAATCTTT	0.388			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.K1536E	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2-3153	0			c.A4606G						.						51	55	53					13																	32913098		2202	4299	6501	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	ATTGCAAAGGAAT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.4606A>G	13.37:g.32913098A>G	ENSP00000369497:p.Lys1536Glu	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_000059	0	0	0	0	0	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662988	0.29515	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.68479	-0.33;-0.33	5.74	4.54	0.55810	.	0.251014	0.35013	N	0.003510	T	0.64735	0.2625	M	0.62723	1.935	0.25827	N	0.984216	P	0.47034	0.889	P	0.50896	0.653	T	0.55224	-0.8174	10	0.16896	T	0.51	.	3.9056	0.09180	0.6124:0.2054:0.1823:0.0	.	1536	P51587	BRCA2_HUMAN	E	1536	ENSP00000369497:K1536E;ENSP00000439902:K1536E	ENSP00000369497:K1536E	K	+	1	0	BRCA2	31811098	0.956000	0.32656	0.377000	0.26055	0.488000	0.33401	1.874000	0.39568	0.979000	0.38497	0.460000	0.39030	AAG	.		0.388	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32913098	A	G	32913098	3	3	47	1	0	0	0	0	1	0	0	0	1502	15	1	3	4644	3	BRCA2	13	32913098	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	3625588	32913098	82256780	61	4289											
ATP7B	540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	52548108	52548108	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaaatcccatgtcttctatAgcagctctgagttcttctgg	8	15	7	11	0	6	1	1	1	5	0	7	1	7	1	1	1	2	3	1	1	3	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:52548108A>T	ENST00000242839.4	-	2	1404	c.1248T>A	c.(1246-1248)gcT>gcA	p.A416A	ATP7B_ENST00000418097.2_Silent_p.A416A|ATP7B_ENST00000400366.3_Silent_p.A305A|ATP7B_ENST00000448424.2_Silent_p.A416A|ATP7B_ENST00000542656.1_Silent_p.A384A|ATP7B_ENST00000344297.5_Silent_p.A416A|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400370.3_Silent_p.A416A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	416	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGTCTTCTATAGCAGCTCTGA	0.458									Wilson disease																												p.A416A		.											.	ATP7B-92	0			c.T1248A						.						100	98	98					13																	52548108		1934	4142	6076	SO:0001819	synonymous_variant	540	exon2	Familial Cancer Database		TTCTATAGCAGCT	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1248T>A	13.37:g.52548108A>T		Somatic	201	0		WXS	Illumina HiSeq	Phase_I	245	90	NM_000053	0	0	2	6	4	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	37	CCDS41892.1																																																																																			.		0.458	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		T	52548108	A	T	52548108	2	4	47	1	0	0	0	0	0	0	0	1	1192	407	15	5		5	ATP7B	13	52548108	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	19635010	52548108	62621770	62	4290											
RNF219	79596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	79190506	79190506	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaacagtcccaaaatcctgTctttggggaagaaaaacatt	16	9	7	9	0	1	1	0	0	1	1	3	2	3	2	2	2	2	0	2	2	6	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:79190506T>A	ENST00000282003.6	-	6	1448	c.1390A>T	c.(1390-1392)Aca>Tca	p.T464S	RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000560209.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	464	Ser-rich.						zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		CAAAATCCTGTCTTTGGGGAA	0.333																																					p.T464S		.											.	RNF219-135	0			c.A1390T						.						38	40	39					13																	79190506		2203	4298	6501	SO:0001583	missense	79596	exon6			ATCCTGTCTTTGG	BC028586	CCDS31997.1	13q31.1	2011-05-23	2008-03-26	2008-03-26	ENSG00000152193	ENSG00000152193		"RING-type (C3HC4) zinc fingers"	20308	protein-coding gene	gene with protein product		615906	"chromosome 13 open reading frame 7"	C13orf7			Standard	XM_006719865		Approved	FLJ13449	uc001vkw.1	Q5W0B1	OTTHUMG00000017122	ENST00000282003.6:c.1390A>T	13.37:g.79190506T>A	ENSP00000282003:p.Thr464Ser	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	58	25	NM_024546	0	0	5	9	4	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813748	0.32053	.	.	ENSG00000152193	ENST00000282003	T	0.13778	2.56	5.86	3.32	0.38043	.	0.182284	0.39475	N	0.001352	T	0.03959	0.0111	N	0.03608	-0.345	0.26073	N	0.9812	B	0.10296	0.003	B	0.08055	0.003	T	0.36841	-0.9731	10	0.10902	T	0.67	-12.2367	1.5693	0.02612	0.3186:0.0903:0.1164:0.4747	.	464	Q5W0B1	RN219_HUMAN	S	464	ENSP00000282003:T464S	ENSP00000282003:T464S	T	-	1	0	RNF219	78088507	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	1.424000	0.34848	1.050000	0.40346	0.533000	0.62120	ACA	.		0.333	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79190506	T	A	79190506	3	1	47	1	0	0	0	0	1	0	0	0	13514	1667	58	5	794	5	RNF219	13	79190506	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	26642398	79190506	35979372	63	4291											
PSME2	5721	ucsc.edu	37	chr14	24613239	24613239	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacgttctgagaagtacCtgccagaagcaagggaatac	13	6	10	12	1	1	2	0	1	1	2	1	4	1	3	4	1	4	3	4	1	6	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr14:24613239C>T	ENST00000216802.5	-	9	1137		c.e9-1		EMC9_ENST00000558200.1_5'Flank|EMC9_ENST00000419198.2_5'Flank|EMC9_ENST00000216799.4_5'Flank|EMC9_ENST00000560403.1_5'Flank|PSME2_ENST00000560410.1_Splice_Site|PSME2_ENST00000471700.2_Intron|RNF31_ENST00000559275.1_5'Flank	NM_002818.2	NP_002809.2	Q9UL46	PSME2_HUMAN	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)				endometrium(1)|lung(3)|prostate(2)	6				GBM - Glioblastoma multiforme(265;0.00839)		TGAGAAGTACCTGCCAGAAGC	0.552																																					.													.	PSME2-90	0			c.498-1G>A						.						118	117	118					14																	24613239		2203	4300	6503	SO:0001630	splice_region_variant	5721	exon10			AAGTACCTGCCAG		CCDS9614.1	14q11.2	2010-03-10			ENSG00000100911	ENSG00000100911		"Proteasome (prosome, macropain) subunits"	9569	protein-coding gene	gene with protein product		602161				7789512	Standard	NM_002818		Approved	PA28beta	uc001wmj.3	Q9UL46	OTTHUMG00000028797	ENST00000216802.5:c.498-1G>A	14.37:g.24613239C>T		Somatic	269	0		WXS	Illumina HiSeq		420	1	NM_002818	0	0	3	3	0	Q15129	Splice_Site	SNP	ENST00000216802.5	37	CCDS9614.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.135818	0.56936	.	.	ENSG00000100911	ENST00000216802	.	.	.	4.83	3.93	0.45458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.307	0.32049	0.0:0.8955:0.0:0.1045	.	.	.	.	.	-1	.	.	.	-	.	.	PSME2	23683079	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.639000	0.67868	2.675000	0.91044	0.555000	0.69702	.	.		0.552	PSME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071918.3	NM_002818	Intron	T	24613239	C	T	24613239	5	4	47	1	0	0	0	0	0	0	1	0	12736	695	24	2	234	2	PSME2	14	24613239	Splice_Site	SNP	C	TCGA-B9-4113-01A-01D-1252-08		24613239	82736301	64	4292											
SDR39U1	23351	hgsc.bcm.edu	37	chr14	24910963	24910963	+	IGR	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaattgggtggtctctaggCggctgccgattacctctttt	5	14	12	10	2	2	0	0	0	2	0	3	1	2	0	2	4	2	2	2	4	3	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr14:24910963C>G	ENST00000251343.5	+	0	6225				SDR39U1_ENST00000555561.1_5'Flank|SDR39U1_ENST00000555365.1_5'UTR|SDR39U1_ENST00000399395.3_Missense_Mutation_p.R82P|SDR39U1_ENST00000554698.1_Intron|SDR39U1_ENST00000553930.1_5'UTR|SDR39U1_ENST00000399390.1_5'Flank|SDR39U1_ENST00000538105.2_Intron			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GGTCTCTAGGCGGCTGCCGAT	0.498																																					p.R82P		.											.	SDR39U1-46	0			c.G245C						.						48	39	42					14																	24910963		1856	4091	5947	SO:0001628	intergenic_variant	56948	exon4			TCTAGGCGGCTGC	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"KIAA0323"	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037			14.37:g.24910963C>G		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	74	6	NM_020195	0	0	0	0	0	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024548	0.93518	.	.	ENSG00000100445	ENST00000399395;ENST00000336353	D	0.93426	-3.22	5.46	5.46	0.80206	NAD(P)-binding domain (1);	0.222455	0.46145	D	0.000301	D	0.96972	0.9011	M	0.84585	2.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97373	0.9977	10	0.87932	D	0	-11.9991	17.1594	0.86800	0.0:1.0:0.0:0.0	.	82;108	Q9NRG7-2;Q9NRG7	.;D39U1_HUMAN	P	82;108	ENSP00000382327:R82P	ENSP00000336854:R108P	R	-	2	0	SDR39U1	23980803	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.215000	0.77966	2.714000	0.92807	0.655000	0.94253	CGC	.		0.498	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			G	24910963	C	G	24910963	1	3	47	0	1	0	0	0	0	0	0	0	14004	768	27	4		4	SDR39U1	14	24910963	IGR	SNP	C	TCGA-B9-4113-01A-01D-1252-08	297724	24910963	82438577	65	4293											
SPINT1	6692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41146021	41146021	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttatggaggctgcttgggCaacaagaacaactaccttcg	11	10	11	9	1	0	1	0	0	0	1	1	2	0	2	1	3	5	4	1	3	6	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:41146021C>T	ENST00000344051.4	+	5	1089	c.855C>T	c.(853-855)ggC>ggT	p.G285G	SPINT1_ENST00000562057.1_Silent_p.G285G|SPINT1_ENST00000431806.1_Silent_p.G285G			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	285	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCTGCTTGGGCAACAAGAACA	0.572																																					p.G285G		.											.	SPINT1-91	0			c.C855T						.						120	128	125					15																	41146021		2203	4300	6503	SO:0001819	synonymous_variant	6692	exon5			CTTGGGCAACAAG		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.855C>T	15.37:g.41146021C>T		Somatic	391	0		WXS	Illumina HiSeq	Phase_I	317	106	NM_181642	0	1	53	99	45	Q7Z7D2	Silent	SNP	ENST00000344051.4	37	CCDS10067.1																																																																																			.		0.572	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		T	41146021	C	T	41146021	2	4	47	1	0	0	0	0	0	0	0	1	15100	697	25	2		2	SPINT1	15	41146021	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08		41146021	61385371	66	4294											
TP53BP1	7158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	43724401	43724401	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgttctctcacctggctatgGagcgactctgtatcatcccc	6	13	8	14	1	4	0	2	0	2	0	6	2	5	1	3	2	1	3	3	2	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:43724401G>A	ENST00000263801.3	-	17	3903	c.3651C>T	c.(3649-3651)ctC>ctT	p.L1217L	TP53BP1_ENST00000382039.3_Silent_p.L1222L|TP53BP1_ENST00000382044.4_Silent_p.L1222L|TP53BP1_ENST00000450115.2_Silent_p.L1222L	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1217					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CCTGGCTATGGAGCGACTCTG	0.483								Other conserved DNA damage response genes																													p.L1222L		.											.	TP53BP1-294	0			c.C3666T						.						137	112	121					15																	43724401		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon17			GCTATGGAGCGAC	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3651C>T	15.37:g.43724401G>A		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	37	13	NM_001141980	0	0	0	0	0	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			.		0.483	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43724401	G	A	43724401	2	1	47	1	0	0	0	0	0	0	0	1	16416	1161	41	2		2	TP53BP1	15	43724401	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	2578380	43724401	58806991	67	4295											
CGNL1	84952	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	57730838	57730838	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggccaaatctggtgtgaCagctattcgtttatgcagct	8	12	10	11	2	1	1	0	1	1	0	2	1	1	1	2	2	3	4	2	2	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:57730838C>G	ENST00000281282.5	+	2	719	c.641C>G	c.(640-642)aCa>aGa	p.T214R		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	214	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TCTGGTGTGACAGCTATTCGT	0.517																																					p.T214R		.											.	CGNL1-100	0			c.C641G						.						132	132	132					15																	57730838		2192	4292	6484	SO:0001583	missense	84952	exon3			GTGTGACAGCTAT	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.641C>G	15.37:g.57730838C>G	ENSP00000281282:p.Thr214Arg	Somatic	625	1		WXS	Illumina HiSeq	Phase_I	467	169	NM_001252335	0	0	2	3	1	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	5.347	0.249277	0.10130	.	.	ENSG00000128849	ENST00000281282	T	0.76968	-1.06	4.98	4.04	0.47022	.	0.178508	0.26851	N	0.022178	T	0.70124	0.3188	L	0.51422	1.61	0.30026	N	0.813928	B	0.27625	0.183	B	0.19666	0.026	T	0.69495	-0.5130	10	0.56958	D	0.05	-12.3608	10.9213	0.47167	0.4244:0.5756:0.0:0.0	.	214	Q0VF96	CGNL1_HUMAN	R	214	ENSP00000281282:T214R	ENSP00000281282:T214R	T	+	2	0	CGNL1	55518130	0.432000	0.25554	0.389000	0.26208	0.182000	0.23217	1.535000	0.36061	1.275000	0.44379	0.650000	0.86243	ACA	.		0.517	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		G	57730838	C	G	57730838	3	3	47	1	0	0	0	0	1	0	0	0	3310	478	17	4	643	4	CGNL1	15	57730838	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	14006437	57730838	44800554	68	4296											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79058483	79058483	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgtccacagctccgccAcgtcaggactaggagaggag	9	6	12	14	2	1	1	1	0	0	1	4	4	4	3	4	3	1	1	4	3	1	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:79058483A>G	ENST00000388820.4	-	19	3980	c.3770T>C	c.(3769-3771)gTg>gCg	p.V1257A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1257					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CAGCTCCGCCACGTCAGGACT	0.682																																					p.V1257A		.											.	ADAMTS7-226	0			c.T3770C						.						18	20	19					15																	79058483		2190	4284	6474	SO:0001583	missense	11173	exon19			TCCGCCACGTCAG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3770T>C	15.37:g.79058483A>G	ENSP00000373472:p.Val1257Ala	Somatic	138	2		WXS	Illumina HiSeq	Phase_I	94	7	NM_014272	0	0	13	13	0	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	a	0.108	-1.142767	0.01728	.	.	ENSG00000136378	ENST00000388820	T	0.58358	0.34	4.07	-1.67	0.08238	.	3.059830	0.01144	N	0.006277	T	0.30417	0.0764	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.14671	-1.0464	10	0.07644	T	0.81	.	4.9595	0.14059	0.4676:0.0:0.3876:0.1449	.	1257	Q9UKP4	ATS7_HUMAN	A	1257	ENSP00000373472:V1257A	ENSP00000373472:V1257A	V	-	2	0	ADAMTS7	76845538	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.896000	0.04114	-0.238000	0.09724	0.387000	0.25754	GTG	.		0.682	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		G	79058483	A	G	79058483	3	3	47	1	0	0	0	0	1	0	0	0	271	159	6	3	1314	3	ADAMTS7	15	79058483	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	21327645	79058483	23472909	69	4297											
ST20	400410	hgsc.bcm.edu;bcgsc.ca	37	chr15	80191469	80191474	+	Splice_Site	DEL	TATGAG	TATGAG	-																															tctttacaaagccattttccTatgagagaataaatttaaca																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	TATGAG	TATGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:80191469_80191474delTATGAG	ENST00000478497.1	-	3	725		c.e3-2		MTHFS_ENST00000258874.3_5'Flank|ST20_ENST00000562759.1_Splice_Site|ST20-MTHFS_ENST00000479961.1_Intron|ST20_ENST00000485386.1_Splice_Site|ST20-MTHFS_ENST00000494999.1_Intron|MTHFS_ENST00000559722.1_5'Flank	NM_001100879.1	NP_001094349.1	Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20						extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						GCCATTTTCCTATGAGAGAATAAATT	0.311																																					.		.											.	ST20-68	0			.						.																																			SO:0001630	splice_region_variant	400410	.			.	AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000478497.1:c.46-2CTCATA>-	15.37:g.80191469_80191474delTATGAG		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	38	11	.	0	0	0	0	0		Splice_Site	DEL	ENST00000478497.1	37	CCDS42067.1																																																																																			.		0.311	ST20-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416728.2		Intron	-	80191474	TATGAG	-	80191469	8	5	47	1	0	1	0	1	0	0	1	0	15245	1536	53	0	199	0	ST20	15	80191469	Splice_Site	DEL	TATGAG	TCGA-B9-4113-01A-01D-1252-08	1132986	80191469	22339923	70	4298											
MCTP2	55784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	94841734	94841734	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctacacctcggtgcccagCagtctgtccactgcagggat	7	9	10	15	1	1	0	0	0	1	0	4	1	3	1	4	2	4	2	4	2	1	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:94841734C>T	ENST00000357742.4	+	1	240	c.240C>T	c.(238-240)agC>agT	p.S80S	MCTP2_ENST00000451018.3_Silent_p.S80S|MCTP2_ENST00000543482.1_Silent_p.S80S|MCTP2_ENST00000331706.4_5'UTR	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	80					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CGGTGCCCAGCAGTCTGTCCA	0.587																																					p.S80S		.											.	MCTP2-93	0			c.C240T						.						60	62	62					15																	94841734		2197	4298	6495	SO:0001819	synonymous_variant	55784	exon1			GCCCAGCAGTCTG	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.240C>T	15.37:g.94841734C>T		Somatic	359	0		WXS	Illumina HiSeq	Phase_I	261	80	NM_001159643	0	0	1	1	0	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			.		0.587	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94841734	C	T	94841734	2	4	47	1	0	0	0	0	0	0	0	1	9426	709	25	2		2	MCTP2	15	94841734	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	14650265	94841734	7689658	71	4299											
KIAA0556	23247	broad.mit.edu	37	chr16	27786370	27786370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaacgacaccagtgatggcCggcacatgtggctggctccc	8	7	13	13	2	0	2	0	2	0	0	1	3	1	2	3	4	1	3	3	4	1	0	rs372682821		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr16:27786370C>T	ENST00000261588.4	+	24	4433	c.4414C>T	c.(4414-4416)Cgg>Tgg	p.R1472W		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1472						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CAGTGATGGCCGGCACATGTG	0.687																																					p.R1472W													.	KIAA0556-141	0			c.C4414T						.	C	TRP/ARG	0,4394		0,0,2197	65	56	59		4414	1	1	16		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA0556	NM_015202.2	101	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1472/1619	27786370	1,12993	2197	4300	6497	SO:0001583	missense	23247	exon24			GATGGCCGGCACA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.4414C>T	16.37:g.27786370C>T	ENSP00000261588:p.Arg1472Trp	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	175	4	NM_015202	0	0	14	14	0	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442453	0.63067	0.0	1.16E-4	ENSG00000047578	ENST00000261588	T	0.15372	2.43	4.78	1.04	0.20106	.	0.000000	0.64402	D	0.000001	T	0.41627	0.1167	M	0.82630	2.6	0.47547	D	0.99945	D	0.89917	1.0	D	0.81914	0.995	T	0.35773	-0.9775	10	0.87932	D	0	-35.2725	12.3331	0.55051	0.5839:0.4161:0.0:0.0	.	1472	O60303	K0556_HUMAN	W	1472	ENSP00000261588:R1472W	ENSP00000261588:R1472W	R	+	1	2	KIAA0556	27693871	0.990000	0.36364	0.995000	0.50966	0.882000	0.50991	1.006000	0.29847	-0.096000	0.12329	-0.823000	0.03104	CGG	.		0.687	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27786370	C	T	27786370	3	4	47	1	0	0	0	0	1	0	0	0	8204	643	23	1	4508	1	KIAA0556	16	27786370	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08		27786370	62568383	72	4300											
FANCA	2175	hgsc.bcm.edu	37	chr16	89883000	89883000	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggtcctggcccgaggcggaGttcgggacccacgagtcgga	6	5	18	12	5	0	0	0	0	0	0	3	5	1	3	3	6	0	1	3	6	0	1	rs76275444	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr16:89883000G>C	ENST00000389301.3	-	1	54	c.24C>G	c.(22-24)aaC>aaG	p.N8K	FANCA_ENST00000563673.1_Missense_Mutation_p.N8K|FANCA_ENST00000389302.3_Missense_Mutation_p.N8K|FANCA_ENST00000534992.1_Missense_Mutation_p.N8K|FANCA_ENST00000543736.1_Missense_Mutation_p.N8K|FANCA_ENST00000568369.1_Missense_Mutation_p.N8K	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	8			N -> K (in FA; unknown pathological significance; dbSNP:rs76275444).		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CCGAGGCGGAGTTCGGGACCC	0.786			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				g|||	250	0.0499201	0.1823	0.013	5008	,	,		7756	0		0	False		,,,				2504	0				p.N8K		.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA-1130	0			c.C24G						.		LYS/ASN,LYS/ASN	326,2924		2,322,1301	2	3	3		24,24	-8.4	0	16	dbSNP_131	3	2,7018		0,2,3508	no	missense,missense	FANCA	NM_000135.2,NM_001018112.1	94,94	2,324,4809	CC,CG,GG		0.0285,10.0308,3.1938	benign,benign	8/1456,8/298	89883000	328,9942	1625	3510	5135	SO:0001583	missense	2175	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGCGGAGTTCGGG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"Fanconi anemia, complementation groups"	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.24C>G	16.37:g.89883000G>C	ENSP00000373952:p.Asn8Lys	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	8	4	NM_000135	0	0	1	1	0	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	68	0.031135531135531136	62	0.12601626016260162	6	0.016574585635359115	0	0.0	0	0.0	G	9.405	1.078943	0.20227	0.100308	2.85E-4	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	D;T;T;T	0.83914	-1.78;0.2;0.19;0.19	4.22	-8.45	0.00946	.	2.015170	0.03142	N	0.166706	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.16396	0.008;0.017;0.017;0.006;0.008	B;B;B;B;B	0.17433	0.004;0.018;0.018;0.01;0.004	T	0.41124	-0.9526	10	0.05959	T	0.93	0.155	2.6799	0.05090	0.3526:0.3821:0.157:0.1083	.	8;8;8;8;8	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360	.;.;.;.;FANCA_HUMAN	K	8	ENSP00000373952:N8K;ENSP00000373953:N8K;ENSP00000443675:N8K;ENSP00000443409:N8K	ENSP00000373952:N8K	N	-	3	2	FANCA	88410501	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-1.977000	0.01495	-1.966000	0.01009	0.187000	0.17357	AAC	G|0.032;C|0.968		0.786	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			C	89883000	G	C	89883000	3	2	47	1	0	0	0	0	1	0	0	0	5681	1020	36	4	4520	4	FANCA	16	89883000	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	62096630	89883000	471753	73	4301											
SLC43A2	124935	hgsc.bcm.edu	37	chr17	1494129	1494129	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgctgaccaggaacttgaGgatgttgttcatagccccca	9	9	11	12	1	1	2	1	2	0	0	1	4	1	4	4	2	2	3	4	2	2	4	rs145755178		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:1494129G>A	ENST00000301335.5	-	9	1133	c.1045C>T	c.(1045-1047)Ctc>Ttc	p.L349F	SLC43A2_ENST00000412517.3_Missense_Mutation_p.L212F|SLC43A2_ENST00000571650.1_Missense_Mutation_p.L349F|SLC43A2_ENST00000382147.4_Missense_Mutation_p.L349F|SLC43A2_ENST00000574274.1_5'Flank	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	349					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		AGGAACTTGAGGATGTTGTTC	0.642													g|||	1	0.000199681	8e-04	0	5008	,	,		16419	0		0	False		,,,				2504	0				p.L349F		.											.	SLC43A2-91	0			c.C1045T						.	-	PHE/LEU	6,4308		0,6,2151	49	42	44		1045	5.7	1	17	dbSNP_134	44	0,8474		0,0,4237	no	missense	SLC43A2	NM_152346.1	22	0,6,6388	AA,AG,GG		0.0,0.1391,0.0469	probably-damaging	349/570	1494129	6,12782	2157	4237	6394	SO:0001583	missense	124935	exon9			ACTTGAGGATGTT	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"Solute carriers"	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.1045C>T	17.37:g.1494129G>A	ENSP00000301335:p.Leu349Phe	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	6	3	NM_152346	0	0	73	126	53	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Missense_Mutation	SNP	ENST00000301335.5	37	CCDS11006.1	.	.	.	.	.	.	.	.	.	.	g	36	5.644218	0.96704	0.001391	0.0	ENSG00000167703	ENST00000301335;ENST00000382147;ENST00000412517	T;T;D	0.82984	0.35;0.35;-1.67	5.69	5.69	0.88448	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.89332	0.6685	L	0.55743	1.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.983;0.998;0.995;0.996	D	0.86314	0.1688	10	0.28530	T	0.3	-0.3735	19.8001	0.96502	0.0:0.0:1.0:0.0	.	212;349;349;349	B7Z6X9;Q8N370-2;Q8N370;Q8N370-3	.;.;LAT4_HUMAN;.	F	349;349;212	ENSP00000301335:L349F;ENSP00000371582:L349F;ENSP00000408284:L212F	ENSP00000301335:L349F	L	-	1	0	SLC43A2	1440879	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.632000	0.83247	2.678000	0.91216	0.556000	0.70494	CTC	G|1.000;A|0.000		0.642	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		A	1494129	G	A	1494129	3	1	47	1	0	0	0	0	1	0	0	0	14665	1000	35	2	688	2	SLC43A2	17	1494129	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		1494129	79701081	74	4302											
ZNF594	84622	ucsc.edu	37	chr17	5085331	5085331	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcctcatccttgctgaaggTtttctcacattcttcaagtt	7	17	5	12	0	4	1	3	1	2	0	7	1	6	1	2	1	1	3	2	1	2	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:5085331T>G	ENST00000399604.4	-	1	2361	c.2221A>C	c.(2221-2223)Acc>Ccc	p.T741P	ZNF594_ENST00000575779.1_Missense_Mutation_p.T741P			Q96JF6	ZN594_HUMAN	zinc finger protein 594	741					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TTGCTGAAGGTTTTCTCACAT	0.443																																					p.T741P													.	ZNF594-71	0			c.A2221C						.						205	211	209					17																	5085331		2088	4237	6325	SO:0001583	missense	84622	exon2			TGAAGGTTTTCTC	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2221A>C	17.37:g.5085331T>G	ENSP00000382513:p.Thr741Pro	Somatic	246	0		WXS	Illumina HiSeq		298	3	NM_032530	0	0	23	30	7	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.521063	0.27211	.	.	ENSG00000180626	ENST00000399604	T	0.16324	2.35	1.04	-2.08	0.07254	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13543	0.0328	L	0.61387	1.9	0.09310	N	0.999994	B	0.30179	0.271	B	0.14023	0.01	T	0.18023	-1.0350	9	0.62326	D	0.03	.	4.1321	0.10154	0.3047:0.0:0.0:0.6953	.	741	Q96JF6	ZN594_HUMAN	P	741	ENSP00000382513:T741P	ENSP00000382513:T741P	T	-	1	0	ZNF594	5026055	0.001000	0.12720	0.016000	0.15963	0.324000	0.28378	0.026000	0.13599	-0.614000	0.05687	0.248000	0.18094	ACC	.		0.443	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		G	5085331	T	G	5085331	3	3	47	1	0	0	0	0	1	0	0	0	18056	1725	60	5	206	5	ZNF594	17	5085331	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	3591202	5085331	76109879	75	4303											
CDRT4	284040	broad.mit.edu	37	chr17	15341130	15341130	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcatcctcatcataggcttgCgggcaaagatgatcttgtta	10	12	10	9	1	3	2	2	1	1	1	4	2	4	2	1	2	1	4	1	2	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:15341130C>T	ENST00000312177.6	-	4	696	c.416G>A	c.(415-417)cGc>cAc	p.R139H	CDRT4_ENST00000519354.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_3'UTR	NM_001204477.1	NP_001191406.1	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4	139										endometrium(3)|skin(1)	4				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)		CATAGGCTTGCGGGCAAAGAT	0.488																																					p.R140H													.	CDRT4-90	0			c.G419A						.						103	85	91					17																	15341130		2203	4300	6503	SO:0001583	missense	284040	exon4			GGCTTGCGGGCAA	BC029542	CCDS73995.1	17p12	2011-09-28			ENSG00000239704	ENSG00000239704			14383	protein-coding gene	gene with protein product						11381029	Standard	NM_001204477		Approved	FLJ36674	uc002gop.2	Q8N9R6	OTTHUMG00000059070	ENST00000312177.6:c.416G>A	17.37:g.15341130C>T	ENSP00000310031:p.Arg139His	Somatic	53	1		WXS	Illumina HiSeq	Phase_I	153	6	NM_001204477	0	0	26	26	0	A8MSL9|Q8IZ19	Missense_Mutation	SNP	ENST00000312177.6	37		.	.	.	.	.	.	.	.	.	.	C	12.34	1.909356	0.33721	.	.	ENSG00000239704	ENST00000520956;ENST00000312177	T	0.38077	1.16	4.98	1.88	0.25563	.	0.505891	0.16231	N	0.223586	T	0.50137	0.1598	M	0.64997	1.995	0.09310	N	1	D	0.89917	1.0	D	0.68039	0.955	T	0.32322	-0.9911	10	0.72032	D	0.01	-8.4552	7.1563	0.25639	0.0:0.7191:0.0:0.2809	.	139	Q8N9R6	CDRT4_HUMAN	H	140;139	ENSP00000310031:R139H	ENSP00000310031:R139H	R	-	2	0	CDRT4	15281855	0.709000	0.27886	0.009000	0.14445	0.110000	0.19582	0.383000	0.20651	0.284000	0.22305	-0.145000	0.13849	CGC	C|1.000;T|0.000		0.488	CDRT4-001	KNOWN	non_canonical_conserved|non_canonical_other|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000130383.7	NM_173622		T	15341130	C	T	15341130	3	4	47	1	0	0	0	0	1	0	0	0	3182	768	27	1	43	1	CDRT4	17	15341130	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	10255799	15341130	65854080	76	4304											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	819	126		WXS	Illumina HiSeq		914	120	NM_145301	0	0	14	72	58	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		T	15457087	C	T	15457087	3	4	47	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	115957	15457087	65738123	77	4305											
ATAD5	79915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	29220728	29220728	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagagacaaaggaaacaaTccagagacaaagaaatctat	21	4	8	8	0	1	3	0	0	1	3	2	6	2	4	2	1	1	0	2	1	6	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:29220728T>G	ENST00000321990.4	+	21	5235	c.4857T>G	c.(4855-4857)aaT>aaG	p.N1619K		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1619					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAGGAAACAATCCAGAGACAA	0.393																																					p.N1619K		.											.	ATAD5-93	0			c.T4857G						.						82	91	88					17																	29220728		2203	4300	6503	SO:0001583	missense	79915	exon21			AAACAATCCAGAG		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4857T>G	17.37:g.29220728T>G	ENSP00000313171:p.Asn1619Lys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	126	28	NM_024857	0	0	2	4	2	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.522716	0.00149	.	.	ENSG00000176208	ENST00000321990	T	0.06218	3.33	4.7	-1.39	0.08997	.	7.549810	0.00481	N	0.000125	T	0.04998	0.0134	L	0.39898	1.24	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.32025	-0.9922	10	0.07325	T	0.83	.	2.0379	0.03544	0.2113:0.3553:0.099:0.3344	.	1619	Q96QE3	ATAD5_HUMAN	K	1619	ENSP00000313171:N1619K	ENSP00000313171:N1619K	N	+	3	2	ATAD5	26244854	0.000000	0.05858	0.027000	0.17364	0.126000	0.20510	-1.140000	0.03210	-0.300000	0.08895	-0.326000	0.08463	AAT	.		0.393	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		G	29220728	T	G	29220728	3	3	47	1	0	0	0	0	1	0	0	0	1077	1432	50	5	4939	5	ATAD5	17	29220728	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	13763641	29220728	51974482	78	4306											
TANC2	26115	hgsc.bcm.edu;broad.mit.edu	37	chr17	61466867	61466867	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctgcagcagcagggtacCtgagcattgtggtgctgctg	7	10	15	9	0	0	1	0	1	0	0	0	1	0	1	1	2	8	8	1	2	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:61466867C>A	ENST00000424789.2	+	15	2795	c.2791C>A	c.(2791-2793)Ctg>Atg	p.L931M	AC015923.1_ENST00000431604.1_RNA|RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.L931M	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	931					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						AGCAGGGTACCTGAGCATTGT	0.537																																					p.L931M		.											.	TANC2-24	0			c.C2791A						.						31	31	31					17																	61466867		2010	4178	6188	SO:0001583	missense	26115	exon15			GGGTACCTGAGCA	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.2791C>A	17.37:g.61466867C>A	ENSP00000387593:p.Leu931Met	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	57	28	NM_025185	0	0	0	0	0	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	37	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	8.463	0.855695	0.17106	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.68765	-0.35;-0.35	5.17	5.17	0.71159	Ankyrin repeat-containing domain (4);	0.063998	0.64402	D	0.000005	T	0.62998	0.2474	L	0.50333	1.59	0.51767	D	0.999933	B;B;B	0.28128	0.082;0.118;0.201	B;B;B	0.31390	0.036;0.091;0.129	T	0.58989	-0.7538	10	0.14656	T	0.56	.	18.698	0.91610	0.0:1.0:0.0:0.0	.	931;841;931	Q9HCD6-2;D3DU10;Q9HCD6	.;.;TANC2_HUMAN	M	931	ENSP00000374171:L931M;ENSP00000387593:L931M	ENSP00000374171:L931M	L	+	1	2	TANC2	58820599	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.060000	0.57477	2.401000	0.81631	0.555000	0.69702	CTG	.		0.537	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			A	61466867	C	A	61466867	3	1	47	1	0	0	0	0	1	0	0	0	15577	680	24	4	2849	4	TANC2	17	61466867	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	32246139	61466867	19728343	79	4307											
SLC16A6	9120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	66270212	66270212	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggactgtggcgaggggagCtgccgggaaagaacaaaacg	13	3	17	8	3	0	1	0	0	0	1	0	5	0	4	1	5	4	1	1	5	4	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:66270212C>A	ENST00000327268.4	-	4	397		c.e4-1		SLC16A6_ENST00000580666.1_Splice_Site|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6						monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	GCGAGGGGAGCTGCCGGGAAA	0.547																																					.		.											.	SLC16A6-90	0			c.233-1G>T						.						63	58	59					17																	66270212		2203	4300	6503	SO:0001630	splice_region_variant	9120	exon4			GGGGAGCTGCCGG	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.233-1G>T	17.37:g.66270212C>A		Somatic	98	1		WXS	Illumina HiSeq	Phase_I	102	43	NM_004694	0	0	0	3	3	Q6P1X3	Splice_Site	SNP	ENST00000327268.4	37	CCDS11675.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290906	0.59976	.	.	ENSG00000108932	ENST00000327268	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0512	0.93046	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC16A6	63781807	1.000000	0.71417	0.991000	0.47740	0.414000	0.31173	7.232000	0.78116	2.735000	0.93741	0.655000	0.94253	.	.		0.547	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	Intron	A	66270212	C	A	66270212	5	1	47	1	0	0	0	0	0	0	1	0	14444	811	28	4	1355	4	SLC16A6	17	66270212	Splice_Site	SNP	C	TCGA-B9-4113-01A-01D-1252-08	4803345	66270212	14924998	80	4308											
PTPRM	5797	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	7567846	7567846	+	Frame_Shift_Del	DEL	T	T	-																															cttgggacttgcctggcgacTttggccggacttttgctaac																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:7567846delT	ENST00000332175.8	+	1	1067	c.30delT	c.(28-30)actfs	p.T10fs	PTPRM_ENST00000400060.4_Frame_Shift_Del_p.T10fs|PTPRM_ENST00000580170.1_Frame_Shift_Del_p.T10fs	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	10					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GCCTGGCGACTTTGGCCGGAC	0.766																																					p.T10fs		.											.	PTPRM-228	0			c.30delT						.						56	56	56					18																	7567846		2203	4300	6503	SO:0001589	frameshift_variant	5797	exon1			.	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.30delT	18.37:g.7567846delT	ENSP00000331418:p.Thr10fs	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	129	46	NM_001105244	0	0	0	0	0	A7MBN1|D3DUH8|J3QL11	Frame_Shift_Del	DEL	ENST00000332175.8	37	CCDS11840.1																																																																																			.		0.766	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			-	7567846	T	-	7567846	7	5	47	1	0	1	0	1	0	0	0	0	12838	1596	56	0	32	0	PTPRM	18	7567846	Frame_Shift_Del	DEL	T	TCGA-B9-4113-01A-01D-1252-08		7567846	70509402	81	4309	48	2									
PTPRM	5797	bcgsc.ca	37	chr18	7567847	7567847	+	Missense_Mutation	SNP	T	T	A																															ttgggacttgcctggcgactTtggccggacttttgctaact																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:7567847T>A	ENST00000332175.8	+	1	1068	c.31T>A	c.(31-33)Ttg>Atg	p.L11M	PTPRM_ENST00000400060.4_Missense_Mutation_p.L11M|PTPRM_ENST00000580170.1_Missense_Mutation_p.L11M	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	11					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CCTGGCGACTTTGGCCGGACT	0.766																																					p.L11M													.	PTPRM-228	0			c.T31A						.						55	56	56					18																	7567847		2203	4300	6503	SO:0001583	missense	5797	exon1			GCGACTTTGGCCG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.31T>A	18.37:g.7567847T>A	ENSP00000331418:p.Leu11Met	Somatic	157	0		WXS	Illumina HiSeq	Phase_1	120	44	NM_001105244	0	0	1	1	0	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	15.78	2.934033	0.52866	.	.	ENSG00000173482	ENST00000332175;ENST00000400060	T;T	0.39056	1.1;1.1	3.47	3.47	0.39725	.	0.140255	0.29328	N	0.012476	T	0.29976	0.0750	L	0.38175	1.15	0.80722	D	1	B;B	0.28324	0.207;0.207	B;B	0.21708	0.036;0.036	T	0.16012	-1.0417	10	0.66056	D	0.02	.	8.2616	0.31788	0.0:0.0:0.2016:0.7984	.	11;11	A7MBN1;P28827	.;PTPRM_HUMAN	M	11	ENSP00000331418:L11M;ENSP00000382933:L11M	ENSP00000331418:L11M	L	+	1	2	PTPRM	7557847	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	1.565000	0.36386	1.228000	0.43614	0.254000	0.18369	TTG	.		0.766	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	7567847	T	A	7567847	3	1	47	1	0	0	0	0	1	0	0	0	12838	1838	64	5	33	5	PTPRM	18	7567847	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	1	7567847	70509401	82	4310	48	2									
TAF4B	6875	broad.mit.edu	37	chr18	23895311	23895311	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cactcattcagtcatgtaaaGatgaaccatttctttttatt	12	17	4	8	0	4	2	3	1	1	1	4	2	4	2	1	0	1	1	1	0	4	7			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:23895311G>C	ENST00000269142.5	+	10	2949	c.1951G>C	c.(1951-1953)Gat>Cat	p.D651H	TAF4B_ENST00000578121.1_Missense_Mutation_p.D656H	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	651					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GTCATGTAAAGATGAACCATT	0.373																																					p.D651H													.	TAF4B-71	0			c.G1951C						.						71	66	67					18																	23895311		1850	4092	5942	SO:0001583	missense	6875	exon10			TGTAAAGATGAAC	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1951G>C	18.37:g.23895311G>C	ENSP00000269142:p.Asp651His	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	108	3	NM_005640	0	0	1	1	0	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990909	0.54041	.	.	ENSG00000141384	ENST00000418698;ENST00000269142	T	0.33438	1.41	5.91	5.91	0.95273	Transcription initiation factor TFIID component TAF4 (1);	0.293009	0.37669	N	0.001992	T	0.60869	0.2302	M	0.82823	2.61	0.80722	D	1	D;D	0.71674	0.998;0.996	D;P	0.67900	0.954;0.89	T	0.61520	-0.7046	10	0.52906	T	0.07	-3.6472	20.2983	0.98569	0.0:0.0:1.0:0.0	.	651;656	Q92750;A4PBF7	TAF4B_HUMAN;.	H	654;651	ENSP00000269142:D651H	ENSP00000269142:D651H	D	+	1	0	TAF4B	22149309	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.802000	0.96397	0.655000	0.94253	GAT	.		0.373	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		C	23895311	G	C	23895311	3	2	47	1	0	0	0	0	1	0	0	0	15559	942	33	4	1989	4	TAF4B	18	23895311	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	16327464	23895311	54181937	83	4311											
SALL3	27164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	76754972	76754972	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcaagagcgcgttggaaaTccactaccgcagccatacta	12	8	9	12	3	0	1	0	0	0	1	1	2	1	2	3	1	5	3	3	1	5	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:76754972T>C	ENST00000537592.2	+	2	2981	c.2981T>C	c.(2980-2982)aTc>aCc	p.I994T	SALL3_ENST00000575389.2_Intron|SALL3_ENST00000536229.3_Intron	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	994					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		GCGTTGGAAATCCACTACCGC	0.562																																					p.I994T		.											.	SALL3-155	0			c.T2981C						.						61	61	61					18																	76754972		2203	4300	6503	SO:0001583	missense	27164	exon2			TGGAAATCCACTA	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"Zinc fingers, C2H2-type"	10527	protein-coding gene	gene with protein product		605079	"sal (Drosophila)-like 3", "sal-like 3 (Drosophila)"			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2981T>C	18.37:g.76754972T>C	ENSP00000441823:p.Ile994Thr	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	86	33	NM_171999	0	0	0	0	0	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890593	0.33348	.	.	ENSG00000256463	ENST00000537592	T	0.07114	3.22	5.15	5.15	0.70609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000142	T	0.10809	0.0264	N	0.12637	0.245	0.80722	D	1	P	0.50819	0.939	P	0.53988	0.739	T	0.22695	-1.0209	10	0.56958	D	0.05	-22.1664	14.9958	0.71431	0.0:0.0:0.0:1.0	.	994	Q9BXA9	SALL3_HUMAN	T	994	ENSP00000441823:I994T	ENSP00000299466:I994T	I	+	2	0	SALL3	74855960	1.000000	0.71417	0.961000	0.40146	0.689000	0.40095	4.390000	0.59646	1.943000	0.56356	0.379000	0.24179	ATC	.		0.562	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		C	76754972	T	C	76754972	3	2	47	1	0	0	0	0	1	0	0	0	13844	1435	50	3	2987	3	SALL3	18	76754972	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	52859661	76754972	1322276	84	4312											
DOT1L	84444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2191111	2191111	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caaccactcggtgaccgaccCcgagaagctcaacaactacg	13	4	8	16	4	1	2	1	1	0	1	2	4	1	2	4	1	5	1	4	1	5	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:2191111C>G	ENST00000398665.3	+	5	401	c.365C>G	c.(364-366)cCc>cGc	p.P122R		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	122	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGACCGACCCCGAGAAGCTC	0.602																																					p.P122R		.											.	DOT1L-132	0			c.C365G						.						70	80	77					19																	2191111		2112	4210	6322	SO:0001583	missense	84444	exon5			CCGACCCCGAGAA	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.365C>G	19.37:g.2191111C>G	ENSP00000381657:p.Pro122Arg	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	116	41	NM_032482	0	0	0	1	1	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.003702	0.93287	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.23754	1.89;1.89	4.75	4.75	0.60458	.	0.053872	0.85682	D	0.000000	T	0.58552	0.2130	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68800	-0.5313	10	0.87932	D	0	-14.6108	16.8009	0.85614	0.0:1.0:0.0:0.0	.	122	Q8TEK3-2	.	R	122;122;98	ENSP00000381657:P122R;ENSP00000404284:P98R	ENSP00000221482:P122R	P	+	2	0	DOT1L	2142111	1.000000	0.71417	0.943000	0.38184	0.962000	0.63368	7.246000	0.78247	2.193000	0.70182	0.555000	0.69702	CCC	.		0.602	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		G	2191111	C	G	2191111	3	3	47	1	0	0	0	0	1	0	0	0	4720	623	22	4	383	4	DOT1L	19	2191111	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08		2191111	56937872	85	4313											
DOT1L	84444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2216711	2216711	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgtgctgaggcggcacctGagccaggaccacacggtgcc	8	6	14	13	2	0	2	0	2	0	0	0	3	0	3	4	4	3	2	4	4	0	1	rs377506676		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:2216711G>A	ENST00000398665.3	+	20	2391	c.2355G>A	c.(2353-2355)ctG>ctA	p.L785L	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	785					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGGCACCTGAGCCAGGACC	0.692																																					p.L785L		.											.	DOT1L-132	0			c.G2355A						.	G		0,4116		0,0,2058	25	30	29		2355	1.9	1	19		29	1,8349		0,1,4174	no	coding-synonymous	DOT1L	NM_032482.2		0,1,6232	AA,AG,GG		0.012,0.0,0.0080		785/1538	2216711	1,12465	2058	4175	6233	SO:0001819	synonymous_variant	84444	exon20			GCACCTGAGCCAG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2355G>A	19.37:g.2216711G>A		Somatic	134	1		WXS	Illumina HiSeq	Phase_I	105	41	NM_032482	0	0	6	10	4	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1																																																																																			.		0.692	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		A	2216711	G	A	2216711	2	1	47	1	0	0	0	0	0	0	0	1	4720	1277	45	2		2	DOT1L	19	2216711	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	25600	2216711	56912272	86	4314											
SLC25A23	79085	hgsc.bcm.edu	37	chr19	6444308	6444308	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaagccaccagttcttcAgagtctggagtggagaaggg	10	8	15	8	0	3	3	1	1	2	2	3	5	3	4	2	3	1	2	2	3	2	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:6444308A>G	ENST00000301454.4	-	9	1182	c.1076T>C	c.(1075-1077)cTg>cCg	p.L359P	SLC25A23_ENST00000601760.1_5'Flank|SLC25A23_ENST00000414491.2_Missense_Mutation_p.L120P|SLC25A23_ENST00000334510.5_Missense_Mutation_p.L359P	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	359					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						CCAGTTCTTCAGAGTCTGGAG	0.607																																					p.L359P		.											.	SLC25A23-92	0			c.T1076C						.						39	40	39					19																	6444308		2203	4300	6503	SO:0001583	missense	79085	exon9			TTCTTCAGAGTCT	AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"Solute carriers", "EF-hand domain containing"	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.1076T>C	19.37:g.6444308A>G	ENSP00000301454:p.Leu359Pro	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_024103	0	0	0	0	0	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Missense_Mutation	SNP	ENST00000301454.4	37	CCDS32882.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314992	0.81358	.	.	ENSG00000125648	ENST00000264088;ENST00000422102;ENST00000301454;ENST00000414491;ENST00000334510	T;T;T;T	0.80994	-1.44;-1.44;-1.34;-1.44	4.93	4.93	0.64822	Mitochondrial carrier domain (2);	0.000000	0.64402	D	0.000010	D	0.92971	0.7763	H	0.97440	4.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.992;0.995	D	0.95055	0.8190	10	0.87932	D	0	-15.6387	13.5424	0.61681	1.0:0.0:0.0:0.0	.	120;359	E7ESZ5;Q9BV35	.;SCMC3_HUMAN	P	406;60;359;120;359	ENSP00000264088:L406P;ENSP00000301454:L359P;ENSP00000408814:L120P;ENSP00000334537:L359P	ENSP00000264088:L406P	L	-	2	0	SLC25A23	6395308	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.848000	0.92172	1.852000	0.53769	0.379000	0.24179	CTG	.		0.607	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103		G	6444308	A	G	6444308	3	3	47	1	0	0	0	0	1	0	0	0	14518	188	7	3	338	3	SLC25A23	19	6444308	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	4227597	6444308	52684675	87	4315											
ZNF136	7695	broad.mit.edu;ucsc.edu	37	chr19	12297631	12297631	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gatacacgtaaccagtgttgGaaacccttcagttctcacca	12	10	7	12	1	2	0	2	0	1	0	3	2	2	1	3	1	3	3	3	1	3	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:12297631G>T	ENST00000343979.4	+	4	578	c.438G>T	c.(436-438)tgG>tgT	p.W146C	ZNF136_ENST00000398616.2_Missense_Mutation_p.W80C	NM_003437.3	NP_003428.1	P52737	ZN136_HUMAN	zinc finger protein 136	146					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|biliary_tract(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	18						ACCAGTGTTGGAAACCCTTCA	0.408																																					p.W146C													.	ZNF136-92	0			c.G438T						.						115	101	106					19																	12297631		2203	4300	6503	SO:0001583	missense	7695	exon4			GTGTTGGAAACCC	U09367	CCDS32916.1	19p13.2	2013-01-08	2006-06-13		ENSG00000196646	ENSG00000196646		"Zinc fingers, C2H2-type", "-"	12920	protein-coding gene	gene with protein product		604078	"zinc finger protein 136 (clone pHZ-20)"			7557990	Standard	NM_003437		Approved	pHZ-20	uc002mti.3	P52737	OTTHUMG00000156429	ENST00000343979.4:c.438G>T	19.37:g.12297631G>T	ENSP00000344162:p.Trp146Cys	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	15	5	NM_003437	0	0	2	7	5		Missense_Mutation	SNP	ENST00000343979.4	37	CCDS32916.1	.	.	.	.	.	.	.	.	.	.	G	8.925	0.961999	0.18583	.	.	ENSG00000196646	ENST00000439995;ENST00000343979;ENST00000398616	T;T;T	0.06449	3.8;3.41;3.3	1.41	-2.82	0.05787	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02727	0.0082	N	0.05124	-0.11	0.09310	N	1	D	0.53462	0.96	B	0.43728	0.429	T	0.28870	-1.0030	8	.	.	.	.	3.1392	0.06450	0.3723:0.0:0.3444:0.2832	.	146	P52737	ZN136_HUMAN	C	80;146;80	ENSP00000388759:W80C;ENSP00000344162:W146C;ENSP00000381617:W80C	.	W	+	3	0	ZNF136	12158631	0.165000	0.22948	0.000000	0.03702	0.050000	0.14768	-0.202000	0.09451	-1.474000	0.01879	-0.140000	0.14226	TGG	.		0.408	ZNF136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344151.2	NM_003437		T	12297631	G	T	12297631	3	4	47	1	0	0	0	0	1	0	0	0	17758	1183	41	4	452	4	ZNF136	19	12297631	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	5853323	12297631	46831352	88	4316											
SLC1A6	6511	broad.mit.edu	37	chr19	15067457	15067457	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagctgaccccccaggaCggccatgtcttccatctcca	7	7	8	19	1	2	1	0	1	2	0	4	2	3	2	7	2	1	1	7	2	0	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:15067457C>T	ENST00000221742.3	-	6	1007	c.1000G>A	c.(1000-1002)Gtc>Atc	p.V334I	SLC1A6_ENST00000600144.1_Intron|SLC1A6_ENST00000430939.2_Missense_Mutation_p.V270I	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	334					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.V334I(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CCCCCCAGGACGGCCATGTCT	0.582																																					p.V334I													.	SLC1A6-186	1	Substitution - Missense(1)	pancreas(1)	c.G1000A						.						130	114	120					19																	15067457		2203	4300	6503	SO:0001583	missense	6511	exon6			CCAGGACGGCCAT		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1000G>A	19.37:g.15067457C>T	ENSP00000221742:p.Val334Ile	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	142	4	NM_005071	0	0	0	0	0	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	10.37	1.332150	0.24167	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.58940	0.3;0.34	3.99	3.99	0.46301	.	0.353602	0.29159	N	0.012978	T	0.52773	0.1755	L	0.39020	1.185	0.34985	D	0.754498	P;B	0.45957	0.869;0.041	P;B	0.45913	0.497;0.028	T	0.67051	-0.5768	10	0.51188	T	0.08	-23.2893	13.9426	0.64064	0.0:1.0:0.0:0.0	.	270;334	E7EV13;P48664	.;EAA4_HUMAN	I	270;334	ENSP00000409386:V270I;ENSP00000221742:V334I	ENSP00000221742:V334I	V	-	1	0	SLC1A6	14928457	0.934000	0.31675	0.408000	0.26446	0.839000	0.47603	1.813000	0.38962	2.238000	0.73509	0.609000	0.83330	GTC	.		0.582	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15067457	C	T	15067457	3	4	47	1	0	0	0	0	1	0	0	0	14468	536	19	1	710	1	SLC1A6	19	15067457	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	2769826	15067457	44061526	89	4317											
CASP14	23581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15164633	15164633	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgtggtactcatggctcaCgggagggaaggcttcctcaa	8	10	13	10	2	3	0	3	0	0	0	5	2	4	2	1	5	1	3	1	5	3	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:15164633C>T	ENST00000427043.3	+	4	575	c.267C>T	c.(265-267)caC>caT	p.H89H	CASP14_ENST00000221740.1_Silent_p.H89H|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	89					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						TCATGGCTCACGGGAGGGAAG	0.552																																					p.H89H		.											.	CASP14-230	0			c.C267T						.						95	83	87					19																	15164633		2203	4300	6503	SO:0001819	synonymous_variant	23581	exon4			GGCTCACGGGAGG		CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.267C>T	19.37:g.15164633C>T		Somatic	281	0		WXS	Illumina HiSeq	Phase_I	244	35	NM_012114	0	0	0	0	0	O95823|Q3SYC9	Silent	SNP	ENST00000427043.3	37	CCDS12323.1																																																																																			.		0.552	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		T	15164633	C	T	15164633	2	4	47	1	0	0	0	0	0	0	0	1	2676	535	19	1		1	CASP14	19	15164633	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	97176	15164633	43964350	90	4318											
NWD1	284434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	16918705	16918705	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccttttacactcagctgcccGagaccctctccagcgtggcc	6	9	8	18	2	2	1	1	0	1	1	3	2	2	1	5	1	4	1	5	1	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:16918705G>A	ENST00000552788.1	+	16	4045	c.4045G>A	c.(4045-4047)Gag>Aag	p.E1349K	NWD1_ENST00000339803.6_Missense_Mutation_p.E1214K|NWD1_ENST00000379808.3_Missense_Mutation_p.E1349K|NWD1_ENST00000549814.1_Missense_Mutation_p.E1307K|NWD1_ENST00000524140.2_Missense_Mutation_p.E1349K|NWD1_ENST00000523826.1_Missense_Mutation_p.E1143K			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1349							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TCAGCTGCCCGAGACCCTCTC	0.567																																					p.E1349K		.											.	NWD1-7	0			c.G4045A						.						152	131	138					19																	16918705		2203	4300	6503	SO:0001583	missense	284434	exon18			CTGCCCGAGACCC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"WD repeat domain containing"	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.4045G>A	19.37:g.16918705G>A	ENSP00000447224:p.Glu1349Lys	Somatic	475	0		WXS	Illumina HiSeq	Phase_I	404	153	NM_001007525	0	0	0	0	0	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	G	12.61	1.989439	0.35131	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.57907	0.45;0.44;0.45;0.37;0.43;0.44	4.95	3.91	0.45181	WD40 repeat-like-containing domain (1);	0.427481	0.20913	N	0.083440	T	0.24509	0.0594	L	0.27053	0.805	0.09310	N	1	P;B;B	0.45078	0.85;0.145;0.089	B;B;B	0.25140	0.058;0.039;0.017	T	0.14952	-1.0454	10	0.09843	T	0.71	-19.7004	6.6582	0.22998	0.1992:0.0:0.8008:0.0	.	1349;1349;1214	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	K	1214;1349;1307;1349;1143;1349;1214	ENSP00000428579:E1349K;ENSP00000447548:E1307K;ENSP00000369136:E1349K;ENSP00000428955:E1143K;ENSP00000447224:E1349K;ENSP00000340159:E1214K	ENSP00000340159:E1214K	E	+	1	0	NWD1	16779705	0.274000	0.24191	0.991000	0.47740	0.505000	0.33919	1.839000	0.39220	2.282000	0.76494	0.655000	0.94253	GAG	.		0.567	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16918705	G	A	16918705	3	1	47	1	0	0	0	0	1	0	0	0	10807	1059	37	1	3694	1	NWD1	19	16918705	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	1754072	16918705	42210278	91	4319											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40395978	40395978	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagcacatacacgcaggtGcccatgaagtcgaagcggcg	11	4	13	13	4	0	1	0	1	0	0	1	2	0	1	2	2	4	2	2	2	3	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:40395978G>A	ENST00000221347.6	-	15	7426	c.7419C>T	c.(7417-7419)ggC>ggT	p.G2473G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2473	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACACGCAGGTGCCCATGAAGT	0.657																																					p.G2473G		.											.	FCGBP-98	0			c.C7419T						.						110	88	96					19																	40395978		2180	3903	6083	SO:0001819	synonymous_variant	8857	exon15			GCAGGTGCCCATG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.7419C>T	19.37:g.40395978G>A		Somatic	271	1		WXS	Illumina HiSeq	Phase_I	248	41	NM_003890	0	0	9	9	0	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			.		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40395978	G	A	40395978	2	1	47	1	0	0	0	0	0	0	0	1	5797	1306	46	2		2	FCGBP	19	40395978	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	23477273	40395978	18733005	92	4320											
ZNF285	26974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44896570	44896570	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caggtttatctgggctttatCcaatagtgccagctcttcct	7	15	8	11	0	2	0	0	0	2	0	4	0	4	0	3	2	2	3	3	2	4	6	rs144077949	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:44896570C>G	ENST00000330997.4	-	3	140	c.76G>C	c.(76-78)Gat>Cat	p.D26H	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.D26H|CTC-512J12.4_ENST00000588655.1_RNA|ZNF285_ENST00000591679.1_Missense_Mutation_p.D33H	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	26	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TGGGCTTTATCCAATAGTGCC	0.453																																					p.D26H		.											.	ZNF285-94	0			c.G76C						.						149	132	138					19																	44896570		2203	4300	6503	SO:0001583	missense	26974	exon3			CTTTATCCAATAG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.76G>C	19.37:g.44896570C>G	ENSP00000333595:p.Asp26His	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	74	33	NM_152354	0	0	1	1	0	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405340	0.62288	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T;T	0.06142	3.34;4.17	3.07	1.89	0.25635	Krueppel-associated box (4);	.	.	.	.	T	0.23054	0.0557	M	0.88310	2.945	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.09640	-1.0665	9	0.87932	D	0	.	3.2985	0.06974	0.2577:0.5999:0.0:0.1424	.	50;26	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	H	49;26	ENSP00000439431:D49H;ENSP00000333595:D26H	ENSP00000333595:D26H	D	-	1	0	ZNF285	49588410	0.829000	0.29322	0.154000	0.22540	0.897000	0.52465	1.205000	0.32308	1.738000	0.51689	0.449000	0.29647	GAT	C|0.997;T|0.003		0.453	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		G	44896570	C	G	44896570	3	3	47	1	0	0	0	0	1	0	0	0	17854	855	30	4	1704	4	ZNF285	19	44896570	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	4500592	44896570	14232413	93	4321											
EML2	24139	hgsc.bcm.edu	37	chr19	46142624	46142624	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggtctcacccagctccaAagctactcatggcggcgggt	9	7	12	13	2	2	0	2	0	1	0	4	0	3	0	2	4	3	2	2	4	3	1	rs201822741	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:46142624A>C	ENST00000245925.3	-	1	61	c.11T>G	c.(10-12)tTt>tGt	p.F4C	EML2_ENST00000536630.1_Intron|MIR330_ENST00000362196.1_RNA|EML2_ENST00000587152.1_Intron|EML2_ENST00000589876.1_Missense_Mutation_p.F4C|AC006132.1_ENST00000593161.1_5'Flank	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	4					negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CCCAGCTCCAAAGCTACTCAT	0.726													A|||	48	0.00958466	0.0325	0.0072	5008	,	,		12182	0		0	False		,,,				2504	0				p.F4C		.											.	EML2-154	0			c.T11G						.		,,CYS/PHE	90,4006		0,90,1958	15	17	16		,,11	4.6	1	19	dbSNP_134	16	1,8033		0,1,4016	yes	intron,intron,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,205	0,91,5974	CC,CA,AA		0.0124,2.1973,0.7502	,,	,,4/650	46142624	91,12039	2048	4017	6065	SO:0001583	missense	24139	exon1			GCTCCAAAGCTAC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"WD repeat domain containing"	18035	protein-coding gene	gene with protein product	"echinoderm MT-associated protein (EMAP)-like protein 70", "microtubule-associated protein like echinoderm EMAP"					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.11T>G	19.37:g.46142624A>C	ENSP00000245925:p.Phe4Cys	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	11	4	NM_012155	0	0	0	1	1	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	13	0.005952380952380952	8	0.016260162601626018	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	A	14.61	2.585437	0.46110	0.021973	1.24E-4	ENSG00000125746	ENST00000245925	T	0.26067	1.76	4.58	4.58	0.56647	.	1.865290	0.03249	U	0.181627	T	0.26666	0.0652	L	0.29908	0.895	0.80722	D	1	D;B	0.76494	0.999;0.118	D;B	0.74674	0.984;0.053	T	0.03034	-1.1080	10	0.59425	D	0.04	44.314	10.2951	0.43618	1.0:0.0:0.0:0.0	.	4;4	B7Z918;O95834	.;EMAL2_HUMAN	C	4	ENSP00000245925:F4C	ENSP00000245925:F4C	F	-	2	0	EML2	50834464	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.633000	0.54295	1.932000	0.55993	0.454000	0.30748	TTT	A|0.994;C|0.006		0.726	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		C	46142624	A	C	46142624	3	2	47	1	0	0	0	0	1	0	0	0	5110	14	1	5	2014	5	EML2	19	46142624	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	1246054	46142624	12986359	94	4322											
DHDH	27294	hgsc.bcm.edu;broad.mit.edu	37	chr19	49438360	49438360	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggagctggccaaggaccCgagcgtgggtgagtggcgag	8	5	20	8	3	0	2	0	2	0	0	0	6	0	4	2	5	2	1	2	5	1	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:49438360C>T	ENST00000221403.2	+	2	234	c.194C>T	c.(193-195)cCg>cTg	p.P65L	DHDH_ENST00000522614.1_Missense_Mutation_p.P65L|DHDH_ENST00000523250.1_Missense_Mutation_p.P65L	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	65					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GCCAAGGACCCGAGCGTGGGT	0.692																																					p.P65L		.											.	DHDH-90	0			c.C194T						.						23	18	20					19																	49438360		2196	4293	6489	SO:0001583	missense	27294	exon2			AGGACCCGAGCGT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.194C>T	19.37:g.49438360C>T	ENSP00000221403:p.Pro65Leu	Somatic	30	1		WXS	Illumina HiSeq	Phase_I	10	6	NM_014475	0	0	0	0	0		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.670182	0.88348	.	.	ENSG00000104808	ENST00000221403;ENST00000523250;ENST00000522614	T;T;T	0.26067	1.76;1.76;1.76	4.84	4.84	0.62591	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.106296	0.64402	D	0.000004	T	0.61652	0.2364	H	0.97240	3.965	0.80722	D	1	D	0.61697	0.99	P	0.57776	0.827	T	0.76567	-0.2912	10	0.72032	D	0.01	-28.9182	15.844	0.78874	0.0:1.0:0.0:0.0	.	65	Q9UQ10	DHDH_HUMAN	L	65	ENSP00000221403:P65L;ENSP00000428935:P65L;ENSP00000428672:P65L	ENSP00000221403:P65L	P	+	2	0	DHDH	54130172	1.000000	0.71417	0.967000	0.41034	0.785000	0.44390	6.706000	0.74649	2.678000	0.91216	0.455000	0.32223	CCG	.		0.692	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		T	49438360	C	T	49438360	3	4	47	1	0	0	0	0	1	0	0	0	4490	652	23	1	200	1	DHDH	19	49438360	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	3295736	49438360	9690623	95	4323											
ZNF665	79788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53669370	53669370	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcccttctatcacgttgagCtcttctaccagggagatttt	8	14	8	11	1	4	2	1	1	3	1	4	3	4	2	2	1	3	2	2	1	2	7			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:53669370C>G	ENST00000600412.1	-	2	293	c.178G>C	c.(178-180)Gct>Cct	p.A60P	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Missense_Mutation_p.A125P			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	60					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)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCACGTTGAGCTCTTCTACCA	0.388																																					p.A125P		.											.	ZNF665-70	0			c.G373C						.						118	124	122					19																	53669370		2073	4226	6299	SO:0001583	missense	79788	exon4			GTTGAGCTCTTCT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.178G>C	19.37:g.53669370C>G	ENSP00000469154:p.Ala60Pro	Somatic	271	0		WXS	Illumina HiSeq	Phase_I	196	64	NM_024733	0	0	0	1	1	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	C	7.108	0.575466	0.13623	.	.	ENSG00000197497	ENST00000396424	T	0.08370	3.1	2.4	-0.298	0.12814	.	.	.	.	.	T	0.04588	0.0125	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44267	-0.9339	9	0.24483	T	0.36	.	6.4255	0.21768	0.1793:0.4658:0.3549:0.0	.	125	Q9H7R5-2	.	P	125	ENSP00000379702:A125P	ENSP00000379702:A125P	A	-	1	0	ZNF665	58361182	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	0.042000	0.13949	0.315000	0.23110	0.543000	0.68304	GCT	.		0.388	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		G	53669370	C	G	53669370	3	3	47	1	0	0	0	0	1	0	0	0	18105	797	28	4	1667	4	ZNF665	19	53669370	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	4231010	53669370	5459613	96	4324											
PRIC285	85441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62193087	62193087	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcttcagctccatccttcTcaggagcagtcctgagggta	7	10	12	12	0	2	1	2	1	1	0	6	2	5	2	3	3	2	4	3	3	1	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr20:62193087T>C	ENST00000467148.1	-	12	6772	c.6703A>G	c.(6703-6705)Aga>Gga	p.R2235G	HELZ2_ENST00000427522.2_Missense_Mutation_p.R1666G	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2235	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCCATCCTTCTCAGGAGCAGT	0.667																																					p.R2235G		.											.	.	0			c.A6703G						.						28	28	28					20																	62193087		2195	4295	6490	SO:0001583	missense	85441	exon13			TCCTTCTCAGGAG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6703A>G	20.37:g.62193087T>C	ENSP00000417401:p.Arg2235Gly	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	63	23	NM_001037335	0	0	2	2	0	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	8.870	0.949007	0.18356	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.81821	-1.54;-1.54	2.96	1.78	0.24846	ATPase, AAA+ type, core (1);	1.202560	0.05584	N	0.573417	T	0.76772	0.4034	L	0.41124	1.26	0.29383	N	0.863141	B;B	0.29270	0.24;0.122	B;B	0.39027	0.288;0.19	T	0.68161	-0.5482	10	0.66056	D	0.02	-9.3242	4.3793	0.11286	0.0:0.1118:0.2045:0.6837	.	2235;1666	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	G	1666;2235	ENSP00000393257:R1666G;ENSP00000417401:R2235G	ENSP00000393257:R1666G	R	-	1	2	RP4-697K14.7	61663531	0.466000	0.25823	0.958000	0.39756	0.288000	0.27193	0.564000	0.23563	0.497000	0.27926	0.402000	0.26972	AGA	.		0.667	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		C	62193087	T	C	62193087	3	2	47	1	0	0	0	0	1	0	0	0	12514	1559	54	3	1278	3	PRIC285	20	62193087	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		62193087	832433	97	4325											
LSS	4047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47626684	47626684	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatttctcatgttcagcagcTgaaatcacagagagcaccct	12	10	8	11	0	3	2	3	1	1	1	4	4	3	2	1	0	3	4	1	0	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr21:47626684T>G	ENST00000397728.3	-	16	1546		c.e16-2		LSS_ENST00000522411.1_Splice_Site|LSS_ENST00000457828.2_Splice_Site|LSS_ENST00000356396.4_Splice_Site	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)						cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					GTTCAGCAGCTGAAATCACAG	0.582																																					.	Pancreas(114;955 2313 34923 50507)	.											.	LSS-90	0			c.1468-2A>C						.						71	60	64					21																	47626684		2203	4300	6503	SO:0001630	splice_region_variant	4047	exon17			AGCAGCTGAAATC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1468-2A>C	21.37:g.47626684T>G		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	154	59	NM_001001438	0	0	0	3	3	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Splice_Site	SNP	ENST00000397728.3	37	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674567	0.47781	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4665	0.75406	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LSS	46451112	1.000000	0.71417	0.974000	0.42286	0.221000	0.24807	7.752000	0.85141	2.206000	0.71126	0.533000	0.62120	.	.		0.582	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		Intron	G	47626684	T	G	47626684	5	3	47	1	0	0	0	0	0	0	1	0	9090	1594	55	5	760	5	LSS	21	47626684	Splice_Site	SNP	T	TCGA-B9-4113-01A-01D-1252-08		47626684	503211	98	4326											
TOP3B	8940	hgsc.bcm.edu;broad.mit.edu	37	chr22	22319734	22319735	+	In_Frame_Ins	INS	-	-	TTG																															cttggccttttctttcctgcINSttgtggcctccacctggaag																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:22319734_22319735insTTG	ENST00000398793.2	-	9	1299_1300	c.865_866insCAA	c.(865-867)agc>aCAAgc	p.288_289insT	TOP3B_ENST00000357179.5_In_Frame_Ins_p.288_289insT|TOP3B_ENST00000413067.2_In_Frame_Ins_p.17_18insT	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	288					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TTCTTTCCTGCTTGTGGCCTCC	0.535																																					p.S289delinsTS		.											.	TOP3B-538	0			c.866_867insCAA						.																																			SO:0001652	inframe_insertion	8940	exon9			.	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.863_865dupCAA	22.37:g.22319735_22319737dupTTG	ENSP00000381773:p.Thr288_Thr288dup	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	55	14	NM_003935	0	0	0	0	0	A0M8Q3|Q9BUP5	In_Frame_Ins	INS	ENST00000398793.2	37	CCDS13797.1																																																																																			.		0.535	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		TTG	22319735	-	TTG	22319734	7	5	47	1	0	1	1	0	0	0	0	0	16401	797	28	0	1762	0	TOP3B	22	22319734	In_Frame_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08		22319734	28984832	99	4327											
CYP2D6	1565	broad.mit.edu	37	chr22	42523507	42523516	+	Frame_Shift_Del	DEL	AGGGGGACGA	AGGGGGACGA	-																															atgtcatatgggtcacacccAgggggacgatgtccccaaag																								rs149686350|rs61745683	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	AGGGGGACGA	AGGGGGACGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:42523507_42523516delAGGGGGACGA	ENST00000360608.5	-	7	1220_1229	c.1106_1115delTCGTCCCCCT	c.(1105-1116)atcgtccccctgfs	p.IVPL369fs	NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000389970.3_Frame_Shift_Del_p.IVPL369fs|NDUFA6-AS1_ENST00000451451.1_RNA|CYP2D6_ENST00000359033.4_Frame_Shift_Del_p.IVPL318fs|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	369			I -> T (in allele CYP2D6*26).		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)	p.I318I(1)|p.I369I(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGTCACACCCAGGGGGACGATGTCCCCAAA	0.624																																					p.369_372del													.	CYP2D6-136	2	Substitution - coding silent(2)	urinary_tract(2)	c.1106_1115del						.																																			SO:0001589	frameshift_variant	1565	exon7			ACACCCAGGGGGA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"Cytochrome P450s"	2625	protein-coding gene	gene with protein product		124030	"cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6", "cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2", "cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2", "cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2", "cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1106_1115delTCGTCCCCCT	22.37:g.42523507_42523516delAGGGGGACGA	ENSP00000353820:p.Ile369fs	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	142	13	NM_000106	0	0	0	0	0	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Frame_Shift_Del	DEL	ENST00000360608.5	37	CCDS46721.1																																																																																			.		0.624	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			-	42523516	AGGGGGACGA	-	42523507	7	5	47	1	0	1	0	1	0	0	0	0	4175	188	7	0	390	0	CYP2D6	22	42523507	Frame_Shift_Del	DEL	AGGGGGACGA	TCGA-B9-4113-01A-01D-1252-08	20203773	42523507	8781059	100	4328											
ARSA	410	broad.mit.edu	37	chr22	51063617	51063617	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcaagctgggcggggggTgcagccaggatgacagcaga	10	3	19	9	1	0	2	0	1	0	1	0	3	0	3	1	5	5	5	1	5	1	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:51063617T>G	ENST00000547307.1	-	8	1885	c.1480A>C	c.(1480-1482)Acc>Ccc	p.T494P	ARSA_ENST00000610191.1_5'Flank|ARSA_ENST00000547805.1_Missense_Mutation_p.T494P|ARSA_ENST00000395621.3_Missense_Mutation_p.T496P|ARSA_ENST00000216124.5_Missense_Mutation_p.T496P|ARSA_ENST00000395619.3_Missense_Mutation_p.T496P|ARSA_ENST00000356098.5_Missense_Mutation_p.T496P|ARSA_ENST00000453344.2_Missense_Mutation_p.T410P			P15289	ARSA_HUMAN	arylsulfatase A	494					autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	GGGCGGGGGGTGCAGCCAGGA	0.692																																					p.T496P													.	ARSA-92	0			c.A1486C						.						10	12	11					22																	51063617		2187	4283	6470	SO:0001583	missense	410	exon9			GGGGGGTGCAGCC	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"Arylsulfatase family"	713	protein-coding gene	gene with protein product	"metachromatic leucodystrophy"	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.1480A>C	22.37:g.51063617T>G	ENSP00000448440:p.Thr494Pro	Somatic	49	13		WXS	Illumina HiSeq	Phase_I	31	7	NM_001085426	0	0	79	84	5	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		.	.	.	.	.	.	.	.	.	.	T	4.511	0.094745	0.08681	.	.	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.14	2.81	0.32909	Alkaline-phosphatase-like, core domain (1);	0.521500	0.22127	N	0.064257	T	0.77772	0.4180	N	0.19112	0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.63550	-0.6612	10	0.30854	T	0.27	.	7.1636	0.25677	0.1435:0.0:0.1486:0.7079	.	494	P15289	ARSA_HUMAN	P	496;496;494;494;496;410;496	ENSP00000348406:T496P;ENSP00000216124:T496P;ENSP00000448440:T494P;ENSP00000448932:T494P;ENSP00000378983:T496P;ENSP00000412542:T410P;ENSP00000378981:T496P	ENSP00000216124:T496P	T	-	1	0	ARSA	49410483	0.258000	0.24033	0.134000	0.22075	0.008000	0.06430	1.796000	0.38794	0.876000	0.35872	0.260000	0.18958	ACC	.		0.692	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487		G	51063617	T	G	51063617	3	3	47	1	0	0	0	0	1	0	0	0	988	1696	59	5	47	5	ARSA	22	51063617	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	8540110	51063617	240949	101	4329											
LONRF3	79836	hgsc.bcm.edu	37	chrX	118109101	118109101	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agaaagtcccgcaaggcgagGcgctggcgccggcgcccccg	7	2	16	16	7	0	1	0	0	0	1	1	2	1	1	4	4	0	2	4	4	2	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chrX:118109101G>T	ENST00000371628.3	+	1	389	c.358G>T	c.(358-360)Gcg>Tcg	p.A120S	LONRF3_ENST00000422289.2_5'Flank|LONRF3_ENST00000304778.7_Missense_Mutation_p.A120S	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	120							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GCAAGGCGAGGCGCTGGCGCC	0.731																																					p.A120S		.											.	LONRF3-289	0			c.G358T						.						2	3	3					X																	118109101		1637	3395	5032	SO:0001583	missense	79836	exon1			GGCGAGGCGCTGG	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.358G>T	X.37:g.118109101G>T	ENSP00000360690:p.Ala120Ser	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	8	7	NM_001031855	0	0	0	0	0	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	G	3.593	-0.083174	0.07141	.	.	ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628	T;T;T	0.80738	-1.41;-1.41;-1.17	4.27	3.38	0.38709	.	1.631660	0.03606	N	0.234137	T	0.65544	0.2701	N	0.08118	0	0.80722	D	1	B;B	0.23249	0.082;0.062	B;B	0.24394	0.053;0.024	T	0.41052	-0.9530	10	0.09590	T	0.72	-3.3969	10.5187	0.44905	0.0:0.1987:0.8013:0.0	.	120;120	Q496Y0-2;Q496Y0	.;LONF3_HUMAN	S	120	ENSP00000360691:A120S;ENSP00000307732:A120S;ENSP00000360690:A120S	ENSP00000307732:A120S	A	+	1	0	LONRF3	117993129	0.999000	0.42202	0.063000	0.19743	0.011000	0.07611	1.162000	0.31786	0.786000	0.33708	0.529000	0.55759	GCG	.		0.731	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		T	118109101	G	T	118109101	3	4	47	1	0	0	0	0	1	0	0	0	8921	1203	42	4	360	4	LONRF3	23	118109101	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		118109101	37161459	102	4330											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19420561	19420561	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcacactggggttggagcGaacaaaggtgctgttgatct	10	9	15	7	1	1	1	0	1	1	0	1	4	1	2	0	4	4	4	0	4	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:19420561G>T	ENST00000375254.3	-	95	13846	c.13819C>A	c.(13819-13821)Cgc>Agc	p.R4607S	UBR4_ENST00000375226.2_Missense_Mutation_p.R4583S|UBR4_ENST00000375267.2_Missense_Mutation_p.R4607S|UBR4_ENST00000375224.1_Missense_Mutation_p.R314S|UBR4_ENST00000467272.2_5'UTR|UBR4_ENST00000543981.1_Missense_Mutation_p.R271S|UBR4_ENST00000375217.2_Missense_Mutation_p.R4600S|UBR4_ENST00000429347.2_Missense_Mutation_p.R130S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4607					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GGGTTGGAGCGAACAAAGGTG	0.532																																					p.R4607S		.											.	UBR4-612	0			c.C13819A						.						111	90	97					1																	19420561		2203	4300	6503	SO:0001583	missense	23352	exon95			TGGAGCGAACAAA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.13819C>A	1.37:g.19420561G>T	ENSP00000364403:p.Arg4607Ser	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	41	11	NM_020765	0	0	19	36	17	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331029	0.95733	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375224;ENST00000429347;ENST00000543981	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	M	0.84683	2.71	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.992	D;D;D;D	0.76575	0.982;0.982;0.988;0.969	T	0.63791	-0.6557	10	0.52906	T	0.07	.	18.7785	0.91922	0.0:0.0:1.0:0.0	.	271;130;4607;4583	B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3	.;.;UBR4_HUMAN;.	S	4607;4607;4600;4583;314;130;271	ENSP00000364403:R4607S;ENSP00000364416:R4607S;ENSP00000364365:R4600S;ENSP00000364374:R4583S;ENSP00000364372:R314S;ENSP00000394173:R130S;ENSP00000444070:R271S	ENSP00000364365:R4600S	R	-	1	0	UBR4	19293148	1.000000	0.71417	0.966000	0.40874	0.992000	0.81027	9.162000	0.94745	2.785000	0.95823	0.591000	0.81541	CGC	.		0.532	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19420561	G	T	19420561	3	4	48	1	0	0	0	0	1	0	0	0	16937	1058	37	4	1780	4	UBR4	1	19420561	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		19420561	229830060	1	4331											
ZYG11B	79699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53236935	53236935	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggtgctgaattcattaaCtctctccctcgaggatcctt	7	14	7	13	1	2	1	1	1	1	0	6	3	4	2	3	2	2	1	3	2	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:53236935C>A	ENST00000294353.6	+	3	585	c.440C>A	c.(439-441)aCt>aAt	p.T147N	ZYG11B_ENST00000443756.2_Missense_Mutation_p.T147N|ZYG11B_ENST00000545132.1_Missense_Mutation_p.T147N	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	147										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						AATTCATTAACTCTCTCCCTC	0.478																																					p.T147N		.											.	ZYG11B-94	0			c.C440A						.						97	94	95					1																	53236935		2203	4300	6503	SO:0001583	missense	79699	exon3			CATTAACTCTCTC	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.440C>A	1.37:g.53236935C>A	ENSP00000294353:p.Thr147Asn	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	73	24	NM_024646	0	0	0	0	0	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	37	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745282	0.49151	.	.	ENSG00000162378	ENST00000443756;ENST00000545132;ENST00000294353	T;T;T	0.07021	3.23;3.23;3.23	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.09686	0.0238	L	0.38175	1.15	0.58432	D	0.999994	B;B	0.24258	0.1;0.027	B;B	0.22753	0.041;0.013	T	0.24977	-1.0145	10	0.23891	T	0.37	.	19.6182	0.95643	0.0:1.0:0.0:0.0	.	147;147	B4DK95;Q9C0D3	.;ZY11B_HUMAN	N	147	ENSP00000400522:T147N;ENSP00000441315:T147N;ENSP00000294353:T147N	ENSP00000294353:T147N	T	+	2	0	ZYG11B	53009523	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.662000	0.68032	2.653000	0.90120	0.650000	0.86243	ACT	.		0.478	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		A	53236935	C	A	53236935	3	1	48	1	0	0	0	0	1	0	0	0	18285	565	20	4	450	4	ZYG11B	1	53236935	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	33816374	53236935	196013686	2	4332											
SGIP1	84251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	67138996	67138996	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agatgacactacggcccttgCtcctctctttggcccaccac	7	10	7	17	1	1	2	0	1	1	1	3	2	2	2	4	2	2	1	4	2	1	3	rs142151342		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:67138996C>A	ENST00000371037.4	+	12	670	c.593C>A	c.(592-594)gCt>gAt	p.A198D	SGIP1_ENST00000371036.3_Missense_Mutation_p.A165D|AL139147.1_ENST00000502413.2_Intron|SGIP1_ENST00000468286.1_3'UTR|SGIP1_ENST00000237247.6_Missense_Mutation_p.A202D|SGIP1_ENST00000371039.1_Missense_Mutation_p.A166D|SGIP1_ENST00000371035.3_Missense_Mutation_p.A155D	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	198	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						ACGGCCCTTGCTCCTCTCTTT	0.363																																					p.A198D		.											.	SGIP1-93	0			c.C593A						.						177	185	183					1																	67138996		2203	4300	6503	SO:0001583	missense	84251	exon12			CCCTTGCTCCTCT	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.593C>A	1.37:g.67138996C>A	ENSP00000360076:p.Ala198Asp	Somatic	620	0		WXS	Illumina HiSeq	Phase_I	301	95	NM_032291	0	0	1	1	0	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	37	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332511	0.41297	.	.	ENSG00000118473	ENST00000237247;ENST00000371039;ENST00000424320;ENST00000371035;ENST00000371038;ENST00000407289;ENST00000371036;ENST00000371037	T;T;T;T;T;T	0.03330	3.97;3.97;3.97;3.97;3.97;3.97	5.73	5.73	0.89815	.	0.171335	0.52532	D	0.000074	T	0.04003	0.0112	N	0.17474	0.49	0.35690	D	0.814803	D	0.71674	0.998	D	0.76071	0.987	T	0.59736	-0.7398	10	0.11485	T	0.65	-18.8968	18.4621	0.90743	0.0:1.0:0.0:0.0	.	198	Q9BQI5	SGIP1_HUMAN	D	202;166;190;155;201;201;165;198	ENSP00000237247:A202D;ENSP00000360078:A166D;ENSP00000410439:A190D;ENSP00000360074:A155D;ENSP00000360075:A165D;ENSP00000360076:A198D	ENSP00000237247:A202D	A	+	2	0	SGIP1	66911584	0.996000	0.38824	1.000000	0.80357	0.595000	0.36748	4.773000	0.62331	2.718000	0.92993	0.650000	0.86243	GCT	C|1.000;G|0.000		0.363	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		A	67138996	C	A	67138996	3	1	48	1	0	0	0	0	1	0	0	0	14238	797	28	4	639	4	SGIP1	1	67138996	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	13902061	67138996	182111625	3	4333											
CDC7	8317	hgsc.bcm.edu	37	chr1	91973853	91973853	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtttatttggccacagcacaGttacaagtaggacctgaaga	13	10	10	8	0	0	2	0	1	0	1	0	3	0	3	2	2	2	4	2	2	5	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:91973853G>C	ENST00000428239.1	+	4	493	c.234G>C	c.(232-234)caG>caC	p.Q78H	CDC7_ENST00000234626.6_Missense_Mutation_p.Q78H|CDC7_ENST00000497611.1_3'UTR|CDC7_ENST00000430031.2_Missense_Mutation_p.Q50H	NM_001134420.1	NP_001127892.1	O00311	CDC7_HUMAN	cell division cycle 7	78	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2)	23		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		CCACAGCACAGTTACAAGTAG	0.343																																					p.Q78H		.											.	CDC7-1125	0			c.G234C						.						58	56	57					1																	91973853		2203	4300	6503	SO:0001583	missense	8317	exon4			AGCACAGTTACAA	AF015592	CCDS734.1	1p22	2013-01-17	2013-01-17	2003-07-23	ENSG00000097046	ENSG00000097046			1745	protein-coding gene	gene with protein product		603311	"CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)"	CDC7L1		9405610, 9250678	Standard	NM_003503		Approved	Hsk1, huCdc7, HsCdc7	uc001dof.3	O00311	OTTHUMG00000047810	ENST00000428239.1:c.234G>C	1.37:g.91973853G>C	ENSP00000393139:p.Gln78His	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_003503	0	0	0	0	0	D3DT31|O00558|Q5T5U5	Missense_Mutation	SNP	ENST00000428239.1	37	CCDS734.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.055516	0.36277	.	.	ENSG00000097046	ENST00000430031;ENST00000234626;ENST00000428239;ENST00000426137	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	6.07	1.06	0.20224	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.160176	0.56097	N	0.000021	T	0.27967	0.0689	N	0.21142	0.635	0.46131	D	0.998887	B;B	0.20459	0.045;0.012	B;B	0.27887	0.084;0.034	T	0.13176	-1.0519	10	0.66056	D	0.02	-3.4716	7.4595	0.27287	0.3535:0.1046:0.5418:0.0	.	50;78	B7Z5H7;O00311	.;CDC7_HUMAN	H	50;78;78;78	ENSP00000407477:Q50H;ENSP00000234626:Q78H;ENSP00000393139:Q78H;ENSP00000398077:Q78H	ENSP00000234626:Q78H	Q	+	3	2	CDC7	91746441	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	2.019000	0.41001	-0.040000	0.13580	0.655000	0.94253	CAG	.		0.343	CDC7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027928.1	NM_003503		C	91973853	G	C	91973853	3	2	48	1	0	0	0	0	1	0	0	0	3090	1020	36	4	244	4	CDC7	1	91973853	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	24834857	91973853	157276768	4	4334											
BCAR3	8412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94054731	94054731	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaagatgatggcgccactCtgctgggagatgggccggcg	7	7	18	9	3	1	3	0	1	1	2	1	5	1	4	2	5	1	1	2	5	1	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:94054731C>T	ENST00000370244.1	-	7	1020	c.732G>A	c.(730-732)caG>caA	p.Q244Q	BCAR3_ENST00000370243.1_Silent_p.Q244Q|BCAR3_ENST00000260502.6_Silent_p.Q244Q|BCAR3_ENST00000370247.3_Silent_p.Q153Q	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	244	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		TGGCGCCACTCTGCTGGGAGA	0.667																																					p.Q244Q		.											.	BCAR3-228	0			c.G732A						.						30	30	30					1																	94054731		2203	4300	6503	SO:0001819	synonymous_variant	8412	exon5			GCCACTCTGCTGG	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"SH2 domain containing"	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.732G>A	1.37:g.94054731C>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	94	35	NM_001261409	0	0	0	1	1	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	ENST00000370244.1	37	CCDS745.1																																																																																			.		0.667	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			T	94054731	C	T	94054731	2	4	48	1	0	0	0	0	0	0	0	1	1350	912	32	2		2	BCAR3	1	94054731	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	2080878	94054731	155195890	5	4335											
ATP1A1	476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	116931576	116931576	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accccagactaggtctccagAtttcacaaatgaaaaccccc	14	7	5	15	0	2	3	1	1	1	2	3	3	2	3	5	1	1	0	5	1	4	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:116931576A>C	ENST00000295598.5	+	7	941	c.689A>C	c.(688-690)gAt>gCt	p.D230A	ATP1A1_ENST00000369496.4_Missense_Mutation_p.D199A|ATP1A1_ENST00000537345.1_Missense_Mutation_p.D230A|ATP1A1_ENST00000491156.1_3'UTR	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	230					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	AGGTCTCCAGATTTCACAAAT	0.453																																					p.D230A		.											.	ATP1A1-91	0			c.A689C						.						86	90	89					1																	116931576		2203	4300	6503	SO:0001583	missense	476	exon7			CTCCAGATTTCAC	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.689A>C	1.37:g.116931576A>C	ENSP00000295598:p.Asp230Ala	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	89	38	NM_000701	0	0	17	45	28	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.674536	0.67928	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	D;D;D	0.90197	-2.63;-2.63;-2.63	5.14	5.14	0.70334	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	T	0.82098	0.4963	L	0.41027	1.25	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.81493	-0.0908	10	0.87932	D	0	.	15.1179	0.72419	1.0:0.0:0.0:0.0	.	230;230	F5H3A1;P05023	.;AT1A1_HUMAN	A	230;230;229;199	ENSP00000295598:D230A;ENSP00000445306:D230A;ENSP00000358508:D199A	ENSP00000295598:D230A	D	+	2	0	ATP1A1	116733099	1.000000	0.71417	0.971000	0.41717	0.988000	0.76386	9.139000	0.94554	2.165000	0.68154	0.533000	0.62120	GAT	.		0.453	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116931576	A	C	116931576	3	2	48	1	0	0	0	0	1	0	0	0	1129	333	12	5	731	5	ATP1A1	1	116931576	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	22876845	116931576	132319045	6	4336											
FAM72B	653820	hgsc.bcm.edu	37	chr1	120839913	120839913	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtaaacaagtgctcagctCtaggggaatgaaggctgttt	11	11	12	7	0	2	1	1	1	1	0	2	2	2	2	0	3	3	5	0	3	6	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:120839913C>A	ENST00000369390.3	+	1	909	c.80C>A	c.(79-81)tCt>tAt	p.S27Y	FAM72B_ENST00000471903.2_Intron|RP11-439A17.7_ENST00000412759.1_RNA|FAM72B_ENST00000355228.4_Intron	NM_001100910.1	NP_001094380.1	Q86X60	FA72B_HUMAN	family with sequence similarity 72, member B	27										large_intestine(1)|lung(2)	3	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)		GTGCTCAGCTCTAGGGGAATG	0.483																																					p.S27Y		.											.	FAM72B-68	0			c.C80A						.						4	4	4					1																	120839913		1473	3170	4643	SO:0001583	missense	653820	exon1			TCAGCTCTAGGGG	AL357493	CCDS72848.1	1p12	2014-05-06			ENSG00000188610	ENSG00000188610			24805	protein-coding gene	gene with protein product		614711					Standard	NM_001100910		Approved	RP11-439A17.6	uc009whp.3	Q86X60	OTTHUMG00000185025	ENST00000369390.3:c.80C>A	1.37:g.120839913C>A	ENSP00000358397:p.Ser27Tyr	Somatic	758	0		WXS	Illumina HiSeq	Phase_I	657	89	NM_001100910	0	0	0	0	0	B2RPQ5|Q5QP15	Missense_Mutation	SNP	ENST00000369390.3	37	CCDS41374.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.605499	0.28623	.	.	ENSG00000188610	ENST00000369390	T	0.32272	1.46	2.52	2.52	0.30459	.	0.148029	0.43416	U	0.000568	T	0.07728	0.0194	L	0.51422	1.61	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22977	-1.0201	10	0.05525	T	0.97	.	5.3489	0.16024	0.0:0.8329:0.0:0.1671	.	27	Q86X60	FA72B_HUMAN	Y	27	ENSP00000358397:S27Y	ENSP00000358397:S27Y	S	+	2	0	FAM72B	120641436	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.637000	0.46553	1.426000	0.47256	0.398000	0.26397	TCT	.		0.483	FAM72B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098437.1			A	120839913	C	A	120839913	3	1	48	1	0	0	0	0	1	0	0	0	5634	913	32	4	82	4	FAM72B	1	120839913	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	3908337	120839913	128410708	7	4337											
CELF3	11189	hgsc.bcm.edu	37	chr1	151678722	151678722	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctttgctgctgctgctgTtgctgctgctgctgctgctg	0	17	12	12	0	1	0	0	0	1	0	2	0	1	0	0	0	10	11	0	0	0	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:151678722T>C	ENST00000290583.4	-	10	1897	c.1104A>G	c.(1102-1104)caA>caG	p.Q368Q	CELF3_ENST00000470688.1_5'UTR|CELF3_ENST00000290585.4_Silent_p.Q318Q|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000392706.3_Silent_p.Q163Q	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	368	Gln-rich.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						gctgctgctgttgctgctgct	0.657																																					p.Q368Q		.											.	CELF3-91	0			c.A1104G						.						19	20	20					1																	151678722		2200	4297	6497	SO:0001819	synonymous_variant	11189	exon10			CTGCTGTTGCTGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1104A>G	1.37:g.151678722T>C		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	35	3	NM_007185	0	0	0	62	62	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Silent	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	4.938	0.174339	0.09391	.	.	ENSG00000159409	ENST00000420342	.	.	.	3.25	1.39	0.22231	.	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19943	-1.0290	4	.	.	.	-0.0118	5.4728	0.16680	0.0:0.7409:0.0:0.2591	.	.	.	.	S	369	.	.	N	-	2	0	CELF3	149945346	0.076000	0.21285	1.000000	0.80357	0.644000	0.38419	-0.812000	0.04496	0.416000	0.25844	-0.389000	0.06534	AAC	.		0.657	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		C	151678722	T	C	151678722	2	2	48	1	0	0	0	0	0	0	0	1	3223	1722	60	3		3	CELF3	1	151678722	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	30838809	151678722	97571899	8	4338											
PGLYRP3	114771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153279661	153279661	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggagctggtctgtgatgatGtaggccacaggcagggtcag	8	8	18	7	0	2	2	1	2	1	0	2	3	2	3	1	5	1	3	1	5	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:153279661G>C	ENST00000290722.1	-	2	190	c.138C>G	c.(136-138)taC>taG	p.Y46*		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	46					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGTGATGATGTAGGCCACAG	0.622																																					p.Y46X		.											.	PGLYRP3-94	0			c.C138G						.						53	47	49					1																	153279661		2203	4300	6503	SO:0001587	stop_gained	114771	exon2			GATGATGTAGGCC	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I alpha precursor"	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.138C>G	1.37:g.153279661G>C	ENSP00000290722:p.Tyr46*	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	74	23	NM_052891	0	0	0	0	0	A1A4U8|Q5SY65	Nonsense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582950	0.46006	.	.	ENSG00000159527	ENST00000290722	.	.	.	4.06	-2.35	0.06684	.	0.381500	0.19389	N	0.115444	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6165	8.7113	0.34385	0.4751:0.0:0.5249:0.0	.	.	.	.	X	46	.	ENSP00000290722:Y46X	Y	-	3	2	PGLYRP3	151546285	0.000000	0.05858	0.045000	0.18777	0.020000	0.10135	-0.301000	0.08232	-0.603000	0.05767	-0.137000	0.14449	TAC	.		0.622	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891		C	153279661	G	C	153279661	4	2	48	1	0	0	0	0	0	1	0	0	11821	1372	48	4	911	4	PGLYRP3	1	153279661	Nonsense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	1600939	153279661	95970960	9	4339											
IRF2BP2	359948	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	234743056	234743058	+	In_Frame_Del	DEL	AGC	AGC	-																															gctttgtctggagcaagggaAgcagaacttgtgcgaaggga																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:234743056_234743058delAGC	ENST00000366609.3	-	2	1619_1621	c.1589_1591delGCT	c.(1588-1593)tgcttc>ttc	p.C530del	IRF2BP2_ENST00000366610.3_In_Frame_Del_p.C514del|IRF2BP2_ENST00000491430.1_5'UTR|RP4-781K5.2_ENST00000436039.1_RNA	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	530	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			GAGCAAGGGAAGCAGAACTTGTG	0.586																																					p.530_531del		.											.	IRF2BP2-90	0			c.1589_1591del						.																																			SO:0001651	inframe_deletion	359948	exon2			.	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1589_1591delGCT	1.37:g.234743056_234743058delAGC	ENSP00000355568:p.Cys530del	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	313	74	NM_182972	0	0	0	0	0	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	In_Frame_Del	DEL	ENST00000366609.3	37	CCDS1602.1																																																																																			.		0.586	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		-	234743058	AGC	-	234743056	7	5	48	1	0	1	0	1	0	0	0	0	7851	72	3	0	176	0	IRF2BP2	1	234743056	In_Frame_Del	DEL	AGC	TCGA-B9-4114-01A-01D-1252-08	81463395	234743056	14507565	10	4340											
LCLAT1	253558	bcgsc.ca	37	chr2	30756180	30756181	+	Splice_Site	INS	-	-	GTAGGTTATTCACACATT																															caaaggtgttcctggatttgINSgtaggttattcacacattat																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:30756180_30756181insGTAGGTTATTCACACATT	ENST00000309052.4	+	4	687	c.478_478insGTAGGTTATTCACACATT	c.(478-480)ggt>GTAGGTTATTCACACATTggt	p.159_160insVGYSHI	LCLAT1_ENST00000379509.3_Splice_Site_p.121_122insVGYSHI|LCLAT1_ENST00000359433.1_Splice_Site_p.159_160insVGYSHI|LCLAT1_ENST00000319406.4_Splice_Site_p.159_160insVGYSHI|LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000540623.1_Splice_Site_p.121_122insVGYSHI	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	159					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						TCCTGGATTTGGTAGGTTATTC	0.381																																					p.G160delinsGRLFTHC													.	LCLAT1-92	0			c.478_479insGTAGGTTATTCACACATT						.																																			SO:0001630	splice_region_variant	253558	exon4			GGATTTGGTAGGT	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.478+1->GTAGGTTATTCACACATT	2.37:g.30756180_30756181insGTAGGTTATTCACACATT		Somatic	434	0		WXS	Illumina HiSeq	Phase_1	223	10	NM_182551	0	0	0	0	0	A6H8Z7|Q8N1Q7	In_Frame_Ins	INS	ENST00000309052.4	37	CCDS1772.1																																																																																			.		0.381	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551	In_Frame_Ins	GTAGGTTATTCACACATT	30756181	-	GTAGGTTATTCACACATT	30756180	8	5	48	1	0	1	1	0	0	0	1	0	8698	1362	47	0	488	0	LCLAT1	2	30756180	Splice_Site	INS	-	TCGA-B9-4114-01A-01D-1252-08		30756180	212443193	11	4341											
CAPN13	92291	hgsc.bcm.edu	37	chr2	30955349	30955349	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagcagaccaggctggggaAgctgaccctgccgacgctgt	9	5	15	12	2	0	2	0	1	0	1	0	5	0	3	3	3	3	4	3	3	2	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:30955349A>T	ENST00000295055.8	-	20	2058	c.1882T>A	c.(1882-1884)Ttc>Atc	p.F628I	CAPN13_ENST00000534090.2_Missense_Mutation_p.F628I	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	628					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AGGCTGGGGAAGCTGACCCTG	0.597																																					p.F628I		.											.	CAPN13-136	0			c.T1882A						.						27	31	30					2																	30955349		2106	4221	6327	SO:0001583	missense	92291	exon20			TGGGGAAGCTGAC		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1882T>A	2.37:g.30955349A>T	ENSP00000295055:p.Phe628Ile	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	52	13	NM_144575	0	0	0	0	0	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	37	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	a	26.8	4.772877	0.90108	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	T;T	0.35789	1.29;1.29	5.5	5.5	0.81552	EF-hand-like domain (1);	0.051382	0.85682	D	0.000000	T	0.63414	0.2509	M	0.87038	2.855	0.43787	D	0.996328	D	0.89917	1.0	D	0.68621	0.959	T	0.70539	-0.4844	10	0.87932	D	0	.	13.1283	0.59368	1.0:0.0:0.0:0.0	.	628	Q6MZZ7	CAN13_HUMAN	I	628	ENSP00000295055:F628I;ENSP00000431298:F628I	ENSP00000295055:F628I	F	-	1	0	CAPN13	30808853	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.047000	0.64232	2.094000	0.63399	0.529000	0.55759	TTC	.		0.597	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		T	30955349	A	T	30955349	3	4	48	1	0	0	0	0	1	0	0	0	2632	72	3	5	139	5	CAPN13	2	30955349	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	199169	30955349	212244024	12	4342											
EIF5B	9669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	99995867	99995867	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcctcttgaagctattaaTgaacagactaagatgattaa	15	13	7	6	0	1	5	0	3	1	2	2	5	2	5	1	0	2	2	1	0	6	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:99995867T>G	ENST00000289371.6	+	12	2239	c.2037T>G	c.(2035-2037)aaT>aaG	p.N679K		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	679	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAGCTATTAATGAACAGACTA	0.343																																					p.N679K	Colon(162;2388 2567 2705 3444)	.											.	EIF5B-93	0			c.T2037G						.						98	87	91					2																	99995867		1852	4096	5948	SO:0001583	missense	9669	exon12			TATTAATGAACAG	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.2037T>G	2.37:g.99995867T>G	ENSP00000289371:p.Asn679Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	10	4	NM_015904	0	0	23	39	16	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Missense_Mutation	SNP	ENST00000289371.6	37	CCDS42721.1	.	.	.	.	.	.	.	.	.	.	T	4.740	0.137561	0.09032	.	.	ENSG00000158417	ENST00000289371	T	0.69806	-0.43	5.63	4.49	0.54785	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	.	.	.	.	T	0.23766	0.0575	N	0.00182	-1.905	0.41010	D	0.984993	B	0.15473	0.013	B	0.17098	0.017	T	0.32161	-0.9917	8	.	.	.	-40.5882	5.3022	0.15783	0.1361:0.1354:0.0:0.7285	.	679	O60841	IF2P_HUMAN	K	679	ENSP00000289371:N679K	.	N	+	3	2	EIF5B	99362299	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.657000	0.24963	2.149000	0.67028	0.260000	0.18958	AAT	.		0.343	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		G	99995867	T	G	99995867	3	3	48	1	0	0	0	0	1	0	0	0	5057	1461	51	5	2083	5	EIF5B	2	99995867	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	69040518	99995867	143203506	13	4343											
COL5A2	1290	hgsc.bcm.edu	37	chr2	189912941	189912941	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatggctcttacacgttcTccaacagcaccatcccgtcc	10	9	6	16	2	2	0	0	0	2	0	5	1	4	0	4	1	3	3	4	1	3	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:189912941T>C	ENST00000374866.3	-	45	3469	c.3195A>G	c.(3193-3195)ggA>ggG	p.G1065G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1065					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TTACACGTTCTCCAACAGCAC	0.348																																					p.G1065G		.											.	COL5A2-92	0			c.A3195G						.						66	69	68					2																	189912941		2203	4300	6503	SO:0001819	synonymous_variant	1290	exon45			ACGTTCTCCAACA	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"Collagens"	2210	protein-coding gene	gene with protein product	"AB collagen"	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3195A>G	2.37:g.189912941T>C		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_000393	0	0	0	0	0	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	37	CCDS33350.1																																																																																			.		0.348	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		C	189912941	T	C	189912941	2	2	48	1	0	0	0	0	0	0	0	1	3703	1538	54	3		3	COL5A2	2	189912941	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	89917074	189912941	53286432	14	4344											
TRAK2	66008	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	202262967	202262967	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gataagctaaaggactcattGaaccgaagaggtgtagaaca	17	7	11	6	1	1	3	1	1	0	2	1	6	1	4	1	2	3	2	1	2	7	4	rs201579398		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:202262967G>A	ENST00000332624.3	-	6	1019	c.591C>T	c.(589-591)ttC>ttT	p.F197F	TRAK2_ENST00000430254.1_Silent_p.F197F	NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	197	HAP1 N-terminal.				protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						AGGACTCATTGAACCGAAGAG	0.438																																					p.F197F		.											.	TRAK2-90	0			c.C591T						.	G		0,4406		0,0,2203	128	123	125		591	4.9	1	2		125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRAK2	NM_015049.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		197/915	202262967	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	66008	exon6			CTCATTGAACCGA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.591C>T	2.37:g.202262967G>A		Somatic	230	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_015049	0	0	0	0	0	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Silent	SNP	ENST00000332624.3	37	CCDS2347.1																																																																																			G|0.999;A|0.001		0.438	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		A	202262967	G	A	202262967	2	1	48	1	0	0	0	0	0	0	0	1	16483	1281	45	2		2	TRAK2	2	202262967	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	12350026	202262967	40936406	15	4345											
FN1	2335	hgsc.bcm.edu	37	chr2	216232668	216232668	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgattcagacattcgttcCcactcatctccaacggcata	10	11	5	15	2	3	2	2	1	1	1	6	2	4	2	3	1	1	2	3	1	2	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:216232668C>G	ENST00000359671.1	-	41	6928	c.6663G>C	c.(6661-6663)tgG>tgC	p.W2221C	FN1_ENST00000421182.1_Missense_Mutation_p.W2075C|FN1_ENST00000345488.5_Missense_Mutation_p.W2019C|FN1_ENST00000357867.4_Missense_Mutation_p.W2011C|FN1_ENST00000443816.1_Missense_Mutation_p.W2100C|FN1_ENST00000323926.6_Missense_Mutation_p.W2281C|FN1_ENST00000336916.4_Missense_Mutation_p.W2190C|FN1_ENST00000432072.2_Missense_Mutation_p.W2102C|FN1_ENST00000346544.3_Intron|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000446046.1_Missense_Mutation_p.W2165C|FN1_ENST00000356005.4_Missense_Mutation_p.W2131C|FN1_ENST00000354785.4_Missense_Mutation_p.W2312C			P02751	FINC_HUMAN	fibronectin 1	2221	Fibrin-binding 2.|Fibronectin type-I 10. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	ACATTCGTTCCCACTCATCTC	0.448																																					p.W2312C		.											.	FN1-584	0			c.G6936C						.						149	125	133					2																	216232668		2203	4300	6503	SO:0001583	missense	2335	exon42			TCGTTCCCACTCA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6663G>C	2.37:g.216232668C>G	ENSP00000352696:p.Trp2221Cys	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_212482	0	0	122	122	0	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	C	17.67	3.445932	0.63178	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000345488;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76	5.67	5.67	0.87782	Fibronectin, type I (4);Complement control module (1);	0.000000	0.64402	D	0.000010	D	0.85600	0.5734	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;0.999;0.998;0.999;1.0;0.999;0.998;0.998;0.999;1.0	D	0.86200	0.1618	10	0.87932	D	0	.	19.7563	0.96294	0.0:1.0:0.0:0.0	.	2102;2281;2011;2131;2165;2190;2222;2075;2100;2312;2221	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15;P02751	.;.;.;.;.;.;.;.;.;.;FINC_HUMAN	C	2075;2281;2190;2011;2312;2222;2221;2019;2165;2100;2102;2131;938	ENSP00000394423:W2075C;ENSP00000323534:W2281C;ENSP00000338200:W2190C;ENSP00000350534:W2011C;ENSP00000346839:W2312C;ENSP00000352696:W2221C;ENSP00000273049:W2019C;ENSP00000410422:W2165C;ENSP00000415018:W2100C;ENSP00000399538:W2102C;ENSP00000348285:W2131C;ENSP00000416139:W938C	ENSP00000265313:W2222C	W	-	3	0	FN1	215940913	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	7.818000	0.86416	2.670000	0.90874	0.585000	0.79938	TGG	.		0.448	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		G	216232668	C	G	216232668	3	3	48	1	0	0	0	0	1	0	0	0	5981	624	22	4	517	4	FN1	2	216232668	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	13969701	216232668	26966705	16	4346											
RUFY4	285180	hgsc.bcm.edu;broad.mit.edu	37	chr2	218954705	218954705	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcctgctctgccatgcttgCtccatggattacaagaagag	9	10	11	11	0	1	2	0	0	1	2	2	3	2	3	3	2	5	3	3	2	3	2	rs368084035	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:218954705C>T	ENST00000344321.7	+	13	2162	c.1644C>T	c.(1642-1644)tgC>tgT	p.C548C	RUFY4_ENST00000374155.3_3'UTR|RUFY4_ENST00000441828.2_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	548							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GCCATGCTTGCTCCATGGATT	0.632													C|||	4	0.000798722	0.003	0	5008	,	,		17867	0		0	False		,,,				2504	0				p.C548C		.											.	RUFY4-46	0			c.C1644T						.	C		20,3988		0,20,1984	36	44	41		1644	3.6	1	2		41	0,8322		0,0,4161	no	coding-synonymous	RUFY4	NM_198483.3		0,20,6145	TT,TC,CC		0.0,0.499,0.1622		548/572	218954705	20,12310	2004	4161	6165	SO:0001819	synonymous_variant	285180	exon13			TGCTTGCTCCATG	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1644C>T	2.37:g.218954705C>T		Somatic	10	1		WXS	Illumina HiSeq	Phase_I	11	6	NM_198483	0	0	0	0	0	Q6ZR96	Silent	SNP	ENST00000344321.7	37																																																																																				.		0.632	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		T	218954705	C	T	218954705	2	4	48	1	0	0	0	0	0	0	0	1	13773	805	28	2		2	RUFY4	2	218954705	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	2722037	218954705	24244668	17	4347											
SP140	11262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	231177371	231177371	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatttcaaggaagtgtttgCtattcaggaaacaaatggga	15	11	11	4	0	2	0	2	0	0	0	2	4	2	3	0	3	2	2	0	3	6	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:231177371C>T	ENST00000392045.3	+	27	2690	c.2576C>T	c.(2575-2577)gCt>gTt	p.A859V	SP140_ENST00000420434.3_Missense_Mutation_p.A832V|SP140_ENST00000417495.3_Missense_Mutation_p.A745V|SP140_ENST00000486687.2_Intron|SP140_ENST00000343805.6_Missense_Mutation_p.A799V|SP140_ENST00000350136.5_Missense_Mutation_p.A728V	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	859					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GAAGTGTTTGCTATTCAGGAA	0.393																																					p.A859V		.											.	SP140-90	0			c.C2576T						.						157	145	149					2																	231177371		1872	4114	5986	SO:0001583	missense	11262	exon27			TGTTTGCTATTCA	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.2576C>T	2.37:g.231177371C>T	ENSP00000375899:p.Ala859Val	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	152	46	NM_007237	0	0	18	18	0	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321189	0.60634	.	.	ENSG00000079263	ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	3.48	2.5	0.30297	Bromodomain (3);	.	.	.	.	T	0.57562	0.2062	M	0.68952	2.095	0.23645	N	0.997215	D;P;D;D	0.64830	0.993;0.956;0.992;0.994	D;B;P;P	0.72625	0.978;0.39;0.708;0.663	T	0.38499	-0.9658	9	0.87932	D	0	-5.2094	7.4406	0.27181	0.2583:0.7417:0.0:0.0	.	832;745;799;859	E7EUR5;E7ESH9;E9PFJ6;Q13342	.;.;.;LY10_HUMAN	V	728;859;745;799;832	ENSP00000345846:A728V;ENSP00000375899:A859V;ENSP00000342096:A799V;ENSP00000398210:A832V	ENSP00000342096:A799V	A	+	2	0	SP140	230885615	0.425000	0.25498	0.936000	0.37596	0.918000	0.54935	0.202000	0.17295	1.966000	0.57179	0.462000	0.41574	GCT	.		0.393	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231177371	C	T	231177371	3	4	48	1	0	0	0	0	1	0	0	0	14994	797	28	2	2799	2	SP140	2	231177371	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	12222666	231177371	12022002	18	4348											
C3orf35	339883	broad.mit.edu	37	chr3	37458846	37458846	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaagaggttattgtgcgcccGaacttttcacacaagaattg	13	11	9	8	2	1	2	1	0	0	2	1	3	1	2	1	1	2	1	1	1	5	5	rs193097162	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:37458846G>A	ENST00000328376.5	+	5	1068	c.89G>A	c.(88-90)cGa>cAa	p.R30Q	C3orf35_ENST00000481400.1_Intron|C3orf35_ENST00000425564.2_Missense_Mutation_p.R30Q|C3orf35_ENST00000425932.1_Missense_Mutation_p.R30Q|C3orf35_ENST00000452017.2_Missense_Mutation_p.R30Q|C3orf35_ENST00000426078.1_Missense_Mutation_p.R30Q	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	30						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						TTGTGCGCCCGAACTTTTCAC	0.433													G|||	4	0.000798722	0.0015	0	5008	,	,		18668	0.001		0	False		,,,				2504	0.001				p.R30Q													.	C3orf35-112	0			c.G89A						.	G	GLN/ARG,GLN/ARG	1,3671		0,1,1835	111	105	107		89,89	-6.6	0	3		107	3,8163		0,3,4080	yes	missense,missense	C3orf35	NM_178339.2,NM_178342.2	43,43	0,4,5915	AA,AG,GG		0.0367,0.0272,0.0338	probably-damaging,probably-damaging	30/171,30/120	37458846	4,11834	1836	4083	5919	SO:0001583	missense	339883	exon5			GCGCCCGAACTTT	AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"AP20 region protein", "APRG1 tumor suppressor candidate"	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.89G>A	3.37:g.37458846G>A	ENSP00000331625:p.Arg30Gln	Somatic	258	0		WXS	Illumina HiSeq	Phase_I	128	4	NM_178342	0	0	1	1	0	B7ZMA0|Q8IVJ5|Q8IVJ9	Missense_Mutation	SNP	ENST00000328376.5	37	CCDS43065.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.692	0.691247	0.15039	2.72E-4	3.67E-4	ENSG00000198590	ENST00000425932;ENST00000328376;ENST00000452017;ENST00000426078;ENST00000425564	T	0.55413	0.52	4.24	-6.63	0.01807	.	.	.	.	.	T	0.26629	0.0651	N	0.08118	0	0.09310	N	1	B;B	0.19706	0.038;0.017	B;B	0.10450	0.005;0.003	T	0.28650	-1.0037	9	0.87932	D	0	.	7.6808	0.28513	0.4534:0.3754:0.1712:0.0	.	30;30	Q8IVJ8-3;Q8IVJ8	.;APRG1_HUMAN	Q	30	ENSP00000331625:R30Q	ENSP00000331625:R30Q	R	+	2	0	C3orf35	37433850	0.011000	0.17503	0.000000	0.03702	0.100000	0.18952	-0.493000	0.06459	-1.614000	0.01575	-0.251000	0.11542	CGA	G|0.999;A|0.001		0.433	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338		A	37458846	G	A	37458846	3	1	48	1	0	0	0	0	1	0	0	0	2231	1058	37	1	91	1	C3orf35	3	37458846	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		37458846	160563584	19	4349											
CCRL2	9034	broad.mit.edu	37	chr3	46449903	46449903	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctcattggactgtacttCgtgggcctgtacagtgagac	8	13	11	9	1	1	1	1	1	1	1	3	3	1	2	1	2	2	2	1	2	2	5	rs371988169		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:46449903C>A	ENST00000399036.3	+	2	685	c.333C>A	c.(331-333)ttC>ttA	p.F111L	CCRL2_ENST00000400880.3_Missense_Mutation_p.F111L|CCRL2_ENST00000400882.2_Missense_Mutation_p.F111L|RP11-24F11.2_ENST00000451485.1_RNA|CCRL2_ENST00000357392.4_Missense_Mutation_p.F123L	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	111					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CCR chemokine receptor binding (GO:0048020)|chemokine receptor activity (GO:0004950)|chemokine receptor binding (GO:0042379)			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		GACTGTACTTCGTGGGCCTGT	0.468																																					p.F123L													.	CCRL2-569	0			c.C369A						.						97	94	95					3																	46449903		1997	4147	6144	SO:0001583	missense	9034	exon2			GTACTTCGTGGGC	AF014958	CCDS43079.1, CCDS46814.1	3p21	2013-07-18	2013-07-18	2013-07-18	ENSG00000121797	ENSG00000121797		"GPCR / Class A : Chemokine receptors : Atypical"	1612	protein-coding gene	gene with protein product	"atypical chemokine receptor 5"	608379				9473515	Standard	NM_001130910		Approved	HCR, CRAM-B, CKRX, CRAM-A, ACKR5	uc003cpp.4	O00421	OTTHUMG00000156318	ENST00000399036.3:c.333C>A	3.37:g.46449903C>A	ENSP00000381994:p.Phe111Leu	Somatic	240	0		WXS	Illumina HiSeq	Phase_I	204	4	NM_001130910	0	0	1	1	0	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Missense_Mutation	SNP	ENST00000399036.3	37	CCDS43079.1	.	.	.	.	.	.	.	.	.	.	C	5.055	0.195853	0.09599	.	.	ENSG00000121797	ENST00000399036;ENST00000357392;ENST00000400880;ENST00000433848;ENST00000400882	T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;-0.49	5.25	-0.613	0.11594	GPCR, rhodopsin-like superfamily (1);	0.631791	0.14943	N	0.289392	T	0.43897	0.1268	N	0.25094	0.71	0.09310	N	1	P;B	0.35821	0.523;0.324	B;B	0.26416	0.041;0.069	T	0.23726	-1.0180	10	0.27082	T	0.32	.	3.7134	0.08428	0.1117:0.4943:0.1005:0.2936	.	123;111	O00421-2;O00421	.;CCRL2_HUMAN	L	111;123;111;111;111	ENSP00000381994:F111L;ENSP00000349967:F123L;ENSP00000383677:F111L;ENSP00000414957:F111L;ENSP00000383678:F111L	ENSP00000349967:F123L	F	+	3	2	CCRL2	46424907	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.241000	0.02911	-0.257000	0.09459	-1.579000	0.00862	TTC	.		0.468	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2			A	46449903	C	A	46449903	3	1	48	1	0	0	0	0	1	0	0	0	2956	883	31	4	375	4	CCRL2	3	46449903	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	8991057	46449903	151572527	20	4350											
OR5H15	403274	hgsc.bcm.edu	37	chr3	97887854	97887854	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagatacaatttttttccaTtgcaattggcgtaaccacag	13	13	6	9	1	0	1	0	0	0	1	1	1	1	1	2	1	3	2	2	1	5	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:97887854T>C	ENST00000356526.2	+	1	311	c.311T>C	c.(310-312)aTt>aCt	p.I104T		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						TTTTTTTCCATTGCAATTGGC	0.388																																					p.I104T		.											.	OR5H15-92	0			c.T311C						.						155	147	150					3																	97887854		2203	4298	6501	SO:0001583	missense	403274	exon1			TTTCCATTGCAAT		CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"GPCR / Class A : Olfactory receptors"	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.311T>C	3.37:g.97887854T>C	ENSP00000373195:p.Ile104Thr	Somatic	406	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_001005515	0	0	0	0	0		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	0.529	-0.858769	0.02610	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.01323	5.01	2.48	2.48	0.30137	GPCR, rhodopsin-like superfamily (1);	0.592858	0.15215	N	0.274263	T	0.01061	0.0035	N	0.16166	0.38	0.09310	N	1	B	0.19583	0.037	B	0.20955	0.032	T	0.47484	-0.9114	10	0.87932	D	0	.	4.8406	0.13489	0.275:0.0:0.0:0.725	.	104	A6NDH6	O5H15_HUMAN	T	104	ENSP00000373195:I104T	ENSP00000373195:I104T	I	+	2	0	OR5H15	99370544	0.012000	0.17670	0.007000	0.13788	0.004000	0.04260	1.381000	0.34362	1.138000	0.42230	0.155000	0.16302	ATT	.		0.388	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1			C	97887854	T	C	97887854	3	2	48	1	0	0	0	0	1	0	0	0	11187	1493	52	3	313	3	OR5H15	3	97887854	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	51437951	97887854	100134576	21	4351											
IFT57	55081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	107937434	107937434	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcttcagcgaagcaatcaaGaacatagcatacatgttctc	14	11	6	10	1	4	1	2	0	2	1	5	2	4	1	0	0	5	3	0	0	6	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:107937434G>C	ENST00000264538.3	-	3	689	c.442C>G	c.(442-444)Ctt>Gtt	p.L148V		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	148					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			AAGCAATCAAGAACATAGCAT	0.343																																					p.L148V		.											.	IFT57-227	0			c.C442G						.						73	74	73					3																	107937434		2203	4299	6502	SO:0001583	missense	55081	exon3			AATCAAGAACATA	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.442C>G	3.37:g.107937434G>C	ENSP00000264538:p.Leu148Val	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	47	7	NM_018010	0	0	27	52	25	Q96DA9	Missense_Mutation	SNP	ENST00000264538.3	37	CCDS2951.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034317	0.75617	.	.	ENSG00000114446	ENST00000264538	.	.	.	5.99	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.84584	0.5504	M	0.90977	3.165	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.87397	0.2367	9	0.51188	T	0.08	.	15.0869	0.72162	0.0674:0.0:0.9326:0.0	.	148	Q9NWB7	IFT57_HUMAN	V	148	.	ENSP00000264538:L148V	L	-	1	0	IFT57	109420124	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.875000	0.69660	1.540000	0.49301	0.655000	0.94253	CTT	.		0.343	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		C	107937434	G	C	107937434	3	2	48	1	0	0	0	0	1	0	0	0	7583	942	33	4	883	4	IFT57	3	107937434	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	10049580	107937434	90084996	22	4352											
PVRL3	25945	hgsc.bcm.edu	37	chr3	110852638	110852638	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccacgatcattgctagtgTagtgggtggggctctcttca	6	13	13	9	1	3	0	2	0	1	0	4	1	3	0	1	3	2	3	1	3	2	4	rs537220727		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:110852638T>G	ENST00000485303.1	+	6	1501	c.1226T>G	c.(1225-1227)gTa>gGa	p.V409G	PVRL3_ENST00000319792.3_3'UTR|PVRL3_ENST00000493615.1_Intron	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	409					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						ATTGCTAGTGTAGTGGGTGGG	0.438																																					p.V409G		.											.	PVRL3-92	0			c.T1226G						.						174	171	172					3																	110852638		2203	4300	6503	SO:0001583	missense	25945	exon6			CTAGTGTAGTGGG	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.1226T>G	3.37:g.110852638T>G	ENSP00000418070:p.Val409Gly	Somatic	354	1		WXS	Illumina HiSeq	Phase_I	38	3	NM_015480	0	0	10	10	0	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Missense_Mutation	SNP	ENST00000485303.1	37	CCDS2957.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.287793	0.23478	.	.	ENSG00000177707	ENST00000485303	T	0.19532	2.14	5.76	4.63	0.57726	Cytochrome c1, transmembrane anchor, C-terminal (1);	0.108700	0.64402	D	0.000009	T	0.15522	0.0374	L	0.38175	1.15	0.80722	D	1	B	0.27229	0.172	B	0.22386	0.039	T	0.05632	-1.0873	10	0.87932	D	0	.	7.2403	0.26092	0.0:0.1282:0.0:0.8717	.	409	Q9NQS3	PVRL3_HUMAN	G	409	ENSP00000418070:V409G	ENSP00000418070:V409G	V	+	2	0	PVRL3	112335328	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.306000	0.51881	2.206000	0.71126	0.383000	0.25322	GTA	.		0.438	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		G	110852638	T	G	110852638	3	3	48	1	0	0	0	0	1	0	0	0	12873	1638	57	5	1248	5	PVRL3	3	110852638	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	2915204	110852638	87169792	23	4353											
STXBP5L	9515	broad.mit.edu	37	chr3	120952528	120952528	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattgtagttgatctgacaCaaagcaagtaagttatccat	14	13	7	7	0	2	2	1	2	1	0	3	2	3	2	1	0	1	5	1	0	5	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:120952528C>A	ENST00000273666.6	+	12	1448	c.1177C>A	c.(1177-1179)Caa>Aaa	p.Q393K	STXBP5L_ENST00000497029.1_Missense_Mutation_p.Q393K|STXBP5L_ENST00000471454.1_Missense_Mutation_p.Q393K|STXBP5L_ENST00000492541.1_Missense_Mutation_p.Q393K|STXBP5L_ENST00000472879.1_Missense_Mutation_p.Q393K	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	393					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		TGATCTGACACAAAGCAAGTA	0.294																																					p.Q393K													.	STXBP5L-77	0			c.C1177A						.						88	83	85					3																	120952528		1814	4076	5890	SO:0001583	missense	9515	exon12			CTGACACAAAGCA	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1177C>A	3.37:g.120952528C>A	ENSP00000273666:p.Gln393Lys	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_014980	0	0	0	0	0	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.443493	0.83993	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.36520	1.94;1.94;1.74;1.25;1.73;1.94	4.27	4.27	0.50696	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.000000	0.85682	D	0.000000	T	0.52581	0.1743	L	0.54323	1.7	0.80722	D	1	D;D	0.60575	0.988;0.988	D;D	0.76071	0.987;0.987	T	0.44251	-0.9340	10	0.15066	T	0.55	-25.6058	16.8666	0.86030	0.0:1.0:0.0:0.0	.	393;393	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	K	393	ENSP00000273666:Q393K;ENSP00000420019:Q393K;ENSP00000419627:Q393K;ENSP00000420287:Q393K;ENSP00000420666:Q393K;ENSP00000420167:Q393K	ENSP00000273666:Q393K	Q	+	1	0	STXBP5L	122435218	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.281000	0.78621	2.194000	0.70268	0.491000	0.48974	CAA	.		0.294	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			A	120952528	C	A	120952528	3	1	48	1	0	0	0	0	1	0	0	0	15389	479	17	4	1219	4	STXBP5L	3	120952528	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	10099890	120952528	77069902	24	4354											
RARRES1	5918	hgsc.bcm.edu;broad.mit.edu	37	chr3	158422600	158422600	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccactgcctcacactagtgaGctgtgccaagtagtagtgtg	9	10	11	11	0	1	1	1	1	0	0	1	1	1	1	3	0	3	3	3	0	4	3	rs140091959		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:158422600G>C	ENST00000237696.5	-	4	932	c.652C>G	c.(652-654)Ctc>Gtc	p.L218V	RARRES1_ENST00000479756.1_Missense_Mutation_p.L218V|RARRES1_ENST00000498640.1_5'UTR	NM_206963.1	NP_996846.1	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene induced) 1	218					negative regulation of cell proliferation (GO:0008285)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	ACACTAGTGAGCTGTGCCAAG	0.443																																					p.L218V		.											.	RARRES1-514	0			c.C652G						.						114	102	106					3																	158422600		2203	4300	6503	SO:0001583	missense	5918	exon4			TAGTGAGCTGTGC	U27185	CCDS3184.1, CCDS54665.1	3q25.32	2013-07-29			ENSG00000118849	ENSG00000118849			9867	protein-coding gene	gene with protein product	"latexin-like"	605090				8601727, 9270552	Standard	NM_002888		Approved	TIG1, LXNL	uc003fci.3	P49788	OTTHUMG00000158834	ENST00000237696.5:c.652C>G	3.37:g.158422600G>C	ENSP00000237696:p.Leu218Val	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	44	11	NM_206963	0	0	44	44	0	Q8N1D7	Missense_Mutation	SNP	ENST00000237696.5	37	CCDS3184.1	.	.	.	.	.	.	.	.	.	.	-	6.185	0.402312	0.11696	.	.	ENSG00000118849	ENST00000237696;ENST00000479756	T;T	0.26660	1.72;1.72	5.2	2.23	0.28157	.	0.201181	0.42821	D	0.000657	T	0.17408	0.0418	L	0.33485	1.01	0.23969	N	0.996317	B;B	0.29136	0.234;0.036	B;B	0.32289	0.143;0.021	T	0.19484	-1.0304	10	0.23891	T	0.37	.	8.0807	0.30744	0.0:0.1549:0.525:0.3201	.	218;218	P49788-2;P49788	.;TIG1_HUMAN	V	218	ENSP00000237696:L218V;ENSP00000418556:L218V	ENSP00000237696:L218V	L	-	1	0	RARRES1	159905294	0.982000	0.34865	0.467000	0.27180	0.899000	0.52679	0.162000	0.16501	0.572000	0.29383	0.387000	0.25754	CTC	G|0.999;A|0.001		0.443	RARRES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352358.1			C	158422600	G	C	158422600	3	2	48	1	0	0	0	0	1	0	0	0	13087	971	34	4	259	4	RARRES1	3	158422600	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	37470072	158422600	39599830	25	4355											
BCHE	590	bcgsc.ca	37	chr3	165504036	165504037	+	Frame_Shift_Ins	INS	-	-	G																															ctgtattcaaggttagatatINSttttgttcagtgcttttgaa																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:165504036_165504037insG	ENST00000264381.3	-	3	1746_1747	c.1580_1581insC	c.(1579-1581)aaafs	p.K527fs	BCHE_ENST00000540653.1_5'UTR	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	527					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)	p.K527R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	AGGTTAGATATTTTTGTTCAGT	0.332																																					p.K527fs													.	BCHE-94	1	Substitution - Missense(1)	lung(1)	c.1581_1582insC						.																																			SO:0001589	frameshift_variant	590	exon3			TAGATATTTTTGT	M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"cholinesterase 1", "cholinesterase (serum) 2"	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1580_1581insC	3.37:g.165504036_165504037insG	ENSP00000264381:p.Lys527fs	Somatic	157	0		WXS	Illumina HiSeq	Phase_1	21	3	NM_000055	0	0	0	0	0	A8K7P8	Frame_Shift_Ins	INS	ENST00000264381.3	37	CCDS3198.1																																																																																			.		0.332	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1			G	165504037	-	G	165504036	7	5	48	1	0	1	1	0	0	0	0	0	1359	1490	52	0	235	0	BCHE	3	165504036	Frame_Shift_Ins	INS	-	TCGA-B9-4114-01A-01D-1252-08	7081436	165504036	32518394	26	4356											
GAK	2580	broad.mit.edu	37	chr4	858925	858925	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cataccttctgtggctggcgTgggggccactgccgatgctg	4	10	15	12	2	1	0	0	0	1	0	1	1	1	0	3	4	3	2	3	4	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:858925T>G	ENST00000314167.4	-	23	3261	c.3151A>C	c.(3151-3153)Acg>Ccg	p.T1051P	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Missense_Mutation_p.T972P	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1051			T -> M (in dbSNP:rs35227944). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GTGGCTGGCGTGGGGGCCACT	0.637																																					p.T1051P													.	GAK-568	0			c.A3151C						.						29	34	32					4																	858925		2200	4296	6496	SO:0001583	missense	2580	exon23			CTGGCGTGGGGGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"Heat shock proteins / DNAJ (HSP40)"	4113	protein-coding gene	gene with protein product	"auxilin-2"	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3151A>C	4.37:g.858925T>G	ENSP00000314499:p.Thr1051Pro	Somatic	36	11		WXS	Illumina HiSeq	Phase_I	68	20	NM_005255	0	0	58	62	4	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.504|7.504	0.653367|0.653367	0.14580|0.14580	.|.	.|.	ENSG00000178950|ENSG00000178950	ENST00000510799|ENST00000398567;ENST00000314167;ENST00000511163	.|T;T	.|0.78707	.|-0.75;-1.2	2.99|2.99	-2.65|-2.65	0.06095|0.06095	.|.	.|1.642800	.|0.02802	.|N	.|0.123304	T|T	0.61135|0.61135	0.2323|0.2323	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.32128	.|0.357;0.001;0.0;0.0	.|B;B;B;B	.|0.31191	.|0.125;0.001;0.001;0.001	T|T	0.52290|0.52290	-0.8595|-0.8595	5|10	.|0.39692	.|T	.|0.17	1.9604|1.9604	7.7425|7.7425	0.28849|0.28849	0.0:0.5379:0.0:0.4621|0.0:0.5379:0.0:0.4621	.|.	.|953;972;1051;936	.|B4DS37;E9PGR2;O14976;Q59HA5	.|.;.;GAK_HUMAN;.	P|P	170|327;1051;972	.|ENSP00000314499:T1051P;ENSP00000421361:T972P	.|ENSP00000314499:T1051P	H|T	-|-	2|1	0|0	GAK|GAK	848925|848925	0.011000|0.011000	0.17503|0.17503	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.699000|-0.699000	0.05087|0.05087	-0.544000|-0.544000	0.06232|0.06232	-1.145000|-1.145000	0.01858|0.01858	CAC|ACG	.		0.637	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		G	858925	T	G	858925	3	3	48	1	0	0	0	0	1	0	0	0	6215	1696	59	5	808	5	GAK	4	858925	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08		858925	190295351	27	4357											
SH3BP2	6452	hgsc.bcm.edu;bcgsc.ca	37	chr4	2831767	2831768	+	Frame_Shift_Ins	INS	-	-	C																															ccatgcccggactctttgtgINSccccccgtggctccccggcc																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:2831767_2831768insC	ENST00000356331.5	+	8	1395_1396	c.1134_1135insC	c.(1135-1137)cccfs	p.P379fs	SH3BP2_ENST00000503393.2_Frame_Shift_Ins_p.P436fs|SH3BP2_ENST00000435136.2_Frame_Shift_Ins_p.P379fs|SH3BP2_ENST00000442312.2_Frame_Shift_Ins_p.P407fs|SH3BP2_ENST00000511747.1_Frame_Shift_Ins_p.P379fs|SH3BP2_ENST00000452765.2_Frame_Shift_Ins_p.P379fs	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	379					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GACTCTTTGTGCCCCCCGTGGC	0.678									Cherubism																												p.V435fs		.											.	SH3BP2-514	0			c.1305_1306insC						.																																			SO:0001589	frameshift_variant	6452	exon8	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	.	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.1140dupC	4.37:g.2831773_2831773dupC	ENSP00000348685:p.Pro379fs	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	187	30	NM_001145856	0	0	0	0	0	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Frame_Shift_Ins	INS	ENST00000356331.5	37	CCDS33944.1																																																																																			.		0.678	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		C	2831768	-	C	2831767	7	5	48	1	0	1	1	0	0	0	0	0	14277	1306	46	0	1419	0	SH3BP2	4	2831767	Frame_Shift_Ins	INS	-	TCGA-B9-4114-01A-01D-1252-08	1972842	2831767	188322509	28	4358											
EVC	2121	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	5721079	5721079	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagagagaagtgcagatgtcGaaggacaaggaagctgttga	16	6	15	4	1	0	4	0	1	0	3	1	8	0	6	0	2	2	3	0	2	5	1	rs373072919		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:5721079G>A	ENST00000264956.6	+	2	463	c.279G>A	c.(277-279)tcG>tcA	p.S93S	EVC_ENST00000509451.1_Silent_p.S93S|EVC_ENST00000382674.2_Silent_p.S93S	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	93					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TGCAGATGTCGAAGGACAAGG	0.512																																					p.S93S		.											.	EVC-92	0			c.G279A						.	G		0,4406		0,0,2203	251	241	245		279	-5.8	0	4		245	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVC	NM_153717.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		93/993	5721079	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon2			GATGTCGAAGGAC	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.279G>A	4.37:g.5721079G>A		Somatic	266	0		WXS	Illumina HiSeq	Phase_I	431	178	NM_153717	0	0	0	0	0		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			.		0.512	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			A	5721079	G	A	5721079	2	1	48	1	0	0	0	0	0	0	0	1	5298	1045	37	1		1	EVC	4	5721079	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	2889312	5721079	185433197	29	4359											
BOD1L	259282	broad.mit.edu	37	chr4	13601241	13601241	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgcttctcttctttttccGcacaaacagcacttggatgg	8	14	7	12	1	2	0	0	0	2	0	4	1	3	1	1	2	3	3	1	2	1	5	rs370936070	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:13601241G>A	ENST00000040738.5	-	10	7418	c.7283C>T	c.(7282-7284)gCg>gTg	p.A2428V		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2428						nucleus (GO:0005634)	DNA binding (GO:0003677)										TTCTTTTTCCGCACAAACAGC	0.547											OREG0016115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0	0.0029	5008	,	,		21537	0		0	False		,,,				2504	0				p.A2428V													.	.	0			c.C7283T						.	G	VAL/ALA	3,4403	8.1+/-20.4	0,3,2200	161	151	154		7283	1	0	4		154	1,8599	1.2+/-3.3	0,1,4299	no	missense	BOD1L	NM_148894.2	64	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	benign	2428/3052	13601241	4,13002	2203	4300	6503	SO:0001583	missense	259282	exon10			TTTTCCGCACAAA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7283C>T	4.37:g.13601241G>A	ENSP00000040738:p.Ala2428Val	Somatic	364	1	688	WXS	Illumina HiSeq	Phase_I	502	6	NM_148894	0	0	0	0	0	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	3.136	-0.177381	0.06380	6.81E-4	1.16E-4	ENSG00000038219	ENST00000040738	T	0.06218	3.33	3.95	1.04	0.20106	.	1.970240	0.02637	N	0.104944	T	0.04452	0.0122	N	0.19112	0.55	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.38779	-0.9645	10	0.08837	T	0.75	.	4.9181	0.13856	0.207:0.1754:0.6176:0.0	.	2428	Q8NFC6	BOD1L_HUMAN	V	2428	ENSP00000040738:A2428V	ENSP00000040738:A2428V	A	-	2	0	BOD1L	13210339	0.111000	0.22076	0.000000	0.03702	0.017000	0.09413	0.903000	0.28475	0.043000	0.15746	0.555000	0.69702	GCG	.		0.547	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13601241	G	A	13601241	3	1	48	1	0	0	0	0	1	0	0	0	1484	1087	38	1	1940	1	BOD1L	4	13601241	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	7880162	13601241	177553035	30	4360											
PDS5A	23244	hgsc.bcm.edu	37	chr4	39929607	39929607	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tttatcatgggaagtatatgGagcttctggggcatagatac	11	13	12	5	0	2	1	1	0	1	1	2	3	2	3	0	4	2	3	0	4	6	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:39929607G>C	ENST00000303538.8	-	3	855	c.316C>G	c.(316-318)Cca>Gca	p.P106A	PDS5A_ENST00000503396.1_Missense_Mutation_p.P106A	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GAAGTATATGGAGCTTCTGGG	0.358																																					p.P106A		.											.	.	0			c.C316G						.						79	73	75					4																	39929607		1873	4100	5973	SO:0001583	missense	23244	exon3			TATATGGAGCTTC	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.316C>G	4.37:g.39929607G>C	ENSP00000303427:p.Pro106Ala	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_001100399	0	0	3	3	0		Missense_Mutation	SNP	ENST00000303538.8	37	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.881480	0.91740	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T	0.65916	-0.18	5.66	5.66	0.87406	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81317	0.4797	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.995;0.999	T	0.81342	-0.0976	9	.	.	.	-11.145	19.7578	0.96301	0.0:0.0:1.0:0.0	.	106;106	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	A	106	ENSP00000303427:P106A	.	P	-	1	0	PDS5A	39606002	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.869000	0.99810	2.657000	0.90304	0.655000	0.94253	CCA	.		0.358	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		C	39929607	G	C	39929607	3	2	48	1	0	0	0	0	1	0	0	0	11717	1174	41	4	3854	4	PDS5A	4	39929607	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	26328366	39929607	151224669	31	4361											
KCTD8	386617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	44449784	44449785	+	Missense_Mutation	DNP	TG	TG	GA																															gtcggggtcgcggctctcgtTgagcgtgtccccgaagacct																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:44449784_44449785TG>GA	ENST00000360029.3	-	1	1039_1040	c.756_757CA>TC	c.(754-759)ctCAac>ctTCac	p.N253H	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	253					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						CGGCTCTCGTTGAGCGTGTCCC	0.658										HNSCC(17;0.042)																											p.N253H		.											.	KCTD8	0			c.C756T						.																																			SO:0001583	missense	386617	exon1			CTCGTTGAGCGTG	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.756_757delinsGA	4.37:g.44449784_44449785delinsGA	ENSP00000353129:p.Asn253His	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	126	51		0	0	0	0	0	A2RU39	Missense_Mutation	DNP	ENST00000360029.3	37	CCDS3467.1																																																																																			.		0.658	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			GA	44449785	TG	GA	44449784	3	3	48	1	0	0	0	0	1	0	0	0	8136	1812	63	5	672	5	KCTD8	4	44449784	Missense_Mutation	DNP	TG	TCGA-B9-4114-01A-01D-1252-08	4520177	44449784	146704492	32	4362											
LNX1	84708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	54343092	54343092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttttcaataatgccactgCctcactccggctgacctctg	7	13	6	15	1	4	1	2	1	2	0	5	1	5	1	4	1	2	1	4	1	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:54343092C>T	ENST00000263925.7	-	9	2034	c.1720G>A	c.(1720-1722)Gca>Aca	p.A574T	FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000306888.2_Missense_Mutation_p.A478T	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	574	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AATGCCACTGCCTCACTCCGG	0.488																																					p.A574T		.											.	LNX1-229	0			c.G1720A						.						166	166	166					4																	54343092		2203	4300	6503	SO:0001583	missense	84708	exon9			CCACTGCCTCACT	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1720G>A	4.37:g.54343092C>T	ENSP00000263925:p.Ala574Thr	Somatic	308	0		WXS	Illumina HiSeq	Phase_I	274	46	NM_001126328	0	0	5	8	3	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304671	0.81136	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.51574	0.7;0.7	5.16	5.16	0.70880	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.76435	0.3987	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82024	-0.0662	10	0.87932	D	0	.	18.8374	0.92168	0.0:1.0:0.0:0.0	.	574;478	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	T	478;412;574	ENSP00000302879:A478T;ENSP00000263925:A574T	ENSP00000263925:A574T	A	-	1	0	LNX1	54037849	1.000000	0.71417	0.998000	0.56505	0.311000	0.27955	6.748000	0.74877	2.687000	0.91594	0.561000	0.74099	GCA	.		0.488	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			T	54343092	C	T	54343092	3	4	48	1	0	0	0	0	1	0	0	0	8888	739	26	2	478	2	LNX1	4	54343092	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	9893308	54343092	136811184	33	4363											
UGT2A3	79799	hgsc.bcm.edu	37	chr4	69816984	69816984	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attctaagtgtgagcacaaaAgggactgcaagcaactcagc	15	7	10	9	0	2	1	1	1	1	0	2	2	2	2	0	1	5	3	0	1	5	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:69816984A>G	ENST00000251566.4	-	1	525	c.495T>C	c.(493-495)ccT>ccC	p.P165P	UGT2A3_ENST00000420231.2_5'UTR	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	165					cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TGAGCACAAAAGGGACTGCAA	0.473																																					p.P165P		.											.	UGT2A3-92	0			c.T495C						.						62	62	62					4																	69816984		2203	4299	6502	SO:0001819	synonymous_variant	79799	exon1			CACAAAAGGGACT		CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220		"UDP glucuronosyltransferases"	28528	protein-coding gene	gene with protein product							Standard	NM_024743		Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.495T>C	4.37:g.69816984A>G		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_024743	0	0	20	20	0	Q9H6S4	Silent	SNP	ENST00000251566.4	37	CCDS3525.1																																																																																			.		0.473	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251564.1	NM_024743		G	69816984	A	G	69816984	2	3	48	1	0	0	0	0	0	0	0	1	16988	59	3	3		3	UGT2A3	4	69816984	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08	15473892	69816984	121337292	34	4364											
AGPAT9	84803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	84457815	84457815	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggaagatcctttccaccTggctgacgctggttctcggc	5	10	12	14	3	1	2	0	1	1	1	4	3	3	3	4	4	0	3	4	4	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:84457815T>C	ENST00000395226.2	+	2	258	c.40T>C	c.(40-42)Tgg>Cgg	p.W14R	AGPAT9_ENST00000264409.4_Missense_Mutation_p.W14R	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	14					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				CCTTTCCACCTGGCTGACGCT	0.582																																					p.W14R		.											.	AGPAT9-91	0			c.T40C						.						88	69	75					4																	84457815		2203	4300	6503	SO:0001583	missense	84803	exon2			TCCACCTGGCTGA	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.40T>C	4.37:g.84457815T>C	ENSP00000378651:p.Trp14Arg	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	214	44	NM_001256421	0	0	3	3	0	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	37	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.459554	0.84317	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.48201	0.82;0.82	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.64405	0.2595	M	0.86028	2.79	0.47374	D	0.999407	D	0.58970	0.984	P	0.54372	0.75	T	0.71341	-0.4622	10	0.59425	D	0.04	-8.2831	13.1799	0.59649	0.0:0.0:0.0:1.0	.	14	Q53EU6	GPAT3_HUMAN	R	14	ENSP00000378651:W14R;ENSP00000264409:W14R	ENSP00000264409:W14R	W	+	1	0	AGPAT9	84676839	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.587000	0.53957	1.760000	0.52011	0.374000	0.22700	TGG	.		0.582	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		C	84457815	T	C	84457815	3	2	48	1	0	0	0	0	1	0	0	0	392	1580	55	3	42	3	AGPAT9	4	84457815	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	14640831	84457815	106696461	35	4365											
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125591236	125591236	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtttggatcagcaccatgctCtaataagacctgaacaacat	14	10	7	10	0	2	2	1	1	1	1	2	3	2	3	2	1	4	3	2	1	4	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:125591236C>G	ENST00000504087.1	-	4	4233	c.3196G>C	c.(3196-3198)Gag>Cag	p.E1066Q	ANKRD50_ENST00000515641.1_Missense_Mutation_p.E887Q	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1066										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						GCACCATGCTCTAATAAGACC	0.428																																					p.E1066Q		.											.	ANKRD50-90	0			c.G3196C						.						107	101	103					4																	125591236		2203	4300	6503	SO:0001583	missense	57182	exon4			CATGCTCTAATAA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.3196G>C	4.37:g.125591236C>G	ENSP00000425658:p.Glu1066Gln	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_020337	0	0	0	0	0	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754517	0.49362	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.67345	-0.26;-0.26	5.24	5.24	0.73138	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.59742	0.2216	L	0.38175	1.15	0.80722	D	1	B	0.25486	0.127	B	0.33960	0.173	T	0.54029	-0.8354	10	0.07482	T	0.82	.	19.0331	0.92965	0.0:1.0:0.0:0.0	.	1066	Q9ULJ7	ANR50_HUMAN	Q	1066;887	ENSP00000425658:E1066Q;ENSP00000425355:E887Q	ENSP00000425658:E1066Q	E	-	1	0	ANKRD50	125810686	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	7.164000	0.77533	2.724000	0.93272	0.561000	0.74099	GAG	.		0.428	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		G	125591236	C	G	125591236	3	3	48	1	0	0	0	0	1	0	0	0	677	922	32	4	1097	4	ANKRD50	4	125591236	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	41133421	125591236	65563040	36	4366											
SEMA5A	9037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	9119220	9119220	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaggtagtgctgcagggAgaccacgaggtccagggagt	10	5	16	10	1	0	1	0	0	0	1	1	4	1	2	3	4	2	3	3	4	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:9119220A>T	ENST00000382496.5	-	15	2480	c.1815T>A	c.(1813-1815)tcT>tcA	p.S605S		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	605	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						TGCTGCAGGGAGACCACGAGG	0.652																																					p.S605S		.											.	SEMA5A-91	0			c.T1815A						.						57	51	53					5																	9119220		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon15			GCAGGGAGACCAC	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1815T>A	5.37:g.9119220A>T		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	79	20	NM_003966	0	0	0	0	0	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			.		0.652	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			T	9119220	A	T	9119220	2	4	48	1	0	0	0	0	0	0	0	1	14069	291	11	5		5	SEMA5A	5	9119220	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08		9119220	171796040	37	4367											
CDH6	1004	hgsc.bcm.edu	37	chr5	31294177	31294177	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacaggcgacatacaggccAccaagaggctggacagggaa	15	2	13	11	1	0	1	0	0	0	1	0	4	0	3	2	5	1	1	2	5	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:31294177A>C	ENST00000265071.2	+	3	602	c.337A>C	c.(337-339)Acc>Ccc	p.T113P	CDH6_ENST00000514738.1_Missense_Mutation_p.T58P	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	113	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CATACAGGCCACCAAGAGGCT	0.463																																					p.T113P		.											.	CDH6-159	0			c.A337C						.						102	104	103					5																	31294177		2203	4300	6503	SO:0001583	missense	1004	exon3			CAGGCCACCAAGA	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.337A>C	5.37:g.31294177A>C	ENSP00000265071:p.Thr113Pro	Somatic	276	2		WXS	Illumina HiSeq	Phase_I	29	2	NM_004932	0	0	3	3	0	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	37	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.143939	0.77888	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.56103	0.48;0.48	5.77	4.59	0.56863	Cadherin (5);Cadherin-like (1);	0.044760	0.85682	D	0.000000	T	0.79684	0.4488	H	0.95884	3.735	0.58432	D	0.999993	D;D	0.67145	0.99;0.996	D;D	0.72625	0.978;0.976	D	0.84659	0.0705	10	0.66056	D	0.02	.	12.3391	0.55083	0.8732:0.0:0.0:0.1268	.	113;113	P55285;P55285-2	CADH6_HUMAN;.	P	58;113	ENSP00000424843:T58P;ENSP00000265071:T113P	ENSP00000265071:T113P	T	+	1	0	CDH6	31329934	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.113000	0.77095	1.076000	0.40961	0.533000	0.62120	ACC	.		0.463	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		C	31294177	A	C	31294177	3	2	48	1	0	0	0	0	1	0	0	0	3120	159	6	5	343	5	CDH6	5	31294177	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	22174957	31294177	149621083	38	4368											
RAI14	26064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	34757668	34757668	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcggcaagaagggggcCagtgccaccaaacacgacag	12	3	13	13	2	0	1	0	0	0	1	1	2	0	1	3	3	3	2	3	3	3	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:34757668C>T	ENST00000265109.3	+	3	419	c.132C>T	c.(130-132)gcC>gcT	p.A44A	RAI14_ENST00000503673.1_Silent_p.A44A|RAI14_ENST00000515799.1_Silent_p.A47A|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000397449.1_Silent_p.A37A|RAI14_ENST00000512629.1_Silent_p.A44A|RAI14_ENST00000428746.2_Silent_p.A44A|RAI14_ENST00000506376.1_Silent_p.A36A	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	44			A -> T (in dbSNP:rs17521570).			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					AGAAGGGGGCCAGTGCCACCA	0.542																																					p.A47A		.											.	RAI14-91	0			c.C141T						.						74	71	72					5																	34757668		2203	4300	6503	SO:0001819	synonymous_variant	26064	exon5			GGGGGCCAGTGCC	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"Ankyrin repeat domain containing"	14873	protein-coding gene	gene with protein product	"novel retinal pigment epithelial"	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.132C>T	5.37:g.34757668C>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	155	28	NM_001145525	0	0	1	1	0	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																			.		0.542	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		T	34757668	C	T	34757668	2	4	48	1	0	0	0	0	0	0	0	1	13040	581	21	2		2	RAI14	5	34757668	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	3463491	34757668	146157592	39	4369											
PARP8	79668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	50123848	50123848	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagccaaagaatccaattTtagagctgctaaaaaactct	17	9	5	10	0	1	2	0	0	1	2	2	2	2	2	3	0	4	2	3	0	7	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:50123848T>A	ENST00000281631.5	+	20	2206	c.2048T>A	c.(2047-2049)tTt>tAt	p.F683Y	PARP8_ENST00000511363.2_3'UTR|PARP8_ENST00000514342.2_Missense_Mutation_p.F394Y|PARP8_ENST00000505697.2_Missense_Mutation_p.F683Y|PARP8_ENST00000503750.2_Missense_Mutation_p.F641Y|PARP8_ENST00000505554.1_Missense_Mutation_p.F662Y|PARP8_ENST00000514067.2_Missense_Mutation_p.F641Y	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	683	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				GAATCCAATTTTAGAGCTGCT	0.383																																					p.F683Y		.											.	PARP8-586	0			c.T2048A						.						127	124	125					5																	50123848		2203	4300	6503	SO:0001583	missense	79668	exon21			CCAATTTTAGAGC	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"Poly (ADP-ribose) polymerases"	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.2048T>A	5.37:g.50123848T>A	ENSP00000281631:p.Phe683Tyr	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	125	41	NM_001178055	0	0	20	33	13	Q3KRB7|Q6DHZ1|Q9H754	Missense_Mutation	SNP	ENST00000281631.5	37	CCDS3954.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379826	0.82682	.	.	ENSG00000151883	ENST00000505697;ENST00000503750;ENST00000514342;ENST00000281631;ENST00000514067;ENST00000505554;ENST00000503561;ENST00000423185	T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21	5.7	5.7	0.88788	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.059647	0.64402	D	0.000002	T	0.34193	0.0889	L	0.48935	1.535	0.54753	D	0.99998	D;P;P	0.53619	0.961;0.954;0.891	P;D;P	0.66351	0.492;0.943;0.492	T	0.01382	-1.1369	9	.	.	.	-16.5844	15.9599	0.79923	0.0:0.0:0.0:1.0	.	575;641;683	B4DQ81;Q8N3A8-2;Q8N3A8	.;.;PARP8_HUMAN	Y	683;641;394;683;641;662;394;394	ENSP00000422217:F683Y;ENSP00000440851:F641Y;ENSP00000439022:F394Y;ENSP00000281631:F683Y;ENSP00000424814:F641Y;ENSP00000423946:F662Y	.	F	+	2	0	PARP8	50159605	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	8.036000	0.88901	2.153000	0.67306	0.533000	0.62120	TTT	.		0.383	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615		A	50123848	T	A	50123848	3	1	48	1	0	0	0	0	1	0	0	0	11491	1841	64	5	2126	5	PARP8	5	50123848	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	15366180	50123848	130791412	40	4370											
GPR98	84059	hgsc.bcm.edu	37	chr5	89923119	89923119	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaattccattgagatcaTcattaagaaaaatgatagtc	17	12	7	5	0	2	3	2	2	0	2	4	5	3	4	1	1	0	0	1	1	6	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:89923119T>C	ENST00000405460.2	+	7	860	c.764T>C	c.(763-765)aTc>aCc	p.I255T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	255					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATTGAGATCATCATTAAGAAA	0.363																																					p.I255T		.											.	GPR98-103	0			c.T764C						.						66	66	66					5																	89923119		1841	4081	5922	SO:0001583	missense	84059	exon7			AGATCATCATTAA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.764T>C	5.37:g.89923119T>C	ENSP00000384582:p.Ile255Thr	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	52	3	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	8.113	0.779170	0.16120	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.20332	2.08	5.79	4.64	0.57946	.	0.306080	0.40302	N	0.001126	T	0.10078	0.0247	N	0.12746	0.255	0.80722	D	1	B	0.12013	0.005	B	0.09377	0.004	T	0.20472	-1.0274	10	0.19590	T	0.45	.	7.1428	0.25566	0.1402:0.073:0.0:0.7869	.	255	Q8WXG9	GPR98_HUMAN	T	255	ENSP00000384582:I255T	ENSP00000296619:I255T	I	+	2	0	GPR98	89958875	0.958000	0.32768	1.000000	0.80357	0.927000	0.56198	0.689000	0.25437	2.215000	0.71742	0.528000	0.53228	ATC	.		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89923119	T	C	89923119	3	2	48	1	0	0	0	0	1	0	0	0	6742	1435	50	3	790	3	GPR98	5	89923119	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	39799271	89923119	90992141	41	4371											
NR2F1	7025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	92929424	92929424	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcgcaccgtgtcctcctCcgtcatcgagcagctcttct	4	11	9	17	4	3	0	1	0	2	0	7	1	6	0	4	0	3	4	4	0	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:92929424C>A	ENST00000327111.3	+	3	2835	c.1148C>A	c.(1147-1149)tCc>tAc	p.S383Y	NR2F1_ENST00000506162.1_3'UTR	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	383					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		GTGTCCTCCTCCGTCATCGAG	0.582																																					p.S383Y		.											.	NR2F1-227	0			c.C1148A						.						123	118	120					5																	92929424		2203	4300	6503	SO:0001583	missense	7025	exon3			CCTCCTCCGTCAT	BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"Nuclear hormone receptors"	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.1148C>A	5.37:g.92929424C>A	ENSP00000325819:p.Ser383Tyr	Somatic	292	0		WXS	Illumina HiSeq	Phase_I	414	121	NM_005654	0	0	34	34	0		Missense_Mutation	SNP	ENST00000327111.3	37	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607237	0.87157	.	.	ENSG00000175745	ENST00000327111	D	0.96856	-4.15	6.17	6.17	0.99709	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.96482	0.8852	L	0.52206	1.635	0.80722	D	1	P	0.48294	0.908	P	0.50490	0.642	D	0.96365	0.9269	10	0.87932	D	0	.	20.4898	0.99202	0.0:1.0:0.0:0.0	.	383	P10589	COT1_HUMAN	Y	383	ENSP00000325819:S383Y	ENSP00000325819:S383Y	S	+	2	0	NR2F1	92955180	1.000000	0.71417	0.974000	0.42286	0.983000	0.72400	6.074000	0.71253	2.941000	0.99782	0.655000	0.94253	TCC	.		0.582	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654		A	92929424	C	A	92929424	3	1	48	1	0	0	0	0	1	0	0	0	10653	855	30	4	1158	4	NR2F1	5	92929424	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	3006305	92929424	87985836	42	4372											
POU5F2	134187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	93076682	93076682	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccattttgcataagcccagAaggttctctgcttccacttc	8	14	6	13	0	1	1	0	0	1	1	5	1	3	1	3	1	3	3	3	1	2	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:93076682A>T	ENST00000510627.4	-	1	661	c.588T>A	c.(586-588)ctT>ctA	p.L196L	FAM172A_ENST00000505869.1_Intron|POU5F2_ENST00000606183.1_5'UTR|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000509163.1_Intron	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	196					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		ATAAGCCCAGAAGGTTCTCTG	0.542																																					p.L196L		.											.	.	0			c.T588A						.						107	107	107					5																	93076682		2115	4250	6365	SO:0001819	synonymous_variant	134187	exon1			GCCCAGAAGGTTC		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.588T>A	5.37:g.93076682A>T		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	208	66	NM_153216	0	0	0	0	0	Q15169|Q6MZL7|Q8N748	Silent	SNP	ENST00000510627.4	37	CCDS59489.1																																																																																			.		0.542	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		T	93076682	A	T	93076682	2	4	48	1	0	0	0	0	0	0	0	1	12309	233	9	5		5	POU5F2	5	93076682	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08	147258	93076682	87838578	43	4373											
FNIP1	96459	broad.mit.edu	37	chr5	131006178	131006178	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcacagcatgagataaatctGacatcagacactgacggaac	16	6	9	10	1	2	4	1	3	1	2	2	6	2	5	0	1	2	2	0	1	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:131006178G>A	ENST00000510461.1	-	15	3181	c.3086C>T	c.(3085-3087)tCa>tTa	p.S1029L	FNIP1_ENST00000307954.8_Missense_Mutation_p.S984L|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.S1001L	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	1029					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		AGATAAATCTGACATCAGACA	0.433																																					p.S1029L													.	FNIP1-92	0			c.C3086T						.						132	120	125					5																	131006178		2203	4300	6503	SO:0001583	missense	96459	exon15			AAATCTGACATCA	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.3086C>T	5.37:g.131006178G>A	ENSP00000421985:p.Ser1029Leu	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	25	6	NM_133372	0	0	2	3	1	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.329940	0.81690	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.12672	2.66;2.66;2.66	6.02	6.02	0.97574	.	.	.	.	.	T	0.20495	0.0493	L	0.45581	1.43	0.80722	D	1	P;P	0.52316	0.868;0.952	B;P	0.46659	0.284;0.523	T	0.00334	-1.1809	9	0.27785	T	0.31	-2.3999	20.5373	0.99239	0.0:0.0:1.0:0.0	.	1001;1029	Q8TF40-3;Q8TF40	.;FNIP1_HUMAN	L	1001;984;781;1029	ENSP00000309266:S1001L;ENSP00000310453:S984L;ENSP00000421985:S1029L	ENSP00000310453:S984L	S	-	2	0	FNIP1	131034077	1.000000	0.71417	0.993000	0.49108	0.804000	0.45430	9.334000	0.96470	2.857000	0.98124	0.650000	0.86243	TCA	.		0.433	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		A	131006178	G	A	131006178	3	1	48	1	0	0	0	0	1	0	0	0	5994	1294	45	2	430	2	FNIP1	5	131006178	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	37929496	131006178	49909082	44	4374											
FNIP1	96459	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	131042155	131042155	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtttggctgcgtcgccaaCgtcgctggtagctgctggca	4	12	14	11	4	0	0	0	0	0	0	2	0	0	0	1	3	4	7	1	3	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:131042155C>A	ENST00000510461.1	-	9	958	c.863G>T	c.(862-864)cGt>cTt	p.R288L	FNIP1_ENST00000307954.8_Missense_Mutation_p.R243L|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000511848.1_Missense_Mutation_p.R288L|FNIP1_ENST00000307968.7_Missense_Mutation_p.R260L	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	288					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		GCGTCGCCAACGTCGCTGGTA	0.453																																					p.R288L		.											.	FNIP1-92	0			c.G863T						.						100	93	96					5																	131042155		2203	4300	6503	SO:0001583	missense	96459	exon9			CGCCAACGTCGCT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.863G>T	5.37:g.131042155C>A	ENSP00000421985:p.Arg288Leu	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	68	15	NM_133372	0	0	0	0	0	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	36	5.709610	0.96821	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.47528	1.83;1.67;1.57;0.84	5.6	5.6	0.85130	.	.	.	.	.	T	0.73473	0.3591	M	0.83012	2.62	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.91635	0.998;0.994;0.998;0.999	T	0.76340	-0.2995	9	0.87932	D	0	-7.1358	19.9737	0.97296	0.0:1.0:0.0:0.0	.	288;288;260;288	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	L	260;243;48;288;288	ENSP00000309266:R260L;ENSP00000310453:R243L;ENSP00000421985:R288L;ENSP00000425619:R288L	ENSP00000310453:R243L	R	-	2	0	FNIP1	131070054	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.776000	0.85560	2.793000	0.96121	0.591000	0.81541	CGT	.		0.453	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		A	131042155	C	A	131042155	3	1	48	1	0	0	0	0	1	0	0	0	5994	536	19	4	2677	4	FNIP1	5	131042155	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	35977	131042155	49873105	45	4375											
PCDHGA12	26025	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140811171	140811177	+	Frame_Shift_Del	DEL	GGTATGT	GGTATGT	-																															ggaagtgaggtattccttccGgtatgtggacgacaaggcgg																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	GGTATGT	GGTATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:140811171_140811177delGGTATGT	ENST00000252085.3	+	1	987_993	c.845_851delGGTATGT	c.(844-852)cggtatgtgfs	p.RYV282fs	PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA11_ENST00000518882.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	282	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATTCCTTCCGGTATGTGGACGACAAG	0.522																																					p.282_284del		.											.	PCDHGA12-27	0			c.845_851del						.																																			SO:0001589	frameshift_variant	26025	exon1			.	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.845_851delGGTATGT	5.37:g.140811171_140811177delGGTATGT	ENSP00000252085:p.Arg282fs	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	254	63	NM_032094	0	0	0	0	0	O15100|Q6UW70|Q9Y5D7	Frame_Shift_Del	DEL	ENST00000252085.3	37	CCDS4260.1																																																																																			.		0.522	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		-	140811177	GGTATGT	-	140811171	7	5	48	1	0	1	0	1	0	0	0	0	11579	1116	39	0	847	0	PCDHGA12	5	140811171	Frame_Shift_Del	DEL	GGTATGT	TCGA-B9-4114-01A-01D-1252-08	9769016	140811171	40104089	46	4376											
HIVEP1	3096	broad.mit.edu	37	chr6	12123740	12123740	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatccaagttccagagattTtggtcacagaagaaccagat	15	9	8	9	0	1	4	1	0	0	4	3	5	3	4	3	1	1	1	3	1	3	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:12123740T>C	ENST00000379388.2	+	4	4044	c.3712T>C	c.(3712-3714)Ttg>Ctg	p.L1238L	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1238					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCCAGAGATTTTGGTCACAGA	0.473																																					p.L1238L													.	HIVEP1-139	0			c.T3712C						.						65	62	63					6																	12123740		1929	4137	6066	SO:0001819	synonymous_variant	3096	exon4			GAGATTTTGGTCA	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.3712T>C	6.37:g.12123740T>C		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_002114	0	0	0	0	0	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	37	CCDS43426.1																																																																																			.		0.473	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		C	12123740	T	C	12123740	2	2	48	1	0	0	0	0	0	0	0	1	7207	1838	64	3		3	HIVEP1	6	12123740	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08		12123740	158991327	47	4377											
HLA-DQA2	3118	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	32713781	32713781	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttacctcaccttcctcccttCtgctgatgagatttatgact	7	16	5	13	0	2	3	1	3	1	1	4	4	4	3	4	0	2	1	4	0	2	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:32713781C>T	ENST00000374940.3	+	3	647	c.545C>T	c.(544-546)tCt>tTt	p.S182F		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	182	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	TTCCTCCCTTCTGCTGATGAG	0.502																																					p.S182F		.											.	HLA-DQA2-90	0			c.C545T						.						191	211	204					6																	32713781		1511	2707	4218	SO:0001583	missense	3118	exon3			TCCCTTCTGCTGA		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.545C>T	6.37:g.32713781C>T	ENSP00000364076:p.Ser182Phe	Somatic	417	1		WXS	Illumina HiSeq	Phase_I	286	92	NM_020056	0	0	437	437	0	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	13.77	2.336406	0.41398	.	.	ENSG00000237541	ENST00000374940	T	0.03152	4.03	3.06	2.06	0.26882	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.585185	0.16577	U	0.208364	T	0.10035	0.0246	M	0.89478	3.035	0.30030	N	0.813521	D	0.89917	1.0	D	0.97110	1.0	T	0.01553	-1.1326	10	0.66056	D	0.02	.	7.1176	0.25424	0.4092:0.5908:0.0:0.0	.	182	P01906	DQA2_HUMAN	F	182	ENSP00000364076:S182F	ENSP00000364076:S182F	S	+	2	0	HLA-DQA2	32821759	0.009000	0.17119	0.999000	0.59377	0.758000	0.43043	0.626000	0.24492	1.700000	0.51204	0.174000	0.16983	TCT	.		0.502	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		T	32713781	C	T	32713781	3	4	48	1	0	0	0	0	1	0	0	0	7226	913	32	2	555	2	HLA-DQA2	6	32713781	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	20590041	32713781	138401286	48	4378											
LEMD2	221496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33748926	33748926	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctggatttccacactcaaaAttacctaggagaaaaaaaac	18	9	5	9	0	2	1	1	0	1	1	3	3	3	2	2	2	2	0	2	2	8	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:33748926A>C	ENST00000293760.5	-	4	877	c.858T>G	c.(856-858)aaT>aaG	p.N286K	LEMD2_ENST00000508327.1_5'UTR|LEMD2_ENST00000502643.1_5'UTR	NM_181336.3	NP_851853.1	Q8NC56	LEMD2_HUMAN	LEM domain containing 2	286					negative regulation of MAPK cascade (GO:0043409)|skeletal muscle cell differentiation (GO:0035914)	integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear membrane (GO:0031965)				central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)|pancreas(1)	9						CACACTCAAAATTACCTAGGA	0.368																																					p.N286K		.											.	LEMD2-90	0			c.T858G						.						74	68	70					6																	33748926		2203	4300	6503	SO:0001583	missense	221496	exon4			CTCAAAATTACCT		CCDS4785.1, CCDS47411.1	6p21.31	2009-11-06			ENSG00000161904	ENSG00000161904			21244	protein-coding gene	gene with protein product						12477932	Standard	NM_001143944		Approved	dJ482C21.1, NET25	uc011drm.2	Q8NC56	OTTHUMG00000014535	ENST00000293760.5:c.858T>G	6.37:g.33748926A>C	ENSP00000293760:p.Asn286Lys	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	152	49	NM_181336	0	0	0	2	2	B4DVH5|E7EVT2|Q5T972|Q5T974	Missense_Mutation	SNP	ENST00000293760.5	37	CCDS4785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.71|19.71	3.877584|3.877584	0.72294|0.72294	.|.	.|.	ENSG00000161904|ENSG00000161904	ENST00000442696|ENST00000293760	.|.	.|.	.|.	5.65|5.65	3.27|3.27	0.37495|0.37495	.|Inner nuclear membrane protein MAN1 (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.33876|0.33876	0.0878|0.0878	L|L	0.35414|0.35414	1.06|1.06	0.80722|0.80722	D|D	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.64595	.|0.927	T|T	0.40664|0.40664	-0.9551|-0.9551	5|9	.|0.06099	.|T	.|0.92	-4.6423|-4.6423	8.5956|8.5956	0.33714|0.33714	0.8505:0.0:0.1495:0.0|0.8505:0.0:0.1495:0.0	.|.	.|286	.|Q8NC56	.|LEMD2_HUMAN	S|K	152|286	.|.	.|ENSP00000293760:N286K	I|N	-|-	2|3	0|2	LEMD2|LEMD2	33856904|33856904	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.063000|2.063000	0.41423|0.41423	0.432000|0.432000	0.26286|0.26286	0.533000|0.533000	0.62120|0.62120	ATT|AAT	.		0.368	LEMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040209.3	XM_166338		C	33748926	A	C	33748926	3	2	48	1	0	0	0	0	1	0	0	0	8741	98	4	5	677	5	LEMD2	6	33748926	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	1035145	33748926	137366141	49	4379											
TTBK1	84630	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43251695	43251695	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcggagccctcaggctcaCtgtcggccaaagagcggtgg	7	6	15	13	3	2	1	2	0	0	1	4	2	2	2	2	5	2	2	2	5	1	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:43251695C>A	ENST00000259750.4	+	14	3300	c.3217C>A	c.(3217-3219)Ctg>Atg	p.L1073M		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1073					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CTCAGGCTCACTGTCGGCCAA	0.687																																					p.L1073M		.											.	TTBK1-353	0			c.C3217A						.						18	19	18					6																	43251695		2183	4238	6421	SO:0001583	missense	84630	exon14			GGCTCACTGTCGG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.3217C>A	6.37:g.43251695C>A	ENSP00000259750:p.Leu1073Met	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	121	46	NM_032538	0	0	0	0	0	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.945410	0.34377	.	.	ENSG00000146216	ENST00000259750	T	0.55413	0.52	5.02	3.14	0.36123	.	0.348022	0.23768	N	0.044741	T	0.27349	0.0671	L	0.36672	1.1	0.80722	D	1	B	0.19200	0.034	B	0.14023	0.01	T	0.30736	-0.9968	10	0.56958	D	0.05	.	11.2746	0.49159	0.1311:0.7259:0.143:0.0	.	1073	Q5TCY1	TTBK1_HUMAN	M	1073	ENSP00000259750:L1073M	ENSP00000259750:L1073M	L	+	1	2	TTBK1	43359673	0.733000	0.28132	0.999000	0.59377	0.950000	0.60333	1.377000	0.34317	2.326000	0.78906	0.455000	0.32223	CTG	.		0.687	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			A	43251695	C	A	43251695	3	1	48	1	0	0	0	0	1	0	0	0	16709	564	20	4	3267	4	TTBK1	6	43251695	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	9502769	43251695	127863372	50	4380											
HTR1B	3351	broad.mit.edu	37	chr6	78172192	78172192	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctagggtcttggtggctttgCgctccctagcggccatgagt	4	12	14	11	2	1	1	0	1	1	0	2	1	2	1	2	4	2	2	2	4	2	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:78172192C>T	ENST00000369947.2	-	1	1298	c.929G>A	c.(928-930)cGc>cAc	p.R310H		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	310					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GGTGGCTTTGCGCTCCCTAGC	0.522																																					p.R310H													.	HTR1B-90	0			c.G929A						.						172	175	174					6																	78172192		2203	4300	6503	SO:0001583	missense	3351	exon1			GCTTTGCGCTCCC	BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5287	protein-coding gene	gene with protein product		182131	"5-hydroxytryptamine (serotonin) receptor 1B"			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.929G>A	6.37:g.78172192C>T	ENSP00000358963:p.Arg310His	Somatic	506	0		WXS	Illumina HiSeq	Phase_I	679	7	NM_000863	0	0	1	1	0	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.084919	0.76642	.	.	ENSG00000135312	ENST00000369947	T	0.73681	-0.77	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.81192	0.4771	L	0.56396	1.775	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.78690	-0.2106	9	.	.	.	.	18.1467	0.89659	0.0:1.0:0.0:0.0	.	310	P28222	5HT1B_HUMAN	H	310	ENSP00000358963:R310H	.	R	-	2	0	HTR1B	78228911	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.798000	0.55522	2.767000	0.95098	0.561000	0.74099	CGC	.		0.522	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		T	78172192	C	T	78172192	3	4	48	1	0	0	0	0	1	0	0	0	7458	768	27	1	247	1	HTR1B	6	78172192	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	34920497	78172192	92942875	51	4381											
ROS1	6098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	117746764	117746764	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccacagaaatccataggCagccaagagttgcaaaattg	16	6	9	10	0	0	2	0	0	0	2	1	2	1	2	3	1	2	4	3	1	5	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:117746764C>G	ENST00000368508.3	-	1	254	c.56G>C	c.(55-57)tGc>tCc	p.C19S	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.C19S	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	19					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AATCCATAGGCAGCCAAGAGT	0.388			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.C19S		.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1-1353	0			c.G56C						.						120	119	119					6																	117746764		2203	4300	6503	SO:0001583	missense	6098	exon1			CATAGGCAGCCAA	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.56G>C	6.37:g.117746764C>G	ENSP00000357494:p.Cys19Ser	Somatic	287	0		WXS	Illumina HiSeq	Phase_I	135	41	NM_002944	0	0	0	0	0	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.155746	0.38021	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70631	-0.5;-0.5	5.11	2.22	0.28083	.	0.273852	0.26757	N	0.022646	T	0.41766	0.1173	L	0.51422	1.61	0.80722	D	1	B	0.14438	0.01	B	0.06405	0.002	T	0.42649	-0.9439	10	0.62326	D	0.03	.	3.545	0.07826	0.175:0.5642:0.1691:0.0917	.	19	P08922	ROS1_HUMAN	S	19	ENSP00000357494:C19S;ENSP00000357493:C19S	ENSP00000357493:C19S	C	-	2	0	ROS1	117853457	0.849000	0.29639	0.992000	0.48379	0.875000	0.50365	0.358000	0.20216	0.366000	0.24427	0.655000	0.94253	TGC	.		0.388	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117746764	C	G	117746764	3	3	48	1	0	0	0	0	1	0	0	0	13563	710	25	4	7159	4	ROS1	6	117746764	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	39574572	117746764	53368303	52	4382											
TMEM184A	202915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	1590513	1590513	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggtggtctccgaggaggaGgaggctgagccaggagtcga	8	6	19	8	2	1	1	0	1	1	0	3	7	1	5	2	7	1	1	2	7	0	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:1590513G>A	ENST00000297477.5	-	3	641	c.325C>T	c.(325-327)Ctc>Ttc	p.L109F		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	109					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		CCGAGGAGGAGGAGGCTGAGC	0.632																																					p.L109F		.											.	TMEM184A-90	0			c.C325T						.						88	97	94					7																	1590513		2203	4300	6503	SO:0001583	missense	202915	exon3			GGAGGAGGAGGCT		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.325C>T	7.37:g.1590513G>A	ENSP00000297477:p.Leu109Phe	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	200	47	NM_001097620	0	0	0	0	0	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	37	CCDS43537.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153532	0.78114	.	.	ENSG00000164855	ENST00000297477;ENST00000319010;ENST00000414730;ENST00000441933;ENST00000431208	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.15	5.15	0.70609	.	0.000000	0.64402	U	0.000001	T	0.52677	0.1749	M	0.70787	2.145	0.80722	D	1	P	0.36599	0.56	B	0.41813	0.367	T	0.56450	-0.7977	10	0.51188	T	0.08	-14.3095	12.9955	0.58644	0.0782:0.0:0.9218:0.0	.	109	Q6ZMB5	T184A_HUMAN	F	109	ENSP00000297477:L109F;ENSP00000325945:L109F;ENSP00000398382:L109F;ENSP00000389092:L109F;ENSP00000403499:L109F	ENSP00000297477:L109F	L	-	1	0	TMEM184A	1557039	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.819000	0.86621	2.396000	0.81511	0.407000	0.27541	CTC	.		0.632	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		A	1590513	G	A	1590513	3	1	48	1	0	0	0	0	1	0	0	0	16136	1000	35	2	944	2	TMEM184A	7	1590513	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		1590513	157548150	53	4383											
TWISTNB	221830	hgsc.bcm.edu	37	chr7	19738026	19738026	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcactgtgttttcttttcttTtttttctttttatggtcact	3	27	4	7	0	5	0	2	0	3	0	5	0	5	0	0	1	0	1	0	1	1	11			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:19738026T>C	ENST00000222567.5	-	4	1000	c.930A>G	c.(928-930)aaA>aaG	p.K310K		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	310	Lys-rich.				transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						TTCTTTTCTTTTTTTTCTTTT	0.373																																					p.K310K		.											.	TWISTNB-91	0			c.A930G						.						106	118	114					7																	19738026		2199	4298	6497	SO:0001819	synonymous_variant	221830	exon4			TTTCTTTTTTTTC	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.930A>G	7.37:g.19738026T>C		Somatic	451	0		WXS	Illumina HiSeq	Phase_I	73	5	NM_001002926	0	0	12	12	0	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																			.		0.373	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			C	19738026	T	C	19738026	2	2	48	1	0	0	0	0	0	0	0	1	16817	1838	64	3		3	TWISTNB	7	19738026	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	18147513	19738026	139400637	54	4384											
UPK3B	80761	hgsc.bcm.edu	37	chr7	76141063	76141063	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactacatgacgctgcccCtgtctccggaccagctgccc	6	7	9	19	2	1	1	0	1	1	0	2	2	1	2	6	1	4	2	6	1	1	1	rs144200247		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:76141063C>G	ENST00000257632.5	+	2	618	c.490C>G	c.(490-492)Ctg>Gtg	p.L164V	UPK3B_ENST00000443097.2_Missense_Mutation_p.L109V|UPK3B_ENST00000334348.3_Missense_Mutation_p.L109V|UPK3B_ENST00000394849.1_Missense_Mutation_p.L109V|UPK3B_ENST00000419923.2_Missense_Mutation_p.L164V|UPK3B_ENST00000448265.3_Missense_Mutation_p.L164V			Q9BT76	UPK3B_HUMAN	uroplakin 3B	164					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L164V(1)		breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				GACGCTGCCCCTGTCTCCGGA	0.697																																					p.L164V		.											.	UPK3B-90	1	Substitution - Missense(1)	skin(1)	c.C490G						.						21	20	20					7																	76141063		2203	4299	6502	SO:0001583	missense	80761	exon2			CTGCCCCTGTCTC	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"uroplakin IIIb"	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.490C>G	7.37:g.76141063C>G	ENSP00000257632:p.Leu164Val	Somatic	19	1		WXS	Illumina HiSeq	Phase_I	25	2	NM_030570	0	0	0	3	3	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	37	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	10.24	1.296352	0.23650	.	.	ENSG00000243566	ENST00000334348;ENST00000419923;ENST00000448265;ENST00000443097;ENST00000257632;ENST00000394849	T;T;T;T;T;T	0.54866	0.55;1.46;1.46;0.55;1.46;1.46	5.23	-0.358	0.12575	.	0.561141	0.16477	N	0.212696	T	0.29556	0.0737	N	0.20986	0.625	0.23747	N	0.996959	P;P;B	0.37731	0.607;0.607;0.211	B;B;B	0.37650	0.187;0.255;0.081	T	0.10359	-1.0633	10	0.30078	T	0.28	-1.9253	1.7196	0.02908	0.156:0.3644:0.305:0.1747	.	109;164;109	Q9BT76-2;Q9BT76;A6NHH5	.;UPK3B_HUMAN;.	V	109;164;164;109;164;109	ENSP00000334938:L109V;ENSP00000441602:L164V;ENSP00000441284:L164V;ENSP00000444585:L109V;ENSP00000257632:L164V;ENSP00000378319:L109V	ENSP00000257632:L164V	L	+	1	2	UPK3B	75978999	0.955000	0.32602	0.996000	0.52242	0.165000	0.22458	0.149000	0.16243	-0.064000	0.13043	0.467000	0.42956	CTG	C|0.500;G|0.500		0.697	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		G	76141063	C	G	76141063	3	3	48	1	0	0	0	0	1	0	0	0	17044	680	24	4	496	4	UPK3B	7	76141063	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	56403037	76141063	82997600	55	4385											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu	37	chr7	82763635	82763635	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcttgcattcagtgcaagtAttgaagttaggaggatcctt	10	15	10	6	0	2	1	1	1	1	0	3	3	3	3	1	2	2	4	1	2	4	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:82763635A>G	ENST00000333891.9	-	3	3568	c.3231T>C	c.(3229-3231)aaT>aaC	p.N1077N	PCLO_ENST00000423517.2_Silent_p.N1077N	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CAGTGCAAGTATTGAAGTTAG	0.368																																					p.N1077N		.											.	PCLO-29	0			c.T3231C						.						50	46	47					7																	82763635		1862	4102	5964	SO:0001819	synonymous_variant	27445	exon3			GCAAGTATTGAAG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3231T>C	7.37:g.82763635A>G		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	51	12	NM_014510	0	0	0	0	0		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			.		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82763635	A	G	82763635	2	3	48	1	0	0	0	0	0	0	0	1	11609	446	16	3		3	PCLO	7	82763635	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08	6622572	82763635	76375028	56	4386											
TFR2	7036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100228607	100228607	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccgcagtcgtggcccggggCccaggtgataaggggagcct	6	5	18	12	3	0	1	0	1	0	0	1	2	0	2	4	6	1	1	4	6	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:100228607C>T	ENST00000462107.1	-	10	1462	c.1175G>A	c.(1174-1176)gGc>gAc	p.G392D	TFR2_ENST00000544242.1_5'UTR|TFR2_ENST00000431692.1_Silent_p.G306G|TFR2_ENST00000223051.3_Missense_Mutation_p.G392D			Q9UP52	TFR2_HUMAN	transferrin receptor 2	392					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	TGGCCCGGGGCCCAGGTGATA	0.612																																					p.G392D		.											.	TFR2-92	0			c.G1175A						.						35	34	35					7																	100228607		2203	4300	6503	SO:0001583	missense	7036	exon9			CCGGGGCCCAGGT	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1175G>A	7.37:g.100228607C>T	ENSP00000420525:p.Gly392Asp	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	83	23	NM_003227	0	0	0	1	1	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	37	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.012638	0.75161	.	.	ENSG00000106327	ENST00000223051;ENST00000462107	T;T	0.52983	0.64;0.64	4.74	4.74	0.60224	.	0.144170	0.45867	D	0.000322	T	0.70684	0.3252	M	0.91768	3.24	0.80722	D	1	D	0.69078	0.997	D	0.64042	0.921	T	0.73943	-0.3823	10	0.34782	T	0.22	-26.2357	13.0917	0.59169	0.0:1.0:0.0:0.0	.	392	Q9UP52	TFR2_HUMAN	D	392	ENSP00000223051:G392D;ENSP00000420525:G392D	ENSP00000223051:G392D	G	-	2	0	TFR2	100066543	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	1.935000	0.40173	2.470000	0.83445	0.561000	0.74099	GGC	.		0.612	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		T	100228607	C	T	100228607	3	4	48	1	0	0	0	0	1	0	0	0	15843	739	26	2	1270	2	TFR2	7	100228607	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	17464972	100228607	58910056	57	4387											
CHRM2	1129	hgsc.bcm.edu	37	chr7	136699700	136699700	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggtgtttattgtcctggtgGctggatccctcagtttggtg	3	17	14	7	0	1	0	1	0	0	0	3	1	3	1	2	5	0	3	2	5	1	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:136699700G>C	ENST00000445907.2	+	3	616	c.88G>C	c.(88-90)Gct>Cct	p.A30P	hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.A30P|CHRM2_ENST00000397608.3_Missense_Mutation_p.A30P|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.A30P|CHRM2_ENST00000453373.1_Missense_Mutation_p.A30P|hsa-mir-490_ENST00000598184.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.A30P|hsa-mir-490_ENST00000439694.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	30					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TGTCCTGGTGGCTGGATCCCT	0.413																																					p.A30P		.											.	CHRM2-94	0			c.G88C						.						133	124	127					7																	136699700		2203	4300	6503	SO:0001583	missense	1129	exon3			CTGGTGGCTGGAT		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.88G>C	7.37:g.136699700G>C	ENSP00000399745:p.Ala30Pro	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_001006632	0	0	0	0	0	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344116	0.82022	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.48714	0.1515	L	0.58810	1.83	0.80722	D	1	D	0.54047	0.964	P	0.50791	0.65	T	0.51474	-0.8701	10	0.62326	D	0.03	-7.9379	18.8324	0.92145	0.0:0.0:1.0:0.0	.	30	P08172	ACM2_HUMAN	P	30	ENSP00000399745:A30P;ENSP00000415386:A30P;ENSP00000319984:A30P;ENSP00000380733:A30P;ENSP00000384937:A30P;ENSP00000384401:A30P	ENSP00000319984:A30P	A	+	1	0	CHRM2	136350240	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.964000	0.87933	2.445000	0.82738	0.585000	0.79938	GCT	.		0.413	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			C	136699700	G	C	136699700	3	2	48	1	0	0	0	0	1	0	0	0	3383	1203	42	4	90	4	CHRM2	7	136699700	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	36471093	136699700	22438963	58	4388											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151882674	151882674	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctctttcttgtgagcttgctTttctccacaatttggcaatt	6	19	6	10	0	3	1	0	1	3	0	4	1	3	1	1	1	2	3	1	1	2	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:151882674T>G	ENST00000262189.6	-	34	5269	c.5051A>C	c.(5050-5052)aAa>aCa	p.K1684T	KMT2C_ENST00000355193.2_Missense_Mutation_p.K1684T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1684					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGAGCTTGCTTTTCTCCACAA	0.343																																					p.K1684T		.											.	MLL3-1398	0			c.A5051C						.						142	123	130					7																	151882674		2202	4300	6502	SO:0001583	missense	58508	exon34			CTTGCTTTTCTCC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5051A>C	7.37:g.151882674T>G	ENSP00000262189:p.Lys1684Thr	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	131	13	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	17.93	3.508980	0.64410	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.93604	-3.25;-3.25	5.03	5.03	0.67393	High mobility group, HMG1/HMG2 (1);	0.000000	0.49305	D	0.000155	D	0.94496	0.8228	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.94705	0.7887	10	0.51188	T	0.08	.	14.7869	0.69810	0.0:0.0:0.0:1.0	.	1684;745	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	T	1684	ENSP00000262189:K1684T;ENSP00000347325:K1684T	ENSP00000262189:K1684T	K	-	2	0	MLL3	151513607	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.888000	0.87302	1.889000	0.54706	0.523000	0.50628	AAA	.		0.343	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151882674	T	G	151882674	3	3	48	1	0	0	0	0	1	0	0	0	9647	1841	64	5	9788	5	MLL3	7	151882674	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	15182974	151882674	7255989	59	4389											
AGPAT5	55326	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	6614714	6614714	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattttatgagtcaccagaTccagaaagaagaaaaagatt	19	9	8	5	0	1	6	1	1	0	5	2	7	2	6	2	0	0	0	2	0	6	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:6614714T>A	ENST00000285518.6	+	8	1212	c.900T>A	c.(898-900)gaT>gaA	p.D300E		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	300					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		AGTCACCAGATCCAGAAAGAA	0.323																																					p.D300E		.											.	AGPAT5-90	0			c.T900A						.						44	45	45					8																	6614714		2203	4300	6503	SO:0001583	missense	55326	exon8			ACCAGATCCAGAA	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.900T>A	8.37:g.6614714T>A	ENSP00000285518:p.Asp300Glu	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_018361	0	0	2	5	3	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	37	CCDS34796.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.60|19.60	3.858531|3.858531	0.71834|0.71834	.|.	.|.	ENSG00000155189|ENSG00000155189	ENST00000285518|ENST00000518327	T|.	0.62232|.	0.04|.	6.04|6.04	2.42|2.42	0.29668|0.29668	.|.	0.087594|.	0.85682|.	D|.	0.000000|.	T|T	0.62624|0.62624	0.2443|0.2443	M|M	0.72576|0.72576	2.205|2.205	0.53005|0.53005	D|D	0.999968|0.999968	P|.	0.37663|.	0.604|.	B|.	0.34779|.	0.189|.	T|T	0.56932|0.56932	-0.7897|-0.7897	10|5	0.09843|.	T|.	0.71|.	-7.4458|-7.4458	7.7568|7.7568	0.28930|0.28930	0.0:0.3185:0.0:0.6815|0.0:0.3185:0.0:0.6815	.|.	300|.	Q9NUQ2|.	PLCE_HUMAN|.	E|N	300|117	ENSP00000285518:D300E|.	ENSP00000285518:D300E|.	D|I	+|+	3|2	2|0	AGPAT5|AGPAT5	6602122|6602122	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.618000|1.618000	0.36954|0.36954	0.190000|0.190000	0.20209|0.20209	0.459000|0.459000	0.35465|0.35465	GAT|ATC	.		0.323	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		A	6614714	T	A	6614714	3	1	48	1	0	0	0	0	1	0	0	0	390	1432	50	5	930	5	AGPAT5	8	6614714	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08		6614714	139749308	60	4390											
TNKS	8658	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	9413684	9413684	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatccgcccgacaggcccCgatccccggacccggttgac	6	4	13	18	5	0	1	0	1	0	0	2	5	2	3	7	4	0	1	7	4	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:9413684C>G	ENST00000310430.6	+	1	261	c.235C>G	c.(235-237)Cga>Gga	p.R79G	TNKS_ENST00000520408.1_Missense_Mutation_p.R79G|TNKS_ENST00000522110.1_Missense_Mutation_p.R79G|RP11-375N15.2_ENST00000607598.1_RNA	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	79					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)	p.R79*(2)		NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		CGACAGGCCCCGATCCCCGGA	0.701																																					p.R79G		.											.	TNKS-660	2	Substitution - Nonsense(2)	large_intestine(2)	c.C235G						.						23	26	25					8																	9413684		2202	4299	6501	SO:0001583	missense	8658	exon1			AGGCCCCGATCCC	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.235C>G	8.37:g.9413684C>G	ENSP00000311579:p.Arg79Gly	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	103	27	NM_003747	0	0	0	0	0	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	37	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	C	13.78	2.337846	0.41398	.	.	ENSG00000173273	ENST00000520408;ENST00000310430;ENST00000522110	T;T	0.62788	0.0;0.05	4.84	2.01	0.26516	.	0.123149	0.33457	N	0.004900	T	0.41096	0.1144	N	0.19112	0.55	0.26334	N	0.977462	B;B	0.17038	0.006;0.02	B;B	0.12837	0.008;0.008	T	0.28618	-1.0038	10	0.51188	T	0.08	.	5.6253	0.17478	0.3245:0.5507:0.0:0.1248	.	79;79	E7EWY6;O95271	.;TNKS1_HUMAN	G	79	ENSP00000428299:R79G;ENSP00000311579:R79G	ENSP00000311579:R79G	R	+	1	2	TNKS	9451094	0.020000	0.18652	0.999000	0.59377	0.985000	0.73830	0.272000	0.18644	0.719000	0.32188	-0.169000	0.13324	CGA	.		0.701	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		G	9413684	C	G	9413684	3	3	48	1	0	0	0	0	1	0	0	0	16351	644	23	4	237	4	TNKS	8	9413684	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	2798970	9413684	136950338	61	4391											
KIAA1967	57805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	22464154	22464154	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgggtcttcactggtattgTtaccagcttgcatgactact	7	14	10	10	1	2	1	1	1	1	0	2	1	2	1	1	2	4	4	1	2	3	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:22464154T>A	ENST00000308511.4	+	4	434	c.185T>A	c.(184-186)gTt>gAt	p.V62D	CCAR2_ENST00000521301.1_Missense_Mutation_p.V62D|CCAR2_ENST00000389279.3_Missense_Mutation_p.V62D|CCAR2_ENST00000520861.1_5'Flank			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	62					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										ACTGGTATTGTTACCAGCTTG	0.463																																					p.V62D		.											.	KIAA1967-92	0			c.T185A						.						154	131	139					8																	22464154		2203	4300	6503	SO:0001583	missense	57805	exon4			GTATTGTTACCAG	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.185T>A	8.37:g.22464154T>A	ENSP00000310670:p.Val62Asp	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	159	51	NM_021174	0	0	6	7	1	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.9|24.9	4.584955|4.584955	0.86748|0.86748	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000523801;ENST00000518989|ENST00000308511;ENST00000521301;ENST00000389279;ENST00000521837;ENST00000523349	.|T;T	.|0.61040	.|0.14;0.14	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	.|T	.|0.76905	.|0.4053	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	.|T	.|0.80108	.|-0.1520	.|10	.|0.87932	.|D	.|0	-21.0092|-21.0092	14.0962|14.0962	0.65023|0.65023	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|62	.|Q8N163	.|K1967_HUMAN	X|D	69;14|62	.|ENSP00000310670:V62D;ENSP00000373930:V62D	.|ENSP00000310670:V62D	C|V	+|+	3|2	2|0	KIAA1967|KIAA1967	22520099|22520099	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	6.291000|6.291000	0.72719|0.72719	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TGT|GTT	.		0.463	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		A	22464154	T	A	22464154	3	1	48	1	0	0	0	0	1	0	0	0	8286	1725	60	5	195	5	KIAA1967	8	22464154	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	13050470	22464154	123899868	62	4392											
ZNF703	80139	hgsc.bcm.edu	37	chr8	37555597	37555597	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggcgcctcgcacctcggcgGctccagctgctccacctgca	4	6	11	20	5	0	0	0	0	0	0	4	0	2	0	5	3	3	5	5	3	0	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:37555597G>A	ENST00000331569.4	+	2	1407	c.1178G>A	c.(1177-1179)gGc>gAc	p.G393D		NM_025069.1	NP_079345.1	Q9H7S9	ZN703_HUMAN	zinc finger protein 703	393	Gly-rich.				adherens junction assembly (GO:0034333)|cellular response to estradiol stimulus (GO:0071392)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)		FGFR1/ZNF703(2)	breast(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)	7			BRCA - Breast invasive adenocarcinoma(5;7.93e-25)|LUSC - Lung squamous cell carcinoma(8;1.05e-09)			CACCTCGGCGGCTCCAGCTGC	0.736																																					p.G393D		.											.	ZNF703-523	0			c.G1178A						.						4	5	4					8																	37555597		1919	4041	5960	SO:0001583	missense	80139	exon2			TCGGCGGCTCCAG	AK024361	CCDS6094.1	8p12	2008-05-02				ENSG00000183779			25883	protein-coding gene	gene with protein product						15897872	Standard	NM_025069		Approved	FLJ14299, ZNF503L	uc003xjy.1	Q9H7S9		ENST00000331569.4:c.1178G>A	8.37:g.37555597G>A	ENSP00000332325:p.Gly393Asp	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	14	5	NM_025069	0	0	2	2	0	Q5XG76	Missense_Mutation	SNP	ENST00000331569.4	37	CCDS6094.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.586864	0.66105	.	.	ENSG00000183779	ENST00000331569	T	0.50277	0.75	4.36	4.36	0.52297	.	0.117667	0.56097	D	0.000023	T	0.60353	0.2262	M	0.62723	1.935	0.49483	D	0.999794	D	0.69078	0.997	P	0.60682	0.878	T	0.64228	-0.6457	10	0.66056	D	0.02	-15.3273	11.8916	0.52633	0.0:0.3359:0.6641:0.0	.	393	Q9H7S9	ZN703_HUMAN	D	393	ENSP00000332325:G393D	ENSP00000332325:G393D	G	+	2	0	ZNF703	37674755	1.000000	0.71417	0.997000	0.53966	0.922000	0.55478	4.127000	0.57944	1.980000	0.57719	0.462000	0.41574	GGC	.		0.736	ZNF703-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376683.2	NM_025069		A	37555597	G	A	37555597	3	1	48	1	0	0	0	0	1	0	0	0	18138	1203	42	2	1184	2	ZNF703	8	37555597	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	15091443	37555597	108808425	63	4393											
WWP1	11059	hgsc.bcm.edu	37	chr8	87460473	87460473	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctattaaggatttggaatctAttgatactgaattttataac	14	17	6	4	0	1	2	0	2	1	0	1	4	1	4	0	2	2	0	0	2	8	9			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:87460473A>G	ENST00000517970.1	+	19	2402	c.2095A>G	c.(2095-2097)Att>Gtt	p.I699V	WWP1_ENST00000349423.2_Missense_Mutation_p.I481V|WWP1_ENST00000265428.4_Missense_Mutation_p.I699V|WWP1_ENST00000341922.2_Missense_Mutation_p.I569V	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	699	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TTTGGAATCTATTGATACTGA	0.294																																					p.I699V		.											.	WWP1-659	0			c.A2095G						.						45	47	47					8																	87460473		2193	4277	6470	SO:0001583	missense	11059	exon19			GAATCTATTGATA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.2095A>G	8.37:g.87460473A>G	ENSP00000427793:p.Ile699Val	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_007013	0	0	14	14	0	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.202|7.202	0.593727|0.593727	0.13875|0.13875	.|.	.|.	ENSG00000123124|ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423|ENST00000520453	T;T;T;T|.	0.58210|.	0.35;0.35;0.35;0.35|.	5.5|5.5	5.5|5.5	0.81552|0.81552	HECT (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.34890|0.34890	0.0913|0.0913	N|N	0.03238|0.03238	-0.38|-0.38	0.80722|0.80722	D|D	1|1	B;B|.	0.14805|.	0.0;0.011|.	B;B|.	0.17722|.	0.001;0.019|.	T|T	0.32613|0.32613	-0.9900|-0.9900	10|5	0.02654|.	T|.	1|.	.|.	15.6043|15.6043	0.76649|0.76649	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	481;699|.	Q9H0M0-6;Q9H0M0|.	.;WWP1_HUMAN|.	V|C	699;699;569;481|199	ENSP00000427793:I699V;ENSP00000265428:I699V;ENSP00000340564:I569V;ENSP00000342665:I481V|.	ENSP00000265428:I699V|.	I|Y	+|+	1|2	0|0	WWP1|WWP1	87529589|87529589	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.998000|0.998000	0.95712|0.95712	7.469000|7.469000	0.80959|0.80959	2.095000|2.095000	0.63458|0.63458	0.533000|0.533000	0.62120|0.62120	ATT|TAT	.		0.294	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		G	87460473	A	G	87460473	3	3	48	1	0	0	0	0	1	0	0	0	17448	449	16	3	2161	3	WWP1	8	87460473	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	49904876	87460473	58903549	64	4394											
MTDH	92140	hgsc.bcm.edu	37	chr8	98657042	98657042	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgcggcccccgacgaccTggccttgctgaagaatctcc	6	6	12	17	4	1	2	0	1	1	1	2	4	1	2	6	3	1	1	6	3	2	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:98657042T>C	ENST00000336273.3	+	1	636	c.308T>C	c.(307-309)cTg>cCg	p.L103P	MTDH_ENST00000519934.1_Missense_Mutation_p.L80P	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	103	Interaction with BCCIP.|Interaction with RELA.				lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			cccgACGACCTGGCCTTGCTG	0.677																																					p.L103P		.											.	MTDH-91	0			c.T308C						.						7	8	8					8																	98657042		1857	3786	5643	SO:0001583	missense	92140	exon1			ACGACCTGGCCTT	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"astrocyte elevated gene 1"	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.308T>C	8.37:g.98657042T>C	ENSP00000338235:p.Leu103Pro	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_178812	0	0	2	2	0	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Missense_Mutation	SNP	ENST00000336273.3	37	CCDS6274.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.560|8.560	0.877643|0.877643	0.17395|0.17395	.|.	.|.	ENSG00000147649|ENSG00000147649	ENST00000336273;ENST00000519934|ENST00000522313	T;T|.	0.08634|.	3.07;3.07|.	4.82|4.82	-6.07|-6.07	0.02158|0.02158	.|.	1.663720|.	0.03201|.	N|.	0.174788|.	T|T	0.13329|0.13329	0.0323|0.0323	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999992|0.999992	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.28004|0.28004	-1.0057|-1.0057	10|5	0.34782|.	T|.	0.22|.	6.3514|6.3514	4.9943|4.9943	0.14230|0.14230	0.1221:0.5219:0.1257:0.2303|0.1221:0.5219:0.1257:0.2303	.|.	103|.	Q86UE4|.	LYRIC_HUMAN|.	P|R	103;80|8	ENSP00000338235:L103P;ENSP00000428168:L80P|.	ENSP00000338235:L103P|.	L|W	+|+	2|1	0|0	MTDH|MTDH	98726218|98726218	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.630000|0.630000	0.37929|0.37929	-0.690000|-0.690000	0.05138|0.05138	-0.831000|-0.831000	0.04256|0.04256	0.482000|0.482000	0.46254|0.46254	CTG|TGG	.		0.677	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2			C	98657042	T	C	98657042	3	2	48	1	0	0	0	0	1	0	0	0	9942	1580	55	3	310	3	MTDH	8	98657042	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	11196569	98657042	47706980	65	4395											
KCNS2	3788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	99441267	99441267	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctacaccattgaaaaggagGagaacgagggcctggccacc	13	4	12	12	1	0	2	0	1	0	1	0	5	0	3	5	4	2	0	5	4	4	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:99441267G>T	ENST00000287042.4	+	2	1410	c.1060G>T	c.(1060-1062)Gag>Tag	p.E354*	KCNS2_ENST00000521839.1_Nonsense_Mutation_p.E354*	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	354					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TGAAAAGGAGGAGAACGAGGG	0.577																																					p.E354X	Pancreas(138;844 2489 9202 24627)	.											.	KCNS2-91	0			c.G1060T						.						89	80	83					8																	99441267		2203	4300	6503	SO:0001587	stop_gained	3788	exon2			AAGGAGGAGAACG	AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.1060G>T	8.37:g.99441267G>T	ENSP00000287042:p.Glu354*	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	202	51	NM_020697	0	0	0	0	0	A8KAN1	Nonsense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	G	40	8.203350	0.98704	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	.	.	.	5.91	5.91	0.95273	.	0.158483	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	.	.	.	X	354	.	ENSP00000287042:E354X	E	+	1	0	KCNS2	99510443	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	9.869000	0.99810	2.808000	0.96608	0.655000	0.94253	GAG	.		0.577	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		T	99441267	G	T	99441267	4	4	48	1	0	0	0	0	0	1	0	0	8110	1175	41	4	1062	4	KCNS2	8	99441267	Nonsense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	784225	99441267	46922755	66	4396											
FAM135B	51059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	139164000	139164000	+	Silent	SNP	G	G	T																															acattcaagtctttaggcatGccctttggggtttcctcaag																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:139164000G>T	ENST00000395297.1	-	13	2888	c.2718C>A	c.(2716-2718)ggC>ggA	p.G906G		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	906										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CTTTAGGCATGCCCTTTGGGG	0.458										HNSCC(54;0.14)																											p.G906G		.											.	FAM135B-31	0			c.C2718A						.						128	126	127					8																	139164000		2203	4300	6503	SO:0001819	synonymous_variant	51059	exon13			AGGCATGCCCTTT	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.2718C>A	8.37:g.139164000G>T		Somatic	307	0		WXS	Illumina HiSeq	Phase_I	335	98	NM_015912	0	0	0	0	0	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			.		0.458	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139164000	G	T	139164000	2	4	48	1	0	0	0	0	0	0	0	1	5465	1306	46	4		4	FAM135B	8	139164000	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	39722733	139164000	7200022	67	4397	49	2									
FAM135B	51059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	139164004	139164004	+	Missense_Mutation	SNP	T	T	C																															tcaagtctttaggcatgcccTttggggtttcctcaagtgct																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:139164004T>C	ENST00000395297.1	-	13	2884	c.2714A>G	c.(2713-2715)aAg>aGg	p.K905R		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	905										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AGGCATGCCCTTTGGGGTTTC	0.468										HNSCC(54;0.14)																											p.K905R		.											.	FAM135B-31	0			c.A2714G						.						125	124	124					8																	139164004		2203	4300	6503	SO:0001583	missense	51059	exon13			ATGCCCTTTGGGG	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.2714A>G	8.37:g.139164004T>C	ENSP00000378710:p.Lys905Arg	Somatic	310	0		WXS	Illumina HiSeq	Phase_I	338	94	NM_015912	0	0	0	0	0	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	T	15.06	2.721538	0.48728	.	.	ENSG00000147724	ENST00000395297	T	0.16597	2.33	5.33	4.15	0.48705	.	0.392353	0.28031	N	0.016877	T	0.19127	0.0459	L	0.32530	0.975	0.09310	N	1	P;P;B	0.51351	0.944;0.728;0.164	P;B;B	0.50617	0.646;0.343;0.04	T	0.04017	-1.0984	10	0.46703	T	0.11	-11.8381	9.5929	0.39557	0.1559:0.0:0.0:0.8441	.	905;905;905	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	R	905	ENSP00000378710:K905R	ENSP00000276737:K905R	K	-	2	0	FAM135B	139233186	0.652000	0.27349	0.013000	0.15412	0.286000	0.27126	4.148000	0.58085	0.833000	0.34828	0.533000	0.62120	AAG	.		0.468	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139164004	T	C	139164004	3	2	48	1	0	0	0	0	1	0	0	0	5465	1609	56	3	1538	3	FAM135B	8	139164004	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	4	139164004	7200018	68	4398	49	2									
UNC13B	10497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35375163	35375163	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcaggaatcacttctgcaAtggctacacgcacttctctt	10	11	8	12	1	3	0	1	0	2	0	4	1	3	1	0	3	2	4	0	3	3	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr9:35375163A>G	ENST00000378495.3	+	13	1555	c.1333A>G	c.(1333-1335)Atg>Gtg	p.M445V	UNC13B_ENST00000396787.1_Missense_Mutation_p.M457V|UNC13B_ENST00000378496.4_Missense_Mutation_p.M445V	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	445					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CACTTCTGCAATGGCTACACG	0.537																																					p.M445V		.											.	UNC13B-157	0			c.A1333G						.						240	213	222					9																	35375163		2203	4300	6503	SO:0001583	missense	10497	exon13			TCTGCAATGGCTA	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.1333A>G	9.37:g.35375163A>G	ENSP00000367756:p.Met445Val	Somatic	447	1		WXS	Illumina HiSeq	Phase_I	369	223	NM_006377	0	0	0	0	0	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.903474	0.33628	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.61040	0.14;0.14;0.14	5.81	3.16	0.36331	.	0.084309	0.85682	D	0.000000	T	0.40932	0.1137	L	0.28504	0.86	0.45295	D	0.998291	B;B	0.23806	0.091;0.03	B;B	0.24006	0.05;0.019	T	0.17228	-1.0376	10	0.26408	T	0.33	-19.0987	8.125	0.30992	0.6561:0.1107:0.0:0.2332	.	445;445	F8W8M9;O14795	.;UN13B_HUMAN	V	457;445;445;32	ENSP00000380006:M457V;ENSP00000367756:M445V;ENSP00000367757:M445V	ENSP00000367756:M445V	M	+	1	0	UNC13B	35365163	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.969000	0.56816	1.010000	0.39314	0.482000	0.46254	ATG	.		0.537	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		G	35375163	A	G	35375163	3	3	48	1	0	0	0	0	1	0	0	0	17018	101	4	3	1383	3	UNC13B	9	35375163	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08		35375163	105838268	69	4399											
TNC	3371	broad.mit.edu;bcgsc.ca	37	chr9	117792668	117792668	+	Frame_Shift_Del	DEL	G	G	-																															tgggagcagtccttggggaaGgggtacaggagtccaactgt																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr9:117792668delG	ENST00000350763.4	-	24	6348	c.5937delC	c.(5935-5937)cccfs	p.P1979fs	TNC_ENST00000345230.3_Frame_Shift_Del_p.P1342fs|TNC_ENST00000535648.1_Frame_Shift_Del_p.P1524fs|TNC_ENST00000346706.3_Frame_Shift_Del_p.P1433fs|TNC_ENST00000341037.4_Frame_Shift_Del_p.P1797fs|TNC_ENST00000340094.3_Frame_Shift_Del_p.P1615fs|TNC_ENST00000423613.2_Frame_Shift_Del_p.P1706fs|TNC_ENST00000537320.1_Frame_Shift_Del_p.P1342fs|TNC_ENST00000542877.1_Frame_Shift_Del_p.P1616fs	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1979	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCTTGGGGAAGGGGTACAGGA	0.498																																					p.P1979fs													.	TNC-517	0			c.5937delC						.						93	77	83					9																	117792668		2203	4300	6503	SO:0001589	frameshift_variant	3371	exon24			GGGGAAGGGGTAC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5937delC	9.37:g.117792668delG	ENSP00000265131:p.Pro1979fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	29	14	NM_002160	0	0	0	0	0	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Frame_Shift_Del	DEL	ENST00000350763.4	37	CCDS6811.1																																																																																			.		0.498	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		-	117792668	G	-	117792668	7	5	48	1	0	1	0	1	0	0	0	0	16302	987	35	0	688	0	TNC	9	117792668	Frame_Shift_Del	DEL	G	TCGA-B9-4114-01A-01D-1252-08	82417505	117792668	23420763	70	4400											
ABL1	25	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	133748371	133748371	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgctgctgtacatggcCactcagatctcgtcagccat	7	11	11	12	1	3	1	2	0	1	1	4	1	3	1	2	2	4	3	2	2	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr9:133748371C>T	ENST00000318560.5	+	6	1413	c.1032C>T	c.(1030-1032)gcC>gcT	p.A344A		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	344	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TGTACATGGCCACTCAGATCT	0.577			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.A363A		.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1-3810	0			c.C1089T						.						73	59	64					9																	133748371		2203	4300	6503	SO:0001819	synonymous_variant	25	exon6			CATGGCCACTCAG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1032C>T	9.37:g.133748371C>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	143	90	NM_007313	0	0	1	1	0	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.		0.577	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133748371	C	T	133748371	2	4	48	1	0	0	0	0	0	0	0	1	92	581	21	2		2	ABL1	9	133748371	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	15955703	133748371	7465060	71	4401											
BMS1	9790	ucsc.edu	37	chr10	43315737	43315737	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagccagagttcagtatgaGggttttcgacctgggatgta	10	11	14	6	1	1	2	1	1	0	1	2	5	1	3	2	2	1	4	2	2	3	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr10:43315737G>T	ENST00000374518.5	+	16	2697	c.2634G>T	c.(2632-2634)gaG>gaT	p.E878D		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	878					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTCAGTATGAGGGTTTTCGAC	0.433																																					p.E878D													.	BMS1-93	0			c.G2634T						.						120	118	118					10																	43315737		2203	4300	6503	SO:0001583	missense	9790	exon16			GTATGAGGGTTTT	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2634G>T	10.37:g.43315737G>T	ENSP00000363642:p.Glu878Asp	Somatic	254	2		WXS	Illumina HiSeq		197	2	NM_014753	0	0	33	52	19	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.115516	0.77323	.	.	ENSG00000165733	ENST00000374518	T	0.17854	2.25	5.05	-4.55	0.03441	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.38506	0.1043	M	0.92122	3.275	0.47778	D	0.999516	D	0.53462	0.96	P	0.58077	0.832	T	0.53995	-0.8359	10	0.39692	T	0.17	.	13.1374	0.59417	0.6341:0.0:0.3659:0.0	.	878	Q14692	BMS1_HUMAN	D	878	ENSP00000363642:E878D	ENSP00000363642:E878D	E	+	3	2	BMS1	42635743	0.998000	0.40836	0.969000	0.41365	0.964000	0.63967	0.474000	0.22148	-0.725000	0.04901	-0.396000	0.06452	GAG	.		0.433	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		T	43315737	G	T	43315737	3	4	48	1	0	0	0	0	1	0	0	0	1473	991	35	4	2692	4	BMS1	10	43315737	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		43315737	92219010	72	4402											
NODAL	4838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	72195424	72195424	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaccctggacatctgcttcTccagggccccagggtgcttc	5	10	10	16	0	2	0	0	0	2	0	4	1	2	1	4	3	3	2	4	3	1	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr10:72195424T>A	ENST00000287139.3	-	2	508	c.509A>T	c.(508-510)gAg>gTg	p.E170V	AC022532.1_ENST00000420338.2_Missense_Mutation_p.L124H	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	170					axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						CATCTGCTTCTCCAGGGCCCC	0.602																																					p.E170V		.											.	NODAL-289	0			c.A509T						.						37	37	37					10																	72195424		2203	4300	6503	SO:0001583	missense	4838	exon2			TGCTTCTCCAGGG	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"nodal, mouse, homolog", "nodal homolog (mouse)"			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.509A>T	10.37:g.72195424T>A	ENSP00000287139:p.Glu170Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	122	38	NM_018055	0	0	0	0	0	Q2M3A5|Q8N4V3	Missense_Mutation	SNP	ENST00000287139.3	37	CCDS7304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.27|14.27	2.486027|2.486027	0.44147|0.44147	.|.	.|.	ENSG00000156574|ENSG00000197604	ENST00000287139;ENST00000414871|ENST00000420338	D;D|.	0.85339|.	-1.97;-1.94|.	5.99|5.99	1.14|1.14	0.20703|0.20703	.|.	0.737242|.	0.13941|.	N|.	0.352164|.	T|T	0.39306|0.39306	0.1073|0.1073	L|L	0.56769|0.56769	1.78|1.78	0.28250|0.28250	N|N	0.925313|0.925313	B|.	0.17268|.	0.021|.	B|.	0.22880|.	0.042|.	T|T	0.46233|0.46233	-0.9206|-0.9206	10|6	0.31617|0.87932	T|D	0.26|0	.|.	1.0685|1.0685	0.01616|0.01616	0.1347:0.2379:0.2788:0.3486|0.1347:0.2379:0.2788:0.3486	.|.	170|.	Q96S42|.	NODAL_HUMAN|.	V|H	170;115|124	ENSP00000287139:E170V;ENSP00000394468:E115V|.	ENSP00000287139:E170V|ENSP00000411125:L124H	E|L	-|+	2|2	0|0	NODAL|AC022532.1	71865430|71865430	0.001000|0.001000	0.12720|0.12720	0.956000|0.956000	0.39512|0.39512	0.792000|0.792000	0.44763|0.44763	0.801000|0.801000	0.27055|0.27055	0.162000|0.162000	0.19483|0.19483	0.533000|0.533000	0.62120|0.62120	GAG|CTC	.		0.602	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055		A	72195424	T	A	72195424	3	1	48	1	0	0	0	0	1	0	0	0	10544	1551	54	5	542	5	NODAL	10	72195424	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	28879687	72195424	63339323	73	4403											
NOLC1	9221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103917239	103917239	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggaaggctgcagccaaagCatcagagagtagcagcagtg	13	5	15	8	0	1	1	1	0	0	1	1	3	1	2	1	2	5	6	1	2	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr10:103917239C>T	ENST00000605788.1	+	4	603	c.368C>T	c.(367-369)gCa>gTa	p.A123V	NOLC1_ENST00000603742.1_5'UTR|NOLC1_ENST00000405356.1_Missense_Mutation_p.A123V|NOLC1_ENST00000488254.2_Missense_Mutation_p.A124V	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	123	11 X 12 AA approximate repeats of an acidic serine cluster.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		GCAGCCAAAGCATCAGAGAGT	0.512																																					p.A123V		.											.	NOLC1-91	0			c.C368T						.						68	65	66					10																	103917239		2203	4300	6503	SO:0001583	missense	9221	exon4			CCAAAGCATCAGA	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.368C>T	10.37:g.103917239C>T	ENSP00000474710:p.Ala123Val	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	75	21	NM_004741	0	0	2	2	0	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978454	0.34942	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.43294	0.95	5.52	5.52	0.82312	.	0.307617	0.28589	N	0.014814	T	0.47967	0.1474	M	0.78801	2.425	0.28217	N	0.926698	P;P;P	0.42296	0.775;0.775;0.666	B;B;B	0.42282	0.382;0.382;0.212	T	0.57207	-0.7851	10	0.66056	D	0.02	-13.6615	11.8733	0.52534	0.272:0.728:0.0:0.0	.	124;123;123	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	V	123	ENSP00000385410:A123V	ENSP00000359024:A123V	A	+	2	0	NOLC1	103907229	0.977000	0.34250	0.998000	0.56505	0.422000	0.31414	2.072000	0.41510	2.620000	0.88729	0.655000	0.94253	GCA	.		0.512	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		T	103917239	C	T	103917239	3	4	48	1	0	0	0	0	1	0	0	0	10555	710	25	2	382	2	NOLC1	10	103917239	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	31721815	103917239	31617508	74	4404											
BRSK2	9024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1466623	1466623	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgaccccgacgtgctggaCagcatgcactcactgggctg	8	7	12	14	3	1	0	1	0	0	0	2	3	1	1	2	2	3	4	2	2	0	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:1466623C>T	ENST00000528841.1	+	10	1296	c.912C>T	c.(910-912)gaC>gaT	p.D304D	BRSK2_ENST00000531197.1_Silent_p.D304D|BRSK2_ENST00000308219.9_Silent_p.D304D|BRSK2_ENST00000528710.1_Silent_p.D244D|BRSK2_ENST00000308230.5_Silent_p.D304D|BRSK2_ENST00000526678.1_Silent_p.D304D|BRSK2_ENST00000544817.1_5'UTR|BRSK2_ENST00000382179.1_Silent_p.D350D			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	304	UBA.				actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		ACGTGCTGGACAGCATGCACT	0.667																																					p.D350D		.											.	BRSK2-333	0			c.C1050T						.						34	42	39					11																	1466623		2132	4245	6377	SO:0001819	synonymous_variant	9024	exon10			GCTGGACAGCATG	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.912C>T	11.37:g.1466623C>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	58	24	NM_001256630	0	0	0	0	0	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Silent	SNP	ENST00000528841.1	37	CCDS58107.1																																																																																			.		0.667	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		T	1466623	C	T	1466623	2	4	48	1	0	0	0	0	0	0	0	1	1527	477	17	2		2	BRSK2	11	1466623	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08		1466623	133539893	75	4405											
EIF3M	493860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	32623898	32623898	+	3'UTR	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacttaatgcctggaaacaaAatctgaacaaagtgaaaaac	20	7	6	8	0	1	2	0	2	1	0	1	3	1	3	1	1	4	0	1	1	8	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:32623898A>T	ENST00000335185.5	-	0	3742				EIF3M_ENST00000524896.1_Missense_Mutation_p.N228Y|EIF3M_ENST00000531120.1_Missense_Mutation_p.N360Y	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73											NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					CTGGAAACAAAATCTGAACAA	0.328																																					p.N360Y		.											.	EIF3M-155	0			c.A1078T						.						93	93	93					11																	32623898		2202	4298	6500	SO:0001624	3_prime_UTR_variant	10480	exon11			AAACAAAATCTGA	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.*459T>A	11.37:g.32623898A>T		Somatic	173	0		WXS	Illumina HiSeq	Phase_I	22	10	NM_006360	0	0	223	416	193	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.454889	0.63290	.	.	ENSG00000149100	ENST00000531120;ENST00000524896;ENST00000526267	T;T;T	0.51325	1.26;0.72;0.71	5.7	5.7	0.88788	.	0.042254	0.85682	D	0.000000	T	0.62889	0.2465	M	0.82056	2.57	0.80722	D	1	D;D	0.61697	0.97;0.99	P;P	0.51615	0.675;0.675	T	0.69986	-0.4996	10	0.87932	D	0	-19.1647	15.9644	0.79956	1.0:0.0:0.0:0.0	.	228;360	B4E2Q4;Q7L2H7	.;EIF3M_HUMAN	Y	360;228;213	ENSP00000436049:N360Y;ENSP00000436787:N228Y;ENSP00000432139:N213Y	ENSP00000436787:N228Y	N	+	1	0	EIF3M	32580474	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.302000	0.89953	2.172000	0.68678	0.460000	0.39030	AAT	.		0.328	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		T	32623898	A	T	32623898	1	4	48	0	1	0	0	0	0	0	0	0	5036	14	1	5		5	EIF3M	11	32623898	3'UTR	SNP	A	TCGA-B9-4114-01A-01D-1252-08	31157275	32623898	102382618	76	4406											
DGKZ	8525	hgsc.bcm.edu	37	chr11	46388524	46388524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaccccaggcctggagcGccctgctcgcgtaggtatag	6	6	14	15	4	0	0	0	0	0	0	1	2	0	2	5	4	2	3	5	4	3	3	rs367886121	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:46388524G>A	ENST00000454345.1	+	2	843	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000525434.1_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000318201.8_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000532868.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000343674.6_Intron	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	240					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GGCCTGGAGCGCCCTGCTCGC	0.711													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		15194	0		0	False		,,,				2504	0				p.A240T		.											.	DGKZ-676	0			c.G718A						.	G	THR/ALA,,,,,,	24,3528		0,24,1752	3	3	3		718,,,,,,	-1.2	1	11		3	0,7448		0,0,3724	no	missense,intron,intron,intron,intron,intron,intron	DGKZ	NM_001105540.1,NM_001199266.1,NM_001199267.1,NM_001199268.1,NM_003646.3,NM_201532.2,NM_201533.3	58,,,,,,	0,24,5476	AA,AG,GG		0.0,0.6757,0.2182	benign,,,,,,	240/1118,,,,,,	46388524	24,10976	1776	3724	5500	SO:0001583	missense	8525	exon2			TGGAGCGCCCTGC	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"diacylglycerol kinase, zeta 104kDa"			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.718G>A	11.37:g.46388524G>A	ENSP00000412178:p.Ala240Thr	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	15	10	NM_001105540	0	0	0	0	0	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.533442	0.45073	0.006757	0.0	ENSG00000149091	ENST00000454345	T	0.70631	-0.5	4.59	-1.22	0.09494	.	2.470100	0.01661	N	0.025119	T	0.35770	0.0943	N	0.04959	-0.14	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.51100	-0.8748	9	.	.	.	.	0.8788	0.01230	0.3054:0.2439:0.3075:0.1432	.	240	Q13574	DGKZ_HUMAN	T	240	ENSP00000412178:A240T	.	A	+	1	0	DGKZ	46345100	0.000000	0.05858	0.996000	0.52242	0.973000	0.67179	-1.483000	0.02318	0.096000	0.17463	0.462000	0.41574	GCC	.		0.711	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		A	46388524	G	A	46388524	3	1	48	1	0	0	0	0	1	0	0	0	4485	1087	38	1	1164	1	DGKZ	11	46388524	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	13764626	46388524	88617992	77	4407											
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237625	56237625	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccatgtatctatcaaaggCcatcgcagcaagaataaaaa	17	8	7	9	1	2	1	1	0	1	1	3	1	2	1	2	1	2	3	2	1	8	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:56237625C>G	ENST00000312240.2	-	1	389	c.349G>C	c.(349-351)Gcc>Ccc	p.A117P		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CTATCAAAGGCCATCGCAGCA	0.363																																					p.A117P		.											.	OR5M3-70	0			c.G349C						.						90	85	87					11																	56237625		2200	4295	6495	SO:0001583	missense	219482	exon1			CAAAGGCCATCGC	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.349G>C	11.37:g.56237625C>G	ENSP00000312208:p.Ala117Pro	Somatic	303	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_001004742	0	0	0	0	0	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.828904	0.71258	.	.	ENSG00000174937	ENST00000312240	T	0.56103	0.48	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000255	T	0.79082	0.4386	H	0.97315	3.98	0.38870	D	0.956688	D	0.60575	0.988	P	0.62491	0.903	D	0.86256	0.1652	10	0.87932	D	0	-8.5722	11.2086	0.48784	0.2878:0.7122:0.0:0.0	.	117	Q8NGP4	OR5M3_HUMAN	P	117	ENSP00000312208:A117P	ENSP00000312208:A117P	A	-	1	0	OR5M3	55994201	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	2.409000	0.44583	2.381000	0.81170	0.478000	0.44815	GCC	.		0.363	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		G	56237625	C	G	56237625	3	3	48	1	0	0	0	0	1	0	0	0	11201	739	26	4	576	4	OR5M3	11	56237625	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	9849101	56237625	78768891	78	4408											
TMX2	51075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57480106	57480106	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaaagatggcggtcttggcaCctctaattgctctcgtgtat	9	13	10	9	2	3	1	0	0	3	1	4	1	3	1	1	3	1	3	1	3	4	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:57480106C>A	ENST00000278422.4	+	1	28	c.16C>A	c.(16-18)Cct>Act	p.P6T	TMX2-CTNND1_ENST00000528395.1_Missense_Mutation_p.P6T|TMX2_ENST00000378312.4_Missense_Mutation_p.P6T|MED19_ENST00000337672.2_5'Flank|MED19_ENST00000431606.2_5'Flank	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	6					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						GGTCTTGGCACCTCTAATTGC	0.592																																					p.P6T		.											.	TMX2-90	0			c.C16A						.						70	57	61					11																	57480106		2201	4296	6497	SO:0001583	missense	51075	exon1			TTGGCACCTCTAA	AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"Protein disulfide isomerases"	30739	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 12"		"thioredoxin domain containing 14"	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.16C>A	11.37:g.57480106C>A	ENSP00000278422:p.Pro6Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	76	27	NM_015959	0	0	17	35	18	B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	Missense_Mutation	SNP	ENST00000278422.4	37	CCDS7967.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.651806	0.67472	.	.	ENSG00000213593	ENST00000378312;ENST00000278422	T	0.53857	0.6	5.98	5.98	0.97165	.	0.128810	0.53938	U	0.000057	T	0.64349	0.2590	L	0.43152	1.355	0.58432	D	0.999993	D;D	0.67145	0.996;0.985	P;P	0.58266	0.836;0.756	T	0.63919	-0.6528	10	0.66056	D	0.02	-4.5842	20.0512	0.97629	0.0:1.0:0.0:0.0	.	6;6	Q9Y320-2;Q9Y320	.;TMX2_HUMAN	T	6	ENSP00000367562:P6T	ENSP00000436274:P6T	P	+	1	0	TMX2	57236682	0.999000	0.42202	0.427000	0.26684	0.277000	0.26821	4.548000	0.60718	2.847000	0.97988	0.591000	0.81541	CCT	.		0.592	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959		A	57480106	C	A	57480106	3	1	48	1	0	0	0	0	1	0	0	0	16299	507	18	4	18	4	TMX2	11	57480106	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	1242481	57480106	77526410	79	4409											
FAU	740	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64889268	64889269	+	5'Flank	DNP	GC	GC	TG																															aaggtgtgtagctcctgggcGcggacaaagagctgcatatt																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:64889268_64889269GC>TG	ENST00000279242.2	+	0	0				MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000531743.1_Missense_Mutation_p.R6P|FAU_ENST00000279259.3_Missense_Mutation_p.R6P|FAU_ENST00000529639.1_Missense_Mutation_p.R6P|FAU_ENST00000434372.2_Missense_Mutation_p.R6P|FAU_ENST00000529259.1_Missense_Mutation_p.R6P|MRPL49_ENST00000534078.1_5'Flank|MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000527548.1_Missense_Mutation_p.R6P|FAU_ENST00000525297.1_Missense_Mutation_p.R6P	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						GCTCCTGGGCGCGGACAAAGAG	0.535																																					p.R6P		.											.	FAU	0			c.G17C						.																																			SO:0001631	upstream_gene_variant	2197	exon2			TGGGCGCGGACAA		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608	Exception_encountered	11.37:g.64889268_64889269delinsTG	Exception_encountered	Somatic	112	1		WXS	Illumina HiSeq	Phase_I	153	37		0	0	0	0	0	B2R4G6	Missense_Mutation	DNP	ENST00000279242.2	37	CCDS8096.1																																																																																			.		0.535	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		TG	64889269	GC	TG	64889268	1	4	48	0	1	0	0	0	0	0	0	0	5713	1074	38	4		4	FAU	11	64889268	5'Flank	DNP	GC	TCGA-B9-4114-01A-01D-1252-08	7409162	64889268	70117248	80	4410											
SIK2	23235	hgsc.bcm.edu;broad.mit.edu	37	chr11	111590501	111590501	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctcccctggcgtttaggtCaatggctgtctgcttgaccc	4	13	10	14	1	3	1	1	1	2	0	4	1	3	1	3	3	1	3	3	3	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:111590501C>T	ENST00000304987.3	+	10	1442	c.1269C>T	c.(1267-1269)gtC>gtT	p.V423V	SIK2_ENST00000533868.1_3'UTR	NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	423					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						GCGTTTAGGTCAATGGCTGTC	0.517																																					p.V423V		.											.	SIK2-783	0			c.C1269T						.						45	30	35					11																	111590501		2201	4297	6498	SO:0001819	synonymous_variant	23235	exon10			TTAGGTCAATGGC	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"SNF1-like kinase 2"	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.1269C>T	11.37:g.111590501C>T		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	59	21	NM_015191	0	0	1	1	0	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Silent	SNP	ENST00000304987.3	37	CCDS8347.1																																																																																			.		0.517	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		T	111590501	C	T	111590501	2	4	48	1	0	0	0	0	0	0	0	1	14350	813	29	2		2	SIK2	11	111590501	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	46701233	111590501	23416015	81	4411											
FAM55A	120400	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr11	114401163	114401163	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgccctccagagagccgaCgccccttcactggggtggat	6	8	12	15	2	1	1	1	0	0	1	2	4	2	2	5	3	2	0	5	3	0	2	rs151227911	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:114401163C>T	ENST00000424269.1	-	2	566	c.567G>A	c.(565-567)gcG>gcA	p.A189A	NXPE1_ENST00000251921.2_Silent_p.A47A|NXPE1_ENST00000536312.1_Silent_p.A189A|NXPE1_ENST00000536271.1_5'Flank			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	189						extracellular region (GO:0005576)											AGAGAGCCGACGCCCCTTCAC	0.507													C|||	2	0.000399361	0	0	5008	,	,		20678	0.002		0	False		,,,				2504	0				p.A47A		.											.	.	0			c.G141A						.	C		0,4402		0,0,2201	75	78	77		141	-8	0	11	dbSNP_134	77	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	FAM55A	NM_152315.2		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		47/406	114401163	1,12993	2201	4296	6497	SO:0001819	synonymous_variant	120400	exon3			AGCCGACGCCCCT	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"family with sequence similarity 55, member A"	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.567G>A	11.37:g.114401163C>T		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	103	19	NM_152315	0	0	0	0	0	B0YJ13	Silent	SNP	ENST00000424269.1	37																																																																																				C|0.999;T|0.001		0.507	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315		T	114401163	C	T	114401163	2	4	48	1	0	0	0	0	0	0	0	1	5603	523	19	1		1	FAM55A	11	114401163	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	2810662	114401163	20605353	82	4412											
OAF	220323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	120097580	120097581	+	Missense_Mutation	DNP	AC	AC	CA																															tcggggtctggagcatctgcAcatggatgtcgctgtcaact																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:120097580_120097581AC>CA	ENST00000328965.4	+	3	935_936	c.422_423AC>CA	c.(421-423)cAC>cCA	p.H141P	OAF_ENST00000531220.1_Missense_Mutation_p.H25P	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	141						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		GAGCATCTGCACATGGATGTCG	0.619																																					p.H141P		.											.	OAF	0			c.C423A						.																																			SO:0001583	missense	220323	exon3			TCTGCACATGGAT	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	Exception_encountered	11.37:g.120097580_120097581delinsCA	ENSP00000332613:p.His141Pro	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	183	57		0	0	0	0	0		Missense_Mutation	DNP	ENST00000328965.4	37	CCDS8430.1																																																																																			.		0.619	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507		CA	120097581	AC	CA	120097580	3	2	48	1	0	0	0	0	1	0	0	0	10824	159	6	5	432	5	OAF	11	120097580	Missense_Mutation	DNP	AC	TCGA-B9-4114-01A-01D-1252-08	5696417	120097580	14908936	83	4413											
SMARCC2	6601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56558312	56558312	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggtgatgcccatgcaggtTaggaggagcggggaggttaa	9	8	19	5	1	0	1	0	1	0	0	0	4	0	4	1	7	3	3	1	7	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:56558312T>G	ENST00000267064.4	-	27	3429	c.3343A>C	c.(3343-3345)Aac>Cac	p.N1115H	SMARCC2_ENST00000550164.1_Missense_Mutation_p.N1146H|SMARCC2_ENST00000394023.3_Intron|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Intron	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1115	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CCATGCAGGTTAGGAGGAGCG	0.592																																					p.N1115H		.											.	SMARCC2-229	0			c.A3343C						.						114	95	101					12																	56558312		2203	4300	6503	SO:0001583	missense	6601	exon27			GCAGGTTAGGAGG	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.3343A>C	12.37:g.56558312T>G	ENSP00000267064:p.Asn1115His	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	259	113	NM_003075	0	0	25	52	27	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622273	0.46840	.	.	ENSG00000139613	ENST00000550164;ENST00000267064	T;T	0.47528	0.85;0.84	5.28	4.1	0.47936	.	1.132090	0.06439	N	0.725536	T	0.33498	0.0865	N	0.14661	0.345	0.27631	N	0.948035	B	0.09022	0.002	B	0.04013	0.001	T	0.23833	-1.0177	9	.	.	.	-9.2359	11.5054	0.50463	0.0:0.0:0.1507:0.8493	.	1115	Q8TAQ2	SMRC2_HUMAN	H	1146;1115	ENSP00000449396:N1146H;ENSP00000267064:N1115H	.	N	-	1	0	SMARCC2	54844579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.575000	0.36493	0.921000	0.36994	0.460000	0.39030	AAC	.		0.592	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			G	56558312	T	G	56558312	3	3	48	1	0	0	0	0	1	0	0	0	14808	1754	61	5	309	5	SMARCC2	12	56558312	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08		56558312	77293583	84	4414											
GLI1	2735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57861143	57861143	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgccggaagtcatactcaCgcctcgaaaacctgaagacg	12	6	11	12	4	2	2	2	1	0	1	3	4	2	3	3	2	3	0	3	2	5	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:57861143C>A	ENST00000228682.2	+	9	1031	c.940C>A	c.(940-942)Cgc>Agc	p.R314S	GLI1_ENST00000543426.1_Missense_Mutation_p.R186S|GLI1_ENST00000546141.1_Missense_Mutation_p.R273S	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	314					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			GTCATACTCACGCCTCGAAAA	0.542																																					p.R314S	Pancreas(157;841 1936 10503 41495 50368)	.											.	GLI1-722	0			c.C940A						.						109	96	101					12																	57861143		2203	4300	6503	SO:0001583	missense	2735	exon9			TACTCACGCCTCG		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.940C>A	12.37:g.57861143C>A	ENSP00000228682:p.Arg314Ser	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	190	38	NM_005269	0	0	0	0	0	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759669	0.89932	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	4.64	3.69	0.42338	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000056	T	0.49098	0.1537	N	0.21448	0.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53906	-0.8372	10	0.87932	D	0	.	13.7621	0.62973	0.1541:0.8459:0.0:0.0	.	314	P08151	GLI1_HUMAN	S	186;314;273;273;186	ENSP00000437607:R186S;ENSP00000228682:R314S;ENSP00000441006:R273S;ENSP00000434408:R273S	ENSP00000228682:R314S	R	+	1	0	GLI1	56147410	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.744000	0.55112	2.575000	0.86900	0.563000	0.77884	CGC	.		0.542	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57861143	C	A	57861143	3	1	48	1	0	0	0	0	1	0	0	0	6457	536	19	4	970	4	GLI1	12	57861143	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	1302831	57861143	75990752	85	4415											
C12orf66	144577	hgsc.bcm.edu;broad.mit.edu	37	chr12	64615826	64615826	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggctgtgatagaccttctcGgccgcggccaggtgcgccaa	7	7	14	13	4	1	2	0	1	1	1	2	2	1	2	4	4	1	1	4	4	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:64615826G>C	ENST00000398055.3	-	1	245	c.192C>G	c.(190-192)gcC>gcG	p.A64A	C12orf66_ENST00000544871.1_Intron|C12orf66_ENST00000311915.8_Silent_p.A64A|C12orf66_ENST00000540673.1_5'UTR|RPS11P6_ENST00000535684.1_RNA	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	64										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						AGACCTTCTCGGCCGCGGCCA	0.637																																					p.A64A		.											.	C12orf66-515	0			c.C192G						.						26	30	29					12																	64615826		1954	4127	6081	SO:0001819	synonymous_variant	144577	exon1			CTTCTCGGCCGCG		CCDS41803.1, CCDS73490.1	12q14.2	2008-08-08			ENSG00000174206	ENSG00000174206			26517	protein-coding gene	gene with protein product						12477932	Standard	NM_152440		Approved	FLJ32549	uc001srw.4	Q96MD2	OTTHUMG00000168763	ENST00000398055.3:c.192C>G	12.37:g.64615826G>C		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	60	18	NM_152440	0	0	1	1	0	C9JX54|Q8IYA0	Silent	SNP	ENST00000398055.3	37	CCDS41803.1																																																																																			.		0.637	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440		C	64615826	G	C	64615826	2	2	48	1	0	0	0	0	0	0	0	1	1713	1103	39	4		4	C12orf66	12	64615826	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	6754683	64615826	69236069	86	4416											
CEP290	80184	ucsc.edu	37	chr12	88482834	88482834	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggctcctttggtatcctttAaagtgcttattaactcttcc	7	17	7	10	0	1	0	0	0	1	0	4	0	4	0	3	2	2	3	3	2	5	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:88482834A>G	ENST00000552810.1	-	31	4347	c.4004T>C	c.(4003-4005)tTa>tCa	p.L1335S	CEP290_ENST00000547691.2_Missense_Mutation_p.L395S|CEP290_ENST00000309041.7_Missense_Mutation_p.L1337S|CEP290_ENST00000397838.3_Missense_Mutation_p.L395S	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1335					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						GGTATCCTTTAAAGTGCTTAT	0.338																																					p.L1335S													.	CEP290-96	0			c.T4004C						.						69	64	66					12																	88482834		1798	4067	5865	SO:0001583	missense	80184	exon31			TCCTTTAAAGTGC	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.4004T>C	12.37:g.88482834A>G	ENSP00000448012:p.Leu1335Ser	Somatic	103	0		WXS	Illumina HiSeq		73	4	NM_025114	0	0	0	0	0	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.194140	0.78902	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.72835	-0.15;-0.69;-0.69;-0.15	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000001	T	0.81456	0.4826	M	0.68952	2.095	0.43110	D	0.99481	D	0.89917	1.0	D	0.80764	0.994	T	0.78797	-0.2063	10	0.21014	T	0.42	.	15.7269	0.77766	1.0:0.0:0.0:0.0	.	1335	O15078	CE290_HUMAN	S	395;1335;1337;395	ENSP00000446905:L395S;ENSP00000448012:L1335S;ENSP00000308021:L1337S;ENSP00000380938:L395S	ENSP00000308021:L1337S	L	-	2	0	CEP290	87006965	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.601000	0.90864	2.123000	0.65237	0.482000	0.46254	TTA	.		0.338	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		G	88482834	A	G	88482834	3	3	48	1	0	0	0	0	1	0	0	0	3259	372	13	3	3531	3	CEP290	12	88482834	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	23867008	88482834	45369061	87	4417											
MYO1H	283446	hgsc.bcm.edu;broad.mit.edu	37	chr12	109834319	109834319	+	Frame_Shift_Del	DEL	A	A	-																															ttctcgagtattttgcagtgAcctgcccaatgacccagtca																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:109834319delA	ENST00000431443.2	+	3	373	c.373delA	c.(373-375)accfs	p.T125fs	MYO1H_ENST00000310903.5_Frame_Shift_Del_p.T125fs	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	125	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						TTTTGCAGTGACCTGCCCAAT	0.498																																					p.T125fs		.											.	.	0			c.373delA						.						71	71	71					12																	109834319		1896	4123	6019	SO:0001589	frameshift_variant	283446	exon3			.		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.373delA	12.37:g.109834319delA	ENSP00000444076:p.Thr125fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	135	21	NM_001101421	0	0	0	0	0	F5H3C6	Frame_Shift_Del	DEL	ENST00000431443.2	37																																																																																				.		0.498	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		-	109834319	A	-	109834319	7	5	48	1	0	1	0	1	0	0	0	0	10100	275	10	0	383	0	MYO1H	12	109834319	Frame_Shift_Del	DEL	A	TCGA-B9-4114-01A-01D-1252-08	21351485	109834319	24017576	88	4418											
PEBP1	5037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	118577333	118577333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtcctctccgattatgtggGctcggggcctcccaagggca	6	9	13	13	2	1	0	0	0	1	0	5	1	3	0	4	4	0	2	4	4	2	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:118577333G>A	ENST00000261313.2	+	3	675	c.323G>A	c.(322-324)gGc>gAc	p.G108D	PEBP1_ENST00000542939.1_3'UTR	NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	108	Interaction with RAF1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GATTATGTGGGCTCGGGGCCT	0.522																																					p.G108D	NSCLC(44;94 1357 12187 49467)	.											.	PEBP1-779	0			c.G323A						.						123	110	115					12																	118577333		2203	4300	6503	SO:0001583	missense	5037	exon3			ATGTGGGCTCGGG	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.323G>A	12.37:g.118577333G>A	ENSP00000261313:p.Gly108Asp	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	249	101	NM_002567	0	1	252	755	502	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	37	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318256	0.95682	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.56776	0.44	5.43	5.43	0.79202	.	0.047800	0.85682	D	0.000000	D	0.82751	0.5105	H	0.96805	3.885	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.85130	0.997;0.994	D	0.88070	0.2800	10	0.59425	D	0.04	.	19.2412	0.93883	0.0:0.0:1.0:0.0	.	108;108	B4DRT4;P30086	.;PEBP1_HUMAN	D	108	ENSP00000261313:G108D	ENSP00000261313:G108D	G	+	2	0	PEBP1	117061716	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.447000	0.97595	2.543000	0.85770	0.563000	0.77884	GGC	.		0.522	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		A	118577333	G	A	118577333	3	1	48	1	0	0	0	0	1	0	0	0	11739	1203	42	2	333	2	PEBP1	12	118577333	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	8743014	118577333	15274562	89	4419											
ZCCHC8	55596	hgsc.bcm.edu;broad.mit.edu	37	chr12	122964832	122964833	+	Frame_Shift_Ins	INS	-	-	A																															ttattctgttgtatttctccINSaacttctgtttccccatcag																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:122964832_122964833insA	ENST00000336229.4	-	11	1174_1175	c.1044_1045insT	c.(1042-1047)gttggafs	p.G349fs	ZCCHC8_ENST00000538116.1_5'Flank|ZCCHC8_ENST00000543897.1_Frame_Shift_Ins_p.G111fs|ZCCHC8_ENST00000536306.1_Frame_Shift_Ins_p.G111fs	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	349					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TGTATTTCTCCAACTTCTGTTT	0.371																																					p.G349fs		.											.	ZCCHC8-90	0			c.1045_1046insT						.																																			SO:0001589	frameshift_variant	55596	exon11			.	BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.1045dupT	12.37:g.122964834_122964834dupA	ENSP00000337313:p.Gly349fs	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	59	26	NM_017612	0	0	0	0	0	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Frame_Shift_Ins	INS	ENST00000336229.4	37																																																																																				.		0.371	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		A	122964833	-	A	122964832	7	5	48	1	0	1	1	0	0	0	0	0	17626	603	21	0	1094	0	ZCCHC8	12	122964832	Frame_Shift_Ins	INS	-	TCGA-B9-4114-01A-01D-1252-08	4387499	122964832	10887063	90	4420											
STX2	2054	ucsc.edu	37	chr12	131280600	131280600	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatcatttgccaactgaCaagccaataattagagcgat	15	9	6	11	1	1	2	1	1	0	1	1	3	1	2	3	0	4	0	3	0	5	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:131280600C>A	ENST00000392373.2	-	10	946	c.852G>T	c.(850-852)ttG>ttT	p.L284F	STX2_ENST00000261653.6_Intron	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	284					acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		TGCCAACTGACAAGCCAATAA	0.393																																					p.L284F													.	STX2-90	0			c.G852T						.						165	146	152					12																	131280600		2203	4300	6503	SO:0001583	missense	2054	exon10			AACTGACAAGCCA	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"epimorphin"	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.852G>T	12.37:g.131280600C>A	ENSP00000376178:p.Leu284Phe	Somatic	171	41		WXS	Illumina HiSeq		229	64	NM_194356	0	0	4	4	0	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	37	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	C	1.821	-0.472205	0.04445	.	.	ENSG00000111450	ENST00000392373	T	0.37584	1.19	4.88	-2.74	0.05932	.	0.329239	0.29126	N	0.013069	T	0.27663	0.0680	M	0.75447	2.3	0.49130	D	0.999758	B	0.25390	0.125	B	0.20184	0.028	T	0.28459	-1.0043	10	0.09843	T	0.71	-5.7483	7.3163	0.26503	0.0:0.4997:0.2737:0.2266	.	284	P32856	STX2_HUMAN	F	284	ENSP00000376178:L284F	ENSP00000376178:L284F	L	-	3	2	STX2	129846553	0.989000	0.36119	0.039000	0.18376	0.007000	0.05969	0.145000	0.16157	-0.821000	0.04312	-0.175000	0.13238	TTG	.		0.393	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356		A	131280600	C	A	131280600	3	1	48	1	0	0	0	0	1	0	0	0	15377	477	17	4	100	4	STX2	12	131280600	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	8315768	131280600	2571295	91	4421											
PARP4	143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	25067776	25067776	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggcttgagaagcatgtgTtccaggtggcccagggcctc	7	9	14	11	0	0	1	0	1	0	1	2	2	1	1	3	4	1	3	3	4	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr13:25067776T>C	ENST00000381989.3	-	8	942	c.837A>G	c.(835-837)gaA>gaG	p.E279E		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	279	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GAAGCATGTGTTCCAGGTGGC	0.478																																					p.E279E		.											.	PARP4-94	0			c.A837G						.						122	99	107					13																	25067776		2203	4300	6503	SO:0001819	synonymous_variant	143	exon8			CATGTGTTCCAGG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.837A>G	13.37:g.25067776T>C		Somatic	70	1		WXS	Illumina HiSeq	Phase_I	22	8	NM_006437	0	0	0	0	0	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			.		0.478	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		C	25067776	T	C	25067776	2	2	48	1	0	0	0	0	0	0	0	1	11489	1722	60	3		3	PARP4	13	25067776	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08		25067776	90102102	92	4422											
ITM2B	9445	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	48830432	48830433	+	In_Frame_Ins	INS	-	-	CAA																															aagaaaatattaaaatctttINSgaagaagaagaagttgaatt																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr13:48830432_48830433insCAA	ENST00000378565.5	+	3	569_570	c.366_367insCAA	c.(367-369)gaa>CAAgaa	p.122_123insQ	ITM2B_ENST00000378549.5_Intron	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	122	Necessary for interaction with APP and inhibitor effects on APP processing.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		TTAAAATCTTTGAAGAAGAAGA	0.401																																					p.F122delinsFQ		.											.	ITM2B-90	0			c.366_367insCAA						.																																			SO:0001652	inframe_insertion	9445	exon3			.	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	Exception_encountered	13.37:g.48830432_48830433insCAA	ENSP00000367828:p.Phe122_Glu123insGln	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	82	26	NM_021999	0	0	0	0	0	Q5W0A3|Q96B24|Q9NYH1	In_Frame_Ins	INS	ENST00000378565.5	37	CCDS9409.1																																																																																			.		0.401	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		CAA	48830433	-	CAA	48830432	7	5	48	1	0	1	1	0	0	0	0	0	7934	1809	63	0	376	0	ITM2B	13	48830432	In_Frame_Ins	INS	-	TCGA-B9-4114-01A-01D-1252-08	23762656	48830432	66339446	93	4423	50	2									
ITM2B	9445	hgsc.bcm.edu	37	chr13	48830433	48830433	+	Missense_Mutation	SNP	G	G	C																															aagaaaatattaaaatctttGaagaagaagaagttgaattt																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr13:48830433G>C	ENST00000378565.5	+	3	570	c.367G>C	c.(367-369)Gaa>Caa	p.E123Q	ITM2B_ENST00000378549.5_Intron	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	123	Necessary for interaction with APP and inhibitor effects on APP processing.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		TAAAATCTTTGAAGAAGAAGA	0.398																																					p.E123Q		.											.	ITM2B-90	0			c.G367C						.						81	82	82					13																	48830433		2203	4300	6503	SO:0001583	missense	9445	exon3			ATCTTTGAAGAAG	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.367G>C	13.37:g.48830433G>C	ENSP00000367828:p.Glu123Gln	Somatic	163	1		WXS	Illumina HiSeq	Phase_I	84	29	NM_021999	1	0	1522	1526	3	Q5W0A3|Q96B24|Q9NYH1	Missense_Mutation	SNP	ENST00000378565.5	37	CCDS9409.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.488250	0.44249	.	.	ENSG00000136156	ENST00000378565	T	0.33865	1.39	5.76	4.92	0.64577	.	0.090715	0.85682	D	0.000000	T	0.33760	0.0874	L	0.59436	1.845	0.80722	D	1	B	0.13594	0.008	B	0.17098	0.017	T	0.13019	-1.0525	10	0.12430	T	0.62	-16.1984	13.6725	0.62434	0.0737:0.0:0.9263:0.0	.	123	Q9Y287	ITM2B_HUMAN	Q	123	ENSP00000367828:E123Q	ENSP00000367828:E123Q	E	+	1	0	ITM2B	47728434	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.037000	0.64170	1.442000	0.47568	0.650000	0.86243	GAA	.		0.398	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		C	48830433	G	C	48830433	3	2	48	1	0	0	0	0	1	0	0	0	7934	1291	45	4	377	4	ITM2B	13	48830433	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	1	48830433	66339445	94	4424	50	2									
RNF31	55072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24617213	24617213	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacctcaacaccctgtccaCggctctgaacatcctggaga	10	8	7	16	1	2	2	1	1	1	1	4	3	4	2	4	2	3	1	4	2	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:24617213C>G	ENST00000324103.6	+	2	541	c.221C>G	c.(220-222)aCg>aGg	p.T74R	RNF31_ENST00000557878.1_3'UTR|PSME2_ENST00000471700.2_5'Flank|PSME2_ENST00000560410.1_5'Flank|RNF31_ENST00000382687.3_5'Flank|RNF31_ENST00000559275.1_5'UTR|PSME2_ENST00000216802.5_5'Flank	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	74	Polyubiquitin-binding.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		ACCCTGTCCACGGCTCTGAAC	0.607																																					p.T74R		.											.	RNF31-90	0			c.C221G						.						80	85	83					14																	24617213		2063	4198	6261	SO:0001583	missense	55072	exon2			TGTCCACGGCTCT	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.221C>G	14.37:g.24617213C>G	ENSP00000315112:p.Thr74Arg	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	176	55	NM_017999	0	0	1	2	1	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498171	0.85069	.	.	ENSG00000092098	ENST00000324103	T	0.47869	0.83	5.31	5.31	0.75309	PUB domain (1);	0.130527	0.51477	D	0.000093	T	0.61135	0.2323	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	T	0.55730	-0.8095	9	.	.	.	-13.9514	17.9131	0.88940	0.0:1.0:0.0:0.0	.	74	Q96EP0	RNF31_HUMAN	R	74	ENSP00000315112:T74R	.	T	+	2	0	RNF31	23687053	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.011000	0.64011	2.779000	0.95612	0.655000	0.94253	ACG	.		0.607	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		G	24617213	C	G	24617213	3	3	48	1	0	0	0	0	1	0	0	0	13519	536	19	4	227	4	RNF31	14	24617213	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		24617213	82732327	95	4425											
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35593087	35593087	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagactttagaacctagaggTtacagtcttctcatccgggg	11	11	10	9	1	2	3	1	0	2	3	4	3	3	3	2	3	2	1	2	3	5	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:35593087T>C	ENST00000557565.1	+	2	1017	c.636T>C	c.(634-636)ggT>ggC	p.G212G	KIAA0391_ENST00000603544.1_Silent_p.G212G|PPP2R3C_ENST00000555644.1_5'Flank|KIAA0391_ENST00000534898.4_Silent_p.G212G|KIAA0391_ENST00000604948.1_Silent_p.G117G|PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000321130.10_Silent_p.G212G|KIAA0391_ENST00000250377.7_Silent_p.G117G|KIAA0391_ENST00000605870.1_Intron	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	212					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		AACCTAGAGGTTACAGTCTTC	0.358																																					p.G212G		.											.	KIAA0391-226	0			c.T636C						.						49	50	49					14																	35593087		2203	4300	6503	SO:0001819	synonymous_variant	9692	exon2			TAGAGGTTACAGT	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.636T>C	14.37:g.35593087T>C		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	69	4	NM_014672	0	0	18	18	0	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Silent	SNP	ENST00000557565.1	37	CCDS32063.1																																																																																			.		0.358	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		C	35593087	T	C	35593087	2	2	48	1	0	0	0	0	0	0	0	1	8193	1712	60	3		3	KIAA0391	14	35593087	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	10975874	35593087	71756453	96	4426											
FAM179B	23116	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	45433529	45433529	+	Frame_Shift_Del	DEL	C	C	-																															cacgtgagggatagcatgcaCatttatggatcttacagccc																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:45433529delC	ENST00000361577.3	+	1	2119	c.1905delC	c.(1903-1905)cacfs	p.H635fs	KLHL28_ENST00000396128.4_5'Flank|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Frame_Shift_Del_p.H635fs|FAM179B_ENST00000382233.2_Frame_Shift_Del_p.H635fs	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	635										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						ATAGCATGCACATTTATGGAT	0.453																																					p.H635fs		.											.	FAM179B-93	0			c.1905delC						.						98	86	90					14																	45433529		2203	4300	6503	SO:0001589	frameshift_variant	23116	exon1			.	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"KIAA0423"	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.1905delC	14.37:g.45433529delC	ENSP00000355045:p.His635fs	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_015091	0	0	0	0	0	Q68D66|Q6PG27	Frame_Shift_Del	DEL	ENST00000361577.3	37	CCDS9681.1																																																																																			.		0.453	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		-	45433529	C	-	45433529	7	5	48	1	0	1	0	1	0	0	0	0	5522	477	17	0	1907	0	FAM179B	14	45433529	Frame_Shift_Del	DEL	C	TCGA-B9-4114-01A-01D-1252-08	9840442	45433529	61916011	97	4427											
C14orf4	64207	ucsc.edu	37	chr14	77491938	77491938	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaaatttgtggctggggAcggaagggcactgaacgaaa	14	6	15	6	2	0	1	0	1	0	0	0	4	0	3	0	5	2	3	0	5	5	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:77491938A>G	ENST00000238647.3	-	1	3096	c.2198T>C	c.(2197-2199)gTc>gCc	p.V733A		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	733					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						GTGGCTGGGGACGGAAGGGCA	0.572																																					p.V733A													.	IRF2BPL-90	0			c.T2198C						.						63	56	58					14																	77491938		2203	4300	6503	SO:0001583	missense	64207	exon1			CTGGGGACGGAAG	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.2198T>C	14.37:g.77491938A>G	ENSP00000238647:p.Val733Ala	Somatic	108	17		WXS	Illumina HiSeq		125	22	NM_024496	0	0	30	39	9	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	37	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164966	0.78339	.	.	ENSG00000119669	ENST00000238647	T	0.68903	-0.36	4.64	4.64	0.57946	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.64402	U	0.000003	T	0.81588	0.4854	M	0.82823	2.61	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	D	0.84635	0.0692	10	0.72032	D	0.01	.	13.3656	0.60682	1.0:0.0:0.0:0.0	.	733	Q9H1B7	I2BPL_HUMAN	A	733	ENSP00000238647:V733A	ENSP00000238647:V733A	V	-	2	0	IRF2BPL	76561691	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	9.097000	0.94193	1.948000	0.56530	0.379000	0.24179	GTC	.		0.572	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		G	77491938	A	G	77491938	3	3	48	1	0	0	0	0	1	0	0	0	1777	275	10	3	196	3	C14orf4	14	77491938	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	32058409	77491938	29857602	98	4428											
SERPINA1	5265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	94849213	94849213	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagggtacggaggagttccTggaagccttcatggatctga	9	10	15	7	1	2	2	1	2	1	0	3	6	3	6	2	5	2	2	2	5	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:94849213T>G	ENST00000448921.1	-	4	934	c.362A>C	c.(361-363)cAg>cCg	p.Q121P	SERPINA1_ENST00000440909.1_Missense_Mutation_p.Q121P|SERPINA1_ENST00000393087.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000404814.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000437397.1_Missense_Mutation_p.Q121P|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000402629.1_Missense_Mutation_p.Q121P|SERPINA1_ENST00000355814.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000449399.3_Missense_Mutation_p.Q121P|SERPINA1_ENST00000393088.4_Missense_Mutation_p.Q121P	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	121					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GAGGAGTTCCTGGAAGCCTTC	0.572																																					p.Q121P		.											.	SERPINA1-226	0			c.A362C						.						57	56	57					14																	94849213		2203	4300	6503	SO:0001583	missense	5265	exon4			AGTTCCTGGAAGC	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"Serine (or cysteine) peptidase inhibitors"	8941	protein-coding gene	gene with protein product	"protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"	107400	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.362A>C	14.37:g.94849213T>G	ENSP00000416066:p.Gln121Pro	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	122	29	NM_001127701	1	2	1426	2592	1163	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.629267	0.46944	.	.	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629;ENST00000554720;ENST00000556091;ENST00000557492	D;D;D;D;D;D;D;D;D;T;D;D	0.88431	-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-0.96;-1.72;-1.72	5.8	-0.59	0.11679	Serpin domain (3);	0.589490	0.16883	N	0.195601	D	0.91472	0.7308	M	0.90082	3.085	0.21020	N	0.999801	B;B	0.25486	0.127;0.091	B;B	0.41946	0.136;0.371	D	0.87168	0.2219	10	0.72032	D	0.01	.	7.1129	0.25401	0.0:0.3182:0.1125:0.5693	.	121;121	P01009-2;P01009	.;A1AT_HUMAN	P	121;121;121;121;121;121;121;121;121;35;121;121	ENSP00000390299:Q121P;ENSP00000416066:Q121P;ENSP00000408474:Q121P;ENSP00000348068:Q121P;ENSP00000376802:Q121P;ENSP00000376803:Q121P;ENSP00000385960:Q121P;ENSP00000416354:Q121P;ENSP00000386094:Q121P;ENSP00000450561:Q35P;ENSP00000452169:Q121P;ENSP00000452452:Q121P	ENSP00000348068:Q121P	Q	-	2	0	SERPINA1	93918966	0.002000	0.14202	0.075000	0.20258	0.907000	0.53573	-0.082000	0.11304	-0.099000	0.12263	-0.379000	0.06801	CAG	.		0.572	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		G	94849213	T	G	94849213	3	3	48	1	0	0	0	0	1	0	0	0	14118	1580	55	5	910	5	SERPINA1	14	94849213	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	17357275	94849213	12500327	99	4429											
WDR20	91833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102675938	102675938	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaggcaccacgagaaagaTcacaagcgaaatcatagcat	18	4	10	9	2	2	3	2	0	0	3	2	6	2	3	1	1	2	2	1	1	4	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:102675938T>C	ENST00000342702.3	+	3	1462	c.1431T>C	c.(1429-1431)gaT>gaC	p.D477D	WDR20_ENST00000424963.2_Silent_p.D353D|WDR20_ENST00000499851.2_Silent_p.D220D|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556807.1_Silent_p.D416D|WDR20_ENST00000556511.2_Silent_p.D416D|WDR20_ENST00000454394.2_Silent_p.D508D|WDR20_ENST00000335263.5_Silent_p.D477D|WDR20_ENST00000545563.1_Silent_p.D304D	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	477										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						ACGAGAAAGATCACAAGCGAA	0.473											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D508D		.											.	WDR20-90	0			c.T1524C						.						114	105	108					14																	102675938		2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			GAAAGATCACAAG	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1431T>C	14.37:g.102675938T>C		Somatic	204	0	1368	WXS	Illumina HiSeq	Phase_I	239	78	NM_001242417	0	0	11	20	9	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	37	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	T	3.721	-0.057478	0.07317	.	.	ENSG00000140153	ENST00000556511	.	.	.	5.73	-3.12	0.05282	.	.	.	.	.	T	0.63604	0.2525	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63093	-0.6714	4	.	.	.	.	14.198	0.65684	0.0:0.4331:0.0:0.5669	.	.	.	.	P	408	.	.	S	+	1	0	WDR20	101745691	0.985000	0.35326	0.982000	0.44146	0.999000	0.98932	0.241000	0.18065	-0.454000	0.07066	0.533000	0.62120	TCA	.		0.473	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		C	102675938	T	C	102675938	2	2	48	1	0	0	0	0	0	0	0	1	17313	1432	50	3		3	WDR20	14	102675938	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	7826725	102675938	4673602	100	4430											
PLCB2	5330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40590557	40590557	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctggcggtacatctcagccGaggagaggcctgagaactgg	9	6	15	11	2	1	2	1	1	1	2	2	5	1	2	3	5	3	1	3	5	2	1	rs201305253	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:40590557G>A	ENST00000260402.3	-	11	1271	c.1022C>T	c.(1021-1023)tCg>tTg	p.S341L	PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000557821.1_Missense_Mutation_p.S341L|PLCB2_ENST00000456256.2_Missense_Mutation_p.S341L	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	341	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CATCTCAGCCGAGGAGAGGCC	0.627													G|||	2	0.000399361	8e-04	0	5008	,	,		20598	0		0	False		,,,				2504	0.001				p.S341L		.											.	PLCB2-275	0			c.C1022T						.						33	36	35					15																	40590557		2082	4236	6318	SO:0001583	missense	5330	exon11			TCAGCCGAGGAGA		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1022C>T	15.37:g.40590557G>A	ENSP00000260402:p.Ser341Leu	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	125	31	NM_004573	0	0	7	7	0	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	37	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	G	32	5.183791	0.94885	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.59772	0.24;0.24	4.38	4.38	0.52667	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.136952	0.50627	D	0.000108	D	0.83151	0.5192	H	0.95712	3.71	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.952;0.997	D	0.88893	0.3347	10	0.87932	D	0	.	17.4798	0.87670	0.0:0.0:1.0:0.0	.	341;341;341	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	L	341	ENSP00000260402:S341L;ENSP00000411991:S341L	ENSP00000260402:S341L	S	-	2	0	PLCB2	38377849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.657000	0.98554	2.438000	0.82558	0.563000	0.77884	TCG	G|0.999;A|0.001		0.627	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40590557	G	A	40590557	3	1	48	1	0	0	0	0	1	0	0	0	12054	1059	37	1	2623	1	PLCB2	15	40590557	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		40590557	61940835	101	4431											
ANKDD1A	348094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65239709	65239709	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagctccgttctgtgctgtGgcggctggcctccaggtatc	3	11	14	13	2	1	0	0	0	1	0	4	0	3	0	3	4	2	6	3	4	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:65239709G>T	ENST00000380230.3	+	13	1276	c.1247G>T	c.(1246-1248)tGg>tTg	p.W416L	ANKDD1A_ENST00000395723.1_Missense_Mutation_p.W293L|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.W384L|ANKDD1A_ENST00000395720.1_Missense_Mutation_p.W416L	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	416	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						TCTGTGCTGTGGCGGCTGGCC	0.597																																					p.W416L		.											.	ANKDD1A-69	0			c.G1247T						.						45	40	42					15																	65239709		2202	4299	6501	SO:0001583	missense	348094	exon13			TGCTGTGGCGGCT		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1247G>T	15.37:g.65239709G>T	ENSP00000369579:p.Trp416Leu	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	65	22	NM_182703	0	0	0	0	0	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	37	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469077	0.84533	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000395723	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	4.63	4.63	0.57726	Death (1);DEATH-like (1);	0.000000	0.64402	D	0.000017	D	0.85758	0.5771	M	0.78637	2.42	0.80722	D	1	P	0.45283	0.855	P	0.48524	0.58	D	0.83545	0.0098	10	0.16420	T	0.52	-16.8697	16.2408	0.82408	0.0:0.0:1.0:0.0	.	416	Q495B1	AKD1A_HUMAN	L	416;384;416;293	ENSP00000369579:W416L;ENSP00000350329:W384L;ENSP00000379070:W416L;ENSP00000379073:W293L	ENSP00000350329:W384L	W	+	2	0	ANKDD1A	63026762	1.000000	0.71417	0.995000	0.50966	0.848000	0.48234	9.170000	0.94795	2.423000	0.82170	0.655000	0.94253	TGG	.		0.597	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		T	65239709	G	T	65239709	3	4	48	1	0	0	0	0	1	0	0	0	624	1357	47	4	1297	4	ANKDD1A	15	65239709	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	24649152	65239709	37291683	102	4432											
DENND4A	10260	hgsc.bcm.edu;broad.mit.edu	37	chr15	65989618	65989618	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctacaggaactacaatcActcccttttttatctttttc	10	17	2	12	0	2	0	1	0	1	0	4	1	3	1	2	1	4	0	2	1	6	8			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:65989618A>T	ENST00000431932.2	-	20	3013	c.2805T>A	c.(2803-2805)agT>agA	p.S935R	snoU13_ENST00000459325.1_RNA|DENND4A_ENST00000443035.3_Missense_Mutation_p.S978R	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	935					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AACTACAATCACTCCCTTTTT	0.303																																					p.S978R		.											.	DENND4A-229	0			c.T2934A						.						110	108	109					15																	65989618		1814	4062	5876	SO:0001583	missense	10260	exon21			ACAATCACTCCCT	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2805T>A	15.37:g.65989618A>T	ENSP00000396830:p.Ser935Arg	Somatic	183	1		WXS	Illumina HiSeq	Phase_I	38	3	NM_001144823	0	0	0	0	0	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.157435	0.38119	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05996	3.42;3.36	5.62	3.24	0.37175	.	1.083580	0.06784	N	0.785821	T	0.09862	0.0242	L	0.58101	1.795	0.53005	D	0.99996	P;B	0.37955	0.612;0.09	B;B	0.37943	0.261;0.05	T	0.14559	-1.0468	10	0.29301	T	0.29	.	9.6916	0.40131	0.8567:0.0:0.1433:0.0	.	978;935	E7EPL3;Q7Z401	.;MYCPP_HUMAN	R	978;935	ENSP00000391167:S978R;ENSP00000396830:S935R	ENSP00000396830:S935R	S	-	3	2	DENND4A	63776672	1.000000	0.71417	1.000000	0.80357	0.533000	0.34776	0.974000	0.29436	0.462000	0.27095	0.383000	0.25322	AGT	.		0.303	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	65989618	A	T	65989618	3	4	48	1	0	0	0	0	1	0	0	0	4444	156	6	5	2838	5	DENND4A	15	65989618	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	749909	65989618	36541774	103	4433											
ISLR2	57611	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	74425252	74425252	+	Frame_Shift_Del	DEL	G	G	-																															cggaaggactgcctgccaacGtgacgacgcttagtctgtcc																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:74425252delG	ENST00000361742.3	+	4	926	c.157delG	c.(157-159)gtgfs	p.V53fs	ISLR2_ENST00000453268.2_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000565159.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000565540.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000445793.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000435464.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000419208.1_Frame_Shift_Del_p.V53fs	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	53					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						GCCTGCCAACGTGACGACGCT	0.632																																					p.V53X		.											.	ISLR2-90	0			c.157delG						.						82	68	73					15																	74425252		2198	4297	6495	SO:0001589	frameshift_variant	57611	exon4			.		CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.157delG	15.37:g.74425252delG	ENSP00000355402:p.Val53fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	234	76	NM_001130138	0	0	0	0	0	A8K352|Q9P263	Nonsense_Mutation	DEL	ENST00000361742.3	37	CCDS10259.1																																																																																			.		0.632	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		-	74425252	G	-	74425252	7	5	48	1	0	1	0	1	0	0	0	0	7880	1145	40	0	159	0	ISLR2	15	74425252	Frame_Shift_Del	DEL	G	TCGA-B9-4114-01A-01D-1252-08	8435634	74425252	28106140	104	4434											
FAM154B	283726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	82574679	82574679	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgccttgattatatacctcAtcagcttgaactcaagtttg	10	15	6	10	1	3	2	3	2	0	0	4	2	3	2	2	0	3	2	2	0	5	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:82574679A>C	ENST00000339465.5	+	3	542	c.473A>C	c.(472-474)cAt>cCt	p.H158P	FAM154B_ENST00000565501.1_3'UTR|FAM154B_ENST00000427381.2_Missense_Mutation_p.H143P	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	158										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						TATATACCTCATCAGCTTGAA	0.433																																					p.H158P		.											.	FAM154B-70	0			c.A473C						.						112	111	111					15																	82574679		2203	4300	6503	SO:0001583	missense	283726	exon3			TACCTCATCAGCT	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.473A>C	15.37:g.82574679A>C	ENSP00000340445:p.His158Pro	Somatic	370	0		WXS	Illumina HiSeq	Phase_I	51	9	NM_001008226	0	0	0	0	0	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.760509	0.69763	.	.	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.14391	2.51;2.51	3.9	3.9	0.45041	.	0.144157	0.45126	D	0.000381	T	0.35219	0.0924	M	0.77103	2.36	0.51012	D	0.999907	D;D	0.67145	0.996;0.992	D;D	0.69824	0.966;0.953	T	0.12142	-1.0559	10	0.37606	T	0.19	-13.415	13.1531	0.59500	1.0:0.0:0.0:0.0	.	143;158	B4E2M2;Q658L1	.;F154B_HUMAN	P	158;143	ENSP00000340445:H158P;ENSP00000403743:H143P	ENSP00000340445:H158P	H	+	2	0	FAM154B	80361734	0.998000	0.40836	0.633000	0.29310	0.980000	0.70556	4.775000	0.62346	1.751000	0.51876	0.438000	0.28831	CAT	.		0.433	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		C	82574679	A	C	82574679	3	2	48	1	0	0	0	0	1	0	0	0	5480	217	8	5	483	5	FAM154B	15	82574679	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	8149427	82574679	19956713	105	4435											
LINS1	55180	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	101114034	101114034	+	Frame_Shift_Del	DEL	C	C	-																															acagacagtgtcttcaacaaCcccgaattcacagcttgcaa																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:101114034delC	ENST00000314742.8	-	5	1266	c.1044delG	c.(1042-1044)gggfs	p.G348fs	LINS_ENST00000559149.1_5'UTR|LINS_ENST00000560133.1_Frame_Shift_Del_p.G229fs|LINS_ENST00000561308.1_Frame_Shift_Del_p.G348fs	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	348										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						TCTTCAACAACCCCGAATTCA	0.448																																					p.G348fs		.											.	LINS-92	0			c.1044delG						.			0,4264		0,0,2132	146	133	137			2.5	0.1	15		137	2,8252		0,2,4125	no	frameshift	LINS	NM_001040616.2		0,2,6257	A1A1,A1R,RR		0.0242,0.0,0.016			101114034	2,12516	2203	4300	6503	SO:0001589	frameshift_variant	55180	exon5			.	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1044delG	15.37:g.101114034delC	ENSP00000318423:p.Gly348fs	Somatic	281	0		WXS	Illumina HiSeq	Phase_I	213	57	NM_001040616	0	0	0	0	0	Q96FW2|Q9NVQ3	Frame_Shift_Del	DEL	ENST00000314742.8	37	CCDS10385.1																																																																																			.		0.448	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		-	101114034	C	-	101114034	7	5	48	1	0	1	0	1	0	0	0	0	8841	494	18	0	1241	0	LINS1	15	101114034	Frame_Shift_Del	DEL	C	TCGA-B9-4114-01A-01D-1252-08	18539355	101114034	1417358	106	4436											
IFT140	9742	broad.mit.edu	37	chr16	1574816	1574816	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccctggaagcagtggatgCggaccagggagaagtggtcc	9	6	17	9	1	0	1	0	0	0	1	1	5	1	4	3	5	3	1	3	5	2	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr16:1574816C>T	ENST00000426508.2	-	23	3329	c.2966G>A	c.(2965-2967)cGc>cAc	p.R989H	IFT140_ENST00000361339.5_Missense_Mutation_p.R183H	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	989					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				GCAGTGGATGCGGACCAGGGA	0.662																																					p.R989H													.	IFT140-95	0			c.G2966A						.						55	65	62					16																	1574816		2199	4300	6499	SO:0001583	missense	9742	exon23			TGGATGCGGACCA	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"Intraflagellar transport homologs", "WD repeat domain containing"	29077	protein-coding gene	gene with protein product		614620	"WD and tetratricopeptide repeats 2", "intraflagellar transport 140 homolog (Chlamydomonas)"	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2966G>A	16.37:g.1574816C>T	ENSP00000406012:p.Arg989His	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	288	6	NM_014714	0	0	11	11	0	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	C	35	5.435616	0.96150	.	.	ENSG00000187535	ENST00000397417;ENST00000361339;ENST00000426508	T;T	0.56275	0.47;0.47	5.53	4.56	0.56223	.	0.062488	0.64402	N	0.000003	T	0.77294	0.4109	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82317	-0.0517	10	0.56958	D	0.05	.	15.571	0.76337	0.1388:0.8612:0.0:0.0	.	989;676	Q96RY7;B4DR58	IF140_HUMAN;.	H	989;183;989	ENSP00000354895:R183H;ENSP00000406012:R989H	ENSP00000354895:R183H	R	-	2	0	IFT140	1514817	1.000000	0.71417	0.807000	0.32361	0.963000	0.63663	7.755000	0.85180	1.291000	0.44653	0.655000	0.94253	CGC	.		0.662	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1574816	C	T	1574816	3	4	48	1	0	0	0	0	1	0	0	0	7577	768	27	1	1458	1	IFT140	16	1574816	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		1574816	88779937	107	4437											
PALB2	79728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23646407	23646407	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcccagcgggagagctgActttagttaatgagagaagt	11	9	15	6	1	0	4	0	2	0	2	0	6	0	4	1	2	2	2	1	2	3	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr16:23646407A>T	ENST00000261584.4	-	4	1612	c.1460T>A	c.(1459-1461)gTc>gAc	p.V487D		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	487	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		GGGAGAGCTGACTTTAGTTAA	0.458			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.V487D		.	yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	.	PALB2-1351	0			c.T1460A						.						131	131	131					16																	23646407		2197	4300	6497	SO:0001583	missense	79728	exon4			GAGCTGACTTTAG		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"Fanconi anemia, complementation groups"	26144	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group N"	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.1460T>A	16.37:g.23646407A>T	ENSP00000261584:p.Val487Asp	Somatic	403	0		WXS	Illumina HiSeq	Phase_I	179	89	NM_024675	0	0	0	0	0	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.479867	0.26511	.	.	ENSG00000083093	ENST00000261584	T	0.15603	2.41	5.67	1.89	0.25635	.	0.327339	0.25935	N	0.027358	T	0.28267	0.0698	M	0.63428	1.95	0.19775	N	0.999954	D	0.67145	0.996	P	0.62298	0.9	T	0.04693	-1.0933	10	0.59425	D	0.04	-1.5018	4.5066	0.11891	0.6154:0.2179:0.1667:0.0	.	487	Q86YC2	PALB2_HUMAN	D	487	ENSP00000261584:V487D	ENSP00000261584:V487D	V	-	2	0	PALB2	23553908	0.059000	0.20769	0.013000	0.15412	0.188000	0.23474	1.278000	0.33179	0.529000	0.28599	0.533000	0.62120	GTC	.		0.458	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		T	23646407	A	T	23646407	3	4	48	1	0	0	0	0	1	0	0	0	11432	275	10	5	2140	5	PALB2	16	23646407	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	22071591	23646407	66708346	108	4438											
RNF40	9810	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30776526	30776526	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgagctccaggataaagtgAcatcggcagagaccaaggtg	13	5	13	10	2	0	2	0	1	0	1	2	5	1	3	3	3	1	2	3	3	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr16:30776526A>T	ENST00000324685.6	+	7	1231	c.796A>T	c.(796-798)Aca>Tca	p.T266S	RNF40_ENST00000563683.1_Missense_Mutation_p.T266S|RNF40_ENST00000357890.5_Missense_Mutation_p.T266S|RNF40_ENST00000402121.3_Intron|C16orf93_ENST00000543610.1_5'Flank	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	266					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			GGATAAAGTGACATCGGCAGA	0.537																																					p.T266S		.											.	RNF40-226	0			c.A796T						.						91	89	90					16																	30776526		2197	4300	6497	SO:0001583	missense	9810	exon7			AAAGTGACATCGG	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"RING-type (C3HC4) zinc fingers"	16867	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"	607700	"ring finger protein 40"			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.796A>T	16.37:g.30776526A>T	ENSP00000325677:p.Thr266Ser	Somatic	159	2		WXS	Illumina HiSeq	Phase_I	311	86	NM_014771	0	0	4	4	0	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.662367	0.88251	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000452273	T;T	0.33438	1.58;1.41	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.56485	0.1988	M	0.78049	2.395	0.80722	D	1	D;P;P	0.67145	0.996;0.653;0.952	D;B;P	0.73380	0.98;0.392;0.558	T	0.58205	-0.7677	10	0.46703	T	0.11	-14.0565	15.105	0.72315	1.0:0.0:0.0:0.0	.	266;266;266	O75150-4;A8K6K1;O75150	.;.;BRE1B_HUMAN	S	266;266;115	ENSP00000325677:T266S;ENSP00000350563:T266S	ENSP00000325677:T266S	T	+	1	0	RNF40	30684027	1.000000	0.71417	0.978000	0.43139	0.905000	0.53344	4.839000	0.62810	2.208000	0.71279	0.533000	0.62120	ACA	.		0.537	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		T	30776526	A	T	30776526	3	4	48	1	0	0	0	0	1	0	0	0	13525	275	10	5	818	5	RNF40	16	30776526	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	7130119	30776526	59578227	109	4439											
CYB5D1	124637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7762716	7762716	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccaggtgggggttctggagtCcatatgggaaatcctacacc	9	9	13	10	0	1	0	0	0	1	0	3	2	3	2	4	5	1	1	4	5	3	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:7762716C>T	ENST00000332439.4	+	4	625	c.473C>T	c.(472-474)tCc>tTc	p.S158F	LSMD1_ENST00000575208.1_5'Flank|LSMD1_ENST00000570555.1_Intron|LSMD1_ENST00000335155.5_5'Flank|LSMD1_ENST00000575771.1_5'Flank|CYB5D1_ENST00000570446.1_Missense_Mutation_p.S30F|LSMD1_ENST00000576861.1_Intron|CYB5D1_ENST00000571846.1_Intron|LSMD1_ENST00000575071.1_5'Flank|LSMD1_ENST00000333775.5_5'Flank|LSMD1_ENST00000576384.1_5'Flank	NM_144607.4	NP_653208.2	Q6P9G0	CB5D1_HUMAN	cytochrome b5 domain containing 1	158							heme binding (GO:0020037)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|skin(2)	6		all_cancers(10;0.11)|Prostate(122;0.219)				GTTCTGGAGTCCATATGGGAA	0.502																																					p.S158F		.											.	CYB5D1-91	0			c.C473T						.						47	45	46					17																	7762716		2203	4300	6503	SO:0001583	missense	124637	exon4			TGGAGTCCATATG	AK057061	CCDS11123.1	17p13.1	2006-01-12	2006-01-12						26516	protein-coding gene	gene with protein product						12477932	Standard	NM_144607		Approved	FLJ32499	uc002gjb.4	Q6P9G0		ENST00000332439.4:c.473C>T	17.37:g.7762716C>T	ENSP00000331479:p.Ser158Phe	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	111	24	NM_144607	0	0	3	4	1	D3DTQ8|Q96DM7	Missense_Mutation	SNP	ENST00000332439.4	37	CCDS11123.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968751	0.74131	.	.	ENSG00000182224	ENST00000332439	T	0.45668	0.89	5.27	5.27	0.74061	.	0.155423	0.42821	D	0.000659	T	0.40372	0.1114	M	0.64997	1.995	0.50467	D	0.999875	B	0.31910	0.346	B	0.26864	0.074	T	0.42447	-0.9451	10	0.72032	D	0.01	-23.6807	13.3117	0.60384	0.1589:0.841:0.0:0.0	.	158	Q6P9G0	CB5D1_HUMAN	F	158	ENSP00000331479:S158F	ENSP00000331479:S158F	S	+	2	0	CYB5D1	7703441	0.999000	0.42202	0.979000	0.43373	0.882000	0.50991	4.339000	0.59322	2.449000	0.82847	0.462000	0.41574	TCC	.		0.502	CYB5D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440841.1	NM_144607		T	7762716	C	T	7762716	3	4	48	1	0	0	0	0	1	0	0	0	4130	855	30	2	487	2	CYB5D1	17	7762716	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		7762716	73432494	110	4440											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	823	112		WXS	Illumina HiSeq		1062	166	NM_145301	0	0	1	4	3	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		T	15457087	C	T	15457087	3	4	48	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	7694371	15457087	65738123	111	4441											
ERBB2	2064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37876080	37876080	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggctgccccgccgagcagAgagccaggttggcctggacc	7	4	16	14	2	0	1	0	0	0	1	0	4	0	2	6	4	3	3	6	4	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:37876080A>C	ENST00000269571.5	+	16	2098	c.1939A>C	c.(1939-1941)Aga>Cga	p.R647R	ERBB2_ENST00000541774.1_Silent_p.R632R|ERBB2_ENST00000406381.2_Silent_p.R617R|ERBB2_ENST00000584601.1_Silent_p.R617R|ERBB2_ENST00000445658.2_Silent_p.R371R|ERBB2_ENST00000540147.1_Silent_p.R617R|ERBB2_ENST00000584450.1_Silent_p.R647R			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	647					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CGCCGAGCAGAGAGCCAGGTT	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.R647R		.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2-9959	0			c.A1939C						.						153	131	138					17																	37876080		2203	4300	6503	SO:0001819	synonymous_variant	2064	exon16			GAGCAGAGAGCCA	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1939A>C	17.37:g.37876080A>C		Somatic	243	0		WXS	Illumina HiSeq	Phase_I	471	93	NM_004448	0	0	0	0	0	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	37	CCDS32642.1																																																																																			.		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			C	37876080	A	C	37876080	2	2	48	1	0	0	0	0	0	0	0	1	5219	296	11	5		5	ERBB2	17	37876080	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08	22418993	37876080	43319130	112	4442											
PLEKHH3	79990	broad.mit.edu	37	chr17	40822333	40822333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctgcaggcgcagcgccGccagggcgcgcagcgtgtcg	4	4	18	15	7	1	0	0	0	1	0	2	0	1	0	2	3	3	4	2	3	0	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:40822333G>A	ENST00000591022.1	-	11	2003	c.1616C>T	c.(1615-1617)gCg>gTg	p.A539V	PLEKHH3_ENST00000412503.1_Intron|PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000293349.6_Missense_Mutation_p.A536V	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	539	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GCGCAGCGCCGCCAGGGCGCG	0.791																																					p.A539V													.	PLEKHH3-158	0			c.C1616T						.						2	2	2					17																	40822333		876	2032	2908	SO:0001583	missense	79990	exon11			AGCGCCGCCAGGG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1616C>T	17.37:g.40822333G>A	ENSP00000468678:p.Ala539Val	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_024927	0	0	0	4	4	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	37	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167754	0.78339	.	.	ENSG00000068137	ENST00000456950;ENST00000293349	.	.	.	4.35	2.36	0.29203	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);	0.577393	0.15545	N	0.256730	T	0.49321	0.1550	M	0.66297	2.02	0.80722	D	1	P;B	0.39624	0.681;0.206	B;B	0.29440	0.102;0.022	T	0.51585	-0.8687	9	0.66056	D	0.02	-11.77	10.2113	0.43143	0.1483:0.0:0.8517:0.0	.	536;539	Q7Z736-2;Q7Z736	.;PKHH3_HUMAN	V	198;539	.	ENSP00000293349:A539V	A	-	2	0	PLEKHH3	38075859	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.679000	0.68160	0.476000	0.27440	0.555000	0.69702	GCG	.		0.791	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		A	40822333	G	A	40822333	3	1	48	1	0	0	0	0	1	0	0	0	12104	1087	38	1	777	1	PLEKHH3	17	40822333	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	2946253	40822333	40372877	113	4443											
ATXN7L3	56970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42275086	42275086	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaccaggtccgcgtatatctCctgagcgatggcctgggccc	6	8	13	14	3	1	1	0	1	1	0	3	3	2	1	5	3	1	1	5	3	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:42275086C>A	ENST00000454077.2	-	2	63	c.64G>T	c.(64-66)Gag>Tag	p.E22*	ATXN7L3_ENST00000389384.4_Nonsense_Mutation_p.E22*|CTB-175E5.7_ENST00000586560.1_RNA|ATXN7L3_ENST00000593073.1_Intron	NM_020218.1	NP_064603.1			ataxin 7-like 3											kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCGTATATCTCCTGAGCGATG	0.577																																					p.E22X		.											.	ATXN7L3-68	0			c.G64T						.						96	95	96					17																	42275086		1985	4163	6148	SO:0001587	stop_gained	56970	exon2			ATATCTCCTGAGC	AK056002	CCDS42345.1, CCDS45697.1	17q21	2010-03-10			ENSG00000087152	ENSG00000087152			25416	protein-coding gene	gene with protein product						15115762	Standard	NM_001098833		Approved	DKFZp761G2113	uc002ifz.3	Q14CW9		ENST00000454077.2:c.64G>T	17.37:g.42275086C>A	ENSP00000397259:p.Glu22*	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	328	58	NM_020218	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000454077.2	37	CCDS45697.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456493	0.63401	.	.	ENSG00000087152	ENST00000454077;ENST00000389384	.	.	.	4.47	4.47	0.54385	.	0.064498	0.64402	U	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	14.0541	0.64756	0.0:1.0:0.0:0.0	.	.	.	.	X	22	.	ENSP00000374035:E22X	E	-	1	0	ATXN7L3	39630612	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	7.490000	0.81461	2.010000	0.58986	0.655000	0.94253	GAG	.		0.577	ATXN7L3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457724.1			A	42275086	C	A	42275086	4	1	48	1	0	0	0	0	0	1	0	0	1219	864	30	4	1044	4	ATXN7L3	17	42275086	Nonsense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	1452753	42275086	38920124	114	4444											
TTLL6	284076	broad.mit.edu	37	chr17	46865176	46865176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cccggatgtcttcctaccggGcatactcctcccgagccctg	5	9	9	18	3	1	0	0	0	1	0	4	2	4	1	6	2	3	1	6	2	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:46865176G>A	ENST00000393382.3	-	11	1727	c.1586C>T	c.(1585-1587)gCc>gTc	p.A529V	TTLL6_ENST00000433608.2_Missense_Mutation_p.A222V	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TTCCTACCGGGCATACTCCTC	0.537																																					p.A529V													.	TTLL6-90	0			c.C1586T						.						79	79	79					17																	46865176		2203	4300	6503	SO:0001583	missense	284076	exon11			TACCGGGCATACT	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.1586C>T	17.37:g.46865176G>A	ENSP00000377043:p.Ala529Val	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	476	6	NM_001130918	0	0	0	0	0		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	.	.	.	.	.	.	.	.	.	.	G	35	5.462977	0.96257	.	.	ENSG00000170703	ENST00000440941;ENST00000305326;ENST00000433608;ENST00000393382	.	.	.	5.38	5.38	0.77491	.	6.121500	0.01008	U	0.003785	D	0.82522	0.5055	M	0.79475	2.455	0.48571	D	0.999675	D;D;D	0.69078	0.99;0.967;0.997	P;P;P	0.60682	0.743;0.792;0.878	T	0.67998	-0.5525	9	0.72032	D	0.01	.	18.3115	0.90201	0.0:0.0:1.0:0.0	.	481;282;222	Q8N841;D3DTW0;G5E937	TTLL6_HUMAN;.;.	V	529;222;207;481	.	ENSP00000302547:A222V	A	-	2	0	TTLL6	44220175	1.000000	0.71417	0.971000	0.41717	0.954000	0.61252	9.381000	0.97205	2.694000	0.91930	0.555000	0.69702	GCC	.		0.537	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		A	46865176	G	A	46865176	3	1	48	1	0	0	0	0	1	0	0	0	16764	1203	42	2	1109	2	TTLL6	17	46865176	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	4590090	46865176	34330034	115	4445											
SPATA20	64847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48628196	48628196	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctcccggagcctgtgttggGtgccaccgagccgctgacct	4	8	13	16	3	0	1	0	1	0	0	1	3	1	2	7	2	3	2	7	2	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:48628196G>C	ENST00000356488.4	+	10	1336	c.1253G>C	c.(1252-1254)gGt>gCt	p.G418A	SPATA20_ENST00000006658.6_Missense_Mutation_p.G434A|SPATA20_ENST00000393244.3_Missense_Mutation_p.G374A|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	418					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CCTGTGTTGGGTGCCACCGAG	0.642											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G434A		.											.	SPATA20-90	0			c.G1301C						.						64	74	70					17																	48628196		2203	4298	6501	SO:0001583	missense	64847	exon11			TGTTGGGTGCCAC		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1253G>C	17.37:g.48628196G>C	ENSP00000348878:p.Gly418Ala	Somatic	208	2	119	WXS	Illumina HiSeq	Phase_I	347	62	NM_022827	0	0	36	53	17	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475913	0.26511	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.25912	1.77;1.79;1.81	5.64	3.66	0.41972	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.100427	0.64402	D	0.000002	T	0.19446	0.0467	L	0.34521	1.04	0.49213	D	0.99976	B;B	0.31879	0.344;0.281	B;B	0.33339	0.112;0.162	T	0.05886	-1.0858	10	0.56958	D	0.05	-13.2905	9.0573	0.36414	0.2195:0.0:0.7805:0.0	.	418;434	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	A	434;418;374	ENSP00000006658:G434A;ENSP00000348878:G418A;ENSP00000376935:G374A	ENSP00000006658:G434A	G	+	2	0	SPATA20	45983195	1.000000	0.71417	0.029000	0.17559	0.008000	0.06430	4.956000	0.63645	1.395000	0.46643	0.655000	0.94253	GGT	.		0.642	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		C	48628196	G	C	48628196	3	2	48	1	0	0	0	0	1	0	0	0	15038	1261	44	4	1343	4	SPATA20	17	48628196	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	1763020	48628196	32567014	116	4446											
ABCA6	23460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	67108373	67108373	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaaaaacatagaagaacCtgcacacttcagtctcccat	15	10	4	12	0	3	2	2	0	1	2	4	2	3	2	2	0	3	1	2	0	5	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:67108373C>T	ENST00000284425.2	-	16	2257	c.2083G>A	c.(2083-2085)Ggt>Agt	p.G695S		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	695	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					ATAGAAGAACCTGCACACTTC	0.368																																					p.G695S		.											.	ABCA6-159	0			c.G2083A						.						156	164	162					17																	67108373		2203	4300	6503	SO:0001583	missense	23460	exon16			AAGAACCTGCACA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.2083G>A	17.37:g.67108373C>T	ENSP00000284425:p.Gly695Ser	Somatic	548	0		WXS	Illumina HiSeq	Phase_I	63	28	NM_080284	0	0	2	2	0	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599754	0.87055	.	.	ENSG00000154262	ENST00000284425	T	0.80393	-1.37	4.65	4.65	0.58169	ABC transporter-like (1);	0.116516	0.38058	N	0.001826	D	0.94308	0.8171	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96675	0.9499	10	0.87932	D	0	.	17.0385	0.86483	0.0:1.0:0.0:0.0	.	695	Q8N139	ABCA6_HUMAN	S	695	ENSP00000284425:G695S	ENSP00000284425:G695S	G	-	1	0	ABCA6	64619968	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	6.512000	0.73737	2.568000	0.86640	0.655000	0.94253	GGT	.		0.368	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		T	67108373	C	T	67108373	3	4	48	1	0	0	0	0	1	0	0	0	36	681	24	2	2866	2	ABCA6	17	67108373	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	18480177	67108373	14086837	117	4447											
TMEM104	54868	broad.mit.edu	37	chr17	72832672	72832672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcctggtgtaccactgccGcagggacacccagctggcct	6	8	11	16	1	0	0	0	0	0	0	1	1	1	1	5	3	3	3	5	3	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:72832672G>A	ENST00000335464.5	+	10	1499	c.1337G>A	c.(1336-1338)cGc>cAc	p.R446H	TMEM104_ENST00000417024.2_Intron|TMEM104_ENST00000582330.1_Missense_Mutation_p.R446H|TMEM104_ENST00000582773.1_Intron	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	446						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TACCACTGCCGCAGGGACACC	0.647																																					p.R446H													.	TMEM104-90	0			c.G1337A						.						56	46	50					17																	72832672		2203	4300	6503	SO:0001583	missense	54868	exon10			ACTGCCGCAGGGA	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.1337G>A	17.37:g.72832672G>A	ENSP00000334849:p.Arg446His	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	207	5	NM_017728	0	0	2	2	0	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	37	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128714	0.94473	.	.	ENSG00000109066	ENST00000335464	T	0.56444	0.46	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.78717	0.4327	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82438	-0.0457	10	0.56958	D	0.05	-31.4614	19.021	0.92916	0.0:0.0:1.0:0.0	.	446	Q8NE00	TM104_HUMAN	H	446	ENSP00000334849:R446H	ENSP00000334849:R446H	R	+	2	0	TMEM104	70344267	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.355000	0.97087	2.584000	0.87258	0.462000	0.41574	CGC	.		0.647	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		A	72832672	G	A	72832672	3	1	48	1	0	0	0	0	1	0	0	0	16050	1087	38	1	1371	1	TMEM104	17	72832672	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	5724299	72832672	8362538	118	4448											
DNAH17	8632	hgsc.bcm.edu;broad.mit.edu	37	chr17	76445563	76445563	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccccgggccgtgtacatgTagacggagtaggtgatctcg	7	9	15	10	4	1	2	0	1	1	1	3	3	2	3	3	3	1	3	3	3	3	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:76445563T>C	ENST00000585328.1	-	69	11253	c.11129A>G	c.(11128-11130)tAc>tGc	p.Y3710C	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Missense_Mutation_p.Y3701C	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3701					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CGTGTACATGTAGACGGAGTA	0.532																																					p.Y3715C		.											.	DNAH17-142	0			c.A11144G						.						125	92	103					17																	76445563		2203	4296	6499	SO:0001583	missense	8632	exon69			TACATGTAGACGG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.11129A>G	17.37:g.76445563T>C	ENSP00000465516:p.Tyr3710Cys	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	34	5	NM_173628	0	0	0	0	0	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	T	13.95	2.390270	0.42410	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.72051	-0.62	4.7	-3.01	0.05463	.	0.381500	0.21964	N	0.066560	T	0.78477	0.4289	H	0.97265	3.97	0.38101	D	0.937258	B	0.15719	0.014	B	0.19946	0.027	T	0.77397	-0.2603	10	0.66056	D	0.02	.	13.6553	0.62336	0.7125:0.0:0.0:0.2875	.	3710	E7EUM8	.	C	3710;3701	ENSP00000374490:Y3701C	ENSP00000300671:Y3710C	Y	-	2	0	DNAH17	73957158	1.000000	0.71417	0.982000	0.44146	0.979000	0.70002	1.592000	0.36676	-0.130000	0.11599	0.459000	0.35465	TAC	.		0.532	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		C	76445563	T	C	76445563	3	2	48	1	0	0	0	0	1	0	0	0	4612	1638	57	3	2296	3	DNAH17	17	76445563	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	3612891	76445563	4749647	119	4449											
TAF4B	6875	broad.mit.edu	37	chr18	23969874	23969874	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccaaacagttgcatcgTccaagaatcacgagaatctg	14	7	8	12	2	2	2	1	0	1	2	4	3	3	2	3	0	2	2	3	0	4	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr18:23969874T>C	ENST00000269142.5	+	15	3485	c.2487T>C	c.(2485-2487)cgT>cgC	p.R829R	TAF4B_ENST00000578121.1_Silent_p.R834R	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	829					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			AGTTGCATCGTCCAAGAATCA	0.423																																					p.R829R													.	TAF4B-71	0			c.T2487C						.						114	110	111					18																	23969874		1901	4125	6026	SO:0001819	synonymous_variant	6875	exon15			GCATCGTCCAAGA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.2487T>C	18.37:g.23969874T>C		Somatic	272	0		WXS	Illumina HiSeq	Phase_I	108	3	NM_005640	0	0	1	1	0	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1																																																																																			.		0.423	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		C	23969874	T	C	23969874	2	2	48	1	0	0	0	0	0	0	0	1	15559	1654	58	3		3	TAF4B	18	23969874	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08		23969874	54107374	120	4450											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558373	11558373	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggaggaggaggaggaggaAgaagaggctgaagaagagga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr19:11558373A>G	ENST00000589838.1	+	10	969	c.969A>G	c.(967-969)gaA>gaG	p.E323E	PRKCSH_ENST00000252455.2_Silent_p.E323E|PRKCSH_ENST00000587327.1_Silent_p.E323E|PRKCSH_ENST00000412601.1_Silent_p.E323E|PRKCSH_ENST00000592741.1_Silent_p.E323E|PRKCSH_ENST00000591462.1_Silent_p.E323E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	323	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaagaagaggctg	0.642																																					p.E323E		.											.	PRKCSH-90	0			c.A969G						.																																			SO:0001819	synonymous_variant	5589	exon11			GGAGGAAGAAGAG		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.969A>G	19.37:g.11558373A>G		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	52	5	NM_001001329	0	0	9	9	0	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																			.		0.642	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			G	11558373	A	G	11558373	2	3	48	1	0	0	0	0	0	0	0	1	12545	69	3	3		3	PRKCSH	19	11558373	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08		11558373	47570610	121	4451											
KIAA0892	23383	broad.mit.edu	37	chr19	19454740	19454740	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acgggtcacaaggccacggcGctgcaggaggtaaggctgga	10	4	17	10	3	1	0	1	0	0	0	1	2	1	2	1	7	1	4	1	7	2	1	rs369999842		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr19:19454740G>A	ENST00000392313.6	+	10	1247	c.1068G>A	c.(1066-1068)gcG>gcA	p.A356A	MAU2_ENST00000262815.8_Silent_p.A356A	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	356					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						AGGCCACGGCGCTGCAGGAGG	0.582																																					p.A356A													.	MAU2-91	0			c.G1068A						.						58	58	58					19																	19454740		2084	4214	6298	SO:0001819	synonymous_variant	23383	exon10			CACGGCGCTGCAG	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.1068G>A	19.37:g.19454740G>A		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	247	5	NM_015329	0	0	0	0	0	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Silent	SNP	ENST00000392313.6	37	CCDS32969.2																																																																																			.		0.582	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		A	19454740	G	A	19454740	2	1	48	1	0	0	0	0	0	0	0	1	8217	1074	38	1		1	KIAA0892	19	19454740	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	7896367	19454740	39674243	122	4452											
ZNF14	7561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19823080	19823080	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggctttcccacattctttaCatttataaggtcgagcccca	10	13	6	12	1	1	0	0	0	1	0	3	1	2	0	3	2	2	1	3	2	3	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr19:19823080C>A	ENST00000344099.3	-	4	1148	c.1010G>T	c.(1009-1011)tGt>tTt	p.C337F		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	337					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)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				ACATTCTTTACATTTATAAGG	0.378																																					p.C337F		.											.	ZNF14-517	0			c.G1010T						.						54	54	54					19																	19823080		2203	4300	6503	SO:0001583	missense	7561	exon4			TCTTTACATTTAT	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.1010G>T	19.37:g.19823080C>A	ENSP00000340514:p.Cys337Phe	Somatic	202	1		WXS	Illumina HiSeq	Phase_I	39	13	NM_021030	0	0	0	0	0	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	37	CCDS12409.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.643725	0.67244	.	.	ENSG00000105708	ENST00000344099	D	0.85088	-1.94	1.8	1.8	0.24995	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92397	0.7587	M	0.90705	3.14	0.30395	N	0.780618	D	0.89917	1.0	D	0.97110	1.0	D	0.87222	0.2254	9	0.87932	D	0	.	9.1514	0.36965	0.0:1.0:0.0:0.0	.	337	P17017	ZNF14_HUMAN	F	337	ENSP00000340514:C337F	ENSP00000340514:C337F	C	-	2	0	ZNF14	19684080	0.951000	0.32395	0.168000	0.22838	0.635000	0.38103	3.634000	0.54302	0.977000	0.38444	0.467000	0.42956	TGT	.		0.378	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		A	19823080	C	A	19823080	3	1	48	1	0	0	0	0	1	0	0	0	17760	478	17	4	922	4	ZNF14	19	19823080	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	368340	19823080	39305903	123	4453											
ATP4A	495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36050918	36050918	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacccccgacgccagcgatGcgatgcgcccaatgatggtg	8	5	12	16	5	0	1	0	1	0	0	0	4	0	1	5	1	3	0	5	1	1	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr19:36050918G>T	ENST00000262623.3	-	7	873	c.845C>A	c.(844-846)gCa>gAa	p.A282E		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	282					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CGCCAGCGATGCGATGCGCCC	0.647																																					p.A282E		.											.	ATP4A-91	0			c.C845A						.						96	73	81					19																	36050918		2203	4300	6503	SO:0001583	missense	495	exon7			AGCGATGCGATGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.845C>A	19.37:g.36050918G>T	ENSP00000262623:p.Ala282Glu	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	257	72	NM_000704	0	0	0	0	0	O00738	Missense_Mutation	SNP	ENST00000262623.3	37	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.140434	0.56936	.	.	ENSG00000105675	ENST00000262623	D	0.92495	-3.05	3.94	3.94	0.45596	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.077790	0.48767	D	0.000178	D	0.96324	0.8801	M	0.91920	3.255	0.80722	D	1	D	0.57899	0.981	D	0.66196	0.942	D	0.97050	0.9763	10	0.87932	D	0	.	13.8309	0.63380	0.0:0.0:1.0:0.0	.	282	P20648	ATP4A_HUMAN	E	282	ENSP00000262623:A282E	ENSP00000262623:A282E	A	-	2	0	ATP4A	40742758	1.000000	0.71417	0.276000	0.24689	0.038000	0.13279	9.600000	0.98282	2.203000	0.70933	0.561000	0.74099	GCA	.		0.647	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36050918	G	T	36050918	3	4	48	1	0	0	0	0	1	0	0	0	1146	1319	46	4	2326	4	ATP4A	19	36050918	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	16227838	36050918	23078065	124	4454											
SOX12	6666	hgsc.bcm.edu	37	chr20	307296	307296	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgaggaaggtgaagaggAgacggtggcgtcgggggagg	9	4	24	4	3	0	4	0	2	0	2	1	7	0	6	0	9	0	1	0	9	2	0	rs73574574	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr20:307296A>G	ENST00000342665.2	+	1	1058	c.728A>G	c.(727-729)gAg>gGg	p.E243G	SOX12_ENST00000544632.1_Missense_Mutation_p.E243G|RP5-1103G7.4_ENST00000442637.1_RNA|RP5-1103G7.4_ENST00000414676.1_RNA	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	243	Asp/Glu-rich (acidic).				cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GGTGAAGAGGAGACGGTGGCG	0.751													A|||	23	0.00459265	0.0166	0.0014	5008	,	,		9282	0		0	False		,,,				2504	0				p.E243G		.											.	SOX12-514	0			c.A728G						.	A	GLY/GLU	48,4096		0,48,2024	13	11	12		728	3.2	1	20	dbSNP_130	12	0,8176		0,0,4088	no	missense	SOX12	NM_006943.2	98	0,48,6112	GG,GA,AA		0.0,1.1583,0.3896	benign	243/316	307296	48,12272	2072	4088	6160	SO:0001583	missense	6666	exon1			AAGAGGAGACGGT	U35612	CCDS12995.1	20p13	2008-07-28	2002-07-22	2002-07-26	ENSG00000177732	ENSG00000177732		"SRY (sex determining region Y)-boxes"	11198	protein-coding gene	gene with protein product		601947	"SRY (sex determining region Y)-box 22"	SOX22		9215677	Standard	NM_006943		Approved		uc002wdh.4	O15370	OTTHUMG00000031623	ENST00000342665.2:c.728A>G	20.37:g.307296A>G	ENSP00000347646:p.Glu243Gly	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	10	5	NM_006943	0	0	5	7	2	Q5D038|Q9NUD4	Missense_Mutation	SNP	ENST00000342665.2	37	CCDS12995.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	9.986	1.229492	0.22542	0.011583	0.0	ENSG00000177732	ENST00000544632;ENST00000342665	D;D	0.98221	-4.8;-4.8	3.23	3.23	0.37069	.	9.611210	0.01410	U	0.013973	D	0.92166	0.7516	N	0.24115	0.695	0.25663	N	0.985977	B	0.09022	0.002	B	0.09377	0.004	D	0.86384	0.1731	10	0.25751	T	0.34	.	10.4928	0.44760	1.0:0.0:0.0:0.0	.	243	O15370	SOX12_HUMAN	G	243	ENSP00000441671:E243G;ENSP00000347646:E243G	ENSP00000347646:E243G	E	+	2	0	SOX12	255296	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	4.263000	0.58853	1.342000	0.45619	0.164000	0.16699	GAG	A|0.995;G|0.005		0.751	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943		G	307296	A	G	307296	3	3	48	1	0	0	0	0	1	0	0	0	14975	304	11	3	730	3	SOX12	20	307296	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08		307296	62718224	125	4455											
UBOX5	22888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	3090943	3090943	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggcacattcggggcccaGgatgctcccaggctgctctg	6	7	15	13	1	1	0	0	0	1	0	3	2	2	2	2	6	2	4	2	6	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr20:3090943G>A	ENST00000217173.2	-	5	1906	c.1435C>T	c.(1435-1437)Ctg>Ttg	p.L479L	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Silent_p.L425L|UBOX5-AS1_ENST00000454019.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						TCGGGGCCCAGGATGCTCCCA	0.587																																					p.P477L		.											.	UBOX5-227	0			c.C1430T						.						60	69	66					20																	3090943		2203	4300	6503	SO:0001819	synonymous_variant	22888	exon5			GGCCCAGGATGCT	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.1435C>T	20.37:g.3090943G>A		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	253	97	NM_001267584	0	0	2	3	1		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1																																																																																			.		0.587	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3090943	G	A	3090943	2	1	48	1	0	0	0	0	0	0	0	1	16927	991	35	2		2	UBOX5	20	3090943	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	2783647	3090943	59934577	126	4456											
ZSWIM1	90204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44512145	44512145	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggcctgtgtgcccagaacaAtcatgctccctcagacacca	10	7	9	15	0	2	2	2	0	0	2	3	2	3	2	4	1	3	1	4	1	2	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr20:44512145A>T	ENST00000372523.1	+	2	1009	c.914A>T	c.(913-915)aAt>aTt	p.N305I	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.N305I	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	305						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				GCCCAGAACAATCATGCTCCC	0.542																																					p.N305I		.											.	ZSWIM1-91	0			c.A914T						.						106	100	102					20																	44512145		2203	4300	6503	SO:0001583	missense	90204	exon2			AGAACAATCATGC	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"Zinc fingers, SWIM-type"	16155	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 162"	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.914A>T	20.37:g.44512145A>T	ENSP00000361601:p.Asn305Ile	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	330	103	NM_080603	0	0	17	23	6	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	37	CCDS13382.2	.	.	.	.	.	.	.	.	.	.	A	1.890	-0.455649	0.04540	.	.	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.23754	1.89;1.89	5.03	-5.13	0.02884	.	1.279150	0.05647	U	0.584537	T	0.15565	0.0375	N	0.19112	0.55	0.09310	N	1	B	0.33379	0.41	B	0.29440	0.102	T	0.20538	-1.0272	10	0.37606	T	0.19	-6.9614	13.0392	0.58889	0.2965:0.0964:0.607:0.0	.	305	Q9BR11	ZSWM1_HUMAN	I	305	ENSP00000361601:N305I;ENSP00000361598:N305I	ENSP00000361598:N305I	N	+	2	0	ZSWIM1	43945552	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	-3.302000	0.00520	-0.994000	0.03463	-0.256000	0.11100	AAT	.		0.542	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		T	44512145	A	T	44512145	3	4	48	1	0	0	0	0	1	0	0	0	18272	101	4	5	916	5	ZSWIM1	20	44512145	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	41421202	44512145	18513375	127	4457											
GRAMD4	23151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	47068788	47068788	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattgatttcatctttaaacGctgcccgaggctgcgcgcca	8	11	9	13	4	2	1	1	1	1	0	2	2	2	1	2	1	3	2	2	1	2	4	rs371794625		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr22:47068788G>A	ENST00000406902.1	+	14	1346	c.1133G>A	c.(1132-1134)cGc>cAc	p.R378H	GRAMD4_ENST00000408031.1_5'Flank|GRAMD4_ENST00000361034.3_Missense_Mutation_p.R378H			Q6IC98	GRAM4_HUMAN	GRAM domain containing 4	378					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		ATCTTTAAACGCTGCCCGAGG	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		16350	0		0	False		,,,				2504	0				p.R378H		.											.	GRAMD4-23	0			c.G1133A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	71	68	69		1133	4.6	1	22		69	0,8600		0,0,4300	no	missense	GRAMD4	NM_015124.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	378/579	47068788	1,13005	2203	4300	6503	SO:0001583	missense	23151	exon13			TTAAACGCTGCCC		CCDS33672.1	22q13.31	2008-03-03			ENSG00000075240	ENSG00000075240			29113	protein-coding gene	gene with protein product	"death-inducing-protein"	613691				15565177	Standard	NM_015124		Approved	KIAA0767, DIP	uc003bhx.3	Q6IC98	OTTHUMG00000150402	ENST00000406902.1:c.1133G>A	22.37:g.47068788G>A	ENSP00000385689:p.Arg378His	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	117	42	NM_015124	0	0	6	11	5	A9IN51|A9IN57|Q68EN0|Q9UGE6|Q9Y4B9	Missense_Mutation	SNP	ENST00000406902.1	37	CCDS33672.1	.	.	.	.	.	.	.	.	.	.	g	29.5	5.010183	0.93346	2.27E-4	0.0	ENSG00000075240	ENST00000406902;ENST00000361034	T;T	0.45276	0.9;0.9	4.63	4.63	0.57726	.	0.079168	0.49916	D	0.000133	T	0.51466	0.1676	L	0.48642	1.525	0.53688	D	0.99997	D	0.71674	0.998	P	0.56216	0.794	T	0.56177	-0.8022	10	0.87932	D	0	-22.1761	15.3516	0.74393	0.0:0.0:1.0:0.0	.	378	Q6IC98	GRAM4_HUMAN	H	378	ENSP00000385689:R378H;ENSP00000354313:R378H	ENSP00000354313:R378H	R	+	2	0	GRAMD4	45447452	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	8.900000	0.92551	2.294000	0.77228	0.563000	0.77884	CGC	.		0.577	GRAMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317969.1	NM_015124		A	47068788	G	A	47068788	3	1	48	1	0	0	0	0	1	0	0	0	6773	1087	38	1	1183	1	GRAMD4	22	47068788	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		47068788	4235778	128	4458											
TBX22	50945	hgsc.bcm.edu	37	chrX	79286336	79286336	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggttcatctgaagactccaGtgatcagtatctacaagcac	12	10	8	11	1	4	3	2	2	2	1	5	3	5	3	1	1	2	3	1	1	4	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chrX:79286336G>C	ENST00000373294.5	+	8	1317	c.1289G>C	c.(1288-1290)aGt>aCt	p.S430T	TBX22_ENST00000373291.1_Missense_Mutation_p.S310T|TBX22_ENST00000442340.1_Missense_Mutation_p.S310T|TBX22_ENST00000373296.3_Missense_Mutation_p.S430T	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	430					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GAAGACTCCAGTGATCAGTAT	0.428																																					p.S430T		.											.	TBX22-628	0			c.G1289C						.						132	125	128					X																	79286336		2203	4300	6503	SO:0001583	missense	50945	exon8			ACTCCAGTGATCA	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"T-boxes"	11600	protein-coding gene	gene with protein product		300307	"cleft palate and/or ankyloglossia"	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.1289G>C	X.37:g.79286336G>C	ENSP00000362390:p.Ser430Thr	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_016954	0	0	0	0	0	Q5JZ06|Q96LC0|Q9HBF1	Missense_Mutation	SNP	ENST00000373294.5	37	CCDS14445.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.568512	0.00133	.	.	ENSG00000122145	ENST00000373296;ENST00000442340;ENST00000373294;ENST00000373291	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	4.12	-6.23	0.02052	.	14.083600	0.00166	N	0.000000	T	0.66287	0.2774	L	0.48642	1.525	0.09310	N	1	B	0.23937	0.094	B	0.22386	0.039	T	0.55541	-0.8125	10	0.07990	T	0.79	.	8.6398	0.33970	0.3387:0.0:0.5484:0.1129	.	430	Q9Y458	TBX22_HUMAN	T	430;310;430;310	ENSP00000362393:S430T;ENSP00000396394:S310T;ENSP00000362390:S430T;ENSP00000362388:S310T	ENSP00000362388:S310T	S	+	2	0	TBX22	79172992	0.362000	0.24980	0.000000	0.03702	0.002000	0.02628	-0.098000	0.11024	-1.700000	0.01414	-0.503000	0.04515	AGT	.		0.428	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954		C	79286336	G	C	79286336	3	2	48	1	0	0	0	0	1	0	0	0	15690	1029	36	4	1319	4	TBX22	23	79286336	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		79286336	75984224	129	4459											
SLC6A8	6535	hgsc.bcm.edu	37	chrX	152956939	152956939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgccatgaagactgtgccaAtgccagcctggccaacctca	10	6	9	16	1	1	2	1	1	0	1	1	2	1	2	7	1	4	0	7	1	3	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chrX:152956939A>G	ENST00000253122.5	+	3	1051	c.575A>G	c.(574-576)aAt>aGt	p.N192S	SLC6A8_ENST00000430077.2_Missense_Mutation_p.N77S	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	192					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	GACTGTGCCAATGCCAGCCTG	0.622																																					p.N192S		.											.	SLC6A8-131	0			c.A575G						.						112	106	108					X																	152956939		2203	4300	6503	SO:0001583	missense	6535	exon3			GTGCCAATGCCAG		CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.575A>G	X.37:g.152956939A>G	ENSP00000253122:p.Asn192Ser	Somatic	216	1		WXS	Illumina HiSeq	Phase_I	335	18	NM_005629	0	0	43	43	0	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Missense_Mutation	SNP	ENST00000253122.5	37	CCDS14726.1	.	.	.	.	.	.	.	.	.	.	a	11.51	1.660944	0.29515	.	.	ENSG00000130821	ENST00000253122;ENST00000430077	T;T	0.74106	-0.81;-0.81	4.05	1.61	0.23674	.	.	.	.	.	T	0.59252	0.2180	L	0.35593	1.075	0.36406	D	0.863427	B;P;B	0.34724	0.213;0.465;0.078	B;B;B	0.33960	0.173;0.101;0.115	T	0.55673	-0.8104	9	0.39692	T	0.17	.	7.1433	0.25568	0.7987:0.0:0.2013:0.0	.	192;211;192	D3DWV2;Q59EV7;P48029	.;.;SC6A8_HUMAN	S	192;77	ENSP00000253122:N192S;ENSP00000403041:N77S	ENSP00000253122:N192S	N	+	2	0	SLC6A8	152610133	.	.	0.975000	0.42487	0.951000	0.60555	.	.	0.054000	0.16065	0.345000	0.21793	AAT	.		0.622	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			G	152956939	A	G	152956939	3	3	48	1	0	0	0	0	1	0	0	0	14722	101	4	3	585	3	SLC6A8	23	152956939	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	73670603	152956939	2313621	130	4460											
EPHA8	2046	hgsc.bcm.edu;broad.mit.edu	37	chr1	22903356	22903356	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtgccggctacgaggagcGgcgggatgcctgtgtgggtg	5	7	20	9	4	0	0	0	0	0	0	0	3	0	2	2	5	4	1	2	5	1	1	rs139777546		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:22903356G>C	ENST00000166244.3	+	3	878	c.806G>C	c.(805-807)cGg>cCg	p.R269P	EPHA8_ENST00000538803.1_Missense_Mutation_p.R269P|EPHA8_ENST00000374644.4_Missense_Mutation_p.R269P	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	269	Cys-rich.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TACGAGGAGCGGCGGGATGCC	0.677																																					p.R269P		.											.	EPHA8-1380	0			c.G806C						.						25	26	26					1																	22903356		2201	4296	6497	SO:0001583	missense	2046	exon3			AGGAGCGGCGGGA	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.806G>C	1.37:g.22903356G>C	ENSP00000166244:p.Arg269Pro	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	82	25	NM_020526	0	0	0	0	0	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330463	0.41297	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.29397	1.57;5.07;5.07	4.09	2.01	0.26516	.	0.231542	0.36893	N	0.002360	T	0.22975	0.0555	L	0.32530	0.975	0.28846	N	0.896308	B;P	0.42010	0.337;0.768	B;P	0.44477	0.147;0.451	T	0.06092	-1.0846	10	0.48119	T	0.1	.	4.9743	0.14133	0.2072:0.0:0.6108:0.1819	.	269;269	P29322;P29322-2	EPHA8_HUMAN;.	P	269	ENSP00000166244:R269P;ENSP00000363775:R269P;ENSP00000440274:R269P	ENSP00000166244:R269P	R	+	2	0	EPHA8	22775943	0.991000	0.36638	1.000000	0.80357	0.979000	0.70002	0.794000	0.26958	0.926000	0.37118	0.442000	0.29010	CGG	G|0.999;A|0.001		0.677	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		C	22903356	G	C	22903356	3	2	49	1	0	0	0	0	1	0	0	0	5186	1116	39	4	816	4	EPHA8	1	22903356	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		22903356	226347265	1	4461											
PIGV	55650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27121059	27121059	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtttgccctcctgacattCagtgccatggggcagctgga	6	12	12	11	0	1	1	1	1	0	0	2	2	2	2	3	3	3	3	3	3	0	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:27121059C>T	ENST00000374145.1	+	3	1216	c.534C>T	c.(532-534)ttC>ttT	p.F178F	PIGV_ENST00000078527.4_Silent_p.F178F|PIGV_ENST00000449950.2_Intron	NM_001202554.1	NP_001189483.1	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class V	178					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	14		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		TCCTGACATTCAGTGCCATGG	0.562																																					p.F178F		.											.	PIGV-91	0			c.C534T						.						79	78	78					1																	27121059		2203	4300	6503	SO:0001819	synonymous_variant	55650	exon3			GACATTCAGTGCC	AK000484	CCDS287.1	1p36.11	2013-02-26	2006-06-28		ENSG00000060642	ENSG00000060642		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	26031	protein-coding gene	gene with protein product	"GPI mannosyltransferase 2", "dol-P-Man dependent GPI mannosyltransferase"	610274	"phosphatidylinositol glycan, class V"			15623507	Standard	NM_017837		Approved	FLJ20477	uc001bmz.3	Q9NUD9	OTTHUMG00000004005	ENST00000374145.1:c.534C>T	1.37:g.27121059C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	180	57	NM_001202554	0	0	8	32	24	D3DPL2|Q5JYG7|Q5JYG8|Q5JYG9|Q9NX26	Silent	SNP	ENST00000374145.1	37	CCDS287.1																																																																																			.		0.562	PIGV-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011441.1	NM_017837		T	27121059	C	T	27121059	2	4	49	1	0	0	0	0	0	0	0	1	11927	825	29	2		2	PIGV	1	27121059	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	4217703	27121059	222129562	2	4462											
SLC9A1	6548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27428600	27428600	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggatgcgctcggaaggCagggacttggggtggatgtt	7	8	20	6	2	0	0	0	0	0	0	1	4	0	4	0	8	1	4	0	8	1	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:27428600C>T	ENST00000263980.3	-	9	2417	c.1842G>A	c.(1840-1842)ctG>ctA	p.L614L	SLC9A1_ENST00000545949.1_Silent_p.L275L|SLC9A1_ENST00000490329.1_5'Flank	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	614					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	GCTCGGAAGGCAGGGACTTGG	0.582																																					p.L614L		.											.	SLC9A1-91	0			c.G1842A						.						136	126	129					1																	27428600		2203	4300	6503	SO:0001819	synonymous_variant	6548	exon9			GGAAGGCAGGGAC	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1842G>A	1.37:g.27428600C>T		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	270	74	NM_003047	0	0	13	20	7	B1ALD6|D3DPL4|Q96EM2	Silent	SNP	ENST00000263980.3	37	CCDS295.1																																																																																			.		0.582	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		T	27428600	C	T	27428600	2	4	49	1	0	0	0	0	0	0	0	1	14741	697	25	2		2	SLC9A1	1	27428600	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	307541	27428600	221822021	3	4463											
EIF2C1	26523	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	36359988	36359988	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtaatgttacccgtcgccCtgctagccatcagacgtaag	9	10	10	12	3	1	1	1	0	0	1	2	1	1	1	3	0	3	4	3	0	4	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:36359988C>T	ENST00000373204.4	+	7	1070	c.857C>T	c.(856-858)cCt>cTt	p.P286L	AGO1_ENST00000373206.1_Missense_Mutation_p.P211L	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	286	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										ACCCGTCGCCCTGCTAGCCAT	0.532																																					p.P286L		.											.	.	0			c.C857T						.						159	117	131					1																	36359988		2203	4300	6503	SO:0001583	missense	26523	exon7			GTCGCCCTGCTAG	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.857C>T	1.37:g.36359988C>T	ENSP00000362300:p.Pro286Leu	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	78	26	NM_012199	0	0	0	0	0	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	37	CCDS398.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485123	0.63962	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.14022	2.54;2.54	5.24	5.24	0.73138	Argonaute/Dicer protein, PAZ (4);	0.000000	0.85682	D	0.000000	T	0.38532	0.1044	H	0.95679	3.705	0.80722	D	1	B	0.13145	0.007	B	0.33121	0.158	T	0.50171	-0.8859	10	0.72032	D	0.01	-19.9943	19.0006	0.92832	0.0:1.0:0.0:0.0	.	286	Q9UL18	AGO1_HUMAN	L	211;286	ENSP00000362302:P211L;ENSP00000362300:P286L	ENSP00000362300:P286L	P	+	2	0	EIF2C1	36132575	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.651000	0.83577	2.721000	0.93114	0.591000	0.81541	CCT	.		0.532	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			T	36359988	C	T	36359988	3	4	49	1	0	0	0	0	1	0	0	0	5016	681	24	2	883	2	EIF2C1	1	36359988	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	8931388	36359988	212890633	4	4464											
MACF1	23499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	39907695	39907695	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgttggcactgacctcaaTactgttaaagatcagttaaa	13	12	7	9	0	2	2	2	1	0	1	2	2	2	2	2	1	1	4	2	1	6	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:39907695T>G	ENST00000372915.3	+	74	18528	c.18441T>G	c.(18439-18441)aaT>aaG	p.N6147K	MACF1_ENST00000545844.1_Missense_Mutation_p.N4189K|MACF1_ENST00000317713.7_Missense_Mutation_p.N4189K|MACF1_ENST00000361689.2_Missense_Mutation_p.N4189K|MACF1_ENST00000289893.4_Missense_Mutation_p.N4691K|MACF1_ENST00000539005.1_Missense_Mutation_p.N4059K|MACF1_ENST00000564288.1_Missense_Mutation_p.N6248K|MACF1_ENST00000567887.1_Missense_Mutation_p.N6285K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6147					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTGACCTCAATACTGTTAAAG	0.353																																					p.N4189K		.											.	MACF1-165	0			c.T12567G						.						118	110	113					1																	39907695		2203	4300	6503	SO:0001583	missense	23499	exon72			CCTCAATACTGTT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18441T>G	1.37:g.39907695T>G	ENSP00000362006:p.Asn6147Lys	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	45	12	NM_012090	0	0	1	3	2	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.72|16.72	3.201648|3.201648	0.58234|0.58234	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.48836|.	0.8;0.8;0.8;0.8;0.8;0.8|.	5.62|5.62	4.71|4.71	0.59529|0.59529	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.33990|0.33990	0.0882|0.0882	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D;P|.	0.55605|.	0.972;0.843|.	P;P|.	0.55455|.	0.776;0.62|.	T|T	0.14727|0.14727	-1.0462|-1.0462	10|5	0.32370|.	T|.	0.25|.	.|.	9.9927|9.9927	0.41881|0.41881	0.0:0.8446:0.0:0.1554|0.0:0.8446:0.0:0.1554	.|.	6147;4189|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	K|D	4189;6147;4189;4189;4059;4691|3193	ENSP00000439537:N4189K;ENSP00000362006:N6147K;ENSP00000354573:N4189K;ENSP00000313438:N4189K;ENSP00000444364:N4059K;ENSP00000289893:N4691K|.	ENSP00000289893:N4691K|.	N|Y	+|+	3|1	2|0	MACF1|MACF1	39680282|39680282	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.512000|2.512000	0.45485|0.45485	1.352000|1.352000	0.45808|0.45808	-0.366000|-0.366000	0.07423|0.07423	AAT|TAC	.		0.353	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39907695	T	G	39907695	3	3	49	1	0	0	0	0	1	0	0	0	9169	1403	49	5	19000	5	MACF1	1	39907695	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	3547707	39907695	209342926	5	4465											
MCOLN3	55283	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	85491700	85491700	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatcataatgtaccatccAttgacaaattccatttgatc	15	14	3	9	0	1	2	1	2	0	0	4	2	3	2	3	0	1	1	3	0	4	6			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:85491700A>G	ENST00000370589.2	-	9	1069	c.1017T>C	c.(1015-1017)aaT>aaC	p.N339N	MCOLN3_ENST00000474447.1_5'Flank|MCOLN3_ENST00000370587.1_3'UTR|MCOLN3_ENST00000341115.4_Silent_p.N283N|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	339					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TGTACCATCCATTGACAAATT	0.333																																					p.N339N		.											.	MCOLN3-91	0			c.T1017C						.						57	56	56					1																	85491700		2203	4300	6503	SO:0001819	synonymous_variant	55283	exon9			CCATCCATTGACA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1017T>C	1.37:g.85491700A>G		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	40	13	NM_018298	0	0	0	0	0	Q5T4H5|Q5T4H6|Q9NV09	Silent	SNP	ENST00000370589.2	37	CCDS701.1																																																																																			.		0.333	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		G	85491700	A	G	85491700	2	3	49	1	0	0	0	0	0	0	0	1	9422	214	8	3		3	MCOLN3	1	85491700	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	45584005	85491700	163758921	6	4466											
ATP1A2	477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160105304	160105304	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacattggcattgccatgggCatctctggctctgacgtctc	6	12	11	12	1	3	1	0	1	3	0	5	2	3	1	1	3	1	3	1	3	0	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:160105304C>A	ENST00000361216.3	+	16	2285	c.2196C>A	c.(2194-2196)ggC>ggA	p.G732G	ATP1A2_ENST00000392233.3_Silent_p.G732G	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	732					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			TTGCCATGGGCATCTCTGGCT	0.602																																					p.G732G		.											.	ATP1A2-518	0			c.C2196A						.						169	125	140					1																	160105304		2203	4300	6503	SO:0001819	synonymous_variant	477	exon16			CATGGGCATCTCT	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2196C>A	1.37:g.160105304C>A		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	246	97	NM_000702	0	0	0	0	0	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	C	5.352	0.250270	0.10130	.	.	ENSG00000018625	ENST00000447527	.	.	.	4.31	2.27	0.28462	.	.	.	.	.	T	0.32406	0.0828	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19844	-1.0293	4	.	.	.	.	4.575	0.12228	0.1513:0.6098:0.1479:0.091	.	.	.	.	E	443	.	.	A	+	2	0	ATP1A2	158371928	0.489000	0.26004	1.000000	0.80357	0.433000	0.31745	-0.303000	0.08210	1.154000	0.42482	0.561000	0.74099	GCA	.		0.602	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160105304	C	A	160105304	2	1	49	1	0	0	0	0	0	0	0	1	1130	697	25	4		4	ATP1A2	1	160105304	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	74613604	160105304	89145317	7	4467											
ATF6	22926	hgsc.bcm.edu	37	chr1	161748090	161748090	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acactgatgagctgcaattgGaagcagcaaatgagacgtat	15	8	11	7	1	0	3	0	3	0	1	0	5	0	4	0	1	4	5	0	1	4	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:161748090G>C	ENST00000367942.3	+	2	206	c.139G>C	c.(139-141)Gaa>Caa	p.E47Q		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	47	Transcription activation.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	GCTGCAATTGGAAGCAGCAAA	0.348																																					p.E47Q		.											.	ATF6-93	0			c.G139C						.						107	102	104					1																	161748090		2203	4300	6503	SO:0001583	missense	22926	exon2			CAATTGGAAGCAG	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"basic leucine zipper proteins"	791	protein-coding gene	gene with protein product	"activating transcription factor 6 alpha"	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.139G>C	1.37:g.161748090G>C	ENSP00000356919:p.Glu47Gln	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_007348	0	0	2	2	0	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	.	.	.	.	.	.	.	.	.	.	G	9.469	1.095154	0.20471	.	.	ENSG00000118217	ENST00000367942	T	0.14266	2.52	4.97	4.06	0.47325	.	0.206931	0.40554	N	0.001061	T	0.02649	0.0080	N	0.14661	0.345	0.22710	N	0.998823	B;B	0.19583	0.01;0.037	B;B	0.20955	0.012;0.032	T	0.40739	-0.9547	9	0.24483	T	0.36	-9.7527	9.4424	0.38677	0.0959:0.0:0.9041:0.0	.	47;48	P18850;Q59H30	ATF6A_HUMAN;.	Q	47	ENSP00000356919:E47Q	ENSP00000356919:E47Q	E	+	1	0	ATF6	160014714	1.000000	0.71417	0.449000	0.26957	0.456000	0.32438	4.229000	0.58625	1.471000	0.48121	-0.147000	0.13772	GAA	.		0.348	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348		C	161748090	G	C	161748090	3	2	49	1	0	0	0	0	1	0	0	0	1085	1175	41	4	145	4	ATF6	1	161748090	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	1642786	161748090	87502531	8	4468											
F13B	2165	broad.mit.edu	37	chr1	197021793	197021794	+	Frame_Shift_Del	DEL	TC	TC	-																															tacataaaggatatttcactTctcctctgttgcactgcaca																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:197021793_197021794delTC	ENST00000367412.1	-	9	1568_1569	c.1525_1526delGA	c.(1525-1527)gaafs	p.E509fs	F13B_ENST00000490002.1_5'Flank	NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	509	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						ATATTTCACTTCTCCTCTGTTG	0.327																																					p.509_509del													.	F13B-92	0			c.1525_1526del						.																																			SO:0001589	frameshift_variant	2165	exon9			TTCACTTCTCCTC	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.1525_1526delGA	1.37:g.197021795_197021796delTC	ENSP00000356382:p.Glu509fs	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001994	0	0	0	0	0	A8K3E5|Q5VYL5	Frame_Shift_Del	DEL	ENST00000367412.1	37	CCDS1388.1																																																																																			.		0.327	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		-	197021794	TC	-	197021793	7	5	49	1	0	1	0	1	0	0	0	0	5354	1783	62	0	475	0	F13B	1	197021793	Frame_Shift_Del	DEL	TC	TCGA-B9-4115-01A-01D-1252-08	35273703	197021793	52228828	9	4469											
IRF6	3664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	209964089	209964089	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggaatttgacctgctccaGgctgacgggaccaaagagct	10	8	13	10	1	0	3	0	2	0	1	1	5	1	5	3	3	2	3	3	3	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:209964089G>C	ENST00000367021.3	-	7	983	c.811C>G	c.(811-813)Ctg>Gtg	p.L271V	IRF6_ENST00000542854.1_Missense_Mutation_p.L176V	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	271					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		ACCTGCTCCAGGCTGACGGGA	0.572										HNSCC(57;0.16)																											p.L271V		.											.	IRF6-92	0			c.C811G						.						80	76	77					1																	209964089		2203	4300	6503	SO:0001583	missense	3664	exon7			GCTCCAGGCTGAC	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"Van der Woude syndrome"	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.811C>G	1.37:g.209964089G>C	ENSP00000355988:p.Leu271Val	Somatic	229	0		WXS	Illumina HiSeq	Phase_I	167	71	NM_006147	0	0	4	12	8	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Missense_Mutation	SNP	ENST00000367021.3	37	CCDS1492.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139845	0.77775	.	.	ENSG00000117595	ENST00000367021;ENST00000542854;ENST00000456314	D;D;D	0.95788	-3.57;-3.57;-3.81	6.17	5.26	0.73747	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.000000	0.85682	D	0.000000	D	0.95557	0.8556	L	0.39397	1.21	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	D	0.93440	0.6793	9	.	.	.	.	9.4637	0.38800	0.1513:0.0:0.8487:0.0	.	271	O14896	IRF6_HUMAN	V	271;176;271	ENSP00000355988:L271V;ENSP00000440532:L176V;ENSP00000403855:L271V	.	L	-	1	2	IRF6	208030712	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.122000	0.57910	2.941000	0.99782	0.655000	0.94253	CTG	.		0.572	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147		C	209964089	G	C	209964089	3	2	49	1	0	0	0	0	1	0	0	0	7855	991	35	4	604	4	IRF6	1	209964089	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	12942296	209964089	39286532	10	4470											
PRKCE	5581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	45879507	45879507	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctttcacgatgcccccataGgctacgacgacttcgtggcc	7	10	9	15	4	2	0	1	0	1	0	3	3	2	0	3	2	2	1	3	2	2	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr2:45879507G>C	ENST00000306156.3	+	1	595	c.268G>C	c.(268-270)Ggc>Cgc	p.G90R		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	90	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	TGCCCCCATAGGCTACGACGA	0.622																																					p.G90R		.											.	PRKCE-1019	0			c.G268C						.						64	54	57					2																	45879507		2203	4300	6503	SO:0001583	missense	5581	exon1			CCCATAGGCTACG		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.268G>C	2.37:g.45879507G>C	ENSP00000306124:p.Gly90Arg	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	98	43	NM_005400	0	0	0	0	0	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Missense_Mutation	SNP	ENST00000306156.3	37	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	34	5.307076	0.95629	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	T;T	0.71461	-0.57;-0.57	4.95	4.95	0.65309	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.062205	0.64402	D	0.000006	D	0.84629	0.5514	M	0.86651	2.83	0.80722	D	1	D	0.67145	0.996	D	0.68943	0.961	T	0.83162	-0.0098	10	0.16896	T	0.51	.	18.1985	0.89830	0.0:0.0:1.0:0.0	.	90	Q02156	KPCE_HUMAN	R	90	ENSP00000394574:G90R;ENSP00000306124:G90R	ENSP00000306124:G90R	G	+	1	0	PRKCE	45733011	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.802000	0.99131	2.270000	0.75569	0.561000	0.74099	GGC	.		0.622	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			C	45879507	G	C	45879507	3	2	49	1	0	0	0	0	1	0	0	0	12540	1000	35	4	270	4	PRKCE	2	45879507	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		45879507	197319866	11	4471											
REV1	51455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	100019166	100019166	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catcattgaattcaacagctCcagctagattgggtgctgga	11	11	10	9	0	2	2	2	1	0	1	3	3	3	3	1	2	4	3	1	2	3	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr2:100019166C>T	ENST00000258428.3	-	21	3710	c.3482G>A	c.(3481-3483)gGa>gAa	p.G1161E	RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000465835.1_5'Flank|REV1_ENST00000393445.3_Missense_Mutation_p.G1160E	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1161	Protein interaction domain; mediates interaction with DNA polymerase zeta.				DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTCAACAGCTCCAGCTAGATT	0.493								Direct reversal of damage																													p.G1161E		.											.	REV1-92	0			c.G3482A						.						99	97	98					2																	100019166		2203	4300	6503	SO:0001583	missense	51455	exon21			ACAGCTCCAGCTA	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"DNA polymerases"	14060	protein-coding gene	gene with protein product		606134	"REV1 (yeast homolog)- like", "REV1-like (yeast)", "REV1 homolog (S. cerevisiae)"	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3482G>A	2.37:g.100019166C>T	ENSP00000258428:p.Gly1161Glu	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	123	51	NM_016316	0	0	38	68	30	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	33	5.204692	0.95033	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.38077	1.16;1.16	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.64046	0.2563	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.63906	-0.6531	10	0.66056	D	0.02	.	20.3854	0.98941	0.0:1.0:0.0:0.0	.	1161;1160	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	E	1160;1161	ENSP00000377091:G1160E;ENSP00000258428:G1161E	ENSP00000258428:G1161E	G	-	2	0	REV1	99385598	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.844000	0.75390	2.825000	0.97269	0.655000	0.94253	GGA	.		0.493	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		T	100019166	C	T	100019166	3	4	49	1	0	0	0	0	1	0	0	0	13271	855	30	2	285	2	REV1	2	100019166	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	54139659	100019166	143180207	12	4472											
LCT	3938	broad.mit.edu	37	chr2	136575050	136575050	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtggagaagcagaaggccGcatagtccaggaaggcatcc	13	5	14	9	1	0	2	0	0	0	2	2	4	2	3	3	4	1	3	3	4	4	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr2:136575050G>A	ENST00000264162.2	-	6	1578	c.1568C>T	c.(1567-1569)gCg>gTg	p.A523V	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	523	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GCAGAAGGCCGCATAGTCCAG	0.612																																					p.A523V													.	LCT-101	0			c.C1568T						.						118	102	108					2																	136575050		2203	4300	6503	SO:0001583	missense	3938	exon6			AAGGCCGCATAGT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1568C>T	2.37:g.136575050G>A	ENSP00000264162:p.Ala523Val	Somatic	127	1		WXS	Illumina HiSeq	Phase_I	187	7	NM_002299	0	0	0	0	0	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	G	33	5.246918	0.95305	.	.	ENSG00000115850	ENST00000264162	T	0.51817	0.69	5.49	5.49	0.81192	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.178976	0.48767	D	0.000163	T	0.72692	0.3492	M	0.86097	2.795	0.58432	D	0.999998	D	0.76494	0.999	D	0.66351	0.943	T	0.76801	-0.2825	10	0.87932	D	0	-8.1849	19.7399	0.96223	0.0:0.0:1.0:0.0	.	523	P09848	LPH_HUMAN	V	523	ENSP00000264162:A523V	ENSP00000264162:A523V	A	-	2	0	LCT	136291520	1.000000	0.71417	0.452000	0.26994	0.949000	0.60115	7.885000	0.87282	2.736000	0.93811	0.561000	0.74099	GCG	.		0.612	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		A	136575050	G	A	136575050	3	1	49	1	0	0	0	0	1	0	0	0	8714	1087	38	1	4263	1	LCT	2	136575050	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	36555884	136575050	106624323	13	4473											
NUP210	23225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	13415370	13415370	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagttcccactgccaccgtGggcctgcggaggaaaagcca	10	5	13	13	2	0	0	0	0	0	0	1	3	1	2	5	3	3	1	5	3	3	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:13415370G>A	ENST00000254508.5	-	12	1517	c.1435C>T	c.(1435-1437)Cac>Tac	p.H479Y		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	479					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CTGCCACCGTGGGCCTGCGGA	0.592																																					p.H479Y		.											.	NUP210-256	0			c.C1435T						.						87	65	72					3																	13415370		2203	4300	6503	SO:0001583	missense	23225	exon12			CACCGTGGGCCTG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.1435C>T	3.37:g.13415370G>A	ENSP00000254508:p.His479Tyr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	65	25	NM_024923	0	0	1	1	0	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.647580	0.29246	.	.	ENSG00000132182	ENST00000254508	T	0.41400	1.0	5.8	3.99	0.46301	Invasin/intimin cell-adhesion (1);	0.386148	0.30003	N	0.010650	T	0.31918	0.0812	L	0.57536	1.79	0.37940	D	0.932281	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.21999	-1.0229	10	0.02654	T	1	.	8.5233	0.33289	0.1373:0.1281:0.7346:0.0	.	479;479	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	Y	479	ENSP00000254508:H479Y	ENSP00000254508:H479Y	H	-	1	0	NUP210	13390370	0.997000	0.39634	0.794000	0.32065	0.780000	0.44128	2.395000	0.44459	0.784000	0.33661	0.655000	0.94253	CAC	.		0.592	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13415370	G	A	13415370	3	1	49	1	0	0	0	0	1	0	0	0	10786	1348	47	2	4344	2	NUP210	3	13415370	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		13415370	184607060	14	4474											
PLCL2	23228	hgsc.bcm.edu	37	chr3	17053310	17053310	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaatcaacctgcctgaactGgccatggtgcgctttgtagt	9	11	10	11	1	1	1	1	1	0	0	1	1	1	1	3	2	4	2	3	2	4	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:17053310G>C	ENST00000418129.2	+	2	2559	c.2094G>C	c.(2092-2094)ctG>ctC	p.L698L	PLCL2_ENST00000432376.1_Silent_p.L698L|PLCL2_ENST00000396755.2_Silent_p.L698L	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	824	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						TGCCTGAACTGGCCATGGTGC	0.463																																					p.L698L		.											.	PLCL2-229	0			c.G2094C						.						83	84	84					3																	17053310		2203	4300	6503	SO:0001819	synonymous_variant	23228	exon2			TGAACTGGCCATG	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"phospholipase C, epsilon 2"	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.2094G>C	3.37:g.17053310G>C		Somatic	178	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_015184	0	0	3	3	0	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1	.	.	.	.	.	.	.	.	.	.	G	5.312	0.243004	0.10077	.	.	ENSG00000154822	ENST00000419842	.	.	.	5.44	3.5	0.40072	.	.	.	.	.	T	0.43612	0.1255	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42548	-0.9445	4	.	.	.	.	0.9473	0.01368	0.2527:0.1661:0.41:0.1711	.	.	.	.	S	442	.	.	W	+	2	0	PLCL2	17028314	1.000000	0.71417	0.999000	0.59377	0.720000	0.41350	1.063000	0.30567	1.409000	0.46915	0.491000	0.48974	TGG	.		0.463	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			C	17053310	G	C	17053310	2	2	49	1	0	0	0	0	0	0	0	1	12066	1335	47	4		4	PLCL2	3	17053310	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	3637940	17053310	180969120	15	4475											
TRANK1	9881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	36873055	36873055	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccacagggtccaaacagagCaggcggtttagtctgacctc	10	8	11	12	1	1	2	0	1	1	1	4	2	3	2	3	3	2	2	3	3	2	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:36873055C>T	ENST00000429976.2	-	21	8134	c.7887G>A	c.(7885-7887)ctG>ctA	p.L2629L	TRANK1_ENST00000301807.6_Silent_p.L2079L|TRANK1_ENST00000428977.2_Silent_p.L2079L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2629							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						CCAAACAGAGCAGGCGGTTTA	0.532																																					p.L2629L		.											.	TRANK1-24	0			c.G7887A						.						60	62	61					3																	36873055		2004	4167	6171	SO:0001819	synonymous_variant	9881	exon21			ACAGAGCAGGCGG	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.7887G>A	3.37:g.36873055C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	85	32	NM_014831	0	0	3	3	0	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			.		0.532	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		T	36873055	C	T	36873055	2	4	49	1	0	0	0	0	0	0	0	1	16487	697	25	2		2	TRANK1	3	36873055	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	19819745	36873055	161149375	16	4476											
ACAA1	30	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38178134	38178134	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagattcacgtccttgagaaCcgcggtcatgactgccgaga	10	8	11	12	4	2	4	2	2	0	3	3	6	3	4	3	1	2	0	3	1	1	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:38178134C>G	ENST00000333167.8	-	2	386	c.214G>C	c.(214-216)Gtt>Ctt	p.V72L	ACAA1_ENST00000301810.7_Missense_Mutation_p.V72L|ACAA1_ENST00000444607.2_Missense_Mutation_p.V72L|MYD88_ENST00000495303.1_5'Flank|MYD88_ENST00000417037.2_5'Flank|MYD88_ENST00000424893.1_5'Flank|MYD88_ENST00000443433.2_5'Flank|MYD88_ENST00000396334.3_5'Flank|ACAA1_ENST00000544624.1_5'UTR|ACAA1_ENST00000450296.1_Missense_Mutation_p.V72L	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	72					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		TCCTTGAGAACCGCGGTCATG	0.642																																					p.V72L		.											.	ACAA1-91	0			c.G214C						.						53	47	49					3																	38178134		2203	4300	6503	SO:0001583	missense	30	exon2			TGAGAACCGCGGT	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.214G>C	3.37:g.38178134C>G	ENSP00000333664:p.Val72Leu	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	94	28	NM_001130410	0	0	16	36	20	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	37	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442786	0.63067	.	.	ENSG00000060971	ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122;ENST00000444607	D;D;D;D	0.93604	-2.13;-2.13;-3.25;-2.13	4.85	4.85	0.62838	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.212850	0.38605	N	0.001627	D	0.87164	0.6109	N	0.17278	0.47	0.80722	D	1	B;B;B;B	0.18863	0.001;0.003;0.031;0.0	B;B;B;B	0.17979	0.003;0.02;0.019;0.004	T	0.82806	-0.0275	10	0.14656	T	0.56	-17.5296	17.9617	0.89087	0.0:1.0:0.0:0.0	.	4;72;72;72	F5GXL8;C9JDE9;G5E935;P09110	.;.;.;THIK_HUMAN	L	72;72;72;4;72	ENSP00000333664:V72L;ENSP00000301810:V72L;ENSP00000395183:V72L;ENSP00000391918:V72L	ENSP00000301810:V72L	V	-	1	0	ACAA1	38153138	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.483000	0.60264	2.230000	0.72887	0.655000	0.94253	GTT	.		0.642	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38178134	C	G	38178134	3	3	49	1	0	0	0	0	1	0	0	0	104	507	18	4	1104	4	ACAA1	3	38178134	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	1305079	38178134	159844296	17	4477											
CTBP1	1487	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	1232016	1232016	+	Frame_Shift_Del	DEL	A	A	-																															tgcgcgtcgcagaaggccacAgtggccacgtccttcaggat																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:1232016delA	ENST00000290921.6	-	2	331	c.150delT	c.(148-150)actfs	p.T50fs	CTBP1_ENST00000515690.1_5'UTR|CTBP1_ENST00000382952.3_Frame_Shift_Del_p.T39fs|CTBP1_ENST00000510568.1_Frame_Shift_Del_p.T39fs	NM_001328.2	NP_001319.1	Q13363	CTBP1_HUMAN	C-terminal binding protein 1	50	Interaction with GLIS2 1. {ECO:0000250}.				Golgi organization (GO:0007030)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone deacetylation (GO:0031065)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of transcription by chromatin organization (GO:0034401)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		AGAAGGCCACAGTGGCCACGT	0.657																																					p.T50fs		.											.	CTBP1-91	0			c.150delT						.						69	66	67					4																	1232016		2202	4298	6500	SO:0001589	frameshift_variant	1487	exon2			.	U37408	CCDS3348.1, CCDS43203.1	4p16	2008-02-05			ENSG00000159692	ENSG00000159692			2494	protein-coding gene	gene with protein product	"brefeldin A-ribosylated substrate"	602618				9479502	Standard	XM_005272261		Approved	BARS	uc003gcv.1	Q13363	OTTHUMG00000089259	ENST00000290921.6:c.150delT	4.37:g.1232016delA	ENSP00000290921:p.Thr50fs	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	275	80	NM_001328	0	0	0	0	0	Q4W5N3|Q7Z2Q5	Frame_Shift_Del	DEL	ENST00000290921.6	37	CCDS3348.1																																																																																			.		0.657	CTBP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000202938.1	NM_001328		-	1232016	A	-	1232016	7	5	49	1	0	1	0	1	0	0	0	0	4003	175	7	0	1204	0	CTBP1	4	1232016	Frame_Shift_Del	DEL	A	TCGA-B9-4115-01A-01D-1252-08		1232016	189922260	18	4478											
HTT	3064	broad.mit.edu	37	chr4	3201562	3201562	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaacttgcgggctcgttcCatgatcaccacccacccggc	7	9	9	16	3	1	2	1	2	0	0	3	2	2	2	4	2	2	2	4	2	1	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:3201562C>T	ENST00000355072.5	+	41	5617	c.5472C>T	c.(5470-5472)tcC>tcT	p.S1824S		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1824					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GGGCTCGTTCCATGATCACCA	0.597																																					p.S1824S													.	HTT-281	0			c.C5472T						.						78	82	81					4																	3201562		2062	4198	6260	SO:0001819	synonymous_variant	3064	exon41			TCGTTCCATGATC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.5472C>T	4.37:g.3201562C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	227	10	NM_002111	0	0	3	3	0	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			.		0.597	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3201562	C	T	3201562	2	4	49	1	0	0	0	0	0	0	0	1	7478	581	21	2		2	HTT	4	3201562	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	1969546	3201562	187952714	19	4479											
HPSE	10855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	84243394	84243394	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggttgacttgagattgccaGtaacttctctcttcaaaggt	9	15	9	8	0	3	2	1	2	2	1	4	3	3	2	1	2	2	2	1	2	2	6			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:84243394G>A	ENST00000405413.2	-	3	487	c.351C>T	c.(349-351)taC>taT	p.Y117Y	HPSE_ENST00000311412.5_Silent_p.Y117Y|HPSE_ENST00000512196.1_Silent_p.Y117Y|HPSE_ENST00000513463.1_Silent_p.Y117Y	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	117					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	GAGATTGCCAGTAACTTCTCT	0.403																																					p.Y117Y		.											.	HPSE-227	0			c.C351T						.						85	87	86					4																	84243394		2203	4300	6503	SO:0001819	synonymous_variant	10855	exon2			TTGCCAGTAACTT	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.351C>T	4.37:g.84243394G>A		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	56	24	NM_001199830	0	0	4	4	0	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			.		0.403	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		A	84243394	G	A	84243394	2	1	49	1	0	0	0	0	0	0	0	1	7365	1024	36	2		2	HPSE	4	84243394	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	81041832	84243394	106910882	20	4480											
FAM198B	51313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	159092402	159092402	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaagtagatggcacacgcAgtgcccagcagaaggtttct	11	7	11	12	1	1	2	0	0	1	2	1	2	1	2	2	2	2	5	2	2	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:159092402A>T	ENST00000296530.8	-	2	747	c.126T>A	c.(124-126)acT>acA	p.T42T	RP11-597D13.9_ENST00000509463.1_RNA|FAM198B_ENST00000585682.1_Silent_p.T42T|RP11-597D13.9_ENST00000514381.1_RNA|RP11-597D13.9_ENST00000503611.1_RNA|FAM198B_ENST00000592057.1_Silent_p.T42T|FAM198B_ENST00000589306.1_Intron|RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000393807.5_Silent_p.T42T	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	42						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						TGGCACACGCAGTGCCCAGCA	0.637																																					p.T42T		.											.	FAM198B-90	0			c.T126A						.						42	44	43					4																	159092402		2202	4299	6501	SO:0001819	synonymous_variant	51313	exon2			ACACGCAGTGCCC		CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 18"	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.126T>A	4.37:g.159092402A>T		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	301	115	NM_016613	0	0	0	0	0	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Silent	SNP	ENST00000296530.8	37	CCDS3798.1																																																																																			.		0.637	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		T	159092402	A	T	159092402	2	4	49	1	0	0	0	0	0	0	0	1	5545	175	7	5		5	FAM198B	4	159092402	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	74849008	159092402	32061874	21	4481											
WDR17	116966	hgsc.bcm.edu	37	chr4	177081146	177081146	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtccttattttattaggAgagctgaccaattaatccag	12	14	7	8	0	0	2	0	1	0	1	2	3	2	2	3	1	1	1	3	1	5	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:177081146A>G	ENST00000280190.4	+	20	2755	c.2599A>G	c.(2599-2601)Aga>Gga	p.R867G	WDR17_ENST00000507824.2_Splice_Site_p.R850G|WDR17_ENST00000393643.2_Splice_Site_p.R843G|WDR17_ENST00000508596.1_Splice_Site_p.R843G			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	867										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TTTTATTAGGAGAGCTGACCA	0.323																																					p.R867G		.											.	WDR17-95	0			c.A2599G						.						63	61	62					4																	177081146		2203	4300	6503	SO:0001630	splice_region_variant	116966	exon20			ATTAGGAGAGCTG	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.2598-1A>G	4.37:g.177081146A>G		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_170710	0	0	0	0	0	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.70|16.70	3.195060|3.195060	0.58017|0.58017	.|.	.|.	ENSG00000150627|ENSG00000150627	ENST00000443118|ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	.|T;T;T	.|0.60040	.|0.24;0.28;0.22	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75236|0.75236	0.3822|0.3822	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.985;0.997;0.997	.|P;D;D	.|0.77004	.|0.661;0.989;0.989	T|T	0.76184|0.76184	-0.3052|-0.3052	5|10	.|0.44086	.|T	.|0.13	-32.4926|-32.4926	15.6261|15.6261	0.76859|0.76859	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|843;843;867	.|E7EP77;E7EQX0;Q8IZU2	.|.;.;WDR17_HUMAN	G|G	109|843;843;867;850	.|ENSP00000422763:R843G;ENSP00000377258:R843G;ENSP00000280190:R867G	.|ENSP00000280190:R867G	E|R	+|+	2|1	0|2	WDR17|WDR17	177318140|177318140	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	4.614000|4.614000	0.61183|0.61183	2.084000|2.084000	0.62774|0.62774	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.		0.323	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		Missense_Mutation	G	177081146	A	G	177081146	5	3	49	1	0	0	0	0	0	0	1	0	17310	318	11	3	2673	3	WDR17	4	177081146	Splice_Site	SNP	A	TCGA-B9-4115-01A-01D-1252-08	17988744	177081146	14073130	22	4482											
FAM173B	134145	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	10249973	10249973	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgctccagcctcacctcCtcctccctccatcgcgagat	6	8	6	21	3	1	1	1	0	0	1	7	2	6	1	8	0	2	1	8	0	0	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:10249973C>T	ENST00000511437.1	-	1	25	c.13G>A	c.(13-15)Gga>Aga	p.G5R	FAM173B_ENST00000280330.8_5'UTR|CTD-2256P15.1_ENST00000509915.1_RNA|CCT5_ENST00000515390.1_5'Flank|CCT5_ENST00000280326.4_5'Flank|CCT5_ENST00000515676.1_5'Flank|CCT5_ENST00000506600.1_5'Flank|CCT5_ENST00000503026.1_5'Flank|FAM173B_ENST00000510047.1_Missense_Mutation_p.G5R|FAM173B_ENST00000510052.1_5'UTR	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	5						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						GCCTCACCTCCTCCTCCCTCC	0.532																																					p.G5R		.											.	FAM173B-91	0			c.G13A						.						21	28	26					5																	10249973		1815	4066	5881	SO:0001583	missense	134145	exon1			CACCTCCTCCTCC		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.13G>A	5.37:g.10249973C>T	ENSP00000422338:p.Gly5Arg	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	122	45	NM_199133	0	0	0	0	0	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	37	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.707244	0.48412	.	.	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.19250	2.16;2.23	4.76	4.76	0.60689	.	2.684740	0.03150	N	0.167810	T	0.32823	0.0842	L	0.34521	1.04	0.30467	N	0.773718	P;P	0.50943	0.94;0.901	P;P	0.51615	0.675;0.476	T	0.30001	-0.9993	10	0.87932	D	0	.	13.2821	0.60222	0.0:1.0:0.0:0.0	.	5;5	E9PBZ4;Q6P4H8	.;F173B_HUMAN	R	5	ENSP00000422338:G5R;ENSP00000420876:G5R	ENSP00000424210:G5R	G	-	1	0	FAM173B	10302973	0.990000	0.36364	0.880000	0.34516	0.780000	0.44128	0.276000	0.18716	2.166000	0.68216	0.561000	0.74099	GGA	.		0.532	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		T	10249973	C	T	10249973	3	4	49	1	0	0	0	0	1	0	0	0	5510	690	24	2	708	2	FAM173B	5	10249973	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08		10249973	170665287	23	4483											
MAST4	375449	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	66438012	66438022	+	Frame_Shift_Del	DEL	AGGCAGAATTT	AGGCAGAATTT	-																															gaacagtttgctgagacagaAggcagaatttattccccaac																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	AGGCAGAATTT	AGGCAGAATTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:66438012_66438022delAGGCAGAATTT	ENST00000403625.2	+	20	2859_2869	c.2564_2574delAGGCAGAATTT	c.(2563-2574)aaggcagaatttfs	p.KAEF855fs	MAST4_ENST00000403666.1_Frame_Shift_Del_p.KAEF666fs|MAST4_ENST00000404260.3_Frame_Shift_Del_p.KAEF858fs|MAST4_ENST00000405643.1_Frame_Shift_Del_p.KAEF676fs|MAST4_ENST00000261569.7_Frame_Shift_Del_p.KAEF661fs	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	858	AGC-kinase C-terminal.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CTGAGACAGAAGGCAGAATTTATTCCCCAAC	0.403																																					p.855_858del		.											.	MAST4-647	0			c.2564_2574del						.																																			SO:0001589	frameshift_variant	375449	exon20			.	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2564_2574delAGGCAGAATTT	5.37:g.66438012_66438022delAGGCAGAATTT	ENSP00000385727:p.Lys855fs	Somatic	271	0		WXS	Illumina HiSeq	Phase_I	41	16	NM_001164664	0	0	0	0	0	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Frame_Shift_Del	DEL	ENST00000403625.2	37	CCDS54861.1																																																																																			.		0.403	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			-	66438022	AGGCAGAATTT	-	66438012	7	5	49	1	0	1	0	1	0	0	0	0	9352	72	3	0	2772	0	MAST4	5	66438012	Frame_Shift_Del	DEL	AGGCAGAATTT	TCGA-B9-4115-01A-01D-1252-08	56188039	66438012	114477248	24	4484											
RGNEF	64283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	73163796	73163796	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctggaaggagggagactgtgGgacaggtccatccattgtcc	9	8	15	9	0	0	1	0	0	0	1	3	5	3	4	3	5	0	0	3	5	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:73163796G>C	ENST00000426542.2	+	18	2268	c.2248G>C	c.(2248-2250)Gga>Cga	p.G750R	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.G750R|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.G750R|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.G750R|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.G750R|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.G437R|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.G750R			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	750					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)	p.G750R(4)									GGAGACTGTGGGACAGGTCCA	0.522																																					p.G750R		.											.	.	4	Substitution - Missense(4)	lung(4)	c.G2248C						.						104	99	101					5																	73163796		1962	4159	6121	SO:0001583	missense	64283	exon19			ACTGTGGGACAGG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2248G>C	5.37:g.73163796G>C	ENSP00000412175:p.Gly750Arg	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_001080479	0	0	2	5	3	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	G	2.497	-0.316052	0.05422	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.10192	3.16;3.16;3.15;2.9;3.16;3.15;3.0	5.67	4.72	0.59763	.	.	.	.	.	T	0.10208	0.0250	L	0.44542	1.39	0.09310	N	1	B;B;B;P	0.36282	0.014;0.027;0.015;0.546	B;B;B;B	0.36244	0.005;0.005;0.019;0.22	T	0.18209	-1.0344	9	0.20519	T	0.43	.	10.1606	0.42849	0.0:0.175:0.6902:0.1348	.	437;750;750;750	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	R	750;750;750;750;750;750;437	ENSP00000296794:G750R;ENSP00000441913:G750R;ENSP00000441436:G750R;ENSP00000287898:G750R;ENSP00000411459:G750R;ENSP00000412175:G750R;ENSP00000296799:G437R	ENSP00000287898:G750R	G	+	1	0	RP11-428C6.1	73199552	0.004000	0.15560	0.021000	0.16686	0.002000	0.02628	1.469000	0.35343	2.671000	0.90904	0.585000	0.79938	GGA	.		0.522	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			C	73163796	G	C	73163796	3	2	49	1	0	0	0	0	1	0	0	0	13315	1233	43	4	2318	4	RGNEF	5	73163796	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	6725784	73163796	107751464	25	4485											
SHROOM1	134549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	132160478	132160478	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctctggggtaactctgcaGgatacatcaccgcagcctct	8	10	10	13	1	4	0	1	0	3	0	4	1	4	1	2	3	5	4	2	3	2	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:132160478G>T	ENST00000378679.3	-	6	1874	c.1070C>A	c.(1069-1071)cCt>cAt	p.P357H	SHROOM1_ENST00000378676.1_Intron|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000319854.3_Missense_Mutation_p.P357H	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	357					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TAACTCTGCAGGATACATCAC	0.567																																					p.P357H		.											.	SHROOM1-91	0			c.C1070A						.						60	62	61					5																	132160478		2203	4300	6503	SO:0001583	missense	134549	exon3			TCTGCAGGATACA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1070C>A	5.37:g.132160478G>T	ENSP00000367950:p.Pro357His	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	204	78	NM_133456	0	0	0	4	4	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	9.923	1.212785	0.22289	.	.	ENSG00000164403	ENST00000378679;ENST00000319854	T;T	0.24350	1.86;1.86	3.93	3.06	0.35304	.	0.509864	0.20038	N	0.100569	T	0.18130	0.0435	L	0.27053	0.805	0.19300	N	0.999977	B;B	0.27498	0.18;0.113	B;B	0.29176	0.099;0.046	T	0.19976	-1.0289	10	0.72032	D	0.01	-3.8793	9.1379	0.36886	0.0:0.0:0.7829:0.2171	.	357;357	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	H	357	ENSP00000367950:P357H;ENSP00000324245:P357H	ENSP00000324245:P357H	P	-	2	0	SHROOM1	132188377	0.141000	0.22595	0.029000	0.17559	0.002000	0.02628	1.458000	0.35223	1.222000	0.43521	-0.268000	0.10319	CCT	.		0.567	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132160478	G	T	132160478	3	4	49	1	0	0	0	0	1	0	0	0	14325	1000	35	4	1508	4	SHROOM1	5	132160478	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	58996682	132160478	48754782	26	4486											
SEC24A	10802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	134002687	134002687	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttcagctgtcaaccaagaagGtaagtgaaccaagaaacaaa	19	6	8	8	0	2	3	2	1	0	2	2	3	2	3	2	1	4	2	2	1	8	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:134002687G>A	ENST00000398844.2	+	3	1027		c.e3+1		SEC24A_ENST00000322887.4_Splice_Site	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AACCAAGAAGGTAAGTGAACC	0.438																																					.		.											.	SEC24A-68	0			c.739+1G>A						.						40	39	39					5																	134002687		1833	4087	5920	SO:0001630	splice_region_variant	10802	exon3			AAGAAGGTAAGTG	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.739+1G>A	5.37:g.134002687G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	137	50	NM_001252231	0	0	0	0	0	A8MVW3|Q8WUV2|Q96GP7	Splice_Site	SNP	ENST00000398844.2	37	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.297202	0.60086	.	.	ENSG00000113615	ENST00000398844;ENST00000322887	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7049	0.85369	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC24A	134030586	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	5.912000	0.69948	2.428000	0.82296	0.603000	0.83216	.	.		0.438	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1		Intron	A	134002687	G	A	134002687	5	1	49	1	0	0	0	0	0	0	1	0	14026	1275	44	2	750	2	SEC24A	5	134002687	Splice_Site	SNP	G	TCGA-B9-4115-01A-01D-1252-08	1842209	134002687	46912573	27	4487											
SPOCK1	6695	hgsc.bcm.edu;broad.mit.edu	37	chr5	136834142	136834142	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcattgtctaggaaattgcCgtggttggggcccgcgcctc	5	11	14	11	3	2	0	1	0	1	0	3	1	2	1	3	4	1	1	3	4	2	4	rs200001053		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:136834142C>A	ENST00000394945.1	-	2	275	c.106G>T	c.(106-108)Ggc>Tgc	p.G36C	SPOCK1_ENST00000282223.7_Missense_Mutation_p.G36C	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	36					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGGAAATTGCCGTGGTTGGGG	0.682																																					p.G36C		.											.	SPOCK1-91	0			c.G106T						.						22	21	21					5																	136834142		2203	4299	6502	SO:0001583	missense	6695	exon2			AATTGCCGTGGTT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.106G>T	5.37:g.136834142C>A	ENSP00000378401:p.Gly36Cys	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	56	17	NM_004598	0	0	1	1	0	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.179946	0.78564	.	.	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.55588	0.54;0.54;0.51	3.66	2.77	0.32553	.	0.371240	0.21081	N	0.080484	T	0.58509	0.2127	L	0.56199	1.76	0.25077	N	0.990954	D	0.62365	0.991	P	0.55965	0.788	T	0.51576	-0.8688	10	0.66056	D	0.02	.	9.9319	0.41528	0.204:0.796:0.0:0.0	.	36	Q08629	TICN1_HUMAN	C	36	ENSP00000378401:G36C;ENSP00000282223:G36C;ENSP00000424517:G36C	ENSP00000282223:G36C	G	-	1	0	SPOCK1	136862041	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.898000	0.63238	0.626000	0.30322	0.462000	0.41574	GGC	C|0.999;G|0.000		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		A	136834142	C	A	136834142	3	1	49	1	0	0	0	0	1	0	0	0	15111	652	23	4	1253	4	SPOCK1	5	136834142	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	2831455	136834142	44081118	28	4488											
HIST1H2AD	3013	broad.mit.edu	37	chr6	26199108	26199109	+	Frame_Shift_Del	DEL	CA	CA	-																															cttggccttgtggtgactctCagtcttcttggggagcagta																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:26199108_26199109delCA	ENST00000341023.1	-	1	362_363	c.363_364delTG	c.(361-366)actgagfs	p.E122fs	HIST1H3D_ENST00000377831.5_5'UTR|HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000356476.2_5'Flank	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	122						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				TGGTGACTCTCAGTCTTCTTGG	0.485																																					p.121_122del													.	HIST1H2AD-90	0			c.363_364del						.																																			SO:0001589	frameshift_variant	3013	exon1			GACTCTCAGTCTT	Z80776	CCDS4591.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196866	ENSG00000196866		"Histones / Replication-dependent"	4729	protein-coding gene	gene with protein product		602792	"H2A histone family, member G", "histone 1, H2ad"	H2AFG		9119399, 12408966	Standard	NM_021065		Approved	H2A/g, H2A.3	uc003ngw.4	P20671	OTTHUMG00000014437	ENST00000341023.1:c.363_364delTG	6.37:g.26199108_26199109delCA	ENSP00000341094:p.Glu122fs	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	281	26	NM_021065	0	0	0	0	0	A0PK91|P57754|Q6FGY6	Frame_Shift_Del	DEL	ENST00000341023.1	37	CCDS4591.1																																																																																			.		0.485	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065		-	26199109	CA	-	26199108	7	5	49	1	0	1	0	1	0	0	0	0	7152	835	29	0	32	0	HIST1H2AD	6	26199108	Frame_Shift_Del	DEL	CA	TCGA-B9-4115-01A-01D-1252-08		26199108	144915959	29	4489											
BTN3A2	11118	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	26370805	26370805	+	Frame_Shift_Del	DEL	A	A	-																															aaattccctcctcggcctggAaaagacagccagcatttcca																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:26370805delA	ENST00000356386.2	+	5	877	c.689delA	c.(688-690)gaafs	p.E230fs	BTN3A2_ENST00000396948.1_Frame_Shift_Del_p.E230fs|BTN3A2_ENST00000508906.2_Frame_Shift_Del_p.E188fs|BTN3A2_ENST00000527422.1_Frame_Shift_Del_p.E230fs|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396934.3_Frame_Shift_Del_p.E207fs|BTN3A2_ENST00000377708.2_Frame_Shift_Del_p.E230fs	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	230					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						CTCGGCCTGGAAAAGACAGCC	0.522																																					p.E230fs		.											.	BTN3A2-90	0			c.689delA						.						105	103	103					6																	26370805		2203	4300	6503	SO:0001589	frameshift_variant	11118	exon3			.	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.689delA	6.37:g.26370805delA	ENSP00000348751:p.Glu230fs	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	196	70	NM_001197246	0	0	0	0	0	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Frame_Shift_Del	DEL	ENST00000356386.2	37	CCDS4605.1																																																																																			.		0.522	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2			-	26370805	A	-	26370805	7	5	49	1	0	1	0	1	0	0	0	0	1566	246	9	0	699	0	BTN3A2	6	26370805	Frame_Shift_Del	DEL	A	TCGA-B9-4115-01A-01D-1252-08	171697	26370805	144744262	30	4490											
KCNK17	89822	hgsc.bcm.edu	37	chr6	39282083	39282083	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctcgggagccgcccgggctCgcggtcggtacatagcggga	5	5	17	14	7	0	0	0	0	0	0	3	2	0	2	3	5	3	2	3	5	2	2	rs139959421	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:39282083C>T	ENST00000373231.4	-	1	246	c.14G>A	c.(13-15)cGa>cAa	p.R5Q	KCNK17_ENST00000453413.2_Missense_Mutation_p.R5Q	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	5					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						CGCCCGGGCTCGCGGTCGGTA	0.746													C|||	53	0.0105831	0.0401	0	5008	,	,		12502	0		0	False		,,,				2504	0				p.R5Q		.											.	KCNK17-227	0			c.G14A						.	C	GLN/ARG,GLN/ARG	62,2676		0,62,1307	2	2	2		14,14	4.6	0.2	6	dbSNP_134	2	1,5981		0,1,2990	no	missense,missense	KCNK17	NM_001135111.1,NM_031460.3	43,43	0,63,4297	TT,TC,CC		0.0167,2.2644,0.7225	possibly-damaging,possibly-damaging	5/272,5/333	39282083	63,8657	1369	2991	4360	SO:0001583	missense	89822	exon1			CGGGCTCGCGGTC	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.14G>A	6.37:g.39282083C>T	ENSP00000362328:p.Arg5Gln	Somatic	2	2		WXS	Illumina HiSeq	Phase_I	10	10	NM_001135111	0	0	0	0	0	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	17.55	3.417886	0.62622	0.022644	1.67E-4	ENSG00000124780	ENST00000373231;ENST00000453413	T;T	0.56275	0.47;0.47	4.59	4.59	0.56863	.	0.875659	0.09342	N	0.815355	T	0.38532	0.1044	L	0.47716	1.5	0.19300	N	0.999975	P;P	0.51933	0.82;0.949	B;P	0.44561	0.186;0.453	T	0.31806	-0.9930	10	0.59425	D	0.04	.	14.691	0.69085	0.0:1.0:0.0:0.0	.	5;5	E9PB46;Q96T54	.;KCNKH_HUMAN	Q	5	ENSP00000362328:R5Q;ENSP00000401271:R5Q	ENSP00000362328:R5Q	R	-	2	0	KCNK17	39390061	0.000000	0.05858	0.150000	0.22450	0.047000	0.14425	-0.137000	0.10389	2.260000	0.74910	0.561000	0.74099	CGA	C|0.989;T|0.011		0.746	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		T	39282083	C	T	39282083	3	4	49	1	0	0	0	0	1	0	0	0	8085	884	31	1	1136	1	KCNK17	6	39282083	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	12911278	39282083	131832984	31	4491											
KIF6	221458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	39313488	39313488	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccacagacctgtcttccagtGgggtgctggtgctgctctgt	4	12	13	12	0	2	1	0	0	2	1	3	1	3	1	3	3	3	3	3	3	0	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:39313488G>T	ENST00000287152.7	-	21	2403	c.2309C>A	c.(2308-2310)cCa>cAa	p.P770Q	KIF6_ENST00000229913.5_Missense_Mutation_p.P221Q|KIF6_ENST00000394362.1_Missense_Mutation_p.P204Q|KIF6_ENST00000373216.3_Missense_Mutation_p.P753Q|KIF6_ENST00000373213.4_Missense_Mutation_p.P609Q|KIF6_ENST00000538893.1_Missense_Mutation_p.P714Q|KIF6_ENST00000373215.3_Missense_Mutation_p.P753Q|KIF6_ENST00000541946.1_Missense_Mutation_p.P221Q	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	770					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GTCTTCCAGTGGGGTGCTGGT	0.557																																					p.P770Q		.											.	KIF6-713	0			c.C2309A						.						124	107	113					6																	39313488		2203	4300	6503	SO:0001583	missense	221458	exon21			TCCAGTGGGGTGC	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.2309C>A	6.37:g.39313488G>T	ENSP00000287152:p.Pro770Gln	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	67	29	NM_145027	0	0	0	0	0	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.700|6.700	0.497738|0.497738	0.12762|0.12762	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000458470|ENST00000287152;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946	.|T;T;T;T;T;T;T;T	.|0.71222	.|-0.49;1.51;-0.53;-0.31;1.53;-0.49;-0.55;1.49	4.12|4.12	-1.35|-1.35	0.09114|0.09114	.|.	.|.	.|.	.|.	.|.	T|T	0.11665|0.11665	0.0284|0.0284	N|N	0.01352|0.01352	-0.895|-0.895	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.26195	.|0.09;0.09;0.144;0.054	.|B;B;B;B	.|0.29440	.|0.048;0.03;0.102;0.022	T|T	0.20940|0.20940	-1.0260|-1.0260	5|9	.|0.09084	.|T	.|0.74	.|.	1.384|1.384	0.02236|0.02236	0.1966:0.3047:0.3385:0.1602|0.1966:0.3047:0.3385:0.1602	.|.	.|753;714;753;770	.|E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9	.|.;.;.;KIF6_HUMAN	N|Q	645|770;204;753;609;221;753;714;221	.|ENSP00000287152:P770Q;ENSP00000377889:P204Q;ENSP00000362312:P753Q;ENSP00000362309:P609Q;ENSP00000229913:P221Q;ENSP00000362311:P753Q;ENSP00000441435:P714Q;ENSP00000439064:P221Q	.|ENSP00000229913:P221Q	H|P	-|-	1|2	0|0	KIF6|KIF6	39421466|39421466	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.191000|0.191000	0.23601|0.23601	-1.263000|-1.263000	0.02850|0.02850	-0.421000|-0.421000	0.07416|0.07416	0.563000|0.563000	0.77884|0.77884	CAC|CCA	.		0.557	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		T	39313488	G	T	39313488	3	4	49	1	0	0	0	0	1	0	0	0	8329	1348	47	4	147	4	KIF6	6	39313488	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	31405	39313488	131801579	32	4492											
NR2E1	7101	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	108499383	108499383	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatcagctgccagacttctcTtcatgagcatcaagtgggct	10	11	9	11	0	4	2	3	1	1	1	5	2	4	2	1	1	3	3	1	1	2	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:108499383T>G	ENST00000368986.4	+	5	1288	c.580T>G	c.(580-582)Ttc>Gtc	p.F194V	NR2E1_ENST00000368983.3_Missense_Mutation_p.F231V	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	194	Ligand-binding. {ECO:0000250}.				aggressive behavior (GO:0002118)|amygdala development (GO:0021764)|anterior commissure morphogenesis (GO:0021960)|behavioral fear response (GO:0001662)|cell fate commitment (GO:0045165)|cerebral cortex neuron differentiation (GO:0021895)|dentate gyrus development (GO:0021542)|extracellular matrix organization (GO:0030198)|forebrain generation of neurons (GO:0021872)|gene expression (GO:0010467)|glial cell migration (GO:0008347)|layer formation in cerebral cortex (GO:0021819)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|olfactory bulb development (GO:0021772)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of stem cell proliferation (GO:2000648)|regulation of cell migration involved in sprouting angiogenesis (GO:0090049)|regulation of dendrite morphogenesis (GO:0048814)|regulation of timing of neuron differentiation (GO:0060164)|retina development in camera-type eye (GO:0060041)|social behavior (GO:0035176)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(16)|prostate(1)|skin(3)	30		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		CAGACTTCTCTTCATGAGCAT	0.527																																					p.F194V		.											.	NR2E1-187	0			c.T580G						.						123	104	110					6																	108499383		2203	4300	6503	SO:0001583	missense	7101	exon5			CTTCTCTTCATGA	Y13276	CCDS5063.1, CCDS69165.1	6q21	2013-01-16			ENSG00000112333	ENSG00000112333		"Nuclear hormone receptors"	7973	protein-coding gene	gene with protein product		603849		TLX		9628820	Standard	NM_003269		Approved	TLL, XTLL	uc003psg.3	Q9Y466	OTTHUMG00000015319	ENST00000368986.4:c.580T>G	6.37:g.108499383T>G	ENSP00000357982:p.Phe194Val	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	79	29	NM_003269	0	0	0	0	0	Q6ZMP8	Missense_Mutation	SNP	ENST00000368986.4	37	CCDS5063.1	.	.	.	.	.	.	.	.	.	.	T	31	5.077084	0.94000	.	.	ENSG00000112333	ENST00000368986;ENST00000368983	T;T	0.50813	0.73;0.73	5.6	5.6	0.85130	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.043698	0.85682	D	0.000000	T	0.30070	0.0753	N	0.26092	0.79	0.80722	D	1	P	0.46621	0.881	P	0.48089	0.566	T	0.07009	-1.0795	10	0.30854	T	0.27	.	14.0221	0.64563	0.0:0.0:0.0:1.0	.	194	Q9Y466	NR2E1_HUMAN	V	194;231	ENSP00000357982:F194V;ENSP00000357979:F231V	ENSP00000357979:F231V	F	+	1	0	NR2E1	108606076	1.000000	0.71417	0.970000	0.41538	0.957000	0.61999	7.698000	0.84413	2.134000	0.65973	0.528000	0.53228	TTC	.		0.527	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			G	108499383	T	G	108499383	3	3	49	1	0	0	0	0	1	0	0	0	10651	1609	56	5	598	5	NR2E1	6	108499383	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	69185895	108499383	62615684	33	4493											
FOXO3	2309	broad.mit.edu	37	chr6	108985136	108985136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtgcacggtggaactgcCacggctgactgatatggcag	8	7	15	11	3	0	2	0	2	0	0	0	3	0	3	2	4	3	3	2	4	2	1	rs34223850		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:108985136C>T	ENST00000343882.6	+	3	1404	c.1100C>T	c.(1099-1101)cCa>cTa	p.P367L	FOXO3_ENST00000540898.1_Missense_Mutation_p.P147L|FOXO3_ENST00000406360.1_Missense_Mutation_p.P367L	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	367				P -> R (in Ref. 6; CAA04860). {ECO:0000305}.	antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		GTGGAACTGCCACGGCTGACT	0.567																																					p.P367L													.	FOXO3-1295	0			c.C1100T						.						53	49	50					6																	108985136		2203	4300	6503	SO:0001583	missense	2309	exon2			AACTGCCACGGCT	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"Forkhead boxes"	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.1100C>T	6.37:g.108985136C>T	ENSP00000339527:p.Pro367Leu	Somatic	110	1		WXS	Illumina HiSeq	Phase_I	210	10	NM_001455	0	0	1	1	0	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Missense_Mutation	SNP	ENST00000343882.6	37	CCDS5068.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786340	0.70337	.	.	ENSG00000118689	ENST00000343882;ENST00000406360;ENST00000540258;ENST00000540898	D;D	0.93366	-3.21;-3.21	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.96904	0.8989	M	0.85462	2.755	0.09310	P	0.999999999663215	D	0.89917	1.0	D	0.76071	0.987	D	0.96301	0.9221	9	0.52906	T	0.07	-29.4118	19.8586	0.96775	0.0:1.0:0.0:0.0	rs34223850	367	O43524	FOXO3_HUMAN	L	367;367;147;147	ENSP00000339527:P367L;ENSP00000385824:P367L	ENSP00000339527:P367L	P	+	2	0	FOXO3	109091829	1.000000	0.71417	0.989000	0.46669	0.788000	0.44548	7.456000	0.80751	2.701000	0.92244	0.462000	0.41574	CCA	C|1.000;|0.000		0.567	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2			T	108985136	C	T	108985136	3	4	49	1	0	0	0	0	1	0	0	0	6043	594	21	2	1106	2	FOXO3	6	108985136	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	485753	108985136	62129931	34	4494											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5415788	5415788	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agctgctgggcgtggtgcagGgggctgcggcccggcgggta	3	6	22	10	4	0	0	0	0	0	0	0	0	0	0	1	7	4	5	1	7	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:5415788G>A	ENST00000430969.1	-	9	3024	c.2676C>T	c.(2674-2676)ccC>ccT	p.P892P	TNRC18_ENST00000399537.4_Silent_p.P892P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	892							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CGTGGTGCAGGGGGCTGCGGC	0.701																																					p.P892P		.											.	TNRC18-46	0			c.C2676T						.						8	11	10					7																	5415788		2005	4157	6162	SO:0001819	synonymous_variant	84629	exon9			GTGCAGGGGGCTG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.2676C>T	7.37:g.5415788G>A		Somatic	12	2		WXS	Illumina HiSeq	Phase_I	40	22	NM_001080495	0	0	0	2	2	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			.		0.701	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5415788	G	A	5415788	2	1	49	1	0	0	0	0	0	0	0	1	16371	1219	43	2		2	TNRC18	7	5415788	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08		5415788	153722875	35	4495											
DNAH11	8701	broad.mit.edu	37	chr7	21730436	21730436	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatcagttggaatatttaTtactatgaacccgggttatg	11	14	9	7	1	1	1	1	1	0	0	1	2	1	2	2	2	2	2	2	2	7	7			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:21730436T>C	ENST00000409508.3	+	35	6009	c.5978T>C	c.(5977-5979)aTt>aCt	p.I1993T	DNAH11_ENST00000328843.6_Missense_Mutation_p.I2000T	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2000	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GGAATATTTATTACTATGAAC	0.378									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						185	176	179					7																	21730436		1825	4085	5910	SO:0001583	missense	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TATTTATTACTAT	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.5978T>C	7.37:g.21730436T>C	ENSP00000475939:p.Ile1993Thr	Somatic	467	0		WXS	Illumina HiSeq	Phase_I	675	6	.	0	0	0	0	0	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	T	24.7	4.564708	0.86439	.	.	ENSG00000105877	ENST00000328843	T	0.14144	2.53	6.17	6.17	0.99709	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.39835	0.1093	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.69142	0.962	T	0.22382	-1.0218	9	0.87932	D	0	.	16.4957	0.84242	0.0:0.0:0.0:1.0	.	2000	Q96DT5	DYH11_HUMAN	T	2000	ENSP00000330671:I2000T	ENSP00000330671:I2000T	I	+	2	0	DNAH11	21696961	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.013000	0.88655	2.371000	0.80710	0.533000	0.62120	ATT	.		0.378	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		C	21730436	T	C	21730436	3	2	49	1	0	0	0	0	1	0	0	0	4610	1493	52	3	6138	3	DNAH11	7	21730436	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	16314648	21730436	137408227	36	4496											
TRIM73	375593	hgsc.bcm.edu	37	chr7	75028469	75028469	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaggctccctggggacccAgagcccaaggtctgcgtgca	7	6	14	14	1	1	2	0	1	1	1	2	3	2	3	3	4	3	2	3	4	1	0	rs142958137	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:75028469A>G	ENST00000437796.1	+	1	271	c.252A>G	c.(250-252)ccA>ccG	p.P84P	TRIM73_ENST00000447409.2_Silent_p.P84P|TRIM73_ENST00000323819.3_Silent_p.P84P|TRIM73_ENST00000450434.1_5'UTR|TRIM73_ENST00000430211.1_Silent_p.P84P			Q86UV7	TRI73_HUMAN	tripartite motif containing 73	84						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)	4						CTGGGGACCCAGAGCCCAAGG	0.667													G|||	3571	0.713059	0.7163	0.6974	5008	,	,		6749	0.874		0.5527	False		,,,				2504	0.7188				p.P84P		.											.	TRIM74-40	0			c.A252G						.						9	28	23					7																	75028469		810	2167	2977	SO:0001819	synonymous_variant	378108	exon2			GGACCCAGAGCCC	AF498998	CCDS34665.1	7q11.23	2013-01-09	2011-01-25	2006-03-31		ENSG00000178809		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	18162	protein-coding gene	gene with protein product		612549	"tripartite motif-containing 50B", "tripartite motif-containing 73"	TRIM50B			Standard	NM_198924		Approved		uc003udc.1	Q86UV7		ENST00000437796.1:c.252A>G	7.37:g.75028469A>G		Somatic	7	2		WXS	Illumina HiSeq	Phase_I	22	14	NM_198853	0	0	0	11	11	Q8N0S3	Silent	SNP	ENST00000437796.1	37	CCDS34665.1																																																																																			.		0.667	TRIM73-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342950.1			G	75028469	A	G	75028469	2	3	49	1	0	0	0	0	0	0	0	1	16579	175	7	3		3	TRIM73	7	75028469	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	53298033	75028469	84110194	37	4497											
MAGI2	9863	broad.mit.edu	37	chr7	79082570	79082571	+	Frame_Shift_Ins	INS	-	-	C																															cccagctggccctccgggttINScctgccaatgacactctcat																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:79082570_79082571insC	ENST00000354212.4	-	1	319_320	c.66_67insG	c.(64-69)aggaacfs	p.N23fs	MAGI2-AS3_ENST00000446159.1_RNA|MAGI2_ENST00000522391.1_Frame_Shift_Ins_p.N23fs|MAGI2-AS3_ENST00000424477.1_RNA|MAGI2-AS3_ENST00000448195.1_RNA|MAGI2-AS3_ENST00000426835.1_RNA|MAGI2-AS3_ENST00000414797.1_RNA|MAGI2-AS3_ENST00000451809.1_RNA|MAGI2_ENST00000419488.1_Frame_Shift_Ins_p.N23fs|MAGI2-AS3_ENST00000429408.1_RNA|MAGI2-AS3_ENST00000422093.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	23	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CCCTCCGGGTTCCTGCCAATGA	0.589																																					p.N23fs													.	MAGI2-461	0			c.67_68insG						.																																			SO:0001589	frameshift_variant	9863	exon1			CCGGGTTCCTGCC	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.67dupG	7.37:g.79082572_79082572dupC	ENSP00000346151:p.Asn23fs	Somatic	347	0		WXS	Illumina HiSeq	Phase_I	916	7	NM_012301	0	0	0	0	0	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Frame_Shift_Ins	INS	ENST00000354212.4	37	CCDS5594.1																																																																																			.		0.589	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	79082571	-	C	79082570	7	5	49	1	0	1	1	0	0	0	0	0	9216	1783	62	0	4388	0	MAGI2	7	79082570	Frame_Shift_Ins	INS	-	TCGA-B9-4115-01A-01D-1252-08	4054101	79082570	80056093	38	4498											
TFR2	7036	hgsc.bcm.edu	37	chr7	100224941	100224941	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgtgcctgaggacgacgtcCccgtagcggccgaagtcgag	8	6	15	12	6	0	1	0	1	0	0	2	5	1	2	4	2	2	1	4	2	2	1	rs111760099	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:100224941C>A	ENST00000462107.1	-	17	2228	c.1941G>T	c.(1939-1941)ggG>ggT	p.G647G	TFR2_ENST00000544242.1_Silent_p.G188G|TFR2_ENST00000223051.3_Silent_p.G647G|TFR2_ENST00000431692.1_3'UTR			Q9UP52	TFR2_HUMAN	transferrin receptor 2	647					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	GGACGACGTCCCCGTAGCGGC	0.687													C|||	26	0.00519169	0.0182	0.0029	5008	,	,		14728	0		0	False		,,,				2504	0				p.G647G		.											.	TFR2-92	0			c.G1941T						.	C	,	35,4107		1,33,2037	11	12	12		1428,1941	-1.7	1	7	dbSNP_132	12	7,8063		0,7,4028	no	coding-synonymous,coding-synonymous	TFR2	NM_001206855.1,NM_003227.3	,	1,40,6065	AA,AC,CC		0.0867,0.845,0.3439	,	476/631,647/802	100224941	42,12170	2071	4035	6106	SO:0001819	synonymous_variant	7036	exon16			GACGTCCCCGTAG	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1941G>T	7.37:g.100224941C>A		Somatic	7	2		WXS	Illumina HiSeq	Phase_I	20	9	NM_003227	0	0	0	0	0	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1																																																																																			C|0.997;A|0.003		0.687	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		A	100224941	C	A	100224941	2	1	49	1	0	0	0	0	0	0	0	1	15843	610	22	4		4	TFR2	7	100224941	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	21142371	100224941	58913722	39	4499											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgacggcgacggcgacgAcggcagcagcggcggcgttg	6	2	20	13	11	0	0	0	0	0	0	0	4	0	0	0	6	2	3	0	6	0	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:131241055A>G	ENST00000378555.3	-	1	311	c.64T>C	c.(64-66)Tcg>Ccg	p.S22P	PODXL_ENST00000537928.1_Missense_Mutation_p.S22P|PODXL_ENST00000541194.1_Missense_Mutation_p.S22P|PODXL_ENST00000322985.9_Missense_Mutation_p.S22P|PODXL_ENST00000465001.1_Intron			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacgacggcagcagc	0.741																																					p.S22P		.											.	PODXL-136	0			c.T64C						.						5	8	7					7																	131241055		1914	3836	5750	SO:0001583	missense	5420	exon1			GCGACGACGGCAG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.64T>C	7.37:g.131241055A>G	ENSP00000367817:p.Ser22Pro	Somatic	12	1		WXS	Illumina HiSeq	Phase_I	22	5	NM_001018111	0	0	0	0	0	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488975	0.26686	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.12774	2.82;2.65;2.82;2.85	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.08670	0.0215	N	0.14661	0.345	0.09310	N	0.999994	.	.	.	.	.	.	T	0.24728	-1.0152	6	0.29301	T	0.29	.	.	.	.	.	22;22	O00592-2;O00592	.;PODXL_HUMAN	P	22	ENSP00000440518:S22P;ENSP00000442655:S22P;ENSP00000367817:S22P;ENSP00000319782:S22P	ENSP00000319782:S22P	S	-	1	0	PODXL	130891595	0.001000	0.12720	0.027000	0.17364	0.027000	0.11550	0.743000	0.26231	0.056000	0.16144	0.055000	0.15244	TCG	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241055	A	G	131241055	3	3	49	1	0	0	0	0	1	0	0	0	12206	275	10	3	1648	3	PODXL	7	131241055	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	31016114	131241055	27897608	40	4500											
HIPK2	28996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	139299101	139299101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgggcacaaatctgggctgTtcctgtctgcaggggcatgc	6	9	14	12	1	2	0	0	0	2	0	3	0	3	0	2	4	2	5	2	4	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:139299101T>C	ENST00000406875.3	-	8	2015	c.1921A>G	c.(1921-1923)Aca>Gca	p.T641A	HIPK2_ENST00000342645.6_Missense_Mutation_p.T641A|HIPK2_ENST00000428878.2_Missense_Mutation_p.T614A	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	641	Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					ATCTGGGCTGTTCCTGTCTGC	0.597																																					p.T641A		.											.	HIPK2-785	0			c.A1921G						.						47	54	52					7																	139299101		1956	4149	6105	SO:0001583	missense	28996	exon8			GGGCTGTTCCTGT	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1921A>G	7.37:g.139299101T>C	ENSP00000385571:p.Thr641Ala	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	107	46	NM_022740	0	0	0	3	3	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	37		.	.	.	.	.	.	.	.	.	.	T	12.91	2.079694	0.36662	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.50277	0.75;0.8;0.78	5.39	2.9	0.33743	.	.	.	.	.	T	0.33847	0.0877	.	.	.	0.43667	D	0.996098	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.06481	-1.0824	8	0.27785	T	0.31	.	9.7368	0.40392	0.0:0.1461:0.0:0.8539	.	641;614	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	A	641;614;641	ENSP00000385571:T641A;ENSP00000413724:T614A;ENSP00000343108:T641A	ENSP00000343108:T641A	T	-	1	0	HIPK2	138949641	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	0.813000	0.27225	0.383000	0.24910	0.460000	0.39030	ACA	.		0.597	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		C	139299101	T	C	139299101	3	2	49	1	0	0	0	0	1	0	0	0	7138	1725	60	3	1707	3	HIPK2	7	139299101	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	8058046	139299101	19839562	41	4501											
WDR86	349136	hgsc.bcm.edu	37	chr7	151078735	151078735	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccgcgagaggctgcgcAtgggcggagggggccgcggg	6	2	23	10	6	0	2	0	0	0	2	0	4	0	3	2	6	2	2	2	6	0	0	rs4141455	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:151078735A>G	ENST00000334493.6	-	6	1494	c.1064T>C	c.(1063-1065)aTg>aCg	p.M355T	WDR86_ENST00000469830.2_Silent_p.H376H|WDR86_ENST00000477459.1_Missense_Mutation_p.C182R|WDR86_ENST00000463000.1_Intron	NM_001284262.1|NM_198285.2	NP_001271191.1|NP_938026.2	Q86TI4	WDR86_HUMAN	WD repeat domain 86	355			M -> T (in dbSNP:rs4141455). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGGCTGCGCATGGGCGGAGG	0.766													G|||	4189	0.836462	0.8691	0.8689	5008	,	,		10617	0.9851		0.7823	False		,,,				2504	0.6718				p.M355T		.											.	.	0			c.T1064C						.						1	1	1					7																	151078735		635	1338	1973	SO:0001583	missense	349136	exon6			CTGCGCATGGGCG	AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260		"WD repeat domain containing"	28020	protein-coding gene	gene with protein product						12477932	Standard	NM_198285		Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000334493.6:c.1064T>C	7.37:g.151078735A>G	ENSP00000335522:p.Met355Thr	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_198285	0	0	0	0	0	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	Missense_Mutation	SNP	ENST00000334493.6	37	CCDS5925.2	1852|1852	0.847985347985348|0.847985347985348	414|414	0.8414634146341463|0.8414634146341463	300|300	0.8287292817679558|0.8287292817679558	568|568	0.993006993006993|0.993006993006993	570|570	0.7519788918205804|0.7519788918205804	G|G	7.749|7.749	0.702921|0.702921	0.15172|0.15172	.|.	.|.	ENSG00000187260|ENSG00000187260	ENST00000477459|ENST00000334493	T|T	0.56444|0.54479	0.46|0.57	4.39|4.39	-2.72|-2.72	0.05968|0.05968	.|Quinoprotein amine dehydrogenase, beta chain-like (1);	0.855198|.	0.09836|.	N|.	0.749514|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03608|0.03608	-0.345|-0.345	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.01281	0.0|0.0;0.0	T|T	0.25641|0.25641	-1.0126|-1.0126	9|8	0.35671|0.11182	T|T	0.21|0.66	-0.0107|-0.0107	2.2812|2.2812	0.04114|0.04114	0.1224:0.1641:0.4024:0.3111|0.1224:0.1641:0.4024:0.3111	rs4141455;rs10385476;rs13246084|rs4141455;rs10385476;rs13246084	182|355;313	C9JAJ5|Q86TI4;D3DX12	.|WDR86_HUMAN;.	R|T	182|355	ENSP00000417512:C182R|ENSP00000335522:M355T	ENSP00000417512:C182R|ENSP00000335522:M355T	C|M	-|-	1|2	0|0	WDR86|WDR86	150709668|150709668	0.215000|0.215000	0.23574|0.23574	0.012000|0.012000	0.15200|0.15200	0.459000|0.459000	0.32528|0.32528	0.077000|0.077000	0.14738|0.14738	-1.008000|-1.008000	0.03404|0.03404	-1.507000|-1.507000	0.00952|0.00952	TGC|ATG	T|0.151;G|0.004		0.766	WDR86-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319999.3	NM_198285		G	151078735	A	G	151078735	3	3	49	1	0	0	0	0	1	0	0	0	17367	217	8	3	70	3	WDR86	7	151078735	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	11779634	151078735	8059928	42	4502											
AMAC1L2	83650	hgsc.bcm.edu;broad.mit.edu	37	chr8	11188719	11188719	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccagcgctgccagccctctgGtgccaccaatggcctgctgg	5	7	12	17	1	1	0	0	0	1	0	1	0	1	0	6	3	5	2	6	3	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr8:11188719G>A	ENST00000382435.4	+	1	323	c.104G>A	c.(103-105)gGt>gAt	p.G35D		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	35						integral component of membrane (GO:0016021)		p.G35D(1)									CAGCCCTCTGGTGCCACCAAT	0.682																																					p.G35D		.											.	.	1	Substitution - Missense(1)	endometrium(1)	c.G104A						.																																			SO:0001583	missense	83650	exon1			CCTCTGGTGCCAC	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"Solute carriers"	15546	protein-coding gene	gene with protein product		615199	"acyl-malonyl condensing enzyme 1-like 2"	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.104G>A	8.37:g.11188719G>A	ENSP00000371872:p.Gly35Asp	Somatic	118	1		WXS	Illumina HiSeq	Phase_I	273	14	NM_054028	0	0	1	1	0	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.973298	0.00452	.	.	ENSG00000177710	ENST00000382435	T	0.23348	1.91	0.34	0.34	0.15985	.	0.293668	0.23411	N	0.048476	T	0.06280	0.0162	N	0.02539	-0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.28267	-1.0049	9	0.09084	T	0.74	0.0032	.	.	.	.	35	Q96KT7	S35G5_HUMAN	D	35	ENSP00000371872:G35D	ENSP00000371872:G35D	G	+	2	0	SLC35G5	11226129	0.973000	0.33851	0.352000	0.25734	0.047000	0.14425	0.142000	0.16096	-1.532000	0.01747	-2.047000	0.00414	GGT	.		0.682	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028		A	11188719	G	A	11188719	3	1	49	1	0	0	0	0	1	0	0	0	560	1261	44	2	106	2	AMAC1L2	8	11188719	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		11188719	135175303	43	4503											
KCNU1	157855	broad.mit.edu	37	chr8	36698474	36698474	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctttctgaagatgcacctCctgttgatagccatcgaata	10	13	8	10	1	1	3	0	2	1	1	3	4	2	3	3	0	3	3	3	0	4	4	rs375978830		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr8:36698474C>A	ENST00000399881.3	+	16	1693	c.1656C>A	c.(1654-1656)ctC>ctA	p.L552L		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	552	Segment S8.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGATGCACCTCCTGTTGATAG	0.413																																					p.L552L													.	KCNU1-23	0			c.C1656A						.						130	124	126					8																	36698474		1997	4172	6169	SO:0001819	synonymous_variant	157855	exon16			GCACCTCCTGTTG	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1656C>A	8.37:g.36698474C>A		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	29	5	NM_001031836	0	0	0	0	0		Silent	SNP	ENST00000399881.3	37	CCDS55220.1																																																																																			.		0.413	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36698474	C	A	36698474	2	1	49	1	0	0	0	0	0	0	0	1	8114	842	30	4		4	KCNU1	8	36698474	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	25509755	36698474	109665548	44	4504											
ERMP1	79956	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	5801231	5801231	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattggagctatatggaaaaAatgttccactgcaaacaagg	16	9	10	6	0	0	0	0	0	0	0	1	3	1	2	1	3	3	3	1	3	7	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:5801231A>T	ENST00000339450.5	-	11	2101	c.2012T>A	c.(2011-2013)tTt>tAt	p.F671Y	ERMP1_ENST00000543230.1_Missense_Mutation_p.F249Y|ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_3'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	671						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		ATATGGAAAAAATGTTCCACT	0.403																																					p.F671Y		.											.	ERMP1-69	0			c.T2012A						.						143	142	142					9																	5801231		2203	4300	6503	SO:0001583	missense	79956	exon11			GGAAAAAATGTTC	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"Felix-ina"	611156	"KIAA1815"	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.2012T>A	9.37:g.5801231A>T	ENSP00000340427:p.Phe671Tyr	Somatic	171	1		WXS	Illumina HiSeq	Phase_I	64	18	NM_024896	0	0	4	9	5	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273899	0.80580	.	.	ENSG00000099219	ENST00000339450;ENST00000543230	T;T	0.25085	1.82;1.82	5.66	5.66	0.87406	.	0.090086	0.85682	D	0.000000	T	0.24084	0.0583	L	0.36672	1.1	0.80722	D	1	D	0.56521	0.976	P	0.47827	0.558	T	0.03278	-1.1053	10	0.02654	T	1	-21.0967	15.8854	0.79244	1.0:0.0:0.0:0.0	.	671	Q7Z2K6	ERMP1_HUMAN	Y	671;249	ENSP00000340427:F671Y;ENSP00000439368:F249Y	ENSP00000340427:F671Y	F	-	2	0	ERMP1	5791231	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	8.243000	0.89821	2.156000	0.67533	0.533000	0.62120	TTT	.		0.403	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		T	5801231	A	T	5801231	3	4	49	1	0	0	0	0	1	0	0	0	5249	14	1	5	722	5	ERMP1	9	5801231	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08		5801231	135412200	45	4505											
TYRP1	7306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	12694339	12694339	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	acaactgtgggacgtgccgtCctggctggagaggagctgcc	7	7	16	11	2	0	1	0	0	0	1	1	4	1	3	3	4	4	2	3	4	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:12694339C>G	ENST00000388918.5	+	2	472	c.343C>G	c.(343-345)Cct>Gct	p.P115A	TYRP1_ENST00000381136.2_5'Flank|TYRP1_ENST00000381137.2_5'UTR	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	115					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		GACGTGCCGTCCTGGCTGGAG	0.507									Oculocutaneous Albinism																												p.P115A		.											.	TYRP1-226	0			c.C343G						.						35	33	34					9																	12694339		2203	4300	6503	SO:0001583	missense	7306	exon2	Familial Cancer Database		TGCCGTCCTGGCT	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.343C>G	9.37:g.12694339C>G	ENSP00000373570:p.Pro115Ala	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	48	14	NM_000550	0	0	0	0	0	P78468|P78469|Q13721|Q15679	Missense_Mutation	SNP	ENST00000388918.5	37	CCDS34990.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937217	0.52972	.	.	ENSG00000107165	ENST00000388918	D	0.98926	-5.24	5.5	5.5	0.81552	Uncharacterised domain, di-copper centre (2);	0.097920	0.64402	D	0.000001	D	0.97324	0.9125	L	0.55834	1.745	0.80722	D	1	B	0.10296	0.003	B	0.14578	0.011	D	0.95286	0.8390	9	.	.	.	-1.287	19.7727	0.96373	0.0:1.0:0.0:0.0	.	115	P17643	TYRP1_HUMAN	A	115	ENSP00000373570:P115A	.	P	+	1	0	TYRP1	12684339	0.998000	0.40836	1.000000	0.80357	0.744000	0.42396	3.774000	0.55341	2.758000	0.94735	0.563000	0.77884	CCT	.		0.507	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		G	12694339	C	G	12694339	3	3	49	1	0	0	0	0	1	0	0	0	16849	855	30	4	345	4	TYRP1	9	12694339	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	6893108	12694339	128519092	46	4506											
UNC13B	10497	hgsc.bcm.edu	37	chr9	35243362	35243362	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccttgggagctgacaatgagGtaggagcagccttatttgca	10	10	13	8	0	0	2	0	2	0	0	0	4	0	4	2	3	4	4	2	3	3	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:35243362G>C	ENST00000378495.3	+	6	690		c.e6+1		UNC13B_ENST00000396787.1_Splice_Site|UNC13B_ENST00000378496.4_Splice_Site	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)						apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TGACAATGAGGTAGGAGCAGC	0.453																																					.		.											.	UNC13B-157	0			c.468+1G>C						.						107	106	107					9																	35243362		2203	4300	6503	SO:0001630	splice_region_variant	10497	exon6			AATGAGGTAGGAG	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"unc-13-like (C. elegans)"	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.468+1G>C	9.37:g.35243362G>C		Somatic	217	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_006377	0	0	0	0	0	Q5VYM8	Splice_Site	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806342	0.70682	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2568	0.82522	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13B	35233362	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.638000	0.91019	2.307000	0.77673	0.655000	0.94253	.	.		0.453	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	Intron	C	35243362	G	C	35243362	5	2	49	1	0	0	0	0	0	0	1	0	17018	1275	44	4	491	4	UNC13B	9	35243362	Splice_Site	SNP	G	TCGA-B9-4115-01A-01D-1252-08	22549023	35243362	105970069	47	4507											
KIF12	113220	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	116859620	116859620	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagggcctccagactcccaaAttccaccacccgcagctgct	9	6	7	19	1	0	1	0	0	0	1	3	1	3	1	6	1	2	3	6	1	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:116859620A>T	ENST00000374118.3	-	4	430	c.193T>A	c.(193-195)Ttt>Att	p.F65I	KIF12_ENST00000473174.1_Intron	NM_138424.1	NP_612433.1	Q96FN5	KIF12_HUMAN	kinesin family member 12	198	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	17						AGACTCCCAAATTCCACCACC	0.602																																					p.F65I		.											.	KIF12-90	0			c.T193A						.						41	43	43					9																	116859620		2203	4300	6503	SO:0001583	missense	113220	exon4			TCCCAAATTCCAC	BC010626	CCDS6801.1	9q33.1	2008-02-05			ENSG00000136883	ENSG00000136883		"Kinesins"	21495	protein-coding gene	gene with protein product		611278					Standard	NM_138424		Approved		uc004bif.3	Q96FN5	OTTHUMG00000020533	ENST00000374118.3:c.193T>A	9.37:g.116859620A>T	ENSP00000363232:p.Phe65Ile	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	92	32	NM_138424	0	0	17	47	30	Q5TBE0	Missense_Mutation	SNP	ENST00000374118.3	37	CCDS6801.1	.	.	.	.	.	.	.	.	.	.	A	6.945	0.544191	0.13312	.	.	ENSG00000136883	ENST00000374118;ENST00000259410	T	0.70045	-0.45	5.5	0.00987	0.14080	Kinesin, motor domain (4);	0.463632	0.22239	N	0.062709	T	0.33000	0.0848	N	0.01817	-0.705	0.23906	N	0.996504	B	0.10296	0.003	B	0.15484	0.013	T	0.21245	-1.0251	10	0.52906	T	0.07	.	4.5522	0.12117	0.4767:0.0:0.0832:0.4401	.	198	Q96FN5	KIF12_HUMAN	I	65;198	ENSP00000363232:F65I	ENSP00000259410:F198I	F	-	1	0	KIF12	115899441	0.889000	0.30405	0.842000	0.33263	0.054000	0.15201	1.421000	0.34815	-0.251000	0.09542	-0.451000	0.05528	TTT	.		0.602	KIF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053751.1	NM_138424		T	116859620	A	T	116859620	3	4	49	1	0	0	0	0	1	0	0	0	8294	101	4	5	1400	5	KIF12	9	116859620	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	81616258	116859620	24353811	48	4508											
COL27A1	85301	hgsc.bcm.edu	37	chr9	117052533	117052533	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgccagggccccggggCgtggtggggagacagggcct	4	4	22	11	2	0	1	0	0	0	1	0	2	0	1	4	8	1	1	4	8	0	0	rs575474490	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:117052533C>G	ENST00000356083.3	+	47	4681	c.4290C>G	c.(4288-4290)ggC>ggG	p.G1430G		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1430	Collagen-like 13.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GGCCCCGGGGCGTGGTGGGGA	0.677																																					p.G1430G		.											.	COL27A1-94	0			c.C4290G						.						15	14	14					9																	117052533		2181	4265	6446	SO:0001819	synonymous_variant	85301	exon47			CCGGGGCGTGGTG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4290C>G	9.37:g.117052533C>G		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	17	2	NM_032888	0	0	1	1	0	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			.		0.677	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		G	117052533	C	G	117052533	2	3	49	1	0	0	0	0	0	0	0	1	3691	755	27	4		4	COL27A1	9	117052533	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	192913	117052533	24160898	49	4509											
CEL	1056	hgsc.bcm.edu	37	chr9	135947023	135947023	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgggtgactccgagaccGcccccgtgccgcccacgggt	5	4	13	19	6	0	2	0	1	0	1	1	3	1	2	7	2	1	0	7	2	0	0	rs374263839|rs75294797	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:135947023G>C	ENST00000372080.4	+	11	2159	c.2143G>C	c.(2143-2145)Gcc>Ccc	p.A715P	CEL_ENST00000351304.7_Missense_Mutation_p.A646P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	712	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CTCCGAGACCGCCCCCGTGCC	0.781																																					p.A715P		.											.	CEL-91	0			c.G2143C						.						5	7	6					9																	135947023		1628	3758	5386	SO:0001583	missense	1056	exon11			GAGACCGCCCCCG	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"bile salt-stimulated lipase"	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.2143G>C	9.37:g.135947023G>C	ENSP00000361151:p.Ala715Pro	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	29	4	NM_001807	0	0	0	0	0	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	g	7.404	0.633289	0.14322	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.70986	-0.34;-0.53	2.27	-2.27	0.06846	.	.	.	.	.	T	0.43678	0.1258	N	0.16368	0.405	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18085	-1.0348	9	0.20519	T	0.43	.	0.5426	0.00648	0.3832:0.178:0.2587:0.1801	.	712	P19835	CEL_HUMAN	P	715;646;681	ENSP00000361151:A715P;ENSP00000342217:A646P	ENSP00000304021:A681P	A	+	1	0	CEL	134936844	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.308000	0.00255	-0.627000	0.05589	-0.698000	0.03680	GCC	.		0.781	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			C	135947023	G	C	135947023	3	2	49	1	0	0	0	0	1	0	0	0	3215	1087	38	4	2185	4	CEL	9	135947023	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	18894490	135947023	5266408	50	4510											
PTEN	5728	broad.mit.edu	37	chr10	89624275	89624275	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcagaaacaaaaggagatatCaagaggatggattcgactta	18	7	11	5	1	1	3	1	0	0	3	2	7	1	5	0	3	1	1	0	3	6	3	rs587781912		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr10:89624275C>T	ENST00000371953.3	+	1	1406	c.49C>T	c.(49-51)Caa>Taa	p.Q17*	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	17	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.Q17*(5)|p.Q17del(2)|p.R15fs*23(1)|p.R14fs*26(1)|p.Y16fs*21(1)|p.N12fs*6(1)|p.R14_D22del(1)|p.Y16fs*1(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AAGGAGATATCAAGAGGATGG	0.478		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.Q17X			yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN-17735	63	Whole gene deletion(37)|Unknown(13)|Substitution - Nonsense(5)|Deletion - Frameshift(5)|Deletion - In frame(3)	prostate(14)|central_nervous_system(13)|endometrium(7)|skin(7)|lung(6)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|breast(3)|bone(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	c.C49T						.						183	175	178					10																	89624275		2203	4300	6503	SO:0001587	stop_gained	5728	exon1	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	AGATATCAAGAGG	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.49C>T	10.37:g.89624275C>T	ENSP00000361021:p.Gln17*	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	205	6	NM_000314	0	0	13	14	1	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	49	15.443228	0.99834	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.05	5.05	0.67936	.	0.062767	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.7659	17.1609	0.86803	0.0:1.0:0.0:0.0	.	.	.	.	X	17	.	.	Q	+	1	0	PTEN	89614255	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.015000	0.76387	2.335000	0.79485	0.561000	0.74099	CAA	.		0.478	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89624275	C	T	89624275	4	4	49	1	0	0	0	0	0	1	0	0	12767	827	29	2	51	2	PTEN	10	89624275	Nonsense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08		89624275	45910472	51	4511											
METTL10	399818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	126477651	126477651	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttccagttccaatatcAagcactgaagcatccagtgg	12	10	7	12	0	1	1	1	1	0	0	4	1	4	1	4	1	2	3	4	1	4	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr10:126477651A>G	ENST00000368836.2	-	3	288	c.252T>C	c.(250-252)ctT>ctC	p.L84L	RP11-12J10.3_ENST00000494792.1_Missense_Mutation_p.L49S	NM_212554.2	NP_997719.2	Q5JPI9	MET10_HUMAN	methyltransferase like 10	84							methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_lung(145;0.0186)|Lung NSC(174;0.0295)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.101)|COAD - Colon adenocarcinoma(40;0.111)		TTCCAATATCAAGCACTGAAG	0.348																																					p.L84L		.											.	METTL10-22	0			c.T252C						.						172	152	159					10																	126477651		2203	4300	6503	SO:0001819	synonymous_variant	399818	exon3			AATATCAAGCACT		CCDS31307.1	10q26.13	2010-01-15			ENSG00000203791	ENSG00000203791			33787	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 138"	C10orf138			Standard	NM_212554		Approved	Em:AC068896.3	uc001lhy.1	Q5JPI9	OTTHUMG00000019217	ENST00000368836.2:c.252T>C	10.37:g.126477651A>G		Somatic	182	0		WXS	Illumina HiSeq	Phase_I	110	39	NM_212554	0	0	3	6	3	A8MPY7	Silent	SNP	ENST00000368836.2	37	CCDS31307.1																																																																																			.		0.348	METTL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050884.1	NM_212554		G	126477651	A	G	126477651	2	3	49	1	0	0	0	0	0	0	0	1	9519	117	5	3		3	METTL10	10	126477651	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	36853376	126477651	9057096	52	4512											
OSBPL5	114879	hgsc.bcm.edu;broad.mit.edu	37	chr11	3143300	3143300	+	Frame_Shift_Del	DEL	T	T	-																															gctgccgtgtggcgcgcttcTtctcctgccggtagttctcc																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:3143300delT	ENST00000263650.7	-	5	488	c.329delA	c.(328-330)aagfs	p.K111fs	OSBPL5_ENST00000348039.5_Frame_Shift_Del_p.K111fs|OSBPL5_ENST00000389989.3_Frame_Shift_Del_p.K111fs|OSBPL5_ENST00000542243.1_Frame_Shift_Del_p.E26fs|OSBPL5_ENST00000525498.1_Frame_Shift_Del_p.K63fs	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	111					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GGCGCGCTTCTTCTCCTGCCG	0.687																																					p.K110fs		.											.	OSBPL5-113	0			c.329delA						.						43	34	37					11																	3143300		2191	4291	6482	SO:0001589	frameshift_variant	114879	exon5			.	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.329delA	11.37:g.3143300delT	ENSP00000263650:p.Lys111fs	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	25	11	NM_145638	0	0	0	0	0	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Frame_Shift_Del	DEL	ENST00000263650.7	37	CCDS31344.1																																																																																			.		0.687	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			-	3143300	T	-	3143300	7	5	49	1	0	1	0	1	0	0	0	0	11306	1609	56	0	2382	0	OSBPL5	11	3143300	Frame_Shift_Del	DEL	T	TCGA-B9-4115-01A-01D-1252-08		3143300	131863216	53	4513											
TRIM3	10612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6486812	6486812	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacctctcacagaaggtgtgCaggcaaggaagaaccttggg	12	6	13	10	0	1	2	1	0	1	2	2	3	1	3	2	4	2	2	2	4	4	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:6486812C>T	ENST00000525074.1	-	2	508	c.114G>A	c.(112-114)ctG>ctA	p.L38L	TRIM3_ENST00000359518.3_Silent_p.L38L|TRIM3_ENST00000345851.3_Silent_p.L38L|TRIM3_ENST00000536344.1_Intron|TRIM3_ENST00000537602.1_Silent_p.L38L	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	38					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGAAGGTGTGCAGGCAAGGAA	0.607																																					p.L38L	Melanoma(6;5 510 1540 25169 29084)	.											.	TRIM3-714	0			c.G114A						.						209	157	174					11																	6486812		2201	4296	6497	SO:0001819	synonymous_variant	10612	exon2			GGTGTGCAGGCAA	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.114G>A	11.37:g.6486812C>T		Somatic	230	1		WXS	Illumina HiSeq	Phase_I	318	107	NM_001248006	0	0	0	1	1	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			.		0.607	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		T	6486812	C	T	6486812	2	4	49	1	0	0	0	0	0	0	0	1	16537	697	25	2		2	TRIM3	11	6486812	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	3343512	6486812	128519704	54	4514											
FJX1	24147	hgsc.bcm.edu	37	chr11	35641295	35641295	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcgtgttccgcgagcggAccgcgcggcgcgtcctggag	3	7	18	13	9	0	0	0	0	0	0	2	3	2	2	3	3	2	1	3	3	0	1	rs202089278	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:35641295A>G	ENST00000317811.4	+	1	1561	c.1111A>G	c.(1111-1113)Acc>Gcc	p.T371A	FJX1_ENST00000532914.1_3'UTR	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	371					retina layer formation (GO:0010842)	extracellular space (GO:0005615)				lung(1)|urinary_tract(1)	2	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				CCGCGAGCGGACCGCGCGGCG	0.706													A|||	14	0.00279553	0.0106	0	5008	,	,		12543	0		0	False		,,,				2504	0				p.T371A	Melanoma(161;10 2587 27165 47356)	.											.	.	0			c.A1111G						.	A	ALA/THR	14,3808		0,14,1897	6	8	7		1111	5.2	1	11		7	0,8144		0,0,4072	yes	missense	FJX1	NM_014344.3	58	0,14,5969	GG,GA,AA		0.0,0.3663,0.117	possibly-damaging	371/438	35641295	14,11952	1911	4072	5983	SO:0001583	missense	24147	exon1			GAGCGGACCGCGC	AJ245599	CCDS44570.1	11p13	2012-05-18				ENSG00000179431			17166	protein-coding gene	gene with protein product	"putative secreted ligand homologous to fjx1"	612206				7647465, 10072791	Standard	NM_014344		Approved	FLJ22416, FLJ25593	uc001mwh.3	Q86VR8		ENST00000317811.4:c.1111A>G	11.37:g.35641295A>G	ENSP00000400223:p.Thr371Ala	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	15	5	NM_014344	0	0	0	1	1	B2RCA9|Q9UGK6	Missense_Mutation	SNP	ENST00000317811.4	37	CCDS44570.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	20.6	4.011909	0.75046	0.003663	0.0	ENSG00000179431	ENST00000317811	D	0.81659	-1.52	5.21	5.21	0.72293	.	.	.	.	.	T	0.78470	0.4288	M	0.73217	2.22	0.38748	D	0.954037	D	0.67145	0.996	D	0.65573	0.936	D	0.85203	0.1016	9	0.72032	D	0.01	-4.633	9.3359	0.38049	0.9184:0.0:0.0816:0.0	.	371	Q86VR8	FJX1_HUMAN	A	371	ENSP00000400223:T371A	ENSP00000400223:T371A	T	+	1	0	FJX1	35597871	1.000000	0.71417	0.994000	0.49952	0.946000	0.59487	5.310000	0.65780	1.968000	0.57251	0.454000	0.30748	ACC	A|0.995;G|0.005		0.706	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344		G	35641295	A	G	35641295	3	3	49	1	0	0	0	0	1	0	0	0	5920	275	10	3	1113	3	FJX1	11	35641295	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	29154483	35641295	99365221	55	4515											
TTC17	55761	hgsc.bcm.edu	37	chr11	43436151	43436151	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttttcagcctctgaccttTttgagcctgggaaatgctta	7	16	8	10	0	3	2	1	2	2	0	3	3	3	3	3	1	3	1	3	1	2	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:43436151T>G	ENST00000039989.4	+	16	2090	c.2076T>G	c.(2074-2076)ttT>ttG	p.F692L	TTC17_ENST00000299240.6_Missense_Mutation_p.F692L|TTC17_ENST00000526774.1_3'UTR	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	692					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						CTCTGACCTTTTTGAGCCTGG	0.398																																					p.F692L		.											.	TTC17-95	0			c.T2076G						.						102	114	110					11																	43436151		2203	4300	6503	SO:0001583	missense	55761	exon16			GACCTTTTTGAGC	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"Tetratricopeptide (TTC) repeat domain containing"	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.2076T>G	11.37:g.43436151T>G	ENSP00000039989:p.Phe692Leu	Somatic	413	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_018259	0	0	0	0	0	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	T	9.464	1.093955	0.20471	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.55588	0.51;0.51	5.6	3.3	0.37823	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.056859	0.64402	D	0.000001	T	0.18341	0.0440	N	0.00750	-1.22	0.31176	N	0.702654	B;B;B	0.12013	0.0;0.005;0.0	B;B;B	0.14023	0.002;0.01;0.001	T	0.09862	-1.0655	10	0.25106	T	0.35	-14.3037	5.3147	0.15849	0.0:0.214:0.138:0.648	.	692;692;692	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	L	692	ENSP00000299240:F692L;ENSP00000039989:F692L	ENSP00000039989:F692L	F	+	3	2	TTC17	43392727	0.972000	0.33761	0.999000	0.59377	0.979000	0.70002	0.393000	0.20817	0.419000	0.25927	-0.400000	0.06385	TTT	.		0.398	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		G	43436151	T	G	43436151	3	3	49	1	0	0	0	0	1	0	0	0	16717	1838	64	5	2138	5	TTC17	11	43436151	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	7794856	43436151	91570365	56	4516											
ZBTB3	79842	broad.mit.edu	37	chr11	62519739	62519739	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgagccttgcggatgtggcgGtagaggtcccctgactgcgt	5	10	16	10	3	0	3	0	2	0	1	1	4	1	4	3	4	3	1	3	4	1	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:62519739G>A	ENST00000394807.3	-	2	1673	c.1548C>T	c.(1546-1548)taC>taT	p.Y516Y		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	516					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(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						GGATGTGGCGGTAGAGGTCCC	0.617																																					p.Y516Y													.	ZBTB3-585	0			c.C1548T						.						95	90	91					11																	62519739		2202	4299	6501	SO:0001819	synonymous_variant	79842	exon2			GTGGCGGTAGAGG	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.1548C>T	11.37:g.62519739G>A		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	160	4	NM_024784	0	0	3	3	0		Silent	SNP	ENST00000394807.3	37	CCDS8034.1																																																																																			.		0.617	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784		A	62519739	G	A	62519739	2	1	49	1	0	0	0	0	0	0	0	1	17566	1256	44	2		2	ZBTB3	11	62519739	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	19083588	62519739	72486777	57	4517											
OTUB1	55611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63756155	63756155	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaaccctctggtgtcagaGcggctggagctctcggtcct	6	9	13	13	2	3	2	1	0	2	2	5	3	4	3	2	4	3	2	2	4	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:63756155G>T	ENST00000538426.1	+	3	194	c.150G>T	c.(148-150)gaG>gaT	p.E50D	OTUB1_ENST00000428192.2_Missense_Mutation_p.E50D|OTUB1_ENST00000543004.1_Missense_Mutation_p.E59D|OTUB1_ENST00000543988.1_Missense_Mutation_p.E20D|OTUB1_ENST00000535715.1_Missense_Mutation_p.E50D|OTUB1_ENST00000541478.1_Intron|OTUB1_ENST00000422031.2_Missense_Mutation_p.E87D|OTUB1_ENST00000536443.1_3'UTR	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1	50					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						TGGTGTCAGAGCGGCTGGAGC	0.537																																					p.E50D		.											.	OTUB1-501	0			c.G150T						.						114	116	115					11																	63756155		2201	4297	6498	SO:0001583	missense	55611	exon3			GTCAGAGCGGCTG	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"OTU domain containing"	23077	protein-coding gene	gene with protein product		608337	"OTU domain, ubiquitin aldehyde binding 1"			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.150G>T	11.37:g.63756155G>T	ENSP00000444357:p.Glu50Asp	Somatic	346	0		WXS	Illumina HiSeq	Phase_I	515	141	NM_017670	0	0	70	118	48	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Missense_Mutation	SNP	ENST00000538426.1	37	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	G	8.534	0.871741	0.17322	.	.	ENSG00000167770	ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004;ENST00000543988	T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85	5.49	5.49	0.81192	.	.	.	.	.	T	0.29491	0.0735	N	0.17248	0.465	0.35424	D	0.793481	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29971	-0.9994	9	0.15952	T	0.53	.	10.7288	0.46085	0.0876:0.0:0.9124:0.0	.	87;50	B4DPD5;Q96FW1	.;OTUB1_HUMAN	D	50;50;87;50;59;20	ENSP00000440211:E50D;ENSP00000402551:E50D;ENSP00000416973:E87D;ENSP00000444357:E50D;ENSP00000437453:E59D;ENSP00000441328:E20D	ENSP00000416973:E87D	E	+	3	2	OTUB1	63512731	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	1.546000	0.36179	2.753000	0.94483	0.591000	0.81541	GAG	.		0.537	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670		T	63756155	G	T	63756155	3	4	49	1	0	0	0	0	1	0	0	0	11337	962	34	4	160	4	OTUB1	11	63756155	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	1236416	63756155	71250361	58	4518											
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	133814179	133814179	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactgctggtccagcatgagCactttgcactcataccagcc	9	10	8	14	0	1	1	1	1	0	0	2	1	2	1	3	1	7	4	3	1	2	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:133814179C>A	ENST00000321016.8	-	3	575	c.345G>T	c.(343-345)gtG>gtT	p.V115V	IGSF9B_ENST00000533871.2_Silent_p.V115V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	115	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCAGCATGAGCACTTTGCACT	0.577																																					p.V115V		.											.	IGSF9B-68	0			c.G345T						.						108	116	113					11																	133814179		2103	4231	6334	SO:0001819	synonymous_variant	22997	exon3			CATGAGCACTTTG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.345G>T	11.37:g.133814179C>A		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	67	32	NM_014987	0	0	0	0	0	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				.		0.577	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133814179	C	A	133814179	2	1	49	1	0	0	0	0	0	0	0	1	7627	697	25	4		4	IGSF9B	11	133814179	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	70058024	133814179	1192337	59	4519											
PRB2	653247	broad.mit.edu	37	chr12	11546691	11546692	+	In_Frame_Ins	INS	-	-	TTG																															gagatcggggacttcgggacINSttgtctccttgtgggggtgg																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr12:11546691_11546692insTTG	ENST00000389362.4	-	3	355_356	c.320_321insCAA	c.(319-321)aag>aaCAAg	p.106_107insN	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	106	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GACTTCGGGACTTGTCTCCTTG	0.604																																					p.K107delinsNK													.	PRB2-22	0			c.321_322insCAA						.																																			SO:0001652	inframe_insertion	653247	exon3			TCGGGACTTGTCT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.318_320dupCAA	12.37:g.11546692_11546694dupTTG	ENSP00000374013:p.Asp106_Lys107insAsn	Somatic	1175	0		WXS	Illumina HiSeq	Phase_I	2149	7	NM_006248	0	0	0	0	0	O00599|P02811|P04281	In_Frame_Ins	INS	ENST00000389362.4	37	CCDS41757.2																																																																																			.		0.604	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		TTG	11546692	-	TTG	11546691	7	5	49	1	0	1	1	0	0	0	0	0	12472	564	20	0	933	0	PRB2	12	11546691	In_Frame_Ins	INS	-	TCGA-B9-4115-01A-01D-1252-08		11546691	122305204	60	4520											
ITGB7	3695	broad.mit.edu	37	chr12	53587039	53587039	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgacagtgaccctttccactGcacaggggccctgtgccatt	7	10	10	14	0	0	2	0	2	0	0	1	2	1	2	4	2	2	1	4	2	0	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr12:53587039G>A	ENST00000267082.5	-	12	1842	c.1611C>T	c.(1609-1611)tgC>tgT	p.C537C	ITGB7_ENST00000550743.2_Intron|ITGB7_ENST00000338737.4_Intron|ITGB7_ENST00000422257.3_Silent_p.C537C	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	537	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCTTTCCACTGCACAGGGGCC	0.627																																					p.C537C													.	ITGB7-231	0			c.C1611T						.						51	48	49					12																	53587039		2203	4300	6503	SO:0001819	synonymous_variant	3695	exon12			TCCACTGCACAGG		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1611C>T	12.37:g.53587039G>A		Somatic	81	1		WXS	Illumina HiSeq	Phase_I	129	5	NM_000889	0	0	24	24	0	Q9UCP7|Q9UCS7	Silent	SNP	ENST00000267082.5	37	CCDS8849.1																																																																																			.		0.627	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			A	53587039	G	A	53587039	2	1	49	1	0	0	0	0	0	0	0	1	7921	1311	46	2		2	ITGB7	12	53587039	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	42040348	53587039	80264856	61	4521											
CEP290	80184	broad.mit.edu	37	chr12	88524957	88524957	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttacctctcttcttaatttGctgttttcattttctgcctc	4	23	3	11	0	4	0	1	0	3	0	6	0	4	0	2	0	3	2	2	0	2	9			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr12:88524957G>T	ENST00000552810.1	-	7	823	c.480C>A	c.(478-480)agC>agA	p.S160R	CEP290_ENST00000309041.7_Missense_Mutation_p.S160R|CEP290_ENST00000397838.3_5'Flank	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	160					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTCTTAATTTGCTGTTTTCAT	0.249																																					p.S160R													.	CEP290-96	0			c.C480A						.						114	102	105					12																	88524957		1765	4036	5801	SO:0001583	missense	80184	exon7			TAATTTGCTGTTT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.480C>A	12.37:g.88524957G>T	ENSP00000448012:p.Ser160Arg	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_025114	0	0	0	0	0	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.746016	0.30955	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.64991	-0.13;-0.13	5.48	5.48	0.80851	.	0.213875	0.48767	D	0.000171	T	0.47210	0.1433	N	0.12182	0.205	0.80722	D	1	B	0.15473	0.013	B	0.16289	0.015	T	0.33111	-0.9881	10	0.25751	T	0.34	.	19.3369	0.94322	0.0:0.0:1.0:0.0	.	160	O15078	CE290_HUMAN	R	160;160;160;62	ENSP00000448012:S160R;ENSP00000308021:S160R	ENSP00000308021:S160R	S	-	3	2	CEP290	87049088	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.396000	0.59684	2.575000	0.86900	0.563000	0.77884	AGC	.		0.249	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88524957	G	T	88524957	3	4	49	1	0	0	0	0	1	0	0	0	3259	1310	46	4	7151	4	CEP290	12	88524957	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	34937918	88524957	45326938	62	4522											
DGKH	160851	hgsc.bcm.edu	37	chr13	42740683	42740683	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacattttcgttctgtgttAgtcctctattggtttttgtc	5	21	7	8	1	2	0	0	0	2	0	5	0	3	0	1	1	1	3	1	1	3	8			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr13:42740683A>C	ENST00000337343.4	+	9	1012	c.991A>C	c.(991-993)Agt>Cgt	p.S331R	DGKH_ENST00000261491.5_Missense_Mutation_p.S331R|DGKH_ENST00000540693.1_Missense_Mutation_p.S331R|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Missense_Mutation_p.S86R|DGKH_ENST00000379274.2_Missense_Mutation_p.S195R|DGKH_ENST00000536612.1_Missense_Mutation_p.S195R	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	331	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		GTTCTGTGTTAGTCCTCTATT	0.363																																					p.S331R		.											.	DGKH-652	0			c.A991C						.						160	154	156					13																	42740683		2203	4300	6503	SO:0001583	missense	160851	exon10			TGTGTTAGTCCTC	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.991A>C	13.37:g.42740683A>C	ENSP00000337572:p.Ser331Arg	Somatic	325	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001204504	0	0	0	0	0	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.642151	0.87859	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	T;T;T;T;T;T	0.80994	-1.44;-1.26;-1.44;-1.42;-1.42;1.81	5.81	5.81	0.92471	Diacylglycerol kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85111	0.5622	L	0.33293	1	0.80722	D	1	D;D;D;D	0.89917	0.997;1.0;0.999;0.998	D;D;D;D	0.83275	0.986;0.981;0.996;0.98	D	0.86762	0.1967	10	0.72032	D	0.01	.	16.1677	0.81782	1.0:0.0:0.0:0.0	.	86;195;331;331	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	R	331;331;331;195;195;86	ENSP00000440823:S331R;ENSP00000337572:S331R;ENSP00000261491:S331R;ENSP00000368576:S195R;ENSP00000445114:S195R;ENSP00000441308:S86R	ENSP00000261491:S331R	S	+	1	0	DGKH	41638683	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	7.333000	0.79214	2.218000	0.71995	0.528000	0.53228	AGT	.		0.363	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		C	42740683	A	C	42740683	3	2	49	1	0	0	0	0	1	0	0	0	4481	420	15	5	1025	5	DGKH	13	42740683	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08		42740683	72429195	63	4523											
DOCK9	23348	broad.mit.edu	37	chr13	99481713	99481713	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctccttcatctgggcggTggccattagcaccgtgcgta	6	11	12	12	3	2	0	1	0	1	0	3	0	3	0	3	3	3	3	3	3	2	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr13:99481713T>C	ENST00000376460.1	-	43	4824	c.4744A>G	c.(4744-4746)Acc>Gcc	p.T1582A	DOCK9_ENST00000339416.2_Missense_Mutation_p.T1583A|DOCK9_ENST00000448493.2_3'UTR|DOCK9-AS1_ENST00000439367.1_RNA	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1583					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ATCTGGGCGGTGGCCATTAGC	0.542																																					.													.	DOCK9-90	0			.						.						84	82	82					13																	99481713		2098	4229	6327	SO:0001583	missense	23348	.			GGGCGGTGGCCAT	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.4744A>G	13.37:g.99481713T>C	ENSP00000365643:p.Thr1582Ala	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	64	13	.	0	0	2	2	0	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.7|28.7	4.945479|4.945479	0.92593|0.92593	.|.	.|.	ENSG00000088387|ENSG00000088387	ENST00000400228|ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000376453;ENST00000340449	.|T;T;T	.|0.64991	.|2.05;2.14;-0.13	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84552|0.84552	0.5497|0.5497	M|M	0.93763|0.93763	3.455|3.455	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D	.|0.89917	.|0.998;0.998;1.0;1.0;1.0;0.981;1.0;1.0	.|D;D;D;D;D;D;D;D	.|0.91635	.|0.986;0.987;0.983;0.999;0.994;0.909;0.987;0.992	D|D	0.88614|0.88614	0.3158|0.3158	5|10	.|0.87932	.|D	.|0	.|.	16.3948|16.3948	0.83586|0.83586	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1583;302;226;1582;226;1583;275;225	.|A8MWZ5;B7Z6H5;B7Z2J2;Q9BZ29-5;Q5JUD8;Q9BZ29;B7Z6G9;F5H1Q4	.|.;.;.;.;.;DOCK9_HUMAN;.;.	R|A	169|1582;1583;1575;1583;1582;513;1583;225;226	.|ENSP00000365643:T1582A;ENSP00000341086:T1583A;ENSP00000344702:T226A	.|ENSP00000341086:T1583A	H|T	-|-	2|1	0|0	DOCK9|DOCK9	98279714|98279714	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.994000|0.994000	0.84299|0.84299	5.854000|5.854000	0.69503|0.69503	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.		0.542	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		C	99481713	T	C	99481713	3	2	49	1	0	0	0	0	1	0	0	0	4705	1696	59	3	1514	3	DOCK9	13	99481713	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	56741030	99481713	15688165	64	4524											
ATP11A	23250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	113516824	113516825	+	Missense_Mutation	DNP	GC	GC	AG																															cgctcctgggactgtttgacGcactggtgttcttctttggt																								rs140812688		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr13:113516824_113516825GC>AG	ENST00000487903.1	+	25	3014_3015	c.2926_2927GC>AG	c.(2926-2928)GCa>AGa	p.A976R	ATP11A_ENST00000375630.2_Missense_Mutation_p.A976R|ATP11A_ENST00000283558.8_Missense_Mutation_p.A976R|ATP11A_ENST00000375645.3_Missense_Mutation_p.A976R			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	976					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACTGTTTGACGCACTGGTGTTC	0.535																																					p.A976R		.											.	ATP11A	0			c.C2927G						.																																			SO:0001583	missense	23250	exon25			TTGACGCACTGGT	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	Exception_encountered	13.37:g.113516824_113516825delinsAG	ENSP00000420387:p.Ala976Arg	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	92	38		0	0	0	0	0	Q5VXT2	Missense_Mutation	DNP	ENST00000487903.1	37	CCDS32011.1																																																																																			.		0.535	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		AG	113516825	GC	AG	113516824	3	1	49	1	0	0	0	0	1	0	0	0	1120	1087	38	1	3024	1	ATP11A	13	113516824	Missense_Mutation	DNP	GC	TCGA-B9-4115-01A-01D-1252-08	14035111	113516824	1653054	65	4525											
PPM1A	5494	broad.mit.edu	37	chr14	60749544	60749544	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaatggaggatgcacatacGgctgtgatcggtttgccaag	11	9	14	7	2	0	1	0	1	0	0	1	4	0	3	1	4	3	3	1	4	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:60749544G>T	ENST00000395076.4	+	2	553	c.123G>T	c.(121-123)acG>acT	p.T41T	PPM1A_ENST00000325658.3_Silent_p.T41T|PPM1A_ENST00000325642.3_Silent_p.T114T|PPM1A_ENST00000529574.1_Silent_p.T41T	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	41					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		ATGCACATACGGCTGTGATCG	0.498																																					p.T114T													.	PPM1A-227	0			c.G342T						.						431	385	401					14																	60749544		2203	4300	6503	SO:0001819	synonymous_variant	5494	exon2			ACATACGGCTGTG	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.123G>T	14.37:g.60749544G>T		Somatic	613	0		WXS	Illumina HiSeq	Phase_I	245	4	NM_177952	0	0	7	8	1	B5BU11|J3KNM0|O75551	Silent	SNP	ENST00000395076.4	37	CCDS9744.1																																																																																			.		0.498	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003		T	60749544	G	T	60749544	2	4	49	1	0	0	0	0	0	0	0	1	12364	1103	39	4		4	PPM1A	14	60749544	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08		60749544	46599996	66	4526											
ZFYVE26	23503	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	68282659	68282659	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgcgaagcagcttcctCttttccaaatggatgattca	9	14	7	11	1	3	1	1	1	2	0	5	3	5	2	2	1	3	2	2	1	2	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:68282659C>A	ENST00000347230.4	-	2	160	c.22G>T	c.(22-24)Gag>Tag	p.E8*	ZFYVE26_ENST00000555452.1_Nonsense_Mutation_p.E8*	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	8					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GCAGCTTCCTCTTTTCCAAAT	0.478																																					p.E8X		.											.	ZFYVE26-162	0			c.G22T						.						30	30	30					14																	68282659		2203	4300	6503	SO:0001587	stop_gained	23503	exon2			CTTCCTCTTTTCC	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.22G>T	14.37:g.68282659C>A	ENSP00000251119:p.Glu8*	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	64	24	NM_015346	0	0	0	0	0	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Nonsense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	37	6.195059	0.97367	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-20.4213	20.2576	0.98430	0.0:1.0:0.0:0.0	.	.	.	.	X	8	.	ENSP00000251119:E8X	E	-	1	0	ZFYVE26	67352412	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.200000	0.72118	2.783000	0.95769	0.655000	0.94253	GAG	.		0.478	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68282659	C	A	68282659	4	1	49	1	0	0	0	0	0	1	0	0	17700	922	32	4	7761	4	ZFYVE26	14	68282659	Nonsense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	7533115	68282659	39066881	67	4527											
DICER1	23405	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	95556880	95556880	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttagctttgaggcttcggagGgctcttcttgctgctgcaga	5	14	13	9	1	2	2	0	1	2	1	3	3	2	3	0	3	4	6	0	3	1	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:95556880G>T	ENST00000526495.1	-	29	6015	c.5724C>A	c.(5722-5724)gcC>gcA	p.A1908A	DICER1_ENST00000527414.1_Silent_p.A1908A|DICER1_ENST00000541352.1_3'UTR|DICER1_ENST00000527416.2_5'UTR|DICER1_ENST00000393063.1_Silent_p.A1908A|DICER1_ENST00000556045.1_Silent_p.A806A|DICER1_ENST00000343455.3_Silent_p.A1908A			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1908	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		GGCTTCGGAGGGCTCTTCTTG	0.413			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.A1908A		.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1-961	0			c.C5724A						.						187	186	187					14																	95556880		2203	4300	6503	SO:0001819	synonymous_variant	23405	exon28	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TCGGAGGGCTCTT	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.5724C>A	14.37:g.95556880G>T		Somatic	468	0		WXS	Illumina HiSeq	Phase_I	95	36	NM_030621	0	0	1	1	0	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Silent	SNP	ENST00000526495.1	37	CCDS9931.1																																																																																			.		0.413	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			T	95556880	G	T	95556880	2	4	49	1	0	0	0	0	0	0	0	1	4532	1219	43	4		4	DICER1	14	95556880	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	27274221	95556880	11792660	68	4528											
SIVA1	10572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	105222013	105222013	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggcccaggcctacctggaCcacgtgtgggatgaaggctg	7	6	17	11	1	0	1	0	1	0	0	0	3	0	3	4	6	1	1	4	6	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:105222013C>T	ENST00000329967.6	+	2	267	c.165C>T	c.(163-165)gaC>gaT	p.D55D	SIVA1_ENST00000347067.5_Intron	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	55	Interaction with BCL2L1 isoform Bcl-x(L) and inhibition of BCL2L1 anti-apoptotic activity.				activation-induced cell death of T cells (GO:0006924)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	CD27 receptor binding (GO:0005175)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|prostate(1)	3		all_cancers(154;0.14)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.173)		CCTACCTGGACCACGTGTGGG	0.607																																					p.D55D		.											.	SIVA1-514	0			c.C165T						.						92	88	89					14																	105222013		2203	4300	6503	SO:0001819	synonymous_variant	10572	exon2			CCTGGACCACGTG	U82938	CCDS9992.1, CCDS9993.1	14q32.33	2007-03-19							17712	protein-coding gene	gene with protein product		605567				9177220	Standard	NM_006427		Approved	SIVA, Siva-1, Siva-2, CD27BP	uc001yph.3	O15304		ENST00000329967.6:c.165C>T	14.37:g.105222013C>T		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	314	98	NM_006427	0	0	58	131	73	Q96P98|Q9UPD6	Silent	SNP	ENST00000329967.6	37	CCDS9992.1	.	.	.	.	.	.	.	.	.	.	C	3.241	-0.155408	0.06544	.	.	ENSG00000184990	ENST00000556195	.	.	.	4.89	3.01	0.34805	.	.	.	.	.	T	0.55641	0.1933	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50499	-0.8821	4	.	.	.	-28.3879	7.3185	0.26513	0.0:0.783:0.0:0.217	.	.	.	.	I	73	.	.	T	+	2	0	SIVA1	104293058	0.105000	0.21958	0.720000	0.30636	0.302000	0.27658	0.003000	0.13083	1.027000	0.39758	0.462000	0.41574	ACC	.		0.607	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427		T	105222013	C	T	105222013	2	4	49	1	0	0	0	0	0	0	0	1	14377	506	18	2		2	SIVA1	14	105222013	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	9665133	105222013	2127527	69	4529											
TP53BP1	7158	broad.mit.edu	37	chr15	43733777	43733777	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttctttcaccagttgcAggctctgaataaaaacaaaa	14	14	5	8	0	3	1	1	1	2	0	3	1	3	1	1	1	2	3	1	1	6	6			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr15:43733777A>G	ENST00000263801.3	-	15	3282	c.3030T>C	c.(3028-3030)ccT>ccC	p.P1010P	TP53BP1_ENST00000382044.4_Silent_p.P1015P|TP53BP1_ENST00000450115.2_Silent_p.P1015P|TP53BP1_ENST00000382039.3_Silent_p.P1015P	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1010					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CACCAGTTGCAGGCTCTGAAT	0.388								Other conserved DNA damage response genes																													p.P1015P													.	TP53BP1-294	0			c.T3045C						.						102	102	102					15																	43733777		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon15			AGTTGCAGGCTCT	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.3030T>C	15.37:g.43733777A>G		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	244	4	NM_001141980	0	0	2	2	0	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			.		0.388	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			G	43733777	A	G	43733777	2	3	49	1	0	0	0	0	0	0	0	1	16416	175	7	3		3	TP53BP1	15	43733777	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08		43733777	58797615	70	4530											
FSD2	123722	broad.mit.edu	37	chr15	83437762	83437764	+	In_Frame_Del	DEL	TAA	TAA	-																															gctccttatctctttggtttTaataatggggggagaaggtg																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	TAA	TAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr15:83437762_83437764delTAA	ENST00000334574.8	-	9	1602_1604	c.1421_1423delTTA	c.(1420-1425)attaaa>aaa	p.I474del	FSD2_ENST00000541889.1_In_Frame_Del_p.I429del			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	474	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TCTTTGGTTTTAATAATGGGGGG	0.483																																					p.474_475del													.	FSD2-90	0			c.1421_1423del						.																																			SO:0001651	inframe_deletion	123722	exon9			TGGTTTTAATAAT	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"Fibronectin type III domain containing"	18024	protein-coding gene	gene with protein product			"SPRY domain containing 1"	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.1421_1423delTTA	15.37:g.83437765_83437767delTAA	ENSP00000335651:p.Ile474del	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	22	9	NM_001007122	0	0	0	0	0	B3KVG1|B7ZM02	In_Frame_Del	DEL	ENST00000334574.8	37	CCDS45332.1																																																																																			.		0.483	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122		-	83437764	TAA	-	83437762	7	5	49	1	0	1	0	1	0	0	0	0	6090	1763	61	0	846	0	FSD2	15	83437762	In_Frame_Del	DEL	TAA	TCGA-B9-4115-01A-01D-1252-08	39703985	83437762	19093630	71	4531											
ACAN	176	hgsc.bcm.edu	37	chr15	89399908	89399908	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggagaagttctagagacTgctgcccctggagtagagga	10	9	14	8	0	2	3	0	0	2	3	2	7	2	5	2	3	2	3	2	3	3	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr15:89399908T>C	ENST00000561243.1	+	11	4092	c.4092T>C	c.(4090-4092)acT>acC	p.T1364T	ACAN_ENST00000352105.7_Silent_p.T1364T|ACAN_ENST00000559004.1_Silent_p.T1364T|ACAN_ENST00000439576.2_Silent_p.T1364T			P16112	PGCA_HUMAN	aggrecan	1364	29 X 19 AA approximate tandem repeats of E-[IVDG]-[LV]-[EV]-[GTI]-[STA]-[ATV]- [SP]-[GA]-[VIFAD]-[GEDL]-[DE]-[LVI]-[SG]- [GERK]-[LV]-P-S-G.|CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TTCTAGAGACTGCTGCCCCTG	0.562																																					p.T1364T		.											.	ACAN-25	0			c.T4092C						.						4	6	6					15																	89399908		687	1791	2478	SO:0001819	synonymous_variant	176	exon12			AGAGACTGCTGCC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4092T>C	15.37:g.89399908T>C		Somatic	434	0		WXS	Illumina HiSeq	Phase_I	312	20	NM_001135	0	0	0	0	0	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			.		0.562	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		C	89399908	T	C	89399908	2	2	49	1	0	0	0	0	0	0	0	1	117	1567	55	3		3	ACAN	15	89399908	Silent	SNP	T	TCGA-B9-4115-01A-01D-1252-08	5962146	89399908	13131484	72	4532											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1251875	1251875	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcaaggtcaagcggcgcagCttgcgcctctacgcccgctg	6	6	13	16	6	2	0	1	0	1	0	2	0	2	0	2	2	4	4	2	2	3	2	rs60537026	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:1251875C>T	ENST00000348261.5	+	9	1673	c.1425C>T	c.(1423-1425)agC>agT	p.S475S	CACNA1H_ENST00000565831.1_Silent_p.S475S|CACNA1H_ENST00000358590.4_Silent_p.S475S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	475					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	AGCGGCGCAGCTTGCGCCTCT	0.677													C|||	4	0.000798722	0.003	0	5008	,	,		16056	0		0	False		,,,				2504	0				p.S475S		.											.	CACNA1H-67	0			c.C1425T						.	C	,	5,4079		0,5,2037	11	13	13		1425,1425	3.9	0.9	16	dbSNP_129	13	0,8256		0,0,4128	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	0,5,6165	TT,TC,CC		0.0,0.1224,0.0405	,	475/2348,475/2354	1251875	5,12335	2042	4128	6170	SO:0001819	synonymous_variant	8912	exon9			GCGCAGCTTGCGC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1425C>T	16.37:g.1251875C>T		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	7	4	NM_021098	0	0	0	0	0	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.985;T|0.015		0.677	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1251875	C	T	1251875	2	4	49	1	0	0	0	0	0	0	0	1	2551	796	28	2		2	CACNA1H	16	1251875	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08		1251875	89102878	73	4533											
KIAA0430	9665	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	15716936	15716936	+	Frame_Shift_Del	DEL	A	A	-																															tgctcgaatttgcaatgttgAaagcaagcggggatgctctg																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:15716936delA	ENST00000396368.3	-	11	2521	c.2315delT	c.(2314-2316)ttcfs	p.F772fs	KIAA0430_ENST00000602337.1_Frame_Shift_Del_p.F769fs|KIAA0430_ENST00000540441.2_Intron|KIAA0430_ENST00000344181.3_Frame_Shift_Del_p.F441fs|KIAA0430_ENST00000551742.1_Frame_Shift_Del_p.F772fs|KIAA0430_ENST00000548025.1_Frame_Shift_Del_p.F769fs	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	772					double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TGCAATGTTGAAAGCAAGCGG	0.408																																					p.F772fs		.											.	KIAA0430-90	0			c.2315delT						.						91	88	89					16																	15716936		1865	4105	5970	SO:0001589	frameshift_variant	9665	exon11			.	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.2315delT	16.37:g.15716936delA	ENSP00000379654:p.Phe772fs	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	195	63	NM_014647	0	0	0	0	0	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Frame_Shift_Del	DEL	ENST00000396368.3	37	CCDS10562.2																																																																																			.		0.408	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		-	15716936	A	-	15716936	7	5	49	1	0	1	0	1	0	0	0	0	8198	246	9	0	2981	0	KIAA0430	16	15716936	Frame_Shift_Del	DEL	A	TCGA-B9-4115-01A-01D-1252-08	14465061	15716936	74637817	74	4534											
TMC5	79838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19498328	19498328	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgattatgcttttcatcatgTtctactccaaaaatgtgagt	11	17	6	7	0	3	2	2	2	1	0	4	2	4	2	1	0	2	2	1	0	4	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:19498328T>G	ENST00000396229.2	+	16	3174	c.2425T>G	c.(2425-2427)Ttc>Gtc	p.F809V	TMC5_ENST00000541464.1_Missense_Mutation_p.F757V|TMC5_ENST00000564959.1_Missense_Mutation_p.F492V|TMC5_ENST00000561503.1_Missense_Mutation_p.F450V|TMC5_ENST00000381414.4_Missense_Mutation_p.F809V|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000542583.2_Missense_Mutation_p.F809V|TMC5_ENST00000219821.5_Missense_Mutation_p.F563V	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	809					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTTCATCATGTTCTACTCCAA	0.517																																					p.F809V		.											.	TMC5-91	0			c.T2425G						.						128	104	112					16																	19498328		2197	4300	6497	SO:0001583	missense	79838	exon16			ATCATGTTCTACT	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2425T>G	16.37:g.19498328T>G	ENSP00000379531:p.Phe809Val	Somatic	118	1		WXS	Illumina HiSeq	Phase_I	116	37	NM_001105249	0	0	0	0	0	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	T	17.82	3.484037	0.63962	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.61	5.61	0.85477	.	0.118609	0.64402	D	0.000006	D	0.84275	0.5436	M	0.89414	3.03	0.58432	D	0.999998	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;1.0;0.999	D	0.87427	0.2386	10	0.87932	D	0	-21.956	14.7798	0.69756	0.0:0.0:0.0:1.0	.	757;492;563;563;809;809	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	V	757;809;809;809;563;492	ENSP00000441227:F757V;ENSP00000370822:F809V;ENSP00000379531:F809V;ENSP00000446274:F809V;ENSP00000219821:F563V	ENSP00000219821:F563V	F	+	1	0	TMC5	19405829	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	6.761000	0.74945	2.130000	0.65690	0.533000	0.62120	TTC	.		0.517	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		G	19498328	T	G	19498328	3	3	49	1	0	0	0	0	1	0	0	0	16020	1725	60	5	2793	5	TMC5	16	19498328	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	3781392	19498328	70856425	75	4535											
CCDC102A	92922	hgsc.bcm.edu;broad.mit.edu	37	chr16	57562850	57562850	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgcgcccgcgcctcctcCagctcccgcagccgcagctc	3	4	10	24	6	0	0	0	0	0	0	4	0	3	0	7	0	3	4	7	0	0	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:57562850C>A	ENST00000258214.2	-	2	486	c.240G>T	c.(238-240)ctG>ctT	p.L80L		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	80										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						GCGCCTCCTCCAGCTCCCGCA	0.761																																					p.L80L		.											.	CCDC102A-91	0			c.G240T						.						6	8	8					16																	57562850		1458	3193	4651	SO:0001819	synonymous_variant	92922	exon2			CTCCTCCAGCTCC	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.240G>T	16.37:g.57562850C>A		Somatic	24	1		WXS	Illumina HiSeq	Phase_I	38	13	NM_033212	0	0	0	0	0	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																			.		0.761	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212		A	57562850	C	A	57562850	2	1	49	1	0	0	0	0	0	0	0	1	2742	581	21	4		4	CCDC102A	16	57562850	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	38064522	57562850	32791903	76	4536											
CES8	283848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67038037	67038037	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgtggtgatcccagatgaCcctttggtgctcctgaccca	6	11	12	12	0	0	4	0	3	0	1	2	4	2	4	4	3	1	1	4	3	0	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:67038037C>A	ENST00000326686.5	+	9	990	c.990C>A	c.(988-990)gaC>gaA	p.D330E	CES4A_ENST00000398354.1_Missense_Mutation_p.D330E|CES4A_ENST00000541479.1_Missense_Mutation_p.D353E|CES4A_ENST00000540579.1_Missense_Mutation_p.D232E|CES4A_ENST00000535696.1_Missense_Mutation_p.D236E|CES4A_ENST00000338718.4_Missense_Mutation_p.D353E|CES4A_ENST00000540947.2_Missense_Mutation_p.D330E			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	330						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						TCCCAGATGACCCTTTGGTGC	0.512																																					p.D330E		.											.	CES4A-91	0			c.C990A						.						232	229	230					16																	67038037		2041	4186	6227	SO:0001583	missense	283848	exon9			AGATGACCCTTTG	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"Carboxylesterases"	26741	protein-coding gene	gene with protein product			"carboxylesterase 8 (putative)"	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.990C>A	16.37:g.67038037C>A	ENSP00000314145:p.Asp330Glu	Somatic	284	0		WXS	Illumina HiSeq	Phase_I	399	143	NM_173815	0	0	0	0	0	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	37		.	.	.	.	.	.	.	.	.	.	c	1.498	-0.552834	0.03996	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	4.63	0.0898	0.14460	Carboxylesterase, type B (1);	0.569501	0.15610	N	0.253409	T	0.52773	0.1755	L	0.41415	1.275	0.09310	N	1	B;B;B;B	0.19331	0.023;0.004;0.02;0.035	B;B;B;B	0.28305	0.022;0.004;0.088;0.021	T	0.45977	-0.9224	10	0.49607	T	0.09	.	4.644	0.12563	0.0:0.4819:0.153:0.3651	.	236;353;330;353	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	E	330;353;353;330;330;293;232;236	ENSP00000444052:D330E;ENSP00000443175:D353E;ENSP00000340714:D353E;ENSP00000381397:D330E;ENSP00000314145:D330E;ENSP00000441103:D293E;ENSP00000441907:D232E;ENSP00000441644:D236E	ENSP00000314145:D330E	D	+	3	2	CES4A	65595538	0.000000	0.05858	0.009000	0.14445	0.083000	0.17756	-0.546000	0.06062	-0.221000	0.09973	0.486000	0.48141	GAC	.		0.512	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815		A	67038037	C	A	67038037	3	1	49	1	0	0	0	0	1	0	0	0	3279	506	18	4	1105	4	CES8	16	67038037	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	9475187	67038037	23316716	77	4537											
TNFSF12-TNFSF13	8741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7464141	7464141	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaaccttcctggggtttgtGaaactgtgattgtgttataa	9	15	12	5	0	0	2	0	2	0	0	1	3	1	3	2	3	2	2	2	3	4	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr17:7464141G>A	ENST00000338784.4	+	6	1187	c.744G>A	c.(742-744)gtG>gtA	p.V248V	TNFSF12_ENST00000557233.1_Silent_p.V328V|SENP3-EIF4A1_ENST00000579777.1_RNA|TNFSF12-TNFSF13_ENST00000293826.4_Silent_p.V328V|SENP3_ENST00000429205.2_5'Flank|TNFSF13_ENST00000396542.1_Silent_p.V203V|TNFSF13_ENST00000380535.4_Silent_p.V220V|TNFSF13_ENST00000349228.4_Silent_p.V232V|TNFSF13_ENST00000483039.1_Silent_p.V112V|TNFSF13_ENST00000396545.4_Intron|SENP3_ENST00000321337.7_5'Flank	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	248					gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				TGGGGTTTGTGAAACTGTGAT	0.473											OREG0024138	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V328V		.											.	TNFSF12-TNFSF13-44	0			c.G984A						.						108	102	104					17																	7464141		2203	4300	6503	SO:0001819	synonymous_variant	407977	exon11			GTTTGTGAAACTG	AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.744G>A	17.37:g.7464141G>A		Somatic	244	1	641	WXS	Illumina HiSeq	Phase_I	503	135	NM_172089	0	0	552	731	179	A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Silent	SNP	ENST00000338784.4	37	CCDS11111.1																																																																																			.		0.473	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226948.2	NM_003808		A	7464141	G	A	7464141	2	1	49	1	0	0	0	0	0	0	0	1	16336	1277	45	2		2	TNFSF12-TNFSF13	17	7464141	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08		7464141	73731069	78	4538											
CNTNAP1	8506	hgsc.bcm.edu;broad.mit.edu	37	chr17	40843435	40843435	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggactgctgacctttgtggaCcatctgcctgtcactcaggt	6	12	11	12	0	3	1	2	1	1	0	3	3	3	3	3	3	2	1	3	3	0	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr17:40843435C>A	ENST00000264638.4	+	15	2467	c.2250C>A	c.(2248-2250)gaC>gaA	p.D750E	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	750	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		CCTTTGTGGACCATCTGCCTG	0.582																																					p.D750E		.											.	CNTNAP1-525	0			c.C2250A						.						99	82	87					17																	40843435		2203	4300	6503	SO:0001583	missense	8506	exon15			TGTGGACCATCTG	U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"neurexin 4"	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.2250C>A	17.37:g.40843435C>A	ENSP00000264638:p.Asp750Glu	Somatic	125	1		WXS	Illumina HiSeq	Phase_I	326	19	NM_003632	0	0	0	0	0		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.710971	0.30322	.	.	ENSG00000108797	ENST00000264638	T	0.08984	3.03	5.31	1.06	0.20224	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.000000	0.85682	D	0.000000	T	0.04092	0.0114	N	0.20357	0.565	0.42527	D	0.993023	B	0.19935	0.04	B	0.21546	0.035	T	0.41070	-0.9529	10	0.05959	T	0.93	.	7.4711	0.27349	0.0:0.6791:0.1198:0.2011	.	750	P78357	CNTP1_HUMAN	E	750	ENSP00000264638:D750E	ENSP00000264638:D750E	D	+	3	2	CNTNAP1	38096961	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.314000	0.33597	0.095000	0.17434	0.561000	0.74099	GAC	.		0.582	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632		A	40843435	C	A	40843435	3	1	49	1	0	0	0	0	1	0	0	0	3652	506	18	4	2308	4	CNTNAP1	17	40843435	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	33379294	40843435	40351775	79	4539											
MYST2	11143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	47869250	47869250	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggatctatggtattacagagGaatgcaggcagtagttcaga	13	10	13	5	0	2	2	1	0	1	2	2	4	2	4	0	4	2	5	0	4	5	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr17:47869250G>T	ENST00000259021.4	+	2	298	c.18G>T	c.(16-18)agG>agT	p.R6S	KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000454930.2_Missense_Mutation_p.R6S|FAM117A_ENST00000514018.1_5'Flank|KAT7_ENST00000424009.2_Missense_Mutation_p.R6S|KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000510819.1_Missense_Mutation_p.R6S|KAT7_ENST00000509773.1_Missense_Mutation_p.R6S	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	6					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TATTACAGAGGAATGCAGGCA	0.423																																					p.R6S		.											.	.	0			c.G18T						.						148	136	140					17																	47869250		2203	4300	6503	SO:0001583	missense	11143	exon2			ACAGAGGAATGCA	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.18G>T	17.37:g.47869250G>T	ENSP00000259021:p.Arg6Ser	Somatic	322	0		WXS	Illumina HiSeq	Phase_I	434	102	NM_001199158	0	0	0	0	0	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848691	0.51164	.	.	ENSG00000136504	ENST00000259021;ENST00000454930;ENST00000509773;ENST00000510819;ENST00000424009	.	.	.	5.6	2.52	0.30459	.	0.093201	0.64402	D	0.000001	T	0.63189	0.2490	L	0.48642	1.525	0.80722	D	1	D;D;D;B;P	0.54601	0.967;0.967;0.967;0.421;0.557	P;P;P;B;B	0.60789	0.879;0.879;0.879;0.058;0.124	T	0.62144	-0.6916	9	0.87932	D	0	-16.1716	9.2677	0.37652	0.3015:0.0:0.6985:0.0	.	6;6;6;6;6	B4DFE0;B4DFB4;E7ER15;O95251;G5E9K7	.;.;.;KAT7_HUMAN;.	S	6	.	ENSP00000259021:R6S	R	+	3	2	KAT7	45224249	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	1.877000	0.39598	0.295000	0.22570	-0.137000	0.14449	AGG	.		0.423	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		T	47869250	G	T	47869250	3	4	49	1	0	0	0	0	1	0	0	0	10128	1165	41	4	24	4	MYST2	17	47869250	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	7025815	47869250	33325960	80	4540											
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288976	74288976	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctgatctgcaccaggttggGccaaaccagactgatccatt	10	9	10	12	0	1	3	0	2	1	1	2	3	2	3	4	2	2	3	4	2	1	2	rs75054966		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr17:74288976G>A	ENST00000262765.5	-	4	1513	c.1334C>T	c.(1333-1335)gCc>gTc	p.A445V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	445	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						accaggttgggccaaaccaga	0.572																																					p.A445V		.											.	QRICH2-94	0			c.C1334T						.						95	94	94					17																	74288976		2203	4300	6503	SO:0001583	missense	84074	exon4			GGTTGGGCCAAAC	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1334C>T	17.37:g.74288976G>A	ENSP00000262765:p.Ala445Val	Somatic	17	1		WXS	Illumina HiSeq	Phase_I	22	4	NM_032134	0	0	0	0	0	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689770	0.29962	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08370	3.1	5.51	-11.0	0.00169	.	.	.	.	.	T	0.01695	0.0054	N	0.01505	-0.83	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.40079	-0.9582	9	0.18710	T	0.47	-3.6749	1.0591	0.01596	0.2559:0.2896:0.2648:0.1898	.	445;445	B5MD94;Q9H0J4	.;QRIC2_HUMAN	V	445	ENSP00000262765:A445V	ENSP00000262765:A445V	A	-	2	0	QRICH2	71800571	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.871000	0.01640	-1.417000	0.02017	-0.423000	0.05987	GCC	A|1.000;|0.000		0.572	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74288976	G	A	74288976	3	1	49	1	0	0	0	0	1	0	0	0	12912	1203	42	2	3721	2	QRICH2	17	74288976	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	26419726	74288976	6906234	81	4541											
CEP192	55125	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	13049324	13049324	+	Frame_Shift_Del	DEL	T	T	-																															agaaaacacagcagctattgTttatgttgaaaatggagaga																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr18:13049324delT	ENST00000325971.8	+	14	2339	c.746delT	c.(745-747)gttfs	p.V249fs	CEP192_ENST00000430049.2_Frame_Shift_Del_p.V370fs|CEP192_ENST00000506447.1_Frame_Shift_Del_p.V845fs			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	249					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GCAGCTATTGTTTATGTTGAA	0.383																																					p.V845fs		.											.	CEP192-27	0			c.2534delT						.						100	95	97					18																	13049324		2203	4300	6503	SO:0001589	frameshift_variant	55125	exon16			.	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.746delT	18.37:g.13049324delT	ENSP00000317156:p.Val249fs	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	61	19	NM_032142	0	0	0	0	0	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Frame_Shift_Del	DEL	ENST00000325971.8	37																																																																																				.		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		-	13049324	T	-	13049324	7	5	49	1	0	1	0	1	0	0	0	0	3257	1725	60	0	2592	0	CEP192	18	13049324	Frame_Shift_Del	DEL	T	TCGA-B9-4115-01A-01D-1252-08		13049324	65027924	82	4542											
COX7A1	1346	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	36642400	36642402	+	In_Frame_Del	DEL	TGT	TGT	-																															cattgtcactcggtacaggaTgttgtcaacgatgccgccct																								rs375983153		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:36642400_36642402delTGT	ENST00000292907.3	-	3	610_612	c.149_151delACA	c.(148-153)aacatc>atc	p.N50del	COX7A1_ENST00000437291.2_5'UTR	NM_001864.2	NP_001855.1	P24310	CX7A1_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)	50					generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)	integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)|large_intestine(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGGTACAGGATGTTGTCAACGAT	0.626																																					p.50_51del		.											.	COX7A1-226	0			c.149_151del						.																																			SO:0001651	inframe_deletion	1346	exon3			.	BC002757	CCDS12490.1	19q13.1	2011-07-04			ENSG00000161281	ENSG00000161281	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2287	protein-coding gene	gene with protein product		123995		COX7A		1327965, 2550906	Standard	NM_001864		Approved	COX7AH	uc002odm.1	P24310	OTTHUMG00000048144	ENST00000292907.3:c.149_151delACA	19.37:g.36642403_36642405delTGT	ENSP00000292907:p.Asn50del	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	242	64	NM_001864	0	0	0	0	0		In_Frame_Del	DEL	ENST00000292907.3	37	CCDS12490.1																																																																																			.		0.626	COX7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109545.2	NM_001864		-	36642402	TGT	-	36642400	7	5	49	1	0	1	0	1	0	0	0	0	3785	1464	51	0	96	0	COX7A1	19	36642400	In_Frame_Del	DEL	TGT	TCGA-B9-4115-01A-01D-1252-08		36642400	22486583	83	4543											
ITPKC	80271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41223385	41223385	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaagcaaaagacggagccAgacaggtccagcctccggac	13	2	11	15	2	0	2	0	0	0	2	2	4	2	4	5	3	3	1	5	3	3	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:41223385A>T	ENST00000263370.2	+	1	378	c.345A>T	c.(343-345)ccA>ccT	p.P115P	ADCK4_ENST00000324464.3_5'Flank|ADCK4_ENST00000450541.1_5'Flank|ADCK4_ENST00000243583.6_5'Flank	NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	115					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			AGACGGAGCCAGACAGGTCCA	0.597																																					p.P115P		.											.	ITPKC-115	0			c.A345T						.						51	58	56					19																	41223385		2202	4300	6502	SO:0001819	synonymous_variant	80271	exon1			GGAGCCAGACAGG	Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	"inositol 1,4,5-trisphosphate 3-kinase C"			11085927	Standard	NM_025194		Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.345A>T	19.37:g.41223385A>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	201	65	NM_025194	0	0	4	7	3	Q9UE25|Q9Y475	Silent	SNP	ENST00000263370.2	37	CCDS12563.1																																																																																			.		0.597	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194		T	41223385	A	T	41223385	2	4	49	1	0	0	0	0	0	0	0	1	7940	175	7	5		5	ITPKC	19	41223385	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	4580985	41223385	17905598	84	4544											
ERF	2077	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	42752789	42752790	+	In_Frame_Ins	INS	-	-	AAA																															cccacccccttcgaggcgacINSagtcttcactccagcgccgc																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:42752789_42752790insAAA	ENST00000222329.4	-	4	1631_1632	c.1474_1475insTTT	c.(1474-1476)tgt>tTTTgt	p.491_492insF	ERF_ENST00000595941.1_5'Flank|ERF_ENST00000440177.2_In_Frame_Ins_p.416_417insF|AC006486.9_ENST00000594664.1_Intron	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	491					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				TTCGAGGCGACAGTCTTCACTC	0.698																																					p.C492delinsFC		.											.	ERF-658	0			c.1475_1476insTTT						.																																			SO:0001652	inframe_insertion	2077	exon4			.	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.1474_1475insTTT	19.37:g.42752789_42752790insAAA	ENSP00000222329:p.Asp491_Cys492insPhe	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	249	60	NM_006494	0	0	0	0	0	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	In_Frame_Ins	INS	ENST00000222329.4	37	CCDS12600.1																																																																																			.		0.698	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		AAA	42752790	-	AAA	42752789	7	5	49	1	0	1	1	0	0	0	0	0	5234	478	17	0	175	0	ERF	19	42752789	In_Frame_Ins	INS	-	TCGA-B9-4115-01A-01D-1252-08	1529404	42752789	16376194	85	4545											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945880	48945880	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacagctgctgcagcgcTgaggccgccccaccgcccgc	6	5	12	18	4	0	1	0	1	0	0	0	1	0	1	5	1	5	5	5	1	1	1	rs62130268	byFrequency	TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:48945880T>C	ENST00000263269.3	+	13	2785	c.2697T>C	c.(2695-2697)gcT>gcC	p.A899A		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	899					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTGCAGCGCTGAGGCCGCCC	0.781													c|||	3742	0.747204	0.6188	0.8545	5008	,	,		4716	0.6548		0.8887	False		,,,				2504	0.7945				p.A899A		.											.	GRIN2D-156	0			c.T2697C						.			1689,437		638,413,12	1	1	1		2697	-3.3	1	19	dbSNP_129	1	3712,202		1757,198,2	no	coding-synonymous	GRIN2D	NM_000836.2		2395,611,14	CC,CT,TT		5.161,20.555,10.5795		899/1337	48945880	5401,639	1063	1957	3020	SO:0001819	synonymous_variant	2906	exon13			CAGCGCTGAGGCC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2697T>C	19.37:g.48945880T>C		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_000836	0	0	0	0	0		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			T|0.245;C|0.755		0.781	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			C	48945880	T	C	48945880	2	2	49	1	0	0	0	0	0	0	0	1	6803	1567	55	3		3	GRIN2D	19	48945880	Silent	SNP	T	TCGA-B9-4115-01A-01D-1252-08	6193091	48945880	10183103	86	4546											
NTN5	126147	broad.mit.edu	37	chr19	49167945	49167945	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggcaccgctcacaaacAcccccactccggccgcccga	8	3	9	21	5	1	0	1	0	0	0	2	1	2	0	6	3	1	2	6	3	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:49167945A>C	ENST00000270235.4	-	3	806	c.711T>G	c.(709-711)ggT>ggG	p.G237G	SEC1P_ENST00000430145.2_RNA	NM_145807.1	NP_665806.1	Q8WTR8	NET5_HUMAN	netrin 5	237	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	10						GCTCACAAACACCCCCACTCC	0.652																																					p.G237G													.	NTN5-136	0			c.T711G						.						18	19	19					19																	49167945		2199	4296	6495	SO:0001819	synonymous_variant	126147	exon3			ACAAACACCCCCA		CCDS33068.1	19q13.33	2013-03-01			ENSG00000142233	ENSG00000142233		"Netrins"	25208	protein-coding gene	gene with protein product	"Netrin-5"					12477932	Standard	NM_145807		Approved		uc002pkb.3	Q8WTR8		ENST00000270235.4:c.711T>G	19.37:g.49167945A>C		Somatic	21	2		WXS	Illumina HiSeq	Phase_I	42	9	NM_145807	0	0	1	1	0	Q8N4X9|Q8WU63	Silent	SNP	ENST00000270235.4	37	CCDS33068.1																																																																																			.		0.652	NTN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466176.1	NM_145807		C	49167945	A	C	49167945	2	2	49	1	0	0	0	0	0	0	0	1	10729	146	6	5		5	NTN5	19	49167945	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	222065	49167945	9961038	87	4547											
ALDH16A1	126133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49971767	49971767	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccctggcctacggcaacActgtggtcatggtgcccagt	6	8	12	15	2	1	0	1	0	0	0	1	0	1	0	4	4	3	1	4	4	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:49971767A>T	ENST00000293350.4	+	15	2231	c.2068A>T	c.(2068-2070)Act>Tct	p.T690S	ALDH16A1_ENST00000540132.1_Missense_Mutation_p.T527S|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.T639S|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.T525S	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	690						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CTACGGCAACACTGTGGTCAT	0.687																																					p.T690S		.											.	ALDH16A1-91	0			c.A2068T						.						123	129	127					19																	49971767		2203	4300	6503	SO:0001583	missense	126133	exon15			GGCAACACTGTGG	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"Aldehyde dehydrogenases"	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.2068A>T	19.37:g.49971767A>T	ENSP00000293350:p.Thr690Ser	Somatic	345	0		WXS	Illumina HiSeq	Phase_I	542	197	NM_153329	0	0	17	26	9	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	A	3.550	-0.091783	0.07053	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	4.37	-5.8	0.02347	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.561034	0.18181	N	0.149153	T	0.53899	0.1825	N	0.20845	0.615	0.09310	N	1	B;B;B	0.13145	0.003;0.007;0.004	B;B;B	0.17098	0.007;0.012;0.017	T	0.46748	-0.9169	10	0.13108	T	0.6	-7.5334	9.9685	0.41738	0.1664:0.0:0.7061:0.1275	.	527;639;690	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	S	690;639;527;525	ENSP00000293350:T690S;ENSP00000410142:T639S;ENSP00000445088:T527S;ENSP00000398675:T525S	ENSP00000293350:T690S	T	+	1	0	ALDH16A1	54663579	0.000000	0.05858	0.003000	0.11579	0.071000	0.16799	-0.795000	0.04580	-0.972000	0.03559	0.397000	0.26171	ACT	.		0.687	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		T	49971767	A	T	49971767	3	4	49	1	0	0	0	0	1	0	0	0	488	159	6	5	2126	5	ALDH16A1	19	49971767	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	803822	49971767	9157216	88	4548											
ZNF134	7693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58131703	58131703	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatgaacaccagggtacacaCcatggactgaaacttcacac	15	6	8	12	0	1	2	1	2	0	0	1	4	1	3	2	2	3	1	2	2	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:58131703C>A	ENST00000396161.5	+	3	526	c.216C>A	c.(214-216)caC>caA	p.H72Q	ZNF134_ENST00000597975.1_3'UTR	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	72					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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		AGGGTACACACCATGGACTGA	0.493																																					p.H72Q		.											.	ZNF134-226	0			c.C216A						.						108	104	105					19																	58131703		2041	4225	6266	SO:0001583	missense	7693	exon3			TACACACCATGGA	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"Zinc fingers, C2H2-type"	12918	protein-coding gene	gene with protein product		604076	"zinc finger protein 134 (clone pHZ-15)"			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.216C>A	19.37:g.58131703C>A	ENSP00000379464:p.His72Gln	Somatic	293	1		WXS	Illumina HiSeq	Phase_I	82	29	NM_003435	0	0	2	5	3	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	37	CCDS42638.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.322492	0.41096	.	.	ENSG00000213762	ENST00000418193;ENST00000396161	T	0.66995	-0.24	4.05	0.456	0.16655	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63153	0.2487	M	0.81682	2.555	0.09310	N	1	B	0.30211	0.273	B	0.28638	0.092	T	0.58719	-0.7587	9	0.87932	D	0	.	5.1641	0.15077	0.163:0.6473:0.0:0.1897	.	72	P52741	ZN134_HUMAN	Q	139;72	ENSP00000379464:H72Q	ENSP00000379464:H72Q	H	+	3	2	ZNF134	62823515	0.000000	0.05858	0.000000	0.03702	0.967000	0.64934	0.316000	0.19469	0.092000	0.17331	0.655000	0.94253	CAC	.		0.493	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		A	58131703	C	A	58131703	3	1	49	1	0	0	0	0	1	0	0	0	17756	506	18	4	222	4	ZNF134	19	58131703	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	8159936	58131703	997280	89	4549											
RIN2	54453	broad.mit.edu	37	chr20	19956190	19956190	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcggggtgttcagctccttCatgaccccggagaagcggat	8	8	14	11	3	2	2	2	1	0	1	3	4	3	3	3	4	3	2	3	4	1	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr20:19956190C>T	ENST00000255006.6	+	8	1817	c.1668C>T	c.(1666-1668)ttC>ttT	p.F556F	RIN2_ENST00000440354.2_Intron|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	507					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						TCAGCTCCTTCATGACCCCGG	0.592																																					p.F556F													.	RIN2-660	0			c.C1668T						.						93	102	99					20																	19956190		2025	4181	6206	SO:0001819	synonymous_variant	54453	exon8			CTCCTTCATGACC	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.1668C>T	20.37:g.19956190C>T		Somatic	249	0		WXS	Illumina HiSeq	Phase_I	343	10	NM_001242581	0	0	9	9	0	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			.		0.592	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19956190	C	T	19956190	2	4	49	1	0	0	0	0	0	0	0	1	13404	825	29	2		2	RIN2	20	19956190	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08		19956190	43069330	90	4550											
CBFA2T2	9139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	32199022	32199022	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatcagcaattgccagccActtgtggtgctcgacaactc	11	9	8	13	1	1	0	1	0	0	0	3	1	1	0	2	1	5	2	2	1	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr20:32199022A>G	ENST00000346541.3	+	4	865	c.328A>G	c.(328-330)Act>Gct	p.T110A	CBFA2T2_ENST00000344201.3_Missense_Mutation_p.T81A|CBFA2T2_ENST00000397798.2_Missense_Mutation_p.T81A|CBFA2T2_ENST00000397800.1_Missense_Mutation_p.T81A|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.T81A|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.T110A|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.T120A|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.T101A	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	110					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						ATTGCCAGCCACTTGTGGTGC	0.527																																					p.T110A	Esophageal Squamous(174;142 1955 14837 21276 28041)	.											.	CBFA2T2-92	0			c.A328G						.						186	158	168					20																	32199022		2203	4300	6503	SO:0001583	missense	9139	exon4			CCAGCCACTTGTG	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"Zinc fingers, MYND-type"	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.328A>G	20.37:g.32199022A>G	ENSP00000262653:p.Thr110Ala	Somatic	240	1		WXS	Illumina HiSeq	Phase_I	97	29	NM_005093	0	0	2	4	2	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	37	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	A	5.376	0.254600	0.10185	.	.	ENSG00000078699	ENST00000375279;ENST00000342704;ENST00000417366;ENST00000344201;ENST00000346541;ENST00000397800;ENST00000397798;ENST00000359606	T;T;T;T;T	0.39229	1.1;1.1;1.1;1.09;1.69	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	N	0.11201	0.11	0.80722	D	1	D;D	0.67145	0.994;0.996	D;D	0.76071	0.97;0.987	T	0.24657	-1.0154	10	0.02654	T	1	-18.4621	15.6678	0.77247	1.0:0.0:0.0:0.0	.	110;101	O43439;F8W6D7	MTG8R_HUMAN;.	A	110;101;101;81;110;81;81;120	ENSP00000364428:T110A;ENSP00000345810:T101A;ENSP00000262653:T110A;ENSP00000380902:T81A;ENSP00000352622:T120A	ENSP00000345810:T101A	T	+	1	0	CBFA2T2	31662683	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.571000	0.60879	2.103000	0.63969	0.533000	0.62120	ACT	.		0.527	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		G	32199022	A	G	32199022	3	3	49	1	0	0	0	0	1	0	0	0	2703	159	6	3	376	3	CBFA2T2	20	32199022	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	12242832	32199022	30826498	91	4551											
SLC32A1	140679	broad.mit.edu	37	chr20	37356313	37356313	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcttcccaacgctgggcggCcgagtggtgaacgtagcgca	7	6	15	13	6	0	1	0	1	0	0	1	2	1	1	2	3	3	4	2	3	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr20:37356313C>T	ENST00000217420.1	+	2	872	c.609C>T	c.(607-609)ggC>ggT	p.G203G		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	203					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CGCTGGGCGGCCGAGTGGTGA	0.632																																					p.G203G													.	SLC32A1-90	0			c.C609T						.						80	66	71					20																	37356313		2203	4300	6503	SO:0001819	synonymous_variant	140679	exon2			GGGCGGCCGAGTG	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"Solute carriers"	11018	protein-coding gene	gene with protein product			"vesicular inhibitory amino acid transporter"	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.609C>T	20.37:g.37356313C>T		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	125	4	NM_080552	0	0	0	0	0	Q8N489	Silent	SNP	ENST00000217420.1	37	CCDS13307.1																																																																																			.		0.632	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		T	37356313	C	T	37356313	2	4	49	1	0	0	0	0	0	0	0	1	14597	726	26	2		2	SLC32A1	20	37356313	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	5157291	37356313	25669207	92	4552											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62191642	62191642	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acggcgatgtcctggggctcTacggtcctccccagggtcag	5	8	14	14	3	2	0	1	0	1	0	5	1	5	0	4	5	1	1	4	5	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr20:62191642T>C	ENST00000467148.1	-	17	7608	c.7539A>G	c.(7537-7539)gtA>gtG	p.V2513V	HELZ2_ENST00000427522.2_Silent_p.V1944V	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2513	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CCTGGGGCTCTACGGTCCTCC	0.677																																					p.V2513V		.											.	.	0			c.A7539G						.						45	33	37					20																	62191642		2191	4295	6486	SO:0001819	synonymous_variant	85441	exon18			GGGCTCTACGGTC	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.7539A>G	20.37:g.62191642T>C		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001037335	0	0	9	9	0	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			.		0.677	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		C	62191642	T	C	62191642	2	2	49	1	0	0	0	0	0	0	0	1	12514	1509	53	3		3	PRIC285	20	62191642	Silent	SNP	T	TCGA-B9-4115-01A-01D-1252-08	24835329	62191642	833878	93	4553											
RFPL3	10738	broad.mit.edu	37	chr22	32756482	32756482	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atctgttcactgcaaagggaAgatccagctgaccacagagc	13	7	10	11	0	2	3	1	1	1	2	3	4	3	4	2	1	3	3	2	1	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr22:32756482A>G	ENST00000249007.4	+	2	822	c.617A>G	c.(616-618)aAg>aGg	p.K206R	RFPL3_ENST00000382088.3_Missense_Mutation_p.K177R|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000397468.1_Missense_Mutation_p.K177R|RFPL3S_ENST00000382084.4_3'UTR|RFPL3S_ENST00000400234.1_3'UTR	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	206	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TGCAAAGGGAAGATCCAGCTG	0.562																																					p.K206R													.	RFPL3-91	0			c.A617G						.						120	116	117					22																	32756482		2203	4300	6503	SO:0001583	missense	10738	exon2			AAGGGAAGATCCA	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.617A>G	22.37:g.32756482A>G	ENSP00000249007:p.Lys206Arg	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	253	9	NM_001098535	0	0	1	1	0	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	.	.	.	.	.	.	.	.	.	.	a	0.121	-1.125578	0.01770	.	.	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.69306	-0.39;-0.39;-0.39	1.36	-2.73	0.05950	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.46560	0.1399	L	0.33137	0.985	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10222	-1.0639	9	0.18276	T	0.48	.	4.5817	0.12262	0.3421:0.1932:0.4647:0.0	.	206	O75679	RFPL3_HUMAN	R	177;206;177	ENSP00000380609:K177R;ENSP00000249007:K206R;ENSP00000371520:K177R	ENSP00000249007:K206R	K	+	2	0	RFPL3	31086482	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.869000	0.04232	-3.519000	0.00148	-3.015000	0.00074	AAG	.		0.562	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		G	32756482	A	G	32756482	3	3	49	1	0	0	0	0	1	0	0	0	13287	72	3	3	623	3	RFPL3	22	32756482	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08		32756482	18548084	94	4554											
CACNA1I	8911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40061912	40061912	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggcaagttctaccactgTctgggcgtggacacccgcaa	10	7	12	12	2	2	0	0	0	2	0	2	1	2	1	2	3	1	3	2	3	4	2	rs370356955		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr22:40061912T>G	ENST00000402142.3	+	23	4005	c.4005T>G	c.(4003-4005)tgT>tgG	p.C1335W	CACNA1I_ENST00000400164.3_Missense_Mutation_p.C1300W|CACNA1I_ENST00000404898.1_Missense_Mutation_p.C1300W|CACNA1I_ENST00000336649.4_Missense_Mutation_p.C1341W|CACNA1I_ENST00000407673.1_Missense_Mutation_p.C1300W|CACNA1I_ENST00000401624.1_Missense_Mutation_p.C1335W	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1335					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TCTACCACTGTCTGGGCGTGG	0.587																																					p.C1335W		.											.	CACNA1I-135	0			c.T4005G						.						124	132	129					22																	40061912		2111	4223	6334	SO:0001583	missense	8911	exon23			CCACTGTCTGGGC	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.4005T>G	22.37:g.40061912T>G	ENSP00000385019:p.Cys1335Trp	Somatic	171	2		WXS	Illumina HiSeq	Phase_I	231	79	NM_021096	0	0	0	0	0	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630186	0.67015	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01;-5.01;-5.01	4.3	-3.89	0.04193	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99199	0.9722	H	0.98333	4.205	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.998;0.998	D	0.98871	1.0766	10	0.87932	D	0	.	13.8835	0.63696	0.0:0.6656:0.0:0.3344	.	1300;1335;1300;1335	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	W	1335;1300;1335;1300;1341;1300	ENSP00000385019:C1335W;ENSP00000384093:C1300W;ENSP00000383887:C1335W;ENSP00000385680:C1300W;ENSP00000337829:C1341W;ENSP00000383028:C1300W	ENSP00000337829:C1341W	C	+	3	2	CACNA1I	38391858	0.613000	0.27009	0.940000	0.37924	0.966000	0.64601	-0.015000	0.12634	-0.931000	0.03746	-0.609000	0.04063	TGT	.		0.587	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		G	40061912	T	G	40061912	3	3	49	1	0	0	0	0	1	0	0	0	2552	1673	58	5	4095	5	CACNA1I	22	40061912	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	7305430	40061912	11242654	95	4555											
GPR112	139378	hgsc.bcm.edu	37	chrX	135431434	135431434	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagacctctcctcctcccAcatcccaaatggttgaattt	11	11	4	15	0	1	2	0	1	1	1	5	2	4	2	5	1	0	1	5	1	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chrX:135431434A>C	ENST00000394143.1	+	6	5860	c.5569A>C	c.(5569-5571)Aca>Cca	p.T1857P	GPR112_ENST00000370652.1_Missense_Mutation_p.T1857P|GPR112_ENST00000412101.1_Missense_Mutation_p.T1652P|GPR112_ENST00000394141.1_Missense_Mutation_p.T1652P|GPR112_ENST00000287534.4_Missense_Mutation_p.T1794P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1857					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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TCCTCCTCCCACATCCCAAAT	0.453																																					p.T1857P		.											.	GPR112-183	0			c.A5569C						.						113	103	106					X																	135431434		2203	4300	6503	SO:0001583	missense	139378	exon6			CCTCCCACATCCC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5569A>C	X.37:g.135431434A>C	ENSP00000377699:p.Thr1857Pro	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_153834	0	0	0	0	0	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	a	11.27	1.589464	0.28357	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.34072	1.41;1.41;1.38;1.51;1.38	3.84	1.39	0.22231	.	.	.	.	.	T	0.33644	0.0870	N	0.24115	0.695	0.09310	N	1	D;D;D	0.64830	0.994;0.982;0.983	P;P;P	0.56960	0.81;0.682;0.637	T	0.12578	-1.0542	9	0.46703	T	0.11	.	5.0436	0.14471	0.7128:0.0:0.2872:0.0	.	1794;1652;1857	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	P	1857;1857;1652;1794;1652	ENSP00000377699:T1857P;ENSP00000359686:T1857P;ENSP00000416526:T1652P;ENSP00000287534:T1794P;ENSP00000377697:T1652P	ENSP00000287534:T1794P	T	+	1	0	GPR112	135259100	0.001000	0.12720	0.000000	0.03702	0.241000	0.25554	1.371000	0.34250	0.002000	0.14630	0.430000	0.28490	ACA	.		0.453	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			C	135431434	A	C	135431434	3	2	49	1	0	0	0	0	1	0	0	0	6649	159	6	5	5579	5	GPR112	23	135431434	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08		135431434	19839126	96	4556											
HTATSF1	27336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	135594033	135594033	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagaagttgtttgatgaggAggaagattccagtgagaagt	13	11	15	2	0	0	5	0	4	0	3	1	9	1	7	1	2	0	2	1	2	3	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chrX:135594033A>T	ENST00000218364.4	+	9	2303	c.2129A>T	c.(2128-2130)gAg>gTg	p.E710V	HTATSF1_ENST00000535601.1_Missense_Mutation_p.E710V	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	710	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					TTTGATGAGGAGGAAGATTCC	0.458																																					p.E710V		.											.	HTATSF1-132	0			c.A2129T						.						221	193	203					X																	135594033		2203	4300	6503	SO:0001583	missense	27336	exon10			ATGAGGAGGAAGA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"RNA binding motif (RRM) containing"	5276	protein-coding gene	gene with protein product		300346	"HIV TAT specific factor 1"			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.2129A>T	X.37:g.135594033A>T	ENSP00000218364:p.Glu710Val	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	17	14	NM_001163280	0	1	3	85	81	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	37	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	A	9.409	1.080079	0.20309	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.34667	1.35;1.35	2.64	2.64	0.31445	.	.	.	.	.	T	0.21227	0.0511	N	0.14661	0.345	0.09310	N	1	P	0.42757	0.789	B	0.38655	0.278	T	0.08006	-1.0743	9	0.87932	D	0	-2.0207	8.2917	0.31960	1.0:0.0:0.0:0.0	.	710	O43719	HTSF1_HUMAN	V	710;710;676	ENSP00000442699:E710V;ENSP00000218364:E710V	ENSP00000218364:E710V	E	+	2	0	HTATSF1	135421699	0.836000	0.29430	0.004000	0.12327	0.938000	0.57974	2.165000	0.42396	1.296000	0.44742	0.235000	0.17854	GAG	.		0.458	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		T	135594033	A	T	135594033	3	4	49	1	0	0	0	0	1	0	0	0	7454	304	11	5	2163	5	HTATSF1	23	135594033	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	162599	135594033	19676527	97	4557											
CA6	765	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	9009376	9009376	+	Frame_Shift_Del	DEL	A	A	-																															ctaccccgcctgtgggggccAgagacagtcgcctatcaacc																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:9009376delA	ENST00000377443.2	+	2	138	c.134delA	c.(133-135)cagfs	p.Q45fs	CA6_ENST00000480186.3_Frame_Shift_Del_p.Q45fs|CA6_ENST00000377436.3_Frame_Shift_Del_p.Q45fs|CA6_ENST00000377442.2_Intron|CA6_ENST00000476083.1_Intron	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	45					bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	TGTGGGGGCCAGAGACAGTCG	0.602																																					p.Q45fs		.											.	CA6-516	0			c.134delA						.						44	42	43					1																	9009376		2203	4300	6503	SO:0001589	frameshift_variant	765	exon2			.	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"Carbonic anhydrases"	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.134delA	1.37:g.9009376delA	ENSP00000366662:p.Gln45fs	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	153	59	NM_001270500	0	0	0	0	0	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Frame_Shift_Del	DEL	ENST00000377443.2	37	CCDS30578.1																																																																																			.		0.602	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1			-	9009376	A	-	9009376	7	5	50	1	0	1	0	1	0	0	0	0	2527	188	7	0	140	0	CA6	1	9009376	Frame_Shift_Del	DEL	A	TCGA-B9-4116-01A-01D-1252-08		9009376	240241245	1	4558											
CLCN6	1185	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	11888206	11888206	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcaccctcaacttcttccGttctgggattcagtttggaa	7	15	7	12	1	5	0	3	0	2	0	6	2	6	2	2	2	1	2	2	2	2	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:11888206G>A	ENST00000346436.6	+	11	936	c.884G>A	c.(883-885)cGt>cAt	p.R295H	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Missense_Mutation_p.R295H|CLCN6_ENST00000312413.6_Missense_Mutation_p.R295H|CLCN6_ENST00000376487.3_Missense_Mutation_p.R273H	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	295					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		AACTTCTTCCGTTCTGGGATT	0.483																																					p.R295H		.											.	CLCN6-90	0			c.G884A						.						224	231	229					1																	11888206		2203	4300	6503	SO:0001583	missense	1185	exon11			TCTTCCGTTCTGG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"Ion channels / Chloride channels : Voltage-sensitive"	2024	protein-coding gene	gene with protein product		602726	"chloride channel 6"			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.884G>A	1.37:g.11888206G>A	ENSP00000234488:p.Arg295His	Somatic	636	0		WXS	Illumina HiSeq	Phase_I	990	54	NM_001286	0	0	3	3	0	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415466	0.96092	.	.	ENSG00000011021	ENST00000312413;ENST00000346436;ENST00000376487;ENST00000376496;ENST00000376492	D;D;D;D	0.94232	-3.36;-3.38;-3.38;-3.38	5.06	5.06	0.68205	Chloride channel, core (2);	0.048615	0.85682	D	0.000000	D	0.96046	0.8712	.	.	.	0.80722	D	1	D;D;D	0.76494	0.989;0.999;0.992	P;P;P	0.60117	0.459;0.869;0.594	D	0.96294	0.9216	9	0.66056	D	0.02	-10.0688	17.6173	0.88071	0.0:0.0:1.0:0.0	.	273;295;295	F8W9R3;P51797-3;P51797	.;.;CLCN6_HUMAN	H	295;295;273;295;295	ENSP00000308367:R295H;ENSP00000234488:R295H;ENSP00000365670:R273H;ENSP00000365679:R295H	ENSP00000308367:R295H	R	+	2	0	CLCN6	11810793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.263000	0.95617	2.625000	0.88918	0.655000	0.94253	CGT	.		0.483	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11888206	G	A	11888206	3	1	50	1	0	0	0	0	1	0	0	0	3473	1145	40	1	936	1	CLCN6	1	11888206	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	2878830	11888206	237362415	2	4559											
PRAMEF18	391003	hgsc.bcm.edu	37	chr1	13474718	13474718	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttccccgcaagcaaaaatTgaactccagttgctcagtgg	11	9	8	13	1	1	1	1	1	0	0	3	1	3	1	4	1	3	4	4	1	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:13474718T>G	ENST00000376126.2	-	3	1410	c.1411A>C	c.(1411-1413)Aat>Cat	p.N471H		NM_001099850.1	NP_001093320.1	Q5VWM3	PRA18_HUMAN	PRAME family member 18	471					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					lung(2)|ovary(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AAGCAAAAATTGAACTCCAGT	0.483																																					p.N471H		.											.	.	0			c.A1411C						.						1	1	1					1																	13474718		362	930	1292	SO:0001583	missense	645414	exon3			AAAAATTGAACTC			1p36.21	2013-01-17			ENSG00000204491			"-"	30693	protein-coding gene	gene with protein product							Standard			Approved	OTTHUMG00000002932		Q5VWM3	OTTHUMG00000002932	ENST00000376126.2:c.1411A>C	1.37:g.13474718T>G	ENSP00000365294:p.Asn471His	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	304	105	NM_001099790	0	0	0	0	0		Missense_Mutation	SNP	ENST00000376126.2	37	CCDS41258.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.563802	0.00903	.	.	ENSG00000204491	ENST00000376126	T	0.01287	5.05	1.25	0.028	0.14157	.	24.652700	0.00166	N	0.000001	T	0.00906	0.0030	N	0.04018	-0.295	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.45556	-0.9253	10	0.15066	T	0.55	.	3.0129	0.06049	0.0:0.2956:0.0:0.7044	.	471	Q5VWM3	PRA18_HUMAN	H	471	ENSP00000365294:N471H	ENSP00000365294:N471H	N	-	1	0	PRAMEF18	13347305	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.371000	0.07513	-0.016000	0.14127	0.164000	0.16699	AAT	.		0.483	PRAMEF18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008177.2	NM_001099850		G	13474718	T	G	13474718	3	3	50	1	0	0	0	0	1	0	0	0	12462	1812	63	5	32	5	PRAMEF18	1	13474718	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	1586512	13474718	235775903	3	4560											
FGR	2268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27943508	27943508	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cccagtcccggatggacaggGagtaggcacctgtggagagg	9	5	17	10	1	0	1	0	0	0	1	1	5	1	4	3	6	0	2	3	6	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:27943508G>A	ENST00000374005.3	-	7	830	c.542C>T	c.(541-543)tCc>tTc	p.S181F	FGR_ENST00000545953.1_Missense_Mutation_p.S115F|FGR_ENST00000374004.1_Missense_Mutation_p.S181F|FGR_ENST00000399173.1_Missense_Mutation_p.S181F	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	181	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GATGGACAGGGAGTAGGCACC	0.567																																					p.S181F		.											.	FGR-547	0			c.C542T						.						103	96	99					1																	27943508		2203	4300	6503	SO:0001583	missense	2268	exon7			GACAGGGAGTAGG	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.542C>T	1.37:g.27943508G>A	ENSP00000363117:p.Ser181Phe	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	225	128	NM_001042729	0	0	0	0	0	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	37	CCDS305.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328135	0.81690	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	D;D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;-2.53	4.38	4.38	0.52667	SH2 motif (5);	0.000000	0.56097	D	0.000031	D	0.95079	0.8406	H	0.98199	4.17	0.50813	D	0.999899	D	0.57571	0.98	P	0.50754	0.649	D	0.97122	0.9812	10	0.87932	D	0	.	16.3789	0.83431	0.0:0.0:1.0:0.0	.	181	P09769	FGR_HUMAN	F	181;115;181;181;181;181	ENSP00000363117:S181F;ENSP00000445302:S115F;ENSP00000382126:S181F;ENSP00000363116:S181F;ENSP00000363115:S181F;ENSP00000407670:S181F	ENSP00000363115:S181F	S	-	2	0	FGR	27816095	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.670000	0.68088	2.348000	0.79779	0.491000	0.48974	TCC	.		0.567	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		A	27943508	G	A	27943508	3	1	50	1	0	0	0	0	1	0	0	0	5893	1174	41	2	1075	2	FGR	1	27943508	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	14468790	27943508	221307113	4	4561											
PABPC4	8761	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	40038242	40038242	+	Frame_Shift_Del	DEL	G	G	-																															atcacatcaaagttcatggtGtccaaagcccgctcagctgt																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:40038242delG	ENST00000372857.3	-	2	1002	c.210delC	c.(208-210)gacfs	p.D70fs	PABPC4_ENST00000372858.3_Frame_Shift_Del_p.D70fs|PABPC4_ENST00000529216.1_5'Flank|PABPC4_ENST00000372862.3_Frame_Shift_Del_p.D70fs|PABPC4_ENST00000372856.3_Frame_Shift_Del_p.D70fs|RP11-69E11.8_ENST00000415255.1_RNA	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	70	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGTTCATGGTGTCCAAAGCCC	0.468																																					p.D70fs		.											.	PABPC4-68	0			c.210delC						.						83	77	79					1																	40038242		2203	4300	6503	SO:0001589	frameshift_variant	8761	exon2			.	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.210delC	1.37:g.40038242delG	ENSP00000361948:p.Asp70fs	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	117	34	NM_001135653	0	0	0	0	0	B1ANQ8|Q4VC03|Q6P0N3	Frame_Shift_Del	DEL	ENST00000372857.3	37	CCDS438.1																																																																																			.		0.468	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		-	40038242	G	-	40038242	7	5	50	1	0	1	0	1	0	0	0	0	11392	1368	48	0	1828	0	PABPC4	1	40038242	Frame_Shift_Del	DEL	G	TCGA-B9-4116-01A-01D-1252-08	12094734	40038242	209212379	5	4562	51	2									
PABPC4	8761	hgsc.bcm.edu;bcgsc.ca	37	chr1	40038244	40038244	+	Missense_Mutation	SNP	C	C	A																															cacatcaaagttcatggtgtCcaaagcccgctcagctgtaa																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:40038244C>A	ENST00000372857.3	-	2	1000	c.208G>T	c.(208-210)Gac>Tac	p.D70Y	PABPC4_ENST00000372858.3_Missense_Mutation_p.D70Y|PABPC4_ENST00000529216.1_5'Flank|PABPC4_ENST00000372862.3_Missense_Mutation_p.D70Y|PABPC4_ENST00000372856.3_Missense_Mutation_p.D70Y|RP11-69E11.8_ENST00000415255.1_RNA	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	70	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TTCATGGTGTCCAAAGCCCGC	0.463																																					p.D70Y		.											.	PABPC4-68	0			c.G208T						.						81	75	77					1																	40038244		2203	4300	6503	SO:0001583	missense	8761	exon2			TGGTGTCCAAAGC	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.208G>T	1.37:g.40038244C>A	ENSP00000361948:p.Asp70Tyr	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	118	35	NM_001135653	0	0	60	60	0	B1ANQ8|Q4VC03|Q6P0N3	Missense_Mutation	SNP	ENST00000372857.3	37	CCDS438.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.994504	0.93167	.	.	ENSG00000090621	ENST00000372862;ENST00000372858;ENST00000372857;ENST00000372856;ENST00000451091	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.69	5.69	0.88448	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.38692	0.1050	L	0.46157	1.445	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.76575	0.964;0.988;0.924	T	0.05649	-1.0872	10	0.87932	D	0	.	19.8057	0.96531	0.0:1.0:0.0:0.0	.	70;70;70	Q13310;Q13310-2;Q4VC03	PABP4_HUMAN;.;.	Y	70	ENSP00000361953:D70Y;ENSP00000361949:D70Y;ENSP00000361948:D70Y;ENSP00000361947:D70Y;ENSP00000406675:D70Y	ENSP00000361947:D70Y	D	-	1	0	PABPC4	39810831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.705000	0.84606	2.682000	0.91365	0.655000	0.94253	GAC	.		0.463	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		A	40038244	C	A	40038244	3	1	50	1	0	0	0	0	1	0	0	0	11392	855	30	4	1830	4	PABPC4	1	40038244	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	2	40038244	209212377	6	4563	51	2									
PBX1	5087	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	164761796	164761796	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgatgcggctggacaacAtgctgttagcggaaggcgtg	9	8	16	8	3	0	1	0	1	0	0	0	3	0	3	0	4	5	4	0	4	3	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:164761796A>T	ENST00000420696.2	+	3	519	c.331A>T	c.(331-333)Atg>Ttg	p.M111L	PBX1_ENST00000560641.1_Missense_Mutation_p.M6L|PBX1_ENST00000559240.1_Missense_Mutation_p.M111L|PBX1_ENST00000401534.1_Missense_Mutation_p.M111L|PBX1_ENST00000540236.1_Missense_Mutation_p.M111L|PBX1_ENST00000540246.1_Missense_Mutation_p.M6L|PBX1_ENST00000367897.1_Missense_Mutation_p.M111L	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	111					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						GCTGGACAACATGCTGTTAGC	0.627			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.M111L		.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1-659	0			c.A331T						.						32	35	34					1																	164761796		2203	4300	6503	SO:0001583	missense	5087	exon3			GACAACATGCTGT	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.331A>T	1.37:g.164761796A>T	ENSP00000405890:p.Met111Leu	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	131	43	NM_001204963	0	0	1	4	3	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	A	34	5.311091	0.95629	.	.	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19	5.5	5.5	0.81552	PBX (1);	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	M	0.87758	2.905	0.09310	N	1.0	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.91635	0.997;0.999;0.998;0.999;0.999	T	0.68640	-0.5355	9	0.72032	D	0.01	-12.8606	15.255	0.73579	1.0:0.0:0.0:0.0	.	6;111;111;111;111	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	L	111;111;111;111;111;6	ENSP00000341455:M111L;ENSP00000405890:M111L;ENSP00000356872:M111L;ENSP00000439943:M111L;ENSP00000384856:M111L;ENSP00000440869:M6L	ENSP00000341455:M111L	M	+	1	0	PBX1	163028420	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.813000	0.91963	2.066000	0.61787	0.460000	0.39030	ATG	.		0.627	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		T	164761796	A	T	164761796	3	4	50	1	0	0	0	0	1	0	0	0	11518	217	8	5	341	5	PBX1	1	164761796	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	124723552	164761796	84488825	7	4564											
CACNA1S	779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201039482	201039482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cagctgcagctcagccagggGacgtggtcgggggctcagcg	6	5	18	12	3	2	0	2	0	0	0	3	1	2	1	1	5	5	4	1	5	0	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:201039482G>A	ENST00000362061.3	-	17	2504	c.2278C>T	c.(2278-2280)Ccc>Tcc	p.P760S	CACNA1S_ENST00000367338.3_Missense_Mutation_p.P760S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	760					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCAGCCAGGGGACGTGGTCGG	0.587																																					p.P760S		.											.	CACNA1S-94	0			c.C2278T						.						70	75	73					1																	201039482		2203	4300	6503	SO:0001583	missense	779	exon17			CCAGGGGACGTGG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.2278C>T	1.37:g.201039482G>A	ENSP00000355192:p.Pro760Ser	Somatic	250	0		WXS	Illumina HiSeq	Phase_I	385	121	NM_000069	0	0	0	0	0	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.105070	0.56291	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.95821	-3.82;-3.73	4.18	4.18	0.49190	.	0.000000	0.85682	D	0.000000	D	0.97492	0.9179	M	0.79805	2.47	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	D	0.97283	0.9919	10	0.37606	T	0.19	.	16.8708	0.86040	0.0:0.0:1.0:0.0	.	760	Q13698	CAC1S_HUMAN	S	760	ENSP00000355192:P760S;ENSP00000356307:P760S	ENSP00000355192:P760S	P	-	1	0	CACNA1S	199306105	1.000000	0.71417	0.292000	0.24919	0.289000	0.27227	7.945000	0.87732	2.032000	0.59987	0.643000	0.83706	CCC	.		0.587	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201039482	G	A	201039482	3	1	50	1	0	0	0	0	1	0	0	0	2553	1174	41	2	3455	2	CACNA1S	1	201039482	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	36277686	201039482	48211139	8	4565											
EGLN1	54583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	231502192	231502192	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accgaccgaatctgaaggttTattgagttcaaccctcacac	12	10	7	12	2	3	2	2	2	1	0	3	4	3	2	3	1	1	2	3	1	4	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:231502192T>A	ENST00000366641.3	-	5	4401	c.1246A>T	c.(1246-1248)Aaa>Taa	p.K416*	EGLN1_ENST00000476717.1_5'UTR	NM_022051.2	NP_071334.1			egl-9 family hypoxia-inducible factor 1											breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	16		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)				TCTGAAGGTTTATTGAGTTCA	0.378																																					p.K416X		.											.	EGLN1-226	0			c.A1246T						.						104	98	100					1																	231502192		2203	4300	6503	SO:0001587	stop_gained	54583	exon5			AAGGTTTATTGAG	AJ310543	CCDS1595.1	1q42.1	2013-08-21	2013-08-21	2001-08-24	ENSG00000135766	ENSG00000135766		"Zinc fingers, MYND-type"	1232	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 2"	606425	"EGL nine (C.elegans) homolog 1", "egl nine homolog 1 (C. elegans)"	C1orf12		11056053	Standard	NM_022051		Approved	SM-20, PHD2, ZMYND6, HIFPH2	uc001huv.2	Q9GZT9	OTTHUMG00000038027	ENST00000366641.3:c.1246A>T	1.37:g.231502192T>A	ENSP00000355601:p.Lys416*	Somatic	143	2		WXS	Illumina HiSeq	Phase_I	68	20	NM_022051	0	0	26	65	39		Nonsense_Mutation	SNP	ENST00000366641.3	37	CCDS1595.1	.	.	.	.	.	.	.	.	.	.	T	57	27.737614	0.99972	.	.	ENSG00000135766	ENST00000366641	.	.	.	5.47	5.47	0.80525	.	0.163488	0.53938	D	0.000058	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.8574	15.562	0.76256	0.0:0.0:0.0:1.0	.	.	.	.	X	416	.	ENSP00000355601:K416X	K	-	1	0	EGLN1	229568815	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.890000	0.75633	2.073000	0.62155	0.533000	0.62120	AAA	.		0.378	EGLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092879.1	NM_022051		A	231502192	T	A	231502192	4	1	50	1	0	0	0	0	0	1	0	0	4979	1763	61	5	38	5	EGLN1	1	231502192	Nonsense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	30462710	231502192	17748429	9	4566											
ZNF692	55657	broad.mit.edu	37	chr1	249150136	249150136	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtagtctgggggcatcAggctcactactgaaaggaga	11	7	15	8	0	3	2	2	1	1	1	3	3	3	2	0	5	1	4	0	5	3	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:249150136A>G	ENST00000306601.4	-	7	835	c.669T>C	c.(667-669)ccT>ccC	p.P223P	ZNF692_ENST00000468455.1_5'UTR|ZNF692_ENST00000451251.1_Silent_p.P228P|ZNF692_ENST00000366469.5_Silent_p.P222P|ZNF692_ENST00000366471.3_Silent_p.P178P|ZNF692_ENST00000427146.1_Silent_p.P178P	NM_017865.3	NP_060335.2	Q9BU19	ZN692_HUMAN	zinc finger protein 692	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)	17	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TGGGGGCATCAGGCTCACTAC	0.567																																					p.P228P													.	ZNF692-90	0			c.T684C						.						36	38	37					1																	249150136		2203	4300	6503	SO:0001819	synonymous_variant	55657	exon7			GGCATCAGGCTCA	BC002948	CCDS31127.1, CCDS44348.1, CCDS53487.1	1q44	2013-01-08			ENSG00000171163	ENSG00000171163		"Zinc fingers, C2H2-type"	26049	protein-coding gene	gene with protein product						12477932	Standard	NM_001136036		Approved	FLJ20531, Zfp692	uc001ifc.2	Q9BU19	OTTHUMG00000040423	ENST00000306601.4:c.669T>C	1.37:g.249150136A>G		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	118	3	NM_001136036	0	0	4	4	0	B4DXZ0|Q5SRA5|Q5SRA6|Q9HBC9|Q9NW93|Q9NWY6|Q9UF97	Silent	SNP	ENST00000306601.4	37	CCDS31127.1	.	.	.	.	.	.	.	.	.	.	A	1.433	-0.569664	0.03910	.	.	ENSG00000171163	ENST00000476503	.	.	.	4.73	-0.628	0.11537	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.1888	4.3099	0.10965	0.4905:0.092:0.0:0.4174	.	.	.	.	R	3	.	.	X	-	1	0	ZNF692	247116759	0.062000	0.20869	0.715000	0.30552	0.101000	0.19017	-0.240000	0.08952	-0.189000	0.10482	-0.695000	0.03696	TGA	.		0.567	ZNF692-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097298.1	NM_017865		G	249150136	A	G	249150136	2	3	50	1	0	0	0	0	0	0	0	1	18129	175	7	3		3	ZNF692	1	249150136	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	17647944	249150136	100485	10	4567											
MYCN	4613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	16086058	16086058	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggaccacgtgccggagttgGtaaagaatgagaaggccgcc	11	5	16	9	3	0	2	0	1	0	2	0	5	0	4	4	4	1	2	4	4	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:16086058G>C	ENST00000281043.3	+	3	1531	c.1234G>C	c.(1234-1236)Gta>Cta	p.V412L		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	412	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GCCGGAGTTGGTAAAGAATGA	0.572			A		neuroblastoma																																p.V412L		.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN-1271	0			c.G1234C						.						90	100	97					2																	16086058		2203	4300	6503	SO:0001583	missense	4613	exon3			GAGTTGGTAAAGA	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.1234G>C	2.37:g.16086058G>C	ENSP00000281043:p.Val412Leu	Somatic	304	0		WXS	Illumina HiSeq	Phase_I	496	163	NM_005378	0	0	0	0	0	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	37	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.959315	0.53400	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	D	0.97976	-4.64	5.14	4.26	0.50523	Helix-loop-helix DNA-binding (5);	0.515918	0.19319	N	0.117200	D	0.94535	0.8240	L	0.27053	0.805	0.39651	D	0.970461	P	0.40144	0.704	B	0.40864	0.342	D	0.93971	0.7249	10	0.56958	D	0.05	-13.1384	10.2421	0.43319	0.1524:0.0:0.8476:0.0	.	412	P04198	MYCN_HUMAN	L	412;330	ENSP00000281043:V412L	ENSP00000281043:V412L	V	+	1	0	MYCN	16003509	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	4.154000	0.58125	1.331000	0.45412	-0.192000	0.12808	GTA	.		0.572	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		C	16086058	G	C	16086058	3	2	50	1	0	0	0	0	1	0	0	0	10046	1261	44	4	1240	4	MYCN	2	16086058	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		16086058	227113315	11	4568											
EMILIN1	11117	hgsc.bcm.edu	37	chr2	27305348	27305348	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggttgcaggagtcctgctcCgtgtgcctggccgggctaga	4	9	16	12	3	0	1	0	0	0	1	2	2	2	2	4	4	3	4	4	4	1	2	rs375569765	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:27305348C>T	ENST00000380320.4	+	4	1408	c.909C>T	c.(907-909)tcC>tcT	p.S303S		NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	303					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTCCTGCTCCGTGTGCCTGG	0.726													C|||	2	0.000399361	0.0015	0	5008	,	,		14262	0		0	False		,,,				2504	0				p.S303S		.											.	EMILIN1-91	0			c.C909T						.	C		5,4113		0,5,2054	4	7	6		909	-10.2	0.7	2		6	1,8207		0,1,4103	no	coding-synonymous	EMILIN1	NM_007046.3		0,6,6157	TT,TC,CC		0.0122,0.1214,0.0487		303/1017	27305348	6,12320	2059	4104	6163	SO:0001819	synonymous_variant	11117	exon4			CTGCTCCGTGTGC	AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"EMI domain containing"	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.909C>T	2.37:g.27305348C>T		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	14	7	NM_007046	0	0	4	8	4	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Silent	SNP	ENST00000380320.4	37	CCDS1733.1																																																																																			.		0.726	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1	NM_007046		T	27305348	C	T	27305348	2	4	50	1	0	0	0	0	0	0	0	1	5106	639	23	1		1	EMILIN1	2	27305348	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	11219290	27305348	215894025	12	4569											
LCLAT1	253558	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	30863165	30863173	+	In_Frame_Del	DEL	GAAGAGAAA	GAAGAGAAA	-																															tctggtgccacaaacggtggGaagagaaagaagagaggctg																								rs200693287|rs150085223	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	GAAGAGAAA	GAAGAGAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:30863165_30863173delGAAGAGAAA	ENST00000309052.4	+	7	1134_1142	c.925_933delGAAGAGAAA	c.(925-933)gaagagaaadel	p.EEK309del	LCLAT1_ENST00000379509.3_In_Frame_Del_p.EEK271del|LCLAT1_ENST00000540623.1_In_Frame_Del_p.EEK271del|LCLAT1_ENST00000491680.2_3'UTR	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	309					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						CAAACGGTGGGAAGAGAAAGAAGAGAGGC	0.498																																					p.309_311del		.											.	LCLAT1-92	0			c.925_933del						.																																			SO:0001651	inframe_deletion	253558	exon7			.	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.925_933delGAAGAGAAA	2.37:g.30863165_30863173delGAAGAGAAA	ENSP00000310551:p.Glu309_Lys311del	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	178	28	NM_182551	0	0	0	0	0	A6H8Z7|Q8N1Q7	In_Frame_Del	DEL	ENST00000309052.4	37	CCDS1772.1																																																																																			.		0.498	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		-	30863173	GAAGAGAAA	-	30863165	7	5	50	1	0	1	0	1	0	0	0	0	8698	1175	41	0	947	0	LCLAT1	2	30863165	In_Frame_Del	DEL	GAAGAGAAA	TCGA-B9-4116-01A-01D-1252-08	3557817	30863165	212336208	13	4570											
ANXA4	307	ucsc.edu	37	chr2	70037724	70037724	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctaatttcactctcttgctAgaatatggacggagccttga	10	13	9	9	1	2	2	1	1	1	1	3	4	2	4	1	2	2	2	1	2	4	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:70037724A>G	ENST00000394295.4	+	7	645		c.e7-1		ANXA4_ENST00000536030.1_Splice_Site|ANXA4_ENST00000409920.1_Splice_Site	NM_001153.3	NP_001144.1	P09525	ANXA4_HUMAN	annexin A4						epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						CTCTCTTGCTAGAATATGGAC	0.488																																					.													.	ANXA4-90	0			c.398-2A>G						.						118	109	112					2																	70037724		2203	4300	6503	SO:0001630	splice_region_variant	307	exon7			CTTGCTAGAATAT	M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"Annexins"	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000394295.4:c.398-1A>G	2.37:g.70037724A>G		Somatic	73	0		WXS	Illumina HiSeq		96	1	NM_001153	0	0	8	8	0	B4DDF9|Q96F33|Q9BWK1	Splice_Site	SNP	ENST00000394295.4	37	CCDS1894.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163658	0.78226	.	.	ENSG00000196975	ENST00000409920;ENST00000394295;ENST00000536030	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9622	0.64188	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANXA4	69891228	1.000000	0.71417	0.961000	0.40146	0.940000	0.58332	7.600000	0.82769	2.190000	0.69967	0.533000	0.62120	.	.		0.488	ANXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251848.2	NM_001153	Intron	G	70037724	A	G	70037724	5	3	50	1	0	0	0	0	0	0	1	0	720	434	15	3	418	3	ANXA4	2	70037724	Splice_Site	SNP	A	TCGA-B9-4116-01A-01D-1252-08	39174559	70037724	173161649	14	4571											
MAT2A	4144	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	85769094	85769097	+	Splice_Site	DEL	AAGT	AAGT	-																															acgccctgattctaaaactcAagtaagtgatgatcataaag																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:85769094_85769097delAAGT	ENST00000306434.3	+	5	671_672	c.548_549delAAGT	c.(547-549)caa>c	p.Q183fs	MAT2A_ENST00000490878.1_3'UTR|MAT2A_ENST00000409017.1_Splice_Site_p.Q120fs	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	183					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TCTAAAACTCAAGTAAGTGATGAT	0.382																																					p.183_183del		.											.	MAT2A-90	0			c.548_549del						.																																			SO:0001630	splice_region_variant	4144	exon5			.		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.549+1AAGT>-	2.37:g.85769098_85769101delAAGT		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	52	14	NM_005911	0	0	0	0	0	A8K511|B4DN45|D6W5L1|Q53SP5	Frame_Shift_Del	DEL	ENST00000306434.3	37	CCDS1977.1																																																																																			.		0.382	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911	Frame_Shift_Del	-	85769097	AAGT	-	85769094	8	5	50	1	0	1	0	1	0	0	1	0	9355	144	5	0	566	0	MAT2A	2	85769094	Splice_Site	DEL	AAGT	TCGA-B9-4116-01A-01D-1252-08	15731370	85769094	157430279	15	4572											
FAM128A	653784	hgsc.bcm.edu	37	chr2	132249519	132249520	+	Frame_Shift_Ins	INS	-	-	A																															ggggctcgctcgctagcctcINStgcccggcacacatggactt																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:132249519_132249520insA	ENST00000309451.6	-	2	293_294	c.248_249insT	c.(247-249)cagfs	p.Q83fs	AC093838.4_ENST00000438378.2_RNA|MIR4784_ENST00000579560.1_RNA|MZT2A_ENST00000410036.2_5'UTR	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	83						centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						TCGCTAGCCTCTGCCCGGCACA	0.703																																					p.Q83fs		.											.	MZT2A-68	0			c.249_250insT						.																																			SO:0001589	frameshift_variant	653784	exon2			.	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"	613449	"family with sequence similarity 128, member A"	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.248_249insT	2.37:g.132249519_132249520insA	ENSP00000311500:p.Gln83fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	49	17	NM_001085365	0	0	0	0	0	Q3SWV8|Q8WVB2	Frame_Shift_Ins	INS	ENST00000309451.6	37	CCDS42758.1																																																																																			.		0.703	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2			A	132249520	-	A	132249519	7	5	50	1	0	1	1	0	0	0	0	0	5450	912	32	0	235	0	FAM128A	2	132249519	Frame_Shift_Ins	INS	-	TCGA-B9-4116-01A-01D-1252-08	46480425	132249519	110949854	16	4573											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160287392	160287392	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagagtgtgggcttgaagTaagtgtggaagaagatgtac	13	9	15	4	0	0	4	0	1	0	3	0	5	0	5	1	2	1	3	1	2	5	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:160287392T>G	ENST00000392783.2	-	10	2671	c.2176A>C	c.(2176-2178)Act>Cct	p.T726P	BAZ2B_ENST00000392782.1_Missense_Mutation_p.T724P|BAZ2B_ENST00000355831.2_Missense_Mutation_p.T726P|BAZ2B_ENST00000343439.5_Intron	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	726					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GGGCTTGAAGTAAGTGTGGAA	0.408																																					p.T726P		.											.	BAZ2B-94	0			c.A2176C						.						110	105	107					2																	160287392		1886	4123	6009	SO:0001583	missense	29994	exon10			TTGAAGTAAGTGT	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2176A>C	2.37:g.160287392T>G	ENSP00000376534:p.Thr726Pro	Somatic	161	1		WXS	Illumina HiSeq	Phase_I	39	2	NM_013450	0	0	3	3	0	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	T	14.40	2.524028	0.44866	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831	T;T;T	0.22743	1.94;1.94;1.94	5.64	4.42	0.53409	DNA-binding, integrase-type (1);	0.219310	0.22744	U	0.056164	T	0.13457	0.0326	N	0.14661	0.345	0.80722	D	1	B;B;B	0.14438	0.01;0.005;0.007	B;B;B	0.15484	0.013;0.011;0.005	T	0.05550	-1.0878	10	0.66056	D	0.02	-15.8483	11.6182	0.51102	0.1332:0.0:0.0:0.8668	.	530;724;726	Q9UIF8-4;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	P	724;726;726	ENSP00000376533:T724P;ENSP00000376534:T726P;ENSP00000348087:T726P	ENSP00000348087:T726P	T	-	1	0	BAZ2B	159995638	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.673000	0.37534	2.148000	0.66965	0.523000	0.50628	ACT	.		0.408	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			G	160287392	T	G	160287392	3	3	50	1	0	0	0	0	1	0	0	0	1333	1638	57	5	4442	5	BAZ2B	2	160287392	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	28037873	160287392	82911981	17	4574											
C2orf80	389073	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	209045533	209045533	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaagacttcctcaatcgggAtactgttctgttaaacaaca	14	12	6	9	1	2	1	1	0	1	1	4	2	3	2	1	1	3	2	1	1	7	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:209045533A>C	ENST00000341287.4	-	6	497	c.302T>G	c.(301-303)aTc>aGc	p.I101S	C2orf80_ENST00000453017.1_Missense_Mutation_p.I101S|C2orf80_ENST00000451346.1_Missense_Mutation_p.I82S	NM_001099334.2	NP_001092804	Q0P641	CB080_HUMAN	chromosome 2 open reading frame 80	101										endometrium(2)|large_intestine(3)|lung(6)|skin(2)	13						CTCAATCGGGATACTGTTCTG	0.363																																					p.I101S		.											.	C2orf80-69	0			c.T302G						.						98	92	94					2																	209045533		1810	4083	5893	SO:0001583	missense	389073	exon6			ATCGGGATACTGT	AC016697, AW136505, BC035737	CCDS42809.1	2q33.3	2013-10-31			ENSG00000188674	ENSG00000188674			34352	protein-coding gene	gene with protein product	"gonad development associated 1"	615536				22080834, 24055526	Standard	NM_001099334		Approved	LOC389073, GONDA1	uc002vcr.3	Q0P641	OTTHUMG00000154751	ENST00000341287.4:c.302T>G	2.37:g.209045533A>C	ENSP00000343171:p.Ile101Ser	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	86	26	NM_001099334	0	0	0	0	0	A6NKZ3	Missense_Mutation	SNP	ENST00000341287.4	37	CCDS42809.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.20|14.20	2.465820|2.465820	0.43839|0.43839	.|.	.|.	ENSG00000188674|ENSG00000188674	ENST00000451342;ENST00000341287;ENST00000451346;ENST00000453017;ENST00000423952|ENST00000428015	T;T;T;T;T|.	0.54866|.	1.04;1.51;1.46;0.55;1.02|.	4.67|4.67	3.47|3.47	0.39725|0.39725	.|.	0.384012|.	0.22416|.	N|.	0.060357|.	T|.	0.33381|.	0.0861|.	L|L	0.32530|0.32530	0.975|0.975	0.28843|0.28843	N|N	0.896464|0.896464	B|.	0.29646|.	0.253|.	B|.	0.33799|.	0.17|.	T|.	0.22068|.	-1.0227|.	10|.	0.87932|.	D|.	0|.	-4.0257|-4.0257	7.2927|7.2927	0.26374|0.26374	0.8979:0.0:0.1021:0.0|0.8979:0.0:0.1021:0.0	.|.	101|.	Q0P641|.	CB080_HUMAN|.	S|X	26;101;82;101;14|52	ENSP00000389385:I26S;ENSP00000343171:I101S;ENSP00000405393:I82S;ENSP00000397144:I101S;ENSP00000413016:I14S|.	ENSP00000343171:I101S|.	I|Y	-|-	2|3	0|2	C2orf80|C2orf80	208753778|208753778	1.000000|1.000000	0.71417|0.71417	0.937000|0.937000	0.37676|0.37676	0.941000|0.941000	0.58515|0.58515	2.253000|2.253000	0.43205|0.43205	0.883000|0.883000	0.36040|0.36040	0.455000|0.455000	0.32223|0.32223	ATC|TAT	.		0.363	C2orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336931.1	NM_001099334		C	209045533	A	C	209045533	3	2	50	1	0	0	0	0	1	0	0	0	2203	333	12	5	295	5	C2orf80	2	209045533	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	48758141	209045533	34153840	18	4575											
SP140	11262	hgsc.bcm.edu	37	chr2	231176275	231176275	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggggtttgtacaagacatgCgcctcatcttccagaaccac	11	9	9	12	1	2	2	1	0	1	2	3	2	3	2	3	2	3	2	3	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:231176275C>G	ENST00000392045.3	+	26	2584	c.2470C>G	c.(2470-2472)Cgc>Ggc	p.R824G	SP140_ENST00000420434.3_Missense_Mutation_p.R797G|SP140_ENST00000350136.5_Missense_Mutation_p.R693G|SP140_ENST00000343805.6_Missense_Mutation_p.R764G|SP140_ENST00000417495.3_Missense_Mutation_p.R710G|SP140_ENST00000486687.2_Missense_Mutation_p.R748G	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	824	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ACAAGACATGCGCCTCATCTT	0.507																																					p.R824G		.											.	SP140-90	0			c.C2470G						.						31	31	31					2																	231176275		1784	4036	5820	SO:0001583	missense	11262	exon26			GACATGCGCCTCA	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"Zinc fingers, PHD-type"	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.2470C>G	2.37:g.231176275C>G	ENSP00000375899:p.Arg824Gly	Somatic	422	0		WXS	Illumina HiSeq	Phase_I	321	22	NM_007237	0	0	24	26	2	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450333	0.43531	.	.	ENSG00000079263	ENST00000486687;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	2.9	-1.45	0.08828	Bromodomain (5);	.	.	.	.	T	0.49490	0.1560	M	0.85373	2.75	0.24352	N	0.994912	D;D;D;D	0.69078	0.997;0.976;0.986;0.989	D;P;P;D	0.70227	0.968;0.727;0.859;0.913	T	0.39396	-0.9616	9	0.87932	D	0	-9.1463	2.5578	0.04764	0.3978:0.3475:0.0:0.2547	.	797;710;764;824	E7EUR5;E7ESH9;E9PFJ6;Q13342	.;.;.;LY10_HUMAN	G	748;693;824;710;764;797	ENSP00000440107:R748G;ENSP00000345846:R693G;ENSP00000375899:R824G;ENSP00000342096:R764G;ENSP00000398210:R797G	ENSP00000342096:R764G	R	+	1	0	SP140	230884519	0.805000	0.28982	0.517000	0.27799	0.964000	0.63967	0.246000	0.18160	-0.360000	0.08138	0.563000	0.77884	CGC	.		0.507	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		G	231176275	C	G	231176275	3	3	50	1	0	0	0	0	1	0	0	0	14994	768	27	4	2689	4	SP140	2	231176275	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	22130742	231176275	12023098	19	4576											
SP140L	93349	hgsc.bcm.edu	37	chr2	231266487	231266487	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggggtttgtacaagacatgCgcctcatcttccagaaccac	11	9	9	12	1	2	2	1	0	1	2	3	2	3	2	3	2	3	2	3	2	3	3	rs367571251		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:231266487C>G	ENST00000415673.2	+	18	1695	c.1609C>G	c.(1609-1611)Cgc>Ggc	p.R537G	SP140L_ENST00000243810.6_3'UTR|SP140L_ENST00000396563.4_3'UTR	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	537	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						ACAAGACATGCGCCTCATCTT	0.507																																					p.R537G		.											.	SP140L-23	0			c.C1609G						.						27	27	27					2																	231266487		1777	4026	5803	SO:0001583	missense	93349	exon18			GACATGCGCCTCA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1609C>G	2.37:g.231266487C>G	ENSP00000397911:p.Arg537Gly	Somatic	378	0		WXS	Illumina HiSeq	Phase_I	278	61	NM_138402	0	0	24	26	2	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.173538	0.38413	.	.	ENSG00000185404	ENST00000415673	T	0.31510	1.49	3.14	1.16	0.20824	.	.	.	.	.	T	0.52517	0.1739	M	0.89414	3.03	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.49579	-0.8925	9	0.87932	D	0	.	3.4797	0.07598	0.2626:0.5932:0.0:0.1442	.	537	Q9H930-4	.	G	537	ENSP00000397911:R537G	ENSP00000397911:R537G	R	+	1	0	SP140L	230974731	0.851000	0.29673	0.755000	0.31263	0.732000	0.41865	0.637000	0.24659	0.136000	0.18733	0.298000	0.19748	CGC	.		0.507	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		G	231266487	C	G	231266487	3	3	50	1	0	0	0	0	1	0	0	0	14995	768	27	4	1679	4	SP140L	2	231266487	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	90212	231266487	11932886	20	4577											
OGG1	4968	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9793597	9793597	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatccagcttgatgatgtcAcctaccatggcttccccagc	8	11	7	15	0	2	2	2	2	0	0	4	2	4	2	5	1	3	2	5	1	1	3	rs144249605	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:9793597A>G	ENST00000344629.7	+	3	872	c.529A>G	c.(529-531)Acc>Gcc	p.T177A	OGG1_ENST00000302036.7_Missense_Mutation_p.T177A|OGG1_ENST00000339511.5_Missense_Mutation_p.T177A|OGG1_ENST00000349503.5_Missense_Mutation_p.T177A|OGG1_ENST00000302008.8_Missense_Mutation_p.T177A|OGG1_ENST00000302003.7_Missense_Mutation_p.T177A|OGG1_ENST00000449570.2_Missense_Mutation_p.T177A|OGG1_ENST00000383826.5_Missense_Mutation_p.T177A			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	177					acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					TGATGATGTCACCTACCATGG	0.572								Base excision repair (BER), DNA glycosylases																													p.T177A		.											.	OGG1-660	0			c.A529G						.						86	82	83					3																	9793597		2203	4300	6503	SO:0001583	missense	4968	exon3			GATGTCACCTACC	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"8-hydroxyguanine DNA glycosylase", "OGG1 type 1e", "OGG1 type 1d", "OGG1 type 1g", "OGG1 type 1h"	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.529A>G	3.37:g.9793597A>G	ENSP00000342851:p.Thr177Ala	Somatic	133	2		WXS	Illumina HiSeq	Phase_I	193	64	NM_016819	0	0	14	22	8	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.43|12.43	1.935498|1.935498	0.34189|0.34189	.|.	.|.	ENSG00000114026|ENSG00000114026	ENST00000352937;ENST00000416333|ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000383826;ENST00000339542	.|T;T;T;T;T;T;T;T	.|0.54071	.|0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.59	5.51|5.51	-3.55|-3.55	0.04639|0.04639	.|HhH-GPD domain (2);DNA glycosylase (2);	.|0.639505	.|0.18056	.|N	.|0.153083	T|T	0.27559|0.27559	0.0677|0.0677	L|L	0.33245|0.33245	0.995|0.995	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B;B;B	.|0.30236	.|0.274;0.002;0.038;0.006;0.0;0.0;0.008;0.0;0.0	.|B;B;B;B;B;B;B;B;B	.|0.31751	.|0.135;0.004;0.004;0.01;0.009;0.005;0.009;0.003;0.002	T|T	0.19745|0.19745	-1.0296|-1.0296	5|10	.|0.12103	.|T	.|0.63	-6.2946|-6.2946	0.5751|0.5751	0.00702|0.00702	0.3173:0.2684:0.2179:0.1964|0.3173:0.2684:0.2179:0.1964	.|.	.|20;177;177;177;177;177;177;177;177	.|F8WA07;E5KPM8;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.|.;.;.;.;.;.;.;OGG1_HUMAN;.	R|A	82;4|177;177;177;177;177;177;177;177;20	.|ENSP00000305584:T177A;ENSP00000342851:T177A;ENSP00000306561:T177A;ENSP00000303132:T177A;ENSP00000345520:T177A;ENSP00000403598:T177A;ENSP00000305527:T177A;ENSP00000373337:T177A	.|ENSP00000305584:T177A	H|T	+|+	2|1	0|0	OGG1|OGG1	9768597|9768597	0.001000|0.001000	0.12720|0.12720	0.928000|0.928000	0.36995|0.36995	0.968000|0.968000	0.65278|0.65278	-0.152000|-0.152000	0.10159|0.10159	-0.208000|-0.208000	0.10171|0.10171	0.533000|0.533000	0.62120|0.62120	CAC|ACC	A|0.999;T|0.001		0.572	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		G	9793597	A	G	9793597	3	3	50	1	0	0	0	0	1	0	0	0	10871	159	6	3	539	3	OGG1	3	9793597	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08		9793597	188228833	21	4578											
MON1A	84315	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49946456	49946456	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acacattcccatcaataggtGaggggcgtgagaatgaagag	14	7	13	7	1	1	4	1	3	0	2	2	5	2	4	1	3	0	0	1	3	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:49946456G>A	ENST00000417270.1	-	7	2376	c.1683C>T	c.(1681-1683)ctC>ctT	p.L561L	MON1A_ENST00000455683.2_Silent_p.L488L|CTD-2330K9.3_ENST00000419183.1_Intron|MON1A_ENST00000483022.1_5'Flank|MON1A_ENST00000296473.3_Silent_p.L650L			Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	553										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		ATCAATAGGTGAGGGGCGTGA	0.607																																					p.L650L		.											.	MON1A-280	0			c.C1950T						.						48	43	45					3																	49946456		2203	4300	6503	SO:0001819	synonymous_variant	84315	exon6			ATAGGTGAGGGGC	AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"MON1 homolog A (yeast)"			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000417270.1:c.1683C>T	3.37:g.49946456G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	126	38	NM_032355	0	0	10	11	1	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Silent	SNP	ENST00000417270.1	37																																																																																				.		0.607	MON1A-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000345538.2	NM_032355		A	49946456	G	A	49946456	2	1	50	1	0	0	0	0	0	0	0	1	9723	1277	45	2		2	MON1A	3	49946456	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	40152859	49946456	148075974	22	4579											
RPL29	6159	hgsc.bcm.edu	37	chr3	52027876	52027876	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggccttggccttggccttGgcctttggccggcacagcct	2	12	13	14	1	0	0	0	0	0	0	0	0	0	0	6	6	1	1	6	6	0	5	rs545891070		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:52027876G>T	ENST00000466397.1	-	4	509	c.369C>A	c.(367-369)gcC>gcA	p.A123A	RPL29_ENST00000475248.1_Silent_p.A123A|RPL29_ENST00000479017.1_Silent_p.A123A|RPL29_ENST00000495383.1_Silent_p.A123A|RPL29_ENST00000294189.6_Silent_p.A123A			P47914	RL29_HUMAN	ribosomal protein L29	123					cellular protein metabolic process (GO:0044267)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ccttggccttggcctttggcc	0.627																																					p.A123A		.											.	RPL29-90	0			c.C369A						.																																			SO:0001819	synonymous_variant	6159	exon4			GGCCTTGGCCTTT	U10248	CCDS2845.1	3p21.3-p21.2	2013-03-11			ENSG00000162244	ENSG00000162244		"L ribosomal proteins"	10331	protein-coding gene	gene with protein product	"60S ribosomal protein L29", "heparin/heparan sulfate-interacting protein", "HP/HS-interacting protein", "heparin/heparan sulfate-binding protein", "cell surface heparin-binding protein HIP"	601832	"ribosomal protein L29 pseudogene 10"	RPL29P10		8597591	Standard	NM_000992		Approved	HIP, HUMRPL29, L29	uc003dcs.3	P47914	OTTHUMG00000155262	ENST00000466397.1:c.369C>A	3.37:g.52027876G>T		Somatic	60	2		WXS	Illumina HiSeq	Phase_I	120	10	NM_000992	0	0	1679	1681	2	A8K0H3|B2R4M8|Q6IPY3	Silent	SNP	ENST00000466397.1	37	CCDS2845.1																																																																																			.		0.627	RPL29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349680.2	NM_000992		T	52027876	G	T	52027876	2	4	50	1	0	0	0	0	0	0	0	1	13610	1335	47	4		4	RPL29	3	52027876	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	2081420	52027876	145994554	23	4580											
TMF1	7110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	69096707	69096707	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcagtgggtataactaaTgtttcatttacttcttcaga	10	17	6	8	0	4	1	3	0	1	1	5	1	5	1	1	1	2	2	1	1	4	8			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:69096707T>C	ENST00000398559.2	-	2	1365	c.1149A>G	c.(1147-1149)acA>acG	p.T383T	CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Silent_p.T383T|MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	383					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		GTATAACTAATGTTTCATTTA	0.383																																					p.T383T		.											.	TMF1-90	0			c.A1149G						.						129	121	123					3																	69096707		1871	4109	5980	SO:0001819	synonymous_variant	7110	exon2			AACTAATGTTTCA		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.1149A>G	3.37:g.69096707T>C		Somatic	229	0		WXS	Illumina HiSeq	Phase_I	106	42	NM_007114	0	0	4	14	10	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	37	CCDS43105.1																																																																																			.		0.383	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69096707	T	C	69096707	2	2	50	1	0	0	0	0	0	0	0	1	16260	1451	51	3		3	TMF1	3	69096707	Silent	SNP	T	TCGA-B9-4116-01A-01D-1252-08	17068831	69096707	128925723	24	4581											
GPR128	84873	hgsc.bcm.edu;broad.mit.edu	37	chr3	100349576	100349576	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgaaaatagtacctataTgggttttacttttgccagaa	12	16	8	5	0	0	2	0	1	0	1	0	2	0	2	2	1	3	2	2	1	8	9			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:100349576T>G	ENST00000273352.3	+	3	525	c.257T>G	c.(256-258)aTg>aGg	p.M86R		NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	86					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)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						AGTACCTATATGGGTTTTACT	0.318																																					p.M86R	Pancreas(87;185 1975 7223 18722)	.											.	GPR128-94	0			c.T257G						.						69	71	70					3																	100349576		2203	4300	6503	SO:0001583	missense	84873	exon3			CCTATATGGGTTT	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"-", "GPCR / Class B : Orphans"	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.257T>G	3.37:g.100349576T>G	ENSP00000273352:p.Met86Arg	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_032787	0	0	0	0	0	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	T	1.740	-0.491891	0.04322	.	.	ENSG00000144820	ENST00000273352	T	0.37915	1.17	5.82	-11.6	0.00059	.	4.439820	0.00397	N	0.000057	T	0.21921	0.0528	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15122	-1.0448	10	0.12430	T	0.62	.	8.0964	0.30831	0.2366:0.0663:0.5446:0.1525	.	86	Q96K78	GP128_HUMAN	R	86	ENSP00000273352:M86R	ENSP00000273352:M86R	M	+	2	0	GPR128	101832266	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.466000	0.02355	-4.377000	0.00053	-0.323000	0.08544	ATG	.		0.318	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			G	100349576	T	G	100349576	3	3	50	1	0	0	0	0	1	0	0	0	6661	1464	51	5	267	5	GPR128	3	100349576	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	31252869	100349576	97672854	25	4582											
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101370247	101370247	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgaggaccactgctttcTtgttcctgcatgcctgctgt	4	16	9	12	0	2	1	0	1	2	0	3	2	3	2	3	1	4	4	3	1	0	4	rs374150569		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:101370247T>G	ENST00000312938.4	-	11	3505	c.2925A>C	c.(2923-2925)caA>caC	p.Q975H		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	975					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						CACTGCTTTCTTGTTCCTGCA	0.448																																					p.Q975H		.											.	ZBTB11-91	0			c.A2925C						.						202	171	181					3																	101370247		2203	4300	6503	SO:0001583	missense	27107	exon11			GCTTTCTTGTTCC	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.2925A>C	3.37:g.101370247T>G	ENSP00000326200:p.Gln975His	Somatic	421	1		WXS	Illumina HiSeq	Phase_I	258	75	NM_014415	0	0	6	10	4	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652999	0.67472	.	.	ENSG00000066422	ENST00000312938	T	0.12672	2.66	5.49	-2.58	0.06228	.	0.060521	0.64402	D	0.000003	T	0.10252	0.0251	N	0.24115	0.695	0.80722	D	1	D	0.62365	0.991	P	0.51999	0.687	T	0.20874	-1.0262	10	0.02654	T	1	-14.7598	12.7952	0.57556	0.0:0.4538:0.0:0.5462	.	975	O95625	ZBT11_HUMAN	H	975	ENSP00000326200:Q975H	ENSP00000326200:Q975H	Q	-	3	2	ZBTB11	102852937	0.931000	0.31567	0.982000	0.44146	0.882000	0.50991	-0.067000	0.11579	-0.456000	0.07043	0.454000	0.30748	CAA	.		0.448	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		G	101370247	T	G	101370247	3	3	50	1	0	0	0	0	1	0	0	0	17556	1606	56	5	240	5	ZBTB11	3	101370247	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	1020671	101370247	96652183	26	4583											
PVRL3	25945	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	110830989	110830989	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	accataacacagatttcatgGgagaagatacatggcaaaag	18	7	9	7	0	1	3	1	0	0	3	1	4	1	3	1	2	2	1	1	2	5	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:110830989G>A	ENST00000485303.1	+	2	548	c.273G>A	c.(271-273)tgG>tgA	p.W91*	PVRL3_ENST00000319792.3_Nonsense_Mutation_p.W91*|PVRL3_ENST00000493615.1_Nonsense_Mutation_p.W68*|PVRL3_ENST00000488016.1_3'UTR	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	91	Ig-like V-type.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						AGATTTCATGGGAGAAGATAC	0.378																																					p.W91X		.											.	PVRL3-92	0			c.G273A						.						79	75	77					3																	110830989		2203	4300	6503	SO:0001587	stop_gained	25945	exon2			TTCATGGGAGAAG	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.273G>A	3.37:g.110830989G>A	ENSP00000418070:p.Trp91*	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_001243286	0	0	4	6	2	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Nonsense_Mutation	SNP	ENST00000485303.1	37	CCDS2957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.619371|5.619371	0.96649|0.96649	.|.	.|.	ENSG00000177707|ENSG00000177707	ENST00000486596|ENST00000461477;ENST00000485303;ENST00000319792;ENST00000493615;ENST00000481766	.|.	.|.	.|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.45875|.	0.1364|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.38001|.	-0.9681|.	3|.	.|0.02654	.|T	.|1	.|.	17.649|17.649	0.88157|0.88157	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	R|X	91|44;91;91;68;76	.|.	.|ENSP00000321514:W91X	G|W	+|+	1|3	0|0	PVRL3|PVRL3	112313679|112313679	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.517000|8.517000	0.90555|0.90555	2.760000|2.760000	0.94817|0.94817	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.		0.378	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		A	110830989	G	A	110830989	4	1	50	1	0	0	0	0	0	1	0	0	12873	1241	43	2	279	2	PVRL3	3	110830989	Nonsense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	9460742	110830989	87191441	27	4584											
C3orf17	25871	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	112736366	112736368	+	In_Frame_Del	DEL	CAT	CAT	-																															gtaaaggactgcacataacaCatctgtttctgcatctaagg																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:112736366_112736368delCAT	ENST00000314400.5	-	2	379_381	c.188_190delATG	c.(187-192)gatgtg>gtg	p.D63del	RP11-572M11.4_ENST00000460707.1_RNA|C3orf17_ENST00000383675.2_In_Frame_Del_p.D63del|RP11-572M11.4_ENST00000496389.1_RNA|RP11-572M11.4_ENST00000467342.1_RNA|C3orf17_ENST00000393857.2_Intron|RP11-572M11.4_ENST00000470313.1_RNA	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	63					negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						GCACATAACACATCTGTTTCTGC	0.478																																					p.63_64del		.											.	C3orf17-90	0			c.188_190del						.																																			SO:0001651	inframe_deletion	25871	exon2			.	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.188_190delATG	3.37:g.112736366_112736368delCAT	ENSP00000320251:p.Asp63del	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	86	23	NM_015412	0	0	0	0	0	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	In_Frame_Del	DEL	ENST00000314400.5	37	CCDS33824.1																																																																																			.		0.478	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412		-	112736368	CAT	-	112736366	7	5	50	1	0	1	0	1	0	0	0	0	2216	478	17	0	1545	0	C3orf17	3	112736366	In_Frame_Del	DEL	CAT	TCGA-B9-4116-01A-01D-1252-08	1905377	112736366	85286064	28	4585											
PIGZ	80235	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	196675120	196675120	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcagccacaatgcctccAagaagccagctgcgccaccg	11	3	9	18	2	0	1	0	0	0	1	1	1	1	1	7	0	6	2	7	0	3	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:196675120A>T	ENST00000412723.1	-	3	794	c.648T>A	c.(646-648)ctT>ctA	p.L216L	PIGZ_ENST00000443835.1_3'UTR	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	216					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		CAATGCCTCCAAGAAGCCAGC	0.637																																					p.L216L		.											.	PIGZ-93	0			c.T648A						.						59	67	64					3																	196675120		2203	4299	6502	SO:0001819	synonymous_variant	80235	exon3			GCCTCCAAGAAGC	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	30596	protein-coding gene	gene with protein product	"GPI mannosyltransferase 4", "dol-P-Man dependent GPI mannosyltransferase"	611671	"phosphatidylinositol glycan, class Z"			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.648T>A	3.37:g.196675120A>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	271	114	NM_025163	0	0	3	10	7	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			.		0.637	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		T	196675120	A	T	196675120	2	4	50	1	0	0	0	0	0	0	0	1	11931	117	5	5		5	PIGZ	3	196675120	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	83938754	196675120	1347310	29	4586											
GRK4	2868	broad.mit.edu	37	chr4	3039108	3039108	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttgctacacagcctcatgCcgtttactgtaaggacgtcc	8	12	8	13	2	2	0	1	0	1	0	3	1	3	1	3	1	5	3	3	1	3	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:3039108C>T	ENST00000398052.4	+	14	1758	c.1415C>T	c.(1414-1416)gCc>gTc	p.A472V	GRK4_ENST00000504933.1_Missense_Mutation_p.A472V|GRK4_ENST00000345167.6_Missense_Mutation_p.A440V|GRK4_ENST00000509545.1_3'UTR|GRK4_ENST00000398051.4_Missense_Mutation_p.A440V	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	472	AGC-kinase C-terminal.				G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CAGCCTCATGCCGTTTACTGT	0.522											OREG0016045	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A472V													.	GRK4-507	0			c.C1415T						.						244	236	239					4																	3039108		2203	4300	6503	SO:0001583	missense	2868	exon14			CTCATGCCGTTTA		CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"G protein-coupled receptor kinase 2-like (Drosophila)"	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.1415C>T	4.37:g.3039108C>T	ENSP00000381129:p.Ala472Val	Somatic	428	1	608	WXS	Illumina HiSeq	Phase_I	695	6	NM_182982	0	0	0	0	0	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Missense_Mutation	SNP	ENST00000398052.4	37	CCDS33946.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.721254	0.48728	.	.	ENSG00000125388	ENST00000398051;ENST00000398052;ENST00000345167;ENST00000504933	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	4.85	4.01	0.46588	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	U	0.000000	T	0.35970	0.0950	L	0.58583	1.82	0.80722	D	1	D;P;D;D	0.64830	0.994;0.944;0.994;0.99	B;B;P;P	0.54346	0.43;0.242;0.749;0.565	T	0.07520	-1.0768	10	0.23891	T	0.37	-12.343	12.6443	0.56725	0.0:0.9193:0.0:0.0807	.	440;440;472;472	P32298-3;P32298-2;P32298-4;P32298	.;.;.;GRK4_HUMAN	V	440;472;440;472	ENSP00000381128:A440V;ENSP00000381129:A472V;ENSP00000264764:A440V;ENSP00000427445:A472V	ENSP00000264764:A440V	A	+	2	0	GRK4	3008906	1.000000	0.71417	0.002000	0.10522	0.010000	0.07245	4.724000	0.61972	1.172000	0.42781	0.511000	0.50034	GCC	.		0.522	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307		T	3039108	C	T	3039108	3	4	50	1	0	0	0	0	1	0	0	0	6812	739	26	2	1469	2	GRK4	4	3039108	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08		3039108	188115168	30	4587											
RFC1	5981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39325032	39325032	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcatcttcatgcaactgcctCtccagctgtaaaatgtgtca	10	13	6	12	0	5	0	3	0	2	0	6	0	5	0	2	0	4	3	2	0	3	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:39325032C>T	ENST00000381897.1	-	7	781	c.648G>A	c.(646-648)gaG>gaA	p.E216E	RFC1_ENST00000349703.2_Silent_p.E216E|RFC1_ENST00000418436.1_5'UTR	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	216					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GCAACTGCCTCTCCAGCTGTA	0.373																																					p.E216E	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	.											.	RFC1-230	0			c.G648A						.						149	124	132					4																	39325032		2203	4300	6503	SO:0001819	synonymous_variant	5981	exon7			CTGCCTCTCCAGC	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.648G>A	4.37:g.39325032C>T		Somatic	169	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_002913	0	0	0	0	0	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																			.		0.373	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		T	39325032	C	T	39325032	2	4	50	1	0	0	0	0	0	0	0	1	13276	912	32	2		2	RFC1	4	39325032	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	36285924	39325032	151829244	31	4588											
UGT2B7	7364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	69968643	69968643	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattgcatcagccctggcccAgatcccacaaaaggtaagat	14	7	8	12	0	1	2	1	0	0	2	2	2	2	2	3	2	2	2	3	2	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:69968643A>T	ENST00000508661.1	+	3	1016	c.989A>T	c.(988-990)cAg>cTg	p.Q330L	UGT2B7_ENST00000305231.7_Missense_Mutation_p.Q330L|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	330					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GCCCTGGCCCAGATCCCACAA	0.428																																					p.Q330L		.											.	UGT2B7-92	0			c.A989T						.						173	167	169					4																	69968643		2203	4300	6503	SO:0001583	missense	7364	exon3			TGGCCCAGATCCC	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"UDP glucuronosyltransferases"	12554	protein-coding gene	gene with protein product		600068	"UDP glycosyltransferase 2 family, polypeptide B7"			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.989A>T	4.37:g.69968643A>T	ENSP00000427659:p.Gln330Leu	Somatic	438	0		WXS	Illumina HiSeq	Phase_I	51	17	NM_001074	0	0	127	334	207	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		.	.	.	.	.	.	.	.	.	.	A	7.768	0.706788	0.15239	.	.	ENSG00000171234	ENST00000502942;ENST00000305231;ENST00000508661	T;T;T	0.61158	0.13;0.13;0.13	3.0	1.8	0.24995	.	0.000000	0.64402	U	0.000001	T	0.75125	0.3807	M	0.93898	3.47	0.22961	N	0.998502	P;P	0.47545	0.875;0.897	P;P	0.59424	0.857;0.657	T	0.66097	-0.6008	9	.	.	.	.	6.2555	0.20872	0.8699:0.0:0.1301:0.0	.	330;330	E9PBP8;P16662	.;UD2B7_HUMAN	L	81;330;330	ENSP00000426206:Q81L;ENSP00000304811:Q330L;ENSP00000427659:Q330L	.	Q	+	2	0	UGT2B7	70003232	1.000000	0.71417	0.097000	0.21041	0.105000	0.19272	6.429000	0.73387	0.370000	0.24538	0.477000	0.44152	CAG	.		0.428	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		T	69968643	A	T	69968643	3	4	50	1	0	0	0	0	1	0	0	0	16995	188	7	5	999	5	UGT2B7	4	69968643	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	30643611	69968643	121185633	32	4589											
SULT1E1	6783	hgsc.bcm.edu	37	chr4	70713508	70713508	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tttataccaggaaccataagGaactaaaattagagagaaaa	21	8	7	5	0	0	2	0	0	0	2	0	5	0	4	2	2	3	0	2	2	10	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:70713508G>C	ENST00000226444.3	-	6	611	c.499C>G	c.(499-501)Cct>Gct	p.P167A		NM_005420.2	NP_005411.1	P49888	ST1E1_HUMAN	sulfotransferase family 1E, estrogen-preferring, member 1	167					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	estrone sulfotransferase activity (GO:0004304)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid binding (GO:0005496)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10					Acetaminophen(DB00316)|Cyclizine(DB01176)	GAACCATAAGGAACTAAAATT	0.338																																					p.P167A		.											.	SULT1E1-91	0			c.C499G						.						70	71	71					4																	70713508		2203	4299	6502	SO:0001583	missense	6783	exon6			CATAAGGAACTAA	BC027956	CCDS3531.1	4q13.1	2008-02-05	2004-02-06	2004-02-04	ENSG00000109193	ENSG00000109193	2.8.2.4	"Sulfotransferases, cytosolic"	11377	protein-coding gene	gene with protein product		600043	"sulfotransferase, estrogen-preferring"	STE		7961757	Standard	NM_005420		Approved	EST	uc003heo.3	P49888	OTTHUMG00000129403	ENST00000226444.3:c.499C>G	4.37:g.70713508G>C	ENSP00000226444:p.Pro167Ala	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_005420	0	0	0	0	0	Q8N6X5	Missense_Mutation	SNP	ENST00000226444.3	37	CCDS3531.1	.	.	.	.	.	.	.	.	.	.	G	0.568	-0.842210	0.02671	.	.	ENSG00000109193	ENST00000226444	D	0.81739	-1.53	4.21	4.21	0.49690	Sulfotransferase domain (1);	0.243367	0.36200	N	0.002727	T	0.64692	0.2621	N	0.21448	0.665	0.34331	D	0.687687	B	0.13145	0.007	B	0.11329	0.006	T	0.63743	-0.6568	9	.	.	.	.	8.1688	0.31243	0.1058:0.0:0.8942:0.0	.	167	P49888	ST1E1_HUMAN	A	167	ENSP00000226444:P167A	.	P	-	1	0	SULT1E1	70748097	0.001000	0.12720	1.000000	0.80357	0.958000	0.62258	-0.134000	0.10436	2.631000	0.89168	0.650000	0.86243	CCT	.		0.338	SULT1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251559.1	NM_005420		C	70713508	G	C	70713508	3	2	50	1	0	0	0	0	1	0	0	0	15412	1174	41	4	397	4	SULT1E1	4	70713508	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	744865	70713508	120440768	33	4590											
ANTXR2	118429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	80992809	80992809	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttgccacactcccagacCtgaaagatgaaattgaactg	14	10	7	10	0	0	5	0	3	0	2	1	5	1	5	3	0	2	0	3	0	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:80992809C>A	ENST00000307333.7	-	2	155		c.e2-1		ANTXR2_ENST00000404191.1_Splice_Site|ANTXR2_ENST00000295465.4_Splice_Site|ANTXR2_ENST00000403729.2_Splice_Site|ANTXR2_ENST00000346652.6_Splice_Site	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2						reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						ACTCCCAGACCTGAAAGATGA	0.383									Juvenile Hyaline Fibromatosis																												.		.											.	ANTXR2-23	0			c.153-1G>T						.						71	71	71					4																	80992809		1839	4093	5932	SO:0001630	splice_region_variant	118429	exon3	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	CCAGACCTGAAAG	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.153-1G>T	4.37:g.80992809C>A		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	79	21	NM_058172	0	0	0	0	0	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Splice_Site	SNP	ENST00000307333.7	37	CCDS47086.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826045	0.50739	.	.	ENSG00000163297	ENST00000403729;ENST00000346652;ENST00000307333;ENST00000295465	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5222	0.84320	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANTXR2	81211833	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.415000	0.66411	2.642000	0.89623	0.563000	0.77884	.	.		0.383	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172	Intron	A	80992809	C	A	80992809	5	1	50	1	0	0	0	0	0	0	1	0	712	695	24	4	1420	4	ANTXR2	4	80992809	Splice_Site	SNP	C	TCGA-B9-4116-01A-01D-1252-08	10279301	80992809	110161467	34	4591											
C4orf37	285555	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	98865112	98865112	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcatatttgttagtcaagTtaggtaattcatcagaaatt	14	15	7	5	0	3	1	3	0	0	1	3	1	3	1	0	1	1	4	0	1	6	7			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:98865112T>G	ENST00000295268.3	-	8	1069	c.980A>C	c.(979-981)aAc>aCc	p.N327T		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	327																	GTTAGTCAAGTTAGGTAATTC	0.323																																					p.N327T		.											.	.	0			c.A980C						.						130	127	128					4																	98865112		2203	4300	6503	SO:0001583	missense	285555	exon8			GTCAAGTTAGGTA	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.980A>C	4.37:g.98865112T>G	ENSP00000295268:p.Asn327Thr	Somatic	329	0		WXS	Illumina HiSeq	Phase_I	29	9	NM_174952	0	0	0	0	0		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	T	4.606	0.112544	0.08831	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.48201	0.82;2.71	4.0	4.0	0.46444	.	1.315340	0.04739	N	0.422540	T	0.38878	0.1057	L	0.29908	0.895	0.25587	N	0.986734	B	0.33694	0.421	B	0.29862	0.108	T	0.32375	-0.9909	10	0.59425	D	0.04	-9.3556	9.6357	0.39806	0.0:0.0:0.0:1.0	.	327	Q8N412	CD037_HUMAN	T	41;327	ENSP00000428346:N41T;ENSP00000295268:N327T	ENSP00000295268:N327T	N	-	2	0	C4orf37	99084135	0.997000	0.39634	0.663000	0.29738	0.803000	0.45373	2.716000	0.47219	2.041000	0.60428	0.456000	0.33151	AAC	.		0.323	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		G	98865112	T	G	98865112	3	3	50	1	0	0	0	0	1	0	0	0	2273	1725	60	5	415	5	C4orf37	4	98865112	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	17872303	98865112	92289164	35	4592											
NPY2R	4887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	156136059	156136059	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccacttttgccaatccccTtctctatggctggatgaaca	8	13	6	14	0	1	1	0	1	1	0	4	2	3	2	4	2	2	1	4	2	3	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:156136059T>G	ENST00000329476.3	+	2	1457	c.968T>G	c.(967-969)cTt>cGt	p.L323R	NPY2R_ENST00000506608.1_Missense_Mutation_p.L323R	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	323					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	GCCAATCCCCTTCTCTATGGC	0.527																																					p.L323R		.											.	NPY2R-523	0			c.T968G						.						116	97	103					4																	156136059		2203	4300	6503	SO:0001583	missense	4887	exon2			ATCCCCTTCTCTA	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"GPCR / Class A : Neuropeptide receptors : Y"	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.968T>G	4.37:g.156136059T>G	ENSP00000332591:p.Leu323Arg	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	247	84	NM_000910	0	0	0	0	0	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	37	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979528	0.74360	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.56275	0.47;0.47	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.285408	0.32970	N	0.005436	T	0.78342	0.4268	M	0.93939	3.475	0.80722	D	1	P	0.51240	0.943	D	0.63113	0.911	D	0.84029	0.0358	10	0.72032	D	0.01	.	15.2138	0.73247	0.0:0.0:0.0:1.0	.	323	P49146	NPY2R_HUMAN	R	323	ENSP00000332591:L323R;ENSP00000426366:L323R	ENSP00000332591:L323R	L	+	2	0	NPY2R	156355509	0.998000	0.40836	0.885000	0.34714	0.928000	0.56348	8.040000	0.89188	2.189000	0.69895	0.523000	0.50628	CTT	.		0.527	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		G	156136059	T	G	156136059	3	3	50	1	0	0	0	0	1	0	0	0	10635	1609	56	5	970	5	NPY2R	4	156136059	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	57270947	156136059	35018217	36	4593											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187549407	187549407	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aacggctgccgattcataaaCccgccctttgtaggaggaag	11	8	11	11	3	1	0	1	0	0	0	1	3	1	2	3	3	3	2	3	3	5	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:187549407C>A	ENST00000441802.2	-	9	4920	c.4711G>T	c.(4711-4713)Gtt>Ttt	p.V1571F		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1571	Cadherin 14. {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						GATTCATAAACCCGCCCTTTG	0.527										HNSCC(5;0.00058)																											p.V1571F	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.G4711T						.						46	48	47					4																	187549407		2090	4237	6327	SO:0001583	missense	2195	exon9			CATAAACCCGCCC	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.4711G>T	4.37:g.187549407C>A	ENSP00000406229:p.Val1571Phe	Somatic	50	2		WXS	Illumina HiSeq	Phase_I	90	34	NM_005245	0	0	19	31	12		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.114458	0.77210	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.57436	0.4	5.49	5.49	0.81192	Cadherin (3);Cadherin-like (1);	0.056071	0.64402	D	0.000001	T	0.77191	0.4094	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79584	-0.1743	10	0.72032	D	0.01	.	19.5755	0.95441	0.0:1.0:0.0:0.0	.	1571	Q14517	FAT1_HUMAN	F	1571;1570	ENSP00000406229:V1571F	ENSP00000260147:V1570F	V	-	1	0	FAT1	187786401	1.000000	0.71417	0.925000	0.36789	0.201000	0.24016	7.651000	0.83577	2.865000	0.98341	0.655000	0.94253	GTT	.		0.527	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187549407	C	A	187549407	3	1	50	1	0	0	0	0	1	0	0	0	5708	507	18	4	9131	4	FAT1	4	187549407	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	31413348	187549407	3604869	37	4594											
CDH9	1007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	26906161	26906161	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcccatctggccacccatgtCtttggcctgtataacaacct	8	12	6	15	0	2	0	0	0	2	0	3	0	3	0	5	2	2	1	5	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:26906161C>T	ENST00000231021.4	-	5	890	c.718G>A	c.(718-720)Gac>Aac	p.D240N		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	240	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D240N(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CCACCCATGTCTTTGGCCTGT	0.448																																					p.D240N	Melanoma(8;187 585 15745 40864 52829)	.											.	CDH9-99	1	Substitution - Missense(1)	lung(1)	c.G718A						.						232	208	216					5																	26906161		2203	4300	6503	SO:0001583	missense	1007	exon5			CCATGTCTTTGGC	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.718G>A	5.37:g.26906161C>T	ENSP00000231021:p.Asp240Asn	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	54	12	NM_016279	0	0	1	2	1	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553655	0.96501	.	.	ENSG00000113100	ENST00000231021	T	0.79940	-1.32	5.6	5.6	0.85130	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92548	0.7633	M	0.93939	3.475	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.93866	0.7158	9	.	.	.	.	18.5289	0.90984	0.0:1.0:0.0:0.0	.	240	Q9ULB4	CADH9_HUMAN	N	240	ENSP00000231021:D240N	.	D	-	1	0	CDH9	26941918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.750000	0.85110	2.802000	0.96397	0.650000	0.86243	GAC	.		0.448	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26906161	C	T	26906161	3	4	50	1	0	0	0	0	1	0	0	0	3123	913	32	2	1683	2	CDH9	5	26906161	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08		26906161	154009099	38	4595											
ANKHD1	54882	hgsc.bcm.edu;broad.mit.edu	37	chr5	139908303	139908303	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggactgttttaccctcagaGtctgctggactagctactgc	7	12	11	11	0	2	1	1	0	1	1	2	3	2	3	1	2	5	3	1	2	3	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:139908303G>C	ENST00000360839.2	+	29	5926	c.5772G>C	c.(5770-5772)gaG>gaC	p.E1924D	ANKHD1_ENST00000544120.1_Missense_Mutation_p.E307D|ANKHD1_ENST00000297183.6_Missense_Mutation_p.E1924D|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.E1924D|SNORD45_ENST00000363181.1_RNA	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1924						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACCCTCAGAGTCTGCTGGAC	0.488																																					p.E1924D		.											.	ANKHD1-185	0			c.G5772C						.						81	77	78					5																	139908303		2203	4300	6503	SO:0001583	missense	54882	exon29			CTCAGAGTCTGCT	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.5772G>C	5.37:g.139908303G>C	ENSP00000354085:p.Glu1924Asp	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	54	4	NM_017747	0	0	70	70	0	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.835|9.835	1.189371|1.189371	0.21954|0.21954	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000536646;ENST00000433049;ENST00000544120;ENST00000532219|ENST00000435794;ENST00000432301	T;T;T;T;T;T|.	0.65916|.	-0.14;-0.18;1.89;1.89;1.48;-0.18|.	4.98|4.98	1.47|1.47	0.22746|0.22746	.|.	0.238205|.	0.41396|.	D|.	0.000887|.	T|T	0.33789|0.33789	0.0875|0.0875	L|L	0.34521|0.34521	1.04|1.04	0.25479|0.25479	N|N	0.987752|0.987752	B;P;B;P;B;B|.	0.42409|.	0.184;0.779;0.28;0.462;0.231;0.231|.	B;B;B;B;B;B|.	0.35510|.	0.055;0.204;0.118;0.121;0.054;0.054|.	T|T	0.25152|0.25152	-1.0140|-1.0140	10|5	0.19590|.	T|.	0.45|.	.|.	8.8813|8.8813	0.35376|0.35376	0.3024:0.0:0.6976:0.0|0.3024:0.0:0.6976:0.0	.|.	307;354;307;1924;1924;1924|.	Q8IWG5;Q9H059;F6WFL0;E9PF56;Q8IWZ2;Q8IWZ3|.	.;.;.;.;.;ANKH1_HUMAN|.	D|L	1924;1924;1924;580;359;446;307;1924|415;375	ENSP00000354085:E1924D;ENSP00000297183:E1924D;ENSP00000393204:E580D;ENSP00000390034:E446D;ENSP00000437687:E307D;ENSP00000432016:E1924D|.	ENSP00000432016:E1924D|.	E|V	+|+	3|1	2|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139888487|139888487	0.997000|0.997000	0.39634|0.39634	0.996000|0.996000	0.52242|0.52242	0.985000|0.985000	0.73830|0.73830	0.224000|0.224000	0.17738|0.17738	0.419000|0.419000	0.25927|0.25927	0.650000|0.650000	0.86243|0.86243	GAG|GTC	.		0.488	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139908303	G	C	139908303	3	2	50	1	0	0	0	0	1	0	0	0	628	1020	36	4	5992	4	ANKHD1	5	139908303	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	113002142	139908303	41006957	39	4596											
PCDHA4	56144	hgsc.bcm.edu;broad.mit.edu	37	chr5	140186954	140186954	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctggcggagctggtgcCgcgcctgttccgggtggcgt	2	8	20	11	5	0	0	0	0	0	0	1	2	1	2	3	6	3	3	3	6	0	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:140186954C>T	ENST00000530339.1	+	1	182	c.182C>T	c.(181-183)cCg>cTg	p.P61L	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.P61L|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.P61L	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCTGGTGCCGCGCCTGTTC	0.632																																					p.P61L		.											.	PCDHA4-96	0			c.C182T						.						44	50	48					5																	140186954		2200	4295	6495	SO:0001583	missense	56144	exon1			TGGTGCCGCGCCT	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"Cadherins / Protocadherins : Clustered"	8670	other	complex locus constituent	"ortholog of mouse CNR1, KIAA0345-like 10"	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.182C>T	5.37:g.140186954C>T	ENSP00000435300:p.Pro61Leu	Somatic	186	2		WXS	Illumina HiSeq	Phase_I	336	29	NM_031500	13	0	1	14	0	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	18.36	3.607643	0.66558	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.26660	1.72;1.72;1.72	4.73	4.73	0.59995	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.191976	0.25214	U	0.032282	T	0.40222	0.1108	M	0.66439	2.03	0.30870	N	0.732594	D;P;D	0.54964	0.969;0.938;0.966	P;B;P	0.49637	0.562;0.366;0.617	T	0.50355	-0.8838	10	0.72032	D	0.01	.	18.1393	0.89634	0.0:1.0:0.0:0.0	.	61;61;61	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	L	61	ENSP00000423470:P61L;ENSP00000349344:P61L;ENSP00000435300:P61L	ENSP00000349344:P61L	P	+	2	0	PCDHA4	140167138	0.002000	0.14202	1.000000	0.80357	0.910000	0.53928	1.293000	0.33353	2.369000	0.80426	0.461000	0.40582	CCG	.		0.632	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140186954	C	T	140186954	3	4	50	1	0	0	0	0	1	0	0	0	11552	652	23	1	184	1	PCDHA4	5	140186954	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	278651	140186954	40728306	40	4597											
PCDHA8	56140	hgsc.bcm.edu;broad.mit.edu	37	chr5	140221088	140221088	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctggcggagctggtgcCgcgcctgttccgggtggcgt	2	8	20	11	5	0	0	0	0	0	0	1	2	1	2	3	6	3	3	3	6	0	1	rs376513525	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:140221088C>T	ENST00000531613.1	+	1	182	c.182C>T	c.(181-183)cCg>cTg	p.P61L	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.P61L|PCDHA5_ENST00000529619.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCTGGTGCCGCGCCTGTTC	0.637																																					p.P61L		.											.	PCDHA8-92	0			c.C182T						.						38	50	46					5																	140221088		2203	4296	6499	SO:0001583	missense	56140	exon1			TGGTGCCGCGCCT	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.182C>T	5.37:g.140221088C>T	ENSP00000434655:p.Pro61Leu	Somatic	241	0		WXS	Illumina HiSeq	Phase_I	455	26	NM_031856	13	0	1	14	0	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.880274	0.72294	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.26660	1.72;1.72	3.95	3.95	0.45737	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.226637	0.22037	U	0.065506	T	0.30759	0.0775	M	0.72118	2.19	0.19775	N	0.999956	P;D	0.59357	0.938;0.985	B;B	0.40506	0.239;0.331	T	0.39583	-0.9607	10	0.87932	D	0	.	16.3451	0.83120	0.0:1.0:0.0:0.0	.	61;61	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	L	61	ENSP00000434655:P61L;ENSP00000367363:P61L	ENSP00000367363:P61L	P	+	2	0	PCDHA8	140201272	0.000000	0.05858	1.000000	0.80357	0.982000	0.71751	-0.108000	0.10857	1.905000	0.55150	0.557000	0.71058	CCG	.		0.637	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140221088	C	T	140221088	3	4	50	1	0	0	0	0	1	0	0	0	11556	652	23	1	184	1	PCDHA8	5	140221088	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	34134	140221088	40694172	41	4598											
MED7	9443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156565887	156565887	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcagcatccattggttcagTttttactctcattcctgctt	7	18	5	11	0	3	0	3	0	1	0	6	0	5	0	2	1	3	4	2	1	1	7			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:156565887T>G	ENST00000286317.5	-	2	937	c.556A>C	c.(556-558)Act>Cct	p.T186P	MED7_ENST00000420343.1_Missense_Mutation_p.T186P	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	186					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATTGGTTCAGTTTTTACTCTC	0.373																																					p.T186P		.											.	MED7-22	0			c.A556C						.						170	159	163					5																	156565887		2203	4300	6503	SO:0001583	missense	9443	exon2			GTTCAGTTTTTAC	AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868			2378	protein-coding gene	gene with protein product		605045	"cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa"	CRSP9		9989412	Standard	NM_004270		Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.556A>C	5.37:g.156565887T>G	ENSP00000286317:p.Thr186Pro	Somatic	267	0		WXS	Illumina HiSeq	Phase_I	121	45	NM_001100816	0	0	21	33	12		Missense_Mutation	SNP	ENST00000286317.5	37	CCDS4334.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.291433	0.40494	.	.	ENSG00000155868	ENST00000286317;ENST00000420343;ENST00000524289	.	.	.	5.81	1.99	0.26369	.	0.426120	0.27048	N	0.021196	T	0.36248	0.0960	L	0.52573	1.65	0.35094	D	0.764574	P	0.45634	0.863	B	0.41271	0.352	T	0.40327	-0.9569	9	0.27082	T	0.32	-13.3431	5.9577	0.19283	0.1123:0.1921:0.0:0.6956	.	186	O43513	MED7_HUMAN	P	186	.	ENSP00000286317:T186P	T	-	1	0	MED7	156498465	0.995000	0.38212	0.985000	0.45067	0.991000	0.79684	0.479000	0.22228	0.098000	0.17522	0.533000	0.62120	ACT	.		0.373	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252567.2	NM_004270		G	156565887	T	G	156565887	3	3	50	1	0	0	0	0	1	0	0	0	9477	1725	60	5	149	5	MED7	5	156565887	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	16344799	156565887	24349373	42	4599											
SLC25A27	9481	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	46630133	46630133	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatcagtcattggagggaTgatggctggtgttattggcc	9	12	15	5	0	2	1	2	1	0	0	2	4	2	3	1	5	0	2	1	5	2	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr6:46630133T>C	ENST00000371347.5	+	4	656	c.404T>C	c.(403-405)aTg>aCg	p.M135T	SLC25A27_ENST00000604908.1_3'UTR|SLC25A27_ENST00000452689.2_Missense_Mutation_p.M49T|SLC25A27_ENST00000411689.2_Missense_Mutation_p.M135T	NM_001204051.1|NM_004277.4	NP_001190980.1|NP_004268.3	O95847	UCP4_HUMAN	solute carrier family 25, member 27	135					cellular triglyceride homeostasis (GO:0035356)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|negative regulation of mitochondrial membrane potential (GO:0010917)|neuron death (GO:0070997)|positive regulation of cell proliferation (GO:0008284)|regulation of glucose import (GO:0046324)|transport (GO:0006810)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)				central_nervous_system(1)|kidney(1)|lung(4)|prostate(1)|urinary_tract(1)	8			Lung(136;0.192)			ATTGGAGGGATGATGGCTGGT	0.388																																					p.M135T		.											.	SLC25A27-90	0			c.T404C						.						97	92	94					6																	46630133		1856	4096	5952	SO:0001583	missense	9481	exon4			GAGGGATGATGGC	AK090871	CCDS43470.1, CCDS56431.1	6p12.3	2013-05-22			ENSG00000153291	ENSG00000153291		"Solute carriers"	21065	protein-coding gene	gene with protein product		613725				10025957, 10772343	Standard	NM_004277		Approved	UCP4, FLJ33552	uc003oyh.3	O95847	OTTHUMG00000014786	ENST00000371347.5:c.404T>C	6.37:g.46630133T>C	ENSP00000360398:p.Met135Thr	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	42	11	NM_001204051	0	0	11	15	4	F5GWR4|Q5VTS9|Q8N518	Missense_Mutation	SNP	ENST00000371347.5	37	CCDS43470.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.544149	0.45280	.	.	ENSG00000153291	ENST00000371347;ENST00000411689;ENST00000452689;ENST00000425120	T;T;T	0.78816	-1.21;-1.21;-1.21	5.48	4.31	0.51392	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.66426	0.2788	M	0.64676	1.99	0.46927	D	0.999258	B;B;B;B	0.29805	0.142;0.257;0.257;0.101	B;B;B;B	0.36030	0.216;0.216;0.216;0.062	T	0.71163	-0.4673	10	0.49607	T	0.09	-8.7623	9.9319	0.41528	0.0:0.0835:0.0:0.9164	.	49;135;135;135	B4DZG4;Q5VTS9;O95847;F5GWR4	.;.;UCP4_HUMAN;.	T	135;135;49;65	ENSP00000360398:M135T;ENSP00000412024:M135T;ENSP00000412223:M49T	ENSP00000360398:M135T	M	+	2	0	SLC25A27	46738092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.266000	0.58871	2.089000	0.63090	0.460000	0.39030	ATG	.		0.388	SLC25A27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040791.1	NM_004277		C	46630133	T	C	46630133	3	2	50	1	0	0	0	0	1	0	0	0	14522	1464	51	3	418	3	SLC25A27	6	46630133	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08		46630133	124484934	43	4600											
SLC22A16	85413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	110757106	110757106	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagataaatgaggccaaatGctgccccgatggcaaatttt	15	9	9	8	1	0	2	0	1	0	1	0	3	0	2	3	2	2	2	3	2	5	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr6:110757106G>A	ENST00000368919.3	-	6	1436	c.1370C>T	c.(1369-1371)gCa>gTa	p.A457V	SLC22A16_ENST00000439654.1_Missense_Mutation_p.A457V|SLC22A16_ENST00000330550.4_Missense_Mutation_p.A423V	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	457					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GAGGCCAAATGCTGCCCCGAT	0.363																																					p.A457V		.											.	SLC22A16-91	0			c.C1370T						.						102	99	100					6																	110757106		2203	4300	6503	SO:0001583	missense	85413	exon6			CCAAATGCTGCCC		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"Solute carriers"	20302	protein-coding gene	gene with protein product		608276	"solute carrier family 22 (organic cation transporter), member 16"			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1370C>T	6.37:g.110757106G>A	ENSP00000357915:p.Ala457Val	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	125	39	NM_033125	0	0	0	0	0	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095193	0.56075	.	.	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	4.75	0.519	0.17035	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.355691	0.31809	N	0.007039	T	0.81814	0.4902	L	0.56124	1.755	0.80722	D	1	B;B	0.31413	0.322;0.275	B;B	0.37550	0.253;0.164	T	0.76924	-0.2779	10	0.72032	D	0.01	.	8.3956	0.32555	0.3527:0.0:0.6473:0.0	.	457;423	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	V	457;374;423;457	ENSP00000357915:A457V;ENSP00000395642:A374V;ENSP00000328583:A423V;ENSP00000408799:A457V	ENSP00000328583:A423V	A	-	2	0	SLC22A16	110863799	0.999000	0.42202	0.000000	0.03702	0.591000	0.36615	2.826000	0.48104	-0.101000	0.12219	-0.339000	0.08088	GCA	.		0.363	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		A	110757106	G	A	110757106	3	1	50	1	0	0	0	0	1	0	0	0	14479	1319	46	2	375	2	SLC22A16	6	110757106	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	64126973	110757106	60357961	44	4601											
MAP7	9053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	136709627	136709627	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcctttccattgtgcgccGtacaacagcttcgtggcgtt	5	13	10	13	4	0	0	0	0	0	0	3	0	2	0	3	1	4	4	3	1	2	5	rs369036954	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr6:136709627G>A	ENST00000354570.3	-	5	840	c.430C>T	c.(430-432)Cgg>Tgg	p.R144W	MAP7_ENST00000438100.2_Missense_Mutation_p.R166W|MAP7_ENST00000432797.2_De_novo_Start_OutOfFrame|MAP7_ENST00000544465.1_Missense_Mutation_p.R129W|MAP7_ENST00000454590.1_Missense_Mutation_p.R166W	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	144					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		ATTGTGCGCCGTACAACAGCT	0.498													G|||	2	0.000399361	0.0015	0	5008	,	,		18906	0		0	False		,,,				2504	0				p.R166W		.											.	MAP7-90	0			c.C496T						.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,,,,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	203	167	179		496,496,496,496,385,430,,,,430	1.8	0	6		179	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,intron,utr-5,utr-5,missense	MAP7	NM_001198608.1,NM_001198609.1,NM_001198611.1,NM_001198614.1,NM_001198615.1,NM_001198616.1,NM_001198617.1,NM_001198618.1,NM_001198619.1,NM_003980.4	101,101,101,101,101,101,,,,101	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,,probably-damaging	166/772,166/780,166/735,166/772,129/735,144/713,,,,144/750	136709627	2,13004	2203	4300	6503	SO:0001583	missense	9053	exon5			TGCGCCGTACAAC	X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.430C>T	6.37:g.136709627G>A	ENSP00000346581:p.Arg144Trp	Somatic	237	1		WXS	Illumina HiSeq	Phase_I	137	46	NM_001198611	0	0	16	30	14	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Missense_Mutation	SNP	ENST00000354570.3	37	CCDS5178.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.448214	0.43429	4.54E-4	0.0	ENSG00000135525	ENST00000354570;ENST00000454590;ENST00000544465;ENST00000438100	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	6.06	1.84	0.25277	.	0.000000	0.51477	D	0.000099	T	0.29945	0.0749	M	0.83953	2.67	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.998;0.999;0.999	T	0.45848	-0.9233	10	0.87932	D	0	-14.4911	15.6295	0.76893	0.0:0.0:0.429:0.571	.	166;166;129;166;166;144;144	B7Z290;B7ZB64;F5H1E2;E9PCP3;B7Z400;Q14244-2;Q14244	.;.;.;.;.;.;MAP7_HUMAN	W	144;166;129;166	ENSP00000346581:R144W;ENSP00000414712:R166W;ENSP00000445737:R129W;ENSP00000400790:R166W	ENSP00000346581:R144W	R	-	1	2	MAP7	136751320	0.998000	0.40836	0.049000	0.19019	0.644000	0.38419	2.739000	0.47409	0.849000	0.35215	0.655000	0.94253	CGG	.		0.498	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		A	136709627	G	A	136709627	3	1	50	1	0	0	0	0	1	0	0	0	9291	1144	40	1	1875	1	MAP7	6	136709627	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	25952521	136709627	34405440	45	4602											
SYNJ2	8871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	158449969	158449969	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgggggtgttctatttctcAtggccaaacgatgggtctcg	6	13	13	9	3	3	0	1	0	3	0	6	1	3	0	1	4	1	1	1	4	2	3	rs140060886		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr6:158449969A>T	ENST00000355585.4	+	3	471	c.396A>T	c.(394-396)tcA>tcT	p.S132S	SYNJ2_ENST00000449859.2_Silent_p.S81S|SYNJ2_ENST00000367121.3_Silent_p.S132S|SYNJ2_ENST00000367122.2_Silent_p.S132S	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	132	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TCTATTTCTCATGGCCAAACG	0.542																																					p.S132S		.											.	SYNJ2-227	0			c.A396T						.						66	67	66					6																	158449969		2203	4300	6503	SO:0001819	synonymous_variant	8871	exon3			TTTCTCATGGCCA	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.396A>T	6.37:g.158449969A>T		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	235	70	NM_003898	0	0	2	2	0	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	A	4.185	0.032976	0.08101	.	.	ENSG00000078269	ENST00000367113	.	.	.	4.62	-9.25	0.00666	.	.	.	.	.	T	0.35219	0.0924	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68868	-0.5295	4	.	.	.	.	9.0699	0.36486	0.2544:0.577:0.1011:0.0675	.	.	.	.	L	107	.	.	H	+	2	0	SYNJ2	158369957	0.008000	0.16893	0.903000	0.35520	0.321000	0.28281	-1.071000	0.03437	1.946000	0.56461	0.533000	0.62120	CAT	A|1.000;G|0.000		0.542	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158449969	A	T	158449969	2	4	50	1	0	0	0	0	0	0	0	1	15485	204	8	5		5	SYNJ2	6	158449969	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	21740342	158449969	12665098	46	4603											
DGKB	1607	broad.mit.edu	37	chr7	14712573	14712573	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagtaccactggacagattGttgtgggtggtaaaatatgg	11	11	13	6	0	0	1	0	0	0	1	0	2	0	2	2	4	1	3	2	4	4	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:14712573G>T	ENST00000403951.2	-	13	1534	c.1115C>A	c.(1114-1116)aCa>aAa	p.T372K	DGKB_ENST00000444700.2_Missense_Mutation_p.T365K|DGKB_ENST00000406247.3_Missense_Mutation_p.T372K|DGKB_ENST00000399322.3_Missense_Mutation_p.T372K|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000402815.1_Missense_Mutation_p.T372K|DGKB_ENST00000258767.5_Missense_Mutation_p.T372K|DGKB_ENST00000407950.1_Missense_Mutation_p.T365K			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	372					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TGGACAGATTGTTGTGGGTGG	0.383																																					p.T372K													.	DGKB-276	0			c.C1115A						.						92	90	91					7																	14712573		1866	4102	5968	SO:0001583	missense	1607	exon12			CAGATTGTTGTGG	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"EF-hand domain containing"	2850	protein-coding gene	gene with protein product		604070	"diacylglycerol kinase, beta (90kD)"	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.1115C>A	7.37:g.14712573G>T	ENSP00000385780:p.Thr372Lys	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_145695	0	0	0	0	0	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.286640	0.40494	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.79454	-1.16;-1.16;-1.16;-1.16;-1.16;-1.17;-1.27	5.77	5.77	0.91146	.	0.312306	0.34507	N	0.003915	T	0.73651	0.3614	L	0.40543	1.245	0.39165	D	0.962478	B;B;B;B	0.21309	0.032;0.016;0.016;0.054	B;B;B;B	0.25614	0.028;0.062;0.062;0.021	T	0.67875	-0.5557	10	0.30854	T	0.27	.	20.0007	0.97408	0.0:0.0:1.0:0.0	.	372;365;372;372	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	K	372;372;372;372;365;365;372	ENSP00000385780:T372K;ENSP00000382260:T372K;ENSP00000258767:T372K;ENSP00000384909:T372K;ENSP00000385031:T365K;ENSP00000388451:T365K;ENSP00000386066:T372K	ENSP00000258767:T372K	T	-	2	0	DGKB	14679098	0.995000	0.38212	0.946000	0.38457	0.998000	0.95712	5.461000	0.66699	2.726000	0.93360	0.650000	0.86243	ACA	.		0.383	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		T	14712573	G	T	14712573	3	4	50	1	0	0	0	0	1	0	0	0	4477	1377	48	4	1370	4	DGKB	7	14712573	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		14712573	144426090	47	4604											
NOD1	10392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	30475651	30475651	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgttctgctgcagggcccTcgcaaggctctttcctcctt	3	13	10	15	2	2	0	0	0	2	0	5	0	4	0	3	2	2	5	3	2	1	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:30475651T>A	ENST00000222823.4	-	11	3109	c.2584A>T	c.(2584-2586)Agg>Tgg	p.R862W		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	862					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						TGCAGGGCCCTCGCAAGGCTC	0.443																																					p.R862W		.											.	NOD1-229	0			c.A2584T						.						129	106	114					7																	30475651		2203	4300	6503	SO:0001583	missense	10392	exon11			GGGCCCTCGCAAG	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"Nucleotide-binding domain and leucine rich repeat containing"	16390	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1", "NLR family, CARD domain containing 1"	605980	"caspase recruitment domain family, member 4"	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.2584A>T	7.37:g.30475651T>A	ENSP00000222823:p.Arg862Trp	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	173	52	NM_006092	0	0	2	7	5	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	.	.	.	.	.	.	.	.	.	.	T	8.038	0.763254	0.15914	.	.	ENSG00000106100	ENST00000222823	T	0.55052	0.54	5.12	-1.83	0.07833	.	0.871180	0.09788	N	0.755710	T	0.39145	0.1067	L	0.49126	1.545	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36866	-0.9730	10	0.62326	D	0.03	.	1.2857	0.02050	0.1549:0.2137:0.3025:0.3289	.	862	Q9Y239	NOD1_HUMAN	W	862	ENSP00000222823:R862W	ENSP00000222823:R862W	R	-	1	2	NOD1	30442176	0.008000	0.16893	0.000000	0.03702	0.092000	0.18411	0.609000	0.24238	-0.810000	0.04375	-0.313000	0.08912	AGG	.		0.443	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			A	30475651	T	A	30475651	3	1	50	1	0	0	0	0	1	0	0	0	10542	1550	54	5	293	5	NOD1	7	30475651	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	15763078	30475651	128663012	48	4605											
EIF4H	7458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	73601993	73601993	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccagaaggagttgcccAcagagcccccctacacagca	12	4	10	15	0	0	2	0	0	0	2	0	3	0	3	5	1	5	3	5	1	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:73601993A>G	ENST00000265753.8	+	2	251	c.112A>G	c.(112-114)Aca>Gca	p.T38A	EIF4H_ENST00000495187.1_3'UTR|EIF4H_ENST00000353999.6_Missense_Mutation_p.T38A	NM_022170.1	NP_071496.1	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	38					cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|sexual reproduction (GO:0019953)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|lung(2)|prostate(1)	4						GGAGTTGCCCACAGAGCCCCC	0.527																																					p.T38A		.											.	EIF4H-90	0			c.A112G						.						93	91	92					7																	73601993		2203	4297	6500	SO:0001583	missense	7458	exon2			TTGCCCACAGAGC		CCDS5564.1, CCDS5565.1	7q11.23	2013-02-12	2006-11-27	2006-11-27	ENSG00000106682	ENSG00000106682		"RNA binding motif (RRM) containing"	12741	protein-coding gene	gene with protein product		603431	"Williams-Beuren syndrome chromosome region 1"	WBSCR1		9516461, 15078951	Standard	NM_022170		Approved	WSCR1, KIAA0038	uc003uad.1	Q15056	OTTHUMG00000023025	ENST00000265753.8:c.112A>G	7.37:g.73601993A>G	ENSP00000265753:p.Thr38Ala	Somatic	296	0		WXS	Illumina HiSeq	Phase_I	422	133	NM_022170	0	0	44	80	35	A8K3R1|D3DXF6|D3DXF8	Missense_Mutation	SNP	ENST00000265753.8	37	CCDS5564.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053342	0.55218	.	.	ENSG00000106682	ENST00000265753;ENST00000353999	T;T	0.74002	-0.8;-0.8	5.05	5.05	0.67936	Nucleotide-binding, alpha-beta plait (1);	0.118143	0.64402	D	0.000020	T	0.72020	0.3409	L	0.55990	1.75	0.54753	D	0.999988	B;B;B;B	0.20368	0.012;0.012;0.044;0.006	B;B;B;B	0.28916	0.096;0.096;0.047;0.054	T	0.70310	-0.4907	10	0.49607	T	0.09	-15.2629	13.9042	0.63823	1.0:0.0:0.0:0.0	.	38;38;38;38	B4DMV6;Q75MU2;Q15056-2;Q15056	.;.;.;IF4H_HUMAN	A	38	ENSP00000265753:T38A;ENSP00000265754:T38A	ENSP00000265753:T38A	T	+	1	0	EIF4H	73239929	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.887000	0.63156	2.029000	0.59856	0.379000	0.24179	ACA	.		0.527	EIF4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252375.2	NM_022170		G	73601993	A	G	73601993	3	3	50	1	0	0	0	0	1	0	0	0	5052	159	6	3	118	3	EIF4H	7	73601993	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	43126342	73601993	85536670	49	4606											
POR	5447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	75615481	75615481	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacccttggccccaggtctAcgtccagcacctgctaaagc	8	7	8	18	1	1	0	0	0	1	0	2	0	2	0	6	2	4	2	6	2	3	3	rs72557954		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:75615481A>G	ENST00000461988.1	+	15	1925	c.1820A>G	c.(1819-1821)tAc>tGc	p.Y607C	POR_ENST00000545601.1_Missense_Mutation_p.Y415C|POR_ENST00000419840.1_Intron|POR_ENST00000394893.1_Missense_Mutation_p.Y607C|POR_ENST00000439269.1_Missense_Mutation_p.Y345C|TMEM120A_ENST00000338761.4_RNA|POR_ENST00000450476.1_Missense_Mutation_p.Y506C|TMEM120A_ENST00000493111.2_RNA	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	604					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	CCCCAGGTCTACGTCCAGCAC	0.632																																					p.Y607C		.											.	POR-23	0			c.A1820G	GRCh37	CM087168	POR	M	rs72557954	.						43	56	52					7																	75615481		2106	4224	6330	SO:0001583	missense	5447	exon15			AGGTCTACGTCCA	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1820A>G	7.37:g.75615481A>G	ENSP00000419970:p.Tyr607Cys	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	41	19	NM_000941	0	0	0	0	0	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	37	CCDS5579.1	.	.	.	.	.	.	.	.	.	.	A	11.75	1.731367	0.30684	.	.	ENSG00000127948	ENST00000461988;ENST00000394893;ENST00000545601;ENST00000450476;ENST00000439269	D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57	3.59	3.59	0.41128	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.127712	0.53938	D	0.000041	D	0.94512	0.8233	H	0.99336	4.52	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95784	0.8819	10	0.87932	D	0	-33.1823	12.3556	0.55174	1.0:0.0:0.0:0.0	.	604;506;415;613	P16435;E7EVY7;F5H468;Q59ED7	NCPR_HUMAN;.;.;.	C	607;607;415;506;345	ENSP00000419970:Y607C;ENSP00000378355:Y607C;ENSP00000446149:Y415C;ENSP00000416572:Y506C;ENSP00000412490:Y345C	ENSP00000378355:Y607C	Y	+	2	0	POR	75453417	1.000000	0.71417	0.956000	0.39512	0.099000	0.18886	5.702000	0.68332	1.863000	0.54032	0.459000	0.35465	TAC	A|0.999;G|0.001		0.632	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		G	75615481	A	G	75615481	3	3	50	1	0	0	0	0	1	0	0	0	12283	391	14	3	1874	3	POR	7	75615481	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	2013488	75615481	83523182	50	4607											
BAIAP2L1	55971	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	97933661	97933661	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctattctcagacaagttcacGgtgctgatgcttctcactgg	8	13	9	11	1	3	2	3	1	2	1	5	2	3	2	0	2	2	3	0	2	2	4	rs555687728		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:97933661G>A	ENST00000005260.8	-	12	1484	c.1269C>T	c.(1267-1269)acC>acT	p.T423T		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	423					filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.T423T(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			ACAAGTTCACGGTGCTGATGC	0.537													G|||	1	0.000199681	0	0	5008	,	,		18777	0		0	False		,,,				2504	0.001				p.T423T		.											.	BAIAP2L1-91	1	Substitution - coding silent(1)	breast(1)	c.C1269T						.						119	99	105					7																	97933661		2203	4300	6503	SO:0001819	synonymous_variant	55971	exon12			GTTCACGGTGCTG	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1269C>T	7.37:g.97933661G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	245	50	NM_018842	0	0	37	48	11	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			.		0.537	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		A	97933661	G	A	97933661	2	1	50	1	0	0	0	0	0	0	0	1	1303	1103	39	1		1	BAIAP2L1	7	97933661	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	22318180	97933661	61205002	51	4608											
POLR2J	5439	hgsc.bcm.edu;broad.mit.edu	37	chr7	102119282	102119282	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cgccctcgaagagcaagaacGactcgaaggctggaggggcg	11	3	16	11	5	0	2	0	0	0	2	2	6	0	3	1	4	2	2	1	4	4	0	rs532470326	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:102119282G>C	ENST00000292614.5	-	1	72	c.26C>G	c.(25-27)tCg>tGg	p.S9W	AC093668.3_ENST00000607525.1_RNA|POLR2J_ENST00000393794.3_Missense_Mutation_p.S9W	NM_006234.4	NP_006225.1	P52435	RPB11_HUMAN	polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa	9					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|LRR domain binding (GO:0030275)			pancreas(2)	2						GAGCAAGAACGACTCGAAGGC	0.682											OREG0018232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3	0.000599042	0.0023	0	5008	,	,		9429	0		0	False		,,,				2504	0				p.S9W		.											.	POLR2J-91	0			c.C26G						.						17	22	20					7																	102119282		1948	3904	5852	SO:0001583	missense	5439	exon1			AAGAACGACTCGA	X98433	CCDS5724.1	7q11.2	2013-01-21	2002-08-29		ENSG00000005075	ENSG00000005075		"RNA polymerase subunits"	9197	protein-coding gene	gene with protein product		604150	"polymerase (RNA) II (DNA directed) polypeptide J (13.3kD)"				Standard	XM_005250452		Approved	RPB11, hRPB14, RPB11A, RPB11m, POLR2J1	uc003uzp.1	P52435	OTTHUMG00000150387	ENST00000292614.5:c.26C>G	7.37:g.102119282G>C	ENSP00000292614:p.Ser9Trp	Somatic	95	2	1364	WXS	Illumina HiSeq	Phase_I	333	18	NM_006234	0	0	1346	1414	68	A5D6V8|O43375	Missense_Mutation	SNP	ENST00000292614.5	37	CCDS5724.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624348	0.87560	.	.	ENSG00000005075	ENST00000292614;ENST00000393794	D;D	0.92752	-3.1;-3.1	5.59	5.59	0.84812	DNA-directed RNA polymerase, RBP11-like (1);	0.000000	0.85682	D	0.000000	D	0.95796	0.8632	M	0.91090	3.175	0.80722	D	1	D	0.69078	0.997	P	0.53809	0.735	D	0.96375	0.9277	10	0.66056	D	0.02	-9.1512	17.0873	0.86614	0.0:0.0:1.0:0.0	.	9	P52435	RPB11_HUMAN	W	9	ENSP00000292614:S9W;ENSP00000377383:S9W	ENSP00000292614:S9W	S	-	2	0	POLR2J	101906287	1.000000	0.71417	1.000000	0.80357	0.455000	0.32408	7.941000	0.87700	2.647000	0.89833	0.555000	0.69702	TCG	.		0.682	POLR2J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317913.1	NM_006234		C	102119282	G	C	102119282	3	2	50	1	0	0	0	0	1	0	0	0	12249	1059	37	4	343	4	POLR2J	7	102119282	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	4185621	102119282	57019381	52	4609											
ANKRD7	56311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	117879989	117879989	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccacaattcactgcgagcCatggaaagaagaaacatgct	16	6	8	11	1	1	2	1	0	0	2	1	4	1	3	2	1	4	1	2	1	4	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:117879989C>A	ENST00000265224.4	+	6	894	c.739C>A	c.(739-741)Cat>Aat	p.H247N	ANKRD7_ENST00000417525.1_Silent_p.A192A|ANKRD7_ENST00000433239.1_Missense_Mutation_p.H194N|ANKRD7_ENST00000477532.1_3'UTR|ANKRD7_ENST00000357099.4_Missense_Mutation_p.H267N	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	247					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						CACTGCGAGCCATGGAAAGAA	0.338																																					p.H247N		.											.	ANKRD7-90	0			c.C739A						.						95	90	92					7																	117879989		1874	4112	5986	SO:0001583	missense	56311	exon6			GCGAGCCATGGAA	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.739C>A	7.37:g.117879989C>A	ENSP00000265224:p.His247Asn	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	221	31	NM_019644	0	0	5	9	4	B4DYF5|Q96QN1|Q9UDM3	Missense_Mutation	SNP	ENST00000265224.4	37	CCDS43638.1	.	.	.	.	.	.	.	.	.	.	C	8.240	0.806672	0.16467	.	.	ENSG00000106013	ENST00000357099;ENST00000265224;ENST00000433239	T;T;T	0.39787	1.07;1.18;1.06	3.96	-7.92	0.01160	.	7.917730	0.01487	U	0.016939	T	0.22551	0.0544	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08722	-1.0708	10	0.42905	T	0.14	-2.3393	0.7429	0.00977	0.3457:0.1668:0.1118:0.3758	.	247	Q92527	ANKR7_HUMAN	N	267;247;194	ENSP00000349612:H267N;ENSP00000265224:H247N;ENSP00000388473:H194N	ENSP00000265224:H247N	H	+	1	0	ANKRD7	117667225	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.364000	0.07583	-2.334000	0.00630	-2.920000	0.00090	CAT	.		0.338	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		A	117879989	C	A	117879989	3	1	50	1	0	0	0	0	1	0	0	0	686	594	21	4	761	4	ANKRD7	7	117879989	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	15760707	117879989	41258674	53	4610											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	7	4	17	13	6	2	0	1	0	1	0	2	4	2	1	2	6	0	0	2	6	0	1	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		.											.	PODXL-136	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	7.37:g.131241029G>C		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001018111	0	0	0	0	0	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	50	1	0	0	0	0	0	0	0	1	12206	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	13361040	131241029	27897634	54	4611											
PRKAG2	51422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151262972	151262972	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggctttggcatatcagacatCtaaacggaagataaacgcaa	16	8	9	8	2	2	2	1	0	1	2	2	3	2	3	0	3	2	3	0	3	7	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:151262972C>T	ENST00000287878.4	-	12	1738		c.e12-1		PRKAG2_ENST00000433631.2_Splice_Site|PRKAG2_ENST00000418337.2_Splice_Site|PRKAG2_ENST00000492843.1_Splice_Site|PRKAG2_ENST00000392801.2_Splice_Site	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit						ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	TATCAGACATCTAAACGGAAG	0.418																																					.		.											.	PRKAG2-658	0			c.1234-1G>A						.						168	137	147					7																	151262972		2203	4300	6503	SO:0001630	splice_region_variant	51422	exon13			AGACATCTAAACG	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"AMPK gamma2"	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.1234-1G>A	7.37:g.151262972C>T		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	87	31	NM_016203	0	0	1	3	2	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Splice_Site	SNP	ENST00000287878.4	37	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459439	0.84317	.	.	ENSG00000106617	ENST00000418337;ENST00000287878;ENST00000492843;ENST00000433631;ENST00000392801	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.609	0.95594	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKAG2	150893905	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	7.538000	0.82048	2.882000	0.98803	0.655000	0.94253	.	.		0.418	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203	Intron	T	151262972	C	T	151262972	5	4	50	1	0	0	0	0	0	0	1	0	12530	927	32	2	496	2	PRKAG2	7	151262972	Splice_Site	SNP	C	TCGA-B9-4116-01A-01D-1252-08	20021943	151262972	7875691	55	4612											
SGCZ	137868	hgsc.bcm.edu	37	chr8	13948004	13948004	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacaagtggaacctactcctGctggagaaaggtaaagtttg	13	9	12	7	0	0	1	0	0	0	1	1	4	1	2	2	3	3	3	2	3	6	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr8:13948004G>C	ENST00000382080.1	-	8	1602	c.887C>G	c.(886-888)gCa>gGa	p.A296G	SGCZ_ENST00000421524.2_Missense_Mutation_p.A249G	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	283					membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		ACCTACTCCTGCTGGAGAAAG	0.498																																					p.A296G		.											.	SGCZ-93	0			c.C887G						.						175	159	164					8																	13948004		2203	4300	6503	SO:0001583	missense	137868	exon8			ACTCCTGCTGGAG	AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053			14075	protein-coding gene	gene with protein product		608113				12189167	Standard	XM_006716287		Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.887C>G	8.37:g.13948004G>C	ENSP00000371512:p.Ala296Gly	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_139167	0	0	0	0	0	Q6REU0	Missense_Mutation	SNP	ENST00000382080.1	37	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512227	0.85389	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	D;D	0.95069	-3.6;-3.6	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.97241	0.9098	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.994	D	0.97464	1.0036	10	0.72032	D	0.01	.	18.7556	0.91832	0.0:0.0:1.0:0.0	.	249;296	Q08AT0;Q96LD1-2	.;.	G	296;249	ENSP00000371512:A296G;ENSP00000405224:A249G	ENSP00000371512:A296G	A	-	2	0	SGCZ	13992375	1.000000	0.71417	0.994000	0.49952	0.955000	0.61496	9.476000	0.97823	2.760000	0.94817	0.655000	0.94253	GCA	.		0.498	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207636.2	NM_139167		C	13948004	G	C	13948004	3	2	50	1	0	0	0	0	1	0	0	0	14236	1319	46	4	55	4	SGCZ	8	13948004	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		13948004	132416018	56	4613											
FAM84B	157638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	127569250	127569250	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tacggcccagtgcgggtactGagcctgcgacacgaactcca	9	6	12	14	4	0	1	0	1	0	0	1	3	1	1	3	2	6	1	3	2	3	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr8:127569250G>C	ENST00000304916.3	-	2	840	c.385C>G	c.(385-387)Cag>Gag	p.Q129E	RP11-89K10.1_ENST00000517773.1_RNA|RP11-89K10.1_ENST00000520512.1_RNA|RP11-89K10.1_ENST00000519880.1_RNA|RP11-103H7.5_ENST00000524320.1_RNA|FAM84B_ENST00000517458.1_5'Flank	NM_174911.4	NP_777571.1	Q96KN1	FA84B_HUMAN	family with sequence similarity 84, member B	129						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	5	Ovarian(5;9.43e-05)|Esophageal squamous(12;0.0012)|Hepatocellular(40;0.128)|Myeloproliferative disorder(2;0.135)		STAD - Stomach adenocarcinoma(47;0.000556)|Colorectal(2;0.0102)|Lung(2;0.0136)|READ - Rectum adenocarcinoma(2;0.0723)			TGCGGGTACTGAGCCTGCGAC	0.637																																					p.Q129E		.											.	FAM84B-22	0			c.C385G						.						27	29	29					8																	127569250		2202	4299	6501	SO:0001583	missense	157638	exon2			GGTACTGAGCCTG	AJ417849	CCDS6358.1	8q24.13	2006-02-09				ENSG00000168672			24166	protein-coding gene	gene with protein product	"breast cancer membrane-associated protein 101", "neurological/sensory 2"	609483				12477722	Standard	NM_174911		Approved	BCMP101, NSE2	uc003yrz.2	Q96KN1		ENST00000304916.3:c.385C>G	8.37:g.127569250G>C	ENSP00000302578:p.Gln129Glu	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	156	43	NM_174911	0	0	17	46	29		Missense_Mutation	SNP	ENST00000304916.3	37	CCDS6358.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.480872	0.44044	.	.	ENSG00000168672	ENST00000304916	T	0.03152	4.03	4.81	4.81	0.61882	.	0.057812	0.64402	D	0.000001	T	0.14270	0.0345	M	0.63428	1.95	0.51767	D	0.999933	D	0.71674	0.998	D	0.67725	0.953	T	0.06215	-1.0839	10	0.27785	T	0.31	-11.9573	16.8556	0.86005	0.0:0.0:1.0:0.0	.	129	Q96KN1	FA84B_HUMAN	E	129	ENSP00000302578:Q129E	ENSP00000302578:Q129E	Q	-	1	0	FAM84B	127638432	1.000000	0.71417	0.977000	0.42913	0.005000	0.04900	7.807000	0.86032	2.181000	0.69327	0.467000	0.42956	CAG	.		0.637	FAM84B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381487.1	NM_174911		C	127569250	G	C	127569250	3	2	50	1	0	0	0	0	1	0	0	0	5661	1299	45	4	551	4	FAM84B	8	127569250	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	113621246	127569250	18794772	57	4614											
NAPRT1	1936	hgsc.bcm.edu	37	chr8	144660318	144660318	+	IGR	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacagtcgcgcaagccggcGgccaaggcgaaggcgccgcc	9	1	15	16	7	0	0	0	0	0	0	1	1	0	0	4	4	1	1	4	4	3	0	rs896951|rs35914195	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr8:144660318G>T	ENST00000529272.1	-	0	1311				RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'Flank|NAPRT1_ENST00000426292.3_Silent_p.A57A|RP11-661A12.7_ENST00000529247.1_RNA|NAPRT1_ENST00000435154.3_Silent_p.A57A|NAPRT1_ENST00000276844.7_Silent_p.A57A|NAPRT1_ENST00000449291.2_Silent_p.A57A			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			GCAAGCCGGCGGCCAAGGCGA	0.756													G|||	105	0.0209665	0.0772	0.0043	5008	,	,		10107	0		0	False		,,,				2504	0				p.A57A		.											.	NAPRT1-91	0			c.C171A						.	G		128,2634		0,128,1253	2	3	3		171	2.1	1	8	dbSNP_86	3	4,5910		0,4,2953	no	coding-synonymous	NAPRT1	NM_145201.4		0,132,4206	TT,TG,GG		0.0676,4.6343,1.5214		57/539	144660318	132,8544	1381	2957	4338	SO:0001628	intergenic_variant	93100	exon1			GCCGGCGGCCAAG	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191		8.37:g.144660318G>T		Somatic	6	2		WXS	Illumina HiSeq	Phase_I	14	9	NM_145201	0	0	3	3	0	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1																																																																																			T|0.001;C|0.985		0.756	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		T	144660318	G	T	144660318	1	4	50	0	1	0	0	0	0	0	0	0	10190	1103	39	4		4	NAPRT1	8	144660318	IGR	SNP	G	TCGA-B9-4116-01A-01D-1252-08	17091068	144660318	1703704	58	4615											
C9orf79	286234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	90501484	90501484	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaaggatgtgcagaagacCgggttcaggagctccggaag	12	5	17	7	2	1	2	1	0	0	2	2	6	2	6	2	5	2	3	2	5	3	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr9:90501484C>T	ENST00000325643.5	+	4	2148	c.2082C>T	c.(2080-2082)acC>acT	p.T694T		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	694					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGCAGAAGACCGGGTTCAGGA	0.612																																					p.T694T		.											.	.	0			c.C2082T						.						54	69	64					9																	90501484		2203	4300	6503	SO:0001819	synonymous_variant	286234	exon4			GAAGACCGGGTTC	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 79", "family with sequence similarity 75, member E1"	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2082C>T	9.37:g.90501484C>T		Somatic	160	0		WXS	Illumina HiSeq	Phase_I	234	65	NM_178828	0	0	0	0	0	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																			.		0.612	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90501484	C	T	90501484	2	4	50	1	0	0	0	0	0	0	0	1	2503	639	23	1		1	C9orf79	9	90501484	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		90501484	50711947	59	4616											
NUP214	8021	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	134010301	134010301	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagaaaaaagaagaaaagcAcccagagatatttgtgaact	20	7	9	5	0	0	5	0	1	0	4	0	6	0	5	1	0	2	2	1	0	9	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr9:134010301A>T	ENST00000359428.5	+	8	992	c.848A>T	c.(847-849)cAc>cTc	p.H283L	NUP214_ENST00000411637.2_Missense_Mutation_p.H283L|RP11-544A12.4_ENST00000415391.2_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.H283L|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	283	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GAAGAAAAGCACCCAGAGATA	0.378			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.H283L	Pancreas(4;24 48 25510 30394 32571)	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214-1131	0			c.A848T						.						69	67	67					9																	134010301		2203	4300	6503	SO:0001583	missense	8021	exon8			AAAAGCACCCAGA	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.848A>T	9.37:g.134010301A>T	ENSP00000352400:p.His283Leu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	57	17	NM_005085	0	0	14	18	4	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	19.58	3.855209	0.71719	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375	D;D;D	0.93488	-3.23;-3.23;-3.23	5.69	3.32	0.38043	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.43110	D	0.000603	T	0.80954	0.4723	N	0.08118	0	0.31118	N	0.709181	B;B	0.33022	0.202;0.394	B;B	0.32022	0.099;0.139	T	0.75227	-0.3392	10	0.23891	T	0.37	-11.0116	3.1676	0.06541	0.5712:0.2182:0.2105:0.0	.	283;283	P35658-4;P35658	.;NU214_HUMAN	L	283	ENSP00000352400:H283L;ENSP00000396576:H283L;ENSP00000405014:H283L	ENSP00000352400:H283L	H	+	2	0	NUP214	133000122	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.069000	0.50026	0.950000	0.37743	0.528000	0.53228	CAC	.		0.378	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134010301	A	T	134010301	3	4	50	1	0	0	0	0	1	0	0	0	10788	159	6	5	878	5	NUP214	9	134010301	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	43508817	134010301	7203130	60	4617											
SEC16A	9919	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	139369195	139369195	+	Frame_Shift_Del	DEL	G	G	-																															ccacacttgtgcttccagcaGggctattagcaaatccggga																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr9:139369195delG	ENST00000371706.3	-	1	2372	c.2339delC	c.(2338-2340)cctfs	p.P780fs	SEC16A_ENST00000313050.7_Frame_Shift_Del_p.P958fs|SEC16A_ENST00000290037.6_Frame_Shift_Del_p.P780fs|SEC16A_ENST00000431893.2_Frame_Shift_Del_p.P780fs			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	780					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GCTTCCAGCAGGGCTATTAGC	0.507																																					p.P958fs		.											.	.	0			c.2873delC						.						65	64	64					9																	139369195		1939	4138	6077	SO:0001589	frameshift_variant	9919	exon3			.	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.2339delC	9.37:g.139369195delG	ENSP00000360771:p.Pro780fs	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	213	76	NM_014866	0	0	0	0	0	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Frame_Shift_Del	DEL	ENST00000371706.3	37																																																																																				.		0.507	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		-	139369195	G	-	139369195	7	5	50	1	0	1	0	1	0	0	0	0	14018	1000	35	0	4320	0	SEC16A	9	139369195	Frame_Shift_Del	DEL	G	TCGA-B9-4116-01A-01D-1252-08	5358894	139369195	1844236	61	4618											
ABI1	10006	hgsc.bcm.edu	37	chr10	27040641	27040641	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cactggtggtggtggtggggGaggtggagagtcatcaaaca	9	8	19	5	0	2	1	2	0	0	1	2	3	2	2	0	8	1	0	0	8	1	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr10:27040641G>C	ENST00000376142.2	-	11	1308	c.1237C>G	c.(1237-1239)Ccc>Gcc	p.P413A	ABI1_ENST00000376170.4_Missense_Mutation_p.P356A|ABI1_ENST00000376139.2_Missense_Mutation_p.P381A|ABI1_ENST00000376160.1_Missense_Mutation_p.P380A|ABI1_ENST00000359188.4_Missense_Mutation_p.P385A|ABI1_ENST00000376137.4_Missense_Mutation_p.P328A|ABI1_ENST00000490841.2_Missense_Mutation_p.P234A|ABI1_ENST00000376134.3_Missense_Mutation_p.P387A|ABI1_ENST00000536334.1_Missense_Mutation_p.P299A|ABI1_ENST00000346832.5_Missense_Mutation_p.P401A|ABI1_ENST00000376166.1_Missense_Mutation_p.P351A|ABI1_ENST00000376140.3_Missense_Mutation_p.P386A|ABI1_ENST00000376138.3_Missense_Mutation_p.P357A|ABI1_ENST00000355394.4_Missense_Mutation_p.P414A	NM_005470.3	NP_005461.2	Q8IZP0	ABI1_HUMAN	abl-interactor 1	413	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium morphogenesis (GO:0072673)|megakaryocyte development (GO:0035855)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|SCAR complex (GO:0031209)	cytoskeletal protein binding (GO:0008092)|protein complex binding (GO:0032403)|protein tyrosine kinase activator activity (GO:0030296)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGTGGTGGGGGAGGTGGAGAG	0.478																																					p.P413A		.											.	ABI1-1082	0			c.C1237G						.						115	123	120					10																	27040641		2203	4300	6503	SO:0001583	missense	10006	exon11			GTGGGGGAGGTGG	U87166	CCDS7150.1, CCDS31169.1, CCDS31170.1, CCDS31171.1, CCDS53497.1, CCDS53498.1, CCDS53499.1, CCDS53500.1, CCDS53501.1, CCDS73077.1, CCDS73078.1	10p12.1	2009-05-29	2004-03-17	2004-03-19	ENSG00000136754	ENSG00000136754			11320	protein-coding gene	gene with protein product		603050	"spectrin SH3 domain binding protein 1"	SSH3BP1		9593709, 9010225	Standard	NM_005470		Approved	E3B1, ABI-1	uc001isx.3	Q8IZP0	OTTHUMG00000017848	ENST00000376142.2:c.1237C>G	10.37:g.27040641G>C	ENSP00000365312:p.Pro413Ala	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_005470	0	0	31	31	0	A9Z1Y6|B3KX62|B4DQ58|H7BXI6|O15147|O76049|O95060|Q5T2R3|Q5T2R4|Q5T2R6|Q5T2R7|Q5T2R9|Q5W070|Q5W072|Q8TB63|Q96S81|Q9NXZ9|Q9NYB8	Missense_Mutation	SNP	ENST00000376142.2	37	CCDS7150.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.846505	0.51164	.	.	ENSG00000136754	ENST00000376138;ENST00000376170;ENST00000376166;ENST00000376160;ENST00000376142;ENST00000359188;ENST00000376139;ENST00000355394;ENST00000346832;ENST00000376134;ENST00000376137;ENST00000536334;ENST00000490841;ENST00000376140	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.47177	2.25;2.25;2.25;0.95;0.92;0.94;0.96;1.02;2.25;0.85;1.1;2.25;1.04;0.94	5.18	4.28	0.50868	Src homology-3 domain (1);	0.357554	0.36200	N	0.002724	T	0.62527	0.2435	L	0.56769	1.78	0.35986	D	0.836389	B;B;B;B;P;B;D;P;P;P;P;P;D	0.89917	0.3;0.018;0.131;0.206;0.948;0.413;0.997;0.917;0.556;0.95;0.855;0.917;1.0	B;B;B;B;P;B;D;P;B;P;P;P;D	0.87578	0.039;0.007;0.039;0.086;0.65;0.265;0.98;0.64;0.403;0.775;0.64;0.709;0.998	T	0.67499	-0.5655	10	0.29301	T	0.29	-2.6224	13.6422	0.62257	0.0764:0.0:0.9236:0.0	.	298;327;234;293;223;351;381;385;401;357;381;386;413	B6VEX4;B6VEX3;B4DQ58;Q8IZP0-10;B4DKX2;Q5T2R9;Q59G41;Q8IZP0-6;B3KX62;Q8IZP0-3;Q8IZP0-5;Q8IZP0-9;Q8IZP0	.;.;.;.;.;.;.;.;.;.;.;.;ABI1_HUMAN	A	357;356;351;380;413;385;381;414;401;387;328;299;234;386	ENSP00000365308:P357A;ENSP00000365340:P356A;ENSP00000365336:P351A;ENSP00000365330:P380A;ENSP00000365312:P413A;ENSP00000352114:P385A;ENSP00000365309:P381A;ENSP00000347555:P414A;ENSP00000279599:P401A;ENSP00000365304:P387A;ENSP00000365307:P328A;ENSP00000439646:P299A;ENSP00000440101:P234A;ENSP00000365310:P386A	ENSP00000279599:P401A	P	-	1	0	ABI1	27080647	1.000000	0.71417	0.753000	0.31225	0.381000	0.30169	7.809000	0.86057	1.318000	0.45170	0.563000	0.77884	CCC	.		0.478	ABI1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047287.1	NM_005470		C	27040641	G	C	27040641	3	2	50	1	0	0	0	0	1	0	0	0	88	1174	41	4	297	4	ABI1	10	27040641	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		27040641	108494106	62	4619											
PGAM1	5223	hgsc.bcm.edu	37	chr10	99192203	99192203	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttgaagcctatcaagccCatgcagtttctgggggatga	11	10	11	9	0	2	2	1	2	1	0	2	3	2	3	2	2	4	2	2	2	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr10:99192203C>T	ENST00000334828.5	+	4	835	c.687C>T	c.(685-687)ccC>ccT	p.P229P	PGAM1_ENST00000467867.1_3'UTR	NM_002629.2	NP_002620.1	P18669	PGAM1_HUMAN	phosphoglycerate mutase 1 (brain)	229					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|regulation of glycolytic process (GO:0006110)|regulation of pentose-phosphate shunt (GO:0043456)|respiratory burst (GO:0045730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)|protein kinase binding (GO:0019901)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(252;0.162)		Epithelial(162;8.36e-10)|all cancers(201;5.62e-08)		CTATCAAGCCCATGCAGTTTC	0.532																																					p.P229P		.											.	PGAM1-226	0			c.C687T						.						102	102	102					10																	99192203		2202	4281	6483	SO:0001819	synonymous_variant	5223	exon4			CAAGCCCATGCAG	BC010038	CCDS7458.1	10q25.3	2012-10-02			ENSG00000171314	ENSG00000171314	5.4.2.1		8888	protein-coding gene	gene with protein product	"Phosphoglycerate mutase A, nonmuscle form"	172250		PGAMA		2846553	Standard	NM_002629		Approved	PGAM-B	uc001knh.3	P18669	OTTHUMG00000018846	ENST00000334828.5:c.687C>T	10.37:g.99192203C>T		Somatic	294	1		WXS	Illumina HiSeq	Phase_I	445	131	NM_002629	0	0	268	488	220	Q9BWC0	Silent	SNP	ENST00000334828.5	37	CCDS7458.1																																																																																			.		0.532	PGAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049652.1	NM_002629		T	99192203	C	T	99192203	2	4	50	1	0	0	0	0	0	0	0	1	11799	581	21	2		2	PGAM1	10	99192203	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	72151562	99192203	36342544	63	4620											
FAM45A	404636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	120879873	120879873	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acattgtatctcagtttggaAtggaaactgttatcttacac	12	15	7	7	0	2	0	1	0	2	0	3	2	2	2	0	2	2	3	0	2	5	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr10:120879873A>T	ENST00000361432.2	+	5	528	c.502A>T	c.(502-504)Atg>Ttg	p.M168L	FAM45A_ENST00000535029.1_Intron|FAM45A_ENST00000489988.1_3'UTR|FAM45A_ENST00000544016.1_Missense_Mutation_p.M17L	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	168										breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		TCAGTTTGGAATGGAAACTGT	0.343																																					p.M168L		.											.	FAM45A-91	0			c.A502T						.						87	84	85					10																	120879873		2203	4300	6503	SO:0001583	missense	404636	exon5			TTTGGAATGGAAA	AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.502A>T	10.37:g.120879873A>T	ENSP00000354688:p.Met168Leu	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	137	42	NM_207009	0	0	11	16	5	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Missense_Mutation	SNP	ENST00000361432.2	37	CCDS7609.1	.	.	.	.	.	.	.	.	.	.	A	8.904	0.957092	0.18507	.	.	ENSG00000119979	ENST00000546291;ENST00000361432;ENST00000544016	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.51719	0.1691	L	0.42245	1.32	0.58432	D	0.999999	B;B;B;B	0.22414	0.051;0.069;0.01;0.051	B;B;B;B	0.24701	0.055;0.04;0.022;0.037	T	0.48625	-0.9019	9	0.02654	T	1	.	15.0195	0.71617	1.0:0.0:0.0:0.0	.	95;17;160;168	B4DNL9;B4DMU4;Q8TCE6-2;Q8TCE6	.;.;.;FA45A_HUMAN	L	168;168;17	.	ENSP00000354688:M168L	M	+	1	0	FAM45A	120869863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.380000	0.90149	2.285000	0.76669	0.533000	0.62120	ATG	.		0.343	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009		T	120879873	A	T	120879873	3	4	50	1	0	0	0	0	1	0	0	0	5583	101	4	5	520	5	FAM45A	10	120879873	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	21687670	120879873	14654874	64	4621											
FANK1	92565	broad.mit.edu	37	chr10	127585218	127585218	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggagcagccgaccatggagCcccagagtaagggaggcccg	10	2	17	12	2	0	1	0	0	0	1	0	5	0	4	5	4	3	2	5	4	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr10:127585218C>A	ENST00000368693.1	+	1	111	c.7C>A	c.(7-9)Ccc>Acc	p.P3T	FANK1_ENST00000449042.2_5'UTR|FANK1_ENST00000368695.1_5'UTR			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	3						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				GACCATGGAGCCCCAGAGTAA	0.761																																					p.P3T													.	FANK1-91	0			c.C7A						.						9	12	11					10																	127585218		2171	4258	6429	SO:0001583	missense	92565	exon1			ATGGAGCCCCAGA	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"Ankyrin repeat domain containing", "Fibronectin type III domain containing"	23527	protein-coding gene	gene with protein product		611640	"fibronectin type 3 and ankyrin repeat domains 1"			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.7C>A	10.37:g.127585218C>A	ENSP00000357682:p.Pro3Thr	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	29	3	NM_145235	0	0	0	0	0	Q6UXY9|Q6X7T6	Missense_Mutation	SNP	ENST00000368693.1	37	CCDS31309.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.288816	0.23478	.	.	ENSG00000203780	ENST00000368693	T	0.43688	0.94	2.62	2.62	0.31277	.	.	.	.	.	T	0.25195	0.0612	N	0.22421	0.69	0.80722	D	1	B;B	0.12013	0.003;0.005	B;B	0.12837	0.007;0.008	T	0.05835	-1.0861	9	0.18276	T	0.48	.	8.8836	0.35389	0.0:1.0:0.0:0.0	.	3;3	Q8TC84-3;Q8TC84	.;FANK1_HUMAN	T	3	ENSP00000357682:P3T	ENSP00000357682:P3T	P	+	1	0	FANK1	127575208	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	2.904000	0.48719	1.756000	0.51951	0.462000	0.41574	CCC	.		0.761	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		A	127585218	C	A	127585218	3	1	50	1	0	0	0	0	1	0	0	0	5691	739	26	4	9	4	FANK1	10	127585218	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	6705345	127585218	7949529	65	4622											
MICAL2	9645	ucsc.edu	37	chr11	12225946	12225946	+	Silent	SNP	G	G	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaccatccatgaccttcgTggcctgggagccaagaagtt	9	10	10	12	1	1	2	1	1	0	1	3	3	2	3	5	2	1	1	5	2	2	3	rs3763823	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:12225946G>A	ENST00000256194.4	+	4	702	c.414G>A	c.(412-414)cgG>cgA	p.R138R	MICAL2_ENST00000537344.1_Silent_p.R138R|MICAL2_ENST00000527195.1_3'UTR|MICAL2_ENST00000379612.3_Silent_p.R138R|MICAL2_ENST00000342902.5_Silent_p.R138R|MICAL2_ENST00000527546.1_Silent_p.R138R	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	138	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ATGACCTTCGTGGCCTGGGAG	0.547																																					p.R138R													.	MICAL2-92	0			c.T414A						.						114	101	105					11																	12225946		2201	4294	6495	SO:0001819	synonymous_variant	9645	exon4			CCTTCGTGGCCTG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.414G>A	11.37:g.12225946G>A		Somatic	198	0		WXS	Illumina HiSeq		234	104	NM_014632	0	0	1	1	0	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			G|0.668;T|0.332		0.547	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		A	12225946	G	A	12225946	2	1	50	1	0	0	0	0	0	0	0	1	9595	1683	59	5		5	MICAL2	11	12225946	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08		12225946	122780570	66	4623											
LRRC4C	57689	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	40136626	40136630	+	Frame_Shift_Del	DEL	AGCAC	AGCAC	-																															aatttaacgtaccatcactgAgcacagctatccgcactttg																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	AGCAC	AGCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:40136626_40136630delAGCAC	ENST00000278198.2	-	2	3176_3180	c.1213_1217delGTGCT	c.(1213-1218)gtgctcfs	p.VL405fs	LRRC4C_ENST00000530763.1_Frame_Shift_Del_p.VL405fs|LRRC4C_ENST00000527150.1_Frame_Shift_Del_p.VL405fs|LRRC4C_ENST00000528697.1_Frame_Shift_Del_p.VL405fs			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	405	Ig-like C2-type.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ACCATCACTGAGCACAGCTATCCGC	0.454																																					p.405_406del		.											.	LRRC4C-521	0			c.1213_1217del						.																																			SO:0001589	frameshift_variant	57689	exon7			.	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1213_1217delGTGCT	11.37:g.40136626_40136630delAGCAC	ENSP00000278198:p.Val405fs	Somatic	484	0		WXS	Illumina HiSeq	Phase_I	222	50	NM_001258419	0	0	0	0	0	A8K0T1|Q7L0N3	Frame_Shift_Del	DEL	ENST00000278198.2	37	CCDS31464.1																																																																																			.		0.454	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		-	40136630	AGCAC	-	40136626	7	5	50	1	0	1	0	1	0	0	0	0	9033	304	11	0	709	0	LRRC4C	11	40136626	Frame_Shift_Del	DEL	AGCAC	TCGA-B9-4116-01A-01D-1252-08	27910680	40136626	94869890	67	4624											
TRIM48	79097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55032729	55032729	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctgtttgctgtgctccaGctctcaggagcaccggtatc	5	12	11	13	1	2	0	1	0	2	0	5	1	3	1	2	2	4	7	2	2	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:55032729G>T	ENST00000417545.2	+	2	484	c.398G>T	c.(397-399)aGc>aTc	p.S133I		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	117						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CTGTGCTCCAGCTCTCAGGAG	0.507																																					p.S133I		.											.	TRIM48-130	0			c.G398T						.						53	49	50					11																	55032729		2190	4261	6451	SO:0001583	missense	79097	exon2			GCTCCAGCTCTCA	AF521869	CCDS7947.2	11q12	2013-01-09	2011-01-25		ENSG00000150244	ENSG00000150244		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19021	protein-coding gene	gene with protein product			"tripartite motif-containing 48"				Standard	NM_024114		Approved	RNF101	uc010rid.2	Q8IWZ4	OTTHUMG00000157011	ENST00000417545.2:c.398G>T	11.37:g.55032729G>T	ENSP00000402414:p.Ser133Ile	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	16	8	NM_024114	0	0	0	0	0	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	37	CCDS7947.2	.	.	.	.	.	.	.	.	.	.	g	7.071	0.568353	0.13560	.	.	ENSG00000150244	ENST00000417545	T	0.42900	0.96	0.596	-1.19	0.09585	Zinc finger, B-box (3);	.	.	.	.	T	0.36524	0.0970	N	0.20610	0.595	0.09310	N	1	P	0.49961	0.93	P	0.57009	0.811	T	0.23797	-1.0178	9	0.62326	D	0.03	.	4.2471	0.10677	0.7213:0.0:0.2787:0.0	.	117	Q8IWZ4	TRI48_HUMAN	I	133	ENSP00000402414:S133I	ENSP00000402414:S133I	S	+	2	0	TRIM48	54789305	0.000000	0.05858	0.045000	0.18777	0.232000	0.25224	-0.139000	0.10358	-0.425000	0.07371	-0.506000	0.04501	AGC	.		0.507	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1			T	55032729	G	T	55032729	3	4	50	1	0	0	0	0	1	0	0	0	16556	971	34	4	404	4	TRIM48	11	55032729	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	14896103	55032729	79973787	68	4625											
COX8A	1351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63743765	63743765	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgggctggatcctgtcacaCctggagacctacaggaggcc	8	6	14	13	1	1	1	1	0	0	1	2	4	2	3	4	5	1	1	4	5	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:63743765C>G	ENST00000314133.3	+	2	257	c.183C>G	c.(181-183)caC>caG	p.H61Q	AP000721.4_ENST00000535431.1_Intron	NM_004074.2	NP_004065.1	P10176	COX8A_HUMAN	cytochrome c oxidase subunit VIIIA (ubiquitous)	61					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)										TCCTGTCACACCTGGAGACCT	0.587																																					p.H61Q		.											.	COX8A-226	0			c.C183G						.						200	160	173					11																	63743765		2201	4297	6498	SO:0001583	missense	1351	exon2			GTCACACCTGGAG	J04823	CCDS8054.1	11q12-q13	2011-07-04	2010-04-27	2004-03-24	ENSG00000176340	ENSG00000176340	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2294	protein-coding gene	gene with protein product		123870	"cytochrome c oxidase subunit VIII", "cytochrome c oxidase subunit 8A (ubiquitous)"	COX8		2543673, 2847943	Standard	NM_004074		Approved	COX8-2, COX8L, VIII-L, COX, VIII	uc001nye.3	P10176	OTTHUMG00000167785	ENST00000314133.3:c.183C>G	11.37:g.63743765C>G	ENSP00000321260:p.His61Gln	Somatic	314	0		WXS	Illumina HiSeq	Phase_I	522	139	NM_004074	0	0	427	745	318	P15955	Missense_Mutation	SNP	ENST00000314133.3	37	CCDS8054.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425954	0.62733	.	.	ENSG00000176340	ENST00000314133	.	.	.	5.75	3.88	0.44766	Cytochrome c oxidase subunit VIII/photosystem I reaction centre subunit IX (1);	0.064498	0.64402	D	0.000010	T	0.47002	0.1422	.	.	.	0.34757	D	0.732368	B	0.33940	0.433	B	0.37091	0.241	T	0.59337	-0.7473	8	0.87932	D	0	-8.3625	8.2466	0.31693	0.0:0.7603:0.1565:0.0832	.	61	P10176	COX8A_HUMAN	Q	61	.	ENSP00000321260:H61Q	H	+	3	2	COX8A	63500341	0.967000	0.33354	0.996000	0.52242	0.629000	0.37895	0.650000	0.24858	0.774000	0.33427	0.655000	0.94253	CAC	.		0.587	COX8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396273.1	NM_004074		G	63743765	C	G	63743765	3	3	50	1	0	0	0	0	1	0	0	0	3791	506	18	4	189	4	COX8A	11	63743765	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	8711036	63743765	71262751	69	4626											
SCYL1	57410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	65305494	65305494	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gagtccgactggagcagctgGgaagctgagggctcctggga	8	6	18	9	1	0	1	0	1	0	0	2	6	2	4	2	4	3	4	2	4	1	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:65305494G>A	ENST00000270176.5	+	16	2165	c.2088G>A	c.(2086-2088)tgG>tgA	p.W696*	SCYL1_ENST00000527009.1_Nonsense_Mutation_p.W553*|SCYL1_ENST00000534462.1_3'UTR|SCYL1_ENST00000533862.1_Missense_Mutation_p.G684E|SCYL1_ENST00000279270.6_Nonsense_Mutation_p.W696*|SCYL1_ENST00000525364.1_Nonsense_Mutation_p.W695*|SCYL1_ENST00000420247.2_Nonsense_Mutation_p.W679*|SCYL1_ENST00000524944.1_Nonsense_Mutation_p.W696*	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	696					peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						GGAGCAGCTGGGAAGCTGAGG	0.637																																					p.W696X		.											.	SCYL1-333	0			c.G2088A						.						34	36	35					11																	65305494		1905	4127	6032	SO:0001587	stop_gained	57410	exon16			CAGCTGGGAAGCT	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"teratoma-associated tyrosine kinase", "telomerase transcriptional elements-interacting factor", "telomerase regulation-associated protein"	607982	"N-terminal kinase-like"	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.2088G>A	11.37:g.65305494G>A	ENSP00000270176:p.Trp696*	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	45	18	NM_020680	0	0	62	73	11	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Nonsense_Mutation	SNP	ENST00000270176.5	37	CCDS41672.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.30|12.30	1.897578|1.897578	0.33535|0.33535	.|.	.|.	ENSG00000142186|ENSG00000142186	ENST00000533862|ENST00000270176;ENST00000525364;ENST00000420247;ENST00000279270;ENST00000524944;ENST00000527009;ENST00000528545	T|.	0.12774|.	2.65|.	4.3|4.3	4.3|4.3	0.51218|0.51218	.|.	.|0.000000	.|0.50627	.|D	.|0.000105	T|.	0.43612|.	0.1255|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	B|.	0.22746|.	0.074|.	B|.	0.20955|.	0.032|.	T|.	0.48375|.	-0.9041|.	7|.	0.05436|0.11485	T|T	0.98|0.65	.|.	12.6154|12.6154	0.56573|0.56573	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	684|.	Q96KG9-6|.	.|.	E|X	684|696;695;679;696;696;553;168	ENSP00000437254:G684E|.	ENSP00000437254:G684E|ENSP00000270176:W696X	G|W	+|+	2|3	0|0	SCYL1|SCYL1	65062070|65062070	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.319000|0.319000	0.28217|0.28217	6.160000|6.160000	0.71862|0.71862	2.126000|2.126000	0.65437|0.65437	0.561000|0.561000	0.74099|0.74099	GGG|TGG	.		0.637	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		A	65305494	G	A	65305494	4	1	50	1	0	0	0	0	0	1	0	0	13979	1241	43	2	2150	2	SCYL1	11	65305494	Nonsense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	1561729	65305494	69701022	70	4627											
FGF3	2248	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	69625463	69625464	+	Frame_Shift_Ins	INS	-	-	T																															actcgcactcggcgctgtagINStgctcctgcggggatgagat																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:69625463_69625464insT	ENST00000334134.2	-	3	419_420	c.329_330insA	c.(328-330)cacfs	p.H110fs		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	110					anatomical structure morphogenesis (GO:0009653)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			CGGCGCTGTAGTGCTCCTGCGG	0.639																																					p.H110fs		.											.	FGF3-847	0			c.330_331insA						.																																			SO:0001589	frameshift_variant	2248	exon3			.		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"INT-2 proto-oncogene protein", "oncogene INT2", "V-INT2 murine mammary tumor virus integration site oncogene homolog", "murine mammary tumor virus integration site 2, mouse"	164950	"fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.330dupA	11.37:g.69625464_69625464dupT	ENSP00000334122:p.His110fs	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	174	54	NM_005247	0	0	0	0	0	Q0VG69	Frame_Shift_Ins	INS	ENST00000334134.2	37	CCDS8195.1																																																																																			.		0.639	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247		T	69625464	-	T	69625463	7	5	50	1	0	1	1	0	0	0	0	0	5872	1020	36	0	393	0	FGF3	11	69625463	Frame_Shift_Ins	INS	-	TCGA-B9-4116-01A-01D-1252-08	4319969	69625463	65381053	71	4628	52	2									
FGF3	2248	hgsc.bcm.edu;bcgsc.ca	37	chr11	69625465	69625465	+	Missense_Mutation	SNP	G	G	T																															ctcgcactcggcgctgtagtGctcctgcggggatgagatat																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:69625465G>T	ENST00000334134.2	-	3	418	c.328C>A	c.(328-330)Cac>Aac	p.H110N		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	110					anatomical structure morphogenesis (GO:0009653)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			GCGCTGTAGTGCTCCTGCGGG	0.637																																					p.H110N		.											.	FGF3-847	0			c.C328A						.						33	37	35					11																	69625465		2194	4284	6478	SO:0001583	missense	2248	exon3			TGTAGTGCTCCTG		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"INT-2 proto-oncogene protein", "oncogene INT2", "V-INT2 murine mammary tumor virus integration site oncogene homolog", "murine mammary tumor virus integration site 2, mouse"	164950	"fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.328C>A	11.37:g.69625465G>T	ENSP00000334122:p.His110Asn	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	168	53	NM_005247	0	0	1	1	0	Q0VG69	Missense_Mutation	SNP	ENST00000334134.2	37	CCDS8195.1	.	.	.	.	.	.	.	.	.	.	G	9.674	1.147585	0.21288	.	.	ENSG00000186895	ENST00000334134	T	0.80214	-1.35	3.92	1.64	0.23874	.	0.604005	0.17897	N	0.158317	T	0.54046	0.1834	N	0.02420	-0.555	0.25235	N	0.989798	B	0.09022	0.002	B	0.08055	0.003	T	0.38714	-0.9648	9	.	.	.	.	10.459	0.44567	0.0:0.0:0.4125:0.5875	.	110	P11487	FGF3_HUMAN	N	110	ENSP00000334122:H110N	.	H	-	1	0	FGF3	69334646	0.322000	0.24634	0.971000	0.41717	0.966000	0.64601	2.097000	0.41748	0.055000	0.16094	0.462000	0.41574	CAC	.		0.637	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247		T	69625465	G	T	69625465	3	4	50	1	0	0	0	0	1	0	0	0	5872	1319	46	4	395	4	FGF3	11	69625465	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	2	69625465	65381051	72	4629	52	2									
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	133805658	133805658	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccctcagcttcaggtcgCtgcaaagcggcatggggaca	9	6	13	13	2	2	0	2	0	0	0	3	1	2	1	1	4	3	5	1	4	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:133805658C>T	ENST00000321016.8	-	7	1052		c.e7-1		IGSF9B_ENST00000533871.2_Splice_Site			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B						homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTTCAGGTCGCTGCAAAGCGG	0.617																																					.		.											.	IGSF9B-68	0			c.822-1G>A						.						20	24	22					11																	133805658		2117	4221	6338	SO:0001630	splice_region_variant	22997	exon8			AGGTCGCTGCAAA	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.822-1G>A	11.37:g.133805658C>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	60	32	NM_014987	0	0	0	7	7	G5EA26	Splice_Site	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	C	33	5.219946	0.95139	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0502	0.93039	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IGSF9B	133310868	1.000000	0.71417	0.166000	0.22797	0.790000	0.44656	5.713000	0.68415	2.560000	0.86352	0.561000	0.74099	.	.		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	Intron	T	133805658	C	T	133805658	5	4	50	1	0	0	0	0	0	0	1	0	7627	811	28	2	3280	2	IGSF9B	11	133805658	Splice_Site	SNP	C	TCGA-B9-4116-01A-01D-1252-08	64180193	133805658	1200858	73	4630											
CACNA1C	775	broad.mit.edu	37	chr12	2794927	2794927	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctaccaggatgacgaaaatCggcaactgacgctcccagag	13	5	10	13	3	0	3	0	2	0	1	2	5	1	4	3	2	2	2	3	2	4	1	rs369421219		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:2794927C>T	ENST00000347598.4	+	46	5743	c.5743C>T	c.(5743-5745)Cgg>Tgg	p.R1915W	CACNA1C_ENST00000399621.1_Missense_Mutation_p.R1886W|CACNA1C_ENST00000335762.5_Missense_Mutation_p.R1892W|CACNA1C_ENST00000399634.1_Missense_Mutation_p.R1938W|CACNA1C_ENST00000399603.1_Missense_Mutation_p.R1867W|CACNA1C_ENST00000399617.1_Missense_Mutation_p.R1902W|CACNA1C_ENST00000399591.1_Missense_Mutation_p.R1875W|CACNA1C_ENST00000399601.1_Missense_Mutation_p.R1867W|CACNA1C_ENST00000399649.1_Missense_Mutation_p.R1873W|CACNA1C_ENST00000402845.3_Missense_Mutation_p.R1886W|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000344100.3_Missense_Mutation_p.R1908W|CACNA1C_ENST00000399655.1_Missense_Mutation_p.R1867W|CACNA1C_ENST00000399595.1_Missense_Mutation_p.R1875W|CACNA1C_ENST00000327702.7_Missense_Mutation_p.R1902W|CACNA1C_ENST00000399629.1_Missense_Mutation_p.R1884W|CACNA1C_ENST00000399606.1_Missense_Mutation_p.R1887W|CACNA1C_ENST00000399641.1_Missense_Mutation_p.R1867W|CACNA1C_ENST00000399637.1_Missense_Mutation_p.R1886W|CACNA1C_ENST00000399597.1_Missense_Mutation_p.R1867W|CACNA1C_ENST00000399644.1_Missense_Mutation_p.R1867W|CACNA1C_ENST00000399638.1_Missense_Mutation_p.R1895W|CACNA1C_ENST00000406454.3_Missense_Mutation_p.R1938W	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1950					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGACGAAAATCGGCAACTGAC	0.602																																					p.R1950W													.	CACNA1C-34	0			c.C5848T						.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4017		0,1,2008	49	49	49		5599,5743,5722,5704,5683,5659,5656,5656,5656,5650,5623,5623,5617,5599,5599,5599,5599,5590,5566,5599,5704,5779,5848	3.3	0.9	12		49	0,8318		0,0,4159	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CACNA1C	NM_000719.6,NM_001129827.1,NM_001129829.1,NM_001129830.1,NM_001129831.1,NM_001129832.1,NM_001129833.1,NM_001129834.1,NM_001129835.1,NM_001129836.1,NM_001129837.1,NM_001129838.1,NM_001129839.1,NM_001129840.1,NM_001129841.1,NM_001129842.1,NM_001129843.1,NM_001129844.1,NM_001129846.1,NM_001167623.1,NM_001167624.1,NM_001167625.1,NM_199460.2	101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101,101	0,1,6167	TT,TC,CC		0.0,0.0249,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1867/2139,1915/2187,1908/2180,1902/2174,1895/2167,1887/2159,1886/2158,1886/2158,1886/2158,1884/2156,1875/2147,1875/2147,1873/2145,1867/2139,1867/2139,1867/2139,1867/2139,1864/2136,1856/2128,1867/2139,1902/2174,1927/2199,1950/2222	2794927	1,12335	2009	4159	6168	SO:0001583	missense	775	exon47			GAAAATCGGCAAC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5743C>T	12.37:g.2794927C>T	ENSP00000266376:p.Arg1915Trp	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	177	12	NM_199460	0	0	2	2	0	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165127	0.57476	2.49E-4	0.0	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51	4.26	3.28	0.37604	.	6.168900	0.00682	N	0.000692	T	0.70596	0.3242	L	0.50333	1.59	0.23478	N	0.997598	D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.995;1.0;0.999;0.84;1.0;1.0;0.999;1.0;0.999;0.999;1.0;0.999;0.998;0.993;0.999;0.975;0.998;0.989;1.0;0.966;0.996;1.0;1.0;0.998;0.999	P;D;D;B;D;D;D;D;D;P;D;P;P;P;P;B;P;P;D;P;P;D;D;P;D	0.85130	0.757;0.977;0.932;0.368;0.997;0.951;0.926;0.967;0.944;0.888;0.967;0.859;0.861;0.685;0.803;0.386;0.861;0.827;0.953;0.71;0.791;0.967;0.953;0.802;0.932	T	0.56896	-0.7903	10	0.87932	D	0	.	11.5771	0.50869	0.2538:0.7462:0.0:0.0	.	558;1908;1864;1950;1902;1886;1867;1884;1895;1867;1887;1867;1898;1915;1867;1902;1938;1875;1873;1875;1856;1886;1886;1867;1867	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	W	1892;1867;1867;1895;1867;1886;1886;1875;1867;1915;1887;1867;1908;1884;1902;1873;1886;1867;1938;1902;1938;1875;1768	ENSP00000336982:R1892W;ENSP00000382563:R1867W;ENSP00000382552:R1867W;ENSP00000382547:R1895W;ENSP00000382506:R1867W;ENSP00000382530:R1886W;ENSP00000382546:R1886W;ENSP00000382500:R1875W;ENSP00000382549:R1867W;ENSP00000266376:R1915W;ENSP00000382515:R1887W;ENSP00000382510:R1867W;ENSP00000341092:R1908W;ENSP00000382537:R1884W;ENSP00000329877:R1902W;ENSP00000382557:R1873W;ENSP00000385724:R1886W;ENSP00000382512:R1867W;ENSP00000382542:R1938W;ENSP00000382526:R1902W;ENSP00000385896:R1938W;ENSP00000382504:R1875W	ENSP00000323129:R1768W	R	+	1	2	CACNA1C	2665188	0.998000	0.40836	0.950000	0.38849	0.685000	0.39939	1.926000	0.40084	2.202000	0.70862	0.449000	0.29647	CGG	.		0.602	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2794927	C	T	2794927	3	4	50	1	0	0	0	0	1	0	0	0	2546	875	31	1	6482	1	CACNA1C	12	2794927	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08		2794927	131056968	74	4631											
CLEC4D	338339	broad.mit.edu;bcgsc.ca	37	chr12	8667926	8667932	+	Splice_Site	DEL	TAAGTTA	TAAGTTA	-																															tttattgcaagttgtttgggTaagttattagccaaagtaga																								rs374422007		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	TAAGTTA	TAAGTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:8667926_8667932delTAAGTTA	ENST00000299665.2	+	2	314		c.e2+2			NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D						innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					GTTGTTTGGGTAAGTTATTAGCCAAAG	0.372																																					.													.	CLEC4D-90	0			.						.																																			SO:0001630	splice_region_variant	338339	.			TTTGGGTAAGTTA	AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"C-type lectin domain containing"	14554	protein-coding gene	gene with protein product		609964	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.121+2TAAGTTA>-	12.37:g.8667926_8667932delTAAGTTA		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	38	7	.	0	0	0	0	0	Q8N5J5	Splice_Site	DEL	ENST00000299665.2	37	CCDS8593.1																																																																																			.		0.372	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387	Intron	-	8667932	TAAGTTA	-	8667926	8	5	50	1	0	1	0	1	0	0	1	0	3520	1652	57	0	129	0	CLEC4D	12	8667926	Splice_Site	DEL	TAAGTTA	TCGA-B9-4116-01A-01D-1252-08	5872999	8667926	125183969	75	4632											
MFSD5	84975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53647275	53647275	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctggcaggggccttggcccTtcgaaactggggggagaact	7	8	16	10	1	1	1	0	0	1	1	2	3	1	1	2	7	2	1	2	7	2	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:53647275T>G	ENST00000329548.4	+	2	847	c.656T>G	c.(655-657)cTt>cGt	p.L219R	MFSD5_ENST00000534842.1_Missense_Mutation_p.L326R	NM_032889.4	NP_116278.3	Q6N075	MFSD5_HUMAN	major facilitator superfamily domain containing 5	219					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(3)|urinary_tract(1)	16						GCCTTGGCCCTTCGAAACTGG	0.662																																					p.L326R		.											.	MFSD5-93	0			c.T977G						.						56	61	59					12																	53647275		2203	4300	6503	SO:0001583	missense	84975	exon2			TGGCCCTTCGAAA	AK097576	CCDS8851.1, CCDS53796.1	12q13.13	2012-03-09			ENSG00000182544	ENSG00000182544			28156	protein-coding gene	gene with protein product							Standard	NM_032889		Approved	MGC11308	uc001sch.2	Q6N075	OTTHUMG00000170028	ENST00000329548.4:c.656T>G	12.37:g.53647275T>G	ENSP00000332624:p.Leu219Arg	Somatic	195	1		WXS	Illumina HiSeq	Phase_I	347	124	NM_001170790	0	0	15	34	19	G3V1N7|Q6NW04|Q8N7W8|Q8NCK0|Q96IA5	Missense_Mutation	SNP	ENST00000329548.4	37	CCDS8851.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009159	0.54361	.	.	ENSG00000182544	ENST00000551660;ENST00000534842;ENST00000328704;ENST00000329548	D;D	0.81659	-1.52;-1.52	4.25	4.25	0.50352	Major facilitator superfamily domain, general substrate transporter (1);	0.083569	0.50627	D	0.000110	T	0.78591	0.4307	L	0.43598	1.365	0.53688	D	0.999976	P;D	0.54601	0.512;0.967	B;P	0.49085	0.286;0.6	T	0.79855	-0.1627	10	0.51188	T	0.08	-3.4608	12.4702	0.55783	0.0:0.0:0.0:1.0	.	219;326	Q6N075;G3V1N7	MFSD5_HUMAN;.	R	326;326;326;219	ENSP00000442688:L326R;ENSP00000332624:L219R	ENSP00000331231:L326R	L	+	2	0	MFSD5	51933542	1.000000	0.71417	0.901000	0.35422	0.859000	0.49053	5.709000	0.68384	1.783000	0.52377	0.459000	0.35465	CTT	.		0.662	MFSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406896.1	NM_032889		G	53647275	T	G	53647275	3	3	50	1	0	0	0	0	1	0	0	0	9559	1609	56	5	983	5	MFSD5	12	53647275	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	44979349	53647275	80204620	76	4633											
ITGA7	3679	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	56096870	56096870	+	Frame_Shift_Del	DEL	T	T	-																															ccactctgtagcagtcagtcTcctccaggctcaacgggcaa																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:56096870delT	ENST00000555728.1	-	2	327	c.299delA	c.(298-300)gagfs	p.E100fs	ITGA7_ENST00000452168.2_Intron|ITGA7_ENST00000347027.6_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000257879.6_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000553804.1_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000394230.2_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000257880.7_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000394229.2_Frame_Shift_Del_p.E100fs			Q13683	ITA7_HUMAN	integrin, alpha 7	100					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GCAGTCAGTCTCCTCCAGGCT	0.642																																					p.E100fs		.											.	ITGA7-229	0			c.299delA						.						106	96	99					12																	56096870		2203	4300	6503	SO:0001589	frameshift_variant	3679	exon2			.		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.299delA	12.37:g.56096870delT	ENSP00000452387:p.Glu100fs	Somatic	250	0		WXS	Illumina HiSeq	Phase_I	363	130	NM_002206	0	0	0	0	0	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Frame_Shift_Del	DEL	ENST00000555728.1	37																																																																																				.		0.642	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		-	56096870	T	-	56096870	7	5	50	1	0	1	0	1	0	0	0	0	7902	1551	54	0	3388	0	ITGA7	12	56096870	Frame_Shift_Del	DEL	T	TCGA-B9-4116-01A-01D-1252-08	2449595	56096870	77755025	77	4634											
SMARCC2	6601	broad.mit.edu;bcgsc.ca	37	chr12	56559482	56559482	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgcctctgatactccAgctgccagtgccaattgagt	7	11	10	13	0	1	2	0	2	1	0	2	2	2	2	4	0	6	3	4	0	2	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:56559482A>G	ENST00000267064.4	-	26	2845	c.2759T>C	c.(2758-2760)cTg>cCg	p.L920P	SMARCC2_ENST00000550164.1_Splice_Site_p.L951P|SMARCC2_ENST00000394023.3_Splice_Site_p.L951P|SMARCC2_ENST00000347471.4_Splice_Site_p.L951P|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	920					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CTGATACTCCAGCTGCCAGTG	0.527																																					p.L951P													.	SMARCC2-229	0			c.T2852C						.						41	42	42					12																	56559482		2195	4272	6467	SO:0001630	splice_region_variant	6601	exon27			TACTCCAGCTGCC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.2758-1T>C	12.37:g.56559482A>G		Somatic	78	2		WXS	Illumina HiSeq	Phase_I	111	29	NM_139067	0	0	2	6	4	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.072625	0.76415	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.64803	1.07;-0.12;-0.01;-0.04	4.51	4.51	0.55191	.	0.109060	0.37178	N	0.002208	T	0.78298	0.4261	M	0.79475	2.455	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.998;0.998;0.999;0.998	D;D;D;D;D	0.83275	0.994;0.996;0.994;0.994;0.996	T	0.81577	-0.0869	10	0.87932	D	0	-3.3912	13.2826	0.60224	1.0:0.0:0.0:0.0	.	840;951;955;920;951	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	P	951;951;951;920	ENSP00000377591:L951P;ENSP00000449396:L951P;ENSP00000302919:L951P;ENSP00000267064:L920P	ENSP00000267064:L920P	L	-	2	0	SMARCC2	54845749	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.755000	0.91646	2.042000	0.60477	0.529000	0.55759	CTG	.		0.527	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		Missense_Mutation	G	56559482	A	G	56559482	5	3	50	1	0	0	0	0	0	0	1	0	14808	202	7	3	897	3	SMARCC2	12	56559482	Splice_Site	SNP	A	TCGA-B9-4116-01A-01D-1252-08	462612	56559482	77292413	78	4635											
PPFIA2	8499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	81661720	81661720	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtgttggaatctgtaataAtaaagctaagctgctgtagt	12	14	10	5	0	1	0	0	0	1	0	1	1	1	1	0	1	3	6	0	1	7	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:81661720A>G	ENST00000549396.1	-	29	3617	c.3457T>C	c.(3457-3459)Tta>Cta	p.L1153L	PPFIA2_ENST00000550359.2_Silent_p.L1000L|PPFIA2_ENST00000407050.4_Silent_p.L1052L|PPFIA2_ENST00000333447.7_Silent_p.L1141L|PPFIA2_ENST00000541570.2_Silent_p.L689L|PPFIA2_ENST00000541017.1_Silent_p.L339L|PPFIA2_ENST00000549325.1_Silent_p.L1138L|PPFIA2_ENST00000548586.1_Silent_p.L1147L|RP11-121G22.3_ENST00000549161.1_lincRNA|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000550584.2_Silent_p.L1153L|PPFIA2_ENST00000443686.3_Silent_p.L1048L|PPFIA2_ENST00000552948.1_Silent_p.L1132L	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	1153	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						ATCTGTAATAATAAAGCTAAG	0.363																																					p.L1153L		.											.	PPFIA2-231	0			c.T3457C						.						68	66	67					12																	81661720		1846	4101	5947	SO:0001819	synonymous_variant	8499	exon28			GTAATAATAAAGC	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.3457T>C	12.37:g.81661720A>G		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	32	8	NM_001220473	0	0	2	2	0	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1																																																																																			.		0.363	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			G	81661720	A	G	81661720	2	3	50	1	0	0	0	0	0	0	0	1	12336	98	4	3		3	PPFIA2	12	81661720	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	25102238	81661720	52190175	79	4636											
KIAA1033	23325	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	105512257	105512259	+	In_Frame_Del	DEL	GTG	GTG	-																															ttgttacgaggtgctatgaaGtggtgatgaacgtagtccac																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:105512257_105512259delGTG	ENST00000332180.5	+	7	556_558	c.469_471delGTG	c.(469-471)gtgdel	p.V158del		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						GTGCTATGAAGTGGTGATGAACG	0.34																																					p.157_157del		.											.	KIAA1033-91	0			c.469_471del						.																																			SO:0001651	inframe_deletion	23325	exon7			.	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.469_471delGTG	12.37:g.105512260_105512262delGTG	ENSP00000328062:p.Val158del	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	36	11	NM_015275	0	0	0	0	0		In_Frame_Del	DEL	ENST00000332180.5	37	CCDS41826.1																																																																																			.		0.34	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		-	105512259	GTG	-	105512257	7	5	50	1	0	1	0	1	0	0	0	0	8227	1029	36	0	495	0	KIAA1033	12	105512257	In_Frame_Del	DEL	GTG	TCGA-B9-4116-01A-01D-1252-08	23850537	105512257	28339638	80	4637											
ATXN2	6311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	111963052	111963052	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgagttcacctgcatcccAgggctccaggtccttctctt	5	13	9	14	0	2	1	1	1	1	0	6	1	5	1	4	2	1	3	4	2	0	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:111963052A>G	ENST00000377617.3	-	6	1281	c.1120T>C	c.(1120-1122)Tgg>Cgg	p.W374R	ATXN2_ENST00000549455.1_5'UTR|ATXN2_ENST00000535949.1_Missense_Mutation_p.W85R|ATXN2_ENST00000608853.1_Missense_Mutation_p.W214R|ATXN2_ENST00000389153.4_Missense_Mutation_p.W109R|ATXN2_ENST00000542287.2_Missense_Mutation_p.W109R|ATXN2_ENST00000550104.1_Missense_Mutation_p.W374R	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	374					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CCTGCATCCCAGGGCTCCAGG	0.418																																					p.W374R		.											.	ATXN2-136	0			c.T1120C						.						160	139	146					12																	111963052		2203	4300	6503	SO:0001583	missense	6311	exon6			CATCCCAGGGCTC	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.1120T>C	12.37:g.111963052A>G	ENSP00000366843:p.Trp374Arg	Somatic	218	1		WXS	Illumina HiSeq	Phase_I	116	42	NM_002973	0	0	12	18	6	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.391860	0.83011	.	.	ENSG00000204842	ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949;ENST00000471866;ENST00000548492	D;D	0.89617	-2.2;-2.54	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.93641	0.7969	M	0.68593	2.085	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.998;1.0	D;D;D;D	0.87578	0.996;0.996;0.994;0.998	D	0.94295	0.7532	10	0.87932	D	0	-4.5283	15.8835	0.79222	1.0:0.0:0.0:0.0	.	109;374;85;109	B3KT59;Q99700;Q24JQ7;F8VQP2	.;ATX2_HUMAN;.;.	R	109;374;374;109;85;50;117	ENSP00000366843:W374R;ENSP00000446576:W374R	ENSP00000366843:W374R	W	-	1	0	ATXN2	110447435	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	8.648000	0.91062	2.212000	0.71576	0.460000	0.39030	TGG	.		0.418	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		G	111963052	A	G	111963052	3	3	50	1	0	0	0	0	1	0	0	0	1212	188	7	3	2901	3	ATXN2	12	111963052	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	6450795	111963052	21888843	81	4638											
ZNF10	7556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	133732280	133732280	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagagacatttgaggcaaGtggcattcacccaaaagaaa	17	6	10	8	0	1	4	1	1	0	3	1	5	1	4	1	2	0	2	1	2	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:133732280G>C	ENST00000248211.6	+	5	670	c.448G>C	c.(448-450)Gtg>Ctg	p.V150L	ZNF10_ENST00000426665.2_Missense_Mutation_p.V150L|ZNF10_ENST00000402932.2_Intron|CTD-2140B24.4_ENST00000540096.2_Intron|ZNF268_ENST00000416488.1_Intron	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	150				Missing (in Ref. 1). {ECO:0000305}.	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)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TTTGAGGCAAGTGGCATTCAC	0.428																																					p.V150L		.											.	ZNF10-154	0			c.G448C						.						110	106	107					12																	133732280		2203	4300	6503	SO:0001583	missense	7556	exon5			AGGCAAGTGGCAT	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.448G>C	12.37:g.133732280G>C	ENSP00000248211:p.Val150Leu	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	43	10	NM_015394	0	0	8	12	4	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	37	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.273178	0.40194	.	.	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000537119	T;T;T	0.05447	3.44;3.44;4.56	4.44	4.44	0.53790	.	0.698949	0.11773	N	0.530882	T	0.04137	0.0115	N	0.16708	0.43	0.80722	D	1	P	0.34662	0.462	B	0.31614	0.133	T	0.51252	-0.8729	9	.	.	.	.	8.5148	0.33239	0.1041:0.0:0.8959:0.0	.	150	P21506	ZNF10_HUMAN	L	150;150;108	ENSP00000248211:V150L;ENSP00000393814:V150L;ENSP00000437397:V108L	.	V	+	1	0	ZNF10	132242353	0.671000	0.27521	1.000000	0.80357	0.991000	0.79684	1.986000	0.40677	2.460000	0.83146	0.655000	0.94253	GTG	.		0.428	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		C	133732280	G	C	133732280	3	2	50	1	0	0	0	0	1	0	0	0	17744	1029	36	4	462	4	ZNF10	12	133732280	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	21769228	133732280	119615	82	4639											
IL17D	53342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	21295994	21295994	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cccgtgggctgcacctgcgtCcccgagccggagaaggacgc	6	4	15	16	5	0	1	0	0	0	1	1	4	1	2	5	3	3	2	5	3	1	0	rs372465901		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr13:21295994C>T	ENST00000304920.3	+	3	618	c.510C>T	c.(508-510)gtC>gtT	p.V170V		NM_138284.1	NP_612141.1	Q8TAD2	IL17D_HUMAN	interleukin 17D	170					inflammatory response (GO:0006954)	extracellular space (GO:0005615)				endometrium(1)|skin(1)	2		all_cancers(29;9.63e-24)|all_epithelial(30;1.09e-19)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000301)|Epithelial(112;0.000633)|OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Lung(94;0.0154)|LUSC - Lung squamous cell carcinoma(192;0.0414)		GCACCTGCGTCCCCGAGCCGG	0.706																																					p.V170V		.											.	IL17D-90	0			c.C510T						.						39	39	39					13																	21295994		2190	4279	6469	SO:0001819	synonymous_variant	53342	exon3			CTGCGTCCCCGAG	AY078238	CCDS9292.1	13q11	2008-07-18			ENSG00000172458	ENSG00000172458		"Interleukins and interleukin receptors"	5984	protein-coding gene	gene with protein product	"interleukin 27"	607587				12097364	Standard	NM_138284		Approved	IL-22, IL-27, IL-17D, IL27, FLJ30846	uc001unm.3	Q8TAD2	OTTHUMG00000016521	ENST00000304920.3:c.510C>T	13.37:g.21295994C>T		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	209	72	NM_138284	0	0	0	0	0	B1AM69	Silent	SNP	ENST00000304920.3	37	CCDS9292.1																																																																																			.		0.706	IL17D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044087.1	NM_138284		T	21295994	C	T	21295994	2	4	50	1	0	0	0	0	0	0	0	1	7658	842	30	2		2	IL17D	13	21295994	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		21295994	93873884	83	4640											
TCL1B	9623	ucsc.edu	37	chr14	96157639	96157639	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctggtcctaacatatcAgccggagaggaaagactgac	13	6	12	10	1	1	3	1	1	0	2	2	5	2	4	2	3	3	2	2	3	3	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr14:96157639A>G	ENST00000340722.7	+	3	419	c.368A>G	c.(367-369)cAg>cGg	p.Q123R	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	123										cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		CTAACATATCAGCCGGAGAGG	0.547																																					p.Q123R													.	TCL1B-91	0			c.A368G						.						90	79	82					14																	96157639		2203	4300	6503	SO:0001583	missense	9623	exon3			CATATCAGCCGGA	AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.368A>G	14.37:g.96157639A>G	ENSP00000343223:p.Gln123Arg	Somatic	38	0		WXS	Illumina HiSeq		51	4	NM_004918	0	0	0	0	0	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	37	CCDS32151.1	.	.	.	.	.	.	.	.	.	.	A	3.956	-0.011387	0.07727	.	.	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.29397	1.57	2.4	-3.21	0.05140	.	.	.	.	.	T	0.10637	0.0260	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.31447	-0.9943	9	0.14656	T	0.56	0.0694	2.2796	0.04111	0.2791:0.0:0.3108:0.4101	.	123	O95988	TCL1B_HUMAN	R	123	ENSP00000343223:Q123R	ENSP00000343223:Q123R	Q	+	2	0	TCL1B	95227392	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.046000	0.01409	-0.616000	0.05671	0.260000	0.18958	CAG	.		0.547	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2			G	96157639	A	G	96157639	3	3	50	1	0	0	0	0	1	0	0	0	15737	188	7	3	378	3	TCL1B	14	96157639	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08		96157639	11191901	84	4641											
AP4E1	23431	hgsc.bcm.edu;broad.mit.edu	37	chr15	51285604	51285604	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaggtataaagaaattgTgggggaaagaaggctatctt	15	10	14	2	0	1	2	0	0	1	2	1	4	1	4	0	5	0	2	0	5	8	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr15:51285604T>G	ENST00000261842.5	+	17	2234	c.2128T>G	c.(2128-2130)Tgg>Ggg	p.W710G	AP4E1_ENST00000560508.1_Missense_Mutation_p.W635G	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	710					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AAAGAAATTGTGGGGGAAAGA	0.383																																					p.W710G		.											.	AP4E1-90	0			c.T2128G						.						66	61	63					15																	51285604		2196	4294	6490	SO:0001583	missense	23431	exon17			AAATTGTGGGGGA	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2128T>G	15.37:g.51285604T>G	ENSP00000261842:p.Trp710Gly	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	25	3	NM_007347	0	0	3	6	3	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936539	0.73442	.	.	ENSG00000081014	ENST00000261842	T	0.60920	0.15	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.66713	0.2817	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70517	-0.4850	10	0.87932	D	0	-4.9167	14.4124	0.67124	0.0:0.0:0.0:1.0	.	710	Q9UPM8	AP4E1_HUMAN	G	710	ENSP00000261842:W710G	ENSP00000261842:W710G	W	+	1	0	AP4E1	49072896	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.406000	0.73276	1.988000	0.58038	0.460000	0.39030	TGG	.		0.383	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51285604	T	G	51285604	3	3	50	1	0	0	0	0	1	0	0	0	752	1696	59	5	2194	5	AP4E1	15	51285604	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08		51285604	51245788	85	4642											
IGF1R	3480	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	99465632	99465632	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggctgcagcgcctccaaCttcgtctttgcaaggactat	7	11	10	13	2	1	0	0	0	1	0	3	1	2	1	2	2	4	3	2	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr15:99465632C>A	ENST00000268035.6	+	11	3068	c.2457C>A	c.(2455-2457)aaC>aaA	p.N819K	IGF1R_ENST00000558762.1_Missense_Mutation_p.N819K	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	819	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GCGCCTCCAACTTCGTCTTTG	0.517																																					p.N819K		.											.	IGF1R-1490	0			c.C2457A						.						105	102	103					15																	99465632		2197	4297	6494	SO:0001583	missense	3480	exon11			CTCCAACTTCGTC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2457C>A	15.37:g.99465632C>A	ENSP00000268035:p.Asn819Lys	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	350	122	NM_000875	0	0	8	18	10	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695512	0.48202	.	.	ENSG00000140443	ENST00000268035	T	0.68624	-0.34	5.5	4.59	0.56863	Immunoglobulin-like fold (1);	0.086755	0.47455	N	0.000239	T	0.57169	0.2035	L	0.44542	1.39	0.50171	D	0.999854	B;B	0.33964	0.434;0.18	B;B	0.34489	0.184;0.109	T	0.58747	-0.7582	10	0.54805	T	0.06	.	9.3354	0.38047	0.1455:0.7829:0.0:0.0716	.	819;819	C9J5X1;P08069	.;IGF1R_HUMAN	K	819	ENSP00000268035:N819K	ENSP00000268035:N819K	N	+	3	2	IGF1R	97283155	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	1.087000	0.30865	1.319000	0.45190	-0.127000	0.14921	AAC	.		0.517	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99465632	C	A	99465632	3	1	50	1	0	0	0	0	1	0	0	0	7592	564	20	4	2499	4	IGF1R	15	99465632	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	48180028	99465632	3065760	86	4643											
MKL2	57496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	14346228	14346228	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttatttgacacagcctagtTcacccccgccaccccagcaa	10	9	5	17	1	1	1	1	1	0	0	1	1	1	1	6	0	2	2	6	0	3	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:14346228T>G	ENST00000341243.5	+	13	2539	c.2539T>G	c.(2539-2541)Tca>Gca	p.S847A	MKL2_ENST00000571589.1_Missense_Mutation_p.S858A|MKL2_ENST00000574045.1_Missense_Mutation_p.S808A|MKL2_ENST00000318282.5_Missense_Mutation_p.S808A			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	847					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ACAGCCTAGTTCACCCCCGCC	0.522																																					p.S808A		.											.	MKL2-95	0			c.T2422G						.						111	107	108					16																	14346228		2197	4300	6497	SO:0001583	missense	57496	exon15			CCTAGTTCACCCC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.2539T>G	16.37:g.14346228T>G	ENSP00000345841:p.Ser847Ala	Somatic	208	0		WXS	Illumina HiSeq	Phase_I	246	70	NM_014048	0	0	2	2	0	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	37		.	.	.	.	.	.	.	.	.	.	T	15.37	2.812492	0.50527	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.98	4.89	0.63831	.	0.443487	0.25106	N	0.033091	T	0.29882	0.0747	L	0.41710	1.295	0.20563	N	0.999886	B;B	0.19583	0.022;0.037	B;B	0.15052	0.005;0.012	T	0.19353	-1.0308	9	0.22706	T	0.39	-7.812	6.5315	0.22330	0.1376:0.0725:0.0:0.7899	.	858;808	B4DGT8;Q9ULH7-4	.;.	A	808;847	.	ENSP00000339086:S808A	S	+	1	0	MKL2	14253729	1.000000	0.71417	0.041000	0.18516	0.317000	0.28152	4.265000	0.58865	1.089000	0.41292	-0.250000	0.11733	TCA	.		0.522	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		G	14346228	T	G	14346228	3	3	50	1	0	0	0	0	1	0	0	0	9627	1783	62	5	2472	5	MKL2	16	14346228	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08		14346228	76008525	87	4644											
BFAR	51283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	14755800	14755800	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tatacgccctcaagagctccCccaggctgagtctgctctac	8	9	8	16	1	3	2	1	1	2	1	4	2	4	2	3	1	4	3	3	1	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:14755800C>G	ENST00000261658.2	+	6	1112	c.835C>G	c.(835-837)Ccc>Gcc	p.P279A	BFAR_ENST00000563971.1_Missense_Mutation_p.P154A|BFAR_ENST00000426842.2_Missense_Mutation_p.P151A	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	279					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						CAAGAGCTCCCCCAGGCTGAG	0.567																																					p.P279A		.											.	BFAR-92	0			c.C835G						.						222	192	202					16																	14755800		2197	4300	6497	SO:0001583	missense	51283	exon6			AGCTCCCCCAGGC	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"RING-type (C3HC4) zinc fingers", "Sterile alpha motif (SAM) domain containing"	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.835C>G	16.37:g.14755800C>G	ENSP00000261658:p.Pro279Ala	Somatic	325	0		WXS	Illumina HiSeq	Phase_I	478	175	NM_016561	0	0	22	36	14	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524396	0.64747	.	.	ENSG00000103429	ENST00000261658;ENST00000426842	T;T	0.55760	2.85;0.5	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.991;0.997;0.996	T	0.67142	-0.5745	10	0.87932	D	0	.	18.1703	0.89743	0.0:1.0:0.0:0.0	.	151;279;279	B4DUT0;B2R9R6;Q9NZS9	.;.;BFAR_HUMAN	A	279;151	ENSP00000261658:P279A;ENSP00000400634:P151A	ENSP00000261658:P279A	P	+	1	0	BFAR	14663301	1.000000	0.71417	0.584000	0.28653	0.249000	0.25844	7.391000	0.79828	2.513000	0.84729	0.655000	0.94253	CCC	.		0.567	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		G	14755800	C	G	14755800	3	3	50	1	0	0	0	0	1	0	0	0	1415	623	22	4	853	4	BFAR	16	14755800	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	409572	14755800	75598953	88	4645											
SMG1	23049	broad.mit.edu;ucsc.edu	37	chr16	18851234	18851234	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cactaggacggggtacaattCcaggattctgaggagtttgg	10	10	14	7	1	1	1	0	1	1	0	2	4	2	4	1	6	1	2	1	6	3	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:18851234C>T	ENST00000446231.2	-	42	7143	c.6731G>A	c.(6730-6732)gGa>gAa	p.G2244E	SMG1_ENST00000389467.3_Missense_Mutation_p.G2244E			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2244	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GGGTACAATTCCAGGATTCTG	0.388																																					p.G2244E													.	SMG1-1160	0			c.G6731A						.						36	32	33					16																	18851234		1802	4074	5876	SO:0001583	missense	23049	exon42			ACAATTCCAGGAT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6731G>A	16.37:g.18851234C>T	ENSP00000402515:p.Gly2244Glu	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_015092	0	0	8	14	6	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.292945	0.60086	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01005	5.45;5.45	5.71	5.71	0.89125	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.101740	0.44483	D	0.000456	T	0.01156	0.0038	N	0.20766	0.605	0.29434	N	0.859676	B;B	0.31413	0.275;0.322	B;B	0.37422	0.161;0.249	T	0.55780	-0.8087	10	0.26408	T	0.33	.	15.3437	0.74317	0.0:0.861:0.139:0.0	.	2104;2244	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	E	2244	ENSP00000402515:G2244E;ENSP00000374118:G2244E	ENSP00000374118:G2244E	G	-	2	0	SMG1	18758735	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.464000	0.53057	2.701000	0.92244	0.563000	0.77884	GGA	.		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18851234	C	T	18851234	3	4	50	1	0	0	0	0	1	0	0	0	14827	855	30	2	4342	2	SMG1	16	18851234	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	4095434	18851234	71503519	89	4646											
GPRC5B	51704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19884048	19884048	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gacacgtactgagggaggagGtccagcccacagcctcggga	10	4	15	12	2	0	1	0	1	0	0	2	5	1	4	3	4	3	1	3	4	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:19884048G>A	ENST00000300571.2	-	2	311	c.120C>T	c.(118-120)gaC>gaT	p.D40D	GPRC5B_ENST00000537135.1_Silent_p.D66D|GPRC5B_ENST00000535671.1_Silent_p.D40D|GPRC5B_ENST00000569479.1_Silent_p.D40D|GPRC5B_ENST00000569847.1_Silent_p.D40D	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	40					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						GAGGGAGGAGGTCCAGCCCAC	0.637																																					p.D40D		.											.	GPRC5B-523	0			c.C120T						.						50	51	51					16																	19884048		2197	4300	6497	SO:0001819	synonymous_variant	51704	exon2			GAGGAGGTCCAGC	AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"GPCR / Class C : Orphans"	13308	protein-coding gene	gene with protein product		605948	"G protein-coupled receptor, family C, group 1, member B", "G protein-coupled receptor, family C, group 5, member B"			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.120C>T	16.37:g.19884048G>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	207	82	NM_016235	0	0	1	7	6	D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	CCDS10581.1																																																																																			.		0.637	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			A	19884048	G	A	19884048	2	1	50	1	0	0	0	0	0	0	0	1	6746	1252	44	2		2	GPRC5B	16	19884048	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	1032814	19884048	70470705	90	4647											
BCL7C	9274	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr16	30899187	30899187	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggacaggcaggccggcttctCaggggtcaggggcatttggg	6	7	19	9	1	2	0	2	0	1	0	3	1	2	1	1	9	0	3	1	9	0	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:30899187C>T	ENST00000215115.4	-	6	1668	c.653G>A	c.(652-654)tGa>tAa	p.*218*	MIR4519_ENST00000564901.1_RNA|MIR4519_ENST00000565573.1_RNA|BCL7C_ENST00000380317.4_Intron|MIR4519_ENST00000570025.1_RNA|AC106782.20_ENST00000572471.1_RNA	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	0					apoptotic process (GO:0006915)			p.*218L(1)		large_intestine(1)|lung(3)|prostate(1)|skin(1)	6			Colorectal(24;0.198)			GCCGGCTTCTCAGGGGTCAGG	0.592																																					p.X218X		.											.	BCL7C-227	1	Nonstop extension(1)	lung(1)	c.G653A						.						81	107	98					16																	30899187		2196	4300	6496	SO:0001819	synonymous_variant	9274	exon6			GCTTCTCAGGGGT	AJ223980	CCDS10693.1, CCDS67012.1	16p11	2012-11-19			ENSG00000099385	ENSG00000099385			1006	protein-coding gene	gene with protein product		605847				9931421	Standard	NM_004765		Approved		uc002dzv.3	Q8WUZ0	OTTHUMG00000177719	ENST00000215115.4:c.653G>A	16.37:g.30899187C>T		Somatic	404	0		WXS	Illumina HiSeq	Phase_I	677	259	NM_004765	0	0	27	54	27	O43770|Q6PD89	Silent	SNP	ENST00000215115.4	37	CCDS10693.1																																																																																			.		0.592	BCL7C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255547.3	NM_004765		T	30899187	C	T	30899187	2	4	50	1	0	0	0	0	0	0	0	1	1381	837	29	2		2	BCL7C	16	30899187	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	11015139	30899187	59455566	91	4648											
ZNF423	23090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	49671278	49671278	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggccttggacttcttgctGtgggccagtggaatgttctt	4	15	13	9	1	2	0	0	0	2	0	3	2	2	2	2	4	1	2	2	4	1	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:49671278G>T	ENST00000561648.1	-	4	1838	c.1785C>A	c.(1783-1785)caC>caA	p.H595Q	ZNF423_ENST00000262383.2_Missense_Mutation_p.H595Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.H478Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.H535Q|ZNF423_ENST00000563137.2_Missense_Mutation_p.H535Q|ZNF423_ENST00000562871.1_Missense_Mutation_p.H535Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.H478Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	595					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ACTTCTTGCTGTGGGCCAGTG	0.572																																					p.H595Q		.											.	ZNF423-228	0			c.C1785A						.						127	100	109					16																	49671278		2198	4300	6498	SO:0001583	missense	23090	exon4			CTTGCTGTGGGCC	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1785C>A	16.37:g.49671278G>T	ENSP00000455426:p.His595Gln	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	318	99	NM_015069	0	0	0	6	6	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	G	8.424	0.846973	0.17034	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08634	3.07;3.14	4.78	2.8	0.32819	.	0.047718	0.85682	D	0.000000	T	0.05273	0.0140	N	0.24115	0.695	0.37616	D	0.921121	B	0.26120	0.142	B	0.24394	0.053	T	0.43702	-0.9375	9	.	.	.	.	8.2567	0.31760	0.2436:0.0:0.7564:0.0	.	595	Q2M1K9	ZN423_HUMAN	Q	595;478	ENSP00000262383:H595Q;ENSP00000442321:H478Q	.	H	-	3	2	ZNF423	48228779	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.823000	0.55715	0.439000	0.26476	0.561000	0.74099	CAC	.		0.572	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49671278	G	T	49671278	3	4	50	1	0	0	0	0	1	0	0	0	17930	1368	48	4	2089	4	ZNF423	16	49671278	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	18772091	49671278	40683475	92	4649											
IRX3	79191	hgsc.bcm.edu	37	chr16	54317587	54317598	+	Stop_Codon_Del	DEL	TTTTTAAAGAAC	TTTTTAAAGAAC	-																															ttttttttgtttttttgtttTttttaaagaactaggatgag																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	TTTTTAAAGAAC	TTTTTAAAGAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:54317587_54317598delTTTTTAAAGAAC	ENST00000329734.3	-	0	2218_2229					NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3						mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						TTTTTTGTTTTTTTTAAAGAACTAGGATGAGG	0.377																																					p.502_502del	GBM(143;1830 1866 4487 4646 37383)	.											.	IRX3-90	0			c.1506_1922del						.																																			SO:0001567	stop_retained_variant	79191	exon4			.	U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"Homeoboxes / TALE class"	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	Exception_encountered	16.37:g.54317587_54317598delTTTTTAAAGAAC	Exception_encountered	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	75	17	NM_024336	0	0	0	0	0	Q7Z4A4|Q7Z4A5|Q8IVC6	Frame_Shift_Del	DEL	ENST00000329734.3	37	CCDS10750.1																																																																																			.		0.377	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2			-	54317598	TTTTTAAAGAAC	-	54317587	7	5	50	1	0	1	0	1	0	0	0	0	7866	1856	64	0		0	IRX3	16	54317587	Stop_Codon_Del	DEL	TTTTTAAAGAAC	TCGA-B9-4116-01A-01D-1252-08	4646309	54317587	36037166	93	4650											
BBS2	583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56531663	56531663	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcattccctcaccttaactaGcacctttcgtaattcctcaa	10	13	3	15	1	2	0	2	0	0	0	5	0	4	0	4	0	2	3	4	0	4	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:56531663G>A	ENST00000245157.5	-	14	2209	c.1789C>T	c.(1789-1791)Cta>Tta	p.L597L	BBS2_ENST00000568104.1_Intron	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	597					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						ACCTTAACTAGCACCTTTCGT	0.373									Bardet-Biedl syndrome																												p.L597L		.											.	BBS2-91	0			c.C1789T						.						141	133	136					16																	56531663		2198	4300	6498	SO:0001819	synonymous_variant	583	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAACTAGCACCTT	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.1789C>T	16.37:g.56531663G>A		Somatic	282	0		WXS	Illumina HiSeq	Phase_I	75	31	NM_031885	0	0	0	4	4	Q96CM0|Q96SN9	Silent	SNP	ENST00000245157.5	37	CCDS32451.1																																																																																			.		0.373	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		A	56531663	G	A	56531663	2	1	50	1	0	0	0	0	0	0	0	1	1339	962	34	2		2	BBS2	16	56531663	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	2214076	56531663	33823090	94	4651											
ZC3H18	124245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	88653023	88653023	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggatgatgacctggaaGaaggtgaagtgaaggacccc	13	7	14	7	0	1	5	1	4	0	1	1	8	1	8	3	4	0	0	3	4	4	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:88653023G>T	ENST00000301011.5	+	3	819	c.619G>T	c.(619-621)Gaa>Taa	p.E207*	ZC3H18_ENST00000452588.2_Nonsense_Mutation_p.E207*	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	207						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		TGACCTGGAAGAAGGTGAAGT	0.542																																					p.E207X	Ovarian(121;375 2276 20373 38669)	.											.	ZC3H18-69	0			c.G619T						.						136	105	116					16																	88653023		2198	4300	6498	SO:0001587	stop_gained	124245	exon3			CTGGAAGAAGGTG	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.619G>T	16.37:g.88653023G>T	ENSP00000301011:p.Glu207*	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	166	40	NM_144604	0	0	12	14	2	Q96DG4|Q96MP7	Nonsense_Mutation	SNP	ENST00000301011.5	37	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	G	41	8.860379	0.98980	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588;ENST00000545404	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-25.7045	18.3833	0.90457	0.0:0.0:1.0:0.0	.	.	.	.	X	207;207;207;90	.	ENSP00000289509:E207X	E	+	1	0	ZC3H18	87180524	1.000000	0.71417	0.978000	0.43139	0.763000	0.43281	9.161000	0.94739	2.350000	0.79820	0.462000	0.41574	GAA	.		0.542	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88653023	G	T	88653023	4	4	50	1	0	0	0	0	0	1	0	0	17600	943	33	4	625	4	ZC3H18	16	88653023	Nonsense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	32121360	88653023	1701730	95	4652											
MINK1	100130311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4800540	4800540	+	5'Flank	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgggggcagcagccaagtTtacttcatgactctgaaccg	9	10	11	11	1	3	2	1	2	2	0	3	2	3	2	2	2	4	3	2	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:4800540T>G	ENST00000381365.3	+	0	0				MINK1_ENST00000347992.7_Silent_p.V1290V|C17orf107_ENST00000521575.1_5'Flank|MINK1_ENST00000453408.3_Silent_p.V1299V|MINK1_ENST00000355280.6_Silent_p.V1319V	NM_001145536.1	NP_001139008.1	Q6ZR85	CQ107_HUMAN	chromosome 17 open reading frame 107											endometrium(2)	2						GCAGCCAAGTTTACTTCATGA	0.612																																					p.V1319V		.											.	MINK1-943	0			c.T3957G						.						71	73	72					17																	4800540		1933	4140	6073	SO:0001631	upstream_gene_variant	50488	exon32			CCAAGTTTACTTC	AK128415	CCDS45591.1	17p13.2	2009-09-30			ENSG00000205710	ENSG00000205710			37238	protein-coding gene	gene with protein product							Standard	NM_001145536		Approved		uc002fzl.3	Q6ZR85	OTTHUMG00000164838		17.37:g.4800540T>G	Exception_encountered	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	96	26	NM_153827	0	0	65	142	77		Silent	SNP	ENST00000381365.3	37	CCDS45591.1																																																																																			.		0.612	C17orf107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380556.1	NM_001145536		G	4800540	T	G	4800540	1	3	50	0	1	0	0	0	0	0	0	0	9612	1828	64	5		5	MINK1	17	4800540	5'Flank	SNP	T	TCGA-B9-4116-01A-01D-1252-08		4800540	76394670	96	4653											
SLC16A13	201232	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	6942168	6942169	+	In_Frame_Ins	INS	-	-	ATA																															gcctgggactgttgcagatgINSatagagagcatcggggggct																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:6942168_6942169insATA	ENST00000308027.6	+	3	1349_1350	c.1041_1042insATA	c.(1042-1044)ata>ATAata	p.348_348I>II		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	348						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TGTTGCAGATGATAGAGAGCAT	0.589																																					p.M347delinsMI		.											.	SLC16A13-92	0			c.1041_1042insATA						.																																			SO:0001652	inframe_insertion	201232	exon3			.	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"Solute carriers"	31037	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 13"		"solute carrier family 16 (monocarboxylic acid transporters), member 13"				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.1042_1044dupATA	17.37:g.6942169_6942171dupATA	ENSP00000309751:p.Ile348dup	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	467	118	NM_201566	0	0	0	0	0	A3KMG3|A5PKU5|Q2VP92	In_Frame_Ins	INS	ENST00000308027.6	37	CCDS11085.1																																																																																			.		0.589	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2			ATA	6942169	-	ATA	6942168	7	5	50	1	0	1	1	0	0	0	0	0	14438	1290	45	0	1051	0	SLC16A13	17	6942168	In_Frame_Ins	INS	-	TCGA-B9-4116-01A-01D-1252-08	2141628	6942168	74253042	97	4654											
YBX2	51087	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7193332	7193332	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcggggggactcgctcatctCcctgctgttggtgcccctcc	2	10	13	16	2	2	0	1	0	1	0	5	1	3	1	4	4	2	3	4	4	0	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:7193332C>A	ENST00000007699.5	-	6	866	c.803G>T	c.(802-804)gGa>gTa	p.G268V	YBX2_ENST00000570627.1_5'Flank	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	268	Pro-rich.|Required for mRNA-binding.				mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						TCGCTCATCTCCCTGCTGTTG	0.632																																					p.G268V		.											.	YBX2-90	0			c.G803T						.						52	55	54					17																	7193332		2203	4300	6503	SO:0001583	missense	51087	exon6			TCATCTCCCTGCT	AF096834	CCDS11098.1	17p13.1	2013-12-20			ENSG00000006047	ENSG00000006047			17948	protein-coding gene	gene with protein product		611447				10100484, 9780336	Standard	NM_015982		Approved	MSY2, CSDA3	uc002gfq.2	Q9Y2T7	OTTHUMG00000177992	ENST00000007699.5:c.803G>T	17.37:g.7193332C>A	ENSP00000007699:p.Gly268Val	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	274	112	NM_015982	0	0	0	0	0	D3DTP1|Q8N4P0	Missense_Mutation	SNP	ENST00000007699.5	37	CCDS11098.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845908	0.51164	.	.	ENSG00000006047	ENST00000007699	T	0.29142	1.58	5.34	5.34	0.76211	.	0.251035	0.34750	N	0.003707	T	0.52370	0.1730	M	0.62723	1.935	0.53688	D	0.999978	D	0.89917	1.0	D	0.74023	0.982	T	0.52426	-0.8577	10	0.72032	D	0.01	-13.9828	14.9276	0.70890	0.0:1.0:0.0:0.0	.	268	Q9Y2T7	YBOX2_HUMAN	V	268	ENSP00000007699:G268V	ENSP00000007699:G268V	G	-	2	0	YBX2	7134056	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.987000	0.49378	2.689000	0.91719	0.462000	0.41574	GGA	.		0.632	YBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440172.2	NM_015982		A	7193332	C	A	7193332	3	1	50	1	0	0	0	0	1	0	0	0	17503	855	30	4	303	4	YBX2	17	7193332	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	251164	7193332	74001878	98	4655											
SPEM1	374768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7324267	7324267	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagcagagttctcctgcagtCcatcttcggtgcaccatgga	9	10	10	12	1	2	1	0	0	2	1	5	2	3	2	3	2	3	4	3	2	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:7324267C>A	ENST00000323675.3	+	3	298	c.273C>A	c.(271-273)gtC>gtA	p.V91V	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	91					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				CTCCTGCAGTCCATCTTCGGT	0.597																																					p.V91V		.											.	SPEM1-90	0			c.C273A						.						112	120	117					17																	7324267		2106	4203	6309	SO:0001819	synonymous_variant	374768	exon3			TGCAGTCCATCTT	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"chromosome 17 open reading frame 83"	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.273C>A	17.37:g.7324267C>A		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	335	133	NM_199339	0	0	0	0	0		Silent	SNP	ENST00000323675.3	37	CCDS42254.1																																																																																			.		0.597	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339		A	7324267	C	A	7324267	2	1	50	1	0	0	0	0	0	0	0	1	15069	842	30	4		4	SPEM1	17	7324267	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	130935	7324267	73870943	99	4656											
GUCY2D	3000	hgsc.bcm.edu;broad.mit.edu	37	chr17	7919305	7919305	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgtgctctggactcgggctAccaggtggagctgcgaggcc	5	7	16	13	3	1	0	0	0	1	0	2	3	1	2	3	5	4	3	3	5	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:7919305A>C	ENST00000254854.4	+	17	3254	c.3104A>C	c.(3103-3105)tAc>tCc	p.Y1035S		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	1035					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				GACTCGGGCTACCAGGTGGAG	0.697																																					p.Y1035S		.											.	GUCY2D-319	0			c.A3104C						.						34	29	30					17																	7919305		2202	4299	6501	SO:0001583	missense	3000	exon17			CGGGCTACCAGGT	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.3104A>C	17.37:g.7919305A>C	ENSP00000254854:p.Tyr1035Ser	Somatic	32	1		WXS	Illumina HiSeq	Phase_I	37	12	NM_000180	0	0	0	0	0	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268354	0.59540	.	.	ENSG00000132518	ENST00000254854	T	0.80824	-1.42	4.22	3.12	0.35913	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.133374	0.34652	N	0.003784	D	0.86797	0.6019	M	0.90977	3.165	0.30085	N	0.808806	P	0.48503	0.911	P	0.51974	0.686	D	0.84338	0.0525	10	0.87932	D	0	.	7.7707	0.29006	0.352:0.0:0.0:0.648	.	1035	Q02846	GUC2D_HUMAN	S	1035	ENSP00000254854:Y1035S	ENSP00000254854:Y1035S	Y	+	2	0	GUCY2D	7860030	0.971000	0.33674	0.996000	0.52242	0.784000	0.44337	1.713000	0.37951	0.753000	0.32945	0.260000	0.18958	TAC	.		0.697	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			C	7919305	A	C	7919305	3	2	50	1	0	0	0	0	1	0	0	0	6918	391	14	5	3166	5	GUCY2D	17	7919305	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	595038	7919305	73275905	100	4657											
NCOR1	9611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	15964734	15964734	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctactagaagagtctgaActttgagagccacgttccct	11	10	9	11	1	1	4	0	2	1	3	2	5	2	4	2	0	4	2	2	0	4	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:15964734A>G	ENST00000268712.3	-	37	6119	c.5862T>C	c.(5860-5862)agT>agC	p.S1954S	NCOR1_ENST00000395851.1_Intron|NCOR1_ENST00000395857.3_Silent_p.S538S	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1954	Interaction with C1D. {ECO:0000250}.|Poly-Ser.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AAGAGTCTGAACTTTGAGAGC	0.428																																					p.S1954S		.											.	NCOR1-229	0			c.T5862C						.						219	200	206					17																	15964734		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon37			GTCTGAACTTTGA	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.5862T>C	17.37:g.15964734A>G		Somatic	367	0		WXS	Illumina HiSeq	Phase_I	325	87	NM_006311	0	0	15	28	13	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			.		0.428	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15964734	A	G	15964734	2	3	50	1	0	0	0	0	0	0	0	1	10261	40	2	3		3	NCOR1	17	15964734	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	8045429	15964734	65230476	101	4658											
MAPK7	5598	hgsc.bcm.edu	37	chr17	19285267	19285267	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggctggggcctctgggggcCcctccactgaccccttggct	2	8	15	16	0	1	1	0	1	1	0	2	1	2	1	6	6	0	2	6	6	0	1	rs144954037	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:19285267C>T	ENST00000308406.5	+	5	2037	c.1651C>T	c.(1651-1653)Ccc>Tcc	p.P551S	MAPK7_ENST00000395604.3_Missense_Mutation_p.P551S|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395602.4_Missense_Mutation_p.P551S|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000299612.7_Missense_Mutation_p.P412S	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	551	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CTCTGGGGGCCCCTCCACTGA	0.677													C|||	36	0.0071885	0.0257	0.0029	5008	,	,		10870	0		0	False		,,,				2504	0				p.P551S		.											.	MAPK7-1402	0			c.C1651T						.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	72,3880		1,70,1905	10	20	17		1651,1234,1651,1651	4.2	1	17	dbSNP_134	17	0,7860		0,0,3930	yes	missense,missense,missense,missense	MAPK7	NM_002749.3,NM_139032.2,NM_139033.2,NM_139034.2	74,74,74,74	1,70,5835	TT,TC,CC		0.0,1.8219,0.6095	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	551/817,412/678,551/817,551/817	19285267	72,11740	1976	3930	5906	SO:0001583	missense	5598	exon5			GGGGGCCCCTCCA	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1651C>T	17.37:g.19285267C>T	ENSP00000311005:p.Pro551Ser	Somatic	3	2		WXS	Illumina HiSeq	Phase_I	9	7	NM_002749	0	0	10	24	14	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	37	CCDS11206.1	22	0.010073260073260074	19	0.03861788617886179	0	0.0	1	0.0017482517482517483	2	0.002638522427440633	C	17.38	3.374357	0.61735	0.018219	0.0	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.73152	-0.49;-0.72;-0.49;-0.49	5.16	4.19	0.49359	.	0.251911	0.30455	N	0.009581	T	0.25044	0.0608	L	0.27053	0.805	0.27227	N	0.959505	B	0.02656	0.0	B	0.04013	0.001	T	0.42310	-0.9459	10	0.59425	D	0.04	-8.4654	11.3923	0.49822	0.0:0.9108:0.0:0.0892	.	551	Q13164	MK07_HUMAN	S	551;412;551;551	ENSP00000311005:P551S;ENSP00000299612:P412S;ENSP00000378968:P551S;ENSP00000378966:P551S	ENSP00000299612:P412S	P	+	1	0	MAPK7	19225860	0.024000	0.19004	0.993000	0.49108	0.942000	0.58702	1.510000	0.35790	1.162000	0.42619	0.561000	0.74099	CCC	C|0.990;T|0.010		0.677	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		T	19285267	C	T	19285267	3	4	50	1	0	0	0	0	1	0	0	0	9307	623	22	2	1665	2	MAPK7	17	19285267	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	3320533	19285267	61909943	102	4659											
PLEKHH3	79990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40821477	40821477	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaggaggagctggctctCtcccaccctcaaggccaggg	7	6	13	15	0	2	0	1	0	1	0	4	2	3	2	3	5	2	3	3	5	1	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:40821477C>A	ENST00000591022.1	-	12	2563	c.2176G>T	c.(2176-2178)Gag>Tag	p.E726*	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000412503.1_Nonsense_Mutation_p.E549*|PLEKHH3_ENST00000293349.6_Nonsense_Mutation_p.E723*	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	726	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		AGCTGGCTCTCTCCCACCCTC	0.622																																					p.E726X		.											.	PLEKHH3-158	0			c.G2176T						.						20	23	22					17																	40821477		2202	4300	6502	SO:0001587	stop_gained	79990	exon12			GGCTCTCTCCCAC	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.2176G>T	17.37:g.40821477C>A	ENSP00000468678:p.Glu726*	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	114	48	NM_024927	0	0	25	49	24	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Nonsense_Mutation	SNP	ENST00000591022.1	37	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	C	41	8.827108	0.98968	.	.	ENSG00000068137	ENST00000293349;ENST00000412503	.	.	.	4.43	4.43	0.53597	.	0.336296	0.21518	N	0.073272	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-10.0927	16.1774	0.81862	0.0:1.0:0.0:0.0	.	.	.	.	X	726;549	.	ENSP00000293349:E726X	E	-	1	0	PLEKHH3	38075003	0.999000	0.42202	0.997000	0.53966	0.955000	0.61496	3.927000	0.56499	2.465000	0.83290	0.655000	0.94253	GAG	.		0.622	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		A	40821477	C	A	40821477	4	1	50	1	0	0	0	0	0	1	0	0	12104	922	32	4	213	4	PLEKHH3	17	40821477	Nonsense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	21536210	40821477	40373733	103	4660											
UBTF	7343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	42289718	42289718	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcggaagcctaacctcgtaCtccttccgctgctccagggc	7	8	10	16	3	0	0	0	0	0	0	4	1	3	1	5	2	5	3	5	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:42289718C>G	ENST00000302904.4	-	8	1257	c.765G>C	c.(763-765)gaG>gaC	p.E255D	UBTF_ENST00000529383.1_Missense_Mutation_p.E255D|UBTF_ENST00000436088.1_Missense_Mutation_p.E255D|UBTF_ENST00000393606.3_Intron|UBTF_ENST00000343638.5_Intron|UBTF_ENST00000526094.1_Intron|UBTF_ENST00000533177.1_Intron|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000527034.1_Intron			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	255					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TAACCTCGTACTCCTTCCGCT	0.617																																					p.E255D		.											.	UBTF-90	0			c.G765C						.						97	90	93					17																	42289718		2203	4300	6503	SO:0001583	missense	7343	exon8			CTCGTACTCCTTC	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.765G>C	17.37:g.42289718C>G	ENSP00000302640:p.Glu255Asp	Somatic	192	2		WXS	Illumina HiSeq	Phase_I	290	103	NM_014233	0	0	0	0	0	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	c	12.04	1.818327	0.32145	.	.	ENSG00000108312	ENST00000302904;ENST00000436088;ENST00000529383	D;D;D	0.98207	-4.79;-4.79;-4.79	4.15	4.15	0.48705	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.520474	0.19709	N	0.107851	D	0.91908	0.7438	N	0.02539	-0.55	0.36012	D	0.838154	B	0.09022	0.002	B	0.15052	0.012	D	0.90257	0.4298	10	0.30078	T	0.28	-23.3092	10.3677	0.44035	0.0:0.9073:0.0:0.0927	.	255	P17480	UBF1_HUMAN	D	255	ENSP00000302640:E255D;ENSP00000390669:E255D;ENSP00000435708:E255D	ENSP00000302640:E255D	E	-	3	2	UBTF	39645244	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.080000	0.50112	2.305000	0.77605	0.456000	0.33151	GAG	.		0.617	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		G	42289718	C	G	42289718	3	3	50	1	0	0	0	0	1	0	0	0	16942	564	20	4	1585	4	UBTF	17	42289718	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	1468241	42289718	38905492	104	4661											
MEX3D	399664	hgsc.bcm.edu	37	chr19	1555892	1555892	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggccctgcgggggtcgccaGgacagcgcgcccaccgggtc	4	3	18	16	5	0	0	0	0	0	0	2	1	0	1	4	5	2	0	4	5	0	0	rs543107043	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:1555892G>A	ENST00000402693.4	-	2	1625	c.1626C>T	c.(1624-1626)tcC>tcT	p.S542S	AC027307.2_ENST00000581992.1_RNA|MEX3D_ENST00000388824.6_Silent_p.S542S|AC027307.1_ENST00000410788.1_RNA	NM_203304.3	NP_976049.3	Q86XN8	MEX3D_HUMAN	mex-3 RNA binding family member D	542					mRNA destabilization (GO:0061157)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|lung(3)	4		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGTCGCCAGGACAGCGCGC	0.816													G|||	65	0.0129792	0.0477	0.0029	5008	,	,		4540	0		0	False		,,,				2504	0				p.S542S		.											.	MEX3D-658	0			c.C1626T						.						1	1	1					19																	1555892		484	1166	1650	SO:0001819	synonymous_variant	399664	exon2			TCGCCAGGACAGC	AB107353	CCDS32865.2	19p13.3	2013-08-21	2013-08-21	2007-07-18	ENSG00000181588	ENSG00000181588		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	16734	protein-coding gene	gene with protein product	"bcl-2 ARE RNA binding protein"	611009	"ring finger and KH domain containing 1", "mex-3 homolog D (C. elegans)"	RKHD1		17267406	Standard	NM_203304		Approved	Tino, KIAA2031, OK/SW-cl.4, RNF193	uc010dsn.3	Q86XN8	OTTHUMG00000150369	ENST00000402693.4:c.1626C>T	19.37:g.1555892G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_203304	0	0	0	0	0	A0PJL8|A1L023|E9PAL6|Q71M49	Silent	SNP	ENST00000402693.4	37	CCDS32865.2																																																																																			.		0.816	MEX3D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317870.2	NM_203304		A	1555892	G	A	1555892	2	1	50	1	0	0	0	0	0	0	0	1	9537	987	35	2		2	MEX3D	19	1555892	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08		1555892	57573091	105	4662											
GNA11	2767	hgsc.bcm.edu	37	chr19	3110145	3110145	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcacgtgccccgtcccccAggcacgggcgagagcgggaa	7	3	14	17	5	1	1	1	0	0	1	2	3	2	2	5	3	2	1	5	3	1	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:3110145A>C	ENST00000078429.4	+	2	378		c.e2-1			NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)						action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		CCCGTCCCCCAGGCACGGGCG	0.692			Mis		uveal melanoma																																.		.		Dom	yes		19	19p13.3	2767	"guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"		E	.	GNA11-1957	0			c.137-2A>C						.						24	19	21					19																	3110145		2202	4299	6501	SO:0001630	splice_region_variant	2767	exon2			TCCCCCAGGCACG	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256			4379	protein-coding gene	gene with protein product		139313	"hypocalciuric hypercalcemia 2"	HHC2		1302014, 23802516	Standard	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.137-1A>C	19.37:g.3110145A>C		Somatic	18	2		WXS	Illumina HiSeq	Phase_I	39	5	NM_002067	0	0	0	0	0	O15109|Q14350|Q6IB00	Splice_Site	SNP	ENST00000078429.4	37	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	A	12.98	2.100153	0.37048	.	.	ENSG00000088256	ENST00000078429	.	.	.	4.05	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8583	0.52451	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GNA11	3061145	1.000000	0.71417	0.957000	0.39632	0.158000	0.22134	9.110000	0.94302	1.468000	0.48064	0.454000	0.30748	.	.		0.692	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2	NM_002067	Intron	C	3110145	A	C	3110145	5	2	50	1	0	0	0	0	0	0	1	0	6519	202	7	5	141	5	GNA11	19	3110145	Splice_Site	SNP	A	TCGA-B9-4116-01A-01D-1252-08	1554253	3110145	56018838	106	4663											
TIMM44	10469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8002997	8002997	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttatactttctttcattTctttgtttttggctaattct	5	27	3	6	0	4	0	1	0	3	0	4	0	4	0	0	1	1	2	0	1	3	12			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:8002997T>A	ENST00000270538.3	-	3	495	c.227A>T	c.(226-228)gAa>gTa	p.E76V		NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	76					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						TTCTTTCATTTCTTTGTTTTT	0.393																																					p.E76V		.											.	TIMM44-91	0			c.A227T						.						194	192	193					19																	8002997		2203	4300	6503	SO:0001583	missense	10469	exon3			TTCATTTCTTTGT	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.227A>T	19.37:g.8002997T>A	ENSP00000270538:p.Glu76Val	Somatic	319	0		WXS	Illumina HiSeq	Phase_I	485	164	NM_006351	0	0	16	32	16	A8K0R9|D6W664|Q8N193	Missense_Mutation	SNP	ENST00000270538.3	37	CCDS12192.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.629496	0.87660	.	.	ENSG00000104980	ENST00000270538	D	0.87491	-2.26	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.93625	0.7964	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94461	0.7676	10	0.87932	D	0	-30.5113	13.3329	0.60500	0.0:0.0:0.0:1.0	.	76	O43615	TIM44_HUMAN	V	76	ENSP00000270538:E76V	ENSP00000270538:E76V	E	-	2	0	TIMM44	7908997	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.452000	0.80683	2.047000	0.60756	0.528000	0.53228	GAA	.		0.393	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3			A	8002997	T	A	8002997	3	1	50	1	0	0	0	0	1	0	0	0	15944	1783	62	5	1175	5	TIMM44	19	8002997	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	4892852	8002997	51125986	107	4664											
RAB11B	9230	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	8468330	8468331	+	Frame_Shift_Del	DEL	CA	CA	-																															cgtgtcacagaaacagatcgCagaccgcgctgcccacgacg																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:8468330_8468331delCA	ENST00000328024.6	+	5	763_764	c.545_546delCA	c.(544-546)gcafs	p.A182fs		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	182					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						AAACAGATCGCAGACCGCGCTG	0.653																																					p.182_182del		.											.	RAB11B-227	0			c.545_546del						.																																			SO:0001589	frameshift_variant	9230	exon5			.	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"RAB, member RAS oncogene"	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.545_546delCA	19.37:g.8468330_8468331delCA	ENSP00000333547:p.Ala182fs	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	255	75	NM_004218	0	0	0	0	0	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Frame_Shift_Del	DEL	ENST00000328024.6	37	CCDS12201.1																																																																																			.		0.653	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218		-	8468331	CA	-	8468330	7	5	50	1	0	1	0	1	0	0	0	0	12924	710	25	0	563	0	RAB11B	19	8468330	Frame_Shift_Del	DEL	CA	TCGA-B9-4116-01A-01D-1252-08	465333	8468330	50660653	108	4665											
OR7E24	26648	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	9362275	9362275	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattatgttacagctcaccTgcttcaaggatgtggacatt	10	14	9	8	0	2	1	2	1	0	0	2	3	2	3	1	2	3	3	1	2	3	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:9362275T>G	ENST00000456448.1	+	1	670	c.556T>G	c.(556-558)Tgc>Ggc	p.C186G		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						ACAGCTCACCTGCTTCAAGGA	0.403																																					p.C186G		.											.	OR7E24-47	0			c.T556G						.						96	100	99					19																	9362275		2015	4185	6200	SO:0001583	missense	26648	exon1			CTCACCTGCTTCA	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.556T>G	19.37:g.9362275T>G	ENSP00000387523:p.Cys186Gly	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	47	12	NM_001079935	0	0	0	0	0	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	37	CCDS45955.1	.	.	.	.	.	.	.	.	.	.	t	10.40	1.340959	0.24339	.	.	ENSG00000237521	ENST00000456448	T	0.00224	8.51	2.21	-0.132	0.13489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00241	0.0007	L	0.53249	1.67	0.09310	N	1	D	0.52996	0.957	P	0.50490	0.642	T	0.48614	-0.9020	9	0.87932	D	0	.	6.5019	0.22174	0.0:0.4011:0.0:0.5989	.	186	Q6IFN5	O7E24_HUMAN	G	186	ENSP00000387523:C186G	ENSP00000387523:C186G	C	+	1	0	OR7E24	9223275	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.214000	0.32419	-0.264000	0.09365	-0.483000	0.04790	TGC	.		0.403	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			G	9362275	T	G	9362275	3	3	50	1	0	0	0	0	1	0	0	0	11247	1580	55	5	558	5	OR7E24	19	9362275	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	893945	9362275	49766708	109	4666											
RDH8	50700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10132218	10132218	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccattctgcaggccattgtCaacgtcatcagctcgactcg	8	11	8	14	3	4	0	3	0	1	0	7	1	5	0	2	1	3	2	2	1	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:10132218C>A	ENST00000171214.1	+	6	978	c.729C>A	c.(727-729)gtC>gtA	p.V243V	RDH8_ENST00000591589.1_Silent_p.V263V	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	243					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	AGGCCATTGTCAACGTCATCA	0.632																																					p.V263V		.											.	RDH8-94	0			c.C789A						.						77	71	73					19																	10132218		2203	4300	6503	SO:0001819	synonymous_variant	50700	exon6			CATTGTCAACGTC	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	14423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 28C, member 2"	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.729C>A	19.37:g.10132218C>A		Somatic	105	1		WXS	Illumina HiSeq	Phase_I	201	67	NM_015725	0	0	0	0	0	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				.		0.632	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	10132218	C	A	10132218	2	1	50	1	0	0	0	0	0	0	0	1	13228	813	29	4		4	RDH8	19	10132218	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	769943	10132218	48996765	110	4667											
DOCK6	57572	broad.mit.edu	37	chr19	11324999	11325018	+	Frame_Shift_Del	DEL	GGCACTCTGGGCACTGCCCA	GGCACTCTGGGCACTGCCCA	-																															aggccatgctgcaagaagagGgcactctgggcactgcccag																								rs201987811		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	GGCACTCTGGGCACTGCCCA	GGCACTCTGGGCACTGCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:11324999_11325018delGGCACTCTGGGCACTGCCCA	ENST00000294618.7	-	34	4282_4301	c.4271_4290delTGGGCAGTGCCCAGAGTGCC	c.(4270-4290)ctgggcagtgcccagagtgccfs	p.LGSAQSA1424fs	DOCK6_ENST00000319867.7_Frame_Shift_Del_p.LGSAQSA763fs|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1424					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCAAGAAGAGGGCACTCTGGGCACTGCCCAGGCTGTACAG	0.568																																					p.1424_1430del													.	DOCK6-93	0			c.4271_4290del						.																																			SO:0001589	frameshift_variant	57572	exon34			GAAGAGGGCACTC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4271_4290delTGGGCAGTGCCCAGAGTGCC	19.37:g.11324999_11325018delGGCACTCTGGGCACTGCCCA	ENSP00000294618:p.Leu1424fs	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	114	14	NM_020812	0	0	0	0	0	A6H8X5|Q7Z7P4|Q9P2F2	Frame_Shift_Del	DEL	ENST00000294618.7	37	CCDS45975.1																																																																																			.		0.568	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		-	11325018	GGCACTCTGGGCACTGCCCA	-	11324999	7	5	50	1	0	1	0	1	0	0	0	0	4702	1219	43	0	1913	0	DOCK6	19	11324999	Frame_Shift_Del	DEL	GGCACTCTGGGCACTGCCCA	TCGA-B9-4116-01A-01D-1252-08	1192781	11324999	47803984	111	4668											
C19orf44	84167	ucsc.edu	37	chr19	16612294	16612294	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcttgatggactcttctagaGaaaaaaacacgaatcaaggc	16	8	9	8	1	3	2	1	1	2	1	3	5	3	3	0	2	1	1	0	2	6	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:16612294G>A	ENST00000221671.3	+	2	847	c.691G>A	c.(691-693)Gaa>Aaa	p.E231K	C19orf44_ENST00000594035.1_Missense_Mutation_p.E231K|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	231										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						CTCTTCTAGAGAAAAAAACAC	0.373																																					p.E231K													.	C19orf44-90	0			c.G691A						.						63	66	65					19																	16612294		2202	4299	6501	SO:0001583	missense	84167	exon2			TCTAGAGAAAAAA	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.691G>A	19.37:g.16612294G>A	ENSP00000221671:p.Glu231Lys	Somatic	148	0		WXS	Illumina HiSeq		266	1	NM_032207	0	0	7	8	1	Q8N6Y7	Missense_Mutation	SNP	ENST00000221671.3	37	CCDS12345.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.886468	0.33348	.	.	ENSG00000105072	ENST00000221671	.	.	.	4.81	2.62	0.31277	.	1.056350	0.07363	N	0.884396	T	0.57344	0.2047	L	0.56769	1.78	0.09310	N	1	D;D	0.89917	0.996;1.0	D;D	0.72338	0.93;0.977	T	0.37009	-0.9724	9	0.38643	T	0.18	-2.8439	7.3233	0.26540	0.0929:0.1729:0.7341:0.0	.	231;231	Q9H6X5;Q9H6X5-2	CS044_HUMAN;.	K	231	.	ENSP00000221671:E231K	E	+	1	0	C19orf44	16473294	0.979000	0.34478	0.028000	0.17463	0.062000	0.15995	3.222000	0.51223	1.130000	0.42092	-0.176000	0.13171	GAA	.		0.373	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		A	16612294	G	A	16612294	3	1	50	1	0	0	0	0	1	0	0	0	1933	943	33	2	693	2	C19orf44	19	16612294	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	5287295	16612294	42516689	112	4669											
UPF1	5976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18963808	18963808	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctcagactcaagataacAtcactgtcaggtgggacctg	11	9	11	10	0	4	2	4	0	0	2	4	3	4	3	1	2	2	1	1	2	2	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:18963808A>G	ENST00000599848.1	+	7	1194	c.985A>G	c.(985-987)Atc>Gtc	p.I329V	UPF1_ENST00000262803.5_Missense_Mutation_p.I329V			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	329	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						TCAAGATAACATCACTGTCAG	0.537																																					p.I329V		.											.	UPF1-91	0			c.A985G						.						131	115	120					19																	18963808		2203	4300	6503	SO:0001583	missense	5976	exon7			GATAACATCACTG	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"UP Frameshift 1", "smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"	601430	"regulator of nonsense transcripts 1"	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.985A>G	19.37:g.18963808A>G	ENSP00000470142:p.Ile329Val	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	287	92	NM_002911	0	0	17	25	8	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	37		.	.	.	.	.	.	.	.	.	.	A	11.03	1.518996	0.27211	.	.	ENSG00000005007	ENST00000262803	D	0.88975	-2.45	4.16	4.16	0.48862	.	0.052684	0.64402	D	0.000001	T	0.79052	0.4381	N	0.16903	0.455	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.12156	0.003;0.007	T	0.72077	-0.4399	10	0.18276	T	0.48	-35.3027	12.395	0.55380	1.0:0.0:0.0:0.0	.	329;329	Q92900;Q92900-2	RENT1_HUMAN;.	V	329	ENSP00000262803:I329V	ENSP00000262803:I329V	I	+	1	0	UPF1	18824808	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.925000	0.92832	1.534000	0.49203	0.438000	0.28831	ATC	.		0.537	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		G	18963808	A	G	18963808	3	3	50	1	0	0	0	0	1	0	0	0	17036	217	8	3	1011	3	UPF1	19	18963808	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	2351514	18963808	40165175	113	4670											
SARS2	54938	broad.mit.edu	37	chr19	39412717	39412717	+	Intron	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacctggatccagccgcAcctgaagccagttttagttt	9	10	9	13	1	0	1	0	1	0	0	1	2	1	2	5	1	3	4	5	1	2	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:39412717A>T	ENST00000221431.6	-	3	553				CTC-360G5.8_ENST00000599996.1_Intron|SARS2_ENST00000430193.3_Intron|SARS2_ENST00000448145.2_Intron|SARS2_ENST00000594171.1_Intron|SARS2_ENST00000600042.1_Splice_Site_p.V132E	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial						gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			atccagccgcacctgaagcca	0.448																																					p.V132E													.	SARS2-93	0			c.T395A						.						60	65	64					19																	39412717		692	1591	2283	SO:0001627	intron_variant	54938	exon4			AGCCGCACCTGAA	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"Aminoacyl tRNA synthetases / Class II"	17697	protein-coding gene	gene with protein product	"serine tRNA ligase 2, mitochondrial"	612804	"serine-tRNA ligase, mitochondrial", "seryl-tRNA synthetase 2"	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.393+160T>A	19.37:g.39412717A>T		Somatic	15	0		WXS	Illumina HiSeq	Phase_I	44	17	NM_001145901	0	0	11	14	3	A6NHW7|B4DE10|Q9BVP3	Missense_Mutation	SNP	ENST00000221431.6	37	CCDS33017.1	.	.	.	.	.	.	.	.	.	.	A	1.368	-0.586872	0.03827	.	.	ENSG00000104835	ENST00000430193	.	.	.	3.73	0.283	0.15696	.	.	.	.	.	T	0.12987	0.0315	N	0.08118	0	.	.	.	B	0.33694	0.421	B	0.34824	0.19	T	0.31280	-0.9949	7	0.02654	T	1	.	3.1998	0.06646	0.5259:0.217:0.2571:0.0	.	132	B4DE10	.	E	132	.	ENSP00000406754:V132E	V	-	2	0	FBXO17	44104557	0.000000	0.05858	0.001000	0.08648	0.059000	0.15707	-0.852000	0.04308	-0.018000	0.14079	0.379000	0.24179	GTG	.		0.448	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		T	39412717	A	T	39412717	1	4	50	0	1	0	0	0	0	0	0	0	13877	173	6	5		5	SARS2	19	39412717	Intron	SNP	A	TCGA-B9-4116-01A-01D-1252-08	20448909	39412717	19716266	114	4671											
HSD17B14	51171	hgsc.bcm.edu;broad.mit.edu	37	chr19	49316535	49316535	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagttcaatgcccgtgcagAagttggcttcggaggccagg	8	8	15	10	2	1	1	1	0	0	1	2	2	1	2	2	4	2	5	2	4	2	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:49316535A>C	ENST00000263278.4	-	9	976	c.710T>G	c.(709-711)tTc>tGc	p.F237C	BCAT2_ENST00000601496.1_5'Flank|BCAT2_ENST00000599246.1_5'Flank|BCAT2_ENST00000402551.1_5'Flank|BCAT2_ENST00000545387.2_5'Flank|BCAT2_ENST00000316273.6_5'Flank|HSD17B14_ENST00000599157.1_Missense_Mutation_p.F213C|BCAT2_ENST00000598162.1_5'Flank|BCAT2_ENST00000597011.1_5'Flank	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	237					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GCCCGTGCAGAAGTTGGCTTC	0.677																																					p.F237C		.											.	HSD17B14-90	0			c.T710G						.						24	22	23					19																	49316535		2201	4294	6495	SO:0001583	missense	51171	exon9			GTGCAGAAGTTGG	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	23238	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 3", "short chain dehydrogenase/reductase family 47C, member 1"	612832	"dehydrogenase/reductase (SDR family) member 10"	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.710T>G	19.37:g.49316535A>C	ENSP00000263278:p.Phe237Cys	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	46	22	NM_016246	0	0	8	14	6	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414225	0.42817	.	.	ENSG00000087076	ENST00000263278	T	0.25250	1.81	4.54	4.54	0.55810	NAD(P)-binding domain (1);	0.056642	0.64402	D	0.000001	T	0.48732	0.1516	M	0.70787	2.145	0.48571	D	0.99967	D	0.89917	1.0	D	0.97110	1.0	T	0.51888	-0.8648	10	0.72032	D	0.01	.	12.4586	0.55718	1.0:0.0:0.0:0.0	.	237	Q9BPX1	DHB14_HUMAN	C	237	ENSP00000263278:F237C	ENSP00000263278:F237C	F	-	2	0	HSD17B14	54008347	1.000000	0.71417	0.995000	0.50966	0.070000	0.16714	4.249000	0.58766	1.991000	0.58162	0.379000	0.24179	TTC	.		0.677	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246		C	49316535	A	C	49316535	3	2	50	1	0	0	0	0	1	0	0	0	7404	246	9	5	106	5	HSD17B14	19	49316535	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	9903818	49316535	9812448	115	4672											
CHGB	1114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	5903027	5903027	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaactgaaaatgaaaacacAaagtttgaagtaagattgtt	20	10	7	4	0	0	4	0	3	0	1	0	4	0	4	0	0	2	3	0	0	8	4	rs199738388		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:5903027A>G	ENST00000378961.4	+	4	441	c.237A>G	c.(235-237)acA>acG	p.T79T		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	79						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						ATGAAAACACAAAGTTTGAAG	0.453													A|||	1	0.000199681	8e-04	0	5008	,	,		19556	0		0	False		,,,				2504	0				p.T79T		.											.	CHGB-96	0			c.A237G						.						61	61	61					20																	5903027		2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			AAACACAAAGTTT		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.237A>G	20.37:g.5903027A>G		Somatic	134	1		WXS	Illumina HiSeq	Phase_I	132	54	NM_001819	0	0	1	1	0	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	37	CCDS13092.1																																																																																			A|0.999;G|0.000		0.453	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		G	5903027	A	G	5903027	2	3	50	1	0	0	0	0	0	0	0	1	3345	117	5	3		3	CHGB	20	5903027	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08		5903027	57122493	116	4673											
NKX2-4	644524	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	21376576	21376576	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcctgccatagagcaggttGgcgcccaggacgccgccgct	6	6	14	15	4	0	1	0	0	0	1	1	2	1	2	5	3	2	3	5	3	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:21376576G>T	ENST00000351817.4	-	2	1666	c.1038C>A	c.(1036-1038)gcC>gcA	p.A346A	RP11-227D2.3_ENST00000552439.1_RNA|RP11-227D2.3_ENST00000419666.2_RNA	NM_033176.1	NP_149416.1	Q9H2Z4	NKX24_HUMAN	NK2 homeobox 4	346					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(2)|upper_aerodigestive_tract(1)	3						AGAGCAGGTTGGCGCCCAGGA	0.736																																					p.A346A		.											.	NKX2-4-22	0			c.C1038A						.						18	19	18					20																	21376576		1266	2943	4209	SO:0001819	synonymous_variant	644524	exon2			CAGGTTGGCGCCC		CCDS42855.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125816	ENSG00000125816		"Homeoboxes / ANTP class : NKL subclass"	7837	protein-coding gene	gene with protein product		607808	"NK-2 (Drosophila) homolog D", "NK2 transcription factor related, locus 4 (Drosophila)"	NKX2D		1346742, 10818213	Standard	NM_033176		Approved	NKX2.4	uc010gcz.3	Q9H2Z4	OTTHUMG00000032022	ENST00000351817.4:c.1038C>A	20.37:g.21376576G>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	105	30	NM_033176	0	0	0	0	0	Q5VZV8	Silent	SNP	ENST00000351817.4	37	CCDS42855.1																																																																																			.		0.736	NKX2-4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078270.2			T	21376576	G	T	21376576	2	4	50	1	0	0	0	0	0	0	0	1	10478	1335	47	4		4	NKX2-4	20	21376576	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	15473549	21376576	41648944	117	4674											
CEP250	11190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	34091451	34091451	+	Frame_Shift_Del	DEL	A	A	-																															tccatgaactccaggagctcAaagaccagctggagcagcag																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:34091451delA	ENST00000397527.1	+	30	5974	c.5254delA	c.(5254-5256)aaafs	p.K1752fs	CEP250_ENST00000342580.4_Frame_Shift_Del_p.K1696fs	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1752	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CCAGGAGCTCAAAGACCAGCT	0.577																																					p.K1752fs		.											.	CEP250-27	0			c.5254delA						.						81	80	80					20																	34091451		2203	4300	6503	SO:0001589	frameshift_variant	11190	exon30			.	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.5254delA	20.37:g.34091451delA	ENSP00000380661:p.Lys1752fs	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	311	105	NM_007186	0	0	0	0	0	E1P5Q3|O14812|O60588|Q9H450	Frame_Shift_Del	DEL	ENST00000397527.1	37	CCDS13255.1																																																																																			.		0.577	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		-	34091451	A	-	34091451	7	5	50	1	0	1	0	1	0	0	0	0	3258	131	5	0	5360	0	CEP250	20	34091451	Frame_Shift_Del	DEL	A	TCGA-B9-4116-01A-01D-1252-08	12714875	34091451	28934069	118	4675											
ACTR5	79913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37400319	37400319	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagagtatgaagaaaagggaGgagagtacctcaaggagcac	18	4	14	5	0	1	4	1	1	0	3	1	7	1	6	1	3	2	3	1	3	7	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:37400319G>C	ENST00000243903.4	+	9	1721	c.1684G>C	c.(1684-1686)Gga>Cga	p.G562R		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	562					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				AGAAAAGGGAGGAGAGTACCT	0.557																																					p.G562R		.											.	ACTR5-90	0			c.G1684C						.						108	88	94					20																	37400319		2203	4300	6503	SO:0001583	missense	79913	exon9			AAGGGAGGAGAGT	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"INO80 complex subunits"	14671	protein-coding gene	gene with protein product	"INO80 complex subunit M"		"ARP5 (actin-related protein 5, yeast) homolog"			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.1684G>C	20.37:g.37400319G>C	ENSP00000243903:p.Gly562Arg	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	187	75	NM_024855	0	0	2	5	3	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Missense_Mutation	SNP	ENST00000243903.4	37	CCDS13308.1	.	.	.	.	.	.	.	.	.	.	G	32	5.160871	0.94727	.	.	ENSG00000101442	ENST00000243903	T	0.07688	3.17	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	M	0.66439	2.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00166	-1.1966	10	0.87932	D	0	-21.9656	20.6086	0.99469	0.0:0.0:1.0:0.0	.	562	Q9H9F9	ARP5_HUMAN	R	562	ENSP00000243903:G562R	ENSP00000243903:G562R	G	+	1	0	ACTR5	36833733	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.960000	0.93117	2.880000	0.98712	0.655000	0.94253	GGA	.		0.557	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		C	37400319	G	C	37400319	3	2	50	1	0	0	0	0	1	0	0	0	215	1001	35	4	1718	4	ACTR5	20	37400319	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	3308868	37400319	25625201	119	4676											
ZNFX1	57169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47864026	47864027	+	Missense_Mutation	DNP	GT	GT	AG																															ccattgcggcacttgaaccaGtgaccacgaggataacctat																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:47864026_47864027GT>AG	ENST00000396105.1	-	14	5780_5781	c.5534_5535AC>CT	c.(5533-5535)cAC>cCT	p.H1845P	ZNFX1_ENST00000469991.1_5'Flank|ZNFX1_ENST00000371752.1_Missense_Mutation_p.H1845P|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1845							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACTTGAACCAGTGACCACGAGG	0.545																																					p.H1845P		.											.	ZNFX1	0			c.A5534C						.																																			SO:0001583	missense	57169	exon14			AACCAGTGACCAC	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.5534_5535delinsAG	20.37:g.47864026_47864027delinsAG	ENSP00000379412:p.His1845Pro	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	229	85		0	0	0	0	0	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	DNP	ENST00000396105.1	37	CCDS13417.1																																																																																			.		0.545	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		AG	47864027	GT	AG	47864026	3	1	50	1	0	0	0	0	1	0	0	0	18237	1020	36	2	225	2	ZNFX1	20	47864026	Missense_Mutation	DNP	GT	TCGA-B9-4116-01A-01D-1252-08	10463707	47864026	15161494	120	4677											
YTHDF1	54915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	61833792	61833792	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcccgggagtttgtgaccggTttgttgtcgttattctccag	4	16	12	9	3	1	1	0	1	1	0	4	2	2	2	3	2	0	4	3	2	1	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:61833792T>C	ENST00000370339.3	-	4	1841	c.1500A>G	c.(1498-1500)aaA>aaG	p.K500K	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Silent_p.K450K	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	500	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.						N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						TTGTGACCGGTTTGTTGTCGT	0.483																																					p.K500K		.											.	YTHDF1-92	0			c.A1500G						.						156	131	139					20																	61833792		2203	4300	6503	SO:0001819	synonymous_variant	54915	exon4			GACCGGTTTGTTG	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"YTH domain family 1"	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1500A>G	20.37:g.61833792T>C		Somatic	134	1		WXS	Illumina HiSeq	Phase_I	275	48	NM_017798	0	0	44	53	9	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	37	CCDS13511.1																																																																																			.		0.483	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		C	61833792	T	C	61833792	2	2	50	1	0	0	0	0	0	0	0	1	17531	1722	60	3		3	YTHDF1	20	61833792	Silent	SNP	T	TCGA-B9-4116-01A-01D-1252-08	13969766	61833792	1191728	121	4678											
PRDM15	63977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43221789	43221789	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagattggtaaactgagtcgCggccgcagtggtgatggggg	8	8	19	6	3	0	3	0	2	0	1	1	4	0	3	1	5	1	2	1	5	2	2	rs139717863		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr21:43221789C>G	ENST00000269844.3	-	31	4245	c.4135G>C	c.(4135-4137)Gcg>Ccg	p.A1379P	PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Missense_Mutation_p.A1050P|PRDM15_ENST00000538201.1_Missense_Mutation_p.A1033P|PRDM15_ENST00000447207.2_Missense_Mutation_p.A1013P|PRDM15_ENST00000422911.1_Missense_Mutation_p.A1070P	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1379					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						AACTGAGTCGCGGCCGCAGTG	0.582																																					p.A1379P		.											.	PRDM15-90	0			c.G4135C						.						47	47	47					21																	43221789		2203	4300	6503	SO:0001583	missense	63977	exon31			GAGTCGCGGCCGC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4135G>C	21.37:g.43221789C>G	ENSP00000269844:p.Ala1379Pro	Somatic	65	1		WXS	Illumina HiSeq	Phase_I	143	54	NM_022115	0	0	1	2	1	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	c	9.656	1.142945	0.21205	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	4.47	4.47	0.54385	.	.	.	.	.	T	0.21590	0.0520	N	0.14661	0.345	0.20975	N	0.999815	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.12293	-1.0553	9	0.34782	T	0.22	-29.0395	16.1585	0.81681	0.0:1.0:0.0:0.0	.	1379;1070;1050	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	P	1070;1050;1033;1013;1379	ENSP00000408592:A1070P;ENSP00000381556:A1050P;ENSP00000444044:A1033P;ENSP00000390245:A1013P;ENSP00000269844:A1379P	ENSP00000269844:A1379P	A	-	1	0	PRDM15	42094858	0.970000	0.33590	0.915000	0.36163	0.244000	0.25665	3.534000	0.53568	2.039000	0.60335	0.558000	0.71614	GCG	C|1.000;T|0.000		0.582	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		G	43221789	C	G	43221789	3	3	50	1	0	0	0	0	1	0	0	0	12485	768	27	4	392	4	PRDM15	21	43221789	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08		43221789	4908106	122	4679											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46925137	46925137	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgaggggcgccagggcccTcccggccccccaggcccccc	4	2	13	22	3	0	0	0	0	0	0	1	1	1	0	9	5	1	0	9	5	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr21:46925137T>C	ENST00000359759.4	+	34	4224	c.4203T>C	c.(4201-4203)ccT>ccC	p.P1401P	SLC19A1_ENST00000567670.1_Intron|COL18A1_ENST00000400337.2_Silent_p.P986P|COL18A1_ENST00000355480.5_Silent_p.P1166P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1401	Triple-helical region 9 (COL9).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GCCAGGGCCCTCCCGGCCCCC	0.741																																					p.P1163P		.											.	COL18A1-90	0			c.T3489C						.						7	11	10					21																	46925137		1716	3956	5672	SO:0001819	synonymous_variant	80781	exon35			GGGCCCTCCCGGC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4203T>C	21.37:g.46925137T>C		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	20	2	NM_030582	0	0	50	50	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				.		0.741	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			C	46925137	T	C	46925137	2	2	50	1	0	0	0	0	0	0	0	1	3681	1538	54	3		3	COL18A1	21	46925137	Silent	SNP	T	TCGA-B9-4116-01A-01D-1252-08	3703348	46925137	1204758	123	4680											
CECR2	27443	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18028580	18028580	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caccactatcagcgaactccTtactatgcctgtccacagag	11	9	6	15	1	1	1	1	0	0	1	3	2	3	1	4	0	4	0	4	0	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr22:18028580T>A	ENST00000400585.2	+	17	3549	c.3111T>A	c.(3109-3111)ccT>ccA	p.P1037P	CECR2_ENST00000400573.5_Silent_p.P1179P|CECR2_ENST00000262608.8_Silent_p.P1180P			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	1221					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		AGCGAACTCCTTACTATGCCT	0.592																																					.													.	CECR2-70	0			.						.						64	67	66					22																	18028580		1998	4157	6155	SO:0001819	synonymous_variant	27443	.			AACTCCTTACTAT	AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.3111T>A	22.37:g.18028580T>A		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	154	53	.	0	0	5	7	2	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Silent	SNP	ENST00000400585.2	37																																																																																				.		0.592	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		A	18028580	T	A	18028580	2	1	50	1	0	0	0	0	0	0	0	1	3212	1596	56	5		5	CECR2	22	18028580	Silent	SNP	T	TCGA-B9-4116-01A-01D-1252-08		18028580	33275986	124	4681											
RGL4	266747	hgsc.bcm.edu;broad.mit.edu	37	chr22	24041048	24041048	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctacaagctgtcctgccAgctggagcccgaaaacccgt	10	6	10	15	2	0	0	0	0	0	0	1	2	1	1	4	1	7	3	4	1	4	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr22:24041048A>T	ENST00000290691.5	+	11	2570	c.1400A>T	c.(1399-1401)cAg>cTg	p.Q467L	RGL4_ENST00000401461.1_Missense_Mutation_p.Q331L|KB-1572G7.2_ENST00000421064.1_RNA	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	467	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						CTGTCCTGCCAGCTGGAGCCC	0.627																																					p.Q467L		.											.	RGL4-228	0			c.A1400T						.						43	37	39					22																	24041048		2203	4300	6503	SO:0001583	missense	266747	exon11			CCTGCCAGCTGGA		CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"RalGDS related oncogene"	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.1400A>T	22.37:g.24041048A>T	ENSP00000290691:p.Gln467Leu	Somatic	29	1		WXS	Illumina HiSeq	Phase_I	51	15	NM_153615	0	0	0	0	0	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	37	CCDS13811.1	.	.	.	.	.	.	.	.	.	.	-	7.165	0.586422	0.13749	.	.	ENSG00000159496	ENST00000401461;ENST00000290691	T;T	0.30182	1.54;1.54	1.53	-0.347	0.12617	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	.	.	.	.	T	0.18299	0.0439	L	0.28192	0.835	0.20563	N	0.999887	B	0.17268	0.021	B	0.12837	0.008	T	0.25012	-1.0144	9	0.87932	D	0	.	3.8135	0.08806	0.4614:0.0:0.0:0.5386	.	467	Q8IZJ4	RGDSR_HUMAN	L	331;467	ENSP00000383951:Q331L;ENSP00000290691:Q467L	ENSP00000290691:Q467L	Q	+	2	0	RGL4	22371048	1.000000	0.71417	0.009000	0.14445	0.002000	0.02628	1.510000	0.35790	-0.226000	0.09899	0.439000	0.28862	CAG	.		0.627	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615		T	24041048	A	T	24041048	3	4	50	1	0	0	0	0	1	0	0	0	13311	188	7	5	1442	5	RGL4	22	24041048	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	6012468	24041048	27263518	125	4682											
MKL1	57591	hgsc.bcm.edu	37	chr22	40814737	40814737	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgggggtgccgaggggggCgggggcgggggcgggctgct	2	3	27	9	5	0	0	0	0	0	0	0	1	0	0	1	10	2	2	1	10	0	0	rs144888766		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr22:40814737C>T	ENST00000355630.3	-	12	2295	c.1705G>A	c.(1705-1707)Gcc>Acc	p.A569T	MKL1_ENST00000402042.1_Missense_Mutation_p.A519T|MKL1_ENST00000407029.1_Missense_Mutation_p.A569T|MKL1_ENST00000396617.3_Missense_Mutation_p.A569T	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	569	Pro-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						CCGAGgggggcgggggcgggg	0.716			T	RBM15	acute megakaryocytic leukemia																																p.A569T		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	0			c.G1705A						.	C	THR/ALA	116,2310		0,116,1097	2	2	2		1705	-3.5	0	22	dbSNP_134	2	5,5439		0,5,2717	yes	missense	MKL1	NM_020831.3	58	0,121,3814	TT,TC,CC		0.0918,4.7815,1.5375	benign	569/932	40814737	121,7749	1213	2722	3935	SO:0001583	missense	57591	exon12			GGGGGGCGGGGGC	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1705G>A	22.37:g.40814737C>T	ENSP00000347847:p.Ala569Thr	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	11	4	NM_020831	0	0	0	1	1	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	44	0.020146520146520148	39	0.07926829268292683	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	9.145	1.014937	0.19355	0.047815	9.18E-4	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	4.41	-3.45	0.04781	.	1.271760	0.05835	N	0.618279	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B;B	0.12630	0.006;0.006;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.12293	-1.0553	10	0.14252	T	0.57	0.1113	2.1801	0.03872	0.1212:0.4293:0.2367:0.2129	.	519;569;569	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	T	569;569;519;569	ENSP00000347847:A569T;ENSP00000379861:A569T;ENSP00000385584:A519T;ENSP00000385835:A569T	ENSP00000347847:A569T	A	-	1	0	MKL1	39144683	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.029000	0.12329	-0.242000	0.09667	-1.320000	0.01293	GCC	C|0.980;T|0.020		0.716	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		T	40814737	C	T	40814737	3	4	50	1	0	0	0	0	1	0	0	0	9626	768	27	1	1106	1	MKL1	22	40814737	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	16773689	40814737	10489829	126	4683											
EP300	2033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	41572951	41572951	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtctctggtccatgctTgccagtgtcggaatgccaat	7	12	10	12	1	1	0	0	0	1	0	5	1	3	1	4	2	3	1	4	2	2	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr22:41572951T>A	ENST00000263253.7	+	31	6455	c.5236T>A	c.(5236-5238)Tgc>Agc	p.C1746S	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1746	Binding region for E1A adenovirus.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GGTCCATGCTTGCCAGTGTCG	0.572			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.C1746S		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300-2011	0			c.T5236A						.						88	74	79					22																	41572951		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	CATGCTTGCCAGT	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.5236T>A	22.37:g.41572951T>A	ENSP00000263253:p.Cys1746Ser	Somatic	142	1		WXS	Illumina HiSeq	Phase_I	241	84	NM_001429	0	0	15	26	11	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.667060	0.67814	.	.	ENSG00000100393	ENST00000263253	D	0.81659	-1.52	5.75	5.75	0.90469	Zinc finger, TAZ-type (5);	0.000000	0.53938	D	0.000056	D	0.86723	0.6001	L	0.51853	1.615	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.85515	0.1200	10	0.35671	T	0.21	-5.0783	16.0573	0.80814	0.0:0.0:0.0:1.0	.	1746	Q09472	EP300_HUMAN	S	1746	ENSP00000263253:C1746S	ENSP00000263253:C1746S	C	+	1	0	EP300	39902897	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.040000	0.89188	2.191000	0.70037	0.528000	0.53228	TGC	.		0.572	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41572951	T	A	41572951	3	1	50	1	0	0	0	0	1	0	0	0	5161	1812	63	5	5358	5	EP300	22	41572951	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	758214	41572951	9731615	127	4684											
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15841260	15841260	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagccggagccggagccgCaggagccgccgcagccggag	7	0	19	15	7	0	0	0	0	0	0	0	5	0	5	6	5	5	2	6	5	0	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chrX:15841260C>G	ENST00000307771.7	+	11	1368	c.1344C>G	c.(1342-1344)cgC>cgG	p.R448R		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	448	Arg/Ser-rich (RS domain).				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					gccggagccgCAGGAGCCGCC	0.647			"F, S, Mis"		"MDS, CLL"																																p.R448R	NSCLC(197;1631 3042 5741 31152)	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2-133	0			c.C1344G						.						7	9	9					X																	15841260		1924	3790	5714	SO:0001819	synonymous_variant	8233	exon11			GAGCCGCAGGAGC	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1344C>G	X.37:g.15841260C>G		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	50	5	NM_005089	0	0	3	3	0	Q14D69	Silent	SNP	ENST00000307771.7	37	CCDS14172.1																																																																																			.		0.647	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		G	15841260	C	G	15841260	2	3	50	1	0	0	0	0	0	0	0	1	18257	697	25	4		4	ZRSR2	23	15841260	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		15841260	139429300	128	4685											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350752	50350752	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcctcctcctcctcctgTtgcttctgctgctgctgttg	0	17	7	17	0	1	0	0	0	1	0	7	0	7	0	6	0	4	6	6	0	0	3	rs534812379		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chrX:50350752T>C	ENST00000289292.7	-	6	3673	c.3390A>G	c.(3388-3390)caA>caG	p.Q1130Q	SHROOM4_ENST00000460112.3_Silent_p.Q1014Q|SHROOM4_ENST00000376020.2_Silent_p.Q1130Q			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1130	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctcctcctgttgcttctgct	0.582																																					p.Q1130Q		.											.	SHROOM4-131	0			c.A3390G						.						15	15	15					X																	50350752		2198	4291	6489	SO:0001819	synonymous_variant	57477	exon6			CTCCTGTTGCTTC	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3390A>G	X.37:g.50350752T>C		Somatic	55	1		WXS	Illumina HiSeq	Phase_I	103	6	NM_020717	0	0	1	1	0	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																			.		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50350752	T	C	50350752	2	2	50	1	0	0	0	0	0	0	0	1	14328	1722	60	3		3	SHROOM4	23	50350752	Silent	SNP	T	TCGA-B9-4116-01A-01D-1252-08	34509492	50350752	104919808	129	4686											
HEPH	9843	hgsc.bcm.edu	37	chrX	65423314	65423314	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccacccctcgccaacgctAccaagctgcaagaatctact	12	6	6	17	2	1	1	0	0	1	1	2	1	1	1	5	0	6	3	5	0	6	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chrX:65423314A>C	ENST00000343002.2	+	12	2850	c.2186A>C	c.(2185-2187)tAc>tCc	p.Y729S	HEPH_ENST00000519389.1_Missense_Mutation_p.Y783S|HEPH_ENST00000336279.5_Missense_Mutation_p.Y462S|HEPH_ENST00000419594.1_Missense_Mutation_p.Y540S|HEPH_ENST00000374727.3_Missense_Mutation_p.Y732S|HEPH_ENST00000441993.2_Missense_Mutation_p.Y732S			Q9BQS7	HEPH_HUMAN	hephaestin	729					cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						CGCCAACGCTACCAAGCTGCA	0.537																																					p.Y783S		.											.	HEPH-135	0			c.A2348C						.						89	71	77					X																	65423314		2203	4300	6503	SO:0001583	missense	9843	exon13			AACGCTACCAAGC	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.2186A>C	X.37:g.65423314A>C	ENSP00000343939:p.Tyr729Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_138737	0	0	2	2	0	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	A	15.22	2.767599	0.49574	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000419594;ENST00000343002;ENST00000425114	D;D;D;D;D;D;D	0.99252	-4.95;-4.95;-4.95;-4.95;-5.63;-4.95;-4.95	4.91	4.91	0.64330	Cupredoxin (1);	0.389120	0.26612	N	0.023404	D	0.98745	0.9578	L	0.45744	1.44	0.34243	D	0.677871	D;P;B;D	0.71674	0.983;0.603;0.203;0.998	P;B;B;P	0.61722	0.852;0.138;0.026;0.893	D	0.99964	1.1808	10	0.36615	T	0.2	.	12.4148	0.55488	1.0:0.0:0.0:0.0	.	783;129;540;729	E9PHN8;B4DFV3;E7ES21;Q9BQS7	.;.;.;HEPH_HUMAN	S	783;732;462;732;540;729;686	ENSP00000430620:Y783S;ENSP00000363859:Y732S;ENSP00000337418:Y462S;ENSP00000411687:Y732S;ENSP00000413211:Y540S;ENSP00000343939:Y729S;ENSP00000398078:Y686S	ENSP00000337418:Y462S	Y	+	2	0	HEPH	65340039	1.000000	0.71417	0.974000	0.42286	0.805000	0.45488	3.735000	0.55044	1.812000	0.52913	0.486000	0.48141	TAC	.		0.537	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		C	65423314	A	C	65423314	3	2	50	1	0	0	0	0	1	0	0	0	7075	391	14	5	2398	5	HEPH	23	65423314	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	15072562	65423314	89847246	130	4687											
TREX2	11219	broad.mit.edu	37	chrX	152710189	152710189	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctggtgctcaggcctccaGgctggggtcatcaggcggca	5	7	15	14	1	3	0	3	0	0	0	4	0	4	0	3	7	1	3	3	7	0	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chrX:152710189G>T	ENST00000334497.2	-	11	1970	c.829C>A	c.(829-831)Ctg>Atg	p.L277M	TREX2_ENST00000330912.2_Missense_Mutation_p.L234M|TREX2_ENST00000338525.2_Missense_Mutation_p.L234M|TREX2_ENST00000370232.1_Missense_Mutation_p.L277M|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000370231.2_Missense_Mutation_p.L234M|TREX2_ENST00000393862.2_Missense_Mutation_p.L234M|TREX2_ENST00000402951.1_Missense_Mutation_p.L277M|TREX2_ENST00000414588.1_Missense_Mutation_p.L276M			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	277					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCCTCCAGGCTGGGGTCA	0.687								Editing and processing nucleases																													p.L234M													.	TREX2-227	0			c.C700A						.						13	10	11					X																	152710189		2184	4267	6451	SO:0001583	missense	11219	exon2			CCTCCAGGCTGGG	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.829C>A	X.37:g.152710189G>T	ENSP00000334993:p.Leu277Met	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_080701	0	0	0	0	0	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	G	11.73	1.725419	0.30593	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.55588	0.69;0.69;0.69;0.55;0.55;0.55;0.51;0.69	4.35	-4.78	0.03209	.	1.591890	0.04555	U	0.390669	T	0.32376	0.0827	L	0.27053	0.805	0.09310	N	1	P;B	0.35982	0.531;0.255	B;B	0.32864	0.154;0.03	T	0.26573	-1.0099	10	0.59425	D	0.04	-15.9683	2.929	0.05793	0.0948:0.243:0.1692:0.493	.	276;277	Q06S70;Q9BQ50	.;TREX2_HUMAN	M	234;234;234;277;277;277;276;234	ENSP00000377442:L234M;ENSP00000333441:L234M;ENSP00000345218:L234M;ENSP00000334993:L277M;ENSP00000359252:L277M;ENSP00000386078:L277M;ENSP00000401692:L276M;ENSP00000359251:L234M	ENSP00000333441:L234M	L	-	1	2	TREX2	152363383	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.322000	0.08007	-0.747000	0.04759	-0.542000	0.04241	CTG	.		0.687	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701		T	152710189	G	T	152710189	3	4	50	1	0	0	0	0	1	0	0	0	16510	991	35	4	13	4	TREX2	23	152710189	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	87286875	152710189	2560371	131	4688											
ATAD3C	219293	bcgsc.ca	37	chr1	1392552	1392552	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggacgccttccttcggaagCgagccactgtgagtgtcact	7	9	12	13	4	1	1	1	1	0	0	3	4	2	3	3	2	2	0	3	2	1	2	rs373927712		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:1392552C>G	ENST00000378785.2	+	8	1728	c.733C>G	c.(733-735)Cga>Gga	p.R245G		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	245							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	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;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCTTCGGAAGCGAGCCACTGT	0.627																																					p.R245G													.	.	0			c.C733G						.						42	42	42					1																	1392552		692	1591	2283	SO:0001583	missense	219293	exon8			CGGAAGCGAGCCA	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"ATPases / AAA-type"	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.733C>G	1.37:g.1392552C>G	ENSP00000368062:p.Arg245Gly	Somatic	97	0		WXS	Illumina HiSeq	Phase_1	142	78	NM_001039211	0	0	0	0	0	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	.	.	.	.	.	.	.	.	.	.	.	8.578	0.881656	0.17467	.	.	ENSG00000215915	ENST00000378785	T	0.77750	-1.12	2.51	0.459	0.16678	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.90390	0.6992	H	0.97365	3.99	0.50813	D	0.999897	D	0.76494	0.999	D	0.77557	0.99	D	0.89146	0.3520	10	0.87932	D	0	.	9.7739	0.40607	0.7125:0.2875:0.0:0.0	.	245	Q5T2N8	ATD3C_HUMAN	G	245	ENSP00000368062:R245G	ENSP00000368062:R245G	R	+	1	2	ATAD3C	1382415	1.000000	0.71417	0.462000	0.27118	0.006000	0.05464	0.868000	0.27982	-0.126000	0.11682	-1.075000	0.02238	CGA	.		0.627	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211		G	1392552	C	G	1392552	3	3	51	1	0	0	0	0	1	0	0	0	1076	760	27	4	763	4	ATAD3C	1	1392552	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08		1392552	247858069	1	4689											
PLA2G2A	5320	bcgsc.ca	37	chr1	20304929	20304929	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acgccacagtggcagccgtaGaagccataactgagtgcggc	11	5	13	12	3	0	2	0	1	0	1	0	2	0	2	3	2	4	2	3	2	3	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:20304929G>A	ENST00000375111.3	-	4	400	c.129C>T	c.(127-129)ttC>ttT	p.F43F	PLA2G2A_ENST00000496748.1_5'UTR|PLA2G2A_ENST00000400520.3_Silent_p.F43F	NM_000300.3|NM_001161727.1	NP_000291.1|NP_001155199.1	P14555	PA2GA_HUMAN	phospholipase A2, group IIA (platelets, synovial fluid)	43					defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of epithelial cell proliferation (GO:0050680)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidic acid metabolic process (GO:0046473)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|small molecule metabolic process (GO:0044281)|somatic stem cell maintenance (GO:0035019)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|phospholipid binding (GO:0005543)			central_nervous_system(1)|lung(6)|prostate(1)|stomach(1)	9		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Diclofenac(DB00586)|Ginkgo biloba(DB01381)|Indomethacin(DB00328)|Suramin(DB04786)	GGCAGCCGTAGAAGCCATAAC	0.562																																					p.F43F													.	PLA2G2A-650	0			c.C129T						.						42	46	45					1																	20304929		2203	4300	6503	SO:0001819	synonymous_variant	5320	exon3			GCCGTAGAAGCCA	BC005919	CCDS201.1	1p35	2008-09-19			ENSG00000188257	ENSG00000188257	3.1.1.4		9031	protein-coding gene	gene with protein product		172411		PLA2B, PLA2L		8838795	Standard	NM_000300		Approved		uc010odb.2	P14555	OTTHUMG00000002699	ENST00000375111.3:c.129C>T	1.37:g.20304929G>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_1	66	39	NM_001161729	0	0	0	0	0	A8K5I7|Q6DN24|Q6IBD9|Q9UCD2	Silent	SNP	ENST00000375111.3	37	CCDS201.1																																																																																			.		0.562	PLA2G2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007675.1	NM_000300		A	20304929	G	A	20304929	2	1	51	1	0	0	0	0	0	0	0	1	12021	933	33	2		2	PLA2G2A	1	20304929	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	18912377	20304929	228945692	2	4690											
ADC	113451	broad.mit.edu	37	chr1	33583680	33583681	+	Frame_Shift_Ins	INS	-	-	C																															ccccttttgggggacccaggINScctgccacatcacctatgcc																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:33583680_33583681insC	ENST00000294517.6	+	11	1794_1795	c.1207_1208insC	c.(1207-1209)gccfs	p.A403fs	ADC_ENST00000484656.1_3'UTR|ADC_ENST00000398167.1_Frame_Shift_Ins_p.A423fs|ADC_ENST00000373441.1_Frame_Shift_Ins_p.A423fs|ADC_ENST00000373443.3_Frame_Shift_Ins_p.A403fs	NM_052998.2	NP_443724.1	Q96A70	AZIN2_HUMAN		403					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of protein catabolic process (GO:0042177)|ornithine metabolic process (GO:0006591)|polyamine biosynthetic process (GO:0006596)|polyamine metabolic process (GO:0006595)|positive regulation of catalytic activity (GO:0043085)|positive regulation of polyamine transmembrane transport (GO:1902269)|putrescine transport (GO:0015847)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|trans-Golgi network membrane organization (GO:0098629)	axon (GO:0030424)|cis-Golgi network (GO:0005801)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|granular vesicle (GO:1990005)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	catalytic activity (GO:0003824)|ornithine decarboxylase activator activity (GO:0042978)|putrescine transmembrane transporter activity (GO:0015489)			NS(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)	GGGGACCCAGGCCTGCCACATC	0.614																																					p.A403fs													.	ADC-92	0			c.1207_1208insC						.																																			SO:0001589	frameshift_variant	113451	exon11			ACCCAGGCCTGCC																												ENST00000294517.6:c.1209dupC	1.37:g.33583682_33583682dupC	ENSP00000294517:p.Ala403fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	199	3	NM_052998	0	0	0	0	0	B2RDU5|D3DPQ9|Q5TIF4|Q5TIF5|Q5TIF6|Q8TF56|Q96L54|Q96L55|Q96L56|Q96L57|Q96MD9	Frame_Shift_Ins	INS	ENST00000294517.6	37	CCDS375.1																																																																																			.		0.614	ADC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011867.1			C	33583681	-	C	33583680	7	5	51	1	0	1	1	0	0	0	0	0	287	1203	42	0	1237	0	ADC	1	33583680	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	13278751	33583680	215666941	3	4691											
PHC2	1912	bcgsc.ca	37	chr1	33832972	33832972	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacaggctgagtgggggTggggcccgaggctgctgccg	5	5	21	10	2	0	1	0	1	0	0	0	3	0	2	2	7	2	3	2	7	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:33832972T>G	ENST00000257118.5	-	6	774	c.721A>C	c.(721-723)Acc>Ccc	p.T241P	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Missense_Mutation_p.T212P|PHC2_ENST00000419414.2_Missense_Mutation_p.T241P	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	241					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TGAGTGGGGGTGGGGCCCGAG	0.632											OREG0013344	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T241P													.	PHC2-227	0			c.A721C						.						69	92	84					1																	33832972		2195	4292	6487	SO:0001583	missense	1912	exon6			TGGGGGTGGGGCC	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"Sterile alpha motif (SAM) domain containing"	3183	protein-coding gene	gene with protein product		602979	"early development regulator 2 (homolog of polyhomeotic 2)", "polyhomeotic-like 2 (Drosophila)"	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.721A>C	1.37:g.33832972T>G	ENSP00000257118:p.Thr241Pro	Somatic	220	3	843	WXS	Illumina HiSeq	Phase_1	375	80	NM_198040	0	0	3	3	0	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.763690	0.31228	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.32272	1.86;1.46;1.87	5.74	-5.55	0.02536	.	0.703679	0.13425	N	0.388856	T	0.14442	0.0349	L	0.29908	0.895	0.38372	D	0.944898	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.11060	-1.0603	10	0.23891	T	0.37	-2.7256	4.1957	0.10441	0.2228:0.0732:0.4939:0.2101	.	241;212;241	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	P	212;241;241	ENSP00000389436:T212P;ENSP00000257118:T241P;ENSP00000391440:T241P	ENSP00000257118:T241P	T	-	1	0	PHC2	33605559	0.001000	0.12720	0.470000	0.27216	0.960000	0.62799	-0.911000	0.04050	-0.880000	0.03997	-0.331000	0.08364	ACC	.		0.632	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		G	33832972	T	G	33832972	3	3	51	1	0	0	0	0	1	0	0	0	11843	1696	59	5	1891	5	PHC2	1	33832972	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	249292	33832972	215417649	4	4692											
ZMYM4	9202	bcgsc.ca	37	chr1	35870649	35870649	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaagtctatagtggctgTggagcccaggagtcttattc	10	11	13	7	0	2	1	0	0	2	1	3	4	2	3	1	3	1	1	1	3	5	4	rs200301387		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:35870649T>G	ENST00000314607.6	+	24	3634	c.3554T>G	c.(3553-3555)gTg>gGg	p.V1185G	ZMYM4_ENST00000373297.2_Missense_Mutation_p.V1096G	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1185					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ATAGTGGCTGTGGAGCCCAGG	0.423																																					p.V1185G													.	ZMYM4-291	0			c.T3554G						.						64	75	71					1																	35870649		2203	4300	6503	SO:0001583	missense	9202	exon24			TGGCTGTGGAGCC	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"Zinc fingers, MYM type"	13055	protein-coding gene	gene with protein product		613568	"zinc finger protein 262"	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.3554T>G	1.37:g.35870649T>G	ENSP00000322915:p.Val1185Gly	Somatic	115	0		WXS	Illumina HiSeq	Phase_1	61	25	NM_005095	0	0	11	11	0	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.54|14.54	2.565382|2.565382	0.45694|0.45694	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000457946|ENST00000314607;ENST00000373297	.|T;T	.|0.24908	.|1.83;1.86	5.95|5.95	3.29|3.29	0.37713|0.37713	.|.	.|0.583284	.|0.17804	.|N	.|0.161469	T|T	0.15782|0.15782	0.0380|0.0380	N|N	0.24115|0.24115	0.695|0.695	0.58432|0.58432	D|D	0.999998|0.999998	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.06162|0.06162	-1.0842|-1.0842	5|10	.|0.23302	.|T	.|0.38	-2.5928|-2.5928	9.5722|9.5722	0.39436|0.39436	0.0:0.0707:0.1226:0.8067|0.0:0.0707:0.1226:0.8067	.|.	.|1185	.|Q5VZL5	.|ZMYM4_HUMAN	W|G	843|1185;1096	.|ENSP00000322915:V1185G;ENSP00000362394:V1096G	.|ENSP00000322915:V1185G	C|V	+|+	3|2	2|0	ZMYM4|ZMYM4	35643236|35643236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.443000|4.443000	0.59994|0.59994	1.059000|1.059000	0.40554|0.40554	0.533000|0.533000	0.62120|0.62120	TGT|GTG	.		0.423	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		G	35870649	T	G	35870649	3	3	51	1	0	0	0	0	1	0	0	0	17734	1696	59	5	3648	5	ZMYM4	1	35870649	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	2037677	35870649	213379972	5	4693											
FHL3	2275	bcgsc.ca	37	chr1	38463740	38463740	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggagcccagtggctgttcAcagccactgcacaggaagca	10	5	13	13	1	1	0	1	0	0	0	1	2	1	2	2	3	4	4	2	3	1	1	rs201163097		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:38463740A>C	ENST00000373016.3	-	4	564	c.396T>G	c.(394-396)tgT>tgG	p.C132W	FHL3_ENST00000485803.1_5'UTR	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN	four and a half LIM domains 3	132	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|muscle organ development (GO:0007517)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)|Z disc (GO:0030018)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GTGGCTGTTCACAGCCACTGC	0.587																																					p.C132W													.	FHL3-90	0			c.T396G						.						67	70	69					1																	38463740		2203	4300	6503	SO:0001583	missense	2275	exon4			CTGTTCACAGCCA	BC011697	CCDS30678.1	1p34.3	2008-02-05			ENSG00000183386	ENSG00000183386			3704	protein-coding gene	gene with protein product		602790				8753811, 10226657	Standard	NM_004468		Approved	SLIM2	uc001cck.3	Q13643	OTTHUMG00000004434	ENST00000373016.3:c.396T>G	1.37:g.38463740A>C	ENSP00000362107:p.Cys132Trp	Somatic	142	0		WXS	Illumina HiSeq	Phase_1	190	80	NM_004468	0	0	9	9	0	D3DPT6|Q6I9T0|Q9BVA2	Missense_Mutation	SNP	ENST00000373016.3	37	CCDS30678.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.539010	0.45176	.	.	ENSG00000183386	ENST00000373016	D	0.99898	-7.61	5.2	2.87	0.33458	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.99923	0.9964	H	0.99697	4.71	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.97083	0.9785	10	0.87932	D	0	.	7.1369	0.25533	0.594:0.0:0.406:0.0	.	132;24;132	Q9P100;Q96C98;Q13643	.;.;FHL3_HUMAN	W	132	ENSP00000362107:C132W	ENSP00000362107:C132W	C	-	3	2	FHL3	38236327	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	1.690000	0.37711	0.313000	0.23062	-0.609000	0.04063	TGT	.		0.587	FHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012958.1	NM_004468		C	38463740	A	C	38463740	3	2	51	1	0	0	0	0	1	0	0	0	5899	157	6	5	458	5	FHL3	1	38463740	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	2593091	38463740	210786881	6	4694											
MACF1	23499	bcgsc.ca	37	chr1	39845028	39845028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtgctgcagtggctggAatcaaaagaggaagtcctga	11	9	13	8	0	2	2	1	1	1	1	3	4	3	4	1	3	2	3	1	3	4	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:39845028A>G	ENST00000372915.3	+	53	13532	c.13445A>G	c.(13444-13446)gAa>gGa	p.E4482G	MACF1_ENST00000539005.1_Missense_Mutation_p.E2394G|MACF1_ENST00000567887.1_Missense_Mutation_p.E4514G|MACF1_ENST00000317713.7_Missense_Mutation_p.E2415G|MACF1_ENST00000564288.1_Missense_Mutation_p.E4477G|MACF1_ENST00000289893.4_Missense_Mutation_p.E2917G|MACF1_ENST00000545844.1_Missense_Mutation_p.E2415G|MACF1_ENST00000361689.2_Missense_Mutation_p.E2415G			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4482					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGTGGCTGGAATCAAAAGAG	0.478																																					p.E2415G													.	MACF1-165	0			c.A7244G						.						218	217	217					1																	39845028		2203	4300	6503	SO:0001583	missense	23499	exon50			GGCTGGAATCAAA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13445A>G	1.37:g.39845028A>G	ENSP00000362006:p.Glu4482Gly	Somatic	342	0		WXS	Illumina HiSeq	Phase_1	160	61	NM_012090	0	0	6	6	0	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	A	13.56	2.275133	0.40194	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	6.04	6.04	0.98038	.	0.000000	0.64402	D	0.000006	T	0.47710	0.1460	L	0.43152	1.355	0.80722	D	1	B;B;B	0.23650	0.089;0.019;0.043	B;B;B	0.32864	0.154;0.088;0.088	T	0.42649	-0.9439	10	0.56958	D	0.05	.	16.6244	0.84952	1.0:0.0:0.0:0.0	.	4482;2415;2359	Q9UPN3;F8W8Q1;Q9UPN3-3	MACF1_HUMAN;.;.	G	2415;4482;2415;2415;2394;2917	ENSP00000439537:E2415G;ENSP00000362006:E4482G;ENSP00000354573:E2415G;ENSP00000313438:E2415G;ENSP00000444364:E2394G;ENSP00000289893:E2917G	ENSP00000289893:E2917G	E	+	2	0	MACF1	39617615	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.140000	0.50585	2.323000	0.78572	0.529000	0.55759	GAA	.		0.478	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39845028	A	G	39845028	3	3	51	1	0	0	0	0	1	0	0	0	9169	246	9	3	13589	3	MACF1	1	39845028	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1381288	39845028	209405593	7	4695											
SCMH1	22955	hgsc.bcm.edu	37	chr1	41579112	41579113	+	Frame_Shift_Ins	INS	-	-	G																															gaacctccccaatagtggctINSgggcaaatgaaatgagggtt																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:41579112_41579113insG	ENST00000326197.7	-	7	856_857	c.557_558insC	c.(556-558)ccafs	p.P186fs	SCMH1_ENST00000397171.2_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000372596.1_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000337495.5_Frame_Shift_Ins_p.P196fs|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000372595.1_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000402904.2_Frame_Shift_Ins_p.P186fs|SCMH1_ENST00000361191.5_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000372597.1_Frame_Shift_Ins_p.P139fs|SCMH1_ENST00000361705.3_Frame_Shift_Ins_p.P139fs|SCMH1_ENST00000397174.2_Frame_Shift_Ins_p.P166fs					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CAATAGTGGCTGGGCAAATGAA	0.53																																					p.P196fs		.											.	SCMH1-90	0			c.588_589insC						.																																			SO:0001589	frameshift_variant	22955	exon8			.	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.558dupC	1.37:g.41579115_41579115dupG	ENSP00000318094:p.Pro186fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	107	20	NM_001172219	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000326197.7	37	CCDS30688.1																																																																																			.		0.53	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			G	41579113	-	G	41579112	7	5	51	1	0	1	1	0	0	0	0	0	13940	1567	55	0	1460	0	SCMH1	1	41579112	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	1734084	41579112	207671509	8	4696											
DOCK7	85440	bcgsc.ca	37	chr1	62923219	62923219	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataagcatacctgtggcaggTgacaggcaatactgccttgt	11	10	11	9	0	0	1	0	1	0	0	0	1	0	1	2	3	4	3	2	3	4	4	rs200939372		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:62923219T>G	ENST00000340370.5	-	48	6294	c.6277A>C	c.(6277-6279)Acc>Ccc	p.T2093P	DOCK7_ENST00000251157.5_Missense_Mutation_p.T2113P	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	2124	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTGTGGCAGGTGACAGGCAAT	0.408																																					p.T2113P													.	DOCK7-92	0			c.A6337C						.																																			SO:0001583	missense	85440	exon48			GGCAGGTGACAGG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.6277A>C	1.37:g.62923219T>G	ENSP00000340742:p.Thr2093Pro	Somatic	105	1		WXS	Illumina HiSeq	Phase_1	83	51	NM_001271999	0	0	0	0	0	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.13|13.13	2.145093|2.145093	0.37825|0.37825	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000454575|ENST00000371140;ENST00000251157;ENST00000340370	.|T;T	.|0.14640	.|2.5;2.49	5.99|5.99	3.51|3.51	0.40186|0.40186	.|.	.|0.939062	.|0.09139	.|N	.|0.843193	T|T	0.06917|0.06917	0.0176|0.0176	N|N	0.04880|0.04880	-0.145|-0.145	0.42996|0.42996	D|D	0.994508|0.994508	.|B;B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B	.|0.08055	.|0.003;0.001;0.001;0.001;0.003;0.002	T|T	0.21895|0.21895	-1.0232|-1.0232	5|10	.|0.35671	.|T	.|0.21	.|.	6.1776|6.1776	0.20453|0.20453	0.252:0.0677:0.0:0.6803|0.252:0.0677:0.0:0.6803	.|.	.|2124;2113;2093;2082;2084;2115	.|Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	.|DOCK7_HUMAN;.;.;.;.;.	P|P	1286|2124;2113;2093	.|ENSP00000251157:T2113P;ENSP00000340742:T2093P	.|ENSP00000251157:T2113P	H|T	-|-	2|1	0|0	DOCK7|DOCK7	62695807|62695807	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.530000|0.530000	0.23036|0.23036	1.049000|1.049000	0.40321|0.40321	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.		0.408	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		G	62923219	T	G	62923219	3	3	51	1	0	0	0	0	1	0	0	0	4703	1696	59	5	60	5	DOCK7	1	62923219	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	21344107	62923219	186327402	9	4697											
WDR78	79819	broad.mit.edu	37	chr1	67390432	67390433	+	Frame_Shift_Ins	INS	-	-	G																															ggtgcaccacccctttttttINSggccgcctctgaagtccctg																								rs557595505		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:67390432_67390433insG	ENST00000371026.3	-	1	137_138	c.82_83insC	c.(82-84)caafs	p.Q28fs	MIER1_ENST00000357692.2_5'Flank|WDR78_ENST00000371022.3_Frame_Shift_Ins_p.Q28fs|MIER1_ENST00000371012.2_5'Flank|WDR78_ENST00000371023.3_Frame_Shift_Ins_p.Q28fs|MIER1_ENST00000401041.1_5'Flank|MIER1_ENST00000371018.3_5'Flank|MIER1_ENST00000355977.6_5'Flank|MIER1_ENST00000371014.1_5'Flank|MIER1_ENST00000371016.1_5'Flank|WDR78_ENST00000431318.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	28					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						CCCCTTTTTTTGGCCGCCTCTG	0.644																																					p.Q28fs													.	WDR78-92	0			c.83_84insC						.																																			SO:0001589	frameshift_variant	79819	exon1			TTTTTTTGGCCGC	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"WD repeat domain containing"	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.83dupC	1.37:g.67390434_67390434dupG	ENSP00000360065:p.Gln28fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	350	12	NM_024763	0	0	0	0	0	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Frame_Shift_Ins	INS	ENST00000371026.3	37	CCDS635.1																																																																																			.		0.644	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		G	67390433	-	G	67390432	7	5	51	1	0	1	1	0	0	0	0	0	17361	1812	63	0	2588	0	WDR78	1	67390432	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	4467213	67390432	181860189	10	4698											
FRRS1	391059	bcgsc.ca	37	chr1	100194174	100194174	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taacaccgtccgccaacctcCaagccatatcctcaagggta	12	7	6	16	2	1	0	1	0	0	0	4	0	4	0	7	1	3	1	7	1	6	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:100194174C>A	ENST00000414213.1	-	9	1482	c.881G>T	c.(880-882)tGg>tTg	p.W294L	FRRS1_ENST00000287474.5_Missense_Mutation_p.W294L			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	294	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		CGCCAACCTCCAAGCCATATC	0.388																																					p.W294L													.	FRRS1-91	0			c.G881T						.						98	96	97					1																	100194174		2203	4300	6503	SO:0001583	missense	391059	exon9			AACCTCCAAGCCA	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"stromal cell derived factor receptor 2 homolog (mouse)"	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.881G>T	1.37:g.100194174C>A	ENSP00000393884:p.Trp294Leu	Somatic	135	0		WXS	Illumina HiSeq	Phase_1	94	43	NM_001013660	0	0	0	0	0	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		.	.	.	.	.	.	.	.	.	.	C	25.6	4.650467	0.87958	.	.	ENSG00000156869	ENST00000414213;ENST00000287474	T;T	0.75260	-0.92;-0.92	5.18	5.18	0.71444	.	0.062752	0.64402	D	0.000001	T	0.65207	0.2669	L	0.54323	1.7	0.80722	D	1	P	0.46395	0.877	P	0.47470	0.548	T	0.65664	-0.6113	10	0.09590	T	0.72	-9.2222	18.684	0.91557	0.0:1.0:0.0:0.0	.	294	Q6ZNA5-2	.	L	294	ENSP00000393884:W294L;ENSP00000287474:W294L	ENSP00000287474:W294L	W	-	2	0	FRRS1	99966762	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.970000	0.70431	2.411000	0.81874	0.484000	0.47621	TGG	.		0.388	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		A	100194174	C	A	100194174	3	1	51	1	0	0	0	0	1	0	0	0	6079	595	21	4	1035	4	FRRS1	1	100194174	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	32803742	100194174	149056447	11	4699											
CLCC1	23155	bcgsc.ca	37	chr1	109486197	109486197	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtacatatgtccacagctcaGtagccactaaaaccacgatg	14	8	7	12	1	1	0	1	0	0	0	2	1	2	0	3	0	4	3	3	0	5	4	rs201600225	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:109486197G>T	ENST00000369971.2	-	6	731	c.602C>A	c.(601-603)aCt>aAt	p.T201N	CLCC1_ENST00000369969.2_Intron|CLCC1_ENST00000356970.2_Missense_Mutation_p.T201N|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369976.1_Missense_Mutation_p.T201N|CLCC1_ENST00000348264.2_Intron|CLCC1_ENST00000369970.3_Missense_Mutation_p.T151N|CLCC1_ENST00000415331.1_Missense_Mutation_p.T151N|CLCC1_ENST00000482889.1_5'UTR|CLCC1_ENST00000369968.2_Intron|CLCC1_ENST00000302500.4_Intron	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	201						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		CCACAGCTCAGTAGCCACTAA	0.393													G|||	4	0.000798722	0	0.0014	5008	,	,		19132	0.002		0.001	False		,,,				2504	0				p.T201N													.	CLCC1-91	0			c.C602A						.						100	105	103					1																	109486197		2203	4300	6503	SO:0001583	missense	23155	exon6			AGCTCAGTAGCCA	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"Mid1-related chloride channel (yeast)"					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.602C>A	1.37:g.109486197G>T	ENSP00000358988:p.Thr201Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_1	63	24	NM_001048210	0	0	2	2	0	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.651578	0.67472	.	.	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369976;ENST00000369970	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.67449	0.2894	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.70861	-0.4757	10	0.66056	D	0.02	-17.6869	14.5247	0.67878	0.073:0.0:0.927:0.0	.	151;201	Q96S66-2;Q96S66	.;CLCC1_HUMAN	N	201;201;151;201;151	ENSP00000349456:T201N;ENSP00000358988:T201N;ENSP00000411591:T151N;ENSP00000358993:T201N;ENSP00000358987:T151N	ENSP00000349456:T201N	T	-	2	0	CLCC1	109287720	1.000000	0.71417	0.929000	0.37066	0.628000	0.37860	4.214000	0.58527	2.616000	0.88540	0.591000	0.81541	ACT	G|0.999;T|0.001		0.393	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127		T	109486197	G	T	109486197	3	4	51	1	0	0	0	0	1	0	0	0	3466	1029	36	4	1077	4	CLCC1	1	109486197	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	9292023	109486197	139764424	12	4700											
AMPD2	271	broad.mit.edu	37	chr1	110167929	110167930	+	Frame_Shift_Ins	INS	-	-	C																															tcactgtctctgcagaggctINScggggtggtctgggggcccc																								rs202115880		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:110167929_110167930insC	ENST00000256578.3	+	2	618_619	c.258_259insC	c.(259-261)cggfs	p.R87fs	AMPD2_ENST00000342115.4_Frame_Shift_Ins_p.R6fs|AMPD2_ENST00000528667.1_Frame_Shift_Ins_p.R87fs|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000358729.4_Intron|AMPD2_ENST00000393688.3_5'Flank|AMPD2_ENST00000528454.1_5'UTR	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	87					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		CTGCAGAGGCTCGGGGTGGTCT	0.703																																					p.A86fs													.	AMPD2-292	0			c.258_259insC						.																																			SO:0001589	frameshift_variant	271	exon3			AGAGGCTCGGGGT	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"AMPD isoform L"	102771	"adenosine monophosphate deaminase 2 (isoform L)"			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.259dupC	1.37:g.110167930_110167930dupC	ENSP00000256578:p.Arg87fs	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	121	22	NM_001257360	0	0	0	0	0	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Frame_Shift_Ins	INS	ENST00000256578.3	37	CCDS805.1																																																																																			.		0.703	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1			C	110167930	-	C	110167929	7	5	51	1	0	1	1	0	0	0	0	0	586	1538	54	0	278	0	AMPD2	1	110167929	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	681732	110167929	139082692	13	4701											
CGN	57530	bcgsc.ca	37	chr1	151491486	151491487	+	Frame_Shift_Ins	INS	-	-	T																															gagctagccccgaaagtggcINSttccccaggtagcaccattg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:151491486_151491487insT	ENST00000271636.7	+	2	624_625	c.491_492insT	c.(490-495)gcttccfs	p.S165fs		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	159	Head.|Interacts with ZO-2.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCGAAAGTGGCTTCCCCAGGTA	0.584																																					p.A164fs													.	CGN-93	0			c.491_492insT						.																																			SO:0001589	frameshift_variant	57530	exon2			AAGTGGCTTCCCC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.493dupT	1.37:g.151491488_151491488dupT	ENSP00000271636:p.Ser165fs	Somatic	129	0		WXS	Illumina HiSeq	Phase_1	364	69	NM_020770	0	0	0	0	0	A6H8L3|A7MD22|Q5T386|Q9NR25	Frame_Shift_Ins	INS	ENST00000271636.7	37	CCDS999.1																																																																																			.		0.584	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151491487	-	T	151491486	7	5	51	1	0	1	1	0	0	0	0	0	3309	797	28	0	493	0	CGN	1	151491486	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	41323557	151491486	97759135	14	4702											
S100A7	6278	bcgsc.ca	37	chr1	153430290	153430291	+	Frame_Shift_Ins	INS	-	-	G																															gtggggctgggtcactggctINSgcccccggaacagggcgctg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:153430290_153430291insG	ENST00000368723.3	-	3	407_408	c.297_298insC	c.(295-300)ggcagcfs	p.S100fs	S100A7_ENST00000368722.1_Frame_Shift_Ins_p.S100fs	NM_002963.3	NP_002954.2	P31151	S10A7_HUMAN	S100 calcium binding protein A7	100					angiogenesis (GO:0001525)|defense response to Gram-negative bacterium (GO:0050829)|epidermis development (GO:0008544)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of granulocyte chemotaxis (GO:0071624)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of T cell chemotaxis (GO:0010820)|response to lipopolysaccharide (GO:0032496)|response to reactive oxygen species (GO:0000302)|sequestering of metal ion (GO:0051238)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|RAGE receptor binding (GO:0050786)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(5)|skin(2)	10	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGTCACTGGCTGCCCCCGGAAC	0.515																																					p.S100fs													.	S100A7-91	0			c.298_299insC						.																																			SO:0001589	frameshift_variant	6278	exon3			ACTGGCTGCCCCC	BC034687	CCDS1039.1	1q21	2013-01-10	2006-09-11		ENSG00000143556	ENSG00000143556		"S100 calcium binding proteins", "EF-hand domain containing"	10497	protein-coding gene	gene with protein product		600353	"S100 calcium-binding protein A7 (psoriasin 1)", "S100 calcium binding protein A7 (psoriasin 1)"	PSOR1		1940442	Standard	NM_002963		Approved	S100A7c	uc001fbv.1	P31151	OTTHUMG00000013123	ENST00000368723.3:c.298dupC	1.37:g.153430291_153430291dupG	ENSP00000357712:p.Ser100fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	199	36	NM_002963	0	0	0	0	0	Q5SY67|Q6FGE3|Q9H1E2	Frame_Shift_Ins	INS	ENST00000368723.3	37	CCDS1039.1																																																																																			.		0.515	S100A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036789.1	NM_002963		G	153430291	-	G	153430290	7	5	51	1	0	1	1	0	0	0	0	0	13815	1580	55	0	11	0	S100A7	1	153430290	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	1938804	153430290	95820331	15	4703											
FCGR2A	2212	bcgsc.ca	37	chr1	161480669	161480669	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggggatcattgtggctgTggtcattgcgactgctgtag	7	13	15	6	1	2	0	2	0	0	0	2	2	2	1	0	4	2	3	0	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:161480669T>G	ENST00000271450.6	+	5	703	c.665T>G	c.(664-666)gTg>gGg	p.V222G	RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000367972.4_Missense_Mutation_p.V221G	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	222					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	ATTGTGGCTGTGGTCATTGCG	0.512																																					p.V222G													.	FCGR2A-91	0			c.T665G						.						232	230	231					1																	161480669		2203	4300	6503	SO:0001583	missense	2212	exon5			TGGCTGTGGTCAT	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3616	protein-coding gene	gene with protein product	"Immunoglobulin G Fc receptor II"	146790	"Fc fragment of IgG, low affinity IIa, receptor for (CD32)"	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.665T>G	1.37:g.161480669T>G	ENSP00000271450:p.Val222Gly	Somatic	177	0		WXS	Illumina HiSeq	Phase_1	285	161	NM_001136219	0	0	23	26	3	Q8WUN1|Q8WW64	Missense_Mutation	SNP	ENST00000271450.6	37	CCDS44264.1	.	.	.	.	.	.	.	.	.	.	.	12.98	2.101851	0.37048	.	.	ENSG00000143226	ENST00000367972;ENST00000271450	T;T	0.01998	4.51;4.51	2.27	-0.676	0.11361	.	2.881450	0.01271	N	0.009457	T	0.01695	0.0054	L	0.60455	1.87	0.25785	N	0.984687	D;P	0.54601	0.967;0.955	P;P	0.48454	0.576;0.578	T	0.35176	-0.9799	9	0.87932	D	0	.	5.0419	0.14463	0.0:0.5402:0.0:0.4598	.	222;221	P12318;P12318-2	FCG2A_HUMAN;.	G	221;222	ENSP00000356949:V221G;ENSP00000271450:V222G	ENSP00000271450:V222G	V	+	2	0	FCGR2A	159747293	0.000000	0.05858	0.006000	0.13384	0.027000	0.11550	-0.017000	0.12590	-0.155000	0.11098	0.459000	0.35465	GTG	.		0.512	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642		G	161480669	T	G	161480669	3	3	51	1	0	0	0	0	1	0	0	0	5800	1696	59	5	683	5	FCGR2A	1	161480669	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8050379	161480669	87769952	16	4704											
ASTN1	460	bcgsc.ca	37	chr1	177030344	177030344	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaagcaaagtgccattcTccagccactgctgcctccag	12	7	8	14	0	1	0	0	0	1	0	3	1	2	0	5	0	5	2	5	0	3	1	rs201383783		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:177030344T>C	ENST00000367654.3	-	2	552	c.341A>G	c.(340-342)gAg>gGg	p.E114G	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000361833.2_Missense_Mutation_p.E114G|ASTN1_ENST00000424564.2_Missense_Mutation_p.E114G|ASTN1_ENST00000367657.3_Missense_Mutation_p.E114G	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	114					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AGTGCCATTCTCCAGCCACTG	0.517																																					p.E114G													.	ASTN1-319	0			c.A341G						.						181	174	176					1																	177030344		2203	4300	6503	SO:0001583	missense	460	exon2			CCATTCTCCAGCC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"astrotactin"	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.341A>G	1.37:g.177030344T>C	ENSP00000356626:p.Glu114Gly	Somatic	202	1		WXS	Illumina HiSeq	Phase_1	67	32	NM_004319	0	0	0	0	0	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		.	.	.	.	.	.	.	.	.	.	T	27.9	4.871764	0.91587	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.25749	1.78;2.19;2.19;1.79	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.48909	0.1526	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.994;0.994	T	0.47209	-0.9135	10	0.87932	D	0	-34.8281	16.2708	0.82618	0.0:0.0:0.0:1.0	.	114;114;114	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	G	114	ENSP00000356629:E114G;ENSP00000354536:E114G;ENSP00000356626:E114G;ENSP00000395041:E114G	ENSP00000354536:E114G	E	-	2	0	ASTN1	175296967	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.897000	0.87356	2.324000	0.78689	0.533000	0.62120	GAG	T|0.999;C|0.001		0.517	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		C	177030344	T	C	177030344	3	2	51	1	0	0	0	0	1	0	0	0	1065	1551	54	3	3635	3	ASTN1	1	177030344	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	15549675	177030344	72220277	17	4705											
GLUL	2752	bcgsc.ca	37	chr1	182354977	182354977	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaatgggcctccacgatgTccctgccataggctctgtct	6	11	11	13	1	2	0	0	0	2	0	4	1	4	0	4	3	1	2	4	3	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:182354977T>C	ENST00000331872.6	-	5	1061	c.521A>G	c.(520-522)gAc>gGc	p.D174G	GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000311223.5_Missense_Mutation_p.D174G|GLUL_ENST00000339526.4_Missense_Mutation_p.D174G|GLUL_ENST00000417584.2_Missense_Mutation_p.D174G	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	174					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	CTCCACGATGTCCCTGCCATA	0.512																																					p.D174G													.	GLUL-90	0			c.A521G						.						135	143	141					1																	182354977		2203	4300	6503	SO:0001583	missense	2752	exon5			ACGATGTCCCTGC	AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"glutamine synthetase"	138290	"glutamate-ammonia ligase (glutamine synthase)"	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.521A>G	1.37:g.182354977T>C	ENSP00000356537:p.Asp174Gly	Somatic	226	2		WXS	Illumina HiSeq	Phase_1	174	81	NM_001033056	0	0	106	124	18	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Missense_Mutation	SNP	ENST00000331872.6	37	CCDS1344.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.193070|5.193070	0.94960|0.94960	.|.	.|.	ENSG00000135821|ENSG00000135821	ENST00000331872;ENST00000311223;ENST00000417584;ENST00000339526|ENST00000435013	D;D;D;D|.	0.87571|.	-2.27;-2.27;-2.27;-2.27|.	5.29|5.29	5.29|5.29	0.74685|0.74685	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);|.	0.145914|.	0.64402|.	D|.	0.000013|.	D|D	0.84120|0.84120	0.5402|0.5402	M|M	0.92412|0.92412	3.305|3.305	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.72075|.	0.976|.	D|D	0.87715|0.87715	0.2569|0.2569	10|6	0.87932|0.59425	D|D	0|0.04	-25.0718|-25.0718	14.0272|14.0272	0.64592|0.64592	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	174|.	P15104|.	GLNA_HUMAN|.	G|A	174|174	ENSP00000356537:D174G;ENSP00000307900:D174G;ENSP00000398320:D174G;ENSP00000344958:D174G|.	ENSP00000307900:D174G|ENSP00000388535:T174A	D|T	-|-	2|1	0|0	GLUL|GLUL	180621600|180621600	1.000000|1.000000	0.71417|0.71417	0.898000|0.898000	0.35279|0.35279	0.981000|0.981000	0.71138|0.71138	7.662000|7.662000	0.83803|0.83803	1.982000|1.982000	0.57802|0.57802	0.528000|0.528000	0.53228|0.53228	GAC|ACA	.		0.512	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065		C	182354977	T	C	182354977	3	2	51	1	0	0	0	0	1	0	0	0	6498	1667	58	3	612	3	GLUL	1	182354977	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	5324633	182354977	66895644	18	4706											
C1orf25	81627	bcgsc.ca	37	chr1	185112542	185112542	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttcgttcctcagccaaaGcagccaatgtacagaatatt	12	12	7	10	1	1	1	1	0	0	1	3	1	2	1	3	0	4	4	3	0	5	6	rs369669193		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:185112542G>C	ENST00000367506.5	-	7	1074	c.806C>G	c.(805-807)gCt>gGt	p.A269G	TRMT1L_ENST00000367504.3_Missense_Mutation_p.A113G	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	269	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.				adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						CTCAGCCAAAGCAGCCAATGT	0.353																																					p.A269G													.	TRMT1L-92	0			c.C806G						.						94	103	100					1																	185112542		2203	4300	6503	SO:0001583	missense	81627	exon7			GCCAAAGCAGCCA	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.806C>G	1.37:g.185112542G>C	ENSP00000356476:p.Ala269Gly	Somatic	149	0		WXS	Illumina HiSeq	Phase_1	47	24	NM_030934	0	0	8	8	0	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Missense_Mutation	SNP	ENST00000367506.5	37	CCDS1366.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350465	0.82132	.	.	ENSG00000121486	ENST00000367504;ENST00000367506	.	.	.	5.34	4.32	0.51571	.	0.056271	0.64402	D	0.000001	T	0.40522	0.1120	L	0.38175	1.15	0.41055	D	0.985335	P	0.39044	0.656	B	0.41894	0.369	T	0.40869	-0.9540	9	0.51188	T	0.08	-13.8742	3.4542	0.07510	0.3709:0.0:0.6291:0.0	.	269	Q7Z2T5	TRM1L_HUMAN	G	113;269	.	ENSP00000356474:A113G	A	-	2	0	TRMT1L	183379165	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.497000	0.60367	2.495000	0.84180	0.591000	0.81541	GCT	.		0.353	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		C	185112542	G	C	185112542	3	2	51	1	0	0	0	0	1	0	0	0	2040	971	34	4	1431	4	C1orf25	1	185112542	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	2757565	185112542	64138079	19	4707											
IPO9	55705	bcgsc.ca	37	chr1	201827623	201827623	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgcagcagccctggctgctGcagccactcgacatttacaa	9	8	10	14	1	0	0	0	0	0	0	1	1	0	0	2	1	7	5	2	1	2	2	rs201551339		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:201827623G>C	ENST00000361565.4	+	12	1339	c.1270G>C	c.(1270-1272)Gca>Cca	p.A424P		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	424					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						CCTGGCTGCTGCAGCCACTCG	0.448																																					p.A424P													.	IPO9-228	0			c.G1270C						.						62	75	70					1																	201827623		2202	4300	6502	SO:0001583	missense	55705	exon12			GCTGCTGCAGCCA	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.1270G>C	1.37:g.201827623G>C	ENSP00000354742:p.Ala424Pro	Somatic	179	0		WXS	Illumina HiSeq	Phase_1	104	75	NM_018085	0	0	14	17	3	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	G	35	5.581101	0.96565	.	.	ENSG00000198700	ENST00000361565	T	0.66460	-0.21	5.54	5.54	0.83059	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80144	0.4569	M	0.82323	2.585	0.80722	D	1	P	0.52692	0.955	P	0.56751	0.805	T	0.79797	-0.1652	10	0.36615	T	0.2	-8.4189	16.9815	0.86328	0.0:0.0:1.0:0.0	.	424	Q96P70	IPO9_HUMAN	P	424	ENSP00000354742:A424P	ENSP00000354742:A424P	A	+	1	0	IPO9	200094246	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.451000	0.80668	2.576000	0.86940	0.557000	0.71058	GCA	.		0.448	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		C	201827623	G	C	201827623	3	2	51	1	0	0	0	0	1	0	0	0	7820	1319	46	4	1316	4	IPO9	1	201827623	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	16715081	201827623	47422998	20	4708											
FCAMR	83953	bcgsc.ca	37	chr1	207135670	207135670	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggacagcctcaccacaaaCaagcctctctgtggaaagtc	12	7	9	13	0	2	0	1	0	1	0	4	2	2	2	3	2	3	0	3	2	3	0	rs199611731		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:207135670C>A	ENST00000324852.4	-	5	1014	c.540G>T	c.(538-540)ttG>ttT	p.L180F	FCAMR_ENST00000486178.1_5'Flank|FCAMR_ENST00000450945.2_Missense_Mutation_p.L180F|FCAMR_ENST00000400962.3_Missense_Mutation_p.L180F	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	135					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TCACCACAAACAAGCCTCTCT	0.517																																					p.L180F	Ovarian(199;1883 2142 16966 44409 45154)												.	FCAMR-91	0			c.G540T						.						105	100	101					1																	207135670		1568	3582	5150	SO:0001583	missense	83953	exon5			CACAAACAAGCCT	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.540G>T	1.37:g.207135670C>A	ENSP00000316491:p.Leu180Phe	Somatic	95	0		WXS	Illumina HiSeq	Phase_1	122	52	NM_001170631	0	0	10	10	0	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.997875	0.35226	.	.	ENSG00000162897	ENST00000400962;ENST00000324852;ENST00000450945;ENST00000367087	T;T;T	0.64991	-0.13;-0.13;-0.13	5.6	-2.7	0.06004	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.888450	0.09618	N	0.777967	T	0.71728	0.3374	M	0.63428	1.95	0.21719	N	0.999576	B;D;B;D	0.76494	0.011;0.999;0.364;0.992	B;D;B;D	0.77557	0.009;0.99;0.341;0.944	T	0.63686	-0.6581	10	0.62326	D	0.03	0.0926	8.852	0.35206	0.1144:0.2096:0.6036:0.0724	.	135;155;135;135	Q8WWV6-4;D2KTA8;Q8WWV6-2;Q8WWV6	.;.;.;FCAMR_HUMAN	F	180;180;180;156	ENSP00000383746:L180F;ENSP00000316491:L180F;ENSP00000392707:L180F	ENSP00000316491:L180F	L	-	3	2	FCAMR	205202293	0.001000	0.12720	0.228000	0.23943	0.138000	0.21146	-0.991000	0.03728	-0.452000	0.07087	-0.963000	0.02626	TTG	C|0.999;A|0.001		0.517	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		A	207135670	C	A	207135670	3	1	51	1	0	0	0	0	1	0	0	0	5791	477	17	4	1209	4	FCAMR	1	207135670	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	5308047	207135670	42114951	21	4709											
PLXNA2	5362	bcgsc.ca	37	chr1	208252715	208252715	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctgcgctcgccgctgcAccagccacactcaaacttcc	8	6	7	20	3	1	0	1	0	0	0	3	0	2	0	5	0	4	4	5	0	1	1	rs202222167		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:208252715A>C	ENST00000367033.3	-	12	3233	c.2476T>G	c.(2476-2478)Tgc>Ggc	p.C826G		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	826					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TCGCCGCTGCACCAGCCACAC	0.627																																					p.C826G													.	PLXNA2-92	0			c.T2476G						.						33	34	34					1																	208252715		2203	4300	6503	SO:0001583	missense	5362	exon12			CGCTGCACCAGCC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2476T>G	1.37:g.208252715A>C	ENSP00000356000:p.Cys826Gly	Somatic	32	1		WXS	Illumina HiSeq	Phase_1	47	32	NM_025179	0	0	6	7	1	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.912439	0.92178	.	.	ENSG00000076356	ENST00000367033	T	0.31769	1.48	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	M	0.92507	3.315	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.75224	-0.3393	10	0.87932	D	0	.	15.7935	0.78388	1.0:0.0:0.0:0.0	.	826	O75051	PLXA2_HUMAN	G	826	ENSP00000356000:C826G	ENSP00000356000:C826G	C	-	1	0	PLXNA2	206319338	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.922000	0.70036	2.125000	0.65367	0.533000	0.62120	TGC	.		0.627	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		C	208252715	A	C	208252715	3	2	51	1	0	0	0	0	1	0	0	0	12146	159	6	5	3292	5	PLXNA2	1	208252715	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1117045	208252715	40997906	22	4710											
LAMB3	3914	hgsc.bcm.edu	37	chr1	209795956	209795956	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccatctgggagcggctggCgctcacctgggtctccaagc	5	8	13	15	2	3	0	1	0	2	0	5	1	4	1	3	4	2	2	3	4	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:209795956C>G	ENST00000356082.4	-	18	2760	c.2626G>C	c.(2626-2628)Gcc>Ccc	p.A876P	LAMB3_ENST00000367030.3_Missense_Mutation_p.A876P|LAMB3_ENST00000391911.1_Missense_Mutation_p.A876P|MIR4260_ENST00000583107.1_RNA	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	876	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GAGCGGCTGGCGCTCACCTGG	0.582																																					p.A876P		.											.	LAMB3-156	0			c.G2626C						.						176	177	177					1																	209795956		2203	4300	6503	SO:0001583	missense	3914	exon18			GGCTGGCGCTCAC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2626G>C	1.37:g.209795956C>G	ENSP00000348384:p.Ala876Pro	Somatic	319	0		WXS	Illumina HiSeq	Phase_I	865	334	NM_000228	0	0	5	5	0	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.869140	0.32977	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.25085	1.82;1.82;1.82	5.56	-2.65	0.06095	.	0.911231	0.09623	N	0.777320	T	0.15998	0.0385	L	0.29908	0.895	0.20196	N	0.999927	B	0.31730	0.337	B	0.26416	0.069	T	0.15521	-1.0434	10	0.30078	T	0.28	.	11.3588	0.49632	0.0:0.363:0.0:0.637	.	876	Q13751	LAMB3_HUMAN	P	876	ENSP00000375778:A876P;ENSP00000348384:A876P;ENSP00000355997:A876P	ENSP00000348384:A876P	A	-	1	0	LAMB3	207862579	0.202000	0.23423	0.922000	0.36590	0.766000	0.43426	-0.483000	0.06536	-0.754000	0.04715	-0.518000	0.04402	GCC	.		0.582	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		G	209795956	C	G	209795956	3	3	51	1	0	0	0	0	1	0	0	0	8633	768	27	4	916	4	LAMB3	1	209795956	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1543241	209795956	39454665	23	4711											
TRAF5	7188	bcgsc.ca	37	chr1	211545690	211545690	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tacaccagccgctgtggctaCcggctctgtgctagagcata	8	9	11	13	2	1	1	0	0	1	1	1	1	1	1	3	2	5	5	3	2	4	4	rs200264560		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:211545690C>A	ENST00000261464.5	+	11	1374	c.1320C>A	c.(1318-1320)taC>taA	p.Y440*	TRAF5_ENST00000336184.2_Nonsense_Mutation_p.Y440*|TRAF5_ENST00000367004.3_Nonsense_Mutation_p.Y440*|TRAF5_ENST00000427925.2_Nonsense_Mutation_p.Y334*	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	440	Interaction with EIF2AK2/PKR.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		GCTGTGGCTACCGGCTCTGTG	0.537																																					p.Y440X													.	TRAF5-661	0			c.C1320A						.						78	84	82					1																	211545690		2203	4300	6503	SO:0001587	stop_gained	7188	exon11			TGGCTACCGGCTC	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.1320C>A	1.37:g.211545690C>A	ENSP00000261464:p.Tyr440*	Somatic	119	0		WXS	Illumina HiSeq	Phase_1	33	10	NM_004619	0	0	9	9	0	B4DIS9|B4E0A2|Q6FHY1	Nonsense_Mutation	SNP	ENST00000261464.5	37	CCDS1497.1	.	.	.	.	.	.	.	.	.	.	C	37	6.095248	0.97276	.	.	ENSG00000082512	ENST00000336184;ENST00000427925;ENST00000261464;ENST00000367004	.	.	.	5.16	2.29	0.28610	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.6191	10.6195	0.45472	0.0:0.791:0.0:0.209	.	.	.	.	X	440;334;440;440	.	ENSP00000261464:Y440X	Y	+	3	2	TRAF5	209612313	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.660000	0.61511	0.291000	0.22468	0.650000	0.86243	TAC	.		0.537	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		A	211545690	C	A	211545690	4	1	51	1	0	0	0	0	0	1	0	0	16477	518	18	4	1358	4	TRAF5	1	211545690	Nonsense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1749734	211545690	37704931	24	4712											
TP53BP2	7159	bcgsc.ca	37	chr1	223990474	223990474	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagagctgccttcttcttccAcagccggtccctcagctcat	6	12	7	16	1	4	1	2	0	2	1	6	1	6	1	4	1	4	2	4	1	1	4	rs199538625		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:223990474A>C	ENST00000343537.7	-	8	1246	c.955T>G	c.(955-957)Tgg>Ggg	p.W319G	TP53BP2_ENST00000391878.2_Missense_Mutation_p.W190G|TP53BP2_ENST00000391879.2_5'Flank|TP53BP2_ENST00000498843.1_5'Flank	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	313					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		TTCTTCTTCCACAGCCGGTCC	0.473																																					p.W319G													.	TP53BP2-229	0			c.T955G						.						184	182	183					1																	223990474		2203	4300	6503	SO:0001583	missense	7159	exon8			TCTTCCACAGCCG	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.955T>G	1.37:g.223990474A>C	ENSP00000341957:p.Trp319Gly	Somatic	192	0		WXS	Illumina HiSeq	Phase_1	85	28	NM_001031685	0	0	23	25	2	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082375	0.76528	.	.	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.33216	1.42;1.42	5.56	5.56	0.83823	.	0.107477	0.64402	D	0.000002	T	0.53834	0.1821	M	0.68317	2.08	0.80722	D	1	D;D	0.76494	0.999;0.991	D;P	0.80764	0.994;0.874	T	0.53041	-0.8494	10	0.44086	T	0.13	.	15.7073	0.77594	1.0:0.0:0.0:0.0	.	319;313	B4DG66;Q13625	.;ASPP2_HUMAN	G	190;319	ENSP00000375750:W190G;ENSP00000341957:W319G	ENSP00000341957:W319G	W	-	1	0	TP53BP2	222057097	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.500000	0.81588	2.098000	0.63641	0.533000	0.62120	TGG	.		0.473	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		C	223990474	A	C	223990474	3	2	51	1	0	0	0	0	1	0	0	0	16417	159	6	5	2493	5	TP53BP2	1	223990474	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	12444784	223990474	25260147	25	4713											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228559225	228559225	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggcgctgccaggcctgcgcGagccactgatggagcaccgc	6	4	16	15	4	0	1	0	1	0	0	0	3	0	2	4	3	4	2	4	3	0	0	rs200269110	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:228559225G>A	ENST00000422127.1	+	94	20790	c.20746G>A	c.(20746-20748)Gag>Aag	p.E6916K	OBSCN_ENST00000570156.2_Missense_Mutation_p.E7873K|OBSCN_ENST00000366707.4_Missense_Mutation_p.E4550K	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6916					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGCCTGCGCGAGCCACTGAT	0.746													G|||	34	0.00678914	0.0257	0	5008	,	,		12917	0		0	False		,,,				2504	0				p.E7873K		.											.	OBSCN-403	0			c.G23617A						.	G	LYS/GLU	70,3774		0,70,1852	5	9	8		20746	4.4	0.9	1		8	0,8116		0,0,4058	yes	missense	OBSCN	NM_001098623.1	56	0,70,5910	AA,AG,GG		0.0,1.821,0.5853	benign	6916/7969	228559225	70,11890	1922	4058	5980	SO:0001583	missense	84033	exon105			CTGCGCGAGCCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.20746G>A	1.37:g.228559225G>A	ENSP00000409493:p.Glu6916Lys	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	13	6	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368034|3.368034	0.61513|0.61513	0.01821|0.01821	0.0|0.0	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|T	0.65549|0.72394	-0.16;-0.1|-0.65	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	.|.	.|.	.|.	.|.	T|T	0.64068|0.64068	0.2565|0.2565	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.72301|0.72301	-0.4334|-0.4334	9|7	0.40728|0.41790	T|T	0.16|0.15	.|.	17.2084|17.2084	0.86924|0.86924	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6916|.	Q5VST9|.	OBSCN_HUMAN|.	K|Q	6916;4550|1532	ENSP00000409493:E6916K;ENSP00000355668:E4550K|ENSP00000388554:R1532Q	ENSP00000355668:E4550K|ENSP00000388554:R1532Q	E|R	+|+	1|2	0|0	OBSCN|OBSCN	226625848|226625848	0.999000|0.999000	0.42202|0.42202	0.931000|0.931000	0.37212|0.37212	0.040000|0.040000	0.13550|0.13550	2.926000|2.926000	0.48892|0.48892	2.300000|2.300000	0.77407|0.77407	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.		0.746	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228559225	G	A	228559225	3	1	51	1	0	0	0	0	1	0	0	0	10838	1059	37	1	22326	1	OBSCN	1	228559225	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	4568751	228559225	20691396	26	4714											
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458346	248458346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caaacgcaccaacacgggggCctcgcagaagaagtgatcga	14	3	12	12	4	0	3	0	1	0	2	2	4	0	3	2	2	2	2	2	2	4	0	rs149479956	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:248458346C>T	ENST00000317996.1	-	1	534	c.535G>A	c.(535-537)Gcc>Acc	p.A179T		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			AACACGGGGGCCTCGCAGAAG	0.562																																					p.A179T		.											.	OR2T12-71	0			c.G535A						.						166	128	141					1																	248458346		2201	4298	6499	SO:0001583	missense	127064	exon1			CGGGGGCCTCGCA	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.535G>A	1.37:g.248458346C>T	ENSP00000324583:p.Ala179Thr	Somatic	102	1		WXS	Illumina HiSeq	Phase_I	249	18	NM_001004692	0	0	0	0	0		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	c	11.86	1.764047	0.31228	.	.	ENSG00000177201	ENST00000317996	T	0.36878	1.23	1.55	0.228	0.15364	GPCR, rhodopsin-like superfamily (1);	0.505346	0.14676	U	0.305046	T	0.22781	0.0550	N	0.17901	0.54	0.09310	N	1	B	0.25563	0.129	B	0.35971	0.215	T	0.28522	-1.0041	10	0.72032	D	0.01	.	3.0778	0.06252	0.0:0.37:0.0:0.63	.	179	Q8NG77	O2T12_HUMAN	T	179	ENSP00000324583:A179T	ENSP00000324583:A179T	A	-	1	0	OR2T12	246524969	0.000000	0.05858	0.074000	0.20217	0.296000	0.27459	-4.436000	0.00234	0.645000	0.30675	0.175000	0.17021	GCC	C|1.000;|0.000		0.562	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		T	248458346	C	T	248458346	3	4	51	1	0	0	0	0	1	0	0	0	11045	739	26	2	430	2	OR2T12	1	248458346	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	19899121	248458346	792275	27	4715											
HS1BP3	64342	bcgsc.ca	37	chr2	20818846	20818846	+	Silent	SNP	C	C	T																															tggatctgctcctgcggcttCtgctgcccagccacagcttc																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:20818846C>T	ENST00000304031.3	-	7	1105	c.1080G>A	c.(1078-1080)caG>caA	p.Q360Q		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	360							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTGCGGCTTCTGCTGCCCAG	0.612																																					p.Q360Q													.	HS1BP3-91	0			c.G1080A						.						91	99	96					2																	20818846		2203	4300	6503	SO:0001819	synonymous_variant	64342	exon7			CGGCTTCTGCTGC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.1080G>A	2.37:g.20818846C>T		Somatic	201	0		WXS	Illumina HiSeq	Phase_1	276	130	NM_022460	0	0	35	37	2	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			.		0.612	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		T	20818846	C	T	20818846	2	4	51	1	0	0	0	0	0	0	0	1	7382	912	32	2		2	HS1BP3	2	20818846	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08		20818846	222380527	28	4716	53	2									
HS1BP3	64342	bcgsc.ca	37	chr2	20818851	20818851	+	Missense_Mutation	SNP	G	G	C																															ctgctcctgcggcttctgctGcccagccacagcttcagccg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:20818851G>C	ENST00000304031.3	-	7	1100	c.1075C>G	c.(1075-1077)Cag>Gag	p.Q359E		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	359							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTTCTGCTGCCCAGCCACA	0.622																																					p.Q359E													.	HS1BP3-91	0			c.C1075G						.						86	95	92					2																	20818851		2203	4300	6503	SO:0001583	missense	64342	exon7			TCTGCTGCCCAGC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.1075C>G	2.37:g.20818851G>C	ENSP00000305193:p.Gln359Glu	Somatic	206	0		WXS	Illumina HiSeq	Phase_1	304	159	NM_022460	0	0	43	45	2	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	37	CCDS1700.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.302154	0.23736	.	.	ENSG00000118960	ENST00000304031	T	0.17691	2.26	5.42	5.42	0.78866	.	1.045250	0.07668	N	0.935044	T	0.20047	0.0482	L	0.46157	1.445	0.80722	D	1	B	0.22276	0.067	B	0.17433	0.018	T	0.04930	-1.0917	10	0.26408	T	0.33	-5.6295	14.7112	0.69232	0.0:0.0:1.0:0.0	.	359	Q53T59	H1BP3_HUMAN	E	359	ENSP00000305193:Q359E	ENSP00000305193:Q359E	Q	-	1	0	HS1BP3	20682332	0.066000	0.20996	0.007000	0.13788	0.718000	0.41266	3.003000	0.49505	2.556000	0.86216	0.655000	0.94253	CAG	.		0.622	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		C	20818851	G	C	20818851	3	2	51	1	0	0	0	0	1	0	0	0	7382	1328	46	4	107	4	HS1BP3	2	20818851	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	5	20818851	222380522	29	4717	53	2									
TMEM214	54867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27259433	27259433	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggccctgggtcaagcaggtTttgccaacctcaccgaggga	8	7	14	12	1	2	0	2	0	0	0	2	2	2	1	4	4	3	2	4	4	2	2	rs564964647		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:27259433T>G	ENST00000238788.9	+	6	861	c.799T>G	c.(799-801)Ttt>Gtt	p.F267V	TMEM214_ENST00000404032.3_Missense_Mutation_p.F222V	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	267					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TCAAGCAGGTTTTGCCAACCT	0.567																																					p.F267V		.											.	TMEM214-115	0			c.T799G						.						103	103	103					2																	27259433		1943	4141	6084	SO:0001583	missense	54867	exon6			GCAGGTTTTGCCA		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.799T>G	2.37:g.27259433T>G	ENSP00000238788:p.Phe267Val	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	611	177	NM_017727	0	0	102	142	40	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	37	CCDS42664.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.873746	0.91664	.	.	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397	T;T	0.52295	0.67;0.67	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.74258	2.255	0.80722	D	1	D;P	0.56746	0.977;0.917	P;P	0.57679	0.794;0.825	T	0.65417	-0.6173	10	0.42905	T	0.14	-14.1771	15.3509	0.74384	0.0:0.0:0.0:1.0	.	222;267	Q6NUQ4-2;Q6NUQ4	.;TM214_HUMAN	V	267;222;9	ENSP00000238788:F267V;ENSP00000384417:F222V	ENSP00000238788:F267V	F	+	1	0	TMEM214	27112937	1.000000	0.71417	0.436000	0.26797	0.968000	0.65278	7.508000	0.81686	2.128000	0.65567	0.459000	0.35465	TTT	.		0.567	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		G	27259433	T	G	27259433	3	3	51	1	0	0	0	0	1	0	0	0	16169	1841	64	5	821	5	TMEM214	2	27259433	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	6440582	27259433	215939940	30	4718											
CGREF1	10669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27327221	27327221	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggattaacactgtcatcGtcaaaggtaacatccttcct	12	11	7	11	1	2	0	2	0	0	0	5	1	4	1	2	2	2	2	2	2	3	3	rs112618911		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:27327221G>T	ENST00000260595.5	-	2	306	c.14C>A	c.(13-15)aCg>aAg	p.T5K	CGREF1_ENST00000405600.1_Missense_Mutation_p.T5K|CGREF1_ENST00000312734.4_Missense_Mutation_p.T5K|CGREF1_ENST00000402394.1_Missense_Mutation_p.T5K|CGREF1_ENST00000452318.2_Intron|CGREF1_ENST00000404694.3_Missense_Mutation_p.T127K|CGREF1_ENST00000402550.1_Missense_Mutation_p.T5K			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	5					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACTGTCATCGTCAAAGGTAA	0.567																																					p.T5K		.											.	CGREF1-91	0			c.C14A						.						67	59	62					2																	27327221		2203	4300	6503	SO:0001583	missense	10669	exon2			GTCATCGTCAAAG	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"EF-hand domain containing"	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.14C>A	2.37:g.27327221G>T	ENSP00000260595:p.Thr5Lys	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	149	38	NM_001166239	0	0	5	5	0	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Missense_Mutation	SNP	ENST00000260595.5	37		.	.	.	.	.	.	.	.	.	.	A	13.14	2.147472	0.37923	.	.	ENSG00000138028	ENST00000402550;ENST00000402394;ENST00000405600;ENST00000389521;ENST00000312734;ENST00000404694;ENST00000260595	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.73	-7.65	0.01281	.	1.833840	0.02770	N	0.119586	T	0.16300	0.0392	N	0.12182	0.205	0.09310	N	1	B;B;B	0.10296	0.002;0.002;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.20638	-1.0269	10	0.44086	T	0.13	-10.5345	8.4971	0.33134	0.1308:0.0:0.5748:0.2945	.	127;5;5	B5MCC9;B5MCP5;Q99674	.;.;CGRE1_HUMAN	K	5;5;5;5;5;127;5	ENSP00000385452:T5K;ENSP00000386113:T5K;ENSP00000324025:T5K;ENSP00000385574:T127K;ENSP00000260595:T5K	ENSP00000260595:T5K	T	-	2	0	CGREF1	27180725	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.719000	0.04974	-2.518000	0.00499	-1.007000	0.02485	ACG	G|0.998;A|0.002		0.567	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569		T	27327221	G	T	27327221	3	4	51	1	0	0	0	0	1	0	0	0	3311	1145	40	4	1154	4	CGREF1	2	27327221	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	67788	27327221	215872152	31	4719											
ZNF512	84450	bcgsc.ca	37	chr2	27840357	27840357	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggaaactttgtggctggAaaatacaaatgtcttctatg	13	13	10	5	0	2	0	0	0	2	0	2	2	2	2	0	3	2	1	0	3	7	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:27840357A>G	ENST00000355467.4	+	13	1397	c.1314A>G	c.(1312-1314)ggA>ggG	p.G438G	ZNF512_ENST00000416005.2_Silent_p.G409G|ZNF512_ENST00000556601.1_Silent_p.G307G|ZNF512_ENST00000413371.2_Silent_p.G361G|ZNF512_ENST00000379717.1_Silent_p.G437G|RP11-158I13.2_ENST00000505973.1_RNA	NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3	NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2	Q96ME7	ZN512_HUMAN	zinc finger protein 512	438					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)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)					TTGTGGCTGGAAAATACAAAT	0.383																																					p.G438G													.	ZNF512-91	0			c.A1314G						.						88	86	87					2																	27840357		2203	4300	6503	SO:0001819	synonymous_variant	84450	exon13			GGCTGGAAAATAC	AL833748	CCDS1758.1, CCDS59428.1, CCDS59429.1	2p23	2008-02-05			ENSG00000243943	ENSG00000243943		"Zinc fingers, C2H2-type"	29380	protein-coding gene	gene with protein product						11347906	Standard	NM_032434		Approved	KIAA1805	uc002rla.4	Q96ME7	OTTHUMG00000097786	ENST00000355467.4:c.1314A>G	2.37:g.27840357A>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_1	73	45	NM_032434	0	0	16	20	4	B4DSM5|Q53RZ7|Q86XK6|Q96JM0	Silent	SNP	ENST00000355467.4	37	CCDS1758.1																																																																																			.		0.383	ZNF512-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215029.2	NM_032434		G	27840357	A	G	27840357	2	3	51	1	0	0	0	0	0	0	0	1	17988	233	9	3		3	ZNF512	2	27840357	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	513136	27840357	215359016	32	4720											
SPAST	6683	hgsc.bcm.edu	37	chr2	32289269	32289269	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagtcttccacaaacaggcCttcgagtacatctccattgc	10	10	7	14	2	2	0	0	0	2	0	5	2	3	0	3	1	3	1	3	1	2	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:32289269C>G	ENST00000315285.3	+	1	494	c.369C>G	c.(367-369)gcC>gcG	p.A123A	SPAST_ENST00000345662.1_Silent_p.A123A	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ACAAACAGGCCTTCGAGTACA	0.711																																					p.A123A		.											.	SPAST-153	0			c.C369G						.						4	4	4					2																	32289269		1808	3894	5702	SO:0001819	synonymous_variant	6683	exon1			ACAGGCCTTCGAG	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"ATPases / AAA-type"	11233	protein-coding gene	gene with protein product		604277	"spastic paraplegia 4 (autosomal dominant; spastin)"	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.369C>G	2.37:g.32289269C>G		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	9	6	NM_199436	0	0	0	2	2		Silent	SNP	ENST00000315285.3	37	CCDS1778.1																																																																																			.		0.711	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		G	32289269	C	G	32289269	2	3	51	1	0	0	0	0	0	0	0	1	15029	668	24	4		4	SPAST	2	32289269	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	4448912	32289269	210910104	33	4721											
FAM98A	25940	bcgsc.ca	37	chr2	33813450	33813450	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatagttatattggctggAggtttggacattcctagagc	11	13	11	6	0	0	1	0	0	0	1	1	3	1	3	1	4	2	3	1	4	5	7			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:33813450A>G	ENST00000238823.8	-	4	614	c.474T>C	c.(472-474)ccT>ccC	p.P158P	FAM98A_ENST00000498340.1_Intron|FAM98A_ENST00000441530.2_Intron|FAM98A_ENST00000403368.1_Silent_p.P158P			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	158							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					TATTGGCTGGAGGTTTGGACA	0.388																																					p.P158P													.	FAM98A-91	0			c.T474C						.						173	174	174					2																	33813450		2203	4300	6503	SO:0001819	synonymous_variant	25940	exon4			GGCTGGAGGTTTG		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.474T>C	2.37:g.33813450A>G		Somatic	169	0		WXS	Illumina HiSeq	Phase_1	55	25	NM_015475	0	0	42	48	6	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																			.		0.388	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		G	33813450	A	G	33813450	2	3	51	1	0	0	0	0	0	0	0	1	5675	291	11	3		3	FAM98A	2	33813450	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1524181	33813450	209385923	34	4722											
CEBPZ	10153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37454852	37454852	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catcaccagtctgggaataaGggtatgccctattcacacct	11	10	8	12	0	3	0	2	0	1	0	3	1	3	1	3	2	1	1	3	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:37454852G>A	ENST00000234170.5	-	2	1629	c.1484C>T	c.(1483-1485)cCt>cTt	p.P495L		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	495					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				CTGGGAATAAGGGTATGCCCT	0.368																																					p.P495L		.											.	CEBPZ-91	0			c.C1484T						.						83	79	80					2																	37454852		2203	4300	6503	SO:0001583	missense	10153	exon2			GAATAAGGGTATG	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1484C>T	2.37:g.37454852G>A	ENSP00000234170:p.Pro495Leu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	34	20	NM_005760	0	0	25	66	41	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.952289	0.73787	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.24538	1.85	5.59	5.59	0.84812	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.64494	0.2603	M	0.93898	3.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74247	-0.3727	10	0.87932	D	0	.	19.6055	0.95580	0.0:0.0:1.0:0.0	.	495	Q03701	CEBPZ_HUMAN	L	495	ENSP00000234170:P495L	ENSP00000234170:P495L	P	-	2	0	CEBPZ	37308356	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	9.296000	0.96104	2.631000	0.89168	0.650000	0.86243	CCT	.		0.368	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37454852	G	A	37454852	3	1	51	1	0	0	0	0	1	0	0	0	3210	1000	35	2	1740	2	CEBPZ	2	37454852	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	3641402	37454852	205744521	35	4723											
ATL2	64225	bcgsc.ca	37	chr2	38525498	38525498	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcaaacagtgtggctggggTacgagcagcatagaagatat	13	7	14	7	2	0	2	0	0	0	2	0	3	0	2	0	3	4	5	0	3	5	3	rs76204302		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:38525498T>G	ENST00000378954.4	-	12	1421	c.1420A>C	c.(1420-1422)Acc>Ccc	p.T474P	ATL2_ENST00000406122.1_Missense_Mutation_p.T303P|ATL2_ENST00000546051.1_Missense_Mutation_p.T303P|ATL2_ENST00000419554.2_Missense_Mutation_p.T474P|ATL2_ENST00000452935.2_Missense_Mutation_p.T456P|ATL2_ENST00000539122.1_Missense_Mutation_p.T303P|ATL2_ENST00000332337.4_Missense_Mutation_p.T456P|ATL2_ENST00000402054.1_Missense_Mutation_p.T303P	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	474					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						GTGGCTGGGGTACGAGCAGCA	0.418																																					p.T474P													.	ATL2-228	0			c.A1420C						.						137	125	129					2																	38525498		2203	4300	6503	SO:0001583	missense	64225	exon12			CTGGGGTACGAGC		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"ADP-ribosylation factor-like 6 interacting protein 2"	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.1420A>C	2.37:g.38525498T>G	ENSP00000368237:p.Thr474Pro	Somatic	95	1		WXS	Illumina HiSeq	Phase_1	36	16	NM_001135673	0	0	33	46	13	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.606237	0.87157	.	.	ENSG00000119787	ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051	D;D;D;D;D;D;D;D	0.96856	-4.15;-4.15;-4.15;-4.15;-4.15;-4.15;-4.15;-4.15	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.98385	0.9463	M	0.89968	3.075	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.997;0.987;0.997;0.997;0.992	D	0.99418	1.0932	10	0.72032	D	0.01	-10.8367	15.3584	0.74448	0.0:0.0:0.0:1.0	.	303;456;456;474;474	B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.;.;.;.;ATLA2_HUMAN	P	474;303;303;303;456;474;456;303	ENSP00000368237:T474P;ENSP00000385446:T303P;ENSP00000384062:T303P;ENSP00000446192:T303P;ENSP00000333393:T456P;ENSP00000415336:T474P;ENSP00000390743:T456P;ENSP00000438938:T303P	ENSP00000333393:T456P	T	-	1	0	ATL2	38379002	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	7.874000	0.87199	2.217000	0.71921	0.482000	0.46254	ACC	.		0.418	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374		G	38525498	T	G	38525498	3	3	51	1	0	0	0	0	1	0	0	0	1108	1638	57	5	451	5	ATL2	2	38525498	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1070646	38525498	204673875	36	4724											
ABCG8	64241	bcgsc.ca	37	chr2	44079968	44079969	+	Frame_Shift_Ins	INS	-	-	A																															gtatttcacagccatcggctINSacccctgtcctcgctacagc																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:44079968_44079969insA	ENST00000272286.2	+	6	1015_1016	c.925_926insA	c.(925-927)tacfs	p.Y309fs		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	309	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	AGCCATCGGCTACCCCTGTCCT	0.594																																					p.Y309_P310delinsX													.	ABCG8-94	0			c.925_926insA						.																																			SO:0001589	frameshift_variant	64241	exon6			ATCGGCTACCCCT	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"ATP binding cassette transporters / subfamily G"	13887	protein-coding gene	gene with protein product	"gallbladder disease 4", "sterolin 2"	605460	"ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.926dupA	2.37:g.44079969_44079969dupA	ENSP00000272286:p.Tyr309fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_1	376	72	NM_022437	0	0	0	0	0	Q53QN8	Nonsense_Mutation	INS	ENST00000272286.2	37	CCDS1815.1																																																																																			.		0.594	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437		A	44079969	-	A	44079968	7	5	51	1	0	1	1	0	0	0	0	0	72	1522	53	0	947	0	ABCG8	2	44079968	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	5554470	44079968	199119405	37	4725											
ZNF514	84874	bcgsc.ca	37	chr2	95818976	95818976	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcccactggctgaattccAcagccacatcttcaaatgtc	11	10	5	15	0	2	1	1	1	1	0	5	1	4	1	3	1	1	1	3	1	2	2	rs79400981		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:95818976A>C	ENST00000295208.2	-	3	485	c.23T>G	c.(22-24)gTg>gGg	p.V8G	ZNF514_ENST00000411425.1_Missense_Mutation_p.V8G	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	8	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			large_intestine(4)|lung(6)|urinary_tract(1)	11						GCTGAATTCCACAGCCACATC	0.478																																					p.V8G													.	ZNF514-90	0			c.T23G						.						70	69	69					2																	95818976		2203	4300	6503	SO:0001583	missense	84874	exon3			AATTCCACAGCCA	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.23T>G	2.37:g.95818976A>C	ENSP00000295208:p.Val8Gly	Somatic	91	0		WXS	Illumina HiSeq	Phase_1	47	21	NM_032788	0	0	36	42	6	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	37	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.522701	0.44866	.	.	ENSG00000144026	ENST00000295208;ENST00000411425;ENST00000447814	T;T;T	0.04758	3.56;3.56;3.56	2.96	1.69	0.24217	Krueppel-associated box (4);	.	.	.	.	T	0.23766	0.0575	H	0.95402	3.665	0.40694	D	0.982426	D	0.71674	0.998	D	0.63113	0.911	T	0.02512	-1.1148	9	0.87932	D	0	.	7.1256	0.25469	0.77:0.23:0.0:0.0	.	8	Q96K75	ZN514_HUMAN	G	8;8;24	ENSP00000295208:V8G;ENSP00000405509:V8G;ENSP00000399647:V24G	ENSP00000295208:V8G	V	-	2	0	ZNF514	95182703	0.990000	0.36364	0.996000	0.52242	0.594000	0.36715	2.815000	0.48018	0.310000	0.22990	0.533000	0.62120	GTG	.		0.478	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		C	95818976	A	C	95818976	3	2	51	1	0	0	0	0	1	0	0	0	17991	159	6	5	1191	5	ZNF514	2	95818976	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	51739008	95818976	147380397	38	4726											
GPR45	11250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	105858582	105858582	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtccctctgctgcatgccCttcaccgccgtcaccctcat	4	11	6	20	2	4	0	3	0	1	0	5	0	5	0	5	0	3	2	5	0	0	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:105858582C>G	ENST00000258456.1	+	1	383	c.267C>G	c.(265-267)ccC>ccG	p.P89P		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						GCTGCATGCCCTTCACCGCCG	0.627																																					p.P89P		.											.	GPR45-154	0			c.C267G						.						125	115	118					2																	105858582		2203	4300	6503	SO:0001819	synonymous_variant	11250	exon1			CATGCCCTTCACC	AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.267C>G	2.37:g.105858582C>G		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	527	245	NM_007227	0	0	0	0	0	Q6NWS4|Q6NXU6	Silent	SNP	ENST00000258456.1	37	CCDS2066.1																																																																																			.		0.627	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		G	105858582	C	G	105858582	2	3	51	1	0	0	0	0	0	0	0	1	6716	668	24	4		4	GPR45	2	105858582	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	10039606	105858582	137340791	39	4727											
TGFBRAP1	9392	bcgsc.ca	37	chr2	105924084	105924085	+	Frame_Shift_Ins	INS	-	-	C																															cctcacccagccctccggggINScccgccagcaggaactcctg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:105924084_105924085insC	ENST00000393359.2	-	2	1100_1101	c.674_675insG	c.(673-675)ggcfs	p.G225fs	TGFBRAP1_ENST00000258449.1_Frame_Shift_Ins_p.G225fs			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	225	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						GCCCTCCGGGGCCCGCCAGCAG	0.594																																					p.G225fs	Esophageal Squamous(183;794 2019 9730 21801 48859)												.	TGFBRAP1-91	0			c.675_676insG						.																																			SO:0001589	frameshift_variant	9392	exon2			TCCGGGGCCCGCC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.675dupG	2.37:g.105924087_105924087dupC	ENSP00000377027:p.Gly225fs	Somatic	235	4		WXS	Illumina HiSeq	Phase_1	747	123	NM_004257	0	0	0	0	0	A8K5R7|D3DVJ8|O60466	Frame_Shift_Ins	INS	ENST00000393359.2	37	CCDS2067.1																																																																																			.		0.594	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		C	105924085	-	C	105924084	7	5	51	1	0	1	1	0	0	0	0	0	15856	1190	42	0	1951	0	TGFBRAP1	2	105924084	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	65502	105924084	137275289	40	4728											
CBWD2	150472	hgsc.bcm.edu	37	chr2	114195459	114195459	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccggaatgttaccggctgTtggatctgcggatgaggagg	7	9	18	7	3	1	1	0	1	1	0	1	5	1	5	2	7	2	3	2	7	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:114195459T>G	ENST00000259199.4	+	1	192	c.14T>G	c.(13-15)gTt>gGt	p.V5G	CBWD2_ENST00000416503.2_Missense_Mutation_p.V5G|RP11-480C16.1_ENST00000608834.1_lincRNA|CBWD2_ENST00000433343.2_5'UTR	NM_172003.3	NP_742000.1	Q8IUF1	CBWD2_HUMAN	COBW domain containing 2	5							ATP binding (GO:0005524)			endometrium(1)|lung(1)	2						TTACCGGCTGTTGGATCTGCG	0.622																																					p.V5G		.											.	CBWD2-90	0			c.T14G						.						33	38	36					2																	114195459		2154	4227	6381	SO:0001583	missense	150472	exon1			CGGCTGTTGGATC	AF452722	CCDS2116.1	2q14.1	2005-08-22			ENSG00000136682	ENSG00000136682			17907	protein-coding gene	gene with protein product		611079				12421752, 15233989	Standard	NM_172003		Approved		uc002tju.3	Q8IUF1	OTTHUMG00000131360	ENST00000259199.4:c.14T>G	2.37:g.114195459T>G	ENSP00000259199:p.Val5Gly	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	571	268	NM_172003	0	0	24	26	2	Q0VAN3	Missense_Mutation	SNP	ENST00000259199.4	37	CCDS2116.1	.	.	.	.	.	.	.	.	.	.	.	10.67	1.415862	0.25552	.	.	ENSG00000136682	ENST00000259199;ENST00000376448;ENST00000448780;ENST00000416503	T;T	0.09538	2.97;2.98	2.85	-1.52	0.08637	.	1.998220	0.02745	N	0.116767	T	0.06872	0.0175	N	0.19112	0.55	0.20196	N	0.999927	B	0.25351	0.124	B	0.24006	0.05	T	0.37502	-0.9703	10	0.87932	D	0	-14.7404	0.3048	0.00278	0.2246:0.1479:0.2295:0.398	.	5	Q8IUF1	CBWD2_HUMAN	G	5	ENSP00000259199:V5G;ENSP00000411906:V5G	ENSP00000259199:V5G	V	+	2	0	CBWD2	113911929	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.562000	0.05950	-0.057000	0.13199	0.327000	0.21459	GTT	.		0.622	CBWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254149.3	NM_172003		G	114195459	T	G	114195459	3	3	51	1	0	0	0	0	1	0	0	0	2719	1725	60	5	16	5	CBWD2	2	114195459	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8271375	114195459	129003914	41	4729											
GLI2	2736	hgsc.bcm.edu	37	chr2	121746538	121746538	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagccacccgagcaccgaCggcggcctggcccgcggcgc	6	1	15	19	7	0	1	0	0	0	1	0	3	0	1	5	4	2	1	5	4	0	0	rs140479803	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:121746538C>T	ENST00000452319.1	+	14	3108	c.3048C>T	c.(3046-3048)gaC>gaT	p.D1016D	GLI2_ENST00000314490.11_Silent_p.D688D|GLI2_ENST00000361492.4_Silent_p.D1016D					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CGAGCACCGACGGCGGCCTGG	0.761													C|||	136	0.0271565	0.0983	0.0072	5008	,	,		7708	0		0.001	False		,,,				2504	0				p.D1016D		.											.	GLI2-954	0			c.C3048T						.	C		158,2180		0,158,1011	3	3	3		3048	-4.9	0	2	dbSNP_134	3	2,4896		0,2,2447	no	coding-synonymous	GLI2	NM_005270.4		0,160,3458	TT,TC,CC		0.0408,6.7579,2.2112		1016/1587	121746538	160,7076	1169	2449	3618	SO:0001819	synonymous_variant	2736	exon13			CACCGACGGCGGC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"Zinc fingers, C2H2-type"	4318	protein-coding gene	gene with protein product	"tax-responsive element-2 holding protein", "tax helper protein 1", "tax helper protein 2"	165230	"GLI-Kruppel family member GLI2", "glioma-associated oncogene family zinc finger 2"			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3048C>T	2.37:g.121746538C>T		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	18	14	NM_005270	0	0	0	0	0		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			C|0.978;T|0.022		0.761	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121746538	C	T	121746538	2	4	51	1	0	0	0	0	0	0	0	1	6458	535	19	1		1	GLI2	2	121746538	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	7551079	121746538	121452835	42	4730											
TFCP2L1	29842	hgsc.bcm.edu;broad.mit.edu	37	chr2	122042681	122042681	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggctgcgtgtgccagaagAgcatggctggaactcccagc	8	6	15	12	2	0	2	0	0	0	2	1	3	1	3	2	3	5	3	2	3	2	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:122042681A>T	ENST00000263707.5	-	1	102	c.5T>A	c.(4-6)cTc>cAc	p.L2H		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	2	Mediate transcriptional repression.				cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					GTGCCAGAAGAGCATGGCTGG	0.756																																					p.L2H		.											.	TFCP2L1-93	0			c.T5A						.						17	16	16					2																	122042681		2192	4286	6478	SO:0001583	missense	29842	exon1			CAGAAGAGCATGG	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.5T>A	2.37:g.122042681A>T	ENSP00000263707:p.Leu2His	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	31	19	NM_014553	0	0	3	10	7	Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	37	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	a	17.41	3.381885	0.61845	.	.	ENSG00000115112	ENST00000263707	T	0.26373	1.74	4.1	4.1	0.47936	.	0.097761	0.43747	U	0.000539	T	0.39835	0.1093	L	0.38175	1.15	0.58432	D	0.999999	D;D	0.89917	1.0;0.988	D;P	0.87578	0.998;0.832	T	0.29518	-1.0009	10	0.87932	D	0	.	12.7432	0.57266	1.0:0.0:0.0:0.0	.	2;2	Q5JV87;Q9NZI6	.;TF2L1_HUMAN	H	2	ENSP00000263707:L2H	ENSP00000263707:L2H	L	-	2	0	TFCP2L1	121759151	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	6.622000	0.74233	1.467000	0.48044	0.398000	0.26397	CTC	.		0.756	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		T	122042681	A	T	122042681	3	4	51	1	0	0	0	0	1	0	0	0	15828	304	11	5	1494	5	TFCP2L1	2	122042681	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	296143	122042681	121156692	43	4731											
IWS1	55677	bcgsc.ca	37	chr2	128262546	128262547	+	Frame_Shift_Ins	INS	-	-	G																															cagtttctgagtcactggcaINSggccccttctgaggcccctc																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:128262546_128262547insG	ENST00000295321.4	-	3	1191_1192	c.932_933insC	c.(931-933)cctfs	p.P311fs	IWS1_ENST00000486662.1_5'Flank|AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000455721.2_Frame_Shift_Ins_p.P318fs	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	311	Glu-rich.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		AGTCACTGGCAGGCCCCTTCTG	0.54																																					p.P311fs													.	IWS1-91	0			c.933_934insC						.																																			SO:0001589	frameshift_variant	55677	exon3			ACTGGCAGGCCCC	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.933dupC	2.37:g.128262548_128262548dupG	ENSP00000295321:p.Pro311fs	Somatic	224	1		WXS	Illumina HiSeq	Phase_1	215	65	NM_017969	0	0	0	0	0	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Frame_Shift_Ins	INS	ENST00000295321.4	37	CCDS2146.1																																																																																			.		0.54	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		G	128262547	-	G	128262546	7	5	51	1	0	1	1	0	0	0	0	0	7952	175	7	0	1574	0	IWS1	2	128262546	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	6219865	128262546	114936827	44	4732											
ZRANB3	84083	bcgsc.ca	37	chr2	136107601	136107601	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgtaagaagaatggctcGtctggctttctgtactattg	8	15	10	8	1	2	2	0	0	2	2	4	2	3	2	1	2	1	4	1	2	5	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:136107601G>C	ENST00000264159.6	-	5	660	c.544C>G	c.(544-546)Cga>Gga	p.R182G	ZRANB3_ENST00000536680.1_Missense_Mutation_p.R182G|ZRANB3_ENST00000401392.1_Missense_Mutation_p.R182G	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	182	DNA annealing helicase activity.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		AGAATGGCTCGTCTGGCTTTC	0.423																																					p.R182G													.	ZRANB3-658	0			c.C544G						.						105	108	107					2																	136107601		1860	4101	5961	SO:0001583	missense	84083	exon5			TGGCTCGTCTGGC	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.544C>G	2.37:g.136107601G>C	ENSP00000264159:p.Arg182Gly	Somatic	67	0		WXS	Illumina HiSeq	Phase_1	45	25	NM_032143	0	0	2	3	1	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.394680	0.62066	.	.	ENSG00000121988	ENST00000401392;ENST00000264159;ENST00000536680;ENST00000397448	D;D;D	0.93133	-3.17;-3.17;-3.17	5.57	0.888	0.19206	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97161	0.9072	M	0.92649	3.33	0.42134	D	0.991483	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.995	D	0.97660	1.0160	10	0.62326	D	0.03	-8.5108	16.2461	0.82446	0.0:0.0:0.447:0.553	.	122;182;182	E9PBP0;Q5FWF4;Q5FWF4-3	.;ZRAB3_HUMAN;.	G	182;182;182;122	ENSP00000383979:R182G;ENSP00000264159:R182G;ENSP00000441320:R182G	ENSP00000264159:R182G	R	-	1	2	ZRANB3	135824071	0.978000	0.34361	0.993000	0.49108	0.997000	0.91878	1.686000	0.37669	0.226000	0.20979	0.591000	0.81541	CGA	.		0.423	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		C	136107601	G	C	136107601	3	2	51	1	0	0	0	0	1	0	0	0	18256	1153	40	4	2763	4	ZRANB3	2	136107601	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	7845055	136107601	107091772	45	4733											
PLA2R1	22925	bcgsc.ca	37	chr2	160898583	160898583	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctctttcataacggcttGtcgtggcacaccacagtaag	10	11	8	12	2	2	0	1	0	1	0	4	0	2	0	1	2	1	3	1	2	2	4	rs200625381		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:160898583G>T	ENST00000283243.7	-	3	826	c.620C>A	c.(619-621)aCa>aAa	p.T207K	PLA2R1_ENST00000392771.1_Missense_Mutation_p.T207K	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	207	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00479}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ATAACGGCTTGTCGTGGCACA	0.428																																					p.T207K													.	PLA2R1-93	0			c.C620A						.						132	127	129					2																	160898583		2203	4300	6503	SO:0001583	missense	22925	exon3			CGGCTTGTCGTGG	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.620C>A	2.37:g.160898583G>T	ENSP00000283243:p.Thr207Lys	Somatic	141	0		WXS	Illumina HiSeq	Phase_1	97	40	NM_001195641	0	0	7	7	0	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.451136	0.84209	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.56941	0.43;0.43	5.59	5.59	0.84812	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.054970	0.64402	D	0.000001	T	0.80539	0.4642	M	0.92459	3.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.999;0.999	D	0.84142	0.0418	10	0.66056	D	0.02	.	19.9651	0.97262	0.0:0.0:1.0:0.0	.	207;207;207	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	K	207	ENSP00000283243:T207K;ENSP00000376524:T207K	ENSP00000283243:T207K	T	-	2	0	PLA2R1	160606829	1.000000	0.71417	0.344000	0.25628	0.988000	0.76386	7.442000	0.80503	2.793000	0.96121	0.655000	0.94253	ACA	G|0.999;T|0.001		0.428	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160898583	G	T	160898583	3	4	51	1	0	0	0	0	1	0	0	0	12036	1377	48	4	3891	4	PLA2R1	2	160898583	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	24790982	160898583	82300790	46	4734											
DPP4	1803	bcgsc.ca	37	chr2	162879272	162879272	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttataacacttactcttccaAcccagccagtagtactcatt	12	13	3	13	0	2	0	1	0	1	0	3	0	3	0	3	0	5	2	3	0	6	7	rs200047090		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:162879272A>C	ENST00000360534.3	-	12	1621	c.1061T>G	c.(1060-1062)gTt>gGt	p.V354G		NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	354					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	TACTCTTCCAACCCAGCCAGT	0.403																																					p.V354G													.	DPP4-93	0			c.T1061G						.						155	150	151					2																	162879272		2203	4300	6503	SO:0001583	missense	1803	exon12			CTTCCAACCCAGC	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"CD molecules"	3009	protein-coding gene	gene with protein product		102720	"dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)", "adenosine deaminase complexing protein 2"	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1061T>G	2.37:g.162879272A>C	ENSP00000353731:p.Val354Gly	Somatic	169	0		WXS	Illumina HiSeq	Phase_1	47	19	NM_001935	0	0	0	0	0	Q53TN1	Missense_Mutation	SNP	ENST00000360534.3	37	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777643	0.70107	.	.	ENSG00000197635	ENST00000360534	T	0.38240	1.15	5.32	5.32	0.75619	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.178535	0.48767	D	0.000167	T	0.66470	0.2792	M	0.88906	2.99	0.80722	D	1	P	0.50369	0.934	D	0.77004	0.989	T	0.73235	-0.4047	10	0.87932	D	0	-28.2942	14.5501	0.68059	1.0:0.0:0.0:0.0	.	354	P27487	DPP4_HUMAN	G	354	ENSP00000353731:V354G	ENSP00000353731:V354G	V	-	2	0	DPP4	162587518	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	5.980000	0.70516	2.126000	0.65437	0.528000	0.53228	GTT	.		0.403	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2			C	162879272	A	C	162879272	3	2	51	1	0	0	0	0	1	0	0	0	4740	43	2	5	1299	5	DPP4	2	162879272	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1980689	162879272	80320101	47	4735											
ALS2	57679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	202626257	202626257	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcgccacacgccaactGtaaaatcctgactgctaaca	12	8	5	16	2	0	1	0	1	0	0	3	1	2	1	4	0	3	2	4	0	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:202626257G>A	ENST00000264276.6	-	4	832	c.460C>T	c.(460-462)Cag>Tag	p.Q154*	ALS2_ENST00000467448.1_Nonsense_Mutation_p.Q154*|ALS2_ENST00000496244.1_5'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	154					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						CACGCCAACTGTAAAATCCTG	0.522																																					p.Q154X		.											.	ALS2-275	0			c.C460T						.						79	79	79					2																	202626257		2073	4196	6269	SO:0001587	stop_gained	57679	exon4			CCAACTGTAAAAT	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.460C>T	2.37:g.202626257G>A	ENSP00000264276:p.Gln154*	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	121	55	NM_001135745	0	0	8	20	12	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Nonsense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.582281	0.86748	.	.	ENSG00000003393	ENST00000264276;ENST00000467448	.	.	.	6.17	6.17	0.99709	.	0.056382	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	154	.	ENSP00000264276:Q154X	Q	-	1	0	ALS2	202334502	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.405000	0.66351	2.941000	0.99782	0.655000	0.94253	CAG	.		0.522	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		A	202626257	G	A	202626257	4	1	51	1	0	0	0	0	0	1	0	0	550	1386	48	2	4715	2	ALS2	2	202626257	Nonsense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	39746985	202626257	40573116	48	4736											
C2orf67	151050	bcgsc.ca	37	chr2	210993868	210993868	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccaactcgtgctctgtctaCaagccacttccattcagtac	9	11	6	15	1	3	0	1	0	2	0	5	0	4	0	3	0	5	2	3	0	4	4	rs78236584		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:210993868C>A	ENST00000281772.9	-	3	1380	c.1117G>T	c.(1117-1119)Gta>Tta	p.V373L	KANSL1L_ENST00000457374.1_Missense_Mutation_p.V373L|KANSL1L_ENST00000418791.1_Missense_Mutation_p.V373L|KANSL1L_ENST00000452086.1_Missense_Mutation_p.V373L	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	373						histone acetyltransferase complex (GO:0000123)											GCTCTGTCTACAAGCCACTTC	0.408																																					p.V373L													.	.	0			c.G1117T						.						139	128	132					2																	210993868		2203	4300	6503	SO:0001583	missense	151050	exon3			TGTCTACAAGCCA	AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"KIAA1267-like"	613833	"chromosome 2 open reading frame 67"	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.1117G>T	2.37:g.210993868C>A	ENSP00000281772:p.Val373Leu	Somatic	127	0		WXS	Illumina HiSeq	Phase_1	19	14	NM_152519	0	0	38	41	3	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Missense_Mutation	SNP	ENST00000281772.9	37	CCDS33370.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	12.68|12.68|12.68	2.010138|2.010138|2.010138	0.35415|0.35415|0.35415	.|.|.	.|.|.	ENSG00000144445|ENSG00000144445|ENSG00000144445	ENST00000428655|ENST00000438563;ENST00000415553|ENST00000281772;ENST00000418791;ENST00000457374;ENST00000452086	.|.|.	.|.|.	.|.|.	5.51|5.51|5.51	3.67|3.67|3.67	0.42095|0.42095|0.42095	.|.|.	.|.|0.378184	.|.|0.22513	.|.|N	.|.|0.059077	T|T|T	0.26268|0.26268|0.26268	0.0641|0.0641|0.0641	L|L|L	0.47716|0.47716|0.47716	1.5|1.5|1.5	0.26138|0.26138|0.26138	N|N|N	0.980312|0.980312|0.980312	.|.|B;P;B;B	.|.|0.38729	.|.|0.132;0.644;0.208;0.208	.|.|B;B;B;B	.|.|0.32677	.|.|0.106;0.15;0.104;0.104	T|T|T	0.09100|0.09100|0.09100	-1.0690|-1.0690|-1.0690	5|6|9	.|0.56958|0.30078	.|D|T	.|0.05|0.28	.|.|.	8.5979|8.5979|8.5979	0.33727|0.33727|0.33727	0.2701:0.6599:0.0:0.07|0.2701:0.6599:0.0:0.07|0.2701:0.6599:0.0:0.07	.|.|.	.|.|373;373;373;373	.|.|A0AUZ9-4;A0AUZ9-3;A0AUZ9-2;A0AUZ9	.|.|.;.;.;CB067_HUMAN	F|F|L	67|46;91|373	.|.|.	.|ENSP00000388182:L91F|ENSP00000281772:V373L	C|L|V	-|-|-	2|3|1	0|2|0	C2orf67|C2orf67|C2orf67	210702113|210702113|210702113	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	1.012000|1.012000|1.012000	0.29924|0.29924|0.29924	0.641000|0.641000|0.641000	0.30601|0.30601|0.30601	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	TGT|TTG|GTA	.		0.408	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519		A	210993868	C	A	210993868	3	1	51	1	0	0	0	0	1	0	0	0	2192	478	17	4	1898	4	C2orf67	2	210993868	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	8367611	210993868	32205505	49	4737											
MYL1	4632	bcgsc.ca	37	chr2	211179729	211179729	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggctggggcagccgcagccGcagccacaggtttcttcacg	6	6	15	14	3	2	0	1	0	1	0	2	0	2	0	3	4	3	5	3	4	0	2	rs142821726		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:211179729G>C	ENST00000352451.3	-	1	185	c.38C>G	c.(37-39)gCg>gGg	p.A13G		NM_079420.2	NP_524144.1	P05976	MYL1_HUMAN	myosin, light chain 1, alkali; skeletal, fast	13					cardiac muscle contraction (GO:0060048)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|sarcomere (GO:0030017)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	16				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)		AGCCGCAGCCGCAGCCACAGG	0.502																																					p.A13G													.	MYL1-91	0			c.C38G						.						73	106	95					2																	211179729		2185	4279	6464	SO:0001583	missense	4632	exon1			GCAGCCGCAGCCA		CCDS2390.1, CCDS2391.1	2q33-q34	2013-01-10	2006-09-29		ENSG00000168530	ENSG00000168530		"Myosins / Light chain", "EF-hand domain containing"	7582	protein-coding gene	gene with protein product		160780	"myosin, light polypeptide 1, alkali; skeletal, fast"			2304459, 3422212	Standard	NM_079422		Approved		uc002vec.3	P05976	OTTHUMG00000132992	ENST00000352451.3:c.38C>G	2.37:g.211179729G>C	ENSP00000307280:p.Ala13Gly	Somatic	342	0		WXS	Illumina HiSeq	Phase_1	702	155	NM_079420	0	0	0	0	0	B2R4N6|B2R4T6|P06741|Q6IBD5	Missense_Mutation	SNP	ENST00000352451.3	37	CCDS2390.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.364961	0.24684	.	.	ENSG00000168530	ENST00000352451	D	0.85556	-2.0	5.3	5.3	0.74995	.	0.358981	0.27966	N	0.017124	D	0.89504	0.6734	L	0.43923	1.385	0.35447	D	0.795389	D	0.63880	0.993	D	0.72075	0.976	D	0.92456	0.5974	10	0.62326	D	0.03	.	16.7514	0.85487	0.0:0.0:1.0:0.0	.	13	P05976	MYL1_HUMAN	G	13	ENSP00000307280:A13G	ENSP00000307280:A13G	A	-	2	0	MYL1	210887974	0.998000	0.40836	0.938000	0.37757	0.230000	0.25150	4.170000	0.58229	2.486000	0.83907	0.561000	0.74099	GCG	G|1.000;C|0.000		0.502	MYL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256566.2	NM_079420		C	211179729	G	C	211179729	3	2	51	1	0	0	0	0	1	0	0	0	10068	1087	38	4	606	4	MYL1	2	211179729	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	185861	211179729	32019644	50	4738											
OBSL1	23363	hgsc.bcm.edu	37	chr2	220435880	220435880	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagctcggcctcggcgccActtaccacccgcacaggccg	6	6	11	18	5	0	1	0	1	0	0	2	1	0	1	5	3	2	2	5	3	1	2	rs376818200		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:220435880A>C	ENST00000404537.1	-	1	131	c.75T>G	c.(73-75)agT>agG	p.S25R	OBSL1_ENST00000373876.1_Missense_Mutation_p.S25R|OBSL1_ENST00000373873.4_Missense_Mutation_p.S25R|OBSL1_ENST00000491370.1_Intron|INHA_ENST00000489456.1_Intron|OBSL1_ENST00000265318.4_Missense_Mutation_p.S25R|OBSL1_ENST00000289656.3_Intron|INHA_ENST00000243786.2_5'Flank|OBSL1_ENST00000603926.1_Missense_Mutation_p.S25R	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	25	Ig-like 1.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CCTCGGCGCCACTTACCACCC	0.736													A|||	1	0.000199681	8e-04	0	5008	,	,		6502	0		0	False		,,,				2504	0				p.S25R		.											.	OBSL1-71	0			c.T75G						.	A	ARG/SER,ARG/SER,ARG/SER	1,3161		0,1,1580	4	4	4		75,75,75	-3.3	1	2		4	0,7030		0,0,3515	no	missense,missense,missense	OBSL1	NM_015311.2,NM_001173431.1,NM_001173408.1	110,110,110	0,1,5095	CC,CA,AA		0.0,0.0316,0.0098	benign,benign,benign	25/1897,25/1544,25/1026	220435880	1,10191	1581	3515	5096	SO:0001583	missense	23363	exon1			GGCGCCACTTACC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.75T>G	2.37:g.220435880A>C	ENSP00000385636:p.Ser25Arg	Somatic	8	1		WXS	Illumina HiSeq	Phase_I	17	7	NM_001173431	0	0	3	7	4	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.924651	0.34002	3.16E-4	0.0	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	3.63	-3.34	0.04943	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.11067	0.0270	N	0.02296	-0.605	0.80722	D	1	B;P	0.52316	0.238;0.952	B;P	0.50192	0.145;0.634	T	0.35325	-0.9793	8	.	.	.	.	6.3881	0.21572	0.4017:0.0:0.4652:0.1331	.	25;25	O75147;O75147-2	OBSL1_HUMAN;.	R	25	ENSP00000265318:S25R;ENSP00000385636:S25R;ENSP00000362983:S25R;ENSP00000362980:S25R	.	S	-	3	2	OBSL1	220144124	0.457000	0.25752	0.975000	0.42487	0.006000	0.05464	-0.406000	0.07187	-0.573000	0.05998	-0.549000	0.04216	AGT	.		0.736	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			C	220435880	A	C	220435880	3	2	51	1	0	0	0	0	1	0	0	0	10839	156	6	5	5851	5	OBSL1	2	220435880	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	9256151	220435880	22763493	51	4739											
SLC19A3	80704	bcgsc.ca	37	chr2	228560681	228560681	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacgcccagatattggctgTgtaatgcatgagaaataaag	14	9	11	7	1	0	2	0	1	0	2	0	3	0	2	1	1	1	4	1	1	5	4	rs201784334		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:228560681T>G	ENST00000258403.3	-	4	1167	c.1096A>C	c.(1096-1098)Aca>Cca	p.T366P	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Missense_Mutation_p.T362P	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	366					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	ATATTGGCTGTGTAATGCATG	0.443																																					p.T366P													.	SLC19A3-92	0			c.A1096C						.						83	92	89					2																	228560681		2203	4300	6503	SO:0001583	missense	80704	exon4			TGGCTGTGTAATG	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"Solute carriers"	16266	protein-coding gene	gene with protein product	"thiamine transporter 2"	606152	"solute carrier family 19, member 3"			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.1096A>C	2.37:g.228560681T>G	ENSP00000258403:p.Thr366Pro	Somatic	102	0		WXS	Illumina HiSeq	Phase_1	47	15	NM_025243	0	0	1	1	0		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811011	0.50421	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.87491	-2.26;-2.26	5.03	3.85	0.44370	Major facilitator superfamily domain, general substrate transporter (1);	0.370968	0.30920	N	0.008618	D	0.93154	0.7820	M	0.91972	3.26	0.09310	N	0.999999	D;D	0.60160	0.987;0.961	P;P	0.62089	0.898;0.811	D	0.86550	0.1834	10	0.49607	T	0.09	-2.3003	10.5027	0.44815	0.2562:0.0:0.0:0.7437	.	362;366	F5H2M8;Q9BZV2	.;S19A3_HUMAN	P	366;362	ENSP00000258403:T366P;ENSP00000445519:T362P	ENSP00000258403:T366P	T	-	1	0	SLC19A3	228268925	1.000000	0.71417	0.813000	0.32504	0.680000	0.39746	1.739000	0.38217	0.902000	0.36520	0.533000	0.62120	ACA	.		0.443	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			G	228560681	T	G	228560681	3	3	51	1	0	0	0	0	1	0	0	0	14462	1696	59	5	406	5	SLC19A3	2	228560681	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8124801	228560681	14638692	52	4740											
CIDEC	63924	hgsc.bcm.edu	37	chr3	9911862	9911862	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctcacctgttctgatggggGctgccatttctgccccttct	3	14	9	15	0	4	1	1	1	3	0	4	1	4	1	5	2	2	2	5	2	0	3	rs201802471|rs368273807		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:9911862G>C	ENST00000336832.2	-	4	491	c.352C>G	c.(352-354)Ccc>Gcc	p.P118A	CIDEC_ENST00000443115.1_Intron|CIDEC_ENST00000383817.1_Intron|CIDEC_ENST00000430427.1_Missense_Mutation_p.P128A|CIDEC_ENST00000455015.1_Missense_Mutation_p.P44A|CIDEC_ENST00000423850.1_Missense_Mutation_p.P44A	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	118	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					TCTGATGGGGGCTGCCATTTC	0.542																																					p.P131A		.											.	CIDEC-90	0			c.C391G						.						70	72	72					3																	9911862		2203	4300	6503	SO:0001583	missense	63924	exon4			ATGGGGGCTGCCA		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.352C>G	3.37:g.9911862G>C	ENSP00000338642:p.Pro118Ala	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	367	90	NM_001199623	0	0	0	0	0	C9JMN7|Q67DW9|Q9GZY9	Missense_Mutation	SNP	ENST00000336832.2	37	CCDS2587.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265024	0.40095	.	.	ENSG00000187288	ENST00000336832;ENST00000455015;ENST00000423850;ENST00000430427	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.78	1.72	0.24424	Caspase-activated nuclease CIDE-N (2);	0.213000	0.49916	N	0.000130	T	0.47040	0.1424	M	0.71036	2.16	0.80722	D	1	B;B	0.33528	0.034;0.416	B;B	0.40506	0.026;0.331	T	0.33701	-0.9858	10	0.51188	T	0.08	-13.7547	5.8544	0.18712	0.2576:0.1378:0.6046:0.0	.	118;128	Q96AQ7;C9JMN7	CIDEC_HUMAN;.	A	118;44;44;128	ENSP00000338642:P118A;ENSP00000392975:P44A;ENSP00000400649:P44A;ENSP00000408631:P128A	ENSP00000338642:P118A	P	-	1	0	CIDEC	9886862	0.940000	0.31905	0.348000	0.25681	0.967000	0.64934	1.716000	0.37981	0.025000	0.15241	0.461000	0.40582	CCC	G|0.999;C|0.001		0.542	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094		C	9911862	G	C	9911862	3	2	51	1	0	0	0	0	1	0	0	0	3433	1203	42	4	376	4	CIDEC	3	9911862	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		9911862	188110568	53	4741											
OR5H15	403274	hgsc.bcm.edu	37	chr3	97888448	97888448	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaagtcatagtttcattcaTaaaaatgttaaaaagaaatg	19	12	6	4	0	3	1	3	0	0	1	3	1	3	1	0	0	0	3	0	0	9	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:97888448T>C	ENST00000356526.2	+	1	905	c.905T>C	c.(904-906)aTa>aCa	p.I302T		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						GTTTCATTCATAAAAATGTTA	0.303																																					p.I302T		.											.	OR5H15-92	0			c.T905C						.						42	45	44					3																	97888448		2180	4289	6469	SO:0001583	missense	403274	exon1			CATTCATAAAAAT		CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"GPCR / Class A : Olfactory receptors"	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.905T>C	3.37:g.97888448T>C	ENSP00000373195:p.Ile302Thr	Somatic	39	2		WXS	Illumina HiSeq	Phase_I	11	2	NM_001005515	0	0	0	0	0		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	0.667	-0.803458	0.02841	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.37915	1.17	2.48	-4.96	0.03038	.	1.714170	0.03383	N	0.200708	T	0.17831	0.0428	N	0.11698	0.16	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09640	-1.0665	10	0.48119	T	0.1	.	2.0532	0.03575	0.3751:0.1679:0.3455:0.1115	.	302	A6NDH6	O5H15_HUMAN	T	302	ENSP00000373195:I302T	ENSP00000373195:I302T	I	+	2	0	OR5H15	99371138	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.896000	0.04114	-1.963000	0.01013	-1.372000	0.01188	ATA	.		0.303	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1			C	97888448	T	C	97888448	3	2	51	1	0	0	0	0	1	0	0	0	11187	1406	49	3	907	3	OR5H15	3	97888448	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	87976586	97888448	100133982	54	4742											
TMPRSS7	344805	bcgsc.ca	37	chr3	111780727	111780727	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagttcaaggctttcagaCaagccacttttggcagaata	12	11	9	9	0	2	2	2	0	0	2	2	2	2	2	1	2	2	4	1	2	4	5	rs200385589		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:111780727C>A	ENST00000452346.2	+	11	1407	c.1404C>A	c.(1402-1404)gaC>gaA	p.D468E	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.D342E			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	468	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GGCTTTCAGACAAGCCACTTT	0.448																																					p.D342E													.	TMPRSS7-70	0			c.C1026A						.						98	100	100					3																	111780727		1908	4126	6034	SO:0001583	missense	344805	exon9			TTCAGACAAGCCA	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.1404C>A	3.37:g.111780727C>A	ENSP00000398236:p.Asp468Glu	Somatic	100	1		WXS	Illumina HiSeq	Phase_1	28	10	NM_001042575	0	0	0	0	0	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	37		.	.	.	.	.	.	.	.	.	.	C	12.86	2.064486	0.36470	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.34859	1.34;1.34	5.62	0.415	0.16411	CUB (1);	0.318108	0.32015	N	0.006704	T	0.14184	0.0343	N	0.04508	-0.205	0.30681	N	0.752324	B;B	0.15930	0.015;0.004	B;B	0.20767	0.031;0.006	T	0.09422	-1.0675	10	0.33141	T	0.24	.	5.4512	0.16566	0.0:0.3667:0.3826:0.2507	.	468;342	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	E	468;456;442;342	ENSP00000398236:D468E;ENSP00000411645:D342E	ENSP00000411645:D342E	D	+	3	2	TMPRSS7	113263417	1.000000	0.71417	0.978000	0.43139	0.784000	0.44337	0.723000	0.25939	0.051000	0.15978	0.557000	0.71058	GAC	.		0.448	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		A	111780727	C	A	111780727	3	1	51	1	0	0	0	0	1	0	0	0	16284	477	17	4	1056	4	TMPRSS7	3	111780727	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	13892279	111780727	86241703	55	4743											
DTX3L	151636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122283388	122283388	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctctaagtcctcgggcggcGgggagtgcacggtcagcacc	6	6	16	13	4	2	0	1	0	1	0	4	1	3	1	2	5	2	3	2	5	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:122283388G>T	ENST00000296161.4	+	1	304	c.115G>T	c.(115-117)Ggg>Tgg	p.G39W	PARP9_ENST00000471785.1_5'Flank|PARP9_ENST00000477522.2_5'UTR|PARP9_ENST00000492382.1_5'Flank|DTX3L_ENST00000383661.3_Missense_Mutation_p.G39W|PARP9_ENST00000360356.2_5'UTR|PARP9_ENST00000462315.1_5'Flank	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	39					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		CTCGGGCGGCGGGGAGTGCAC	0.672																																					p.G39W		.											.	DTX3L-587	0			c.G115T						.						48	57	54					3																	122283388		2203	4299	6502	SO:0001583	missense	151636	exon1			GGCGGCGGGGAGT		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"RING-type (C3HC4) zinc fingers"	30323	protein-coding gene	gene with protein product	"rhysin 2"	613143	"deltex 3-like (Drosophila)"			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.115G>T	3.37:g.122283388G>T	ENSP00000296161:p.Gly39Trp	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	365	62	NM_138287	0	0	13	19	6	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	37	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.152626	0.57259	.	.	ENSG00000163840	ENST00000296161;ENST00000383661	T;T	0.69040	0.13;-0.37	4.59	4.59	0.56863	.	0.000000	0.47455	D	0.000228	T	0.81749	0.4888	M	0.80982	2.52	0.37919	D	0.931622	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86218	0.1629	10	0.87932	D	0	-25.6532	14.2431	0.65971	0.0:0.0:1.0:0.0	.	39;39	Q8TDB6-2;Q8TDB6	.;DTX3L_HUMAN	W	39	ENSP00000296161:G39W;ENSP00000373157:G39W	ENSP00000296161:G39W	G	+	1	0	DTX3L	123766078	1.000000	0.71417	1.000000	0.80357	0.039000	0.13416	5.884000	0.69729	2.342000	0.79632	0.655000	0.94253	GGG	.		0.672	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		T	122283388	G	T	122283388	3	4	51	1	0	0	0	0	1	0	0	0	4807	1116	39	4	117	4	DTX3L	3	122283388	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	10502661	122283388	75739042	56	4744											
SLC12A8	84561	broad.mit.edu	37	chr3	124896700	124896700	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgacacctgcgaggttaatgCccagcaaggccagaagcacc	12	5	11	13	1	0	2	0	1	0	1	0	3	0	2	4	2	4	3	4	2	3	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:124896700C>T	ENST00000393469.4	-	4	558	c.509G>A	c.(508-510)gGc>gAc	p.G170D	SLC12A8_ENST00000469902.1_Missense_Mutation_p.G170D|SLC12A8_ENST00000423114.2_Missense_Mutation_p.G199D|SLC12A8_ENST00000314584.7_5'UTR	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	170					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						GAGGTTAATGCCCAGCAAGGC	0.542																																					p.G170D													.	SLC12A8-22	0			c.G509A						.						72	83	79					3																	124896700		2079	4211	6290	SO:0001583	missense	84561	exon5			TTAATGCCCAGCA		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"Solute carriers"	15595	protein-coding gene	gene with protein product	"solute carrier family 12 (sodium/potassium/chloride transporters), member 8", "cation-chloride cotransporter 9"	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.509G>A	3.37:g.124896700C>T	ENSP00000377112:p.Gly170Asp	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	190	5	NM_024628	0	0	8	8	0	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	.	.	.	.	.	.	.	.	.	.	c	19.18	3.777697	0.70107	.	.	ENSG00000221955	ENST00000393469;ENST00000423114;ENST00000469902	D;D;D	0.98876	-5.2;-5.2;-5.2	5.64	5.64	0.86602	Amino acid permease domain (1);	.	.	.	.	D	0.99064	0.9679	M	0.77712	2.385	0.80722	D	1	D;P;D	0.89917	1.0;0.86;0.988	D;P;P	0.97110	1.0;0.661;0.863	D	0.99705	1.1005	9	0.51188	T	0.08	.	17.8866	0.88856	0.0:1.0:0.0:0.0	.	62;199;170	B5MDT1;A0AV02-2;A0AV02	.;.;S12A8_HUMAN	D	170;199;170	ENSP00000377112:G170D;ENSP00000404243:G199D;ENSP00000418783:G170D	ENSP00000377112:G170D	G	-	2	0	SLC12A8	126379390	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.467000	0.80930	2.668000	0.90789	0.551000	0.68910	GGC	.		0.542	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628		T	124896700	C	T	124896700	3	4	51	1	0	0	0	0	1	0	0	0	14421	739	26	2	1675	2	SLC12A8	3	124896700	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	2613312	124896700	73125730	57	4745											
SLC41A3	54946	bcgsc.ca	37	chr3	125786910	125786911	+	Frame_Shift_Ins	INS	-	-	T																															taggctcagtctccagtggcINSttgggggtcacgctttggct																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:125786910_125786911insT	ENST00000315891.6	-	2	390_391	c.152_153insA	c.(151-153)aagfs	p.K51fs	SLC41A3_ENST00000346785.5_Frame_Shift_Ins_p.K51fs|AC117422.1_ENST00000581281.1_RNA|SLC41A3_ENST00000514023.1_5'UTR|SLC41A3_ENST00000508835.1_Intron|SLC41A3_ENST00000360370.4_Frame_Shift_Ins_p.K51fs	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		TCTCCAGTGGCTTGGGGGTCAC	0.639																																					p.K51fs													.	SLC41A3-90	0			c.153_154insA						.																																			SO:0001589	frameshift_variant	54946	exon2			CAGTGGCTTGGGG		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"Solute carriers"	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.153dupA	3.37:g.125786912_125786912dupT	ENSP00000326070:p.Lys51fs	Somatic	167	0		WXS	Illumina HiSeq	Phase_1	709	137	NM_001008486	0	0	0	0	0	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Frame_Shift_Ins	INS	ENST00000315891.6	37	CCDS33843.1																																																																																			.		0.639	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836		T	125786911	-	T	125786910	7	5	51	1	0	1	1	0	0	0	0	0	14663	796	28	0	1711	0	SLC41A3	3	125786910	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	890210	125786910	72235520	58	4746											
SEC61A1	29927	bcgsc.ca	37	chr3	127774579	127774579	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctattggatgagagtgattCtagcctctaacagaggtagg	11	12	12	6	0	3	3	0	2	3	2	3	5	3	4	1	3	2	1	1	3	4	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:127774579C>T	ENST00000243253.3	+	4	389	c.205C>T	c.(205-207)Cta>Tta	p.L69L	SEC61A1_ENST00000464451.1_Silent_p.L75L|SEC61A1_ENST00000424880.2_Intron	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	69					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)|cell growth (GO:0016049)|endoplasmic reticulum organization (GO:0007029)|posttranslational protein targeting to membrane (GO:0006620)|protein targeting to ER (GO:0045047)|response to interferon-gamma (GO:0034341)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)			central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						GAGAGTGATTCTAGCCTCTAA	0.433																																					p.L69L													.	SEC61A1-91	0			c.C205T						.						134	127	130					3																	127774579		2203	4300	6503	SO:0001819	synonymous_variant	29927	exon4			GTGATTCTAGCCT	AF077032	CCDS3046.1	3q21.3	2008-02-05			ENSG00000058262	ENSG00000058262			18276	protein-coding gene	gene with protein product		609213					Standard	NM_013336		Approved		uc003ekb.3	P61619	OTTHUMG00000159624	ENST00000243253.3:c.205C>T	3.37:g.127774579C>T		Somatic	150	1		WXS	Illumina HiSeq	Phase_1	116	41	NM_013336	0	0	191	206	15	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Silent	SNP	ENST00000243253.3	37	CCDS3046.1																																																																																			.		0.433	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336		T	127774579	C	T	127774579	2	4	51	1	0	0	0	0	0	0	0	1	14032	912	32	2		2	SEC61A1	3	127774579	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1987669	127774579	70247851	59	4747											
CDV3	55573	bcgsc.ca	37	chr3	133306868	133306868	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgcttgaaaatcagaaaaGcagccactcacaatacaatt	17	9	6	9	0	2	2	2	1	0	1	2	2	2	2	1	0	4	2	1	0	7	3	rs558085907	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:133306868G>C	ENST00000264993.3	+	5	1070	c.755G>C	c.(754-756)aGc>aCc	p.S252T	CDV3_ENST00000515421.1_Intron|CDV3_ENST00000420115.2_3'UTR|CDV3_ENST00000508481.1_Missense_Mutation_p.S150T	NM_001134422.1|NM_001282763.1|NM_017548.4	NP_001127894.1|NP_001269692.1|NP_060018.1	Q9UKY7	CDV3_HUMAN	CDV3 homolog (mouse)	252					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				kidney(3)|lung(1)|prostate(1)	5						AATCAGAAAAGCAGCCACTCA	0.423																																					p.S252T													.	CDV3-90	0			c.G755C						.						80	81	81					3																	133306868		2203	4300	6503	SO:0001583	missense	55573	exon5			AGAAAAGCAGCCA	AK096865	CCDS3079.1, CCDS46917.1, CCDS46918.1, CCDS75013.1, CCDS75014.1, CCDS75015.1	3q22.1	2008-02-05			ENSG00000091527	ENSG00000091527			26928	protein-coding gene	gene with protein product						10497265	Standard	NM_017548		Approved	H41	uc003epq.3	Q9UKY7	OTTHUMG00000159764	ENST00000264993.3:c.755G>C	3.37:g.133306868G>C	ENSP00000264993:p.Ser252Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_1	43	19	NM_017548	0	0	99	102	3	B3KUC2|Q96IP9	Missense_Mutation	SNP	ENST00000264993.3	37	CCDS3079.1	.	.	.	.	.	.	.	.	.	.	G	9.924	1.212860	0.22289	.	.	ENSG00000091527	ENST00000264993;ENST00000508481	.	.	.	5.51	2.55	0.30701	.	0.753004	0.12282	N	0.482767	T	0.39091	0.1065	L	0.29908	0.895	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.10109	-1.0644	9	0.08599	T	0.76	.	7.81	0.29226	0.1491:0.1339:0.717:0.0	.	252	Q9UKY7	CDV3_HUMAN	T	252;150	.	ENSP00000264993:S252T	S	+	2	0	CDV3	134789558	1.000000	0.71417	0.905000	0.35620	0.998000	0.95712	2.344000	0.44010	0.683000	0.31428	0.650000	0.86243	AGC	.		0.423	CDV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357203.1	NM_017548		C	133306868	G	C	133306868	3	2	51	1	0	0	0	0	1	0	0	0	3187	971	34	4	793	4	CDV3	3	133306868	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	5532289	133306868	64715562	60	4748											
PCOLCE2	26577	hgsc.bcm.edu	37	chr3	142607735	142607735	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccaggcgttcgcgccccTcatggcagcgtagacgctcg	5	6	13	17	7	1	1	1	0	0	1	3	1	1	1	3	2	1	4	3	2	1	2	rs202134327	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:142607735T>G	ENST00000295992.3	-	1	310	c.4A>C	c.(4-6)Agg>Cgg	p.R2R	PCOLCE2_ENST00000461818.1_5'UTR|PCOLCE2_ENST00000485766.1_Silent_p.R2R	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	2					positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						TTCGCGCCCCTCATGGCAGCG	0.741													T|||	30	0.00599042	0.0227	0	5008	,	,		11668	0		0	False		,,,				2504	0				p.R2R		.											.	PCOLCE2-93	0			c.A4C						.	T		39,4315		0,39,2138	14	21	18		4	2.3	1	3		18	0,8542		0,0,4271	no	coding-synonymous	PCOLCE2	NM_013363.3		0,39,6409	GG,GT,TT		0.0,0.8957,0.3024		2/416	142607735	39,12857	2177	4271	6448	SO:0001819	synonymous_variant	26577	exon1			CGCCCCTCATGGC	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.4A>C	3.37:g.142607735T>G		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	40	18	NM_013363	0	0	1	1	0	B2RCH9|D3DNG4|Q9BRH3	Silent	SNP	ENST00000295992.3	37	CCDS3127.1																																																																																			T|0.993;G|0.007		0.741	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363		G	142607735	T	G	142607735	2	3	51	1	0	0	0	0	0	0	0	1	11621	1550	54	5		5	PCOLCE2	3	142607735	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	9300867	142607735	55414695	61	4749											
GPR149	344758	bcgsc.ca	37	chr3	154055935	154055935	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctattttcttagaggctggAgttattttttgcccttctgc	5	20	8	8	0	3	1	0	0	3	1	3	2	3	2	1	2	2	2	1	2	3	9			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:154055935A>G	ENST00000389740.2	-	4	1848	c.1749T>C	c.(1747-1749)acT>acC	p.T583T		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	583					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TAGAGGCTGGAGTTATTTTTT	0.448																																					p.T583T													.	GPR149-96	0			c.T1749C						.						140	141	141					3																	154055935		1849	4088	5937	SO:0001819	synonymous_variant	344758	exon4			GGCTGGAGTTATT	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"GPCR / Class A : Orphans"	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1749T>C	3.37:g.154055935A>G		Somatic	206	0		WXS	Illumina HiSeq	Phase_1	90	26	NM_001038705	0	0	0	0	0		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			.		0.448	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		G	154055935	A	G	154055935	2	3	51	1	0	0	0	0	0	0	0	1	6674	291	11	3		3	GPR149	3	154055935	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	11448200	154055935	43966495	62	4750											
PSMD2	5708	hgsc.bcm.edu	37	chr3	184019770	184019770	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatgcagagcatgaggcttgCgacctgcttatggaaattga	12	10	12	7	1	0	3	0	2	0	1	0	5	0	4	1	2	4	4	1	2	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:184019770C>T	ENST00000310118.4	+	5	1173	c.615C>T	c.(613-615)tgC>tgT	p.C205C	PSMD2_ENST00000435761.1_Silent_p.C46C|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Silent_p.C75C	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	205					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	ATGAGGCTTGCGACCTGCTTA	0.507																																					p.C205C	Colon(24;313 636 6917 9932 15554)	.											.	PSMD2-90	0			c.C615T						.						115	106	109					3																	184019770		2203	4300	6503	SO:0001819	synonymous_variant	5708	exon5			GGCTTGCGACCTG	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"Proteasome (prosome, macropain) subunits"	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.615C>T	3.37:g.184019770C>T		Somatic	114	2		WXS	Illumina HiSeq	Phase_I	184	11	NM_002808	0	1	149	150	0	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Silent	SNP	ENST00000310118.4	37	CCDS3258.1																																																																																			.		0.507	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		T	184019770	C	T	184019770	2	4	51	1	0	0	0	0	0	0	0	1	12727	776	27	1		1	PSMD2	3	184019770	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	29963835	184019770	14002660	63	4751											
FAM43A	131583	hgsc.bcm.edu	37	chr3	194408136	194408136	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctctaccagacgtcggccaAcgcgctggcggaatttaaac	10	7	11	13	5	1	1	0	0	1	1	2	2	1	2	2	3	3	2	2	3	5	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:194408136A>G	ENST00000329759.4	+	1	1515	c.581A>G	c.(580-582)aAc>aGc	p.N194S		NM_153690.4	NP_710157.2	Q8N2R8	FA43A_HUMAN	family with sequence similarity 43, member A	194										breast(2)|central_nervous_system(1)|lung(6)|skin(1)	10	all_cancers(143;2.04e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.147)	OV - Ovarian serous cystadenocarcinoma(49;8.37e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.78e-05)		ACGTCGGCCAACGCGCTGGCG	0.672																																					p.N194S		.											.	FAM43A-90	0			c.A581G						.						5	4	4					3																	194408136		2020	3974	5994	SO:0001583	missense	131583	exon1			CGGCCAACGCGCT	AK074503	CCDS33923.1	3q29	2004-07-28			ENSG00000185112	ENSG00000185112			26888	protein-coding gene	gene with protein product						12477932	Standard	NM_153690		Approved	FLJ90022	uc003fuj.3	Q8N2R8	OTTHUMG00000156016	ENST00000329759.4:c.581A>G	3.37:g.194408136A>G	ENSP00000371397:p.Asn194Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	24	5	NM_153690	0	0	5	13	8	A3KME2|Q8IXP4|Q8WZ07	Missense_Mutation	SNP	ENST00000329759.4	37	CCDS33923.1	.	.	.	.	.	.	.	.	.	.	A	8.875	0.950325	0.18431	.	.	ENSG00000185112	ENST00000329759	T	0.62364	0.03	5.07	3.85	0.44370	Pleckstrin homology-type (1);	0.222998	0.44688	D	0.000422	T	0.40119	0.1104	N	0.13098	0.295	0.31328	N	0.685214	B	0.33171	0.4	B	0.33960	0.173	T	0.40403	-0.9565	10	0.07644	T	0.81	-38.1095	12.0384	0.53438	0.8111:0.1889:0.0:0.0	.	194	Q8N2R8	FA43A_HUMAN	S	194	ENSP00000371397:N194S	ENSP00000371397:N194S	N	+	2	0	FAM43A	195889425	0.999000	0.42202	1.000000	0.80357	0.903000	0.53119	3.528000	0.53524	1.913000	0.55393	0.379000	0.24179	AAC	.		0.672	FAM43A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342734.1	NM_153690		G	194408136	A	G	194408136	3	3	51	1	0	0	0	0	1	0	0	0	5581	43	2	3	583	3	FAM43A	3	194408136	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	10388366	194408136	3614294	64	4752											
FAM193A	8603	bcgsc.ca	37	chr4	2674038	2674038	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctttgcacactgttccacAcctgccacgccctctcatcc	6	10	5	20	1	1	0	1	0	1	0	4	0	3	0	6	0	2	2	6	0	0	2	rs201152034		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:2674038A>C	ENST00000324666.5	+	11	1748	c.1397A>C	c.(1396-1398)cAc>cCc	p.H466P	FAM193A_ENST00000545951.1_Missense_Mutation_p.H466P|FAM193A_ENST00000505311.1_Missense_Mutation_p.H466P|FAM193A_ENST00000502458.1_Missense_Mutation_p.H488P|FAM193A_ENST00000382839.3_Missense_Mutation_p.H466P	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	466										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						ACTGTTCCACACCTGCCACGC	0.552																																					p.H488P													.	FAM193A-93	0			c.A1463C						.						144	100	115					4																	2674038		2203	4300	6503	SO:0001583	missense	8603	exon12			TTCCACACCTGCC	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.1397A>C	4.37:g.2674038A>C	ENSP00000324587:p.His466Pro	Somatic	63	4		WXS	Illumina HiSeq	Phase_1	69	37	NM_001256667	0	0	7	8	1	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.048080	0.75846	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	4.82	4.82	0.62117	.	0.061911	0.64402	D	0.000004	T	0.44850	0.1313	L	0.54323	1.7	0.58432	D	0.999998	D;D;D;D;D	0.69078	0.997;0.995;0.997;0.997;0.997	D;D;D;D;D	0.80764	0.994;0.984;0.994;0.994;0.994	T	0.30416	-0.9979	10	0.42905	T	0.14	-25.7798	13.8593	0.63550	1.0:0.0:0.0:0.0	.	466;488;466;488;466	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	P	466;466;466;488;320	ENSP00000372290:H466P;ENSP00000324587:H466P;ENSP00000443617:H466P;ENSP00000427505:H488P;ENSP00000427260:H320P	ENSP00000324587:H466P	H	+	2	0	FAM193A	2643836	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.875000	0.87205	1.920000	0.55613	0.528000	0.53228	CAC	.		0.552	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		C	2674038	A	C	2674038	3	2	51	1	0	0	0	0	1	0	0	0	5540	159	6	5	1431	5	FAM193A	4	2674038	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		2674038	188480238	65	4753											
OTOP1	133060	hgsc.bcm.edu	37	chr4	4228479	4228479	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ggggggccggggattccgggGacctcggggccgaggacgag	5	3	23	10	5	0	0	0	0	0	0	2	5	1	3	4	10	0	0	4	10	0	1	rs199890951		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:4228479G>C	ENST00000296358.4	-	1	137	c.113C>G	c.(112-114)tCc>tGc	p.S38C		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	38					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ggATTCCGGGGACCTCGGGGC	0.746																																					p.S38C		.											.	OTOP1-92	0			c.C113G						.						3	3	3					4																	4228479		1773	3481	5254	SO:0001583	missense	133060	exon1			TCCGGGGACCTCG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.113C>G	4.37:g.4228479G>C	ENSP00000296358:p.Ser38Cys	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	11	3	NM_177998	0	0	0	0	0	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	7.656	0.683978	0.14907	.	.	ENSG00000163982	ENST00000296358	T	0.08896	3.04	2.01	0.00709	0.14069	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	P	0.52463	0.953	B	0.31390	0.129	T	0.44559	-0.9320	9	0.49607	T	0.09	-0.0197	7.5462	0.27768	0.0:0.5332:0.4668:0.0	.	38	Q7RTM1	OTOP1_HUMAN	C	38	ENSP00000296358:S38C	ENSP00000296358:S38C	S	-	2	0	OTOP1	4279380	0.001000	0.12720	0.002000	0.10522	0.057000	0.15508	0.411000	0.21115	-0.016000	0.14127	-0.472000	0.04984	TCC	.		0.746	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		C	4228479	G	C	4228479	3	2	51	1	0	0	0	0	1	0	0	0	11331	1174	41	4	1749	4	OTOP1	4	4228479	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	1554441	4228479	186925797	66	4754											
ACOX3	8310	bcgsc.ca	37	chr4	8383307	8383307	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctctcggagcaggtagcaaAccagccacttgtatgctgcc	9	9	10	13	1	1	0	0	0	1	0	3	1	1	1	3	2	6	5	3	2	3	3	rs200650508		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:8383307A>C	ENST00000356406.5	-	14	1642	c.1565T>G	c.(1564-1566)gTt>gGt	p.V522G	ACOX3_ENST00000503233.1_Missense_Mutation_p.V522G|ACOX3_ENST00000413009.2_Missense_Mutation_p.V522G	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	522					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CAGGTAGCAAACCAGCCACTT	0.438																																					p.V522G													.	ACOX3-90	0			c.T1565G						.						86	95	92					4																	8383307		2203	4300	6503	SO:0001583	missense	8310	exon14			TAGCAAACCAGCC	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1565T>G	4.37:g.8383307A>C	ENSP00000348775:p.Val522Gly	Somatic	66	0		WXS	Illumina HiSeq	Phase_1	235	187	NM_001101667	0	0	14	15	1	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.366704	0.82463	.	.	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	T;T;T	0.46819	0.86;0.86;0.86	4.96	4.96	0.65561	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	M	0.89904	3.07	0.80722	D	1	D;D;D	0.63880	0.993;0.991;0.993	D;D;D	0.69142	0.962;0.949;0.962	T	0.79325	-0.1850	10	0.87932	D	0	-39.6665	13.7232	0.62740	1.0:0.0:0.0:0.0	.	522;522;522	B2R856;O15254-2;O15254	.;.;ACOX3_HUMAN	G	522	ENSP00000413994:V522G;ENSP00000348775:V522G;ENSP00000421625:V522G	ENSP00000348775:V522G	V	-	2	0	ACOX3	8434207	1.000000	0.71417	0.984000	0.44739	0.980000	0.70556	7.111000	0.77077	2.083000	0.62718	0.533000	0.62120	GTT	A|0.999;C|0.001		0.438	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			C	8383307	A	C	8383307	3	2	51	1	0	0	0	0	1	0	0	0	160	43	2	5	557	5	ACOX3	4	8383307	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	4154828	8383307	182770969	67	4755											
LGI2	55203	bcgsc.ca	37	chr4	25005443	25005443	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcattcggaagctcttcAcagccagtacgtcctccatg	8	12	8	13	2	2	0	1	0	1	0	5	1	4	1	3	1	4	3	3	1	2	4	rs77736957		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:25005443A>C	ENST00000382114.4	-	8	1453	c.1268T>G	c.(1267-1269)gTg>gGg	p.V423G		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	423						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				GAAGCTCTTCACAGCCAGTAC	0.532																																					p.V423G													.	LGI2-90	0			c.T1268G						.						217	225	222					4																	25005443		2203	4300	6503	SO:0001583	missense	55203	exon8			CTCTTCACAGCCA	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1268T>G	4.37:g.25005443A>C	ENSP00000371548:p.Val423Gly	Somatic	405	0		WXS	Illumina HiSeq	Phase_1	298	73	NM_018176	0	0	0	0	0	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	37	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	A	19.30	3.801055	0.70567	.	.	ENSG00000153012	ENST00000382114;ENST00000282970	D	0.83914	-1.78	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.89791	0.6817	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90847	0.4728	10	0.87932	D	0	-25.8133	15.7705	0.78164	1.0:0.0:0.0:0.0	.	423	Q8N0V4	LGI2_HUMAN	G	423;71	ENSP00000371548:V423G	ENSP00000282970:V71G	V	-	2	0	LGI2	24614541	1.000000	0.71417	0.997000	0.53966	0.716000	0.41182	9.339000	0.96797	2.116000	0.64780	0.455000	0.32223	GTG	.		0.532	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			C	25005443	A	C	25005443	3	2	51	1	0	0	0	0	1	0	0	0	8774	159	6	5	373	5	LGI2	4	25005443	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	16622136	25005443	166148833	68	4756											
SLAIN2	57606	broad.mit.edu	37	chr4	48422364	48422364	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tactctaaccagacctgcagGgacaactgcaatgagaagtg	14	7	10	10	0	1	2	0	1	1	2	1	4	1	3	2	1	5	2	2	1	5	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:48422364G>A	ENST00000264313.6	+	7	2001	c.1583G>A	c.(1582-1584)gGg>gAg	p.G528E	SLAIN2_ENST00000512093.1_Missense_Mutation_p.G361E	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	528					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						AGACCTGCAGGGACAACTGCA	0.557																																					p.G528E													.	.	0			c.G1583A						.						133	134	134					4																	48422364		2038	4203	6241	SO:0001583	missense	57606	exon7			CTGCAGGGACAAC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"KIAA1458"	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1583G>A	4.37:g.48422364G>A	ENSP00000264313:p.Gly528Glu	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	160	4	NM_020846	0	0	41	41	0	A8K4P1|Q8N5R3	Missense_Mutation	SNP	ENST00000264313.6	37	CCDS47051.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592341	0.46214	.	.	ENSG00000109171	ENST00000264313;ENST00000512093	.	.	.	4.87	4.87	0.63330	.	0.182928	0.47455	D	0.000235	T	0.65026	0.2652	L	0.49778	1.585	0.43313	D	0.995324	D	0.65815	0.995	P	0.58721	0.844	T	0.65207	-0.6224	9	0.45353	T	0.12	-8.1445	12.6914	0.56976	0.0:0.0:0.8349:0.1651	.	528	Q9P270	SLAI2_HUMAN	E	528;361	.	ENSP00000264313:G528E	G	+	2	0	SLAIN2	48117121	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	6.329000	0.72920	2.275000	0.75901	0.557000	0.71058	GGG	.		0.557	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846		A	48422364	G	A	48422364	3	1	51	1	0	0	0	0	1	0	0	0	14398	1232	43	2	1609	2	SLAIN2	4	48422364	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	23416921	48422364	142731912	69	4757											
LPHN3	23284	bcgsc.ca	37	chr4	62542580	62542580	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgtgcagtggtggcaggTcctgatgtttttccagaccc	6	12	13	10	0	0	2	0	1	0	1	2	2	2	2	3	3	1	3	3	3	0	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:62542580T>G	ENST00000514591.1	+	5	635	c.306T>G	c.(304-306)ggT>ggG	p.G102G	LPHN3_ENST00000504896.1_Silent_p.G102G|LPHN3_ENST00000506746.1_Silent_p.G170G|LPHN3_ENST00000508946.1_Silent_p.G102G|LPHN3_ENST00000507164.1_Silent_p.G170G|LPHN3_ENST00000506700.1_Silent_p.G102G|LPHN3_ENST00000512091.2_Silent_p.G102G|LPHN3_ENST00000506720.1_Silent_p.G170G|LPHN3_ENST00000514157.1_Silent_p.G102G|LPHN3_ENST00000508693.1_Silent_p.G170G|LPHN3_ENST00000545650.1_Silent_p.G102G|LPHN3_ENST00000507625.1_Silent_p.G170G|LPHN3_ENST00000509896.1_Silent_p.G170G|LPHN3_ENST00000514996.1_Silent_p.G102G|LPHN3_ENST00000511324.1_Silent_p.G170G			Q9HAR2	LPHN3_HUMAN	latrophilin 3	102	SUEL-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00260}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						TGGTGGCAGGTCCTGATGTTT	0.383																																					p.G102G													.	LPHN3-508	0			c.T306G						.						229	229	229					4																	62542580		1975	4191	6166	SO:0001819	synonymous_variant	23284	exon3			GGCAGGTCCTGAT	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"-", "GPCR / Class B : Orphans"	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.306T>G	4.37:g.62542580T>G		Somatic	238	1		WXS	Illumina HiSeq	Phase_1	36	19	NM_015236	0	0	1	1	0	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	CCDS54768.1																																																																																			.		0.383	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			G	62542580	T	G	62542580	2	3	51	1	0	0	0	0	0	0	0	1	8942	1654	58	5		5	LPHN3	4	62542580	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	14120216	62542580	128611696	70	4758											
CFI	3426	bcgsc.ca	37	chr4	110670458	110670458	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggcatccttaattgccAcctgccatgggaggtctccc	7	10	9	15	0	1	0	0	0	1	0	3	1	2	1	5	3	2	1	5	3	1	2	rs199838992		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:110670458A>C	ENST00000394634.2	-	10	1271	c.1064T>G	c.(1063-1065)gTg>gGg	p.V355G	CFI_ENST00000394635.3_Missense_Mutation_p.V363G|CFI_ENST00000512148.1_Missense_Mutation_p.V348G	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	355	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		CTTAATTGCCACCTGCCATGG	0.453																																					p.V355G													.	CFI-90	0			c.T1064G						.						146	152	150					4																	110670458		2203	4300	6503	SO:0001583	missense	3426	exon10			ATTGCCACCTGCC	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"Complement system"	5394	protein-coding gene	gene with protein product	"Konglutinogen-activating factor", "C3b-inactivator"	217030	"I factor (complement)"	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.1064T>G	4.37:g.110670458A>C	ENSP00000378130:p.Val355Gly	Somatic	280	5		WXS	Illumina HiSeq	Phase_1	221	103	NM_000204	0	0	266	343	77	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.081198	0.76528	.	.	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000512148	D;D;D	0.95853	-3.83;-3.83;-3.83	5.71	5.71	0.89125	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.182235	0.47093	D	0.000259	D	0.97679	0.9239	M	0.85197	2.74	0.80722	D	1	D;P;D	0.76494	0.997;0.521;0.999	D;P;D	0.69824	0.955;0.508;0.966	D	0.98427	1.0580	10	0.87932	D	0	-6.8988	14.5977	0.68419	1.0:0.0:0.0:0.0	.	363;348;355	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	G	363;355;348	ENSP00000378131:V363G;ENSP00000378130:V355G;ENSP00000427438:V348G	ENSP00000378130:V355G	V	-	2	0	CFI	110889907	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.606000	0.82863	2.178000	0.69098	0.524000	0.50904	GTG	A|0.999;C|0.001		0.453	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204		C	110670458	A	C	110670458	3	2	51	1	0	0	0	0	1	0	0	0	3295	159	6	5	703	5	CFI	4	110670458	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	48127878	110670458	80483818	71	4759											
NEUROG2	63973	hgsc.bcm.edu	37	chr4	113436466	113436466	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctgcccggcctcagcccCgcgctgccgacgcgccccgc	2	3	11	25	7	1	0	1	0	0	0	1	1	1	0	9	1	3	1	9	1	0	0	rs200923931	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:113436466C>G	ENST00000313341.3	-	2	492	c.166G>C	c.(166-168)Ggg>Cgg	p.G56R	RP11-402J6.1_ENST00000506057.1_RNA|RP11-402J6.1_ENST00000504009.1_RNA	NM_024019.3	NP_076924.1	Q9H2A3	NGN2_HUMAN	neurogenin 2	56					axon guidance (GO:0007411)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(3)|lung(6)|skin(2)	12		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)		gcctcagccccgcgctgccga	0.776													C|||	25	0.00499201	0.0166	0.0029	5008	,	,		8213	0		0.001	False		,,,				2504	0				p.G56R		.											.	NEUROG2-92	0			c.G166C						.						3	4	4					4																	113436466		1749	3372	5121	SO:0001583	missense	63973	exon2			CAGCCCCGCGCTG	AF303002	CCDS3698.1	4q25	2013-05-21			ENSG00000178403	ENSG00000178403		"Basic helix-loop-helix proteins"	13805	protein-coding gene	gene with protein product		606624					Standard	NM_024019		Approved	Atoh4, Math4A, ngn-2, bHLHa8, NGN2	uc003ias.3	Q9H2A3	OTTHUMG00000132907	ENST00000313341.3:c.166G>C	4.37:g.113436466C>G	ENSP00000317333:p.Gly56Arg	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	26	17	NM_024019	0	0	0	0	0	Q8N416	Missense_Mutation	SNP	ENST00000313341.3	37	CCDS3698.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	3.865	-0.029028	0.07589	.	.	ENSG00000178403	ENST00000313341	D	0.90620	-2.7	3.36	1.47	0.22746	.	.	.	.	.	T	0.67088	0.2856	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.59773	-0.7391	9	0.16896	T	0.51	-5.8759	5.1708	0.15108	0.2372:0.5317:0.2311:0.0	.	56	Q9H2A3	NGN2_HUMAN	R	56	ENSP00000317333:G56R	ENSP00000317333:G56R	G	-	1	0	NEUROG2	113655915	0.000000	0.05858	0.030000	0.17652	0.080000	0.17528	0.492000	0.22435	1.729000	0.51567	0.306000	0.20318	GGG	C|0.996;G|0.004		0.776	NEUROG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256414.1	NM_024019		G	113436466	C	G	113436466	3	3	51	1	0	0	0	0	1	0	0	0	10379	652	23	4	656	4	NEUROG2	4	113436466	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	2766008	113436466	77717810	72	4760											
ANK2	287	bcgsc.ca	37	chr4	114275831	114275831	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacaaatcagcaaaacaaaaGcagccacaagagaaaggtaa	23	2	7	9	0	1	1	1	0	0	1	1	2	1	1	1	1	4	3	1	1	8	1	rs201005444		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:114275831G>C	ENST00000357077.4	+	38	6110	c.6057G>C	c.(6055-6057)aaG>aaC	p.K2019N	ANK2_ENST00000264366.6_Missense_Mutation_p.K1986N|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2019					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CAAAACAAAAGCAGCCACAAG	0.438																																					p.K2019N													.	ANK2-583	0			c.G6057C						.						43	50	47					4																	114275831		2197	4299	6496	SO:0001583	missense	287	exon38			ACAAAAGCAGCCA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.6057G>C	4.37:g.114275831G>C	ENSP00000349588:p.Lys2019Asn	Somatic	91	0		WXS	Illumina HiSeq	Phase_1	68	32	NM_001148	0	0	1	1	0	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.519176	0.44866	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.69806	-0.42;-0.43	5.53	0.508	0.16972	.	0.000000	0.64402	D	0.000016	T	0.73171	0.3553	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.994;0.997	T	0.68100	-0.5498	9	.	.	.	.	6.1849	0.20491	0.4325:0.0:0.4502:0.1173	.	1986;2019	Q01484;Q01484-4	ANK2_HUMAN;.	N	2019;1986	ENSP00000349588:K2019N;ENSP00000264366:K1986N	.	K	+	3	2	ANK2	114495280	0.770000	0.28543	0.525000	0.27900	0.799000	0.45148	0.923000	0.28757	0.054000	0.16065	0.563000	0.77884	AAG	.		0.438	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		C	114275831	G	C	114275831	3	2	51	1	0	0	0	0	1	0	0	0	621	962	34	4	6272	4	ANK2	4	114275831	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	839365	114275831	76878445	73	4761											
MAML3	55534	bcgsc.ca	37	chr4	140646955	140646955	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggattccgctgtggctggAggtgctgccggggtagatgt	5	11	18	7	2	0	1	0	0	0	1	1	3	1	3	2	6	2	4	2	6	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:140646955A>G	ENST00000509479.2	-	4	3222	c.2366T>C	c.(2365-2367)cTc>cCc	p.L789P	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					CTGTGGCTGGAGGTGCTGCCG	0.512																																					p.L785P													.	MAML3-455	0			c.T2354C						.						89	94	92					4																	140646955		2082	4228	6310	SO:0001583	missense	55534	exon5			GGCTGGAGGTGCT	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.2366T>C	4.37:g.140646955A>G	ENSP00000421180:p.Leu789Pro	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	29	13	NM_018717	0	0	0	0	0		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.41|11.41	1.631090|1.631090	0.28978|0.28978	.|.	.|.	ENSG00000196782|ENSG00000196782	ENST00000509479;ENST00000538400|ENST00000502696	T|.	0.22743|.	1.94|.	5.29|5.29	4.08|4.08	0.47627|0.47627	.|.	0.274240|.	0.31347|.	N|.	0.007812|.	T|T	0.64843|0.64843	0.2635|0.2635	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	B;B|.	0.10296|.	0.003;0.003|.	B;B|.	0.09377|.	0.004;0.004|.	T|T	0.62248|0.62248	-0.6894|-0.6894	9|5	.|.	.|.	.|.	.|.	11.2123|11.2123	0.48806|0.48806	0.9274:0.0:0.0726:0.0|0.9274:0.0:0.0726:0.0	.|.	789;785|.	E7EVW8;Q96JK9|.	.;MAML3_HUMAN|.	P|P	789;96|133	ENSP00000421180:L789P|.	.|.	L|S	-|-	2|1	0|0	MAML3|MAML3	140866405|140866405	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	2.384000|2.384000	0.44362|0.44362	0.821000|0.821000	0.34540|0.34540	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.		0.512	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			G	140646955	A	G	140646955	3	3	51	1	0	0	0	0	1	0	0	0	9232	304	11	3	1058	3	MAML3	4	140646955	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	26371124	140646955	50507321	74	4762											
TBC1D9	23158	broad.mit.edu	37	chr4	141580761	141580761	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccacaactctggtgttgtaGtaatctgggagcatgcgctc	8	11	11	11	1	2	0	0	0	2	0	3	1	2	1	1	2	3	5	1	2	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr4:141580761G>C	ENST00000442267.2	-	11	1976	c.1902C>G	c.(1900-1902)taC>taG	p.Y634*		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	634	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TGGTGTTGTAGTAATCTGGGA	0.458																																					p.Y634X													.	TBC1D9-23	0			c.C1902G						.						59	60	60					4																	141580761		2054	4210	6264	SO:0001587	stop_gained	23158	exon11			GTTGTAGTAATCT	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1902C>G	4.37:g.141580761G>C	ENSP00000411197:p.Tyr634*	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_015130	0	0	19	19	0	A6H8U8|D3DNZ1|O94958	Nonsense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	G	39	7.814800	0.98504	.	.	ENSG00000109436	ENST00000442267	.	.	.	5.62	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.5126	0.67797	0.0702:0.0:0.9297:0.0	.	.	.	.	X	634	.	ENSP00000411197:Y634X	Y	-	3	2	TBC1D9	141800211	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.869000	0.99810	1.370000	0.46153	0.655000	0.94253	TAC	.		0.458	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		C	141580761	G	C	141580761	4	2	51	1	0	0	0	0	0	1	0	0	15659	1024	36	4	1942	4	TBC1D9	4	141580761	Nonsense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	933806	141580761	49573515	75	4763											
PDCD6	10016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	311485	311485	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacgggggcagattgccttcGacgacttcatccagggctgc	7	8	14	12	3	1	1	1	0	0	1	3	4	2	1	2	3	2	2	2	3	0	3	rs368897410		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:311485G>A	ENST00000264933.4	+	5	545	c.445G>A	c.(445-447)Gac>Aac	p.D149N	AHRR_ENST00000505113.1_Intron|AHRR_ENST00000316418.5_Intron|PDCD6_ENST00000511482.1_3'UTR|PDCD6_ENST00000505221.1_Intron|AHRR_ENST00000512529.1_Intron|PDCD6_ENST00000507528.1_Missense_Mutation_p.D147N	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	149	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			GATTGCCTTCGACGACTTCAT	0.582																																					p.D149N		.											.	PDCD6-290	0			c.G445A						.	G	,ASN/ASP,	1,4405	2.1+/-5.4	0,1,2202	92	76	81		,445,	5.7	0.9	5		81	0,8600		0,0,4300	no	intron,missense,intron	PDCD6,AHRR	NM_001242412.1,NM_013232.3,NM_020731.4	,23,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,probably-damaging,	,149/192,	311485	1,13005	2203	4300	6503	SO:0001583	missense	10016	exon5			GCCTTCGACGACT	AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"EF-hand domain containing"	8765	protein-coding gene	gene with protein product	"apoptosis-linked gene-2"	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.445G>A	5.37:g.311485G>A	ENSP00000264933:p.Asp149Asn	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	163	44	NM_013232	0	0	162	162	0	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	37	CCDS3854.1	.	.	.	.	.	.	.	.	.	.	g	36	5.640171	0.96693	2.27E-4	0.0	ENSG00000249915	ENST00000264933;ENST00000507528;ENST00000507473	T;T;T	0.79141	1.36;1.36;-1.24	5.72	5.72	0.89469	EF-hand-like domain (1);	.	.	.	.	D	0.88789	0.6532	M	0.82132	2.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.89735	0.3929	9	0.87932	D	0	.	17.3651	0.87362	0.0:0.0:1.0:0.0	.	147;149	Q2YDC2;O75340	.;PDCD6_HUMAN	N	149;147;62	ENSP00000264933:D149N;ENSP00000423815:D147N;ENSP00000425370:D62N	ENSP00000264933:D149N	D	+	1	0	PDCD6	364485	1.000000	0.71417	0.914000	0.36105	0.835000	0.47333	9.347000	0.97059	2.692000	0.91855	0.655000	0.94253	GAC	.		0.582	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232		A	311485	G	A	311485	3	1	51	1	0	0	0	0	1	0	0	0	11649	1058	37	1	463	1	PDCD6	5	311485	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		311485	180603775	76	4764											
NSUN2	54888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	6616902	6616902	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatagggtttagtgaacacGtggaatacaccatccttcca	13	10	8	10	1	0	1	0	1	0	0	2	2	2	2	3	2	2	1	3	2	6	5	rs138724893		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:6616902G>T	ENST00000264670.6	-	9	1270	c.959C>A	c.(958-960)aCg>aAg	p.T320K	NSUN2_ENST00000539938.1_Missense_Mutation_p.T84K|NSUN2_ENST00000506139.1_Missense_Mutation_p.T285K	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	320					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)	p.T320M(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TAGTGAACACGTGGAATACAC	0.468																																					p.T320K		.											.	NSUN2-91	1	Substitution - Missense(1)	prostate(1)	c.C959A						.						151	133	139					5																	6616902		2203	4300	6503	SO:0001583	missense	54888	exon9			GAACACGTGGAAT	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.959C>A	5.37:g.6616902G>T	ENSP00000264670:p.Thr320Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	86	38	NM_017755	0	0	12	29	17	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517699	0.85495	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.26810	1.71;1.71;1.71	5.56	4.69	0.59074	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.092104	0.85682	D	0.000000	T	0.70133	0.3189	H	0.99507	4.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84435	0.0579	10	0.87932	D	0	-41.0989	14.8419	0.70233	0.0693:0.0:0.9307:0.0	.	285;320	B4DQW2;Q08J23	.;NSUN2_HUMAN	K	320;84;285	ENSP00000264670:T320K;ENSP00000444338:T84K;ENSP00000420957:T285K	ENSP00000264670:T320K	T	-	2	0	NSUN2	6669902	1.000000	0.71417	0.047000	0.18901	0.855000	0.48748	8.772000	0.91757	1.498000	0.48600	0.650000	0.86243	ACG	G|1.000;A|0.000		0.468	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6616902	G	T	6616902	3	4	51	1	0	0	0	0	1	0	0	0	10704	1145	40	4	1388	4	NSUN2	5	6616902	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	6305417	6616902	174298358	77	4765											
C5orf51	285636	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	41911262	41911262	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagagagtggctcttaagaaAatccagtttgcttaaaaagg	16	10	10	5	0	1	2	0	0	1	2	2	3	2	2	1	2	1	3	1	2	7	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:41911262A>T	ENST00000381647.2	+	4	486	c.467A>T	c.(466-468)aAa>aTa	p.K156I	C5orf51_ENST00000505931.2_3'UTR	NM_175921.4	NP_787117.3	A6NDU8	CE051_HUMAN	chromosome 5 open reading frame 51	156										endometrium(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						CTCTTAAGAAAATCCAGTTTG	0.383																																					p.K156I													.	C5orf51-68	0			c.A467T						.						82	81	82					5																	41911262		2203	4300	6503	SO:0001583	missense	285636	exon4			TAAGAAAATCCAG	AL833916, AK094002	CCDS34151.1	5p13.1	2008-07-18			ENSG00000205765	ENSG00000205765			27750	protein-coding gene	gene with protein product						14702039	Standard	NM_175921		Approved	LOC285636	uc003jmo.3	A6NDU8	OTTHUMG00000162084	ENST00000381647.2:c.467A>T	5.37:g.41911262A>T	ENSP00000371061:p.Lys156Ile	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	11	7	NM_175921	0	0	4	8	4	A2RRM9	Missense_Mutation	SNP	ENST00000381647.2	37	CCDS34151.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.179632	0.78564	.	.	ENSG00000205765	ENST00000381647	D	0.83163	-1.69	5.7	5.7	0.88788	.	0.046992	0.85682	D	0.000000	D	0.84831	0.5559	N	0.24115	0.695	0.29480	N	0.856424	D	0.89917	1.0	D	0.71656	0.974	T	0.82432	-0.0460	10	0.72032	D	0.01	-7.918	14.5359	0.67960	1.0:0.0:0.0:0.0	.	156	A6NDU8	CE051_HUMAN	I	156	ENSP00000371061:K156I	ENSP00000371061:K156I	K	+	2	0	C5orf51	41947019	1.000000	0.71417	0.939000	0.37840	0.970000	0.65996	4.742000	0.62103	2.175000	0.68902	0.383000	0.25322	AAA	.		0.383	C5orf51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367144.1	NM_175921		T	41911262	A	T	41911262	3	4	51	1	0	0	0	0	1	0	0	0	2314	14	1	5	481	5	C5orf51	5	41911262	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	35294360	41911262	139003998	78	4766											
FGF10	2255	broad.mit.edu	37	chr5	44388715	44388717	+	In_Frame_Del	DEL	AGC	AGC	-																															caccaagaacagcaacaaaaAgcagcagcagcagcagccgg																								rs576181814		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:44388715_44388717delAGC	ENST00000264664.4	-	1	182_184	c.68_70delGCT	c.(67-72)tgcttt>ttt	p.C23del	RP11-473L15.2_ENST00000502457.1_RNA	NM_004465.1	NP_004456.1	O15520	FGF10_HUMAN	fibroblast growth factor 10	23					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchiole morphogenesis (GO:0060436)|bud elongation involved in lung branching (GO:0060449)|bud outgrowth involved in lung branching (GO:0060447)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell migration (GO:0010631)|epithelial cell proliferation (GO:0050673)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|ERK1 and ERK2 cascade (GO:0070371)|establishment of mitotic spindle orientation (GO:0000132)|Fc-epsilon receptor signaling pathway (GO:0038095)|female genitalia morphogenesis (GO:0048807)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|hair follicle morphogenesis (GO:0031069)|Harderian gland development (GO:0070384)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte proliferation (GO:0043616)|lacrimal gland development (GO:0032808)|limb bud formation (GO:0060174)|lung epithelium development (GO:0060428)|lung proximal/distal axis specification (GO:0061115)|lung saccule development (GO:0060430)|male genitalia morphogenesis (GO:0048808)|mammary gland bud formation (GO:0060615)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal-epithelial cell signaling involved in lung development (GO:0060496)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|metanephros morphogenesis (GO:0003338)|muscle cell fate commitment (GO:0042693)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|pancreas development (GO:0031016)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of ATPase activity (GO:0032781)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urothelial cell proliferation (GO:0050677)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of white fat cell proliferation (GO:0070352)|prostatic bud formation (GO:0060513)|protein localization to cell surface (GO:0034394)|radial glial cell differentiation (GO:0060019)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of saliva secretion (GO:0046877)|regulation of smoothened signaling pathway (GO:0008589)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|salivary gland development (GO:0007431)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|semicircular canal fusion (GO:0060879)|smooth muscle cell differentiation (GO:0051145)|somatic stem cell maintenance (GO:0035019)|spleen development (GO:0048536)|submandibular salivary gland formation (GO:0060661)|tear secretion (GO:0070075)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tissue regeneration (GO:0042246)|Type II pneumocyte differentiation (GO:0060510)|urothelial cell proliferation (GO:0050674)|white fat cell differentiation (GO:0050872)|wound healing (GO:0042060)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chemoattractant activity (GO:0042056)|fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|type 2 fibroblast growth factor receptor binding (GO:0005111)			haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1)	13	Lung NSC(6;1.12e-06)					AGCAACAAAAAGCAGCAGCAGCA	0.537																																					p.23_24del													.	FGF10-522	0			c.68_70del						.																																			SO:0001651	inframe_deletion	2255	exon1			ACAAAAAGCAGCA		CCDS3950.1	5p13-p12	2008-02-05			ENSG00000070193	ENSG00000070193			3666	protein-coding gene	gene with protein product		602115				9287324	Standard	NM_004465		Approved		uc003jog.1	O15520	OTTHUMG00000131153	ENST00000264664.4:c.68_70delGCT	5.37:g.44388724_44388726delAGC	ENSP00000264664:p.Cys23del	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	245	6	NM_004465	0	0	0	0	0	C7FDY0|Q6FHR3|Q6FHT6|Q96P59	In_Frame_Del	DEL	ENST00000264664.4	37	CCDS3950.1																																																																																			.		0.537	FGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253845.2	NM_004465		-	44388717	AGC	-	44388715	7	5	51	1	0	1	0	1	0	0	0	0	5858	72	3	0	568	0	FGF10	5	44388715	In_Frame_Del	DEL	AGC	TCGA-B9-4117-01A-01D-1252-08	2477453	44388715	136526545	79	4767											
SV2C	22987	bcgsc.ca	37	chr5	75490896	75490896	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaaggttatggcttctttCtcttctgtcgcttactttct	4	20	6	11	1	4	0	0	0	4	0	7	0	5	0	1	2	1	3	1	2	3	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:75490896C>T	ENST00000502798.2	+	3	1175	c.733C>T	c.(733-735)Ctc>Ttc	p.L245F	SV2C_ENST00000322285.7_Missense_Mutation_p.L245F	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	245					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		TGGCTTCTTTCTCTTCTGTCG	0.388																																					p.L245F													.	SV2C-91	0			c.C733T						.						335	316	322					5																	75490896		1860	4100	5960	SO:0001583	missense	22987	exon3			TTCTTTCTCTTCT	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.733C>T	5.37:g.75490896C>T	ENSP00000423541:p.Leu245Phe	Somatic	267	0		WXS	Illumina HiSeq	Phase_1	86	10	NM_014979	0	0	0	0	0	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	37	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333761	0.81801	.	.	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.74106	-0.81;-0.81	5.27	5.27	0.74061	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.061421	0.64402	D	0.000002	D	0.86644	0.5982	M	0.77616	2.38	0.80722	D	1	D	0.67145	0.996	D	0.70716	0.97	D	0.87838	0.2649	10	0.72032	D	0.01	-28.5958	19.2542	0.93940	0.0:1.0:0.0:0.0	.	245	Q496J9	SV2C_HUMAN	F	245	ENSP00000423541:L245F;ENSP00000316983:L245F	ENSP00000316983:L245F	L	+	1	0	SV2C	75526652	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.880000	0.69698	2.617000	0.88574	0.655000	0.94253	CTC	.		0.388	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			T	75490896	C	T	75490896	3	4	51	1	0	0	0	0	1	0	0	0	15451	913	32	2	739	2	SV2C	5	75490896	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	31102181	75490896	105424364	80	4768											
BHMT	635	bcgsc.ca	37	chr5	78426877	78426877	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccgagctgatgcagcagaaaGaagccacaactgagcagcag	15	3	12	11	1	0	4	0	2	0	2	0	5	0	4	2	0	7	5	2	0	3	0	rs201007228		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:78426877G>A	ENST00000274353.5	+	8	1266	c.1159G>A	c.(1159-1161)Gaa>Aaa	p.E387K	BHMT_ENST00000524080.1_Missense_Mutation_p.E234K|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	387					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)	p.E387*(1)		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)	GCAGCAGAAAGAAGCCACAAC	0.458																																					p.E387K													.	BHMT-91	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1159A						.						111	124	120					5																	78426877		2203	4300	6503	SO:0001583	missense	635	exon8			CAGAAAGAAGCCA	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.1159G>A	5.37:g.78426877G>A	ENSP00000274353:p.Glu387Lys	Somatic	167	0		WXS	Illumina HiSeq	Phase_1	98	38	NM_001713	0	0	106	114	8	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028421	0.93518	.	.	ENSG00000145692	ENST00000274353;ENST00000524080	T;T	0.36157	1.35;1.27	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.53562	0.1804	M	0.80616	2.505	0.80722	D	1	D;P	0.54207	0.965;0.907	P;B	0.49301	0.606;0.312	T	0.57860	-0.7738	10	0.48119	T	0.1	-14.6116	19.5116	0.95144	0.0:0.0:1.0:0.0	.	234;387	E5RJH0;Q93088	.;BHMT1_HUMAN	K	387;234	ENSP00000274353:E387K;ENSP00000428240:E234K	ENSP00000274353:E387K	E	+	1	0	BHMT	78462633	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.813000	0.99286	2.619000	0.88677	0.655000	0.94253	GAA	.		0.458	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		A	78426877	G	A	78426877	3	1	51	1	0	0	0	0	1	0	0	0	1426	943	33	2	1189	2	BHMT	5	78426877	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	2935981	78426877	102488383	81	4769											
SNCAIP	9627	bcgsc.ca	37	chr5	121776345	121776345	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaagattcttctgtggcttCttcagtttatgcaagaacag	12	14	8	7	0	4	2	1	0	3	2	4	2	4	2	0	1	2	3	0	1	5	6	rs200684003		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:121776345C>T	ENST00000261368.8	+	7	1580	c.1318C>T	c.(1318-1320)Ctt>Ttt	p.L440F	SNCAIP_ENST00000503116.2_Missense_Mutation_p.L487F|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000542191.1_5'UTR|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000414317.2_Missense_Mutation_p.L42F|SNCAIP_ENST00000261367.7_Missense_Mutation_p.L487F|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.L380F|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000379538.3_Missense_Mutation_p.L74F|SNCAIP_ENST00000379533.2_Missense_Mutation_p.L487F|CTC-210G5.1_ENST00000506053.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	440					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TCTGTGGCTTCTTCAGTTTAT	0.423																																					p.L440F													.	SNCAIP-92	0			c.C1318T						.																																			SO:0001583	missense	9627	exon7			TGGCTTCTTCAGT	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1318C>T	5.37:g.121776345C>T	ENSP00000261368:p.Leu440Phe	Somatic	96	0		WXS	Illumina HiSeq	Phase_1	49	18	NM_005460	0	0	1	1	0	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.022509	0.93462	.	.	ENSG00000064692	ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854;ENST00000503116	T;T;T;T;T;T;T;T	0.72725	-0.67;-0.63;-0.63;-0.67;-0.67;-0.63;-0.22;-0.68	5.22	5.22	0.72569	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.86748	0.6007	M	0.87097	2.86	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D;D	0.91635	0.998;0.998;0.999;0.974;0.999;0.997;0.999;0.994;0.999	D	0.88628	0.3167	10	0.87932	D	0	-14.0135	18.9723	0.92719	0.0:1.0:0.0:0.0	.	380;68;42;487;380;74;74;487;440	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-6;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;.;SNCAP_HUMAN	F	380;440;487;380;74;487;42;80;487	ENSP00000422106:L380F;ENSP00000261368:L440F;ENSP00000368848:L487F;ENSP00000368851:L380F;ENSP00000368854:L74F;ENSP00000261367:L487F;ENSP00000394392:L42F;ENSP00000423199:L487F	ENSP00000261367:L487F	L	+	1	0	SNCAIP	121804244	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.347000	0.79356	2.717000	0.92951	0.650000	0.86243	CTT	.		0.423	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			T	121776345	C	T	121776345	3	4	51	1	0	0	0	0	1	0	0	0	14873	913	32	2	1340	2	SNCAIP	5	121776345	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	43349468	121776345	59138915	82	4770											
MEGF10	84466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	126753406	126753406	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtaatgagacatgttctcctGgattctacggggaagcttgc	9	12	12	8	1	2	1	0	1	2	1	3	4	2	3	1	3	3	3	1	3	3	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:126753406G>A	ENST00000274473.6	+	11	1474	c.1207G>A	c.(1207-1209)Gga>Aga	p.G403R	MEGF10_ENST00000418761.2_Missense_Mutation_p.G403R|MEGF10_ENST00000508365.1_Missense_Mutation_p.G403R|MEGF10_ENST00000503335.2_Missense_Mutation_p.G403R	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	403	Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		ATGTTCTCCTGGATTCTACGG	0.532																																					p.G403R		.											.	MEGF10-94	0			c.G1207A						.						121	103	109					5																	126753406		2203	4300	6503	SO:0001583	missense	84466	exon11			TCTCCTGGATTCT	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.1207G>A	5.37:g.126753406G>A	ENSP00000274473:p.Gly403Arg	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	106	49	NM_032446	0	0	0	0	0	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226760	0.95173	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.69	5.69	0.88448	EGF-like, laminin (2);	0.000000	0.64402	D	0.000001	D	0.89392	0.6702	H	0.95816	3.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.90450	0.4438	10	0.44086	T	0.13	-11.0125	19.8251	0.96614	0.0:0.0:1.0:0.0	.	403;403	Q96KG7-2;Q96KG7	.;MEG10_HUMAN	R	403	ENSP00000423354:G403R;ENSP00000423195:G403R;ENSP00000416284:G403R;ENSP00000274473:G403R	ENSP00000274473:G403R	G	+	1	0	MEGF10	126781305	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.864000	0.99589	2.692000	0.91855	0.655000	0.94253	GGA	.		0.532	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		A	126753406	G	A	126753406	3	1	51	1	0	0	0	0	1	0	0	0	9485	1349	47	2	1241	2	MEGF10	5	126753406	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	4977061	126753406	54161854	83	4771											
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856534	140856534	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgaaattatttactccttcgGcagccacaaccgcgccggcg	9	9	9	14	5	0	1	0	1	0	0	2	1	1	1	4	2	3	1	4	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:140856534G>C	ENST00000308177.3	+	1	955	c.851G>C	c.(850-852)gGc>gCc	p.G284A	PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB6_ENST00000520790.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	284	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACTCCTTCGGCAGCCACAAC	0.592																																					p.G284A		.											.	PCDHGC3-24	0			c.G851C						.						49	55	53					5																	140856534		2203	4300	6503	SO:0001583	missense	5098	exon1			CCTTCGGCAGCCA	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.851G>C	5.37:g.140856534G>C	ENSP00000312070:p.Gly284Ala	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	386	102	NM_032402	0	0	27	27	0	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	37	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.905262	0.33628	.	.	ENSG00000240184	ENST00000308177	T	0.48522	0.81	5.38	5.38	0.77491	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.49457	0.1558	N	0.16233	0.39	0.36092	D	0.843523	D;D	0.61697	0.984;0.99	P;D	0.63113	0.847;0.911	T	0.47471	-0.9115	9	0.16896	T	0.51	.	17.4859	0.87688	0.0:0.0:1.0:0.0	.	284;284	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	A	284	ENSP00000312070:G284A	ENSP00000312070:G284A	G	+	2	0	PCDHGC3	140836718	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.632000	0.83247	2.806000	0.96561	0.655000	0.94253	GGC	.		0.592	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		C	140856534	G	C	140856534	3	2	51	1	0	0	0	0	1	0	0	0	11595	1203	42	4	853	4	PCDHGC3	5	140856534	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	14103128	140856534	40058726	84	4772											
FGF1	2246	bcgsc.ca	37	chr5	141974880	141974880	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagagactggcagggggAgaaacaagattgctttctgg	13	7	15	6	0	1	4	0	0	1	4	1	6	1	4	0	4	2	2	0	4	3	2	rs201277854		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:141974880A>G	ENST00000359370.6	-	4	522	c.443T>C	c.(442-444)cTc>cCc	p.L148P	FGF1_ENST00000378046.1_Missense_Mutation_p.L148P|FGF1_ENST00000494579.1_5'UTR|AC005592.2_ENST00000443800.1_RNA|AC005592.2_ENST00000414314.1_RNA|FGF1_ENST00000360966.5_3'UTR|FGF1_ENST00000419524.2_Missense_Mutation_p.L148P|FGF1_ENST00000337706.2_Missense_Mutation_p.L148P|FGF1_ENST00000407758.1_3'UTR	NM_000800.4|NM_001144892.2|NM_001144934.1|NM_001144935.1|NM_001257205.1|NM_001257206.1|NM_001257207.1|NM_001257210.1|NM_001257212.1|NM_033137.2	NP_000791.1|NP_001138364.1|NP_001138406.1|NP_001138407.1|NP_001244134.1|NP_001244135.1|NP_001244136.1|NP_001244139.1|NP_001244141.1|NP_149128.1	P05230	FGF1_HUMAN	fibroblast growth factor 1 (acidic)	148					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|branch elongation involved in ureteric bud branching (GO:0060681)|cell differentiation (GO:0030154)|cellular response to heat (GO:0034605)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesonephric epithelium development (GO:0072163)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|S100 protein binding (GO:0044548)			large_intestine(1)|lung(2)	3		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Amlexanox(DB01025)|Pazopanib(DB06589)|Pentosan Polysulfate(DB00686)	TGGCAGGGGGAGAAACAAGAT	0.493																																					p.L148P													.	FGF1-947	0			c.T443C						.						83	81	82					5																	141974880		2203	4300	6503	SO:0001583	missense	2246	exon4			AGGGGGAGAAACA	X59065	CCDS4275.1, CCDS4276.1	5q31.3-q33.2	2014-01-30			ENSG00000113578	ENSG00000113578		"Endogenous ligands"	3665	protein-coding gene	gene with protein product	"heparin-binding growth factor 1", "endothelial cell growth factor, alpha", "endothelial cell growth factor, beta"	131220		FGFA		1697263, 3523756	Standard	NM_033137		Approved	AFGF, ECGF, ECGFA, ECGFB, HBGF1, ECGF-beta, FGF-alpha, GLIO703	uc031slo.1	P05230	OTTHUMG00000059703	ENST00000359370.6:c.443T>C	5.37:g.141974880A>G	ENSP00000352329:p.Leu148Pro	Somatic	57	0		WXS	Illumina HiSeq	Phase_1	42	20	NM_001257209	0	0	1	1	0	B2R5T0|D3DQF2|P07502|Q16588	Missense_Mutation	SNP	ENST00000359370.6	37	CCDS4275.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.570251	0.86542	.	.	ENSG00000113578	ENST00000359370;ENST00000378046;ENST00000337706;ENST00000441680;ENST00000419524	D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48	5.87	5.87	0.94306	.	0.000000	0.64402	D	0.000003	D	0.96278	0.8786	H	0.95294	3.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97431	1.0015	10	0.87932	D	0	.	16.2718	0.82624	1.0:0.0:0.0:0.0	.	147;148	A8K147;P05230	.;FGF1_HUMAN	P	148	ENSP00000352329:L148P;ENSP00000367285:L148P;ENSP00000338548:L148P;ENSP00000404742:L148P;ENSP00000396195:L148P	ENSP00000338548:L148P	L	-	2	0	FGF1	141955064	1.000000	0.71417	0.995000	0.50966	0.944000	0.59088	8.782000	0.91809	2.239000	0.73571	0.528000	0.53228	CTC	A|0.999;G|0.001		0.493	FGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132735.2	NM_000800		G	141974880	A	G	141974880	3	3	51	1	0	0	0	0	1	0	0	0	5857	304	11	3	28	3	FGF1	5	141974880	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1118346	141974880	38940380	85	4773											
HAVCR1	26762	bcgsc.ca	37	chr5	156482504	156482504	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtagtgtgacagatggAcctgcctctccaccaacctt	9	9	10	13	0	1	2	0	1	1	1	2	3	1	3	5	2	2	1	5	2	2	2	rs141472249		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:156482504A>C	ENST00000339252.3	-	2	619	c.87T>G	c.(85-87)ggT>ggG	p.G29G	HAVCR1_ENST00000425854.1_Silent_p.G29G|HAVCR1_ENST00000523175.1_Silent_p.G29G|HAVCR1_ENST00000544197.1_Silent_p.G29G|HAVCR1_ENST00000522693.1_Silent_p.G29G	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	Ig-like V-type.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.G29G(1)		endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGACAGATGGACCTGCCTCTC	0.473																																					p.G29G													.	HAVCR1-92	1	Substitution - coding silent(1)	skin(1)	c.T87G						.						52	55	54					5																	156482504		1955	4153	6108	SO:0001819	synonymous_variant	26762	exon3			AGATGGACCTGCC	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"Immunoglobulin superfamily / V-set domain containing"	17866	protein-coding gene	gene with protein product	"T-cell immunoglobulin mucin family member 1"	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.87T>G	5.37:g.156482504A>C		Somatic	38	3		WXS	Illumina HiSeq	Phase_1	54	35	NM_001099414	0	0	43	80	37	O43656	Silent	SNP	ENST00000339252.3	37	CCDS43392.1																																																																																			A|0.998;C|0.002		0.473	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			C	156482504	A	C	156482504	2	2	51	1	0	0	0	0	0	0	0	1	6994	262	10	5		5	HAVCR1	5	156482504	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	14507624	156482504	24432756	86	4774											
PANK3	79646	bcgsc.ca	37	chr5	167991022	167991022	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagcctcttcaaaactttcAcagccagtcaataaactgca	15	9	5	12	0	4	1	3	0	1	1	4	1	4	1	2	0	5	1	2	0	5	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:167991022A>C	ENST00000239231.6	-	4	1000	c.684T>G	c.(682-684)tgT>tgG	p.C228W	PANK3_ENST00000520504.1_Intron	NM_024594.3	NP_078870.1	Q9H999	PANK3_HUMAN	pantothenate kinase 3	228					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.C228C(1)		NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		CAAAACTTTCACAGCCAGTCA	0.383																																					p.C228W													.	PANK3-91	1	Substitution - coding silent(1)	lung(1)	c.T684G						.						129	144	139					5																	167991022		2203	4300	6503	SO:0001583	missense	79646	exon4			ACTTTCACAGCCA	AK022961	CCDS4368.1	5q35.1	2008-02-05			ENSG00000120137	ENSG00000120137			19365	protein-coding gene	gene with protein product		606161				11479594	Standard	NM_024594		Approved	FLJ12899	uc003lzz.2	Q9H999	OTTHUMG00000130410	ENST00000239231.6:c.684T>G	5.37:g.167991022A>C	ENSP00000239231:p.Cys228Trp	Somatic	247	0		WXS	Illumina HiSeq	Phase_1	91	33	NM_024594	0	0	15	17	2	D3DQL1|Q53FJ9|Q7RTX4	Missense_Mutation	SNP	ENST00000239231.6	37	CCDS4368.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.201052	0.58234	.	.	ENSG00000120137	ENST00000239231	D	0.99552	-6.15	4.73	3.56	0.40772	.	0.000000	0.85682	D	0.000000	D	0.99619	0.9861	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98750	1.0720	10	0.72032	D	0.01	-15.015	9.6307	0.39778	0.9168:0.0:0.0832:0.0	.	228	Q9H999	PANK3_HUMAN	W	228	ENSP00000239231:C228W	ENSP00000239231:C228W	C	-	3	2	PANK3	167923600	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	1.680000	0.37607	0.771000	0.33359	0.383000	0.25322	TGT	.		0.383	PANK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252793.2	NM_024594		C	167991022	A	C	167991022	3	2	51	1	0	0	0	0	1	0	0	0	11444	157	6	5	444	5	PANK3	5	167991022	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	11508518	167991022	12924238	87	4775											
FBXW11	23291	bcgsc.ca	37	chr5	171384675	171384675	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctaccaggttggcgcagcCtagccacaaagaccttggca	10	7	10	14	1	1	1	0	0	1	1	1	1	1	1	4	3	3	3	4	3	3	4	rs201948522		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:171384675C>T	ENST00000265094.5	-	2	210	c.73G>A	c.(73-75)Ggc>Agc	p.G25S	FBXW11_ENST00000425623.2_Intron|FBXW11_ENST00000296933.6_Intron|FBXW11_ENST00000393802.2_Intron	NM_012300.2	NP_036432.2	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11	25					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	21	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTGGCGCAGCCTAGCCACAAA	0.512																																					p.G25S													.	FBXW11-272	0			c.G73A						.						94	95	94					5																	171384675		2203	4300	6503	SO:0001583	missense	23291	exon2			CGCAGCCTAGCCA	AB014596	CCDS34289.1, CCDS47340.1, CCDS47341.1	5q35.1	2013-01-09	2007-02-08	2004-06-16	ENSG00000072803	ENSG00000072803		"F-boxes / WD-40 domains", "WD repeat domain containing"	13607	protein-coding gene	gene with protein product		605651	"F-box and WD-40 domain protein 1B", "F-box and WD-40 domain protein 11"	FBXW1B		10531035, 10694485	Standard	NM_033644		Approved	KIAA0696, Fbw1b, BTRCP2, BTRC2, Hos, Fbw11	uc003mbm.1	Q9UKB1	OTTHUMG00000163267	ENST00000265094.5:c.73G>A	5.37:g.171384675C>T	ENSP00000265094:p.Gly25Ser	Somatic	144	1		WXS	Illumina HiSeq	Phase_1	99	58	NM_012300	0	0	0	0	0	B2RC98|Q9P2S8|Q9P2S9|Q9Y4C6	Missense_Mutation	SNP	ENST00000265094.5	37	CCDS34289.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.713661	0.89112	.	.	ENSG00000072803	ENST00000265094;ENST00000517395	T;T	0.71103	0.01;-0.54	5.49	5.49	0.81192	.	0.133777	0.48767	D	0.000161	T	0.51363	0.1670	N	0.08118	0	0.80722	D	1	P	0.48694	0.914	B	0.44044	0.439	T	0.56733	-0.7930	10	0.02654	T	1	-12.0164	17.1698	0.86826	0.0:1.0:0.0:0.0	.	25	Q9UKB1	FBW1B_HUMAN	S	25	ENSP00000265094:G25S;ENSP00000428753:G25S	ENSP00000265094:G25S	G	-	1	0	FBXW11	171317280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.615000	0.61190	2.565000	0.86533	0.655000	0.94253	GGC	.		0.512	FBXW11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372382.1	NM_012300		T	171384675	C	T	171384675	3	4	51	1	0	0	0	0	1	0	0	0	5783	681	24	2	1666	2	FBXW11	5	171384675	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	3393653	171384675	9530585	88	4776											
TFAP2A	7020	hgsc.bcm.edu	37	chr6	10398708	10398708	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgttgttgtccgtgtggctgTtggggttgttgctgaggtac	2	16	17	6	2	0	1	0	1	0	0	1	1	1	1	1	4	2	8	1	4	1	6	rs201591227		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:10398708T>G	ENST00000482890.1	-	8	1608	c.1256A>C	c.(1255-1257)aAc>aCc	p.N419T	TFAP2A_ENST00000379608.3_Missense_Mutation_p.N413T|TFAP2A_ENST00000497266.1_5'Flank|TFAP2A_ENST00000379604.2_Missense_Mutation_p.N419T|TFAP2A_ENST00000319516.4_Missense_Mutation_p.N415T|TFAP2A_ENST00000379613.3_Missense_Mutation_p.N421T			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	419					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				CGTGTGGCTGTTGGGGTTGTT	0.622																																					p.N419T		.											.	TFAP2A-91	0			c.A1256C						.						317	330	326					6																	10398708		2203	4300	6503	SO:0001583	missense	7020	exon7			TGGCTGTTGGGGT	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1256A>C	6.37:g.10398708T>G	ENSP00000418541:p.Asn419Thr	Somatic	715	1		WXS	Illumina HiSeq	Phase_I	1832	626	NM_003220	0	0	0	0	0	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	37	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.825513	0.32237	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.97114	-4.25;-4.25;-4.25;-4.25;-4.25	5.41	5.41	0.78517	.	0.042320	0.85682	D	0.000000	D	0.97247	0.9100	L	0.55481	1.735	0.80722	D	1	D;D;D	0.71674	0.993;0.983;0.998	D;P;D	0.83275	0.968;0.829;0.996	D	0.96866	0.9636	10	0.34782	T	0.22	-13.6146	15.4442	0.75216	0.0:0.0:0.0:1.0	.	415;419;413	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	T	421;419;415;413;419	ENSP00000368933:N421T;ENSP00000368924:N419T;ENSP00000316516:N415T;ENSP00000368928:N413T;ENSP00000418541:N419T	ENSP00000316516:N415T	N	-	2	0	TFAP2A	10506694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.249000	0.58766	2.048000	0.60808	0.533000	0.62120	AAC	.		0.622	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220		G	10398708	T	G	10398708	3	3	51	1	0	0	0	0	1	0	0	0	15819	1725	60	5	61	5	TFAP2A	6	10398708	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		10398708	160716359	89	4777											
ELOVL2	54898	bcgsc.ca	37	chr6	11005704	11005704	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgttcttcatatacttgttAcccagccatattgagagcag	10	14	7	10	0	2	1	1	1	1	1	2	2	2	1	2	0	4	3	2	0	4	8			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:11005704A>C	ENST00000354666.3	-	3	239	c.156T>G	c.(154-156)ggT>ggG	p.G52G		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	52					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	fatty acid elongase activity (GO:0009922)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(2)	14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			TATACTTGTTACCCAGCCATA	0.443																																					p.G52G													.	ELOVL2-90	0			c.T156G						.																																			SO:0001819	synonymous_variant	54898	exon3			CTTGTTACCCAGC	AK000341	CCDS4518.1	6p24.1	2011-05-25	2011-05-25		ENSG00000197977	ENSG00000197977			14416	protein-coding gene	gene with protein product		611814	"elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"			12371743, 16564093	Standard	NM_017770		Approved	Ssc2	uc003mzp.4	Q9NXB9	OTTHUMG00000014252	ENST00000354666.3:c.156T>G	6.37:g.11005704A>C		Somatic	55	0		WXS	Illumina HiSeq	Phase_1	38	21	NM_017770	0	0	0	0	0	Q6P9E1|Q86W94	Silent	SNP	ENST00000354666.3	37	CCDS4518.1																																																																																			.		0.443	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1			C	11005704	A	C	11005704	2	2	51	1	0	0	0	0	0	0	0	1	5087	378	14	5		5	ELOVL2	6	11005704	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	606996	11005704	160109363	90	4778											
CAP2	10486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	17507928	17507928	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacgctgccaccttttacacTaacagggtcttaaaggacta	12	10	8	11	1	1	0	0	0	1	0	1	2	1	1	2	2	3	1	2	2	5	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:17507928T>C	ENST00000229922.2	+	6	1033	c.501T>C	c.(499-501)acT>acC	p.T167T	CAP2_ENST00000378990.2_Silent_p.T141T|CAP2_ENST00000465994.1_Intron|CAP2_ENST00000489374.1_Intron|CAP2_ENST00000493172.1_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	167					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			CCTTTTACACTAACAGGGTCT	0.413																																					p.T167T		.											.	CAP2-91	0			c.T501C						.						138	124	129					6																	17507928		2203	4300	6503	SO:0001819	synonymous_variant	10486	exon6			TTACACTAACAGG	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.501T>C	6.37:g.17507928T>C		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	132	50	NM_006366	0	0	4	13	9	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			.		0.413	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			C	17507928	T	C	17507928	2	2	51	1	0	0	0	0	0	0	0	1	2626	1509	53	3		3	CAP2	6	17507928	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	6502224	17507928	153607139	91	4779											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056427	26056427	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaccaagtttgatacggctgTtgtttttctccacatcatag	9	15	8	9	1	2	1	1	1	1	0	3	2	2	1	2	1	1	4	2	1	3	6	rs182693914		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:26056427T>G	ENST00000343677.2	-	1	272	c.230A>C	c.(229-231)aAc>aCc	p.N77T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	77	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						GATACGGCTGTTGTTTTTCTC	0.527																																					p.N77T		.											.	HIST1H1C-231	0			c.A230C						.						106	111	109					6																	26056427		2203	4300	6503	SO:0001583	missense	3006	exon1			CGGCTGTTGTTTT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"Histones / Replication-dependent"	4716	protein-coding gene	gene with protein product		142710	"H1 histone family, member 2", "histone 1, H1c"	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.230A>C	6.37:g.26056427T>G	ENSP00000339566:p.Asn77Thr	Somatic	162	2		WXS	Illumina HiSeq	Phase_I	476	201	NM_005319	0	0	40	46	6	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.688031	0.68271	.	.	ENSG00000187837	ENST00000343677	T	0.08984	3.03	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.152097	0.56097	D	0.000023	T	0.24275	0.0588	M	0.85945	2.785	0.80722	D	1	D	0.64830	0.994	D	0.71870	0.975	T	0.02617	-1.1133	10	0.66056	D	0.02	-32.5039	15.3144	0.74062	0.0:0.0:0.0:1.0	.	77	P16403	H12_HUMAN	T	77	ENSP00000339566:N77T	ENSP00000339566:N77T	N	-	2	0	HIST1H1C	26164406	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	6.087000	0.71362	2.271000	0.75665	0.533000	0.62120	AAC	.		0.527	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056427	T	G	26056427	3	3	51	1	0	0	0	0	1	0	0	0	7145	1725	60	5	415	5	HIST1H1C	6	26056427	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8548499	26056427	145058640	92	4780											
BTN3A2	11118	bcgsc.ca	37	chr6	26370630	26370630	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgcaggtccaccggctggTacccccaaccccaaatacag	11	5	9	16	1	0	0	0	0	0	0	1	0	1	0	6	3	4	3	6	3	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:26370630T>G	ENST00000356386.2	+	5	702	c.514T>G	c.(514-516)Tac>Gac	p.Y172D	BTN3A2_ENST00000396948.1_Missense_Mutation_p.Y172D|BTN3A2_ENST00000396934.3_Missense_Mutation_p.Y149D|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000508906.2_Missense_Mutation_p.Y130D|BTN3A2_ENST00000377708.2_Missense_Mutation_p.Y172D|BTN3A2_ENST00000527422.1_Missense_Mutation_p.Y172D	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	172					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						CACCGGCTGGTACCCCCAACC	0.537																																					p.Y172D													.	BTN3A2-90	0			c.T514G						.						118	106	110					6																	26370630		2203	4300	6503	SO:0001583	missense	11118	exon3			GGCTGGTACCCCC	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.514T>G	6.37:g.26370630T>G	ENSP00000348751:p.Tyr172Asp	Somatic	106	0		WXS	Illumina HiSeq	Phase_1	96	51	NM_001197246	0	0	68	75	7	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	.	.	.	.	.	.	.	.	.	.	t	11.20	1.569103	0.28003	.	.	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.15952	2.38;3.13;3.13;3.13;3.13;3.13;3.13	2.31	1.11	0.20524	Immunoglobulin-like fold (1);	.	.	.	.	T	0.19087	0.0458	M	0.92649	3.33	0.09310	N	1	P;P	0.49783	0.928;0.747	P;B	0.49922	0.626;0.422	T	0.09015	-1.0694	9	0.87932	D	0	.	4.3039	0.10937	0.0:0.1712:0.0:0.8288	.	149;172	F8W6E0;P78410	.;BT3A2_HUMAN	D	130;172;172;172;149;172;172;130	ENSP00000435952:Y130D;ENSP00000432138:Y172D;ENSP00000348751:Y172D;ENSP00000380140:Y149D;ENSP00000366937:Y172D;ENSP00000380152:Y172D;ENSP00000442687:Y130D	ENSP00000348751:Y172D	Y	+	1	0	BTN3A2	26478609	0.958000	0.32768	0.007000	0.13788	0.004000	0.04260	1.202000	0.32271	0.320000	0.23234	-0.722000	0.03604	TAC	.		0.537	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2			G	26370630	T	G	26370630	3	3	51	1	0	0	0	0	1	0	0	0	1566	1638	57	5	524	5	BTN3A2	6	26370630	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	314203	26370630	144744437	93	4781											
TRIM39	56658	bcgsc.ca	37	chr6	30297131	30297131	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttagaggctggggcctctGcagcctctacagctgcggct	5	10	14	12	1	2	1	0	0	2	1	2	1	2	1	2	4	5	5	2	4	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:30297131G>C	ENST00000396547.1	+	2	197	c.37G>C	c.(37-39)Gca>Cca	p.A13P	HCG18_ENST00000413358.2_RNA|HCG18_ENST00000602290.1_RNA|HCG18_ENST00000602550.1_RNA|TRIM39_ENST00000396548.1_Missense_Mutation_p.A13P|HCG18_ENST00000426882.1_RNA|TRIM39_ENST00000540416.1_Missense_Mutation_p.A13P|TRIM39_ENST00000376656.4_Missense_Mutation_p.A13P|HCG18_ENST00000412685.2_RNA|TRIM39-RPP21_ENST00000513556.1_5'Flank|HCG18_ENST00000454269.1_RNA|TRIM39_ENST00000376659.5_Missense_Mutation_p.A13P|HCG18_ENST00000438412.1_RNA|HCG18_ENST00000454129.1_RNA|TRIM39_ENST00000396551.3_Missense_Mutation_p.A13P			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	13					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						TGGGGCCTCTGCAGCCTCTAC	0.478																																					p.A13P													.	TRIM39-161	0			c.G37C						.						104	138	126					6																	30297131		1507	2708	4215	SO:0001583	missense	56658	exon3			GCCTCTGCAGCCT	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10065	protein-coding gene	gene with protein product		605700	"ring finger protein 23", "tripartite motif-containing 39"	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.37G>C	6.37:g.30297131G>C	ENSP00000379796:p.Ala13Pro	Somatic	271	1		WXS	Illumina HiSeq	Phase_1	148	70	NM_172016	0	0	6	7	1	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Missense_Mutation	SNP	ENST00000396547.1	37	CCDS34377.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.621641	0.46736	.	.	ENSG00000204599	ENST00000458516;ENST00000440271;ENST00000396551;ENST00000376656;ENST00000545104;ENST00000540416;ENST00000449040;ENST00000428728;ENST00000396548;ENST00000428404;ENST00000376659;ENST00000428555;ENST00000396547	T;T;T;T;T;T;T;T;T;T;T	0.80909	-0.34;-1.3;-0.0;-0.03;0.03;-0.28;-0.0;-1.43;-0.0;1.25;-0.03	4.87	4.0	0.46444	.	0.000000	0.40908	D	0.000988	T	0.39545	0.1082	N	0.08118	0	0.35341	D	0.786512	B;P	0.35656	0.38;0.514	B;B	0.29524	0.103;0.093	T	0.38520	-0.9657	10	0.29301	T	0.29	.	7.4849	0.27427	0.1893:0.0:0.8107:0.0	.	13;13	Q9HCM9;Q9HCM9-2	TRI39_HUMAN;.	P	13	ENSP00000405928:A13P;ENSP00000394768:A13P;ENSP00000379800:A13P;ENSP00000365844:A13P;ENSP00000439400:A13P;ENSP00000406019:A13P;ENSP00000379797:A13P;ENSP00000405498:A13P;ENSP00000365847:A13P;ENSP00000397952:A13P;ENSP00000379796:A13P	ENSP00000365844:A13P	A	+	1	0	TRIM39	30405110	0.994000	0.37717	1.000000	0.80357	0.958000	0.62258	2.069000	0.41481	1.275000	0.44379	0.561000	0.74099	GCA	.		0.478	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016		C	30297131	G	C	30297131	3	2	51	1	0	0	0	0	1	0	0	0	16546	1319	46	4	39	4	TRIM39	6	30297131	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	3926501	30297131	140817936	94	4782											
DST	667	bcgsc.ca	37	chr6	56417908	56417908	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgagcaagctattggctgTgttgttcagtaattctacca	10	14	9	8	0	2	1	1	1	1	0	2	1	2	1	1	1	3	6	1	1	4	7	rs78180015		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:56417908T>G	ENST00000361203.3	-	57	15056	c.15049A>C	c.(15049-15051)Aca>Cca	p.T5017P	DST_ENST00000421834.2_Missense_Mutation_p.T2931P|DST_ENST00000244364.6_Missense_Mutation_p.T2605P|DST_ENST00000370788.2_Missense_Mutation_p.T2931P|DST_ENST00000446842.2_Missense_Mutation_p.T4693P|DST_ENST00000370769.4_Missense_Mutation_p.T5019P|DST_ENST00000370754.5_Missense_Mutation_p.T5197P|DST_ENST00000312431.6_3'UTR			Q03001	DYST_HUMAN	dystonin	5017					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTATTGGCTGTGTTGTTCAGT	0.413																																					p.T2605P													.	DST-523	0			c.A7813C						.						152	151	151					6																	56417908		1883	4123	6006	SO:0001583	missense	667	exon42			TGGCTGTGTTGTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.15049A>C	6.37:g.56417908T>G	ENSP00000354508:p.Thr5017Pro	Somatic	159	0		WXS	Illumina HiSeq	Phase_1	151	60	NM_015548	0	0	9	10	1	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	T	9.647	1.140469	0.21205	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.76	2.67	0.31697	.	0.535968	0.16734	N	0.201714	T	0.10337	0.0253	L	0.40543	1.245	0.27971	N	0.936394	P;P;B;B;B	0.37398	0.593;0.592;0.449;0.09;0.211	B;B;B;B;B	0.34489	0.124;0.184;0.12;0.046;0.104	T	0.13150	-1.0520	9	0.32370	T	0.25	.	5.3734	0.16152	0.2714:0.5297:0.0:0.1989	.	2931;5019;5197;5017;2605	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	P	2605;5197;5019;2931;4693;2931;5017	ENSP00000244364:T2605P;ENSP00000359790:T5197P;ENSP00000359805:T5019P;ENSP00000400883:T2931P;ENSP00000393645:T4693P;ENSP00000359824:T2931P;ENSP00000354508:T5017P	ENSP00000244364:T2605P	T	-	1	0	DST	56525867	0.683000	0.27633	0.300000	0.25030	0.984000	0.73092	1.334000	0.33827	0.288000	0.22398	0.533000	0.62120	ACA	.		0.413	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56417908	T	G	56417908	3	3	51	1	0	0	0	0	1	0	0	0	4794	1696	59	5	7874	5	DST	6	56417908	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	26120777	56417908	114697159	95	4783											
SMPD2	6610	broad.mit.edu	37	chr6	109764877	109764877	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgtgtcctggcggctggAggaggggccggggaagctgc	4	7	21	9	2	0	0	0	0	0	0	1	3	1	3	2	8	2	2	2	8	1	0	rs142982624|rs370460899	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:109764877A>G	ENST00000258052.3	+	10	1400	c.1041A>G	c.(1039-1041)ggA>ggG	p.G347G	PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	347					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		TGGCGGCTGGAGGAGGGGCCG	0.632																																					p.G347G													.	SMPD2-90	0			c.A1041G						.						41	52	48					6																	109764877		2202	4300	6502	SO:0001819	synonymous_variant	6610	exon10			GGCTGGAGGAGGG	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.1041A>G	6.37:g.109764877A>G		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	111	30	NM_003080	0	0	6	6	0	Q5TED1|Q9BWR3	Silent	SNP	ENST00000258052.3	37	CCDS5075.1																																																																																			.		0.632	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			G	109764877	A	G	109764877	2	3	51	1	0	0	0	0	0	0	0	1	14837	291	11	3		3	SMPD2	6	109764877	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	53346969	109764877	61350190	96	4784											
VGLL2	245806	bcgsc.ca	37	chr6	117589438	117589438	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctcctcattttccagccaaAccccagccagtataaaagag	13	8	6	14	0	1	1	1	0	0	1	3	1	3	1	6	0	3	2	6	0	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:117589438A>C	ENST00000326274.5	+	2	365	c.175A>C	c.(175-177)Acc>Ccc	p.T59P	VGLL2_ENST00000352536.3_Missense_Mutation_p.T59P	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	59					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		TTCCAGCCAAACCCCAGCCAG	0.532																																					p.T59P													.	VGLL2-90	0			c.A175C						.						108	134	125					6																	117589438		2202	4300	6502	SO:0001583	missense	245806	exon2			AGCCAAACCCCAG	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"vestigial like 2 (Drosophila)"			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.175A>C	6.37:g.117589438A>C	ENSP00000320957:p.Thr59Pro	Somatic	320	2		WXS	Illumina HiSeq	Phase_1	602	210	NM_182645	0	0	0	0	0	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	37	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.342450	0.41498	.	.	ENSG00000170162	ENST00000352536;ENST00000326274	T	0.46819	0.86	5.05	5.05	0.67936	.	0.409080	0.24147	N	0.041111	T	0.10594	0.0259	N	0.08118	0	0.30774	N	0.742725	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.10177	-1.0641	10	0.26408	T	0.33	-11.3886	7.1855	0.25797	0.8309:0.0:0.1691:0.0	.	59;59	Q8N8G2-2;Q8N8G2	.;VGLL2_HUMAN	P	59	ENSP00000320957:T59P	ENSP00000320957:T59P	T	+	1	0	VGLL2	117696131	0.377000	0.25106	1.000000	0.80357	0.993000	0.82548	0.615000	0.24329	2.123000	0.65237	0.459000	0.35465	ACC	.		0.532	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		C	117589438	A	C	117589438	3	2	51	1	0	0	0	0	1	0	0	0	17192	43	2	5	181	5	VGLL2	6	117589438	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	7824561	117589438	53525629	97	4785											
FAM184A	79632	bcgsc.ca	37	chr6	119282964	119282964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttaggtggcactggctgTggaagtggtttgctgctgtt	4	15	15	7	0	0	0	0	0	0	0	0	1	0	1	1	5	2	6	1	5	2	4	rs534758163	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:119282964T>G	ENST00000338891.7	-	17	3746	c.3303A>C	c.(3301-3303)ccA>ccC	p.P1101P	FAM184A_ENST00000352896.5_Silent_p.P932P|FAM184A_ENST00000368475.4_Silent_p.P897P|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000521531.1_Silent_p.P1017P	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	1101						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GCACTGGCTGTGGAAGTGGTT	0.448													T|||	6	0.00119808	0.0023	0	5008	,	,		15675	0		0.003	False		,,,				2504	0				p.P1101P													.	FAM184A-519	0			c.A3303C						.						191	198	196					6																	119282964		1937	4147	6084	SO:0001819	synonymous_variant	79632	exon17			TGGCTGTGGAAGT	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.3303A>C	6.37:g.119282964T>G		Somatic	278	1		WXS	Illumina HiSeq	Phase_1	51	23	NM_024581	0	0	6	6	0	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Silent	SNP	ENST00000338891.7	37	CCDS43499.1																																																																																			.		0.448	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		G	119282964	T	G	119282964	2	3	51	1	0	0	0	0	0	0	0	1	5527	1683	59	5		5	FAM184A	6	119282964	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1693526	119282964	51832103	98	4786											
PBOV1	59351	bcgsc.ca	37	chr6	138539226	138539226	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caatgtgaataatatggcttCtgaagataatgaggaacatt	16	12	9	4	0	1	4	0	3	1	1	1	5	1	5	0	2	1	1	0	2	7	5	rs200344940		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:138539226C>T	ENST00000527246.2	-	1	401	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	103						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		AATATGGCTTCTGAAGATAAT	0.388																																					p.E103K													.	.	0			c.G307A						.						187	193	191					6																	138539226		2203	4300	6503	SO:0001583	missense	59351	exon1			TGGCTTCTGAAGA	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.307G>A	6.37:g.138539226C>T	ENSP00000432353:p.Glu103Lys	Somatic	127	0		WXS	Illumina HiSeq	Phase_1	62	24	NM_021635	0	0	0	0	0		Missense_Mutation	SNP	ENST00000527246.2	37	CCDS5190.1	.	.	.	.	.	.	.	.	.	.	C	7.997	0.754479	0.15778	.	.	ENSG00000254440	ENST00000527246	T	0.44482	0.92	3.24	-2.56	0.06268	.	.	.	.	.	T	0.06005	0.0156	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.31503	-0.9941	9	0.87932	D	0	.	0.2202	0.00167	0.2162:0.2517:0.185:0.3472	.	103	Q9GZY1	PBOV1_HUMAN	K	103	ENSP00000432353:E103K	ENSP00000432353:E103K	E	-	1	0	PBOV1	138580919	0.927000	0.31430	0.000000	0.03702	0.050000	0.14768	2.144000	0.42197	-0.465000	0.06953	-0.492000	0.04666	GAA	.		0.388	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635		T	138539226	C	T	138539226	3	4	51	1	0	0	0	0	1	0	0	0	11516	922	32	2	104	2	PBOV1	6	138539226	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	19256262	138539226	32575841	99	4787											
PHACTR2	9749	bcgsc.ca	37	chr6	144086447	144086447	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctaaagcatcagcttcGccatccacttcatccacctc	9	10	5	17	1	3	0	2	0	1	0	7	0	5	0	4	1	2	3	4	1	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:144086447G>C	ENST00000427704.2	+	6	841	c.711G>C	c.(709-711)tcG>tcC	p.S237S	PHACTR2_ENST00000440869.2_Silent_p.S248S|PHACTR2_ENST00000305766.6_Silent_p.S157S|PHACTR2_ENST00000367584.4_Silent_p.S225S|PHACTR2_ENST00000367582.3_Silent_p.S168S	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	237							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		CATCAGCTTCGCCATCCACTT	0.433																																					p.S248S	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)												.	PHACTR2-92	0			c.G744C						.						96	97	97					6																	144086447		1963	4155	6118	SO:0001819	synonymous_variant	9749	exon6			AGCTTCGCCATCC	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"Phosphatase and actin regulators"	20956	protein-coding gene	gene with protein product		608724	"chromosome 6 open reading frame 56"	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.711G>C	6.37:g.144086447G>C		Somatic	142	0		WXS	Illumina HiSeq	Phase_1	76	30	NM_001100164	0	0	11	11	0	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	37	CCDS47492.1																																																																																			.		0.433	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721		C	144086447	G	C	144086447	2	2	51	1	0	0	0	0	0	0	0	1	11836	1074	38	4		4	PHACTR2	6	144086447	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	5547221	144086447	27028620	100	4788											
UTRN	7402	bcgsc.ca	37	chr6	144808805	144808805	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgagaaactggaggctttcaAcagccgatatgaagatctaa	15	9	10	7	1	2	3	1	2	1	2	2	6	2	4	1	2	3	1	1	2	5	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:144808805A>C	ENST00000367545.3	+	28	3944	c.3944A>C	c.(3943-3945)aAc>aCc	p.N1315T		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1315					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAGGCTTTCAACAGCCGATAT	0.478																																					p.N1315T													.	UTRN-95	0			c.A3944C						.						88	95	93					6																	144808805		2203	4300	6503	SO:0001583	missense	7402	exon28			CTTTCAACAGCCG	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"utrophin (homologous to dystrophin)"	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.3944A>C	6.37:g.144808805A>C	ENSP00000356515:p.Asn1315Thr	Somatic	147	0		WXS	Illumina HiSeq	Phase_1	98	52	NM_007124	0	0	4	4	0	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.970742	0.74246	.	.	ENSG00000152818	ENST00000367545	T	0.14144	2.53	5.13	3.95	0.45737	.	0.000000	0.56097	D	0.000040	T	0.24160	0.0585	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.02457	-1.1156	10	0.72032	D	0.01	.	11.1426	0.48411	0.927:0.0:0.073:0.0	.	1315	P46939	UTRO_HUMAN	T	1315	ENSP00000356515:N1315T	ENSP00000356515:N1315T	N	+	2	0	UTRN	144850498	1.000000	0.71417	0.635000	0.29338	0.932000	0.56968	9.287000	0.95975	0.885000	0.36088	0.533000	0.62120	AAC	.		0.478	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			C	144808805	A	C	144808805	3	2	51	1	0	0	0	0	1	0	0	0	17136	43	2	5	4054	5	UTRN	6	144808805	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	722358	144808805	26306262	101	4789											
SYNE1	23345	bcgsc.ca	37	chr6	152470619	152470619	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatgttacatacaggcaggCggatcagtttcttatggtat	11	13	10	7	1	2	0	1	0	1	0	2	1	2	1	0	4	2	4	0	4	5	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:152470619C>G	ENST00000367255.5	-	136	25236	c.24635G>C	c.(24634-24636)cGc>cCc	p.R8212P	SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000354674.4_Missense_Mutation_p.R367P|SYNE1_ENST00000423061.1_Missense_Mutation_p.R8141P|SYNE1_ENST00000539504.1_Missense_Mutation_p.R367P|SYNE1_ENST00000341594.5_Missense_Mutation_p.R7824P|SYNE1_ENST00000448038.1_Missense_Mutation_p.R8141P|SYNE1_ENST00000265368.4_Missense_Mutation_p.R8212P|SYNE1_ENST00000356820.4_Missense_Mutation_p.R2736P	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8212					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TACAGGCAGGCGGATCAGTTT	0.468										HNSCC(10;0.0054)																											p.R8212P													.	SYNE1-607	0			c.G24635C						.						83	80	81					6																	152470619		2203	4300	6503	SO:0001583	missense	23345	exon136			GGCAGGCGGATCA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.24635G>C	6.37:g.152470619C>G	ENSP00000356224:p.Arg8212Pro	Somatic	101	1		WXS	Illumina HiSeq	Phase_1	89	39	NM_182961	0	0	0	0	0	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918688	0.92249	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.58358	0.41;4.54;1.35;0.38;0.34;0.39;0.55;2.45;1.52;4.53	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000012	T	0.65228	0.2671	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.998	D;D;D;D;D	0.87578	0.992;0.992;0.996;0.998;0.953	T	0.67027	-0.5774	10	0.72032	D	0.01	.	19.4997	0.95089	0.0:1.0:0.0:0.0	.	8212;8212;8141;8141;414	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	P	8212;367;858;8141;8212;8141;7824;2736;374;369;1134;367	ENSP00000356224:R8212P;ENSP00000441052:R367P;ENSP00000356226:R858P;ENSP00000396024:R8141P;ENSP00000265368:R8212P;ENSP00000390975:R8141P;ENSP00000341887:R7824P;ENSP00000349276:R2736P;ENSP00000356220:R1134P;ENSP00000346701:R367P	ENSP00000265368:R8212P	R	-	2	0	SYNE1	152512312	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.674000	0.54598	2.611000	0.88343	0.655000	0.94253	CGC	.		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152470619	C	G	152470619	3	3	51	1	0	0	0	0	1	0	0	0	15477	768	27	4	1875	4	SYNE1	6	152470619	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	7661814	152470619	18644448	102	4790											
NOX3	50508	bcgsc.ca	37	chr6	155776042	155776042	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtgcggatgctcgtgccCaagccagtgttgactgtcca	8	9	12	12	2	0	1	0	1	0	0	2	2	1	2	3	1	4	2	3	1	1	1	rs200865731		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:155776042C>A	ENST00000159060.2	-	3	260	c.158G>T	c.(157-159)tGg>tTg	p.W53L		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	53					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TGCTCGTGCCCAAGCCAGTGT	0.368																																					p.W53L													.	NOX3-91	0			c.G158T						.																																			SO:0001583	missense	50508	exon3			CGTGCCCAAGCCA	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.158G>T	6.37:g.155776042C>A	ENSP00000159060:p.Trp53Leu	Somatic	38	0		WXS	Illumina HiSeq	Phase_1	12	9	NM_015718	0	0	0	0	0	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	C	9.987	1.229856	0.22542	.	.	ENSG00000074771	ENST00000159060	D	0.94931	-3.56	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000014	D	0.93429	0.7904	L	0.35854	1.095	0.52501	D	0.999955	D	0.89917	1.0	D	0.83275	0.996	D	0.88911	0.3359	10	0.02654	T	1	-13.8466	20.3011	0.98612	0.0:1.0:0.0:0.0	.	53	Q9HBY0	NOX3_HUMAN	L	53	ENSP00000159060:W53L	ENSP00000159060:W53L	W	-	2	0	NOX3	155817734	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	6.321000	0.72881	2.804000	0.96469	0.650000	0.86243	TGG	C|0.999;A|0.001		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			A	155776042	C	A	155776042	3	1	51	1	0	0	0	0	1	0	0	0	10583	595	21	4	1592	4	NOX3	6	155776042	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	3305423	155776042	15339025	103	4791											
PLG	5340	broad.mit.edu	37	chr6	161152867	161152867	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggactgggctgcccaggagcCccatagacacagcattttca	10	7	11	13	0	1	1	1	0	0	1	1	3	1	3	3	3	3	2	3	3	1	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:161152867C>A	ENST00000308192.9	+	12	1592	c.1529C>A	c.(1528-1530)cCc>cAc	p.P510H		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	510	Kringle 5. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	GCCCAGGAGCCCCATAGACAC	0.527																																					p.P510H													.	PLG-94	0			c.C1529A	GRCh37	CM068062	PLG	M		.						89	96	93					6																	161152867		2203	4300	6503	SO:0001583	missense	5340	exon12			AGGAGCCCCATAG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1529C>A	6.37:g.161152867C>A	ENSP00000308938:p.Pro510His	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	110	4	NM_000301	0	0	0	0	0	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.296297	0.60086	.	.	ENSG00000122194	ENST00000308192	T	0.66638	-0.22	4.47	4.47	0.54385	Kringle (4);Kringle-like fold (1);	0.000000	0.39146	U	0.001457	D	0.84871	0.5568	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88999	0.3420	10	0.87932	D	0	.	12.4909	0.55899	0.0:1.0:0.0:0.0	.	510	P00747	PLMN_HUMAN	H	510	ENSP00000308938:P510H	ENSP00000308938:P510H	P	+	2	0	PLG	161072857	1.000000	0.71417	0.999000	0.59377	0.285000	0.27093	5.440000	0.66563	2.305000	0.77605	0.557000	0.71058	CCC	.		0.527	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		A	161152867	C	A	161152867	3	1	51	1	0	0	0	0	1	0	0	0	12112	623	22	4	1579	4	PLG	6	161152867	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	5376825	161152867	9962200	104	4792											
SFT2D1	113402	bcgsc.ca	37	chr6	166738061	166738061	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcaatatgcagaataacAcagccagtcccttcttatgc	13	10	6	12	0	1	1	0	0	1	1	2	1	2	1	2	0	5	2	2	0	5	4	rs78154309		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:166738061A>C	ENST00000361731.3	-	6	483	c.374T>G	c.(373-375)gTg>gGg	p.V125G	SFT2D1_ENST00000487841.1_5'UTR	NM_145169.1	NP_660152.1			SFT2 domain containing 1											NS(1)|central_nervous_system(1)|large_intestine(3)|upper_aerodigestive_tract(1)	6		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)		OV - Ovarian serous cystadenocarcinoma(33;2.63e-19)|BRCA - Breast invasive adenocarcinoma(81;4.92e-06)|GBM - Glioblastoma multiforme(31;4.58e-05)		GCAGAATAACACAGCCAGTCC	0.368																																					p.V125G													.	SFT2D1-514	0			c.T374G						.						117	106	110					6																	166738061		2203	4300	6503	SO:0001583	missense	113402	exon6			AATAACACAGCCA	AF041429	CCDS5292.1	6q27	2008-02-05	2005-07-25	2005-07-25	ENSG00000198818	ENSG00000198818			21102	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 83"	C6orf83			Standard	NM_145169		Approved	MGC19825, pRGR1	uc003qux.3	Q8WV19	OTTHUMG00000016001	ENST00000361731.3:c.374T>G	6.37:g.166738061A>C	ENSP00000354590:p.Val125Gly	Somatic	69	0		WXS	Illumina HiSeq	Phase_1	51	22	NM_145169	0	0	53	72	19		Missense_Mutation	SNP	ENST00000361731.3	37	CCDS5292.1	.	.	.	.	.	.	.	.	.	.	A	9.538	1.112522	0.20795	.	.	ENSG00000198818	ENST00000361731	T	0.60797	0.16	5.07	3.9	0.45041	.	0.327095	0.28595	N	0.014781	T	0.32041	0.0816	L	0.53617	1.68	0.21020	N	0.999807	B	0.30937	0.301	B	0.29440	0.102	T	0.25710	-1.0124	10	0.87932	D	0	-17.8432	9.058	0.36416	0.9119:0.0:0.0881:0.0	.	125	Q8WV19	SFT2A_HUMAN	G	125	ENSP00000354590:V125G	ENSP00000354590:V125G	V	-	2	0	SFT2D1	166658051	0.575000	0.26692	0.001000	0.08648	0.312000	0.27988	6.815000	0.75242	0.762000	0.33152	0.519000	0.50382	GTG	.		0.368	SFT2D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043061.2	NM_145169		C	166738061	A	C	166738061	3	2	51	1	0	0	0	0	1	0	0	0	14217	159	6	5	117	5	SFT2D1	6	166738061	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	5585194	166738061	4377006	105	4793											
INTS1	26173	bcgsc.ca	37	chr7	1524994	1524994	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggcgaggcaggtcccgcaGcagccactgatagccctgca	9	4	13	15	2	0	1	0	1	0	0	1	2	1	1	3	3	4	4	3	3	1	1	rs201952847		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:1524994G>C	ENST00000404767.3	-	23	3173	c.3088C>G	c.(3088-3090)Ctg>Gtg	p.L1030V	INTS1_ENST00000389470.4_Missense_Mutation_p.L1192V	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	1030					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		AGGTCCCGCAGCAGCCACTGA	0.692																																					p.L1030V													.	.	0			c.C3088G						.						32	46	41					7																	1524994		2087	4208	6295	SO:0001583	missense	26173	exon23			CCCGCAGCAGCCA	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.3088C>G	7.37:g.1524994G>C	ENSP00000385722:p.Leu1030Val	Somatic	62	0		WXS	Illumina HiSeq	Phase_1	104	57	NM_001080453	0	0	10	10	0	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	37	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734445	0.69189	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.53857	0.6;0.62	5.31	4.23	0.50019	.	0.000000	0.64402	D	0.000001	T	0.60521	0.2275	L	0.61387	1.9	0.52501	D	0.999954	P;P	0.52316	0.897;0.952	P;P	0.54924	0.764;0.764	T	0.60835	-0.7184	10	0.45353	T	0.12	.	11.3697	0.49692	0.1569:0.0:0.8431:0.0	.	1198;1030	A4D213;Q8N201	.;INT1_HUMAN	V	1030;1192	ENSP00000385722:L1030V;ENSP00000374121:L1192V	ENSP00000374121:L1192V	L	-	1	2	INTS1	1491520	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.675000	0.46875	2.485000	0.83878	0.561000	0.74099	CTG	.		0.692	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			C	1524994	G	C	1524994	3	2	51	1	0	0	0	0	1	0	0	0	7796	962	34	4	3588	4	INTS1	7	1524994	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		1524994	157613669	106	4794											
HOXA4	3201	hgsc.bcm.edu	37	chr7	27170159	27170159	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcagtgggctctcggccgCcgcccgcgtgagggagctgg	4	5	19	13	5	1	1	0	1	1	0	2	2	1	2	3	5	1	3	3	5	0	0	rs6962314	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:27170159C>T	ENST00000360046.5	-	1	259	c.194G>A	c.(193-195)gGc>gAc	p.G65D	HOXA3_ENST00000521401.1_Intron|HOXA-AS2_ENST00000521687.1_RNA|HOXA-AS2_ENST00000521159.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000517550.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA4_ENST00000428284.2_Missense_Mutation_p.G65D	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	65	Pro-rich (part of the transcriptional activation domain).				anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						CTCTCGGCCGCCGCCCGCGTG	0.801													C|||	762	0.152157	0.2284	0.232	5008	,	,		3644	0.1359		0.1014	False		,,,				2504	0.0613				p.G65D		.											.	HOXA4-153	0			c.G194A						.	C	ASP/GLY	255,1391		4,247,572	1	1	1		194	2	1	7	dbSNP_116	1	269,3643		9,251,1696	no	missense	HOXA4	NM_002141.4	94	13,498,2268	TT,TC,CC		6.8763,15.4921,9.4279	probably-damaging	65/321	27170159	524,5034	823	1956	2779	SO:0001583	missense	3201	exon1			CGGCCGCCGCCCG		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"Homeoboxes / ANTP class : HOXL subclass"	5105	protein-coding gene	gene with protein product		142953	"homeo box A4"	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.194G>A	7.37:g.27170159C>T	ENSP00000353151:p.Gly65Asp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	7	NM_002141	0	0	0	0	0	A4D180|O43366	Missense_Mutation	SNP	ENST00000360046.5	37	CCDS5405.1	367	0.16804029304029305	137	0.2784552845528455	73	0.20165745856353592	75	0.13111888111888112	82	0.10817941952506596	C	17.17	3.321133	0.60634	0.154921	0.068763	ENSG00000197576	ENST00000360046;ENST00000428284	T;T	0.50277	0.75;0.75	4.04	2.04	0.26737	.	3.419590	0.01272	U	0.009493	T	0.00012	0.0000	L	0.29908	0.895	0.45634	P	0.001434999999999964	B	0.24186	0.099	B	0.19391	0.025	T	0.10776	-1.0615	9	0.33141	T	0.24	.	5.9117	0.19031	0.0:0.5528:0.2427:0.2045	rs6962314;rs58352262	65	Q00056	HXA4_HUMAN	D	65	ENSP00000353151:G65D;ENSP00000408845:G65D	ENSP00000353151:G65D	G	-	2	0	HOXA4	27136684	0.002000	0.14202	0.997000	0.53966	0.870000	0.49936	1.131000	0.31406	0.828000	0.34709	0.298000	0.19748	GGC	C|0.832;T|0.168		0.801	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4			T	27170159	C	T	27170159	3	4	51	1	0	0	0	0	1	0	0	0	7315	739	26	2	776	2	HOXA4	7	27170159	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	25645165	27170159	131968504	107	4795											
URGCP	55665	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	43916495	43916495	+	Frame_Shift_Del	DEL	C	C	-																															ccagtgcccggaagccgtcgCcctgtttctccatctgggct																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:43916495delC	ENST00000453200.1	-	6	3060	c.2567delG	c.(2566-2568)ggcfs	p.G856fs	URGCP_ENST00000443736.1_Frame_Shift_Del_p.G813fs|URGCP_ENST00000447717.3_Frame_Shift_Del_p.G813fs|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000223341.7_Frame_Shift_Del_p.G813fs|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000336086.6_Frame_Shift_Del_p.G813fs|URGCP_ENST00000402306.3_Frame_Shift_Del_p.G847fs			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	856	VLIG-type G.				cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAAGCCGTCGCCCTGTTTCTC	0.637																																					p.G856fs		.											.	URGCP-94	0			c.2567delG						.						29	31	30					7																	43916495		1994	4175	6169	SO:0001589	frameshift_variant	55665	exon6			.		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2567delG	7.37:g.43916495delC	ENSP00000396918:p.Gly856fs	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	167	39	NM_001077663	0	0	0	0	0	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	37	CCDS47578.1																																																																																			.		0.637	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		-	43916495	C	-	43916495	7	5	51	1	0	1	0	1	0	0	0	0	17059	739	26	0	232	0	URGCP	7	43916495	Frame_Shift_Del	DEL	C	TCGA-B9-4117-01A-01D-1252-08	16746336	43916495	115222168	108	4796											
GCK	2645	ucsc.edu	37	chr7	44186168	44186168	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccacgagcctgagcagcaCaagccgcaccagctcgccca	10	3	10	18	3	0	1	0	1	0	0	2	2	1	1	5	0	5	4	5	0	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:44186168C>A	ENST00000403799.3	-	8	1382	c.913G>T	c.(913-915)Gtg>Ttg	p.V305L	GCK_ENST00000395796.3_Missense_Mutation_p.V304L|GCK_ENST00000437084.1_Missense_Mutation_p.V288L|GCK_ENST00000345378.2_Missense_Mutation_p.V306L	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	305	Hexokinase type-2.				calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						CTGAGCAGCACAAGCCGCACC	0.627																																					p.V306L													.	GCK-416	0			c.G916T						.						100	88	92					7																	44186168		2203	4300	6503	SO:0001583	missense	2645	exon8			GCAGCACAAGCCG	AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.913G>T	7.37:g.44186168C>A	ENSP00000384247:p.Val305Leu	Somatic	81	0		WXS	Illumina HiSeq		346	107	NM_033507	0	0	0	0	0	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	ENST00000403799.3	37	CCDS5479.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.921425	0.52653	.	.	ENSG00000106633	ENST00000403799;ENST00000395796;ENST00000345378;ENST00000437084	D;D;D;D	0.96940	-4.18;-4.18;-4.18;-4.18	4.77	2.9	0.33743	Hexokinase, C-terminal (1);	0.192236	0.44097	N	0.000484	D	0.94470	0.8220	M	0.67625	2.065	0.58432	D	0.999999	B;B;B	0.33044	0.395;0.013;0.343	B;B;B	0.28916	0.096;0.027;0.058	D	0.91605	0.5298	10	0.56958	D	0.05	-17.2758	14.3797	0.66902	0.0:0.7175:0.2825:0.0	.	305;306;304	P35557;P35557-2;P35557-3	HXK4_HUMAN;.;.	L	305;304;306;288	ENSP00000384247:V305L;ENSP00000379142:V304L;ENSP00000223366:V306L;ENSP00000402840:V288L	ENSP00000223366:V306L	V	-	1	0	GCK	44152693	0.936000	0.31750	0.464000	0.27143	0.554000	0.35429	2.046000	0.41260	0.402000	0.25451	-0.282000	0.10007	GTG	.		0.627	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			A	44186168	C	A	44186168	3	1	51	1	0	0	0	0	1	0	0	0	6313	478	17	4	496	4	GCK	7	44186168	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	269673	44186168	114952495	109	4797											
TRIM73	375593	hgsc.bcm.edu	37	chr7	75028469	75028469	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaggctccctggggacccAgagcccaaggtctgcgtgca	7	6	14	14	1	1	2	0	1	1	1	2	3	2	3	3	4	3	2	3	4	1	0	rs142958137	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:75028469A>G	ENST00000437796.1	+	1	271	c.252A>G	c.(250-252)ccA>ccG	p.P84P	TRIM73_ENST00000323819.3_Silent_p.P84P|TRIM73_ENST00000447409.2_Silent_p.P84P|TRIM73_ENST00000450434.1_5'UTR|TRIM73_ENST00000430211.1_Silent_p.P84P			Q86UV7	TRI73_HUMAN	tripartite motif containing 73	84						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)	4						CTGGGGACCCAGAGCCCAAGG	0.667													G|||	3571	0.713059	0.7163	0.6974	5008	,	,		6749	0.874		0.5527	False		,,,				2504	0.7188				p.P84P		.											.	TRIM74-40	0			c.A252G						.						9	28	23					7																	75028469		810	2167	2977	SO:0001819	synonymous_variant	378108	exon2			GGACCCAGAGCCC	AF498998	CCDS34665.1	7q11.23	2013-01-09	2011-01-25	2006-03-31		ENSG00000178809		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	18162	protein-coding gene	gene with protein product		612549	"tripartite motif-containing 50B", "tripartite motif-containing 73"	TRIM50B			Standard	NM_198924		Approved		uc003udc.1	Q86UV7		ENST00000437796.1:c.252A>G	7.37:g.75028469A>G		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	14	11	NM_198853	0	0	0	8	8	Q8N0S3	Silent	SNP	ENST00000437796.1	37	CCDS34665.1																																																																																			.		0.667	TRIM73-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342950.1			G	75028469	A	G	75028469	2	3	51	1	0	0	0	0	0	0	0	1	16579	175	7	3		3	TRIM73	7	75028469	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	30842301	75028469	84110194	110	4798											
ABCB4	5244	bcgsc.ca	37	chr7	87072688	87072688	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctggaccgttgtgctctTcccacagccactacttccaa	8	10	7	16	1	1	0	0	0	1	0	3	1	3	1	4	1	4	3	4	1	2	4	rs201292029	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:87072688T>C	ENST00000265723.4	-	12	1414	c.1303A>G	c.(1303-1305)Aag>Gag	p.K435E	ABCB4_ENST00000359206.3_Missense_Mutation_p.K435E|ABCB4_ENST00000545634.1_Missense_Mutation_p.K435E|ABCB4_ENST00000453593.1_Missense_Mutation_p.K435E|ABCB4_ENST00000358400.3_Missense_Mutation_p.K435E	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	435	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	GTTGTGCTCTTCCCACAGCCA	0.512													t|||	742	0.148163	0.0756	0.1931	5008	,	,		17284	0.2688		0.2237	False		,,,				2504	0.0123				p.K435E													.	ABCB4-96	0			c.A1303G						.						145	134	138					7																	87072688		2203	4300	6503	SO:0001583	missense	5244	exon12			TGCTCTTCCCACA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1303A>G	7.37:g.87072688T>C	ENSP00000265723:p.Lys435Glu	Somatic	183	1		WXS	Illumina HiSeq	Phase_1	85	47	NM_018850	0	0	3	3	0	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	t	27.9	4.870037	0.91587	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.98914	-5.23;-5.23;-5.23;-5.23;-5.23	5.05	5.05	0.67936	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.99563	0.9843	H	0.99475	4.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.99;0.984	D	0.97526	1.0076	10	0.87932	D	0	-14.9061	14.7881	0.69819	0.0:0.0:0.0:1.0	.	435;435;435	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	E	435	ENSP00000352135:K435E;ENSP00000351172:K435E;ENSP00000265723:K435E;ENSP00000392983:K435E;ENSP00000437465:K435E	ENSP00000265723:K435E	K	-	1	0	ABCB4	86910624	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	6.293000	0.72731	1.893000	0.54813	0.383000	0.25322	AAG	.		0.512	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		C	87072688	T	C	87072688	3	2	51	1	0	0	0	0	1	0	0	0	43	1792	62	3	2625	3	ABCB4	7	87072688	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	12044219	87072688	72065975	111	4799											
MUC17	140453	bcgsc.ca	37	chr7	100675714	100675714	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactccattaacaagtacGcctgccagcaccatgccggt	11	7	8	15	2	0	0	0	0	0	0	1	0	1	0	5	1	6	3	5	1	3	2	rs538405099	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:100675714G>C	ENST00000306151.4	+	3	1081	c.1017G>C	c.(1015-1017)acG>acC	p.T339T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	339	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TAACAAGTACGCCTGCCAGCA	0.478													G|||	197	0.0393371	0.0408	0.0648	5008	,	,		24116	0.0278		0.0696	False		,,,				2504	0				p.T339T													.	MUC17-95	0			c.G1017C						.						169	179	176					7																	100675714		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AAGTACGCCTGCC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.1017G>C	7.37:g.100675714G>C		Somatic	334	0		WXS	Illumina HiSeq	Phase_1	250	93	NM_001040105	0	0	0	0	0	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100675714	G	C	100675714	2	2	51	1	0	0	0	0	0	0	0	1	9999	1074	38	4		4	MUC17	7	100675714	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	13603026	100675714	58462949	112	4800											
CAV2	858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116140377	116140377	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgacaaagtgtggatcTgcagccatgccctctttgaa	9	12	9	11	0	2	2	0	2	2	0	2	3	2	3	3	1	3	1	3	1	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:116140377T>A	ENST00000222693.4	+	2	606	c.214T>A	c.(214-216)Tgc>Agc	p.C72S	AC002066.1_ENST00000446355.2_RNA|CAV2_ENST00000462876.1_3'UTR|CAV2_ENST00000393480.2_Missense_Mutation_p.C72S|CAV2_ENST00000343213.2_Intron	NM_001206747.1|NM_001206748.1|NM_001233.4	NP_001193676.1|NP_001193677.1|NP_001224.1	P51636	CAV2_HUMAN	caveolin 2	72					caveola assembly (GO:0070836)|endoplasmic reticulum organization (GO:0007029)|mitochondrion organization (GO:0007005)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of endothelial cell proliferation (GO:0001938)|protein oligomerization (GO:0051259)|regulation of mitosis (GO:0007088)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)|vesicle docking (GO:0048278)|vesicle fusion (GO:0006906)|vesicle organization (GO:0016050)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	D1 dopamine receptor binding (GO:0031748)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|skin(1)	3	all_epithelial(6;1.53e-06)|Lung NSC(10;0.00592)|all_lung(10;0.00642)		STAD - Stomach adenocarcinoma(10;0.00878)			AGTGTGGATCTGCAGCCATGC	0.542																																					p.C72S		.											.	CAV2-90	0			c.T214A						.						169	138	149					7																	116140377		2203	4300	6503	SO:0001583	missense	858	exon2			TGGATCTGCAGCC	AF035752	CCDS5765.1, CCDS5766.1	7q31	2006-02-09			ENSG00000105971	ENSG00000105971			1528	protein-coding gene	gene with protein product		601048				8552590, 10087206	Standard	NM_001233		Approved	CAV	uc003vid.3	P51636	OTTHUMG00000023414	ENST00000222693.4:c.214T>A	7.37:g.116140377T>A	ENSP00000222693:p.Cys72Ser	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	348	92	NM_001233	0	1	100	156	55	A4D0U2|Q9UGM7	Missense_Mutation	SNP	ENST00000222693.4	37	CCDS5766.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420268	0.83559	.	.	ENSG00000105971	ENST00000222693;ENST00000393480	D;D	0.92249	-3.0;-3.0	4.6	4.6	0.57074	.	0.193833	0.56097	D	0.000032	D	0.93213	0.7838	M	0.85197	2.74	0.39643	D	0.970342	P	0.35656	0.514	B	0.41135	0.348	D	0.93194	0.6586	10	0.36615	T	0.2	-15.4697	14.2879	0.66258	0.0:0.0:0.0:1.0	.	72	P51636	CAV2_HUMAN	S	72	ENSP00000222693:C72S;ENSP00000377120:C72S	ENSP00000222693:C72S	C	+	1	0	CAV2	115927613	0.972000	0.33761	1.000000	0.80357	0.995000	0.86356	1.530000	0.36007	1.828000	0.53243	0.460000	0.39030	TGC	.		0.542	CAV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059735.4	NM_001233		A	116140377	T	A	116140377	3	1	51	1	0	0	0	0	1	0	0	0	2700	1580	55	5	220	5	CAV2	7	116140377	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	15464663	116140377	42998286	113	4801											
MET	4233	bcgsc.ca	37	chr7	116380999	116380999	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgttcagtgtggctggTgccacgacaaatgtgtgcga	7	12	13	9	2	1	0	1	0	0	0	1	2	1	0	2	2	2	2	2	2	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:116380999T>G	ENST00000318493.6	+	5	1808	c.1621T>G	c.(1621-1623)Tgc>Ggc	p.C541G	MET_ENST00000495962.1_3'UTR|MET_ENST00000436117.2_Missense_Mutation_p.C541G|MET_ENST00000397752.3_Missense_Mutation_p.C541G			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGTGGCTGGTGCCACGACAA	0.522			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.C541G				Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.T1621G						.						112	115	114					7																	116380999		1964	4139	6103	SO:0001583	missense	4233	exon5	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGCTGGTGCCACG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1621T>G	7.37:g.116380999T>G	ENSP00000317272:p.Cys541Gly	Somatic	115	0		WXS	Illumina HiSeq	Phase_1	81	35	NM_000245	0	0	139	161	22	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557636	0.86231	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.31769	1.48;1.48;1.48	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.60521	0.2275	M	0.83953	2.67	0.80722	D	1	D;P;D;D;D;D;D;D	0.89917	1.0;0.931;0.978;0.998;0.999;0.999;0.995;0.999	D;D;P;D;D;D;P;D	0.87578	0.998;0.948;0.872;0.996;0.99;0.986;0.878;0.976	T	0.65865	-0.6064	10	0.72032	D	0.01	.	16.3594	0.83251	0.0:0.0:0.0:1.0	.	541;541;541;541;541;541;541;541	B5A929;E7EQ94;B5A930;B5A934;B5A937;B5A939;P08581-2;P08581	.;.;.;.;.;.;.;MET_HUMAN	G	541	ENSP00000380860:C541G;ENSP00000317272:C541G;ENSP00000410980:C541G	ENSP00000317272:C541G	C	+	1	0	MET	116168235	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.208000	0.58486	2.266000	0.75297	0.455000	0.32223	TGC	.		0.522	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116380999	T	G	116380999	3	3	51	1	0	0	0	0	1	0	0	0	9510	1696	59	5	1635	5	MET	7	116380999	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	240622	116380999	42757664	114	4802											
NUP205	23165	bcgsc.ca	37	chr7	135290919	135290919	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcagaaactaatggctggAtttgtggagtgtttggattg	10	14	14	3	0	1	1	1	0	0	1	1	4	1	4	0	4	1	2	0	4	2	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:135290919A>G	ENST00000285968.6	+	20	2876	c.2850A>G	c.(2848-2850)ggA>ggG	p.G950G		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	950					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TAATGGCTGGATTTGTGGAGT	0.318																																					p.G950G													.	NUP205-207	0			c.A2850G						.						186	186	186					7																	135290919		2203	4300	6503	SO:0001819	synonymous_variant	23165	exon20			GGCTGGATTTGTG	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.2850A>G	7.37:g.135290919A>G		Somatic	224	0		WXS	Illumina HiSeq	Phase_1	182	63	NM_015135	0	0	16	19	3	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			.		0.318	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			G	135290919	A	G	135290919	2	3	51	1	0	0	0	0	0	0	0	1	10785	320	12	3		3	NUP205	7	135290919	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	18909920	135290919	23847744	115	4803											
SLC13A4	26266	bcgsc.ca	37	chr7	135384143	135384143	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaggaagatgaggctggTggaggtgccgatgatggtgg	8	9	19	5	1	0	3	0	2	0	1	1	6	1	5	2	7	1	1	2	7	1	1	rs201310555		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:135384143T>G	ENST00000354042.4	-	8	1554	c.865A>C	c.(865-867)Acc>Ccc	p.T289P		NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	289					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						ATGAGGCTGGTGGAGGTGCCG	0.507																																					p.T289P													.	SLC13A4-90	0			c.A865C						.						128	113	118					7																	135384143		2203	4300	6503	SO:0001583	missense	26266	exon8			GGCTGGTGGAGGT	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.865A>C	7.37:g.135384143T>G	ENSP00000297282:p.Thr289Pro	Somatic	39	1		WXS	Illumina HiSeq	Phase_1	75	45	NM_012450	0	0	0	0	0	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	37	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.996515	0.35226	.	.	ENSG00000164707	ENST00000354042	T	0.02177	4.41	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.04182	0.0116	N	0.13198	0.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.52815	-0.8525	10	0.02654	T	1	.	14.2529	0.66031	0.0:0.0:0.0:1.0	.	158;289	Q59HF0;Q9UKG4	.;S13A4_HUMAN	P	289	ENSP00000297282:T289P	ENSP00000297282:T289P	T	-	1	0	SLC13A4	135034683	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.054000	0.64275	2.246000	0.74042	0.533000	0.62120	ACC	T|0.999;G|0.001		0.507	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		G	135384143	T	G	135384143	3	3	51	1	0	0	0	0	1	0	0	0	14426	1696	59	5	1051	5	SLC13A4	7	135384143	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	93224	135384143	23754520	116	4804											
OR9A2	135924	hgsc.bcm.edu	37	chr7	142724166	142724166	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgtggtgtagtccttgggaCccagggaagcctagaaggtg	9	9	16	7	0	0	1	0	0	0	1	1	3	1	3	3	4	1	1	3	4	4	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:142724166C>G	ENST00000350513.2	-	1	116	c.54G>C	c.(52-54)ggG>ggC	p.G18G		NM_001001658.1	NP_001001658.1	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A, member 2	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(3)|endometrium(4)|large_intestine(1)|lung(14)|skin(3)	25	Melanoma(164;0.059)					GTCCTTGGGACCCAGGGAAGC	0.408																																					p.G18G		.											.	OR9A2-69	0			c.G54C						.						77	75	76					7																	142724166		2203	4300	6503	SO:0001819	synonymous_variant	135924	exon1			TTGGGACCCAGGG		CCDS34767.1	7q34	2014-07-10			ENSG00000179468	ENSG00000179468		"GPCR / Class A : Olfactory receptors"	15093	protein-coding gene	gene with protein product							Standard	NM_001001658		Approved		uc003wcc.1	Q8NGT5	OTTHUMG00000158386	ENST00000350513.2:c.54G>C	7.37:g.142724166C>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_001001658	0	0	0	0	0	B9EH51|Q6IF71|Q8NGD9	Silent	SNP	ENST00000350513.2	37	CCDS34767.1																																																																																			.		0.408	OR9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350862.1			G	142724166	C	G	142724166	2	3	51	1	0	0	0	0	0	0	0	1	11274	494	18	4		4	OR9A2	7	142724166	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	7340023	142724166	16414497	117	4805											
SSPO	23145	hgsc.bcm.edu	37	chr7	149485465	149485465	+	RNA	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggccccacgtgtccccccAcctgccatgagcagcatcct	6	7	9	19	1	0	1	0	1	0	0	2	1	2	1	8	1	3	2	8	1	0	0	rs200617080		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:149485465A>C	ENST00000378016.2	+	0	3871							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GTGTCCCCCCACCTGCCATGA	0.652																																					p.T1291P		.											.	.	0			c.A3871C						.						32	39	37					7																	149485465		2072	4192	6264			23145	exon27			CCCCCCACCTGCC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149485465A>C		Somatic	36	1		WXS	Illumina HiSeq	Phase_I	175	96	NM_198455	0	0	0	0	0	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.996;C|0.004		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149485465	A	C	149485465	1	2	51	0	1	0	0	0	0	0	0	0	15221	159	6	5		5	SSPO	7	149485465	RNA	SNP	A	TCGA-B9-4117-01A-01D-1252-08	6761299	149485465	9653198	118	4806											
LRRC61	65999	hgsc.bcm.edu	37	chr7	150033986	150033986	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaagccgggagaggctggCggactgcagatcacacccca	11	3	15	12	2	1	3	1	0	0	3	1	6	1	4	3	4	2	2	3	4	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:150033986C>G	ENST00000359623.4	+	3	624	c.36C>G	c.(34-36)ggC>ggG	p.G12G	LRRC61_ENST00000493307.1_Silent_p.G12G|LRRC61_ENST00000323078.7_Silent_p.G12G	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	12										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GAGAGGCTGGCGGACTGCAGA	0.637																																					p.G12G		.											.	LRRC61-90	0			c.C36G						.						47	54	51					7																	150033986		2203	4300	6503	SO:0001819	synonymous_variant	65999	exon2			GGCTGGCGGACTG	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.36C>G	7.37:g.150033986C>G		Somatic	109	2		WXS	Illumina HiSeq	Phase_I	413	108	NM_023942	0	1	43	44	0	B3KUW0|D3DWY8	Silent	SNP	ENST00000359623.4	37	CCDS5901.1																																																																																			.		0.637	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942		G	150033986	C	G	150033986	2	3	51	1	0	0	0	0	0	0	0	1	9042	755	27	4		4	LRRC61	7	150033986	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	548521	150033986	9104677	119	4807											
TMEM176A	55365	ucsc.edu	37	chr7	150500797	150500797	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaagatttccgatatggctaCtcttattacaacagtgcctg	11	13	8	9	1	1	1	0	0	1	1	2	3	2	1	2	1	4	1	2	1	6	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:150500797C>A	ENST00000484928.1	+	5	1013	c.432C>A	c.(430-432)taC>taA	p.Y144*	TMEM176A_ENST00000461345.1_Nonsense_Mutation_p.Y85*|TMEM176A_ENST00000004103.3_Nonsense_Mutation_p.Y144*|TMEM176B_ENST00000447204.2_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	144					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GATATGGCTACTCTTATTACA	0.537																																					p.Y144X													.	TMEM176A-92	0			c.C432A						.						70	75	73					7																	150500797		2203	4300	6503	SO:0001587	stop_gained	55365	exon5			TGGCTACTCTTAT	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.432C>A	7.37:g.150500797C>A	ENSP00000417626:p.Tyr144*	Somatic	76	1		WXS	Illumina HiSeq		204	54	NM_018487	1	2	861	895	31	D3DX00|Q9NYC7	Nonsense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	.	.	.	.	.	.	.	.	.	.	C	8.438	0.850128	0.17034	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	.	.	.	.	.	.	.	3.470060	0.00622	N	0.000457	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-3.8712	.	.	.	.	.	.	.	X	144;144;85;96;85	.	ENSP00000004103:Y144X	Y	+	3	2	TMEM176A	150131730	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.145000	0.16157	0.119000	0.18210	0.121000	0.15741	TAC	.		0.537	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		A	150500797	C	A	150500797	4	1	51	1	0	0	0	0	0	1	0	0	16124	576	20	4	446	4	TMEM176A	7	150500797	Nonsense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	466811	150500797	8637866	120	4808											
GALNTL5	168391	bcgsc.ca	37	chr7	151699853	151699853	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaacagagtatggctggAgcccctgctgcatgccattg	8	9	14	10	0	0	2	0	1	0	1	0	3	0	3	3	3	5	4	3	3	2	2	rs200114484		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:151699853A>G	ENST00000392800.2	+	6	967	c.713A>G	c.(712-714)gAg>gGg	p.E238G	GALNTL5_ENST00000431418.2_Missense_Mutation_p.E238G|GALNTL5_ENST00000483959.1_3'UTR	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	238	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GTATGGCTGGAGCCCCTGCTG	0.517																																					p.E238G													.	GALNTL5-92	0			c.A713G						.						95	90	91					7																	151699853		2203	4300	6503	SO:0001583	missense	168391	exon6			GGCTGGAGCCCCT	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"Glycosyltransferase family 2 domain containing"	21725	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 5"	615133	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.713A>G	7.37:g.151699853A>G	ENSP00000376548:p.Glu238Gly	Somatic	63	0		WXS	Illumina HiSeq	Phase_1	60	31	NM_145292	0	0	0	0	0	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.084186	0.76642	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.68025	-0.3;-0.3	4.83	4.83	0.62350	Glycosyl transferase, family 2 (1);	0.143577	0.32386	N	0.006165	D	0.87309	0.6145	H	0.98048	4.135	0.45747	D	0.998645	D	0.63880	0.993	D	0.65323	0.934	D	0.91788	0.5441	10	0.87932	D	0	.	14.04	0.64669	1.0:0.0:0.0:0.0	.	238	Q7Z4T8	GLTL5_HUMAN	G	238	ENSP00000392582:E238G;ENSP00000376548:E238G	ENSP00000376548:E238G	E	+	2	0	GALNTL5	151330786	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	6.923000	0.75817	2.160000	0.67779	0.528000	0.53228	GAG	.		0.517	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292		G	151699853	A	G	151699853	3	3	51	1	0	0	0	0	1	0	0	0	6244	304	11	3	731	3	GALNTL5	7	151699853	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1199056	151699853	7438810	121	4809											
PAXIP1	22976	bcgsc.ca	37	chr7	154745994	154745994	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgacacctgaagcattctTccagccactctggcgtcact	8	11	7	15	1	4	2	1	2	3	0	5	2	5	2	3	1	2	1	3	1	1	2	rs78770148		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:154745994T>C	ENST00000404141.1	-	16	2946	c.2792A>G	c.(2791-2793)gAa>gGa	p.E931G	PAXIP1_ENST00000397192.1_Missense_Mutation_p.E931G|RP11-5C23.1_ENST00000608064.1_RNA|PAXIP1_ENST00000473219.1_5'UTR|RP11-5C23.2_ENST00000609134.1_RNA			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	931	BRCT 5. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GAAGCATTCTTCCAGCCACTC	0.448																																					p.E931G													.	PAXIP1-228	0			c.A2792G						.						100	100	100					7																	154745994		1994	4181	6175	SO:0001583	missense	22976	exon16			CATTCTTCCAGCC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2792A>G	7.37:g.154745994T>C	ENSP00000384048:p.Glu931Gly	Somatic	124	0		WXS	Illumina HiSeq	Phase_1	68	26	NM_007349	0	0	4	5	1	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.832103	0.50845	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.79845	-1.31;-1.31	4.61	4.61	0.57282	BRCT (4);	0.109676	0.38164	U	0.001800	D	0.87505	0.6194	M	0.75615	2.305	0.58432	D	0.999997	D;D;D	0.76494	0.999;0.992;0.992	D;P;P	0.66351	0.943;0.853;0.812	D	0.86385	0.1732	10	0.30078	T	0.28	-31.4357	14.3281	0.66534	0.0:0.0:0.0:1.0	.	884;897;931	B4DEQ6;Q6ZW49-1;Q6ZW49	.;.;PAXI1_HUMAN	G	931;931;755;884	ENSP00000384048:E931G;ENSP00000380376:E931G	ENSP00000319149:E884G	E	-	2	0	PAXIP1	154376927	1.000000	0.71417	0.970000	0.41538	0.666000	0.39218	7.702000	0.84576	1.847000	0.53656	0.528000	0.53228	GAA	.		0.448	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		C	154745994	T	C	154745994	3	2	51	1	0	0	0	0	1	0	0	0	11513	1783	62	3	441	3	PAXIP1	7	154745994	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3046141	154745994	4392669	122	4810											
CSMD1	64478	bcgsc.ca	37	chr8	2820801	2820801	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttcacaggagaggatggCggagtgagagagctggtaac	12	6	16	7	1	1	3	1	1	0	2	1	7	1	5	1	5	2	2	1	5	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:2820801C>G	ENST00000520002.1	-	61	9955	c.9400G>C	c.(9400-9402)Gcc>Ccc	p.A3134P	CSMD1_ENST00000602557.1_Missense_Mutation_p.A3134P|CSMD1_ENST00000400186.3_Missense_Mutation_p.A2957P|CSMD1_ENST00000542608.1_Missense_Mutation_p.A2956P|CSMD1_ENST00000602723.1_Missense_Mutation_p.A2957P|CSMD1_ENST00000537824.1_Missense_Mutation_p.A3133P			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3134	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.A3133S(1)|p.A2862S(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GAGAGGATGGCGGAGTGAGAG	0.582																																					p.A3133P													.	CSMD1-86	2	Substitution - Missense(2)	large_intestine(2)	c.G9397C						.																																			SO:0001583	missense	64478	exon60			GGATGGCGGAGTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9400G>C	8.37:g.2820801C>G	ENSP00000430733:p.Ala3134Pro	Somatic	156	0		WXS	Illumina HiSeq	Phase_1	132	44	NM_033225	0	0	0	0	0	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.70|11.70	1.717641|1.717641	0.30413|0.30413	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.64618|.	-0.11;-0.11;-0.11;-0.11|.	5.69|5.69	4.82|4.82	0.62117|0.62117	Complement control module (2);Sushi/SCR/CCP (3);|.	0.072136|.	0.53938|.	D|.	0.000044|.	T|T	0.61286|0.61286	0.2335|0.2335	L|L	0.54863|0.54863	1.705|1.705	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.998;0.995|.	D;D;D|.	0.91635|.	0.999;0.991;0.947|.	T|T	0.59359|0.59359	-0.7469|-0.7469	10|5	0.39692|.	T|.	0.17|.	.|.	11.0295|11.0295	0.47763|0.47763	0.0:0.8583:0.0:0.1417|0.0:0.8583:0.0:0.1417	.|.	3134;3134;2956|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	P|P	2957;3134;2995;3133;2956|2550	ENSP00000383047:A2957P;ENSP00000430733:A3134P;ENSP00000441462:A3133P;ENSP00000446243:A2956P|.	ENSP00000320445:A2995P|.	A|R	-|-	1|2	0|0	CSMD1|CSMD1	2808208|2808208	0.981000|0.981000	0.34729|0.34729	0.885000|0.885000	0.34714|0.34714	0.079000|0.079000	0.17450|0.17450	2.561000|2.561000	0.45905|0.45905	1.418000|1.418000	0.47098|0.47098	-0.126000|-0.126000	0.14955|0.14955	GCC|CGC	.		0.582	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2820801	C	G	2820801	3	3	51	1	0	0	0	0	1	0	0	0	3950	768	27	4	1341	4	CSMD1	8	2820801	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08		2820801	143543221	123	4811											
DPYSL2	1808	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	26505196	26505196	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctgtgaccagcaccaaTgcagccaaagtcttcaacct	11	8	9	13	0	2	1	1	1	1	0	2	1	2	1	4	1	4	3	4	1	3	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:26505196T>A	ENST00000311151.5	+	11	1573	c.1161T>A	c.(1159-1161)aaT>aaA	p.N387K	DPYSL2_ENST00000523027.1_Missense_Mutation_p.N351K|DPYSL2_ENST00000521913.1_Missense_Mutation_p.N351K	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	387					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		CCAGCACCAATGCAGCCAAAG	0.552																																					p.N492K		.											.	DPYSL2-153	0			c.T1476A						.						133	121	125					8																	26505196		2203	4300	6503	SO:0001583	missense	1808	exon11			CACCAATGCAGCC	D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.1161T>A	8.37:g.26505196T>A	ENSP00000309539:p.Asn387Lys	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	190	118	NM_001197293	0	0	25	84	59	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	37	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.898016	0.72639	.	.	ENSG00000092964	ENST00000545637;ENST00000521913;ENST00000311151;ENST00000522745;ENST00000523027	D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07	5.22	-6.76	0.01732	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.96144	0.8743	M	0.92367	3.3	0.53688	D	0.999974	D;P	0.76494	0.999;0.835	D;B	0.83275	0.996;0.269	D	0.94988	0.8132	10	0.66056	D	0.02	-27.4582	18.9516	0.92643	0.0:0.601:0.0:0.399	.	387;443	Q16555;Q59GB4	DPYL2_HUMAN;.	K	26;351;387;387;351	ENSP00000427985:N351K;ENSP00000309539:N387K;ENSP00000428909:N387K;ENSP00000431117:N351K	ENSP00000309539:N387K	N	+	3	2	DPYSL2	26561113	0.000000	0.05858	0.783000	0.31826	0.973000	0.67179	-2.232000	0.01205	-1.277000	0.02411	-1.098000	0.02139	AAT	.		0.552	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386		A	26505196	T	A	26505196	3	1	51	1	0	0	0	0	1	0	0	0	4758	1461	51	5	1203	5	DPYSL2	8	26505196	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	23684395	26505196	119858826	124	4812											
TMEM67	91147	bcgsc.ca	37	chr8	94800161	94800161	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattgatatcaaagatgccaAcagccagtctgtgaaggtga	14	9	10	8	0	2	4	1	3	1	1	2	4	2	4	2	1	3	0	2	1	4	2	rs79555627		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:94800161A>C	ENST00000453321.3	+	14	1560	c.1502A>C	c.(1501-1503)aAc>aCc	p.N501T	TMEM67_ENST00000409623.3_Missense_Mutation_p.N420T	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	501					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			AAAGATGCCAACAGCCAGTCT	0.378																																					p.N501T													.	TMEM67-92	0			c.A1502C						.						164	145	152					8																	94800161		2203	4300	6503	SO:0001583	missense	91147	exon14			ATGCCAACAGCCA	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1502A>C	8.37:g.94800161A>C	ENSP00000389998:p.Asn501Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	74	40	NM_153704	0	0	6	6	0	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	37	CCDS6258.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.205|0.205	-1.041705|-1.041705	0.02013|0.02013	.|.	.|.	ENSG00000164953|ENSG00000164953	ENST00000453321;ENST00000409623|ENST00000520680	D;D|.	0.96685|.	-4.09;-4.09|.	5.94|5.94	-3.96|-3.96	0.04106|0.04106	.|.	1.048890|.	0.07378|.	N|.	0.886978|.	T|T	0.17450|0.17450	0.0419|0.0419	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B|.	0.28055|.	0.01;0.014;0.199|.	B;B;B|.	0.27076|.	0.013;0.033;0.076|.	T|T	0.29088|0.29088	-1.0023|-1.0023	9|5	.|.	.|.	.|.	0.2887|0.2887	6.3924|6.3924	0.21593|0.21593	0.4842:0.2195:0.2963:0.0|0.4842:0.2195:0.2963:0.0	.|.	501;420;420|.	Q5HYA8;B3KRU5;G5E9H2|.	MKS3_HUMAN;.;.|.	T|H	501;420|108	ENSP00000389998:N501T;ENSP00000386966:N420T|.	.|.	N|Q	+|+	2|3	0|2	TMEM67|TMEM67	94869337|94869337	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.034000|-0.034000	0.12225|0.12225	-0.993000|-0.993000	0.03467|0.03467	-0.379000|-0.379000	0.06801|0.06801	AAC|CAA	.		0.378	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94800161	A	C	94800161	3	2	51	1	0	0	0	0	1	0	0	0	16228	43	2	5	1694	5	TMEM67	8	94800161	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	68294965	94800161	51563861	125	4813											
UBR5	51366	bcgsc.ca	37	chr8	103300468	103300468	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcatgatgatcctcttcTccagccacaccctccaccac	9	10	3	19	0	4	2	2	2	2	0	7	2	6	2	6	0	1	0	6	0	0	1	rs199686475		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:103300468T>C	ENST00000520539.1	-	36	5346	c.4740A>G	c.(4738-4740)ggA>ggG	p.G1580G	UBR5_ENST00000519528.1_5'UTR|UBR5_ENST00000220959.4_Silent_p.G1580G|UBR5_ENST00000521922.1_Silent_p.G1574G	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	1580					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			GATCCTCTTCTCCAGCCACAC	0.423																																					p.G1580G	Ovarian(131;96 1741 5634 7352 27489)												.	UBR5-761	0			c.A4740G						.						177	154	162					8																	103300468		2203	4300	6503	SO:0001819	synonymous_variant	51366	exon36			CTCTTCTCCAGCC	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.4740A>G	8.37:g.103300468T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_1	105	61	NM_015902	0	0	14	18	4	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																			T|0.999;C|0.001		0.423	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		C	103300468	T	C	103300468	2	2	51	1	0	0	0	0	0	0	0	1	16938	1538	54	3		3	UBR5	8	103300468	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8500307	103300468	43063554	126	4814											
TTC35	9694	hgsc.bcm.edu;broad.mit.edu	37	chr8	109498794	109498794	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttaaggctgtcgaagaCatgttggaaacattgcagat	12	12	10	7	1	1	2	0	0	1	2	3	4	1	3	0	2	2	3	0	2	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:109498794C>G	ENST00000220853.3	+	11	896	c.861C>G	c.(859-861)gaC>gaG	p.D287E	EMC2_ENST00000520294.1_3'UTR	NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	287						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CTGTCGAAGACATGTTGGAAA	0.338																																					p.D287E		.											.	.	0			c.C861G						.						80	80	80					8																	109498794		2203	4300	6503	SO:0001583	missense	9694	exon11			CGAAGACATGTTG	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.861C>G	8.37:g.109498794C>G	ENSP00000220853:p.Asp287Glu	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	26	3	NM_014673	0	0	48	48	0	Q8WUE1	Missense_Mutation	SNP	ENST00000220853.3	37	CCDS6309.1	.	.	.	.	.	.	.	.	.	.	C	9.035	0.988299	0.18966	.	.	ENSG00000104412	ENST00000220853	.	.	.	5.95	5.95	0.96441	.	0.043479	0.85682	D	0.000000	T	0.23330	0.0564	N	0.01800	-0.715	0.45076	D	0.998095	B	0.02656	0.0	B	0.01281	0.0	T	0.28073	-1.0055	9	0.02654	T	1	-19.3849	13.5585	0.61775	0.0:0.9292:0.0:0.0708	.	287	Q15006	TTC35_HUMAN	E	287	.	ENSP00000220853:D287E	D	+	3	2	TTC35	109567970	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.646000	0.46630	2.817000	0.96982	0.563000	0.77884	GAC	.		0.338	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		G	109498794	C	G	109498794	3	3	51	1	0	0	0	0	1	0	0	0	16736	477	17	4	903	4	TTC35	8	109498794	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	6198326	109498794	36865228	127	4815											
LRRC24	441381	hgsc.bcm.edu	37	chr8	145748092	145748092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctccctcccccggaggccCccgcgccttttttcgcctgc	1	9	9	22	5	0	0	0	0	0	0	3	1	2	1	7	2	1	1	7	2	0	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:145748092C>T	ENST00000529415.2	-	5	1426	c.1309G>A	c.(1309-1311)Ggg>Agg	p.G437R	LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Missense_Mutation_p.G434R|LRRC14_ENST00000292524.1_3'UTR			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	437						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCCGGAGGCCCCCGCGCCTTT	0.692																																					p.G437R		.											.	LRRC24-90	0			c.G1309A						.						9	10	10					8																	145748092		2166	4273	6439	SO:0001583	missense	441381	exon5			GAGGCCCCCGCGC	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"Immunoglobulin superfamily / I-set domain containing"	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.1309G>A	8.37:g.145748092C>T	ENSP00000434849:p.Gly437Arg	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	22	19	NM_001024678	0	0	0	5	5		Missense_Mutation	SNP	ENST00000529415.2	37	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	C	8.413	0.844629	0.16963	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.55234	0.67;0.53	4.06	3.17	0.36434	.	1.184250	0.05990	N	0.645793	T	0.36386	0.0965	N	0.24115	0.695	0.09310	N	1	B;B	0.33583	0.418;0.047	B;B	0.33521	0.165;0.017	T	0.27571	-1.0070	10	0.15066	T	0.55	.	5.7465	0.18122	0.0:0.6941:0.2006:0.1053	.	434;437	G3V1D8;Q50LG9	.;LRC24_HUMAN	R	437;434	ENSP00000434849:G437R;ENSP00000435653:G434R	ENSP00000434849:G437R	G	-	1	0	LRRC24	145718900	0.462000	0.25791	0.003000	0.11579	0.002000	0.02628	2.025000	0.41059	1.286000	0.44565	-0.305000	0.09177	GGG	.		0.692	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		T	145748092	C	T	145748092	3	4	51	1	0	0	0	0	1	0	0	0	9004	623	22	2	236	2	LRRC24	8	145748092	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	36249298	145748092	615930	128	4816											
PTPRD	5789	bcgsc.ca	37	chr9	8507427	8507427	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gctttgaagtttagtggctgCcctggtactaaaaacaggga	11	11	12	7	0	0	1	0	1	0	0	0	2	0	2	1	3	3	4	1	3	6	5	rs202247306		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:8507427C>G	ENST00000381196.4	-	19	2094	c.1551G>C	c.(1549-1551)ggG>ggC	p.G517G	PTPRD_ENST00000537002.1_Silent_p.G514G|PTPRD_ENST00000360074.4_Silent_p.G504G|PTPRD_ENST00000358503.5_Silent_p.G504G|PTPRD_ENST00000355233.5_Silent_p.G517G|PTPRD_ENST00000397617.3_Silent_p.G507G|PTPRD_ENST00000486161.1_Silent_p.G517G|PTPRD_ENST00000540109.1_Silent_p.G517G|PTPRD_ENST00000356435.5_Silent_p.G517G|PTPRD_ENST00000397606.3_Silent_p.G507G|PTPRD_ENST00000397611.3_Silent_p.G514G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	517					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TTAGTGGCTGCCCTGGTACTA	0.428										TSP Lung(15;0.13)																											p.G517G													.	PTPRD-912	0			c.G1551C						.						152	144	147					9																	8507427		2203	4300	6503	SO:0001819	synonymous_variant	5789	exon11			TGGCTGCCCTGGT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1551G>C	9.37:g.8507427C>G		Somatic	139	0		WXS	Illumina HiSeq	Phase_1	44	16	NM_130392	0	0	0	0	0	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	37	CCDS43786.1																																																																																			C|0.999;G|0.001		0.428	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			G	8507427	C	G	8507427	2	3	51	1	0	0	0	0	0	0	0	1	12831	726	26	4		4	PTPRD	9	8507427	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08		8507427	132706004	129	4817											
TEK	7010	bcgsc.ca	37	chr9	27173339	27173339	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcctgtgccacaggctggAagggtctgcagtgcaatgaa	9	9	14	9	0	1	1	0	1	1	0	2	2	2	2	2	3	3	4	2	3	3	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:27173339A>G	ENST00000380036.4	+	6	1322	c.880A>G	c.(880-882)Aag>Gag	p.K294E	TEK_ENST00000406359.4_Missense_Mutation_p.K294E|TEK_ENST00000519097.1_Missense_Mutation_p.K190E	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	294	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CACAGGCTGGAAGGGTCTGCA	0.488																																					p.K294E													.	TEK-1584	0			c.A880G						.						158	126	137					9																	27173339		2203	4300	6503	SO:0001583	missense	7010	exon6			GGCTGGAAGGGTC	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.880A>G	9.37:g.27173339A>G	ENSP00000369375:p.Lys294Glu	Somatic	93	0		WXS	Illumina HiSeq	Phase_1	30	12	NM_000459	0	0	0	0	0	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.323590	0.41096	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.53	1.67	0.24075	Epidermal growth factor-like (1);EGF-like region, conserved site (2);	0.649250	0.14087	N	0.342261	T	0.73257	0.3564	M	0.66939	2.045	0.28602	N	0.909084	B;B;B;B;B;B	0.27823	0.002;0.06;0.002;0.19;0.008;0.161	B;B;B;B;B;B	0.24155	0.007;0.025;0.002;0.051;0.007;0.026	T	0.60429	-0.7265	10	0.25751	T	0.34	.	13.1595	0.59537	0.5962:0.4038:0.0:0.0	.	190;327;294;147;294;294	E7EWI2;Q59HG2;B5A953;E5RIV9;B4DHD3;Q02763	.;.;.;.;.;TIE2_HUMAN	E	190;294;294;294;147	ENSP00000430686:K190E;ENSP00000369375:K294E;ENSP00000383977:K294E;ENSP00000428337:K147E	ENSP00000343716:K294E	K	+	1	0	TEK	27163339	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.642000	0.37207	0.091000	0.17302	0.528000	0.53228	AAG	.		0.488	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			G	27173339	A	G	27173339	3	3	51	1	0	0	0	0	1	0	0	0	15783	247	9	3	902	3	TEK	9	27173339	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	18665912	27173339	114040092	130	4818											
PIGO	84720	bcgsc.ca	37	chr9	35089137	35089137	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaccaggagctcacagcAccatccactctcatcaccaa	13	6	5	17	0	3	1	3	1	1	0	5	2	4	2	4	1	3	2	4	1	2	0	rs200684520		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:35089137A>C	ENST00000378617.3	-	11	3616	c.3222T>G	c.(3220-3222)ggT>ggG	p.G1074G	PIGO_ENST00000341666.3_Silent_p.G1074G|PIGO_ENST00000361778.2_Silent_p.G657G|PIGO_ENST00000298004.5_Silent_p.G657G	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	1074					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.G1074G(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AGCTCACAGCACCATCCACTC	0.522																																					p.G1074G													.	PIGO-290	1	Substitution - coding silent(1)	prostate(1)	c.T3222G						.						124	113	117					9																	35089137		2203	4300	6503	SO:0001819	synonymous_variant	84720	exon11			CACAGCACCATCC	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"Phosphatidylinositol glycan anchor biosynthesis"	23215	protein-coding gene	gene with protein product		614730	"phosphatidylinositol glycan, class O"			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.3222T>G	9.37:g.35089137A>C		Somatic	107	0		WXS	Illumina HiSeq	Phase_1	98	63	NM_032634	0	0	36	48	12	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Silent	SNP	ENST00000378617.3	37	CCDS6575.1																																																																																			A|0.999;C|0.001		0.522	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634		C	35089137	A	C	35089137	2	2	51	1	0	0	0	0	0	0	0	1	11920	146	6	5		5	PIGO	9	35089137	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	7915798	35089137	106124294	131	4819											
TLN1	7094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35711016	35711016	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagggcgttatcacactcCttctggccgggtgcctgctg	4	10	13	14	3	2	0	1	0	1	0	3	0	3	0	3	3	2	3	3	3	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:35711016C>T	ENST00000314888.9	-	31	4436	c.4083G>A	c.(4081-4083)aaG>aaA	p.K1361K	TLN1_ENST00000540444.1_Silent_p.K1361K	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1361	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TATCACACTCCTTCTGGCCGG	0.532																																					p.K1361K		.											.	TLN1-609	0			c.G4083A						.						107	94	98					9																	35711016		2203	4300	6503	SO:0001819	synonymous_variant	7094	exon31			ACACTCCTTCTGG	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.4083G>A	9.37:g.35711016C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	184	49	NM_006289	0	0	84	135	51	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			.		0.532	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35711016	C	T	35711016	2	4	51	1	0	0	0	0	0	0	0	1	15979	680	24	2		2	TLN1	9	35711016	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	621879	35711016	105502415	132	4820											
RASEF	158158	bcgsc.ca	37	chr9	85615928	85615928	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggatctctcaaggtagaCaagccgctgtcgaagcagct	10	9	12	10	2	2	1	1	0	1	1	4	3	2	2	1	2	3	4	1	2	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:85615928C>A	ENST00000376447.3	-	10	1580	c.1320G>T	c.(1318-1320)ttG>ttT	p.L440F		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	440					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TCAAGGTAGACAAGCCGCTGT	0.527																																					p.L440F													.	RASEF-280	0			c.G1320T						.						77	73	74					9																	85615928		2203	4300	6503	SO:0001583	missense	158158	exon10			GGTAGACAAGCCG	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.1320G>T	9.37:g.85615928C>A	ENSP00000365630:p.Leu440Phe	Somatic	65	0		WXS	Illumina HiSeq	Phase_1	50	23	NM_152573	0	0	5	5	0	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760639	0.69763	.	.	ENSG00000165105	ENST00000376447	T	0.62232	0.04	5.92	4.08	0.47627	.	0.157867	0.43919	D	0.000512	T	0.70090	0.3184	L	0.60455	1.87	0.80722	D	1	D	0.65815	0.995	P	0.61533	0.89	T	0.72279	-0.4340	10	0.72032	D	0.01	.	9.1415	0.36906	0.0:0.7804:0.0:0.2196	.	440	Q8IZ41	RASEF_HUMAN	F	440	ENSP00000365630:L440F	ENSP00000365630:L440F	L	-	3	2	RASEF	84805748	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.556000	0.36288	1.523000	0.49018	0.585000	0.79938	TTG	.		0.527	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		A	85615928	C	A	85615928	3	1	51	1	0	0	0	0	1	0	0	0	13100	477	17	4	934	4	RASEF	9	85615928	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	49904912	85615928	55597503	133	4821											
ZCCHC6	79670	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	88940291	88940291	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gggccaatccttcaattcccGagataccaattctttgacac	11	11	6	13	1	2	2	1	1	1	1	4	3	4	2	4	1	1	0	4	1	4	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:88940291G>C	ENST00000375963.3	-	12	1919	c.1747C>G	c.(1747-1749)Cgg>Ggg	p.R583G	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.R583G|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.R460G|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000469004.1_5'Flank	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	583	PAP-associated 1.				RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						TTCAATTCCCGAGATACCAAT	0.403																																					p.R583G		.											.	ZCCHC6-92	0			c.C1747G						.						101	98	99					9																	88940291		2203	4300	6503	SO:0001583	missense	79670	exon12			ATTCCCGAGATAC	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.1747C>G	9.37:g.88940291G>C	ENSP00000365130:p.Arg583Gly	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	34	12	NM_024617	0	0	6	7	1	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.583577	0.65992	.	.	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.78707	-1.2;-1.2;-1.2	5.1	5.1	0.69264	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.87358	0.6157	M	0.76838	2.35	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88322	0.2963	10	0.72032	D	0.01	-11.8038	13.6554	0.62336	0.0:0.0:0.8455:0.1544	.	460;583	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	G	460;583;583	ENSP00000365127:R460G;ENSP00000365128:R583G;ENSP00000365130:R583G	ENSP00000365127:R460G	R	-	1	2	ZCCHC6	88130111	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.937000	0.56575	2.658000	0.90341	0.650000	0.86243	CGG	.		0.403	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		C	88940291	G	C	88940291	3	2	51	1	0	0	0	0	1	0	0	0	17624	1057	37	4	2804	4	ZCCHC6	9	88940291	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	3324363	88940291	52273140	134	4822											
HSDL2	84263	bcgsc.ca	37	chr9	115166387	115166387	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttattgctgcaaagaccGcccagccacatccaaaactt	12	10	6	13	1	0	1	0	0	0	1	1	1	1	1	4	0	4	3	4	0	4	4	rs184202621	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:115166387G>C	ENST00000398805.3	+	2	357	c.130G>C	c.(130-132)Gcc>Ccc	p.A44P	HSDL2_ENST00000539114.1_5'UTR|HSDL2_ENST00000398803.1_Missense_Mutation_p.A44P|HSDL2_ENST00000262542.7_Intron|HSDL2_ENST00000488101.1_Intron	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	44						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						TGCAAAGACCGCCCAGCCACA	0.418													G|||	311	0.0621006	0.0416	0.1124	5008	,	,		18257	0.0804		0.0954	False		,,,				2504	0.001				p.A44P													.	HSDL2-90	0			c.G130C						.						87	83	84					9																	115166387		1965	4150	6115	SO:0001583	missense	84263	exon2			AAGACCGCCCAGC	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18572	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 13C, member 1"		"chromosome 9 open reading frame 99"	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.130G>C	9.37:g.115166387G>C	ENSP00000381785:p.Ala44Pro	Somatic	84	1		WXS	Illumina HiSeq	Phase_1	84	35	NM_032303	0	0	50	50	0	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.366799	0.41902	.	.	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.87729	-2.29;-2.29	6.07	-1.25	0.09405	NAD(P)-binding domain (1);	0.313593	0.38663	N	0.001613	D	0.85137	0.5628	M	0.67397	2.05	0.37713	D	0.924656	P;D	0.54964	0.879;0.969	B;P	0.44811	0.276;0.461	D	0.85039	0.0922	10	0.62326	D	0.03	.	13.4084	0.60926	0.4014:0.0:0.5986:0.0	.	44;44	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	P	44	ENSP00000381785:A44P;ENSP00000381783:A44P	ENSP00000381783:A44P	A	+	1	0	HSDL2	114206208	0.044000	0.20184	0.000000	0.03702	0.127000	0.20565	1.192000	0.32150	-0.401000	0.07644	-0.982000	0.02568	GCC	A|0.001;G|0.999		0.418	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		C	115166387	G	C	115166387	3	2	51	1	0	0	0	0	1	0	0	0	7415	1087	38	4	136	4	HSDL2	9	115166387	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	26226096	115166387	26047044	135	4823											
AKNA	80709	broad.mit.edu	37	chr9	117139572	117139572	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcttgttcgccagaagccAcccagcccctggcctgacca	7	7	10	17	1	0	2	0	1	0	1	1	2	0	2	7	2	2	2	7	2	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:117139572A>C	ENST00000307564.4	-	3	676	c.515T>G	c.(514-516)gTg>gGg	p.V172G	AKNA_ENST00000312033.3_Missense_Mutation_p.V172G|AKNA_ENST00000223791.3_5'Flank|AKNA_ENST00000374088.3_Missense_Mutation_p.V172G|AKNA_ENST00000374075.5_Missense_Mutation_p.V91G	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	172					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GCCAGAAGCCACCCAGCCCCT	0.592																																					p.V172G													.	AKNA-94	0			c.T515G						.						58	54	55					9																	117139572		2203	4300	6503	SO:0001583	missense	80709	exon3			GAAGCCACCCAGC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.515T>G	9.37:g.117139572A>C	ENSP00000303769:p.Val172Gly	Somatic	76	2		WXS	Illumina HiSeq	Phase_I	187	34	NM_030767	0	0	10	12	2	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093091	0.56075	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	T;T;T;T	0.48836	2.05;2.05;2.05;0.8	4.64	-1.48	0.08745	.	1.095500	0.07239	N	0.863913	T	0.41373	0.1156	L	0.32530	0.975	0.09310	N	1	B;B;D	0.57571	0.005;0.006;0.98	B;B;P	0.52957	0.007;0.003;0.714	T	0.30909	-0.9962	10	0.44086	T	0.13	-3.2628	2.0987	0.03675	0.4642:0.2985:0.0918:0.1455	.	172;172;91	Q7Z591-6;Q7Z591;Q7Z591-2	.;AKNA_HUMAN;.	G	172;172;91;172;172	ENSP00000303769:V172G;ENSP00000363201:V172G;ENSP00000363188:V91G;ENSP00000309222:V172G	ENSP00000303769:V172G	V	-	2	0	AKNA	116179393	0.000000	0.05858	0.022000	0.16811	0.296000	0.27459	0.023000	0.13533	-0.083000	0.12618	0.379000	0.24179	GTG	.		0.592	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117139572	A	C	117139572	3	2	51	1	0	0	0	0	1	0	0	0	463	159	6	5	3884	5	AKNA	9	117139572	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1973185	117139572	24073859	136	4824											
CRAT	1384	bcgsc.ca	37	chr9	131864811	131864812	+	Frame_Shift_Ins	INS	-	-	T																															actggttcatgcacagtggcINSttcccccccaggtactccac																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:131864811_131864812insT	ENST00000318080.2	-	5	791_792	c.497_498insA	c.(496-498)aagfs	p.K166fs	RP11-247A12.1_ENST00000434250.1_RNA|CRAT_ENST00000464290.1_5'UTR	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	166					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	TGCACAGTGGCTTCCCCCCCAG	0.609																																					p.K166fs													.	CRAT-90	0			c.498_499insA						.																																			SO:0001589	frameshift_variant	1384	exon5			CAGTGGCTTCCCC	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"carnitine acetyltransferase"			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.498dupA	9.37:g.131864813_131864813dupT	ENSP00000315013:p.Lys166fs	Somatic	295	0		WXS	Illumina HiSeq	Phase_1	956	174	NM_000755	0	0	0	0	0	Q5T952|Q9BW16	Frame_Shift_Ins	INS	ENST00000318080.2	37	CCDS6919.1																																																																																			.		0.609	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			T	131864812	-	T	131864811	7	5	51	1	0	1	1	0	0	0	0	0	3853	796	28	0	1422	0	CRAT	9	131864811	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	14725239	131864811	9348620	137	4825											
C10orf18	54906	bcgsc.ca	37	chr10	5788304	5788304	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacagtggcactgttactCaagccacattcaccaggact	11	10	7	13	0	2	0	2	0	0	0	2	1	2	1	2	2	3	2	2	2	3	3	rs72772328		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:5788304C>A	ENST00000328090.5	+	15	3545	c.2920C>A	c.(2920-2922)Caa>Aaa	p.Q974K	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	974																	CACTGTTACTCAAGCCACATT	0.463																																					p.Q974K													.	.	0			c.C2920A						.						72	76	75					10																	5788304		1996	4169	6165	SO:0001583	missense	54906	exon15			GTTACTCAAGCCA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.2920C>A	10.37:g.5788304C>A	ENSP00000328426:p.Gln974Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_1	32	16	NM_017782	0	0	10	10	0	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.250700	0.39797	.	.	ENSG00000108021	ENST00000328090	T	0.43688	0.94	4.78	4.78	0.61160	.	0.260060	0.27504	N	0.019074	T	0.62865	0.2463	M	0.70595	2.14	0.25318	N	0.989145	D	0.69078	0.997	D	0.87578	0.998	T	0.56860	-0.7909	10	0.72032	D	0.01	.	14.0255	0.64584	0.0:1.0:0.0:0.0	.	974	Q5VWN6	F208B_HUMAN	K	974	ENSP00000328426:Q974K	ENSP00000328426:Q974K	Q	+	1	0	C10orf18	5828310	0.394000	0.25246	0.128000	0.21923	0.039000	0.13416	1.854000	0.39368	2.557000	0.86248	0.655000	0.94253	CAA	.		0.463	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		A	5788304	C	A	5788304	3	1	51	1	0	0	0	0	1	0	0	0	1600	827	29	4	2966	4	C10orf18	10	5788304	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08		5788304	129746443	138	4826											
ANK3	288	hgsc.bcm.edu	37	chr10	61819138	61819138	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	taacccaccagttactcttcGagcttgagcgcaggactcta	10	10	8	13	2	2	1	0	1	2	0	3	3	2	2	2	1	4	3	2	1	3	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:61819138G>C	ENST00000280772.2	-	41	12837	c.12646C>G	c.(12646-12648)Cga>Gga	p.R4216G	ANK3_ENST00000373827.2_Missense_Mutation_p.R1700G|ANK3_ENST00000503366.1_Missense_Mutation_p.R1707G|RP11-388P9.2_ENST00000414383.1_RNA|ANK3_ENST00000355288.2_Missense_Mutation_p.R840G	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4216					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GTTACTCTTCGAGCTTGAGCG	0.408																																					p.R4216G		.											.	ANK3-107	0			c.C12646G						.						201	175	184					10																	61819138		2203	4300	6503	SO:0001583	missense	288	exon41			CTCTTCGAGCTTG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.12646C>G	10.37:g.61819138G>C	ENSP00000280772:p.Arg4216Gly	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_020987	0	0	65	65	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315261	0.40996	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000373820;ENST00000355288;ENST00000503366;ENST00000395299;ENST00000373817	T;T;T;T;T	0.79352	-0.67;-1.26;0.38;-0.38;-1.22	5.56	4.65	0.58169	.	0.000000	0.30329	U	0.009875	T	0.73783	0.3631	L	0.29908	0.895	0.80722	D	1	P;P;P;P;B;P;D	0.58268	0.889;0.543;0.889;0.945;0.447;0.543;0.982	B;B;B;P;B;B;P	0.49752	0.301;0.162;0.394;0.597;0.307;0.162;0.621	T	0.77464	-0.2578	10	0.72032	D	0.01	.	13.835	0.63404	0.0733:0.0:0.9267:0.0	.	1707;840;1700;4216;941;840;239	E9PE32;A8KA62;Q5CZH9;Q12955;F5GXK0;B1AQT2;B1AQT0	.;.;.;ANK3_HUMAN;.;.;.	G	4216;1700;298;840;1707;1686;941	ENSP00000280772:R4216G;ENSP00000362933:R1700G;ENSP00000362926:R298G;ENSP00000347436:R840G;ENSP00000425236:R1707G	ENSP00000280772:R4216G	R	-	1	2	ANK3	61489144	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.006000	0.76329	2.623000	0.88846	0.455000	0.32223	CGA	.		0.408	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61819138	G	C	61819138	3	2	51	1	0	0	0	0	1	0	0	0	622	1066	37	4	499	4	ANK3	10	61819138	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	56030834	61819138	73715609	139	4827											
DNA2	1763	bcgsc.ca	37	chr10	70196869	70196869	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttacaataactctgtcAcctgccattagatttgtgac	11	13	5	12	0	2	2	1	1	1	1	2	2	2	2	3	0	3	0	3	0	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:70196869A>C	ENST00000358410.3	-	10	1595	c.1545T>G	c.(1543-1545)ggT>ggG	p.G515G	DNA2_ENST00000399179.2_Silent_p.G515G|DNA2_ENST00000399180.2_Silent_p.G601G	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	515	Nuclease activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TAACTCTGTCACCTGCCATTA	0.353																																					p.G515G													.	.	0			c.T1545G						.						182	176	178					10																	70196869		1887	4114	6001	SO:0001819	synonymous_variant	1763	exon10			TCTGTCACCTGCC	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.1545T>G	10.37:g.70196869A>C		Somatic	134	5		WXS	Illumina HiSeq	Phase_1	122	69	NM_001080449	0	0	7	8	1	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.		0.353	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			C	70196869	A	C	70196869	2	2	51	1	0	0	0	0	0	0	0	1	4607	146	6	5		5	DNA2	10	70196869	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	8377731	70196869	65337878	140	4828											
ENTPD1	953	bcgsc.ca	37	chr10	97604357	97604357	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaaggtgcctatggctggAttactatcaactatctgctg	10	12	11	8	0	2	0	1	0	1	0	2	2	2	2	1	4	4	2	1	4	6	4	rs80329743		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:97604357A>G	ENST00000371205.4	+	5	821	c.538A>G	c.(538-540)Att>Gtt	p.I180V	ENTPD1_ENST00000543964.1_Missense_Mutation_p.I72V|ENTPD1_ENST00000453258.2_Missense_Mutation_p.I187V|ENTPD1_ENST00000371203.5_Missense_Mutation_p.I42V|ENTPD1_ENST00000539125.1_Missense_Mutation_p.I42V|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000490659.1_3'UTR|ENTPD1_ENST00000371207.3_Missense_Mutation_p.I192V|RP11-429G19.3_ENST00000433113.1_RNA			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	180					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		CTATGGCTGGATTACTATCAA	0.522																																					p.I192V													.	ENTPD1-93	0			c.A574G						.						158	153	154					10																	97604357		2203	4300	6503	SO:0001583	missense	953	exon5			GGCTGGATTACTA	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"CD molecules"	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.538A>G	10.37:g.97604357A>G	ENSP00000360248:p.Ile180Val	Somatic	169	0		WXS	Illumina HiSeq	Phase_1	77	23	NM_001164178	0	0	25	28	3	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	ENST00000371205.4	37	CCDS7444.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.861384	0.51482	.	.	ENSG00000138185	ENST00000453258;ENST00000371206;ENST00000371207;ENST00000543964;ENST00000539125;ENST00000371203;ENST00000371205	T;T;T;T;T;T	0.15372	2.43;2.43;2.43;2.43;2.43;2.43	5.83	5.83	0.93111	.	0.159980	0.56097	D	0.000038	T	0.19967	0.0480	L	0.39245	1.2	0.58432	D	0.999993	P;P;B;P;P	0.47034	0.889;0.865;0.153;0.889;0.568	P;B;B;P;B	0.46940	0.532;0.396;0.113;0.532;0.279	T	0.01904	-1.1250	10	0.25106	T	0.35	-25.9621	14.1648	0.65469	1.0:0.0:0.0:0.0	.	192;192;187;180;187	B4DWB9;G3XAF6;P49961-2;P49961;P49961-3	.;.;.;ENTP1_HUMAN;.	V	187;187;192;72;42;42;180	ENSP00000390955:I187V;ENSP00000360250:I192V;ENSP00000442968:I72V;ENSP00000440027:I42V;ENSP00000360246:I42V;ENSP00000360248:I180V	ENSP00000360246:I42V	I	+	1	0	ENTPD1	97594347	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.762000	0.68809	2.236000	0.73375	0.533000	0.62120	ATT	.		0.522	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776		G	97604357	A	G	97604357	3	3	51	1	0	0	0	0	1	0	0	0	5151	333	12	3	653	3	ENTPD1	10	97604357	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	27407488	97604357	37930390	141	4829											
ABCC2	1244	bcgsc.ca	37	chr10	101603581	101603581	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaccctgaactggctggTgaggatgacatcagaaatag	15	7	11	8	0	1	4	1	3	0	1	1	5	1	5	1	3	2	1	1	3	4	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:101603581T>G	ENST00000370449.4	+	27	3880	c.3767T>G	c.(3766-3768)gTg>gGg	p.V1256G		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1256	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AACTGGCTGGTGAGGATGACA	0.418																																					p.V1256G													.	ABCC2-91	0			c.T3767G						.						293	304	300					10																	101603581		2203	4300	6503	SO:0001583	missense	1244	exon27			GGCTGGTGAGGAT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3767T>G	10.37:g.101603581T>G	ENSP00000359478:p.Val1256Gly	Somatic	414	1		WXS	Illumina HiSeq	Phase_1	276	60	NM_000392	0	0	5	6	1	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.552029	0.86127	.	.	ENSG00000023839	ENST00000370449	D	0.83992	-1.79	5.33	5.33	0.75918	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.000000	0.85682	D	0.000000	D	0.94335	0.8179	H	0.97587	4.035	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96281	0.9206	10	0.87932	D	0	-15.3424	15.3291	0.74193	0.0:0.0:0.0:1.0	.	1256	Q92887	MRP2_HUMAN	G	1256	ENSP00000359478:V1256G	ENSP00000359478:V1256G	V	+	2	0	ABCC2	101593571	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.037000	0.88933	2.017000	0.59298	0.533000	0.62120	GTG	.		0.418	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		G	101603581	T	G	101603581	3	3	51	1	0	0	0	0	1	0	0	0	53	1696	59	5	3873	5	ABCC2	10	101603581	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3999224	101603581	33931166	142	4830											
SEC31B	25956	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102255181	102255181	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccaatctgtaagatgatgtCtctttagagtggagggtagc	10	12	12	7	0	2	3	0	1	2	2	3	4	2	4	1	2	1	2	1	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:102255181C>G	ENST00000370345.3	-	19	2530	c.2433G>C	c.(2431-2433)gaG>gaC	p.E811D	SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	811					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		AAGATGATGTCTCTTTAGAGT	0.488																																					p.E811D		.											.	SEC31B-91	0			c.G2433C						.						69	61	63					10																	102255181		2203	4300	6503	SO:0001583	missense	25956	exon19			TGATGTCTCTTTA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"WD repeat domain containing"	23197	protein-coding gene	gene with protein product		610258	"SEC31-like 2 (S. cerevisiae)"	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.2433G>C	10.37:g.102255181C>G	ENSP00000359370:p.Glu811Asp	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	33	17	NM_015490	0	0	2	3	1	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.927568	0.34002	.	.	ENSG00000075826	ENST00000370345	T	0.51325	0.71	5.76	-1.7	0.08159	.	0.960732	0.08733	N	0.901781	T	0.18676	0.0448	N	0.08118	0	0.09310	N	0.999998	B;B	0.32893	0.017;0.389	B;B	0.25987	0.006;0.065	T	0.13308	-1.0514	10	0.33141	T	0.24	-8.994	0.6819	0.00876	0.1758:0.2806:0.2804:0.2633	.	810;811	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	D	811	ENSP00000359370:E811D	ENSP00000359370:E811D	E	-	3	2	SEC31B	102245171	.	.	0.335000	0.25508	0.480000	0.33159	.	.	-0.009000	0.14296	0.561000	0.74099	GAG	.		0.488	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		G	102255181	C	G	102255181	3	3	51	1	0	0	0	0	1	0	0	0	14031	912	32	4	1138	4	SEC31B	10	102255181	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	651600	102255181	33279566	143	4831											
ITPRIP	85450	bcgsc.ca	37	chr10	106074688	106074689	+	Frame_Shift_Ins	INS	-	-	G																															gccagtctgtgctggaggctINSggggtgccctcagagggctc																								rs536937676	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:106074688_106074689insG	ENST00000337478.1	-	2	1292_1293	c.1121_1122insC	c.(1120-1122)ccafs	p.P374fs	ITPRIP_ENST00000358187.2_Frame_Shift_Ins_p.P374fs|ITPRIP_ENST00000278071.2_Frame_Shift_Ins_p.P374fs|RP11-127L20.5_ENST00000472915.2_RNA	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	374						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						TGCTGGAGGCTGGGGTGCCCTC	0.589																																					p.P374fs													.	ITPRIP-90	0			c.1122_1123insC						.																																			SO:0001589	frameshift_variant	85450	exon2			GGAGGCTGGGGTG	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.1122dupC	10.37:g.106074692_106074692dupG	ENSP00000337178:p.Pro374fs	Somatic	104	0		WXS	Illumina HiSeq	Phase_1	339	96	NM_001272013	0	0	0	0	0	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Frame_Shift_Ins	INS	ENST00000337478.1	37	CCDS7557.1																																																																																			.		0.589	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		G	106074689	-	G	106074688	7	5	51	1	0	1	1	0	0	0	0	0	7944	1567	55	0	525	0	ITPRIP	10	106074688	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	3819507	106074688	29460059	144	4832											
XPNPEP1	7511	bcgsc.ca	37	chr10	111667523	111667523	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagagttcctcatggcttGtctcagctgccgaagcagct	7	11	10	13	1	3	1	3	0	1	1	5	2	4	1	2	1	4	5	2	1	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:111667523G>T	ENST00000502935.1	-	3	291	c.172C>A	c.(172-174)Caa>Aaa	p.Q58K	XPNPEP1_ENST00000430337.1_5'UTR|XPNPEP1_ENST00000369680.4_Missense_Mutation_p.Q15K|XPNPEP1_ENST00000322238.8_Missense_Mutation_p.Q58K|XPNPEP1_ENST00000369683.1_5'UTR					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble											endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		CTCATGGCTTGTCTCAGCTGC	0.537																																					p.Q58K													.	XPNPEP1-94	0			c.C172A						.						222	191	201					10																	111667523		2203	4300	6503	SO:0001583	missense	7511	exon3			TGGCTTGTCTCAG		CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"X-prolyl aminopeptidase (aminopeptidase P)-like"	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.172C>A	10.37:g.111667523G>T	ENSP00000421566:p.Gln58Lys	Somatic	239	0		WXS	Illumina HiSeq	Phase_1	222	110	NM_001167604	0	0	39	41	2		Missense_Mutation	SNP	ENST00000502935.1	37	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434498	0.43224	.	.	ENSG00000108039	ENST00000502935;ENST00000322238;ENST00000369680;ENST00000403138;ENST00000423625	.	.	.	5.33	5.33	0.75918	Creatinase (1);	0.119653	0.64402	D	0.000017	T	0.40297	0.1111	N	0.11698	0.16	0.51233	D	0.999916	B;B;B	0.14012	0.009;0.007;0.009	B;B;B	0.12837	0.008;0.004;0.008	T	0.21211	-1.0252	9	0.23302	T	0.38	-6.8452	15.934	0.79688	0.0:0.0:1.0:0.0	.	58;58;15	B4E2P4;G5E9Y2;Q9NQW7	.;.;XPP1_HUMAN	K	58;58;15;15;15	.	ENSP00000324011:Q58K	Q	-	1	0	XPNPEP1	111657513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.635000	0.67841	2.504000	0.84457	0.655000	0.94253	CAA	.		0.537	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2			T	111667523	G	T	111667523	3	4	51	1	0	0	0	0	1	0	0	0	17475	1386	48	4	1904	4	XPNPEP1	10	111667523	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	5592835	111667523	23867224	145	4833											
DCLRE1A	9937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115608965	115608965	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctacatctctttttttgAcgctgtgacctctcactaga	7	18	5	11	1	3	3	1	2	3	1	5	3	3	3	1	0	1	1	1	0	2	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:115608965A>G	ENST00000361384.2	-	2	2816	c.1899T>C	c.(1897-1899)cgT>cgC	p.R633R	DCLRE1A_ENST00000369305.1_Silent_p.R633R	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	633					mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		TCTTTTTTTGACGCTGTGACC	0.368								Other identified genes with known or suspected DNA repair function																													p.R633R		.											.	DCLRE1A-228	0			c.T1899C						.						162	164	163					10																	115608965		2203	4300	6503	SO:0001819	synonymous_variant	9937	exon2			TTTTTGACGCTGT		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.1899T>C	10.37:g.115608965A>G		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	225	84	NM_014881	0	0	2	5	3	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Silent	SNP	ENST00000361384.2	37	CCDS7584.1																																																																																			.		0.368	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		G	115608965	A	G	115608965	2	3	51	1	0	0	0	0	0	0	0	1	4300	262	10	3		3	DCLRE1A	10	115608965	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	3941442	115608965	19925782	146	4834											
MRGPRX2	117194	bcgsc.ca	37	chr11	19077079	19077079	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgaggatcggctgctgcaGccgccactgcttcctaaaag	8	9	11	13	2	0	1	0	1	0	0	2	2	1	2	3	2	4	4	3	2	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:19077079G>C	ENST00000329773.2	-	2	958	c.871C>G	c.(871-873)Ctg>Gtg	p.L291V		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	291					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)			NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						GGCTGCTGCAGCCGCCACTGC	0.532																																					p.L291V	GBM(198;1966 2199 4849 37227 49954)												.	MRGPRX2-91	0			c.C871G						.						35	43	41					11																	19077079		2198	4293	6491	SO:0001583	missense	117194	exon2			GCTGCAGCCGCCA		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"GPCR / Class A : Orphans"	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.871C>G	11.37:g.19077079G>C	ENSP00000333800:p.Leu291Val	Somatic	82	2		WXS	Illumina HiSeq	Phase_1	96	47	NM_054030	0	0	0	0	0	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	37	CCDS7847.1	.	.	.	.	.	.	.	.	.	.	.	8.321	0.824218	0.16678	.	.	ENSG00000183695	ENST00000329773	T	0.07114	3.22	5.25	-3.39	0.04868	.	1.848080	0.02775	N	0.120139	T	0.07954	0.0199	L	0.47016	1.485	0.09310	N	1	B	0.25441	0.126	B	0.21546	0.035	T	0.38351	-0.9665	10	0.14252	T	0.57	.	7.955	0.30038	0.1138:0.0:0.1876:0.6985	.	291	Q96LB1	MRGX2_HUMAN	V	291	ENSP00000333800:L291V	ENSP00000333800:L291V	L	-	1	2	MRGPRX2	19033655	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.070000	0.00301	-0.322000	0.08615	-0.188000	0.12872	CTG	.		0.532	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030		C	19077079	G	C	19077079	3	2	51	1	0	0	0	0	1	0	0	0	9792	962	34	4	125	4	MRGPRX2	11	19077079	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		19077079	115929437	147	4835											
PDHX	8050	bcgsc.ca	37	chr11	34988257	34988258	+	Frame_Shift_Ins	INS	-	-	ACTCCAGCCCCCC																															cagaccaactccagcccccaINScagccactcccacagcacct																								rs146230351|rs118054792		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:34988257_34988258insACTCCAGCCCCCC	ENST00000227868.4	+	6	796_797	c.712_713insACTCCAGCCCCCC	c.(712-714)acafs	p.T238fs	PDHX_ENST00000430469.2_Intron|PDHX_ENST00000448838.3_Frame_Shift_Ins_p.T223fs			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	238					cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)	p.T238P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TCCAGCCCCCACAGCCACTCCC	0.53																																					p.T238fs													.	PDHX-226	1	Substitution - Missense(1)	large_intestine(1)	c.712_713insACTCCAGCCCCCC						.																																			SO:0001589	frameshift_variant	8050	exon6			GCCCCCACAGCCA	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	Exception_encountered	11.37:g.34988257_34988258insACTCCAGCCCCCC	ENSP00000227868:p.Thr238fs	Somatic	119	0		WXS	Illumina HiSeq	Phase_1	180	0	NM_003477	0	0	0	0	0	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Frame_Shift_Ins	INS	ENST00000227868.4	37	CCDS7896.1																																																																																			.		0.53	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		ACTCCAGCCCCCC	34988258	-	ACTCCAGCCCCCC	34988257	7	5	51	1	0	1	1	0	0	0	0	0	11693	159	6	0	853	0	PDHX	11	34988257	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	15911178	34988257	100018259	148	4836											
SLC43A3	29015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57188512	57188512	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acagagtgatgatggtcgaaCggtgttggccaaataggttc	11	10	14	6	2	0	3	0	2	0	1	2	4	0	3	1	4	1	2	1	4	3	3	rs148055054		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:57188512C>T	ENST00000395123.2	-	7	768	c.464G>A	c.(463-465)cGt>cAt	p.R155H	SLC43A3_ENST00000395124.1_Missense_Mutation_p.R155H|SLC43A3_ENST00000529554.1_Missense_Mutation_p.R155H|SLC43A3_ENST00000352187.1_Missense_Mutation_p.R155H|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000533524.1_Missense_Mutation_p.R168H	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	155					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						GATGGTCGAACGGTGTTGGCC	0.448																																					p.R155H		.											.	SLC43A3-90	0			c.G464A						.	C	HIS/ARG,HIS/ARG,HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	156	128	138		464,464,464	5.8	1	11	dbSNP_134	138	0,8592		0,0,4296	no	missense,missense,missense	SLC43A3	NM_014096.2,NM_017611.2,NM_199329.1	29,29,29	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	155/492,155/492,155/492	57188512	1,12993	2201	4296	6497	SO:0001583	missense	29015	exon7			GTCGAACGGTGTT	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.464G>A	11.37:g.57188512C>T	ENSP00000378555:p.Arg155His	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	91	35	NM_017611	0	0	8	10	2	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	C	35	5.465074	0.96257	2.27E-4	0.0	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005;ENST00000529113;ENST00000525474	T;T;T;T;T;T;D;D	0.84146	-0.35;-0.35;-0.35;-0.35;-0.35;-0.46;-1.81;-1.81	5.85	5.85	0.93711	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.93468	0.7916	M	0.87180	2.865	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.997;0.998	D	0.93715	0.7027	10	0.62326	D	0.03	-17.6544	17.9537	0.89062	0.0:1.0:0.0:0.0	.	155;168;155;155	B4DV87;E7EQD2;Q8NBI5;A8K2X6	.;.;S43A3_HUMAN;.	H	155;155;155;155;168;155;102;155	ENSP00000378555:R155H;ENSP00000378556:R155H;ENSP00000337561:R155H;ENSP00000436254:R155H;ENSP00000434515:R168H;ENSP00000435893:R155H;ENSP00000434293:R102H;ENSP00000436055:R155H	ENSP00000337561:R155H	R	-	2	0	SLC43A3	56945088	1.000000	0.71417	0.993000	0.49108	0.945000	0.59286	6.437000	0.73421	2.782000	0.95742	0.655000	0.94253	CGT	C|1.000;T|0.000		0.448	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		T	57188512	C	T	57188512	3	4	51	1	0	0	0	0	1	0	0	0	14666	536	19	1	1043	1	SLC43A3	11	57188512	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	22200255	57188512	77818004	149	4837											
DAGLA	747	broad.mit.edu	37	chr11	61495728	61495729	+	Frame_Shift_Ins	INS	-	-	G																															gtgctgctccggcagcggcaINSgcgggccaagcgcaacgccg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:61495728_61495729insG	ENST00000257215.5	+	7	856_857	c.740_741insG	c.(739-744)cagcggfs	p.R248fs		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	248					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CGGCAGCGGCAGCGGGCCAAGC	0.624																																					p.Q247fs													.	DAGLA-92	0			c.740_741insG						.																																			SO:0001589	frameshift_variant	747	exon7			AGCGGCAGCGGGC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"neural stem cell-derived dendrite regulator"	614015	"chromosome 11 open reading frame 11"	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.741dupG	11.37:g.61495729_61495729dupG	ENSP00000257215:p.Arg248fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	314	5	NM_006133	0	0	0	0	0	A7E233|Q6WQJ0	Frame_Shift_Ins	INS	ENST00000257215.5	37	CCDS31578.1																																																																																			.		0.624	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		G	61495729	-	G	61495728	7	5	51	1	0	1	1	0	0	0	0	0	4232	188	7	0	762	0	DAGLA	11	61495728	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	4307216	61495728	73510788	150	4838											
SLC22A10	387775	bcgsc.ca	37	chr11	63071626	63071626	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatgtctgggaatcggctgTtctgctgctactttttccag	5	15	11	10	1	2	0	0	0	2	0	4	1	3	1	1	2	3	5	1	2	2	4	rs76578107		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:63071626T>G	ENST00000332793.6	+	8	1334	c.1332T>G	c.(1330-1332)tgT>tgG	p.C444W	SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000544661.1_Missense_Mutation_p.V243G	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	444						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	GAATCGGCTGTTCTGCTGCTA	0.488																																					p.C444W													.	SLC22A10-92	0			c.T1332G						.						207	213	211					11																	63071626		2086	4261	6347	SO:0001583	missense	387775	exon8			CGGCTGTTCTGCT	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.1332T>G	11.37:g.63071626T>G	ENSP00000327569:p.Cys444Trp	Somatic	215	1		WXS	Illumina HiSeq	Phase_1	63	26	NM_001039752	0	0	0	0	0	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.960|6.960	0.547063|0.547063	0.13312|0.13312	.|.	.|.	ENSG00000184999|ENSG00000184999	ENST00000332793|ENST00000544661	T|T	0.59224|0.69306	0.28|-0.39	3.05|3.05	1.81|1.81	0.25067|0.25067	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.427522|.	0.24630|.	U|.	0.036882|.	T|T	0.69602|0.69602	0.3129|0.3129	M|M	0.88377|0.88377	2.95|2.95	0.09310|0.09310	N|N	1|1	P|P	0.47841|0.34684	0.901|0.463	B|B	0.42386|0.37888	0.386|0.26	T|T	0.64474|0.64474	-0.6399|-0.6399	10|9	0.38643|0.72032	T|D	0.18|0.01	.|.	5.2147|5.2147	0.15336|0.15336	0.2588:0.0:0.0:0.7412|0.2588:0.0:0.0:0.7412	.|.	444|238	Q63ZE4|E9PJB1	S22AA_HUMAN|.	W|G	444|243	ENSP00000327569:C444W|ENSP00000445667:V243G	ENSP00000327569:C444W|ENSP00000433817:V238G	C|V	+|+	3|2	2|0	SLC22A10|SLC22A10	62828202|62828202	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.288000|0.288000	0.18939|0.18939	0.348000|0.348000	0.23949|0.23949	0.472000|0.472000	0.43445|0.43445	TGT|GTT	.		0.488	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		G	63071626	T	G	63071626	3	3	51	1	0	0	0	0	1	0	0	0	14473	1731	60	5	1362	5	SLC22A10	11	63071626	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1575898	63071626	71934890	151	4839											
SYVN1	84447	bcgsc.ca	37	chr11	64898255	64898255	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggacatccatacggcaggTggggcaggtctgctgccgct	8	7	15	11	2	1	0	0	0	1	0	2	1	2	1	2	6	3	4	2	6	2	1	rs199952384		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:64898255T>G	ENST00000377190.3	-	11	1076	c.982A>C	c.(982-984)Acc>Ccc	p.T328P	SYVN1_ENST00000526121.1_5'UTR|SYVN1_ENST00000526060.1_Missense_Mutation_p.T328P|SYVN1_ENST00000294256.8_Missense_Mutation_p.T328P|SYVN1_ENST00000307289.6_Missense_Mutation_p.T277P	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	328					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						ATACGGCAGGTGGGGCAGGTC	0.711																																					p.T328P													.	SYVN1-91	0			c.A982C						.						21	25	24					11																	64898255		2190	4272	6462	SO:0001583	missense	84447	exon11			GGCAGGTGGGGCA	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.982A>C	11.37:g.64898255T>G	ENSP00000366395:p.Thr328Pro	Somatic	52	3		WXS	Illumina HiSeq	Phase_1	149	101	NM_172230	0	0	4	6	2	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	37	CCDS31605.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.449287	0.84101	.	.	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.22	5.22	0.72569	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.68513	0.3009	M	0.78223	2.4	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.73161	-0.4070	10	0.87932	D	0	-30.9766	13.0856	0.59138	0.0:0.0:0.0:1.0	.	277;328;328	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	P	328;328;328;277;328	ENSP00000366395:T328P;ENSP00000294256:T328P;ENSP00000302035:T277P;ENSP00000436984:T328P	ENSP00000294256:T328P	T	-	1	0	SYVN1	64654831	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	6.057000	0.71119	1.966000	0.57179	0.379000	0.24179	ACC	.		0.711	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		G	64898255	T	G	64898255	3	3	51	1	0	0	0	0	1	0	0	0	15519	1696	59	5	895	5	SYVN1	11	64898255	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1826629	64898255	70108261	152	4840											
LTBP3	4054	hgsc.bcm.edu	37	chr11	65306859	65306859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacactcgcacacggcgcCgcccggccgcggcacgcagc	6	1	15	19	8	0	0	0	0	0	0	1	1	0	1	3	4	1	3	3	4	0	0	rs372367914	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:65306859C>T	ENST00000301873.5	-	27	3968	c.3700G>A	c.(3700-3702)Ggc>Agc	p.G1234S	LTBP3_ENST00000529189.1_Missense_Mutation_p.G190S|LTBP3_ENST00000536982.1_Missense_Mutation_p.G813S|LTBP3_ENST00000322147.4_Missense_Mutation_p.G1187S|LTBP3_ENST00000530785.1_Missense_Mutation_p.G237S|LTBP3_ENST00000532932.1_Missense_Mutation_p.G664S	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	1234					bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CACACGGCGCCGCCCGGCCGC	0.721													C|||	2	0.000399361	8e-04	0	5008	,	,		7392	0		0.001	False		,,,				2504	0				p.G1234S		.											.	LTBP3-91	0			c.G3700A						.	C	SER/GLY,SER/GLY,SER/GLY	2,3936		0,2,1967	18	21	20		3700,3208,3559	4.8	0.4	11		20	0,7628		0,0,3814	no	missense,missense,missense	LTBP3	NM_001130144.2,NM_001164266.1,NM_021070.4	56,56,56	0,2,5781	TT,TC,CC		0.0,0.0508,0.0173	probably-damaging,probably-damaging,probably-damaging	1234/1304,1070/1140,1187/1257	65306859	2,11564	1969	3814	5783	SO:0001583	missense	4054	exon27			CGGCGCCGCCCGG	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.3700G>A	11.37:g.65306859C>T	ENSP00000301873:p.Gly1234Ser	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	13	9	NM_001130144	0	0	12	37	25	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	37	CCDS44647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.48|18.48	3.632392|3.632392	0.67015|0.67015	5.08E-4|5.08E-4	0.0|0.0	ENSG00000168056|ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000530785;ENST00000529189;ENST00000532932;ENST00000536982;ENST00000532661;ENST00000529371|ENST00000526927	T;T;T;T;T;T;D;T|.	0.86097|.	1.72;1.72;1.72;1.72;1.72;1.72;-2.07;1.72|.	4.79|4.79	4.79|4.79	0.61399|0.61399	Matrix fibril-associated (1);Epidermal growth factor-like (1);|.	0.057494|.	0.64402|.	D|.	0.000002|.	T|T	0.40372|0.40372	0.1114|0.1114	N|N	0.11201|0.11201	0.11|0.11	0.47778|0.47778	D|D	0.999511|0.999511	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	1.0;0.999;0.999;1.0;1.0;0.998|.	T|T	0.30534|0.30534	-0.9975|-0.9975	10|5	0.02654|.	T|.	1|.	.|.	15.3249|15.3249	0.74154|0.74154	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	813;1070;1234;1187;664;813|.	F5GWC4;B9EG76;Q9NS15;Q9NS15-2;E9PJR2;B4DQL8|.	.;.;LTBP3_HUMAN;.;.;.|.	S|Q	1187;1234;237;190;664;813;190;107|837	ENSP00000326647:G1187S;ENSP00000301873:G1234S;ENSP00000434315:G237S;ENSP00000434406:G190S;ENSP00000435530:G664S;ENSP00000441912:G813S;ENSP00000436341:G190S;ENSP00000436032:G107S|.	ENSP00000301873:G1234S|.	G|R	-|-	1|2	0|0	LTBP3|LTBP3	65063435|65063435	0.999000|0.999000	0.42202|0.42202	0.445000|0.445000	0.26908|0.26908	0.187000|0.187000	0.23431|0.23431	4.535000|4.535000	0.60629|0.60629	2.204000|2.204000	0.70986|0.70986	0.561000|0.561000	0.74099|0.74099	GGC|CGG	.		0.721	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		T	65306859	C	T	65306859	3	4	51	1	0	0	0	0	1	0	0	0	9100	652	23	1	219	1	LTBP3	11	65306859	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	408604	65306859	69699657	153	4841											
SF3B2	10992	hgsc.bcm.edu	37	chr11	65835460	65835460	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtgttgccagagaagagaAcagccactgttggaggggcc	10	7	15	9	0	0	2	0	0	0	2	0	5	0	3	3	3	3	2	3	3	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:65835460A>C	ENST00000322535.6	+	20	2423	c.2374A>C	c.(2374-2376)Aca>Cca	p.T792P	SF3B2_ENST00000528302.1_Missense_Mutation_p.T775P|RP11-1167A19.2_ENST00000529036.1_Intron|PACS1_ENST00000320580.4_5'Flank	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	792					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AGAGAAGAGAACAGCCACTGT	0.512											OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T792P		.											.	SF3B2-92	0			c.A2374C						.						138	141	140					11																	65835460		2201	4295	6496	SO:0001583	missense	10992	exon20			AAGAGAACAGCCA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.2374A>C	11.37:g.65835460A>C	ENSP00000318861:p.Thr792Pro	Somatic	139	0	1087	WXS	Illumina HiSeq	Phase_I	482	138	NM_006842	0	0	179	208	29	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	37	CCDS31612.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.7|28.7	4.939948|4.939948	0.92526|0.92526	.|.	.|.	ENSG00000087365|ENSG00000087365	ENST00000530981|ENST00000528302;ENST00000322535;ENST00000355456	.|.	.|.	.|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.092804	.|0.64402	.|D	.|0.000001	T|T	0.77974|0.77974	0.4211|0.4211	M|M	0.84585|0.84585	2.705|2.705	0.80722|0.80722	D|D	1|1	.|D	.|0.61080	.|0.989	.|P	.|0.58331	.|0.837	T|T	0.81818|0.81818	-0.0758|-0.0758	5|9	.|0.66056	.|D	.|0.02	-9.2765|-9.2765	14.0383|14.0383	0.64658|0.64658	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|792	.|Q13435	.|SF3B2_HUMAN	D|P	211|775;792;696	.|.	.|ENSP00000318861:T792P	E|T	+|+	3|1	2|0	SF3B2|SF3B2	65592036|65592036	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.032000|7.032000	0.76498|0.76498	2.197000|2.197000	0.70478|0.70478	0.454000|0.454000	0.30748|0.30748	GAA|ACA	.		0.512	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			C	65835460	A	C	65835460	3	2	51	1	0	0	0	0	1	0	0	0	14183	43	2	5	2452	5	SF3B2	11	65835460	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	528601	65835460	69171056	154	4842											
FOLR2	2350	hgsc.bcm.edu	37	chr11	71932098	71932098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctggggccctggatccAgcaggtagggtgtctccccc	6	7	13	15	0	1	0	0	0	1	0	3	1	2	1	5	5	2	2	5	5	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:71932098A>G	ENST00000298223.6	+	3	522	c.335A>G	c.(334-336)cAg>cGg	p.Q112R	FOLR2_ENST00000454954.2_Missense_Mutation_p.Q71R|FOLR2_ENST00000449475.2_Missense_Mutation_p.Q129R	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	112				IQ -> VR (in Ref. 6; AA sequence). {ECO:0000305}.	folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)			breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	CCCTGGATCCAGCAGGTAGGG	0.637																																					p.Q112R		.											.	FOLR2-290	0			c.A335G						.						17	18	18					11																	71932098		2200	4291	6491	SO:0001583	missense	2350	exon3			GGATCCAGCAGGT	AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.335A>G	11.37:g.71932098A>G	ENSP00000298223:p.Gln112Arg	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	64	7	NM_001113535	0	0	1	1	0	Q05CA5|Q6GTE8	Missense_Mutation	SNP	ENST00000298223.6	37	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	N	8.068	0.769589	0.15983	.	.	ENSG00000165457	ENST00000449475;ENST00000298223;ENST00000454954;ENST00000539412;ENST00000536778;ENST00000535625;ENST00000321324;ENST00000538353	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	4.37	-0.643	0.11482	Folate receptor-like (1);	0.224016	0.38005	N	0.001858	T	0.68824	0.3043	L	0.53249	1.67	0.23023	N	0.998413	B	0.17038	0.02	B	0.25405	0.06	T	0.54450	-0.8292	10	0.25106	T	0.35	.	9.9831	0.41826	0.6851:0.0:0.3149:0.0	.	112	P14207	FOLR2_HUMAN	R	129;112;71;123;127;112;125;112	ENSP00000405638:Q129R;ENSP00000298223:Q112R;ENSP00000414094:Q71R;ENSP00000441547:Q123R;ENSP00000438568:Q127R;ENSP00000444794:Q112R;ENSP00000321957:Q125R;ENSP00000440337:Q112R	ENSP00000298223:Q112R	Q	+	2	0	FOLR2	71609746	0.010000	0.17322	0.901000	0.35422	0.462000	0.32619	0.950000	0.29122	-0.662000	0.05338	-1.815000	0.00603	CAG	.		0.637	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		G	71932098	A	G	71932098	3	3	51	1	0	0	0	0	1	0	0	0	6001	188	7	3	341	3	FOLR2	11	71932098	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	6096638	71932098	63074418	155	4843											
P2RY6	5031	bcgsc.ca	37	chr11	73007682	73007682	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcggcggtgctggcggctgGcctgccgctgaacatctgtg	3	10	16	12	4	1	1	0	1	1	0	2	1	1	1	2	5	3	3	2	5	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:73007682G>C	ENST00000393590.2	+	2	418	c.119G>C	c.(118-120)gGc>gCc	p.G40A	P2RY6_ENST00000540342.1_Missense_Mutation_p.G40A|P2RY6_ENST00000393591.1_Missense_Mutation_p.G40A|P2RY6_ENST00000542092.1_Missense_Mutation_p.G40A|P2RY6_ENST00000538328.1_Missense_Mutation_p.G40A|P2RY6_ENST00000540124.1_Missense_Mutation_p.G40A|P2RY6_ENST00000349767.2_Missense_Mutation_p.G40A|P2RY6_ENST00000393592.2_Missense_Mutation_p.G40A	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	40					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)	p.G40V(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						CTGGCGGCTGGCCTGCCGCTG	0.632																																					p.G40A													.	P2RY6-501	1	Substitution - Missense(1)	lung(1)	c.G119C						.						113	124	120					11																	73007682		2200	4293	6493	SO:0001583	missense	5031	exon4			CGGCTGGCCTGCC		CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.119G>C	11.37:g.73007682G>C	ENSP00000377215:p.Gly40Ala	Somatic	277	0		WXS	Illumina HiSeq	Phase_1	596	132	NM_176796	0	0	12	12	0	Q15754	Missense_Mutation	SNP	ENST00000393590.2	37	CCDS8220.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.621250	0.87460	.	.	ENSG00000171631	ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000544437;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000535931;ENST00000538328	T;T;T;T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.67785	0.2930	M	0.69523	2.12	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.72769	-0.4193	10	0.87932	D	0	.	16.265	0.82571	0.0:0.0:1.0:0.0	.	40	Q15077	P2RY6_HUMAN	A	40	ENSP00000443427:G40A;ENSP00000445652:G40A;ENSP00000309771:G40A;ENSP00000377217:G40A;ENSP00000441079:G40A;ENSP00000377216:G40A;ENSP00000442551:G40A;ENSP00000377215:G40A;ENSP00000440770:G40A;ENSP00000442990:G40A	ENSP00000309771:G40A	G	+	2	0	P2RY6	72685330	1.000000	0.71417	0.994000	0.49952	0.959000	0.62525	6.528000	0.73807	2.367000	0.80283	0.491000	0.48974	GGC	.		0.632	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			C	73007682	G	C	73007682	3	2	51	1	0	0	0	0	1	0	0	0	11380	1203	42	4	121	4	P2RY6	11	73007682	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	1075584	73007682	61998834	156	4844											
GDPD5	81544	broad.mit.edu	37	chr11	75146590	75146591	+	Frame_Shift_Ins	INS	-	-	G																															atgagggtcttggtgtggctINSgccaccccctcgggggccca																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:75146590_75146591insG	ENST00000336898.3	-	17	2616_2617	c.1779_1780insC	c.(1777-1782)ggcagcfs	p.S594fs	GDPD5_ENST00000533784.1_Frame_Shift_Ins_p.S475fs|GDPD5_ENST00000529721.1_Frame_Shift_Ins_p.S594fs|GDPD5_ENST00000376282.3_Frame_Shift_Ins_p.S475fs|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000526177.1_Frame_Shift_Ins_p.S456fs|GDPD5_ENST00000533805.1_Frame_Shift_Ins_p.S349fs	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	594					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						TTGGTGTGGCTGCCACCCCCTC	0.579																																					p.S594fs													.	GDPD5-91	0			c.1780_1781insC						.																																			SO:0001589	frameshift_variant	81544	exon17			TGTGGCTGCCACC	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1780dupC	11.37:g.75146591_75146591dupG	ENSP00000337972:p.Ser594fs	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	307	4	NM_030792	0	0	0	0	0	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Frame_Shift_Ins	INS	ENST00000336898.3	37	CCDS8238.1																																																																																			.		0.579	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		G	75146591	-	G	75146590	7	5	51	1	0	1	1	0	0	0	0	0	6347	1580	55	0	41	0	GDPD5	11	75146590	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	2138908	75146590	59859926	157	4845											
FAT3	120114	bcgsc.ca	37	chr11	92533292	92533292	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agatcaatagatagtggcttCccatcactgagcagtgaggt	12	10	11	8	0	2	4	2	2	0	2	3	4	3	4	1	2	1	2	1	2	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:92533292C>T	ENST00000298047.6	+	9	7130	c.7113C>T	c.(7111-7113)ttC>ttT	p.F2371F	FAT3_ENST00000409404.2_Silent_p.F2371F|FAT3_ENST00000525166.1_Silent_p.F2221F			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2371	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ATAGTGGCTTCCCATCACTGA	0.413										TCGA Ovarian(4;0.039)																											p.F2371F													.	FAT3-73	0			c.C7113T						.						120	118	119					11																	92533292		1934	4134	6068	SO:0001819	synonymous_variant	120114	exon9			TGGCTTCCCATCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7113C>T	11.37:g.92533292C>T		Somatic	134	0		WXS	Illumina HiSeq	Phase_1	62	19	NM_001008781	0	0	0	0	0	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.		0.413	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92533292	C	T	92533292	2	4	51	1	0	0	0	0	0	0	0	1	5710	854	30	2		2	FAT3	11	92533292	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	17386702	92533292	42473224	158	4846											
ARHGAP20	57569	hgsc.bcm.edu;broad.mit.edu	37	chr11	110454361	110454361	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acacacagctaaattaaatgCagtcatctgattggatgagg	15	10	9	7	0	2	2	1	2	1	0	2	3	2	3	0	2	2	2	0	2	4	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:110454361C>G	ENST00000260283.4	-	14	1800	c.1516G>C	c.(1516-1518)Gca>Cca	p.A506P	ARHGAP20_ENST00000524756.1_Missense_Mutation_p.A483P|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.A49P|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.A470P|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.A480P|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.A470P|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.A480P	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	506	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		AAATTAAATGCAGTCATCTGA	0.418																																					p.A506P		.											.	ARHGAP20-230	0			c.G1516C						.						138	119	125					11																	110454361		2201	4298	6499	SO:0001583	missense	57569	exon14			TAAATGCAGTCAT	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.1516G>C	11.37:g.110454361C>G	ENSP00000260283:p.Ala506Pro	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	10	3	NM_020809	0	0	1	1	0	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	19.51	3.840548	0.71488	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13;2.13	5.78	3.9	0.45041	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.059348	0.64402	D	0.000006	T	0.35307	0.0927	L	0.45051	1.395	0.47407	D	0.999418	P;P;P	0.50066	0.931;0.89;0.867	D;D;D	0.67103	0.931;0.949;0.915	T	0.03493	-1.1031	10	0.56958	D	0.05	.	11.2223	0.48862	0.1286:0.8054:0.0:0.066	.	480;506;483	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	P	506;480;49;483;470;480;470	ENSP00000260283:A506P;ENSP00000349660:A480P;ENSP00000437905:A49P;ENSP00000432076:A483P;ENSP00000436319:A470P;ENSP00000436522:A480P;ENSP00000431399:A470P	ENSP00000260283:A506P	A	-	1	0	ARHGAP20	109959571	0.996000	0.38824	0.448000	0.26945	0.922000	0.55478	3.402000	0.52608	0.889000	0.36185	0.591000	0.81541	GCA	.		0.418	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		G	110454361	C	G	110454361	3	3	51	1	0	0	0	0	1	0	0	0	870	710	25	4	2071	4	ARHGAP20	11	110454361	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	17921069	110454361	24552155	159	4847											
ST3GAL4	6484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	126276866	126276866	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttcccatcccagagaagaagGagccgtgcctccagggtgag	10	6	13	12	1	0	3	0	1	0	2	3	5	3	4	5	2	2	0	5	2	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:126276866G>C	ENST00000526727.1	+	3	504	c.130G>C	c.(130-132)Gag>Cag	p.E44Q	ST3GAL4_ENST00000534083.1_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000392669.2_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000227495.6_Missense_Mutation_p.E40Q|ST3GAL4_ENST00000356132.4_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000532243.1_Missense_Mutation_p.E43Q|ST3GAL4_ENST00000530591.1_Missense_Mutation_p.E40Q|ST3GAL4_ENST00000534457.1_Missense_Mutation_p.E39Q|ST3GAL4_ENST00000444328.2_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000449406.2_Missense_Mutation_p.E33Q|ST3GAL4_ENST00000526756.1_3'UTR			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	44					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)			endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		AGAGAAGAAGGAGCCGTGCCT	0.547																																					p.E44Q		.											.	ST3GAL4-90	0			c.G130C						.						85	86	86					11																	126276866		2201	4298	6499	SO:0001583	missense	6484	exon4			AAGAAGGAGCCGT	X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"Sialyltransferases"	10864	protein-coding gene	gene with protein product	"ST3Gal IV"	104240	"sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.130G>C	11.37:g.126276866G>C	ENSP00000436047:p.Glu44Gln	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	419	165	NM_001254757	0	0	14	50	36	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Missense_Mutation	SNP	ENST00000526727.1	37	CCDS58193.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.349790	0.41599	.	.	ENSG00000110080	ENST00000227495;ENST00000444328;ENST00000356132;ENST00000530591;ENST00000534083;ENST00000526311;ENST00000528858;ENST00000534452;ENST00000392669;ENST00000526727;ENST00000449406;ENST00000532243;ENST00000534457	T;T;T;T;T;T;T;T;T;T;T	0.43688	0.94;0.94;0.97;0.94;0.94;0.94;0.94;0.94;0.95;0.94;0.94	5.4	3.42	0.39159	.	0.741690	0.13270	N	0.400600	T	0.28234	0.0697	L	0.50333	1.59	0.09310	N	1	P;P;P	0.49559	0.925;0.454;0.454	B;B;B	0.37346	0.247;0.105;0.105	T	0.09530	-1.0670	10	0.13470	T	0.59	.	6.0778	0.19925	0.1787:0.1907:0.6306:0.0	.	25;40;44	Q9HAA9;Q6IBE6;Q11206	.;.;SIA4C_HUMAN	Q	40;44;44;40;44;44;44;44;44;44;33;43;39	ENSP00000227495:E40Q;ENSP00000394354:E44Q;ENSP00000348451:E44Q;ENSP00000433989:E40Q;ENSP00000433318:E44Q;ENSP00000432424:E44Q;ENSP00000376437:E44Q;ENSP00000436047:E44Q;ENSP00000399444:E33Q;ENSP00000434349:E43Q;ENSP00000434668:E39Q	ENSP00000227495:E40Q	E	+	1	0	ST3GAL4	125782076	0.018000	0.18449	0.992000	0.48379	0.963000	0.63663	1.290000	0.33319	2.527000	0.85204	0.561000	0.74099	GAG	.		0.547	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278		C	126276866	G	C	126276866	3	2	51	1	0	0	0	0	1	0	0	0	15249	1175	41	4	128	4	ST3GAL4	11	126276866	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	15822505	126276866	8729650	160	4848											
ACAD8	27034	bcgsc.ca	37	chr11	134127129	134127129	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacaggctgcaccagcaccAcagcctatataagcatccac	13	6	6	16	0	0	0	0	0	0	0	1	0	1	0	4	1	5	4	4	1	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:134127129A>C	ENST00000281182.4	+	3	464	c.358A>C	c.(358-360)Aca>Cca	p.T120P	ACAD8_ENST00000374752.4_Intron|ACAD8_ENST00000543332.1_Intron|ACAD8_ENST00000537423.1_Missense_Mutation_p.T43P|ACAD8_ENST00000524547.1_Intron	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	120					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	CACCAGCACCACAGCCTATAT	0.512																																					p.T120P	GBM(65;238 1125 33403 41853 48889)												.	ACAD8-90	0			c.A358C						.						69	63	65					11																	134127129		2201	4297	6498	SO:0001583	missense	27034	exon3			AGCACCACAGCCT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.358A>C	11.37:g.134127129A>C	ENSP00000281182:p.Thr120Pro	Somatic	55	0		WXS	Illumina HiSeq	Phase_1	97	39	NM_014384	0	0	26	26	0	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.944585	0.92593	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000537915	D;D	0.99709	-6.48;-6.48	5.73	5.73	0.89815	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99674	0.9878	M	0.83692	2.655	0.80722	D	1	D;D;D	0.76494	0.983;0.998;0.999	D;D;D	0.76575	0.922;0.981;0.988	D	0.97633	1.0143	10	0.72032	D	0.01	.	16.0021	0.80301	1.0:0.0:0.0:0.0	.	61;43;120	B7Z767;B7Z5W4;Q9UKU7	.;.;ACAD8_HUMAN	P	120;43;82	ENSP00000281182:T120P;ENSP00000443763:T43P	ENSP00000281182:T120P	T	+	1	0	ACAD8	133632339	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.167000	0.94773	2.192000	0.70111	0.533000	0.62120	ACA	.		0.512	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		C	134127129	A	C	134127129	3	2	51	1	0	0	0	0	1	0	0	0	110	159	6	5	368	5	ACAD8	11	134127129	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	7850263	134127129	879387	161	4849											
WNK1	65125	bcgsc.ca	37	chr12	977305	977305	+	Intron	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgtagttatgttgggtactAcagccagtagagtaactgga	11	11	12	7	1	0	1	0	0	0	1	0	2	0	2	2	2	4	6	2	2	6	7	rs375911794		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:977305A>C	ENST00000315939.6	+	9	2782				WNK1_ENST00000535572.1_Intron|WNK1_ENST00000537687.1_Missense_Mutation_p.T805P|WNK1_ENST00000574564.1_Missense_Mutation_p.T104P|WNK1_ENST00000530271.2_Missense_Mutation_p.T890P|WNK1_ENST00000340908.4_Intron	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.T805P(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GTTGGGTACTACAGCCAGTAG	0.493																																					p.T890P	Colon(19;451 567 6672 12618 28860)												.	WNK1-916	1	Substitution - Missense(1)	prostate(1)	c.A2668C						.						78	77	77					12																	977305		1926	4131	6057	SO:0001627	intron_variant	65125	exon10			GGTACTACAGCCA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2140-3126A>C	12.37:g.977305A>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_1	114	53	NM_213655	0	0	0	0	0	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	4.389	0.071873	0.08436	.	.	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.15718	2.4;2.4	5.15	-0.612	0.11597	.	.	.	.	.	T	0.05410	0.0143	.	.	.	0.80722	D	1	B	0.19583	0.037	B	0.21151	0.033	T	0.41395	-0.9511	8	0.02654	T	1	.	4.0408	0.09750	0.4731:0.0:0.2889:0.2381	.	890	F5H2M7	.	P	805;890	ENSP00000444465:T805P;ENSP00000433548:T890P	ENSP00000433548:T890P	T	+	1	0	WNK1	847566	0.661000	0.27430	0.556000	0.28293	0.869000	0.49853	1.016000	0.29976	0.047000	0.15862	0.383000	0.25322	ACA	.		0.493	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		C	977305	A	C	977305	1	2	51	0	1	0	0	0	0	0	0	0	17410	391	14	5		5	WNK1	12	977305	Intron	SNP	A	TCGA-B9-4117-01A-01D-1252-08		977305	132874590	162	4850											
WNK1	65125	bcgsc.ca	37	chr12	988849	988849	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcatttccttccagtgggAcagccgctccctactccctt	5	12	7	17	1	1	0	1	0	0	0	5	1	5	1	5	1	2	2	5	1	1	4	rs201077153		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:988849A>C	ENST00000315939.6	+	11	3127	c.2484A>C	c.(2482-2484)ggA>ggC	p.G828G	WNK1_ENST00000535572.1_Intron|WNK1_ENST00000537687.1_Intron|WNK1_ENST00000530271.2_Silent_p.G1326G|WNK1_ENST00000340908.4_Silent_p.G421G	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	828					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTCCAGTGGGACAGCCGCTCC	0.547																																					p.G828G	Colon(19;451 567 6672 12618 28860)												.	WNK1-916	0			c.A2484C						.						164	140	148					12																	988849		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon11			AGTGGGACAGCCG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2484A>C	12.37:g.988849A>C		Somatic	140	0		WXS	Illumina HiSeq	Phase_1	85	20	NM_018979	0	0	4	4	0	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			.		0.547	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		C	988849	A	C	988849	2	2	51	1	0	0	0	0	0	0	0	1	17410	262	10	5		5	WNK1	12	988849	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	11544	988849	132863046	163	4851											
C1S	716	bcgsc.ca	37	chr12	7171607	7171607	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agattttgtagatgtcccttGtagccacttctgcaacaatt	10	15	7	9	0	1	2	0	0	1	2	2	2	2	2	2	0	3	3	2	0	4	7	rs201505473		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:7171607G>T	ENST00000406697.1	+	8	1056	c.428G>T	c.(427-429)tGt>tTt	p.C143F	C1S_ENST00000328916.3_Missense_Mutation_p.C143F|C1S_ENST00000360817.5_Missense_Mutation_p.C143F|C1S_ENST00000402681.3_5'UTR			P09871	C1S_HUMAN	complement component 1, s subcomponent	143	EGF-like; calcium-binding.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GATGTCCCTTGTAGCCACTTC	0.433																																					p.C143F	GBM(156;750 1943 12971 24779 31015)												.	C1S-91	0			c.G428T						.						183	183	183					12																	7171607		2203	4300	6503	SO:0001583	missense	716	exon5			TCCCTTGTAGCCA		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"Complement system"	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.428G>T	12.37:g.7171607G>T	ENSP00000385035:p.Cys143Phe	Somatic	213	0		WXS	Illumina HiSeq	Phase_1	168	36	NM_201442	1	0	91	92	0	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.428176	0.83667	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000403949	D;D;D;D	0.99818	-6.92;-6.92;-6.92;-5.91	5.96	5.96	0.96718	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.000000	0.46145	D	0.000314	D	0.99921	0.9963	H	0.99368	4.535	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96217	0.9157	10	0.87932	D	0	.	19.4101	0.94667	0.0:0.0:1.0:0.0	.	143	P09871	C1S_HUMAN	F	143;143;143;132;143	ENSP00000385035:C143F;ENSP00000328173:C143F;ENSP00000354057:C143F;ENSP00000384464:C143F	ENSP00000328173:C143F	C	+	2	0	C1S	7041868	1.000000	0.71417	0.989000	0.46669	0.839000	0.47603	8.555000	0.90693	2.832000	0.97577	0.655000	0.94253	TGT	.		0.433	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		T	7171607	G	T	7171607	3	4	51	1	0	0	0	0	1	0	0	0	1980	1377	48	4	442	4	C1S	12	7171607	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	6182758	7171607	126680288	164	4852											
CD163	9332	bcgsc.ca	37	chr12	7654024	7654024	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccgctacacttgttttcAccatccactagcctcagctc	7	12	4	18	1	2	0	2	0	0	0	5	0	4	0	4	0	3	3	4	0	2	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:7654024A>C	ENST00000359156.4	-	3	370	c.168T>G	c.(166-168)ggT>ggG	p.G56G	CD163_ENST00000432237.2_Silent_p.G56G|CD163_ENST00000396620.3_Silent_p.G56G|CD163_ENST00000541972.1_Silent_p.G44G	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	56	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	ACTTGTTTTCACCATCCACTA	0.458																																					p.G56G													.	CD163-98	0			c.T168G						.						136	123	127					12																	7654024		2203	4300	6503	SO:0001819	synonymous_variant	9332	exon3			GTTTTCACCATCC	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.168T>G	12.37:g.7654024A>C		Somatic	156	0		WXS	Illumina HiSeq	Phase_1	57	28	NM_203416	0	0	34	37	3	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1																																																																																			.		0.458	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		C	7654024	A	C	7654024	2	2	51	1	0	0	0	0	0	0	0	1	2973	146	6	5		5	CD163	12	7654024	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	482417	7654024	126197871	165	4853											
PRB2	653247	broad.mit.edu	37	chr12	11545949	11545951	+	In_Frame_Del	DEL	TGC	TGC	-																															agatcgggcacttcgggactTgctgcctccttgtgggggtg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:11545949_11545951delTGC	ENST00000389362.4	-	3	1096_1098	c.1061_1063delGCA	c.(1060-1065)agcaag>aag	p.S354del	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	354	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			CTTCGGGACTTGCTGCCTCCTTG	0.601																																					p.354_355del													.	PRB2-22	0			c.1061_1063del						.																																			SO:0001651	inframe_deletion	653247	exon3			GGGACTTGCTGCC	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.1061_1063delGCA	12.37:g.11545952_11545954delTGC	ENSP00000374013:p.Ser354del	Somatic	554	0		WXS	Illumina HiSeq	Phase_I	1460	15	NM_006248	0	0	0	0	0	O00599|P02811|P04281	In_Frame_Del	DEL	ENST00000389362.4	37	CCDS41757.2																																																																																			.		0.601	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248		-	11545951	TGC	-	11545949	7	5	51	1	0	1	0	1	0	0	0	0	12472	1821	63	0	191	0	PRB2	12	11545949	In_Frame_Del	DEL	TGC	TCGA-B9-4117-01A-01D-1252-08	3891925	11545949	122305946	166	4854											
PKP2	5318	bcgsc.ca	37	chr12	32974403	32974403	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttataacaatggaatgccAcagccactccacgcccttgg	11	8	7	15	1	0	0	0	0	0	0	1	1	1	1	5	2	3	0	5	2	4	3	rs200327989		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:32974403A>C	ENST00000070846.6	-	10	2056	c.2032T>G	c.(2032-2034)Tgg>Ggg	p.W678G	PKP2_ENST00000340811.4_Missense_Mutation_p.W634G	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	678					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					ATGGAATGCCACAGCCACTCC	0.502																																					p.W678G													.	PKP2-92	0			c.T2032G						.						95	80	85					12																	32974403		2203	4300	6503	SO:0001583	missense	5318	exon10			AATGCCACAGCCA	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"Armadillo repeat containing"	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.2032T>G	12.37:g.32974403A>C	ENSP00000070846:p.Trp678Gly	Somatic	70	1		WXS	Illumina HiSeq	Phase_1	32	14	NM_004572	0	0	1	1	0	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.053939	0.75960	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	D;D	0.84223	-1.82;-1.82	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.92708	0.7682	M	0.86420	2.815	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.93797	0.7097	10	0.87932	D	0	-20.5891	13.0643	0.59024	1.0:0.0:0.0:0.0	.	634;634;678	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	G	634;678;678	ENSP00000342800:W634G;ENSP00000070846:W678G	ENSP00000070846:W678G	W	-	1	0	PKP2	32865670	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	7.949000	0.87791	1.815000	0.52974	0.460000	0.39030	TGG	.		0.502	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		C	32974403	A	C	32974403	3	2	51	1	0	0	0	0	1	0	0	0	12011	159	6	5	633	5	PKP2	12	32974403	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	21428454	32974403	100877492	167	4855											
SLC11A2	4891	bcgsc.ca	37	chr12	51384724	51384724	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagattcctcctgcaatccGccagcctctgtaaaagaaat	13	9	6	13	1	1	2	0	0	1	2	4	2	4	2	5	0	2	2	5	0	5	2	rs199589052		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:51384724G>C	ENST00000262051.7	-	15	1516	c.1429C>G	c.(1429-1431)Cgg>Ggg	p.R477G	SLC11A2_ENST00000546743.1_Missense_Mutation_p.R398G|SLC11A2_ENST00000541174.2_Missense_Mutation_p.R477G|SLC11A2_ENST00000547688.1_Missense_Mutation_p.R506G|SLC11A2_ENST00000262052.5_Missense_Mutation_p.R477G|SLC11A2_ENST00000394904.3_Missense_Mutation_p.R506G|SLC11A2_ENST00000547198.1_Missense_Mutation_p.R477G|SLC11A2_ENST00000545993.2_Missense_Mutation_p.R473G	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	477					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						CCTGCAATCCGCCAGCCTCTG	0.438																																					p.R506G													.	SLC11A2-153	0			c.C1516G						.						70	63	65					12																	51384724		2203	4300	6503	SO:0001583	missense	4891	exon15			CAATCCGCCAGCC	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"Solute carriers"	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1429C>G	12.37:g.51384724G>C	ENSP00000262051:p.Arg477Gly	Somatic	78	0		WXS	Illumina HiSeq	Phase_1	29	12	NM_001174125	0	0	0	0	0	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.811787	0.50527	.	.	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.30714	1.92;1.92;1.92;1.91;1.91;1.92;1.92;1.52	5.91	2.1	0.27182	.	0.090350	0.85682	D	0.000000	T	0.34861	0.0912	M	0.63428	1.95	0.37707	D	0.924444	B;B;B;B;B;B	0.30033	0.105;0.169;0.266;0.169;0.005;0.001	B;B;B;B;B;B	0.36335	0.051;0.222;0.222;0.109;0.013;0.004	T	0.37911	-0.9685	10	0.72032	D	0.01	-11.6909	12.8814	0.58020	0.0:0.0:0.4077:0.5923	.	440;473;506;477;326;477	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	G	477;477;477;506;506;477;473;398	ENSP00000262051:R477G;ENSP00000446769:R477G;ENSP00000262052:R477G;ENSP00000378364:R506G;ENSP00000449200:R506G;ENSP00000444542:R477G;ENSP00000442810:R473G;ENSP00000446914:R398G	ENSP00000262051:R477G	R	-	1	2	SLC11A2	49670991	1.000000	0.71417	0.999000	0.59377	0.898000	0.52572	2.789000	0.47813	0.105000	0.17753	-0.271000	0.10264	CGG	G|0.998;C|0.002		0.438	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1			C	51384724	G	C	51384724	3	2	51	1	0	0	0	0	1	0	0	0	14413	1086	38	4	346	4	SLC11A2	12	51384724	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	18410321	51384724	82467171	168	4856											
GEFT	115557	bcgsc.ca	37	chr12	58010627	58010628	+	Frame_Shift_Ins	INS	-	-	C																															agtctctccaactccaaaaaINScccctccctgccaagccaga																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:58010627_58010628insC	ENST00000286494.4	+	15	2153_2154	c.1693_1694insC	c.(1693-1695)accfs	p.T565fs	AC025165.8_ENST00000444467.1_RNA|ARHGEF25_ENST00000477314.1_3'UTR|AC025165.8_ENST00000610219.1_RNA|ARHGEF25_ENST00000333972.7_Frame_Shift_Ins_p.T604fs|AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000356672.3_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	565						cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						AACTCCAAAAACCCCTCCCTGC	0.54																																					p.T604fs													.	ARHGEF25-653	0			c.1810_1811insC						.																																			SO:0001589	frameshift_variant	115557	exon16			CCAAAAACCCCTC		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1697dupC	12.37:g.58010631_58010631dupC	ENSP00000286494:p.Thr565fs	Somatic	205	0		WXS	Illumina HiSeq	Phase_1	252	71	NM_001111270	0	0	0	0	0	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Frame_Shift_Ins	INS	ENST00000286494.4	37	CCDS8947.1																																																																																			.		0.54	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		C	58010628	-	C	58010627	7	5	51	1	0	1	1	0	0	0	0	0	6348	43	2	0	1973	0	GEFT	12	58010627	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	6625903	58010627	75841268	169	4857											
SLC26A10	65012	bcgsc.ca	37	chr12	58017668	58017669	+	Frame_Shift_Ins	INS	-	-	G																															ctgtcggtgctgctgtggctINSggggcccttcttttactatc																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:58017668_58017669insG	ENST00000320442.4	+	8	1414_1415	c.1103_1104insG	c.(1102-1107)ctggggfs	p.LG368fs	SLC26A10_ENST00000379218.2_Frame_Shift_Ins_p.LG368fs	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	368						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					CTGCTGTGGCTGGGGCCCTTCT	0.569																																					p.L368fs													.	SLC26A10-531	0			c.1103_1104insG						.																																			SO:0001589	frameshift_variant	65012	exon8			TGTGGCTGGGGCC		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1107dupG	12.37:g.58017672_58017672dupG	ENSP00000320217:p.Leu368fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_1	289	72	NM_133489	0	0	0	0	0	A6NMJ2|B6ZDQ3|Q6ZWI7	Frame_Shift_Ins	INS	ENST00000320442.4	37	CCDS8949.2																																																																																			.		0.569	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			G	58017669	-	G	58017668	7	5	51	1	0	1	1	0	0	0	0	0	14547	1580	55	0	1133	0	SLC26A10	12	58017668	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	7041	58017668	75834227	170	4858											
CCDC59	29080	bcgsc.ca	37	chr12	82750844	82750844	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcttcaagcaacggctggTgaacttgttctgacaaagga	11	11	11	8	1	3	2	1	2	2	0	3	3	3	3	0	3	3	4	0	3	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:82750844T>G	ENST00000256151.7	-	2	770	c.359A>C	c.(358-360)cAc>cCc	p.H120P	METTL25_ENST00000248306.3_5'Flank|CCDC59_ENST00000548126.1_5'UTR	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	120					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						CAACGGCTGGTGAACTTGTTC	0.413																																					p.H120P													.	CCDC59-90	0			c.A359C						.						194	172	179					12																	82750844		2203	4300	6503	SO:0001583	missense	29080	exon2			GGCTGGTGAACTT	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.359A>C	12.37:g.82750844T>G	ENSP00000256151:p.His120Pro	Somatic	140	3		WXS	Illumina HiSeq	Phase_1	107	53	NM_014167	0	0	27	27	0	Q9H2V5|Q9NW62	Missense_Mutation	SNP	ENST00000256151.7	37	CCDS9023.1	.	.	.	.	.	.	.	.	.	.	T	3.450	-0.112256	0.06881	.	.	ENSG00000133773	ENST00000552377;ENST00000256151	.	.	.	4.05	0.154	0.14901	.	0.563015	0.19793	N	0.105924	T	0.20414	0.0491	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.18555	-1.0333	9	0.31617	T	0.26	-37.4784	9.771	0.40589	0.0:0.0:0.5532:0.4468	.	120	Q9P031	TAP26_HUMAN	P	120	.	ENSP00000256151:H120P	H	-	2	0	CCDC59	81274975	0.000000	0.05858	0.000000	0.03702	0.151000	0.21798	0.221000	0.17680	0.024000	0.15214	-0.313000	0.08912	CAC	.		0.413	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167		G	82750844	T	G	82750844	3	3	51	1	0	0	0	0	1	0	0	0	2835	1696	59	5	378	5	CCDC59	12	82750844	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	24733176	82750844	51101051	171	4859											
UBE2N	7334	bcgsc.ca	37	chr12	93804525	93804525	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatacctgtttctatggcttGggcttcgttggtcttccact	4	17	10	10	1	2	0	0	0	2	0	4	1	3	0	2	3	1	4	2	3	2	7			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:93804525G>T	ENST00000318066.2	-	3	780	c.403C>A	c.(403-405)Caa>Aaa	p.Q135K	UBE2N_ENST00000552442.1_Intron|UBE2N_ENST00000550657.1_3'UTR|UBE2N_ENST00000549833.1_Missense_Mutation_p.Q72K	NM_003348.3	NP_003339.1	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	135					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						TCTATGGCTTGGGCTTCGTTG	0.428								Direct reversal of damage;Rad6 pathway																													p.Q135K	Pancreas(197;738 2228 30225 32034 33454)												.	UBE2N-659	0			c.C403A						.						177	154	162					12																	93804525		2203	4300	6503	SO:0001583	missense	7334	exon3			TGGCTTGGGCTTC	D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889		"Ubiquitin-conjugating enzymes E2"	12492	protein-coding gene	gene with protein product		603679	"ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13)", "ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)"			8902611	Standard	NM_003348		Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000318066.2:c.403C>A	12.37:g.93804525G>T	ENSP00000316176:p.Gln135Lys	Somatic	206	0		WXS	Illumina HiSeq	Phase_1	110	30	NM_003348	0	0	110	116	6	Q16781|Q53Y81	Missense_Mutation	SNP	ENST00000318066.2	37	CCDS31875.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.395622	0.42512	.	.	ENSG00000177889	ENST00000318066;ENST00000549833	T;T	0.36340	1.26;1.26	5.94	5.94	0.96194	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	.	.	.	.	T	0.21468	0.0517	N	0.11341	0.13	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.15549	-1.0433	9	0.02654	T	1	.	20.3736	0.98901	0.0:0.0:1.0:0.0	.	135	P61088	UBE2N_HUMAN	K	135;72	ENSP00000316176:Q135K;ENSP00000450260:Q72K	ENSP00000316176:Q135K	Q	-	1	0	UBE2N	92328656	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.814000	0.62627	2.820000	0.97059	0.650000	0.86243	CAA	.		0.428	UBE2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407710.1	NM_003348		T	93804525	G	T	93804525	3	4	51	1	0	0	0	0	1	0	0	0	16899	1357	47	4	63	4	UBE2N	12	93804525	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	11053681	93804525	40047370	172	4860											
MYBPC1	4604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	102038482	102038482	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgcatatcaggttgacaaAggaggcagagtgaggtttgt	11	10	14	6	0	1	3	1	2	0	1	1	4	1	4	1	4	1	4	1	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:102038482A>T	ENST00000550270.1	+	10	798	c.798A>T	c.(796-798)aaA>aaT	p.K266N	MYBPC1_ENST00000547509.1_Missense_Mutation_p.K252N|MYBPC1_ENST00000541119.1_Missense_Mutation_p.K254N|MYBPC1_ENST00000551300.1_Missense_Mutation_p.K167N|MYBPC1_ENST00000545503.2_Missense_Mutation_p.K266N|MYBPC1_ENST00000550501.1_Intron|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000452455.2_Missense_Mutation_p.K266N|MYBPC1_ENST00000441232.1_Missense_Mutation_p.K266N|MYBPC1_ENST00000360610.2_Missense_Mutation_p.K266N|MYBPC1_ENST00000361685.2_Missense_Mutation_p.K291N|MYBPC1_ENST00000536007.1_Missense_Mutation_p.K247N|MYBPC1_ENST00000547405.1_Missense_Mutation_p.K240N|MYBPC1_ENST00000361466.2_Missense_Mutation_p.K291N|MYBPC1_ENST00000553190.1_Missense_Mutation_p.K266N|MYBPC1_ENST00000392934.3_Missense_Mutation_p.K253N|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000549145.1_Missense_Mutation_p.K279N			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	266	Ig-like C2-type 2.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						AGGTTGACAAAGGAGGCAGAG	0.368																																					p.K291N		.											.	MYBPC1-94	0			c.A873T						.						86	82	83					12																	102038482		2203	4300	6503	SO:0001583	missense	4604	exon12			TGACAAAGGAGGC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.798A>T	12.37:g.102038482A>T	ENSP00000449702:p.Lys266Asn	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	65	18	NM_206819	0	0	0	0	0	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.395297	0.83011	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000037	T	0.69806	0.3152	M	0.87328	2.875	0.80722	D	1	P;D;D;D;D;P;D;D;P;D;D	0.89917	0.623;1.0;0.999;1.0;0.999;0.623;0.999;1.0;0.863;0.999;0.999	P;D;D;D;D;P;D;D;P;D;D	0.91635	0.499;0.999;0.993;0.999;0.998;0.627;0.998;0.999;0.614;0.998;0.999	T	0.75926	-0.3145	10	0.87932	D	0	.	15.8202	0.78633	1.0:0.0:0.0:0.0	.	247;254;266;266;253;240;266;266;291;291;279	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	N	240;266;266;266;253;252;291;279;266;291;266;247;254;291;167;266	ENSP00000448175:K240N;ENSP00000400908:K266N;ENSP00000388989:K266N;ENSP00000353822:K266N;ENSP00000376665:K253N;ENSP00000447362:K252N;ENSP00000354845:K291N;ENSP00000447660:K279N;ENSP00000447900:K266N;ENSP00000440034:K266N;ENSP00000446128:K247N;ENSP00000442847:K254N;ENSP00000354849:K291N;ENSP00000447116:K167N;ENSP00000449702:K266N	ENSP00000353822:K266N	K	+	3	2	MYBPC1	100562613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.038000	0.64177	2.212000	0.71576	0.533000	0.62120	AAA	.		0.368	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102038482	A	T	102038482	3	4	51	1	0	0	0	0	1	0	0	0	10036	69	3	5	919	5	MYBPC1	12	102038482	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	8233957	102038482	31813413	173	4861											
STAB2	55576	bcgsc.ca	37	chr12	104030938	104030938	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaaaattccagatgttcGccttccactgaagatgaaaa	15	9	7	10	1	0	5	0	2	0	3	3	5	2	5	4	0	0	1	4	0	5	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:104030938G>C	ENST00000388887.2	+	7	837	c.633G>C	c.(631-633)tcG>tcC	p.S211S		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCAGATGTTCGCCTTCCACTG	0.433																																					p.S211S													.	STAB2-104	0			c.G633C						.						117	116	116					12																	104030938		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon7			ATGTTCGCCTTCC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"hyaluronic acid receptor for endocytosis"	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.633G>C	12.37:g.104030938G>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_1	78	35	NM_017564	0	0	0	0	0		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			.		0.433	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			C	104030938	G	C	104030938	2	2	51	1	0	0	0	0	0	0	0	1	15270	1074	38	4		4	STAB2	12	104030938	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	1992456	104030938	29820957	174	4862											
ACAD10	80724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112174685	112174685	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatccctgctgcagaggagTatttcaggatgtactgtctc	9	12	11	9	0	2	1	1	0	1	1	4	4	3	3	1	2	3	4	1	2	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:112174685T>A	ENST00000313698.4	+	12	1746	c.1591T>A	c.(1591-1593)Tat>Aat	p.Y531N	ACAD10_ENST00000392636.2_Missense_Mutation_p.Y133N|ACAD10_ENST00000549590.1_Missense_Mutation_p.Y531N|ACAD10_ENST00000455480.2_Missense_Mutation_p.Y562N|ACAD10_ENST00000413681.3_3'UTR	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	531						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						TGCAGAGGAGTATTTCAGGAT	0.502																																					p.Y562N		.											.	ACAD10-92	0			c.T1684A						.						124	112	116					12																	112174685		2203	4300	6503	SO:0001583	missense	80724	exon13			GAGGAGTATTTCA	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"acyl-Coenzyme A dehydrogenase family, member 10"			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.1591T>A	12.37:g.112174685T>A	ENSP00000325137:p.Tyr531Asn	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	132	50	NM_001136538	0	0	13	26	13	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	37	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.801553	0.70682	.	.	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000549590;ENST00000455480;ENST00000313698	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.29	4.14	0.48551	Protein kinase-like domain (1);	0.289517	0.34133	N	0.004238	T	0.61887	0.2383	M	0.92880	3.355	0.37403	D	0.912927	D;D;D	0.89917	0.997;0.999;1.0	P;D;D	0.91635	0.879;0.957;0.999	T	0.72020	-0.4416	10	0.66056	D	0.02	.	10.4594	0.44570	0.0:0.0776:0.0:0.9224	.	562;531;531	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	N	133;531;531;562;531	ENSP00000376411:Y133N;ENSP00000446959:Y531N;ENSP00000389813:Y562N;ENSP00000325137:Y531N	ENSP00000325137:Y531N	Y	+	1	0	ACAD10	110659068	0.972000	0.33761	0.981000	0.43875	0.974000	0.67602	1.626000	0.37039	0.863000	0.35553	0.459000	0.35465	TAT	.		0.502	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		A	112174685	T	A	112174685	3	1	51	1	0	0	0	0	1	0	0	0	108	1638	57	5	1730	5	ACAD10	12	112174685	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8143747	112174685	21677210	175	4863											
KNTC1	9735	broad.mit.edu;ucsc.edu	37	chr12	123105091	123105091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatatccagttagaacttcCggcttttgcattagcttgtc	8	16	8	9	1	0	1	0	0	0	1	3	1	2	1	2	1	3	5	2	1	5	8	rs370269719		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:123105091C>T	ENST00000333479.7	+	60	6392	c.6215C>T	c.(6214-6216)cCg>cTg	p.P2072L	KNTC1_ENST00000450485.2_Missense_Mutation_p.P997L|HCAR1_ENST00000356987.2_3'UTR|KNTC1_ENST00000537348.1_3'UTR|KNTC1_ENST00000436959.3_5'UTR|KNTC1_ENST00000534995.1_5'UTR	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	2072					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TTAGAACTTCCGGCTTTTGCA	0.458																																					p.P2072L													.	KNTC1-543	0			c.C6215T						.	C	LEU/PRO	2,3962		0,2,1980	87	82	84		6215	5.6	1	12		84	0,8364		0,0,4182	no	missense	KNTC1	NM_014708.4	98	0,2,6162	TT,TC,CC		0.0,0.0505,0.0162	probably-damaging	2072/2210	123105091	2,12326	1982	4182	6164	SO:0001583	missense	9735	exon60			AACTTCCGGCTTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"rough deal homolog (Drosophila)"	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.6215C>T	12.37:g.123105091C>T	ENSP00000328236:p.Pro2072Leu	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	51	4	NM_014708	0	0	7	7	0	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.028470	0.75390	5.05E-4	0.0	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.33216	1.42;1.42	5.62	5.62	0.85841	RZZ complex, subunit KNTC1/ROD, C-terminal (1);	0.048083	0.85682	D	0.000000	T	0.55893	0.1949	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.984;0.998	T	0.49062	-0.8978	10	0.37606	T	0.19	-18.0077	19.2653	0.93983	0.0:1.0:0.0:0.0	.	997;2072	E7ES84;P50748	.;KNTC1_HUMAN	L	997;2072	ENSP00000397992:P997L;ENSP00000328236:P2072L	ENSP00000328236:P2072L	P	+	2	0	KNTC1	121671044	1.000000	0.71417	0.956000	0.39512	0.220000	0.24768	6.355000	0.73041	2.665000	0.90641	0.650000	0.86243	CCG	.		0.458	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			T	123105091	C	T	123105091	3	4	51	1	0	0	0	0	1	0	0	0	8449	652	23	1	6449	1	KNTC1	12	123105091	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	10930406	123105091	10746804	176	4864											
RIMBP2	23504	bcgsc.ca	37	chr12	130892349	130892349	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgcgtcgataccgaatgAcgcctgccacttctcctgct	6	10	8	17	5	1	1	0	1	1	0	4	3	2	1	5	0	3	1	5	0	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:130892349A>C	ENST00000261655.4	-	16	3010	c.2847T>G	c.(2845-2847)cgT>cgG	p.R949R		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	949					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		ATACCGAATGACGCCTGCCAC	0.532																																					p.R949R													.	RIMBP2-142	0			c.T2847G						.						210	166	181					12																	130892349		2203	4300	6503	SO:0001819	synonymous_variant	23504	exon16			CGAATGACGCCTG	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2847T>G	12.37:g.130892349A>C		Somatic	190	0		WXS	Illumina HiSeq	Phase_1	299	110	NM_015347	0	0	0	0	0	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			.		0.532	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		C	130892349	A	C	130892349	2	2	51	1	0	0	0	0	0	0	0	1	13395	262	10	5		5	RIMBP2	12	130892349	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	7787258	130892349	2959546	177	4865											
EP400	57634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132551479	132551479	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccatgaacgtcgcggggaTcagcgtggcgatcggtcagc	7	6	16	12	6	2	1	2	1	0	0	4	3	2	2	1	4	3	0	1	4	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:132551479T>A	ENST00000333577.4	+	50	8931	c.8822T>A	c.(8821-8823)aTc>aAc	p.I2941N	EP400_ENST00000330386.6_Missense_Mutation_p.I2824N|EP400_ENST00000389562.2_Missense_Mutation_p.I2904N|EP400_ENST00000389561.2_Missense_Mutation_p.I2905N|EP400_ENST00000332482.4_Missense_Mutation_p.I2868N			Q96L91	EP400_HUMAN	E1A binding protein p400	2941					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		GTCGCGGGGATCAGCGTGGCG	0.687																																					p.I2905N		.											.	EP400-520	0			c.T8714A						.						29	29	29					12																	132551479		2203	4299	6502	SO:0001583	missense	57634	exon49			CGGGGATCAGCGT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8822T>A	12.37:g.132551479T>A	ENSP00000333602:p.Ile2941Asn	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	89	35	NM_015409	0	0	9	15	6	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	T	18.43	3.621758	0.66787	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.92545	-3.06;-3.05;-2.99;-3.01;-3.02	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.93112	0.7807	L	0.34521	1.04	0.44899	D	0.997913	D;D;D;D	0.89917	0.992;1.0;1.0;1.0	D;D;D;D	0.87578	0.976;0.998;0.998;0.998	D	0.92827	0.6277	10	0.40728	T	0.16	.	14.4084	0.67099	0.0:0.0:0.0:1.0	.	2941;2905;2824;2904	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	N	2941;2905;2904;2868;2824;2905	ENSP00000333602:I2941N;ENSP00000374212:I2905N;ENSP00000374213:I2904N;ENSP00000331737:I2868N;ENSP00000330620:I2824N	ENSP00000330620:I2824N	I	+	2	0	EP400	131117432	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	1.817000	0.53016	0.454000	0.30748	ATC	.		0.687	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132551479	T	A	132551479	3	1	51	1	0	0	0	0	1	0	0	0	5162	1435	50	5	8901	5	EP400	12	132551479	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1659130	132551479	1300416	178	4866											
IFT88	8100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	21189985	21189985	+	Missense_Mutation	SNP	T	T	G																															tgcaaaactcattgctcctgTaattgaaacatcttttgctg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:21189985T>G	ENST00000319980.6	+	16	1520	c.1193T>G	c.(1192-1194)gTa>gGa	p.V398G	IFT88_ENST00000461115.1_3'UTR|IFT88_ENST00000537103.1_Missense_Mutation_p.V370G|IFT88_ENST00000382778.4_Missense_Mutation_p.V398G|IFT88_ENST00000351808.5_Missense_Mutation_p.V389G	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	398					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		ATTGCTCCTGTAATTGAAACA	0.279																																					p.V398G		.											.	IFT88-91	0			c.T1193G						.						81	91	87					13																	21189985		2203	4295	6498	SO:0001583	missense	8100	exon16			CTCCTGTAATTGA	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.1193T>G	13.37:g.21189985T>G	ENSP00000323580:p.Val398Gly	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	181	63	NM_175605	0	0	15	15	0	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863350	0.71949	.	.	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.35789	1.31;1.29;1.29;1.31	5.59	3.19	0.36642	.	0.122813	0.56097	D	0.000035	T	0.34978	0.0916	M	0.74647	2.275	0.80722	D	1	B;P;P;B	0.37985	0.433;0.594;0.613;0.104	B;B;B;B	0.36845	0.234;0.164;0.197;0.058	T	0.22765	-1.0207	10	0.66056	D	0.02	-16.2168	6.1242	0.20170	0.0:0.3259:0.0:0.6741	.	370;398;196;398	F5H6C2;E7EW86;Q6MZX0;Q13099	.;.;.;IFT88_HUMAN	G	398;261;389;398;370	ENSP00000372228:V398G;ENSP00000261632:V389G;ENSP00000323580:V398G;ENSP00000437719:V370G	ENSP00000323580:V398G	V	+	2	0	IFT88	20087985	0.997000	0.39634	0.988000	0.46212	0.997000	0.91878	2.622000	0.46427	0.942000	0.37525	0.528000	0.53228	GTA	.		0.279	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		G	21189985	T	G	21189985	3	3	51	1	0	0	0	0	1	0	0	0	7587	1638	57	5	1247	5	IFT88	13	21189985	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		21189985	93979893	179	4867	54	2									
IFT88	8100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	21189988	21189988	+	Missense_Mutation	SNP	T	T	A																															aaaactcattgctcctgtaaTtgaaacatcttttgctgcag																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:21189988T>A	ENST00000319980.6	+	16	1523	c.1196T>A	c.(1195-1197)aTt>aAt	p.I399N	IFT88_ENST00000461115.1_3'UTR|IFT88_ENST00000537103.1_Missense_Mutation_p.I371N|IFT88_ENST00000382778.4_Missense_Mutation_p.I399N|IFT88_ENST00000351808.5_Missense_Mutation_p.I390N	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	399					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GCTCCTGTAATTGAAACATCT	0.279																																					p.I399N		.											.	IFT88-91	0			c.T1196A						.						81	90	87					13																	21189988		2203	4293	6496	SO:0001583	missense	8100	exon16			CTGTAATTGAAAC	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	20606	protein-coding gene	gene with protein product	"polaris homolog"	600595	"tetratricopeptide repeat domain 10", "intraflagellar transport 88 homolog (Chlamydomonas)"	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.1196T>A	13.37:g.21189988T>A	ENSP00000323580:p.Ile399Asn	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	180	60	NM_175605	0	0	19	19	0	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.408083	0.83340	.	.	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.40756	1.03;1.02;1.02;1.04	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.69717	0.3142	M	0.88105	2.93	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.998	D;D;D;D	0.79784	0.986;0.979;0.993;0.991	T	0.76564	-0.2913	10	0.87932	D	0	-20.545	14.7446	0.69480	0.0:0.0:0.0:1.0	.	371;399;197;399	F5H6C2;E7EW86;Q6MZX0;Q13099	.;.;.;IFT88_HUMAN	N	399;262;390;399;371	ENSP00000372228:I399N;ENSP00000261632:I390N;ENSP00000323580:I399N;ENSP00000437719:I371N	ENSP00000323580:I399N	I	+	2	0	IFT88	20087988	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.260000	0.78391	2.121000	0.65114	0.528000	0.53228	ATT	.		0.279	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		A	21189988	T	A	21189988	3	1	51	1	0	0	0	0	1	0	0	0	7587	1493	52	5	1250	5	IFT88	13	21189988	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3	21189988	93979890	180	4868	54	2									
ATP8A2	51761	ucsc.edu	37	chr13	26156055	26156055	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aaggcagaaattaaaatatgGgtgttgacaggagacaaaca	19	7	11	4	0	0	3	0	1	0	2	0	4	0	3	0	3	1	2	0	3	6	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:26156055G>T	ENST00000381655.2	+	23	2248	c.2106G>T	c.(2104-2106)tgG>tgT	p.W702C	ATP8A2_ENST00000491840.1_3'UTR|ATP8A2_ENST00000255283.8_Missense_Mutation_p.W662C	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	662					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		TTAAAATATGGGTGTTGACAG	0.373																																					p.W702C													.	ATP8A2-138	0			c.G2106T						.						85	79	81					13																	26156055		1831	4083	5914	SO:0001583	missense	51761	exon23			AATATGGGTGTTG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2106G>T	13.37:g.26156055G>T	ENSP00000371070:p.Trp702Cys	Somatic	72	0		WXS	Illumina HiSeq		76	4	NM_016529	0	0	0	0	0	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615120	0.87359	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	D;D	0.96427	-4.01;-4.01	6.17	6.17	0.99709	HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.99010	0.9662	H	0.97758	4.07	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98844	1.0756	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	662;482;662	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	C	702;662;482	ENSP00000371070:W702C;ENSP00000255283:W662C	ENSP00000255283:W662C	W	+	3	0	ATP8A2	25054055	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.756000	0.98918	2.941000	0.99782	0.655000	0.94253	TGG	.		0.373	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		T	26156055	G	T	26156055	3	4	51	1	0	0	0	0	1	0	0	0	1194	1241	43	4	2196	4	ATP8A2	13	26156055	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	4966067	26156055	89013823	181	4869											
BRCA2	675	bcgsc.ca	37	chr13	32906983	32906983	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctagcctaccaaaatcagaGaagccattaaatgaggaaac	18	7	7	9	0	2	2	1	1	1	1	2	4	2	3	3	1	4	0	3	1	8	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:32906983G>A	ENST00000380152.3	+	10	1601	c.1368G>A	c.(1366-1368)gaG>gaA	p.E456E	BRCA2_ENST00000544455.1_Silent_p.E456E			P51587	BRCA2_HUMAN	breast cancer 2, early onset	456					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.E456D(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CAAAATCAGAGAAGCCATTAA	0.363			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.E456E	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2-3153	2	Substitution - Missense(2)	large_intestine(2)	c.G1368A						.						62	71	68					13																	32906983		2201	4296	6497	SO:0001819	synonymous_variant	675	exon10	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	ATCAGAGAAGCCA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1368G>A	13.37:g.32906983G>A		Somatic	88	0		WXS	Illumina HiSeq	Phase_1	49	22	NM_000059	0	0	1	1	0	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			.		0.363	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32906983	G	A	32906983	2	1	51	1	0	0	0	0	0	0	0	1	1502	933	33	2		2	BRCA2	13	32906983	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	6750928	32906983	82262895	182	4870											
BRCA2	675	bcgsc.ca	37	chr13	32913965	32913965	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccctgcaaaaataaaaatGcagccattaaattgtccata	18	9	4	10	0	0	0	0	0	0	0	1	0	1	0	3	0	3	2	3	0	8	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:32913965G>C	ENST00000380152.3	+	11	5706	c.5473G>C	c.(5473-5475)Gca>Cca	p.A1825P	BRCA2_ENST00000544455.1_Missense_Mutation_p.A1825P			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1825					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAATAAAAATGCAGCCATTAA	0.363			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.A1825P	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2-3153	0			c.G5473C						.						61	69	66					13																	32913965		2203	4300	6503	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AAAAATGCAGCCA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5473G>C	13.37:g.32913965G>C	ENSP00000369497:p.Ala1825Pro	Somatic	89	0		WXS	Illumina HiSeq	Phase_1	58	22	NM_000059	0	0	0	0	0	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	5.883	0.347062	0.11126	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.71222	-0.55;-0.55	5.24	-8.48	0.00935	.	1.380380	0.04407	N	0.365374	T	0.53400	0.1794	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.44544	-0.9321	10	0.41790	T	0.15	.	11.6232	0.51130	0.4691:0.084:0.4469:0.0	.	1825	P51587	BRCA2_HUMAN	P	1825	ENSP00000369497:A1825P;ENSP00000439902:A1825P	ENSP00000369497:A1825P	A	+	1	0	BRCA2	31811965	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-0.210000	0.09345	-1.691000	0.01430	-0.345000	0.07892	GCA	.		0.363	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		C	32913965	G	C	32913965	3	2	51	1	0	0	0	0	1	0	0	0	1502	1319	46	4	5511	4	BRCA2	13	32913965	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	6982	32913965	82255913	183	4871											
ELF1	1997	bcgsc.ca	37	chr13	41508016	41508016	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtgatgatggaatggcttGtaaaataaacttctgagatc	13	13	10	5	0	1	3	0	3	1	1	2	5	1	4	0	2	1	2	0	2	5	4	rs79846574		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:41508016G>T	ENST00000239882.3	-	9	1719	c.1405C>A	c.(1405-1407)Caa>Aaa	p.Q469K	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.Q445K	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	469					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		GGAATGGCTTGTAAAATAAAC	0.468																																					p.Q469K													.	ELF1-227	0			c.C1405A						.																																			SO:0001583	missense	1997	exon9			TGGCTTGTAAAAT	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1405C>A	13.37:g.41508016G>T	ENSP00000239882:p.Gln469Lys	Somatic	237	0		WXS	Illumina HiSeq	Phase_1	121	44	NM_172373	0	0	92	105	13	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.827067	0.71143	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.55052	0.54;0.54	5.44	5.44	0.79542	.	0.063340	0.64402	D	0.000004	T	0.65739	0.2720	L	0.36672	1.1	0.49915	D	0.999836	D;D	0.69078	0.994;0.997	D;D	0.72338	0.968;0.977	T	0.68375	-0.5425	10	0.87932	D	0	.	19.2715	0.94011	0.0:0.0:1.0:0.0	.	445;469	E9PDQ9;P32519	.;ELF1_HUMAN	K	445;211;469	ENSP00000405580:Q445K;ENSP00000239882:Q469K	ENSP00000239882:Q469K	Q	-	1	0	ELF1	40406016	1.000000	0.71417	0.984000	0.44739	0.900000	0.52787	7.562000	0.82300	2.539000	0.85634	0.655000	0.94253	CAA	.		0.468	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		T	41508016	G	T	41508016	3	4	51	1	0	0	0	0	1	0	0	0	5066	1386	48	4	458	4	ELF1	13	41508016	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	8594051	41508016	73661862	184	4872											
KIAA0564	23078	bcgsc.ca	37	chr13	42273324	42273324	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atatcaaaaaagtccacaaaGaagccacttttcccagtcat	17	9	4	11	0	2	1	2	0	0	1	4	1	4	1	3	0	1	0	3	0	6	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:42273324G>A	ENST00000379310.3	-	29	3515	c.3447C>T	c.(3445-3447)ttC>ttT	p.F1149F		NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1149						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										AGTCCACAAAGAAGCCACTTT	0.433																																					p.F1149F													.	.	0			c.C3447T						.						89	91	91					13																	42273324		1877	4101	5978	SO:0001819	synonymous_variant	23078	exon29			CACAAAGAAGCCA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.3447C>T	13.37:g.42273324G>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_1	89	26	NM_015058	0	0	16	16	0	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Silent	SNP	ENST00000379310.3	37	CCDS41881.1																																																																																			.		0.433	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		A	42273324	G	A	42273324	2	1	51	1	0	0	0	0	0	0	0	1	8206	933	33	2		2	KIAA0564	13	42273324	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	765308	42273324	72896554	185	4873											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42876808	42876808	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagttggatatagaggctgTagtgcacccaagagaagtgg	13	8	15	5	0	0	2	0	0	0	2	0	5	0	3	1	3	1	4	1	3	6	4	rs201995333		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:42876808T>G	ENST00000025301.2	+	8	4101	c.3926T>G	c.(3925-3927)gTa>gGa	p.V1309G		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1309					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		ATAGAGGCTGTAGTGCACCCA	0.388																																					p.V1309G		.											.	AKAP11-227	0			c.T3926G						.						78	79	78					13																	42876808		2203	4300	6503	SO:0001583	missense	11215	exon8			AGGCTGTAGTGCA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	369	protein-coding gene	gene with protein product	"AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44"	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.3926T>G	13.37:g.42876808T>G	ENSP00000025301:p.Val1309Gly	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	47	12	NM_016248	0	0	45	47	2	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	T	9.177	1.022549	0.19433	.	.	ENSG00000023516	ENST00000025301	T	0.52983	0.64	5.75	1.75	0.24633	.	1.406730	0.04625	N	0.402539	T	0.37210	0.0995	L	0.51422	1.61	0.09310	N	0.999999	B	0.30439	0.279	B	0.25140	0.058	T	0.25222	-1.0138	10	0.34782	T	0.22	.	0.6864	0.00883	0.2429:0.1806:0.1137:0.4628	.	1309	Q9UKA4	AKA11_HUMAN	G	1309	ENSP00000025301:V1309G	ENSP00000025301:V1309G	V	+	2	0	AKAP11	41774808	0.206000	0.23470	0.000000	0.03702	0.219000	0.24729	2.655000	0.46707	0.451000	0.26802	0.533000	0.62120	GTA	.		0.388	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42876808	T	G	42876808	3	3	51	1	0	0	0	0	1	0	0	0	447	1638	57	5	3948	5	AKAP11	13	42876808	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	603484	42876808	72293070	186	4874											
C13orf18	80183	bcgsc.ca	37	chr13	46942947	46942947	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcttctactgacttgaacaGcacctgccaatatagcaaat	13	12	5	11	0	2	2	0	2	2	0	2	2	2	2	2	0	5	2	2	0	6	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:46942947G>C	ENST00000429979.1	-	4	1143	c.539C>G	c.(538-540)gCt>gGt	p.A180G	KIAA0226L_ENST00000409879.2_Missense_Mutation_p.A23G|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.A45G|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.A113G|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.A23G|KIAA0226L_ENST00000378781.3_Missense_Mutation_p.A180G|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.A180G|KIAA0226L_ENST00000378787.3_Missense_Mutation_p.A180G|KIAA0226L_ENST00000378797.2_Missense_Mutation_p.A180G	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	180										NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GACTTGAACAGCACCTGCCAA	0.338																																					p.A180G													.	.	0			c.C539G						.						82	89	87					13																	46942947		2203	4300	6503	SO:0001583	missense	80183	exon4			TGAACAGCACCTG	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 18"	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.539C>G	13.37:g.46942947G>C	ENSP00000396935:p.Ala180Gly	Somatic	115	4		WXS	Illumina HiSeq	Phase_1	48	25	NM_025113	0	0	0	0	0	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.	.	.	.	.	.	.	.	.	.	G	13.14	2.149540	0.37923	.	.	ENSG00000102445	ENST00000378781;ENST00000429979;ENST00000378797;ENST00000378784;ENST00000389908;ENST00000378787;ENST00000409879;ENST00000322896;ENST00000534925;ENST00000417405	T;T;T;T;T;T;T;T	0.48201	0.82;0.86;0.85;0.86;0.86;0.85;0.88;0.83	6.17	3.41	0.39046	.	0.417022	0.23062	N	0.052365	T	0.53238	0.1784	L	0.38175	1.15	0.22851	N	0.998653	D;P;P;P;P;P;P	0.76494	0.999;0.682;0.925;0.682;0.877;0.925;0.925	D;B;P;B;B;P;P	0.69479	0.964;0.156;0.691;0.156;0.339;0.54;0.616	T	0.41448	-0.9508	10	0.62326	D	0.03	-2.7621	7.9961	0.30269	0.0726:0.0:0.6336:0.2937	.	180;23;180;23;180;113;180	E7EMA2;B7ZBN5;Q9H714-1;B7Z6E4;Q9H714;Q9H714-3;Q9H714-4	.;.;.;.;K226L_HUMAN;.;.	G	180;180;180;113;180;180;23;23;45;45	ENSP00000368057:A180G;ENSP00000396935:A180G;ENSP00000368074:A180G;ENSP00000368061:A113G;ENSP00000374558:A180G;ENSP00000368064:A180G;ENSP00000437501:A45G;ENSP00000402357:A45G	ENSP00000315633:A23G	A	-	2	0	KIAA0226L	45840948	0.833000	0.29383	0.933000	0.37362	0.725000	0.41563	1.486000	0.35530	0.422000	0.26005	0.655000	0.94253	GCT	.		0.338	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113		C	46942947	G	C	46942947	3	2	51	1	0	0	0	0	1	0	0	0	1724	971	34	4	1497	4	C13orf18	13	46942947	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	4066139	46942947	68226931	187	4875											
DIS3	22894	bcgsc.ca	37	chr13	73349455	73349455	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactcttggggagaagctccAcagccacaatatcttcgtga	11	9	10	11	1	2	2	0	1	2	1	4	4	3	2	2	2	2	1	2	2	3	3	rs201006124	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:73349455A>C	ENST00000377767.4	-	6	981	c.881T>G	c.(880-882)gTg>gGg	p.V294G	DIS3_ENST00000377780.4_Missense_Mutation_p.V264G|DIS3_ENST00000545453.1_Missense_Mutation_p.V132G	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	294					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		GAGAAGCTCCACAGCCACAAT	0.398										Multiple Myeloma(4;0.011)			A|||	71	0.0141773	0.0121	0.0173	5008	,	,		16942	0.0169		0.0258	False		,,,				2504	0				p.V294G													.	DIS3-90	0			c.T881G						.						129	133	132					13																	73349455		2203	4300	6503	SO:0001583	missense	22894	exon6			AGCTCCACAGCCA	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"exosome component 11"	607533	"KIAA1008", "DIS3 mitotic control homolog (S. cerevisiae)"	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.881T>G	13.37:g.73349455A>C	ENSP00000366997:p.Val294Gly	Somatic	103	0		WXS	Illumina HiSeq	Phase_1	53	23	NM_014953	0	0	36	41	5	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	.	.	.	.	.	.	.	.	.	.	A	33	5.237692	0.95240	.	.	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.46451	0.87;0.87;0.87	6.06	6.06	0.98353	.	0.117437	0.64402	D	0.000019	T	0.71476	0.3344	M	0.92833	3.35	0.80722	D	1	D;P	0.53619	0.961;0.934	P;P	0.61940	0.896;0.864	T	0.79035	-0.1968	10	0.87932	D	0	.	16.6245	0.84952	1.0:0.0:0.0:0.0	.	264;294	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	G	294;264;132	ENSP00000366997:V294G;ENSP00000367011:V264G;ENSP00000440058:V132G	ENSP00000366997:V294G	V	-	2	0	DIS3	72247456	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.251000	0.95483	2.323000	0.78572	0.528000	0.53228	GTG	.		0.398	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		C	73349455	A	C	73349455	3	2	51	1	0	0	0	0	1	0	0	0	4546	159	6	5	2059	5	DIS3	13	73349455	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	26406508	73349455	41820423	188	4876											
COCH	1690	bcgsc.ca	37	chr14	31355025	31355025	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtctgtcggaataatggcttCttctcttaccacatgcccaa	9	13	7	12	1	3	0	0	0	3	0	5	1	3	1	2	2	2	1	2	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:31355025C>T	ENST00000396618.3	+	11	1040	c.984C>T	c.(982-984)ttC>ttT	p.F328F	RP11-829H16.3_ENST00000555421.1_RNA|RP11-829H16.3_ENST00000468444.2_RNA|COCH_ENST00000460581.2_Silent_p.F216F|RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000216361.4_Silent_p.F328F|COCH_ENST00000475087.1_Silent_p.F328F|COCH_ENST00000382493.4_Silent_p.F179F|RP11-829H16.3_ENST00000555108.1_RNA	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	328	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		ATAATGGCTTCTTCTCTTACC	0.418																																					p.F328F													.	COCH-228	0			c.C984T						.						104	100	102					14																	31355025		2203	4300	6503	SO:0001819	synonymous_variant	1690	exon11			TGGCTTCTTCTCT		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.984C>T	14.37:g.31355025C>T		Somatic	107	0		WXS	Illumina HiSeq	Phase_1	34	6	NM_004086	0	0	2	2	0	A8K9K9|D3DS84|Q96IU6	Silent	SNP	ENST00000396618.3	37	CCDS9640.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.722560	0.48728	.	.	ENSG00000100473	ENST00000468826	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	T	0.77046	0.4073	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74134	-0.3763	4	.	.	.	-11.6452	20.327	0.98704	0.0:1.0:0.0:0.0	.	.	.	.	F	212	.	.	S	+	2	0	COCH	30424776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.015000	0.70791	2.794000	0.96219	0.650000	0.86243	TCT	.		0.418	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		T	31355025	C	T	31355025	2	4	51	1	0	0	0	0	0	0	0	1	3662	912	32	2		2	COCH	14	31355025	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08		31355025	75994515	189	4877											
PPM1A	5494	bcgsc.ca	37	chr14	60749549	60749549	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggatgcacatacggctgTgatcggtttgccaagtggac	9	9	15	8	2	0	1	0	1	0	0	1	4	0	4	1	5	3	3	1	5	2	2	rs74713917		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:60749549T>G	ENST00000395076.4	+	2	558	c.128T>G	c.(127-129)gTg>gGg	p.V43G	PPM1A_ENST00000325642.3_Missense_Mutation_p.V116G|PPM1A_ENST00000325658.3_Missense_Mutation_p.V43G|PPM1A_ENST00000529574.1_Missense_Mutation_p.V43G	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	43					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		CATACGGCTGTGATCGGTTTG	0.493																																					p.V116G													.	PPM1A-227	0			c.T347G						.						438	391	407					14																	60749549		2203	4300	6503	SO:0001583	missense	5494	exon2			CGGCTGTGATCGG	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.128T>G	14.37:g.60749549T>G	ENSP00000378514:p.Val43Gly	Somatic	492	0		WXS	Illumina HiSeq	Phase_1	327	121	NM_177952	0	0	49	52	3	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313734	0.60414	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076;ENST00000325658;ENST00000528241;ENST00000525399;ENST00000531937	T;T;T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88;2.88;2.88	5.75	5.75	0.90469	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.24392	0.0591	M	0.86028	2.79	0.80722	D	1	B;B;B	0.24132	0.098;0.041;0.098	B;B;B	0.33750	0.169;0.16;0.169	T	0.02539	-1.1144	10	0.56958	D	0.05	-3.9804	16.0345	0.80612	0.0:0.0:0.0:1.0	.	43;43;43	P35813;P35813-2;B2R8E4	PPM1A_HUMAN;.;.	G	116;43;43;43;43;43;43	ENSP00000327255:V116G;ENSP00000432966:V43G;ENSP00000378514:V43G;ENSP00000314850:V43G;ENSP00000431453:V43G;ENSP00000435398:V43G;ENSP00000435575:V43G	ENSP00000327255:V116G	V	+	2	0	PPM1A	59819302	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.183000	0.69458	0.482000	0.46254	GTG	.		0.493	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003		G	60749549	T	G	60749549	3	3	51	1	0	0	0	0	1	0	0	0	12364	1696	59	5	353	5	PPM1A	14	60749549	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	29394524	60749549	46599991	190	4878											
SYT16	83851	hgsc.bcm.edu	37	chr14	62463094	62463094	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaggactcatgttccacAatgtcccagtggcccaattg	11	9	9	12	0	1	0	1	0	0	0	3	1	3	1	3	2	0	2	3	2	3	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:62463094A>C	ENST00000430451.2	+	1	554	c.357A>C	c.(355-357)acA>acC	p.T119T	SYT16_ENST00000446982.2_Silent_p.T119T	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	119					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CATGTTCCACAATGTCCCAGT	0.458																																					p.T119T		.											.	SYT16-23	0			c.A357C						.						131	125	127					14																	62463094		1910	4127	6037	SO:0001819	synonymous_variant	83851	exon1			TTCCACAATGTCC	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"Synaptotagmins"	23142	protein-coding gene	gene with protein product	"synaptotagmin XIV-related", " chr14 synaptotagmin"	610950	"synaptotagmin XIV-like"	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.357A>C	14.37:g.62463094A>C		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_031914	0	0	6	6	0	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																			.		0.458	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		C	62463094	A	C	62463094	2	2	51	1	0	0	0	0	0	0	0	1	15504	117	5	5		5	SYT16	14	62463094	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1713545	62463094	44886446	191	4879											
AKAP5	9495	bcgsc.ca	37	chr14	64935947	64935947	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagatcaacaaattgtggaaGaagccagtaacagtacccta	17	7	8	9	0	1	2	1	0	0	2	1	3	1	3	2	1	4	2	2	1	7	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:64935947G>A	ENST00000394718.4	+	2	1213	c.835G>A	c.(835-837)Gaa>Aaa	p.E279K	ZBTB25_ENST00000555220.1_Intron|ZBTB25_ENST00000555424.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.E279K	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	279					energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.E279*(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		AATTGTGGAAGAAGCCAGTAA	0.413																																					p.E279K													.	AKAP5-226	1	Substitution - Nonsense(1)	large_intestine(1)	c.G835A						.						73	76	75					14																	64935947		2203	4300	6503	SO:0001583	missense	9495	exon2			GTGGAAGAAGCCA	M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"A-kinase anchor proteins"	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.835G>A	14.37:g.64935947G>A	ENSP00000378207:p.Glu279Lys	Somatic	132	0		WXS	Illumina HiSeq	Phase_1	73	20	NM_004857	0	0	2	3	1	A2RRB8	Missense_Mutation	SNP	ENST00000394718.4	37	CCDS9764.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.099867	0.37048	.	.	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.32515	1.45;1.45	5.9	5.01	0.66863	.	0.426594	0.22125	N	0.064266	T	0.32615	0.0835	M	0.61703	1.905	0.30000	N	0.816116	B	0.18461	0.028	B	0.19148	0.024	T	0.24048	-1.0171	10	0.41790	T	0.15	-2.0645	12.8171	0.57671	0.0754:0.0:0.9246:0.0	.	279	P24588	AKAP5_HUMAN	K	279	ENSP00000378207:E279K;ENSP00000315615:E279K	ENSP00000315615:E279K	E	+	1	0	AKAP5	64005700	0.883000	0.30277	0.724000	0.30704	0.166000	0.22503	2.392000	0.44433	1.500000	0.48636	0.650000	0.86243	GAA	.		0.413	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3			A	64935947	G	A	64935947	3	1	51	1	0	0	0	0	1	0	0	0	454	943	33	2	837	2	AKAP5	14	64935947	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	2472853	64935947	42413593	192	4880											
CLMN	79789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	95669398	95669398	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggagtccaggtctggcataTagccctctggctcttcgaga	7	11	12	11	1	3	1	0	0	3	1	5	3	4	2	2	4	1	2	2	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:95669398T>C	ENST00000298912.4	-	9	2401	c.2288A>G	c.(2287-2289)tAt>tGt	p.Y763C		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	763					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		GTCTGGCATATAGCCCTCTGG	0.567																																					p.Y763C		.											.	CLMN-90	0			c.A2288G						.						38	39	39					14																	95669398		2203	4300	6503	SO:0001583	missense	79789	exon9			GGCATATAGCCCT	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2288A>G	14.37:g.95669398T>C	ENSP00000298912:p.Tyr763Cys	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	206	84	NM_024734	0	0	16	28	12	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	T	9.014	0.983104	0.18889	.	.	ENSG00000165959	ENST00000298912	D	0.92647	-3.08	5.22	-4.75	0.03239	.	0.879712	0.09454	N	0.800049	D	0.83718	0.5315	L	0.39397	1.21	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.68055	-0.5510	10	0.40728	T	0.16	.	3.381	0.07255	0.1129:0.3809:0.1154:0.3907	.	763	Q96JQ2	CLMN_HUMAN	C	763	ENSP00000298912:Y763C	ENSP00000298912:Y763C	Y	-	2	0	CLMN	94739151	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.163000	0.03138	-0.982000	0.03515	-1.236000	0.01555	TAT	.		0.567	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			C	95669398	T	C	95669398	3	2	51	1	0	0	0	0	1	0	0	0	3548	1406	49	3	740	3	CLMN	14	95669398	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	30733451	95669398	11680142	193	4881											
AHNAK2	113146	ucsc.edu	37	chr14	105415291	105415291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgatggacttgcctggggcaGacaccccaaacgacggcatc	10	5	12	14	3	0	1	0	0	0	1	1	4	0	2	3	4	2	2	3	4	1	1	rs568117634		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:105415291G>A	ENST00000333244.5	-	7	6616	c.6497C>T	c.(6496-6498)tCt>tTt	p.S2166F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2166						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCTGGGGCAGACACCCCAAA	0.592													.|||	0	0	0	0	5008	,	,		16538	0		0	False		,,,				2504	0				p.S2166F													.	AHNAK2-47	0			c.C6497T						.						208	149	170					14																	105415291		1940	3520	5460	SO:0001583	missense	113146	exon7			GGGGCAGACACCC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6497C>T	14.37:g.105415291G>A	ENSP00000353114:p.Ser2166Phe	Somatic	485	4		WXS	Illumina HiSeq		2022	16	NM_138420	0	0	72	72	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	16.92	3.256462	0.59321	.	.	ENSG00000185567	ENST00000333244	T	0.01025	5.43	4.35	4.35	0.52113	.	.	.	.	.	T	0.08403	0.0209	M	0.91406	3.205	0.09310	N	1	D	0.71674	0.998	D	0.87578	0.998	T	0.04752	-1.0929	9	0.52906	T	0.07	.	16.9291	0.86184	0.0:0.0:1.0:0.0	.	2166	Q8IVF2	AHNK2_HUMAN	F	2166	ENSP00000353114:S2166F	ENSP00000353114:S2166F	S	-	2	0	AHNAK2	104486336	0.018000	0.18449	0.006000	0.13384	0.001000	0.01503	1.888000	0.39708	1.995000	0.58328	0.306000	0.20318	TCT	.		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105415291	G	A	105415291	3	1	51	1	0	0	0	0	1	0	0	0	415	942	33	2	10894	2	AHNAK2	14	105415291	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	9745893	105415291	1934249	194	4882											
BMF	90427	bcgsc.ca	37	chr15	40396521	40396521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgggaaactggcagggagagGaagccgatagccagcattgc	12	5	16	8	1	0	1	0	0	0	1	0	5	0	3	2	4	5	2	2	4	3	2	rs77642791		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:40396521G>A	ENST00000354670.4	-	4	547	c.313C>T	c.(313-315)Cct>Tct	p.P105S	BMF_ENST00000561360.1_Missense_Mutation_p.P105S|BMF_ENST00000431415.3_Missense_Mutation_p.P105S|BMF_ENST00000559701.1_Intron|BMF_ENST00000558774.1_Intron|BMF_ENST00000397573.1_Missense_Mutation_p.P105S|BMF_ENST00000220446.4_Intron|BMF_ENST00000561282.1_Missense_Mutation_p.P105S	NM_001003940.1	NP_001003940.1	Q96LC9	BMF_HUMAN	Bcl2 modifying factor	105					anoikis (GO:0043276)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6		all_cancers(109;4.18e-18)|all_epithelial(112;6.15e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.29e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0516)		GCAGGGAGAGGAAGCCGATAG	0.567																																					p.P105S													.	BMF-228	0			c.C313T						.						98	96	97					15																	40396521		2203	4300	6503	SO:0001583	missense	90427	exon2			GGAGAGGAAGCCG	BC060783	CCDS10052.1, CCDS32196.1, CCDS45223.1	15q14	2014-03-07			ENSG00000104081	ENSG00000104081			24132	protein-coding gene	gene with protein product		606266				11546872	Standard	NM_001003943		Approved	FLJ00065	uc001zkw.4	Q96LC9	OTTHUMG00000129875	ENST00000354670.4:c.313C>T	15.37:g.40396521G>A	ENSP00000346697:p.Pro105Ser	Somatic	148	0		WXS	Illumina HiSeq	Phase_1	267	131	NM_001003942	0	0	10	11	1	Q2M396|Q6NT30|Q6NT56|Q6P9F6|Q7Z7D4|Q7Z7D5|Q9H7K7	Missense_Mutation	SNP	ENST00000354670.4	37	CCDS10052.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553055	0.65425	.	.	ENSG00000104081	ENST00000354670;ENST00000397573;ENST00000431415	.	.	.	5.91	4.99	0.66335	.	0.186495	0.37530	N	0.002053	T	0.32255	0.0823	N	0.24115	0.695	0.80722	D	1	B;P	0.37370	0.218;0.592	B;B	0.29440	0.038;0.102	T	0.10291	-1.0636	9	0.25106	T	0.35	-9.2573	10.6792	0.45804	0.1416:0.0:0.8584:0.0	.	105;105	Q96LC9;Q96LC9-2	BMF_HUMAN;.	S	105	.	ENSP00000346697:P105S	P	-	1	0	BMF	38183813	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.773000	0.55333	2.802000	0.96397	0.655000	0.94253	CCT	.		0.567	BMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252119.1	NM_033503		A	40396521	G	A	40396521	3	1	51	1	0	0	0	0	1	0	0	0	1455	1174	41	2	249	2	BMF	15	40396521	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		40396521	62134871	195	4883											
TTBK2	146057	bcgsc.ca	37	chr15	43132600	43132600	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaatcgatcattcctcccAcagccaataaatctacaaac	15	10	3	13	1	2	1	1	1	1	0	5	2	4	1	3	0	3	0	3	0	6	4	rs141523080		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:43132600A>C	ENST00000267890.6	-	4	357	c.249T>G	c.(247-249)tgT>tgG	p.C83W	TTBK2_ENST00000567840.1_Missense_Mutation_p.C83W|TTBK2_ENST00000567274.1_Missense_Mutation_p.C83W	NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	83	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CATTCCTCCCACAGCCAATAA	0.318																																					p.C83W													.	TTBK2-338	0			c.T249G						.						133	126	128					15																	43132600		1820	4084	5904	SO:0001583	missense	146057	exon4			CCTCCCACAGCCA	AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.249T>G	15.37:g.43132600A>C	ENSP00000267890:p.Cys83Trp	Somatic	132	1		WXS	Illumina HiSeq	Phase_1	94	39	NM_173500	0	0	2	2	0	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.750201	0.30955	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.64438	-0.1	5.31	4.18	0.49190	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.082061	0.85682	D	0.000000	T	0.73892	0.3645	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.999	T	0.75193	-0.3404	10	0.87932	D	0	.	11.2089	0.48786	0.9264:0.0:0.0736:0.0	.	63;14;83;83	Q8IWY7;Q6IQ55-2;Q6IQ55-3;Q6IQ55	.;.;.;TTBK2_HUMAN	W	83;13;63	ENSP00000267890:C83W	ENSP00000263802:C63W	C	-	3	2	TTBK2	40919892	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.929000	0.48916	0.955000	0.37878	0.477000	0.44152	TGT	.		0.318	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		C	43132600	A	C	43132600	3	2	51	1	0	0	0	0	1	0	0	0	16710	157	6	5	3533	5	TTBK2	15	43132600	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	2736079	43132600	59398792	196	4884											
ONECUT1	3175	broad.mit.edu	37	chr15	53081466	53081467	+	Frame_Shift_Ins	INS	-	-	G																															atcttgtcggtgggcatggcINSggcccccgggtgggcatagt																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:53081466_53081467insG	ENST00000305901.5	-	1	742_743	c.615_616insC	c.(613-618)gccgccfs	p.A206fs	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	206					B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		GTGGGCATGGCGGCCCCCGGGT	0.713																																					p.A206fs													.	ONECUT1-68	0			c.616_617insC						.																																			SO:0001589	frameshift_variant	3175	exon1			GCATGGCGGCCCC	U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"Homeoboxes / CUT class"	8138	protein-coding gene	gene with protein product		604164	"one cut domain, family member 1"	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.616dupC	15.37:g.53081468_53081468dupG	ENSP00000302630:p.Ala206fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	311	6	NM_004498	0	0	0	0	0	B2RTV4|Q99744|Q9UMR6	Frame_Shift_Ins	INS	ENST00000305901.5	37	CCDS10150.1																																																																																			.		0.713	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2			G	53081467	-	G	53081466	7	5	51	1	0	1	1	0	0	0	0	0	10894	768	27	0	789	0	ONECUT1	15	53081466	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	9948866	53081466	49449926	197	4885											
PYGO1	26108	bcgsc.ca	37	chr15	55838604	55838604	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agggttattgtttgtggcttCagtgctacttgaacggctgt	6	16	13	6	1	1	1	1	1	0	0	1	1	1	1	0	3	3	5	0	3	3	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:55838604C>T	ENST00000302000.6	-	3	971	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	PYGO1_ENST00000563719.1_Missense_Mutation_p.E293K	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	293	Asn-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		TTTGTGGCTTCAGTGCTACTT	0.408																																					p.E293K													.	PYGO1-228	0			c.G877A						.						301	299	300					15																	55838604		2193	4292	6485	SO:0001583	missense	26108	exon3			TGGCTTCAGTGCT	AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"Zinc fingers, PHD-type"	30256	protein-coding gene	gene with protein product		606902	"pygopus homolog 1 (Drosophila)"			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.877G>A	15.37:g.55838604C>T	ENSP00000302327:p.Glu293Lys	Somatic	348	0		WXS	Illumina HiSeq	Phase_1	117	27	NM_015617	0	0	2	2	0	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	37	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744774	0.49151	.	.	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.44881	0.91	5.24	5.24	0.73138	.	0.203869	0.42420	D	0.000703	T	0.27134	0.0665	N	0.19112	0.55	0.40068	D	0.97598	B;P	0.34522	0.247;0.455	B;B	0.32211	0.091;0.142	T	0.09164	-1.0687	10	0.06625	T	0.88	-15.9589	18.1934	0.89813	0.0:1.0:0.0:0.0	.	293;293	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	K	293	ENSP00000302327:E293K	ENSP00000302327:E293K	E	-	1	0	PYGO1	53625896	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	3.818000	0.55678	2.605000	0.88082	0.591000	0.81541	GAA	.		0.408	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		T	55838604	C	T	55838604	3	4	51	1	0	0	0	0	1	0	0	0	12895	835	29	2	386	2	PYGO1	15	55838604	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	2757138	55838604	46692788	198	4886											
GCNT3	9245	bcgsc.ca	37	chr15	59911342	59911342	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaatgcgtacattgtggcttCccgagatttcgtccaacatg	9	12	10	10	3	0	1	0	0	0	1	3	3	2	1	2	1	3	2	2	1	3	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:59911342C>T	ENST00000396065.1	+	3	1353	c.905C>T	c.(904-906)tCc>tTc	p.S302F	GCNT3_ENST00000560585.1_Missense_Mutation_p.S302F	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	302					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ATTGTGGCTTCCCGAGATTTC	0.428																																					p.S302F													.	GCNT3-91	0			c.C905T						.						165	165	165					15																	59911342		2190	4290	6480	SO:0001583	missense	9245	exon3			TGGCTTCCCGAGA	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.905C>T	15.37:g.59911342C>T	ENSP00000379377:p.Ser302Phe	Somatic	205	0		WXS	Illumina HiSeq	Phase_1	137	27	NM_004751	0	0	19	19	0		Missense_Mutation	SNP	ENST00000396065.1	37	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.962315	0.53400	.	.	ENSG00000140297	ENST00000396065	T	0.14893	2.47	5.41	4.43	0.53597	.	0.309345	0.35838	N	0.002944	T	0.44871	0.1314	M	0.85945	2.785	0.40043	D	0.975673	D	0.71674	0.998	D	0.68483	0.958	T	0.53521	-0.8427	10	0.87932	D	0	.	14.7569	0.69572	0.0:0.6617:0.3383:0.0	.	302	O95395	GCNT3_HUMAN	F	302	ENSP00000379377:S302F	ENSP00000379377:S302F	S	+	2	0	GCNT3	57698634	0.081000	0.21417	0.998000	0.56505	0.843000	0.47879	1.250000	0.32850	2.535000	0.85469	0.655000	0.94253	TCC	.		0.428	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		T	59911342	C	T	59911342	3	4	51	1	0	0	0	0	1	0	0	0	6322	855	30	2	907	2	GCNT3	15	59911342	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	4072738	59911342	42620050	199	4887											
FBXO22	26263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	76196905	76196905	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgtaacctggatctccgcaGgcctggcggaggccggccac	6	5	15	15	4	1	0	0	0	1	0	2	2	1	2	5	6	1	2	5	6	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:76196905G>A	ENST00000308275.3	+	2	319	c.214G>A	c.(214-216)Ggc>Agc	p.G72S	FBXO22_ENST00000565131.1_3'UTR|FBXO22_ENST00000540507.1_Intron|FBXO22_ENST00000453211.2_Missense_Mutation_p.G72S	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	72					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GATCTCCGCAGGCCTGGCGGA	0.602																																					p.G72S		.											.	FBXO22-658	0			c.G214A						.						108	101	103					15																	76196905		2197	4294	6491	SO:0001583	missense	26263	exon2			TCCGCAGGCCTGG	AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"F-boxes /  "other""	13593	protein-coding gene	gene with protein product	"FIST domain containing 1"	609096	"F-box only protein 22"			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.214G>A	15.37:g.76196905G>A	ENSP00000307833:p.Gly72Ser	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	305	92	NM_012170	0	0	22	42	20	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	37	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	G	6.702	0.498156	0.12762	.	.	ENSG00000167196	ENST00000308275;ENST00000453211	.	.	.	3.51	0.501	0.16925	.	0.746536	0.11012	N	0.609403	T	0.13841	0.0335	N	0.03608	-0.345	0.09310	N	0.999993	B;B	0.09022	0.0;0.002	B;B	0.08055	0.001;0.003	T	0.33599	-0.9862	9	0.12103	T	0.63	-1.7367	7.3984	0.26950	0.0987:0.332:0.5694:0.0	.	72;72	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	S	72	.	ENSP00000307833:G72S	G	+	1	0	FBXO22	73983960	0.001000	0.12720	0.002000	0.10522	0.591000	0.36615	0.233000	0.17911	0.106000	0.17784	0.563000	0.77884	GGC	.		0.602	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188		A	76196905	G	A	76196905	3	1	51	1	0	0	0	0	1	0	0	0	5753	1000	35	2	220	2	FBXO22	15	76196905	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	16285563	76196905	26334487	200	4888											
MFGE8	4240	bcgsc.ca	37	chr15	89453134	89453135	+	Frame_Shift_Ins	INS	-	-	G																															cataaaccaccgttgtggcaINSggggtttttggaacagatat																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:89453134_89453135insG	ENST00000566497.1	-	2	154_155	c.93_94insC	c.(91-96)ccctgcfs	p.C32fs	MFGE8_ENST00000539437.1_Frame_Shift_Ins_p.C24fs|MFGE8_ENST00000268151.7_Frame_Shift_Ins_p.C32fs|MFGE8_ENST00000268150.8_Frame_Shift_Ins_p.C32fs|MFGE8_ENST00000559997.1_Intron|MFGE8_ENST00000542878.1_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	32	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CCGTTGTGGCAGGGGTTTTTGG	0.545																																					p.C32fs													.	MFGE8-91	0			c.94_95insC						.																																			SO:0001589	frameshift_variant	4240	exon2			TGTGGCAGGGGTT	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.94dupC	15.37:g.89453138_89453138dupG	ENSP00000456281:p.Cys32fs	Somatic	104	3		WXS	Illumina HiSeq	Phase_1	257	68	NM_001114614	0	0	0	0	0	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Frame_Shift_Ins	INS	ENST00000566497.1	37	CCDS10347.1																																																																																			.		0.545	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		G	89453135	-	G	89453134	7	5	51	1	0	1	1	0	0	0	0	0	9545	188	7	0	1097	0	MFGE8	15	89453134	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	13256229	89453134	13078258	201	4889											
SYNM	23336	ucsc.edu	37	chr15	99671486	99671486	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtccgccctcaccagagAggggcagggtgggccgggga	6	4	19	12	2	1	1	1	0	0	1	2	3	2	2	4	6	0	2	4	6	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:99671486A>G	ENST00000560674.1	+	4	2532	c.2063A>G	c.(2062-2064)gAg>gGg	p.E688G	RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000561323.1_3'UTR|SYNM_ENST00000328642.7_Missense_Mutation_p.E973G|SYNM_ENST00000336292.6_Missense_Mutation_p.E973G			O15061	SYNEM_HUMAN	synemin, intermediate filament protein	974	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						CTCACCAGAGAGGGGCAGGGT	0.642																																					.	Pancreas(125;1071 1762 21750 40003 40381)												.	SYNM-26	0			.						.						32	38	36					15																	99671486		2007	4151	6158	SO:0001583	missense	23336	.			CCAGAGAGGGGCA	AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"A-kinase anchor proteins", "Intermediate filaments type IV"	24466	protein-coding gene	gene with protein product	"synemin alpha", "synemin beta"	606087	"desmuslin"	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000560674.1:c.2063A>G	15.37:g.99671486A>G	ENSP00000453040:p.Glu688Gly	Somatic	17	0		WXS	Illumina HiSeq		57	1	.	0	0	3	4	1	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Missense_Mutation	SNP	ENST00000560674.1	37		.	.	.	.	.	.	.	.	.	.	A	11.52	1.662170	0.29515	.	.	ENSG00000182253	ENST00000336292;ENST00000328642	D;D	0.84944	-1.9;-1.92	5.64	4.52	0.55395	.	.	.	.	.	T	0.81725	0.4883	.	.	.	0.20074	N	0.999933	P;P	0.50272	0.933;0.933	B;B	0.40901	0.343;0.276	T	0.73078	-0.4096	8	0.87932	D	0	.	12.3478	0.55130	0.8587:0.1412:0.0:0.0	.	974;973	O15061;C9JIE4	SYNEM_HUMAN;.	G	973	ENSP00000336775:E973G;ENSP00000330469:E973G	ENSP00000330469:E973G	E	+	2	0	SYNM	97489009	0.998000	0.40836	0.017000	0.16124	0.013000	0.08279	2.672000	0.46850	0.967000	0.38186	-0.264000	0.10439	GAG	.		0.642	SYNM-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000415698.2	NM_145728		G	99671486	A	G	99671486	3	3	51	1	0	0	0	0	1	0	0	0	15487	304	11	3	2934	3	SYNM	15	99671486	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	10218352	99671486	2859906	202	4890											
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1394683	1394683	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttctgctacagtgtgtacGccagcctcttccacaggtgg	7	11	11	12	1	2	0	0	0	2	0	3	0	3	0	3	2	4	3	3	2	2	4	rs565955956	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:1394683G>C	ENST00000324385.5	+	19	2004	c.1846G>C	c.(1846-1848)Gcc>Ccc	p.A616P	BAIAP3_ENST00000562208.1_Missense_Mutation_p.A558P|BAIAP3_ENST00000397489.1_Missense_Mutation_p.A598P|BAIAP3_ENST00000568887.1_Missense_Mutation_p.A553P|BAIAP3_ENST00000397488.2_Missense_Mutation_p.A598P|BAIAP3_ENST00000426824.3_Missense_Mutation_p.A581P|BAIAP3_ENST00000421665.2_Missense_Mutation_p.A545P	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	616					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				CAGTGTGTACGCCAGCCTCTT	0.647													G|||	369	0.0736821	0.0545	0.1455	5008	,	,		18128	0.0724		0.1054	False		,,,				2504	0.0174				p.A616P		.											.	BAIAP3-91	0			c.G1846C						.						118	128	125					16																	1394683		2199	4300	6499	SO:0001583	missense	8938	exon19			GTGTACGCCAGCC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.1846G>C	16.37:g.1394683G>C	ENSP00000324510:p.Ala616Pro	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	662	325	NM_003933	0	0	8	9	1	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125077	0.37533	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.71934	-0.6;-0.59;-0.61;-0.59;-0.6	4.51	2.5	0.30297	.	0.373843	0.27189	N	0.020501	T	0.67192	0.2867	L	0.51422	1.61	0.35007	D	0.756553	D;P;P;P	0.61080	0.989;0.845;0.845;0.845	P;P;P;B	0.52217	0.693;0.469;0.469;0.369	T	0.69829	-0.5039	10	0.30854	T	0.27	-24.8112	6.0006	0.19519	0.3171:0.0:0.6829:0.0	.	545;558;616;598	E7EUB9;B4DIK3;O94812;A2A2B2	.;.;BAIP3_HUMAN;.	P	581;598;616;598;545	ENSP00000407242:A581P;ENSP00000380625:A598P;ENSP00000324510:A616P;ENSP00000380626:A598P;ENSP00000409533:A545P	ENSP00000324510:A616P	A	+	1	0	BAIAP3	1334684	0.997000	0.39634	0.726000	0.30738	0.069000	0.16628	3.026000	0.49689	0.855000	0.35359	0.436000	0.28706	GCC	.		0.647	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			C	1394683	G	C	1394683	3	2	51	1	0	0	0	0	1	0	0	0	1305	1087	38	4	1920	4	BAIAP3	16	1394683	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		1394683	88960070	203	4891											
C16orf42	84572	hgsc.bcm.edu	37	chr16	1401500	1401500	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgcggcccgtgcagcgcCgggggtcgcagtggcccaac	4	5	17	15	5	0	0	0	0	0	0	1	0	0	0	3	4	4	3	3	4	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:1401500C>T	ENST00000204679.4	+	0	0				TSR3_ENST00000007390.2_Missense_Mutation_p.R71Q	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit						carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				CGTGCAGCGCCGGGGGTCGCA	0.771																																					p.R71Q		.											.	.	0			c.G212A						.						3	4	4					16																	1401500		1707	3466	5173	SO:0001631	upstream_gene_variant	115939	exon2			CAGCGCCGGGGGT	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"GlcNAc-phosphotransferase gamma-subunit"	607838	"N-acetylglucosamine-1-phosphotransferase, gamma subunit", "chromosome 16 open reading frame 27"	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835		16.37:g.1401500C>T	Exception_encountered	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	37	20	NM_001001410	0	0	2	10	8	B2R556|Q6XYD7|Q96L13	Missense_Mutation	SNP	ENST00000204679.4	37	CCDS10436.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316172	0.81469	.	.	ENSG00000007520	ENST00000007390	.	.	.	4.74	1.64	0.23874	RNase L inhibitor RLI, possible metal-binding domain (1);	0.131915	0.48767	D	0.000175	T	0.43322	0.1242	M	0.73372	2.23	0.26712	N	0.970953	P	0.52170	0.951	P	0.49276	0.605	T	0.39742	-0.9599	9	0.72032	D	0.01	-15.2852	3.4374	0.07450	0.0:0.4866:0.2002:0.3132	.	71	Q9UJK0	TSR3_HUMAN	Q	71	.	ENSP00000007390:R71Q	R	-	2	0	C16orf42	1341501	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	2.346000	0.44027	0.396000	0.25283	0.462000	0.41574	CGG	.		0.771	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		T	1401500	C	T	1401500	1	4	51	0	1	0	0	0	0	0	0	0	1817	652	23	1		1	C16orf42	16	1401500	5'Flank	SNP	C	TCGA-B9-4117-01A-01D-1252-08	6817	1401500	88953253	204	4892											
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3808859	3808859	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatgaattaacttactggaAttccgaggagctggggatct	11	13	11	6	1	1	1	0	1	1	0	2	5	2	4	1	4	3	1	1	4	5	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:3808859A>G	ENST00000262367.5	-	17	4174	c.3365T>C	c.(3364-3366)aTt>aCt	p.I1122T	CREBBP_ENST00000382070.3_Missense_Mutation_p.I1084T	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1122	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACTTACTGGAATTCCGAGGAG	0.438			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.I1122T		.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP-1807	0			c.T3365C						.						69	68	68					16																	3808859		2197	4300	6497	SO:0001583	missense	1387	exon17			ACTGGAATTCCGA	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3365T>C	16.37:g.3808859A>G	ENSP00000262367:p.Ile1122Thr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	62	14	NM_004380	0	0	0	0	0	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.568041	0.45798	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	T;T	0.19532	2.14;2.14	5.05	5.05	0.67936	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000001	T	0.54303	0.1850	M	0.89534	3.04	0.80722	D	1	D;D	0.59767	0.986;0.986	D;D	0.97110	1.0;1.0	T	0.64952	-0.6286	10	0.72032	D	0.01	-13.4551	15.0885	0.72174	1.0:0.0:0.0:0.0	.	1152;1122	Q4LE28;Q92793	.;CBP_HUMAN	T	1122;1152;1084	ENSP00000262367:I1122T;ENSP00000371502:I1084T	ENSP00000262367:I1122T	I	-	2	0	CREBBP	3748860	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.067000	0.93955	2.022000	0.59522	0.459000	0.35465	ATT	.		0.438	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3808859	A	G	3808859	3	3	51	1	0	0	0	0	1	0	0	0	3867	101	4	3	4023	3	CREBBP	16	3808859	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	2407359	3808859	86545894	205	4893											
C16orf68	79091	bcgsc.ca	37	chr16	8736397	8736398	+	Frame_Shift_Ins	INS	-	-	TCCCTCCC																															cagattgaaaaatgcctgcaINScagccatactgtcggtggag																								rs138698854|rs202173100		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:8736397_8736398insTCCCTCCC	ENST00000381920.3	+	9	1243_1244	c.985_986insTCCCTCCC	c.(985-987)acafs	p.T329fs	METTL22_ENST00000568967.1_3'UTR|METTL22_ENST00000561758.1_Frame_Shift_Ins_p.T273fs	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	329						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						AAATGCCTGCACAGCCATACTG	0.535																																					p.T329fs													.	METTL22-90	0			c.985_986insTCCCTCCC						.																																			SO:0001589	frameshift_variant	79091	exon9			GCCTGCACAGCCA	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"chromosome 16 open reading frame 68"	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	Exception_encountered	16.37:g.8736397_8736398insTCCCTCCC	ENSP00000371345:p.Thr329fs	Somatic	230	0		WXS	Illumina HiSeq	Phase_1	312	0	NM_024109	0	0	0	0	0	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Frame_Shift_Ins	INS	ENST00000381920.3	37	CCDS10533.2																																																																																			.		0.535	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109		TCCCTCCC	8736398	-	TCCCTCCC	8736397	7	5	51	1	0	1	1	0	0	0	0	0	1831	159	6	0	1015	0	C16orf68	16	8736397	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	4927538	8736397	81618356	206	4894											
SETD1A	9739	broad.mit.edu	37	chr16	30974861	30974861	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaagttccaaggctcgggtGcagccactgagacggtgaga	11	6	15	9	2	0	3	0	2	0	3	2	5	1	3	2	3	2	3	2	3	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:30974861G>C	ENST00000262519.8	+	5	1311	c.625G>C	c.(625-627)Gca>Cca	p.A209P		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	209					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						AGGCTCGGGTGCAGCCACTGA	0.577																																					p.A209P													.	SETD1A-93	0			c.G625C						.																																			SO:0001583	missense	9739	exon5			TCGGGTGCAGCCA	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.625G>C	16.37:g.30974861G>C	ENSP00000262519:p.Ala209Pro	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	236	57	NM_014712	0	0	10	12	2	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	37	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	6.515	0.463221	0.12402	.	.	ENSG00000099381	ENST00000262519;ENST00000452917	D	0.94280	-3.39	5.93	2.51	0.30379	.	0.628623	0.15550	N	0.256486	D	0.83667	0.5304	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.71265	-0.4644	10	0.26408	T	0.33	.	10.6274	0.45516	0.2471:0.0:0.7529:0.0	.	209	O15047	SET1A_HUMAN	P	209	ENSP00000262519:A209P	ENSP00000262519:A209P	A	+	1	0	SETD1A	30882362	0.778000	0.28640	0.992000	0.48379	0.302000	0.27658	0.180000	0.16860	0.863000	0.35553	-0.150000	0.13652	GCA	.		0.577	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		C	30974861	G	C	30974861	3	2	51	1	0	0	0	0	1	0	0	0	14162	1319	46	4	639	4	SETD1A	16	30974861	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	22238464	30974861	59379892	207	4895											
ITGAM	3684	hgsc.bcm.edu	37	chr16	31335785	31335785	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcccacattcccgcgccGtcttcaatgagacaaagaac	11	6	8	16	4	2	2	1	1	1	2	3	3	3	2	4	0	1	0	4	0	3	2	rs139908772	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:31335785G>A	ENST00000287497.8	+	17	2143	c.2068G>A	c.(2068-2070)Gtc>Atc	p.V690I	ITGAM_ENST00000544665.3_Missense_Mutation_p.V691I			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	690					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TTCCCGCGCCGTCTTCAATGA	0.582													G|||	6	0.00119808	0.0038	0	5008	,	,		18615	0		0.001	False		,,,				2504	0				p.V691I		.											.	ITGAM-226	0			c.G2071A						.	G	ILE/VAL,ILE/VAL	14,3950		0,14,1968	22	23	23		2071,2068	-7.7	0	16	dbSNP_134	23	0,8326		0,0,4163	yes	missense,missense	ITGAM	NM_001145808.1,NM_000632.3	29,29	0,14,6131	AA,AG,GG		0.0,0.3532,0.1139	benign,benign	691/1154,690/1153	31335785	14,12276	1982	4163	6145	SO:0001583	missense	3684	exon17			CGCGCCGTCTTCA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2068G>A	16.37:g.31335785G>A	ENSP00000287497:p.Val690Ile	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	27	17	NM_001145808	0	0	10	23	13	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	1.225	-0.625646	0.03610	0.003532	0.0	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.50001	0.76;0.76	4.81	-7.71	0.01254	Integrin alpha-2 (1);	.	.	.	.	T	0.17195	0.0413	N	0.04686	-0.185	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.13407	0.009;0.006;0.006	T	0.35798	-0.9774	9	0.02654	T	1	.	8.3033	0.32027	0.2458:0.0:0.6241:0.1301	.	96;690;690	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	I	691;690	ENSP00000441691:V691I;ENSP00000287497:V690I	ENSP00000287497:V690I	V	+	1	0	ITGAM	31243286	0.052000	0.20516	0.001000	0.08648	0.001000	0.01503	-0.785000	0.04628	-1.588000	0.01627	-1.008000	0.02478	GTC	G|0.999;A|0.001		0.582	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31335785	G	A	31335785	3	1	51	1	0	0	0	0	1	0	0	0	7908	1145	40	1	2137	1	ITGAM	16	31335785	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	360924	31335785	59018968	208	4896											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31474046	31474046	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcaccctcgtattgtggctgCccttgtggggtttctgtatg	3	15	13	10	1	1	0	0	0	1	0	2	0	1	0	2	3	1	5	2	3	2	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:31474046C>G	ENST00000563544.1	+	4	1724	c.1178C>G	c.(1177-1179)gCc>gGc	p.A393G	ARMC5_ENST00000538189.1_Missense_Mutation_p.A425G|ARMC5_ENST00000457010.2_Missense_Mutation_p.A393G|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000268314.4_Missense_Mutation_p.A393G|ARMC5_ENST00000408912.3_Missense_Mutation_p.A488G|ARMC5_ENST00000412665.2_Intron			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	393										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						ATTGTGGCTGCCCTTGTGGGG	0.647																																					p.A393G		.											.	ARMC5-24	0			c.C1178G						.						51	56	55					16																	31474046		1985	4176	6161	SO:0001583	missense	79798	exon3			TGGCTGCCCTTGT	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1178C>G	16.37:g.31474046C>G	ENSP00000456877:p.Ala393Gly	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	269	63	NM_024742	0	0	10	10	0	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	c	22.5	4.302423	0.81136	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.53423	1.55;1.58;1.59;0.62	4.87	4.87	0.63330	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65291	0.2677	L	0.58101	1.795	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.68868	-0.5295	10	0.87932	D	0	-28.7614	15.5059	0.75739	0.0:1.0:0.0:0.0	.	425;488;393;393	F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;ARMC5_HUMAN;.	G	488;425;393;393	ENSP00000386125:A488G;ENSP00000443995:A425G;ENSP00000268314:A393G;ENSP00000399561:A393G	ENSP00000268314:A393G	A	+	2	0	ARMC5	31381547	1.000000	0.71417	0.996000	0.52242	0.851000	0.48451	6.214000	0.72200	2.251000	0.74343	0.457000	0.33378	GCC	.		0.647	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		G	31474046	C	G	31474046	3	3	51	1	0	0	0	0	1	0	0	0	955	739	26	4	1188	4	ARMC5	16	31474046	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	138261	31474046	58880707	209	4897											
LONP2	83752	bcgsc.ca	37	chr16	48286156	48286156	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgtacaggtcttaaaagaGaagccatatcccattgctga	14	11	8	8	0	1	2	0	1	1	1	2	3	2	2	2	1	3	2	2	1	5	5	rs202207335		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:48286156G>A	ENST00000285737.4	+	2	441	c.348G>A	c.(346-348)gaG>gaA	p.E116E	LONP2_ENST00000535754.1_Silent_p.E116E	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCTTAAAAGAGAAGCCATATC	0.502																																					p.E116E													.	LONP2-90	0			c.G348A						.						79	71	74					16																	48286156		2200	4300	6500	SO:0001819	synonymous_variant	83752	exon2			AAAAGAGAAGCCA	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.348G>A	16.37:g.48286156G>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_1	29	18	NM_031490	0	0	10	13	3		Silent	SNP	ENST00000285737.4	37	CCDS10734.1																																																																																			G|0.999;A|0.001		0.502	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		A	48286156	G	A	48286156	2	1	51	1	0	0	0	0	0	0	0	1	8918	933	33	2		2	LONP2	16	48286156	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	16812110	48286156	42068597	210	4898											
HERPUD1	9709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56970652	56970652	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatcggggacagtatcctgaGgattcctcaagtgatggttt	10	12	12	7	1	1	2	1	2	0	0	4	4	3	4	2	4	0	2	2	4	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:56970652G>T	ENST00000439977.2	+	4	551	c.354G>T	c.(352-354)gaG>gaT	p.E118D	HERPUD1_ENST00000344114.4_Missense_Mutation_p.E117D|HERPUD1_ENST00000570273.1_3'UTR|HERPUD1_ENST00000379792.2_Missense_Mutation_p.E93D|HERPUD1_ENST00000300302.5_Missense_Mutation_p.E117D	NM_001010989.1|NM_014685.2	NP_001010989.1|NP_055500.1	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	118					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of protein binding (GO:0032092)|regulation of protein ubiquitination (GO:0031396)|response to unfolded protein (GO:0006986)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	11						AGTATCCTGAGGATTCCTCAA	0.443			T	ERG	prostate																																p.E118D		.		Dom	yes		16	16q12.2-q13	9709	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"		E	.	HERPUD1-90	0			c.G354T						.						142	131	135					16																	56970652		2198	4300	6498	SO:0001583	missense	9709	exon4			TCCTGAGGATTCC	AB034989	CCDS10771.1, CCDS45492.1	16q13	2008-05-14			ENSG00000051108	ENSG00000051108			13744	protein-coding gene	gene with protein product		608070				10922362, 10708769	Standard	NM_001010989		Approved	KIAA0025, Mif1, HERP, SUP	uc002eke.2	Q15011	OTTHUMG00000133276	ENST00000439977.2:c.354G>T	16.37:g.56970652G>T	ENSP00000409555:p.Glu118Asp	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	77	41	NM_014685	0	0	265	515	250	E9PGD1|O60644|Q6IAN8|Q96D92	Missense_Mutation	SNP	ENST00000439977.2	37	CCDS10771.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.631353	0.28978	.	.	ENSG00000051108	ENST00000439977;ENST00000379792;ENST00000300302;ENST00000344114	T;T	0.44881	1.51;0.91	6.16	3.15	0.36227	.	0.708796	0.14867	N	0.293775	T	0.20577	0.0495	N	0.08118	0	0.26730	N	0.970611	B;B;B;B;B;B	0.20988	0.017;0.008;0.033;0.0;0.05;0.029	B;B;B;B;B;B	0.19666	0.008;0.026;0.022;0.0;0.019;0.009	T	0.21552	-1.0242	10	0.14656	T	0.56	-20.3489	8.8344	0.35104	0.2378:0.0:0.7622:0.0	.	118;117;118;93;117;118	B4E3N8;Q15011-3;A4UAE9;E9PGD1;Q15011-2;Q15011	.;.;.;.;.;HERP1_HUMAN	D	117;93;118;117	ENSP00000369118:E93D;ENSP00000340931:E117D	ENSP00000300302:E118D	E	+	3	2	HERPUD1	55528153	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	0.509000	0.22707	0.939000	0.37446	0.650000	0.86243	GAG	.		0.443	HERPUD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257056.5			T	56970652	G	T	56970652	3	4	51	1	0	0	0	0	1	0	0	0	7084	991	35	4	368	4	HERPUD1	16	56970652	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	8684496	56970652	33384101	211	4899											
SF3B3	23450	broad.mit.edu	37	chr16	70569300	70569300	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtgaccagccagatatcCgctgtccaattcccaggagg	9	9	11	12	1	0	2	0	1	0	1	3	3	3	3	5	3	1	1	5	3	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:70569300C>T	ENST00000302516.5	+	6	1013	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C	SNORD111_ENST00000408139.1_RNA	NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	268					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)	p.R268C(1)|p.R268S(1)		breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				GCCAGATATCCGCTGTCCAAT	0.413																																					p.R268C													.	SF3B3-91	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.C802T						.						130	135	133					16																	70569300		2198	4300	6498	SO:0001583	missense	23450	exon6			GATATCCGCTGTC	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.802C>T	16.37:g.70569300C>T	ENSP00000305790:p.Arg268Cys	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	285	5	NM_012426	0	0	46	46	0	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	37	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863904	0.51482	.	.	ENSG00000189091	ENST00000302516	T	0.44881	0.91	4.84	3.79	0.43588	.	0.000000	0.85682	D	0.000000	T	0.58018	0.2093	M	0.78223	2.4	0.80722	D	1	D	0.54047	0.964	P	0.54889	0.763	T	0.63567	-0.6608	10	0.44086	T	0.13	.	15.9059	0.79430	0.1767:0.8233:0.0:0.0	.	268	Q15393	SF3B3_HUMAN	C	268	ENSP00000305790:R268C	ENSP00000305790:R268C	R	+	1	0	SF3B3	69126801	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.092000	0.50207	2.236000	0.73375	0.484000	0.47621	CGC	.		0.413	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70569300	C	T	70569300	3	4	51	1	0	0	0	0	1	0	0	0	14184	652	23	1	820	1	SF3B3	16	70569300	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	13598648	70569300	19785453	212	4900											
MARVELD3	91862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	71674415	71674415	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcggtggctttgggaacaacTactactcaccgttcgagggc	8	9	13	11	3	1	0	1	0	0	0	2	2	1	1	1	4	4	2	1	4	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:71674415T>A	ENST00000299952.4	+	3	761	c.718T>A	c.(718-720)Tac>Aac	p.Y240N	MARVELD3_ENST00000561682.1_Intron|PHLPP2_ENST00000540628.1_Intron|MARVELD3_ENST00000565261.1_3'UTR	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	240	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				TGGGAACAACTACTACTCACC	0.572																																					p.Y240N		.											.	MARVELD3-91	0			c.T718A						.						113	95	101					16																	71674415		2198	4300	6498	SO:0001583	missense	91862	exon3			AACAACTACTACT	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.718T>A	16.37:g.71674415T>A	ENSP00000299952:p.Tyr240Asn	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	329	87	NM_001017967	0	0	2	5	3	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000299952.4	37	CCDS32478.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397934	0.62177	.	.	ENSG00000140832	ENST00000299952	D	0.85861	-2.04	5.63	5.63	0.86233	.	0.319419	0.34802	N	0.003668	D	0.90950	0.7155	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	D	0.90548	0.4507	9	0.40728	T	0.16	-16.1302	13.8397	0.63430	0.0:0.0:0.0:1.0	.	240	Q96A59-2	.	N	240	ENSP00000299952:Y240N	ENSP00000299952:Y240N	Y	+	1	0	MARVELD3	70231916	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.127000	0.50484	2.154000	0.67381	0.456000	0.33151	TAC	.		0.572	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268990.1	NM_052858		A	71674415	T	A	71674415	3	1	51	1	0	0	0	0	1	0	0	0	9344	1522	53	5	1343	5	MARVELD3	16	71674415	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1105115	71674415	18680338	213	4901											
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72984698	72984698	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgctccacgttcatgtgcagGcccagcatgtccaggttgtc	6	10	11	14	2	1	0	1	0	0	0	4	0	3	0	3	2	2	5	3	2	0	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:72984698G>A	ENST00000268489.5	-	3	3558	c.2886C>T	c.(2884-2886)ggC>ggT	p.G962G	ZFHX3_ENST00000397992.5_Silent_p.G48G	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	962					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TCATGTGCAGGCCCAGCATGT	0.607																																					p.G962G		.											.	ZFHX3-72	0			c.C2886T						.						106	90	96					16																	72984698		2198	4300	6498	SO:0001819	synonymous_variant	463	exon3			GTGCAGGCCCAGC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2886C>T	16.37:g.72984698G>A		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	260	65	NM_006885	0	0	9	11	2	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.		0.607	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		A	72984698	G	A	72984698	2	1	51	1	0	0	0	0	0	0	0	1	17666	1190	42	2		2	ZFHX3	16	72984698	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	1310283	72984698	17370055	214	4902											
ANKRD11	29123	broad.mit.edu	37	chr16	89352564	89352565	+	Frame_Shift_Ins	INS	-	-	C																															ctgttgctctgctgcgggttINSccctccgtaccgcagcagca																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:89352564_89352565insC	ENST00000301030.4	-	8	1234_1235	c.774_775insG	c.(772-777)gggaacfs	p.N259fs	ANKRD11_ENST00000378330.2_Frame_Shift_Ins_p.N259fs	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	259					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TGCTGCGGGTTCCCTCCGTACC	0.579																																					p.N259fs													.	ANKRD11-139	0			c.775_776insG						.																																			SO:0001589	frameshift_variant	29123	exon8			GCGGGTTCCCTCC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.775dupG	16.37:g.89352567_89352567dupC	ENSP00000301030:p.Asn259fs	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	536	7	NM_013275	0	0	0	0	0	Q6NTG1|Q6QMF8	Frame_Shift_Ins	INS	ENST00000301030.4	37	CCDS32513.1																																																																																			.		0.579	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89352565	-	C	89352564	7	5	51	1	0	1	1	0	0	0	0	0	639	1783	62	0	7240	0	ANKRD11	16	89352564	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	16367866	89352564	1002189	215	4903											
USP6	9098	hgsc.bcm.edu	37	chr17	5042939	5042939	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggaggaccagctggccAcctgctggcaggctgaacac	9	4	13	15	0	0	1	0	1	0	0	0	3	0	3	4	5	3	4	4	5	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:5042939A>C	ENST00000574788.1	+	22	3698	c.1468A>C	c.(1468-1470)Acc>Ccc	p.T490P	USP6_ENST00000304328.5_Missense_Mutation_p.T173P|USP6_ENST00000332776.4_Missense_Mutation_p.T490P|USP6_ENST00000250066.6_Missense_Mutation_p.T490P			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	490					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CCAGCTGGCCACCTGCTGGCA	0.607			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.T490P		.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6-662	0			c.A1468C						.						44	48	47					17																	5042939		2203	4300	6503	SO:0001583	missense	9098	exon14			CTGGCCACCTGCT	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"Ubiquitin-specific peptidases"	12629	protein-coding gene	gene with protein product	"ubiquitin carboxyl-terminal hydrolase 6", "TBC1D3 and USP32 fusion", "Tre-2 oncogene"	604334	"ubiquitin specific protease 6 (Tre-2 oncogene)", "TRE oncogene, Smith Magenis syndrome chromosome region", "ubiquitin specific peptidase 6 (Tre-2 oncogene)"	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1468A>C	17.37:g.5042939A>C	ENSP00000460380:p.Thr490Pro	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	325	20	NM_004505	0	0	0	38	38	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.512750	0.00975	.	.	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.13901	2.55;3.03;2.73	0.0465	0.0465	0.14256	.	0.094876	0.64402	D	0.000001	T	0.09423	0.0232	N	0.08118	0	0.09310	N	1	P;P	0.47106	0.89;0.797	P;B	0.52554	0.702;0.321	T	0.20773	-1.0265	9	0.38643	T	0.18	.	.	.	.	.	173;490	P35125-2;P35125	.;UBP6_HUMAN	P	490;490;173	ENSP00000328010:T490P;ENSP00000250066:T490P;ENSP00000305473:T173P	ENSP00000250066:T490P	T	+	1	0	USP6	4983663	0.933000	0.31639	0.264000	0.24511	0.260000	0.26232	-0.165000	0.09968	0.115000	0.18071	0.113000	0.15668	ACC	.		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		C	5042939	A	C	5042939	3	2	51	1	0	0	0	0	1	0	0	0	17119	159	6	5	1518	5	USP6	17	5042939	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		5042939	76152271	216	4904											
PER1	5187	hgsc.bcm.edu	37	chr17	8047043	8047043	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaagggggtagtggctggTggggtgggccagggggtgga	5	6	27	3	0	0	0	0	0	0	0	0	2	0	2	1	11	0	2	1	11	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:8047043T>G	ENST00000317276.4	-	19	2850	c.2613A>C	c.(2611-2613)ccA>ccC	p.P871P	PER1_ENST00000581082.1_Silent_p.P848P|PER1_ENST00000578089.1_5'UTR	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	871	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TAGTGGCTGGTGGGGTGGGCC	0.672			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.P871P		.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1-723	0			c.A2613C						.						9	11	10					17																	8047043		2183	4270	6453	SO:0001819	synonymous_variant	5187	exon19			GGCTGGTGGGGTG	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"period (Drosophila) homolog 1", "period homolog 1 (Drosophila)"	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2613A>C	17.37:g.8047043T>G		Somatic	11	1		WXS	Illumina HiSeq	Phase_I	52	29	NM_002616	0	0	13	14	1	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			.		0.672	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			G	8047043	T	G	8047043	2	3	51	1	0	0	0	0	0	0	0	1	11755	1683	59	5		5	PER1	17	8047043	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3004104	8047043	73148167	217	4905											
COX10	1352	hgsc.bcm.edu;bcgsc.ca	37	chr17	14110451	14110451	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcttctgcagcctgtggcAcctgccgctgctgctgctgc	2	12	12	15	1	2	0	0	0	2	0	2	0	2	0	3	1	7	7	3	1	0	2	rs200435051		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:14110451A>C	ENST00000261643.3	+	7	1330	c.1253A>C	c.(1252-1254)cAc>cCc	p.H418P	COX10_ENST00000537334.1_Missense_Mutation_p.H201P|COX10_ENST00000536205.1_Missense_Mutation_p.H226P	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	418					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		AGCCTGTGGCACCTGCCGCTG	0.672																																					p.H418P		.											.	COX10-226	0			c.A1253C						.						34	35	34					17																	14110451		2200	4293	6493	SO:0001583	missense	1352	exon7			TGTGGCACCTGCC	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.1253A>C	17.37:g.14110451A>C	ENSP00000261643:p.His418Pro	Somatic	81	2		WXS	Illumina HiSeq	Phase_I	161	96	NM_001303	0	0	10	10	0	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.623350	0.87460	.	.	ENSG00000006695	ENST00000261643;ENST00000536205;ENST00000537334	D;D;D	0.92397	-3.03;-3.03;-3.03	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	D	0.97133	0.9063	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79784	0.981;0.993	D	0.98325	1.0530	10	0.87932	D	0	.	14.6208	0.68582	1.0:0.0:0.0:0.0	.	226;418	B4DJ50;Q12887	.;COX10_HUMAN	P	418;226;201	ENSP00000261643:H418P;ENSP00000439494:H226P;ENSP00000443354:H201P	ENSP00000261643:H418P	H	+	2	0	COX10	14051176	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.822000	0.92013	1.932000	0.55993	0.459000	0.35465	CAC	.		0.672	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		C	14110451	A	C	14110451	3	2	51	1	0	0	0	0	1	0	0	0	3768	159	6	5	1279	5	COX10	17	14110451	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	6063408	14110451	67084759	218	4906											
FAM18B2	201158	bcgsc.ca	37	chr17	15449097	15449097	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagttctacactgatactcAccagccactttactgtgaag	13	11	6	11	0	2	2	1	2	1	0	2	2	2	2	2	0	4	1	2	0	5	5	rs199732389		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:15449097A>C	ENST00000225576.3	-	5	558		c.e5+1		TVP23C_ENST00000518321.1_Splice_Site|TVP23C_ENST00000428082.2_Splice_Site|TVP23C_ENST00000519970.1_Splice_Site|TVP23C-CDRT4_ENST00000522212.2_Splice_Site|TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000584811.1_Splice_Site	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)							integral component of membrane (GO:0016021)											ACTGATACTCACCAGCCACTT	0.403																																					.													.	.	0			c.462+2T>G						.						151	145	147					17																	15449097		2203	4300	6503	SO:0001630	splice_region_variant	201158	exon6			ATACTCACCAGCC	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.462+1T>G	17.37:g.15449097A>C		Somatic	147	2		WXS	Illumina HiSeq	Phase_1	53	17	NM_145301	0	0	0	0	0	Q3LIC7	Splice_Site	SNP	ENST00000225576.3	37	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838878	0.51057	.	.	ENSG00000259024;ENSG00000259024;ENSG00000259024;ENSG00000175106;ENSG00000175106;ENSG00000175106;ENSG00000175106;ENSG00000175106	ENST00000522212;ENST00000557349;ENST00000481756;ENST00000519970;ENST00000225576;ENST00000428082;ENST00000438826;ENST00000419890	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6393	0.68711	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RP11-726O12.1;FAM18B2	15389822	1.000000	0.71417	1.000000	0.80357	0.564000	0.35744	8.864000	0.92294	2.160000	0.67779	0.528000	0.53228	.	.		0.403	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301	Intron	C	15449097	A	C	15449097	5	2	51	1	0	0	0	0	0	0	1	0	5536	173	6	5	528	5	FAM18B2	17	15449097	Splice_Site	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1338646	15449097	65746113	219	4907											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR	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	265	268					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	303	45		WXS	Illumina HiSeq		858	112	NM_145301	0	1	15	47	31	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		T	15457087	C	T	15457087	3	4	51	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	7990	15457087	65738123	220	4908											
WSB1	26118	bcgsc.ca	37	chr17	25639347	25639347	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccacccaagaagttcaggaGctgccgattccttccaagct	10	8	8	15	1	1	1	1	0	0	1	3	3	3	2	5	1	3	3	5	1	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:25639347G>C	ENST00000262394.2	+	9	1534	c.1218G>C	c.(1216-1218)gaG>gaC	p.E406D	RP11-173M1.8_ENST00000578929.1_lincRNA|WSB1_ENST00000348811.2_Missense_Mutation_p.E260D	NM_015626.8	NP_056441.6	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box containing 1	406	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				lung(3)	3	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		AAGTTCAGGAGCTGCCGATTC	0.468																																					p.E406D													.	WSB1-226	0			c.G1218C						.						286	272	277					17																	25639347		2203	4300	6503	SO:0001583	missense	26118	exon9			TCAGGAGCTGCCG	AF069313	CCDS11220.1, CCDS11221.1	17q11.2	2013-01-09	2011-01-25		ENSG00000109046	ENSG00000109046		"WD repeat domain containing"	19221	protein-coding gene	gene with protein product		610091	"WD repeat and SOCS box-containing 1"			10354473, 12076535	Standard	XR_243778		Approved	DKFZp564A122, DKFZp564B0482, SWIP1	uc002gzd.1	Q9Y6I7	OTTHUMG00000132293	ENST00000262394.2:c.1218G>C	17.37:g.25639347G>C	ENSP00000262394:p.Glu406Asp	Somatic	450	0		WXS	Illumina HiSeq	Phase_1	403	122	NM_015626	0	0	126	140	14	Q9NRB1|Q9UBH9|Q9UG25|Q9UNN6|Q9Y656	Missense_Mutation	SNP	ENST00000262394.2	37	CCDS11220.1	.	.	.	.	.	.	.	.	.	.	G	8.222	0.802733	0.16397	.	.	ENSG00000109046	ENST00000262394;ENST00000348811	T;T	0.44083	0.93;0.93	5.91	-0.263	0.12954	SOCS protein, C-terminal (4);	0.583212	0.17272	N	0.180325	T	0.24928	0.0605	L	0.28014	0.82	0.22728	N	0.998802	B;B	0.14012	0.009;0.003	B;B	0.15870	0.014;0.014	T	0.13308	-1.0514	10	0.36615	T	0.2	-28.0638	6.7073	0.23258	0.4017:0.1213:0.477:0.0	.	260;406	Q9Y6I7-2;Q9Y6I7	.;WSB1_HUMAN	D	406;260	ENSP00000262394:E406D;ENSP00000327055:E260D	ENSP00000262394:E406D	E	+	3	2	WSB1	22663474	0.995000	0.38212	0.940000	0.37924	0.141000	0.21300	0.353000	0.20130	-0.232000	0.09811	0.655000	0.94253	GAG	.		0.468	WSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255391.4	NM_015626		C	25639347	G	C	25639347	3	2	51	1	0	0	0	0	1	0	0	0	17437	962	34	4	1252	4	WSB1	17	25639347	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	10182260	25639347	55555863	221	4909											
ALDOC	230	bcgsc.ca	37	chr17	26900783	26900784	+	Frame_Shift_Ins	INS	-	-	G																															tgatgaactcctcagtggcaINSgccccagcattgtcccgttg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:26900783_26900784insG	ENST00000226253.4	-	8	1443_1444	c.968_969insC	c.(967-969)gctfs	p.A323fs	PIGS_ENST00000543734.1_5'Flank|PIGS_ENST00000308360.7_5'Flank|PIGS_ENST00000395346.2_5'Flank|ALDOC_ENST00000395319.3_Frame_Shift_Ins_p.A295fs|RP11-192H23.5_ENST00000585189.1_RNA|ALDOC_ENST00000395321.2_Frame_Shift_Ins_p.A323fs	NM_005165.2	NP_005156.1	P09972	ALDOC_HUMAN	aldolase C, fructose-bisphosphate	323					aging (GO:0007568)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|organ regeneration (GO:0031100)|protein heterotetramerization (GO:0051290)|protein homotetramerization (GO:0051289)|response to hypoxia (GO:0001666)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	cytoskeletal protein binding (GO:0008092)|fructose-bisphosphate aldolase activity (GO:0004332)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Lung NSC(42;0.00431)					CCTCAGTGGCAGCCCCAGCATT	0.653																																					p.A323fs													.	ALDOC-651	0			c.969_970insC						.																																			SO:0001589	frameshift_variant	230	exon8			AGTGGCAGCCCCA	AF054987	CCDS11236.1	17q11.2	2013-09-20			ENSG00000109107	ENSG00000109107	4.1.2.13		418	protein-coding gene	gene with protein product		103870					Standard	XM_005257947		Approved		uc002hbp.3	P09972	OTTHUMG00000132605	ENST00000226253.4:c.969dupC	17.37:g.26900784_26900784dupG	ENSP00000226253:p.Ala323fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_1	567	121	NM_005165	0	0	0	0	0	B2R5R3|Q3SYL3|Q6FH94|Q6P0L5	Frame_Shift_Ins	INS	ENST00000226253.4	37	CCDS11236.1																																																																																			.		0.653	ALDOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255839.4			G	26900784	-	G	26900783	7	5	51	1	0	1	1	0	0	0	0	0	509	175	7	0	133	0	ALDOC	17	26900783	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	1261436	26900783	54294427	222	4910											
SLFN5	162394	bcgsc.ca	37	chr17	33586030	33586030	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatggaacacagaggctggTgtgccacttgctaccttatg	9	11	11	10	0	1	1	1	0	0	1	1	2	1	2	2	3	4	2	2	3	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:33586030T>G	ENST00000299977.4	+	2	469	c.321T>G	c.(319-321)ggT>ggG	p.G107G	SLFN5_ENST00000592325.1_Silent_p.G107G|SLFN5_ENST00000542451.1_Silent_p.G107G	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	107					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		CAGAGGCTGGTGTGCCACTTG	0.433																																					p.G107G													.	SLFN5-92	0			c.T321G						.						110	110	110					17																	33586030		2203	4300	6503	SO:0001819	synonymous_variant	162394	exon2			GGCTGGTGTGCCA	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.321T>G	17.37:g.33586030T>G		Somatic	144	1		WXS	Illumina HiSeq	Phase_1	106	45	NM_144975	0	0	20	20	0	Q08AF2|Q8WU54|Q96A82	Silent	SNP	ENST00000299977.4	37	CCDS32619.1																																																																																			.		0.433	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		G	33586030	T	G	33586030	2	3	51	1	0	0	0	0	0	0	0	1	14769	1683	59	5		5	SLFN5	17	33586030	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	6685247	33586030	47609180	223	4911											
ACACA	31	bcgsc.ca	37	chr17	35445967	35445967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcctctgtcagctgtttctCtagccactccgccagatcct	5	13	6	17	1	3	1	1	0	2	1	7	1	6	1	5	0	2	2	5	0	1	2	rs199660893		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:35445967C>T	ENST00000394406.2	-	55	7013	c.6823G>A	c.(6823-6825)Gag>Aag	p.E2275K	ACACA_ENST00000353139.5_Missense_Mutation_p.E2312K|ACACA_ENST00000335166.5_Missense_Mutation_p.E2197K|ACACA_ENST00000360679.3_Missense_Mutation_p.E2217K|ACACA_ENST00000361253.5_Missense_Mutation_p.E401K	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2275					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGCTGTTTCTCTAGCCACTCC	0.507																																					p.E2312K	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)												.	ACACA-154	0			c.G6934A						.						175	160	165					17																	35445967		2203	4300	6503	SO:0001583	missense	31	exon55			GTTTCTCTAGCCA	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.6823G>A	17.37:g.35445967C>T	ENSP00000377928:p.Glu2275Lys	Somatic	196	0		WXS	Illumina HiSeq	Phase_1	185	72	NM_198834	0	0	25	28	3	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234586	0.95207	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330;ENST00000361253	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	5.77	4.78	0.61160	.	0.052201	0.85682	D	0.000000	T	0.69296	0.3095	M	0.81341	2.54	0.80722	D	1	D;P;P;B;B	0.54397	0.966;0.907;0.744;0.056;0.093	P;P;B;B;B	0.55055	0.484;0.767;0.402;0.009;0.02	T	0.75955	-0.3135	10	0.87932	D	0	-17.632	16.7077	0.85376	0.0:0.8704:0.1296:0.0	.	313;974;2312;2275;2217	B4DIG6;F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;.;ACACA_HUMAN;.	K	2312;2217;2275;2299;2197;974;401	ENSP00000344789:E2312K;ENSP00000353898:E2217K;ENSP00000377928:E2275K;ENSP00000335323:E2197K;ENSP00000354565:E401K	ENSP00000335323:E2197K	E	-	1	0	ACACA	32520080	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.800000	0.85949	1.398000	0.46701	0.655000	0.94253	GAG	.		0.507	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35445967	C	T	35445967	3	4	51	1	0	0	0	0	1	0	0	0	106	922	32	2	225	2	ACACA	17	35445967	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1859937	35445967	45749243	224	4912											
KRTAP4-2	85291	hgsc.bcm.edu	37	chr17	39334233	39334233	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctggcagcagctggggcTgcagcaggtgggctggcagc	5	6	20	10	0	1	0	0	0	1	0	1	0	1	0	0	7	5	8	0	7	0	0	rs560495299	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:39334233T>G	ENST00000377726.2	-	1	227	c.184A>C	c.(184-186)Agc>Cgc	p.S62R		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	62	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			CAGCTGGGGCTGCAGCAGGTG	0.657													T|||	17	0.00339457	0.0023	0.0014	5008	,	,		17958	0.0099		0	False		,,,				2504	0.0031				p.S62R		.											.	KRTAP4-2-44	0			c.A184C						.						40	46	44					17																	39334233		2201	4298	6499	SO:0001583	missense	85291	exon1			TGGGGCTGCAGCA	AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"Keratin associated proteins"	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.184A>C	17.37:g.39334233T>G	ENSP00000366955:p.Ser62Arg	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	477	30	NM_033062	0	0	0	0	0	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	37	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	0.738	-0.777466	0.02929	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.00603	6.28	4.67	-1.59	0.08453	.	1.674050	0.04249	N	0.338307	T	0.00178	0.0005	N	0.00011	-3.005	0.09310	N	1	B	0.16802	0.019	B	0.20955	0.032	T	0.51608	-0.8684	10	0.12766	T	0.61	.	14.1242	0.65210	0.0:0.0:0.3626:0.6374	.	62	Q9BYR5	KRA42_HUMAN	R	62;179	ENSP00000366955:S62R	ENSP00000366955:S62R	S	-	1	0	KRTAP4-2	36587759	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	-2.321000	0.01119	-0.438000	0.07232	-1.986000	0.00452	AGC	.		0.657	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1			G	39334233	T	G	39334233	3	3	51	1	0	0	0	0	1	0	0	0	8572	1580	55	5	230	5	KRTAP4-2	17	39334233	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3888266	39334233	41860977	225	4913											
KRT9	3857	broad.mit.edu	37	chr17	39724451	39724451	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaaggaggttgtggtaggTctcgatttccttctccagcc	6	13	11	11	1	3	0	1	0	2	0	6	2	4	1	3	4	1	2	3	4	2	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:39724451T>G	ENST00000246662.4	-	6	1422	c.1357A>C	c.(1357-1359)Acc>Ccc	p.T453P	KRT9_ENST00000588431.1_Missense_Mutation_p.T220P	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	453	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TTGTGGTAGGTCTCGATTTCC	0.557																																					p.T453P													.	KRT9-92	0			c.A1357C						.						90	84	86					17																	39724451		2203	4300	6503	SO:0001583	missense	3857	exon6			GGTAGGTCTCGAT		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"-", "Intermediate filaments type I, keratins (acidic)"	6447	protein-coding gene	gene with protein product	"cytokeratin 9", "type I cytoskeletal 9", "epidermolytic palmoplantar keratoderma"	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1357A>C	17.37:g.39724451T>G	ENSP00000246662:p.Thr453Pro	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	209	59	NM_000226	0	0	0	0	0	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.798153	0.50208	.	.	ENSG00000171403	ENST00000246662	D	0.91945	-2.94	4.93	4.93	0.64822	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.33364	N	0.004999	D	0.96522	0.8865	M	0.92367	3.3	0.19945	N	0.999942	D	0.76494	0.999	D	0.75020	0.985	D	0.91494	0.5214	10	0.87932	D	0	.	11.6733	0.51415	0.0:0.0:0.2295:0.7705	.	453	P35527	K1C9_HUMAN	P	453	ENSP00000246662:T453P	ENSP00000246662:T453P	T	-	1	0	KRT9	36977977	0.001000	0.12720	0.928000	0.36995	0.572000	0.35998	0.824000	0.27379	1.828000	0.53243	0.386000	0.25728	ACC	.		0.557	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		G	39724451	T	G	39724451	3	3	51	1	0	0	0	0	1	0	0	0	8522	1667	58	5	522	5	KRT9	17	39724451	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	390218	39724451	41470759	226	4914											
FKBP10	60681	broad.mit.edu	37	chr17	39975558	39975559	+	Frame_Shift_Ins	INS	-	-	C																															cagctagagacgctggagctINScccccccggctgtgtccgca																								rs137853883		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:39975558_39975559insC	ENST00000321562.4	+	5	928_929	c.824_825insC	c.(823-828)ctccccfs	p.LP275fs	FKBP10_ENST00000544340.1_5'UTR	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	275					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		ACGCTGGAGCTCCCCCCCGGCT	0.634																																					p.L275fs													.	FKBP10-227	0			c.824_825insC						.																																			SO:0001589	frameshift_variant	60681	exon5			TGGAGCTCCCCCC	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"EF-hand domain containing"	18169	protein-coding gene	gene with protein product		607063	"FK506 binding protein 10 (65 kDa)"			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.831dupC	17.37:g.39975565_39975565dupC	ENSP00000317232:p.Leu275fs	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	492	6	NM_021939	0	0	0	0	0	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Frame_Shift_Ins	INS	ENST00000321562.4	37	CCDS11409.1																																																																																			.		0.634	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		C	39975559	-	C	39975558	7	5	51	1	0	1	1	0	0	0	0	0	5921	1551	54	0	842	0	FKBP10	17	39975558	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	251107	39975558	41219652	227	4915											
GHDC	84514	broad.mit.edu	37	chr17	40344321	40344322	+	Frame_Shift_Ins	INS	-	-	C																															gcaccacaaggccccgagggINScagccacagcctcggcctgg																								rs371381917		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:40344321_40344322insC	ENST00000301671.8	-	4	1267_1268	c.826_827insG	c.(826-828)gccfs	p.A276fs	GHDC_ENST00000593209.1_Frame_Shift_Ins_p.A276fs|GHDC_ENST00000428494.2_Frame_Shift_Ins_p.A237fs|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000436923.2_Frame_Shift_Ins_p.A276fs|GHDC_ENST00000587427.1_Frame_Shift_Ins_p.A276fs|GHDC_ENST00000414034.3_Frame_Shift_Ins_p.A276fs			Q8N2G8	GHDC_HUMAN	GH3 domain containing	276						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		GGCCCCGAGGGCAGCCACAGCC	0.663																																					p.A276fs													.	GHDC-90	0			c.827_828insG						.																																			SO:0001589	frameshift_variant	84514	exon5			CCGAGGGCAGCCA	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.827dupG	17.37:g.40344322_40344322dupC	ENSP00000301671:p.Ala276fs	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	507	13	NM_001142623	0	0	0	0	0	B4DQS4|E9PDB5|Q9BXM6	Frame_Shift_Ins	INS	ENST00000301671.8	37	CCDS11422.1																																																																																			.		0.663	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		C	40344322	-	C	40344321	7	5	51	1	0	1	1	0	0	0	0	0	6389	1203	42	0	878	0	GHDC	17	40344321	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	368763	40344321	40850889	228	4916			1	16		3	3	652	N	G_C_-	1.926372e-05
GHDC	84514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40344945	40344945	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcagagaggcctccccaagGtcctggtttgaggtcggggg	6	8	17	10	1	0	2	0	1	0	1	3	3	2	2	4	6	1	2	4	6	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:40344945G>T	ENST00000301671.8	-	3	807	c.366C>A	c.(364-366)gaC>gaA	p.D122E	GHDC_ENST00000593209.1_Missense_Mutation_p.D122E|GHDC_ENST00000428494.2_Intron|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000436923.2_Missense_Mutation_p.D122E|GHDC_ENST00000587427.1_Missense_Mutation_p.D122E|GHDC_ENST00000414034.3_Missense_Mutation_p.D122E			Q8N2G8	GHDC_HUMAN	GH3 domain containing	122						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CCTCCCCAAGGTCCTGGTTTG	0.607																																					p.D122E		.											.	GHDC-90	0			c.C366A						.						105	118	113					17																	40344945		2203	4300	6503	SO:0001583	missense	84514	exon4			CCCAAGGTCCTGG	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.366C>A	17.37:g.40344945G>T	ENSP00000301671:p.Asp122Glu	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	674	230	NM_001142623	0	0	42	72	30	B4DQS4|E9PDB5|Q9BXM6	Missense_Mutation	SNP	ENST00000301671.8	37	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	G	0.862	-0.734923	0.03111	.	.	ENSG00000167925	ENST00000393854;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.61	1.41	0.22369	.	1.247040	0.05644	N	0.583915	T	0.19886	0.0478	N	0.14661	0.345	0.09310	N	1	B;B	0.26400	0.148;0.009	B;B	0.24394	0.053;0.007	T	0.25082	-1.0142	9	0.18276	T	0.48	-0.018	4.8152	0.13363	0.1998:0.1781:0.6221:0.0	.	122;122	Q8N2G8-2;Q8N2G8	.;GHDC_HUMAN	E	66;122;122;122	.	ENSP00000301671:D122E	D	-	3	2	GHDC	37598471	0.000000	0.05858	0.002000	0.10522	0.094000	0.18550	0.158000	0.16422	0.544000	0.28883	0.561000	0.74099	GAC	.		0.607	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		T	40344945	G	T	40344945	3	4	51	1	0	0	0	0	1	0	0	0	6389	1252	44	4	1343	4	GHDC	17	40344945	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	624	40344945	40850265	229	4917			1	16		3	3	652	N	G_C_-	1.926372e-05
GHDC	84514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40344972	40344972	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgaggtcgggggcagtggCtgctctccactgtcttcctg	3	13	14	11	1	2	1	0	1	2	0	5	1	3	1	2	4	1	3	2	4	0	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:40344972C>T	ENST00000301671.8	-	3	780	c.339G>A	c.(337-339)caG>caA	p.Q113Q	GHDC_ENST00000593209.1_Silent_p.Q113Q|GHDC_ENST00000428494.2_Intron|GHDC_ENST00000590520.1_5'UTR|GHDC_ENST00000436923.2_Silent_p.Q113Q|GHDC_ENST00000587427.1_Silent_p.Q113Q|GHDC_ENST00000414034.3_Silent_p.Q113Q			Q8N2G8	GHDC_HUMAN	GH3 domain containing	113						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		GGGGCAGTGGCTGCTCTCCAC	0.592																																					p.Q113Q		.											.	GHDC-90	0			c.G339A						.						118	133	128					17																	40344972		2203	4300	6503	SO:0001819	synonymous_variant	84514	exon4			CAGTGGCTGCTCT	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.339G>A	17.37:g.40344972C>T		Somatic	191	1		WXS	Illumina HiSeq	Phase_I	869	325	NM_001142623	0	0	40	76	36	B4DQS4|E9PDB5|Q9BXM6	Silent	SNP	ENST00000301671.8	37	CCDS11422.1																																																																																			.		0.592	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		T	40344972	C	T	40344972	2	4	51	1	0	0	0	0	0	0	0	1	6389	796	28	2		2	GHDC	17	40344972	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	27	40344972	40850238	230	4918			1	16		3	3	652	N	G_C_-	1.926372e-05
BRCA1	672	bcgsc.ca	37	chr17	41197706	41197707	+	In_Frame_Ins	INS	-	-	GGGGGGGGT																															ggctgcagtcagtagtggctINSgtgggggatctggggtatca																								rs138690298		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:41197706_41197707insGGGGGGGGT	ENST00000357654.3	-	23	5698_5699	c.5580_5581insACCCCCCCC	c.(5578-5583)cacagc>cacACCCCCCCCagc	p.1860_1861HS>HTPPS	BRCA1_ENST00000346315.3_In_Frame_Ins_p.1621_1622HS>HTPPS|BRCA1_ENST00000354071.3_In_Frame_Ins_p.1595_1596HS>HTPPS|BRCA1_ENST00000491747.2_In_Frame_Ins_p.756_757HS>HTPPS|BRCA1_ENST00000586385.1_In_Frame_Ins_p.170_171HS>HTPPS|BRCA1_ENST00000468300.1_3'UTR|BRCA1_ENST00000471181.2_In_Frame_Ins_p.1881_1882HS>HTPPS|BRCA1_ENST00000493795.1_In_Frame_Ins_p.1813_1814HS>HTPPS|BRCA1_ENST00000591534.1_In_Frame_Ins_p.351_352HS>HTPPS|BRCA1_ENST00000591849.1_In_Frame_Ins_p.93_94HS>HTPPS|BRCA1_ENST00000309486.4_In_Frame_Ins_p.1564_1565HS>HTPPS|BRCA1_ENST00000351666.3_In_Frame_Ins_p.677_678HS>HTPPS|BRCA1_ENST00000352993.3_In_Frame_Ins_p.718_719HS>HTPPS	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1860					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CAGTAGTGGCTGTGGGGGATCT	0.584			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.S1882delinsTPPS			yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1-3415	0			c.5644_5645insACCCCCCCC						.		,,,,	345,583,3336		0,0,345,0,583,1204					,,,,	1.9	0		dbSNP_134	62	468,928,6858		0,0,468,0,928,2731	no	codingComplex,utr-3,codingComplex,codingComplex,codingComplex	BRCA1	NM_007300.3,NM_007299.3,NM_007298.3,NM_007297.3,NM_007294.3	,,,,	0,0,813,0,1511,3935	A1A1,A1A2,A1R,A2A2,A2R,RR		16.913,21.7636,18.5653	,,,,	,,,,		813,1511,10194				SO:0001652	inframe_insertion	672	exon24	Familial Cancer Database		AGTGGCTGTGGGG	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5580_5581insACCCCCCCC	17.37:g.41197706_41197707insGGGGGGGGT	ENSP00000350283:p.His1860_Ser1861insThrProPro	Somatic	37	0		WXS	Illumina HiSeq	Phase_1	111	8	NM_007300	0	0	0	0	0	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	In_Frame_Ins	INS	ENST00000357654.3	37	CCDS11453.1																																																																																			.		0.584	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		GGGGGGGGT	41197707	-	GGGGGGGGT	41197706	7	5	51	1	0	1	1	0	0	0	0	0	1501	1580	55	0	14	0	BRCA1	17	41197706	In_Frame_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	852734	41197706	39997504	231	4919											
WNT3	7473	bcgsc.ca	37	chr17	44851096	44851097	+	Frame_Shift_Ins	INS	-	-	G																															ggtggtgcagttccagcggcINSggccccggaactggtgctgg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:44851096_44851097insG	ENST00000225512.5	-	2	421_422	c.259_260insC	c.(259-261)cgcfs	p.R87fs		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	87					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GTTCCAGCGGCGGCCCCGGAAC	0.644																																					p.W87fs													.	WNT3-522	0			c.260_261insC						.																																			SO:0001589	frameshift_variant	7473	exon2			CAGCGGCGGCCCC	AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"Wingless-type MMTV integration sites", "Endogenous ligands"	12782	protein-coding gene	gene with protein product	"WNT-3 proto-oncogene protein"	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.260dupC	17.37:g.44851098_44851098dupG	ENSP00000225512:p.Arg87fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_1	313	80	NM_030753	0	0	0	0	0	Q2M237|Q9H1J9	Frame_Shift_Ins	INS	ENST00000225512.5	37	CCDS11505.1																																																																																			.		0.644	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753		G	44851097	-	G	44851096	7	5	51	1	0	1	1	0	0	0	0	0	17421	768	27	0	819	0	WNT3	17	44851096	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	3653390	44851096	36344114	232	4920											
INTS2	57508	bcgsc.ca	37	chr17	59946430	59946430	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatgacattgacagctaaaCgagccacactaagtgacttt	14	9	7	11	1	0	3	0	3	0	0	0	4	0	3	2	0	3	1	2	0	3	4	rs372415686		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:59946430C>G	ENST00000444766.3	-	23	3308	c.3233G>C	c.(3232-3234)cGt>cCt	p.R1078P	INTS2_ENST00000251334.6_Missense_Mutation_p.R1070P	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1078					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						GACAGCTAAACGAGCCACACT	0.338																																					p.R1078P													.	INTS2-206	0			c.G3233C						.						90	88	89					17																	59946430		1856	4098	5954	SO:0001583	missense	57508	exon23			GCTAAACGAGCCA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.3233G>C	17.37:g.59946430C>G	ENSP00000414237:p.Arg1078Pro	Somatic	98	6		WXS	Illumina HiSeq	Phase_1	34	13	NM_020748	0	0	12	12	0	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	37	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.317342	0.81469	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.47177	0.85	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.66351	0.943	T	0.66268	-0.5966	9	.	.	.	-6.2183	16.8778	0.86056	0.0:1.0:0.0:0.0	.	1078	Q9H0H0	INT2_HUMAN	P	1078;1077	ENSP00000414237:R1078P	.	R	-	2	0	INTS2	57301212	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.239000	0.78182	2.220000	0.72140	0.650000	0.86243	CGT	.		0.338	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		G	59946430	C	G	59946430	3	3	51	1	0	0	0	0	1	0	0	0	7799	536	19	4	393	4	INTS2	17	59946430	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	15095334	59946430	21248780	233	4921											
COG1	9382	bcgsc.ca	37	chr17	71196858	71196858	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctatgtcggcggcttctggaGaagccgctcttgttctggga	5	12	14	10	3	3	1	0	0	3	1	4	3	3	2	1	4	1	3	1	4	2	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:71196858G>A	ENST00000299886.4	+	6	1304	c.1224G>A	c.(1222-1224)gaG>gaA	p.E408E		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	408					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GGCTTCTGGAGAAGCCGCTCT	0.527																																					p.E408E													.	COG1-91	0			c.G1224A						.						55	58	57					17																	71196858		2203	4300	6503	SO:0001819	synonymous_variant	9382	exon6			TCTGGAGAAGCCG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1224G>A	17.37:g.71196858G>A		Somatic	86	0		WXS	Illumina HiSeq	Phase_1	179	59	NM_018714	0	0	59	78	19	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	37	CCDS11692.1																																																																																			.		0.527	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			A	71196858	G	A	71196858	2	1	51	1	0	0	0	0	0	0	0	1	3663	933	33	2		2	COG1	17	71196858	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	11250428	71196858	9998352	234	4922											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73732406	73732406	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggccactgtgagtgtggccGctgccactgccaccagcagt	6	8	13	14	1	0	1	0	1	0	0	0	1	0	1	5	2	3	2	5	2	0	0	rs201929789		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:73732406G>C	ENST00000200181.3	+	15	1986	c.1799G>C	c.(1798-1800)cGc>cCc	p.R600P	ITGB4_ENST00000339591.3_Missense_Mutation_p.R600P|ITGB4_ENST00000579662.1_Missense_Mutation_p.R600P|ITGB4_ENST00000450894.3_Missense_Mutation_p.R600P|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000449880.2_Missense_Mutation_p.R600P	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	600	Cysteine-rich tandem repeats.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GAGTGTGGCCGCTGCCACTGC	0.632																																					p.R600P		.											.	ITGB4-227	0			c.G1799C						.						65	69	67					17																	73732406		2203	4300	6503	SO:0001583	missense	3691	exon15			GTGGCCGCTGCCA		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.1799G>C	17.37:g.73732406G>C	ENSP00000200181:p.Arg600Pro	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	385	151	NM_001005731	0	0	19	19	0	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314176	0.40996	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.94862	-3.54;-3.54;-3.54	4.6	4.6	0.57074	.	0.067612	0.64402	D	0.000010	D	0.97222	0.9092	M	0.83774	2.66	0.58432	D	0.999999	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.916;0.961;0.993;0.985;0.985	D	0.98032	1.0377	10	0.72032	D	0.01	.	16.4661	0.84079	0.0:0.0:1.0:0.0	.	560;600;600;600;600	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	P	516;600;600;600	ENSP00000200181:R600P;ENSP00000344079:R600P;ENSP00000400217:R600P	ENSP00000200181:R600P	R	+	2	0	ITGB4	71244001	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.642000	0.67888	2.095000	0.63458	0.558000	0.71614	CGC	G|0.998;C|0.002		0.632	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			C	73732406	G	C	73732406	3	2	51	1	0	0	0	0	1	0	0	0	7918	1087	38	4	1853	4	ITGB4	17	73732406	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	2535548	73732406	7462804	235	4923											
SEPT9	10801	hgsc.bcm.edu	37	chr17	75488782	75488782	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcggaggaccggctggTgaacgagaagttccgggtga	9	6	18	8	4	0	3	0	2	0	1	2	7	1	6	2	6	1	2	2	6	2	1	rs376712636		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:75488782T>G	ENST00000427177.1	+	9	1586	c.1460T>G	c.(1459-1461)gTg>gGg	p.V487G	SEPT9_ENST00000588690.1_Missense_Mutation_p.V323G|SEPT9_ENST00000591198.1_Missense_Mutation_p.V468G|SEPT9_ENST00000591088.1_Missense_Mutation_p.V236G|SEPT9_ENST00000541152.2_Missense_Mutation_p.V236G|SEPT9_ENST00000427674.2_Missense_Mutation_p.V323G|SEPT9_ENST00000592481.1_3'UTR|SEPT9_ENST00000592951.1_Missense_Mutation_p.V236G|SEPT9_ENST00000431235.2_Missense_Mutation_p.V323G|SEPT9_ENST00000329047.8_Missense_Mutation_p.V469G|SEPT9_ENST00000427180.1_Missense_Mutation_p.V375G|SEPT9_ENST00000585930.1_Missense_Mutation_p.V263G|SEPT9_ENST00000423034.2_Missense_Mutation_p.V480G|SEPT9_ENST00000590294.1_Missense_Mutation_p.V469G|SEPT9_ENST00000449803.2_Missense_Mutation_p.V323G	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9	487	Septin-type G.			V -> E (in Ref. 5; BAB14057). {ECO:0000305}.	cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			GACCGGCTGGTGAACGAGAAG	0.582																																					p.V487G		.											.	SEPT9-659	0			c.T1460G						.						135	147	143					17																	75488782		1981	4158	6139	SO:0001583	missense	10801	exon9			GGCTGGTGAACGA	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"Septins"	7323	protein-coding gene	gene with protein product	"Ov/Br septin"	604061	"MLL septin-like fusion"	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.1460T>G	17.37:g.75488782T>G	ENSP00000391249:p.Val487Gly	Somatic	206	1		WXS	Illumina HiSeq	Phase_I	873	208	NM_001113491	0	0	174	229	55	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Missense_Mutation	SNP	ENST00000427177.1	37	CCDS45790.1	.	.	.	.	.	.	.	.	.	.	t	16.89	3.247092	0.59103	.	.	ENSG00000184640	ENST00000427177;ENST00000449803;ENST00000329047;ENST00000423034;ENST00000427674;ENST00000541152;ENST00000431235;ENST00000427180	T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71	4.99	3.9	0.45041	.	0.062830	0.64402	D	0.000005	T	0.50701	0.1631	L	0.39898	1.24	0.58432	D	0.999998	P;D;B;B;B;B	0.58620	0.716;0.983;0.275;0.354;0.354;0.407	B;P;B;B;B;B	0.54590	0.386;0.756;0.219;0.283;0.283;0.405	T	0.51371	-0.8714	10	0.66056	D	0.02	.	11.4247	0.50003	0.1353:0.0:0.0:0.8647	.	263;468;375;480;469;487	Q9UHD8-9;Q9UHD8-7;Q9UHD8-8;Q9UHD8-5;Q9UHD8-2;Q9UHD8	.;.;.;.;.;SEPT9_HUMAN	G	487;323;469;480;323;263;236;375	ENSP00000391249:V487G;ENSP00000400181:V323G;ENSP00000329161:V469G;ENSP00000405877:V480G;ENSP00000403194:V323G;ENSP00000415624:V375G	ENSP00000329161:V469G	V	+	2	0	SEPT9	73000377	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	3.186000	0.50942	0.835000	0.34877	0.359000	0.22050	GTG	.		0.582	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640		G	75488782	T	G	75488782	3	3	51	1	0	0	0	0	1	0	0	0	14103	1696	59	5	1968	5	SEPT9	17	75488782	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1756376	75488782	5706428	236	4924											
PLEKHJ1	55111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2234038	2234038	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcgttcctgtagaagatgaGgcttctccgcatgaactcgt	8	13	10	10	3	1	4	0	2	1	2	5	4	2	4	2	1	1	4	2	1	3	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:2234038G>T	ENST00000589097.1	-	6	1456	c.343C>A	c.(343-345)Ctc>Atc	p.L115I	PLEKHJ1_ENST00000326631.2_Missense_Mutation_p.L115I|PLEKHJ1_ENST00000587962.2_Missense_Mutation_p.L115I|PLEKHJ1_ENST00000591099.2_Silent_p.A84A|PLEKHJ1_ENST00000589791.1_5'UTR|PLEKHJ1_ENST00000586608.2_Missense_Mutation_p.L116I|PLEKHJ1_ENST00000587394.2_Missense_Mutation_p.L115I|MIR1227_ENST00000408484.1_RNA|SF3A2_ENST00000221494.5_5'Flank			Q9NW61	PKHJ1_HUMAN	pleckstrin homology domain containing, family J member 1	115										endometrium(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAGAAGATGAGGCTTCTCCGC	0.642																																					p.L115I		.											.	PLEKHJ1-90	0			c.C343A						.						119	107	111					19																	2234038		2203	4300	6503	SO:0001583	missense	55111	exon5			AGATGAGGCTTCT	AK001159	CCDS12083.1, CCDS74251.1	19p13.3	2013-01-10				ENSG00000104886		"Pleckstrin homology (PH) domain containing"	18211	protein-coding gene	gene with protein product	"guanine nucleotide releasing protein x"					11602354	Standard	XM_006722784		Approved	FLJ10297	uc002lvf.1	Q9NW61		ENST00000589097.1:c.343C>A	19.37:g.2234038G>T	ENSP00000465391:p.Leu115Ile	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	567	185	NM_018049	0	0	22	40	18	B3KUQ9|D6W604	Missense_Mutation	SNP	ENST00000589097.1	37	CCDS12083.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.836779	0.32421	.	.	ENSG00000104886	ENST00000326631	.	.	.	4.05	2.94	0.34122	.	0.176721	0.36591	N	0.002508	T	0.28234	0.0697	L	0.32530	0.975	0.42701	D	0.993613	P	0.42692	0.787	B	0.33121	0.158	T	0.06881	-1.0802	9	0.33940	T	0.23	-16.6324	7.7627	0.28961	0.0916:0.0:0.7474:0.161	.	115	Q9NW61	PKHJ1_HUMAN	I	115	.	ENSP00000318075:L115I	L	-	1	0	PLEKHJ1	2185038	1.000000	0.71417	0.983000	0.44433	0.410000	0.31052	5.117000	0.64667	1.788000	0.52465	0.561000	0.74099	CTC	.		0.642	PLEKHJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451255.1	NM_018049		T	2234038	G	T	2234038	3	4	51	1	0	0	0	0	1	0	0	0	12105	1000	35	4	114	4	PLEKHJ1	19	2234038	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		2234038	56894945	237	4925											
TMIGD2	126259	bcgsc.ca	37	chr19	4294632	4294632	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accaggcaccccacacgatcGcagccacacccatgcttccc	10	4	6	21	2	0	0	0	0	0	0	2	1	1	0	6	1	2	3	6	1	0	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:4294632G>C	ENST00000301272.2	-	4	539	c.494C>G	c.(493-495)gCg>gGg	p.A165G	TMIGD2_ENST00000595645.1_Missense_Mutation_p.A165G|TMIGD2_ENST00000600349.1_Intron|TMIGD2_ENST00000600114.1_Missense_Mutation_p.A45G	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	165					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACACGATCGCAGCCACACC	0.637																																					p.A165G													.	TMIGD2-90	0			c.C494G						.						129	151	144					19																	4294632		2203	4300	6503	SO:0001583	missense	126259	exon4			ACGATCGCAGCCA	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.494C>G	19.37:g.4294632G>C	ENSP00000301272:p.Ala165Gly	Somatic	394	0		WXS	Illumina HiSeq	Phase_1	661	151	NM_144615	0	0	0	0	0	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	.	.	.	.	.	.	.	.	.	.	G	6.658	0.489899	0.12702	.	.	ENSG00000167664	ENST00000301272	T	0.46819	0.86	2.58	-4.34	0.03666	.	.	.	.	.	T	0.25531	0.0621	N	0.24115	0.695	0.09310	N	1	B;B	0.22909	0.077;0.046	B;B	0.13407	0.009;0.004	T	0.16424	-1.0403	9	0.38643	T	0.18	.	4.069	0.09874	0.558:0.2014:0.2406:0.0	.	165;165	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	G	165	ENSP00000301272:A165G	ENSP00000301272:A165G	A	-	2	0	TMIGD2	4245632	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.887000	0.04152	-0.521000	0.06426	0.543000	0.68304	GCG	.		0.637	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615		C	4294632	G	C	4294632	3	2	51	1	0	0	0	0	1	0	0	0	16263	1087	38	4	362	4	TMIGD2	19	4294632	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	2060594	4294632	54834351	238	4926											
KDM4B	23030	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	5131903	5131903	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgtgtgtttcaggcaccGtccacattttccaaattgaa	9	15	8	9	1	1	1	1	1	0	0	3	1	3	1	3	1	0	3	3	1	2	5	rs544835411		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:5131903G>C	ENST00000159111.4	+	13	2009	c.1791G>C	c.(1789-1791)ccG>ccC	p.P597P	KDM4B_ENST00000536461.1_Silent_p.P631P	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	597					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TTCAGGCACCGTCCACATTTT	0.652																																					p.P597P		.											.	KDM4B-226	0			c.G1791C						.						36	39	38					19																	5131903		2201	4299	6500	SO:0001819	synonymous_variant	23030	exon13			GGCACCGTCCACA	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1791G>C	19.37:g.5131903G>C		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	89	20	NM_015015	0	0	0	0	0	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			.		0.652	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		C	5131903	G	C	5131903	2	2	51	1	0	0	0	0	0	0	0	1	8150	1132	40	4		4	KDM4B	19	5131903	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	837271	5131903	53997080	239	4927											
MUC16	94025	bcgsc.ca	37	chr19	9021175	9021175	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggtaccaggagagggccaGcagccataactggaatggga	13	5	15	8	0	0	1	0	0	0	1	0	4	0	3	3	5	4	2	3	5	3	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:9021175G>C	ENST00000397910.4	-	19	37351	c.37148C>G	c.(37147-37149)gCt>gGt	p.A12383G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12385					cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGAGGGCCAGCAGCCATAAC	0.443																																					p.A12383G													.	MUC16-566	0			c.C37148G						.						123	103	109					19																	9021175		1924	4126	6050	SO:0001583	missense	94025	exon19			GGGCCAGCAGCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.37148C>G	19.37:g.9021175G>C	ENSP00000381008:p.Ala12383Gly	Somatic	132	0		WXS	Illumina HiSeq	Phase_1	74	23	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	3.215	-0.160863	0.06502	.	.	ENSG00000181143	ENST00000397910	T	0.33438	1.41	2.92	-3.21	0.05140	.	.	.	.	.	T	0.13756	0.0333	N	0.08118	0	.	.	.	B	0.24483	0.104	B	0.29353	0.101	T	0.28870	-1.0030	8	0.87932	D	0	.	3.6223	0.08100	0.2396:0.0:0.441:0.3194	.	12383	B5ME49	.	G	12383	ENSP00000381008:A12383G	ENSP00000381008:A12383G	A	-	2	0	MUC16	8882175	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.083000	0.14871	-0.657000	0.05373	-1.644000	0.00765	GCT	.		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9021175	G	C	9021175	3	2	51	1	0	0	0	0	1	0	0	0	9998	971	34	4	6639	4	MUC16	19	9021175	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	3889272	9021175	50107808	240	4928											
ZNF559	84527	bcgsc.ca	37	chr19	9449897	9449897	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctttgaggatgtggctgTggacttcacccaggaggagt	8	10	15	8	0	1	1	1	1	0	0	1	6	1	5	2	5	0	1	2	5	0	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:9449897T>G	ENST00000393883.2	+	4	710	c.62T>G	c.(61-63)gTg>gGg	p.V21G	ZNF559_ENST00000592896.1_Missense_Mutation_p.V49G|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.V21G|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000587557.1_Missense_Mutation_p.V85G|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000586255.1_Missense_Mutation_p.V49G|ZNF559_ENST00000317221.7_Missense_Mutation_p.V21G|ZNF559_ENST00000538743.1_Intron|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000592504.1_Missense_Mutation_p.V21G|ZNF559_ENST00000585352.1_Missense_Mutation_p.V21G|ZNF177_ENST00000446085.4_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	21	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						GATGTGGCTGTGGACTTCACC	0.473																																					p.V85G													.	ZNF559-91	0			c.T254G						.						224	189	201					19																	9449897		2203	4300	6503	SO:0001583	missense	84527	exon4			TGGCTGTGGACTT	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.62T>G	19.37:g.9449897T>G	ENSP00000377461:p.Val21Gly	Somatic	169	0		WXS	Illumina HiSeq	Phase_1	170	56	NM_001202408	0	0	8	10	2	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.580504	0.46006	.	.	ENSG00000188321	ENST00000317221;ENST00000393883	T;T	0.04758	3.56;3.56	2.42	2.42	0.29668	Krueppel-associated box (4);	.	.	.	.	T	0.34919	0.0914	H	0.99357	4.53	0.26138	N	0.980326	D	0.89917	1.0	D	0.85130	0.997	T	0.32188	-0.9916	9	0.87932	D	0	.	8.7135	0.34397	0.0:0.0:0.0:1.0	.	21	Q9BR84	ZN559_HUMAN	G	21	ENSP00000325393:V21G;ENSP00000377461:V21G	ENSP00000325393:V21G	V	+	2	0	ZNF559	9310897	0.040000	0.19996	0.004000	0.12327	0.946000	0.59487	0.881000	0.28173	1.363000	0.46019	0.260000	0.18958	GTG	.		0.473	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		G	9449897	T	G	9449897	3	3	51	1	0	0	0	0	1	0	0	0	18022	1696	59	5	68	5	ZNF559	19	9449897	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	428722	9449897	49679086	241	4929											
ZNF426	79088	bcgsc.ca	37	chr19	9644614	9644614	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctcctgggtgaagtccAcagccacatcgtcaaaggtc	10	8	9	14	1	1	1	1	1	0	0	6	1	4	1	4	2	1	0	4	2	2	0	rs77003677		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:9644614A>C	ENST00000535489.1	-	3	482	c.146T>G	c.(145-147)gTg>gGg	p.V49G	ZNF426_ENST00000253115.2_Missense_Mutation_p.V49G|ZNF426_ENST00000593003.1_Missense_Mutation_p.V11G|ZNF426_ENST00000589289.1_Missense_Mutation_p.V49G			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	49	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						GGTGAAGTCCACAGCCACATC	0.517																																					p.V49G													.	ZNF426-91	0			c.T146G						.																																			SO:0001583	missense	79088	exon5			AAGTCCACAGCCA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"Zinc fingers, C2H2-type", "-"	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.146T>G	19.37:g.9644614A>C	ENSP00000439017:p.Val49Gly	Somatic	120	0		WXS	Illumina HiSeq	Phase_1	80	28	NM_024106	0	0	6	6	0	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.127870	0.56721	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.04758	3.56;3.56	1.41	1.41	0.22369	Krueppel-associated box (4);	.	.	.	.	T	0.29223	0.0727	H	0.99011	4.4	0.47584	D	0.999469	P;P	0.52842	0.956;0.956	P;P	0.62885	0.908;0.908	T	0.17501	-1.0367	9	0.87932	D	0	.	6.8709	0.24121	1.0:0.0:0.0:0.0	.	36;49	Q59EH4;Q9BUY5	.;ZN426_HUMAN	G	36;49;49	ENSP00000253115:V49G;ENSP00000439017:V49G	ENSP00000253115:V49G	V	-	2	0	ZNF426	9505614	0.018000	0.18449	0.211000	0.23655	0.573000	0.36030	3.550000	0.53691	0.886000	0.36113	0.260000	0.18958	GTG	.		0.517	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		C	9644614	A	C	9644614	3	2	51	1	0	0	0	0	1	0	0	0	17932	159	6	5	1534	5	ZNF426	19	9644614	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	194717	9644614	49484369	242	4930											
MRI1	81576	hgsc.bcm.edu	37	chr19	13875777	13875777	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaccgggactcgccgcgctCgtggccttcgtgcgcgacaa	5	6	15	15	8	0	0	0	0	0	0	3	3	0	2	3	3	1	1	3	3	1	1	rs558173579	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:13875777C>T	ENST00000586600.1	+	0	1922				MRI1_ENST00000040663.6_Silent_p.L75L|MRI1_ENST00000319545.8_Silent_p.L75L			P13994	CC130_HUMAN	coiled-coil domain containing 130						response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			TCGCCGCGCTCGTGGCCTTCG	0.756													C|||	13	0.00259585	0.0098	0	5008	,	,		6863	0		0	False		,,,				2504	0				p.L75L		.											.	MRI1-91	0			c.C225T						.						4	5	4					19																	13875777		1806	3486	5292	SO:0001628	intergenic_variant	84245	exon2			CGCGCTCGTGGCC	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994			19.37:g.13875777C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	8	6	NM_001031727	0	0	13	34	21	Q9BQ72	Silent	SNP	ENST00000586600.1	37	CCDS12296.1																																																																																			.		0.756	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		T	13875777	C	T	13875777	1	4	51	0	1	0	0	0	0	0	0	0	9795	871	31	1		1	MRI1	19	13875777	IGR	SNP	C	TCGA-B9-4117-01A-01D-1252-08	4231163	13875777	45253206	243	4931											
OR10H2	26538	broad.mit.edu	37	chr19	15839311	15839311	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgctcctgggctggtggctCggtcatggggatggtggtga	3	11	19	8	1	1	1	1	1	0	0	3	2	2	2	1	8	1	3	1	8	0	0	rs139469467		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:15839311C>T	ENST00000305899.3	+	1	478	c.458C>T	c.(457-459)tCg>tTg	p.S153L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					GCTGGTGGCTCGGTCATGGGG	0.592																																					p.S153L													.	OR10H2-70	0			c.C458T						.						91	75	81					19																	15839311		2203	4300	6503	SO:0001583	missense	26538	exon1			GTGGCTCGGTCAT	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.458C>T	19.37:g.15839311C>T	ENSP00000306095:p.Ser153Leu	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	199	6	NM_013939	0	0	0	0	0	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	37	CCDS12333.1	.	.	.	.	.	.	.	.	.	.	.	0.360	-0.939686	0.02322	.	.	ENSG00000171942	ENST00000305899	T	0.00019	9.06	3.4	-2.39	0.06602	GPCR, rhodopsin-like superfamily (1);	1.096810	0.07137	N	0.846687	T	0.00039	0.0001	N	0.02973	-0.45	0.09310	N	1	B	0.12630	0.006	B	0.19946	0.027	T	0.00510	-1.1697	10	0.10902	T	0.67	.	6.8361	0.23937	0.0:0.2906:0.0:0.7094	.	153	O60403	O10H2_HUMAN	L	153	ENSP00000306095:S153L	ENSP00000306095:S153L	S	+	2	0	OR10H2	15700311	0.000000	0.05858	0.002000	0.10522	0.174000	0.22865	-0.238000	0.08977	-0.296000	0.08947	0.537000	0.68136	TCG	C|1.000;T|0.000		0.592	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			T	15839311	C	T	15839311	3	4	51	1	0	0	0	0	1	0	0	0	10932	893	31	1	460	1	OR10H2	19	15839311	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1963534	15839311	43289672	244	4932											
USE1	55850	bcgsc.ca	37	chr19	17330035	17330035	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatcagtggagtggcagggTcccagccagtgagtgagaag	12	6	16	7	0	1	2	1	2	0	1	2	4	2	3	2	3	1	1	2	3	2	0	rs201210102	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:17330035T>C	ENST00000263897.5	+	7	483	c.436T>C	c.(436-438)Tcc>Ccc	p.S146P	USE1_ENST00000379776.4_Intron|USE1_ENST00000596136.1_Intron|USE1_ENST00000445667.2_Missense_Mutation_p.S146P	NM_018467.3	NP_060937	Q9NZ43	USE1_HUMAN	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	146					endoplasmic reticulum tubular network organization (GO:0071786)|lysosomal transport (GO:0007041)|protein catabolic process (GO:0030163)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|secretion by cell (GO:0032940)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|lung(3)	6						AGTGGCAGGGTCCCAGCCAGT	0.517																																					p.S146P													.	.	0			c.T436C						.						34	40	38					19																	17330035		2011	4194	6205	SO:0001583	missense	55850	exon7			GCAGGGTCCCAGC	AF220052	CCDS46011.1	19p13.11	2007-08-20				ENSG00000053501			30882	protein-coding gene	gene with protein product	"Q-SNARE", "SNARE-like tail-anchored protein 1 homolog (S. cerevisiae)"	610675				16354670, 15029241	Standard	NM_018467		Approved	p31, SLT1, MDS032	uc002nfo.2	Q9NZ43		ENST00000263897.5:c.436T>C	19.37:g.17330035T>C	ENSP00000263897:p.Ser146Pro	Somatic	38	0		WXS	Illumina HiSeq	Phase_1	107	41	NM_018467	0	0	1	1	0	Q8NCK1|Q9BRT4	Missense_Mutation	SNP	ENST00000263897.5	37	CCDS46011.1	.	.	.	.	.	.	.	.	.	.	T	1.143	-0.648945	0.03506	.	.	ENSG00000053501	ENST00000263897;ENST00000445667	T;T	0.43294	0.95;0.95	4.43	-2.55	0.06288	.	0.812302	0.11216	N	0.587183	T	0.15132	0.0365	N	0.02802	-0.49	0.49130	D	0.999757	B	0.02656	0.0	B	0.01281	0.0	T	0.13415	-1.0510	10	0.22706	T	0.39	-10.2664	6.5631	0.22497	0.0:0.4171:0.2073:0.3757	.	146	Q9NZ43	USE1_HUMAN	P	146	ENSP00000263897:S146P;ENSP00000390287:S146P	ENSP00000263897:S146P	S	+	1	0	USE1	17191035	0.870000	0.30015	0.005000	0.12908	0.026000	0.11368	0.046000	0.14035	-0.162000	0.10964	-0.415000	0.06103	TCC	T|0.966;G|0.034		0.517	USE1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463295.1	NM_018467		C	17330035	T	C	17330035	3	2	51	1	0	0	0	0	1	0	0	0	17064	1667	58	3	462	3	USE1	19	17330035	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1490724	17330035	41798948	245	4933											
LRRC25	126364	broad.mit.edu	37	chr19	18507298	18507298	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagttgcagaggccaggccaGgggcgcagctgacctccagg	8	5	16	12	1	0	2	0	1	0	1	1	2	1	2	4	5	2	4	4	5	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:18507298G>T	ENST00000339007.3	-	1	1129	c.476C>A	c.(475-477)cCt>cAt	p.P159H	LRRC25_ENST00000595840.1_Missense_Mutation_p.P159H	NM_145256.2	NP_660299.2	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25	159						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|skin(1)	8						GGCCAGGCCAGGGGCGCAGCT	0.642																																					p.P159H													.	LRRC25-90	0			c.C476A						.						29	28	28					19																	18507298		2202	4299	6501	SO:0001583	missense	126364	exon1			AGGCCAGGGGCGC	AK095435	CCDS12377.1	19p13.11	2013-09-20			ENSG00000175489	ENSG00000175489			29806	protein-coding gene	gene with protein product		607518				12384430	Standard	NM_145256		Approved	MAPA, FLJ38116	uc002niw.3	Q8N386	OTTHUMG00000183361	ENST00000339007.3:c.476C>A	19.37:g.18507298G>T	ENSP00000340983:p.Pro159His	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	142	7	NM_145256	0	0	2	2	0	Q6IQ00|Q8N9A5	Missense_Mutation	SNP	ENST00000339007.3	37	CCDS12377.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670912	0.47781	.	.	ENSG00000175489	ENST00000339007	T	0.34275	1.37	3.76	1.43	0.22495	.	0.764210	0.11156	N	0.593588	T	0.38904	0.1058	L	0.55481	1.735	0.09310	N	1	D	0.64830	0.994	P	0.51415	0.669	T	0.18366	-1.0339	10	0.46703	T	0.11	-0.5814	4.9166	0.13849	0.118:0.0:0.6746:0.2074	.	159	Q8N386	LRC25_HUMAN	H	159	ENSP00000340983:P159H	ENSP00000340983:P159H	P	-	2	0	LRRC25	18368298	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.010000	0.12743	0.303000	0.22785	0.491000	0.48974	CCT	.		0.642	LRRC25-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466342.1	NM_145256		T	18507298	G	T	18507298	3	4	51	1	0	0	0	0	1	0	0	0	9005	1000	35	4	449	4	LRRC25	19	18507298	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	1177263	18507298	40621685	246	4934											
UBA2	10054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	34921484	34921484	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggtttatgcatttgtagattGatctggatactattgatgta	10	18	10	3	0	1	3	0	2	1	1	1	4	1	4	0	2	2	4	0	2	5	9			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:34921484G>C	ENST00000246548.4	+	2	212	c.142G>C	c.(142-144)Gat>Cat	p.D48H	UBA2_ENST00000439527.2_5'UTR|CTD-2588C8.8_ENST00000592220.1_RNA	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	48					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TTTGTAGATTGATCTGGATAC	0.358																																					p.D48H		.											.	UBA2-227	0			c.G142C						.						185	170	175					19																	34921484		2203	4300	6503	SO:0001583	missense	10054	exon2			TAGATTGATCTGG	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.142G>C	19.37:g.34921484G>C	ENSP00000246548:p.Asp48His	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	152	52	NM_005499	0	0	0	0	0	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Missense_Mutation	SNP	ENST00000246548.4	37	CCDS12439.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624070	0.87560	.	.	ENSG00000126261	ENST00000246548	D	0.84442	-1.85	5.22	5.22	0.72569	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.100210	0.64402	D	0.000001	D	0.96565	0.8879	H	0.99937	4.99	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.98698	1.0699	10	0.87932	D	0	-19.2256	17.8923	0.88876	0.0:0.0:1.0:0.0	.	48	Q9UBT2	SAE2_HUMAN	H	48	ENSP00000246548:D48H	ENSP00000246548:D48H	D	+	1	0	UBA2	39613324	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.953000	0.93041	2.603000	0.88011	0.563000	0.77884	GAT	.		0.358	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499		C	34921484	G	C	34921484	3	2	51	1	0	0	0	0	1	0	0	0	16861	1290	45	4	148	4	UBA2	19	34921484	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	16414186	34921484	24207499	247	4935											
KIRREL2	84063	bcgsc.ca	37	chr19	36353426	36353426	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtgcggatagtggccggAgtggccgctgccaccacaac	8	6	14	13	3	0	0	0	0	0	0	0	2	0	2	4	4	3	1	4	4	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:36353426A>G	ENST00000360202.5	+	12	1740	c.1542A>G	c.(1540-1542)ggA>ggG	p.G514G	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000262625.7_Silent_p.G514G|KIRREL2_ENST00000347900.6_Silent_p.G464G|KIRREL2_ENST00000592409.1_Intron	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	514					cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TAGTGGCCGGAGTGGCCGCTG	0.652																																					p.G514G													.	KIRREL2-93	0			c.A1542G						.						101	103	102					19																	36353426		2203	4300	6503	SO:0001819	synonymous_variant	84063	exon12			GGCCGGAGTGGCC	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1542A>G	19.37:g.36353426A>G		Somatic	210	1		WXS	Illumina HiSeq	Phase_1	344	129	NM_199180	0	0	0	0	0	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			.		0.652	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		G	36353426	A	G	36353426	2	3	51	1	0	0	0	0	0	0	0	1	8346	291	11	3		3	KIRREL2	19	36353426	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1431942	36353426	22775557	248	4936											
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39039030	39039030	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactacgtaacggatccccgTggcctcatctccaagaagga	11	7	10	13	3	2	1	1	0	1	1	4	4	3	3	4	3	2	1	4	3	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:39039030T>C	ENST00000359596.3	+	89	12252	c.12252T>C	c.(12250-12252)cgT>cgC	p.R4084R	RYR1_ENST00000360985.3_Silent_p.R4079R|RYR1_ENST00000355481.4_Silent_p.R4079R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4084					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGGATCCCCGTGGCCTCATCT	0.557																																					p.R4084R		.											.	RYR1-100	0			c.T12252C						.						132	113	119					19																	39039030		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon89			TCCCCGTGGCCTC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.12252T>C	19.37:g.39039030T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	299	101	NM_000540	0	0	1	1	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			.		0.557	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	39039030	T	C	39039030	2	2	51	1	0	0	0	0	0	0	0	1	13800	1683	59	3		3	RYR1	19	39039030	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	2685604	39039030	20089953	249	4937											
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40366038	40366038	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtactcacgacagaagtcCggccgcctccactcgccgag	9	5	10	17	5	1	1	1	0	0	1	4	3	3	1	5	1	1	1	5	1	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:40366038C>G	ENST00000221347.6	-	30	14203	c.14196G>C	c.(14194-14196)ccG>ccC	p.P4732P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4732						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGAAGTCCGGCCGCCTCC	0.647																																					p.P4732P		.											.	FCGBP-98	0			c.G14196C						.																																			SO:0001819	synonymous_variant	8857	exon30			GAAGTCCGGCCGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14196G>C	19.37:g.40366038C>G		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	205	59	NM_003890	0	0	0	0	0	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			.		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40366038	C	G	40366038	2	3	51	1	0	0	0	0	0	0	0	1	5797	639	23	4		4	FCGBP	19	40366038	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1327008	40366038	18762945	250	4938											
ZNF227	7770	bcgsc.ca	37	chr19	44732627	44732627	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacattcaaggatgtggctgTggtcttctccagggaggaac	9	10	14	8	0	3	0	1	0	2	0	4	4	3	3	1	5	1	1	1	5	2	2	rs77864769		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:44732627T>G	ENST00000313040.7	+	4	294	c.89T>G	c.(88-90)gTg>gGg	p.V30G	ZNF227_ENST00000589707.1_5'UTR|ZNF227_ENST00000391961.2_5'UTR|ZNF227_ENST00000589237.1_3'UTR|ZNF227_ENST00000589005.1_5'UTR|ZNF227_ENST00000586228.1_Intron	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				GATGTGGCTGTGGTCTTCTCC	0.488																																					p.V30G													.	ZNF227-91	0			c.T89G						.						229	199	209					19																	44732627		2203	4300	6503	SO:0001583	missense	7770	exon4			TGGCTGTGGTCTT	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.89T>G	19.37:g.44732627T>G	ENSP00000321049:p.Val30Gly	Somatic	130	1		WXS	Illumina HiSeq	Phase_1	103	40	NM_182490	0	0	3	4	1	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.636184	0.47049	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000418980	T	0.04758	3.56	3.84	3.84	0.44239	Krueppel-associated box (4);	.	.	.	.	T	0.35970	0.0950	H	0.99312	4.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.56823	-0.7915	9	0.87932	D	0	.	10.8844	0.46957	0.0:0.0:0.0:1.0	.	16;10;30	Q658S5;Q9NS43;Q86WZ6	.;.;ZN227_HUMAN	G	30;15;16	ENSP00000321049:V30G	ENSP00000321049:V30G	V	+	2	0	ZNF227	49424467	1.000000	0.71417	0.979000	0.43373	0.361000	0.29550	4.585000	0.60977	1.743000	0.51761	0.397000	0.26171	GTG	.		0.488	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		G	44732627	T	G	44732627	3	3	51	1	0	0	0	0	1	0	0	0	17813	1696	59	5	95	5	ZNF227	19	44732627	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	4366589	44732627	14396356	251	4939											
RELB	5971	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	45515450	45515452	+	In_Frame_Del	DEL	CCG	CCG	-																															aagcagcgcggcatgcgcttCcgctacgagtgcgagggccg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:45515450_45515452delCCG	ENST00000221452.8	+	4	570_572	c.420_422delCCG	c.(418-423)ttccgc>ttc	p.R141del	RELB_ENST00000505236.1_In_Frame_Del_p.R138del|RELB_ENST00000540120.1_In_Frame_Del_p.R141del	NM_006509.3	NP_006500.2	Q01201	RELB_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog B	141	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				antigen processing and presentation (GO:0019882)|circadian regulation of gene expression (GO:0032922)|myeloid dendritic cell differentiation (GO:0043011)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of gene expression (GO:0010628)|T-helper 1 cell differentiation (GO:0045063)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(3)|skin(1)	12		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)		GCATGCGCTTCCGCTACGAGTGC	0.754																																					.		.											.	RELB-847	0			.						.																																			SO:0001651	inframe_deletion	5971	.			.	M83221	CCDS46110.1	19q13.32	2013-07-09	2013-07-09		ENSG00000104856	ENSG00000104856			9956	protein-coding gene	gene with protein product		604758	"v-rel avian reticuloendotheliosis viral oncogene homolog B (nuclear factor of kappa light polypeptide gene enhancer in B-cells 3)"			1531086	Standard	NM_006509		Approved	REL-B	uc021uvp.1	Q01201	OTTHUMG00000162116	ENST00000221452.8:c.420_422delCCG	19.37:g.45515450_45515452delCCG	ENSP00000221452:p.Arg141del	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	74	33	.	0	0	0	0	0	Q6GTX7|Q9UEI7	Targeted_Region	DEL	ENST00000221452.8	37	CCDS46110.1																																																																																			.		0.754	RELB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000367361.2			-	45515452	CCG	-	45515450	7	5	51	1	0	1	0	1	0	0	0	0	13249	854	30	0	426	0	RELB	19	45515450	In_Frame_Del	DEL	CCG	TCGA-B9-4117-01A-01D-1252-08	782823	45515450	13613533	252	4940											
SFRS16	11129	ucsc.edu	37	chr19	45572384	45572384	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggagcatgagcggcaggTgaagtgggaaagggagggct	11	4	21	5	1	0	2	0	2	0	0	0	5	0	5	0	6	2	4	0	6	2	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:45572384T>G	ENST00000221455.3	+	17	1925		c.e17+2		CLASRP_ENST00000391953.4_Splice_Site|CLASRP_ENST00000544944.2_Splice_Site	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						GAGCGGCAGGTGAAGTGGGAA	0.597																																					.													.	CLASRP-154	0			c.1827+2T>G						.						107	119	115					19																	45572384		2203	4300	6503	SO:0001630	splice_region_variant	11129	exon17			GGCAGGTGAAGTG	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"Clk4 associating SR-related protein"		"splicing factor, arginine/serine-rich 16"	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.1827+2T>G	19.37:g.45572384T>G		Somatic	104	11		WXS	Illumina HiSeq		302	88	NM_007056	0	0	0	0	0	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Splice_Site	SNP	ENST00000221455.3	37	CCDS12652.2	.	.	.	.	.	.	.	.	.	.	T	14.73	2.623388	0.46840	.	.	ENSG00000104859	ENST00000221455;ENST00000391953;ENST00000544944	.	.	.	4.84	3.82	0.43975	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2182	0.25971	0.0:0.0998:0.0:0.9002	.	.	.	.	.	-1	.	.	.	+	.	.	CLASRP	50264224	1.000000	0.71417	0.781000	0.31783	0.488000	0.33401	3.750000	0.55157	0.996000	0.38943	0.454000	0.30748	.	.		0.597	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	Intron	G	45572384	T	G	45572384	5	3	51	1	0	0	0	0	0	0	1	0	14204	1710	59	5	1891	5	SFRS16	19	45572384	Splice_Site	SNP	T	TCGA-B9-4117-01A-01D-1252-08	56934	45572384	13556599	253	4941											
FOSB	2354	bcgsc.ca	37	chr19	45974012	45974013	+	Frame_Shift_Ins	INS	-	-	C																															ccatggcccagtcccaggggINScagccactggcctcccagcc																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:45974012_45974013insC	ENST00000353609.3	+	2	844_845	c.252_253insC	c.(253-255)cagfs	p.Q85fs	ERCC1_ENST00000423698.2_Intron|FOSB_ENST00000592436.1_Frame_Shift_Ins_p.Q85fs|FOSB_ENST00000586615.1_Frame_Shift_Ins_p.Q36fs|FOSB_ENST00000590335.1_Frame_Shift_Ins_p.Q85fs|FOSB_ENST00000585836.1_Frame_Shift_Ins_p.Q46fs|FOSB_ENST00000591858.1_Frame_Shift_Ins_p.Q46fs|FOSB_ENST00000417353.2_Frame_Shift_Ins_p.Q85fs|FOSB_ENST00000443841.2_Intron|FOSB_ENST00000592811.1_Frame_Shift_Ins_p.Q36fs	NM_006732.2	NP_006723.2	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B	85					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	13		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)		AGTCCCAGGGGCAGCCACTGGC	0.658																																					p.G84fs													.	FOSB-848	0			c.252_253insC						.																																			SO:0001589	frameshift_variant	2354	exon2			CCAGGGGCAGCCA		CCDS12664.1, CCDS46113.1	19q13.3	2013-01-10						"basic leucine zipper proteins"	3797	protein-coding gene	gene with protein product	"oncogene FOS-B", "activator protein 1"	164772				1301997	Standard	NM_006732		Approved	G0S3, GOSB, GOS3, AP-1, MGC42291, DKFZp686C0818	uc002pbx.4	P53539		ENST00000353609.3:c.253dupC	19.37:g.45974013_45974013dupC	ENSP00000245919:p.Gln85fs	Somatic	209	0		WXS	Illumina HiSeq	Phase_1	426	79	NM_006732	0	0	0	0	0	A8K9K5|A8VJE1|A8VJE6|A8VJF0|A8VJF3|A8VJF7|A8VJG1|A8VJG5|A8VJG9|E7EPR6|E9PHJ3|K7EMJ6|Q49AD7	Frame_Shift_Ins	INS	ENST00000353609.3	37	CCDS12664.1																																																																																			.		0.658	FOSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459561.1	NM_006732		C	45974013	-	C	45974012	7	5	51	1	0	1	1	0	0	0	0	0	6005	1190	42	0	258	0	FOSB	19	45974012	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	401628	45974012	13154971	254	4942											
NUCB1	4924	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49422348	49422348	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgggagatggaggaggagcGactgcgcatgcgggagcatg	9	4	21	7	4	0	1	0	0	0	1	0	7	0	5	0	5	4	2	0	5	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:49422348G>A	ENST00000405315.4	+	9	1212	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	NUCB1-AS1_ENST00000416432.1_RNA|NUCB1_ENST00000407032.1_Missense_Mutation_p.R293Q|NUCB1_ENST00000485798.1_Intron|NUCB1_ENST00000263273.5_Missense_Mutation_p.R293Q	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	293	Binds to GNAI2 and GNAI3. {ECO:0000250}.|EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		GAGGAGGAGCGACTGCGCATG	0.612																																					p.R293Q		.											.	NUCB1-90	0			c.G878A						.						56	58	58					19																	49422348		2203	4300	6503	SO:0001583	missense	4924	exon9			AGGAGCGACTGCG	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.878G>A	19.37:g.49422348G>A	ENSP00000385923:p.Arg293Gln	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	126	43	NM_006184	0	0	147	342	195	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Missense_Mutation	SNP	ENST00000405315.4	37	CCDS12740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.875643|5.875643	0.97055|0.97055	.|.	.|.	ENSG00000104805|ENSG00000104805	ENST00000424608|ENST00000405315;ENST00000407032;ENST00000263273	.|T;T;T	.|0.71698	.|-0.59;-0.59;-0.59	5.01|5.01	5.01|5.01	0.66863|0.66863	.|EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81437|0.81437	0.4822|0.4822	M|M	0.64630|0.64630	1.985|1.985	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.72982	.|0.979;0.979	T|T	0.80596|0.80596	-0.1312|-0.1312	5|10	.|0.40728	.|T	.|0.16	.|.	16.1855|16.1855	0.81948|0.81948	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|293;293	.|Q02818;Q53GX6	.|NUCB1_HUMAN;.	N|Q	263|293	.|ENSP00000385923:R293Q;ENSP00000385211:R293Q;ENSP00000263273:R293Q	.|ENSP00000263273:R293Q	D|R	+|+	1|2	0|0	NUCB1|NUCB1	54114160|54114160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	9.177000|9.177000	0.94849|0.94849	2.514000|2.514000	0.84764|0.84764	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.		0.612	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		A	49422348	G	A	49422348	3	1	51	1	0	0	0	0	1	0	0	0	10744	1058	37	1	908	1	NUCB1	19	49422348	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	3448336	49422348	9706635	255	4943											
NUP62	23636	bcgsc.ca	37	chr19	50411672	50411673	+	Frame_Shift_Ins	INS	-	-	G																															agtgggtcactggtgtcggcINSgggggccccggacgtgttca																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:50411672_50411673insG	ENST00000596217.1	-	2	3279_3280	c.1392_1393insC	c.(1390-1395)cccgccfs	p.A465fs	NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000413454.1_Frame_Shift_Ins_p.A465fs|NUP62_ENST00000597029.1_Frame_Shift_Ins_p.A465fs|NUP62_ENST00000597723.1_Frame_Shift_Ins_p.A389fs|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Frame_Shift_Ins_p.A465fs|NUP62_ENST00000352066.3_Frame_Shift_Ins_p.A465fs			P37198	NUP62_HUMAN	nucleoporin 62kDa	465					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CTGGTGTCGGCGGGGGCCCCGG	0.579																																					p.A465fs													.	NUP62-615	0			c.1393_1394insC						.																																			SO:0001589	frameshift_variant	23636	exon2			TGTCGGCGGGGGC	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.1393dupC	19.37:g.50411677_50411677dupG	ENSP00000471191:p.Ala465fs	Somatic	248	2		WXS	Illumina HiSeq	Phase_1	695	114	NM_001193357	0	0	0	0	0	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Frame_Shift_Ins	INS	ENST00000596217.1	37	CCDS12788.1																																																																																			.		0.579	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		G	50411673	-	G	50411672	7	5	51	1	0	1	1	0	0	0	0	0	10794	768	27	0	179	0	NUP62	19	50411672	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	989324	50411672	8717311	256	4944											
VRK3	51231	bcgsc.ca	37	chr19	50493004	50493004	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgggcaatagcggaaggCgaagccatagcctgccaaag	13	5	13	10	2	0	0	0	0	0	0	0	2	0	1	3	3	4	1	3	3	6	3	rs200282632		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:50493004C>G	ENST00000599538.1	-	11	1652	c.988G>C	c.(988-990)Gcc>Ccc	p.A330P	VRK3_ENST00000424804.2_5'UTR|VRK3_ENST00000594948.1_Missense_Mutation_p.A330P|VRK3_ENST00000377011.2_Missense_Mutation_p.A280P|VRK3_ENST00000601912.1_Missense_Mutation_p.A280P|VRK3_ENST00000601341.1_Missense_Mutation_p.A280P|VRK3_ENST00000593919.1_Missense_Mutation_p.A330P|VRK3_ENST00000316763.3_Missense_Mutation_p.A330P|VRK3_ENST00000443401.2_Missense_Mutation_p.A99P|VRK3_ENST00000594092.1_Missense_Mutation_p.A330P			Q8IV63	VRK3_HUMAN	vaccinia related kinase 3	330	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)|stomach(2)|urinary_tract(1)	23		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		TAGCGGAAGGCGAAGCCATAG	0.547																																					p.A330P	Pancreas(6;90 181 4352 12603 17050 34726 35237 44094)												.	VRK3-359	0			c.G988C						.						63	51	55					19																	50493004		2203	4300	6503	SO:0001583	missense	51231	exon11			GGAAGGCGAAGCC	AB031052	CCDS12791.1, CCDS33076.1	19q13.33	2011-01-14			ENSG00000105053	ENSG00000105053			18996	protein-coding gene	gene with protein product							Standard	XM_005258971		Approved		uc002prh.1	Q8IV63		ENST00000599538.1:c.988G>C	19.37:g.50493004C>G	ENSP00000469880:p.Ala330Pro	Somatic	48	0		WXS	Illumina HiSeq	Phase_1	54	26	NM_016440	0	0	36	40	4	A6NEG5|A8KA53|Q502Y2|Q9P2V8	Missense_Mutation	SNP	ENST00000599538.1	37	CCDS12791.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171142	0.78452	.	.	ENSG00000105053	ENST00000316763;ENST00000377011;ENST00000443401	T;T;T	0.76186	-1.0;-1.0;-1.0	4.57	-7.34	0.01427	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.347807	0.32343	N	0.006231	D	0.83774	0.5327	M	0.91140	3.18	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	D	0.84263	0.0484	10	0.72032	D	0.01	-3.1814	9.4534	0.38741	0.2248:0.6043:0.0:0.1709	.	99;330;280;330	B4DGW1;Q8IV63-2;A6NEG5;Q8IV63	.;.;.;VRK3_HUMAN	P	330;280;99	ENSP00000324636:A330P;ENSP00000366210:A280P;ENSP00000414907:A99P	ENSP00000324636:A330P	A	-	1	0	VRK3	55184816	0.902000	0.30710	0.705000	0.30386	0.953000	0.61014	0.076000	0.14712	-1.586000	0.01632	-0.345000	0.07892	GCC	.		0.547	VRK3-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464815.1	NM_016440		G	50493004	C	G	50493004	3	3	51	1	0	0	0	0	1	0	0	0	17254	768	27	4	452	4	VRK3	19	50493004	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	81332	50493004	8635979	257	4945											
ZNF649	65251	bcgsc.ca	37	chr19	52400203	52400203	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctcccaggtgaagtccAcagccacatcctccagggtc	9	7	8	17	0	0	1	0	1	0	0	6	1	5	1	6	2	1	0	6	2	1	0	rs149586071		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:52400203A>C	ENST00000354957.3	-	3	328	c.44T>G	c.(43-45)gTg>gGg	p.V15G	ZNF649_ENST00000600738.1_Missense_Mutation_p.V15G|CTC-429C10.2_ENST00000600329.1_RNA	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		GGTGAAGTCCACAGCCACATC	0.488																																					p.V15G													.	ZNF649-92	0			c.T44G						.						173	167	169					19																	52400203		2203	4300	6503	SO:0001583	missense	65251	exon3			AAGTCCACAGCCA	BC005368	CCDS12843.1	19q13.41	2013-01-08				ENSG00000198093		"Zinc fingers, C2H2-type", "-"	25741	protein-coding gene	gene with protein product		611903				15950191	Standard	NM_023074		Approved	FLJ12644	uc002pxy.3	Q9BS31		ENST00000354957.3:c.44T>G	19.37:g.52400203A>C	ENSP00000347043:p.Val15Gly	Somatic	216	0		WXS	Illumina HiSeq	Phase_1	130	48	NM_023074	0	0	12	16	4	A8MYJ5|B2RDC4|Q9H9N2	Missense_Mutation	SNP	ENST00000354957.3	37	CCDS12843.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.203643	0.38905	.	.	ENSG00000198093	ENST00000354957	T	0.04758	3.56	2.51	1.39	0.22231	Krueppel-associated box (4);	.	.	.	.	T	0.31544	0.0800	H	0.99312	4.51	0.38484	D	0.947792	D	0.76494	0.999	D	0.87578	0.998	T	0.10753	-1.0616	9	0.87932	D	0	.	5.2869	0.15706	0.6995:0.3005:0.0:0.0	.	15	Q9BS31	ZN649_HUMAN	G	15	ENSP00000347043:V15G	ENSP00000347043:V15G	V	-	2	0	ZNF649	57092015	0.017000	0.18338	0.752000	0.31206	0.747000	0.42532	1.960000	0.40422	0.172000	0.19760	0.443000	0.29094	GTG	.		0.488	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074		C	52400203	A	C	52400203	3	2	51	1	0	0	0	0	1	0	0	0	18096	159	6	5	1485	5	ZNF649	19	52400203	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1907199	52400203	6728780	258	4946											
ZNF614	80110	bcgsc.ca	37	chr19	52521719	52521719	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctcccagctgaattccAcagccacatcctccagggtc	9	8	6	18	0	0	1	0	1	0	0	6	1	5	1	6	1	2	1	6	1	1	1	rs76388547		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:52521719A>C	ENST00000270649.6	-	3	588	c.44T>G	c.(43-45)gTg>gGg	p.V15G	ZNF614_ENST00000356322.6_Missense_Mutation_p.V15G	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GCTGAATTCCACAGCCACATC	0.418																																					p.V15G													.	ZNF614-95	0			c.T44G						.						87	84	85					19																	52521719		2203	4300	6503	SO:0001583	missense	80110	exon3			AATTCCACAGCCA	BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"Zinc fingers, C2H2-type", "-"	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.44T>G	19.37:g.52521719A>C	ENSP00000270649:p.Val15Gly	Somatic	111	0		WXS	Illumina HiSeq	Phase_1	80	29	NM_025040	0	0	7	8	1	Q494T8|Q8TCF4|Q9BSN8	Missense_Mutation	SNP	ENST00000270649.6	37	CCDS12847.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.477112	0.63849	.	.	ENSG00000142556	ENST00000356322;ENST00000270649	T;T	0.04758	3.56;3.56	3.22	3.22	0.36961	Krueppel-associated box (4);	.	.	.	.	T	0.34890	0.0913	H	0.99117	4.435	0.44492	D	0.997432	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.53085	-0.8488	9	0.87932	D	0	.	9.7872	0.40684	1.0:0.0:0.0:0.0	.	15;15	Q8N883;Q9BSN8	ZN614_HUMAN;.	G	15	ENSP00000348674:V15G;ENSP00000270649:V15G	ENSP00000270649:V15G	V	-	2	0	ZNF614	57213531	0.984000	0.35163	0.963000	0.40424	0.975000	0.68041	4.979000	0.63806	1.464000	0.47987	0.477000	0.44152	GTG	.		0.418	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040		C	52521719	A	C	52521719	3	2	51	1	0	0	0	0	1	0	0	0	18071	159	6	5	1725	5	ZNF614	19	52521719	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	121516	52521719	6607264	259	4947											
ZNF665	79788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53668284	53668284	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaccacattcatcacactTgtaaggtttctctccagaat	11	15	4	11	0	3	1	2	0	1	1	5	1	4	1	2	1	1	2	2	1	3	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:53668284T>A	ENST00000600412.1	-	2	1379	c.1264A>T	c.(1264-1266)Aag>Tag	p.K422*	ZNF665_ENST00000396424.3_Nonsense_Mutation_p.K487*|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	422					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)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCATCACACTTGTAAGGTTTC	0.413																																					p.K487X		.											.	ZNF665-70	0			c.A1459T						.						91	95	93					19																	53668284		2203	4300	6503	SO:0001587	stop_gained	79788	exon4			CACACTTGTAAGG		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1264A>T	19.37:g.53668284T>A	ENSP00000469154:p.Lys422*	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	217	68	NM_024733	0	0	1	1	0	A8K5T8	Nonsense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	T	17.85	3.490740	0.64074	.	.	ENSG00000197497	ENST00000396424	.	.	.	2.18	1.14	0.20703	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.3597	0.21420	0.0:0.1475:0.0:0.8525	.	.	.	.	X	487	.	ENSP00000379702:K487X	K	-	1	0	ZNF665	58360096	0.000000	0.05858	0.027000	0.17364	0.049000	0.14656	-2.447000	0.01010	1.001000	0.39076	0.358000	0.22013	AAG	.		0.413	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53668284	T	A	53668284	4	1	51	1	0	0	0	0	0	1	0	0	18105	1821	63	5	581	5	ZNF665	19	53668284	Nonsense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1146565	53668284	5460699	260	4948											
LILRB2	10288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54783677	54783677	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaccagggggtcactgagCtcagaccaccgagcgcggct	9	4	14	14	3	2	2	2	1	0	1	2	3	2	2	3	3	3	3	3	3	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:54783677C>T	ENST00000391749.4	-	4	595	c.324G>A	c.(322-324)gaG>gaA	p.E108E	LILRB2_ENST00000314446.5_Silent_p.E108E|LILRB2_ENST00000391748.1_Silent_p.E108E|MIR4752_ENST00000579672.1_RNA|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000434421.1_5'UTR|LILRB2_ENST00000391746.1_Silent_p.E108E	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	108	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTCACTGAGCTCAGACCACC	0.602																																					p.E108E		.											.	LILRB2-91	0			c.G324A						.						105	105	105					19																	54783677		2203	4300	6503	SO:0001819	synonymous_variant	10288	exon4			ACTGAGCTCAGAC	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.324G>A	19.37:g.54783677C>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	359	108	NM_005874	0	0	4	4	0	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	37	CCDS12886.1																																																																																			.		0.602	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			T	54783677	C	T	54783677	2	4	51	1	0	0	0	0	0	0	0	1	8813	796	28	2		2	LILRB2	19	54783677	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1115393	54783677	4345306	261	4949											
NLRP8	126205	bcgsc.ca	37	chr19	56490765	56490765	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttctgtgtcacaggctggAaaactgcctgttcacctcca	8	12	9	12	0	3	0	2	0	1	0	4	1	4	1	3	2	2	3	3	2	2	2	rs77160817		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:56490765A>G	ENST00000291971.3	+	9	2953	c.2882A>G	c.(2881-2883)gAa>gGa	p.E961G	NLRP8_ENST00000590542.1_Missense_Mutation_p.E942G	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	961					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CACAGGCTGGAAAACTGCCTG	0.512																																					p.E961G													.	NLRP8-361	0			c.A2882G						.						106	101	103					19																	56490765		2203	4300	6503	SO:0001583	missense	126205	exon9			GGCTGGAAAACTG	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2882A>G	19.37:g.56490765A>G	ENSP00000291971:p.Glu961Gly	Somatic	129	0		WXS	Illumina HiSeq	Phase_1	70	25	NM_176811	0	0	0	0	0	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	A	6.389	0.439869	0.12104	.	.	ENSG00000179709	ENST00000291971	T	0.52983	0.64	2.27	-1.68	0.08212	.	.	.	.	.	T	0.38321	0.1036	L	0.44542	1.39	0.09310	N	1	P;B	0.44690	0.841;0.37	P;B	0.49708	0.62;0.41	T	0.22173	-1.0224	9	0.22109	T	0.4	.	0.2333	0.00183	0.3798:0.2347:0.1554:0.2301	.	942;961	Q86W28-2;Q86W28	.;NALP8_HUMAN	G	961	ENSP00000291971:E961G	ENSP00000291971:E961G	E	+	2	0	NLRP8	61182577	0.102000	0.21896	0.002000	0.10522	0.002000	0.02628	0.040000	0.13905	-0.500000	0.06614	-0.633000	0.03987	GAA	.		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		G	56490765	A	G	56490765	3	3	51	1	0	0	0	0	1	0	0	0	10509	246	9	3	2916	3	NLRP8	19	56490765	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1707088	56490765	2638218	262	4950											
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133670	57133670	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaggccttcagccagagcTcctacctcatccagcaccag	10	6	8	17	0	2	1	2	0	0	1	4	1	4	1	6	1	4	3	6	1	2	2	rs575219516		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:57133670T>G	ENST00000328070.6	+	3	1249	c.1015T>G	c.(1015-1017)Tcc>Gcc	p.S339A		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S339A(1)		endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		CAGCCAGAGCTCCTACCTCAT	0.632													.|||	1	0.000199681	0	0.0014	5008	,	,		21342	0		0	False		,,,				2504	0				p.S339A		.											.	ZNF71-91	1	Substitution - Missense(1)	endometrium(1)	c.T1015G						.						87	80	82					19																	57133670		2203	4300	6503	SO:0001583	missense	58491	exon3			CAGAGCTCCTACC	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"Zinc fingers, C2H2-type"	13141	protein-coding gene	gene with protein product		194545	"zinc finger protein 71 (Cos26)"			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.1015T>G	19.37:g.57133670T>G	ENSP00000328245:p.Ser339Ala	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	180	9	NM_021216	0	0	4	4	0	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	37	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.726062	0.30593	.	.	ENSG00000197951	ENST00000328070	T	0.35421	1.31	3.76	1.4	0.22301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34135	0.0887	M	0.69358	2.11	0.09310	N	1	B	0.21452	0.056	B	0.15052	0.012	T	0.27157	-1.0082	9	0.44086	T	0.13	.	8.5519	0.33458	0.0:0.0:0.3775:0.6225	.	339	Q9NQZ8	ZNF71_HUMAN	A	339	ENSP00000328245:S339A	ENSP00000328245:S339A	S	+	1	0	ZNF71	61825482	0.000000	0.05858	0.996000	0.52242	0.982000	0.71751	-3.336000	0.00507	0.480000	0.27534	0.459000	0.35465	TCC	.		0.632	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		G	57133670	T	G	57133670	3	3	51	1	0	0	0	0	1	0	0	0	18146	1551	54	5	1017	5	ZNF71	19	57133670	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	642905	57133670	1995313	263	4951											
ESF1	51575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	13695769	13695769	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaggggtccaaattgaacaAgtgggaagtgtacattgcct	12	10	13	6	0	0	2	0	2	0	0	1	3	1	3	2	3	3	1	2	3	5	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr20:13695769A>T	ENST00000202816.1	-	14	2415	c.2308T>A	c.(2308-2310)Ttg>Atg	p.L770M		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	770	Lys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						AAATTGAACAAGTGGGAAGTG	0.348																																					p.L770M		.											.	ESF1-91	0			c.T2308A						.						96	100	98					20																	13695769		2203	4300	6503	SO:0001583	missense	51575	exon14			TGAACAAGTGGGA		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.2308T>A	20.37:g.13695769A>T	ENSP00000202816:p.Leu770Met	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	89	38	NM_001276380	0	0	10	17	7	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	37	CCDS13117.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.698422	0.68386	.	.	ENSG00000089048	ENST00000202816	T	0.23348	1.91	6.05	4.93	0.64822	NUC153 (1);	0.000000	0.56097	D	0.000024	T	0.47857	0.1468	M	0.72894	2.215	0.43588	D	0.995936	D	0.89917	1.0	D	0.97110	1.0	T	0.41840	-0.9486	10	0.45353	T	0.12	-6.0E-4	11.0101	0.47657	0.8699:0.0:0.1301:0.0	.	770	Q9H501	ESF1_HUMAN	M	770	ENSP00000202816:L770M	ENSP00000202816:L770M	L	-	1	2	ESF1	13643769	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.302000	0.59092	1.065000	0.40693	0.528000	0.53228	TTG	.		0.348	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		T	13695769	A	T	13695769	3	4	51	1	0	0	0	0	1	0	0	0	5264	69	3	5	251	5	ESF1	20	13695769	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		13695769	49329751	264	4952											
RALGAPA2	57186	bcgsc.ca	37	chr20	20501647	20501647	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacatttgccagtggcaggAaggggtcataatccgtggat	10	10	13	8	1	2	0	2	0	0	0	3	2	3	2	2	5	1	1	2	5	2	2	rs77346211		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr20:20501647A>G	ENST00000202677.7	-	31	4005	c.3998T>C	c.(3997-3999)tTc>tCc	p.F1333S		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1333					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						CAGTGGCAGGAAGGGGTCATA	0.498																																					p.F1333S													.	RALGAPA2-24	0			c.T3998C						.						105	107	106					20																	20501647		1969	4170	6139	SO:0001583	missense	57186	exon31			GGCAGGAAGGGGT	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.3998T>C	20.37:g.20501647A>G	ENSP00000202677:p.Phe1333Ser	Somatic	77	4		WXS	Illumina HiSeq	Phase_1	57	33	NM_020343	0	0	9	9	0	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.82|16.82	3.227385|3.227385	0.58668|0.58668	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	T|.	0.30448|.	1.53|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.133079|.	0.53938|.	D|.	0.000058|.	T|T	0.75133|0.75133	0.3808|0.3808	M|M	0.72894|0.72894	2.215|2.215	0.53005|0.53005	D|D	0.99996|0.99996	B;D;B|.	0.76494|.	0.057;0.999;0.057|.	B;D;B|.	0.83275|.	0.053;0.996;0.053|.	T|T	0.74466|0.74466	-0.3656|-0.3656	10|5	0.23302|.	T|.	0.38|.	.|.	16.8222|16.8222	0.85835|0.85835	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1171;1333;1333|.	A8MSM5;Q2PPJ7-2;Q2PPJ7|.	.;.;RGPA2_HUMAN|.	S|P	1333|1150	ENSP00000202677:F1333S|.	ENSP00000202677:F1333S|.	F|S	-|-	2|1	0|0	RALGAPA2|RALGAPA2	20449647|20449647	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.996000|0.996000	0.88848|0.88848	6.366000|6.366000	0.73095|0.73095	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TTC|TCC	A|0.996;G|0.004		0.498	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		G	20501647	A	G	20501647	3	3	51	1	0	0	0	0	1	0	0	0	13046	246	9	3	1659	3	RALGAPA2	20	20501647	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	6805878	20501647	42523873	265	4953											
AHCY	191	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	32868894	32868914	+	In_Frame_Del	DEL	CTGGGCTTGCTTCTCAGTTAG	CTGGGCTTGCTTCTCAGTTAG	-																															tcacaggacatgcccaggtaCtgggcttgcttctcagttag																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	CTGGGCTTGCTTCTCAGTTAG	CTGGGCTTGCTTCTCAGTTAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr20:32868894_32868914delCTGGGCTTGCTTCTCAGTTAG	ENST00000217426.2	-	10	1302_1322	c.1225_1245delCTAACTGAGAAGCAAGCCCAG	c.(1225-1245)ctaactgagaagcaagcccagdel	p.LTEKQAQ409del	CTD-3216D2.5_ENST00000609218.1_RNA|RP4-785G19.5_ENST00000512005.1_RNA|AHCY_ENST00000538132.1_In_Frame_Del_p.LTEKQAQ381del	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	409					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGCCCAGGTACTGGGCTTGCTTCTCAGTTAGCTTGGTCAAC	0.566																																					p.409_415del		.											.	AHCY-91	0			c.1225_1245del						.																																			SO:0001651	inframe_deletion	191	exon10			.	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.1225_1245delCTAACTGAGAAGCAAGCCCAG	20.37:g.32868894_32868914delCTGGGCTTGCTTCTCAGTTAG	ENSP00000217426:p.Leu409_Gln415del	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	104	26	NM_000687	0	0	0	0	0	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	In_Frame_Del	DEL	ENST00000217426.2	37	CCDS13233.1																																																																																			.		0.566	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		-	32868914	CTGGGCTTGCTTCTCAGTTAG	-	32868894	7	5	51	1	0	1	0	1	0	0	0	0	409	564	20	0	57	0	AHCY	20	32868894	In_Frame_Del	DEL	CTGGGCTTGCTTCTCAGTTAG	TCGA-B9-4117-01A-01D-1252-08	12367247	32868894	30156626	266	4954											
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44512073	44512073	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgagaaacaaggtatggcttCtctgttccgttacatgcagc	10	12	10	9	1	1	1	0	1	1	1	3	2	2	1	1	2	4	5	1	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr20:44512073C>T	ENST00000372523.1	+	2	937	c.842C>T	c.(841-843)tCt>tTt	p.S281F	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.S281F	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	281						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				GGTATGGCTTCTCTGTTCCGT	0.542																																					p.S281F		.											.	ZSWIM1-91	0			c.C842T						.						114	106	109					20																	44512073		2203	4300	6503	SO:0001583	missense	90204	exon2			TGGCTTCTCTGTT	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"Zinc fingers, SWIM-type"	16155	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 162"	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.842C>T	20.37:g.44512073C>T	ENSP00000361601:p.Ser281Phe	Somatic	165	1		WXS	Illumina HiSeq	Phase_I	754	280	NM_080603	0	0	7	12	5	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	37	CCDS13382.2	.	.	.	.	.	.	.	.	.	.	C	11.18	1.562391	0.27915	.	.	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.25579	1.79;1.79	5.27	3.33	0.38152	.	0.405963	0.20859	U	0.084384	T	0.19167	0.0460	L	0.27053	0.805	0.09310	N	1	B	0.30406	0.278	B	0.34385	0.181	T	0.16778	-1.0391	10	0.54805	T	0.06	-14.0609	9.3261	0.37993	0.0:0.779:0.1441:0.077	.	281	Q9BR11	ZSWM1_HUMAN	F	281	ENSP00000361601:S281F;ENSP00000361598:S281F	ENSP00000361598:S281F	S	+	2	0	ZSWIM1	43945480	0.010000	0.17322	0.018000	0.16275	0.968000	0.65278	1.435000	0.34969	0.785000	0.33685	0.655000	0.94253	TCT	.		0.542	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		T	44512073	C	T	44512073	3	4	51	1	0	0	0	0	1	0	0	0	18272	913	32	2	844	2	ZSWIM1	20	44512073	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	11643179	44512073	18513447	267	4955											
GRIK1	2897	hgsc.bcm.edu	37	chr21	30927529	30927529	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcttcctcggggcagccAttcccacgccaccacttctc	5	11	7	18	2	2	0	0	0	2	0	6	0	4	0	5	2	1	1	5	2	0	4	rs201323952		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr21:30927529A>C	ENST00000399907.1	-	16	2862	c.2451T>G	c.(2449-2451)aaT>aaG	p.N817K	GRIK1_ENST00000399909.1_Missense_Mutation_p.N802K|GRIK1_ENST00000389125.3_Missense_Mutation_p.N802K|GRIK1_ENST00000389124.2_Missense_Mutation_p.N817K|GRIK1_ENST00000309434.7_Missense_Mutation_p.N819K|GRIK1_ENST00000327783.4_Missense_Mutation_p.N817K|GRIK1_ENST00000399914.1_Missense_Mutation_p.N802K|GRIK1_ENST00000535441.1_Missense_Mutation_p.N819K|GRIK1_ENST00000399913.1_Missense_Mutation_p.N817K	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	817					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	CGGGGCAGCCATTCCCACGCC	0.478																																					p.N817K		.											.	GRIK1-137	0			c.T2451G						.						98	100	100					21																	30927529		2203	4300	6503	SO:0001583	missense	2897	exon16			GCAGCCATTCCCA		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.2451T>G	21.37:g.30927529A>C	ENSP00000382791:p.Asn817Lys	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	40	3	NM_000830	0	0	0	0	0	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	37	CCDS42913.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.413038	0.42817	.	.	ENSG00000171189	ENST00000327783;ENST00000389125;ENST00000399913;ENST00000399914;ENST00000535441;ENST00000541508;ENST00000389124;ENST00000399907;ENST00000399909;ENST00000309434	T;T;T;T;T;T;T;T;T	0.10192	2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9	4.88	-2.03	0.07365	Ionotropic glutamate receptor (1);	0.043179	0.85682	N	0.000000	T	0.03871	0.0109	N	0.12746	0.255	0.58432	D	0.999993	B;B;P;B	0.36125	0.238;0.395;0.538;0.177	B;B;B;B	0.35312	0.2;0.132;0.2;0.037	T	0.44997	-0.9291	10	0.06494	T	0.89	.	7.7865	0.29095	0.3408:0.1458:0.5135:0.0	.	802;817;817;802	E7EPY9;E9PD61;P39086;P39086-2	.;.;GRIK1_HUMAN;.	K	817;802;817;802;819;678;817;817;802;819	ENSP00000327687:N817K;ENSP00000373777:N802K;ENSP00000382797:N817K;ENSP00000382798:N802K;ENSP00000446326:N819K;ENSP00000373776:N817K;ENSP00000382791:N817K;ENSP00000382793:N802K;ENSP00000311646:N819K	ENSP00000311646:N819K	N	-	3	2	GRIK1	29849400	0.081000	0.21417	0.963000	0.40424	0.988000	0.76386	-0.395000	0.07287	-0.418000	0.07450	-0.263000	0.10527	AAT	A|0.999;G|0.001		0.478	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1			C	30927529	A	C	30927529	3	2	51	1	0	0	0	0	1	0	0	0	6794	214	8	5	473	5	GRIK1	21	30927529	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		30927529	17202366	268	4956											
KRTAP22-1	337979	bcgsc.ca	37	chr21	31973511	31973511	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggctgcagctatggctgTggtcttagcggctatggcta	5	12	15	9	1	1	0	0	0	1	0	1	0	1	0	0	5	3	6	0	5	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr21:31973511T>G	ENST00000334680.2	+	1	98	c.72T>G	c.(70-72)tgT>tgG	p.C24W	KRTAP6-2_ENST00000334897.3_5'Flank	NM_181620.1	NP_853651.1	Q3MIV0	KR221_HUMAN	keratin associated protein 22-1	24						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	8						GCTATGGCTGTGGTCTTAGCG	0.478																																					p.C24W													.	KRTAP22-1-68	0			c.T72G						.																																			SO:0001583	missense	337979	exon1			TGGCTGTGGTCTT	AP001708	CCDS13601.1	21q22.1	2011-02-10			ENSG00000186924	ENSG00000186924		"Keratin associated proteins"	18947	protein-coding gene	gene with protein product						12359730	Standard	NM_181620		Approved	KAP22.1	uc011add.2	Q3MIV0	OTTHUMG00000057778	ENST00000334680.2:c.72T>G	21.37:g.31973511T>G	ENSP00000333887:p.Cys24Trp	Somatic	175	0		WXS	Illumina HiSeq	Phase_1	110	40	NM_181620	0	0	0	0	0		Missense_Mutation	SNP	ENST00000334680.2	37	CCDS13601.1	.	.	.	.	.	.	.	.	.	.	T	9.604	1.129475	0.21041	.	.	ENSG00000186924	ENST00000334680	T	0.20200	2.09	3.93	-1.38	0.09027	.	2.982100	0.01786	N	0.032038	T	0.36358	0.0964	.	.	.	0.09310	N	1	D	0.76494	0.999	D	0.63703	0.917	T	0.22487	-1.0215	9	0.87932	D	0	.	2.5716	0.04796	0.3438:0.1913:0.0:0.4649	.	24	Q3MIV0	KR221_HUMAN	W	24	ENSP00000333887:C24W	ENSP00000333887:C24W	C	+	3	2	KRTAP22-1	30895382	0.000000	0.05858	0.002000	0.10522	0.105000	0.19272	-0.869000	0.04232	-0.234000	0.09782	0.383000	0.25322	TGT	.		0.478	KRTAP22-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128230.2			G	31973511	T	G	31973511	3	3	51	1	0	0	0	0	1	0	0	0	8561	1702	59	5	74	5	KRTAP22-1	21	31973511	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1045982	31973511	16156384	269	4957											
SLC5A3	6526	bcgsc.ca	37	chr21	35468406	35468406	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctactcttatggctggCttcttaaagctcctgccaat	7	14	8	12	0	3	0	0	0	3	0	4	0	4	0	2	3	3	4	2	3	5	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr21:35468406C>G	ENST00000381151.3	+	2	1421	c.909C>G	c.(907-909)ggC>ggG	p.G303G	SLC5A3_ENST00000608209.1_Silent_p.G303G|AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	303					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						TTATGGCTGGCTTCTTAAAGC	0.463																																					p.G303G													.	SLC5A3-92	0			c.C909G						.						86	93	91					21																	35468406		2203	4300	6503	SO:0001819	synonymous_variant	6526	exon2			GGCTGGCTTCTTA		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.909C>G	21.37:g.35468406C>G		Somatic	127	0		WXS	Illumina HiSeq	Phase_1	100	53	NM_006933	0	0	1	1	0	O43489	Silent	SNP	ENST00000381151.3	37	CCDS33549.1																																																																																			.		0.463	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			G	35468406	C	G	35468406	2	3	51	1	0	0	0	0	0	0	0	1	14698	784	28	4		4	SLC5A3	21	35468406	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	3494895	35468406	12661489	270	4958											
CABIN1	23523	ucsc.edu	37	chr22	24494089	24494089	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgacatccccaccttacAcagccactccgattgaccac	10	8	5	18	1	1	2	0	2	1	0	3	3	3	2	6	0	2	0	6	0	1	2	rs77920906		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr22:24494089A>C	ENST00000398319.2	+	26	4436	c.4051A>C	c.(4051-4053)Aca>Cca	p.T1351P	CABIN1_ENST00000405822.2_Intron|CABIN1_ENST00000263119.5_Missense_Mutation_p.T1351P	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1351					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CCCACCTTACACAGCCACTCC	0.622																																					p.T1351P													.	CABIN1-94	0			c.A4051C						.						89	82	84					22																	24494089		2203	4300	6503	SO:0001583	missense	23523	exon26			CCTTACACAGCCA	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.4051A>C	22.37:g.24494089A>C	ENSP00000381364:p.Thr1351Pro	Somatic	97	1		WXS	Illumina HiSeq		278	87	NM_001199281	0	0	7	7	0	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.966900	0.74131	.	.	ENSG00000099991	ENST00000263119;ENST00000398319	T;T	0.63417	-0.04;-0.04	4.77	4.77	0.60923	.	0.111718	0.64402	D	0.000011	T	0.52108	0.1714	L	0.43152	1.355	0.80722	D	1	B	0.30824	0.296	B	0.19946	0.027	T	0.55198	-0.8178	10	0.49607	T	0.09	.	13.83	0.63375	1.0:0.0:0.0:0.0	.	1351	Q9Y6J0	CABIN_HUMAN	P	1351	ENSP00000263119:T1351P;ENSP00000381364:T1351P	ENSP00000263119:T1351P	T	+	1	0	CABIN1	22824089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.927000	0.63440	1.935000	0.56089	0.529000	0.55759	ACA	.		0.622	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		C	24494089	A	C	24494089	3	2	51	1	0	0	0	0	1	0	0	0	2534	159	6	5	4149	5	CABIN1	22	24494089	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		24494089	26810477	271	4959											
NEFH	4744	broad.mit.edu	37	chr22	29885754	29885777	+	In_Frame_Del	DEL	AAGTCCCCAGTGAAGGAAGAAGCA	AAGTCCCCAGTGAAGGAAGAAGCA	-																															caaagtcccctgagaaggccAagtccccagtgaaggaagaa																								rs139600064|rs531060059	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	AAGTCCCCAGTGAAGGAAGAAGCA	AAGTCCCCAGTGAAGGAAGAAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr22:29885754_29885777delAAGTCCCCAGTGAAGGAAGAAGCA	ENST00000310624.6	+	4	2158_2181	c.2125_2148delAAGTCCCCAGTGAAGGAAGAAGCA	c.(2125-2148)aagtccccagtgaaggaagaagcadel	p.KSPVKEEA709del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	715	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.E715K(1)		cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TGAGAAGGCCAAGTCCCCAGTGAAGGAAGAAGCAAAGTCCCCTG	0.562																																					p.709_716del													.	NEFH-90	1	Substitution - Missense(1)	skin(1)	c.2125_2148del						.																																			SO:0001651	inframe_deletion	4744	exon4			AAGGCCAAGTCCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2125_2148delAAGTCCCCAGTGAAGGAAGAAGCA	22.37:g.29885754_29885777delAAGTCCCCAGTGAAGGAAGAAGCA	ENSP00000311997:p.Lys709_Ala716del	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	379	8	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	37	CCDS13858.1																																																																																			.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		-	29885777	AAGTCCCCAGTGAAGGAAGAAGCA	-	29885754	7	5	51	1	0	1	0	1	0	0	0	0	10340	131	5	0	2139	0	NEFH	22	29885754	In_Frame_Del	DEL	AAGTCCCCAGTGAAGGAAGAAGCA	TCGA-B9-4117-01A-01D-1252-08	5391665	29885754	21418812	272	4960											
NF2	4771	hgsc.bcm.edu	37	chr22	30000103	30000103	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatggagttcaattgcgaggTaaccggccggcagccccgac	9	6	14	12	4	1	0	1	0	0	0	1	4	1	1	4	4	3	3	4	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr22:30000103T>G	ENST00000338641.4	+	1	555		c.e1+2		NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000413209.2_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000347330.5_Splice_Site|NF2_ENST00000361676.4_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.?(1)		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						AATTGCGAGGTAACCGGCCGG	0.562			"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	1	Unknown(1)	lung(1)	c.114+2T>G						.						35	25	29					22																	30000103		2202	4299	6501	SO:0001630	splice_region_variant	4771	exon1	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GCGAGGTAACCGG	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.114+2T>G	22.37:g.30000103T>G		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	17	15	NM_016418	0	0	0	5	5	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.472138	0.84533	.	.	ENSG00000186575	ENST00000413209;ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0321	0.71717	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28330103	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	5.795000	0.69074	2.034000	0.60081	0.459000	0.35465	.	.		0.562	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	G	30000103	T	G	30000103	5	3	51	1	0	0	0	0	0	0	1	0	10383	1652	57	5	118	5	NF2	22	30000103	Splice_Site	SNP	T	TCGA-B9-4117-01A-01D-1252-08	114349	30000103	21304463	273	4961											
ADSL	158	bcgsc.ca	37	chr22	40750276	40750276	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagtgatctctcggcttGccgactttgctaaggaacga	9	10	11	11	3	1	2	0	1	1	1	3	5	1	3	2	2	3	2	2	2	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr22:40750276G>T	ENST00000216194.7	+	4	483	c.427G>T	c.(427-429)Gcc>Tcc	p.A143S	ADSL_ENST00000342312.6_Missense_Mutation_p.A143S|ADSL_ENST00000454266.2_Missense_Mutation_p.A157S	NM_000026.2	NP_000017.1	P30566	PUR8_HUMAN	adenylosuccinate lyase	143					'de novo' AMP biosynthetic process (GO:0044208)|'de novo' IMP biosynthetic process (GO:0006189)|aerobic respiration (GO:0009060)|AMP biosynthetic process (GO:0006167)|metabolic process (GO:0008152)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity (GO:0070626)|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity (GO:0004018)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(2)|ovary(1)|prostate(1)	19						CTCTCGGCTTGCCGACTTTGC	0.393																																					p.A143S	Colon(4;65 130 1097 1516)												.	ADSL-652	0			c.G427T						.						219	216	217					22																	40750276		2203	4300	6503	SO:0001583	missense	158	exon4			CGGCTTGCCGACT	X65867	CCDS14001.1, CCDS46714.1	22q13.1	2011-02-17			ENSG00000239900	ENSG00000239900	4.3.2.2		291	protein-coding gene	gene with protein product		608222				8404037	Standard	NM_000026		Approved		uc003ayp.4	P30566	OTTHUMG00000166425	ENST00000216194.7:c.427G>T	22.37:g.40750276G>T	ENSP00000216194:p.Ala143Ser	Somatic	228	0		WXS	Illumina HiSeq	Phase_1	408	111	NM_001123378	0	0	79	81	2	B0QY76|O75495|Q5TI34	Missense_Mutation	SNP	ENST00000216194.7	37	CCDS14001.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398744	0.25205	.	.	ENSG00000239900	ENST00000216194;ENST00000425605;ENST00000454266;ENST00000342312	D;D;D	0.99329	-5.75;-5.75;-5.75	5.75	3.69	0.42338	Lyase 1, N-terminal (1);L-Aspartase-like (1);	0.096122	0.64402	D	0.000001	D	0.96269	0.8783	N	0.12920	0.275	0.80722	D	1	B;B;B;B	0.19200	0.01;0.006;0.034;0.034	B;B;B;B	0.32090	0.032;0.058;0.14;0.14	D	0.93579	0.6911	10	0.06365	T	0.9	-9.9191	11.5473	0.50700	0.1421:0.0:0.8579:0.0	.	157;143;143;143	E7ERF4;P30566-2;Q71UA4;P30566	.;.;.;PUR8_HUMAN	S	143;157;157;143	ENSP00000216194:A143S;ENSP00000390107:A157S;ENSP00000341429:A143S	ENSP00000216194:A143S	A	+	1	0	ADSL	39080222	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.553000	0.45837	1.437000	0.47472	0.655000	0.94253	GCC	.		0.393	ADSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321386.1	NM_000026		T	40750276	G	T	40750276	3	4	51	1	0	0	0	0	1	0	0	0	346	1319	46	4	441	4	ADSL	22	40750276	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	10750173	40750276	10554290	274	4962											
EP300	2033	broad.mit.edu	37	chr22	41543893	41543893	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagccccctattgtaccccgGcaaacccctcctcttcagca	8	8	5	20	1	2	0	1	0	1	0	3	0	3	0	7	1	4	3	7	1	3	4	rs187938527		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr22:41543893G>A	ENST00000263253.7	+	12	3403	c.2184G>A	c.(2182-2184)cgG>cgA	p.R728R		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	728					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TTGTACCCCGGCAAACCCCTC	0.478			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.R728R				Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300-2011	0			c.G2184A						.						105	98	101					22																	41543893		2203	4300	6503	SO:0001819	synonymous_variant	2033	exon12	Familial Cancer Database	Broad Thumb-Hallux syndrome	ACCCCGGCAAACC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2184G>A	22.37:g.41543893G>A		Somatic	82	1		WXS	Illumina HiSeq	Phase_I	191	7	NM_001429	0	0	26	26	0	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																			G|0.999;T|0.000		0.478	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41543893	G	A	41543893	2	1	51	1	0	0	0	0	0	0	0	1	5161	1190	42	2		2	EP300	22	41543893	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	793617	41543893	9760673	275	4963											
GLRA2	2742	bcgsc.ca	37	chrX	14599357	14599357	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaatgattcacggctggCgtacagtgagtacccagatg	10	9	14	8	2	1	3	1	2	0	1	1	4	1	4	1	3	2	3	1	3	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:14599357C>G	ENST00000218075.4	+	4	853	c.323C>G	c.(322-324)gCg>gGg	p.A108G	GLRA2_ENST00000443437.2_Missense_Mutation_p.A19G|GLRA2_ENST00000355020.4_Missense_Mutation_p.A108G	NM_002063.3	NP_002054.1	P23416	GLRA2_HUMAN	glycine receptor, alpha 2	108					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)|synapse assembly (GO:0007416)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(22)|ovary(1)|prostate(1)|skin(2)	37	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)|Lindane(DB00431)	TCACGGCTGGCGTACAGTGAG	0.483													C|||	367	0.0972185	0.0386	0.0951	3775	,	,		14374	0.129		0.1143	False		,,,				2504	0.0051				p.A108G													.	GLRA2-131	0			c.C323G						.						124	114	117					X																	14599357		2203	4300	6503	SO:0001583	missense	2742	exon5			GGCTGGCGTACAG		CCDS14160.1, CCDS48085.1, CCDS55371.1	Xp22.2	2012-02-07			ENSG00000101958	ENSG00000101958		"Ligand-gated ion channels / Glycine receptors"	4327	protein-coding gene	gene with protein product		305990		GLR			Standard	NM_002063		Approved		uc010nep.3	P23416	OTTHUMG00000021166	ENST00000218075.4:c.323C>G	X.37:g.14599357C>G	ENSP00000218075:p.Ala108Gly	Somatic	133	0		WXS	Illumina HiSeq	Phase_1	82	35	NM_001118885	0	0	0	0	0	A8K0J6|B2R6I8|B7Z4F5|J3KQ59|Q53YX7|Q6ICQ0|Q99862	Missense_Mutation	SNP	ENST00000218075.4	37	CCDS14160.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078293	0.76528	.	.	ENSG00000101958	ENST00000443437;ENST00000218075;ENST00000355020;ENST00000415367	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36	5.72	5.72	0.89469	Neurotransmitter-gated ion-channel ligand-binding (3);	0.052089	0.85682	D	0.000000	D	0.87943	0.6305	M	0.74258	2.255	0.80722	D	1	P;B;B	0.44877	0.845;0.093;0.271	P;B;B	0.54372	0.75;0.161;0.275	D	0.88632	0.3170	10	0.66056	D	0.02	.	18.8728	0.92322	0.0:1.0:0.0:0.0	.	92;108;108	B7Z4E9;P23416;P23416-2	.;GLRA2_HUMAN;.	G	19;108;108;92	ENSP00000387756:A19G;ENSP00000218075:A108G;ENSP00000347123:A108G;ENSP00000391606:A92G	ENSP00000218075:A108G	A	+	2	0	GLRA2	14509278	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.701000	0.84566	2.404000	0.81709	0.600000	0.82982	GCG	.		0.483	GLRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055829.1			G	14599357	C	G	14599357	3	3	51	1	0	0	0	0	1	0	0	0	6475	768	27	4	409	4	GLRA2	23	14599357	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08		14599357	140671203	276	4964											
CDKL5	6792	hgsc.bcm.edu	37	chrX	18646492	18646492	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcatcctttctttcagaGccagccattaaaatcactgc	10	14	4	13	0	4	1	3	0	2	1	6	1	5	1	3	0	3	0	3	0	2	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:18646492G>C	ENST00000379989.3	+	19	2783	c.2498G>C	c.(2497-2499)aGc>aCc	p.S833T	CDKL5_ENST00000379996.3_Splice_Site_p.S833T	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	833					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					TTCTTTCAGAGCCAGCCATTA	0.522																																					p.S833T		.											.	CDKL5-838	0			c.G2498C						.						228	244	238					X																	18646492		2203	4300	6503	SO:0001630	splice_region_variant	6792	exon18			TTCAGAGCCAGCC	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"Cyclin-dependent kinases"	11411	protein-coding gene	gene with protein product		300203	"serine/threonine kinase 9"	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2497-1G>C	X.37:g.18646492G>C		Somatic	576	0		WXS	Illumina HiSeq	Phase_I	2096	296	NM_003159	0	0	0	0	0	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.577737	0.28180	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.72394	-0.65;-0.65	5.73	4.81	0.61882	.	0.074767	0.85682	D	0.000000	T	0.57125	0.2032	N	0.19112	0.55	0.31747	N	0.635103	B	0.21071	0.051	B	0.15052	0.012	T	0.63075	-0.6718	10	0.52906	T	0.07	-18.3408	15.1993	0.73122	0.0:0.1372:0.8628:0.0	.	833	O76039	CDKL5_HUMAN	T	833	ENSP00000369332:S833T;ENSP00000369325:S833T	ENSP00000369325:S833T	S	+	2	0	CDKL5	18556413	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.004000	0.49513	2.398000	0.81561	0.594000	0.82650	AGC	.		0.522	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Missense_Mutation	C	18646492	G	C	18646492	5	2	51	1	0	0	0	0	0	0	1	0	3163	985	34	4	2564	4	CDKL5	23	18646492	Splice_Site	SNP	G	TCGA-B9-4117-01A-01D-1252-08	4047135	18646492	136624068	277	4965											
DMD	1756	bcgsc.ca	37	chrX	31854856	31854856	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcactggctgagtggctggTttttccttgtacaaatgctg	6	16	11	8	0	1	1	1	1	0	0	2	1	2	1	1	3	2	5	1	3	2	5	rs202090289		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:31854856T>G	ENST00000357033.4	-	49	7385	c.7179A>C	c.(7177-7179)aaA>aaC	p.K2393N	DMD_ENST00000474231.1_5'UTR|DMD_ENST00000359836.1_5'UTR|DMD_ENST00000343523.2_5'UTR|DMD_ENST00000378677.2_Missense_Mutation_p.K2389N|DMD_ENST00000378707.3_5'UTR|DMD_ENST00000541735.1_5'UTR	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2393					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GAGTGGCTGGTTTTTCCTTGT	0.428																																					p.K2393N													.	DMD-265	0			c.A7179C						.						221	181	194					X																	31854856		2202	4300	6502	SO:0001583	missense	1756	exon49			GGCTGGTTTTTCC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.7179A>C	X.37:g.31854856T>G	ENSP00000354923:p.Lys2393Asn	Somatic	108	0		WXS	Illumina HiSeq	Phase_1	57	30	NM_004006	0	0	0	0	0	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.23|10.23	1.291994|1.291994	0.23564|0.23564	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280|ENST00000465285	T;T;T|.	0.34275|.	1.37;1.37;1.37|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.37012|.	U|.	0.002288|.	T|T	0.53916|0.53916	0.1826|0.1826	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	P;P;P;P;P|.	0.44139|.	0.827;0.734;0.734;0.734;0.734|.	P;B;B;B;B|.	0.49192|.	0.602;0.398;0.398;0.243;0.243|.	T|T	0.51387|0.51387	-0.8712|-0.8712	10|5	0.17832|.	T|.	0.49|.	.|.	13.4217|13.4217	0.61001|0.61001	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2385;2393;2389;1052;1049|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6|.	.;DMD_HUMAN;.;.;.|.	N|P	2385;1052;1049;89;2389;2393;2393;2270|122	ENSP00000350765:K89N;ENSP00000367948:K2389N;ENSP00000354923:K2393N|.	ENSP00000354923:K2393N|.	K|T	-|-	3|1	2|0	DMD|DMD	31764777|31764777	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	2.978000|2.978000	0.49305|0.49305	1.887000|1.887000	0.54652|0.54652	0.345000|0.345000	0.21793|0.21793	AAA|ACC	.		0.428	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	31854856	T	G	31854856	3	3	51	1	0	0	0	0	1	0	0	0	4591	1722	60	5	4150	5	DMD	23	31854856	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	13208364	31854856	123415704	278	4966											
RPGR	6103	hgsc.bcm.edu	37	chrX	38145451	38145451	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccccttctccttcctccTcttccccctccccttctcct	0	16	0	25	0	3	0	0	0	3	0	10	0	8	0	10	0	0	0	10	0	0	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:38145451T>C	ENST00000339363.3	-	14	2688				RPGR_ENST00000309513.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.E934G|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tccttcctcctcttccccctc	0.607																																					p.E934G		.											.	RPGR-131	0			c.A2801G						.						7	4	5					X																	38145451		1732	3246	4978	SO:0001627	intron_variant	6103	exon15			TCCTCCTCTTCCC	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"retinitis pigmentosa 15", "cone dystrophy 1 (X-linked)"	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+895A>G	X.37:g.38145451T>C		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_001034853	0	0	0	0	0	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	-	4.134	0.023256	0.08006	.	.	ENSG00000156313	ENST00000378505	T	0.39056	1.1	1.68	-2.28	0.06826	.	971.910000	0.00824	N	0.001616	T	0.33381	0.0861	L	0.47716	1.5	0.09310	N	0.999997	B	0.09022	0.002	B	0.04013	0.001	T	0.14699	-1.0463	10	0.39692	T	0.17	.	2.8465	0.05545	0.2182:0.1695:0.0:0.6124	.	934	E9PE28	.	G	934	ENSP00000367766:E934G	ENSP00000367766:E934G	E	-	2	0	RPGR	38030395	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-0.472000	0.06623	-0.068000	0.12953	0.000000	0.15137	GAG	.		0.607	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		C	38145451	T	C	38145451	1	2	51	0	1	0	0	0	0	0	0	0	13580	1551	54	3		3	RPGR	23	38145451	Intron	SNP	T	TCGA-B9-4117-01A-01D-1252-08	6290595	38145451	117125109	279	4967											
MAOA	4128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	43590945	43590945	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgtgtgtgttttagtgcaAatacgtaattaatgcgatcc	10	16	9	6	2	0	0	0	0	0	0	1	1	1	0	1	0	3	3	1	0	5	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:43590945A>C	ENST00000338702.3	+	8	923	c.800A>C	c.(799-801)aAa>aCa	p.K267T	MAOA_ENST00000542639.1_Missense_Mutation_p.K134T	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	267					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	TTTTAGTGCAAATACGTAATT	0.418																																					p.K267T		.											.	MAOA-194	0			c.A800C						.						110	82	92					X																	43590945		2203	4300	6503	SO:0001583	missense	4128	exon8			AGTGCAAATACGT		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.800A>C	X.37:g.43590945A>C	ENSP00000340684:p.Lys267Thr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	95	30	NM_000240	0	0	0	0	0	B4DF46|Q16426	Missense_Mutation	SNP	ENST00000338702.3	37	CCDS14260.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.367611	0.24771	.	.	ENSG00000189221	ENST00000338702;ENST00000542639	D;D	0.92699	-3.09;-3.09	5.81	-4.19	0.03835	Amine oxidase (1);	0.452762	0.27682	N	0.018281	D	0.92280	0.7551	M	0.86420	2.815	0.40067	D	0.975962	B	0.20887	0.049	B	0.28991	0.097	T	0.76729	-0.2852	10	0.72032	D	0.01	.	16.9162	0.86152	0.7596:0.0:0.2404:0.0	.	267	P21397	AOFA_HUMAN	T	267;134	ENSP00000340684:K267T;ENSP00000440846:K134T	ENSP00000340684:K267T	K	+	2	0	MAOA	43475889	0.137000	0.22531	0.008000	0.14137	0.362000	0.29581	-0.156000	0.10100	-1.760000	0.01312	-0.488000	0.04728	AAA	.		0.418	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		C	43590945	A	C	43590945	3	2	51	1	0	0	0	0	1	0	0	0	9250	14	1	5	830	5	MAOA	23	43590945	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	5445494	43590945	111679615	280	4968											
NDUFB11	54539	broad.mit.edu;bcgsc.ca	37	chrX	47002143	47002143	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaccatgggagtctgggtTctgtggagaaatagaggtca	12	10	14	5	0	3	2	1	0	2	2	3	4	3	3	1	4	1	1	1	4	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:47002143T>G	ENST00000377811.3	-	2	1032	c.208A>C	c.(208-210)Aac>Cac	p.N70H	RBM10_ENST00000377604.3_5'Flank|RBM10_ENST00000345781.6_5'Flank|NDUFB11_ENST00000276062.8_Splice_Site_p.N70H|RBM10_ENST00000329236.7_5'Flank	NM_001135998.2	NP_001129470.1	Q9NX14	NDUBB_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa	70					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	7						GAGTCTGGGTTCTGTGGAGAA	0.512																																					p.N70H	Ovarian(77;454 1296 7908 21551 37072)												.	NDUFB11-130	0			c.A208C						.						128	108	114					X																	47002143		2203	4300	6503	SO:0001630	splice_region_variant	54539	exon2			CTGGGTTCTGTGG	AF044213	CCDS14273.1, CCDS48100.1	Xp11.3	2011-07-04			ENSG00000147123	ENSG00000147123		"Mitochondrial respiratory chain complex / Complex I"	20372	protein-coding gene	gene with protein product	"complex I NP17.3 subunit"	300403				10544803, 12381726	Standard	NM_019056		Approved	ESSS, NP17.3, Np15	uc004dhc.3	Q9NX14	OTTHUMG00000021433	ENST00000377811.3:c.208-1A>C	X.37:g.47002143T>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	187	7	NM_019056	0	0	0	0	0	Q5JRR3|Q5JRR4|Q6IAB6|Q8WZ96|Q9BXX9	Missense_Mutation	SNP	ENST00000377811.3	37	CCDS48100.1	.	.	.	.	.	.	.	.	.	.	t	18.64	3.666621	0.67814	.	.	ENSG00000147123	ENST00000377811;ENST00000447793;ENST00000276062	.	.	.	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.68522	0.3010	M	0.76574	2.34	0.47407	D	0.999411	P;P	0.51933	0.948;0.949	P;P	0.57425	0.82;0.786	T	0.71948	-0.4438	9	0.72032	D	0.01	-20.6174	9.3073	0.37883	0.0:0.0:0.0:1.0	.	70;70	Q9NX14;Q9NX14-2	NDUBB_HUMAN;.	H	70;74;70	.	ENSP00000276062:N70H	N	-	1	0	NDUFB11	46887087	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	5.736000	0.68597	1.653000	0.50694	0.437000	0.28790	AAC	.		0.512	NDUFB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056382.1	NM_019056	Missense_Mutation	G	47002143	T	G	47002143	5	3	51	1	0	0	0	0	0	0	1	0	10306	1797	62	5	291	5	NDUFB11	23	47002143	Splice_Site	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3411198	47002143	108268417	281	4969											
GNL3L	54552	hgsc.bcm.edu	37	chrX	54578752	54578752	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagcttctatataccaccAccagccactcacactctgcc	11	9	3	18	0	4	0	2	0	2	0	4	0	4	0	5	0	4	1	5	0	3	4	rs201849856		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:54578752A>C	ENST00000336470.4	+	13	1348	c.1209A>C	c.(1207-1209)ccA>ccC	p.P403P	GNL3L_ENST00000360845.2_Silent_p.P403P	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	403					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						ATATACCACCACCAGCCACTC	0.502																																					p.P403P		.											.	GNL3L-131	0			c.A1209C						.						181	141	155					X																	54578752		2203	4300	6503	SO:0001819	synonymous_variant	54552	exon13			ACCACCACCAGCC	AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.1209A>C	X.37:g.54578752A>C		Somatic	145	2		WXS	Illumina HiSeq	Phase_I	558	198	NM_001184819	0	0	16	16	0		Silent	SNP	ENST00000336470.4	37	CCDS14360.1																																																																																			.		0.502	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067		C	54578752	A	C	54578752	2	2	51	1	0	0	0	0	0	0	0	1	6558	146	6	5		5	GNL3L	23	54578752	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	7576609	54578752	100691808	282	4970											
APEX2	27301	broad.mit.edu	37	chrX	55033524	55033525	+	Frame_Shift_Ins	INS	-	-	A																															gccctcccctagctgtccccINSaagcctctcctgacatagag																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:55033524_55033525insA	ENST00000374987.3	+	6	1279_1280	c.1213_1214insA	c.(1213-1215)caafs	p.Q405fs	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	405					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						TAGCTGTCCCCAAGCCTCTCCT	0.584								Other BER factors																													p.Q405fs													.	APEX2-659	0			c.1213_1214insA						.																																			SO:0001589	frameshift_variant	27301	exon6			TGTCCCCAAGCCT	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.1215dupA	X.37:g.55033526_55033526dupA	ENSP00000364126:p.Gln405fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	171	7	NM_014481	0	0	0	0	0	Q9Y5X7	Frame_Shift_Ins	INS	ENST00000374987.3	37	CCDS14365.1																																																																																			.		0.584	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			A	55033525	-	A	55033524	7	5	51	1	0	1	1	0	0	0	0	0	770	595	21	0	1235	0	APEX2	23	55033524	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	454772	55033524	100237036	283	4971											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412720	63412720	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacagctttctctgtggcTccagccacagatgtcttaca	8	11	8	14	0	2	1	0	0	2	1	4	1	3	1	3	1	3	2	3	1	1	2	rs200897699		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:63412720T>C	ENST00000330258.3	-	2	719	c.447A>G	c.(445-447)ggA>ggG	p.G149G	AMER1_ENST00000374869.3_Silent_p.G149G|AMER1_ENST00000403336.1_Silent_p.G149G	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	149					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TCTCTGTGGCTCCAGCCACAG	0.532																																					p.G149G		.											.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A447G						.						34	37	36					X																	63412720		2203	4297	6500	SO:0001819	synonymous_variant	139285	exon2			TGTGGCTCCAGCC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.447A>G	X.37:g.63412720T>C		Somatic	71	1		WXS	Illumina HiSeq	Phase_I	407	137	NM_152424	0	0	1	1	0	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			.		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		C	63412720	T	C	63412720	2	2	51	1	0	0	0	0	0	0	0	1	5439	1538	54	3		3	FAM123B	23	63412720	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8379196	63412720	91857840	284	4972											
NLGN3	54413	hgsc.bcm.edu	37	chrX	70387444	70387444	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcatgcccgctacggctcGcctacctacttctacgcctt	5	11	7	18	4	1	0	0	0	1	0	2	0	1	0	4	1	6	3	4	1	4	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:70387444G>C	ENST00000358741.3	+	7	1800	c.1497G>C	c.(1495-1497)tcG>tcC	p.S499S	NLGN3_ENST00000536169.1_Silent_p.S459S|NLGN3_ENST00000374051.3_Silent_p.S479S|NLGN3_ENST00000476589.1_3'UTR	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	499					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					GCTACGGCTCGCCTACCTACT	0.567																																					p.S499S	Esophageal Squamous(103;760 1488 16849 22250 40351)	.											.	NLGN3-131	0			c.G1497C						.						83	69	74					X																	70387444		2203	4300	6503	SO:0001819	synonymous_variant	54413	exon7			CGGCTCGCCTACC	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.1497G>C	X.37:g.70387444G>C		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	339	160	NM_181303	0	0	0	0	0	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Silent	SNP	ENST00000358741.3	37	CCDS55441.1																																																																																			.		0.567	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977		C	70387444	G	C	70387444	2	2	51	1	0	0	0	0	0	0	0	1	10489	1074	38	4		4	NLGN3	23	70387444	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	6974724	70387444	84883116	285	4973											
NOX1	27035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	100099033	100099033	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcaggctctttgccaaagTccgagggccacataagaaaa	13	6	11	11	2	1	1	0	0	1	1	2	2	2	1	3	2	1	2	3	2	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:100099033T>C	ENST00000372966.3	-	13	1808	c.1603A>G	c.(1603-1605)Act>Gct	p.T535A	NOX1_ENST00000217885.5_Missense_Mutation_p.T486A|NOX1_ENST00000372960.4_Missense_Mutation_p.T498A|NOX1_ENST00000372964.1_Intron	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	535	Interaction with NOXO1.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						TTTGCCAAAGTCCGAGGGCCA	0.433																																					p.T535A		.											.	NOX1-131	0			c.A1603G						.						65	51	55					X																	100099033		2202	4299	6501	SO:0001583	missense	27035	exon13			CCAAAGTCCGAGG	AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)", "NADPH oxidase homolog-1", "NADPH oxidase 1 variant NOH-1L"	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.1603A>G	X.37:g.100099033T>C	ENSP00000362057:p.Thr535Ala	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	34	13	NM_007052	0	0	0	0	0	A8K836|O95691|Q2PP02	Missense_Mutation	SNP	ENST00000372966.3	37	CCDS14474.1	.	.	.	.	.	.	.	.	.	.	t	0.927	-0.714078	0.03206	.	.	ENSG00000007952	ENST00000372966;ENST00000217885;ENST00000372960	D;T;D	0.94650	-3.48;0.09;-3.48	5.09	-0.337	0.12654	Ferric reductase, NAD binding (1);	0.458064	0.22296	N	0.061923	T	0.70456	0.3226	N	0.00277	-1.72	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.70938	-0.4736	10	0.02654	T	1	-0.2036	5.1658	0.15084	0.0:0.3874:0.3302:0.2825	.	498;486;535	A6NGA6;Q9Y5S8-3;Q9Y5S8	.;.;NOX1_HUMAN	A	535;486;498	ENSP00000362057:T535A;ENSP00000217885:T486A;ENSP00000362051:T498A	ENSP00000217885:T486A	T	-	1	0	NOX1	99985689	0.000000	0.05858	0.000000	0.03702	0.904000	0.53231	0.069000	0.14552	-0.326000	0.08564	0.483000	0.47432	ACT	.		0.433	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052		C	100099033	T	C	100099033	3	2	51	1	0	0	0	0	1	0	0	0	10582	1667	58	3	95	3	NOX1	23	100099033	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	29711589	100099033	55171527	286	4974											
RNF128	79589	broad.mit.edu	37	chrX	105970391	105970391	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggagcctgtggctggggTcctggtaccgcccgacgggc	3	7	18	13	3	0	0	0	0	0	0	1	2	1	1	4	6	2	3	4	6	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:105970391T>G	ENST00000255499.2	+	1	498	c.248T>G	c.(247-249)gTc>gGc	p.V83G	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	83	PA.				negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						GTGGCTGGGGTCCTGGTACCG	0.672																																					p.V83G													.	RNF128-227	0			c.T248G						.						15	14	14					X																	105970391		2176	4243	6419	SO:0001583	missense	79589	exon1			CTGGGGTCCTGGT	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.248T>G	X.37:g.105970391T>G	ENSP00000255499:p.Val83Gly	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	116	42	NM_194463	0	0	19	28	9	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Missense_Mutation	SNP	ENST00000255499.2	37	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.501839	0.64298	.	.	ENSG00000133135	ENST00000255499	T	0.13778	2.56	4.53	3.36	0.38483	.	0.583687	0.17419	N	0.174901	T	0.24890	0.0604	M	0.67700	2.07	0.47037	D	0.999294	P	0.52061	0.95	P	0.55303	0.773	T	0.00844	-1.1543	10	0.48119	T	0.1	.	7.2331	0.26053	0.0:0.1061:0.0:0.8939	.	83	Q8TEB7	RN128_HUMAN	G	83	ENSP00000255499:V83G	ENSP00000255499:V83G	V	+	2	0	RNF128	105857047	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	1.620000	0.36976	0.553000	0.29044	-0.438000	0.05819	GTC	.		0.672	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		G	105970391	T	G	105970391	3	3	51	1	0	0	0	0	1	0	0	0	13468	1667	58	5	660	5	RNF128	23	105970391	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	5871358	105970391	49300169	287	4975											
NXT2	55916	bcgsc.ca	37	chrX	108779193	108779193	+	5'Flank	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actattatgaggggccacacAccagccactcaaggtaaaac	15	6	8	12	0	1	1	1	1	0	0	1	1	1	1	3	3	2	1	3	3	5	3	rs201184200		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:108779193A>C	ENST00000372106.1	+	0	0				NXT2_ENST00000218004.1_Missense_Mutation_p.T28P|NXT2_ENST00000372107.1_5'Flank|NXT2_ENST00000372103.1_5'Flank	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2						mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						GGGGCCACACACCAGCCACTC	0.413																																					p.T28P													.	NXT2-109	0			c.A82C						.						45	42	43					X																	108779193		2203	4300	6503	SO:0001631	upstream_gene_variant	55916	exon1			CCACACACCAGCC	AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185		X.37:g.108779193A>C	Exception_encountered	Somatic	26	2		WXS	Illumina HiSeq	Phase_1	33	24	NM_018698	0	0	0	0	0	D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Missense_Mutation	SNP	ENST00000372106.1	37	CCDS56605.1	.	.	.	.	.	.	.	.	.	.	A	6.093	0.385362	0.11524	.	.	ENSG00000101888	ENST00000218004	.	.	.	4.23	-4.18	0.03846	.	3.130020	0.01274	N	0.009521	T	0.24928	0.0605	.	.	.	0.09310	N	1	P	0.39624	0.681	B	0.38755	0.281	T	0.12785	-1.0534	8	0.48119	T	0.1	.	2.0266	0.03520	0.2841:0.1585:0.4006:0.1568	.	28	Q9NPJ8-3	.	P	28	.	ENSP00000218004:T28P	T	+	1	0	NXT2	108665849	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.474000	0.06607	-1.039000	0.03275	-0.553000	0.04205	ACC	.		0.413	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057886.1	NM_018698		C	108779193	A	C	108779193	1	2	51	0	1	0	0	0	0	0	0	0	10821	159	6	5		5	NXT2	23	108779193	5'Flank	SNP	A	TCGA-B9-4117-01A-01D-1252-08	2808802	108779193	46491367	288	4976											
DOCK11	139818	bcgsc.ca	37	chrX	117761500	117761500	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttccatgtggctttactTcacctgccaatagagggagt	9	13	10	9	0	1	1	1	0	0	1	2	2	2	2	3	2	2	2	3	2	3	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:117761500T>C	ENST00000276202.7	+	33	3685	c.3622T>C	c.(3622-3624)Tca>Cca	p.S1208P	DOCK11_ENST00000276204.6_Missense_Mutation_p.S1208P	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1208					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						TGGCTTTACTTCACCTGCCAA	0.393																																					p.S1208P													.	DOCK11-93	0			c.T3622C						.						124	123	123					X																	117761500		2203	4300	6503	SO:0001583	missense	139818	exon33			TTTACTTCACCTG	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.3622T>C	X.37:g.117761500T>C	ENSP00000276202:p.Ser1208Pro	Somatic	139	0		WXS	Illumina HiSeq	Phase_1	69	22	NM_144658	0	0	23	23	0	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.507611	0.44558	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.18657	2.2;2.2	5.67	5.67	0.87782	.	1.404080	0.04119	N	0.316040	T	0.30324	0.0761	L	0.59436	1.845	0.49299	D	0.999775	B;B	0.24533	0.105;0.0	B;B	0.22601	0.04;0.001	T	0.05920	-1.0856	10	0.36615	T	0.2	-0.8924	15.0248	0.71659	0.0:0.0:0.0:1.0	.	1208;1208	A6NIW2;Q5JSL3	.;DOC11_HUMAN	P	1208	ENSP00000276204:S1208P;ENSP00000276202:S1208P	ENSP00000276202:S1208P	S	+	1	0	DOCK11	117645528	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.126000	0.64721	1.999000	0.58509	0.481000	0.45027	TCA	.		0.393	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		C	117761500	T	C	117761500	3	2	51	1	0	0	0	0	1	0	0	0	4697	1783	62	3	3752	3	DOCK11	23	117761500	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8982307	117761500	37509060	289	4977											
UTP14A	10813	broad.mit.edu	37	chrX	129045830	129045831	+	Frame_Shift_Ins	INS	-	-	G																															aaccggcaggcagagcagctINSggtttttcccctggagaaag																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:129045830_129045831insG	ENST00000394422.3	+	6	498_499	c.470_471insG	c.(469-474)ctggttfs	p.V158fs	UTP14A_ENST00000371042.3_5'Flank|UTP14A_ENST00000371051.5_Frame_Shift_Ins_p.V104fs|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000425117.2_Intron	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	158					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						GCAGAGCAGCTGGTTTTTCCCC	0.5																																					p.L157fs													.	UTP14A-132	0			c.470_471insG						.																																			SO:0001589	frameshift_variant	10813	exon6			AGCAGCTGGTTTT	AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"serologically defined colon cancer antigen 16"	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.472dupG	X.37:g.129045832_129045832dupG	ENSP00000377944:p.Val158fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	315	9	NM_006649	0	0	0	0	0	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Frame_Shift_Ins	INS	ENST00000394422.3	37	CCDS14615.1																																																																																			.		0.5	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		G	129045831	-	G	129045830	7	5	51	1	0	1	1	0	0	0	0	0	17128	1580	55	0	492	0	UTP14A	23	129045830	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	11284330	129045830	26224730	290	4978											
BCORL1	63035	broad.mit.edu	37	chrX	129146953	129146954	+	Frame_Shift_Ins	INS	-	-	G																															cacggcagttggaagtggcaINSgcaatgcccggggggcagac																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:129146953_129146954insG	ENST00000218147.7	+	4	402_403	c.205_206insG	c.(205-207)agcfs	p.S69fs	BCORL1_ENST00000359304.2_Frame_Shift_Ins_p.S69fs|BCORL1_ENST00000303743.5_Frame_Shift_Ins_p.S69fs|BCORL1_ENST00000540052.1_Frame_Shift_Ins_p.S69fs			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	69					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						TGGAAGTGGCAGCAATGCCCGG	0.574																																					p.S69fs													.	BCORL1-294	0			c.205_206insG						.			70,3624		0,55,15,1529,511						4.1	1			70	78,6349		0,54,24,2296,1703	no	frameshift	BCORL1	NM_021946.4		0,109,39,3825,2214	A1A1,A1R,A1,RR,R		1.2136,1.895,1.4623				148,9973				SO:0001589	frameshift_variant	63035	exon3			AGTGGCAGCAATG	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.206dupG	X.37:g.129146954_129146954dupG	ENSP00000218147:p.Ser69fs	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	765	9	NM_021946	0	0	0	0	0	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Frame_Shift_Ins	INS	ENST00000218147.7	37	CCDS14616.1																																																																																			.		0.574	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		G	129146954	-	G	129146953	7	5	51	1	0	1	1	0	0	0	0	0	1388	188	7	0	215	0	BCORL1	23	129146953	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	101123	129146953	26123607	291	4979											
AIFM1	9131	bcgsc.ca	37	chrX	129270135	129270135	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattgggctccaggcccacaGctgccactatgtggtcagtt	7	10	11	13	0	1	0	1	0	0	0	2	0	2	0	3	3	2	3	3	3	1	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:129270135G>C	ENST00000287295.3	-	12	1420	c.1190C>G	c.(1189-1191)gCt>gGt	p.A397G	AIFM1_ENST00000319908.3_Missense_Mutation_p.A393G|AIFM1_ENST00000460436.2_Missense_Mutation_p.A58G|AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000440263.1_Missense_Mutation_p.A45G|AIFM1_ENST00000346424.2_Missense_Mutation_p.A110G	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	397	FAD-dependent oxidoreductase. {ECO:0000250}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	CAGGCCCACAGCTGCCACTAT	0.483																																					p.A397G													.	AIFM1-586	0			c.C1190G						.						46	42	43					X																	129270135		2203	4300	6503	SO:0001583	missense	9131	exon12			CCCACAGCTGCCA	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"programmed cell death 8 (apoptosis-inducing factor)", "neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.1190C>G	X.37:g.129270135G>C	ENSP00000287295:p.Ala397Gly	Somatic	87	1		WXS	Illumina HiSeq	Phase_1	71	45	NM_004208	0	0	17	17	0	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Missense_Mutation	SNP	ENST00000287295.3	37	CCDS14618.1	.	.	.	.	.	.	.	.	.	.	G	35	5.524927	0.96431	.	.	ENSG00000156709	ENST00000460436;ENST00000346424;ENST00000319908;ENST00000440263;ENST00000287295	T;T;D;T;D	0.88046	0.92;0.93;-2.33;0.96;-2.33	6.01	6.01	0.97437	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.88789	0.6532	L	0.46885	1.475	0.80722	D	1	P;D;P	0.60575	0.876;0.988;0.898	P;P;P	0.56434	0.575;0.779;0.798	D	0.84579	0.0660	10	0.09084	T	0.74	-13.2159	19.3824	0.94542	0.0:0.0:1.0:0.0	.	110;393;397	O95831-2;O95831-3;O95831	.;.;AIFM1_HUMAN	G	58;110;393;45;397	ENSP00000431222:A58G;ENSP00000316320:A110G;ENSP00000315122:A393G;ENSP00000405879:A45G;ENSP00000287295:A397G	ENSP00000287295:A397G	A	-	2	0	AIFM1	129097816	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.620000	0.83070	2.531000	0.85337	0.600000	0.82982	GCT	.		0.483	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2			C	129270135	G	C	129270135	3	2	51	1	0	0	0	0	1	0	0	0	426	971	34	4	671	4	AIFM1	23	129270135	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	123182	129270135	26000425	292	4980											
FRMD7	90167	bcgsc.ca	37	chrX	131219749	131219749	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgtcagattcagctgggcTcctgccactgaaaggggaaa	12	8	12	9	0	2	2	2	1	0	1	3	3	3	3	2	3	2	2	2	3	3	1	rs201803600		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:131219749T>C	ENST00000298542.4	-	7	680	c.505A>G	c.(505-507)Agc>Ggc	p.S169G	FRMD7_ENST00000370879.1_Missense_Mutation_p.S49G|FRMD7_ENST00000464296.1_Missense_Mutation_p.S154G	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	169	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					TCAGCTGGGCTCCTGCCACTG	0.493																																					p.S169G													.	FRMD7-228	0			c.A505G						.						71	61	64					X																	131219749		2203	4300	6503	SO:0001583	missense	90167	exon7			CTGGGCTCCTGCC	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"nystagmus 1, congenital"	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.505A>G	X.37:g.131219749T>C	ENSP00000298542:p.Ser169Gly	Somatic	80	0		WXS	Illumina HiSeq	Phase_1	35	19	NM_194277	0	0	0	0	0	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629900	0.67015	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	T;T;T	0.81415	-0.81;-1.49;-1.49	5.71	5.71	0.89125	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.202977	0.51477	D	0.000093	D	0.88104	0.6347	M	0.85542	2.76	0.54753	D	0.999983	P;D	0.64830	0.86;0.994	P;P	0.60949	0.453;0.881	D	0.89393	0.3690	10	0.87932	D	0	.	9.0861	0.36581	0.2791:0.0:0.0:0.7209	.	154;169	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	G	49;169;154	ENSP00000359916:S49G;ENSP00000298542:S169G;ENSP00000417996:S154G	ENSP00000298542:S169G	S	-	1	0	FRMD7	131047430	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.195000	0.51013	1.920000	0.55613	0.486000	0.48141	AGC	.		0.493	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		C	131219749	T	C	131219749	3	2	51	1	0	0	0	0	1	0	0	0	6074	1551	54	3	1663	3	FRMD7	23	131219749	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	1949614	131219749	24050811	293	4981											
GPC4	2239	bcgsc.ca	37	chrX	132437060	132437060	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagggcactgctgatactcAcagccacttccacttccttc	9	10	7	15	0	1	1	1	1	0	0	4	2	3	1	3	1	3	2	3	1	2	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:132437060A>C	ENST00000370828.3	-	9	2030	c.1506T>G	c.(1504-1506)tgT>tgG	p.C502W	GPC4_ENST00000535467.1_Missense_Mutation_p.C432W	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	502					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GCTGATACTCACAGCCACTTC	0.453																																					p.C502W													.	GPC4-226	0			c.T1506G						.						218	192	201					X																	132437060		2203	4300	6503	SO:0001583	missense	2239	exon9			ATACTCACAGCCA	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"Proteoglycans / Cell Surface : Glypicans"	4452	protein-coding gene	gene with protein product	"glypican proteoglycan 4"	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1506T>G	X.37:g.132437060A>C	ENSP00000359864:p.Cys502Trp	Somatic	406	0		WXS	Illumina HiSeq	Phase_1	332	109	NM_001448	0	0	79	106	27	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	37	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	a	15.11	2.735606	0.49045	.	.	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.52057	0.68;0.68	5.42	3.02	0.34903	.	0.000000	0.85682	D	0.000000	T	0.66336	0.2779	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.64672	-0.6352	10	0.87932	D	0	-20.3119	7.2693	0.26248	0.7483:0.0:0.2517:0.0	.	502	O75487	GPC4_HUMAN	W	502;496;432	ENSP00000359864:C502W;ENSP00000444959:C432W	ENSP00000359864:C502W	C	-	3	2	GPC4	132264726	0.930000	0.31532	0.997000	0.53966	0.896000	0.52359	0.017000	0.13399	0.223000	0.20920	-0.365000	0.07479	TGT	.		0.453	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448		C	132437060	A	C	132437060	3	2	51	1	0	0	0	0	1	0	0	0	6620	157	6	5	168	5	GPC4	23	132437060	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	1217311	132437060	22833500	294	4982											
SAGE1	55511	bcgsc.ca	37	chrX	134990742	134990742	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcttattaatatggcaggAgctagtattccagcaatgag	12	11	12	6	0	0	1	0	1	0	0	1	2	1	2	1	3	2	5	1	3	6	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:134990742A>G	ENST00000370709.3	+	11	1407	c.1407A>G	c.(1405-1407)ggA>ggG	p.G469G	SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000324447.3_Silent_p.G469G|SAGE1_ENST00000535938.1_Silent_p.G469G			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	469						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					ATATGGCAGGAGCTAGTATTC	0.423																																					p.G469G													.	SAGE1-133	0			c.A1407G						.						157	153	154					X																	134990742		2203	4300	6503	SO:0001819	synonymous_variant	55511	exon12			GGCAGGAGCTAGT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"cancer/testis antigen 14"	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1407A>G	X.37:g.134990742A>G		Somatic	196	2		WXS	Illumina HiSeq	Phase_1	86	33	NM_018666	0	0	0	0	0	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			.		0.423	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666		G	134990742	A	G	134990742	2	3	51	1	0	0	0	0	0	0	0	1	13841	291	11	3		3	SAGE1	23	134990742	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	2553682	134990742	20279818	295	4983											
CNGA2	1260	hgsc.bcm.edu	37	chrX	150906986	150906986	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccaatggtgtgaagagcTccccagccaataatcacaac	16	6	7	12	0	1	2	1	1	0	1	2	2	2	2	4	1	4	1	4	1	6	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:150906986T>C	ENST00000329903.4	+	1	64	c.31T>C	c.(31-33)Tcc>Ccc	p.S11P		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	11					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					TGTGAAGAGCTCCCCAGCCAA	0.517																																					p.S11P		.											.	CNGA2-193	0			c.T31C						.						208	153	171					X																	150906986		2203	4300	6503	SO:0001583	missense	1260	exon2			AAGAGCTCCCCAG	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.31T>C	X.37:g.150906986T>C	ENSP00000328478:p.Ser11Pro	Somatic	171	1		WXS	Illumina HiSeq	Phase_I	613	160	NM_005140	0	0	0	0	0	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.356630	0.41801	.	.	ENSG00000183862	ENST00000329903	D	0.97870	-4.58	4.85	4.85	0.62838	.	0.438060	0.23624	N	0.046217	D	0.95714	0.8606	N	0.08118	0	0.29499	N	0.855084	D	0.54601	0.967	D	0.63033	0.91	D	0.91985	0.5598	10	0.52906	T	0.07	.	9.6231	0.39734	0.0:0.0:0.0:1.0	.	11	Q16280	CNGA2_HUMAN	P	11	ENSP00000328478:S11P	ENSP00000328478:S11P	S	+	1	0	CNGA2	150657642	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	2.734000	0.47368	1.794000	0.52575	0.486000	0.48141	TCC	.		0.517	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		C	150906986	T	C	150906986	3	2	51	1	0	0	0	0	1	0	0	0	3603	1551	54	3	33	3	CNGA2	23	150906986	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	15916244	150906986	4363574	296	4984											
PLXNA3	55558	broad.mit.edu	37	chrX	153688565	153688565	+	Frame_Shift_Del	DEL	G	G	-																															ctgctgctcttccttgccgtGgggggggccctgggcaacag																								rs375310385		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:153688565delG	ENST00000369682.3	+	2	217	c.42delG	c.(40-42)gtgfs	p.V14fs		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	14					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)	p.A17fs*39(1)		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)					TCCTTGCCGTGGGGGGGGCCC	0.682																																					p.V14fs													.	PLXNA3-132	1	Insertion - Frameshift(1)	ovary(1)	c.42delG						.			47,59,3613		1,0,29,16,2,35,20,1525,499	34	32	33			0.6	0	X		33	69,109,6290		1,0,27,40,3,50,53,2275,1663	no	codingComplex	PLXNA3	NM_017514.3		2,0,56,56,5,85,73,3800,2162	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		2.752,2.8502,2.7879			153688565	116,168,9903	2202	4292	6494	SO:0001589	frameshift_variant	55558	exon2			TGCCGTGGGGGGG	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.42delG	X.37:g.153688565delG	ENSP00000358696:p.Val14fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	408	7	NM_017514	0	0	0	0	0	Q5HY36	Frame_Shift_Del	DEL	ENST00000369682.3	37	CCDS14752.1																																																																																			.		0.682	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		-	153688565	G	-	153688565	7	5	51	1	0	1	0	1	0	0	0	0	12147	1335	47	0	44	0	PLXNA3	23	153688565	Frame_Shift_Del	DEL	G	TCGA-B9-4117-01A-01D-1252-08	2781579	153688565	1581995	297	4985											
F8	2157	bcgsc.ca	37	chrX	154124444	154124444	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagagatgtagaggctggAgaacttctgacgggcaccct	10	8	14	9	1	1	5	0	2	1	3	1	7	1	5	1	3	1	3	1	3	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:154124444A>G	ENST00000360256.4	-	22	6537	c.6337T>C	c.(6337-6339)Tcc>Ccc	p.S2113P		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	2113	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TAGAGGCTGGAGAACTTCTGA	0.403																																					p.S2113P													.	F8-182	0			c.T6337C						.						158	152	154					X																	154124444		2203	4300	6503	SO:0001583	missense	2157	exon22			GGCTGGAGAACTT	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.6337T>C	X.37:g.154124444A>G	ENSP00000353393:p.Ser2113Pro	Somatic	256	1		WXS	Illumina HiSeq	Phase_1	158	48	NM_000132	0	0	1	1	0	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	a	19.08	3.757309	0.69648	.	.	ENSG00000185010	ENST00000360256	D	0.98296	-4.85	5.56	4.32	0.51571	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.265891	0.42548	D	0.000681	D	0.98226	0.9413	M	0.73598	2.24	0.38720	D	0.953421	D	0.76494	0.999	D	0.71414	0.973	D	0.98824	1.0748	10	0.72032	D	0.01	-5.8601	4.594	0.12320	0.7353:0.0:0.0915:0.1732	.	2113	P00451	FA8_HUMAN	P	2113	ENSP00000353393:S2113P	ENSP00000353393:S2113P	S	-	1	0	F8	153777638	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	3.782000	0.55401	1.850000	0.53721	0.486000	0.48141	TCC	.		0.403	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			G	154124444	A	G	154124444	3	3	51	1	0	0	0	0	1	0	0	0	5363	304	11	3	766	3	F8	23	154124444	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	435879	154124444	1146116	298	4986											
TMEM82	388595	hgsc.bcm.edu	37	chr1	16070782	16070782	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcacgctgaacctgctgcTgagcctcgggctggccacgc	5	6	13	17	4	0	2	0	2	0	0	1	2	0	2	4	2	4	5	4	2	1	0	rs374481924		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:16070782T>G	ENST00000375782.1	+	4	602	c.464T>G	c.(463-465)cTg>cGg	p.L155R	TMEM82_ENST00000465575.1_3'UTR|RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	155	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AACCTGCTGCTGAGCCTCGGG	0.706																																					p.L155R		.											.	TMEM82-90	0			c.T464G						.	T	ARG/LEU	0,4300		0,0,2150	8	8	8		464	5.3	1	1		8	1,8421		0,1,4210	no	missense	TMEM82	NM_001013641.1	102	0,1,6360	GG,GT,TT		0.0119,0.0,0.0079	probably-damaging	155/344	16070782	1,12721	2150	4211	6361	SO:0001583	missense	388595	exon4			TGCTGCTGAGCCT		CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460			32350	protein-coding gene	gene with protein product							Standard	NM_001013641		Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.464T>G	1.37:g.16070782T>G	ENSP00000364938:p.Leu155Arg	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	5	3	NM_001013641	0	0	20	34	14	B2RP27|Q5VVD4	Missense_Mutation	SNP	ENST00000375782.1	37	CCDS30608.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.700784	0.88924	0.0	1.19E-4	ENSG00000162460	ENST00000375782	T	0.60424	0.19	5.33	5.33	0.75918	.	0.077205	0.53938	D	0.000060	T	0.75796	0.3898	M	0.76328	2.33	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.79359	-0.1836	10	0.87932	D	0	-12.7185	15.2878	0.73843	0.0:0.0:0.0:1.0	.	155	A0PJX8	TMM82_HUMAN	R	155	ENSP00000364938:L155R	ENSP00000364938:L155R	L	+	2	0	TMEM82	15943369	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.610000	0.82949	2.014000	0.59158	0.533000	0.62120	CTG	.		0.706	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641		G	16070782	T	G	16070782	3	3	52	1	0	0	0	0	1	0	0	0	16238	1580	55	5	478	5	TMEM82	1	16070782	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08		16070782	233179839	1	4987											
ARHGEF19	128272	broad.mit.edu;ucsc.edu	37	chr1	16532837	16532837	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatcagctcaaacttggccTgagggagggcacacacgggg	10	6	15	10	1	2	2	2	2	0	0	2	3	2	3	1	5	2	2	1	5	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:16532837T>G	ENST00000270747.3	-	7	1274		c.e7-2		ARHGEF19_ENST00000478117.1_Splice_Site	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19						regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		AAACTTGGCCTGAGGGAGGGC	0.647																																					.													.	ARHGEF19-229	0			c.1138-2A>C						.						34	30	31					1																	16532837		2200	4289	6489	SO:0001630	splice_region_variant	128272	exon8			TTGGCCTGAGGGA	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"Rho guanine nucleotide exchange factors"	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.1138-2A>C	1.37:g.16532837T>G		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	7	3	NM_153213	0	0	1	5	4	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Splice_Site	SNP	ENST00000270747.3	37	CCDS170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.98|16.98	3.271016|3.271016	0.59540|0.59540	.|.	.|.	ENSG00000142632|ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607|ENST00000441785	.|T	.|0.17370	.|2.28	4.85|4.85	4.85|4.85	0.62838|0.62838	.|.	.|.	.|.	.|.	.|.	.|T	.|0.27419	.|0.0673	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.01298	.|-1.1392	.|5	.|.	.|.	.|.	.|.	12.4596|12.4596	0.55725|0.55725	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	.|P	-1|62	.|ENSP00000414370:Q62P	.|.	.|Q	-|-	.|2	.|0	ARHGEF19|ARHGEF19	16405424|16405424	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.716000|0.716000	0.41182|0.41182	7.267000|7.267000	0.78462|0.78462	1.845000|1.845000	0.53610|0.53610	0.454000|0.454000	0.30748|0.30748	.|CAG	.		0.647	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	Intron	G	16532837	T	G	16532837	5	3	52	1	0	0	0	0	0	0	1	0	902	1594	55	5	1312	5	ARHGEF19	1	16532837	Splice_Site	SNP	T	TCGA-B9-5156-01A-01D-1589-08	462055	16532837	232717784	2	4988											
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19166252	19166252	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaggtccacgatggtgacCagcaccccgctgtaggcaga	11	5	13	12	2	0	3	0	1	0	2	1	4	1	3	4	3	1	4	4	3	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:19166252C>G	ENST00000375371.3	-	6	2382	c.2361G>C	c.(2359-2361)ctG>ctC	p.L787L		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	787					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CGATGGTGACCAGCACCCCGC	0.567																																					p.L787L		.											.	TAS1R2-93	0			c.G2361C						.						125	94	105					1																	19166252		2203	4300	6503	SO:0001819	synonymous_variant	80834	exon6			GGTGACCAGCACC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.2361G>C	1.37:g.19166252C>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	37	16	NM_152232	0	0	0	0	0	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			.		0.567	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			G	19166252	C	G	19166252	2	3	52	1	0	0	0	0	0	0	0	1	15595	581	21	4		4	TAS1R2	1	19166252	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08	2633415	19166252	230084369	3	4989											
EIF2C1	26523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36354062	36354062	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgccccccctgcagcaggtGttccaggcacctcgccggcc	4	6	11	20	2	0	0	0	0	0	0	2	0	1	0	7	3	3	4	7	3	0	1	rs79428335		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:36354062G>A	ENST00000373204.4	+	2	273	c.60G>A	c.(58-60)gtG>gtA	p.V20V	AGO1_ENST00000373206.1_5'UTR	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	20					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										TGCAGCAGGTGTTCCAGGCAC	0.562																																					p.V20V		.											.	.	0			c.G60A						.						73	70	71					1																	36354062		2203	4300	6503	SO:0001819	synonymous_variant	26523	exon2			GCAGGTGTTCCAG	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"Argonaute/PIWI family"	3262	protein-coding gene	gene with protein product	"argonaute 1"	606228	"eukaryotic translation initiation factor 2C, 1"	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.60G>A	1.37:g.36354062G>A		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	107	30	NM_012199	0	0	8	13	5	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																			.		0.562	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			A	36354062	G	A	36354062	2	1	52	1	0	0	0	0	0	0	0	1	5016	1364	48	2		2	EIF2C1	1	36354062	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	17187810	36354062	212896559	4	4990											
UROD	7389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45478626	45478626	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgacacattcctgcgagcagCctggggagaggaaacagact	12	6	13	10	1	0	3	0	1	0	2	1	6	1	4	2	3	4	1	2	3	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:45478626C>T	ENST00000246337.4	+	2	187	c.68C>T	c.(67-69)gCc>gTc	p.A23V	HECTD3_ENST00000372172.4_5'Flank|UROD_ENST00000494399.1_3'UTR	NM_000374.4	NP_000365.3	P06132	DCUP_HUMAN	uroporphyrinogen decarboxylase	23					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	uroporphyrinogen decarboxylase activity (GO:0004853)			endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					CTGCGAGCAGCCTGGGGAGAG	0.557									Porphyria Cutanea Tarda, Type II																												p.A23V		.											.	UROD-90	0			c.C68T						.						56	50	52					1																	45478626		2203	4300	6503	SO:0001583	missense	7389	exon2	Familial Cancer Database	PCT-II	GAGCAGCCTGGGG	BC001778	CCDS518.1	1p34	2012-10-02			ENSG00000126088	ENSG00000126088	4.1.1.37		12591	protein-coding gene	gene with protein product		613521				3015909, 3460962	Standard	NM_000374		Approved		uc001cna.2	P06132	OTTHUMG00000008949	ENST00000246337.4:c.68C>T	1.37:g.45478626C>T	ENSP00000246337:p.Ala23Val	Somatic	66	1		WXS	Illumina HiSeq	Phase_I	61	17	NM_000374	0	0	44	81	37	A8K762|Q16863|Q16883|Q53YB8|Q53ZP6|Q6IB28|Q9BUZ0	Missense_Mutation	SNP	ENST00000246337.4	37	CCDS518.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.921742	0.92319	.	.	ENSG00000126088	ENST00000246337;ENST00000434478;ENST00000372135;ENST00000372139	D;D	0.94497	-3.44;-3.37	6.07	6.07	0.98685	Uroporphyrinogen decarboxylase (URO-D) (1);	0.000000	0.85682	D	0.000000	D	0.97380	0.9143	M	0.79805	2.47	0.80722	D	1	D;D	0.76494	0.999;0.993	D;P	0.68765	0.96;0.565	D	0.97184	0.9853	10	0.72032	D	0.01	-17.4135	20.6439	0.99570	0.0:1.0:0.0:0.0	.	23;23	B4DHV6;P06132	.;DCUP_HUMAN	V	23;23;23;16	ENSP00000246337:A23V;ENSP00000404489:A23V	ENSP00000246337:A23V	A	+	2	0	UROD	45251213	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.679000	0.84048	2.884000	0.98904	0.655000	0.94253	GCC	.		0.557	UROD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024803.1	NM_000374		T	45478626	C	T	45478626	3	4	52	1	0	0	0	0	1	0	0	0	17062	739	26	2	74	2	UROD	1	45478626	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	9124564	45478626	203771995	5	4991											
PDE4DIP	9659	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	144915498	144915498	+	Frame_Shift_Del	DEL	T	T	-																															aagcaggccttgaatctccaTttcatgttccagcacttgtt																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:144915498delT	ENST00000369354.3	-	14	2116	c.1927delA	c.(1927-1929)atgfs	p.M643fs	PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.M643fs|PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.M709fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.M643fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.M780fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.M806fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.M643fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.M430fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.M806fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.M780fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	643				M -> V (in Ref. 4; CAD91152). {ECO:0000305}.	cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGAATCTCCATTTCATGTTCC	0.468			T	PDGFRB	MPD																																p.M806fs		.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP-663	0			c.2416delA						.						319	290	300					1																	144915498		2203	4296	6499	SO:0001589	frameshift_variant	9659	exon10			.	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1927delA	1.37:g.144915498delT	ENSP00000358360:p.Met643fs	Somatic	452	0		WXS	Illumina HiSeq	Phase_I	447	85	NM_001002811	0	0	0	0	0	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			.		0.468	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		-	144915498	T	-	144915498	7	5	52	1	0	1	0	1	0	0	0	0	11669	1493	52	0	5247	0	PDE4DIP	1	144915498	Frame_Shift_Del	DEL	T	TCGA-B9-5156-01A-01D-1589-08	99436872	144915498	104335123	6	4992											
PDZK1	5174	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	145752477	145752477	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacctcaaggtgtggctatGagagctggagttctggctga	9	10	14	8	0	2	2	1	2	1	1	2	4	2	3	1	4	1	4	1	4	2	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:145752477G>T	ENST00000344770.2	+	4	583	c.510G>T	c.(508-510)atG>atT	p.M170I	PDZK1_ENST00000451928.2_Intron|PDZK1_ENST00000417171.1_Missense_Mutation_p.M170I	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	170	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			GTGTGGCTATGAGAGCTGGAG	0.473																																					p.M170I		.											.	PDZK1-90	0			c.G510T						.						91	74	80					1																	145752477		2202	4299	6501	SO:0001583	missense	5174	exon5			GGCTATGAGAGCT	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.510G>T	1.37:g.145752477G>T	ENSP00000342143:p.Met170Ile	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	158	41	NM_002614	0	0	255	436	181	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Missense_Mutation	SNP	ENST00000344770.2	37	CCDS924.1	.	.	.	.	.	.	.	.	.	.	G	6.882	0.532176	0.13127	.	.	ENSG00000174827	ENST00000443667;ENST00000417171;ENST00000344770	T;T;T	0.26518	1.73;1.73;1.73	5.31	4.33	0.51752	PDZ/DHR/GLGF (4);	0.808792	0.11445	N	0.563343	T	0.08492	0.0211	N	0.12961	0.28	0.80722	D	1	B	0.26672	0.156	B	0.33960	0.173	T	0.13872	-1.0493	10	0.66056	D	0.02	-4.121	6.0081	0.19557	0.1032:0.195:0.7018:0.0	.	170	Q5T2W1	NHRF3_HUMAN	I	170	ENSP00000409291:M170I;ENSP00000394485:M170I;ENSP00000342143:M170I	ENSP00000342143:M170I	M	+	3	0	PDZK1	144463834	1.000000	0.71417	1.000000	0.80357	0.045000	0.14185	0.963000	0.29293	2.767000	0.95098	0.591000	0.81541	ATG	.		0.473	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		T	145752477	G	T	145752477	3	4	52	1	0	0	0	0	1	0	0	0	11733	1290	45	4	520	4	PDZK1	1	145752477	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	836979	145752477	103498144	7	4993											
RPRD2	23248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150390094	150390094	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatatccccaccgtttgaaTctcttttaccttgccaatga	9	14	5	13	1	1	2	0	2	1	0	3	2	2	2	5	0	2	2	5	0	4	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:150390094T>C	ENST00000369068.4	+	2	232	c.228T>C	c.(226-228)aaT>aaC	p.N76N	RPRD2_ENST00000401000.4_Silent_p.N76N|RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000539519.1_Silent_p.N76N|RPRD2_ENST00000369067.3_Silent_p.N76N	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	76	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ACCGTTTGAATCTCTTTTACC	0.363																																					p.N76N		.											.	RPRD2-23	0			c.T228C						.						231	217	221					1																	150390094		1865	4102	5967	SO:0001819	synonymous_variant	23248	exon2			TTTGAATCTCTTT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.228T>C	1.37:g.150390094T>C		Somatic	298	0		WXS	Illumina HiSeq	Phase_I	284	97	NM_015203	0	0	17	44	27	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Silent	SNP	ENST00000369068.4	37	CCDS44216.1																																																																																			.		0.363	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150390094	T	C	150390094	2	2	52	1	0	0	0	0	0	0	0	1	13649	1432	50	3		3	RPRD2	1	150390094	Silent	SNP	T	TCGA-B9-5156-01A-01D-1589-08	4637617	150390094	98860527	8	4994											
POGZ	23126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151395875	151395875	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagagtttccaaacttactaGtagattcatagggactatga	15	12	8	6	0	1	3	1	1	0	2	2	4	2	4	1	1	2	2	1	1	7	7			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:151395875G>T	ENST00000271715.2	-	10	1990	c.1676C>A	c.(1675-1677)aCt>aAt	p.T559N	POGZ_ENST00000531094.1_Missense_Mutation_p.T497N|POGZ_ENST00000392723.1_Missense_Mutation_p.T506N|POGZ_ENST00000368863.2_Missense_Mutation_p.T464N|POGZ_ENST00000409503.1_Missense_Mutation_p.T550N|POGZ_ENST00000361398.3_Missense_Mutation_p.T506N|POGZ_ENST00000491586.1_Missense_Mutation_p.T506N|POGZ_ENST00000540984.1_5'UTR	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	559					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AAACTTACTAGTAGATTCATA	0.443																																					p.T559N		.											.	POGZ-93	0			c.C1676A						.						104	95	98					1																	151395875		2203	4300	6503	SO:0001583	missense	23126	exon10			TTACTAGTAGATT	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.1676C>A	1.37:g.151395875G>T	ENSP00000271715:p.Thr559Asn	Somatic	108	1		WXS	Illumina HiSeq	Phase_I	82	35	NM_015100	0	0	0	0	0	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988053	0.93106	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000491586;ENST00000529669	T;T;T;T;T;T;T;T	0.15372	5.84;5.87;5.84;5.83;5.85;5.85;5.33;2.43	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000003	T	0.26085	0.0636	L	0.39898	1.24	0.80722	D	1	D;D;D;D;D;D	0.67145	0.993;0.963;0.996;0.996;0.996;0.993	P;P;P;D;D;P	0.77557	0.787;0.55;0.895;0.99;0.99;0.787	T	0.00708	-1.1600	10	0.54805	T	0.06	-15.1724	17.7138	0.88330	0.0:0.0:1.0:0.0	.	497;550;464;506;506;559	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	N	506;559;506;464;550;497;506;8	ENSP00000376484:T506N;ENSP00000271715:T559N;ENSP00000354467:T506N;ENSP00000357856:T464N;ENSP00000386836:T550N;ENSP00000431259:T497N;ENSP00000418408:T506N;ENSP00000432295:T8N	ENSP00000271715:T559N	T	-	2	0	POGZ	149662499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.361000	0.79497	2.763000	0.94921	0.563000	0.77884	ACT	.		0.443	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		T	151395875	G	T	151395875	3	4	52	1	0	0	0	0	1	0	0	0	12212	1029	36	4	2596	4	POGZ	1	151395875	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	1005781	151395875	97854746	9	4995											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173545857	173545857	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaatctaaattcagtcctAcagcggctaaggcaagagtg	15	8	10	8	1	2	2	1	0	1	2	3	2	3	2	1	2	2	2	1	2	7	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:173545857A>G	ENST00000367714.3	-	8	1267	c.845T>C	c.(844-846)gTa>gCa	p.V282A	SLC9C2_ENST00000536496.1_Missense_Mutation_p.V180A|RP3-436N22.3_ENST00000431459.1_RNA|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	282					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										ATTCAGTCCTACAGCGGCTAA	0.368																																					p.V282A		.											.	.	0			c.T845C						.						68	68	68					1																	173545857		2203	4300	6503	SO:0001583	missense	284525	exon8			AGTCCTACAGCGG	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.845T>C	1.37:g.173545857A>G	ENSP00000356687:p.Val282Ala	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_178527	0	0	0	0	0	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.285972	0.40394	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.06687	3.27;3.27	5.48	4.36	0.52297	Cation/H+ exchanger (1);	0.426381	0.19800	N	0.105771	T	0.02727	0.0082	L	0.50333	1.59	0.09310	N	1	B	0.18166	0.026	B	0.23275	0.045	T	0.42548	-0.9445	10	0.23302	T	0.38	-14.6781	8.1183	0.30957	0.9095:0.0:0.0905:0.0	.	282	Q5TAH2	S9A11_HUMAN	A	282;180	ENSP00000356687:V282A;ENSP00000445437:V180A	ENSP00000356687:V282A	V	-	2	0	SLC9A11	171812480	0.049000	0.20398	0.097000	0.21041	0.518000	0.34316	4.102000	0.57776	0.925000	0.37094	-0.250000	0.11733	GTA	.		0.368	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		G	173545857	A	G	173545857	3	3	52	1	0	0	0	0	1	0	0	0	14743	391	14	3	2613	3	SLC9A11	1	173545857	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	22149982	173545857	75704764	10	4996											
HMCN1	83872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	186158954	186158954	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctacagtgccaatgggaccAttgaatatcagaccacattc	13	9	7	12	0	1	2	1	1	0	1	2	3	1	3	4	1	2	0	4	1	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:186158954A>G	ENST00000271588.4	+	107	17081	c.16852A>G	c.(16852-16854)Att>Gtt	p.I5618V	HMCN1_ENST00000367492.2_Missense_Mutation_p.I5501V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5618					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CAATGGGACCATTGAATATCA	0.448																																					p.I5618V		.											.	HMCN1-113	0			c.A16852G						.						122	111	115					1																	186158954		2203	4300	6503	SO:0001583	missense	83872	exon107			GGGACCATTGAAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.16852A>G	1.37:g.186158954A>G	ENSP00000271588:p.Ile5618Val	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	115	31	NM_031935	0	0	1	1	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	5.555	0.287307	0.10513	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.62364	0.03;0.03	5.91	-0.414	0.12359	.	0.153154	0.56097	N	0.000026	T	0.40670	0.1126	N	0.20986	0.625	0.23896	N	0.996533	B	0.06786	0.001	B	0.06405	0.002	T	0.20538	-1.0272	10	0.45353	T	0.12	.	6.395	0.21607	0.5367:0.2325:0.2308:0.0	.	5618	Q96RW7	HMCN1_HUMAN	V	5618;5501	ENSP00000271588:I5618V;ENSP00000356462:I5501V	ENSP00000271588:I5618V	I	+	1	0	HMCN1	184425577	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	2.129000	0.42055	-0.086000	0.12550	0.533000	0.62120	ATT	.		0.448	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186158954	A	G	186158954	3	3	52	1	0	0	0	0	1	0	0	0	7241	217	8	3	17278	3	HMCN1	1	186158954	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	12613097	186158954	63091667	11	4997											
LRRN2	10446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204588079	204588079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctgctggtgcaaggcacTgagagcgttgttgttgagca	7	11	15	8	2	1	2	0	2	1	1	1	3	1	2	0	2	4	7	0	2	1	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:204588079T>C	ENST00000367175.1	-	1	3254	c.1042A>G	c.(1042-1044)Agt>Ggt	p.S348G	LRRN2_ENST00000367176.3_Missense_Mutation_p.S348G|RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.S348G			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	348					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TGCAAGGCACTGAGAGCGTTG	0.617																																					p.S348G		.											.	LRRN2-514	0			c.A1042G						.						66	59	62					1																	204588079		2203	4300	6503	SO:0001583	missense	10446	exon3			AGGCACTGAGAGC	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1042A>G	1.37:g.204588079T>C	ENSP00000356143:p.Ser348Gly	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_006338	0	0	0	0	0	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.988226	0.53934	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.58797	0.31;0.31;0.31	5.69	5.69	0.88448	.	0.000000	0.50627	D	0.000109	T	0.74030	0.3663	M	0.68952	2.095	0.49213	D	0.999765	D	0.76494	0.999	D	0.74023	0.982	T	0.76394	-0.2975	10	0.62326	D	0.03	.	15.6141	0.76750	0.0:0.0:0.0:1.0	.	348	O75325	LRRN2_HUMAN	G	348	ENSP00000356144:S348G;ENSP00000356145:S348G;ENSP00000356143:S348G	ENSP00000356143:S348G	S	-	1	0	LRRN2	202854702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.287000	0.72671	2.171000	0.68590	0.460000	0.39030	AGT	.		0.617	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		C	204588079	T	C	204588079	3	2	52	1	0	0	0	0	1	0	0	0	9060	1580	55	3	1103	3	LRRN2	1	204588079	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	18429125	204588079	44662542	12	4998											
URB2	9816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	229771856	229771856	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gggcccctccacggtactctCtgcatgcctcctggagctgc	4	9	11	17	1	1	0	0	0	1	0	4	1	3	1	5	3	5	3	5	3	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:229771856C>T	ENST00000258243.2	+	4	1632	c.1496C>T	c.(1495-1497)tCt>tTt	p.S499F		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	499						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.S499F(1)		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						ACGGTACTCTCTGCATGCCTC	0.577																																					p.S499F		.											.	URB2-174	1	Substitution - Missense(1)	lung(1)	c.C1496T						.						113	118	116					1																	229771856		2203	4300	6503	SO:0001583	missense	9816	exon4			TACTCTCTGCATG	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.1496C>T	1.37:g.229771856C>T	ENSP00000258243:p.Ser499Phe	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	174	57	NM_014777	0	0	6	7	1	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	C	4.911	0.169357	0.09339	.	.	ENSG00000135763	ENST00000258243	T	0.33216	1.42	5.35	0.996	0.19844	.	1.134710	0.06163	N	0.676348	T	0.23094	0.0558	L	0.34521	1.04	0.09310	N	1	B	0.33448	0.412	B	0.27887	0.084	T	0.24261	-1.0165	9	.	.	.	0.0631	11.0794	0.48051	0.0671:0.3671:0.5657:0.0	.	499	Q14146	URB2_HUMAN	F	499	ENSP00000258243:S499F	.	S	+	2	0	URB2	227838479	0.357000	0.24938	0.001000	0.08648	0.004000	0.04260	1.775000	0.38584	0.327000	0.23409	-0.153000	0.13522	TCT	.		0.577	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229771856	C	T	229771856	3	4	52	1	0	0	0	0	1	0	0	0	17058	913	32	2	1506	2	URB2	1	229771856	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	25183777	229771856	19478765	13	4999											
CPSF3	51692	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	9570989	9570994	+	In_Frame_Del	DEL	TTCTGA	TTCTGA	-																															gctatttatagatggcttctTtctgattatgtcaaagttag																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	TTCTGA	TTCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:9570989_9570994delTTCTGA	ENST00000238112.3	+	4	527_532	c.321_326delTTCTGA	c.(319-327)ctttctgat>ctt	p.SD108del	CPSF3_ENST00000460593.1_In_Frame_Del_p.SD71del	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	108					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GATGGCTTCTTTCTGATTATGTCAAA	0.35																																					p.107_109del	Colon(194;1259 2048 3845 5218 19985)	.											.	CPSF3-153	0			c.321_326del						.																																			SO:0001651	inframe_deletion	51692	exon4			.	AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"cleavage and polyadenylation specific factor 3, 73kD subunit"			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.321_326delTTCTGA	2.37:g.9570989_9570994delTTCTGA	ENSP00000238112:p.Ser108_Asp109del	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	133	41	NM_016207	0	0	0	0	0	O14769|Q53RS2|Q96F36	In_Frame_Del	DEL	ENST00000238112.3	37	CCDS1664.1																																																																																			.		0.35	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207		-	9570994	TTCTGA	-	9570989	7	5	52	1	0	1	0	1	0	0	0	0	3832	1828	64	0	335	0	CPSF3	2	9570989	In_Frame_Del	DEL	TTCTGA	TCGA-B9-5156-01A-01D-1589-08		9570989	233628384	14	5000											
SLC3A1	6519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44507998	44507998	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttttggaacgatggaaGattttgagaatctggttgca	11	14	11	5	1	1	2	0	1	1	2	1	6	1	4	1	3	2	2	1	3	3	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:44507998G>T	ENST00000260649.6	+	2	650	c.574G>T	c.(574-576)Gat>Tat	p.D192Y	SLC3A1_ENST00000410056.3_Missense_Mutation_p.D192Y|SLC3A1_ENST00000409387.1_Missense_Mutation_p.D192Y|SLC3A1_ENST00000409741.1_Missense_Mutation_p.D192Y|SLC3A1_ENST00000409229.3_Missense_Mutation_p.D192Y	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	192					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	AACGATGGAAGATTTTGAGAA	0.373																																					p.D192Y		.											.	SLC3A1-90	0			c.G574T						.						111	107	108					2																	44507998		2203	4300	6503	SO:0001583	missense	6519	exon2			ATGGAAGATTTTG		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.574G>T	2.37:g.44507998G>T	ENSP00000260649:p.Asp192Tyr	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	125	37	NM_000341	0	2	340	694	352	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	37	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.563097	0.65538	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000410056;ENST00000409741;ENST00000409229;ENST00000541289	D;D;D;D;D	0.99758	-6.65;-6.65;-5.38;-6.65;-6.65	4.74	3.86	0.44501	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.054412	0.64402	D	0.000001	D	0.99862	0.9935	H	0.98256	4.185	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.81914	0.995;0.995;0.995;0.988;0.984	D	0.96726	0.9536	10	0.87932	D	0	-14.6276	13.4464	0.61144	0.0768:0.0:0.9232:0.0	.	192;192;192;192;192	Q07837;B8ZZK1;Q4J6B5;Q4J6B6;Q4J6B8	SLC31_HUMAN;.;.;.;.	Y	192;192;128;192;192;192;192	ENSP00000260649:D192Y;ENSP00000387308:D192Y;ENSP00000387337:D192Y;ENSP00000386954:D192Y;ENSP00000386620:D192Y	ENSP00000260649:D192Y	D	+	1	0	SLC3A1	44361502	1.000000	0.71417	0.989000	0.46669	0.730000	0.41778	7.381000	0.79718	1.110000	0.41699	0.655000	0.94253	GAT	.		0.373	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		T	44507998	G	T	44507998	3	4	52	1	0	0	0	0	1	0	0	0	14658	942	33	4	580	4	SLC3A1	2	44507998	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	34937009	44507998	198691375	15	5001											
PNPT1	87178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55908004	55908004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttaccgccattaattgctAggacatcaggctcatttaca	12	12	6	11	1	2	0	2	0	0	0	2	1	2	1	2	2	3	2	2	2	4	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:55908004A>G	ENST00000447944.2	-	6	589	c.503T>C	c.(502-504)cTa>cCa	p.L168P		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	168					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ATTAATTGCTAGGACATCAGG	0.313																																					p.L168P		.											.	PNPT1-90	0			c.T503C						.						57	60	59					2																	55908004		2203	4299	6502	SO:0001583	missense	87178	exon6			ATTGCTAGGACAT	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.503T>C	2.37:g.55908004A>G	ENSP00000400646:p.Leu168Pro	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	78	23	NM_033109	0	0	0	0	0	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.910089	0.72983	.	.	ENSG00000138035	ENST00000447944	T	0.68025	-0.3	5.24	5.24	0.73138	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.000000	0.64402	D	0.000001	T	0.79470	0.4451	M	0.67625	2.065	0.80722	D	1	D	0.67145	0.996	D	0.77004	0.989	T	0.78602	-0.2140	10	0.36615	T	0.2	-15.1193	15.4288	0.75075	1.0:0.0:0.0:0.0	.	168	Q8TCS8	PNPT1_HUMAN	P	168	ENSP00000400646:L168P	ENSP00000260604:L168P	L	-	2	0	PNPT1	55761508	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.590000	0.90821	2.107000	0.64212	0.383000	0.25322	CTA	.		0.313	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		G	55908004	A	G	55908004	3	3	52	1	0	0	0	0	1	0	0	0	12199	420	15	3	1940	3	PNPT1	2	55908004	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	11400006	55908004	187291369	16	5002											
FANCL	55120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	58431304	58431304	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgattaaatgctctctaccAgaagcatcttctgcttttaa	11	15	6	9	0	3	2	0	1	3	1	4	2	3	2	1	0	4	3	1	0	5	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:58431304A>G	ENST00000233741.4	-	6	468	c.432T>C	c.(430-432)tcT>tcC	p.S144S	FANCL_ENST00000403676.1_Silent_p.S27S|FANCL_ENST00000402135.3_Silent_p.S144S|FANCL_ENST00000540646.1_Intron|FANCL_ENST00000403295.3_Silent_p.S144S	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	144	UBC-RWD region (URD).		S -> F (in dbSNP:rs36059257).		cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						GCTCTCTACCAGAAGCATCTT	0.408								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S144S		.											.	FANCL-661	0			c.T432C						.						137	133	135					2																	58431304		2203	4300	6503	SO:0001819	synonymous_variant	55120	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCTACCAGAAGCA	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"Zinc fingers, PHD-type", "Fanconi anemia, complementation groups"	20748	protein-coding gene	gene with protein product		608111	"PHD finger protein 9"	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.432T>C	2.37:g.58431304A>G		Somatic	197	0		WXS	Illumina HiSeq	Phase_I	166	45	NM_018062	0	0	8	11	3	Q6GU60	Silent	SNP	ENST00000233741.4	37	CCDS1860.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.550764	0.27739	.	.	ENSG00000115392	ENST00000427708	.	.	.	6.03	1.08	0.20341	.	.	.	.	.	T	0.55784	0.1942	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47045	-0.9147	4	.	.	.	-18.6795	8.6392	0.33968	0.7171:0.0:0.2829:0.0	.	.	.	.	R	144	.	.	W	-	1	0	FANCL	58284808	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.352000	0.44080	0.161000	0.19458	0.533000	0.62120	TGG	.		0.408	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062		G	58431304	A	G	58431304	2	3	52	1	0	0	0	0	0	0	0	1	5689	175	7	3		3	FANCL	2	58431304	Silent	SNP	A	TCGA-B9-5156-01A-01D-1589-08	2523300	58431304	184768069	17	5003											
TET3	200424	hgsc.bcm.edu	37	chr2	74275021	74275021	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggctctgctgtgcccctgccCccagaaccttctcttgcgct	3	11	9	18	1	2	1	0	0	2	1	3	1	2	1	5	1	5	3	5	1	1	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:74275021C>T	ENST00000409262.3	+	1	1572	c.1572C>T	c.(1570-1572)ccC>ccT	p.P524P		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	524					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGCCCCTGCCCCCAGAACCTT	0.632																																					p.P524P		.											.	.	0			c.C1572T						.						23	25	24					2																	74275021		1993	4171	6164	SO:0001819	synonymous_variant	200424	exon1			CCTGCCCCCAGAA		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1572C>T	2.37:g.74275021C>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_144993	0	0	3	6	3	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																			.		0.632	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74275021	C	T	74275021	2	4	52	1	0	0	0	0	0	0	0	1	15803	610	22	2		2	TET3	2	74275021	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08	15843717	74275021	168924352	18	5004											
THNSL2	55258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	88482283	88482283	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtgaaccgcaatgacAtcatccacaggactgtccag	12	7	10	12	1	1	2	1	2	0	0	3	3	3	3	3	2	1	2	3	2	2	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:88482283A>G	ENST00000324166.5	+	5	2559	c.868A>G	c.(868-870)Atc>Gtc	p.I290V	THNSL2_ENST00000402102.1_Missense_Mutation_p.I290V|THNSL2_ENST00000343544.4_Missense_Mutation_p.I290V|THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000358591.2_Missense_Mutation_p.I290V|THNSL2_ENST00000377254.3_Missense_Mutation_p.I290V|THNSL2_ENST00000449349.1_Intron	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	290					2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)			breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						CCGCAATGACATCATCCACAG	0.512																																					p.I290V		.											.	THNSL2-91	0			c.A868G						.						93	89	90					2																	88482283		2203	4300	6503	SO:0001583	missense	55258	exon5			AATGACATCATCC		CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.868A>G	2.37:g.88482283A>G	ENSP00000327323:p.Ile290Val	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	88	27	NM_018271	0	0	38	74	36	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Missense_Mutation	SNP	ENST00000324166.5	37	CCDS2002.2	.	.	.	.	.	.	.	.	.	.	A	27.0	4.789980	0.90367	.	.	ENSG00000144115	ENST00000358591;ENST00000377254;ENST00000402102;ENST00000544063;ENST00000343544;ENST00000324166	T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78	5.81	5.81	0.92471	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	T	0.20495	0.0493	L	0.37561	1.115	0.49389	D	0.999788	D;D;D	0.62365	0.991;0.987;0.979	P;P;P	0.59703	0.844;0.862;0.784	T	0.00701	-1.1603	10	0.38643	T	0.18	.	15.3313	0.74215	1.0:0.0:0.0:0.0	.	132;290;290	A8K0C1;Q86YJ6;Q86YJ6-2	.;THNS2_HUMAN;.	V	290;290;290;132;290;290	ENSP00000351402:I290V;ENSP00000366464:I290V;ENSP00000384475:I290V;ENSP00000339563:I290V;ENSP00000327323:I290V	ENSP00000327323:I290V	I	+	1	0	THNSL2	88263398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.322000	0.90000	2.219000	0.72066	0.533000	0.62120	ATC	.		0.512	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271		G	88482283	A	G	88482283	3	3	52	1	0	0	0	0	1	0	0	0	15895	217	8	3	886	3	THNSL2	2	88482283	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	14207262	88482283	154717090	19	5005											
TRIM43	129868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	96260855	96260855	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattcaagaaaatcagagaAatctatatgaggagggaaga	20	7	11	3	0	3	5	2	1	1	4	3	8	3	7	0	2	0	0	0	2	7	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:96260855A>T	ENST00000272395.2	+	3	605	c.469A>T	c.(469-471)Aat>Tat	p.N157Y		NM_001164464.1|NM_138800.1	NP_001157936.1|NP_620155.1	Q96BQ3	TRI43_HUMAN	tripartite motif containing 43	157						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|lung(7)|ovary(1)	12						AAATCAGAGAAATCTATATGA	0.403																																					p.N157Y		.											.	TRIM43-63	0			c.A469T						.						58	56	56					2																	96260855		2203	4299	6502	SO:0001583	missense	129868	exon3			CAGAGAAATCTAT	BK000505	CCDS2015.1	2q11	2014-02-17	2011-01-25		ENSG00000144015	ENSG00000144015		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19015	protein-coding gene	gene with protein product			"tripartite motif-containing 43"				Standard	NM_138800		Approved	TRIM43A	uc002suv.3	Q96BQ3	OTTHUMG00000130401	ENST00000272395.2:c.469A>T	2.37:g.96260855A>T	ENSP00000272395:p.Asn157Tyr	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	46	14	NM_138800	0	0	0	0	0	Q53TJ7	Missense_Mutation	SNP	ENST00000272395.2	37	CCDS2015.1	.	.	.	.	.	.	.	.	.	.	.	11.90	1.776990	0.31411	.	.	ENSG00000144015	ENST00000272395	T	0.06608	3.28	0.911	0.911	0.19343	.	.	.	.	.	T	0.12178	0.0296	L	0.59436	1.845	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.17137	-1.0379	9	0.02654	T	1	-3.9711	4.1749	0.10348	1.0:0.0:0.0:0.0	.	157	Q96BQ3	TRI43_HUMAN	Y	157	ENSP00000272395:N157Y	ENSP00000272395:N157Y	N	+	1	0	TRIM43	95624582	0.197000	0.23362	0.060000	0.19600	0.268000	0.26511	0.953000	0.29162	0.680000	0.31366	0.308000	0.20428	AAT	.		0.403	TRIM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252784.1	NM_138800		T	96260855	A	T	96260855	3	4	52	1	0	0	0	0	1	0	0	0	16551	14	1	5	475	5	TRIM43	2	96260855	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	7778572	96260855	146938518	20	5006											
DARS	1615	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	136673870	136673871	+	Frame_Shift_Ins	INS	-	-	A																															cttcacaatattctagtcttINSagagttggctccaaaaattt																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:136673870_136673871insA	ENST00000264161.4	-	11	1246_1247	c.1031_1032insT	c.(1030-1032)ctafs	p.L344fs	DARS_ENST00000537273.1_Frame_Shift_Ins_p.L244fs	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	344					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	ATTCTAGTCTTAGAGTTGGCTC	0.366																																					p.L344fs		.											.	DARS-91	0			c.1032_1033insT						.																																			SO:0001589	frameshift_variant	1615	exon11			.	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.1032dupT	2.37:g.136673871_136673871dupA	ENSP00000264161:p.Leu344fs	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	153	48	NM_001349	0	0	0	0	0	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Frame_Shift_Ins	INS	ENST00000264161.4	37	CCDS2180.1																																																																																			.		0.366	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349		A	136673871	-	A	136673870	7	5	52	1	0	1	1	0	0	0	0	0	4247	1741	61	0	497	0	DARS	2	136673870	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	40413015	136673870	106525503	21	5007											
ZEB2	9839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	145156027	145156027	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggtctggactggtggcatGaaagtagcagggggaaatgc	10	8	17	6	0	1	1	0	1	1	0	1	3	1	3	0	6	2	3	0	6	3	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:145156027G>A	ENST00000558170.2	-	8	3911	c.2727C>T	c.(2725-2727)ttC>ttT	p.F909F	ZEB2_ENST00000303660.4_Silent_p.F909F|ZEB2_ENST00000539609.3_Silent_p.F885F|ZEB2_ENST00000409487.3_Silent_p.F909F	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	909					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		CTGGTGGCATGAAAGTAGCAG	0.498																																					p.F909F	Melanoma(33;1235 1264 5755 16332)	.											.	ZEB2-297	0			c.C2727T						.						176	170	172					2																	145156027		2203	4300	6503	SO:0001819	synonymous_variant	9839	exon8			TGGCATGAAAGTA	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.2727C>T	2.37:g.145156027G>A		Somatic	240	0		WXS	Illumina HiSeq	Phase_I	172	60	NM_014795	0	0	18	21	3	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	37	CCDS2186.1																																																																																			.		0.498	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145156027	G	A	145156027	2	1	52	1	0	0	0	0	0	0	0	1	17656	1281	45	2		2	ZEB2	2	145156027	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	8482157	145156027	98043346	22	5008											
CD302	9936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160637446	160637446	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catctgggcctttccattgcTttttcaaagtatccagtata	9	16	6	10	0	2	0	1	0	1	0	4	0	4	0	3	1	1	3	3	1	4	7			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:160637446T>C	ENST00000259053.4	-	3	285	c.242A>G	c.(241-243)aAg>aGg	p.K81R	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1722R|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1666R|LY75_ENST00000554112.1_Missense_Mutation_p.K1722R|CD302_ENST00000480212.1_5'UTR|CD302_ENST00000429078.2_Missense_Mutation_p.K81R|LY75_ENST00000553424.1_Missense_Mutation_p.K1666R	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	81	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						TTTCCATTGCTTTTTCAAAGT	0.338																																					p.K1722R		.											.	.	0			c.A5165G						.						153	141	145					2																	160637446		2203	4300	6503	SO:0001583	missense	100526664	exon36			CATTGCTTTTTCA	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"CD molecules", "C-type lectin domain containing"	30843	protein-coding gene	gene with protein product	"C-type lectin domain family 13, member A"	612246	"CD302 antigen"			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.242A>G	2.37:g.160637446T>C	ENSP00000259053:p.Lys81Arg	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	103	27	NM_001198759	0	0	21	21	0	A8K5G4|B4E2T9|Q15009	Missense_Mutation	SNP	ENST00000259053.4	37	CCDS33308.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.151609	0.78001	.	.	ENSG00000241399;ENSG00000241399;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000259053;ENST00000429078;ENST00000554112;ENST00000553424;ENST00000504764;ENST00000505052	T;T;T;T;T;T	0.08370	3.1;3.1;3.1;3.1;3.1;3.1	5.21	3.98	0.46160	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.222293	0.36854	N	0.002374	T	0.14874	0.0359	L	0.51422	1.61	0.21445	N	0.99969	P;B;P;D	0.58620	0.901;0.386;0.642;0.983	P;B;B;P	0.57324	0.702;0.178;0.178;0.818	T	0.09100	-1.0690	10	0.19590	T	0.45	-28.4385	10.1369	0.42712	0.0:0.0:0.3327:0.6673	.	81;1666;1722;81	B4E2T9;O60449-3;O60449-2;Q8IX05	.;.;.;CD302_HUMAN	R	81;81;1722;1666;1722;1666	ENSP00000259053:K81R;ENSP00000394301:K81R;ENSP00000451511:K1722R;ENSP00000451446:K1666R;ENSP00000423463:K1722R;ENSP00000421035:K1666R	ENSP00000259053:K81R	K	-	2	0	LY75;CD302;LY75-CD302	160345692	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.111000	0.31159	2.097000	0.63578	0.533000	0.62120	AAG	.		0.338	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880		C	160637446	T	C	160637446	3	2	52	1	0	0	0	0	1	0	0	0	3009	1609	56	3	472	3	CD302	2	160637446	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	15481419	160637446	82561927	23	5009											
UBR3	130507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170843265	170843265	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gtggcccctcctctgaagatCgacctactggattagttgta	8	12	10	11	1	1	2	0	1	1	1	3	4	2	3	4	2	1	2	4	2	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:170843265C>G	ENST00000272793.5	+	25	3795	c.3745C>G	c.(3745-3747)Cga>Gga	p.R1249G	UBR3_ENST00000392631.1_Missense_Mutation_p.R70G|UBR3_ENST00000418381.1_Missense_Mutation_p.R1249G			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1249					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CTCTGAAGATCGACCTACTGG	0.408																																					p.R1249G		.											.	UBR3-68	0			c.C3745G						.						109	108	108					2																	170843265		2203	4300	6503	SO:0001583	missense	130507	exon25			GAAGATCGACCTA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3745C>G	2.37:g.170843265C>G	ENSP00000272793:p.Arg1249Gly	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	103	29	NM_172070	0	0	7	17	10	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.13|17.13	3.312099|3.312099	0.60414|0.60414	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000392632|ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631	.|T;T;T	.|0.57907	.|0.37;0.37;0.89	5.27|5.27	3.38|3.38	0.38709|0.38709	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67748|0.67748	0.2926|0.2926	M|M	0.71581|0.71581	2.175|2.175	0.32414|0.32414	N|N	0.550296|0.550296	.|D;D;D	.|0.67145	.|0.993;0.996;0.987	.|D;D;D	.|0.79108	.|0.982;0.992;0.953	T|T	0.71481|0.71481	-0.4580|-0.4580	5|10	.|0.20519	.|T	.|0.43	.|.	13.7422|13.7422	0.62855|0.62855	0.4588:0.5412:0.0:0.0|0.4588:0.5412:0.0:0.0	.|.	.|1249;70;1249	.|Q6ZT12;Q6ZT12-2;E7EVK3	.|UBR3_HUMAN;.;.	M|G	306|1249;1249;1249;70	.|ENSP00000272793:R1249G;ENSP00000396068:R1249G;ENSP00000376408:R70G	.|ENSP00000272793:R1249G	I|R	+|+	3|1	3|2	UBR3|UBR3	170551511|170551511	0.662000|0.662000	0.27439|0.27439	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.024000|1.024000	0.30077|0.30077	0.530000|0.530000	0.28619|0.28619	0.585000|0.585000	0.79938|0.79938	ATC|CGA	.		0.408	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		G	170843265	C	G	170843265	3	3	52	1	0	0	0	0	1	0	0	0	16936	876	31	4	3843	4	UBR3	2	170843265	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	10205819	170843265	72356108	24	5010											
DYTN	391475	hgsc.bcm.edu	37	chr2	207564616	207564616	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattgctgggctcaacaccTgaaaaacaatggcactctaa	14	9	8	10	0	2	2	1	2	1	0	2	2	2	2	1	2	3	3	1	2	5	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:207564616T>C	ENST00000452335.2	-	7	672		c.e7-2		DYTN_ENST00000477734.1_Splice_Site|Y_RNA_ENST00000384589.1_RNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin							plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GCTCAACACCTGAAAAACAAT	0.438																																					.		.											.	DYTN-23	0			c.556-2A>G						.						67	69	68					2																	207564616		1887	4116	6003	SO:0001630	splice_region_variant	391475	exon8			AACACCTGAAAAA	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.556-2A>G	2.37:g.207564616T>C		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	49	3	NM_001093730	0	0	0	0	0		Splice_Site	SNP	ENST00000452335.2	37	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.386607	0.42308	.	.	ENSG00000232125	ENST00000452335	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8833	0.70550	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DYTN	207272861	1.000000	0.71417	0.997000	0.53966	0.389000	0.30415	5.505000	0.66981	2.254000	0.74563	0.459000	0.35465	.	.		0.438	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		Intron	C	207564616	T	C	207564616	5	2	52	1	0	0	0	0	0	0	1	0	4872	1594	55	3	1206	3	DYTN	2	207564616	Splice_Site	SNP	T	TCGA-B9-5156-01A-01D-1589-08	36721351	207564616	35634757	25	5011											
ANKMY1	51281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	241468551	241468551	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgaacggaggaatttcatTgaggaagatgcgggcgtcca	13	7	14	7	4	1	2	1	1	0	1	2	6	2	5	1	4	3	0	1	4	4	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:241468551T>G	ENST00000272972.3	-	4	803	c.589A>C	c.(589-591)Aat>Cat	p.N197H	ANKMY1_ENST00000373318.2_Intron|ANKMY1_ENST00000405523.3_Intron|ANKMY1_ENST00000462004.1_Intron|ANKMY1_ENST00000405002.1_Intron|ANKMY1_ENST00000536462.1_Intron|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000403283.1_Intron|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000401804.1_Missense_Mutation_p.N286H|ANKMY1_ENST00000391987.1_Missense_Mutation_p.N197H|ANKMY1_ENST00000373320.4_Intron	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	197							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GGAATTTCATTGAGGAAGATG	0.483																																					p.N197H		.											.	ANKMY1-90	0			c.A589C						.						155	155	155					2																	241468551		2203	4300	6503	SO:0001583	missense	51281	exon4			TTTCATTGAGGAA	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.589A>C	2.37:g.241468551T>G	ENSP00000272972:p.Asn197His	Somatic	200	1		WXS	Illumina HiSeq	Phase_I	153	46	NM_016552	0	0	0	1	1	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.289|4.289	0.052793|0.052793	0.08291|0.08291	.|.	.|.	ENSG00000144504|ENSG00000144504	ENST00000272972;ENST00000391987;ENST00000401804;ENST00000539830;ENST00000418708|ENST00000443318	T;T;T;T|.	0.44881|.	0.91;0.91;0.91;0.91|.	4.79|4.79	-4.57|-4.57	0.03421|0.03421	.|.	0.571564|.	0.17218|.	N|.	0.182438|.	T|T	0.49490|0.49490	0.1560|0.1560	M|M	0.72118|0.72118	2.19|2.19	0.09310|0.09310	N|N	1|1	B;B|.	0.13594|.	0.008;0.008|.	B;B|.	0.11329|.	0.006;0.006|.	T|T	0.54944|0.54944	-0.8217|-0.8217	10|5	0.66056|.	D|.	0.02|.	-7.6409|-7.6409	8.6712|8.6712	0.34152|0.34152	0.0:0.0966:0.5195:0.3839|0.0:0.0966:0.5195:0.3839	.|.	197;197|.	Q4ZFV3;Q9P2S6|.	.;ANKY1_HUMAN|.	H|P	197;197;286;197;197|141	ENSP00000272972:N197H;ENSP00000375847:N197H;ENSP00000385887:N286H;ENSP00000407015:N197H|.	ENSP00000272972:N197H|.	N|Q	-|-	1|2	0|0	ANKMY1|ANKMY1	241117224|241117224	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.190000|-0.190000	0.09615|0.09615	-0.388000|-0.388000	0.07797|0.07797	-0.313000|-0.313000	0.08912|0.08912	AAT|CAA	.		0.483	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		G	241468551	T	G	241468551	3	3	52	1	0	0	0	0	1	0	0	0	634	1812	63	5	2292	5	ANKMY1	2	241468551	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	33903935	241468551	1730822	26	5012											
EXOSC7	23016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	45038724	45038724	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtcctcgggagcactgctggGttctctatgtggatgtgctg	4	13	15	9	1	1	0	0	0	1	0	4	2	2	2	1	3	3	4	1	3	1	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:45038724G>C	ENST00000265564.7	+	4	448	c.400G>C	c.(400-402)Gtt>Ctt	p.V134L	EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	134					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		GCACTGCTGGGTTCTCTATGT	0.468																																					p.V134L		.											.	EXOSC7-90	0			c.G400C						.						128	118	121					3																	45038724		2203	4300	6503	SO:0001583	missense	23016	exon4			TGCTGGGTTCTCT	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.400G>C	3.37:g.45038724G>C	ENSP00000265564:p.Val134Leu	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	101	44	NM_015004	0	0	26	52	26	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	37	CCDS2725.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.573110	0.45902	.	.	ENSG00000075914	ENST00000265564	T	0.62232	0.04	5.71	-7.06	0.01568	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.510215	0.21639	N	0.071362	T	0.55940	0.1952	M	0.67625	2.065	0.49130	D	0.999757	B;B	0.09022	0.002;0.002	B;B	0.16289	0.015;0.015	T	0.26643	-1.0097	10	0.30078	T	0.28	-1.5027	19.6631	0.95882	0.2416:0.0:0.7584:0.0	.	134;134	B2RDZ9;Q15024	.;EXOS7_HUMAN	L	134	ENSP00000265564:V134L	ENSP00000265564:V134L	V	+	1	0	EXOSC7	45013728	0.981000	0.34729	0.040000	0.18447	0.953000	0.61014	0.073000	0.14640	-1.400000	0.02061	-0.224000	0.12420	GTT	.		0.468	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		C	45038724	G	C	45038724	3	2	52	1	0	0	0	0	1	0	0	0	5332	1261	44	4	414	4	EXOSC7	3	45038724	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		45038724	152983706	27	5013											
ROBO1	6091	broad.mit.edu;ucsc.edu	37	chr3	78735047	78735047	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggctggatgactgtggtggTtgatatgagaaaagtagatt	11	12	15	3	1	0	4	0	3	0	2	0	6	0	5	0	4	0	3	0	4	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:78735047T>A	ENST00000464233.1	-	10	1304	c.1191A>T	c.(1189-1191)caA>caT	p.Q397H	ROBO1_ENST00000436010.2_Missense_Mutation_p.Q358H|ROBO1_ENST00000495273.1_Missense_Mutation_p.Q361H|ROBO1_ENST00000467549.1_Missense_Mutation_p.Q361H	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	397	Ig-like C2-type 4.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ACTGTGGTGGTTGATATGAGA	0.393																																					p.Q397H													.	ROBO1-67	0			c.A1191T						.						46	47	47					3																	78735047		1907	4095	6002	SO:0001583	missense	6091	exon10			TGGTGGTTGATAT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.1191A>T	3.37:g.78735047T>A	ENSP00000420321:p.Gln397His	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	25	4	NM_002941	0	0	9	15	6	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990616	0.35131	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.75154	-0.91;-0.91;1.62;1.62	5.42	0.145	0.14829	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.111195	0.64402	D	0.000005	T	0.68586	0.3017	N	0.21545	0.675	0.49051	D	0.999749	P;P;B;P;P	0.48998	0.814;0.918;0.012;0.469;0.778	P;P;B;B;P	0.59643	0.861;0.539;0.053;0.405;0.834	T	0.61855	-0.6977	9	.	.	.	.	7.4025	0.26973	0.0:0.42:0.1116:0.4684	.	361;397;361;361;358	Q1RMC7;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	H	358;361;397;361;361;397	ENSP00000406043:Q358H;ENSP00000420321:Q397H;ENSP00000420637:Q361H;ENSP00000417992:Q361H	.	Q	-	3	2	ROBO1	78817737	0.047000	0.20315	0.998000	0.56505	0.644000	0.38419	-0.561000	0.05957	0.068000	0.16574	-0.468000	0.05107	CAA	.		0.393	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78735047	T	A	78735047	3	1	52	1	0	0	0	0	1	0	0	0	13545	1722	60	5	3852	5	ROBO1	3	78735047	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	33696323	78735047	119287383	28	5014											
OR5H1	26341	broad.mit.edu	37	chr3	97852336	97852336	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatgtgggccctgcatctccGcaagcagatgatcaagatat	11	10	10	10	1	2	3	1	1	1	2	3	3	2	3	2	1	2	3	2	1	4	2	rs138973744		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:97852336G>A	ENST00000354565.2	+	1	795	c.795G>A	c.(793-795)ccG>ccA	p.P265P	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CTGCATCTCCGCAAGCAGATG	0.438																																					p.P265P													.	OR5H1-136	0			c.G795A						.	G		0,4404		0,0,2202	107	115	112		795	-7.1	0	3	dbSNP_134	112	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	OR5H1	NM_001005338.1		0,1,6500	AA,AG,GG		0.0116,0.0,0.0077		265/314	97852336	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	26341	exon1			ATCTCCGCAAGCA	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"GPCR / Class A : Olfactory receptors"	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.795G>A	3.37:g.97852336G>A		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	207	5	NM_001005338	0	0	0	0	0		Silent	SNP	ENST00000354565.2	37	CCDS33797.1																																																																																			G|1.000;A|0.000		0.438	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		A	97852336	G	A	97852336	2	1	52	1	0	0	0	0	0	0	0	1	11185	1074	38	1		1	OR5H1	3	97852336	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	19117289	97852336	100170094	29	5015											
BOC	91653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	112991328	112991328	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcgtcaccaaaggccagAgtctcattctggagtgtgtg	9	11	11	10	1	4	1	3	0	2	1	6	2	4	2	2	2	0	0	2	2	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:112991328A>C	ENST00000495514.1	+	7	1443	c.739A>C	c.(739-741)Agt>Cgt	p.S247R	BOC_ENST00000273395.4_Missense_Mutation_p.S247R|BOC_ENST00000355385.3_Missense_Mutation_p.S247R			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	247	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CAAAGGCCAGAGTCTCATTCT	0.617																																					p.S247R		.											.	BOC-157	0			c.A739C						.						164	157	159					3																	112991328		2203	4300	6503	SO:0001583	missense	91653	exon7			GGCCAGAGTCTCA	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17173	protein-coding gene	gene with protein product	"brother of CDO", "brother of CDON", "cell adhesion associated, oncogene regulated 2"	608708	"Boc homolog (mouse)"			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.739A>C	3.37:g.112991328A>C	ENSP00000418663:p.Ser247Arg	Somatic	261	0		WXS	Illumina HiSeq	Phase_I	318	73	NM_033254	0	0	2	3	1	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110475	0.56398	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.69685	-0.42;-0.42;-0.42	5.93	5.93	0.95920	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.043438	0.85682	D	0.000000	T	0.60932	0.2307	L	0.41573	1.285	0.50313	D	0.999862	B;B	0.16603	0.014;0.018	B;B	0.21360	0.033;0.034	T	0.56275	-0.8006	10	0.44086	T	0.13	.	16.3797	0.83452	1.0:0.0:0.0:0.0	.	247;247	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	R	247	ENSP00000418663:S247R;ENSP00000273395:S247R;ENSP00000347546:S247R	ENSP00000273395:S247R	S	+	1	0	BOC	114474018	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.474000	0.73578	2.271000	0.75665	0.533000	0.62120	AGT	.		0.617	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		C	112991328	A	C	112991328	3	2	52	1	0	0	0	0	1	0	0	0	1482	304	11	5	757	5	BOC	3	112991328	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	15138992	112991328	85031102	30	5016											
RPN1	6184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	128348859	128348859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtaatgggtcttccacccgCcaaagagagggaagcgaggc	11	6	14	10	2	1	1	0	0	1	1	2	4	2	2	3	3	1	1	3	3	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:128348859C>T	ENST00000296255.3	-	5	1019	c.971G>A	c.(970-972)gGc>gAc	p.G324D	RPN1_ENST00000490166.1_5'Flank|RPN1_ENST00000497289.1_Missense_Mutation_p.G152D	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	324					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		CTTCCACCCGCCAAAGAGAGG	0.458			T	EVI1	AML																																p.G324D		.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	.	RPN1-652	0			c.G971A						.						76	74	74					3																	128348859		2203	4300	6503	SO:0001583	missense	6184	exon5			CACCCGCCAAAGA		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"oligosaccharyltransferase 1 homolog (S. cerevisiae)", "oligosaccharyltransferase complex subunit (non-catalytic)"	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.971G>A	3.37:g.128348859C>T	ENSP00000296255:p.Gly324Asp	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	87	41	NM_002950	0	0	282	802	520	B2R5Z0|D3DNB6|Q68DT1	Missense_Mutation	SNP	ENST00000296255.3	37	CCDS3051.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165154	0.94768	.	.	ENSG00000163902	ENST00000296255;ENST00000497289;ENST00000537139;ENST00000545956	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.87051	0.6081	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90352	0.4367	9	0.87932	D	0	-19.9225	19.0082	0.92861	0.0:1.0:0.0:0.0	.	324	P04843	RPN1_HUMAN	D	324;152;95;298	.	ENSP00000296255:G324D	G	-	2	0	RPN1	129831549	1.000000	0.71417	0.920000	0.36463	0.991000	0.79684	7.380000	0.79704	2.487000	0.83934	0.591000	0.81541	GGC	.		0.458	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950		T	128348859	C	T	128348859	3	4	52	1	0	0	0	0	1	0	0	0	13639	739	26	2	876	2	RPN1	3	128348859	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	15357531	128348859	69673571	31	5017											
ATR	545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142268491	142268491	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgctttggcagcaagatCaggtagtagaacttgtaatg	11	12	12	6	0	1	2	1	0	0	2	1	2	1	2	0	2	3	7	0	2	5	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:142268491C>A	ENST00000350721.4	-	15	3122	c.3001G>T	c.(3001-3003)Gat>Tat	p.D1001Y	ATR_ENST00000383101.3_Missense_Mutation_p.D937Y	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1001					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GCAGCAAGATCAGGTAGTAGA	0.348								Other conserved DNA damage response genes																													p.D1001Y		.											.	ATR-1139	0			c.G3001T						.						50	51	51					3																	142268491		2203	4299	6502	SO:0001583	missense	545	exon15			CAAGATCAGGTAG	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.3001G>T	3.37:g.142268491C>A	ENSP00000343741:p.Asp1001Tyr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	82	37	NM_001184	0	0	3	11	8	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	4.829	0.154136	0.09236	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.63417	-0.04;-0.04	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.062472	0.64402	D	0.000004	T	0.34919	0.0914	N	0.02539	-0.55	0.43453	D	0.995646	B	0.06786	0.001	B	0.08055	0.003	T	0.41466	-0.9507	10	0.02654	T	1	-18.3072	17.7702	0.88489	0.0:1.0:0.0:0.0	.	1001	Q13535	ATR_HUMAN	Y	1001;937	ENSP00000343741:D1001Y;ENSP00000372581:D937Y	ENSP00000343741:D1001Y	D	-	1	0	ATR	143751181	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.835000	0.69368	2.635000	0.89317	0.655000	0.94253	GAT	.		0.348	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142268491	C	A	142268491	3	1	52	1	0	0	0	0	1	0	0	0	1205	826	29	4	5065	4	ATR	3	142268491	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	13919632	142268491	55753939	32	5018											
SH3TC1	54436	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	8229750	8229752	+	In_Frame_Del	DEL	ACC	ACC	-																															ggcaagcgctggcctccctgAccccgggcacaggccaggcg																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	ACC	ACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:8229750_8229752delACC	ENST00000245105.3	+	12	2396_2398	c.2329_2331delACC	c.(2329-2331)accdel	p.T777del	SH3TC1_ENST00000539824.1_In_Frame_Del_p.T701del	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	777										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGCCTCCCTGACCCCGGGCACAG	0.685																																					p.777_777del	NSCLC(145;2298 2623 35616 37297)	.											.	SH3TC1-154	0			c.2329_2331del						.																																			SO:0001651	inframe_deletion	54436	exon12			.	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2329_2331delACC	4.37:g.8229750_8229752delACC	ENSP00000245105:p.Thr777del	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	49	12	NM_018986	0	0	0	0	0	Q4W5G5	In_Frame_Del	DEL	ENST00000245105.3	37	CCDS3399.1																																																																																			.		0.685	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		-	8229752	ACC	-	8229750	7	5	52	1	0	1	0	1	0	0	0	0	14293	275	10	0	2371	0	SH3TC1	4	8229750	In_Frame_Del	DEL	ACC	TCGA-B9-5156-01A-01D-1589-08		8229750	182924526	33	5019											
FBXL5	26234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	15640266	15640266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcaatcactttctttttaaTatccttaagctcttcatagg	10	18	4	9	0	4	0	2	0	2	0	5	0	5	0	1	1	2	2	1	1	5	8			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:15640266T>C	ENST00000341285.3	-	4	572	c.448A>G	c.(448-450)Att>Gtt	p.I150V	FBXL5_ENST00000412094.2_Missense_Mutation_p.I133V|FBXL5_ENST00000382358.4_Missense_Mutation_p.I24V	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	150	Hemerythrin-like.				iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						TTCTTTTTAATATCCTTAAGC	0.368																																					p.I150V		.											.	FBXL5-226	0			c.A448G						.						76	67	70					4																	15640266		2201	4299	6500	SO:0001583	missense	26234	exon4			TTTTAATATCCTT	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"F-boxes / Leucine-rich repeats"	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.448A>G	4.37:g.15640266T>C	ENSP00000344866:p.Ile150Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	65	21	NM_001193534	0	0	78	159	81	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	37	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	31|31	5.081114|5.081114	0.94050|0.94050	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000341285;ENST00000412094;ENST00000382358;ENST00000512066;ENST00000503196;ENST00000509314|ENST00000513163	T;T;T|.	0.38722|.	1.18;1.17;1.12|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59169|0.59169	0.2174|0.2174	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	P;P|.	0.51791|.	0.948;0.913|.	D;P|.	0.67103|.	0.949;0.891|.	T|T	0.55431|0.55431	-0.8142|-0.8142	10|5	0.72032|.	D|.	0.01|.	-22.925|-22.925	16.1306|16.1306	0.81436|0.81436	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	133;150|.	Q9UKA1-2;Q9UKA1|.	.;FBXL5_HUMAN|.	V|C	150;133;24;112;95;95|70	ENSP00000344866:I150V;ENSP00000408679:I133V;ENSP00000371795:I24V|.	ENSP00000344866:I150V|.	I|Y	-|-	1|2	0|0	FBXL5|FBXL5	15249364|15249364	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.034000|8.034000	0.88864|0.88864	2.209000|2.209000	0.71365|0.71365	0.528000|0.528000	0.53228|0.53228	ATT|TAT	.		0.368	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			C	15640266	T	C	15640266	3	2	52	1	0	0	0	0	1	0	0	0	5741	1406	49	3	1659	3	FBXL5	4	15640266	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	7410516	15640266	175514010	34	5020											
GC	2638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	72620174	72620174	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctgaataatctgcacataGttcttgtcccttgtcaatga	10	16	6	9	0	4	2	1	2	3	0	5	2	5	2	1	0	1	2	1	0	4	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:72620174G>A	ENST00000273951.8	-	10	1559	c.1216C>T	c.(1216-1218)Cta>Tta	p.L406L	GC_ENST00000513476.1_Silent_p.L406L|GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Silent_p.L425L	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	406	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)|vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	actin binding (GO:0003779)|calcidiol binding (GO:1902118)|vitamin D binding (GO:0005499)|vitamin transporter activity (GO:0051183)			endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	TCTGCACATAGTTCTTGTCCC	0.308																																					p.L425L		.											.	GC-93	0			c.C1273T						.						77	76	76					4																	72620174		2203	4300	6503	SO:0001819	synonymous_variant	2638	exon11			CACATAGTTCTTG	L10641	CCDS3550.1, CCDS56332.1	4q12-q13	2008-08-29			ENSG00000145321	ENSG00000145321			4187	protein-coding gene	gene with protein product		139200				558959	Standard	NM_000583		Approved	DBP, VDBP, hDBP	uc010iif.3	P02774	OTTHUMG00000129915	ENST00000273951.8:c.1216C>T	4.37:g.72620174G>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	54	16	NM_001204307	0	0	0	0	0	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	37	CCDS3550.1																																																																																			.		0.308	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			A	72620174	G	A	72620174	2	1	52	1	0	0	0	0	0	0	0	1	6302	1020	36	2		2	GC	4	72620174	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	56979908	72620174	118534102	35	5021											
USO1	8615	broad.mit.edu;ucsc.edu	37	chr4	76703850	76703850	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtatagtagttgaagatTgtttgattttgctccaaaac	12	15	9	5	0	0	3	0	2	0	1	1	3	1	3	1	1	2	5	1	1	6	8			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:76703850T>A	ENST00000538159.1	+	9	700	c.700T>A	c.(700-702)Tgt>Agt	p.C234S	USO1_ENST00000514213.2_Missense_Mutation_p.C217S			O60763	USO1_HUMAN	USO1 vesicle transport factor	232	Globular head.				ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi vesicle docking (GO:0048211)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|mitotic cell cycle (GO:0000278)|transcytosis (GO:0045056)|vesicle fusion with Golgi apparatus (GO:0048280)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AGTTGAAGATTGTTTGATTTT	0.308																																					.													.	USO1-25	0			.						.						29	27	27					4																	76703850		1801	4055	5856	SO:0001583	missense	8615	.			GAAGATTGTTTGA	AL832010	CCDS75144.1	4q21.1	2012-12-10	2012-12-10		ENSG00000138768	ENSG00000138768			30904	protein-coding gene	gene with protein product	"vesicle docking protein", "transcytosis associated protein"	603344	"USO1 homolog, vesicle docking protein (yeast)", "USO1 vesicle docking protein homolog (yeast)"			9478999, 9150144, 12077354, 15979508, 14736916	Standard	XM_006714395		Approved	TAP, VDP, p115	uc003hiu.3	O60763	OTTHUMG00000160952	ENST00000538159.1:c.700T>A	4.37:g.76703850T>A	ENSP00000440586:p.Cys234Ser	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	8	5	.	0	0	36	50	14	B2RAQ0|Q6PK63|Q86TB8|Q8N592	Missense_Mutation	SNP	ENST00000538159.1	37		.	.	.	.	.	.	.	.	.	.	T	22.9	4.354011	0.82243	.	.	ENSG00000138768	ENST00000508939;ENST00000538159;ENST00000514213;ENST00000264904	T;T	0.46819	0.86;0.86	5.82	5.82	0.92795	Armadillo-type fold (2);	0.000000	0.85682	D	0.000000	T	0.68577	0.3016	M	0.80746	2.51	0.80722	D	1	D;D	0.65815	0.985;0.995	P;P	0.62089	0.891;0.898	T	0.72364	-0.4316	10	0.56958	D	0.05	.	16.1917	0.81992	0.0:0.0:0.0:1.0	.	234;232	F5GYR8;O60763	.;USO1_HUMAN	S	67;234;217;160	ENSP00000440586:C234S;ENSP00000444850:C217S	ENSP00000264904:C160S	C	+	1	0	USO1	76922874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.481000	0.81124	2.216000	0.71823	0.533000	0.62120	TGT	.		0.308	USO1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003715		A	76703850	T	A	76703850	3	1	52	1	0	0	0	0	1	0	0	0	17072	1812	63	5	569	5	USO1	4	76703850	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	4083676	76703850	114450426	36	5022											
CENPE	1062	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	104041471	104041471	+	Frame_Shift_Del	DEL	T	T	-																															ctttagcttcatgcagtgaaTtttccagctctcgaattttc																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:104041471delT	ENST00000265148.3	-	44	7252	c.7163delA	c.(7162-7164)aatfs	p.N2388fs	CENPE_ENST00000380026.3_Frame_Shift_Del_p.N2267fs	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2388	Kinetochore-binding domain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ATGCAGTGAATTTTCCAGCTC	0.333																																					p.N2388fs		.											.	CENPE-277	0			c.7163delA						.						106	90	96					4																	104041471		2202	4296	6498	SO:0001589	frameshift_variant	1062	exon44			.	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.7163delA	4.37:g.104041471delT	ENSP00000265148:p.Asn2388fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	62	18	NM_001813	0	0	0	0	0	A6NKY9|A8K2U7|Q4LE75	Frame_Shift_Del	DEL	ENST00000265148.3	37	CCDS34042.1																																																																																			.		0.333	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	104041471	T	-	104041471	7	5	52	1	0	1	0	1	0	0	0	0	3236	1493	52	0	966	0	CENPE	4	104041471	Frame_Shift_Del	DEL	T	TCGA-B9-5156-01A-01D-1589-08	27337621	104041471	87112805	37	5023											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	151827133	151827134	+	Frame_Shift_Ins	INS	-	-	T																															actgctctgctaacatgagaINStttggaagactgcaaaaaaa																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:151827133_151827134insT	ENST00000357115.3	-	13	1854_1855	c.1611_1612insA	c.(1609-1614)aaatctfs	p.S538fs	LRBA_ENST00000507224.1_Frame_Shift_Ins_p.S538fs|LRBA_ENST00000510413.1_Frame_Shift_Ins_p.S538fs|LRBA_ENST00000535741.1_Frame_Shift_Ins_p.S538fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	538						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CTAACATGAGATTTGGAAGACT	0.396																																					p.S538fs		.											.	LRBA-157	0			c.1612_1613insA						.																																			SO:0001589	frameshift_variant	987	exon13			.	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1612dupA	4.37:g.151827136_151827136dupT	ENSP00000349629:p.Ser538fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	67	27	NM_006726	0	0	0	0	0	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Ins	INS	ENST00000357115.3	37	CCDS3773.1																																																																																			.		0.396	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151827134	-	T	151827133	7	5	52	1	0	1	1	0	0	0	0	0	8956	333	12	0	7163	0	LRBA	4	151827133	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	47785662	151827133	39327143	38	5024											
TERT	7015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1282605	1282605	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtagaaaaagagcctgttctTttgaaacgtggtctccgtga	11	12	11	7	2	2	4	0	2	2	2	3	4	2	4	2	1	2	2	2	1	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:1282605T>G	ENST00000310581.5	-	3	1765	c.1708A>C	c.(1708-1710)Aag>Cag	p.K570Q	TERT_ENST00000296820.5_Missense_Mutation_p.K570Q|TERT_ENST00000508104.2_Missense_Mutation_p.K570Q|TERT_ENST00000334602.6_Missense_Mutation_p.K570Q	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	570			K -> N (in AA susceptibility; abolishes telomerase catalytic activity but no effect on binding to TERC). {ECO:0000269|PubMed:16990594, ECO:0000269|PubMed:19760749}.		DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	AGCCTGTTCTTTTGAAACGTG	0.517									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.K570Q		.											.	TERT-1272	0			c.A1708C						.						119	114	116					5																	1282605		2203	4300	6503	SO:0001583	missense	7015	exon3	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	TGTTCTTTTGAAA	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.1708A>C	5.37:g.1282605T>G	ENSP00000309572:p.Lys570Gln	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	51	13	NM_001193376	0	0	0	0	0	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	T	15.08	2.727919	0.48833	.	.	ENSG00000164362	ENST00000310581;ENST00000296820;ENST00000334602;ENST00000508104	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	4.64	3.42	0.39159	Telomerase ribonucleoprotein complex - RNA-binding domain (2);	0.049349	0.85682	D	0.000000	D	0.93969	0.8069	M	0.92026	3.265	0.49213	D	0.999767	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.97110	0.952;1.0;0.972	D	0.93578	0.6910	10	0.72032	D	0.01	-0.3505	11.0502	0.47882	0.0:0.0:0.1562:0.8438	.	570;570;570	O14746-3;O14746;Q8NG38	.;TERT_HUMAN;.	Q	570	ENSP00000309572:K570Q;ENSP00000296820:K570Q;ENSP00000334346:K570Q;ENSP00000426042:K570Q	ENSP00000296820:K570Q	K	-	1	0	TERT	1335605	1.000000	0.71417	0.999000	0.59377	0.854000	0.48673	2.991000	0.49409	0.585000	0.29608	0.379000	0.24179	AAG	.		0.517	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			G	1282605	T	G	1282605	3	3	52	1	0	0	0	0	1	0	0	0	15796	1850	64	5	1746	5	TERT	5	1282605	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08		1282605	179632655	39	5025											
CDH6	1004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	31323226	31323226	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaatgacacggaccccacTgccccgccatacgactcctt	11	6	7	17	3	0	1	0	1	0	0	1	4	1	2	6	1	2	0	6	1	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:31323226T>G	ENST00000265071.2	+	12	2449	c.2184T>G	c.(2182-2184)acT>acG	p.T728T		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	728					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGGACCCCACTGCCCCGCCAT	0.557																																					p.T728T		.											.	CDH6-159	0			c.T2184G						.						42	43	42					5																	31323226		2203	4300	6503	SO:0001819	synonymous_variant	1004	exon12			CCCCACTGCCCCG	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"Cadherins / Major cadherins"	1765	protein-coding gene	gene with protein product	"K-Cadherin"	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.2184T>G	5.37:g.31323226T>G		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	34	5	NM_004932	0	1	186	233	46	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			.		0.557	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		G	31323226	T	G	31323226	2	3	52	1	0	0	0	0	0	0	0	1	3120	1567	55	5		5	CDH6	5	31323226	Silent	SNP	T	TCGA-B9-5156-01A-01D-1589-08	30040621	31323226	149592034	40	5026											
TRIM36	55521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	114515696	114515696	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctttagctatcaattccatGatgtagccaaattcactcat	12	14	4	11	0	3	1	3	1	0	0	4	1	4	1	3	0	2	2	3	0	5	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:114515696G>A	ENST00000282369.3	-	1	160	c.39C>T	c.(37-39)atC>atT	p.I13I	TRIM36_ENST00000379618.2_Silent_p.I13I|TRIM36_ENST00000379617.2_Silent_p.I13I|TRIM36_ENST00000514154.1_5'UTR	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	13					acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TCAATTCCATGATGTAGCCAA	0.577																																					p.I13I		.											.	TRIM36-725	0			c.C39T						.						116	117	117					5																	114515696		2202	4300	6502	SO:0001819	synonymous_variant	55521	exon1			TTCCATGATGTAG	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.39C>T	5.37:g.114515696G>A		Somatic	162	0		WXS	Illumina HiSeq	Phase_I	137	47	NM_001017397	0	0	0	0	0	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	37	CCDS4115.1																																																																																			.		0.577	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		A	114515696	G	A	114515696	2	1	52	1	0	0	0	0	0	0	0	1	16543	1280	45	2		2	TRIM36	5	114515696	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	83192470	114515696	66399564	41	5027											
PCDHGA1	56114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140712438	140712438	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctgctacaggcttcgggAggcggcttagcgagcatgcc	6	8	15	12	4	1	0	0	0	1	0	2	2	1	1	1	4	5	4	1	4	2	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:140712438A>G	ENST00000517417.1	+	1	2187	c.2187A>G	c.(2185-2187)ggA>ggG	p.G729G	PCDHGA1_ENST00000378105.3_Silent_p.G729G	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	729					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCTTCGGGAGGCGGCTTAG	0.662																																					p.G729G		.											.	PCDHGA1-137	0			c.A2187G						.						64	69	68					5																	140712438		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			TTCGGGAGGCGGC	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2187A>G	5.37:g.140712438A>G		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	98	37	NM_018912	0	0	3	3	0	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																			.		0.662	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140712438	A	G	140712438	2	3	52	1	0	0	0	0	0	0	0	1	11576	291	11	3		3	PCDHGA1	5	140712438	Silent	SNP	A	TCGA-B9-5156-01A-01D-1589-08	26196742	140712438	40202822	42	5028											
LARS	51520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	145506033	145506033	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatggcatgactttcttcaTgtatttcttcagttctggca	9	17	7	8	0	5	1	2	1	3	0	5	1	5	1	0	2	0	4	0	2	2	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:145506033T>C	ENST00000394434.2	-	28	3122	c.2956A>G	c.(2956-2958)Atg>Gtg	p.M986V	LARS_ENST00000510191.1_Missense_Mutation_p.M932V|LARS_ENST00000274562.9_Missense_Mutation_p.M959V|LARS_ENST00000545646.1_Missense_Mutation_p.M940V	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	986					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	ACTTTCTTCATGTATTTCTTC	0.428																																					p.M986V		.											.	LARS-90	0			c.A2956G						.						202	156	171					5																	145506033		2202	4300	6502	SO:0001583	missense	51520	exon28			TCTTCATGTATTT	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	6512	protein-coding gene	gene with protein product	"leucine tRNA ligase 1, cytoplasmic"	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2956A>G	5.37:g.145506033T>C	ENSP00000377954:p.Met986Val	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	86	24	NM_020117	0	0	24	58	34	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	37	CCDS34265.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.399675	0.42512	.	.	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000540713;ENST00000510191;ENST00000274562	T;T;T;T	0.63913	-0.06;-0.06;-0.06;-0.07	5.17	5.17	0.71159	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.037152	0.85682	D	0.000000	T	0.66157	0.2761	M	0.86864	2.845	0.80722	D	1	B;P;B	0.38335	0.007;0.627;0.001	B;B;B	0.36030	0.007;0.216;0.007	T	0.68401	-0.5418	10	0.25751	T	0.34	.	15.1805	0.72952	0.0:0.0:0.0:1.0	.	959;940;986	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	V	986;940;295;932;959	ENSP00000377954:M986V;ENSP00000437791:M940V;ENSP00000426005:M932V;ENSP00000274562:M959V	ENSP00000274562:M959V	M	-	1	0	LARS	145486226	1.000000	0.71417	0.937000	0.37676	0.899000	0.52679	5.892000	0.69790	2.178000	0.69098	0.455000	0.32223	ATG	.		0.428	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		C	145506033	T	C	145506033	3	2	52	1	0	0	0	0	1	0	0	0	8655	1464	51	3	594	3	LARS	5	145506033	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	4793595	145506033	35409227	43	5029											
PDGFRB	5159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149511592	149511592	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctcagcatcctcatggaagGcccgcatggtgtagtggcca	8	8	12	13	1	2	0	2	0	0	0	3	1	3	1	4	4	1	3	4	4	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:149511592G>T	ENST00000261799.4	-	8	1662	c.1193C>A	c.(1192-1194)gCc>gAc	p.A398D		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	398	Ig-like C2-type 4.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTCATGGAAGGCCCGCATGGT	0.607			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.A398D		.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB-1499	0			c.C1193A						.						129	106	114					5																	149511592		2203	4300	6503	SO:0001583	missense	5159	exon8			TGGAAGGCCCGCA	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1193C>A	5.37:g.149511592G>T	ENSP00000261799:p.Ala398Asp	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	53	11	NM_002609	0	0	10	10	0	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.318803	0.81469	.	.	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.76968	-1.06	5.52	4.65	0.58169	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000079	D	0.86908	0.6046	M	0.79805	2.47	0.41506	D	0.988315	D;D	0.89917	0.992;1.0	D;D	0.77004	0.959;0.989	D	0.88006	0.2759	10	0.87932	D	0	.	10.3808	0.44110	0.1488:0.0:0.8512:0.0	.	398;398	A8KAM8;P09619	.;PGFRB_HUMAN	D	398;68	ENSP00000261799:A398D	ENSP00000261799:A398D	A	-	2	0	PDGFRB	149491785	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	4.122000	0.57910	1.325000	0.45301	0.655000	0.94253	GCC	.		0.607	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		T	149511592	G	T	149511592	3	4	52	1	0	0	0	0	1	0	0	0	11688	1203	42	4	2191	4	PDGFRB	5	149511592	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	4005559	149511592	31403668	44	5030											
SLC34A1	6569	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176824798	176824800	+	In_Frame_Del	DEL	CTT	CTT	-																															ctgcagattgccctctgtcaCttcttcttcaacatctcggg																								rs387907506		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:176824798_176824800delCTT	ENST00000324417.5	+	13	1522_1524	c.1431_1433delCTT	c.(1429-1434)cacttc>cac	p.F480del	SLC34A1_ENST00000513614.1_3'UTR	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	480					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCTCTGTCACTTCTTCTTCAAC	0.616																																					p.477_478del		.											.	SLC34A1-91	0			c.1431_1433del						.																																			SO:0001651	inframe_deletion	6569	exon13			.	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.1431_1433delCTT	5.37:g.176824804_176824806delCTT	ENSP00000321424:p.Phe480del	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	118	26	NM_003052	0	0	0	0	0	B4DPE3	In_Frame_Del	DEL	ENST00000324417.5	37	CCDS4418.1																																																																																			.		0.616	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052		-	176824800	CTT	-	176824798	7	5	52	1	0	1	0	1	0	0	0	0	14599	564	20	0	1568	0	SLC34A1	5	176824798	In_Frame_Del	DEL	CTT	TCGA-B9-5156-01A-01D-1589-08	27313206	176824798	4090462	45	5031											
PRPF4B	8899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	4032504	4032504	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaggcgatctcaagagaaAattggtaaggccagatctcc	15	7	11	8	1	2	3	1	0	2	3	4	5	2	3	2	3	0	1	2	3	5	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr6:4032504A>C	ENST00000337659.6	+	2	853	c.753A>C	c.(751-753)aaA>aaC	p.K251N	PRPF4B_ENST00000538861.1_Missense_Mutation_p.K237N	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	251	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				CTCAAGAGAAAATTGGTAAGG	0.343																																					p.K251N		.											.	PRPF4B-1308	0			c.A753C						.						123	134	131					6																	4032504		2203	4300	6503	SO:0001583	missense	8899	exon2			AGAGAAAATTGGT	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.753A>C	6.37:g.4032504A>C	ENSP00000337194:p.Lys251Asn	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	188	79	NM_003913	0	0	17	28	11	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997406	0.54147	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.67865	-0.29;-0.29	5.61	-1.1	0.09872	.	0.000000	0.85682	D	0.000000	T	0.28699	0.0711	L	0.36672	1.1	0.32528	N	0.535323	P	0.43477	0.808	B	0.33960	0.173	T	0.13255	-1.0516	10	0.32370	T	0.25	.	10.743	0.46164	0.6402:0.0:0.3598:0.0	.	251	Q13523	PRP4B_HUMAN	N	251;237	ENSP00000337194:K251N;ENSP00000439331:K237N	ENSP00000337194:K251N	K	+	3	2	PRPF4B	3977503	0.997000	0.39634	0.223000	0.23860	0.955000	0.61496	1.838000	0.39211	-0.329000	0.08527	0.533000	0.62120	AAA	.		0.343	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			C	4032504	A	C	4032504	3	2	52	1	0	0	0	0	1	0	0	0	12602	11	1	5	759	5	PRPF4B	6	4032504	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		4032504	167082563	46	5032											
MUC21	394263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30954340	30954340	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagtccagcacaccctccAgtggggccagcacagccacc	9	4	10	18	0	0	1	0	1	0	0	2	1	2	1	6	2	3	2	6	2	0	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr6:30954340A>T	ENST00000376296.3	+	2	629	c.388A>T	c.(388-390)Agt>Tgt	p.S130C	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	130	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CACACCCTCCAGTGGGGCCAG	0.607																																					p.S130C		.											.	MUC21-92	0			c.A388T						.						164	155	158					6																	30954340		2203	4300	6503	SO:0001583	missense	394263	exon2			CCCTCCAGTGGGG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.388A>T	6.37:g.30954340A>T	ENSP00000365473:p.Ser130Cys	Somatic	255	0		WXS	Illumina HiSeq	Phase_I	249	57	NM_001010909	0	0	0	0	0	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	9.389	1.074974	0.20227	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.03301	3.98	3.34	-1.87	0.07737	.	.	.	.	.	T	0.01092	0.0036	N	0.24115	0.695	0.09310	N	1	D	0.53619	0.961	P	0.47162	0.54	T	0.47433	-0.9118	8	.	.	.	.	4.8046	0.13314	0.3103:0.0:0.5043:0.1854	.	130	Q5SSG8	MUC21_HUMAN	C	130	ENSP00000365473:S130C	.	S	+	1	0	MUC21	31062319	0.007000	0.16637	0.000000	0.03702	0.014000	0.08584	1.200000	0.32247	-0.218000	0.10018	-0.425000	0.05940	AGT	.		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30954340	A	T	30954340	3	4	52	1	0	0	0	0	1	0	0	0	10002	188	7	5	394	5	MUC21	6	30954340	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	26921836	30954340	140160727	47	5033											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51889440	51889440	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggcagatgaggcccaccctCtgatgcagtcatagcctctg	8	8	12	13	0	3	3	1	2	2	1	3	3	3	3	3	2	2	2	3	2	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr6:51889440C>G	ENST00000371117.3	-	32	5443	c.5168G>C	c.(5167-5169)aGa>aCa	p.R1723T	PKHD1_ENST00000340994.4_Missense_Mutation_p.R1723T	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1723	IPT/TIG 12; atypical.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGCCCACCCTCTGATGCAGTC	0.532																																					p.R1723T		.											.	PKHD1-603	0			c.G5168C						.						87	86	86					6																	51889440		2203	4300	6503	SO:0001583	missense	5314	exon32			CACCCTCTGATGC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5168G>C	6.37:g.51889440C>G	ENSP00000360158:p.Arg1723Thr	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	97	28	NM_170724	0	0	5	12	7	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071085	0.55646	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87256	-2.05;-2.23	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.91543	0.7329	M	0.66939	2.045	0.35080	D	0.763272	D;D	0.76494	0.99;0.999	D;D	0.77557	0.96;0.99	D	0.91115	0.4925	10	0.45353	T	0.12	.	18.6881	0.91573	0.0:1.0:0.0:0.0	.	1723;1723	P08F94-2;P08F94	.;PKHD1_HUMAN	T	1723	ENSP00000360158:R1723T;ENSP00000341097:R1723T	ENSP00000341097:R1723T	R	-	2	0	PKHD1	51997399	1.000000	0.71417	0.878000	0.34440	0.146000	0.21551	5.086000	0.64474	2.659000	0.90383	0.650000	0.86243	AGA	.		0.532	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51889440	C	G	51889440	3	3	52	1	0	0	0	0	1	0	0	0	11997	913	32	4	7239	4	PKHD1	6	51889440	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	20935100	51889440	119225627	48	5034											
LIMK1	3984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	73530183	73530183	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggcgcgtctcatggtggacGagaagactcagcctgagggc	8	7	16	10	3	2	3	2	1	1	2	3	5	2	4	1	4	1	0	1	4	1	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:73530183G>A	ENST00000336180.2	+	13	1513	c.1462G>A	c.(1462-1464)Gag>Aag	p.E488K	LIMK1_ENST00000418310.1_Missense_Mutation_p.E518K|LIMK1_ENST00000538333.3_Missense_Mutation_p.E454K	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	488	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CATGGTGGACGAGAAGACTCA	0.607																																					p.E488K		.											.	LIMK1-523	0			c.G1462A						.						101	83	89					7																	73530183		2203	4300	6503	SO:0001583	missense	3984	exon13			GTGGACGAGAAGA	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1462G>A	7.37:g.73530183G>A	ENSP00000336740:p.Glu488Lys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	76	22	NM_002314	0	0	40	50	10	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	g	14.48	2.547545	0.45383	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000538333	T;T;T	0.62232	0.04;0.04;0.04	5.25	3.45	0.39498	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.210321	0.48767	D	0.000162	T	0.43942	0.1270	N	0.17345	0.48	0.50813	D	0.999895	P;P	0.48834	0.543;0.916	B;B	0.42386	0.364;0.386	T	0.28427	-1.0044	10	0.39692	T	0.17	-19.111	8.804	0.34927	0.0834:0.1523:0.7643:0.0	.	454;488	B7Z6I8;P53667	.;LIMK1_HUMAN	K	518;488;488;454	ENSP00000409717:E518K;ENSP00000336740:E488K;ENSP00000444452:E454K	ENSP00000336740:E488K	E	+	1	0	LIMK1	73168119	1.000000	0.71417	0.039000	0.18376	0.059000	0.15707	7.647000	0.83462	0.627000	0.30340	-0.240000	0.12126	GAG	.		0.607	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		A	73530183	G	A	73530183	3	1	52	1	0	0	0	0	1	0	0	0	8823	1059	37	1	1512	1	LIMK1	7	73530183	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		73530183	85608480	49	5035											
STYXL1	51657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	75633079	75633079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggaacgctccttaccaaTgaagtgacacatgtggcgta	13	8	10	10	2	0	2	0	2	0	0	1	3	1	3	2	2	2	2	2	2	6	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:75633079T>C	ENST00000248600.1	-	7	1036	c.694A>G	c.(694-696)Att>Gtt	p.I232V	STYXL1_ENST00000359697.3_Missense_Mutation_p.I232V|STYXL1_ENST00000340062.5_Missense_Mutation_p.I136V|STYXL1_ENST00000360591.3_3'UTR|STYXL1_ENST00000431581.1_Missense_Mutation_p.I232V|STYXL1_ENST00000451157.1_Missense_Mutation_p.I232V	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	232	Tyrosine-protein phosphatase.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						TCCTTACCAATGAAGTGACAC	0.537																																					p.I232V		.											.	STYXL1-278	0			c.A694G						.						113	87	96					7																	75633079		2203	4300	6503	SO:0001583	missense	51657	exon7			TACCAATGAAGTG	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	18165	protein-coding gene	gene with protein product			"dual specificity phosphatase 24 (putative)"	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.694A>G	7.37:g.75633079T>C	ENSP00000248600:p.Ile232Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	80	47	NM_016086	0	0	0	0	0	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Missense_Mutation	SNP	ENST00000248600.1	37	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.347287	0.24426	.	.	ENSG00000127952	ENST00000248600;ENST00000359697;ENST00000340062;ENST00000404050;ENST00000431581;ENST00000454618;ENST00000451157	D;D;D;D;T;D	0.88124	-2.34;-2.34;-2.34;-2.34;0.0;-2.34	3.74	-3.86	0.04230	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.287194	0.36374	N	0.002630	T	0.79435	0.4445	L	0.52823	1.66	0.80722	D	1	B;B;B;B;B;B	0.33748	0.423;0.172;0.096;0.01;0.087;0.086	B;B;B;B;B;B	0.32805	0.153;0.133;0.081;0.007;0.12;0.124	T	0.66212	-0.5980	10	0.62326	D	0.03	.	8.0828	0.30754	0.0:0.0993:0.6291:0.2716	.	232;232;232;136;232;136	Q9Y6J8-3;C9J4H0;Q9Y6J8-2;Q9Y6J8-4;Q9Y6J8;Q7Z3H6	.;.;.;.;STYL1_HUMAN;.	V	232;232;136;232;232;187;232	ENSP00000248600:I232V;ENSP00000352726:I232V;ENSP00000343383:I136V;ENSP00000392221:I232V;ENSP00000406073:I187V;ENSP00000411812:I232V	ENSP00000248600:I232V	I	-	1	0	STYXL1	75471015	0.998000	0.40836	0.219000	0.23793	0.709000	0.40893	0.666000	0.25097	-0.708000	0.05015	0.460000	0.39030	ATT	.		0.537	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086		C	75633079	T	C	75633079	3	2	52	1	0	0	0	0	1	0	0	0	15393	1464	51	3	259	3	STYXL1	7	75633079	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	2102896	75633079	83505584	50	5036											
STYXL1	51657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	75643205	75643205	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgcttgaggcacaagaTctgagagtggagaccaaaga	13	7	14	7	0	1	5	0	2	1	4	1	7	1	5	1	3	1	3	1	3	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:75643205T>C	ENST00000248600.1	-	5	650	c.308A>G	c.(307-309)gAt>gGt	p.D103G	STYXL1_ENST00000359697.3_Splice_Site_p.D103G|STYXL1_ENST00000340062.5_Intron|STYXL1_ENST00000360591.3_Intron|STYXL1_ENST00000431581.1_Splice_Site_p.D103G|STYXL1_ENST00000460184.2_5'UTR|STYXL1_ENST00000451157.1_Splice_Site_p.D103G	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	103	Rhodanese.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						AGGCACAAGATCTGAGAGTGG	0.498																																					p.D103G		.											.	STYXL1-278	0			c.A308G						.						125	109	114					7																	75643205		2203	4300	6503	SO:0001630	splice_region_variant	51657	exon5			ACAAGATCTGAGA	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	18165	protein-coding gene	gene with protein product			"dual specificity phosphatase 24 (putative)"	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.308-1A>G	7.37:g.75643205T>C		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	189	89	NM_016086	0	0	0	0	0	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Missense_Mutation	SNP	ENST00000248600.1	37	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	T	9.558	1.117639	0.20877	.	.	ENSG00000127952	ENST00000248600;ENST00000359697;ENST00000404050;ENST00000431581;ENST00000454618;ENST00000451157	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.26	-5.09	0.02920	Rhodanese-like (4);	2.770220	0.00966	N	0.003162	T	0.14787	0.0357	N	0.16478	0.41	0.26750	N	0.970228	B;B;B	0.10296	0.003;0.001;0.002	B;B;B	0.11329	0.006;0.001;0.003	T	0.18209	-1.0344	10	0.22706	T	0.39	.	7.9066	0.29765	0.1461:0.5762:0.0:0.2777	.	103;103;103	C9J4H0;Q9Y6J8-2;Q9Y6J8	.;.;STYL1_HUMAN	G	103;103;103;103;58;103	ENSP00000248600:D103G;ENSP00000352726:D103G;ENSP00000392221:D103G;ENSP00000411812:D103G	ENSP00000248600:D103G	D	-	2	0	STYXL1	75481141	0.053000	0.20554	0.002000	0.10522	0.015000	0.08874	-0.109000	0.10840	-0.873000	0.04032	0.454000	0.30748	GAT	.		0.498	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	Missense_Mutation	C	75643205	T	C	75643205	5	2	52	1	0	0	0	0	0	0	1	0	15393	1449	50	3	653	3	STYXL1	7	75643205	Splice_Site	SNP	T	TCGA-B9-5156-01A-01D-1589-08	10126	75643205	83495458	51	5037											
ZNF3	7551	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99669265	99669266	+	Frame_Shift_Ins	INS	-	-	C																															attacattcatagggtttctINScccccgtgtggatcctccga																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:99669265_99669266insC	ENST00000424697.1	-	6	1147_1148	c.841_842insG	c.(841-843)gagfs	p.E281fs	ZNF3_ENST00000299667.4_Frame_Shift_Ins_p.E281fs|ZNF3_ENST00000413658.2_Intron|ZNF3_ENST00000303915.6_Frame_Shift_Ins_p.E281fs	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	281					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			ATAGGGTTTCTCCCCCGTGTGG	0.515																																					p.E281fs		.											.	ZNF3-91	0			c.842_843insG						.																																			SO:0001589	frameshift_variant	7551	exon6			.	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.842dupG	7.37:g.99669270_99669270dupC	ENSP00000415358:p.Glu281fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	113	28	NM_032924	0	0	0	0	0	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Frame_Shift_Ins	INS	ENST00000424697.1	37	CCDS43619.1																																																																																			.		0.515	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		C	99669266	-	C	99669265	7	5	52	1	0	1	1	0	0	0	0	0	17861	1551	54	0	631	0	ZNF3	7	99669265	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	24026060	99669265	59469398	52	5038											
NRCAM	4897	hgsc.bcm.edu;broad.mit.edu	37	chr7	107836289	107836289	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgacctggtagagtgtgtttGcaggtgtgaggattcgtggt	6	14	17	4	1	0	3	0	2	0	1	1	4	0	4	1	4	1	3	1	4	1	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:107836289G>T	ENST00000425651.2	-	12	1378	c.1379C>A	c.(1378-1380)gCa>gAa	p.A460E	NRCAM_ENST00000379022.4_Missense_Mutation_p.A460E|NRCAM_ENST00000351718.4_Missense_Mutation_p.A454E|NRCAM_ENST00000379024.4_Missense_Mutation_p.A441E|NRCAM_ENST00000413765.2_Missense_Mutation_p.A441E|NRCAM_ENST00000379028.3_Missense_Mutation_p.A460E	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	460	Ig-like 5.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GAGTGTGTTTGCAGGTGTGAG	0.403																																					p.A460E		.											.	NRCAM-156	0			c.C1379A						.						153	133	140					7																	107836289		2203	4300	6503	SO:0001583	missense	4897	exon12			GTGTTTGCAGGTG		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.1379C>A	7.37:g.107836289G>T	ENSP00000401244:p.Ala460Glu	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_001037132	0	0	17	17	0	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	G	4.258	0.046854	0.08243	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979	T;T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66;1.66	5.2	2.26	0.28386	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.402640	0.27650	N	0.018433	T	0.13798	0.0334	N	0.25825	0.765	0.35757	D	0.819842	B;B;B;B;B	0.10296	0.001;0.002;0.003;0.002;0.001	B;B;B;B;B	0.17979	0.005;0.02;0.013;0.008;0.006	T	0.24404	-1.0161	10	0.02654	T	1	.	2.5345	0.04711	0.1394:0.1264:0.4743:0.2599	.	460;441;441;454;460	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	E	460;460;441;460;454;441;460;460;454	ENSP00000368314:A460E;ENSP00000407858:A441E;ENSP00000325269:A454E;ENSP00000368310:A441E;ENSP00000401244:A460E;ENSP00000368308:A460E	ENSP00000325269:A454E	A	-	2	0	NRCAM	107623525	0.894000	0.30519	0.896000	0.35187	0.983000	0.72400	1.999000	0.40806	0.512000	0.28257	0.563000	0.77884	GCA	.		0.403	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		T	107836289	G	T	107836289	3	4	52	1	0	0	0	0	1	0	0	0	10670	1319	46	4	2641	4	NRCAM	7	107836289	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	8167024	107836289	51302374	53	5039											
ZNF786	136051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	148767681	148767681	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacaggcaaagggcctctcgGgcctgtggatgcgctggtgc	6	7	16	12	2	1	0	0	0	1	0	2	1	1	1	2	5	2	2	2	5	1	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:148767681G>T	ENST00000491431.1	-	4	2247	c.2183C>A	c.(2182-2184)cCc>cAc	p.P728H	ZNF786_ENST00000451334.3_Missense_Mutation_p.P691H|ZNF786_ENST00000316286.9_Missense_Mutation_p.P642H	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	728					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(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GGGCCTCTCGGGCCTGTGGAT	0.567																																					p.P728H		.											.	ZNF786-50	0			c.C2183A						.						131	135	133					7																	148767681		2045	4211	6256	SO:0001583	missense	136051	exon4			CTCTCGGGCCTGT	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"Zinc fingers, C2H2-type", "-"	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2183C>A	7.37:g.148767681G>T	ENSP00000417470:p.Pro728His	Somatic	241	1		WXS	Illumina HiSeq	Phase_I	297	138	NM_152411	0	0	2	2	0	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	37	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678888	0.47886	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	T;T;T	0.19394	2.15;2.15;2.15	4.62	3.7	0.42460	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36444	N	0.002595	T	0.34745	0.0908	L	0.42581	1.335	0.31365	N	0.68091	D	0.89917	1.0	D	0.77004	0.989	T	0.21484	-1.0244	10	0.87932	D	0	-21.2407	10.48	0.44687	0.0:0.3127:0.6873:0.0	.	728	Q8N393	ZN786_HUMAN	H	642;728;691	ENSP00000313516:P642H;ENSP00000417470:P728H;ENSP00000404984:P691H	ENSP00000313516:P642H	P	-	2	0	ZNF786	148398614	0.001000	0.12720	0.900000	0.35374	0.789000	0.44602	0.774000	0.26675	2.411000	0.81874	0.591000	0.81541	CCC	.		0.567	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411		T	148767681	G	T	148767681	3	4	52	1	0	0	0	0	1	0	0	0	18190	1232	43	4	169	4	ZNF786	7	148767681	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	40931392	148767681	10370982	54	5040											
GIMAP6	474344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	150325338	150325338	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggccctggggcggataagacGatggcttggcagatagcgtc	8	7	17	9	3	0	2	0	0	0	2	1	4	0	3	1	6	1	2	1	6	2	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:150325338G>A	ENST00000328902.5	-	3	564	c.348C>T	c.(346-348)atC>atT	p.I116I	GIMAP6_ENST00000493969.1_Missense_Mutation_p.R42C	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	116	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CGGATAAGACGATGGCTTGGC	0.632																																					p.R42C		.											.	GIMAP6-93	0			c.C124T						.						57	59	58					7																	150325338		2203	4300	6503	SO:0001819	synonymous_variant	474344	exon3			TAAGACGATGGCT	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"GTPases, IMAP"	21918	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 6"					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.348C>T	7.37:g.150325338G>A		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	155	36	NM_001244071	0	0	6	6	0	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	.	.	.	.	.	.	.	.	.	.	G	8.530	0.870870	0.17322	.	.	ENSG00000133561	ENST00000493969	.	.	.	4.07	-6.18	0.02085	.	.	.	.	.	T	0.30386	0.0763	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44034	-0.9354	5	0.87932	D	0	.	2.4155	0.04435	0.2705:0.4128:0.199:0.1177	.	.	.	.	C	42	.	ENSP00000418304:R42C	R	-	1	0	GIMAP6	149956271	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.968000	0.03817	-1.017000	0.03367	-1.157000	0.01802	CGT	.		0.632	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		A	150325338	G	A	150325338	2	1	52	1	0	0	0	0	0	0	0	1	6403	1048	37	1		1	GIMAP6	7	150325338	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	1557657	150325338	8813325	55	5041											
PXDNL	137902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	52336162	52336162	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtaagaaacatgttggtcaCagcaaggccaaaagaattcc	16	8	9	8	0	1	2	1	0	0	2	2	2	2	2	2	2	2	3	2	2	6	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr8:52336162C>G	ENST00000356297.4	-	14	1868	c.1768G>C	c.(1768-1770)Gtg>Ctg	p.V590L	PXDNL_ENST00000543296.1_Missense_Mutation_p.V590L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	590	Ig-like C2-type 4.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				ATGTTGGTCACAGCAAGGCCA	0.453																																					p.V590L		.											.	PXDNL-70	0			c.G1768C						.						109	115	113					8																	52336162		2106	4234	6340	SO:0001583	missense	137902	exon14			TGGTCACAGCAAG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1768G>C	8.37:g.52336162C>G	ENSP00000348645:p.Val590Leu	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_144651	0	0	0	0	0	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	9.782	1.175500	0.21704	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.66638	-0.22;-0.22	4.59	2.79	0.32731	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50633	0.1627	N	0.25789	0.76	0.09310	N	1	B	0.14438	0.01	B	0.21151	0.033	T	0.36986	-0.9725	9	0.30854	T	0.27	.	7.6374	0.28274	0.0:0.7996:0.0:0.2004	.	590	A1KZ92	PXDNL_HUMAN	L	590	ENSP00000348645:V590L;ENSP00000444865:V590L	ENSP00000348645:V590L	V	-	1	0	PXDNL	52498715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.388000	0.07352	0.476000	0.27440	-0.757000	0.03467	GTG	.		0.453	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		G	52336162	C	G	52336162	3	3	52	1	0	0	0	0	1	0	0	0	12880	478	17	4	2663	4	PXDNL	8	52336162	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08		52336162	94027860	56	5042											
TMEM67	91147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	94797545	94797546	+	Missense_Mutation	DNP	TA	TA	CT																															gatgaaaatcaacatcaataTattttggctgtgcctgtgtt																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr8:94797545_94797546TA>CT	ENST00000453321.3	+	12	1285_1286	c.1227_1228TA>CT	c.(1225-1230)taTAtt>taCTtt	p.I410F	TMEM67_ENST00000409623.3_Missense_Mutation_p.I329F	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	410					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			AACATCAATATATTTTGGCTGT	0.337																																					p.I410F		.											.	TMEM67	0			c.A1228T						.																																			SO:0001583	missense	91147	exon12			CAATATATTTTGG	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	Exception_encountered	8.37:g.94797545_94797546delinsCT	ENSP00000389998:p.Ile410Phe	Somatic	268	1		WXS	Illumina HiSeq	Phase_I	228	69		0	0	0	0	0	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	DNP	ENST00000453321.3	37	CCDS6258.2																																																																																			.		0.337	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		CT	94797546	TA	CT	94797545	3	2	52	1	0	0	0	0	1	0	0	0	16228	1413	49	3	1411	3	TMEM67	8	94797545	Missense_Mutation	DNP	TA	TCGA-B9-5156-01A-01D-1589-08	42461383	94797545	51566477	57	5043											
DMRT2	10655	hgsc.bcm.edu	37	chr9	1051930	1051930	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtccccgagagcgctgcaCtcccgcgggcggcggcgcgg	3	3	18	17	9	0	1	0	0	0	1	2	2	2	1	3	5	2	2	3	5	0	0	rs112585712	byFrequency	TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr9:1051930C>G	ENST00000358146.2	+	1	317	c.317C>G	c.(316-318)aCt>aGt	p.T106S	DMRT2_ENST00000382251.3_Missense_Mutation_p.T106S|DMRT2_ENST00000302441.6_Missense_Mutation_p.T106S|DMRT2_ENST00000412350.2_Missense_Mutation_p.T106S|DMRT2_ENST00000259622.6_Missense_Mutation_p.T106S|DMRT2_ENST00000382255.3_Missense_Mutation_p.T106S			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	106					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		GAGCGCTGCACTCCCGCGGGC	0.786													C|||	131	0.0261581	0.0015	0.0187	5008	,	,		9377	0.006		0.0537	False		,,,				2504	0.0573				p.T106S		.											.	DMRT2-514	0			c.C317G						.						1	1	1					9																	1051930		747	1711	2458	SO:0001583	missense	10655	exon2			GCTGCACTCCCGC	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"terra-like protein"	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.317C>G	9.37:g.1051930C>G	ENSP00000350865:p.Thr106Ser	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_006557	0	0	0	0	0	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	52	0.023809523809523808	4	0.008130081300813009	8	0.022099447513812154	1	0.0017482517482517483	39	0.051451187335092345	C	8.378	0.836916	0.16891	.	.	ENSG00000173253	ENST00000382255;ENST00000382251;ENST00000412350;ENST00000302441;ENST00000358146;ENST00000259622	T;T;T;T;T;T	0.39997	1.05;2.04;1.05;2.04;2.04;1.05	3.82	0.583	0.17417	.	1.094080	0.07099	N	0.840084	T	0.03739	0.0106	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.14420	-1.0473	10	0.10636	T	0.68	0.1877	8.3816	0.32474	0.0:0.6844:0.1394:0.1761	.	106;106	Q05C20;Q9Y5R5	.;DMRT2_HUMAN	S	106	ENSP00000371690:T106S;ENSP00000371686:T106S;ENSP00000397494:T106S;ENSP00000305785:T106S;ENSP00000350865:T106S;ENSP00000259622:T106S	ENSP00000259622:T106S	T	+	2	0	DMRT2	1041930	0.001000	0.12720	0.003000	0.11579	0.005000	0.04900	-0.165000	0.09968	0.267000	0.21916	0.491000	0.48974	ACT	C|0.976;G|0.024		0.786	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		G	1051930	C	G	1051930	3	3	52	1	0	0	0	0	1	0	0	0	4597	565	20	4	319	4	DMRT2	9	1051930	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08		1051930	140161501	58	5044											
TOR1A	1861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	132576423	132576423	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggatacacatttttaggTgtttgtattccagggggagg	8	14	13	6	1	0	0	0	0	0	0	2	2	1	2	1	5	1	2	1	5	3	7			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr9:132576423T>G	ENST00000351698.4	-	5	875	c.827A>C	c.(826-828)cAc>cCc	p.H276P		NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	276	Interaction with KLC1.				ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				CATTTTTAGGTGTTTGTATTC	0.453																																					p.H276P		.											.	TOR1A-90	0			c.A827C						.						163	156	159					9																	132576423		2203	4300	6503	SO:0001583	missense	1861	exon5			TTTAGGTGTTTGT	AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"dystonia 1, torsion (autosomal dominant; torsin A)"	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.827A>C	9.37:g.132576423T>G	ENSP00000345719:p.His276Pro	Somatic	263	0		WXS	Illumina HiSeq	Phase_I	231	69	NM_000113	0	0	18	40	22	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269693	0.80469	.	.	ENSG00000136827	ENST00000427355;ENST00000351698	T	0.71579	-0.58	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.87740	0.6253	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90894	0.4763	10	0.87932	D	0	-9.1277	14.3493	0.66688	0.0:0.0:0.0:1.0	.	276	O14656	TOR1A_HUMAN	P	245;276	ENSP00000345719:H276P	ENSP00000345719:H276P	H	-	2	0	TOR1A	131616244	1.000000	0.71417	0.928000	0.36995	0.803000	0.45373	7.698000	0.84413	1.974000	0.57490	0.459000	0.35465	CAC	.		0.453	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113		G	132576423	T	G	132576423	3	3	52	1	0	0	0	0	1	0	0	0	16404	1696	59	5	175	5	TOR1A	9	132576423	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	131524493	132576423	8637008	59	5045											
FUT7	2529	broad.mit.edu	37	chr9	139925712	139925712	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcggtggcgagggccccCagtggggctccaggcggcca	5	3	19	14	3	0	0	0	0	0	0	1	1	1	0	4	7	1	2	4	7	0	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr9:139925712C>A	ENST00000314412.6	-	2	1497	c.479G>T	c.(478-480)tGg>tTg	p.W160L	ABCA2_ENST00000371605.3_5'Flank|ABCA2_ENST00000265662.5_5'Flank|C9orf139_ENST00000314330.2_Intron	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	160					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|leukocyte migration involved in immune response (GO:0002522)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|lung(4)|ovary(1)|skin(1)	8	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CGAGGGCCCCCAGTGGGGCTC	0.687																																					p.W160L													.	FUT7-90	0			c.G479T						.						13	17	15					9																	139925712		2171	4262	6433	SO:0001583	missense	2529	exon2			GGCCCCCAGTGGG	X78031, AB012668	CCDS7022.1	9q34.3	2013-02-26			ENSG00000180549	ENSG00000180549		"Fucosyltransferases"	4018	protein-coding gene	gene with protein product		602030				8207002, 8182079	Standard	NM_004479		Approved		uc004ckq.2	Q11130	OTTHUMG00000020964	ENST00000314412.6:c.479G>T	9.37:g.139925712C>A	ENSP00000318142:p.Trp160Leu	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	15	3	NM_004479	0	0	0	0	0	B2R7U7|Q6DK54	Missense_Mutation	SNP	ENST00000314412.6	37	CCDS7022.1	.	.	.	.	.	.	.	.	.	.	c	2.448	-0.327108	0.05350	.	.	ENSG00000180549	ENST00000314412	T	0.21543	2.0	4.74	-2.18	0.07037	.	6.541200	0.00678	N	0.000671	T	0.09158	0.0226	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23655	-1.0182	10	0.49607	T	0.09	5.1204	2.6034	0.04872	0.0942:0.3189:0.2336:0.3533	.	160	Q11130	FUT7_HUMAN	L	160	ENSP00000318142:W160L	ENSP00000318142:W160L	W	-	2	0	FUT7	139045533	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-1.554000	0.02172	-0.380000	0.07894	-0.251000	0.11542	TGG	.		0.687	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479		A	139925712	C	A	139925712	3	1	52	1	0	0	0	0	1	0	0	0	6128	595	21	4	553	4	FUT7	9	139925712	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	7349289	139925712	1287719	60	5046											
WNT8B	7479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102239758	102239758	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcagctgtccagccatggtgGgcttcgcagtggtaagaaaa	10	8	14	9	1	0	1	0	0	0	1	2	1	1	1	2	3	2	5	2	3	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr10:102239758G>A	ENST00000343737.5	+	3	358	c.230G>A	c.(229-231)gGg>gAg	p.G77E		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	77					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		AGCCATGGTGGGCTTCGCAGT	0.582																																					p.G77E		.											.	WNT8B-625	0			c.G230A						.						54	49	50					10																	102239758		2203	4300	6503	SO:0001583	missense	7479	exon3			ATGGTGGGCTTCG	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"Wingless-type MMTV integration sites"	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.230G>A	10.37:g.102239758G>A	ENSP00000340677:p.Gly77Glu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	31	8	NM_003393	0	0	0	0	0	O00771|Q5VX55|Q8WYK9	Missense_Mutation	SNP	ENST00000343737.5	37	CCDS7494.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.368885	0.42003	.	.	ENSG00000075290	ENST00000343737	T	0.74947	-0.89	5.7	5.7	0.88788	.	1.622190	0.03427	N	0.207152	T	0.75606	0.3872	N	0.21373	0.66	0.54753	D	0.999988	P	0.38535	0.635	P	0.48982	0.597	T	0.60999	-0.7151	10	0.05351	T	0.99	.	19.8354	0.96655	0.0:0.0:1.0:0.0	.	77	Q93098	WNT8B_HUMAN	E	77	ENSP00000340677:G77E	ENSP00000340677:G77E	G	+	2	0	WNT8B	102229748	1.000000	0.71417	0.990000	0.47175	0.759000	0.43091	9.476000	0.97823	2.686000	0.91538	0.555000	0.69702	GGG	.		0.582	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393		A	102239758	G	A	102239758	3	1	52	1	0	0	0	0	1	0	0	0	17430	1232	43	2	240	2	WNT8B	10	102239758	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		102239758	33294989	61	5047											
NLRP14	338323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	7064099	7064099	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtgcgaagactggacccAagaacacccagtgtccttcc	11	7	9	14	1	0	2	0	0	0	2	2	4	2	3	4	1	2	0	4	1	3	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:7064099A>C	ENST00000299481.4	+	4	1188	c.842A>C	c.(841-843)cAa>cCa	p.Q281P		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	281	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GACTGGACCCAAGAACACCCA	0.448																																					p.Q281P		.											.	NLRP14-295	0			c.A842C						.						88	84	85					11																	7064099		2201	4296	6497	SO:0001583	missense	338323	exon4			GGACCCAAGAACA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"Nucleotide-binding domain and leucine rich repeat containing"	22939	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"	609665	"NACHT, leucine rich repeat and PYD containing 14"	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.842A>C	11.37:g.7064099A>C	ENSP00000299481:p.Gln281Pro	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	101	33	NM_176822	0	0	0	0	0	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.059980	0.36373	.	.	ENSG00000158077	ENST00000299481	T	0.78924	-1.22	4.57	2.08	0.27032	NACHT nucleoside triphosphatase (1);	0.164316	0.29133	N	0.013042	D	0.85186	0.5639	M	0.80183	2.485	0.09310	N	1	D	0.71674	0.998	D	0.68621	0.959	T	0.75596	-0.3263	10	0.72032	D	0.01	.	8.1401	0.31078	0.6792:0.0:0.0:0.3208	.	281	Q86W24	NAL14_HUMAN	P	281	ENSP00000299481:Q281P	ENSP00000299481:Q281P	Q	+	2	0	NLRP14	7020675	0.832000	0.29368	0.494000	0.27515	0.657000	0.38888	3.500000	0.53318	0.308000	0.22923	0.533000	0.62120	CAA	.		0.448	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		C	7064099	A	C	7064099	3	2	52	1	0	0	0	0	1	0	0	0	10502	130	5	5	852	5	NLRP14	11	7064099	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		7064099	127942417	62	5048											
MADD	8567	hgsc.bcm.edu	37	chr11	47346058	47346058	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagttccctgtgcaggaccTgaagactggtgagggtggcc	7	8	16	10	1	0	3	0	2	0	1	1	5	1	4	3	4	1	2	3	4	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:47346058T>C	ENST00000311027.5	+	33	4817	c.4652T>C	c.(4651-4653)cTg>cCg	p.L1551P	MADD_ENST00000349238.3_Missense_Mutation_p.L1512P|MADD_ENST00000402799.1_Missense_Mutation_p.L1449P|MADD_ENST00000406482.1_Missense_Mutation_p.L1449P|MADD_ENST00000342922.4_Missense_Mutation_p.L1492P|MADD_ENST00000402192.2_Missense_Mutation_p.L1491P|MADD_ENST00000407859.3_Missense_Mutation_p.L1469P|MADD_ENST00000395344.3_Missense_Mutation_p.L1445P|MADD_ENST00000405573.2_Missense_Mutation_p.L361P|MADD_ENST00000395336.3_Missense_Mutation_p.L1551P	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GTGCAGGACCTGAAGACTGGT	0.602																																					p.L1551P		.											.	MADD-682	0			c.T4652C						.						78	76	77					11																	47346058		2201	4298	6499	SO:0001583	missense	8567	exon33			AGGACCTGAAGAC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4652T>C	11.37:g.47346058T>C	ENSP00000310933:p.Leu1551Pro	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	38	3	NM_130475	0	0	31	31	0		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.565942	0.86439	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192;ENST00000405573	T;T;T;T;T;T;T;T;T;T	0.50813	3.37;3.24;3.24;3.37;3.37;3.24;3.25;3.37;3.38;0.73	5.83	5.83	0.93111	.	0.035200	0.85682	D	0.000000	T	0.51652	0.1687	L	0.27053	0.805	0.58432	D	0.999999	D;B;B;P;B;B;B;B;B;P;B	0.58970	0.984;0.215;0.133;0.785;0.21;0.321;0.321;0.199;0.312;0.679;0.199	P;B;B;P;B;B;B;B;B;B;B	0.55871	0.786;0.039;0.039;0.512;0.085;0.152;0.085;0.105;0.105;0.314;0.057	T	0.56141	-0.8028	10	0.87932	D	0	-17.8484	16.1883	0.81967	0.0:0.0:0.0:1.0	.	361;1445;1445;1551;1449;1449;1449;1512;1469;1551;1492	F8W8U2;B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;.;MADD_HUMAN;.	P	1492;1449;1449;1449;1512;1551;1469;1445;1551;1491;361	ENSP00000343902:L1492P;ENSP00000385585:L1449P;ENSP00000384435:L1449P;ENSP00000304505:L1512P;ENSP00000310933:L1551P;ENSP00000384204:L1469P;ENSP00000378753:L1445P;ENSP00000378745:L1551P;ENSP00000384287:L1491P;ENSP00000384483:L361P	ENSP00000310933:L1551P	L	+	2	0	MADD	47302634	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.689000	0.84165	2.231000	0.72958	0.454000	0.30748	CTG	.		0.602	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			C	47346058	T	C	47346058	3	2	52	1	0	0	0	0	1	0	0	0	9177	1580	55	3	4778	3	MADD	11	47346058	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	40281959	47346058	87660458	63	5049											
PRPF19	27339	hgsc.bcm.edu	37	chr11	60670932	60670932	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcttgcaggaactcaccCactcatcctgcaaagctttc	9	12	5	15	0	3	0	2	0	1	0	6	1	4	1	2	1	4	3	2	1	2	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:60670932C>A	ENST00000227524.4	-	3	450	c.245G>T	c.(244-246)tGg>tTg	p.W82L		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						GGAACTCACCCACTCATCCTG	0.532																																					p.W82L		.											.	PRPF19-91	0			c.G245T						.						52	52	52					11																	60670932		2203	4298	6501	SO:0001630	splice_region_variant	27339	exon3			CTCACCCACTCAT	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.246+1G>T	11.37:g.60670932C>A		Somatic	15	1		WXS	Illumina HiSeq	Phase_I	22	11	NM_014502	0	0	0	0	0		Missense_Mutation	SNP	ENST00000227524.4	37	CCDS7995.1	.	.	.	.	.	.	.	.	.	.	C	32	5.171353	0.94807	.	.	ENSG00000110107	ENST00000227524;ENST00000541371	T	0.73469	-0.75	5.08	5.08	0.68730	Pre-mRNA-splicing factor 19 (1);	0.066474	0.64402	D	0.000003	D	0.89876	0.6842	M	0.93594	3.435	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.92305	0.5853	10	0.87932	D	0	-8.8421	18.2782	0.90089	0.0:1.0:0.0:0.0	.	82	Q9UMS4	PRP19_HUMAN	L	82	ENSP00000227524:W82L	ENSP00000227524:W82L	W	-	2	0	PRPF19	60427508	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.280000	0.78610	2.646000	0.89796	0.561000	0.74099	TGG	.		0.532	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502	Missense_Mutation	A	60670932	C	A	60670932	5	1	52	1	0	0	0	0	0	0	1	0	12593	608	21	4	1325	4	PRPF19	11	60670932	Splice_Site	SNP	C	TCGA-B9-5156-01A-01D-1589-08	13324874	60670932	74335584	64	5050											
PRKRIR	5612	hgsc.bcm.edu;broad.mit.edu	37	chr11	76062971	76062971	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctttactgttctgaaaaAgaacagaaattacgttgtca	14	15	6	6	1	3	3	1	1	2	2	3	3	3	3	0	0	3	2	0	0	6	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:76062971A>T	ENST00000260045.3	-	5	1328	c.1223T>A	c.(1222-1224)cTt>cAt	p.L408H	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	408					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						GTTCTGAAAAAGAACAGAAAT	0.388																																					p.L408H		.											.	PRKRIR-93	0			c.T1223A						.						19	19	19					11																	76062971		2163	4223	6386	SO:0001583	missense	5612	exon5			TGAAAAAGAACAG	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.1223T>A	11.37:g.76062971A>T	ENSP00000260045:p.Leu408His	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	79	22	NM_004705	0	0	12	18	6	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	37	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	A	6.750	0.507246	0.12883	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	.	.	.	4.78	4.78	0.61160	Ribonuclease H-like (1);	0.052433	0.85682	D	0.000000	T	0.50103	0.1596	L	0.45581	1.43	0.46131	D	0.998889	B	0.31318	0.319	B	0.26310	0.068	T	0.52764	-0.8532	9	0.46703	T	0.11	.	14.7428	0.69469	1.0:0.0:0.0:0.0	.	408	O43422	P52K_HUMAN	H	233;408	.	ENSP00000260045:L408H	L	-	2	0	PRKRIR	75740619	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	2.504000	0.45416	1.956000	0.56807	0.524000	0.50904	CTT	.		0.388	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		T	76062971	A	T	76062971	3	4	52	1	0	0	0	0	1	0	0	0	12555	72	3	5	1066	5	PRKRIR	11	76062971	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	15392039	76062971	58943545	65	5051											
SYTL2	54843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	85445140	85445140	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggaaaagaaccagaagtcAttggctgatgtgtttcactt	12	13	10	6	0	2	3	2	1	0	2	2	4	2	4	1	2	1	2	1	2	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:85445140A>T	ENST00000528231.1	-	6	1506	c.1229T>A	c.(1228-1230)aTg>aAg	p.M410K	SYTL2_ENST00000316356.4_Missense_Mutation_p.M411K|SYTL2_ENST00000389960.4_Missense_Mutation_p.M410K|SYTL2_ENST00000527523.1_Missense_Mutation_p.M362K|SYTL2_ENST00000524452.1_Missense_Mutation_p.M410K	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	410					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		ACCAGAAGTCATTGGCTGATG	0.403																																					p.M411K		.											.	SYTL2-137	0			c.T1232A						.						152	146	148					11																	85445140		2203	4299	6502	SO:0001583	missense	54843	exon6			GAAGTCATTGGCT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1229T>A	11.37:g.85445140A>T	ENSP00000431701:p.Met410Lys	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	156	43	NM_001162953	0	0	14	28	14	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	A	7.911	0.736457	0.15574	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.23348	2.0;2.01;2.01;1.91;2.0	5.81	-5.21	0.02815	.	.	.	.	.	T	0.10981	0.0268	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001	T	0.34104	-0.9842	8	.	.	.	.	1.191	0.01864	0.3579:0.26:0.0884:0.2937	.	362;410;410;411;268	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	K	410;411;410;362;410	ENSP00000374610:M410K;ENSP00000318803:M411K;ENSP00000431701:M410K;ENSP00000434010:M362K;ENSP00000435238:M410K	.	M	-	2	0	SYTL2	85122788	0.000000	0.05858	0.002000	0.10522	0.675000	0.39556	-2.151000	0.01289	-0.378000	0.07918	0.533000	0.62120	ATG	.		0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85445140	A	T	85445140	3	4	52	1	0	0	0	0	1	0	0	0	15515	217	8	5	4108	5	SYTL2	11	85445140	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	9382169	85445140	49561376	66	5052											
ADAMTS8	11095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	130284505	130284505	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgcacggcgtgccgtcaGcccagggcaggctgccattc	5	5	14	17	4	1	0	1	0	0	0	2	0	1	0	4	3	3	3	4	3	0	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:130284505G>T	ENST00000257359.6	-	5	2193	c.1487C>A	c.(1486-1488)gCt>gAt	p.A496D		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	496	Disintegrin.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		CGTGCCGTCAGCCCAGGGCAG	0.657																																					p.A496D		.											.	ADAMTS8-226	0			c.C1487A						.						49	56	53					11																	130284505		2029	4184	6213	SO:0001583	missense	11095	exon5			CCGTCAGCCCAGG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"ADAM metallopeptidases with thrombospondin type 1 motif"	224	protein-coding gene	gene with protein product		605175	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1487C>A	11.37:g.130284505G>T	ENSP00000257359:p.Ala496Asp	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	124	39	NM_007037	0	0	0	0	0	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	37	CCDS41732.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252974	0.80135	.	.	ENSG00000134917	ENST00000257359;ENST00000414575	T	0.63255	-0.03	5.59	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.84234	0.5427	H	0.94964	3.605	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88705	0.3218	10	0.87932	D	0	.	14.45	0.67379	0.0708:0.0:0.9292:0.0	.	496	Q9UP79	ATS8_HUMAN	D	496;525	ENSP00000257359:A496D	ENSP00000257359:A496D	A	-	2	0	ADAMTS8	129789715	1.000000	0.71417	0.873000	0.34254	0.657000	0.38888	3.871000	0.56077	1.355000	0.45865	0.655000	0.94253	GCT	.		0.657	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		T	130284505	G	T	130284505	3	4	52	1	0	0	0	0	1	0	0	0	272	971	34	4	1202	4	ADAMTS8	11	130284505	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	44839365	130284505	4722011	67	5053											
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	26553127	26553127	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgaggccctggttcagcacGgtgacaatgcacataaggag	11	7	13	10	1	1	2	1	2	0	0	1	3	1	3	1	4	2	3	1	4	2	2	rs560385893		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:26553127G>A	ENST00000381340.3	-	53	7880	c.7464C>T	c.(7462-7464)acC>acT	p.T2488T	RP11-513G19.1_ENST00000535324.1_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2488					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGTTCAGCACGGTGACAATGC	0.413													g|||	1	0.000199681	0	0	5008	,	,		14883	0		0	False		,,,				2504	0.001				p.T2488T		.											.	ITPR2-542	0			c.C7464T						.						122	119	120					12																	26553127		1920	4128	6048	SO:0001819	synonymous_variant	3709	exon53			CAGCACGGTGACA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.7464C>T	12.37:g.26553127G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	229	53	NM_002223	0	0	8	10	2	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			.		0.413	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26553127	G	A	26553127	2	1	52	1	0	0	0	0	0	0	0	1	7942	1103	39	1		1	ITPR2	12	26553127	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08		26553127	107298768	68	5054											
TMBIM6	7009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	50149442	50149442	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgctgtctgccttgggcTccctgatattgatgatttgg	4	15	12	10	0	1	3	0	3	1	0	2	3	2	3	3	2	2	2	3	2	1	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:50149442T>C	ENST00000267115.5	+	4	275	c.190T>C	c.(190-192)Tcc>Ccc	p.S64P	TMBIM6_ENST00000395006.4_Missense_Mutation_p.S64P|TMBIM6_ENST00000549385.1_Missense_Mutation_p.S64P|TMBIM6_ENST00000552699.1_Missense_Mutation_p.S122P|TMBIM6_ENST00000547798.1_Missense_Mutation_p.S27P|TMBIM6_ENST00000423828.1_Missense_Mutation_p.S122P	NM_003217.2	NP_003208.2	P55061	BI1_HUMAN	transmembrane BAX inhibitor motif containing 6	64					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						TGCCTTGGGCTCCCTGATATT	0.418																																					p.S122P		.											.	TMBIM6-90	0			c.T364C						.						175	173	174					12																	50149442		2203	4300	6503	SO:0001583	missense	7009	exon4			TTGGGCTCCCTGA	X75861	CCDS31797.1, CCDS44875.1	12q13.12	2013-10-08	2008-09-17	2008-09-17	ENSG00000139644	ENSG00000139644			11723	protein-coding gene	gene with protein product	"BAX inhibitor 1"	600748	"testis enhanced gene transcript"	TEGT		8530040, 9660918	Standard	NM_001098576		Approved	BI-1, BAXI1	uc001ruy.2	P55061	OTTHUMG00000169652	ENST00000267115.5:c.190T>C	12.37:g.50149442T>C	ENSP00000267115:p.Ser64Pro	Somatic	256	2		WXS	Illumina HiSeq	Phase_I	319	70	NM_001098576	2	2	1468	2069	597	B2R5M4|F8W034|O14938|Q643A7|Q96J50	Missense_Mutation	SNP	ENST00000267115.5	37	CCDS31797.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.817632	0.32145	.	.	ENSG00000139644	ENST00000546796;ENST00000549966;ENST00000547832;ENST00000547187;ENST00000546914;ENST00000552699;ENST00000267115;ENST00000541612;ENST00000549445;ENST00000549385;ENST00000548201;ENST00000423828;ENST00000542631;ENST00000550445;ENST00000549130;ENST00000552370;ENST00000395006;ENST00000547798	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03;1.03	5.65	4.49	0.54785	.	0.056827	0.64402	D	0.000001	T	0.51770	0.1694	M	0.90198	3.095	0.58432	D	0.999993	B;B;B	0.28470	0.013;0.206;0.213	B;B;B	0.31614	0.025;0.133;0.089	T	0.54234	-0.8324	10	0.45353	T	0.12	.	11.4766	0.50302	0.0:0.0:0.2833:0.7167	.	64;122;64	B7Z984;F8W034;P55061	.;.;BI1_HUMAN	P	64;64;64;64;64;122;64;64;64;64;64;122;64;64;64;64;64;27	ENSP00000450159:S64P;ENSP00000446668:S64P;ENSP00000448269:S64P;ENSP00000447400:S64P;ENSP00000448612:S64P;ENSP00000446734:S122P;ENSP00000267115:S64P;ENSP00000449904:S64P;ENSP00000448036:S64P;ENSP00000450265:S64P;ENSP00000389277:S122P;ENSP00000449907:S64P;ENSP00000450158:S64P;ENSP00000378454:S64P;ENSP00000447030:S27P	ENSP00000267115:S64P	S	+	1	0	TMBIM6	48435709	1.000000	0.71417	1.000000	0.80357	0.527000	0.34593	3.264000	0.51553	1.118000	0.41863	0.533000	0.62120	TCC	.		0.418	TMBIM6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405289.1	NM_003217		C	50149442	T	C	50149442	3	2	52	1	0	0	0	0	1	0	0	0	16015	1551	54	3	378	3	TMBIM6	12	50149442	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	23596315	50149442	83702453	69	5055											
AMHR2	269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53824991	53824991	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggctgagggagctcctagaaGactgttgggatgcagaccca	10	7	15	9	0	0	4	0	1	0	3	1	6	1	6	2	3	2	4	2	3	2	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:53824991G>C	ENST00000257863.4	+	11	1536	c.1456G>C	c.(1456-1458)Gac>Cac	p.D486H	AMHR2_ENST00000550311.1_3'UTR|AMHR2_ENST00000379791.3_Missense_Mutation_p.D391H	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	486	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	GCTCCTAGAAGACTGTTGGGA	0.592																																					p.D486H		.											.	AMHR2-628	0			c.G1456C						.						77	78	78					12																	53824991		2203	4300	6503	SO:0001583	missense	269	exon11			CTAGAAGACTGTT	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1456G>C	12.37:g.53824991G>C	ENSP00000257863:p.Asp486His	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	166	83	NM_020547	0	0	0	0	0	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	37	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579839	0.86645	.	.	ENSG00000135409	ENST00000257863;ENST00000379791	T;D	0.93247	-0.21;-3.19	4.86	4.86	0.63082	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.39834	N	0.001257	D	0.95484	0.8533	L	0.56340	1.77	0.30411	N	0.779055	D	0.89917	1.0	D	0.97110	1.0	D	0.92996	0.6419	10	0.87932	D	0	.	15.3949	0.74784	0.0:0.0:1.0:0.0	.	486	Q16671	AMHR2_HUMAN	H	486;391	ENSP00000257863:D486H;ENSP00000369117:D391H	ENSP00000257863:D486H	D	+	1	0	AMHR2	52111258	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.206000	0.77891	2.691000	0.91804	0.563000	0.77884	GAC	.		0.592	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		C	53824991	G	C	53824991	3	2	52	1	0	0	0	0	1	0	0	0	573	942	33	4	1498	4	AMHR2	12	53824991	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	3675549	53824991	80026904	70	5056											
WSCD2	9671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	108641980	108641980	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaggatggcaacttcaagCgctcagggctccggaagctc	11	6	13	11	2	2	1	2	0	0	1	4	3	3	3	1	4	3	4	1	4	4	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:108641980C>T	ENST00000332082.4	+	10	2376	c.1558C>T	c.(1558-1560)Cgc>Tgc	p.R520C	WSCD2_ENST00000549903.1_Missense_Mutation_p.R540C|WSCD2_ENST00000261400.3_Missense_Mutation_p.R540C|WSCD2_ENST00000547525.1_Missense_Mutation_p.R520C			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	520						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						CAACTTCAAGCGCTCAGGGCT	0.602																																					p.R520C		.											.	WSCD2-136	0			c.C1558T						.						59	66	64					12																	108641980		2036	4193	6229	SO:0001583	missense	9671	exon9			TTCAAGCGCTCAG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1558C>T	12.37:g.108641980C>T	ENSP00000331933:p.Arg520Cys	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	95	19	NM_014653	0	0	0	0	0	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.809847	0.70797	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.58060	0.36;3.98;0.36;3.98	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.73071	0.3540	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.78285	-0.2263	10	0.87932	D	0	-44.2877	16.1113	0.81266	0.0:1.0:0.0:0.0	.	540;520	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	C	520;540;520;540	ENSP00000448047:R520C;ENSP00000261400:R540C;ENSP00000331933:R520C;ENSP00000447272:R540C	ENSP00000261400:R540C	R	+	1	0	WSCD2	107166110	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	5.717000	0.68446	2.029000	0.59856	0.655000	0.94253	CGC	.		0.602	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		T	108641980	C	T	108641980	3	4	52	1	0	0	0	0	1	0	0	0	17440	768	27	1	1588	1	WSCD2	12	108641980	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	54816989	108641980	25209915	71	5057											
FREM2	341640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	39452997	39452997	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccagagacacaagcgacCagttttggaaatgtcctatt	13	9	9	10	1	0	1	0	0	0	1	1	4	1	2	3	1	2	1	3	1	3	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr13:39452997C>G	ENST00000280481.7	+	23	9105	c.8889C>G	c.(8887-8889)acC>acG	p.T2963T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2963					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)		CACAAGCGACCAGTTTTGGAA	0.448																																					p.T2963T		.											.	FREM2-100	0			c.C8889G						.						162	148	153					13																	39452997		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon23			AGCGACCAGTTTT	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.8889C>G	13.37:g.39452997C>G		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	122	35	NM_207361	0	0	10	22	12	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			.		0.448	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39452997	C	G	39452997	2	3	52	1	0	0	0	0	0	0	0	1	6064	581	21	4		4	FREM2	13	39452997	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08		39452997	75716881	72	5058											
C13orf23	80209	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	39587574	39587574	+	Frame_Shift_Del	DEL	A	A	-																															gtgggctcagttttgatcatAacaggaagagttgttgcagc																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr13:39587574delA	ENST00000352251.3	-	11	2648	c.1815delT	c.(1813-1815)gttfs	p.V605fs	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Frame_Shift_Del_p.V583fs	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	605	Ser-rich.																TTTTGATCATAACAGGAAGAG	0.517																																					p.V605fs		.											.	.	0			c.1815delT						.						153	163	159					13																	39587574		2203	4300	6503	SO:0001589	frameshift_variant	80209	exon11			.	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1815delT	13.37:g.39587574delA	ENSP00000332034:p.Val605fs	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	191	72	NM_025138	0	0	0	0	0	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Frame_Shift_Del	DEL	ENST00000352251.3	37	CCDS9368.2																																																																																			.		0.517	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		-	39587574	A	-	39587574	7	5	52	1	0	1	0	1	0	0	0	0	1725	349	13	0	1031	0	C13orf23	13	39587574	Frame_Shift_Del	DEL	A	TCGA-B9-5156-01A-01D-1589-08	134577	39587574	75582304	73	5059											
ANKRD10	55608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	111532214	111532214	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcaggtgcagagaaccgcAcaactcagggttagctctca	11	8	11	11	1	3	1	3	0	1	1	4	2	3	1	1	2	4	5	1	2	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr13:111532214A>T	ENST00000267339.2	-	6	1167	c.1033T>A	c.(1033-1035)Tgc>Agc	p.C345S	ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	345										central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			AGAGAACCGCACAACTCAGGG	0.547																																					p.C345S		.											.	ANKRD10-226	0			c.T1033A						.						101	87	92					13																	111532214		2203	4300	6503	SO:0001583	missense	55608	exon6			AACCGCACAACTC	AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"Ankyrin repeat domain containing"	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.1033T>A	13.37:g.111532214A>T	ENSP00000267339:p.Cys345Ser	Somatic	117	2		WXS	Illumina HiSeq	Phase_I	102	30	NM_017664	0	0	46	92	46	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	37	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.379004	0.42207	.	.	ENSG00000088448	ENST00000267339	T	0.77358	-1.09	5.28	5.28	0.74379	.	0.052781	0.85682	D	0.000000	T	0.76608	0.4011	M	0.74258	2.255	0.80722	D	1	P	0.39282	0.666	B	0.35039	0.194	T	0.79725	-0.1683	10	0.54805	T	0.06	-5.8478	15.2197	0.73303	1.0:0.0:0.0:0.0	.	345	Q9NXR5	ANR10_HUMAN	S	345	ENSP00000267339:C345S	ENSP00000267339:C345S	C	-	1	0	ANKRD10	110330215	1.000000	0.71417	0.826000	0.32828	0.377000	0.30045	5.271000	0.65553	1.996000	0.58369	0.455000	0.32223	TGC	.		0.547	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			T	111532214	A	T	111532214	3	4	52	1	0	0	0	0	1	0	0	0	638	159	6	5	233	5	ANKRD10	13	111532214	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	71944640	111532214	3637664	74	5060											
MYH6	4624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23862897	23862897	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttctctgttgcatgcttcTccttctccaccttggccagt	3	17	7	14	0	3	0	0	0	3	0	6	0	3	0	4	1	2	4	4	1	0	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:23862897T>G	ENST00000356287.3	-	21	2935	c.2906A>C	c.(2905-2907)gAg>gCg	p.E969A	MYH6_ENST00000405093.3_Missense_Mutation_p.E969A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	969					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TGCATGCTTCTCCTTCTCCAC	0.562																																					p.E969A		.											.	MYH6-94	0			c.A2906C						.						206	174	185					14																	23862897		2203	4300	6503	SO:0001583	missense	4624	exon22			TGCTTCTCCTTCT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"Myosins / Myosin superfamily : Class II"	7576	protein-coding gene	gene with protein product	"cardiomyopathy, hypertrophic 1"	160710	"myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2906A>C	14.37:g.23862897T>G	ENSP00000348634:p.Glu969Ala	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	113	33	NM_002471	0	0	0	0	0	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	t	18.08	3.544179	0.65198	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.92911	-3.13;-3.13	4.95	4.95	0.65309	.	.	.	.	.	D	0.95143	0.8426	H	0.94964	3.605	0.58432	D	0.999999	P	0.35527	0.507	B	0.41764	0.366	D	0.95789	0.8823	9	0.62326	D	0.03	.	14.9359	0.70954	0.0:0.0:0.0:1.0	.	969	P13533	MYH6_HUMAN	A	969	ENSP00000386041:E969A;ENSP00000348634:E969A	ENSP00000348634:E969A	E	-	2	0	MYH6	22932737	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	1.992000	0.58205	0.528000	0.53228	GAG	.		0.562	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			G	23862897	T	G	23862897	3	3	52	1	0	0	0	0	1	0	0	0	10063	1551	54	5	2985	5	MYH6	14	23862897	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08		23862897	83486643	75	5061											
MYH7	4625	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	23897724	23897724	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccttctcgatgaggtcAatgcaggcctgcaggtccat	8	9	12	12	1	2	1	1	1	1	0	4	2	3	1	3	4	2	3	3	4	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:23897724A>C	ENST00000355349.3	-	15	1725	c.1563T>G	c.(1561-1563)atT>atG	p.I521M		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	521	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CGATGAGGTCAATGCAGGCCT	0.517																																					p.I521M		.											.	MYH7-94	0			c.T1563G						.						231	168	189					14																	23897724		2203	4300	6503	SO:0001583	missense	4625	exon15			GAGGTCAATGCAG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1563T>G	14.37:g.23897724A>C	ENSP00000347507:p.Ile521Met	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	82	6	NM_000257	0	0	0	0	0	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.084286	0.55861	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.96396	-4.0	4.63	-6.69	0.01772	Myosin head, motor domain (3);	.	.	.	.	D	0.98865	0.9616	H	0.98769	4.325	0.47476	D	0.999438	P	0.35551	0.509	D	0.63192	0.912	D	0.97432	1.0016	9	0.87932	D	0	.	16.9993	0.86377	0.8517:0.0:0.1483:0.0	.	521	P12883	MYH7_HUMAN	M	521	ENSP00000347507:I521M	ENSP00000347507:I521M	I	-	3	3	MYH7	22967564	0.716000	0.27956	0.769000	0.31535	0.940000	0.58332	-0.030000	0.12308	-1.432000	0.01979	-1.028000	0.02416	ATT	.		0.517	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		C	23897724	A	C	23897724	3	2	52	1	0	0	0	0	1	0	0	0	10064	126	5	5	4348	5	MYH7	14	23897724	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	34827	23897724	83451816	76	5062											
RIPK3	11035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24805465	24805465	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcttgcgaacctactggtggGgggtgctgcaagcccctccc	5	9	13	14	1	1	0	0	0	1	0	2	1	2	0	4	4	6	2	4	4	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:24805465G>T	ENST00000216274.5	-	10	1691	c.1473C>A	c.(1471-1473)ccC>ccA	p.P491P	ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000558563.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank|RP11-934B9.3_ENST00000555591.1_Intron	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	491					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CTACTGGTGGGGGGTGCTGCA	0.542																																					p.P491P	Pancreas(58;918 1191 4668 13304 15331)	.											.	RIPK3-946	0			c.C1473A						.						75	78	77					14																	24805465		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon10			TGGTGGGGGGTGC	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1473C>A	14.37:g.24805465G>T		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	102	27	NM_006871	0	0	3	3	0	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	37	CCDS9628.1																																																																																			.		0.542	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24805465	G	T	24805465	2	4	52	1	0	0	0	0	0	0	0	1	13414	1219	43	4		4	RIPK3	14	24805465	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	907741	24805465	82544075	77	5063											
SEC23A	10484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	39524378	39524378	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgtctgtccagccacctaAgcacatctggaccttcttct	7	12	7	15	0	4	0	0	0	4	0	5	1	5	1	4	1	2	2	4	1	1	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:39524378A>T	ENST00000307712.6	-	14	2145	c.1628T>A	c.(1627-1629)cTt>cAt	p.L543H	SEC23A_ENST00000536508.1_Missense_Mutation_p.L417H|SEC23A_ENST00000537403.1_Missense_Mutation_p.L341H|SEC23A_ENST00000545328.2_Missense_Mutation_p.L514H	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	543					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		CAGCCACCTAAGCACATCTGG	0.418																																					p.L543H		.											.	SEC23A-95	0			c.T1628A						.						137	129	132					14																	39524378		2203	4300	6503	SO:0001583	missense	10484	exon14			CACCTAAGCACAT	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"Sec23 (S. cerevisiae) homolog A"			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.1628T>A	14.37:g.39524378A>T	ENSP00000306881:p.Leu543His	Somatic	222	1		WXS	Illumina HiSeq	Phase_I	174	50	NM_006364	0	0	34	59	25	B2R5P4|B3KXI2|Q8NE16	Missense_Mutation	SNP	ENST00000307712.6	37	CCDS9668.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.993863	0.93167	.	.	ENSG00000100934	ENST00000537403;ENST00000307712;ENST00000536508;ENST00000545328	D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58	5.81	5.81	0.92471	Sec23/Sec24, helical domain (2);	0.130937	0.51477	D	0.000089	D	0.95893	0.8663	H	0.94183	3.505	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.996	D;D;D	0.67382	0.94;0.94;0.951	D	0.96995	0.9725	10	0.87932	D	0	-22.7375	16.1603	0.81700	1.0:0.0:0.0:0.0	.	514;417;543	F5H365;F5H6C4;Q15436	.;.;SC23A_HUMAN	H	341;543;417;514	ENSP00000444193:L341H;ENSP00000306881:L543H;ENSP00000437715:L417H;ENSP00000445393:L514H	ENSP00000306881:L543H	L	-	2	0	SEC23A	38594129	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.138000	0.94501	2.218000	0.71995	0.450000	0.29827	CTT	.		0.418	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			T	39524378	A	T	39524378	3	4	52	1	0	0	0	0	1	0	0	0	14023	72	3	5	697	5	SEC23A	14	39524378	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	14718913	39524378	67825162	78	5064											
HERC2	8924	broad.mit.edu	37	chr15	28460930	28460930	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccggtgttgctccctgtacAccagcctgtttggagaagct	6	12	11	12	1	0	1	0	0	0	1	2	2	2	1	4	2	4	5	4	2	2	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr15:28460930A>C	ENST00000261609.7	-	39	6155	c.6047T>G	c.(6046-6048)gTg>gGg	p.V2016G		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTCCCTGTACACCAGCCTGTT	0.527																																					p.V2016G													.	HERC2-234	0			c.T6047G						.						19	19	19					15																	28460930		1991	3968	5959	SO:0001583	missense	8924	exon39			CTGTACACCAGCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6047T>G	15.37:g.28460930A>C	ENSP00000261609:p.Val2016Gly	Somatic	76	3		WXS	Illumina HiSeq	Phase_I	83	9	NM_004667	0	0	10	11	1		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.926984	0.34002	.	.	ENSG00000128731	ENST00000261609	T	0.40756	1.02	4.28	4.28	0.50868	.	0.000000	0.64402	D	0.000002	T	0.35158	0.0922	L	0.47716	1.5	0.80722	D	1	B	0.33073	0.396	B	0.26416	0.069	T	0.36040	-0.9764	10	0.66056	D	0.02	.	13.573	0.61858	1.0:0.0:0.0:0.0	.	2016	O95714	HERC2_HUMAN	G	2016	ENSP00000261609:V2016G	ENSP00000261609:V2016G	V	-	2	0	HERC2	26134525	1.000000	0.71417	0.070000	0.20053	0.381000	0.30169	6.710000	0.74670	1.800000	0.52685	0.397000	0.26171	GTG	.		0.527	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28460930	A	C	28460930	3	2	52	1	0	0	0	0	1	0	0	0	7079	159	6	5	8677	5	HERC2	15	28460930	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		28460930	74070462	79	5065											
NR2E3	10002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	72104834	72104834	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgcctgtgttctccagcCtgcccttccgggatcaggta	5	11	10	15	1	2	0	1	0	1	0	4	1	3	1	6	2	3	2	6	2	1	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr15:72104834C>T	ENST00000398840.2	+	0	920							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(1)	3						GTTCTCCAGCCTGCCCTTCCG	0.647																																					p.L244L		.											.	NR2E3-22	0			c.C730T						.						48	54	52					15																	72104834		2027	4165	6192			10002	exon5			TCCAGCCTGCCCT		CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"Nuclear hormone receptors"	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72104834C>T		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	28	10	NM_016346	0	0	0	0	0	B6ZGU0|Q9UHM4	Silent	SNP	ENST00000398840.2	37																																																																																				.		0.647	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		T	72104834	C	T	72104834	1	4	52	0	1	0	0	0	0	0	0	0	10652	680	24	2		2	NR2E3	15	72104834	RNA	SNP	C	TCGA-B9-5156-01A-01D-1589-08	43643904	72104834	30426558	80	5066											
CHTF18	63922	broad.mit.edu;ucsc.edu	37	chr16	842454	842454	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaggccgccatcaacgtcCtcctgagcatcctgaaccgc	9	6	8	18	3	1	2	1	2	0	0	4	2	4	2	7	1	3	1	7	1	3	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:842454C>G	ENST00000262315.9	+	11	1405	c.1342C>G	c.(1342-1344)Ctc>Gtc	p.L448V	CHTF18_ENST00000317063.6_Missense_Mutation_p.L643V|CHTF18_ENST00000455171.2_Missense_Mutation_p.L476V	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	448					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CATCAACGTCCTCCTGAGCAT	0.721																																					p.L448V													.	CHTF18-227	0			c.C1342G						.						8	11	10					16																	842454		2017	4101	6118	SO:0001583	missense	63922	exon11			AACGTCCTCCTGA	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.1342C>G	16.37:g.842454C>G	ENSP00000262315:p.Leu448Val	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_022092	0	0	5	6	1	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	c	18.01	3.528711	0.64860	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.28895	1.59;1.59;1.59	4.6	4.6	0.57074	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	M	0.83852	2.665	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.60434	-0.7264	10	0.34782	T	0.22	-30.9585	16.3448	0.83120	0.0:1.0:0.0:0.0	.	476;448	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	643;476;448	ENSP00000313029:L643V;ENSP00000406252:L476V;ENSP00000262315:L448V	ENSP00000262315:L448V	L	+	1	0	CHTF18	782455	0.997000	0.39634	0.767000	0.31495	0.512000	0.34134	2.862000	0.48388	2.264000	0.75181	0.457000	0.33378	CTC	.		0.721	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		G	842454	C	G	842454	3	3	52	1	0	0	0	0	1	0	0	0	3420	681	24	4	1384	4	CHTF18	16	842454	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08		842454	89512299	81	5067											
MAPK8IP3	23162	broad.mit.edu	37	chr16	1815160	1815160	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcaacgcgcacgtgctGtgcatctccagcatccccgg	6	8	11	16	4	2	0	0	0	2	0	4	0	3	0	3	1	5	5	3	1	1	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:1815160G>A	ENST00000250894.4	+	20	2581	c.2424G>A	c.(2422-2424)ctG>ctA	p.L808L	MAPK8IP3_ENST00000356010.5_Silent_p.L802L	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	808					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						CGCACGTGCTGTGCATCTCCA	0.612																																					p.L808L													.	MAPK8IP3-1109	0			c.G2424A						.						29	33	32					16																	1815160		2126	4234	6360	SO:0001819	synonymous_variant	23162	exon20			CGTGCTGTGCATC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"homolog of Drosophila Sunday driver 2"	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2424G>A	16.37:g.1815160G>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	38	3	NM_015133	0	0	6	6	0	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			.		0.612	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439		A	1815160	G	A	1815160	2	1	52	1	0	0	0	0	0	0	0	1	9311	1364	48	2		2	MAPK8IP3	16	1815160	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	972706	1815160	88539593	82	5068											
PKD1	5310	hgsc.bcm.edu	37	chr16	2155892	2155892	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcacggtgaccagggccaAcgagtactcgatgacgtgct	10	6	13	12	4	0	2	0	2	0	0	1	4	0	2	2	2	4	3	2	2	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2613L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		Missing (in PKD1; unknown pathological significance). {ECO:0000269|PubMed:11571556}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.L2613L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACCAGGGCCAACGAGTACTCG	0.657																																					p.L2613L		.											.	PKD1-91	1	Substitution - coding silent(1)	lung(1)	c.T7837C						.						46	45	45					16																	2155892		1400	2465	3865	SO:0001819	synonymous_variant	5310	exon20			GGGCCAACGAGTA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.7837T>C	16.37:g.2155892A>G		Somatic	48	2		WXS	Illumina HiSeq	Phase_I	67	4	NM_000296	0	0	5	6	1	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2155892	A	G	2155892	2	3	52	1	0	0	0	0	0	0	0	1	11989	40	2	3		3	PKD1	16	2155892	Silent	SNP	A	TCGA-B9-5156-01A-01D-1589-08	340732	2155892	88198861	83	5069											
MYLK3	91807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	46766187	46766187	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcttcagctctcaccggagcCctggctgcacagtcctgctc	5	9	10	17	1	2	0	2	0	1	0	5	1	3	1	3	2	4	5	3	2	0	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:46766187C>T	ENST00000394809.4	-	4	1510	c.1395G>A	c.(1393-1395)agG>agA	p.R465R	MYLK3_ENST00000536476.1_Silent_p.R124R	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	465					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TCACCGGAGCCCTGGCTGCAC	0.657																																					p.R465R		.											.	MYLK3-374	0			c.G1395A						.						35	39	37					16																	46766187		2203	4300	6503	SO:0001819	synonymous_variant	91807	exon4			CGGAGCCCTGGCT	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1395G>A	16.37:g.46766187C>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	110	57	NM_182493	0	0	0	0	0	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Silent	SNP	ENST00000394809.4	37	CCDS10723.2																																																																																			.		0.657	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46766187	C	T	46766187	2	4	52	1	0	0	0	0	0	0	0	1	10083	622	22	2		2	MYLK3	16	46766187	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08	44610295	46766187	43588566	84	5070											
AMFR	267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56435720	56435720	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatggcacagtcgtcattgTtgacagccagctcctctgga	9	10	11	11	1	2	2	1	1	1	1	4	3	3	3	2	2	2	3	2	2	0	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:56435720T>C	ENST00000290649.5	-	8	1220	c.1010A>G	c.(1009-1011)aAc>aGc	p.N337S		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	337					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						GTCGTCATTGTTGACAGCCAG	0.522																																					p.N337S	Pancreas(2;144 323 39528)	.											.	AMFR-1009	0			c.A1010G						.						113	106	109					16																	56435720		2198	4300	6498	SO:0001583	missense	267	exon8			TCATTGTTGACAG	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1010A>G	16.37:g.56435720T>C	ENSP00000290649:p.Asn337Ser	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	174	85	NM_001144	0	0	23	62	39	P26442|Q8IZ70	Missense_Mutation	SNP	ENST00000290649.5	37	CCDS10758.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.281024	0.80692	.	.	ENSG00000159461	ENST00000290649	T	0.66280	-0.2	5.63	5.63	0.86233	Zinc finger, RING/FYVE/PHD-type (1);	0.083860	0.85682	D	0.000000	T	0.54515	0.1863	L	0.50333	1.59	0.80722	D	1	P	0.37061	0.58	B	0.34590	0.186	T	0.52823	-0.8524	10	0.13108	T	0.6	-19.7475	15.8526	0.78943	0.0:0.0:0.0:1.0	.	337	Q9UKV5	AMFR2_HUMAN	S	337	ENSP00000290649:N337S	ENSP00000290649:N337S	N	-	2	0	AMFR	54993221	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.862000	0.87013	2.141000	0.66446	0.528000	0.53228	AAC	.		0.522	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			C	56435720	T	C	56435720	3	2	52	1	0	0	0	0	1	0	0	0	571	1725	60	3	949	3	AMFR	16	56435720	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	9669533	56435720	33919033	85	5071											
NDEL1	81565	broad.mit.edu	37	chr17	8370302	8370302	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtctgggctcctcgcgTccatcgtcagcgccgggtat	3	10	13	15	5	2	0	1	0	1	0	6	0	4	0	4	3	1	2	4	3	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr17:8370302T>C	ENST00000334527.7	+	9	1196	c.999T>C	c.(997-999)cgT>cgC	p.R333R	NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000380025.4_3'UTR|NDEL1_ENST00000299734.7_Intron|NDEL1_ENST00000402554.3_3'UTR	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	333	Interaction with CENPF.|Interaction with NEFL. {ECO:0000250}.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						GCTCCTCGCGTCCATCGTCAG	0.627																																					p.R333R													.	NDEL1-90	0			c.T999C						.						112	108	109					17																	8370302		2203	4300	6503	SO:0001819	synonymous_variant	81565	exon9			CTCGCGTCCATCG	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.999T>C	17.37:g.8370302T>C		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	185	5	NM_030808	0	0	45	45	0	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Silent	SNP	ENST00000334527.7	37	CCDS11143.1																																																																																			.		0.627	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		C	8370302	T	C	8370302	2	2	52	1	0	0	0	0	0	0	0	1	10270	1654	58	3		3	NDEL1	17	8370302	Silent	SNP	T	TCGA-B9-5156-01A-01D-1589-08		8370302	72824908	86	5072											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|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	265	268					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	525	83		WXS	Illumina HiSeq		659	90	NM_145301	0	0	13	69	56	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		T	15457087	C	T	15457087	3	4	52	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	7086785	15457087	65738123	87	5073											
EFCAB5	374786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	28405254	28405255	+	Frame_Shift_Ins	INS	-	-	A																															aaactacacatccaatttccINSaaagccacaccctggtcacg																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr17:28405254_28405255insA	ENST00000394835.3	+	15	2951_2952	c.2759_2760insA	c.(2758-2763)ccaaagfs	p.PK920fs	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Frame_Shift_Ins_p.PK796fs	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	920							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						ATCCAATTTCCAAAGCCACACC	0.411																																					p.P920fs		.											.	EFCAB5-70	0			c.2759_2760insA						.																																			SO:0001589	frameshift_variant	374786	exon15			.	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.2762dupA	17.37:g.28405257_28405257dupA	ENSP00000378312:p.Pro920fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	88	19	NM_198529	0	0	0	0	0	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Frame_Shift_Ins	INS	ENST00000394835.3	37	CCDS11254.2																																																																																			.		0.411	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28405255	-	A	28405254	7	5	52	1	0	1	1	0	0	0	0	0	4949	594	21	0	2984	0	EFCAB5	17	28405254	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	12948167	28405254	52789956	88	5074											
PEX12	5193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33903043	33903043	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tacaggtggtggtggagtagGcagggcagtcaatgacttga	10	9	17	5	0	1	2	1	2	0	0	1	3	1	3	0	6	1	3	0	6	3	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr17:33903043G>A	ENST00000225873.4	-	3	1445	c.838C>T	c.(838-840)Cct>Tct	p.P280S	SNORD7_ENST00000384567.1_RNA|RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	280	Poly-Pro.				peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGTGGAGTAGGCAGGGCAGTC	0.478																																					p.P280S		.											.	PEX12-90	0			c.C838T						.						215	172	187					17																	33903043		2203	4300	6503	SO:0001583	missense	5193	exon3			GAGTAGGCAGGGC	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.838C>T	17.37:g.33903043G>A	ENSP00000225873:p.Pro280Ser	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	147	65	NM_000286	0	0	11	17	6	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	37	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.510383	0.85389	.	.	ENSG00000108733	ENST00000424525;ENST00000225873	D	0.85484	-1.99	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	D	0.87541	0.6203	M	0.71920	2.185	0.80722	D	1	D	0.54772	0.968	P	0.50231	0.635	D	0.84965	0.0879	10	0.18710	T	0.47	-19.5682	17.5698	0.87932	0.0:0.0:1.0:0.0	.	280	O00623	PEX12_HUMAN	S	280	ENSP00000225873:P280S	ENSP00000225873:P280S	P	-	1	0	PEX12	30927156	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.022000	0.93678	2.614000	0.88457	0.655000	0.94253	CCT	.		0.478	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		A	33903043	G	A	33903043	3	1	52	1	0	0	0	0	1	0	0	0	11766	1203	42	2	245	2	PEX12	17	33903043	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	5497789	33903043	47292167	89	5075											
ENGASE	64772	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	77077140	77077141	+	Missense_Mutation	DNP	TC	TC	CG																															gctcaaatggcaagacgaacTcaaccagcacaacaggtgag																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr17:77077140_77077141TC>CG	ENST00000579016.1	+	6	857_858	c.857_858TC>CG	c.(856-858)cTC>cCG	p.L286P	ENGASE_ENST00000539857.2_Missense_Mutation_p.L100P	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	286						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CAAGACGAACTCAACCAGCACA	0.658																																					p.L286P		.											.	ENGASE	0			c.C858G						.																																			SO:0001583	missense	64772	exon6			CGAACTCAACCAG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	Exception_encountered	17.37:g.77077140_77077141delinsCG	ENSP00000462333:p.Leu286Pro	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	28	16		0	0	0	0	0	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	DNP	ENST00000579016.1	37	CCDS42394.1																																																																																			.		0.658	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		CG	77077141	TC	CG	77077140	3	2	52	1	0	0	0	0	1	0	0	0	5131	1551	54	3	879	3	ENGASE	17	77077140	Missense_Mutation	DNP	TC	TCGA-B9-5156-01A-01D-1589-08	43174097	77077140	4118070	90	5076											
SMAD4	4089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	48581177	48581177	+	Missense_Mutation	SNP	G	G	A																															caagtatgatggtgaaggatGaatatgtgcatgactttgag																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:48581177G>A	ENST00000342988.3	+	5	1019	c.481G>A	c.(481-483)Gaa>Aaa	p.E161K	RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000588745.1_Missense_Mutation_p.E161K|SMAD4_ENST00000452201.2_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.E161K	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	161					atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGTGAAGGATGAATATGTGCA	0.358																																					p.E161K		.											.	SMAD4-4758	39	Whole gene deletion(36)|Unknown(3)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	c.G481A						.						127	92	104					18																	48581177		2203	4300	6503	SO:0001583	missense	4089	exon5			AAGGATGAATATG	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.481G>A	18.37:g.48581177G>A	ENSP00000341551:p.Glu161Lys	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	86	19	NM_005359	0	0	30	30	0	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	35	5.555908	0.96514	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.97688	-4.49;-4.49	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.96975	0.9012	M	0.67397	2.05	0.80722	D	1	P	0.44195	0.828	B	0.41666	0.363	D	0.97207	0.9868	10	0.59425	D	0.04	.	19.1262	0.93386	0.0:0.0:1.0:0.0	.	161	Q13485	SMAD4_HUMAN	K	161	ENSP00000341551:E161K;ENSP00000381452:E161K	ENSP00000341551:E161K	E	+	1	0	SMAD4	46835175	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.567000	0.98161	2.890000	0.99128	0.585000	0.79938	GAA	.		0.358	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48581177	G	A	48581177	3	1	52	1	0	0	0	0	1	0	0	0	14792	1291	45	2	495	2	SMAD4	18	48581177	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		48581177	29496071	91	5077	55	2									
SMAD4	4089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	48581187	48581187	+	Missense_Mutation	SNP	A	A	G																															ggtgaaggatgaatatgtgcAtgactttgagggacagccat																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:48581187A>G	ENST00000342988.3	+	5	1029	c.491A>G	c.(490-492)cAt>cGt	p.H164R	RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000588745.1_Missense_Mutation_p.H164R|SMAD4_ENST00000452201.2_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.H164R	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	164					atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GAATATGTGCATGACTTTGAG	0.368																																					p.H164R		.											.	SMAD4-4758	39	Whole gene deletion(36)|Unknown(3)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	c.A491G						.						148	105	119					18																	48581187		2203	4300	6503	SO:0001583	missense	4089	exon5			ATGTGCATGACTT	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.491A>G	18.37:g.48581187A>G	ENSP00000341551:p.His164Arg	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	102	26	NM_005359	0	0	16	16	0	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154905	0.38021	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.97378	-4.36;-4.36	5.86	4.64	0.57946	.	0.115658	0.64402	D	0.000020	D	0.92753	0.7696	L	0.29908	0.895	0.80722	D	1	B	0.25904	0.137	B	0.17979	0.02	D	0.90115	0.4195	10	0.20046	T	0.44	.	12.835	0.57767	0.8649:0.1351:0.0:0.0	.	164	Q13485	SMAD4_HUMAN	R	164	ENSP00000341551:H164R;ENSP00000381452:H164R	ENSP00000341551:H164R	H	+	2	0	SMAD4	46835185	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.912000	0.48782	2.367000	0.80283	0.528000	0.53228	CAT	.		0.368	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48581187	A	G	48581187	3	3	52	1	0	0	0	0	1	0	0	0	14792	217	8	3	505	3	SMAD4	18	48581187	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	10	48581187	29496061	92	5078	55	2									
TCF4	6925	hgsc.bcm.edu	37	chr18	52921883	52921883	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cactgcatggttccggagaaCatgaatagcatcatccagtc	12	9	9	11	1	1	2	1	1	0	1	4	3	3	2	2	2	3	3	2	2	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:52921883C>G	ENST00000356073.4	-	15	1806	c.1195G>C	c.(1195-1197)Gtt>Ctt	p.V399L	TCF4_ENST00000544241.2_Missense_Mutation_p.V328L|TCF4_ENST00000354452.3_Missense_Mutation_p.V399L|TCF4_ENST00000564999.1_Missense_Mutation_p.V399L|TCF4_ENST00000570177.2_Missense_Mutation_p.V269L|TCF4_ENST00000568740.1_Missense_Mutation_p.V374L|TCF4_ENST00000561992.1_Missense_Mutation_p.V269L|TCF4_ENST00000564228.1_Missense_Mutation_p.V328L|TCF4_ENST00000398339.1_Missense_Mutation_p.V501L|TCF4_ENST00000540999.1_Missense_Mutation_p.V375L|TCF4_ENST00000564403.2_Missense_Mutation_p.V405L|TCF4_ENST00000561831.3_Missense_Mutation_p.V239L|TCF4_ENST00000567880.1_Missense_Mutation_p.V339L|TCF4_ENST00000457482.3_Missense_Mutation_p.V239L|TCF4_ENST00000570287.2_Missense_Mutation_p.V239L|TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000537578.1_Missense_Mutation_p.V375L|TCF4_ENST00000537856.3_Missense_Mutation_p.V269L|TCF4_ENST00000565018.2_Missense_Mutation_p.V399L|TCF4_ENST00000543082.1_Missense_Mutation_p.V357L|TCF4_ENST00000566286.1_Missense_Mutation_p.V396L|TCF4_ENST00000568673.1_Missense_Mutation_p.V375L|TCF4_ENST00000566279.1_Missense_Mutation_p.V339L	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	399	Leucine-zipper.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TTCCGGAGAACATGAATAGCA	0.453																																					p.V501L		.											.	TCF4-523	0			c.G1501C						.						100	97	98					18																	52921883		2203	4300	6503	SO:0001583	missense	6925	exon16			GGAGAACATGAAT	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"Basic helix-loop-helix proteins"	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1195G>C	18.37:g.52921883C>G	ENSP00000348374:p.Val399Leu	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_001243226	0	0	14	14	0	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	37	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.754277	0.89843	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26;0.26;0.26;0.26;0.26	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.76463	0.3991	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.989;1.0;0.997;0.992;1.0;0.994;0.999;0.982;1.0	D;D;D;D;D;D;D;D;D	0.87578	0.961;0.998;0.97;0.992;0.996;0.961;0.961;0.911;0.994	T	0.78285	-0.2263	10	0.87932	D	0	-8.9972	18.4277	0.90614	0.0:1.0:0.0:0.0	.	375;399;239;501;399;357;328;239;396	B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;ITF2_HUMAN;.;.;.;.	L	399;239;399;357;375;375;328;269;501	ENSP00000346440:V399L;ENSP00000409447:V239L;ENSP00000348374:V399L;ENSP00000439656:V357L;ENSP00000445202:V375L;ENSP00000440731:V375L;ENSP00000441562:V328L;ENSP00000439827:V269L;ENSP00000381382:V501L	ENSP00000346440:V399L	V	-	1	0	TCF4	51072881	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.042000	0.70996	2.653000	0.90120	0.585000	0.79938	GTT	.		0.453	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		G	52921883	C	G	52921883	3	3	52	1	0	0	0	0	1	0	0	0	15727	478	17	4	840	4	TCF4	18	52921883	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	4340696	52921883	25155365	93	5079											
RNF152	220441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	59483577	59483577	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctggctggtcctcatctgCtgcaggcacactgaacagca	8	10	10	13	0	3	1	1	1	2	0	4	1	4	1	1	3	4	5	1	3	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:59483577C>A	ENST00000312828.3	-	2	1219	c.120G>T	c.(118-120)caG>caT	p.Q40H		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	40					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				TCCTCATCTGCTGCAGGCACA	0.622																																					p.Q40H		.											.	RNF152-226	0			c.G120T						.						48	50	49					18																	59483577		2203	4300	6503	SO:0001583	missense	220441	exon2			CATCTGCTGCAGG	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"RING-type (C3HC4) zinc fingers"	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.120G>T	18.37:g.59483577C>A	ENSP00000316628:p.Gln40His	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	70	29	NM_173557	0	0	4	8	4	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	37	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404965	0.62288	.	.	ENSG00000176641	ENST00000312828	D	0.92545	-3.06	4.97	4.97	0.65823	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.427187	0.24662	N	0.036625	D	0.91355	0.7273	L	0.37561	1.115	0.41272	D	0.986853	P	0.37781	0.608	P	0.45998	0.5	D	0.91326	0.5086	10	0.48119	T	0.1	-30.3756	18.4187	0.90579	0.0:1.0:0.0:0.0	.	40	Q8N8N0	RN152_HUMAN	H	40	ENSP00000316628:Q40H	ENSP00000316628:Q40H	Q	-	3	2	RNF152	57634557	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.177000	0.58276	2.600000	0.87896	0.655000	0.94253	CAG	.		0.622	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557		A	59483577	C	A	59483577	3	1	52	1	0	0	0	0	1	0	0	0	13485	796	28	4	495	4	RNF152	18	59483577	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	6561694	59483577	18593671	94	5080											
FZR1	51343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	3527659	3527659	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccggtccccccggaaaccCacccgcaagatctccaagat	10	5	7	19	3	1	2	0	0	1	2	4	3	3	3	7	2	1	1	7	2	3	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:3527659C>A	ENST00000395095.3	+	6	501	c.501C>A	c.(499-501)ccC>ccA	p.P167P	FZR1_ENST00000441788.2_Silent_p.P167P|FZR1_ENST00000313639.8_Intron	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	167					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCGGAAACCCACCCGCAAGA	0.622																																					p.P167P		.											.	FZR1-227	0			c.C501A						.						65	55	59					19																	3527659		2199	4296	6495	SO:0001819	synonymous_variant	51343	exon6			GAAACCCACCCGC	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.501C>A	19.37:g.3527659C>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	42	9	NM_001136198	0	0	17	32	15	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Silent	SNP	ENST00000395095.3	37	CCDS45916.1																																																																																			.		0.622	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3527659	C	A	3527659	2	1	52	1	0	0	0	0	0	0	0	1	6157	581	21	4		4	FZR1	19	3527659	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08		3527659	55601324	95	5081											
MAP2K2	5605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4117623	4117623	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctgcaggtccaccaggtTtgccctgcagagacccccca	7	8	9	17	0	1	1	0	0	1	1	2	2	2	1	6	2	3	3	6	2	0	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:4117623T>G	ENST00000262948.5	-	2	350	c.97A>C	c.(97-99)Aac>Cac	p.N33H	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	33					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	TCCACCAGGTTTGCCCTGCAG	0.607																																					p.N33H		.											.	MAP2K2-510	0			c.A97C						.						61	63	62					19																	4117623		2203	4300	6503	SO:0001583	missense	5605	exon2			CCAGGTTTGCCCT	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.97A>C	19.37:g.4117623T>G	ENSP00000262948:p.Asn33His	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	64	23	NM_030662	0	0	0	0	0		Missense_Mutation	SNP	ENST00000262948.5	37	CCDS12120.1	.	.	.	.	.	.	.	.	.	.	t	10.40	1.339579	0.24339	.	.	ENSG00000126934	ENST00000262948	D	0.93189	-3.18	4.14	1.96	0.26148	.	0.114851	0.56097	N	0.000021	D	0.92057	0.7483	M	0.64997	1.995	0.80722	D	1	P	0.41597	0.756	P	0.45829	0.494	D	0.88376	0.2998	10	0.45353	T	0.12	-24.2755	10.059	0.42263	0.0:0.0:0.3226:0.6774	.	33	P36507	MP2K2_HUMAN	H	33	ENSP00000262948:N33H	ENSP00000262948:N33H	N	-	1	0	MAP2K2	4068623	1.000000	0.71417	0.448000	0.26945	0.147000	0.21601	4.829000	0.62737	0.137000	0.18759	0.454000	0.30748	AAC	.		0.607	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			G	4117623	T	G	4117623	3	3	52	1	0	0	0	0	1	0	0	0	9262	1841	64	5	1145	5	MAP2K2	19	4117623	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	589964	4117623	55011360	96	5082											
KDM4B	23030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	5082512	5082513	+	Missense_Mutation	DNP	TC	TC	CA																															gactacggcaaagtggccacTcaggtaaaagcttgcctgct																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:5082512_5082513TC>CA	ENST00000159111.4	+	9	1133_1134	c.915_916TC>CA	c.(913-918)acTCag>acCAag	p.Q306K	KDM4B_ENST00000381759.4_Missense_Mutation_p.Q306K|KDM4B_ENST00000536461.1_Missense_Mutation_p.Q306K	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	306	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						AAGTGGCCACTCAGGTAAAAGC	0.594																																					p.Q306K		.											.	KDM4B	0			c.C916A						.																																			SO:0001583	missense	23030	exon9			GCCACTCAGGTAA	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		Exception_encountered	19.37:g.5082512_5082513delinsCA	ENSP00000159111:p.Gln306Lys	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	38	9		0	0	0	0	0	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	DNP	ENST00000159111.4	37	CCDS12138.1																																																																																			.		0.594	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		CA	5082513	TC	CA	5082512	3	2	52	1	0	0	0	0	1	0	0	0	8150	1538	54	3	941	3	KDM4B	19	5082512	Missense_Mutation	DNP	TC	TCGA-B9-5156-01A-01D-1589-08	964889	5082512	54046471	97	5083											
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11144150	11144150	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctccagccatgagcggcGcgccttcctgcaggccatcc	5	7	11	18	3	0	1	0	1	0	0	4	1	4	1	7	2	3	1	7	2	0	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:11144150G>C	ENST00000429416.3	+	27	4012	c.3731G>C	c.(3730-3732)cGc>cCc	p.R1244P	SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1244P|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1244P|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1244P|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1244P|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1244P|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1244P|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1244P|SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1244P	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1244	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CATGAGCGGCGCGCCTTCCTG	0.642			"F, N, Mis"		NSCLC																																p.R1244P		.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.G3731C						.						80	80	80					19																	11144150		2203	4300	6503	SO:0001583	missense	6597	exon26			AGCGGCGCGCCTT	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3731G>C	19.37:g.11144150G>C	ENSP00000395654:p.Arg1244Pro	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	92	21	NM_003072	0	0	49	87	38	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948702	0.73787	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;T;T;T;T	0.87650	-2.28;-2.28;-2.28;-1.15;-1.15;-1.15;-1.15	4.74	4.74	0.60224	Helicase, C-terminal (1);	0.122489	0.48286	D	0.000187	D	0.90079	0.6901	M	0.64997	1.995	0.40709	D	0.982558	D;D;D;P;D;P;P	0.62365	0.963;0.963;0.963;0.754;0.991;0.927;0.867	P;P;P;P;P;P;P	0.60286	0.82;0.872;0.872;0.575;0.863;0.669;0.796	D	0.90809	0.4700	10	0.87932	D	0	-24.5941	10.3285	0.43807	0.0918:0.0:0.9082:0.0	.	1244;1244;1244;1244;1244;464;1244	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	P	1244;1244;1308;1244;1244;1244;1244;1244	ENSP00000395654:R1244P;ENSP00000350720:R1244P;ENSP00000343896:R1244P;ENSP00000445036:R1244P;ENSP00000392837:R1244P;ENSP00000397783:R1244P;ENSP00000414727:R1244P	ENSP00000343896:R1244P	R	+	2	0	SMARCA4	11005150	0.985000	0.35326	0.998000	0.56505	0.972000	0.66771	6.337000	0.72958	2.488000	0.83962	0.558000	0.71614	CGC	.		0.642	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11144150	G	C	11144150	3	2	52	1	0	0	0	0	1	0	0	0	14802	1087	38	4	3829	4	SMARCA4	19	11144150	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	6061638	11144150	47984833	98	5084											
KANK2	25959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11304538	11304538	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagccagggccacggggcAgcgagctcaggcgggggcgg	7	1	22	11	4	1	0	1	0	0	0	1	2	1	1	2	8	3	2	2	8	0	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:11304538A>T	ENST00000586659.1	-	4	532	c.218T>A	c.(217-219)cTg>cAg	p.L73Q	KANK2_ENST00000355150.5_Missense_Mutation_p.L73Q|KANK2_ENST00000432929.2_Missense_Mutation_p.L73Q|KANK2_ENST00000589359.1_Missense_Mutation_p.L73Q|KANK2_ENST00000589894.1_Missense_Mutation_p.L73Q			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	73					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GCCACGGGGCAGCGAGCTCAG	0.672																																					p.L73Q		.											.	KANK2-68	0			c.T218A						.						35	37	36					19																	11304538		2203	4297	6500	SO:0001583	missense	25959	exon2			CGGGGCAGCGAGC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	29300	protein-coding gene	gene with protein product		614610	"matrix-remodelling associated 3", "ankyrin repeat domain 25"	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.218T>A	19.37:g.11304538A>T	ENSP00000465650:p.Leu73Gln	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	51	19	NM_015493	0	0	14	20	6	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.853681	0.32791	.	.	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.48836	0.8;0.82	4.38	4.38	0.52667	.	0.000000	0.56097	D	0.000029	T	0.61800	0.2376	L	0.57536	1.79	0.35815	D	0.824149	D;D;D	0.89917	1.0;0.965;1.0	D;P;D	0.91635	0.999;0.862;0.999	T	0.67201	-0.5730	10	0.28530	T	0.3	-25.9043	12.5808	0.56390	1.0:0.0:0.0:0.0	.	73;73;73	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	Q	73	ENSP00000395650:L73Q;ENSP00000347276:L73Q	ENSP00000347276:L73Q	L	-	2	0	KANK2	11165538	1.000000	0.71417	0.540000	0.28089	0.038000	0.13279	6.295000	0.72744	1.616000	0.50265	0.379000	0.24179	CTG	.		0.672	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11304538	A	T	11304538	3	4	52	1	0	0	0	0	1	0	0	0	7998	188	7	5	2401	5	KANK2	19	11304538	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	160388	11304538	47824445	99	5085											
ZNF791	163049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12739559	12739559	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaaatccacaagagaaatCacactggagaaaaaccctat	20	6	6	9	0	1	3	1	1	0	2	2	5	2	3	2	1	1	0	2	1	7	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:12739559C>A	ENST00000343325.4	+	4	1378	c.1216C>A	c.(1216-1218)Cac>Aac	p.H406N	AC010422.1_ENST00000408416.1_RNA|ZNF791_ENST00000446165.1_3'UTR|ZNF791_ENST00000458122.3_Missense_Mutation_p.H374N|ZNF490_ENST00000465656.1_Intron|ZNF791_ENST00000540038.1_Missense_Mutation_p.H297N	NM_153358.2	NP_699189.2	Q3KP31	ZN791_HUMAN	zinc finger protein 791	406					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						CAAGAGAAATCACACTGGAGA	0.393																																					p.H406N		.											.	ZNF791-92	0			c.C1216A						.						90	99	96					19																	12739559		2203	4300	6503	SO:0001583	missense	163049	exon4			AGAAATCACACTG	AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875		"Zinc fingers, C2H2-type", "-"	26895	protein-coding gene	gene with protein product							Standard	NM_153358		Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000343325.4:c.1216C>A	19.37:g.12739559C>A	ENSP00000342974:p.His406Asn	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	207	77	NM_153358	0	0	2	6	4	B7Z586|Q8NC99	Missense_Mutation	SNP	ENST00000343325.4	37	CCDS12273.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828830	0.50845	.	.	ENSG00000173875	ENST00000343325;ENST00000393303;ENST00000458122;ENST00000540038	T;T;T	0.67345	-0.26;-0.26;-0.26	1.83	1.83	0.25207	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81959	0.4933	M	0.88640	2.97	0.30637	N	0.756821	D	0.76494	0.999	D	0.91635	0.999	T	0.77763	-0.2466	9	0.87932	D	0	.	9.2247	0.37398	0.0:1.0:0.0:0.0	.	406	Q3KP31	ZN791_HUMAN	N	406;388;374;297	ENSP00000342974:H406N;ENSP00000441761:H374N;ENSP00000441038:H297N	ENSP00000342974:H406N	H	+	1	0	ZNF791	12600559	1.000000	0.71417	0.865000	0.33974	0.967000	0.64934	4.955000	0.63638	1.007000	0.39238	0.491000	0.48974	CAC	.		0.393	ZNF791-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344140.1	NM_153358		A	12739559	C	A	12739559	3	1	52	1	0	0	0	0	1	0	0	0	18195	826	29	4	1230	4	ZNF791	19	12739559	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	1435021	12739559	46389424	100	5086											
ZNF260	339324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	37005333	37005333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtagggtttctctccaatatGaattttctcatgctctgtga	8	17	8	8	0	3	2	1	2	3	0	6	2	4	2	1	1	1	3	1	1	4	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:37005333G>A	ENST00000523638.1	-	3	1929	c.808C>T	c.(808-810)Cat>Tat	p.H270Y	ZNF260_ENST00000588993.1_Missense_Mutation_p.H270Y|ZNF260_ENST00000593142.1_Missense_Mutation_p.H270Y|ZNF260_ENST00000592282.1_Missense_Mutation_p.H270Y	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	270					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					TCTCCAATATGAATTTTCTCA	0.398																																					p.H270Y		.											.	ZNF260-90	0			c.C808T						.						123	122	122					19																	37005333		2203	4300	6503	SO:0001583	missense	339324	exon3			CAATATGAATTTT	AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004		"Zinc fingers, C2H2-type"	13499	protein-coding gene	gene with protein product		613749					Standard	NM_001166036		Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.808C>T	19.37:g.37005333G>A	ENSP00000429803:p.His270Tyr	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	134	42	NM_001166038	0	0	3	6	3	Q0VF43	Missense_Mutation	SNP	ENST00000523638.1	37	CCDS33003.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335259	0.81801	.	.	ENSG00000254004	ENST00000523638	T	0.67523	-0.27	4.54	4.54	0.55810	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85720	0.5762	M	0.92412	3.305	0.50632	D	0.999883	D	0.89917	1.0	D	0.91635	0.999	D	0.89435	0.3719	9	0.87932	D	0	.	16.5613	0.84567	0.0:0.0:1.0:0.0	.	270	Q3ZCT1	ZN260_HUMAN	Y	270	ENSP00000429803:H270Y	ENSP00000429803:H270Y	H	-	1	0	ZNF260	41697173	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.645000	0.83430	2.496000	0.84212	0.561000	0.74099	CAT	.		0.398	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109564.2	NM_001012756		A	37005333	G	A	37005333	3	1	52	1	0	0	0	0	1	0	0	0	17834	1290	45	2	434	2	ZNF260	19	37005333	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	24265774	37005333	22123650	101	5087											
GSK3A	2931	hgsc.bcm.edu	37	chr19	42746451	42746451	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccccgacgcccccacccAtggccccgacagatgccttt	7	5	9	20	3	0	1	0	0	0	1	0	3	0	1	8	2	1	0	8	2	0	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:42746451A>G	ENST00000222330.3	-	1	294	c.167T>C	c.(166-168)aTg>aCg	p.M56T	AC006486.1_ENST00000378108.1_5'Flank|GSK3A_ENST00000398249.4_5'Flank|AC006486.9_ENST00000594664.1_Intron	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	56	Gly-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				GCCCCCACCCATGGCCCCGAC	0.821																																					p.M56T		.											.	GSK3A-981	0			c.T167C						.																																			SO:0001583	missense	2931	exon1			CCACCCATGGCCC		CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.167T>C	19.37:g.42746451A>G	ENSP00000222330:p.Met56Thr	Somatic	3	2		WXS	Illumina HiSeq	Phase_I	4	2	NM_019884	0	0	1	4	3	O14959	Missense_Mutation	SNP	ENST00000222330.3	37	CCDS12599.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340070	0.41398	.	.	ENSG00000105723	ENST00000222330;ENST00000544315	T	0.20738	2.05	3.88	3.88	0.44766	.	.	.	.	.	T	0.12646	0.0307	N	0.24115	0.695	0.80722	D	1	B	0.14012	0.009	B	0.10450	0.005	T	0.09530	-1.0670	9	0.16420	T	0.52	-7.7159	9.2973	0.37824	1.0:0.0:0.0:0.0	.	56	P49840	GSK3A_HUMAN	T	56;1	ENSP00000222330:M56T	ENSP00000222330:M56T	M	-	2	0	GSK3A	47438291	0.999000	0.42202	0.998000	0.56505	0.897000	0.52465	1.556000	0.36288	1.771000	0.52183	0.459000	0.35465	ATG	.		0.821	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1			G	42746451	A	G	42746451	3	3	52	1	0	0	0	0	1	0	0	0	6844	217	8	3	1328	3	GSK3A	19	42746451	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	5741118	42746451	16382532	102	5088											
NOSIP	51070	hgsc.bcm.edu;broad.mit.edu	37	chr19	50063190	50063190	+	Splice_Site	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatccctgttcccagctcaCgtgacaacaggatcgtggca	9	8	9	15	2	1	1	1	1	0	0	4	2	3	2	3	2	2	3	3	2	1	1	rs150449733		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:50063190C>G	ENST00000596358.1	-	3	235		c.e3+1		NOSIP_ENST00000391853.3_Splice_Site|NOSIP_ENST00000339093.3_Splice_Site	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein						negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		TCCCAGCTCACGTGACAACAG	0.622																																					.		.											.	NOSIP-91	0			c.176+1G>C						.						83	59	67					19																	50063190		2203	4300	6503	SO:0001630	splice_region_variant	51070	exon4			AGCTCACGTGACA	AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.176+1G>C	19.37:g.50063190C>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	16	3	NM_001270960	0	0	0	0	0	Q96FD2	Splice_Site	SNP	ENST00000596358.1	37	CCDS12772.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.652985	0.67472	.	.	ENSG00000142546	ENST00000339093;ENST00000391853	.	.	.	5.5	2.05	0.26809	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7205	0.62723	0.4016:0.5984:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOSIP	54755002	1.000000	0.71417	0.925000	0.36789	0.978000	0.69477	4.870000	0.63035	0.241000	0.21283	0.585000	0.79938	.	C|1.000;T|0.000		0.622	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1		Intron	G	50063190	C	G	50063190	5	3	52	1	0	0	0	0	0	0	1	0	10571	550	19	4	756	4	NOSIP	19	50063190	Splice_Site	SNP	C	TCGA-B9-5156-01A-01D-1589-08	7316739	50063190	9065793	103	5089											
TTYH1	57348	broad.mit.edu	37	chr19	54932519	54932519	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgtcccagctcagctctgCgctgctgcacgccaaccaca	7	7	10	17	2	2	0	1	0	1	0	3	0	3	0	3	1	6	5	3	1	1	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:54932519C>T	ENST00000376530.3	+	3	477	c.374C>T	c.(373-375)gCg>gTg	p.A125V	TTYH1_ENST00000301194.4_Missense_Mutation_p.A125V|TTYH1_ENST00000391739.3_Missense_Mutation_p.A174V|TTYH1_ENST00000376531.3_Missense_Mutation_p.A125V	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	125					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)			endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CTCAGCTCTGCGCTGCTGCAC	0.622																																					p.A125V													.	TTYH1-90	0			c.C374T						.						125	102	110					19																	54932519		2203	4300	6503	SO:0001583	missense	57348	exon3			GCTCTGCGCTGCT	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.374C>T	19.37:g.54932519C>T	ENSP00000365713:p.Ala125Val	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	82	4	NM_020659	0	0	0	0	0	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	37	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404884	0.83230	.	.	ENSG00000167614	ENST00000423529;ENST00000301194;ENST00000376530;ENST00000445095;ENST00000391739;ENST00000376531	T;T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46;2.46	3.75	3.75	0.43078	.	0.071799	0.56097	D	0.000029	T	0.34978	0.0916	L	0.55481	1.735	0.51482	D	0.999929	D;D;D;D;D	0.89917	1.0;0.995;0.99;0.995;1.0	D;P;P;P;D	0.83275	0.976;0.837;0.718;0.837;0.996	T	0.04840	-1.0923	9	.	.	.	-10.4751	13.8879	0.63719	0.0:1.0:0.0:0.0	.	174;40;125;125;125	B7Z1H9;Q9H313-5;Q9H313-2;Q9H313-3;Q9H313	.;.;.;.;TTYH1_HUMAN	V	121;125;125;174;174;125	ENSP00000391282:A121V;ENSP00000301194:A125V;ENSP00000365713:A125V;ENSP00000393592:A174V;ENSP00000375619:A174V;ENSP00000365714:A125V	.	A	+	2	0	TTYH1	59624331	1.000000	0.71417	0.483000	0.27378	0.558000	0.35554	6.882000	0.75589	2.021000	0.59480	0.655000	0.94253	GCG	.		0.622	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1			T	54932519	C	T	54932519	3	4	52	1	0	0	0	0	1	0	0	0	16772	768	27	1	384	1	TTYH1	19	54932519	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	4869329	54932519	4196464	104	5090											
FITM2	128486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42935425	42935425	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acaagttgtggaaataaacaGctgtgcacagaaacatcaac	18	7	8	8	0	1	1	1	0	0	1	1	2	1	2	0	1	5	3	0	1	6	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr20:42935425G>T	ENST00000396825.3	-	2	649	c.629C>A	c.(628-630)gCt>gAt	p.A210D		NM_001080472.1	NP_001073941.1	Q8N6M3	FITM2_HUMAN	fat storage-inducing transmembrane protein 2	210					cellular triglyceride homeostasis (GO:0035356)|cytoskeleton organization (GO:0007010)|lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of cell morphogenesis (GO:0022604)|regulation of triglyceride biosynthetic process (GO:0010866)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)				endometrium(2)|lung(2)|skin(2)	6						GAAATAAACAGCTGTGCACAG	0.522																																					p.A210D		.											.	FITM2-24	0			c.C629A						.						99	83	88					20																	42935425		2203	4300	6503	SO:0001583	missense	128486	exon2			TAAACAGCTGTGC	BC029662	CCDS33473.1	20q13.12	2009-04-29	2009-04-29	2009-04-29	ENSG00000197296	ENSG00000197296			16135	protein-coding gene	gene with protein product	"fat inducing transcript 2"	612029	"chromosome 20 open reading frame 142"	C20orf142		18160536	Standard	NM_001080472		Approved	dJ881L22.2, FIT2	uc002xlr.1	Q8N6M3	OTTHUMG00000032522	ENST00000396825.3:c.629C>A	20.37:g.42935425G>T	ENSP00000380037:p.Ala210Asp	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	55	18	NM_001080472	0	0	8	18	10	A1L492|B9EGQ4|Q5TE59|Q9H3Y1	Missense_Mutation	SNP	ENST00000396825.3	37	CCDS33473.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600365	0.87055	.	.	ENSG00000197296	ENST00000396825	.	.	.	5.57	5.57	0.84162	.	0.217055	0.48286	D	0.000191	D	0.82747	0.5104	M	0.84082	2.675	0.80722	D	1	D	0.63880	0.993	D	0.63877	0.919	T	0.83306	-0.0025	9	0.48119	T	0.1	.	19.5462	0.95299	0.0:0.0:1.0:0.0	.	210	Q8N6M3	FITM2_HUMAN	D	210	.	ENSP00000380037:A210D	A	-	2	0	FITM2	42368839	1.000000	0.71417	0.620000	0.29132	0.912000	0.54170	9.397000	0.97276	2.609000	0.88269	0.563000	0.77884	GCT	.		0.522	FITM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079342.2	XM_371399		T	42935425	G	T	42935425	3	4	52	1	0	0	0	0	1	0	0	0	5918	971	34	4	163	4	FITM2	20	42935425	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		42935425	20090095	105	5091											
MYH9	4627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	36716872	36716872	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctccagccccagacaggAgataatagaagatgtggaag	14	6	12	9	0	1	4	0	0	1	4	2	6	1	5	3	2	1	1	3	2	4	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr22:36716872A>T	ENST00000216181.5	-	8	1069	c.839T>A	c.(838-840)cTc>cAc	p.L280H		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	280	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CCCAGACAGGAGATAATAGAA	0.532			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.L280H		.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9-292	0			c.T839A						.						74	70	71					22																	36716872		2203	4300	6503	SO:0001583	missense	4627	exon8	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GACAGGAGATAAT		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.839T>A	22.37:g.36716872A>T	ENSP00000216181:p.Leu280His	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	40	11	NM_002473	1	0	183	306	122	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.937579	0.92458	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	D	0.94092	-3.35	5.13	5.13	0.70059	Myosin head, motor domain (2);	0.073236	0.53938	D	0.000057	D	0.97405	0.9151	H	0.99357	4.53	0.80722	D	1	D	0.63880	0.993	P	0.51895	0.683	D	0.98753	1.0721	10	0.87932	D	0	.	14.9048	0.70709	1.0:0.0:0.0:0.0	.	280	P35579	MYH9_HUMAN	H	144;280	ENSP00000216181:L280H	ENSP00000216181:L280H	L	-	2	0	MYH9	35046818	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	9.287000	0.95975	2.053000	0.61076	0.482000	0.46254	CTC	.		0.532	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36716872	A	T	36716872	3	4	52	1	0	0	0	0	1	0	0	0	10067	304	11	5	5179	5	MYH9	22	36716872	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		36716872	14587694	106	5092											
EP300	2033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	41489069	41489069	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	agcggcctaaactctcatctCcggccctctcggcgtccgcc	5	8	9	19	5	3	0	1	0	3	0	7	0	4	0	5	3	2	0	5	3	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr22:41489069C>G	ENST00000263253.7	+	1	1280	c.61C>G	c.(61-63)Ccg>Gcg	p.P21A	MIR1281_ENST00000408233.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	21	Interaction with ALX1.|Interaction with RORA.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACTCTCATCTCCGGCCCTCTC	0.547			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.P21A		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300-2011	0			c.C61G						.						56	66	63					22																	41489069		2203	4300	6503	SO:0001583	missense	2033	exon1	Familial Cancer Database	Broad Thumb-Hallux syndrome	TCATCTCCGGCCC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.61C>G	22.37:g.41489069C>G	ENSP00000263253:p.Pro21Ala	Somatic	179	2		WXS	Illumina HiSeq	Phase_I	159	41	NM_001429	0	0	5	7	2	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929891	0.92389	.	.	ENSG00000100393	ENST00000263253	D	0.94537	-3.45	4.7	4.7	0.59300	.	0.000000	0.39020	N	0.001484	D	0.95974	0.8689	L	0.51914	1.62	0.49389	D	0.999785	D	0.76494	0.999	D	0.80764	0.994	D	0.95834	0.8860	10	0.51188	T	0.08	.	15.9919	0.80211	0.0:1.0:0.0:0.0	.	21	Q09472	EP300_HUMAN	A	21	ENSP00000263253:P21A	ENSP00000263253:P21A	P	+	1	0	EP300	39819015	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.738000	0.74822	2.449000	0.82847	0.591000	0.81541	CCG	.		0.547	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41489069	C	G	41489069	3	3	52	1	0	0	0	0	1	0	0	0	5161	855	30	4	63	4	EP300	22	41489069	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	4772197	41489069	9815497	107	5093											
USP9X	8239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	40999924	40999924	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacagggttggctagtggatCttctcaacaaatttggcact	10	13	10	8	0	2	0	1	0	2	0	3	1	2	1	0	4	2	3	0	4	4	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chrX:40999924C>A	ENST00000324545.8	+	7	1303	c.670C>A	c.(670-672)Ctt>Att	p.L224I	USP9X_ENST00000378308.2_Missense_Mutation_p.L224I	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	224					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						GCTAGTGGATCTTCTCAACAA	0.318																																					p.L224I	Ovarian(172;1807 2695 35459 49286)	.											.	USP9X-563	0			c.C670A						.						111	99	103					X																	40999924		2203	4298	6501	SO:0001583	missense	8239	exon7			GTGGATCTTCTCA	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.670C>A	X.37:g.40999924C>A	ENSP00000316357:p.Leu224Ile	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	80	55	NM_001039591	0	0	7	38	31	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.926912	0.73327	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.03982	3.75;3.74	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.24044	0.0582	M	0.79475	2.455	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.74348	0.983;0.963	T	0.00104	-1.2059	10	0.45353	T	0.12	.	19.5004	0.95091	0.0:1.0:0.0:0.0	.	224;224	Q93008-1;Q93008	.;USP9X_HUMAN	I	224	ENSP00000367558:L224I;ENSP00000316357:L224I	ENSP00000316357:L224I	L	+	1	0	USP9X	40884868	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.611000	0.61162	2.560000	0.86352	0.594000	0.82650	CTT	.		0.318	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		A	40999924	C	A	40999924	3	1	52	1	0	0	0	0	1	0	0	0	17123	913	32	4	692	4	USP9X	23	40999924	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08		40999924	114270636	108	5094											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350698	50350698	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctctgcctcctcctcCtcctcttcctcttcctcttc	0	17	1	23	0	4	0	0	0	4	0	13	0	12	0	9	0	1	0	9	0	0	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chrX:50350698C>T	ENST00000289292.7	-	6	3727	c.3444G>A	c.(3442-3444)gaG>gaA	p.E1148E	SHROOM4_ENST00000376020.2_Silent_p.E1148E|SHROOM4_ENST00000460112.3_Silent_p.E1032E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1148	Glu-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctcctcctcctcctcttcct	0.557													C|||	1	0.000264901	0	0.0014	3775	,	,		12007	0		0	False		,,,				2504	0				p.E1148E		.											.	SHROOM4-131	0			c.G3444A						.						22	20	21					X																	50350698		2203	4298	6501	SO:0001819	synonymous_variant	57477	exon6			CTCCTCCTCCTCT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3444G>A	X.37:g.50350698C>T		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_020717	0	0	0	0	0	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																			.		0.557	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50350698	C	T	50350698	2	4	52	1	0	0	0	0	0	0	0	1	14328	680	24	2		2	SHROOM4	23	50350698	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08	9350774	50350698	104919862	109	5095											
SKI	6497	hgsc.bcm.edu	37	chr1	2160390	2160390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgcggccgcggtgccggCgccggtgcccgcagccaccg	2	2	19	18	9	0	0	0	0	0	0	0	0	0	0	6	5	3	1	6	5	0	0	rs28384811	byFrequency	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:2160390C>G	ENST00000378536.4	+	1	257	c.185C>G	c.(184-186)gCg>gGg	p.A62G		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	62					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		gcggtgccggcgccggTGCCC	0.776													C|||	229	0.0457268	0.0234	0.0576	5008	,	,		4535	0.0079		0.0706	False		,,,				2504	0.0808				p.A62G	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.C185G						.						1	1	1					1																	2160390		788	1840	2628	SO:0001583	missense	6497	exon1			TGCCGGCGCCGGT	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.185C>G	1.37:g.2160390C>G	ENSP00000367797:p.Ala62Gly	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_003036	0	0	0	1	1	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	37	CCDS39.1	102	0.046703296703296704	20	0.04065040650406504	28	0.07734806629834254	3	0.005244755244755245	51	0.06728232189973615	C	9.688	1.151208	0.21371	.	.	ENSG00000157933	ENST00000378536	D	0.95821	-3.82	2.3	2.3	0.28687	.	.	.	.	.	T	0.47857	0.1468	N	0.08118	0	0.45733	P	0.001363000000000003	D	0.57899	0.981	P	0.58520	0.84	T	0.76271	-0.3020	8	0.20519	T	0.43	-11.9718	7.7374	0.28823	0.0:1.0:0.0:0.0	rs28384811	62	P12755	SKI_HUMAN	G	62	ENSP00000367797:A62G	ENSP00000367797:A62G	A	+	2	0	SKI	2150250	0.994000	0.37717	0.998000	0.56505	0.971000	0.66376	0.878000	0.28126	1.104000	0.41587	0.185000	0.17295	GCG	C|0.953;G|0.047		0.776	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		G	2160390	C	G	2160390	3	3	53	1	0	0	0	0	1	0	0	0	14389	768	27	4	187	4	SKI	1	2160390	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		2160390	247090231	1	5096											
FUCA1	2517	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24192102	24192102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttcgtgatgctttgtcgTcaaaactacatacctgtgga	9	13	9	10	2	1	1	1	1	0	0	3	2	1	2	2	1	4	1	2	1	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:24192102T>C	ENST00000374479.3	-	2	410	c.403A>G	c.(403-405)Acg>Gcg	p.T135A		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	135					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		TGCTTTGTCGTCAAAACTACA	0.488																																					p.T135A		.											.	FUCA1-153	0			c.A403G						.						107	101	103					1																	24192102		2203	4300	6503	SO:0001583	missense	2517	exon2			TTGTCGTCAAAAC	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.403A>G	1.37:g.24192102T>C	ENSP00000363603:p.Thr135Ala	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	153	34	NM_000147	0	0	0	0	0	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	37	CCDS244.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.276474	0.80580	.	.	ENSG00000179163	ENST00000374479	T	0.62105	0.05	5.38	5.38	0.77491	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.88451	0.6440	H	0.99404	4.55	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.93482	0.6828	10	0.87932	D	0	-11.1115	15.685	0.77402	0.0:0.0:0.0:1.0	.	135	P04066	FUCO_HUMAN	A	135	ENSP00000363603:T135A	ENSP00000363603:T135A	T	-	1	0	FUCA1	24064689	1.000000	0.71417	0.944000	0.38274	0.576000	0.36127	7.551000	0.82182	2.163000	0.67991	0.459000	0.35465	ACG	.		0.488	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		C	24192102	T	C	24192102	3	2	53	1	0	0	0	0	1	0	0	0	6113	1667	58	3	1025	3	FUCA1	1	24192102	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	22031712	24192102	225058519	2	5097											
CATSPER4	378807	ucsc.edu	37	chr1	26528995	26528995	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggttcatgactctagcTcacaaatactccttaaaaaa	15	11	5	10	0	3	1	2	1	1	0	4	1	4	1	1	1	3	3	1	1	6	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:26528995T>C	ENST00000456354.2	+	10	1448	c.1381T>C	c.(1381-1383)Tca>Cca	p.S461P		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	461					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TGACTCTAGCTCACAAATACT	0.552																																					p.S461P													.	CATSPER4-91	0			c.T1381C						.						40	39	39					1																	26528995		2203	4300	6503	SO:0001583	missense	378807	exon10			TCTAGCTCACAAA	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"Voltage-gated ion channels / Cation channels, sperm associated"	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1381T>C	1.37:g.26528995T>C	ENSP00000390423:p.Ser461Pro	Somatic	21	0		WXS	Illumina HiSeq		31	4	NM_198137	0	0	0	0	0	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	.	.	.	.	.	.	.	.	.	.	T	2.653	-0.281491	0.05642	.	.	ENSG00000188782	ENST00000456354	D	0.97529	-4.42	4.42	-2.63	0.06133	.	2.363080	0.02142	N	0.057251	D	0.91005	0.7171	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	D	0.84668	0.0710	10	0.44086	T	0.13	0.0864	5.949	0.19235	0.3484:0.4045:0.0:0.2471	.	461	Q7RTX7	CTSR4_HUMAN	P	461	ENSP00000390423:S461P	ENSP00000390423:S461P	S	+	1	0	CATSPER4	26401582	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.066000	0.14489	-0.456000	0.07043	-0.509000	0.04479	TCA	.		0.552	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137		C	26528995	T	C	26528995	3	2	53	1	0	0	0	0	1	0	0	0	2696	1551	54	3	1419	3	CATSPER4	1	26528995	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	2336893	26528995	222721626	3	5098											
PABPC4	8761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40029530	40029530	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagactggcagctgtcagtCagcccttgctgggcggcacc	6	7	13	15	1	2	1	2	0	0	1	2	1	2	1	3	3	3	4	3	3	0	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:40029530C>T	ENST00000372857.3	-	11	2262	c.1470G>A	c.(1468-1470)ctG>ctA	p.L490L	PABPC4_ENST00000372862.3_Intron|PABPC4_ENST00000372858.3_Silent_p.L506L|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372856.3_Intron	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	490					blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGCTGTCAGTCAGCCCTTGCT	0.557																																					p.L506L		.											.	PABPC4-68	0			c.G1518A						.						60	61	61					1																	40029530		2203	4300	6503	SO:0001819	synonymous_variant	8761	exon11			GTCAGTCAGCCCT	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1470G>A	1.37:g.40029530C>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	116	51	NM_001135653	0	0	85	140	55	B1ANQ8|Q4VC03|Q6P0N3	Silent	SNP	ENST00000372857.3	37	CCDS438.1																																																																																			.		0.557	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		T	40029530	C	T	40029530	2	4	53	1	0	0	0	0	0	0	0	1	11392	813	29	2		2	PABPC4	1	40029530	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	13500535	40029530	209221091	4	5099											
BEST4	266675	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	45250593	45250593	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacctgcaagttgcggtctAtgagctgatttgtctcaaag	9	13	10	9	1	3	2	2	2	2	0	4	2	3	2	1	1	3	3	1	1	3	3	rs377207881		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:45250593A>G	ENST00000372207.3	-	7	976	c.977T>C	c.(976-978)aTa>aCa	p.I326T		NM_153274.2	NP_695006.1	Q8NFU0	BEST4_HUMAN	bestrophin 4	326						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)					GTTGCGGTCTATGAGCTGATT	0.562																																					p.I326T		.											.	BEST4-91	0			c.T977C						.						76	81	79					1																	45250593		2203	4300	6503	SO:0001583	missense	266675	exon7			CGGTCTATGAGCT	AF440757	CCDS514.1	1p33-p32.3	2012-09-26	2006-10-18	2006-10-18	ENSG00000142959	ENSG00000142959		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17106	protein-coding gene	gene with protein product		607336	"vitelliform macular dystrophy 2-like 2"	VMD2L2		12032738, 16702355	Standard	NM_153274		Approved		uc001cmm.3	Q8NFU0	OTTHUMG00000008488	ENST00000372207.3:c.977T>C	1.37:g.45250593A>G	ENSP00000361281:p.Ile326Thr	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	135	11	NM_153274	0	0	1	1	0	Q5JR93	Missense_Mutation	SNP	ENST00000372207.3	37	CCDS514.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.072846	0.76415	.	.	ENSG00000142959	ENST00000372207	D	0.99270	-5.66	5.19	4.07	0.47477	.	0.051148	0.85682	D	0.000000	D	0.99518	0.9828	H	0.96269	3.795	0.51767	D	0.999939	D	0.71674	0.998	D	0.74348	0.983	D	0.98708	1.0703	10	0.87932	D	0	-16.684	9.7184	0.40289	0.9183:0.0:0.0816:0.0	.	326	Q8NFU0	BEST4_HUMAN	T	326	ENSP00000361281:I326T	ENSP00000361281:I326T	I	-	2	0	BEST4	45023180	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.946000	0.70234	0.998000	0.38996	0.533000	0.62120	ATA	.		0.562	BEST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023425.1	NM_153274		G	45250593	A	G	45250593	3	3	53	1	0	0	0	0	1	0	0	0	1408	449	16	3	456	3	BEST4	1	45250593	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	5221063	45250593	204000028	5	5100											
STXBP3	6814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109302625	109302625	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtttgccctgataatctctTtaacaaaattaaggcttctt	12	16	5	8	0	2	1	0	1	2	0	3	1	2	1	1	1	2	2	1	1	5	7			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:109302625T>G	ENST00000370008.3	+	6	406	c.356T>G	c.(355-357)tTt>tGt	p.F119C		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	119	Mediates interaction with DOC2B. {ECO:0000250}.				blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GATAATCTCTTTAACAAAATT	0.289																																					p.F119C		.											.	STXBP3-93	0			c.T356G						.						92	106	101					1																	109302625		2203	4288	6491	SO:0001583	missense	6814	exon6			ATCTCTTTAACAA	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.356T>G	1.37:g.109302625T>G	ENSP00000359025:p.Phe119Cys	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	216	94	NM_007269	0	0	18	34	16	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	37	CCDS790.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861971	0.71949	.	.	ENSG00000116266	ENST00000370008	T	0.77098	-1.07	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.87083	0.6089	M	0.84846	2.72	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.89069	0.3468	10	0.62326	D	0.03	-18.7523	15.3518	0.74396	0.0:0.0:0.0:1.0	.	119	O00186	STXB3_HUMAN	C	119	ENSP00000359025:F119C	ENSP00000359025:F119C	F	+	2	0	STXBP3	109104148	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.164000	0.71885	2.110000	0.64415	0.477000	0.44152	TTT	.		0.289	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		G	109302625	T	G	109302625	3	3	53	1	0	0	0	0	1	0	0	0	15386	1841	64	5	378	5	STXBP3	1	109302625	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	64052032	109302625	139947996	6	5101											
CHD1L	9557	hgsc.bcm.edu	37	chr1	146727559	146727559	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgaaacaggagtcacgttttCatgtgctactgactacctat	11	13	8	9	1	2	2	2	2	0	0	2	3	2	3	1	1	4	2	1	1	4	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:146727559C>G	ENST00000369258.4	+	4	459	c.439C>G	c.(439-441)Cat>Gat	p.H147D	CHD1L_ENST00000369259.3_Intron|CHD1L_ENST00000361293.5_Intron|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000431239.1_Missense_Mutation_p.H147D	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	147	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					GTCACGTTTTCATGTGCTACT	0.433																																					p.H147D		.											.	CHD1L-231	0			c.C439G						.						79	67	71					1																	146727559		2203	4300	6503	SO:0001583	missense	9557	exon4			CGTTTTCATGTGC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.439C>G	1.37:g.146727559C>G	ENSP00000358262:p.His147Asp	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_004284	0	0	9	9	0	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	.	.	.	.	.	.	.	.	.	.	C	1.555	-0.538188	0.04082	.	.	ENSG00000131778	ENST00000431239;ENST00000369258;ENST00000436230;ENST00000254086	D;D	0.91686	-2.89;-2.89	5.66	5.66	0.87406	DEAD-like helicase (2);SNF2-related (1);	0.198583	0.53938	D	0.000060	D	0.82912	0.5140	N	0.02368	-0.58	0.80722	D	1	D;B	0.89917	1.0;0.007	D;B	0.83275	0.996;0.038	T	0.81709	-0.0809	10	0.02654	T	1	.	15.6157	0.76767	0.0:1.0:0.0:0.0	.	147;147	Q86WJ1-2;Q86WJ1	.;CHD1L_HUMAN	D	147;147;47;108	ENSP00000389031:H147D;ENSP00000358262:H147D	ENSP00000254086:H108D	H	+	1	0	CHD1L	145194183	1.000000	0.71417	1.000000	0.80357	0.290000	0.27261	2.913000	0.48790	2.832000	0.97577	0.655000	0.94253	CAT	.		0.433	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		G	146727559	C	G	146727559	3	3	53	1	0	0	0	0	1	0	0	0	3330	826	29	4	453	4	CHD1L	1	146727559	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	37424934	146727559	102523062	7	5102											
C1orf54	79630	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	150248209	150248212	+	Splice_Site	DEL	GTGA	GTGA	-																															ttgagtcagaggacaggctgGtgagtgaactctacatctaa																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	GTGA	GTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:150248209_150248212delGTGA	ENST00000369102.1	+	5	959		c.e5+1		C1orf54_ENST00000369098.3_Splice_Site|C1orf54_ENST00000369099.3_Splice_Site			Q8WWF1	CA054_HUMAN	chromosome 1 open reading frame 54							extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGACAGGCTGGTGAGTGAACTCTA	0.407																																					.		.											.	C1orf54-90	0			.						.																																			SO:0001630	splice_region_variant	79630	.			.	BC017761	CCDS948.1, CCDS72905.1	1q21.2	2012-06-25			ENSG00000118292	ENSG00000118292			26258	protein-coding gene	gene with protein product						12477932	Standard	NM_024579		Approved	FLJ23221	uc001eud.3	Q8WWF1	OTTHUMG00000012546	ENST00000369102.1:c.189+1GTGA>-	1.37:g.150248213_150248216delGTGA		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	75	17	.	0	0	0	0	0	Q9H5P3	Splice_Site	DEL	ENST00000369102.1	37	CCDS948.1																																																																																			.		0.407	C1orf54-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035055.1	NM_024579	Intron	-	150248212	GTGA	-	150248209	8	5	53	1	0	1	0	1	0	0	1	0	2052	1275	44	0	200	0	C1orf54	1	150248209	Splice_Site	DEL	GTGA	TCGA-B9-7268-01A-11D-2136-08	3520650	150248209	99002412	8	5103											
ZNF687	57592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151259373	151259373	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccctcttcctttgagctggcCcaggagaatggcccaggcat	7	9	11	14	0	1	2	0	1	1	1	2	3	2	2	4	4	1	2	4	4	1	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:151259373C>G	ENST00000368879.2	+	2	704	c.606C>G	c.(604-606)gcC>gcG	p.A202A		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	202	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTGAGCTGGCCCAGGAGAATG	0.652																																					p.A202A		.											.	ZNF687-92	0			c.C606G						.						44	49	47					1																	151259373		2203	4300	6503	SO:0001819	synonymous_variant	57592	exon2			GCTGGCCCAGGAG		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.606C>G	1.37:g.151259373C>G		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	122	59	NM_020832	1	0	14	28	13	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	37																																																																																				.		0.652	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		G	151259373	C	G	151259373	2	3	53	1	0	0	0	0	0	0	0	1	18124	610	22	4		4	ZNF687	1	151259373	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	1011164	151259373	97991248	9	5104											
SPRR1A	6698	hgsc.bcm.edu;broad.mit.edu	37	chr1	152957850	152957850	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccccaaggtgcctgagccCtgccaccccaaagtgcctga	9	5	9	18	0	0	2	0	2	0	0	0	2	0	2	8	1	4	0	8	1	2	0	rs267598046		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:152957850C>T	ENST00000368762.1	+	1	144	c.144C>T	c.(142-144)ccC>ccT	p.P48P	SPRR1A_ENST00000307122.2_Silent_p.P48P			P35321	SPR1A_HUMAN	small proline-rich protein 1A	48	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCCTGAGCCCTGCCACCCCA	0.642																																					p.P48P		.											.	SPRR1A-68	0			c.C144T						.						120	120	120					1																	152957850		2203	4300	6503	SO:0001819	synonymous_variant	6698	exon2			TGAGCCCTGCCAC	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.144C>T	1.37:g.152957850C>T		Somatic	212	0		WXS	Illumina HiSeq	Phase_I	254	17	NM_005987	0	0	0	0	0	B1AN47|D3DV31|Q2M303|Q9UDG4	Silent	SNP	ENST00000368762.1	37	CCDS1032.1																																																																																			.		0.642	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987		T	152957850	C	T	152957850	2	4	53	1	0	0	0	0	0	0	0	1	15127	668	24	2		2	SPRR1A	1	152957850	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	1698477	152957850	96292771	10	5105											
SPRR1B	6699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153004965	153004965	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccccaaggtgcctgagccCtgccaccccaaagtgcccga	9	4	9	19	1	0	1	0	1	0	0	0	2	0	1	8	1	4	0	8	1	2	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:153004965C>T	ENST00000307098.4	+	2	209	c.144C>T	c.(142-144)ccC>ccT	p.P48P	SPRR1B_ENST00000392661.3_Silent_p.P48P	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	48	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCCTGAGCCCTGCCACCCCA	0.627																																					p.P48P		.											.	SPRR1B-69	1	Deletion - In frame(1)	ovary(1)	c.C144T						.						123	123	123					1																	153004965		2203	4300	6503	SO:0001819	synonymous_variant	6699	exon2			TGAGCCCTGCCAC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"cornifin"	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.144C>T	1.37:g.153004965C>T		Somatic	274	0		WXS	Illumina HiSeq	Phase_I	264	105	NM_003125	0	0	0	0	0	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	37	CCDS30863.1																																																																																			.		0.627	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125		T	153004965	C	T	153004965	2	4	53	1	0	0	0	0	0	0	0	1	15128	668	24	2		2	SPRR1B	1	153004965	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	47115	153004965	96245656	11	5106											
DCAF8	50717	hgsc.bcm.edu	37	chr1	160209974	160209974	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagtgtcctccatgctgTcagagtccttatcttcacct	7	13	7	14	0	3	1	2	0	1	1	6	2	6	1	5	0	1	1	5	0	1	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:160209974T>G	ENST00000368073.3	-	4	670	c.236A>C	c.(235-237)gAc>gCc	p.D79A	DCAF8_ENST00000368074.1_Missense_Mutation_p.D79A|DCAF8_ENST00000326837.2_Missense_Mutation_p.D79A|DCAF8_ENST00000610139.1_Missense_Mutation_p.D79A|DCAF8_ENST00000475733.1_Missense_Mutation_p.D79A|DCAF8_ENST00000608310.1_Missense_Mutation_p.D233A|DCAF8_ENST00000556710.1_Missense_Mutation_p.D233A			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	79					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(16)|skin(3)|upper_aerodigestive_tract(1)	33						CTCCATGCTGTCAGAGTCCTT	0.512																																					p.D79A		.											.	DCAF8-92	0			c.A236C						.						126	90	102					1																	160209974		2203	4300	6503	SO:0001583	missense	50717	exon4			ATGCTGTCAGAGT	AK093176	CCDS1200.1	1q22-q23	2013-01-09	2009-07-17	2009-07-17	ENSG00000132716	ENSG00000132716		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24891	protein-coding gene	gene with protein product		615820	"WD repeat domain 42A"	WDR42A		11401431	Standard	NM_015726		Approved	H326, FLJ35857	uc010pjb.1	Q5TAQ9	OTTHUMG00000031604	ENST00000368073.3:c.236A>C	1.37:g.160209974T>G	ENSP00000357052:p.Asp79Ala	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_015726	0	0	65	65	0	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	Missense_Mutation	SNP	ENST00000368073.3	37	CCDS1200.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094041	0.76870	.	.	ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000258465;ENSG00000258465	ENST00000368073;ENST00000326837;ENST00000368074;ENST00000555195;ENST00000447377;ENST00000440682;ENST00000407642;ENST00000556710;ENST00000485079	T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.23;-0.23	5.03	5.03	0.67393	.	0.000000	0.64402	U	0.000002	T	0.51975	0.1706	L	0.40543	1.245	0.58432	D	0.999997	P;P;B	0.49253	0.884;0.921;0.329	B;P;B	0.47206	0.382;0.541;0.077	T	0.54827	-0.8235	10	0.37606	T	0.19	-12.1696	13.7732	0.63038	0.0:0.0:0.0:1.0	.	233;79;79	G3V3G9;Q5TAQ9-2;Q5TAQ9	.;.;DCAF8_HUMAN	A	79;79;79;233;79;79;79;233;291	ENSP00000357052:D79A;ENSP00000318227:D79A;ENSP00000357053:D79A;ENSP00000451989:D233A;ENSP00000451235:D233A	ENSP00000318227:D79A	D	-	2	0	RP11-574F21.3;DCAF8	158476598	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.172000	0.65003	1.889000	0.54706	0.528000	0.53228	GAC	.		0.512	DCAF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077402.2	NM_015726		G	160209974	T	G	160209974	3	3	53	1	0	0	0	0	1	0	0	0	4282	1667	58	5	1601	5	DCAF8	1	160209974	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	7205009	160209974	89040647	12	5107											
IFT172	26160	hgsc.bcm.edu	37	chr2	27704121	27704121	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggacacgggtggttaaccaActtcccctaagacagaagta	13	8	10	10	1	0	2	0	0	0	2	1	3	1	3	3	3	2	2	3	3	5	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:27704121A>G	ENST00000260570.3	-	8	680	c.577T>C	c.(577-579)Ttg>Ctg	p.L193L	IFT172_ENST00000416524.2_Silent_p.L172L|IFT172_ENST00000359466.6_Silent_p.L193L	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	193					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TGGTTAACCAACTTCCCCTAA	0.493																																					p.L193L		.											.	IFT172-154	0			c.T577C						.						43	40	41					2																	27704121		2203	4300	6503	SO:0001819	synonymous_variant	26160	exon8			TAACCAACTTCCC	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.577T>C	2.37:g.27704121A>G		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_015662	0	0	0	0	0	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Silent	SNP	ENST00000260570.3	37	CCDS1755.1																																																																																			.		0.493	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		G	27704121	A	G	27704121	2	3	53	1	0	0	0	0	0	0	0	1	7578	40	2	3		3	IFT172	2	27704121	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08		27704121	215495252	13	5108											
LTBP1	4052	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	33412000	33412000	+	Frame_Shift_Del	DEL	G	G	-																															agtgccctccaaatttcacaGgaaaactttgtcagatccca																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:33412000delG	ENST00000404816.2	+	6	1632	c.1279delG	c.(1279-1281)ggafs	p.G427fs	LTBP1_ENST00000418533.2_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000407925.1_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000354476.3_Frame_Shift_Del_p.G427fs|LTBP1_ENST00000390003.4_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000404525.1_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000402934.1_Frame_Shift_Del_p.G101fs			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	427	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAATTTCACAGGAAAACTTTG	0.473																																					p.G427fs		.											.	LTBP1-230	0			c.1279delG						.						115	107	110					2																	33412000		2203	4300	6503	SO:0001589	frameshift_variant	4052	exon6			.		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1279delG	2.37:g.33412000delG	ENSP00000386043:p.Gly427fs	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	57	20	NM_206943	0	0	0	0	0	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Frame_Shift_Del	DEL	ENST00000404816.2	37	CCDS33177.2																																																																																			.		0.473	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		-	33412000	G	-	33412000	7	5	53	1	0	1	0	1	0	0	0	0	9098	1001	35	0	1356	0	LTBP1	2	33412000	Frame_Shift_Del	DEL	G	TCGA-B9-7268-01A-11D-2136-08	5707879	33412000	209787373	14	5109	56	2									
LTBP1	4052	hgsc.bcm.edu;bcgsc.ca	37	chr2	33412006	33412006	+	Missense_Mutation	SNP	C	C	A																															ctccaaatttcacaggaaaaCtttgtcagatcccagtccat																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:33412006C>A	ENST00000404816.2	+	6	1638	c.1285C>A	c.(1285-1287)Ctt>Att	p.L429I	LTBP1_ENST00000418533.2_Missense_Mutation_p.L103I|LTBP1_ENST00000407925.1_Missense_Mutation_p.L103I|LTBP1_ENST00000354476.3_Missense_Mutation_p.L429I|LTBP1_ENST00000390003.4_Missense_Mutation_p.L103I|LTBP1_ENST00000404525.1_Missense_Mutation_p.L103I|LTBP1_ENST00000402934.1_Missense_Mutation_p.L103I			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	429	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CACAGGAAAACTTTGTCAGAT	0.478																																					p.L429I		.											.	LTBP1-230	0			c.C1285A						.						116	108	110					2																	33412006		2203	4300	6503	SO:0001583	missense	4052	exon6			GGAAAACTTTGTC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1285C>A	2.37:g.33412006C>A	ENSP00000386043:p.Leu429Ile	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	57	20	NM_206943	0	0	0	0	0	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	C	15.88	2.962600	0.53400	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000432635;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95	5.3	5.3	0.74995	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.87849	0.6281	L	0.32530	0.975	0.80722	D	1	B;B;B;B;B;B	0.25441	0.077;0.028;0.016;0.033;0.096;0.126	B;B;B;B;B;B	0.28709	0.043;0.016;0.017;0.027;0.05;0.093	D	0.85678	0.1299	9	0.66056	D	0.02	.	12.3249	0.55005	0.0:0.9228:0.0:0.0772	.	429;103;103;103;103;429	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	I	429;429;118;103;103;103;103;103	ENSP00000386043:L429I;ENSP00000346467:L429I;ENSP00000374653:L103I;ENSP00000393057:L103I;ENSP00000384373:L103I;ENSP00000385359:L103I;ENSP00000384091:L103I	ENSP00000346467:L429I	L	+	1	0	LTBP1	33265510	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	4.239000	0.58694	2.468000	0.83385	0.655000	0.94253	CTT	.		0.478	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33412006	C	A	33412006	3	1	53	1	0	0	0	0	1	0	0	0	9098	565	20	4	1362	4	LTBP1	2	33412006	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	6	33412006	209787367	15	5110	56	2									
GGCX	2677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	85777685	85777685	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtgaacttacctgcggcGaaagacatagagctttcgca	11	10	11	9	3	0	3	0	1	0	2	1	4	0	3	1	1	4	3	1	1	4	4	rs372492949		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:85777685G>T	ENST00000233838.4	-	14	2157	c.2077C>A	c.(2077-2079)Cgc>Agc	p.R693S	GGCX_ENST00000473665.1_5'Flank|GGCX_ENST00000430215.3_Missense_Mutation_p.R636S	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	693					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	TACCTGCGGCGAAAGACATAG	0.468																																					p.R693S		.											.	GGCX-91	0			c.C2077A						.						53	56	55					2																	85777685		2203	4300	6503	SO:0001583	missense	2677	exon14			TGCGGCGAAAGAC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"vitamin K-dependent gamma-carboxylase"	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.2077C>A	2.37:g.85777685G>T	ENSP00000233838:p.Arg693Ser	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	92	42	NM_000821	0	0	0	0	0	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	37	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.395574	0.83011	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	T;T	0.28895	1.59;1.59	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.56673	0.2001	M	0.72118	2.19	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.998	T	0.55302	-0.8162	10	0.54805	T	0.06	-15.286	17.5141	0.87768	0.0:0.0:1.0:0.0	.	636;509;693	E9PEE1;B4DQW4;P38435	.;.;VKGC_HUMAN	S	693;636	ENSP00000233838:R693S;ENSP00000408045:R636S	ENSP00000233838:R693S	R	-	1	0	GGCX	85631196	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.029000	0.57253	2.730000	0.93505	0.655000	0.94253	CGC	.		0.468	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		T	85777685	G	T	85777685	3	4	53	1	0	0	0	0	1	0	0	0	6376	1058	37	4	207	4	GGCX	2	85777685	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	52365679	85777685	157421688	16	5111											
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152507333	152507333	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggacaacacaagttttgggtCatcttgcagactccggaatc	11	10	10	10	1	2	1	1	0	1	1	4	3	3	3	1	3	2	2	1	3	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:152507333C>T	ENST00000172853.10	-	53	7129	c.6982G>A	c.(6982-6984)Gac>Aac	p.D2328N	NEB_ENST00000397345.3_Missense_Mutation_p.D2328N|NEB_ENST00000427231.2_Missense_Mutation_p.D2328N|NEB_ENST00000604864.1_Missense_Mutation_p.D2328N|NEB_ENST00000603639.1_Missense_Mutation_p.D2328N|NEB_ENST00000409198.1_Missense_Mutation_p.D2328N			P20929	NEBU_HUMAN	nebulin	2328					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		AGTTTTGGGTCATCTTGCAGA	0.413																																					p.D2328N		.											.	NEB-145	0			c.G6982A						.						187	191	190					2																	152507333		1983	4164	6147	SO:0001583	missense	4703	exon53			TTGGGTCATCTTG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.6982G>A	2.37:g.152507333C>T	ENSP00000172853:p.Asp2328Asn	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	287	142	NM_004543	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	34	5.297627	0.95574	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.75903	0.3913	M	0.91249	3.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77461	-0.2579	10	0.34782	T	0.22	.	19.3325	0.94297	0.0:1.0:0.0:0.0	.	2328	P20929	NEBU_HUMAN	N	2328	ENSP00000386259:D2328N;ENSP00000380505:D2328N;ENSP00000416578:D2328N;ENSP00000172853:D2328N	ENSP00000172853:D2328N	D	-	1	0	NEB	152215579	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.770000	0.85390	2.583000	0.87209	0.650000	0.86243	GAC	.		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152507333	C	T	152507333	3	4	53	1	0	0	0	0	1	0	0	0	10328	826	29	2	19224	2	NEB	2	152507333	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	66729648	152507333	90692040	17	5112											
RAPGEF4	11069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	173832042	173832042	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tattctatcgatttctggatGatgagcacgaggatgcccct	9	13	10	9	2	2	2	0	2	2	0	3	6	2	4	2	2	2	1	2	2	2	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:173832042G>A	ENST00000397081.3	+	10	1017	c.874G>A	c.(874-876)Gat>Aat	p.D292N	RAPGEF4_ENST00000539331.1_Missense_Mutation_p.D139N|RAPGEF4_ENST00000535187.1_Missense_Mutation_p.D72N|RAPGEF4_ENST00000409036.1_Missense_Mutation_p.D292N|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.D291N|RAPGEF4_ENST00000397087.3_Missense_Mutation_p.D148N|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.D139N|RAPGEF4_ENST00000473043.1_3'UTR|RAPGEF4_ENST00000538974.1_Missense_Mutation_p.D121N	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	292					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			ATTTCTGGATGATGAGCACGA	0.527																																					p.D292N		.											.	RAPGEF4-274	0			c.G874A						.						51	53	52					2																	173832042		2072	4228	6300	SO:0001583	missense	11069	exon10			CTGGATGATGAGC	U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"cAMP-regulated guanine nucleotide exchange factor II", " exchange protein directly activated by cAMP 2"	606058	"RAP guanine-nucleotide-exchange factor (GEF) 4"			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.874G>A	2.37:g.173832042G>A	ENSP00000380271:p.Asp292Asn	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	33	18	NM_007023	0	0	0	0	0	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	37	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453522	0.96223	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000539767;ENST00000535187	T;T;T;T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5	5.31	5.31	0.75309	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.40862	0.1134	M	0.74258	2.255	0.80722	D	1	D;D;D;D;D	0.89917	0.993;1.0;0.996;0.992;1.0	P;D;D;P;D	0.87578	0.897;0.998;0.948;0.889;0.996	T	0.28681	-1.0036	10	0.72032	D	0.01	.	18.9765	0.92738	0.0:0.0:1.0:0.0	.	119;121;148;292;292	B7Z805;B7Z2R0;Q8WZA2-3;Q8WZA2;E9PB94	.;.;.;RPGF4_HUMAN;.	N	291;292;292;148;121;139;139;119;72	ENSP00000264111:D291N;ENSP00000380271:D292N;ENSP00000387104:D292N;ENSP00000380276:D148N;ENSP00000440135:D121N;ENSP00000440250:D139N;ENSP00000437384:D139N;ENSP00000438011:D72N	ENSP00000264111:D291N	D	+	1	0	RAPGEF4	173540288	1.000000	0.71417	0.999000	0.59377	0.885000	0.51271	9.822000	0.99363	2.478000	0.83669	0.561000	0.74099	GAT	.		0.527	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		A	173832042	G	A	173832042	3	1	53	1	0	0	0	0	1	0	0	0	13078	1290	45	2	928	2	RAPGEF4	2	173832042	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	21324709	173832042	69367331	18	5113											
TNS1	7145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	218712984	218712984	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	accggagctgggggcagctgGggttcagcttccgaaaagga	9	6	17	9	2	1	0	1	0	0	0	2	3	2	2	2	6	3	5	2	6	2	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:218712984G>C	ENST00000171887.4	-	17	2333	c.1881C>G	c.(1879-1881)ccC>ccG	p.P627P	TNS1_ENST00000419504.1_Silent_p.P627P|TNS1_ENST00000430930.1_Silent_p.P627P|TNS1_ENST00000480665.1_5'Flank	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	627					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGGGCAGCTGGGGTTCAGCTT	0.652																																					p.P627P		.											.	TNS1-156	0			c.C1881G						.						45	38	40					2																	218712984		2203	4299	6502	SO:0001819	synonymous_variant	7145	exon17			CAGCTGGGGTTCA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1881C>G	2.37:g.218712984G>C		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	79	37	NM_022648	0	0	20	31	11	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			.		0.652	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		C	218712984	G	C	218712984	2	2	53	1	0	0	0	0	0	0	0	1	16375	1219	43	4		4	TNS1	2	218712984	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	44880942	218712984	24486389	19	5114											
MYEOV2	150678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	241073371	241073371	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttaaaaaagtctgcatgaaCggccttttcattggctgcca	11	12	9	9	1	2	1	1	1	1	0	2	1	2	1	2	2	3	3	2	2	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:241073371C>G	ENST00000607357.1	-	2	133	c.115G>C	c.(115-117)Gtt>Ctt	p.V39L	MYEOV2_ENST00000489698.1_5'UTR|MYEOV2_ENST00000307266.3_Missense_Mutation_p.V70L	NM_001163424.1	NP_001156896.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	39								p.V70F(1)		breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		TCTGCATGAACGGCCTTTTCA	0.483																																					p.V70L		.											.	MYEOV2-68	1	Substitution - Missense(1)	lung(1)	c.G208C						.						127	130	129					2																	241073371		2203	4300	6503	SO:0001583	missense	150678	exon2			CATGAACGGCCTT	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000607357.1:c.115G>C	2.37:g.241073371C>G	ENSP00000475979:p.Val39Leu	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	168	65	NM_138336	0	0	79	142	63	Q8N110	Missense_Mutation	SNP	ENST00000607357.1	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.096434	0.76870	.	.	ENSG00000172428	ENST00000307266;ENST00000403160	.	.	.	4.55	3.67	0.42095	.	0.000000	0.64402	U	0.000001	T	0.74137	0.3677	.	.	.	0.58432	D	0.999999	B;D	0.57899	0.04;0.981	B;P	0.62382	0.041;0.901	T	0.76203	-0.3045	8	0.72032	D	0.01	-4.0557	10.5952	0.45333	0.0:0.9036:0.0:0.0963	.	39;70	Q8WXC6;Q8WXC6-1	MYOV2_HUMAN;.	L	70;60	.	ENSP00000304147:V70L	V	-	1	0	MYEOV2	240722044	1.000000	0.71417	0.472000	0.27241	0.971000	0.66376	6.092000	0.71414	1.042000	0.40150	0.650000	0.86243	GTT	.		0.483	MYEOV2-005	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470698.1	NM_138336		G	241073371	C	G	241073371	3	3	53	1	0	0	0	0	1	0	0	0	10051	536	19	4	570	4	MYEOV2	2	241073371	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	22360387	241073371	2126002	20	5115											
TTLL3	26140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9877081	9877081	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaaataaaaagaaacaaGtgaagtatttggggcttgac	18	8	9	6	0	0	3	0	2	0	1	0	3	0	3	1	2	1	2	1	2	8	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr3:9877081G>A	ENST00000547186.1	+	13	2443	c.2227G>A	c.(2227-2229)Gtg>Atg	p.V743M	TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000383827.1_3'UTR|ARPC4-TTLL3_ENST00000397256.1_3'UTR|TTLL3_ENST00000397241.1_3'UTR|TTLL3_ENST00000426895.4_Missense_Mutation_p.V886M	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	743					axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					AAAGAAACAAGTGAAGTATTT	0.567																																					p.V886M		.											.	TTLL3-585	0			c.G2656A						.						122	128	126					3																	9877081		1906	4123	6029	SO:0001583	missense	26140	exon13			AAACAAGTGAAGT		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"Tubulin tyrosine ligase-like family"	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.2227G>A	3.37:g.9877081G>A	ENSP00000446659:p.Val743Met	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	311	108	NM_001025930	0	0	2	2	0	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Missense_Mutation	SNP	ENST00000547186.1	37		.	.	.	.	.	.	.	.	.	.	G	9.673	1.147353	0.21288	.	.	ENSG00000214021	ENST00000426895;ENST00000547186	T;T	0.06294	3.32;3.44	3.94	-1.13	0.09775	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.42275	-0.9461	9	0.87932	D	0	.	3.4181	0.07382	0.437:0.0:0.3814:0.1815	.	743	Q9Y4R7	TTLL3_HUMAN	M	886;743	ENSP00000392549:V886M;ENSP00000446659:V743M	ENSP00000392549:V886M	V	+	1	0	TTLL3	9852081	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.357000	0.07651	-0.239000	0.09710	-0.314000	0.08810	GTG	.		0.567	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		A	9877081	G	A	9877081	3	1	53	1	0	0	0	0	1	0	0	0	16761	1029	36	2	2273	2	TTLL3	3	9877081	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08		9877081	188145349	21	5116											
NISCH	11188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52526307	52526307	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacgtgcaaggtcatgacCtcatgggcagtgtcaccctg	9	9	12	11	1	3	2	3	2	0	0	3	2	3	2	2	2	1	2	2	2	1	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr3:52526307C>A	ENST00000479054.1	+	22	4396	c.4324C>A	c.(4324-4326)Ctc>Atc	p.L1442I	NISCH_ENST00000345716.4_Missense_Mutation_p.L1442I			Q9Y2I1	NISCH_HUMAN	nischarin	1442					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	AGGTCATGACCTCATGGGCAG	0.657																																					p.L1442I		.											.	NISCH-93	0			c.C4324A						.						154	153	153					3																	52526307		2203	4300	6503	SO:0001583	missense	11188	exon21			CATGACCTCATGG	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.4324C>A	3.37:g.52526307C>A	ENSP00000418232:p.Leu1442Ile	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	441	133	NM_007184	0	0	32	48	16	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	37	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107084	0.77096	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000414197	T;T	0.13089	2.62;2.62	5.37	4.3	0.51218	.	0.078630	0.51477	D	0.000098	T	0.18800	0.0451	L	0.27053	0.805	0.37589	D	0.920105	D	0.67145	0.996	P	0.58210	0.835	T	0.02307	-1.1179	10	0.72032	D	0.01	-30.3479	11.4769	0.50304	0.0:0.8448:0.0:0.1552	.	1442	Q9Y2I1	NISCH_HUMAN	I	1442;1442;366;786	ENSP00000418232:L1442I;ENSP00000339958:L1442I	ENSP00000339958:L1442I	L	+	1	0	NISCH	52501347	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.763000	0.47605	2.535000	0.85469	0.561000	0.74099	CTC	.		0.657	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		A	52526307	C	A	52526307	3	1	53	1	0	0	0	0	1	0	0	0	10458	681	24	4	4406	4	NISCH	3	52526307	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	42649226	52526307	145496123	22	5117											
KIAA2018	205717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113376680	113376680	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggtccaggaggttgactGccataggagctagatgaaac	12	8	14	7	0	0	3	0	2	0	1	1	6	1	5	2	4	3	2	2	4	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr3:113376680G>T	ENST00000478658.1	-	5	3866	c.3849C>A	c.(3847-3849)ggC>ggA	p.G1283G	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.G1283G			Q68DE3	K2018_HUMAN	KIAA2018	1283						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						GAGGTTGACTGCCATAGGAGC	0.468																																					p.G1283G		.											.	KIAA2018-93	0			c.C3849A						.						109	105	106					3																	113376680		1947	4151	6098	SO:0001819	synonymous_variant	205717	exon7			TTGACTGCCATAG	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.3849C>A	3.37:g.113376680G>T		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	222	140	NM_001009899	0	0	0	2	2	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.468	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376680	G	T	113376680	2	4	53	1	0	0	0	0	0	0	0	1	8289	1306	46	4		4	KIAA2018	3	113376680	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	60850373	113376680	84645750	23	5118											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123254840	123254840	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcaccttcaaaaaagaagaAgtttcaaactaattatgctt	17	13	4	7	0	3	2	3	0	0	2	3	2	3	2	1	0	2	2	1	0	8	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:123254840A>G	ENST00000264501.4	+	68	11895	c.11522A>G	c.(11521-11523)aAg>aGg	p.K3841R	KIAA1109_ENST00000388738.3_Missense_Mutation_p.K3841R			Q2LD37	K1109_HUMAN	KIAA1109	3841	Poly-Lys.				regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AAAAAGAAGAAGTTTCAAACT	0.348																																					p.K3841R		.											.	KIAA1109-80	0			c.A11522G						.						80	72	74					4																	123254840		1827	4081	5908	SO:0001583	missense	84162	exon66			AGAAGAAGTTTCA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.11522A>G	4.37:g.123254840A>G	ENSP00000264501:p.Lys3841Arg	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	46	23	NM_015312	0	0	5	16	11	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.9|24.9	4.586223|4.586223	0.86851|0.86851	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	T;T;T|.	0.35421|.	2.32;2.32;1.31|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72120|0.72120	0.3421|0.3421	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.974;0.997|.	D;D|.	0.73380|.	0.969;0.98|.	T|T	0.70941|0.70941	-0.4735|-0.4735	10|5	0.45353|.	T|.	0.12|.	.|.	16.1413|16.1413	0.81528|0.81528	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	3840;3841|.	Q2LD37-4;Q2LD37|.	.;K1109_HUMAN|.	R|G	3841;3841;545|252	ENSP00000264501:K3841R;ENSP00000373390:K3841R;ENSP00000410874:K545R|.	ENSP00000264501:K3841R|.	K|S	+|+	2|1	0|0	KIAA1109|KIAA1109	123474290|123474290	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	8.910000|8.910000	0.92685|0.92685	2.270000|2.270000	0.75569|0.75569	0.482000|0.482000	0.46254|0.46254	AAG|AGT	.		0.348	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123254840	A	G	123254840	3	3	53	1	0	0	0	0	1	0	0	0	8229	72	3	3	11784	3	KIAA1109	4	123254840	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		123254840	67899436	24	5119											
NUDT6	11162	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123843660	123843660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggcccagcggtaacccgccGaaggcccggggccgtaggtt	7	4	16	14	5	0	0	0	0	0	0	0	1	0	0	5	6	2	3	5	6	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:123843660G>A	ENST00000304430.5	-	1	101	c.68C>T	c.(67-69)tCg>tTg	p.S23L	SPATA5_ENST00000274008.4_5'Flank|NUDT6_ENST00000339154.2_Intron	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	23						mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						GTAACCCGCCGAAGGCCCGGG	0.677																																					p.S23L													.	NUDT6-90	0			c.C68T						.						14	18	17					4																	123843660		1877	4043	5920	SO:0001583	missense	11162	exon1			CCCGCCGAAGGCC	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"Nudix motif containing"	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.68C>T	4.37:g.123843660G>A	ENSP00000306070:p.Ser23Leu	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	39	5	NM_007083	0	0	5	6	1	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.823757	0.32237	.	.	ENSG00000170917	ENST00000304430	T	0.22945	1.93	3.97	-7.94	0.01152	.	2.861800	0.01561	N	0.020112	T	0.08044	0.0201	N	0.02539	-0.55	0.09310	N	0.999995	B	0.06786	0.001	B	0.04013	0.001	T	0.22103	-1.0226	10	0.09843	T	0.71	3.0083	6.3736	0.21495	0.2466:0.543:0.1195:0.091	.	23	P53370	NUDT6_HUMAN	L	23	ENSP00000306070:S23L	ENSP00000306070:S23L	S	-	2	0	NUDT6	124063110	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.472000	0.02341	-2.060000	0.00893	0.462000	0.41574	TCG	.		0.677	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		A	123843660	G	A	123843660	3	1	53	1	0	0	0	0	1	0	0	0	10769	1059	37	1	902	1	NUDT6	4	123843660	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	588820	123843660	67310616	25	5120											
CBR4	84869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	169931208	169931208	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acagctctgccaatgcctcgGgagcctccaaaaacagcaca	13	5	8	15	1	1	0	0	0	1	0	3	1	2	1	4	1	6	2	4	1	3	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:169931208G>T	ENST00000306193.3	-	1	201	c.33C>A	c.(31-33)tcC>tcA	p.S11S	CBR4_ENST00000504480.1_Silent_p.S11S|RP11-483A20.3_ENST00000506933.1_RNA	NM_032783.4	NP_116172.2	Q8N4T8	CBR4_HUMAN	carbonyl reductase 4	11					daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|fatty acid biosynthetic process (GO:0006633)|protein homotetramerization (GO:0051289)	mitochondrial matrix (GO:0005759)	NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|NADPH binding (GO:0070402)|NADPH dehydrogenase (quinone) activity (GO:0008753)|quinone binding (GO:0048038)			kidney(1)|large_intestine(2)|lung(2)	5		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		CAATGCCTCGGGAGCCTCCAA	0.602											OREG0016397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S11S		.											.	CBR4-90	0			c.C33A						.						50	54	52					4																	169931208		2203	4300	6503	SO:0001819	synonymous_variant	84869	exon1			GCCTCGGGAGCCT	BC021973	CCDS3812.1	4q32.3	2013-10-11			ENSG00000145439	ENSG00000145439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	25891	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 45C, member 1"					19027726	Standard	NM_032783		Approved	FLJ14431, SDR45C1	uc003iry.3	Q8N4T8	OTTHUMG00000161025	ENST00000306193.3:c.33C>A	4.37:g.169931208G>T		Somatic	49	0	1881	WXS	Illumina HiSeq	Phase_I	44	22	NM_032783	0	0	20	35	15	Q8WTW8|Q96K93	Silent	SNP	ENST00000306193.3	37	CCDS3812.1																																																																																			.		0.602	CBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363441.2	NM_032783		T	169931208	G	T	169931208	2	4	53	1	0	0	0	0	0	0	0	1	2716	1219	43	4		4	CBR4	4	169931208	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	46087548	169931208	21223068	26	5121											
FAT1	2195	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	187540602	187540602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attatcattgaggtcggtaaCgtccaccgtgacaatcacat	12	11	8	10	3	2	2	2	2	0	0	4	2	3	2	2	2	1	1	2	2	3	3	rs201352448		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:187540602C>T	ENST00000441802.2	-	10	7347	c.7138G>A	c.(7138-7140)Gtt>Att	p.V2380I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2380	Cadherin 21. {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						AGGTCGGTAACGTCCACCGTG	0.502										HNSCC(5;0.00058)																											p.V2380I	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.G7138A						.						67	68	67					4																	187540602		2106	4223	6329	SO:0001583	missense	2195	exon10			CGGTAACGTCCAC	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.7138G>A	4.37:g.187540602C>T	ENSP00000406229:p.Val2380Ile	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	67	35	NM_005245	0	0	36	79	43		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.092207	0.36952	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.61510	0.1	5.14	4.3	0.51218	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.121633	0.56097	N	0.000035	T	0.38799	0.1054	N	0.26130	0.795	0.58432	D	0.999996	B	0.30851	0.297	B	0.25614	0.062	T	0.20306	-1.0279	10	0.22109	T	0.4	.	9.4366	0.38643	0.0:0.8376:0.0:0.1624	.	2380	Q14517	FAT1_HUMAN	I	2380;2382	ENSP00000406229:V2380I	ENSP00000260147:V2382I	V	-	1	0	FAT1	187777596	0.992000	0.36948	0.999000	0.59377	0.398000	0.30690	1.481000	0.35476	1.527000	0.49086	0.650000	0.86243	GTT	C|0.999;T|0.001		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187540602	C	T	187540602	3	4	53	1	0	0	0	0	1	0	0	0	5708	536	19	1	6700	1	FAT1	4	187540602	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	17609394	187540602	3613674	27	5122											
RGNEF	64283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	73136427	73136427	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccttcctacagaaaccagTcccagtgtgtacccacttag	11	9	6	15	0	0	1	0	0	0	1	2	1	2	1	5	0	3	1	5	0	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr5:73136427T>C	ENST00000426542.2	+	10	1289	c.1269T>C	c.(1267-1269)agT>agC	p.S423S	ARHGEF28_ENST00000296799.4_Silent_p.S110S|ARHGEF28_ENST00000513841.1_3'UTR|ARHGEF28_ENST00000513042.2_Silent_p.S423S|ARHGEF28_ENST00000545377.1_Silent_p.S423S|ARHGEF28_ENST00000296794.6_Silent_p.S423S|ARHGEF28_ENST00000287898.5_Silent_p.S423S|ARHGEF28_ENST00000437974.1_Silent_p.S423S			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	423					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										CAGAAACCAGTCCCAGTGTGT	0.493																																					p.S423S		.											.	.	0			c.T1269C						.						69	68	68					5																	73136427		2002	4162	6164	SO:0001819	synonymous_variant	64283	exon11			AACCAGTCCCAGT		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1269T>C	5.37:g.73136427T>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	57	27	NM_001080479	0	0	3	6	3	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			.		0.493	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			C	73136427	T	C	73136427	2	2	53	1	0	0	0	0	0	0	0	1	13315	1664	58	3		3	RGNEF	5	73136427	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08		73136427	107778833	28	5123											
CDKL3	51265	hgsc.bcm.edu	37	chr5	133695635	133695635	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgaaggatctggaagaggtAttttctaagtcgcttactct	10	14	10	7	2	3	1	0	0	3	1	5	4	3	3	0	3	1	2	0	3	5	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr5:133695635A>C	ENST00000265334.4	-	3	431	c.313T>G	c.(313-315)Tac>Gac	p.Y105D	CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000521755.1_Intron|CDKL3_ENST00000523054.1_5'UTR|CDKL3_ENST00000536186.1_Intron|CDKL3_ENST00000435211.1_Missense_Mutation_p.Y105D|CDKL3_ENST00000609654.1_Intron|CDKL3_ENST00000435240.2_Intron|CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000523832.1_Missense_Mutation_p.Y105D|CDKL3_ENST00000521118.1_Missense_Mutation_p.Y105D|CDKL3_ENST00000522501.1_Intron	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGGAAGAGGTATTTTCTAAGT	0.328																																					p.Y105D		.											.	CDKL3-389	0			c.T313G						.						99	90	93					5																	133695635		1826	4085	5911	SO:0001583	missense	51265	exon3			AGAGGTATTTTCT	AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"Cyclin-dependent kinases"	15483	protein-coding gene	gene with protein product	"serine-threonine protein kinase NKIAMRE"	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.313T>G	5.37:g.133695635A>C	ENSP00000265334:p.Tyr105Asp	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	17	8	NM_001113575	0	0	0	0	0	D3DQA0|D3DQA1|Q9P114	Missense_Mutation	SNP	ENST00000265334.4	37	CCDS47264.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106870	0.77096	.	.	ENSG00000006837	ENST00000265334;ENST00000521118;ENST00000523832;ENST00000435211	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000039	T	0.82171	0.4979	M	0.81614	2.55	0.45733	D	0.998634	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.84940	0.0865	10	0.87932	D	0	-6.1958	14.5773	0.68258	1.0:0.0:0.0:0.0	.	105;105	E7ET86;Q8IVW4	.;CDKL3_HUMAN	D	105	ENSP00000265334:Y105D;ENSP00000428689:Y105D;ENSP00000430496:Y105D;ENSP00000395559:Y105D	ENSP00000265334:Y105D	Y	-	1	0	CDKL3	133723534	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.231000	0.72307	2.141000	0.66446	0.482000	0.46254	TAC	.		0.328	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575		C	133695635	A	C	133695635	3	2	53	1	0	0	0	0	1	0	0	0	3161	449	16	5	1513	5	CDKL3	5	133695635	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	60559208	133695635	47219625	29	5124											
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	38704982	38704982	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaagcagggagaatctgAaaaacatattttcactgaaa	17	9	8	7	0	2	3	1	2	1	1	3	4	3	3	1	1	2	1	1	1	6	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr6:38704982A>T	ENST00000359357.3	+	4	505	c.251A>T	c.(250-252)gAa>gTa	p.E84V	DNAH8_ENST00000441566.1_Missense_Mutation_p.E84V|DNAH8_ENST00000449981.2_Missense_Mutation_p.E301V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	84					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GGAGAATCTGAAAAACATATT	0.313																																					p.E301V		.											.	DNAH8-615	0			c.A902T						.						74	77	76					6																	38704982		2203	4300	6503	SO:0001583	missense	1769	exon6			AATCTGAAAAACA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.251A>T	6.37:g.38704982A>T	ENSP00000352312:p.Glu84Val	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	108	50	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	6.965	0.548009	0.13312	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.23950	1.91;1.9;1.88	5.2	5.2	0.72013	.	0.348200	0.29980	N	0.010705	T	0.08268	0.0206	L	0.41236	1.265	0.32224	N	0.57484	B	0.02656	0.0	B	0.04013	0.001	T	0.17868	-1.0355	10	0.14252	T	0.57	.	11.237	0.48946	0.8476:0.1523:0.0:0.0	.	84	Q96JB1	DYH8_HUMAN	V	289;289;84;84	ENSP00000333363:E289V;ENSP00000352312:E84V;ENSP00000402294:E84V	ENSP00000333363:E289V	E	+	2	0	DNAH8	38812960	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.440000	0.44855	2.073000	0.62155	0.482000	0.46254	GAA	.		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38704982	A	T	38704982	3	4	53	1	0	0	0	0	1	0	0	0	4618	246	9	5	257	5	DNAH8	6	38704982	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		38704982	132410085	30	5125											
BCLAF1	9774	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	136582550	136582550	+	Frame_Shift_Del	DEL	T	T	-																															ttaaagcgccctctgccacgTtgaaaagtaccacgacctct																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr6:136582550delT	ENST00000531224.1	-	12	2862	c.2610delA	c.(2608-2610)caafs	p.Q870fs	BCLAF1_ENST00000392348.2_Frame_Shift_Del_p.Q819fs|BCLAF1_ENST00000031135.9_Frame_Shift_Del_p.Q88fs|BCLAF1_ENST00000527536.1_Frame_Shift_Del_p.Q821fs|BCLAF1_ENST00000530767.1_Frame_Shift_Del_p.Q697fs|BCLAF1_ENST00000353331.4_Frame_Shift_Del_p.Q819fs|BCLAF1_ENST00000527759.1_Frame_Shift_Del_p.Q868fs|BCLAF1_ENST00000529917.1_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	870					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		CTCTGCCACGTTGAAAAGTAC	0.418																																					p.Q870fs	Colon(142;1534 1789 5427 7063 28491)	.											.	BCLAF1-228	0			c.2610delA						.						218	218	218					6																	136582550		2203	4300	6503	SO:0001589	frameshift_variant	9774	exon12			.	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2610delA	6.37:g.136582550delT	ENSP00000435210:p.Gln870fs	Somatic	379	0		WXS	Illumina HiSeq	Phase_I	614	103	NM_014739	0	0	0	0	0	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Frame_Shift_Del	DEL	ENST00000531224.1	37	CCDS5177.1																																																																																			.		0.418	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		-	136582550	T	-	136582550	7	5	53	1	0	1	0	1	0	0	0	0	1384	1722	60	0	160	0	BCLAF1	6	136582550	Frame_Shift_Del	DEL	T	TCGA-B9-7268-01A-11D-2136-08	97877568	136582550	34532517	31	5126											
DFNA5	1687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	24745817	24745817	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttacctgcgagggcactgAccaagaagtaggctgtcata	11	8	11	11	1	1	2	1	1	0	1	1	3	1	2	3	2	2	3	3	2	5	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr7:24745817A>T	ENST00000342947.3	-	8	1594	c.1169T>A	c.(1168-1170)gTc>gAc	p.V390D	DFNA5_ENST00000409970.1_Missense_Mutation_p.V226D|DFNA5_ENST00000545231.1_Missense_Mutation_p.V226D|DFNA5_ENST00000419307.1_Missense_Mutation_p.V226D|DFNA5_ENST00000409775.3_Missense_Mutation_p.V390D	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	390					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GAGGGCACTGACCAAGAAGTA	0.537																																					p.V390D	GBM(78;184 1250 20134 20900 23600)	.											.	DFNA5-91	0			c.T1169A						.						75	76	76					7																	24745817		2203	4300	6503	SO:0001583	missense	1687	exon8			GCACTGACCAAGA	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.1169T>A	7.37:g.24745817A>T	ENSP00000339587:p.Val390Asp	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	164	95	NM_001127453	0	0	0	0	0	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.752032	0.49362	.	.	ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775;ENST00000430096	T;T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7;1.7	5.0	5.0	0.66597	.	0.415630	0.25613	N	0.029475	T	0.44074	0.1276	M	0.68317	2.08	0.80722	D	1	D	0.60575	0.988	P	0.59357	0.856	T	0.43048	-0.9415	10	0.87932	D	0	-18.5588	12.3301	0.55035	1.0:0.0:0.0:0.0	.	390	O60443	DFNA5_HUMAN	D	390;226;226;226;390;10	ENSP00000339587:V390D;ENSP00000401332:V226D;ENSP00000442661:V226D;ENSP00000387119:V226D;ENSP00000386670:V390D;ENSP00000395540:V10D	ENSP00000339587:V390D	V	-	2	0	DFNA5	24712342	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	5.025000	0.64097	2.091000	0.63221	0.460000	0.39030	GTC	.		0.537	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		T	24745817	A	T	24745817	3	4	53	1	0	0	0	0	1	0	0	0	4465	275	10	5	333	5	DFNA5	7	24745817	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		24745817	134392846	32	5127											
REPIN1	29803	hgsc.bcm.edu;broad.mit.edu	37	chr7	150068863	150068864	+	Frame_Shift_Ins	INS	-	-	A																															ccggaggcccggcccttcatINSatgcggcaactgtggccgga																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr7:150068863_150068864insA	ENST00000425389.2	+	1	611_612	c.533_534insA	c.(532-537)atatgcfs	p.C179fs	REPIN1_ENST00000397281.2_Frame_Shift_Ins_p.C179fs|REPIN1_ENST00000540729.1_Frame_Shift_Ins_p.C179fs|REPIN1_ENST00000444957.1_Frame_Shift_Ins_p.C179fs|REPIN1_ENST00000489432.2_Frame_Shift_Ins_p.C236fs|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000479668.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000482680.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	179					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			CGGCCCTTCATATGCGGCAACT	0.658																																					p.I235fs		.											.	REPIN1-69	0			c.704_705insA						.																																			SO:0001589	frameshift_variant	29803	exon3			.	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"Zinc fingers, C2H2-type"	17922	protein-coding gene	gene with protein product	"replication initiation region protein (60kD)", "zinc finger protein AP4", "zinc finger protein 464 (RIP60)"		"zinc finger protein 464 (RIP60)"	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.534dupA	7.37:g.150068864_150068864dupA	ENSP00000388287:p.Cys179fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	41	10	NM_001099695	0	0	0	0	0	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Frame_Shift_Ins	INS	ENST00000425389.2	37	CCDS43677.1																																																																																			.		0.658	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		A	150068864	-	A	150068863	7	5	53	1	0	1	1	0	0	0	0	0	13259	1406	49	0	710	0	REPIN1	7	150068863	Frame_Shift_Ins	INS	-	TCGA-B9-7268-01A-11D-2136-08	125323046	150068863	9069800	33	5128											
SGK223	157285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	8235103	8235103	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgccccgggaacctgcAgtctgggaggcagccttggc	5	7	15	14	1	1	0	0	0	1	0	1	2	1	2	5	4	5	2	5	4	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:8235103A>T	ENST00000520004.1	-	3	1080	c.816T>A	c.(814-816)acT>acA	p.T272T	SGK223_ENST00000330777.4_Silent_p.T272T			Q86YV5	SG223_HUMAN		272							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGGAACCTGCAGTCTGGGAGG	0.677																																					p.T272T	GBM(34;731 755 10259 33573 33867)	.											.	.	0			c.T816A						.						22	27	25					8																	8235103		1995	4154	6149	SO:0001819	synonymous_variant	0	exon2			ACCTGCAGTCTGG																												ENST00000520004.1:c.816T>A	8.37:g.8235103A>T		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	34	22	NM_001080826	0	0	12	18	6	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			.		0.677	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8235103	A	T	8235103	2	4	53	1	0	0	0	0	0	0	0	1	14242	175	7	5		5	SGK223	8	8235103	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08		8235103	138128919	34	5129											
GPR124	25960	hgsc.bcm.edu	37	chr8	37699293	37699293	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctggcccagagtcaggTgtgcgaggcgggggcggcgg	5	4	22	10	4	1	1	1	0	0	1	1	2	1	1	1	7	2	2	1	7	0	0	rs111828443	byFrequency	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:37699293T>C	ENST00000412232.2	+	19	3450	c.3437T>C	c.(3436-3438)gTg>gCg	p.V1146A	GPR124_ENST00000315215.7_Missense_Mutation_p.V929A	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	1146					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CAGAGTCAGGTGTGCGAggcg	0.746													T|||	6	0.00119808	0	0.0014	5008	,	,		8221	0		0.005	False		,,,				2504	0				p.V1146A		.											.	GPR124-157	0			c.T3437C						.	T	ALA/VAL	2,2230		0,2,1114	1	2	2		3437	-8.5	0	8	dbSNP_132	2	31,5047		0,31,2508	no	missense	GPR124	NM_032777.9	64	0,33,3622	CC,CT,TT		0.6105,0.0896,0.4514	benign	1146/1339	37699293	33,7277	1116	2539	3655	SO:0001583	missense	25960	exon19			GTCAGGTGTGCGA	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.3437T>C	8.37:g.37699293T>C	ENSP00000406367:p.Val1146Ala	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	4	2	NM_032777	0	0	0	0	0	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	T	0.107	-1.144334	0.01728	8.96E-4	0.006105	ENSG00000020181	ENST00000315215;ENST00000412232	T;T	0.59224	0.28;0.4	4.26	-8.52	0.00920	.	0.697471	0.13568	N	0.378295	T	0.20700	0.0498	N	0.16790	0.44	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13388	-1.0511	10	0.13108	T	0.6	-1.0774	6.7924	0.23707	0.089:0.5225:0.2609:0.1276	.	929;1146	Q96PE1-2;Q96PE1	.;GP124_HUMAN	A	929;1146	ENSP00000323508:V929A;ENSP00000406367:V1146A	ENSP00000323508:V929A	V	+	2	0	GPR124	37818451	0.000000	0.05858	0.016000	0.15963	0.559000	0.35586	-1.039000	0.03550	-2.808000	0.00349	-0.425000	0.05940	GTG	T|0.500;C|0.500		0.746	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			C	37699293	T	C	37699293	3	2	53	1	0	0	0	0	1	0	0	0	6658	1696	59	3	3490	3	GPR124	8	37699293	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	29464190	37699293	108664729	35	5130											
NPBWR1	2831	ucsc.edu	37	chr8	53852861	53852861	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcctcaccgtcatgagcGccgaccgctacctggtggtg	6	9	11	15	4	2	1	2	1	0	0	3	2	3	1	5	2	2	1	5	2	1	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:53852861G>A	ENST00000331251.3	+	1	1871	c.394G>A	c.(394-396)Gcc>Acc	p.A132T		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	132					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				CGTCATGAGCGCCGACCGCTA	0.677																																					p.A132T													.	NPBWR1-155	0			c.G394A						.						31	31	31					8																	53852861		2199	4292	6491	SO:0001583	missense	2831	exon1			ATGAGCGCCGACC	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"GPCR / Class A : Neuropeptide receptors : W/B"	4522	protein-coding gene	gene with protein product		600730	"G protein-coupled receptor 7"	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.394G>A	8.37:g.53852861G>A	ENSP00000330284:p.Ala132Thr	Somatic	39	0		WXS	Illumina HiSeq		37	4	NM_005285	0	0	0	0	0	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474654	0.84640	.	.	ENSG00000183729	ENST00000331251	T	0.37235	1.21	5.06	4.1	0.47936	GPCR, rhodopsin-like superfamily (1);	0.391699	0.20883	N	0.083979	T	0.27731	0.0682	L	0.35593	1.075	0.32441	N	0.546692	P	0.49358	0.923	B	0.43680	0.427	T	0.38972	-0.9636	10	0.87932	D	0	.	6.9066	0.24313	0.2626:0.0:0.7374:0.0	.	132	P48145	NPBW1_HUMAN	T	132	ENSP00000330284:A132T	ENSP00000330284:A132T	A	+	1	0	NPBWR1	54015414	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.744000	0.55112	2.623000	0.88846	0.655000	0.94253	GCC	.		0.677	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285		A	53852861	G	A	53852861	3	1	53	1	0	0	0	0	1	0	0	0	10594	1087	38	1	396	1	NPBWR1	8	53852861	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	16153568	53852861	92511161	36	5131											
CSPP1	79848	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	68070755	68070755	+	Frame_Shift_Del	DEL	G	G	-																															agaagaaaaagaagaaagacGgcttgcagaacagagggcac																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:68070755delG	ENST00000262210.5	+	18	2331	c.2300delG	c.(2299-2301)cggfs	p.R767fs	CSPP1_ENST00000521168.1_3'UTR|CSPP1_ENST00000412460.1_Frame_Shift_Del_p.R422fs	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	802					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GAAGAAAGACGGCTTGCAGAA	0.388																																					p.R767fs		.											.	CSPP1-138	0			c.2300delG						.						68	67	67					8																	68070755		1860	4092	5952	SO:0001589	frameshift_variant	79848	exon18			.	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.2300delG	8.37:g.68070755delG	ENSP00000262210:p.Arg767fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	47	13	NM_024790	0	0	0	0	0	A6ND63|Q70F00|Q8TBC1	Frame_Shift_Del	DEL	ENST00000262210.5	37	CCDS43744.1																																																																																			.		0.388	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		-	68070755	G	-	68070755	7	5	53	1	0	1	0	1	0	0	0	0	3968	1116	39	0	2483	0	CSPP1	8	68070755	Frame_Shift_Del	DEL	G	TCGA-B9-7268-01A-11D-2136-08	14217894	68070755	78293267	37	5132											
NIPAL2	79815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	99215364	99215364	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggcactgattgtaaagaaAatatgattaactggcaccac	16	10	8	7	0	0	3	0	2	0	1	0	3	0	3	1	2	1	3	1	2	6	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:99215364A>T	ENST00000341166.3	-	8	1107	c.852T>A	c.(850-852)atT>atA	p.I284I	NIPAL2_ENST00000520545.1_5'UTR|NIPAL2_ENST00000430223.2_Silent_p.I284I	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	284						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						TTGTAAAGAAAATATGATTAA	0.408																																					p.I284I		.											.	NIPAL2-90	0			c.T852A						.						185	162	170					8																	99215364		2203	4300	6503	SO:0001819	synonymous_variant	79815	exon8			AAAGAAAATATGA	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.852T>A	8.37:g.99215364A>T		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	122	58	NM_024759	0	0	1	2	1	A2RTY8	Silent	SNP	ENST00000341166.3	37	CCDS6278.1																																																																																			.		0.408	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759		T	99215364	A	T	99215364	2	4	53	1	0	0	0	0	0	0	0	1	10451	10	1	5		5	NIPAL2	8	99215364	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08	31144609	99215364	47148658	38	5133											
JRK	8629	hgsc.bcm.edu	37	chr8	143745894	143745894	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcaccacgccgcctcctcaCctgctgctggctccggaaca	6	6	10	19	3	1	0	1	0	0	0	3	1	3	1	6	3	3	4	6	3	1	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:143745894C>G	ENST00000507178.2	-	0	1916							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				CGCCTCCTCACCTGCTGCTGG	0.692																																					p.V528L		.											.	.	0			c.G1582C						.						19	24	23					8																	143745894		2165	4270	6435			8629	exon3			TCCTCACCTGCTG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"jerky (mouse) homolog", "jerky homolog (mouse)"			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143745894C>G		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_003724	0	0	2	2	0	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				.		0.692	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		G	143745894	C	G	143745894	1	3	53	0	1	0	0	0	0	0	0	0	7985	521	18	4		4	JRK	8	143745894	RNA	SNP	C	TCGA-B9-7268-01A-11D-2136-08	44530530	143745894	2618128	39	5134											
C9orf91	203197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	117400851	117400851	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagaagcagattgagccagTtgtgtgttgtcatggagact	10	12	14	5	0	1	4	1	2	0	3	1	6	1	4	1	1	2	3	1	1	1	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr9:117400851T>C	ENST00000288502.4	+	8	1131	c.694T>C	c.(694-696)Ttg>Ctg	p.L232L	C9orf91_ENST00000374049.4_Silent_p.L233L			Q5VZI3	CI091_HUMAN	chromosome 9 open reading frame 91	232						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	13						ATTGAGCCAGTTGTGTGTTGT	0.562																																					p.L232L		.											.	C9orf91-91	0			c.T694C						.						149	136	140					9																	117400851		2203	4300	6503	SO:0001819	synonymous_variant	203197	exon8			AGCCAGTTGTGTG	BX649023	CCDS6808.1	9q33.1	2008-02-05			ENSG00000157693	ENSG00000157693			24513	protein-coding gene	gene with protein product						14702039	Standard	NM_153045		Approved	DKFZp547P234, FLJ38045	uc004bjd.4	Q5VZI3	OTTHUMG00000020541	ENST00000288502.4:c.694T>C	9.37:g.117400851T>C		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	175	76	NM_153045	0	0	5	10	5	A0PJA3|Q3KNS4|Q5VZI2|Q6P5Z7|Q8N1P3|Q8ND43	Silent	SNP	ENST00000288502.4	37	CCDS6808.1																																																																																			.		0.562	C9orf91-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053780.1	NM_153045		C	117400851	T	C	117400851	2	2	53	1	0	0	0	0	0	0	0	1	2511	1722	60	3		3	C9orf91	9	117400851	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08		117400851	23812580	40	5135											
LIPA	3988	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	90974746	90974746	+	Frame_Shift_Del	DEL	G	G	-																															gacgtcgtagacatctgcaaGccagtcgtgacccccgctcc																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr10:90974746delG	ENST00000336233.5	-	10	1361	c.1039delC	c.(1039-1041)cttfs	p.L347fs	LIPA_ENST00000371837.1_Frame_Shift_Del_p.L291fs|LIPA_ENST00000456827.1_Frame_Shift_Del_p.L347fs			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	347					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)			endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		ACATCTGCAAGCCAGTCGTGA	0.493																																					p.L347fs		.											.	LIPA-90	0			c.1039delC						.						93	84	87					10																	90974746		2203	4300	6503	SO:0001589	frameshift_variant	3988	exon10			.	M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"Wolman disease"	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.1039delC	10.37:g.90974746delG	ENSP00000337354:p.Leu347fs	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	156	63	NM_000235	0	0	0	0	0	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Frame_Shift_Del	DEL	ENST00000336233.5	37	CCDS7401.1																																																																																			.		0.493	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235		-	90974746	G	-	90974746	7	5	53	1	0	1	0	1	0	0	0	0	8842	971	34	0	164	0	LIPA	10	90974746	Frame_Shift_Del	DEL	G	TCGA-B9-7268-01A-11D-2136-08		90974746	44560001	41	5136											
CUTC	51076	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101507060	101507060	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagctctggagaccctcttAaccttgggatttgaacgcgt	8	11	11	11	2	2	2	0	1	2	1	2	4	2	3	2	2	3	2	2	2	2	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr10:101507060A>C	ENST00000370476.5	+	6	615	c.486A>C	c.(484-486)ttA>ttC	p.L162F		NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	162					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		AGACCCTCTTAACCTTGGGAT	0.438																																					p.L162F		.											.	CUTC-153	0			c.A486C						.						178	165	170					10																	101507060		2203	4300	6503	SO:0001583	missense	51076	exon6			CCTCTTAACCTTG	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"cutC copper transporter homolog (E. coli)"			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.486A>C	10.37:g.101507060A>C	ENSP00000359507:p.Leu162Phe	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	179	42	NM_015960	0	0	26	32	6	Q5TCZ8|Q9Y321	Missense_Mutation	SNP	ENST00000370476.5	37	CCDS7483.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.863855	0.51482	.	.	ENSG00000119929	ENST00000370476;ENST00000370472	.	.	.	5.75	1.83	0.25207	Copper homeostasis CutC domain (2);	0.362596	0.26478	N	0.024153	T	0.47097	0.1427	M	0.66439	2.03	0.40178	D	0.977255	P;B	0.35844	0.524;0.358	B;B	0.40940	0.241;0.344	T	0.52003	-0.8633	9	0.87932	D	0	-2.0266	1.2816	0.02042	0.5158:0.1141:0.1618:0.2083	.	162;162	B4DYM2;Q9NTM9	.;CUTC_HUMAN	F	162;99	.	ENSP00000359503:L99F	L	+	3	2	CUTC	101497050	0.287000	0.24315	0.936000	0.37596	0.989000	0.77384	-0.314000	0.08092	0.960000	0.38005	0.460000	0.39030	TTA	.		0.438	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960		C	101507060	A	C	101507060	3	2	53	1	0	0	0	0	1	0	0	0	4069	359	13	5	508	5	CUTC	10	101507060	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	10532314	101507060	34027687	42	5137											
C10orf119	79892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	121598084	121598084	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgttccaggagagtctcAtcgattacaagggaagtatt	11	11	10	9	1	1	1	1	0	1	1	4	4	2	2	2	2	1	2	2	2	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr10:121598084A>G	ENST00000360003.3	-	12	1546	c.1377T>C	c.(1375-1377)gaT>gaC	p.D459D	MCMBP_ENST00000369077.3_Silent_p.D457D|MCMBP_ENST00000466047.1_5'UTR	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	459					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						GGAGAGTCTCATCGATTACAA	0.483																																					p.D459D		.											.	MCMBP-93	0			c.T1377C						.						75	73	74					10																	121598084		2203	4300	6503	SO:0001819	synonymous_variant	79892	exon12			AGTCTCATCGATT	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"chromosome 10 open reading frame 119"	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.1377T>C	10.37:g.121598084A>G		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	80	29	NM_024834	0	0	37	59	22	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			.		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		G	121598084	A	G	121598084	2	3	53	1	0	0	0	0	0	0	0	1	1592	214	8	3		3	C10orf119	10	121598084	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08	20091024	121598084	13936663	43	5138											
ENDOD1	23052	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	94862157	94862157	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagagttctagtcccctttCtagcaccaggagcaagaggt	12	9	10	10	0	2	2	0	0	2	2	3	3	3	3	3	2	2	3	3	2	4	4	rs61734147	byFrequency	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr11:94862157C>G	ENST00000278505.4	+	2	1035	c.917C>G	c.(916-918)tCt>tGt	p.S306C		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	306						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.S306C(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				AGTCCCCTTTCTAGCACCAGG	0.448																																					p.S306C		.											.	ENDOD1-68	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C917G						.						85	82	83					11																	94862157		1855	4087	5942	SO:0001583	missense	23052	exon2			CCCTTTCTAGCAC	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.917C>G	11.37:g.94862157C>G	ENSP00000278505:p.Ser306Cys	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	116	47	NM_015036	0	0	32	62	30	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450542	0.43531	.	.	ENSG00000149218	ENST00000278505	T	0.35973	1.28	5.79	5.79	0.91817	.	0.494397	0.18919	N	0.127530	T	0.44767	0.1309	M	0.62723	1.935	0.28948	N	0.890571	P	0.45283	0.855	B	0.44163	0.443	T	0.50171	-0.8859	10	0.87932	D	0	-0.6278	17.5334	0.87820	0.0:1.0:0.0:0.0	.	306	O94919	ENDD1_HUMAN	C	306	ENSP00000278505:S306C	ENSP00000278505:S306C	S	+	2	0	ENDOD1	94501805	0.020000	0.18652	0.551000	0.28230	0.151000	0.21798	2.730000	0.47335	2.742000	0.94016	0.455000	0.32223	TCT	C|0.998;T|0.002		0.448	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		G	94862157	C	G	94862157	3	3	53	1	0	0	0	0	1	0	0	0	5127	913	32	4	923	4	ENDOD1	11	94862157	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		94862157	40144359	44	5139											
UBE4A	9354	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118243839	118243839	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtttctggaagaggtcattGaagccttgatattggatgag	11	13	13	4	0	2	4	1	3	1	1	2	6	2	6	1	3	1	1	1	3	3	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr11:118243839G>A	ENST00000431736.2	+	7	853	c.781G>A	c.(781-783)Gaa>Aaa	p.E261K	UBE4A_ENST00000252108.3_Missense_Mutation_p.E254K					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		AGAGGTCATTGAAGCCTTGAT	0.368																																					p.E261K		.											.	UBE4A-229	0			c.G781A						.						117	113	115					11																	118243839		2200	4296	6496	SO:0001583	missense	9354	exon7			GTCATTGAAGCCT	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.781G>A	11.37:g.118243839G>A	ENSP00000387362:p.Glu261Lys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	89	42	NM_004788	0	0	10	13	3		Missense_Mutation	SNP	ENST00000431736.2	37	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	g	14.87	2.663910	0.47572	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.46063	0.88;0.88	6.04	1.95	0.26073	.	0.407974	0.28815	N	0.014059	T	0.23766	0.0575	N	0.24115	0.695	0.80722	D	1	B;B	0.19200	0.02;0.034	B;B	0.21708	0.016;0.036	T	0.05903	-1.0857	10	0.08837	T	0.75	-0.6425	8.9731	0.35919	0.1267:0.245:0.6283:0.0	.	254;261	Q14139;Q14139-2	UBE4A_HUMAN;.	K	254;261	ENSP00000252108:E254K;ENSP00000387362:E261K	ENSP00000252108:E254K	E	+	1	0	UBE4A	117749049	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.805000	0.55575	0.437000	0.26423	-0.213000	0.12676	GAA	.		0.368	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		A	118243839	G	A	118243839	3	1	53	1	0	0	0	0	1	0	0	0	16915	1291	45	2	803	2	UBE4A	11	118243839	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	23381682	118243839	16762677	45	5140											
MCAM	4162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119183001	119183001	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagtagttcctgtggttcActcagcagcgatatcatggt	9	12	10	10	1	3	0	3	0	0	0	4	1	4	0	2	2	2	4	2	2	2	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr11:119183001A>C	ENST00000264036.4	-	8	1013	c.999T>G	c.(997-999)agT>agG	p.S333R	MCAM_ENST00000392814.1_Missense_Mutation_p.S282R|MCAM_ENST00000530144.2_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	333					anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CCTGTGGTTCACTCAGCAGCG	0.622																																					p.S333R		.											.	MCAM-137	0			c.T999G						.						96	92	94					11																	119183001		2199	4295	6494	SO:0001583	missense	4162	exon8			TGGTTCACTCAGC	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.999T>G	11.37:g.119183001A>C	ENSP00000264036:p.Ser333Arg	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	107	38	NM_006500	1	0	119	234	114	O95812|Q59E86|Q6PHR3|Q6ZTR2	Missense_Mutation	SNP	ENST00000264036.4	37	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.399560	0.25291	.	.	ENSG00000076706	ENST00000264036;ENST00000392814	T;T	0.06849	3.25;3.25	5.53	-3.57	0.04612	Immunoglobulin-like fold (1);	.	.	.	.	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	B	0.19331	0.035	B	0.15484	0.013	T	0.45614	-0.9249	9	0.18276	T	0.48	-16.5141	2.4635	0.04547	0.3729:0.2069:0.3187:0.1015	.	333	P43121	MUC18_HUMAN	R	333;282	ENSP00000264036:S333R;ENSP00000376561:S282R	ENSP00000264036:S333R	S	-	3	2	MCAM	118688211	0.000000	0.05858	0.024000	0.17045	0.080000	0.17528	-0.422000	0.07043	-0.700000	0.05070	-0.411000	0.06167	AGT	.		0.622	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			C	119183001	A	C	119183001	3	2	53	1	0	0	0	0	1	0	0	0	9393	156	6	5	977	5	MCAM	11	119183001	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	939162	119183001	15823515	46	5141											
APOLD1	81575	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	12940182	12940182	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgatcttctgcaactccCgggagctgcggagggtgcag	6	8	15	12	3	2	1	0	1	2	0	3	3	3	3	1	3	5	4	1	3	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:12940182C>T	ENST00000326765.6	+	2	506	c.436C>T	c.(436-438)Cgg>Tgg	p.R146W	APOLD1_ENST00000356591.4_Missense_Mutation_p.R115W	NM_001130415.1	NP_001123887.1	Q96LR9	APLD1_HUMAN	apolipoprotein L domain containing 1	146					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|endothelial cell activation (GO:0042118)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|regulation of endothelial cell differentiation (GO:0045601)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	5		Prostate(47;0.0632)		BRCA - Breast invasive adenocarcinoma(232;0.0338)|GBM - Glioblastoma multiforme(207;0.149)		CTGCAACTCCCGGGAGCTGCG	0.682																																					p.R146W		.											.	APOLD1-91	0			c.C436T						.						27	31	30					12																	12940182		2203	4300	6503	SO:0001583	missense	81575	exon2			AACTCCCGGGAGC	AL136783	CCDS8654.1, CCDS44833.1	12p13.2	2006-02-03	2006-01-23		ENSG00000178878	ENSG00000178878			25268	protein-coding gene	gene with protein product		612456				11230166	Standard	NM_030817		Approved	FLJ25138, DKFZP434F0318	uc001rau.4	Q96LR9	OTTHUMG00000153561	ENST00000326765.6:c.436C>T	12.37:g.12940182C>T	ENSP00000324277:p.Arg146Trp	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	93	23	NM_001130415	0	0	3	3	0	Q8IVR2|Q9H0I5	Missense_Mutation	SNP	ENST00000326765.6	37	CCDS44833.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040822	0.75732	.	.	ENSG00000178878	ENST00000326765;ENST00000356591	T;T	0.03386	3.95;3.95	4.91	4.01	0.46588	.	0.395551	0.24623	U	0.036942	T	0.09730	0.0239	L	0.43152	1.355	0.31300	N	0.688457	D;D	0.76494	0.999;0.999	D;D	0.65987	0.94;0.94	T	0.02758	-1.1114	10	0.44086	T	0.13	-18.6983	9.3604	0.38192	0.2848:0.5756:0.1396:0.0	.	115;146	A0AVN6;Q96LR9	.;APLD1_HUMAN	W	146;115	ENSP00000324277:R146W;ENSP00000348998:R115W	ENSP00000324277:R146W	R	+	1	2	APOLD1	12831449	0.938000	0.31826	1.000000	0.80357	0.994000	0.84299	0.853000	0.27777	1.179000	0.42884	0.478000	0.44815	CGG	.		0.682	APOLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331627.1	NM_030817		T	12940182	C	T	12940182	3	4	53	1	0	0	0	0	1	0	0	0	811	643	23	1	449	1	APOLD1	12	12940182	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		12940182	120911713	47	5142											
ANP32D	23519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48866497	48866497	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcggaacaggacgccctCcgatgtgaaagaacttttcc	10	8	11	12	3	0	2	0	1	0	1	2	5	2	4	3	2	3	1	3	2	3	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:48866497C>A	ENST00000266594.1	+	1	50	c.50C>A	c.(49-51)tCc>tAc	p.S17Y		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	17						nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						AGGACGCCCTCCGATGTGAAA	0.448																																					p.S17Y		.											.	ANP32D-227	0			c.C50A						.						115	117	117					12																	48866497		2203	4300	6503	SO:0001583	missense	23519	exon1			CGCCCTCCGATGT	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"ANP32 acidic nuclear phosphoproteins"	16676	protein-coding gene	gene with protein product	"pp32 related 2"	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.50C>A	12.37:g.48866497C>A	ENSP00000266594:p.Ser17Tyr	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	258	135	NM_012404	0	0	0	0	0	Q6NTC4	Missense_Mutation	SNP	ENST00000266594.1	37	CCDS31788.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.624087	0.46840	.	.	ENSG00000139223	ENST00000266594	T	0.00468	7.22	1.48	0.203	0.15195	.	0.288521	0.34986	N	0.003527	T	0.00552	0.0018	M	0.86343	2.81	0.38870	D	0.95666	P	0.47106	0.89	B	0.41088	0.347	T	0.68458	-0.5403	10	0.72032	D	0.01	.	4.9765	0.14144	0.0:0.6111:0.3889:0.0	.	17	O95626	AN32D_HUMAN	Y	17	ENSP00000266594:S17Y	ENSP00000266594:S17Y	S	+	2	0	ANP32D	47152764	0.897000	0.30589	0.027000	0.17364	0.572000	0.35998	-0.183000	0.09712	0.856000	0.35383	0.289000	0.19496	TCC	.		0.448	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404		A	48866497	C	A	48866497	3	1	53	1	0	0	0	0	1	0	0	0	708	855	30	4	52	4	ANP32D	12	48866497	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	35926315	48866497	84985398	48	5143											
KRT77	374454	hgsc.bcm.edu	37	chr12	53086342	53086342	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgcagggcctcctccagGtcctgcagcttctgccacgc	4	9	11	17	1	1	0	0	0	1	0	4	0	4	0	5	2	5	4	5	2	0	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:53086342G>C	ENST00000341809.3	-	7	1318	c.1290C>G	c.(1288-1290)gaC>gaG	p.D430E	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_Missense_Mutation_p.D197E	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	430	Coil 2.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.Q429fs*17(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CCTCCTCCAGGTCCTGCAGCT	0.612																																					p.D430E		.											.	KRT77-187	1	Deletion - Frameshift(1)	ovary(1)	c.C1290G						.						44	41	42					12																	53086342		2203	4276	6479	SO:0001583	missense	374454	exon7			CTCCAGGTCCTGC	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"-", "Intermediate filaments type II, keratins (basic)"	20411	protein-coding gene	gene with protein product		611158	"keratin 1B"	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1290C>G	12.37:g.53086342G>C	ENSP00000342710:p.Asp430Glu	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_175078	0	0	0	0	0	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.132215	0.00338	.	.	ENSG00000189182	ENST00000341809;ENST00000537195	T;D	0.87887	-0.76;-2.31	4.29	0.889	0.19212	Filament (1);	.	.	.	.	T	0.63212	0.2492	N	0.03209	-0.39	0.09310	N	0.999999	B	0.27264	0.173	B	0.26614	0.071	T	0.57653	-0.7774	9	0.02654	T	1	.	3.5163	0.07726	0.0919:0.2007:0.4813:0.2261	.	430	Q7Z794	K2C1B_HUMAN	E	430;197	ENSP00000342710:D430E;ENSP00000440803:D197E	ENSP00000342710:D430E	D	-	3	2	KRT77	51372609	0.000000	0.05858	0.002000	0.10522	0.087000	0.18053	-0.966000	0.03825	0.368000	0.24481	-0.487000	0.04747	GAC	.		0.612	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		C	53086342	G	C	53086342	3	2	53	1	0	0	0	0	1	0	0	0	8511	1252	44	4	458	4	KRT77	12	53086342	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	4219845	53086342	80765553	49	5144											
KRT4	3851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53205646	53205646	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagctgcttcctcaggacaCtgaggtaggtctcaaagagg	10	9	12	10	0	2	2	2	1	1	1	4	3	3	3	1	4	2	3	1	4	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:53205646C>G	ENST00000551956.1	-	2	1070	c.578G>C	c.(577-579)aGt>aCt	p.S193T	KRT4_ENST00000293774.4_Missense_Mutation_p.S267T|KRT4_ENST00000458244.2_Missense_Mutation_p.S173T			P19013	K2C4_HUMAN	keratin 4	207	Linker 1.|Rod.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCTCAGGACACTGAGGTAGGT	0.537																																					p.S193T	Pancreas(190;284 2995 41444 45903)	.											.	KRT4-96	0			c.G578C						.						114	119	117					12																	53205646		2030	4201	6231	SO:0001583	missense	3851	exon2			AGGACACTGAGGT		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"-", "Intermediate filaments type II, keratins (basic)"	6441	protein-coding gene	gene with protein product	"cytokeratin 4", "keratin, type II cytoskeletal 4"	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.578G>C	12.37:g.53205646C>G	ENSP00000448220:p.Ser193Thr	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	124	44	NM_002272	0	0	0	0	0	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	37	CCDS41787.2	.	.	.	.	.	.	.	.	.	.	C	4.151	0.026479	0.08054	.	.	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	T;T;T	0.76316	-1.01;-1.01;-1.01	4.54	-1.88	0.07713	Filament (1);	0.363501	0.23947	N	0.042986	T	0.65291	0.2677	L	0.61218	1.895	0.19945	N	0.999941	B	0.21452	0.056	B	0.25614	0.062	T	0.51818	-0.8657	10	0.34782	T	0.22	.	0.9077	0.01288	0.2253:0.3089:0.1121:0.3537	.	207	P19013	K2C4_HUMAN	T	193;267;173	ENSP00000448220:S193T;ENSP00000293774:S267T;ENSP00000387904:S173T	ENSP00000293774:S267T	S	-	2	0	KRT4	51491913	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-1.038000	0.03553	-0.350000	0.08262	-0.137000	0.14449	AGT	.		0.537	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272		G	53205646	C	G	53205646	3	3	53	1	0	0	0	0	1	0	0	0	8498	565	20	4	1016	4	KRT4	12	53205646	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	119304	53205646	80646249	50	5145											
LRRIQ1	84125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	85449852	85449852	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatatagccaaaaatctagtGgatgaaaattcaaagaagca	20	8	8	5	0	2	2	1	1	1	1	2	4	2	3	1	1	2	1	1	1	9	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:85449852G>T	ENST00000393217.2	+	8	1342	c.1281G>T	c.(1279-1281)gtG>gtT	p.V427V		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	427										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AAAATCTAGTGGATGAAAATT	0.294																																					p.V427V		.											.	LRRIQ1-95	0			c.G1281T						.						83	95	91					12																	85449852		2200	4297	6497	SO:0001819	synonymous_variant	84125	exon8			TCTAGTGGATGAA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1281G>T	12.37:g.85449852G>T		Somatic	160	0		WXS	Illumina HiSeq	Phase_I	279	34	NM_001079910	0	0	1	1	0	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	37	CCDS41816.1																																																																																			.		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85449852	G	T	85449852	2	4	53	1	0	0	0	0	0	0	0	1	9054	1335	47	4		4	LRRIQ1	12	85449852	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	32244206	85449852	48402043	51	5146											
SYCP3	50511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	102125409	102125409	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggctctgaacaattctagaTtgttgaagaatcttttgttg	10	17	9	5	0	3	4	0	2	3	2	3	4	3	4	0	1	1	3	0	1	5	7			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:102125409T>C	ENST00000392927.3	-	7	620	c.489A>G	c.(487-489)caA>caG	p.Q163Q	SYCP3_ENST00000392924.1_Silent_p.Q163Q|SYCP3_ENST00000266743.2_Silent_p.Q163Q	NM_001177948.1|NM_001177949.1|NM_153694.4	NP_001171419.1|NP_001171420.1|NP_710161.1	Q8IZU3	SYCP3_HUMAN	synaptonemal complex protein 3	163	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						CAATTCTAGATTGTTGAAGAA	0.264																																					p.Q163Q		.											.	SYCP3-90	0			c.A489G						.						61	59	60					12																	102125409		2202	4281	6483	SO:0001819	synonymous_variant	50511	exon7			TCTAGATTGTTGA	AF492003, AI075991	CCDS9087.1	12q23.2	2007-02-05			ENSG00000139351	ENSG00000139351			18130	protein-coding gene	gene with protein product		604759				12213195, 10854409	Standard	NM_153694		Approved		uc001tis.3	Q8IZU3	OTTHUMG00000150132	ENST00000392927.3:c.489A>G	12.37:g.102125409T>C		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	41	24	NM_001177949	0	0	0	0	0		Silent	SNP	ENST00000392927.3	37	CCDS9087.1																																																																																			.		0.264	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		C	102125409	T	C	102125409	2	2	53	1	0	0	0	0	0	0	0	1	15466	1490	52	3		3	SYCP3	12	102125409	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08	16675557	102125409	31726486	52	5147											
GATC	51499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120884511	120884511	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacctggagcgtctagcgCttgtggacttcggcagccgc	6	8	14	13	4	1	0	0	0	1	0	2	2	1	2	2	3	4	3	2	3	1	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:120884511C>T	ENST00000546954.1	-	0	0				AL021546.6_ENST00000551806.1_Missense_Mutation_p.A76V|GATC_ENST00000551765.1_Missense_Mutation_p.L45F|TRIAP1_ENST00000302432.3_5'Flank	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGTCTAGCGCTTGTGGACTT	0.682																																					p.L45F		.											.	GATC-22	0			c.C133T						.						29	33	32					12																	120884511		2202	4295	6497	SO:0001631	upstream_gene_variant	283459	exon2			CTAGCGCTTGTGG		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"p53-inducible cell-survival factor", "mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		12.37:g.120884511C>T	Exception_encountered	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	121	34	NM_176818	0	0	27	42	15	B2R4Z7|Q5RKS5|Q6LCA7	Missense_Mutation	SNP	ENST00000546954.1	37	CCDS9198.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.450683|4.450683	0.84101|0.84101	.|.	.|.	ENSG00000111780|ENSG00000257218	ENST00000551806|ENST00000551765	.|T	.|0.55413	.|0.52	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.46483|0.46483	0.1395|0.1395	L|L	0.55213|0.55213	1.73|1.73	0.58432|0.58432	D|D	0.999996|0.999996	.|P	.|0.35456	.|0.502	.|B	.|0.31337	.|0.128	T|T	0.53272|0.53272	-0.8462|-0.8462	6|10	0.72032|0.87932	D|D	0.01|0	-15.3352|-15.3352	12.1028|12.1028	0.53794|0.53794	0.0:0.9221:0.0:0.0779|0.0:0.9221:0.0:0.0779	.|.	.|45	.|O43716	.|GATC_HUMAN	V|F	76|45	.|ENSP00000446872:L45F	ENSP00000450281:A76V|ENSP00000448397:L45F	A|L	+|+	2|1	0|0	GATC|AL021546.1	119368894|119368894	0.992000|0.992000	0.36948|0.36948	0.685000|0.685000	0.30070|0.30070	0.991000|0.991000	0.79684|0.79684	2.195000|2.195000	0.42677|0.42677	2.646000|2.646000	0.89796|0.89796	0.644000|0.644000	0.83932|0.83932	GCT|CTT	.		0.682	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399		T	120884511	C	T	120884511	1	4	53	0	1	0	0	0	0	0	0	0	6282	797	28	2		2	GATC	12	120884511	5'Flank	SNP	C	TCGA-B9-7268-01A-11D-2136-08	18759102	120884511	12967384	53	5148											
GPR133	283383	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	131590407	131590407	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttccgcctcgagccgggCacggtgagtgggcgcagctc	5	7	16	13	5	0	1	0	1	0	0	3	2	1	1	3	3	2	4	3	3	0	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:131590407C>A	ENST00000261654.5	+	17	2443	c.1884C>A	c.(1882-1884)ggC>ggA	p.G628G	GPR133_ENST00000543617.1_Silent_p.G147G|GPR133_ENST00000376682.4_Silent_p.G314G|GPR133_ENST00000535015.1_Silent_p.G660G	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	628					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(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		TCGAGCCGGGCACGGTGAGTG	0.612																																					p.G628G		.											.	GPR133-191	0			c.C1884A						.						112	74	87					12																	131590407		2203	4300	6503	SO:0001819	synonymous_variant	283383	exon17			GCCGGGCACGGTG	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.1884C>A	12.37:g.131590407C>A		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	33	17	NM_198827	0	0	0	0	0	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Silent	SNP	ENST00000261654.5	37	CCDS9272.1																																																																																			.		0.612	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		A	131590407	C	A	131590407	2	1	53	1	0	0	0	0	0	0	0	1	6663	697	25	4		4	GPR133	12	131590407	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	10705896	131590407	2261488	54	5149											
MNAT1	4331	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	61434959	61434959	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttttaggtatttaaaccaTgtcagagctgcctcaccaca	11	13	7	10	0	2	1	2	0	0	1	2	1	2	1	3	1	3	3	3	1	4	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr14:61434959T>C	ENST00000261245.4	+	8	923	c.822T>C	c.(820-822)caT>caC	p.H274H	MNAT1_ENST00000539616.2_Silent_p.H232H|RP11-193F5.1_ENST00000553946.1_RNA	NM_002431.3	NP_002422.1	P51948	MAT1_HUMAN	MNAT CDK-activating kinase assembly factor 1	274					7-methylguanosine mRNA capping (GO:0006370)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to calcium ion (GO:0051592)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|ventricular system development (GO:0021591)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		ATTTAAACCATGTCAGAGCTG	0.388								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.H274H		.											.	MNAT1-523	0			c.T822C						.						128	116	120					14																	61434959		2203	4300	6503	SO:0001819	synonymous_variant	4331	exon8			AAACCATGTCAGA	X87843	CCDS9750.1, CCDS53899.1	14q23	2013-07-31	2013-07-31		ENSG00000020426	ENSG00000020426		"RING-type (C3HC4) zinc fingers", "General transcription factor IIH complex subunits"	7181	protein-coding gene	gene with protein product	"CDK-activating kinase assembly factor"	602659	"menage a trois 1 (CAK assembly factor)", "menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)"			9465303	Standard	NM_002431		Approved	MAT1, RNF66	uc001xfd.3	P51948	OTTHUMG00000152340	ENST00000261245.4:c.822T>C	14.37:g.61434959T>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	102	33	NM_002431	0	0	0	0	0	G3V1U8|Q15817|Q6ICQ7	Silent	SNP	ENST00000261245.4	37	CCDS9750.1																																																																																			.		0.388	MNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276956.1	NM_002431		C	61434959	T	C	61434959	2	2	53	1	0	0	0	0	0	0	0	1	9699	1461	51	3		3	MNAT1	14	61434959	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08		61434959	45914581	55	5150											
MARK3	4140	hgsc.bcm.edu	37	chr14	103894758	103894758	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattgacaaaactcagttgaAtccaacaagtctacaaaagg	19	8	6	8	0	2	2	1	2	1	0	3	2	3	2	1	1	3	1	1	1	9	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr14:103894758A>G	ENST00000429436.2	+	3	788	c.278A>G	c.(277-279)aAt>aGt	p.N93S	MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000416682.2_Missense_Mutation_p.N93S|MARK3_ENST00000440884.3_Missense_Mutation_p.N93S|MARK3_ENST00000553942.1_Missense_Mutation_p.N93S|MARK3_ENST00000303622.9_Missense_Mutation_p.N93S|MARK3_ENST00000335102.5_Missense_Mutation_p.N93S|MARK3_ENST00000216288.7_Missense_Mutation_p.N93S	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	93	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			ACTCAGTTGAATCCAACAAGT	0.284																																					p.N93S		.											.	MARK3-360	0			c.A278G						.						21	19	20					14																	103894758		1762	4021	5783	SO:0001583	missense	4140	exon3			AGTTGAATCCAAC	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.278A>G	14.37:g.103894758A>G	ENSP00000411397:p.Asn93Ser	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	12	8	NM_001128921	0	0	15	30	15	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.	.	.	.	.	.	.	.	.	.	A	8.139	0.784865	0.16189	.	.	ENSG00000075413	ENST00000335102;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	T;T;T;T;T;T;T	0.64618	-0.11;3.26;-0.11;-0.11;-0.11;-0.11;-0.11	5.27	4.12	0.48240	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.093621	0.64402	D	0.000001	T	0.40694	0.1127	N	0.10685	0.025	0.54753	D	0.99998	B;P;B;B;B;B	0.36183	0.164;0.542;0.026;0.04;0.366;0.021	B;B;B;B;B;B	0.34180	0.127;0.177;0.038;0.043;0.136;0.009	T	0.40683	-0.9550	10	0.54805	T	0.06	.	11.4976	0.50417	0.8493:0.1507:0.0:0.0	.	93;93;93;93;93;93	P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.;.;MARK3_HUMAN;.;.;.	S	93	ENSP00000335347:N93S;ENSP00000402104:N93S;ENSP00000408092:N93S;ENSP00000411397:N93S;ENSP00000303698:N93S;ENSP00000216288:N93S;ENSP00000450772:N93S	ENSP00000216288:N93S	N	+	2	0	MARK3	102964511	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	6.709000	0.74665	0.836000	0.34901	-0.313000	0.08912	AAT	.		0.284	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		G	103894758	A	G	103894758	3	3	53	1	0	0	0	0	1	0	0	0	9339	101	4	3	288	3	MARK3	14	103894758	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	42459799	103894758	3454782	56	5151											
PKD1	5310	ucsc.edu	37	chr16	2153595	2153595	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaagatgagctgcaccacGtcactgaggttggccagggc	11	6	14	10	1	1	4	1	2	0	2	1	4	1	4	2	3	2	3	2	3	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr16:2153595G>A	ENST00000262304.4	-	23	8671	c.8463C>T	c.(8461-8463)gaC>gaT	p.D2821D	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.D2821D	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2821	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GCTGCACCACGTCACTGAGGT	0.622																																					p.D2821D													.	PKD1-91	0			c.C8463T						.						40	44	43					16																	2153595		2190	4282	6472	SO:0001819	synonymous_variant	5310	exon23			CACCACGTCACTG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.8463C>T	16.37:g.2153595G>A		Somatic	146	1		WXS	Illumina HiSeq		248	3	NM_000296	0	0	54	67	13	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.622	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2153595	G	A	2153595	2	1	53	1	0	0	0	0	0	0	0	1	11989	1136	40	1		1	PKD1	16	2153595	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08		2153595	88201158	57	5152											
TERF2	7014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	69402345	69402345	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtttatcttccttccctgtaCttgaggcagcggactcagat	7	14	9	11	1	2	2	1	1	1	1	4	3	4	3	2	2	2	3	2	2	2	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr16:69402345C>G	ENST00000254942.3	-	6	897	c.881G>C	c.(880-882)aGt>aCt	p.S294T	TERF2_ENST00000603068.1_Missense_Mutation_p.S252T|TERF2_ENST00000569611.2_5'Flank	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	294					age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				CTTCCCTGTACTTGAGGCAGC	0.478																																					p.S294T	Ovarian(13;63 524 30420 31710 34037)	.											.	TERF2-227	0			c.G881C						.						133	121	125					16																	69402345		2198	4300	6498	SO:0001583	missense	7014	exon6			CCTGTACTTGAGG		CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604			11729	protein-coding gene	gene with protein product		602027		TRBF2		9326950, 10226653	Standard	NM_005652		Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.881G>C	16.37:g.69402345C>G	ENSP00000254942:p.Ser294Thr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	160	61	NM_005652	0	1	12	31	18		Missense_Mutation	SNP	ENST00000254942.3	37		.	.	.	.	.	.	.	.	.	.	C	4.457	0.084724	0.08583	.	.	ENSG00000132604	ENST00000254942	.	.	.	4.95	0.394	0.16299	.	0.964177	0.08668	N	0.911414	T	0.36826	0.0981	L	0.43152	1.355	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.31024	-0.9958	9	0.15066	T	0.55	0.7302	9.5105	0.39074	0.0:0.5756:0.3285:0.0959	.	252	Q15554	TERF2_HUMAN	T	252	.	ENSP00000254942:S252T	S	-	2	0	TERF2	67959846	.	.	0.002000	0.10522	0.255000	0.26057	.	.	0.218000	0.20820	0.555000	0.69702	AGT	.		0.478	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2			G	69402345	C	G	69402345	3	3	53	1	0	0	0	0	1	0	0	0	15794	565	20	4	767	4	TERF2	16	69402345	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	67248750	69402345	20952408	58	5153											
GINS2	51659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	85715212	85715212	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaacaggagcttcgtaagtTccatgtagtaagggctgggc	10	11	13	7	1	0	0	0	0	0	0	2	1	1	1	1	3	2	6	1	3	4	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr16:85715212T>C	ENST00000253462.3	-	3	381	c.281A>G	c.(280-282)gAa>gGa	p.E94G		NM_016095.2	NP_057179.1	Q9Y248	PSF2_HUMAN	GINS complex subunit 2 (Psf2 homolog)	94					DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(2)|lung(2)	6						CTTCGTAAGTTCCATGTAGTA	0.448																																					p.E94G		.											.	GINS2-90	0			c.A281G						.						183	164	170					16																	85715212		2198	4300	6498	SO:0001583	missense	51659	exon3			GTAAGTTCCATGT	BC003186	CCDS10953.1	16q24.1	2008-02-05			ENSG00000131153	ENSG00000131153			24575	protein-coding gene	gene with protein product		610609				11042152, 10810093	Standard	NM_016095		Approved	PSF2, Pfs2	uc002fja.3	Q9Y248	OTTHUMG00000137646	ENST00000253462.3:c.281A>G	16.37:g.85715212T>C	ENSP00000253462:p.Glu94Gly	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	130	66	NM_016095	1	0	18	30	11	D3DUM5|Q6IAG9	Missense_Mutation	SNP	ENST00000253462.3	37	CCDS10953.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643560	0.87859	.	.	ENSG00000131153	ENST00000253462	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.81259	0.4785	M	0.86420	2.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84916	0.0851	9	0.72032	D	0.01	-30.9692	14.3362	0.66592	0.0:0.0:0.0:1.0	.	94;94	Q53G08;Q9Y248	.;PSF2_HUMAN	G	94	.	ENSP00000253462:E94G	E	-	2	0	GINS2	84272713	1.000000	0.71417	0.970000	0.41538	0.939000	0.58152	7.531000	0.81973	1.874000	0.54306	0.459000	0.35465	GAA	.		0.448	GINS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269098.1	NM_016095		C	85715212	T	C	85715212	3	2	53	1	0	0	0	0	1	0	0	0	6408	1783	62	3	288	3	GINS2	16	85715212	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	16312867	85715212	4639541	59	5154											
YBX2	51087	hgsc.bcm.edu	37	chr17	7197633	7197633	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggattgccaggggtgcgggAgcccggcgccgagggggtcc	4	4	21	12	5	0	0	0	0	0	0	1	3	1	2	4	7	3	0	4	7	0	1	rs8069533	byFrequency	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr17:7197633A>G	ENST00000007699.5	-	1	250	c.187T>C	c.(187-189)Tcc>Ccc	p.S63P	YBX2_ENST00000570627.1_Intron	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	63	Gly-rich.		S -> P (in dbSNP:rs8069533).		mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						GGGGTGCGGGAGCCCGGCGCC	0.816													G|||	1889	0.377196	0.3079	0.4769	5008	,	,		5716	0.245		0.5447	False		,,,				2504	0.364				p.S63P		.											.	YBX2-90	0			c.T187C	GRCh37	CM085124	YBX2	M	rs8069533	.						1	1	1					17																	7197633		363	837	1200	SO:0001583	missense	51087	exon1			TGCGGGAGCCCGG	AF096834	CCDS11098.1	17p13.1	2013-12-20			ENSG00000006047	ENSG00000006047			17948	protein-coding gene	gene with protein product		611447				10100484, 9780336	Standard	NM_015982		Approved	MSY2, CSDA3	uc002gfq.2	Q9Y2T7	OTTHUMG00000177992	ENST00000007699.5:c.187T>C	17.37:g.7197633A>G	ENSP00000007699:p.Ser63Pro	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	2	NM_015982	0	0	0	0	0	D3DTP1|Q8N4P0	Missense_Mutation	SNP	ENST00000007699.5	37	CCDS11098.1	910	0.4166666666666667	158	0.32113821138211385	182	0.5027624309392266	158	0.2762237762237762	412	0.5435356200527705	G	2.549	-0.304467	0.05495	.	.	ENSG00000006047	ENST00000007699	T	0.22945	1.93	4.06	0.88	0.19161	.	0.434820	0.17110	N	0.186656	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	9	0.11182	T	0.66	0.3984	6.9711	0.24648	0.4087:0.0:0.5913:0.0	rs8069533	63	Q9Y2T7	YBOX2_HUMAN	P	63	ENSP00000007699:S63P	ENSP00000007699:S63P	S	-	1	0	YBX2	7138357	.	.	0.863000	0.33907	0.401000	0.30781	.	.	-0.213000	0.10094	-0.665000	0.03846	TCC	A|0.584;G|0.416		0.816	YBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440172.2	NM_015982		G	7197633	A	G	7197633	3	3	53	1	0	0	0	0	1	0	0	0	17503	304	11	3	939	3	YBX2	17	7197633	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		7197633	73997577	60	5155											
COX10	1352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	14005508	14005508	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactggccctgtttcctgctTacttctgttgggacaggcct	4	14	11	12	0	1	0	0	0	1	0	2	2	2	1	3	3	2	3	3	3	1	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr17:14005508T>A	ENST00000261643.3	+	4	650	c.573T>A	c.(571-573)ctT>ctA	p.L191L	COX10_ENST00000536205.1_Intron|COX10_ENST00000537334.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	191					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GTTTCCTGCTTACTTCTGTTG	0.473																																					p.L191L		.											.	COX10-226	0			c.T573A						.						174	152	160					17																	14005508		2203	4300	6503	SO:0001819	synonymous_variant	1352	exon4			CCTGCTTACTTCT	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.573T>A	17.37:g.14005508T>A		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	300	190	NM_001303	0	0	3	9	6	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1																																																																																			.		0.473	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		A	14005508	T	A	14005508	2	1	53	1	0	0	0	0	0	0	0	1	3768	1741	61	5		5	COX10	17	14005508	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08	6807875	14005508	67189702	61	5156											
AATK	9625	hgsc.bcm.edu	37	chr17	79096100	79096100	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggggcgcagccggcgcagtCagggtcgtggccggcggcgg	3	3	23	12	7	1	0	1	0	0	0	2	0	1	0	2	8	1	2	2	8	0	0	rs62073020	byFrequency	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr17:79096100C>G	ENST00000326724.4	-	11	1660	c.1636G>C	c.(1636-1638)Gac>Cac	p.D546H	MIR657_ENST00000385003.1_RNA|AATK_ENST00000417379.1_Missense_Mutation_p.D443H|AATK_ENST00000572339.1_5'Flank	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	546					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCGGCGCAGTCAGGGTCGTGG	0.746													C|||	10	0.00199681	0	0.0014	5008	,	,		8349	0		0.004	False		,,,				2504	0.0051				p.D546H		.											.	AATK-933	0			c.G1636C						.	C	HIS/ASP,HIS/ASP	3,2899		0,3,1448	2	3	2		1636,1327	4	0.5	17	dbSNP_129	2	5,5973		0,5,2984	no	missense,missense	AATK	NM_001080395.2,NM_004920.2	81,81	0,8,4432	GG,GC,CC		0.0836,0.1034,0.0901	probably-damaging,probably-damaging	546/1375,443/1272	79096100	8,8872	1451	2989	4440	SO:0001583	missense	9625	exon11			CGCAGTCAGGGTC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.1636G>C	17.37:g.79096100C>G	ENSP00000324196:p.Asp546His	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_001080395	0	0	0	0	0	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.104323	0.56291	0.001034	8.36E-4	ENSG00000181409	ENST00000326724;ENST00000374792	T;T	0.79653	-1.27;-1.29	3.96	3.96	0.45880	.	0.218250	0.36893	N	0.002349	D	0.85881	0.5800	L	0.52573	1.65	0.40902	D	0.984165	D	0.89917	1.0	D	0.72625	0.978	D	0.87951	0.2723	10	0.87932	D	0	.	13.7929	0.63152	0.0:1.0:0.0:0.0	rs62073020	546	Q6ZMQ8	LMTK1_HUMAN	H	546;510	ENSP00000324196:D546H;ENSP00000363924:D510H	ENSP00000324196:D546H	D	-	1	0	AATK	76710695	1.000000	0.71417	0.461000	0.27105	0.273000	0.26683	4.564000	0.60830	1.742000	0.51746	0.561000	0.74099	GAC	.		0.746	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		G	79096100	C	G	79096100	3	3	53	1	0	0	0	0	1	0	0	0	26	826	29	4	2504	4	AATK	17	79096100	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	65090592	79096100	2099110	62	5157											
TXNL1	9352	bcgsc.ca	37	chr18	54293655	54293655	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tatttattactcatagaactGaatgctggggcaatcctcaa	13	13	7	8	0	2	2	2	1	0	1	3	2	3	2	1	2	3	2	1	2	8	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr18:54293655G>C	ENST00000217515.6	-	2	336	c.132C>G	c.(130-132)ttC>ttG	p.F44L	TXNL1_ENST00000540155.1_5'UTR|TXNL1_ENST00000590954.1_Missense_Mutation_p.F44L	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN	thioredoxin-like 1	44	Thioredoxin.				cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		TCATAGAACTGAATGCTGGGG	0.343																																					p.F44L													.	TXNL1-90	0			c.C132G						.						118	124	122					18																	54293655		2203	4300	6503	SO:0001583	missense	9352	exon2			AGAACTGAATGCT	AF003938	CCDS11961.1	18q21.31	2011-01-17	2004-05-06	2004-05-07	ENSG00000091164	ENSG00000091164			12436	protein-coding gene	gene with protein product	"thioredoxin-like, 32kD"	603049	"thioredoxin-like, 32kDa"	TXNL		9473519, 9668102	Standard	NM_004786		Approved	Txl, TRP32	uc002lgg.3	O43396	OTTHUMG00000132722	ENST00000217515.6:c.132C>G	18.37:g.54293655G>C	ENSP00000217515:p.Phe44Leu	Somatic	123	0		WXS	Illumina HiSeq	Phase_1	166	5	NM_004786	0	0	60	62	2		Missense_Mutation	SNP	ENST00000217515.6	37	CCDS11961.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600187	0.87055	.	.	ENSG00000091164	ENST00000217515	T	0.16743	2.32	5.56	3.76	0.43208	Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.20780	0.0500	L	0.47190	1.495	0.80722	D	1	P;P	0.50443	0.935;0.905	P;P	0.47981	0.548;0.563	T	0.01448	-1.1352	10	0.42905	T	0.14	.	12.0451	0.53475	0.1438:0.0:0.8562:0.0	.	44;44	B2R960;O43396	.;TXNL1_HUMAN	L	44	ENSP00000217515:F44L	ENSP00000217515:F44L	F	-	3	2	TXNL1	52444653	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.041000	0.49807	1.360000	0.45960	0.655000	0.94253	TTC	.		0.343	TXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256064.2			C	54293655	G	C	54293655	3	2	53	1	0	0	0	0	1	0	0	0	16837	1281	45	4	765	4	TXNL1	18	54293655	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08		54293655	23783593	63	5158											
SMARCA4	6597	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11144469	11144469	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgcagcacgggcagcggCagtgccagcttcgcccacac	8	4	12	17	3	0	0	0	0	0	0	1	0	0	0	2	2	5	5	2	2	0	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:11144469C>A	ENST00000429416.3	+	28	4082	c.3801C>A	c.(3799-3801)ggC>ggA	p.G1267G	SMARCA4_ENST00000590574.1_Intron|SMARCA4_ENST00000444061.3_Intron|SMARCA4_ENST00000344626.4_Silent_p.G1267G|SMARCA4_ENST00000450717.3_Intron|SMARCA4_ENST00000589677.1_Intron|SMARCA4_ENST00000538456.3_Intron|SMARCA4_ENST00000358026.2_Silent_p.G1267G|SMARCA4_ENST00000541122.2_Intron|SMARCA4_ENST00000413806.3_Intron	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1267					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				cgggcagcggcagtgccagct	0.577			"F, N, Mis"		NSCLC																																p.G1267G				Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.C3801A						.						24	28	27					19																	11144469		2201	4297	6498	SO:0001819	synonymous_variant	6597	exon27			CAGCGGCAGTGCC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3801C>A	19.37:g.11144469C>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	69	9	NM_003072	0	0	13	17	4	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																			.		0.577	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11144469	C	A	11144469	2	1	53	1	0	0	0	0	0	0	0	1	14802	697	25	4		4	SMARCA4	19	11144469	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08		11144469	47984514	64	5159											
FAM187B	148109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35718874	35718874	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccatcacctgtacatggatCctaagggacagtcgagccac	11	8	9	13	1	1	0	1	0	0	0	4	3	3	2	4	2	2	1	4	2	2	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:35718874C>T	ENST00000324675.3	-	1	758	c.710G>A	c.(709-711)gGa>gAa	p.G237E		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	237						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						GTACATGGATCCTAAGGGACA	0.507																																					p.G237E		.											.	FAM187B-92	0			c.G710A						.						67	57	60					19																	35718874		2203	4300	6503	SO:0001583	missense	148109	exon1			ATGGATCCTAAGG	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"transmembrane protein 162"	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.710G>A	19.37:g.35718874C>T	ENSP00000323355:p.Gly237Glu	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	37	13	NM_152481	0	0	0	0	0	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687642	0.29962	.	.	ENSG00000177558	ENST00000324675	T	0.39592	1.07	4.91	1.25	0.21368	.	0.519698	0.15947	N	0.236896	T	0.50274	0.1606	L	0.57536	1.79	0.09310	N	1	D	0.57899	0.981	P	0.53401	0.725	T	0.49041	-0.8980	10	0.72032	D	0.01	-2.2526	13.4884	0.61379	0.0:0.4094:0.5906:0.0	.	237	Q17R55	F187B_HUMAN	E	237	ENSP00000323355:G237E	ENSP00000323355:G237E	G	-	2	0	FAM187B	40410714	0.319000	0.24607	0.289000	0.24876	0.145000	0.21501	0.869000	0.27996	0.564000	0.29238	-0.175000	0.13238	GGA	.		0.507	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481		T	35718874	C	T	35718874	3	4	53	1	0	0	0	0	1	0	0	0	5529	855	30	2	407	2	FAM187B	19	35718874	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	24574405	35718874	23410109	65	5160											
ZNF780B	163131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40540794	40540794	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcatgaatactctgatgttGaacaaggtttgagacacgat	14	11	10	6	1	1	4	0	4	1	1	1	6	1	4	0	1	3	3	0	1	4	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:40540794G>C	ENST00000434248.1	-	5	2037	c.1972C>G	c.(1972-1974)Caa>Gaa	p.Q658E	ZNF780B_ENST00000221355.6_Missense_Mutation_p.Q510E	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	658					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)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTCTGATGTTGAACAAGGTTT	0.388																																					p.Q658E		.											.	ZNF780B-47	0			c.C1972G						.						167	180	176					19																	40540794		2201	4300	6501	SO:0001583	missense	163131	exon5			GATGTTGAACAAG	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1972C>G	19.37:g.40540794G>C	ENSP00000391641:p.Gln658Glu	Somatic	263	2		WXS	Illumina HiSeq	Phase_I	310	113	NM_001005851	0	0	5	6	1	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	g	0.438	-0.899982	0.02472	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.15139	2.45;2.45	2.56	-0.573	0.11742	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05273	0.0140	N	0.04669	-0.19	0.09310	N	1	B	0.30709	0.291	B	0.29663	0.105	T	0.37056	-0.9722	9	0.02654	T	1	.	5.8975	0.18947	0.0:0.4996:0.321:0.1794	.	658	Q9Y6R6	Z780B_HUMAN	E	658;510	ENSP00000391641:Q658E;ENSP00000221355:Q510E	ENSP00000221355:Q510E	Q	-	1	0	ZNF780B	45232634	0.000000	0.05858	0.312000	0.25196	0.637000	0.38172	-0.905000	0.04075	0.184000	0.20083	0.462000	0.41574	CAA	.		0.388	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		C	40540794	G	C	40540794	3	2	53	1	0	0	0	0	1	0	0	0	18185	1299	45	4	533	4	ZNF780B	19	40540794	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	4821920	40540794	18588189	66	5161											
ATP1A3	478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42492245	42492245	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggtggcgtgagtgcgttaGgcccatcccgggccaggatc	5	7	17	12	4	0	1	0	1	0	0	2	2	1	2	3	5	1	1	3	5	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:42492245G>A	ENST00000302102.5	-	4	350	c.200C>T	c.(199-201)cCt>cTt	p.P67L	ATP1A3_ENST00000543770.1_Missense_Mutation_p.P78L|ATP1A3_ENST00000545399.1_Missense_Mutation_p.P80L|ATP1A3_ENST00000468774.2_5'UTR|ATP1A3_ENST00000602133.1_Missense_Mutation_p.P37L	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	67					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						GAGTGCGTTAGGCCCATCCCG	0.637																																					p.P80L		.											.	ATP1A3-92	0			c.C239T						.						103	107	106					19																	42492245		2203	4300	6503	SO:0001583	missense	478	exon4			GCGTTAGGCCCAT		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"ATPases / P-type"	801	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-3", "sodium pump subunit alpha-3", "sodium-potassium ATPase catalytic subunit alpha-3"	182350	"dystonia 12"	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.200C>T	19.37:g.42492245G>A	ENSP00000302397:p.Pro67Leu	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	133	16	NM_001256214	0	0	0	0	0	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	37	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095660	0.56075	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000543770;ENST00000448429	T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43	4.09	4.09	0.47781	ATPase, P-type cation-transporter, N-terminal (2);	0.185108	0.46758	D	0.000274	D	0.89065	0.6609	M	0.80616	2.505	0.80722	D	1	B;D;D;D	0.76494	0.383;0.998;0.999;0.997	B;D;D;D	0.75484	0.126;0.965;0.986;0.979	D	0.90107	0.4189	10	0.54805	T	0.06	.	14.1703	0.65506	0.0:0.0:1.0:0.0	.	80;78;67;67	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	L	67;67;80;37;78;80	ENSP00000302397:P67L;ENSP00000411503:P67L;ENSP00000444688:P80L;ENSP00000437577:P78L	ENSP00000302397:P67L	P	-	2	0	ATP1A3	47184085	1.000000	0.71417	0.945000	0.38365	0.021000	0.10359	9.808000	0.99193	2.010000	0.58986	0.491000	0.48974	CCT	.		0.637	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42492245	G	A	42492245	3	1	53	1	0	0	0	0	1	0	0	0	1131	1000	35	2	2921	2	ATP1A3	19	42492245	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	1951451	42492245	16636738	67	5162											
ZNF836	162962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52660096	52660096	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattttgtctgaagatcttGccacatacaccacattgata	13	13	6	9	0	2	3	0	2	2	1	2	4	2	3	2	0	2	0	2	0	4	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:52660096G>A	ENST00000322146.8	-	5	1361	c.840C>T	c.(838-840)ggC>ggT	p.G280G	ZNF836_ENST00000597252.1_Silent_p.G280G|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	280					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)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TGAAGATCTTGCCACATACAC	0.413																																					p.G280G		.											.	ZNF836-46	0			c.C840T						.						85	90	88					19																	52660096		2176	4286	6462	SO:0001819	synonymous_variant	162962	exon5			GATCTTGCCACAT	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.840C>T	19.37:g.52660096G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	114	46	NM_001102657	0	0	4	4	0		Silent	SNP	ENST00000322146.8	37	CCDS46162.1																																																																																			.		0.413	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52660096	G	A	52660096	2	1	53	1	0	0	0	0	0	0	0	1	18219	1306	46	2		2	ZNF836	19	52660096	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	10167851	52660096	6468887	68	5163											
ZNF264	9422	bcgsc.ca	37	chr19	57724137	57724137	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctcgtccctcactcagcatCaaaggatgcatactgggaaa	12	8	9	12	1	3	0	3	0	0	0	5	2	4	2	1	2	3	3	1	2	3	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:57724137C>G	ENST00000263095.6	+	4	2086	c.1672C>G	c.(1672-1674)Caa>Gaa	p.Q558E	ZNF264_ENST00000536056.1_Missense_Mutation_p.Q558E	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	558					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(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		CACTCAGCATCAAAGGATGCA	0.453																																					p.Q558E													.	ZNF264-92	0			c.C1672G						.						100	97	98					19																	57724137		2203	4300	6503	SO:0001583	missense	9422	exon4			CAGCATCAAAGGA	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"Zinc fingers, C2H2-type", "-"	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.1672C>G	19.37:g.57724137C>G	ENSP00000263095:p.Gln558Glu	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	108	5	NM_003417	0	0	1	1	0	A8K8Y9|Q9P1V0	Missense_Mutation	SNP	ENST00000263095.6	37	CCDS33127.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.241123	0.22711	.	.	ENSG00000083844	ENST00000263095;ENST00000536056	T;T	0.07327	3.2;3.2	2.35	2.35	0.29111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06234	0.0161	L	0.28014	0.82	0.21553	N	0.999646	B	0.27853	0.191	B	0.18263	0.021	T	0.27226	-1.0080	9	0.59425	D	0.04	.	8.9199	0.35605	0.0:0.7681:0.2319:0.0	.	558	O43296	ZN264_HUMAN	E	558	ENSP00000263095:Q558E;ENSP00000440376:Q558E	ENSP00000263095:Q558E	Q	+	1	0	ZNF264	62415949	0.000000	0.05858	0.624000	0.29186	0.955000	0.61496	0.743000	0.26231	1.644000	0.50603	0.491000	0.48974	CAA	.		0.453	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			G	57724137	C	G	57724137	3	3	53	1	0	0	0	0	1	0	0	0	17836	827	29	4	1686	4	ZNF264	19	57724137	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	5064041	57724137	1404846	69	5164											
SCARF2	91179	broad.mit.edu	37	chr22	20791897	20791897	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcacacgttgcggccgcGagggttcagttcctgaggcg	6	7	16	12	6	1	1	1	1	0	0	2	2	2	1	2	4	1	4	2	4	0	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr22:20791897G>T	ENST00000266214.5	-	1	249	c.145C>A	c.(145-147)Cgc>Agc	p.R49S	SCARF2_ENST00000405555.3_Missense_Mutation_p.R49S	NM_153334.4	NP_699165.2	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2	49					cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			TTGCGGCCGCGAGGGTTCAGT	0.741																																					p.R49S													.	SCARF2-341	0			c.C145A						.						5	7	7					22																	20791897		2125	4206	6331	SO:0001583	missense	91179	exon1			GGCCGCGAGGGTT	AF522196	CCDS13779.1, CCDS46666.1	22q11.21	2011-10-10			ENSG00000244486	ENSG00000244486			19869	protein-coding gene	gene with protein product		613619				12154095	Standard	XM_006724364		Approved	SREC-II, SREC2, HUMZD58C02	uc002zsk.2	Q96GP6	OTTHUMG00000150779	ENST00000266214.5:c.145C>A	22.37:g.20791897G>T	ENSP00000266214:p.Arg49Ser	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_182895	0	0	0	0	0	E5RFB8|Q58A83|Q8IXF3|Q9BW74	Missense_Mutation	SNP	ENST00000266214.5	37	CCDS13779.1	.	.	.	.	.	.	.	.	.	.	G	1.646	-0.515131	0.04200	.	.	ENSG00000244486	ENST00000405555;ENST00000341328;ENST00000266214	T;T	0.19105	2.23;2.17	2.65	1.57	0.23409	.	0.223960	0.29451	U	0.012102	T	0.06371	0.0164	N	0.02225	-0.63	0.54753	D	0.999987	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28332	-1.0047	10	0.10111	T	0.7	-16.2973	7.303	0.26432	0.0:0.2762:0.7238:0.0	.	49;49	E5RFB8;Q96GP6	.;SREC2_HUMAN	S	49	ENSP00000385589:R49S;ENSP00000266214:R49S	ENSP00000266214:R49S	R	-	1	0	SCARF2	19121897	0.998000	0.40836	0.988000	0.46212	0.206000	0.24218	2.710000	0.47169	0.438000	0.26450	-0.547000	0.04224	CGC	.		0.741	SCARF2-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320047.1			T	20791897	G	T	20791897	3	4	53	1	0	0	0	0	1	0	0	0	13916	1058	37	4	2511	4	SCARF2	22	20791897	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08		20791897	30512669	70	5165											
PHF16	9767	hgsc.bcm.edu	37	chrX	46918438	46918438	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacgggattgccatggtaaaAgcaagacacatcccctttcc	12	8	9	12	1	0	1	0	0	0	1	2	3	2	2	4	2	2	2	4	2	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chrX:46918438A>G	ENST00000218343.4	+	11	2729	c.2431A>G	c.(2431-2433)Agc>Ggc	p.S811G	PHF16_ENST00000397189.1_Missense_Mutation_p.S811G	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CCATGGTAAAAGCAAGACACA	0.458																																					p.S811G		.											.	PHF16-130	0			c.A2431G						.						40	34	36					X																	46918438		2203	4293	6496	SO:0001583	missense	9767	exon11			GGTAAAAGCAAGA																												ENST00000218343.4:c.2431A>G	X.37:g.46918438A>G	ENSP00000218343:p.Ser811Gly	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	52	3	NM_001077445	0	0	14	14	0		Missense_Mutation	SNP	ENST00000218343.4	37	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	A	5.227	0.227339	0.09916	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	T;T	0.50813	0.73;0.73	5.18	2.75	0.32379	.	1.092960	0.06637	N	0.760394	T	0.22975	0.0555	N	0.04508	-0.205	0.22081	N	0.999376	B	0.02656	0.0	B	0.01281	0.0	T	0.26815	-1.0092	10	0.11794	T	0.64	.	5.0228	0.14370	0.6887:0.153:0.1583:0.0	.	811	Q92613	JADE3_HUMAN	G	811	ENSP00000380373:S811G;ENSP00000218343:S811G	ENSP00000218343:S811G	S	+	1	0	PHF16	46803382	1.000000	0.71417	0.859000	0.33776	0.840000	0.47671	1.976000	0.40579	0.274000	0.22072	0.481000	0.45027	AGC	.		0.458	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			G	46918438	A	G	46918438	3	3	53	1	0	0	0	0	1	0	0	0	11853	72	3	3	2469	3	PHF16	23	46918438	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		46918438	108352122	71	5166											
HUWE1	10075	ucsc.edu	37	chrX	53607789	53607789	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccaggagcaagcgaaacttAccagttcctgagcctcgagg	11	6	12	12	2	0	1	0	1	0	0	2	4	1	2	4	2	5	2	4	2	3	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chrX:53607789A>G	ENST00000342160.3	-	42	6174		c.e42+1		HUWE1_ENST00000262854.6_Splice_Site			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase						base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						AGCGAAACTTACCAGTTCCTG	0.498																																					.													.	HUWE1-280	0			c.5716+2T>C						.						55	41	46					X																	53607789		2203	4300	6503	SO:0001630	splice_region_variant	10075	exon44			AAACTTACCAGTT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.5716+1T>C	X.37:g.53607789A>G		Somatic	28	0		WXS	Illumina HiSeq		40	4	NM_031407	0	0	0	0	0	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Splice_Site	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.418952	0.83559	.	.	ENSG00000086758	ENST00000342160;ENST00000427052;ENST00000262854	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0818	0.64929	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HUWE1	53624514	1.000000	0.71417	0.971000	0.41717	0.927000	0.56198	8.857000	0.92250	1.971000	0.57363	0.486000	0.48141	.	.		0.498	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	Intron	G	53607789	A	G	53607789	5	3	53	1	0	0	0	0	0	0	1	0	7482	405	14	3	7574	3	HUWE1	23	53607789	Splice_Site	SNP	A	TCGA-B9-7268-01A-11D-2136-08	6689351	53607789	101662771	72	5167											
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70468027	70468027	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttaccttcgctgcagaagcTtttctccactccgctgaatc	7	13	6	15	2	1	2	0	1	1	1	5	2	2	2	3	0	3	4	3	0	3	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chrX:70468027T>C	ENST00000353904.2	-	11	2147	c.1960A>G	c.(1960-1962)Agc>Ggc	p.S654G	ZMYM3_ENST00000373988.1_Missense_Mutation_p.S656G|ZMYM3_ENST00000373984.3_Missense_Mutation_p.S656G|ZMYM3_ENST00000314425.5_Missense_Mutation_p.S654G|ZMYM3_ENST00000373998.1_Missense_Mutation_p.S654G|ZMYM3_ENST00000489332.1_5'UTR	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	654					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					CTGCAGAAGCTTTTCTCCACT	0.562																																					p.S654G		.											.	ZMYM3-131	0			c.A1960G						.						70	48	55					X																	70468027		2203	4299	6502	SO:0001583	missense	9203	exon11			AGAAGCTTTTCTC	AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"Zinc fingers, MYM type"	13054	protein-coding gene	gene with protein product		300061	"zinc finger protein 261"	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.1960A>G	X.37:g.70468027T>C	ENSP00000343909:p.Ser654Gly	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_005096	0	0	16	16	0	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	37	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	t	3.943	-0.013893	0.07681	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988	T;T;T;T;T	0.46063	1.48;0.88;1.48;1.48;1.48	4.37	4.37	0.52481	TRASH (1);Zinc finger, MYM-type (1);	0.073908	0.64402	D	0.000019	T	0.31358	0.0794	N	0.24115	0.695	0.26074	N	0.981187	B;B	0.22800	0.061;0.075	B;B	0.27380	0.047;0.079	T	0.25984	-1.0116	10	0.44086	T	0.13	-1.9223	12.9702	0.58508	0.0:0.0:0.0:1.0	.	654;654	Q14202-2;Q14202	.;ZMYM3_HUMAN	G	654;654;654;656;656	ENSP00000322845:S654G;ENSP00000363110:S654G;ENSP00000343909:S654G;ENSP00000363096:S656G;ENSP00000363100:S656G	ENSP00000322845:S654G	S	-	1	0	ZMYM3	70384752	1.000000	0.71417	0.998000	0.56505	0.226000	0.24999	3.014000	0.49590	1.629000	0.50426	0.350000	0.21858	AGC	.		0.562	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		C	70468027	T	C	70468027	3	2	53	1	0	0	0	0	1	0	0	0	17733	1609	56	3	2212	3	ZMYM3	23	70468027	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	16860238	70468027	84802533	73	5168											
PHKA1	5255	hgsc.bcm.edu;ucsc.edu	37	chrX	71822085	71822085	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacagcaccaatctcgtggaTagaaatagcaggactgacat	16	7	9	9	1	1	2	0	1	1	1	2	4	1	4	1	2	3	2	1	2	5	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chrX:71822085T>C	ENST00000373542.4	-	27	3115	c.2956A>G	c.(2956-2958)Atc>Gtc	p.I986V	PHKA1_ENST00000541944.1_Missense_Mutation_p.I927V|PHKA1_ENST00000373545.3_Missense_Mutation_p.I927V|PHKA1_ENST00000373539.3_Missense_Mutation_p.I986V|PHKA1_ENST00000339490.3_Missense_Mutation_p.I986V	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	986					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					ATCTCGTGGATAGAAATAGCA	0.403																																					p.I986V		.											.	PHKA1-134	0			c.A2956G						.						120	96	104					X																	71822085		2203	4300	6503	SO:0001583	missense	5255	exon27			CGTGGATAGAAAT		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.2956A>G	X.37:g.71822085T>C	ENSP00000362643:p.Ile986Val	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	39	4	NM_002637	0	0	5	5	0	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.931761	0.52866	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91295	-2.77;-2.79;-2.82;-2.78;-2.76	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.89884	0.6844	M	0.73372	2.23	0.52099	D	0.999948	B;B;B	0.19200	0.025;0.016;0.034	B;B;B	0.27608	0.038;0.073;0.081	D	0.86249	0.1648	10	0.34782	T	0.22	-12.1844	12.9234	0.58245	0.0:0.0:0.0:1.0	.	927;986;986	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	V	927;986;927;986;986	ENSP00000362646:I927V;ENSP00000362643:I986V;ENSP00000441251:I927V;ENSP00000342469:I986V;ENSP00000362640:I986V	ENSP00000342469:I986V	I	-	1	0	PHKA1	71738810	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.818000	0.69236	1.960000	0.56953	0.417000	0.27973	ATC	.		0.403	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			C	71822085	T	C	71822085	3	2	53	1	0	0	0	0	1	0	0	0	11869	1406	49	3	739	3	PHKA1	23	71822085	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	1354058	71822085	83448475	74	5169											
CCDC160	347475	hgsc.bcm.edu	37	chrX	133379028	133379028	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatttaagaggaaaaaataTattttccaactaaatgaaat	22	12	4	3	0	0	2	0	1	0	1	1	3	1	3	1	1	1	0	1	1	11	7	rs367640741		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chrX:133379028T>C	ENST00000517294.1	+	3	581	c.198T>C	c.(196-198)taT>taC	p.Y66Y	CCDC160_ENST00000370809.4_Silent_p.Y66Y			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	66										endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GGAAAAAATATATTTTCCAAC	0.303													T|||	1	0.000264901	0	0	3775	,	,		12364	0		0.001	False		,,,				2504	0				p.Y66Y		.											.	CCDC160-40	0			c.T198C						.	T		0,2994		0,0,0,1219,556	16	14	15		198	1.2	0	X		15	2,6295		0,0,2,2278,1739	no	coding-synonymous	CCDC160	NM_001101357.1		0,0,2,3497,2295	CC,CT,C,TT,T		0.0318,0.0,0.0215		66/326	133379028	2,9289	1775	4019	5794	SO:0001819	synonymous_variant	347475	exon2			AAAATATATTTTC	BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.198T>C	X.37:g.133379028T>C		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	5	4	NM_001101357	0	0	0	2	2		Silent	SNP	ENST00000517294.1	37	CCDS48171.1																																																																																			.		0.303	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		C	133379028	T	C	133379028	2	2	53	1	0	0	0	0	0	0	0	1	2798	1413	49	3		3	CCDC160	23	133379028	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08	61556943	133379028	21891532	75	5170											
FAM132A	388581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1179848	1179848	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agccatgtcatgtgggcgtcGgagaactcaggtcctgaggc	8	8	15	10	2	2	2	2	1	0	1	4	3	3	2	2	4	2	0	2	4	1	0	rs200735866		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:1179848G>C	ENST00000330388.2	-	2	238	c.207C>G	c.(205-207)tcC>tcG	p.S69S		NM_001014980.2	NP_001014980.1	Q5T7M4	ADIPL_HUMAN	family with sequence similarity 132, member A	69					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)		TGTGGGCGTCGGAGAACTCAG	0.682																																					p.S69S		.											.	FAM132A-68	0			c.C207G						.						44	49	47					1																	1179848		2190	4289	6479	SO:0001819	synonymous_variant	388581	exon2			GGCGTCGGAGAAC	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.207C>G	1.37:g.1179848G>C		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	90	18	NM_001014980	0	0	0	0	0	Q5EBL5	Silent	SNP	ENST00000330388.2	37	CCDS30554.1																																																																																			G|0.999;A|0.000		0.682	FAM132A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004080.4	XM_371208		C	1179848	G	C	1179848	2	2	54	1	0	0	0	0	0	0	0	1	5458	1103	39	4		4	FAM132A	1	1179848	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		1179848	248070773	1	5171											
KCNAB2	8514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6142274	6142274	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatggcagagcagctcatgaCcttggcctatgataatggca	11	9	12	9	0	1	3	1	2	0	1	1	4	1	3	2	3	2	4	2	3	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:6142274C>A	ENST00000164247.1	+	6	785	c.221C>A	c.(220-222)aCc>aAc	p.T74N	KCNAB2_ENST00000602612.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000341524.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000378111.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000378083.3_Missense_Mutation_p.T107N|KCNAB2_ENST00000378087.3_Missense_Mutation_p.T74N|KCNAB2_ENST00000378092.1_Missense_Mutation_p.T60N|KCNAB2_ENST00000378097.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000458166.2_Missense_Mutation_p.T7N|KCNAB2_ENST00000352527.1_Missense_Mutation_p.T60N	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 2	74					hematopoietic progenitor cell differentiation (GO:0002244)|protein heterooligomerization (GO:0051291)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(1)|lung(4)|skin(3)	8	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCTCATGACCTTGGCCTAT	0.562																																					p.T107N		.											.	KCNAB2-514	0			c.C320A						.						138	123	129					1																	6142274		2203	4300	6503	SO:0001583	missense	8514	exon5			TCATGACCTTGGC	U33429	CCDS55.1, CCDS56.1, CCDS55570.1, CCDS55571.1	1p36.3	2008-02-05			ENSG00000069424	ENSG00000069424		"Potassium channels", "Aldo-keto reductases"	6229	protein-coding gene	gene with protein product		601142				8838324	Standard	NM_003636		Approved	AKR6A5, KCNA2B, HKvbeta2.1, HKvbeta2.2	uc001aly.2	Q13303	OTTHUMG00000000795	ENST00000164247.1:c.221C>A	1.37:g.6142274C>A	ENSP00000164247:p.Thr74Asn	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	80	29	NM_001199862	0	0	0	0	0	A0AVM9|A8K1A4|B0AZR7|O43659|Q5TG82|Q5TG83|Q6ZNE4|Q99411	Missense_Mutation	SNP	ENST00000164247.1	37	CCDS55.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332367	0.81801	.	.	ENSG00000069424	ENST00000378111;ENST00000378097;ENST00000378092;ENST00000428161;ENST00000389632;ENST00000378087;ENST00000341524;ENST00000352527;ENST00000435937;ENST00000164247;ENST00000378083;ENST00000458166	T;T;T;T;T;T;T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99	5.33	5.33	0.75918	NADP-dependent oxidoreductase domain (3);	0.095392	0.64402	D	0.000001	T	0.37019	0.0988	L	0.39467	1.215	0.58432	D	0.999997	D;D;D;D	0.65815	0.971;0.995;0.979;0.964	D;D;P;P	0.66979	0.948;0.936;0.88;0.766	T	0.02042	-1.1224	10	0.33940	T	0.23	-23.7432	17.5837	0.87974	0.0:1.0:0.0:0.0	.	107;60;74;74	Q13303-3;Q13303-2;Q13303;Q2YD85	.;.;KCAB2_HUMAN;.	N	74;74;60;60;74;74;74;60;60;74;107;7	ENSP00000367351:T74N;ENSP00000367337:T74N;ENSP00000367332:T60N;ENSP00000400285:T60N;ENSP00000374283:T74N;ENSP00000367327:T74N;ENSP00000340824:T74N;ENSP00000318772:T60N;ENSP00000389151:T60N;ENSP00000164247:T74N;ENSP00000367323:T107N;ENSP00000396167:T7N	ENSP00000164247:T74N	T	+	2	0	KCNAB2	6064861	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.706000	0.74649	2.482000	0.83794	0.563000	0.77884	ACC	.		0.562	KCNAB2-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002114.3	NM_172130		A	6142274	C	A	6142274	3	1	54	1	0	0	0	0	1	0	0	0	8031	507	18	4	239	4	KCNAB2	1	6142274	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4962426	6142274	243108347	2	5172											
CASZ1	54897	broad.mit.edu	37	chr1	10699156	10699158	+	In_Frame_Del	DEL	TCG	TCG	-																															ggtcctcgtcgtcgtcgtccTcgtcgtcgtcctcgtcgtcg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TCG	TCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:10699156_10699158delTCG	ENST00000377022.3	-	21	5438_5440	c.5121_5123delCGA	c.(5119-5124)gacgag>gag	p.D1707del	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1707	Asp-rich.|Glu-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		gtcgtcgtcctcgtcgtcgtcct	0.744																																					p.1707_1708del													.	CASZ1-113	0			c.5121_5123del						.																																			SO:0001651	inframe_deletion	54897	exon21			TCGTCCTCGTCGT	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.5121_5123delCGA	1.37:g.10699162_10699164delTCG	ENSP00000366221:p.Asp1707del	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001079843	0	0	0	0	0	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	In_Frame_Del	DEL	ENST00000377022.3	37	CCDS41246.1																																																																																			-|0.032;TCGTCG|0.968		0.744	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		-	10699158	TCG	-	10699156	7	5	54	1	0	1	0	1	0	0	0	0	2691	1551	54	0	160	0	CASZ1	1	10699156	In_Frame_Del	DEL	TCG	TCGA-B9-A44B-01A-11D-A25F-10	4556882	10699156	238551465	3	5173											
SPEN	23013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	16258337	16258337	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcacagaagcttttggaaTtgaagatggaggcagagaag	16	7	14	4	0	0	4	0	1	0	3	0	7	0	6	0	3	2	3	0	3	5	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:16258337T>G	ENST00000375759.3	+	11	5806	c.5602T>G	c.(5602-5604)Ttg>Gtg	p.L1868V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1868					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCTTTTGGAATTGAAGATGGA	0.498																																					p.L1868V		.											.	SPEN-298	0			c.T5602G						.						67	73	71					1																	16258337		2203	4300	6503	SO:0001583	missense	23013	exon11			TTGGAATTGAAGA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.5602T>G	1.37:g.16258337T>G	ENSP00000364912:p.Leu1868Val	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	67	48	NM_015001	0	0	1	4	3	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	8.066	0.769236	0.15983	.	.	ENSG00000065526	ENST00000375759	T	0.08807	3.05	5.27	-2.9	0.05648	.	.	.	.	.	T	0.06416	0.0165	L	0.36672	1.1	0.09310	N	1	B	0.22276	0.067	B	0.24155	0.051	T	0.40059	-0.9583	9	0.29301	T	0.29	-8.6361	7.649	0.28337	0.0:0.4283:0.1213:0.4504	.	1868	Q96T58	MINT_HUMAN	V	1868	ENSP00000364912:L1868V	ENSP00000364912:L1868V	L	+	1	2	SPEN	16130924	0.919000	0.31177	0.007000	0.13788	0.912000	0.54170	0.155000	0.16362	-0.878000	0.04007	0.383000	0.25322	TTG	.		0.498	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16258337	T	G	16258337	3	3	54	1	0	0	0	0	1	0	0	0	15070	1490	52	5	5644	5	SPEN	1	16258337	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	5559181	16258337	232992284	4	5174											
RCAN3	11123	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	24840954	24840954	+	Frame_Shift_Del	DEL	A	A	-																															agaagagatgatttttggtgAaaatgaagatgatttggatg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:24840954delA	ENST00000374395.4	+	2	405	c.92delA	c.(91-93)gaafs	p.E31fs	RCAN3_ENST00000436717.2_Frame_Shift_Del_p.E31fs|RCAN3_ENST00000374393.2_Frame_Shift_Del_p.E31fs|RCAN3_ENST00000412742.2_Frame_Shift_Del_p.E31fs|RCAN3_ENST00000538532.1_Frame_Shift_Del_p.E31fs	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	31					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		ATTTTTGGTGAAAATGAAGAT	0.438																																					p.E31fs		.											.	RCAN3-90	0			c.92delA						.						199	184	189					1																	24840954		2203	4300	6503	SO:0001589	frameshift_variant	11123	exon1			.		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"Down syndrome critical region gene 1-like 2"	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.92delA	1.37:g.24840954delA	ENSP00000363516:p.Glu31fs	Somatic	325	0		WXS	Illumina HiSeq	Phase_I	264	121	NM_001251980	0	0	0	0	0	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Frame_Shift_Del	DEL	ENST00000374395.4	37	CCDS254.1																																																																																			.		0.438	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2			-	24840954	A	-	24840954	7	5	54	1	0	1	0	1	0	0	0	0	13202	246	9	0	94	0	RCAN3	1	24840954	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	8582617	24840954	224409667	5	5175											
DNALI1	7802	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	38027791	38027793	+	In_Frame_Del	DEL	AGA	AGA	-																															cgagaggcggcaggtggaggAgaagaagcacaatgaggaga																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:38027791_38027793delAGA	ENST00000296218.7	+	5	762_764	c.752_754delAGA	c.(751-756)gagaag>gag	p.K253del	DNALI1_ENST00000497858.1_3'UTR|DNALI1_ENST00000541606.1_In_Frame_Del_p.K105del	NM_003462.3	NP_003453.2	O14645	IDLC_HUMAN	dynein, axonemal, light intermediate chain 1	231					cellular component movement (GO:0006928)|metabolic process (GO:0008152)|single fertilization (GO:0007338)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|filopodium (GO:0030175)	microtubule motor activity (GO:0003777)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CAGGTGGAGGAGAAGAAGCACAA	0.567																																					p.251_252del		.											.	DNALI1-154	0			c.752_754del						.			3,4263		0,3,2130						5.4	1			104	1,8253		0,1,4126	no	coding	DNALI1	NM_003462.3		0,4,6256	A1A1,A1R,RR		0.0121,0.0703,0.0319				4,12516				SO:0001651	inframe_deletion	7802	exon5			.	AF006386	CCDS420.1	1p35.1	2008-07-18	2006-09-04		ENSG00000163879	ENSG00000163879		"Axonemal dyneins"	14353	protein-coding gene	gene with protein product	"inner dynein arm, homolog of clamydomonas", "dJ423B22.5 (axonemal dynein light chain (hp28))"	602135	"dynein, axonemal, light intermediate polypeptide 1"			9284741	Standard	NM_003462		Approved	P28, hp28, dJ423B22.5	uc001cbj.3	O14645	OTTHUMG00000004222	ENST00000296218.7:c.752_754delAGA	1.37:g.38027794_38027796delAGA	ENSP00000296218:p.Lys253del	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	110	56	NM_003462	0	0	0	0	0	A8K387|B4DHN6|Q05BL9|Q5HYE2|Q5TGH0|Q7L0I5	In_Frame_Del	DEL	ENST00000296218.7	37	CCDS420.1																																																																																			.		0.567	DNALI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012159.1	NM_003462		-	38027793	AGA	-	38027791	7	5	54	1	0	1	0	1	0	0	0	0	4670	304	11	0	770	0	DNALI1	1	38027791	In_Frame_Del	DEL	AGA	TCGA-B9-A44B-01A-11D-A25F-10	13186837	38027791	211222830	6	5176											
KIAA0494	9813	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	47144193	47144194	+	Frame_Shift_Del	DEL	AA	AA	-																															cttccatctccatcggaatcAaatgctctcaagctctctgg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:47144193_47144194delAA	ENST00000371933.3	-	11	2403_2404	c.1427_1428delTT	c.(1426-1428)tttfs	p.F476fs	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14_ENST00000544071.1_Intron	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	476	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										CATCGGAATCAAATGCTCTCAA	0.475																																					p.476_476del		.											.	.	0			c.1427_1428del						.																																			SO:0001589	frameshift_variant	9813	exon11			.	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1427_1428delTT	1.37:g.47144193_47144194delAA	ENSP00000361001:p.Phe476fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	56	21	NM_014774	0	0	0	0	0	D3DQ23|Q5SXB8	Frame_Shift_Del	DEL	ENST00000371933.3	37	CCDS30706.1																																																																																			.		0.475	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		-	47144194	AA	-	47144193	7	5	54	1	0	1	0	1	0	0	0	0	8200	127	5	0	63	0	KIAA0494	1	47144193	Frame_Shift_Del	DEL	AA	TCGA-B9-A44B-01A-11D-A25F-10	9116402	47144193	202106428	7	5177											
SLC44A3	126969	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	95360468	95360468	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggaacagaactccaggccaTtgtgagatagatacccattt	13	9	10	9	0	0	3	0	1	0	3	1	5	1	4	3	2	3	0	3	2	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:95360468T>C	ENST00000271227.6	+	15	2054	c.1952T>C	c.(1951-1953)aTt>aCt	p.I651T	SLC44A3_ENST00000532427.1_Missense_Mutation_p.I571T|SLC44A3_ENST00000529450.1_Missense_Mutation_p.I618T|SLC44A3_ENST00000467909.1_Missense_Mutation_p.I603T|SLC44A3_ENST00000446120.2_Missense_Mutation_p.I615T|SLC44A3_ENST00000527077.1_Missense_Mutation_p.I583T	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	651					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	CTCCAGGCCATTGTGAGATAG	0.403																																					p.I651T		.											.	SLC44A3-91	0			c.T1952C						.						93	83	87					1																	95360468		2203	4300	6503	SO:0001583	missense	126969	exon15			AGGCCATTGTGAG	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1952T>C	1.37:g.95360468T>C	ENSP00000271227:p.Ile651Thr	Somatic	295	0		WXS	Illumina HiSeq	Phase_I	294	58	NM_001114106	0	0	38	53	15	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	T	9.568	1.120299	0.20877	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427;ENST00000532670	T;T;T;T;T;T	0.20069	2.58;2.78;2.1;2.1;2.59;2.11	5.91	2.35	0.29111	.	1.131400	0.06831	N	0.793947	T	0.04861	0.0131	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.001	T	0.44574	-0.9319	10	0.72032	D	0.01	-0.1874	9.3576	0.38175	0.0:0.1722:0.0:0.8278	.	571;615;583;618;651	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	T	615;651;583;618;603;571;107	ENSP00000389143:I615T;ENSP00000271227:I651T;ENSP00000433641:I583T;ENSP00000431836:I618T;ENSP00000432789:I603T;ENSP00000436661:I571T	ENSP00000271227:I651T	I	+	2	0	SLC44A3	95133056	0.132000	0.22450	0.000000	0.03702	0.004000	0.04260	1.121000	0.31283	0.153000	0.19213	0.454000	0.30748	ATT	.		0.403	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		C	95360468	T	C	95360468	3	2	54	1	0	0	0	0	1	0	0	0	14669	1493	52	3	2010	3	SLC44A3	1	95360468	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	48216275	95360468	153890153	8	5178											
ATXN7L2	127002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110029635	110029635	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cctcctggtgacagaaagaaGacatgggcccctcagcaagc	12	5	11	13	0	1	4	1	1	0	3	2	4	2	4	4	2	2	1	4	2	3	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:110029635G>C	ENST00000369870.3	+	4	320	c.305G>C	c.(304-306)aGa>aCa	p.R102T		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	102										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		ACAGAAAGAAGACATGGGCCC	0.547																																					p.R102T		.											.	ATXN7L2-92	0			c.G305C						.						28	34	32					1																	110029635		2203	4299	6502	SO:0001583	missense	127002	exon4			AAAGAAGACATGG	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.305G>C	1.37:g.110029635G>C	ENSP00000358886:p.Arg102Thr	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	130	17	NM_153340	0	0	0	0	0		Missense_Mutation	SNP	ENST00000369870.3	37	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.640777	0.67244	.	.	ENSG00000162650	ENST00000369870;ENST00000541125	T	0.29397	1.57	4.57	4.57	0.56435	.	0.000000	0.52532	D	0.000067	T	0.38931	0.1059	L	0.56199	1.76	0.80722	D	1	D	0.54601	0.967	D	0.63597	0.916	T	0.31251	-0.9950	10	0.72032	D	0.01	-7.5006	14.2772	0.66187	0.0:0.0:1.0:0.0	.	102	Q5T6C5	AT7L2_HUMAN	T	102	ENSP00000358886:R102T	ENSP00000358886:R102T	R	+	2	0	ATXN7L2	109831158	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.555000	0.73928	2.090000	0.63153	0.591000	0.81541	AGA	.		0.547	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		C	110029635	G	C	110029635	3	2	54	1	0	0	0	0	1	0	0	0	1218	942	33	4	319	4	ATXN7L2	1	110029635	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	14669167	110029635	139220986	9	5179											
CTTNBP2NL	55917	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	112999419	112999419	+	Frame_Shift_Del	DEL	G	G	-																															tcttcgccggtactcactaaGcgtttattggggtcatcagc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:112999419delG	ENST00000271277.6	+	6	1530	c.1305delG	c.(1303-1305)aagfs	p.K435fs		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	435					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTCACTAAGCGTTTATTGG	0.557																																					p.K435fs		.											.	CTTNBP2NL-92	0			c.1305delG						.						255	260	258					1																	112999419		2203	4300	6503	SO:0001589	frameshift_variant	55917	exon6			.	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1305delG	1.37:g.112999419delG	ENSP00000271277:p.Lys435fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	142	88	NM_018704	0	0	0	0	0	B3KMS5|Q96B40	Frame_Shift_Del	DEL	ENST00000271277.6	37	CCDS845.1																																																																																			.		0.557	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		-	112999419	G	-	112999419	7	5	54	1	0	1	0	1	0	0	0	0	4052	962	34	0	1319	0	CTTNBP2NL	1	112999419	Frame_Shift_Del	DEL	G	TCGA-B9-A44B-01A-11D-A25F-10	2969784	112999419	136251202	10	5180											
CELF3	11189	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151688462	151688462	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccagatgcctcgggatctgcCccacaaacagcttgatggca	10	7	10	14	1	1	2	0	1	1	1	2	3	1	3	4	2	4	2	4	2	1	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:151688462C>T	ENST00000290583.4	-	1	828	c.35G>A	c.(34-36)gGg>gAg	p.G12E	CELF3_ENST00000290585.4_Missense_Mutation_p.G12E|AL589765.1_ENST00000442233.2_Intron|RIIAD1_ENST00000326413.3_Intron	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	12	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						CGGGATCTGCCCCACAAACAG	0.607																																					p.G12E													.	CELF3-91	0			c.G35A						.						84	74	77					1																	151688462		2203	4300	6503	SO:0001583	missense	11189	exon1			ATCTGCCCCACAA	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.35G>A	1.37:g.151688462C>T	ENSP00000290583:p.Gly12Glu	Somatic	139	1		WXS	Illumina HiSeq	Phase_I	145	95	NM_007185	0	0	0	0	0	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520584	0.85495	.	.	ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000368833	T;T	0.80566	-1.39;2.01	4.88	4.88	0.63580	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.	.	.	.	D	0.92140	0.7508	H	0.95982	3.75	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.94117	0.7376	9	0.87932	D	0	.	15.6407	0.76997	0.0:1.0:0.0:0.0	.	12;12;12;12	Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	E	12	ENSP00000290585:G12E;ENSP00000290583:G12E	ENSP00000290583:G12E	G	-	2	0	CELF3	149955086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.255000	0.78338	2.558000	0.86282	0.478000	0.44815	GGG	.		0.607	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		T	151688462	C	T	151688462	3	4	54	1	0	0	0	0	1	0	0	0	3223	623	22	2	1418	2	CELF3	1	151688462	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	38689043	151688462	97562159	11	5181											
MRPL24	79590	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156707893	156707893	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actagggatcatggttccccGgtaatccatggtcttgccaa	9	11	10	11	1	2	0	1	0	1	0	4	1	4	1	4	4	1	2	4	4	3	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:156707893G>A	ENST00000361531.2	-	4	449	c.313C>T	c.(313-315)Cgg>Tgg	p.R105W	MRPL24_ENST00000478899.1_5'UTR|MRPL24_ENST00000368211.4_Missense_Mutation_p.R105W			Q96A35	RM24_HUMAN	mitochondrial ribosomal protein L24	105					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(1)|lung(4)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ATGGTTCCCCGGTAATCCATG	0.572																																					p.R105W													.	MRPL24-90	0			c.C313T						.						92	91	92					1																	156707893		2203	4300	6503	SO:0001583	missense	79590	exon4			TTCCCCGGTAATC	AB051341	CCDS1155.1	1q23.1	2012-11-14			ENSG00000143314	ENSG00000143314		"Mitochondrial ribosomal proteins / large subunits"	14037	protein-coding gene	gene with protein product		611836					Standard	NM_145729		Approved	MRP-L18	uc001fpx.1	Q96A35	OTTHUMG00000041296	ENST00000361531.2:c.313C>T	1.37:g.156707893G>A	ENSP00000354525:p.Arg105Trp	Somatic	344	1		WXS	Illumina HiSeq	Phase_I	371	70	NM_145729	0	0	122	156	34	D3DVC8|Q53G65|Q53HT0|Q5SYZ9|Q5SZ00|Q5SZ02|Q96Q70|Q9H7G3	Missense_Mutation	SNP	ENST00000361531.2	37	CCDS1155.1	.	.	.	.	.	.	.	.	.	.	G	9.204	1.029302	0.19512	.	.	ENSG00000143314	ENST00000361531;ENST00000368211;ENST00000434558	.	.	.	5.44	4.53	0.55603	Translation protein SH3-like (1);Ribosomal protein L24, SH3-like (1);	0.188218	0.46758	D	0.000276	T	0.39835	0.1093	M	0.85197	2.74	0.21553	N	0.999647	B	0.11235	0.004	B	0.06405	0.002	T	0.42999	-0.9418	9	0.72032	D	0.01	-4.2736	9.1512	0.36965	0.0972:0.0:0.9028:0.0	.	105	Q96A35	RM24_HUMAN	W	105	.	ENSP00000354525:R105W	R	-	1	2	MRPL24	154974517	0.989000	0.36119	0.452000	0.26994	0.186000	0.23388	2.276000	0.43408	2.565000	0.86533	0.557000	0.71058	CGG	.		0.572	MRPL24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098955.1	NM_145729		A	156707893	G	A	156707893	3	1	54	1	0	0	0	0	1	0	0	0	9815	1115	39	1	349	1	MRPL24	1	156707893	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	5019431	156707893	92542728	12	5182											
C1orf125	126859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	179460842	179460842	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcgattgaactgacaaggaAgttgtaccaatactccagct	13	10	9	9	1	0	2	0	2	0	0	1	4	1	3	2	1	5	3	2	1	6	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:179460842A>C	ENST00000367618.3	+	19	2648	c.2261A>C	c.(2260-2262)aAg>aCg	p.K754T		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	754										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						CTGACAAGGAAGTTGTACCAA	0.423																																					p.K754T		.											.	AXDND1-93	0			c.A2261C						.						162	155	158					1																	179460842		2203	4300	6503	SO:0001583	missense	126859	exon19			CAAGGAAGTTGTA	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2261A>C	1.37:g.179460842A>C	ENSP00000356590:p.Lys754Thr	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	309	52	NM_144696	0	0	0	0	0	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	A	8.397	0.841178	0.16891	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.27256	1.68;1.68	5.5	-3.94	0.04130	.	0.252664	0.37393	N	0.002104	T	0.15609	0.0376	L	0.60455	1.87	0.09310	N	1	B;B	0.22800	0.028;0.075	B;B	0.17098	0.01;0.017	T	0.11518	-1.0584	10	0.35671	T	0.21	-0.2597	1.2029	0.01889	0.2479:0.137:0.3481:0.2669	.	712;754	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	T	754;712;688	ENSP00000356590:K754T;ENSP00000391716:K688T	ENSP00000353471:K712T	K	+	2	0	AXDND1	177727465	0.109000	0.22037	0.000000	0.03702	0.156000	0.22039	-0.033000	0.12246	-0.147000	0.11254	-0.326000	0.08463	AAG	.		0.423	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179460842	A	C	179460842	3	2	54	1	0	0	0	0	1	0	0	0	1999	72	3	5	2331	5	C1orf125	1	179460842	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	22752949	179460842	69789779	13	5183											
ZNF648	127665	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	182026912	182026918	+	Frame_Shift_Del	DEL	TTCCTCT	TTCCTCT	-																															gaggagtcagagaatttctcTtcctctttgcccagtggatg																								rs145733361	byFrequency	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TTCCTCT	TTCCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:182026912_182026918delTTCCTCT	ENST00000339948.3	-	2	435_441	c.228_234delAGAGGAA	c.(226-234)aaagaggaafs	p.KEE76fs		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E77D(1)		breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						AGAATTTCTCTTCCTCTTTGCCCAGTG	0.56																																					p.76_78del	NSCLC(71;908 1374 5429 20458 35642)	.											.	ZNF648-91	1	Substitution - Missense(1)	large_intestine(1)	c.228_234del						.																																			SO:0001589	frameshift_variant	127665	exon2			.	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"Zinc fingers, C2H2-type"	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.228_234delAGAGGAA	1.37:g.182026912_182026918delTTCCTCT	ENSP00000344129:p.Lys76fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	160	31	NM_001009992	0	0	0	0	0	B2RP16	Frame_Shift_Del	DEL	ENST00000339948.3	37	CCDS30952.1																																																																																			.		0.56	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		-	182026918	TTCCTCT	-	182026912	7	5	54	1	0	1	0	1	0	0	0	0	18095	1606	56	0	1476	0	ZNF648	1	182026912	Frame_Shift_Del	DEL	TTCCTCT	TCGA-B9-A44B-01A-11D-A25F-10	2566070	182026912	67223709	14	5184											
ZNF281	23528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	200376815	200376815	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggatttttcaaaagcctgTtggaggtatttggagtattc	9	16	12	4	0	1	0	1	0	0	0	2	3	1	3	1	4	1	3	1	4	4	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:200376815T>C	ENST00000294740.3	-	2	2143	c.2019A>G	c.(2017-2019)caA>caG	p.Q673Q	ZNF281_ENST00000367352.3_Silent_p.Q637Q|ZNF281_ENST00000367353.1_Silent_p.Q673Q	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	673					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						CAAAAGCCTGTTGGAGGTATT	0.398																																					p.Q673Q		.											.	ZNF281-154	0			c.A2019G						.						118	130	126					1																	200376815		2203	4300	6503	SO:0001819	synonymous_variant	23528	exon2			AGCCTGTTGGAGG	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.2019A>G	1.37:g.200376815T>C		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	66	13	NM_012482	0	0	1	1	0	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	37	CCDS1402.1																																																																																			.		0.398	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		C	200376815	T	C	200376815	2	2	54	1	0	0	0	0	0	0	0	1	17850	1722	60	3		3	ZNF281	1	200376815	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	18349903	200376815	48873806	15	5185											
HS1BP3	64342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	20818857	20818857	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgcggcttctgctgcccagCcacagcttcagccgggcccg	4	7	12	18	3	2	0	1	0	1	0	2	0	2	0	4	2	6	3	4	2	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:20818857C>G	ENST00000304031.3	-	7	1094	c.1069G>C	c.(1069-1071)Gct>Cct	p.A357P		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	357							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTGCCCAGCCACAGCTTCA	0.622																																					p.A357P		.											.	HS1BP3-91	0			c.G1069C						.						86	96	93					2																	20818857		2203	4300	6503	SO:0001583	missense	64342	exon7			GCCCAGCCACAGC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.1069G>C	2.37:g.20818857C>G	ENSP00000305193:p.Ala357Pro	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	210	93	NM_022460	0	0	84	149	65	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	37	CCDS1700.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.376332	0.42105	.	.	ENSG00000118960	ENST00000304031	T	0.19532	2.14	5.64	0.323	0.15893	.	1.521430	0.04126	N	0.317110	T	0.17280	0.0415	L	0.39898	1.24	0.09310	N	0.999997	B	0.10296	0.003	B	0.09377	0.004	T	0.29852	-0.9998	10	0.51188	T	0.08	-2.0508	3.1138	0.06367	0.2876:0.3492:0.2805:0.0827	.	357	Q53T59	H1BP3_HUMAN	P	357	ENSP00000305193:A357P	ENSP00000305193:A357P	A	-	1	0	HS1BP3	20682338	0.000000	0.05858	0.000000	0.03702	0.388000	0.30384	0.116000	0.15561	0.037000	0.15575	0.655000	0.94253	GCT	.		0.622	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		G	20818857	C	G	20818857	3	3	54	1	0	0	0	0	1	0	0	0	7382	739	26	4	113	4	HS1BP3	2	20818857	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		20818857	222380516	16	5186											
CCDC121	79635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27850548	27850548	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgttagtcaggtattccAgaaagaatctgttttcagcc	10	16	8	7	0	3	2	2	0	1	2	4	2	4	2	2	1	1	3	2	1	4	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:27850548A>G	ENST00000324364.3	-	2	299	c.119T>C	c.(118-120)cTg>cCg	p.L40P	GPN1_ENST00000458167.2_5'Flank|GPN1_ENST00000515877.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_Intron|GPN1_ENST00000407583.3_5'Flank|CCDC121_ENST00000394775.3_Missense_Mutation_p.L202P|GPN1_ENST00000424214.1_5'Flank|GPN1_ENST00000264718.3_5'Flank|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000503738.1_5'Flank	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121	40										breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					CAGGTATTCCAGAAAGAATCT	0.418																																					p.L202P		.											.	CCDC121-68	0			c.T605C						.						115	120	119					2																	27850548		2203	4300	6503	SO:0001583	missense	79635	exon2			TATTCCAGAAAGA	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.119T>C	2.37:g.27850548A>G	ENSP00000339087:p.Leu40Pro	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	129	39	NM_001142683	0	0	0	1	1	B3KW66|J3KQZ8|Q9H8G6	Missense_Mutation	SNP	ENST00000324364.3	37	CCDS1759.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.174659	0.57692	.	.	ENSG00000176714	ENST00000324364;ENST00000394775	T;T	0.48201	0.82;0.82	5.09	1.14	0.20703	.	0.656444	0.13268	N	0.400745	T	0.62502	0.2433	M	0.70275	2.135	0.09310	N	0.999997	D	0.76494	0.999	D	0.70016	0.967	T	0.51663	-0.8677	10	0.72032	D	0.01	-22.9356	8.2278	0.31579	0.5274:0.0:0.0:0.4726	.	40	Q6ZUS5	CC121_HUMAN	P	40;202	ENSP00000339087:L40P;ENSP00000412150:L202P	ENSP00000339087:L40P	L	-	2	0	CCDC121	27704052	0.720000	0.27996	0.001000	0.08648	0.370000	0.29829	1.010000	0.29898	-0.057000	0.13199	0.482000	0.46254	CTG	.		0.418	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		G	27850548	A	G	27850548	3	3	54	1	0	0	0	0	1	0	0	0	2763	188	7	3	721	3	CCDC121	2	27850548	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	7031691	27850548	215348825	17	5187											
ALK	238	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	29420473	29420473	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacaaactccagaacttcCtggttgcttttgctggggta	8	13	11	9	0	0	2	0	1	0	1	2	2	2	2	2	3	4	4	2	3	3	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:29420473C>A	ENST00000389048.3	-	27	4914	c.4008G>T	c.(4006-4008)caG>caT	p.Q1336H	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1336	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CCAGAACTTCCTGGTTGCTTT	0.507			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.Q1336H		.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK-3833	0			c.G4008T						.						92	96	95					2																	29420473		2203	4300	6503	SO:0001583	missense	238	exon27	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AACTTCCTGGTTG	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"CD molecules"	427	protein-coding gene	gene with protein product		105590	"anaplastic lymphoma kinase (Ki-1)"			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4008G>T	2.37:g.29420473C>A	ENSP00000373700:p.Gln1336His	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	82	37	NM_004304	0	0	0	0	0	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093137	0.76756	.	.	ENSG00000171094	ENST00000389048	D	0.82984	-1.67	5.8	4.0	0.46444	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.44688	U	0.000424	D	0.84383	0.5460	L	0.31578	0.945	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.81876	-0.0731	9	.	.	.	.	12.0878	0.53708	0.0:0.8616:0.0:0.1384	.	1336	Q9UM73	ALK_HUMAN	H	1336	ENSP00000373700:Q1336H	.	Q	-	3	2	ALK	29273977	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.181000	0.42547	0.788000	0.33755	0.561000	0.74099	CAG	.		0.507	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29420473	C	A	29420473	3	1	54	1	0	0	0	0	1	0	0	0	525	680	24	4	866	4	ALK	2	29420473	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	1569925	29420473	213778900	18	5188											
LOC285033	285033	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	96906416	96906416	+	RNA	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acactcctgcttccttccttCcctgcagttggtgagtatct	5	15	7	14	0	1	1	0	1	1	0	5	1	5	1	4	1	2	4	4	1	1	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:96906416C>A	ENST00000446816.1	+	0	799																											TTCCTTCCTTCCCTGCAGTTG	0.552																																					.													.	.	0			.						.						40	42	41					2																	96906416		2004	4194	6198			0	.			TTCCTTCCCTGCA																													2.37:g.96906416C>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	44	14	.	0	0	0	0	0		RNA	SNP	ENST00000446816.1	37																																																																																				.		0.552	AC012307.3-001	KNOWN	basic|exp_conf	antisense	processed_transcript	OTTHUMT00000338796.1			A	96906416	C	A	96906416	1	1	54	0	1	0	0	0	0	0	0	0	8898	855	30	4		4	LOC285033	2	96906416	RNA	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	67485943	96906416	146292957	19	5189											
RGPD3	653489	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	107073432	107073432	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttgtttgtttacctttaGtttataaattgcaggacttc	8	21	7	5	0	0	0	0	0	0	0	1	1	0	1	1	1	2	5	1	1	5	12			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:107073432G>A	ENST00000409886.3	-	4	487	c.400C>T	c.(400-402)Cta>Tta	p.L134L	RGPD3_ENST00000304514.7_Silent_p.L134L	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	134					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTTACCTTTAGTTTATAAATT	0.333																																					p.L134L		.											.	RGPD3-23	0			c.C400T						.						9	21	17					2																	107073432		628	1473	2101	SO:0001819	synonymous_variant	653489	exon4			CCTTTAGTTTATA		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"Tetratricopeptide (TTC) repeat domain containing"	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.400C>T	2.37:g.107073432G>A		Somatic	342	0		WXS	Illumina HiSeq	Phase_I	384	132	NM_001144013	0	0	0	0	0	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			.		0.333	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		A	107073432	G	A	107073432	2	1	54	1	0	0	0	0	0	0	0	1	13319	1020	36	2		2	RGPD3	2	107073432	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	10167016	107073432	136125941	20	5190											
RABL2A	11159	broad.mit.edu	37	chr2	114391751	114391751	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccacagcagctgtccacGtacgccctgaccctgtacaa	10	6	8	17	2	0	1	0	1	0	0	1	1	1	1	4	0	5	4	4	0	3	2	rs551772490		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:114391751G>A	ENST00000393167.3	+	4	384	c.159G>A	c.(157-159)acG>acA	p.T53T	RABL2A_ENST00000393165.3_Silent_p.T53T|RABL2A_ENST00000409875.1_Silent_p.T53T|RABL2A_ENST00000409842.1_Silent_p.T53T|RABL2A_ENST00000393166.3_Silent_p.T53T|RABL2A_ENST00000376439.3_Silent_p.T53T	NM_013412.2	NP_038198.1	Q9UBK7	RBL2A_HUMAN	RAB, member of RAS oncogene family-like 2A	53					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|stomach(3)	9						AGCTGTCCACGTACGCCCTGA	0.537													G|||	1	0.000199681	0	0	5008	,	,		20415	0		0	False		,,,				2504	0.001				p.T53T													.	RABL2A-86	0			c.G159A						.						84	50	61					2																	114391751		2203	4297	6500	SO:0001819	synonymous_variant	11159	exon4			GTCCACGTACGCC		CCDS2118.1	2q13	2014-05-09			ENSG00000144134	ENSG00000144134		"RAB, member RAS oncogene"	9799	protein-coding gene	gene with protein product		605412				10444334	Standard	NM_007082		Approved		uc010flb.3	Q9UBK7	OTTHUMG00000047828	ENST00000393167.3:c.159G>A	2.37:g.114391751G>A		Somatic	181	0		WXS	Illumina HiSeq	Phase_I	215	7	NM_013412	0	0	33	34	1	B7ZBD6|Q9NU37	Silent	SNP	ENST00000393167.3	37	CCDS2118.1																																																																																			.		0.537	RABL2A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000109047.2			A	114391751	G	A	114391751	2	1	54	1	0	0	0	0	0	0	0	1	13002	1132	40	1		1	RABL2A	2	114391751	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	7318319	114391751	128807622	21	5191											
SCN2A	6326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	166153545	166153545	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacgtttatagtattgaatAaagggaaagcaatctctcga	16	11	9	5	2	1	2	0	1	1	1	3	4	1	3	0	1	1	3	0	1	8	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:166153545A>T	ENST00000375437.2	+	3	576	c.286A>T	c.(286-288)Aaa>Taa	p.K96*	SCN2A_ENST00000375427.2_Nonsense_Mutation_p.K96*|SCN2A_ENST00000283256.6_Nonsense_Mutation_p.K96*|SCN2A_ENST00000357398.3_Nonsense_Mutation_p.K96*	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	96					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGTATTGAATAAAGGGAAAGC	0.289																																					p.K96X		.											.	SCN2A-142	0			c.A286T						.						58	56	57					2																	166153545		2203	4298	6501	SO:0001587	stop_gained	6326	exon2			TTGAATAAAGGGA	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.286A>T	2.37:g.166153545A>T	ENSP00000364586:p.Lys96*	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	200	105	NM_001040143	0	0	0	0	0	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Nonsense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	38	6.708516	0.97780	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	.	.	.	5.32	5.32	0.75619	.	0.077674	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5789	0.76418	1.0:0.0:0.0:0.0	.	.	.	.	X	96	.	ENSP00000283256:K96X	K	+	1	0	SCN2A	165861791	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.801000	0.55545	2.151000	0.67156	0.482000	0.46254	AAA	.		0.289	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166153545	A	T	166153545	4	4	54	1	0	0	0	0	0	1	0	0	13948	363	13	5	292	5	SCN2A	2	166153545	Nonsense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	51761794	166153545	77045828	22	5192											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170055306	170055306	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttactcactgcaataagtAgggttttcatcactgttatc	10	16	6	9	0	4	0	3	0	1	0	5	0	4	0	0	1	2	4	0	1	5	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:170055306A>G	ENST00000263816.3	-	45	8853	c.8568T>C	c.(8566-8568)ccT>ccC	p.P2856P		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2856	LDL-receptor class A 19. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	TGCAATAAGTAGGGTTTTCAT	0.383																																					p.P2856P		.											.	LRP2-175	0			c.T8568C						.						155	142	147					2																	170055306		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon45			ATAAGTAGGGTTT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8568T>C	2.37:g.170055306A>G		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	149	49	NM_004525	0	0	0	0	0	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			.		0.383	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170055306	A	G	170055306	2	3	54	1	0	0	0	0	0	0	0	1	8981	407	15	3		3	LRP2	2	170055306	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	3901761	170055306	73144067	23	5193											
PGAP1	80055	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197784853	197784853	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcgggatagcgttttgccaGtttctttggaagttctattt	6	18	11	6	2	2	0	0	0	2	0	2	2	2	2	1	2	3	3	1	2	3	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:197784853G>T	ENST00000354764.4	-	2	283	c.169C>A	c.(169-171)Ctg>Atg	p.L57M	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409475.1_Missense_Mutation_p.L57M|PGAP1_ENST00000409188.1_Missense_Mutation_p.L15M	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	57					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						CGTTTTGCCAGTTTCTTTGGA	0.343																																					p.L57M		.											.	PGAP1-93	0			c.C169A						.						120	125	123					2																	197784853		2203	4300	6503	SO:0001583	missense	80055	exon2			TTGCCAGTTTCTT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.169C>A	2.37:g.197784853G>T	ENSP00000346809:p.Leu57Met	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	56	28	NM_024989	0	0	0	0	0	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.258007	0.59321	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	.	.	.	5.11	3.32	0.38043	.	0.237063	0.36519	N	0.002555	T	0.33847	0.0877	L	0.29908	0.895	0.27991	N	0.935656	D;D	0.71674	0.958;0.998	P;P	0.59221	0.66;0.854	T	0.13202	-1.0518	9	0.35671	T	0.21	-5.081	2.3431	0.04264	0.1595:0.2325:0.4637:0.1442	.	57;57	Q75T13-3;Q75T13	.;PGAP1_HUMAN	M	57;57;15	.	ENSP00000346809:L57M	L	-	1	2	PGAP1	197493098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.666000	0.37460	0.852000	0.35287	0.655000	0.94253	CTG	.		0.343	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		T	197784853	G	T	197784853	3	4	54	1	0	0	0	0	1	0	0	0	11803	1020	36	4	2703	4	PGAP1	2	197784853	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	27729547	197784853	45414520	24	5194											
COL6A3	1293	broad.mit.edu;bcgsc.ca	37	chr2	238275565	238275565	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcctgtgcatcttccacCgactttcctcccgtgatcac	7	12	5	17	2	2	1	1	1	1	0	6	2	6	1	5	0	1	1	5	0	0	2	rs140699766		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:238275565C>T	ENST00000295550.4	-	11	5717	c.5265G>A	c.(5263-5265)tcG>tcA	p.S1755S	COL6A3_ENST00000409809.1_Silent_p.S1549S|COL6A3_ENST00000472056.1_Silent_p.S1148S|COL6A3_ENST00000346358.4_Silent_p.S1555S|COL6A3_ENST00000347401.3_Silent_p.S1554S|COL6A3_ENST00000353578.4_Silent_p.S1549S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1755	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S1755S(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CATCTTCCACCGACTTTCCTC	0.582													C|||	1	0.000199681	0	0	5008	,	,		20328	0		0	False		,,,				2504	0.001				p.S1755S													.	COL6A3-526	1	Substitution - coding silent(1)	large_intestine(1)	c.G5265A						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	79	81	80		5265,3444,4647	-5.6	0.7	2	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	1755/3178,1148/2571,1549/2972	238275565	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon11			TTCCACCGACTTT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5265G>A	2.37:g.238275565C>T		Somatic	196	1		WXS	Illumina HiSeq	Phase_I	266	10	NM_004369	0	0	3	3	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|1.000;T|0.000		0.582	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238275565	C	T	238275565	2	4	54	1	0	0	0	0	0	0	0	1	3707	639	23	1		1	COL6A3	2	238275565	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	40490712	238275565	4923808	25	5195											
FARP2	9855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242407764	242407764	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgcggacattacagcccCgggcaccatgactacgctga	10	7	10	14	3	0	2	0	2	0	0	0	3	0	3	3	2	4	2	3	2	3	3	rs138469271		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:242407764C>G	ENST00000264042.3	+	18	2273	c.2103C>G	c.(2101-2103)ccC>ccG	p.P701P		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	701	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		ATTACAGCCCCGGGCACCATG	0.637																																					p.P701P		.											.	FARP2-93	0			c.C2103G						.						42	36	38					2																	242407764		2203	4300	6503	SO:0001819	synonymous_variant	9855	exon18			CAGCCCCGGGCAC	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.2103C>G	2.37:g.242407764C>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	93	36	NM_014808	0	0	0	1	1	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	37	CCDS33424.1																																																																																			C|1.000;T|0.000		0.637	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			G	242407764	C	G	242407764	2	3	54	1	0	0	0	0	0	0	0	1	5696	639	23	4		4	FARP2	2	242407764	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4132199	242407764	791609	26	5196											
MKRN2	23609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	12611673	12611673	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtcctcaccctccttccgagGtcactgcatccattgtgaaa	8	11	7	15	1	2	1	2	1	0	0	6	2	6	1	5	1	1	1	5	1	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:12611673G>A	ENST00000170447.7	+	3	396	c.259G>A	c.(259-261)Gtc>Atc	p.V87I	MKRN2_ENST00000411987.1_Missense_Mutation_p.V44I|MKRN2_ENST00000448482.1_Missense_Mutation_p.V85I	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	87					protein ubiquitination (GO:0016567)	intracellular (GO:0005622)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)	16						TCCTTCCGAGGTCACTGCATC	0.547																																					p.V87I		.											.	MKRN2-90	0			c.G259A						.						97	82	87					3																	12611673		2203	4300	6503	SO:0001583	missense	23609	exon3			TCCGAGGTCACTG		CCDS33702.1, CCDS63545.1	3p25	2008-08-13	2008-08-13		ENSG00000075975	ENSG00000075975		"RING-type (C3HC4) zinc fingers"	7113	protein-coding gene	gene with protein product		608426				11597136	Standard	NM_014160		Approved	RNF62, HSPC070	uc003bxd.4	Q9H000	OTTHUMG00000155371	ENST00000170447.7:c.259G>A	3.37:g.12611673G>A	ENSP00000170447:p.Val87Ile	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	83	77	NM_014160	0	0	0	2	2	A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Missense_Mutation	SNP	ENST00000170447.7	37	CCDS33702.1	.	.	.	.	.	.	.	.	.	.	G	2.117	-0.402351	0.04865	.	.	ENSG00000075975	ENST00000170447;ENST00000411987;ENST00000448482	T;T;T	0.22539	2.79;1.96;1.95	5.53	-1.17	0.09648	.	0.892392	0.09710	N	0.765804	T	0.05686	0.0149	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.35773	-0.9775	10	0.33141	T	0.24	.	4.2105	0.10509	0.361:0.332:0.2385:0.0685	.	44;85;87	B4DPR4;C9J494;Q9H000	.;.;MKRN2_HUMAN	I	87;44;85	ENSP00000170447:V87I;ENSP00000396340:V44I;ENSP00000397983:V85I	ENSP00000170447:V87I	V	+	1	0	MKRN2	12586673	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.048000	0.14078	0.001000	0.14605	-0.311000	0.09066	GTC	.		0.547	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160		A	12611673	G	A	12611673	3	1	54	1	0	0	0	0	1	0	0	0	9632	1261	44	2	269	2	MKRN2	3	12611673	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		12611673	185410757	27	5197											
RPSA	3921	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	39453553	39453556	+	Splice_Site	DEL	GTAT	GTAT	-																															tattcagcaattccctactgGtatgtatcaggatagaggtg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	GTAT	GTAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:39453553_39453556delGTAT	ENST00000301821.6	+	6	902		c.e6+1		SNORA62_ENST00000365493.1_RNA|RPSA_ENST00000443003.1_Splice_Site|RPSA_ENST00000478027.1_Splice_Site	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		TTCCCTACTGGTATGTATCAGGAT	0.431																																					.		.											.	RPSA-278	0			.						.																																			SO:0001630	splice_region_variant	3921	.			.	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"laminin receptor 1 (67kD, ribosomal protein SA)"	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.793+1GTAT>-	3.37:g.39453557_39453560delGTAT		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	23	17	.	0	0	0	0	0		Splice_Site	DEL	ENST00000301821.6	37	CCDS2686.1																																																																																			.		0.431	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295	Intron	-	39453556	GTAT	-	39453553	8	5	54	1	0	1	0	1	0	0	1	0	13695	1275	44	0	812	0	RPSA	3	39453553	Splice_Site	DEL	GTAT	TCGA-B9-A44B-01A-11D-A25F-10	26841880	39453553	158568877	28	5198											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	47163966	47163967	+	Frame_Shift_Ins	INS	-	-	C																															acctactaatattctgaaatINSccatttgatgaaagcatgca																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:47163966_47163967insC	ENST00000409792.3	-	3	2201_2202	c.2159_2160insG	c.(2158-2160)ggafs	p.G720fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	720					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TATTCTGAAATCCATTTGATGA	0.391			"N, F, S, Mis"		clear cell renal carcinoma																																p.G720fs		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.2160_2161insG						.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2160dupG	3.37:g.47163968_47163968dupC	ENSP00000386759:p.Gly720fs	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	49	37	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.391	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47163967	-	C	47163966	7	5	54	1	0	1	1	0	0	0	0	0	14163	1422	50	0	5610	0	SETD2	3	47163966	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	7710413	47163966	150858464	29	5199											
POC1A	25886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52181040	52181040	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgagtggacacattcccggCtgctcttgtcccacagctta	8	10	9	14	2	1	0	0	0	1	0	3	2	3	1	2	2	2	3	2	2	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:52181040C>A	ENST00000296484.2	-	5	566	c.527G>T	c.(526-528)aGc>aTc	p.S176I	POC1A_ENST00000394970.2_Missense_Mutation_p.S176I|POC1A_ENST00000474012.1_Missense_Mutation_p.S138I	NM_015426.4	NP_056241.3	Q8NBT0	POC1A_HUMAN	POC1 centriolar protein A	176					cell projection organization (GO:0030030)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|large_intestine(4)|liver(1)|lung(4)|prostate(3)|skin(1)	14						ACATTCCCGGCTGCTCTTGTC	0.592																																					p.S176I		.											.	POC1A-90	0			c.G527T						.						107	98	101					3																	52181040		2203	4300	6503	SO:0001583	missense	25886	exon5			TCCCGGCTGCTCT	AL117629	CCDS2846.1, CCDS54591.1, CCDS54592.1	3p21.2	2014-05-02	2013-08-21	2010-03-26	ENSG00000164087	ENSG00000164087		"WD repeat domain containing"	24488	protein-coding gene	gene with protein product		614783	"WD repeat domain 51A", "POC1 centriolar protein homolog A (Chlamydomonas)"	WDR51A		19109428, 22840364	Standard	NM_015426		Approved	DKFZP434C245	uc003dcu.3	Q8NBT0	OTTHUMG00000157817	ENST00000296484.2:c.527G>T	3.37:g.52181040C>A	ENSP00000296484:p.Ser176Ile	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	127	32	NM_015426	0	0	0	0	0	A4FUW4|E9PFC6|Q0VDF8|Q2TAK6|Q96IK6|Q9UFJ8	Missense_Mutation	SNP	ENST00000296484.2	37	CCDS2846.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831256	0.91036	.	.	ENSG00000164087	ENST00000296484;ENST00000394970;ENST00000474012	D;D;D	0.82803	-1.65;-1.65;-1.65	5.13	4.19	0.49359	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.041315	0.85682	D	0.000000	D	0.89160	0.6636	M	0.84082	2.675	0.80722	D	1	D;D	0.62365	0.974;0.991	P;P	0.56163	0.767;0.793	D	0.91017	0.4854	10	0.87932	D	0	.	15.0503	0.71862	0.0:0.8574:0.1426:0.0	.	176;176	Q8NBT0-2;Q8NBT0	.;POC1A_HUMAN	I	176;176;138	ENSP00000296484:S176I;ENSP00000378421:S176I;ENSP00000418968:S138I	ENSP00000296484:S176I	S	-	2	0	POC1A	52156080	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.074000	0.50065	2.555000	0.86185	0.563000	0.77884	AGC	.		0.592	POC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349685.1	NM_015426		A	52181040	C	A	52181040	3	1	54	1	0	0	0	0	1	0	0	0	12201	797	28	4	724	4	POC1A	3	52181040	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	5017074	52181040	145841390	30	5200											
STAB1	23166	hgsc.bcm.edu	37	chr3	52555670	52555671	+	Frame_Shift_Ins	INS	-	-	T																															ttgggggctctggctcctgcINSttctgtgatgaaggctggac																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:52555670_52555671insT	ENST00000321725.6	+	57	6193_6194	c.6117_6118insT	c.(6118-6120)ttcfs	p.F2040fs		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2040					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CTGGCTCCTGCTTCTGTGATGA	0.604																																					p.C2039fs		.											.	STAB1-139	0			c.6117_6118insT						.																																			SO:0001589	frameshift_variant	23166	exon57			.	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.6119dupT	3.37:g.52555672_52555672dupT	ENSP00000312946:p.Phe2040fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	92	14	NM_015136	0	0	0	0	0	A7E297|Q8IUH0|Q8IUH1|Q93072	Frame_Shift_Ins	INS	ENST00000321725.6	37	CCDS33768.1																																																																																			.		0.604	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52555671	-	T	52555670	7	5	54	1	0	1	1	0	0	0	0	0	15269	805	28	0	6343	0	STAB1	3	52555670	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	374630	52555670	145466760	31	5201											
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52637647	52637647	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttgtggtatagctgagtGccggtgaaagaagaatctct	10	13	13	5	1	1	4	0	2	1	2	2	4	1	4	1	2	2	3	1	2	5	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:52637647G>T	ENST00000296302.7	-	17	2670	c.2669C>A	c.(2668-2670)gCa>gAa	p.A890E	PBRM1_ENST00000409057.1_Missense_Mutation_p.A890E|PBRM1_ENST00000410007.1_Missense_Mutation_p.A890E|PBRM1_ENST00000394830.3_Missense_Mutation_p.A890E|PBRM1_ENST00000409767.1_Missense_Mutation_p.A905E|PBRM1_ENST00000337303.4_Missense_Mutation_p.A890E|PBRM1_ENST00000409114.3_Missense_Mutation_p.A905E|PBRM1_ENST00000356770.4_Missense_Mutation_p.A858E			Q86U86	PB1_HUMAN	polybromo 1	890					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ATAGCTGAGTGCCGGTGAAAG	0.338			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.A890E		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.C2669A						.						82	78	79					3																	52637647		2203	4299	6502	SO:0001583	missense	55193	exon18			CTGAGTGCCGGTG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2669C>A	3.37:g.52637647G>T	ENSP00000296302:p.Ala890Glu	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	32	28	NM_018313	0	0	1	2	1	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	33	5.240611	0.95240	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T;T	0.54675	0.67;0.59;0.71;0.66;0.68;0.56;1.14;0.67;0.69;0.97	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.76018	0.3929	M	0.80422	2.495	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;1.0;1.0;0.999;0.999;1.0	T	0.78237	-0.2282	10	0.87932	D	0	.	19.9278	0.97110	0.0:0.0:1.0:0.0	.	890;890;890;890;905;905;890;858;890	Q86U86-9;E7EVG2;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.;.	E	858;890;890;890;890;890;905;905;890;849	ENSP00000349213:A858E;ENSP00000378307:A890E;ENSP00000296302:A890E;ENSP00000338302:A890E;ENSP00000386593:A890E;ENSP00000386529:A890E;ENSP00000386643:A905E;ENSP00000386601:A905E;ENSP00000387775:A890E;ENSP00000397662:A849E	ENSP00000296302:A890E	A	-	2	0	PBRM1	52612687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.779000	0.99018	2.770000	0.95276	0.650000	0.86243	GCA	.		0.338	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52637647	G	T	52637647	3	4	54	1	0	0	0	0	1	0	0	0	11517	1319	46	4	2287	4	PBRM1	3	52637647	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	81977	52637647	145384783	32	5202											
SLMAP	7871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	57743531	57743531	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttttgattgcaaagtgctAtcaaggaaccacgctctcgt	11	12	8	10	2	2	1	1	1	1	0	3	2	2	2	1	1	3	3	1	1	4	4	rs147270008		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:57743531A>G	ENST00000428312.1	+	1	247	c.153A>G	c.(151-153)ctA>ctG	p.L51L	SLMAP_ENST00000449503.2_Silent_p.L51L|SLMAP_ENST00000295952.3_Silent_p.L51L|SLMAP_ENST00000295951.3_Silent_p.L51L|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000383718.3_Silent_p.L51L			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	51	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.|Necessary for targeting to centrosomes. {ECO:0000250}.				muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GCAAAGTGCTATCAAGGAACC	0.498																																					p.L51L		.											.	SLMAP-90	0			c.A153G						.	A		1,4405		0,1,2202	78	70	73		153	1.8	1	3	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	SLMAP	NM_007159.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		51/812	57743531	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7871	exon1			AGTGCTATCAAGG	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.153A>G	3.37:g.57743531A>G		Somatic	317	2		WXS	Illumina HiSeq	Phase_I	282	236	NM_007159	0	0	0	0	0	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37																																																																																				A|1.000;G|0.000		0.498	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		G	57743531	A	G	57743531	2	3	54	1	0	0	0	0	0	0	0	1	14781	436	16	3		3	SLMAP	3	57743531	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	5105884	57743531	140278899	33	5203											
THPO	7066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	184090635	184090635	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgttcaggtatccggggAtttggtccagggacctggag	6	11	15	9	1	1	0	1	0	0	0	4	3	4	3	4	6	0	2	4	6	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:184090635A>C	ENST00000204615.7	-	6	942	c.728T>G	c.(727-729)aTc>aGc	p.I243S	THPO_ENST00000445696.2_Missense_Mutation_p.I239S|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000477594.1_5'Flank|THPO_ENST00000421442.2_Missense_Mutation_p.N204K	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	243					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GTATCCGGGGATTTGGTCCAG	0.552																																					p.I243S		.											.	THPO-91	0			c.T728G						.						88	86	87					3																	184090635		2203	4300	6503	SO:0001583	missense	7066	exon6			CCGGGGATTTGGT		CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"Endogenous ligands"	11795	protein-coding gene	gene with protein product	"prepro-thrombopoietin", "megakaryocyte stimulating factor", "myeloproliferative leukemia virus oncogene ligand", "megakaryocyte growth and development factor", "MPL ligand", "megakaryocyte colony-stimulating factor", "c-mpl ligand", "thrombopoietin nirs variant 1"	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.728T>G	3.37:g.184090635A>C	ENSP00000204615:p.Ile243Ser	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	150	49	NM_000460	0	0	0	0	0	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	37	CCDS3265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.184|0.184	-1.059924|-1.059924	0.01950|0.01950	.|.	.|.	ENSG00000090534|ENSG00000090534	ENST00000204615;ENST00000445696;ENST00000353488|ENST00000421442	T;T|T	0.34859|0.36157	1.34;1.35|1.27	4.34|4.34	-1.07|-1.07	0.09968|0.09968	Four-helical cytokine, core (1);|.	1.174950|.	0.06383|.	N|.	0.715527|.	T|T	0.21718|0.21718	0.0523|0.0523	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B;B|B	0.24426|0.28291	0.103;0.063|0.206	B;B|B	0.25140|0.28139	0.058;0.026|0.086	T|T	0.23547|0.23547	-1.0185|-1.0185	10|9	0.66056|0.42905	D|T	0.02|0.14	-23.2862|-23.2862	3.8944|3.8944	0.09133|0.09133	0.3909:0.3883:0.2208:0.0|0.3909:0.3883:0.2208:0.0	.|.	239;243|204	P40225-2;P40225|F8W6L1	.;TPO_HUMAN|.	S|K	243;239;204|204	ENSP00000204615:I243S;ENSP00000410763:I239S|ENSP00000411704:N204K	ENSP00000204615:I243S|ENSP00000411704:N204K	I|N	-|-	2|3	0|2	THPO|THPO	185573329|185573329	0.002000|0.002000	0.14202|0.14202	0.093000|0.093000	0.20910|0.20910	0.720000|0.720000	0.41350|0.41350	-0.313000|-0.313000	0.08103|0.08103	0.205000|0.205000	0.20568|0.20568	0.378000|0.378000	0.23410|0.23410	ATC|AAT	.		0.552	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460		C	184090635	A	C	184090635	3	2	54	1	0	0	0	0	1	0	0	0	15904	333	12	5	337	5	THPO	3	184090635	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	126347104	184090635	13931795	34	5204											
EIF4A2	1974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186503770	186503770	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgaaatgcaaaaactgcaGgctgaagcaccacatattgt	17	8	8	8	0	0	2	0	2	0	0	0	2	0	2	1	1	4	4	1	1	6	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:186503770G>T	ENST00000323963.5	+	5	511	c.447G>T	c.(445-447)caG>caT	p.Q149H	EIF4A2_ENST00000356531.5_Missense_Mutation_p.Q54H|RP11-573D15.9_ENST00000577781.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.Q150H|SNORA63_ENST00000363450.1_RNA|SNORA63_ENST00000363548.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORA4_ENST00000584302.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	149	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		AAAAACTGCAGGCTGAAGCAC	0.393			T	BCL6	NHL																																p.Q149H		.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2-291	0			c.G447T						.						94	87	90					3																	186503770		2203	4300	6503	SO:0001583	missense	1974	exon5			ACTGCAGGCTGAA	D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"DEAD-boxes"	3284	protein-coding gene	gene with protein product		601102	"eukaryotic translation initiation factor 4A, isoform 2"	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.447G>T	3.37:g.186503770G>T	ENSP00000326381:p.Gln149His	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	149	34	NM_001967	0	0	32	39	7	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.761816	0.69763	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.04917	3.53;3.53;3.53	4.51	4.51	0.55191	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.40818	U	0.001006	T	0.15089	0.0364	L	0.45051	1.395	0.80722	D	1	D;P;P;P	0.67145	0.996;0.913;0.836;0.865	P;P;B;P	0.59115	0.852;0.71;0.382;0.516	T	0.00389	-1.1770	10	0.87932	D	0	-9.8507	15.0932	0.72211	0.0:0.0:1.0:0.0	.	5;54;150;149	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	H	149;150;54	ENSP00000326381:Q149H;ENSP00000398370:Q150H;ENSP00000348925:Q54H	ENSP00000326381:Q149H	Q	+	3	2	EIF4A2	187986464	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.890000	0.69774	2.497000	0.84241	0.650000	0.86243	CAG	.		0.393	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		T	186503770	G	T	186503770	3	4	54	1	0	0	0	0	1	0	0	0	5038	991	35	4	465	4	EIF4A2	3	186503770	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	2413135	186503770	11518660	35	5205											
SLC30A9	10463	bcgsc.ca	37	chr4	42051440	42051440	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcttgcctggatttataccGgttcagcaagtatgttctca	8	16	8	9	1	3	0	2	0	2	0	4	1	3	1	2	2	3	4	2	2	4	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr4:42051440G>T	ENST00000264451.7	+	9	964	c.784G>T	c.(784-786)Ggt>Tgt	p.G262C		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	262					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GATTTATACCGGTTCAGCAAG	0.318																																					p.G262C													.	SLC30A9-91	0			c.G784T						.						160	164	162					4																	42051440		2203	4299	6502	SO:0001583	missense	10463	exon9			TATACCGGTTCAG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.784G>T	4.37:g.42051440G>T	ENSP00000264451:p.Gly262Cys	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	68	4	NM_006345	0	0	3	3	0	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686311	0.88639	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.70516	-0.49	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.90167	0.6927	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91970	0.5586	10	0.87932	D	0	-13.3774	20.4745	0.99168	0.0:0.0:1.0:0.0	.	262	Q6PML9	ZNT9_HUMAN	C	262;90	ENSP00000264451:G262C	ENSP00000264451:G262C	G	+	1	0	SLC30A9	41746197	1.000000	0.71417	0.991000	0.47740	0.797000	0.45037	8.866000	0.92307	2.941000	0.99782	0.655000	0.94253	GGT	.		0.318	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			T	42051440	G	T	42051440	3	4	54	1	0	0	0	0	1	0	0	0	14594	1116	39	4	818	4	SLC30A9	4	42051440	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		42051440	149102836	36	5206											
TMPRSS11A	339967	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	68777111	68777111	+	Frame_Shift_Del	DEL	G	G	-																															cggtaataagtcacttgtgtGtagactccaggcttgtcctt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr4:68777111delG	ENST00000334830.7	-	10	1961	c.1215delC	c.(1213-1215)tacfs	p.Y405fs	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000396188.2_Frame_Shift_Del_p.Y402fs|TMPRSS11A_ENST00000508048.1_Frame_Shift_Del_p.Y401fs			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	405	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						TCACTTGTGTGTAGACTCCAG	0.408																																					p.Y405X	NSCLC(26;2 894 10941 14480 22546)	.											.	TMPRSS11A-69	0			c.1215delC						.						192	181	185					4																	68777111		2203	4300	6503	SO:0001589	frameshift_variant	339967	exon10			.	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1215delC	4.37:g.68777111delG	ENSP00000334611:p.Tyr405fs	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	163	70	NM_182606	0	0	0	0	0	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Nonsense_Mutation	DEL	ENST00000334830.7	37	CCDS3519.1																																																																																			.		0.408	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		-	68777111	G	-	68777111	7	5	54	1	0	1	0	1	0	0	0	0	16271	1372	48	0	54	0	TMPRSS11A	4	68777111	Frame_Shift_Del	DEL	G	TCGA-B9-A44B-01A-11D-A25F-10	26725671	68777111	122377165	37	5207	57	2									
TMPRSS11A	339967	bcgsc.ca	37	chr4	68777112	68777112	+	Missense_Mutation	SNP	T	T	A																															ggtaataagtcacttgtgtgTagactccaggcttgtccttt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr4:68777112T>A	ENST00000334830.7	-	10	1960	c.1214A>T	c.(1213-1215)tAc>tTc	p.Y405F	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.Y402F|TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.Y401F			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	405	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						CACTTGTGTGTAGACTCCAGG	0.413																																					p.Y405F	NSCLC(26;2 894 10941 14480 22546)												.	TMPRSS11A-69	0			c.A1214T						.						191	181	184					4																	68777112		2203	4300	6503	SO:0001583	missense	339967	exon10			TGTGTGTAGACTC	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1214A>T	4.37:g.68777112T>A	ENSP00000334611:p.Tyr405Phe	Somatic	205	0		WXS	Illumina HiSeq	Phase_1	163	70	NM_182606	0	0	0	0	0	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.983616	0.93044	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46	5.66	5.66	0.87406	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.48286	D	0.000190	D	0.96445	0.8840	M	0.64080	1.96	0.47778	D	0.999512	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.96859	0.9631	10	0.87932	D	0	.	13.8496	0.63487	0.0:0.0:0.0:1.0	.	402;405	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	F	401;405;402;369	ENSP00000426911:Y401F;ENSP00000334611:Y405F;ENSP00000379491:Y402F;ENSP00000427621:Y369F	ENSP00000334611:Y405F	Y	-	2	0	TMPRSS11A	68459707	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.673000	0.83973	2.155000	0.67459	0.377000	0.23210	TAC	.		0.413	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		A	68777112	T	A	68777112	3	1	54	1	0	0	0	0	1	0	0	0	16271	1638	57	5	55	5	TMPRSS11A	4	68777112	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	1	68777112	122377164	38	5208	57	2									
ZNF622	90441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	16465479	16465479	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccgattcactgcctgcAcggccttcttctccagctca	5	13	6	17	2	4	0	2	0	2	0	6	1	5	0	4	1	3	2	4	1	0	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:16465479A>G	ENST00000308683.2	-	1	422	c.296T>C	c.(295-297)gTg>gCg	p.V99A		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	99					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						CACTGCCTGCACGGCCTTCTT	0.537																																					p.V99A		.											.	ZNF622-91	0			c.T296C						.						155	139	145					5																	16465479		2203	4300	6503	SO:0001583	missense	90441	exon1			GCCTGCACGGCCT	AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.296T>C	5.37:g.16465479A>G	ENSP00000310042:p.Val99Ala	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	155	31	NM_033414	0	0	16	22	6		Missense_Mutation	SNP	ENST00000308683.2	37	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.814522	0.50527	.	.	ENSG00000173545	ENST00000308683	.	.	.	4.81	3.65	0.41850	.	0.199006	0.45126	D	0.000388	T	0.46639	0.1403	M	0.65975	2.015	0.41784	D	0.989838	B	0.15141	0.012	B	0.09377	0.004	T	0.36432	-0.9748	9	0.02654	T	1	-37.7849	7.9359	0.29929	0.8407:0.0:0.1593:0.0	.	99	Q969S3	ZN622_HUMAN	A	99	.	ENSP00000310042:V99A	V	-	2	0	ZNF622	16518479	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	5.190000	0.65104	0.855000	0.35359	0.528000	0.53228	GTG	.		0.537	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		G	16465479	A	G	16465479	3	3	54	1	0	0	0	0	1	0	0	0	18078	159	6	3	1161	3	ZNF622	5	16465479	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		16465479	164449781	39	5209											
MYO10	4651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	16685914	16685914	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtccgtggacgcgtggAcctgactcagcacgctgaac	7	7	13	14	4	1	2	1	2	0	0	2	4	2	4	3	3	2	2	3	3	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:16685914A>C	ENST00000513610.1	-	29	4377	c.3923T>G	c.(3922-3924)gTc>gGc	p.V1308G	MYO10_ENST00000505695.1_Missense_Mutation_p.V647G|MYO10_ENST00000515803.1_Missense_Mutation_p.V647G|MYO10_ENST00000274203.9_Missense_Mutation_p.V665G|MYO10_ENST00000427430.2_Missense_Mutation_p.V665G	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1308	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GGACGCGTGGACCTGACTCAG	0.592																																					p.V1308G		.											.	MYO10-3	0			c.T3923G						.						61	61	61					5																	16685914		2160	4271	6431	SO:0001583	missense	4651	exon29			GCGTGGACCTGAC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.3923T>G	5.37:g.16685914A>C	ENSP00000421280:p.Val1308Gly	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	56	24	NM_012334	0	0	2	4	2	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889699	0.91889	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51	5.51	5.51	0.81932	Pleckstrin homology domain (3);	.	.	.	.	T	0.46151	0.1378	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.57057	-0.7876	9	0.87932	D	0	.	15.6429	0.77020	1.0:0.0:0.0:0.0	.	187;949;1308	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	G	1308;647;665;647;665	ENSP00000421280:V1308G;ENSP00000425051:V647G;ENSP00000274203:V665G;ENSP00000421170:V647G;ENSP00000391106:V665G	ENSP00000274203:V665G	V	-	2	0	MYO10	16738914	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.331000	0.96430	2.092000	0.63282	0.523000	0.50628	GTC	.		0.592	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		C	16685914	A	C	16685914	3	2	54	1	0	0	0	0	1	0	0	0	10087	275	10	5	2305	5	MYO10	5	16685914	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	220435	16685914	164229346	40	5210											
CDH9	1007	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	26915851	26915851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgattccggttccacctgcCgcccagtttttctgtctata	5	14	7	15	3	2	0	0	0	2	0	4	1	4	0	6	1	1	2	6	1	2	6	rs150604531		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:26915851C>T	ENST00000231021.4	-	3	582	c.410G>A	c.(409-411)cGg>cAg	p.R137Q		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	137	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TTCCACCTGCCGCCCAGTTTT	0.383																																					p.R137Q	Melanoma(8;187 585 15745 40864 52829)												.	CDH9-99	0			c.G410A						.	C	GLN/ARG	0,4406		0,0,2203	136	136	136		410	4.6	0.5	5	dbSNP_134	136	3,8595	3.0+/-9.4	0,3,4296	no	missense	CDH9	NM_016279.3	43	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	benign	137/790	26915851	3,13001	2203	4299	6502	SO:0001583	missense	1007	exon3			ACCTGCCGCCCAG	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"Cadherins / Major cadherins"	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.410G>A	5.37:g.26915851C>T	ENSP00000231021:p.Arg137Gln	Somatic	112	1		WXS	Illumina HiSeq	Phase_I	112	37	NM_016279	0	0	0	0	0	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.525965	0.44969	0.0	3.49E-4	ENSG00000113100	ENST00000231021	T	0.50548	0.74	4.62	4.62	0.57501	Cadherin (4);Cadherin-like (1);	0.353060	0.31031	N	0.008396	T	0.35595	0.0937	L	0.39514	1.22	0.09310	N	1	B	0.28512	0.214	B	0.25405	0.06	T	0.16424	-1.0403	9	.	.	.	.	10.1395	0.42728	0.0:0.9063:0.0:0.0937	.	137	Q9ULB4	CADH9_HUMAN	Q	137	ENSP00000231021:R137Q	.	R	-	2	0	CDH9	26951608	0.001000	0.12720	0.540000	0.28089	0.988000	0.76386	1.388000	0.34442	2.275000	0.75901	0.650000	0.86243	CGG	C|1.000;T|0.000		0.383	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26915851	C	T	26915851	3	4	54	1	0	0	0	0	1	0	0	0	3123	652	23	1	1999	1	CDH9	5	26915851	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	10229937	26915851	153999409	41	5211											
PRRC1	133619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	126860514	126860514	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttcgggtcctcctatatcagGattttctgttggttcaactt	6	18	8	9	1	3	0	2	0	1	0	6	1	5	1	2	3	1	2	2	3	3	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:126860514G>C	ENST00000296666.8	+	3	583	c.395G>C	c.(394-396)gGa>gCa	p.G132A	PRRC1_ENST00000512635.2_Missense_Mutation_p.G132A|PRRC1_ENST00000442138.2_Missense_Mutation_p.G132A	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	132						Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		CCTATATCAGGATTTTCTGTT	0.507																																					p.G132A		.											.	PRRC1-68	0			c.G395C						.						145	149	148					5																	126860514		2203	4300	6503	SO:0001583	missense	133619	exon3			TATCAGGATTTTC	AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244			28164	protein-coding gene	gene with protein product						15541471	Standard	NM_130809		Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.395G>C	5.37:g.126860514G>C	ENSP00000296666:p.Gly132Ala	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	182	83	NM_130809	0	0	3	4	1	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	Missense_Mutation	SNP	ENST00000296666.8	37	CCDS4143.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.265327	0.59431	.	.	ENSG00000164244	ENST00000296666;ENST00000442138;ENST00000330542;ENST00000414018;ENST00000512635;ENST00000512535	.	.	.	5.06	5.06	0.68205	.	0.174179	0.49916	D	0.000122	T	0.41926	0.1180	L	0.31207	0.915	0.53005	D	0.999966	B;P	0.42375	0.214;0.778	B;B	0.37989	0.052;0.262	T	0.29971	-0.9994	9	0.30078	T	0.28	-20.0859	17.5874	0.87986	0.0:0.0:1.0:0.0	.	132;132	Q96M27;Q96M27-5	PRRC1_HUMAN;.	A	132	.	ENSP00000296666:G132A	G	+	2	0	PRRC1	126888413	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.592000	0.67543	2.632000	0.89209	0.655000	0.94253	GGA	.		0.507	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250971.3	NM_130809		C	126860514	G	C	126860514	3	2	54	1	0	0	0	0	1	0	0	0	12633	1174	41	4	401	4	PRRC1	5	126860514	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	99944663	126860514	54054746	42	5212											
MATR3	9782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	138643239	138643239	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagcatctcttggaaggatGaaccagggtactgcacgcct	10	8	11	12	1	1	1	0	1	1	0	2	3	1	3	3	3	4	3	3	3	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:138643239G>A	ENST00000394805.3	+	2	470	c.135G>A	c.(133-135)atG>atA	p.M45I	MATR3_ENST00000361059.2_Missense_Mutation_p.M45I|MATR3_ENST00000503811.1_Intron|MATR3_ENST00000510056.1_Missense_Mutation_p.M45I|MATR3_ENST00000502499.1_Intron|MATR3_ENST00000394800.2_Missense_Mutation_p.M45I|MATR3_ENST00000504203.1_Intron|MATR3_ENST00000502929.1_Missense_Mutation_p.M45I|MATR3_ENST00000509990.1_Missense_Mutation_p.M45I	NM_001194955.1|NM_018834.5	NP_001181884.1|NP_061322.2	P43243	MATR3_HUMAN	matrin 3	45					cell death (GO:0008219)	membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTGGAAGGATGAACCAGGGTA	0.488																																					p.M45I		.											.	MATR3-91	0			c.G135A						.						144	135	138					5																	138643239		2203	4300	6503	SO:0001583	missense	9782	exon2			AAGGATGAACCAG	M63483	CCDS4210.1, CCDS54908.1, CCDS75316.1	5q31.3	2010-08-12			ENSG00000015479	ENSG00000015479			6912	protein-coding gene	gene with protein product		164015	"myopathy, distal 2"	MPD2		2033075, 19344878	Standard	NM_018834		Approved	KIAA0723, MGC9105, VCPDM	uc003ldx.3	P43243	OTTHUMG00000129229	ENST00000394805.3:c.135G>A	5.37:g.138643239G>A	ENSP00000378284:p.Met45Ile	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	198	84	NM_018834	0	0	3	6	3	B7ZAV5|D3DQC3|Q9UHW0|Q9UQ27	Missense_Mutation	SNP	ENST00000394805.3	37	CCDS4210.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461853	0.43736	.	.	ENSG00000015479	ENST00000509990;ENST00000361059;ENST00000514694;ENST00000502929;ENST00000394800;ENST00000505016;ENST00000502394;ENST00000394805;ENST00000504045;ENST00000510056;ENST00000508689;ENST00000514488;ENST00000503340;ENST00000504023	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	N	0.14661	0.345	0.51233	D	0.999917	P;B;P	0.45126	0.851;0.018;0.851	P;B;P	0.55391	0.775;0.131;0.775	T	0.83121	-0.0118	10	0.72032	D	0.01	-7.6365	20.4366	0.99092	0.0:0.0:1.0:0.0	.	45;45;45	D6REM6;A8MXP9;P43243	.;.;MATR3_HUMAN	I	45	ENSP00000423533:M45I;ENSP00000354346:M45I;ENSP00000422233:M45I;ENSP00000422319:M45I;ENSP00000378279:M45I;ENSP00000424431:M45I;ENSP00000427168:M45I;ENSP00000378284:M45I;ENSP00000423290:M45I;ENSP00000426743:M45I;ENSP00000422137:M45I;ENSP00000426801:M45I;ENSP00000422590:M45I;ENSP00000421145:M45I	ENSP00000354346:M45I	M	+	3	0	MATR3	138671138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.685000	0.74543	2.843000	0.97960	0.585000	0.79938	ATG	.		0.488	MATR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251324.2	NM_018834		A	138643239	G	A	138643239	3	1	54	1	0	0	0	0	1	0	0	0	9362	1290	45	2	137	2	MATR3	5	138643239	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	11782725	138643239	42272021	43	5213											
PCDHB13	56123	broad.mit.edu	37	chr5	140595249	140595249	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgttcgccctcaggtcTctggactacgaggccctgca	6	9	10	16	2	2	0	1	0	1	0	4	2	2	1	3	3	2	2	3	3	1	2	rs144959109	byFrequency	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:140595249T>C	ENST00000341948.4	+	1	1741	c.1554T>C	c.(1552-1554)tcT>tcC	p.S518S		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	518	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S518S(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTCAGGTCTCTGGACTACG	0.692																																					p.S518S													.	PCDHB13-93	1	Substitution - coding silent(1)	kidney(1)	c.T1554C						.						89	96	93					5																	140595249		2203	4300	6503	SO:0001819	synonymous_variant	56123	exon1			CAGGTCTCTGGAC	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"Cadherins / Protocadherins : Clustered"	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1554T>C	5.37:g.140595249T>C		Somatic	123	1		WXS	Illumina HiSeq	Phase_I	89	3	NM_018933	0	0	0	0	0	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			T|0.999;G|0.001		0.692	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		C	140595249	T	C	140595249	2	2	54	1	0	0	0	0	0	0	0	1	11564	1538	54	3		3	PCDHB13	5	140595249	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	1952010	140595249	40320011	44	5214											
GRPEL2	134266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	148730494	148730494	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctgcaggaatccagagtttCtgtaaggacttggtggaggt	9	12	14	6	0	2	1	0	0	2	1	3	4	3	4	1	5	1	3	1	5	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:148730494C>T	ENST00000329271.3	+	4	437	c.327C>T	c.(325-327)ttC>ttT	p.F109F	GRPEL2-AS1_ENST00000521295.1_RNA|GRPEL2_ENST00000507562.1_3'UTR|GRPEL2_ENST00000416916.2_Missense_Mutation_p.S82F	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	109					cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	adenyl-nucleotide exchange factor activity (GO:0000774)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGAGTTTCTGTAAGGACT	0.478																																					p.F109F		.											.	GRPEL2-91	0			c.C327T						.						90	99	96					5																	148730494		2203	4300	6503	SO:0001819	synonymous_variant	134266	exon4			GAGTTTCTGTAAG	AL832325	CCDS4295.1	5q33.1	2008-02-05			ENSG00000164284	ENSG00000164284			21060	protein-coding gene	gene with protein product							Standard	NM_152407		Approved	DKFZp451C205, Mt-GrpE#2, FLJ23713	uc003lqj.3	Q8TAA5	OTTHUMG00000130048	ENST00000329271.3:c.327C>T	5.37:g.148730494C>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	81	20	NM_152407	0	0	0	0	0	B4DFA6|Q49AJ6	Silent	SNP	ENST00000329271.3	37	CCDS4295.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.925419	0.73213	.	.	ENSG00000164284	ENST00000416916	.	.	.	6.06	4.27	0.50696	.	.	.	.	.	T	0.26882	0.0658	.	.	.	0.29129	N	0.879743	B	0.23249	0.082	B	0.22386	0.039	T	0.20739	-1.0266	6	.	.	.	-1.559	7.4128	0.27027	0.1374:0.7272:0.0:0.1354	.	82	B4DFA6	.	F	82	.	.	S	+	2	0	GRPEL2	148710687	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.587000	0.36622	0.866000	0.35629	0.655000	0.94253	TCT	.		0.478	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		T	148730494	C	T	148730494	2	4	54	1	0	0	0	0	0	0	0	1	6828	912	32	2		2	GRPEL2	5	148730494	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	8135245	148730494	32184766	45	5215											
DSP	1832	hgsc.bcm.edu;bcgsc.ca	37	chr6	7562996	7562996	+	Frame_Shift_Del	DEL	A	A	-																															actatcgctggcagctggacAaaatcaaagccgacctggta																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:7562996delA	ENST00000379802.3	+	5	1050	c.709delA	c.(709-711)aaafs	p.K237fs	DSP_ENST00000418664.2_Frame_Shift_Del_p.K237fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	237	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GCAGCTGGACAAAATCAAAGC	0.507																																					p.K237fs		.											.	DSP-518	0			c.709delA						.						119	119	119					6																	7562996		2203	4300	6503	SO:0001589	frameshift_variant	1832	exon5			.	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.709delA	6.37:g.7562996delA	ENSP00000369129:p.Lys237fs	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	103	29	NM_004415	0	0	0	0	0	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Del	DEL	ENST00000379802.3	37	CCDS4501.1																																																																																			.		0.507	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		-	7562996	A	-	7562996	7	5	54	1	0	1	0	1	0	0	0	0	4792	131	5	0	727	0	DSP	6	7562996	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10		7562996	163552071	46	5216											
SLC17A3	10786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	25850278	25850278	+	Frame_Shift_Del	DEL	A	A	-																															ctcaagctctgttcttacctAaaattgtggcaattttcctc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:25850278delA	ENST00000360657.3	-	8	1172	c.887delT	c.(886-888)ttafs	p.L296fs	SLC17A3_ENST00000397060.4_Frame_Shift_Del_p.L374fs|SLC17A3_ENST00000361703.6_Frame_Shift_Del_p.L296fs			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	296					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						GTTCTTACCTAAAATTGTGGC	0.408																																					p.L374X		.											.	SLC17A3-91	0			c.1121delT						.						97	96	97					6																	25850278		2203	4300	6503	SO:0001589	frameshift_variant	10786	exon9			.	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"Solute carriers"	10931	protein-coding gene	gene with protein product		611034	"solute carrier family 17 (sodium phosphate), member 3"			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.887delT	6.37:g.25850278delA	ENSP00000353873:p.Leu296fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	99	41	NM_001098486	0	0	0	0	0	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Nonsense_Mutation	DEL	ENST00000360657.3	37	CCDS4566.2																																																																																			.		0.408	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2			-	25850278	A	-	25850278	7	5	54	1	0	1	0	1	0	0	0	0	14450	372	13	0	391	0	SLC17A3	6	25850278	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	18287282	25850278	145264789	47	5217											
MDC1	9656	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	30681013	30681013	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtggcacctcttctggcagCtgaggaggcctcctctgtgg	5	10	14	12	0	3	1	0	1	3	0	4	2	4	2	3	5	1	3	3	5	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:30681013C>A	ENST00000376406.3	-	5	1353	c.706G>T	c.(706-708)Gct>Tct	p.A236S	MDC1_ENST00000376405.2_Missense_Mutation_p.A236S|MDC1_ENST00000494654.1_5'Flank|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	236	Required for nuclear localization (NLS1).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CTTCTGGCAGCTGAGGAGGCC	0.537								Other conserved DNA damage response genes																													p.A236S		.											.	MDC1-273	0			c.G706T						.						90	99	96					6																	30681013		1509	2708	4217	SO:0001583	missense	9656	exon5			TGGCAGCTGAGGA	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.706G>T	6.37:g.30681013C>A	ENSP00000365588:p.Ala236Ser	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	126	7	NM_014641	0	0	3	3	0	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.58|10.58	1.390558|1.390558	0.25118|0.25118	.|.	.|.	ENSG00000137337|ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104;ENST00000435797|ENST00000452213	T;T|.	0.04119|.	3.79;3.7|.	5.31|5.31	-0.775|-0.775	0.10988|0.10988	.|.	0.429453|.	0.17269|.	N|.	0.180468|.	T|T	0.08802|0.08802	0.0218|0.0218	L|L	0.35723|0.35723	1.085|1.085	0.09310|0.09310	N|N	1|1	P;B;B|.	0.36392|.	0.551;0.129;0.261|.	B;B;B|.	0.31751|.	0.135;0.082;0.063|.	T|T	0.35624|0.35624	-0.9781|-0.9781	10|6	0.41790|0.30854	T|T	0.15|0.27	-1.711|-1.711	0.5485|0.5485	0.00658|0.00658	0.2846:0.3351:0.1383:0.242|0.2846:0.3351:0.1383:0.242	.|.	236;108;236|.	Q14676-2;B4DYH4;Q14676|.	.;.;MDC1_HUMAN|.	S|I	236;236;236;108;236|235	ENSP00000365588:A236S;ENSP00000365587:A236S|.	ENSP00000365587:A236S|ENSP00000404936:S235I	A|S	-|-	1|2	0|0	MDC1|MDC1	30788992|30788992	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.005000|0.005000	0.13129|0.13129	-0.368000|-0.368000	0.08040|0.08040	-0.844000|-0.844000	0.03045|0.03045	GCT|AGC	.		0.537	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30681013	C	A	30681013	3	1	54	1	0	0	0	0	1	0	0	0	9428	797	28	4	5607	4	MDC1	6	30681013	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4830735	30681013	140434054	48	5218											
TCP11	6954	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35086064	35086064	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcaaacagactccactttTgtttccagtgcctgggctgg	8	13	9	11	0	1	1	1	0	0	1	3	1	3	1	3	2	2	2	3	2	2	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:35086064T>G	ENST00000512012.1	-	9	1650	c.1494A>C	c.(1492-1494)acA>acC	p.T498T	TCP11_ENST00000311875.5_Silent_p.T511T|TCP11_ENST00000373979.2_Silent_p.T436T|TCP11_ENST00000444780.2_Silent_p.T506T|TCP11_ENST00000412155.2_Silent_p.T460T|TCP11_ENST00000244645.3_Silent_p.T436T|TCP11_ENST00000373974.4_Silent_p.T465T|TCP11_ENST00000418521.2_Silent_p.T435T			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	498					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						ACTCCACTTTTGTTTCCAGTG	0.498																																					p.T511T		.											.	TCP11-95	0			c.A1533C						.						133	135	134					6																	35086064		2203	4300	6503	SO:0001819	synonymous_variant	6954	exon10			CACTTTTGTTTCC		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"fertilization-promoting peptide receptor"	186982	"t-complex 11 (a murine tcp homolog)", "t-complex 11 homolog (mouse)"	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.1494A>C	6.37:g.35086064T>G		Somatic	179	0		WXS	Illumina HiSeq	Phase_I	202	87	NM_001093728	0	0	0	0	0	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Silent	SNP	ENST00000512012.1	37		.	.	.	.	.	.	.	.	.	.	T	11.91	1.779912	0.31502	.	.	ENSG00000124678	ENST00000502480	.	.	.	5.32	-1.75	0.08031	.	.	.	.	.	T	0.28200	0.0696	.	.	.	0.38093	D	0.937032	.	.	.	.	.	.	T	0.22765	-1.0207	4	.	.	.	-4.2485	6.0586	0.19824	0.0:0.1544:0.2928:0.5527	.	.	.	.	Q	240	.	.	K	-	1	0	TCP11	35194042	0.000000	0.05858	0.064000	0.19789	0.809000	0.45718	-1.209000	0.03002	-0.281000	0.09141	0.460000	0.39030	AAA	.		0.498	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728		G	35086064	T	G	35086064	2	3	54	1	0	0	0	0	0	0	0	1	15745	1799	63	5		5	TCP11	6	35086064	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	4405051	35086064	136029003	49	5219											
KLC4	89953	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43041642	43041643	+	Frame_Shift_Ins	INS	-	-	CAACACGA																															tccgttttccattgtagcagINScaacatgaagcgagcagcct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:43041642_43041643insCAACACGA	ENST00000394056.2	+	16	2243_2244	c.1748_1749insCAACACGA	c.(1747-1752)agcaacfs	p.-584fs	PTK7_ENST00000349241.2_5'Flank|KLC4_ENST00000479388.1_Frame_Shift_Ins_p.-584fs|PTK7_ENST00000471863.1_5'Flank|PTK7_ENST00000230419.4_5'Flank|PTK7_ENST00000352931.2_5'Flank|PTK7_ENST00000481273.1_5'Flank|PTK7_ENST00000345201.2_5'Flank|KLC4_ENST00000394058.1_Frame_Shift_Ins_p.-584fs|KLC4_ENST00000347162.5_Frame_Shift_Ins_p.-584fs|PTK7_ENST00000476760.1_5'Flank|KLC4_ENST00000259708.3_Frame_Shift_Ins_p.-602fs|KLC4_ENST00000453940.2_Frame_Shift_Ins_p.-507fs|RP11-387M24.5_ENST00000606123.1_RNA			Q9NSK0	KLC4_HUMAN	kinesin light chain 4							cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			CATTGTAGCAGCAACATGAAGC	0.54																																					p.S601fs		.											.	KLC4-94	0			c.1802_1803insCAACACGA						.																																			SO:0001589	frameshift_variant	89953	exon15			.	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	Exception_encountered	6.37:g.43041642_43041643insCAACACGA	ENSP00000377620:p.Asn584fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	126	24	NM_201523	0	0	0	0	0	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Frame_Shift_Ins	INS	ENST00000394056.2	37	CCDS4883.1																																																																																			.		0.54	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		CAACACGA	43041643	-	CAACACGA	43041642	7	5	54	1	0	1	1	0	0	0	0	0	8357	971	34	0	1929	0	KLC4	6	43041642	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	7955578	43041642	128073425	50	5220	58	2									
KLC4	89953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43041648	43041648	+	Missense_Mutation	SNP	T	T	C																															tttccattgtagcagcaacaTgaagcgagcagcctccttga																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:43041648T>C	ENST00000394056.2	+	16	2249	c.1754T>C	c.(1753-1755)aTg>aCg	p.M585T	PTK7_ENST00000349241.2_5'Flank|KLC4_ENST00000479388.1_Missense_Mutation_p.M585T|PTK7_ENST00000471863.1_5'Flank|PTK7_ENST00000230419.4_5'Flank|PTK7_ENST00000352931.2_5'Flank|PTK7_ENST00000481273.1_5'Flank|PTK7_ENST00000345201.2_5'Flank|KLC4_ENST00000394058.1_Missense_Mutation_p.M585T|KLC4_ENST00000347162.5_Missense_Mutation_p.M585T|PTK7_ENST00000476760.1_5'Flank|KLC4_ENST00000259708.3_Missense_Mutation_p.M603T|KLC4_ENST00000453940.2_Missense_Mutation_p.M508T|RP11-387M24.5_ENST00000606123.1_RNA			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	585						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			AGCAGCAACATGAAGCGAGCA	0.537																																					p.M603T		.											.	KLC4-94	0			c.T1808C						.						138	119	125					6																	43041648		2203	4300	6503	SO:0001583	missense	89953	exon15			GCAACATGAAGCG	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1754T>C	6.37:g.43041648T>C	ENSP00000377620:p.Met585Thr	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	128	40	NM_201523	0	0	2	2	0	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.745697	0.49151	.	.	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	D;D;D;D;D;D	0.85088	-1.86;-1.94;-1.87;-1.86;-1.86;-1.86	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	D	0.85141	0.5629	M	0.73217	2.22	0.53688	D	0.999979	P;D;P	0.53462	0.791;0.96;0.717	B;P;P	0.61397	0.212;0.888;0.599	D	0.83770	0.0219	10	0.11794	T	0.64	-11.1696	11.8821	0.52581	0.0:0.0:0.0:1.0	.	508;603;585	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	T	585;508;603;585;585;585	ENSP00000340221:M585T;ENSP00000395806:M508T;ENSP00000259708:M603T;ENSP00000418031:M585T;ENSP00000377620:M585T;ENSP00000377622:M585T	ENSP00000259708:M603T	M	+	2	0	KLC4	43149626	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.911000	0.69939	2.054000	0.61138	0.459000	0.35465	ATG	.		0.537	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		C	43041648	T	C	43041648	3	2	54	1	0	0	0	0	1	0	0	0	8357	1464	51	3	1935	3	KLC4	6	43041648	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	6	43041648	128073419	51	5221	58	2									
YIPF3	25844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43480515	43480515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaccatgcgcagtgtggacAgtccacccaccaacagccag	11	6	9	15	1	0	0	0	0	0	0	1	1	1	1	5	1	4	1	5	1	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:43480515A>G	ENST00000372422.2	-	7	946	c.764T>C	c.(763-765)cTg>cCg	p.L255P	LRRC73_ENST00000372441.1_5'Flank|YIPF3_ENST00000506469.1_Missense_Mutation_p.L261P	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	255					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			CAGTGTGGACAGTCCACCCAC	0.567																																					p.L255P		.											.	YIPF3-90	0			c.T764C						.						89	76	81					6																	43480515		2203	4300	6503	SO:0001583	missense	25844	exon7			GTGGACAGTCCAC	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.764T>C	6.37:g.43480515A>G	ENSP00000361499:p.Leu255Pro	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	189	75	NM_015388	0	0	66	101	35	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Missense_Mutation	SNP	ENST00000372422.2	37	CCDS4899.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.404720	0.62288	.	.	ENSG00000137207	ENST00000372422;ENST00000506469;ENST00000503972	T;T;T	0.53857	0.61;0.6;0.71	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000001	T	0.58680	0.2139	L	0.49126	1.545	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.998;0.997;0.998	T	0.59653	-0.7414	10	0.41790	T	0.15	-11.2654	15.19	0.73035	1.0:0.0:0.0:0.0	.	261;220;255	E7EQR8;Q5JTD5;Q9GZM5	.;.;YIPF3_HUMAN	P	255;261;221	ENSP00000361499:L255P;ENSP00000425494:L261P;ENSP00000421461:L221P	ENSP00000361499:L255P	L	-	2	0	YIPF3	43588493	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.982000	0.93471	1.996000	0.58369	0.460000	0.39030	CTG	.		0.567	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		G	43480515	A	G	43480515	3	3	54	1	0	0	0	0	1	0	0	0	17512	188	7	3	300	3	YIPF3	6	43480515	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	438867	43480515	127634552	52	5222											
SNAP91	9892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	84371294	84371294	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcattcaaatatctactatAgcgccttatgaaggtagaca	14	13	6	8	1	3	2	2	1	1	1	3	2	3	2	1	1	2	1	1	1	8	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:84371294A>T	ENST00000439399.2	-	5	695	c.379T>A	c.(379-381)Tat>Aat	p.Y127N	SNAP91_ENST00000369694.2_Missense_Mutation_p.Y127N|SNAP91_ENST00000521743.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000437520.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000520302.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000520213.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000428679.2_Missense_Mutation_p.Y127N|SNAP91_ENST00000195649.6_Missense_Mutation_p.Y127N|SNAP91_ENST00000521485.1_Missense_Mutation_p.Y127N	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	127	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TATCTACTATAGCGCCTTATG	0.328																																					p.Y127N		.											.	SNAP91-23	0			c.T379A						.						56	54	54					6																	84371294		1805	4074	5879	SO:0001583	missense	9892	exon5			TACTATAGCGCCT	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"synaptosomal-associated protein, 91 kDa (mouse) homolog", "synaptosomal-associated protein, 91kDa homolog (mouse)"			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.379T>A	6.37:g.84371294A>T	ENSP00000400459:p.Tyr127Asn	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	100	59	NM_001242794	0	0	0	0	0	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	37	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.551977	0.86127	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000521931;ENST00000519779;ENST00000518309;ENST00000369690	T;T;T;T;T;T;T;T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.13	5.13	0.70059	ENTH/VHS (2);ANTH (1);Epsin-like, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87358	0.6157	H	0.96547	3.84	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.996;0.999	D	0.91513	0.5228	10	0.87932	D	0	-8.3087	15.2297	0.73378	1.0:0.0:0.0:0.0	.	127;127;127;127	O60641-3;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	N	127	ENSP00000429776:Y127N;ENSP00000358708:Y127N;ENSP00000400459:Y127N;ENSP00000195649:Y127N;ENSP00000412492:Y127N;ENSP00000413277:Y127N;ENSP00000428511:Y127N;ENSP00000428215:Y127N;ENSP00000428026:Y127N;ENSP00000430071:Y127N;ENSP00000429429:Y127N;ENSP00000430441:Y127N;ENSP00000358704:Y127N	ENSP00000195649:Y127N	Y	-	1	0	SNAP91	84428013	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.210000	0.95106	2.056000	0.61249	0.460000	0.39030	TAT	.		0.328	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			T	84371294	A	T	84371294	3	4	54	1	0	0	0	0	1	0	0	0	14865	420	15	5	2440	5	SNAP91	6	84371294	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	40890779	84371294	86743773	53	5223											
SPACA1	81833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	88775941	88775941	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggcaaaagcctctacacCtgaggtacaatccgagcaga	13	5	12	11	1	1	2	0	1	1	1	2	3	2	2	3	3	4	3	3	3	5	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:88775941C>A	ENST00000237201.1	+	7	890	c.773C>A	c.(772-774)cCt>cAt	p.P258H	SPACA1_ENST00000462690.1_3'UTR	NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	258					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		GCCTCTACACCTGAGGTACAA	0.413																																					p.P258H		.											.	SPACA1-90	0			c.C773A						.						100	109	106					6																	88775941		2203	4300	6503	SO:0001583	missense	81833	exon7			CTACACCTGAGGT	AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.773C>A	6.37:g.88775941C>A	ENSP00000237201:p.Pro258His	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	39	14	NM_030960	0	0	0	0	0		Missense_Mutation	SNP	ENST00000237201.1	37	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.734402	0.30774	.	.	ENSG00000118434	ENST00000237201	T	0.30448	1.53	4.81	4.81	0.61882	.	0.410909	0.23356	N	0.049061	T	0.16171	0.0389	N	0.22421	0.69	0.09310	N	0.999999	P	0.49447	0.924	P	0.47941	0.562	T	0.03545	-1.1026	10	0.66056	D	0.02	-5.1836	13.254	0.60068	0.0:1.0:0.0:0.0	.	258	Q9HBV2	SACA1_HUMAN	H	258	ENSP00000237201:P258H	ENSP00000237201:P258H	P	+	2	0	SPACA1	88832660	0.530000	0.26330	0.533000	0.28001	0.013000	0.08279	1.999000	0.40806	2.507000	0.84556	0.467000	0.42956	CCT	.		0.413	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			A	88775941	C	A	88775941	3	1	54	1	0	0	0	0	1	0	0	0	15004	681	24	4	799	4	SPACA1	6	88775941	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4404647	88775941	82339126	54	5224											
MDN1	23195	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90402313	90402313	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttccagctcctttcctcctGagcgcttgaggattagcttc	5	14	8	14	1	0	2	0	2	0	0	5	3	4	3	4	1	3	3	4	1	1	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:90402313G>C	ENST00000369393.3	-	63	10551	c.10436C>G	c.(10435-10437)tCa>tGa	p.S3479*	MDN1_ENST00000428876.1_Nonsense_Mutation_p.S3479*			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3479					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTTTCCTCCTGAGCGCTTGAG	0.567																																					p.S3479X													.	MDN1-100	0			c.C10436G						.						92	88	89					6																	90402313		2203	4300	6503	SO:0001587	stop_gained	23195	exon63			CCTCCTGAGCGCT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.10436C>G	6.37:g.90402313G>C	ENSP00000358400:p.Ser3479*	Somatic	180	1		WXS	Illumina HiSeq	Phase_I	208	44	NM_014611	0	0	0	0	0	O15019|Q5T794	Nonsense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	50	16.516527	0.99865	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	.	.	.	5.27	1.31	0.21738	.	0.321294	0.27072	N	0.021070	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	8.301	0.32014	0.1364:0.2565:0.6071:0.0	.	.	.	.	X	3479	.	ENSP00000358400:S3479X	S	-	2	0	MDN1	90459034	0.260000	0.24053	0.004000	0.12327	0.332000	0.28634	1.104000	0.31074	-0.054000	0.13266	0.462000	0.41574	TCA	.		0.567	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90402313	G	C	90402313	4	2	54	1	0	0	0	0	0	1	0	0	9440	1294	45	4	6514	4	MDN1	6	90402313	Nonsense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	1626372	90402313	80712754	55	5225											
HACE1	57531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	105298839	105298839	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaatgcataattgacatcaAattttgaatttgatagtagt	15	15	7	4	1	1	3	1	3	0	0	1	4	1	3	0	0	1	2	0	0	6	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:105298839A>T	ENST00000262903.4	-	3	440	c.164T>A	c.(163-165)tTt>tAt	p.F55Y	HACE1_ENST00000369125.2_Missense_Mutation_p.F55Y	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	55					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		ATTGACATCAAATTTTGAATT	0.299																																					p.F55Y		.											.	HACE1-663	0			c.T164A						.						152	157	156					6																	105298839		2203	4300	6503	SO:0001583	missense	57531	exon3			ACATCAAATTTTG	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.164T>A	6.37:g.105298839A>T	ENSP00000262903:p.Phe55Tyr	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	105	61	NM_020771	0	0	0	0	0	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	37	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.488630	0.84854	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645;ENST00000524020	T;T;T;T	0.72282	-0.64;-0.64;-0.09;1.51	5.97	5.97	0.96955	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	N	0.21545	0.675	0.80722	D	1	D;D	0.53885	0.963;0.963	D;D	0.69824	0.966;0.966	T	0.73538	-0.3951	10	0.51188	T	0.08	.	15.4434	0.75208	1.0:0.0:0.0:0.0	.	55;55	E9PGP0;Q8IYU2	.;HACE1_HUMAN	Y	55;55;55;21	ENSP00000262903:F55Y;ENSP00000358121:F55Y;ENSP00000429765:F55Y;ENSP00000427901:F21Y	ENSP00000262903:F55Y	F	-	2	0	HACE1	105405532	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.328000	0.90014	2.288000	0.76882	0.533000	0.62120	TTT	.		0.299	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		T	105298839	A	T	105298839	3	4	54	1	0	0	0	0	1	0	0	0	6961	14	1	5	2653	5	HACE1	6	105298839	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	14896526	105298839	65816228	56	5226											
SOBP	55084	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	107827527	107827527	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacaggctattcagggcttgCcactggaaatggactcagtg	10	9	12	10	0	2	0	2	0	0	0	2	2	2	2	1	4	1	2	1	4	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:107827527C>A	ENST00000317357.5	+	3	976	c.317C>A	c.(316-318)gCc>gAc	p.A106D		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		TCAGGGCTTGCCACTGGAAAT	0.413																																					p.A106D		.											.	SOBP-91	0			c.C317A						.						193	185	188					6																	107827527		1908	4136	6044	SO:0001583	missense	55084	exon3			GGCTTGCCACTGG	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.317C>A	6.37:g.107827527C>A	ENSP00000318900:p.Ala106Asp	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	89	16	NM_018013	0	0	0	0	0		Missense_Mutation	SNP	ENST00000317357.5	37	CCDS43488.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145200	0.77888	.	.	ENSG00000112320	ENST00000317357	T	0.11277	2.79	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.07413	0.0187	N	0.08118	0	0.58432	D	0.999996	D	0.53312	0.959	P	0.52957	0.714	T	0.40720	-0.9548	10	0.66056	D	0.02	-11.9919	19.1981	0.93698	0.0:1.0:0.0:0.0	.	106	A7XYQ1	SOBP_HUMAN	D	106	ENSP00000318900:A106D	ENSP00000318900:A106D	A	+	2	0	SOBP	107934220	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.422000	0.66453	2.615000	0.88500	0.655000	0.94253	GCC	.		0.413	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		A	107827527	C	A	107827527	3	1	54	1	0	0	0	0	1	0	0	0	14944	739	26	4	327	4	SOBP	6	107827527	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2528688	107827527	63287540	57	5227											
NUS1	116150	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	118015319	118015319	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagacccacagatttggatGtagatacgttagccagttta	13	11	10	7	1	0	3	0	0	0	3	0	5	0	4	2	1	2	3	2	1	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:118015319G>A	ENST00000368494.3	+	3	836	c.667G>A	c.(667-669)Gta>Ata	p.V223I		NM_138459.3	NP_612468.1	Q96E22	NGBR_HUMAN	nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae)	223					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|intracellular cholesterol transport (GO:0032367)|protein glycosylation (GO:0006486)|sterol homeostasis (GO:0055092)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|prostate(2)	8		all_cancers(87;0.0395)|all_epithelial(87;0.0301)		GBM - Glioblastoma multiforme(226;0.02)|OV - Ovarian serous cystadenocarcinoma(136;0.115)|all cancers(137;0.146)		AGATTTGGATGTAGATACGTT	0.373																																					p.V223I		.											.	NUS1-108	0			c.G667A						.						89	91	90					6																	118015319		2203	4300	6503	SO:0001583	missense	116150	exon3			TTGGATGTAGATA	BC013026	CCDS5118.1	6q22.1	2012-12-13	2006-11-24	2006-11-24	ENSG00000153989	ENSG00000153989			21042	protein-coding gene	gene with protein product	"Nogo-B receptor", "transport and golgi organization 14 homolog (Drosophila)"	610463	"chromosome 6 open reading frame 68"	C6orf68			Standard	NM_138459		Approved	MGC7199, NgBR, TANGO14	uc003pxw.3	Q96E22	OTTHUMG00000015458	ENST00000368494.3:c.667G>A	6.37:g.118015319G>A	ENSP00000357480:p.Val223Ile	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	87	50	NM_138459	0	0	2	3	1	B2RWQ4|O00251	Missense_Mutation	SNP	ENST00000368494.3	37	CCDS5118.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.550972	0.45383	.	.	ENSG00000153989	ENST00000368494	T	0.29397	1.57	5.1	5.1	0.69264	.	0.115570	0.64402	D	0.000015	T	0.16128	0.0388	L	0.47078	1.49	0.58432	D	0.999992	P	0.36086	0.536	B	0.34873	0.191	T	0.02713	-1.1120	10	0.37606	T	0.19	-0.3662	13.2505	0.60050	0.0769:0.0:0.9231:0.0	.	223	Q96E22	NGBR_HUMAN	I	223	ENSP00000357480:V223I	ENSP00000357480:V223I	V	+	1	0	NUS1	118122012	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.487000	0.60293	2.537000	0.85549	0.650000	0.86243	GTA	.		0.373	NUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041989.1	NM_138459		A	118015319	G	A	118015319	3	1	54	1	0	0	0	0	1	0	0	0	10803	1377	48	2	677	2	NUS1	6	118015319	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	10187792	118015319	53099748	58	5228											
GPR126	57211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	142691578	142691578	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgaataatgcattacctgtCaaagaaaaagaagacatttt	18	12	6	5	0	1	4	1	1	0	3	1	4	1	4	1	0	2	1	1	0	7	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:142691578C>T	ENST00000230173.6	+	4	1193	c.717C>T	c.(715-717)gtC>gtT	p.V239V	GPR126_ENST00000367608.2_Silent_p.V239V|GPR126_ENST00000296932.8_Silent_p.V239V|GPR126_ENST00000367609.3_Silent_p.V239V|GPR126_ENST00000545477.1_Intron	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	239	Pentaxin.				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)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		CATTACCTGTCAAAGAAAAAG	0.353																																					p.V239V		.											.	GPR126-91	0			c.C717T						.						64	63	63					6																	142691578		1828	4081	5909	SO:0001819	synonymous_variant	57211	exon4			ACCTGTCAAAGAA	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.717C>T	6.37:g.142691578C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	38	8	NM_198569	0	0	0	0	0	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Silent	SNP	ENST00000230173.6	37	CCDS47490.1																																																																																			.		0.353	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142691578	C	T	142691578	2	4	54	1	0	0	0	0	0	0	0	1	6660	813	29	2		2	GPR126	6	142691578	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	24676259	142691578	28423489	59	5229											
ARID1B	57492	broad.mit.edu	37	chr6	157099342	157099342	+	Frame_Shift_Del	DEL	C	C	-																															caccaccatgcccaccaccaCcaccaccatgcccaccacct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:157099342delC	ENST00000350026.5	+	1	280	c.279delC	c.(277-279)cacfs	p.H96fs	RP11-230C9.2_ENST00000603191.1_lincRNA|ARID1B_ENST00000275248.4_Frame_Shift_Del_p.H38fs|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000367148.1_Frame_Shift_Del_p.H96fs|ARID1B_ENST00000346085.5_Frame_Shift_Del_p.H96fs|MIR4466_ENST00000606121.1_RNA	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	96	His-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		cccaccaccaccaccaccatg	0.652																																					p.H93fs													.	ARID1B-154	0			c.279delC						.						11	20	17					6																	157099342		1813	3513	5326	SO:0001589	frameshift_variant	57492	exon1			CCACCACCACCAC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.279delC	6.37:g.157099342delC	ENSP00000055163:p.His96fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_017519	0	0	0	0	0	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Del	DEL	ENST00000350026.5	37	CCDS5251.2																																																																																			.		0.652	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		-	157099342	C	-	157099342	7	5	54	1	0	1	0	1	0	0	0	0	914	506	18	0	281	0	ARID1B	6	157099342	Frame_Shift_Del	DEL	C	TCGA-B9-A44B-01A-11D-A25F-10	14407764	157099342	14015725	60	5230											
IGF2R	3482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	160445676	160445676	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatcaagcttagtggtgccTacttggtggatgactccgat	8	13	12	8	1	1	2	1	2	0	0	2	4	2	3	2	3	3	1	2	3	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:160445676T>C	ENST00000356956.1	+	5	734	c.586T>C	c.(586-588)Tac>Cac	p.Y196H		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	196					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TAGTGGTGCCTACTTGGTGGA	0.473																																					p.Y196H		.											.	IGF2R-118	0			c.T586C						.						277	241	253					6																	160445676		2203	4300	6503	SO:0001583	missense	3482	exon5			GGTGCCTACTTGG	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.586T>C	6.37:g.160445676T>C	ENSP00000349437:p.Tyr196His	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	172	47	NM_000876	0	0	0	0	0	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.109386	0.56398	.	.	ENSG00000197081	ENST00000356956	T	0.02682	4.2	5.47	5.47	0.80525	Mannose-6-phosphate receptor, binding (1);	0.232876	0.45361	D	0.000378	T	0.08891	0.0220	M	0.77103	2.36	0.39897	D	0.97384	D	0.89917	1.0	D	0.91635	0.999	T	0.21109	-1.0255	10	0.30854	T	0.27	-3.4455	15.5981	0.76602	0.0:0.0:0.0:1.0	.	196	P11717	MPRI_HUMAN	H	196	ENSP00000349437:Y196H	ENSP00000349437:Y196H	Y	+	1	0	IGF2R	160365666	1.000000	0.71417	0.672000	0.29872	0.761000	0.43186	4.495000	0.60353	2.077000	0.62373	0.374000	0.22700	TAC	.		0.473	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160445676	T	C	160445676	3	2	54	1	0	0	0	0	1	0	0	0	7597	1522	53	3	604	3	IGF2R	6	160445676	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	3346334	160445676	10669391	61	5231											
CARD11	84433	broad.mit.edu	37	chr7	2959068	2959068	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgaaagggtcgacccgcgcGcacagccactcgtgcctgtc	7	6	13	15	5	0	1	0	1	0	0	3	2	0	1	3	1	2	1	3	1	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:2959068G>A	ENST00000396946.4	-	18	2851	c.2448C>T	c.(2446-2448)tgC>tgT	p.C816C		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	816					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CGACCCGCGCGCACAGCCACT	0.607			Mis		DLBCL																																p.C816C				Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11-870	0			c.C2448T						.						92	70	77					7																	2959068		2203	4300	6503	SO:0001819	synonymous_variant	84433	exon18			CCGCGCGCACAGC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2448C>T	7.37:g.2959068G>A		Somatic	226	0		WXS	Illumina HiSeq	Phase_I	290	8	NM_032415	0	0	2	2	0	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			.		0.607	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2959068	G	A	2959068	2	1	54	1	0	0	0	0	0	0	0	1	2651	1079	38	1		1	CARD11	7	2959068	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		2959068	156179595	62	5232											
NEUROD6	63974	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	31378439	31378440	+	Missense_Mutation	DNP	TT	TT	AA																															ctcttgccgattctcagaatTtcagaaagtgcccagatgta																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:31378439_31378440TT>AA	ENST00000297142.3	-	2	765_766	c.443_444AA>TT	c.(442-444)gAA>gTT	p.E148V		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	148					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						TTCTCAGAATTTCAGAAAGTGC	0.441																																					p.E148V													.	NEUROD6-92	0			c.A443T						.																																			SO:0001583	missense	63974	exon2			AGAATTTCAGAAA	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"Basic helix-loop-helix proteins"	13804	protein-coding gene	gene with protein product		611513	"neurogenic differentiation 6"			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.443_444delinsAA	7.37:g.31378439_31378440delinsAA	ENSP00000297142:p.Glu148Val	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	97	36	NM_022728	0	0	0	0	0	Q548T9|Q9H3H6	Missense_Mutation	DNP	ENST00000297142.3	37	CCDS5434.1																																																																																			.		0.441	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		AA	31378440	TT	AA	31378439	3	1	54	1	0	0	0	0	1	0	0	0	10377	1838	64	5	573	5	NEUROD6	7	31378439	Missense_Mutation	DNP	TT	TCGA-B9-A44B-01A-11D-A25F-10	28419371	31378439	127760224	63	5233											
CCDC129	223075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	31682718	31682718	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgtcacagaaatgcaggaCagttttgtgaggcctgaggg	11	8	14	8	1	1	3	1	2	0	1	1	4	1	4	1	3	1	2	1	3	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:31682718C>A	ENST00000407970.3	+	11	1772	c.1734C>A	c.(1732-1734)gaC>gaA	p.D578E	CCDC129_ENST00000451887.2_Missense_Mutation_p.D604E|CCDC129_ENST00000319386.3_Missense_Mutation_p.D430E|CCDC129_ENST00000409210.1_Missense_Mutation_p.D486E	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	578										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAATGCAGGACAGTTTTGTGA	0.488																																					p.D604E		.											.	.	0			c.C1812A						.						173	173	173					7																	31682718		2203	4300	6503	SO:0001583	missense	223075	exon11			GCAGGACAGTTTT	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1734C>A	7.37:g.31682718C>A	ENSP00000384416:p.Asp578Glu	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	138	61	NM_001257968	0	0	0	0	0	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	C	14.17	2.456804	0.43634	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.25414	1.8;2.12;2.1;1.86	5.93	-11.6	0.00059	.	0.467692	0.20346	N	0.094142	T	0.15219	0.0367	M	0.69823	2.125	0.09310	N	1	P;P;P;P	0.41450	0.75;0.565;0.565;0.734	B;B;B;B	0.39503	0.168;0.107;0.107;0.301	T	0.00216	-1.1910	10	0.38643	T	0.18	-37.2348	1.7051	0.02880	0.2799:0.2778:0.079:0.3633	.	604;588;578;430	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	E	430;578;604;588;486	ENSP00000313062:D430E;ENSP00000384416:D578E;ENSP00000395835:D604E;ENSP00000387214:D486E	ENSP00000313062:D430E	D	+	3	2	CCDC129	31649243	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.334000	0.02665	-2.216000	0.00732	-1.094000	0.02160	GAC	.		0.488	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		A	31682718	C	A	31682718	3	1	54	1	0	0	0	0	1	0	0	0	2770	477	17	4	1772	4	CCDC129	7	31682718	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	304279	31682718	127455945	64	5234											
HERPUD2	64224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	35733937	35733937	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aatctccatcccactttggtCcatggtgcccccaaagtcag	9	10	7	15	0	2	0	1	0	1	0	5	0	4	0	5	2	1	0	5	2	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:35733937C>T	ENST00000396081.1	-	1	808	c.4G>A	c.(4-6)Gac>Aac	p.D2N	RP11-379H18.1_ENST00000605778.1_RNA|HERPUD2_ENST00000311350.3_Missense_Mutation_p.D2N	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	2					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						CCACTTTGGTCCATGGTGCCC	0.537																																					p.D2N		.											.	HERPUD2-93	0			c.G4A						.						106	108	107					7																	35733937		2203	4300	6503	SO:0001583	missense	64224	exon2			TTTGGTCCATGGT	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.4G>A	7.37:g.35733937C>T	ENSP00000379390:p.Asp2Asn	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	166	62	NM_022373	0	0	3	5	2	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	37	CCDS5446.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.779789	0.90195	.	.	ENSG00000122557	ENST00000396081;ENST00000311350;ENST00000438224;ENST00000413517;ENST00000427455	T;T;T;T;T	0.57436	1.52;1.52;1.21;1.55;0.4	3.53	3.53	0.40419	.	0.275735	0.39985	N	0.001216	T	0.57504	0.2058	L	0.50333	1.59	0.38724	D	0.953506	D	0.59767	0.986	P	0.55615	0.78	T	0.64275	-0.6446	10	0.72032	D	0.01	-3.5396	10.7536	0.46223	0.1906:0.8094:0.0:0.0	.	2	Q9BSE4	HERP2_HUMAN	N	2	ENSP00000379390:D2N;ENSP00000310729:D2N;ENSP00000415475:D2N;ENSP00000391015:D2N;ENSP00000412895:D2N	ENSP00000310729:D2N	D	-	1	0	HERPUD2	35700462	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.641000	0.74324	2.253000	0.74438	0.467000	0.42956	GAC	.		0.537	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		T	35733937	C	T	35733937	3	4	54	1	0	0	0	0	1	0	0	0	7085	855	30	2	1248	2	HERPUD2	7	35733937	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4051219	35733937	123404726	65	5235											
PKD1L1	168507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	47853600	47853600	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tattaggtagcattttcctcCaagagctccaggctgaaagg	11	11	10	9	0	0	2	0	1	0	1	3	2	3	2	3	3	2	4	3	3	5	5	rs147316882		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:47853600C>T	ENST00000289672.2	-	48	7152	c.7102G>A	c.(7102-7104)Gga>Aga	p.G2368R	C7orf69_ENST00000418326.2_Intron|C7orf69_ENST00000258776.4_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2368					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CATTTTCCTCCAAGAGCTCCA	0.458																																					p.G2368R		.											.	PKD1L1-145	0			c.G7102A						.	C	,ARG/GLY	0,4406		0,0,2203	73	68	70		,7102	3.5	0.6	7	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,probably-damaging	,2368/2850	47853600	1,13005	2203	4300	6503	SO:0001583	missense	168507	exon48			TTCCTCCAAGAGC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7102G>A	7.37:g.47853600C>T	ENSP00000289672:p.Gly2368Arg	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	51	26	NM_138295	0	0	0	0	0	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.772575	0.49680	0.0	1.16E-4	ENSG00000158683	ENST00000289672	T	0.19250	2.16	5.3	3.48	0.39840	.	0.260784	0.26903	N	0.021910	T	0.35393	0.0930	L	0.60455	1.87	0.80722	D	1	D	0.65815	0.995	P	0.62435	0.902	T	0.02813	-1.1107	10	0.49607	T	0.09	-7.9894	9.0941	0.36629	0.0:0.7697:0.148:0.0823	.	2368	Q8TDX9	PK1L1_HUMAN	R	2368	ENSP00000289672:G2368R	ENSP00000289672:G2368R	G	-	1	0	PKD1L1	47820125	0.492000	0.26027	0.605000	0.28930	0.632000	0.37999	1.534000	0.36051	0.604000	0.29930	-0.172000	0.13284	GGA	C|1.000;T|0.000		0.458	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47853600	C	T	47853600	3	4	54	1	0	0	0	0	1	0	0	0	11990	603	21	2	1487	2	PKD1L1	7	47853600	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	12119663	47853600	111285063	66	5236											
VWC2	375567	hgsc.bcm.edu	37	chr7	49815193	49815193	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgagcacgcctctcgggaCggcccggggcgggtgaacga	6	4	18	13	7	1	2	0	2	1	0	2	4	1	3	2	5	2	1	2	5	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:49815193C>T	ENST00000340652.4	+	2	718	c.162C>T	c.(160-162)gaC>gaT	p.D54D		NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	54					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)				cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						CCTCTCGGGACGGCCCGGGGC	0.741																																					p.D54D		.											.	VWC2-514	0			c.C162T						.						6	6	6					7																	49815193		2074	4046	6120	SO:0001819	synonymous_variant	375567	exon2			TCGGGACGGCCCG	AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"brorin", "brain-specific chordin-like"	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.162C>T	7.37:g.49815193C>T		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	8	7	NM_198570	0	0	0	0	0	Q6UXE2	Silent	SNP	ENST00000340652.4	37	CCDS5508.1																																																																																			.		0.741	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570		T	49815193	C	T	49815193	2	4	54	1	0	0	0	0	0	0	0	1	17276	535	19	1		1	VWC2	7	49815193	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	1961593	49815193	109323470	67	5237											
RHBDD2	57414	broad.mit.edu;bcgsc.ca	37	chr7	75511278	75511278	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgccactgcttcttcaccGtgatcttcgccatcttctcc	4	14	5	18	3	5	1	1	1	4	0	8	1	6	1	5	0	1	1	5	0	0	4	rs375383259		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:75511278G>A	ENST00000006777.6	+	2	445	c.310G>A	c.(310-312)Gtg>Atg	p.V104M	RHBDD2_ENST00000428119.1_5'Flank|RHBDD2_ENST00000318622.4_5'UTR|RHBDD2_ENST00000468304.1_Intron	NM_001040456.1	NP_001035546.1	Q6NTF9	RHBD2_HUMAN	rhomboid domain containing 2	104						Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|lung(4)|prostate(1)	6						CTTCTTCACCGTGATCTTCGC	0.562																																					p.V104M													.	RHBDD2-90	0			c.G310A						.	G	MET/VAL,	0,4300		0,0,2150	155	167	163		310,	-1.9	1	7		163	1,8509		0,1,4254	no	missense,utr-5	RHBDD2	NM_001040456.1,NM_001040457.1	21,	0,1,6404	AA,AG,GG		0.0118,0.0,0.0078	possibly-damaging,	104/365,	75511278	1,12809	2150	4255	6405	SO:0001583	missense	57414	exon2			TTCACCGTGATCT	AF226732	CCDS43602.1, CCDS43603.1	7q11	2008-09-04	2006-02-22	2006-02-22	ENSG00000005486	ENSG00000005486			23082	protein-coding gene	gene with protein product		615203	"rhomboid, veinlet-like 7 (Drosophila)"	RHBDL7		12838346	Standard	XM_005250511		Approved	NPD007	uc003udw.1	Q6NTF9	OTTHUMG00000156435	ENST00000006777.6:c.310G>A	7.37:g.75511278G>A	ENSP00000006777:p.Val104Met	Somatic	337	1		WXS	Illumina HiSeq	Phase_I	399	22	NM_001040456	0	0	81	82	1	Q7L534|Q9H5W6|Q9HBK7|Q9UDT2	Missense_Mutation	SNP	ENST00000006777.6	37	CCDS43602.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.574233	0.45902	0.0	1.18E-4	ENSG00000005486	ENST00000006777;ENST00000413229	T	0.14022	2.54	5.63	-1.94	0.07571	Peptidase S54, rhomboid domain (1);	0.633406	0.14408	N	0.321425	T	0.08044	0.0201	N	0.19112	0.55	0.24848	N	0.992425	B	0.32365	0.367	B	0.31245	0.126	T	0.28299	-1.0048	10	0.33141	T	0.24	-2.1708	11.7139	0.51641	0.0:0.3837:0.4834:0.133	.	104	Q6NTF9	RHBD2_HUMAN	M	104;149	ENSP00000006777:V104M	ENSP00000006777:V104M	V	+	1	0	RHBDD2	75349214	0.000000	0.05858	0.979000	0.43373	0.994000	0.84299	-1.372000	0.02570	-0.262000	0.09392	-0.262000	0.10625	GTG	.		0.562	RHBDD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344176.1	NM_020684		A	75511278	G	A	75511278	3	1	54	1	0	0	0	0	1	0	0	0	13349	1145	40	1	316	1	RHBDD2	7	75511278	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	25696085	75511278	83627385	68	5238											
POMZP3	22932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	76240801	76240801	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gttacagggaagcagacgtgGaccactggctcacgacacga	12	5	13	11	3	1	1	1	0	0	1	1	5	1	3	1	3	2	3	1	3	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:76240801G>T	ENST00000310842.4	-	6	1229	c.545C>A	c.(544-546)tCc>tAc	p.S182Y	AC004980.7_ENST00000418663.1_RNA|UPK3B_ENST00000419923.2_Intron|UPK3B_ENST00000443097.2_Intron|POMZP3_ENST00000275569.4_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	182										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				AGCAGACGTGGACCACTGGCT	0.537																																					p.S182Y		.											.	POMZP3-90	0			c.C545A						.						72	71	72					7																	76240801		2200	4279	6479	SO:0001583	missense	22932	exon6			GACGTGGACCACT	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"POM-ZP3 fusion protein", "POM121/ZP3 fusion protein"	600587	"POM (POM121 rat homolog) and ZP3 fusion", "POM (POM121 homolog, rat) and ZP3 fusion"			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.545C>A	7.37:g.76240801G>T	ENSP00000309233:p.Ser182Tyr	Somatic	373	1		WXS	Illumina HiSeq	Phase_I	382	118	NM_012230	0	0	10	18	8	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	37	CCDS43606.1	.	.	.	.	.	.	.	.	.	.	N	8.381	0.837429	0.16891	.	.	ENSG00000146707	ENST00000310842	T	0.23950	1.88	0.786	-1.57	0.08506	.	3.392970	0.01303	U	0.010346	T	0.28134	0.0694	L	0.38175	1.15	0.09310	N	1	D	0.57257	0.979	P	0.50970	0.655	T	0.18241	-1.0343	10	0.87932	D	0	.	3.7228	0.08463	0.0:0.0:0.477:0.523	.	182	Q6PJE2	POZP3_HUMAN	Y	182	ENSP00000309233:S182Y	ENSP00000309233:S182Y	S	-	2	0	POMZP3	76078737	0.000000	0.05858	0.089000	0.20774	0.299000	0.27559	-0.671000	0.05250	-0.344000	0.08338	0.372000	0.22366	TCC	.		0.537	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230		T	76240801	G	T	76240801	3	4	54	1	0	0	0	0	1	0	0	0	12273	1174	41	4	29	4	POMZP3	7	76240801	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	729523	76240801	82897862	69	5239											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	82579041	82579041	+	Frame_Shift_Del	DEL	T	T	-																															gagatgggtgagtaaaggacTttgggggatttgggtgggga																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:82579041delT	ENST00000333891.9	-	6	11200	c.10863delA	c.(10861-10863)aaafs	p.K3621fs	PCLO_ENST00000437081.1_Frame_Shift_Del_p.K341fs|PCLO_ENST00000423517.2_Frame_Shift_Del_p.K3621fs	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGTAAAGGACTTTGGGGGATT	0.478																																					p.K3621fs		.											.	PCLO-29	0			c.10863delA						.						106	107	106					7																	82579041		2005	4186	6191	SO:0001589	frameshift_variant	27445	exon6			.	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.10863delA	7.37:g.82579041delT	ENSP00000334319:p.Lys3621fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	111	46	NM_014510	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000333891.9	37	CCDS47630.1																																																																																			.		0.478	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		-	82579041	T	-	82579041	7	5	54	1	0	1	0	1	0	0	0	0	11609	1606	56	0	4662	0	PCLO	7	82579041	Frame_Shift_Del	DEL	T	TCGA-B9-A44B-01A-11D-A25F-10	6338240	82579041	76559622	70	5240											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	82585266	82585266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactgttgagctcaattgttTtaaatcggcgtagccctcct	8	15	8	10	2	1	1	1	1	0	0	3	1	2	1	2	1	3	4	2	1	5	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:82585266T>C	ENST00000333891.9	-	5	5340	c.5003A>G	c.(5002-5004)aAa>aGa	p.K1668R	PCLO_ENST00000423517.2_Missense_Mutation_p.K1668R	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTCAATTGTTTTAAATCGGCG	0.368																																					p.K1668R		.											.	PCLO-29	0			c.A5003G						.						107	99	102					7																	82585266		1859	4098	5957	SO:0001583	missense	27445	exon5			ATTGTTTTAAATC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5003A>G	7.37:g.82585266T>C	ENSP00000334319:p.Lys1668Arg	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	99	44	NM_014510	0	0	0	0	0		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	7.727	0.698443	0.15106	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.26810	1.71;1.73	5.31	5.31	0.75309	.	.	.	.	.	T	0.35068	0.0919	M	0.74881	2.28	0.80722	D	1	P;P	0.45715	0.865;0.865	B;B	0.42555	0.391;0.391	T	0.36359	-0.9751	9	0.87932	D	0	.	15.2616	0.73628	0.0:0.0:0.0:1.0	.	1668;1668	Q9Y6V0-5;Q9Y6V0-6	.;.	R	1599;1668;1668	ENSP00000334319:K1668R;ENSP00000388393:K1668R	ENSP00000334319:K1668R	K	-	2	0	PCLO	82423202	1.000000	0.71417	0.847000	0.33407	0.907000	0.53573	5.048000	0.64238	2.005000	0.58758	0.528000	0.53228	AAA	.		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82585266	T	C	82585266	3	2	54	1	0	0	0	0	1	0	0	0	11609	1841	64	3	10526	3	PCLO	7	82585266	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	6225	82585266	76553397	71	5241											
ANKIB1	54467	ucsc.edu;bcgsc.ca	37	chr7	91957150	91957150	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactaaaagatatgcttatTgtggaaactgcagacatgct	15	11	9	6	0	0	3	0	0	0	3	0	4	0	4	0	1	4	3	0	1	5	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:91957150T>C	ENST00000265742.3	+	5	1099	c.723T>C	c.(721-723)atT>atC	p.I241I		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	241							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ATATGCTTATTGTGGAAACTG	0.368																																					p.I241I													.	ANKIB1-432	0			c.T723C						.						85	83	84					7																	91957150		1844	4092	5936	SO:0001819	synonymous_variant	54467	exon5			GCTTATTGTGGAA	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.723T>C	7.37:g.91957150T>C		Somatic	56	1		WXS	Illumina HiSeq		67	30	NM_019004	0	0	0	1	1	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																			.		0.368	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			C	91957150	T	C	91957150	2	2	54	1	0	0	0	0	0	0	0	1	630	1800	63	3		3	ANKIB1	7	91957150	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	9371884	91957150	67181513	72	5242											
PRKAR2B	5577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	106799967	106799967	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaggaacatcgctacctaTgaagaacagttagttgccct	15	9	8	9	1	0	2	0	1	0	1	1	3	0	3	2	1	4	3	2	1	8	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:106799967T>A	ENST00000265717.4	+	11	1456	c.1197T>A	c.(1195-1197)taT>taA	p.Y399*		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	399					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TCGCTACCTATGAAGAACAGT	0.388																																					p.Y399X		.											.	PRKAR2B-1083	0			c.T1197A						.						135	118	124					7																	106799967		2203	4300	6503	SO:0001587	stop_gained	5577	exon11			TACCTATGAAGAA		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1197T>A	7.37:g.106799967T>A	ENSP00000265717:p.Tyr399*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	114	42	NM_002736	0	0	0	0	0	A4D0R9	Nonsense_Mutation	SNP	ENST00000265717.4	37	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.821472	0.71028	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	.	.	.	5.68	2.05	0.26809	.	0.110083	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.3785	9.0728	0.36502	0.0:0.277:0.0:0.723	.	.	.	.	X	399;399;386	.	ENSP00000265717:Y399X	Y	+	3	2	PRKAR2B	106587203	0.950000	0.32346	1.000000	0.80357	0.997000	0.91878	0.030000	0.13688	0.113000	0.18004	0.528000	0.53228	TAT	.		0.388	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			A	106799967	T	A	106799967	4	1	54	1	0	0	0	0	0	1	0	0	12535	1471	51	5	1239	5	PRKAR2B	7	106799967	Nonsense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	14842817	106799967	52338696	73	5243											
ADCK2	90956	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	140380887	140380887	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcaggcaggaattcccgtgGacttgaaaaggaagattgca	14	7	13	7	1	0	2	0	1	0	1	1	5	1	5	1	4	2	3	1	4	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:140380887G>T	ENST00000072869.4	+	4	1433	c.1255G>T	c.(1255-1257)Gac>Tac	p.D419Y	ADCK2_ENST00000476491.1_Missense_Mutation_p.D419Y	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	419	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					AATTCCCGTGGACTTGAAAAG	0.562																																					p.D419Y		.											.	ADCK2-333	0			c.G1255T						.						137	114	122					7																	140380887		2203	4300	6503	SO:0001583	missense	90956	exon4			CCCGTGGACTTGA	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.1255G>T	7.37:g.140380887G>T	ENSP00000072869:p.Asp419Tyr	Somatic	278	0		WXS	Illumina HiSeq	Phase_I	287	122	NM_052853	0	0	16	31	15	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	37	CCDS5861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.78|14.78	2.638582|2.638582	0.47153|0.47153	.|.	.|.	ENSG00000133597|ENSG00000133597	ENST00000072869;ENST00000476491;ENST00000473512|ENST00000483369	T;T;T|.	0.12039|.	2.72;2.72;2.72|.	4.18|4.18	3.2|3.2	0.36748|0.36748	.|.	0.234009|.	0.34245|.	N|.	0.004140|.	T|T	0.55609|0.55609	0.1931|0.1931	M|M	0.70595|0.70595	2.14|2.14	0.19945|0.19945	N|N	0.999942|0.999942	D;D|.	0.54397|.	0.966;0.966|.	P;P|.	0.46718|.	0.525;0.525|.	T|T	0.46735|0.46735	-0.9170|-0.9170	10|5	0.66056|.	D|.	0.02|.	-50.6212|-50.6212	10.5732|10.5732	0.45212|0.45212	0.1074:0.0:0.8926:0.0|0.1074:0.0:0.8926:0.0	.|.	419;419|.	C9JE15;Q7Z695|.	.;ADCK2_HUMAN|.	Y|V	419;419;59|256	ENSP00000072869:D419Y;ENSP00000420512:D419Y;ENSP00000420288:D59Y|.	ENSP00000072869:D419Y|.	D|G	+|+	1|2	0|0	ADCK2|ADCK2	140027356|140027356	0.982000|0.982000	0.34865|0.34865	0.077000|0.077000	0.20336|0.20336	0.837000|0.837000	0.47467|0.47467	4.292000|4.292000	0.59031|0.59031	2.154000|2.154000	0.67381|0.67381	0.561000|0.561000	0.74099|0.74099	GAC|GGA	.		0.562	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		T	140380887	G	T	140380887	3	4	54	1	0	0	0	0	1	0	0	0	289	1174	41	4	1269	4	ADCK2	7	140380887	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	33580920	140380887	18757776	74	5244											
RBM33	155435	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	155534581	155534582	+	Frame_Shift_Ins	INS	-	-	A																															ccactgcgccaaggaacagcINSaatttgcgtgaattacccat																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:155534581_155534582insA	ENST00000401878.3	+	13	2316_2317	c.2118_2119insA	c.(2119-2121)aatfs	p.N707fs		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	707							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CAAGGAACAGCAATTTGCGTGA	0.49																																					p.S706fs		.											.	RBM33-23	0			c.2118_2119insA						.																																			SO:0001589	frameshift_variant	155435	exon13			.	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.2120dupA	7.37:g.155534583_155534583dupA	ENSP00000384160:p.Asn707fs	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	165	69	NM_053043	0	0	0	0	0	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Ins	INS	ENST00000401878.3	37	CCDS5941.2																																																																																			.		0.49	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		A	155534582	-	A	155534581	7	5	54	1	0	1	1	0	0	0	0	0	13162	709	25	0	2168	0	RBM33	7	155534581	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	15153694	155534581	3604082	75	5245											
FUT10	84750	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	33246682	33246683	+	Frame_Shift_Ins	INS	-	-	A																															catcagaatccagtcgtctgINSatgtaacttgccagttccct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:33246682_33246683insA	ENST00000327671.5	-	4	1641_1642	c.1010_1011insT	c.(1009-1011)atcfs	p.I337fs	FUT10_ENST00000524021.1_Frame_Shift_Ins_p.I309fs|FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Frame_Shift_Ins_p.I275fs|FUT10_ENST00000518672.1_Frame_Shift_Ins_p.I309fs	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	337					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CCAGTCGTCTGATGTAACTTGC	0.46																																					p.I337fs		.											.	FUT10-92	0			c.1011_1012insT						.																																			SO:0001589	frameshift_variant	84750	exon4			.	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1011dupT	8.37:g.33246683_33246683dupA	ENSP00000332757:p.Ile337fs	Somatic	301	0		WXS	Illumina HiSeq	Phase_I	311	126	NM_032664	0	0	0	0	0	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Frame_Shift_Ins	INS	ENST00000327671.5	37	CCDS6088.1																																																																																			.		0.46	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		A	33246683	-	A	33246682	7	5	54	1	0	1	1	0	0	0	0	0	6121	1280	45	0	436	0	FUT10	8	33246682	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10		33246682	113117340	76	5246											
RNF19A	25897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	101276971	101276971	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctgctatggccaaattccGtttgtgctttgaaacatcct	9	14	7	11	1	0	1	0	1	0	0	2	1	2	1	4	1	3	3	4	1	3	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:101276971G>A	ENST00000519449.1	-	7	1550	c.1234C>T	c.(1234-1236)Cgg>Tgg	p.R412W	RNF19A_ENST00000341084.2_Missense_Mutation_p.R412W|RNF19A_ENST00000523255.1_5'UTR	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	412					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R412W(1)		breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	30	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			GCCAAATTCCGTTTGTGCTTT	0.373																																					p.R412W		.											.	RNF19A-229	1	Substitution - Missense(1)	endometrium(1)	c.C1234T						.						239	211	220					8																	101276971		2203	4300	6503	SO:0001583	missense	25897	exon7			AATTCCGTTTGTG	AB029316	CCDS6286.1	8q22	2013-10-03	2013-10-03	2007-08-20		ENSG00000034677		"RING-type (C3HC4) zinc fingers"	13432	protein-coding gene	gene with protein product		607119	"ring finger protein 19", "ring finger protein 19A", "ring finger protein 19A, E3 ubiquitin protein ligase"	RNF19		11237715, 10976766	Standard	NM_183419		Approved	dorfin, DKFZp566B1346	uc003yjj.1	Q9NV58		ENST00000519449.1:c.1234C>T	8.37:g.101276971G>A	ENSP00000428968:p.Arg412Trp	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	98	23	NM_015435	0	0	7	9	2	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012643	0.75161	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.86297	-2.1;-2.1	5.17	4.28	0.50868	.	0.053565	0.64402	D	0.000002	D	0.92704	0.7681	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93259	0.6641	10	0.87932	D	0	.	12.7055	0.57058	0.0:0.0:0.5807:0.4193	.	412	Q9NV58	RN19A_HUMAN	W	412	ENSP00000428968:R412W;ENSP00000342667:R412W	ENSP00000342667:R412W	R	-	1	2	RNF19A	101346147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.083000	0.41615	1.305000	0.44909	0.650000	0.86243	CGG	.		0.373	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		A	101276971	G	A	101276971	3	1	54	1	0	0	0	0	1	0	0	0	13502	1144	40	1	1302	1	RNF19A	8	101276971	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	68030289	101276971	45087051	77	5247											
RSPO2	340419	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	108970372	108970372	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaatggttggacacagtatTgtgtctttcactggcttttt	7	17	10	7	0	2	0	1	0	1	0	2	1	2	1	0	3	0	4	0	3	2	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:108970372T>C	ENST00000276659.5	-	5	1172	c.552A>G	c.(550-552)acA>acG	p.T184T	RSPO2_ENST00000378439.2_Silent_p.T120T|RSPO2_ENST00000517939.1_Silent_p.T117T|RSPO2_ENST00000517781.1_Silent_p.T120T	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	184	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			GACACAGTATTGTGTCTTTCA	0.443																																					p.T184T		.											.	RSPO2-231	0			c.A552G						.						328	281	297					8																	108970372		2203	4300	6503	SO:0001819	synonymous_variant	340419	exon5			CAGTATTGTGTCT	AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.552A>G	8.37:g.108970372T>C		Somatic	217	0		WXS	Illumina HiSeq	Phase_I	239	112	NM_178565	0	0	0	0	0	B3KVP0|Q4G0U4|Q8N6X6	Silent	SNP	ENST00000276659.5	37	CCDS6307.1																																																																																			.		0.443	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		C	108970372	T	C	108970372	2	2	54	1	0	0	0	0	0	0	0	1	13742	1799	63	3		3	RSPO2	8	108970372	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	7693401	108970372	37393650	78	5248											
FLJ43860	389690	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	142486196	142486196	+	RNA	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaaacacgctgcggaagcaGgtggacaggagctgagactt	12	5	15	9	2	0	1	0	1	0	1	0	5	0	4	0	4	4	4	0	4	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:142486196G>A	ENST00000430863.1	-	0	1577					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		TGCGGAAGCAGGTGGACAGGA	0.617																																					.													.	.	0			.						.						21	27	25					8																	142486196		2046	4199	6245			389690	.			GAAGCAGGTGGAC			8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142486196G>A		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	133	71	.	0	0	0	0	0		Silent	SNP	ENST00000430863.1	37																																																																																				.		0.617	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		A	142486196	G	A	142486196	1	1	54	0	1	0	0	0	0	0	0	0	5949	987	35	2		2	FLJ43860	8	142486196	RNA	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	33515824	142486196	3877826	79	5249											
EEF1D	1936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144661995	144661995	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagctgcgatatcgacactCtgcacctgaggagaggcgga	12	6	13	10	3	1	2	0	1	1	1	2	6	1	3	1	3	3	2	1	3	2	1	rs11548159		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:144661995C>G	ENST00000529272.1	-	8	1213	c.813G>C	c.(811-813)caG>caC	p.Q271H	EEF1D_ENST00000524624.1_Missense_Mutation_p.Q247H|EEF1D_ENST00000317198.6_Missense_Mutation_p.Q271H|EEF1D_ENST00000423316.2_Missense_Mutation_p.Q637H|NAPRT1_ENST00000276844.7_5'Flank|EEF1D_ENST00000419152.2_Missense_Mutation_p.Q271H|EEF1D_ENST00000442189.2_Missense_Mutation_p.Q637H|NAPRT1_ENST00000435154.3_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|EEF1D_ENST00000531621.1_Missense_Mutation_p.Q228H|EEF1D_ENST00000532400.1_Missense_Mutation_p.R87T|EEF1D_ENST00000395119.3_Missense_Mutation_p.Q271H|EEF1D_ENST00000526838.1_Missense_Mutation_p.Q252H|EEF1D_ENST00000532741.1_Missense_Mutation_p.Q687H|RP11-661A12.7_ENST00000529247.1_RNA|NAPRT1_ENST00000449291.2_5'Flank|EEF1D_ENST00000528610.1_Missense_Mutation_p.Q247H|NAPRT1_ENST00000426292.3_5'Flank			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	271	Catalytic (GEF).				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			TATCGACACTCTGCACCTGAG	0.612																																					p.Q637H		.											.	EEF1D-228	0			c.G1911C						.						116	108	111					8																	144661995		2203	4300	6503	SO:0001583	missense	1936	exon10			GACACTCTGCACC	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.813G>C	8.37:g.144661995C>G	ENSP00000434872:p.Gln271His	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	112	42	NM_001130053	0	0	0	0	0	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|C|C|C	16.30|16.30|16.30|16.30	3.083562|3.083562|3.083562|3.083562	0.55861|0.55861|0.55861|0.55861	.|.|.|.	.|.|.|.	ENSG00000104529|ENSG00000104529|ENSG00000104529|ENSG00000104529	ENST00000529576|ENST00000530109|ENST00000419152;ENST00000532741;ENST00000526838;ENST00000442189;ENST00000528610;ENST00000395119;ENST00000529272;ENST00000423316;ENST00000356793;ENST00000317198;ENST00000531621;ENST00000524624|ENST00000532400	.|.|.|.	.|.|.|.	.|.|.|.	4.94|4.94|4.94|4.94	2.14|2.14|2.14|2.14	0.27477|0.27477|0.27477|0.27477	.|.|Translation elongation factor EF1B/ribosomal protein S6 (1);Translation elongation factor EF1B, beta/delta chains, conserved site (1);Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange (3);|.	.|.|0.121518|.	.|.|0.64402|.	.|.|D|.	.|.|0.000014|.	.|D|D|D	.|0.87525|0.87525|0.87525	.|0.6199|0.6199|0.6199	H|H|H|H	0.99182|0.99182|0.99182|0.99182	4.46|4.46|4.46|4.46	0.58432|0.58432|0.58432|0.58432	D|D|D|D	0.999996|0.999996|0.999996|0.999996	.|.|D;D;D;D;D;D|.	.|.|0.89917|.	.|.|1.0;0.999;1.0;0.999;1.0;1.0|.	.|.|D;D;D;D;D;D|.	.|.|0.97110|.	.|.|0.998;0.998;0.999;0.99;1.0;0.996|.	.|D|D|D	.|0.87780|0.87780|0.87780	.|0.2611|0.2611|0.2611	.|5|9|6	.|.|0.87932|0.87932	.|.|D|D	.|.|0|0	.|.|.|.	9.1243|9.1243|9.1243|9.1243	0.36805|0.36805|0.36805|0.36805	0.0:0.6883:0.0:0.3117|0.0:0.6883:0.0:0.3117|0.0:0.6883:0.0:0.3117|0.0:0.6883:0.0:0.3117	.|.|.|.	.|.|252;637;565;271;687;637|.	.|.|E9PBQ9;D3DWK1;F8W934;P29692;E9PRY8;P29692-2|.	.|.|.;.;.;EF1D_HUMAN;.;.|.	.|Q|H|T	-1|146|271;687;252;637;247;271;271;637;565;271;228;247|87	.|.|.|.	.|.|ENSP00000317399:Q271H|ENSP00000433784:R87T	.|E|Q|R	-|-|-|-	.|1|3|2	.|0|2|0	EEF1D|EEF1D|EEF1D|EEF1D	144733138|144733138|144733138|144733138	1.000000|1.000000|1.000000|1.000000	0.71417|0.71417|0.71417|0.71417	1.000000|1.000000|1.000000|1.000000	0.80357|0.80357|0.80357|0.80357	0.953000|0.953000|0.953000|0.953000	0.61014|0.61014|0.61014|0.61014	2.428000|2.428000|2.428000|2.428000	0.44749|0.44749|0.44749|0.44749	0.622000|0.622000|0.622000|0.622000	0.30249|0.30249|0.30249|0.30249	-0.136000|-0.136000|-0.136000|-0.136000	0.14681|0.14681|0.14681|0.14681	.|GAG|CAG|AGA	.		0.612	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		G	144661995	C	G	144661995	3	3	54	1	0	0	0	0	1	0	0	0	4937	912	32	4	36	4	EEF1D	8	144661995	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2175799	144661995	1702027	80	5250											
STOML2	30968	broad.mit.edu	37	chr9	35101165	35101165	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatctgttcagccttttctgCttcggaggccaggatctggg	5	14	12	10	1	4	0	1	0	3	0	5	2	4	2	2	4	2	2	2	4	1	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr9:35101165C>A	ENST00000356493.5	-	7	753	c.691G>T	c.(691-693)Gca>Tca	p.A231S	STOML2_ENST00000487490.1_5'Flank|STOML2_ENST00000452248.2_Missense_Mutation_p.A186S	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	231					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GCCTTTTCTGCTTCGGAGGCC	0.587																																					p.A231S													.	STOML2-90	0			c.G691T						.						100	99	99					9																	35101165		2203	4300	6503	SO:0001583	missense	30968	exon7			TTTCTGCTTCGGA	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.691G>T	9.37:g.35101165C>A	ENSP00000348886:p.Ala231Ser	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	108	7	NM_013442	0	0	121	123	2	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	ENST00000356493.5	37	CCDS6577.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766411	0.90020	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.98835	-4.12;-5.17	5.26	5.26	0.73747	.	0.117594	0.56097	D	0.000021	D	0.99211	0.9726	M	0.90309	3.105	0.80722	D	1	D;P	0.60575	0.988;0.882	P;P	0.62382	0.901;0.718	D	0.99338	1.0911	10	0.66056	D	0.02	-6.2121	19.0555	0.93062	0.0:1.0:0.0:0.0	.	186;231	B4E1K7;Q9UJZ1	.;STML2_HUMAN	S	231;186	ENSP00000348886:A231S;ENSP00000395743:A186S	ENSP00000348886:A231S	A	-	1	0	STOML2	35091165	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.623000	0.83113	2.739000	0.93911	0.563000	0.77884	GCA	.		0.587	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442		A	35101165	C	A	35101165	3	1	54	1	0	0	0	0	1	0	0	0	15346	797	28	4	395	4	STOML2	9	35101165	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		35101165	106112266	81	5251											
MELK	9833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	36583634	36583634	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctacttaggtggctttgcAaaggtcaaacttgcctgcca	9	12	9	11	0	1	0	1	0	0	0	2	0	2	0	3	3	5	2	3	3	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr9:36583634A>G	ENST00000298048.2	+	3	253	c.69A>G	c.(67-69)gcA>gcG	p.A23A	MELK_ENST00000536860.1_Silent_p.A23A|MELK_ENST00000545008.1_Silent_p.A23A|MELK_ENST00000541717.1_Silent_p.A23A|MELK_ENST00000538311.1_Intron|MELK_ENST00000536329.1_Intron|MELK_ENST00000543751.1_Intron|MELK_ENST00000536987.1_Intron|MELK_ENST00000487398.1_Intron	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	23	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			GTGGCTTTGCAAAGGTCAAAC	0.323																																					p.A23A	Ovarian(82;980 1317 7225 14391 18624)	.											.	MELK-760	0			c.A69G						.						66	65	65					9																	36583634		2203	4300	6503	SO:0001819	synonymous_variant	9833	exon3			CTTTGCAAAGGTC	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.69A>G	9.37:g.36583634A>G		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	31	13	NM_001256688	0	0	0	0	0	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	37	CCDS6606.1																																																																																			.		0.323	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		G	36583634	A	G	36583634	2	3	54	1	0	0	0	0	0	0	0	1	9495	117	5	3		3	MELK	9	36583634	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	1482469	36583634	104629797	82	5252											
ZMYND17	118490	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	75187422	75187422	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagcccactagggagtgctCtacagtgagcacagaatcga	14	6	11	10	1	1	2	0	1	1	1	2	4	1	3	1	1	4	2	1	1	4	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:75187422C>A	ENST00000372912.1	-	2	328	c.326G>T	c.(325-327)aGa>aTa	p.R109I	AL353731.1_ENST00000584907.1_RNA|MSS51_ENST00000299432.2_Missense_Mutation_p.R109I			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	109					social behavior (GO:0035176)		metal ion binding (GO:0046872)										AGGGAGTGCTCTACAGTGAGC	0.488																																					p.R109I		.											.	.	0			c.G326T						.						150	152	151					10																	75187422		2203	4300	6503	SO:0001583	missense	118490	exon3			AGTGCTCTACAGT	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.326G>T	10.37:g.75187422C>A	ENSP00000362003:p.Arg109Ile	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	83	43	NM_001024593	0	0	0	0	0	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	37	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.006937	0.74932	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.47528	0.84;0.84	5.93	1.82	0.25136	Zinc finger, MYND-type (3);	0.272901	0.39985	N	0.001207	T	0.45915	0.1366	L	0.46157	1.445	0.28419	N	0.917817	P;P	0.42941	0.794;0.755	P;P	0.49192	0.602;0.466	T	0.37957	-0.9683	10	0.52906	T	0.07	-1.0575	7.4501	0.27234	0.0:0.5461:0.0:0.4539	.	109;109	Q4VC12;F6VAV3	ZMY17_HUMAN;.	I	109	ENSP00000299432:R109I;ENSP00000362003:R109I	ENSP00000299432:R109I	R	-	2	0	ZMYND17	74857428	0.998000	0.40836	0.944000	0.38274	0.974000	0.67602	0.901000	0.28445	0.332000	0.23536	0.591000	0.81541	AGA	.		0.488	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		A	75187422	C	A	75187422	3	1	54	1	0	0	0	0	1	0	0	0	17741	913	32	4	1076	4	ZMYND17	10	75187422	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		75187422	60347325	83	5253											
FUT11	170384	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	75533456	75533456	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgccgagaaagcccacgCggcctctcccggggacagcc	8	3	14	16	4	1	1	0	0	1	1	2	4	1	3	5	4	3	0	5	4	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:75533456C>T	ENST00000372841.3	+	2	1260	c.1217C>T	c.(1216-1218)gCg>gTg	p.A406V	AC022400.2_ENST00000595757.1_5'Flank|FUT11_ENST00000465695.1_3'UTR|FUT11_ENST00000394790.1_Missense_Mutation_p.A406V|RMRPP1_ENST00000517236.1_RNA	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	406					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					AAAGCCCACGCGGCCTCTCCC	0.597																																					p.A406V		.											.	FUT11-90	0			c.C1217T						.						70	73	72					10																	75533456		2203	4300	6503	SO:0001583	missense	170384	exon2			CCCACGCGGCCTC	BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"Fucosyltransferases"	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.1217C>T	10.37:g.75533456C>T	ENSP00000361932:p.Ala406Val	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	98	50	NM_173540	0	0	4	5	1	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	37	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411217	0.42817	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.35605	1.32;1.3	5.68	-3.31	0.04988	.	0.603818	0.19087	N	0.123083	T	0.12263	0.0298	N	0.14661	0.345	0.09310	N	1	B;B	0.34349	0.156;0.45	B;B	0.27500	0.061;0.08	T	0.33085	-0.9882	10	0.13853	T	0.58	-31.9131	4.6888	0.12771	0.5766:0.2067:0.0844:0.1324	.	406;406	Q495W5;Q495W5-2	FUT11_HUMAN;.	V	406	ENSP00000361932:A406V;ENSP00000378270:A406V	ENSP00000361932:A406V	A	+	2	0	FUT11	75203462	0.000000	0.05858	0.000000	0.03702	0.968000	0.65278	0.215000	0.17562	-0.197000	0.10350	0.563000	0.77884	GCG	.		0.597	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540		T	75533456	C	T	75533456	3	4	54	1	0	0	0	0	1	0	0	0	6122	768	27	1	1223	1	FUT11	10	75533456	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	346034	75533456	60001291	84	5254											
MYST4	23522	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	76781667	76781667	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctaatggaacaagctagctGctgggagaaggaggaacaag	15	5	15	6	0	0	1	0	0	0	1	0	5	0	4	0	4	5	4	0	4	7	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:76781667G>C	ENST00000287239.4	+	16	3539	c.3050G>C	c.(3049-3051)tGc>tCc	p.C1017S	KAT6B_ENST00000372724.1_Missense_Mutation_p.C725S|RP11-77G23.5_ENST00000436608.1_RNA|RP11-77G23.2_ENST00000413431.1_RNA|KAT6B_ENST00000372711.1_Missense_Mutation_p.C834S|KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372714.1_Missense_Mutation_p.C725S|KAT6B_ENST00000372725.1_Missense_Mutation_p.C725S	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1017					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CAAGCTAGCTGCTGGGAGAAG	0.483											OREG0020273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C1017S													.	.	0			c.G3050C						.						68	67	67					10																	76781667		2203	4300	6503	SO:0001583	missense	23522	exon16			CTAGCTGCTGGGA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.3050G>C	10.37:g.76781667G>C	ENSP00000287239:p.Cys1017Ser	Somatic	106	1	1170	WXS	Illumina HiSeq	Phase_I	79	29	NM_012330	0	0	0	0	0	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.211104	0.39102	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.76186	2.36;2.36;0.26;2.36;-1.0	5.98	5.02	0.67125	.	0.122386	0.37623	N	0.002015	T	0.50394	0.1613	N	0.05351	-0.065	0.53688	D	0.999977	B;B;B	0.26483	0.105;0.027;0.15	B;B;B	0.20767	0.031;0.031;0.027	T	0.52518	-0.8565	10	0.02654	T	1	-8.3168	15.0568	0.71921	0.0:0.1412:0.8588:0.0	.	834;725;1017	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	S	725;725;1017;725;834	ENSP00000361810:C725S;ENSP00000361809:C725S;ENSP00000287239:C1017S;ENSP00000361799:C725S;ENSP00000361796:C834S	ENSP00000287239:C1017S	C	+	2	0	KAT6B	76451673	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.698000	0.74608	2.833000	0.97629	0.655000	0.94253	TGC	.		0.483	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		C	76781667	G	C	76781667	3	2	54	1	0	0	0	0	1	0	0	0	10130	1319	46	4	3104	4	MYST4	10	76781667	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	1248211	76781667	58753080	85	5255											
GRID1	2894	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	87484287	87484287	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacacagcgaaatcaaaTggagcaaagagggagaagat	18	3	12	8	1	1	3	1	0	0	3	1	6	1	4	1	2	2	1	1	2	4	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:87484287T>G	ENST00000327946.7	-	11	1765	c.1680A>C	c.(1678-1680)ccA>ccC	p.P560P	GRID1_ENST00000536331.1_Silent_p.P131P	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	560					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.P560P(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CGAAATCAAATGGAGCAAAGA	0.498										Multiple Myeloma(13;0.14)																											p.P560P													.	GRID1-142	1	Substitution - coding silent(1)	ovary(1)	c.A1680C						.						88	79	82					10																	87484287		2203	4300	6503	SO:0001819	synonymous_variant	2894	exon11			ATCAAATGGAGCA	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1680A>C	10.37:g.87484287T>G		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	36	5	NM_017551	0	0	3	3	0	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			.		0.498	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		G	87484287	T	G	87484287	2	3	54	1	0	0	0	0	0	0	0	1	6792	1451	51	5		5	GRID1	10	87484287	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	10702620	87484287	48050460	86	5256											
SUFU	51684	broad.mit.edu	37	chr10	104263976	104263982	+	Frame_Shift_Del	DEL	CCCCCGG	CCCCCGG	-																															cggcccctggcccgactgccCccccggccttcgcttcgctc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	CCCCCGG	CCCCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:104263976_104263982delCCCCCGG	ENST00000369902.3	+	1	233_239	c.67_73delCCCCCGG	c.(67-75)cccccggccfs	p.PPA23fs	ACTR1A_ENST00000545684.1_5'Flank|SUFU_ENST00000423559.2_Frame_Shift_Del_p.PPA23fs|SUFU_ENST00000369899.2_Frame_Shift_Del_p.PPA23fs|ACTR1A_ENST00000369905.4_5'Flank|ACTR1A_ENST00000446605.2_5'Flank|ACTR1A_ENST00000487599.1_5'Flank	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	23					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		cccgactgcccccccggccTTCGCTTC	0.729			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																												p.23_25del			yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU-2246	0			c.67_73del						.																																			SO:0001589	frameshift_variant	51684	exon1	Familial Cancer Database		ACTGCCCCCCCGG	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.67_73delCCCCCGG	10.37:g.104263976_104263982delCCCCCGG	ENSP00000358918:p.Pro23fs	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	12	10	NM_001178133	0	0	0	0	0	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Frame_Shift_Del	DEL	ENST00000369902.3	37	CCDS7537.1																																																																																			.		0.729	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		-	104263982	CCCCCGG	-	104263976	7	5	54	1	0	1	0	1	0	0	0	0	15400	623	22	0	69	0	SUFU	10	104263976	Frame_Shift_Del	DEL	CCCCCGG	TCGA-B9-A44B-01A-11D-A25F-10	16779689	104263976	31270771	87	5257											
PDCD11	22984	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	105205187	105205189	+	In_Frame_Del	DEL	TTC	TTC	-																															tggcccccaagagaatgaagTtcttcttcaagcgctacctg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:105205187_105205189delTTC	ENST00000369797.3	+	36	5591_5593	c.5497_5499delTTC	c.(5497-5499)ttcdel	p.F1835del		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1835					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GAGAATGAAGTTCTTCTTCAAGC	0.542																																					p.1833_1833del		.											.	PDCD11-275	0			c.5497_5499del						.																																			SO:0001651	inframe_deletion	22984	exon36			.	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5497_5499delTTC	10.37:g.105205193_105205195delTTC	ENSP00000358812:p.Phe1835del	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	209	56	NM_014976	0	0	0	0	0	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	In_Frame_Del	DEL	ENST00000369797.3	37	CCDS31276.1																																																																																			.		0.542	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			-	105205189	TTC	-	105205187	7	5	54	1	0	1	0	1	0	0	0	0	11643	1725	60	0	5635	0	PDCD11	10	105205187	In_Frame_Del	DEL	TTC	TCGA-B9-A44B-01A-11D-A25F-10	941211	105205187	30329560	88	5258											
MUC2	4583	broad.mit.edu	37	chr11	1093326	1093326	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaccccaacacccaccggCacacagaccccaaccccgac	13	0	4	24	2	0	1	0	0	0	1	0	2	0	1	9	1	3	1	9	1	3	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:1093326C>A	ENST00000441003.2	+	30	5172	c.5145C>A	c.(5143-5145)ggC>ggA	p.G1715G	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.G3G|MUC2_ENST00000359061.5_Silent_p.G1682G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cacccaccggcacacagaccc	0.637																																					p.G1715G													.	MUC2-90	0			c.C5145A						.						186	232	216					11																	1093326		1932	3660	5592	SO:0001819	synonymous_variant	4583	exon30			CACCGGCACACAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5145C>A	11.37:g.1093326C>A		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	82	4	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093326	C	A	1093326	2	1	54	1	0	0	0	0	0	0	0	1	10000	697	25	4		4	MUC2	11	1093326	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		1093326	133913190	89	5259											
DCHS1	8642	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6654032	6654032	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccctggggcagtgtttggtGgtagcaataccgtgtcttca	6	13	13	9	1	2	0	1	0	1	0	3	0	3	0	2	4	2	4	2	4	3	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:6654032G>T	ENST00000299441.3	-	6	3122	c.2711C>A	c.(2710-2712)cCa>cAa	p.P904Q	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	904	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGTGTTTGGTGGTAGCAATAC	0.572																																					p.P904Q													.	DCHS1-73	0			c.C2711A						.						155	137	143					11																	6654032		2201	4296	6497	SO:0001583	missense	8642	exon6			TTTGGTGGTAGCA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.2711C>A	11.37:g.6654032G>T	ENSP00000299441:p.Pro904Gln	Somatic	189	1		WXS	Illumina HiSeq	Phase_I	233	108	NM_003737	0	0	1	1	0	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.896684	0.52121	.	.	ENSG00000166341	ENST00000299441	T	0.63417	-0.04	4.71	2.83	0.33086	Cadherin (2);Cadherin-like (1);	0.141093	0.32935	N	0.005467	T	0.69424	0.3109	M	0.64567	1.98	0.48696	D	0.999698	D	0.89917	1.0	D	0.91635	0.999	T	0.65088	-0.6253	10	0.25751	T	0.34	.	5.2844	0.15692	0.1701:0.0:0.667:0.1629	.	904	Q96JQ0	PCD16_HUMAN	Q	904	ENSP00000299441:P904Q	ENSP00000299441:P904Q	P	-	2	0	DCHS1	6610608	1.000000	0.71417	0.902000	0.35471	0.931000	0.56810	7.408000	0.80041	0.706000	0.31912	0.462000	0.41574	CCA	.		0.572	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6654032	G	T	6654032	3	4	54	1	0	0	0	0	1	0	0	0	4293	1348	47	4	7249	4	DCHS1	11	6654032	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	5560706	6654032	128352484	90	5260											
FBXO3	26273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	33770331	33770331	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgggttccataccaactactCcaggtccttgaacttcttcc	8	13	6	14	0	1	1	0	1	1	0	5	1	5	1	5	2	4	1	5	2	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:33770331C>T	ENST00000265651.3	-	9	1058	c.1040G>A	c.(1039-1041)gGa>gAa	p.G347E	FBXO3_ENST00000532057.1_Missense_Mutation_p.G34E|FBXO3_ENST00000534136.1_Missense_Mutation_p.G347E|FBXO3_ENST00000448981.2_Missense_Mutation_p.G347E|FBXO3_ENST00000526785.1_Missense_Mutation_p.G234E|FBXO3_ENST00000531080.1_Missense_Mutation_p.G34E|FBXO3_ENST00000530401.1_Missense_Mutation_p.G342E	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	347	ApaG. {ECO:0000255|PROSITE- ProRule:PRU00412}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		ACCAACTACTCCAGGTCCTTG	0.373																																					p.G347E		.											.	FBXO3-227	0			c.G1040A						.						99	99	99					11																	33770331		2202	4298	6500	SO:0001583	missense	26273	exon9			ACTACTCCAGGTC	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1040G>A	11.37:g.33770331C>T	ENSP00000265651:p.Gly347Glu	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	51	14	NM_012175	0	0	0	0	0	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	37	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567786	0.86439	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000531080;ENST00000532057;ENST00000534136;ENST00000448981	T;T;T;T;T	0.71934	-0.51;-0.61;-0.5;-0.54;-0.51	5.61	4.68	0.58851	ApaG domain (4);	0.000000	0.85682	D	0.000000	D	0.89518	0.6738	H	0.96633	3.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.993;0.993;0.999	D	0.93248	0.6632	10	0.87932	D	0	-21.1763	16.4024	0.83644	0.0:0.8681:0.1319:0.0	.	342;347;347	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	E	234;347;342;34;34;347;347	ENSP00000435680:G234E;ENSP00000265651:G347E;ENSP00000433781:G342E;ENSP00000431745:G347E;ENSP00000408836:G347E	ENSP00000265651:G347E	G	-	2	0	FBXO3	33726907	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.294000	0.78760	1.355000	0.45865	0.491000	0.48974	GGA	.		0.373	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		T	33770331	C	T	33770331	3	4	54	1	0	0	0	0	1	0	0	0	5758	855	30	2	396	2	FBXO3	11	33770331	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	27116299	33770331	101236185	91	5261											
CD6	923	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	60778597	60778605	+	In_Frame_Del	DEL	AGTCACTAT	AGTCACTAT	-																															gtccctgcaagtgttcagacAgtcactataggtaagtgttg																								rs374328736		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AGTCACTAT	AGTCACTAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:60778597_60778605delAGTCACTAT	ENST00000313421.7	+	6	1326_1334	c.1140_1148delAGTCACTAT	c.(1138-1149)acagtcactata>aca	p.VTI381del	CD6_ENST00000545105.1_3'UTR|CD6_ENST00000346437.4_In_Frame_Del_p.VTI381del|CD6_ENST00000344028.5_In_Frame_Del_p.VTI381del|CD6_ENST00000352009.5_In_Frame_Del_p.VTI381del|CD6_ENST00000452451.2_In_Frame_Del_p.VTI381del	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	381					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GTGTTCAGACAGTCACTATAGGTAAGTGT	0.526																																					p.380_383del	Pancreas(169;904 2017 4767 38890 42505)	.											.	CD6-227	0			c.1140_1148del						.																																			SO:0001651	inframe_deletion	923	exon6			.		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1140_1148delAGTCACTAT	11.37:g.60778597_60778605delAGTCACTAT	ENSP00000323280:p.Val381_Ile383del	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	171	38	NM_006725	0	0	0	0	0	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	In_Frame_Del	DEL	ENST00000313421.7	37	CCDS7999.1																																																																																			.		0.526	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		-	60778605	AGTCACTAT	-	60778597	7	5	54	1	0	1	0	1	0	0	0	0	3034	175	7	0	1162	0	CD6	11	60778597	In_Frame_Del	DEL	AGTCACTAT	TCGA-B9-A44B-01A-11D-A25F-10	27008266	60778597	74227919	92	5262											
HNRNPUL2	221092	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	62491416	62491416	+	Frame_Shift_Del	DEL	C	C	-																															gttcacaagagtttgatcctCctcctcatcttttgcctctt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:62491416delC	ENST00000301785.5	-	3	913	c.721delG	c.(721-723)gagfs	p.E241fs	HNRNPUL2-BSCL2_ENST00000403734.2_Frame_Shift_Del_p.E241fs	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	241	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Glu-rich. {ECO:0000255}.					membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTTTGATCCTCCTCCTCATCT	0.383																																					p.E241fs		.											.	HNRNPUL2-22	0			c.721delG						.						196	187	190					11																	62491416		1958	4148	6106	SO:0001589	frameshift_variant	221092	exon3			.		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.721delG	11.37:g.62491416delC	ENSP00000301785:p.Glu241fs	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	157	95	NM_001079559	0	0	0	0	0	Q8N3B3	Frame_Shift_Del	DEL	ENST00000301785.5	37	CCDS41659.1																																																																																			.		0.383	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		-	62491416	C	-	62491416	7	5	54	1	0	1	0	1	0	0	0	0	7296	864	30	0	1570	0	HNRNPUL2	11	62491416	Frame_Shift_Del	DEL	C	TCGA-B9-A44B-01A-11D-A25F-10	1712819	62491416	72515100	93	5263											
PPP2R5B	5526	hgsc.bcm.edu	37	chr11	64694184	64694184	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgccctctcctccccagAtgtgccggcttccgagctgc	4	9	11	17	2	1	1	0	0	1	1	4	3	3	2	6	2	4	2	6	2	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:64694184A>G	ENST00000164133.2	+	3	822	c.200A>G	c.(199-201)gAt>gGt	p.D67G		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	67					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						TCCTCCCCAGATGTGCCGGCT	0.662																																					p.D67G		.											.	PPP2R5B-660	0			c.A200G						.						55	61	59					11																	64694184		2201	4297	6498	SO:0001630	splice_region_variant	5526	exon3			CCCCAGATGTGCC	L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9310	protein-coding gene	gene with protein product	"PP2A, B subunit, B' beta isoform", "PP2A, B subunit, B56 beta isoform", "PP2A, B subunit, PR61 beta isoform", "PP2A, B subunit, R5 beta isoform", "serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"	601644	"protein phosphatase 2, regulatory subunit B (B56), beta isoform", "protein phosphatase 2, regulatory subunit B', beta isoform"			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.200-1A>G	11.37:g.64694184A>G		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	35	6	NM_006244	0	0	0	0	0	Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.654294	0.47467	.	.	ENSG00000068971	ENST00000526559;ENST00000164133;ENST00000359279;ENST00000527441	.	.	.	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	M	0.82517	2.595	0.80722	D	1	B	0.14012	0.009	B	0.24974	0.057	T	0.66748	-0.5845	8	.	.	.	.	12.2855	0.54789	1.0:0.0:0.0:0.0	.	67	Q15173	2A5B_HUMAN	G	67;67;94;67	.	.	D	+	2	0	PPP2R5B	64450760	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	8.597000	0.90847	2.077000	0.62373	0.528000	0.53228	GAT	.		0.662	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244	Missense_Mutation	G	64694184	A	G	64694184	5	3	54	1	0	0	0	0	0	0	1	0	12422	347	12	3	206	3	PPP2R5B	11	64694184	Splice_Site	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	2202768	64694184	70312332	94	5264											
HEPHL1	341208	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	93797512	93797529	+	In_Frame_Del	DEL	ATTCAGGGACACGGAATG	ATTCAGGGACACGGAATG	-																															gacaggtatcctgaatagatAttcagggacacggaatgatg																								rs200031155|rs368679862|rs556983825		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	ATTCAGGGACACGGAATG	ATTCAGGGACACGGAATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:93797512_93797529delATTCAGGGACACGGAATG	ENST00000315765.9	+	4	652_669	c.644_661delATTCAGGGACACGGAATG	c.(643-663)tattcagggacacggaatgat>tat	p.SGTRND216del		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	216					copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				CTGAATAGATATTCAGGGACACGGAATGATGTGGATCG	0.394																																					p.215_221del		.											.	HEPHL1-71	0			c.644_661del						.																																			SO:0001651	inframe_deletion	341208	exon4			.	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.644_661delATTCAGGGACACGGAATG	11.37:g.93797512_93797529delATTCAGGGACACGGAATG	ENSP00000313699:p.Ser216_Asp221del	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	72	18	NM_001098672	0	0	0	0	0	Q3C1W7	In_Frame_Del	DEL	ENST00000315765.9	37	CCDS44710.1																																																																																			.		0.394	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		-	93797529	ATTCAGGGACACGGAATG	-	93797512	7	5	54	1	0	1	0	1	0	0	0	0	7076	449	16	0	658	0	HEPHL1	11	93797512	In_Frame_Del	DEL	ATTCAGGGACACGGAATG	TCGA-B9-A44B-01A-11D-A25F-10	29103328	93797512	41209004	95	5265											
PHLDB1	23187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118509935	118509935	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccactcactcacagggggcaGgcctttcccgaagaccacat	10	6	9	16	1	2	1	2	0	0	1	3	2	3	1	4	3	0	1	4	3	1	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:118509935G>A	ENST00000361417.2	+	13	3113	c.2702G>A	c.(2701-2703)aGg>aAg	p.R901K	PHLDB1_ENST00000524713.1_5'Flank|PHLDB1_ENST00000527898.1_5'UTR|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Missense_Mutation_p.R901K|AP002954.3_ENST00000530198.1_RNA	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	901										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ACAGGGGGCAGGCCTTTCCCG	0.562																																					p.R901K		.											.	PHLDB1-90	0			c.G2702A						.						97	84	88					11																	118509935		2200	4295	6495	SO:0001583	missense	23187	exon12			GGGGCAGGCCTTT		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2702G>A	11.37:g.118509935G>A	ENSP00000354498:p.Arg901Lys	Somatic	169	1		WXS	Illumina HiSeq	Phase_I	95	77	NM_001144758	0	0	8	31	23	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890173	0.52014	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063	T;T	0.41065	1.01;1.01	4.39	4.39	0.52855	.	0.120998	0.49916	D	0.000123	T	0.28067	0.0692	L	0.31065	0.9	0.80722	D	1	B;B;B;B	0.30482	0.002;0.281;0.062;0.003	B;B;B;B	0.34093	0.004;0.175;0.025;0.005	T	0.05954	-1.0854	10	0.02654	T	1	-25.2439	12.056	0.53536	0.0:0.1734:0.8266:0.0	.	645;901;901;901	Q5W9G0;Q86UU1-3;Q86UU1-2;Q86UU1	.;.;.;PHLB1_HUMAN	K	901;660;265;901	ENSP00000354498:R901K;ENSP00000348359:R901K	ENSP00000348359:R901K	R	+	2	0	PHLDB1	118015145	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.292000	0.51772	2.010000	0.58986	0.456000	0.33151	AGG	.		0.562	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		A	118509935	G	A	118509935	3	1	54	1	0	0	0	0	1	0	0	0	11877	1000	35	2	2744	2	PHLDB1	11	118509935	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	24712423	118509935	16496581	96	5266											
CACNA2D4	93589	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	1902856	1902856	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcagtagcccccaggcacAcacaggcagcaggagtaggg	11	2	16	12	0	0	0	0	0	0	0	0	1	0	1	2	5	2	6	2	5	2	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:1902856A>G	ENST00000382722.5	-	38	3741	c.3379T>C	c.(3379-3381)Tgt>Cgt	p.C1127R	CACNA2D4_ENST00000587995.1_Missense_Mutation_p.C1102R|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.C1063R|CACNA2D4_ENST00000538027.2_Missense_Mutation_p.C272R|CACNA2D4_ENST00000538450.1_Missense_Mutation_p.C257R	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	1127					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		CCCCAGGCACACACAGGCAGC	0.642																																					p.C1127R	Colon(2;101 179 21030 23310 28141)												.	CACNA2D4-23	0			c.T3379C						.						39	47	44					12																	1902856		2082	4209	6291	SO:0001583	missense	93589	exon38			AGGCACACACAGG	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"Calcium channel subunits"	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.3379T>C	12.37:g.1902856A>G	ENSP00000372169:p.Cys1127Arg	Somatic	165	1		WXS	Illumina HiSeq	Phase_I	150	46	NM_172364	0	0	0	0	0	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	A	11.49	1.655480	0.29425	.	.	ENSG00000151062	ENST00000456077;ENST00000537784;ENST00000545595;ENST00000382722;ENST00000538027;ENST00000538450	T;T	0.17370	3.26;2.28	4.8	-5.5	0.02576	.	1.054930	0.07441	N	0.897387	T	0.15652	0.0377	L	0.44542	1.39	0.09310	N	0.999991	B	0.26975	0.165	B	0.25405	0.06	T	0.23904	-1.0175	10	0.25106	T	0.35	.	18.1264	0.89587	0.205:0.795:0.0:0.0	.	1127	Q7Z3S7	CA2D4_HUMAN	R	1063;194;194;1127;194;257	ENSP00000372169:C1127R;ENSP00000446341:C257R	ENSP00000372169:C1127R	C	-	1	0	CACNA2D4	1773117	0.414000	0.25408	0.151000	0.22473	0.101000	0.19017	-0.064000	0.11636	-0.641000	0.05487	0.459000	0.35465	TGT	.		0.642	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			G	1902856	A	G	1902856	3	3	54	1	0	0	0	0	1	0	0	0	2557	159	6	3	38	3	CACNA2D4	12	1902856	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		1902856	131949039	97	5267											
KIAA0528	9847	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	22670928	22670928	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaagcgccttaccagttttgGgtgtcaaactcaaatctgtg	10	12	10	9	1	3	0	2	0	1	0	3	1	3	0	2	1	3	1	2	1	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:22670928G>T	ENST00000333957.4	-	8	1199	c.944C>A	c.(943-945)cCc>cAc	p.P315H	C2CD5_ENST00000545552.1_Intron|C2CD5_ENST00000544930.1_Intron|C2CD5_ENST00000396028.2_Intron|C2CD5_ENST00000542676.1_Missense_Mutation_p.P315H|C2CD5_ENST00000446597.1_Missense_Mutation_p.P315H|C2CD5_ENST00000536386.1_Intron|C2CD5_ENST00000540703.1_5'Flank	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	315					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										ACCAGTTTTGGGTGTCAAACT	0.383																																					p.P315H		.											.	.	0			c.C944A						.						177	174	175					12																	22670928		2203	4300	6503	SO:0001583	missense	9847	exon8			GTTTTGGGTGTCA	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.944C>A	12.37:g.22670928G>T	ENSP00000334229:p.Pro315His	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	85	36	NM_014802	0	0	0	0	0	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	37	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536609	0.65085	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000542676	T;T;T	0.50001	0.76;0.76;0.76	6.04	5.14	0.70334	.	.	.	.	.	T	0.66268	0.2772	M	0.75777	2.31	0.80722	D	1	D;D	0.65815	0.995;0.957	P;P	0.59288	0.855;0.58	T	0.71758	-0.4496	9	0.72032	D	0.01	-3.34	17.3582	0.87342	0.0:0.125:0.875:0.0	.	315;315	B4DRN7;Q86YS7	.;K0528_HUMAN	H	315	ENSP00000334229:P315H;ENSP00000388756:P315H;ENSP00000441951:P315H	ENSP00000334229:P315H	P	-	2	0	KIAA0528	22562195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.606000	0.98325	1.538000	0.49270	0.561000	0.74099	CCC	.		0.383	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		T	22670928	G	T	22670928	3	4	54	1	0	0	0	0	1	0	0	0	8203	1232	43	4	2130	4	KIAA0528	12	22670928	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	20768072	22670928	111180967	98	5268											
KIF21A	55605	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	39726729	39726729	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccggcgttggtaaggcctGgactctcgccacaggaattc	7	9	13	12	3	1	0	0	0	1	0	3	2	1	2	3	5	1	2	3	5	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:39726729G>C	ENST00000361418.5	-	19	2683	c.2668C>G	c.(2668-2670)Cag>Gag	p.Q890E	KIF21A_ENST00000395670.3_Missense_Mutation_p.Q890E|KIF21A_ENST00000361961.3_Missense_Mutation_p.Q877E|KIF21A_ENST00000544797.2_Missense_Mutation_p.Q877E|KIF21A_ENST00000541463.2_Missense_Mutation_p.Q854E			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	890					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GGTAAGGCCTGGACTCTCGCC	0.478																																					p.Q890E													.	KIF21A-97	0			c.C2668G						.						75	76	75					12																	39726729		2203	4300	6503	SO:0001583	missense	55605	exon19			AGGCCTGGACTCT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2668C>G	12.37:g.39726729G>C	ENSP00000354878:p.Gln890Glu	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	179	72	NM_001173464	0	0	4	8	4	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696135	0.30052	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T	0.68903	-0.36;-0.33;-0.36;-0.28;-0.34	5.58	4.67	0.58626	.	0.000000	0.49305	D	0.000142	T	0.61664	0.2365	L	0.54323	1.7	0.43467	D	0.995677	B;P;B;B;P	0.46142	0.266;0.491;0.041;0.266;0.873	B;B;B;B;B	0.44133	0.142;0.199;0.027;0.142;0.442	T	0.62840	-0.6769	10	0.02654	T	1	.	16.3349	0.83056	0.0:0.1323:0.8677:0.0	.	877;854;890;877;890	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3	.;.;KI21A_HUMAN;.;.	E	877;890;890;877;890;854	ENSP00000354851:Q877E;ENSP00000379029:Q890E;ENSP00000445606:Q877E;ENSP00000354878:Q890E;ENSP00000438075:Q854E	ENSP00000344501:Q890E	Q	-	1	0	KIF21A	38012996	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	3.519000	0.53458	1.318000	0.45170	0.557000	0.71058	CAG	.		0.478	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		C	39726729	G	C	39726729	3	2	54	1	0	0	0	0	1	0	0	0	8309	1357	47	4	2436	4	KIF21A	12	39726729	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	17055801	39726729	94125166	99	5269											
ARID2	196528	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	46205220	46205221	+	Frame_Shift_Del	DEL	AA	AA	-																															gttacctagaaaagtacgagAaagttcatcattttggggag																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:46205220_46205221delAA	ENST00000334344.6	+	4	476_477	c.304_305delAA	c.(304-306)aaafs	p.K102fs	ARID2_ENST00000422737.1_5'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	102	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAAGTACGAGAAAGTTCATCAT	0.366			"N, S, F"		hepatocellular carcinoma																																p.102_102del		.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2-100	0			c.304_305del						.																																			SO:0001589	frameshift_variant	196528	exon4			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.304_305delAA	12.37:g.46205220_46205221delAA	ENSP00000335044:p.Lys102fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	82	33	NM_152641	0	0	0	0	0	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	37	CCDS31783.1																																																																																			.		0.366	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46205221	AA	-	46205220	7	5	54	1	0	1	0	1	0	0	0	0	915	247	9	0	318	0	ARID2	12	46205220	Frame_Shift_Del	DEL	AA	TCGA-B9-A44B-01A-11D-A25F-10	6478491	46205220	87646675	100	5270											
PRPH	5630	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49690229	49690229	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaaggacgtggacgatgcCactctgtcccgcctggaact	8	8	12	13	4	1	0	0	0	1	0	3	5	2	3	3	3	2	0	3	3	2	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:49690229C>T	ENST00000257860.4	+	3	2120	c.621C>T	c.(619-621)gcC>gcT	p.A207A	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						TGGACGATGCCACTCTGTCCC	0.567																																					p.A207A		.											.	PRPH-90	0			c.C621T						.						86	77	80					12																	49690229		2203	4300	6503	SO:0001819	synonymous_variant	5630	exon3			CGATGCCACTCTG		CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.621C>T	12.37:g.49690229C>T		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	151	9	NM_006262	0	0	1	1	0	Q5TFH5|Q6DK65	Silent	SNP	ENST00000257860.4	37	CCDS8783.1																																																																																			.		0.567	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		T	49690229	C	T	49690229	2	4	54	1	0	0	0	0	0	0	0	1	12605	581	21	2		2	PRPH	12	49690229	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	3485009	49690229	84161666	101	5271											
KCNH3	23416	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49951017	49951018	+	Frame_Shift_Del	DEL	AC	AC	-																															cagcgaggcaaggaacacagAcacactggacaagcttcggc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:49951017_49951018delAC	ENST00000257981.6	+	14	2887_2888	c.2627_2628delAC	c.(2626-2628)gacfs	p.D876fs	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	876					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						AGGAACACAGACACACTGGACA	0.619																																					p.876_876del		.											.	KCNH3-90	0			c.2627_2628del						.																																			SO:0001589	frameshift_variant	23416	exon14			.	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2627_2628delAC	12.37:g.49951021_49951022delAC	ENSP00000257981:p.Asp876fs	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	126	51	NM_012284	0	0	0	0	0	Q9UQ06	Frame_Shift_Del	DEL	ENST00000257981.6	37	CCDS8786.1																																																																																			.		0.619	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		-	49951018	AC	-	49951017	7	5	54	1	0	1	0	1	0	0	0	0	8054	275	10	0	2681	0	KCNH3	12	49951017	Frame_Shift_Del	DEL	AC	TCGA-B9-A44B-01A-11D-A25F-10	260788	49951017	83900878	102	5272											
KRT85	3891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52754642	52754642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctccatgactctactaggCaaagcggaccgaccggctac	10	6	11	14	3	1	1	0	1	1	0	2	3	2	2	3	4	3	3	3	4	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:52754642C>T	ENST00000257901.3	-	9	1594	c.1519G>A	c.(1519-1521)Gcc>Acc	p.A507T	KRT85_ENST00000544265.1_Missense_Mutation_p.A295T	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	507	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTCTACTAGGCAAAGCGGACC	0.607																																					p.A507T		.											.	KRT85-91	0			c.G1519A						.						44	52	49					12																	52754642		2201	4300	6501	SO:0001583	missense	3891	exon9			ACTAGGCAAAGCG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.1519G>A	12.37:g.52754642C>T	ENSP00000257901:p.Ala507Thr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	68	29	NM_002283	0	0	0	0	0	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746175	0.30955	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;D	0.82255	-1.59;-1.5	5.22	3.31	0.37934	.	0.000000	0.44097	D	0.000485	T	0.72104	0.3419	N	0.22421	0.69	0.09310	N	1	B	0.27498	0.18	B	0.26517	0.07	T	0.67952	-0.5537	10	0.87932	D	0	.	12.1399	0.53993	0.0:0.6712:0.3288:0.0	.	507	P78386	KRT85_HUMAN	T	507;295	ENSP00000257901:A507T;ENSP00000440240:A295T	ENSP00000257901:A507T	A	-	1	0	KRT85	51040909	0.619000	0.27059	0.841000	0.33234	0.099000	0.18886	0.941000	0.29005	1.427000	0.47276	0.609000	0.83330	GCC	.		0.607	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		T	52754642	C	T	52754642	3	4	54	1	0	0	0	0	1	0	0	0	8520	710	25	2	8	2	KRT85	12	52754642	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2803625	52754642	81097253	103	5273											
PTPRB	5787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	70932007	70932007	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagcttcactcgcgtggcAtcatctggaaggagagattt	10	10	13	8	2	3	2	2	0	1	2	4	6	3	4	0	3	1	2	0	3	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:70932007A>T	ENST00000261266.5	-	26	5249	c.5220T>A	c.(5218-5220)gaT>gaA	p.D1740E	PTPRB_ENST00000538708.1_Missense_Mutation_p.D1650E|PTPRB_ENST00000334414.6_Missense_Mutation_p.D1958E|RP11-588H23.3_ENST00000551438.1_RNA|RP11-588H23.3_ENST00000549460.1_RNA|RP11-588H23.3_ENST00000548687.1_RNA|PTPRB_ENST00000550857.1_Missense_Mutation_p.D1650E|PTPRB_ENST00000451516.2_Missense_Mutation_p.D1650E|PTPRB_ENST00000550358.1_Missense_Mutation_p.D1870E|RP11-588H23.3_ENST00000547656.1_RNA|RP11-588H23.3_ENST00000546836.1_RNA	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1740	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTCGCGTGGCATCATCTGGAA	0.478																																					p.D1958E		.											.	PTPRB-226	0			c.T5874A						.						162	159	160					12																	70932007		2102	4245	6347	SO:0001583	missense	5787	exon28			CGTGGCATCATCT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.5220T>A	12.37:g.70932007A>T	ENSP00000261266:p.Asp1740Glu	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	184	74	NM_001109754	0	0	0	0	0	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.952571	0.73787	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	5.67	0.844	0.18943	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.91623	0.7353	M	0.78801	2.425	0.53688	D	0.999979	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.89983	0.4102	10	0.87932	D	0	.	9.5604	0.39366	0.6532:0.0:0.3468:0.0	.	1650;1650;1958;1740;1870	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	E	1958;1650;1870;1650;1650;1740	ENSP00000334928:D1958E;ENSP00000393028:D1650E;ENSP00000448058:D1870E;ENSP00000438927:D1650E;ENSP00000447302:D1650E;ENSP00000261266:D1740E	ENSP00000261266:D1740E	D	-	3	2	PTPRB	69218274	1.000000	0.71417	0.996000	0.52242	0.783000	0.44284	1.253000	0.32886	0.122000	0.18314	-0.371000	0.07208	GAT	.		0.478	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70932007	A	T	70932007	3	4	54	1	0	0	0	0	1	0	0	0	12828	214	8	5	801	5	PTPRB	12	70932007	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	18177365	70932007	62919888	104	5274											
TMCC3	57458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	94965249	94965249	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctttctatggcacacaggaTatggtcccagtttttacaaa	11	13	7	10	0	1	0	0	0	1	0	2	1	2	1	2	3	1	2	2	3	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:94965249T>C	ENST00000261226.4	-	4	1527	c.1396A>G	c.(1396-1398)Atc>Gtc	p.I466V	TMCC3_ENST00000551457.1_Missense_Mutation_p.I435V	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	466						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCACACAGGATATGGTCCCAG	0.418																																					p.I466V		.											.	TMCC3-92	0			c.A1396G						.						113	108	110					12																	94965249		2203	4300	6503	SO:0001583	missense	57458	exon4			ACAGGATATGGTC	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1396A>G	12.37:g.94965249T>C	ENSP00000261226:p.Ile466Val	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	139	66	NM_020698	0	0	1	1	0	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	37	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.378687	0.24944	.	.	ENSG00000057704	ENST00000261226;ENST00000551457	T;T	0.40756	1.02;1.02	5.33	5.33	0.75918	.	0.057274	0.64402	D	0.000001	T	0.49847	0.1581	L	0.32530	0.975	0.48185	D	0.999604	D	0.61697	0.99	D	0.68192	0.956	T	0.36212	-0.9757	10	0.13470	T	0.59	-18.6633	15.2998	0.73940	0.0:0.0:0.0:1.0	.	466	Q9ULS5	TMCC3_HUMAN	V	466;435	ENSP00000261226:I466V;ENSP00000449888:I435V	ENSP00000261226:I466V	I	-	1	0	TMCC3	93489380	1.000000	0.71417	0.950000	0.38849	0.986000	0.74619	2.358000	0.44134	2.019000	0.59389	0.459000	0.35465	ATC	.		0.418	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		C	94965249	T	C	94965249	3	2	54	1	0	0	0	0	1	0	0	0	16026	1406	49	3	41	3	TMCC3	12	94965249	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	24033242	94965249	38886646	105	5275											
C12orf51	283450	broad.mit.edu	37	chr12	112623045	112623046	+	Frame_Shift_Ins	INS	-	-	C																															gccctggtcaccggccgccgINScccccccggagcccccgcag																								rs368404348		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:112623045_112623046insC	ENST00000430131.2	-	60	9603_9604	c.8458_8459insG	c.(8458-8460)gcgfs	p.A2820fs	HECTD4_ENST00000550722.1_Frame_Shift_Ins_p.A3096fs|HECTD4_ENST00000377560.5_Frame_Shift_Ins_p.A3070fs			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2820					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										Accggccgccgcccccccggag	0.639																																					p.A3108fs													.	.	0			c.9323_9324insG						.																																			SO:0001589	frameshift_variant	283450	exon61			GCCGCCGCCCCCC	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.8459dupG	12.37:g.112623052_112623052dupC	ENSP00000404379:p.Ala2820fs	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	14	6	NM_001109662	0	0	0	0	0	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Frame_Shift_Ins	INS	ENST00000430131.2	37																																																																																				.		0.639	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112623046	-	C	112623045	7	5	54	1	0	1	1	0	0	0	0	0	1700	1087	38	0	3595	0	C12orf51	12	112623045	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	17657796	112623045	21228850	106	5276											
PXN	5829	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	120653013	120653013	+	Frame_Shift_Del	DEL	G	G	-																															ccccagcatgctgtccagctGgctcccgggcttcgggggcc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:120653013delG	ENST00000228307.7	-	8	1138	c.997delC	c.(997-999)cagfs	p.Q333fs	PXN_ENST00000536957.1_Frame_Shift_Del_p.Q331fs|PXN-AS1_ENST00000535200.1_RNA|PXN_ENST00000267257.7_Frame_Shift_Del_p.Q347fs|PXN-AS1_ENST00000542265.1_RNA|PXN_ENST00000458477.2_Frame_Shift_Del_p.Q166fs|PXN_ENST00000424649.2_Frame_Shift_Del_p.Q299fs|PXN_ENST00000538144.1_5'UTR|PXN_ENST00000397506.3_Frame_Shift_Del_p.Q145fs	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	333					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTGTCCAGCTGGCTCCCGGGC	0.677																																					p.Q347fs		.											.	PXN-660	0			c.1039delC						.						11	13	12					12																	120653013		2038	4192	6230	SO:0001589	frameshift_variant	5829	exon7			.	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.997delC	12.37:g.120653013delG	ENSP00000228307:p.Gln333fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	68	28	NM_001243756	0	0	0	0	0	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Frame_Shift_Del	DEL	ENST00000228307.7	37	CCDS44997.1																																																																																			.		0.677	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		-	120653013	G	-	120653013	7	5	54	1	0	1	0	1	0	0	0	0	12884	1357	47	0	798	0	PXN	12	120653013	Frame_Shift_Del	DEL	G	TCGA-B9-A44B-01A-11D-A25F-10	8029968	120653013	13198882	107	5277											
BRCA2	675	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	32912283	32912283	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aataagtttatcttcaagtaAatgtcatgattctgttgttt	12	19	6	4	0	4	1	2	1	2	0	4	1	4	1	0	0	0	4	0	0	6	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr13:32912283A>G	ENST00000380152.3	+	11	4024	c.3791A>G	c.(3790-3792)aAa>aGa	p.K1264R	BRCA2_ENST00000544455.1_Missense_Mutation_p.K1264R			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1264					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCTTCAAGTAAATGTCATGAT	0.284			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.K1264R	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2-3153	0			c.A3791G						.						32	33	33					13																	32912283		2203	4298	6501	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	CAAGTAAATGTCA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3791A>G	13.37:g.32912283A>G	ENSP00000369497:p.Lys1264Arg	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_000059	0	0	0	0	0	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	8.292	0.817933	0.16607	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00669	5.9;5.9	5.72	1.46	0.22682	.	0.702869	0.14340	N	0.325776	T	0.01029	0.0034	M	0.63428	1.95	0.09310	N	1	B	0.21381	0.055	B	0.17433	0.018	T	0.44003	-0.9356	10	0.22706	T	0.39	.	7.1182	0.25429	0.6276:0.2868:0.0856:0.0	.	1264	P51587	BRCA2_HUMAN	R	1264	ENSP00000369497:K1264R;ENSP00000439902:K1264R	ENSP00000369497:K1264R	K	+	2	0	BRCA2	31810283	0.001000	0.12720	0.001000	0.08648	0.564000	0.35744	1.013000	0.29937	0.406000	0.25560	0.528000	0.53228	AAA	.		0.284	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32912283	A	G	32912283	3	3	54	1	0	0	0	0	1	0	0	0	1502	14	1	3	3829	3	BRCA2	13	32912283	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		32912283	82257595	108	5278											
ABCC4	10257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	95840715	95840715	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attctaactcaccttccctgCtcccacggggccgaccacag	8	8	7	18	2	2	0	1	0	1	0	4	1	4	0	5	2	2	1	5	2	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr13:95840715C>A	ENST00000376887.4	-	10	1459	c.1345G>T	c.(1345-1347)Gca>Tca	p.A449S	ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000431522.1_Missense_Mutation_p.A449S|ABCC4_ENST00000412704.1_Missense_Mutation_p.A449S|ABCC4_ENST00000536256.1_Missense_Mutation_p.A374S	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	449	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	ACCTTCCCTGCTCCCACGGGG	0.468																																					p.A449S		.											.	ABCC4-515	0			c.G1345T						.						120	109	113					13																	95840715		2203	4300	6503	SO:0001583	missense	10257	exon10			TCCCTGCTCCCAC	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"ATP binding cassette transporters / subfamily C"	55	protein-coding gene	gene with protein product	"canalicular multispecific organic anion transporter (ABC superfamily)", "bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)", "multidrug resistance-associated protein 4", "multispecific organic anion transporter B"	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.1345G>T	13.37:g.95840715C>A	ENSP00000366084:p.Ala449Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	112	23	NM_005845	0	0	0	0	0	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	37	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673351	0.47781	.	.	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49	5.22	4.29	0.51040	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.050917	0.85682	D	0.000000	D	0.84316	0.5445	N	0.02751	-0.505	0.80722	D	1	B;B;B;B;B	0.27117	0.032;0.068;0.028;0.168;0.038	B;B;B;B;B	0.27262	0.039;0.05;0.076;0.078;0.034	T	0.81959	-0.0694	10	0.07175	T	0.84	.	16.4591	0.84031	0.1401:0.8598:0.0:0.0	.	374;449;449;449;449	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	S	449;449;374;449	ENSP00000388657:A449S;ENSP00000366084:A449S;ENSP00000442024:A374S;ENSP00000398562:A449S	ENSP00000366084:A449S	A	-	1	0	ABCC4	94638716	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	3.665000	0.54532	2.447000	0.82792	0.637000	0.83480	GCA	.		0.468	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		A	95840715	C	A	95840715	3	1	54	1	0	0	0	0	1	0	0	0	55	797	28	4	2769	4	ABCC4	13	95840715	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	62928432	95840715	19329163	109	5279											
DOCK9	23348	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99449739	99449739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catatgctagtgggccagcaTtgacctagacaaagagcaaa	15	7	10	9	0	0	3	0	1	0	2	0	3	0	3	2	1	3	3	2	1	5	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr13:99449739T>C	ENST00000376460.1	-	54	6043	c.5963A>G	c.(5962-5964)aAt>aGt	p.N1988S	DOCK9_ENST00000339416.2_Missense_Mutation_p.N1975S	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1989	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TGGGCCAGCATTGACCTAGAC	0.428																																					.													.	DOCK9-90	0			.						.						102	86	91					13																	99449739		1906	4132	6038	SO:0001583	missense	23348	.			CCAGCATTGACCT	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.5963A>G	13.37:g.99449739T>C	ENSP00000365643:p.Asn1988Ser	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	116	18	.	0	0	0	0	0	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.992364	0.54041	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000376453	T;T	0.25250	1.81;1.81	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	H	0.94582	3.555	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;0.994;1.0;0.997;0.997	T	0.74873	-0.3516	10	0.87932	D	0	.	14.8041	0.69938	0.0:0.0:0.0:1.0	.	694;607;1988;1989;644;606	B7Z6H5;B7Z2J2;Q9BZ29-5;Q9BZ29;B7Z6G9;F5H1Q4	.;.;.;DOCK9_HUMAN;.;.	S	1988;1989;1981;1966;1988;896;1975;606	ENSP00000365643:N1988S;ENSP00000341086:N1975S	ENSP00000341086:N1975S	N	-	2	0	DOCK9	98247740	1.000000	0.71417	0.995000	0.50966	0.097000	0.18754	7.698000	0.84413	1.893000	0.54813	0.459000	0.35465	AAT	.		0.428	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		C	99449739	T	C	99449739	3	2	54	1	0	0	0	0	1	0	0	0	4705	1493	52	3	259	3	DOCK9	13	99449739	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	3609024	99449739	15720139	110	5280											
ACIN1	22985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23549484	23549484	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	taaaggtggaggagtctcctCctcgctggcagtttgctctg	6	12	13	10	1	2	0	0	0	2	0	5	2	3	2	2	4	1	4	2	4	2	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:23549484C>G	ENST00000262710.1	-	6	1561	c.1234G>C	c.(1234-1236)Gag>Cag	p.E412Q	ACIN1_ENST00000457657.1_Missense_Mutation_p.E372Q|ACIN1_ENST00000605057.1_Missense_Mutation_p.E354Q|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_Missense_Mutation_p.E412Q	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	412	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		GGAGTCTCCTCCTCGCTGGCA	0.517																																					p.E412Q		.											.	ACIN1-156	0			c.G1234C						.						59	61	61					14																	23549484		2203	4300	6503	SO:0001583	missense	22985	exon6			TCTCCTCCTCGCT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1234G>C	14.37:g.23549484C>G	ENSP00000262710:p.Glu412Gln	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	239	111	NM_001164814	0	0	1	1	0	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.780380	0.70222	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.30448	1.53;1.53;1.53	5.27	5.27	0.74061	.	0.000000	0.41605	D	0.000851	T	0.40886	0.1135	L	0.27053	0.805	0.34634	D	0.719933	D;D;D	0.67145	0.996;0.993;0.993	D;D;D	0.75484	0.986;0.968;0.968	T	0.43605	-0.9381	10	0.32370	T	0.25	-13.6658	14.2703	0.66147	0.0:1.0:0.0:0.0	.	412;412;372	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	Q	412;372;412	ENSP00000262710:E412Q;ENSP00000405677:E372Q;ENSP00000451328:E412Q	ENSP00000262710:E412Q	E	-	1	0	ACIN1	22619324	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.347000	0.52200	2.752000	0.94435	0.650000	0.86243	GAG	.		0.517	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		G	23549484	C	G	23549484	3	3	54	1	0	0	0	0	1	0	0	0	142	864	30	4	2994	4	ACIN1	14	23549484	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		23549484	83800056	111	5281											
SAMD4A	23034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55203876	55203876	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctagaggaccccagtgcCtcccatccgatcatgccccc	8	6	9	18	1	1	1	1	0	0	1	3	4	3	2	7	1	3	1	7	1	1	1	rs138744574	byFrequency	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:55203876C>T	ENST00000554335.1	+	4	1513	c.850C>T	c.(850-852)Ctc>Ttc	p.L284F	SAMD4A_ENST00000392067.3_Missense_Mutation_p.L284F|SAMD4A_ENST00000357634.3_Missense_Mutation_p.L283F|SAMD4A_ENST00000251091.5_Intron			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	284					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						ACCCCAGTGCCTCCCATCCGA	0.537																																					p.L284F		.											.	SAMD4A-90	0			c.C850T						.						226	210	215					14																	55203876		2203	4300	6503	SO:0001583	missense	23034	exon3			CAGTGCCTCCCAT	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"Sterile alpha motif (SAM) domain containing"	23023	protein-coding gene	gene with protein product	"smaug homolog (Drosophila)"	610747	"sterile alpha motif domain containing 4"	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.850C>T	14.37:g.55203876C>T	ENSP00000452535:p.Leu284Phe	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	130	52	NM_015589	0	0	0	0	0	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354282	0.41700	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000357634	.	.	.	5.15	4.19	0.49359	.	0.203527	0.35615	N	0.003096	T	0.39410	0.1077	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33317	-0.9873	9	0.56958	D	0.05	-16.9697	8.4253	0.32725	0.1972:0.7168:0.0:0.086	.	284	Q9UPU9	SMAG1_HUMAN	F	284;284;283	.	ENSP00000350261:L283F	L	+	1	0	SAMD4A	54273626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.201000	0.32259	2.673000	0.90976	0.655000	0.94253	CTC	C|0.999;A|0.001		0.537	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55203876	C	T	55203876	3	4	54	1	0	0	0	0	1	0	0	0	13853	681	24	2	857	2	SAMD4A	14	55203876	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	31654392	55203876	52145664	112	5282											
SYNE2	23224	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64522891	64522891	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aatgatatccagccccgaagCcaaactacaacttcagtata	16	8	5	12	1	1	1	1	1	0	0	2	2	2	1	4	0	5	1	4	0	8	5	rs377173620	byFrequency	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:64522891C>A	ENST00000344113.4	+	49	10186	c.9974C>A	c.(9973-9975)gCc>gAc	p.A3325D	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.A3358D|SYNE2_ENST00000358025.3_Missense_Mutation_p.A3325D	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3325					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGCCCCGAAGCCAAACTACAA	0.438																																					p.A3325D													.	SYNE2-164	0			c.C9974A						.						67	61	63					14																	64522891		1894	4113	6007	SO:0001583	missense	23224	exon49			CCGAAGCCAAACT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9974C>A	14.37:g.64522891C>A	ENSP00000341781:p.Ala3325Asp	Somatic	144	1		WXS	Illumina HiSeq	Phase_I	132	59	NM_182914	0	0	2	2	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.965603	0.34659	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.50813	0.73;1.48;1.56	5.79	4.87	0.63330	.	0.203443	0.33772	N	0.004564	T	0.30759	0.0775	N	0.14661	0.345	0.80722	D	1	B;B	0.18461	0.017;0.028	B;B	0.19946	0.012;0.027	T	0.08146	-1.0736	10	0.18276	T	0.48	.	14.6434	0.68742	0.2533:0.7467:0.0:0.0	.	3325;3325	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	D	3325;3325;3358;3358	ENSP00000350719:A3325D;ENSP00000341781:A3325D;ENSP00000452570:A3358D	ENSP00000261678:A3358D	A	+	2	0	SYNE2	63592644	1.000000	0.71417	0.312000	0.25196	0.261000	0.26267	1.072000	0.30678	2.749000	0.94314	0.491000	0.48974	GCC	.		0.438	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64522891	C	A	64522891	3	1	54	1	0	0	0	0	1	0	0	0	15478	739	26	4	10164	4	SYNE2	14	64522891	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	9319015	64522891	42826649	113	5283											
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64610587	64610587	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgtagaaagcaagcgctAtgaaagaacggagtttgcag	15	8	13	5	2	0	4	0	2	0	2	0	5	0	5	0	1	4	5	0	1	6	3	rs556819169		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:64610587A>G	ENST00000344113.4	+	83	15616	c.15404A>G	c.(15403-15405)tAt>tGt	p.Y5135C	SYNE2_ENST00000357395.3_Missense_Mutation_p.Y1520C|SYNE2_ENST00000394768.2_Missense_Mutation_p.Y1520C|SYNE2_ENST00000554584.1_Missense_Mutation_p.Y5052C|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000358025.3_Missense_Mutation_p.Y5135C|SYNE2_ENST00000555002.1_Missense_Mutation_p.Y1769C	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5135					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGCAAGCGCTATGAAAGAACG	0.458													A|||	1	0.000199681	8e-04	0	5008	,	,		19135	0		0	False		,,,				2504	0				p.Y5135C		.											.	SYNE2-164	0			c.A15404G						.						276	278	277					14																	64610587		2203	4300	6503	SO:0001583	missense	23224	exon83			AGCGCTATGAAAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15404A>G	14.37:g.64610587A>G	ENSP00000341781:p.Tyr5135Cys	Somatic	216	1		WXS	Illumina HiSeq	Phase_I	169	88	NM_182914	0	0	2	2	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.096384	0.56075	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.52754	1.32;0.65;1.32;1.32;0.67;0.65	5.33	5.33	0.75918	.	0.000000	0.48286	D	0.000190	T	0.67979	0.2951	M	0.73598	2.24	0.80722	D	1	B;D;B;P	0.89917	0.081;1.0;0.382;0.644	B;D;B;B	0.73380	0.094;0.98;0.146;0.307	T	0.70633	-0.4818	10	0.51188	T	0.08	.	15.2733	0.73723	1.0:0.0:0.0:0.0	.	1520;5052;5135;5135	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	C	5135;1520;5135;5052;5058;1769;1520	ENSP00000350719:Y5135C;ENSP00000349969:Y1520C;ENSP00000341781:Y5135C;ENSP00000452570:Y5052C;ENSP00000450831:Y1769C;ENSP00000378249:Y1520C	ENSP00000261678:Y5058C	Y	+	2	0	SYNE2	63680340	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.285000	0.65633	2.004000	0.58718	0.528000	0.53228	TAT	.		0.458	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64610587	A	G	64610587	3	3	54	1	0	0	0	0	1	0	0	0	15478	449	16	3	15730	3	SYNE2	14	64610587	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	87696	64610587	42738953	114	5284											
MTHFD1	4522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64924942	64924942	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatcctagatgagcacaaTgcctggactccccacccggc	10	7	8	16	1	0	2	0	1	0	1	2	3	2	3	5	2	3	1	5	2	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:64924942T>C	ENST00000216605.8	+	27	2807	c.2729T>C	c.(2728-2730)aTg>aCg	p.M910T	ZBTB25_ENST00000555424.1_Intron|MTHFD1_ENST00000556284.1_3'UTR|MTHFD1_ENST00000545908.1_Intron|ZBTB25_ENST00000555220.1_Intron	NM_005956.3	NP_005947.3	P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	910	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	ATGAGCACAATGCCTGGACTC	0.448																																					p.M910T	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	.											.	MTHFD1-92	0			c.T2729C						.						141	140	141					14																	64924942		2203	4300	6503	SO:0001583	missense	4522	exon27			GCACAATGCCTGG	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000216605.8:c.2729T>C	14.37:g.64924942T>C	ENSP00000216605:p.Met910Thr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	57	24	NM_005956	0	0	2	3	1	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000216605.8	37	CCDS9763.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.906782	0.72868	.	.	ENSG00000100714	ENST00000555709;ENST00000216605	T;T	0.29142	1.58;1.58	5.27	5.27	0.74061	.	0.179769	0.64402	D	0.000011	T	0.65831	0.2729	H	0.98199	4.17	0.80722	D	1	P	0.43909	0.821	P	0.54140	0.743	T	0.78607	-0.2138	10	0.87932	D	0	-32.6795	14.6571	0.68841	0.0:0.0:0.0:1.0	.	910	G3V2B8	.	T	910;966	ENSP00000450560:M910T;ENSP00000216605:M966T	ENSP00000216605:M910T	M	+	2	0	MTHFD1	63994695	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.503000	0.81632	2.117000	0.64856	0.482000	0.46254	ATG	.		0.448	MTHFD1-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471593.1			C	64924942	T	C	64924942	3	2	54	1	0	0	0	0	1	0	0	0	9952	1464	51	3	2835	3	MTHFD1	14	64924942	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	314355	64924942	42424598	115	5285											
RDH11	51109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	68159767	68159767	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaccccactggacagcattTtcctgcagacagagaaggag	13	6	10	12	0	0	2	0	0	0	2	1	5	1	4	3	2	2	2	3	2	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:68159767T>G	ENST00000381346.4	-	2	187	c.77A>C	c.(76-78)aAa>aCa	p.K26T	RDH11_ENST00000428130.2_Missense_Mutation_p.K26T|RDH11_ENST00000553384.1_Missense_Mutation_p.K26T|RP11-1012A1.4_ENST00000553306.1_5'Flank|RP11-1012A1.4_ENST00000554493.1_5'Flank	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	26					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	GGACAGCATTTTCCTGCAGAC	0.483																																					p.K26T		.											.	RDH11-91	0			c.A77C						.						94	86	89					14																	68159767		2203	4300	6503	SO:0001583	missense	51109	exon2			AGCATTTTCCTGC	AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	17964	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 1", "androgen-regulated short-chain dehydrogenase/reductase 1"	607849	"retinol dehydrogenase 11 (all-trans and 9-cis)"			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.77A>C	14.37:g.68159767T>G	ENSP00000370750:p.Lys26Thr	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	93	35	NM_001252650	0	0	0	0	0	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	37	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.669280	0.47677	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000557273;ENST00000557726	D;D;D;D;D	0.90133	-1.78;-1.5;-1.91;-2.34;-2.62	5.31	4.17	0.49024	.	0.298500	0.36234	N	0.002701	D	0.83459	0.5259	N	0.19112	0.55	0.38302	D	0.943	P;P;P	0.47910	0.902;0.716;0.594	P;P;B	0.45681	0.476;0.49;0.295	T	0.81688	-0.0819	10	0.34782	T	0.22	.	7.5042	0.27534	0.0:0.1787:0.0:0.8213	.	26;26;26	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	T	26	ENSP00000370750:K26T;ENSP00000452079:K26T;ENSP00000416395:K26T;ENSP00000450651:K26T;ENSP00000450435:K26T	ENSP00000370750:K26T	K	-	2	0	RDH11	67229520	0.987000	0.35691	0.999000	0.59377	0.943000	0.58893	1.910000	0.39927	1.044000	0.40200	0.533000	0.62120	AAA	.		0.483	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			G	68159767	T	G	68159767	3	3	54	1	0	0	0	0	1	0	0	0	13222	1841	64	5	903	5	RDH11	14	68159767	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	3234825	68159767	39189773	116	5286											
FLVCR2	55640	broad.mit.edu;bcgsc.ca	37	chr14	76107380	76107380	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatcagaaggcatctcctccGgcctcctcaacatatctgca	11	9	6	15	1	4	1	2	0	2	1	7	1	6	1	4	2	2	2	4	2	4	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:76107380G>A	ENST00000238667.4	+	7	1674	c.1318G>A	c.(1318-1320)Ggc>Agc	p.G440S	FLVCR2_ENST00000539311.1_Missense_Mutation_p.G235S|FLVCR2_ENST00000556241.1_Intron|FLVCR2_ENST00000556856.1_Intron|FLVCR2_ENST00000553587.1_Intron|FLVCR2_ENST00000555027.1_Missense_Mutation_p.G155S	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	440					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		CATCTCCTCCGGCCTCCTCAA	0.502																																					p.G440S													.	FLVCR2-90	0			c.G1318A						.						126	111	116					14																	76107380		2203	4300	6503	SO:0001583	missense	55640	exon7			TCCTCCGGCCTCC	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"Solute carriers"	20105	protein-coding gene	gene with protein product		610865	"chromosome 14 open reading frame 58", "feline leukemia virus subgroup C cellular receptor 2"	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.1318G>A	14.37:g.76107380G>A	ENSP00000238667:p.Gly440Ser	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	227	7	NM_017791	0	0	3	3	0	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Missense_Mutation	SNP	ENST00000238667.4	37	CCDS9844.1	.	.	.	.	.	.	.	.	.	.	G	32	5.109740	0.94292	.	.	ENSG00000119686	ENST00000238667;ENST00000539311;ENST00000553341;ENST00000554580;ENST00000555027	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.26	5.26	0.73747	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.046377	0.85682	D	0.000000	D	0.84101	0.5398	M	0.88181	2.935	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71184	0.972;0.972	D	0.85430	0.1148	10	0.42905	T	0.14	-14.4478	17.6351	0.88120	0.0:0.0:1.0:0.0	.	235;440	B7Z485;Q9UPI3	.;FLVC2_HUMAN	S	440;235;141;140;155	ENSP00000238667:G440S;ENSP00000443439:G235S;ENSP00000452584:G141S;ENSP00000451781:G140S;ENSP00000452453:G155S	ENSP00000238667:G440S	G	+	1	0	AC007182.1	75177133	1.000000	0.71417	0.998000	0.56505	0.780000	0.44128	9.405000	0.97313	2.452000	0.82932	0.655000	0.94253	GGC	.		0.502	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791		A	76107380	G	A	76107380	3	1	54	1	0	0	0	0	1	0	0	0	5965	1116	39	1	1344	1	FLVCR2	14	76107380	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	7947613	76107380	31242160	117	5287											
WDR20	91833	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102675669	102675669	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaccttacagaagatatcCttttccctcaccaacccctc	10	10	5	16	0	1	2	1	0	0	2	4	3	3	3	6	1	2	0	6	1	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:102675669C>A	ENST00000342702.3	+	3	1193	c.1162C>A	c.(1162-1164)Ctt>Att	p.L388I	WDR20_ENST00000556807.1_Missense_Mutation_p.L327I|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000424963.2_Missense_Mutation_p.L264I|WDR20_ENST00000454394.2_Missense_Mutation_p.L419I|WDR20_ENST00000335263.5_Missense_Mutation_p.L388I|WDR20_ENST00000499851.2_Missense_Mutation_p.L131I|WDR20_ENST00000545563.1_Missense_Mutation_p.L215I|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000556511.2_Missense_Mutation_p.L327I	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	388										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AGAAGATATCCTTTTCCCTCA	0.517											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L419I													.	WDR20-90	0			c.C1255A						.						100	90	93					14																	102675669		2203	4300	6503	SO:0001583	missense	91833	exon4			GATATCCTTTTCC	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1162C>A	14.37:g.102675669C>A	ENSP00000341037:p.Leu388Ile	Somatic	166	1	1368	WXS	Illumina HiSeq	Phase_I	155	59	NM_001242417	0	0	1	2	1	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	37	CCDS9969.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.04|16.04	3.010031|3.010031	0.54361|0.54361	.|.	.|.	ENSG00000140153|ENSG00000140153	ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563|ENST00000556511	T;T;T;T;T;T;T|.	0.74947|.	-0.89;-0.89;-0.89;-0.89;-0.89;-0.89;-0.89|.	5.56|5.56	5.56|5.56	0.83823|0.83823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72195|0.72195	0.3430|0.3430	L|L	0.55213|0.55213	1.73|1.73	0.80722|0.80722	D|D	1|1	D;D;P;D;D;P;D|.	0.69078|.	0.985;0.991;0.884;0.995;0.997;0.956;0.985|.	P;P;B;P;D;D;P|.	0.65010|.	0.831;0.669;0.41;0.895;0.919;0.931;0.866|.	T|T	0.68409|0.68409	-0.5416|-0.5416	10|5	0.46703|.	T|.	0.11|.	.|.	19.5351|19.5351	0.95247|0.95247	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	419;400;327;388;327;264;388|.	E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3|.	.;.;.;.;.;.;WDR20_HUMAN|.	I|H	388;327;264;388;327;131;419;318;215|318	ENSP00000335434:L388I;ENSP00000395793:L264I;ENSP00000341037:L388I;ENSP00000450636:L327I;ENSP00000443641:L131I;ENSP00000406084:L419I;ENSP00000437927:L215I|.	ENSP00000299135:L327I|.	L|P	+|+	1|2	0|0	WDR20|WDR20	101745422|101745422	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.480000|7.480000	0.81109|0.81109	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	CTT|CCT	.		0.517	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		A	102675669	C	A	102675669	3	1	54	1	0	0	0	0	1	0	0	0	17313	681	24	4	1189	4	WDR20	14	102675669	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	26568289	102675669	4673871	118	5288											
C15orf41	84529	broad.mit.edu;bcgsc.ca	37	chr15	37002072	37002072	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttagctgtagaagggcacaTaattcactggattgaaagca	14	10	10	7	0	1	2	1	1	0	1	1	3	1	3	0	2	2	4	0	2	5	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:37002072T>A	ENST00000566621.1	+	10	876	c.626T>A	c.(625-627)aTa>aAa	p.I209K	C15orf41_ENST00000338183.4_Missense_Mutation_p.I111K|C15orf41_ENST00000562877.1_Missense_Mutation_p.I111K|C15orf41_ENST00000567389.1_Missense_Mutation_p.I111K|C15orf41_ENST00000569302.1_Missense_Mutation_p.I215K|C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000437989.2_Missense_Mutation_p.I209K|C15orf41_ENST00000562489.1_Missense_Mutation_p.I33K	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	209										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GAAGGGCACATAATTCACTGG	0.453																																					p.I209K													.	C15orf41-46	0			c.T626A						.						129	122	124					15																	37002072		1894	4110	6004	SO:0001583	missense	84529	exon10			GGCACATAATTCA	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.626T>A	15.37:g.37002072T>A	ENSP00000455397:p.Ile209Lys	Somatic	131	2		WXS	Illumina HiSeq	Phase_I	131	59	NM_001130010	0	0	0	1	1	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	37	CCDS45215.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.032004	0.75504	.	.	ENSG00000186073	ENST00000437989;ENST00000338183	T	0.46819	0.86	6.0	4.88	0.63580	.	0.136861	0.64402	D	0.000003	T	0.54255	0.1847	L	0.53249	1.67	0.80722	D	1	D	0.53151	0.958	P	0.53649	0.731	T	0.53099	-0.8486	10	0.44086	T	0.13	-11.1729	11.8294	0.52285	0.0:0.068:0.0:0.932	.	209	Q9Y2V0	CO041_HUMAN	K	209;111	ENSP00000401362:I209K	ENSP00000342433:I111K	I	+	2	0	C15orf41	34789364	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.103000	0.41568	0.528000	0.53228	ATA	.		0.453	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		A	37002072	T	A	37002072	3	1	54	1	0	0	0	0	1	0	0	0	1799	1406	49	5	664	5	C15orf41	15	37002072	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10		37002072	65529320	119	5289											
NUSAP1	51203	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41657726	41657726	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggccctgcaagtcagagtAccttgggtctgaaggggtca	8	9	15	9	0	3	2	2	1	1	1	3	2	3	2	2	4	2	2	2	4	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:41657726A>G	ENST00000559596.1	+	7	874	c.787A>G	c.(787-789)Acc>Gcc	p.T263A	NUSAP1_ENST00000414849.2_Missense_Mutation_p.T262A|NUSAP1_ENST00000560747.1_Missense_Mutation_p.T261A|NUSAP1_ENST00000450592.2_Missense_Mutation_p.T239A|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T248A|NUSAP1_ENST00000450318.1_Missense_Mutation_p.T263A|NUSAP1_ENST00000560177.1_Missense_Mutation_p.T262A|NUSAP1_ENST00000558123.1_3'UTR			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	263	Interaction with microtubules. {ECO:0000250}.				establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		AAGTCAGAGTACCTTGGGTCT	0.512																																					p.T263A		.											.	.	0			c.A787G						.						35	34	34					15																	41657726		1905	4133	6038	SO:0001583	missense	51203	exon7			CAGAGTACCTTGG	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.787A>G	15.37:g.41657726A>G	ENSP00000453403:p.Thr263Ala	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	88	32	NM_016359	0	0	3	4	1	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	SNP	ENST00000559596.1	37	CCDS45234.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417901	0.25552	.	.	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318;ENST00000450592	T;T;T	0.33438	1.41;1.41;1.41	4.64	0.0292	0.14161	.	0.492803	0.22030	N	0.065603	T	0.18383	0.0441	L	0.45137	1.4	0.09310	N	1	B;B;B;B;B;B;B	0.20671	0.018;0.018;0.047;0.037;0.023;0.047;0.047	B;B;B;B;B;B;B	0.20767	0.007;0.016;0.031;0.022;0.007;0.031;0.031	T	0.22800	-1.0206	10	0.15499	T	0.54	.	3.8119	0.08801	0.5416:0.1864:0.272:0.0	.	239;263;261;262;263;263;262	E7ERR5;E9PB35;Q9BXS6-3;Q9BXS6-5;A8K4B4;Q9BXS6;Q9BXS6-2	.;.;.;.;.;NUSAP_HUMAN;.	A	263;262;263;239	ENSP00000400746:T262A;ENSP00000401351:T263A;ENSP00000401014:T239A	ENSP00000260359:T263A	T	+	1	0	NUSAP1	39445018	0.167000	0.22975	0.004000	0.12327	0.008000	0.06430	1.620000	0.36976	-0.153000	0.11137	-0.438000	0.05819	ACC	.		0.512	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359		G	41657726	A	G	41657726	3	3	54	1	0	0	0	0	1	0	0	0	10804	391	14	3	813	3	NUSAP1	15	41657726	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	4655654	41657726	60873666	120	5290											
TP53BP1	7158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43771711	43771711	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atatcttcgttggactgttcTtcatgcttaattgctgagag	8	17	9	7	1	3	1	1	1	2	1	4	3	3	2	0	1	2	4	0	1	2	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:43771711T>C	ENST00000263801.3	-	7	909	c.657A>G	c.(655-657)gaA>gaG	p.E219E	TP53BP1_ENST00000450115.2_Silent_p.E224E|TP53BP1_ENST00000382039.3_Silent_p.E224E|TP53BP1_ENST00000382044.4_Silent_p.E224E	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	219					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		TGGACTGTTCTTCATGCTTAA	0.378								Other conserved DNA damage response genes																													p.E224E		.											.	TP53BP1-294	0			c.A672G						.						233	184	201					15																	43771711		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon7			CTGTTCTTCATGC	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.657A>G	15.37:g.43771711T>C		Somatic	270	0		WXS	Illumina HiSeq	Phase_I	287	103	NM_001141980	0	0	0	0	0	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			.		0.378	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			C	43771711	T	C	43771711	2	2	54	1	0	0	0	0	0	0	0	1	16416	1606	56	3		3	TP53BP1	15	43771711	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	2113985	43771711	58759681	121	5291											
CATSPER2	117155	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43940128	43940128	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctgaccaagtaactccctGatagtgtgccgcggcacagc	9	8	11	13	2	0	2	0	2	0	0	1	2	1	2	3	1	4	3	3	1	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:43940128G>A	ENST00000321596.5	-	2	331	c.132C>T	c.(130-132)atC>atT	p.I44I	STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000355438.2_Silent_p.I44I|CATSPER2_ENST00000464721.1_Intron|CATSPER2_ENST00000396879.1_Silent_p.I44I|CATSPER2_ENST00000381761.1_Silent_p.I50I|CATSPER2_ENST00000354127.4_Silent_p.I44I			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	44					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GTAACTCCCTGATAGTGTGCC	0.453																																					p.I44I													.	CATSPER2-91	0			c.C132T						.						118	123	122					15																	43940128		2199	4296	6495	SO:0001819	synonymous_variant	117155	exon2			CTCCCTGATAGTG	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.132C>T	15.37:g.43940128G>A		Somatic	486	2		WXS	Illumina HiSeq	Phase_I	454	183	NM_172097	0	0	1	1	0	Q8NHT9|Q96P54|Q96P55	Silent	SNP	ENST00000321596.5	37	CCDS10099.1																																																																																			.		0.453	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		A	43940128	G	A	43940128	2	1	54	1	0	0	0	0	0	0	0	1	2694	1280	45	2		2	CATSPER2	15	43940128	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	168417	43940128	58591264	122	5292											
DAPK2	23604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64204316	64204316	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctggacacaccttccaccgCctgcggacatactgcttcct	7	9	7	18	2	0	0	0	0	0	0	2	2	2	2	6	2	3	1	6	2	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:64204316C>G	ENST00000457488.1	-	10	969	c.939G>C	c.(937-939)agG>agC	p.R313S	DAPK2_ENST00000261891.3_Missense_Mutation_p.R313S	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	313	Calmodulin-binding.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CCTTCCACCGCCTGCGGACAT	0.622																																					p.R313S		.											.	DAPK2-333	0			c.G939C						.						59	48	52					15																	64204316		2203	4300	6503	SO:0001583	missense	23604	exon10			CCACCGCCTGCGG	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.939G>C	15.37:g.64204316C>G	ENSP00000408277:p.Arg313Ser	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	64	38	NM_014326	0	0	0	0	0	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	37	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.777111	0.70107	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.68025	-0.3;-0.3	5.15	3.28	0.37604	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000011	T	0.74191	0.3684	M	0.70275	2.135	0.43054	D	0.994667	D	0.67145	0.996	P	0.58454	0.839	T	0.74213	-0.3738	10	0.62326	D	0.03	.	8.8262	0.35057	0.0:0.8244:0.0:0.1756	.	313	Q9UIK4	DAPK2_HUMAN	S	313	ENSP00000261891:R313S;ENSP00000408277:R313S	ENSP00000261891:R313S	R	-	3	2	DAPK2	61991369	1.000000	0.71417	0.982000	0.44146	0.974000	0.67602	1.554000	0.36266	0.573000	0.29400	-0.192000	0.12808	AGG	.		0.622	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		G	64204316	C	G	64204316	3	3	54	1	0	0	0	0	1	0	0	0	4242	738	26	4	185	4	DAPK2	15	64204316	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	20264188	64204316	38327076	123	5293											
SENP8	123228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72432461	72432461	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctatgactgtgggatgtAcgtgatatgtaacactgagg	11	11	13	6	1	0	3	0	3	0	0	0	4	0	4	0	2	3	3	0	2	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:72432461A>T	ENST00000542035.2	+	2	830	c.497A>T	c.(496-498)tAc>tTc	p.Y166F	SENP8_ENST00000544411.1_Missense_Mutation_p.Y166F|SENP8_ENST00000544171.1_Missense_Mutation_p.Y166F|RP11-2I17.4_ENST00000568984.1_RNA|SENP8_ENST00000340912.4_Missense_Mutation_p.Y166F	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	166	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						TGTGGGATGTACGTGATATGT	0.478																																					p.Y166F		.											.	SENP8-660	0			c.A497T						.						117	113	114					15																	72432461		2199	4297	6496	SO:0001583	missense	123228	exon2			GGATGTACGTGAT	BC031411	CCDS10240.1	15q22.33	2005-08-17	2005-08-17	2004-01-30	ENSG00000166192	ENSG00000166192			22992	protein-coding gene	gene with protein product	"NEDD8-specific protease 1", "sentrin/SUMO-specific protease SENP8", "deneddylase 1"	608659	"protease, cysteine, 2 (NEDD8 specific)", "SUMO/sentrin specific protease family member 8"	PRSC2		12730221, 12759362	Standard	NM_145204		Approved	NEDP1, DEN1, HsT17512	uc021spt.1	Q96LD8	OTTHUMG00000133441	ENST00000542035.2:c.497A>T	15.37:g.72432461A>T	ENSP00000446057:p.Tyr166Phe	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	33	10	NM_001166340	0	0	1	1	0	Q96QA4	Missense_Mutation	SNP	ENST00000542035.2	37	CCDS10240.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.150452	0.78001	.	.	ENSG00000166192	ENST00000542035;ENST00000544411;ENST00000340912;ENST00000544171	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.86	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	L	0.51853	1.615	0.58432	D	0.999999	D	0.56521	0.976	P	0.56751	0.805	T	0.24657	-1.0154	10	0.25106	T	0.35	-15.1718	13.2186	0.59875	0.867:0.133:0.0:0.0	.	166	Q96LD8	SENP8_HUMAN	F	166	ENSP00000446057:Y166F;ENSP00000441753:Y166F;ENSP00000340505:Y166F;ENSP00000439415:Y166F	ENSP00000340505:Y166F	Y	+	2	0	SENP8	70219515	1.000000	0.71417	0.921000	0.36526	0.907000	0.53573	9.228000	0.95250	1.018000	0.39521	-0.323000	0.08544	TAC	.		0.478	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204		T	72432461	A	T	72432461	3	4	54	1	0	0	0	0	1	0	0	0	14084	391	14	5	499	5	SENP8	15	72432461	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	8228145	72432461	30098931	124	5294											
PARP6	56965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72543559	72543559	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtcacttaccctgctgagagGtagtttgacaatgtgtgacc	9	12	11	9	0	1	3	1	3	0	1	1	4	1	3	2	1	2	3	2	1	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:72543559G>A	ENST00000569795.1	-	17	1984	c.1297C>T	c.(1297-1299)Cct>Tct	p.P433S	PARP6_ENST00000287196.9_Missense_Mutation_p.P433S|PARP6_ENST00000260376.7_Missense_Mutation_p.P433S|PARP6_ENST00000413097.2_5'UTR			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	433	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CTGCTGAGAGGTAGTTTGACA	0.413																																					p.P433S		.											.	PARP6-522	0			c.C1297T						.						104	99	101					15																	72543559		1869	4113	5982	SO:0001583	missense	56965	exon16			TGAGAGGTAGTTT	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.1297C>T	15.37:g.72543559G>A	ENSP00000456348:p.Pro433Ser	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	100	48	NM_020214	0	0	0	0	0	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	37	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	G	23.1	4.378759	0.82682	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000413097	.	.	.	5.14	4.22	0.49857	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66317	0.2777	L	0.41824	1.3	0.80722	D	1	B;D;D	0.89917	0.374;0.993;1.0	B;D;D	0.80764	0.117;0.979;0.994	T	0.66586	-0.5886	9	0.46703	T	0.11	-4.7079	12.9482	0.58384	0.0779:0.0:0.9221:0.0	.	433;433;365	Q0VDG0;Q2NL67;A0PJ50	.;PARP6_HUMAN;.	S	433;433;433;278	.	ENSP00000260376:P433S	P	-	1	0	PARP6	70330613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.539000	0.98076	1.386000	0.46466	0.655000	0.94253	CCT	.		0.413	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		A	72543559	G	A	72543559	3	1	54	1	0	0	0	0	1	0	0	0	11490	1261	44	2	627	2	PARP6	15	72543559	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	111098	72543559	29987833	125	5295											
FANCI	55215	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	89801970	89801970	+	Frame_Shift_Del	DEL	A	A	-																															cagaatcaagcagtgaaaggAaaagttgctggagcactcct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:89801970delA	ENST00000310775.7	+	3	206	c.120delA	c.(118-120)ggafs	p.G40fs	FANCI_ENST00000567996.1_Frame_Shift_Del_p.G40fs|FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000300027.8_Frame_Shift_Del_p.G40fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	40					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CAGTGAAAGGAAAAGTTGCTG	0.388								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G40fs		.											.	FANCI-92	0			c.120delA						.						181	178	179					15																	89801970		2200	4299	6499	SO:0001589	frameshift_variant	55215	exon3	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.120delA	15.37:g.89801970delA	ENSP00000310842:p.Gly40fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	102	46	NM_001113378	0	0	0	0	0	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	37	CCDS45346.1																																																																																			.		0.388	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		-	89801970	A	-	89801970	7	5	54	1	0	1	0	1	0	0	0	0	5688	233	9	0	126	0	FANCI	15	89801970	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	17258411	89801970	12729422	126	5296											
OR4F6	390648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	102346642	102346642	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaggctttctctatgctGtcagctcatgtcattgtggt	6	17	9	9	0	5	0	4	0	1	0	6	0	5	0	0	2	2	3	0	2	2	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:102346642G>T	ENST00000328882.4	+	1	741	c.720G>T	c.(718-720)ctG>ctT	p.L240L		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(1)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			TCTCTATGCTGTCAGCTCATG	0.353																																					p.L240L		.											.	OR4F6-69	0			c.G720T						.						172	165	167					15																	102346642		2202	4300	6502	SO:0001819	synonymous_variant	390648	exon1			TATGCTGTCAGCT	AC025234	CCDS32341.1	15q26.3	2014-02-19	2002-02-28		ENSG00000184140	ENSG00000184140		"GPCR / Class A : Olfactory receptors"	15372	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily F, member 12"	OR4F12			Standard	NM_001005326		Approved		uc010utr.2	Q8NGB9	OTTHUMG00000172267	ENST00000328882.4:c.720G>T	15.37:g.102346642G>T		Somatic	180	0		WXS	Illumina HiSeq	Phase_I	124	42	NM_001005326	0	0	0	0	0	B9EH28|Q6IF95	Silent	SNP	ENST00000328882.4	37	CCDS32341.1																																																																																			.		0.353	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1			T	102346642	G	T	102346642	2	4	54	1	0	0	0	0	0	0	0	1	11092	1364	48	4		4	OR4F6	15	102346642	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	12544672	102346642	184750	127	5297											
PLK1	5347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23690422	23690422	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcgctatgtgcggggcCgctttttgggcaagggcggc	3	8	20	10	5	0	0	0	0	0	0	0	0	0	0	1	7	1	3	1	7	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr16:23690422C>A	ENST00000300093.4	+	1	280	c.169C>A	c.(169-171)Cgc>Agc	p.R57S	PLK1_ENST00000564202.1_3'UTR	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	57	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		TGTGCGGGGCCGCTTTTTGGG	0.657																																					p.R57S	Colon(12;240 564 27038 33155)	.											.	PLK1-766	0			c.C169A						.						16	19	18					16																	23690422		2197	4300	6497	SO:0001583	missense	5347	exon1			CGGGGCCGCTTTT		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"polo-like kinase (Drosophila)"	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.169C>A	16.37:g.23690422C>A	ENSP00000300093:p.Arg57Ser	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	157	60	NM_005030	0	0	5	8	3	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.861173	0.71949	.	.	ENSG00000166851	ENST00000300093;ENST00000330792	T	0.25579	1.79	4.08	3.09	0.35607	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.24699	0.0599	L	0.37630	1.12	0.80722	D	1	P	0.49090	0.919	P	0.49752	0.621	T	0.01600	-1.1315	10	0.44086	T	0.13	-18.3883	7.0374	0.25000	0.198:0.6098:0.1921:0.0	.	57	P53350	PLK1_HUMAN	S	57	ENSP00000300093:R57S	ENSP00000300093:R57S	R	+	1	0	PLK1	23597923	0.986000	0.35501	0.991000	0.47740	0.995000	0.86356	2.740000	0.47418	1.026000	0.39733	0.561000	0.74099	CGC	.		0.657	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		A	23690422	C	A	23690422	3	1	54	1	0	0	0	0	1	0	0	0	12120	652	23	4	171	4	PLK1	16	23690422	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		23690422	66664331	128	5298											
LONP2	83752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	48311386	48311386	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatccagcagcagctctgcTtgaggtaagatttggaaaat	12	11	11	7	0	1	3	0	2	1	1	2	4	2	4	1	2	4	5	1	2	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr16:48311386T>G	ENST00000285737.4	+	8	1472	c.1379T>G	c.(1378-1380)cTt>cGt	p.L460R	LONP2_ENST00000535754.1_Missense_Mutation_p.L416R	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GCAGCTCTGCTTGAGGTAAGA	0.438																																					p.L460R		.											.	LONP2-90	0			c.T1379G						.						81	73	76					16																	48311386		2200	4300	6500	SO:0001583	missense	83752	exon8			CTCTGCTTGAGGT	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.1379T>G	16.37:g.48311386T>G	ENSP00000285737:p.Leu460Arg	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	188	63	NM_031490	0	0	0	0	0		Missense_Mutation	SNP	ENST00000285737.4	37	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.426428	0.83667	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754;ENST00000416006	T;T;T	0.55760	0.5;0.5;0.5	5.96	5.96	0.96718	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.85592	0.5732	H	0.99705	4.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92181	0.5751	10	0.87932	D	0	-17.8825	16.4277	0.83824	0.0:0.0:0.0:1.0	.	416;460	B7ZKL7;Q86WA8	.;LONP2_HUMAN	R	460;189;416;416	ENSP00000285737:L460R;ENSP00000445426:L416R;ENSP00000415983:L416R	ENSP00000285737:L460R	L	+	2	0	LONP2	46868887	1.000000	0.71417	0.992000	0.48379	0.761000	0.43186	7.996000	0.88334	2.279000	0.76181	0.533000	0.62120	CTT	.		0.438	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		G	48311386	T	G	48311386	3	3	54	1	0	0	0	0	1	0	0	0	8918	1609	56	5	1409	5	LONP2	16	48311386	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	24620964	48311386	42043367	129	5299											
MINK1	50488	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4789856	4789856	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccgggaccagcccacggAgcggcaggtccgcatccagc	8	3	13	17	4	0	0	0	0	0	0	3	2	3	2	5	4	3	2	5	4	0	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:4789856A>G	ENST00000355280.6	+	10	1080	c.884A>G	c.(883-885)gAg>gGg	p.E295G	MINK1_ENST00000453408.3_Missense_Mutation_p.E295G|MINK1_ENST00000347992.7_Missense_Mutation_p.E295G	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						CAGCCCACGGAGCGGCAGGTC	0.582																																					p.E295G													.	MINK1-943	0			c.A884G						.						60	64	63					17																	4789856		1962	4131	6093	SO:0001583	missense	50488	exon10			CCACGGAGCGGCA	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"misshapen/NIK-related kinase"	609426	"misshapen-like kinase 1 (zebrafish)"			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.884A>G	17.37:g.4789856A>G	ENSP00000347427:p.Glu295Gly	Somatic	136	1		WXS	Illumina HiSeq	Phase_I	118	37	NM_170663	0	0	4	7	3		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757426	0.89843	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;D	0.97688	-1.06;-0.01;-4.49	4.81	4.81	0.61882	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.98485	0.9495	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.996	D;D;D;D	0.71870	0.975;0.975;0.945;0.975	D	0.99312	1.0904	10	0.87932	D	0	.	12.3647	0.55222	1.0:0.0:0.0:0.0	.	295;295;295;295	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	G	295	ENSP00000347427:E295G;ENSP00000406487:E295G;ENSP00000269296:E295G	ENSP00000269296:E295G	E	+	2	0	MINK1	4730639	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.139000	0.94554	2.036000	0.60181	0.459000	0.35465	GAG	.		0.582	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		G	4789856	A	G	4789856	3	3	54	1	0	0	0	0	1	0	0	0	9612	304	11	3	661	3	MINK1	17	4789856	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		4789856	76405354	130	5300											
GUCY2D	3000	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	7910749	7910749	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctttctccaccaggcaccGgctacttcacatgcaaatgg	9	10	7	15	1	3	0	1	0	2	0	4	0	3	0	3	3	2	3	3	3	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:7910749G>A	ENST00000254854.4	+	6	1619	c.1469G>A	c.(1468-1470)cGg>cAg	p.R490Q		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	490					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.R490Q(1)		skin(1)	1		Prostate(122;0.157)				ACCAGGCACCGGCTACTTCAC	0.592																																					p.R490Q		.											.	GUCY2D-319	1	Substitution - Missense(1)	lung(1)	c.G1469A						.						105	102	103					17																	7910749		2203	4300	6503	SO:0001583	missense	3000	exon6			GGCACCGGCTACT	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.1469G>A	17.37:g.7910749G>A	ENSP00000254854:p.Arg490Gln	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	88	6	NM_000180	0	0	0	0	0	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.388655	0.42308	.	.	ENSG00000132518	ENST00000254854	D	0.83591	-1.74	5.52	0.753	0.18404	.	0.440036	0.19338	N	0.116724	T	0.74261	0.3693	L	0.41710	1.295	0.18873	N	0.999989	B	0.22146	0.065	B	0.11329	0.006	T	0.59768	-0.7392	10	0.28530	T	0.3	.	14.1923	0.65646	0.2084:0.0:0.7916:0.0	.	490	Q02846	GUC2D_HUMAN	Q	490	ENSP00000254854:R490Q	ENSP00000254854:R490Q	R	+	2	0	GUCY2D	7851474	0.946000	0.32159	0.998000	0.56505	0.972000	0.66771	2.884000	0.48562	0.309000	0.22966	-1.267000	0.01435	CGG	.		0.592	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			A	7910749	G	A	7910749	3	1	54	1	0	0	0	0	1	0	0	0	6918	1116	39	1	1487	1	GUCY2D	17	7910749	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	3120893	7910749	73284461	131	5301											
MAP2K3	5606	broad.mit.edu;bcgsc.ca	37	chr17	21208389	21208389	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggatcaacccagagctgaaCcagaagggctacaatgtcaa	16	5	10	10	0	2	3	2	1	0	2	2	4	2	4	2	2	4	2	2	2	6	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:21208389C>A	ENST00000342679.4	+	9	972	c.723C>A	c.(721-723)aaC>aaA	p.N241K	MAP2K3_ENST00000316920.6_Missense_Mutation_p.N212K|MAP2K3_ENST00000361818.5_Missense_Mutation_p.N212K	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAGAGCTGAACCAGAAGGGCT	0.632																																					p.N241K													.	MAP2K3-790	0			c.C723A						.						179	153	162					17																	21208389		2203	4300	6503	SO:0001583	missense	5606	exon9			GCTGAACCAGAAG	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"Mitogen-activated protein kinase cascade / Kinase kinases"	6843	protein-coding gene	gene with protein product	"MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3"	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.723C>A	17.37:g.21208389C>A	ENSP00000345083:p.Asn241Lys	Somatic	126	2		WXS	Illumina HiSeq	Phase_I	131	19	NM_145109	0	0	35	35	0	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.234453	0.58886	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.63255	-0.03;-0.03	5.13	3.12	0.35913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.38957	0.1060	N	0.01649	-0.78	0.58432	D	0.999999	P	0.44986	0.847	P	0.46237	0.508	T	0.49943	-0.8885	10	0.59425	D	0.04	-46.6714	10.6286	0.45523	0.0:0.8414:0.0:0.1586	.	241	P46734	MP2K3_HUMAN	K	241;212;212;245	ENSP00000345083:N241K;ENSP00000355081:N212K	ENSP00000319139:N245K	N	+	3	2	MAP2K3	21148982	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.537000	0.53590	0.541000	0.28827	0.462000	0.41574	AAC	.		0.632	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		A	21208389	C	A	21208389	3	1	54	1	0	0	0	0	1	0	0	0	9263	506	18	4	757	4	MAP2K3	17	21208389	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	13297640	21208389	59986821	132	5302											
SGK494	9703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26938587	26938587	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctttaacctctctcacccAtgtactgaagagtgccacag	11	10	7	13	0	2	2	1	1	1	1	3	2	2	2	3	0	4	2	3	0	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:26938587A>G	ENST00000528896.2	-	0	7407				SPAG5-AS1_ENST00000554154.1_RNA|SGK494_ENST00000469832.3_5'Flank|SPAG5-AS1_ENST00000414744.1_RNA|SGK494_ENST00000301037.5_Missense_Mutation_p.M270T|RP11-192H23.4_ENST00000534850.1_3'UTR|RP11-192H23.4_ENST00000577790.1_Intron|RP11-192H23.6_ENST00000579019.2_RNA|SPAG5-AS1_ENST00000424210.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100							extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TCTCTCACCCATGTACTGAAG	0.502																																					p.M270T		.											.	.	0			c.T809C						.						184	156	165					17																	26938587		2203	4300	6503	SO:0001628	intergenic_variant	0	exon9			TCACCCATGTACT	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587		17.37:g.26938587A>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	116	39	NM_001174103	0	0	2	2	0	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.245285	0.59103	.	.	ENSG00000167524	ENST00000301037	T	0.09817	2.94	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.41766	0.1173	M	0.91972	3.26	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53229	-0.8468	10	0.87932	D	0	-18.3153	14.6957	0.69121	1.0:0.0:0.0:0.0	.	270	Q96LW2	SG494_HUMAN	T	270	ENSP00000301037:M270T	ENSP00000301037:M270T	M	-	2	0	AC005726.6	23962714	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.546000	0.73887	2.074000	0.62210	0.383000	0.25322	ATG	.		0.502	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		G	26938587	A	G	26938587	1	3	54	0	1	0	0	0	0	0	0	0	14245	217	8	3		3	SGK494	17	26938587	IGR	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	5730198	26938587	54256623	133	5303											
EFCAB5	374786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	28296149	28296149	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgcatatttgcttgacaaActtctacccaccttagttcc	10	14	4	13	0	1	1	0	1	1	0	2	1	2	1	3	0	4	3	3	0	4	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:28296149A>T	ENST00000394835.3	+	4	723	c.531A>T	c.(529-531)aaA>aaT	p.K177N	EFCAB5_ENST00000378738.3_Missense_Mutation_p.K177N|EFCAB5_ENST00000536908.2_Missense_Mutation_p.K121N|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000394832.2_Missense_Mutation_p.K177N|EFCAB5_ENST00000534836.2_Intron|EFCAB5_ENST00000320856.5_Missense_Mutation_p.K177N	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	177							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TGCTTGACAAACTTCTACCCA	0.373																																					p.K177N		.											.	EFCAB5-70	0			c.A531T						.						45	43	44					17																	28296149		1839	4090	5929	SO:0001583	missense	374786	exon4			TGACAAACTTCTA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"EF-hand domain containing"	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.531A>T	17.37:g.28296149A>T	ENSP00000378312:p.Lys177Asn	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	118	52	NM_198529	0	0	0	0	0	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	A	11.59	1.682704	0.29872	.	.	ENSG00000176927	ENST00000536908;ENST00000421238;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598	T;T;T;T;T	0.32023	1.51;2.55;2.51;1.81;1.47	5.57	-0.614	0.11590	.	.	.	.	.	T	0.36771	0.0979	L	0.33485	1.01	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.995;0.995	D;D;D;D	0.91635	0.999;0.999;0.909;0.909	T	0.10177	-1.0641	8	.	.	.	-14.4895	8.1332	0.31039	0.4603:0.1168:0.4229:0.0	.	121;177;177;177	F5GYL2;B5MEA3;E7EVS9;A4FU69	.;.;.;EFCB5_HUMAN	N	121;121;177;177;177;177;121	ENSP00000440619:K121N;ENSP00000378312:K177N;ENSP00000322003:K177N;ENSP00000378309:K177N;ENSP00000368012:K177N	.	K	+	3	2	EFCAB5	25320275	1.000000	0.71417	0.998000	0.56505	0.492000	0.33523	0.654000	0.24918	-0.080000	0.12685	-0.290000	0.09829	AAA	.		0.373	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		T	28296149	A	T	28296149	3	4	54	1	0	0	0	0	1	0	0	0	4949	40	2	5	545	5	EFCAB5	17	28296149	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	1357562	28296149	52899061	134	5304											
LRRC37B	114659	hgsc.bcm.edu;bcgsc.ca	37	chr17	30349520	30349520	+	Frame_Shift_Del	DEL	C	C	-																															gcctccagacccggggcttgCcataactccagaacccacta																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:30349520delC	ENST00000341671.7	+	1	1360	c.1355delC	c.(1354-1356)gccfs	p.A452fs	LRRC37B_ENST00000543378.2_Frame_Shift_Del_p.A370fs|LRRC37B_ENST00000394713.3_Frame_Shift_Del_p.A452fs|LRRC37B_ENST00000584368.1_Frame_Shift_Del_p.A464fs|LRRC37B_ENST00000327564.7_Frame_Shift_Del_p.A479fs|LRRC37B_ENST00000581786.1_3'UTR	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	452						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				CCGGGGCTTGCCATAACTCCA	0.542																																					p.A452fs		.											.	LRRC37B-92	0			c.1355delC						.						95	101	99					17																	30349520		2203	4300	6503	SO:0001589	frameshift_variant	114659	exon1			.	AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.1355delC	17.37:g.30349520delC	ENSP00000340519:p.Ala452fs	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	268	45	NM_052888	0	0	0	0	0	Q17RC9|Q5YKG6	Frame_Shift_Del	DEL	ENST00000341671.7	37	CCDS32609.1																																																																																			.		0.542	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		-	30349520	C	-	30349520	7	5	54	1	0	1	0	1	0	0	0	0	9019	739	26	0	1357	0	LRRC37B	17	30349520	Frame_Shift_Del	DEL	C	TCGA-B9-A44B-01A-11D-A25F-10	2053371	30349520	50845690	135	5305											
PTRF	284119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40557359	40557359	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctggcagcgcctccgactcTttcagcgatttgctgatgct	5	13	10	13	3	3	1	1	1	2	0	4	3	4	1	2	1	4	3	2	1	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:40557359T>A	ENST00000357037.5	-	2	938	c.519A>T	c.(517-519)aaA>aaT	p.K173N		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		CCTCCGACTCTTTCAGCGATT	0.652																																					p.K173N		.											.	PTRF-153	0			c.A519T						.						79	86	83					17																	40557359		2202	4300	6502	SO:0001583	missense	284119	exon2			CGACTCTTTCAGC	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.519A>T	17.37:g.40557359T>A	ENSP00000349541:p.Lys173Asn	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	20	4	NM_012232	0	0	37	47	10		Missense_Mutation	SNP	ENST00000357037.5	37	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.186520	0.57909	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.60171	0.21	5.35	-3.31	0.04988	.	0.183494	0.47455	D	0.000233	T	0.61924	0.2386	M	0.72353	2.195	0.50813	D	0.999894	D;D	0.56035	0.974;0.974	P;P	0.53146	0.719;0.719	T	0.65352	-0.6189	10	0.30078	T	0.28	-16.9364	14.7183	0.69286	0.0:0.6953:0.0:0.3047	.	155;173	B4DNU9;Q6NZI2	.;PTRF_HUMAN	N	173;128	ENSP00000349541:K173N	ENSP00000349541:K173N	K	-	3	2	PTRF	37810885	0.929000	0.31497	0.985000	0.45067	0.776000	0.43924	0.061000	0.14366	-0.544000	0.06232	-0.490000	0.04691	AAA	.		0.652	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		A	40557359	T	A	40557359	3	1	54	1	0	0	0	0	1	0	0	0	12847	1606	56	5	657	5	PTRF	17	40557359	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	10207839	40557359	40637851	136	5306											
MBTD1	54799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	49302371	49302371	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggttataaatactcacccAtgccagatttaccatctggg	13	11	7	10	0	2	1	1	0	1	1	2	1	2	1	3	2	3	1	3	2	6	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:49302371A>C	ENST00000586178.1	-	3	495	c.152T>G	c.(151-153)aTg>aGg	p.M51R	MBTD1_ENST00000376381.2_Missense_Mutation_p.M51R|MBTD1_ENST00000593259.1_5'Flank|MBTD1_ENST00000415868.1_Missense_Mutation_p.M51R	NM_017643.2	NP_060113.2	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	51					chromatin modification (GO:0016568)|embryonic skeletal system development (GO:0048706)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			ATACTCACCCATGCCAGATTT	0.393																																					p.M51R		.											.	MBTD1-92	0			c.T152G						.						145	135	138					17																	49302371		692	1591	2283	SO:0001583	missense	54799	exon3			TCACCCATGCCAG	AK000062	CCDS11581.2	17q24.1	2003-01-15			ENSG00000011258	ENSG00000011258			19866	protein-coding gene	gene with protein product							Standard	NM_017643		Approved	SA49P01, FLJ20055	uc002itr.4	Q05BQ5	OTTHUMG00000150442	ENST00000586178.1:c.152T>G	17.37:g.49302371A>C	ENSP00000468304:p.Met51Arg	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	86	26	NM_017643	0	0	0	0	0	Q6ZVU7|Q9NXU1	Missense_Mutation	SNP	ENST00000586178.1	37	CCDS11581.2	.	.	.	.	.	.	.	.	.	.	A	23.1	4.377416	0.82682	.	.	ENSG00000011258	ENST00000405860;ENST00000415868;ENST00000376381	T;T	0.23950	1.9;1.88	5.21	5.21	0.72293	Zinc finger, FCS-type (1);	0.073350	0.85682	D	0.000000	T	0.39759	0.1090	L	0.40543	1.245	0.80722	D	1	D;D	0.60575	0.988;0.96	P;D	0.69142	0.701;0.962	T	0.06789	-1.0807	10	0.23891	T	0.37	.	15.3505	0.74380	1.0:0.0:0.0:0.0	.	51;51	Q05BQ5;Q05BQ5-2	MBTD1_HUMAN;.	R	51	ENSP00000403946:M51R;ENSP00000365561:M51R	ENSP00000365561:M51R	M	-	2	0	MBTD1	46657370	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.248000	0.95456	2.089000	0.63090	0.482000	0.46254	ATG	.		0.393	MBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318124.1			C	49302371	A	C	49302371	3	2	54	1	0	0	0	0	1	0	0	0	9385	217	8	5	1794	5	MBTD1	17	49302371	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	8745012	49302371	31892839	137	5307											
AKAP1	8165	ucsc.edu;bcgsc.ca	37	chr17	55197616	55197616	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aactttcttttctaggtggtGttgataaaccggtccctggt	7	16	10	8	1	2	1	0	1	2	0	3	1	3	1	2	4	2	1	2	4	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:55197616G>A	ENST00000337714.3	+	11	2876	c.2643G>A	c.(2641-2643)gtG>gtA	p.V881V	AKAP1_ENST00000571629.1_Silent_p.V881V|AKAP1_ENST00000572557.1_Silent_p.V881V|AKAP1_ENST00000539273.1_Silent_p.V881V	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	881					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					TCTAGGTGGTGTTGATAAACC	0.532																																					p.V881V													.	AKAP1-227	0			c.G2643A						.						159	129	139					17																	55197616		2203	4300	6503	SO:0001819	synonymous_variant	8165	exon12			GGTGGTGTTGATA	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Tudor domain containing"	367	protein-coding gene	gene with protein product	"protein kinase anchoring protein 1", "dual specificity A-kinase-anchoring protein 1", "protein phosphatase 1, regulatory subunit 43", "tudor domain containing 17"	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.2643G>A	17.37:g.55197616G>A		Somatic	233	2		WXS	Illumina HiSeq		215	71	NM_001242902	0	0	0	1	1	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Silent	SNP	ENST00000337714.3	37	CCDS11594.1																																																																																			.		0.532	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			A	55197616	G	A	55197616	2	1	54	1	0	0	0	0	0	0	0	1	445	1364	48	2		2	AKAP1	17	55197616	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	5895245	55197616	25997594	138	5308											
BZRAP1	9256	broad.mit.edu;bcgsc.ca	37	chr17	56382447	56382447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tctcagcctggggtgtcctgGgttccctgtccaggccgcct	2	11	13	15	1	1	0	1	0	1	0	5	0	4	0	6	4	1	1	6	4	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:56382447G>A	ENST00000343736.4	-	30	5682	c.5519C>T	c.(5518-5520)cCc>cTc	p.P1840L	BZRAP1_ENST00000268893.6_Missense_Mutation_p.P1780L|BZRAP1_ENST00000355701.3_Missense_Mutation_p.P1840L			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1840						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGGTGTCCTGGGTTCCCTGTC	0.637																																					p.P1840L													.	BZRAP1-229	0			c.C5519T						.						43	49	47					17																	56382447		2203	4300	6503	SO:0001583	missense	9256	exon30			GTCCTGGGTTCCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.5519C>T	17.37:g.56382447G>A	ENSP00000345824:p.Pro1840Leu	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	151	6	NM_004758	0	0	0	0	0	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.532801	0.45073	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.06849	3.46;3.25;3.27	5.42	4.45	0.53987	.	0.288216	0.32935	N	0.005468	T	0.11707	0.0285	L	0.27053	0.805	0.09310	N	1	B;D;P;P	0.54601	0.005;0.967;0.883;0.856	B;P;B;B	0.53861	0.003;0.736;0.444;0.357	T	0.05716	-1.0868	10	0.56958	D	0.05	.	11.0111	0.47663	0.087:0.0:0.913:0.0	.	1831;1780;1840;1780	B7ZVZ7;O95153-2;O95153;A7E2C5	.;.;RIMB1_HUMAN;.	L	1840;1840;1780	ENSP00000347929:P1840L;ENSP00000345824:P1840L;ENSP00000268893:P1780L	ENSP00000268893:P1780L	P	-	2	0	BZRAP1	53737446	0.186000	0.23225	0.236000	0.24074	0.576000	0.36127	1.208000	0.32345	1.308000	0.44962	0.449000	0.29647	CCC	.		0.637	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		A	56382447	G	A	56382447	3	1	54	1	0	0	0	0	1	0	0	0	1580	1232	43	2	62	2	BZRAP1	17	56382447	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	1184831	56382447	24812763	139	5309											
MED13	9969	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	60042511	60042511	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagacatggatcctgcagcaTtactgttcatactgccaaag	12	11	8	10	0	1	1	1	0	0	1	2	2	2	2	2	1	5	3	2	1	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:60042511T>C	ENST00000397786.2	-	20	4776	c.4700A>G	c.(4699-4701)aAt>aGt	p.N1567S		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1567	Ser-rich.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TCCTGCAGCATTACTGTTCAT	0.443																																					p.N1567S													.	MED13-136	0			c.A4700G						.						139	133	135					17																	60042511		2013	4177	6190	SO:0001583	missense	9969	exon20			GCAGCATTACTGT	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4700A>G	17.37:g.60042511T>C	ENSP00000380888:p.Asn1567Ser	Somatic	246	1		WXS	Illumina HiSeq	Phase_I	252	98	NM_005121	0	0	2	3	1	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	4.460	0.085281	0.08583	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.72942	-0.7	5.86	1.31	0.21738	.	0.512331	0.22363	N	0.061055	T	0.44623	0.1302	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.26744	-1.0094	10	0.02654	T	1	-29.4536	4.8439	0.13503	0.0:0.4:0.2672:0.3328	.	1567	Q9UHV7	MED13_HUMAN	S	1567;1566	ENSP00000380888:N1567S	ENSP00000262436:N1566S	N	-	2	0	MED13	57397293	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	0.587000	0.23909	0.752000	0.32923	0.533000	0.62120	AAT	.		0.443	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		C	60042511	T	C	60042511	3	2	54	1	0	0	0	0	1	0	0	0	9455	1493	52	3	1868	3	MED13	17	60042511	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	3660064	60042511	21152699	140	5310											
KCNH6	81033	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61623068	61623068	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaacggacaaaactctggcAccatcctcagaacaggaaca	16	4	8	13	1	2	1	1	0	1	1	3	3	3	3	2	3	4	2	2	3	5	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:61623068A>G	ENST00000583023.1	+	14	2801	c.2790A>G	c.(2788-2790)gcA>gcG	p.A930A	KCNH6_ENST00000456941.2_Silent_p.A841A|KCNH6_ENST00000581784.1_Silent_p.A841A|KCNH6_ENST00000314672.5_Silent_p.A894A	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	930					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AAACTCTGGCACCATCCTCAG	0.567																																					p.A930A													.	KCNH6-91	0			c.A2790G						.						109	97	101					17																	61623068		2203	4300	6503	SO:0001819	synonymous_variant	81033	exon14			TCTGGCACCATCC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2790A>G	17.37:g.61623068A>G		Somatic	112	1		WXS	Illumina HiSeq	Phase_I	123	51	NM_030779	0	0	3	7	4	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			.		0.567	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		G	61623068	A	G	61623068	2	3	54	1	0	0	0	0	0	0	0	1	8057	146	6	3		3	KCNH6	17	61623068	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	1580557	61623068	19572142	141	5311											
NAT9	26151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72768142	72768142	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatccggatgcttggttcaTttccttgcccaattttagcc	7	15	7	12	1	1	0	1	0	0	0	3	1	3	1	4	2	3	2	4	2	2	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:72768142T>G	ENST00000357814.3	-	6	519	c.446A>C	c.(445-447)aAt>aCt	p.N149T	NAT9_ENST00000583476.1_Intron|NAT9_ENST00000580216.1_5'Flank|NAT9_ENST00000581136.1_Missense_Mutation_p.N144T|NAT9_ENST00000582870.1_Missense_Mutation_p.N153T|NAT9_ENST00000580632.1_Missense_Mutation_p.N149T|NAT9_ENST00000578822.1_Missense_Mutation_p.N154T|NAT9_ENST00000583757.1_Intron|NAT9_ENST00000582524.1_Intron|NAT9_ENST00000580301.1_Missense_Mutation_p.N148T	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	149	N-acetyltransferase.					protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						GCTTGGTTCATTTCCTTGCCC	0.567																																					p.N149T		.											.	NAT9-90	0			c.A446C						.						168	164	165					17																	72768142		2203	4300	6503	SO:0001583	missense	26151	exon6			GGTTCATTTCCTT	AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"N-acetyltransferase 9"			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.446A>C	17.37:g.72768142T>G	ENSP00000350467:p.Asn149Thr	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	126	54	NM_015654	0	0	11	25	14	B2R7F0|Q9BTD0|Q9Y3T3	Missense_Mutation	SNP	ENST00000357814.3	37	CCDS11706.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499275	0.44455	.	.	ENSG00000109065	ENST00000357814	T	0.78364	-1.17	5.09	5.09	0.68999	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.92704	0.7681	H	0.98295	4.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95440	0.8524	10	0.87932	D	0	-19.1654	15.1669	0.72837	0.0:0.0:0.0:1.0	.	148;149	Q9BTE0-2;Q9BTE0	.;NAT9_HUMAN	T	149	ENSP00000350467:N149T	ENSP00000350467:N149T	N	-	2	0	NAT9	70279737	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.519000	0.81809	2.055000	0.61198	0.459000	0.35465	AAT	.		0.567	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654		G	72768142	T	G	72768142	3	3	54	1	0	0	0	0	1	0	0	0	10207	1493	52	5	185	5	NAT9	17	72768142	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	11145074	72768142	8427068	142	5312											
CARD14	79092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	78166392	78166392	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgccccagagacgacagcGactgcagcctcgtcagctcc	8	6	10	17	3	2	1	1	0	1	1	4	4	3	1	4	0	5	2	4	0	0	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:78166392G>A	ENST00000573882.1	+	11	1866	c.1330G>A	c.(1330-1332)Gac>Aac	p.D444N	CARD14_ENST00000570421.1_Missense_Mutation_p.D444N|CARD14_ENST00000344227.2_Missense_Mutation_p.D444N|CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000392434.2_Missense_Mutation_p.D207N			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	444					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			AGACGACAGCGACTGCAGCCT	0.662																																					p.D444N		.											.	CARD14-231	0			c.G1330A						.						50	51	51					17																	78166392		2203	4300	6503	SO:0001583	missense	79092	exon9			GACAGCGACTGCA	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"psoriasis susceptibility 2"	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.1330G>A	17.37:g.78166392G>A	ENSP00000458715:p.Asp444Asn	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	203	43	NM_024110	0	0	0	0	0	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	G	2.678	-0.275943	0.05679	.	.	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	T;T	0.32515	1.45;1.45	3.64	0.451	0.16629	.	1.109330	0.06805	N	0.789318	T	0.16938	0.0407	L	0.27053	0.805	0.09310	N	1	B;B;B	0.14438	0.002;0.01;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.29088	-1.0023	10	0.08599	T	0.76	-9.737	3.7718	0.08645	0.3225:0.1839:0.4936:0.0	.	444;207;444	B8QQJ3;E7ETJ2;Q9BXL6	.;.;CAR14_HUMAN	N	444;207;207	ENSP00000344549:D444N;ENSP00000376229:D207N	ENSP00000308507:D207N	D	+	1	0	CARD14	75780987	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.205000	0.09411	-0.044000	0.13491	-1.162000	0.01777	GAC	.		0.662	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78166392	G	A	78166392	3	1	54	1	0	0	0	0	1	0	0	0	2652	1058	37	1	1360	1	CARD14	17	78166392	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	5398250	78166392	3028818	143	5313											
NPTX1	4884	hgsc.bcm.edu;bcgsc.ca	37	chr17	78449367	78449367	+	Frame_Shift_Del	DEL	A	A	-																															tcagggcggtctcgatcttgAccctctcctcggtgtcgttc																								rs375303530		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:78449367delA	ENST00000306773.4	-	2	753	c.596delT	c.(595-597)gtcfs	p.V199fs	NPTX1_ENST00000575212.1_5'UTR	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	199					axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CTCGATCTTGACCCTCTCCTC	0.657																																					p.V199fs		.											.	NPTX1-90	0			c.596delT						.						55	41	46					17																	78449367		2202	4300	6502	SO:0001589	frameshift_variant	4884	exon2			.	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.596delT	17.37:g.78449367delA	ENSP00000307549:p.Val199fs	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	130	55	NM_002522	0	0	0	0	0	B3KXH3|Q5FWE6	Frame_Shift_Del	DEL	ENST00000306773.4	37	CCDS32762.1																																																																																			.		0.657	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			-	78449367	A	-	78449367	7	5	54	1	0	1	0	1	0	0	0	0	10628	275	10	0	718	0	NPTX1	17	78449367	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	282975	78449367	2745843	144	5314											
DSG3	1830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	29038453	29038453	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaaatcacctaccgaatcTctggagtgggaatcgatcag	14	8	10	9	2	3	1	2	0	1	1	5	5	3	3	2	2	1	0	2	2	5	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr18:29038453T>G	ENST00000257189.4	+	4	345	c.262T>G	c.(262-264)Tct>Gct	p.S88A		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTACCGAATCTCTGGAGTGGG	0.448																																					p.S88A		.											.	DSG3-98	0			c.T262G						.						103	102	102					18																	29038453		2203	4300	6503	SO:0001583	missense	1830	exon4			CGAATCTCTGGAG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"Cadherins / Major cadherins"	3050	protein-coding gene	gene with protein product	"pemphigus vulgaris antigen"	169615	"desmoglein 3 (pemphigus vulgaris antigen)"			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.262T>G	18.37:g.29038453T>G	ENSP00000257189:p.Ser88Ala	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	108	56	NM_001944	0	0	0	0	0	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.280611	0.80692	.	.	ENSG00000134757	ENST00000257189	T	0.52057	0.68	5.76	3.2	0.36748	Cadherin (4);Cadherin-like (1);	0.141448	0.32563	N	0.005937	T	0.69360	0.3102	M	0.91920	3.255	0.35383	D	0.790079	D	0.55385	0.971	P	0.60068	0.868	T	0.81453	-0.0926	10	0.87932	D	0	.	11.3024	0.49314	0.2412:0.0:0.0:0.7588	.	88	P32926	DSG3_HUMAN	A	88	ENSP00000257189:S88A	ENSP00000257189:S88A	S	+	1	0	DSG3	27292451	0.993000	0.37304	0.857000	0.33713	0.922000	0.55478	2.362000	0.44169	1.080000	0.41073	0.528000	0.53228	TCT	.		0.448	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		G	29038453	T	G	29038453	3	3	54	1	0	0	0	0	1	0	0	0	4789	1551	54	5	276	5	DSG3	18	29038453	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10		29038453	49038795	145	5315											
ABCA7	10347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1059069	1059069	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gttgaccgcttgtgcctgggGattccccctggtgaggtgag	4	11	16	10	1	0	3	0	3	0	0	1	4	1	4	4	4	1	2	4	4	0	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:1059069G>T	ENST00000263094.6	+	40	5679	c.5448G>T	c.(5446-5448)ggG>ggT	p.G1816G	ABCA7_ENST00000433129.1_Silent_p.G1816G|ABCA7_ENST00000435683.2_Silent_p.G1678G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1816	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTGCCTGGGGATTCCCCCTG	0.617																																					p.G1816G		.											.	ABCA7-98	0			c.G5448T						.						81	68	73					19																	1059069		2202	4300	6502	SO:0001819	synonymous_variant	10347	exon40			CCTGGGGATTCCC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5448G>T	19.37:g.1059069G>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	118	28	NM_019112	0	0	12	38	26	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.		0.617	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1059069	G	T	1059069	2	4	54	1	0	0	0	0	0	0	0	1	37	1161	41	4		4	ABCA7	19	1059069	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		1059069	58069914	146	5316											
C19orf28	126321	broad.mit.edu;bcgsc.ca	37	chr19	3546268	3546268	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctaccgtgtggggaccgatGaggtcggccgtcatggccag	6	7	16	12	4	1	1	1	1	0	0	2	3	1	2	5	5	1	0	5	5	1	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:3546268G>A	ENST00000355415.2	-	7	1348	c.1179C>T	c.(1177-1179)ctC>ctT	p.L393L	MFSD12_ENST00000591878.1_5'Flank|MFSD12_ENST00000398558.4_Silent_p.L393L|MFSD12_ENST00000389395.3_Silent_p.L393L|AC005786.7_ENST00000589360.1_RNA	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	393					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						GGGGACCGATGAGGTCGGCCG	0.687																																					p.L393L													.	.	0			c.C1179T						.						17	23	21					19																	3546268		2141	4246	6387	SO:0001819	synonymous_variant	126321	exon7			ACCGATGAGGTCG	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 28"	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1179C>T	19.37:g.3546268G>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_001042680	1	0	102	124	21	A8MXP7|D6W615|E9PAJ8|Q8N459	Silent	SNP	ENST00000355415.2	37	CCDS42465.1																																																																																			.		0.687	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983		A	3546268	G	A	3546268	2	1	54	1	0	0	0	0	0	0	0	1	1923	1277	45	2		2	C19orf28	19	3546268	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	2487199	3546268	55582715	147	5317											
ZNF799	90576	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12502558	12502558	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatggtttctctccagtgtgCgttctctcatgcatatgtaa	7	17	8	9	1	3	0	1	0	2	0	6	0	4	0	1	1	2	4	1	1	3	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:12502558C>T	ENST00000430385.3	-	4	854	c.654G>A	c.(652-654)acG>acA	p.T218T	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Silent_p.T186T	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	218					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T218T(2)|p.T5T(2)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CTCCAGTGTGCGTTCTCTCAT	0.403																																					p.T218T													.	ZNF799-74	4	Substitution - coding silent(4)	lung(4)	c.G654A						.						105	109	108					19																	12502558		2202	4298	6500	SO:0001819	synonymous_variant	90576	exon4			AGTGTGCGTTCTC	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.654G>A	19.37:g.12502558C>T		Somatic	160	1		WXS	Illumina HiSeq	Phase_I	99	39	NM_001080821	0	0	0	0	0		Silent	SNP	ENST00000430385.3	37	CCDS45989.1																																																																																			.		0.403	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		T	12502558	C	T	12502558	2	4	54	1	0	0	0	0	0	0	0	1	18198	755	27	1		1	ZNF799	19	12502558	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	8956290	12502558	46626425	148	5318											
CD97	976	hgsc.bcm.edu;broad.mit.edu	37	chr19	14517156	14517156	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcaggtggggctgcgctGccgcctggtggccgggctgc	1	6	19	15	4	0	0	0	0	0	0	0	0	0	0	4	6	3	4	4	6	0	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:14517156G>T	ENST00000242786.5	+	15	1915	c.1835G>T	c.(1834-1836)tGc>tTc	p.C612F	CD97_ENST00000358600.3_Missense_Mutation_p.C519F|CD97_ENST00000357355.3_Missense_Mutation_p.C563F|CTC-548K16.5_ENST00000590626.1_RNA	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	612					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GGGCTGCGCTGCCGCCTGGTG	0.706											OREG0025312	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C612F		.											.	CD97-570	0			c.G1835T						.						30	24	26					19																	14517156		2190	4280	6470	SO:0001583	missense	976	exon15			TGCGCTGCCGCCT		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1835G>T	19.37:g.14517156G>T	ENSP00000242786:p.Cys612Phe	Somatic	18	0	695	WXS	Illumina HiSeq	Phase_I	28	15	NM_078481	0	0	11	22	11	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	37	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158116	0.78114	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	D;D;D	0.82433	-1.61;-1.61;-1.61	4.42	3.33	0.38152	GPCR, family 2-like (1);	0.000000	0.36303	N	0.002674	D	0.93517	0.7931	H	0.97291	3.975	0.48236	D	0.999613	D;D;D	0.71674	0.959;0.976;0.998	D;D;D	0.87578	0.91;0.938;0.998	D	0.93810	0.7109	10	0.87932	D	0	.	11.004	0.47622	0.0:0.0:0.8118:0.1882	.	519;563;612	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	F	612;563;519;562	ENSP00000242786:C612F;ENSP00000349918:C563F;ENSP00000351413:C519F	ENSP00000242786:C612F	C	+	2	0	CD97	14378156	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.174000	0.89682	0.778000	0.33520	0.505000	0.49811	TGC	.		0.706	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14517156	G	T	14517156	3	4	54	1	0	0	0	0	1	0	0	0	3055	1319	46	4	1893	4	CD97	19	14517156	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	2014598	14517156	44611827	149	5319											
EPS15L1	58513	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	16548668	16548669	+	Frame_Shift_Del	DEL	AT	AT	-																															gccaccagtctcagtgcaacAtagaaaccctgcaagtccaa																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:16548668_16548669delAT	ENST00000248070.6	-	5	360_361	c.221_222delAT	c.(220-222)tatfs	p.Y74fs	EPS15L1_ENST00000455140.2_Frame_Shift_Del_p.Y74fs|EPS15L1_ENST00000602009.1_5'Flank|EPS15L1_ENST00000594975.1_Frame_Shift_Del_p.Y74fs|EPS15L1_ENST00000535753.2_Frame_Shift_Del_p.Y74fs|EPS15L1_ENST00000597937.1_Frame_Shift_Del_p.Y74fs	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	74	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TCAGTGCAACATAGAAACCCTG	0.5																																					p.74_74del		.											.	EPS15L1-95	0			c.221_222del						.																																			SO:0001589	frameshift_variant	58513	exon5			.	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.221_222delAT	19.37:g.16548668_16548669delAT	ENSP00000248070:p.Tyr74fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	113	34	NM_021235	0	0	0	0	0	A2RRF3|A5PL29|B4DKA3	Frame_Shift_Del	DEL	ENST00000248070.6	37	CCDS32944.1																																																																																			.		0.5	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		-	16548669	AT	-	16548668	7	5	54	1	0	1	0	1	0	0	0	0	5206	224	8	0	2448	0	EPS15L1	19	16548668	Frame_Shift_Del	DEL	AT	TCGA-B9-A44B-01A-11D-A25F-10	2031512	16548668	42580315	150	5320											
IFI30	10437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18288015	18288015	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgtgcaatgggggaccgCggcatgcagctcatgcacgc	8	6	16	11	3	1	0	1	0	0	0	1	2	1	1	1	3	4	5	1	3	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:18288015C>T	ENST00000407280.3	+	5	724	c.549C>T	c.(547-549)cgC>cgT	p.R183R	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	183					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 II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						TGGGGGACCGCGGCATGCAGC	0.617																																					p.R183R		.											.	IFI30-226	0			c.C549T						.						32	34	33					19																	18288015		2111	4231	6342	SO:0001819	synonymous_variant	10437	exon5			GGACCGCGGCATG	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"gamma-interferon-inducible lysosomal thiol reductase", "interferon gamma-inducible protein 30 preproprotein"	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.549C>T	19.37:g.18288015C>T		Somatic	215	0		WXS	Illumina HiSeq	Phase_I	160	34	NM_006332	0	0	54	67	13	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	37	CCDS46015.1																																																																																			.		0.617	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332		T	18288015	C	T	18288015	2	4	54	1	0	0	0	0	0	0	0	1	7536	755	27	1		1	IFI30	19	18288015	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	1739347	18288015	40840968	151	5321											
ZNF507	22847	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	32873421	32873421	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcctccttctttgaagtcTcatatgtggaaacatgcaag	11	13	7	10	0	2	1	1	1	2	0	5	2	4	2	2	1	2	1	2	1	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:32873421T>A	ENST00000311921.4	+	5	2601	c.2409T>A	c.(2407-2409)tcT>tcA	p.S803S	ZNF507_ENST00000355898.5_Silent_p.S803S|ZNF507_ENST00000544431.1_Silent_p.S807S	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	803					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					CTTTGAAGTCTCATATGTGGA	0.438																																					p.S803S													.	ZNF507-230	0			c.T2409A						.						277	268	271					19																	32873421		2203	4300	6503	SO:0001819	synonymous_variant	22847	exon6			GAAGTCTCATATG	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"Zinc fingers, C2H2-type"	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.2409T>A	19.37:g.32873421T>A		Somatic	203	2		WXS	Illumina HiSeq	Phase_I	202	106	NM_001136156	0	0	2	5	3	A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Silent	SNP	ENST00000311921.4	37	CCDS32985.1																																																																																			.		0.438	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		A	32873421	T	A	32873421	2	1	54	1	0	0	0	0	0	0	0	1	17985	1538	54	5		5	ZNF507	19	32873421	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	14585406	32873421	26255562	152	5322											
CEACAM20	125931	broad.mit.edu;bcgsc.ca	37	chr19	45016957	45016957	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgtggggtgctcctccttCgggatgggttgtgaggtctc	2	14	16	9	1	2	1	0	1	2	0	6	2	4	2	2	5	1	2	2	5	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:45016957C>T	ENST00000454753.1	-	0	1761							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				GCTCCTCCTTCGGGATGGGTT	0.592											OREG0025538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P494P													.	CEACAM20-67	0			c.G1482A						.						97	103	101					19																	45016957		1927	4129	6056			125931	exon9			CTCCTTCGGGATG	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Immunoglobulin superfamily / I-set domain containing"	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45016957C>T		Somatic	206	0	928	WXS	Illumina HiSeq	Phase_I	204	7	NM_001102600	0	0	0	0	0		Silent	SNP	ENST00000454753.1	37																																																																																				.		0.592	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		T	45016957	C	T	45016957	1	4	54	0	1	0	0	0	0	0	0	0	3197	893	31	1		1	CEACAM20	19	45016957	RNA	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	12143536	45016957	14112026	153	5323											
FAM83E	54854	broad.mit.edu	37	chr19	49114033	49114033	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggtagacaggtacccagcgGcgcgtggcagcatccaccaa	11	4	13	13	3	0	1	0	0	0	1	1	1	1	1	3	4	3	4	3	4	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:49114033G>A	ENST00000263266.3	-	2	726	c.537C>T	c.(535-537)cgC>cgT	p.R179R		NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	179										NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GTACCCAGCGGCGCGTGGCAG	0.652																																					p.R179R													.	FAM83E-91	0			c.C537T						.						14	19	17					19																	49114033		2104	4233	6337	SO:0001819	synonymous_variant	54854	exon2			CCAGCGGCGCGTG	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.537C>T	19.37:g.49114033G>A		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	180	6	NM_017708	0	0	6	6	0	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			.		0.652	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708		A	49114033	G	A	49114033	2	1	54	1	0	0	0	0	0	0	0	1	5656	1190	42	2		2	FAM83E	19	49114033	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	4097076	49114033	10014950	154	5324											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		.											.	.	0			c.C968A						.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	131	13	NM_001144989	0	0	2	2	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	54	1	0	0	0	0	1	0	0	0	18208	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	9271757	58385790	743193	155	5325	59	3									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		.											.	.	0			c.G965A						.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	122	12	NM_001144989	0	0	1	1	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	54	1	0	0	0	0	1	0	0	0	18208	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	3	58385793	743190	156	5326	59	3									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385798	58385799	+	Missense_Mutation	DNP	CC	CC	TT																															ccacattcataaggtcttttCccagtgtgaactctctgatg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:58385798_58385799CC>TT	ENST00000435989.2	-	3	1193_1194	c.959_960GG>AA	c.(958-960)gGG>gAA	p.G320E	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	320					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G320E(1)|p.G320G(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AAGGTCTTTTCCCAGTGTGAAC	0.356																																					p.G320E		.											.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	central_nervous_system(2)	c.G959A						.																																			SO:0001583	missense	730051	exon3			CTTTTCCCAGTGT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.959_960delinsTT	19.37:g.58385798_58385799delinsTT	ENSP00000410545:p.Gly320Glu	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	119	13	NM_001144989	0	0	0	0	0	A6NF35	Missense_Mutation	DNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.356	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		TT	58385799	CC	TT	58385798	3	4	54	1	0	0	0	0	1	0	0	0	18208	842	30	2	1611	2	ZNF814	19	58385798	Missense_Mutation	DNP	CC	TCGA-B9-A44B-01A-11D-A25F-10	5	58385798	743185	157	5327	59	3									
CHD6	84181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	40143495	40143495	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactccgcagagatgggttCgtcaggccctgatccagctc	7	8	13	13	2	1	2	1	1	0	1	5	4	3	3	3	3	1	3	3	3	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:40143495C>A	ENST00000373233.3	-	4	828	c.651G>T	c.(649-651)acG>acT	p.T217T	CHD6_ENST00000373222.3_Silent_p.T252T|CHD6_ENST00000309279.7_Silent_p.T217T	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	217	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GAGATGGGTTCGTCAGGCCCT	0.537																																					p.T217T		.											.	CHD6-238	0			c.G651T						.						131	122	125					20																	40143495		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon4			TGGGTTCGTCAGG	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.651G>T	20.37:g.40143495C>A		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	99	38	NM_032221	0	0	0	3	3	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1																																																																																			.		0.537	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40143495	C	A	40143495	2	1	54	1	0	0	0	0	0	0	0	1	3335	871	31	4		4	CHD6	20	40143495	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		40143495	22882025	158	5328											
MYBL2	4605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42328636	42328636	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaggcagctaacctcctcatCcctgctgtgggttctagcct	6	11	10	14	0	2	0	1	0	1	0	4	1	4	0	4	2	4	4	4	2	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:42328636C>T	ENST00000217026.4	+	7	1030	c.903C>T	c.(901-903)atC>atT	p.I301I	MYBL2_ENST00000396863.4_Silent_p.I277I	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	301					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			ACCTCCTCATCCCTGCTGTGG	0.572																																					p.I301I		.											.	MYBL2-415	0			c.C903T						.						78	56	63					20																	42328636		2203	4300	6503	SO:0001819	synonymous_variant	4605	exon7			CCTCATCCCTGCT		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.903C>T	20.37:g.42328636C>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	82	34	NM_002466	0	0	0	0	0	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	37	CCDS13322.1																																																																																			.		0.572	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42328636	C	T	42328636	2	4	54	1	0	0	0	0	0	0	0	1	10035	845	30	2		2	MYBL2	20	42328636	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2185141	42328636	20696884	159	5329											
WFDC8	90199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44181865	44181865	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtcactgtgacatgaaggtgGacactccttacgttcagtga	10	11	11	9	1	2	3	2	3	0	0	3	4	3	4	1	2	1	1	1	2	2	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:44181865G>T	ENST00000357199.4	-	5	574	c.496C>A	c.(496-498)Cca>Aca	p.P166T	WFDC8_ENST00000289953.2_Missense_Mutation_p.P166T	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	166	WAP 2. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|stomach(1)|upper_aerodigestive_tract(1)	15		Myeloproliferative disorder(115;0.0122)				CATGAAGGTGGACACTCCTTA	0.488																																					p.P166T		.											.	WFDC8-90	0			c.C496A						.						139	111	121					20																	44181865		2203	4300	6503	SO:0001583	missense	90199	exon5			AAGGTGGACACTC	AL031663	CCDS13361.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000158901	ENSG00000158901		"WAP four-disulfide core domain containing"	16163	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 170"	C20orf170		12206714	Standard	NM_130896		Approved	dJ461P17.1, WAP8	uc002xow.3	Q8IUA0	OTTHUMG00000046342	ENST00000357199.4:c.496C>A	20.37:g.44181865G>T	ENSP00000361735:p.Pro166Thr	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	131	51	NM_181510	0	0	0	0	0	E1P623|Q5TDV2|Q96A34	Missense_Mutation	SNP	ENST00000357199.4	37	CCDS13361.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.218036	0.39201	.	.	ENSG00000158901	ENST00000357199;ENST00000289953	T;T	0.71934	-0.61;-0.61	4.91	0.245	0.15512	Whey acidic protein, 4-disulphide core (5);	0.596324	0.15342	N	0.267433	T	0.59074	0.2167	L	0.48986	1.54	0.26237	N	0.978939	P	0.36412	0.552	B	0.42462	0.388	T	0.49597	-0.8923	10	0.07175	T	0.84	.	4.7744	0.13171	0.2342:0.0:0.5927:0.1732	.	166	Q8IUA0	WFDC8_HUMAN	T	166	ENSP00000361735:P166T;ENSP00000289953:P166T	ENSP00000289953:P166T	P	-	1	0	WFDC8	43615279	0.501000	0.26099	0.751000	0.31187	0.050000	0.14768	-0.083000	0.11286	0.202000	0.20498	0.655000	0.94253	CCA	.		0.488	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1			T	44181865	G	T	44181865	3	4	54	1	0	0	0	0	1	0	0	0	17389	1174	41	4	237	4	WFDC8	20	44181865	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	1853229	44181865	18843655	160	5330											
BCAS4	55653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49458324	49458324	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcgtcaagatggttggaCaccacgtcgccttcctggaa	8	10	10	13	3	1	1	1	0	0	1	4	3	2	3	4	3	0	1	4	3	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:49458324C>T	ENST00000358791.5	+	4	476	c.376C>T	c.(376-378)Cac>Tac	p.H126Y	BCAS4_ENST00000262591.5_Intron|BCAS4_ENST00000371608.2_Missense_Mutation_p.H126Y|BCAS4_ENST00000609336.1_Missense_Mutation_p.H96Y	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	126						cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						GATGGTTGGACACCACGTCGC	0.657																																					p.H126Y		.											.	BCAS4-204	0			c.C376T						.						76	59	65					20																	49458324		2203	4300	6503	SO:0001583	missense	55653	exon4			GTTGGACACCACG	AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243			14367	protein-coding gene	gene with protein product		607471				12378525	Standard	NM_001010974		Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.376C>T	20.37:g.49458324C>T	ENSP00000351642:p.His126Tyr	Somatic	333	0		WXS	Illumina HiSeq	Phase_I	250	109	NM_198799	0	0	6	9	3	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Missense_Mutation	SNP	ENST00000358791.5	37	CCDS33487.1	.	.	.	.	.	.	.	.	.	.	C	1.847	-0.465944	0.04476	.	.	ENSG00000124243	ENST00000358791;ENST00000355583;ENST00000371608	T;T	0.45276	1.9;0.9	4.48	3.5	0.40072	.	0.340201	0.30593	N	0.009290	T	0.37919	0.1021	L	0.51422	1.61	0.50632	D	0.999888	P;P	0.50528	0.763;0.936	B;P	0.44359	0.181;0.447	T	0.11941	-1.0567	10	0.39692	T	0.17	-17.6017	9.5663	0.39400	0.2101:0.7899:0.0:0.0	.	126;126	Q8TDM0-3;Q8TDM0	.;BCAS4_HUMAN	Y	126	ENSP00000351642:H126Y;ENSP00000360669:H126Y	ENSP00000347789:H126Y	H	+	1	0	BCAS4	48891731	0.746000	0.28272	0.137000	0.22149	0.014000	0.08584	1.544000	0.36158	0.837000	0.34925	0.561000	0.74099	CAC	.		0.657	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843		T	49458324	C	T	49458324	3	4	54	1	0	0	0	0	1	0	0	0	1354	478	17	2	390	2	BCAS4	20	49458324	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	5276459	49458324	13567196	161	5331											
NTSR1	4923	broad.mit.edu;bcgsc.ca	37	chr20	61389632	61389632	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcaggtgcagtggtcatcGcctttgtggtctgctggctg	3	13	14	11	1	3	0	2	0	1	0	4	0	3	0	2	4	2	3	2	4	0	1	rs201489051		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:61389632G>A	ENST00000370501.3	+	3	1302	c.931G>A	c.(931-933)Gcc>Acc	p.A311T	NTSR1_ENST00000482259.1_3'UTR	NM_002531.2	NP_002522.2	P30989	NTR1_HUMAN	neurotensin receptor 1 (high affinity)	311					adult locomotory behavior (GO:0008344)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(16)|prostate(1)|skin(3)	27	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			AGTGGTCATCGCCTTTGTGGT	0.612													G|||	1	0.000199681	0	0.0014	5008	,	,		21734	0		0	False		,,,				2504	0				p.A311T	GBM(37;400 780 6403 19663 35669)												.	NTSR1-524	0			c.G931A						.	G	THR/ALA	1,4403	2.1+/-5.4	0,1,2201	166	110	129		931	4.4	1	20		129	0,8600		0,0,4300	no	missense	NTSR1	NM_002531.2	58	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	311/419	61389632	1,13003	2202	4300	6502	SO:0001583	missense	4923	exon3			GTCATCGCCTTTG		CCDS13502.1	20q13	2012-08-08			ENSG00000101188	ENSG00000101188		"GPCR / Class A : Neurotensin receptors"	8039	protein-coding gene	gene with protein product		162651				8075503	Standard	NM_002531		Approved	NTR	uc002ydf.3	P30989	OTTHUMG00000032932	ENST00000370501.3:c.931G>A	20.37:g.61389632G>A	ENSP00000359532:p.Ala311Thr	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	201	10	NM_002531	0	0	0	0	0	Q9H4H1|Q9H4T5	Missense_Mutation	SNP	ENST00000370501.3	37	CCDS13502.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	23.7	4.447578	0.84101	2.27E-4	0.0	ENSG00000101188	ENST00000370501	T	0.72394	-0.65	4.36	4.36	0.52297	GPCR, rhodopsin-like superfamily (1);	0.066521	0.64402	D	0.000016	T	0.76062	0.3935	L	0.31476	0.935	0.47094	D	0.999311	D	0.89917	1.0	D	0.87578	0.998	T	0.75966	-0.3131	10	0.35671	T	0.21	-37.0465	16.8674	0.86033	0.0:0.0:1.0:0.0	.	311	P30989	NTR1_HUMAN	T	311	ENSP00000359532:A311T	ENSP00000359532:A311T	A	+	1	0	NTSR1	60860077	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	5.289000	0.65656	1.976000	0.57569	0.467000	0.42956	GCC	G|0.999;A|0.000		0.612	NTSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080061.1			A	61389632	G	A	61389632	3	1	54	1	0	0	0	0	1	0	0	0	10736	1087	38	1	941	1	NTSR1	20	61389632	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	11931308	61389632	1635888	162	5332											
POTEH	23784	broad.mit.edu;bcgsc.ca	37	chr22	16266950	16266950	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgatactgttcattctcaGtgtcaggaaattgctggctt	8	16	10	7	0	3	1	3	1	1	0	4	2	3	2	0	2	2	3	0	2	2	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr22:16266950G>T	ENST00000343518.6	-	9	1550	c.1499C>A	c.(1498-1500)aCt>aAt	p.T500N		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	500										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TTCATTCTCAGTGTCAGGAAA	0.398																																					p.T500N													.	POTEH-1	0			c.C1499A						.						2	1	2					22																	16266950		136	404	540	SO:0001583	missense	23784	exon9			TTCTCAGTGTCAG	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.1499C>A	22.37:g.16266950G>T	ENSP00000340610:p.Thr500Asn	Somatic	1499	1		WXS	Illumina HiSeq	Phase_I	1342	145	NM_001136213	0	0	0	0	0	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	37	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	G	0.065	-1.214312	0.01555	.	.	ENSG00000198062	ENST00000359587;ENST00000343518	T	0.24723	1.84	1.4	-2.79	0.05841	.	.	.	.	.	T	0.11750	0.0286	N	0.17082	0.46	0.09310	N	1	B;B	0.14012	0.009;0.001	B;B	0.11329	0.006;0.001	T	0.22800	-1.0206	9	0.30078	T	0.28	.	3.0928	0.06299	0.1861:0.0:0.3761:0.4378	.	500;463	Q6S545;A6NKF6	POTEH_HUMAN;.	N	463;500	ENSP00000340610:T500N	ENSP00000340610:T500N	T	-	2	0	POTEH	14646950	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.697000	0.05098	-1.658000	0.01490	0.184000	0.17185	ACT	.		0.398	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		T	16266950	G	T	16266950	3	4	54	1	0	0	0	0	1	0	0	0	12293	1029	36	4	146	4	POTEH	22	16266950	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		16266950	35037616	163	5333											
CECR2	27443	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18029082	18029082	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttactcttcccctgtggctGccctcccacctcaccaccca	5	10	4	22	0	2	0	1	0	1	0	4	0	4	0	7	1	2	1	7	1	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr22:18029082G>A	ENST00000400585.2	+	17	4051	c.3613G>A	c.(3613-3615)Gcc>Acc	p.A1205T	CECR2_ENST00000262608.8_Missense_Mutation_p.A1348T|CECR2_ENST00000400573.5_Missense_Mutation_p.A1347T			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	1389					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		CCCTGTGGCTGCCCTCCCACC	0.637																																					.													.	CECR2-70	0			.						.						28	33	32					22																	18029082		1931	4119	6050	SO:0001583	missense	27443	.			GTGGCTGCCCTCC	AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.3613G>A	22.37:g.18029082G>A	ENSP00000383428:p.Ala1205Thr	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	62	30	.	0	0	0	1	1	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400585.2	37		.	.	.	.	.	.	.	.	.	.	G	4.253	0.046012	0.08243	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.27720	1.77;1.77;1.65	5.25	1.98	0.26296	.	0.528428	0.17011	N	0.190539	T	0.24967	0.0606	L	0.53249	1.67	0.09310	N	0.999999	B;B;B	0.13145	0.007;0.007;0.007	B;B;B	0.12156	0.007;0.004;0.004	T	0.21793	-1.0235	10	0.26408	T	0.33	-3.498	6.879	0.24163	0.2126:0.1271:0.6603:0.0	.	1389;1205;1347	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	T	1205;1347;1348	ENSP00000383428:A1205T;ENSP00000383417:A1347T;ENSP00000262608:A1348T	ENSP00000262608:A1348T	A	+	1	0	CECR2	16409082	0.882000	0.30256	0.026000	0.17262	0.008000	0.06430	0.894000	0.28350	0.223000	0.20920	0.484000	0.47621	GCC	.		0.637	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		A	18029082	G	A	18029082	3	1	54	1	0	0	0	0	1	0	0	0	3212	1319	46	2	4103	2	CECR2	22	18029082	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	1762132	18029082	33275484	164	5334											
ZDHHC8	29801	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	20128194	20128194	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccgaggctgctgtgggAatgtggagcacgtgctgtgt	6	10	16	9	2	1	0	1	0	0	0	1	3	1	2	1	3	3	4	1	3	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr22:20128194A>T	ENST00000334554.7	+	6	856	c.715A>T	c.(715-717)Aat>Tat	p.N239Y	ZDHHC8_ENST00000405930.3_Missense_Mutation_p.N239Y|ZDHHC8_ENST00000320602.7_Missense_Mutation_p.N147Y|ZDHHC8_ENST00000468112.1_3'UTR	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	239					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CTGCTGTGGGAATGTGGAGCA	0.697																																					p.N239Y		.											.	ZDHHC8-91	0			c.A715T						.						39	35	36					22																	20128194		2198	4299	6497	SO:0001583	missense	29801	exon6			TGTGGGAATGTGG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.715A>T	22.37:g.20128194A>T	ENSP00000334490:p.Asn239Tyr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	32	16	NM_001185024	0	0	7	7	0	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Missense_Mutation	SNP	ENST00000334554.7	37	CCDS13776.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.624495	0.87560	.	.	ENSG00000099904	ENST00000334554;ENST00000320602;ENST00000405930	T;T;T	0.79845	-0.2;-1.31;-0.32	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.89618	0.3846	10	0.72032	D	0.01	.	15.1958	0.73088	1.0:0.0:0.0:0.0	.	147;239;239	Q9ULC8-2;Q9ULC8-3;Q9ULC8	.;.;ZDHC8_HUMAN	Y	239;147;239	ENSP00000334490:N239Y;ENSP00000317804:N147Y;ENSP00000384716:N239Y	ENSP00000317804:N147Y	N	+	1	0	ZDHHC8	18508194	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.875000	0.92372	2.035000	0.60131	0.533000	0.62120	AAT	.		0.697	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20128194	A	T	20128194	3	4	54	1	0	0	0	0	1	0	0	0	17653	246	9	5	737	5	ZDHHC8	22	20128194	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	2099112	20128194	31176372	165	5335											
C22orf42	150297	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	32555017	32555019	+	In_Frame_Del	DEL	CTG	CTG	-																															gtcttcgggaggctgaggtaCtgcatgagttgggccttctt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr22:32555017_32555019delCTG	ENST00000382097.3	-	1	256_258	c.184_186delCAG	c.(184-186)cagdel	p.Q62del	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	62										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GGCTGAGGTACTGCATGAGTTGG	0.537																																					p.62_62del		.											.	C22orf42-92	0			c.184_186del						.																																			SO:0001651	inframe_deletion	150297	exon1			.	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.184_186delCAG	22.37:g.32555017_32555019delCTG	ENSP00000371529:p.Gln62del	Somatic	290	0		WXS	Illumina HiSeq	Phase_I	274	49	NM_001010859	0	0	0	0	0	A4QPH5	In_Frame_Del	DEL	ENST00000382097.3	37	CCDS33639.1																																																																																			.		0.537	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		-	32555019	CTG	-	32555017	7	5	54	1	0	1	0	1	0	0	0	0	2155	564	20	0	605	0	C22orf42	22	32555017	In_Frame_Del	DEL	CTG	TCGA-B9-A44B-01A-11D-A25F-10	12426823	32555017	18749549	166	5336											
ACOT9	23597	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	23723676	23723676	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcatatgccttcctcataagGaaaccaccaaagatccgatt	14	10	5	12	1	2	1	2	0	0	1	4	3	4	2	5	1	2	0	5	1	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:23723676G>A	ENST00000336430.7	-	12	1073	c.942C>T	c.(940-942)ttC>ttT	p.F314F	ACOT9_ENST00000379295.1_Silent_p.F254F|ACOT9_ENST00000379303.5_Silent_p.F323F	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	314					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)			breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						TCCTCATAAGGAAACCACCAA	0.393																																					p.F323F													.	ACOT9-133	0			c.C969T						.						156	145	149					X																	23723676		2203	4300	6503	SO:0001819	synonymous_variant	23597	exon13			CATAAGGAAACCA	AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"Acyl CoA thioesterases"	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.942C>T	X.37:g.23723676G>A		Somatic	130	2		WXS	Illumina HiSeq	Phase_I	66	48	NM_001037171	0	0	2	5	3	B3KNC9|B7ZM94	Silent	SNP	ENST00000336430.7	37	CCDS35216.1																																																																																			.		0.393	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332		A	23723676	G	A	23723676	2	1	54	1	0	0	0	0	0	0	0	1	157	1165	41	2		2	ACOT9	23	23723676	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		23723676	131546884	167	5337											
POLA1	5422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	24744126	24744126	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaactatgcttttgagaTacctgatgttccagaaaaat	16	12	7	6	0	0	4	0	2	0	3	1	5	1	4	2	0	3	2	2	0	6	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:24744126T>A	ENST00000379059.3	+	13	1343	c.1328T>A	c.(1327-1329)aTa>aAa	p.I443K	POLA1_ENST00000379068.3_Missense_Mutation_p.I449K	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	443					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GCTTTTGAGATACCTGATGTT	0.328																																					p.I443K		.											.	POLA1-229	0			c.T1328A						.						71	69	70					X																	24744126		2203	4300	6503	SO:0001583	missense	5422	exon13			TTGAGATACCTGA		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1328T>A	X.37:g.24744126T>A	ENSP00000368349:p.Ile443Lys	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	34	26	NM_016937	0	0	0	0	0	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	t	11.79	1.743738	0.30865	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.42900	0.96;0.96	5.36	4.2	0.49525	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.046811	0.85682	D	0.000000	T	0.30479	0.0766	L	0.42744	1.35	0.80722	D	1	B;B	0.14438	0.001;0.01	B;B	0.20384	0.016;0.029	T	0.08534	-1.0717	10	0.05959	T	0.93	-6.4004	10.4411	0.44466	0.0:0.0769:0.0:0.9231	.	449;443	A6NMQ1;P09884	.;DPOLA_HUMAN	K	449;443	ENSP00000368358:I449K;ENSP00000368349:I443K	ENSP00000368349:I443K	I	+	2	0	POLA1	24654047	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	7.333000	0.79214	0.832000	0.34804	-0.392000	0.06488	ATA	.		0.328	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24744126	T	A	24744126	3	1	54	1	0	0	0	0	1	0	0	0	12213	1406	49	5	1378	5	POLA1	23	24744126	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	1020450	24744126	130526434	168	5338											
OPHN1	4983	bcgsc.ca	37	chrX	67283721	67283721	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgtggtgggccaggggccgGggagctggtctctttatgtg	3	12	19	7	1	1	0	0	0	1	0	2	1	1	1	2	7	1	1	2	7	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:67283721G>A	ENST00000355520.5	-	21	2774	c.2133C>T	c.(2131-2133)ccC>ccT	p.P711P	OPHN1_ENST00000540071.1_Intron|OPHN1_ENST00000484842.1_5'UTR	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	711	Pro-rich.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						CCAGGGGCCGGGGAGCTGGTC	0.577																																					p.P711P													.	OPHN1-110	0			c.C2133T						.						25	21	22					X																	67283721		2195	4281	6476	SO:0001819	synonymous_variant	4983	exon21			GGGCCGGGGAGCT	AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"Rho GTPase activating proteins"	8148	protein-coding gene	gene with protein product		300127	"mental retardation, X-linked 60"	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.2133C>T	X.37:g.67283721G>A		Somatic	28	1		WXS	Illumina HiSeq	Phase_1	68	62	NM_002547	0	0	0	0	0	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Silent	SNP	ENST00000355520.5	37	CCDS14388.1																																																																																			.		0.577	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		A	67283721	G	A	67283721	2	1	54	1	0	0	0	0	0	0	0	1	10901	1219	43	2		2	OPHN1	23	67283721	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	42539595	67283721	87986839	169	5339											
MCART6	401612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	103349337	103349337	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccttgctctgccaggcCatcctggatggggtccttga	5	10	13	13	0	1	1	0	1	1	0	3	2	3	2	5	5	2	1	5	5	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:103349337C>T	ENST00000357421.4	-	2	784	c.604G>A	c.(604-606)Ggc>Agc	p.G202S		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	202					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											TCTGCCAGGCCATCCTGGATG	0.552																																					p.G202S		.											.	.	0			c.G604A						.						62	65	64					X																	103349337		2202	4300	6502	SO:0001583	missense	401612	exon2			CCAGGCCATCCTG		CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"Solute carriers"	31894	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 6"	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.604G>A	X.37:g.103349337C>T	ENSP00000361681:p.Gly202Ser	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	84	12	NM_001012755	0	0	0	0	0	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	37	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	c	9.080	0.999007	0.19121	.	.	ENSG00000176274	ENST00000357421	T	0.77620	-1.11	4.18	2.25	0.28309	Mitochondrial carrier domain (2);	0.586966	0.16485	N	0.212372	T	0.48259	0.1490	N	0.01751	-0.74	0.29543	N	0.85193	B	0.02656	0.0	B	0.06405	0.002	T	0.39881	-0.9592	10	0.22109	T	0.4	-18.0741	7.4625	0.27304	0.0:0.7591:0.0:0.2409	.	202	Q5H9E4	MCAR6_HUMAN	S	202	ENSP00000361681:G202S	ENSP00000361681:G202S	G	-	1	0	MCART6	103235993	0.000000	0.05858	0.980000	0.43619	0.966000	0.64601	-0.866000	0.04245	0.295000	0.22570	0.594000	0.82650	GGC	.		0.552	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755		T	103349337	C	T	103349337	3	4	54	1	0	0	0	0	1	0	0	0	9396	594	21	2	323	2	MCART6	23	103349337	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	36065616	103349337	51921223	170	5340											
COL4A5	1287	broad.mit.edu;bcgsc.ca	37	chrX	107938134	107938134	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgggattctctgtggattGgttattccttcatgatggta	7	17	12	5	0	2	1	1	1	1	0	4	4	3	3	1	4	0	2	1	4	2	6	rs104886424		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:107938134G>A	ENST00000361603.2	+	49	5030	c.4786G>A	c.(4786-4788)Ggt>Agt	p.G1596S	COL4A5_ENST00000328300.6_Missense_Mutation_p.G1602S	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1596	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.		G -> D (in APSX). {ECO:0000269|PubMed:9452056}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						TCTGTGGATTGGTTATTCCTT	0.453									Alport syndrome with Diffuse Leiomyomatosis																												p.G1596S													.	COL4A5-133	0			c.G4786A						.						321	202	242					X																	107938134		2203	4300	6503	SO:0001583	missense	1287	exon49	Familial Cancer Database		TGGATTGGTTATT	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"Collagens"	2207	protein-coding gene	gene with protein product		303630	"Alport syndrome"	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4786G>A	X.37:g.107938134G>A	ENSP00000354505:p.Gly1596Ser	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	219	9	NM_000495	0	0	11	12	1	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	34	5.313598	0.95655	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186;ENST00000504541	D;D;D	0.99557	-6.16;-6.16;-4.07	5.57	5.57	0.84162	C-type lectin fold (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	H	0.97265	3.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96778	0.9573	10	0.87932	D	0	.	18.5959	0.91229	0.0:0.0:1.0:0.0	.	1599;1596	E7EVY4;P29400	.;CO4A5_HUMAN	S	1602;1596;1602;68	ENSP00000331902:G1602S;ENSP00000354505:G1596S;ENSP00000424845:G68S	ENSP00000331902:G1602S	G	+	1	0	COL4A5	107824790	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.335000	0.79485	0.594000	0.82650	GGT	.		0.453	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107938134	G	A	107938134	3	1	54	1	0	0	0	0	1	0	0	0	3700	1348	47	2	4991	2	COL4A5	23	107938134	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	4588797	107938134	47332426	171	5341											
HP1BP3	50809	bcgsc.ca	37	chr1	21071364	21071364	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttacttcctttcttgcacTggttgcaggcttctttgagg	4	19	9	9	0	2	1	0	1	2	0	3	1	3	1	1	3	3	4	1	3	1	8			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr1:21071364T>C	ENST00000312239.5	-	13	1727	c.1588A>G	c.(1588-1590)Agt>Ggt	p.S530G	RP5-930J4.4_ENST00000413451.1_RNA|HP1BP3_ENST00000375003.2_Missense_Mutation_p.S378G	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	530	Lys-rich.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TTTCTTGCACTGGTTGCAGGC	0.453																																					p.S530G													.	HP1BP3-91	0			c.A1588G						.						99	101	101					1																	21071364		2203	4300	6503	SO:0001583	missense	50809	exon13			TTGCACTGGTTGC	BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.1588A>G	1.37:g.21071364T>C	ENSP00000312625:p.Ser530Gly	Somatic	102	3		WXS	Illumina HiSeq	Phase_1	75	30	NM_016287	0	0	48	86	38	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	ENST00000312239.5	37	CCDS30621.1	.	.	.	.	.	.	.	.	.	.	T	10.32	1.318001	0.23994	.	.	ENSG00000127483	ENST00000312239;ENST00000375004;ENST00000375003	T;T	0.51574	0.7;0.72	5.74	4.61	0.57282	.	0.757026	0.13544	N	0.380000	T	0.35998	0.0951	L	0.27053	0.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13495	-1.0507	10	0.72032	D	0.01	0.037	10.0226	0.42053	0.0:0.0765:0.0:0.9235	.	530	Q5SSJ5	HP1B3_HUMAN	G	530;492;378	ENSP00000312625:S530G;ENSP00000364142:S378G	ENSP00000312625:S530G	S	-	1	0	HP1BP3	20943951	0.651000	0.27340	0.212000	0.23672	0.206000	0.24218	1.784000	0.38674	1.101000	0.41535	0.459000	0.35465	AGT	.		0.453	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287		C	21071364	T	C	21071364	3	2	55	1	0	0	0	0	1	0	0	0	7349	1580	55	3	77	3	HP1BP3	1	21071364	Missense_Mutation	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10		21071364	228179257	1	5342											
DHX9	1660	ucsc.edu;bcgsc.ca	37	chr1	182856445	182856445	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggtggctttagaggcaactCtggaggagactacagagggc	11	7	16	7	0	1	3	0	0	1	3	1	5	1	4	0	6	2	2	0	6	3	3			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr1:182856445C>G	ENST00000367549.3	+	28	3799	c.3689C>G	c.(3688-3690)tCt>tGt	p.S1230C	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1230	NTD.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AGAGGCAACTCTGGAGGAGAC	0.582																																					p.S1230C	Colon(69;210 1162 3697 13559 39565)												.	DHX9-92	0			c.C3689G						.						65	70	68					1																	182856445		1877	4097	5974	SO:0001583	missense	1660	exon28			GCAACTCTGGAGG	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.3689C>G	1.37:g.182856445C>G	ENSP00000356520:p.Ser1230Cys	Somatic	163	4		WXS	Illumina HiSeq		110	42	NM_001357	0	0	73	166	93	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	C	9.774	1.173556	0.21704	.	.	ENSG00000135829	ENST00000367549	D	0.82803	-1.65	4.43	2.11	0.27256	.	0.450874	0.19787	N	0.106070	T	0.65291	0.2677	N	0.19112	0.55	0.09310	N	1	B;B	0.28512	0.214;0.07	B;B	0.23852	0.049;0.049	T	0.53899	-0.8373	10	0.40728	T	0.16	.	3.7511	0.08566	0.1804:0.5673:0.0:0.2523	.	509;1230	B3KU66;Q08211	.;DHX9_HUMAN	C	1230	ENSP00000356520:S1230C	ENSP00000356520:S1230C	S	+	2	0	DHX9	181123068	0.000000	0.05858	0.019000	0.16419	0.907000	0.53573	0.262000	0.18460	0.555000	0.29079	0.561000	0.74099	TCT	.		0.582	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182856445	C	G	182856445	3	3	55	1	0	0	0	0	1	0	0	0	4527	913	32	4	3795	4	DHX9	1	182856445	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10	161785081	182856445	66394176	2	5343											
AGBL5	60509	broad.mit.edu	37	chr2	27276801	27276801	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgttatcctttgttcatcGtttcgtggagggccgtgggg	3	16	15	7	3	1	0	1	0	0	0	4	1	2	1	2	4	0	3	2	4	1	4			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr2:27276801G>T	ENST00000360131.4	+	4	584	c.425G>T	c.(424-426)cGt>cTt	p.R142L	AGBL5_ENST00000323064.8_Missense_Mutation_p.R142L|RP11-503P10.1_ENST00000607407.1_RNA	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	142					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTGTTCATCGTTTCGTGGAG	0.542																																					p.R142L													.	AGBL5-154	0			c.G425T						.						196	173	180					2																	27276801		2203	4300	6503	SO:0001583	missense	60509	exon4			TTCATCGTTTCGT	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.425G>T	2.37:g.27276801G>T	ENSP00000353249:p.Arg142Leu	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	90	3	NM_021831	0	0	33	33	0	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	37	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	G	21.0	4.084963	0.76642	.	.	ENSG00000084693	ENST00000453161;ENST00000323064;ENST00000360131	T;T	0.16196	2.39;2.36	5.51	4.64	0.57946	.	0.142751	0.64402	D	0.000004	T	0.32793	0.0841	L	0.53617	1.68	0.58432	D	0.999995	D;D;D	0.63880	0.988;0.993;0.993	P;D;D	0.63488	0.825;0.915;0.915	T	0.02109	-1.1212	10	0.32370	T	0.25	-8.9665	13.3669	0.60689	0.0773:0.0:0.9227:0.0	.	142;142;142	Q8NDL9;Q8NDL9-3;Q8NDL9-2	CBPC5_HUMAN;.;.	L	142	ENSP00000323681:R142L;ENSP00000353249:R142L	ENSP00000323681:R142L	R	+	2	0	AGBL5	27130305	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.166000	0.94766	1.331000	0.45412	0.561000	0.74099	CGT	.		0.542	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		T	27276801	G	T	27276801	3	4	55	1	0	0	0	0	1	0	0	0	378	1145	40	4	435	4	AGBL5	2	27276801	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		27276801	215922572	3	5344											
SPTBN1	6711	ucsc.edu;bcgsc.ca	37	chr2	54855278	54855278	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaaacacttacttggtgtGgaagacctgttacagaagca	13	9	11	8	0	0	2	0	0	0	2	0	3	0	3	1	3	4	3	1	3	5	3			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr2:54855278G>C	ENST00000356805.4	+	13	1970	c.1689G>C	c.(1687-1689)gtG>gtC	p.V563V	SPTBN1_ENST00000333896.5_Silent_p.V550V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	563					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			TACTTGGTGTGGAAGACCTGT	0.498																																					p.V563V													.	SPTBN1-140	0			c.G1689C						.						187	153	165					2																	54855278		2203	4300	6503	SO:0001819	synonymous_variant	6711	exon13			TGGTGTGGAAGAC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.1689G>C	2.37:g.54855278G>C		Somatic	126	2		WXS	Illumina HiSeq		105	39	NM_003128	0	0	29	60	31	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			.		0.498	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			C	54855278	G	C	54855278	2	2	55	1	0	0	0	0	0	0	0	1	15151	1335	47	4		4	SPTBN1	2	54855278	Silent	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	27578477	54855278	188344095	4	5345											
ERCC3	2071	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	128051174	128051174	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	catattcatccactttggtgCctgactcatccacctgcttc	7	14	5	15	0	2	1	2	1	0	0	5	1	4	1	4	1	2	1	4	1	1	4			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr2:128051174C>G	ENST00000285398.2	-	2	243	c.149G>C	c.(148-150)gGc>gCc	p.G50A	ERCC3_ENST00000493187.2_5'UTR	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	50					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CACTTTGGTGCCTGACTCATC	0.597			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.G50A			yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3-723	0			c.G149C						.						108	100	103					2																	128051174		2203	4300	6503	SO:0001583	missense	2071	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TTGGTGCCTGACT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.149G>C	2.37:g.128051174C>G	ENSP00000285398:p.Gly50Ala	Somatic	153	1		WXS	Illumina HiSeq	Phase_I	86	6	NM_000122	0	0	13	16	3	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	37	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	C	3.976	-0.007366	0.07773	.	.	ENSG00000163161	ENST00000285398	T	0.61980	0.06	4.65	3.78	0.43462	.	0.406249	0.29480	N	0.012028	T	0.42630	0.1211	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.23726	-1.0180	10	0.08179	T	0.78	-9.8038	12.7961	0.57560	0.0:0.9206:0.0:0.0794	.	50;50	A8K359;P19447	.;ERCC3_HUMAN	A	50	ENSP00000285398:G50A	ENSP00000285398:G50A	G	-	2	0	ERCC3	127767644	0.959000	0.32827	0.934000	0.37439	0.609000	0.37215	3.327000	0.52045	1.174000	0.42811	-0.136000	0.14681	GGC	.		0.597	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		G	128051174	C	G	128051174	3	3	55	1	0	0	0	0	1	0	0	0	5227	739	26	4	2255	4	ERCC3	2	128051174	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10	73195896	128051174	115148199	5	5346											
OSBPL6	114880	bcgsc.ca	37	chr2	179255928	179255928	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtggccccctctgcaaaGtgcatttggagaccaggtga	8	9	14	10	0	1	2	0	1	1	1	1	3	1	2	3	4	2	2	3	4	1	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr2:179255928G>A	ENST00000190611.4	+	22	2806	c.2430G>A	c.(2428-2430)aaG>aaA	p.K810K	OSBPL6_ENST00000409045.3_Silent_p.K779K|OSBPL6_ENST00000315022.2_Silent_p.K814K|OSBPL6_ENST00000409631.1_Silent_p.K774K|OSBPL6_ENST00000392505.2_Silent_p.K835K|OSBPL6_ENST00000359685.3_Silent_p.K774K	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	810					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CCTCTGCAAAGTGCATTTGGA	0.537																																					p.K835K													.	OSBPL6-69	0			c.G2505A						.						145	128	134					2																	179255928		2203	4300	6503	SO:0001819	synonymous_variant	114880	exon23			TGCAAAGTGCATT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"Oxysterol binding proteins"	16388	protein-coding gene	gene with protein product	"OSBP-related protein 6"	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.2430G>A	2.37:g.179255928G>A		Somatic	139	3		WXS	Illumina HiSeq	Phase_1	90	35	NM_001201480	0	0	0	0	0	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			.		0.537	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		A	179255928	G	A	179255928	2	1	55	1	0	0	0	0	0	0	0	1	11307	1020	36	2		2	OSBPL6	2	179255928	Silent	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	51204754	179255928	63943445	6	5347											
PIK3R4	30849	broad.mit.edu;bcgsc.ca	37	chr3	130425829	130425831	+	In_Frame_Del	DEL	GAG	GAG	-																															aagggacacaaatgccagcaGaggactcggaacgaggaggt																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr3:130425829_130425831delGAG	ENST00000356763.3	-	11	3239_3241	c.2682_2684delCTC	c.(2680-2685)tcctct>tct	p.894_895SS>S		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	894					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						AATGCCAGCAGAGGACTCGGAAC	0.502																																					p.894_895del													.	PIK3R4-1471	0			c.2682_2684del						.																																			SO:0001651	inframe_deletion	30849	exon11			CCAGCAGAGGACT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.2682_2684delCTC	3.37:g.130425829_130425831delGAG	ENSP00000349205:p.Ser895del	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	114	12	NM_014602	0	0	0	0	0	Q2TBF4	In_Frame_Del	DEL	ENST00000356763.3	37	CCDS3067.1																																																																																			.		0.502	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		-	130425831	GAG	-	130425829	7	5	55	1	0	1	0	1	0	0	0	0	11947	942	33	0	1432	0	PIK3R4	3	130425829	In_Frame_Del	DEL	GAG	TCGA-B9-A5W7-01A-11D-A31X-10		130425829	67596601	7	5348											
MUC4	4585	broad.mit.edu	37	chr3	195488976	195488976	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acccaggagcccctccgtgcGgttctggtactcgggcggga	5	7	15	14	4	1	0	0	0	1	0	3	2	2	2	4	5	3	2	4	5	1	2			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr3:195488976G>A	ENST00000346145.4	-	13	1825	c.1786C>T	c.(1786-1788)Cgc>Tgc	p.R596C	MUC4_ENST00000349607.4_Missense_Mutation_p.R545C|MUC4_ENST00000475231.1_Missense_Mutation_p.R4780C|MUC4_ENST00000463781.3_Missense_Mutation_p.R4832C	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1589					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCCTCCGTGCGGTTCTGGTAC	0.741																																					p.R4832C													.	MUC4-90	0			c.C14494T						.						18	19	18					3																	195488976		2199	4295	6494	SO:0001583	missense	4585	exon14			CCGTGCGGTTCTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"Mucins"	7514	protein-coding gene	gene with protein product		158372	"mucin 4, tracheobronchial"			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.1786C>T	3.37:g.195488976G>A	ENSP00000304207:p.Arg596Cys	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_018406	0	0	0	0	0	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	7.202	0.593705	0.13875	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.60424	0.19;0.19;0.19;0.19	4.97	4.09	0.47781	.	0.926209	0.09124	N	0.845258	T	0.68604	0.3019	L	0.50333	1.59	0.09310	N	1	D;D;D;D;D;D	0.76494	0.999;0.998;0.998;0.994;0.994;0.998	D;P;P;P;P;P	0.68621	0.959;0.738;0.738;0.765;0.765;0.784	T	0.53373	-0.8448	10	0.62326	D	0.03	-4.6337	8.1797	0.31302	0.0:0.1524:0.5328:0.3147	.	4704;545;596;4832;4780;1537	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	C	545;596;4832;4780;1332	ENSP00000338109:R545C;ENSP00000304207:R596C;ENSP00000417498:R4832C;ENSP00000420243:R4780C	ENSP00000304207:R596C	R	-	1	0	MUC4	196974647	0.073000	0.21202	0.017000	0.16124	0.007000	0.05969	0.864000	0.27926	1.065000	0.40693	0.561000	0.74099	CGC	.		0.741	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		A	195488976	G	A	195488976	3	1	55	1	0	0	0	0	1	0	0	0	10003	1116	39	1	1792	1	MUC4	3	195488976	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	65063147	195488976	2533454	8	5349											
COPS4	51138	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	83996480	83996480	+	Frame_Shift_Del	DEL	A	A	-																															cctgccaacgtgggataagcAgatccaatcactttgtttcc																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr4:83996480delA	ENST00000264389.2	+	10	1253	c.1118delA	c.(1117-1119)cagfs	p.Q373fs	COPS4_ENST00000509093.1_Frame_Shift_Del_p.R345fs|COPS4_ENST00000503682.1_Frame_Shift_Del_p.Q405fs|COPS4_ENST00000511653.1_3'UTR	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	373					cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				TGGGATAAGCAGATCCAATCA	0.403																																					p.Q373fs		.											.	COPS4-226	0			c.1118delA						.						87	85	86					4																	83996480		2203	4300	6503	SO:0001589	frameshift_variant	51138	exon10			.	AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.1118delA	4.37:g.83996480delA	ENSP00000264389:p.Gln373fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	71	15	NM_016129	0	0	0	0	0	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Frame_Shift_Del	DEL	ENST00000264389.2	37	CCDS3600.1																																																																																			.		0.403	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1			-	83996480	A	-	83996480	7	5	55	1	0	1	0	1	0	0	0	0	3741	188	7	0	1156	0	COPS4	4	83996480	Frame_Shift_Del	DEL	A	TCGA-B9-A5W7-01A-11D-A31X-10		83996480	107157796	9	5350											
IL6ST	3572	ucsc.edu	37	chr5	55237518	55237518	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccttcagtattaattttttCctttttgaacaggtccaatg	9	19	5	8	0	1	1	1	1	0	0	4	1	4	1	3	1	1	1	3	1	4	8			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr5:55237518C>T	ENST00000381298.2	-	17	2461	c.2149G>A	c.(2149-2151)Gaa>Aaa	p.E717K	IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000502326.3_Missense_Mutation_p.E717K|CTD-2031P19.5_ENST00000576302.1_RNA|IL6ST_ENST00000336909.5_Missense_Mutation_p.E717K|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381294.3_Missense_Mutation_p.E656K	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	717					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TTAATTTTTTCCTTTTTGAAC	0.383			O		hepatocellular ca																																p.E717K				Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST-290	0			c.G2149A						.						141	148	146					5																	55237518		2203	4300	6503	SO:0001583	missense	3572	exon17			TTTTTTCCTTTTT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.2149G>A	5.37:g.55237518C>T	ENSP00000370698:p.Glu717Lys	Somatic	283	0		WXS	Illumina HiSeq		294	1	NM_002184	0	0	19	20	1	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911763	0.92178	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.42900	1.25;1.25;0.96	5.4	5.4	0.78164	.	3.018200	0.01740	N	0.029358	T	0.45216	0.1331	N	0.24115	0.695	0.80722	D	1	P;P;P	0.48911	0.862;0.917;0.862	B;P;P	0.48627	0.424;0.584;0.501	T	0.23404	-1.0189	10	0.49607	T	0.09	.	12.8542	0.57876	0.0:0.9252:0.0:0.0748	.	717;656;717	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	K	717;717;656	ENSP00000370698:E717K;ENSP00000338799:E717K;ENSP00000370694:E656K	ENSP00000338799:E717K	E	-	1	0	IL6ST	55273275	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.416000	0.66417	2.687000	0.91594	0.557000	0.71058	GAA	.		0.383	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		T	55237518	C	T	55237518	3	4	55	1	0	0	0	0	1	0	0	0	7724	864	30	2	611	2	IL6ST	5	55237518	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10		55237518	125677742	10	5351											
NKX2-5	1482	broad.mit.edu	37	chr5	172659920	172659920	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcaggcggcggcggcggCgggggcagccccaccagctc	4	1	20	16	6	0	0	0	0	0	0	1	0	0	0	3	8	2	3	3	8	0	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr5:172659920C>G	ENST00000329198.4	-	2	900	c.627G>C	c.(625-627)ccG>ccC	p.P209P	NKX2-5_ENST00000521848.1_3'UTR|NKX2-5_ENST00000424406.2_3'UTR	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	209	Ala/Pro-rich.				adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			gcggcggcggcgggggcAGCC	0.701																																					p.P209P	Esophageal Squamous(72;810 1219 2387 13420 44943)												.	NKX2-5-90	0			c.G627C						.						5	6	6					5																	172659920		1935	3790	5725	SO:0001819	synonymous_variant	1482	exon2			CGGCGGCGGGGGC	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.627G>C	5.37:g.172659920C>G		Somatic	85	2		WXS	Illumina HiSeq	Phase_I	76	6	NM_004387	0	0	0	0	0	A8K3K0|B4DNB6|E9PBU6	Silent	SNP	ENST00000329198.4	37	CCDS4387.1																																																																																			.		0.701	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			G	172659920	C	G	172659920	2	3	55	1	0	0	0	0	0	0	0	1	10479	755	27	4		4	NKX2-5	5	172659920	Silent	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10	117422402	172659920	8255340	11	5352											
PRIM2	5558	broad.mit.edu;bcgsc.ca	37	chr6	57393114	57393114	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttctttttttaaagtcAttcctacactagccaagatt	10	20	3	8	0	2	1	1	0	1	1	3	1	3	1	2	0	2	0	2	0	5	11	rs551418169		TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr6:57393114A>G	ENST00000607273.1	+	9	851	c.764A>G	c.(763-765)cAt>cGt	p.H255R	PRIM2_ENST00000389488.2_3'UTR	NM_000947.3	NP_000938.2	P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	255					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ttttaaaGTCATTCCTACACT	0.269																																					.													.	PRIM2-227	0			.						.						71	63	65					6																	57393114		1797	4065	5862	SO:0001583	missense	5558	.			AAAGTCATTCCTA		CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000607273.1:c.764A>G	6.37:g.57393114A>G	ENSP00000475738:p.His255Arg	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	96	11	.	0	0	0	0	0	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Missense_Mutation	SNP	ENST00000607273.1	37																																																																																				.		0.269	PRIM2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000947		G	57393114	A	G	57393114	3	3	55	1	0	0	0	0	1	0	0	0	12520	217	8	3	794	3	PRIM2	6	57393114	Missense_Mutation	SNP	A	TCGA-B9-A5W7-01A-11D-A31X-10		57393114	113721953	12	5353											
TNRC18	84629	broad.mit.edu	37	chr7	5352666	5352668	+	In_Frame_Del	DEL	GAG	GAG	-																															aggaggaggaggaggaggatGaggaggaggaggaggaggcc																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:5352666_5352668delGAG	ENST00000430969.1	-	27	8202_8204	c.7854_7856delCTC	c.(7852-7857)tcctca>tca	p.2618_2619SS>S	TNRC18_ENST00000399537.4_In_Frame_Del_p.2618_2619SS>S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2618	Ser-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ggaggaggatgaggaggaggagg	0.66																																					p.2618_2619del													.	TNRC18-46	0			c.7854_7856del						.																																			SO:0001651	inframe_deletion	84629	exon27			GAGGATGAGGAGG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7854_7856delCTC	7.37:g.5352675_5352677delGAG	ENSP00000395538:p.Ser2671del	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	1	NM_001080495	0	0	0	0	0	A8MX41|Q96JH1|Q96K91	In_Frame_Del	DEL	ENST00000430969.1	37	CCDS47534.1																																																																																			.		0.66	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	5352668	GAG	-	5352666	7	5	55	1	0	1	0	1	0	0	0	0	16371	1294	45	0	1066	0	TNRC18	7	5352666	In_Frame_Del	DEL	GAG	TCGA-B9-A5W7-01A-11D-A31X-10		5352666	153785997	13	5354											
PHKG1	5260	ucsc.edu;bcgsc.ca	37	chr7	56151013	56151013	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctggcaggaaaagccaaAgtctgtgagcttgatgttca	12	9	12	8	0	2	2	1	2	1	0	2	3	2	3	1	2	3	4	1	2	3	2			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:56151013A>C	ENST00000297373.2	-	6	699	c.505T>G	c.(505-507)Ttt>Gtt	p.F169V	PHKG1_ENST00000452681.2_Missense_Mutation_p.F201V|PHKG1_ENST00000489604.1_5'Flank|PHKG1_ENST00000537360.1_Missense_Mutation_p.F115V	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	169	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GAAAAGCCAAAGTCTGTGAGC	0.562																																					p.F201V	Melanoma(184;580 2064 5329 24177 35303)												.	PHKG1-424	0			c.T601G						.						83	80	81					7																	56151013		2203	4300	6503	SO:0001583	missense	5260	exon7			AGCCAAAGTCTGT	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.505T>G	7.37:g.56151013A>C	ENSP00000297373:p.Phe169Val	Somatic	125	3		WXS	Illumina HiSeq		145	34	NM_001258459	0	0	0	0	0	B7Z1D0|F5H2S1|Q75LP5	Missense_Mutation	SNP	ENST00000297373.2	37	CCDS5525.1	.	.	.	.	.	.	.	.	.	.	A	33	5.223987	0.95139	.	.	ENSG00000164776	ENST00000452681;ENST00000537360;ENST00000297373;ENST00000446428;ENST00000432123	T;T;T;T;T	0.73897	1.58;-0.79;-0.79;-0.04;-0.04	5.62	5.62	0.85841	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.92443	0.7601	H	0.99475	4.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.996;1.0	D	0.95527	0.8600	10	0.87932	D	0	-15.785	15.306	0.73992	1.0:0.0:0.0:0.0	.	115;160;201;169	B7Z5U3;B7Z6U2;F5H2S1;Q16816	.;.;.;PHKG1_HUMAN	V	201;115;169;91;91	ENSP00000445440:F201V;ENSP00000441528:F115V;ENSP00000297373:F169V;ENSP00000389721:F91V;ENSP00000397193:F91V	ENSP00000297373:F169V	F	-	1	0	PHKG1	56118507	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.256000	0.95535	2.275000	0.75901	0.528000	0.53228	TTT	.		0.562	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213		C	56151013	A	C	56151013	3	2	55	1	0	0	0	0	1	0	0	0	11872	72	3	5	678	5	PHKG1	7	56151013	Missense_Mutation	SNP	A	TCGA-B9-A5W7-01A-11D-A31X-10	50798347	56151013	102987650	14	5355											
SBDS	51119	ucsc.edu;bcgsc.ca	37	chr7	66456233	66456233	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggatgaaccgaagcctcAtgtgagcacgttctatcttc	11	10	10	10	2	3	2	1	2	2	0	4	5	3	3	2	1	3	2	2	1	4	3			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:66456233A>C	ENST00000246868.2	-	4	698	c.515T>G	c.(514-516)aTg>aGg	p.M172R		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	172					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						CCGAAGCCTCATGTGAGCACG	0.388			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.M172R			yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS-523	0			c.T515G						.						131	111	118					7																	66456233		2203	4300	6503	SO:0001583	missense	51119	exon4	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	AGCCTCATGTGAG	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.515T>G	7.37:g.66456233A>C	ENSP00000246868:p.Met172Arg	Somatic	164	3		WXS	Illumina HiSeq		170	95	NM_016038	0	0	59	158	99	A8K0P4|Q96FX0|Q9NV53	Missense_Mutation	SNP	ENST00000246868.2	37	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.590324	0.66105	.	.	ENSG00000126524	ENST00000246868	D	0.97430	-4.38	5.04	3.87	0.44632	Ribosome maturation protein SBDS, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98741	0.9577	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98476	1.0603	10	0.54805	T	0.06	-39.0865	10.1837	0.42984	0.8322:0.1678:0.0:0.0	.	172	Q9Y3A5	SBDS_HUMAN	R	172	ENSP00000246868:M172R	ENSP00000246868:M172R	M	-	2	0	SBDS	66093668	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	8.335000	0.90031	0.935000	0.37341	0.454000	0.30748	ATG	.		0.388	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038		C	66456233	A	C	66456233	3	2	55	1	0	0	0	0	1	0	0	0	13889	217	8	5	245	5	SBDS	7	66456233	Missense_Mutation	SNP	A	TCGA-B9-A5W7-01A-11D-A31X-10	10305220	66456233	92682430	15	5356											
CACNA2D1	781	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	81588631	81588631	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacatcaggcccttttcggTatctgggttgcttaaccatg	8	13	10	10	1	2	1	1	0	1	1	3	1	2	1	2	3	2	3	2	3	2	5			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:81588631T>G	ENST00000356253.5	-	38	3410	c.3155A>C	c.(3154-3156)tAc>tCc	p.Y1052S	CACNA2D1_ENST00000535308.1_Missense_Mutation_p.Y252S|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.Y1040S			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	1052					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CCCTTTTCGGTATCTGGGTTG	0.358																																					p.Y1040S													.	CACNA2D1-96	0			c.A3119C						.						114	104	107					7																	81588631		2203	4300	6503	SO:0001583	missense	781	exon38			TTTCGGTATCTGG	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"Calcium channel subunits"	1399	protein-coding gene	gene with protein product		114204	"long intergenic non-protein coding RNA 1112"	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.3155A>C	7.37:g.81588631T>G	ENSP00000348589:p.Tyr1052Ser	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	167	40	NM_000722	0	0	1	2	1	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	T	24.8	4.566128	0.86439	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253;ENST00000535308	T;T;T	0.68479	-0.33;-0.33;-0.33	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.82568	0.5065	M	0.82517	2.595	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.82476	-0.0438	10	0.35671	T	0.21	-11.6328	16.2135	0.82186	0.0:0.0:0.0:1.0	.	252;1040	B7Z658;P54289-2	.;.	S	1040;1059;1052;252	ENSP00000349320:Y1040S;ENSP00000348589:Y1052S;ENSP00000443124:Y252S	ENSP00000284088:Y1059S	Y	-	2	0	CACNA2D1	81426567	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.492000	0.81482	2.227000	0.72691	0.460000	0.39030	TAC	.		0.358	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				G	81588631	T	G	81588631	3	3	55	1	0	0	0	0	1	0	0	0	2554	1638	57	5	164	5	CACNA2D1	7	81588631	Missense_Mutation	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10	15132398	81588631	77550032	16	5357											
LAMB1	3912	broad.mit.edu	37	chr7	107569606	107569607	+	Missense_Mutation	DNP	TC	TC	AA																															tttctgcttcttccagagctTcctttaccatatctgcagtg																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:107569606_107569607TC>AA	ENST00000222399.6	-	31	5019_5020	c.4789_4790GA>TT	c.(4789-4791)GAa>TTa	p.E1597L	LAMB1_ENST00000393561.1_Missense_Mutation_p.E1621L|LAMB1_ENST00000474380.1_5'Flank	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1597	Domain I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TTCCAGAGCTTCCTTTACCATA	0.401																																					p.E1621L													.	LAMB1-97	0			c.G4789T						.																																			SO:0001583	missense	3912	exon31			GAGCTTCCTTTAC	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.4789_4790delinsAA	7.37:g.107569606_107569607delinsAA	ENSP00000222399:p.Glu1597Leu	Somatic	208	1		WXS	Illumina HiSeq	Phase_I	254	7	NM_002291	0	0	0	0	0	Q14D91	Missense_Mutation	DNP	ENST00000222399.6	37	CCDS5750.1																																																																																			.		0.401	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		AA	107569607	TC	AA	107569606	3	1	55	1	0	0	0	0	1	0	0	0	8631	1783	62	5	586	5	LAMB1	7	107569606	Missense_Mutation	DNP	TC	TCGA-B9-A5W7-01A-11D-A31X-10	25980975	107569606	51569057	17	5358											
LMOD2	442721	broad.mit.edu	37	chr7	123302918	123302918	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacctcctcctcctcccccTcctcctcctcctccccctcc	2	10	0	29	0	0	0	0	0	0	0	10	0	10	0	13	0	0	0	13	0	0	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:123302918T>C	ENST00000458573.2	+	2	1435	c.1278T>C	c.(1276-1278)ccT>ccC	p.P426P	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	426	Pro-rich.					cytoskeleton (GO:0005856)											ctcctccccctcctcctcctc	0.592																																					p.P426P													.	LMOD2-68	0			c.T1278C						.						17	18	18					7																	123302918		1917	4112	6029	SO:0001819	synonymous_variant	442721	exon2			TCCCCCTCCTCCT	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.1278T>C	7.37:g.123302918T>C		Somatic	62	10		WXS	Illumina HiSeq	Phase_I	61	16	NM_207163	0	0	0	0	0	A4D0W9|A4D0Y2|Q8WVJ8	Silent	SNP	ENST00000458573.2	37	CCDS47693.1																																																																																			.		0.592	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			C	123302918	T	C	123302918	2	2	55	1	0	0	0	0	0	0	0	1	8880	1538	54	3		3	LMOD2	7	123302918	Silent	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10	15733312	123302918	35835745	18	5359											
TSPAN33	340348	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	128804350	128804350	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgagatcatcaacaatgcCattgtgcactaccgagatga	14	9	9	9	1	2	3	2	2	0	2	2	5	2	3	2	0	4	1	2	0	3	2			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:128804350C>A	ENST00000289407.4	+	5	508	c.399C>A	c.(397-399)gcC>gcA	p.A133A	Y_RNA_ENST00000363759.1_RNA	NM_178562.3	NP_848657.1	Q86UF1	TSN33_HUMAN	tetraspanin 33	133					establishment of protein localization to plasma membrane (GO:0090002)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14						TCAACAATGCCATTGTGCACT	0.498											OREG0018304	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A133A		.											.	TSPAN33-91	0			c.C399A						.						211	180	190					7																	128804350		2203	4300	6503	SO:0001819	synonymous_variant	340348	exon5			CAATGCCATTGTG		CCDS5810.1	7q32.3	2013-02-14			ENSG00000158457	ENSG00000158457		"Tetraspanins"	28743	protein-coding gene	gene with protein product		610120				16213355, 16242907	Standard	XM_006715960		Approved	MGC50844, Penumbra	uc003vop.2	Q86UF1	OTTHUMG00000158420	ENST00000289407.4:c.399C>A	7.37:g.128804350C>A		Somatic	54	0	1567	WXS	Illumina HiSeq	Phase_I	76	48	NM_178562	0	0	94	253	159		Silent	SNP	ENST00000289407.4	37	CCDS5810.1																																																																																			.		0.498	TSPAN33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350983.1	NM_178562		A	128804350	C	A	128804350	2	1	55	1	0	0	0	0	0	0	0	1	16681	581	21	4		4	TSPAN33	7	128804350	Silent	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10	5501432	128804350	30334313	19	5360											
MAFA	389692	broad.mit.edu	37	chr8	144511742	144511742	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgctctccagaatgtgccGctgctgcacccgcttgaagc	6	9	10	16	3	1	2	0	1	1	1	3	2	1	2	3	0	4	5	3	0	2	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr8:144511742G>A	ENST00000333480.2	-	1	834	c.835C>T	c.(835-837)Cgg>Tgg	p.R279W	MAFA_ENST00000528185.1_5'UTR	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	279	Basic motif.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				insulin secretion (GO:0030073)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(1)|upper_aerodigestive_tract(2)	4	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)			AGAATGTGCCGCTGCTGCACC	0.642										HNSCC(29;0.082)																											p.R279W													.	MAFA-278	0			c.C835T						.						17	18	17					8																	144511742		2195	4291	6486	SO:0001583	missense	389692	exon1			TGTGCCGCTGCTG	AY083269	CCDS34955.1	8q24.3	2013-07-09	2013-07-09			ENSG00000182759			23145	protein-coding gene	gene with protein product		610303					Standard	NM_201589		Approved	RIPE3b1, hMafA	uc003yyc.2	Q8NHW3		ENST00000333480.2:c.835C>T	8.37:g.144511742G>A	ENSP00000328364:p.Arg279Trp	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	32	3	NM_201589	0	0	0	0	0		Missense_Mutation	SNP	ENST00000333480.2	37	CCDS34955.1	.	.	.	.	.	.	.	.	.	.	g	18.54	3.645833	0.67358	.	.	ENSG00000182759	ENST00000333480	D	0.92199	-2.99	2.95	1.98	0.26296	Basic-leucine zipper (bZIP) transcription factor (2);Maf transcription factor (1);	0.000000	0.64402	U	0.000008	D	0.94122	0.8115	M	0.68952	2.095	0.48288	D	0.999623	D	0.89917	1.0	D	0.81914	0.995	D	0.93186	0.6579	10	0.59425	D	0.04	.	9.6689	0.40000	0.0:0.0:0.7917:0.2082	.	279	Q8NHW3	MAFA_HUMAN	W	279	ENSP00000328364:R279W	ENSP00000328364:R279W	R	-	1	2	MAFA	144582885	0.990000	0.36364	1.000000	0.80357	0.978000	0.69477	0.007000	0.13174	1.183000	0.42943	0.282000	0.19409	CGG	.		0.642	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2	NM_201589		A	144511742	G	A	144511742	3	1	55	1	0	0	0	0	1	0	0	0	9182	1086	38	1	230	1	MAFA	8	144511742	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		144511742	1852280	20	5361											
INPP5E	56623	ucsc.edu	37	chr9	139327715	139327715	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagcgtctcctgcagacGagtctcccactcccgcctgc	5	7	9	20	3	2	1	0	0	2	1	5	2	3	1	5	0	3	1	5	0	0	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr9:139327715G>T	ENST00000371712.3	-	4	1453	c.1051C>A	c.(1051-1053)Cgt>Agt	p.R351S		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		TCCTGCAGACGAGTCTCCCAC	0.682																																					p.R351S													.	INPP5E-227	0			c.C1051A						.						16	17	16					9																	139327715		2183	4289	6472	SO:0001583	missense	56623	exon4			GCAGACGAGTCTC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"Joubert syndrome 1"	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1051C>A	9.37:g.139327715G>T	ENSP00000360777:p.Arg351Ser	Somatic	17	0		WXS	Illumina HiSeq		23	4	NM_019892	0	0	7	7	0	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371712.3	37	CCDS7000.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611634	0.66558	.	.	ENSG00000148384	ENST00000371712	T	0.79352	-1.26	4.87	2.97	0.34412	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.061110	0.64402	D	0.000005	T	0.72358	0.3450	L	0.48877	1.53	0.58432	D	0.999997	P	0.44578	0.838	P	0.46049	0.502	T	0.67205	-0.5729	10	0.39692	T	0.17	-23.2799	8.3299	0.32180	0.0822:0.0:0.7625:0.1553	.	351	Q9NRR6	INP5E_HUMAN	S	351	ENSP00000360777:R351S	ENSP00000360777:R351S	R	-	1	0	INPP5E	138447536	1.000000	0.71417	0.194000	0.23346	0.845000	0.48019	2.512000	0.45485	0.445000	0.26639	0.561000	0.74099	CGT	.		0.682	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892		T	139327715	G	T	139327715	3	4	55	1	0	0	0	0	1	0	0	0	7778	1058	37	4	911	4	INPP5E	9	139327715	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		139327715	1885716	21	5362											
C10orf140	387640	broad.mit.edu	37	chr10	21805502	21805502	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctcctcctcctctcccTcctcctcctcttcctctgag	1	14	2	24	0	3	1	0	1	3	0	12	1	11	1	10	0	0	0	10	0	0	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr10:21805502T>C	ENST00000449193.2	-	4	3502	c.1250A>G	c.(1249-1251)gAg>gGg	p.E417G	SKIDA1_ENST00000444772.3_Missense_Mutation_p.E338G|SKIDA1_ENST00000487107.1_5'Flank	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	336						nucleus (GO:0005634)											ctcctctccctcctcctcctc	0.622																																					p.E417G													.	.	0			c.A1250G						.						5	6	5					10																	21805502		1959	4052	6011	SO:0001583	missense	387640	exon4			TCTCCCTCCTCCT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1250A>G	10.37:g.21805502T>C	ENSP00000410041:p.Glu417Gly	Somatic	64	1		WXS	Illumina HiSeq	Phase_I	46	3	NM_207371	0	0	0	0	0	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	37	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.473065	0.26423	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	.	.	.	4.85	4.85	0.62838	.	0.092390	0.40064	U	0.001195	T	0.34077	0.0885	N	0.12182	0.205	0.36349	D	0.859968	B	0.23540	0.087	B	0.20577	0.03	T	0.35351	-0.9792	9	0.28530	T	0.3	-8.3992	13.4017	0.60887	0.0:0.0:0.0:1.0	.	417	E9PAX1	.	G	417;338	.	ENSP00000442432:E338G	E	-	2	0	C10orf140	21845508	1.000000	0.71417	0.979000	0.43373	0.894000	0.52154	1.575000	0.36493	1.826000	0.53198	0.454000	0.30748	GAG	.		0.622	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		C	21805502	T	C	21805502	3	2	55	1	0	0	0	0	1	0	0	0	1599	1551	54	3	1480	3	C10orf140	10	21805502	Missense_Mutation	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10		21805502	113729245	22	5363											
TM7SF2	7108	broad.mit.edu	37	chr11	64883476	64883476	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtacggcctggcctggcAggagtactgccggcgtgtgc	6	7	17	11	3	0	0	0	0	0	0	0	2	0	1	3	5	4	3	3	5	3	2			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr11:64883476A>G	ENST00000279263.7	+	10	1370	c.1208A>G	c.(1207-1209)cAg>cGg	p.Q403R	TM7SF2_ENST00000345348.5_Missense_Mutation_p.Q376R|TM7SF2_ENST00000540748.1_Missense_Mutation_p.Q287R|AP003068.12_ENST00000527789.1_RNA	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	403					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTGGCCTGGCAGGAGTACTGC	0.642																																					p.Q403R													.	TM7SF2-91	0			c.A1208G						.						40	45	44					11																	64883476		2087	4206	6293	SO:0001583	missense	7108	exon10			CCTGGCAGGAGTA	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"delta(14)-sterol reductase"	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.1208A>G	11.37:g.64883476A>G	ENSP00000279263:p.Gln403Arg	Somatic	49	1		WXS	Illumina HiSeq	Phase_I	28	7	NM_003273	0	0	43	113	70	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	37	CCDS41669.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.049827	0.36181	.	.	ENSG00000149809	ENST00000279263;ENST00000540748;ENST00000345348	D;D;D	0.97941	-4.62;-4.62;-4.62	5.39	-4.76	0.03229	Sterol reductase, conserved site (1);	1.553580	0.03419	N	0.205992	D	0.90191	0.6934	N	0.03294	-0.36	0.18873	N	0.999987	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	D	0.85001	0.0900	10	0.36615	T	0.2	-9.9488	3.2742	0.06892	0.3929:0.1167:0.3764:0.114	.	287;376;403	F5GYV3;O76062-2;O76062	.;.;ERG24_HUMAN	R	403;287;376	ENSP00000279263:Q403R;ENSP00000441215:Q287R;ENSP00000329520:Q376R	ENSP00000279263:Q403R	Q	+	2	0	TM7SF2	64640052	0.051000	0.20477	0.008000	0.14137	0.836000	0.47400	0.654000	0.24918	-0.739000	0.04809	-0.250000	0.11733	CAG	.		0.642	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		G	64883476	A	G	64883476	3	3	55	1	0	0	0	0	1	0	0	0	16006	188	7	3	1246	3	TM7SF2	11	64883476	Missense_Mutation	SNP	A	TCGA-B9-A5W7-01A-11D-A31X-10		64883476	70123040	23	5364											
P2RY2	5029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	72945937	72945937	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggccaagcgcaagtccgtgCgcaccatcgccgtggtgctg	6	6	15	14	5	0	0	0	0	0	0	2	0	1	0	4	2	3	3	4	2	2	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr11:72945937C>T	ENST00000311131.2	+	3	1200	c.733C>T	c.(733-735)Cgc>Tgc	p.R245C	P2RY2_ENST00000393596.2_Missense_Mutation_p.R245C|P2RY2_ENST00000393597.2_Missense_Mutation_p.R245C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	245					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CAAGTCCGTGCGCACCATCGC	0.642																																					p.R245C		.											.	P2RY2-503	0			c.C733T						.						101	92	95					11																	72945937		2200	4293	6493	SO:0001583	missense	5029	exon3			TCCGTGCGCACCA	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.733C>T	11.37:g.72945937C>T	ENSP00000310305:p.Arg245Cys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	33	13	NM_176071	0	0	0	0	0	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076082	0.55646	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.37411	1.2;1.2;1.2	4.42	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.057192	0.64402	D	0.000005	T	0.60830	0.2299	M	0.88450	2.955	0.52501	D	0.999954	D	0.89917	1.0	D	0.71414	0.973	T	0.66999	-0.5781	10	0.87932	D	0	.	9.3877	0.38354	0.4324:0.5676:0.0:0.0	.	245	P41231	P2RY2_HUMAN	C	245	ENSP00000377222:R245C;ENSP00000310305:R245C;ENSP00000377221:R245C	ENSP00000310305:R245C	R	+	1	0	P2RY2	72623585	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.622000	0.54217	2.170000	0.68504	0.561000	0.74099	CGC	.		0.642	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072		T	72945937	C	T	72945937	3	4	55	1	0	0	0	0	1	0	0	0	11378	768	27	1	735	1	P2RY2	11	72945937	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10	8062461	72945937	62060579	24	5365											
MCAM	4162	broad.mit.edu	37	chr11	119187759	119187761	+	In_Frame_Del	DEL	CAG	CAG	-																															actcacccgcgacgcgaggaCagcagcagcaggcggcgagc																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr11:119187759_119187761delCAG	ENST00000264036.4	-	1	65_67	c.51_53delCTG	c.(49-54)tgctgt>tgt	p.17_18CC>C	MCAM_ENST00000530144.2_Intron|MCAM_ENST00000392814.1_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	17					anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		GACGCGAGGACAGCAGCAGCAGG	0.744																																					p.17_18del													.	MCAM-137	0			c.51_53del						.			6,3438		0,6,1716						1.2	1			7	14,6786		2,10,3388	no	coding	MCAM	NM_006500.2		2,16,5104	A1A1,A1R,RR		0.2059,0.1742,0.1952				20,10224				SO:0001651	inframe_deletion	4162	exon1			CGAGGACAGCAGC	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.51_53delCTG	11.37:g.119187768_119187770delCAG	ENSP00000264036:p.Cys18del	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_006500	0	0	0	0	0	O95812|Q59E86|Q6PHR3|Q6ZTR2	In_Frame_Del	DEL	ENST00000264036.4	37	CCDS31690.1																																																																																			.		0.744	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			-	119187761	CAG	-	119187759	7	5	55	1	0	1	0	1	0	0	0	0	9393	478	17	0	1951	0	MCAM	11	119187759	In_Frame_Del	DEL	CAG	TCGA-B9-A5W7-01A-11D-A31X-10	46241822	119187759	15818757	25	5366											
SMARCC2	6601	broad.mit.edu	37	chr12	56558430	56558430	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcaaacccaaaggagcattAcccgccacgcctgggtgccc	10	4	11	16	2	0	0	0	0	0	0	0	1	0	1	5	3	4	2	5	3	3	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr12:56558430A>C	ENST00000267064.4	-	27	3311	c.3225T>G	c.(3223-3225)ggT>ggG	p.G1075G	SMARCC2_ENST00000347471.4_Splice_Site|SMARCC2_ENST00000550164.1_Silent_p.G1106G|SMARCC2_ENST00000394023.3_Splice_Site|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1075	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.G1075G(2)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			AAGGAGCATTACCCGCCACGC	0.567																																					p.G1075G													.	SMARCC2-229	2	Substitution - coding silent(2)	kidney(2)	c.T3225G						.						57	53	55					12																	56558430		2203	4300	6503	SO:0001819	synonymous_variant	6601	exon27			AGCATTACCCGCC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.3225T>G	12.37:g.56558430A>C		Somatic	47	17		WXS	Illumina HiSeq	Phase_I	66	16	NM_003075	0	0	26	28	2	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	A	19.51	3.841392	0.71488	.	.	ENSG00000139613	ENST00000394023;ENST00000347471	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7728	0.63036	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SMARCC2	54844697	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.668000	0.68074	2.045000	0.60652	0.455000	0.32223	.	.		0.567	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			C	56558430	A	C	56558430	2	2	55	1	0	0	0	0	0	0	0	1	14808	405	14	5		5	SMARCC2	12	56558430	Silent	SNP	A	TCGA-B9-A5W7-01A-11D-A31X-10		56558430	77293465	26	5367											
SLITRK5	26050	ucsc.edu;bcgsc.ca	37	chr13	88327922	88327922	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgttgtccggaaaccttttGaaccgtctctatcccaatga	9	14	7	11	2	1	2	0	2	1	0	4	3	3	3	4	1	2	1	4	1	4	5			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr13:88327922G>C	ENST00000325089.6	+	2	498	c.279G>C	c.(277-279)ttG>ttC	p.L93F	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	93					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GAAACCTTTTGAACCGTCTCT	0.463																																					p.L93F													.	SLITRK5-94	0			c.G279C						.						159	165	163					13																	88327922		2203	4300	6503	SO:0001583	missense	26050	exon2			CCTTTTGAACCGT	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"leucine rich repeat containing 11"	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.279G>C	13.37:g.88327922G>C	ENSP00000366283:p.Leu93Phe	Somatic	276	3		WXS	Illumina HiSeq		210	66	NM_015567	0	0	0	0	0	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.201266	0.38905	.	.	ENSG00000165300	ENST00000325089	T	0.60424	0.19	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000003	T	0.70029	0.3177	L	0.58925	1.835	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.68610	-0.5363	9	.	.	.	-7.6811	11.1672	0.48550	0.0829:0.0:0.9171:0.0	.	93	O94991	SLIK5_HUMAN	F	93	ENSP00000366283:L93F	.	L	+	3	2	SLITRK5	87125923	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.494000	0.35616	2.826000	0.97356	0.561000	0.74099	TTG	.		0.463	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			C	88327922	G	C	88327922	3	2	55	1	0	0	0	0	1	0	0	0	14778	1281	45	4	281	4	SLITRK5	13	88327922	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		88327922	26841956	27	5368											
OR4N2	390429	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20296302	20296302	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgagggtcttcttctgaggCaaaaaacaaggccatgtcca	13	8	10	10	1	3	1	0	1	3	0	4	2	4	1	2	3	1	1	2	3	4	2	rs567489106		TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr14:20296302C>A	ENST00000315947.1	+	1	695	c.695C>A	c.(694-696)gCa>gAa	p.A232E	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCTTCTGAGGCAAAAAACAAG	0.493																																					p.A232E													.	OR4N2-71	0			c.C695A						.						105	106	106					14																	20296302		2203	4300	6503	SO:0001583	missense	390429	exon1			CTGAGGCAAAAAA		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"GPCR / Class A : Olfactory receptors"	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.695C>A	14.37:g.20296302C>A	ENSP00000319601:p.Ala232Glu	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	127	21	NM_001004723	0	0	0	0	0	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	6.956	0.546326	0.13312	.	.	ENSG00000176294	ENST00000315947	T	0.00091	8.74	4.66	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.130056	0.35262	N	0.003337	T	0.00144	0.0004	L	0.28694	0.88	0.09310	N	1	B	0.16802	0.019	B	0.25759	0.063	T	0.32052	-0.9921	10	0.66056	D	0.02	-4.9296	11.5944	0.50964	0.0:0.355:0.645:0.0	.	232	Q8NGD1	OR4N2_HUMAN	E	232	ENSP00000319601:A232E	ENSP00000319601:A232E	A	+	2	0	OR4N2	19366142	0.036000	0.19791	0.988000	0.46212	0.123000	0.20343	0.859000	0.27858	1.313000	0.45069	-0.234000	0.12200	GCA	.		0.493	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			A	20296302	C	A	20296302	3	1	55	1	0	0	0	0	1	0	0	0	11103	710	25	4	697	4	OR4N2	14	20296302	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10		20296302	87053238	28	5369											
SETD3	84193	bcgsc.ca	37	chr14	99925507	99925507	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caattttcgtggaacccataAaaacaattcttctgcctagg	13	12	6	10	1	2	0	0	0	2	0	3	1	2	1	2	2	3	0	2	2	7	6			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr14:99925507A>T	ENST00000331768.5	-	5	520	c.361T>A	c.(361-363)Tta>Ata	p.L121I	SETD3_ENST00000329331.3_Missense_Mutation_p.L121I|SETD3_ENST00000436070.2_Missense_Mutation_p.L121I|SETD3_ENST00000453938.1_5'UTR	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	121	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				GGAACCCATAAAAACAATTCT	0.358																																					p.L121I													.	SETD3-514	0			c.T361A						.						96	102	100					14																	99925507		2203	4300	6503	SO:0001583	missense	84193	exon5			CCCATAAAAACAA	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.361T>A	14.37:g.99925507A>T	ENSP00000327436:p.Leu121Ile	Somatic	308	5		WXS	Illumina HiSeq	Phase_1	244	98	NM_032233	0	0	41	65	24	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Missense_Mutation	SNP	ENST00000331768.5	37	CCDS9951.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273978	0.80580	.	.	ENSG00000183576	ENST00000331768;ENST00000329331;ENST00000436070	T;T;T	0.16897	2.31;2.31;2.31	5.47	1.88	0.25563	SET domain (1);	0.000000	0.64402	D	0.000002	T	0.20495	0.0493	N	0.25647	0.755	0.58432	D	0.999997	B;D;P	0.65815	0.067;0.995;0.505	B;D;P	0.81914	0.152;0.995;0.522	T	0.11641	-1.0579	10	0.15066	T	0.55	-8.4561	6.7996	0.23744	0.5324:0.0:0.4676:0.0	.	121;121;121	Q6NXR6;A0PJU3;Q86TU7	.;.;SETD3_HUMAN	I	121	ENSP00000327436:L121I;ENSP00000327910:L121I;ENSP00000408602:L121I	ENSP00000327910:L121I	L	-	1	2	SETD3	98995260	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.416000	0.59815	0.463000	0.27118	0.455000	0.32223	TTA	.		0.358	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		T	99925507	A	T	99925507	3	4	55	1	0	0	0	0	1	0	0	0	14164	11	1	5	1505	5	SETD3	14	99925507	Missense_Mutation	SNP	A	TCGA-B9-A5W7-01A-11D-A31X-10	79629205	99925507	7424033	29	5370											
C14orf73	91828	broad.mit.edu	37	chr14	103570687	103570687	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggtccccgaggtgctgcaGggcctctaccaggcgccgct	5	6	15	15	3	1	0	0	0	1	0	2	2	2	0	5	4	3	3	5	4	1	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr14:103570687G>A	ENST00000380069.3	+	4	1321	c.1245G>A	c.(1243-1245)caG>caA	p.Q415Q		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	415					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						AGGTGCTGCAGGGCCTCTACC	0.667																																					p.Q415Q													.	EXOC3L4-23	0			c.G1245A						.						11	12	12					14																	103570687		2194	4287	6481	SO:0001819	synonymous_variant	91828	exon4			GCTGCAGGGCCTC	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 73"	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.1245G>A	14.37:g.103570687G>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_001077594	0	0	16	16	0	Q14CR2	Silent	SNP	ENST00000380069.3	37	CCDS32163.1																																																																																			.		0.667	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093		A	103570687	G	A	103570687	2	1	55	1	0	0	0	0	0	0	0	1	1783	991	35	2		2	C14orf73	14	103570687	Silent	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	3645180	103570687	3778853	30	5371											
KIF26A	26153	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	104639376	104639376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgggcatcgtgccctgcGccatctcctggctcttcagg	3	10	12	16	2	3	0	1	0	2	0	5	0	3	0	4	3	2	2	4	3	0	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr14:104639376G>A	ENST00000423312.2	+	8	1483	c.1483G>A	c.(1483-1485)Gcc>Acc	p.A495T	KIF26A_ENST00000315264.7_Missense_Mutation_p.A356T	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	495	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CGTGCCCTGCGCCATCTCCTG	0.682																																					p.A495T		.											.	KIF26A-24	0			c.G1483A						.						21	27	25					14																	104639376		2117	4214	6331	SO:0001583	missense	26153	exon8			CCCTGCGCCATCT	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"Kinesins"	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1483G>A	14.37:g.104639376G>A	ENSP00000388241:p.Ala495Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	76	6	NM_015656	0	0	0	0	0	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	37	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	G	35	5.536616	0.96460	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.48522	0.81;0.81	4.84	4.84	0.62591	Kinesin, motor domain (4);	.	.	.	.	T	0.65616	0.2708	L	0.53617	1.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68891	-0.5289	9	0.66056	D	0.02	.	17.9375	0.89017	0.0:0.0:1.0:0.0	.	495	Q9ULI4	KI26A_HUMAN	T	495;356	ENSP00000388241:A495T;ENSP00000325452:A356T	ENSP00000325452:A356T	A	+	1	0	KIF26A	103709129	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	7.702000	0.84576	2.223000	0.72356	0.462000	0.41574	GCC	.		0.682	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			A	104639376	G	A	104639376	3	1	55	1	0	0	0	0	1	0	0	0	8315	1087	38	1	1513	1	KIF26A	14	104639376	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	1068689	104639376	2710164	31	5372											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79058942	79058944	+	In_Frame_Del	DEL	GCA	GCA	-																															cggggctacccgtggagggcGcagcaggatggctgtgtggt																								rs529497330|rs201562030|rs543268667	byFrequency	TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr15:79058942_79058944delGCA	ENST00000388820.4	-	19	3519_3521	c.3309_3311delTGC	c.(3307-3312)gctgcg>gcg	p.1103_1104AA>A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1103					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CGTGGAGGGCGCAGCAGGATGGC	0.675																																					p.1103_1104del		.											.	ADAMTS7-226	0			c.3309_3311del						.																																			SO:0001651	inframe_deletion	11173	exon19			.	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3309_3311delTGC	15.37:g.79058945_79058947delGCA	ENSP00000373472:p.Ala1104del	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	39	23	NM_014272	0	0	0	0	0	Q14F51|Q6P7J9	In_Frame_Del	DEL	ENST00000388820.4	37	CCDS32303.1																																																																																			.		0.675	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		-	79058944	GCA	-	79058942	7	5	55	1	0	1	0	1	0	0	0	0	271	1087	38	0	1773	0	ADAMTS7	15	79058942	In_Frame_Del	DEL	GCA	TCGA-B9-A5W7-01A-11D-A31X-10		79058942	23472450	32	5373											
CNOT1	23019	broad.mit.edu	37	chr16	58566190	58566190	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaacacatgctcaggtgcaTtgagttccaagagaagcatg	13	8	10	10	0	1	2	1	1	0	1	2	3	2	2	2	1	4	4	2	1	3	2			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr16:58566190T>C	ENST00000317147.5	-	41	6337	c.6005A>G	c.(6004-6006)aAt>aGt	p.N2002S	CNOT1_ENST00000245138.4_Missense_Mutation_p.N853S|CNOT1_ENST00000569240.1_Missense_Mutation_p.N1997S	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2002					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CTCAGGTGCATTGAGTTCCAA	0.398																																					p.N2002S													.	CNOT1-95	0			c.A6005G						.						95	89	91					16																	58566190		2198	4300	6498	SO:0001583	missense	23019	exon41			GGTGCATTGAGTT	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.6005A>G	16.37:g.58566190T>C	ENSP00000320949:p.Asn2002Ser	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	141	5	NM_016284	0	0	69	72	3	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	13.01	2.110146	0.37242	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000546037;ENST00000245138;ENST00000394200	T	0.44482	0.92	5.85	5.85	0.93711	CCR4-Not complex component, Not1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.29093	0.0723	N	0.21508	0.67	0.80722	D	1	B;B;B	0.29341	0.065;0.242;0.235	B;B;B	0.29353	0.028;0.101;0.069	T	0.09509	-1.0671	10	0.07644	T	0.81	.	16.2355	0.82371	0.0:0.0:0.0:1.0	.	853;2002;1997	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	S	2002;696;7;853;1997	ENSP00000320949:N2002S	ENSP00000245138:N853S	N	-	2	0	CNOT1	57123691	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.238000	0.73509	0.533000	0.62120	AAT	.		0.398	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58566190	T	C	58566190	3	2	55	1	0	0	0	0	1	0	0	0	3623	1493	52	3	1161	3	CNOT1	16	58566190	Missense_Mutation	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10		58566190	31788563	33	5374											
KRTAP4-11	653240	broad.mit.edu	37	chr17	39274432	39274432	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctgcagcagctggacaCacagcagctggggcgacagt	9	4	16	12	1	0	0	0	0	0	0	0	2	0	1	1	4	5	5	1	4	0	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr17:39274432C>T	ENST00000391413.2	-	1	174	c.136G>A	c.(136-138)Gtg>Atg	p.V46M		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	46	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGACACACAGCAGCTG	0.677																																					p.V46M													.	.	0			c.G136A						.						14	18	17					17																	39274432		690	1591	2281	SO:0001583	missense	653240	exon1			TGGACACACAGCA	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"Keratin associated proteins"	18911	protein-coding gene	gene with protein product			"keratin associated protein 4-14"	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.136G>A	17.37:g.39274432C>T	ENSP00000375232:p.Val46Met	Somatic	77	2		WXS	Illumina HiSeq	Phase_I	86	5	NM_033059	0	0	0	0	0	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	10.56	1.385842	0.25031	.	.	ENSG00000212721	ENST00000391413	T	0.01430	4.9	3.76	-6.69	0.01772	.	0.911881	0.08829	U	0.887602	T	0.03739	0.0106	M	0.84948	2.725	0.09310	N	1	P	0.40266	0.71	P	0.46585	0.521	T	0.02144	-1.1206	10	0.54805	T	0.06	.	8.7851	0.34816	0.0:0.3102:0.5247:0.1651	.	46	Q9BYQ6	KR411_HUMAN	M	46	ENSP00000375232:V46M	ENSP00000375232:V46M	V	-	1	0	KRTAP4-11	36527958	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.396000	0.01052	-0.895000	0.03920	-1.166000	0.01754	GTG	.		0.677	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274432	C	T	39274432	3	4	55	1	0	0	0	0	1	0	0	0	8570	478	17	2	455	2	KRTAP4-11	17	39274432	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10		39274432	41920778	34	5375											
KIAA1012	22878	broad.mit.edu	37	chr18	29497627	29497627	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagactcaaaccatggagtaGtggctaaaattaacaatata	19	9	7	6	0	1	1	1	0	0	1	1	2	1	2	1	2	2	2	1	2	9	5			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr18:29497627G>T	ENST00000283351.4	-	3	691	c.356C>A	c.(355-357)aCt>aAt	p.T119N	TRAPPC8_ENST00000582513.1_Missense_Mutation_p.T119N|TRAPPC8_ENST00000582539.1_Missense_Mutation_p.T65N	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	119					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CCATGGAGTAGTGGCTAAAAT	0.318																																					p.T119N													.	TRAPPC8-159	0			c.C356A						.						110	116	114					18																	29497627		2203	4300	6503	SO:0001583	missense	22878	exon3			GGAGTAGTGGCTA	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.356C>A	18.37:g.29497627G>T	ENSP00000283351:p.Thr119Asn	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_014939	0	0	0	0	0	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.073869	0.55646	.	.	ENSG00000153339	ENST00000283351	T	0.08807	3.05	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.09730	0.0239	L	0.31664	0.95	0.80722	D	1	B;B	0.33266	0.404;0.27	B;B	0.34489	0.132;0.184	T	0.30880	-0.9963	10	0.25751	T	0.34	-26.1221	20.8598	0.99761	0.0:0.0:1.0:0.0	.	119;119	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	N	119	ENSP00000283351:T119N	ENSP00000283351:T119N	T	-	2	0	TRAPPC8	27751625	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	ACT	.		0.318	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		T	29497627	G	T	29497627	3	4	55	1	0	0	0	0	1	0	0	0	8225	1029	36	4	4059	4	KIAA1012	18	29497627	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		29497627	48579621	35	5376											
GRIK5	2901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42525580	42525580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctccaggatgtgggggcGtgcccgcaggcatgggtgtg	4	9	19	9	2	1	0	0	0	1	0	2	1	1	1	2	5	1	3	2	5	0	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr19:42525580G>A	ENST00000262895.3	-	14	1743	c.1744C>T	c.(1744-1746)Cgc>Tgc	p.R582C	GRIK5_ENST00000301218.4_Missense_Mutation_p.R582C|GRIK5_ENST00000593562.1_Missense_Mutation_p.R582C	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	582					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.R582C(2)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				ATGTGGGGGCGTGCCCGCAGG	0.652																																					p.R582C		.											.	GRIK5-90	2	Substitution - Missense(2)	prostate(2)	c.C1744T						.						35	29	31					19																	42525580		2203	4300	6503	SO:0001583	missense	2901	exon14			GGGGGCGTGCCCG		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.1744C>T	19.37:g.42525580G>A	ENSP00000262895:p.Arg582Cys	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	62	16	NM_002088	0	0	0	0	0	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	37	CCDS12595.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194809	0.58017	.	.	ENSG00000105737	ENST00000262895;ENST00000301218	T;T	0.14022	2.59;2.54	4.51	4.51	0.55191	Ionotropic glutamate receptor (2);	0.153806	0.42821	D	0.000644	T	0.24353	0.0590	L	0.32530	0.975	0.45621	D	0.99855	D	0.89917	1.0	D	0.70016	0.967	T	0.01114	-1.1447	10	0.62326	D	0.03	.	11.8849	0.52596	0.0:0.0:0.8248:0.1752	.	582	Q16478	GRIK5_HUMAN	C	582	ENSP00000262895:R582C;ENSP00000301218:R582C	ENSP00000262895:R582C	R	-	1	0	GRIK5	47217420	0.846000	0.29590	0.903000	0.35520	0.645000	0.38454	1.338000	0.33873	2.055000	0.61198	0.563000	0.77884	CGC	.		0.652	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			A	42525580	G	A	42525580	3	1	55	1	0	0	0	0	1	0	0	0	6798	1145	40	1	1222	1	GRIK5	19	42525580	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		42525580	16603403	36	5377											
CRX	1406	broad.mit.edu	37	chr19	48343201	48343201	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggactacaaggatcagagtGcctggaagtttcagatcttg	11	11	12	7	0	3	2	2	0	1	2	3	5	3	5	1	3	2	1	1	3	3	3			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr19:48343201G>T	ENST00000221996.7	+	4	1083	c.877G>T	c.(877-879)Gcc>Tcc	p.A293S	CRX_ENST00000539067.1_Missense_Mutation_p.A293S|TPRX2P_ENST00000535362.1_Intron	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	293					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		GGATCAGAGTGCCTGGAAGTT	0.537																																					p.A293S	Pancreas(57;461 1196 22201 40716 47188)												.	CRX-153	0			c.G877T						.						72	74	73					19																	48343201		2171	4203	6374	SO:0001583	missense	1406	exon4			CAGAGTGCCTGGA	AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"Homeoboxes / PRD class"	2383	protein-coding gene	gene with protein product	"orthodenticle homeobox 3"	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.877G>T	19.37:g.48343201G>T	ENSP00000221996:p.Ala293Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	63	5	NM_000554	0	0	0	0	0	Q0QD45	Missense_Mutation	SNP	ENST00000221996.7	37	CCDS12706.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.239964	0.22711	.	.	ENSG00000105392	ENST00000221996;ENST00000539067	D;D	0.85773	-2.03;-2.03	3.88	2.77	0.32553	.	0.069568	0.64402	D	0.000017	T	0.56247	0.1972	N	0.01473	-0.845	0.28983	N	0.88852	B	0.19073	0.033	B	0.10450	0.005	T	0.53669	-0.8406	10	0.02654	T	1	-12.4857	8.1058	0.30885	0.0:0.0:0.6293:0.3707	.	293	O43186	CRX_HUMAN	S	293	ENSP00000221996:A293S;ENSP00000445565:A293S	ENSP00000221996:A293S	A	+	1	0	CRX	53035013	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.817000	0.62650	1.988000	0.58038	0.313000	0.20887	GCC	.		0.537	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554		T	48343201	G	T	48343201	3	4	55	1	0	0	0	0	1	0	0	0	3908	1319	46	4	887	4	CRX	19	48343201	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	5817621	48343201	10785782	37	5378											
ZNF808	388558	broad.mit.edu	37	chr19	53057180	53057180	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaattcataaggcaattcaTactggagagaaaccttacaa	17	10	7	7	0	2	1	2	0	0	1	2	3	2	2	1	2	3	2	1	2	7	6			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr19:53057180T>C	ENST00000359798.4	+	5	1191	c.1011T>C	c.(1009-1011)caT>caC	p.H337H		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	337					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)			endometrium(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		AGGCAATTCATACTGGAGAGA	0.393																																					p.H337H													.	.	0			c.T1011C						.						82	87	85					19																	53057180		2203	4300	6503	SO:0001819	synonymous_variant	388558	exon5			AATTCATACTGGA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"Zinc fingers, C2H2-type", "-"	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1011T>C	19.37:g.53057180T>C		Somatic	135	3		WXS	Illumina HiSeq	Phase_I	130	5	NM_001039886	0	0	19	19	0	Q68CN7	Silent	SNP	ENST00000359798.4	37	CCDS46167.1																																																																																			.		0.393	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		C	53057180	T	C	53057180	2	2	55	1	0	0	0	0	0	0	0	1	18205	1403	49	3		3	ZNF808	19	53057180	Silent	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10	4713979	53057180	6071803	38	5379											
TTLL12	23170	ucsc.edu;bcgsc.ca	37	chr22	43569808	43569808	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcgccaggttccagggcttGcagatccagtggttgtcctc	5	10	13	13	2	0	1	0	0	0	1	4	1	3	1	4	3	1	4	4	3	0	3			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr22:43569808G>T	ENST00000216129.6	-	9	1317	c.1254C>A	c.(1252-1254)tgC>tgA	p.C418*	TTLL12_ENST00000484118.1_5'Flank|TTLL12_ENST00000494035.1_5'Flank	NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	418	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				TCCAGGGCTTGCAGATCCAGT	0.687																																					p.C418X													.	TTLL12-90	0			c.C1254A						.						58	51	53					22																	43569808		2203	4300	6503	SO:0001587	stop_gained	23170	exon9			GGGCTTGCAGATC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"Tubulin tyrosine ligase-like family"	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.1254C>A	22.37:g.43569808G>T	ENSP00000216129:p.Cys418*	Somatic	32	0		WXS	Illumina HiSeq		26	4	NM_015140	0	0	37	37	0	Q20WK5|Q9UGU3	Nonsense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	.	.	.	.	.	.	.	.	.	.	G	37	6.535621	0.97646	.	.	ENSG00000100304	ENST00000216129;ENST00000423379	.	.	.	4.96	3.94	0.45596	.	0.098590	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.6038	13.2367	0.59972	0.0776:0.0:0.9224:0.0	.	.	.	.	X	418	.	ENSP00000216129:C418X	C	-	3	2	TTLL12	41899752	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.967000	0.49216	1.061000	0.40601	0.467000	0.42956	TGC	.		0.687	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140		T	43569808	G	T	43569808	4	4	55	1	0	0	0	0	0	1	0	0	16758	1311	46	4	704	4	TTLL12	22	43569808	Nonsense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		43569808	7734758	39	5380											
RBM3	5935	broad.mit.edu	37	chrX	48434994	48434994	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagactataatggcaggTgggtagccaaagggctggga	12	6	16	7	0	0	1	0	0	0	1	0	3	0	2	2	5	1	3	2	5	4	3			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chrX:48434994T>G	ENST00000376759.3	+	5	476		c.e5+2		RBM3_ENST00000354480.2_Splice_Site|RBM3_ENST00000430348.2_Splice_Site|AC115618.1_ENST00000376775.2_5'Flank|RBM3_ENST00000376755.1_Splice_Site|RBM3_ENST00000466764.1_Splice_Site	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3						positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)	p.?(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TAATGGCAGGTGGGTAGCCAA	0.517																																					.													.	RBM3-131	1	Unknown(1)	ovary(1)	c.413+2T>G						.						59	56	57					X																	48434994		2193	4272	6465	SO:0001630	splice_region_variant	5935	exon5			GGCAGGTGGGTAG	BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"RNA binding motif (RRM) containing"	9900	protein-coding gene	gene with protein product		300027	"RNA binding motif protein 3"			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.413+2T>G	X.37:g.48434994T>G		Somatic	31	5		WXS	Illumina HiSeq	Phase_I	27	5	NM_006743	0	0	0	0	0		Splice_Site	SNP	ENST00000376759.3	37	CCDS14301.1	.	.	.	.	.	.	.	.	.	.	t	11.97	1.798592	0.31777	.	.	ENSG00000102317	ENST00000376759;ENST00000430348;ENST00000376755;ENST00000354480	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3004	0.43648	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM3	48319938	1.000000	0.71417	0.999000	0.59377	0.387000	0.30353	2.025000	0.41059	1.792000	0.52537	0.481000	0.45027	.	.		0.517	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060755.1	NM_006743	Intron	G	48434994	T	G	48434994	5	3	55	1	0	0	0	0	0	0	1	0	13161	1710	59	5	429	5	RBM3	23	48434994	Splice_Site	SNP	T	TCGA-B9-A5W7-01A-11D-A31X-10		48434994	106835566	40	5381											
ACTRT2	140625	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	2938841	2938841	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagctcctcatgcagctgctCctggccagcggccacacctt	6	8	10	17	1	1	0	1	0	0	0	3	1	3	0	5	2	5	4	5	2	0	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:2938841C>A	ENST00000378404.2	+	1	796	c.591C>A	c.(589-591)ctC>ctA	p.L197L		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	197						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		TGCAGCTGCTCCTGGCCAGCG	0.627																																					p.L197L													.	ACTRT2-90	0			c.C591A						.						38	39	39					1																	2938841		2203	4299	6502	SO:0001819	synonymous_variant	140625	exon1			GCTGCTCCTGGCC	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.591C>A	1.37:g.2938841C>A		Somatic	243	1		WXS	Illumina HiSeq	Phase_I	189	71	NM_080431	0	0	0	0	0	B1AN52|Q8NHS6|Q8TDG1	Silent	SNP	ENST00000378404.2	37	CCDS45.1																																																																																			.		0.627	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431		A	2938841	C	A	2938841	2	1	56	1	0	0	0	0	0	0	0	1	219	842	30	4		4	ACTRT2	1	2938841	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		2938841	246311780	1	5382											
TMOD4	29765	broad.mit.edu	37	chr1	151146999	151146999	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttgtctggtcacgttgtcTtagtccagctggcaggagca	6	13	12	10	1	3	0	1	0	2	0	4	1	4	1	1	3	2	4	1	3	1	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:151146999T>A	ENST00000416280.2	-	3	247	c.148A>T	c.(148-150)Aga>Tga	p.R50*	VPS72_ENST00000496809.1_5'Flank|TMOD4_ENST00000601585.1_5'Flank			Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)	0					muscle contraction (GO:0006936)	striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCACGTTGTCTTAGTCCAGCT	0.537																																					p.R50X													.	TMOD4-91	0			c.A148T						.						163	157	159					1																	151146999		2203	4300	6503	SO:0001587	stop_gained	29765	exon3			GTTGTCTTAGTCC	AF177173	CCDS988.1	1q12	2008-05-23			ENSG00000163157	ENSG00000163157			11874	protein-coding gene	gene with protein product	"actin-capping protein"	605834				10662549, 10497209	Standard	NM_013353		Approved	Sk-Tmod	uc001exc.4	Q9NZQ9	OTTHUMG00000012350	ENST00000416280.2:c.148A>T	1.37:g.151146999T>A	ENSP00000414180:p.Arg50*	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_013353	0	0	0	0	0	B7Z6N9|Q5JR83|Q8WVL3|Q9UKH2	Nonsense_Mutation	SNP	ENST00000416280.2	37		.	.	.	.	.	.	.	.	.	.	.	29.1	4.976337	0.92982	.	.	ENSG00000163157	ENST00000295314;ENST00000416280;ENST00000441701	.	.	.	5.62	3.09	0.35607	.	0.117111	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.6159	10.3631	0.44006	0.0:0.0:0.4458:0.5542	.	.	.	.	X	50	.	ENSP00000295314:R50X	R	-	1	2	TMOD4	149413623	1.000000	0.71417	0.988000	0.46212	0.952000	0.60782	3.215000	0.51169	0.915000	0.36847	0.459000	0.35465	AGA	.		0.537	TMOD4-201	KNOWN	basic	protein_coding	protein_coding				A	151146999	T	A	151146999	4	1	56	1	0	0	0	0	0	1	0	0	16268	1617	56	5	921	5	TMOD4	1	151146999	Nonsense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	148208158	151146999	98103622	2	5383											
PBX1	5087	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	164761953	164761953	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatcagacaaatctaccataCggagctggagaaatacgagc	16	6	10	9	2	2	2	1	0	1	2	2	6	2	3	1	2	5	1	1	2	5	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:164761953C>T	ENST00000420696.2	+	3	676	c.488C>T	c.(487-489)aCg>aTg	p.T163M	PBX1_ENST00000367897.1_Missense_Mutation_p.T163M|PBX1_ENST00000540236.1_Missense_Mutation_p.T163M|PBX1_ENST00000540246.1_Missense_Mutation_p.T58M|PBX1_ENST00000560641.1_Missense_Mutation_p.T58M|PBX1_ENST00000401534.1_Missense_Mutation_p.T163M|PBX1_ENST00000559240.1_Missense_Mutation_p.T163M	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	163					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						ATCTACCATACGGAGCTGGAG	0.577			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.T163M		.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1-659	0			c.C488T						.						27	31	30					1																	164761953		2202	4300	6502	SO:0001583	missense	5087	exon3			ACCATACGGAGCT	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.488C>T	1.37:g.164761953C>T	ENSP00000405890:p.Thr163Met	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	60	30	NM_001204963	0	0	0	0	0	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709033	0.89018	.	.	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5	5.23	5.23	0.72850	PBX (1);	0.000000	0.85682	D	0.000000	T	0.43144	0.1234	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.65815	0.995;0.994;0.993;0.994;0.994	P;P;P;D;P	0.64877	0.738;0.806;0.852;0.93;0.82	T	0.39643	-0.9604	10	0.72032	D	0.01	-9.5716	18.3959	0.90497	0.0:1.0:0.0:0.0	.	58;163;163;163;163	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	M	163;163;163;163;163;58	ENSP00000341455:T163M;ENSP00000405890:T163M;ENSP00000356872:T163M;ENSP00000439943:T163M;ENSP00000384856:T163M;ENSP00000440869:T58M	ENSP00000341455:T163M	T	+	2	0	PBX1	163028577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.376000	0.79658	2.405000	0.81733	0.563000	0.77884	ACG	.		0.577	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		T	164761953	C	T	164761953	3	4	56	1	0	0	0	0	1	0	0	0	11518	536	19	1	498	1	PBX1	1	164761953	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	13614954	164761953	84488668	3	5384											
SUSD4	55061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223438095	223438095	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagatcacagtccccaccgGgaaggaggtctggagctcag	10	5	15	11	1	3	1	2	0	1	1	4	5	4	4	3	5	1	1	3	5	1	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:223438095G>A	ENST00000343846.3	-	4	1234	c.601C>T	c.(601-603)Ccg>Tcg	p.P201S	SUSD4_ENST00000494793.2_Missense_Mutation_p.P201S|SUSD4_ENST00000344029.6_Missense_Mutation_p.P201S|SUSD4_ENST00000484758.2_Missense_Mutation_p.P130S|SUSD4_ENST00000478605.1_Intron|SUSD4_ENST00000454695.2_Missense_Mutation_p.P41S|SUSD4_ENST00000366878.4_Missense_Mutation_p.P201S			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	201	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GTCCCCACCGGGAAGGAGGTC	0.498																																					p.P201S		.											.	SUSD4-68	0			c.C601T						.						85	91	89					1																	223438095		2203	4300	6503	SO:0001583	missense	55061	exon5			CCACCGGGAAGGA	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.601C>T	1.37:g.223438095G>A	ENSP00000344219:p.Pro201Ser	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	88	18	NM_017982	0	0	0	0	0	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	37	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775431	0.49786	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000454695;ENST00000344029	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.32	4.38	0.52667	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.47093	D	0.000255	T	0.58764	0.2145	N	0.20685	0.6	0.80722	D	1	B;D;P	0.71674	0.426;0.998;0.626	B;D;B	0.80764	0.329;0.994;0.432	T	0.56890	-0.7904	10	0.05721	T	0.95	-16.3711	10.3108	0.43708	0.0756:0.1375:0.7869:0.0	.	130;201;201	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	S	201;201;130;41;201	ENSP00000344219:P201S;ENSP00000355843:P201S;ENSP00000399288:P41S;ENSP00000339926:P201S	ENSP00000344219:P201S	P	-	1	0	SUSD4	221504718	1.000000	0.71417	0.997000	0.53966	0.827000	0.46813	4.506000	0.60428	1.415000	0.47037	0.491000	0.48974	CCG	.		0.498	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		A	223438095	G	A	223438095	3	1	56	1	0	0	0	0	1	0	0	0	15442	1232	43	2	1044	2	SUSD4	1	223438095	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	58676142	223438095	25812526	4	5385											
CAD	790	broad.mit.edu	37	chr2	27462296	27462296	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagtgaagggcaccgtccGccgtgtggtcctgcgagggg	7	6	18	10	4	0	1	0	1	0	0	2	3	2	1	4	4	1	1	4	4	2	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:27462296G>A	ENST00000403525.1	+	32	5306	c.5162G>A	c.(5161-5163)cGc>cAc	p.R1721H	CAD_ENST00000264705.4_Missense_Mutation_p.R1784H			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCACCGTCCGCCGTGTGGTC	0.577																																					p.R1784H													.	CAD-295	0			c.G5351A						.						84	72	76					2																	27462296		2203	4300	6503	SO:0001583	missense	790	exon33			CCGTCCGCCGTGT	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5162G>A	2.37:g.27462296G>A	ENSP00000384510:p.Arg1721His	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	151	5	NM_004341	0	0	21	24	3	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	3.326	-0.137714	0.06711	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.98455	-4.94;-4.88	4.88	4.88	0.63580	Metal-dependent hydrolase, composite domain (1);	0.105066	0.64402	D	0.000004	D	0.96334	0.8804	N	0.26162	0.8	0.48901	D	0.99972	B;D	0.65815	0.005;0.995	B;P	0.53146	0.006;0.719	D	0.94637	0.7827	10	0.02654	T	1	-15.6878	16.9731	0.86305	0.0:0.0:1.0:0.0	.	1721;1784	F8VPD4;P27708	.;PYR1_HUMAN	H	1784;1721	ENSP00000264705:R1784H;ENSP00000384510:R1721H	ENSP00000264705:R1784H	R	+	2	0	CAD	27315800	1.000000	0.71417	0.999000	0.59377	0.438000	0.31896	5.691000	0.68249	2.407000	0.81776	0.561000	0.74099	CGC	.		0.577	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27462296	G	A	27462296	3	1	56	1	0	0	0	0	1	0	0	0	2571	1087	38	1	5481	1	CAD	2	27462296	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		27462296	215737077	5	5386											
NEUROD1	4760	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	182543048	182543051	+	Frame_Shift_Del	DEL	GGTG	GGTG	-																															cagcccgcaaccaggttggtGgtgggttgggataagccctt																								rs565522208		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GGTG	GGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:182543048_182543051delGGTG	ENST00000295108.3	-	2	994_997	c.537_540delCACC	c.(535-540)cccaccfs	p.PT179fs	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	179					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CCAGGTTGGTGGTGGGTTGGGATA	0.598																																					p.179_180del		.											.	NEUROD1-91	0			c.537_540del						.																																			SO:0001589	frameshift_variant	4760	exon2			.	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.537_540delCACC	2.37:g.182543048_182543051delGGTG	ENSP00000295108:p.Pro179fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	80	22	NM_002500	0	0	0	0	0	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Frame_Shift_Del	DEL	ENST00000295108.3	37	CCDS2283.1																																																																																			.		0.598	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		-	182543051	GGTG	-	182543048	7	5	56	1	0	1	0	1	0	0	0	0	10374	1335	47	0	534	0	NEUROD1	2	182543048	Frame_Shift_Del	DEL	GGTG	TCGA-B9-A5W8-01A-11D-A28G-10	155080752	182543048	60656325	6	5387											
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233651899	233651899	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggtggaccaacatcagtagGgagaaagcatgaatttatac	16	8	11	6	0	1	2	1	1	0	1	1	4	1	3	1	3	3	2	1	3	6	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:233651899G>C	ENST00000409547.1	+	11	883	c.572G>C	c.(571-573)gGg>gCg	p.G191A	GIGYF2_ENST00000409196.3_Missense_Mutation_p.G191A|GIGYF2_ENST00000452341.2_Missense_Mutation_p.G22A|GIGYF2_ENST00000373563.4_Missense_Mutation_p.G191A|GIGYF2_ENST00000373566.3_Missense_Mutation_p.G213A|GIGYF2_ENST00000409451.3_Missense_Mutation_p.G213A|GIGYF2_ENST00000409480.1_Missense_Mutation_p.G213A	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	191	Arg-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		ACATCAGTAGGGAGAAAGCAT	0.403																																					p.G213A		.											.	GIGYF2-28	0			c.G638C						.						104	106	106					2																	233651899		2203	4300	6503	SO:0001583	missense	26058	exon11			CAGTAGGGAGAAA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.572G>C	2.37:g.233651899G>C	ENSP00000386537:p.Gly191Ala	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	92	16	NM_001103147	0	0	0	3	3	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.498686	0.64298	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000445650;ENST00000452341;ENST00000421778	T;T;T;T;T;T;T;T;T;T	0.78364	-0.69;-0.69;-0.69;-0.69;-1.02;-0.7;-0.69;-0.82;-1.17;-0.89	5.63	5.63	0.86233	.	0.192608	0.46442	D	0.000288	D	0.86247	0.5887	L	0.57536	1.79	0.36437	D	0.865276	D;D;P;D	0.76494	0.999;0.982;0.953;0.989	D;P;B;P	0.75484	0.986;0.898;0.371;0.874	D	0.84937	0.0863	10	0.29301	T	0.29	-24.5013	20.0345	0.97552	0.0:0.0:1.0:0.0	.	22;213;191;191	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	A	213;140;191;213;191;191;140;191;213;191;22;22;18	ENSP00000362667:G213A;ENSP00000362664:G191A;ENSP00000386765:G213A;ENSP00000386537:G191A;ENSP00000404195:G140A;ENSP00000387070:G191A;ENSP00000387170:G213A;ENSP00000410297:G191A;ENSP00000392218:G22A;ENSP00000411505:G22A	ENSP00000362664:G191A	G	+	2	0	GIGYF2	233360143	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.552000	0.67281	2.797000	0.96272	0.655000	0.94253	GGG	.		0.403	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		C	233651899	G	C	233651899	3	2	56	1	0	0	0	0	1	0	0	0	6398	1232	43	4	668	4	GIGYF2	2	233651899	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	51108851	233651899	9547474	7	5388											
NUP210	23225	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	13438880	13438880	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggagtccagggcctggatcTtcagctccaggggggagtcc	6	7	16	12	1	2	0	1	0	1	0	5	3	5	3	4	6	1	1	4	6	0	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:13438880T>C	ENST00000254508.5	-	3	495	c.413A>G	c.(412-414)aAg>aGg	p.K138R		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	138					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GGCCTGGATCTTCAGCTCCAG	0.602																																					p.K138R		.											.	NUP210-256	0			c.A413G						.						67	63	64					3																	13438880		2203	4300	6503	SO:0001583	missense	23225	exon3			TGGATCTTCAGCT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.413A>G	3.37:g.13438880T>C	ENSP00000254508:p.Lys138Arg	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	85	25	NM_024923	0	0	1	4	3	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	T	5.986	0.365927	0.11352	.	.	ENSG00000132182	ENST00000254508	T	0.04758	3.56	3.96	2.77	0.32553	.	0.049223	0.85682	D	0.000000	T	0.03608	0.0103	L	0.33137	0.985	0.43203	D	0.995057	B	0.31817	0.341	B	0.31245	0.126	T	0.39099	-0.9630	10	0.07325	T	0.83	-12.7074	9.9009	0.41346	0.0:0.0:0.172:0.8279	.	138	Q8TEM1	PO210_HUMAN	R	138	ENSP00000254508:K138R	ENSP00000254508:K138R	K	-	2	0	NUP210	13413880	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	2.196000	0.42686	0.680000	0.31366	0.454000	0.30748	AAG	.		0.602	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		C	13438880	T	C	13438880	3	2	56	1	0	0	0	0	1	0	0	0	10786	1609	56	3	5402	3	NUP210	3	13438880	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10		13438880	184583550	8	5389											
NME6	10201	broad.mit.edu	37	chr3	48336157	48336157	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctaggcctcctgttccagcTacatagtggacacctccctc	7	10	7	17	0	0	0	0	0	0	0	4	1	3	1	6	2	2	2	6	2	3	4	rs148416956		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:48336157T>C	ENST00000452211.1	-	7	768	c.531A>G	c.(529-531)gtA>gtG	p.V177V	NME6_ENST00000451657.1_Nonstop_Mutation_p.*164W|NME6_ENST00000421967.1_Silent_p.V185V|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000415644.1_Silent_p.V110V|NME6_ENST00000447314.1_Silent_p.V132V|NME6_ENST00000444069.1_5'UTR|NME6_ENST00000442597.1_Silent_p.V177V|NME6_ENST00000435684.1_Nonstop_Mutation_p.*164W|NME6_ENST00000415053.1_Silent_p.V177V|NME6_ENST00000450160.1_Nonstop_Mutation_p.*164W|NME6_ENST00000426689.2_Silent_p.V177V|NME6_ENST00000426723.1_Silent_p.V110V			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	177					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		CTGTTCCAGCTACATAGTGGA	0.537																																					p.V185V													.	NME6-115	0			c.A555G						.						106	96	99					3																	48336157		2203	4300	6503	SO:0001819	synonymous_variant	10201	exon6			TCCAGCTACATAG	AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113			20567	protein-coding gene	gene with protein product		608294	"non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)"			10453732, 19852809	Standard	NM_005793		Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000452211.1:c.531A>G	3.37:g.48336157T>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	124	3	NM_005793	0	0	12	12	0	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Silent	SNP	ENST00000452211.1	37		.	.	.	.	.	.	.	.	.	.	T	10.38	1.333284	0.24167	.	.	ENSG00000172113	ENST00000450160;ENST00000451657;ENST00000435684	.	.	.	4.24	-2.59	0.06209	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.1032	1.421	0.02312	0.1641:0.3655:0.1684:0.3019	.	.	.	.	W	164	.	.	X	-	2	0	NME6	48311161	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.893000	0.04127	-0.303000	0.08856	0.459000	0.35465	TAG	T|1.000;A|0.000		0.537	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793		C	48336157	T	C	48336157	2	2	56	1	0	0	0	0	0	0	0	1	10521	1509	53	3		3	NME6	3	48336157	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	34897277	48336157	149686273	9	5390											
RBM5	10181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50147868	50147868	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggccccagccgcttccccTactggtgtagttcctggtac	5	10	10	16	1	0	0	0	0	0	0	2	0	2	0	6	3	3	4	6	3	3	5			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:50147868T>C	ENST00000347869.3	+	16	1510	c.1335T>C	c.(1333-1335)ccT>ccC	p.P445P	RBM5_ENST00000441812.2_Intron	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	445	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCGCTTCCCCTACTGGTGTAG	0.458																																					p.P445P		.											.	RBM5-278	0			c.T1335C						.						54	58	56					3																	50147868		2203	4300	6503	SO:0001819	synonymous_variant	10181	exon16			TTCCCCTACTGGT	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.1335T>C	3.37:g.50147868T>C		Somatic	180	0		WXS	Illumina HiSeq	Phase_I	149	36	NM_005778	0	0	14	32	18	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			.		0.458	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		C	50147868	T	C	50147868	2	2	56	1	0	0	0	0	0	0	0	1	13175	1509	53	3		3	RBM5	3	50147868	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	1811711	50147868	147874562	10	5391											
GOLIM4	27333	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	167747034	167747034	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctctccttggattcccTggtcctctgctccctgaacg	3	14	7	17	1	2	1	0	1	2	0	7	2	6	2	5	2	2	1	5	2	1	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:167747034T>C	ENST00000470487.1	-	11	2179	c.1490A>G	c.(1489-1491)cAg>cGg	p.Q497R	GOLIM4_ENST00000309027.4_Missense_Mutation_p.Q469R	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	497	Gln-rich.|Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TTGGATTCCCTGGTCCTCTGC	0.383																																					p.Q497R		.											.	GOLIM4-291	0			c.A1490G						.						133	116	122					3																	167747034		2203	4300	6503	SO:0001583	missense	27333	exon11			ATTCCCTGGTCCT	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1490A>G	3.37:g.167747034T>C	ENSP00000417354:p.Gln497Arg	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	90	6	NM_014498	0	0	9	9	0		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305022	0.60305	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	4.97	4.97	0.65823	.	0.242984	0.44097	D	0.000487	T	0.69575	0.3126	M	0.74881	2.28	0.43029	D	0.994599	D;D	0.64830	0.994;0.989	D;P	0.67103	0.949;0.814	T	0.68405	-0.5417	9	0.09590	T	0.72	-18.1647	11.9183	0.52778	0.0:0.0:0.1451:0.8549	.	469;497	F8W785;O00461	.;GOLI4_HUMAN	R	497;469	.	ENSP00000309893:Q469R	Q	-	2	0	GOLIM4	169229728	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	4.279000	0.58953	1.884000	0.54569	0.449000	0.29647	CAG	.		0.383	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			C	167747034	T	C	167747034	3	2	56	1	0	0	0	0	1	0	0	0	6586	1580	55	3	624	3	GOLIM4	3	167747034	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	117599166	167747034	30275396	11	5392											
HTT	3064	broad.mit.edu	37	chr4	3123099	3123099	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgggggcattgggcagctcAccgctgctaaggaggagtct	7	8	16	10	2	2	0	1	0	1	0	3	2	2	2	1	5	2	5	1	5	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:3123099A>C	ENST00000355072.5	+	9	1358	c.1213A>C	c.(1213-1215)Acc>Ccc	p.T405P		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	405					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGGGCAGCTCACCGCTGCTAA	0.547																																					p.T405P													.	HTT-281	0			c.A1213C						.						63	65	65					4																	3123099		1951	4145	6096	SO:0001583	missense	3064	exon9			CAGCTCACCGCTG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1213A>C	4.37:g.3123099A>C	ENSP00000347184:p.Thr405Pro	Somatic	138	1		WXS	Illumina HiSeq	Phase_I	142	5	NM_002111	0	0	3	3	0	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.188909	0.38707	.	.	ENSG00000197386	ENST00000355072	T	0.05258	3.47	4.52	-9.03	0.00737	Armadillo-type fold (1);	0.764838	0.12277	N	0.483307	T	0.02533	0.0077	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33523	-0.9865	10	0.33141	T	0.24	.	0.7871	0.01051	0.2351:0.186:0.3049:0.2739	.	405	P42858	HD_HUMAN	P	405	ENSP00000347184:T405P	ENSP00000347184:T405P	T	+	1	0	HTT	3092897	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.501000	0.06398	-2.465000	0.00533	0.533000	0.62120	ACC	.		0.547	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		C	3123099	A	C	3123099	3	2	56	1	0	0	0	0	1	0	0	0	7478	159	6	5	1247	5	HTT	4	3123099	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10		3123099	188031177	12	5393											
EVC	2121	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	5754739	5754739	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggagctgctcacgcagcaGcacaaggccttctggcagga	10	5	14	12	1	2	0	1	0	1	0	2	3	2	2	1	4	4	6	1	4	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:5754739G>A	ENST00000264956.6	+	9	1459	c.1275G>A	c.(1273-1275)caG>caA	p.Q425Q	EVC_ENST00000382674.2_Silent_p.Q425Q|EVC_ENST00000509451.1_Silent_p.Q425Q	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	425					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TCACGCAGCAGCACAAGGCCT	0.692																																					p.Q425Q													.	EVC-92	0			c.G1275A						.						20	20	20					4																	5754739		2203	4297	6500	SO:0001819	synonymous_variant	2121	exon9			GCAGCAGCACAAG	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1275G>A	4.37:g.5754739G>A		Somatic	157	2		WXS	Illumina HiSeq	Phase_I	134	43	NM_153717	0	0	10	32	22		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			.		0.692	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			A	5754739	G	A	5754739	2	1	56	1	0	0	0	0	0	0	0	1	5298	962	34	2		2	EVC	4	5754739	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	2631640	5754739	185399537	13	5394											
KIAA0232	9778	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	6860177	6860177	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagattcacaaaaagttagaGgggtctccctctccagaggc	13	8	10	10	0	3	3	1	0	2	3	5	3	3	3	2	3	0	1	2	3	4	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:6860177G>A	ENST00000307659.5	+	6	917	c.462G>A	c.(460-462)gaG>gaA	p.E154E	KIAA0232_ENST00000425103.1_Silent_p.E154E	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	154							ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						AAAAGTTAGAGGGGTCTCCCT	0.328																																					p.E154E													.	KIAA0232-92	0			c.G462A						.						41	39	40					4																	6860177		1811	4075	5886	SO:0001819	synonymous_variant	9778	exon6			GTTAGAGGGGTCT	D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.462G>A	4.37:g.6860177G>A		Somatic	398	2		WXS	Illumina HiSeq	Phase_I	292	86	NM_014743	0	0	1	2	1	A7E2D2	Silent	SNP	ENST00000307659.5	37	CCDS43209.1																																																																																			.		0.328	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		A	6860177	G	A	6860177	2	1	56	1	0	0	0	0	0	0	0	1	8184	991	35	2		2	KIAA0232	4	6860177	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	1105438	6860177	184294099	14	5395											
APBB2	323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	40818110	40818110	+	Nonstop_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtccttttgcatgtgcagcTatggcatttcggtgacaggg	7	13	13	8	1	0	1	0	1	0	0	2	1	1	1	1	3	3	4	1	3	1	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:40818110T>A	ENST00000295974.8	-	18	2905	c.2276A>T	c.(2275-2277)tAg>tTg	p.*759L	APBB2_ENST00000504305.1_Nonstop_Mutation_p.*211L|RP11-632F7.3_ENST00000513127.1_RNA|APBB2_ENST00000506352.1_Nonstop_Mutation_p.*738L|APBB2_ENST00000508593.1_Nonstop_Mutation_p.*760L|APBB2_ENST00000513140.1_Nonstop_Mutation_p.*737L|APBB2_ENST00000543538.1_Nonstop_Mutation_p.*211L|APBB2_ENST00000502841.1_Nonstop_Mutation_p.*211L	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	0					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CATGTGCAGCTATGGCATTTC	0.458																																					p.X760L	Ovarian(3;20 75 16686 49997)	.											.	APBB2-92	0			c.A2279T						.						255	249	251					4																	40818110		1979	4157	6136	SO:0001578	stop_lost	323	exon18			TGCAGCTATGGCA	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.2276A>T	4.37:g.40818110T>A		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	99	22	NM_004307	0	0	4	6	2	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	37	CCDS54761.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614383	0.46631	.	.	ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000543538;ENST00000513140;ENST00000508593;ENST00000502841;ENST00000506352;ENST00000504305	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3812	0.74658	0.0:0.0:0.0:1.0	.	.	.	.	L	759;758;211;737;760;211;738;211	.	.	X	-	2	0	APBB2	40512867	1.000000	0.71417	0.936000	0.37596	0.073000	0.16967	8.000000	0.88501	2.040000	0.60383	0.477000	0.44152	TAG	.		0.458	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		A	40818110	T	A	40818110	4	1	56	1	0	0	0	0	0	0	0	0	761	1535	53	5	4	5	APBB2	4	40818110	Nonstop_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	33957933	40818110	150336166	15	5396											
FRYL	285527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48536646	48536646	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcaatatgactcaatagActataaataatctgtagtaa	18	12	6	5	0	3	2	2	1	1	1	3	2	3	2	0	1	0	2	0	1	10	7			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:48536646A>G	ENST00000503238.1	-	46	6620	c.6621T>C	c.(6619-6621)agT>agC	p.S2207S	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.S2207S|FRYL_ENST00000537810.1_Silent_p.S2207S|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	2207					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GACTCAATAGACTATAAATAA	0.333																																					p.S2207S		.											.	FRYL-69	0			c.T6621C						.						76	72	73					4																	48536646		1829	4086	5915	SO:0001819	synonymous_variant	285527	exon49			CAATAGACTATAA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.6621T>C	4.37:g.48536646A>G		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	67	10	NM_015030	0	0	4	4	0	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	A	0.350	-0.945182	0.02304	.	.	ENSG00000075539	ENST00000514617	T	0.12879	2.64	5.57	-1.09	0.09904	.	0.000000	0.85682	D	0.000000	T	0.18882	0.0453	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02844	-1.1103	7	0.35671	T	0.21	.	10.974	0.47454	0.529:0.0:0.471:0.0	.	.	.	.	P	1077	ENSP00000425344:S1077P	ENSP00000425344:S1077P	S	-	1	0	FRYL	48231403	1.000000	0.71417	0.766000	0.31476	0.006000	0.05464	1.028000	0.30128	0.032000	0.15435	-0.256000	0.11100	TCT	.		0.333	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			G	48536646	A	G	48536646	2	3	56	1	0	0	0	0	0	0	0	1	6083	272	10	3		3	FRYL	4	48536646	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	7718536	48536646	142617630	16	5397											
SMARCAD1	56916	broad.mit.edu	37	chr4	95204298	95204298	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tctaattgatgagtttaataCcgatatggatatctttgtgt	11	18	8	4	1	2	2	0	2	2	0	2	4	2	3	1	1	1	1	1	1	5	8			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:95204298C>G	ENST00000354268.4	+	22	2826	c.2753C>G	c.(2752-2754)aCc>aGc	p.T918S	SMARCAD1_ENST00000457823.2_Missense_Mutation_p.T920S|SMARCAD1_ENST00000509418.1_Missense_Mutation_p.T488S			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	918	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		GAGTTTAATACCGATATGGAT	0.289																																					p.T920S													.	SMARCAD1-229	0			c.C2759G						.						83	82	82					4																	95204298		2203	4300	6503	SO:0001583	missense	56916	exon22			TTAATACCGATAT	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.2753C>G	4.37:g.95204298C>G	ENSP00000346217:p.Thr918Ser	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	101	3	NM_001128429	0	0	5	5	0	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	C	7.713	0.695510	0.15106	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268;ENST00000509418	T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85	5.33	5.33	0.75918	Helicase, C-terminal (3);	0.000000	0.51477	D	0.000097	T	0.53142	0.1778	N	0.02802	-0.49	0.58432	D	0.999992	B;B	0.14012	0.009;0.007	B;B	0.16722	0.016;0.009	T	0.51560	-0.8690	10	0.14656	T	0.56	-9.5026	19.0231	0.92922	0.0:1.0:0.0:0.0	.	918;920	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	S	920;920;918;488	ENSP00000351947:T920S;ENSP00000415576:T920S;ENSP00000346217:T918S;ENSP00000423286:T488S	ENSP00000346217:T918S	T	+	2	0	SMARCAD1	95423321	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.835000	0.55805	2.493000	0.84123	0.591000	0.81541	ACC	.		0.289	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		G	95204298	C	G	95204298	3	3	56	1	0	0	0	0	1	0	0	0	14804	507	18	4	2841	4	SMARCAD1	4	95204298	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	46667652	95204298	95949978	17	5398											
BBS7	55212	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	122774226	122774226	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccacaatgtcaaagctgTcaatacacaaaataccttta	17	9	3	12	0	2	0	2	0	0	0	2	0	2	0	2	0	3	1	2	0	8	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:122774226T>A	ENST00000264499.4	-	8	917	c.734A>T	c.(733-735)gAc>gTc	p.D245V	BBS7_ENST00000506636.1_Missense_Mutation_p.D245V	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	245					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GTCAAAGCTGTCAATACACAA	0.333									Bardet-Biedl syndrome																												p.D245V													.	BBS7-91	0			c.A734T						.						115	100	105					4																	122774226		2203	4300	6503	SO:0001583	missense	55212	exon8	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AAGCTGTCAATAC	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.734A>T	4.37:g.122774226T>A	ENSP00000264499:p.Asp245Val	Somatic	215	1		WXS	Illumina HiSeq	Phase_I	193	58	NM_018190	0	0	3	5	2	Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	37	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169776	0.78452	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	D;D	0.91843	-2.92;-2.92	5.26	5.26	0.73747	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.89962	0.6867	L	0.52126	1.63	0.80722	D	1	B	0.32350	0.366	B	0.37091	0.241	D	0.87512	0.2440	10	0.22109	T	0.4	-16.8022	15.156	0.72743	0.0:0.0:0.0:1.0	.	245	Q8IWZ6	BBS7_HUMAN	V	245	ENSP00000264499:D245V;ENSP00000423626:D245V	ENSP00000264499:D245V	D	-	2	0	BBS7	122993676	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.777000	0.85628	1.990000	0.58119	0.477000	0.44152	GAC	.		0.333	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			A	122774226	T	A	122774226	3	1	56	1	0	0	0	0	1	0	0	0	1342	1667	58	5	1466	5	BBS7	4	122774226	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	27569928	122774226	68380050	18	5399											
PDLIM4	8572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131602211	131602211	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagcaaggctcaggcacaCaggatccacatcgatcctga	13	5	10	13	1	1	1	1	1	0	0	4	4	3	2	2	3	1	3	2	3	1	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:131602211C>T	ENST00000253754.3	+	3	364	c.300C>T	c.(298-300)caC>caT	p.H100H	PDLIM4_ENST00000379018.3_Silent_p.H100H|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	100							zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCAGGCACACAGGATCCACA	0.592																																					p.H100H		.											.	PDLIM4-91	0			c.C300T						.						93	69	77					5																	131602211		2203	4300	6503	SO:0001819	synonymous_variant	8572	exon3			GGCACACAGGATC	AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.300C>T	5.37:g.131602211C>T		Somatic	251	0		WXS	Illumina HiSeq	Phase_I	235	70	NM_003687	0	0	1	1	0	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Silent	SNP	ENST00000253754.3	37	CCDS4152.1																																																																																			.		0.592	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687		T	131602211	C	T	131602211	2	4	56	1	0	0	0	0	0	0	0	1	11708	477	17	2		2	PDLIM4	5	131602211	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		131602211	49313049	19	5400											
SLC22A4	6583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131647952	131647952	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgtgtccgggcagctgtcAgacaggtaagcacatgggag	9	8	15	9	2	1	1	1	0	0	1	3	2	2	2	1	3	2	4	1	3	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:131647952A>C	ENST00000200652.3	+	2	666	c.492A>C	c.(490-492)tcA>tcC	p.S164S	SLC22A4_ENST00000491257.1_3'UTR|AC034220.3_ENST00000417795.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	164					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	GGCAGCTGTCAGACAGGTAAG	0.572																																					p.S164S		.											.	SLC22A4-90	0			c.A492C						.						132	107	116					5																	131647952		2203	4300	6503	SO:0001819	synonymous_variant	6583	exon2			GCTGTCAGACAGG	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"Solute carriers"	10968	protein-coding gene	gene with protein product		604190	"solute carrier family 22 (organic cation/ergothioneine transporter), member 4"			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.492A>C	5.37:g.131647952A>C		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	56	18	NM_003059	0	0	0	0	0	O14546	Silent	SNP	ENST00000200652.3	37	CCDS4153.1																																																																																			.		0.572	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059		C	131647952	A	C	131647952	2	2	56	1	0	0	0	0	0	0	0	1	14488	175	7	5		5	SLC22A4	5	131647952	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	45741	131647952	49267308	20	5401											
TIFAB	140947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	134785315	134785315	+	5'Flank	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atctggatgcctgagaaggaGaccctgttgacggtgctcag	9	9	14	9	1	2	3	1	2	1	2	2	6	2	4	2	3	2	2	2	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:134785315G>C	ENST00000503143.2	-	0	0				CTB-138E5.1_ENST00000510230.1_RNA|TIFAB_ENST00000537858.1_Silent_p.V105V	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGAGAAGGAGACCCTGTTGA	0.577																																					p.V105V		.											.	TIFAB-22	0			c.C315G						.						101	104	103					5																	134785315		2082	4221	6303	SO:0001631	upstream_gene_variant	497189	exon2			GAAGGAGACCCTG																													5.37:g.134785315G>C	Exception_encountered	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	133	24	NM_001099221	0	0	0	0	0		Silent	SNP	ENST00000503143.2	37	CCDS4186.1																																																																																			.		0.577	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			C	134785315	G	C	134785315	1	2	56	0	1	0	0	0	0	0	0	0	15927	929	33	4		4	TIFAB	5	134785315	5'Flank	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	3137363	134785315	46129945	21	5402											
PCDHGA1	56114	broad.mit.edu	37	chr5	140710540	140710540	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagaccgggaggagctctgcGctcagagcatgccgtgtctc	7	8	14	12	3	3	2	1	0	2	2	4	4	3	4	2	2	4	3	2	2	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:140710540G>T	ENST00000517417.1	+	1	289	c.289G>T	c.(289-291)Gct>Tct	p.A97S	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.A97S	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	97	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A97S(2)		breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTCTGCGCTCAGAGCAT	0.473																																					p.A97S													.	PCDHGA1-137	2	Substitution - Missense(2)	kidney(2)	c.G289T						.						110	123	118					5																	140710540		2203	4300	6503	SO:0001583	missense	56114	exon1			CTCTGCGCTCAGA	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.289G>T	5.37:g.140710540G>T	ENSP00000431083:p.Ala97Ser	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	113	9	NM_018912	0	0	4	4	0	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	G	17.17	3.320750	0.60634	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.27402	1.67;1.67	4.37	3.49	0.39957	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.138694	0.32328	N	0.006242	T	0.37404	0.1002	M	0.79011	2.435	0.23813	N	0.99677	P;P	0.42010	0.726;0.768	B;B	0.43658	0.3;0.426	T	0.35375	-0.9791	10	0.59425	D	0.04	.	9.5567	0.39343	0.0857:0.1484:0.7659:0.0	.	97;97	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	S	97	ENSP00000431083:A97S;ENSP00000367345:A97S	ENSP00000367345:A97S	A	+	1	0	PCDHGA1	140690724	0.066000	0.20996	1.000000	0.80357	0.686000	0.39977	2.217000	0.42880	2.432000	0.82394	0.655000	0.94253	GCT	.		0.473	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		T	140710540	G	T	140710540	3	4	56	1	0	0	0	0	1	0	0	0	11576	1087	38	4	291	4	PCDHGA1	5	140710540	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	5925225	140710540	40204720	22	5403											
GABRA6	2559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	161116041	161116041	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actgagattctgagtctgaaTaatttgatggtcagtaaaat	14	14	9	4	0	3	4	1	4	2	1	3	5	3	4	0	1	0	1	0	1	4	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:161116041T>C	ENST00000274545.5	+	4	745	c.312T>C	c.(310-312)aaT>aaC	p.N104N	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Silent_p.N94N			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	104					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TGAGTCTGAATAATTTGATGG	0.403										TCGA Ovarian(5;0.080)																											p.N104N		.											.	GABRA6-163	0			c.T312C						.						76	77	77					5																	161116041		2203	4299	6502	SO:0001819	synonymous_variant	2559	exon4			TCTGAATAATTTG		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4080	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 6"	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.312T>C	5.37:g.161116041T>C		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	85	17	NM_000811	0	0	0	0	0	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	37	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	T	8.919	0.960604	0.18583	.	.	ENSG00000145863	ENST00000520000	.	.	.	5.65	2.01	0.26516	.	.	.	.	.	T	0.54581	0.1867	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	.	6.8819	0.24179	0.0:0.4395:0.0:0.5605	.	.	.	.	T	44	.	.	I	+	2	0	GABRA6	161048619	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.646000	0.46630	0.507000	0.28148	-0.274000	0.10170	ATA	.		0.403	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			C	161116041	T	C	161116041	2	2	56	1	0	0	0	0	0	0	0	1	6184	1403	49	3		3	GABRA6	5	161116041	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	20405501	161116041	19799219	23	5404											
DTNBP1	84062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	15523339	15523339	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaccctcactgatgtccCgggtggccgagtcggtgcag	5	7	13	16	3	1	1	1	1	0	0	3	2	2	1	5	3	1	1	5	3	0	0	rs374085686		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:15523339C>G	ENST00000344537.5	-	10	1095	c.923G>C	c.(922-924)cGg>cCg	p.R308P	DTNBP1_ENST00000462989.2_Missense_Mutation_p.R152P|DTNBP1_ENST00000355917.3_Missense_Mutation_p.R309P	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	308	Dysbindin.				actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			ACTGATGTCCCGGGTGGCCGA	0.567									Hermansky-Pudlak syndrome																												p.R308P		.											.	DTNBP1-90	0			c.G923C						.						137	142	141					6																	15523339		2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	ATGTCCCGGGTGG	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"Biogenesis of lysosomal organelles complex-1 subunits"	17328	protein-coding gene	gene with protein product	"dysbindin-1", "biogenesis of lysosomal organelles complex-1, subunit 8"	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.923G>C	6.37:g.15523339C>G	ENSP00000341680:p.Arg308Pro	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	197	32	NM_032122	0	0	13	29	16	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	37	CCDS4534.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.710179	0.30322	.	.	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.62	-7.93	0.01156	.	1.163890	0.06365	N	0.712440	T	0.01558	0.0050	N	0.01297	-0.9	0.19300	N	0.999978	B	0.02656	0.0	B	0.08055	0.003	T	0.27331	-1.0077	10	0.08179	T	0.78	-9.2314	4.2873	0.10862	0.0902:0.1668:0.4361:0.307	.	308	Q96EV8	DTBP1_HUMAN	P	308;152;309;227;125	ENSP00000341680:R308P;ENSP00000427239:R152P;ENSP00000348183:R309P;ENSP00000421797:R125P	ENSP00000341680:R308P	R	-	2	0	DTNBP1	15631318	0.501000	0.26099	0.000000	0.03702	0.022000	0.10575	0.142000	0.16096	-2.293000	0.00664	-0.254000	0.11334	CGG	.		0.567	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122		G	15523339	C	G	15523339	3	3	56	1	0	0	0	0	1	0	0	0	4801	652	23	4	136	4	DTNBP1	6	15523339	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		15523339	155591728	24	5405											
ACOT13	55856	broad.mit.edu;bcgsc.ca	37	chr6	24701750	24701750	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacatgttctgaagcaaggAaaaacacttgcatttacctc	14	10	7	10	0	1	1	0	1	1	0	2	2	1	2	1	1	4	4	1	1	5	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:24701750A>T	ENST00000230048.4	+	3	523	c.330A>T	c.(328-330)ggA>ggT	p.G110G	ACOT13_ENST00000537591.1_Silent_p.G87G|RP1-30M3.5_ENST00000607014.1_RNA|ACOT13_ENST00000476436.1_3'UTR	NM_018473.3	NP_060943.1	Q9NPJ3	ACO13_HUMAN	acyl-CoA thioesterase 13	110					metabolic process (GO:0008152)|protein homotetramerization (GO:0051289)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA hydrolase activity (GO:0047617)			large_intestine(1)	1						TGAAGCAAGGAAAAACACTTG	0.378																																					p.G110G													.	ACOT13-90	0			c.A330T						.						155	153	154					6																	24701750		2203	4300	6503	SO:0001819	synonymous_variant	55856	exon3			GCAAGGAAAAACA	AF220186	CCDS4558.1, CCDS54972.1	6p22.1	2009-11-20	2009-05-05	2009-05-05	ENSG00000112304	ENSG00000112304		"Acyl CoA thioesterases"	20999	protein-coding gene	gene with protein product		615652	"thioesterase superfamily member 2"	THEM2		16934754, 19405909	Standard	NM_018473		Approved	HT012	uc003nek.3	Q9NPJ3	OTTHUMG00000014359	ENST00000230048.4:c.330A>T	6.37:g.24701750A>T		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	213	8	NM_018473	0	0	48	48	0	F5H2L4|O95549	Silent	SNP	ENST00000230048.4	37	CCDS4558.1																																																																																			.		0.378	ACOT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040010.2	NM_018473		T	24701750	A	T	24701750	2	4	56	1	0	0	0	0	0	0	0	1	151	233	9	5		5	ACOT13	6	24701750	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	9178411	24701750	146413317	25	5406											
HIST1H2AL	8332	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	27833355	27833357	+	In_Frame_Del	DEL	AAG	AAG	-																															gcaacgccgcccgcgacaacAagaagacccgcattatcccg																								rs376667817		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:27833355_27833357delAAG	ENST00000357320.2	+	1	322_324	c.223_225delAAG	c.(223-225)aagdel	p.K76del		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	76						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						CCGCGACAACAAGAAGACCCGCA	0.665																																					p.75_75del		.											.	HIST1H2AL-68	0			c.223_225del						.																																			SO:0001651	inframe_deletion	8332	exon1			.	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"Histones / Replication-dependent"	4730	protein-coding gene	gene with protein product		602793	"H2A histone family, member I", "histone 1, H2al"	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.223_225delAAG	6.37:g.27833358_27833360delAAG	ENSP00000349873:p.Lys76del	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	217	47	NM_003511	0	0	0	0	0	P02261|Q2M1R2|Q76PA6	In_Frame_Del	DEL	ENST00000357320.2	37	CCDS4634.1																																																																																			.		0.665	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511		-	27833357	AAG	-	27833355	7	5	56	1	0	1	0	1	0	0	0	0	7159	131	5	0	225	0	HIST1H2AL	6	27833355	In_Frame_Del	DEL	AAG	TCGA-B9-A5W8-01A-11D-A28G-10	3131605	27833355	143281712	26	5407											
HIST1H3J	8356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	27858516	27858516	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccttggtggccagctgctTccgcggtgccttgccgccgg	1	10	15	15	4	0	0	0	0	0	0	1	0	1	0	6	4	5	2	6	4	0	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:27858516T>G	ENST00000359303.2	-	1	54	c.55A>C	c.(55-57)Aag>Cag	p.K19Q	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	19					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GCCAGCTGCTTCCGCGGTGCC	0.617																																					p.K19Q		.											.	HIST1H3J-69	0			c.A55C						.						29	33	31					6																	27858516		2203	4299	6502	SO:0001583	missense	8356	exon1			GCTGCTTCCGCGG	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"Histones / Replication-dependent"	4774	protein-coding gene	gene with protein product		602817	"H3 histone family, member J", "histone 1, H3j"	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.55A>C	6.37:g.27858516T>G	ENSP00000352252:p.Lys19Gln	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	89	25	NM_003535	0	0	0	0	0	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000359303.2	37	CCDS4638.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572970	0.45798	.	.	ENSG00000197153	ENST00000359303	T	0.48522	0.81	4.06	4.06	0.47325	.	.	.	.	.	T	0.52224	0.1721	.	.	.	0.42070	D	0.991202	.	.	.	.	.	.	T	0.59316	-0.7477	6	0.87932	D	0	.	12.8321	0.57752	0.0:0.0:0.0:1.0	.	.	.	.	Q	19	ENSP00000352252:K19Q	ENSP00000352252:K19Q	K	-	1	0	HIST1H3J	27966495	1.000000	0.71417	0.997000	0.53966	0.747000	0.42532	7.496000	0.81526	2.071000	0.62044	0.533000	0.62120	AAG	.		0.617	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535		G	27858516	T	G	27858516	3	3	56	1	0	0	0	0	1	0	0	0	7185	1792	62	5	359	5	HIST1H3J	6	27858516	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	25161	27858516	143256551	27	5408											
DNAH8	1769	broad.mit.edu	37	chr6	38875811	38875811	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaagagggagctacctcGccatcctcctacctttgata	10	10	9	12	1	0	3	0	2	0	1	3	5	2	4	5	1	3	1	5	1	4	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:38875811G>A	ENST00000359357.3	+	62	9031	c.8777G>A	c.(8776-8778)cGc>cAc	p.R2926H	DNAH8_ENST00000441566.1_Missense_Mutation_p.R2890H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R3143H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2926	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GAGCTACCTCGCCATCCTCCT	0.383																																					p.R3143H													.	DNAH8-615	0			c.G9428A						.						121	116	118					6																	38875811		2203	4300	6503	SO:0001583	missense	1769	exon64			TACCTCGCCATCC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.8777G>A	6.37:g.38875811G>A	ENSP00000352312:p.Arg2926His	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	80	4	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	21.8	4.202583	0.79127	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.26223	1.77;1.77;1.75	5.74	4.88	0.63580	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	M	0.84773	2.715	0.58432	D	0.999998	D	0.89917	1.0	D	0.79784	0.993	T	0.54323	-0.8311	10	0.51188	T	0.08	.	14.9621	0.71164	0.0685:0.0:0.9315:0.0	.	2926	Q96JB1	DYH8_HUMAN	H	3131;3131;2926;2890	ENSP00000333363:R3131H;ENSP00000352312:R2926H;ENSP00000402294:R2890H	ENSP00000333363:R3131H	R	+	2	0	DNAH8	38983789	1.000000	0.71417	0.967000	0.41034	0.733000	0.41908	7.863000	0.87023	1.431000	0.47355	0.650000	0.86243	CGC	.		0.383	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38875811	G	A	38875811	3	1	56	1	0	0	0	0	1	0	0	0	4618	1087	38	1	9015	1	DNAH8	6	38875811	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	11017295	38875811	132239256	28	5409											
ENPP1	5167	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	132171207	132171207	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcctgtgttgagcttggaAactgctgtttagattaccag	8	14	11	8	0	0	2	0	1	0	1	0	3	0	3	2	1	5	4	2	1	3	5			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:132171207A>C	ENST00000360971.2	+	3	411	c.391A>C	c.(391-393)Aac>Cac	p.N131H		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	131	SMB 1. {ECO:0000255|PROSITE- ProRule:PRU00350}.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	TGAGCTTGGAAACTGCTGTTT	0.423																																					p.N131H	Colon(104;336 1535 5856 11019 33782)												.	ENPP1-95	0			c.A391C						.						157	145	149					6																	132171207		2203	4300	6503	SO:0001583	missense	5167	exon3			CTTGGAAACTGCT	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.391A>C	6.37:g.132171207A>C	ENSP00000354238:p.Asn131His	Somatic	203	1		WXS	Illumina HiSeq	Phase_I	158	48	NM_006208	0	0	0	0	0	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	37	CCDS5150.2	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210856	0.79240	.	.	ENSG00000197594	ENST00000360971	T	0.46451	0.87	5.53	5.53	0.82687	Somatomedin B domain (4);Somatomedin B, chordata (1);	0.063724	0.64402	D	0.000008	T	0.61198	0.2328	M	0.82823	2.61	0.49130	D	0.999752	D	0.89917	1.0	D	0.83275	0.996	T	0.68428	-0.5411	10	0.87932	D	0	-26.8529	14.9356	0.70951	1.0:0.0:0.0:0.0	.	131	P22413	ENPP1_HUMAN	H	131	ENSP00000354238:N131H	ENSP00000354238:N131H	N	+	1	0	ENPP1	132212900	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.000000	0.70678	2.227000	0.72691	0.528000	0.53228	AAC	.		0.423	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			C	132171207	A	C	132171207	3	2	56	1	0	0	0	0	1	0	0	0	5142	14	1	5	401	5	ENPP1	6	132171207	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	93295396	132171207	38943860	29	5410											
MICALL2	79778	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	1477990	1477990	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccggggacaagggtctccCtggagaaggagcagggtgag	9	4	20	8	1	1	2	0	1	1	1	2	5	1	4	2	7	1	1	2	7	2	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:1477990C>G	ENST00000297508.7	-	11	2298		c.e11-1		MICALL2_ENST00000471899.1_Splice_Site|MICALL2_ENST00000405088.4_Splice_Site	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2						actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		AAGGGTCTCCCTGGAGAAGGA	0.672																																					.													.	MICALL2-90	0			c.2123-1G>C						.						32	21	24					7																	1477990		2186	4293	6479	SO:0001630	splice_region_variant	79778	exon12			GTCTCCCTGGAGA	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"junctional Rab13-binding protein"					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2123-1G>C	7.37:g.1477990C>G		Somatic	192	2		WXS	Illumina HiSeq	Phase_I	160	36	NM_182924	0	0	1	4	3	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Splice_Site	SNP	ENST00000297508.7	37	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	C	5.718	0.316910	0.10845	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	.	.	.	3.43	2.49	0.30216	.	.	.	.	.	.	.	.	.	.	.	0.28847	N	0.896255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.9901	0.36019	0.2221:0.7778:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MICALL2	1444516	0.309000	0.24518	0.059000	0.19551	0.370000	0.29829	1.806000	0.38892	0.728000	0.32382	0.455000	0.32223	.	.		0.672	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	Intron	G	1477990	C	G	1477990	5	3	56	1	0	0	0	0	0	0	1	0	9599	695	24	4	620	4	MICALL2	7	1477990	Splice_Site	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		1477990	157660673	30	5411											
CBLL1	79872	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107398636	107398636	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagtgtacacgaggttctctCttcatgtgtagcattgttca	8	15	9	9	1	4	0	2	0	2	0	5	1	4	0	0	1	2	5	0	1	2	6			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:107398636C>T	ENST00000440859.3	+	6	956	c.489C>T	c.(487-489)ctC>ctT	p.L163L	CBLL1_ENST00000222597.2_Silent_p.L162L|CBLL1_ENST00000415884.2_3'UTR	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	163	HYB domain. {ECO:0000250}.				negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						GAGGTTCTCTCTTCATGTGTA	0.398																																					p.L163L													.	CBLL1-229	0			c.C489T						.						112	99	104					7																	107398636		2203	4300	6503	SO:0001819	synonymous_variant	79872	exon6			TTCTCTCTTCATG	AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879		"RING-type (C3HC4) zinc fingers"	21225	protein-coding gene	gene with protein product	"Casitas B-lineage lymphoma-like"	606872	"Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1"			11836526, 11944035	Standard	NM_001284291		Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000440859.3:c.489C>T	7.37:g.107398636C>T		Somatic	143	1		WXS	Illumina HiSeq	Phase_I	152	33	NM_024814	0	0	5	9	4	B7ZM03|Q8TAJ4|Q9H5S6	Silent	SNP	ENST00000440859.3	37	CCDS5747.1																																																																																			.		0.398	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	NM_024814		T	107398636	C	T	107398636	2	4	56	1	0	0	0	0	0	0	0	1	2709	900	32	2		2	CBLL1	7	107398636	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	105920646	107398636	51740027	31	5412											
DNAJB9	4189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	108212287	108212287	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccaaaatcggcatcagaGcgccaaatcaagaaggcctt	14	6	10	11	2	2	2	2	0	0	2	3	2	2	2	3	2	2	1	3	2	5	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:108212287G>A	ENST00000249356.3	+	2	663	c.117G>A	c.(115-117)gaG>gaA	p.E39E	THAP5_ENST00000438865.1_5'Flank|THAP5_ENST00000493722.1_5'Flank|THAP5_ENST00000415914.3_5'Flank|DNAJB9_ENST00000465725.1_3'UTR|THAP5_ENST00000313516.5_5'Flank	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	39	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						CGGCATCAGAGCGCCAAATCA	0.403																																					p.E39E		.											.	DNAJB9-226	0			c.G117A						.						107	116	113					7																	108212287		2203	4300	6503	SO:0001819	synonymous_variant	4189	exon2			ATCAGAGCGCCAA	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"Heat shock proteins / DNAJ (HSP40)"	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.117G>A	7.37:g.108212287G>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	137	43	NM_012328	0	0	14	29	15		Silent	SNP	ENST00000249356.3	37	CCDS5752.1																																																																																			.		0.403	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			A	108212287	G	A	108212287	2	1	56	1	0	0	0	0	0	0	0	1	4638	962	34	2		2	DNAJB9	7	108212287	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	813651	108212287	50926376	32	5413											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	151859497	151859497	+	Frame_Shift_Del	DEL	T	T	-																															ggcaggactctgtctcagccTtttccagttttatctcttct																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:151859497delT	ENST00000262189.6	-	43	11383	c.11165delA	c.(11164-11166)aagfs	p.K3722fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K3722fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3722					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGTCTCAGCCTTTTCCAGTTT	0.468																																					p.K3722fs		.											.	MLL3-1398	0			c.11165delA						.						178	182	181					7																	151859497		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon43			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11165delA	7.37:g.151859497delT	ENSP00000262189:p.Lys3722fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	80	23	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151859497	T	-	151859497	7	5	56	1	0	1	0	1	0	0	0	0	9647	1609	56	0	3638	0	MLL3	7	151859497	Frame_Shift_Del	DEL	T	TCGA-B9-A5W8-01A-11D-A28G-10	43647210	151859497	7279166	33	5414											
DLGAP2	9228	broad.mit.edu	37	chr8	1497770	1497770	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaggccaaggaggcctaccGcaagagctcgctgaacctgg	10	4	13	14	2	0	2	0	1	0	1	1	3	0	3	5	4	3	3	5	4	4	1	rs370050230		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:1497770G>A	ENST00000421627.2	+	2	1045	c.911G>A	c.(910-912)cGc>cAc	p.R304H		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	383					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GAGGCCTACCGCAAGAGCTCG	0.672																																					p.R304H													.	DLGAP2-22	0			c.G911A						.						9	10	10					8																	1497770		2127	4234	6361	SO:0001583	missense	9228	exon2			CCTACCGCAAGAG	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.911G>A	8.37:g.1497770G>A	ENSP00000400258:p.Arg304His	Somatic	151	2		WXS	Illumina HiSeq	Phase_I	151	5	NM_004745	0	0	0	0	0	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.213135|5.213135	0.95069|0.95069	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000520901|ENST00000356067;ENST00000421627	.|T	.|0.14022	.|2.54	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.39358|0.39358	0.1075|0.1075	M|M	0.70275|0.70275	2.135|2.135	0.53005|0.53005	D|D	0.999967|0.999967	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.994	T|T	0.11036|0.11036	-1.0604|-1.0604	5|10	.|0.51188	.|T	.|0.08	-16.7352|-16.7352	18.9482|18.9482	0.92630|0.92630	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|383;383	.|Q9P1A6-2;Q9P1A6	.|.;DLGP2_HUMAN	T|H	321|349;304	.|ENSP00000400258:R304H	.|ENSP00000348366:R349H	A|R	+|+	1|2	0|0	DLGAP2|DLGAP2	1485177|1485177	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.085000|7.085000	0.76875|0.76875	2.463000|2.463000	0.83235|0.83235	0.655000|0.655000	0.94253|0.94253	GCA|CGC	.		0.672	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1497770	G	A	1497770	3	1	56	1	0	0	0	0	1	0	0	0	4571	1087	38	1	913	1	DLGAP2	8	1497770	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		1497770	144866252	34	5415											
NEFM	4741	broad.mit.edu	37	chr8	24771576	24771576	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacggcggctccggaccCggcggcgactacaagctgtc	7	5	13	16	6	1	0	1	0	0	0	3	2	2	1	2	5	3	2	2	5	3	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:24771576C>T	ENST00000221166.5	+	1	1052	c.270C>T	c.(268-270)ccC>ccT	p.P90P	NEFM_ENST00000437366.2_Silent_p.P90P|NEFM_ENST00000518131.1_Silent_p.P90P|GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000521540.1_3'UTR|RP11-624C23.1_ENST00000519689.1_RNA|NEFM_ENST00000433454.2_5'Flank			P07197	NFM_HUMAN	neurofilament, medium polypeptide	90	Head.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		GCTCCGGACCCGGCGGCGACT	0.657																																					p.P90P													.	NEFM-577	0			c.C270T						.						16	19	18					8																	24771576		2179	4255	6434	SO:0001819	synonymous_variant	4741	exon1			CGGACCCGGCGGC	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"Intermediate filaments type IV"	7734	protein-coding gene	gene with protein product		162250	"neurofilament, medium polypeptide 150kDa"	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.270C>T	8.37:g.24771576C>T		Somatic	118	1		WXS	Illumina HiSeq	Phase_I	144	4	NM_005382	0	0	0	0	0	B4DGN2|E9PBF7|Q4QRK6	Silent	SNP	ENST00000221166.5	37	CCDS6046.1																																																																																			.		0.657	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		T	24771576	C	T	24771576	2	4	56	1	0	0	0	0	0	0	0	1	10342	639	23	1		1	NEFM	8	24771576	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	23273806	24771576	121592446	35	5416											
FAM83H	286077	hgsc.bcm.edu	37	chr8	144809730	144809730	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaccttggtggggaaggctGctgggacgcggaaggccgag	7	5	21	8	3	0	0	0	0	0	0	0	5	0	4	2	8	1	2	2	8	2	1	rs367877690	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:144809730G>C	ENST00000388913.3	-	5	2026	c.1901C>G	c.(1900-1902)gCa>gGa	p.A634G		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	634					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GGGGAAGGCTGCTGGGACGCG	0.751													G|||	5	0.000998403	0.0038	0	5008	,	,		9374	0		0	False		,,,				2504	0				p.A634G		.											.	FAM83H-92	0			c.C1901G						.	G	GLY/ALA	5,3093		0,5,1544	6	8	7		1901	0.6	0	8		7	0,7130		0,0,3565	no	missense	FAM83H	NM_198488.3	60	0,5,5109	CC,CG,GG		0.0,0.1614,0.0489	benign	634/1180	144809730	5,10223	1549	3565	5114	SO:0001583	missense	286077	exon5			AAGGCTGCTGGGA	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1901C>G	8.37:g.144809730G>C	ENSP00000373565:p.Ala634Gly	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_198488	0	0	0	3	3	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	0.018	-1.474564	0.01044	0.001614	0.0	ENSG00000180921	ENST00000388913	T	0.14516	2.5	3.85	0.608	0.17569	.	16.316900	0.01476	U	0.016496	T	0.08980	0.0222	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27054	-1.0085	10	0.20519	T	0.43	.	5.3436	0.15996	0.2787:0.3057:0.4156:0.0	.	634	Q6ZRV2	FA83H_HUMAN	G	634	ENSP00000373565:A634G	ENSP00000373565:A634G	A	-	2	0	FAM83H	144881718	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	0.100000	0.15231	0.258000	0.21686	0.561000	0.74099	GCA	.		0.751	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		C	144809730	G	C	144809730	3	2	56	1	0	0	0	0	1	0	0	0	5659	1319	46	4	1642	4	FAM83H	8	144809730	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	120038154	144809730	1554292	36	5417											
PLEC	5339	hgsc.bcm.edu	37	chr8	145001217	145001217	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggccaccggctcaagctgCgccttgtacgtcaccagctg	7	7	12	15	3	2	0	2	0	0	0	2	1	2	0	4	2	4	4	4	2	2	2	rs374669316		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:145001217C>T	ENST00000322810.4	-	29	4453	c.4284G>A	c.(4282-4284)gcG>gcA	p.A1428A	PLEC_ENST00000527096.1_Silent_p.A1314A|PLEC_ENST00000354958.2_Silent_p.A1269A|PLEC_ENST00000398774.2_Silent_p.A1259A|PLEC_ENST00000357649.2_Silent_p.A1295A|PLEC_ENST00000345136.3_Silent_p.A1291A|PLEC_ENST00000354589.3_Silent_p.A1291A|PLEC_ENST00000356346.3_Silent_p.A1277A|PLEC_ENST00000436759.2_Silent_p.A1318A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1428	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCTCAAGCTGCGCCTTGTACG	0.637																																					p.A1428A		.											.	PLEC-141	0			c.G4284A						.	C	,,,,,,,	1,4183		0,1,2091	58	63	62		3954,3831,3807,4284,3777,3873,3885,3873	-9.9	0.3	8		62	0,8434		0,0,4217	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	0,1,6308	TT,TC,CC		0.0,0.0239,0.0079	,,,,,,,	1318/4575,1277/4534,1269/4526,1428/4685,1259/4516,1291/4548,1295/4552,1291/4548	145001217	1,12617	2092	4217	6309	SO:0001819	synonymous_variant	5339	exon29			AAGCTGCGCCTTG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4284G>A	8.37:g.145001217C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	69	4	NM_201380	0	0	20	20	0	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	145001217	C	T	145001217	2	4	56	1	0	0	0	0	0	0	0	1	12078	755	27	1		1	PLEC	8	145001217	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	191487	145001217	1362805	37	5418											
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971184	21971184	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcagcagctccgccacTcgggcgctgcccatcatcat	8	6	10	17	3	2	0	2	0	0	0	4	0	3	0	3	1	5	5	3	1	0	0	rs201208890	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:21971184T>G	ENST00000304494.5	-	2	444	c.174A>C	c.(172-174)cgA>cgC	p.R58R	CDKN2A_ENST00000578845.2_Silent_p.R7R|CDKN2A_ENST00000361570.3_Missense_Mutation_p.S114R|CDKN2A_ENST00000494262.1_Silent_p.R7R|CDKN2A_ENST00000446177.1_Silent_p.R58R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000497750.1_Silent_p.R7R|CDKN2A_ENST00000530628.2_Missense_Mutation_p.S73R|CDKN2A_ENST00000498628.2_Silent_p.R7R|CDKN2A_ENST00000498124.1_Silent_p.R58R|CDKN2A_ENST00000579122.1_Silent_p.R58R|CDKN2A_ENST00000479692.2_Silent_p.R7R|CDKN2A_ENST00000579755.1_Missense_Mutation_p.S73R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	58			R -> Q (in dbSNP:rs36204273).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(45)|p.M53_R58del(3)|p.R58fs*59(2)|p.V59fs*82(2)|p.0(1)|p.V28_V51del(1)|p.V59fs*63(1)|p.V59fs*61(1)|p.V59fs*60(1)|p.G55fs*86(1)|p.A57fs*85(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCTCCGCCACTCGGGCGCTGC	0.682		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			G|||	15	0.00299521	0.0113	0	5008	,	,		11788	0		0	False		,,,				2504	0				p.S73R		.											.	CDKN2A-23992	1374	Whole gene deletion(1316)|Unknown(45)|Deletion - Frameshift(7)|Deletion - In frame(4)|Insertion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(285)|skin(176)|central_nervous_system(167)|lung(145)|urinary_tract(92)|bone(74)|soft_tissue(57)|upper_aerodigestive_tract(55)|oesophagus(52)|pleura(51)|ovary(37)|kidney(32)|breast(32)|pancreas(30)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.A217C						.	G	,,,ARG/SER	25,4025		0,25,2000	7	9	8		174,174,,217	-4.5	0	9		8	0,8162		0,0,4081	no	coding-synonymous,coding-synonymous,utr-3,missense	CDKN2A	NM_000077.4,NM_001195132.1,NM_058197.4,NM_058195.3	,,,110	0,25,6081	GG,GT,TT		0.0,0.6173,0.2047	,,,benign	58/157,58/168,,73/133	21971184	25,12187	2025	4081	6106	SO:0001819	synonymous_variant	1029	exon2			CGCCACTCGGGCG	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.174A>C	9.37:g.21971184T>G		Somatic	4	2		WXS	Illumina HiSeq	Phase_I	34	18	NM_058195	0	0	0	0	0	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	37	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	G	6.483	0.457206	0.12342	0.006173	0.0	ENSG00000147889	ENST00000361570;ENST00000530628	T;T	0.76186	-1.0;-0.95	5.79	-4.48	0.03515	.	0.576553	0.14595	N	0.309984	T	0.41789	0.1174	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22941	-1.0202	8	.	.	.	-3.0019	5.0452	0.14480	0.1174:0.1641:0.1404:0.5781	.	114	Q8N726	CD2A2_HUMAN	R	114;73	ENSP00000355153:S114R;ENSP00000432664:S73R	.	S	-	1	0	CDKN2A	21961184	0.000000	0.05858	0.001000	0.08648	0.194000	0.23727	-2.443000	0.01013	-1.206000	0.02641	-2.190000	0.00312	AGT	.		0.682	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		G	21971184	T	G	21971184	2	3	56	1	0	0	0	0	0	0	0	1	3167	1551	54	5		5	CDKN2A	9	21971184	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10		21971184	119242247	38	5419											
HRCT1	646962	broad.mit.edu	37	chr9	35906600	35906601	+	Frame_Shift_Ins	INS	-	-	A																															cctccaccaccaccaccaccINScccaccgccaccatccccgc																								rs565823201|rs112212538		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:35906600_35906601insA	ENST00000354323.2	+	1	412_413	c.316_317insA	c.(316-318)cccfs	p.P106fs	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	106	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						ccaccaccacccccaccgccac	0.673																																					p.P106fs													.	HRCT1-22	0			c.316_317insA						.																																			SO:0001589	frameshift_variant	646962	exon1			CACCACCCCCACC		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	Exception_encountered	9.37:g.35906600_35906601insA	ENSP00000346283:p.Pro106fs	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_001039792	0	0	0	0	0	B7ZBJ1	Frame_Shift_Ins	INS	ENST00000354323.2	37	CCDS35012.1																																																																																			.		0.673	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		A	35906601	-	A	35906600	7	5	56	1	0	1	1	0	0	0	0	0	7374	623	22	0	318	0	HRCT1	9	35906600	Frame_Shift_Ins	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	13935416	35906600	105306831	39	5420	60	2									
HRCT1	646962	broad.mit.edu	37	chr9	35906601	35906602	+	Frame_Shift_Ins	INS	-	-	CA																															ctccaccaccaccaccacccINSccaccgccaccatccccgcc																								rs565823201|rs112212538		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:35906601_35906602insCA	ENST00000354323.2	+	1	413_414	c.317_318insCA	c.(316-321)ccccacfs	p.H107fs	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	107	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						caccaccacccccaccgccacc	0.678																																					p.P106fs													.	HRCT1-22	0			c.317_318insCA						.																																			SO:0001589	frameshift_variant	646962	exon1			ACCACCCCCACCG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	Exception_encountered	9.37:g.35906601_35906602insCA	ENSP00000346283:p.His107fs	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_001039792	0	0	0	0	0	B7ZBJ1	Frame_Shift_Ins	INS	ENST00000354323.2	37	CCDS35012.1																																																																																			.		0.678	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		CA	35906602	-	CA	35906601	7	5	56	1	0	1	1	0	0	0	0	0	7374	623	22	0	319	0	HRCT1	9	35906601	Frame_Shift_Ins	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	1	35906601	105306830	40	5421	60	2									
PIP5K1B	8395	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	71509346	71509346	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatatcaggattgtggtgaTgaacaacgttttgccacgct	11	13	10	7	2	1	2	1	2	0	0	1	3	1	3	1	2	3	2	1	2	4	5			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:71509346T>C	ENST00000265382.3	+	8	868	c.563T>C	c.(562-564)aTg>aCg	p.M188T	PIP5K1B_ENST00000541509.1_Missense_Mutation_p.M188T	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	188	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		ATTGTGGTGATGAACAACGTT	0.403																																					p.M188T													.	PIP5K1B-240	0			c.T563C						.						98	88	91					9																	71509346		2203	4300	6503	SO:0001583	missense	8395	exon8			TGGTGATGAACAA	U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.563T>C	9.37:g.71509346T>C	ENSP00000265382:p.Met188Thr	Somatic	227	2		WXS	Illumina HiSeq	Phase_I	216	53	NM_003558	0	0	1	4	3	A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Missense_Mutation	SNP	ENST00000265382.3	37	CCDS6624.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370255	0.82573	.	.	ENSG00000107242	ENST00000541509;ENST00000377290;ENST00000265382;ENST00000419747	T;T	0.43294	0.95;0.95	5.82	5.82	0.92795	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.89904	3.07	0.80722	D	1	D	0.64830	0.994	D	0.65323	0.934	T	0.77316	-0.2633	10	0.87932	D	0	-12.8359	16.1966	0.82029	0.0:0.0:0.0:1.0	.	188	O14986	PI51B_HUMAN	T	188;188;188;135	ENSP00000438082:M188T;ENSP00000265382:M188T	ENSP00000265382:M188T	M	+	2	0	PIP5K1B	70699166	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.895000	0.87343	2.232000	0.73038	0.528000	0.53228	ATG	.		0.403	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558		C	71509346	T	C	71509346	3	2	56	1	0	0	0	0	1	0	0	0	11966	1464	51	3	581	3	PIP5K1B	9	71509346	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	35602745	71509346	69704085	41	5422											
TLR4	7099	broad.mit.edu	37	chr9	120475890	120475890	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagatatcttcacagagcTgagaaacttgaccttcctgg	11	11	8	11	0	2	4	1	2	1	3	4	5	4	4	3	1	2	1	3	1	2	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:120475890T>C	ENST00000355622.6	+	3	1585	c.1484T>C	c.(1483-1485)cTg>cCg	p.L495P	TLR4_ENST00000394487.4_Missense_Mutation_p.L455P|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	495					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.L495P(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TTCACAGAGCTGAGAAACTTG	0.448																																					p.L495P													.	TLR4-577	1	Substitution - Missense(1)	endometrium(1)	c.T1484C						.						79	77	78					9																	120475890		2203	4300	6503	SO:0001583	missense	7099	exon3			CAGAGCTGAGAAA	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"CD molecules"	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.1484T>C	9.37:g.120475890T>C	ENSP00000363089:p.Leu495Pro	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	71	3	NM_138554	0	0	2	2	0	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.049512	0.36181	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.72167	-0.63;-0.63	5.72	4.59	0.56863	.	0.885833	0.09654	N	0.773349	D	0.88789	0.6532	H	0.96547	3.84	0.43608	D	0.995976	D	0.89917	1.0	D	0.91635	0.999	D	0.84225	0.0463	10	0.42905	T	0.14	.	10.9103	0.47106	0.0:0.0745:0.0:0.9255	.	495	O00206	TLR4_HUMAN	P	455;495	ENSP00000377997:L455P;ENSP00000363089:L495P	ENSP00000363089:L495P	L	+	2	0	TLR4	119515711	0.598000	0.26882	0.021000	0.16686	0.009000	0.06853	4.192000	0.58378	1.012000	0.39366	0.528000	0.53228	CTG	.		0.448	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		C	120475890	T	C	120475890	3	2	56	1	0	0	0	0	1	0	0	0	15985	1580	55	3	1494	3	TLR4	9	120475890	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	48966544	120475890	20737541	42	5423											
SORCS1	114815	ucsc.edu;bcgsc.ca	37	chr10	108371705	108371705	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgatgactcgaccgatgtcCctcctccactcagggatgtc	7	11	9	14	2	1	2	1	2	0	0	6	5	4	3	4	1	0	0	4	1	0	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr10:108371705C>A	ENST00000263054.6	-	22	3004	c.2997G>T	c.(2995-2997)agG>agT	p.R999S	SORCS1_ENST00000478809.2_5'UTR|SORCS1_ENST00000369698.1_Missense_Mutation_p.R534S|SORCS1_ENST00000344440.6_Missense_Mutation_p.R999S	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	999					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GACCGATGTCCCTCCTCCACT	0.493																																					p.R999S													.	SORCS1-153	0			c.G2997T						.						114	102	106					10																	108371705		2203	4300	6503	SO:0001583	missense	114815	exon22			GATGTCCCTCCTC	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2997G>T	10.37:g.108371705C>A	ENSP00000263054:p.Arg999Ser	Somatic	166	3		WXS	Illumina HiSeq		151	34	NM_001206572	0	0	0	0	0	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.19|16.19	3.052900|3.052900	0.55218|0.55218	.|.	.|.	ENSG00000108018|ENSG00000108018	ENST00000452214|ENST00000369698;ENST00000263054;ENST00000344440	.|T;T;T	.|0.21543	.|2.0;2.55;2.56	5.41|5.41	-1.66|-1.66	0.08265|0.08265	.|.	.|0.116409	.|0.56097	.|D	.|0.000026	T|T	0.12774|0.12774	0.0310|0.0310	L|L	0.40543|0.40543	1.245|1.245	0.43088|0.43088	D|D	0.994752|0.994752	.|B;B;B;B;B	.|0.30146	.|0.176;0.27;0.27;0.176;0.27	.|B;B;B;B;B	.|0.35114	.|0.096;0.196;0.196;0.096;0.196	T|T	0.11084|0.11084	-1.0602|-1.0602	5|9	.|.	.|.	.|.	-25.7275|-25.7275	1.9546|1.9546	0.03373|0.03373	0.1101:0.3946:0.2156:0.2796|0.1101:0.3946:0.2156:0.2796	.|.	.|999;999;999;999;999	.|A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.|.;.;.;SORC1_HUMAN;.	V|S	14|534;999;999	.|ENSP00000358712:R534S;ENSP00000263054:R999S;ENSP00000345964:R999S	.|.	G|R	-|-	2|3	0|2	SORCS1|SORCS1	108361695|108361695	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.999000|0.999000	0.98932|0.98932	0.766000|0.766000	0.26560|0.26560	0.024000|0.024000	0.15214|0.15214	0.655000|0.655000	0.94253|0.94253	GGG|AGG	.		0.493	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108371705	C	A	108371705	3	1	56	1	0	0	0	0	1	0	0	0	14962	622	22	4	763	4	SORCS1	10	108371705	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		108371705	27163042	43	5424											
C10orf118	55088	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115917414	115917414	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatgtctacgaagagctcctGatgcttcttattttctttaa	10	17	6	8	1	3	2	0	1	3	1	4	3	4	2	1	0	3	2	1	0	5	7			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr10:115917414G>A	ENST00000369287.3	-	3	924	c.658C>T	c.(658-660)Cag>Tag	p.Q220*		NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		220										NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		AAGAGCTCCTGATGCTTCTTA	0.274																																					p.Q220X													.	C10orf118-92	0			c.C658T						.						74	74	74					10																	115917414		2202	4298	6500	SO:0001587	stop_gained	55088	exon3			GCTCCTGATGCTT																												ENST00000369287.3:c.658C>T	10.37:g.115917414G>A	ENSP00000358293:p.Gln220*	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	24	8	NM_018017	0	0	0	0	0	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Nonsense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	G	39	7.580594	0.98371	.	.	ENSG00000165813	ENST00000369287;ENST00000430353	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	16.5904	0.84763	0.0:0.0:1.0:0.0	.	.	.	.	X	220;326	.	ENSP00000358293:Q220X	Q	-	1	0	C10orf118	115907404	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.469000	0.90395	2.578000	0.87016	0.650000	0.86243	CAG	.		0.274	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1			A	115917414	G	A	115917414	4	1	56	1	0	0	0	0	0	1	0	0	1591	1299	45	2	2094	2	C10orf118	10	115917414	Nonsense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	7545709	115917414	19617333	44	5425											
EPS8L2	64787	broad.mit.edu	37	chr11	726471	726471	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcgcctggctggaagccaagGccttcagcccgcggtgagcg	6	5	16	14	4	1	1	1	1	0	0	1	2	1	2	4	4	3	1	4	4	2	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:726471G>T	ENST00000533256.1	+	20	2296	c.1921G>T	c.(1921-1923)Gcc>Tcc	p.A641S	EPS8L2_ENST00000530636.1_Missense_Mutation_p.A641S|EPS8L2_ENST00000318562.8_Missense_Mutation_p.A641S|EPS8L2_ENST00000526198.1_Missense_Mutation_p.A657S|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	641					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGAAGCCAAGGCCTTCAGCCC	0.756																																					p.A641S													.	EPS8L2-91	0			c.G1921T						.																																			SO:0001583	missense	64787	exon19			GCCAAGGCCTTCA	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.1921G>T	11.37:g.726471G>T	ENSP00000435585:p.Ala641Ser	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	75	7	NM_022772	0	0	0	0	0	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Missense_Mutation	SNP	ENST00000533256.1	37	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212487	0.39102	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	T;T;T;T	0.16196	2.36;2.36;2.36;2.36	3.3	1.09	0.20402	.	0.208508	0.29383	U	0.012303	T	0.11153	0.0272	L	0.27053	0.805	0.26101	N	0.980812	B;B	0.14438	0.01;0.01	B;B	0.10450	0.005;0.003	T	0.23297	-1.0192	10	0.45353	T	0.12	-19.1124	9.8968	0.41322	0.0:0.0:0.5629:0.4371	.	657;641	B7ZKL3;Q9H6S3	.;ES8L2_HUMAN	S	641;641;641;657	ENSP00000320828:A641S;ENSP00000435585:A641S;ENSP00000436035:A641S;ENSP00000436230:A657S	ENSP00000320828:A641S	A	+	1	0	EPS8L2	716471	1.000000	0.71417	0.995000	0.50966	0.558000	0.35554	2.264000	0.43302	0.706000	0.31912	0.298000	0.19748	GCC	.		0.756	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		T	726471	G	T	726471	3	4	56	1	0	0	0	0	1	0	0	0	5209	1203	42	4	1991	4	EPS8L2	11	726471	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		726471	134280045	45	5426											
GLYATL2	219970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	58601915	58601915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatcaatcaacaatatttcTtgggggtgcatttccactga	12	13	8	8	0	3	1	2	1	1	0	4	2	4	1	1	2	2	1	1	2	5	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:58601915T>C	ENST00000287275.1	-	6	1262	c.872A>G	c.(871-873)aAg>aGg	p.K291R	GLYATL2_ENST00000533636.1_5'Flank|GLYATL2_ENST00000532258.1_Missense_Mutation_p.K291R	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	291						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	ACAATATTTCTTGGGGGTGCA	0.363																																					p.K291R		.											.	GLYATL2-92	0			c.A872G						.						53	49	50					11																	58601915		1831	4083	5914	SO:0001583	missense	219970	exon6			TATTTCTTGGGGG	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.872A>G	11.37:g.58601915T>C	ENSP00000287275:p.Lys291Arg	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	37	11	NM_145016	0	0	0	0	0	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	37	CCDS41649.1	.	.	.	.	.	.	.	.	.	.	T	7.457	0.643799	0.14451	.	.	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.14640	2.49;2.49	2.81	-1.38	0.09027	.	0.816947	0.10184	U	0.705518	T	0.08133	0.0203	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.39921	-0.9590	10	0.25106	T	0.35	.	3.0975	0.06314	0.0:0.2741:0.2254:0.5005	.	291	Q8WU03	GLYL2_HUMAN	R	291	ENSP00000287275:K291R;ENSP00000434277:K291R	ENSP00000287275:K291R	K	-	2	0	GLYATL2	58358491	0.008000	0.16893	0.022000	0.16811	0.453000	0.32348	0.974000	0.29436	-0.398000	0.07679	-1.222000	0.01597	AAG	.		0.363	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016		C	58601915	T	C	58601915	3	2	56	1	0	0	0	0	1	0	0	0	6501	1609	56	3	16	3	GLYATL2	11	58601915	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	57875444	58601915	76404601	46	5427											
PCF11	51585	broad.mit.edu	37	chr11	82879804	82879804	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgagatttgaggggccAcaaggtcagctaggaggtgg	9	9	16	7	0	1	2	1	2	0	1	1	4	1	3	2	6	1	1	2	6	2	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:82879804A>T	ENST00000298281.4	+	8	2879	c.2427A>T	c.(2425-2427)ccA>ccT	p.P809P		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	809	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TTGAGGGGCCACAAGGTCAGC	0.562																																					p.P809P													.	PCF11-23	0			c.A2427T						.						55	56	56					11																	82879804		1914	4115	6029	SO:0001819	synonymous_variant	51585	exon8			GGGGCCACAAGGT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2427A>T	11.37:g.82879804A>T		Somatic	183	1		WXS	Illumina HiSeq	Phase_I	174	5	NM_015885	0	0	1	1	0	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			.		0.562	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82879804	A	T	82879804	2	4	56	1	0	0	0	0	0	0	0	1	11599	146	6	5		5	PCF11	11	82879804	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	24277889	82879804	52126712	47	5428											
MAML2	84441	broad.mit.edu;bcgsc.ca	37	chr11	95825356	95825356	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttgctgttgctgttgctgTtgctgctgctgctgctgttg	0	19	14	8	0	0	0	0	0	0	0	0	0	0	0	0	0	8	13	0	0	0	5			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:95825356T>C	ENST00000524717.1	-	2	3123	c.1839A>G	c.(1837-1839)caA>caG	p.Q613Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	613					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgttgctgctgct	0.542			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q613Q				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.A1839G						.						50	53	52					11																	95825356		2075	4054	6129	SO:0001819	synonymous_variant	84441	exon2			TTGCTGTTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1839A>G	11.37:g.95825356T>C		Somatic	123	1		WXS	Illumina HiSeq	Phase_I	110	9	NM_032427	0	0	10	47	37	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.542	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825356	T	C	95825356	2	2	56	1	0	0	0	0	0	0	0	1	9231	1722	60	3		3	MAML2	11	95825356	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	12945552	95825356	39181160	48	5429											
MAML2	84441	broad.mit.edu	37	chr11	95825392	95825392	+	Frame_Shift_Del	DEL	C	C	-																															tgttgctgctgctgctgctgCtgctgctgctgctgctgctg																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:95825392delC	ENST00000524717.1	-	2	3087	c.1803delG	c.(1801-1803)cagfs	p.Q621fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	621				Missing (in Ref. 1; AAK93831/AAK93833, 3; BAB47448, 5; AAI52450 and 6; AAP12462). {ECO:0000305}.	gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgct	0.537			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q601fs				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.1803delG						.						21	29	26					11																	95825392		1960	3863	5823	SO:0001589	frameshift_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1803delG	11.37:g.95825392delC	ENSP00000434552:p.Gln621fs	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	135	7	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Del	DEL	ENST00000524717.1	37	CCDS44714.1																																																																																			-|0.034;TGC|0.966		0.537	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			-	95825392	C	-	95825392	7	5	56	1	0	1	0	1	0	0	0	0	9231	796	28	0	1683	0	MAML2	11	95825392	Frame_Shift_Del	DEL	C	TCGA-B9-A5W8-01A-11D-A28G-10	36	95825392	39181124	49	5430	61	3									
MAML2	84441	broad.mit.edu	37	chr11	95825394	95825395	+	Frame_Shift_Del	DEL	GC	GC	-																															ttgctgctgctgctgctgctGctgctgctgctgctgctgct																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:95825394_95825395delGC	ENST00000524717.1	-	2	3084_3085	c.1800_1801delGC	c.(1798-1803)cagcagfs	p.QQ600fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	600					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				tgctgctgctgctgctgctgct	0.54			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.600_601del				Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.1800_1801del						.																																			SO:0001589	frameshift_variant	84441	exon2			GCTGCTGCTGCTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1800_1801delGC	11.37:g.95825394_95825395delGC	ENSP00000434552:p.Gln600fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	135	7	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Del	DEL	ENST00000524717.1	37	CCDS44714.1																																																																																			-|0.034;TGC|0.966		0.54	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			-	95825395	GC	-	95825394	7	5	56	1	0	1	0	1	0	0	0	0	9231	1328	46	0	1685	0	MAML2	11	95825394	Frame_Shift_Del	DEL	GC	TCGA-B9-A5W8-01A-11D-A28G-10	2	95825394	39181122	50	5431	61	3									
MAML2	84441	hgsc.bcm.edu;bcgsc.ca	37	chr11	95825395	95825395	+	Silent	SNP	C	C	T																															tgctgctgctgctgctgctgCtgctgctgctgctgctgctg																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:95825395C>T	ENST00000524717.1	-	2	3084	c.1800G>A	c.(1798-1800)caG>caA	p.Q600Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	600					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgct	0.537			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q600Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.G1800A						.						21	29	26					11																	95825395		1989	3928	5917	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1800G>A	11.37:g.95825395C>T		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	137	16	NM_032427	2	1	1345	1412	64	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.537	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825395	C	T	95825395	2	4	56	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825395	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	1	95825395	39181121	51	5432	61	3									
CD163L1	283316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7526000	7526001	+	Missense_Mutation	DNP	GC	GC	TT																															gcactgccatatggagatatGcgttttaggacactgaatgt																								rs368002565		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:7526000_7526001GC>TT	ENST00000313599.3	-	14	3702_3703	c.3645_3646GC>AA	c.(3643-3648)acGCat>acAAat	p.H1216N	CD163L1_ENST00000396630.1_Missense_Mutation_p.H1216N|CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Missense_Mutation_p.H1226N			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1216	SRCR 11. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						ATGGAGATATGCGTTTTAGGAC	0.525																																					p.H1226N		.											.	CD163L1-100	0			c.G3645A						.																																			SO:0001583	missense	283316	exon14			GATATGCGTTTTA	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3645_3646delinsTT	12.37:g.7526000_7526001delinsTT	ENSP00000315945:p.His1216Asn	Somatic	332	0		WXS	Illumina HiSeq	Phase_I	280	46	NM_174941	0	0	0	0	0	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	DNP	ENST00000313599.3	37	CCDS8577.1																																																																																			.		0.525	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		TT	7526001	GC	TT	7526000	3	4	56	1	0	0	0	0	1	0	0	0	2974	1319	46	4	739	4	CD163L1	12	7526000	Missense_Mutation	DNP	GC	TCGA-B9-A5W8-01A-11D-A28G-10		7526000	126325895	52	5433											
SLC38A4	55089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	47170779	47170779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccgtttgcatttttctcCgggaccgactggaaaaagaa	12	10	9	10	3	1	1	0	0	1	1	2	4	1	3	3	2	1	2	3	2	3	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:47170779C>T	ENST00000447411.1	-	12	1288	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	SLC38A4_ENST00000266579.4_Missense_Mutation_p.R361Q	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	361					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					CATTTTTCTCCGGGACCGACT	0.358																																					p.R361Q		.											.	SLC38A4-93	0			c.G1082A						.						87	88	88					12																	47170779		2203	4299	6502	SO:0001583	missense	55089	exon12			TTTCTCCGGGACC	AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"Solute carriers"	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.1082G>A	12.37:g.47170779C>T	ENSP00000389843:p.Arg361Gln	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	64	16	NM_001143824	0	0	0	0	0	A8K553	Missense_Mutation	SNP	ENST00000447411.1	37	CCDS8750.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.479698	0.26511	.	.	ENSG00000139209	ENST00000447411;ENST00000266579	T;T	0.02158	4.42;4.42	5.96	3.18	0.36537	.	0.116259	0.64402	N	0.000017	T	0.03871	0.0109	L	0.49640	1.575	0.45607	D	0.998544	B	0.24258	0.1	B	0.33890	0.172	T	0.41288	-0.9517	10	0.17369	T	0.5	-4.6085	15.3035	0.73972	0.0:0.872:0.0:0.128	.	361	Q969I6	S38A4_HUMAN	Q	361	ENSP00000389843:R361Q;ENSP00000266579:R361Q	ENSP00000266579:R361Q	R	-	2	0	SLC38A4	45457046	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	1.399000	0.34566	0.425000	0.26087	-0.940000	0.02684	CGG	.		0.358	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1			T	47170779	C	T	47170779	3	4	56	1	0	0	0	0	1	0	0	0	14638	652	23	1	581	1	SLC38A4	12	47170779	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	39644779	47170779	86681116	53	5434											
METTL7A	25840	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	51319010	51319030	+	In_Frame_Del	DEL	GGAGTTTGCGGGCCCCTCCGG	GGAGTTTGCGGGCCCCTCCGG	-																															gagctcttcagtaacctgcaGgagtttgcgggcccctccgg																								rs142438796		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GGAGTTTGCGGGCCCCTCCGG	GGAGTTTGCGGGCCCCTCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:51319010_51319030delGGAGTTTGCGGGCCCCTCCGG	ENST00000548553.1	+	2	1170_1190	c.189_209delGGAGTTTGCGGGCCCCTCCGG	c.(187-210)caggagtttgcgggcccctccggg>cag	p.EFAGPSG64del	METTL7A_ENST00000332160.4_In_Frame_Del_p.EFAGPSG64del			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	64						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)	p.A66V(1)		endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GTAACCTGCAGGAGTTTGCGGGCCCCTCCGGGAAACTCTCC	0.543																																					p.63_70del		.											.	METTL7A-90	1	Substitution - Missense(1)	lung(1)	c.189_209del						.																																			SO:0001651	inframe_deletion	25840	exon1			.		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.189_209delGGAGTTTGCGGGCCCCTCCGG	12.37:g.51319010_51319030delGGAGTTTGCGGGCCCCTCCGG	ENSP00000448785:p.Glu64_Gly70del	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	80	12	NM_014033	0	0	0	0	0	Q9H7R3|Q9UHZ7|Q9Y422	In_Frame_Del	DEL	ENST00000548553.1	37	CCDS8804.1																																																																																			.		0.543	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033		-	51319030	GGAGTTTGCGGGCCCCTCCGG	-	51319010	7	5	56	1	0	1	0	1	0	0	0	0	9530	991	35	0	191	0	METTL7A	12	51319010	In_Frame_Del	DEL	GGAGTTTGCGGGCCCCTCCGG	TCGA-B9-A5W8-01A-11D-A28G-10	4148231	51319010	82532885	54	5435											
XPOT	11260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64808728	64808728	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaaaatttccccagatgcCtggcaggtgtgtgcagaagc	11	10	11	9	0	0	2	0	0	0	2	1	2	1	2	3	2	3	2	3	2	4	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:64808728C>A	ENST00000332707.5	+	3	631	c.102C>A	c.(100-102)gcC>gcA	p.A34A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	34	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		CCCCAGATGCCTGGCAGGTGT	0.388																																					p.A34A		.											.	XPOT-652	0			c.C102A						.						91	97	95					12																	64808728		2203	4300	6503	SO:0001819	synonymous_variant	11260	exon3			AGATGCCTGGCAG	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.102C>A	12.37:g.64808728C>A		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	37	5	NM_007235	0	0	6	8	2	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	37	CCDS31852.1																																																																																			.		0.388	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		A	64808728	C	A	64808728	2	1	56	1	0	0	0	0	0	0	0	1	17483	668	24	4		4	XPOT	12	64808728	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	13489718	64808728	69043167	55	5436											
TMCC3	57458	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	94975986	94975987	+	Frame_Shift_Ins	INS	-	-	A																															ctctctgagctttcgatgatINSactgctctaacttcttctgc																								rs530422400		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:94975986_94975987insA	ENST00000261226.4	-	2	537_538	c.406_407insT	c.(406-408)tatfs	p.Y136fs	TMCC3_ENST00000551457.1_Frame_Shift_Ins_p.Y105fs	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	136						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						CTTTCGATGATACTGCTCTAAC	0.475																																					p.Y136fs		.											.	TMCC3-92	0			c.407_408insT						.																																			SO:0001589	frameshift_variant	57458	exon2			.	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.407dupT	12.37:g.94975987_94975987dupA	ENSP00000261226:p.Tyr136fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	73	12	NM_020698	0	0	0	0	0	Q8IWB2	Frame_Shift_Ins	INS	ENST00000261226.4	37	CCDS31877.1																																																																																			.		0.475	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		A	94975987	-	A	94975986	7	5	56	1	0	1	1	0	0	0	0	0	16026	1406	49	0	1038	0	TMCC3	12	94975986	Frame_Shift_Ins	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	30167258	94975986	38875909	56	5437											
METAP2	84101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	95907438	95907438	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcctcttaggcttccaagaAcaaaacacttgttaaatgtc	13	12	5	11	0	1	1	0	0	1	1	4	1	3	1	2	1	2	2	2	1	7	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:95907438A>G	ENST00000258499.3	-	0	4022				METAP2_ENST00000546753.1_Missense_Mutation_p.T376A|METAP2_ENST00000323666.5_Missense_Mutation_p.T399A|METAP2_ENST00000261220.9_Missense_Mutation_p.T376A|METAP2_ENST00000551840.1_Missense_Mutation_p.T398A|METAP2_ENST00000550777.1_Missense_Mutation_p.T363A	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44						mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						GCTTCCAAGAACAAAACACTT	0.418																																					p.T399A		.											.	METAP2-90	0			c.A1195G						.						84	82	83					12																	95907438		2203	4300	6503	SO:0001628	intergenic_variant	10988	exon11			CCAAGAACAAAAC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"Ubiquitin-specific peptidases"	20064	protein-coding gene	gene with protein product		610993	"ubiquitin specific protease 44"			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7			12.37:g.95907438A>G		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	88	21	NM_006838	0	0	1	1	0	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	A	2.554	-0.303387	0.05495	.	.	ENSG00000111142	ENST00000323666;ENST00000546753;ENST00000261220;ENST00000550777;ENST00000551840	.	.	.	5.83	2.17	0.27698	Winged helix-turn-helix transcription repressor DNA-binding (1);Peptidase M24, structural domain (2);	0.135470	0.64402	N	0.000002	T	0.03220	0.0094	N	0.00003	-3.5	0.39326	D	0.96532	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.40194	-0.9576	9	0.02654	T	1	-9.0542	6.8846	0.24193	0.3929:0.0:0.6071:0.0	.	376;363;376;398;399	B4DUX5;F8VRR3;G3XA91;F8VQZ7;P50579	.;.;.;.;AMPM2_HUMAN	A	399;376;376;363;398	.	ENSP00000261220:T376A	T	+	1	0	METAP2	94431569	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.393000	0.59665	0.466000	0.27193	0.533000	0.62120	ACA	.		0.418	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		G	95907438	A	G	95907438	1	3	56	0	1	0	0	0	0	0	0	0	9512	43	2	3		3	METAP2	12	95907438	IGR	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	931452	95907438	37944457	57	5438											
RFC5	5985	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	118462664	118462664	+	Frame_Shift_Del	DEL	A	A	-																															ttctcttactagtaattgagAaattcacagaaaataccaga																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:118462664delA	ENST00000454402.2	+	6	548	c.430delA	c.(430-432)aaafs	p.K144fs	RFC5_ENST00000229043.3_Frame_Shift_Del_p.K59fs|RFC5_ENST00000392542.2_Frame_Shift_Del_p.K123fs	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	144					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGTAATTGAGAAATTCACAGA	0.428																																					p.K144fs		.											.	RFC5-227	0			c.430delA						.						75	81	79					12																	118462664		2203	4300	6503	SO:0001589	frameshift_variant	5985	exon6			.		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.430delA	12.37:g.118462664delA	ENSP00000408295:p.Lys144fs	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	53	15	NM_007370	0	0	0	0	0	A8MZ62|B3KSX8	Frame_Shift_Del	DEL	ENST00000454402.2	37	CCDS9185.1																																																																																			.		0.428	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		-	118462664	A	-	118462664	7	5	56	1	0	1	0	1	0	0	0	0	13280	247	9	0	458	0	RFC5	12	118462664	Frame_Shift_Del	DEL	A	TCGA-B9-A5W8-01A-11D-A28G-10	22555226	118462664	15389231	58	5439											
PABPC3	5042	ucsc.edu	37	chr13	25672007	25672007	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaagcaaaagcaaatgttAggtgaacggctctttcctct	14	10	8	9	1	2	1	0	1	2	0	3	1	3	1	1	2	3	4	1	2	7	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr13:25672007A>G	ENST00000281589.3	+	1	1708	c.1671A>G	c.(1669-1671)ttA>ttG	p.L557L		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	557	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AGCAAATGTTAGGTGAACGGC	0.433																																					p.L557L													.	PABPC3-72	0			c.A1671G						.						118	107	110					13																	25672007		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			AATGTTAGGTGAA	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1671A>G	13.37:g.25672007A>G		Somatic	154	1		WXS	Illumina HiSeq		182	1	NM_030979	0	0	0	1	1	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																			.		0.433	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		G	25672007	A	G	25672007	2	3	56	1	0	0	0	0	0	0	0	1	11391	417	15	3		3	PABPC3	13	25672007	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10		25672007	89497871	59	5440											
FRY	10129	broad.mit.edu	37	chr13	32841388	32841388	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcctttcagcccgcagcCtgtgacgatgccgaggaggc	6	6	14	15	4	1	1	1	1	0	0	1	4	1	2	5	2	3	1	5	2	0	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr13:32841388C>A	ENST00000380250.3	+	55	8524	c.8028C>A	c.(8026-8028)gcC>gcA	p.A2676A	FRY_ENST00000542859.1_Silent_p.A46A	NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2676						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AGCCCGCAGCCTGTGACGATG	0.552																																					p.A2676A													.	FRY-142	0			c.C8028A						.						99	107	104					13																	32841388		2065	4205	6270	SO:0001819	synonymous_variant	10129	exon55			CGCAGCCTGTGAC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"chromosome 13 open reading frame 14"	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.8028C>A	13.37:g.32841388C>A		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_023037	0	0	3	4	1	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																			.		0.552	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32841388	C	A	32841388	2	1	56	1	0	0	0	0	0	0	0	1	6082	668	24	4		4	FRY	13	32841388	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	7169381	32841388	82328490	60	5441											
LRRC16B	90668	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	24528535	24528547	+	Frame_Shift_Del	DEL	CATCAATGCCCTG	CATCAATGCCCTG	-																															aagcttcgcaccagcatcctCatcaatgccctgggcagcaa																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	CATCAATGCCCTG	CATCAATGCCCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr14:24528535_24528547delCATCAATGCCCTG	ENST00000342740.5	+	21	1837_1849	c.1683_1695delCATCAATGCCCTG	c.(1681-1695)ctcatcaatgccctgfs	p.LINAL561fs	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	561						cytoplasm (GO:0005737)		p.N563D(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		CCAGCATCCTCATCAATGCCCTGGGCAGCAACA	0.62																																					p.561_565del		.											.	LRRC16B-139	1	Substitution - Missense(1)	large_intestine(1)	c.1683_1695del						.																																			SO:0001589	frameshift_variant	90668	exon21			.	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"chromosome 14 open reading frame 121"	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1683_1695delCATCAATGCCCTG	14.37:g.24528535_24528547delCATCAATGCCCTG	ENSP00000340467:p.Leu561fs	Somatic	288	0		WXS	Illumina HiSeq	Phase_I	154	40	NM_138360	0	0	0	0	0	Q8TEF7|Q96HS9	Frame_Shift_Del	DEL	ENST00000342740.5	37	CCDS32054.1																																																																																			.		0.62	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		-	24528547	CATCAATGCCCTG	-	24528535	7	5	56	1	0	1	0	1	0	0	0	0	8997	813	29	0	1765	0	LRRC16B	14	24528535	Frame_Shift_Del	DEL	CATCAATGCCCTG	TCGA-B9-A5W8-01A-11D-A28G-10		24528535	82821005	61	5442											
RALGAPA1	253959	ucsc.edu;bcgsc.ca	37	chr14	36103887	36103887	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggatcataatctacagatGccaaatcagagaggctcatg	16	8	9	8	0	4	2	3	0	1	2	4	4	4	3	1	2	2	1	1	2	4	2	rs554131227	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr14:36103887G>A	ENST00000389698.3	-	32	4760	c.4370C>T	c.(4369-4371)gCa>gTa	p.A1457V	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.A1470V|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.A1457V|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.A1504V	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1457	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATCTACAGATGCCAAATCAGA	0.438													G|||	10	0.00199681	0.0076	0	5008	,	,		15122	0		0	False		,,,				2504	0				p.A1457V													.	RALGAPA1-138	0			c.C4370T						.						53	51	52					14																	36103887		2203	4297	6500	SO:0001583	missense	253959	exon32			ACAGATGCCAAAT	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4370C>T	14.37:g.36103887G>A	ENSP00000374348:p.Ala1457Val	Somatic	136	3		WXS	Illumina HiSeq		111	21	NM_194301	0	0	3	3	0	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.097606	0.56075	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42	5.38	5.38	0.77491	.	0.293400	0.37577	N	0.002036	T	0.34077	0.0885	L	0.53249	1.67	0.33807	D	0.627326	P;B;B;B	0.38827	0.649;0.382;0.452;0.215	B;B;B;B	0.36567	0.228;0.146;0.228;0.101	T	0.50303	-0.8844	10	0.52906	T	0.07	-16.2934	19.5007	0.95093	0.0:0.0:1.0:0.0	.	1504;1470;1457;1457	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	V	1457;1457;1457;1504;95;1470;1504	ENSP00000374348:A1457V;ENSP00000302647:A1457V;ENSP00000258840:A1504V;ENSP00000451133:A95V;ENSP00000371803:A1470V;ENSP00000451877:A1504V	ENSP00000258840:A1504V	A	-	2	0	RALGAPA1	35173638	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.259000	0.58828	2.673000	0.90976	0.650000	0.86243	GCA	.		0.438	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		A	36103887	G	A	36103887	3	1	56	1	0	0	0	0	1	0	0	0	13045	1319	46	2	1929	2	RALGAPA1	14	36103887	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	11575352	36103887	71245653	62	5443											
SPTBN5	51332	ucsc.edu	37	chr15	42147764	42147764	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctttctgggttcttcctGctctccaggagtgctgctgt	3	15	10	13	0	3	0	0	0	3	0	5	1	4	1	3	2	3	4	3	2	0	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr15:42147764G>A	ENST00000320955.6	-	54	9428	c.9201C>T	c.(9199-9201)agC>agT	p.S3067S		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3067					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GGTTCTTCCTGCTCTCCAGGA	0.632																																					p.S3032S													.	SPTBN5-91	0			c.C9096T						.						20	23	22					15																	42147764		2032	4171	6203	SO:0001819	synonymous_variant	51332	exon54			CTTCCTGCTCTCC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9201C>T	15.37:g.42147764G>A		Somatic	48	0		WXS	Illumina HiSeq		41	4	NM_016642	0	0	0	0	0		Silent	SNP	ENST00000320955.6	37																																																																																				.		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42147764	G	A	42147764	2	1	56	1	0	0	0	0	0	0	0	1	15154	1310	46	2		2	SPTBN5	15	42147764	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		42147764	60383628	63	5444											
DAPK2	23604	broad.mit.edu;bcgsc.ca	37	chr15	64217047	64217047	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtctgagagcctcttggaTtgtgagccgtttcctgcaat	6	14	12	9	1	2	2	0	2	2	1	3	4	3	3	3	1	3	2	3	1	1	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr15:64217047T>C	ENST00000457488.1	-	9	856	c.826A>G	c.(826-828)Atc>Gtc	p.I276V	DAPK2_ENST00000261891.3_Missense_Mutation_p.I276V|DAPK2_ENST00000558069.1_Missense_Mutation_p.I276V	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	276	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		GCCTCTTGGATTGTGAGCCGT	0.532																																					p.I276V													.	DAPK2-333	0			c.A826G						.						136	106	116					15																	64217047		2203	4300	6503	SO:0001583	missense	23604	exon9			CTTGGATTGTGAG	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.826A>G	15.37:g.64217047T>C	ENSP00000408277:p.Ile276Val	Somatic	246	0		WXS	Illumina HiSeq	Phase_I	151	6	NM_014326	0	0	0	0	0	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	37	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.967289	0.34754	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.39229	1.09;1.09	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.30823	0.0777	N	0.20766	0.605	0.80722	D	1	B	0.18166	0.026	B	0.30179	0.112	T	0.11060	-1.0603	10	0.13470	T	0.59	.	14.7185	0.69289	0.0:0.0:0.0:1.0	.	276	Q9UIK4	DAPK2_HUMAN	V	276	ENSP00000261891:I276V;ENSP00000408277:I276V	ENSP00000261891:I276V	I	-	1	0	DAPK2	62004100	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	5.074000	0.64401	2.198000	0.70561	0.533000	0.62120	ATC	.		0.532	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		C	64217047	T	C	64217047	3	2	56	1	0	0	0	0	1	0	0	0	4242	1493	52	3	302	3	DAPK2	15	64217047	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	22069283	64217047	38314345	64	5445											
KBTBD13	390594	hgsc.bcm.edu	37	chr15	65369367	65369367	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcggcgaccggccggcgCtggcggcggaggacgagctg	4	3	21	13	9	0	0	0	0	0	0	0	4	0	2	2	7	2	2	2	7	0	0	rs550537101	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr15:65369367C>T	ENST00000432196.2	+	1	214	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	72	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						CCGGCCGGCGCTGGCGGCGGA	0.736													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		9554	0		0	False		,,,				2504	0				p.L72L		.											.	.	0			c.C214T						.						2	2	2					15																	65369367		1202	2816	4018	SO:0001819	synonymous_variant	390594	exon1			CCGGCGCTGGCGG		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"BTB/POZ domain containing"	37227	protein-coding gene	gene with protein product	"nemaline myopathy type 6"	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.214C>T	15.37:g.65369367C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	5	NM_001101362	0	0	0	0	0		Silent	SNP	ENST00000432196.2	37	CCDS45281.1																																																																																			.		0.736	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362		T	65369367	C	T	65369367	2	4	56	1	0	0	0	0	0	0	0	1	8013	796	28	2		2	KBTBD13	15	65369367	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	1152320	65369367	37162025	65	5446											
FBXO22	26263	broad.mit.edu	37	chr15	76225142	76225142	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgagaagactgctgaggCtgcgatgcagcgcctcaaag	11	7	14	9	2	1	4	1	3	0	2	1	6	1	4	1	1	4	3	1	1	2	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr15:76225142C>A	ENST00000308275.3	+	7	1016	c.911C>A	c.(910-912)gCt>gAt	p.A304D	FBXO22_ENST00000540507.1_Missense_Mutation_p.A200D	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	304					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						ACTGCTGAGGCTGCGATGCAG	0.537																																					p.A304D													.	FBXO22-658	0			c.C911A						.						133	121	125					15																	76225142		2197	4294	6491	SO:0001583	missense	26263	exon7			CTGAGGCTGCGAT	AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"F-boxes /  "other""	13593	protein-coding gene	gene with protein product	"FIST domain containing 1"	609096	"F-box only protein 22"			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.911C>A	15.37:g.76225142C>A	ENSP00000307833:p.Ala304Asp	Somatic	142	2		WXS	Illumina HiSeq	Phase_I	115	7	NM_147188	0	0	15	15	0	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	37	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592872	0.86953	.	.	ENSG00000167196	ENST00000308275;ENST00000540507	.	.	.	5.52	5.52	0.82312	FIST C domain (1);	0.000000	0.85682	D	0.000000	T	0.78635	0.4314	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.79401	-0.1819	9	0.66056	D	0.02	-26.0739	18.7902	0.91971	0.0:1.0:0.0:0.0	.	304	Q8NEZ5	FBX22_HUMAN	D	304;200	.	ENSP00000307833:A304D	A	+	2	0	FBXO22	74012197	0.999000	0.42202	0.966000	0.40874	0.542000	0.35054	4.175000	0.58263	2.752000	0.94435	0.655000	0.94253	GCT	.		0.537	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188		A	76225142	C	A	76225142	3	1	56	1	0	0	0	0	1	0	0	0	5753	797	28	4	974	4	FBXO22	15	76225142	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	10855775	76225142	26306250	66	5447											
CDR2	1039	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	22358803	22358803	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctggctgggctctttgAaaggaacatacagagagtct	10	10	13	8	0	3	2	0	1	3	1	3	4	3	3	0	4	2	3	0	4	3	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:22358803A>G	ENST00000268383.2	-	5	1155	c.848T>C	c.(847-849)tTc>tCc	p.F283S		NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	283						cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		GGGCTCTTTGAAAGGAACATA	0.532																																					p.F283S		.											.	CDR2-91	0			c.T848C						.						38	39	39					16																	22358803		2197	4300	6497	SO:0001583	missense	1039	exon5			TCTTTGAAAGGAA	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"Yo paraneoplastic antigen"	117340	"cerebellar degeneration-related protein (62kD)"			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.848T>C	16.37:g.22358803A>G	ENSP00000268383:p.Phe283Ser	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	64	15	NM_001802	0	0	18	45	27	A8K8A8|Q13977	Missense_Mutation	SNP	ENST00000268383.2	37	CCDS32404.1	.	.	.	.	.	.	.	.	.	.	A	3.865	-0.029069	0.07589	.	.	ENSG00000140743	ENST00000268383	T	0.41065	1.01	5.79	4.68	0.58851	.	0.159588	0.56097	D	0.000023	T	0.29093	0.0723	L	0.27053	0.805	0.38438	D	0.946635	B	0.23185	0.081	B	0.20577	0.03	T	0.09100	-1.0690	10	0.15952	T	0.53	-9.0507	13.0653	0.59030	0.8657:0.1343:0.0:0.0	.	283	Q01850	CDR2_HUMAN	S	283	ENSP00000268383:F283S	ENSP00000268383:F283S	F	-	2	0	CDR2	22266304	0.890000	0.30428	0.599000	0.28851	0.617000	0.37484	3.322000	0.52007	0.991000	0.38814	0.533000	0.62120	TTC	.		0.532	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1			G	22358803	A	G	22358803	3	3	56	1	0	0	0	0	1	0	0	0	3178	246	9	3	520	3	CDR2	16	22358803	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10		22358803	67995950	67	5448											
ZNF629	23361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30794425	30794425	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgacgctgaagctcttGccgcactctgggcacttgta	7	10	12	12	2	2	2	0	2	2	0	2	3	2	2	1	1	3	6	1	1	2	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:30794425G>A	ENST00000262525.4	-	3	1431	c.1224C>T	c.(1222-1224)ggC>ggT	p.G408G	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	408					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)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			TGAAGCTCTTGCCGCACTCTG	0.652																																					p.G408G		.											.	.	0			c.C1224T						.						47	51	49					16																	30794425		2197	4300	6497	SO:0001819	synonymous_variant	23361	exon3			GCTCTTGCCGCAC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"Zinc fingers, C2H2-type"	29008	protein-coding gene	gene with protein product			"zinc finger protein 65"	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.1224C>T	16.37:g.30794425G>A		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	179	51	NM_001080417	0	0	2	4	2	Q15938	Silent	SNP	ENST00000262525.4	37	CCDS45463.1																																																																																			.		0.652	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30794425	G	A	30794425	2	1	56	1	0	0	0	0	0	0	0	1	18085	1306	46	2		2	ZNF629	16	30794425	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	8435622	30794425	59560328	68	5449											
ZNF646	9726	broad.mit.edu	37	chr16	31087650	31087650	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctacgttgccccatggAggacacacccccctcactca	8	8	7	18	1	3	0	2	0	1	0	3	2	3	2	5	2	3	2	5	2	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:31087650A>G	ENST00000394979.2	+	1	428	c.5A>G	c.(4-6)gAg>gGg	p.E2G	ZNF668_ENST00000300849.4_5'Flank|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000538906.1_5'Flank|ZNF646_ENST00000300850.5_Missense_Mutation_p.E2G|ZNF668_ENST00000394983.2_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						TGCCCCATGGAGGACACACCC	0.622																																					p.E2G													.	ZNF646-153	0			c.A5G						.						60	58	59					16																	31087650		2197	4300	6497	SO:0001583	missense	9726	exon2			CCATGGAGGACAC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.5A>G	16.37:g.31087650A>G	ENSP00000378429:p.Glu2Gly	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	107	3	NM_014699	0	0	0	0	0	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		.	.	.	.	.	.	.	.	.	.	A	21.5	4.163319	0.78226	.	.	ENSG00000167395	ENST00000428260;ENST00000300850;ENST00000394979	T;T;T	0.12039	3.06;2.72;2.74	5.69	5.69	0.88448	.	.	.	.	.	T	0.15089	0.0364	N	0.24115	0.695	0.34472	D	0.702912	P	0.51537	0.946	P	0.49301	0.606	T	0.14868	-1.0457	9	0.59425	D	0.04	-19.4918	12.342	0.55099	1.0:0.0:0.0:0.0	.	2	O15015-2	.	G	2	ENSP00000391271:E2G;ENSP00000300850:E2G;ENSP00000378429:E2G	ENSP00000300850:E2G	E	+	2	0	ZNF646	30995151	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	1.981000	0.40628	2.167000	0.68274	0.460000	0.39030	GAG	.		0.622	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		G	31087650	A	G	31087650	3	3	56	1	0	0	0	0	1	0	0	0	18094	304	11	3	7	3	ZNF646	16	31087650	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	293225	31087650	59267103	69	5450											
MMP15	4324	broad.mit.edu	37	chr16	58074478	58074478	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtggcagtgcatgagctgggCcacgcgctggggctggagca	6	6	19	10	2	0	1	0	1	0	0	0	2	0	2	1	5	3	6	1	5	0	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:58074478C>A	ENST00000219271.3	+	5	1571	c.786C>A	c.(784-786)ggC>ggA	p.G262G		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	262					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	ATGAGCTGGGCCACGCGCTGG	0.602																																					p.G262G													.	MMP15-713	0			c.C786A						.						77	64	68					16																	58074478		2198	4300	6498	SO:0001819	synonymous_variant	4324	exon5			GCTGGGCCACGCG	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.786C>A	16.37:g.58074478C>A		Somatic	112	1		WXS	Illumina HiSeq	Phase_I	111	5	NM_002428	0	0	11	11	0	A0A2U6|Q14111	Silent	SNP	ENST00000219271.3	37	CCDS10792.1																																																																																			.		0.602	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		A	58074478	C	A	58074478	2	1	56	1	0	0	0	0	0	0	0	1	9679	726	26	4		4	MMP15	16	58074478	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	26986828	58074478	32280275	70	5451											
NFAT5	10725	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	69727578	69727578	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacagcagcagcaacaacaaCagagcattttattcagtaat	18	8	6	9	0	1	1	1	0	0	1	1	1	1	1	0	0	8	5	0	0	6	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:69727578C>T	ENST00000354436.2	+	12	4114	c.3796C>T	c.(3796-3798)Cag>Tag	p.Q1266*	NFAT5_ENST00000393742.2_Nonsense_Mutation_p.Q1190*|NFAT5_ENST00000432919.1_Nonsense_Mutation_p.Q1284*|NFAT5_ENST00000349945.1_Nonsense_Mutation_p.Q1190*|NFAT5_ENST00000566899.1_Nonsense_Mutation_p.Q1190*|NFAT5_ENST00000567239.1_Nonsense_Mutation_p.Q1283*	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	1266	Poly-Gln.				cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						gcaacaacaacagAGCATTTT	0.468																																					p.Q1284X													.	NFAT5-90	0			c.C3850T						.						59	53	55					16																	69727578		2198	4300	6498	SO:0001587	stop_gained	10725	exon13			CAACAACAGAGCA	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.3796C>T	16.37:g.69727578C>T	ENSP00000346420:p.Gln1266*	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	87	23	NM_138713	0	0	5	5	0	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Nonsense_Mutation	SNP	ENST00000354436.2	37	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	C	37	6.228520	0.97394	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	.	.	.	5.06	5.06	0.68205	.	2.340300	0.01863	N	0.036730	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-1.0247	14.2685	0.66138	0.0:1.0:0.0:0.0	.	.	.	.	X	1284;1283;1190;1266;1190	.	ENSP00000338806:Q1190X	Q	+	1	0	NFAT5	68285079	1.000000	0.71417	0.944000	0.38274	0.119000	0.20118	4.177000	0.58276	2.507000	0.84556	0.555000	0.69702	CAG	.		0.468	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		T	69727578	C	T	69727578	4	4	56	1	0	0	0	0	0	1	0	0	10386	479	17	2	3900	2	NFAT5	16	69727578	Nonsense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	11653100	69727578	20627175	71	5452											
OSGIN1	29948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	83994295	83994295	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgaagtcggtcctcacctGgaagcaccggaaggagcacg	11	5	13	12	3	1	1	1	1	0	0	3	4	2	4	3	4	2	2	3	4	3	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:83994295G>A	ENST00000343939.2	+	5	958	c.575G>A	c.(574-576)tGg>tAg	p.W192*	OSGIN1_ENST00000393306.1_Nonsense_Mutation_p.W109*|OSGIN1_ENST00000361711.3_Nonsense_Mutation_p.W109*|OSGIN1_ENST00000565123.1_Nonsense_Mutation_p.W109*			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	192					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GTCCTCACCTGGAAGCACCGG	0.652																																					p.W109X		.											.	OSGIN1-68	0			c.G326A						.						61	60	60					16																	83994295		2200	4300	6500	SO:0001587	stop_gained	29948	exon4			TCACCTGGAAGCA	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived growth inhibitor", "pregnancy induced growth inhibitor"	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.575G>A	16.37:g.83994295G>A	ENSP00000343376:p.Trp192*	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	185	62	NM_182981	0	0	4	5	1	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Nonsense_Mutation	SNP	ENST00000343939.2	37		.	.	.	.	.	.	.	.	.	.	G	38	7.081125	0.98051	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.1195	16.9387	0.86210	0.0:0.0:1.0:0.0	.	.	.	.	X	192;109;109	.	ENSP00000343376:W192X	W	+	2	0	OSGIN1	82551796	1.000000	0.71417	0.998000	0.56505	0.495000	0.33615	5.463000	0.66712	2.228000	0.72767	0.491000	0.48974	TGG	.		0.652	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		A	83994295	G	A	83994295	4	1	56	1	0	0	0	0	0	1	0	0	11315	1357	47	2	593	2	OSGIN1	16	83994295	Nonsense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	14266717	83994295	6360458	72	5453											
MTHFSD	64779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	86565821	86565821	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggtcactcacacgggcGtccccggggaggttcccaac	7	7	12	15	3	3	0	3	0	0	0	5	1	5	1	3	5	1	1	3	5	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:86565821G>A	ENST00000360900.6	-	8	973	c.948C>T	c.(946-948)gaC>gaT	p.D316D	MTHFSD_ENST00000543303.2_Silent_p.D315D|MTHFSD_ENST00000322911.6_Silent_p.D315D|MTHFSD_ENST00000381214.5_Silent_p.D316D|MTHFSD_ENST00000546093.1_Silent_p.D153D	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	316	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TCACACGGGCGTCCCCGGGGA	0.682																																					p.D316D		.											.	MTHFSD-90	0			c.C948T						.						11	14	13					16																	86565821		1876	4097	5973	SO:0001819	synonymous_variant	64779	exon8			ACGGGCGTCCCCG	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"RNA binding motif (RRM) containing"	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.948C>T	16.37:g.86565821G>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	143	25	NM_001159377	0	0	0	0	0	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Silent	SNP	ENST00000360900.6	37	CCDS54047.1																																																																																			.		0.682	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		A	86565821	G	A	86565821	2	1	56	1	0	0	0	0	0	0	0	1	9958	1136	40	1		1	MTHFSD	16	86565821	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	2571526	86565821	3788932	73	5454											
MYH10	4628	ucsc.edu;bcgsc.ca	37	chr17	8424548	8424548	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttggttttatatgcggaGccaaaagctgtctcagtcat	9	15	9	8	1	3	0	2	0	2	0	4	1	3	1	1	2	3	2	1	2	4	5			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr17:8424548G>A	ENST00000269243.4	-	16	2058	c.1920C>T	c.(1918-1920)ggC>ggT	p.G640G	MYH10_ENST00000379980.4_Silent_p.G656G|MYH10_ENST00000360416.3_Silent_p.G671G|MYH10_ENST00000396239.1_Silent_p.G661G	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	640	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TATATGCGGAGCCAAAAGCTG	0.473																																					p.G671G													.	MYH10-92	0			c.C2013T						.						174	165	168					17																	8424548		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon18			TGCGGAGCCAAAA	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.1920C>T	17.37:g.8424548G>A		Somatic	222	2		WXS	Illumina HiSeq		185	42	NM_001256012	0	0	3	5	2	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.		0.473	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			A	8424548	G	A	8424548	2	1	56	1	0	0	0	0	0	0	0	1	10055	958	34	2		2	MYH10	17	8424548	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		8424548	72770662	74	5455											
GIT1	28964	bcgsc.ca	37	chr17	27902918	27902918	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacacccctttccggatcTgaaacccagggcagcgctgg	9	6	11	15	2	1	2	0	1	1	1	2	3	2	3	4	3	2	2	4	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr17:27902918T>C	ENST00000225394.3	-	16	1914		c.e16-2		GIT1_ENST00000394869.3_Splice_Site|RP11-68I3.2_ENST00000581474.1_RNA|GIT1_ENST00000579937.1_Splice_Site|GIT1_ENST00000581348.1_Intron	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1						regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		TTTCCGGATCTGAAACCCAGG	0.622																																					.	Colon(81;41 1719 20078 35068)												.	GIT1-251	0			c.1666-2A>G						.						85	91	89					17																	27902918		2200	4294	6494	SO:0001630	splice_region_variant	28964	exon17			CGGATCTGAAACC	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4272	protein-coding gene	gene with protein product		608434	"G protein-coupled receptor kinase interactor 1"			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.1666-2A>G	17.37:g.27902918T>C		Somatic	128	0		WXS	Illumina HiSeq	Phase_1	126	5	NM_014030	0	0	0	0	0	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Splice_Site	SNP	ENST00000225394.3	37	CCDS11250.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.150346	0.57151	.	.	ENSG00000108262	ENST00000225394;ENST00000394869	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.811	0.69994	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GIT1	24927044	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	5.079000	0.64431	2.157000	0.67596	0.379000	0.24179	.	.		0.622	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030	Intron	C	27902918	T	C	27902918	5	2	56	1	0	0	0	0	0	0	1	0	6416	1594	55	3	641	3	GIT1	17	27902918	Splice_Site	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	19478370	27902918	53292292	75	5456											
ACLY	47	ucsc.edu	37	chr17	40028342	40028342	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctttcccagctcgcgcacaAatgatggtgttgtgggctcc	6	12	11	12	2	1	1	0	1	1	0	4	1	3	1	2	2	1	4	2	2	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr17:40028342A>T	ENST00000352035.2	-	24	2866	c.2736T>A	c.(2734-2736)atT>atA	p.I912I	ACLY_ENST00000537919.1_Silent_p.I641I|ACLY_ENST00000588779.1_5'Flank|ACLY_ENST00000353196.1_Silent_p.I902I|ACLY_ENST00000393896.2_Silent_p.I902I|ACLY_ENST00000590151.1_Silent_p.I912I	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	912					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CTCGCGCACAAATGATGGTGT	0.562																																					p.I912I	Colon(64;807 1396 15971 30971)												.	ACLY-228	0			c.T2736A						.						82	69	74					17																	40028342		2203	4300	6503	SO:0001819	synonymous_variant	47	exon24			CGCACAAATGATG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.2736T>A	17.37:g.40028342A>T		Somatic	173	0		WXS	Illumina HiSeq		143	6	NM_001096	0	0	40	45	5	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	37	CCDS11412.1																																																																																			.		0.562	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		T	40028342	A	T	40028342	2	4	56	1	0	0	0	0	0	0	0	1	143	10	1	5		5	ACLY	17	40028342	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	12125424	40028342	41166868	76	5457											
ACSF2	80221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48541577	48541577	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcagccctctctctgattcAggtgtcattgctgggtcccc	4	13	10	14	0	5	1	3	1	2	0	7	1	6	1	3	2	2	1	3	2	0	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr17:48541577A>G	ENST00000300441.4	+	10	1242		c.e10-1		ACSF2_ENST00000502667.1_Splice_Site|ACSF2_ENST00000427954.2_Splice_Site|ACSF2_ENST00000504392.1_Splice_Site|ACSF2_ENST00000541920.1_Splice_Site	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2						fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCTCTGATTCAGGTGTCATTG	0.547																																					.		.											.	ACSF2-68	0			c.1139-2A>G						.						130	117	121					17																	48541577		2203	4300	6503	SO:0001630	splice_region_variant	80221	exon10			TGATTCAGGTGTC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1139-1A>G	17.37:g.48541577A>G		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	129	44	NM_025149	0	0	0	1	1	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Splice_Site	SNP	ENST00000300441.4	37	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562393	0.65538	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	.	.	.	4.48	4.48	0.54585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.256	0.66053	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACSF2	45896576	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.372000	0.79612	2.016000	0.59253	0.533000	0.62120	.	.		0.547	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	Intron	G	48541577	A	G	48541577	5	3	56	1	0	0	0	0	0	0	1	0	175	202	7	3	1175	3	ACSF2	17	48541577	Splice_Site	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	8513235	48541577	32653633	77	5458											
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11134286	11134286	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cgacgactcaagaaggaagtCgaggcccagttgcccgaaaa	14	4	12	11	4	1	1	1	0	0	1	2	6	1	2	2	2	1	1	2	2	5	1	rs371276213		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:11134286C>G	ENST00000429416.3	+	21	3233	c.2952C>G	c.(2950-2952)gtC>gtG	p.V984V	SMARCA4_ENST00000358026.2_Silent_p.V984V|SMARCA4_ENST00000444061.3_Silent_p.V984V|SMARCA4_ENST00000589677.1_Silent_p.V984V|SMARCA4_ENST00000413806.3_Silent_p.V984V|SMARCA4_ENST00000344626.4_Silent_p.V984V|SMARCA4_ENST00000590574.1_Silent_p.V984V|SMARCA4_ENST00000541122.2_Silent_p.V984V|SMARCA4_ENST00000450717.3_Silent_p.V984V	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	984					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				AGAAGGAAGTCGAGGCCCAGT	0.597			"F, N, Mis"		NSCLC																																p.V984V		.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.C2952G						.						46	42	44					19																	11134286		2202	4300	6502	SO:0001819	synonymous_variant	6597	exon20			GGAAGTCGAGGCC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2952C>G	19.37:g.11134286C>G		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	142	26	NM_003072	0	0	24	33	9	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																			.		0.597	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11134286	C	G	11134286	2	3	56	1	0	0	0	0	0	0	0	1	14802	871	31	4		4	SMARCA4	19	11134286	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		11134286	47994697	78	5459											
NCCRP1	342897	hgsc.bcm.edu	37	chr19	39687743	39687743	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgccgtcgccgccaccaCtgccctcgccgccgtcgctg	2	5	11	23	9	0	0	0	0	0	0	3	0	0	0	8	0	1	1	8	0	0	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:39687743C>T	ENST00000339852.4	+	1	143	c.121C>T	c.(121-123)Ctg>Ttg	p.L41L		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	41	Pro-rich.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						gccgccaccactgccctcgcc	0.776																																					p.L41L	Melanoma(107;1207 1556 14956 29427 52130)	.											.	NCCRP1-91	0			c.C121T						.						2	3	3					19																	39687743		1158	2257	3415	SO:0001819	synonymous_variant	342897	exon1			CCACCACTGCCCT	AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.121C>T	19.37:g.39687743C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	9	5	NM_001001414	0	0	0	0	0	Q6NVV5	Silent	SNP	ENST00000339852.4	37	CCDS12529.1																																																																																			.		0.776	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463829.1	NM_001001414		T	39687743	C	T	39687743	2	4	56	1	0	0	0	0	0	0	0	1	10239	564	20	2		2	NCCRP1	19	39687743	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	28553457	39687743	19441240	79	5460											
ZNF225	7768	broad.mit.edu	37	chr19	44636876	44636878	+	In_Frame_Del	DEL	AAA	AAA	-																															acgcttttgtcattatttttAaatgacacataactgttgta																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	AAA	AAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:44636876_44636878delAAA	ENST00000262894.6	+	5	2389_2391	c.2109_2111delAAA	c.(2107-2112)ttaaat>ttt	p.703_704LN>F	ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_In_Frame_Del_p.703_704LN>F	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	703					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				CAttatttttaaatgacacataa	0.355																																					p.703_704del													.	.	0			c.2109_2111del						.																																			SO:0001651	inframe_deletion	7768	exon5			ATTTTTAAATGAC	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.2109_2111delAAA	19.37:g.44636876_44636878delAAA	ENSP00000262894:p.Leu703_Asn704delinsPhe	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	101	8	NM_013362	0	0	0	0	0	A8K8S2|Q53F12|Q9NS46|Q9UID8	In_Frame_Del	DEL	ENST00000262894.6	37	CCDS46100.1																																																																																			.		0.355	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			-	44636878	AAA	-	44636876	7	5	56	1	0	1	0	1	0	0	0	0	17811	359	13	0	2123	0	ZNF225	19	44636876	In_Frame_Del	DEL	AAA	TCGA-B9-A5W8-01A-11D-A28G-10	4949133	44636876	14492107	80	5461	62	2									
ZNF225	7768	broad.mit.edu;bcgsc.ca	37	chr19	44636880	44636885	+	In_Frame_Del	DEL	GACACA	GACACA	-																															ttttgtcattatttttaaatGacacataactgttgtactca																								rs143348426	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GACACA	GACACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:44636880_44636885delGACACA	ENST00000262894.6	+	5	2393_2398	c.2113_2118delGACACA	c.(2113-2118)gacacadel	p.DT705del	ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_In_Frame_Del_p.DT705del	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	705					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				atttttaaatgacacataactgttgt	0.359																																					p.705_706del													.	.	0			c.2113_2118del						.																																			SO:0001651	inframe_deletion	7768	exon5			TTAAATGACACAT	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.2113_2118delGACACA	19.37:g.44636880_44636885delGACACA	ENSP00000262894:p.Asp705_Thr706del	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	88	8	NM_013362	0	0	0	0	0	A8K8S2|Q53F12|Q9NS46|Q9UID8	In_Frame_Del	DEL	ENST00000262894.6	37	CCDS46100.1																																																																																			.		0.359	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			-	44636885	GACACA	-	44636880	7	5	56	1	0	1	0	1	0	0	0	0	17811	1290	45	0	2127	0	ZNF225	19	44636880	In_Frame_Del	DEL	GACACA	TCGA-B9-A5W8-01A-11D-A28G-10	4	44636880	14492103	81	5462	62	2									
DHX34	9704	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	47856826	47856826	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgctgaaggagcaccaggTggtggtagtggccggtgaca	9	6	18	8	2	0	2	0	2	0	0	0	4	0	3	2	6	1	3	2	6	2	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:47856826T>C	ENST00000328771.4	+	2	888	c.539T>C	c.(538-540)gTg>gCg	p.V180A		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	180	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		GAGCACCAGGTGGTGGTAGTG	0.662																																					p.V180A													.	DHX34-231	0			c.T539C						.						34	38	36					19																	47856826		2203	4299	6502	SO:0001583	missense	9704	exon2			ACCAGGTGGTGGT	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.539T>C	19.37:g.47856826T>C	ENSP00000331907:p.Val180Ala	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	56	19	NM_014681	0	0	2	2	0	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.493784	0.84962	.	.	ENSG00000134815	ENST00000328771;ENST00000257252	T	0.14266	2.52	5.26	5.26	0.73747	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.47852	D	0.000215	T	0.42063	0.1186	M	0.84846	2.72	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	T	0.47368	-0.9123	10	0.87932	D	0	-25.0325	14.1501	0.65378	0.0:0.0:0.0:1.0	.	180;180	Q14147;B4E3G3	DHX34_HUMAN;.	A	180	ENSP00000331907:V180A	ENSP00000257252:V180A	V	+	2	0	DHX34	52548666	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	7.672000	0.83956	1.992000	0.58205	0.454000	0.30748	GTG	.		0.662	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		C	47856826	T	C	47856826	3	2	56	1	0	0	0	0	1	0	0	0	4518	1696	59	3	541	3	DHX34	19	47856826	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	3219946	47856826	11272157	82	5463											
LILRB1	10859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55143956	55143956	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcagtgcagccaggtcctAtcgtggcccctgaggagacc	7	8	12	14	1	1	2	1	1	1	1	4	3	2	2	5	3	2	1	5	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:55143956A>G	ENST00000396331.1	+	7	1060	c.703A>G	c.(703-705)Atc>Gtc	p.I235V	LILRB1_ENST00000448689.1_Missense_Mutation_p.I235V|LILRB1_ENST00000396332.4_Missense_Mutation_p.I235V|LILRB1_ENST00000434867.2_Missense_Mutation_p.I235V|LILRB1_ENST00000396327.3_Missense_Mutation_p.I235V|LILRB1_ENST00000418536.2_Missense_Mutation_p.I235V|LILRB1_ENST00000396317.1_Missense_Mutation_p.I235V|LILRB1_ENST00000427581.2_Missense_Mutation_p.I271V|LILRB1_ENST00000324602.7_Missense_Mutation_p.I235V|LILRB1_ENST00000396315.1_Missense_Mutation_p.I235V|LILRB1_ENST00000396321.2_Missense_Mutation_p.I235V	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	235	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GCCAGGTCCTATCGTGGCCCC	0.537										HNSCC(37;0.09)																											p.I235V		.											.	LILRB1-137	0			c.A703G						.						98	102	101					19																	55143956		2203	4300	6503	SO:0001583	missense	10859	exon6			GGTCCTATCGTGG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.703A>G	19.37:g.55143956A>G	ENSP00000379622:p.Ile235Val	Somatic	333	0		WXS	Illumina HiSeq	Phase_I	264	83	NM_001081637	0	0	9	9	0	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.218786	0.00286	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87	1.49	-1.31	0.09230	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.873016	0.09637	N	0.775542	T	0.01592	0.0051	N	0.00219	-1.825	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.001;0.001;0.006;0.001;0.002	T	0.39014	-0.9634	10	0.02654	T	1	.	2.0446	0.03557	0.3776:0.0:0.3682:0.2542	.	235;235;235;235;235	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	V	235;235;235;235;235;235;235;235;271;235;235	ENSP00000379614:I235V;ENSP00000391514:I235V;ENSP00000409968:I235V;ENSP00000379622:I235V;ENSP00000379618:I235V;ENSP00000315997:I235V;ENSP00000405243:I235V;ENSP00000379623:I235V;ENSP00000395004:I271V;ENSP00000379610:I235V;ENSP00000379608:I235V	ENSP00000315997:I235V	I	+	1	0	LILRB1	59835768	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.930000	0.03972	-0.750000	0.04740	-1.160000	0.01791	ATC	.		0.537	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			G	55143956	A	G	55143956	3	3	56	1	0	0	0	0	1	0	0	0	8812	449	16	3	721	3	LILRB1	19	55143956	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	7287130	55143956	3985027	83	5464											
HNF4A	3172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42984469	42984469	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagcgtgaacgcgcccctcGgggctccagtggagagttct	6	8	14	13	4	2	2	1	1	1	1	4	3	3	2	3	3	2	2	3	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr20:42984469G>T	ENST00000316673.4	+	1	130	c.25G>T	c.(25-27)Ggg>Tgg	p.G9W	HNF4A_ENST00000609795.1_Missense_Mutation_p.G9W|RP5-881L22.5_ENST00000438702.1_RNA|HNF4A_ENST00000457232.1_Missense_Mutation_p.G9W			P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	157					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.G9W(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CGCGCCCCTCGGGGCTCCAGT	0.682																																					p.G9W	Colon(79;2 1269 8820 14841 52347)	.											.	HNF4A-227	1	Substitution - Missense(1)	lung(1)	c.G25T						.						24	28	26					20																	42984469		2037	4184	6221	SO:0001583	missense	3172	exon1			CCCCTCGGGGCTC	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316673.4:c.25G>T	20.37:g.42984469G>T	ENSP00000315180:p.Gly9Trp	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	75	16	NM_001030003	0	0	0	0	0	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316673.4	37	CCDS42876.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213853	0.39102	.	.	ENSG00000101076	ENST00000316673;ENST00000457232	D;D	0.92595	-3.07;-3.06	4.98	3.04	0.35103	.	.	.	.	.	D	0.91099	0.7198	N	0.24115	0.695	0.80722	D	1	D;D;P	0.71674	0.998;0.998;0.948	D;D;P	0.70227	0.93;0.968;0.759	D	0.89491	0.3757	9	0.72032	D	0.01	.	7.9382	0.29941	0.1907:0.0:0.8093:0.0	.	9;9;9	F1D8T0;P41235-6;P41235-7	.;.;.	W	9	ENSP00000315180:G9W;ENSP00000396216:G9W	ENSP00000315180:G9W	G	+	1	0	HNF4A	42417883	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	2.571000	0.45990	0.635000	0.30488	-0.136000	0.14681	GGG	.		0.682	HNF4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079362.2			T	42984469	G	T	42984469	3	4	56	1	0	0	0	0	1	0	0	0	7274	1116	39	4	27	4	HNF4A	20	42984469	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		42984469	20041051	84	5465											
GGT5	2687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24628898	24628898	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agcagcgcgatggtgggctgGaacagctgcgcccagggcag	8	4	18	11	3	0	0	0	0	0	0	0	2	0	1	1	4	5	4	1	4	1	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:24628898G>C	ENST00000327365.4	-	4	905	c.489C>G	c.(487-489)ttC>ttG	p.F163L	GGT5_ENST00000398292.3_Missense_Mutation_p.F163L|GGT5_ENST00000263112.7_Missense_Mutation_p.F131L|GGT5_ENST00000418439.2_Missense_Mutation_p.P88A	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	163					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						TGGTGGGCTGGAACAGCTGCG	0.701																																					p.F163L		.											.	GGT5-71	0			c.C489G						.						23	25	24					22																	24628898		2184	4285	6469	SO:0001583	missense	2687	exon4			GGGCTGGAACAGC	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"Gamma-glutamyltransferases"	4260	protein-coding gene	gene with protein product		137168	"gamma-glutamyltransferase-like activity 1"	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.489C>G	22.37:g.24628898G>C	ENSP00000330080:p.Phe163Leu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	193	36	NM_001099781	0	0	1	1	0	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	37	CCDS13825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.533985|4.533985	0.85812|0.85812	.|.	.|.	ENSG00000099998|ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292|ENST00000418439	T;T;T|T	0.03717|0.66638	3.83;3.83;3.83|-0.22	4.32|4.32	3.3|3.3	0.37823|0.37823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58264|0.58264	0.2110|0.2110	M|M	0.64997|0.64997	1.995|1.995	0.25198|0.25198	N|N	0.990074|0.990074	D;D;B;D|B	0.69078|0.25667	0.967;0.997;0.095;0.997|0.131	P;D;B;D|B	0.67900|0.25140	0.775;0.954;0.129;0.954|0.058	T|T	0.45469|0.45469	-0.9259|-0.9259	10|9	0.72032|0.17369	D|T	0.01|0.5	-37.4629|-37.4629	6.7667|6.7667	0.23571|0.23571	0.2119:0.0:0.7881:0.0|0.2119:0.0:0.7881:0.0	.|.	131;163;163;163|88	P36269-2;Q53XM9;Q6GMP0;P36269|E7EUG3	.;.;.;GGT5_HUMAN|.	L|A	163;131;78;163|88	ENSP00000330080:F163L;ENSP00000263112:F131L;ENSP00000381340:F163L|ENSP00000392146:P88A	ENSP00000263112:F131L|ENSP00000392146:P88A	F|P	-|-	3|1	2|0	GGT5|GGT5	22958898|22958898	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	1.180000|1.180000	0.32005|0.32005	1.170000|1.170000	0.42753|0.42753	0.585000|0.585000	0.79938|0.79938	TTC|CCA	.		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		C	24628898	G	C	24628898	3	2	56	1	0	0	0	0	1	0	0	0	6382	1165	41	4	1310	4	GGT5	22	24628898	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		24628898	26675668	85	5466											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885571	29885572	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT																															aacgaaggaggaagcaaagtINScccctgagaaggccaagtcc																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:29885571_29885572insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1975_1976	c.1942_1943insCCCCTGAGAAGGCCAAGT	c.(1942-1944)tcc>tCCCCTGAGAAGGCCAAGTcc	p.648_648S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GGAAGCAAAGTCCCCTGAGAAG	0.569																																					p.S648delinsSPEKAKS		.											.	NEFH-90	0			c.1942_1943insCCCCTGAGAAGGCCAAGT						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	22.37:g.29885571_29885572insCCCCTGAGAAGGCCAAGT	Exception_encountered	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	223	71	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																			.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CCCCTGAGAAGGCCAAGT	29885572	-	CCCCTGAGAAGGCCAAGT	29885571	7	5	56	1	0	1	1	0	0	0	0	0	10340	1667	58	0	1956	0	NEFH	22	29885571	In_Frame_Ins	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	5256673	29885571	21418995	86	5467											
CSNK1E	1454	broad.mit.edu	37	chr22	38699223	38699223	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcacacactccagcttgatgGcgacttcctcaccagaggcg	9	8	9	15	2	2	2	2	1	0	1	4	3	4	2	3	2	1	1	3	2	0	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:38699223G>A	ENST00000396832.1	-	3	367	c.107C>T	c.(106-108)gCc>gTc	p.A36V	CSNK1E_ENST00000413574.2_Missense_Mutation_p.A36V|CSNK1E_ENST00000400206.2_Missense_Mutation_p.A36V|CSNK1E_ENST00000405675.3_Missense_Mutation_p.A36V|CSNK1E_ENST00000359867.3_Missense_Mutation_p.A36V|CSNK1E_ENST00000403904.1_Missense_Mutation_p.A36V	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	36	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					CAGCTTGATGGCGACTTCCTC	0.632																																					p.A36V	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)												.	CSNK1E-1193	0			c.C107T						.						67	38	48					22																	38699223		2202	4300	6502	SO:0001583	missense	1454	exon3			TTGATGGCGACTT		CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.107C>T	22.37:g.38699223G>A	ENSP00000380044:p.Ala36Val	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	57	4	NM_001894	0	0	18	18	0		Missense_Mutation	SNP	ENST00000396832.1	37	CCDS13970.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.501307	0.64298	.	.	ENSG00000213923	ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904;ENST00000413574;ENST00000405675;ENST00000430335	T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.64	4.63	0.57726	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050330	0.85682	D	0.000000	D	0.88157	0.6361	M	0.90145	3.09	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.83275	0.8;0.988;0.996	D	0.90538	0.4500	10	0.87932	D	0	.	14.2141	0.65781	0.0723:0.0:0.9277:0.0	.	36;36;36	B0QY35;B0QY34;P49674	.;.;KC1E_HUMAN	V	36	ENSP00000352929:A36V;ENSP00000380044:A36V;ENSP00000383067:A36V;ENSP00000384074:A36V;ENSP00000407235:A36V;ENSP00000384426:A36V;ENSP00000412335:A36V	ENSP00000352929:A36V	A	-	2	0	CSNK1E	37029169	1.000000	0.71417	0.960000	0.40013	0.000000	0.00434	9.869000	0.99810	1.399000	0.46721	-0.136000	0.14681	GCC	.		0.632	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		A	38699223	G	A	38699223	3	1	56	1	0	0	0	0	1	0	0	0	3959	1203	42	2	1175	2	CSNK1E	22	38699223	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	8813652	38699223	12605343	87	5468											
TCEANC	170082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	13680806	13680808	+	In_Frame_Del	DEL	CCT	CCT	-																															cagagtcctcaaaaactgccCctctgtggctttgaaaaaga																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:13680806_13680808delCCT	ENST00000380600.1	+	2	266_268	c.179_181delCCT	c.(178-183)ccctct>cct	p.S61del	TCEANC_ENST00000490617.1_3'UTR|TCEANC_ENST00000545566.1_In_Frame_Del_p.S61del|TCEANC_ENST00000544987.1_In_Frame_Del_p.S61del|TCEANC_ENST00000314720.4_In_Frame_Del_p.S91del			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	61	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						AAAAACTGCCCCTCTGTGGCTTT	0.443																																					p.90_91del		.											.	TCEANC-41	0			c.269_271del						.																																			SO:0001651	inframe_deletion	170082	exon4			.		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.179_181delCCT	X.37:g.13680806_13680808delCCT	ENSP00000369974:p.Ser61del	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	58	33	NM_152634	0	0	0	0	0	A6NI06|B2RDM3	In_Frame_Del	DEL	ENST00000380600.1	37																																																																																				.		0.443	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634		-	13680808	CCT	-	13680806	7	5	56	1	0	1	0	1	0	0	0	0	15710	623	22	0	275	0	TCEANC	23	13680806	In_Frame_Del	DEL	CCT	TCGA-B9-A5W8-01A-11D-A28G-10		13680806	141589754	88	5469											
SH3KBP1	30011	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	19560042	19560043	+	Splice_Site	INS	-	-	T																															aagagtccccaggcactcacINSttctgctggtccttcatggt																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:19560042_19560043insT	ENST00000397821.3	-	16	2182_2183		c.e16+1		SH3KBP1_ENST00000541422.1_Splice_Site|SH3KBP1_ENST00000379698.4_Splice_Site|SH3KBP1_ENST00000379716.1_Splice_Site	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1						apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						CAGGCACTCACTTCTGCTGGTC	0.634																																					.		.											.	SH3KBP1-130	0			c.1178+1->A						.																																			SO:0001630	splice_region_variant	30011	exon12			.	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1892+1->A	X.37:g.19560044_19560044dupT		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	81	41	NM_001184960	0	0	0	0	0	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Splice_Site	INS	ENST00000397821.3	37	CCDS14193.1																																																																																			.		0.634	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892	Intron	T	19560043	-	T	19560042	8	5	56	1	0	1	1	0	0	0	1	0	14287	579	20	0	116	0	SH3KBP1	23	19560042	Splice_Site	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	5879236	19560042	135710518	89	5470	63	2									
SH3KBP1	30011	hgsc.bcm.edu;bcgsc.ca	37	chrX	19560045	19560045	+	Missense_Mutation	SNP	C	C	A																															gagtccccaggcactcacttCtgctggtccttcatggtctc																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:19560045C>A	ENST00000397821.3	-	16	2180	c.1890G>T	c.(1888-1890)caG>caT	p.Q630H	SH3KBP1_ENST00000541422.1_Missense_Mutation_p.Q369H|SH3KBP1_ENST00000379698.4_Missense_Mutation_p.Q593H|SH3KBP1_ENST00000379716.1_Missense_Mutation_p.Q392H	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	630					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						GCACTCACTTCTGCTGGTCCT	0.627																																					p.Q630H		.											.	SH3KBP1-130	0			c.G1890T						.						106	96	100					X																	19560045		2203	4300	6503	SO:0001583	missense	30011	exon16			TCACTTCTGCTGG	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1890G>T	X.37:g.19560045C>A	ENSP00000380921:p.Gln630His	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	81	40	NM_031892	0	0	0	0	0	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Missense_Mutation	SNP	ENST00000397821.3	37	CCDS14193.1	.	.	.	.	.	.	.	.	.	.	C	3.308	-0.141521	0.06669	.	.	ENSG00000147010	ENST00000379702;ENST00000397821;ENST00000379716;ENST00000379698;ENST00000541422;ENST00000379726	T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4	5.39	4.41	0.53225	.	0.000000	0.64402	D	0.000010	T	0.30541	0.0768	N	0.12887	0.27	0.37413	D	0.9133	D;B;D	0.89917	1.0;0.156;0.997	D;B;D	0.85130	0.997;0.031;0.99	T	0.44050	-0.9353	10	0.02654	T	1	-14.024	6.2238	0.20695	0.0:0.7735:0.0:0.2265	.	392;630;593	Q5JPT4;Q96B97;Q5JPT5	.;SH3K1_HUMAN;.	H	615;630;392;593;369;610	ENSP00000380921:Q630H;ENSP00000369039:Q392H;ENSP00000369020:Q593H;ENSP00000442499:Q369H;ENSP00000369049:Q610H	ENSP00000369020:Q593H	Q	-	3	2	SH3KBP1	19469966	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.388000	0.34442	2.265000	0.75225	0.529000	0.55759	CAG	.		0.627	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		A	19560045	C	A	19560045	3	1	56	1	0	0	0	0	1	0	0	0	14287	912	32	4	119	4	SH3KBP1	23	19560045	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	3	19560045	135710515	90	5471	63	2									
TAF1	6872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70618524	70618524	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttaagaggaaccaggaaaaGgagaagcttaagggtcctcc	15	6	12	8	0	0	2	0	0	0	2	2	5	2	4	3	4	2	1	3	4	6	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:70618524G>A	ENST00000373790.4	+	24	3771	c.3720G>A	c.(3718-3720)aaG>aaA	p.K1240K	TAF1_ENST00000449580.1_Silent_p.K1240K|TAF1_ENST00000423759.1_Silent_p.K1261K|TAF1_ENST00000276072.3_Silent_p.K1261K	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1240					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ACCAGGAAAAGGAGAAGCTTA	0.458																																					p.K1261K		.											.	TAF1-900	0			c.G3783A						.						93	79	84					X																	70618524		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon24			GGAAAAGGAGAAG		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3720G>A	X.37:g.70618524G>A		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	129	74	NM_004606	0	0	2	3	1	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	9.733	1.162842	0.21538	.	.	ENSG00000147133	ENST00000483985	.	.	.	5.54	3.77	0.43336	.	.	.	.	.	T	0.59074	0.2167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53129	-0.8482	4	.	.	.	.	9.3163	0.37937	0.2564:0.0:0.7436:0.0	.	.	.	.	K	151	.	.	R	+	2	0	TAF1	70535249	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.737000	0.26144	0.520000	0.28426	0.468000	0.43344	AGG	.		0.458	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70618524	G	A	70618524	2	1	56	1	0	0	0	0	0	0	0	1	15545	991	35	2		2	TAF1	23	70618524	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	51058479	70618524	84652036	91	5472											
ARMCX5	64860	broad.mit.edu;bcgsc.ca	37	chrX	101857944	101857944	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	taggcaaagggaaaagtatgGgcctaatccgaaggcctgcc	13	6	13	9	1	0	0	0	0	0	0	1	2	1	1	4	4	1	2	4	4	7	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:101857944G>T	ENST00000604957.1	+	1	3497	c.875G>T	c.(874-876)gGg>gTg	p.G292V	RP4-769N13.7_ENST00000602441.1_RNA|ARMCX5_ENST00000372742.1_Missense_Mutation_p.G292V|ARMCX5_ENST00000541409.1_Missense_Mutation_p.G292V|ARMCX5_ENST00000246174.2_Missense_Mutation_p.G292V|ARMCX5_ENST00000536530.1_Missense_Mutation_p.G292V|ARMCX5_ENST00000537008.1_Missense_Mutation_p.G292V|RP4-769N13.6_ENST00000476910.2_RNA	NM_001168478.1	NP_001161950.1	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	292										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	22						GAAAAGTATGGGCCTAATCCG	0.443																																					p.G292V													.	ARMCX5-131	0			c.G875T						.						69	64	66					X																	101857944		2203	4299	6502	SO:0001583	missense	64860	exon3			AGTATGGGCCTAA		CCDS14500.1	Xq22.1-q22.3	2014-03-21			ENSG00000125962	ENSG00000125962		"Armadillo repeat containing"	25772	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_022838		Approved	FLJ12969, GASP5	uc004ejh.3	Q6P1M9	OTTHUMG00000022062	ENST00000604957.1:c.875G>T	X.37:g.101857944G>T	ENSP00000474720:p.Gly292Val	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	72	5	NM_022838	0	0	0	0	0	B3KU88|D3DX99|Q68DB4|Q9BVZ3|Q9H969	Missense_Mutation	SNP	ENST00000604957.1	37	CCDS14500.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951432	0.53186	.	.	ENSG00000125962	ENST00000246174;ENST00000537008;ENST00000541409;ENST00000536530;ENST00000372742	T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02	3.67	3.67	0.42095	.	0.166576	0.29034	N	0.013357	T	0.31009	0.0783	L	0.29908	0.895	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.04268	-1.0964	10	0.72032	D	0.01	-4.0369	10.0142	0.42006	0.0:0.0:1.0:0.0	.	292	Q6P1M9	ARMX5_HUMAN	V	292	ENSP00000246174:G292V;ENSP00000439001:G292V;ENSP00000446385:G292V;ENSP00000445851:G292V;ENSP00000361827:G292V	ENSP00000246174:G292V	G	+	2	0	ARMCX5	101744600	0.992000	0.36948	1.000000	0.80357	0.921000	0.55340	0.919000	0.28692	2.114000	0.64651	0.600000	0.82982	GGG	.		0.443	ARMCX5-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469659.1	NM_022838		T	101857944	G	T	101857944	3	4	56	1	0	0	0	0	1	0	0	0	963	1232	43	4	877	4	ARMCX5	23	101857944	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	31239420	101857944	53412616	92	5473											
GLUD2	2747	ucsc.edu	37	chrX	120183026	120183026	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acggcagagttccaagacagTatatcgggtgcatctgagaa	13	8	12	8	2	1	3	0	1	1	3	3	4	2	3	1	2	1	4	1	2	4	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:120183026T>G	ENST00000328078.1	+	1	1565	c.1488T>G	c.(1486-1488)agT>agG	p.S496R		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	496					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						TCCAAGACAGTATATCGGGTG	0.453																																					p.S496R													.	GLUD2-131	0			c.T1488G						.						163	129	141					X																	120183026		2203	4300	6503	SO:0001583	missense	2747	exon1			AGACAGTATATCG	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1488T>G	X.37:g.120183026T>G	ENSP00000327589:p.Ser496Arg	Somatic	89	0		WXS	Illumina HiSeq		107	1	NM_012084	0	0	2	152	150	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.467675	0.00011	.	.	ENSG00000182890	ENST00000328078	D	0.95918	-3.85	1.99	-3.98	0.04082	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.045906	0.85682	N	0.000000	T	0.72961	0.3526	N	0.00453	-1.485	0.19300	N	0.999976	B	0.02656	0.0	B	0.01281	0.0	T	0.76277	-0.3018	10	0.02654	T	1	.	4.3409	0.11110	0.6313:0.0:0.1881:0.1806	.	496	P49448	DHE4_HUMAN	R	496	ENSP00000327589:S496R	ENSP00000327589:S496R	S	+	3	2	GLUD2	120010707	1.000000	0.71417	0.043000	0.18650	0.080000	0.17528	0.344000	0.19962	-1.074000	0.03132	-1.405000	0.01134	AGT	.		0.453	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		G	120183026	T	G	120183026	3	3	56	1	0	0	0	0	1	0	0	0	6497	1635	57	5	1490	5	GLUD2	23	120183026	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	18325082	120183026	35087534	93	5474											
HTR6	3362	broad.mit.edu	37	chr1	20005583	20005583	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggagcgccaggccagcctgGcctcgccatcactgcgcacc	6	4	13	18	3	1	0	1	0	0	0	2	1	1	1	6	3	3	1	6	3	0	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:20005583G>T	ENST00000289753.1	+	3	1512	c.1045G>T	c.(1045-1047)Gcc>Tcc	p.A349S		NM_000871.1	NP_000862.1	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled	349					brain development (GO:0007420)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|long-term synaptic potentiation (GO:0060291)|negative regulation of acetylcholine secretion, neurotransmission (GO:0014058)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|synaptic transmission (GO:0007268)	cilium (GO:0005929)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)|serotonin receptor activity (GO:0004993)			endometrium(1)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Mianserin(DB06148)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Quetiapine(DB01224)|Sertindole(DB06144)|Ziprasidone(DB00246)	GGCCAGCCTGGCCTCGCCATC	0.687																																					p.A349S	Esophageal Squamous(168;1879 2619 6848 21062)												.	HTR6-91	0			c.G1045T						.						30	34	33					1																	20005583		2201	4298	6499	SO:0001583	missense	3362	exon3			AGCCTGGCCTCGC	L41147	CCDS197.1	1p36-p35	2012-08-08	2012-02-03		ENSG00000158748	ENSG00000158748		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5301	protein-coding gene	gene with protein product		601109	"5-hydroxytryptamine (serotonin) receptor 6"			8522988	Standard	NM_000871		Approved	5-HT6, 5-HT6R	uc001bcl.3	P50406	OTTHUMG00000002713	ENST00000289753.1:c.1045G>T	1.37:g.20005583G>T	ENSP00000289753:p.Ala349Ser	Somatic	43	2		WXS	Illumina HiSeq	Phase_I	80	11	NM_000871	0	0	0	0	0	Q13640|Q5TGZ1	Missense_Mutation	SNP	ENST00000289753.1	37	CCDS197.1	.	.	.	.	.	.	.	.	.	.	G	9.626	1.135033	0.21123	.	.	ENSG00000158748	ENST00000289753	T	0.32988	1.43	5.39	4.25	0.50352	.	0.303975	0.23513	N	0.047376	T	0.16514	0.0397	N	0.14661	0.345	0.23113	N	0.998271	P	0.45044	0.849	B	0.42738	0.396	T	0.07849	-1.0751	9	.	.	.	.	4.8529	0.13545	0.2699:0.0:0.7301:0.0	.	349	P50406	5HT6R_HUMAN	S	349	ENSP00000289753:A349S	.	A	+	1	0	HTR6	19878170	0.724000	0.28038	0.959000	0.39883	0.135000	0.20990	1.057000	0.30492	2.698000	0.92095	0.561000	0.74099	GCC	.		0.687	HTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007704.1	NM_000871		T	20005583	G	T	20005583	3	4	57	1	0	0	0	0	1	0	0	0	7472	1203	42	4	1055	4	HTR6	1	20005583	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		20005583	229245038	1	5475											
C1orf128	57095	hgsc.bcm.edu	37	chr1	24105128	24105128	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcgacctggagcggctgcaAtgccttaacgagagccgcga	10	6	13	12	5	0	1	0	0	0	1	1	5	0	2	3	2	5	2	3	2	2	1	rs562148184		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:24105128A>G	ENST00000246151.4	+	1	234	c.123A>G	c.(121-123)caA>caG	p.Q41Q	RP5-886K2.3_ENST00000427796.1_RNA	NM_020362.4	NP_065095.2	Q9GZP4	PITH1_HUMAN	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	41	PITH. {ECO:0000255|PROSITE- ProRule:PRU00864}.					nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	6						AGCGGCTGCAATGCCTTAACG	0.751													G|||	1	0.000199681	0	0.0014	5008	,	,		6646	0		0	False		,,,				2504	0				p.Q41Q		.											.	PITHD1-90	0			c.A123G						.																																			SO:0001819	synonymous_variant	57095	exon1			GCTGCAATGCCTT		CCDS240.1	1p36.11	2011-02-21	2011-02-21	2011-02-21	ENSG00000057757	ENSG00000057757			25022	protein-coding gene	gene with protein product	"TXNL1 C-terminal like"		"chromosome 1 open reading frame 128"	C1orf128		12477932	Standard	NM_020362		Approved	HT014, TXNL1CL	uc001bhq.3	Q9GZP4	OTTHUMG00000002960	ENST00000246151.4:c.123A>G	1.37:g.24105128A>G		Somatic	4	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_020362	0	0	10	14	4	B2R7J4|Q5QPN6|Q5QPN7|Q9NRI8	Silent	SNP	ENST00000246151.4	37	CCDS240.1																																																																																			.		0.751	PITHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008243.1	NM_020362		G	24105128	A	G	24105128	2	3	57	1	0	0	0	0	0	0	0	1	2001	98	4	3		3	C1orf128	1	24105128	Silent	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	4099545	24105128	225145493	2	5476											
CATSPER4	378807	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	26524220	26524220	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattatcgtctttatcttgcTcttgcggttcttcattaatg	6	20	6	9	2	5	0	1	0	4	0	6	0	5	0	0	1	2	2	0	1	3	8			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:26524220T>A	ENST00000456354.2	+	4	570	c.503T>A	c.(502-504)cTc>cAc	p.L168H		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	168					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TTTATCTTGCTCTTGCGGTTC	0.542																																					p.L168H													.	CATSPER4-91	0			c.T503A						.						105	88	94					1																	26524220		2203	4300	6503	SO:0001583	missense	378807	exon4			TCTTGCTCTTGCG	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"Voltage-gated ion channels / Cation channels, sperm associated"	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.503T>A	1.37:g.26524220T>A	ENSP00000390423:p.Leu168His	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	84	29	NM_198137	0	0	0	0	0	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	.	.	.	.	.	.	.	.	.	.	T	15.51	2.855937	0.51376	.	.	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.98807	-5.15;-5.15	5.32	4.16	0.48862	Ion transport (1);	0.974000	0.08402	N	0.951329	D	0.98658	0.9550	M	0.71920	2.185	0.09310	N	1	D	0.69078	0.997	P	0.60173	0.87	D	0.93664	0.6984	10	0.48119	T	0.1	-7.1998	9.1267	0.36818	0.0:0.0:0.1847:0.8153	.	168	Q7RTX7	CTSR4_HUMAN	H	168	ENSP00000341006:L168H;ENSP00000390423:L168H	ENSP00000341006:L168H	L	+	2	0	CATSPER4	26396807	0.256000	0.24012	0.166000	0.22797	0.043000	0.13939	2.574000	0.46016	0.820000	0.34516	0.460000	0.39030	CTC	.		0.542	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137		A	26524220	T	A	26524220	3	1	57	1	0	0	0	0	1	0	0	0	2696	1551	54	5	517	5	CATSPER4	1	26524220	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	2419092	26524220	222726401	3	5477											
RLF	6018	broad.mit.edu;bcgsc.ca	37	chr1	40702398	40702398	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agatttgtatccatgtcccgGtacagactgttcccgtgtgt	7	14	10	10	2	0	2	0	0	0	2	3	2	3	2	3	1	1	3	3	1	2	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:40702398G>A	ENST00000372771.4	+	8	2051	c.2024G>A	c.(2023-2025)gGt>gAt	p.G675D		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	675					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			CCATGTCCCGGTACAGACTGT	0.388																																					p.G675D													.	RLF-93	0			c.G2024A						.						111	111	111					1																	40702398		2203	4300	6503	SO:0001583	missense	6018	exon8			GTCCCGGTACAGA		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.2024G>A	1.37:g.40702398G>A	ENSP00000361857:p.Gly675Asp	Somatic	51	1		WXS	Illumina HiSeq	Phase_I	46	20	NM_012421	0	0	2	7	5	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658618	0.47467	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.39056	1.1	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.045241	0.85682	D	0.000000	T	0.60457	0.2270	L	0.44542	1.39	0.58432	D	0.999997	D;D	0.89917	0.998;1.0	D;D	0.91635	0.976;0.999	T	0.56631	-0.7947	10	0.52906	T	0.07	-12.1306	20.4387	0.99107	0.0:0.0:1.0:0.0	.	368;675	F5H2M5;Q13129	.;RLF_HUMAN	D	675;368	ENSP00000361857:G675D	ENSP00000361857:G675D	G	+	2	0	RLF	40474985	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.167000	0.58209	2.836000	0.97738	0.655000	0.94253	GGT	.		0.388	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40702398	G	A	40702398	3	1	57	1	0	0	0	0	1	0	0	0	13421	1261	44	2	2054	2	RLF	1	40702398	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	14178178	40702398	208548223	4	5478											
HFM1	164045	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	91742587	91742587	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttacaaagatgattgcattCtcggttcccaggttttttgc	8	17	8	8	1	1	2	0	1	1	1	3	2	2	2	1	2	3	3	1	2	2	8			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:91742587C>G	ENST00000370425.3	-	31	3522	c.3424G>C	c.(3424-3426)Gaa>Caa	p.E1142Q	HFM1_ENST00000370424.3_Missense_Mutation_p.E821Q|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Missense_Mutation_p.E374Q	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1142					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGATTGCATTCTCGGTTCCCA	0.289																																					p.E1142Q		.											.	HFM1-112	0			c.G3424C						.						129	128	129					1																	91742587		2203	4299	6502	SO:0001583	missense	164045	exon31			TGCATTCTCGGTT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3424G>C	1.37:g.91742587C>G	ENSP00000359454:p.Glu1142Gln	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	88	30	NM_001017975	0	0	0	1	1	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	12.44|12.44|12.44	1.937796|1.937796|1.937796	0.34189|0.34189|0.34189	.|.|.	.|.|.	ENSG00000162669|ENSG00000162669|ENSG00000162669	ENST00000430465|ENST00000370425;ENST00000294696;ENST00000370424|ENST00000370421	.|T;T;T|.	.|0.64618|.	.|0.25;0.63;-0.11|.	5.71|5.71|5.71	5.71|5.71|5.71	0.89125|0.89125|0.89125	.|.|.	0.237508|0.237508|.	0.33005|0.33005|.	N|N|.	0.005389|0.005389|.	T|T|T	0.55481|0.55481|0.55481	0.1923|0.1923|0.1923	M|M|M	0.64997|0.64997|0.64997	1.995|1.995|1.995	0.36745|0.36745|0.36745	D|D|D	0.882419|0.882419|0.882419	.|B;B;B|.	.|0.28378|.	.|0.082;0.209;0.105|.	.|B;B;B|.	.|0.25614|.	.|0.045;0.062;0.034|.	T|T|T	0.59461|0.59461|0.59461	-0.7450|-0.7450|-0.7450	6|10|6	.|0.40728|0.42905	.|T|T	.|0.16|0.14	.|.|.	10.7947|10.7947|10.7947	0.46453|0.46453|0.46453	0.0:0.9137:0.0:0.0863|0.0:0.9137:0.0:0.0863|0.0:0.9137:0.0:0.0863	.|.|.	.|821;353;1142|.	.|A6NGI5;B1B0B5;A2PYH4|.	.|.;.;HFM1_HUMAN|.	D|Q|T	353|1142;374;821|825	.|ENSP00000359454:E1142Q;ENSP00000294696:E374Q;ENSP00000359453:E821Q|.	.|ENSP00000294696:E374Q|ENSP00000359450:R825T	E|E|R	-|-|-	3|1|2	2|0|0	HFM1|HFM1|HFM1	91515175|91515175|91515175	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.815000|0.815000|0.815000	0.46073|0.46073|0.46073	3.562000|3.562000|3.562000	0.53777|0.53777|0.53777	2.698000|2.698000|2.698000	0.92095|0.92095|0.92095	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	GAG|GAA|AGA	.		0.289	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		G	91742587	C	G	91742587	3	3	57	1	0	0	0	0	1	0	0	0	7104	922	32	4	919	4	HFM1	1	91742587	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	51040189	91742587	157508034	5	5479											
SLC44A3	126969	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	95330398	95330398	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagggtcatttttaatctcTgtggtgaggattccgagaat	11	14	11	5	1	2	2	1	1	1	1	4	4	3	3	1	3	0	0	1	3	3	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:95330398T>A	ENST00000271227.6	+	11	1440	c.1338T>A	c.(1336-1338)tcT>tcA	p.S446S	SLC44A3_ENST00000532427.1_Silent_p.S366S|SLC44A3_ENST00000467909.1_Silent_p.S398S|SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000529450.1_Silent_p.S414S|SLC44A3_ENST00000527077.1_Silent_p.S378S|SLC44A3_ENST00000446120.2_Silent_p.S410S	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	446					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	TTTTAATCTCTGTGGTGAGGA	0.433																																					p.S446S		.											.	SLC44A3-91	0			c.T1338A						.						217	202	207					1																	95330398		2203	4300	6503	SO:0001819	synonymous_variant	126969	exon11			AATCTCTGTGGTG	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"Solute carriers"	28689	protein-coding gene	gene with protein product			"solute carrier family, member 3"			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1338T>A	1.37:g.95330398T>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	68	22	NM_001114106	0	0	127	210	83	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																			.		0.433	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		A	95330398	T	A	95330398	2	1	57	1	0	0	0	0	0	0	0	1	14669	1567	55	5		5	SLC44A3	1	95330398	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	3587811	95330398	153920223	6	5480											
CHD1L	9557	ucsc.edu;bcgsc.ca	37	chr1	146765335	146765335	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgatcgttccaatgtccTgtctggcattaagatggcag	8	13	11	9	2	1	2	0	1	1	1	5	2	3	2	2	2	0	3	2	2	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:146765335T>C	ENST00000369258.4	+	21	2455	c.2435T>C	c.(2434-2436)cTg>cCg	p.L812P	CHD1L_ENST00000369259.3_Missense_Mutation_p.L608P|CHD1L_ENST00000431239.1_Missense_Mutation_p.L718P|CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000361293.5_Missense_Mutation_p.L531P	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	812	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					TCCAATGTCCTGTCTGGCATT	0.458																																					p.L812P													.	CHD1L-231	0			c.T2435C						.						187	182	184					1																	146765335		2203	4300	6503	SO:0001583	missense	9557	exon21			ATGTCCTGTCTGG	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.2435T>C	1.37:g.146765335T>C	ENSP00000358262:p.Leu812Pro	Somatic	59	0		WXS	Illumina HiSeq		43	4	NM_004284	0	0	21	21	0	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	.	.	.	.	.	.	.	.	.	.	T	19.21	3.784525	0.70222	.	.	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.27	5.27	0.74061	Appr-1-p processing (1);	0.072961	0.56097	D	0.000022	T	0.52008	0.1708	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.987;0.999;0.991	T	0.55604	-0.8115	10	0.51188	T	0.08	.	11.8759	0.52548	0.0:0.0:0.0:1.0	.	718;608;812	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	P	718;608;812;531	ENSP00000389031:L718P;ENSP00000358263:L608P;ENSP00000358262:L812P;ENSP00000355100:L531P	ENSP00000355100:L531P	L	+	2	0	CHD1L	145231959	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.989000	0.63870	2.118000	0.64928	0.455000	0.32223	CTG	.		0.458	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		C	146765335	T	C	146765335	3	2	57	1	0	0	0	0	1	0	0	0	3330	1580	55	3	2517	3	CHD1L	1	146765335	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	51434937	146765335	102485286	7	5481											
RGL1	23179	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	183885769	183885769	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtttacaaccaacagaaTgaagacacctgcataatccg	15	8	6	12	1	0	3	0	1	0	2	1	3	1	3	4	0	4	2	4	0	6	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:183885769T>G	ENST00000360851.3	+	16	2116	c.1938T>G	c.(1936-1938)aaT>aaG	p.N646K	RGL1_ENST00000536277.1_Missense_Mutation_p.N644K|RGL1_ENST00000539189.1_Missense_Mutation_p.N617K|RGL1_ENST00000304685.4_Missense_Mutation_p.N681K			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	646					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						ACCAACAGAATGAAGACACCT	0.527																																					p.N681K													.	RGL1-725	0			c.T2043G						.						144	135	138					1																	183885769		2203	4300	6503	SO:0001583	missense	23179	exon17			ACAGAATGAAGAC	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1938T>G	1.37:g.183885769T>G	ENSP00000354097:p.Asn646Lys	Somatic	97	1		WXS	Illumina HiSeq	Phase_I	93	41	NM_015149	0	0	3	8	5	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	T	12.79	2.044074	0.36085	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.43	-2.84	0.05751	.	0.338661	0.34959	N	0.003544	T	0.19208	0.0461	L	0.36672	1.1	0.23872	N	0.996605	P;B;B;B	0.34587	0.458;0.118;0.118;0.118	B;B;B;B	0.32465	0.146;0.018;0.018;0.018	T	0.35325	-0.9793	10	0.06757	T	0.87	.	3.1668	0.06539	0.1095:0.3105:0.1084:0.4716	.	617;644;646;681	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	K	681;681;644;646;617	ENSP00000303192:N681K;ENSP00000356501:N681K;ENSP00000438662:N644K;ENSP00000354097:N646K;ENSP00000437355:N617K	ENSP00000303192:N681K	N	+	3	2	RGL1	182152392	0.000000	0.05858	0.939000	0.37840	0.995000	0.86356	-1.705000	0.01896	-0.313000	0.08728	-0.137000	0.14449	AAT	.		0.527	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		G	183885769	T	G	183885769	3	3	57	1	0	0	0	0	1	0	0	0	13308	1461	51	5	2105	5	RGL1	1	183885769	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	37120434	183885769	65364852	8	5482											
KLHDC8A	55220	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205308913	205308913	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtaggtccaggcccatccCgcctgccgcatatactcggt	7	8	10	16	4	0	0	0	0	0	0	3	0	2	0	5	3	2	2	5	3	3	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:205308913C>T	ENST00000367156.3	-	6	1216	c.400G>A	c.(400-402)Ggg>Agg	p.G134R	KLHDC8A_ENST00000367155.3_Missense_Mutation_p.G134R|KLHDC8A_ENST00000537168.1_Missense_Mutation_p.G21R|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.G134R|KLHDC8A_ENST00000460687.1_5'UTR	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	134										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGGCCCATCCCGCCTGCCGCA	0.557																																					p.G134R													.	KLHDC8A-91	0			c.G400A						.						107	87	94					1																	205308913		2203	4300	6503	SO:0001583	missense	55220	exon3			CCATCCCGCCTGC		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.400G>A	1.37:g.205308913C>T	ENSP00000356124:p.Gly134Arg	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	93	51	NM_018203	0	0	0	0	0	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	37	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486904	0.84854	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253;ENST00000537168	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-1.85	5.87	5.87	0.94306	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.97639	0.9226	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.97864	1.0282	10	0.87932	D	0	-20.5621	19.803	0.96516	0.0:1.0:0.0:0.0	.	21;134	F5H5F1;Q8IYD2	.;KLD8A_HUMAN	R	134;134;134;21	ENSP00000356123:G134R;ENSP00000356124:G134R;ENSP00000442229:G134R;ENSP00000443447:G21R	ENSP00000356123:G134R	G	-	1	0	KLHDC8A	203575536	1.000000	0.71417	0.999000	0.59377	0.493000	0.33554	7.774000	0.85478	2.781000	0.95711	0.655000	0.94253	GGG	.		0.557	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		T	205308913	C	T	205308913	3	4	57	1	0	0	0	0	1	0	0	0	8383	652	23	1	668	1	KLHDC8A	1	205308913	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	21423144	205308913	43941708	9	5483											
DHX57	90957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	39088916	39088916	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaggagatgctctagtgaTgctcccacatctccatcaca	11	10	8	12	0	3	2	1	1	2	1	5	3	4	2	2	1	2	3	2	1	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:39088916T>C	ENST00000295373.6	-	5	762	c.636A>G	c.(634-636)gcA>gcG	p.A212A	AC018693.6_ENST00000442829.1_RNA|DHX57_ENST00000479345.2_5'UTR	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	212	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GCTCTAGTGATGCTCCCACAT	0.448																																					p.A212A	Melanoma(191;1090 2095 4375 23729 47341)	.											.	DHX57-228	0			c.A636G						.						84	79	81					2																	39088916		2203	4300	6503	SO:0001819	synonymous_variant	90957	exon5			TAGTGATGCTCCC	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.636A>G	2.37:g.39088916T>C		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	120	66	NM_198963	0	0	4	10	6	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	37	CCDS1800.1																																																																																			.		0.448	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		C	39088916	T	C	39088916	2	2	57	1	0	0	0	0	0	0	0	1	4524	1451	51	3		3	DHX57	2	39088916	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		39088916	204110457	10	5484											
PDE11A	50940	broad.mit.edu	37	chr2	178936708	178936708	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccggagaagtgccctccgtcGtacactactcaggggttcct	7	9	11	14	3	1	1	1	0	0	1	4	2	3	1	4	3	3	2	4	3	3	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:178936708G>A	ENST00000286063.6	-	1	774	c.457C>T	c.(457-459)Cga>Tga	p.R153*	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	153					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.R153*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GCCCTCCGTCGTACACTACTC	0.587									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.R153X													.	PDE11A-93	1	Substitution - Nonsense(1)	large_intestine(1)	c.C457T						.						78	75	76					2																	178936708		2203	4300	6503	SO:0001587	stop_gained	50940	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TCCGTCGTACACT	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"Phosphodiesterases"	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.457C>T	2.37:g.178936708G>A	ENSP00000286063:p.Arg153*	Somatic	145	1		WXS	Illumina HiSeq	Phase_I	120	4	NM_016953	0	0	0	0	0	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Nonsense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	40	8.081797	0.98643	.	.	ENSG00000128655	ENST00000286063	.	.	.	5.04	4.06	0.47325	.	0.504890	0.20822	N	0.085054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6094	0.62068	0.0:0.0:0.7542:0.2457	.	.	.	.	X	153	.	ENSP00000286063:R153X	R	-	1	2	PDE11A	178644954	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.726000	0.38085	2.341000	0.79615	0.655000	0.94253	CGA	.		0.587	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178936708	G	A	178936708	4	1	57	1	0	0	0	0	0	1	0	0	11657	1153	40	1	2424	1	PDE11A	2	178936708	Nonsense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	139847792	178936708	64262665	11	5485											
NBEAL1	65065	hgsc.bcm.edu;bcgsc.ca	37	chr2	204009565	204009566	+	Frame_Shift_Ins	INS	-	-	T																															ttaccaatggtagctcctcaINSttttttgaagattttcaaga																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:204009565_204009566insT	ENST00000449802.1	+	31	5337_5338	c.5004_5005insT	c.(5005-5007)tttfs	p.F1669fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1669										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GTAGCTCCTCATTTTTTGAAGA	0.317																																					p.S1668fs		.											.	NBEAL1-92	0			c.5004_5005insT						.																																			SO:0001589	frameshift_variant	65065	exon31			.	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.5010dupT	2.37:g.204009571_204009571dupT	ENSP00000399903:p.Phe1669fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	45	16	NM_001114132	0	0	0	0	0	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Frame_Shift_Ins	INS	ENST00000449802.1	37	CCDS46495.1																																																																																			.		0.317	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204009566	-	T	204009565	7	5	57	1	0	1	1	0	0	0	0	0	10213	204	8	0	5122	0	NBEAL1	2	204009565	Frame_Shift_Ins	INS	-	TCGA-B9-A5W9-01A-11D-A28G-10	25072857	204009565	39189808	12	5486											
STK11IP	114790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220473931	220473931	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgatgcccacgcagctgTccaggtgatggcgcccagag	7	6	14	14	2	0	3	0	2	0	1	1	3	1	3	4	2	2	2	4	2	0	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:220473931T>C	ENST00000456909.1	+	16	2012	c.1922T>C	c.(1921-1923)gTc>gCc	p.V641A	STK11IP_ENST00000295641.10_Missense_Mutation_p.V652A			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	652					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CACGCAGCTGTCCAGGTGATG	0.662																																					p.V652A		.											.	STK11IP-91	0			c.T1955C						.						23	22	23					2																	220473931		2018	4164	6182	SO:0001583	missense	114790	exon16			CAGCTGTCCAGGT	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1922T>C	2.37:g.220473931T>C	ENSP00000389383:p.Val641Ala	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	89	35	NM_052902	0	0	0	0	0	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		.	.	.	.	.	.	.	.	.	.	T	12.88	2.071525	0.36566	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.05025	3.51;3.51	5.0	-0.564	0.11774	.	1.280970	0.05320	N	0.526447	T	0.07683	0.0193	L	0.43152	1.355	0.20821	N	0.999844	B;B;B	0.14012	0.009;0.004;0.002	B;B;B	0.15484	0.013;0.003;0.006	T	0.43956	-0.9359	10	0.72032	D	0.01	-0.0971	8.4014	0.32588	0.0:0.3626:0.0:0.6374	.	620;652;652	B4DUE4;Q8N1F8-2;Q8N1F8	.;.;S11IP_HUMAN	A	641;620;652	ENSP00000389383:V641A;ENSP00000295641:V652A	ENSP00000295641:V652A	V	+	2	0	STK11IP	220182175	0.431000	0.25546	0.117000	0.21633	0.652000	0.38707	0.654000	0.24918	-0.222000	0.09958	-0.250000	0.11733	GTC	.		0.662	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		C	220473931	T	C	220473931	3	2	57	1	0	0	0	0	1	0	0	0	15320	1667	58	3	2017	3	STK11IP	2	220473931	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	16464366	220473931	22725442	13	5487											
INPP5D	3635	broad.mit.edu	37	chr2	234102516	234102516	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcagctgcccatctacacGcctctcacccaccatgggga	9	6	8	18	2	2	0	1	0	2	0	3	1	2	1	4	2	3	2	4	2	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:234102516G>T	ENST00000359570.5	+	25	2469	c.2469G>T	c.(2467-2469)acG>acT	p.T823T	INPP5D_ENST00000450745.1_Silent_p.T587T|INPP5D_ENST00000455936.2_Silent_p.T587T			Q92835	SHIP1_HUMAN	inositol polyphosphate-5-phosphatase, 145kDa	835					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|determination of adult lifespan (GO:0008340)|immunoglobulin mediated immune response (GO:0016064)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of bone resorption (GO:0045779)|negative regulation of immune response (GO:0050777)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of neutrophil differentiation (GO:0045659)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of signal transduction (GO:0009968)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of erythrocyte differentiation (GO:0045648)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|membrane (GO:0016020)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)			central_nervous_system(1)|ovary(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CCATCTACACGCCTCTCACCC	0.597																																					.	NSCLC(82;1215 1426 16163 20348 41018)												.	INPP5D-652	0			.						.						80	83	82					2																	234102516		2057	4190	6247	SO:0001819	synonymous_variant	3635	.			CTACACGCCTCTC	U57650	CCDS74672.1	2q37.1	2013-02-14	2002-08-29		ENSG00000168918	ENSG00000168918		"SH2 domain containing"	6079	protein-coding gene	gene with protein product		601582	"inositol polyphosphate-5-phosphatase, 145kD"			8643691, 8874179	Standard	NM_001017915		Approved	SHIP, hp51CN	uc010zmp.2	Q92835	OTTHUMG00000133688	ENST00000359570.5:c.2469G>T	2.37:g.234102516G>T		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	81	5	.	0	0	5	5	0	O00145|Q13544|Q13545|Q6P5A4|Q92656|Q9UE80	Silent	SNP	ENST00000359570.5	37																																																																																				.		0.597	INPP5D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001017915		T	234102516	G	T	234102516	2	4	57	1	0	0	0	0	0	0	0	1	7777	1074	38	4		4	INPP5D	2	234102516	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	13628585	234102516	9096857	14	5488											
XIRP1	165904	broad.mit.edu	37	chr3	39229085	39229085	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgcctcagccttggctgTgggatctgtgacctctgacc	4	12	12	13	0	3	2	1	2	2	0	3	3	3	3	4	2	2	1	4	2	0	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:39229085T>A	ENST00000340369.3	-	2	2080	c.1852A>T	c.(1852-1854)Aca>Tca	p.T618S	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Missense_Mutation_p.T618S	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	618	Interaction with CTNNB1. {ECO:0000250}.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GCCTTGGCTGTGGGATCTGTG	0.607																																					p.T618S													.	XIRP1-158	0			c.A1852T						.						81	71	74					3																	39229085		2203	4300	6503	SO:0001583	missense	165904	exon2			TGGCTGTGGGATC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"cardiomyopathy associated 1"	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.1852A>T	3.37:g.39229085T>A	ENSP00000343140:p.Thr618Ser	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_001198621	0	0	0	0	0	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	T	3.269	-0.149600	0.06585	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05025	3.51;3.9	4.59	0.404	0.16355	.	1.428260	0.04215	U	0.332466	T	0.06280	0.0162	L	0.46157	1.445	0.09310	N	1	B;B	0.22909	0.028;0.077	B;B	0.17979	0.02;0.019	T	0.42155	-0.9468	10	0.36615	T	0.2	.	0.7335	0.00961	0.3376:0.1046:0.1732:0.3846	.	618;618	Q702N8;Q702N8-2	XIRP1_HUMAN;.	S	618	ENSP00000379550:T618S;ENSP00000343140:T618S	ENSP00000343140:T618S	T	-	1	0	XIRP1	39204089	0.000000	0.05858	0.002000	0.10522	0.935000	0.57460	-0.544000	0.06077	0.217000	0.20800	0.379000	0.24179	ACA	.		0.607	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39229085	T	A	39229085	3	1	57	1	0	0	0	0	1	0	0	0	17462	1696	59	5	3683	5	XIRP1	3	39229085	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		39229085	158793345	15	5489											
DOCK3	1795	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	51393580	51393580	+	Frame_Shift_Del	DEL	G	G	-																															ggatgttctgcagatggataGggtaccagatcgagtcaaga																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:51393580delG	ENST00000266037.9	+	42	4333	c.4310delG	c.(4309-4311)aggfs	p.R1437fs		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1437	DHR-2.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CAGATGGATAGGGTACCAGAT	0.493																																					p.R1437fs		.											.	DOCK3-22	0			c.4310delG						.						147	140	142					3																	51393580		1982	4180	6162	SO:0001589	frameshift_variant	1795	exon42			.	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"dedicator of cyto-kinesis 3"			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.4310delG	3.37:g.51393580delG	ENSP00000266037:p.Arg1437fs	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	199	65	NM_004947	0	0	0	0	0	O15017	Frame_Shift_Del	DEL	ENST00000266037.9	37	CCDS46835.1																																																																																			.		0.493	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		-	51393580	G	-	51393580	7	5	57	1	0	1	0	1	0	0	0	0	4699	1000	35	0	4476	0	DOCK3	3	51393580	Frame_Shift_Del	DEL	G	TCGA-B9-A5W9-01A-11D-A28G-10	12164495	51393580	146628850	16	5490											
DNAH1	25981	hgsc.bcm.edu;bcgsc.ca	37	chr3	52402933	52402934	+	Splice_Site	INS	-	-	G																															gagatcatcaagctcacagaINSggtgcacctacctgtccacc																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:52402933_52402934insG	ENST00000420323.2	+	37	6203_6204	c.5942_5943insG	c.(5941-5946)gaggca>gaGggca	p.A1982fs		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1982	AAA 2. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AAGCTCACAGAGGTGCACCTAC	0.584																																					p.E1981fs		.											.	DNAH1-67	0			c.5942_5943insG						.																																			SO:0001630	splice_region_variant	25981	exon37			.	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.5943+1->G	3.37:g.52402935_52402935dupG		Somatic	178	0		WXS	Illumina HiSeq	Phase_I	131	33	NM_015512	0	0	0	0	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Frame_Shift_Ins	INS	ENST00000420323.2	37	CCDS46842.1																																																																																			.		0.584	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	Frame_Shift_Ins	G	52402934	-	G	52402933	8	5	57	1	0	1	1	0	0	0	1	0	4608	318	11	0	6084	0	DNAH1	3	52402933	Splice_Site	INS	-	TCGA-B9-A5W9-01A-11D-A28G-10	1009353	52402933	145619497	17	5491											
ATXN7	6314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	63983337	63983337	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgaacaggaatttcagcaaCatcaccccagagccctgact	14	6	7	14	1	2	2	2	1	0	1	2	4	2	3	3	1	4	1	3	1	3	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:63983337C>T	ENST00000295900.6	+	12	3211				ATXN7_ENST00000398590.3_Missense_Mutation_p.T901I|ATXN7_ENST00000484332.1_Intron|ATXN7_ENST00000487717.1_Intron|ATXN7_ENST00000538065.1_Missense_Mutation_p.T901I	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7						cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		ATTTCAGCAACATCACCCCAG	0.428																																					p.T901I		.											.	ATXN7-90	0			c.C2702T						.						296	237	255					3																	63983337		692	1591	2283	SO:0001627	intron_variant	6314	exon12			CAGCAACATCACC	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2661+1178C>T	3.37:g.63983337C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_001177387	0	0	1	3	2	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045840	0.36085	.	.	ENSG00000163635	ENST00000398590;ENST00000538065;ENST00000522345	T;T;T	0.51071	2.49;2.49;0.72	4.03	3.14	0.36123	.	0.628911	0.14004	N	0.347922	T	0.26159	0.0638	N	0.08118	0	0.22521	N	0.99903	B	0.12013	0.005	B	0.11329	0.006	T	0.15321	-1.0441	10	0.56958	D	0.05	0.0408	7.1588	0.25652	0.0:0.8751:0.0:0.1249	.	901	O15265-2	.	I	901;901;72	ENSP00000381590:T901I;ENSP00000439585:T901I;ENSP00000428067:T72I	ENSP00000381590:T901I	T	+	2	0	ATXN7	63958377	0.005000	0.15991	0.963000	0.40424	0.987000	0.75469	0.983000	0.29552	1.254000	0.44035	0.644000	0.83932	ACA	.		0.428	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		T	63983337	C	T	63983337	1	4	57	0	1	0	0	0	0	0	0	0	1216	478	17	2		2	ATXN7	3	63983337	Intron	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	11580404	63983337	134039093	18	5492											
ITGB5	3693	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	124515325	124515325	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaactcgctctcgaagcAggagcactggttgcagctgc	9	7	12	13	2	1	0	0	0	1	0	3	2	1	1	1	2	6	6	1	2	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:124515325A>T	ENST00000296181.4	-	10	1899	c.1603T>A	c.(1603-1605)Tgc>Agc	p.C535S		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	535	Cysteine-rich tandem repeats.				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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		CTCTCGAAGCAGGAGCACTGG	0.597																																					p.C535S													.	ITGB5-227	0			c.T1603A						.						103	92	96					3																	124515325		2203	4300	6503	SO:0001583	missense	3693	exon10			CGAAGCAGGAGCA	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1603T>A	3.37:g.124515325A>T	ENSP00000296181:p.Cys535Ser	Somatic	100	1		WXS	Illumina HiSeq	Phase_I	77	29	NM_002213	0	0	42	65	23	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	37	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.715465	0.89112	.	.	ENSG00000082781	ENST00000296181	D	0.98207	-4.79	5.26	5.26	0.73747	.	0.136977	0.64402	D	0.000003	D	0.99290	0.9752	H	0.95884	3.735	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98816	1.0745	10	0.87932	D	0	.	15.3487	0.74363	1.0:0.0:0.0:0.0	.	535	P18084	ITB5_HUMAN	S	535	ENSP00000296181:C535S	ENSP00000296181:C535S	C	-	1	0	ITGB5	125998015	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	9.049000	0.93837	2.208000	0.71279	0.460000	0.39030	TGC	.		0.597	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		T	124515325	A	T	124515325	3	4	57	1	0	0	0	0	1	0	0	0	7919	188	7	5	820	5	ITGB5	3	124515325	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	60531988	124515325	73507105	19	5493											
TOPBP1	11073	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	133331389	133331389	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcactgcttttctatcacCaatccaccttaagcagagaa	14	10	5	12	0	2	1	1	0	1	1	3	2	3	1	3	0	3	3	3	0	5	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:133331389C>T	ENST00000260810.5	-	24	4010	c.3879G>A	c.(3877-3879)ttG>ttA	p.L1293L		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1293	BRCT 7. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TTTCTATCACCAATCCACCTT	0.383								Other conserved DNA damage response genes																													p.L1293L	Ovarian(21;193 658 4424 15423 17362)	.											.	TOPBP1-540	0			c.G3879A						.						50	48	49					3																	133331389		1904	4132	6036	SO:0001819	synonymous_variant	11073	exon24			TATCACCAATCCA	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3879G>A	3.37:g.133331389C>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	52	20	NM_007027	0	0	0	0	0	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																			.		0.383	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		T	133331389	C	T	133331389	2	4	57	1	0	0	0	0	0	0	0	1	16402	593	21	2		2	TOPBP1	3	133331389	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	8816064	133331389	64691041	20	5494											
KLHL6	89857	broad.mit.edu	37	chr3	183217515	183217515	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagggggtccaggcaggtcAcctctgccacaaaccgttca	9	7	11	14	1	4	0	3	0	1	0	5	0	5	0	4	4	2	2	4	4	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:183217515A>C	ENST00000341319.3	-	4	1045	c.1010T>G	c.(1009-1011)gTg>gGg	p.V337G		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	337					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			CAGGCAGGTCACCTCTGCCAC	0.567																																					p.V337G													.	KLHL6-93	0			c.T1010G						.						82	71	75					3																	183217515		2203	4300	6503	SO:0001583	missense	89857	exon4			CAGGTCACCTCTG	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"Kelch-like", "BTB/POZ domain containing"	18653	protein-coding gene	gene with protein product	"kelch-like protein KLHL6"	614214	"kelch-like 6 (Drosophila)"			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1010T>G	3.37:g.183217515A>C	ENSP00000341342:p.Val337Gly	Somatic	91	4		WXS	Illumina HiSeq	Phase_I	73	7	NM_130446	0	0	2	2	0	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	A	22.0	4.224479	0.79576	.	.	ENSG00000172578	ENST00000341319	T	0.69175	-0.38	5.12	5.12	0.69794	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.79155	0.4398	M	0.78049	2.395	0.80722	D	1	D	0.56035	0.974	P	0.57911	0.829	T	0.82682	-0.0336	10	0.87932	D	0	.	15.234	0.73413	1.0:0.0:0.0:0.0	.	337	Q8WZ60	KLHL6_HUMAN	G	337	ENSP00000341342:V337G	ENSP00000341342:V337G	V	-	2	0	KLHL6	184700209	1.000000	0.71417	0.999000	0.59377	0.815000	0.46073	8.910000	0.92685	2.068000	0.61886	0.454000	0.30748	GTG	.		0.567	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		C	183217515	A	C	183217515	3	2	57	1	0	0	0	0	1	0	0	0	8414	159	6	5	871	5	KLHL6	3	183217515	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	49886126	183217515	14804915	21	5495											
CLDN16	10686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	190126252	190126252	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgggtctctgggttgctttTtggctggagctgttctcacc	2	16	13	10	0	2	0	1	0	2	0	4	1	2	1	1	4	2	5	1	4	0	4	rs143316426	byFrequency	TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:190126252T>G	ENST00000264734.2	+	4	990	c.742T>G	c.(742-744)Ttg>Gtg	p.L248V	CLDN16_ENST00000456423.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	248					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		GGGTTGCTTTTTGGCTGGAGC	0.393																																					p.L248V		.											.	CLDN16-227	0			c.T742G						.						142	138	140					3																	190126252		2203	4300	6503	SO:0001583	missense	10686	exon4			TGCTTTTTGGCTG	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"Claudins"	2037	protein-coding gene	gene with protein product	"paracellin-1", "hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.742T>G	3.37:g.190126252T>G	ENSP00000264734:p.Leu248Val	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	78	40	NM_006580	0	0	5	5	0		Missense_Mutation	SNP	ENST00000264734.2	37	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.084809	0.36758	.	.	ENSG00000113946	ENST00000264734	D	0.89875	-2.58	5.6	3.12	0.35913	.	0.099830	0.43919	D	0.000514	D	0.82282	0.5003	L	0.39326	1.205	0.80722	D	1	P	0.42296	0.775	B	0.39660	0.306	T	0.78966	-0.1995	10	0.44086	T	0.13	-2.4464	8.0251	0.30431	0.0:0.0724:0.135:0.7926	.	248	Q9Y5I7	CLD16_HUMAN	V	248	ENSP00000264734:L248V	ENSP00000264734:L248V	L	+	1	2	CLDN16	191608946	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	1.133000	0.31430	0.909000	0.36697	0.455000	0.32223	TTG	T|0.999;C|0.001		0.393	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580		G	190126252	T	G	190126252	3	3	57	1	0	0	0	0	1	0	0	0	3483	1838	64	5	756	5	CLDN16	3	190126252	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	6908737	190126252	7896178	22	5496											
PLK4	10733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	128813596	128813596	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatctcccaaaatcacttaTtttacaagatatgctaaatg	17	13	3	8	0	2	1	1	0	1	1	3	1	2	1	1	0	2	1	1	0	9	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr4:128813596T>C	ENST00000270861.5	+	10	2389	c.2115T>C	c.(2113-2115)taT>taC	p.Y705Y	PLK4_ENST00000515069.1_Silent_p.Y627Y|PLK4_ENST00000514379.1_Silent_p.Y664Y|PLK4_ENST00000507249.1_Silent_p.Y644Y|PLK4_ENST00000513090.1_Silent_p.Y673Y|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	705					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AAATCACTTATTTTACAAGAT	0.313																																					p.Y705Y	Colon(135;508 1718 19061 31832 42879)	.											.	PLK4-333	0			c.T2115C						.						121	116	118					4																	128813596		2202	4299	6501	SO:0001819	synonymous_variant	10733	exon10			CACTTATTTTACA	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2115T>C	4.37:g.128813596T>C		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	115	31	NM_014264	0	0	2	5	3	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																			.		0.313	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			C	128813596	T	C	128813596	2	2	57	1	0	0	0	0	0	0	0	1	12124	1500	52	3		3	PLK4	4	128813596	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		128813596	62340680	23	5497											
CPE	1363	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	166300624	166300624	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggtggggcgcagcttcgAgggccgggagctcctggtca	5	6	18	12	4	1	0	1	0	0	0	3	2	2	1	2	6	2	3	2	6	0	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr4:166300624A>C	ENST00000402744.4	+	1	531	c.251A>C	c.(250-252)gAg>gCg	p.E84A		NM_001873.2	NP_001864.1	P16870	CBPE_HUMAN	carboxypeptidase E	84					cardiac left ventricle morphogenesis (GO:0003214)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|insulin processing (GO:0030070)|metabolic process (GO:0008152)|neuropeptide signaling pathway (GO:0007218)|protein localization to membrane (GO:0072657)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)	carboxypeptidase activity (GO:0004180)|cell adhesion molecule binding (GO:0050839)|metallocarboxypeptidase activity (GO:0004181)|neurexin family protein binding (GO:0042043)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CGCAGCTTCGAGGGCCGGGAG	0.682																																					p.E84A		.											.	CPE-155	0			c.A251C						.						13	14	14					4																	166300624		2161	4236	6397	SO:0001583	missense	1363	exon1			GCTTCGAGGGCCG	X51405	CCDS3810.1	4q32.3	2012-02-10			ENSG00000109472	ENSG00000109472	3.4.17.10		2303	protein-coding gene	gene with protein product	"carboxypeptidase H", "enkephalin convertase", "insulin granule-associated carboxypeptidase", "cobalt-stimulated chromaffin granule carboxypeptidase"	114855				2334405	Standard	NM_001873		Approved		uc003irg.4	P16870	OTTHUMG00000150252	ENST00000402744.4:c.251A>C	4.37:g.166300624A>C	ENSP00000386104:p.Glu84Ala	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	156	91	NM_001873	0	0	15	67	52	A8K4N1|B3KR42|B4DFN4|D3DP33|Q9UIU9	Missense_Mutation	SNP	ENST00000402744.4	37	CCDS3810.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301811	0.81136	.	.	ENSG00000109472	ENST00000402744;ENST00000261510	T	0.15372	2.43	4.1	4.1	0.47936	Peptidase M14, carboxypeptidase A (2);	0.098707	0.64402	D	0.000002	T	0.27697	0.0681	M	0.84082	2.675	0.58432	D	0.999999	B	0.24576	0.106	B	0.31245	0.126	T	0.14615	-1.0466	10	0.59425	D	0.04	-28.9098	12.8978	0.58109	1.0:0.0:0.0:0.0	.	84	P16870	CBPE_HUMAN	A	84;48	ENSP00000386104:E84A	ENSP00000261510:E48A	E	+	2	0	CPE	166520074	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.494000	0.73661	1.707000	0.51288	0.254000	0.18369	GAG	.		0.682	CPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317094.2	NM_001873		C	166300624	A	C	166300624	3	2	57	1	0	0	0	0	1	0	0	0	3805	304	11	5	253	5	CPE	4	166300624	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	37487028	166300624	24853652	24	5498											
SHROOM1	134549	broad.mit.edu	37	chr5	132160935	132160935	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctccgactccgactggcggGcctgaaggcatcaccgagct	7	6	13	15	4	1	1	1	1	0	0	3	4	3	1	4	3	1	3	4	3	1	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr5:132160935G>T	ENST00000378679.3	-	4	1702	c.898C>A	c.(898-900)Ccc>Acc	p.P300T	SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000378676.1_Missense_Mutation_p.P300T|SHROOM1_ENST00000319854.3_Missense_Mutation_p.P300T	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	300					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGACTGGCGGGCCTGAAGGCA	0.592																																					p.P300T													.	SHROOM1-91	0			c.C898A						.						30	33	32					5																	132160935		2203	4300	6503	SO:0001583	missense	134549	exon1			TGGCGGGCCTGAA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.898C>A	5.37:g.132160935G>T	ENSP00000367950:p.Pro300Thr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	87	8	NM_133456	0	0	3	3	0	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.578119	0.65878	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676;ENST00000440118	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.7	4.7	0.59300	.	0.362631	0.24720	N	0.036146	T	0.38878	0.1057	L	0.32530	0.975	0.09310	N	0.999999	D;D	0.76494	0.999;0.999	D;D	0.76575	0.988;0.973	T	0.11665	-1.0578	10	0.52906	T	0.07	-15.8128	13.8589	0.63548	0.0:0.0:1.0:0.0	.	300;300	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	T	300	ENSP00000367950:P300T;ENSP00000324245:P300T;ENSP00000367947:P300T;ENSP00000388049:P300T	ENSP00000324245:P300T	P	-	1	0	SHROOM1	132188834	0.006000	0.16342	0.662000	0.29724	0.016000	0.09150	0.732000	0.26072	2.542000	0.85734	0.561000	0.74099	CCC	.		0.592	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132160935	G	T	132160935	3	4	57	1	0	0	0	0	1	0	0	0	14325	1203	42	4	1688	4	SHROOM1	5	132160935	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		132160935	48754325	25	5499											
FAM13B	51306	broad.mit.edu	37	chr5	137289150	137289150	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgaactaaaggatgatcttcGaattctgaattaaaacaaaa	19	11	6	5	1	2	3	0	3	2	0	3	5	2	4	0	1	2	0	0	1	9	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr5:137289150G>A	ENST00000033079.3	-	15	2108	c.1657C>T	c.(1657-1659)Cga>Tga	p.R553*	FAM13B_ENST00000425075.2_Nonsense_Mutation_p.R457*|FAM13B_ENST00000420893.2_Nonsense_Mutation_p.R553*	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	553					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						GATGATCTTCGAATTCTGAAT	0.353																																					p.R553X													.	.	0			c.C1657T						.						115	111	112					5																	137289150		2203	4299	6502	SO:0001587	stop_gained	51306	exon15			ATCTTCGAATTCT	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.1657C>T	5.37:g.137289150G>A	ENSP00000033079:p.Arg553*	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	80	5	NM_001101800	0	0	0	0	0	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Nonsense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	G	41	9.156967	0.99084	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	.	.	.	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.9213	13.6288	0.62183	0.0:0.0:0.8451:0.1549	.	.	.	.	X	553;457;553	.	ENSP00000033079:R553X	R	-	1	2	FAM13B	137317049	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.454000	0.52986	2.403000	0.81681	0.585000	0.79938	CGA	.		0.353	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			A	137289150	G	A	137289150	4	1	57	1	0	0	0	0	0	1	0	0	5469	1066	37	1	1126	1	FAM13B	5	137289150	Nonsense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	5128215	137289150	43626110	26	5500											
HIGD2A	192286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	175816407	175816407	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacagccagcgctctcagcTcatgatgcgcacccggatcg	9	6	10	16	4	2	1	2	1	1	0	4	2	2	2	2	1	5	3	2	1	1	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr5:175816407T>A	ENST00000274787.2	+	2	303	c.230T>A	c.(229-231)cTc>cAc	p.L77H	NOP16_ENST00000510123.1_5'Flank|NOP16_ENST00000389158.5_5'Flank|NOP16_ENST00000509257.1_5'Flank|NOP16_ENST00000507413.1_5'Flank	NM_138820.2	NP_620175.1	Q9BW72	HIG2A_HUMAN	HIG1 hypoxia inducible domain family, member 2A	77	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.				negative regulation of apoptotic process (GO:0043066)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)				large_intestine(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		CGCTCTCAGCTCATGATGCGC	0.647																																					p.L77H		.											.	HIGD2A-90	0			c.T230A						.						67	74	71					5																	175816407		2203	4300	6503	SO:0001583	missense	192286	exon2			CTCAGCTCATGAT	BC007502	CCDS4401.1	5q35.2	2009-03-17	2009-03-17		ENSG00000146066	ENSG00000146066			28311	protein-coding gene	gene with protein product			"HIG1 domain family, member 2A"			12477932	Standard	NM_138820		Approved	MGC2198	uc003meg.3	Q9BW72	OTTHUMG00000130657	ENST00000274787.2:c.230T>A	5.37:g.175816407T>A	ENSP00000274787:p.Leu77His	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	141	35	NM_138820	0	0	517	788	271		Missense_Mutation	SNP	ENST00000274787.2	37	CCDS4401.1	.	.	.	.	.	.	.	.	.	.	T	32	5.165072	0.94727	.	.	ENSG00000146066	ENST00000274787	.	.	.	5.89	5.89	0.94794	Hypoxia induced protein, domain (2);	0.244211	0.42548	D	0.000699	T	0.63965	0.2556	L	0.33710	1.025	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.57911	-0.7729	9	0.13853	T	0.58	-17.0539	16.3158	0.82923	0.0:0.0:0.0:1.0	.	77	Q9BW72	HIG2A_HUMAN	H	77	.	ENSP00000274787:L77H	L	+	2	0	HIGD2A	175749013	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.646000	0.83445	2.254000	0.74563	0.533000	0.62120	CTC	.		0.647	HIGD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253147.1	NM_138820		A	175816407	T	A	175816407	3	1	57	1	0	0	0	0	1	0	0	0	7130	1551	54	5	236	5	HIGD2A	5	175816407	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	38527257	175816407	5098853	27	5501											
UNC5A	90249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176300996	176300996	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccctgaggacgtggcccTctatgtgggcctcatcgccg	4	9	14	14	3	2	1	1	1	1	0	3	2	2	2	4	4	0	0	4	4	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr5:176300996T>G	ENST00000329542.4	+	7	1188	c.914T>G	c.(913-915)cTc>cGc	p.L305R	UNC5A_ENST00000261961.3_Missense_Mutation_p.L265R	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	305					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACGTGGCCCTCTATGTGGGC	0.627																																					p.L305R		.											.	UNC5A-91	0			c.T914G						.						96	81	86					5																	176300996		2203	4300	6503	SO:0001583	missense	90249	exon7			TGGCCCTCTATGT	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"Immunoglobulin superfamily / I-set domain containing"	12567	protein-coding gene	gene with protein product		607869	"unc5 (C.elegans homolog) a"				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.914T>G	5.37:g.176300996T>G	ENSP00000332737:p.Leu305Arg	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	113	68	NM_133369	0	0	0	0	0	B2RXE6|Q8TF26|Q96GP4	Missense_Mutation	SNP	ENST00000329542.4	37	CCDS34299.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.466120	0.84425	.	.	ENSG00000113763	ENST00000329542;ENST00000261961	T;T	0.58506	0.33;0.68	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000001	T	0.74261	0.3693	M	0.69248	2.105	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.77603	-0.2526	10	0.87932	D	0	-27.0982	15.222	0.73320	0.0:0.0:0.0:1.0	.	265;305	Q6ZN44-3;Q6ZN44	.;UNC5A_HUMAN	R	305;265	ENSP00000332737:L305R;ENSP00000261961:L265R	ENSP00000261961:L265R	L	+	2	0	UNC5A	176233602	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.627000	0.83176	2.010000	0.58986	0.402000	0.26972	CTC	.		0.627	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		G	176300996	T	G	176300996	3	3	57	1	0	0	0	0	1	0	0	0	17024	1551	54	5	940	5	UNC5A	5	176300996	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	484589	176300996	4614264	28	5502											
PECI	10455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	4130664	4130664	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgatctttgtgatgccaTcttcggaggtcaccaccaga	10	11	9	11	1	3	3	1	2	2	1	4	4	3	4	3	2	1	0	3	2	0	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:4130664T>G	ENST00000380118.3	-	4	479	c.443A>C	c.(442-444)gAt>gCt	p.D148A	C6orf201_ENST00000380175.4_Intron|C6orf201_ENST00000333388.5_Intron|ECI2_ENST00000380125.2_Missense_Mutation_p.D118A|ECI2_ENST00000465828.1_Missense_Mutation_p.D118A|ECI2_ENST00000361538.2_Missense_Mutation_p.D118A|ECI2_ENST00000413766.2_5'UTR			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	148					fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						TGTGATGCCATCTTCGGAGGT	0.458																																					p.D148A													.	ECI2-90	0			c.A443C						.						199	172	181					6																	4130664		2203	4300	6503	SO:0001583	missense	10455	exon4			ATGCCATCTTCGG	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"acyl-Coenzyme A binding domain containing 2", " Hepatocellular carcinoma-associated antigen 88"	608024	"peroxisomal D3,D2-enoyl-CoA isomerase"	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.443A>C	6.37:g.4130664T>G	ENSP00000369461:p.Asp148Ala	Somatic	106	1		WXS	Illumina HiSeq	Phase_I	88	24	NM_206836	0	0	72	131	59	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	37	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	T	14.64	2.594282	0.46214	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000361538;ENST00000465828;ENST00000495548	T;T;T;T;T	0.49720	0.79;0.79;0.79;0.79;0.77	5.95	0.473	0.16763	.	0.524869	0.21650	N	0.071183	T	0.28764	0.0713	M	0.82433	2.59	0.80722	D	1	B	0.28667	0.219	B	0.31751	0.135	T	0.07947	-1.0746	10	0.33940	T	0.23	.	4.8584	0.13571	0.1281:0.2415:0.0:0.6304	.	148	O75521	ECI2_HUMAN	A	148;118;118;118;195	ENSP00000369461:D148A;ENSP00000369468:D118A;ENSP00000354737:D118A;ENSP00000420309:D118A;ENSP00000417459:D195A	ENSP00000354737:D118A	D	-	2	0	ECI2	4075663	0.969000	0.33509	0.093000	0.20910	0.844000	0.47949	2.042000	0.41222	0.098000	0.17522	0.533000	0.62120	GAT	.		0.458	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117		G	4130664	T	G	4130664	3	3	57	1	0	0	0	0	1	0	0	0	11742	1435	50	5	769	5	PECI	6	4130664	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		4130664	166984403	29	5503											
TNFRSF21	27242	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	47254097	47254097	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattggccatgggcatggctGactacagtcatggcatttct	8	12	11	10	0	2	1	1	1	1	0	2	1	2	1	1	4	1	3	1	4	1	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:47254097G>A	ENST00000296861.2	-	2	724	c.331C>T	c.(331-333)Cag>Tag	p.Q111*		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	111					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GGGCATGGCTGACTACAGTCA	0.522																																					p.Q111X		.											.	TNFRSF21-227	0			c.C331T						.						162	141	149					6																	47254097		2203	4300	6503	SO:0001587	stop_gained	27242	exon2			ATGGCTGACTACA	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.331C>T	6.37:g.47254097G>A	ENSP00000296861:p.Gln111*	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	136	61	NM_014452	0	0	33	47	14	B2RDI9|Q0D2P5|Q96D86	Nonsense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	G	39	7.562418	0.98361	.	.	ENSG00000146072	ENST00000296861	.	.	.	5.65	4.72	0.59763	.	0.399599	0.28612	N	0.014733	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	8.9938	0.36039	0.0:0.1192:0.6376:0.2432	.	.	.	.	X	111	.	ENSP00000296861:Q111X	Q	-	1	0	TNFRSF21	47362056	0.996000	0.38824	0.998000	0.56505	0.998000	0.95712	2.242000	0.43106	2.826000	0.97356	0.563000	0.77884	CAG	.		0.522	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		A	47254097	G	A	47254097	4	1	57	1	0	0	0	0	0	1	0	0	16327	1299	45	2	1656	2	TNFRSF21	6	47254097	Nonsense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	43123433	47254097	123860970	30	5504											
C6orf204	387119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	118790282	118790282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggctccttgccctgagcaCgctgattaagaatactacac	11	10	8	12	1	0	3	0	2	0	1	1	3	1	3	2	1	4	3	2	1	5	5	rs371610026		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:118790282C>T	ENST00000368491.3	-	12	2828	c.2207G>A	c.(2206-2208)cGt>cAt	p.R736H	CEP85L_ENST00000368488.5_Missense_Mutation_p.R739H	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	736						centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCCCTGAGCACGCTGATTAAG	0.378																																					p.R739H		.											.	.	0			c.G2216A						.						93	91	92					6																	118790282		1996	4188	6184	SO:0001583	missense	387119	exon13			TGAGCACGCTGAT	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 204"	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.2207G>A	6.37:g.118790282C>T	ENSP00000357477:p.Arg736His	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	105	22	NM_001178035	0	0	0	1	1	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236142	0.95240	.	.	ENSG00000111860	ENST00000368491;ENST00000368488	T;T	0.12465	2.68;2.68	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.33411	0.0862	M	0.72118	2.19	0.52501	D	0.999954	D	0.89917	1.0	D	0.91635	0.999	T	0.01621	-1.1310	10	0.62326	D	0.03	-8.4553	20.6208	0.99490	0.0:1.0:0.0:0.0	.	736	Q5SZL2	CF204_HUMAN	H	736;739	ENSP00000357477:R736H;ENSP00000357474:R739H	ENSP00000357474:R739H	R	-	2	0	C6orf204	118896975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.059000	0.64306	2.882000	0.98803	0.655000	0.94253	CGT	.		0.378	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		T	118790282	C	T	118790282	3	4	57	1	0	0	0	0	1	0	0	0	2359	536	19	1	218	1	C6orf204	6	118790282	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	71536185	118790282	52324785	31	5505											
KIAA1244	57221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	138656258	138656258	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgcgacaggacaagaGgccccgctcaggctccaccg	8	4	13	16	3	1	1	1	0	0	1	2	3	2	2	4	3	2	4	4	3	1	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:138656258G>A	ENST00000251691.4	+	33	6441	c.6275G>A	c.(6274-6276)aGg>aAg	p.R2092K		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAGGACAAGAGGCCCCGCTCA	0.647																																					p.R2092K		.											.	KIAA1244-228	0			c.G6275A						.						19	19	19					6																	138656258		2203	4297	6500	SO:0001583	missense	57221	exon33			ACAAGAGGCCCCG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 33"		"chromosome 6 open reading frame 92"	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.6275G>A	6.37:g.138656258G>A	ENSP00000251691:p.Arg2092Lys	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	19	8	NM_020340	0	0	0	0	0		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.215145|5.215145	0.95104|0.95104	.|.	.|.	ENSG00000112379|ENSG00000112379	ENST00000367706|ENST00000251691	.|T	.|0.20598	.|2.06	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.156972	.|0.56097	.|D	.|0.000026	.|T	.|0.24812	.|0.0602	L|L	0.32530|0.32530	0.975|0.975	0.51012|0.51012	D|D	0.999903|0.999903	.|D	.|0.58268	.|0.982	.|D	.|0.67548	.|0.952	.|T	.|0.01301	.|-1.1391	.|10	.|0.18276	.|T	.|0.48	.|-24.3666	19.9626|19.9626	0.97256|0.97256	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2092	.|Q5TH69	.|BIG3_HUMAN	.|K	-1|2092	.|ENSP00000251691:R2092K	.|ENSP00000251691:R2092K	.|R	+|+	.|2	.|0	KIAA1244|KIAA1244	138697951|138697951	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	9.198000|9.198000	0.94994|0.94994	2.723000|2.723000	0.93209|0.93209	0.511000|0.511000	0.50034|0.50034	.|AGG	.		0.647	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138656258	G	A	138656258	3	1	57	1	0	0	0	0	1	0	0	0	8238	1000	35	2	6405	2	KIAA1244	6	138656258	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	19865976	138656258	32458809	32	5506											
ANLN	54443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	36446013	36446013	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtaccgcttgtttatccaaAttttcctctgcaagtggagc	8	14	9	10	1	1	0	0	0	1	0	3	1	3	1	3	2	3	4	3	2	4	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr7:36446013A>C	ENST00000265748.2	+	4	932	c.711A>C	c.(709-711)aaA>aaC	p.K237N	ANLN_ENST00000396068.2_Missense_Mutation_p.K237N	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	237	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						GTTTATCCAAATTTTCCTCTG	0.428																																					p.K237N		.											.	ANLN-517	0			c.A711C						.						125	118	120					7																	36446013		2203	4300	6503	SO:0001583	missense	54443	exon4			ATCCAAATTTTCC	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.711A>C	7.37:g.36446013A>C	ENSP00000265748:p.Lys237Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	89	49	NM_018685	0	0	0	0	0	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	37	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.239520	0.58995	.	.	ENSG00000011426	ENST00000265748;ENST00000396068	T;T	0.03004	4.08;4.08	5.51	4.35	0.52113	.	0.142348	0.64402	D	0.000007	T	0.16214	0.0390	M	0.71581	2.175	0.44067	D	0.99681	D;D;D;D	0.89917	1.0;0.998;0.999;0.998	D;D;D;D	0.87578	0.998;0.913;0.973;0.913	T	0.00176	-1.1953	10	0.72032	D	0.01	-27.164	12.9765	0.58540	0.8648:0.1352:0.0:0.0	.	114;237;237;237	B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.;.;.;ANLN_HUMAN	N	237	ENSP00000265748:K237N;ENSP00000379380:K237N	ENSP00000265748:K237N	K	+	3	2	ANLN	36412538	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.978000	0.63799	1.024000	0.39682	0.528000	0.53228	AAA	.		0.428	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		C	36446013	A	C	36446013	3	2	57	1	0	0	0	0	1	0	0	0	694	98	4	5	725	5	ANLN	7	36446013	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		36446013	122692650	33	5507											
ASH2L	9070	broad.mit.edu	37	chr8	37978552	37978552	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attctagctgagcctgatccGcacgcccctgaccccgagaa	9	7	9	16	3	1	4	0	3	1	1	2	5	2	4	6	0	2	2	6	0	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr8:37978552G>A	ENST00000343823.6	+	10	1359	c.1050G>A	c.(1048-1050)ccG>ccA	p.P350P	ASH2L_ENST00000545394.1_Silent_p.P211P|ASH2L_ENST00000250635.7_Silent_p.P256P|RP11-90P5.5_ENST00000476186.2_RNA|ASH2L_ENST00000521652.1_Silent_p.P256P|ASH2L_ENST00000428278.2_Silent_p.P256P|RP11-90P5.4_ENST00000519081.1_RNA	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	350					cellular response to DNA damage stimulus (GO:0006974)|hemopoiesis (GO:0030097)|histone H3-K4 methylation (GO:0051568)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)	19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				AGCCTGATCCGCACGCCCCTG	0.522											OREG0018719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P350P													.	ASH2L-131	0			c.G1050A						.						134	126	128					8																	37978552		2203	4300	6503	SO:0001819	synonymous_variant	9070	exon10			TGATCCGCACGCC	AF056717	CCDS6101.1, CCDS47840.1, CCDS59100.1, CCDS64872.1	8p11.2	2013-01-28	2001-11-28		ENSG00000129691	ENSG00000129691		"Zinc fingers, PHD-type"	744	protein-coding gene	gene with protein product		604782	"ash2 (absent, small, or homeotic, Drosophila, homolog)-like"	ASH2L1		10393421	Standard	NM_004674		Approved	ASH2L2, ASH2, Bre2	uc003xkt.5	Q9UBL3	OTTHUMG00000164016	ENST00000343823.6:c.1050G>A	8.37:g.37978552G>A		Somatic	120	1	874	WXS	Illumina HiSeq	Phase_I	204	6	NM_004674	0	1	86	87	0	A8K7C3|D3DSW9|O60659|O60660|Q96B62	Silent	SNP	ENST00000343823.6	37	CCDS6101.1																																																																																			.		0.522	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	NM_004674		A	37978552	G	A	37978552	2	1	57	1	0	0	0	0	0	0	0	1	1043	1074	38	1		1	ASH2L	8	37978552	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		37978552	108385470	34	5508											
RECQL4	113655	broad.mit.edu	37	chr8	145738764	145738764	+	IGR	DEL	A	A	-																															aggccaccgtggccaccaccAcccggcaactggccctgcat																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr8:145738764delA	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Frame_Shift_Del_p.V769fs|RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GGCCACCACCACCCGGCAACT	0.687																																					p.V767fs													.	RECQL4-1083	0			c.2300delT						.						15	20	19					8																	145738764		2073	4204	6277	SO:0001628	intergenic_variant	9401	exon15			ACCACCACCCGGC		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		8.37:g.145738764delA		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	181	7	NM_004260	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000301327.4	37	CCDS6431.1																																																																																			.		0.687	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		-	145738764	A	-	145738764	6	5	57	0	1	1	0	1	0	0	0	0	13234	146	6	0		0	RECQL4	8	145738764	IGR	DEL	A	TCGA-B9-A5W9-01A-11D-A28G-10	107760212	145738764	625258	35	5509											
MGC70857	414919	hgsc.bcm.edu	37	chr8	145753110	145753110	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaggaaggggaaagcggcCtcgtagcgcccgctgcggtt	8	5	18	10	5	0	1	0	0	0	1	1	4	0	3	2	5	3	3	2	5	3	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr8:145753110C>A	ENST00000524821.1	-	3	482	c.267G>T	c.(265-267)gaG>gaT	p.E89D	LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank|C8orf82_ENST00000313465.5_3'UTR			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	89										endometrium(1)|urinary_tract(1)	2						GGAAAGCGGCCTCGTAGCGCC	0.682																																					p.E89D		.											.	C8orf82-44	0			c.G267T						.						38	48	45					8																	145753110		2179	4287	6466	SO:0001583	missense	414919	exon3			AGCGGCCTCGTAG		CCDS34970.1	8q24	2012-04-18			ENSG00000213563	ENSG00000213563			33826	protein-coding gene	gene with protein product						12477932	Standard	NM_001001795		Approved	MGC70857	uc003zdp.1	Q6P1X6	OTTHUMG00000165181	ENST00000524821.1:c.267G>T	8.37:g.145753110C>A	ENSP00000436621:p.Glu89Asp	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	30	16	NM_001001795	0	0	46	87	41	Q6GMR2|Q6P2Q7	Missense_Mutation	SNP	ENST00000524821.1	37	CCDS34970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.998184|3.998184	0.74818|0.74818	.|.	.|.	ENSG00000213563|ENSG00000213563	ENST00000524821|ENST00000532827	.|.	.|.	.|.	3.97|3.97	2.88|2.88	0.33553|0.33553	.|.	0.238001|.	0.26891|.	U|.	0.021962|.	T|T	0.55752|0.55752	0.1940|0.1940	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D;P|.	0.58268|.	0.982;0.939|.	P;P|.	0.58013|.	0.831;0.554|.	T|T	0.51872|0.51872	-0.8650|-0.8650	9|5	0.44086|.	T|.	0.13|.	-10.1373|-10.1373	3.8003|3.8003	0.08756|0.08756	0.0:0.6552:0.0:0.3448|0.0:0.6552:0.0:0.3448	.|.	81;89|.	Q6P1X6-2;Q6P1X6|.	.;CH082_HUMAN|.	D|C	89|134	.|.	ENSP00000436621:E89D|.	E|G	-|-	3|1	2|0	C8orf82|C8orf82	145723918|145723918	0.969000|0.969000	0.33509|0.33509	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	1.066000|1.066000	0.30604|0.30604	0.810000|0.810000	0.34279|0.34279	0.563000|0.563000	0.77884|0.77884	GAG|GGC	.		0.682	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795		A	145753110	C	A	145753110	3	1	57	1	0	0	0	0	1	0	0	0	9578	680	24	4	387	4	MGC70857	8	145753110	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	14346	145753110	610912	36	5510											
CERCAM	51148	broad.mit.edu	37	chr9	131186698	131186698	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttccccagggctactacCgccgcacagccgagtacttc	7	9	8	17	3	0	0	0	0	0	0	2	1	1	0	5	1	4	3	5	1	3	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr9:131186698C>T	ENST00000372838.4	+	5	969	c.571C>T	c.(571-573)Cgc>Tgc	p.R191C	CERCAM_ENST00000372842.1_Missense_Mutation_p.R113C	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	191					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						GGGCTACTACCGCCGCACAGC	0.662																																					p.R191C													.	CERCAM-69	0			c.C571T						.						47	51	50					9																	131186698		2203	4300	6503	SO:0001583	missense	51148	exon5			TACTACCGCCGCA	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"glycosyltransferase 25 domain containing 3"		"cerebral cell adhesion molecule"	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.571C>T	9.37:g.131186698C>T	ENSP00000361929:p.Arg191Cys	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_016174	0	0	9	9	0	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Missense_Mutation	SNP	ENST00000372838.4	37	CCDS6901.2	.	.	.	.	.	.	.	.	.	.	C	22.0	4.231933	0.79688	.	.	ENSG00000167123	ENST00000372842;ENST00000420512;ENST00000372838;ENST00000413863	T;T;T	0.21932	1.98;1.98;1.98	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.45478	0.1344	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.63703	0.917	T	0.48927	-0.8991	10	0.87932	D	0	0.3165	16.4921	0.84205	0.0:1.0:0.0:0.0	.	191	Q5T4B2	GT253_HUMAN	C	113;113;191;144	ENSP00000361933:R113C;ENSP00000416676:R113C;ENSP00000361929:R191C	ENSP00000361929:R191C	R	+	1	0	CERCAM	130226519	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	1.964000	0.40462	2.473000	0.83533	0.467000	0.42956	CGC	.		0.662	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174		T	131186698	C	T	131186698	3	4	57	1	0	0	0	0	1	0	0	0	3272	652	23	1	589	1	CERCAM	9	131186698	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		131186698	10026733	37	5511											
HK1	3098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	71128300	71128300	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcttctttgcaggccatcctGatcacctggacaaagcgatt	9	12	8	12	1	3	1	1	1	2	0	4	3	4	2	3	2	2	1	3	2	1	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr10:71128300G>A	ENST00000359426.6	+	5	608	c.504G>A	c.(502-504)ctG>ctA	p.L168L	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000298649.3_Silent_p.L167L|HK1_ENST00000448642.2_Silent_p.L203L|HK1_ENST00000360289.2_Silent_p.L156L|HK1_ENST00000404387.2_Silent_p.L172L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	168	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AGGCCATCCTGATCACCTGGA	0.547																																					p.L172L		.											.	HK1-252	0			c.G516A						.						97	85	89					10																	71128300		2203	4300	6503	SO:0001819	synonymous_variant	3098	exon8			CATCCTGATCACC	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.504G>A	10.37:g.71128300G>A		Somatic	180	0		WXS	Illumina HiSeq	Phase_I	171	68	NM_033498	0	0	0	0	0	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			.		0.547	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		A	71128300	G	A	71128300	2	1	57	1	0	0	0	0	0	0	0	1	7211	1277	45	2		2	HK1	10	71128300	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		71128300	64406447	38	5512											
DHDPSL	112817	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	99358955	99358955	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcatgagcagtgcggccctCattcaccactacaccaaggt	10	7	9	15	2	2	1	2	1	0	0	2	1	2	1	3	2	3	2	3	2	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr10:99358955C>T	ENST00000370646.4	+	3	811	c.450C>T	c.(448-450)ctC>ctT	p.L150L	HOGA1_ENST00000370647.4_Intron|PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron	NM_138413.3	NP_612422.2	Q86XE5	HOGA1_HUMAN	4-hydroxy-2-oxoglutarate aldolase 1	150					4-hydroxyproline catabolic process (GO:0019470)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|oxalate metabolic process (GO:0033609)|pyruvate biosynthetic process (GO:0042866)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	4-hydroxy-2-oxoglutarate aldolase activity (GO:0008700)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|stomach(1)	14						GTGCGGCCCTCATTCACCACT	0.612																																					p.L150L		.											.	HOGA1-90	0			c.C450T						.						52	47	49					10																	99358955		2203	4300	6503	SO:0001819	synonymous_variant	112817	exon3			GGCCCTCATTCAC	BC011916	CCDS7467.1, CCDS44469.1	10q24.1	2010-12-19	2010-12-19	2010-12-19	ENSG00000241935	ENSG00000241935			25155	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 2 (E. coli)", "N-acetylneuraminate pyruvate lyase 2 (putative)"	613597	"chromosome 10 open reading frame 65", "dihydrodipicolinate synthase-like, mitochondrial"	C10orf65, DHDPSL		20797690	Standard	NM_001134670		Approved	FLJ37472, DHDPS2, NPL2		Q86XE5	OTTHUMG00000018859	ENST00000370646.4:c.450C>T	10.37:g.99358955C>T		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	88	35	NM_138413	0	0	70	102	32	A8K075|Q5T680|Q5T684|Q711P0|Q8N9F2|Q96EV5	Silent	SNP	ENST00000370646.4	37	CCDS7467.1																																																																																			.		0.612	HOGA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049726.1	NM_138413		T	99358955	C	T	99358955	2	4	57	1	0	0	0	0	0	0	0	1	4491	813	29	2		2	DHDPSL	10	99358955	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	28230655	99358955	36175792	39	5513											
SLC18A2	6571	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	119003520	119003520	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtacagcattaagcatGagaagaatgctacagaaatc	17	9	8	7	0	1	3	0	1	1	3	2	4	1	3	0	0	5	4	0	0	6	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr10:119003520G>T	ENST00000298472.5	+	3	303	c.160G>T	c.(160-162)Gag>Tag	p.E54*	SLC18A2_ENST00000497497.1_3'UTR|RP11-501J20.5_ENST00000425264.1_RNA	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	54					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	CATTAAGCATGAGAAGAATGC	0.478																																					p.E54X		.											.	SLC18A2-90	0			c.G160T						.						70	61	64					10																	119003520		2203	4300	6503	SO:0001587	stop_gained	6571	exon3			AAGCATGAGAAGA	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"Solute carriers"	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.160G>T	10.37:g.119003520G>T	ENSP00000298472:p.Glu54*	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	64	29	NM_003054	0	0	0	0	0	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Nonsense_Mutation	SNP	ENST00000298472.5	37	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307301	0.81247	.	.	ENSG00000165646	ENST00000298472	.	.	.	5.82	5.82	0.92795	.	0.167513	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-19.4478	14.7287	0.69365	0.0:0.144:0.856:0.0	.	.	.	.	X	54	.	ENSP00000298472:E54X	E	+	1	0	SLC18A2	118993510	0.976000	0.34144	0.990000	0.47175	0.418000	0.31294	1.665000	0.37449	2.756000	0.94617	0.563000	0.77884	GAG	.		0.478	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		T	119003520	G	T	119003520	4	4	57	1	0	0	0	0	0	1	0	0	14458	1291	45	4	166	4	SLC18A2	10	119003520	Nonsense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	19644565	119003520	16531227	40	5514											
C11orf46	120534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	30352522	30352522	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gatccatgttcagttggagtCcagcttcgtactacaaatga	11	12	9	9	1	1	1	1	1	0	0	4	3	3	2	2	1	3	4	2	1	3	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr11:30352522C>T	ENST00000282032.3	+	2	242	c.27C>T	c.(25-27)gtC>gtT	p.V9V		NM_152316.1	NP_689529.1	Q8N8R7	AL14E_HUMAN	ADP-ribosylation factor-like 14 effector protein	9						cytoplasm (GO:0005737)											CAGTTGGAGTCCAGCTTCGTA	0.378																																					p.V9V		.											.	.	0			c.C27T						.						76	70	72					11																	30352522		2202	4299	6501	SO:0001819	synonymous_variant	120534	exon2			TGGAGTCCAGCTT	AK096287	CCDS7869.1	11p14.1	2014-09-17	2012-07-09	2012-07-09	ENSG00000152219	ENSG00000152219			26798	protein-coding gene	gene with protein product		612295	"chromosome 11 open reading frame 46"	C11orf46		21458045	Standard	XM_005252792		Approved	FLJ38968, ARF7EP	uc001mso.1	Q8N8R7	OTTHUMG00000166154	ENST00000282032.3:c.27C>T	11.37:g.30352522C>T		Somatic	360	0		WXS	Illumina HiSeq	Phase_I	328	142	NM_152316	0	0	7	20	13	Q5HYH9	Silent	SNP	ENST00000282032.3	37	CCDS7869.1																																																																																			.		0.378	ARL14EP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388129.1	NM_152316		T	30352522	C	T	30352522	2	4	57	1	0	0	0	0	0	0	0	1	1647	842	30	2		2	C11orf46	11	30352522	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		30352522	104653994	41	5515											
CCDC85B	11007	hgsc.bcm.edu	37	chr11	65658488	65658488	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagaaccgtgagctgcgCgacctctgctgcttcctgga	7	8	13	13	3	1	2	0	1	1	1	2	5	2	3	3	1	5	4	3	1	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr11:65658488C>T	ENST00000312579.2	+	1	614	c.234C>T	c.(232-234)cgC>cgT	p.R78R	FIBP_ENST00000533045.1_5'Flank|FIBP_ENST00000357519.4_5'Flank|FIBP_ENST00000338369.2_5'Flank|FIBP_ENST00000426652.2_5'Flank	NM_006848.2	NP_006839.2	Q15834	CC85B_HUMAN	coiled-coil domain containing 85B	78					cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)									READ - Rectum adenocarcinoma(159;0.166)		GTGAGCTGCGCGACCTCTGCT	0.701																																					p.R78R		.											.	CCDC85B-90	0			c.C234T						.						5	6	5					11																	65658488		2076	4086	6162	SO:0001819	synonymous_variant	11007	exon1			GCTGCGCGACCTC	BC008796	CCDS8120.1	11q13.1	2010-12-24				ENSG00000175602			24926	protein-coding gene	gene with protein product	"hepatitis delta antigen interacting protein A"	605360				8810253, 15644333, 17873903	Standard	NM_006848		Approved	DIPA	uc001ogf.3	Q15834		ENST00000312579.2:c.234C>T	11.37:g.65658488C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_006848	0	0	9	22	13	B2R598|Q96HA0	Silent	SNP	ENST00000312579.2	37	CCDS8120.1																																																																																			.		0.701	CCDC85B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391196.1	NM_006848		T	65658488	C	T	65658488	2	4	57	1	0	0	0	0	0	0	0	1	2866	755	27	1		1	CCDC85B	11	65658488	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	35305966	65658488	69348028	42	5516											
SDHD	6392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	111958619	111958619	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtggtcagacctgctcatAtctcagcatttcttcaggac	9	12	8	12	0	5	1	4	0	2	1	6	2	5	2	1	2	2	2	1	2	1	3	rs397514034		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr11:111958619A>G	ENST00000375549.3	+	2	226	c.91A>G	c.(91-93)Atc>Gtc	p.I31V	TIMM8B_ENST00000541231.1_5'Flank|SDHD_ENST00000532699.1_Missense_Mutation_p.I31V|SDHD_ENST00000528182.1_Missense_Mutation_p.I31V|SDHD_ENST00000528048.1_Missense_Mutation_p.I31V|SDHD_ENST00000525291.1_Intron|SDHD_ENST00000528021.1_Missense_Mutation_p.I31V|SDHD_ENST00000526592.1_Missense_Mutation_p.I31V|TIMM8B_ENST00000504148.2_5'Flank|TIMM8B_ENST00000507614.1_5'Flank	NM_003002.2	NP_002993.1	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D, integral membrane protein	31					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|succinate dehydrogenase activity (GO:0000104)|ubiquinone binding (GO:0048039)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Hexachlorophene(DB00756)|Succinic acid(DB00139)	ACCTGCTCATATCTCAGCATT	0.473			"Mis, N, F, S"			"paraganglioma, pheochromocytoma"			Familial Paragangliomas;Cowden syndrome;Carney-Stratakis syndrome																												p.T31A		.	yes	Rec		Familial paraganglioma	11	11q23	6392	"succinate dehydrogenase complex, subunit D, integral membrane protein"		O	.	SDHD-226	0			c.A91G						.						178	155	163					11																	111958619		2201	4297	6498	SO:0001583	missense	6392	exon2	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	GCTCATATCTCAG	AB006202	CCDS31678.1, CCDS60958.1, CCDS60959.1, CCDS60960.1	11q23	2014-09-17				ENSG00000204370		"Mitochondrial respiratory chain complex / Complex II"	10683	protein-coding gene	gene with protein product		602690		PGL, PGL1		9533030, 1301144	Standard	NM_003002		Approved		uc001pmz.4	O14521		ENST00000375549.3:c.91A>G	11.37:g.111958619A>G	ENSP00000364699:p.Ile31Val	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	60	26	NM_003002	0	0	77	150	73	A6ND90|B3KQQ8|E9PIC0|E9PIG3|E9PQI9|Q53XW5|Q6IRW2	Missense_Mutation	SNP	ENST00000375549.3	37	CCDS31678.1	.	.	.	.	.	.	.	.	.	.	A	0.223	-1.026824	0.02045	.	.	ENSG00000204370	ENST00000375549;ENST00000528182;ENST00000528048;ENST00000528021;ENST00000526592	D;D;T;D;D	0.94497	-3.44;-2.77;-1.48;-2.76;-2.9	4.81	2.78	0.32641	.	0.321128	0.32244	N	0.006373	T	0.77624	0.4158	N	0.01168	-0.975	0.19300	N	0.999977	B	0.02656	0.0	B	0.01281	0.0	T	0.68224	-0.5465	10	0.02654	T	1	-1.6835	6.2353	0.20760	0.2591:0.0:0.7409:0.0	.	31	O14521	DHSD_HUMAN	V	31	ENSP00000364699:I31V;ENSP00000435475:I31V;ENSP00000436217:I31V;ENSP00000432465:I31V;ENSP00000432005:I31V	ENSP00000436395:I31V	I	+	1	0	SDHD	111463829	0.331000	0.24713	0.060000	0.19600	0.783000	0.44284	0.435000	0.21510	0.511000	0.28236	-0.248000	0.11899	ATC	.		0.473	SDHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392351.1	NM_003002		G	111958619	A	G	111958619	3	3	57	1	0	0	0	0	1	0	0	0	13999	449	16	3	97	3	SDHD	11	111958619	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	46300131	111958619	23047897	43	5517											
C12orf41	54934	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49073468	49073468	+	Frame_Shift_Del	DEL	T	T	-																															gctggcttcactgcgactacTttctggagtctgagacccca																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:49073468delT	ENST00000420613.2	-	3	447	c.400delA	c.(400-402)agtfs	p.S135fs	KANSL2_ENST00000357861.3_5'UTR|KANSL2_ENST00000550347.1_Frame_Shift_Del_p.S318fs|KANSL2_ENST00000553086.1_Frame_Shift_Del_p.S135fs	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	135					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											CTGCGACTACTTTCTGGAGTC	0.493																																					p.S134fs		.											.	.	0			c.400delA						.						50	47	48					12																	49073468		1915	4135	6050	SO:0001589	frameshift_variant	54934	exon3			.	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.400delA	12.37:g.49073468delT	ENSP00000415436:p.Ser135fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	122	64	NM_017822	0	0	0	0	0	Q8N3B5|Q96CV0|Q9NX51	Frame_Shift_Del	DEL	ENST00000420613.2	37	CCDS44869.1																																																																																			.		0.493	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		-	49073468	T	-	49073468	7	5	57	1	0	1	0	1	0	0	0	0	1691	1609	56	0	1110	0	C12orf41	12	49073468	Frame_Shift_Del	DEL	T	TCGA-B9-A5W9-01A-11D-A28G-10		49073468	84778427	44	5518	64	2									
C12orf41	54934	bcgsc.ca	37	chr12	49073469	49073469	+	Missense_Mutation	SNP	T	T	A																															ctggcttcactgcgactactTtctggagtctgagaccccag																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:49073469T>A	ENST00000420613.2	-	3	446	c.399A>T	c.(397-399)gaA>gaT	p.E133D	KANSL2_ENST00000357861.3_5'UTR|KANSL2_ENST00000550347.1_Missense_Mutation_p.E316D|KANSL2_ENST00000553086.1_Missense_Mutation_p.E133D	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	133					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											TGCGACTACTTTCTGGAGTCT	0.493																																					p.E133D													.	.	0			c.A399T						.						50	47	48					12																	49073469		1917	4135	6052	SO:0001583	missense	54934	exon3			ACTACTTTCTGGA	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.399A>T	12.37:g.49073469T>A	ENSP00000415436:p.Glu133Asp	Somatic	82	0		WXS	Illumina HiSeq	Phase_1	122	64	NM_017822	0	0	14	14	0	Q8N3B5|Q96CV0|Q9NX51	Missense_Mutation	SNP	ENST00000420613.2	37	CCDS44869.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.790834	0.50102	.	.	ENSG00000139620	ENST00000550347;ENST00000420613;ENST00000553086;ENST00000550931	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.95	2.33	0.28932	.	0.051599	0.85682	D	0.000000	T	0.52484	0.1737	N	0.11560	0.145	0.80722	D	1	B;B	0.31931	0.347;0.06	B;B	0.26416	0.069;0.03	T	0.37526	-0.9702	10	0.25106	T	0.35	-23.2646	7.0563	0.25102	0.0:0.3922:0.0:0.6078	.	316;133	F8VX10;Q9H9L4	.;CL041_HUMAN	D	316;133;133;70	ENSP00000449747:E316D;ENSP00000415436:E133D;ENSP00000448833:E133D;ENSP00000448129:E70D	ENSP00000415436:E133D	E	-	3	2	C12orf41	47359736	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.459000	0.21908	0.507000	0.28148	0.533000	0.62120	GAA	.		0.493	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		A	49073469	T	A	49073469	3	1	57	1	0	0	0	0	1	0	0	0	1691	1838	64	5	1111	5	C12orf41	12	49073469	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	1	49073469	84778426	45	5519	64	2									
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49432161	49432161	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcatcaaaatcgtcatccAgctcgggatcctcacagggc	10	7	11	13	2	3	0	3	0	0	0	7	1	5	1	2	3	1	2	2	3	2	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:49432161A>C	ENST00000301067.7	-	34	8977	c.8978T>G	c.(8977-8979)cTg>cGg	p.L2993R	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2993					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										ATCGTCATCCAGCTCGGGATC	0.597																																					p.L2993R		.											.	MLL2-612	0			c.T8978G						.						85	85	85					12																	49432161		2025	4193	6218	SO:0001583	missense	8085	exon34			TCATCCAGCTCGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8978T>G	12.37:g.49432161A>C	ENSP00000301067:p.Leu2993Arg	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	173	49	NM_003482	0	0	5	7	2	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	10.65	1.408624	0.25378	.	.	ENSG00000167548	ENST00000301067	D	0.83335	-1.71	5.46	5.46	0.80206	.	0.000000	0.30428	N	0.009645	D	0.86053	0.5841	L	0.29908	0.895	0.38041	D	0.935458	D	0.89917	1.0	D	0.75484	0.986	D	0.88960	0.3393	10	0.87932	D	0	.	14.8421	0.70233	1.0:0.0:0.0:0.0	.	2993	O14686	MLL2_HUMAN	R	2993	ENSP00000301067:L2993R	ENSP00000301067:L2993R	L	-	2	0	MLL2	47718428	0.520000	0.26250	0.999000	0.59377	0.717000	0.41224	4.553000	0.60753	2.207000	0.71202	0.533000	0.62120	CTG	.		0.597	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49432161	A	C	49432161	3	2	57	1	0	0	0	0	1	0	0	0	9646	188	7	5	7719	5	MLL2	12	49432161	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	358692	49432161	84419734	46	5520											
RHEBL1	121268	broad.mit.edu;bcgsc.ca	37	chr12	49460045	49460045	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatctgccttgttccccaCtagaaccactggcaccctgt	8	10	8	15	0	1	2	0	0	1	2	2	3	2	2	5	1	2	2	5	1	2	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:49460045C>A	ENST00000301068.6	-	6	588	c.349G>T	c.(349-351)Gtg>Ttg	p.V117L		NM_144593.1	NP_653194.1	Q8TAI7	REBL1_HUMAN	Ras homolog enriched in brain like 1	117					GTP catabolic process (GO:0006184)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|small GTPase mediated signal transduction (GO:0007264)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(2)|large_intestine(2)|lung(5)	9						TTGTTCCCCACTAGAACCACT	0.498																																					p.V117L													.	RHEBL1-659	0			c.G349T						.						114	106	108					12																	49460045		2203	4300	6503	SO:0001583	missense	121268	exon6			TCCCCACTAGAAC	AK098663	CCDS8778.1	12q13.12	2014-05-09				ENSG00000167550			21166	protein-coding gene	gene with protein product						12477932	Standard	NM_144593		Approved	MGC34869, FLJ25797	uc001rtc.1	Q8TAI7	OTTHUMG00000170407	ENST00000301068.6:c.349G>T	12.37:g.49460045C>A	ENSP00000301068:p.Val117Leu	Somatic	99	2		WXS	Illumina HiSeq	Phase_I	112	68	NM_144593	0	0	0	0	0	Q56VH8	Missense_Mutation	SNP	ENST00000301068.6	37	CCDS8778.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035378	0.75617	.	.	ENSG00000167550	ENST00000301068	T	0.81330	-1.48	5.25	4.36	0.52297	Small GTP-binding protein domain (1);	0.059229	0.64402	D	0.000003	D	0.89153	0.6634	M	0.85197	2.74	0.48571	D	0.999678	D	0.89917	1.0	D	0.77557	0.99	D	0.89836	0.3999	10	0.87932	D	0	.	10.0518	0.42221	0.0:0.9062:0.0:0.0938	.	117	Q8TAI7	REBL1_HUMAN	L	117	ENSP00000301068:V117L	ENSP00000301068:V117L	V	-	1	0	RHEBL1	47746312	0.915000	0.31059	0.998000	0.56505	0.940000	0.58332	1.598000	0.36740	1.347000	0.45714	0.591000	0.81541	GTG	.		0.498	RHEBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408969.1	NM_144593		A	49460045	C	A	49460045	3	1	57	1	0	0	0	0	1	0	0	0	13361	565	20	4	214	4	RHEBL1	12	49460045	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	27884	49460045	84391850	47	5521											
RAB5B	5869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56384574	56384574	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgacctggccaacaaacgtAtggtggagtatgaagtaagg	13	8	13	7	1	0	2	0	2	0	0	0	3	0	3	2	4	2	3	2	4	6	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:56384574A>G	ENST00000360299.5	+	4	645	c.424A>G	c.(424-426)Atg>Gtg	p.M142V	RAB5B_ENST00000448789.2_Intron|RAB5B_ENST00000553116.1_Missense_Mutation_p.M142V	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	142					antigen processing and presentation (GO:0019882)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1)	9			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			CAACAAACGTATGGTGGAGTA	0.522																																					p.M142V		.											.	RAB5B-227	0			c.A424G						.						126	120	122					12																	56384574		2203	4300	6503	SO:0001583	missense	5869	exon4			AAACGTATGGTGG		CCDS8900.1, CCDS58244.1	12q13	2008-07-30						"RAB, member RAS oncogene"	9784	protein-coding gene	gene with protein product		179514				1541686, 10403367	Standard	NM_001252037		Approved		uc001siw.3	P61020		ENST00000360299.5:c.424A>G	12.37:g.56384574A>G	ENSP00000353444:p.Met142Val	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	151	87	NM_002868	0	0	58	159	101	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Missense_Mutation	SNP	ENST00000360299.5	37	CCDS8900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.481|9.481	1.098275|1.098275	0.20552|0.20552	.|.	.|.	ENSG00000111540|ENSG00000111540	ENST00000553116;ENST00000360299|ENST00000549218	T;T|.	0.78364|.	-1.17;-1.17|.	4.81|4.81	3.66|3.66	0.41972|0.41972	Small GTP-binding protein domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.15782|0.15782	0.0380|0.0380	N|N	0.00633|0.00633	-1.31|-1.31	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.06991|0.06991	-1.0796|-1.0796	10|5	0.09843|.	T|.	0.71|.	-6.2164|-6.2164	9.8491|9.8491	0.41046|0.41046	0.9168:0.0:0.0832:0.0|0.9168:0.0:0.0832:0.0	.|.	142;142|.	Q6FI54;P61020|.	.;RAB5B_HUMAN|.	V|C	142|61	ENSP00000450168:M142V;ENSP00000353444:M142V|.	ENSP00000353444:M142V|.	M|Y	+|+	1|2	0|0	RAB5B|RAB5B	54670841|54670841	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.607000|1.607000	0.36836|0.36836	0.974000|0.974000	0.38366|0.38366	0.477000|0.477000	0.44152|0.44152	ATG|TAT	.		0.522	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1			G	56384574	A	G	56384574	3	3	57	1	0	0	0	0	1	0	0	0	12981	449	16	3	434	3	RAB5B	12	56384574	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	6924529	56384574	77467321	48	5522											
SLC17A8	246213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	100811853	100811853	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccacgctatgccagcatTctcatggggatctcaaacgg	9	8	10	14	2	2	0	2	0	2	0	4	1	2	1	3	3	3	2	3	3	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:100811853T>G	ENST00000323346.5	+	11	1657	c.1344T>G	c.(1342-1344)atT>atG	p.I448M	SLC17A8_ENST00000552697.1_3'UTR|SLC17A8_ENST00000392989.3_Missense_Mutation_p.I398M	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	448					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						ATGCCAGCATTCTCATGGGGA	0.478																																					p.I448M		.											.	SLC17A8-93	0			c.T1344G						.						177	163	167					12																	100811853		2203	4300	6503	SO:0001583	missense	246213	exon11			CAGCATTCTCATG	AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1344T>G	12.37:g.100811853T>G	ENSP00000316909:p.Ile448Met	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	103	73	NM_139319	0	0	0	1	1	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	37	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261452	0.59431	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.55588	0.51;0.51	5.55	1.98	0.26296	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.73636	0.3612	M	0.90542	3.125	0.58432	D	0.999993	D;D	0.89917	0.999;1.0	D;D	0.87578	0.987;0.998	T	0.74121	-0.3767	10	0.66056	D	0.02	.	9.7886	0.40692	0.0:0.349:0.0:0.651	.	448;398	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	M	448;398	ENSP00000316909:I448M;ENSP00000376715:I398M	ENSP00000316909:I448M	I	+	3	3	SLC17A8	99335984	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	0.508000	0.22692	0.164000	0.19529	-0.250000	0.11733	ATT	.		0.478	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		G	100811853	T	G	100811853	3	3	57	1	0	0	0	0	1	0	0	0	14455	1771	62	5	1386	5	SLC17A8	12	100811853	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	44427279	100811853	33040042	49	5523											
ACACB	32	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	109702126	109702126	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctccccatctaccaccagGtggcggtgcagttcgccgac	6	8	11	16	3	1	0	0	0	1	0	3	1	2	0	5	3	3	3	5	3	1	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:109702126G>A	ENST00000338432.7	+	50	6996	c.6877G>A	c.(6877-6879)Gtg>Atg	p.V2293M	ACACB_ENST00000543201.1_3'UTR|ACACB_ENST00000377854.5_Missense_Mutation_p.V2223M|ACACB_ENST00000377848.3_Missense_Mutation_p.V2293M			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2293	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	CTACCACCAGGTGGCGGTGCA	0.622											OREG0022102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V2293M													.	ACACB-98	0			c.G6877A						.						68	70	69					12																	109702126		2203	4300	6503	SO:0001583	missense	32	exon49			CACCAGGTGGCGG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6877G>A	12.37:g.109702126G>A	ENSP00000341044:p.Val2293Met	Somatic	125	1	1421	WXS	Illumina HiSeq	Phase_I	104	55	NM_001093	0	0	7	25	18	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106643	0.94292	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	D;D;D	0.97772	-4.53;-4.53;-4.53	4.79	4.79	0.61399	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.000000	0.85682	D	0.000000	D	0.98789	0.9592	M	0.85041	2.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99764	1.1022	10	0.66056	D	0.02	.	18.2354	0.89948	0.0:0.0:1.0:0.0	.	2293	O00763	ACACB_HUMAN	M	2293;2293;2223;1524	ENSP00000341044:V2293M;ENSP00000367079:V2293M;ENSP00000367085:V2223M	ENSP00000341044:V2293M	V	+	1	0	ACACB	108186509	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.389000	0.81357	0.655000	0.94253	GTG	.		0.622	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109702126	G	A	109702126	3	1	57	1	0	0	0	0	1	0	0	0	107	1261	44	2	7071	2	ACACB	12	109702126	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	8890273	109702126	24149769	50	5524											
PEBP1	5037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	118575948	118575948	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccagcaggaaggatcccaaAtacaggtgagaggtgagaaa	16	4	13	8	0	0	2	0	2	0	2	1	6	1	4	2	4	2	1	2	4	4	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:118575948A>C	ENST00000261313.2	+	2	592	c.240A>C	c.(238-240)aaA>aaC	p.K80N		NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	80						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGATCCCAAATACAGGTGAG	0.517																																					p.K80N	NSCLC(44;94 1357 12187 49467)	.											.	PEBP1-779	0			c.A240C						.						41	36	38					12																	118575948		2203	4300	6503	SO:0001583	missense	5037	exon2			TCCCAAATACAGG	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.240A>C	12.37:g.118575948A>C	ENSP00000261313:p.Lys80Asn	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	73	24	NM_002567	0	0	0	0	0	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	37	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425675	0.43020	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.48522	0.81	4.42	0.684	0.18003	Phosphatidylethanolamine-binding, conserved site (1);	0.048518	0.85682	D	0.000000	T	0.37433	0.1003	L	0.60904	1.88	0.54753	D	0.999985	B;B	0.12013	0.005;0.001	B;B	0.23716	0.048;0.046	T	0.08554	-1.0716	10	0.30078	T	0.28	-8.474	4.709	0.12863	0.5104:0.0:0.3477:0.142	.	80;80	B4DRT4;P30086	.;PEBP1_HUMAN	N	80	ENSP00000261313:K80N	ENSP00000261313:K80N	K	+	3	2	PEBP1	117060331	0.829000	0.29322	0.997000	0.53966	0.937000	0.57800	0.050000	0.14120	-0.044000	0.13491	-0.274000	0.10170	AAA	.		0.517	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		C	118575948	A	C	118575948	3	2	57	1	0	0	0	0	1	0	0	0	11739	98	4	5	246	5	PEBP1	12	118575948	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	8873822	118575948	15275947	51	5525											
KDM2B	84678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	121881832	121881833	+	Missense_Mutation	DNP	GC	GC	AA																															tacccgcttgcgtccactcaGctcctggggcttctcgtatt																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:121881832_121881833GC>AA	ENST00000377071.4	-	16	2505_2506	c.2433_2434GC>TT	c.(2431-2436)gaGCtg>gaTTtg	p.E811D	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Missense_Mutation_p.E179D|KDM2B_ENST00000377069.4_Missense_Mutation_p.E780D	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	811					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CGTCCACTCAGCTCCTGGGGCT	0.649											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E811D		.											.	KDM2B-638	0			c.G2340T						.																																			SO:0001583	missense	84678	exon16			ACTCAGCTCCTGG	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2433_2434delinsAA	12.37:g.121881832_121881833delinsAA	ENSP00000366271:p.Glu811Asp	Somatic	55	0	1514	WXS	Illumina HiSeq	Phase_I	53	12	NM_001005366	0	0	0	0	0	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	DNP	ENST00000377071.4	37	CCDS41850.1																																																																																			.		0.649	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		AA	121881833	GC	AA	121881832	3	1	57	1	0	0	0	0	1	0	0	0	8146	962	34	2	1660	2	KDM2B	12	121881832	Missense_Mutation	DNP	GC	TCGA-B9-A5W9-01A-11D-A28G-10	3305884	121881832	11970063	52	5526											
RXFP2	122042	bcgsc.ca	37	chr13	32360573	32360573	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcacctttttaaagactTgaagcttctacaaaagctgt	13	13	5	10	0	2	2	1	1	1	1	2	2	2	2	2	0	3	2	2	0	6	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr13:32360573T>C	ENST00000298386.2	+	12	1054	c.983T>C	c.(982-984)tTg>tCg	p.L328S	RXFP2_ENST00000380314.1_Missense_Mutation_p.L304S	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	328					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		TTTAAAGACTTGAAGCTTCTA	0.338																																					p.L328S													.	RXFP2-90	0			c.T983C						.						99	92	95					13																	32360573		2203	4300	6503	SO:0001583	missense	122042	exon12			AAGACTTGAAGCT	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.983T>C	13.37:g.32360573T>C	ENSP00000298386:p.Leu328Ser	Somatic	58	0		WXS	Illumina HiSeq	Phase_1	67	5	NM_130806	0	0	0	0	0	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.083863	0.55861	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.72282	-0.64;-0.64	5.72	4.51	0.55191	.	0.000000	0.64402	D	0.000001	D	0.83422	0.5251	M	0.83223	2.63	0.25477	N	0.987777	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.75875	-0.3163	10	0.48119	T	0.1	.	11.3401	0.49527	0.1361:0.0:0.0:0.8639	.	304;328	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	S	304;328	ENSP00000369670:L304S;ENSP00000298386:L328S	ENSP00000298386:L328S	L	+	2	0	RXFP2	31258573	0.974000	0.33945	0.992000	0.48379	0.974000	0.67602	4.820000	0.62671	0.963000	0.38082	0.533000	0.62120	TTG	.		0.338	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		C	32360573	T	C	32360573	3	2	57	1	0	0	0	0	1	0	0	0	13792	1821	63	3	1029	3	RXFP2	13	32360573	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		32360573	82809305	53	5527											
MYCBP2	23077	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	77714983	77714983	+	De_novo_Start_OutOfFrame	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattcattctgccctaacctTattaggctgaggttcagact	10	14	7	10	0	3	2	2	1	1	1	3	2	3	2	2	2	2	2	2	2	4	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr13:77714983T>C	ENST00000360084.5	-	0	7377				MYCBP2_ENST00000357337.6_Missense_Mutation_p.K2429E|MYCBP2_ENST00000407578.2_Missense_Mutation_p.K2467E|MYCBP2_ENST00000544440.2_Missense_Mutation_p.K2429E					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GCCCTAACCTTATTAGGCTGA	0.403																																					p.K2467E		.											.	MYCBP2-236	0			c.A7399G						.						220	222	222					13																	77714983		2203	4300	6503			23077	exon50			TAACCTTATTAGG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000360084.5:c.-327A>G	13.37:g.77714983T>C		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	107	6	NM_015057	0	0	0	0	0		Missense_Mutation	SNP	ENST00000360084.5	37		.	.	.	.	.	.	.	.	.	.	T	20.4	3.985587	0.74589	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.36520	1.26;1.25;1.26	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.56277	0.1974	M	0.61703	1.905	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.59658	-0.7413	10	0.72032	D	0.01	.	15.2435	0.73488	0.0:0.0:0.0:1.0	.	2429	O75592	MYCB2_HUMAN	E	2429;2467;2429	ENSP00000349892:K2429E;ENSP00000384288:K2467E;ENSP00000444596:K2429E	ENSP00000349892:K2429E	K	-	1	0	MYCBP2	76612984	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.642000	0.83385	2.012000	0.59069	0.482000	0.46254	AAG	.		0.403	MYCBP2-202	KNOWN	basic	protein_coding	protein_coding		NM_015057		C	77714983	T	C	77714983	1	2	57	1	0	1	0	0	0	0	0	0	10043	1763	61	3		3	MYCBP2	13	77714983	De_novo_Start_OutOfFrame	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	45354410	77714983	37454895	54	5528											
TM9SF1	10548	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	24661497	24661519	+	Frame_Shift_Del	DEL	CTGCTGAGTTAATGGCCCCATGA	CTGCTGAGTTAATGGCCCCATGA	-																															cagggcatacaacaagatggCtgctgagttaatggccccat																								rs150862560		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	CTGCTGAGTTAATGGCCCCATGA	CTGCTGAGTTAATGGCCCCATGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr14:24661497_24661519delCTGCTGAGTTAATGGCCCCATGA	ENST00000261789.4	-	4	1369_1391	c.1011_1033delTCATGGGGCCATTAACTCAGCAG	c.(1009-1035)cgtcatggggccattaactcagcagccfs	p.HGAINSAA338fs	TM9SF1_ENST00000530611.1_Frame_Shift_Del_p.HGAINSAA547fs|TM9SF1_ENST00000396854.4_Frame_Shift_Del_p.HGAINSAA338fs|TM9SF1_ENST00000524835.1_Frame_Shift_Del_p.HGAINSAA251fs|TM9SF1_ENST00000528669.1_Frame_Shift_Del_p.HGAINSAA338fs|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000556387.1_Frame_Shift_Del_p.HGAINSAA547fs	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	338					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.S343P(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		AACAAGATGGCTGCTGAGTTAATGGCCCCATGACGGTGCACAT	0.538																																					p.337_345del		.											.	TM9SF1-91	1	Substitution - Missense(1)	large_intestine(1)	c.1011_1033del						.																																			SO:0001589	frameshift_variant	10548	exon4			.	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.1011_1033delTCATGGGGCCATTAACTCAGCAG	14.37:g.24661497_24661519delCTGCTGAGTTAATGGCCCCATGA	ENSP00000261789:p.His338fs	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	209	48	NM_001014842	0	0	0	0	0	D3DS65|Q86SZ6|Q96FI8	Frame_Shift_Del	DEL	ENST00000261789.4	37	CCDS9617.1																																																																																			.		0.538	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		-	24661519	CTGCTGAGTTAATGGCCCCATGA	-	24661497	7	5	57	1	0	1	0	1	0	0	0	0	16009	797	28	0	842	0	TM9SF1	14	24661497	Frame_Shift_Del	DEL	CTGCTGAGTTAATGGCCCCATGA	TCGA-B9-A5W9-01A-11D-A28G-10		24661497	82688043	55	5529											
SPTB	6710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	65253201	65253201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcactgagcgagggtgtggCtgcggctctcccacatcctg	5	8	15	13	2	1	1	0	1	1	0	3	2	2	1	2	4	2	3	2	4	0	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr14:65253201C>T	ENST00000389721.5	-	15	3514	c.3482G>A	c.(3481-3483)aGc>aAc	p.S1161N	SPTB_ENST00000556626.1_Missense_Mutation_p.S1161N|SPTB_ENST00000542895.1_Missense_Mutation_p.S1161N|SPTB_ENST00000389722.3_Missense_Mutation_p.S1161N|SPTB_ENST00000389720.3_Missense_Mutation_p.S1161N	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1161					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GAGGGTGTGGCTGCGGCTCTC	0.612																																					p.S1161N		.											.	SPTB-100	0			c.G3482A						.						58	59	59					14																	65253201		2203	4300	6503	SO:0001583	missense	6710	exon15			GTGTGGCTGCGGC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"Pleckstrin homology (PH) domain containing"	11274	protein-coding gene	gene with protein product	"spherocytosis, clinical type I"	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.3482G>A	14.37:g.65253201C>T	ENSP00000374371:p.Ser1161Asn	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	80	30	NM_001024858	0	0	0	0	0	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851576	0.32699	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	4.78	3.86	0.44501	.	0.412688	0.27549	N	0.018876	T	0.18551	0.0445	N	0.01352	-0.895	0.22096	N	0.999368	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13176	-1.0519	10	0.59425	D	0.04	.	6.711	0.23276	0.0:0.7003:0.0:0.2997	.	1161;1165	P11277;Q59FP5	SPTB1_HUMAN;.	N	1165;1161;1161;1161;1161;1161	ENSP00000374372:S1161N;ENSP00000451752:S1161N;ENSP00000374371:S1161N;ENSP00000443882:S1161N;ENSP00000374370:S1161N	ENSP00000374370:S1161N	S	-	2	0	SPTB	64322954	0.429000	0.25530	0.066000	0.19879	0.879000	0.50718	3.324000	0.52022	1.079000	0.41038	0.549000	0.68633	AGC	.		0.612	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65253201	C	T	65253201	3	4	57	1	0	0	0	0	1	0	0	0	15150	797	28	2	3657	2	SPTB	14	65253201	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	40591704	65253201	42096339	56	5530											
HERC2	8924	bcgsc.ca	37	chr15	28456185	28456185	+	Frame_Shift_Del	DEL	A	A	-																															gtctcctgaacagctggctgAgacaggatctgccgcagttt																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:28456185delA	ENST00000261609.7	-	44	7140	c.7032delT	c.(7030-7032)tctfs	p.S2344fs		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAGCTGGCTGAGACAGGATCT	0.488																																					p.S2344fs													.	HERC2-234	0			c.7032delT						.						36	37	36					15																	28456185		2202	4297	6499	SO:0001589	frameshift_variant	8924	exon44			TGGCTGAGACAGG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7032delT	15.37:g.28456185delA	ENSP00000261609:p.Ser2344fs	Somatic	409	1		WXS	Illumina HiSeq	Phase_1	406	140	NM_004667	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000261609.7	37	CCDS10021.1																																																																																			.		0.488	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		-	28456185	A	-	28456185	7	5	57	1	0	1	0	1	0	0	0	0	7079	291	11	0	7672	0	HERC2	15	28456185	Frame_Shift_Del	DEL	A	TCGA-B9-A5W9-01A-11D-A28G-10		28456185	74075207	57	5531											
SPTBN5	51332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42166194	42166194	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggctccgcccagaactcAgcacccgttgcacctgcccc	7	5	8	21	2	1	1	1	0	0	1	2	1	2	1	7	1	4	4	7	1	1	1	rs199969875		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:42166194A>C	ENST00000320955.6	-	25	4966	c.4739T>G	c.(4738-4740)cTg>cGg	p.L1580R		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1580					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCCAGAACTCAGCACCCGTTG	0.652																																					p.L1545R		.											.	SPTBN5-91	0			c.T4634G						.						26	31	29					15																	42166194		2009	4188	6197	SO:0001583	missense	51332	exon25			GAACTCAGCACCC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4739T>G	15.37:g.42166194A>C	ENSP00000317790:p.Leu1580Arg	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	26	10	NM_016642	0	0	0	0	0		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	16.38	3.107363	0.56291	.	.	ENSG00000137877	ENST00000320955	T	0.51071	0.72	5.26	5.26	0.73747	.	0.111511	0.39909	N	0.001223	T	0.71484	0.3345	M	0.84683	2.71	0.34983	D	0.754273	D	0.89917	1.0	D	0.87578	0.998	T	0.83027	-0.0164	10	0.87932	D	0	.	14.1772	0.65549	1.0:0.0:0.0:0.0	.	1580	Q9NRC6	SPTN5_HUMAN	R	1580	ENSP00000317790:L1580R	ENSP00000317790:L1580R	L	-	2	0	SPTBN5	39953486	1.000000	0.71417	0.240000	0.24138	0.217000	0.24651	6.813000	0.75231	1.979000	0.57680	0.529000	0.55759	CTG	.		0.652	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		C	42166194	A	C	42166194	3	2	57	1	0	0	0	0	1	0	0	0	15154	188	7	5	6461	5	SPTBN5	15	42166194	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	13710009	42166194	60365198	58	5532											
TGM7	116179	broad.mit.edu	37	chr15	43571977	43571977	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accctctggatacgcagcagCagctgcaggtcctggcccca	8	6	11	16	1	1	0	0	0	1	0	2	1	2	1	4	3	5	5	4	3	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:43571977C>A	ENST00000452443.2	-	10	1528	c.1524G>T	c.(1522-1524)ctG>ctT	p.L508L		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	508					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TACGCAGCAGCAGCTGCAGGT	0.657																																					p.L508L													.	TGM7-92	0			c.G1524T						.						38	44	42					15																	43571977		2201	4297	6498	SO:0001819	synonymous_variant	116179	exon10			CAGCAGCAGCTGC	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1524G>T	15.37:g.43571977C>A		Somatic	36	1		WXS	Illumina HiSeq	Phase_I	35	5	NM_052955	0	0	0	0	0		Silent	SNP	ENST00000452443.2	37	CCDS32213.1																																																																																			.		0.657	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		A	43571977	C	A	43571977	2	1	57	1	0	0	0	0	0	0	0	1	15867	697	25	4		4	TGM7	15	43571977	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	1405783	43571977	58959415	59	5533											
VPS13C	54832	broad.mit.edu	37	chr15	62207846	62207846	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacaccttatttttagtaaAaatgttcttcttcttgaaag	12	17	4	8	0	3	1	0	1	3	0	3	1	3	1	2	0	0	2	2	0	6	9			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:62207846A>T	ENST00000261517.5	-	61	8504	c.8431T>A	c.(8431-8433)Ttt>Att	p.F2811I	VPS13C_ENST00000395898.3_Missense_Mutation_p.F2768I|RN7SL613P_ENST00000584412.1_RNA|VPS13C_ENST00000249837.3_Missense_Mutation_p.F2768I|VPS13C_ENST00000395896.4_Missense_Mutation_p.F2811I	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTTTTAGTAAAAATGTTCTTC	0.338																																					p.F2811I													.	VPS13C-92	0			c.T8431A						.						23	25	24					15																	62207846		2195	4296	6491	SO:0001583	missense	54832	exon61			TAGTAAAAATGTT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.8431T>A	15.37:g.62207846A>T	ENSP00000261517:p.Phe2811Ile	Somatic	34	1		WXS	Illumina HiSeq	Phase_I	31	4	NM_020821	0	0	7	7	0		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813000	0.90707	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.31510	1.49;1.49;1.49	5.52	5.52	0.82312	Vacuolar protein sorting-associated protein (1);	0.000000	0.85682	D	0.000000	T	0.60856	0.2301	M	0.86502	2.82	0.80722	D	1	D;D;D;D;D	0.69078	0.995;0.957;0.963;0.997;0.97	D;D;P;D;D	0.73708	0.981;0.936;0.886;0.981;0.93	T	0.66991	-0.5783	10	0.52906	T	0.07	.	15.6453	0.77042	1.0:0.0:0.0:0.0	.	2811;2768;2811;2768;2811	F5GZG8;Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;.;VP13C_HUMAN	I	2768;2811;2811;2811	ENSP00000249837:F2768I;ENSP00000261517:F2811I;ENSP00000379233:F2811I	ENSP00000249837:F2768I	F	-	1	0	VPS13C	59995138	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.896000	0.92521	2.088000	0.63022	0.528000	0.53228	TTT	.		0.338	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62207846	A	T	62207846	3	4	57	1	0	0	0	0	1	0	0	0	17224	14	1	5	2958	5	VPS13C	15	62207846	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	18635869	62207846	40323546	60	5534											
SMAD6	4091	hgsc.bcm.edu	37	chr15	66995735	66995735	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcagccgagctgagccggccCcgcgggcaagagagggcgga	8	1	19	13	5	0	2	0	1	0	1	0	5	0	3	4	4	3	3	4	4	1	0	rs368960350	byFrequency	TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:66995735C>T	ENST00000288840.5	+	1	1170	c.139C>T	c.(139-141)Ccg>Tcg	p.P47S	SMAD6_ENST00000457357.2_Missense_Mutation_p.P47S	NM_005585.4	NP_005576.3	O43541	SMAD6_HUMAN	SMAD family member 6	47					BMP signaling pathway (GO:0030509)|cell-substrate adhesion (GO:0031589)|fat cell differentiation (GO:0045444)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|response to estrogen (GO:0043627)|response to laminar fluid shear stress (GO:0034616)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|R-SMAD binding (GO:0070412)|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 activin receptor binding (GO:0070698)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			lung(1)|skin(1)	2						TGAGCCGGCCCCGCGGGCAAG	0.781													C|||	28	0.00559105	0.0212	0	5008	,	,		7406	0		0	False		,,,				2504	0				p.P47S	Esophageal Squamous(179;72 2004 22333 39628 47290)	.											.	SMAD6-415	0			c.C139T						.	C	SER/PRO	19,2291		0,19,1136	1	2	2		139	1.6	1	15		2	0,5124		0,0,2562	no	missense	SMAD6	NM_005585.4	74	0,19,3698	TT,TC,CC		0.0,0.8225,0.2556	possibly-damaging	47/497	66995735	19,7415	1155	2562	3717	SO:0001583	missense	4091	exon1			CCGGCCCCGCGGG	BC012986	CCDS10221.1	15q22.31	2014-09-11	2006-11-06	2004-05-26	ENSG00000137834	ENSG00000137834		"SMADs"	6772	protein-coding gene	gene with protein product		602931	"MAD, mothers against decapentaplegic homolog 6 (Drosophila)", "SMAD, mothers against DPP homolog 6 (Drosophila)"	MADH7, MADH6		9256479	Standard	NR_027654		Approved	HsT17432	uc002aqf.3	O43541	OTTHUMG00000133218	ENST00000288840.5:c.139C>T	15.37:g.66995735C>T	ENSP00000288840:p.Pro47Ser	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	43	26	NM_005585	0	0	1	1	0	A9J6M5|O43654|Q15799|Q7Z7L4|Q96E31|Q9UKZ3	Missense_Mutation	SNP	ENST00000288840.5	37	CCDS10221.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.578776	0.46006	0.008225	0.0	ENSG00000137834	ENST00000288840;ENST00000457357	T;T	0.73789	-0.78;-0.78	3.56	1.62	0.23740	.	0.217966	0.39475	N	0.001355	T	0.47948	0.1473	L	0.27053	0.805	0.80722	D	1	B	0.10296	0.003	B	0.09377	0.004	T	0.43032	-0.9416	10	0.62326	D	0.03	.	4.743	0.13024	0.0:0.6512:0.2231:0.1257	.	47	O43541	SMAD6_HUMAN	S	47	ENSP00000288840:P47S;ENSP00000396961:P47S	ENSP00000288840:P47S	P	+	1	0	SMAD6	64782789	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	2.369000	0.44231	0.205000	0.20568	0.462000	0.41574	CCG	.		0.781	SMAD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256953.2	NM_005585		T	66995735	C	T	66995735	3	4	57	1	0	0	0	0	1	0	0	0	14794	623	22	2	141	2	SMAD6	15	66995735	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	4787889	66995735	35535657	61	5535											
ISLR	3671	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	74468065	74468065	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccccaacgtgggcactgatgGgcgtgccctgcctggcaccc	5	6	13	17	2	0	1	0	1	0	0	0	1	0	1	5	3	3	2	5	3	1	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:74468065G>T	ENST00000249842.3	+	2	1223	c.866G>T	c.(865-867)gGg>gTg	p.G289V	ISLR_ENST00000395118.1_Missense_Mutation_p.G289V|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	289	Ig-like.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						GGCACTGATGGGCGTGCCCTG	0.637																																					p.G289V													.	ISLR-155	0			c.G866T						.						78	79	78					15																	74468065		2198	4297	6495	SO:0001583	missense	3671	exon2			CTGATGGGCGTGC	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"Immunoglobulin superfamily / I-set domain containing"	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.866G>T	15.37:g.74468065G>T	ENSP00000249842:p.Gly289Val	Somatic	125	1		WXS	Illumina HiSeq	Phase_I	121	69	NM_201526	0	0	1	1	0		Missense_Mutation	SNP	ENST00000249842.3	37	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.142217	0.37825	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.64085	-0.08;-0.08	4.37	4.37	0.52481	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42548	U	0.000696	D	0.83672	0.5305	H	0.95328	3.655	0.48395	D	0.999649	D	0.64830	0.994	P	0.61477	0.889	D	0.89755	0.3943	10	0.87932	D	0	.	16.9283	0.86182	0.0:0.0:1.0:0.0	.	289	O14498	ISLR_HUMAN	V	289	ENSP00000249842:G289V;ENSP00000378550:G289V	ENSP00000249842:G289V	G	+	2	0	ISLR	72255118	0.995000	0.38212	0.217000	0.23759	0.095000	0.18619	2.221000	0.42917	1.987000	0.57996	0.313000	0.20887	GGG	.		0.637	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		T	74468065	G	T	74468065	3	4	57	1	0	0	0	0	1	0	0	0	7879	1232	43	4	868	4	ISLR	15	74468065	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	7472330	74468065	28063327	62	5536											
ADAMTS7	11173	broad.mit.edu	37	chr15	79083052	79083052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatggtgcaggggatgggCatcccccttcatgttgatgc	6	11	14	10	0	2	1	2	1	0	0	3	2	3	2	2	4	2	3	2	4	0	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:79083052C>T	ENST00000388820.4	-	6	1198	c.988G>A	c.(988-990)Gcc>Acc	p.A330T	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	330	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGGGGATGGGCATCCCCCTTC	0.597																																					p.A330T													.	ADAMTS7-226	0			c.G988A						.						183	136	152					15																	79083052		2196	4293	6489	SO:0001583	missense	11173	exon6			GATGGGCATCCCC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.988G>A	15.37:g.79083052C>T	ENSP00000373472:p.Ala330Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	78	4	NM_014272	0	0	2	2	0	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	C	0.048	-1.260469	0.01445	.	.	ENSG00000136378	ENST00000388820;ENST00000456326	D	0.86865	-2.18	4.86	-9.71	0.00518	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	1.854880	0.02471	N	0.087547	T	0.73916	0.3648	N	0.13371	0.34	0.09310	N	1	B;B;B	0.14012	0.009;0.001;0.005	B;B;B	0.24006	0.05;0.008;0.01	T	0.64300	-0.6440	10	0.14252	T	0.57	.	11.2082	0.48782	0.165:0.6694:0.0:0.1656	.	330;330;330	E7EP58;A8MQ00;Q9UKP4	.;.;ATS7_HUMAN	T	330	ENSP00000373472:A330T	ENSP00000373472:A330T	A	-	1	0	ADAMTS7	76870107	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.472000	0.02341	-3.126000	0.00237	-1.786000	0.00637	GCC	.		0.597	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79083052	C	T	79083052	3	4	57	1	0	0	0	0	1	0	0	0	271	710	25	2	4148	2	ADAMTS7	15	79083052	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	4614987	79083052	23448340	63	5537											
VASN	114990	broad.mit.edu	37	chr16	4432543	4432543	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcggggaggcccatacAcccccagccgtccactccaa	8	4	10	19	2	0	0	0	0	0	0	2	1	2	1	7	3	3	0	7	3	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:4432543A>C	ENST00000304735.3	+	2	1820	c.1665A>C	c.(1663-1665)acA>acC	p.T555T	CORO7_ENST00000539968.1_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000537233.2_Intron|CORO7_ENST00000251166.4_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000423908.2_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	555	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						AGGCCCATACACCCCCAGCCG	0.731																																					p.T555T													.	VASN-68	0			c.A1665C						.						11	17	15					16																	4432543		2155	4252	6407	SO:0001819	synonymous_variant	114990	exon2			CCATACACCCCCA	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"slit-like 2 (Drosophila)"	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1665A>C	16.37:g.4432543A>C		Somatic	20	2		WXS	Illumina HiSeq	Phase_I	135	32	NM_138440	0	0	17	17	0	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			.		0.731	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		C	4432543	A	C	4432543	2	2	57	1	0	0	0	0	0	0	0	1	17160	146	6	5		5	VASN	16	4432543	Silent	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		4432543	85922210	64	5538											
GPR97	222487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57713092	57713092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gatctcccctttcacagggcCcccggctcggcctgggagat	5	8	12	16	2	2	1	1	0	1	1	4	3	2	1	5	4	0	1	5	4	0	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:57713092C>T	ENST00000333493.4	+	5	657	c.496C>T	c.(496-498)Ccc>Tcc	p.P166S	GPR97_ENST00000450388.3_Missense_Mutation_p.P46S|GPR97_ENST00000327655.6_5'UTR|RP11-405F3.4_ENST00000563062.1_RNA	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	166					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTCACAGGGCCCCCGGCTCGG	0.632																																					p.P166S		.											.	GPR97-91	0			c.C496T						.						60	61	61					16																	57713092		2198	4300	6498	SO:0001583	missense	222487	exon5			CAGGGCCCCCGGC	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"-", "GPCR / Class B : Orphans"	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.496C>T	16.37:g.57713092C>T	ENSP00000332900:p.Pro166Ser	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	90	25	NM_170776	0	0	0	0	0	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	37	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	C	6.016	0.371299	0.11409	.	.	ENSG00000182885	ENST00000333493;ENST00000450388	T;T	0.28454	1.61;1.7	4.3	-0.0636	0.13776	.	0.491076	0.17461	N	0.173450	T	0.19248	0.0462	L	0.38838	1.175	0.34925	D	0.748776	B	0.21071	0.051	B	0.18561	0.022	T	0.09015	-1.0694	10	0.52906	T	0.07	.	4.2438	0.10662	0.0:0.5249:0.1709:0.3042	.	166	Q86Y34	GPR97_HUMAN	S	166;46	ENSP00000332900:P166S;ENSP00000404803:P46S	ENSP00000332900:P166S	P	+	1	0	GPR97	56270593	0.001000	0.12720	0.670000	0.29842	0.078000	0.17371	-0.024000	0.12435	0.104000	0.17725	0.313000	0.20887	CCC	.		0.632	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		T	57713092	C	T	57713092	3	4	57	1	0	0	0	0	1	0	0	0	6741	623	22	2	514	2	GPR97	16	57713092	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	53280549	57713092	32641661	65	5539											
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72821093	72821093	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggtgtccgttcctacactGgtcagaccactgtccttggg	7	11	11	12	1	1	1	1	0	0	1	4	1	4	1	4	3	1	1	4	3	2	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:72821093G>T	ENST00000268489.5	-	10	11754	c.11082C>A	c.(11080-11082)acC>acA	p.T3694T	AC004943.1_ENST00000584072.1_RNA|ZFHX3_ENST00000397992.5_Silent_p.T2780T|RP5-991G20.4_ENST00000569195.1_RNA|RP5-991G20.1_ENST00000563328.2_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3694					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TTCCTACACTGGTCAGACCAC	0.463																																					p.T3694T		.											.	ZFHX3-72	0			c.C11082A						.						161	173	169					16																	72821093		2198	4300	6498	SO:0001819	synonymous_variant	463	exon10			TACACTGGTCAGA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.11082C>A	16.37:g.72821093G>T		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	127	37	NM_006885	0	0	2	4	2	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.		0.463	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72821093	G	T	72821093	2	4	57	1	0	0	0	0	0	0	0	1	17666	1335	47	4		4	ZFHX3	16	72821093	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	15108001	72821093	17533660	66	5540											
CLEC18B	497190	broad.mit.edu;bcgsc.ca	37	chr16	74444869	74444869	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtctccaggcggcccaGatagaaggcgaggatgtcct	8	7	16	10	2	1	2	0	0	1	2	3	4	2	3	3	6	0	0	3	6	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:74444869G>T	ENST00000339953.5	-	9	1169	c.1048C>A	c.(1048-1050)Ctg>Atg	p.L350M		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	350	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						AGGCGGCCCAGATAGAAGGCG	0.587																																					p.L350M													.	CLEC18B-90	0			c.C1048A						.						2	2	2					16																	74444869		706	1402	2108	SO:0001583	missense	497190	exon9			GGCCCAGATAGAA	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"C-type lectin domain containing"	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.1048C>A	16.37:g.74444869G>T	ENSP00000341051:p.Leu350Met	Somatic	592	0		WXS	Illumina HiSeq	Phase_I	588	122	NM_001011880	0	0	0	0	0	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	37	CCDS32484.1	.	.	.	.	.	.	.	.	.	.	N	15.98	2.992397	0.54041	.	.	ENSG00000140839	ENST00000429489;ENST00000339953	T	0.22336	1.96	3.14	1.05	0.20165	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.64402	D	0.000007	T	0.36524	0.0970	M	0.67569	2.06	0.32862	D	0.508097	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.44711	-0.9310	10	0.72032	D	0.01	.	5.3462	0.16010	0.2931:0.0:0.7069:0.0	.	350;350	C9JSV1;Q6UXF7	.;CL18B_HUMAN	M	350	ENSP00000341051:L350M	ENSP00000341051:L350M	L	-	1	2	CLEC18B	73002370	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.317000	0.51968	0.532000	0.28657	0.425000	0.28330	CTG	.		0.587	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880		T	74444869	G	T	74444869	3	4	57	1	0	0	0	0	1	0	0	0	3509	933	33	4	339	4	CLEC18B	16	74444869	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	1623776	74444869	15909884	67	5541											
GALNS	2588	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	88889080	88889080	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcttccagattgtgagttgtGacccctgaaacgttctgccc	7	13	9	12	1	2	4	0	3	2	1	3	4	3	4	4	0	2	2	4	0	1	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:88889080G>A	ENST00000268695.5	-	12	1369	c.1281C>T	c.(1279-1281)gtC>gtT	p.V427V	GALNS_ENST00000542788.1_Silent_p.V352V	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	427					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		TGTGAGTTGTGACCCCTGAAA	0.622																																					p.V427V	GBM(129;1929 2344 25209 33204)	.											.	GALNS-153	0			c.C1281T						.						105	88	94					16																	88889080		2196	4299	6495	SO:0001819	synonymous_variant	2588	exon12			AGTTGTGACCCCT	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"Arylsulfatase family"	4122	protein-coding gene	gene with protein product	"Morquio syndrome", "mucopolysaccharidosis type IVA"	612222	"galactosamine (N-acetyl)-6-sulfate sulfatase"			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1281C>T	16.37:g.88889080G>A		Somatic	205	0		WXS	Illumina HiSeq	Phase_I	251	75	NM_000512	0	0	20	31	11	Q86VK3	Silent	SNP	ENST00000268695.5	37	CCDS10970.1																																																																																			.		0.622	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1			A	88889080	G	A	88889080	2	1	57	1	0	0	0	0	0	0	0	1	6226	1277	45	2		2	GALNS	16	88889080	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	14444211	88889080	1465673	68	5542											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	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_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y	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	265	268					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	325	23		WXS	Illumina HiSeq		498	29	NM_145301	0	0	8	40	32	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		T	15457087	C	T	15457087	3	4	57	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		15457087	65738123	69	5543											
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18058522	18058522	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggaggtctacttctccCgcatcttccccgccacggtg	4	10	10	17	3	3	0	0	0	3	0	5	1	4	1	5	3	1	1	5	3	1	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:18058522C>T	ENST00000205890.5	+	46	8661	c.8323C>T	c.(8323-8325)Cgc>Tgc	p.R2775C	MYO15A_ENST00000585180.1_Missense_Mutation_p.R39C|MYO15A_ENST00000418233.3_Missense_Mutation_p.R39C	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2775	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CTACTTCTCCCGCATCTTCCC	0.607																																					p.R2775C		.											.	MYO15A-97	0			c.C8323T						.						39	48	45					17																	18058522		2100	4218	6318	SO:0001583	missense	51168	exon45			TTCTCCCGCATCT	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8323C>T	17.37:g.18058522C>T	ENSP00000205890:p.Arg2775Cys	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	108	12	NM_016239	0	0	0	0	0	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898121	0.52227	.	.	ENSG00000091536	ENST00000205890	D	0.93488	-3.23	5.1	5.1	0.69264	.	.	.	.	.	D	0.97164	0.9073	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	D	0.97931	1.0320	9	0.87932	D	0	.	18.5096	0.90911	0.0:1.0:0.0:0.0	.	39;2775	B4DFC7;Q9UKN7	.;MYO15_HUMAN	C	2775	ENSP00000205890:R2775C	ENSP00000205890:R2775C	R	+	1	0	MYO15A	17999247	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	7.086000	0.76885	2.363000	0.80096	0.561000	0.74099	CGC	.		0.607	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18058522	C	T	18058522	3	4	57	1	0	0	0	0	1	0	0	0	10088	652	23	1	8497	1	MYO15A	17	18058522	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	2601435	18058522	63136688	70	5544											
AATF	26574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	35345926	35345926	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggactatcccagcttcatGgcaaagcgctttgccgactt	9	10	10	12	2	1	0	1	0	0	0	2	3	2	1	2	2	3	3	2	2	2	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:35345926G>A	ENST00000225402.5	+	6	1307	c.1056G>A	c.(1054-1056)atG>atA	p.M352I		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	352	RB1 binding.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				CCAGCTTCATGGCAAAGCGCT	0.493																																					p.M352I	NSCLC(49;901 1159 19183 41572 46244)	.											.	AATF-90	0			c.G1056A						.						97	90	93					17																	35345926		2203	4300	6503	SO:0001583	missense	26574	exon6			CTTCATGGCAAAG	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.1056G>A	17.37:g.35345926G>A	ENSP00000225402:p.Met352Ile	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	157	84	NM_012138	0	0	22	69	47	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	37	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740923	0.30865	.	.	ENSG00000108270	ENST00000225402	.	.	.	5.58	4.62	0.57501	.	0.033193	0.85682	D	0.000000	T	0.43722	0.1260	L	0.33339	1.005	0.52501	D	0.999955	B	0.12013	0.005	B	0.17098	0.017	T	0.26224	-1.0109	9	0.15066	T	0.55	-8.411	11.471	0.50268	0.1564:0.0:0.8436:0.0	.	352	Q9NY61	AATF_HUMAN	I	352	.	ENSP00000225402:M352I	M	+	3	0	AATF	32420039	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.264000	0.72527	1.370000	0.46153	0.561000	0.74099	ATG	.		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138		A	35345926	G	A	35345926	3	1	57	1	0	0	0	0	1	0	0	0	25	1348	47	2	1078	2	AATF	17	35345926	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	17287404	35345926	45849284	71	5545											
SCPEP1	59342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	55058480	55058480	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccacagaggagggcaaggaAgtatgggattatgtgacggt	12	7	16	6	1	0	2	0	1	0	1	0	5	0	5	1	5	0	2	1	5	4	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:55058480A>C	ENST00000262288.3	+	2	169	c.114A>C	c.(112-114)gaA>gaC	p.E38D	RP5-1107A17.4_ENST00000572877.1_RNA|SCPEP1_ENST00000571898.1_3'UTR	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	38					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					AGGGCAAGGAAGTATGGGATT	0.493																																					p.E38D		.											.	SCPEP1-91	0			c.A114C						.						128	105	113					17																	55058480		2203	4300	6503	SO:0001583	missense	59342	exon2			CAAGGAAGTATGG	AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"retinoid inducible serine carboxypeptidase"					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.114A>C	17.37:g.55058480A>C	ENSP00000262288:p.Glu38Asp	Somatic	235	1		WXS	Illumina HiSeq	Phase_I	338	161	NM_021626	0	0	4	9	5	Q96A94|Q9H3F0	Missense_Mutation	SNP	ENST00000262288.3	37	CCDS11593.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093414	0.56075	.	.	ENSG00000121064	ENST00000262288	D	0.85955	-2.05	5.84	3.64	0.41730	.	0.000000	0.85682	D	0.000000	D	0.91331	0.7266	M	0.89414	3.03	0.46954	D	0.99926	D	0.65815	0.995	D	0.70716	0.97	D	0.90110	0.4191	10	0.66056	D	0.02	-12.7064	5.5755	0.17220	0.71:0.0:0.29:0.0	.	38	Q9HB40	RISC_HUMAN	D	38	ENSP00000262288:E38D	ENSP00000262288:E38D	E	+	3	2	SCPEP1	52413479	0.816000	0.29132	0.975000	0.42487	0.312000	0.27988	0.445000	0.21677	1.036000	0.39998	0.533000	0.62120	GAA	.		0.493	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626		C	55058480	A	C	55058480	3	2	57	1	0	0	0	0	1	0	0	0	13967	69	3	5	120	5	SCPEP1	17	55058480	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	19712554	55058480	26136730	72	5546											
NACA2	342538	ucsc.edu	37	chr17	59668318	59668318	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacatagccttccgtgccCtcttttcactccgactctgt	5	14	7	15	2	3	0	1	0	2	0	5	2	5	1	4	1	2	0	4	1	1	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:59668318C>T	ENST00000521764.1	-	1	245	c.224G>A	c.(223-225)aGg>aAg	p.R75K		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	75	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					CTTCCGTGCCCTCTTTTCACT	0.458																																					p.R75K													.	NACA2-91	0			c.G224A						.						246	229	234					17																	59668318		2203	4300	6503	SO:0001583	missense	342538	exon1			CGTGCCCTCTTTT	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.224G>A	17.37:g.59668318C>T	ENSP00000427802:p.Arg75Lys	Somatic	137	1		WXS	Illumina HiSeq		277	4	NM_199290	0	0	0	1895	1895	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976583	0.34848	.	.	ENSG00000253506	ENST00000521764	T	0.17528	2.27	0.753	-0.748	0.11087	Nascent polypeptide-associated complex NAC (2);	0.072360	0.50627	N	0.000118	T	0.01489	0.0048	N	0.00010	-3.04	0.23577	N	0.997375	B	0.02656	0.0	B	0.01281	0.0	T	0.46076	-0.9217	9	.	.	.	.	4.0866	0.09950	0.0:0.257:0.0:0.743	.	75	Q9H009	NACA2_HUMAN	K	75	ENSP00000427802:R75K	.	R	-	2	0	NACA2	57023100	1.000000	0.71417	0.973000	0.42090	0.773000	0.43773	3.300000	0.51834	-0.188000	0.10499	-0.624000	0.04008	AGG	.		0.458	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		T	59668318	C	T	59668318	3	4	57	1	0	0	0	0	1	0	0	0	10159	681	24	2	427	2	NACA2	17	59668318	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	4609838	59668318	21526892	73	5547											
SPHK1	8877	hgsc.bcm.edu	37	chr17	74381682	74381682	+	5'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccacgggcagcgcccccaCagcgccagggaccccctggc	6	1	13	21	4	0	0	0	0	0	0	0	1	0	1	6	3	2	1	6	3	0	0	rs56342542	byFrequency	TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:74381682C>T	ENST00000545180.1	+	0	766				SPHK1_ENST00000592299.1_5'UTR|SPHK1_ENST00000590959.1_5'UTR|SPHK1_ENST00000323374.4_Missense_Mutation_p.T72I|SPHK1_ENST00000392496.3_5'UTR			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1						'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	AGCGCCCCCACAGCGCCAGGG	0.716													C|||	43	0.00858626	0	0.0173	5008	,	,		12154	0		0.0278	False		,,,				2504	0.0031				p.T72I	GBM(90;966 1307 27369 33775 44498)	.											.	SPHK1-1107	0			c.C215T						.	C	,,,ILE/THR	16,3798		0,16,1891	6	10	9		,,,215	3.8	0	17	dbSNP_129	9	114,7334		0,114,3610	no	utr-5,utr-5,utr-5,missense	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	,,,89	0,130,5501	TT,TC,CC		1.5306,0.4195,1.1543	,,,possibly-damaging	,,,72/471	74381682	130,11132	1907	3724	5631	SO:0001623	5_prime_UTR_variant	8877	exon2			CCCCCACAGCGCC	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.-44C>T	17.37:g.74381682C>T		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	43	15	NM_182965	0	0	1	3	2	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	37	CCDS45785.1	26	0.011904761904761904	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	18	0.023746701846965697	C	12.88	2.071524	0.36566	0.004195	0.015306	ENSG00000176170	ENST00000323374	T	0.23950	1.88	5.03	3.83	0.44106	.	1.434080	0.04181	N	0.326590	T	0.10766	0.0263	.	.	.	0.22489	N	0.999055	B	0.29646	0.253	B	0.27500	0.08	T	0.08066	-1.0740	9	0.35671	T	0.21	-13.0527	11.1919	0.48690	0.0:0.8948:0.0:0.1052	rs56342542;rs61751847	72	Q9NYA1-2	.	I	72	ENSP00000313681:T72I	ENSP00000313681:T72I	T	+	2	0	SPHK1	71893277	0.000000	0.05858	0.031000	0.17742	0.031000	0.12232	0.145000	0.16157	2.337000	0.79520	0.462000	0.41574	ACA	C|0.988;T|0.012		0.716	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		T	74381682	C	T	74381682	1	4	57	0	1	0	0	0	0	0	0	0	15078	478	17	2		2	SPHK1	17	74381682	5'UTR	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	14713364	74381682	6813528	74	5548											
P4HB	5034	broad.mit.edu	37	chr17	79813349	79813349	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttgaagaagccgatgacagCcacctcgctggactccacca	11	6	9	15	2	0	3	0	2	0	1	2	5	1	4	5	1	2	1	5	1	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:79813349C>A	ENST00000331483.4	-	3	688	c.466G>T	c.(466-468)Gct>Tct	p.A156S	P4HB_ENST00000439918.2_Intron|P4HB_ENST00000576390.1_Intron|P4HB_ENST00000472244.1_5'UTR	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	156					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			CCGATGACAGCCACCTCGCTG	0.602																																					p.A156S	Colon(49;444 983 1296 7887 42561)												.	P4HB-46	0			c.G466T						.						58	63	61					17																	79813349		2203	4300	6503	SO:0001583	missense	5034	exon3			TGACAGCCACCTC	J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"Protein disulfide isomerases"	8548	protein-coding gene	gene with protein product	"protein disulfide isomerase-associated 1", "protein disulfide isomerase family A, member 1", "collagen prolyl 4-hydroxylase beta"	176790	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)", "procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)", "procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.466G>T	17.37:g.79813349C>A	ENSP00000327801:p.Ala156Ser	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	104	5	NM_000918	1	0	598	600	1	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Missense_Mutation	SNP	ENST00000331483.4	37	CCDS11787.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206607	0.58343	.	.	ENSG00000185624	ENST00000331483;ENST00000436463	T	0.22336	1.96	4.75	0.549	0.17213	Thioredoxin-like fold (2);	0.324426	0.35677	N	0.003055	T	0.16642	0.0400	L	0.35414	1.06	0.80722	D	1	B	0.18610	0.029	B	0.30316	0.114	T	0.07309	-1.0779	10	0.59425	D	0.04	.	9.5234	0.39149	0.0:0.7428:0.0:0.2572	.	156	P07237	PDIA1_HUMAN	S	156;140	ENSP00000327801:A156S	ENSP00000327801:A156S	A	-	1	0	P4HB	77406638	0.996000	0.38824	0.235000	0.24058	0.848000	0.48234	2.629000	0.46485	-0.171000	0.10797	0.462000	0.41574	GCT	.		0.602	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918		A	79813349	C	A	79813349	3	1	57	1	0	0	0	0	1	0	0	0	11385	739	26	4	1096	4	P4HB	17	79813349	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	5431667	79813349	1381861	75	5549											
DCC	1630	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	50985743	50985743	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccctgcaggaagggactcTcccatccaaagttgccaaga	12	6	10	13	0	1	1	0	0	1	1	3	4	2	3	4	2	2	2	4	2	3	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr18:50985743T>A	ENST00000442544.2	+	24	4150	c.3534T>A	c.(3532-3534)tcT>tcA	p.S1178S	DCC_ENST00000581580.1_Silent_p.S813S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1178					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GAAGGGACTCTCCCATCCAAA	0.478																																					p.S1178S													.	DCC-225	0			c.T3534A						.						140	138	139					18																	50985743		2203	4300	6503	SO:0001819	synonymous_variant	1630	exon24			GGACTCTCCCATC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3534T>A	18.37:g.50985743T>A		Somatic	55	1		WXS	Illumina HiSeq	Phase_I	45	24	NM_005215	0	0	0	0	0		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			.		0.478	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		A	50985743	T	A	50985743	2	1	57	1	0	0	0	0	0	0	0	1	4288	1538	54	5		5	DCC	18	50985743	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		50985743	27091505	76	5550											
SERPINB8	5271	broad.mit.edu	37	chr18	61654493	61654493	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caactgcatcttgttctgtgGcaggttctcttctccgtaaa	7	15	8	11	1	4	0	0	0	4	0	6	0	4	0	1	2	2	5	1	2	3	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr18:61654493G>T	ENST00000397985.2	+	7	1362	c.1106G>T	c.(1105-1107)gGc>gTc	p.G369V	SERPINB8_ENST00000353706.2_Missense_Mutation_p.G369V|SERPINB8_ENST00000493661.1_Intron|SERPINB8_ENST00000542677.1_Missense_Mutation_p.G187V	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	369					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				TTGTTCTGTGGCAGGTTCTCT	0.468																																					p.G369V													.	SERPINB8-226	0			c.G1106T						.						96	97	97					18																	61654493		2203	4300	6503	SO:0001583	missense	5271	exon7			TCTGTGGCAGGTT	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"Serine (or cysteine) peptidase inhibitors"	8952	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase 2"	601697	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.1106G>T	18.37:g.61654493G>T	ENSP00000381072:p.Gly369Val	Somatic	78	2		WXS	Illumina HiSeq	Phase_I	71	7	NM_198833	0	0	2	2	0	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.496901	0.64186	.	.	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677	D;D;T	0.98044	-4.68;-4.68;-0.1	5.38	5.38	0.77491	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.99296	0.9754	H	0.97983	4.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98676	1.0690	10	0.87932	D	0	.	18.3101	0.90195	0.0:0.0:1.0:0.0	.	369	P50452	SPB8_HUMAN	V	369;369;187	ENSP00000381072:G369V;ENSP00000331368:G369V;ENSP00000438328:G187V	ENSP00000331368:G369V	G	+	2	0	SERPINB8	59805473	1.000000	0.71417	0.997000	0.53966	0.099000	0.18886	9.555000	0.98123	2.793000	0.96121	0.655000	0.94253	GGC	.		0.468	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848		T	61654493	G	T	61654493	3	4	57	1	0	0	0	0	1	0	0	0	14139	1203	42	4	1141	4	SERPINB8	18	61654493	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	10668750	61654493	16422755	77	5551											
DOHH	83475	broad.mit.edu	37	chr19	3496745	3496745	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaacagcgcccggaagcggGcctgcaggggctgcttgggg	6	5	19	11	3	0	1	0	1	0	0	0	2	0	2	2	6	5	3	2	6	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:3496745G>T	ENST00000427575.1	-	2	519	c.68C>A	c.(67-69)gCc>gAc	p.A23D	DOHH_ENST00000250937.3_Missense_Mutation_p.A23D	NM_001145165.1	NP_001138637.1			deoxyhypusine hydroxylase/monooxygenase											central_nervous_system(1)|large_intestine(1)|lung(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGAAGCGGGCCTGCAGGGG	0.672																																					p.A23D													.	DOHH-90	0			c.C68A						.						30	34	33					19																	3496745		2203	4299	6502	SO:0001583	missense	83475	exon2			AAGCGGGCCTGCA	BC002817	CCDS12108.1	19p13.3	2008-02-05	2006-05-22	2006-05-22		ENSG00000129932			28662	protein-coding gene	gene with protein product		611262	"HEAT-like (PBS lyase) repeat containing 1"	HLRC1		16371467, 16533814	Standard	NM_031304		Approved	MGC4293	uc002lxs.3	Q9BU89		ENST00000427575.1:c.68C>A	19.37:g.3496745G>T	ENSP00000398882:p.Ala23Asp	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	82	6	NM_001145165	0	0	20	20	0		Missense_Mutation	SNP	ENST00000427575.1	37	CCDS12108.1	.	.	.	.	.	.	.	.	.	.	G	6.366	0.435651	0.12104	.	.	ENSG00000129932	ENST00000427575;ENST00000250937	.	.	.	4.28	4.28	0.50868	Armadillo-like helical (1);	0.572614	0.17864	N	0.159432	T	0.30324	0.0761	L	0.45352	1.415	0.26414	N	0.97622	B	0.06786	0.001	B	0.08055	0.003	T	0.16364	-1.0405	9	0.12766	T	0.61	-7.5811	8.1479	0.31124	0.1119:0.0:0.8881:0.0	.	23	Q9BU89	DOHH_HUMAN	D	23	.	ENSP00000250937:A23D	A	-	2	0	DOHH	3447745	0.999000	0.42202	1.000000	0.80357	0.689000	0.40095	4.666000	0.61554	1.947000	0.56498	0.561000	0.74099	GCC	.		0.672	DOHH-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452932.1	NM_031304		T	3496745	G	T	3496745	3	4	57	1	0	0	0	0	1	0	0	0	4706	1203	42	4	856	4	DOHH	19	3496745	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		3496745	55632238	78	5552											
ZNF443	10224	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12541862	12541862	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcagtgaactaggacaaTcaaagcctttcccacatatc	13	11	6	11	0	1	1	1	1	0	0	3	2	2	2	2	1	3	1	2	1	5	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:12541862T>C	ENST00000301547.5	-	4	1321	c.1124A>G	c.(1123-1125)gAt>gGt	p.D375G	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	375					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						ACTAGGACAATCAAAGCCTTT	0.423																																					p.D375G													.	ZNF443-91	0			c.A1124G						.						191	179	183					19																	12541862		2203	4298	6501	SO:0001583	missense	10224	exon4			GGACAATCAAAGC	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1124A>G	19.37:g.12541862T>C	ENSP00000301547:p.Asp375Gly	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	127	39	NM_005815	0	0	3	5	2		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	T	9.235	1.036915	0.19669	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07800	3.16	1.37	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06826	0.0174	N	0.04043	-0.29	0.09310	N	1	D	0.56035	0.974	P	0.62885	0.908	T	0.26573	-1.0099	9	0.30854	T	0.27	.	3.7751	0.08657	0.0:0.3:0.4706:0.2293	.	375	Q9Y2A4	ZN443_HUMAN	G	375	ENSP00000301547:D375G	ENSP00000301547:D375G	D	-	2	0	ZNF443	12402862	0.000000	0.05858	0.002000	0.10522	0.169000	0.22640	-4.305000	0.00256	-0.500000	0.06614	0.378000	0.23410	GAT	.		0.423	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		C	12541862	T	C	12541862	3	2	57	1	0	0	0	0	1	0	0	0	17948	1435	50	3	895	3	ZNF443	19	12541862	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	9045117	12541862	46587121	79	5553											
ZSWIM4	65249	broad.mit.edu	37	chr19	13928686	13928686	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggggctgtacgcccaggacaAggtggtgcgcaacgaggagc	9	4	18	10	3	0	0	0	0	0	0	0	3	0	2	1	6	4	3	1	6	3	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:13928686A>T	ENST00000254323.2	+	8	1658	c.1469A>T	c.(1468-1470)aAg>aTg	p.K490M	RN7SL619P_ENST00000581753.1_RNA|ZSWIM4_ENST00000440752.2_Missense_Mutation_p.K324M	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	490							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GCCCAGGACAAGGTGGTGCGC	0.701																																					p.K490M													.	ZSWIM4-90	0			c.A1469T						.						48	25	33					19																	13928686		2137	4198	6335	SO:0001583	missense	65249	exon8			AGGACAAGGTGGT	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1469A>T	19.37:g.13928686A>T	ENSP00000254323:p.Lys490Met	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	130	5	NM_023072	0	0	21	21	0		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.789084	0.90367	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.54279	0.59;0.58	4.51	4.51	0.55191	.	0.192153	0.33772	N	0.004568	T	0.68632	0.3022	M	0.67397	2.05	0.43824	D	0.996399	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	T	0.71889	-0.4456	10	0.72032	D	0.01	-31.4044	11.7679	0.51941	1.0:0.0:0.0:0.0	.	324;490	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	M	490;324	ENSP00000254323:K490M;ENSP00000405278:K324M	ENSP00000254323:K490M	K	+	2	0	ZSWIM4	13789686	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.944000	0.75940	1.669000	0.50854	0.379000	0.24179	AAG	.		0.701	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		T	13928686	A	T	13928686	3	4	57	1	0	0	0	0	1	0	0	0	18275	72	3	5	1499	5	ZSWIM4	19	13928686	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	1386824	13928686	45200297	80	5554											
PODNL1	79883	hgsc.bcm.edu	37	chr19	14044012	14044012	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctggaggcacgcggtccaGcccattgccatagaggtgca	8	6	15	12	2	0	1	0	0	0	1	1	2	1	2	3	5	3	3	3	5	1	2	rs79400921	byFrequency	TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:14044012G>A	ENST00000339560.5	-	8	1318	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	PODNL1_ENST00000254320.3_Silent_p.L267L|PODNL1_ENST00000538371.2_Silent_p.L347L|PODNL1_ENST00000538517.2_Silent_p.L258L	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	349	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			ACGCGGTCCAGCCCATTGCCA	0.726													G|||	17	0.00339457	0.0129	0	5008	,	,		12628	0		0	False		,,,				2504	0				p.L349L		.											.	PODNL1-90	0			c.C1045T						.	G	,,	25,3857		0,25,1916	4	6	6		1039,772,1045	2.1	0.7	19	dbSNP_131	6	1,7563		0,1,3781	no	coding-synonymous,coding-synonymous,coding-synonymous	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	,,	0,26,5697	AA,AG,GG		0.0132,0.644,0.2272	,,	347/511,258/422,349/513	14044012	26,11420	1941	3782	5723	SO:0001819	synonymous_variant	79883	exon8			GGTCCAGCCCATT	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1045C>T	19.37:g.14044012G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	24	9	NM_024825	0	0	0	0	0	B7Z564|Q9H5G9	Silent	SNP	ENST00000339560.5	37	CCDS12300.1																																																																																			.		0.726	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		A	14044012	G	A	14044012	2	1	57	1	0	0	0	0	0	0	0	1	12205	962	34	2		2	PODNL1	19	14044012	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	115326	14044012	45084971	81	5555											
CYP4F3	4051	ucsc.edu;bcgsc.ca	37	chr19	15760902	15760902	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtcatccaggagcggcgccGcaccctccctagccagggtg	6	5	13	17	4	1	0	1	0	0	0	3	1	3	1	5	3	2	1	5	3	1	1	rs113330239		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:15760902G>A	ENST00000221307.8	+	7	874	c.827G>A	c.(826-828)cGc>cAc	p.R276H	CYP4F3_ENST00000585846.1_Missense_Mutation_p.R276H|CYP4F3_ENST00000591058.1_Missense_Mutation_p.R276H|CYP4F3_ENST00000586182.2_Missense_Mutation_p.R276H	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	276					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)	p.R276H(1)		endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						GAGCGGCGCCGCACCCTCCCT	0.577													.|||	1	0.000199681	8e-04	0	5008	,	,		18604	0		0	False		,,,				2504	0				p.R276H													.	CYP4F3-93	1	Substitution - Missense(1)	large_intestine(1)	c.G827A						.						106	96	99					19																	15760902		2203	4300	6503	SO:0001583	missense	4051	exon7			GGCGCCGCACCCT	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"Cytochrome P450s"	2646	protein-coding gene	gene with protein product		601270	"cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.827G>A	19.37:g.15760902G>A	ENSP00000221307:p.Arg276His	Somatic	254	2		WXS	Illumina HiSeq		202	91	NM_001199209	0	0	0	0	0	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	37	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	14.12	2.441442	0.43326	.	.	ENSG00000186529	ENST00000538865;ENST00000221307	T	0.69561	-0.41	3.99	-0.166	0.13351	.	0.712480	0.12645	U	0.450940	T	0.63117	0.2484	M	0.77406	2.37	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.19148	0.015;0.024	T	0.58188	-0.7680	10	0.52906	T	0.07	.	7.3165	0.26503	0.4513:0.0:0.5487:0.0	.	276;276	B7Z8Z3;Q08477	.;CP4F3_HUMAN	H	203;276	ENSP00000221307:R276H	ENSP00000221307:R276H	R	+	2	0	CYP4F3	15621902	0.000000	0.05858	0.009000	0.14445	0.817000	0.46193	-1.012000	0.03649	0.173000	0.19788	0.313000	0.20887	CGC	G|0.500;A|0.500		0.577	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		A	15760902	G	A	15760902	3	1	57	1	0	0	0	0	1	0	0	0	4196	1087	38	1	849	1	CYP4F3	19	15760902	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	1716890	15760902	43368081	82	5556											
CPAMD8	27151	broad.mit.edu	37	chr19	17086849	17086849	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaacccagacctgagcaggTagacactcttatcaactgcg	12	7	10	12	1	2	3	1	1	1	2	2	4	2	4	2	2	4	2	2	2	4	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:17086849T>C	ENST00000443236.1	-	16	2043	c.2012A>G	c.(2011-2013)tAc>tGc	p.Y671C	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	624	Poly-Arg.	Cleavage; by furin-like protease. {ECO:0000305}.				extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCTGAGCAGGTAGACACTCTT	0.597																																					p.Y671C													.	CPAMD8-141	0			c.A2012G						.						40	47	45					19																	17086849		2155	4268	6423	SO:0001583	missense	27151	exon16			AGCAGGTAGACAC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2012A>G	19.37:g.17086849T>C	ENSP00000402505:p.Tyr671Cys	Somatic	174	2		WXS	Illumina HiSeq	Phase_I	154	3	NM_015692	0	0	0	0	0	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.08|16.08	3.020616|3.020616	0.54576|0.54576	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	2.74|2.74	2.74|2.74	0.32292|0.32292	.|Alpha-2-macroglobulin, N-terminal 2 (1);	.|0.000000	.|0.64402	.|D	.|0.000011	T|T	0.77505|0.77505	0.4140|0.4140	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.79108	.|0.992	T|T	0.78645|0.78645	-0.2123|-0.2123	5|9	.|0.51188	.|T	.|0.08	.|.	11.0186|11.0186	0.47705|0.47705	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|624	.|Q8IZJ3	.|CPMD8_HUMAN	A|C	682|671	.|.	.|ENSP00000291440:Y671C	T|Y	-|-	1|2	0|0	CPAMD8|CPAMD8	16947849|16947849	1.000000|1.000000	0.71417|0.71417	0.834000|0.834000	0.33040|0.33040	0.815000|0.815000	0.46073|0.46073	3.865000|3.865000	0.56033|0.56033	1.047000|1.047000	0.40274|0.40274	0.454000|0.454000	0.30748|0.30748	ACC|TAC	.		0.597	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		C	17086849	T	C	17086849	3	2	57	1	0	0	0	0	1	0	0	0	3801	1638	57	3	3894	3	CPAMD8	19	17086849	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	1325947	17086849	42042134	83	5557											
LRRC25	126364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18507658	18507658	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaattcaggcacgtggcaCtgaactccgcgttccagtcc	9	9	10	13	3	1	2	1	2	0	0	4	2	4	2	3	2	1	3	3	2	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:18507658C>G	ENST00000339007.3	-	1	769	c.116G>C	c.(115-117)aGt>aCt	p.S39T	LRRC25_ENST00000595840.1_Missense_Mutation_p.S39T	NM_145256.2	NP_660299.2	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|skin(1)	8						GCACGTGGCACTGAACTCCGC	0.622																																					p.S39T		.											.	LRRC25-90	0			c.G116C						.						76	57	64					19																	18507658		2203	4300	6503	SO:0001583	missense	126364	exon1			GTGGCACTGAACT	AK095435	CCDS12377.1	19p13.11	2013-09-20			ENSG00000175489	ENSG00000175489			29806	protein-coding gene	gene with protein product		607518				12384430	Standard	NM_145256		Approved	MAPA, FLJ38116	uc002niw.3	Q8N386	OTTHUMG00000183361	ENST00000339007.3:c.116G>C	19.37:g.18507658C>G	ENSP00000340983:p.Ser39Thr	Somatic	256	1		WXS	Illumina HiSeq	Phase_I	195	85	NM_145256	0	0	4	4	0	Q6IQ00|Q8N9A5	Missense_Mutation	SNP	ENST00000339007.3	37	CCDS12377.1	.	.	.	.	.	.	.	.	.	.	C	0.518	-0.863567	0.02590	.	.	ENSG00000175489	ENST00000339007	T	0.31510	1.49	4.4	-4.55	0.03441	.	2.202890	0.02302	N	0.071289	T	0.10680	0.0261	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20739	-1.0266	10	0.02654	T	1	2.5899	1.3392	0.02151	0.2155:0.2315:0.3888:0.1642	.	39	Q8N386	LRC25_HUMAN	T	39	ENSP00000340983:S39T	ENSP00000340983:S39T	S	-	2	0	LRRC25	18368658	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.684000	0.05173	-0.454000	0.07066	-0.367000	0.07326	AGT	.		0.622	LRRC25-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466342.1	NM_145256		G	18507658	C	G	18507658	3	3	57	1	0	0	0	0	1	0	0	0	9005	565	20	4	809	4	LRRC25	19	18507658	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	1420809	18507658	40621325	84	5558											
ZNF14	7561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19822257	19822257	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcattcataaggtttctcTccagtgtgagacctttcatg	8	16	8	9	0	3	1	2	1	1	1	5	2	4	1	2	1	1	2	2	1	1	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:19822257T>G	ENST00000344099.3	-	4	1971	c.1833A>C	c.(1831-1833)ggA>ggC	p.G611G		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	611					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)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				AAGGTTTCTCTCCAGTGTGAG	0.408																																					p.G611G		.											.	ZNF14-517	0			c.A1833C						.						83	81	82					19																	19822257		2203	4300	6503	SO:0001819	synonymous_variant	7561	exon4			TTTCTCTCCAGTG	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.1833A>C	19.37:g.19822257T>G		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	84	38	NM_021030	0	0	7	13	6	B9EGA4|Q9ULZ5	Silent	SNP	ENST00000344099.3	37	CCDS12409.1																																																																																			.		0.408	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		G	19822257	T	G	19822257	2	3	57	1	0	0	0	0	0	0	0	1	17760	1538	54	5		5	ZNF14	19	19822257	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	1314599	19822257	39306726	85	5559											
LIN37	126393	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	36243734	36243734	+	IGR	DEL	G	G	-																															catcgcagccactggcaaaaGgtaaggtggcagggtcccag																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:36243734delG	ENST00000592984.1	-	0	1634				LIN37_ENST00000301159.9_Splice_Site_p.R64fs|AC002398.9_ENST00000591613.2_3'UTR|AC002398.12_ENST00000587767.1_RNA|AC002398.11_ENST00000591091.1_RNA			O14558	HSPB6_HUMAN	heat shock protein, alpha-crystallin-related, B6						regulation of muscle contraction (GO:0006937)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			lung(1)	1	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACTGGCAAAAGGTAAGGTGGC	0.627																																					p.R64fs		.											.	.	0			c.191delG						.						27	33	31					19																	36243734		2060	4204	6264	SO:0001628	intergenic_variant	55957	exon4			.	AJ278121	CCDS12475.1	19q13.13	2014-06-12			ENSG00000004776	ENSG00000004776		"Heat shock proteins / HSPB"	26511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 91"	610695				12820654, 14717697	Standard	NM_144617		Approved	FLJ32389, Hsp20, PPP1R91	uc002obn.2	O14558	OTTHUMG00000048122		19.37:g.36243734delG		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	73	28	NM_019104	0	0	0	0	0	O14551|Q6NVI3|Q96MG9	Frame_Shift_Del	DEL	ENST00000592984.1	37	CCDS12475.1																																																																																			.		0.627	HSPB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109498.3	NM_144617		-	36243734	G	-	36243734	6	5	57	0	1	1	0	1	0	0	0	0	8830	1014	35	0		0	LIN37	19	36243734	IGR	DEL	G	TCGA-B9-A5W9-01A-11D-A28G-10	16421477	36243734	22885249	86	5560											
ZNF180	7733	bcgsc.ca	37	chr19	44981544	44981544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgaaggattttccacatTcactacattcataaggtttc	11	14	7	9	0	2	1	2	1	0	0	4	2	3	2	1	3	1	2	1	3	3	7			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:44981544T>C	ENST00000221327.4	-	5	1435	c.1154A>G	c.(1153-1155)gAa>gGa	p.E385G	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.E360G|ZNF180_ENST00000592529.1_Missense_Mutation_p.E358G	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TTTTCCACATTCACTACATTC	0.448																																					p.E385G	Esophageal Squamous(180;1353 2003 32862 46574 49854)												.	ZNF180-92	0			c.A1154G						.						71	72	71					19																	44981544		2203	4299	6502	SO:0001583	missense	7733	exon5			CCACATTCACTAC	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1154A>G	19.37:g.44981544T>C	ENSP00000221327:p.Glu385Gly	Somatic	62	0		WXS	Illumina HiSeq	Phase_1	51	4	NM_013256	0	0	6	6	0	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	3.784	-0.045104	0.07452	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07444	3.19;3.19	5.28	4.07	0.47477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.363008	0.19929	N	0.102906	T	0.09774	0.0240	L	0.46819	1.47	0.09310	N	0.999997	P;P;P	0.43412	0.768;0.806;0.806	B;B;B	0.41440	0.243;0.357;0.357	T	0.12016	-1.0564	10	0.87932	D	0	-5.0445	9.1013	0.36669	0.3914:0.0:0.0:0.6086	.	360;384;385	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	G	385;360	ENSP00000221327:E385G;ENSP00000375818:E360G	ENSP00000221327:E385G	E	-	2	0	ZNF180	49673384	0.000000	0.05858	0.231000	0.23993	0.114000	0.19823	0.269000	0.18589	0.526000	0.28541	0.533000	0.62120	GAA	.		0.448	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44981544	T	C	44981544	3	2	57	1	0	0	0	0	1	0	0	0	17780	1783	62	3	928	3	ZNF180	19	44981544	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	8737810	44981544	14147439	87	5561											
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175950	57175950	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctgggtcaggtgcgtgAcgcgcgtgaaggccttgccg	4	8	19	10	5	1	2	1	2	0	0	1	2	1	2	2	4	3	1	2	4	1	1	rs369897881		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:57175950A>G	ENST00000537055.2	-	2	848	c.617T>C	c.(616-618)gTc>gCc	p.V206A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	206					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CAGGTGCGTGACGCGCGTGAA	0.716																																					p.V206A		.											.	ZNF835-72	0			c.T617C						.	A	ALA/VAL	3,4319		0,3,2158	15	16	16		617	-3.4	0	19		16	0,8402		0,0,4201	no	missense	ZNF835	NM_001005850.2	64	0,3,6359	GG,GA,AA		0.0,0.0694,0.0236	benign	206/538	57175950	3,12721	2161	4201	6362	SO:0001583	missense	90485	exon2			TGCGTGACGCGCG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.617T>C	19.37:g.57175950A>G	ENSP00000444747:p.Val206Ala	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	46	19	NM_001005850	0	0	0	0	0	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	A	7.598	0.672178	0.14776	6.94E-4	0.0	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.07114	3.22	2.12	-3.43	0.04810	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02807	0.0084	N	0.04245	-0.25	0.09310	N	1	B	0.11235	0.004	B	0.14578	0.011	T	0.45920	-0.9228	9	0.16896	T	0.51	.	4.1371	0.10176	0.246:0.0:0.5433:0.2107	.	228	Q9Y2P0	ZN835_HUMAN	A	228;206	ENSP00000444747:V206A	ENSP00000341756:V228A	V	-	2	0	ZNF835	61867762	0.000000	0.05858	0.000000	0.03702	0.296000	0.27459	-1.731000	0.01853	-0.977000	0.03537	-0.411000	0.06167	GTC	.		0.716	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		G	57175950	A	G	57175950	3	3	57	1	0	0	0	0	1	0	0	0	18218	275	10	3	998	3	ZNF835	19	57175950	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	12194406	57175950	1953033	88	5562											
C20orf186	149954	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31685559	31685559	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtcatggtctcccagcccaAagacctggagactaccatct	10	8	9	14	0	3	2	1	0	2	2	4	3	3	2	4	3	2	0	4	3	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr20:31685559A>T	ENST00000375483.3	+	11	1535	c.1535A>T	c.(1534-1536)aAa>aTa	p.K512I		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	512						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCCAGCCCAAAGACCTGGAG	0.577																																					p.K512I		.											.	.	0			c.A1535T						.						100	72	81					20																	31685559		2203	4300	6503	SO:0001583	missense	149954	exon11			AGCCCAAAGACCT	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"BPI fold containing"	16179	protein-coding gene	gene with protein product		615718	"chromosome 20 open reading frame 186"	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1535A>T	20.37:g.31685559A>T	ENSP00000364632:p.Lys512Ile	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	169	79	NM_182519	0	0	0	0	0	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582504	0.46006	.	.	ENSG00000186191	ENST00000375483	T	0.07327	3.2	5.26	5.26	0.73747	.	0.240028	0.35067	N	0.003468	T	0.07279	0.0184	N	0.24115	0.695	0.24134	N	0.995755	B	0.30937	0.301	B	0.31812	0.136	T	0.27773	-1.0064	10	0.62326	D	0.03	-11.2987	11.8323	0.52303	1.0:0.0:0.0:0.0	.	512	P59827	BPIB4_HUMAN	I	512	ENSP00000364632:K512I	ENSP00000364632:K512I	K	+	2	0	BPIFB4	31149220	0.981000	0.34729	0.940000	0.37924	0.577000	0.36160	2.261000	0.43276	2.108000	0.64289	0.379000	0.24179	AAA	.		0.577	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31685559	A	T	31685559	3	4	57	1	0	0	0	0	1	0	0	0	2104	14	1	5	1577	5	C20orf186	20	31685559	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		31685559	31339961	89	5563											
COL18A1	80781	broad.mit.edu	37	chr21	46911183	46911183	+	Frame_Shift_Del	DEL	C	C	-																															gggcagccgggcctccctggCccccccggacccccgggacc																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr21:46911183delC	ENST00000359759.4	+	21	3378	c.3357delC	c.(3355-3357)ggcfs	p.G1119fs	COL18A1_ENST00000400337.2_Frame_Shift_Del_p.G704fs|COL18A1_ENST00000355480.5_Frame_Shift_Del_p.G884fs			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1119	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GCCTCCCTGGCCCCCCCGGAC	0.692																																					p.G884fs													.	COL18A1-90	0			c.2652delC						.						19	26	24					21																	46911183		1917	4091	6008	SO:0001589	frameshift_variant	80781	exon21			CCCTGGCCCCCCC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3357delC	21.37:g.46911183delC	ENSP00000352798:p.Gly1119fs	Somatic	260	0		WXS	Illumina HiSeq	Phase_I	451	7	NM_030582	0	0	0	0	0	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Frame_Shift_Del	DEL	ENST00000359759.4	37																																																																																				.		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			-	46911183	C	-	46911183	7	5	57	1	0	1	0	1	0	0	0	0	3681	726	26	0	3553	0	COL18A1	21	46911183	Frame_Shift_Del	DEL	C	TCGA-B9-A5W9-01A-11D-A28G-10		46911183	1218712	90	5564											
KIAA1210	57481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	118219440	118219440	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggccttgaaactcttctgcTtctgctttgccatagttatc	6	16	8	11	0	3	1	0	1	3	0	4	1	3	1	2	1	4	3	2	1	3	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chrX:118219440T>G	ENST00000402510.2	-	12	4753	c.4754A>C	c.(4753-4755)aAg>aCg	p.K1585T		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1585										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						ACTCTTCTGCTTCTGCTTTGC	0.448																																					p.K1585T		.											.	KIAA1210-67	0			c.A4754C						.						108	96	99					X																	118219440		1887	4103	5990	SO:0001583	missense	57481	exon12			TTCTGCTTCTGCT	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.4754A>C	X.37:g.118219440T>G	ENSP00000384670:p.Lys1585Thr	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	46	6	NM_020721	0	0	0	0	0	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.05|11.05	1.525709|1.525709	0.27299|0.27299	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.22743	.|1.94	5.16|5.16	-4.73|-4.73	0.03259|0.03259	.|.	.|.	.|.	.|.	.|.	T|T	0.32912|0.32912	0.0845|0.0845	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	.|D	.|0.62365	.|0.991	.|P	.|0.61070	.|0.883	T|T	0.21930|0.21930	-1.0231|-1.0231	5|9	.|0.35671	.|T	.|0.21	.|.	12.3761|12.3761	0.55281|0.55281	0.0:0.2909:0.0:0.7091|0.0:0.2909:0.0:0.7091	.|.	.|1585	.|Q9ULL0	.|K1210_HUMAN	D|T	991|1585	.|ENSP00000384670:K1585T	.|ENSP00000384670:K1585T	E|K	-|-	3|2	2|0	KIAA1210|RP13-347D8.6	118103468|118103468	0.049000|0.049000	0.20398|0.20398	0.001000|0.001000	0.08648|0.08648	0.044000|0.044000	0.14063|0.14063	-0.389000|-0.389000	0.07342|0.07342	-1.098000|-1.098000	0.03038|0.03038	0.486000|0.486000	0.48141|0.48141	GAA|AAG	.		0.448	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		G	118219440	T	G	118219440	3	3	57	1	0	0	0	0	1	0	0	0	8235	1609	56	5	387	5	KIAA1210	23	118219440	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		118219440	37051120	91	5565											
ALPL	249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	21889674	21889674	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctgtgtggggtgaaggcCaatgagggcaccgtgggggt	7	8	19	7	1	0	2	0	2	0	0	0	2	0	2	3	6	1	1	3	6	3	1	rs201342272		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:21889674C>A	ENST00000374840.3	+	5	619	c.369C>A	c.(367-369)gcC>gcA	p.A123A	ALPL_ENST00000540617.1_Silent_p.A68A|ALPL_ENST00000374832.1_Silent_p.A123A|ALPL_ENST00000425315.2_Silent_p.A123A|ALPL_ENST00000468526.1_3'UTR|ALPL_ENST00000539907.1_Silent_p.A46A	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	123					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	GGGTGAAGGCCAATGAGGGCA	0.652													C|||	1	0.000199681	0	0	5008	,	,		17698	0		0	False		,,,				2504	0.001				p.A123A		.											.	ALPL-94	0			c.C369A						.						84	75	78					1																	21889674		2203	4300	6503	SO:0001819	synonymous_variant	249	exon5			GAAGGCCAATGAG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.369C>A	1.37:g.21889674C>A		Somatic	263	0		WXS	Illumina HiSeq	Phase_I	179	71	NM_000478	0	0	2	48	46	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	37	CCDS217.1																																																																																			C|0.999;A|0.001		0.652	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		A	21889674	C	A	21889674	2	1	58	1	0	0	0	0	0	0	0	1	547	581	21	4		4	ALPL	1	21889674	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		21889674	227360947	1	5566											
FAM46B	115572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27333078	27333078	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggagtctatgctgaattcaAactggcgtctcaccgagtcc	10	10	10	11	2	3	1	2	1	2	0	5	3	4	2	2	2	2	1	2	2	3	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:27333078A>T	ENST00000289166.5	-	2	800	c.635T>A	c.(634-636)tTt>tAt	p.F212Y		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	212										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GCTGAATTCAAACTGGCGTCT	0.552																																					p.F212Y		.											.	FAM46B-90	0			c.T635A						.						108	110	110					1																	27333078		2203	4300	6503	SO:0001583	missense	115572	exon2			AATTCAAACTGGC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.635T>A	1.37:g.27333078A>T	ENSP00000289166:p.Phe212Tyr	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_052943	0	0	1	6	5		Missense_Mutation	SNP	ENST00000289166.5	37	CCDS294.2	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507004	0.85282	.	.	ENSG00000158246	ENST00000289166	T	0.28454	1.61	5.2	5.2	0.72013	Domain of unknown function DUF1693 (1);	0.045170	0.85682	D	0.000000	T	0.57066	0.2028	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.61133	-0.7124	10	0.56958	D	0.05	-1.9476	15.2153	0.73261	1.0:0.0:0.0:0.0	.	212	Q96A09	FA46B_HUMAN	Y	212	ENSP00000289166:F212Y	ENSP00000289166:F212Y	F	-	2	0	FAM46B	27205665	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	9.135000	0.94478	2.178000	0.69098	0.459000	0.35465	TTT	.		0.552	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		T	27333078	A	T	27333078	3	4	58	1	0	0	0	0	1	0	0	0	5585	14	1	5	646	5	FAM46B	1	27333078	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	5443404	27333078	221917543	2	5567											
C1orf94	84970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	34643683	34643683	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccctgtggttggaactctaaGaggcaatgagctcagctttc	9	11	11	10	0	2	2	1	1	1	1	3	3	2	3	1	3	3	4	1	3	3	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:34643683G>C	ENST00000488417.1	+	1	413	c.293G>C	c.(292-294)aGa>aCa	p.R98T	AC115286.1_ENST00000408126.1_RNA|C1orf94_ENST00000373374.3_Intron	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	98										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				GGAACTCTAAGAGGCAATGAG	0.537																																					p.R98T		.											.	C1orf94-90	0			c.G293C						.						73	69	70					1																	34643683		692	1591	2283	SO:0001583	missense	84970	exon1			CTCTAAGAGGCAA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.293G>C	1.37:g.34643683G>C	ENSP00000435634:p.Arg98Thr	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	77	24	NM_001134734	0	0	0	0	0	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	0.083	-1.180380	0.01633	.	.	ENSG00000142698	ENST00000488417	T	0.44881	0.91	4.99	2.08	0.27032	.	.	.	.	.	T	0.26666	0.0652	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.23261	-1.0193	9	0.66056	D	0.02	.	5.0027	0.14273	0.1877:0.173:0.6393:0.0	.	98	Q6P1W5	CA094_HUMAN	T	98	ENSP00000435634:R98T	ENSP00000435634:R98T	R	+	2	0	C1orf94	34416270	0.867000	0.29959	0.005000	0.12908	0.004000	0.04260	1.134000	0.31442	0.277000	0.22141	0.655000	0.94253	AGA	.		0.537	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		C	34643683	G	C	34643683	3	2	58	1	0	0	0	0	1	0	0	0	2077	942	33	4	295	4	C1orf94	1	34643683	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	7310605	34643683	214606938	3	5568											
ZCCHC11	23318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52897102	52897102	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagttctgtggaaatggctGaggctgaggagaataagatg	13	9	16	3	0	1	5	0	2	1	3	1	7	1	6	0	4	0	3	0	4	3	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:52897102G>T	ENST00000371544.3	-	28	4553	c.4291C>A	c.(4291-4293)Cag>Aag	p.Q1431K	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.Q1432K	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1431	Gln-rich.|Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GGAAATGGCTGAGGCTGAGGA	0.393																																					p.Q1432K		.											.	ZCCHC11-93	0			c.C4294A						.						32	29	30					1																	52897102		2203	4298	6501	SO:0001583	missense	23318	exon28			ATGGCTGAGGCTG	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4291C>A	1.37:g.52897102G>T	ENSP00000360599:p.Gln1431Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	60	19	NM_001009881	0	0	3	15	12	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.48|15.48	2.847224|2.847224	0.51164|0.51164	.|.	.|.	ENSG00000134744|ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000531722|ENST00000474453	T;T|.	0.46451|.	0.87;0.88|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.248184|.	0.35466|.	N|.	0.003196|.	T|.	0.55433|.	0.1920|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	P|.	0.40144|.	0.704|.	B|.	0.32022|.	0.139|.	T|.	0.50668|.	-0.8801|.	10|.	0.40728|.	T|.	0.16|.	.|.	18.8838|18.8838	0.92367|0.92367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1431|.	Q5TAX3|.	TUT4_HUMAN|.	K|X	1432;1431;269|276	ENSP00000257177:Q1432K;ENSP00000360599:Q1431K|.	ENSP00000257177:Q1432K|.	Q|S	-|-	1|2	0|0	ZCCHC11|ZCCHC11	52669690|52669690	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.423000|5.423000	0.66458|0.66458	2.459000|2.459000	0.83118|0.83118	0.557000|0.557000	0.71058|0.71058	CAG|TCA	.		0.393	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		T	52897102	G	T	52897102	3	4	58	1	0	0	0	0	1	0	0	0	17612	1299	45	4	655	4	ZCCHC11	1	52897102	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	18253419	52897102	196353519	4	5569											
HS2ST1	9653	broad.mit.edu	37	chr1	87570377	87570377	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatttaccctaagtcgaacTgagtataaggtgtgactatt	13	13	9	6	1	0	3	0	2	0	1	1	4	0	3	1	1	2	1	1	1	6	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:87570377T>C	ENST00000370550.5	+	7	1432	c.1069T>C	c.(1069-1071)Tga>Cga	p.*357R	RP5-1052I5.2_ENST00000370548.2_Intron|HS2ST1_ENST00000356813.4_Intron	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	0					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		TAAGTCGAACTGAGTATAAGG	0.413																																					p.X357R													.	HS2ST1-90	0			c.T1069C						.						29	31	30					1																	87570377		2203	4296	6499	SO:0001578	stop_lost	9653	exon7			TCGAACTGAGTAT	AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"Sulfotransferases, membrane-bound"	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.1069T>C	1.37:g.87570377T>C	ENSP00000359581:p.*357Argext*2	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	41	13	NM_012262	0	0	2	3	1	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Missense_Mutation	SNP	ENST00000370550.5	37	CCDS711.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.450662	0.43531	.	.	ENSG00000153936	ENST00000370550	.	.	.	5.83	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2373	0.54522	0.1275:0.0:0.0:0.8724	.	.	.	.	R	357	.	.	X	+	1	0	HS2ST1	87342965	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.841000	0.86834	0.986000	0.38683	0.528000	0.53228	TGA	.		0.413	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262		C	87570377	T	C	87570377	4	2	58	1	0	0	0	0	0	0	0	0	7383	1593	55	3	1099	3	HS2ST1	1	87570377	Nonstop_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	34673275	87570377	161680244	5	5570											
RUSC1	23623	broad.mit.edu	37	chr1	155292770	155292770	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtcccgccccggcccccAcccccgcctgtccctccccg	1	6	8	26	4	0	0	0	0	0	0	3	0	3	0	11	2	0	0	11	2	0	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:155292770A>C	ENST00000368352.5	+	2	1357	c.1206A>C	c.(1204-1206)ccA>ccC	p.P402P	RUSC1_ENST00000292254.4_5'Flank|RUSC1_ENST00000368349.4_5'Flank|RUSC1_ENST00000368354.3_Silent_p.P402P|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000543656.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	402					positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			CCCGGCCCCCACCCCCGCCTG	0.726																																					p.P402P													.	RUSC1-92	0			c.A1206C						.																																			SO:0001819	synonymous_variant	23623	exon2			GCCCCCACCCCCG	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.1206A>C	1.37:g.155292770A>C		Somatic	17	4		WXS	Illumina HiSeq	Phase_I	24	8	NM_001105203	0	0	0	0	0	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																			.		0.726	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1			C	155292770	A	C	155292770	2	2	58	1	0	0	0	0	0	0	0	1	13782	146	6	5		5	RUSC1	1	155292770	Silent	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	67722393	155292770	93957851	6	5571											
SPTA1	6708	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	158639217	158639217	+	Frame_Shift_Del	DEL	G	G	-																															ccttgtaatcttcatcatctGccaactttttcttcttgttg																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:158639217delG	ENST00000368147.4	-	14	1994	c.1814delC	c.(1813-1815)gcafs	p.A605fs		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	605					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCATCATCTGCCAACTTTTT	0.408																																					p.A605fs		.											.	SPTA1-142	0			c.1814delC						.						285	268	273					1																	158639217		1915	4136	6051	SO:0001589	frameshift_variant	6708	exon14			.	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1814delC	1.37:g.158639217delG	ENSP00000357129:p.Ala605fs	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	73	19	NM_003126	0	0	0	0	0	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Frame_Shift_Del	DEL	ENST00000368147.4	37	CCDS41423.1																																																																																			.		0.408	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		-	158639217	G	-	158639217	7	5	58	1	0	1	0	1	0	0	0	0	15148	1319	46	0	5601	0	SPTA1	1	158639217	Frame_Shift_Del	DEL	G	TCGA-B9-A69E-01A-11D-A31X-10	3346447	158639217	90611404	7	5572											
RABIF	5877	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	202850297	202850297	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcctggaggagatcgccgtCaggattgctgccgtcagaca	8	9	13	11	3	2	2	2	0	0	2	4	5	3	4	3	3	2	1	3	3	0	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:202850297C>T	ENST00000367262.3	-	2	217	c.181G>A	c.(181-183)Gac>Aac	p.D61N		NM_002871.4	NP_002862.2	P47224	MSS4_HUMAN	RAB interacting factor	61					membrane fusion (GO:0061025)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(75;0.166)			AGATCGCCGTCAGGATTGCTG	0.507																																					p.D61N		.											.	RABIF-227	0			c.G181A						.						68	64	65					1																	202850297		2203	4300	6503	SO:0001583	missense	5877	exon2			CGCCGTCAGGATT	S78873	CCDS1428.1	1q32.1	2008-05-14			ENSG00000183155	ENSG00000183155			9797	protein-coding gene	gene with protein product		603417		RASGRF3		9441742, 7619808	Standard	NM_002871		Approved	mss4	uc001gyl.3	P47224	OTTHUMG00000041400	ENST00000367262.3:c.181G>A	1.37:g.202850297C>T	ENSP00000356231:p.Asp61Asn	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	48	18	NM_002871	0	0	10	14	4	B2R4P4|Q92992	Missense_Mutation	SNP	ENST00000367262.3	37	CCDS1428.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382058	0.24944	.	.	ENSG00000183155	ENST00000367262	.	.	.	5.75	4.84	0.62591	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.332353	0.37136	N	0.002226	T	0.55955	0.1953	L	0.40543	1.245	0.80722	D	1	B	0.25809	0.135	B	0.29176	0.099	T	0.55528	-0.8127	9	0.51188	T	0.08	-57.0511	14.6684	0.68926	0.0:0.9296:0.0:0.0704	.	61	P47224	MSS4_HUMAN	N	61	.	ENSP00000356231:D61N	D	-	1	0	RABIF	201116920	1.000000	0.71417	0.009000	0.14445	0.008000	0.06430	5.492000	0.66893	1.447000	0.47661	-0.254000	0.11334	GAC	.		0.507	RABIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099183.1			T	202850297	C	T	202850297	3	4	58	1	0	0	0	0	1	0	0	0	13001	826	29	2	194	2	RABIF	1	202850297	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	44211080	202850297	46400324	8	5573											
CENPF	1063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214826247	214826247	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagttcacagaagctggagaTagaccttttaaagtctagta	14	11	9	7	0	2	3	1	0	1	3	2	4	2	3	1	1	1	3	1	1	6	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:214826247T>C	ENST00000366955.3	+	16	8405	c.8237T>C	c.(8236-8238)aTa>aCa	p.I2746T	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2842	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGCTGGAGATAGACCTTTTA	0.328																																					p.I2746T	Colon(80;575 1284 11000 14801 43496)	.											.	CENPF-567	0			c.T8237C						.						91	94	93					1																	214826247		2203	4300	6503	SO:0001583	missense	1063	exon16			TGGAGATAGACCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8237T>C	1.37:g.214826247T>C	ENSP00000355922:p.Ile2746Thr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	120	25	NM_016343	0	0	2	2	0	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.757432	0.31137	.	.	ENSG00000117724	ENST00000366955;ENST00000391896	T	0.04234	3.67	3.93	3.93	0.45458	.	.	.	.	.	T	0.05410	0.0143	L	0.47716	1.5	0.20489	N	0.999898	B	0.33694	0.421	B	0.22152	0.038	T	0.28106	-1.0054	9	0.42905	T	0.14	.	11.9872	0.53155	0.0:0.0:0.0:1.0	.	2842	P49454	CENPF_HUMAN	T	2746;145	ENSP00000355922:I2746T	ENSP00000355922:I2746T	I	+	2	0	CENPF	212892870	0.990000	0.36364	0.042000	0.18584	0.923000	0.55619	3.757000	0.55212	1.429000	0.47314	0.418000	0.28097	ATA	.		0.328	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214826247	T	C	214826247	3	2	58	1	0	0	0	0	1	0	0	0	3237	1406	49	3	8295	3	CENPF	1	214826247	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	11975950	214826247	34424374	9	5574											
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228511117	228511117	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgacaggtcagcccatGcccagtgtgcgctggttcaa	7	9	14	11	1	2	1	2	1	0	0	2	1	2	1	2	3	3	2	2	3	1	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:228511117G>A	ENST00000422127.1	+	56	15506	c.15462G>A	c.(15460-15462)atG>atA	p.M5154I	OBSCN_ENST00000366709.4_Missense_Mutation_p.M2273I|OBSCN_ENST00000366707.4_Missense_Mutation_p.M2788I|OBSCN_ENST00000284548.11_Missense_Mutation_p.M5154I|OBSCN_ENST00000570156.2_Missense_Mutation_p.M6111I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5154	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTCAGCCCATGCCCAGTGTGC	0.522																																					p.M6111I		.											.	OBSCN-403	0			c.G18333A						.						92	94	93					1																	228511117		2155	4253	6408	SO:0001583	missense	84033	exon67			GCCCATGCCCAGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15462G>A	1.37:g.228511117G>A	ENSP00000409493:p.Met5154Ile	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	102	23	NM_001271223	0	0	1	1	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431705	0.25813	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.660669	0.14435	N	0.319744	T	0.46034	0.1372	N	0.04959	-0.14	0.27969	N	0.936468	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13629	-1.0502	10	0.16896	T	0.51	.	15.681	0.77367	0.0:0.2016:0.7984:0.0	.	5154;5154	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	5154;5154;2788;2273	ENSP00000284548:M5154I;ENSP00000409493:M5154I;ENSP00000355668:M2788I;ENSP00000355670:M2273I	ENSP00000284548:M5154I	M	+	3	0	OBSCN	226577740	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	1.113000	0.31184	2.629000	0.89072	0.655000	0.94253	ATG	.		0.522	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228511117	G	A	228511117	3	1	58	1	0	0	0	0	1	0	0	0	10838	1319	46	2	15680	2	OBSCN	1	228511117	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	13684870	228511117	20739504	10	5575											
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059782	248059782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcagaaacagagaggtgaaGggggcactgggaaggttgct	12	6	17	6	0	1	3	1	1	0	2	1	5	1	4	0	5	2	3	0	5	3	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:248059782G>A	ENST00000360358.3	+	1	894	c.894G>A	c.(892-894)aaG>aaA	p.K298K	OR2W3_ENST00000537741.1_Silent_p.K298K	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GAGAGGTGAAGGGGGCACTGG	0.537																																					p.K298K		.											.	OR2W3-115	0			c.G894A						.						39	40	40					1																	248059782		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			GGTGAAGGGGGCA	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"GPCR / Class A : Olfactory receptors"	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.894G>A	1.37:g.248059782G>A		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	80	5	NM_001001957	0	0	0	0	0	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	37	CCDS31099.1																																																																																			.		0.537	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		A	248059782	G	A	248059782	2	1	58	1	0	0	0	0	0	0	0	1	11059	991	35	2		2	OR2W3	1	248059782	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	19548665	248059782	1190839	11	5576											
LRPPRC	10128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44116985	44116986	+	Missense_Mutation	DNP	GC	GC	AG																															cagtcaaatgttcatacagtGctttagcagatgtgacatct																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:44116985_44116986GC>AG	ENST00000260665.7	-	37	4072_4073	c.4015_4016GC>CT	c.(4015-4017)GCa>CTa	p.A1339L	RNU6-1048P_ENST00000364054.1_RNA	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1339	RNA-binding.				mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TTCATACAGTGCTTTAGCAGAT	0.366																																					p.A1339L		.											.	LRPPRC-93	0			c.G4015C						.																																			SO:0001583	missense	10128	exon37			ACAGTGCTTTAGC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.4015_4016delinsAG	2.37:g.44116985_44116986delinsAG	ENSP00000260665:p.Ala1339Leu	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	217	48	NM_133259	0	0	0	0	0	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	DNP	ENST00000260665.7	37	CCDS33189.1																																																																																			.		0.366	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		AG	44116986	GC	AG	44116985	3	1	58	1	0	0	0	0	1	0	0	0	8990	1319	46	2	176	2	LRPPRC	2	44116985	Missense_Mutation	DNP	GC	TCGA-B9-A69E-01A-11D-A31X-10		44116985	199082388	12	5577											
CYP27C1	339761	ucsc.edu	37	chr2	127950814	127950814	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctcaggccggaactccttGgcccgagggaagttctcatc	7	8	12	14	3	2	0	2	0	1	0	5	3	3	2	3	4	1	2	3	4	2	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:127950814G>T	ENST00000335247.7	-	7	988	c.858C>A	c.(856-858)gcC>gcA	p.A286A	CYP27C1_ENST00000409327.1_Silent_p.A286A	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	286						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		GGAACTCCTTGGCCCGAGGGA	0.542																																					p.A286A													.	CYP27C1-90	0			c.C858A						.						96	91	93					2																	127950814		2203	4300	6503	SO:0001819	synonymous_variant	339761	exon7			CTCCTTGGCCCGA	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"Cytochrome P450s"	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.858C>A	2.37:g.127950814G>T		Somatic	137	4		WXS	Illumina HiSeq		124	34	NM_001001665	0	0	0	0	0	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			.		0.542	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665		T	127950814	G	T	127950814	2	4	58	1	0	0	0	0	0	0	0	1	4166	1335	47	4		4	CYP27C1	2	127950814	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	83833829	127950814	115248559	13	5578											
CHRNA1	1134	broad.mit.edu;ucsc.edu	37	chr2	175614800	175614800	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcatgtattttccaatcaaGggcacagcactggacgtgga	12	9	11	9	1	1	0	1	0	0	0	2	2	2	2	1	3	2	4	1	3	3	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:175614800G>A	ENST00000261007.5	-	8	1017	c.951C>T	c.(949-951)ccC>ccT	p.P317P	CHRNA1_ENST00000348749.5_Silent_p.P292P|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409219.1_Silent_p.P292P|CHRNA1_ENST00000409542.1_Silent_p.P210P	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	317					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TTCCAATCAAGGGCACAGCAC	0.517																																					p.P317P													.	CHRNA1-518	0			c.C951T						.						204	156	172					2																	175614800		2203	4300	6503	SO:0001819	synonymous_variant	1134	exon8			AATCAAGGGCACA	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.951C>T	2.37:g.175614800G>A		Somatic	87	2		WXS	Illumina HiSeq	Phase_I	132	22	NM_001039523	0	0	0	0	0	B4DRV6|D3DPE8	Silent	SNP	ENST00000261007.5	37	CCDS33331.1																																																																																			.		0.517	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			A	175614800	G	A	175614800	2	1	58	1	0	0	0	0	0	0	0	1	3387	987	35	2		2	CHRNA1	2	175614800	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	47663986	175614800	67584573	14	5579											
ROBO2	6092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	77671536	77671536	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcccctgagagcactggAccagactcctggatccagca	10	5	11	15	0	0	2	0	1	0	2	2	5	2	4	5	3	2	2	5	3	0	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:77671536A>T	ENST00000461745.1	+	23	4613	c.3713A>T	c.(3712-3714)gAc>gTc	p.D1238V	ROBO2_ENST00000332191.8_Missense_Mutation_p.D1238V|ROBO2_ENST00000487694.3_Missense_Mutation_p.D1254V	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1238					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		AGAGCACTGGACCAGACTCCT	0.463																																					p.D1238V		.											.	ROBO2-328	0			c.A3713T						.						74	77	76					3																	77671536		1902	4120	6022	SO:0001583	missense	6092	exon23			CACTGGACCAGAC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3713A>T	3.37:g.77671536A>T	ENSP00000417164:p.Asp1238Val	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_002942	0	0	0	0	0	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917020	0.52546	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	T;T;T	0.61510	0.1;0.14;0.12	5.56	5.56	0.83823	.	0.299670	0.23303	N	0.049659	T	0.43897	0.1268	N	0.08118	0	0.30052	N	0.811715	B;B;B	0.26512	0.151;0.096;0.151	B;B;B	0.34093	0.086;0.175;0.086	T	0.56667	-0.7941	9	0.56958	D	0.05	.	15.6959	0.77499	1.0:0.0:0.0:0.0	.	1254;1238;1238	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	V	1254;1254;1238;1238	ENSP00000417335:D1254V;ENSP00000417164:D1238V;ENSP00000327536:D1238V	ENSP00000327536:D1238V	D	+	2	0	ROBO2	77754226	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	8.962000	0.93254	2.110000	0.64415	0.528000	0.53228	GAC	.		0.463	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77671536	A	T	77671536	3	4	58	1	0	0	0	0	1	0	0	0	13546	275	10	5	3805	5	ROBO2	3	77671536	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		77671536	120350894	15	5580											
MRPL3	11222	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	131190046	131190046	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagctccaggtctcctgtggGttttcgtttgaccatgcgta	5	14	11	11	2	1	1	0	1	1	0	4	1	2	1	3	2	2	4	3	2	1	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:131190046G>T	ENST00000264995.3	-	7	854	c.707C>A	c.(706-708)aCc>aAc	p.T236N	MRPL3_ENST00000425847.2_Missense_Mutation_p.T263N	NM_007208.3	NP_009139.1	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	236					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						TCTCCTGTGGGTTTTCGTTTG	0.418																																					p.T236N													.	MRPL3-90	0			c.C707A						.						123	125	124					3																	131190046		2203	4300	6503	SO:0001583	missense	11222	exon7			CTGTGGGTTTTCG	X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686		"Mitochondrial ribosomal proteins / large subunits"	10379	protein-coding gene	gene with protein product		607118		RPML3		2891103	Standard	NM_007208		Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000264995.3:c.707C>A	3.37:g.131190046G>T	ENSP00000264995:p.Thr236Asn	Somatic	100	1		WXS	Illumina HiSeq	Phase_I	95	17	NM_007208	0	0	55	95	40	Q6IBT2	Missense_Mutation	SNP	ENST00000264995.3	37	CCDS3071.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.6|25.6	4.650246|4.650246	0.87958|0.87958	.|.	.|.	ENSG00000114686|ENSG00000114686	ENST00000511168|ENST00000264995;ENST00000425847;ENST00000507669	.|T;T;T	.|0.41758	.|0.99;0.99;0.99	5.56|5.56	5.56|5.56	0.83823|0.83823	.|Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61035|0.61035	0.2315|0.2315	L|L	0.49699|0.49699	1.58|1.58	0.80722|0.80722	D|D	1|1	.|D;D	.|0.65815	.|0.979;0.995	.|D;D	.|0.76575	.|0.976;0.988	T|T	0.61860|0.61860	-0.6976|-0.6976	5|10	.|0.72032	.|D	.|0.01	-16.478|-16.478	18.2922|18.2922	0.90134|0.90134	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|263;236	.|E7ETU7;P09001	.|.;RM03_HUMAN	K|N	250|236;263;131	.|ENSP00000264995:T236N;ENSP00000398536:T263N;ENSP00000422419:T131N	.|ENSP00000264995:T236N	N|T	-|-	3|2	2|0	MRPL3|MRPL3	132672736|132672736	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	8.563000|8.563000	0.90723|0.90723	2.614000|2.614000	0.88457|0.88457	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.		0.418	MRPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356471.3	NM_007208		T	131190046	G	T	131190046	3	4	58	1	0	0	0	0	1	0	0	0	9818	1261	44	4	355	4	MRPL3	3	131190046	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	53518510	131190046	66832384	16	5581											
AMOTL2	51421	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	134078995	134078995	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagtgagcagaccctcAttgaagctgctgctgggtga	9	8	12	12	0	1	4	1	3	0	1	1	4	1	4	3	1	4	4	3	1	1	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:134078995A>C	ENST00000422605.2	-	7	2002	c.1836T>G	c.(1834-1836)aaT>aaG	p.N612K	AMOTL2_ENST00000514516.1_Missense_Mutation_p.N670K|AMOTL2_ENST00000513145.1_Missense_Mutation_p.N610K|AMOTL2_ENST00000249883.5_Missense_Mutation_p.N612K			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	612					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						GCAGACCCTCATTGAAGCTGC	0.622																																					p.N612K		.											.	AMOTL2-135	0			c.T1836G						.						57	50	52					3																	134078995		2203	4300	6503	SO:0001583	missense	51421	exon7			ACCCTCATTGAAG	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"Leman coiled-coil protein", "angiomotin-like protein 2"	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1836T>G	3.37:g.134078995A>C	ENSP00000409999:p.Asn612Lys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_016201	0	0	28	50	22	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	37		.	.	.	.	.	.	.	.	.	.	A	16.66	3.183876	0.57800	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.17370	2.29;2.29;2.28;2.29	5.23	-0.975	0.10289	.	0.000000	0.85682	D	0.000000	T	0.26810	0.0656	L	0.57536	1.79	0.58432	D	0.999996	D;D;D	0.64830	0.992;0.992;0.994	P;P;D	0.63793	0.866;0.866;0.918	T	0.14727	-1.0462	10	0.11794	T	0.64	-26.2587	11.2577	0.49063	0.5554:0.0:0.4446:0.0	.	610;612;670	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	K	612;612;670;610	ENSP00000249883:N612K;ENSP00000409999:N612K;ENSP00000424765:N670K;ENSP00000425475:N610K	ENSP00000249883:N612K	N	-	3	2	AMOTL2	135561685	0.461000	0.25783	0.993000	0.49108	0.925000	0.55904	-0.316000	0.08071	-0.263000	0.09378	-0.441000	0.05720	AAT	.		0.622	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		C	134078995	A	C	134078995	3	2	58	1	0	0	0	0	1	0	0	0	584	214	8	5	522	5	AMOTL2	3	134078995	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	2888949	134078995	63943435	17	5582											
SLC25A36	55186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	140675502	140675502	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggagccagtgtcaaccgaGtagtgtctcccggacctctt	7	10	11	13	2	3	0	1	0	2	0	4	3	3	2	4	2	2	1	4	2	2	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:140675502G>A	ENST00000324194.6	+	2	343	c.175G>A	c.(175-177)Gta>Ata	p.V59I	SLC25A36_ENST00000393015.4_3'UTR|SLC25A36_ENST00000446041.2_Missense_Mutation_p.V59I|SLC25A36_ENST00000507429.1_Missense_Mutation_p.V59I|SLC25A36_ENST00000453248.2_Missense_Mutation_p.V59I			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	59					response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						TGTCAACCGAGTAGTGTCTCC	0.433																																					p.V59I		.											.	SLC25A36-90	0			c.G175A						.						140	135	137					3																	140675502		2203	4300	6503	SO:0001583	missense	55186	exon2			AACCGAGTAGTGT	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"Solute carriers"	25554	protein-coding gene	gene with protein product			"solute carrier family 25, member 36"				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.175G>A	3.37:g.140675502G>A	ENSP00000320688:p.Val59Ile	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	73	24	NM_018155	0	0	5	10	5	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	37	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666084	0.29604	.	.	ENSG00000114120	ENST00000446041;ENST00000507429;ENST00000324194;ENST00000453248;ENST00000513887	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.17	5.29	-0.772	0.10998	Mitochondrial carrier domain (2);	0.517046	0.21808	N	0.068811	T	0.62551	0.2437	L	0.31578	0.945	0.09310	N	0.999996	B;B;B;B	0.13594	0.0;0.001;0.008;0.0	B;B;B;B	0.13407	0.005;0.003;0.009;0.005	T	0.43130	-0.9410	10	0.23302	T	0.38	-6.1006	11.8956	0.52654	0.3779:0.0:0.6221:0.0	.	59;59;59;59	B4DL01;Q96CQ1-3;Q96CQ1;F6SDC8	.;.;S2536_HUMAN;.	I	59;59;59;59;9	ENSP00000401938:V59I;ENSP00000421470:V59I;ENSP00000320688:V59I;ENSP00000391521:V59I	ENSP00000320688:V59I	V	+	1	0	SLC25A36	142158192	0.994000	0.37717	0.770000	0.31555	0.903000	0.53119	1.349000	0.33998	-0.689000	0.05149	-0.813000	0.03139	GTA	.		0.433	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155		A	140675502	G	A	140675502	3	1	58	1	0	0	0	0	1	0	0	0	14532	1029	36	2	181	2	SLC25A36	3	140675502	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	6596507	140675502	57346928	18	5583											
MED12L	116931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151107816	151107816	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctaattactcgcctaTctcctcccaaatgatgcacc	9	11	4	17	1	1	1	0	1	1	0	5	1	3	1	6	0	2	1	6	0	4	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:151107816T>G	ENST00000474524.1	+	36	5434	c.5396T>G	c.(5395-5397)aTc>aGc	p.I1799S	MED12L_ENST00000273432.4_Missense_Mutation_p.I1659S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1799						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TACTCGCCTATCTCCTCCCAA	0.468																																					p.I1799S		.											.	MED12L-576	0			c.T5396G						.						175	171	172					3																	151107816		2203	4300	6503	SO:0001583	missense	116931	exon36			CGCCTATCTCCTC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5396T>G	3.37:g.151107816T>G	ENSP00000417235:p.Ile1799Ser	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	88	37	NM_053002	0	0	0	0	0	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440148	0.43326	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60171	0.43;0.21	5.73	5.73	0.89815	.	0.222920	0.46442	D	0.000300	T	0.39682	0.1087	N	0.08118	0	0.32093	N	0.591569	B;B	0.23058	0.005;0.079	B;B	0.19666	0.002;0.026	T	0.52132	-0.8616	10	0.87932	D	0	-5.497	14.2508	0.66019	0.0:0.0:0.0:1.0	.	1659;1799	F8WAE6;Q86YW9	.;MD12L_HUMAN	S	1799;1659	ENSP00000417235:I1799S;ENSP00000273432:I1659S	ENSP00000273432:I1659S	I	+	2	0	MED12L	152590506	0.493000	0.26035	0.865000	0.33974	0.987000	0.75469	3.781000	0.55394	2.186000	0.69663	0.459000	0.35465	ATC	.		0.468	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	151107816	T	G	151107816	3	3	58	1	0	0	0	0	1	0	0	0	9454	1435	50	5	5538	5	MED12L	3	151107816	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	10432314	151107816	46914614	19	5584											
SMC4	10051	hgsc.bcm.edu;bcgsc.ca	37	chr3	160134136	160134136	+	Frame_Shift_Del	DEL	A	A	-																															gaaggaaaaagagaaagaagAaaaaaaattaaaggaagtta																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:160134136delA	ENST00000357388.3	+	10	1821	c.1370delA	c.(1369-1371)gaafs	p.E457fs	SMC4_ENST00000462787.1_Frame_Shift_Del_p.E457fs|SMC4_ENST00000469762.1_Frame_Shift_Del_p.E432fs|SMC4_ENST00000344722.5_Frame_Shift_Del_p.E457fs|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000360111.2_Frame_Shift_Del_p.E457fs	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	457					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GAGAAAGAAGAAAAAAAATTA	0.308																																					p.E457fs		.											.	SMC4-291	0			c.1370delA						.						53	62	59					3																	160134136		2202	4290	6492	SO:0001589	frameshift_variant	10051	exon9			.	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1370delA	3.37:g.160134136delA	ENSP00000349961:p.Glu457fs	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	230	36	NM_005496	0	0	0	0	0	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Frame_Shift_Del	DEL	ENST00000357388.3	37	CCDS3189.1																																																																																			.		0.308	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			-	160134136	A	-	160134136	7	5	58	1	0	1	0	1	0	0	0	0	14817	246	9	0	1404	0	SMC4	3	160134136	Frame_Shift_Del	DEL	A	TCGA-B9-A69E-01A-11D-A31X-10	9026320	160134136	37888294	20	5585											
DOK7	285489	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	3478120	3478121	+	Frame_Shift_Ins	INS	-	-	GGCTA																															accaagttggagagcggcccINSggctaccctgcacctctgca																								rs376659660|rs539942267		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:3478120_3478121insGGCTA	ENST00000340083.5	+	4	448_449	c.383_384insGGCTA	c.(382-387)ccggctfs	p.-129fs	DOK7_ENST00000389653.2_Frame_Shift_Ins_p.-129fs|DOK7_ENST00000507039.1_Frame_Shift_Ins_p.-129fs	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7						neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GAGAGCGGCCCGGCTACCCTGC	0.668																																					p.P128fs		.											.	DOK7-91	0			c.383_384insGGCTA						.																																			SO:0001589	frameshift_variant	285489	exon4			.	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"chromosome 4 open reading frame 25"	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.384_388dupGGCTA	4.37:g.3478121_3478125dupGGCTA	ENSP00000344432:p.Ala129fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	86	21	NM_001164673	0	0	0	0	0	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Frame_Shift_Ins	INS	ENST00000340083.5	37	CCDS3370.2																																																																																			.		0.668	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660		GGCTA	3478121	-	GGCTA	3478120	7	5	58	1	0	1	1	0	0	0	0	0	4713	652	23	0	397	0	DOK7	4	3478120	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10		3478120	187676156	21	5586											
TLR10	81793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	38776735	38776735	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcagatgagcaattttctgGaaatctgatttttgtatttt	10	19	8	4	0	2	3	0	2	2	1	2	4	2	4	0	1	2	3	0	1	3	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:38776735G>T	ENST00000308973.4	-	4	1082	c.477C>A	c.(475-477)ttC>ttA	p.F159L	TLR10_ENST00000361424.2_Missense_Mutation_p.F159L|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Missense_Mutation_p.F159L|TLR10_ENST00000506111.1_Missense_Mutation_p.F159L	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	159					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CAATTTTCTGGAAATCTGATT	0.398																																					p.F159L		.											.	TLR10-522	0			c.C477A						.						57	61	59					4																	38776735		2202	4299	6501	SO:0001583	missense	81793	exon2			TTTCTGGAAATCT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.477C>A	4.37:g.38776735G>T	ENSP00000308925:p.Phe159Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	43	9	NM_001017388	0	0	0	0	0	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	1.875	-0.459352	0.04508	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.23	2.42	0.29668	.	0.111310	0.38272	N	0.001753	T	0.07503	0.0189	N	0.17082	0.46	0.41978	D	0.990781	B	0.09022	0.002	B	0.10450	0.005	T	0.20107	-1.0285	10	0.10636	T	0.68	.	4.4622	0.11671	0.1433:0.1228:0.6077:0.1263	.	159	Q9BXR5	TLR10_HUMAN	L	159	ENSP00000308925:F159L;ENSP00000421483:F159L;ENSP00000354459:F159L;ENSP00000424923:F159L	ENSP00000308925:F159L	F	-	3	2	TLR10	38453130	0.010000	0.17322	1.000000	0.80357	0.982000	0.71751	-0.202000	0.09451	1.211000	0.43351	0.655000	0.94253	TTC	.		0.398	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			T	38776735	G	T	38776735	3	4	58	1	0	0	0	0	1	0	0	0	15982	1165	41	4	1962	4	TLR10	4	38776735	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	35298615	38776735	152377541	22	5587											
MUC7	4589	ucsc.edu;bcgsc.ca	37	chr4	71347168	71347168	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctccaccagagaccacagCtgccccacccacaccttctg	10	5	6	20	0	1	1	0	0	1	1	2	2	2	1	7	0	3	2	7	0	0	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:71347168C>T	ENST00000304887.5	+	3	897	c.707C>T	c.(706-708)gCt>gTt	p.A236V	MUC7_ENST00000413702.1_Missense_Mutation_p.A236V|MUC7_ENST00000456088.1_Missense_Mutation_p.A236V	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	236	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			GAGACCACAGCTGCCCCACCC	0.587																																					p.A236V													.	MUC7-93	0			c.C707T						.						386	317	340					4																	71347168		2203	4300	6503	SO:0001583	missense	4589	exon4			CCACAGCTGCCCC	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"Mucins"	7518	protein-coding gene	gene with protein product		158375	"mucin 7, salivary"			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.707C>T	4.37:g.71347168C>T	ENSP00000302021:p.Ala236Val	Somatic	689	2		WXS	Illumina HiSeq		547	131	NM_001145007	0	0	0	0	0	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.263054	0.23051	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.45668	0.89;0.89;0.89	2.03	2.03	0.26663	.	.	.	.	.	T	0.40767	0.1130	N	0.19112	0.55	0.29493	N	0.855503	D	0.60160	0.987	P	0.58970	0.849	T	0.26258	-1.0108	8	.	.	.	-3.0E-4	10.0947	0.42469	0.0:1.0:0.0:0.0	.	236	Q8TAX7	MUC7_HUMAN	V	236	ENSP00000407422:A236V;ENSP00000400585:A236V;ENSP00000302021:A236V	.	A	+	2	0	MUC7	71381757	0.001000	0.12720	0.167000	0.22817	0.132000	0.20833	0.201000	0.17276	1.420000	0.47138	0.655000	0.94253	GCT	.		0.587	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		T	71347168	C	T	71347168	3	4	58	1	0	0	0	0	1	0	0	0	10006	797	28	2	713	2	MUC7	4	71347168	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	32570433	71347168	119807108	23	5588											
SYNPO2	171024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	119952865	119952865	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaatgcatccttgtttactTtccaacctccagatgcaaag	11	13	5	12	0	1	1	1	0	0	1	4	1	4	1	4	0	4	3	4	0	4	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:119952865T>A	ENST00000429713.2	+	4	3117	c.2935T>A	c.(2935-2937)Ttc>Atc	p.F979I	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.F979I|SYNPO2_ENST00000434046.2_Missense_Mutation_p.F979I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	979						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTTGTTTACTTTCCAACCTCC	0.498																																					p.F979I		.											.	SYNPO2-92	0			c.T2935A						.						96	78	84					4																	119952865		2203	4300	6503	SO:0001583	missense	171024	exon4			TTTACTTTCCAAC	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2935T>A	4.37:g.119952865T>A	ENSP00000395143:p.Phe979Ile	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	140	28	NM_001128934	0	0	2	2	0	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.425277|4.425277	0.83667|0.83667	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.16324|.	2.35;2.39;2.37|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000004|0.000004	T|T	0.75398|0.75398	0.3844|0.3844	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.991|.	D;D;D;D|.	0.80764|.	0.994;0.992;0.991;0.955|.	T|T	0.76713|0.76713	-0.2858|-0.2858	9|6	.|.	.|.	.|.	-21.6986|-21.6986	15.246|15.246	0.73507|0.73507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	979;979;979;979|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	979|930	ENSP00000306015:F979I;ENSP00000395143:F979I;ENSP00000390965:F979I|.	.|.	F|F	+|+	1|2	0|0	SYNPO2|SYNPO2	120172313|120172313	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	7.841000|7.841000	0.86834|0.86834	2.013000|2.013000	0.59113|0.59113	0.533000|0.533000	0.62120|0.62120	TTC|TTT	.		0.498	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			A	119952865	T	A	119952865	3	1	58	1	0	0	0	0	1	0	0	0	15489	1841	64	5	2949	5	SYNPO2	4	119952865	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	48605697	119952865	71201411	24	5589											
ODZ3	55714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	183245385	183245385	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggatttggttcacagagaagCagacgagttcactagacaag	14	8	12	7	1	2	3	2	0	0	3	2	6	2	4	0	2	1	3	0	2	3	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:183245385C>A	ENST00000511685.1	+	2	335	c.212C>A	c.(211-213)gCa>gAa	p.A71E	TENM3_ENST00000406950.2_Missense_Mutation_p.A71E			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	71	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CACAGAGAAGCAGACGAGTTC	0.458																																					p.A71E		.											.	.	0			c.C212A						.						98	97	98					4																	183245385		1955	4146	6101	SO:0001583	missense	55714	exon1			GAGAAGCAGACGA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.212C>A	4.37:g.183245385C>A	ENSP00000424226:p.Ala71Glu	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	66	9	NM_001080477	0	0	0	0	0	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184679	0.57909	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.31769	1.48;1.48;1.48	5.65	5.65	0.86999	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.52256	0.1723	L	0.60455	1.87	0.30938	N	0.726181	D;P	0.62365	0.991;0.77	P;B	0.61132	0.884;0.255	T	0.51934	-0.8642	9	0.72032	D	0.01	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	71;71	D6RGC5;Q9P273	.;TEN3_HUMAN	E	71	ENSP00000421320:A71E;ENSP00000424226:A71E;ENSP00000385276:A71E	ENSP00000385276:A71E	A	+	2	0	ODZ3	183482379	0.995000	0.38212	0.986000	0.45419	0.986000	0.74619	3.658000	0.54482	2.941000	0.99782	0.655000	0.94253	GCA	.		0.458	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183245385	C	A	183245385	3	1	58	1	0	0	0	0	1	0	0	0	10862	710	25	4	214	4	ODZ3	4	183245385	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	63292520	183245385	7908891	25	5590											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187517964	187517964	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggcacctggggtggtatgtCtgagtaaatgttcttattta	9	15	12	5	0	2	1	0	1	2	0	2	1	2	1	1	4	0	4	1	4	5	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:187517964C>G	ENST00000441802.2	-	25	12939	c.12730G>C	c.(12730-12732)Gac>Cac	p.D4244H	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4244					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						GGTGGTATGTCTGAGTAAATG	0.478										HNSCC(5;0.00058)																											p.D4244H	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.G12730C						.						70	69	69					4																	187517964		1861	4100	5961	SO:0001583	missense	2195	exon25			GTATGTCTGAGTA	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.12730G>C	4.37:g.187517964C>G	ENSP00000406229:p.Asp4244His	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	97	26	NM_005245	0	0	24	45	21		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.443680|4.443680	0.83993|0.83993	.|.	.|.	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.70869|.	-0.52|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72961|0.72961	0.3526|0.3526	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.69304|0.69304	-0.5180|-0.5180	10|5	0.66056|.	D|.	0.02|.	.|.	19.3359|19.3359	0.94319|0.94319	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4244|.	Q14517|.	FAT1_HUMAN|.	H|T	4244;4246|11	ENSP00000406229:D4244H|.	ENSP00000260147:D4246H|.	D|R	-|-	1|2	0|0	FAT1|FAT1	187754958|187754958	1.000000|1.000000	0.71417|0.71417	0.831000|0.831000	0.32960|0.32960	0.737000|0.737000	0.42083|0.42083	7.651000|7.651000	0.83577|0.83577	2.809000|2.809000	0.96659|0.96659	0.555000|0.555000	0.69702|0.69702	GAC|AGA	.		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187517964	C	G	187517964	3	3	58	1	0	0	0	0	1	0	0	0	5708	913	32	4	1048	4	FAT1	4	187517964	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	4272579	187517964	3636312	26	5591											
TRIP13	9319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	908120	908120	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtggcaagctggtaacCaagatgtttcagaagattca	14	9	11	7	0	2	4	2	0	0	4	2	4	2	4	1	2	2	4	1	2	4	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:908120C>T	ENST00000166345.3	+	8	1046	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	230					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			AGCTGGTAACCAAGATGTTTC	0.498																																					p.T230T		.											.	TRIP13-90	0			c.C690T						.						169	149	155					5																	908120		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon8			GGTAACCAAGATG	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.690C>T	5.37:g.908120C>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	123	38	NM_004237	0	0	0	0	0	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	37	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	8.882	0.951814	0.18431	.	.	ENSG00000071539	ENST00000513435	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.41259	0.1151	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	4	.	.	.	-32.367	5.2498	0.15515	0.143:0.5019:0.2154:0.1397	.	.	.	.	L	226	.	.	P	+	2	0	TRIP13	961120	0.006000	0.16342	0.087000	0.20705	0.969000	0.65631	-1.282000	0.02799	-2.592000	0.00456	-0.345000	0.07892	CCA	.		0.498	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		T	908120	C	T	908120	2	4	58	1	0	0	0	0	0	0	0	1	16590	581	21	2		2	TRIP13	5	908120	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		908120	180007140	27	5592											
SRD5A1	6715	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	6663046	6663047	+	Frame_Shift_Ins	INS	-	-	T																															tttgctttcttcacgttttgINSttttttatctggtagagcaa																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:6663046_6663047insT	ENST00000274192.5	+	4	914_915	c.680_681insT	c.(679-684)tgttttfs	p.CF227fs	SRD5A1_ENST00000538824.1_Frame_Shift_Ins_p.CF180fs|SRD5A1_ENST00000537411.1_3'UTR	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	227					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)			endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TTCACGTTTTGTTTTTTATCTG	0.396																																					p.C227fs		.											.	SRD5A1-90	0			c.680_681insT						.																																			SO:0001589	frameshift_variant	6715	exon4			.	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.686dupT	5.37:g.6663052_6663052dupT	ENSP00000274192:p.Cys227fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	91	23	NM_001047	0	0	0	0	0	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Frame_Shift_Ins	INS	ENST00000274192.5	37	CCDS3870.1																																																																																			.		0.396	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047		T	6663047	-	T	6663046	7	5	58	1	0	1	1	0	0	0	0	0	15170	1377	48	0	694	0	SRD5A1	5	6663046	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	5754926	6663046	174252214	28	5593											
CDH12	1010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	21752166	21752166	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggttttatatccctgcgaaTtttgttctcctcaatcactt	7	19	5	10	1	3	0	2	0	1	0	5	1	4	0	2	1	1	2	2	1	4	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:21752166T>C	ENST00000382254.1	-	15	3151	c.2065A>G	c.(2065-2067)Att>Gtt	p.I689V	CDH12_ENST00000522262.1_Missense_Mutation_p.I649V|RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000521384.1_5'UTR|CDH12_ENST00000504376.2_Missense_Mutation_p.I689V	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	689					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TCCCTGCGAATTTTGTTCTCC	0.458										HNSCC(59;0.17)																											p.I689V		.											.	CDH12-92	0			c.A2065G						.						188	161	171					5																	21752166		2203	4300	6503	SO:0001583	missense	1010	exon15			TGCGAATTTTGTT	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2065A>G	5.37:g.21752166T>C	ENSP00000371689:p.Ile689Val	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	221	60	NM_004061	0	0	0	0	0	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	T	5.372	0.253855	0.10185	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.76186	-1.0;-1.0;-1.0	5.12	3.92	0.45320	Cadherin, cytoplasmic domain (1);	0.479938	0.25538	N	0.029988	T	0.51958	0.1705	N	0.14661	0.345	0.31334	N	0.684456	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.46938	-0.9155	10	0.17369	T	0.5	.	6.6994	0.23217	0.0:0.0776:0.1551:0.7673	.	649;689	B7Z2U6;P55289	.;CAD12_HUMAN	V	689;689;649	ENSP00000423577:I689V;ENSP00000371689:I689V;ENSP00000428786:I649V	ENSP00000371689:I689V	I	-	1	0	CDH12	21787923	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	1.798000	0.38814	0.765000	0.33221	0.383000	0.25322	ATT	.		0.458	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		C	21752166	T	C	21752166	3	2	58	1	0	0	0	0	1	0	0	0	3104	1493	52	3	323	3	CDH12	5	21752166	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	15089120	21752166	159163094	29	5594											
IL31RA	133396	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	55212822	55212822	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagcttctcttttctggTcaaagtttagtaccagatca	10	14	8	9	0	4	1	2	0	2	1	5	2	4	1	1	1	3	4	1	1	3	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:55212822T>C	ENST00000447346.2	+	15	2234	c.2169T>C	c.(2167-2169)ggT>ggC	p.G723G	IL31RA_ENST00000490985.1_Silent_p.G581G|IL31RA_ENST00000359040.5_Intron|IL31RA_ENST00000354961.4_Intron|IL31RA_ENST00000396834.1_Intron	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	691					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				TCTTTTCTGGTCAAAGTTTAG	0.468																																					p.G723G													.	IL31RA-91	0			c.T2169C						.						56	63	61					5																	55212822		2203	4300	6503	SO:0001819	synonymous_variant	133396	exon15			TTCTGGTCAAAGT	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.2169T>C	5.37:g.55212822T>C		Somatic	158	1		WXS	Illumina HiSeq	Phase_I	162	47	NM_139017	0	0	0	0	0	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Silent	SNP	ENST00000447346.2	37	CCDS3970.2																																																																																			.		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		C	55212822	T	C	55212822	2	2	58	1	0	0	0	0	0	0	0	1	7712	1654	58	3		3	IL31RA	5	55212822	Silent	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	33460656	55212822	125702438	30	5595											
KIF2A	3796	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	61662304	61662304	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaatacattaagatatgcaAataggtatgagagatagttc	17	13	8	3	0	0	3	0	1	0	2	1	4	0	3	0	1	2	3	0	1	8	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:61662304A>T	ENST00000401507.3	+	16	1953	c.1642A>T	c.(1642-1644)Aat>Tat	p.N548Y	KIF2A_ENST00000381103.2_Missense_Mutation_p.N528Y|KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000407818.3_Missense_Mutation_p.N548Y|KIF2A_ENST00000506857.1_Missense_Mutation_p.N502Y	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	548	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		AAGATATGCAAATAGGTATGA	0.368																																					p.N548Y													.	KIF2A-228	0			c.A1642T						.						47	49	48					5																	61662304		2202	4297	6499	SO:0001583	missense	3796	exon16			TATGCAAATAGGT	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"Kinesins"	6318	protein-coding gene	gene with protein product		602591	"kinesin heavy chain member 2"	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.1642A>T	5.37:g.61662304A>T	ENSP00000385622:p.Asn548Tyr	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	132	31	NM_001098511	0	0	0	0	0	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Missense_Mutation	SNP	ENST00000401507.3	37	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135292	0.77662	.	.	ENSG00000068796	ENST00000401507;ENST00000381103;ENST00000407818;ENST00000506857	T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95	5.95	5.95	0.96441	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	T	0.79799	0.4508	L	0.28649	0.875	0.58432	D	0.999997	D;D;D;D	0.58970	0.984;0.98;0.979;0.979	D;D;P;D	0.68353	0.957;0.929;0.905;0.951	T	0.82165	-0.0592	10	0.87932	D	0	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	548;548;548;528	B4DM85;O00139-4;O00139;E9PB70	.;.;KIF2A_HUMAN;.	Y	548;528;548;502	ENSP00000385622:N548Y;ENSP00000370493:N528Y;ENSP00000385000:N548Y;ENSP00000423772:N502Y	ENSP00000370493:N528Y	N	+	1	0	KIF2A	61698061	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.341000	0.72977	2.279000	0.76181	0.533000	0.62120	AAT	.		0.368	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520		T	61662304	A	T	61662304	3	4	58	1	0	0	0	0	1	0	0	0	8318	14	1	5	1704	5	KIF2A	5	61662304	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	6449482	61662304	119252956	31	5596											
SLC12A2	6558	broad.mit.edu	37	chr5	127420207	127420209	+	In_Frame_Del	DEL	CGG	CGG	-																															gagggcagcagcctgcactcCggcggcggcggcggcagtgg																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:127420207_127420209delCGG	ENST00000262461.2	+	1	750_752	c.561_563delCGG	c.(559-564)tccggc>tcc	p.G192del	SLC12A2_ENST00000343225.4_In_Frame_Del_p.G192del|CTC-228N24.3_ENST00000501702.2_lincRNA	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	192	Poly-Gly.				ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	GCCTGCACTCCGGCGGCGGCGGC	0.65																																					p.187_188del													.	SLC12A2-94	0			c.561_563del						.																																			SO:0001651	inframe_deletion	6558	exon1			GCACTCCGGCGGC		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.561_563delCGG	5.37:g.127420216_127420218delCGG	ENSP00000262461:p.Gly192del	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	187	9	NM_001046	0	0	0	0	0	Q8N713|Q8WWH7	In_Frame_Del	DEL	ENST00000262461.2	37	CCDS4144.1																																																																																			.		0.65	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		-	127420209	CGG	-	127420207	7	5	58	1	0	1	0	1	0	0	0	0	14415	639	23	0	563	0	SLC12A2	5	127420207	In_Frame_Del	DEL	CGG	TCGA-B9-A69E-01A-11D-A31X-10	65757903	127420207	53495053	32	5597											
NDST1	3340	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149921206	149921206	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaccgcttcccaaagctcctCatcatcggcccccagaaaac	11	6	6	18	2	2	1	2	0	0	1	5	2	4	1	5	1	2	2	5	1	3	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:149921206C>T	ENST00000261797.6	+	9	2326	c.1824C>T	c.(1822-1824)ctC>ctT	p.L608L	NDST1_ENST00000523767.1_Silent_p.L608L|snoU13_ENST00000459561.1_RNA	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	608	Heparan sulfate N-sulfotransferase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAAGCTCCTCATCATCGGCC	0.552																																					p.L608L													.	NDST1-136	0			c.C1824T						.						84	69	75					5																	149921206		2203	4300	6503	SO:0001819	synonymous_variant	3340	exon9			GCTCCTCATCATC	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"Sulfotransferases, membrane-bound"	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.1824C>T	5.37:g.149921206C>T		Somatic	104	1		WXS	Illumina HiSeq	Phase_I	91	30	NM_001543	0	0	18	23	5	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			.		0.552	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		T	149921206	C	T	149921206	2	4	58	1	0	0	0	0	0	0	0	1	10281	813	29	2		2	NDST1	5	149921206	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	22500999	149921206	30994054	33	5598											
DST	667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	56504731	56504731	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaaattcacatacctcaCtgattttagcttctttgaga	11	18	4	8	0	3	2	2	2	1	1	3	3	3	2	1	0	2	1	1	0	4	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:56504731C>T	ENST00000361203.3	-	15	1989	c.1982G>A	c.(1981-1983)aGt>aAt	p.S661N	DST_ENST00000370765.6_Missense_Mutation_p.S335N|DST_ENST00000370769.4_Missense_Mutation_p.S661N|DST_ENST00000370754.5_Missense_Mutation_p.S839N|DST_ENST00000370788.2_Missense_Mutation_p.S661N|DST_ENST00000312431.6_Missense_Mutation_p.S661N|DST_ENST00000421834.2_Missense_Mutation_p.S661N|DST_ENST00000244364.6_Missense_Mutation_p.S335N|DST_ENST00000446842.2_Missense_Mutation_p.S335N|DST_ENST00000518935.1_Missense_Mutation_p.S335N			Q03001	DYST_HUMAN	dystonin	661					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACATACCTCACTGATTTTAGC	0.284																																					p.S335N		.											.	DST-523	0			c.G1004A						.						47	51	50					6																	56504731		2203	4299	6502	SO:0001583	missense	667	exon5			ACCTCACTGATTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1982G>A	6.37:g.56504731C>T	ENSP00000354508:p.Ser661Asn	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	81	30	NM_001723	0	0	0	0	0	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	17.97	3.519255	0.64634	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;D;T;T;T;D;T;T	0.83992	1.18;0.02;0.02;0.17;0.96;-1.53;0.13;-0.0;-0.3;-1.79;-0.69;-0.14	5.45	4.58	0.56647	.	0.000000	0.64402	D	0.000017	T	0.80486	0.4632	L	0.44542	1.39	0.29528	N	0.852973	P;B;P;B;D;B;B;P;B;B	0.55385	0.899;0.235;0.944;0.354;0.971;0.016;0.115;0.917;0.235;0.277	B;B;D;B;P;B;B;P;B;B	0.63597	0.401;0.149;0.916;0.149;0.73;0.02;0.134;0.897;0.149;0.329	T	0.78265	-0.2271	9	0.17832	T	0.49	.	14.2099	0.65756	0.0:0.9287:0.0:0.0713	.	690;661;661;839;777;335;335;335;661;335	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	N	335;839;661;661;335;661;661;661;335;701;335;335	ENSP00000244364:S335N;ENSP00000359790:S839N;ENSP00000359805:S661N;ENSP00000400883:S661N;ENSP00000393645:S335N;ENSP00000307959:S661N;ENSP00000359824:S661N;ENSP00000354508:S661N;ENSP00000404924:S335N;ENSP00000431030:S701N;ENSP00000359801:S335N;ENSP00000431003:S335N	ENSP00000244364:S335N	S	-	2	0	DST	56612690	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.897000	0.56273	1.525000	0.49052	0.655000	0.94253	AGT	.		0.284	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56504731	C	T	56504731	3	4	58	1	0	0	0	0	1	0	0	0	4794	565	20	2	19471	2	DST	6	56504731	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		56504731	114610336	34	5599											
RIMS1	22999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	72960096	72960096	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgttctgcaagcaacagatCtacctgctagagtagatgga	13	10	10	8	0	2	3	0	0	2	3	2	4	2	4	1	1	5	5	1	1	5	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:72960096C>G	ENST00000521978.1	+	13	2305	c.2305C>G	c.(2305-2307)Cta>Gta	p.L769V	RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000520567.1_Missense_Mutation_p.L769V|RIMS1_ENST00000491071.2_Missense_Mutation_p.L769V|RIMS1_ENST00000517827.1_Missense_Mutation_p.L228V|RIMS1_ENST00000523963.1_Missense_Mutation_p.L243V|RIMS1_ENST00000425662.2_Missense_Mutation_p.L162V|RIMS1_ENST00000517960.1_Missense_Mutation_p.L769V|RIMS1_ENST00000264839.7_Missense_Mutation_p.L769V|RIMS1_ENST00000401910.3_Missense_Mutation_p.L243V|RIMS1_ENST00000348717.5_Missense_Mutation_p.L769V|RIMS1_ENST00000522291.1_Missense_Mutation_p.L769V|RIMS1_ENST00000518273.1_Missense_Mutation_p.L769V	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	769	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGCAACAGATCTACCTGCTAG	0.348																																					p.L769V		.											.	RIMS1-144	0			c.C2305G						.						89	83	84					6																	72960096		1846	4102	5948	SO:0001583	missense	22999	exon13			ACAGATCTACCTG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2305C>G	6.37:g.72960096C>G	ENSP00000428417:p.Leu769Val	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	90	14	NM_014989	0	0	0	0	0	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.83|18.83	3.706633|3.706633	0.68615|0.68615	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827|ENST00000517433	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.82344|.	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6|.	5.28|5.28	4.38|4.38	0.52667|0.52667	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.52532|.	D|.	0.000072|.	T|T	0.69663|0.69663	0.3136|0.3136	M|M	0.87971|0.87971	2.92|2.92	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.962;0.99;0.99;0.998;0.994;0.99|.	D;D;D;D;D;D;D|.	0.97110|.	1.0;0.983;0.996;0.996;0.999;0.996;0.996|.	T|T	0.74475|0.74475	-0.3653|-0.3653	10|5	0.87932|.	D|.	0|.	-12.8523|-12.8523	10.4795|10.4795	0.44684|0.44684	0.0:0.8222:0.0:0.1778|0.0:0.8222:0.0:0.1778	.|.	228;243;769;228;243;769;769|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;C9JNW6;Q86UR5|.	.;.;.;.;.;.;RIMS1_HUMAN|.	V|C	769;769;769;769;769;769;769;769;769;769;769;769;243;243;162;162;228|342	ENSP00000430101:L769V;ENSP00000275037:L769V;ENSP00000264839:L769V;ENSP00000429959:L769V;ENSP00000430408:L769V;ENSP00000430502:L769V;ENSP00000430932:L769V;ENSP00000428417:L769V;ENSP00000385649:L243V;ENSP00000428328:L243V;ENSP00000411235:L162V;ENSP00000389503:L162V;ENSP00000428367:L228V|.	ENSP00000264839:L769V|.	L|S	+|+	1|2	2|0	RIMS1|RIMS1	73016817|73016817	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	4.060000|4.060000	0.57477|0.57477	1.279000|1.279000	0.44446|0.44446	0.585000|0.585000	0.79938|0.79938	CTA|TCT	.		0.348	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	72960096	C	G	72960096	3	3	58	1	0	0	0	0	1	0	0	0	13399	912	32	4	2518	4	RIMS1	6	72960096	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	16455365	72960096	98154971	35	5600											
AKD1	221264	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	109977966	109977966	+	Frame_Shift_Del	DEL	G	G	-																															attttgttcttacttctaaaGtttggagaattgtttcctta																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:109977966delG	ENST00000424296.2	-	8	828	c.752delC	c.(751-753)actfs	p.T251fs	AK9_ENST00000285397.5_Frame_Shift_Del_p.T251fs|AK9_ENST00000368948.2_Frame_Shift_Del_p.T251fs|AK9_ENST00000341338.6_5'UTR	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	251	Adenylate kinase 1.|Glu-rich.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TACTTCTAAAGTTTGGAGAAT	0.318																																					p.T251fs		.											.	AKD1-91	0			c.752delC						.						57	58	58					6																	109977966		2203	4294	6497	SO:0001589	frameshift_variant	221264	exon8			.	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1"	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.752delC	6.37:g.109977966delG	ENSP00000410186:p.Thr251fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	103	32	NM_145025	0	0	0	0	0	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Frame_Shift_Del	DEL	ENST00000424296.2	37	CCDS55048.1																																																																																			.		0.318	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		-	109977966	G	-	109977966	7	5	58	1	0	1	0	1	0	0	0	0	460	1029	36	0	5131	0	AKD1	6	109977966	Frame_Shift_Del	DEL	G	TCGA-B9-A69E-01A-11D-A31X-10	37017870	109977966	61137101	36	5601											
VGLL2	245806	hgsc.bcm.edu	37	chr6	117591730	117591730	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccttcccgatgagccagcGcagcttccccgcctccttct	4	10	7	20	3	1	1	0	1	1	0	5	2	5	1	7	0	3	2	7	0	0	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:117591730G>T	ENST00000326274.5	+	3	606	c.416G>T	c.(415-417)cGc>cTc	p.R139L	VGLL2_ENST00000352536.3_Intron	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	139					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		ATGAGCCAGCGCAGCTTCCCC	0.697																																					p.R139L		.											.	VGLL2-90	0			c.G416T						.						13	15	14					6																	117591730		2195	4285	6480	SO:0001583	missense	245806	exon3			GCCAGCGCAGCTT	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"vestigial like 2 (Drosophila)"			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.416G>T	6.37:g.117591730G>T	ENSP00000320957:p.Arg139Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	53	4	NM_182645	0	0	0	0	0	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	37	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331271	0.95733	.	.	ENSG00000170162	ENST00000326274	T	0.54866	0.55	4.86	4.86	0.63082	.	0.056880	0.64402	D	0.000003	T	0.68393	0.2996	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.72360	-0.4317	10	0.72032	D	0.01	-24.0493	18.1693	0.89740	0.0:0.0:1.0:0.0	.	139	Q8N8G2	VGLL2_HUMAN	L	139	ENSP00000320957:R139L	ENSP00000320957:R139L	R	+	2	0	VGLL2	117698423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.078000	0.94023	2.528000	0.85240	0.549000	0.68633	CGC	.		0.697	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		T	117591730	G	T	117591730	3	4	58	1	0	0	0	0	1	0	0	0	17192	1087	38	4	426	4	VGLL2	6	117591730	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	7613764	117591730	53523337	37	5602											
C6orf170	221322	hgsc.bcm.edu	37	chr6	121433801	121433801	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccagcataattcccttgcagGcagactgaaaaacacagtta	15	8	7	11	0	0	2	0	1	0	1	1	2	1	2	2	1	3	4	2	1	4	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:121433801G>T	ENST00000398212.2	-	29	3223	c.3174C>A	c.(3172-3174)tgC>tgA	p.C1058*	TBC1D32_ENST00000275159.6_Nonsense_Mutation_p.C1099*|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1058					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCCCTTGCAGGCAGACTGAAA	0.274																																					p.C1058X		.											.	C6orf170-92	0			c.C3174A						.						54	49	50					6																	121433801		1803	4070	5873	SO:0001587	stop_gained	221322	exon29			TTGCAGGCAGACT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3174C>A	6.37:g.121433801G>T	ENSP00000381270:p.Cys1058*	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_152730	0	0	0	0	0	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Nonsense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220888	0.95139	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	.	.	.	5.41	3.63	0.41609	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3109	0.32071	0.3125:0.0:0.6875:0.0	.	.	.	.	X	1099;1058	.	ENSP00000275159:C1099X	C	-	3	2	C6orf170	121475500	1.000000	0.71417	0.998000	0.56505	0.007000	0.05969	2.668000	0.46816	0.674000	0.31244	0.585000	0.79938	TGC	.		0.274	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121433801	G	T	121433801	4	4	58	1	0	0	0	0	0	1	0	0	2350	1195	42	4	615	4	C6orf170	6	121433801	Nonsense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3842071	121433801	49681266	38	5603											
FNDC1	84624	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	159655428	159655428	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttctccaccaccccgaTgctgtccttgcgccagagga	7	8	8	18	2	1	1	0	0	1	1	3	3	2	2	7	1	2	1	7	1	0	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:159655428T>G	ENST00000297267.9	+	11	4084	c.3884T>G	c.(3883-3885)aTg>aGg	p.M1295R	FNDC1_ENST00000340366.6_Missense_Mutation_p.M1232R	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1295				M -> K (in Ref. 6; CAE51894). {ECO:0000305}.	cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		ACCACCCCGATGCTGTCCTTG	0.632																																					p.M1295R													.	FNDC1-138	0			c.T3884G						.						25	27	26					6																	159655428		2055	4145	6200	SO:0001583	missense	84624	exon11			CCCCGATGCTGTC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"Fibronectin type III domain containing"	21184	protein-coding gene	gene with protein product		609991	"fibronectin type III domain containing 2"	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3884T>G	6.37:g.159655428T>G	ENSP00000297267:p.Met1295Arg	Somatic	199	1		WXS	Illumina HiSeq	Phase_I	136	45	NM_032532	0	0	0	0	0	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.10|12.10	1.835380|1.835380	0.32421|0.32421	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.08807	.|3.05;3.83	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.276491	.|0.34906	.|N	.|0.003600	T|T	0.08044|0.08044	0.0201|0.0201	L|L	0.34521|0.34521	1.04|1.04	0.32639|0.32639	N|N	0.520991|0.520991	.|D;D	.|0.76494	.|0.999;0.998	.|D;P	.|0.74023	.|0.982;0.895	T|T	0.18840|0.18840	-1.0324|-1.0324	5|10	.|0.32370	.|T	.|0.25	-34.3204|-34.3204	8.2561|8.2561	0.31758|0.31758	0.0:0.088:0.0:0.912|0.0:0.088:0.0:0.912	.|.	.|1232;1295	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	E|R	1190|1295;1232	.|ENSP00000297267:M1295R;ENSP00000342460:M1232R	.|ENSP00000297267:M1295R	D|M	+|+	3|2	2|0	FNDC1|FNDC1	159575418|159575418	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.202000|0.202000	0.24057|0.24057	3.172000|3.172000	0.50832|0.50832	2.112000|2.112000	0.64535|0.64535	0.528000|0.528000	0.53228|0.53228	GAT|ATG	.		0.632	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		G	159655428	T	G	159655428	3	3	58	1	0	0	0	0	1	0	0	0	5987	1464	51	5	3926	5	FNDC1	6	159655428	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	38221627	159655428	11459639	39	5604											
ACTB	60	broad.mit.edu	37	chr7	5567474	5567474	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggacagcgaggccaggaTggagccgccgatccacacgg	9	3	17	12	4	0	0	0	0	0	0	1	5	1	3	4	6	2	0	4	6	0	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:5567474T>G	ENST00000331789.5	-	6	1224	c.1033A>C	c.(1033-1035)Atc>Ctc	p.I345L	ACTB_ENST00000464611.1_5'UTR|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	345					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GAGGCCAGGATGGAGCCGCCG	0.607																																					p.I345L													.	ACTB-226	0			c.A1033C						.						68	71	70					7																	5567474		2203	4300	6503	SO:0001583	missense	60	exon6			CCAGGATGGAGCC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.1033A>C	7.37:g.5567474T>G	ENSP00000349960:p.Ile345Leu	Somatic	143	10		WXS	Illumina HiSeq	Phase_I	105	16	NM_001101	3	3	4318	4419	95	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.555820	0.45487	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713	D	0.95447	-3.71	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000013	D	0.96528	0.8867	M	0.86740	2.835	0.48975	D	0.999733	B	0.06786	0.001	B	0.35655	0.207	D	0.95309	0.8410	10	0.87932	D	0	.	14.9227	0.70851	0.0:0.0:0.0:1.0	.	345	P60709	ACTB_HUMAN	L	345;321;317;264	ENSP00000349960:I345L	ENSP00000440549:I264L	I	-	1	0	ACTB	5534000	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.747000	0.85070	2.114000	0.64651	0.529000	0.55759	ATC	.		0.607	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		G	5567474	T	G	5567474	3	3	58	1	0	0	0	0	1	0	0	0	193	1464	51	5	98	5	ACTB	7	5567474	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		5567474	153571189	40	5605											
THSD7A	221981	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	11500346	11500346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggctgtcttgttgcaCgctccaagggactaattggc	7	11	12	11	1	1	0	0	0	1	0	3	1	3	1	2	3	1	4	2	3	2	4	rs199705914		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:11500346C>T	ENST00000423059.4	-	11	2799	c.2548G>A	c.(2548-2550)Gtg>Atg	p.V850M	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	850					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCTTGTTGCACGCTCCAAGGG	0.552										HNSCC(18;0.044)			C|||	1	0.000199681	0	0.0014	5008	,	,		18566	0		0	False		,,,				2504	0				p.V850M													.	THSD7A-71	0			c.G2548A						.	C	MET/VAL	3,3953		0,3,1975	50	51	50		2548	3.4	0.9	7		50	0,8324		0,0,4162	yes	missense	THSD7A	NM_015204.2	21	0,3,6137	TT,TC,CC		0.0,0.0758,0.0244	possibly-damaging	850/1658	11500346	3,12277	1978	4162	6140	SO:0001583	missense	221981	exon11			GTTGCACGCTCCA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2548G>A	7.37:g.11500346C>T	ENSP00000406482:p.Val850Met	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	62	9	NM_015204	0	0	1	1	0		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.16	2.752331	0.49362	7.58E-4	0.0	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.60920	0.15	5.2	3.38	0.38709	.	0.257298	0.39834	N	0.001257	T	0.53610	0.1807	L	0.60455	1.87	0.39852	D	0.973256	B	0.28258	0.205	B	0.32624	0.149	T	0.51647	-0.8679	10	0.35671	T	0.21	.	11.4413	0.50099	0.0:0.8729:0.0:0.1271	.	850	Q9UPZ6	THS7A_HUMAN	M	850	ENSP00000406482:V850M	ENSP00000262042:V850M	V	-	1	0	THSD7A	11466871	0.045000	0.20229	0.911000	0.35937	0.977000	0.68977	0.420000	0.21263	0.688000	0.31529	0.655000	0.94253	GTG	C|0.999;T|0.000		0.552	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11500346	C	T	11500346	3	4	58	1	0	0	0	0	1	0	0	0	15911	536	19	1	2493	1	THSD7A	7	11500346	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	5932872	11500346	147638317	41	5606											
TRIP6	7205	broad.mit.edu;bcgsc.ca	37	chr7	100466248	100466248	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	accgccagcaccccggctggCccagccttccccgtgcaagt	6	5	10	20	3	0	0	0	0	0	0	1	0	1	0	8	2	3	3	8	2	1	1	rs548658866		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:100466248C>T	ENST00000200457.4	+	4	855	c.495C>T	c.(493-495)ggC>ggT	p.G165G		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	165					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCCGGCTGGCCCAGCCTTCC	0.721													C|||	1	0.000199681	0	0.0014	5008	,	,		13231	0		0	False		,,,				2504	0				p.G165G													.	TRIP6-514	0			c.C495T						.						14	17	16					7																	100466248		2149	4196	6345	SO:0001819	synonymous_variant	7205	exon4			GGCTGGCCCAGCC	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.495C>T	7.37:g.100466248C>T		Somatic	54	1		WXS	Illumina HiSeq	Phase_I	78	26	NM_003302	0	0	64	104	40	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Silent	SNP	ENST00000200457.4	37	CCDS5708.1																																																																																			.		0.721	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		T	100466248	C	T	100466248	2	4	58	1	0	0	0	0	0	0	0	1	16592	726	26	2		2	TRIP6	7	100466248	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	88965902	100466248	58672415	42	5607											
GPR85	54329	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	112724144	112724146	+	In_Frame_Del	DEL	ATC	ATC	-																															actggcttcatttttcttcgAtcgtggacgaaaaatatcag																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:112724144_112724146delATC	ENST00000297146.3	-	3	1234_1236	c.631_633delGAT	c.(631-633)gatdel	p.D211del	GPR85_ENST00000424100.1_In_Frame_Del_p.D211del|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000501255.2_In_Frame_Del_p.D211del|GPR85_ENST00000449591.1_In_Frame_Del_p.D211del	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	211					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TTTTTCTTCGATCGTGGACGAAA	0.493																																					p.211_211del		.											.	GPR85-91	0			c.631_633del						.																																			SO:0001651	inframe_deletion	54329	exon3			.	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"GPCR / Class A : Orphans"	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.631_633delGAT	7.37:g.112724144_112724146delATC	ENSP00000297146:p.Asp211del	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	63	14	NM_001146265	0	0	0	0	0	Q9JHI6|Q9NPD1	In_Frame_Del	DEL	ENST00000297146.3	37	CCDS5758.1																																																																																			.		0.493	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2			-	112724146	ATC	-	112724144	7	5	58	1	0	1	0	1	0	0	0	0	6735	330	12	0	483	0	GPR85	7	112724144	In_Frame_Del	DEL	ATC	TCGA-B9-A69E-01A-11D-A31X-10	12257896	112724144	46414519	43	5608											
RBM28	55131	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	127958110	127958111	+	In_Frame_Ins	INS	-	-	GAC																															aaaggcgtagcccagggactINSgacccttcatgttcccatga																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:127958110_127958111insGAC	ENST00000223073.2	-	15	1726_1727	c.1612_1613insGTC	c.(1612-1614)cag>cGTCag	p.537_538insR	RBM28_ENST00000481788.1_Intron|RBM28_ENST00000415472.2_In_Frame_Ins_p.396_397insR	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	537	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						GCCCAGGGACTGACCCTTCATG	0.485																																					p.Q538delinsRQ		.											.	RBM28-92	0			c.1613_1614insGTC						.																																			SO:0001652	inframe_insertion	55131	exon15			.	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"RNA binding motif (RRM) containing"	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1610_1612dupGTC	7.37:g.127958111_127958113dupGAC	ENSP00000223073:p.Gly537_Gln538insArg	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	88	19	NM_018077	0	0	0	0	0	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	In_Frame_Ins	INS	ENST00000223073.2	37	CCDS5801.1																																																																																			.		0.485	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		GAC	127958111	-	GAC	127958110	7	5	58	1	0	1	1	0	0	0	0	0	13160	1580	55	0	686	0	RBM28	7	127958110	In_Frame_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	15233966	127958110	31180553	44	5609											
LSM1	27257	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	38027436	38027436	+	Splice_Site	DEL	C	C	-																															ctgatgtagcactaagtttgCtgtaagtgtatagggaaaaa																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:38027436delC	ENST00000311351.4	-	3	511		c.e3-1		LSM1_ENST00000522515.1_Splice_Site|LSM1_ENST00000520755.1_Intron	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					ACTAAGTTTGCTGTAAGTGTA	0.363																																					.		.											.	LSM1-90	0			c.116-1G>-						.						127	118	121					8																	38027436		2203	4300	6503	SO:0001630	splice_region_variant	27257	exon4			.	AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.116-1G>-	8.37:g.38027436delC		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	129	33	NM_014462	0	0	0	0	0	B2R5E6	Splice_Site	DEL	ENST00000311351.4	37	CCDS6103.1																																																																																			.		0.363	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462	Intron	-	38027436	C	-	38027436	8	5	58	1	0	1	0	1	0	0	1	0	9075	811	28	0	294	0	LSM1	8	38027436	Splice_Site	DEL	C	TCGA-B9-A69E-01A-11D-A31X-10		38027436	108336586	45	5610											
TMEM67	91147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	94805453	94805453	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggtgtattgggtgggctaGctgttttagcatctcttttg	4	18	14	5	0	1	0	0	0	1	0	2	0	1	0	0	3	2	5	0	3	3	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:94805453G>C	ENST00000453321.3	+	16	1661	c.1603G>C	c.(1603-1605)Gct>Cct	p.A535P	TMEM67_ENST00000409623.3_Missense_Mutation_p.A454P	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	535					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			GGGTGGGCTAGCTGTTTTAGC	0.368																																					p.A535P		.											.	TMEM67-92	0			c.G1603C						.						157	153	154					8																	94805453		2203	4300	6503	SO:0001583	missense	91147	exon16			GGGCTAGCTGTTT	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1603G>C	8.37:g.94805453G>C	ENSP00000389998:p.Ala535Pro	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	116	31	NM_153704	0	0	2	2	0	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	37	CCDS6258.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.1|26.1	4.706160|4.706160	0.89018|0.89018	.|.	.|.	ENSG00000164953|ENSG00000164953	ENST00000453321;ENST00000409623|ENST00000520680	D;D|.	0.97256|.	-4.31;-4.31|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.111849|.	0.64402|.	D|.	0.000016|.	T|T	0.78317|0.78317	0.4264|0.4264	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.83275|.	0.993;0.996;0.992|.	T|T	0.77584|0.77584	-0.2533|-0.2533	10|5	0.66056|.	D|.	0.02|.	-17.8669|-17.8669	19.6017|19.6017	0.95566|0.95566	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	535;454;454|.	Q5HYA8;B3KRU5;G5E9H2|.	MKS3_HUMAN;.;.|.	P|T	535;454|183	ENSP00000389998:A535P;ENSP00000386966:A454P|.	ENSP00000314488:A525P|.	A|S	+|+	1|2	0|0	TMEM67|TMEM67	94874629|94874629	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.997000|0.997000	0.91878|0.91878	6.318000|6.318000	0.72866|0.72866	2.622000|2.622000	0.88805|0.88805	0.655000|0.655000	0.94253|0.94253	GCT|AGC	.		0.368	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94805453	G	C	94805453	3	2	58	1	0	0	0	0	1	0	0	0	16228	971	34	4	1803	4	TMEM67	8	94805453	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	56778017	94805453	51558569	46	5611											
FAM91A1	157769	broad.mit.edu	37	chr8	124796777	124796777	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttgaaactctactctataaGatatttgtttcaatagatga	14	17	5	5	0	3	4	1	2	2	2	3	4	3	4	0	0	2	1	0	0	7	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:124796777G>C	ENST00000334705.7	+	9	1017	c.771G>C	c.(769-771)aaG>aaC	p.K257N	FAM91A1_ENST00000521166.1_Missense_Mutation_p.K257N	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	257										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TACTCTATAAGATATTTGTTT	0.328																																					p.K257N													.	FAM91A1-91	0			c.G771C						.						72	67	69					8																	124796777		1806	4060	5866	SO:0001583	missense	157769	exon9			CTATAAGATATTT	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.771G>C	8.37:g.124796777G>C	ENSP00000335082:p.Lys257Asn	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	32	6	NM_144963	0	0	5	14	9	B6YY23|Q658T5|Q8TE89	Missense_Mutation	SNP	ENST00000334705.7	37	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685454	0.68157	.	.	ENSG00000176853	ENST00000521166;ENST00000334705	T;T	0.53423	0.62;1.19	5.68	1.72	0.24424	.	0.000000	0.85682	D	0.000000	T	0.61035	0.2315	L	0.60455	1.87	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.60084	-0.7332	10	0.72032	D	0.01	.	11.3042	0.49325	0.2407:0.0:0.7593:0.0	.	257;257	E7ER68;Q658Y4	.;F91A1_HUMAN	N	257	ENSP00000429491:K257N;ENSP00000335082:K257N	ENSP00000335082:K257N	K	+	3	2	FAM91A1	124865958	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.983000	0.40648	0.089000	0.17243	0.644000	0.83932	AAG	.		0.328	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		C	124796777	G	C	124796777	3	2	58	1	0	0	0	0	1	0	0	0	5670	933	33	4	805	4	FAM91A1	8	124796777	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	29991324	124796777	21567245	47	5612											
DNAJC25	548645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	114412019	114412019	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccttttcacctatgctcatAtatagtttggtattgtcggt	7	19	7	8	1	2	0	2	0	0	0	4	0	3	0	2	2	1	3	2	2	5	9			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:114412019A>G	ENST00000313525.3	+	3	832	c.776A>G	c.(775-777)tAt>tGt	p.Y259C	DNAJC25-GNG10_ENST00000374294.3_Intron|DNAJC25_ENST00000556107.1_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	259						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						CTATGCTCATATATAGTTTGG	0.328																																					p.Y259C		.											.	DNAJC25-22	0			c.A776G						.						48	50	49					9																	114412019		1817	4067	5884	SO:0001583	missense	548645	exon3			GCTCATATATAGT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"Heat shock proteins / DNAJ (HSP40)"	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.776A>G	9.37:g.114412019A>G	ENSP00000320650:p.Tyr259Cys	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	178	41	NM_001015882	0	0	6	18	12	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	37	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039309	0.55003	.	.	ENSG00000059769	ENST00000313525	T	0.52057	0.68	6.17	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.49729	0.1574	M	0.79475	2.455	0.80722	D	1	B	0.20887	0.049	B	0.19666	0.026	T	0.49244	-0.8960	10	0.56958	D	0.05	-6.1843	11.1739	0.48588	0.9308:0.0:0.0692:0.0	.	259	Q9H1X3	DJC25_HUMAN	C	259	ENSP00000320650:Y259C	ENSP00000320650:Y259C	Y	+	2	0	DNAJC25	113451840	1.000000	0.71417	0.055000	0.19348	0.793000	0.44817	6.943000	0.75934	1.144000	0.42321	0.533000	0.62120	TAT	.		0.328	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882		G	114412019	A	G	114412019	3	3	58	1	0	0	0	0	1	0	0	0	4654	449	16	3	786	3	DNAJC25	9	114412019	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		114412019	26801412	48	5613											
ANGPTL2	23452	broad.mit.edu	37	chr9	129870363	129870363	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggcggggcagcggggggTggctgggggacgggcctggc	2	3	27	9	4	0	0	0	0	0	0	0	1	0	1	1	12	1	2	1	12	0	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:129870363T>G	ENST00000373425.3	-	2	1265	c.648A>C	c.(646-648)ccA>ccC	p.P216P	RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000259351.5_Intron|ANGPTL2_ENST00000491991.1_5'Flank|ANGPTL2_ENST00000373417.1_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	216					multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CAGCGGGGGGTGGCTGGGGGA	0.637																																					p.P216P													.	ANGPTL2-90	0			c.A648C						.						23	24	24					9																	129870363		2203	4300	6503	SO:0001819	synonymous_variant	23452	exon2			GGGGGGTGGCTGG	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"Fibrinogen C domain containing"	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.648A>C	9.37:g.129870363T>G		Somatic	76	10		WXS	Illumina HiSeq	Phase_I	68	10	NM_012098	0	0	33	35	2	Q5JT58|Q8NCH7	Silent	SNP	ENST00000373425.3	37	CCDS6868.1																																																																																			.		0.637	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		G	129870363	T	G	129870363	2	3	58	1	0	0	0	0	0	0	0	1	614	1683	59	5		5	ANGPTL2	9	129870363	Silent	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	15458344	129870363	11343068	49	5614											
MLLT10	8028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	21970293	21970293	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatcggcatgatggagctTgcccaacaactagtaagttg	12	10	11	8	1	0	1	0	1	0	0	1	2	0	2	1	2	4	5	1	2	5	5			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:21970293T>A	ENST00000307729.7	+	12	1832	c.1654T>A	c.(1654-1656)Tgc>Agc	p.C552S	MLLT10_ENST00000446906.2_Missense_Mutation_p.C552S|MLLT10_ENST00000377072.3_Missense_Mutation_p.C552S|MLLT10_ENST00000377059.3_Missense_Mutation_p.C552S			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	552	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						TGATGGAGcttgcccaacaac	0.428			T	"MLL, PICALM, CDK6"	AL																																p.C552S		.		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	.	MLLT10-658	0			c.T1654A						.						118	114	115					10																	21970293		2203	4300	6503	SO:0001583	missense	8028	exon11			GGAGCTTGCCCAA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.1654T>A	10.37:g.21970293T>A	ENSP00000307411:p.Cys552Ser	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	97	29	NM_001195626	0	0	0	1	1	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	37	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.266891	0.23136	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059;ENST00000438473;ENST00000538639	T;T;T;T	0.14766	2.5;2.48;2.48;2.48	4.67	4.67	0.58626	.	0.392955	0.33309	N	0.005051	T	0.08670	0.0215	L	0.38175	1.15	0.48135	D	0.999596	B;B;B;B	0.33694	0.008;0.001;0.421;0.0	B;B;B;B	0.21360	0.004;0.0;0.034;0.001	T	0.22034	-1.0228	10	0.13470	T	0.59	.	10.6549	0.45669	0.0:0.0:0.0:1.0	.	247;552;552;552	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	S	552;552;552;398;552;195;194	ENSP00000366272:C552S;ENSP00000401406:C552S;ENSP00000307411:C552S;ENSP00000366258:C552S	ENSP00000307411:C552S	C	+	1	0	MLLT10	22010299	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.116000	0.41930	2.095000	0.63458	0.477000	0.44152	TGC	.		0.428	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1			A	21970293	T	A	21970293	3	1	58	1	0	0	0	0	1	0	0	0	9651	1812	63	5	1696	5	MLLT10	10	21970293	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		21970293	113564454	50	5615											
ENKUR	219670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	25288439	25288439	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagttttagctttttgcatGtcatcttttacagttgcctt	6	20	7	8	0	2	0	1	0	1	0	2	0	2	0	1	0	4	5	1	0	2	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:25288439G>T	ENST00000331161.4	-	2	333	c.114C>A	c.(112-114)gaC>gaA	p.D38E	ENKUR_ENST00000376363.1_Missense_Mutation_p.D38E	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	38						motile cilium (GO:0031514)				endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CTTTTTGCATGTCATCTTTTA	0.299																																					p.D38E		.											.	ENKUR-90	0			c.C114A						.						107	95	99					10																	25288439		2201	4297	6498	SO:0001583	missense	219670	exon2			TTGCATGTCATCT	AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"chromosome 10 open reading frame 63"	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.114C>A	10.37:g.25288439G>T	ENSP00000331044:p.Asp38Glu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	86	19	NM_145010	0	0	0	0	0	A8K8Y0|D3DRV2	Missense_Mutation	SNP	ENST00000331161.4	37	CCDS7146.1	.	.	.	.	.	.	.	.	.	.	G	2.150	-0.394650	0.04899	.	.	ENSG00000151023	ENST00000331161;ENST00000376363	.	.	.	5.98	0.497	0.16902	.	0.090535	0.85682	D	0.000000	T	0.07413	0.0187	N	0.02539	-0.55	0.09310	N	0.999997	B	0.06786	0.001	B	0.01281	0.0	T	0.32079	-0.9920	9	0.02654	T	1	-22.9569	2.4844	0.04595	0.1405:0.2598:0.3993:0.2004	.	38	Q8TC29	ENKUR_HUMAN	E	38	.	ENSP00000331044:D38E	D	-	3	2	ENKUR	25328445	0.018000	0.18449	0.721000	0.30653	0.930000	0.56654	-0.003000	0.12901	0.428000	0.26173	0.591000	0.81541	GAC	.		0.299	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010		T	25288439	G	T	25288439	3	4	58	1	0	0	0	0	1	0	0	0	5133	1368	48	4	676	4	ENKUR	10	25288439	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3318146	25288439	110246308	51	5616											
HK1	3098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	71136714	71136714	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagaagatggtcagtggcatGtacttgggagagctggttcg	9	10	17	5	1	1	3	1	0	0	3	2	5	1	3	0	4	2	4	0	4	2	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:71136714G>T	ENST00000359426.6	+	8	1004	c.900G>T	c.(898-900)atG>atT	p.M300I	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000360289.2_Missense_Mutation_p.M288I|HK1_ENST00000448642.2_Missense_Mutation_p.M335I|HK1_ENST00000298649.3_Missense_Mutation_p.M299I|HK1_ENST00000404387.2_Missense_Mutation_p.M304I	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	300	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						TCAGTGGCATGTACTTGGGAG	0.567																																					p.M304I		.											.	HK1-252	0			c.G912T						.						163	143	150					10																	71136714		2203	4300	6503	SO:0001583	missense	3098	exon11			TGGCATGTACTTG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.900G>T	10.37:g.71136714G>T	ENSP00000352398:p.Met300Ile	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	255	59	NM_033498	0	0	20	27	7	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	37	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413479	0.62511	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7	4.94	4.94	0.65067	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	M	0.86573	2.825	0.80722	D	1	B;B;B;B;B;P	0.39717	0.191;0.191;0.004;0.013;0.05;0.684	B;B;B;B;B;B	0.37267	0.243;0.16;0.012;0.089;0.078;0.245	T	0.30880	-0.9963	10	0.72032	D	0.01	-26.1047	18.1516	0.89676	0.0:0.0:1.0:0.0	.	300;300;299;335;304;288	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	I	288;335;304;299;300;300	ENSP00000353433:M288I;ENSP00000402103:M335I;ENSP00000384774:M304I;ENSP00000298649:M299I;ENSP00000352398:M300I	ENSP00000298649:M299I	M	+	3	0	HK1	70806720	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	7.941000	0.87700	2.293000	0.77203	0.585000	0.79938	ATG	.		0.567	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		T	71136714	G	T	71136714	3	4	58	1	0	0	0	0	1	0	0	0	7211	1377	48	4	1108	4	HK1	10	71136714	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	45848275	71136714	64398033	52	5617											
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104103846	104103846	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaatgtattccttcgacctTttctggaagtgattcgctct	7	16	7	11	2	2	1	0	1	2	0	5	3	3	2	3	1	0	2	3	1	3	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:104103846T>G	ENST00000369983.3	+	4	462	c.202T>G	c.(202-204)Ttt>Gtt	p.F68V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	68					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTTCGACCTTTTCTGGAAGT	0.428																																					p.F68V		.											.	GBF1-91	0			c.T202G						.						163	145	151					10																	104103846		2203	4300	6503	SO:0001583	missense	8729	exon4			CGACCTTTTCTGG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.202T>G	10.37:g.104103846T>G	ENSP00000359000:p.Phe68Val	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	116	27	NM_001199378	0	0	4	5	1	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.967181	0.92855	.	.	ENSG00000107862	ENST00000369983	T	0.68025	-0.3	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.85741	0.5767	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.998;0.999;0.994;0.999	D	0.88884	0.3341	10	0.87932	D	0	-13.687	16.3736	0.83374	0.0:0.0:0.0:1.0	.	68;68;68;68	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	68	ENSP00000359000:F68V	ENSP00000359000:F68V	F	+	1	0	GBF1	104093836	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.922000	0.87538	2.273000	0.75805	0.482000	0.46254	TTT	.		0.428	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104103846	T	G	104103846	3	3	58	1	0	0	0	0	1	0	0	0	6291	1841	64	5	212	5	GBF1	10	104103846	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	32967132	104103846	31430901	53	5618											
OR52M1	119772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4567069	4567069	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatcctggactcagtggctAttgctgcatcctatgtgatg	7	14	11	9	0	1	2	1	2	0	0	3	3	3	3	2	2	2	3	2	2	2	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:4567069A>T	ENST00000360213.1	+	1	649	c.649A>T	c.(649-651)Att>Ttt	p.I217F		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCAGTGGCTATTGCTGCATC	0.532																																					p.I217F		.											.	OR52M1-68	0			c.A649T						.						267	251	257					11																	4567069		2201	4298	6499	SO:0001583	missense	119772	exon1			GTGGCTATTGCTG	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"GPCR / Class A : Olfactory receptors"	15225	protein-coding gene	gene with protein product			"olfactory receptor, family 52, subfamily M, member 1 pseudogene"	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.649A>T	11.37:g.4567069A>T	ENSP00000353343:p.Ile217Phe	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	144	32	NM_001004137	0	0	0	0	0		Missense_Mutation	SNP	ENST00000360213.1	37	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838966	0.51057	.	.	ENSG00000197790	ENST00000360213	T	0.00333	8.07	5.01	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000207	T	0.01092	0.0036	H	0.96916	3.905	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.35450	-0.9788	10	0.87932	D	0	.	5.4232	0.16411	0.7442:0.0:0.0856:0.1702	.	217	Q8NGK5	O52M1_HUMAN	F	217	ENSP00000353343:I217F	ENSP00000353343:I217F	I	+	1	0	OR52M1	4523645	1.000000	0.71417	0.265000	0.24526	0.813000	0.45954	4.973000	0.63763	0.995000	0.38917	0.528000	0.53228	ATT	.		0.532	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		T	4567069	A	T	4567069	3	4	58	1	0	0	0	0	1	0	0	0	11152	449	16	5	651	5	OR52M1	11	4567069	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		4567069	130439447	54	5619											
RIC3	79608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	8132577	8132577	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcccattctttcagctatttCttcagcagaaagttcttttg	8	18	5	10	0	5	1	2	0	3	1	6	1	6	1	1	0	2	3	1	0	2	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:8132577C>T	ENST00000309737.6	-	6	777	c.778G>A	c.(778-780)Gaa>Aaa	p.E260K	RIC3_ENST00000425599.2_Missense_Mutation_p.E179K|RIC3_ENST00000343202.4_Missense_Mutation_p.E259K|RIC3_ENST00000335425.7_Missense_Mutation_p.E78K|RIC3_ENST00000539720.1_Missense_Mutation_p.E211K|RIC3_ENST00000396677.2_Missense_Mutation_p.E98K|RIC3_ENST00000530060.1_5'UTR			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	260					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCAGCTATTTCTTCAGCAGAA	0.428																																					p.E260K		.											.	RIC3-155	0			c.G778A						.						112	111	112					11																	8132577		2201	4296	6497	SO:0001583	missense	79608	exon6			CTATTTCTTCAGC		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.778G>A	11.37:g.8132577C>T	ENSP00000308820:p.Glu260Lys	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	231	47	NM_001206671	0	0	1	4	3	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626069	0.87560	.	.	ENSG00000166405	ENST00000396677;ENST00000335425;ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.37752	1.24;1.24;1.26;1.18;1.2	6.06	6.06	0.98353	.	0.154914	0.45606	D	0.000353	T	0.57651	0.2068	M	0.72118	2.19	0.51233	D	0.999912	D;D;D;D;D;D	0.67145	0.996;0.971;0.99;0.99;0.99;0.99	P;P;P;P;P;P	0.62560	0.904;0.651;0.817;0.857;0.857;0.766	T	0.58250	-0.7669	10	0.72032	D	0.01	.	16.0307	0.80574	0.0:0.8665:0.1335:0.0	.	288;179;78;260;259;98	B7Z1U4;B0B1U0;Q7Z5B4-3;Q7Z5B4;Q7Z5B4-5;D3DQU6	.;.;.;RIC3_HUMAN;.;.	K	98;78;259;260;288;211;179;288	ENSP00000344904:E259K;ENSP00000308820:E260K;ENSP00000443871:E211K;ENSP00000395320:E179K;ENSP00000431658:E288K	ENSP00000308820:E260K	E	-	1	0	RIC3	8089153	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.792000	0.62467	2.882000	0.98803	0.655000	0.94253	GAA	.		0.428	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557		T	8132577	C	T	8132577	3	4	58	1	0	0	0	0	1	0	0	0	13386	922	32	2	335	2	RIC3	11	8132577	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	3565508	8132577	126873939	55	5620											
LRP4	4038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46895104	46895104	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggtcttcagccctcgccCgatcactgtctccatgttgc	5	12	9	15	2	4	0	2	0	2	0	6	1	4	0	3	1	2	1	3	1	0	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:46895104C>G	ENST00000378623.1	-	29	4512	c.4270G>C	c.(4270-4272)Ggg>Cgg	p.G1424R	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1424					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		AGCCCTCGCCCGATCACTGTC	0.572																																					p.G1424R		.											.	LRP4-94	0			c.G4270C						.						80	72	75					11																	46895104		2201	4299	6500	SO:0001583	missense	4038	exon29			CTCGCCCGATCAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4270G>C	11.37:g.46895104C>G	ENSP00000367888:p.Gly1424Arg	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	84	25	NM_002334	0	0	3	5	2	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347774	0.82022	.	.	ENSG00000134569	ENST00000378623	D	0.95690	-3.78	5.91	5.91	0.95273	Six-bladed beta-propeller, TolB-like (1);	0.048798	0.85682	D	0.000000	D	0.91975	0.7458	N	0.12527	0.23	0.80722	D	1	P	0.35107	0.484	B	0.41088	0.347	D	0.89603	0.3836	10	0.22706	T	0.39	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	1424	O75096	LRP4_HUMAN	R	1424	ENSP00000367888:G1424R	ENSP00000367888:G1424R	G	-	1	0	LRP4	46851680	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	5.943000	0.70211	2.793000	0.96121	0.655000	0.94253	GGG	.		0.572	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		G	46895104	C	G	46895104	3	3	58	1	0	0	0	0	1	0	0	0	8984	652	23	4	1487	4	LRP4	11	46895104	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	38762527	46895104	88111412	56	5621											
BRMS1	25855	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr11	66108763	66108763	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctcagcccccacttccTccagccgcaaccgcagctga	7	7	6	21	2	2	1	1	1	1	0	5	1	4	1	6	0	4	3	6	0	1	1	rs199933125	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:66108763T>A	ENST00000359957.3	-	4	432	c.272A>T	c.(271-273)gAg>gTg	p.E91V	RP11-867G23.12_ENST00000526655.1_RNA|BRMS1_ENST00000425825.2_Missense_Mutation_p.E91V	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1	91					apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						CCCCACTTCCTCCAGCCGCAA	0.602																																					p.E91V	GBM(7;55 307 2662 20856 28942)	.											.	BRMS1-90	0			c.A272T						.						32	36	35					11																	66108763		2200	4295	6495	SO:0001583	missense	25855	exon4			ACTTCCTCCAGCC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.272A>T	11.37:g.66108763T>A	ENSP00000353042:p.Glu91Val	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	72	15	NM_015399	3	0	15	30	12	Q6IAI2	Missense_Mutation	SNP	ENST00000359957.3	37	CCDS8135.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.718118	0.68844	.	.	ENSG00000174744	ENST00000425825;ENST00000359957;ENST00000530756	.	.	.	4.17	4.17	0.49024	.	0.121890	0.53938	D	0.000052	T	0.54431	0.1858	L	0.45228	1.405	0.44175	D	0.99698	B;B	0.31790	0.256;0.34	B;B	0.41135	0.348;0.343	T	0.55075	-0.8197	9	0.38643	T	0.18	-29.1846	11.4756	0.50295	0.0:0.0:0.0:1.0	.	91;91	Q9HCU9;G5E9I4	BRMS1_HUMAN;.	V	91	.	ENSP00000353042:E91V	E	-	2	0	BRMS1	65865339	0.983000	0.35010	1.000000	0.80357	0.998000	0.95712	1.690000	0.37711	1.889000	0.54706	0.460000	0.39030	GAG	T|0.993;C|0.007		0.602	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399		A	66108763	T	A	66108763	3	1	58	1	0	0	0	0	1	0	0	0	1519	1551	54	5	640	5	BRMS1	11	66108763	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	19213659	66108763	68897753	57	5622											
CASP1	834	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	104901192	104901192	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattgcagataatgagagcAagacgtgtgcggcttgactt	11	11	12	7	2	1	4	1	2	0	3	1	5	1	4	0	1	3	3	0	1	2	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:104901192A>C	ENST00000533400.1	-	5	527	c.492T>G	c.(490-492)ctT>ctG	p.L164L	CASP1_ENST00000526568.1_Silent_p.L71L|CASP1_ENST00000594519.1_Silent_p.L71L|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000393136.4_Silent_p.L143L|CASP1_ENST00000534497.1_Silent_p.L71L|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000436863.3_Silent_p.L164L|CASP1_ENST00000528974.1_Silent_p.L125L|CASP1_ENST00000525825.1_Silent_p.L143L|CASP1_ENST00000598974.1_Silent_p.L164L|CASP1_ENST00000593315.1_Silent_p.L143L|CASP1_ENST00000446369.1_Silent_p.L71L|CASP1_ENST00000527979.1_Silent_p.L127L|CASP1_ENST00000415981.2_Intron	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	164					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TAATGAGAGCAAGACGTGTGC	0.403																																					p.L164L	NSCLC(41;1246 1743 4934)												.	CASP1-661	0			c.T492G						.						127	112	117					11																	104901192		2202	4299	6501	SO:0001819	synonymous_variant	834	exon5			GAGAGCAAGACGT	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"Caspases"	1499	protein-coding gene	gene with protein product	"caspase-1", "interleukin 1, beta, convertase"	147678	"caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)", "caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.492T>G	11.37:g.104901192A>C		Somatic	75	1		WXS	Illumina HiSeq	Phase_I	57	14	NM_001257118	0	0	25	28	3	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																			.		0.403	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292		C	104901192	A	C	104901192	2	2	58	1	0	0	0	0	0	0	0	1	2674	117	5	5		5	CASP1	11	104901192	Silent	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	38792429	104901192	30105324	58	5623											
OR10G9	219870	bcgsc.ca	37	chr11	123894195	123894195	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tctgcactctgctgtccagaCcatattgactttccatttgc	7	15	6	13	0	2	2	0	1	2	1	4	2	4	2	3	0	3	2	3	0	1	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:123894195C>T	ENST00000375024.1	+	1	476	c.476C>T	c.(475-477)aCc>aTc	p.T159I		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GCTGTCCAGACCATATTGACT	0.552																																					p.T159I													.	OR10G9-92	0			c.C476T						.						181	158	166					11																	123894195		2201	4296	6497	SO:0001583	missense	219870	exon1			TCCAGACCATATT	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"GPCR / Class A : Olfactory receptors"	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.476C>T	11.37:g.123894195C>T	ENSP00000364164:p.Thr159Ile	Somatic	361	2		WXS	Illumina HiSeq	Phase_1	307	81	NM_001001953	0	0	0	0	0		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	6.764	0.509912	0.12883	.	.	ENSG00000236981	ENST00000375024	T	0.00245	8.45	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.139097	0.33075	N	0.005307	T	0.00328	0.0010	M	0.62088	1.915	0.09310	N	0.999995	D	0.56287	0.975	P	0.62491	0.903	T	0.54029	-0.8354	10	0.13470	T	0.59	.	7.6951	0.28590	0.1822:0.6402:0.1775:0.0	.	159	Q8NGN4	O10G9_HUMAN	I	159	ENSP00000364164:T159I	ENSP00000364164:T159I	T	+	2	0	OR10G9	123399405	0.000000	0.05858	0.704000	0.30370	0.076000	0.17211	0.121000	0.15667	1.938000	0.56188	0.655000	0.94253	ACC	.		0.552	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		T	123894195	C	T	123894195	3	4	58	1	0	0	0	0	1	0	0	0	10930	507	18	2	478	2	OR10G9	11	123894195	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	18993003	123894195	11112321	59	5624											
BCDIN3D	144233	ucsc.edu;bcgsc.ca	37	chr12	50232259	50232259	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tttgccctgaagagcagaagGcttctgtcccaactggtgtt	8	12	11	10	0	1	3	0	1	1	2	2	3	2	3	2	2	3	3	2	2	3	3	rs559976366		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr12:50232259G>T	ENST00000333924.4	-	2	815	c.774C>A	c.(772-774)agC>agA	p.S258R	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	258	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						AGAGCAGAAGGCTTCTGTCCC	0.443																																					p.S258R													.	BCDIN3D-69	0			c.C774A						.						145	139	141					12																	50232259		2203	4300	6503	SO:0001583	missense	144233	exon2			CAGAAGGCTTCTG		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.774C>A	12.37:g.50232259G>T	ENSP00000335201:p.Ser258Arg	Somatic	41	0		WXS	Illumina HiSeq		38	4	NM_181708	0	0	9	9	0	A8K829	Missense_Mutation	SNP	ENST00000333924.4	37	CCDS8790.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.193431	0.38707	.	.	ENSG00000186666	ENST00000333924	T	0.45668	0.89	5.44	1.62	0.23740	Bin3-type S-adenosyl-L-methionine binding domain (1);	0.077387	0.85682	D	0.000000	T	0.41442	0.1159	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.57152	0.814	T	0.09015	-1.0694	10	0.34782	T	0.22	.	8.9521	0.35796	0.3107:0.0:0.6893:0.0	.	258	Q7Z5W3	BN3D2_HUMAN	R	258	ENSP00000335201:S258R	ENSP00000335201:S258R	S	-	3	2	BCDIN3D	48518526	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	0.640000	0.24705	0.099000	0.17552	0.491000	0.48974	AGC	.		0.443	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708		T	50232259	G	T	50232259	3	4	58	1	0	0	0	0	1	0	0	0	1358	1194	42	4	108	4	BCDIN3D	12	50232259	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		50232259	83619636	60	5625											
TAOK3	51347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	118651868	118651868	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcattctgggcaatgtgatAtaaggcactcattgcattca	11	13	9	8	0	4	1	3	1	1	0	4	1	4	1	0	2	1	3	0	2	3	5			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr12:118651868A>T	ENST00000392533.3	-	10	1181	c.691T>A	c.(691-693)Tat>Aat	p.Y231N	TAOK3_ENST00000419821.2_Missense_Mutation_p.Y231N	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCAATGTGATATAAGGCACTC	0.413																																					p.Y231N		.											.	TAOK3-933	0			c.T691A						.						153	148	150					12																	118651868		2203	4300	6503	SO:0001583	missense	51347	exon10			TGTGATATAAGGC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.691T>A	12.37:g.118651868A>T	ENSP00000376317:p.Tyr231Asn	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	83	17	NM_016281	0	0	10	14	4	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	37	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.731562	0.89390	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000538601	D;D;D	0.85484	-1.99;-1.99;-1.99	5.24	5.24	0.73138	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.072210	0.64402	D	0.000020	D	0.89245	0.6660	L	0.45228	1.405	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.90431	0.4424	10	0.87932	D	0	.	15.3625	0.74492	1.0:0.0:0.0:0.0	.	231	Q9H2K8	TAOK3_HUMAN	N	231;231;129	ENSP00000416374:Y231N;ENSP00000376317:Y231N;ENSP00000437389:Y129N	ENSP00000376317:Y231N	Y	-	1	0	TAOK3	117136251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.087000	0.94110	2.210000	0.71456	0.472000	0.43445	TAT	.		0.413	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		T	118651868	A	T	118651868	3	4	58	1	0	0	0	0	1	0	0	0	15581	449	16	5	2053	5	TAOK3	12	118651868	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	68419609	118651868	15200027	61	5626											
ATP7B	540	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	52509756	52509756	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagggatgagagcaccAcagacacagaggaggctgcc	12	3	15	11	0	0	3	0	1	0	3	0	6	0	5	2	3	3	4	2	3	0	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr13:52509756A>G	ENST00000242839.4	-	20	4253	c.4097T>C	c.(4096-4098)gTg>gCg	p.V1366A	ATP7B_ENST00000400370.3_Missense_Mutation_p.V936A|ATP7B_ENST00000344297.5_Missense_Mutation_p.V1159A|ATP7B_ENST00000418097.2_Missense_Mutation_p.V1301A|ATP7B_ENST00000400366.3_Missense_Mutation_p.V1255A|ATP7B_ENST00000417240.2_Missense_Mutation_p.V577A|ATP7B_ENST00000448424.2_Missense_Mutation_p.V1288A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1366					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGAGAGCACCACAGACACAGA	0.592									Wilson disease																												p.V1366A													.	ATP7B-92	0			c.T4097C	GRCh37	CD033178	ATP7B	D		.						28	34	32					13																	52509756		2120	4230	6350	SO:0001583	missense	540	exon20	Familial Cancer Database		AGCACCACAGACA	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.4097T>C	13.37:g.52509756A>G	ENSP00000242839:p.Val1366Ala	Somatic	186	1		WXS	Illumina HiSeq	Phase_I	144	37	NM_000053	0	0	1	5	4	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.100115	0.76983	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.99714	-6.5;-6.5;-6.5;-6.5;-6.5;-6.5;-6.5	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.99789	0.9911	H	0.94183	3.505	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.986;0.995;0.996;0.997;0.996;0.999;0.996;0.999	D	0.96956	0.9698	10	0.87932	D	0	-21.8479	15.2853	0.73822	1.0:0.0:0.0:0.0	.	1288;1318;1301;577;936;1255;1159;1366	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	A	1366;1255;1159;577;1288;936;1301	ENSP00000242839:V1366A;ENSP00000383217:V1255A;ENSP00000342559:V1159A;ENSP00000390360:V577A;ENSP00000416738:V1288A;ENSP00000383221:V936A;ENSP00000393343:V1301A	ENSP00000242839:V1366A	V	-	2	0	ATP7B	51407757	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.629000	0.90983	2.201000	0.70794	0.533000	0.62120	GTG	.		0.592	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		G	52509756	A	G	52509756	3	3	58	1	0	0	0	0	1	0	0	0	1192	159	6	3	308	3	ATP7B	13	52509756	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		52509756	62660122	62	5627											
G2E3	55632	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31081505	31081505	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggatgtctcagacttataacGacattaagtgataaatatat	16	13	7	5	1	1	2	1	1	1	1	2	4	1	3	0	1	1	0	0	1	7	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:31081505G>A	ENST00000206595.6	+	13	1747	c.1593G>A	c.(1591-1593)acG>acA	p.T531T	G2E3_ENST00000438909.2_Silent_p.T485T|G2E3_ENST00000553504.1_Silent_p.T561T	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	531	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						GACTTATAACGACATTAAGTG	0.313																																					p.T531T		.											.	G2E3-660	0			c.G1593A						.						100	103	102					14																	31081505		2203	4295	6498	SO:0001819	synonymous_variant	55632	exon13			TATAACGACATTA	AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"Zinc fingers, PHD-type"	20338	protein-coding gene	gene with protein product	"PHD finger protein 7B"	611299	"KIAA1333"	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.1593G>A	14.37:g.31081505G>A		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	175	40	NM_017769	0	0	3	3	0	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Silent	SNP	ENST00000206595.6	37	CCDS9638.1																																																																																			.		0.313	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		A	31081505	G	A	31081505	2	1	58	1	0	0	0	0	0	0	0	1	6159	1045	37	1		1	G2E3	14	31081505	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		31081505	76268035	63	5628											
FANCM	57697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	45645152	45645152	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tatccatctgaaaaaagttgCctttatgatatacctaatga	15	14	5	7	0	1	3	0	3	1	0	2	3	2	3	3	0	2	1	3	0	8	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:45645152C>G	ENST00000267430.5	+	14	3280	c.3195C>G	c.(3193-3195)tgC>tgG	p.C1065W	FANCM_ENST00000542564.2_Missense_Mutation_p.C1039W	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1065					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAAAAAGTTGCCTTTATGATA	0.299								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.C1065W		.											.	FANCM-569	0			c.C3195G						.						25	26	25					14																	45645152		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGTTGCCTTTAT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3195C>G	14.37:g.45645152C>G	ENSP00000267430:p.Cys1065Trp	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	123	31	NM_020937	0	0	1	1	0	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	6.697	0.497283	0.12762	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18657	2.79;2.79;2.2	5.23	-2.33	0.06724	.	1.440870	0.03493	N	0.216880	T	0.30885	0.0779	L	0.56769	1.78	0.09310	N	0.999999	D;D	0.58620	0.964;0.983	P;P	0.53006	0.624;0.715	T	0.38067	-0.9678	10	0.66056	D	0.02	.	5.9826	0.19415	0.0:0.3342:0.137:0.5287	.	1039;1065	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	W	1065;1039;581	ENSP00000267430:C1065W;ENSP00000442493:C1039W;ENSP00000452033:C581W	ENSP00000267430:C1065W	C	+	3	2	FANCM	44714902	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.431000	0.06965	-0.270000	0.09285	-0.229000	0.12294	TGC	.		0.299	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45645152	C	G	45645152	3	3	58	1	0	0	0	0	1	0	0	0	5690	747	26	4	3249	4	FANCM	14	45645152	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	14563647	45645152	61704388	64	5629											
DLGAP5	9787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55642723	55642723	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccaaaatttcttttgttgCttgagactcatcactaaaaa	13	15	5	8	0	3	1	2	1	1	1	3	2	3	1	1	0	2	2	1	0	5	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:55642723C>A	ENST00000247191.2	-	9	1279	c.1063G>T	c.(1063-1065)Gca>Tca	p.A355S	DLGAP5_ENST00000395425.2_Missense_Mutation_p.A355S	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	355					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TCTTTTGTTGCTTGAGACTCA	0.313																																					p.A355S		.											.	DLGAP5-92	0			c.G1063T						.						131	125	127					14																	55642723		2203	4297	6500	SO:0001583	missense	9787	exon9			TTGTTGCTTGAGA	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1063G>T	14.37:g.55642723C>A	ENSP00000247191:p.Ala355Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	73	10	NM_014750	0	0	0	0	0	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720936	0.30503	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.15952	2.38;2.38	3.83	2.93	0.34026	.	1.470090	0.03875	N	0.276195	T	0.16342	0.0393	L	0.36672	1.1	0.24747	N	0.993003	B;B	0.26902	0.163;0.095	B;B	0.30105	0.111;0.078	T	0.32798	-0.9893	10	0.13108	T	0.6	.	9.5155	0.39102	0.0:0.7848:0.2152:0.0	.	355;355	A8MTM6;Q15398	.;DLGP5_HUMAN	S	355	ENSP00000378815:A355S;ENSP00000247191:A355S	ENSP00000247191:A355S	A	-	1	0	DLGAP5	54712476	0.784000	0.28713	0.566000	0.28421	0.957000	0.61999	1.018000	0.30002	1.213000	0.43380	0.650000	0.86243	GCA	.		0.313	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		A	55642723	C	A	55642723	3	1	58	1	0	0	0	0	1	0	0	0	4574	797	28	4	1616	4	DLGAP5	14	55642723	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	9997571	55642723	51706817	65	5630											
APBA2	321	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	29346718	29346718	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccggcgcctccccctacCgcctgaggcgtggggatggg	5	5	15	16	4	0	1	0	1	0	0	1	2	1	2	6	5	1	0	6	5	1	1	rs149847107		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:29346718C>T	ENST00000558402.1	+	5	1230	c.631C>T	c.(631-633)Cgc>Tgc	p.R211C	APBA2_ENST00000558330.1_Missense_Mutation_p.R211C|APBA2_ENST00000411764.1_Missense_Mutation_p.R211C|APBA2_ENST00000558259.1_Missense_Mutation_p.R211C|APBA2_ENST00000561069.1_Missense_Mutation_p.R211C			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	211	STXBP1-binding.			DEPSVLEAHDQEEDGHYCASKEGYQDYYPEEANGNTGASPY RLRR -> MSPPSLRPMTRKKMVTMCQQRGLPGLLPRGGQR EHRRLPLPPEA (in Ref. 1; AAC39767). {ECO:0000305}.	in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CTCCCCCTACCGCCTGAGGCG	0.602													C|||	1	0.000199681	0	0	5008	,	,		20367	0		0.001	False		,,,				2504	0				p.R211C		.											.	APBA2-90	0			c.C631T						.	C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	44	34	37		631,631	2.9	0.1	15	dbSNP_134	37	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	APBA2	NM_001130414.1,NM_005503.3	180,180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	211/738,211/750	29346718	1,13001	2201	4300	6501	SO:0001583	missense	321	exon3			CCCTACCGCCTGA	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.631C>T	15.37:g.29346718C>T	ENSP00000453293:p.Arg211Cys	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	162	10	NM_005503	0	0	0	0	0	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.31	1.898247	0.33535	0.0	1.16E-4	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.47177	0.85	4.77	2.89	0.33648	.	0.517876	0.20604	N	0.089082	T	0.42720	0.1215	L	0.54323	1.7	0.18873	N	0.999985	B;D;B	0.63046	0.122;0.992;0.06	B;B;B	0.42916	0.008;0.402;0.006	T	0.35895	-0.9770	10	0.72032	D	0.01	.	10.2679	0.43466	0.0:0.8387:0.0:0.1613	.	211;211;211	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	C	211	ENSP00000409312:R211C	ENSP00000219865:R211C	R	+	1	0	APBA2	27134010	0.000000	0.05858	0.085000	0.20634	0.465000	0.32709	0.245000	0.18142	0.541000	0.28827	-0.142000	0.14014	CGC	C|1.000;T|0.000		0.602	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29346718	C	T	29346718	3	4	58	1	0	0	0	0	1	0	0	0	757	652	23	1	633	1	APBA2	15	29346718	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		29346718	73184674	66	5631											
AP4E1	23431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51285700	51285700	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtataatggagaatgtaGatcaagctataactaaaaag	20	9	9	3	0	1	3	1	0	0	3	1	4	1	3	0	1	2	3	0	1	10	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:51285700G>T	ENST00000261842.5	+	17	2330	c.2224G>T	c.(2224-2226)Gat>Tat	p.D742Y	AP4E1_ENST00000560508.1_Missense_Mutation_p.D667Y	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	742					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GGAGAATGTAGATCAAGCTAT	0.408																																					p.D742Y		.											.	AP4E1-90	0			c.G2224T						.						105	92	97					15																	51285700		2196	4294	6490	SO:0001583	missense	23431	exon17			AATGTAGATCAAG	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2224G>T	15.37:g.51285700G>T	ENSP00000261842:p.Asp742Tyr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	56	8	NM_007347	0	0	2	2	0	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969624	0.53614	.	.	ENSG00000081014	ENST00000261842	T	0.19250	2.16	5.29	5.29	0.74685	.	0.278842	0.38778	N	0.001568	T	0.22898	0.0553	N	0.24115	0.695	0.35318	D	0.784497	P	0.51653	0.947	P	0.47744	0.556	T	0.19844	-1.0293	10	0.72032	D	0.01	-17.9497	17.9229	0.88973	0.0:0.0:1.0:0.0	.	742	Q9UPM8	AP4E1_HUMAN	Y	742	ENSP00000261842:D742Y	ENSP00000261842:D742Y	D	+	1	0	AP4E1	49072992	0.989000	0.36119	0.774000	0.31636	0.968000	0.65278	3.111000	0.50360	2.455000	0.83008	0.563000	0.77884	GAT	.		0.408	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51285700	G	T	51285700	3	4	58	1	0	0	0	0	1	0	0	0	752	942	33	4	2290	4	AP4E1	15	51285700	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	21938982	51285700	51245692	67	5632											
PKM2	5315	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72499107	72499107	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctccagaggatagtcccCtttggctgtttctccagaca	8	11	9	13	0	1	2	0	0	1	2	4	3	3	3	5	2	1	2	5	2	1	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:72499107C>T	ENST00000335181.5	-	8	1205	c.1102G>A	c.(1102-1104)Ggg>Agg	p.G368R	PKM_ENST00000319622.6_Missense_Mutation_p.G368R|PKM_ENST00000568883.1_Missense_Mutation_p.G203R|PKM_ENST00000568459.1_Missense_Mutation_p.G368R|PKM_ENST00000449901.2_Missense_Mutation_p.G353R|PKM_ENST00000565184.1_Missense_Mutation_p.G368R|PKM_ENST00000565154.1_Missense_Mutation_p.G368R|PKM_ENST00000389093.3_Missense_Mutation_p.G368R	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	368	Interaction with POU5F1.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	GGATAGTCCCCTTTGGCTGTT	0.622																																					p.G442R													.	.	0			c.G1324A						.						55	51	53					15																	72499107		2199	4297	6496	SO:0001583	missense	5315	exon9			AGTCCCCTTTGGC	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.1102G>A	15.37:g.72499107C>T	ENSP00000334983:p.Gly368Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	36	4	NM_001206796	0	0	492	889	397	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Missense_Mutation	SNP	ENST00000335181.5	37	CCDS32284.1	.	.	.	.	.	.	.	.	.	.	C	34	5.293462	0.95546	.	.	ENSG00000067225	ENST00000319622;ENST00000335181;ENST00000434220;ENST00000327974;ENST00000389093;ENST00000449901	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.23	5.23	0.72850	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	H	0.99642	4.675	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97965	1.0340	10	0.87932	D	0	-24.602	19.1591	0.93524	0.0:1.0:0.0:0.0	.	294;353;348;348;368;368;203;295;203	B4DNK4;B4DUU6;B4DRT3;E7EUQ8;P14618;P14618-2;Q504U3;E9PF79;E7EUJ4	.;.;.;.;KPYM_HUMAN;.;.;.;.	R	368;368;295;203;368;353	ENSP00000320171:G368R;ENSP00000334983:G368R;ENSP00000373745:G368R;ENSP00000403365:G353R	ENSP00000320171:G368R	G	-	1	0	PKM2	70286161	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.818000	0.86416	2.596000	0.87737	0.561000	0.74099	GGG	.		0.622	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1			T	72499107	C	T	72499107	3	4	58	1	0	0	0	0	1	0	0	0	12003	681	24	2	680	2	PKM2	15	72499107	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	21213407	72499107	30032285	68	5633											
MESP2	145873	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90321562	90321562	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccgcctgggcatcttctaCtaaatggcctcggcttccct	5	11	9	16	2	2	0	0	0	2	0	4	0	3	0	4	3	1	2	4	3	3	4	rs375171689		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:90321562C>T	ENST00000341735.3	+	2	1191	c.1191C>T	c.(1189-1191)taC>taT	p.Y397Y	MESP2_ENST00000560219.1_Silent_p.Y99Y|MESP2_ENST00000558723.1_3'UTR	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	397					mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			GCATCTTCTACTAAATGGCCT	0.537																																					p.Y397Y													.	MESP2-68	0			c.C1191T						.	T		1,3677		0,1,1838	25	28	27		1191	1.2	0.3	15		27	0,8160		0,0,4080	no	coding-synonymous	MESP2	NM_001039958.1		0,1,5918	TT,TC,CC		0.0,0.0272,0.0084		397/398	90321562	1,11837	1839	4080	5919	SO:0001819	synonymous_variant	145873	exon2			CTTCTACTAAATG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"Basic helix-loop-helix proteins"	29659	protein-coding gene	gene with protein product		605195	"mesoderm posterior 2 homolog (mouse)"			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.1191C>T	15.37:g.90321562C>T		Somatic	156	1		WXS	Illumina HiSeq	Phase_I	143	32	NM_001039958	0	0	1	1	0	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																			.		0.537	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		T	90321562	C	T	90321562	2	4	58	1	0	0	0	0	0	0	0	1	9508	576	20	2		2	MESP2	15	90321562	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	17822455	90321562	12209830	69	5634											
CHD2	1106	hgsc.bcm.edu	37	chr15	93541851	93541851	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgacaggtggggaagaGgtgagtacgctgccagctgg	8	7	19	7	1	0	3	0	2	0	1	0	4	0	4	1	5	3	4	1	5	2	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:93541851G>T	ENST00000394196.4	+	31	5076	c.4008G>T	c.(4006-4008)gaG>gaT	p.E1336D	CHD2_ENST00000557381.1_Splice_Site_p.E1336D	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1336					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GTGGGGAAGAGGTGAGTACGC	0.552																																					p.E1336D		.											.	CHD2-229	0			c.G4008T						.						92	92	92					15																	93541851		2197	4298	6495	SO:0001630	splice_region_variant	1106	exon31			GGAAGAGGTGAGT	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4008+1G>T	15.37:g.93541851G>T		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_001271	0	0	1	1	0	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702923	0.48412	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.89939	-2.59;-2.58	5.16	5.16	0.70880	.	0.000000	0.34484	U	0.003936	D	0.92410	0.7591	L	0.59436	1.845	0.80722	D	1	D;D	0.67145	0.984;0.996	D;P	0.68192	0.956;0.789	D	0.89962	0.4087	10	0.22109	T	0.4	-32.7161	17.2006	0.86904	0.0:0.0:1.0:0.0	.	1336;1336	O14647;O14647-2	CHD2_HUMAN;.	D	1336	ENSP00000377747:E1336D;ENSP00000451366:E1336D	ENSP00000377747:E1336D	E	+	3	2	CHD2	91342855	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	8.987000	0.93497	2.578000	0.87016	0.561000	0.74099	GAG	.		0.552	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	Missense_Mutation	T	93541851	G	T	93541851	5	4	58	1	0	0	0	0	0	0	1	0	3331	1014	35	4	4130	4	CHD2	15	93541851	Splice_Site	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3220289	93541851	8989541	70	5635											
CCDC64B	146439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3078701	3078701	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcaatggcttgaggcttacTtgttcacggcctcgtcccgg	5	12	12	12	3	2	1	2	1	0	0	4	1	3	1	2	4	1	3	2	4	2	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3078701T>A	ENST00000572449.1	-	8	1300	c.1238A>T	c.(1237-1239)aAg>aTg	p.K413M	CCDC64B_ENST00000389347.4_Splice_Site_p.K413M|CCDC64B_ENST00000573514.1_Splice_Site_p.K206M			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	413										breast(1)|endometrium(2)|large_intestine(1)	4						TGAGGCTTACTTGTTCACGGC	0.637																																					p.K413M		.											.	.	0			c.A1238T						.						35	49	44					16																	3078701		1994	4127	6121	SO:0001630	splice_region_variant	146439	exon7			GCTTACTTGTTCA	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1238+1A>T	16.37:g.3078701T>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	70	16	NM_001103175	0	0	0	0	0	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.656736	0.67586	.	.	ENSG00000162069	ENST00000389347	T	0.39592	1.07	4.28	4.28	0.50868	.	0.067259	0.56097	D	0.000027	T	0.57989	0.2091	M	0.72118	2.19	0.58432	D	0.999993	D	0.76494	0.999	D	0.63192	0.912	T	0.59936	-0.7360	9	.	.	.	-53.638	11.4408	0.50096	0.0:0.0:0.0:1.0	.	413	A1A5D9	BICR2_HUMAN	M	413	ENSP00000373998:K413M	.	K	-	2	0	CCDC64B	3018702	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	2.792000	0.47837	1.814000	0.52955	0.459000	0.35465	AAG	.		0.637	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		Missense_Mutation	A	3078701	T	A	3078701	5	1	58	1	0	0	0	0	0	0	1	0	2842	1623	56	5	300	5	CCDC64B	16	3078701	Splice_Site	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		3078701	87276052	71	5636											
ZNF75A	7627	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3367508	3367508	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagagttagctctgaccttaTtaagcaccaaagaattcaca	15	10	6	10	0	2	3	1	1	1	2	2	3	2	3	2	0	2	3	2	0	5	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3367508T>C	ENST00000574298.1	+	6	1003	c.530T>C	c.(529-531)aTt>aCt	p.I177T	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	177					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)|large_intestine(3)|lung(7)|prostate(1)	12						TCTGACCTTATTAAGCACCAA	0.378																																					p.I177T													.	ZNF75A-153	0			c.T530C						.						80	78	79					16																	3367508		2197	4300	6497	SO:0001583	missense	7627	exon6			ACCTTATTAAGCA	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"Zinc fingers, C2H2-type", "-"	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.530T>C	16.37:g.3367508T>C	ENSP00000459566:p.Ile177Thr	Somatic	161	1		WXS	Illumina HiSeq	Phase_I	174	43	NM_153028	0	0	7	11	4	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	37	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	T	9.976	1.226686	0.22542	.	.	ENSG00000162086	ENST00000293995	.	.	.	4.57	3.47	0.39725	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45606	D	0.000353	T	0.12518	0.0304	N	0.04805	-0.155	0.21933	N	0.999462	B	0.18013	0.025	B	0.18561	0.022	T	0.33394	-0.9870	9	0.02654	T	1	.	4.0488	0.09785	0.181:0.0983:0.0:0.7207	.	177	Q96N20	ZN75A_HUMAN	T	177	.	ENSP00000293995:I177T	I	+	2	0	ZNF75A	3307509	0.000000	0.05858	1.000000	0.80357	0.986000	0.74619	0.323000	0.19593	0.889000	0.36185	0.455000	0.32223	ATT	.		0.378	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028		C	3367508	T	C	3367508	3	2	58	1	0	0	0	0	1	0	0	0	18165	1493	52	3	540	3	ZNF75A	16	3367508	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	288807	3367508	86987245	72	5637											
NLRC3	197358	ucsc.edu	37	chr16	3593429	3593429	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactggaatacttactcgaGaatctccaaggttctgttca	12	12	8	9	1	3	2	1	0	2	2	5	4	3	3	1	2	2	2	1	2	5	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3593429G>T	ENST00000301749.7	-	0	3340				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ACTTACTCGAGAATCTCCAAG	0.493																																					p.L979I													.	NLRC3-96	0			c.C2935A						.						42	45	44					16																	3593429		1916	4131	6047			197358	exon18			ACTCGAGAATCTC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3593429G>T		Somatic	36	0		WXS	Illumina HiSeq		44	4	NM_178844	0	0	0	0	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	G	16.73	3.203059	0.58234	.	.	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.77229	-1.08;-1.08;-1.08	4.86	3.9	0.45041	.	0.000000	0.64402	D	0.000011	D	0.85336	0.5673	M	0.79011	2.435	0.22001	N	0.999423	D	0.64830	0.994	D	0.74348	0.983	T	0.75563	-0.3274	10	0.87932	D	0	.	8.3586	0.32346	0.104:0.0:0.896:0.0	.	1025	C9JLH9	.	I	979;950;1025	ENSP00000301749:L979I;ENSP00000352039:L950I;ENSP00000414415:L1025I	ENSP00000301749:L979I	L	-	1	0	NLRC3	3533430	1.000000	0.71417	0.986000	0.45419	0.576000	0.36127	3.522000	0.53480	2.675000	0.91044	0.561000	0.74099	CTC	.		0.493	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3593429	G	T	3593429	1	4	58	0	1	0	0	0	0	0	0	0	10494	942	33	4		4	NLRC3	16	3593429	RNA	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	225921	3593429	86761324	73	5638											
TMC5	79838	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19474632	19474632	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaaagaaaaaagcaaacaGacccatcgtatccttcagct	18	6	6	11	1	1	2	1	0	0	2	3	3	2	2	2	0	3	3	2	0	6	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:19474632G>T	ENST00000396229.2	+	7	1928	c.1179G>T	c.(1177-1179)caG>caT	p.Q393H	TMC5_ENST00000564959.1_Missense_Mutation_p.Q76H|TMC5_ENST00000381414.4_Missense_Mutation_p.Q393H|TMC5_ENST00000541464.1_Missense_Mutation_p.Q393H|TMC5_ENST00000542583.2_Missense_Mutation_p.Q393H|TMC5_ENST00000219821.5_Missense_Mutation_p.Q147H|TMC5_ENST00000561503.1_Missense_Mutation_p.Q34H	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	393					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						AAAGCAAACAGACCCATCGTA	0.393																																					p.Q393H													.	TMC5-91	0			c.G1179T						.						130	117	121					16																	19474632		2197	4300	6497	SO:0001583	missense	79838	exon7			CAAACAGACCCAT	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1179G>T	16.37:g.19474632G>T	ENSP00000379531:p.Gln393His	Somatic	68	2		WXS	Illumina HiSeq	Phase_I	71	18	NM_001105249	0	0	0	0	0	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	9.374	1.071196	0.20147	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	4.52	-3.67	0.04476	.	2.274450	0.01221	N	0.008115	T	0.37919	0.1021	L	0.46157	1.445	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B	0.09377	0.004;0.002;0.004;0.002;0.002;0.004	T	0.04495	-1.0947	10	0.15499	T	0.54	-0.1905	0.9076	0.01288	0.3654:0.2379:0.2531:0.1436	.	393;76;147;147;393;393	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	H	393;393;393;393;147;76	ENSP00000441227:Q393H;ENSP00000370822:Q393H;ENSP00000379531:Q393H;ENSP00000446274:Q393H;ENSP00000219821:Q147H	ENSP00000219821:Q147H	Q	+	3	2	TMC5	19382133	0.001000	0.12720	0.002000	0.10522	0.205000	0.24178	-0.007000	0.12810	-0.220000	0.09988	-0.142000	0.14014	CAG	.		0.393	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		T	19474632	G	T	19474632	3	4	58	1	0	0	0	0	1	0	0	0	16020	933	33	4	1511	4	TMC5	16	19474632	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	15881203	19474632	70880121	74	5639											
GTF3C1	2975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27549611	27549611	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttcaggtcgggatccccCtcctggcctatcaaggccct	6	9	10	16	1	2	0	2	0	0	0	5	1	4	1	5	4	1	1	5	4	2	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:27549611C>T	ENST00000356183.4	-	3	513	c.498G>A	c.(496-498)gaG>gaA	p.E166E	GTF3C1_ENST00000561623.1_Silent_p.E166E	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	166					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CGGGATCCCCCTCCTGGCCTA	0.582																																					p.E166E		.											.	GTF3C1-94	0			c.G498A						.						70	66	68					16																	27549611		2197	4300	6497	SO:0001819	synonymous_variant	2975	exon3			ATCCCCCTCCTGG	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.498G>A	16.37:g.27549611C>T		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	74	20	NM_001520	0	0	13	18	5	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	8.560	0.877594	0.17395	.	.	ENSG00000077235	ENST00000388971	.	.	.	5.5	1.98	0.26296	.	.	.	.	.	T	0.61640	0.2363	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	5	0.38643	T	0.18	-3.8349	11.4639	0.50227	0.0:0.6864:0.0:0.3136	.	.	.	.	R	166	.	ENSP00000373623:G166R	G	-	1	0	GTF3C1	27457112	0.875000	0.30112	0.996000	0.52242	0.914000	0.54420	-0.027000	0.12371	0.389000	0.25086	-1.945000	0.00491	GGG	.		0.582	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27549611	C	T	27549611	2	4	58	1	0	0	0	0	0	0	0	1	6893	680	24	2		2	GTF3C1	16	27549611	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	8074979	27549611	62805142	75	5640											
CDH1	999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	68853183	68853183	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcttgtccccgttcagAtatcggatttggagagacac	10	10	11	10	2	1	3	1	0	0	3	3	6	2	5	2	2	1	2	2	2	1	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:68853183A>C	ENST00000261769.5	+	11	1757	c.1566A>C	c.(1564-1566)acA>acC	p.T522T	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Splice_Site_p.T461T|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	522	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CCCCGTTCAGATATCGGATTT	0.493			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.T522T		.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1-3377	1	Unknown(1)	breast(1)	c.A1566C						.						89	78	82					16																	68853183		2198	4300	6498	SO:0001630	splice_region_variant	999	exon11	Familial Cancer Database	HDGC	GTTCAGATATCGG	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1566-1A>C	16.37:g.68853183A>C		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	92	22	NM_004360	0	0	0	0	0	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																			.		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Silent	C	68853183	A	C	68853183	5	2	58	1	0	0	0	0	0	0	1	0	3101	347	12	5	1608	5	CDH1	16	68853183	Splice_Site	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	41303572	68853183	21501570	76	5641											
CPNE7	27132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89650107	89650107	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgcctctgacttacagatTgtggcccagaagaaggtgac	11	8	12	10	1	1	5	0	2	1	3	1	6	1	5	2	2	1	0	2	2	3	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:89650107T>A	ENST00000268720.5	+	5	715	c.585T>A	c.(583-585)atT>atA	p.I195I	CPNE7_ENST00000319518.8_Silent_p.I120I	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	195					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		ACTTACAGATTGTGGCCCAGA	0.672																																					p.I195I		.											.	CPNE7-90	0			c.T585A						.						48	45	46					16																	89650107		2198	4300	6498	SO:0001819	synonymous_variant	27132	exon5			ACAGATTGTGGCC	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.585T>A	16.37:g.89650107T>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	107	29	NM_014427	0	0	0	0	0		Silent	SNP	ENST00000268720.5	37	CCDS10980.1																																																																																			.		0.672	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			A	89650107	T	A	89650107	2	1	58	1	0	0	0	0	0	0	0	1	3823	1800	63	5		5	CPNE7	16	89650107	Silent	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	20796924	89650107	704646	77	5642											
C17orf81	23587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7157996	7157996	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggagccttgagagccatgTgcaagaggacagatcctgtt	10	9	14	8	0	0	3	0	1	0	3	1	6	1	5	3	2	3	2	3	2	1	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:7157996T>C	ENST00000396628.2	+	4	548	c.331T>C	c.(331-333)Tgc>Cgc	p.C111R	ELP5_ENST00000396627.2_Missense_Mutation_p.C111R|ELP5_ENST00000573657.1_Missense_Mutation_p.C111R|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000354429.2_Missense_Mutation_p.C111R|ELP5_ENST00000574993.1_Missense_Mutation_p.C111R|ELP5_ENST00000574255.1_Missense_Mutation_p.C111R|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000356683.2_Missense_Mutation_p.C111R|CTDNEP1_ENST00000318988.6_5'Flank|CTDNEP1_ENST00000572043.1_5'Flank	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	111					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GAGAGCCATGTGCAAGAGGAC	0.562																																					p.C111R		.											.	.	0			c.T331C						.						126	93	104					17																	7157996		2203	4300	6503	SO:0001583	missense	23587	exon4			GCCATGTGCAAGA	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"Elongator acetyltransferase complex subunits"	30617	protein-coding gene	gene with protein product	"dermal papilla derived protein 6", "S-phase 2 protein"	615019	"chromosome 17 open reading frame 81"	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.331T>C	17.37:g.7157996T>C	ENSP00000379869:p.Cys111Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	71	19	NM_203414	1	0	42	129	86	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	37	CCDS11094.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009540	0.35415	.	.	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.47869	1.54;1.54;1.54;0.83	5.51	0.78	0.18556	.	0.815021	0.11405	N	0.567376	T	0.41858	0.1177	L	0.56769	1.78	0.19575	N	0.999968	B;B;B;B	0.26002	0.029;0.114;0.139;0.021	B;B;B;B	0.31290	0.025;0.053;0.127;0.025	T	0.43925	-0.9361	10	0.56958	D	0.05	-0.1605	4.5046	0.11881	0.0:0.2406:0.3505:0.4089	.	111;111;111;111	Q8TE02-2;Q8TE02-3;A8K1M5;Q8TE02	.;.;.;DERP6_HUMAN	R	111	ENSP00000346412:C111R;ENSP00000379869:C111R;ENSP00000379868:C111R;ENSP00000349111:C111R	ENSP00000346412:C111R	C	+	1	0	C17orf81	7098720	0.003000	0.15002	0.001000	0.08648	0.794000	0.44872	0.167000	0.16602	0.127000	0.18452	0.482000	0.46254	TGC	.		0.562	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362		C	7157996	T	C	7157996	3	2	58	1	0	0	0	0	1	0	0	0	1891	1696	59	3	345	3	C17orf81	17	7157996	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		7157996	74037214	78	5643											
ATPAF2	91647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17925092	17925092	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgttgtaagatgccaggtGgctgacgagcacctcccgag	8	9	14	10	2	0	2	0	1	0	1	1	4	1	2	3	2	2	4	3	2	1	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:17925092G>A	ENST00000474627.3	-	6	737	c.583C>T	c.(583-585)Cac>Tac	p.H195Y	ATPAF2_ENST00000585101.1_Intron|ATPAF2_ENST00000469327.1_5'UTR	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	195					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					GATGCCAGGTGGCTGACGAGC	0.547																																					p.H195Y		.											.	ATPAF2-90	0			c.C583T						.						234	205	215					17																	17925092		2203	4300	6503	SO:0001583	missense	91647	exon6			CCAGGTGGCTGAC	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"Mitochondrial respiratory chain complex assembly factors"	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.583C>T	17.37:g.17925092G>A	ENSP00000417190:p.His195Tyr	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	125	34	NM_145691	0	0	31	51	20	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	37	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247071	0.59103	.	.	ENSG00000171953	ENST00000474627;ENST00000444058	T;T	0.75821	-0.97;-0.97	5.41	5.41	0.78517	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	T	0.78767	0.4335	L	0.38175	1.15	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.70182	-0.4942	10	0.02654	T	1	4.9557	19.5423	0.95278	0.0:0.0:1.0:0.0	.	195	Q8N5M1	ATPF2_HUMAN	Y	195	ENSP00000417190:H195Y;ENSP00000397198:H195Y	ENSP00000434980:H195Y	H	-	1	0	ATPAF2	17865817	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	7.369000	0.79578	2.692000	0.91855	0.655000	0.94253	CAC	.		0.547	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691		A	17925092	G	A	17925092	3	1	58	1	0	0	0	0	1	0	0	0	1202	1348	47	2	298	2	ATPAF2	17	17925092	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	10767096	17925092	63270118	79	5644											
POLDIP2	7126	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	26675218	26675218	+	IGR	DEL	A	A	-																															aagggaggaatccgaacatcAaagtgggagccatcaggtct																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:26675218delA	ENST00000226225.2	+	0	3627				POLDIP2_ENST00000540200.1_Frame_Shift_Del_p.F343fs|POLDIP2_ENST00000003607.4_5'UTR	NM_021137.4	NP_066960.1	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1 (endothelial)						apoptotic process (GO:0006915)|cell migration (GO:0016477)|DNA replication (GO:0006260)|embryo development (GO:0009790)|immune response (GO:0006955)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleolus (GO:0005730)	GTP-Rho binding (GO:0017049)			endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	12	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		TCCGAACATCAAAGTGGGAGC	0.547																																					.		.											.	.	0			.						.						96	97	97					17																	26675218		1904	4126	6030	SO:0001628	intergenic_variant	26073	.			.		CCDS11227.1	17q22-q23	2013-01-09			ENSG00000109079	ENSG00000109079		"BTB/POZ domain containing"	11894	protein-coding gene	gene with protein product		191161		EDP1		2406243, 2233719	Standard	NM_021137		Approved	B61, B12, MGC2317, BTBD34	uc002hay.3	Q13829	OTTHUMG00000132501		17.37:g.26675218delA		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	100	20	.	0	0	0	0	0	B7Z6M4|Q5TZQ1	Targeted_Region	DEL	ENST00000226225.2	37	CCDS11227.1																																																																																			.		0.547	TNFAIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255681.2	NM_021137		-	26675218	A	-	26675218	6	5	58	0	1	1	0	1	0	0	0	0	12220	127	5	0		0	POLDIP2	17	26675218	IGR	DEL	A	TCGA-B9-A69E-01A-11D-A31X-10	8750126	26675218	54519992	80	5645											
C17orf57	124989	hgsc.bcm.edu;bcgsc.ca	37	chr17	45468874	45468875	+	Frame_Shift_Ins	INS	-	-	G																															ttatgaggatctaaatacttINSgtcttcaaaattttggtatt																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:45468874_45468875insG	ENST00000331493.2	+	15	2065_2066	c.1654_1655insG	c.(1654-1656)tgtfs	p.C552fs	EFCAB13_ENST00000517484.1_Frame_Shift_Ins_p.C456fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	552	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TCTAAATACTTGTCTTCAAAAT	0.327																																					p.C552fs		.											.	.	0			c.1654_1655insG						.																																			SO:0001589	frameshift_variant	124989	exon15			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1655dupG	17.37:g.45468875_45468875dupG	ENSP00000332111:p.Cys552fs	Somatic	277	0		WXS	Illumina HiSeq	Phase_I	342	63	NM_152347	0	0	0	0	0	G3V128|Q49AG9	Frame_Shift_Ins	INS	ENST00000331493.2	37	CCDS11512.1																																																																																			.		0.327	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		G	45468875	-	G	45468874	7	5	58	1	0	1	1	0	0	0	0	0	1870	1812	63	0	1700	0	C17orf57	17	45468874	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	18793656	45468874	35726336	81	5646											
TIMP2	7077	hgsc.bcm.edu	37	chr17	76921135	76921135	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcgccagcagcaggaggccGagcgccagccgcagggtgcg	7	2	18	14	5	0	0	0	0	0	0	1	2	0	1	4	3	5	3	4	3	0	0	rs577686887	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:76921135G>A	ENST00000262768.7	-	1	334	c.36C>T	c.(34-36)ctC>ctT	p.L12L	TIMP2_ENST00000536189.2_5'Flank	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	12					aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			GCAGGAGGCCGAGCGCCAGCC	0.781													G|||	90	0.0179712	0.0098	0.0159	5008	,	,		2705	0		0.0398	False		,,,				2504	0.0266				p.L12L		.											.	TIMP2-650	0			c.C36T						.						2	2	2					17																	76921135		972	1756	2728	SO:0001819	synonymous_variant	7077	exon1			GAGGCCGAGCGCC		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"tissue inhibitor of metalloproteinase 2"			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.36C>T	17.37:g.76921135G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_003255	0	0	0	4	4	Q16121|Q93006|Q9UDF7	Silent	SNP	ENST00000262768.7	37	CCDS11758.1																																																																																			.		0.781	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255		A	76921135	G	A	76921135	2	1	58	1	0	0	0	0	0	0	0	1	15950	1045	37	1		1	TIMP2	17	76921135	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	31452261	76921135	4274075	82	5647											
NDC80	10403	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	2610806	2610806	+	Frame_Shift_Del	DEL	A	A	-																															gaagaaagacgaaaagtgggAaataacttgcaacgtctgtt																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:2610806delA	ENST00000261597.4	+	16	1919	c.1737delA	c.(1735-1737)ggafs	p.G579fs		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	579	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GAAAAGTGGGAAATAACTTGC	0.368																																					p.G579fs		.											.	NDC80-91	0			c.1737delA						.						194	172	180					18																	2610806		2203	4300	6503	SO:0001589	frameshift_variant	10403	exon16			.	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1737delA	18.37:g.2610806delA	ENSP00000261597:p.Gly579fs	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	157	36	NM_006101	0	0	0	0	0	Q6PJX2	Frame_Shift_Del	DEL	ENST00000261597.4	37	CCDS11827.1																																																																																			.		0.368	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		-	2610806	A	-	2610806	7	5	58	1	0	1	0	1	0	0	0	0	10268	233	9	0	1795	0	NDC80	18	2610806	Frame_Shift_Del	DEL	A	TCGA-B9-A69E-01A-11D-A31X-10		2610806	75466442	83	5648											
DYM	54808	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	46798650	46798650	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcctttcttcaacatgataCagaatctcaagaattggtaa	14	14	5	8	0	3	3	2	1	2	2	5	3	4	3	1	1	2	1	1	1	6	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:46798650C>G	ENST00000269445.6	-	11	1606	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L	DYM_ENST00000442713.2_Silent_p.L193L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	383					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						CAACATGATACAGAATCTCAA	0.299																																					p.L383L													.	DYM-226	0			c.G1149C						.						77	72	74					18																	46798650		2203	4299	6502	SO:0001819	synonymous_variant	54808	exon11			ATGATACAGAATC	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1149G>C	18.37:g.46798650C>G		Somatic	151	1		WXS	Illumina HiSeq	Phase_I	123	35	NM_017653	0	0	25	35	10	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Silent	SNP	ENST00000269445.6	37	CCDS11937.1																																																																																			.		0.299	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		G	46798650	C	G	46798650	2	3	58	1	0	0	0	0	0	0	0	1	4851	465	17	4		4	DYM	18	46798650	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	44187844	46798650	31278598	84	5649											
HMHA1	23526	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	1082889	1082889	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taccacgagctcgtagggctGgccaaggacagcctgaaggc	10	5	14	12	2	0	1	0	1	0	0	1	3	0	2	3	4	3	3	3	4	4	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:1082889G>T	ENST00000313093.2	+	20	2799	c.2568G>T	c.(2566-2568)ctG>ctT	p.L856L	HMHA1_ENST00000539243.2_Silent_p.L872L|HMHA1_ENST00000543365.1_Silent_p.L739L|HMHA1_ENST00000536472.1_Silent_p.L724L|HMHA1_ENST00000586866.1_Silent_p.L860L|HMHA1_ENST00000590577.1_Silent_p.L491L|HMHA1_ENST00000590214.1_Silent_p.L883L	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	856	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGTAGGGCTGGCCAAGGACA	0.711																																					p.L872L		.											.	HMHA1-91	0			c.G2616T						.						13	12	12					19																	1082889		2193	4288	6481	SO:0001819	synonymous_variant	23526	exon20			AGGGCTGGCCAAG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"Rho GTPase activating proteins"	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.2568G>T	19.37:g.1082889G>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	49	19	NM_001258328	0	0	33	33	0	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			.		0.711	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			T	1082889	G	T	1082889	2	4	58	1	0	0	0	0	0	0	0	1	7261	1335	47	4		4	HMHA1	19	1082889	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		1082889	58046094	85	5650											
SAFB	6294	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	5653148	5653148	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggcgccaaggttgtgaCaaatgcccggagtcctggag	8	7	17	9	2	0	1	0	1	0	0	1	3	1	3	3	5	1	1	3	5	2	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:5653148C>T	ENST00000292123.5	+	10	1423	c.1316C>T	c.(1315-1317)aCa>aTa	p.T439I	SAFB_ENST00000538656.1_Missense_Mutation_p.T282I|SAFB_ENST00000454510.1_Missense_Mutation_p.T370I|SAFB_ENST00000588852.1_Missense_Mutation_p.T439I|SAFB_ENST00000592224.1_Missense_Mutation_p.T439I|SAFB_ENST00000433404.1_Missense_Mutation_p.T269I|SAFB_ENST00000586934.1_3'UTR	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	439	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		AAGGTTGTGACAAATGCCCGG	0.547																																					p.T439I	Colon(88;338 1345 6184 8214 20897)												.	SAFB-228	0			c.C1316T						.						102	86	92					19																	5653148		2203	4300	6503	SO:0001583	missense	6294	exon10			TTGTGACAAATGC	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.1316C>T	19.37:g.5653148C>T	ENSP00000292123:p.Thr439Ile	Somatic	227	1		WXS	Illumina HiSeq	Phase_I	178	57	NM_002967	0	0	34	57	23	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	37	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989341	0.74589	.	.	ENSG00000160633	ENST00000454510;ENST00000540206;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.08008	3.14;3.14;3.14;3.14	4.81	4.81	0.61882	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.56097	D	0.000021	T	0.21103	0.0508	L	0.32530	0.975	0.80722	D	1	D;D;D;P;D;D;D	0.89917	1.0;0.998;1.0;0.886;0.998;0.989;0.998	D;D;D;P;D;D;D	0.91635	0.999;0.99;0.999;0.806;0.994;0.963;0.994	T	0.01105	-1.1450	10	0.87932	D	0	-21.1697	18.4417	0.90669	0.0:1.0:0.0:0.0	.	238;282;370;439;439;439;439	B7Z1C7;B7Z2F6;F5H0H3;B7ZLP5;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	I	370;334;269;439;282	ENSP00000415895:T370I;ENSP00000404545:T269I;ENSP00000292123:T439I;ENSP00000438880:T282I	ENSP00000292123:T439I	T	+	2	0	SAFB	5604148	1.000000	0.71417	0.967000	0.41034	0.964000	0.63967	7.491000	0.81471	2.654000	0.90174	0.563000	0.77884	ACA	.		0.547	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			T	5653148	C	T	5653148	3	4	58	1	0	0	0	0	1	0	0	0	13838	478	17	2	1354	2	SAFB	19	5653148	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	4570259	5653148	53475835	86	5651											
MRI1	28974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13883025	13883025	+	5'Flank	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggggtctttgcccctgAggagctccggacagccctaa	7	8	13	13	1	1	1	0	1	1	0	2	3	2	3	4	4	3	1	4	4	1	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:13883025A>T	ENST00000588234.1	+	0	0				C19orf53_ENST00000593274.1_5'Flank|MRI1_ENST00000040663.6_Missense_Mutation_p.E347V|CTB-5E10.3_ENST00000586297.1_RNA|MRI1_ENST00000319545.8_Missense_Mutation_p.E300V|CTB-5E10.3_ENST00000586894.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53											breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			TTTGCCCCTGAGGAGCTCCGG	0.577																																					p.E347V		.											.	MRI1-91	0			c.A1040T						.						95	88	91					19																	13883025		2203	4300	6503	SO:0001631	upstream_gene_variant	84245	exon6			CCCCTGAGGAGCT	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"leydig cell tumor 10 kDa protein homolog"					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5			19.37:g.13883025A>T	Exception_encountered	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	208	48	NM_001031727	0	0	17	21	4	B2R4J9	Missense_Mutation	SNP	ENST00000588234.1	37	CCDS12298.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611851	0.28712	.	.	ENSG00000037757	ENST00000040663;ENST00000319545	T;T	0.31247	1.5;1.5	4.88	3.84	0.44239	.	0.235842	0.36409	N	0.002620	T	0.27900	0.0687	L	0.48986	1.54	0.32290	N	0.566403	B;B	0.29085	0.232;0.011	B;B	0.30251	0.113;0.027	T	0.29518	-1.0009	10	0.42905	T	0.14	-48.5554	10.0893	0.42436	0.8314:0.1686:0.0:0.0	.	300;347	Q9BV20-2;Q9BV20	.;MTNA_HUMAN	V	347;300	ENSP00000040663:E347V;ENSP00000314871:E300V	ENSP00000040663:E347V	E	+	2	0	MRI1	13744025	0.000000	0.05858	0.400000	0.26346	0.621000	0.37620	0.854000	0.27791	0.685000	0.31468	0.397000	0.26171	GAG	.		0.577	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047		T	13883025	A	T	13883025	1	4	58	0	1	0	0	0	0	0	0	0	9795	304	11	5		5	MRI1	19	13883025	5'Flank	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	8229877	13883025	45245958	87	5652											
PRKACA	5566	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	14211641	14211641	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggtggcccgcttacctgAaccttccgatccgccgtagg	5	8	14	14	4	0	1	0	1	0	0	2	2	2	1	6	4	2	2	6	4	3	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:14211641A>G	ENST00000308677.4	-	5	612	c.416T>C	c.(415-417)tTc>tCc	p.F139S	PRKACA_ENST00000350356.3_5'UTR|PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000589994.1_Missense_Mutation_p.F131S	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	139	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						CGCTTACCTGAACCTTCCGAT	0.592																																					p.F139S													.	PRKACA-978	0			c.T416C						.						101	75	84					19																	14211641		2203	4300	6503	SO:0001583	missense	5566	exon5			TACCTGAACCTTC		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.416T>C	19.37:g.14211641A>G	ENSP00000309591:p.Phe139Ser	Somatic	143	1		WXS	Illumina HiSeq	Phase_I	131	40	NM_002730	0	0	0	0	0	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Missense_Mutation	SNP	ENST00000308677.4	37	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.778024	0.70107	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695;ENST00000536649	T	0.67345	-0.26	4.75	4.75	0.60458	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.283528	0.25267	N	0.031918	D	0.83815	0.5336	M	0.90082	3.085	0.46542	D	0.999096	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.86854	0.2025	10	0.87932	D	0	.	12.2465	0.54574	1.0:0.0:0.0:0.0	.	81;122;139;131	B7Z708;Q15136;P17612;P17612-2	.;.;KAPCA_HUMAN;.	S	139;131;139;81	ENSP00000309591:F139S	ENSP00000309591:F139S	F	-	2	0	PRKACA	14072641	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	9.217000	0.95160	1.796000	0.52611	0.378000	0.23410	TTC	.		0.592	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730		G	14211641	A	G	14211641	3	3	58	1	0	0	0	0	1	0	0	0	12526	246	9	3	663	3	PRKACA	19	14211641	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	328616	14211641	44917342	88	5653											
USHBP1	83878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17366410	17366410	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgaagcatcaggtccgccagGgcctcctgtgggaccaagga	9	5	14	13	2	1	0	1	0	0	0	3	3	3	2	5	4	1	1	5	4	2	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:17366410G>A	ENST00000252597.3	-	10	1649	c.1476C>T	c.(1474-1476)gcC>gcT	p.A492A	USHBP1_ENST00000431146.2_Silent_p.A428A|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						GGTCCGCCAGGGCCTCCTGTG	0.632																																					p.A492A		.											.	USHBP1-91	0			c.C1476T						.						10	12	11					19																	17366410		2188	4264	6452	SO:0001819	synonymous_variant	83878	exon10			CGCCAGGGCCTCC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1476C>T	19.37:g.17366410G>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	79	14	NM_031941	0	0	0	0	0		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			.		0.632	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		A	17366410	G	A	17366410	2	1	58	1	0	0	0	0	0	0	0	1	17070	1219	43	2		2	USHBP1	19	17366410	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3154769	17366410	41762573	89	5654											
NCAN	1463	broad.mit.edu	37	chr19	19360601	19360603	+	In_Frame_Del	DEL	CAC	CAC	-																															gttcacatcggatgcggcgaCaccaccaccaccaccaacac																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:19360601_19360603delCAC	ENST00000252575.6	+	15	3946_3948	c.3847_3849delCAC	c.(3847-3849)cacdel	p.H1287del	NCAN_ENST00000538881.1_In_Frame_Del_p.H738del	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1287					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	GATGCGGCGAcaccaccaccacc	0.596																																					p.1283_1283del													.	NCAN-94	0			c.3847_3849del						.																																			SO:0001651	inframe_deletion	1463	exon15			CGGCGACACCACC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans", "Endogenous ligands"	2465	protein-coding gene	gene with protein product	"neurocan proteoglycan"	600826	"chondroitin sulfate proteoglycan 3"	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3847_3849delCAC	19.37:g.19360610_19360612delCAC	ENSP00000252575:p.His1287del	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	193	7	NM_004386	0	0	0	0	0	Q9UPK6	In_Frame_Del	DEL	ENST00000252575.6	37	CCDS12397.1																																																																																			.		0.596	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		-	19360603	CAC	-	19360601	7	5	58	1	0	1	0	1	0	0	0	0	10230	478	17	0	3901	0	NCAN	19	19360601	In_Frame_Del	DEL	CAC	TCGA-B9-A69E-01A-11D-A31X-10	1994191	19360601	39768382	90	5655											
C19orf40	91442	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	33464971	33464972	+	Frame_Shift_Ins	INS	-	-	A																															tttttcctttcaagtccaatINSaatcttaaaggaattgtagt																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:33464971_33464972insA	ENST00000588258.1	+	4	359_360	c.249_250insA	c.(250-252)aatfs	p.N84fs	CEP89_ENST00000590597.2_5'Flank|CEP89_ENST00000305768.5_5'Flank|CEP89_ENST00000591863.1_5'Flank|C19orf40_ENST00000589646.1_5'UTR|C19orf40_ENST00000590179.1_5'UTR|C19orf40_ENST00000590281.1_Frame_Shift_Ins_p.N84fs	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	84					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					TCAAGTCCAATAATCTTAAAGG	0.406								Direct reversal of damage																													p.N83fs		.											.	C19orf40-90	0			c.249_250insA						.																																			SO:0001589	frameshift_variant	91442	exon4			.	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 24kDa"	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.251dupA	19.37:g.33464973_33464973dupA	ENSP00000466121:p.Asn84fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	170	43	NM_152266	0	0	0	0	0	B3KY46|Q8WUJ7|Q96FX6	Frame_Shift_Ins	INS	ENST00000588258.1	37	CCDS12426.1																																																																																			.		0.406	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266		A	33464972	-	A	33464971	7	5	58	1	0	1	1	0	0	0	0	0	1929	1403	49	0	259	0	C19orf40	19	33464971	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	14104370	33464971	25664012	91	5656											
CBLC	23624	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	45281521	45281521	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	agtgccaacgacgagctcttCcgggcgggctccagactcag	8	6	13	14	4	2	1	1	0	1	1	4	3	4	1	3	2	3	2	3	2	1	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:45281521C>G	ENST00000270279.3	+	1	396	c.333C>G	c.(331-333)ttC>ttG	p.F111L	CBLC_ENST00000341505.4_Missense_Mutation_p.F111L	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	111	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				ACGAGCTCTTCCGGGCGGGCT	0.657			M		AML																																p.F111L		.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC-849	0			c.C333G						.						4	5	5					19																	45281521		1948	3848	5796	SO:0001583	missense	23624	exon1			GCTCTTCCGGGCG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"RING-type (C3HC4) zinc fingers"	15961	protein-coding gene	gene with protein product		608453	"Cas-Br-M (murine) ectropic retroviral transforming sequence c", "Cas-Br-M (murine) ecotropic retroviral transforming sequence c"			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.333C>G	19.37:g.45281521C>G	ENSP00000270279:p.Phe111Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_001130852	0	0	3	3	0	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	.	.	.	.	.	.	.	.	.	.	.	14.98	2.697608	0.48307	.	.	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.78924	-1.22;-1.22	3.49	3.49	0.39957	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.64402	D	0.000016	T	0.78978	0.4369	M	0.81497	2.545	0.39134	D	0.961902	P;D	0.52996	0.939;0.957	P;P	0.45310	0.476;0.469	D	0.83554	0.0103	10	0.66056	D	0.02	-25.9304	10.6934	0.45884	0.0:1.0:0.0:0.0	.	111;111	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	L	111	ENSP00000270279:F111L;ENSP00000340250:F111L	ENSP00000270279:F111L	F	+	3	2	CBLC	49973361	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	2.404000	0.44539	1.962000	0.57031	0.556000	0.70494	TTC	.		0.657	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		G	45281521	C	G	45281521	3	3	58	1	0	0	0	0	1	0	0	0	2708	854	30	4	335	4	CBLC	19	45281521	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	11816550	45281521	13847462	92	5657											
ZNF577	84765	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	52376955	52376955	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcttctactctggattacAaaacctaaatgagatttcaa	15	14	4	8	0	4	1	1	1	3	1	4	3	4	2	1	1	3	0	1	1	8	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:52376955A>G	ENST00000301399.5	-	7	653	c.288T>C	c.(286-288)ttT>ttC	p.F96F	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	96					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)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCTGGATTACAAAACCTAAAT	0.358																																					p.F96F		.											.	ZNF577-91	0			c.T288C						.						37	34	35					19																	52376955		2203	4299	6502	SO:0001819	synonymous_variant	84765	exon7			GATTACAAAACCT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.288T>C	19.37:g.52376955A>G		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	59	13	NM_032679	0	0	0	0	0	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			.		0.358	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		G	52376955	A	G	52376955	2	3	58	1	0	0	0	0	0	0	0	1	18041	127	5	3		3	ZNF577	19	52376955	Silent	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	7095434	52376955	6752028	93	5658											
ZNF606	80095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58489700	58489700	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttcactgtgatttctcTggtgttgaagtagggctgag	6	16	12	7	0	3	3	1	3	2	0	5	3	3	3	0	2	0	3	0	2	2	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:58489700T>C	ENST00000341164.4	-	7	2968	c.2348A>G	c.(2347-2349)cAg>cGg	p.Q783R	ZNF606_ENST00000536132.1_Missense_Mutation_p.Q693R	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	783					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		GTGATTTCTCTGGTGTTGAAG	0.368																																					p.Q783R		.											.	ZNF606-92	0			c.A2348G						.						91	84	86					19																	58489700		2203	4300	6503	SO:0001583	missense	80095	exon7			TTTCTCTGGTGTT	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2348A>G	19.37:g.58489700T>C	ENSP00000343617:p.Gln783Arg	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	152	39	NM_025027	0	0	5	8	3	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185460	0.21870	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.25749	1.78;1.78	4.77	2.52	0.30459	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40302	N	0.001121	T	0.18882	0.0453	L	0.39147	1.195	0.23988	N	0.996254	B	0.11235	0.004	B	0.10450	0.005	T	0.16217	-1.0410	10	0.49607	T	0.09	.	7.2862	0.26340	0.0:0.0828:0.145:0.7722	.	783	Q8WXB4	ZN606_HUMAN	R	783;693	ENSP00000343617:Q783R;ENSP00000445624:Q693R	ENSP00000343617:Q783R	Q	-	2	0	ZNF606	63181512	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.272000	0.18644	0.941000	0.37499	0.528000	0.53228	CAG	.		0.368	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		C	58489700	T	C	58489700	3	2	58	1	0	0	0	0	1	0	0	0	18064	1580	55	3	34	3	ZNF606	19	58489700	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	6112745	58489700	639283	94	5659											
SIRPA	140885	bcgsc.ca	37	chr20	1902142	1902142	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcttctcacccagagacAtcaccctgaaatggttcaaa	13	8	7	13	1	3	2	3	1	1	1	4	3	3	2	2	2	0	2	2	2	2	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:1902142A>G	ENST00000358771.4	+	3	690	c.538A>G	c.(538-540)Atc>Gtc	p.I180V	SIRPA_ENST00000400068.3_Missense_Mutation_p.I180V|SIRPA_ENST00000356025.3_Missense_Mutation_p.I180V	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	180	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		ACCCAGAGACATCACCCTGAA	0.592																																					p.I180V	GBM(155;1668 1920 5945 42733 48121)												.	SIRPA-227	0			c.A538G						.						80	77	78					20																	1902142		2203	4297	6500	SO:0001583	missense	140885	exon4			AGAGACATCACCC	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	9662	protein-coding gene	gene with protein product		602461	"protein tyrosine phosphatase, non-receptor type substrate 1"	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.538A>G	20.37:g.1902142A>G	ENSP00000351621:p.Ile180Val	Somatic	383	2		WXS	Illumina HiSeq	Phase_1	316	79	NM_001040022	0	0	32	70	38	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	A	7.686	0.690124	0.15039	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02863	4.13;4.13;4.13	4.38	-0.0461	0.13848	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.416111	0.22732	N	0.056306	T	0.05868	0.0153	M	0.77103	2.36	0.26965	N	0.965718	B;P;B	0.34909	0.045;0.475;0.149	B;B;B	0.41619	0.055;0.361;0.081	T	0.11941	-1.0567	10	0.54805	T	0.06	.	6.9109	0.24335	0.6134:0.0:0.3866:0.0	.	160;180;180	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	V	180	ENSP00000382941:I180V;ENSP00000348307:I180V;ENSP00000351621:I180V	ENSP00000348307:I180V	I	+	1	0	SIRPA	1850142	0.954000	0.32549	0.989000	0.46669	0.163000	0.22366	2.005000	0.40864	0.003000	0.14656	-0.475000	0.04921	ATC	.		0.592	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		G	1902142	A	G	1902142	3	3	58	1	0	0	0	0	1	0	0	0	14364	217	8	3	548	3	SIRPA	20	1902142	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		1902142	61123378	95	5660											
BPIL3	128859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31627181	31627181	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcttatcccaagtcaaagcCcttgacgacccagatcaaga	14	7	7	13	1	2	3	2	1	0	2	3	4	3	3	3	0	2	1	3	0	4	2	rs370022331		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:31627181C>A	ENST00000349552.1	+	10	929	c.929C>A	c.(928-930)cCc>cAc	p.P310H		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	310						extracellular region (GO:0005576)	lipid binding (GO:0008289)										AAGTCAAAGCCCTTGACGACC	0.522																																					p.P310H		.											.	.	0			c.C929A						.						102	107	105					20																	31627181		2203	4300	6503	SO:0001583	missense	128859	exon10			CAAAGCCCTTGAC	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"BPI fold containing"	16504	protein-coding gene	gene with protein product		614110	"bactericidal/permeability-increasing protein-like 3"	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.929C>A	20.37:g.31627181C>A	ENSP00000344929:p.Pro310His	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	88	33	NM_174897	0	0	0	0	0		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703220	0.30232	.	.	ENSG00000167104	ENST00000349552	T	0.08896	3.04	4.44	3.47	0.39725	.	0.000000	0.56097	D	0.000035	T	0.25606	0.0623	M	0.81497	2.545	0.29520	N	0.853577	D	0.71674	0.998	D	0.66716	0.946	T	0.05354	-1.0890	10	0.46703	T	0.11	.	10.1046	0.42526	0.0:0.7964:0.2036:0.0	.	310	Q8NFQ5	BPIB6_HUMAN	H	310	ENSP00000344929:P310H	ENSP00000344929:P310H	P	+	2	0	BPIFB6	31090842	1.000000	0.71417	0.986000	0.45419	0.039000	0.13416	1.937000	0.40193	1.047000	0.40274	0.561000	0.74099	CCC	.		0.522	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897		A	31627181	C	A	31627181	3	1	58	1	0	0	0	0	1	0	0	0	1496	623	22	4	967	4	BPIL3	20	31627181	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	29725039	31627181	31398339	96	5661											
TTPAL	79183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	43108944	43108944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgcagctcctcgtcaactAccacagctgtagaagaagct	11	8	8	14	1	1	2	1	0	0	2	3	2	2	2	3	0	6	5	3	0	5	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43108944A>G	ENST00000372904.3	+	3	448	c.305A>G	c.(304-306)tAc>tGc	p.Y102C	TTPAL_ENST00000372906.2_Missense_Mutation_p.Y102C|TTPAL_ENST00000262605.4_Missense_Mutation_p.Y102C	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	102						intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						CTCGTCAACTACCACAGCTGT	0.567																																					p.Y102C		.											.	TTPAL-153	0			c.A305G						.						51	44	46					20																	43108944		2203	4300	6503	SO:0001583	missense	79183	exon2			TCAACTACCACAG	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 121"	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.305A>G	20.37:g.43108944A>G	ENSP00000361995:p.Tyr102Cys	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	153	49	NM_001039199	0	0	1	2	1	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	37	CCDS13332.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306489	0.81247	.	.	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000372906;ENST00000456317	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.1	5.1	0.69264	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92886	0.7737	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93787	0.7089	10	0.87932	D	0	-22.794	14.903	0.70696	1.0:0.0:0.0:0.0	.	102	Q9BTX7	TTPAL_HUMAN	C	102	ENSP00000262605:Y102C;ENSP00000361995:Y102C;ENSP00000361997:Y102C;ENSP00000412720:Y102C	ENSP00000262605:Y102C	Y	+	2	0	TTPAL	42542358	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	1.909000	0.55274	0.533000	0.62120	TAC	.		0.567	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331		G	43108944	A	G	43108944	3	3	58	1	0	0	0	0	1	0	0	0	16770	391	14	3	307	3	TTPAL	20	43108944	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	11481763	43108944	19916576	97	5662											
ADA	100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	43251682	43251682	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggccgagcccacctccccgGcgtggacagtacggtgaatg	7	5	14	15	5	0	1	0	1	0	0	1	3	1	2	5	4	2	1	5	4	2	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43251682G>A	ENST00000372874.4	-	7	778	c.644C>T	c.(643-645)gCc>gTc	p.A215V	ADA_ENST00000464097.1_5'UTR|PKIG_ENST00000372882.3_Intron|ADA_ENST00000537820.1_Intron|PKIG_ENST00000372887.1_Intron	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	215			A -> T (in ADASCID; dbSNP:rs114025668). {ECO:0000269|PubMed:2166947}.		adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	CACCTCCCCGGCGTGGACAGT	0.657									Adenosine Deaminase Deficiency																												p.A215V		.											.	ADA-653	0			c.C644T						.						67	68	68					20																	43251682		2203	4300	6503	SO:0001583	missense	100	exon7	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	TCCCCGGCGTGGA	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.644C>T	20.37:g.43251682G>A	ENSP00000361965:p.Ala215Val	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	98	20	NM_000022	0	0	10	14	4	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	37	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377508	0.61735	.	.	ENSG00000196839	ENST00000372874	D	0.97114	-4.25	4.89	3.9	0.45041	Adenosine/AMP deaminase (1);	0.048514	0.85682	D	0.000000	D	0.98466	0.9489	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.63113	0.911	D	0.98951	1.0794	10	0.87932	D	0	-9.5965	15.4157	0.74966	0.0:0.1385:0.8615:0.0	.	215	P00813	ADA_HUMAN	V	215	ENSP00000361965:A215V	ENSP00000361965:A215V	A	-	2	0	ADA	42685096	1.000000	0.71417	0.136000	0.22124	0.136000	0.21042	6.472000	0.73567	2.549000	0.85964	0.563000	0.77884	GCC	.		0.657	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022		A	43251682	G	A	43251682	3	1	58	1	0	0	0	0	1	0	0	0	230	1203	42	2	471	2	ADA	20	43251682	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	142738	43251682	19773838	98	5663											
KCNE2	9992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	35743124	35743124	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catccatgagaacattggtgCggctgggttcaaaatgtccc	10	10	11	10	1	1	1	1	1	0	1	3	2	3	1	2	3	2	2	2	3	3	2	rs199473367		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:35743124C>T	ENST00000290310.3	+	2	487	c.347C>T	c.(346-348)gCg>gTg	p.A116V	AP000320.6_ENST00000440403.1_RNA	NM_172201.1	NP_751951.1	Q9Y6J6	KCNE2_HUMAN	potassium voltage-gated channel, Isk-related family, member 2	116					aging (GO:0007568)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular protein localization (GO:0034613)|cellular response to drug (GO:0035690)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|positive regulation of proteasomal protein catabolic process (GO:1901800)|potassium ion export (GO:0071435)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of cyclic nucleotide-gated ion channel activity (GO:1902159)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of inward rectifier potassium channel activity (GO:1901979)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|tongue development (GO:0043586)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|large_intestine(1)	2						AACATTGGTGCGGCTGGGTTC	0.488																																					p.A116V		.											.	KCNE2-68	0			c.C347T	GRCh37	CM003450	KCNE2	M		.						44	40	42					21																	35743124		2203	4300	6503	SO:0001583	missense	9992	exon2			TTGGTGCGGCTGG	AF071002	CCDS13635.1	21q22.1	2014-09-17			ENSG00000159197	ENSG00000159197		"Potassium channels"	6242	protein-coding gene	gene with protein product		603796				10219239	Standard	NM_172201		Approved	MiRP1, LQT6	uc002ytt.1	Q9Y6J6	OTTHUMG00000086189	ENST00000290310.3:c.347C>T	21.37:g.35743124C>T	ENSP00000290310:p.Ala116Val	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	99	26	NM_172201	0	0	4	4	0	A5H1P3|D3DSF8|Q52LJ5	Missense_Mutation	SNP	ENST00000290310.3	37	CCDS13635.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805758	0.70682	.	.	ENSG00000159197	ENST00000290310	D	0.93307	-3.2	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	D	0.94686	0.8286	L	0.32530	0.975	0.42882	D	0.994175	D	0.89917	1.0	D	0.78314	0.991	D	0.95265	0.8372	10	0.66056	D	0.02	-27.5208	17.5309	0.87814	0.0:1.0:0.0:0.0	.	116	Q9Y6J6	KCNE2_HUMAN	V	116	ENSP00000290310:A116V	ENSP00000290310:A116V	A	+	2	0	KCNE2	34664994	0.991000	0.36638	0.150000	0.22450	0.102000	0.19082	3.221000	0.51215	2.657000	0.90304	0.655000	0.94253	GCG	.		0.488	KCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194068.2			T	35743124	C	T	35743124	3	4	58	1	0	0	0	0	1	0	0	0	8044	768	27	1	349	1	KCNE2	21	35743124	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		35743124	12386771	99	5664											
KCNJ15	3772	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	39671646	39671649	+	Frame_Shift_Del	DEL	TTGA	TTGA	-																															ctcagttggtcatcacgaccTtgattgagatcttcatcacc																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	TTGA	TTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:39671646_39671649delTTGA	ENST00000328656.4	+	4	766_769	c.463_466delTTGA	c.(463-468)ttgattfs	p.LI155fs	KCNJ15_ENST00000398932.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398934.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398930.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398938.2_Frame_Shift_Del_p.LI155fs	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	155					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CATCACGACCTTGATTGAGATCTT	0.515																																					p.155_156del		.											.	KCNJ15-157	0			c.463_466del						.																																			SO:0001589	frameshift_variant	3772	exon4			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.463_466delTTGA	21.37:g.39671650_39671653delTTGA	ENSP00000331698:p.Leu155fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	105	28	NM_002243	0	0	0	0	0	D3DSH5|O00564|Q96L28|Q99446	Frame_Shift_Del	DEL	ENST00000328656.4	37	CCDS13656.1																																																																																			.		0.515	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		-	39671649	TTGA	-	39671646	7	5	58	1	0	1	0	1	0	0	0	0	8070	1606	56	0	465	0	KCNJ15	21	39671646	Frame_Shift_Del	DEL	TTGA	TCGA-B9-A69E-01A-11D-A31X-10	3928522	39671646	8458249	100	5665											
USP9X	8239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	41043810	41043810	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tatggaaactcgaaggggtgCctacctcaatgctcttaaaa	13	10	9	9	1	2	0	1	0	1	0	3	2	2	1	2	3	4	1	2	3	7	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:41043810C>T	ENST00000324545.8	+	23	4073	c.3440C>T	c.(3439-3441)gCc>gTc	p.A1147V	USP9X_ENST00000378308.2_Missense_Mutation_p.A1147V	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1147					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CGAAGGGGTGCCTACCTCAAT	0.463																																					p.A1147V	Ovarian(172;1807 2695 35459 49286)	.											.	USP9X-563	0			c.C3440T						.						107	99	101					X																	41043810		2177	4280	6457	SO:0001583	missense	8239	exon23			GGGGTGCCTACCT	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3440C>T	X.37:g.41043810C>T	ENSP00000316357:p.Ala1147Val	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	143	72	NM_001039591	0	0	4	16	12	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984913	0.74474	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.11712	2.75;2.75	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.10723	0.0262	L	0.35723	1.085	0.80722	D	1	B;B	0.16802	0.019;0.019	B;B	0.17098	0.017;0.017	T	0.15321	-1.0441	10	0.09843	T	0.71	.	18.7017	0.91623	0.0:1.0:0.0:0.0	.	1147;1147	Q93008-1;Q93008	.;USP9X_HUMAN	V	1147	ENSP00000367558:A1147V;ENSP00000316357:A1147V	ENSP00000316357:A1147V	A	+	2	0	USP9X	40928754	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.729000	0.84864	2.361000	0.80049	0.513000	0.50165	GCC	.		0.463	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		T	41043810	C	T	41043810	3	4	58	1	0	0	0	0	1	0	0	0	17123	739	26	2	3526	2	USP9X	23	41043810	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		41043810	114226750	101	5666											
WDR13	64743	ucsc.edu;bcgsc.ca	37	chrX	48462761	48462761	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcccctcatgtccttccGccagggggcctgcgtgggtg	2	10	14	15	2	1	0	1	0	0	0	4	0	4	0	6	3	1	0	6	3	0	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:48462761G>A	ENST00000218056.5	+	8	1761	c.1256G>A	c.(1255-1257)cGc>cAc	p.R419H	WDR13_ENST00000376729.5_Missense_Mutation_p.R419H	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	419						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						ATGTCCTTCCGCCAGGGGGCC	0.632																																					p.R419H													.	WDR13-132	0			c.G1256A						.						55	42	46					X																	48462761		2203	4300	6503	SO:0001583	missense	64743	exon8			CCTTCCGCCAGGG	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"WD repeat domain containing"	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.1256G>A	X.37:g.48462761G>A	ENSP00000218056:p.Arg419His	Somatic	67	0		WXS	Illumina HiSeq		40	4	NM_017883	1	0	288	290	1	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	37	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	G	32	5.118173	0.94385	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.73152	-0.72;-0.72	5.74	5.74	0.90152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76863	0.4047	M	0.75264	2.295	0.80722	D	1	D	0.53885	0.963	P	0.48488	0.579	T	0.79855	-0.1627	10	0.56958	D	0.05	-3.1215	16.085	0.81038	0.0:0.0:1.0:0.0	.	419	Q9H1Z4	WDR13_HUMAN	H	419	ENSP00000365919:R419H;ENSP00000218056:R419H	ENSP00000218056:R419H	R	+	2	0	WDR13	48347705	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.978000	0.93450	2.400000	0.81607	0.597000	0.82753	CGC	.		0.632	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			A	48462761	G	A	48462761	3	1	58	1	0	0	0	0	1	0	0	0	17308	1087	38	1	1286	1	WDR13	23	48462761	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	7418951	48462761	106807799	102	5667											
GPR174	84636	hgsc.bcm.edu;bcgsc.ca	37	chrX	78426874	78426874	+	Frame_Shift_Del	DEL	T	T	-																															tttggtttctcatgtaccccTttcgcttccatgactgcaaa																								rs137871290		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:78426874delT	ENST00000276077.1	+	1	406	c.370delT	c.(370-372)tttfs	p.F124fs		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CATGTACCCCTTTCGCTTCCA	0.458										HNSCC(63;0.18)																											p.F124fs		.											.	GPR174-130	0			c.370delT						.						217	194	202					X																	78426874		2203	4300	6503	SO:0001589	frameshift_variant	84636	exon1			.	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.370delT	X.37:g.78426874delT	ENSP00000276077:p.Phe124fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	144	59	NM_032553	0	0	0	0	0	Q2M3F7	Frame_Shift_Del	DEL	ENST00000276077.1	37	CCDS14443.1																																																																																			.		0.458	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		-	78426874	T	-	78426874	7	5	58	1	0	1	0	1	0	0	0	0	6692	1609	56	0	372	0	GPR174	23	78426874	Frame_Shift_Del	DEL	T	TCGA-B9-A69E-01A-11D-A31X-10	29964113	78426874	76843686	103	5668											
UPF3B	65109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	118977251	118977251	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcataactttccaaaaacttTctatattctggatctaaata	15	15	3	8	0	3	0	0	0	3	0	4	1	4	1	1	1	2	1	1	1	8	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:118977251T>C	ENST00000276201.2	-	5	552	c.483A>G	c.(481-483)agA>agG	p.R161R	UPF3B_ENST00000478840.1_5'UTR|UPF3B_ENST00000345865.2_Silent_p.R161R	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	161	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCAAAAACTTTCTATATTCTG	0.279																																					p.R161R		.											.	UPF3B-133	0			c.A483G						.						161	144	150					X																	118977251		2202	4300	6502	SO:0001819	synonymous_variant	65109	exon5			AAACTTTCTATAT	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.483A>G	X.37:g.118977251T>C		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	31	17	NM_023010	0	0	0	0	0	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Silent	SNP	ENST00000276201.2	37	CCDS14588.1																																																																																			.		0.279	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			C	118977251	T	C	118977251	2	2	58	1	0	0	0	0	0	0	0	1	17039	1780	62	3		3	UPF3B	23	118977251	Silent	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	40550377	118977251	36293309	104	5669											
RERE	473	broad.mit.edu;bcgsc.ca	37	chr1	8425998	8425998	+	Frame_Shift_Del	DEL	T	T	-																															ggagctggctgcttcgggggTcttcttccaatagtaataga																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:8425998delT	ENST00000337907.3	-	14	1955	c.1321delA	c.(1321-1323)accfs	p.T441fs	RERE_ENST00000476556.1_5'UTR|RERE_ENST00000460659.1_5'UTR|RERE_ENST00000377464.1_Frame_Shift_Del_p.T173fs|RERE_ENST00000400908.2_Frame_Shift_Del_p.T441fs|RERE_ENST00000400907.2_Frame_Shift_Del_p.T441fs	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	441	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GCTTCGGGGGTCTTCTTCCAA	0.622																																					p.T441fs													.	RERE-515	0			c.1321delA						.						47	47	47					1																	8425998		2203	4300	6503	SO:0001589	frameshift_variant	473	exon14			CGGGGGTCTTCTT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1321delA	1.37:g.8425998delT	ENSP00000338629:p.Thr441fs	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	37	9	NM_012102	0	0	0	0	0	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Del	DEL	ENST00000337907.3	37	CCDS95.1																																																																																			.		0.622	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			-	8425998	T	-	8425998	7	5	59	1	0	1	0	1	0	0	0	0	13263	1667	58	0	3423	0	RERE	1	8425998	Frame_Shift_Del	DEL	T	TCGA-BQ-5875-01A-11D-1589-08		8425998	240824623	1	5670											
DNAJC16	23341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15894410	15894410	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catggagcgtgactacactgGttatgtactggctctgaatg	9	12	12	8	1	1	2	0	2	1	0	1	3	1	3	0	3	3	3	0	3	4	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:15894410G>A	ENST00000375847.3	+	15	2251	c.2087G>A	c.(2086-2088)gGt>gAt	p.G696D	RP4-680D5.8_ENST00000606186.1_RNA|DNAJC16_ENST00000375849.1_Intron|DNAJC16_ENST00000483270.1_3'UTR	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	696					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GACTACACTGGTTATGTACTG	0.443																																					p.G696D		.											.	DNAJC16-226	0			c.G2087A						.						148	134	139					1																	15894410		2203	4300	6503	SO:0001583	missense	23341	exon15			ACACTGGTTATGT	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.2087G>A	1.37:g.15894410G>A	ENSP00000365007:p.Gly696Asp	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	123	26	NM_015291	0	0	8	21	13	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	37	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059726	0.93846	.	.	ENSG00000116138	ENST00000375847	D	0.94417	-3.42	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.97173	0.9076	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97352	0.9964	10	0.87932	D	0	-20.3895	18.8118	0.92061	0.0:0.0:1.0:0.0	.	696	Q9Y2G8	DJC16_HUMAN	D	696	ENSP00000365007:G696D	ENSP00000365007:G696D	G	+	2	0	DNAJC16	15766997	1.000000	0.71417	0.501000	0.27601	0.987000	0.75469	9.238000	0.95380	2.790000	0.95986	0.655000	0.94253	GGT	.		0.443	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		A	15894410	G	A	15894410	3	1	59	1	0	0	0	0	1	0	0	0	4646	1261	44	2	2141	2	DNAJC16	1	15894410	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	7468412	15894410	233356211	2	5671											
DNAJC16	23341	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	15894493	15894493	+	Frame_Shift_Del	DEL	G	G	-																															tcgaagaggaggaagccataGggtcgtgcagtgatgttgac																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:15894493delG	ENST00000375847.3	+	15	2334	c.2170delG	c.(2170-2172)gggfs	p.G724fs	RP4-680D5.8_ENST00000606186.1_RNA|DNAJC16_ENST00000375849.1_Intron|DNAJC16_ENST00000483270.1_3'UTR	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	724					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GGAAGCCATAGGGTCGTGCAG	0.512																																					p.G724fs		.											.	DNAJC16-226	0			c.2170delG						.						124	103	110					1																	15894493		2203	4300	6503	SO:0001589	frameshift_variant	23341	exon15			.	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.2170delG	1.37:g.15894493delG	ENSP00000365007:p.Gly724fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	75	17	NM_015291	0	0	0	0	0	Q68D57|Q86X32|Q8N5P4	Frame_Shift_Del	DEL	ENST00000375847.3	37	CCDS30606.1																																																																																			.		0.512	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		-	15894493	G	-	15894493	7	5	59	1	0	1	0	1	0	0	0	0	4646	1000	35	0	2224	0	DNAJC16	1	15894493	Frame_Shift_Del	DEL	G	TCGA-BQ-5875-01A-11D-1589-08	83	15894493	233356128	3	5672											
BAI2	576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	32203282	32203282	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcggcatagatggcgagcagGgtgagcagcgccatgcacga	10	4	17	10	4	0	2	0	1	0	1	0	4	0	2	1	3	4	4	1	3	1	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:32203282G>A	ENST00000373658.3	-	19	3188	c.2847C>T	c.(2845-2847)acC>acT	p.T949T	BAI2_ENST00000527361.1_Silent_p.T949T|BAI2_ENST00000398556.3_Silent_p.T897T|BAI2_ENST00000398547.1_Silent_p.T882T|BAI2_ENST00000398538.1_Silent_p.T937T|BAI2_ENST00000440175.2_Silent_p.T591T|BAI2_ENST00000373655.2_Silent_p.T949T|BAI2_ENST00000465256.1_5'Flank|BAI2_ENST00000257070.4_Silent_p.T949T|BAI2_ENST00000398542.1_Silent_p.T882T	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	949					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		TGGCGAGCAGGGTGAGCAGCG	0.667																																					p.T949T		.											.	BAI2-526	0			c.C2847T						.						40	39	39					1																	32203282		2202	4299	6501	SO:0001819	synonymous_variant	576	exon19			GAGCAGGGTGAGC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.2847C>T	1.37:g.32203282G>A		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	56	22	NM_001703	0	0	0	1	1	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			.		0.667	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32203282	G	A	32203282	2	1	59	1	0	0	0	0	0	0	0	1	1300	1219	43	2		2	BAI2	1	32203282	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	16308789	32203282	217047339	4	5673											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34128679	34128679	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aacctcctctgtgtcaaacaCcaggaagtgtagcctgcacg	11	8	9	13	1	2	0	1	0	1	0	3	1	3	1	4	1	4	2	4	1	4	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:34128679C>G	ENST00000373380.1	-	5	905	c.685G>C	c.(685-687)Gtg>Ctg	p.V229L	CSMD2_ENST00000373381.4_Missense_Mutation_p.V1356L|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1316	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTGTCAAACACCAGGAAGTGT	0.592																																					p.V1316L		.											.	CSMD2-103	0			c.G3946C						.						69	62	65					1																	34128679		2203	4300	6503	SO:0001583	missense	114784	exon26			CAAACACCAGGAA	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.685G>C	1.37:g.34128679C>G	ENSP00000362478:p.Val229Leu	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_052896	0	0	0	0	0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37		.	.	.	.	.	.	.	.	.	.	C	26.3	4.720946	0.89205	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.17528	2.27;2.27	5.22	5.22	0.72569	CUB (5);	0.000000	0.85682	D	0.000000	T	0.33731	0.0873	L	0.46947	1.48	0.80722	D	1	P;D;D	0.65815	0.816;0.995;0.96	P;P;P	0.62382	0.667;0.901;0.838	T	0.00872	-1.1532	10	0.42905	T	0.14	.	18.1292	0.89596	0.0:1.0:0.0:0.0	.	229;1316;1356	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	L	1356;229	ENSP00000362479:V1356L;ENSP00000362478:V229L	ENSP00000241312:V1316L	V	-	1	0	CSMD2	33901266	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.606000	0.88127	0.561000	0.74099	GTG	.		0.592	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		G	34128679	C	G	34128679	3	3	59	1	0	0	0	0	1	0	0	0	3951	507	18	4	6693	4	CSMD2	1	34128679	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	1925397	34128679	215121942	5	5674											
LEPROT	54741	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	65895651	65895651	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcaaccagtagtgcctgtCgggaactggcatatttcttc	9	12	10	10	1	1	0	0	0	1	0	3	1	1	1	2	2	4	3	2	2	4	4	rs147651845	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:65895651C>A	ENST00000371065.4	+	3	337	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	LEPR_ENST00000349533.6_Intron|LEPR_ENST00000371059.3_Intron|LEPR_ENST00000371060.3_Intron|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000344610.8_Intron|LEPROT_ENST00000484243.1_3'UTR	NM_001198681.1|NM_017526.4	NP_001185610.1|NP_059996.1	O15243	OBRG_HUMAN	leptin receptor overlapping transcript	67					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			kidney(1)|large_intestine(1)|lung(5)	7				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TAGTGCCTGTCGGGAACTGGC	0.453																																					p.R76R		.											.	LEPROT-90	0			c.C226A						.						337	318	325					1																	65895651		2203	4300	6503	SO:0001819	synonymous_variant	54741	exon4			GCCTGTCGGGAAC	Y12670	CCDS630.1, CCDS72801.1	1p31.2	2008-02-05			ENSG00000213625	ENSG00000213625			29477	protein-coding gene	gene with protein product	"leptin receptor gene related protein"	613461				9207021	Standard	NM_001198681		Approved	OBRGRP, OB-RGRP, VPS55, FLJ90360	uc001dcf.3	O15243	OTTHUMG00000009065	ENST00000371065.4:c.199C>A	1.37:g.65895651C>A		Somatic	428	2		WXS	Illumina HiSeq	Phase_I	189	17	NM_001198681	0	0	175	175	0	Q6FHL5	Silent	SNP	ENST00000371065.4	37	CCDS630.1																																																																																			C|1.000;T|0.000		0.453	LEPROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025132.4	NM_017526		A	65895651	C	A	65895651	2	1	59	1	0	0	0	0	0	0	0	1	8753	875	31	4		4	LEPROT	1	65895651	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	31766972	65895651	183354970	6	5675											
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94502837	94502837	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaaggaagataagttcttgaCcaatgcactccaccagcttt	13	10	8	10	0	1	2	0	1	1	1	2	4	2	3	3	1	2	3	3	1	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:94502837C>A	ENST00000370225.3	-	25	3763	c.3677G>T	c.(3676-3678)gGt>gTt	p.G1226V		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1226					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AAGTTCTTGACCAATGCACTC	0.478																																					p.G1226V		.											.	ABCA4-162	0			c.G3677T						.						120	117	118					1																	94502837		2203	4300	6503	SO:0001583	missense	24	exon25			TCTTGACCAATGC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3677G>T	1.37:g.94502837C>A	ENSP00000359245:p.Gly1226Val	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	80	14	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.522436	0.85600	.	.	ENSG00000198691	ENST00000546054;ENST00000370225	T	0.80123	-1.34	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.90954	0.7156	H	0.96080	3.765	0.80722	D	1	D	0.56746	0.977	P	0.55011	0.766	D	0.93070	0.6482	10	0.87932	D	0	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	1226	P78363	ABCA4_HUMAN	V	18;1226	ENSP00000359245:G1226V	ENSP00000359245:G1226V	G	-	2	0	ABCA4	94275425	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.320000	0.79064	2.861000	0.98227	0.655000	0.94253	GGT	.		0.478	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94502837	C	A	94502837	3	1	59	1	0	0	0	0	1	0	0	0	34	507	18	4	3248	4	ABCA4	1	94502837	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	28607186	94502837	154747784	7	5676											
KCNA2	3737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	111146524	111146524	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttaccaaccggatgacaCggaggatggccagtgacatg	11	7	12	11	2	1	2	0	2	1	0	1	5	1	5	3	4	2	0	3	4	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:111146524C>A	ENST00000485317.1	-	3	1554	c.881G>T	c.(880-882)cGt>cTt	p.R294L	KCNA2_ENST00000440270.1_Missense_Mutation_p.R294L|KCNA2_ENST00000369770.3_Missense_Mutation_p.R294L|KCNA2_ENST00000316361.4_Missense_Mutation_p.R294L|KCNA2_ENST00000525120.1_5'Flank			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	294					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	CCGGATGACACGGAGGATGGC	0.537																																					p.R294L	Pancreas(18;568 735 10587 23710 36357)	.											.	KCNA2-91	0			c.G881T						.						102	103	103					1																	111146524		2203	4300	6503	SO:0001583	missense	3737	exon3			ATGACACGGAGGA	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.881G>T	1.37:g.111146524C>A	ENSP00000433109:p.Arg294Leu	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	92	33	NM_001204269	0	0	0	1	1	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212566	0.58452	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	D;D;D;D	0.99005	-4.93;-5.32;-5.32;-5.32	5.87	5.87	0.94306	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	H	0.98818	4.34	0.80722	D	1	D;D	0.71674	0.998;0.962	D;P	0.71414	0.973;0.748	D	0.97484	1.0049	10	0.87932	D	0	.	20.2182	0.98305	0.0:1.0:0.0:0.0	.	294;294	Q86XG6;P16389	.;KCNA2_HUMAN	L	294	ENSP00000358785:R294L;ENSP00000433109:R294L;ENSP00000415257:R294L;ENSP00000314520:R294L	ENSP00000314520:R294L	R	-	2	0	KCNA2	110948047	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.770000	0.85390	2.785000	0.95823	0.655000	0.94253	CGT	.		0.537	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111146524	C	A	111146524	3	1	59	1	0	0	0	0	1	0	0	0	8024	536	19	4	622	4	KCNA2	1	111146524	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	16643687	111146524	138104097	8	5677											
SPAG17	200162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	118535132	118535132	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcacctcattctttatgAcctcatgctgaatgaattgg	9	16	7	9	0	4	3	3	3	1	0	4	3	4	3	2	1	1	2	2	1	3	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:118535132A>T	ENST00000336338.5	-	36	5383	c.5318T>A	c.(5317-5319)gTc>gAc	p.V1773D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1773						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ATTCTTTATGACCTCATGCTG	0.473																																					p.V1773D		.											.	SPAG17-158	0			c.T5318A						.						116	112	113					1																	118535132		2203	4300	6503	SO:0001583	missense	200162	exon36			TTTATGACCTCAT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5318T>A	1.37:g.118535132A>T	ENSP00000337804:p.Val1773Asp	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	100	25	NM_206996	0	0	0	0	0	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562988	0.65538	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.19105	2.17	5.38	3.1	0.35709	.	0.311094	0.33854	N	0.004486	T	0.13329	0.0323	L	0.54323	1.7	0.41943	D	0.990622	P	0.47677	0.899	P	0.48227	0.571	T	0.02301	-1.1180	10	0.66056	D	0.02	.	5.9646	0.19318	0.6602:0.0:0.3398:0.0	.	1773	Q6Q759	SPG17_HUMAN	D	1773;253	ENSP00000337804:V1773D	ENSP00000337804:V1773D	V	-	2	0	SPAG17	118336655	1.000000	0.71417	0.993000	0.49108	0.946000	0.59487	3.048000	0.49862	0.886000	0.36113	-0.250000	0.11733	GTC	.		0.473	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118535132	A	T	118535132	3	4	59	1	0	0	0	0	1	0	0	0	15011	275	10	5	1405	5	SPAG17	1	118535132	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	7388608	118535132	130715489	9	5678											
HRNR	388697	hgsc.bcm.edu	37	chr1	152187192	152187192	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcccggaaccggacccatGtcggccgcgactaggagact	8	5	14	14	5	0	1	0	0	0	1	1	5	0	3	4	4	2	0	4	4	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:152187192G>A	ENST00000368801.2	-	3	6988	c.6913C>T	c.(6913-6915)Cat>Tat	p.H2305Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2305					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGGACCCATGTCGGCCGCGA	0.612																																					p.H2305Y		.											.	HRNR-93	0			c.C6913T						.						7	12	11					1																	152187192		1487	3704	5191	SO:0001583	missense	388697	exon3			ACCCATGTCGGCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6913C>T	1.37:g.152187192G>A	ENSP00000357791:p.His2305Tyr	Somatic	1440	0		WXS	Illumina HiSeq	Phase_I	1346	83	NM_001009931	0	0	0	0	0	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	5.809	0.333472	0.11013	.	.	ENSG00000197915	ENST00000368801	T	0.18810	2.19	3.38	1.4	0.22301	.	.	.	.	.	T	0.04543	0.0124	L	0.48642	1.525	0.09310	N	1	B	0.21821	0.061	B	0.14578	0.011	T	0.44406	-0.9330	9	0.11485	T	0.65	.	5.4473	0.16541	0.1147:0.0:0.6863:0.199	.	2305	Q86YZ3	HORN_HUMAN	Y	2305	ENSP00000357791:H2305Y	ENSP00000357791:H2305Y	H	-	1	0	HRNR	150453816	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.807000	0.04520	0.232000	0.21100	0.650000	0.86243	CAT	.		0.612	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152187192	G	A	152187192	3	1	59	1	0	0	0	0	1	0	0	0	7380	1377	48	2	1643	2	HRNR	1	152187192	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	33652060	152187192	97063429	10	5679											
CADM3	57863	broad.mit.edu	37	chr1	159169659	159169659	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cttggccactacttgatccgGcacaaaggtcagaggcacaa	12	7	10	12	1	1	2	1	1	0	1	2	2	2	2	2	4	1	2	2	4	3	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:159169659G>A	ENST00000368125.4	+	8	1228	c.1071G>A	c.(1069-1071)cgG>cgA	p.R357R	CADM3_ENST00000497636.1_3'UTR|CTA-134P22.2_ENST00000609696.1_RNA|CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000368124.4_Silent_p.R391R	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	357					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.R391R(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					ACTTGATCCGGCACAAAGGTC	0.562																																					p.R391R													.	CADM3-92	2	Substitution - coding silent(2)	endometrium(1)|central_nervous_system(1)	c.G1173A						.						95	75	82					1																	159169659		2203	4300	6503	SO:0001819	synonymous_variant	57863	exon9			GATCCGGCACAAA	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.1071G>A	1.37:g.159169659G>A		Somatic	35	1		WXS	Illumina HiSeq	Phase_I	44	4	NM_021189	0	0	0	0	0	Q8IZQ9|Q9NVJ5|Q9UJP1	Silent	SNP	ENST00000368125.4	37	CCDS44251.1																																																																																			.		0.562	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		A	159169659	G	A	159169659	2	1	59	1	0	0	0	0	0	0	0	1	2574	1190	42	2		2	CADM3	1	159169659	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	6982467	159169659	90080962	11	5680											
FMO4	2329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171303684	171303684	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggacagtggaagaaaacaTtgatgttgtgatcttcacta	13	12	11	5	0	2	3	1	2	1	1	2	5	2	5	0	2	1	1	0	2	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:171303684T>C	ENST00000367749.3	+	8	1292	c.962T>C	c.(961-963)aTt>aCt	p.I321T		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	321					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GAAGAAAACATTGATGTTGTG	0.368																																					p.I321T	Pancreas(24;816 862 7754 7993 32832)	.											.	FMO4-537	0			c.T962C						.						92	95	94					1																	171303684		2203	4300	6503	SO:0001583	missense	2329	exon8			AAAACATTGATGT	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.962T>C	1.37:g.171303684T>C	ENSP00000356723:p.Ile321Thr	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	79	31	NM_002022	0	0	4	8	4	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.668252	0.67814	.	.	ENSG00000076258	ENST00000367749	T	0.56941	0.43	5.63	4.47	0.54385	.	0.249916	0.40144	N	0.001171	T	0.72170	0.3427	M	0.93978	3.48	0.41142	D	0.985967	D	0.69078	0.997	D	0.77557	0.99	T	0.80176	-0.1491	10	0.87932	D	0	-9.0886	12.3662	0.55230	0.0:0.0:0.1412:0.8588	.	321	P31512	FMO4_HUMAN	T	321	ENSP00000356723:I321T	ENSP00000356723:I321T	I	+	2	0	FMO4	169570308	1.000000	0.71417	0.246000	0.24233	0.910000	0.53928	6.102000	0.71486	0.918000	0.36919	0.528000	0.53228	ATT	.		0.368	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		C	171303684	T	C	171303684	3	2	59	1	0	0	0	0	1	0	0	0	5976	1493	52	3	984	3	FMO4	1	171303684	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	12134025	171303684	77946937	12	5681											
CEP350	9857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	180063597	180063597	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaatccagcttagcaatcAggagcttcttggtgatgacc	12	10	10	9	0	2	2	1	2	1	0	3	4	3	3	2	2	3	3	2	2	4	3	rs573430116		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:180063597A>T	ENST00000367607.3	+	34	8775	c.8357A>T	c.(8356-8358)cAg>cTg	p.Q2786L	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2786					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						CTTAGCAATCAGGAGCTTCTT	0.388																																					p.Q2786L		.											.	CEP350-26	0			c.A8357T						.						59	59	59					1																	180063597		2203	4300	6503	SO:0001583	missense	9857	exon34			GCAATCAGGAGCT	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.8357A>T	1.37:g.180063597A>T	ENSP00000356579:p.Gln2786Leu	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	47	16	NM_014810	0	0	7	12	5	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377132	0.61735	.	.	ENSG00000135837	ENST00000367607;ENST00000417046	T	0.61859	0.07	5.31	5.31	0.75309	.	0.000000	0.44902	D	0.000414	T	0.70657	0.3249	M	0.72118	2.19	0.45662	D	0.998587	D;P	0.60160	0.987;0.935	D;P	0.67725	0.953;0.614	T	0.72007	-0.4420	9	.	.	.	.	9.4328	0.38620	0.9192:0.0:0.0808:0.0	.	2786;2786	E7EU22;Q5VT06	.;CE350_HUMAN	L	2786;250	ENSP00000356579:Q2786L	.	Q	+	2	0	CEP350	178330220	1.000000	0.71417	0.993000	0.49108	0.935000	0.57460	2.342000	0.43992	2.126000	0.65437	0.482000	0.46254	CAG	.		0.388	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180063597	A	T	180063597	3	4	59	1	0	0	0	0	1	0	0	0	3260	188	7	5	8487	5	CEP350	1	180063597	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	8759913	180063597	69187024	13	5682											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228494611	228494611	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccctgcagctgcgcctgTgcggttcctccgagagctgc	3	9	12	17	3	0	1	0	0	0	1	3	2	3	1	5	1	6	4	5	1	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:228494611T>C	ENST00000422127.1	+	45	11980	c.11936T>C	c.(11935-11937)gTg>gCg	p.V3979A	OBSCN_ENST00000570156.2_Missense_Mutation_p.V4936A|OBSCN_ENST00000366709.4_Missense_Mutation_p.V1098A|OBSCN_ENST00000366707.4_Missense_Mutation_p.V1613A|OBSCN_ENST00000284548.11_Missense_Mutation_p.V3979A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3979	Ig-like 41.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGCGCCTGTGCGGTTCCTC	0.662																																					p.V4936A		.											.	OBSCN-403	0			c.T14807C						.						10	12	11					1																	228494611		2080	4192	6272	SO:0001583	missense	84033	exon56			CGCCTGTGCGGTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11936T>C	1.37:g.228494611T>C	ENSP00000409493:p.Val3979Ala	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	9	8	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657906	0.47467	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.05382	3.45;3.45;3.45;3.45	5.75	5.75	0.90469	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	T	0.10252	0.0251	M	0.71206	2.165	0.33071	D	0.535386	B;P	0.35872	0.333;0.525	B;B	0.39660	0.306;0.116	T	0.06807	-1.0806	10	0.10111	T	0.7	.	11.8999	0.52678	0.0:0.0698:0.0:0.9302	.	3979;3979	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	A	3979;3979;1613;1098	ENSP00000284548:V3979A;ENSP00000409493:V3979A;ENSP00000355668:V1613A;ENSP00000355670:V1098A	ENSP00000284548:V3979A	V	+	2	0	OBSCN	226561234	0.986000	0.35501	0.213000	0.23690	0.014000	0.08584	2.048000	0.41278	2.198000	0.70561	0.379000	0.24179	GTG	.		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228494611	T	C	228494611	3	2	59	1	0	0	0	0	1	0	0	0	10838	1696	59	3	12110	3	OBSCN	1	228494611	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	48431014	228494611	20756010	14	5683											
OR2M3	127062	broad.mit.edu	37	chr1	248367073	248367073	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggatctggagagggtcgtcGcaaagcttttactacttgtt	8	13	13	7	2	1	1	0	0	1	1	3	3	1	2	0	3	3	3	0	3	3	5	rs138010167	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:248367073G>A	ENST00000456743.1	+	1	742	c.704G>A	c.(703-705)cGc>cAc	p.R235H		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R235H(2)		endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GAGGGTCGTCGCAAAGCTTTT	0.468													g|||	2	0.000399361	0	0	5008	,	,		20996	0.001		0.001	False		,,,				2504	0				p.R235H													.	OR2M3-70	2	Substitution - Missense(2)	large_intestine(2)	c.G704A						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	257	244	248		704	-3.3	0	1	dbSNP_134	248	0,8600		0,0,4300	no	missense	OR2M3	NM_001004689.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	235/313	248367073	1,13005	2203	4300	6503	SO:0001583	missense	127062	exon1			GTCGTCGCAAAGC		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.704G>A	1.37:g.248367073G>A	ENSP00000389625:p.Arg235His	Somatic	399	0		WXS	Illumina HiSeq	Phase_I	253	5	NM_001004689	0	0	0	0	0	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.305	0.424298	0.11928	2.27E-4	0.0	ENSG00000228198	ENST00000456743	T	0.00034	8.87	2.25	-3.31	0.04988	GPCR, rhodopsin-like superfamily (1);	1.276350	0.06104	N	0.665935	T	0.00073	0.0002	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04386	-1.0955	10	0.41790	T	0.15	.	7.4052	0.26987	0.6672:0.0:0.3328:0.0	.	235	Q8NG83	OR2M3_HUMAN	H	235	ENSP00000389625:R235H	ENSP00000389625:R235H	R	+	2	0	OR2M3	246433696	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.791000	0.00767	-0.925000	0.03775	0.398000	0.26397	CGC	G|1.000;A|0.000		0.468	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		A	248367073	G	A	248367073	3	1	59	1	0	0	0	0	1	0	0	0	11037	1087	38	1	706	1	OR2M3	1	248367073	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	19872462	248367073	883548	15	5684											
ADAM17	6868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	9630624	9630624	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcgaaccgatgcagaatcCatgctgctcagcatttcgac	11	9	9	12	3	1	1	1	0	0	1	3	4	2	1	2	0	6	4	2	0	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:9630624C>T	ENST00000310823.3	-	19	2339	c.2157G>A	c.(2155-2157)atG>atA	p.M719I	IAH1_ENST00000545602.1_Intron	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	719					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		ATGCAGAATCCATGCTGCTCA	0.537																																					p.M719I		.											.	ADAM17-659	0			c.G2157A						.						54	51	52					2																	9630624		2203	4300	6503	SO:0001583	missense	6868	exon19			AGAATCCATGCTG	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.2157G>A	2.37:g.9630624C>T	ENSP00000309968:p.Met719Ile	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	55	11	NM_003183	0	0	12	17	5	O60226	Missense_Mutation	SNP	ENST00000310823.3	37	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	C	9.835	1.189343	0.21954	.	.	ENSG00000151694	ENST00000310823	T	0.19806	2.12	5.46	5.46	0.80206	.	0.145332	0.64402	N	0.000007	T	0.14399	0.0348	N	0.12182	0.205	0.80722	D	1	B;B;B	0.13145	0.0;0.007;0.007	B;B;B	0.12156	0.0;0.007;0.007	T	0.11792	-1.0573	10	0.19590	T	0.45	.	19.3715	0.94490	0.0:1.0:0.0:0.0	.	438;719;719	Q53RS1;B2RNB2;P78536	.;.;ADA17_HUMAN	I	719	ENSP00000309968:M719I	ENSP00000309968:M719I	M	-	3	0	ADAM17	9548075	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	2.684000	0.46951	2.570000	0.86706	0.456000	0.33151	ATG	.		0.537	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			T	9630624	C	T	9630624	3	4	59	1	0	0	0	0	1	0	0	0	238	594	21	2	321	2	ADAM17	2	9630624	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		9630624	233568749	16	5685											
FAM49A	81553	hgsc.bcm.edu;broad.mit.edu	37	chr2	16736394	16736394	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgctccttcaaaacttttAtgcagcctttcatctaggag	9	14	6	12	0	3	0	2	0	1	0	4	1	4	1	3	1	4	2	3	1	4	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:16736394A>T	ENST00000381323.3	-	11	1071	c.851T>A	c.(850-852)aTa>aAa	p.I284K	FAM49A_ENST00000355549.2_Missense_Mutation_p.I284K|FAM49A_ENST00000406434.1_Missense_Mutation_p.I284K	NM_030797.3	NP_110424.1	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	284						intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)			CAAAACTTTTATGCAGCCTTT	0.458																																					p.I284K		.											.	FAM49A-226	0			c.T851A						.						52	51	51					2																	16736394		2203	4300	6503	SO:0001583	missense	81553	exon11			ACTTTTATGCAGC	AK001942	CCDS1688.1	2p24.3	2008-02-05			ENSG00000197872	ENSG00000197872			25373	protein-coding gene	gene with protein product							Standard	NM_030797		Approved	DKFZP566A1524, FLJ11080	uc002rck.2	Q9H0Q0	OTTHUMG00000090615	ENST00000381323.3:c.851T>A	2.37:g.16736394A>T	ENSP00000370724:p.Ile284Lys	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	34	7	NM_030797	0	0	0	0	0	B3KNZ1|Q53QW2	Missense_Mutation	SNP	ENST00000381323.3	37	CCDS1688.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.832727	0.91036	.	.	ENSG00000197872	ENST00000381323;ENST00000406434;ENST00000355549	T;T;T	0.55234	0.53;0.53;0.53	5.37	5.37	0.77165	.	0.041280	0.85682	D	0.000000	T	0.74642	0.3743	M	0.84683	2.71	0.80722	D	1	D	0.61080	0.989	D	0.71656	0.974	T	0.79593	-0.1739	10	0.87932	D	0	-26.8426	14.8606	0.70379	1.0:0.0:0.0:0.0	.	284	Q9H0Q0	FA49A_HUMAN	K	284	ENSP00000370724:I284K;ENSP00000384771:I284K;ENSP00000347744:I284K	ENSP00000347744:I284K	I	-	2	0	FAM49A	16599875	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.288000	0.96055	2.170000	0.68504	0.533000	0.62120	ATA	.		0.458	FAM49A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207203.2	NM_030797		T	16736394	A	T	16736394	3	4	59	1	0	0	0	0	1	0	0	0	5594	449	16	5	128	5	FAM49A	2	16736394	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	7105770	16736394	226462979	17	5686											
PIGF	5281	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	46815297	46815297	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggagagatctataagtgcTacgttttctttctactgtca	10	16	8	7	1	4	1	1	0	3	1	4	3	4	2	0	1	3	2	0	1	4	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:46815297T>C	ENST00000281382.6	-	5	717				PIGF_ENST00000306465.4_Missense_Mutation_p.S190G	NM_002643.3	NP_002634.1	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class F						C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ethanolaminephosphotransferase activity (GO:0004307)			breast(1)|endometrium(1)|lung(1)|stomach(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ctataagtgctaCGTTTTCTT	0.388																																					p.S190G		.											.	PIGF-226	0			c.A568G						.						107	95	100					2																	46815297		2203	4300	6503	SO:0001627	intron_variant	5281	exon6			AAGTGCTACGTTT		CCDS1827.1, CCDS1828.1	2p21-p16	2013-02-26	2006-06-28		ENSG00000151665	ENSG00000151665		"Phosphatidylinositol glycan anchor biosynthesis"	8962	protein-coding gene	gene with protein product		600153	"phosphatidylinositol glycan, class F"			8575782, 8463218	Standard	NM_173074		Approved		uc002rvd.3	Q07326	OTTHUMG00000128816	ENST00000281382.6:c.546+4316A>G	2.37:g.46815297T>C		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	46	22	NM_173074	0	0	1	13	12	Q8WW20	Missense_Mutation	SNP	ENST00000281382.6	37	CCDS1827.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.485331	0.26598	.	.	ENSG00000151665	ENST00000306465	.	.	.	4.19	-1.01	0.10169	.	.	.	.	.	T	0.27559	0.0677	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.11329	0.006	T	0.28681	-1.0036	7	0.87932	D	0	.	4.1091	0.10050	0.0:0.1982:0.3574:0.4443	.	190	Q07326-2	.	G	190	.	ENSP00000302663:S190G	S	-	1	0	PIGF	46668801	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.098000	0.11024	-0.159000	0.11021	-0.438000	0.05819	AGC	.		0.388	PIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250749.2	NM_173074		C	46815297	T	C	46815297	1	2	59	0	1	0	0	0	0	0	0	0	11913	1522	53	3		3	PIGF	2	46815297	Intron	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	30078903	46815297	196384076	18	5687											
TTC7A	57217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	47300864	47300864	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgatgctgagtcggctgggCcacaagagcttggcccagaa	9	7	14	11	1	0	4	0	2	0	2	1	4	0	4	2	3	2	3	2	3	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:47300864C>T	ENST00000319190.5	+	20	2747	c.2379C>T	c.(2377-2379)ggC>ggT	p.G793G	TTC7A_ENST00000409245.1_Silent_p.G759G|C2orf61_ENST00000464527.2_Intron|TTC7A_ENST00000394850.2_Silent_p.G817G|AC073283.7_ENST00000421759.1_RNA|RP11-761B3.1_ENST00000422269.1_Intron|TTC7A_ENST00000263737.6_Silent_p.G439G	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	793					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GTCGGCTGGGCCACAAGAGCT	0.652																																					p.G793G		.											.	TTC7A-136	0			c.C2379T						.						66	61	63					2																	47300864		2203	4300	6503	SO:0001819	synonymous_variant	57217	exon20			GCTGGGCCACAAG	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"Tetratricopeptide (TTC) repeat domain containing"	19750	protein-coding gene	gene with protein product		609332	"tetratricopeptide repeat domain 7"	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.2379C>T	2.37:g.47300864C>T		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	62	24	NM_020458	0	0	14	25	11	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			.		0.652	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		T	47300864	C	T	47300864	2	4	59	1	0	0	0	0	0	0	0	1	16745	726	26	2		2	TTC7A	2	47300864	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	485567	47300864	195898509	19	5688											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54876308	54876308	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggtcccatgaactgggacAggactatgagcatgtcacgg	11	7	14	9	1	1	2	1	2	0	0	2	4	2	4	1	4	2	1	1	4	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:54876308A>G	ENST00000356805.4	+	25	5464	c.5183A>G	c.(5182-5184)cAg>cGg	p.Q1728R	SPTBN1_ENST00000333896.5_Missense_Mutation_p.Q1715R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1728	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAACTGGGACAGGACTATGAG	0.552																																					p.Q1728R		.											.	SPTBN1-140	0			c.A5183G						.						82	70	74					2																	54876308		2203	4300	6503	SO:0001583	missense	6711	exon25			TGGGACAGGACTA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"Pleckstrin homology (PH) domain containing"	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.5183A>G	2.37:g.54876308A>G	ENSP00000349259:p.Gln1728Arg	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_003128	0	0	169	169	0	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.936737	0.92458	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.48201	0.82;0.82	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.73385	0.3580	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.985;0.996	T	0.77840	-0.2438	10	0.59425	D	0.04	.	16.2826	0.82703	1.0:0.0:0.0:0.0	.	1715;1728	Q01082-3;Q01082	.;SPTB2_HUMAN	R	1728;1715	ENSP00000349259:Q1728R;ENSP00000334156:Q1715R	ENSP00000334156:Q1715R	Q	+	2	0	SPTBN1	54729812	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.281000	0.95811	2.253000	0.74438	0.454000	0.30748	CAG	.		0.552	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54876308	A	G	54876308	3	3	59	1	0	0	0	0	1	0	0	0	15151	188	7	3	5390	3	SPTBN1	2	54876308	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	7575444	54876308	188323065	20	5689											
IL1R2	7850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	102626224	102626224	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agacacggatgtgggcccagGacggtgctctgtggcttctg	6	9	16	10	2	2	1	0	0	2	1	2	3	2	3	1	5	1	2	1	5	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:102626224G>T	ENST00000332549.3	+	3	497	c.268G>T	c.(268-270)Gac>Tac	p.D90Y	IL1R2_ENST00000441002.1_Missense_Mutation_p.D90Y|IL1R2_ENST00000393414.2_Missense_Mutation_p.D90Y	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	90	Ig-like C2-type 1.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						GTGGGCCCAGGACGGTGCTCT	0.597																																					p.D90Y	Pancreas(106;189 1628 2302 5133 12295)	.											.	IL1R2-522	0			c.G268T						.						139	147	145					2																	102626224		2203	4300	6503	SO:0001583	missense	7850	exon3			GCCCAGGACGGTG	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"Interleukins and interleukin receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.268G>T	2.37:g.102626224G>T	ENSP00000330959:p.Asp90Tyr	Somatic	359	1		WXS	Illumina HiSeq	Phase_I	270	85	NM_001261419	0	0	0	0	0	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.711212	0.30322	.	.	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000457817;ENST00000441002	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.8	4.92	0.64577	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.512100	0.21363	N	0.075776	T	0.59770	0.2218	M	0.76002	2.32	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.57039	-0.7879	10	0.56958	D	0.05	.	7.7685	0.28993	0.0807:0.0:0.756:0.1633	.	90	P27930	IL1R2_HUMAN	Y	90	ENSP00000330959:D90Y;ENSP00000377066:D90Y;ENSP00000408415:D90Y;ENSP00000414611:D90Y	ENSP00000330959:D90Y	D	+	1	0	IL1R2	101992656	0.347000	0.24853	0.015000	0.15790	0.125000	0.20455	1.279000	0.33191	1.466000	0.48025	-0.268000	0.10319	GAC	.		0.597	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		T	102626224	G	T	102626224	3	4	59	1	0	0	0	0	1	0	0	0	7680	1174	41	4	274	4	IL1R2	2	102626224	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	47749916	102626224	140573149	21	5690											
SLC4A10	57282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	162711596	162711597	+	Missense_Mutation	DNP	CT	CT	AG																															aagttgtattctgaatggaaCtgtgttgctggacatgcatg																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:162711596_162711597CT>AG	ENST00000446997.1	+	5	626_627	c.533_534CT>AG	c.(532-534)aCT>aAG	p.T178K	SLC4A10_ENST00000272716.5_Missense_Mutation_p.T178K|SLC4A10_ENST00000415876.2_Missense_Mutation_p.T178K|SLC4A10_ENST00000535165.1_Missense_Mutation_p.T178K|SLC4A10_ENST00000375514.5_Missense_Mutation_p.T189K|SLC4A10_ENST00000421911.1_Missense_Mutation_p.T178K|SLC4A10_ENST00000493021.1_3'UTR	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	178					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	CTGAATGGAACTGTGTTGCTGG	0.396																																					p.T178K		.											.	SLC4A10	0			c.T567G						.																																			SO:0001583	missense	57282	exon6			TGGAACTGTGTTG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	Exception_encountered	2.37:g.162711596_162711597delinsAG	ENSP00000393066:p.Thr178Lys	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	76	33		0	0	0	0	0	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	DNP	ENST00000446997.1	37	CCDS54411.1																																																																																			.		0.396	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		AG	162711597	CT	AG	162711596	3	1	59	1	0	0	0	0	1	0	0	0	14683	565	20	4	636	4	SLC4A10	2	162711596	Missense_Mutation	DNP	CT	TCGA-BQ-5875-01A-11D-1589-08	60085372	162711596	80487777	22	5691											
CYBRD1	79901	broad.mit.edu	37	chr2	172379114	172379114	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggggtcggcactgctcgtcgGcttcctgtcggtgatcttcg	2	12	15	12	5	1	1	0	1	1	0	7	1	2	1	1	5	1	3	1	5	0	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:172379114G>A	ENST00000321348.4	+	1	257	c.59G>A	c.(58-60)gGc>gAc	p.G20D	CYBRD1_ENST00000468308.1_3'UTR|CYBRD1_ENST00000375252.3_Missense_Mutation_p.G20D|CYBRD1_ENST00000409484.1_Intron	NM_024843.3	NP_079119.3	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1	20	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				cellular iron ion homeostasis (GO:0006879)|response to iron ion (GO:0010039)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|oxidoreductase activity, oxidizing metal ions (GO:0016722)			endometrium(1)|kidney(1)|large_intestine(3)|liver(2)|lung(3)	10						CTGCTCGTCGGCTTCCTGTCG	0.652																																					p.G20D													.	CYBRD1-90	0			c.G59A						.						68	64	65					2																	172379114		2203	4300	6503	SO:0001583	missense	79901	exon1			TCGTCGGCTTCCT	AK027115	CCDS2244.1, CCDS46449.1, CCDS58736.1	2q31	2013-03-14			ENSG00000071967	ENSG00000071967		"Cytochrome b genes"	20797	protein-coding gene	gene with protein product	"ferric-chelate reductase 3", "cytochrome b561 family, member A2"	605745				11230685	Standard	NM_001127383		Approved	DCYTB, FLJ23462, FRRS3, CYB561A2	uc002ugy.4	Q53TN4	OTTHUMG00000132260	ENST00000321348.4:c.59G>A	2.37:g.172379114G>A	ENSP00000319141:p.Gly20Asp	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	37	4	NM_024843	0	0	13	15	2	B2RE79|B4DWD7|Q6KC16|Q6KC17|Q6P147|Q6ZR51|Q9H0Q8|Q9H5G5	Missense_Mutation	SNP	ENST00000321348.4	37	CCDS2244.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041589	0.93685	.	.	ENSG00000071967	ENST00000321348;ENST00000375252	T	0.64991	-0.13	4.85	3.97	0.46021	Cytochrome b561/ferric reductase transmembrane (1);	0.000000	0.85682	D	0.000000	D	0.83857	0.5345	H	0.95187	3.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87446	0.2398	10	0.87932	D	0	-8.9137	12.2705	0.54704	0.0833:0.0:0.9167:0.0	.	20;20	Q53TN4-2;Q53TN4	.;CYBR1_HUMAN	D	20	ENSP00000319141:G20D	ENSP00000319141:G20D	G	+	2	0	CYBRD1	172087360	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	8.808000	0.91939	1.030000	0.39839	0.563000	0.77884	GGC	.		0.652	CYBRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255344.2	NM_024843		A	172379114	G	A	172379114	3	1	59	1	0	0	0	0	1	0	0	0	4140	1203	42	2	61	2	CYBRD1	2	172379114	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	9667518	172379114	70820259	23	5692											
RAPH1	65059	broad.mit.edu	37	chr2	204305855	204305855	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatcactgggggtgttggCggcttaaacagggcccctga	7	9	15	10	1	1	1	1	1	0	0	1	1	1	1	2	5	2	3	2	5	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:204305855C>T	ENST00000319170.5	-	14	2357	c.2058G>A	c.(2056-2058)ccG>ccA	p.P686P	RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000374493.3_Silent_p.P738P	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	686					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGGGTGTTGGCGGCTTAAACA	0.577																																					p.P686P													.	RAPH1-1151	0			c.G2058A						.						62	61	61					2																	204305855		2203	4299	6502	SO:0001819	synonymous_variant	65059	exon14			TGTTGGCGGCTTA	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.2058G>A	2.37:g.204305855C>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	92	5	NM_213589	0	0	0	0	0	Q96Q37|Q9C0I2	Silent	SNP	ENST00000319170.5	37	CCDS2359.1																																																																																			.		0.577	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		T	204305855	C	T	204305855	2	4	59	1	0	0	0	0	0	0	0	1	13082	755	27	1		1	RAPH1	2	204305855	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	31926741	204305855	38893518	24	5693											
ITPR1	3708	bcgsc.ca	37	chr3	4685828	4685828	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttccattccaggtggtcatAggtgacaaggtggttctgaa	9	13	12	7	0	2	2	1	2	1	0	4	2	4	2	2	5	0	1	2	5	3	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:4685828A>T	ENST00000443694.2	+	6	534	c.534A>T	c.(532-534)atA>atT	p.I178I	ITPR1_ENST00000354582.6_Silent_p.I178I|ITPR1_ENST00000544951.1_Silent_p.I178I|ITPR1_ENST00000456211.2_Silent_p.I178I|ITPR1_ENST00000357086.4_Silent_p.I178I|ITPR1_ENST00000423119.2_Silent_p.I178I|ITPR1_ENST00000302640.8_Silent_p.I178I			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	178	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AGGTGGTCATAGGTGACAAGG	0.493																																					p.I178I													.	ITPR1-710	0			c.A534T						.						100	97	98					3																	4685828		2008	4180	6188	SO:0001819	synonymous_variant	3708	exon8			GGTCATAGGTGAC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.534A>T	3.37:g.4685828A>T		Somatic	19	0		WXS	Illumina HiSeq	Phase_1	24	4	NM_001099952	0	0	0	0	0	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																			.		0.493	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4685828	A	T	4685828	2	4	59	1	0	0	0	0	0	0	0	1	7941	410	15	5		5	ITPR1	3	4685828	Silent	SNP	A	TCGA-BQ-5875-01A-11D-1589-08		4685828	193336602	25	5694											
STAC	6769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	36587768	36587768	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcatcccccttgatgtacTagaaaacatctgattgctgg	10	12	7	12	0	2	3	1	2	1	1	3	3	3	3	3	1	3	2	3	1	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:36587768T>G	ENST00000273183.3	+	11	1496	c.1196T>G	c.(1195-1197)cTa>cGa	p.L399R	STAC_ENST00000457375.2_Missense_Mutation_p.L338R	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	399					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						CTTGATGTACTAGAAAACATC	0.493																																					p.L399R		.											.	STAC-94	0			c.T1196G						.						151	131	138					3																	36587768		2203	4300	6503	SO:0001583	missense	6769	exon11			ATGTACTAGAAAA	D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.1196T>G	3.37:g.36587768T>G	ENSP00000273183:p.Leu399Arg	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	80	62	NM_003149	0	0	0	0	0	B2R8S8	Missense_Mutation	SNP	ENST00000273183.3	37	CCDS2662.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126023	0.77436	.	.	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000544687	T;T	0.09445	2.98;2.98	5.17	5.17	0.71159	Src homology-3 domain (1);Variant SH3 (1);	0.074155	0.56097	D	0.000036	T	0.33904	0.0879	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.10200	-1.0640	10	0.87932	D	0	.	13.5546	0.61751	0.0:0.0:0.0:1.0	.	338;399	E9PEA7;Q99469	.;STAC_HUMAN	R	399;338;331	ENSP00000273183:L399R;ENSP00000393713:L338R	ENSP00000273183:L399R	L	+	2	0	STAC	36562772	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.936000	0.70153	2.074000	0.62210	0.533000	0.62120	CTA	.		0.493	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		G	36587768	T	G	36587768	3	3	59	1	0	0	0	0	1	0	0	0	15271	1522	53	5	1238	5	STAC	3	36587768	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	31901940	36587768	161434662	26	5695											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47061276	47061276	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaatacttctttgctttTctttgctagttcactggagg	6	19	8	8	0	4	1	1	1	3	0	4	2	4	2	0	2	3	3	0	2	3	8			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:47061276T>A	ENST00000409792.3	-	19	7447	c.7405A>T	c.(7405-7407)Aaa>Taa	p.K2469*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2469	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCTTTGCTTTTCTTTGCTAGT	0.428			"N, F, S, Mis"		clear cell renal carcinoma																																p.K2469X		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.A7405T						.						286	251	263					3																	47061276		2203	4300	6503	SO:0001587	stop_gained	29072	exon19			TGCTTTTCTTTGC	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7405A>T	3.37:g.47061276T>A	ENSP00000386759:p.Lys2469*	Somatic	151	1		WXS	Illumina HiSeq	Phase_I	85	72	NM_014159	0	0	5	11	6	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	48	14.332947	0.99790	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6824	0.77381	0.0:0.0:0.0:1.0	.	.	.	.	X	2469	.	ENSP00000386759:K2469X	K	-	1	0	SETD2	47036280	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.701000	0.84566	2.367000	0.80283	0.528000	0.53228	AAA	.		0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47061276	T	A	47061276	4	1	59	1	0	0	0	0	0	1	0	0	14163	1792	62	5	301	5	SETD2	3	47061276	Nonsense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	10473508	47061276	150961154	27	5696											
NPRL2	10641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50386372	50386372	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggtaaagacaggtacaTcatactcctgggccaccgga	11	9	10	11	1	1	1	1	0	0	1	2	2	2	2	3	4	2	2	3	4	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:50386372T>A	ENST00000232501.3	-	5	956	c.518A>T	c.(517-519)gAt>gTt	p.D173V	CYB561D2_ENST00000418577.1_5'Flank|CYB561D2_ENST00000232508.5_5'Flank|XXcos-LUCA11.5_ENST00000606589.1_5'Flank|CYB561D2_ENST00000425346.1_5'Flank|CYB561D2_ENST00000424512.1_5'Flank|ZMYND10_ENST00000231749.3_5'Flank|NPRL2_ENST00000493465.1_5'Flank	NM_006545.4	NP_006536.3	Q8WTW4	NPRL2_HUMAN	nitrogen permease regulator-like 2 (S. cerevisiae)	173					negative regulation of kinase activity (GO:0033673)|protein phosphorylation (GO:0006468)		GTPase activator activity (GO:0005096)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	11						GACAGGTACATCATACTCCTG	0.537																																					p.D173V		.											.	NPRL2-278	0			c.A518T						.						133	126	128					3																	50386372		2203	4300	6503	SO:0001583	missense	10641	exon5			GGTACATCATACT	AF040708	CCDS2826.1	3p21.3	2010-03-30	2010-03-30	2010-03-30	ENSG00000114388	ENSG00000114388			24969	protein-coding gene	gene with protein product		607072	"tumor suppressor candidate 4"	TUSC4		11085536	Standard	NM_006545		Approved	NPR2L, NPR2	uc003daj.1	Q8WTW4	OTTHUMG00000156864	ENST00000232501.3:c.518A>T	3.37:g.50386372T>A	ENSP00000232501:p.Asp173Val	Somatic	165	1		WXS	Illumina HiSeq	Phase_I	149	107	NM_006545	0	0	0	14	14	A8K831|Q6FGS2|Q9Y249|Q9Y497	Missense_Mutation	SNP	ENST00000232501.3	37	CCDS2826.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945242	0.73672	.	.	ENSG00000114388	ENST00000232501	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.72534	0.3472	M	0.80422	2.495	0.80722	D	1	P	0.51057	0.941	P	0.51016	0.656	T	0.73113	-0.4085	9	0.30854	T	0.27	-20.1441	15.7486	0.77967	0.0:0.0:0.0:1.0	.	173	Q8WTW4	NPRL2_HUMAN	V	173	.	ENSP00000232501:D173V	D	-	2	0	NPRL2	50361376	1.000000	0.71417	0.990000	0.47175	0.940000	0.58332	7.968000	0.87980	2.122000	0.65172	0.533000	0.62120	GAT	.		0.537	NPRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346299.1	NM_006545		A	50386372	T	A	50386372	3	1	59	1	0	0	0	0	1	0	0	0	10623	1435	50	5	652	5	NPRL2	3	50386372	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	3325096	50386372	147636058	28	5697											
BAP1	8314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52441190	52441190	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagctcatggtgcctacCatggtcaatggggtagacct	8	10	11	12	0	2	1	2	0	0	1	3	1	3	1	4	4	3	2	4	4	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:52441190C>T	ENST00000460680.1	-	7	1051	c.580G>A	c.(580-582)Ggg>Agg	p.G194R	BAP1_ENST00000296288.5_Splice_Site_p.G194R	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TGGTGCCTACCATGGTCAATG	0.597			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.G194R	GBM(101;493 1458 7992 21037 25532)	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1-1032	1	Unknown(1)	eye(1)	c.G580A						.						59	57	58					3																	52441190		2203	4300	6503	SO:0001630	splice_region_variant	8314	exon7			GCCTACCATGGTC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.580+1G>A	3.37:g.52441190C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	52	34	NM_004656	0	0	0	6	6	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425433	0.96131	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.66995	-0.24;-0.24	6.05	6.05	0.98169	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	D	0.86756	0.6009	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87932	0.2711	10	0.66056	D	0.02	-7.544	20.6086	0.99469	0.0:1.0:0.0:0.0	.	194	Q92560	BAP1_HUMAN	R	194	ENSP00000417132:G194R;ENSP00000296288:G194R	ENSP00000296288:G194R	G	-	1	0	BAP1	52416230	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.783000	0.85696	2.880000	0.98712	0.655000	0.94253	GGG	.		0.597	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Missense_Mutation	T	52441190	C	T	52441190	5	4	59	1	0	0	0	0	0	0	1	0	1312	608	21	2	1653	2	BAP1	3	52441190	Splice_Site	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	2054818	52441190	145581240	29	5698											
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101378652	101378652	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcatgtggctttacacctGtgtgctttaacatatgtatt	9	17	8	7	0	0	0	0	0	0	0	0	0	0	0	1	1	4	4	1	1	4	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:101378652G>C	ENST00000312938.4	-	6	2601	c.2021C>G	c.(2020-2022)aCa>aGa	p.T674R	Y_RNA_ENST00000364251.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	674					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						CTTTACACCTGTGTGCTTTAA	0.373																																					p.T674R		.											.	ZBTB11-91	0			c.C2021G						.						118	117	117					3																	101378652		2203	4300	6503	SO:0001583	missense	27107	exon6			ACACCTGTGTGCT	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.2021C>G	3.37:g.101378652G>C	ENSP00000326200:p.Thr674Arg	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	99	36	NM_014415	0	0	2	7	5	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.560004	0.86335	.	.	ENSG00000066422	ENST00000312938	T	0.25749	1.78	5.09	5.09	0.68999	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.054542	0.64402	D	0.000001	T	0.47838	0.1467	L	0.52206	1.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48103	-0.9064	10	0.87932	D	0	-12.7873	18.48	0.90808	0.0:0.0:1.0:0.0	.	674	O95625	ZBT11_HUMAN	R	674	ENSP00000326200:T674R	ENSP00000326200:T674R	T	-	2	0	ZBTB11	102861342	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.181000	0.94874	2.387000	0.81309	0.491000	0.48974	ACA	.		0.373	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		C	101378652	G	C	101378652	3	2	59	1	0	0	0	0	1	0	0	0	17556	1377	48	4	1164	4	ZBTB11	3	101378652	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	48937462	101378652	96643778	30	5699											
KCTD8	386617	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	44450342	44450342	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catgctggccaaagtactgtCcgggacgctgagcagcgtcg	8	7	14	12	4	0	1	0	1	0	0	2	2	1	2	2	2	4	4	2	2	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr4:44450342C>T	ENST00000360029.3	-	1	482	c.199G>A	c.(199-201)Gac>Aac	p.D67N	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	67	BTB.				protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						AAAGTACTGTCCGGGACGCTG	0.682										HNSCC(17;0.042)																											p.D67N		.											.	KCTD8-92	0			c.G199A						.						25	21	22					4																	44450342		2190	4277	6467	SO:0001583	missense	386617	exon1			TACTGTCCGGGAC	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.199G>A	4.37:g.44450342C>T	ENSP00000353129:p.Asp67Asn	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	36	14	NM_198353	0	0	2	4	2	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	37	CCDS3467.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.187972	0.57909	.	.	ENSG00000183783	ENST00000360029	T	0.46451	0.87	3.59	3.59	0.41128	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	D	0.000001	T	0.34337	0.0894	L	0.28014	0.82	0.58432	D	0.999992	B	0.31640	0.333	B	0.37091	0.241	T	0.28902	-1.0029	10	0.42905	T	0.14	.	14.3619	0.66779	0.0:1.0:0.0:0.0	.	67	Q6ZWB6	KCTD8_HUMAN	N	67	ENSP00000353129:D67N	ENSP00000353129:D67N	D	-	1	0	KCTD8	44145099	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.682000	0.68182	1.810000	0.52873	0.467000	0.42956	GAC	.		0.682	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44450342	C	T	44450342	3	4	59	1	0	0	0	0	1	0	0	0	8136	855	30	2	1230	2	KCTD8	4	44450342	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		44450342	146703934	31	5700											
PPAT	5471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57262889	57262889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatatttaattggtggtgaaGctactcgaatgtgtaccttg	10	15	11	5	1	0	1	0	1	0	0	1	3	0	1	1	2	3	2	1	2	6	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr4:57262889G>A	ENST00000264220.2	-	10	1390	c.1253C>T	c.(1252-1254)gCt>gTt	p.A418V	RP11-646I6.6_ENST00000602749.1_lincRNA	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	418					'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TGGTGGTGAAGCTACTCGAAT	0.338																																					p.A418V		.											.	PPAT-90	0			c.C1253T						.						130	121	124					4																	57262889		2203	4299	6502	SO:0001583	missense	5471	exon10			GGTGAAGCTACTC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.1253C>T	4.37:g.57262889G>A	ENSP00000264220:p.Ala418Val	Somatic	154	1		WXS	Illumina HiSeq	Phase_I	77	30	NM_002703	0	0	7	8	1		Missense_Mutation	SNP	ENST00000264220.2	37	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	G	34	5.298750	0.95574	.	.	ENSG00000128059	ENST00000264220	D	0.99252	-5.63	5.77	5.77	0.91146	Phosphoribosyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.99483	0.9816	M	0.86097	2.795	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.98931	1.0787	10	0.87932	D	0	-26.581	19.9883	0.97356	0.0:0.0:1.0:0.0	.	418	Q06203	PUR1_HUMAN	V	418	ENSP00000264220:A418V	ENSP00000264220:A418V	A	-	2	0	PPAT	56957646	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.649000	0.98487	2.722000	0.93159	0.555000	0.69702	GCT	.		0.338	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		A	57262889	G	A	57262889	3	1	59	1	0	0	0	0	1	0	0	0	12328	971	34	2	308	2	PPAT	4	57262889	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	12812547	57262889	133891387	32	5701											
TMEM144	55314	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	159138552	159138552	+	Frame_Shift_Del	DEL	A	A	-																															tggggatcatttaatgccttAactggctgggcaagctcaag																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr4:159138552delA	ENST00000296529.6	+	5	832	c.312delA	c.(310-312)ttafs	p.L104fs	TMEM144_ENST00000514558.1_Frame_Shift_Del_p.L104fs	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	104						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		TTAATGCCTTAACTGGCTGGG	0.378																																					p.L104fs		.											.	TMEM144-90	0			c.312delA						.						110	105	107					4																	159138552		2203	4300	6503	SO:0001589	frameshift_variant	55314	exon5			.	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.312delA	4.37:g.159138552delA	ENSP00000296529:p.Leu104fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	62	26	NM_018342	0	0	0	0	0	D3DP24|Q49A05|Q9NUT3	Frame_Shift_Del	DEL	ENST00000296529.6	37	CCDS3799.1																																																																																			.		0.378	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		-	159138552	A	-	159138552	7	5	59	1	0	1	0	1	0	0	0	0	16090	359	13	0	322	0	TMEM144	4	159138552	Frame_Shift_Del	DEL	A	TCGA-BQ-5875-01A-11D-1589-08	101875663	159138552	32015724	33	5702											
CDC20B	166979	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	54429246	54429246	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgataacttacagtagtCatttcgaagaccagtaatat	17	12	6	6	1	1	2	1	1	0	1	2	3	1	2	1	0	2	2	1	0	7	6			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:54429246C>A	ENST00000381375.2	-	6	836	c.691G>T	c.(691-693)Gac>Tac	p.D231Y	CDC20B_ENST00000334206.5_Missense_Mutation_p.D231Y|CDC20B_ENST00000322374.6_Missense_Mutation_p.D231Y|CDC20B_ENST00000296733.1_Missense_Mutation_p.D231Y			Q86Y33	CD20B_HUMAN	cell division cycle 20B	231										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TTACAGTAGTCATTTCGAAGA	0.353																																					p.D231Y		.											.	CDC20B-90	0			c.G691T						.						99	100	100					5																	54429246		2203	4300	6503	SO:0001583	missense	166979	exon6			AGTAGTCATTTCG	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.691G>T	5.37:g.54429246C>A	ENSP00000370781:p.Asp231Tyr	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	99	37	NM_001170402	0	0	0	0	0	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.642068	0.67244	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374	T;T;T;T	0.10099	2.91;2.91;2.91;2.91	4.97	4.1	0.47936	WD40 repeat-like-containing domain (1);	0.000000	0.49305	D	0.000156	T	0.41789	0.1174	M	0.93328	3.405	0.80722	D	1	D;D;P;D	0.89917	0.999;0.97;0.949;1.0	D;P;P;D	0.74348	0.976;0.808;0.648;0.983	T	0.56607	-0.7951	10	0.87932	D	0	-6.0811	13.2244	0.59907	0.0:0.9223:0.0:0.0777	.	231;231;231;231	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	Y	231	ENSP00000335664:D231Y;ENSP00000296733:D231Y;ENSP00000370781:D231Y;ENSP00000315720:D231Y	ENSP00000296733:D231Y	D	-	1	0	CDC20B	54465003	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.180000	0.65048	1.303000	0.44873	0.650000	0.86243	GAC	.		0.353	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		A	54429246	C	A	54429246	3	1	59	1	0	0	0	0	1	0	0	0	3066	826	29	4	896	4	CDC20B	5	54429246	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		54429246	126486014	34	5703											
OTP	23440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	76932809	76932809	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gttggccctgctgctggccgGcttggctggggttcgggccg	0	10	19	12	3	0	0	0	0	0	0	1	0	0	0	3	7	2	6	3	7	0	3	rs148662448	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:76932809G>C	ENST00000306422.3	-	2	1422	c.284C>G	c.(283-285)gCc>gGc	p.A95G	OTP_ENST00000515716.1_5'UTR	NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	95					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		CTGCTGGCCGGCTTGGCTGGG	0.677																																					p.A95G		.											.	OTP-69	0			c.C284G						.						56	64	61					5																	76932809		2203	4300	6503	SO:0001583	missense	23440	exon2			TGGCCGGCTTGGC		CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"Homeoboxes / PRD class"	8518	protein-coding gene	gene with protein product		604529	"orthopedia homolog (Drosophila)"			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.284C>G	5.37:g.76932809G>C	ENSP00000302814:p.Ala95Gly	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	152	49	NM_032109	0	0	0	0	0		Missense_Mutation	SNP	ENST00000306422.3	37	CCDS4039.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506573	0.64410	.	.	ENSG00000171540	ENST00000306422	D	0.95588	-3.75	5.42	4.53	0.55603	Homeodomain-related (1);Homeodomain-like (1);	1.125700	0.06735	N	0.777347	D	0.90143	0.6920	N	0.08118	0	0.36166	D	0.848472	B	0.06786	0.001	B	0.04013	0.001	T	0.76332	-0.2998	10	0.21014	T	0.42	.	15.0725	0.72049	0.0:0.1428:0.8572:0.0	.	95	Q5XKR4	OTP_HUMAN	G	95	ENSP00000302814:A95G	ENSP00000302814:A95G	A	-	2	0	OTP	76968565	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	4.154000	0.58125	1.376000	0.46267	0.655000	0.94253	GCC	G|0.995;A|0.005		0.677	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2			C	76932809	G	C	76932809	3	2	59	1	0	0	0	0	1	0	0	0	11336	1203	42	4	701	4	OTP	5	76932809	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	22503563	76932809	103982451	35	5704											
AFF4	27125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	132270292	132270292	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcccactattgttataTgactcacggtcgtgcctctg	6	14	8	13	2	2	1	1	1	1	0	4	1	3	1	2	1	2	2	2	1	3	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:132270292T>G	ENST00000265343.5	-	3	844	c.465A>C	c.(463-465)tcA>tcC	p.S155S	AFF4_ENST00000378595.3_Silent_p.S155S|AFF4_ENST00000491831.1_5'UTR	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	155	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATTGTTATATGACTCACGGT	0.522																																					p.S155S	Ovarian(126;889 1733 2942 10745 11605)	.											.	AFF4-229	0			c.A465C						.						146	141	143					5																	132270292		2203	4300	6503	SO:0001819	synonymous_variant	27125	exon3			GTTATATGACTCA	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"ALL1 fused gene from 5q31"	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.465A>C	5.37:g.132270292T>G		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	147	65	NM_014423	0	0	15	25	10	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Silent	SNP	ENST00000265343.5	37	CCDS4164.1																																																																																			.		0.522	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		G	132270292	T	G	132270292	2	3	59	1	0	0	0	0	0	0	0	1	359	1451	51	5		5	AFF4	5	132270292	Silent	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	55337483	132270292	48644968	36	5705											
DST	667	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	56480769	56480769	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgcaaagcttcggccaccCggtactttttgccagtaaga	10	11	9	11	2	0	1	0	0	0	1	1	1	0	1	3	2	4	4	3	2	4	6	rs148062292		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr6:56480769C>T	ENST00000370765.6	-	24	7603	c.7496G>A	c.(7495-7497)cGg>cAg	p.R2499Q	DST_ENST00000244364.6_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1795					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TTCGGCCACCCGGTACTTTTT	0.512																																					p.R2499Q		.											.	DST-523	0			c.G7496A						.	C	GLN/ARG,	0,4406		0,0,2203	71	77	75		7496,	5.9	1	6	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	DST	NM_001723.5,NM_015548.4	43,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	2499/2650,	56480769	1,13005	2203	4300	6503	SO:0001583	missense	667	exon24			GCCACCCGGTACT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.7496G>A	6.37:g.56480769C>T	ENSP00000359801:p.Arg2499Gln	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	114	44	NM_001723	0	0	0	0	0	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	9.658	1.143434	0.21205	0.0	1.16E-4	ENSG00000151914	ENST00000370765	T	0.72725	-0.68	5.94	5.94	0.96194	.	.	.	.	.	T	0.55033	0.1895	.	.	.	0.09310	N	0.999998	B	0.29253	0.239	B	0.15870	0.014	T	0.58730	-0.7585	7	0.66056	D	0.02	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	2499	Q03001-3	.	Q	2499	ENSP00000359801:R2499Q	ENSP00000359801:R2499Q	R	-	2	0	DST	56588728	0.989000	0.36119	0.993000	0.49108	0.251000	0.25915	3.295000	0.51794	2.822000	0.97130	0.557000	0.71058	CGG	C|1.000;T|0.000		0.512	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56480769	C	T	56480769	3	4	59	1	0	0	0	0	1	0	0	0	4794	652	23	1	12903	1	DST	6	56480769	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		56480769	114634298	37	5706											
SEPT7	989	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	35930341	35930341	+	Frame_Shift_Del	DEL	A	A	-																															tatgagaactacagaagcagAaaacttgcagctgtgactta																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:35930341delA	ENST00000435235.1	+	10	1209	c.777delA	c.(775-777)agafs	p.R259fs	SEPT7_ENST00000432293.2_Intron|SEPT7_ENST00000399034.2_Frame_Shift_Del_p.R313fs|SEPT7_ENST00000350320.6_Frame_Shift_Del_p.R311fs|SEPT7_ENST00000494488.2_Frame_Shift_Del_p.R298fs|SEPT7_ENST00000399035.3_Frame_Shift_Del_p.R311fs			Q16181	SEPT7_HUMAN	septin 7	312	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						ACAGAAGCAGAAAACTTGCAG	0.333																																					p.R311fs		.											.	.	0			c.933delA						.						51	46	48					7																	35930341		1835	4089	5924	SO:0001589	frameshift_variant	989	exon10			.	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.777delA	7.37:g.35930341delA	ENSP00000413507:p.Arg259fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	31	15	NM_001011553	0	0	0	0	0	Q52M76|Q6NX50	Frame_Shift_Del	DEL	ENST00000435235.1	37																																																																																				.		0.333	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		-	35930341	A	-	35930341	7	5	59	1	0	1	0	1	0	0	0	0	14101	243	9	0	972	0	SEPT7	7	35930341	Frame_Shift_Del	DEL	A	TCGA-BQ-5875-01A-11D-1589-08		35930341	123208322	38	5707	65	2									
SEPT7	989	hgsc.bcm.edu;bcgsc.ca	37	chr7	35930344	35930344	+	Missense_Mutation	SNP	A	A	T																															gagaactacagaagcagaaaActtgcagctgtgacttataa																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:35930344A>T	ENST00000435235.1	+	10	1212	c.780A>T	c.(778-780)aaA>aaT	p.K260N	SEPT7_ENST00000432293.2_Intron|SEPT7_ENST00000399034.2_Missense_Mutation_p.K314N|SEPT7_ENST00000350320.6_Missense_Mutation_p.K312N|SEPT7_ENST00000494488.2_Missense_Mutation_p.K299N|SEPT7_ENST00000399035.3_Missense_Mutation_p.K312N			Q16181	SEPT7_HUMAN	septin 7	313	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						GAAGCAGAAAACTTGCAGCTG	0.338																																					p.K312N		.											.	.	0			c.A936T						.						51	46	48					7																	35930344		1836	4089	5925	SO:0001583	missense	989	exon10			CAGAAAACTTGCA	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.780A>T	7.37:g.35930344A>T	ENSP00000413507:p.Lys260Asn	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	27	15	NM_001011553	0	0	48	48	0	Q52M76|Q6NX50	Missense_Mutation	SNP	ENST00000435235.1	37		.	.	.	.	.	.	.	.	.	.	A	15.31	2.797066	0.50208	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	4.94	0.725	0.18242	.	0.000000	0.85682	U	0.000000	T	0.52338	0.1728	M	0.71920	2.185	0.80722	D	1	P;P;P	0.38420	0.63;0.63;0.63	B;B;B	0.42625	0.393;0.393;0.393	T	0.54364	-0.8305	10	0.62326	D	0.03	.	9.3111	0.37905	0.7223:0.0:0.2777:0.0	.	258;312;313	B4DNE4;E7EPK1;Q16181	.;.;SEPT7_HUMAN	N	260;314;312;312;258;260;299	ENSP00000413507:K260N;ENSP00000381992:K314N;ENSP00000344868:K312N;ENSP00000381993:K312N;ENSP00000438395:K299N	ENSP00000344868:K312N	K	+	3	2	SEPT7	35896869	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.373000	0.34272	0.300000	0.22699	0.460000	0.39030	AAA	.		0.338	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		T	35930344	A	T	35930344	3	4	59	1	0	0	0	0	1	0	0	0	14101	40	2	5	975	5	SEPT7	7	35930344	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	3	35930344	123208319	39	5708	65	2									
CDK13	8621	broad.mit.edu	37	chr7	40134552	40134552	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attagcacatcaactggcagAggcagaggcagagggttacc	13	6	13	9	0	1	3	1	0	0	3	1	3	1	3	1	4	3	5	1	4	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:40134552A>G	ENST00000181839.4	+	14	5117	c.4512A>G	c.(4510-4512)agA>agG	p.R1504R	CDK13_ENST00000340829.5_Silent_p.R1444R	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	1504					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						CAACTGGCAGAGGCAGAGGCA	0.483																																					p.R1504R													.	CDK13-548	0			c.A4512G						.						102	103	103					7																	40134552		2203	4300	6503	SO:0001819	synonymous_variant	8621	exon14			TGGCAGAGGCAGA	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.4512A>G	7.37:g.40134552A>G		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	162	3	NM_003718	0	0	19	19	0	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Silent	SNP	ENST00000181839.4	37	CCDS5461.1																																																																																			.		0.483	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		G	40134552	A	G	40134552	2	3	59	1	0	0	0	0	0	0	0	1	3135	301	11	3		3	CDK13	7	40134552	Silent	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	4204208	40134552	119004111	40	5709											
FOXP2	93986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	114299729	114299729	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtaatgcagcaacttggaagGtaactacttttccagcagtt	12	12	9	8	0	0	0	0	0	0	0	1	1	1	1	1	2	6	6	1	2	5	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:114299729G>A	ENST00000393494.2	+	13	1926		c.e13+1		FOXP2_ENST00000393498.2_Splice_Site|FOXP2_ENST00000393489.3_Splice_Site|FOXP2_ENST00000403559.4_Splice_Site|FOXP2_ENST00000408937.3_Splice_Site|FOXP2_ENST00000350908.4_Splice_Site|FOXP2_ENST00000393491.3_Splice_Site|FOXP2_ENST00000393500.3_Splice_Site			O15409	FOXP2_HUMAN	forkhead box P2						camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						AACTTGGAAGGTAACTACTTT	0.388																																					.		.											.	FOXP2-295	0			c.1647+1G>A						.						109	103	105					7																	114299729		2203	4300	6503	SO:0001630	splice_region_variant	93986	exon13			TGGAAGGTAACTA	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1647+1G>A	7.37:g.114299729G>A		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	58	25	NM_014491	0	0	0	0	0	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Splice_Site	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189262	0.57909	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6243	0.99512	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FOXP2	114086965	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.879000	0.98667	0.650000	0.86243	.	.		0.388	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491	Intron	A	114299729	G	A	114299729	5	1	59	1	0	0	0	0	0	0	1	0	6046	1275	44	2	1861	2	FOXP2	7	114299729	Splice_Site	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	74165177	114299729	44838934	41	5710											
NDUFB2	4708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	140402766	140402766	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcagcggactcatgtggTtctggattctctggcgcttt	4	16	11	10	2	5	0	2	0	3	0	6	2	5	2	0	4	1	2	0	4	0	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:140402766T>A	ENST00000476279.1	+	2	273	c.199T>A	c.(199-201)Ttc>Atc	p.F67I	NDUFB2_ENST00000482954.1_Missense_Mutation_p.F3I|NDUFB2_ENST00000476470.1_Missense_Mutation_p.F3I|NDUFB2_ENST00000472695.1_Missense_Mutation_p.F3I|NDUFB2_ENST00000475276.1_Missense_Mutation_p.F40I|NDUFB2_ENST00000460088.1_Missense_Mutation_p.F3I|NDUFB2_ENST00000471136.1_Missense_Mutation_p.F55I|NDUFB2_ENST00000204307.5_Missense_Mutation_p.F57I|NDUFB2_ENST00000465506.1_Missense_Mutation_p.F67I|NDUFB2_ENST00000464564.2_3'UTR|NDUFB2_ENST00000461457.1_Intron|NDUFB2_ENST00000247866.4_Missense_Mutation_p.F67I			O95178	NDUB2_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa	67					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|stomach(1)	10	Melanoma(164;0.00956)					ACTCATGTGGTTCTGGATTCT	0.547																																					p.F67I		.											.	NDUFB2-91	0			c.T199A						.						183	180	181					7																	140402766		2203	4300	6503	SO:0001583	missense	4708	exon2			ATGTGGTTCTGGA	AF050639	CCDS5862.1	7q34	2011-07-04	2002-08-29		ENSG00000090266	ENSG00000090266		"Mitochondrial respiratory chain complex / Complex I"	7697	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase AGGG subunit", "complex I AGGG subunit"	603838	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2 (8kD, AGGG)"			9763677, 9878551	Standard	NM_004546		Approved	AGGG, CI-AGGG	uc003vwa.3	O95178	OTTHUMG00000157424	ENST00000476279.1:c.199T>A	7.37:g.140402766T>A	ENSP00000419087:p.Phe67Ile	Somatic	216	1		WXS	Illumina HiSeq	Phase_I	231	73	NM_004546	1	0	305	619	313	Q6FGI6	Missense_Mutation	SNP	ENST00000476279.1	37	CCDS5862.1	.	.	.	.	.	.	.	.	.	.	T	32	5.121335	0.94385	.	.	ENSG00000090266	ENST00000482954;ENST00000476279;ENST00000247866;ENST00000465506;ENST00000204307;ENST00000464566;ENST00000460088;ENST00000472695;ENST00000476470;ENST00000471136;ENST00000475276	.	.	.	6.06	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.79986	0.4541	M	0.84511	2.7	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82341	-0.0505	9	0.87932	D	0	-19.9545	11.7302	0.51732	0.0:0.0689:0.0:0.9311	.	67	O95178	NDUB2_HUMAN	I	3;67;67;67;57;66;3;3;3;55;40	.	ENSP00000204307:F57I	F	+	1	0	NDUFB2	140049235	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.019000	0.76412	1.127000	0.42034	0.533000	0.62120	TTC	.		0.547	NDUFB2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348784.1	NM_004546		A	140402766	T	A	140402766	3	1	59	1	0	0	0	0	1	0	0	0	10307	1725	60	5	205	5	NDUFB2	7	140402766	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	26103037	140402766	18735897	42	5711											
SGK223	157285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	8234118	8234118	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtcactgatagcgacacCgttggtccggcaggaaggag	9	7	16	9	3	1	1	1	1	0	0	2	4	2	3	2	5	1	2	2	5	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:8234118C>A	ENST00000520004.1	-	3	2065	c.1801G>T	c.(1801-1803)Ggt>Tgt	p.G601C	SGK223_ENST00000330777.4_Missense_Mutation_p.G601C			Q86YV5	SG223_HUMAN		603							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ATAGCGACACCGTTGGTCCGG	0.662																																					p.G601C	GBM(34;731 755 10259 33573 33867)	.											.	.	0			c.G1801T						.						33	37	36					8																	8234118		1991	4172	6163	SO:0001583	missense	0	exon2			CGACACCGTTGGT																												ENST00000520004.1:c.1801G>T	8.37:g.8234118C>A	ENSP00000428054:p.Gly601Cys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	88	23	NM_001080826	0	0	2	6	4	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.965915	0.53507	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.60299	0.2;0.2	4.16	3.28	0.37604	.	0.672928	0.13029	N	0.419511	T	0.62588	0.2440	L	0.29908	0.895	0.25653	N	0.986074	D	0.76494	0.999	D	0.65010	0.931	T	0.54077	-0.8347	10	0.72032	D	0.01	.	11.5527	0.50729	0.0:0.9104:0.0:0.0896	.	601	Q86YV5	SG223_HUMAN	C	601	ENSP00000330930:G601C;ENSP00000428054:G601C	ENSP00000330930:G601C	G	-	1	0	AC068353.1	8271528	0.017000	0.18338	0.019000	0.16419	0.011000	0.07611	0.576000	0.23744	1.057000	0.40506	0.467000	0.42956	GGT	.		0.662	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8234118	C	A	8234118	3	1	59	1	0	0	0	0	1	0	0	0	14242	652	23	4	2423	4	SGK223	8	8234118	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		8234118	138129904	43	5712											
ZNF395	55893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	28209093	28209093	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagggcagggaggactcCgggccaggatgttctgggcc	6	6	18	11	1	1	1	0	1	1	0	2	4	2	4	4	6	0	2	4	6	0	1	rs145491469	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:28209093C>A	ENST00000344423.5	-	7	1283	c.1152G>T	c.(1150-1152)ccG>ccT	p.P384P	ZNF395_ENST00000523095.1_Silent_p.P384P|ZNF395_ENST00000523202.1_Silent_p.P384P	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	384					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GGGAGGACTCCGGGCCAGGAT	0.642																																					p.P384P		.											.	ZNF395-90	0			c.G1152T						.						62	73	69					8																	28209093		2203	4299	6502	SO:0001819	synonymous_variant	55893	exon7			GGACTCCGGGCCA	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1152G>T	8.37:g.28209093C>A		Somatic	160	1		WXS	Illumina HiSeq	Phase_I	178	62	NM_018660	0	0	11	19	8	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Silent	SNP	ENST00000344423.5	37	CCDS6067.1																																																																																			C|1.000;T|0.000		0.642	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			A	28209093	C	A	28209093	2	1	59	1	0	0	0	0	0	0	0	1	17913	639	23	4		4	ZNF395	8	28209093	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	19974975	28209093	118154929	44	5713											
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81399527	81399527	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcgagggccggcgactgTggatctggagctggacgcgc	5	6	20	10	5	1	0	0	0	1	0	1	5	1	3	1	6	1	1	1	6	0	0	rs185916023	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:81399527T>G	ENST00000430430.1	+	2	1261	c.482T>G	c.(481-483)gTg>gGg	p.V161G	ZBTB10_ENST00000379091.4_Intron|ZBTB10_ENST00000455036.3_Missense_Mutation_p.V161G|Y_RNA_ENST00000605948.1_RNA|ZBTB10_ENST00000426744.2_Missense_Mutation_p.V161G	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	161	Gly-rich.				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)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			CCGGCGACTGTGGATCTGGAG	0.706													T|||	8	0.00159744	0.0015	0	5008	,	,		13529	0		0.006	False		,,,				2504	0				p.V161G		.											.	ZBTB10-522	0			c.T482G						.	T	GLY/VAL,GLY/VAL	5,3779		0,5,1887	9	11	10		482,482	-0.7	0.8	8		10	26,8024		0,26,3999	yes	missense,missense	ZBTB10	NM_001105539.1,NM_023929.3	109,109	0,31,5886	GG,GT,TT		0.323,0.1321,0.262	benign,benign	161/872,161/848	81399527	31,11803	1892	4025	5917	SO:0001583	missense	65986	exon1			CGACTGTGGATCT	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.482T>G	8.37:g.81399527T>G	ENSP00000387462:p.Val161Gly	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	4	2	NM_023929	0	1	1	2	0	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Missense_Mutation	SNP	ENST00000430430.1	37	CCDS47880.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	0	0.0	6	0.0079155672823219	T	13.00	2.106749	0.37145	0.001321	0.00323	ENSG00000205189	ENST00000430430;ENST00000455036;ENST00000426744	T;T;T	0.10573	2.87;2.87;2.86	3.75	-0.741	0.11112	.	1.665380	0.04291	N	0.345463	T	0.05090	0.0136	N	0.19112	0.55	0.47511	D	0.999447	B;B	0.13145	0.004;0.007	B;B	0.16289	0.004;0.015	T	0.23833	-1.0177	10	0.72032	D	0.01	.	4.1032	0.10025	0.396:0.1092:0.0:0.4948	.	161;161	Q96DT7;Q96DT7-2	ZBT10_HUMAN;.	G	161	ENSP00000387462:V161G;ENSP00000412036:V161G;ENSP00000416134:V161G	ENSP00000416134:V161G	V	+	2	0	ZBTB10	81562082	0.995000	0.38212	0.796000	0.32109	0.801000	0.45260	0.316000	0.19469	0.047000	0.15862	0.379000	0.24179	GTG	T|0.997;G|0.003		0.706	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		G	81399527	T	G	81399527	3	3	59	1	0	0	0	0	1	0	0	0	17555	1696	59	5	484	5	ZBTB10	8	81399527	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	53190434	81399527	64964495	45	5714											
PLEC	5339	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	144998457	144998457	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgcgcggcctgctcctcCagccgccgccgctggaaggc	3	7	14	17	5	0	0	0	0	0	0	2	1	2	1	6	3	3	3	6	3	1	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:144998457C>T	ENST00000322810.4	-	31	6220	c.6051G>A	c.(6049-6051)ctG>ctA	p.L2017L	PLEC_ENST00000398774.2_Silent_p.L1848L|PLEC_ENST00000527096.1_Silent_p.L1903L|PLEC_ENST00000436759.2_Silent_p.L1907L|PLEC_ENST00000354589.3_Silent_p.L1880L|PLEC_ENST00000354958.2_Silent_p.L1858L|PLEC_ENST00000357649.2_Silent_p.L1884L|PLEC_ENST00000345136.3_Silent_p.L1880L|PLEC_ENST00000356346.3_Silent_p.L1866L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2017	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCTGCTCCTCCAGCCGCCGCC	0.706																																					p.L2017L		.											.	PLEC-141	0			c.G6051A						.						7	9	8					8																	144998457		1983	4065	6048	SO:0001819	synonymous_variant	5339	exon31			CTCCTCCAGCCGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.6051G>A	8.37:g.144998457C>T		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	18	8	NM_201380	0	0	6	11	5	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.		0.706	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144998457	C	T	144998457	2	4	59	1	0	0	0	0	0	0	0	1	12078	581	21	2		2	PLEC	8	144998457	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	63598930	144998457	1365565	46	5715											
VPS13A	23230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	79955424	79955424	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaataccatatatcagtggcTgaagaaggaaatgataaatg	19	9	9	4	0	1	3	1	2	0	1	1	4	1	4	1	2	1	1	1	2	9	4	rs144477984	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr9:79955424T>A	ENST00000360280.3	+	50	7244	c.6984T>A	c.(6982-6984)gcT>gcA	p.A2328A	VPS13A_ENST00000376636.3_Silent_p.A2289A|VPS13A_ENST00000357409.5_Silent_p.A2328A|VPS13A_ENST00000376634.4_Silent_p.A2328A	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2328					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TATCAGTGGCTGAAGAAGGAA	0.333																																					p.A2328A		.											.	VPS13A-161	0			c.T6984A						.						88	91	90					9																	79955424		2203	4295	6498	SO:0001819	synonymous_variant	23230	exon50			AGTGGCTGAAGAA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.6984T>A	9.37:g.79955424T>A		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	91	42	NM_001018038	0	0	7	14	7	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			T|1.000;C|0.000		0.333	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79955424	T	A	79955424	2	1	59	1	0	0	0	0	0	0	0	1	17222	1567	55	5		5	VPS13A	9	79955424	Silent	SNP	T	TCGA-BQ-5875-01A-11D-1589-08		79955424	61258007	47	5716											
CDC14B	8555	bcgsc.ca	37	chr9	99296440	99296441	+	Splice_Site	INS	-	-	TACA																															ggagaatgttggtggtaaccINStacataaagaaatgcaccag																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr9:99296440_99296441insTACA	ENST00000375241.1	-	9	1167		c.e9-1		CDC14B_ENST00000375236.1_Splice_Site|CDC14B_ENST00000463569.1_Splice_Site|CDC14B_ENST00000375242.3_Splice_Site|CDC14B_ENST00000375240.3_Splice_Site|CDC14B_ENST00000265659.2_Splice_Site	NM_003671.3|NM_033331.2	NP_003662.1|NP_201588.1	O60729	CC14B_HUMAN	cell division cycle 14B						activation of anaphase-promoting complex activity (GO:0051488)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	15		Acute lymphoblastic leukemia(62;0.0559)				TGGTGGTAACCTACATAAAGAA	0.337																																					.													.	CDC14B-228	0			c.605-1->TGTA						.																																			SO:0001630	splice_region_variant	8555	exon10			GGTAACCTACATA	AF023158	CCDS6721.1, CCDS6722.1, CCDS43853.1	9q22.3	2013-01-17	2013-01-17		ENSG00000081377	ENSG00000081377		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1719	protein-coding gene	gene with protein product		603505	"CDC14 (cell division cycle 14, S. cerevisiae) homolog B", "CDC14 cell division cycle 14 homolog B (S. cerevisiae)"			9367992	Standard	NM_003671		Approved	Cdc14B1, Cdc14B2, CDC14B3, hCDC14B	uc004awj.3	O60729	OTTHUMG00000020300	ENST00000375241.1:c.716-1->TGTA	9.37:g.99296441_99296444dupTACA		Somatic	34	0		WXS	Illumina HiSeq	Phase_1	16	5	NM_001077181	0	0	0	0	0	A6N5X8|A8MQ20|B1AL31|B1AL32|O43183|O60730|Q5JU08	Splice_Site	INS	ENST00000375241.1	37	CCDS6722.1																																																																																			.		0.337	CDC14B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053278.2	NM_033331	Intron	TACA	99296441	-	TACA	99296440	8	5	59	1	0	1	1	0	0	0	1	0	3063	695	24	0	805	0	CDC14B	9	99296440	Splice_Site	INS	-	TCGA-BQ-5875-01A-11D-1589-08	19341016	99296440	41916991	48	5717											
MUSK	4593	broad.mit.edu	37	chr9	113530177	113530177	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcagtcctggcaaaagatgCtcttgtttttctcaacacct	9	14	7	11	0	2	1	1	0	2	1	4	1	3	1	2	1	3	4	2	1	3	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr9:113530177C>G	ENST00000374448.4	+	9	1132	c.998C>G	c.(997-999)gCt>gGt	p.A333G	MUSK_ENST00000416899.2_Missense_Mutation_p.A333G|MUSK_ENST00000189978.5_Missense_Mutation_p.A333G	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	333	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						GCAAAAGATGCTCTTGTTTTT	0.493																																					p.A333G													.	MUSK-1379	0			c.C998G						.						109	111	110					9																	113530177		1933	4142	6075	SO:0001583	missense	4593	exon8			AAGATGCTCTTGT	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.998C>G	9.37:g.113530177C>G	ENSP00000363571:p.Ala333Gly	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	137	3	NM_005592	0	0	0	0	0	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.584564	0.28268	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000416899	T	0.76709	-1.04	5.08	4.18	0.49190	Frizzled domain (3);	0.565076	0.19549	N	0.111619	T	0.69342	0.3100	L	0.35487	1.065	0.39963	D	0.974694	B	0.16802	0.019	B	0.30105	0.111	T	0.63532	-0.6616	10	0.23891	T	0.37	.	12.7243	0.57162	0.0:0.9202:0.0:0.0798	.	333	O15146	MUSK_HUMAN	G	339;333;333;339	ENSP00000363571:A333G	ENSP00000189978:A339G	A	+	2	0	MUSK	112569998	0.262000	0.24073	0.667000	0.29798	0.696000	0.40369	2.200000	0.42724	1.291000	0.44653	0.591000	0.81541	GCT	.		0.493	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	113530177	C	G	113530177	3	3	59	1	0	0	0	0	1	0	0	0	10014	797	28	4	1062	4	MUSK	9	113530177	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	14233737	113530177	27683254	49	5718											
TLL2	7093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	98136535	98136535	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcaggccagttggggctcgCcagggtcccctccacactgc	5	7	13	16	1	1	0	1	0	0	0	4	0	3	0	5	4	1	2	5	4	0	1	rs150738442		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr10:98136535C>A	ENST00000357947.3	-	18	2587	c.2362G>T	c.(2362-2364)Gcg>Tcg	p.A788S		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	788	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		TTGGGGCTCGCCAGGGTCCCC	0.567																																					p.A788S		.											.	TLL2-93	0			c.G2362T						.						66	66	66					10																	98136535		2203	4300	6503	SO:0001583	missense	7093	exon18			GGCTCGCCAGGGT	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.2362G>T	10.37:g.98136535C>A	ENSP00000350630:p.Ala788Ser	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	104	33	NM_012465	0	0	0	0	0	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609563	0.28623	.	.	ENSG00000095587	ENST00000357947	T	0.16897	2.31	4.98	4.07	0.47477	CUB (5);	1.170570	0.06454	N	0.728224	T	0.05044	0.0135	N	0.00666	-1.275	0.22842	N	0.998661	B	0.10296	0.003	B	0.11329	0.006	T	0.36648	-0.9739	10	0.17832	T	0.49	.	3.874	0.09048	0.193:0.6039:0.0:0.2031	.	788	Q9Y6L7	TLL2_HUMAN	S	788	ENSP00000350630:A788S	ENSP00000350630:A788S	A	-	1	0	TLL2	98126525	0.000000	0.05858	0.988000	0.46212	0.744000	0.42396	0.481000	0.22260	1.431000	0.47355	0.655000	0.94253	GCG	C|1.000;T|0.000		0.567	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			A	98136535	C	A	98136535	3	1	59	1	0	0	0	0	1	0	0	0	15978	739	26	4	701	4	TLL2	10	98136535	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		98136535	37398212	50	5719											
GBF1	8729	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr10	104130546	104130546	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaagatttctgcttccttGtggagcgggcagtggtgggg	6	11	16	8	1	1	1	0	0	1	1	2	2	2	2	1	5	2	2	1	5	1	3	rs7894865	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr10:104130546G>T	ENST00000369983.3	+	29	3846	c.3586G>T	c.(3586-3588)Gtg>Ttg	p.V1196L		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1196					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CTGCTTCCTTGTGGAGCGGGC	0.542																																					p.V1197L		.											.	GBF1-91	0			c.G3589T						.						182	147	159					10																	104130546		2203	4300	6503	SO:0001583	missense	8729	exon29			TTCCTTGTGGAGC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.3586G>T	10.37:g.104130546G>T	ENSP00000359000:p.Val1196Leu	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	101	40	NM_001199378	0	0	15	33	18	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.360689	0.24598	.	.	ENSG00000107862	ENST00000369983	T	0.12569	2.67	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.22936	0.0554	N	0.17872	0.535	0.80722	D	1	B;B;D	0.58970	0.107;0.025;0.984	B;B;D	0.68192	0.037;0.016;0.956	T	0.05289	-1.0894	10	0.19590	T	0.45	-16.6116	19.277	0.94036	0.0:0.0:1.0:0.0	.	1196;1196;1196	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	L	1196	ENSP00000359000:V1196L	ENSP00000359000:V1196L	V	+	1	0	GBF1	104120536	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	7.674000	0.83992	2.782000	0.95742	0.655000	0.94253	GTG	G|0.996;A|0.004		0.542	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			T	104130546	G	T	104130546	3	4	59	1	0	0	0	0	1	0	0	0	6291	1377	48	4	3696	4	GBF1	10	104130546	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	5994011	104130546	31404201	51	5720											
SUFU	51684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104353417	104353417	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttggtgtctgcactgaagagCtacactcagcccagcagtgg	9	9	12	11	0	2	2	1	1	1	1	2	2	2	2	1	2	5	3	1	2	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr10:104353417C>A	ENST00000369902.3	+	5	788	c.622C>A	c.(622-624)Cta>Ata	p.L208I	SUFU_ENST00000369899.2_Missense_Mutation_p.L208I|RNU6-43P_ENST00000384302.1_RNA|SUFU_ENST00000423559.2_Missense_Mutation_p.L208I|SUFU_ENST00000471000.1_3'UTR	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	208					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		CACTGAAGAGCTACACTCAGC	0.607			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																												p.L208I		.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU-2246	0			c.C622A						.						99	83	89					10																	104353417		2203	4300	6503	SO:0001583	missense	51684	exon5	Familial Cancer Database		GAAGAGCTACACT	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.622C>A	10.37:g.104353417C>A	ENSP00000358918:p.Leu208Ile	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	73	39	NM_001178133	0	0	13	26	13	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Missense_Mutation	SNP	ENST00000369902.3	37	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614385	0.87359	.	.	ENSG00000107882	ENST00000369902;ENST00000369899;ENST00000423559	D;D;D	0.83755	-1.76;-1.76;-1.76	6.08	4.21	0.49690	Suppressor of fused domain (1);	0.062987	0.64402	D	0.000004	D	0.91088	0.7195	M	0.93763	3.455	0.53005	D	0.999963	P;P;D	0.61697	0.816;0.78;0.99	P;P;P	0.61132	0.789;0.683;0.884	D	0.91841	0.5483	10	0.72032	D	0.01	-14.0459	8.8655	0.35282	0.0:0.7723:0.0:0.2277	.	208;208;208	Q9UMX1;Q9UMX1-2;Q9UMX1-3	SUFU_HUMAN;.;.	I	208	ENSP00000358918:L208I;ENSP00000358915:L208I;ENSP00000411597:L208I	ENSP00000358915:L208I	L	+	1	2	SUFU	104343407	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	2.022000	0.41030	1.557000	0.49525	0.655000	0.94253	CTA	.		0.607	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		A	104353417	C	A	104353417	3	1	59	1	0	0	0	0	1	0	0	0	15400	796	28	4	640	4	SUFU	10	104353417	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	222871	104353417	31181330	52	5721											
POLR2L	5441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	840428	840428	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatcaggtccacgtgggccaGcagcatccggcggcagcagt	8	5	15	13	3	1	0	1	0	0	0	3	1	3	0	3	4	3	4	3	4	0	0			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:840428G>A	ENST00000322028.4	-	2	184	c.148C>T	c.(148-150)Ctg>Ttg	p.L50L	TSPAN4_ENST00000397397.2_5'Flank|TSPAN4_ENST00000397411.2_5'Flank|TSPAN4_ENST00000397408.1_5'Flank|TSPAN4_ENST00000397396.1_5'Flank	NM_021128.4	NP_066951.1	P62875	RPAB5_HUMAN	polymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa	50					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|RNA splicing (GO:0008380)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			lung(1)	1		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;4.1e-25)|Epithelial(43;3.15e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACGTGGGCCAGCAGCATCCGG	0.637																																					p.L50L		.											.	POLR2L-90	0			c.C148T						.						159	125	137					11																	840428		2203	4298	6501	SO:0001819	synonymous_variant	5441	exon2			GGGCCAGCAGCAT	U37690	CCDS7720.1	11p15	2013-01-21	2002-08-29		ENSG00000177700	ENSG00000177700		"RNA polymerase subunits"	9199	protein-coding gene	gene with protein product		601189	"polymerase (RNA) II (DNA directed) polypeptide L (7.6kD)"			8786124	Standard	NM_021128		Approved	RPB10beta, RBP10, RPABC5, RPB7.6, hRPB7.6, hsRPB10b	uc001lsc.3	P62875	OTTHUMG00000133316	ENST00000322028.4:c.148C>T	11.37:g.840428G>A		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	173	48	NM_021128	0	0	162	311	149	P52436|Q6FHX3	Silent	SNP	ENST00000322028.4	37	CCDS7720.1																																																																																			.		0.637	POLR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257114.1	NM_021128		A	840428	G	A	840428	2	1	59	1	0	0	0	0	0	0	0	1	12253	962	34	2		2	POLR2L	11	840428	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		840428	134166088	53	5722											
OR51A4	401666	broad.mit.edu	37	chr11	4967850	4967856	+	Frame_Shift_Del	DEL	AGGGAAG	AGGGAAG	-																															gtttcttaaagtgaaagggaAgggaagaaccaggagcatgc																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	AGGGAAG	AGGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:4967850_4967856delAGGGAAG	ENST00000380373.2	-	1	500_506	c.475_481delCTTCCCT	c.(475-483)cttcccttcfs	p.LPF159fs	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGAAAGGGAAGGGAAGAACCAGGAGC	0.44																																					p.159_161del													.	OR51A4-71	0			c.475_481del						.																																			SO:0001589	frameshift_variant	401666	exon1			AAGGGAAGGGAAG	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"GPCR / Class A : Olfactory receptors"	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.475_481delCTTCCCT	11.37:g.4967850_4967856delAGGGAAG	ENSP00000369731:p.Leu159fs	Somatic	318	0		WXS	Illumina HiSeq	Phase_I	351	43	NM_001005329	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000380373.2	37	CCDS31367.1																																																																																			.		0.44	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329		-	4967856	AGGGAAG	-	4967850	7	5	59	1	0	1	0	1	0	0	0	0	11113	72	3	0	462	0	OR51A4	11	4967850	Frame_Shift_Del	DEL	AGGGAAG	TCGA-BQ-5875-01A-11D-1589-08	4127422	4967850	130038666	54	5723											
OR51A2	401667	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	4976463	4976469	+	Frame_Shift_Del	DEL	AGGGAAG	AGGGAAG	-																															gcttcttaaagtgaaagggaAgggaagaaccaggagcatgc																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	AGGGAAG	AGGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:4976463_4976469delAGGGAAG	ENST00000380371.1	-	1	474_480	c.475_481delCTTCCCT	c.(475-483)cttcccttcfs	p.LPF159fs	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGAAAGGGAAGGGAAGAACCAGGAGC	0.44																																					p.159_161del		.											.	OR51A2-68	0			c.475_481del						.																																			SO:0001589	frameshift_variant	401667	exon1			.	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"GPCR / Class A : Olfactory receptors"	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.475_481delCTTCCCT	11.37:g.4976463_4976469delAGGGAAG	ENSP00000369729:p.Leu159fs	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	164	27	NM_001004748	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000380371.1	37	CCDS31368.1																																																																																			.		0.44	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748		-	4976469	AGGGAAG	-	4976463	7	5	59	1	0	1	0	1	0	0	0	0	11112	72	3	0	462	0	OR51A2	11	4976463	Frame_Shift_Del	DEL	AGGGAAG	TCGA-BQ-5875-01A-11D-1589-08	8613	4976463	130030053	55	5724											
SAAL1	113174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	18101957	18101957	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	attcaggttttaagtctgaaCcttcaaacttgggaagtttt	11	16	8	6	0	3	1	2	1	1	0	3	2	3	2	1	2	2	2	1	2	4	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:18101957C>G	ENST00000524803.1	-	12	1463	c.1414G>C	c.(1414-1416)Gtt>Ctt	p.V472L	SAAL1_ENST00000529318.1_Missense_Mutation_p.V474L|SAAL1_ENST00000300013.4_Missense_Mutation_p.V471L			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	472										breast(2)|large_intestine(5)|lung(8)	15						TAAGTCTGAACCTTCAAACTT	0.318																																					p.V472L		.											.	SAAL1-90	0			c.G1414C						.						59	62	61					11																	18101957		2200	4293	6493	SO:0001583	missense	113174	exon12			TCTGAACCTTCAA	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.1414G>C	11.37:g.18101957C>G	ENSP00000432487:p.Val472Leu	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	68	16	NM_138421	0	0	2	5	3	A6NH05	Missense_Mutation	SNP	ENST00000524803.1	37	CCDS31439.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.29|11.29	1.595377|1.595377	0.28445|0.28445	.|.	.|.	ENSG00000166788|ENSG00000166788	ENST00000532452|ENST00000524803;ENST00000300013;ENST00000529318	.|T;T;T	.|0.32023	.|1.47;1.47;1.47	5.56|5.56	4.65|4.65	0.58169|0.58169	.|.	.|0.883413	.|0.10083	.|N	.|0.718158	T|T	0.25568|0.25568	0.0622|0.0622	L|L	0.40543|0.40543	1.245|1.245	0.25551|0.25551	N|N	0.987081|0.987081	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.08055	.|0.003;0.003;0.003	T|T	0.20207|0.20207	-1.0282|-1.0282	5|10	.|0.22109	.|T	.|0.4	-0.1106|-0.1106	9.5663|9.5663	0.39400|0.39400	0.0:0.783:0.1416:0.0753|0.0:0.783:0.1416:0.0753	.|.	.|474;472;472	.|E9PRZ1;G1UCX3;Q96ER3	.|.;.;SAAL1_HUMAN	S|L	130|472;471;474	.|ENSP00000432487:V472L;ENSP00000300013:V471L;ENSP00000432216:V474L	.|ENSP00000300013:V471L	R|V	-|-	3|1	2|0	SAAL1|SAAL1	18058533|18058533	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.389000|0.389000	0.30415|0.30415	1.161000|1.161000	0.31773|0.31773	1.485000|1.485000	0.48380|0.48380	0.549000|0.549000	0.68633|0.68633	AGG|GTT	.		0.318	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421		G	18101957	C	G	18101957	3	3	59	1	0	0	0	0	1	0	0	0	13833	507	18	4	14	4	SAAL1	11	18101957	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	13125494	18101957	116904559	56	5725											
ARRB1	408	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74979954	74979954	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcccgatgcgggggttcctCtttgggcttggggtgcatta	3	14	15	9	2	1	0	0	0	1	0	3	1	3	0	2	5	2	3	2	5	1	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:74979954C>T	ENST00000420843.2	-	14	1169	c.1072G>A	c.(1072-1074)Gag>Aag	p.E358K	ARRB1_ENST00000393505.4_Missense_Mutation_p.E358K|ARRB1_ENST00000360025.3_Missense_Mutation_p.E350K	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	358	Interaction with TRAF6.				activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						GGGGGTTCCTCTTTGGGCTTG	0.622																																					p.E358K		.											.	ARRB1-567	0			c.G1072A						.						125	113	117					11																	74979954		2200	4293	6493	SO:0001583	missense	408	exon14			GTTCCTCTTTGGG	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"arrestin 2"	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.1072G>A	11.37:g.74979954C>T	ENSP00000409581:p.Glu358Lys	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	98	33	NM_004041	0	0	7	7	0	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Missense_Mutation	SNP	ENST00000420843.2	37	CCDS44684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.999914|3.999914	0.74818|0.74818	.|.	.|.	ENSG00000137486|ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025|ENST00000532447	T;T;T|.	0.10960|.	2.83;2.84;2.82|.	4.36|4.36	4.36|4.36	0.52297|0.52297	Immunoglobulin E-set (1);Arrestin, C-terminal (1);|.	0.142117|.	0.44483|.	D|.	0.000450|.	T|T	0.38134|0.38134	0.1029|0.1029	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B|.	0.25850|.	0.12;0.136|.	B;B|.	0.31495|.	0.079;0.131|.	T|T	0.25641|0.25641	-1.0126|-1.0126	10|5	0.41790|.	T|.	0.15|.	-10.8909|-10.8909	14.4868|14.4868	0.67622|0.67622	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	350;358|.	P49407-2;P49407|.	.;ARRB1_HUMAN|.	K|K	358;358;350|174	ENSP00000409581:E358K;ENSP00000377141:E358K;ENSP00000353124:E350K|.	ENSP00000353124:E350K|.	E|R	-|-	1|2	0|0	ARRB1|ARRB1	74657602|74657602	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	6.899000|6.899000	0.75682|0.75682	2.281000|2.281000	0.76405|0.76405	0.555000|0.555000	0.69702|0.69702	GAG|AGA	.		0.622	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041		T	74979954	C	T	74979954	3	4	59	1	0	0	0	0	1	0	0	0	981	922	32	2	196	2	ARRB1	11	74979954	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	56877997	74979954	60026562	57	5726											
GAB2	9846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	77934564	77934564	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgatgggtagccaagtgaGtcaaagtgatgggcccctgg	9	9	16	7	0	1	3	1	3	0	0	1	3	1	3	3	3	1	2	3	3	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:77934564G>A	ENST00000361507.4	-	6	1546	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	GAB2_ENST00000340149.2_Silent_p.D449D	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	487					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			AGCCAAGTGAGTCAAAGTGAT	0.557																																					p.D487D		.											.	GAB2-663	0			c.C1461T						.						218	207	211					11																	77934564		2200	4292	6492	SO:0001819	synonymous_variant	9846	exon6			AAGTGAGTCAAAG	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1461C>T	11.37:g.77934564G>A		Somatic	270	0		WXS	Illumina HiSeq	Phase_I	229	70	NM_080491	0	0	2	2	0	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			.		0.557	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		A	77934564	G	A	77934564	2	1	59	1	0	0	0	0	0	0	0	1	6168	1020	36	2		2	GAB2	11	77934564	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	2954610	77934564	57071952	58	5727											
CASP5	838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	104879534	104879534	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtaaaatatccagtcttacTttttacactggtcgactttt	10	18	5	8	1	1	0	0	0	1	0	3	1	2	0	1	1	2	1	1	1	5	8			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:104879534T>G	ENST00000260315.3	-	2	180	c.181A>C	c.(181-183)Aaa>Caa	p.K61Q	CASP5_ENST00000393139.2_Splice_Site_p.K28Q|CASP5_ENST00000418434.1_Intron|CASP5_ENST00000444749.2_Intron|CASP5_ENST00000393141.2_Splice_Site_p.K74Q|CASP5_ENST00000526056.1_Splice_Site_p.K74Q|CASP5_ENST00000531367.1_Intron			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	61	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		CCAGTCTTACTTTTTACACTG	0.388																																					p.K74Q		.											.	CASP5-661	0			c.A220C						.						101	95	97					11																	104879534		2202	4299	6501	SO:0001630	splice_region_variant	838	exon2			TCTTACTTTTTAC		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"Caspases"	1506	protein-coding gene	gene with protein product		602665	"caspase 5, apoptosis-related cysteine protease"			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.181+1A>C	11.37:g.104879534T>G		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	58	23	NM_001136112	0	0	0	0	0	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	.	8.417	0.845448	0.16963	.	.	ENSG00000137757	ENST00000393141;ENST00000393139;ENST00000260315;ENST00000526056;ENST00000456094	T;T;T;T;T	0.26810	4.66;1.71;4.68;4.66;2.75	1.45	0.338	0.15974	DEATH-like (1);Caspase Recruitment (2);	0.671852	0.11352	U	0.572858	T	0.09642	0.0237	N	0.08118	0	0.09310	N	1	B;B	0.28636	0.218;0.183	B;B	0.21546	0.035;0.021	T	0.31916	-0.9926	9	.	.	.	.	3.7847	0.08695	0.0:0.7446:0.0:0.2554	.	61;74	P51878;P51878-5	CASP5_HUMAN;.	Q	74;28;61;74;45	ENSP00000376849:K74Q;ENSP00000376847:K28Q;ENSP00000260315:K61Q;ENSP00000436877:K74Q;ENSP00000415241:K45Q	.	K	-	1	0	CASP5	104384744	0.989000	0.36119	0.124000	0.21820	0.011000	0.07611	0.266000	0.18534	0.155000	0.19261	-0.182000	0.12963	AAA	.		0.388	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	Missense_Mutation	G	104879534	T	G	104879534	5	3	59	1	0	0	0	0	0	0	1	0	2680	1623	56	5	1155	5	CASP5	11	104879534	Splice_Site	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	26944970	104879534	30126982	59	5728											
KDM5A	5927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	404935	404935	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaccaaagggctcttccgaGgttgtttccttggggtgcta	6	12	13	10	1	1	0	0	0	1	0	3	1	3	0	3	4	1	5	3	4	2	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:404935G>C	ENST00000399788.2	-	26	4621	c.4259C>G	c.(4258-4260)cCt>cGt	p.P1420R	KDM5A_ENST00000540838.1_5'Flank|KDM5A_ENST00000382815.4_Missense_Mutation_p.P1420R	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1420					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GCTCTTCCGAGGTTGTTTCCT	0.408			T	NUP98	AML																																p.P1420R		.		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A-227	0			c.C4259G						.						97	94	95					12																	404935		1825	4074	5899	SO:0001583	missense	5927	exon26			TTCCGAGGTTGTT		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4259C>G	12.37:g.404935G>C	ENSP00000382688:p.Pro1420Arg	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	143	54	NM_001042603	0	0	7	18	11	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551819	0.65311	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	D;D	0.85171	-1.95;-1.77	5.42	5.42	0.78866	.	0.118506	0.64402	D	0.000015	D	0.88254	0.6387	L	0.29908	0.895	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.85541	0.1215	10	0.25751	T	0.34	-15.9882	19.5762	0.95446	0.0:0.0:1.0:0.0	.	1420;1420	P29375;P29375-2	KDM5A_HUMAN;.	R	1420	ENSP00000382688:P1420R;ENSP00000372265:P1420R	ENSP00000372265:P1420R	P	-	2	0	KDM5A	275196	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.505000	0.97989	2.699000	0.92147	0.561000	0.74099	CCT	.		0.408	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		C	404935	G	C	404935	3	2	59	1	0	0	0	0	1	0	0	0	8154	1000	35	4	825	4	KDM5A	12	404935	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		404935	133446960	60	5729											
AEBP2	121536	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	19615463	19615463	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gcataagcagtactataatgGatgtagacagcacaatttcc	15	10	8	8	0	0	1	0	0	0	1	1	2	1	2	1	1	3	5	1	1	6	6			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:19615463G>C	ENST00000398864.3	+	2	717	c.691G>C	c.(691-693)Gat>Cat	p.D231H	AEBP2_ENST00000541908.1_Missense_Mutation_p.D2H|AEBP2_ENST00000360995.4_Missense_Mutation_p.D15H|AEBP2_ENST00000266508.9_Missense_Mutation_p.D231H	NM_001114176.1	NP_001107648.1	Q6ZN18	AEBP2_HUMAN	AE binding protein 2	231	Interaction with RBBP4.|Ser-rich.				chromatin modification (GO:0016568)	ESC/E(Z) complex (GO:0035098)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					TACTATAATGGATGTAGACAG	0.328																																					p.D231H		.											.	AEBP2-23	0			c.G691C						.						57	51	53					12																	19615463		1877	4113	5990	SO:0001583	missense	121536	exon2			ATAATGGATGTAG		CCDS44841.1, CCDS44842.1, CCDS58215.1	12p12.3	2012-10-02			ENSG00000139154	ENSG00000139154			24051	protein-coding gene	gene with protein product						10329662	Standard	NM_153207		Approved	MGC17922	uc001ref.2	Q6ZN18	OTTHUMG00000168906	ENST00000398864.3:c.691G>C	12.37:g.19615463G>C	ENSP00000381840:p.Asp231His	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	32	13	NM_001114176	0	0	9	17	8	Q59FS5|Q6ZN62|Q96BG3	Missense_Mutation	SNP	ENST00000398864.3	37	CCDS44841.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961310	0.74016	.	.	ENSG00000139154	ENST00000538425;ENST00000541908;ENST00000398864;ENST00000435841;ENST00000266508;ENST00000360995	D;T;D;D;T	0.91631	-2.52;-0.65;-2.88;-2.88;-0.45	5.55	4.66	0.58398	.	.	.	.	.	D	0.91938	0.7447	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	P	0.62885	0.908	D	0.93102	0.6509	9	0.66056	D	0.02	4.244	14.732	0.69388	0.0692:0.0:0.9308:0.0	.	231	Q6ZN18	AEBP2_HUMAN	H	2;2;231;165;231;15	ENSP00000444255:D2H;ENSP00000437983:D2H;ENSP00000381840:D231H;ENSP00000266508:D231H;ENSP00000354267:D15H	ENSP00000266508:D231H	D	+	1	0	AEBP2	19506730	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.263000	0.95617	1.578000	0.49821	0.655000	0.94253	GAT	.		0.328	AEBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401575.1	NM_153207		C	19615463	G	C	19615463	3	2	59	1	0	0	0	0	1	0	0	0	350	1174	41	4	697	4	AEBP2	12	19615463	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	19210528	19615463	114236432	61	5730											
PFKM	5213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48538849	48538849	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttgataggaattttgcCactaagatgggcgccaaggc	11	10	11	9	1	0	2	0	1	0	1	0	3	0	3	3	3	1	0	3	3	4	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:48538849C>A	ENST00000312352.7	+	21	2067	c.2028C>A	c.(2026-2028)gcC>gcA	p.A676A	PFKM_ENST00000340802.6_Silent_p.A747A|PFKM_ENST00000547587.1_Silent_p.A676A|PFKM_ENST00000359794.5_Silent_p.A676A|PFKM_ENST00000551804.1_Silent_p.A645A|PFKM_ENST00000395233.2_Silent_p.A645A	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	676	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GGAATTTTGCCACTAAGATGG	0.473																																					p.A747A		.											.	PFKM-254	0			c.C2241A						.						99	96	97					12																	48538849		2203	4300	6503	SO:0001819	synonymous_variant	5213	exon23			TTTTGCCACTAAG	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.2028C>A	12.37:g.48538849C>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	119	42	NM_001166686	0	0	160	289	129	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	37	CCDS8760.1																																																																																			.		0.473	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		A	48538849	C	A	48538849	2	1	59	1	0	0	0	0	0	0	0	1	11791	581	21	4		4	PFKM	12	48538849	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	28923386	48538849	85313046	62	5731											
NCKAP1L	3071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54903761	54903761	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgattaaccctgctaatTcagatacagtgagtgccctt	11	12	7	11	0	1	3	1	2	0	1	1	3	1	3	3	0	4	1	3	0	3	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:54903761T>G	ENST00000293373.6	+	7	806	c.727T>G	c.(727-729)Tca>Gca	p.S243A	NCKAP1L_ENST00000552211.1_3'UTR|NCKAP1L_ENST00000545638.2_Missense_Mutation_p.S193A	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	243					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CCCTGCTAATTCAGATACAGT	0.488																																					p.S243A		.											.	NCKAP1L-93	0			c.T727G						.						146	139	141					12																	54903761		2203	4300	6503	SO:0001583	missense	3071	exon7			GCTAATTCAGATA	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.727T>G	12.37:g.54903761T>G	ENSP00000293373:p.Ser243Ala	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	150	56	NM_005337	0	0	0	0	0	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	T	15.83	2.948714	0.53186	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.32515	1.45;1.45	5.83	5.83	0.93111	.	0.066512	0.64402	D	0.000007	T	0.25791	0.0628	L	0.38838	1.175	0.40526	D	0.980889	P	0.38473	0.633	B	0.38194	0.267	T	0.06058	-1.0848	10	0.18276	T	0.48	-7.392	14.1522	0.65392	0.0:0.0:0.0:1.0	.	243	P55160	NCKPL_HUMAN	A	243;193	ENSP00000293373:S243A;ENSP00000445596:S193A	ENSP00000293373:S243A	S	+	1	0	NCKAP1L	53190028	1.000000	0.71417	0.930000	0.37139	0.606000	0.37113	7.701000	0.84566	2.216000	0.71823	0.460000	0.39030	TCA	.		0.488	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		G	54903761	T	G	54903761	3	3	59	1	0	0	0	0	1	0	0	0	10248	1783	62	5	753	5	NCKAP1L	12	54903761	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	6364912	54903761	78948134	63	5732											
RFC5	5985	broad.mit.edu	37	chr12	118462710	118462710	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatctgtaactatctgtCaaagatcatccctgccttgc	9	13	5	14	0	5	1	3	0	2	1	6	1	6	1	3	0	3	1	3	0	3	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:118462710C>A	ENST00000454402.2	+	6	594	c.476C>A	c.(475-477)tCa>tAa	p.S159*	RFC5_ENST00000392542.2_Nonsense_Mutation_p.S138*|RFC5_ENST00000229043.3_Nonsense_Mutation_p.S74*	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	159					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AACTATCTGTCAAAGATCATC	0.458																																					p.S159X													.	RFC5-227	0			c.C476A						.						85	86	85					12																	118462710		2203	4300	6503	SO:0001587	stop_gained	5985	exon6			ATCTGTCAAAGAT		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.476C>A	12.37:g.118462710C>A	ENSP00000408295:p.Ser159*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	57	4	NM_007370	0	0	17	17	0	A8MZ62|B3KSX8	Nonsense_Mutation	SNP	ENST00000454402.2	37	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	C	43	9.842294	0.99277	.	.	ENSG00000111445	ENST00000449641;ENST00000537315;ENST00000229043;ENST00000454402;ENST00000392542	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.9222	18.1093	0.89530	0.0:1.0:0.0:0.0	.	.	.	.	X	74;74;74;159;138	.	ENSP00000229043:S74X	S	+	2	0	RFC5	116947093	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.715000	0.84713	2.561000	0.86390	0.563000	0.77884	TCA	.		0.458	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		A	118462710	C	A	118462710	4	1	59	1	0	0	0	0	0	1	0	0	13280	838	29	4	504	4	RFC5	12	118462710	Nonsense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	63558949	118462710	15389185	64	5733											
DCAF4	26094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	73412735	73412735	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctacttcaccaaccggaaGgtacgttgcccatccctgta	9	10	7	15	2	2	0	1	0	1	0	3	1	3	1	4	2	4	3	4	2	5	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr14:73412735G>A	ENST00000358377.2	+	7	898	c.678G>A	c.(676-678)aaG>aaA	p.K226K	DCAF4_ENST00000509153.1_Splice_Site_p.K165K|DCAF4_ENST00000394234.2_Splice_Site_p.K126K|DCAF4_ENST00000555042.1_Splice_Site_p.K226K|DCAF4_ENST00000553457.1_Splice_Site_p.K126K|DCAF4_ENST00000353777.3_Splice_Site_p.K165K	NM_001163509.1|NM_015604.3	NP_001156981.1|NP_056419.2	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4	226					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|skin(1)	22						CCAACCGGAAGGTACGTTGCC	0.527																																					p.K226K		.											.	DCAF4-92	0			c.G678A						.						142	128	132					14																	73412735		2203	4300	6503	SO:0001630	splice_region_variant	26094	exon7			CCGGAAGGTACGT	BC018979	CCDS9809.1, CCDS9810.1, CCDS41968.1, CCDS41968.2, CCDS55926.1	14q24.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000119599		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20229	protein-coding gene	gene with protein product			"WD repeat domain 21", "WD repeat domain 21A"	WDR21, WDR21A			Standard	NM_015604		Approved	DKFZp434K114	uc010ttr.2	Q8WV16		ENST00000358377.2:c.678+1G>A	14.37:g.73412735G>A		Somatic	135	1		WXS	Illumina HiSeq	Phase_I	146	53	NM_001163508	0	0	0	0	0	B4DUT6|G3V522|Q86U31|Q8IV10|Q96K22|Q9Y4P5	Silent	SNP	ENST00000358377.2	37	CCDS9809.1																																																																																			.		0.527	DCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361058.1	NM_015604	Silent	A	73412735	G	A	73412735	5	1	59	1	0	0	0	0	0	0	1	0	4276	1014	35	2	700	2	DCAF4	14	73412735	Splice_Site	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		73412735	33936805	65	5734											
ATXN3	4287	hgsc.bcm.edu	37	chr14	92537397	92537397	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgctgcttttgctgctgTctgaaacattcaaaagtgaa	10	15	9	7	0	2	2	1	2	1	0	2	2	2	2	0	0	5	5	0	0	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr14:92537397T>C	ENST00000532032.1	-	10	882	c.873A>G	c.(871-873)aaA>aaG	p.K291K	ATXN3_ENST00000545170.1_Silent_p.R300R|ATXN3_ENST00000393287.5_Splice_Site_p.K291K|ATXN3_ENST00000429774.2_Splice_Site_p.K284K|ATXN3_ENST00000340660.6_Splice_Site_p.K236K|ATXN3_ENST00000502250.1_Splice_Site_p.K112K|ATXN3_ENST00000503767.1_Splice_Site_p.K276K|ATXN3_ENST00000554491.1_5'UTR			P54252	ATX3_HUMAN	ataxin 3	291					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		tttgctgctgTCTGAAACATT	0.403																																					p.T130A	Esophageal Squamous(190;752 2094 29897 44875 49530)	.											.	ATXN3-522	0			c.A388G						.						24	28	27					14																	92537397		2182	4295	6477	SO:0001630	splice_region_variant	4287	exon6			CTGCTGTCTGAAA	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"Ataxins"	7106	protein-coding gene	gene with protein product		607047	"Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.873-1A>G	14.37:g.92537397T>C		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	29	3	NM_001164778	0	0	0	0	0	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37																																																																																				.		0.403	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	Silent	C	92537397	T	C	92537397	5	2	59	1	0	0	0	0	0	0	1	0	1214	1681	58	3	220	3	ATXN3	14	92537397	Splice_Site	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	19124662	92537397	14812143	66	5735											
GDE1	51573	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19516303	19516303	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaatgtccatcataacaaAtataaaatgtttccagaaag	20	10	4	7	0	1	1	1	0	0	1	3	1	3	1	2	0	1	1	2	0	8	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:19516303A>C	ENST00000353258.3	-	5	928	c.748T>G	c.(748-750)Ttt>Gtt	p.F250V	CTA-363E6.7_ENST00000569345.1_RNA	NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	250	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	13						ATCATAACAAATATAAAATGT	0.403																																					p.F250V		.											.	GDE1-70	0			c.T748G						.						161	151	154					16																	19516303		2197	4300	6497	SO:0001583	missense	51573	exon5			TAACAAATATAAA		CCDS10578.1	16p12-p11.2	2011-01-25			ENSG00000006007	ENSG00000006007	3.1.4.46		29644	protein-coding gene	gene with protein product	"membrane interacting protein of RGS16"	605943				12576545, 16472945	Standard	NM_016641		Approved	MIR16	uc002dgh.3	Q9NZC3	OTTHUMG00000131454	ENST00000353258.3:c.748T>G	16.37:g.19516303A>C	ENSP00000261386:p.Phe250Val	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	164	51	NM_016641	0	0	58	88	30	O43334|Q6PKF7|Q7KYR4	Missense_Mutation	SNP	ENST00000353258.3	37	CCDS10578.1	.	.	.	.	.	.	.	.	.	.	A	5.389	0.256908	0.10185	.	.	ENSG00000006007	ENST00000353258	T	0.27557	1.66	5.66	3.41	0.39046	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.193879	0.56097	D	0.000040	T	0.13884	0.0336	N	0.08118	0	0.23533	N	0.997474	B	0.24368	0.102	B	0.24701	0.055	T	0.20840	-1.0263	10	0.28530	T	0.3	-7.2402	5.9584	0.19286	0.7453:0.0:0.1327:0.122	.	250	Q9NZC3	GDE1_HUMAN	V	250	ENSP00000261386:F250V	ENSP00000261386:F250V	F	-	1	0	GDE1	19423804	0.998000	0.40836	0.125000	0.21846	0.104000	0.19210	3.728000	0.54991	0.417000	0.25871	0.533000	0.62120	TTT	.		0.403	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	NM_016641		C	19516303	A	C	19516303	3	2	59	1	0	0	0	0	1	0	0	0	6330	101	4	5	255	5	GDE1	16	19516303	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08		19516303	70838450	67	5736											
EEF2K	29904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	22237117	22237117	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagtccccccgagctggcCatgatggtgattctgatggg	6	9	14	12	1	1	3	0	3	1	0	2	4	2	3	5	3	1	1	5	3	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:22237117C>T	ENST00000263026.5	+	2	541	c.67C>T	c.(67-69)Cat>Tat	p.H23Y		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	23			H -> R (in dbSNP:rs9935059). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CCGAGCTGGCCATGATGGTGA	0.557																																					p.H23Y	NSCLC(195;1411 2157 20319 27471 51856)	.											.	EEF2K-856	0			c.C67T						.						56	55	55					16																	22237117		2197	4300	6497	SO:0001583	missense	29904	exon2			GCTGGCCATGATG	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.67C>T	16.37:g.22237117C>T	ENSP00000263026:p.His23Tyr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	92	20	NM_013302	0	0	0	2	2	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	C	1.297	-0.605948	0.03717	.	.	ENSG00000103319	ENST00000263026	T	0.08102	3.13	5.82	5.82	0.92795	.	0.750933	0.13237	N	0.403188	T	0.06142	0.0159	L	0.34521	1.04	0.09310	N	1	B	0.18863	0.031	B	0.19148	0.024	T	0.45891	-0.9230	10	0.02654	T	1	-9.8593	8.7204	0.34436	0.1519:0.7677:0.0:0.0804	.	23	O00418	EF2K_HUMAN	Y	23	ENSP00000263026:H23Y	ENSP00000263026:H23Y	H	+	1	0	EEF2K	22144618	0.005000	0.15991	0.338000	0.25549	0.158000	0.22134	0.566000	0.23593	2.757000	0.94681	0.655000	0.94253	CAT	.		0.557	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		T	22237117	C	T	22237117	3	4	59	1	0	0	0	0	1	0	0	0	4941	594	21	2	69	2	EEF2K	16	22237117	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	2720814	22237117	68117636	68	5737											
CX3CL1	6376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57413588	57413588	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcaacatcacgtgcagcaAgatgacatcaaagatacctg	16	7	8	10	1	2	3	2	1	0	2	2	3	2	3	1	0	5	3	1	0	4	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:57413588A>G	ENST00000006053.6	+	2	224	c.113A>G	c.(112-114)aAg>aGg	p.K38R	CX3CL1_ENST00000565912.1_5'UTR|CX3CL1_ENST00000564948.1_Intron|CX3CL1_ENST00000563383.1_Missense_Mutation_p.K44R	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	38	Chemokine.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						ACGTGCAGCAAGATGACATCA	0.522																																					p.K38R		.											.	CX3CL1-226	0			c.A113G						.						181	129	146					16																	57413588		2198	4300	6498	SO:0001583	missense	6376	exon2			GCAGCAAGATGAC	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"Endogenous ligands"	10647	protein-coding gene	gene with protein product		601880	"small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.113A>G	16.37:g.57413588A>G	ENSP00000006053:p.Lys38Arg	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	85	19	NM_002996	0	0	121	166	45	O00672	Missense_Mutation	SNP	ENST00000006053.6	37	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.382853	0.25031	.	.	ENSG00000006210	ENST00000006053	T	0.05199	3.48	2.87	0.504	0.16946	Chemokine interleukin-8-like domain (3);	0.903877	0.09116	N	0.846367	T	0.05777	0.0151	L	0.41710	1.295	0.23421	N	0.997716	B	0.17268	0.021	B	0.18871	0.023	T	0.42481	-0.9449	10	0.87932	D	0	-13.2272	3.0514	0.06171	0.602:0.2553:0.1427:0.0	.	38	P78423	X3CL1_HUMAN	R	38	ENSP00000006053:K38R	ENSP00000006053:K38R	K	+	2	0	CX3CL1	55971089	0.037000	0.19845	0.149000	0.22428	0.245000	0.25701	-0.164000	0.09983	0.081000	0.16988	0.254000	0.18369	AAG	.		0.522	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		G	57413588	A	G	57413588	3	3	59	1	0	0	0	0	1	0	0	0	4080	72	3	3	119	3	CX3CL1	16	57413588	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	35176471	57413588	32941165	69	5738											
SLC12A4	6560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67981315	67981315	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcagggacaggcctcggatcCcgtcaccccactccttctca	7	8	8	18	2	3	0	3	0	1	0	7	2	5	2	5	3	0	0	5	3	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:67981315C>G	ENST00000316341.3	-	16	2131	c.1991G>C	c.(1990-1992)gGg>gCg	p.G664A	CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000338335.3_Missense_Mutation_p.G664A|SLC12A4_ENST00000576616.1_Missense_Mutation_p.G664A|SLC12A4_ENST00000422611.2_Missense_Mutation_p.G666A|SLC12A4_ENST00000572037.1_Missense_Mutation_p.G616A|SLC12A4_ENST00000537830.2_Missense_Mutation_p.G658A|SLC12A4_ENST00000541864.2_Missense_Mutation_p.G633A	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	664					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GCCTCGGATCCCGTCACCCCA	0.672																																					p.G666A		.											.	SLC12A4-91	0			c.G1997C						.						46	56	53					16																	67981315		2195	4299	6494	SO:0001583	missense	6560	exon15			CGGATCCCGTCAC		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1991G>C	16.37:g.67981315C>G	ENSP00000318557:p.Gly664Ala	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	34	8	NM_001145962	0	0	32	53	21	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	C	35	5.435871	0.96168	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.98550	-4.99;-4.99;-4.99;-4.99;-4.99	5.76	5.76	0.90799	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.98748	0.9579	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D	0.89917	0.994;0.999;1.0;0.982;0.982;0.986	D;D;D;P;P;D	0.97110	0.95;0.992;1.0;0.854;0.854;0.91	D	0.99872	1.1098	10	0.72032	D	0.01	.	19.9738	0.97296	0.0:1.0:0.0:0.0	.	666;664;633;658;664;664	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	A	666;633;658;664;664	ENSP00000395983:G666A;ENSP00000438334:G633A;ENSP00000445962:G658A;ENSP00000343374:G664A;ENSP00000318557:G664A	ENSP00000318557:G664A	G	-	2	0	SLC12A4	66538816	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.760000	0.85248	2.732000	0.93576	0.655000	0.94253	GGG	.		0.672	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		G	67981315	C	G	67981315	3	3	59	1	0	0	0	0	1	0	0	0	14417	623	22	4	1302	4	SLC12A4	16	67981315	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	10567727	67981315	22373438	70	5739											
NFATC3	4775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	68224719	68224719	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gattgatttgtcttcagttcCatctttgcctgtgcctcatc	5	18	7	11	0	4	1	2	1	2	0	6	2	5	1	3	0	2	1	3	0	0	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:68224719C>A	ENST00000346183.3	+	9	2171	c.2147C>A	c.(2146-2148)cCa>cAa	p.P716Q	NFATC3_ENST00000329524.4_Missense_Mutation_p.P716Q|NFATC3_ENST00000349223.5_Missense_Mutation_p.P716Q|NFATC3_ENST00000575270.1_Missense_Mutation_p.P716Q|SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000535127.2_3'UTR	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	716					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TCTTCAGTTCCATCTTTGCCT	0.383																																					p.P716Q		.											.	NFATC3-92	0			c.C2147A						.						107	99	101					16																	68224719		2198	4300	6498	SO:0001583	missense	4775	exon9			CAGTTCCATCTTT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2147C>A	16.37:g.68224719C>A	ENSP00000300659:p.Pro716Gln	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	171	95	NM_173163	0	0	3	11	8	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.808656	0.70797	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.14516	2.5;2.5;2.5	5.55	4.59	0.56863	.	0.059669	0.64402	D	0.000002	T	0.33206	0.0855	M	0.72894	2.215	0.44079	D	0.996834	P;D;P;P	0.57257	0.747;0.979;0.747;0.747	P;P;P;P	0.58970	0.499;0.849;0.499;0.499	T	0.14144	-1.0483	10	0.72032	D	0.01	-2.556	15.7347	0.77834	0.1378:0.8622:0.0:0.0	.	716;716;716;716	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	Q	716;716;716;237	ENSP00000264008:P716Q;ENSP00000300659:P716Q;ENSP00000331324:P716Q	ENSP00000331324:P716Q	P	+	2	0	NFATC3	66782220	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.294000	0.78760	1.330000	0.45394	-0.321000	0.08615	CCA	.		0.383	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		A	68224719	C	A	68224719	3	1	59	1	0	0	0	0	1	0	0	0	10390	594	21	4	2181	4	NFATC3	16	68224719	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	243404	68224719	22130034	71	5740											
CHMP1A	5119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89715819	89715819	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcgtctacgcgggacgccatCcgaagccagttcacaccttc	8	7	10	16	5	2	0	1	0	1	0	4	2	3	1	4	1	2	1	4	1	2	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:89715819C>T	ENST00000397901.3	-	4	448	c.192G>A	c.(190-192)cgG>cgA	p.R64R	CHMP1A_ENST00000535997.2_5'UTR|CHMP1A_ENST00000253475.5_Missense_Mutation_p.D58N|CHMP1A_ENST00000547614.1_5'UTR|CHMP1A_ENST00000550102.1_Silent_p.R64R	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	64					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)		GGGACGCCATCCGAAGCCAGT	0.602																																					p.D58N		.											.	.	0			c.G172A						.						90	104	99					16																	89715819		2154	4245	6399	SO:0001819	synonymous_variant	5119	exon3			CGCCATCCGAAGC	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.192G>A	16.37:g.89715819C>T		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	210	63	NM_001083314	0	0	58	89	31	A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	37	CCDS45552.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674550	0.29693	.	.	ENSG00000131165	ENST00000253475	.	.	.	5.38	-6.01	0.02199	.	0.480369	0.15538	N	0.257085	T	0.22244	0.0536	.	.	.	0.09310	N	0.999992	B	0.12013	0.005	B	0.09377	0.004	T	0.15009	-1.0452	8	0.87932	D	0	0.0142	3.6277	0.08119	0.1185:0.3755:0.2125:0.2936	.	58	A6NG32	.	N	58	.	ENSP00000253475:D58N	D	-	1	0	CHMP1A	88243320	0.002000	0.14202	0.974000	0.42286	0.700000	0.40528	-1.471000	0.02344	-0.529000	0.06358	-1.157000	0.01802	GAT	.		0.602	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		T	89715819	C	T	89715819	2	4	59	1	0	0	0	0	0	0	0	1	3358	855	30	2		2	CHMP1A	16	89715819	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	21491100	89715819	638934	72	5741											
CDK10	8558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89756963	89756963	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatgtgtttccattccagatCgggcccgggacacccagaca	10	8	10	13	2	0	2	0	0	0	2	3	3	2	3	4	2	0	1	4	2	1	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:89756963C>T	ENST00000353379.7	+	3	206	c.163C>T	c.(163-165)Cgg>Tgg	p.R55W	CDK10_ENST00000514965.1_3'UTR|CDK10_ENST00000331006.8_Missense_Mutation_p.R8W|CDK10_ENST00000505473.1_5'UTR	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	55	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		CATTCCAGATCGGGCCCGGGA	0.592																																					p.R55W		.											.	CDK10-508	0			c.C163T						.						195	162	173					16																	89756963		2198	4300	6498	SO:0001583	missense	8558	exon3			CCAGATCGGGCCC	L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"Cyclin-dependent kinases"	1770	protein-coding gene	gene with protein product		603464	"cyclin-dependent kinase (CDC2-like) 10"			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.163C>T	16.37:g.89756963C>T	ENSP00000338673:p.Arg55Trp	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	144	28	NM_052988	0	0	0	1	1	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Missense_Mutation	SNP	ENST00000353379.7	37	CCDS10984.2	.	.	.	.	.	.	.	.	.	.	C	25.2	4.617358	0.87359	.	.	ENSG00000185324	ENST00000331006;ENST00000393082;ENST00000353379	T;T	0.66995	0.87;-0.24	5.1	3.11	0.35812	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84906	0.5576	M	0.92268	3.29	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.996;0.999	D	0.87752	0.2592	10	0.87932	D	0	-35.2961	14.2251	0.65853	0.2716:0.7284:0.0:0.0	.	49;55;49	B7Z319;Q15131;B3KQJ3	.;CDK10_HUMAN;.	W	8;26;55	ENSP00000329957:R8W;ENSP00000338673:R55W	ENSP00000329957:R8W	R	+	1	2	CDK10	88284464	1.000000	0.71417	0.996000	0.52242	0.815000	0.46073	3.632000	0.54287	0.517000	0.28361	0.561000	0.74099	CGG	.		0.592	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2			T	89756963	C	T	89756963	3	4	59	1	0	0	0	0	1	0	0	0	3131	875	31	1	173	1	CDK10	16	89756963	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	41144	89756963	597790	73	5742											
ACAP1	9744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7250507	7250507	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgggagccagccccggagtGggccagcatcaaccttggtg	7	5	15	14	2	1	0	1	0	0	0	1	2	1	2	6	4	4	1	6	4	1	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:7250507G>A	ENST00000158762.3	+	14	1495	c.1289G>A	c.(1288-1290)tGg>tAg	p.W430*		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	430	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.|Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GCCCCGGAGTGGGCCAGCATC	0.657																																					p.W430X		.											.	ACAP1-153	0			c.G1289A						.						75	86	82					17																	7250507		2203	4300	6503	SO:0001587	stop_gained	9744	exon14			CGGAGTGGGCCAG	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1289G>A	17.37:g.7250507G>A	ENSP00000158762:p.Trp430*	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	121	38	NM_014716	0	0	2	2	0	Q53XN9	Nonsense_Mutation	SNP	ENST00000158762.3	37	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	G	40	8.222149	0.98712	.	.	ENSG00000072818	ENST00000158762	.	.	.	4.77	4.77	0.60923	.	0.120594	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3166	0.74085	0.0:0.0:1.0:0.0	.	.	.	.	X	430	.	ENSP00000158762:W430X	W	+	2	0	ACAP1	7191231	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.244000	0.95423	2.480000	0.83734	0.462000	0.41574	TGG	.		0.657	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		A	7250507	G	A	7250507	4	1	59	1	0	0	0	0	0	1	0	0	118	1357	47	2	1343	2	ACAP1	17	7250507	Nonsense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		7250507	73944703	74	5743											
ATAD5	79915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	29162059	29162059	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcccagcaggtacgctttaaGacagttactgttcttgcaca	10	12	8	11	1	1	1	0	0	1	1	2	1	2	1	1	1	4	6	1	1	3	6			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:29162059G>C	ENST00000321990.4	+	2	1338	c.960G>C	c.(958-960)aaG>aaC	p.K320N	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	320					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TACGCTTTAAGACAGTTACTG	0.378																																					p.K320N		.											.	ATAD5-93	0			c.G960C						.						51	54	53					17																	29162059		2173	4287	6460	SO:0001583	missense	79915	exon2			CTTTAAGACAGTT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.960G>C	17.37:g.29162059G>C	ENSP00000313171:p.Lys320Asn	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	61	22	NM_024857	0	0	0	0	0	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	9.891	1.204236	0.22205	.	.	ENSG00000176208	ENST00000321990	T	0.11930	2.73	5.91	2.57	0.30868	.	0.221364	0.38778	N	0.001570	T	0.29061	0.0722	M	0.66939	2.045	0.29942	N	0.821002	D;D	0.76494	0.999;0.997	D;P	0.71656	0.974;0.879	T	0.06789	-1.0807	10	0.87932	D	0	.	7.1115	0.25392	0.4358:0.0:0.5642:0.0	.	320;320	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	N	320	ENSP00000313171:K320N	ENSP00000313171:K320N	K	+	3	2	ATAD5	26186185	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	1.162000	0.31786	0.850000	0.35239	-0.136000	0.14681	AAG	.		0.378	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		C	29162059	G	C	29162059	3	2	59	1	0	0	0	0	1	0	0	0	1077	933	33	4	966	4	ATAD5	17	29162059	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	21911552	29162059	52033151	75	5744											
LRRC37B	114659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	30348539	30348539	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaggacttaaatgacaagcGgactccagaagaaaggctcc	15	6	10	10	1	1	3	1	1	0	2	3	5	3	5	2	3	1	1	2	3	5	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:30348539G>T	ENST00000341671.7	+	1	379	c.374G>T	c.(373-375)cGg>cTg	p.R125L	LRRC37B_ENST00000394713.3_Missense_Mutation_p.R125L|LRRC37B_ENST00000584368.1_Missense_Mutation_p.R137L|LRRC37B_ENST00000543378.2_Missense_Mutation_p.R43L|LRRC37B_ENST00000327564.7_Missense_Mutation_p.R152L	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	125						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AATGACAAGCGGACTCCAGAA	0.537																																					p.R125L		.											.	LRRC37B-92	0			c.G374T						.						67	72	70					17																	30348539		2203	4299	6502	SO:0001583	missense	114659	exon1			ACAAGCGGACTCC	AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.374G>T	17.37:g.30348539G>T	ENSP00000340519:p.Arg125Leu	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	153	49	NM_052888	0	0	1	1	0	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	0	-2.679426	0.00102	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.48836	1.03;0.8;1.92;0.83	1.88	-3.76	0.04359	.	.	.	.	.	T	0.08846	0.0219	N	0.00210	-1.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08027	-1.0742	9	0.09338	T	0.73	.	1.1007	0.01683	0.17:0.2722:0.3459:0.2118	.	125;125	Q17RC9;Q96QE4	.;LR37B_HUMAN	L	43;152;125;125	ENSP00000443345:R43L;ENSP00000332536:R152L;ENSP00000378202:R125L;ENSP00000340519:R125L	ENSP00000332536:R152L	R	+	2	0	LRRC37B	27372652	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.498000	0.06420	-2.354000	0.00614	-1.626000	0.00786	CGG	.		0.537	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		T	30348539	G	T	30348539	3	4	59	1	0	0	0	0	1	0	0	0	9019	1116	39	4	376	4	LRRC37B	17	30348539	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	1186480	30348539	50846671	76	5745											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324228	39324228	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcggcagcaggtggtcCtgcagcagctgggtttgcag	5	8	19	9	1	0	0	0	0	0	0	1	0	1	0	1	6	5	7	1	6	0	1	rs192418439	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:39324228C>A	ENST00000391356.2	-	1	196	c.197G>T	c.(196-198)aGg>aTg	p.R66M		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	66	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			gcaggtggtcctgcagcagct	0.627																																					p.R66M		.											.	KRTAP4-3-22	0			c.G197T						.						3	5	4					17																	39324228		1442	3508	4950	SO:0001583	missense	85290	exon1			GTGGTCCTGCAGC	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"Keratin associated proteins"	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.197G>T	17.37:g.39324228C>A	ENSP00000375151:p.Arg66Met	Somatic	19	2		WXS	Illumina HiSeq	Phase_I	29	9	NM_033187	0	0	0	0	0		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	272	0.12454212454212454	19	0.03861788617886179	47	0.1298342541436464	119	0.20804195804195805	87	0.11477572559366754	.	5.704	0.314484	0.10789	.	.	ENSG00000196156	ENST00000391356	T	0.01446	4.88	4.66	-9.31	0.00646	.	.	.	.	.	T	0.00012	0.0000	M	0.86953	2.85	0.09310	N	1	P	0.36438	0.553	B	0.33042	0.157	T	0.10776	-1.0615	9	0.56958	D	0.05	.	0.7924	0.01060	0.2961:0.1605:0.1481:0.3953	.	66	Q9BYR4	KRA43_HUMAN	M	66	ENSP00000375151:R66M	ENSP00000375151:R66M	R	-	2	0	KRTAP4-3	36577754	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.405000	0.00239	-5.285000	0.00017	-0.913000	0.02753	AGG	C|0.876;A|0.125		0.627	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			A	39324228	C	A	39324228	3	1	59	1	0	0	0	0	1	0	0	0	8573	681	24	4	394	4	KRTAP4-3	17	39324228	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	8975689	39324228	41870982	77	5746											
ABI3	51225	broad.mit.edu	37	chr17	47299547	47299547	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccaccaggatttgggccTgatgagcccagctgggtgcc	6	7	13	15	0	0	2	0	2	0	0	0	3	0	3	6	3	3	1	6	3	0	1	rs572814048		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:47299547T>C	ENST00000225941.1	+	7	1395	c.897T>C	c.(895-897)ccT>ccC	p.P299P	ABI3_ENST00000419580.2_Silent_p.P293P	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	299	Pro-rich.				cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			GATTTGGGCCTGATGAGCCCA	0.622										HNSCC(55;0.14)																											p.P299P													.	ABI3-90	0			c.T897C						.						79	77	77					17																	47299547		2203	4300	6503	SO:0001819	synonymous_variant	51225	exon7			TGGGCCTGATGAG	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.897T>C	17.37:g.47299547T>C		Somatic	149	0		WXS	Illumina HiSeq	Phase_I	183	4	NM_016428	0	0	24	24	0	C9IZN8|Q9H0P6	Silent	SNP	ENST00000225941.1	37	CCDS11546.1																																																																																			.		0.622	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428		C	47299547	T	C	47299547	2	2	59	1	0	0	0	0	0	0	0	1	90	1567	55	3		3	ABI3	17	47299547	Silent	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	7975319	47299547	33895663	78	5747											
MFSD11	79157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74772621	74772621	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgccatcttcaagtttgttCaggtaacctcttcagattgt	8	17	7	9	0	5	1	3	0	2	1	5	1	5	1	2	1	2	3	2	1	2	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:74772621C>T	ENST00000588460.1	+	12	3225	c.1183C>T	c.(1183-1185)Cag>Tag	p.Q395*	MFSD11_ENST00000336509.4_Nonsense_Mutation_p.Q395*|MFSD11_ENST00000355954.3_Nonsense_Mutation_p.Q343*|MFSD11_ENST00000590514.1_Nonsense_Mutation_p.Q395*|MFSD11_ENST00000586622.1_Nonsense_Mutation_p.Q395*|MFSD11_ENST00000593181.1_Nonsense_Mutation_p.Q343*|MFSD11_ENST00000590070.1_3'UTR	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	395						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						CAAGTTTGTTCAGGTAACCTC	0.423																																					p.Q395X		.											.	MFSD11-91	0			c.C1183T						.						165	158	160					17																	74772621		2203	4300	6503	SO:0001587	stop_gained	79157	exon12			TTTGTTCAGGTAA	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.1183C>T	17.37:g.74772621C>T	ENSP00000464932:p.Gln395*	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	220	108	NM_001242532	0	0	0	0	0	O43442|Q9NXI5	Nonsense_Mutation	SNP	ENST00000588460.1	37	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	C	39	7.628628	0.98399	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-9.9106	19.2358	0.93858	0.0:1.0:0.0:0.0	.	.	.	.	X	395;343	.	ENSP00000337240:Q395X	Q	+	1	0	MFSD11	72284216	1.000000	0.71417	0.995000	0.50966	0.966000	0.64601	7.624000	0.83124	2.529000	0.85273	0.563000	0.77884	CAG	.		0.423	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		T	74772621	C	T	74772621	4	4	59	1	0	0	0	0	0	1	0	0	9554	827	29	2	1229	2	MFSD11	17	74772621	Nonsense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	27473074	74772621	6422589	79	5748											
RPTOR	57521	hgsc.bcm.edu	37	chr17	78858927	78858927	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcccagctggtcagcgaCgggagccccatggtccggaa	7	5	15	14	3	1	0	1	0	0	0	2	3	2	2	4	5	3	1	4	5	1	0			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:78858927C>T	ENST00000306801.3	+	17	2324	c.1962C>T	c.(1960-1962)gaC>gaT	p.D654D	RPTOR_ENST00000544334.2_Intron|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	654					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TGGTCAGCGACGGGAGCCCCA	0.687																																					p.D654D		.											.	RPTOR-847	0			c.C1962T						.						36	27	30					17																	78858927		2192	4283	6475	SO:0001819	synonymous_variant	57521	exon17			CAGCGACGGGAGC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1962C>T	17.37:g.78858927C>T		Somatic	5	2		WXS	Illumina HiSeq	Phase_I	12	6	NM_020761	0	0	11	35	24	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			.		0.687	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		T	78858927	C	T	78858927	2	4	59	1	0	0	0	0	0	0	0	1	13697	535	19	1		1	RPTOR	17	78858927	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	4086306	78858927	2336283	80	5749											
SYT4	6860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	40853823	40853823	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtcattttgatatatgggtCagaggtcatcgactgctcat	9	14	10	8	2	4	2	4	1	0	1	5	3	4	2	0	2	1	1	0	2	2	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr18:40853823C>T	ENST00000255224.3	-	2	939	c.571G>A	c.(571-573)Gac>Aac	p.D191N	SYT4_ENST00000590752.1_Missense_Mutation_p.D173N|SYT4_ENST00000586678.1_Intron	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	191	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						ATATATGGGTCAGAGGTCATC	0.438																																					p.D191N	NSCLC(85;81 1419 2855 22820 35912)	.											.	SYT4-132	0			c.G571A						.						78	77	78					18																	40853823		2203	4300	6503	SO:0001583	missense	6860	exon2			ATGGGTCAGAGGT	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.571G>A	18.37:g.40853823C>T	ENSP00000255224:p.Asp191Asn	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	112	46	NM_020783	0	0	0	0	0	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	37	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.979225	0.92982	.	.	ENSG00000132872	ENST00000255224	T	0.14516	2.5	5.87	5.87	0.94306	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.19192	-1.0313	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	173;191	B4DEU3;Q9H2B2	.;SYT4_HUMAN	N	191	ENSP00000255224:D191N	ENSP00000255224:D191N	D	-	1	0	SYT4	39107821	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.729000	0.84864	2.941000	0.99782	0.655000	0.94253	GAC	.		0.438	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		T	40853823	C	T	40853823	3	4	59	1	0	0	0	0	1	0	0	0	15508	826	29	2	718	2	SYT4	18	40853823	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		40853823	37223425	81	5750											
MRPL54	116541	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	3765208	3765208	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaggtgcagtgaccagcgagGccctcaaggaccccgacgta	11	4	13	13	3	1	1	1	1	0	0	1	4	1	2	4	3	2	2	4	3	3	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:3765208G>A	ENST00000330133.4	+	2	200	c.163G>A	c.(163-165)Gcc>Acc	p.A55T		NM_172251.2	NP_758455.1	Q6P161	RM54_HUMAN	mitochondrial ribosomal protein L54	55						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GACCAGCGAGGCCCTCAAGGA	0.572																																					p.A55T		.											.	MRPL54-90	0			c.G163A						.						109	90	96					19																	3765208		2202	4300	6502	SO:0001583	missense	116541	exon2			AGCGAGGCCCTCA		CCDS12111.1	19p13.3	2012-11-14			ENSG00000183617	ENSG00000183617		"Mitochondrial ribosomal proteins / large subunits"	16685	protein-coding gene	gene with protein product		611858				11551941	Standard	NM_172251		Approved		uc002lyq.4	Q6P161	OTTHUMG00000180873	ENST00000330133.4:c.163G>A	19.37:g.3765208G>A	ENSP00000331849:p.Ala55Thr	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	50	24	NM_172251	1	0	75	142	66		Missense_Mutation	SNP	ENST00000330133.4	37	CCDS12111.1	.	.	.	.	.	.	.	.	.	.	G	5.440	0.266338	0.10294	.	.	ENSG00000183617	ENST00000330133	.	.	.	4.9	1.59	0.23543	.	0.387651	0.25753	N	0.028522	T	0.22704	0.0548	N	0.19112	0.55	0.09310	N	0.999999	B	0.14438	0.01	B	0.12837	0.008	T	0.18840	-1.0324	9	0.16420	T	0.52	-5.8698	8.109	0.30903	0.2723:0.0:0.7277:0.0	.	55	Q6P161	RM54_HUMAN	T	55	.	ENSP00000331849:A55T	A	+	1	0	MRPL54	3716208	0.988000	0.35896	0.368000	0.25939	0.019000	0.09904	2.395000	0.44459	0.485000	0.27652	0.462000	0.41574	GCC	.		0.572	MRPL54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453443.1	NM_172251		A	3765208	G	A	3765208	3	1	59	1	0	0	0	0	1	0	0	0	9843	1203	42	2	169	2	MRPL54	19	3765208	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		3765208	55363775	82	5751											
ANKLE1	126549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17396342	17396342	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgggcaaagggacgagggcCcggccatatgtccacctctg	8	6	15	12	2	1	0	0	0	1	0	2	2	2	1	4	4	0	1	4	4	2	1	rs111432888		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:17396342C>T	ENST00000394458.3	+	7	1755	c.1479C>T	c.(1477-1479)gcC>gcT	p.A493A	ANKLE1_ENST00000433424.2_3'UTR|ANKLE1_ENST00000594072.1_Silent_p.A456A|ANKLE1_ENST00000404085.1_Silent_p.A489A|ANKLE1_ENST00000598347.1_Silent_p.A467A	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	493	GIY-YIG. {ECO:0000255|PROSITE- ProRule:PRU00977}.									large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GGACGAGGGCCCGGCCATATG	0.617																																					p.A493A		.											.	.	0			c.C1479T						.						85	93	91					19																	17396342		2203	4300	6503	SO:0001819	synonymous_variant	126549	exon7			GAGGGCCCGGCCA	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"Ankyrin repeat domain containing"	26812	protein-coding gene	gene with protein product	"LEM domain containing 6"		"ankyrin repeat domain 41"	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.1479C>T	19.37:g.17396342C>T		Somatic	126	1		WXS	Illumina HiSeq	Phase_I	167	54	NM_152363	0	0	0	0	0	A8VU82|Q8N8J8	Silent	SNP	ENST00000394458.3	37	CCDS12354.2																																																																																			C|0.500;T|0.500		0.617	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363		T	17396342	C	T	17396342	2	4	59	1	0	0	0	0	0	0	0	1	632	610	22	2		2	ANKLE1	19	17396342	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	13631134	17396342	41732641	83	5752											
ZNF30	90075	broad.mit.edu;bcgsc.ca	37	chr19	35434608	35434608	+	Frame_Shift_Del	DEL	G	G	-																															gcttttctagtatatggaaaGcttacccggcatcagagtac																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:35434608delG	ENST00000601142.1	+	5	975	c.738delG	c.(736-738)aagfs	p.K246fs	ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Frame_Shift_Del_p.K165fs|ZNF30_ENST00000303586.7_Frame_Shift_Del_p.K247fs|ZNF30_ENST00000439785.1_Frame_Shift_Del_p.K247fs			P17039	ZNF30_HUMAN	zinc finger protein 30	246					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)		TATATGGAAAGCTTACCCGGC	0.443																																					p.K247fs													.	ZNF30-24	0			c.741delG						.						42	49	47					19																	35434608		2115	4243	6358	SO:0001589	frameshift_variant	90075	exon5			TGGAAAGCTTACC	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.738delG	19.37:g.35434608delG	ENSP00000469954:p.Lys246fs	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	19	8	NM_001099438	0	0	0	0	0	A5PLP1|A8K320|B4DIC0|Q6N068	Frame_Shift_Del	DEL	ENST00000601142.1	37	CCDS46045.1																																																																																			.		0.443	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		-	35434608	G	-	35434608	7	5	59	1	0	1	0	1	0	0	0	0	17862	962	34	0	755	0	ZNF30	19	35434608	Frame_Shift_Del	DEL	G	TCGA-BQ-5875-01A-11D-1589-08	18038266	35434608	23694375	84	5753											
ZFP14	57677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36831787	36831787	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggctttcccacattccttaCattcatagagcttttcagca	10	14	5	12	0	2	1	2	0	0	1	4	1	4	1	2	1	3	3	2	1	2	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:36831787C>T	ENST00000270001.7	-	5	1056	c.941G>A	c.(940-942)tGt>tAt	p.C314Y		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	314					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)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					ACATTCCTTACATTCATAGAG	0.418																																					p.C314Y		.											.	ZFP14-91	0			c.G941A						.						97	100	99					19																	36831787		2203	4300	6503	SO:0001583	missense	57677	exon5			TCCTTACATTCAT	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.941G>A	19.37:g.36831787C>T	ENSP00000270001:p.Cys314Tyr	Somatic	212	1		WXS	Illumina HiSeq	Phase_I	104	39	NM_020917	0	0	1	3	2	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	c	17.95	3.513281	0.64522	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	D	0.85088	-1.94	3.92	3.92	0.45320	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000146	D	0.94584	0.8255	H	0.96518	3.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96261	0.9191	10	0.87932	D	0	.	15.2044	0.73165	0.0:1.0:0.0:0.0	.	314;314	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	Y	314	ENSP00000270001:C314Y	ENSP00000270001:C314Y	C	-	2	0	ZFP14	41523627	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.282000	0.78630	2.177000	0.69029	0.549000	0.68633	TGT	.		0.418	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		T	36831787	C	T	36831787	3	4	59	1	0	0	0	0	1	0	0	0	17671	478	17	2	664	2	ZFP14	19	36831787	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	1397179	36831787	22297196	85	5754											
ZNF225	7768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44635911	44635911	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaatgtggaaagagcttcAgatgggcctcaggtctttca	12	10	12	7	0	4	3	3	0	1	3	4	4	4	4	1	3	1	1	1	3	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:44635911A>C	ENST00000262894.6	+	5	1424	c.1144A>C	c.(1144-1146)Aga>Cga	p.R382R	ZNF225_ENST00000590612.1_Silent_p.R382R|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				AAAGAGCTTCAGATGGGCCTC	0.408																																					p.R382R		.											.	.	0			c.A1144C						.						74	80	78					19																	44635911		2182	4282	6464	SO:0001819	synonymous_variant	7768	exon5			AGCTTCAGATGGG	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.1144A>C	19.37:g.44635911A>C		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	101	47	NM_013362	0	0	0	1	1	A8K8S2|Q53F12|Q9NS46|Q9UID8	Silent	SNP	ENST00000262894.6	37	CCDS46100.1																																																																																			.		0.408	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			C	44635911	A	C	44635911	2	2	59	1	0	0	0	0	0	0	0	1	17811	180	7	5		5	ZNF225	19	44635911	Silent	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	7804124	44635911	14493072	86	5755											
ZNF547	284306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57888699	57888699	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agggactgtacacgtgtccaGcacatcttcaccagcaccaa	12	7	8	14	1	2	0	1	0	1	0	3	1	3	1	3	1	3	3	3	1	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:57888699G>A	ENST00000282282.3	+	4	505	c.355G>A	c.(355-357)Gca>Aca	p.A119T	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	119					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CACGTGTCCAGCACATCTTCA	0.517																																					p.A119T		.											.	ZNF547-91	0			c.G355A						.						100	88	92					19																	57888699		2203	4300	6503	SO:0001583	missense	284306	exon4			TGTCCAGCACATC	AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.355G>A	19.37:g.57888699G>A	ENSP00000282282:p.Ala119Thr	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	91	27	NM_173631	0	0	0	1	1	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	37	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.727951	0.30593	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.05855	3.38	2.09	-1.39	0.08997	.	.	.	.	.	T	0.05823	0.0152	L	0.37800	1.135	0.09310	N	1	P;B;P	0.51057	0.728;0.141;0.941	B;B;B	0.43889	0.358;0.031;0.435	T	0.36311	-0.9753	9	0.42905	T	0.14	.	6.7967	0.23729	0.4946:0.0:0.5054:0.0	.	119;119;119	Q8IVP9-2;C9JTQ3;Q8IVP9	.;.;ZN547_HUMAN	T	119	ENSP00000282282:A119T	ENSP00000282282:A119T	A	+	1	0	ZNF547	62580511	0.000000	0.05858	0.004000	0.12327	0.227000	0.25037	-0.074000	0.11450	-0.246000	0.09611	0.491000	0.48974	GCA	.		0.517	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		A	57888699	G	A	57888699	3	1	59	1	0	0	0	0	1	0	0	0	18011	971	34	2	365	2	ZNF547	19	57888699	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	13252788	57888699	1240284	87	5756											
NINL	22981	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	25457543	25457543	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgatacgcacatctgggcgCgcttctcgctcgcacagggc	7	7	12	15	6	2	0	0	0	2	0	4	1	2	0	0	2	1	4	0	2	1	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr20:25457543C>T	ENST00000278886.6	-	17	2457	c.2384G>A	c.(2383-2385)cGc>cAc	p.R795H	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	795					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CATCTGGGCGCGCTTCTCGCT	0.692																																					p.R795H													.	NINL-94	0			c.G2384A						.						43	36	39					20																	25457543		2203	4300	6503	SO:0001583	missense	22981	exon17			TGGGCGCGCTTCT		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2384G>A	20.37:g.25457543C>T	ENSP00000278886:p.Arg795His	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	26	4	NM_025176	0	0	6	18	12	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	C	7.781	0.709555	0.15239	.	.	ENSG00000101004	ENST00000278886	T	0.25912	1.77	3.48	2.25	0.28309	.	1.732920	0.03095	N	0.160239	T	0.10465	0.0256	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28396	-1.0045	10	0.10636	T	0.68	-0.6342	5.269	0.15615	0.0:0.1397:0.0:0.8603	.	795	Q9Y2I6	NINL_HUMAN	H	795	ENSP00000278886:R795H	ENSP00000278886:R795H	R	-	2	0	NINL	25405543	0.015000	0.18098	0.001000	0.08648	0.000000	0.00434	0.998000	0.29744	0.426000	0.26116	-0.672000	0.03802	CGC	.		0.692	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		T	25457543	C	T	25457543	3	4	59	1	0	0	0	0	1	0	0	0	10446	768	27	1	1796	1	NINL	20	25457543	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		25457543	37567977	88	5757											
UMODL1	89766	broad.mit.edu	37	chr21	43529716	43529716	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggaacacgactgctcaccgGctgcctggtgcatcaacctg	8	7	11	15	3	2	0	2	0	0	0	2	2	2	1	3	3	5	3	3	3	2	0			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr21:43529716G>A	ENST00000408910.2	+	10	1564	c.1564G>A	c.(1564-1566)Gct>Act	p.A522T	UMODL1_ENST00000400427.1_Missense_Mutation_p.A450T|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400424.2_Missense_Mutation_p.A450T|UMODL1_ENST00000408989.2_Missense_Mutation_p.A522T	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	522	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CTGCTCACCGGCTGCCTGGTG	0.627																																					p.A522T	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)												.	UMODL1-93	0			c.G1564A						.						70	83	79					21																	43529716		2051	4178	6229	SO:0001583	missense	89766	exon10			TCACCGGCTGCCT		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1564G>A	21.37:g.43529716G>A	ENSP00000386147:p.Ala522Thr	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	89	4	NM_173568	0	0	0	0	0	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	6.981	0.551127	0.13374	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;D;D;D	0.92149	-1.54;-2.98;-1.54;-2.98	3.23	1.34	0.21922	EGF-like calcium-binding, conserved site (1);Epidermal growth factor-like (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.885950	0.03158	N	0.168966	D	0.87010	0.6071	N	0.16790	0.44	0.09310	N	1	B;B	0.32753	0.383;0.055	B;B	0.40009	0.316;0.093	T	0.77357	-0.2618	10	0.27785	T	0.31	-3.9791	5.9046	0.18986	0.2526:0.0:0.7474:0.0	.	522;522	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	T	450;450;522;522	ENSP00000383279:A450T;ENSP00000383276:A450T;ENSP00000386126:A522T;ENSP00000386147:A522T	ENSP00000383276:A450T	A	+	1	0	UMODL1	42402785	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	0.384000	0.20668	0.364000	0.24374	-0.150000	0.13652	GCT	.		0.627	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43529716	G	A	43529716	3	1	59	1	0	0	0	0	1	0	0	0	17013	1203	42	2	1602	2	UMODL1	21	43529716	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		43529716	4600179	89	5758											
ITGB2	3689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46306670	46306670	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgttccactgggacttgAgcttctccttctcaaagcgc	7	13	8	13	1	2	1	1	1	2	0	5	2	3	2	2	1	2	2	2	1	1	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr21:46306670A>C	ENST00000397850.2	-	16	2680	c.2228T>G	c.(2227-2229)cTc>cGc	p.L743R	ITGB2_ENST00000302347.5_Missense_Mutation_p.L743R|ITGB2_ENST00000397854.3_Missense_Mutation_p.L686R|ITGB2_ENST00000397857.1_Missense_Mutation_p.L743R|ITGB2_ENST00000355153.4_Missense_Mutation_p.L743R|ITGB2_ENST00000397852.1_Missense_Mutation_p.L743R			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	743					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	CTGGGACTTGAGCTTCTCCTT	0.617																																					p.L743R		.											.	ITGB2-717	0			c.T2228G						.						110	88	96					21																	46306670		2203	4300	6503	SO:0001583	missense	3689	exon15			GACTTGAGCTTCT	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"CD molecules", "Complement system", "Integrins"	6155	protein-coding gene	gene with protein product		600065	"integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.2228T>G	21.37:g.46306670A>C	ENSP00000380948:p.Leu743Arg	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	43	6	NM_000211	0	0	126	126	0	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	37	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	A	2.100	-0.406333	0.04832	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347	D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	4.62	2.16	0.27623	Integrin beta subunit, cytoplasmic (2);	.	.	.	.	T	0.78483	0.4290	L	0.34521	1.04	0.30302	N	0.789334	P;P	0.37276	0.589;0.589	B;B	0.43018	0.405;0.315	T	0.67795	-0.5578	9	0.15066	T	0.55	.	1.6167	0.02705	0.5553:0.1773:0.0964:0.171	.	686;743	A8MYE6;P05107	.;ITB2_HUMAN	R	743;743;686;743;743;743	ENSP00000380950:L743R;ENSP00000380955:L743R;ENSP00000380952:L686R;ENSP00000347279:L743R;ENSP00000380948:L743R;ENSP00000303242:L743R	ENSP00000303242:L743R	L	-	2	0	ITGB2	45131098	1.000000	0.71417	0.996000	0.52242	0.100000	0.18952	1.319000	0.33655	0.157000	0.19338	-0.250000	0.11733	CTC	.		0.617	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		C	46306670	A	C	46306670	3	2	59	1	0	0	0	0	1	0	0	0	7915	304	11	5	89	5	ITGB2	21	46306670	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	2776954	46306670	1823225	90	5759											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30038223	30038223	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attttagatgaaaagatctaCtgccctcctgaggcttctgt	10	14	8	9	0	2	4	0	2	2	2	3	4	3	4	2	1	2	1	2	1	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr22:30038223C>A	ENST00000338641.4	+	4	837	c.396C>A	c.(394-396)taC>taA	p.Y132*	NF2_ENST00000397789.3_Nonsense_Mutation_p.Y132*|NF2_ENST00000403999.3_Nonsense_Mutation_p.Y132*|NF2_ENST00000353887.4_Nonsense_Mutation_p.Y49*|NF2_ENST00000347330.5_Nonsense_Mutation_p.Y49*|NF2_ENST00000403435.1_Nonsense_Mutation_p.Y132*|NF2_ENST00000334961.7_Nonsense_Mutation_p.Y49*|NF2_ENST00000361676.4_Nonsense_Mutation_p.Y90*|NF2_ENST00000413209.2_Nonsense_Mutation_p.Y132*|NF2_ENST00000361452.4_Nonsense_Mutation_p.Y91*|NF2_ENST00000361166.4_Nonsense_Mutation_p.Y132*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	132	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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.V122_K149del(5)|p.?(3)|p.L127_P134del(1)|p.K123fs*2(1)		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						AAAAGATCTACTGCCCTCCTG	0.468			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.Y132X		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	10	Deletion - In frame(6)|Unknown(3)|Deletion - Frameshift(1)	soft_tissue(8)|large_intestine(1)|stomach(1)	c.C396A						.						95	90	92					22																	30038223		2203	4300	6503	SO:0001587	stop_gained	4771	exon4	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GATCTACTGCCCT	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.396C>A	22.37:g.30038223C>A	ENSP00000344666:p.Tyr132*	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	37	NM_000268	0	0	1	3	2	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	39	7.545417	0.98348	.	.	ENSG00000186575	ENST00000413209;ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.45	2.11	0.27256	.	0.116668	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5018	0.50441	0.0:0.7981:0.0:0.2019	.	.	.	.	X	132;49;132;132;91;132;132;49;49;132;90;132	.	.	Y	+	3	2	NF2	28368223	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.702000	0.37836	0.657000	0.30906	0.655000	0.94253	TAC	.		0.468	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		A	30038223	C	A	30038223	4	1	59	1	0	0	0	0	0	1	0	0	10383	576	20	4	410	4	NF2	22	30038223	Nonsense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		30038223	21266343	91	5760											
SLC9A7	84679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	46491075	46491075	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggtcttgatcggggtcAacaccaactctgaaagtcac	10	9	12	10	1	4	2	2	2	2	0	5	2	4	2	1	4	2	0	1	4	3	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:46491075A>T	ENST00000328306.4	-	14	1708	c.1683T>A	c.(1681-1683)gtT>gtA	p.V561V	SLC9A7_ENST00000464933.1_5'UTR	NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	561					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						GATCGGGGTCAACACCAACTC	0.498																																					p.V562V	Pancreas(118;454 1696 1930 13865 39976)	.											.	SLC9A7-132	0			c.T1686A						.						110	90	97					X																	46491075		2203	4300	6503	SO:0001819	synonymous_variant	84679	exon14			GGGGTCAACACCA	AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"Solute carriers"	17123	protein-coding gene	gene with protein product		300368	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 7", "solute carrier family 9 (sodium/hydrogen exchanger), member 7"			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.1683T>A	X.37:g.46491075A>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	48	17	NM_001257291	0	0	0	0	0	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	37	CCDS14269.1																																																																																			.		0.498	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591		T	46491075	A	T	46491075	2	4	59	1	0	0	0	0	0	0	0	1	14751	117	5	5		5	SLC9A7	23	46491075	Silent	SNP	A	TCGA-BQ-5875-01A-11D-1589-08		46491075	108779485	92	5761											
HUWE1	10075	hgsc.bcm.edu;broad.mit.edu	37	chrX	53564649	53564649	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaacgctccagctcttggCggaaatatcttgggaggtag	10	10	12	9	2	2	0	0	0	2	0	3	2	3	2	1	4	2	3	1	4	5	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:53564649C>T	ENST00000342160.3	-	77	12462	c.12005G>A	c.(12004-12006)cGc>cAc	p.R4002H	HUWE1_ENST00000262854.6_Missense_Mutation_p.R4002H			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4002					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CAGCTCTTGGCGGAAATATCT	0.473																																					p.R4002H		.											.	HUWE1-280	0			c.G12005A						.						55	43	47					X																	53564649		2203	4300	6503	SO:0001583	missense	10075	exon78			TCTTGGCGGAAAT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12005G>A	X.37:g.53564649C>T	ENSP00000340648:p.Arg4002His	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	36	3	NM_031407	0	0	0	0	0	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.197762	0.58126	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.76709	-1.04;-1.04	5.78	5.78	0.91487	HECT (1);	0.000000	0.85682	D	0.000000	D	0.85358	0.5678	L	0.53617	1.68	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.74674	0.984;0.958;0.981	D	0.85951	0.1464	10	0.62326	D	0.03	.	15.9981	0.80268	0.0:1.0:0.0:0.0	.	824;4002;3986	Q5H935;Q7Z6Z7;Q7Z6Z7-2	.;HUWE1_HUMAN;.	H	4002	ENSP00000340648:R4002H;ENSP00000262854:R4002H	ENSP00000262854:R4002H	R	-	2	0	HUWE1	53581374	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.019000	0.76412	2.580000	0.87095	0.600000	0.82982	CGC	.		0.473	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53564649	C	T	53564649	3	4	59	1	0	0	0	0	1	0	0	0	7482	768	27	1	1147	1	HUWE1	23	53564649	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	7073574	53564649	101705911	93	5762											
POU3F4	5456	hgsc.bcm.edu	37	chrX	82764046	82764046	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atctgcaggttcgaaggcttGcagctgagcttcaaaaatat	12	11	10	8	1	2	1	1	1	1	0	3	2	2	1	0	2	4	6	0	2	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:82764046G>T	ENST00000373200.2	+	1	778	c.714G>T	c.(712-714)ttG>ttT	p.L238F	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	238	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						TCGAAGGCTTGCAGCTGAGCT	0.567																																					p.L238F		.											.	POU3F4-131	0			c.G714T						.						67	53	58					X																	82764046		2203	4300	6503	SO:0001583	missense	5456	exon1			AGGCTTGCAGCTG	X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"Homeoboxes / POU class"	9217	protein-coding gene	gene with protein product	"brain-4"	300039	"POU domain class 3, transcription factor 4"	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.714G>T	X.37:g.82764046G>T	ENSP00000362296:p.Leu238Phe	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	75	4	NM_000307	0	0	0	0	0	B2RC71|Q5H9G9|Q99410	Missense_Mutation	SNP	ENST00000373200.2	37	CCDS14450.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.854438	0.51376	.	.	ENSG00000196767	ENST00000373200	D	0.86694	-2.16	5.07	0.844	0.18943	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.64402	D	0.000006	D	0.93367	0.7885	M	0.93638	3.44	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	D	0.90691	0.4613	10	0.87932	D	0	.	6.3022	0.21119	0.2413:0.0:0.631:0.1276	.	238	P49335	PO3F4_HUMAN	F	238	ENSP00000362296:L238F	ENSP00000362296:L238F	L	+	3	2	POU3F4	82650702	1.000000	0.71417	0.997000	0.53966	0.845000	0.48019	1.627000	0.37050	0.096000	0.17463	0.525000	0.51046	TTG	.		0.567	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		T	82764046	G	T	82764046	3	4	59	1	0	0	0	0	1	0	0	0	12303	1310	46	4	716	4	POU3F4	23	82764046	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	29199397	82764046	72506514	94	5763											
NXF3	56000	broad.mit.edu	37	chrX	102332664	102332664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaagagcttgtcattcaCgatgcacagactggaggaaa	15	7	10	9	1	2	2	2	0	0	2	2	5	2	4	0	2	2	2	0	2	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:102332664C>T	ENST00000395065.3	-	18	1563	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M	NXF3_ENST00000425644.1_Missense_Mutation_p.V160M	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	488	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				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						TTGTCATTCACGATGCACAGA	0.557																																					p.V488M													.	NXF3-205	0			c.G1462A						.						183	123	143					X																	102332664		2203	4300	6503	SO:0001583	missense	56000	exon18			CATTCACGATGCA	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.1462G>A	X.37:g.102332664C>T	ENSP00000378504:p.Val488Met	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	149	5	NM_022052	0	0	0	0	0	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	37	CCDS14503.1	.	.	.	.	.	.	.	.	.	.	C	4.378	0.069632	0.08436	.	.	ENSG00000147206	ENST00000395065;ENST00000425644	T	0.51325	0.71	4.44	-8.88	0.00789	Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);	0.751316	0.12753	N	0.441969	T	0.44932	0.1317	M	0.67953	2.075	0.80722	D	1	D	0.58620	0.983	P	0.49332	0.607	T	0.73094	-0.4091	10	0.48119	T	0.1	0.7011	9.1203	0.36784	0.0:0.1538:0.2768:0.5694	.	488	Q9H4D5	NXF3_HUMAN	M	488;160	ENSP00000378504:V488M	ENSP00000378504:V488M	V	-	1	0	NXF3	102219320	0.125000	0.22332	0.005000	0.12908	0.007000	0.05969	-0.114000	0.10757	-3.615000	0.00132	-1.314000	0.01303	GTG	.		0.557	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		T	102332664	C	T	102332664	3	4	59	1	0	0	0	0	1	0	0	0	10811	536	19	1	141	1	NXF3	23	102332664	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	19568618	102332664	52937896	95	5764											
MCTS1	28985	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	119739292	119739293	+	Frame_Shift_Ins	INS	-	-	AT																															aagaaaatgtgtccaactgcINSatccagttgaaaacttcagt																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:119739292_119739293insAT	ENST00000371317.5	+	2	299_300	c.42_43insAT	c.(43-45)atcfs	p.I15fs	MCTS1_ENST00000371315.3_Frame_Shift_Ins_p.I16fs|MCTS1_ENST00000487133.1_3'UTR	NM_014060.2	NP_054779.1	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1	15					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|ribosome disassembly (GO:0032790)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|stomach(1)|urinary_tract(1)	10						TGTCCAACTGCATCCAGTTGAA	0.332																																					p.C15fs		.											.	MCTS1-130	0			c.45_46insAT						.																																			SO:0001589	frameshift_variant	28985	exon2			.	AB034206	CCDS14601.1, CCDS48160.1	Xq24	2008-05-14			ENSG00000232119	ENSG00000232119			23357	protein-coding gene	gene with protein product		300587				9766643	Standard	NM_014060		Approved	MCT-1	uc011mub.2	Q9ULC4	OTTHUMG00000022303	ENST00000371317.5:c.43_44dupAT	X.37:g.119739293_119739294dupAT	ENSP00000360367:p.Ile15fs	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	131	28	NM_001137554	0	0	0	0	0	B4DGY2|Q502X6	Frame_Shift_Ins	INS	ENST00000371317.5	37	CCDS14601.1																																																																																			.		0.332	MCTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058110.1	NM_014060		AT	119739293	-	AT	119739292	7	5	59	1	0	1	1	0	0	0	0	0	9427	718	25	0	66	0	MCTS1	23	119739292	Frame_Shift_Ins	INS	-	TCGA-BQ-5875-01A-11D-1589-08	17406628	119739292	35531268	96	5765	66	2									
MCTS1	28985	hgsc.bcm.edu	37	chrX	119739295	119739296	+	Frame_Shift_Del	DEL	CC	CC	-																															gaaaatgtgtccaactgcatCcagttgaaaacttcagttat																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:119739295_119739296delCC	ENST00000371317.5	+	2	302_303	c.45_46delCC	c.(43-48)atccagfs	p.Q16fs	MCTS1_ENST00000371315.3_Frame_Shift_Del_p.Q17fs|MCTS1_ENST00000487133.1_3'UTR	NM_014060.2	NP_054779.1	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1	16					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|ribosome disassembly (GO:0032790)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|stomach(1)|urinary_tract(1)	10						CCAACTGCATCCAGTTGAAAAC	0.337																																					p.16_17del		.											.	MCTS1-130	0			c.48_49del						.																																			SO:0001589	frameshift_variant	28985	exon2			.	AB034206	CCDS14601.1, CCDS48160.1	Xq24	2008-05-14			ENSG00000232119	ENSG00000232119			23357	protein-coding gene	gene with protein product		300587				9766643	Standard	NM_014060		Approved	MCT-1	uc011mub.2	Q9ULC4	OTTHUMG00000022303	ENST00000371317.5:c.45_46delCC	X.37:g.119739295_119739296delCC	ENSP00000360367:p.Gln16fs	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	127	19	NM_001137554	0	0	0	0	0	B4DGY2|Q502X6	Frame_Shift_Del	DEL	ENST00000371317.5	37	CCDS14601.1																																																																																			.		0.337	MCTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058110.1	NM_014060		-	119739296	CC	-	119739295	7	5	59	1	0	1	0	1	0	0	0	0	9427	845	30	0	69	0	MCTS1	23	119739295	Frame_Shift_Del	DEL	CC	TCGA-BQ-5875-01A-11D-1589-08	3	119739295	35531265	97	5766	66	2									
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	123184115	123184118	+	Frame_Shift_Del	DEL	AATG	AATG	-																															tgtatagtgatgcctttcttAatgacagttatttaaaatat																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	AATG	AATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:123184115_123184118delAATG	ENST00000371160.1	+	11	1263_1266	c.973_976delAATG	c.(973-978)aatgacfs	p.ND325fs	STAG2_ENST00000371157.3_Frame_Shift_Del_p.ND325fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.ND325fs|STAG2_ENST00000371145.3_Frame_Shift_Del_p.ND325fs|STAG2_ENST00000354548.5_Frame_Shift_Del_p.ND256fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Del_p.ND325fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	325	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TGCCTTTCTTAATGACAGTTATTT	0.412																																					p.325_326del		.											.	STAG2-134	0			c.973_976del						.																																			SO:0001589	frameshift_variant	10735	exon11			.	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.973_976delAATG	X.37:g.123184115_123184118delAATG	ENSP00000360202:p.Asn325fs	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	179	61	NM_001042749	0	0	0	0	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	37	CCDS14607.1																																																																																			.		0.412	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123184118	AATG	-	123184115	7	5	59	1	0	1	0	1	0	0	0	0	15275	362	13	0	1007	0	STAG2	23	123184115	Frame_Shift_Del	DEL	AATG	TCGA-BQ-5875-01A-11D-1589-08	3444820	123184115	32086445	98	5767											
PLCH2	9651	ucsc.edu;bcgsc.ca	37	chr1	2415964	2415964	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tacaagatgatgtccacccgCcgggacctctacctgctcat	9	9	8	15	2	2	2	1	1	1	1	3	3	3	3	5	1	3	1	5	1	3	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:2415964C>T	ENST00000419816.2	+	5	997	c.723C>T	c.(721-723)cgC>cgT	p.R241R	PLCH2_ENST00000288766.5_Intron|PLCH2_ENST00000378488.3_Silent_p.R241R|PLCH2_ENST00000378486.3_Silent_p.R241R|PLCH2_ENST00000449969.1_Silent_p.R214R			O75038	PLCH2_HUMAN	phospholipase C, eta 2	241	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		TGTCCACCCGCCGGGACCTCT	0.592																																					p.R241R													.	PLCH2-229	0			c.C723T						.						51	60	57					1																	2415964		2053	4195	6248	SO:0001819	synonymous_variant	9651	exon5			CACCCGCCGGGAC	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.723C>T	1.37:g.2415964C>T		Somatic	57	0		WXS	Illumina HiSeq		39	4	NM_014638	0	0	0	0	0	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37																																																																																				.		0.592	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		T	2415964	C	T	2415964	2	4	60	1	0	0	0	0	0	0	0	1	12064	726	26	2		2	PLCH2	1	2415964	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		2415964	246834657	1	5768											
VPS13D	55187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	12327038	12327038	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacctggctacagaaggaacTatgtttcctcttctagtctt	9	14	8	10	0	3	1	0	0	3	1	4	3	4	2	2	2	2	2	2	2	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:12327038T>C	ENST00000358136.3	+	14	1825	c.1695T>C	c.(1693-1695)acT>acC	p.T565T	VPS13D_ENST00000356315.4_Silent_p.T565T	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CAGAAGGAACTATGTTTCCTC	0.408																																					p.T565T		.											.	VPS13D-95	0			c.T1695C						.						124	114	117					1																	12327038		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon14			AGGAACTATGTTT	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.1695T>C	1.37:g.12327038T>C		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	168	30	NM_015378	0	0	1	1	0		Silent	SNP	ENST00000358136.3	37	CCDS30588.1																																																																																			.		0.408	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12327038	T	C	12327038	2	2	60	1	0	0	0	0	0	0	0	1	17225	1509	53	3		3	VPS13D	1	12327038	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	9911074	12327038	236923583	2	5769											
MTF1	4520	broad.mit.edu	37	chr1	38323066	38323066	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcacataaccctgggacaTtgcttcatgatctatcaggt	10	12	8	11	0	3	1	2	1	1	0	3	2	3	2	1	2	3	2	1	2	2	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:38323066T>C	ENST00000373036.4	-	2	405	c.265A>G	c.(265-267)Atg>Gtg	p.M89V	MTF1_ENST00000468190.1_5'UTR	NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	89					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CCCTGGGACATTGCTTCATGA	0.468																																					p.M89V													.	MTF1-92	0			c.A265G						.						201	170	180					1																	38323066		2203	4300	6503	SO:0001583	missense	4520	exon2			GGGACATTGCTTC	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.265A>G	1.37:g.38323066T>C	ENSP00000362127:p.Met89Val	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	179	4	NM_005955	0	0	1	1	0	B2RAK6|Q96CB1	Missense_Mutation	SNP	ENST00000373036.4	37	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	T	15.34	2.805707	0.50315	.	.	ENSG00000188786	ENST00000373036	T	0.10288	2.89	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.09512	0.0234	L	0.50333	1.59	0.45515	D	0.998474	B	0.18610	0.029	B	0.12156	0.007	T	0.07404	-1.0774	10	0.02654	T	1	.	11.135	0.48368	0.0:0.0715:0.0:0.9285	.	89	Q14872	MTF1_HUMAN	V	89	ENSP00000362127:M89V	ENSP00000362127:M89V	M	-	1	0	MTF1	38095653	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.968000	0.70413	2.177000	0.69029	0.533000	0.62120	ATG	.		0.468	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		C	38323066	T	C	38323066	3	2	60	1	0	0	0	0	1	0	0	0	9947	1493	52	3	2036	3	MTF1	1	38323066	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	25996028	38323066	210927555	3	5770											
PTPRF	5792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	44058242	44058242	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggggtgggcgtcttcaccCccaccattgaggcccgcaca	6	7	13	15	2	2	1	1	1	1	0	2	1	2	1	4	4	0	1	4	4	0	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:44058242C>G	ENST00000359947.4	+	11	2123	c.1783C>G	c.(1783-1785)Ccc>Gcc	p.P595A	PTPRF_ENST00000438120.1_Missense_Mutation_p.P595A|PTPRF_ENST00000422171.2_Missense_Mutation_p.P54A|PTPRF_ENST00000372413.3_Missense_Mutation_p.P595A|PTPRF_ENST00000372414.3_Missense_Mutation_p.P595A	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	595	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CGTCTTCACCCCCACCATTGA	0.602																																					p.P595A		.											.	PTPRF-232	0			c.C1783G						.						99	83	88					1																	44058242		2203	4300	6503	SO:0001583	missense	5792	exon11			TTCACCCCCACCA	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.1783C>G	1.37:g.44058242C>G	ENSP00000353030:p.Pro595Ala	Somatic	96	1		WXS	Illumina HiSeq	Phase_I	81	32	NM_002840	0	0	1	7	6	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.664|9.664	1.144961|1.144961	0.21288|0.21288	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171|ENST00000412568;ENST00000414879	T;T;T;T;T|.	0.52754|.	0.65;2.31;0.65;2.31;0.65|.	4.43|4.43	4.43|4.43	0.53597|0.53597	Fibronectin, type III (2);Immunoglobulin-like fold (1);|.	0.000000|0.000000	0.34002|0.34002	N|N	0.004350|0.004350	T|T	0.36468|0.36468	0.0968|0.0968	N|N	0.17901|0.17901	0.54|0.54	0.23519|0.23519	N|N	0.9975|0.9975	B;B;B;P;P|.	0.49090|.	0.004;0.0;0.118;0.919;0.552|.	B;B;B;P;B|.	0.48454|.	0.013;0.0;0.026;0.578;0.146|.	T|T	0.24297|0.24297	-1.0164|-1.0164	10|6	0.06494|.	T|.	0.89|.	.|.	17.924|17.924	0.88977|0.88977	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	251;54;354;595;595|.	Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586|.	.;.;.;.;PTPRF_HUMAN|.	A|R	595;595;595;595;54|262;119	ENSP00000353030:P595A;ENSP00000398822:P595A;ENSP00000361491:P595A;ENSP00000361490:P595A;ENSP00000387885:P54A|.	ENSP00000353030:P595A|.	P|P	+|+	1|2	0|0	PTPRF|PTPRF	43830829|43830829	0.792000|0.792000	0.28813|0.28813	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	1.791000|1.791000	0.38744|0.38744	2.398000|2.398000	0.81561|0.81561	0.561000|0.561000	0.74099|0.74099	CCC|CCC	.		0.602	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			G	44058242	C	G	44058242	3	3	60	1	0	0	0	0	1	0	0	0	12833	623	22	4	1817	4	PTPRF	1	44058242	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	5735176	44058242	205192379	4	5771											
FAM73A	374986	bcgsc.ca	37	chr1	78325733	78325733	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atattttttcaggtaattctTtcagaatcagctaacaggat	13	16	6	6	0	4	1	3	0	1	1	4	2	4	2	0	2	2	2	0	2	4	8			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:78325733T>C	ENST00000370791.3	+	11	1229	c.1197T>C	c.(1195-1197)ctT>ctC	p.L399L	FAM73A_ENST00000443751.2_Silent_p.L361L	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	399						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		AGGTAATTCTTTCAGAATCAG	0.343																																					p.L399L													.	FAM73A-91	0			c.T1197C						.						43	44	44					1																	78325733		2203	4300	6503	SO:0001819	synonymous_variant	374986	exon11			AATTCTTTCAGAA		CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.1197T>C	1.37:g.78325733T>C		Somatic	46	0		WXS	Illumina HiSeq	Phase_1	82	4	NM_198549	0	0	12	12	0	Q6MZG0	Silent	SNP	ENST00000370791.3	37	CCDS681.1																																																																																			.		0.343	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		C	78325733	T	C	78325733	2	2	60	1	0	0	0	0	0	0	0	1	5636	1828	64	3		3	FAM73A	1	78325733	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	34267491	78325733	170924888	5	5772											
C1orf52	148423	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	85725088	85725088	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccagtctatctgtttgtTgagcggattgtagagaaagg	9	13	12	7	1	2	2	0	1	2	1	3	4	3	3	1	2	1	3	1	2	3	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:85725088T>G	ENST00000471115.1	-	1	237	c.229A>C	c.(229-231)Aac>Cac	p.N77H	C1orf52_ENST00000294661.4_5'UTR|C1orf52_ENST00000344356.5_Missense_Mutation_p.N77H	NM_198077.3	NP_932343.1	Q8N6N3	CA052_HUMAN	chromosome 1 open reading frame 52	77							poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)	10				all cancers(265;0.0105)|Epithelial(280;0.0293)		ATCTGTTTGTTGAGCGGATTG	0.652											OREG0013580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N77H		.											.	C1orf52-91	0			c.A229C						.						52	58	56					1																	85725088		2203	4300	6503	SO:0001583	missense	148423	exon1			GTTTGTTGAGCGG	BC029538	CCDS703.1	1p22.3	2008-02-05			ENSG00000162642	ENSG00000162642			24871	protein-coding gene	gene with protein product						11891061	Standard	NM_198077		Approved	gm117, FLJ44982	uc001dkv.3	Q8N6N3	OTTHUMG00000009966	ENST00000471115.1:c.229A>C	1.37:g.85725088T>G	ENSP00000419417:p.Asn77His	Somatic	90	1	1239	WXS	Illumina HiSeq	Phase_I	85	32	NM_198077	0	0	3	9	6	B3KX89|Q8TDK5|Q8TDK6	Missense_Mutation	SNP	ENST00000471115.1	37	CCDS703.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937500	0.73557	.	.	ENSG00000162642	ENST00000471115;ENST00000344356	.	.	.	5.74	3.39	0.38822	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	L	0.59436	1.845	0.44000	D	0.996708	B;B	0.24368	0.102;0.102	B;B	0.25291	0.051;0.059	T	0.35822	-0.9773	9	0.52906	T	0.07	-1.2675	4.3274	0.11046	0.1115:0.0677:0.196:0.6248	.	77;77	Q8N6N3-2;Q8N6N3	.;CA052_HUMAN	H	77	.	ENSP00000345092:N77H	N	-	1	0	C1orf52	85497676	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.383000	0.52471	1.080000	0.41073	0.519000	0.50382	AAC	.		0.652	C1orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027616.2	NM_198077		G	85725088	T	G	85725088	3	3	60	1	0	0	0	0	1	0	0	0	2050	1812	63	5	331	5	C1orf52	1	85725088	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	7399355	85725088	163525533	6	5773											
LRRC8D	55144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90399406	90399406	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatcaataaaactggctttaAattttcagctgagaagcctg	14	12	8	7	0	2	1	2	1	0	1	2	3	2	1	1	1	3	2	1	1	6	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:90399406A>T	ENST00000337338.5	+	3	1186	c.779A>T	c.(778-780)aAa>aTa	p.K260I	LRRC8D_ENST00000394593.3_Missense_Mutation_p.K260I	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	260					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		ACTGGCTTTAAATTTTCAGCT	0.458																																					p.K260I		.											.	LRRC8D-92	0			c.A779T						.						44	42	43					1																	90399406		2203	4300	6503	SO:0001583	missense	55144	exon3			GCTTTAAATTTTC	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.779A>T	1.37:g.90399406A>T	ENSP00000338887:p.Lys260Ile	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	44	16	NM_018103	0	0	10	20	10	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	37	CCDS726.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.464588	0.43736	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000441269	T;T;T	0.49432	1.35;1.35;0.78	5.88	5.88	0.94601	.	0.111169	0.64402	D	0.000017	T	0.30070	0.0753	L	0.36672	1.1	0.48696	D	0.99969	P	0.40376	0.715	B	0.42062	0.374	T	0.07121	-1.0789	9	.	.	.	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	260	Q7L1W4	LRC8D_HUMAN	I	260	ENSP00000338887:K260I;ENSP00000378093:K260I;ENSP00000405784:K260I	.	K	+	2	0	LRRC8D	90171994	1.000000	0.71417	0.980000	0.43619	0.959000	0.62525	4.701000	0.61810	2.246000	0.74042	0.533000	0.62120	AAA	.		0.458	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		T	90399406	A	T	90399406	3	4	60	1	0	0	0	0	1	0	0	0	9049	14	1	5	781	5	LRRC8D	1	90399406	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	4674318	90399406	158851215	7	5774											
DNTTIP2	30836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94342829	94342829	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttctcatttcctggtacaAtcttactatctttcttttca	7	21	3	10	0	5	0	2	0	4	0	7	0	6	0	1	1	2	2	1	1	4	8			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:94342829A>C	ENST00000436063.2	-	2	719	c.662T>G	c.(661-663)aTt>aGt	p.I221S	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TCCTGGTACAATCTTACTATC	0.393																																					p.I221S		.											.	.	0			c.T662G						.						157	156	157					1																	94342829		1874	4097	5971	SO:0001583	missense	30836	exon2			GGTACAATCTTAC	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"acidic 82 kDa protein mRNA"	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.662T>G	1.37:g.94342829A>C	ENSP00000411010:p.Ile221Ser	Somatic	264	0		WXS	Illumina HiSeq	Phase_I	295	109	NM_014597	0	0	23	38	15	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	A	7.865	0.726984	0.15439	.	.	ENSG00000067334	ENST00000436063	T	0.16743	2.32	4.97	-4.84	0.03151	.	1.525530	0.03836	N	0.269774	T	0.04998	0.0134	L	0.56769	1.78	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.45308	-0.9270	10	0.72032	D	0.01	.	0.8184	0.01107	0.315:0.2126:0.2868:0.1855	.	221	Q5QJE6	TDIF2_HUMAN	S	221	ENSP00000411010:I221S	ENSP00000352137:I221S	I	-	2	0	DNTTIP2	94115417	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	0.416000	0.21198	-0.444000	0.07170	0.533000	0.62120	ATT	.		0.393	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		C	94342829	A	C	94342829	3	2	60	1	0	0	0	0	1	0	0	0	4693	101	4	5	1632	5	DNTTIP2	1	94342829	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	3943423	94342829	154907792	8	5775											
SASS6	163786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	100572514	100572514	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgctttcttcaagttttttAactgtagcttctaattgttc	7	22	5	7	0	3	0	1	0	2	0	4	0	3	0	0	0	3	5	0	0	4	11			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:100572514A>C	ENST00000287482.5	-	12	1502	c.1362T>G	c.(1360-1362)gtT>gtG	p.V454V	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Silent_p.V287V	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	454					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		CAAGTTTTTTAACTGTAGCTT	0.249																																					p.V454V		.											.	SASS6-70	0			c.T1362G						.						68	68	68					1																	100572514		2189	4293	6482	SO:0001819	synonymous_variant	163786	exon12			TTTTTTAACTGTA	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1362T>G	1.37:g.100572514A>C		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	38	11	NM_194292	0	0	0	2	2	D3DT55|Q8N3K0	Silent	SNP	ENST00000287482.5	37	CCDS764.1																																																																																			.		0.249	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		C	100572514	A	C	100572514	2	2	60	1	0	0	0	0	0	0	0	1	13882	349	13	5		5	SASS6	1	100572514	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	6229685	100572514	148678107	9	5776											
HORMAD1	84072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150679129	150679129	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagtatagttgagtcaataTtttccattcgttctctctca	10	18	5	8	1	3	1	2	1	2	0	7	1	4	1	1	0	0	3	1	0	5	9			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:150679129T>A	ENST00000361824.2	-	10	809	c.704A>T	c.(703-705)aAt>aTt	p.N235I	HORMAD1_ENST00000368995.4_Missense_Mutation_p.N155I|HORMAD1_ENST00000368993.2_Missense_Mutation_p.N235I|HORMAD1_ENST00000322343.7_Missense_Mutation_p.N228I	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	235					blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TGAGTCAATATTTTCCATTCG	0.343																																					p.N235I		.											.	HORMAD1-92	0			c.A704T						.						202	191	195					1																	150679129		2203	4300	6503	SO:0001583	missense	84072	exon10			TCAATATTTTCCA	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"cancer/testis antigen 46"	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.704A>T	1.37:g.150679129T>A	ENSP00000355167:p.Asn235Ile	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	226	86	NM_032132	0	0	0	0	0	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Missense_Mutation	SNP	ENST00000361824.2	37	CCDS967.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.617697	0.66787	.	.	ENSG00000143452	ENST00000368995;ENST00000368993;ENST00000368992;ENST00000540570;ENST00000322343;ENST00000361824;ENST00000368987;ENST00000442853	T;T;T;T	0.47177	0.85;1.42;1.43;1.42	5.48	4.34	0.51931	.	0.219611	0.53938	D	0.000043	T	0.38188	0.1031	L	0.32530	0.975	0.28943	N	0.890864	D;D;D	0.71674	0.998;0.988;0.964	D;P;P	0.65010	0.931;0.878;0.65	T	0.28004	-1.0057	10	0.72032	D	0.01	-12.6203	7.2033	0.25893	0.0:0.2218:0.0:0.7781	.	155;228;235	Q86X24-4;Q86X24-2;Q86X24	.;.;HORM1_HUMAN	I	155;235;164;155;228;235;164;157	ENSP00000357991:N155I;ENSP00000357989:N235I;ENSP00000326489:N228I;ENSP00000355167:N235I	ENSP00000326489:N228I	N	-	2	0	HORMAD1	148945753	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	1.692000	0.37731	2.092000	0.63282	0.383000	0.25322	AAT	.		0.343	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132		A	150679129	T	A	150679129	3	1	60	1	0	0	0	0	1	0	0	0	7307	1493	52	5	504	5	HORMAD1	1	150679129	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	50106615	150679129	98571492	10	5777											
RAB13	5872	hgsc.bcm.edu	37	chr1	153954883	153954921	+	Splice_Site	DEL	GACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	GACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	-																															ttactgatctccggcctcctGacttgagcaagatgtcccgg																								rs556345789|rs202131118|rs553808166|rs371012129|rs56791628		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	GACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	GACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:153954883_153954921delGACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	ENST00000368575.3	-	7	596_633	c.481_518delGGCTTTTAGTTCCCTGGCCCGGGACATCTTGCTCAAGTC	c.(481-519)ggcttttagttccctggcccgggacatcttgctcaagtc>c	p.GF*FPGPGHLAQV161del	RAB13_ENST00000462680.1_5'UTR	NM_002870.2	NP_002861.1	P51153	RAB13_HUMAN	RAB13, member RAS oncogene family	161					cellular response to insulin stimulus (GO:0032869)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endosomal transport (GO:0016197)|endothelial cell chemotaxis (GO:0035767)|establishment of protein localization to plasma membrane (GO:0090002)|establishment of Sertoli cell barrier (GO:0097368)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|protein kinase A signaling (GO:0010737)|protein localization to cell leading edge (GO:1902463)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)|trans-Golgi network to recycling endosome transport (GO:0044795)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R167L(2)		breast(1)|endometrium(3)|kidney(1)|lung(5)|urinary_tract(1)	11	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCGGCCTCCTGACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCCTAAAGTGGGG	0.506																																					p.161_173del	Ovarian(138;395 2427 24306 43415)	.											.	RAB13-227	2	Substitution - Missense(2)	lung(2)	c.481_518del						.																																			SO:0001630	splice_region_variant	5872	exon7			.	X75593	CCDS1058.1, CCDS72921.1	1q21.2	2008-02-05			ENSG00000143545	ENSG00000143545		"RAB, member RAS oncogene"	9762	protein-coding gene	gene with protein product		602672				8294494	Standard	NM_002870		Approved		uc001fdt.2	P51153	OTTHUMG00000036589	ENST00000368575.3:c.481-1GGCTTTTAGTTCCCTGGCCCGGGACATCTTGCTCAAGTC>-	1.37:g.153954883_153954921delGACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC		Somatic	245	0		WXS	Illumina HiSeq	Phase_I	149	30	NM_002870	0	0	0	0	0	A8K6B5|D3DV67|Q5U0A6|Q6GPG6|Q96GU4	Frame_Shift_Del	DEL	ENST00000368575.3	37	CCDS1058.1																																																																																			.		0.506	RAB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088992.1	NM_002870	In_Frame_Del	-	153954921	GACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	-	153954883	8	5	60	1	0	1	0	1	0	0	1	0	12931	1294	45	0	101	0	RAB13	1	153954883	Splice_Site	DEL	GACTTGAGCAAGATGTCCCGGGCCAGGGAACTAAAAGCC	TCGA-BQ-5876-01A-11D-1589-08	3275754	153954883	95295738	11	5778											
DARC	2532	ucsc.edu;bcgsc.ca	37	chr1	159176128	159176128	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aattttgcactgtgtggctaCgcccctgctcctcgccctat	5	13	8	15	2	0	0	0	0	0	0	2	0	1	0	4	1	3	3	4	1	3	4	rs1801482		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:159176128C>A	ENST00000368122.2	+	2	1578	c.899C>A	c.(898-900)aCg>aAg	p.T300K	DARC_ENST00000368121.2_Missense_Mutation_p.T302K|DARC_ENST00000537147.1_Missense_Mutation_p.T300K|CTA-134P22.2_ENST00000609696.1_RNA	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		300					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					TGTGTGGCTACGCCCCTGCTC	0.602																																					p.T302K													.	DARC-659	0			c.C905A						.						175	186	183					1																	159176128		2203	4300	6503	SO:0001583	missense	2532	exon1			TGGCTACGCCCCT																												ENST00000368122.2:c.899C>A	1.37:g.159176128C>A	ENSP00000357104:p.Thr300Lys	Somatic	547	4		WXS	Illumina HiSeq		550	203	NM_001122951	0	0	0	0	0	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	37	CCDS1183.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156946	0.57259	.	.	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000368121	T;T;T	0.37235	1.21;1.21;1.21	5.4	3.5	0.40072	.	0.000000	0.32970	U	0.005426	T	0.33731	0.0873	L	0.46157	1.445	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.12760	-1.0535	10	0.72032	D	0.01	-3.3211	7.7112	0.28679	0.0:0.7476:0.1643:0.0881	rs1801482	302;300	Q5Y7A1;Q16570	.;DUFFY_HUMAN	K	300;300;300;302	ENSP00000357104:T300K;ENSP00000441985:T300K;ENSP00000357103:T302K	ENSP00000352341:T300K	T	+	2	0	DARC	157442752	0.000000	0.05858	0.001000	0.08648	0.794000	0.44872	-0.106000	0.10890	0.738000	0.32606	0.655000	0.94253	ACG	.		0.602	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2			A	159176128	C	A	159176128	3	1	60	1	0	0	0	0	1	0	0	0	4246	536	19	4	932	4	DARC	1	159176128	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	5221245	159176128	90074493	12	5779											
ARHGAP30	257106	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161019045	161019045	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccagcggagtccagggaaCagcagctgggggccaagaca	11	2	17	11	1	0	1	0	0	0	1	1	3	1	3	3	5	4	2	3	5	2	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:161019045C>T	ENST00000368013.3	-	12	2086	c.1766G>A	c.(1765-1767)tGt>tAt	p.C589Y	ARHGAP30_ENST00000368015.1_Missense_Mutation_p.C412Y|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.C589Y	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	589					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GTCCAGGGAACAGCAGCTGGG	0.572																																					p.C589Y		.											.	ARHGAP30-25	0			c.G1766A						.						95	101	99					1																	161019045		2203	4300	6503	SO:0001583	missense	257106	exon12			AGGGAACAGCAGC	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1766G>A	1.37:g.161019045C>T	ENSP00000356992:p.Cys589Tyr	Somatic	203	1		WXS	Illumina HiSeq	Phase_I	212	52	NM_001025598	0	0	0	0	0	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166948	0.57476	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.39592	2.8;2.61;1.07	5.18	5.18	0.71444	.	0.000000	0.53938	D	0.000049	T	0.52041	0.1710	M	0.71581	2.175	0.36206	D	0.851054	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.59742	-0.7397	10	0.66056	D	0.02	.	9.7641	0.40550	0.0:0.906:0.0:0.094	.	589;589	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	Y	589;589;441;412	ENSP00000356995:C589Y;ENSP00000356992:C589Y;ENSP00000356994:C412Y	ENSP00000356992:C589Y	C	-	2	0	ARHGAP30	159285669	0.999000	0.42202	0.997000	0.53966	0.980000	0.70556	3.126000	0.50477	2.422000	0.82143	0.555000	0.69702	TGT	.		0.572	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161019045	C	T	161019045	3	4	60	1	0	0	0	0	1	0	0	0	879	478	17	2	1543	2	ARHGAP30	1	161019045	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	1842917	161019045	88231576	13	5780											
CREG1	8804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167515357	167515357	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgaactgtgacattataatAttcttctggtgtcacgattt	10	17	7	7	1	3	2	1	2	2	0	3	3	3	2	0	1	1	0	0	1	4	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:167515357A>G	ENST00000370509.4	-	3	665	c.640T>C	c.(640-642)Tat>Cat	p.Y214H	CREG1_ENST00000466652.1_5'UTR	NM_003851.2	NP_003842.1	O75629	CREG1_HUMAN	cellular repressor of E1A-stimulated genes 1	214					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|transcription factor complex (GO:0005667)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)|transcription corepressor activity (GO:0003714)										ACATTATAATATTCTTCTGGT	0.438																																					p.Y214H		.											.	CREG1-186	0			c.T640C						.						70	73	72					1																	167515357		2203	4300	6503	SO:0001583	missense	8804	exon3			TATAATATTCTTC	AF084523	CCDS1262.1	1q24	2008-02-05	2004-09-22	2004-09-22	ENSG00000143162	ENSG00000143162			2351	protein-coding gene	gene with protein product			"cellular repressor of E1A-stimulated genes"	CREG		9710587	Standard	NM_003851		Approved		uc001gel.3	O75629	OTTHUMG00000034682	ENST00000370509.4:c.640T>C	1.37:g.167515357A>G	ENSP00000359540:p.Tyr214His	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	67	29	NM_003851	0	0	68	125	57	B2RDD4|Q8N9A3	Missense_Mutation	SNP	ENST00000370509.4	37	CCDS1262.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.891151	0.72524	.	.	ENSG00000143162	ENST00000370509	.	.	.	5.86	5.86	0.93980	FMN-binding split barrel-related (1);FMN-binding split barrel (1);	0.000000	0.85682	D	0.000000	D	0.83326	0.5230	M	0.91818	3.245	0.53005	D	0.999968	D	0.89917	1.0	D	0.97110	1.0	D	0.87426	0.2385	8	0.87932	D	0	-7.3711	16.2453	0.82441	1.0:0.0:0.0:0.0	.	214	O75629	CREG1_HUMAN	H	214	.	ENSP00000359540:Y214H	Y	-	1	0	CREG1	165781981	1.000000	0.71417	0.810000	0.32431	0.581000	0.36288	8.428000	0.90278	2.241000	0.73720	0.533000	0.62120	TAT	.		0.438	CREG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083911.1	NM_003851		G	167515357	A	G	167515357	3	3	60	1	0	0	0	0	1	0	0	0	3870	449	16	3	30	3	CREG1	1	167515357	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	6496312	167515357	81735264	14	5781											
HMCN1	83872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	185984290	185984290	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgttctgaaatcctttgtaGttccacctagtattaaagga	11	16	7	7	0	1	1	0	1	1	0	3	2	3	2	3	1	0	4	3	1	6	8	rs568290303	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:185984290G>A	ENST00000271588.4	+	31	4859		c.e31-1		HMCN1_ENST00000367492.2_Splice_Site	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1						response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATCCTTTGTAGTTCCACCTAG	0.338																																					.		.											.	HMCN1-113	0			c.4631-1G>A						.						72	71	71					1																	185984290		2203	4299	6502	SO:0001630	splice_region_variant	83872	exon31			TTTGTAGTTCCAC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4631-1G>A	1.37:g.185984290G>A		Somatic	129	1		WXS	Illumina HiSeq	Phase_I	93	37	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Splice_Site	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501313	0.85176	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1551	0.93507	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HMCN1	184250913	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	8.911000	0.92721	2.583000	0.87209	0.557000	0.71058	.	.		0.338	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Intron	A	185984290	G	A	185984290	5	1	60	1	0	0	0	0	0	0	1	0	7241	1043	36	2	4752	2	HMCN1	1	185984290	Splice_Site	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	18468933	185984290	63266331	15	5782											
PLEKHA6	22874	broad.mit.edu;ucsc.edu	37	chr1	204199641	204199641	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccactctggtgccgccgcAttcggtcaatctgctcctcc	5	10	9	17	3	3	0	1	0	2	0	6	0	5	0	5	2	3	2	5	2	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:204199641A>G	ENST00000272203.3	-	18	2799	c.2483T>C	c.(2482-2484)aTg>aCg	p.M828T	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.M848T	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	828										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GTGCCGCCGCATTCGGTCAAT	0.652																																					p.M828T													.	PLEKHA6-654	0			c.T2483C						.						36	30	32					1																	204199641		2203	4298	6501	SO:0001583	missense	22874	exon18			CGCCGCATTCGGT	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2483T>C	1.37:g.204199641A>G	ENSP00000272203:p.Met828Thr	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	9	3	NM_014935	0	0	12	15	3	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.726061	0.69074	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.13538	2.58;3.04	5.24	5.24	0.73138	.	0.044871	0.85682	D	0.000000	T	0.32734	0.0839	M	0.73962	2.25	0.53688	D	0.999974	P	0.45827	0.867	P	0.55112	0.769	T	0.05954	-1.0854	10	0.72032	D	0.01	-30.7964	14.7958	0.69876	1.0:0.0:0.0:0.0	.	828	Q9Y2H5	PKHA6_HUMAN	T	828;848	ENSP00000272203:M828T;ENSP00000402046:M848T	ENSP00000272203:M828T	M	-	2	0	PLEKHA6	202466264	1.000000	0.71417	0.997000	0.53966	0.716000	0.41182	8.402000	0.90205	1.972000	0.57404	0.379000	0.24179	ATG	.		0.652	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		G	204199641	A	G	204199641	3	3	60	1	0	0	0	0	1	0	0	0	12086	217	8	3	683	3	PLEKHA6	1	204199641	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	18215351	204199641	45050980	16	5783											
ASAP2	8853	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	9533671	9533671	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagcgtaatggaagcctTgagccagccgagcaagcctg	10	5	13	13	2	0	1	0	1	0	0	0	3	0	2	5	1	6	2	5	1	3	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:9533671T>C	ENST00000281419.3	+	24	2919	c.2579T>C	c.(2578-2580)tTg>tCg	p.L860S	ASAP2_ENST00000315273.4_Missense_Mutation_p.L815S|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	860	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ATGGAAGCCTTGAGCCAGCCG	0.701																																					p.L860S		.											.	ASAP2-90	0			c.T2579C						.						13	15	14					2																	9533671		2199	4294	6493	SO:0001583	missense	8853	exon24			AAGCCTTGAGCCA	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2579T>C	2.37:g.9533671T>C	ENSP00000281419:p.Leu860Ser	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	19	6	NM_003887	0	0	8	8	0	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	37	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.260257	0.23051	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.58506	0.42;0.33	5.36	5.36	0.76844	Src homology-3 domain (1);	4.673060	0.00166	N	0.000005	T	0.67702	0.2921	N	0.19112	0.55	0.35637	D	0.81066	D;B	0.69078	0.997;0.011	D;B	0.75484	0.986;0.01	T	0.56956	-0.7893	10	0.18710	T	0.47	.	15.3426	0.74309	0.0:0.0:0.0:1.0	.	815;860	O43150-2;O43150	.;ASAP2_HUMAN	S	860;815	ENSP00000281419:L860S;ENSP00000316404:L815S	ENSP00000281419:L860S	L	+	2	0	ASAP2	9451122	1.000000	0.71417	0.799000	0.32177	0.419000	0.31324	4.442000	0.59988	2.034000	0.60081	0.379000	0.24179	TTG	.		0.701	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9533671	T	C	9533671	3	2	60	1	0	0	0	0	1	0	0	0	1012	1821	63	3	2673	3	ASAP2	2	9533671	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		9533671	233665702	17	5784											
NRBP1	29959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27664588	27664588	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccccaggctgaccagagccGgttgacttctctgctagaag	8	8	11	14	1	1	4	0	2	1	2	2	4	1	4	4	2	2	3	4	2	2	3	rs141700147	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:27664588G>A	ENST00000233557.3	+	19	2349	c.1517G>A	c.(1516-1518)cGg>cAg	p.R506Q	KRTCAP3_ENST00000288873.3_5'Flank|KRTCAP3_ENST00000407293.1_5'Flank|NRBP1_ENST00000379863.3_Missense_Mutation_p.R514Q|KRTCAP3_ENST00000543753.1_5'Flank|NRBP1_ENST00000379852.3_Missense_Mutation_p.R506Q			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	506					ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)	p.R506Q(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GACCAGAGCCGGTTGACTTCT	0.547													G|||	6	0.00119808	0.0045	0	5008	,	,		18142	0		0	False		,,,				2504	0				p.R506Q		.											.	NRBP1-334	1	Substitution - Missense(1)	large_intestine(1)	c.G1517A						.	G	GLN/ARG	4,4402	9.9+/-24.2	0,4,2199	179	183	182		1517	5.7	1	2	dbSNP_134	182	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NRBP1	NM_013392.2	43	0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384	possibly-damaging	506/536	27664588	5,13001	2203	4300	6503	SO:0001583	missense	29959	exon18			AGAGCCGGTTGAC	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.1517G>A	2.37:g.27664588G>A	ENSP00000233557:p.Arg506Gln	Somatic	314	1		WXS	Illumina HiSeq	Phase_I	334	127	NM_013392	0	0	27	62	35	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	37	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944186	0.73672	9.08E-4	1.16E-4	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863	T;T;T	0.14022	2.84;2.84;2.54	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.14399	0.0348	L	0.43152	1.355	0.58432	D	0.999999	B;B;B	0.32302	0.363;0.239;0.154	B;B;B	0.24701	0.022;0.055;0.025	T	0.02093	-1.1215	10	0.45353	T	0.12	-8.6676	18.2912	0.90131	0.0:0.0:1.0:0.0	.	486;514;506	B4DW31;F8W6G1;Q9UHY1	.;.;NRBP_HUMAN	Q	506;486;506;514	ENSP00000233557:R506Q;ENSP00000369181:R506Q;ENSP00000369192:R514Q	ENSP00000233557:R506Q	R	+	2	0	NRBP1	27518092	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	6.787000	0.75099	2.662000	0.90505	0.561000	0.74099	CGG	G|1.000;A|0.000		0.547	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		A	27664588	G	A	27664588	3	1	60	1	0	0	0	0	1	0	0	0	10668	1116	39	1	1583	1	NRBP1	2	27664588	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	18130917	27664588	215534785	18	5785											
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu	37	chr2	32693046	32693046	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattttactatggtcataccTacatcttgccttgggaaagt	10	15	8	8	0	2	0	1	0	1	0	2	2	2	1	2	2	4	0	2	2	5	7			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:32693046T>C	ENST00000421745.2	+	28	5781	c.5647T>C	c.(5647-5649)Tac>Cac	p.Y1883H		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1883					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TGGTCATACCTACATCTTGCC	0.388																																					p.Y1883H	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.T5647C						.						66	68	68					2																	32693046		2203	4300	6503	SO:0001583	missense	57448	exon28			CATACCTACATCT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5647T>C	2.37:g.32693046T>C	ENSP00000393596:p.Tyr1883His	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_016252	0	0	10	10	0	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	24.2	4.501275	0.85176	.	.	ENSG00000115760	ENST00000421745	T	0.74421	-0.84	5.9	5.9	0.94986	.	0.147925	0.47852	D	0.000217	T	0.82208	0.4987	L	0.44542	1.39	0.54753	D	0.999989	D	0.71674	0.998	D	0.78314	0.991	D	0.83740	0.0203	10	0.72032	D	0.01	.	16.378	0.83412	0.0:0.0:0.0:1.0	.	1883	Q9NR09	BIRC6_HUMAN	H	1883	ENSP00000393596:Y1883H	ENSP00000393596:Y1883H	Y	+	1	0	BIRC6	32546550	1.000000	0.71417	0.990000	0.47175	0.982000	0.71751	7.846000	0.86887	2.277000	0.76020	0.529000	0.55759	TAC	.		0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32693046	T	C	32693046	3	2	60	1	0	0	0	0	1	0	0	0	1439	1522	53	3	5757	3	BIRC6	2	32693046	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	5028458	32693046	210506327	19	5786											
SLC8A1	6546	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	40656328	40656328	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgagtagcttgaatgcGataaaatgctctactttttt	11	14	10	6	2	1	1	0	1	1	0	1	4	1	1	0	1	4	3	0	1	5	7	rs370199920		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:40656328G>T	ENST00000403092.1	-	2	1126	c.1093C>A	c.(1093-1095)Cgc>Agc	p.R365S	SLC8A1_ENST00000408028.2_Missense_Mutation_p.R365S|SLC8A1_ENST00000405269.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000405901.3_Missense_Mutation_p.R365S|SLC8A1_ENST00000402441.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000542024.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000406391.2_Missense_Mutation_p.R365S|SLC8A1_ENST00000406785.2_Missense_Mutation_p.R365S|SLC8A1_ENST00000542756.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000332839.4_Missense_Mutation_p.R365S			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	365					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	GCTTGAATGCGATAAAATGCT	0.433																																					p.R365S		.											.	SLC8A1-93	0			c.C1093A						.						165	157	160					2																	40656328		2203	4300	6503	SO:0001583	missense	6546	exon1			GAATGCGATAAAA		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"Solute carriers"	11068	protein-coding gene	gene with protein product	"Na+/Ca++ exchanger"	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.1093C>A	2.37:g.40656328G>T	ENSP00000384763:p.Arg365Ser	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	267	14	NM_001252624	0	0	1	1	0	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509948	0.64522	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.53857	0.65;0.68;0.67;0.68;0.65;0.65;0.67;0.6;0.65;0.64	6.17	5.29	0.74685	Heat shock protein DnaJ, N-terminal (1);	0.049164	0.85682	D	0.000000	T	0.78233	0.4251	M	0.91663	3.23	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.996;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.995;1.0;0.996;1.0	D	0.83814	0.0243	10	0.87932	D	0	.	14.9877	0.71362	0.0:0.0:0.857:0.143	.	365;365;365;365;365	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	S	365	ENSP00000383886:R365S;ENSP00000440727:R365S;ENSP00000384763:R365S;ENSP00000385678:R365S;ENSP00000385188:R365S;ENSP00000385535:R365S;ENSP00000332931:R365S;ENSP00000384908:R365S;ENSP00000385811:R365S;ENSP00000443515:R365S	ENSP00000332931:R365S	R	-	1	0	SLC8A1	40509832	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	7.812000	0.86109	1.600000	0.50102	0.655000	0.94253	CGC	.		0.433	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		T	40656328	G	T	40656328	3	4	60	1	0	0	0	0	1	0	0	0	14738	1058	37	4	1976	4	SLC8A1	2	40656328	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	7963282	40656328	202543045	20	5787											
MSH6	2956	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	48027125	48027125	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tatgacttcagagtctgattCcattgggttgacaccaggag	10	12	11	8	0	2	4	1	3	1	1	3	5	3	5	2	2	0	1	2	2	1	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:48027125C>G	ENST00000234420.5	+	4	2155	c.2003C>G	c.(2002-2004)tCc>tGc	p.S668C	MSH6_ENST00000538136.1_Missense_Mutation_p.S366C|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000540021.1_Missense_Mutation_p.S538C	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	668					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAGTCTGATTCCATTGGGTTG	0.433			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.S668C		.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6-3014	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.C2003G						.						152	146	148					2																	48027125		2203	4300	6503	SO:0001583	missense	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTGATTCCATTGG	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2003C>G	2.37:g.48027125C>G	ENSP00000234420:p.Ser668Cys	Somatic	274	0		WXS	Illumina HiSeq	Phase_I	282	107	NM_000179	0	0	5	13	8	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735857	0.49045	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.88664	-2.04;-2.12;-2.41	4.8	3.92	0.45320	DNA mismatch repair protein MutS, connector (1);	0.361706	0.32518	N	0.005990	D	0.93112	0.7807	M	0.76574	2.34	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.976	D;D;P	0.67231	0.95;0.95;0.738	D	0.93502	0.6845	10	0.72032	D	0.01	-2.7325	12.8528	0.57867	0.0:0.9212:0.0:0.0788	.	538;668;668	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	C	668;666;538;366	ENSP00000234420:S668C;ENSP00000446475:S538C;ENSP00000438580:S366C	ENSP00000234420:S668C	S	+	2	0	MSH6	47880629	1.000000	0.71417	0.996000	0.52242	0.942000	0.58702	5.875000	0.69660	1.243000	0.43853	0.460000	0.39030	TCC	.		0.433	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		G	48027125	C	G	48027125	3	3	60	1	0	0	0	0	1	0	0	0	9899	855	30	4	2017	4	MSH6	2	48027125	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	7370797	48027125	195172248	21	5788											
CCDC88A	55704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55566741	55566741	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagcttcaataatctactTgatgtcaactcattcacctc	11	15	3	12	0	6	1	4	1	2	0	7	1	6	1	1	0	3	1	1	0	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:55566741T>G	ENST00000436346.1	-	13	2218	c.1377A>C	c.(1375-1377)tcA>tcC	p.S459S	CCDC88A_ENST00000263630.8_Silent_p.S459S|CCDC88A_ENST00000413716.2_Silent_p.S459S|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000608103.1_RNA|CCDC88A_ENST00000336838.6_Silent_p.S459S|AC012358.8_ENST00000594078.1_RNA|AC012358.8_ENST00000599475.1_RNA|AC012358.8_ENST00000599352.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	459					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						ATAATCTACTTGATGTCAACT	0.363																																					p.S459S		.											.	CCDC88A-94	0			c.A1377C						.						92	91	92					2																	55566741		2203	4300	6503	SO:0001819	synonymous_variant	55704	exon13			TCTACTTGATGTC	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.1377A>C	2.37:g.55566741T>G		Somatic	105	1		WXS	Illumina HiSeq	Phase_I	95	29	NM_018084	0	0	2	3	1	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Silent	SNP	ENST00000436346.1	37																																																																																				.		0.363	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		G	55566741	T	G	55566741	2	3	60	1	0	0	0	0	0	0	0	1	2869	1799	63	5		5	CCDC88A	2	55566741	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	7539616	55566741	187632632	22	5789											
TCF7L1	83439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	85536242	85536242	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctcctcccacgggagcaTgctggactccccggccactc	5	7	10	19	2	0	0	0	0	0	0	4	2	3	2	6	3	3	2	6	3	0	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:85536242T>C	ENST00000282111.3	+	12	1699	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	475					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CACGGGAGCATGCTGGACTCC	0.652																																					p.M475T		.											.	TCF7L1-585	0			c.T1424C						.						93	102	99					2																	85536242		2203	4300	6503	SO:0001583	missense	83439	exon12			GGAGCATGCTGGA	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.1424T>C	2.37:g.85536242T>C	ENSP00000282111:p.Met475Thr	Somatic	307	1		WXS	Illumina HiSeq	Phase_I	264	89	NM_031283	0	0	1	1	0	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	37	CCDS1971.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.097296	0.56075	.	.	ENSG00000152284	ENST00000282111	T	0.34072	1.38	5.11	0.36	0.16097	.	0.117117	0.85682	N	0.000000	T	0.37972	0.1023	L	0.54323	1.7	0.29754	N	0.836071	P	0.50156	0.932	P	0.58391	0.838	T	0.35301	-0.9794	10	0.13108	T	0.6	.	3.6615	0.08240	0.1572:0.2705:0.0:0.5722	.	475	Q9HCS4	TF7L1_HUMAN	T	475	ENSP00000282111:M475T	ENSP00000282111:M475T	M	+	2	0	TCF7L1	85389753	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	2.286000	0.43496	-0.075000	0.12798	0.448000	0.29417	ATG	.		0.652	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		C	85536242	T	C	85536242	3	2	60	1	0	0	0	0	1	0	0	0	15729	1464	51	3	1470	3	TCF7L1	2	85536242	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	29969501	85536242	157663131	23	5790											
EIF5B	9669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	100015354	100015354	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagacattttgaagctacAgatattcttgttagtaaggt	13	14	10	4	0	1	3	0	1	1	2	1	4	1	4	0	2	2	3	0	2	6	8			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:100015354A>C	ENST00000289371.6	+	23	3739	c.3537A>C	c.(3535-3537)acA>acC	p.T1179T		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	1179					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TTGAAGCTACAGATATTCTTG	0.398																																					p.T1179T	Colon(162;2388 2567 2705 3444)	.											.	EIF5B-93	0			c.A3537C						.						70	64	66					2																	100015354		1859	4090	5949	SO:0001819	synonymous_variant	9669	exon23			AGCTACAGATATT	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.3537A>C	2.37:g.100015354A>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	86	33	NM_015904	0	0	63	109	46	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			.		0.398	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		C	100015354	A	C	100015354	2	2	60	1	0	0	0	0	0	0	0	1	5057	175	7	5		5	EIF5B	2	100015354	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	14479112	100015354	143184019	24	5791											
WDR33	55339	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	128484249	128484249	+	Frame_Shift_Del	DEL	T	T	-																															ttgcaagactctgcccagtcTtgggatcccagaacttgatt																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:128484249delT	ENST00000322313.4	-	8	985	c.827delA	c.(826-828)aagfs	p.K276fs		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	276					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTGCCCAGTCTTGGGATCCCA	0.468																																					p.K276fs		.											.	WDR33-90	0			c.827delA						.						154	153	153					2																	128484249		2203	4300	6503	SO:0001589	frameshift_variant	55339	exon8			.		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.827delA	2.37:g.128484249delT	ENSP00000325377:p.Lys276fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	136	38	NM_018383	0	0	0	0	0	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Frame_Shift_Del	DEL	ENST00000322313.4	37	CCDS2150.1																																																																																			.		0.468	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		-	128484249	T	-	128484249	7	5	60	1	0	1	0	1	0	0	0	0	17320	1609	56	0	3243	0	WDR33	2	128484249	Frame_Shift_Del	DEL	T	TCGA-BQ-5876-01A-11D-1589-08	28468895	128484249	114715124	25	5792											
CXCR4	7852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	136873381	136873381	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtagatggtgggcaggaaGattttattgaaattagcatt	13	13	13	2	0	0	3	0	1	0	2	0	5	0	4	0	3	1	3	0	3	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:136873381G>T	ENST00000241393.3	-	2	221	c.117C>A	c.(115-117)atC>atA	p.I39I	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Silent_p.I43I	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	39					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	TGGGCAGGAAGATTTTATTGA	0.438																																					p.I43I		.											.	CXCR4-1082	0			c.C129A						.						128	129	128					2																	136873381		2203	4300	6503	SO:0001819	synonymous_variant	7852	exon1			CAGGAAGATTTTA	AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	2561	protein-coding gene	gene with protein product		162643	"chemokine (C-X-C motif), receptor 4 (fusin)"			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.117C>A	2.37:g.136873381G>T		Somatic	145	1		WXS	Illumina HiSeq	Phase_I	163	61	NM_001008540	0	0	14	15	1	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Silent	SNP	ENST00000241393.3	37	CCDS46420.1																																																																																			.		0.438	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			T	136873381	G	T	136873381	2	4	60	1	0	0	0	0	0	0	0	1	4099	932	33	4		4	CXCR4	2	136873381	Silent	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	8389132	136873381	106325992	26	5793											
TTN	7273	hgsc.bcm.edu;broad.mit.edu	37	chr2	179585887	179585887	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaatggattctccctgctttGcaacttttgaagcttctaat	9	16	7	9	0	2	1	0	1	2	0	3	3	2	2	1	1	4	3	1	1	4	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:179585887G>A	ENST00000591111.1	-	77	22132	c.21908C>T	c.(21907-21909)gCa>gTa	p.A7303V	TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.A7620V|TTN_ENST00000342992.6_Missense_Mutation_p.A6376V|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12867	Ig-like 55.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCCTGCTTTGCAACTTTTGA	0.358																																					p.A7620V		.											.	TTN-636	0			c.C22859T						.						60	55	57					2																	179585887		1801	4069	5870	SO:0001583	missense	7273	exon79			TGCTTTGCAACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.21908C>T	2.37:g.179585887G>A	ENSP00000465570:p.Ala7303Val	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	58	6	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.67	1.706674	0.30232	.	.	ENSG00000155657	ENST00000342992	T	0.62788	-0.0	6.16	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.26448	0.0646	N	0.00611	-1.325	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31943	-0.9925	9	0.87932	D	0	.	3.744	0.08541	0.2145:0.2654:0.5201:0.0	.	7303	Q8WZ42	TITIN_HUMAN	V	6376	ENSP00000343764:A6376V	ENSP00000343764:A6376V	A	-	2	0	TTN	179294132	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.296000	0.51802	2.937000	0.99478	0.650000	0.86243	GCA	.		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179585887	G	A	179585887	3	1	60	1	0	0	0	0	1	0	0	0	16768	1319	46	2	81806	2	TTN	2	179585887	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	42712506	179585887	63613486	27	5794											
DNAH7	56171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	196749321	196749321	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actcttacctcagtgacaaaTtgataatcataaattgttcc	14	14	4	9	0	3	2	2	2	1	0	4	2	4	2	2	0	1	1	2	0	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:196749321T>C	ENST00000312428.6	-	35	5851	c.5751A>G	c.(5749-5751)caA>caG	p.Q1917Q		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1917					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						CAGTGACAAATTGATAATCAT	0.433																																					p.Q1917Q		.											.	DNAH7-102	0			c.A5751G						.						77	75	76					2																	196749321		1911	4123	6034	SO:0001819	synonymous_variant	56171	exon35			GACAAATTGATAA	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"Axonemal dyneins", "EF-hand domain containing"	18661	protein-coding gene	gene with protein product		610061	"dynein, axonemal, heavy polypeptide 7"			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.5751A>G	2.37:g.196749321T>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	106	33	NM_018897	0	0	0	0	0	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			.		0.433	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196749321	T	C	196749321	2	2	60	1	0	0	0	0	0	0	0	1	4617	1490	52	3		3	DNAH7	2	196749321	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	17163434	196749321	46450052	28	5795											
GTF3C3	9330	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197636546	197636546	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagggcatgattttctgggTttttcagcatcaaacggaga	11	13	11	6	1	3	2	2	1	1	1	3	3	3	2	0	3	2	3	0	3	2	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:197636546T>G	ENST00000263956.3	-	15	2275	c.2186A>C	c.(2185-2187)aAc>aCc	p.N729T		NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	729					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ATTTTCTGGGTTTTTCAGCAT	0.423																																					p.N729T													.	GTF3C3-97	0			c.A2186C						.						172	154	160					2																	197636546		2203	4300	6503	SO:0001583	missense	9330	exon15			TCTGGGTTTTTCA	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.2186A>C	2.37:g.197636546T>G	ENSP00000263956:p.Asn729Thr	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	114	5	NM_012086	0	0	25	32	7	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Missense_Mutation	SNP	ENST00000263956.3	37	CCDS2316.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458810	0.43634	.	.	ENSG00000119041	ENST00000263956	T	0.46063	0.88	5.21	5.21	0.72293	Tetratricopeptide-like helical (1);	0.144557	0.64402	D	0.000010	T	0.31482	0.0798	L	0.29908	0.895	0.80722	D	1	B	0.27068	0.167	B	0.22880	0.042	T	0.07809	-1.0753	10	0.23891	T	0.37	-14.7458	15.2501	0.73539	0.0:0.0:0.0:1.0	.	729	Q9Y5Q9	TF3C3_HUMAN	T	729	ENSP00000263956:N729T	ENSP00000263956:N729T	N	-	2	0	GTF3C3	197344791	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.868000	0.87116	2.180000	0.69256	0.528000	0.53228	AAC	.		0.423	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1			G	197636546	T	G	197636546	3	3	60	1	0	0	0	0	1	0	0	0	6895	1725	60	5	490	5	GTF3C3	2	197636546	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	887225	197636546	45562827	29	5796											
ERBB4	2066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	212426810	212426810	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catacttgccatgatcagagCttcctgtaagaaaaaaatgc	15	10	7	9	0	1	3	1	1	0	2	2	3	2	3	2	0	4	2	2	0	5	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:212426810C>A	ENST00000342788.4	-	20	2615	c.2305G>T	c.(2305-2307)Gct>Tct	p.A769S	ERBB4_ENST00000436443.1_Missense_Mutation_p.A769S|ERBB4_ENST00000402597.1_Missense_Mutation_p.A759S	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	769	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ATGATCAGAGCTTCCTGTAAG	0.403										TSP Lung(8;0.080)																											p.A769S		.											.	ERBB4-1461	0			c.G2305T						.						81	75	77					2																	212426810		2203	4300	6503	SO:0001583	missense	2066	exon20			TCAGAGCTTCCTG	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2305G>T	2.37:g.212426810C>A	ENSP00000342235:p.Ala769Ser	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	107	42	NM_001042599	0	0	0	0	0	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	32	5.153661	0.94645	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.64085	-0.08;-0.08;-0.08	5.36	5.36	0.76844	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81847	0.4909	M	0.82517	2.595	0.80722	D	1	D;P;D;D	0.76494	0.999;0.738;0.999;0.999	D;D;D;D	0.91635	0.999;0.911;0.998;0.999	D	0.83933	0.0307	10	0.72032	D	0.01	.	19.4633	0.94927	0.0:1.0:0.0:0.0	.	759;759;769;769	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	S	769;769;759	ENSP00000342235:A769S;ENSP00000403204:A769S;ENSP00000385565:A759S	ENSP00000342235:A769S	A	-	1	0	ERBB4	212135055	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.776000	0.85560	2.666000	0.90696	0.655000	0.94253	GCT	.		0.403	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212426810	C	A	212426810	3	1	60	1	0	0	0	0	1	0	0	0	5222	797	28	4	1657	4	ERBB4	2	212426810	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	14790264	212426810	30772563	30	5797											
UBP1	7342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	33434887	33434887	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagggatattaaacaccaGcgcaagttttcgagcaactt	14	9	10	8	2	0	1	0	0	0	1	1	4	0	2	1	1	4	3	1	1	5	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr3:33434887G>C	ENST00000283629.3	-	14	1979	c.1450C>G	c.(1450-1452)Ctg>Gtg	p.L484V	UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000283628.5_Missense_Mutation_p.L484V|UBP1_ENST00000447368.2_Missense_Mutation_p.L448V	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	484					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TTAAACACCAGCGCAAGTTTT	0.348																																					p.L484V		.											.	UBP1-537	0			c.C1450G						.						80	80	80					3																	33434887		2203	4300	6503	SO:0001583	missense	7342	exon14			ACACCAGCGCAAG	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.1450C>G	3.37:g.33434887G>C	ENSP00000283629:p.Leu484Val	Somatic	98	1		WXS	Illumina HiSeq	Phase_I	114	86	NM_014517	0	0	1	8	7	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.638021	0.29157	.	.	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628	T;T;T	0.17054	2.31;2.3;2.31	5.89	-10.4	0.00318	.	0.543122	0.21143	N	0.079443	T	0.08670	0.0215	L	0.29908	0.895	0.09310	N	1	B;B	0.22683	0.073;0.002	B;B	0.27380	0.079;0.004	T	0.09058	-1.0692	10	0.30854	T	0.27	-0.7132	10.5024	0.44813	0.239:0.0:0.5623:0.1987	.	448;484	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	V	484;448;484	ENSP00000283629:L484V;ENSP00000395558:L448V;ENSP00000283628:L484V	ENSP00000283628:L484V	L	-	1	2	UBP1	33409891	0.000000	0.05858	0.002000	0.10522	0.981000	0.71138	-0.034000	0.12225	-2.077000	0.00874	-0.262000	0.10625	CTG	.		0.348	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		C	33434887	G	C	33434887	3	2	60	1	0	0	0	0	1	0	0	0	16928	962	34	4	184	4	UBP1	3	33434887	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		33434887	164587543	31	5798											
SETD2	29072	hgsc.bcm.edu;bcgsc.ca	37	chr3	47125642	47125643	+	Frame_Shift_Ins	INS	-	-	A																															ttttcagtctgcgaaacattINSagtttcttgggagtgtctgt																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr3:47125642_47125643insA	ENST00000409792.3	-	12	5669_5670	c.5627_5628insT	c.(5626-5628)ctafs	p.L1876fs	SETD2_ENST00000492397.1_5'Flank	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1876					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGCGAAACATTAGTTTCTTGGG	0.446			"N, F, S, Mis"		clear cell renal carcinoma																																p.L1876fs		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.5628_5629insT						.																																			SO:0001589	frameshift_variant	29072	exon12			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5628dupT	3.37:g.47125643_47125643dupA	ENSP00000386759:p.Leu1876fs	Somatic	288	0		WXS	Illumina HiSeq	Phase_I	334	75	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.446	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47125643	-	A	47125642	7	5	60	1	0	1	1	0	0	0	0	0	14163	1741	61	0	2106	0	SETD2	3	47125642	Frame_Shift_Ins	INS	-	TCGA-BQ-5876-01A-11D-1589-08	13690755	47125642	150896788	32	5799											
POLQ	10721	broad.mit.edu	37	chr3	121207671	121207673	+	In_Frame_Del	DEL	CTT	CTT	-																															ggaaaaggaatgtgacactcCttctgaaaagagttcattga																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr3:121207671_121207673delCTT	ENST00000264233.5	-	16	4233_4235	c.4105_4107delAAG	c.(4105-4107)aagdel	p.K1369del		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1369					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TGTGACACTCCTTCTGAAAAGAG	0.448								DNA polymerases (catalytic subunits)																													p.1369_1369del	Pancreas(152;907 1925 26081 31236 36904)												.	POLQ-664	0			c.4105_4107del						.			1,4265		0,1,2132						2.9	0			178	0,8254		0,0,4127	no	coding	POLQ	NM_199420.3		0,1,6259	A1A1,A1R,RR		0.0,0.0234,0.0080				1,12519				SO:0001651	inframe_deletion	10721	exon16			ACACTCCTTCTGA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4105_4107delAAG	3.37:g.121207671_121207673delCTT	ENSP00000264233:p.Lys1369del	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	267	13	NM_199420	0	0	0	0	0	O95160|Q6VMB5	In_Frame_Del	DEL	ENST00000264233.5	37	CCDS33833.1																																																																																			.		0.448	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		-	121207673	CTT	-	121207671	7	5	60	1	0	1	0	1	0	0	0	0	12234	680	24	0	3725	0	POLQ	3	121207671	In_Frame_Del	DEL	CTT	TCGA-BQ-5876-01A-11D-1589-08	74082029	121207671	76814759	33	5800											
FBXO45	200933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	196304554	196304554	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgggcccccatgcagtgccaAggttatgtggcattgctggg	6	9	15	11	1	0	0	0	0	0	0	0	0	0	0	3	4	3	4	3	4	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr3:196304554A>T	ENST00000311630.6	+	2	846	c.549A>T	c.(547-549)caA>caT	p.Q183H	FBXO45_ENST00000440469.1_Missense_Mutation_p.Q4H	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	183	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		TGCAGTGCCAAGGTTATGTGG	0.547																																					p.Q183H		.											.	FBXO45-614	0			c.A549T						.						48	49	49					3																	196304554		1953	4148	6101	SO:0001583	missense	200933	exon2			GTGCCAAGGTTAT	AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"F-boxes /  "other""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.549A>T	3.37:g.196304554A>T	ENSP00000310332:p.Gln183His	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	27	23	NM_001105573	0	0	0	3	3	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	A	9.264	1.043862	0.19748	.	.	ENSG00000174013	ENST00000440469;ENST00000311630	T;T	0.60171	0.21;0.21	4.95	2.42	0.29668	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.052694	0.85682	N	0.000000	T	0.25754	0.0627	N	0.01789	-0.72	0.54753	D	0.999983	B	0.11235	0.004	B	0.12156	0.007	T	0.02450	-1.1157	10	0.25106	T	0.35	-22.4406	6.7957	0.23725	0.6401:0.0:0.3599:0.0	.	183	P0C2W1	FBSP1_HUMAN	H	4;183	ENSP00000389868:Q4H;ENSP00000310332:Q183H	ENSP00000310332:Q183H	Q	+	3	2	FBXO45	197788951	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.363000	0.52321	0.403000	0.25479	0.374000	0.22700	CAA	.		0.547	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			T	196304554	A	T	196304554	3	4	60	1	0	0	0	0	1	0	0	0	5773	69	3	5	555	5	FBXO45	3	196304554	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	75096883	196304554	1717876	34	5801											
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69202908	69202908	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctcctcctcctcctcCtcttcctcctcctcctcttc	0	17	0	24	0	3	0	0	0	3	0	14	0	13	0	10	0	0	0	10	0	0	3	rs548927284	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr4:69202908C>T	ENST00000344157.4	-	4	1055	c.720G>A	c.(718-720)gaG>gaA	p.E240E	YTHDC1_ENST00000579690.1_Silent_p.E240E|YTHDC1_ENST00000355665.3_Silent_p.E240E	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	240	Glu-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						cctcctcctcctcttcctcct	0.478																																					p.E240E		.											.	YTHDC1-92	0			c.G720A						.						141	100	114					4																	69202908		2203	4300	6503	SO:0001819	synonymous_variant	91746	exon4			CTCCTCCTCTTCC	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.720G>A	4.37:g.69202908C>T		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_001031732	0	0	7	10	3	Q4W5Q3|Q7Z622|Q8TF35	Silent	SNP	ENST00000344157.4	37	CCDS33992.1																																																																																			.		0.478	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		T	69202908	C	T	69202908	2	4	60	1	0	0	0	0	0	0	0	1	17529	680	24	2		2	YTHDC1	4	69202908	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		69202908	121951368	35	5802											
MFAP3L	9848	bcgsc.ca	37	chr4	170913237	170913237	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttctttagatggctgctcatCatgcacaggcgggtgatatt	8	14	11	8	1	3	2	2	1	1	1	3	2	3	2	0	3	2	3	0	3	2	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr4:170913237C>G	ENST00000361618.3	-	3	829	c.522G>C	c.(520-522)atG>atC	p.M174I	MFAP3L_ENST00000393704.3_Missense_Mutation_p.M71I|RP11-6E9.4_ENST00000508955.1_RNA	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		GGCTGCTCATCATGCACAGGC	0.517																																					p.M174I													.	MFAP3L-91	0			c.G522C						.						136	131	133					4																	170913237		2203	4300	6503	SO:0001583	missense	9848	exon3			GCTCATCATGCAC	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"Immunoglobulin superfamily / I-set domain containing"	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.522G>C	4.37:g.170913237C>G	ENSP00000354583:p.Met174Ile	Somatic	119	1		WXS	Illumina HiSeq	Phase_1	96	4	NM_021647	0	0	26	26	0	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Missense_Mutation	SNP	ENST00000361618.3	37	CCDS34103.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678269	0.88542	.	.	ENSG00000198948	ENST00000393704;ENST00000361618;ENST00000512698	D;D;D	0.98192	-4.78;-1.79;-4.71	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.98261	0.9424	M	0.61703	1.905	0.80722	D	1	P	0.51537	0.946	P	0.55161	0.77	D	0.98186	1.0460	10	0.39692	T	0.17	-2.1688	19.4847	0.95025	0.0:1.0:0.0:0.0	.	174	O75121	MFA3L_HUMAN	I	71;174;71	ENSP00000377307:M71I;ENSP00000354583:M174I;ENSP00000422791:M71I	ENSP00000354583:M174I	M	-	3	0	MFAP3L	171149812	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.602000	0.87976	0.555000	0.69702	ATG	.		0.517	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		G	170913237	C	G	170913237	3	3	60	1	0	0	0	0	1	0	0	0	9541	826	29	4	711	4	MFAP3L	4	170913237	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	101710329	170913237	20241039	36	5803											
TRIO	7204	broad.mit.edu	37	chr5	14381318	14381318	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagtatacagcacacccAggagctcctgaaagagcacg	13	5	9	14	1	0	2	0	1	0	1	2	3	2	3	3	1	4	4	3	1	3	2	rs34701068		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:14381318A>G	ENST00000344204.4	+	21	3551	c.3527A>G	c.(3526-3528)cAg>cGg	p.Q1176R	TRIO_ENST00000509967.2_Missense_Mutation_p.Q1127R|TRIO_ENST00000537187.1_Missense_Mutation_p.Q1176R	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1176					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CAGCACACCCAGGAGCTCCTG	0.493																																					p.Q1176R													.	TRIO-562	0			c.A3527G						.						78	77	77					5																	14381318		2203	4300	6503	SO:0001583	missense	7204	exon21			ACACCCAGGAGCT	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.3527A>G	5.37:g.14381318A>G	ENSP00000339299:p.Gln1176Arg	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	119	6	NM_007118	0	0	9	9	0	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908445	0.52333	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.42513	0.97;0.97;0.97	5.28	5.28	0.74379	.	0.122258	0.56097	D	0.000026	T	0.44726	0.1307	L	0.38838	1.175	0.51482	D	0.999921	P;P;B	0.48640	0.913;0.73;0.006	P;B;B	0.50314	0.637;0.312;0.012	T	0.32745	-0.9895	10	0.40728	T	0.16	.	15.2206	0.73308	1.0:0.0:0.0:0.0	.	1127;1176;1176	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	R	1176;1176;1127;863	ENSP00000339299:Q1176R;ENSP00000446348:Q1176R;ENSP00000445592:Q1127R	ENSP00000339299:Q1176R	Q	+	2	0	TRIO	14434318	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.310000	0.96267	2.000000	0.58554	0.533000	0.62120	CAG	.		0.493	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		G	14381318	A	G	14381318	3	3	60	1	0	0	0	0	1	0	0	0	16585	188	7	3	3609	3	TRIO	5	14381318	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		14381318	166533942	37	5804											
MYO10	4651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	16764479	16764479	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcacgcatacagagccatGgccagggagtccctgctgtc	9	6	12	14	1	0	1	0	0	0	1	2	2	1	2	3	2	4	3	3	2	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:16764479G>T	ENST00000513610.1	-	12	1660	c.1206C>A	c.(1204-1206)gcC>gcA	p.A402A		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	402	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						ACAGAGCCATGGCCAGGGAGT	0.547																																					p.A402A		.											.	MYO10-3	0			c.C1206A						.						107	103	105					5																	16764479		2098	4241	6339	SO:0001819	synonymous_variant	4651	exon12			AGCCATGGCCAGG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1206C>A	5.37:g.16764479G>T		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	103	44	NM_012334	0	0	4	5	1	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			.		0.547	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16764479	G	T	16764479	2	4	60	1	0	0	0	0	0	0	0	1	10087	1335	47	4		4	MYO10	5	16764479	Silent	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	2383161	16764479	164150781	38	5805											
ADAMTS12	81792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	33561191	33561191	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaggtggcatctttttgcagGgtcaggtctctggatggccg	5	12	16	8	1	3	0	1	0	2	0	4	2	3	1	1	6	1	2	1	6	0	2	rs183308563	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:33561191G>C	ENST00000504830.1	-	20	4401	c.4066C>G	c.(4066-4068)Cct>Gct	p.P1356A	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.P1271A	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1356	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CTTTTTGCAGGGTCAGGTCTC	0.572										HNSCC(64;0.19)			G|||	2	0.000399361	0	0	5008	,	,		13628	0.002		0	False		,,,				2504	0				p.P1356A		.											.	ADAMTS12-232	0			c.C4066G						.						131	118	123					5																	33561191		2203	4300	6503	SO:0001583	missense	81792	exon20			TTGCAGGGTCAGG	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"ADAM metallopeptidases with thrombospondin type 1 motif"	14605	protein-coding gene	gene with protein product		606184	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4066C>G	5.37:g.33561191G>C	ENSP00000422554:p.Pro1356Ala	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	180	67	NM_030955	0	0	0	0	0	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	17.73	3.461381	0.63513	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59638	0.25;0.25	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.66982	0.2845	L	0.31120	0.905	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.974;0.985	T	0.67397	-0.5681	10	0.46703	T	0.11	.	18.7866	0.91957	0.0:0.0:1.0:0.0	.	1271;1356	P58397-3;P58397	.;ATS12_HUMAN	A	1356;1271	ENSP00000422554:P1356A;ENSP00000344847:P1271A	ENSP00000344847:P1271A	P	-	1	0	ADAMTS12	33596948	1.000000	0.71417	0.998000	0.56505	0.557000	0.35523	6.077000	0.71275	2.528000	0.85240	0.650000	0.86243	CCT	G|0.999;C|0.001		0.572	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		C	33561191	G	C	33561191	3	2	60	1	0	0	0	0	1	0	0	0	257	1232	43	4	738	4	ADAMTS12	5	33561191	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	16796712	33561191	147354069	39	5806											
SPEF2	79925	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	35771741	35771743	+	In_Frame_Del	DEL	GAA	GAA	-																															aaattcatcagaggcttatgGaagaagaaaaagaaaaccag																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:35771741_35771743delGAA	ENST00000356031.3	+	27	3986_3988	c.3832_3834delGAA	c.(3832-3834)gaadel	p.E1280del	SPEF2_ENST00000440995.2_In_Frame_Del_p.E1275del|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1280					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GAGGCTTATGGAAGAAGAAAAAG	0.399																																					p.1278_1278del		.											.	SPEF2-26	0			c.3832_3834del						.																																			SO:0001651	inframe_deletion	79925	exon27			.	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.3832_3834delGAA	5.37:g.35771747_35771749delGAA	ENSP00000348314:p.Glu1280del	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	58	12	NM_024867	0	0	0	0	0	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	In_Frame_Del	DEL	ENST00000356031.3	37	CCDS43309.1																																																																																			.		0.399	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		-	35771743	GAA	-	35771741	7	5	60	1	0	1	0	1	0	0	0	0	15067	1175	41	0	3959	0	SPEF2	5	35771741	In_Frame_Del	DEL	GAA	TCGA-BQ-5876-01A-11D-1589-08	2210550	35771741	145143519	40	5807											
PARP8	79668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	50137860	50137860	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagaaggaggcattcacaaAgagatcctccgagtaattgg	15	7	11	8	1	1	2	1	0	0	2	3	5	3	3	2	3	0	2	2	3	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:50137860A>T	ENST00000281631.5	+	26	2681	c.2523A>T	c.(2521-2523)aaA>aaT	p.K841N	PARP8_ENST00000511363.2_3'UTR|PARP8_ENST00000503750.2_Missense_Mutation_p.K799N|PARP8_ENST00000505697.2_Missense_Mutation_p.K841N|PARP8_ENST00000514067.2_Missense_Mutation_p.K799N|PARP8_ENST00000505554.1_Missense_Mutation_p.K820N	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	841	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				GCATTCACAAAGAGATCCTCC	0.358																																					p.K841N		.											.	PARP8-586	0			c.A2523T						.						86	82	83					5																	50137860		2203	4300	6503	SO:0001583	missense	79668	exon27			TCACAAAGAGATC	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"Poly (ADP-ribose) polymerases"	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.2523A>T	5.37:g.50137860A>T	ENSP00000281631:p.Lys841Asn	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	101	43	NM_001178055	0	0	9	18	9	Q3KRB7|Q6DHZ1|Q9H754	Missense_Mutation	SNP	ENST00000281631.5	37	CCDS3954.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.855481	0.51376	.	.	ENSG00000151883	ENST00000505697;ENST00000503750;ENST00000281631;ENST00000514067;ENST00000505554	.	.	.	6.08	3.7	0.42460	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.058378	0.64402	D	0.000002	T	0.41465	0.1160	L	0.44542	1.39	0.80722	D	1	P;B;B	0.37781	0.608;0.447;0.319	B;B;B	0.35114	0.193;0.196;0.096	T	0.12941	-1.0528	8	.	.	.	-15.5759	10.485	0.44717	0.8695:0.0:0.1305:0.0	.	733;799;841	B4DQ81;Q8N3A8-2;Q8N3A8	.;.;PARP8_HUMAN	N	841;799;841;799;820	.	.	K	+	3	2	PARP8	50173617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.471000	0.45127	0.545000	0.28902	-0.256000	0.11100	AAA	.		0.358	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615		T	50137860	A	T	50137860	3	4	60	1	0	0	0	0	1	0	0	0	11491	69	3	5	2625	5	PARP8	5	50137860	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	14366119	50137860	130777400	41	5808											
VCAN	1462	broad.mit.edu	37	chr5	82835856	82835856	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggagcagaaggacccaCggtggcacctctccctttct	8	8	10	15	1	2	1	0	0	2	1	3	3	2	3	3	4	1	2	3	4	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:82835856C>A	ENST00000265077.3	+	8	7599	c.7034C>A	c.(7033-7035)aCg>aAg	p.T2345K	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.T1358K|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2345	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GAAGGACCCACGGTGGCACCT	0.468																																					p.T2345K													.	VCAN-238	0			c.C7034A						.						87	81	83					5																	82835856		2203	4300	6503	SO:0001583	missense	1462	exon8			GACCCACGGTGGC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7034C>A	5.37:g.82835856C>A	ENSP00000265077:p.Thr2345Lys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	104	3	NM_004385	0	0	2	2	0	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	7.177	0.588857	0.13812	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.15256	2.44;2.44	6.07	5.16	0.70880	.	0.394765	0.24534	N	0.037699	T	0.20414	0.0491	L	0.48642	1.525	0.09310	N	0.999993	D;D	0.62365	0.991;0.984	P;P	0.52672	0.706;0.607	T	0.14282	-1.0478	10	0.24483	T	0.36	.	5.2285	0.15408	0.1423:0.6391:0.1377:0.081	.	1358;2345	P13611-2;P13611	.;CSPG2_HUMAN	K	2345;1358	ENSP00000265077:T2345K;ENSP00000340062:T1358K	ENSP00000265077:T2345K	T	+	2	0	VCAN	82871612	0.027000	0.19231	0.016000	0.15963	0.113000	0.19764	1.141000	0.31528	1.471000	0.48121	0.650000	0.86243	ACG	.		0.468	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82835856	C	A	82835856	3	1	60	1	0	0	0	0	1	0	0	0	17171	536	19	4	7060	4	VCAN	5	82835856	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	32697996	82835856	98079404	42	5809											
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	89989974	89989974	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagtgtttctggatgacAtcatggatcagcccagctgt	8	11	10	12	0	3	1	2	1	1	0	3	3	3	3	3	2	2	2	3	2	0	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:89989974A>T	ENST00000405460.2	+	33	7497	c.7401A>T	c.(7399-7401)acA>acT	p.T2467T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2467	Calx-beta 17. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCTGGATGACATCATGGATCA	0.488																																					p.T2467T		.											.	GPR98-103	0			c.A7401T						.						67	66	66					5																	89989974		1926	4127	6053	SO:0001819	synonymous_variant	84059	exon33			GATGACATCATGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7401A>T	5.37:g.89989974A>T		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	51	23	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	9.244	1.039019	0.19669	.	.	ENSG00000164199	ENST00000509621	.	.	.	5.92	-3.15	0.05233	.	.	.	.	.	T	0.36908	0.0984	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35968	-0.9767	4	.	.	.	.	1.1269	0.01736	0.4642:0.1847:0.1714:0.1797	.	.	.	.	L	33	.	.	H	+	2	0	GPR98	90025730	0.645000	0.27286	0.979000	0.43373	0.943000	0.58893	-0.090000	0.11163	-0.108000	0.12066	0.533000	0.62120	CAT	.		0.488	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89989974	A	T	89989974	2	4	60	1	0	0	0	0	0	0	0	1	6742	204	8	5		5	GPR98	5	89989974	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	7154118	89989974	90925286	43	5810											
PCDHGC4	56098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140865325	140865325	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	agcctggtcccagagctgctCctggagaagcctttggatcg	7	9	13	12	1	0	2	0	0	0	2	3	4	2	3	4	3	4	2	4	3	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:140865325C>G	ENST00000306593.1	+	1	585	c.585C>G	c.(583-585)ctC>ctG	p.L195L	PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	195	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAGCTGCTCCTGGAGAAGC	0.582																																					p.L195L		.											.	PCDHGC4-72	0			c.C585G						.						35	40	38					5																	140865325		2203	4300	6503	SO:0001819	synonymous_variant	56098	exon1			GCTGCTCCTGGAG	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.585C>G	5.37:g.140865325C>G		Somatic	61	1		WXS	Illumina HiSeq	Phase_I	78	26	NM_018928	0	0	0	0	0	Q495T2|Q9Y5C3	Silent	SNP	ENST00000306593.1	37	CCDS4262.1																																																																																			.		0.582	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		G	140865325	C	G	140865325	2	3	60	1	0	0	0	0	0	0	0	1	11596	842	30	4		4	PCDHGC4	5	140865325	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	50875351	140865325	40049935	44	5811											
TRIM41	90933	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	180661231	180661232	+	Frame_Shift_Ins	INS	-	-	C																															ctgatgctgtcccctgaccgINSccggggggtccgcctggcag																								rs138245799		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:180661231_180661232insC	ENST00000315073.5	+	6	2059_2060	c.1349_1350insC	c.(1348-1353)cgccggfs	p.R451fs	TRIM41_ENST00000351937.5_Frame_Shift_Ins_p.R451fs|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCCCTGACCGCCGGGGGGTCC	0.698																																					p.R450fs		.											.	TRIM41-226	0			c.1349_1350insC						.																																			SO:0001589	frameshift_variant	90933	exon6			.	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19013	protein-coding gene	gene with protein product	"RING-finger protein that interacts with C kinase"	610530	"tripartite motif-containing 41"			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1351dupC	5.37:g.180661233_180661233dupC	ENSP00000320869:p.Arg451fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	104	38	NM_201627	0	0	0	0	0	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Frame_Shift_Ins	INS	ENST00000315073.5	37	CCDS4466.1																																																																																			.		0.698	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		C	180661232	-	C	180661231	7	5	60	1	0	1	1	0	0	0	0	0	16549	1087	38	0	1371	0	TRIM41	5	180661231	Frame_Shift_Ins	INS	-	TCGA-BQ-5876-01A-11D-1589-08	39795906	180661231	254029	45	5812											
RANBP9	10048	broad.mit.edu;bcgsc.ca	37	chr6	13622632	13622632	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtggcaaatgcgcaggAtccaattcctgatcgagcca	11	8	10	12	2	0	1	0	1	0	0	3	3	2	2	3	2	2	2	3	2	2	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:13622632A>G	ENST00000011619.3	-	14	2210	c.2152T>C	c.(2152-2154)Tcc>Ccc	p.S718P	RANBP9_ENST00000469916.1_5'UTR|RANBP9_ENST00000539980.1_Missense_Mutation_p.S489P|AL441883.1_ENST00000600057.1_5'Flank|NOL7_ENST00000474485.1_Intron	NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	718	Interaction with FMR1.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			AATGCGCAGGATCCAATTCCT	0.473																																					p.S718P													.	RANBP9-414	0			c.T2152C						.						126	104	111					6																	13622632		2203	4300	6503	SO:0001583	missense	10048	exon14			CGCAGGATCCAAT	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.2152T>C	6.37:g.13622632A>G	ENSP00000011619:p.Ser718Pro	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	113	5	NM_005493	0	0	31	31	0	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Missense_Mutation	SNP	ENST00000011619.3	37	CCDS4529.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.593002	0.66219	.	.	ENSG00000010017	ENST00000011619;ENST00000539980	T	0.79653	-1.29	6.17	4.99	0.66335	Ran binding protein, CRA domain (1);	0.047828	0.85682	D	0.000000	T	0.70527	0.3234	M	0.63843	1.955	0.80722	D	1	P	0.50710	0.938	B	0.43508	0.422	T	0.71241	-0.4651	10	0.37606	T	0.19	-7.4467	13.5284	0.61607	0.8699:0.1301:0.0:0.0	.	718	Q96S59	RANB9_HUMAN	P	718;489	ENSP00000011619:S718P	ENSP00000011619:S718P	S	-	1	0	RANBP9	13730611	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.101000	0.76997	1.119000	0.41883	0.533000	0.62120	TCC	.		0.473	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			G	13622632	A	G	13622632	3	3	60	1	0	0	0	0	1	0	0	0	13064	333	12	3	41	3	RANBP9	6	13622632	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		13622632	157492435	46	5813											
CRIP3	401262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43275360	43275360	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagccttacttttcttgccTtgggggaggccagtccttgg	4	13	12	12	0	1	0	0	0	1	0	2	1	2	1	5	4	3	0	5	4	1	6	rs568254475		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:43275360T>C	ENST00000274990.4	-	4	322	c.318A>G	c.(316-318)caA>caG	p.Q106Q	ZNF318_ENST00000607252.1_5'UTR|CRIP3_ENST00000372569.3_Silent_p.Q106Q			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	106					T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TTTTCTTGCCTTGGGGGAGGC	0.642													T|||	1	0.000199681	0	0	5008	,	,		16423	0		0	False		,,,				2504	0.001				p.Q106Q		.											.	CRIP3-91	0			c.A318G						.						44	50	48					6																	43275360		2203	4300	6503	SO:0001819	synonymous_variant	401262	exon4			CTTGCCTTGGGGG	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.318A>G	6.37:g.43275360T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	121	46	NM_206922	0	0	0	0	0	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Silent	SNP	ENST00000274990.4	37		.	.	.	.	.	.	.	.	.	.	T	3.522	-0.097611	0.07010	.	.	ENSG00000146215	ENST00000416431	.	.	.	5.28	-4.75	0.03239	.	.	.	.	.	T	0.06735	0.0172	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.34054	-0.9844	4	.	.	.	0.0414	3.3614	0.07188	0.1112:0.4248:0.1114:0.3527	.	.	.	.	G	54	.	.	R	-	1	2	CRIP3	43383338	0.138000	0.22547	0.008000	0.14137	0.650000	0.38633	-0.340000	0.07821	-0.788000	0.04504	0.533000	0.62120	AGG	.		0.642	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			C	43275360	T	C	43275360	2	2	60	1	0	0	0	0	0	0	0	1	3882	1606	56	3		3	CRIP3	6	43275360	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	29652728	43275360	127839707	47	5814											
OGFRL1	79627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	72011098	72011098	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcttccaggtcccagcaCaactatttaagaatcactcg	11	11	5	14	1	2	1	1	0	1	1	6	1	4	1	2	1	2	1	2	1	4	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:72011098C>A	ENST00000370435.4	+	7	836	c.702C>A	c.(700-702)caC>caA	p.H234Q	RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	234						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GGTCCCAGCACAACTATTTAA	0.358																																					p.H234Q		.											.	OGFRL1-68	0			c.C702A						.						224	259	247					6																	72011098		2203	4299	6502	SO:0001583	missense	79627	exon7			CCAGCACAACTAT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.702C>A	6.37:g.72011098C>A	ENSP00000359464:p.His234Gln	Somatic	782	1		WXS	Illumina HiSeq	Phase_I	745	267	NM_024576	0	0	0	0	0	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	37	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561728	0.65538	.	.	ENSG00000119900	ENST00000370435	T	0.67345	-0.26	5.94	4.16	0.48862	Opioid growth factor receptor (OGFr) conserved domain (1);	0.094242	0.85682	D	0.000000	T	0.74535	0.3729	M	0.83012	2.62	0.46749	D	0.999187	D	0.76494	0.999	D	0.68039	0.955	T	0.78663	-0.2116	10	0.87932	D	0	-12.2653	10.4706	0.44635	0.0:0.741:0.0:0.259	.	234	Q5TC84	OGRL1_HUMAN	Q	234	ENSP00000359464:H234Q	ENSP00000359464:H234Q	H	+	3	2	OGFRL1	72067819	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.730000	0.47335	0.846000	0.35142	0.563000	0.77884	CAC	.		0.358	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		A	72011098	C	A	72011098	3	1	60	1	0	0	0	0	1	0	0	0	10870	477	17	4	728	4	OGFRL1	6	72011098	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	28735738	72011098	99103969	48	5815											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152658075	152658075	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tcagcatcttgcaggtaaatCcagagctcagacttcaggtg	11	10	10	10	0	4	2	3	0	1	2	5	2	5	2	1	2	3	4	1	2	2	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:152658075C>G	ENST00000367255.5	-	76	13030	c.12429G>C	c.(12427-12429)tgG>tgC	p.W4143C	SYNE1_ENST00000341594.5_Missense_Mutation_p.W4008C|SYNE1_ENST00000265368.4_Missense_Mutation_p.W4143C|SYNE1_ENST00000448038.1_Missense_Mutation_p.W4072C|SYNE1_ENST00000423061.1_Missense_Mutation_p.W4072C	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4143					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCAGGTAAATCCAGAGCTCAG	0.458										HNSCC(10;0.0054)																											p.W4143C		.											.	SYNE1-607	0			c.G12429C						.						109	99	102					6																	152658075		2203	4300	6503	SO:0001583	missense	23345	exon76			GTAAATCCAGAGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.12429G>C	6.37:g.152658075C>G	ENSP00000356224:p.Trp4143Cys	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	73	22	NM_182961	0	0	2	7	5	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309305	0.40895	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52754	0.74;0.7;0.65;0.7;0.73	5.47	5.47	0.80525	.	0.000000	0.56097	D	0.000036	T	0.50154	0.1599	L	0.57536	1.79	0.80722	D	1	D;D;D;D	0.71674	0.996;0.996;0.996;0.998	P;P;P;P	0.59703	0.608;0.608;0.608;0.862	T	0.49513	-0.8932	10	0.44086	T	0.13	.	12.6398	0.56702	0.0:0.9245:0.0:0.0755	.	4143;4143;4143;4072	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	C	4143;4072;4143;4072;4008	ENSP00000356224:W4143C;ENSP00000396024:W4072C;ENSP00000265368:W4143C;ENSP00000390975:W4072C;ENSP00000341887:W4008C	ENSP00000265368:W4143C	W	-	3	0	SYNE1	152699768	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	1.774000	0.38573	2.572000	0.86782	0.655000	0.94253	TGG	.		0.458	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152658075	C	G	152658075	3	3	60	1	0	0	0	0	1	0	0	0	15477	856	30	4	14321	4	SYNE1	6	152658075	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	80646977	152658075	18456992	49	5816											
RNF216	54476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5781025	5781025	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actctcctagatttgataacAgctctgtctctgagtcttcg	8	15	7	11	1	4	3	0	2	4	1	7	3	4	3	1	0	2	1	1	0	2	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr7:5781025A>G	ENST00000425013.2	-	4	676	c.452T>C	c.(451-453)cTg>cCg	p.L151P	RNF216_ENST00000389902.3_Missense_Mutation_p.L208P	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	151					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		ATTTGATAACAGCTCTGTCTC	0.458																																					p.L208P		.											.	RNF216-274	0			c.T623C						.						172	174	174					7																	5781025		2203	4300	6503	SO:0001583	missense	54476	exon4			GATAACAGCTCTG	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.452T>C	7.37:g.5781025A>G	ENSP00000404602:p.Leu151Pro	Somatic	328	1		WXS	Illumina HiSeq	Phase_I	350	117	NM_207111	0	0	6	20	14	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Missense_Mutation	SNP	ENST00000425013.2	37	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.515649	0.64634	.	.	ENSG00000011275	ENST00000425013;ENST00000389902	T;T	0.64803	-0.12;0.2	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000002	T	0.73737	0.3625	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.67548	0.952;0.916	T	0.75593	-0.3264	10	0.62326	D	0.03	-11.2668	13.8294	0.63370	1.0:0.0:0.0:0.0	.	151;208	Q9NWF9;Q9NWF9-1	RN216_HUMAN;.	P	151;208	ENSP00000404602:L151P;ENSP00000374552:L208P	ENSP00000374550:L151P	L	-	2	0	RNF216	5747551	1.000000	0.71417	0.836000	0.33094	0.819000	0.46315	3.643000	0.54374	2.289000	0.77006	0.459000	0.35465	CTG	.		0.458	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		G	5781025	A	G	5781025	3	3	60	1	0	0	0	0	1	0	0	0	13512	188	7	3	2204	3	RNF216	7	5781025	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		5781025	153357638	50	5817											
POMZP3	22932	hgsc.bcm.edu	37	chr7	76241120	76241120	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggtgaccttcaggtggcagGtgatgtatatctgcaaggaa	10	10	15	6	0	2	2	1	2	1	0	2	3	2	3	1	5	1	3	1	5	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr7:76241120G>C	ENST00000310842.4	-	5	1040	c.356C>G	c.(355-357)aCc>aGc	p.T119S	UPK3B_ENST00000443097.2_Intron|AC004980.7_ENST00000418663.1_RNA|UPK3B_ENST00000419923.2_Intron|POMZP3_ENST00000275569.4_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	119										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CAGGTGGCAGGTGATGTATAT	0.512																																					p.T119S		.											.	POMZP3-90	0			c.C356G						.						44	48	46					7																	76241120		2167	4245	6412	SO:0001583	missense	22932	exon5			TGGCAGGTGATGT	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"POM-ZP3 fusion protein", "POM121/ZP3 fusion protein"	600587	"POM (POM121 rat homolog) and ZP3 fusion", "POM (POM121 homolog, rat) and ZP3 fusion"			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.356C>G	7.37:g.76241120G>C	ENSP00000309233:p.Thr119Ser	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	55	5	NM_012230	0	0	0	0	0	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	37	CCDS43606.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	12.85|12.85	2.062333|2.062333	0.36373|0.36373	.|.	.|.	ENSG00000146707|ENSG00000146707	ENST00000441393|ENST00000310842;ENST00000454397	.|D;D	.|0.81659	.|-1.52;-1.52	0.786|0.786	0.786|0.786	0.18590|0.18590	.|Zona pellucida sperm-binding protein (1);	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.83450|0.83450	0.5257|0.5257	M|M	0.78916|0.78916	2.43|2.43	0.38260|0.38260	D|D	0.941854|0.941854	.|D	.|0.52996	.|0.957	.|P	.|0.56563	.|0.801	T|T	0.81636|0.81636	-0.0843|-0.0843	5|10	.|0.35671	.|T	.|0.21	.|.	7.5453|7.5453	0.27764|0.27764	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|119	.|Q6PJE2	.|POZP3_HUMAN	Q|S	43|119;224	.|ENSP00000309233:T119S;ENSP00000405319:T224S	.|ENSP00000309233:T119S	H|T	-|-	3|2	2|0	POMZP3|POMZP3	76079056|76079056	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.653000|0.653000	0.38743|0.38743	2.607000|2.607000	0.46300|0.46300	0.733000|0.733000	0.32492|0.32492	0.372000|0.372000	0.22366|0.22366	CAC|ACC	.		0.512	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230		C	76241120	G	C	76241120	3	2	60	1	0	0	0	0	1	0	0	0	12273	1261	44	4	222	4	POMZP3	7	76241120	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	70460095	76241120	82897543	51	5818											
CPA5	93979	broad.mit.edu	37	chr7	129987643	129987643	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctggccaaagatgagaaGcagctttcacttctcgggga	10	9	12	10	1	2	2	1	1	1	2	4	4	3	3	2	3	2	2	2	3	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr7:129987643G>T	ENST00000485477.1	+	3	1282	c.153G>T	c.(151-153)aaG>aaT	p.K51N	CPA5_ENST00000461828.1_Missense_Mutation_p.K51N|CPA5_ENST00000393213.3_Missense_Mutation_p.K51N|CPA5_ENST00000474905.1_Missense_Mutation_p.K51N|CPA5_ENST00000355388.3_Missense_Mutation_p.K51N|CPA5_ENST00000431780.2_Missense_Mutation_p.K51N|CPA5_ENST00000466363.2_Missense_Mutation_p.K51N			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	51						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					AAGATGAGAAGCAGCTTTCAC	0.582																																					p.K51N													.	CPA5-92	0			c.G153T						.						75	70	72					7																	129987643		2203	4300	6503	SO:0001583	missense	93979	exon4			TGAGAAGCAGCTT	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.153G>T	7.37:g.129987643G>T	ENSP00000420237:p.Lys51Asn	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_080385	0	0	0	0	0	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.960439	0.34565	.	.	ENSG00000158525	ENST00000355388;ENST00000463587;ENST00000461828;ENST00000466363;ENST00000485477;ENST00000431780;ENST00000474905;ENST00000393213	T;T;T;T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52;2.52;2.52;2.52	5.63	4.74	0.60224	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.806159	0.11253	N	0.583444	T	0.12433	0.0302	L	0.31420	0.93	0.32060	N	0.595808	P;B	0.36909	0.573;0.336	B;B	0.40134	0.32;0.21	T	0.03773	-1.1005	9	.	.	.	.	9.4917	0.38965	0.0927:0.0:0.9073:0.0	.	51;51	G3V0G8;Q8WXQ8	.;CBPA5_HUMAN	N	51	ENSP00000347549:K51N;ENSP00000420060:K51N;ENSP00000418183:K51N;ENSP00000419025:K51N;ENSP00000420237:K51N;ENSP00000393045:K51N;ENSP00000417314:K51N;ENSP00000376907:K51N	.	K	+	3	2	CPA5	129774879	1.000000	0.71417	0.993000	0.49108	0.861000	0.49209	1.701000	0.37825	2.652000	0.90054	0.655000	0.94253	AAG	.		0.582	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441		T	129987643	G	T	129987643	3	4	60	1	0	0	0	0	1	0	0	0	3799	962	34	4	159	4	CPA5	7	129987643	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	53746523	129987643	29151020	52	5819											
OR2A14	135941	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	143826220	143826220	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagcatggaaggcaacaaGacatggatcacagacatcac	18	4	10	9	0	2	3	2	0	0	3	2	5	2	5	0	3	2	2	0	3	4	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr7:143826220G>T	ENST00000408899.2	+	1	70	c.15G>T	c.(13-15)aaG>aaT	p.K5N		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					AAGGCAACAAGACATGGATCA	0.498																																					p.K5N		.											.	OR2A14-90	0			c.G15T						.						80	77	78					7																	143826220		2034	4193	6227	SO:0001583	missense	135941	exon1			CAACAAGACATGG		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"GPCR / Class A : Olfactory receptors"	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.15G>T	7.37:g.143826220G>T	ENSP00000386137:p.Lys5Asn	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	53	23	NM_001001659	0	0	0	0	0	Q6IF41|Q8NGT8	Missense_Mutation	SNP	ENST00000408899.2	37	CCDS43672.1	.	.	.	.	.	.	.	.	.	.	G	8.070	0.770134	0.15983	.	.	ENSG00000221938	ENST00000408899	T	0.00348	8.0	4.18	4.18	0.49190	.	.	.	.	.	T	0.00144	0.0004	N	0.04320	-0.23	0.09310	N	1	B	0.23591	0.088	B	0.20184	0.028	T	0.50372	-0.8836	9	0.48119	T	0.1	-2.9556	12.1908	0.54270	0.0:0.0:1.0:0.0	.	5	Q96R47	O2A14_HUMAN	N	5	ENSP00000386137:K5N	ENSP00000386137:K5N	K	+	3	2	OR2A14	143457153	0.000000	0.05858	0.341000	0.25589	0.476000	0.33039	-0.561000	0.05957	2.303000	0.77524	0.561000	0.74099	AAG	.		0.498	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1			T	143826220	G	T	143826220	3	4	60	1	0	0	0	0	1	0	0	0	11002	933	33	4	17	4	OR2A14	7	143826220	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	13838577	143826220	15312443	53	5820											
FGFR1	2260	broad.mit.edu	37	chr8	38314950	38314950	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcccagaagaggaggcaCttccagctccacatcccagt	12	5	9	15	0	0	2	0	0	0	2	3	3	3	3	4	2	2	2	4	2	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr8:38314950C>T	ENST00000447712.2	-	2	956	c.15G>A	c.(13-15)aaG>aaA	p.K5K	FGFR1_ENST00000397103.1_Silent_p.K5K|FGFR1_ENST00000532791.1_Silent_p.K5K|FGFR1_ENST00000356207.5_Silent_p.K5K|FGFR1_ENST00000397108.4_Silent_p.K5K|FGFR1_ENST00000425967.3_Silent_p.K38K|FGFR1_ENST00000341462.5_Silent_p.K5K|FGFR1_ENST00000335922.5_De_novo_Start_InFrame|FGFR1_ENST00000326324.6_Silent_p.K5K|FGFR1_ENST00000397091.5_Silent_p.K5K|FGFR1_ENST00000397113.2_Silent_p.K5K	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	5					angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGAGGAGGCACTTCCAGCTCC	0.577		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														p.K38K	Melanoma(146;1153 1840 21453 21841 43625)			Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	.	FGFR1-1793	0			c.G114A						.						71	63	66					8																	38314950		2203	4300	6503	SO:0001819	synonymous_variant	2260	exon3			GAGGCACTTCCAG	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.15G>A	8.37:g.38314950C>T		Somatic	77	2		WXS	Illumina HiSeq	Phase_I	72	4	NM_001174067	0	0	36	42	6	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	ENST00000447712.2	37	CCDS6107.2																																																																																			.		0.577	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	38314950	C	T	38314950	2	4	60	1	0	0	0	0	0	0	0	1	5882	564	20	2		2	FGFR1	8	38314950	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		38314950	108049072	54	5821											
C9orf150	286343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	12821680	12821680	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagacttggaccaattcaGtgacagctccctcatagagg	11	10	9	11	0	3	3	3	1	0	2	4	4	4	4	2	2	1	1	2	2	2	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr9:12821680G>T	ENST00000319264.3	+	2	1303	c.608G>T	c.(607-609)aGt>aTt	p.S203I		NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	206																	GACCAATTCAGTGACAGCTCC	0.507																																					p.S203I		.											.	.	0			c.G608T						.						192	171	178					9																	12821680		2203	4300	6503	SO:0001583	missense	286343	exon2			AATTCAGTGACAG	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"		"chromosome 9 open reading frame 150"	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.608G>T	9.37:g.12821680G>T	ENSP00000321026:p.Ser203Ile	Somatic	215	1		WXS	Illumina HiSeq	Phase_I	219	87	NM_203403	0	0	20	32	12	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.729611	0.48833	.	.	ENSG00000153714	ENST00000319264	T	0.50001	0.76	5.59	5.59	0.84812	.	0.891402	0.09724	N	0.764037	T	0.46425	0.1392	L	0.32530	0.975	0.36995	D	0.894971	B	0.26845	0.161	B	0.27380	0.079	T	0.48328	-0.9045	10	0.87932	D	0	.	19.5985	0.95549	0.0:0.0:1.0:0.0	.	206	Q8IV03	CI150_HUMAN	I	203	ENSP00000321026:S203I	ENSP00000321026:S203I	S	+	2	0	C9orf150	12811680	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.943000	0.40253	2.636000	0.89361	0.563000	0.77884	AGT	.		0.507	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403		T	12821680	G	T	12821680	3	4	60	1	0	0	0	0	1	0	0	0	2468	1029	36	4	614	4	C9orf150	9	12821680	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		12821680	128391751	55	5822											
IFNA2	3440	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	21385064	21385067	+	Frame_Shift_Del	DEL	GATT	GATT	-																															tgagtcctttgtgctgaagaGattgaagatctgctggatca																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	GATT	GATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr9:21385064_21385067delGATT	ENST00000380206.2	-	1	329_332	c.262_265delAATC	c.(262-267)aatctcfs	p.NL88fs		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	88					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		GTGCTGAAGAGATTGAAGATCTGC	0.49																																					p.88_89del		.											.	IFNA2-153	0			c.262_265del						.																																			SO:0001589	frameshift_variant	3440	exon1			.		CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"Interferons"	5423	protein-coding gene	gene with protein product	"alpha-2a interferon", "interferon alpha 2b", "interferon alpha A"	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.262_265delAATC	9.37:g.21385064_21385067delGATT	ENSP00000369554:p.Asn88fs	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	215	87	NM_000605	0	0	0	0	0	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Frame_Shift_Del	DEL	ENST00000380206.2	37	CCDS6506.1																																																																																			.		0.49	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605		-	21385067	GATT	-	21385064	7	5	60	1	0	1	0	1	0	0	0	0	7558	942	33	0	305	0	IFNA2	9	21385064	Frame_Shift_Del	DEL	GATT	TCGA-BQ-5876-01A-11D-1589-08	8563384	21385064	119828367	56	5823											
ENTPD7	57089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101460770	101460770	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcggtactaactcagagatTcaagaatggcctcttttcat	11	13	8	9	1	4	2	3	0	1	2	5	3	4	2	1	2	2	1	1	2	4	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr10:101460770T>G	ENST00000370489.4	+	11	1554	c.1376T>G	c.(1375-1377)tTc>tGc	p.F459C		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	459						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		ACTCAGAGATTCAAGAATGGC	0.433																																					p.F459C		.											.	ENTPD7-91	0			c.T1376G						.						361	321	334					10																	101460770		2203	4300	6503	SO:0001583	missense	57089	exon11			AGAGATTCAAGAA	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.1376T>G	10.37:g.101460770T>G	ENSP00000359520:p.Phe459Cys	Somatic	407	0		WXS	Illumina HiSeq	Phase_I	272	93	NM_020354	0	0	11	18	7	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.321910	0.81580	.	.	ENSG00000198018	ENST00000370489	T	0.12255	2.7	5.21	5.21	0.72293	.	0.056019	0.64402	D	0.000001	T	0.41282	0.1152	M	0.85197	2.74	0.53688	D	0.999977	D	0.76494	0.999	D	0.70935	0.971	T	0.42949	-0.9421	10	0.59425	D	0.04	-26.5929	14.9011	0.70681	0.0:0.0:0.0:1.0	.	459	Q9NQZ7	ENTP7_HUMAN	C	459	ENSP00000359520:F459C	ENSP00000359520:F459C	F	+	2	0	ENTPD7	101450760	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	7.860000	0.86993	2.192000	0.70111	0.523000	0.50628	TTC	.		0.433	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		G	101460770	T	G	101460770	3	3	60	1	0	0	0	0	1	0	0	0	5157	1783	62	5	1414	5	ENTPD7	10	101460770	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		101460770	34073977	57	5824											
OR56A5	0	broad.mit.edu;ucsc.edu	37	chr11	5989644	5989644	+	IGR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggggcagagacagccagtgCtgccagctctggaaactggg	10	5	16	10	0	1	1	0	0	1	1	1	3	1	2	2	4	5	3	2	4	1	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:5989644C>A								OR56A3 (20053 upstream) : OR52L1 (17477 downstream)																							ACAGCCAGTGCTGCCAGCTCT	0.532																																					p.Q27H													.	.	0			c.G81T						.						80	86	84					11																	5989644		692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			CCAGTGCTGCCAG																													11.37:g.5989644C>A		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	15	7	NM_001146033	0	0	0	0	0		Missense_Mutation	SNP		37																																																																																				.	0	0.532									A	5989644	C	A	5989644	1	1	60	0	1	0	0	0	0	0	0	0	11162	796	28	4		4	OR56A5	11	5989644	IGR	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		5989644	129016872	58	5825											
AGBL2	79841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47711964	47711964	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtgagcaagtaaacggtaTttcctgctaggctcctgcat	9	12	11	9	1	0	1	0	1	0	0	2	1	2	1	2	3	4	6	2	3	5	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:47711964T>G	ENST00000525123.1	-	10	1580	c.1295A>C	c.(1294-1296)aAt>aCt	p.N432T	AGBL2_ENST00000298861.4_Missense_Mutation_p.N432T|AGBL2_ENST00000357610.3_Missense_Mutation_p.N432T|AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000528244.1_Missense_Mutation_p.N394T	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	432						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						GTAAACGGTATTTCCTGCTAG	0.498																																					p.N432T		.											.	AGBL2-92	0			c.A1295C						.						123	112	116					11																	47711964		2201	4298	6499	SO:0001583	missense	79841	exon10			ACGGTATTTCCTG		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.1295A>C	11.37:g.47711964T>G	ENSP00000435582:p.Asn432Thr	Somatic	173	1		WXS	Illumina HiSeq	Phase_I	132	32	NM_024783	0	0	3	5	2	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.092430	0.76756	.	.	ENSG00000165923	ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244	T;T;T;T	0.11169	2.8;2.8;2.8;2.8	5.57	5.57	0.84162	Peptidase M14, carboxypeptidase A (1);	0.000000	0.85682	D	0.000000	T	0.45915	0.1366	H	0.95004	3.61	0.54753	D	0.999988	D;D;D	0.89917	1.0;0.999;0.997	D;D;D	0.85130	0.997;0.994;0.986	T	0.61342	-0.7082	9	.	.	.	-23.8875	16.0241	0.80528	0.0:0.0:0.0:1.0	.	394;394;432	F6U0I4;B4DZS1;Q5U5Z8	.;.;CBPC2_HUMAN	T	432;432;432;394	ENSP00000435582:N432T;ENSP00000350228:N432T;ENSP00000298861:N432T;ENSP00000436630:N394T	.	N	-	2	0	AGBL2	47668540	1.000000	0.71417	0.510000	0.27712	0.857000	0.48899	7.429000	0.80309	2.248000	0.74166	0.533000	0.62120	AAT	.		0.498	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		G	47711964	T	G	47711964	3	3	60	1	0	0	0	0	1	0	0	0	376	1493	52	5	1453	5	AGBL2	11	47711964	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	41722320	47711964	87294552	59	5826											
TMEM132A	54972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	60696113	60696113	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcacagccatccctgggcGcctgcgtggtggagctggag	5	8	15	13	2	1	0	1	0	0	0	2	2	2	2	3	4	3	1	3	4	0	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:60696113G>C	ENST00000453848.2	+	4	705	c.547G>C	c.(547-549)Gcc>Ccc	p.A183P	TMEM132A_ENST00000005286.4_Missense_Mutation_p.A183P			Q24JP5	T132A_HUMAN	transmembrane protein 132A	183						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						ATCCCTGGGCGCCTGCGTGGT	0.642																																					p.A183P		.											.	TMEM132A-227	0			c.G547C						.						45	49	48					11																	60696113		2171	4243	6414	SO:0001583	missense	54972	exon4			CTGGGCGCCTGCG	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.547G>C	11.37:g.60696113G>C	ENSP00000405823:p.Ala183Pro	Somatic	151	1		WXS	Illumina HiSeq	Phase_I	94	44	NM_178031	0	0	0	1	1	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.989179	0.74589	.	.	ENSG00000006118	ENST00000453848;ENST00000005286	T;T	0.06142	3.34;3.34	4.32	4.32	0.51571	.	0.800173	0.10694	N	0.644830	T	0.19127	0.0459	L	0.44542	1.39	0.40027	D	0.975487	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.69307	0.946;0.963;0.963	T	0.01844	-1.1262	10	0.87932	D	0	.	14.9848	0.71339	0.0:0.0:1.0:0.0	.	172;183;183	Q24JP5-3;Q24JP5;Q24JP5-2	.;T132A_HUMAN;.	P	183	ENSP00000405823:A183P;ENSP00000005286:A183P	ENSP00000005286:A183P	A	+	1	0	TMEM132A	60452689	0.909000	0.30893	0.990000	0.47175	0.909000	0.53808	4.221000	0.58574	2.136000	0.66102	0.462000	0.41574	GCC	.		0.642	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		C	60696113	G	C	60696113	3	2	60	1	0	0	0	0	1	0	0	0	16077	1087	38	4	561	4	TMEM132A	11	60696113	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	12984149	60696113	74310403	60	5827											
CCDC88B	283234	broad.mit.edu	37	chr11	64111815	64111815	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagatcctctctccagagccCtgcctctgtggccccacctc	5	10	7	19	0	2	2	0	0	2	2	6	2	4	2	7	1	2	0	7	1	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:64111815C>A	ENST00000356786.5	+	14	1846	c.1802C>A	c.(1801-1803)cCt>cAt	p.P601H	CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	601						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTCCAGAGCCCTGCCTCTGTG	0.642																																					p.P601H													.	CCDC88B-94	0			c.C1802A						.						33	36	35					11																	64111815		2201	4297	6498	SO:0001583	missense	283234	exon14			AGAGCCCTGCCTC	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"brain leucine zipper protein", "GRP78-interacting protein induced by ER stress"	611205	"coiled-coil domain containing 88"	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1802C>A	11.37:g.64111815C>A	ENSP00000349238:p.Pro601His	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_032251	0	0	1	1	0	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	.	.	.	.	.	.	.	.	.	.	c	9.520	1.108125	0.20714	.	.	ENSG00000168071	ENST00000377638;ENST00000356786	T	0.28069	1.63	3.54	1.52	0.23074	.	.	.	.	.	T	0.21267	0.0512	L	0.32530	0.975	0.09310	N	0.999998	B;B;B	0.14805	0.011;0.004;0.011	B;B;B	0.14023	0.007;0.004;0.01	T	0.21552	-1.0242	9	0.46703	T	0.11	.	6.1863	0.20500	0.1954:0.6944:0.0:0.1102	.	601;250;601	B2RTU8;A6NC98-3;A6NC98	.;.;CC88B_HUMAN	H	601	ENSP00000349238:P601H	ENSP00000349238:P601H	P	+	2	0	CCDC88B	63868391	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.875000	0.04205	0.253000	0.21552	0.450000	0.29827	CCT	.		0.642	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251		A	64111815	C	A	64111815	3	1	60	1	0	0	0	0	1	0	0	0	2870	681	24	4	1856	4	CCDC88B	11	64111815	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	3415702	64111815	70894701	61	5828											
DPF2	5977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65113198	65113198	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactatgcccactcccacttGgctgaggaggagggcgagga	9	6	14	12	1	0	1	0	1	0	0	1	5	1	4	2	5	1	1	2	5	1	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:65113198G>A	ENST00000528416.1	+	7	832	c.699G>A	c.(697-699)ttG>ttA	p.L233L	DPF2_ENST00000415073.2_Intron|DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Silent_p.L247L	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	233					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						ACTCCCACTTGGCTGAGGAGG	0.512																																					p.L233L		.											.	DPF2-91	0			c.G699A						.						78	71	73					11																	65113198		2201	4297	6498	SO:0001819	synonymous_variant	5977	exon7			CCACTTGGCTGAG	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.699G>A	11.37:g.65113198G>A		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_006268	0	0	9	24	15	A8K7C9|B4DT58	Silent	SNP	ENST00000528416.1	37	CCDS8100.1																																																																																			.		0.512	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		A	65113198	G	A	65113198	2	1	60	1	0	0	0	0	0	0	0	1	4728	1339	47	2		2	DPF2	11	65113198	Silent	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	1001383	65113198	69893318	62	5829											
SPTBN2	6712	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66468283	66468283	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggcctctgcctcaggcaggGtggccggcccttcttcagag	4	8	15	14	1	4	1	2	0	2	1	4	1	4	1	4	5	1	1	4	5	0	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:66468283G>T	ENST00000533211.1	-	17	3618	c.3287C>A	c.(3286-3288)aCc>aAc	p.T1096N	SPTBN2_ENST00000529997.1_Missense_Mutation_p.T1096N|SPTBN2_ENST00000309996.2_Missense_Mutation_p.T1096N			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1096					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTCAGGCAGGGTGGCCGGCCC	0.692																																					p.T1096N		.											.	SPTBN2-155	0			c.C3287A						.						16	18	17					11																	66468283		2193	4285	6478	SO:0001583	missense	6712	exon16			GGCAGGGTGGCCG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.3287C>A	11.37:g.66468283G>T	ENSP00000432568:p.Thr1096Asn	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	27	15	NM_006946	0	0	0	0	0	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414677	0.62511	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.34275	1.37;1.37;1.37	4.7	4.7	0.59300	.	0.059484	0.64402	D	0.000001	T	0.20981	0.0505	N	0.12182	0.205	0.36280	D	0.855746	B	0.28026	0.198	B	0.28305	0.088	T	0.20075	-1.0286	10	0.27785	T	0.31	.	11.7357	0.51763	0.0:0.0:0.8233:0.1767	.	1096	O15020	SPTN2_HUMAN	N	1096	ENSP00000432568:T1096N;ENSP00000311489:T1096N;ENSP00000433593:T1096N	ENSP00000311489:T1096N	T	-	2	0	SPTBN2	66224859	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.377000	0.73145	2.446000	0.82766	0.491000	0.48974	ACC	.		0.692	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66468283	G	T	66468283	3	4	60	1	0	0	0	0	1	0	0	0	15152	1261	44	4	3973	4	SPTBN2	11	66468283	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	1355085	66468283	68538233	63	5830											
LRP5	4041	hgsc.bcm.edu	37	chr11	68125147	68125147	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggacagactggggtgagaCgccccggattgagcgggcag	8	5	18	10	3	0	3	0	2	0	2	0	6	0	5	2	5	1	1	2	5	0	1	rs80358306		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:68125147C>G	ENST00000294304.7	+	3	624	c.518C>G	c.(517-519)aCg>aGg	p.T173R		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	173	Beta-propeller 1.		T -> M (in EVR4; an individual with abnormal retinal vasculature and retinal folds). {ECO:0000269|PubMed:15024691}.		adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGGGGTGAGACGCCCCGGATT	0.547																																					p.T173R		.											.	LRP5-661	0			c.C518G	GRCh37	CM041034	LRP5	M	rs80358306	.						62	55	58					11																	68125147		2200	4294	6494	SO:0001583	missense	4041	exon3			GTGAGACGCCCCG	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.518C>G	11.37:g.68125147C>G	ENSP00000294304:p.Thr173Arg	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_002335	0	0	5	5	0	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801004	0.31869	.	.	ENSG00000162337	ENST00000294304	D	0.95069	-3.6	3.56	1.67	0.24075	Six-bladed beta-propeller, TolB-like (1);	0.121287	0.34291	U	0.004093	D	0.87406	0.6169	N	0.08118	0	0.29685	N	0.841388	P	0.39624	0.681	B	0.44044	0.439	T	0.82792	-0.0282	10	0.27082	T	0.32	.	10.4313	0.44409	0.0:0.8325:0.0:0.1675	.	173	O75197	LRP5_HUMAN	R	173	ENSP00000294304:T173R	ENSP00000294304:T173R	T	+	2	0	LRP5	67881723	0.014000	0.17966	0.966000	0.40874	0.693000	0.40251	0.181000	0.16880	0.495000	0.27882	-0.463000	0.05309	ACG	C|0.999;T|0.001		0.547	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		G	68125147	C	G	68125147	3	3	60	1	0	0	0	0	1	0	0	0	8985	536	19	4	528	4	LRP5	11	68125147	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	1656864	68125147	66881369	64	5831											
RSF1	51773	ucsc.edu	37	chr11	77412780	77412780	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctttctcaagctcacctgtTttcatacttgttatgacaga	9	17	5	10	0	4	2	3	1	2	1	5	2	4	2	1	0	2	3	1	0	3	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:77412780T>C	ENST00000308488.6	-	6	1796	c.1494A>G	c.(1492-1494)aaA>aaG	p.K498K	RSF1_ENST00000480887.1_Silent_p.K246K|RSF1_ENST00000360355.2_Silent_p.K467K			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	498					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			GCTCACCTGTTTTCATACTTG	0.398																																					p.K498K													.	RSF1-93	0			c.A1494G						.						141	137	138					11																	77412780		2200	4292	6492	SO:0001819	synonymous_variant	51773	exon6			ACCTGTTTTCATA	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"Zinc fingers, PHD-type"	18118	protein-coding gene	gene with protein product		608522	"hepatitis B virus x associated protein"	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.1494A>G	11.37:g.77412780T>C		Somatic	308	0		WXS	Illumina HiSeq		256	2	NM_016578	0	0	8	8	0	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			.		0.398	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		C	77412780	T	C	77412780	2	2	60	1	0	0	0	0	0	0	0	1	13731	1838	64	3		3	RSF1	11	77412780	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	9287633	77412780	57593736	65	5832											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877600	82877600	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactaaacaggatattcgggAtccaaggcgaatgaaaaaga	18	7	10	6	2	0	2	0	1	0	1	2	5	1	4	1	3	2	0	1	3	8	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:82877600A>G	ENST00000298281.4	+	5	2113	c.1661A>G	c.(1660-1662)gAt>gGt	p.D554G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	554					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GATATTCGGGATCCAAGGCGA	0.423																																					p.D554G		.											.	PCF11-23	0			c.A1661G						.						80	76	77					11																	82877600		1873	4113	5986	SO:0001583	missense	51585	exon5			TTCGGGATCCAAG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1661A>G	11.37:g.82877600A>G	ENSP00000298281:p.Asp554Gly	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	73	19	NM_015885	0	0	5	6	1	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.007795	0.75046	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.56611	1.4;0.45;0.46	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000008	T	0.63189	0.2490	L	0.32530	0.975	0.58432	D	0.999996	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.94	T	0.60409	-0.7269	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	554;554	E9PQ01;O94913	.;PCF11_HUMAN	G	554	ENSP00000298281:D554G;ENSP00000434540:D554G;ENSP00000431567:D554G	.	D	+	2	0	PCF11	82555248	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.615000	0.90920	2.326000	0.78906	0.533000	0.62120	GAT	.		0.423	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877600	A	G	82877600	3	3	60	1	0	0	0	0	1	0	0	0	11599	333	12	3	1679	3	PCF11	11	82877600	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	5464820	82877600	52128916	66	5833											
SNX19	399979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	130785820	130785820	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcctggaacggtggcacTgtttctgtcttcatggctga	5	15	12	9	1	3	1	1	1	2	0	4	2	4	2	1	4	1	4	1	4	1	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:130785820T>A	ENST00000265909.4	-	1	584	c.15A>T	c.(13-15)acA>acT	p.T5T	SNX19_ENST00000539184.1_Intron|SNX19_ENST00000533214.1_Silent_p.T5T|SNX19_ENST00000533318.1_Intron|SNX19_ENST00000530356.1_Intron|SNX19_ENST00000528555.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	5					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		ACGGTGGCACTGTTTCTGTCT	0.542																																					p.T5T		.											.	SNX19-229	0			c.A15T						.						50	44	46					11																	130785820		2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			TGGCACTGTTTCT	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.15A>T	11.37:g.130785820T>A		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	29	13	NM_014758	0	0	2	6	4	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	37	CCDS31721.1																																																																																			.		0.542	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		A	130785820	T	A	130785820	2	1	60	1	0	0	0	0	0	0	0	1	14922	1567	55	5		5	SNX19	11	130785820	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	47908220	130785820	4220696	67	5834											
ATN1	1822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7045767	7045767	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagggtcccccaccacctcCtccctatggccgcctcttag	5	8	7	21	1	1	0	0	0	1	0	4	0	4	0	9	2	0	0	9	2	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:7045767C>A	ENST00000356654.4	+	5	1574	c.1337C>A	c.(1336-1338)cCt>cAt	p.P446H	ATN1_ENST00000396684.2_Missense_Mutation_p.P446H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	446	Poly-Pro.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						CCACCACCTCCTCCCTATGGC	0.627																																					p.P446H		.											.	ATN1-139	0			c.C1337A						.						149	144	146					12																	7045767		2203	4300	6503	SO:0001583	missense	1822	exon5			CACCTCCTCCCTA	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1337C>A	12.37:g.7045767C>A	ENSP00000349076:p.Pro446His	Somatic	377	0		WXS	Illumina HiSeq	Phase_I	366	144	NM_001007026	0	0	12	25	13	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	37	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	c	12.53	1.964846	0.34659	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.55413	0.52;0.52;0.52	3.88	3.88	0.44766	.	.	.	.	.	T	0.63390	0.2507	L	0.40543	1.245	0.46416	D	0.999032	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.988	T	0.63721	-0.6573	9	0.38643	T	0.18	.	16.2396	0.82401	0.0:1.0:0.0:0.0	.	446;446	Q86V38;P54259	.;ATN1_HUMAN	H	446;446;446;31	ENSP00000349076:P446H;ENSP00000379915:P446H;ENSP00000441744:P446H	ENSP00000229279:P31H	P	+	2	0	ATN1	6916028	0.028000	0.19301	0.947000	0.38551	0.354000	0.29330	0.722000	0.25925	1.883000	0.54544	0.586000	0.80456	CCT	.		0.627	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		A	7045767	C	A	7045767	3	1	60	1	0	0	0	0	1	0	0	0	1112	681	24	4	1351	4	ATN1	12	7045767	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		7045767	126806128	68	5835											
AEBP2	121536	hgsc.bcm.edu	37	chr12	19665400	19665400	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattggatgcctgaagacatGtaagtatttgaaatattatg	14	14	9	4	0	0	3	0	2	0	1	0	4	0	4	1	1	1	2	1	1	6	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:19665400G>C	ENST00000398864.3	+	6	1393		c.e6+1		AEBP2_ENST00000541908.1_Splice_Site|AEBP2_ENST00000266508.9_Splice_Site|AEBP2_ENST00000360995.4_Splice_Site	NM_001114176.1	NP_001107648.1	Q6ZN18	AEBP2_HUMAN	AE binding protein 2						chromatin modification (GO:0016568)	ESC/E(Z) complex (GO:0035098)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					CTGAAGACATGTAAGTATTTG	0.249																																					.		.											.	AEBP2-23	0			c.1367+1G>C						.						61	57	58					12																	19665400		1792	4062	5854	SO:0001630	splice_region_variant	121536	exon6			AGACATGTAAGTA		CCDS44841.1, CCDS44842.1, CCDS58215.1	12p12.3	2012-10-02			ENSG00000139154	ENSG00000139154			24051	protein-coding gene	gene with protein product						10329662	Standard	NM_153207		Approved	MGC17922	uc001ref.2	Q6ZN18	OTTHUMG00000168906	ENST00000398864.3:c.1367+1G>C	12.37:g.19665400G>C		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	16	2	NM_153207	0	0	0	0	0	Q59FS5|Q6ZN62|Q96BG3	Splice_Site	SNP	ENST00000398864.3	37	CCDS44841.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.424790	0.83667	.	.	ENSG00000139154	ENST00000541908;ENST00000398864;ENST00000435841;ENST00000266508;ENST00000360995;ENST00000512223;ENST00000398731	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5514	0.95322	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AEBP2	19556667	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.609000	0.90898	2.705000	0.92388	0.650000	0.86243	.	.		0.249	AEBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401575.1	NM_153207	Intron	C	19665400	G	C	19665400	5	2	60	1	0	0	0	0	0	0	1	0	350	1391	48	4	1390	4	AEBP2	12	19665400	Splice_Site	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	12619633	19665400	114186495	69	5836											
NAB2	4665	hgsc.bcm.edu	37	chr12	57487273	57487273	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggctatggagccgacacAtcctgcagcagacactgatg	11	7	12	11	1	0	2	0	1	0	1	1	4	1	3	2	2	3	3	2	2	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:57487273A>G	ENST00000300131.3	+	6	1738	c.1360A>G	c.(1360-1362)Atc>Gtc	p.I454V	NAB2_ENST00000357680.4_3'UTR|NAB2_ENST00000342556.6_Intron	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	454					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GAGCCGACACATCCTGCAGCA	0.687																																					p.I454V		.											.	NAB2-92	0			c.A1360G						.						12	13	13					12																	57487273		2160	4249	6409	SO:0001583	missense	4665	exon6			CGACACATCCTGC	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.1360A>G	12.37:g.57487273A>G	ENSP00000300131:p.Ile454Val	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	13	6	NM_005967	0	0	8	10	2	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.937547	0.52972	.	.	ENSG00000166886	ENST00000300131	.	.	.	4.62	4.62	0.57501	.	0.073328	0.53938	D	0.000047	T	0.33030	0.0849	N	0.14661	0.345	0.80722	D	1	B	0.29508	0.246	B	0.21546	0.035	T	0.17623	-1.0363	9	0.33940	T	0.23	-2.7571	12.2861	0.54793	1.0:0.0:0.0:0.0	.	454	Q15742	NAB2_HUMAN	V	454	.	ENSP00000300131:I454V	I	+	1	0	NAB2	55773540	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.437000	0.66544	2.077000	0.62373	0.459000	0.35465	ATC	.		0.687	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		G	57487273	A	G	57487273	3	3	60	1	0	0	0	0	1	0	0	0	10157	217	8	3	1382	3	NAB2	12	57487273	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	37821873	57487273	76364622	70	5837											
C12orf64	283310	broad.mit.edu	37	chr12	80726809	80726813	+	Splice_Site	DEL	ACATC	ACATC	-																															ggaaatgattactccatcagAcatcactgtgtttgatatgc																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	ACATC	ACATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:80726809_80726813delACATC	ENST00000547103.1	+	37	4317_4320	c.4311_4314delACATC	c.(4309-4314)ccacat>cc	p.PH1437fs	OTOGL_ENST00000458043.2_Frame_Shift_Del_p.DI1449fs			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1437					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						ACTCCATCAGACATCACTGTGTTTG	0.371																																					p.1449_1450del													.	.	0			c.4346_4350del						.																																			SO:0001630	splice_region_variant	283310	exon37			CATCAGACATCAC	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.4312-1ACATC>-	12.37:g.80726809_80726813delACATC		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	26	7	NM_173591	0	0	0	0	0	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Frame_Shift_Del	DEL	ENST00000547103.1	37																																																																																				.		0.371	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	Frame_Shift_Del	-	80726813	ACATC	-	80726809	8	5	60	1	0	1	0	1	0	0	1	0	1711	275	10	0	4492	0	C12orf64	12	80726809	Splice_Site	DEL	ACATC	TCGA-BQ-5876-01A-11D-1589-08	23239536	80726809	53125086	71	5838											
PITPNM2	57605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123479959	123479959	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacaggaaggcctggtgctgCtggatggtatccagctcgta	8	9	15	9	1	0	0	0	0	0	0	2	3	1	2	2	5	3	5	2	5	3	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:123479959C>T	ENST00000542749.1	-	12	2094	c.2031G>A	c.(2029-2031)caG>caA	p.Q677Q	PITPNM2_ENST00000392428.1_Silent_p.Q398Q|PITPNM2_ENST00000280562.5_Silent_p.Q677Q|PITPNM2_ENST00000320201.4_Silent_p.Q677Q			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	677					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CCTGGTGCTGCTGGATGGTAT	0.637																																					p.Q677Q		.											.	PITPNM2-228	0			c.G2031A						.						58	67	64					12																	123479959		2203	4299	6502	SO:0001819	synonymous_variant	57605	exon13			GTGCTGCTGGATG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.2031G>A	12.37:g.123479959C>T		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	150	43	NM_020845	0	0	1	3	2	Q9P271	Silent	SNP	ENST00000542749.1	37	CCDS9242.1																																																																																			.		0.637	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		T	123479959	C	T	123479959	2	4	60	1	0	0	0	0	0	0	0	1	11977	796	28	2		2	PITPNM2	12	123479959	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	42753150	123479959	10371936	72	5839											
ERCC5	2073	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	103510748	103510748	+	Frame_Shift_Del	DEL	T	T	-																															tcaccaagcgcagaagaacaTtatttgaagcaatgccagag																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr13:103510748delT	ENST00000355739.4	+	6	2075	c.652delT	c.(652-654)ttafs	p.L218fs	BIVM-ERCC5_ENST00000602836.1_Frame_Shift_Del_p.I644fs|ERCC5_ENST00000535557.1_Frame_Shift_Del_p.L218fs	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	218					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CAGAAGAACATTATTTGAAGC	0.373			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.L672fs		.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"		E	.	.	0			c.2014delT						.						96	99	98					13																	103510748		2203	4300	6503	SO:0001589	frameshift_variant	0	exon14	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	.	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"Cockayne syndrome"	133530	"xeroderma pigmentosum, complementation group G", "excision repair cross-complementing rodent repair deficiency, complementation group 5"	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.652delT	13.37:g.103510748delT	ENSP00000347978:p.Leu218fs	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	144	51	NM_001204425	0	0	0	0	0	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Frame_Shift_Del	DEL	ENST00000355739.4	37	CCDS32004.1																																																																																			.		0.373	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			-	103510748	T	-	103510748	7	5	60	1	0	1	0	1	0	0	0	0	5229	1490	52	0	674	0	ERCC5	13	103510748	Frame_Shift_Del	DEL	T	TCGA-BQ-5876-01A-11D-1589-08		103510748	11659130	73	5840											
PYGL	5836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	51387749	51387749	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagtgttattcatgtagcCgggcacgggggtgtcatatg	8	11	15	7	2	2	0	2	0	0	0	2	1	2	0	1	3	1	3	1	3	3	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr14:51387749C>T	ENST00000216392.7	-	6	1029	c.697G>A	c.(697-699)Ggc>Agc	p.G233S	PYGL_ENST00000532462.1_Missense_Mutation_p.G233S|PYGL_ENST00000544180.2_Missense_Mutation_p.G199S	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	233					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	TTCATGTAGCCGGGCACGGGG	0.512																																					p.G233S		.											.	PYGL-91	0			c.G697A						.						91	93	92					14																	51387749		2203	4300	6503	SO:0001583	missense	5836	exon6			TGTAGCCGGGCAC		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"Glycogen phosphorylases"	9725	protein-coding gene	gene with protein product	"Hers disease", "glycogen storage disease type VI", "glycogen phosphorylase, liver form"	613741	"phosphorylase, glycogen; liver"			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.697G>A	14.37:g.51387749C>T	ENSP00000216392:p.Gly233Ser	Somatic	103	1		WXS	Illumina HiSeq	Phase_I	71	42	NM_002863	0	0	1	3	2	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	37	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.389863	0.82902	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.97138	-4.26;-4.26;-4.26	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.99143	0.9704	H	0.97564	4.03	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.99026	1.0819	10	0.87932	D	0	-14.2229	19.3504	0.94381	0.0:1.0:0.0:0.0	.	199;233;233	F5H816;E9PK47;P06737	.;.;PYGL_HUMAN	S	233;199;233	ENSP00000431657:G233S;ENSP00000443787:G199S;ENSP00000216392:G233S	ENSP00000216392:G233S	G	-	1	0	PYGL	50457499	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	7.750000	0.85110	2.885000	0.99019	0.655000	0.94253	GGC	.		0.512	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		T	51387749	C	T	51387749	3	4	60	1	0	0	0	0	1	0	0	0	12893	652	23	1	1906	1	PYGL	14	51387749	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		51387749	55961791	74	5841											
TTC7B	145567	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	91161893	91161893	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caactgctctgagaagctctCtaaatcttccgactcctctt	9	13	5	14	1	4	1	0	1	4	1	7	3	6	1	2	0	3	2	2	0	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr14:91161893C>G	ENST00000328459.6	-	6	849	c.728G>C	c.(727-729)aGa>aCa	p.R243T	TTC7B_ENST00000357056.2_Missense_Mutation_p.R243T|RP11-661G16.2_ENST00000553712.1_RNA	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	243										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GAGAAGCTCTCTAAATCTTCC	0.413																																					p.R243T		.											.	TTC7B-92	0			c.G728C						.						138	111	120					14																	91161893		2203	4300	6503	SO:0001583	missense	145567	exon6			AGCTCTCTAAATC	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.728G>C	14.37:g.91161893C>G	ENSP00000336127:p.Arg243Thr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	42	23	NM_001010854	0	0	0	3	3	Q86U24|Q86VT3	Missense_Mutation	SNP	ENST00000328459.6	37	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.671065	0.47781	.	.	ENSG00000165914	ENST00000555768;ENST00000357056;ENST00000328459;ENST00000557766	T;T	0.66638	0.45;-0.22	5.72	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.69278	0.3093	M	0.82517	2.595	0.80722	D	1	B	0.30482	0.281	B	0.27796	0.083	T	0.72279	-0.4340	10	0.87932	D	0	-14.3324	14.3423	0.66636	0.0:0.9283:0.0:0.0717	.	243	Q86TV6	TTC7B_HUMAN	T	141;243;243;163	ENSP00000349564:R243T;ENSP00000336127:R243T	ENSP00000336127:R243T	R	-	2	0	TTC7B	90231646	1.000000	0.71417	0.781000	0.31783	0.002000	0.02628	7.184000	0.77705	1.420000	0.47138	-0.229000	0.12294	AGA	.		0.413	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			G	91161893	C	G	91161893	3	3	60	1	0	0	0	0	1	0	0	0	16746	913	32	4	1863	4	TTC7B	14	91161893	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	39774144	91161893	16187647	75	5842											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41854918	41854918	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttttaaatgtaacaggTgagcagcctcagaagggggc	11	10	13	7	0	2	2	1	1	1	1	2	2	2	2	1	3	3	3	1	3	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:41854918T>G	ENST00000263798.3	+	4	804		c.e4+2		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		ATGTAACAGGTGAGCAGCCTC	0.582																																					.		.											.	TYRO3-1388	0			c.580+2T>G						.						22	20	21					15																	41854918		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon4			AACAGGTGAGCAG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.580+2T>G	15.37:g.41854918T>G		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	31	8	NM_006293	0	0	0	0	0	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.113398	0.77210	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5013	0.67724	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39642210	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.037000	0.70956	2.007000	0.58848	0.387000	0.25754	.	.		0.582	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron	G	41854918	T	G	41854918	5	3	60	1	0	0	0	0	0	0	1	0	16847	1710	59	5	596	5	TYRO3	15	41854918	Splice_Site	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		41854918	60676474	76	5843											
MAPKBP1	23005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42105966	42105966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggacagacattgctagcGtcaccgaggccaggtgagct	9	7	15	10	2	1	2	1	1	0	1	1	4	1	3	2	4	3	2	2	4	1	2	rs374717785		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:42105966G>A	ENST00000456763.2	+	10	1181	c.985G>A	c.(985-987)Gtc>Atc	p.V329I	MAPKBP1_ENST00000221214.6_Intron|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.V211I|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.V323I|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.V323I	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	329								p.V323I(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		CATTGCTAGCGTCACCGAGGC	0.592																																					p.V329I		.											.	MAPKBP1-589	1	Substitution - Missense(1)	large_intestine(1)	c.G985A						.	A	ILE/VAL,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	115	106	109		985,967	-6.3	0.1	15		109	0,8600		0,0,4300	no	missense,missense	MAPKBP1	NM_001128608.1,NM_014994.2	29,29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign,benign	329/1515,323/1509	42105966	3,13003	2203	4300	6503	SO:0001583	missense	23005	exon10			GCTAGCGTCACCG	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.985G>A	15.37:g.42105966G>A	ENSP00000393099:p.Val329Ile	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	153	42	NM_001128608	0	0	0	0	0	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	g	0.324	-0.960053	0.02267	6.81E-4	0.0	ENSG00000137802	ENST00000457542;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T	0.42131	1.08;0.98;1.15;1.24	5.64	-6.33	0.01988	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.593302	0.19314	N	0.117308	T	0.28962	0.0719	L	0.38531	1.155	0.09310	N	0.999993	B;B;B;B	0.12013	0.001;0.005;0.001;0.001	B;B;B;B	0.13407	0.001;0.009;0.001;0.002	T	0.05053	-1.0909	10	0.21014	T	0.42	-1.6987	18.1757	0.89760	0.2499:0.0:0.7501:0.0	.	211;323;329;323	F8WC21;O60336-2;O60336;O60336-6	.;.;MABP1_HUMAN;.	I	323;211;329;323	ENSP00000397570:V323I;ENSP00000260357:V211I;ENSP00000393099:V329I;ENSP00000426154:V323I	ENSP00000260357:V211I	V	+	1	0	MAPKBP1	39893258	0.000000	0.05858	0.055000	0.19348	0.822000	0.46500	-0.443000	0.06862	-1.516000	0.01782	-1.913000	0.00520	GTC	.		0.592	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42105966	G	A	42105966	3	1	60	1	0	0	0	0	1	0	0	0	9317	1145	40	1	1019	1	MAPKBP1	15	42105966	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	251048	42105966	60425426	77	5844											
AP4E1	23431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51289917	51289917	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaagaaactactgaatacaTacactcaaatgctatggaag	18	8	8	7	0	1	2	1	1	0	1	1	4	1	4	0	2	5	1	0	2	9	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:51289917T>A	ENST00000261842.5	+	18	2847	c.2741T>A	c.(2740-2742)aTa>aAa	p.I914K	AP4E1_ENST00000560508.1_Missense_Mutation_p.I839K	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	914					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ACTGAATACATACACTCAAAT	0.353																																					p.I914K		.											.	AP4E1-90	0			c.T2741A						.						66	68	67					15																	51289917		2196	4294	6490	SO:0001583	missense	23431	exon18			AATACATACACTC	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2741T>A	15.37:g.51289917T>A	ENSP00000261842:p.Ile914Lys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	146	65	NM_007347	0	0	0	1	1	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	T	4.902	0.167570	0.09339	.	.	ENSG00000081014	ENST00000261842	T	0.16457	2.34	5.2	4.06	0.47325	Coatomer, beta subunit, C-terminal (1);	0.708362	0.14326	N	0.326718	T	0.08179	0.0204	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.26430	-1.0103	10	0.52906	T	0.07	-0.4045	3.9914	0.09538	0.0:0.1738:0.2024:0.6238	.	914	Q9UPM8	AP4E1_HUMAN	K	914	ENSP00000261842:I914K	ENSP00000261842:I914K	I	+	2	0	AP4E1	49077209	0.972000	0.33761	0.226000	0.23910	0.357000	0.29423	2.092000	0.41700	0.804000	0.34136	0.383000	0.25322	ATA	.		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			A	51289917	T	A	51289917	3	1	60	1	0	0	0	0	1	0	0	0	752	1406	49	5	2811	5	AP4E1	15	51289917	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	9183951	51289917	51241475	78	5845											
PIAS1	8554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	68479999	68479999	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttcttgatcagttaagTgcaggaggcagtacttctct	9	15	10	7	0	3	1	1	1	2	0	4	2	3	2	0	2	2	5	0	2	2	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:68479999T>C	ENST00000249636.6	+	14	1930	c.1782T>C	c.(1780-1782)agT>agC	p.S594S	PIAS1_ENST00000545237.1_Silent_p.S596S	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	594	4 X 4 AA repeats of N-T-S-L.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						ATCAGTTAAGTGCAGGAGGCA	0.502																																					p.S594S		.											.	PIAS1-637	0			c.T1782C						.						85	83	83					15																	68479999		2018	4191	6209	SO:0001819	synonymous_variant	8554	exon14			GTTAAGTGCAGGA	AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"Zinc fingers, MIZ-type"	2752	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 3"	603566	"DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.1782T>C	15.37:g.68479999T>C		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	77	34	NM_016166	0	0	3	8	5	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Silent	SNP	ENST00000249636.6	37	CCDS45290.1																																																																																			.		0.502	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2			C	68479999	T	C	68479999	2	2	60	1	0	0	0	0	0	0	0	1	11901	1693	59	3		3	PIAS1	15	68479999	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	17190082	68479999	34051393	79	5846											
ZNF688	146542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30581595	30581595	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcctgtggtcgggtcccagGcagcatttttgggtggctgt	3	13	15	10	1	0	0	0	0	0	0	3	0	2	0	2	5	1	3	2	5	0	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr16:30581595G>A	ENST00000223459.6	-	3	1577	c.473C>T	c.(472-474)gCc>gTc	p.A158V	AC002310.7_ENST00000492040.1_RNA|AC002310.7_ENST00000486926.1_RNA|ZNF688_ENST00000395219.1_Missense_Mutation_p.A144V	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CGGGTCCCAGGCAGCATTTTT	0.672																																					p.A158V		.											.	ZNF688-68	0			c.C473T						.						29	32	31					16																	30581595		2197	4299	6496	SO:0001583	missense	146542	exon3			TCCCAGGCAGCAT	AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"Zinc fingers, C2H2-type", "-"	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.473C>T	16.37:g.30581595G>A	ENSP00000223459:p.Ala158Val	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	46	19	NM_145271	0	0	2	4	2	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000223459.6	37	CCDS10684.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.817925	0.32145	.	.	ENSG00000229809	ENST00000395219;ENST00000223459	T;T	0.04194	3.68;3.91	4.26	0.961	0.19638	.	.	.	.	.	T	0.04003	0.0112	L	0.41236	1.265	0.09310	N	1	B;B	0.14438	0.002;0.01	B;B	0.11329	0.003;0.006	T	0.43523	-0.9386	9	0.28530	T	0.3	.	3.1826	0.06589	0.2262:0.0:0.5648:0.209	.	158;144	P0C7X2;A8MV39	ZN688_HUMAN;.	V	144;158	ENSP00000378645:A144V;ENSP00000223459:A158V	ENSP00000223459:A158V	A	-	2	0	ZNF688	30489096	0.018000	0.18449	0.721000	0.30653	0.192000	0.23643	1.655000	0.37345	0.546000	0.28920	0.460000	0.39030	GCC	.		0.672	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271		A	30581595	G	A	30581595	3	1	60	1	0	0	0	0	1	0	0	0	18125	1203	42	2	361	2	ZNF688	16	30581595	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		30581595	59773158	80	5847											
RPGRIP1L	23322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	53708941	53708941	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtacctcttgaagctgAataaattttccttccattgc	10	15	5	11	0	1	2	0	2	1	0	3	2	3	2	3	0	3	2	3	0	5	7			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr16:53708941A>C	ENST00000379925.3	-	7	920	c.870T>G	c.(868-870)atT>atG	p.I290M	RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.I290M|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.I290M|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.I290M	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	290					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CTTGAAGCTGAATAAATTTTC	0.308																																					p.I290M		.											.	RPGRIP1L-91	0			c.T870G						.						131	117	122					16																	53708941		2197	4297	6494	SO:0001583	missense	23322	exon7			AAGCTGAATAAAT		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.870T>G	16.37:g.53708941A>C	ENSP00000369257:p.Ile290Met	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	71	31	NM_001127897	0	0	0	0	0	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597979	0.28445	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	D;D	0.89875	-2.58;-2.58	5.98	4.87	0.63330	.	0.287071	0.33834	N	0.004504	T	0.77638	0.4160	L	0.36672	1.1	0.80722	D	1	B;B;B;P	0.38250	0.351;0.241;0.241;0.624	B;B;B;B	0.32342	0.071;0.071;0.071;0.144	T	0.76244	-0.3030	10	0.48119	T	0.1	-8.1579	0.3735	0.00383	0.3487:0.18:0.1302:0.3411	.	290;290;290;290	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	M	290	ENSP00000369257:I290M;ENSP00000262135:I290M	ENSP00000262135:I290M	I	-	3	3	RPGRIP1L	52266442	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.557000	0.36299	2.293000	0.77203	0.477000	0.44152	ATT	.		0.308	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		C	53708941	A	C	53708941	3	2	60	1	0	0	0	0	1	0	0	0	13582	242	9	5	3161	5	RPGRIP1L	16	53708941	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	23127346	53708941	36645812	81	5848											
SLC16A13	201232	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	6942204	6942204	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggctgctggggcctcctctCtcaggtaagtggaatggggt	5	10	17	9	0	2	0	1	0	1	0	4	1	3	1	2	7	1	3	2	7	2	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:6942204C>G	ENST00000308027.6	+	3	1385	c.1077C>G	c.(1075-1077)ctC>ctG	p.L359L		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	359						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						GGCCTCCTCTCTCAGGTAAGT	0.537																																					p.L359L		.											.	SLC16A13-92	0			c.C1077G						.						56	70	65					17																	6942204		2188	4242	6430	SO:0001819	synonymous_variant	201232	exon3			TCCTCTCTCAGGT	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"Solute carriers"	31037	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 13"		"solute carrier family 16 (monocarboxylic acid transporters), member 13"				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.1077C>G	17.37:g.6942204C>G		Somatic	172	1		WXS	Illumina HiSeq	Phase_I	198	13	NM_201566	0	0	0	0	0	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			.		0.537	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2			G	6942204	C	G	6942204	2	3	60	1	0	0	0	0	0	0	0	1	14438	900	32	4		4	SLC16A13	17	6942204	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		6942204	74253006	82	5849											
CHRNB1	1140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7357711	7357711	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgagacctcactatcagtaCccattattatcaagtacctc	12	12	4	13	0	3	1	3	1	0	1	4	2	3	1	3	0	2	2	3	0	6	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:7357711C>G	ENST00000306071.2	+	8	983	c.916C>G	c.(916-918)Ccc>Gcc	p.P306A	CHRNB1_ENST00000575379.1_5'Flank|CHRNB1_ENST00000576360.1_Intron|CHRNB1_ENST00000536404.2_Missense_Mutation_p.P234A	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	306					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	ACTATCAGTACCCATTATTAT	0.512																																					p.P306A		.											.	CHRNB1-92	0			c.C916G						.						307	238	262					17																	7357711		2203	4300	6503	SO:0001583	missense	1140	exon8			TCAGTACCCATTA	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1961	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 1 (muscle)"	100710	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.916C>G	17.37:g.7357711C>G	ENSP00000304290:p.Pro306Ala	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	214	60	NM_000747	0	0	0	0	0	B7Z5H1|Q8IZ46|Q96FB8	Missense_Mutation	SNP	ENST00000306071.2	37	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212473	0.58452	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	D;D	0.85339	-1.97;-1.97	4.92	4.92	0.64577	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95245	0.8458	H	0.99074	4.42	0.80722	D	1	D	0.63880	0.993	P	0.61132	0.884	D	0.97341	0.9957	10	0.87932	D	0	.	15.675	0.77311	0.0:1.0:0.0:0.0	.	306	P11230	ACHB_HUMAN	A	306;234	ENSP00000304290:P306A;ENSP00000439209:P234A	ENSP00000304290:P306A	P	+	1	0	CHRNB1	7298435	1.000000	0.71417	0.998000	0.56505	0.270000	0.26580	7.818000	0.86416	2.300000	0.77407	0.298000	0.19748	CCC	.		0.512	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3			G	7357711	C	G	7357711	3	3	60	1	0	0	0	0	1	0	0	0	3396	507	18	4	946	4	CHRNB1	17	7357711	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	415507	7357711	73837499	83	5850											
SHBG	6462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7536218	7536218	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcctcccttaggcctggCtcccctccttaacctctggg	3	11	8	19	0	1	0	0	0	1	0	4	0	4	0	8	3	2	1	8	3	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:7536218C>A	ENST00000380450.4	+	7	1032	c.1001C>A	c.(1000-1002)gCt>gAt	p.A334D	SHBG_ENST00000416273.3_Intron|SHBG_ENST00000441599.2_Intron|SHBG_ENST00000576728.1_Intron|SHBG_ENST00000572262.1_Missense_Mutation_p.A222D|SHBG_ENST00000340624.5_Intron|SHBG_ENST00000575314.1_Missense_Mutation_p.A276D|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000575903.1_Missense_Mutation_p.A316D|SHBG_ENST00000574539.1_Intron	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	334	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.			A -> L (in Ref. 2; AAC18778). {ECO:0000305}.	primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.0?(1)|p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	TTAGGCCTGGCTCCCCTCCTT	0.557											OREG0024140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A334D		.											.	SHBG-90	2	Unknown(1)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)|bone(1)	c.C1001A						.						60	53	55					17																	7536218		2203	4300	6503	SO:0001583	missense	6462	exon7			GCCTGGCTCCCCT		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"androgen binding protein"	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.1001C>A	17.37:g.7536218C>A	ENSP00000369816:p.Ala334Asp	Somatic	79	1	642	WXS	Illumina HiSeq	Phase_I	73	35	NM_001040	0	0	0	0	0	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	C	9.158	1.018027	0.19355	.	.	ENSG00000129214	ENST00000380450	T	0.79749	-1.3	4.68	-9.36	0.00629	Concanavalin A-like lectin/glucanase (1);	2.122320	0.01800	N	0.032838	T	0.65048	0.2654	L	0.38175	1.15	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.50558	-0.8814	10	0.17369	T	0.5	3.0464	5.421	0.16400	0.303:0.4871:0.12:0.0899	.	334	P04278	SHBG_HUMAN	D	334	ENSP00000369816:A334D	ENSP00000369816:A334D	A	+	2	0	SHBG	7476943	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.654000	0.00855	-1.994000	0.00972	-0.344000	0.07964	GCT	.		0.557	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		A	7536218	C	A	7536218	3	1	60	1	0	0	0	0	1	0	0	0	14301	797	28	4	1027	4	SHBG	17	7536218	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	178507	7536218	73658992	84	5851											
ALOXE3	59344	broad.mit.edu	37	chr17	8018295	8018295	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagttgtcgtctttgtcaagGcaaatttcttgtctgactcc	8	16	8	9	1	4	1	1	1	3	0	6	1	5	1	1	1	0	2	1	1	3	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:8018295G>A	ENST00000448843.2	-	5	855	c.515C>T	c.(514-516)gCc>gTc	p.A172V	ALOXE3_ENST00000318227.3_Missense_Mutation_p.A304V|ALOXE3_ENST00000380149.1_Missense_Mutation_p.A328V	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	172	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						CTTTGTCAAGGCAAATTTCTT	0.507																																					p.A304V													.	ALOXE3-229	0			c.C911T						.						222	199	207					17																	8018295		2203	4300	6503	SO:0001583	missense	59344	exon5			GTCAAGGCAAATT	AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"Arachidonate lipoxygenases"	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.515C>T	17.37:g.8018295G>A	ENSP00000400581:p.Ala172Val	Somatic	371	0		WXS	Illumina HiSeq	Phase_I	356	7	NM_001165960	0	0	0	0	0	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Missense_Mutation	SNP	ENST00000448843.2	37	CCDS11130.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.773525	0.49786	.	.	ENSG00000179148	ENST00000380149;ENST00000318227;ENST00000448843	D;D;D	0.89485	-2.52;-2.52;-2.52	5.85	4.88	0.63580	Lipoxygenase, C-terminal (2);	0.312877	0.26939	N	0.021729	D	0.83161	0.5194	L	0.47716	1.5	0.28933	N	0.891461	B;B;B	0.34181	0.44;0.003;0.062	B;B;B	0.30646	0.118;0.003;0.011	T	0.80025	-0.1555	10	0.72032	D	0.01	-12.3324	7.6914	0.28569	0.0822:0.0:0.7559:0.1619	.	304;172;172	B7Z3W0;Q9BYJ1;B3KVD2	.;LOXE3_HUMAN;.	V	328;304;172	ENSP00000369494:A328V;ENSP00000314879:A304V;ENSP00000400581:A172V	ENSP00000314879:A304V	A	-	2	0	ALOXE3	7959020	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	5.429000	0.66495	1.477000	0.48234	0.655000	0.94253	GCC	.		0.507	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1			A	8018295	G	A	8018295	3	1	60	1	0	0	0	0	1	0	0	0	542	1203	42	2	1668	2	ALOXE3	17	8018295	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	482077	8018295	73176915	85	5852											
SLC6A4	6532	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	28543164	28543164	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaacacccctccaggctccaGggagggtggcacccctcacc	8	4	11	18	0	1	0	1	0	0	0	3	2	3	1	7	4	1	2	7	4	1	0	rs200924626		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:28543164G>T	ENST00000401766.2	-	6	1420	c.908C>A	c.(907-909)cCt>cAt	p.P303H	SLC6A4_ENST00000261707.3_Missense_Mutation_p.P303H			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	303					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	CCAGGCTCCAGGGAGGGTGGC	0.522													G|||	1	0.000199681	0	0.0014	5008	,	,		12429	0		0	False		,,,				2504	0				p.P303H		.											.	SLC6A4-94	0			c.C908A						.						70	71	71					17																	28543164		2203	4300	6503	SO:0001583	missense	6532	exon7			GCTCCAGGGAGGG	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.908C>A	17.37:g.28543164G>T	ENSP00000385822:p.Pro303His	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	118	40	NM_001045	0	0	0	0	0	Q5EE02	Missense_Mutation	SNP	ENST00000401766.2	37	CCDS11256.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	33	5.232955	0.95207	.	.	ENSG00000108576	ENST00000394821;ENST00000401766;ENST00000261707	T;T	0.78481	-1.18;-1.18	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.90335	0.6976	M	0.87617	2.895	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90653	0.4584	10	0.87932	D	0	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	303	P31645	SC6A4_HUMAN	H	345;303;303	ENSP00000385822:P303H;ENSP00000261707:P303H	ENSP00000261707:P303H	P	-	2	0	SLC6A4	25567290	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.803000	0.99136	2.941000	0.99782	0.655000	0.94253	CCT	G|0.999;T|0.000		0.522	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045		T	28543164	G	T	28543164	3	4	60	1	0	0	0	0	1	0	0	0	14718	1000	35	4	1020	4	SLC6A4	17	28543164	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	20524869	28543164	52652046	86	5853											
SPATA20	64847	broad.mit.edu	37	chr17	48627419	48627419	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctctcgggcccagcagatGgccttgcataccctgaaaat	9	8	11	13	1	1	2	0	1	1	1	2	2	1	2	3	3	3	3	3	3	3	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:48627419G>A	ENST00000356488.4	+	7	971	c.888G>A	c.(886-888)atG>atA	p.M296I	SPATA20_ENST00000006658.6_Missense_Mutation_p.M312I|SPATA20_ENST00000393244.3_Missense_Mutation_p.M252I|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	296					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CCCAGCAGATGGCCTTGCATA	0.617																																					p.M312I													.	SPATA20-90	0			c.G936A						.						158	163	161					17																	48627419		2203	4300	6503	SO:0001583	missense	64847	exon8			GCAGATGGCCTTG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"hypothetical protein FLJ21347"	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.888G>A	17.37:g.48627419G>A	ENSP00000348878:p.Met296Ile	Somatic	451	0		WXS	Illumina HiSeq	Phase_I	430	6	NM_022827	0	0	84	87	3	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	32	5.126463	0.94429	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.31510	1.49;1.49;1.49	5.53	5.53	0.82687	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.000000	0.85682	D	0.000000	T	0.49830	0.1580	M	0.72353	2.195	0.80722	D	1	P;P;P	0.51240	0.609;0.943;0.863	B;P;P	0.53722	0.168;0.733;0.614	T	0.44651	-0.9314	10	0.44086	T	0.13	-5.8568	19.4936	0.95062	0.0:0.0:1.0:0.0	.	322;296;312	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	I	312;296;252	ENSP00000006658:M312I;ENSP00000348878:M296I;ENSP00000376935:M252I	ENSP00000006658:M312I	M	+	3	0	SPATA20	45982418	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.029000	0.88807	2.605000	0.88082	0.655000	0.94253	ATG	.		0.617	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48627419	G	A	48627419	3	1	60	1	0	0	0	0	1	0	0	0	15038	1348	47	2	966	2	SPATA20	17	48627419	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	20084255	48627419	32567791	87	5854											
HDHD2	84064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	44639349	44639349	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatacagaagatacataccAgtctttactaagatgcccag	15	11	6	9	0	1	3	0	0	1	3	1	3	1	3	2	0	5	0	2	0	7	7			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr18:44639349A>T	ENST00000300605.6	-	6	827	c.675T>A	c.(673-675)acT>acA	p.T225T	HDHD2_ENST00000587841.1_5'UTR	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	225						extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						GATACATACCAGTCTTTACTA	0.408																																					p.T225T		.											.	HDHD2-90	0			c.T675A						.						115	100	105					18																	44639349		2203	4300	6503	SO:0001630	splice_region_variant	84064	exon6			CATACCAGTCTTT	AL136681	CCDS32829.1	18q21.1	2008-02-05				ENSG00000167220			25364	protein-coding gene	gene with protein product						11230166	Standard	NM_032124		Approved	DKFZP564D1378	uc002lcs.3	Q9H0R4		ENST00000300605.6:c.676+1T>A	18.37:g.44639349A>T		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	86	28	NM_032124	0	0	0	1	1	A8K7T3|Q96NV4	Silent	SNP	ENST00000300605.6	37	CCDS32829.1																																																																																			.		0.408	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124	Silent	T	44639349	A	T	44639349	5	4	60	1	0	0	0	0	0	0	1	0	7044	202	7	5	112	5	HDHD2	18	44639349	Splice_Site	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		44639349	33437899	88	5855											
GRIN3B	116444	bcgsc.ca	37	chr19	1004657	1004657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccccggcctgggccacggTgggcagctggcgggacggcc	3	3	19	16	5	0	0	0	0	0	0	0	1	0	1	5	7	1	2	5	7	0	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:1004657T>C	ENST00000234389.3	+	3	1176	c.1157T>C	c.(1156-1158)gTg>gCg	p.V386A	AC004528.4_ENST00000588380.1_RNA|GRIN3B_ENST00000588335.1_Intron	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	386					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGGGCCACGGTGGGCAGCTGG	0.716																																					p.V386A													.	GRIN3B-90	0			c.T1157C						.						9	10	10					19																	1004657		2141	4171	6312	SO:0001583	missense	116444	exon3			CCACGGTGGGCAG		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1157T>C	19.37:g.1004657T>C	ENSP00000234389:p.Val386Ala	Somatic	21	0		WXS	Illumina HiSeq	Phase_1	11	7	NM_138690	0	0	0	0	0	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756680	0.49362	.	.	ENSG00000116032	ENST00000234389	D	0.91631	-2.88	4.4	4.4	0.53042	.	0.067157	0.64402	D	0.000017	D	0.89660	0.6779	L	0.59436	1.845	0.37366	D	0.911436	P	0.52316	0.952	B	0.41510	0.359	D	0.91764	0.5422	10	0.66056	D	0.02	.	12.4879	0.55883	0.0:0.0:0.0:1.0	.	386	O60391	NMD3B_HUMAN	A	386	ENSP00000234389:V386A	ENSP00000234389:V386A	V	+	2	0	GRIN3B	955657	1.000000	0.71417	0.947000	0.38551	0.713000	0.41058	4.393000	0.59665	1.648000	0.50643	0.382000	0.24955	GTG	.		0.716	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			C	1004657	T	C	1004657	3	2	60	1	0	0	0	0	1	0	0	0	6805	1696	59	3	1167	3	GRIN3B	19	1004657	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		1004657	58124326	89	5856											
REXO1	57455	broad.mit.edu	37	chr19	1821535	1821535	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacctgtaaggatggactgtGggcgattcgcttagggatga	9	11	15	6	2	0	1	0	1	0	0	1	5	0	4	1	4	1	2	1	4	3	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:1821535G>A	ENST00000170168.4	-	5	2471	c.2377C>T	c.(2377-2379)Cac>Tac	p.H793Y	CTB-31O20.4_ENST00000590531.1_RNA|CTB-31O20.4_ENST00000587741.1_RNA|CTB-31O20.4_ENST00000593201.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	793						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GATGGACTGTGGGCGATTCGC	0.642																																					p.H793Y													.	REXO1-90	0			c.C2377T						.						204	154	171					19																	1821535		2203	4300	6503	SO:0001583	missense	57455	exon5			GACTGTGGGCGAT	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.2377C>T	19.37:g.1821535G>A	ENSP00000170168:p.His793Tyr	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	123	5	NM_020695	0	0	8	8	0	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.900374	0.52227	.	.	ENSG00000079313	ENST00000170168;ENST00000543452	T	0.24723	1.84	4.5	4.5	0.54988	.	0.474100	0.20491	N	0.091291	T	0.34745	0.0908	M	0.76002	2.32	0.58432	D	0.999999	B;B	0.28998	0.026;0.23	B;B	0.33690	0.038;0.168	T	0.33650	-0.9860	10	0.72032	D	0.01	-37.2863	14.4921	0.67657	0.0:0.0:1.0:0.0	.	102;793	B4DWY3;Q8N1G1	.;REXO1_HUMAN	Y	793;65	ENSP00000170168:H793Y	ENSP00000170168:H793Y	H	-	1	0	REXO1	1772535	1.000000	0.71417	0.930000	0.37139	0.671000	0.39405	7.646000	0.83445	2.314000	0.78098	0.561000	0.74099	CAC	.		0.642	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		A	1821535	G	A	1821535	3	1	60	1	0	0	0	0	1	0	0	0	13273	1348	47	2	1336	2	REXO1	19	1821535	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	816878	1821535	57307448	90	5857											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9083127	9083127	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagtatccaaacttgggacCtcagaaaactcaaatgtcaa	16	10	6	9	0	3	1	3	0	0	1	4	2	4	2	2	1	2	1	2	1	7	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:9083127C>A	ENST00000397910.4	-	1	8891	c.8688G>T	c.(8686-8688)gaG>gaT	p.E2896D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2897	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AACTTGGGACCTCAGAAAACT	0.507																																					p.E2896D		.											.	MUC16-566	0			c.G8688T						.						75	69	71					19																	9083127		1897	4124	6021	SO:0001583	missense	94025	exon1			TGGGACCTCAGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8688G>T	19.37:g.9083127C>A	ENSP00000381008:p.Glu2896Asp	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	29	6	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	2.382	-0.341788	0.05243	.	.	ENSG00000181143	ENST00000397910	T	0.02606	4.23	0.773	-1.55	0.08558	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.19817	0.039	B	0.15484	0.013	T	0.45906	-0.9229	8	0.87932	D	0	.	2.2074	0.03939	0.0:0.3584:0.3406:0.301	.	2896	B5ME49	.	D	2896	ENSP00000381008:E2896D	ENSP00000381008:E2896D	E	-	3	2	MUC16	8944127	0.000000	0.05858	0.000000	0.03702	0.154000	0.21943	-0.875000	0.04205	-0.903000	0.03881	0.313000	0.20887	GAG	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9083127	C	A	9083127	3	1	60	1	0	0	0	0	1	0	0	0	9998	680	24	4	35171	4	MUC16	19	9083127	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	7261592	9083127	50045856	91	5858											
CACNA1A	773	broad.mit.edu	37	chr19	13338336	13338336	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatgtccaggtaaggcatgCggcccctggcagcaccgaaa	11	5	12	13	2	0	0	0	0	0	0	1	1	1	0	4	4	2	4	4	4	2	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:13338336C>T	ENST00000360228.5	-	37	5533	c.5534G>A	c.(5533-5535)cGc>cAc	p.R1845H	CACNA1A_ENST00000573710.2_Intron|CACNA1A_ENST00000574822.1_5'Flank	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1846					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GTAAGGCATGCGGCCCCTGGC	0.493																																					p.R1845H													.	CACNA1A-67	0			c.G5534A						.						48	49	49					19																	13338336		1877	4112	5989	SO:0001583	missense	773	exon37			GGCATGCGGCCCC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.5534G>A	19.37:g.13338336C>T	ENSP00000353362:p.Arg1845His	Somatic	91	1		WXS	Illumina HiSeq	Phase_I	56	3	NM_001127222	0	0	0	0	0	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	c	24.9	4.580140	0.86645	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018	D	0.96459	-4.02	4.55	4.55	0.56014	.	0.000000	0.64402	D	0.000001	D	0.98264	0.9425	M	0.88640	2.97	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	D	0.99581	1.0973	10	0.87932	D	0	.	16.0868	0.81060	0.0:1.0:0.0:0.0	.	1845	Q9NS88	.	H	1845;1851;1846	ENSP00000353362:R1845H	ENSP00000349520:R1846H	R	-	2	0	CACNA1A	13199336	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.764000	0.85297	2.079000	0.62486	0.298000	0.19748	CGC	.		0.493	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13338336	C	T	13338336	3	4	60	1	0	0	0	0	1	0	0	0	2544	768	27	1	2030	1	CACNA1A	19	13338336	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	4255209	13338336	45790647	92	5859											
SFRS14	10147	broad.mit.edu	37	chr19	19141834	19141834	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatatcgtttggctttttctTgtaatacagcatcaaaagtc	11	16	7	7	1	2	0	1	0	1	0	4	1	2	0	0	1	2	4	0	1	5	7			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:19141834T>G	ENST00000601879.1	-	2	344	c.47A>C	c.(46-48)cAa>cCa	p.Q16P	ARMC6_ENST00000269932.6_5'Flank|ARMC6_ENST00000392335.2_5'Flank|ARMC6_ENST00000535612.1_5'Flank|SUGP2_ENST00000452918.2_Missense_Mutation_p.Q16P|SUGP2_ENST00000337018.6_Missense_Mutation_p.Q16P|SUGP2_ENST00000598202.1_Intron|SUGP2_ENST00000600377.1_Missense_Mutation_p.Q30P|SUGP2_ENST00000456085.2_5'UTR|ARMC6_ENST00000546344.1_5'Flank			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	16					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GGCTTTTTCTTGTAATACAGC	0.393																																					p.Q16P													.	SUGP2-91	0			c.A47C						.						276	249	258					19																	19141834		2203	4300	6503	SO:0001583	missense	10147	exon2			TTTTCTTGTAATA	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.47A>C	19.37:g.19141834T>G	ENSP00000472286:p.Gln16Pro	Somatic	311	0		WXS	Illumina HiSeq	Phase_I	183	5	NM_014884	0	0	7	7	0	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	37	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.025814	0.75390	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918	T;T;T	0.15372	2.43;2.43;2.43	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000007	T	0.29158	0.0725	L	0.27053	0.805	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.78314	0.979;0.991	T	0.05370	-1.0889	10	0.87932	D	0	-17.7682	14.0226	0.64565	0.0:0.0:0.0:1.0	.	16;16	A8K5G0;Q8IX01	.;SUGP2_HUMAN	P	16	ENSP00000337926:Q16P;ENSP00000332373:Q16P;ENSP00000389380:Q16P	ENSP00000332373:Q16P	Q	-	2	0	SUGP2	19002834	1.000000	0.71417	0.919000	0.36401	0.970000	0.65996	4.512000	0.60469	1.987000	0.57996	0.528000	0.53228	CAA	.		0.393	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		G	19141834	T	G	19141834	3	3	60	1	0	0	0	0	1	0	0	0	14202	1812	63	5	3237	5	SFRS14	19	19141834	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	5803498	19141834	39987149	93	5860											
IRF2BP1	26145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46387423	46387423	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccccggccgggccctgcGccttgatgaactcccgggag	4	6	13	18	4	0	2	0	2	0	0	2	3	2	3	7	3	2	0	7	3	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:46387423G>A	ENST00000302165.3	-	1	1953	c.1610C>T	c.(1609-1611)gCg>gTg	p.A537V		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	537	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		CGGGCCCTGCGCCTTGATGAA	0.677																																					p.A537V		.											.	IRF2BP1-90	0			c.C1610T						.						30	30	30					19																	46387423		2203	4299	6502	SO:0001583	missense	26145	exon1			CCCTGCGCCTTGA	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1610C>T	19.37:g.46387423G>A	ENSP00000307265:p.Ala537Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	67	7	NM_015649	0	0	1	1	0	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Missense_Mutation	SNP	ENST00000302165.3	37	CCDS12678.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.574987	0.65878	.	.	ENSG00000170604	ENST00000302165	D	0.86230	-2.09	4.58	4.58	0.56647	Zinc finger, C3HC4 RING-type (1);	0.382217	0.24182	N	0.040786	T	0.75961	0.3921	N	0.22421	0.69	0.30785	N	0.741587	P	0.43750	0.816	B	0.32533	0.147	T	0.77253	-0.2656	10	0.33940	T	0.23	.	14.914	0.70781	0.0:0.0:1.0:0.0	.	537	Q8IU81	I2BP1_HUMAN	V	537	ENSP00000307265:A537V	ENSP00000307265:A537V	A	-	2	0	IRF2BP1	51079263	0.964000	0.33143	0.999000	0.59377	0.968000	0.65278	2.896000	0.48656	2.362000	0.80069	0.563000	0.77884	GCG	.		0.677	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		A	46387423	G	A	46387423	3	1	60	1	0	0	0	0	1	0	0	0	7850	1087	38	1	148	1	IRF2BP1	19	46387423	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	27245589	46387423	12741560	94	5861											
SLC6A16	28968	broad.mit.edu	37	chr19	49793532	49793532	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccgctcttgggcctgaaggGaatcctatgtatgcggcagt	7	11	13	10	2	1	1	0	1	1	0	3	2	3	2	3	3	1	3	3	3	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:49793532G>T	ENST00000335875.4	-	12	2300	c.2059C>A	c.(2059-2061)Ccc>Acc	p.P687T	SLC6A16_ENST00000454748.3_3'UTR	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	687					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		GGCCTGAAGGGAATCCTATGT	0.512																																					p.P687T													.	SLC6A16-94	0			c.C2059A						.						134	131	132					19																	49793532		1973	4140	6113	SO:0001583	missense	28968	exon12			TGAAGGGAATCCT	AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"Solute carriers"	13622	protein-coding gene	gene with protein product	"NTT5 protein"	607972	"solute carrier family 6 (neurotransmitter transporter), member 16"			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.2059C>A	19.37:g.49793532G>T	ENSP00000338627:p.Pro687Thr	Somatic	249	1		WXS	Illumina HiSeq	Phase_I	241	7	NM_014037	0	0	8	8	0	Q8IYV4|Q9Y5I9	Missense_Mutation	SNP	ENST00000335875.4	37	CCDS42590.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225175	0.39300	.	.	ENSG00000063127	ENST00000335875	T	0.73575	-0.76	4.48	-6.15	0.02105	.	4.217680	0.00807	N	0.001479	T	0.43986	0.1272	N	0.14661	0.345	0.20196	N	0.999923	P	0.38148	0.62	B	0.29176	0.099	T	0.48456	-0.9034	10	0.14656	T	0.56	.	0.1872	0.00130	0.2591:0.257:0.223:0.2609	.	687	Q9GZN6	S6A16_HUMAN	T	687	ENSP00000338627:P687T	ENSP00000338627:P687T	P	-	1	0	SLC6A16	54485344	0.000000	0.05858	0.001000	0.08648	0.190000	0.23558	0.031000	0.13710	-0.642000	0.05480	0.543000	0.68304	CCC	.		0.512	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		T	49793532	G	T	49793532	3	4	60	1	0	0	0	0	1	0	0	0	14711	1174	41	4	155	4	SLC6A16	19	49793532	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	3406109	49793532	9335451	95	5862											
FAM71E1	112703	hgsc.bcm.edu;broad.mit.edu	37	chr19	50970929	50970929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcagagaggaagcgcaggcGgtagagcagccgcacccact	12	2	15	12	3	0	2	0	0	0	2	0	4	0	3	2	3	4	5	2	3	2	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:50970929G>A	ENST00000600100.1	-	4	1061	c.697C>T	c.(697-699)Cgc>Tgc	p.R233C	FAM71E1_ENST00000595790.1_Missense_Mutation_p.R217C			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	233										breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		AAGCGCAGGCGGTAGAGCAGC	0.612																																					p.R217C		.											.	FAM71E1-44	0			c.C649T						.						26	27	26					19																	50970929		2195	4290	6485	SO:0001583	missense	112703	exon4			GCAGGCGGTAGAG		CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.697C>T	19.37:g.50970929G>A	ENSP00000472421:p.Arg233Cys	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	11	4	NM_138411	0	0	1	2	1	Q96EJ5|Q9BSM9	Missense_Mutation	SNP	ENST00000600100.1	37		.	.	.	.	.	.	.	.	.	.	g	15.85	2.955383	0.53293	.	.	ENSG00000142530	ENST00000391816;ENST00000270620	T;T	0.17854	2.25;2.25	4.0	0.356	0.16074	.	0.791977	0.10938	N	0.617646	T	0.29914	0.0748	L	0.51422	1.61	0.42510	D	0.992969	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.95	T	0.19877	-1.0292	10	0.66056	D	0.02	-6.3609	5.8158	0.18492	0.096:0.0:0.5658:0.3382	.	233;217	Q6IPT2;Q6IPT2-2	F71E1_HUMAN;.	C	233;217	ENSP00000375692:R233C;ENSP00000270620:R217C	ENSP00000270620:R217C	R	-	1	0	FAM71E1	55662741	1.000000	0.71417	0.998000	0.56505	0.724000	0.41520	2.576000	0.46033	0.057000	0.16193	0.462000	0.41574	CGC	.		0.612	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2			A	50970929	G	A	50970929	3	1	60	1	0	0	0	0	1	0	0	0	5630	1116	39	1	50	1	FAM71E1	19	50970929	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	1177397	50970929	8158054	96	5863											
ZFP28	140612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57066282	57066282	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtatggaatgtgggaaggccTttggtgataactcatcctgt	9	13	13	6	0	1	1	1	1	0	0	2	3	2	3	2	4	1	1	2	4	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:57066282T>C	ENST00000301318.3	+	8	2199	c.2128T>C	c.(2128-2130)Ttt>Ctt	p.F710L	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	710					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)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		TGGGAAGGCCTTTGGTGATAA	0.443																																					p.F710L	Ovarian(124;554 1662 19430 21141 52494)	.											.	ZFP28-91	0			c.T2128C						.						105	105	105					19																	57066282		2203	4300	6503	SO:0001583	missense	140612	exon8			AAGGCCTTTGGTG		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.2128T>C	19.37:g.57066282T>C	ENSP00000301318:p.Phe710Leu	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	128	45	NM_020828	0	0	0	0	0	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.714627	0.68730	.	.	ENSG00000196867	ENST00000301318	T	0.46063	0.88	4.0	2.98	0.34508	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000249	T	0.64659	0.2618	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66488	-0.5911	10	0.87932	D	0	.	8.4668	0.32960	0.0:0.0964:0.0:0.9036	.	710	Q8NHY6	ZFP28_HUMAN	L	710	ENSP00000301318:F710L	ENSP00000301318:F710L	F	+	1	0	ZFP28	61758094	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.655000	0.67981	0.710000	0.31997	0.454000	0.30748	TTT	.		0.443	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		C	57066282	T	C	57066282	3	2	60	1	0	0	0	0	1	0	0	0	17674	1609	56	3	2158	3	ZFP28	19	57066282	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	6095353	57066282	2062701	97	5864			1	17		2	2	17	N	T_C	5.685195e-05
ZFP28	140612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57066298	57066298	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcctttggtgataactcatCctgtactcaacatcaaagac	12	11	7	11	0	3	2	3	1	0	1	4	2	4	2	2	2	3	1	2	2	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:57066298C>A	ENST00000301318.3	+	8	2215	c.2144C>A	c.(2143-2145)tCc>tAc	p.S715Y	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	715					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)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		GATAACTCATCCTGTACTCAA	0.433																																					p.S715Y	Ovarian(124;554 1662 19430 21141 52494)	.											.	ZFP28-91	0			c.C2144A						.						108	108	108					19																	57066298		2203	4300	6503	SO:0001583	missense	140612	exon8			ACTCATCCTGTAC		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"Zinc fingers, C2H2-type", "-"	17801	protein-coding gene	gene with protein product			"zinc finger protein 28 homolog (mouse)"				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.2144C>A	19.37:g.57066298C>A	ENSP00000301318:p.Ser715Tyr	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	130	45	NM_020828	0	0	0	0	0	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	0.336	-0.953021	0.02285	.	.	ENSG00000196867	ENST00000301318	T	0.36878	1.23	4.0	2.86	0.33363	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000413	T	0.22742	0.0549	L	0.35723	1.085	0.20074	N	0.999935	P	0.39181	0.663	B	0.37346	0.247	T	0.07481	-1.0770	10	0.17832	T	0.49	.	7.0155	0.24885	0.0:0.7197:0.1785:0.1018	.	715	Q8NHY6	ZFP28_HUMAN	Y	715	ENSP00000301318:S715Y	ENSP00000301318:S715Y	S	+	2	0	ZFP28	61758110	0.001000	0.12720	0.992000	0.48379	0.984000	0.73092	1.178000	0.31981	2.228000	0.72767	0.555000	0.69702	TCC	.		0.433	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		A	57066298	C	A	57066298	3	1	60	1	0	0	0	0	1	0	0	0	17674	855	30	4	2174	4	ZFP28	19	57066298	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	16	57066298	2062685	98	5865			1	17		2	2	17	N	T_C	5.685195e-05
NCOA6	23054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33329544	33329544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctgtaagcccagggggttTaattgtcacattgggagctc	9	12	12	8	0	2	0	1	0	1	0	3	1	2	1	1	3	2	3	1	3	2	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr20:33329544T>C	ENST00000374796.2	-	12	7086	c.4516A>G	c.(4516-4518)Aaa>Gaa	p.K1506E	NCOA6_ENST00000359003.2_Missense_Mutation_p.K1506E			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1506					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CCAGGGGGTTTAATTGTCACA	0.463																																					p.K1506E		.											.	NCOA6-292	0			c.A4516G						.						78	70	73					20																	33329544		2203	4300	6503	SO:0001583	missense	23054	exon11			GGGGTTTAATTGT	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4516A>G	20.37:g.33329544T>C	ENSP00000363929:p.Lys1506Glu	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	107	43	NM_014071	0	0	2	10	8	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.203458	0.58234	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.34859	1.34;1.34	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000002	T	0.38852	0.1056	L	0.27053	0.805	0.39212	D	0.963341	D	0.60575	0.988	P	0.54759	0.76	T	0.16482	-1.0401	10	0.25106	T	0.35	-8.9946	15.5409	0.76048	0.0:0.0:0.0:1.0	.	1506	Q14686	NCOA6_HUMAN	E	1506	ENSP00000363929:K1506E;ENSP00000351894:K1506E	ENSP00000351894:K1506E	K	-	1	0	NCOA6	32793205	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.330000	0.65899	2.254000	0.74563	0.482000	0.46254	AAA	.		0.463	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33329544	T	C	33329544	3	2	60	1	0	0	0	0	1	0	0	0	10259	1763	61	3	1695	3	NCOA6	20	33329544	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		33329544	29695976	99	5866											
KCNK15	140730	hgsc.bcm.edu	37	chr20	43379383	43379383	+	IGR	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgcacaagctggagaggtgCgcccgcgacaacctgggctt	8	6	15	12	3	0	1	0	0	0	1	0	3	0	1	2	3	4	3	2	3	2	1	rs199821276	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr20:43379383C>G	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Missense_Mutation_p.C299W	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				TGGAGAGGTGCGCCCGCGACA	0.741													C|||	12	0.00239617	0	0.0029	5008	,	,		10240	0		0.0089	False		,,,				2504	0.001				p.C299W		.											.	KCNK15-90	0			c.C897G						.	C	TRP/CYS	2,3470		0,2,1734	4	3	3		897	-4.4	0	20		3	6,6426		0,6,3210	yes	missense	KCNK15	NM_022358.3	215	0,8,4944	GG,GC,CC		0.0933,0.0576,0.0808	benign	299/331	43379383	8,9896	1736	3216	4952	SO:0001628	intergenic_variant	60598	exon2			GAGGTGCGCCCGC		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		20.37:g.43379383C>G		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_022358	0	0	3	11	8	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	C	9.082	0.999523	0.19121	5.76E-4	9.33E-4	ENSG00000124249	ENST00000372861	T	0.12255	2.7	4.16	-4.41	0.03590	.	647.572000	0.00589	U	0.000342	T	0.09113	0.0225	N	0.12182	0.205	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	10	0.56958	D	0.05	.	11.1373	0.48381	0.0:0.6098:0.1794:0.2108	.	299	Q9H427	KCNKF_HUMAN	W	299	ENSP00000361952:C299W	ENSP00000361952:C299W	C	+	3	2	KCNK15	42812797	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.239000	0.18023	-0.430000	0.07318	0.563000	0.77884	TGC	.		0.741	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		G	43379383	C	G	43379383	1	3	60	0	1	0	0	0	0	0	0	0	8083	776	27	4		4	KCNK15	20	43379383	IGR	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	10049839	43379383	19646137	100	5867											
SLC5A3	6526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	35468362	35468362	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgcagagggtccttgcaGccaaaaacattgctcatgcc	10	9	10	12	1	1	1	1	0	0	1	3	1	2	1	3	1	6	3	3	1	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr21:35468362G>A	ENST00000381151.3	+	2	1377	c.865G>A	c.(865-867)Gcc>Acc	p.A289T	SLC5A3_ENST00000608209.1_Missense_Mutation_p.A289T|AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	289					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						GGTCCTTGCAGCCAAAAACAT	0.478																																					p.A289T		.											.	SLC5A3-92	0			c.G865A						.						102	98	100					21																	35468362		2203	4300	6503	SO:0001583	missense	6526	exon2			CTTGCAGCCAAAA		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.865G>A	21.37:g.35468362G>A	ENSP00000370543:p.Ala289Thr	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	190	80	NM_006933	0	0	2	2	0	O43489	Missense_Mutation	SNP	ENST00000381151.3	37	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936080	0.73442	.	.	ENSG00000198743	ENST00000381151	D	0.88975	-2.45	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.96482	0.8852	H	0.96365	3.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	D	0.97583	1.0112	10	0.87932	D	0	.	18.2056	0.89853	0.0:0.0:1.0:0.0	.	289	P53794	SC5A3_HUMAN	T	289	ENSP00000370543:A289T	ENSP00000370543:A289T	A	+	1	0	SLC5A3	34390232	1.000000	0.71417	0.922000	0.36590	0.963000	0.63663	9.869000	0.99810	2.589000	0.87451	0.609000	0.83330	GCC	.		0.478	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			A	35468362	G	A	35468362	3	1	60	1	0	0	0	0	1	0	0	0	14698	971	34	2	867	2	SLC5A3	21	35468362	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		35468362	12661533	101	5868											
ZNF295	49854	broad.mit.edu	37	chr21	43412280	43412280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtccctgaaaaccaggcttgCcgcgccttaacttaatgatc	10	10	8	13	2	0	2	0	2	0	0	2	2	1	2	4	1	3	1	4	1	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr21:43412280C>T	ENST00000310826.5	-	3	2108	c.1925G>A	c.(1924-1926)gGc>gAc	p.G642D	ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Missense_Mutation_p.G642D|ZBTB21_ENST00000398511.3_Missense_Mutation_p.G642D|ZBTB21_ENST00000398505.3_Intron	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	642					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										ACCAGGCTTGCCGCGCCTTAA	0.438																																					p.G642D													.	.	0			c.G1925A						.						65	63	64					21																	43412280		2203	4300	6503	SO:0001583	missense	49854	exon3			GGCTTGCCGCGCC	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13083	protein-coding gene	gene with protein product			"zinc finger protein 295"	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.1925G>A	21.37:g.43412280C>T	ENSP00000308759:p.Gly642Asp	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	137	4	NM_001098402	0	0	5	5	0	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.130570	0.37630	.	.	ENSG00000173276	ENST00000310826;ENST00000398499;ENST00000398511	T;T;T	0.08008	3.14;3.14;3.14	5.44	3.52	0.40303	.	0.508219	0.20986	N	0.082125	T	0.06280	0.0162	N	0.14661	0.345	0.26287	N	0.978185	B	0.31383	0.321	B	0.29267	0.1	T	0.20773	-1.0265	10	0.48119	T	0.1	-2.4439	15.4343	0.75133	0.0:0.7363:0.2636:0.0	.	642	Q9ULJ3	ZN295_HUMAN	D	642	ENSP00000308759:G642D;ENSP00000381512:G642D;ENSP00000381523:G642D	ENSP00000308759:G642D	G	-	2	0	ZNF295	42285349	1.000000	0.71417	0.943000	0.38184	0.996000	0.88848	1.579000	0.36536	0.591000	0.29711	0.591000	0.81541	GGC	.		0.438	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		T	43412280	C	T	43412280	3	4	60	1	0	0	0	0	1	0	0	0	17859	739	26	2	1279	2	ZNF295	21	43412280	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	7943918	43412280	4717615	102	5869											
POTEH	23784	hgsc.bcm.edu;bcgsc.ca	37	chr22	16287580	16287580	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcaggggaagcagtggcaGcaccacttgcccatcttgct	9	7	12	13	0	1	0	0	0	1	0	1	1	1	1	2	3	5	5	2	3	1	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr22:16287580G>T	ENST00000343518.6	-	1	357	c.306C>A	c.(304-306)tgC>tgA	p.C102*		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	102										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						AGCAGTGGCAGCACCACTTGC	0.597																																					p.C102X		.											.	POTEH-1	0			c.C306A						.						67	81	76					22																	16287580		1945	3669	5614	SO:0001587	stop_gained	23784	exon1			GTGGCAGCACCAC	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	133	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 7"	608913	"actin, beta-like 1", "ANKRD26-like family C, member 3"	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.306C>A	22.37:g.16287580G>T	ENSP00000340610:p.Cys102*	Somatic	1092	2		WXS	Illumina HiSeq	Phase_I	417	167	NM_001136213	0	0	0	0	0	A2CEK4|A6NCI1|A9Z1W0	Nonsense_Mutation	SNP	ENST00000343518.6	37	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	13.12	2.143668	0.37825	.	.	ENSG00000198062	ENST00000343518;ENST00000355872	.	.	.	0.168	0.168	0.15012	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	102	.	ENSP00000340610:C102X	C	-	3	2	POTEH	14667580	0.005000	0.15991	0.025000	0.17156	0.026000	0.11368	0.263000	0.18478	0.278000	0.22164	0.283000	0.19423	TGC	.		0.597	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		T	16287580	G	T	16287580	4	4	60	1	0	0	0	0	0	1	0	0	12293	963	34	4	1371	4	POTEH	22	16287580	Nonsense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		16287580	35016986	103	5870											
SMARCB1	6598	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	24167461	24167461	+	Frame_Shift_Del	DEL	A	A	-																															ggtggaccagtttgagtgggAcatgtcagagaaggagaact																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr22:24167461delA	ENST00000263121.7	+	7	1041	c.845delA	c.(844-846)gacfs	p.D282fs	SMARCB1_ENST00000344921.6_Frame_Shift_Del_p.D291fs|SMARCB1_ENST00000407082.3_Frame_Shift_Del_p.D236fs|SMARCB1_ENST00000407422.3_Frame_Shift_Del_p.D273fs|SMARCB1_ENST00000477836.1_3'UTR	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	282	2 X approximate tandem repeats.				ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(6)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				TTTGAGTGGGACATGTCAGAG	0.537			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.D282fs		.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1-2699	7	Unknown(6)|Deletion - In frame(1)	central_nervous_system(6)|soft_tissue(1)	c.845delA						.						126	101	110					22																	24167461		2203	4300	6503	SO:0001589	frameshift_variant	6598	exon7			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.845delA	22.37:g.24167461delA	ENSP00000263121:p.Asp282fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	75	57	NM_003073	0	0	0	0	0	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Del	DEL	ENST00000263121.7	37	CCDS13817.1																																																																																			.		0.537	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		-	24167461	A	-	24167461	7	5	60	1	0	1	0	1	0	0	0	0	14806	275	10	0	871	0	SMARCB1	22	24167461	Frame_Shift_Del	DEL	A	TCGA-BQ-5876-01A-11D-1589-08	7879881	24167461	27137105	104	5871											
CENPM	79019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42342456	42342456	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gcgcagtcctctttgagcatCgagtccgccagctgctgcag	6	9	12	14	3	1	1	0	1	1	0	4	2	3	1	3	0	4	5	3	0	0	1	rs372178394		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr22:42342456C>G	ENST00000215980.5	-	2	189	c.102G>C	c.(100-102)tcG>tcC	p.S34S	CENPM_ENST00000407253.3_Silent_p.S34S|CENPM_ENST00000402420.1_5'UTR|CENPM_ENST00000402338.1_5'UTR|CENPM_ENST00000404067.1_5'UTR	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	34					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						CTTTGAGCATCGAGTCCGCCA	0.647											OREG0026600	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S34S		.											.	CENPM-90	0			c.G102C						.						36	31	33					22																	42342456		2203	4299	6502	SO:0001819	synonymous_variant	79019	exon2			GAGCATCGAGTCC	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"chromosome 22 open reading frame 18"	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.102G>C	22.37:g.42342456C>G		Somatic	39	0	908	WXS	Illumina HiSeq	Phase_I	32	4	NM_024053	0	0	3	4	1	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	37	CCDS14025.1																																																																																			.		0.647	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053		G	42342456	C	G	42342456	2	3	60	1	0	0	0	0	0	0	0	1	3243	871	31	4		4	CENPM	22	42342456	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	18174995	42342456	8962110	105	5872											
ZXDB	158586	hgsc.bcm.edu	37	chrX	57618703	57618703	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccctggcccaagcctgttGgcgccgaggaccgatcaacc	7	5	13	16	3	1	0	1	0	0	0	1	3	1	1	6	4	2	1	6	4	2	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:57618703G>C	ENST00000374888.1	+	1	435	c.222G>C	c.(220-222)ttG>ttC	p.L74F		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	74					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.L74F(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						CAAGCCTGTTGGCGCCGAGGA	0.766																																					p.L74F		.											.	ZXDB-130	1	Substitution - Missense(1)	skin(1)	c.G222C						.																																			SO:0001583	missense	158586	exon1			CCTGTTGGCGCCG	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.222G>C	X.37:g.57618703G>C	ENSP00000364023:p.Leu74Phe	Somatic	14	2		WXS	Illumina HiSeq	Phase_I	14	6	NM_007157	0	0	0	0	0	A8K151|Q9UBB3	Missense_Mutation	SNP	ENST00000374888.1	37	CCDS35313.1	.	.	.	.	.	.	.	.	.	.	.	10.02	1.236808	0.22711	.	.	ENSG00000198455	ENST00000374888	T	0.38560	1.13	2.35	2.35	0.29111	.	0.163913	0.25238	N	0.032116	T	0.37156	0.0993	L	0.29908	0.895	0.28113	N	0.930925	D	0.54964	0.969	P	0.53912	0.737	T	0.10200	-1.0640	10	0.28530	T	0.3	.	7.4225	0.27079	0.0:0.0:1.0:0.0	.	74	P98169	ZXDB_HUMAN	F	74	ENSP00000364023:L74F	ENSP00000364023:L74F	L	+	3	2	ZXDB	57635428	0.372000	0.25064	0.949000	0.38748	0.420000	0.31355	3.802000	0.55553	1.447000	0.47661	0.483000	0.47432	TTG	.		0.766	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		C	57618703	G	C	57618703	3	2	60	1	0	0	0	0	1	0	0	0	18283	1339	47	4	224	4	ZXDB	23	57618703	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		57618703	97651857	106	5873											
TAF1	6872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70643918	70643918	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagagaccatacgtaaggTgagtgagtgatttgatctaa	13	13	11	4	1	1	5	0	4	1	1	1	6	1	5	1	1	1	1	1	1	4	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:70643918T>C	ENST00000373790.4	+	31	4716		c.e31+2		TAF1_ENST00000449580.1_Splice_Site|TAF1_ENST00000423759.1_Splice_Site|TAF1_ENST00000461764.1_Splice_Site|TAF1_ENST00000276072.3_Splice_Site	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa						cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ATACGTAAGGTGAGTGAGTGA	0.373																																					.		.											.	TAF1-900	0			c.4728+2T>C						.						133	107	116					X																	70643918		2203	4300	6503	SO:0001630	splice_region_variant	6872	exon31			GTAAGGTGAGTGA		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"Chromatin-modifying enzymes / K-acetyltransferases"	11535	protein-coding gene	gene with protein product		313650	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD", "dystonia 3 (with Parkinsonism)"	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.4665+2T>C	X.37:g.70643918T>C		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	65	49	NM_004606	0	0	0	0	0	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Splice_Site	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255554	0.59321	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000538124;ENST00000276072;ENST00000437147	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8076	0.63243	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TAF1	70560643	1.000000	0.71417	0.992000	0.48379	0.831000	0.47069	7.412000	0.80091	1.704000	0.51252	0.486000	0.48141	.	.		0.373	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	Intron	C	70643918	T	C	70643918	5	2	60	1	0	0	0	0	0	0	1	0	15545	1710	59	3	4852	3	TAF1	23	70643918	Splice_Site	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	13025215	70643918	84626642	107	5874											
RLIM	51132	hgsc.bcm.edu	37	chrX	73811737	73811737	+	Silent	SNP	T	T	A																															ctaggactggaactggaactTgaactggaactggaactcga																								rs113198776		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:73811737T>A	ENST00000332687.6	-	4	1631	c.1413A>T	c.(1411-1413)tcA>tcT	p.S471S	RLIM_ENST00000349225.2_Silent_p.S471S	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	471	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						aactggaacttgaactggaac	0.478																																					p.S471S	Esophageal Squamous(169;1899 1923 14997 18818 32118)	.											.	RLIM-228	0			c.A1413T						.						38	38	38					X																	73811737		2203	4300	6503	SO:0001819	synonymous_variant	51132	exon5			GGAACTTGAACTG	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1413A>T	X.37:g.73811737T>A		Somatic	38	1		WXS	Illumina HiSeq	Phase_I	40	3	NM_183353	28	0	18	46	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Silent	SNP	ENST00000332687.6	37	CCDS14427.1																																																																																			.		0.478	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73811737	T	A	73811737	2	1	60	1	0	0	0	0	0	0	0	1	13422	1799	63	5		5	RLIM	23	73811737	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	3167819	73811737	81458823	108	5875	67	2									
RLIM	51132	hgsc.bcm.edu	37	chrX	73811739	73811739	+	Missense_Mutation	SNP	A	A	G																															aggactggaactggaacttgAactggaactggaactcgaac																								rs201164156		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:73811739A>G	ENST00000332687.6	-	4	1629	c.1411T>C	c.(1411-1413)Tca>Cca	p.S471P	RLIM_ENST00000349225.2_Missense_Mutation_p.S471P	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	471	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ctggaacttgaactggaactg	0.483																																					p.S471P	Esophageal Squamous(169;1899 1923 14997 18818 32118)	.											.	RLIM-228	0			c.T1411C						.																																			SO:0001583	missense	51132	exon5			AACTTGAACTGGA	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1411T>C	X.37:g.73811739A>G	ENSP00000328059:p.Ser471Pro	Somatic	36	1		WXS	Illumina HiSeq	Phase_I	40	3	NM_183353	0	0	21	21	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.619369	0.00118	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	D;D	0.85258	-1.96;-1.96	1.66	0.0881	0.14453	.	0.638142	0.11946	U	0.514165	T	0.59032	0.2164	N	0.08118	0	0.09310	N	1	P	0.44734	0.842	B	0.29267	0.1	T	0.56607	-0.7951	10	0.34782	T	0.22	-0.2213	3.7245	0.08469	0.5962:0.4038:0.0:0.0	.	471	Q9NVW2	RNF12_HUMAN	P	471	ENSP00000328059:S471P;ENSP00000253571:S471P	ENSP00000328059:S471P	S	-	1	0	RLIM	73728464	0.991000	0.36638	0.012000	0.15200	0.011000	0.07611	0.068000	0.14531	0.675000	0.31264	0.441000	0.28932	TCA	.		0.483	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		G	73811739	A	G	73811739	3	3	60	1	0	0	0	0	1	0	0	0	13422	246	9	3	467	3	RLIM	23	73811739	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	2	73811739	81458821	109	5876	67	2									
ODZ1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123518587	123518587	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaagatctataggcaaagggGtttcattgattacagcttgc	13	12	10	6	0	2	2	1	1	1	1	2	2	2	2	0	3	3	3	0	3	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:123518587G>C	ENST00000371130.3	-	29	6236	c.6173C>G	c.(6172-6174)aCc>aGc	p.T2058S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.T2065S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2058					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGGCAAAGGGGTTTCATTGAT	0.393																																					p.T2065S		.											.	.	0			c.C6194G						.						125	106	112					X																	123518587		2203	4300	6503	SO:0001583	missense	10178	exon30			AAAGGGGTTTCAT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.6173C>G	X.37:g.123518587G>C	ENSP00000360171:p.Thr2058Ser	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	97	81	NM_001163278	0	0	0	0	0	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184284	0.78677	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86097	-2.07;-2.03	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.90992	0.7167	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	D;D;D	0.70716	0.97;0.918;0.937	D	0.90198	0.4255	10	0.39692	T	0.17	.	18.3227	0.90244	0.0:0.0:1.0:0.0	.	2064;2065;2058	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2058;2065	ENSP00000360171:T2058S;ENSP00000403954:T2065S	ENSP00000360171:T2058S	T	-	2	0	ODZ1	123346268	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.964000	0.87933	2.265000	0.75225	0.600000	0.82982	ACC	.		0.393	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123518587	G	C	123518587	3	2	60	1	0	0	0	0	1	0	0	0	10860	1261	44	4	2016	4	ODZ1	23	123518587	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	49706848	123518587	31751973	110	5877											
CXorf48	54967	hgsc.bcm.edu	37	chrX	134303602	134303602	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttttagaggcacgttgccAgtcacaacatcactactgaa	13	10	7	11	1	2	2	2	1	0	1	2	2	2	2	1	1	3	2	1	1	4	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:134303602A>G	ENST00000276241.6	-	2	421	c.195T>C	c.(193-195)acT>acC	p.T65T	CXorf48_ENST00000344129.2_Silent_p.T65T	NM_001031705.2	NP_001026875.1	Q8WUE5	CT55_HUMAN		65										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5	Acute lymphoblastic leukemia(192;0.000127)					GCACGTTGCCAGTCACAACAT	0.428																																					p.T65T		.											.	CXorf48-130	0			c.T195C						.						121	88	99					X																	134303602		2203	4297	6500	SO:0001819	synonymous_variant	54967	exon2			GTTGCCAGTCACA																												ENST00000276241.6:c.195T>C	X.37:g.134303602A>G		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_017863	0	0	0	0	0	Q9NWY8	Silent	SNP	ENST00000276241.6	37	CCDS35400.1																																																																																			.		0.428	CXorf48-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058404.1			G	134303602	A	G	134303602	2	3	60	1	0	0	0	0	0	0	0	1	4117	175	7	3		3	CXorf48	23	134303602	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	10785015	134303602	20966958	111	5878											
CTRC	11330	hgsc.bcm.edu	37	chr1	15766798	15766798	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctcctgtctccccagccTccagctgtggggtgcccagc	3	8	12	18	0	1	0	0	0	1	0	4	0	3	0	7	3	4	1	7	3	0	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:15766798T>C	ENST00000375949.4	+	2	69	c.43T>C	c.(43-45)Tcc>Ccc	p.S15P	CTRC_ENST00000375943.2_Intron	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	15					proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCCAGCCTCCAGCTGTGG	0.662																																					p.S15P		.											.	CTRC-90	0			c.T43C						.						13	15	14					1																	15766798		2195	4289	6484	SO:0001583	missense	11330	exon2			CCAGCCTCCAGCT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.43T>C	1.37:g.15766798T>C	ENSP00000365116:p.Ser15Pro	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	26	4	NM_007272	0	0	0	0	0	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	37	CCDS156.1	.	.	.	.	.	.	.	.	.	.	.	12.00	1.806468	0.31961	.	.	ENSG00000162438	ENST00000375949	D	0.92699	-3.09	4.94	3.78	0.43462	.	0.380815	0.30293	N	0.009943	D	0.82522	0.5055	N	0.12961	0.28	0.80722	D	1	P;B	0.34837	0.472;0.198	B;B	0.30943	0.122;0.122	T	0.78914	-0.2016	10	0.35671	T	0.21	-29.5492	10.7713	0.46325	0.0:0.0:0.1596:0.8404	.	15;15	A8MTQ9;Q99895	.;CTRC_HUMAN	P	15	ENSP00000365116:S15P	ENSP00000365116:S15P	S	+	1	0	CTRC	15639385	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	1.777000	0.38604	0.881000	0.35993	0.533000	0.62120	TCC	.		0.662	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		C	15766798	T	C	15766798	3	2	61	1	0	0	0	0	1	0	0	0	4033	1551	54	3	49	3	CTRC	1	15766798	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		15766798	233483823	1	5879											
YBX1	4904	hgsc.bcm.edu	37	chr1	43166460	43166460	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttcattgcaggggccctcCtcgccaaagacagcctagag	9	7	11	14	2	1	2	1	0	0	2	3	2	2	2	4	2	2	2	4	2	2	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:43166460C>T	ENST00000321358.7	+	7	888	c.749C>T	c.(748-750)cCt>cTt	p.P250L		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	250					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGGGGCCCTCCTCGCCAAAGA	0.498																																					p.P250L		.											.	YBX1-95	0			c.C749T						.						28	25	26					1																	43166460		2203	4300	6503	SO:0001583	missense	4904	exon7			GCCCTCCTCGCCA	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.749C>T	1.37:g.43166460C>T	ENSP00000361626:p.Pro250Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	24	4	NM_004559	0	0	0	0	0	P16990|P16991|Q14972|Q15325|Q5FVF0	Missense_Mutation	SNP	ENST00000321358.7	37	CCDS470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.49|17.49	3.403460|3.403460	0.62288|0.62288	.|.	.|.	ENSG00000065978|ENSG00000065978	ENST00000318612;ENST00000436427|ENST00000321358	.|T	.|0.36340	.|1.26	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.148105	.|0.64402	.|D	.|0.000006	T|T	0.41050|0.41050	0.1142|0.1142	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	.|B	.|0.29862	.|0.259	.|B	.|0.30179	.|0.112	T|T	0.36817|0.36817	-0.9732|-0.9732	6|10	0.30078|0.56958	T|D	0.28|0.05	-2.6639|-2.6639	16.6288|16.6288	0.85011|0.85011	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|250	.|P67809	.|YBOX1_HUMAN	F|L	241;300|250	.|ENSP00000361626:P250L	ENSP00000361621:L241F|ENSP00000361626:P250L	L|P	+|+	1|2	0|0	YBX1|YBX1	42939047|42939047	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.152000|7.152000	0.77419|0.77419	2.501000|2.501000	0.84356|0.84356	0.552000|0.552000	0.68991|0.68991	CTC|CCT	.		0.498	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559		T	43166460	C	T	43166460	3	4	61	1	0	0	0	0	1	0	0	0	17502	681	24	2	775	2	YBX1	1	43166460	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	27399662	43166460	206084161	2	5880											
BCAN	63827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156628454	156628454	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggactggcccagcgcaatCtgccgctgatccgatgccaa	10	6	11	14	3	1	1	0	1	1	0	2	3	2	2	4	2	3	2	4	2	3	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:156628454C>A	ENST00000329117.5	+	13	2893	c.2557C>A	c.(2557-2559)Ctg>Atg	p.L853M	RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	853	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCAGCGCAATCTGCCGCTGAT	0.647																																					p.L853M		.											.	BCAN-516	0			c.C2557A						.						76	82	80					1																	156628454		2203	4300	6503	SO:0001583	missense	63827	exon13			CGCAATCTGCCGC	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.2557C>A	1.37:g.156628454C>A	ENSP00000331210:p.Leu853Met	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	203	83	NM_021948	0	0	0	0	0	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.488032	0.44249	.	.	ENSG00000132692	ENST00000329117	T	0.63744	-0.06	4.96	2.91	0.33838	Complement control module (2);Sushi/SCR/CCP (3);	0.749157	0.11026	N	0.607755	T	0.48352	0.1495	L	0.45051	1.395	0.30868	N	0.73272	D	0.56287	0.975	P	0.55011	0.766	T	0.36456	-0.9747	10	0.44086	T	0.13	-3.4908	5.7222	0.17992	0.0:0.6921:0.0:0.3079	.	853	Q96GW7	PGCB_HUMAN	M	853	ENSP00000331210:L853M	ENSP00000331210:L853M	L	+	1	2	BCAN	154895078	0.002000	0.14202	0.999000	0.59377	0.591000	0.36615	0.020000	0.13466	1.299000	0.44798	0.555000	0.69702	CTG	.		0.647	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156628454	C	A	156628454	3	1	61	1	0	0	0	0	1	0	0	0	1346	912	32	4	2677	4	BCAN	1	156628454	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	113461994	156628454	92622167	3	5881											
HMCN1	83872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	186072770	186072770	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtgcaaactctaggaggAggagaggttcttcgaatttc	12	10	12	7	1	2	1	0	0	2	1	4	5	2	3	0	4	2	2	0	4	4	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:186072770A>G	ENST00000271588.4	+	69	10969	c.10740A>G	c.(10738-10740)ggA>ggG	p.G3580G	HMCN1_ENST00000367492.2_Silent_p.G3580G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3580	Ig-like C2-type 34.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTCTAGGAGGAGGAGAGGTTC	0.433																																					p.G3580G		.											.	HMCN1-113	0			c.A10740G						.						58	60	59					1																	186072770		2203	4299	6502	SO:0001819	synonymous_variant	83872	exon69			AGGAGGAGGAGAG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.10740A>G	1.37:g.186072770A>G		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	74	18	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186072770	A	G	186072770	2	3	61	1	0	0	0	0	0	0	0	1	7241	291	11	3		3	HMCN1	1	186072770	Silent	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	29444316	186072770	63177851	4	5882											
KIF21B	23046	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	200974516	200974517	+	Frame_Shift_Del	DEL	TC	TC	-																															gcgtgagctctgcacgttcaTctgggtgctggctgtggtgc																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:200974516_200974517delTC	ENST00000422435.2	-	5	967_968	c.651_652delGA	c.(649-654)cagatgfs	p.QM217fs	KIF21B_ENST00000332129.2_Frame_Shift_Del_p.QM217fs|KIF21B_ENST00000461742.2_Frame_Shift_Del_p.QM217fs|KIF21B_ENST00000360529.5_Frame_Shift_Del_p.QM217fs	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	217	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TGCACGTTCATCTGGGTGCTGG	0.639																																					p.217_218del		.											.	KIF21B-96	0			c.651_652del						.																																			SO:0001589	frameshift_variant	23046	exon5			.	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.651_652delGA	1.37:g.200974516_200974517delTC	ENSP00000411831:p.Gln217fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	142	48	NM_017596	0	0	0	0	0	B2RP62|B7ZMI0|Q5T4J3	Frame_Shift_Del	DEL	ENST00000422435.2	37	CCDS58056.1																																																																																			.		0.639	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		-	200974517	TC	-	200974516	7	5	61	1	0	1	0	1	0	0	0	0	8310	1435	50	0	4342	0	KIF21B	1	200974516	Frame_Shift_Del	DEL	TC	TCGA-BQ-5877-01A-11D-1589-08	14901746	200974516	48276105	5	5883											
TMEM206	55248	hgsc.bcm.edu	37	chr1	212588063	212588064	+	Splice_Site	INS	-	-	CTCCTGGTAGGATGTGGAGCG																															cgtctctcacaacctcgtacINSctcctggtaggatgtggagc																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:212588063_212588064insCTCCTGGTAGGATGTGGAGCG	ENST00000261455.4	-	1	173_174		c.e1+1		TMEM206_ENST00000471937.1_Splice_Site|TMEM206_ENST00000535273.1_Splice_Site	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206							cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		CAACCTCGTACCTCCTGGTAGG	0.703																																					.		.											.	TMEM206-153	0			c.36+1->CGCTCCACATCCTACCAGGAG						.																																			SO:0001630	splice_region_variant	55248	exon2			.	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.36+1->CGCTCCACATCCTACCAGGAG	1.37:g.212588063_212588064insCTCCTGGTAGGATGTGGAGCG		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	50	10	NM_001198862	0	0	0	0	0	B7Z4D6|Q6IA87|Q9NV85	Splice_Site	INS	ENST00000261455.4	37	CCDS1504.1																																																																																			.		0.703	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252	Intron	CTCCTGGTAGGATGTGGAGCG	212588064	-	CTCCTGGTAGGATGTGGAGCG	212588063	8	5	61	1	0	1	1	0	0	0	1	0	16163	521	18	0	1047	0	TMEM206	1	212588063	Splice_Site	INS	-	TCGA-BQ-5877-01A-11D-1589-08	11613547	212588063	36662558	6	5884											
TRIM17	51127	ucsc.edu;bcgsc.ca	37	chr1	228596833	228596833	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtggggcatcgccaagaGatcctgggtcagaggtcctg	9	7	15	10	1	1	2	1	0	0	2	4	3	3	2	3	4	0	1	3	4	1	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:228596833G>T	ENST00000366697.2	-	5	1840				TRIM11_ENST00000366699.3_5'Flank|TRIM11_ENST00000284551.6_5'Flank|TRIM17_ENST00000366698.2_Intron|TRIM17_ENST00000456946.2_Missense_Mutation_p.S308Y|RP11-245P10.4_ENST00000436779.1_RNA|TRIM17_ENST00000295033.3_Intron			Q9Y577	TRI17_HUMAN	tripartite motif containing 17						protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				ATCGCCAAGAGATCCTGGGTC	0.587																																					p.S308Y													.	TRIM17-659	0			c.C923A						.						80	84	83					1																	228596833		2203	4300	6503	SO:0001627	intron_variant	51127	exon6			CCAAGAGATCCTG	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13430	protein-coding gene	gene with protein product	"ring finger protein 16", "RING finger protein terf", "testis RING finger protein"	606123	"tripartite motif-containing 17"	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.883+39C>A	1.37:g.228596833G>T		Somatic	94	1		WXS	Illumina HiSeq		133	47	NM_001134855	0	0	0	1	1	B4DVJ2|Q5VST8	Missense_Mutation	SNP	ENST00000366697.2	37	CCDS1571.1	.	.	.	.	.	.	.	.	.	.	G	8.908	0.958055	0.18507	.	.	ENSG00000162931	ENST00000456946	T	0.34859	1.34	2.77	0.748	0.18376	.	.	.	.	.	T	0.18383	0.0441	N	0.14661	0.345	0.09310	N	1	P	0.35328	0.495	B	0.31191	0.125	T	0.13098	-1.0522	9	0.59425	D	0.04	.	6.2084	0.20615	0.1192:0.1894:0.6914:0.0	.	308	Q9Y577-2	.	Y	308	ENSP00000403312:S308Y	ENSP00000403312:S308Y	S	-	2	0	TRIM17	226663456	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	0.072000	0.14617	0.191000	0.20236	0.655000	0.94253	TCT	.		0.587	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102		T	228596833	G	T	228596833	1	4	61	0	1	0	0	0	0	0	0	0	16526	942	33	4		4	TRIM17	1	228596833	Intron	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	16008770	228596833	20653788	7	5885											
EXOC8	149371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	231472695	231472695	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actctcgtttgattttagcaTtttcggcctggaaaatacgg	9	15	9	8	3	1	1	0	1	1	0	3	2	1	2	1	3	2	2	1	3	4	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:231472695T>A	ENST00000360394.2	-	1	883	c.797A>T	c.(796-798)aAt>aTt	p.N266I	SPRTN_ENST00000391858.4_5'Flank|SPRTN_ENST00000295050.7_5'Flank|EXOC8_ENST00000366645.1_Missense_Mutation_p.N262I|SPRTN_ENST00000008440.9_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	266	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				GATTTTAGCATTTTCGGCCTG	0.547																																					p.N266I		.											.	EXOC8-91	0			c.A797T						.						69	70	69					1																	231472695		2203	4300	6503	SO:0001583	missense	149371	exon1			TTAGCATTTTCGG	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.797A>T	1.37:g.231472695T>A	ENSP00000353564:p.Asn266Ile	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	172	67	NM_175876	0	0	6	12	6	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	37	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175994	0.78564	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.79653	-1.29;-1.29	5.69	5.69	0.88448	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.88130	0.6354	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.88677	0.3199	10	0.56958	D	0.05	-22.853	15.9478	0.79806	0.0:0.0:0.0:1.0	.	266	Q8IYI6	EXOC8_HUMAN	I	266;262	ENSP00000353564:N266I;ENSP00000355605:N262I	ENSP00000353564:N266I	N	-	2	0	EXOC8	229539318	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.165000	0.68154	0.459000	0.35465	AAT	.		0.547	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472695	T	A	231472695	3	1	61	1	0	0	0	0	1	0	0	0	5324	1493	52	5	1384	5	EXOC8	1	231472695	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	2875862	231472695	17777926	8	5886											
NBAS	51594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	15542368	15542368	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttcgttcacaggtatagaTgcactctagtgctattgcca	10	14	8	9	1	2	1	1	0	1	1	3	1	2	1	1	1	3	4	1	1	4	7			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:15542368T>G	ENST00000281513.5	-	26	3020	c.2995A>C	c.(2995-2997)Atc>Ctc	p.I999L	NBAS_ENST00000441750.1_Missense_Mutation_p.I879L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	999					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CAGGTATAGATGCACTCTAGT	0.383																																					p.I999L		.											.	NBAS-94	0			c.A2995C						.						156	148	151					2																	15542368		2203	4300	6503	SO:0001583	missense	51594	exon26			TATAGATGCACTC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.2995A>C	2.37:g.15542368T>G	ENSP00000281513:p.Ile999Leu	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	137	43	NM_015909	0	0	21	28	7	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.90|16.90	3.250228|3.250228	0.59212|0.59212	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000429842|ENST00000441750;ENST00000281513;ENST00000441755	.|T;T;T	.|0.18016	.|2.24;2.24;2.24	5.65|5.65	4.5|4.5	0.54988|0.54988	.|Secretory pathway Sec39 (1);	.|0.044348	.|0.85682	.|D	.|0.000000	T|T	0.24890|0.24890	0.0604|0.0604	M|M	0.67953|0.67953	2.075|2.075	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.43024	.|0.798;0.771	.|B;P	.|0.45428	.|0.39;0.48	T|T	0.01613|0.01613	-1.1312|-1.1312	5|10	.|0.87932	.|D	.|0	.|.	10.3793|10.3793	0.44101|0.44101	0.0:0.0774:0.0:0.9226|0.0:0.0774:0.0:0.9226	.|.	.|879;999	.|A2RRP1-2;A2RRP1	.|.;NBAS_HUMAN	P|L	96|879;999;46	.|ENSP00000413201:I879L;ENSP00000281513:I999L;ENSP00000396501:I46L	.|ENSP00000281513:I999L	H|I	-|-	2|1	0|0	NBAS|NBAS	15459819|15459819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	4.514000|4.514000	0.60482|0.60482	0.976000|0.976000	0.38417|0.38417	0.533000|0.533000	0.62120|0.62120	CAT|ATC	.		0.383	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15542368	T	G	15542368	3	3	61	1	0	0	0	0	1	0	0	0	10211	1464	51	5	4228	5	NBAS	2	15542368	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		15542368	227657005	9	5887											
CENPA	1058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27016052	27016052	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatctctttgaggacgccTatctcctcaccttacatgca	8	14	5	14	1	4	1	2	1	2	0	6	2	4	2	3	1	2	1	3	1	2	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:27016052T>C	ENST00000335756.4	+	4	528	c.328T>C	c.(328-330)Tat>Cat	p.Y110H	CENPA_ENST00000233505.8_Missense_Mutation_p.Y84H|CENPA_ENST00000475662.1_3'UTR	NM_001809.3	NP_001800.1	P49450	CENPA_HUMAN	centromere protein A	110	CATD.|H3-like.				CENP-A containing nucleosome assembly (GO:0034080)|establishment of mitotic spindle orientation (GO:0000132)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|protein localization to chromosome, centromeric region (GO:0071459)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|condensed chromosome inner kinetochore (GO:0000939)|condensed nuclear chromosome kinetochore (GO:0000778)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(3)|lung(3)|urinary_tract(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGAGGACGCCTATCTCCTCAC	0.542																																					p.Y110H	Pancreas(28;769 878 30250 30578 41330)	.											.	CENPA-181	0			c.T328C						.						185	191	189					2																	27016052		2203	4300	6503	SO:0001583	missense	1058	exon4			GACGCCTATCTCC	U14518	CCDS1729.1, CCDS42662.1	2p23.3	2013-11-05	2006-06-16		ENSG00000115163	ENSG00000115163			1851	protein-coding gene	gene with protein product	"centromere-specific histone", "histone H3-like centromeric protein A"	117139	"centromere protein A (17kD)", "centromere protein A, 17kDa"				Standard	NM_001042426		Approved	CENP-A, CenH3	uc002rhr.3	P49450	OTTHUMG00000097073	ENST00000335756.4:c.328T>C	2.37:g.27016052T>C	ENSP00000336868:p.Tyr110His	Somatic	336	1		WXS	Illumina HiSeq	Phase_I	433	159	NM_001809	0	0	3	3	0	D6W544|Q53T74|Q9BVW2	Missense_Mutation	SNP	ENST00000335756.4	37	CCDS1729.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.184197	0.57800	.	.	ENSG00000115163	ENST00000335756;ENST00000233505	T;T	0.68331	-0.32;-0.32	5.96	5.96	0.96718	Histone-fold (2);Histone core (1);	0.408748	0.26258	N	0.025404	T	0.79137	0.4395	L	0.61387	1.9	0.41321	D	0.987178	D;D	0.76494	0.999;0.999	D;D	0.71184	0.968;0.972	T	0.81182	-0.1049	10	0.72032	D	0.01	-24.0282	14.3967	0.67015	0.0:0.0:0.0:1.0	.	84;110	P49450-2;P49450	.;CENPA_HUMAN	H	110;84	ENSP00000336868:Y110H;ENSP00000233505:Y84H	ENSP00000233505:Y84H	Y	+	1	0	CENPA	26869556	1.000000	0.71417	0.741000	0.31004	0.367000	0.29736	4.210000	0.58500	2.284000	0.76573	0.528000	0.53228	TAT	.		0.542	CENPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214190.2	NM_001809		C	27016052	T	C	27016052	3	2	61	1	0	0	0	0	1	0	0	0	3232	1522	53	3	342	3	CENPA	2	27016052	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	11473684	27016052	216183321	10	5888											
SLC5A6	8884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27427450	27427450	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggaaggggaacactgcaTaacaggagctgcaaaagagg	15	4	15	7	0	0	1	0	0	0	1	0	4	0	4	0	5	5	4	0	5	5	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:27427450T>C	ENST00000310574.3	-	9	1357	c.884A>G	c.(883-885)tAt>tGt	p.Y295C	SLC5A6_ENST00000461319.1_5'Flank|SLC5A6_ENST00000408041.1_Missense_Mutation_p.Y295C	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	295					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	GAACACTGCATAACAGGAGCT	0.572																																					p.Y295C		.											.	SLC5A6-92	0			c.A884G						.						80	74	76					2																	27427450		2203	4300	6503	SO:0001583	missense	8884	exon9			ACTGCATAACAGG	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.884A>G	2.37:g.27427450T>C	ENSP00000310208:p.Tyr295Cys	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	104	35	NM_021095	0	0	0	0	0	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	37	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.389077	0.61956	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.87809	-2.3;-2.3	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.92714	0.7684	M	0.81802	2.56	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.93087	0.6496	10	0.54805	T	0.06	.	12.8283	0.57733	0.0:0.0:0.0:1.0	.	295	Q9Y289	SC5A6_HUMAN	C	295	ENSP00000310208:Y295C;ENSP00000384853:Y295C	ENSP00000310208:Y295C	Y	-	2	0	SLC5A6	27280954	1.000000	0.71417	0.958000	0.39756	0.397000	0.30659	5.786000	0.69006	1.986000	0.57962	0.533000	0.62120	TAT	.		0.572	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		C	27427450	T	C	27427450	3	2	61	1	0	0	0	0	1	0	0	0	14701	1406	49	3	1059	3	SLC5A6	2	27427450	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	411398	27427450	215771923	11	5889											
TTC27	55622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	33036148	33036148	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgactgatcgaagtggagatGttgcaactggcctcaaagga	12	9	13	7	1	1	3	1	2	0	1	2	6	1	4	1	3	2	2	1	3	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:33036148G>A	ENST00000317907.4	+	17	2287	c.2056G>A	c.(2056-2058)Gtt>Att	p.V686I		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	686										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						AAGTGGAGATGTTGCAACTGG	0.428																																					p.V686I		.											.	TTC27-90	0			c.G2056A						.						129	122	125					2																	33036148		2203	4300	6503	SO:0001583	missense	55622	exon17			GGAGATGTTGCAA	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.2056G>A	2.37:g.33036148G>A	ENSP00000313953:p.Val686Ile	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	130	51	NM_017735	0	0	13	25	12	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	1.700	-0.501793	0.04261	.	.	ENSG00000018699	ENST00000317907	T	0.37584	1.19	5.22	2.23	0.28157	.	0.494754	0.21950	N	0.066749	T	0.11153	0.0272	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19031	-1.0318	10	0.32370	T	0.25	-11.2027	5.2727	0.15634	0.2963:0.0:0.5626:0.1412	.	686	Q6P3X3	TTC27_HUMAN	I	686	ENSP00000313953:V686I	ENSP00000313953:V686I	V	+	1	0	TTC27	32889652	0.000000	0.05858	0.868000	0.34077	0.084000	0.17831	0.052000	0.14163	0.765000	0.33221	0.650000	0.86243	GTT	.		0.428	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		A	33036148	G	A	33036148	3	1	61	1	0	0	0	0	1	0	0	0	16728	1377	48	2	2122	2	TTC27	2	33036148	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	5608698	33036148	210163225	12	5890											
THUMPD2	80745	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	39983057	39983058	+	Frame_Shift_Ins	INS	-	-	T																															tttagcagcttccaaaagtaINSttgttccaagtccacacatt																								rs202183716		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:39983057_39983058insT	ENST00000505747.1	-	7	961_962	c.934_935insA	c.(934-936)atafs	p.I312fs	THUMPD2_ENST00000260619.6_Frame_Shift_Ins_p.I282fs	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	312							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				TTCCAAAAGTATTGTTCCAAGT	0.322																																					p.I312fs		.											.	THUMPD2-91	0			c.935_936insA						.																																			SO:0001589	frameshift_variant	80745	exon7			.	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.935dupA	2.37:g.39983059_39983059dupT	ENSP00000423933:p.Ile312fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	98	32	NM_025264	0	0	0	0	0	A8K7I7|Q53TT8|Q53TV0	Frame_Shift_Ins	INS	ENST00000505747.1	37	CCDS1805.2																																																																																			.		0.322	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264		T	39983058	-	T	39983057	7	5	61	1	0	1	1	0	0	0	0	0	15915	449	16	0	592	0	THUMPD2	2	39983057	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	6946909	39983057	203216316	13	5891											
PSME4	23198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	54125075	54125075	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggcacgaagaggcaacaCtcggtcatctctcagcagta	12	8	10	11	2	3	1	2	0	1	1	5	2	3	1	0	3	2	4	0	3	4	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:54125075C>G	ENST00000404125.1	-	31	3593	c.3538G>C	c.(3538-3540)Gtg>Ctg	p.V1180L	PSME4_ENST00000421748.2_Missense_Mutation_p.V324L	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1180					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)			AGAGGCAACACTCGGTCATCT	0.408																																					p.V1180L		.											.	PSME4-275	0			c.G3538C						.						155	149	151					2																	54125075		2203	4300	6503	SO:0001583	missense	23198	exon31			GCAACACTCGGTC	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.3538G>C	2.37:g.54125075C>G	ENSP00000384211:p.Val1180Leu	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	162	44	NM_014614	0	0	19	28	9	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	C	13.13	2.143792	0.37825	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.63417	-0.04;-0.04	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.196755	0.45361	D	0.000375	T	0.47525	0.1450	N	0.22421	0.69	0.37075	D	0.898738	B;B;B	0.15473	0.009;0.013;0.013	B;B;B	0.15484	0.007;0.013;0.008	T	0.47686	-0.9098	10	0.25106	T	0.35	.	13.4018	0.60887	0.0:0.9192:0.0:0.0808	.	555;324;1180	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	L	324;1180	ENSP00000410830:V324L;ENSP00000384211:V1180L	ENSP00000384211:V1180L	V	-	1	0	PSME4	53978579	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.276000	0.58933	2.667000	0.90743	0.655000	0.94253	GTG	.		0.408	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54125075	C	G	54125075	3	3	61	1	0	0	0	0	1	0	0	0	12738	565	20	4	2057	4	PSME4	2	54125075	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	14142018	54125075	189074298	14	5892											
RGPD1	729857	hgsc.bcm.edu	37	chr2	88081658	88081659	+	Frame_Shift_Ins	INS	-	-	A																															ctacccttttctggtgttttINSaaatgtgtagttgattgaag																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:88081658_88081659insA	ENST00000398146.3	-	20	5106_5107	c.4884_4885insT	c.(4882-4887)tttaaafs	p.K1629fs	RGPD2_ENST00000420840.2_Frame_Shift_Ins_p.K1621fs|RGPD2_ENST00000327544.6_Frame_Shift_Ins_p.K886fs|RGPD2_ENST00000494592.1_5'UTR			P0DJD1	RGPD2_HUMAN	RANBP2-like and GRIP domain containing 2	1629					protein targeting to Golgi (GO:0000042)					breast(1)|pancreas(1)	2						TCTGGTGTTTTAAATGTGTAGT	0.342																																					p.K1629_T1630delinsX		.											.	.	0			c.4885_4886insT						.																																			SO:0001589	frameshift_variant	729857	exon20			.		CCDS42710.1, CCDS42710.2	2p11.2	2013-01-10			ENSG00000185304	ENSG00000185304		"Tetratricopeptide (TTC) repeat domain containing"	32415	protein-coding gene	gene with protein product		612705				15710750, 15815621	Standard	NM_001078170		Approved	RGP2, RANBP2L2		P0DJD1	OTTHUMG00000153276	ENST00000398146.3:c.4885dupT	2.37:g.88081661_88081661dupA	ENSP00000381214:p.Lys1629fs	Somatic	417	0		WXS	Illumina HiSeq	Phase_I	532	88	NM_001078170	0	0	0	0	0	P0C839|Q68DN6|Q6V1X0	Nonsense_Mutation	INS	ENST00000398146.3	37	CCDS42710.2																																																																																			.		0.342	RGPD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330534.2	NM_001078170		A	88081659	-	A	88081658	7	5	61	1	0	1	1	0	0	0	0	0	13317	1763	61	0	5740	0	RGPD1	2	88081658	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	33956583	88081658	155117715	15	5893											
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109392304	109392304	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattctattaccaaatccatTagttcaccatctgtttcctc	10	16	3	12	0	3	0	1	0	2	0	6	1	5	0	4	0	1	2	4	0	4	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:109392304T>C	ENST00000283195.6	+	24	8535	c.8409T>C	c.(8407-8409)atT>atC	p.I2803I		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2803					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CCAAATCCATTAGTTCACCAT	0.363																																					p.I2803I		.											.	RANBP2-675	0			c.T8409C						.						130	130	130					2																	109392304		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon24			ATCCATTAGTTCA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.8409T>C	2.37:g.109392304T>C		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	113	46	NM_006267	0	0	27	44	17	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			.		0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109392304	T	C	109392304	2	2	61	1	0	0	0	0	0	0	0	1	13060	1742	61	3		3	RANBP2	2	109392304	Silent	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	21310646	109392304	133807069	16	5894											
TMEM87B	84910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	112863589	112863589	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctctcgtagccgaaggaatAaaattaagagcctcaaaatc	16	9	7	9	2	2	1	1	0	1	1	5	3	2	2	2	1	2	1	2	1	8	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:112863589A>G	ENST00000283206.4	+	16	1830	c.1461A>G	c.(1459-1461)atA>atG	p.I487M		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	487						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						CCGAAGGAATAAAATTAAGAG	0.284																																					p.I487M		.											.	TMEM87B-90	0			c.A1461G						.						136	144	142					2																	112863589		2203	4300	6503	SO:0001583	missense	84910	exon16			AGGAATAAAATTA	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.1461A>G	2.37:g.112863589A>G	ENSP00000283206:p.Ile487Met	Somatic	216	1		WXS	Illumina HiSeq	Phase_I	250	87	NM_032824	0	0	0	0	0	A8K2M9|Q1RLN2|Q53R54	Missense_Mutation	SNP	ENST00000283206.4	37	CCDS33275.1	.	.	.	.	.	.	.	.	.	.	A	1.631	-0.518867	0.04171	.	.	ENSG00000153214	ENST00000283206	.	.	.	5.36	5.36	0.76844	.	0.129072	0.64402	D	0.000002	T	0.26666	0.0652	N	0.11131	0.1	0.37625	D	0.92144	B	0.11235	0.004	B	0.10450	0.005	T	0.23013	-1.0200	9	0.02654	T	1	-18.044	7.9709	0.30127	0.9085:0.0:0.0915:0.0	.	487	Q96K49	TM87B_HUMAN	M	487	.	ENSP00000283206:I487M	I	+	3	3	TMEM87B	112580060	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.770000	0.38532	2.027000	0.59764	0.533000	0.62120	ATA	.		0.284	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		G	112863589	A	G	112863589	3	3	61	1	0	0	0	0	1	0	0	0	16243	352	13	3	1523	3	TMEM87B	2	112863589	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	3471285	112863589	130335784	17	5895											
ORC2L	4999	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	201790562	201790562	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctacttcatgttaccttCtttaaatttgtttactatcc	9	20	2	10	0	3	0	1	0	2	0	4	0	4	0	2	0	3	2	2	0	6	10			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:201790562C>A	ENST00000234296.2	-	13	1393	c.1144G>T	c.(1144-1146)Gaa>Taa	p.E382*	RN7SL694P_ENST00000584245.1_RNA	NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	382					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						ATGTTACCTTCTTTAAATTTG	0.308																																					p.E382X		.											.	ORC2-209	0			c.G1144T						.						139	133	135					2																	201790562		2203	4300	6503	SO:0001587	stop_gained	4999	exon13			TACCTTCTTTAAA		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1144G>T	2.37:g.201790562C>A	ENSP00000234296:p.Glu382*	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	168	49	NM_006190	0	0	0	0	0	Q13204|Q53TX5	Nonsense_Mutation	SNP	ENST00000234296.2	37	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	C	39	7.716939	0.98450	.	.	ENSG00000115942	ENST00000234296	.	.	.	5.34	5.34	0.76211	.	0.148032	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	19.3943	0.94601	0.0:1.0:0.0:0.0	.	.	.	.	X	382	.	ENSP00000234296:E382X	E	-	1	0	ORC2	201498807	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	3.237000	0.51344	2.671000	0.90904	0.585000	0.79938	GAA	.		0.308	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		A	201790562	C	A	201790562	4	1	61	1	0	0	0	0	0	1	0	0	11288	922	32	4	613	4	ORC2L	2	201790562	Nonsense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	88926973	201790562	41408811	18	5896											
KAT2B	8850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	20187858	20187858	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcacaaattcgaaaagtttaCcctggactttcatgttttaa	13	14	6	8	1	1	0	1	0	0	0	2	2	1	1	1	1	1	3	1	1	5	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:20187858C>T	ENST00000263754.4	+	14	2510	c.2055C>T	c.(2053-2055)taC>taT	p.Y685Y		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	685					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						GAAAAGTTTACCCTGGACTTT	0.333																																					p.Y685Y		.											.	KAT2B-228	0			c.C2055T						.						127	135	132					3																	20187858		2203	4300	6503	SO:0001819	synonymous_variant	8850	exon14			AGTTTACCCTGGA	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.2055C>T	3.37:g.20187858C>T		Somatic	209	0		WXS	Illumina HiSeq	Phase_I	146	70	NM_003884	0	0	5	29	24	Q6NSK1	Silent	SNP	ENST00000263754.4	37	CCDS2634.1																																																																																			.		0.333	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		T	20187858	C	T	20187858	2	4	61	1	0	0	0	0	0	0	0	1	8003	518	18	2		2	KAT2B	3	20187858	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		20187858	177834572	19	5897											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	47161751	47161757	+	Frame_Shift_Del	DEL	GCTGTGG	GCTGTGG	-																															cttggcacattccttccatcGctgtgggtccctgaagtcat																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	GCTGTGG	GCTGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:47161751_47161757delGCTGTGG	ENST00000409792.3	-	3	4411_4417	c.4369_4375delCCACAGC	c.(4369-4377)ccacagcgafs	p.PQR1457fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1457					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCCTTCCATCGCTGTGGGTCCCTGAAG	0.444			"N, F, S, Mis"		clear cell renal carcinoma																																p.1457_1459del		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.4369_4375del						.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4369_4375delCCACAGC	3.37:g.47161751_47161757delGCTGTGG	ENSP00000386759:p.Pro1457fs	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	92	40	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.444	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47161757	GCTGTGG	-	47161751	7	5	61	1	0	1	0	1	0	0	0	0	14163	1095	38	0	3395	0	SETD2	3	47161751	Frame_Shift_Del	DEL	GCTGTGG	TCGA-BQ-5877-01A-11D-1589-08	26973893	47161751	150860679	20	5898											
BAP1	8314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52439900	52439900	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgagacttgtgggtctgaAtcagctctggctgtgttact	6	15	12	8	0	3	2	1	2	2	1	3	3	3	2	0	2	2	3	0	2	2	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:52439900A>G	ENST00000460680.1	-	10	1283	c.812T>C	c.(811-813)aTt>aCt	p.I271T	BAP1_ENST00000296288.5_Missense_Mutation_p.I253T	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I271fs*61(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTGGGTCTGAATCAGCTCTGG	0.542			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.I271T	GBM(101;493 1458 7992 21037 25532)	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1-1032	1	Deletion - Frameshift(1)	eye(1)	c.T812C						.						67	68	68					3																	52439900		2203	4300	6503	SO:0001583	missense	8314	exon10			GTCTGAATCAGCT	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.812T>C	3.37:g.52439900A>G	ENSP00000417132:p.Ile271Thr	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	37	14	NM_004656	0	0	8	34	26	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.864400	0.51482	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.56275	0.47;0.49	5.35	5.35	0.76521	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.102540	0.64402	D	0.000002	T	0.46249	0.1383	L	0.54323	1.7	0.50813	D	0.999895	B	0.27068	0.167	B	0.16722	0.016	T	0.39722	-0.9600	10	0.15066	T	0.55	-9.2188	15.6343	0.76937	1.0:0.0:0.0:0.0	.	271	Q92560	BAP1_HUMAN	T	271;253	ENSP00000417132:I271T;ENSP00000296288:I253T	ENSP00000296288:I253T	I	-	2	0	BAP1	52414940	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.318000	0.72866	2.152000	0.67230	0.459000	0.35465	ATT	.		0.542	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			G	52439900	A	G	52439900	3	3	61	1	0	0	0	0	1	0	0	0	1312	101	4	3	1409	3	BAP1	3	52439900	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	5278149	52439900	145582530	21	5899											
CADM2	253559	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	86114798	86114799	+	Frame_Shift_Ins	INS	-	-	T																															atggccctgaccatgctctcINSataggaggaatagtggctgt																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:86114798_86114799insT	ENST00000407528.2	+	9	1169_1170	c.1107_1108insT	c.(1108-1110)atafs	p.I370fs	CADM2_ENST00000383699.3_Frame_Shift_Ins_p.I339fs|CADM2_ENST00000405615.2_Frame_Shift_Ins_p.I372fs	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	370					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		ACCATGCTCTCATAGGAGGAAT	0.406																																					p.L371fs		.											.	CADM2-228	0			c.1113_1114insT						.																																			SO:0001589	frameshift_variant	253559	exon9			.	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	29849	protein-coding gene	gene with protein product	"nectin-like 3"	609938	"immunoglobulin superfamily, member 4D"	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	Exception_encountered	3.37:g.86114798_86114799insT	ENSP00000384575:p.Ile370fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	62	28	NM_153184	0	0	0	0	0	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Frame_Shift_Ins	INS	ENST00000407528.2	37	CCDS54614.1																																																																																			.		0.406	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		T	86114799	-	T	86114798	7	5	61	1	0	1	1	0	0	0	0	0	2573	813	29	0	1212	0	CADM2	3	86114798	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	33674898	86114798	111907632	22	5900											
CCDC80	151887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	112324460	112324460	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaatcgtacacaatcaccAtggaccacattggggaagga	15	8	9	9	1	1	0	1	0	0	0	2	3	1	3	2	4	1	1	2	4	5	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:112324460A>T	ENST00000206423.3	-	8	3610	c.2657T>A	c.(2656-2658)aTg>aAg	p.M886K	CCDC80_ENST00000439685.2_Missense_Mutation_p.M886K	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	886					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						CACAATCACCATGGACCACAT	0.463																																					p.M886K		.											.	CCDC80-92	0			c.T2657A						.						122	101	108					3																	112324460		2203	4300	6503	SO:0001583	missense	151887	exon8			ATCACCATGGACC	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2657T>A	3.37:g.112324460A>T	ENSP00000206423:p.Met886Lys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	51	20	NM_199511	0	0	46	59	13	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	37	CCDS2968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.1|24.1	4.497724|4.497724	0.85069|0.85069	.|.	.|.	ENSG00000091986|ENSG00000091986	ENST00000461431|ENST00000206423;ENST00000439685;ENST00000444594;ENST00000479368	.|T;T;T	.|0.43688	.|0.94;0.94;0.94	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64918|0.64918	0.2642|0.2642	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	.|D;D	.|0.58268	.|0.978;0.982	.|D;D	.|0.77004	.|0.98;0.989	T|T	0.67856|0.67856	-0.5562|-0.5562	5|10	.|0.72032	.|D	.|0.01	-33.8731|-33.8731	16.1894|16.1894	0.81975|0.81975	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|897;886	.|Q76M96-2;Q76M96	.|.;CCD80_HUMAN	Q|K	256|886;886;487;164	.|ENSP00000206423:M886K;ENSP00000411814:M886K;ENSP00000418188:M164K	.|ENSP00000206423:M886K	H|M	-|-	3|2	2|0	CCDC80|CCDC80	113807150|113807150	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.287000|9.287000	0.95975|0.95975	2.222000|2.222000	0.72286|0.72286	0.477000|0.477000	0.44152|0.44152	CAT|ATG	.		0.463	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		T	112324460	A	T	112324460	3	4	61	1	0	0	0	0	1	0	0	0	2860	217	8	5	199	5	CCDC80	3	112324460	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	26209662	112324460	85697970	23	5901											
MCF2L2	23101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183013205	183013205	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttcatcagactcacttGcctcttgtgaaatatttcct	9	16	5	11	0	4	2	3	1	1	1	5	2	5	2	2	0	1	1	2	0	2	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:183013205G>A	ENST00000328913.3	-	13	1855	c.1558C>T	c.(1558-1560)Caa>Taa	p.Q520*	MCF2L2_ENST00000414362.2_Nonsense_Mutation_p.Q520*|MCF2L2_ENST00000473233.1_Nonsense_Mutation_p.Q520*|B3GNT5_ENST00000462559.1_Intron|MCF2L2_ENST00000447025.2_Nonsense_Mutation_p.Q520*	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	520							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AGACTCACTTGCCTCTTGTGA	0.468																																					p.Q520X		.											.	MCF2L2-293	0			c.C1558T						.						173	146	156					3																	183013205		2203	4300	6503	SO:0001587	stop_gained	23101	exon13			TCACTTGCCTCTT	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"Rho guanine nucleotide exchange factors"	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1558C>T	3.37:g.183013205G>A	ENSP00000328118:p.Gln520*	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	118	39	NM_015078	0	0	0	0	0	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Nonsense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	G	39	7.604425	0.98384	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362	.	.	.	4.82	4.82	0.62117	.	0.064498	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	18.1577	0.89699	0.0:0.0:1.0:0.0	.	.	.	.	X	520;520;520;56;520	.	ENSP00000328118:Q520X	Q	-	1	0	MCF2L2	184495899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.725000	0.68507	2.535000	0.85469	0.650000	0.86243	CAA	.		0.468	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		A	183013205	G	A	183013205	4	1	61	1	0	0	0	0	0	1	0	0	9405	1328	46	2	1858	2	MCF2L2	3	183013205	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	70688745	183013205	15009225	24	5902											
CLCN2	1181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	184071937	184071937	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtagggcagtttcttgattCggatgatgctgtcatagagg	8	13	15	5	1	2	3	1	2	1	1	3	4	2	4	0	4	1	4	0	4	2	5	rs199539697		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:184071937C>T	ENST00000265593.4	-	15	1844	c.1673G>A	c.(1672-1674)cGa>cAa	p.R558Q	CLCN2_ENST00000423355.2_3'UTR|CLCN2_ENST00000457512.1_Missense_Mutation_p.R558Q|CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000344937.7_Missense_Mutation_p.R541Q|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Missense_Mutation_p.R514Q	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	558					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	TTTCTTGATTCGGATGATGCT	0.632											OREG0015949	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0	0	5008	,	,		18861	0		0.001	False		,,,				2504	0				p.R558Q		.											.	CLCN2-90	0			c.G1673A						.						71	66	68					3																	184071937		2203	4300	6503	SO:0001583	missense	1181	exon15			TTGATTCGGATGA	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"Ion channels / Chloride channels : Voltage-sensitive"	2020	protein-coding gene	gene with protein product		600570	"chloride channel 2"			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.1673G>A	3.37:g.184071937C>T	ENSP00000265593:p.Arg558Gln	Somatic	66	0	1989	WXS	Illumina HiSeq	Phase_I	90	26	NM_004366	0	0	5	7	2	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	37	CCDS3263.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	16.38	3.108237	0.56291	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12	5.32	5.32	0.75619	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.91676	0.7369	L	0.28556	0.865	0.80722	D	1	D;D;D;D;P	0.65815	0.995;0.985;0.991;0.974;0.898	P;P;P;P;B	0.59056	0.714;0.447;0.851;0.447;0.369	D	0.88415	0.3024	10	0.11182	T	0.66	-1.4549	18.635	0.91374	0.0:1.0:0.0:0.0	.	514;558;541;558;514	E9PBD9;E9PCD2;P51788-3;P51788;B4DZ58	.;.;.;CLCN2_HUMAN;.	Q	558;541;514;558	ENSP00000265593:R558Q;ENSP00000345056:R541Q;ENSP00000400425:R514Q;ENSP00000391928:R558Q	ENSP00000265593:R558Q	R	-	2	0	CLCN2	185554631	0.998000	0.40836	0.996000	0.52242	0.995000	0.86356	3.905000	0.56333	2.494000	0.84150	0.563000	0.77884	CGA	C|1.000;T|0.000		0.632	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			T	184071937	C	T	184071937	3	4	61	1	0	0	0	0	1	0	0	0	3469	884	31	1	1063	1	CLCN2	3	184071937	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	1058732	184071937	13950493	25	5903											
TACC3	10460	hgsc.bcm.edu	37	chr4	1741486	1741486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaggtgtgaggagctccacGggaagaacctggaactgggg	10	5	18	8	1	0	2	0	1	0	1	1	5	1	5	2	6	3	2	2	6	3	0	rs148906614		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:1741486G>A	ENST00000313288.4	+	11	2105	c.1999G>A	c.(1999-2001)Ggg>Agg	p.G667R		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	667					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GGAGCTCCACGGGAAGAACCT	0.652																																					p.G667R	Ovarian(120;482 2294 11894 35824)	.											.	TACC3-91	0			c.G1999A						.	G	ARG/GLY	1,4379		0,1,2189	95	70	78		1999	0.3	0	4	dbSNP_134	78	1,8585		0,1,4292	yes	missense	TACC3	NM_006342.1	125	0,2,6481	AA,AG,GG		0.0116,0.0228,0.0154	benign	667/839	1741486	2,12964	2190	4293	6483	SO:0001583	missense	10460	exon11			CTCCACGGGAAGA	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.1999G>A	4.37:g.1741486G>A	ENSP00000326550:p.Gly667Arg	Somatic	7	1		WXS	Illumina HiSeq	Phase_I	12	6	NM_006342	0	0	21	36	15	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	.	.	.	.	.	.	.	.	.	.	G	5.473	0.272328	0.10349	2.28E-4	1.16E-4	ENSG00000013810	ENST00000313288	T	0.40225	1.04	4.17	0.332	0.15938	.	1.934300	0.02905	N	0.135884	T	0.15003	0.0362	N	0.01297	-0.9	0.09310	N	1	B;B	0.26081	0.002;0.141	B;B	0.17722	0.002;0.019	T	0.12167	-1.0558	10	0.15952	T	0.53	-3.4805	4.2667	0.10766	0.2974:0.3231:0.3795:0.0	.	667;667	Q2NKK4;Q9Y6A5	.;TACC3_HUMAN	R	667	ENSP00000326550:G667R	ENSP00000326550:G667R	G	+	1	0	TACC3	1711284	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.537000	0.06128	-0.081000	0.12662	-0.827000	0.03088	GGG	G|1.000;A|0.000		0.652	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			A	1741486	G	A	1741486	3	1	61	1	0	0	0	0	1	0	0	0	15535	1116	39	1	2037	1	TACC3	4	1741486	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		1741486	189412790	26	5904											
TRIM2	23321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	154249812	154249812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtggccgactggggaaacaGcaggatccaggtagatcaat	12	7	14	8	1	1	1	1	0	0	1	2	4	2	3	2	5	2	2	2	5	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:154249812G>A	ENST00000437508.2	+	11	2273	c.2072G>A	c.(2071-2073)aGc>aAc	p.S691N	TRIM2_ENST00000338700.5_Missense_Mutation_p.S718N	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	691					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TGGGGAAACAGCAGGATCCAG	0.418																																					p.S718N		.											.	TRIM2-650	0			c.G2153A						.						150	142	144					4																	154249812		2203	4300	6503	SO:0001583	missense	23321	exon11			GAAACAGCAGGAT	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.2072G>A	4.37:g.154249812G>A	ENSP00000415812:p.Ser691Asn	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	121	44	NM_015271	0	0	0	0	0	D3DP09|O60272|Q9BSI9|Q9UFZ1	Missense_Mutation	SNP	ENST00000437508.2	37	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.058382	0.76074	.	.	ENSG00000109654	ENST00000437508;ENST00000338700	T;T	0.71222	-0.55;-0.55	5.42	5.42	0.78866	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.69052	0.3068	N	0.10664	0.02	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.74023	0.982;0.982	T	0.65709	-0.6102	10	0.11485	T	0.65	-19.2289	19.2133	0.93766	0.0:0.0:1.0:0.0	.	718;691	D3DP09;Q9C040	.;TRIM2_HUMAN	N	691;718	ENSP00000415812:S691N;ENSP00000339659:S718N	ENSP00000339659:S718N	S	+	2	0	TRIM2	154469262	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.865000	0.99609	2.534000	0.85438	0.650000	0.86243	AGC	.		0.418	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			A	154249812	G	A	154249812	3	1	61	1	0	0	0	0	1	0	0	0	16527	971	34	2	2195	2	TRIM2	4	154249812	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	152508326	154249812	36904464	27	5905											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	187541245	187541245	+	Frame_Shift_Del	DEL	T	T	-																															atcggaacgataacttccgcTgaaaaggccgggttccctcc																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:187541245delT	ENST00000441802.2	-	10	6704	c.6495delA	c.(6493-6495)tcafs	p.S2165fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2165	Cadherin 19. {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						TAACTTCCGCTGAAAAGGCCG	0.423										HNSCC(5;0.00058)																											p.S2165fs	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.6495delA						.						59	58	59					4																	187541245		1894	4111	6005	SO:0001589	frameshift_variant	2195	exon10			.	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.6495delA	4.37:g.187541245delT	ENSP00000406229:p.Ser2165fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	79	26	NM_005245	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187541245	T	-	187541245	7	5	61	1	0	1	0	1	0	0	0	0	5708	1567	55	0	7343	0	FAT1	4	187541245	Frame_Shift_Del	DEL	T	TCGA-BQ-5877-01A-11D-1589-08	33291433	187541245	3613031	28	5906	68	3									
FAT1	2195	hgsc.bcm.edu;bcgsc.ca	37	chr4	187541246	187541246	+	Missense_Mutation	SNP	G	G	A																															tcggaacgataacttccgctGaaaaggccgggttccctcca																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:187541246G>A	ENST00000441802.2	-	10	6703	c.6494C>T	c.(6493-6495)tCa>tTa	p.S2165L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2165	Cadherin 19. {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						AACTTCCGCTGAAAAGGCCGG	0.423										HNSCC(5;0.00058)																											p.S2165L	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.C6494T						.						59	58	59					4																	187541246		1893	4111	6004	SO:0001583	missense	2195	exon10			TCCGCTGAAAAGG	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.6494C>T	4.37:g.187541246G>A	ENSP00000406229:p.Ser2165Leu	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	55	5	NM_005245	0	0	44	44	0		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.585000	0.46110	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.03553	3.89	5.05	5.05	0.67936	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.19927	0.0479	M	0.85099	2.735	0.80722	D	1	D	0.59767	0.986	D	0.63033	0.91	T	0.00679	-1.1613	10	0.44086	T	0.13	.	18.5902	0.91208	0.0:0.0:1.0:0.0	.	2165	Q14517	FAT1_HUMAN	L	2165;2167	ENSP00000406229:S2165L	ENSP00000260147:S2167L	S	-	2	0	FAT1	187778240	1.000000	0.71417	0.148000	0.22405	0.036000	0.12997	9.615000	0.98356	2.619000	0.88677	0.655000	0.94253	TCA	.		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187541246	G	A	187541246	3	1	61	1	0	0	0	0	1	0	0	0	5708	1294	45	2	7344	2	FAT1	4	187541246	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	1	187541246	3613030	29	5907	68	3									
FAT1	2195	hgsc.bcm.edu	37	chr4	187541250	187541250	+	Frame_Shift_Del	DEL	A	A	-																															aacgataacttccgctgaaaAggccgggttccctccatctt																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:187541250delA	ENST00000441802.2	-	10	6699	c.6490delT	c.(6490-6492)tttfs	p.F2164fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2164	Cadherin 19. {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						TCCGCTGAAAAGGCCGGGTTC	0.423										HNSCC(5;0.00058)																											p.F2164fs	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.6490delT						.						60	59	59					4																	187541250		1892	4111	6003	SO:0001589	frameshift_variant	2195	exon10			.	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.6490delT	4.37:g.187541250delA	ENSP00000406229:p.Phe2164fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	79	12	NM_005245	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187541250	A	-	187541250	7	5	61	1	0	1	0	1	0	0	0	0	5708	72	3	0	7348	0	FAT1	4	187541250	Frame_Shift_Del	DEL	A	TCGA-BQ-5877-01A-11D-1589-08	4	187541250	3613026	30	5908	68	3									
MAP1B	4131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	71479648	71479648	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttctgatgaagcagtcagcaCcgaggtaagcattcagctct	11	10	10	10	1	4	2	2	2	2	0	4	3	4	2	1	1	4	5	1	1	2	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:71479648C>A	ENST00000296755.7	+	3	663	c.365C>A	c.(364-366)aCc>aAc	p.T122N		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	122					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GCAGTCAGCACCGAGGTAAGC	0.527																																					p.T122N	Melanoma(17;367 822 11631 31730 47712)	.											.	MAP1B-155	0			c.C365A						.						129	124	126					5																	71479648		2203	4300	6503	SO:0001583	missense	4131	exon3			TCAGCACCGAGGT	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.365C>A	5.37:g.71479648C>A	ENSP00000296755:p.Thr122Asn	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	143	44	NM_005909	0	0	0	0	0	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.846103	0.71603	.	.	ENSG00000131711	ENST00000512974;ENST00000296755;ENST00000511641	T;T;T	0.19806	3.77;2.12;2.12	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000004	T	0.44435	0.1293	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28996	-1.0026	10	0.56958	D	0.05	-15.6336	18.9656	0.92695	0.0:1.0:0.0:0.0	.	122	P46821	MAP1B_HUMAN	N	122	ENSP00000426312:T122N;ENSP00000296755:T122N;ENSP00000423444:T122N	ENSP00000296755:T122N	T	+	2	0	MAP1B	71515404	1.000000	0.71417	0.983000	0.44433	0.241000	0.25554	7.301000	0.78850	2.543000	0.85770	0.637000	0.83480	ACC	.		0.527	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71479648	C	A	71479648	3	1	61	1	0	0	0	0	1	0	0	0	9253	507	18	4	375	4	MAP1B	5	71479648	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		71479648	109435612	31	5909											
RGNEF	64283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	73165934	73165934	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagtgacctcagcagtgaTgcccaggagtttgaagcaga	11	8	14	8	0	1	4	1	3	0	1	1	6	1	6	2	2	3	3	2	2	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:73165934T>A	ENST00000426542.2	+	20	2486	c.2466T>A	c.(2464-2466)gaT>gaA	p.D822E	ARHGEF28_ENST00000287898.5_Missense_Mutation_p.D822E|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.D822E|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.D822E|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.D822E|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.D509E|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.D822E			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	822					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TCAGCAGTGATGCCCAGGAGT	0.413																																					p.D822E		.											.	.	0			c.T2466A						.						196	184	188					5																	73165934		1924	4131	6055	SO:0001583	missense	64283	exon21			CAGTGATGCCCAG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2466T>A	5.37:g.73165934T>A	ENSP00000412175:p.Asp822Glu	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	185	67	NM_001080479	0	0	28	56	28	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.182575	0.38511	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.11821	2.92;2.91;2.91;2.8;2.91;2.91;2.74	5.95	-3.02	0.05446	.	.	.	.	.	T	0.10294	0.0252	L	0.55834	1.745	0.26232	N	0.979	B;B;B;B	0.26318	0.146;0.09;0.017;0.029	B;B;B;B	0.23852	0.036;0.047;0.049;0.045	T	0.35226	-0.9797	9	0.25106	T	0.35	.	4.0067	0.09605	0.1088:0.3977:0.1124:0.3811	.	509;822;822;822	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	E	822;822;822;822;822;822;509	ENSP00000296794:D822E;ENSP00000441913:D822E;ENSP00000441436:D822E;ENSP00000287898:D822E;ENSP00000411459:D822E;ENSP00000412175:D822E;ENSP00000296799:D509E	ENSP00000287898:D822E	D	+	3	2	RP11-428C6.1	73201690	0.517000	0.26226	0.967000	0.41034	0.996000	0.88848	-0.287000	0.08388	-0.749000	0.04747	-0.250000	0.11733	GAT	.		0.413	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73165934	T	A	73165934	3	1	61	1	0	0	0	0	1	0	0	0	13315	1461	51	5	2544	5	RGNEF	5	73165934	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	1686286	73165934	107749326	32	5910											
SNCAIP	9627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	121787084	121787084	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggactctccagcggaccTccacaagtaacgaatcgggg	11	5	12	13	3	1	0	0	0	1	0	4	3	2	2	3	4	2	2	3	4	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:121787084T>G	ENST00000261368.8	+	10	2804	c.2542T>G	c.(2542-2544)Tcc>Gcc	p.S848A	CTC-210G5.1_ENST00000505546.1_RNA|CTC-210G5.1_ENST00000506053.1_RNA|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000379538.3_Missense_Mutation_p.S482A|SNCAIP_ENST00000542191.1_Missense_Mutation_p.S406A|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000379533.2_Missense_Mutation_p.S895A|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000503116.2_3'UTR|SNCAIP_ENST00000261367.7_Missense_Mutation_p.S895A|SNCAIP_ENST00000414317.2_Missense_Mutation_p.S450A|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.S788A	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	848					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CCAGCGGACCTCCACAAGTAA	0.463																																					p.S848A		.											.	SNCAIP-92	0			c.T2542G						.						88	92	91					5																	121787084		2203	4300	6503	SO:0001583	missense	9627	exon10			CGGACCTCCACAA	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"Ankyrin repeat domain containing"	11139	protein-coding gene	gene with protein product	"synphilin"	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.2542T>G	5.37:g.121787084T>G	ENSP00000261368:p.Ser848Ala	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	96	31	NM_005460	0	0	2	2	0	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.252348	0.22880	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317	T;T;T;T;T;T;T;T	0.14266	4.35;4.88;2.57;2.52;4.88;4.81;2.52;4.56	5.69	2.03	0.26663	.	0.412591	0.28730	N	0.014337	T	0.08935	0.0221	L	0.36672	1.1	0.22737	N	0.998792	B;B;B;B;B;B;B;B	0.33777	0.3;0.048;0.252;0.264;0.425;0.264;0.264;0.104	B;B;B;B;B;B;B;B	0.31101	0.049;0.024;0.035;0.124;0.105;0.124;0.124;0.058	T	0.25257	-1.0137	10	0.31617	T	0.26	-3.6974	6.4307	0.21794	0.0:0.5607:0.0:0.4393	.	788;476;450;788;482;482;895;848	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	A	406;788;848;895;788;482;895;450	ENSP00000441681:S406A;ENSP00000422106:S788A;ENSP00000261368:S848A;ENSP00000368848:S895A;ENSP00000368851:S788A;ENSP00000368854:S482A;ENSP00000261367:S895A;ENSP00000394392:S450A	ENSP00000261367:S895A	S	+	1	0	SNCAIP	121814983	0.997000	0.39634	0.066000	0.19879	0.144000	0.21451	1.753000	0.38359	0.438000	0.26450	0.533000	0.62120	TCC	.		0.463	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			G	121787084	T	G	121787084	3	3	61	1	0	0	0	0	1	0	0	0	14873	1551	54	5	2576	5	SNCAIP	5	121787084	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	48621150	121787084	59128176	33	5911											
FAT2	2196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	150946163	150946163	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggtggcttcatagtccaagGgagcagctacagtgagcagc	10	8	14	9	0	1	1	1	1	0	0	2	2	2	2	1	3	5	4	1	3	3	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:150946163G>C	ENST00000261800.5	-	1	2342	c.2330C>G	c.(2329-2331)cCc>cGc	p.P777R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	777	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATAGTCCAAGGGAGCAGCTAC	0.498																																					p.P777R		.											.	FAT2-96	0			c.C2330G						.						60	60	60					5																	150946163		2203	4300	6503	SO:0001583	missense	2196	exon1			TCCAAGGGAGCAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2330C>G	5.37:g.150946163G>C	ENSP00000261800:p.Pro777Arg	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	69	25	NM_001447	0	0	0	0	0	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907163	0.52333	.	.	ENSG00000086570	ENST00000261800	T	0.54071	0.59	5.78	4.91	0.64330	Cadherin (4);Cadherin-like (1);	0.317848	0.27336	N	0.019825	T	0.64227	0.2579	M	0.76002	2.32	0.35862	D	0.827587	D	0.55172	0.97	P	0.57101	0.813	T	0.69771	-0.5055	10	0.21540	T	0.41	.	12.0874	0.53706	0.1385:0.0:0.8615:0.0	.	777	Q9NYQ8	FAT2_HUMAN	R	777	ENSP00000261800:P777R	ENSP00000261800:P777R	P	-	2	0	FAT2	150926356	1.000000	0.71417	0.369000	0.25952	0.700000	0.40528	6.639000	0.74314	1.580000	0.49851	0.655000	0.94253	CCC	.		0.498	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150946163	G	C	150946163	3	2	61	1	0	0	0	0	1	0	0	0	5709	1232	43	4	10811	4	FAT2	5	150946163	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	29159079	150946163	29969097	34	5912											
ATP6V0E1	8992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	172410944	172410944	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcttcttggtgccttggttCatccctaagggtcctaaccg	5	13	11	12	1	2	0	1	0	1	0	4	0	4	0	4	4	2	2	4	4	2	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:172410944C>T	ENST00000519374.1	+	1	185	c.81C>T	c.(79-81)ttC>ttT	p.F27F	ATP6V0E1_ENST00000265093.4_Silent_p.F27F|ATP6V0E1_ENST00000517669.1_Silent_p.F27F|ATP6V0E1_ENST00000519911.1_Silent_p.F27F	NM_003945.3	NP_003936.1	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1	27					ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|response to amino acid (GO:0043200)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			lung(2)	2	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGCCTTGGTTCATCCCTAAGG	0.647																																					p.F27F		.											.	ATP6V0E1-90	0			c.C81T						.						188	172	177					5																	172410944		2203	4300	6503	SO:0001819	synonymous_variant	8992	exon1			TTGGTTCATCCCT	Y15286	CCDS4383.1	5q35.2	2010-04-21	2006-10-12	2006-10-12	ENSG00000113732	ENSG00000113732		"ATPases / V-type"	863	protein-coding gene	gene with protein product		603931	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 9kD", "ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e"	ATP6H, ATP6V0E		9556572, 14970230	Standard	NM_003945		Approved	M9.2	uc003mcd.1	O15342	OTTHUMG00000130518	ENST00000519374.1:c.81C>T	5.37:g.172410944C>T		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	261	93	NM_003945	0	0	233	388	155	B2R557|D3DQM1|Q6IBE8	Silent	SNP	ENST00000519374.1	37	CCDS4383.1																																																																																			.		0.647	ATP6V0E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252935.2	NM_003945		T	172410944	C	T	172410944	2	4	61	1	0	0	0	0	0	0	0	1	1176	825	29	2		2	ATP6V0E1	5	172410944	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	21464781	172410944	8504316	35	5913											
DSP	1832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	7562980	7562980	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaactccatcggcgactaTcgctggcagctggacaaaat	12	7	9	13	3	0	0	0	0	0	0	3	2	1	1	1	3	2	3	1	3	4	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:7562980T>A	ENST00000379802.3	+	5	1034	c.693T>A	c.(691-693)taT>taA	p.Y231*	DSP_ENST00000418664.2_Nonsense_Mutation_p.Y231*	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	231	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TCGGCGACTATCGCTGGCAGC	0.522																																					p.Y231X		.											.	DSP-518	0			c.T693A						.						119	121	120					6																	7562980		2203	4300	6503	SO:0001587	stop_gained	1832	exon5			CGACTATCGCTGG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.693T>A	6.37:g.7562980T>A	ENSP00000369129:p.Tyr231*	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	117	82	NM_004415	0	0	1	2	1	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Nonsense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	39	7.901730	0.98551	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	.	.	.	5.76	-1.12	0.09808	.	0.000000	0.53938	D	0.000046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	11.7621	0.51910	0.0:0.2532:0.0:0.7468	.	.	.	.	X	231;231;36	.	ENSP00000369129:Y231X	Y	+	3	2	DSP	7507979	0.948000	0.32251	0.998000	0.56505	0.948000	0.59901	0.032000	0.13732	-0.099000	0.12263	0.533000	0.62120	TAT	.		0.522	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7562980	T	A	7562980	4	1	61	1	0	0	0	0	0	1	0	0	4792	1442	50	5	711	5	DSP	6	7562980	Nonsense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		7562980	163552087	36	5914											
HCRTR2	3062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	55142265	55142265	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggacagccaacgaagTcccggatgagcgctgtggcg	9	4	16	12	4	0	1	0	1	0	0	1	4	1	3	3	4	3	1	3	4	2	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:55142265T>C	ENST00000370862.3	+	5	1186	c.850T>C	c.(850-852)Tcc>Ccc	p.S284P		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	284					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)			breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GCCAACGAAGTCCCGGATGAG	0.507																																					p.S284P		.											.	HCRTR2-525	0			c.T850C						.						70	74	73					6																	55142265		2203	4300	6503	SO:0001583	missense	3062	exon5			ACGAAGTCCCGGA	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.850T>C	6.37:g.55142265T>C	ENSP00000359899:p.Ser284Pro	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	75	28	NM_001526	0	0	0	0	0	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	37	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	T	9.734	1.163040	0.21538	.	.	ENSG00000137252	ENST00000370862	T	0.63580	-0.05	5.84	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	0.177378	0.51477	D	0.000100	T	0.28896	0.0717	L	0.44542	1.39	0.33540	D	0.594739	B	0.02656	0.0	B	0.08055	0.003	T	0.04607	-1.0939	10	0.25751	T	0.34	.	8.2143	0.31503	0.0:0.0661:0.262:0.6719	.	284	O43614	OX2R_HUMAN	P	284	ENSP00000359899:S284P	ENSP00000359899:S284P	S	+	1	0	HCRTR2	55250224	1.000000	0.71417	0.999000	0.59377	0.622000	0.37654	2.200000	0.42724	0.123000	0.18342	0.528000	0.53228	TCC	.		0.507	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			C	55142265	T	C	55142265	3	2	61	1	0	0	0	0	1	0	0	0	7023	1667	58	3	868	3	HCRTR2	6	55142265	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	47579285	55142265	115972802	37	5915											
AMD1	262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	111213388	111213388	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcagcatattgtatgggacGtatgaattctgactgttggt	10	14	12	5	1	1	2	0	2	1	0	1	3	1	3	0	2	2	5	0	2	4	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:111213388G>A	ENST00000368885.3	+	5	788	c.452G>A	c.(451-453)cGt>cAt	p.R151H	AMD1_ENST00000368877.5_Missense_Mutation_p.R122H|AMD1_ENST00000368876.1_Missense_Mutation_p.R82H|AMD1_ENST00000368882.3_Missense_Mutation_p.R3H|AMD1_ENST00000451850.2_Intron	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	151					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	TGTATGGGACGTATGAATTCT	0.333																																					p.R151H		.											.	AMD1-91	0			c.G452A						.						316	293	301					6																	111213388		2203	4300	6503	SO:0001583	missense	262	exon5			TGGGACGTATGAA	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.452G>A	6.37:g.111213388G>A	ENSP00000357880:p.Arg151His	Somatic	358	0		WXS	Illumina HiSeq	Phase_I	392	130	NM_001634	0	0	17	35	18	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Missense_Mutation	SNP	ENST00000368885.3	37	CCDS5086.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816905	0.50633	.	.	ENSG00000123505	ENST00000368885;ENST00000368882;ENST00000368877;ENST00000368876	.	.	.	5.3	4.43	0.53597	S-adenosylmethionine decarboxylase, core (2);	0.108147	0.64402	D	0.000006	T	0.26011	0.0634	N	0.20304	0.555	0.58432	D	0.999999	B;B	0.24721	0.038;0.11	B;B	0.21546	0.007;0.035	T	0.13019	-1.0525	9	0.46703	T	0.11	.	12.2225	0.54441	0.0796:0.0:0.9204:0.0	.	122;151	A6NNH3;P17707	.;DCAM_HUMAN	H	151;3;122;82	.	ENSP00000357870:R82H	R	+	2	0	AMD1	111320081	1.000000	0.71417	0.985000	0.45067	0.991000	0.79684	7.503000	0.81632	1.237000	0.43756	0.491000	0.48974	CGT	.		0.333	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			A	111213388	G	A	111213388	3	1	61	1	0	0	0	0	1	0	0	0	566	1145	40	1	470	1	AMD1	6	111213388	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	56071123	111213388	59901679	38	5916											
FAM54A	113115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	136562761	136562761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acagtggatcccgaactagtCgcaaaggatgaaaaatttcc	15	8	9	9	2	0	1	0	1	0	0	3	4	2	3	2	2	1	1	2	2	5	2	rs150447506		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:136562761C>T	ENST00000420702.1	-	5	724	c.335G>A	c.(334-336)cGa>cAa	p.R112Q	MTFR2_ENST00000451457.2_Missense_Mutation_p.R112Q	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	112					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CCGAACTAGTCGCAAAGGATG	0.368																																					p.R112Q		.											.	.	0			c.G335A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	103	98	100		335,335	0.4	0	6	dbSNP_134	100	0,8600		0,0,4300	no	missense,missense	FAM54A	NM_001099286.1,NM_138419.3	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	112/386,112/386	136562761	1,13005	2203	4300	6503	SO:0001583	missense	113115	exon5			ACTAGTCGCAAAG	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"DUF729 domain containing 1", "family with sequence similarity 54, member A"	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.335G>A	6.37:g.136562761C>T	ENSP00000395232:p.Arg112Gln	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	108	26	NM_138419	0	0	3	3	0	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	37	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	C	7.761	0.705340	0.15172	2.27E-4	0.0	ENSG00000146410	ENST00000451457;ENST00000420702;ENST00000418509	T;T;T	0.40225	1.04;1.04;1.04	5.59	0.386	0.16254	.	1.138940	0.06310	N	0.702535	T	0.04543	0.0124	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	10	0.12103	T	0.63	-2.0017	7.6241	0.28202	0.0:0.1662:0.5365:0.2973	.	112	Q6P444	FA54A_HUMAN	Q	112;112;69	ENSP00000407010:R112Q;ENSP00000395232:R112Q;ENSP00000410861:R69Q	ENSP00000410861:R69Q	R	-	2	0	FAM54A	136604454	0.001000	0.12720	0.029000	0.17559	0.165000	0.22458	0.681000	0.25320	0.072000	0.16694	-1.673000	0.00743	CGA	C|1.000;T|0.000		0.368	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		T	136562761	C	T	136562761	3	4	61	1	0	0	0	0	1	0	0	0	5601	884	31	1	838	1	FAM54A	6	136562761	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	25349373	136562761	34552306	39	5917											
POU6F2	11281	hgsc.bcm.edu	37	chr7	39379265	39379265	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatccctgaactcccagcTccagcagctccagctccagc	8	7	6	20	0	1	1	1	1	0	0	6	1	6	1	5	0	6	4	5	0	1	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr7:39379265T>C	ENST00000403058.1	+	6	690	c.536T>C	c.(535-537)cTc>cCc	p.L179P	POU6F2_ENST00000518318.2_Missense_Mutation_p.L179P|POU6F2_ENST00000559001.1_Missense_Mutation_p.L171P|POU6F2_ENST00000517348.1_3'UTR	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	179	Gln-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						AACTCCCAGCTCcagcagctc	0.597																																					p.L179P		.											.	POU6F2-90	0			c.T536C						.						23	22	22					7																	39379265		2157	4246	6403	SO:0001583	missense	11281	exon6			CCCAGCTCCAGCA	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.536T>C	7.37:g.39379265T>C	ENSP00000384004:p.Leu179Pro	Somatic	37	1		WXS	Illumina HiSeq	Phase_I	40	2	NM_007252	0	0	0	0	0	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	T	15.61	2.885697	0.51908	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.87966	0.92;-2.32	4.81	4.81	0.61882	.	0.558894	0.15782	U	0.244891	D	0.90995	0.7168	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.995	D	0.90270	0.4307	10	0.49607	T	0.09	.	14.3463	0.66665	0.0:0.0:0.0:1.0	.	179;179	P78424-2;P78424	.;PO6F2_HUMAN	P	179	ENSP00000384004:L179P;ENSP00000430514:L179P	ENSP00000384004:L179P	L	+	2	0	POU6F2	39345790	1.000000	0.71417	0.912000	0.35992	0.996000	0.88848	6.212000	0.72188	1.785000	0.52413	0.455000	0.32223	CTC	.		0.597	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		C	39379265	T	C	39379265	3	2	61	1	0	0	0	0	1	0	0	0	12311	1551	54	3	554	3	POU6F2	7	39379265	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		39379265	119759398	40	5918											
ABCA13	154664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48284203	48284203	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtggaaattgcaaagcttGctgcaaaacctgccccagtg	11	9	10	11	0	0	0	0	0	0	0	0	1	0	1	3	1	6	4	3	1	4	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr7:48284203G>A	ENST00000435803.1	+	11	1317	c.1293G>A	c.(1291-1293)ttG>ttA	p.L431L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	431					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGCAAAGCTTGCTGCAAAACC	0.388																																					p.L431L		.											.	ABCA13-521	0			c.G1293A						.						58	57	57					7																	48284203		1824	4082	5906	SO:0001819	synonymous_variant	154664	exon11			AAGCTTGCTGCAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.1293G>A	7.37:g.48284203G>A		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	54	21	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.		0.388	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48284203	G	A	48284203	2	1	61	1	0	0	0	0	0	0	0	1	31	1310	46	2		2	ABCA13	7	48284203	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	8904938	48284203	110854460	41	5919											
CTAGE6P	340307	hgsc.bcm.edu	37	chr7	143454218	143454218	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgagggattttgactcatcTtctagagactgtatactttt	9	18	8	6	0	3	3	1	2	2	1	3	5	3	4	0	1	1	1	0	1	3	9			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr7:143454218T>G	ENST00000470691.2	-	1	571	c.534A>C	c.(532-534)gaA>gaC	p.E178D	RNU6-267P_ENST00000516714.1_RNA	NM_178561.4	NP_848656.2	Q86UF2	CTGE6_HUMAN	CTAGE family, member 6	178						integral component of membrane (GO:0016021)						Melanoma(164;0.0903)					TTGACTCATCTTCTAGAGACT	0.338																																					p.E178D		.											.	.	0			c.A534C						.						1	1	1					7																	143454218		5	6	11	SO:0001583	missense	340307	exon1			CTCATCTTCTAGA	BC043153	CCDS64790.1	7q35	2013-05-22	2013-02-25	2013-02-25	ENSG00000271321	ENSG00000271321			28644	protein-coding gene	gene with protein product			"CTAGE family, member 6, pseudogene"	CTAGE6P		12477932	Standard	NM_178561		Approved	MGC41943	uc003wdk.4	Q86UF2	OTTHUMG00000157770	ENST00000470691.2:c.534A>C	7.37:g.143454218T>G	ENSP00000474388:p.Glu178Asp	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	215	17	NM_178561	0	0	18	18	0	A4FU29|Q3ZCM5	Missense_Mutation	SNP	ENST00000470691.2	37																																																																																				.		0.338	CTAGE6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349580.2	NM_178561		G	143454218	T	G	143454218	3	3	61	1	0	0	0	0	1	0	0	0	4001	1606	56	5	1803	5	CTAGE6P	7	143454218	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	95170015	143454218	15684445	42	5920											
EBF2	64641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	25766046	25766046	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaaacaattctgattgcActtgaggaaaaattttaaaa	17	14	5	5	0	2	2	1	2	1	0	2	3	2	3	0	1	2	1	0	1	6	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:25766046A>C	ENST00000520164.1	-	7	1114	c.577T>G	c.(577-579)Tgc>Ggc	p.C193G	EBF2_ENST00000408929.3_Missense_Mutation_p.C45G	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	193					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		TTCTGATTGCACTTGAGGAAA	0.373																																					p.C193G	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	.											.	EBF2-26	0			c.T577G						.						73	71	72					8																	25766046		1820	4100	5920	SO:0001583	missense	64641	exon7			GATTGCACTTGAG	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.577T>G	8.37:g.25766046A>C	ENSP00000430241:p.Cys193Gly	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	65	23	NM_022659	0	0	0	0	0	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.770471	0.69992	.	.	ENSG00000221818	ENST00000520164;ENST00000408929	T;T	0.52057	0.69;0.68	5.77	5.77	0.91146	.	0.000000	0.85682	U	0.000000	T	0.69984	0.3172	M	0.80183	2.485	0.80722	D	1	D	0.71674	0.998	D	0.67231	0.95	T	0.74621	-0.3604	10	0.87932	D	0	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	193	Q9HAK2	COE2_HUMAN	G	193;45	ENSP00000430241:C193G;ENSP00000386178:C45G	ENSP00000386178:C45G	C	-	1	0	EBF2	25821963	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.287000	0.95975	2.326000	0.78906	0.533000	0.62120	TGC	.		0.373	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		C	25766046	A	C	25766046	3	2	61	1	0	0	0	0	1	0	0	0	4892	159	6	5	1190	5	EBF2	8	25766046	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08		25766046	120597976	43	5921											
XKR4	114786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	56015502	56015504	+	In_Frame_Del	DEL	GTG	GTG	-																															tcgggctcacgctcttcttcGtggtgctcggctctctgtcg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:56015502_56015504delGTG	ENST00000327381.6	+	1	554_556	c.454_456delGTG	c.(454-456)gtgdel	p.V153del		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	153						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)			GCTCTTCTTCGTGGTGCTCGGCT	0.655																																					p.152_152del		.											.	XKR4-92	0			c.454_456del						.																																			SO:0001651	inframe_deletion	114786	exon1			.	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.454_456delGTG	8.37:g.56015505_56015507delGTG	ENSP00000328326:p.Val153del	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	80	22	NM_052898	0	0	0	0	0	Q96PZ8	In_Frame_Del	DEL	ENST00000327381.6	37	CCDS34893.1																																																																																			.		0.655	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		-	56015504	GTG	-	56015502	7	5	61	1	0	1	0	1	0	0	0	0	17466	1145	40	0	456	0	XKR4	8	56015502	In_Frame_Del	DEL	GTG	TCGA-BQ-5877-01A-11D-1589-08	30249456	56015502	90348520	44	5922											
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81431606	81431606	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccaggagggcaagaaggtgTagatcagggacaggatacag	14	4	17	6	0	1	2	1	0	0	2	1	5	1	5	1	5	1	2	1	5	4	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:81431606T>C	ENST00000430430.1	+	7	3238	c.2459T>C	c.(2458-2460)gTa>gCa	p.V820A	ZBTB10_ENST00000379091.4_Missense_Mutation_p.V528A|ZBTB10_ENST00000426744.2_Missense_Mutation_p.V796A|ZBTB10_ENST00000455036.3_Missense_Mutation_p.V820A	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	820					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)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			CAAGAAGGTGTAGATCAGGGA	0.453																																					p.V820A		.											.	ZBTB10-522	0			c.T2459C						.						103	100	101					8																	81431606		1932	4142	6074	SO:0001583	missense	65986	exon6			AAGGTGTAGATCA	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.2459T>C	8.37:g.81431606T>C	ENSP00000387462:p.Val820Ala	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_001105539	0	0	23	23	0	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Missense_Mutation	SNP	ENST00000430430.1	37	CCDS47880.1	.	.	.	.	.	.	.	.	.	.	T	4.550	0.102223	0.08731	.	.	ENSG00000205189	ENST00000379091;ENST00000430430;ENST00000455036;ENST00000426744;ENST00000519370	T;T	0.09445	2.98;2.98	5.54	5.54	0.83059	.	0.615543	0.16142	N	0.227662	T	0.07007	0.0178	N	0.14661	0.345	0.26201	N	0.979445	B;B;B;B	0.15473	0.0;0.0;0.013;0.001	B;B;B;B	0.10450	0.001;0.001;0.004;0.005	T	0.30995	-0.9959	10	0.25751	T	0.34	.	10.3859	0.44140	0.0:0.0827:0.0:0.9173	.	674;820;796;528	A8E4L4;Q96DT7;Q96DT7-2;Q96DT7-4	.;ZBT10_HUMAN;.;.	A	528;820;796;820;646	ENSP00000368384:V528A;ENSP00000387462:V820A	ENSP00000368384:V528A	V	+	2	0	ZBTB10	81594161	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.649000	0.37281	2.107000	0.64212	0.482000	0.46254	GTA	.		0.453	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		C	81431606	T	C	81431606	3	2	61	1	0	0	0	0	1	0	0	0	17555	1638	57	3	2481	3	ZBTB10	8	81431606	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	25416104	81431606	64932416	45	5923											
TG	7038	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	133898849	133898849	+	Frame_Shift_Del	DEL	C	C	-																															tgccacatcctgcccacccaCgatcaaggagctctttgtgg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:133898849delC	ENST00000220616.4	+	9	1272	c.1232delC	c.(1231-1233)acgfs	p.T411fs	TG_ENST00000377869.1_Frame_Shift_Del_p.T411fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	411					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TGCCCACCCACGATCAAGGAG	0.537																																					p.T411fs		.											.	TG-145	0			c.1232delC						.						144	152	150					8																	133898849		2203	4300	6503	SO:0001589	frameshift_variant	7038	exon9			.	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1232delC	8.37:g.133898849delC	ENSP00000220616:p.Thr411fs	Somatic	258	0		WXS	Illumina HiSeq	Phase_I	368	113	NM_003235	0	0	0	0	0	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Frame_Shift_Del	DEL	ENST00000220616.4	37	CCDS34944.1																																																																																			.		0.537	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		-	133898849	C	-	133898849	7	5	61	1	0	1	0	1	0	0	0	0	15845	536	19	0	1266	0	TG	8	133898849	Frame_Shift_Del	DEL	C	TCGA-BQ-5877-01A-11D-1589-08	52467243	133898849	12465173	46	5924											
NAPRT1	1936	hgsc.bcm.edu	37	chr8	144658981	144658981	+	IGR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctttggccgccaggtccaccCcagggccctcaccagctgct	5	7	10	19	1	1	0	1	0	0	0	2	0	2	0	7	3	2	2	7	3	0	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:144658981C>A	ENST00000529272.1	-	0	1311				RP11-661A12.7_ENST00000529247.1_RNA|NAPRT1_ENST00000449291.2_Missense_Mutation_p.G239V|NAPRT1_ENST00000435154.3_Missense_Mutation_p.G239V|NAPRT1_ENST00000276844.7_Missense_Mutation_p.G239V|NAPRT1_ENST00000460623.1_5'Flank|NAPRT1_ENST00000426292.3_Missense_Mutation_p.G239V|RP11-661A12.9_ENST00000531730.1_RNA			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CAGGTCCACCCCAGGGCCCTC	0.672																																					p.G239V		.											.	NAPRT1-91	0			c.G716T						.						10	13	12					8																	144658981		2168	4249	6417	SO:0001628	intergenic_variant	93100	exon6			TCCACCCCAGGGC	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191		8.37:g.144658981C>A		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	30	7	NM_145201	0	0	9	36	27	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	C	8.836	0.941072	0.18281	.	.	ENSG00000147813	ENST00000435154;ENST00000449291;ENST00000340490;ENST00000426292;ENST00000276844	T;T;T;T;T	0.43688	0.98;0.99;0.94;0.98;0.98	4.42	-8.84	0.00803	Quinolinate phosphoribosyl transferase, C-terminal (1);	1.965940	0.02914	N	0.137039	T	0.20007	0.0481	N	0.08118	0	0.09310	N	1	B;B;B;B	0.23249	0.049;0.01;0.082;0.029	B;B;B;B	0.18871	0.01;0.01;0.023;0.01	T	0.13710	-1.0499	10	0.25106	T	0.35	-1.437	9.7047	0.40209	0.0:0.2126:0.439:0.3484	.	239;239;239;239	C9J8U2;G5E977;Q6XQN6-3;Q6XQN6	.;.;.;PNCB_HUMAN	V	239	ENSP00000405670:G239V;ENSP00000401508:G239V;ENSP00000341136:G239V;ENSP00000390949:G239V;ENSP00000276844:G239V	ENSP00000276844:G239V	G	-	2	0	NAPRT1	144730124	0.000000	0.05858	0.000000	0.03702	0.204000	0.24138	-5.716000	0.00102	-2.660000	0.00419	-0.119000	0.15052	GGG	.		0.672	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		A	144658981	C	A	144658981	1	1	61	0	1	0	0	0	0	0	0	0	10190	623	22	4		4	NAPRT1	8	144658981	IGR	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	10760132	144658981	1705041	47	5925											
KIAA1797	54914	bcgsc.ca	37	chr9	20758140	20758140	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaacacagacctgattgctgGccagtgtttttgcagcagct	9	11	11	10	0	0	2	0	1	0	1	0	3	0	2	2	1	5	5	2	1	1	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr9:20758140G>A	ENST00000380249.1	+	8	808	c.444G>A	c.(442-444)tgG>tgA	p.W148*	FOCAD_ENST00000338382.6_Nonsense_Mutation_p.W148*	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	148						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CTGATTGCTGGCCAGTGTTTT	0.413																																					p.W148X													.	.	0			c.G444A						.						106	95	99					9																	20758140		2203	4300	6503	SO:0001587	stop_gained	54914	exon8			TTGCTGGCCAGTG	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.444G>A	9.37:g.20758140G>A	ENSP00000369599:p.Trp148*	Somatic	90	0		WXS	Illumina HiSeq	Phase_1	106	5	NM_017794	0	0	5	5	0	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Nonsense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	40	8.252373	0.98727	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1331	16.8915	0.86088	0.0:0.0:1.0:0.0	.	.	.	.	X	148	.	ENSP00000344307:W148X	W	+	3	0	KIAA1797	20748140	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.575000	0.74018	2.521000	0.84997	0.555000	0.69702	TGG	.		0.413	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20758140	G	A	20758140	4	1	61	1	0	0	0	0	0	1	0	0	8279	1212	42	2	462	2	KIAA1797	9	20758140	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		20758140	120455291	48	5926											
SPINK4	27290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	33246702	33246702	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggctcacatatacgaatgAatgccagctctgcttggccc	9	10	10	12	1	2	1	1	1	1	0	2	2	2	1	2	2	4	3	2	2	4	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr9:33246702A>G	ENST00000379721.3	+	3	236	c.191A>G	c.(190-192)gAa>gGa	p.E64G	SPINK4_ENST00000379723.1_Missense_Mutation_p.E87G|SPINK4_ENST00000379725.1_Missense_Mutation_p.E87G	NM_014471.1	NP_055286.1	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	64	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				response to drug (GO:0042493)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			TATACGAATGAATGCCAGCTC	0.552																																					p.E64G		.											.	SPINK4-90	0			c.A191G						.						173	145	154					9																	33246702		2203	4300	6503	SO:0001583	missense	27290	exon3			CGAATGAATGCCA	AF048700	CCDS6536.1	9p13.3	2011-08-31	2005-08-17		ENSG00000122711	ENSG00000122711		"Serine peptidase inhibitors, Kazal type"	16646	protein-coding gene	gene with protein product		613929	"serine protease inhibitor, Kazal type 4"			1400298, 17333166	Standard	NM_014471		Approved	PEC-60, MGC133107	uc003zsh.3	O60575	OTTHUMG00000019762	ENST00000379721.3:c.191A>G	9.37:g.33246702A>G	ENSP00000369045:p.Glu64Gly	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	128	39	NM_014471	0	0	0	0	0	Q2YDT7	Missense_Mutation	SNP	ENST00000379721.3	37	CCDS6536.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.738172	0.49045	.	.	ENSG00000122711	ENST00000379725;ENST00000379723;ENST00000379721	T;T;T	0.79554	-1.28;-1.28;-1.28	4.81	4.81	0.61882	Proteinase inhibitor I1, Kazal (3);	0.000000	0.64402	D	0.000001	D	0.86698	0.5995	.	.	.	0.46564	D	0.999105	D	0.58620	0.983	P	0.60473	0.875	D	0.88001	0.2756	9	0.87932	D	0	-33.3681	10.9375	0.47253	1.0:0.0:0.0:0.0	.	64	O60575	ISK4_HUMAN	G	87;87;64	ENSP00000369048:E87G;ENSP00000369046:E87G;ENSP00000369045:E64G	ENSP00000369045:E64G	E	+	2	0	SPINK4	33236702	1.000000	0.71417	0.995000	0.50966	0.167000	0.22549	4.175000	0.58263	2.165000	0.68154	0.379000	0.24179	GAA	.		0.552	SPINK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052035.1	NM_014471		G	33246702	A	G	33246702	3	3	61	1	0	0	0	0	1	0	0	0	15093	246	9	3	201	3	SPINK4	9	33246702	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	12488562	33246702	107966729	49	5927											
PCDH15	65217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	55626411	55626411	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatctacttacgagtacatcGgctttgccgctcagtccctt	7	14	7	13	3	2	0	1	0	1	0	4	1	3	0	2	1	4	3	2	1	4	6	rs374185988		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:55626411G>A	ENST00000320301.6	-	27	4102	c.3708C>T	c.(3706-3708)gcC>gcT	p.A1236A	PCDH15_ENST00000361849.3_Silent_p.A1236A|PCDH15_ENST00000373965.2_Silent_p.A1243A|PCDH15_ENST00000395438.1_Silent_p.A1236A|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000437009.1_Silent_p.A1165A|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Silent_p.A847A|PCDH15_ENST00000395445.1_Silent_p.A1243A|PCDH15_ENST00000395432.2_Silent_p.A1199A|PCDH15_ENST00000414778.1_Silent_p.A1241A|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395430.1_Silent_p.A1236A|PCDH15_ENST00000395433.1_Silent_p.A1214A|PCDH15_ENST00000395442.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1236	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CGAGTACATCGGCTTTGCCGC	0.383										HNSCC(58;0.16)																											p.A1241A		.											.	PCDH15-193	0			c.C3723T						.	G	,,,,,,,,,,,	0,4406		0,0,2203	94	81	86		3723,3708,3495,3708,3597,3642,3744,3708,3723,3708,3642,3708	-2.8	1	10		86	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,,,,,,,,,	1241/1963,1236/1958,1165/1887,1236/1953,1199/1916,1214/1936,1248/1791,1236/1540,1241/1683,1236/1678,1214/1933,1236/1956	55626411	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65217	exon28			TACATCGGCTTTG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3708C>T	10.37:g.55626411G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	118	31	NM_001142763	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55626411	G	A	55626411	2	1	61	1	0	0	0	0	0	0	0	1	11537	1103	39	1		1	PCDH15	10	55626411	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		55626411	79908336	50	5928											
TTC18	118491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	75037057	75037057	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catgaagatggtggtagtttGagaaacaccataatgaaggc	15	9	12	5	0	0	4	0	3	0	2	0	5	0	4	1	3	1	2	1	3	5	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:75037057G>A	ENST00000310715.3	-	22	2791	c.2671C>T	c.(2671-2673)Caa>Taa	p.Q891*	TTC18_ENST00000394865.1_Nonsense_Mutation_p.Q891*|TTC18_ENST00000401621.2_Nonsense_Mutation_p.Q891*|TTC18_ENST00000493787.1_Intron|TTC18_ENST00000355577.3_Nonsense_Mutation_p.Q360*|RNU6-833P_ENST00000363486.1_RNA|TTC18_ENST00000340329.3_Intron|DNAJC9-AS1_ENST00000440197.2_RNA	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		891						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					GTGGTAGTTTGAGAAACACCA	0.378																																					p.Q891X		.											.	TTC18-92	0			c.C2671T						.						127	123	124					10																	75037057		2203	4300	6503	SO:0001587	stop_gained	118491	exon22			TAGTTTGAGAAAC																												ENST00000310715.3:c.2671C>T	10.37:g.75037057G>A	ENSP00000310829:p.Gln891*	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	195	64	NM_145170	0	0	5	5	0	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Nonsense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	G	39	7.846379	0.98522	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	.	.	.	5.62	4.66	0.58398	.	0.570630	0.17764	N	0.162782	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	1.6662	11.0106	0.47661	0.0:0.0:0.8145:0.1855	.	.	.	.	X	891;891;891;298;891	.	ENSP00000310829:Q891X	Q	-	1	0	TTC18	74707063	0.996000	0.38824	0.998000	0.56505	0.827000	0.46813	3.669000	0.54561	2.642000	0.89623	0.655000	0.94253	CAA	.		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	75037057	G	A	75037057	4	1	61	1	0	0	0	0	0	1	0	0	16718	1299	45	2	722	2	TTC18	10	75037057	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	19410646	75037057	60497690	51	5929											
TTC18	118491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	75104981	75104981	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taaaggctctgccactaataCtttaacttcaagactgcact	13	12	5	11	0	2	1	1	0	1	1	2	1	2	1	1	1	4	2	1	1	6	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:75104981C>T	ENST00000310715.3	-	6	571	c.451G>A	c.(451-453)Gta>Ata	p.V151I	TTC18_ENST00000394865.1_Missense_Mutation_p.V151I|TTC18_ENST00000401621.2_Missense_Mutation_p.V151I|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000355577.3_5'UTR|Y_RNA_ENST00000384742.1_RNA|TTC18_ENST00000340329.3_Missense_Mutation_p.V151I	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		151						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					GCCACTAATACTTTAACTTCA	0.413																																					p.V151I		.											.	TTC18-92	0			c.G451A						.						91	89	90					10																	75104981		2203	4300	6503	SO:0001583	missense	118491	exon6			CTAATACTTTAAC																												ENST00000310715.3:c.451G>A	10.37:g.75104981C>T	ENSP00000310829:p.Val151Ile	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	132	45	NM_145170	0	0	0	0	0	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	C	13.80	2.344903	0.41498	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000340329;ENST00000372928;ENST00000394865	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.29288	0.0729	L	0.52011	1.625	0.51767	D	0.999936	P	0.41910	0.764	B	0.35971	0.215	T	0.03287	-1.1052	10	0.31617	T	0.26	-11.3704	17.4191	0.87510	0.0:1.0:0.0:0.0	.	151	Q5T0N1	TTC18_HUMAN	I	151	ENSP00000310829:V151I;ENSP00000384479:V151I;ENSP00000343650:V151I;ENSP00000378334:V151I	ENSP00000310829:V151I	V	-	1	0	TTC18	74774987	1.000000	0.71417	0.994000	0.49952	0.152000	0.21847	4.158000	0.58150	2.692000	0.91855	0.650000	0.86243	GTA	.		0.413	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75104981	C	T	75104981	3	4	61	1	0	0	0	0	1	0	0	0	16718	565	20	2	3006	2	TTC18	10	75104981	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	67924	75104981	60429766	52	5930											
FAM22D	728130	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	89118099	89118099	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctggtgagccaggtcactCtctgggtcttacccttggct	5	13	11	12	0	4	1	1	1	3	0	5	1	4	1	2	4	2	1	2	4	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:89118099C>A	ENST00000381697.2	+	1	675	c.77C>A	c.(76-78)tCt>tAt	p.S26Y	NUTM2D_ENST00000412718.1_Missense_Mutation_p.S26Y|LINC00863_ENST00000439559.2_lincRNA			Q5VT03	NTM2D_HUMAN	NUT family member 2D	26																	CCAGGTCACTCTCTGGGTCTT	0.507																																					.													.	FAM22D-22	0			.						.						189	225	214					10																	89118099		1943	4159	6102	SO:0001583	missense	728130	.			GTCACTCTCTGGG			10q23.31	2013-03-14	2013-03-14	2013-03-14	ENSG00000214562	ENSG00000214562			23447	protein-coding gene	gene with protein product			"family with sequence similarity 22, member D"	FAM22D			Standard	NR_075100		Approved		uc001kes.3	Q5VT03	OTTHUMG00000018672	ENST00000381697.2:c.77C>A	10.37:g.89118099C>A	ENSP00000371116:p.Ser26Tyr	Somatic	284	0		WXS	Illumina HiSeq	Phase_I	312	52	.	0	0	7	10	3	A6NGV9	RNA	SNP	ENST00000381697.2	37		.	.	.	.	.	.	.	.	.	.	C	6.550	0.469839	0.12461	.	.	ENSG00000214562	ENST00000330762;ENST00000381697;ENST00000412718	T;T	0.27720	2.47;1.65	0.86	0.86	0.19042	.	.	.	.	.	T	0.19005	0.0456	.	.	.	0.09310	N	1	B;B	0.30664	0.289;0.191	B;B	0.23275	0.045;0.02	T	0.20273	-1.0280	8	0.72032	D	0.01	.	5.11	0.14804	0.0:1.0:0.0:0.0	.	26;26	Q5VT03-2;Q5VT03	.;FA22D_HUMAN	Y	97;26;26	ENSP00000371116:S26Y;ENSP00000396080:S26Y	ENSP00000328439:S97Y	S	+	2	0	FAM22D	89108079	0.086000	0.21541	0.013000	0.15412	0.054000	0.15201	0.919000	0.28692	0.769000	0.33313	0.175000	0.17021	TCT	.		0.507	NUTM2D-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000470142.1	NR_075100		A	89118099	C	A	89118099	3	1	61	1	0	0	0	0	1	0	0	0	5560	913	32	4	79	4	FAM22D	10	89118099	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	14013118	89118099	46416648	53	5931											
C10orf79	80217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105944865	105944865	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcattgactgaatcccatGaccctggtgagaatgactcc	10	11	8	12	0	1	5	1	5	1	1	4	6	3	5	3	1	0	0	3	1	2	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:105944865G>T	ENST00000278064.2	-	16	2168	c.1843C>A	c.(1843-1845)Cat>Aat	p.H615N	WDR96_ENST00000357060.3_Missense_Mutation_p.H684N|WDR96_ENST00000428666.1_Missense_Mutation_p.H685N														p.H684Y(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TGAATCCCATGACCCTGGTGA	0.403																																					p.H684N		.											.	WDR96-95	1	Substitution - Missense(1)	lung(1)	c.C2050A						.						174	152	160					10																	105944865		2203	4300	6503	SO:0001583	missense	80217	exon16			TCCCATGACCCTG																												ENST00000278064.2:c.1843C>A	10.37:g.105944865G>T	ENSP00000278064:p.His615Asn	Somatic	127	1		WXS	Illumina HiSeq	Phase_I	150	52	NM_025145	0	0	0	0	0		Missense_Mutation	SNP	ENST00000278064.2	37		.	.	.	.	.	.	.	.	.	.	G	0.191	-1.053696	0.01965	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064	T;T;T	0.12879	2.65;2.64;2.66	5.24	3.28	0.37604	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.001350	0.08054	N	0.997084	T	0.16300	0.0392	L	0.57536	1.79	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.09377	0.004;0.003	T	0.06881	-1.0802	10	0.51188	T	0.08	.	9.3605	0.38192	0.0:0.2545:0.6054:0.1402	.	685;684	B4DHB6;Q8NDM7	.;WDR96_HUMAN	N	684;685;615	ENSP00000349568:H684N;ENSP00000400289:H685N;ENSP00000278064:H615N	ENSP00000278064:H615N	H	-	1	0	WDR96	105934855	0.000000	0.05858	0.014000	0.15608	0.983000	0.72400	0.646000	0.24797	2.439000	0.82584	0.655000	0.94253	CAT	.		0.403	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			T	105944865	G	T	105944865	3	4	61	1	0	0	0	0	1	0	0	0	1622	1290	45	4	3039	4	C10orf79	10	105944865	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	16826766	105944865	29589882	54	5932											
EBF3	253738	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	131755589	131755589	+	Splice_Site	DEL	G	G	-																															acttttcttgtcacagcaccGgctgtggagcaattgtaaac																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:131755589delG	ENST00000355311.5	-	6	559	c.487delC	c.(487-489)cgg>gg	p.R163fs	EBF3_ENST00000368648.3_Splice_Site_p.R163fs			Q9H4W6	COE3_HUMAN	early B-cell factor 3	163		Interaction with DNA. {ECO:0000250}.			multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		TCACAGCACCGGCTGTGGAGC	0.388																																					p.R163fs		.											.	EBF3-91	0			c.487delC						.						127	119	121					10																	131755589		2203	4300	6503	SO:0001630	splice_region_variant	253738	exon6			.		CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.486-1C>-	10.37:g.131755589delG		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	181	50	NM_001005463	0	0	0	0	0	A0AUY1|Q5T6H9|Q9H4W5	Frame_Shift_Del	DEL	ENST00000355311.5	37																																																																																				.		0.388	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463	Frame_Shift_Del	-	131755589	G	-	131755589	8	5	61	1	0	1	0	1	0	0	1	0	4893	1130	39	0	1212	0	EBF3	10	131755589	Splice_Site	DEL	G	TCGA-BQ-5877-01A-11D-1589-08	25810724	131755589	3779158	55	5933											
MUC2	4583	hgsc.bcm.edu;ucsc.edu	37	chr11	1087972	1087972	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagacctgcaggaccatcaaCggcatccactccaacatctc	12	6	7	16	1	2	1	1	0	1	1	5	3	4	2	4	2	3	2	4	2	2	0	rs10902088	byFrequency	TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr11:1087972C>G	ENST00000441003.2	+	25	3474	c.3447C>G	c.(3445-3447)aaC>aaG	p.N1149K	MUC2_ENST00000359061.5_Missense_Mutation_p.N1149K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1149					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GGACCATCAACGGCATCCACT	0.622																																					p.N1149K		.											.	MUC2-90	0			c.C3447G						.						56	61	60					11																	1087972		2138	4242	6380	SO:0001583	missense	4583	exon25			CATCAACGGCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3447C>G	11.37:g.1087972C>G	ENSP00000415183:p.Asn1149Lys	Somatic	18	1		WXS	Illumina HiSeq	Phase_I	17	9	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	c	5.692	0.312306	0.10789	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.54675	0.56;0.56	3.98	-2.94	0.05581	.	1.123720	0.07056	N	0.832867	T	0.52306	0.1726	L	0.56769	1.78	0.80722	P	0.0	P	0.35628	0.513	P	0.44477	0.451	T	0.56080	-0.8038	9	0.12430	T	0.62	.	11.5782	0.50877	0.0:0.3997:0.0:0.6003	.	1149	E7EUV1	.	K	1149	ENSP00000415183:N1149K;ENSP00000351956:N1149K	ENSP00000351956:N1149K	N	+	3	2	MUC2	1077972	0.000000	0.05858	0.042000	0.18584	0.284000	0.27059	-1.939000	0.01545	-0.522000	0.06417	-1.075000	0.02238	AAC	C|0.712;T|0.288		0.622	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1087972	C	G	1087972	3	3	61	1	0	0	0	0	1	0	0	0	10000	535	19	4	3545	4	MUC2	11	1087972	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		1087972	133918544	56	5934											
LSP1	4046	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	1907965	1907965	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttttcctcctctgcagaccGctggccggacccccaagcta	6	9	8	18	2	1	1	0	0	1	1	3	2	3	2	6	2	2	3	6	2	2	3	rs370626038		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr11:1907965G>T	ENST00000311604.3	+	8	896	c.721G>T	c.(721-723)Gct>Tct	p.A241S	LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000406638.2_Missense_Mutation_p.A179S|LSP1_ENST00000405957.2_Missense_Mutation_p.A179S|LSP1_ENST00000381775.1_Missense_Mutation_p.A369S	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	241					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		TCTGCAGACCGCTGGCCGGAC	0.602																																					p.A369S		.											.	LSP1-90	0			c.G1105T						.						76	81	79					11																	1907965		2202	4299	6501	SO:0001583	missense	4046	exon9			CAGACCGCTGGCC	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.721G>T	11.37:g.1907965G>T	ENSP00000308383:p.Ala241Ser	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	106	44	NM_001242932	0	0	0	0	0	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	37	CCDS31334.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.516709	0.00151	.	.	ENSG00000130592	ENST00000311604;ENST00000381775;ENST00000405957;ENST00000457279;ENST00000406638;ENST00000417766;ENST00000432093	T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19	3.3	1.31	0.21738	.	0.438819	0.16421	N	0.215179	T	0.19565	0.0470	N	0.16307	0.4	0.09310	N	0.99999	B;B	0.33299	0.407;0.039	B;B	0.37387	0.248;0.056	T	0.25813	-1.0121	10	0.02654	T	1	-10.7455	10.0636	0.42290	0.0:0.0:0.3863:0.6137	.	369;241	E9PFP3;P33241	.;LSP1_HUMAN	S	241;369;179;232;179;179;179	ENSP00000308383:A241S;ENSP00000371194:A369S;ENSP00000383932:A179S;ENSP00000400346:A232S;ENSP00000384022:A179S;ENSP00000416363:A179S;ENSP00000412405:A179S	ENSP00000308383:A241S	A	+	1	0	LSP1	1864541	0.342000	0.24809	0.255000	0.24374	0.071000	0.16799	1.196000	0.32198	0.203000	0.20529	-0.493000	0.04662	GCT	.		0.602	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339		T	1907965	G	T	1907965	3	4	61	1	0	0	0	0	1	0	0	0	9088	1087	38	4	751	4	LSP1	11	1907965	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	819993	1907965	133098551	57	5935											
TNKS1BP1	85456	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57080232	57080232	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctcctcctcaacaggcaGtgcctgtccaggctcagggg	6	7	13	15	0	2	0	2	0	0	0	5	0	5	0	5	5	2	2	5	5	1	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr11:57080232G>T	ENST00000532437.1	-	4	2241	c.1930C>A	c.(1930-1932)Ctg>Atg	p.L644M	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.L644M|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	644	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCAACAGGCAGTGCCTGTCCA	0.652																																					p.L644M		.											.	TNKS1BP1-91	0			c.C1930A						.						40	43	42					11																	57080232		2201	4296	6497	SO:0001583	missense	85456	exon5			CAGGCAGTGCCTG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1930C>A	11.37:g.57080232G>T	ENSP00000437271:p.Leu644Met	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	62	17	NM_033396	0	0	22	30	8	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	G	3.119	-0.180918	0.06380	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.33865	1.39;1.39	3.52	-7.04	0.01578	.	0.599176	0.12691	N	0.447197	T	0.14743	0.0356	L	0.27053	0.805	0.09310	N	1	B	0.32101	0.356	B	0.28305	0.088	T	0.11991	-1.0565	10	0.32370	T	0.25	-3.6489	2.1814	0.03876	0.1527:0.1225:0.4815:0.2434	.	644	Q9C0C2	TB182_HUMAN	M	644	ENSP00000350990:L644M;ENSP00000437271:L644M	ENSP00000350990:L644M	L	-	1	2	TNKS1BP1	56836808	0.000000	0.05858	0.005000	0.12908	0.035000	0.12851	-1.072000	0.03434	-0.816000	0.04340	0.455000	0.32223	CTG	.		0.652	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57080232	G	T	57080232	3	4	61	1	0	0	0	0	1	0	0	0	16352	1020	36	4	3287	4	TNKS1BP1	11	57080232	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	55172267	57080232	77926284	58	5936											
CACNA1C	775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2760913	2760913	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcatccggacgctgctgtgGaccttcatcaagtccttcca	7	10	10	14	2	2	0	2	0	0	0	5	2	5	2	4	3	1	3	4	3	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr12:2760913G>T	ENST00000347598.4	+	34	4197	c.4197G>T	c.(4195-4197)tgG>tgT	p.W1399C	CACNA1C_ENST00000399601.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399638.1_Missense_Mutation_p.W1379C|CACNA1C_ENST00000399641.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399603.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000335762.5_Missense_Mutation_p.W1376C|CACNA1C_ENST00000399644.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000402845.3_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399649.1_Missense_Mutation_p.W1338C|CACNA1C_ENST00000399591.1_Missense_Mutation_p.W1340C|CACNA1C_ENST00000399597.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000344100.3_Missense_Mutation_p.W1373C|CACNA1C_ENST00000399655.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399637.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399617.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399595.1_Missense_Mutation_p.W1340C|CACNA1C_ENST00000327702.7_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399634.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000406454.3_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399629.1_Missense_Mutation_p.W1368C|CACNA1C_ENST00000399621.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399606.1_Missense_Mutation_p.W1371C	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1399					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGCTGCTGTGGACCTTCATCA	0.632																																					p.W1399C		.											.	CACNA1C-34	0			c.G4197T						.						44	53	50					12																	2760913		2195	4295	6490	SO:0001583	missense	775	exon34			GCTGTGGACCTTC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.4197G>T	12.37:g.2760913G>T	ENSP00000266376:p.Trp1399Cys	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	50	14	NM_199460	0	0	1	2	1	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.274714	0.80580	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.17	4.27	0.50696	Ion transport (1);	0.125129	0.64402	D	0.000017	D	0.99275	0.9747	H	0.97186	3.955	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.998;0.995;0.999;0.998;0.995;0.995;0.996;0.999;0.999;0.995;0.995;0.999;0.999;0.999;0.998;0.995;1.0;0.999;0.997;0.995;0.999;0.999;0.995;0.995	D	0.98781	1.0732	10	0.87932	D	0	.	13.5755	0.61873	0.0758:0.0:0.9242:0.0	.	42;1373;1348;1399;1351;1351;1351;1368;1379;1351;1371;1351;1311;1399;1351;1351;1351;1340;1338;1340;1340;1351;1351;1351;1351	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	C	1376;1351;1351;1379;1351;1351;1351;1340;1351;1399;1371;1351;1373;1368;1351;1338;1351;1351;1351;1351;1351;1340;1181	ENSP00000336982:W1376C;ENSP00000382563:W1351C;ENSP00000382552:W1351C;ENSP00000382547:W1379C;ENSP00000382506:W1351C;ENSP00000382530:W1351C;ENSP00000382546:W1351C;ENSP00000382500:W1340C;ENSP00000382549:W1351C;ENSP00000266376:W1399C;ENSP00000382515:W1371C;ENSP00000382510:W1351C;ENSP00000341092:W1373C;ENSP00000382537:W1368C;ENSP00000329877:W1351C;ENSP00000382557:W1338C;ENSP00000385724:W1351C;ENSP00000382512:W1351C;ENSP00000382542:W1351C;ENSP00000382526:W1351C;ENSP00000385896:W1351C;ENSP00000382504:W1340C	ENSP00000323129:W1181C	W	+	3	0	CACNA1C	2631174	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.805000	0.99149	1.171000	0.42768	0.491000	0.48974	TGG	.		0.632	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2760913	G	T	2760913	3	4	61	1	0	0	0	0	1	0	0	0	2546	1183	41	4	4505	4	CACNA1C	12	2760913	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		2760913	131090982	59	5937											
GPR133	283383	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	131439188	131439188	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggtgcgtggcgtctactccaGatcgcaggaccatccaggta	8	8	13	12	3	1	1	0	0	1	1	4	2	3	2	3	4	2	2	3	4	2	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr12:131439188G>C	ENST00000261654.5	+	2	645	c.86G>C	c.(85-87)aGa>aCa	p.R29T	GPR133_ENST00000535015.1_Missense_Mutation_p.R29T	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	29					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(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GTCTACTCCAGATCGCAGGAC	0.562																																					p.R29T		.											.	GPR133-191	0			c.G86C						.						114	98	103					12																	131439188		2203	4300	6503	SO:0001583	missense	283383	exon2			ACTCCAGATCGCA	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.86G>C	12.37:g.131439188G>C	ENSP00000261654:p.Arg29Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	163	37	NM_198827	0	0	3	3	0	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.695276	0.30052	.	.	ENSG00000111452	ENST00000261654;ENST00000543826;ENST00000542091;ENST00000535015	T;T	0.41400	1.0;1.03	4.42	1.96	0.26148	.	0.754074	0.11519	N	0.555971	T	0.33673	0.0871	L	0.56769	1.78	0.09310	N	1	B;B	0.29432	0.244;0.118	B;B	0.26770	0.073;0.023	T	0.37798	-0.9690	10	0.72032	D	0.01	.	2.9661	0.05908	0.2203:0.2806:0.4991:0.0	.	29;29	B7ZLF7;Q6QNK2	.;GP133_HUMAN	T	29	ENSP00000261654:R29T;ENSP00000444425:R29T	ENSP00000261654:R29T	R	+	2	0	GPR133	130005141	0.001000	0.12720	0.007000	0.13788	0.055000	0.15305	0.979000	0.29500	2.023000	0.59567	0.561000	0.74099	AGA	.		0.562	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		C	131439188	G	C	131439188	3	2	61	1	0	0	0	0	1	0	0	0	6663	942	33	4	92	4	GPR133	12	131439188	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	128678275	131439188	2412707	60	5938											
JPH4	84502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24040204	24040204	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaggcacccagcatcaggaCccctcgaggacgagcccctc	9	4	10	18	2	2	0	2	0	0	0	4	4	2	2	5	3	2	2	5	3	0	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:24040204C>G	ENST00000397118.3	-	6	2638	c.1736G>C	c.(1735-1737)gGt>gCt	p.G579A	JPH4_ENST00000544177.1_Missense_Mutation_p.G244A|RP11-66N24.3_ENST00000555968.1_RNA|JPH4_ENST00000356300.4_Missense_Mutation_p.G579A|AP1G2_ENST00000308724.5_5'Flank	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	579					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		AGCATCAGGACCCCTCGAGGA	0.687																																					p.G579A		.											.	JPH4-92	0			c.G1736C						.						31	33	32					14																	24040204		2203	4299	6502	SO:0001583	missense	84502	exon5			TCAGGACCCCTCG	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"junctophilin like 1"	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1736G>C	14.37:g.24040204C>G	ENSP00000380307:p.Gly579Ala	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	46	15	NM_001146028	0	0	0	0	0	D3DS53|Q8ND44|Q96DQ0	Missense_Mutation	SNP	ENST00000397118.3	37	CCDS9603.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.792770	0.31685	.	.	ENSG00000092051	ENST00000356300;ENST00000397118;ENST00000543864;ENST00000267407;ENST00000544177	T;T;T	0.54866	0.55;0.55;0.93	4.93	0.601	0.17529	.	0.326972	0.16970	U	0.192130	T	0.27419	0.0673	N	0.12182	0.205	0.26864	N	0.967898	B;B	0.11235	0.004;0.001	B;B	0.11329	0.006;0.002	T	0.17410	-1.0370	10	0.16420	T	0.52	.	6.9268	0.24419	0.3209:0.3658:0.3132:0.0	.	244;579	F5H1L9;Q96JJ6	.;JPH4_HUMAN	A	579;579;579;580;244	ENSP00000348648:G579A;ENSP00000380307:G579A;ENSP00000439562:G244A	ENSP00000267407:G580A	G	-	2	0	JPH4	23110044	0.797000	0.28877	0.998000	0.56505	0.975000	0.68041	0.344000	0.19962	0.546000	0.28920	-0.152000	0.13540	GGT	.		0.687	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452		G	24040204	C	G	24040204	3	3	61	1	0	0	0	0	1	0	0	0	7984	507	18	4	158	4	JPH4	14	24040204	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		24040204	83309336	61	5939											
NYNRIN	57523	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	24885007	24885007	+	Frame_Shift_Del	DEL	C	C	-																															ctgctccccttacacgccaaCctatgcccacctggcagccg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:24885007delC	ENST00000382554.3	+	9	4370	c.4052delC	c.(4051-4053)accfs	p.T1351fs		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1351					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						TACACGCCAACCTATGCCCAC	0.602																																					p.T1351fs		.											.	NYNRIN-3	0			c.4052delC						.						95	101	99					14																	24885007		2016	4157	6173	SO:0001589	frameshift_variant	57523	exon9			.	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.4052delC	14.37:g.24885007delC	ENSP00000371994:p.Thr1351fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	152	48	NM_025081	0	0	0	0	0	Q6P153|Q86TR3|Q9HAC4	Frame_Shift_Del	DEL	ENST00000382554.3	37	CCDS45090.1																																																																																			.		0.602	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			-	24885007	C	-	24885007	7	5	61	1	0	1	0	1	0	0	0	0	10822	507	18	0	4082	0	NYNRIN	14	24885007	Frame_Shift_Del	DEL	C	TCGA-BQ-5877-01A-11D-1589-08	844803	24885007	82464533	62	5940											
FBXO33	254170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	39868808	39868808	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgattcgatgtccatgactGcatgccaaggttgacccagg	9	10	12	10	1	0	3	0	3	0	0	2	4	1	3	3	2	2	2	3	2	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:39868808G>A	ENST00000298097.7	-	4	1917	c.1580C>T	c.(1579-1581)gCa>gTa	p.A527V	FBXO33_ENST00000554190.1_3'UTR	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	527					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		GTCCATGACTGCATGCCAAGG	0.438																																					p.A527V		.											.	FBXO33-658	0			c.C1580T						.						127	98	108					14																	39868808		2203	4300	6503	SO:0001583	missense	254170	exon4			ATGACTGCATGCC	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"F-boxes /  "other""	19833	protein-coding gene	gene with protein product		609103	"F-box only protein 33"				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.1580C>T	14.37:g.39868808G>A	ENSP00000298097:p.Ala527Val	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	52	18	NM_203301	0	0	5	8	3	Q6PIR2|Q86TR2|Q86YE0	Missense_Mutation	SNP	ENST00000298097.7	37	CCDS9677.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347997	0.61183	.	.	ENSG00000165355	ENST00000298097	T	0.34072	1.38	5.85	5.85	0.93711	.	0.051431	0.85682	D	0.000000	T	0.38108	0.1028	N	0.14661	0.345	0.80722	D	1	D	0.60575	0.988	P	0.54759	0.76	T	0.09885	-1.0654	9	.	.	.	-19.5419	20.1542	0.98100	0.0:0.0:1.0:0.0	.	527	Q7Z6M2	FBX33_HUMAN	V	527	ENSP00000298097:A527V	.	A	-	2	0	FBXO33	38938559	1.000000	0.71417	0.508000	0.27688	0.970000	0.65996	9.124000	0.94394	2.767000	0.95098	0.563000	0.77884	GCA	.		0.438	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			A	39868808	G	A	39868808	3	1	61	1	0	0	0	0	1	0	0	0	5762	1319	46	2	91	2	FBXO33	14	39868808	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	14983801	39868808	67480732	63	5941											
NUMB	8650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	73750966	73750966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccggcgtgggatggcatgagGattgttcatctccagagagg	8	9	16	8	2	2	2	1	1	1	1	3	5	2	4	2	5	0	2	2	5	0	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:73750966G>A	ENST00000355058.3	-	10	1050	c.772C>T	c.(772-774)Cct>Tct	p.P258S	NUMB_ENST00000555238.1_Missense_Mutation_p.P258S|NUMB_ENST00000359560.3_Missense_Mutation_p.P247S|NUMB_ENST00000555738.2_Intron|NUMB_ENST00000559312.1_Intron|NUMB_ENST00000535282.1_Missense_Mutation_p.P247S|NUMB_ENST00000554521.2_Intron|NUMB_ENST00000556772.1_Missense_Mutation_p.P114S|NUMB_ENST00000555394.1_Missense_Mutation_p.P258S|NUMB_ENST00000554546.1_Missense_Mutation_p.P247S|NUMB_ENST00000560335.1_Intron|NUMB_ENST00000356296.4_Missense_Mutation_p.P258S|NUMB_ENST00000454166.4_Intron|NUMB_ENST00000544991.3_Intron|NUMB_ENST00000557597.1_Missense_Mutation_p.P247S			P49757	NUMB_HUMAN	numb homolog (Drosophila)	258					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		ATGGCATGAGGATTGTTCATC	0.542																																					p.P258S		.											.	NUMB-1062	0			c.C772T						.						177	165	169					14																	73750966		2203	4300	6503	SO:0001583	missense	8650	exon10			CATGAGGATTGTT	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.772C>T	14.37:g.73750966G>A	ENSP00000347169:p.Pro258Ser	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	210	62	NM_001005744	0	0	41	69	28	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Missense_Mutation	SNP	ENST00000355058.3	37	CCDS32116.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596077	0.86953	.	.	ENSG00000133961	ENST00000554546;ENST00000356296;ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000555394;ENST00000535282;ENST00000326018;ENST00000555859;ENST00000555307;ENST00000554394	T;T;T;T;T;T;T;T;T;T;T	0.66815	0.28;0.24;0.66;0.66;1.27;0.66;0.66;0.24;0.66;-0.23;-0.23	5.39	5.39	0.77823	NUMB domain (1);	0.000000	0.85682	D	0.000000	T	0.76564	0.4005	L	0.38175	1.15	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.97110	1.0;0.998;0.999;0.992;0.992;0.98	T	0.77616	-0.2521	10	0.66056	D	0.02	-12.4282	19.34	0.94337	0.0:0.0:1.0:0.0	.	4;247;247;258;247;258	B1P2N9;B2RCI6;P49757-4;P49757-2;P49757-3;P49757	.;.;.;.;.;NUMB_HUMAN	S	247;258;247;258;114;258;247;258;247;222;222;258;258	ENSP00000452416:P247S;ENSP00000348644:P258S;ENSP00000451117:P247S;ENSP00000451300:P258S;ENSP00000451513:P114S;ENSP00000347169:P258S;ENSP00000352563:P247S;ENSP00000451625:P258S;ENSP00000441258:P247S;ENSP00000452357:P258S;ENSP00000451374:P258S	ENSP00000315193:P222S	P	-	1	0	NUMB	72820719	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.343000	0.72986	2.808000	0.96608	0.655000	0.94253	CCT	.		0.542	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			A	73750966	G	A	73750966	3	1	61	1	0	0	0	0	1	0	0	0	10777	1174	41	2	1199	2	NUMB	14	73750966	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	33882158	73750966	33598574	64	5942											
CLMN	79789	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	95660233	95660233	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccagatctgctgcgttcctCaactgaacatagctaaaatg	12	11	7	11	1	2	2	1	1	1	1	4	2	4	2	2	0	5	3	2	0	5	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:95660233C>G	ENST00000298912.4	-	12	2906	c.2793G>C	c.(2791-2793)ttG>ttC	p.L931F	CLMN_ENST00000556441.1_5'UTR|CLMN_ENST00000557215.1_5'UTR	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	931					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTGCGTTCCTCAACTGAACAT	0.373																																					p.L931F		.											.	CLMN-90	0			c.G2793C						.						116	111	112					14																	95660233		2203	4300	6503	SO:0001583	missense	79789	exon12			GTTCCTCAACTGA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2793G>C	14.37:g.95660233C>G	ENSP00000298912:p.Leu931Phe	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	100	19	NM_024734	0	0	7	9	2	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211197	0.58343	.	.	ENSG00000165959	ENST00000298912	D	0.93426	-3.22	4.77	3.87	0.44632	.	0.800724	0.10248	N	0.697563	D	0.94571	0.8251	M	0.64997	1.995	0.80722	D	1	D	0.59767	0.986	P	0.56916	0.809	D	0.91007	0.4847	10	0.46703	T	0.11	.	10.1749	0.42933	0.1987:0.8012:0.0:0.0	.	931	Q96JQ2	CLMN_HUMAN	F	931	ENSP00000298912:L931F	ENSP00000298912:L931F	L	-	3	2	CLMN	94729986	0.998000	0.40836	0.922000	0.36590	0.861000	0.49209	3.347000	0.52200	1.223000	0.43536	-0.314000	0.08810	TTG	.		0.373	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			G	95660233	C	G	95660233	3	3	61	1	0	0	0	0	1	0	0	0	3548	825	29	4	223	4	CLMN	14	95660233	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	21909267	95660233	11689307	65	5943											
AK7	122481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	96924426	96924426	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtggtatgcaggaggcgAttgttgcccctaacgatgta	8	11	13	9	2	0	0	0	0	0	0	0	3	0	1	3	3	3	4	3	3	3	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:96924426A>T	ENST00000267584.4	+	12	1278	c.1234A>T	c.(1234-1236)Att>Ttt	p.I412F		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	412	Adenylate kinase.|NMPbind. {ECO:0000250}.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GCAGGAGGCGATTGTTGCCCC	0.493																																					p.I412F		.											.	AK7-228	0			c.A1234T						.						98	86	90					14																	96924426		2203	4300	6503	SO:0001583	missense	122481	exon12			GAGGCGATTGTTG	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1234A>T	14.37:g.96924426A>T	ENSP00000267584:p.Ile412Phe	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_152327	0	0	0	0	0	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	37	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	A	3.590	-0.083768	0.07141	.	.	ENSG00000140057	ENST00000267584	D	0.92858	-3.12	4.89	2.31	0.28768	.	0.577652	0.18744	N	0.132380	D	0.85418	0.5692	L	0.29908	0.895	0.09310	N	0.999999	B	0.13594	0.008	B	0.24394	0.053	T	0.76263	-0.3023	10	0.52906	T	0.07	-2.9231	7.0702	0.25173	0.7494:0.1595:0.0911:0.0	.	412	Q96M32	KAD7_HUMAN	F	412	ENSP00000267584:I412F	ENSP00000267584:I412F	I	+	1	0	AK7	95994179	0.939000	0.31865	0.041000	0.18516	0.049000	0.14656	2.486000	0.45259	0.720000	0.32209	0.260000	0.18958	ATT	.		0.493	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			T	96924426	A	T	96924426	3	4	61	1	0	0	0	0	1	0	0	0	444	333	12	5	1280	5	AK7	14	96924426	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	1264193	96924426	10425114	66	5944											
CAPN3	825	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42691695	42691695	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cttccaacctctcaggatgtCctatgaggatttcatctacc	9	13	6	13	0	3	1	2	1	2	0	6	3	5	3	4	2	2	0	4	2	3	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr15:42691695C>G	ENST00000397163.3	+	10	1418	c.1199C>G	c.(1198-1200)tCc>tGc	p.S400C	CAPN3_ENST00000357568.3_Missense_Mutation_p.S400C|CAPN3_ENST00000356316.3_Missense_Mutation_p.S313C|CAPN3_ENST00000349748.3_Missense_Mutation_p.S352C|CAPN3_ENST00000318023.7_Missense_Mutation_p.S400C|CAPN3_ENST00000397200.4_5'Flank|RP11-164J13.1_ENST00000495723.1_RNA	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	400	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		CTCAGGATGTCCTATGAGGAT	0.498																																					p.S400C		.											.	CAPN3-514	0			c.C1199G						.						79	77	78					15																	42691695		2203	4299	6502	SO:0001583	missense	825	exon10			GGATGTCCTATGA	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"EF-hand domain containing"	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1199C>G	15.37:g.42691695C>G	ENSP00000380349:p.Ser400Cys	Somatic	104	1		WXS	Illumina HiSeq	Phase_I	63	23	NM_000070	0	0	0	0	0	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Missense_Mutation	SNP	ENST00000397163.3	37	CCDS45245.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513014	0.85389	.	.	ENSG00000092529	ENST00000356316;ENST00000397163;ENST00000357568;ENST00000349748;ENST00000318023	D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.94;-2.94	5.16	5.16	0.70880	Peptidase C2, calpain, catalytic domain (3);	0.074033	0.56097	U	0.000031	D	0.91372	0.7278	L	0.42008	1.315	0.80722	D	1	P;B;P;P;P;B	0.44478	0.691;0.289;0.836;0.482;0.538;0.049	P;B;B;B;P;B	0.45998	0.5;0.33;0.367;0.333;0.464;0.111	D	0.92205	0.5771	10	0.66056	D	0.02	.	18.8563	0.92254	0.0:1.0:0.0:0.0	.	265;313;352;400;400;313	C6EVS4;C6EVS3;P20807-2;P20807-3;P20807;Q762C8	.;.;.;.;CAN3_HUMAN;.	C	313;400;400;352;400	ENSP00000348667:S313C;ENSP00000380349:S400C;ENSP00000350181:S400C;ENSP00000183936:S352C;ENSP00000326281:S400C	ENSP00000326281:S400C	S	+	2	0	CAPN3	40478987	1.000000	0.71417	0.986000	0.45419	0.956000	0.61745	7.651000	0.83577	2.679000	0.91253	0.650000	0.86243	TCC	.		0.498	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			G	42691695	C	G	42691695	3	3	61	1	0	0	0	0	1	0	0	0	2634	855	30	4	1289	4	CAPN3	15	42691695	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		42691695	59839697	67	5945											
DUOX1	53905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	45445603	45445603	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cacagtgtgggccatgtggtGaatgtgtacctgttctccat	7	13	12	9	0	1	1	0	1	1	0	2	1	1	1	3	2	1	2	3	2	2	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr15:45445603G>C	ENST00000321429.4	+	27	3857	c.3450G>C	c.(3448-3450)gtG>gtC	p.V1150V	CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000389037.3_Silent_p.V1150V|DUOX1_ENST00000561166.1_Silent_p.V796V|DUOX1_ENST00000559221.1_3'UTR	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1150	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GCCATGTGGTGAATGTGTACC	0.547																																					p.V1150V		.											.	DUOX1-142	0			c.G3450C						.						311	237	262					15																	45445603		2198	4298	6496	SO:0001819	synonymous_variant	53905	exon27			TGTGGTGAATGTG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3450G>C	15.37:g.45445603G>C		Somatic	167	0		WXS	Illumina HiSeq	Phase_I	194	69	NM_017434	0	0	7	7	0	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			.		0.547	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		C	45445603	G	C	45445603	2	2	61	1	0	0	0	0	0	0	0	1	4811	1277	45	4		4	DUOX1	15	45445603	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	2753908	45445603	57085789	68	5946											
CILP	8483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65490142	65490142	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgcagttcctccccagccaGgcttgccaagacataggcag	9	8	10	14	0	0	1	0	0	0	1	2	1	2	1	5	2	3	4	5	2	2	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr15:65490142G>A	ENST00000261883.4	-	9	2648	c.2482C>T	c.(2482-2484)Ctg>Ttg	p.L828L		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	828					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						TCCCCAGCCAGGCTTGCCAAG	0.557																																					p.L828L		.											.	CILP-97	0			c.C2482T						.						63	57	59					15																	65490142		2200	4295	6495	SO:0001819	synonymous_variant	8483	exon9			CAGCCAGGCTTGC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.2482C>T	15.37:g.65490142G>A		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	98	31	NM_003613	0	0	0	0	0	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																			.		0.557	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65490142	G	A	65490142	2	1	61	1	0	0	0	0	0	0	0	1	3435	991	35	2		2	CILP	15	65490142	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	20044539	65490142	37041250	69	5947											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_178167	0	0	0	4	4	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	61	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		2059674	88295079	70	5948											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2817459	2817459	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccttggcagctctgagTctcacaggctctggcacacc	6	9	11	15	0	3	1	1	1	3	0	4	1	3	1	2	3	2	5	2	3	0	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:2817459T>C	ENST00000301740.8	+	11	7479	c.6930T>C	c.(6928-6930)agT>agC	p.S2310S	AC092117.2_ENST00000581119.1_RNA	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2310	Ala-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CAGCTCTGAGTCTCACAGGCT	0.622																																					p.S2310S		.											.	SRRM2-93	0			c.T6930C						.						162	169	166					16																	2817459		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TCTGAGTCTCACA	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.6930T>C	16.37:g.2817459T>C		Somatic	409	1		WXS	Illumina HiSeq	Phase_I	501	143	NM_016333	0	0	130	229	99	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																			.		0.622	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2817459	T	C	2817459	2	2	61	1	0	0	0	0	0	0	0	1	15201	1664	58	3		3	SRRM2	16	2817459	Silent	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	757785	2817459	87537294	71	5949											
MEFV	4210	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	3297239	3297240	+	Frame_Shift_Ins	INS	-	-	T																															ccgctgcttcagcgcttcagINStttgtttctggggagcagag																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:3297239_3297240insT	ENST00000219596.1	-	5	1402_1403	c.1363_1364insA	c.(1363-1365)actfs	p.T455fs	MEFV_ENST00000339854.4_Frame_Shift_Ins_p.T275fs|MEFV_ENST00000541159.1_Frame_Shift_Ins_p.T244fs|MEFV_ENST00000536379.1_Frame_Shift_Ins_p.T244fs	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	455	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CAGCGCTTCAGTTTGTTTCTGG	0.594																																					p.T455fs		.											.	MEFV-228	0			c.1364_1365insA						.																																			SO:0001589	frameshift_variant	4210	exon5			.	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1364dupA	16.37:g.3297242_3297242dupT	ENSP00000219596:p.Thr455fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	146	45	NM_000243	0	0	0	0	0	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Frame_Shift_Ins	INS	ENST00000219596.1	37	CCDS10498.1																																																																																			.		0.594	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3297240	-	T	3297239	7	5	61	1	0	1	1	0	0	0	0	0	9484	1029	36	0	1005	0	MEFV	16	3297239	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	479780	3297239	87057514	72	5950											
ANKS4B	257629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21261659	21261659	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agttgtcagcagaggaggacGgcagtgtgcaccatgaatcc	11	7	14	9	1	1	2	1	1	0	1	2	4	2	4	2	3	2	4	2	3	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:21261659G>A	ENST00000311620.5	+	2	845	c.772G>A	c.(772-774)Ggc>Agc	p.G258S		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	258					response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|lung(11)|ovary(2)	20				GBM - Glioblastoma multiforme(48;0.0565)		AGAGGAGGACGGCAGTGTGCA	0.478																																					p.G258S		.											.	ANKS4B-92	0			c.G772A						.						105	113	111					16																	21261659		2087	4214	6301	SO:0001583	missense	257629	exon2			GAGGACGGCAGTG	AK096138	CCDS42130.1	16p12.2	2013-01-10				ENSG00000175311		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26795	protein-coding gene	gene with protein product		609901					Standard	NM_145865		Approved	FLJ38819, HARP	uc010bwp.1	Q8N8V4		ENST00000311620.5:c.772G>A	16.37:g.21261659G>A	ENSP00000308772:p.Gly258Ser	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	90	17	NM_145865	0	0	0	1	1		Missense_Mutation	SNP	ENST00000311620.5	37	CCDS42130.1	.	.	.	.	.	.	.	.	.	.	A	3.131	-0.178370	0.06380	.	.	ENSG00000175311	ENST00000311620	T	0.39997	1.05	5.77	-1.61	0.08399	.	1.096410	0.06713	N	0.773573	T	0.22513	0.0543	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29549	-1.0008	10	0.08179	T	0.78	0.0056	16.0383	0.80645	0.3534:0.0:0.6466:0.0	.	258	Q8N8V4	ANS4B_HUMAN	S	258	ENSP00000308772:G258S	ENSP00000308772:G258S	G	+	1	0	ANKS4B	21169160	0.000000	0.05858	0.000000	0.03702	0.834000	0.47266	0.038000	0.13862	-0.644000	0.05465	-0.332000	0.08345	GGC	.		0.478	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865		A	21261659	G	A	21261659	3	1	61	1	0	0	0	0	1	0	0	0	691	1116	39	1	778	1	ANKS4B	16	21261659	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	17964420	21261659	69093094	73	5951											
SALL1	6299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	51174769	51174769	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcactcccaaagaccttcGcgcagaacctgcacttgtgt	9	10	8	14	2	1	2	1	0	0	2	3	2	2	2	3	0	2	2	3	0	2	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:51174769G>C	ENST00000251020.4	-	2	1397	c.1364C>G	c.(1363-1365)gCg>gGg	p.A455G	SALL1_ENST00000440970.1_Missense_Mutation_p.A358G|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	455					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			AAAGACCTTCGCGCAGAACCT	0.512																																					p.A455G	GBM(103;1352 1446 1855 4775 8890)	.											.	SALL1-98	0			c.C1364G						.						104	96	99					16																	51174769		2198	4300	6498	SO:0001583	missense	6299	exon2			ACCTTCGCGCAGA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1364C>G	16.37:g.51174769G>C	ENSP00000251020:p.Ala455Gly	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	188	57	NM_002968	0	0	30	65	35	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.550286	0.27739	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.07800	3.16;3.16	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.048774	0.85682	D	0.000000	T	0.05090	0.0136	N	0.11560	0.145	0.58432	D	0.999992	B	0.17667	0.023	B	0.13407	0.009	T	0.17899	-1.0354	10	0.02654	T	1	.	18.685	0.91560	0.0:0.0:1.0:0.0	.	455	Q9NSC2	SALL1_HUMAN	G	455;358;419	ENSP00000251020:A455G;ENSP00000407914:A358G	ENSP00000251020:A455G	A	-	2	0	SALL1	49732270	1.000000	0.71417	0.817000	0.32601	0.990000	0.78478	6.217000	0.72218	2.386000	0.81285	0.563000	0.77884	GCG	.		0.512	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51174769	G	C	51174769	3	2	61	1	0	0	0	0	1	0	0	0	13842	1087	38	4	2618	4	SALL1	16	51174769	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	29913110	51174769	39179984	74	5952											
IRX5	10265	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	54966812	54966813	+	Frame_Shift_Del	DEL	GC	GC	-																															gcgaccccgagggccccgaaGcaggttggtggacatgggaa																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:54966812_54966813delGC	ENST00000394636.4	+	2	989_990	c.652_653delGC	c.(652-654)gcafs	p.A218fs	IRX5_ENST00000560154.1_Intron|IRX5_ENST00000320990.5_Frame_Shift_Del_p.A218fs|CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000558597.1_Frame_Shift_Del_p.A152fs			P78411	IRX5_HUMAN	iroquois homeobox 5	218					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						GGGCCCCGAAGCAGGTTGGTGG	0.649																																					p.218_218del		.											.	IRX5-90	0			c.652_653del						.																																			SO:0001589	frameshift_variant	10265	exon2			.	U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"Homeoboxes / TALE class"	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.652_653delGC	16.37:g.54966812_54966813delGC	ENSP00000378132:p.Ala218fs	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	225	71	NM_001252197	0	0	0	0	0	H0YMS7|P78416|Q7Z2E1	Frame_Shift_Del	DEL	ENST00000394636.4	37	CCDS10751.1																																																																																			.		0.649	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2			-	54966813	GC	-	54966812	7	5	61	1	0	1	0	1	0	0	0	0	7868	971	34	0	658	0	IRX5	16	54966812	Frame_Shift_Del	DEL	GC	TCGA-BQ-5877-01A-11D-1589-08	3792043	54966812	35387941	75	5953											
SLC6A2	6530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	55705980	55705980	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaccgactgtggccacacCtggaacagccccaactgtac	10	6	10	15	1	0	0	0	0	0	0	0	3	0	2	5	3	4	1	5	3	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:55705980C>T	ENST00000379906.2	+	3	792	c.537C>T	c.(535-537)acC>acT	p.T179T	SLC6A2_ENST00000567238.1_Silent_p.T74T|SLC6A2_ENST00000414754.3_Silent_p.T179T|SLC6A2_ENST00000566163.1_Silent_p.T179T|SLC6A2_ENST00000219833.8_Silent_p.T179T|SLC6A2_ENST00000568943.1_Silent_p.T179T|SLC6A2_ENST00000561820.1_Silent_p.T179T	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	179					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GTGGCCACACCTGGAACAGCC	0.567																																					p.T179T		.											.	SLC6A2-526	0			c.C537T						.						164	114	131					16																	55705980		2198	4300	6498	SO:0001819	synonymous_variant	6530	exon4			CCACACCTGGAAC		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"Solute carriers"	11048	protein-coding gene	gene with protein product	"norepinephrine transporter"	163970	"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.537C>T	16.37:g.55705980C>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	66	15	NM_001172501	0	0	0	0	0	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	37	CCDS10754.1																																																																																			.		0.567	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			T	55705980	C	T	55705980	2	4	61	1	0	0	0	0	0	0	0	1	14715	668	24	2		2	SLC6A2	16	55705980	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	739168	55705980	34648773	76	5954											
SPAG7	9552	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4862852	4862852	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggaggttggcggcaactcttCcccactctgccgcagacgct	6	8	12	15	3	2	1	0	0	2	1	3	2	3	2	3	4	2	4	3	4	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:4862852C>T	ENST00000206020.3	-	7	728	c.661G>A	c.(661-663)Gaa>Aaa	p.E221K	SPAG7_ENST00000573366.1_Missense_Mutation_p.E170K|SPAG7_ENST00000575142.1_3'UTR	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	221						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						GGCAACTCTTCCCCACTCTGC	0.622																																					p.E221K		.											.	SPAG7-91	0			c.G661A						.						69	71	70					17																	4862852		1938	4137	6075	SO:0001583	missense	9552	exon7			ACTCTTCCCCACT	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.661G>A	17.37:g.4862852C>T	ENSP00000206020:p.Glu221Lys	Somatic	142	1		WXS	Illumina HiSeq	Phase_I	156	33	NM_004890	0	0	116	184	68	Q96EU5	Missense_Mutation	SNP	ENST00000206020.3	37	CCDS42240.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195946	0.58126	.	.	ENSG00000091640	ENST00000206020	.	.	.	5.26	5.26	0.73747	.	0.117279	0.56097	D	0.000023	T	0.26304	0.0642	N	0.08118	0	0.47994	D	0.999564	P	0.45044	0.849	B	0.37015	0.239	T	0.09228	-1.0684	9	0.16896	T	0.51	-8.7006	16.4689	0.84094	0.0:1.0:0.0:0.0	.	221	O75391	SPAG7_HUMAN	K	221	.	ENSP00000206020:E221K	E	-	1	0	SPAG7	4803575	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.103000	0.57783	2.753000	0.94483	0.650000	0.86243	GAA	.		0.622	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		T	4862852	C	T	4862852	3	4	61	1	0	0	0	0	1	0	0	0	15015	864	30	2	26	2	SPAG7	17	4862852	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		4862852	76332358	77	5955											
MYH4	4622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10366488	10366488	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctttagctgaaaagtaactcGggacttctctagcagatctg	11	12	9	9	1	2	2	0	1	2	1	4	3	2	3	0	1	3	3	0	1	5	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:10366488G>A	ENST00000255381.2	-	10	933	c.823C>T	c.(823-825)Cga>Tga	p.R275*	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	275	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AAAGTAACTCGGGACTTCTCT	0.353																																					p.R275X		.											.	MYH4-102	0			c.C823T						.						76	78	77					17																	10366488		2203	4300	6503	SO:0001587	stop_gained	4622	exon10			TAACTCGGGACTT		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.823C>T	17.37:g.10366488G>A	ENSP00000255381:p.Arg275*	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	103	20	NM_017533	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	34	5.353656	0.95830	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.37	-0.0246	0.13938	.	0.000000	0.35320	U	0.003296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5683	0.76313	0.0:0.0:0.2102:0.7898	.	.	.	.	X	275	.	ENSP00000255381:R275X	R	-	1	2	MYH4	10307213	0.139000	0.22563	0.530000	0.27963	0.997000	0.91878	0.358000	0.20216	0.248000	0.21435	0.650000	0.86243	CGA	.		0.353	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		A	10366488	G	A	10366488	4	1	61	1	0	0	0	0	0	1	0	0	10062	1124	39	1	5120	1	MYH4	17	10366488	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	5503636	10366488	70828722	78	5956											
PLD6	201164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17106274	17106274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacgtactcgtcgtcctccGtgatgagaacattctccctg	7	11	9	14	4	1	2	0	2	1	1	6	3	3	2	3	0	2	2	3	0	2	2	rs139543758		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:17106274G>A	ENST00000321560.3	-	2	594	c.566C>T	c.(565-567)aCg>aTg	p.T189M	RP11-45M22.4_ENST00000427497.3_3'UTR	NM_178836.3	NP_849158.2	Q8N2A8	PLD6_HUMAN	phospholipase D family, member 6	189					DNA methylation involved in gamete generation (GO:0043046)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|meiotic nuclear division (GO:0007126)|mitochondrial fusion (GO:0008053)|P granule organization (GO:0030719)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|piRNA metabolic process (GO:0034587)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	cardiolipin hydrolase activity (GO:0035755)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(1)	2						GTCGTCCTCCGTGATGAGAAC	0.488																																					p.T189M		.											.	PLD6-90	0			c.C566T						.						158	143	148					17																	17106274		2203	4300	6503	SO:0001583	missense	201164	exon2			TCCTCCGTGATGA	AK090899	CCDS11182.1	17p11.2	2008-08-14			ENSG00000179598	ENSG00000179598			30447	protein-coding gene	gene with protein product		614960				12477932	Standard	NM_178836		Approved		uc002gqz.3	Q8N2A8	OTTHUMG00000059278	ENST00000321560.3:c.566C>T	17.37:g.17106274G>A	ENSP00000317177:p.Thr189Met	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	109	29	NM_178836	0	0	11	22	11	Q8N5Y1	Missense_Mutation	SNP	ENST00000321560.3	37	CCDS11182.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.302941	0.23736	.	.	ENSG00000179598	ENST00000321560	T	0.24350	1.86	5.6	5.6	0.85130	.	0.181068	0.49916	N	0.000129	T	0.27629	0.0679	M	0.74258	2.255	0.24632	N	0.993617	B	0.29136	0.234	B	0.28784	0.094	T	0.27434	-1.0074	10	0.26408	T	0.33	-6.0E-4	8.0312	0.30465	0.782:0.0:0.218:0.0	.	189	Q8N2A8	PLD6_HUMAN	M	189	ENSP00000317177:T189M	ENSP00000317177:T189M	T	-	2	0	PLD6	17046999	0.974000	0.33945	0.967000	0.41034	0.665000	0.39181	2.538000	0.45710	0.963000	0.38082	-0.254000	0.11334	ACG	G|1.000;T|0.000		0.488	PLD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131600.2	NM_178836		A	17106274	G	A	17106274	3	1	61	1	0	0	0	0	1	0	0	0	12076	1145	40	1	196	1	PLD6	17	17106274	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	6739786	17106274	64088936	79	5957											
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18039921	18039921	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcactgctgttcagctggcTcatcaccagggtcaacgcgc	7	9	11	14	2	4	0	4	0	0	0	4	0	4	0	1	2	4	5	1	2	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:18039921T>G	ENST00000205890.5	+	15	5038	c.4700T>G	c.(4699-4701)cTc>cGc	p.L1567R		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1567	Myosin motor.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TTCAGCTGGCTCATCACCAGG	0.622																																					p.L1567R		.											.	MYO15A-97	0			c.T4700G						.						68	73	71					17																	18039921		2194	4278	6472	SO:0001583	missense	51168	exon14			GCTGGCTCATCAC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.4700T>G	17.37:g.18039921T>G	ENSP00000205890:p.Leu1567Arg	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	71	19	NM_016239	0	0	0	0	0	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.536870	0.65085	.	.	ENSG00000091536	ENST00000205890	D	0.89939	-2.59	5.7	5.7	0.88788	Myosin head, motor domain (2);	.	.	.	.	D	0.96599	0.8890	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98055	1.0390	9	0.87932	D	0	.	15.97	0.80008	0.0:0.0:0.0:1.0	.	1567	Q9UKN7	MYO15_HUMAN	R	1567	ENSP00000205890:L1567R	ENSP00000205890:L1567R	L	+	2	0	MYO15A	17980646	1.000000	0.71417	0.982000	0.44146	0.669000	0.39330	7.902000	0.87389	2.189000	0.69895	0.459000	0.35465	CTC	.		0.622	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18039921	T	G	18039921	3	3	61	1	0	0	0	0	1	0	0	0	10088	1551	54	5	4750	5	MYO15A	17	18039921	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	933647	18039921	63155289	80	5958											
KRTAP1-5	83895	hgsc.bcm.edu	37	chr17	39183083	39183083	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgggtgctcacagctccacTgctgccctcctggccatagc	6	8	10	17	1	1	0	1	0	0	0	3	0	3	0	4	2	5	3	4	2	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:39183083T>C	ENST00000361883.5	-	1	371	c.325A>G	c.(325-327)Agt>Ggt	p.S109G		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	109	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			ACAGCTCCACTGCTGCCCTCC	0.642																																					p.S109G		.											.	.	0			c.A325G						.																																			SO:0001583	missense	83895	exon1			CTCCACTGCTGCC	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"Keratin associated proteins"	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.325A>G	17.37:g.39183083T>C	ENSP00000355302:p.Ser109Gly	Somatic	31	1		WXS	Illumina HiSeq	Phase_I	48	5	NM_031957	0	0	2	2	0	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Missense_Mutation	SNP	ENST00000361883.5	37	CCDS42321.1	.	.	.	.	.	.	.	.	.	.	T	3.113	-0.182242	0.06340	.	.	ENSG00000221852	ENST00000361883;ENST00000543389	T	0.38077	1.16	5.49	-11.0	0.00169	.	.	.	.	.	T	0.18383	0.0441	L	0.31578	0.945	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.18681	-1.0329	9	0.42905	T	0.14	.	4.8707	0.13631	0.1605:0.1834:0.0639:0.5922	.	109	Q9BYS1	KRA15_HUMAN	G	109;99	ENSP00000355302:S109G	ENSP00000355302:S109G	S	-	1	0	KRTAP1-5	36436609	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.571000	0.02138	-2.795000	0.00354	-1.982000	0.00454	AGT	.		0.642	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1			C	39183083	T	C	39183083	3	2	61	1	0	0	0	0	1	0	0	0	8525	1580	55	3	203	3	KRTAP1-5	17	39183083	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	21143162	39183083	42012127	81	5959											
KRTAP1-5	83895	hgsc.bcm.edu	37	chr17	39183129	39183129	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccaccaatgccacagccAgttccgcaggagctgatctg	10	6	9	16	1	1	1	0	1	1	0	2	2	2	2	6	1	3	3	6	1	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:39183129A>G	ENST00000361883.5	-	1	325	c.279T>C	c.(277-279)acT>acC	p.T93T		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	93	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			TGCCACAGCCAGTTCCGCAGG	0.637																																					p.T93T		.											.	.	0			c.T279C						.						24	28	26					17																	39183129		2076	4218	6294	SO:0001819	synonymous_variant	83895	exon1			ACAGCCAGTTCCG	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"Keratin associated proteins"	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.279T>C	17.37:g.39183129A>G		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	51	4	NM_031957	0	0	0	0	0	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Silent	SNP	ENST00000361883.5	37	CCDS42321.1																																																																																			.		0.637	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1			G	39183129	A	G	39183129	2	3	61	1	0	0	0	0	0	0	0	1	8525	175	7	3		3	KRTAP1-5	17	39183129	Silent	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	46	39183129	42012081	82	5960											
NSF	4905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	44806264	44806264	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttcaaatcttgtattacaGgctcttctcgttttactgaa	9	19	5	8	1	4	1	1	1	3	0	5	1	4	1	0	1	2	3	0	1	5	8			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:44806264G>A	ENST00000398238.4	+	17	1979	c.1872G>A	c.(1870-1872)caG>caA	p.Q624Q	NSF_ENST00000575068.1_Silent_p.Q619Q|NSF_ENST00000225282.8_Silent_p.Q530Q	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	624					exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)			kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		TTGTATTACAGGCTCTTCTCG	0.323																																					p.Q624Q	Ovarian(25;472 742 1472 36813 50223)	.											.	NSF-91	0			c.G1872A						.						141	120	126					17																	44806264		1805	4065	5870	SO:0001819	synonymous_variant	4905	exon17			ATTACAGGCTCTT		CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"ATPases / AAA-type"	8016	protein-coding gene	gene with protein product	"N-ethylmaleimide-sensitive factor-like protein"	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.1872G>A	17.37:g.44806264G>A		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	118	40	NM_006178	0	0	23	32	9	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Silent	SNP	ENST00000398238.4	37	CCDS42354.1																																																																																			.		0.323	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178		A	44806264	G	A	44806264	2	1	61	1	0	0	0	0	0	0	0	1	10697	991	35	2		2	NSF	17	44806264	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	5623135	44806264	36388946	83	5961											
USP32	84669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58348812	58348812	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttcaataaccaatagcgtTtctcaagatcaatgatgtct	13	13	5	10	1	4	2	3	1	2	1	5	2	4	2	2	0	2	1	2	0	6	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:58348812T>G	ENST00000300896.4	-	6	796	c.602A>C	c.(601-603)aAa>aCa	p.K201T	USP32_ENST00000393003.3_Missense_Mutation_p.K201T	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	201					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CCAATAGCGTTTCTCAAGATC	0.398																																					p.K201T		.											.	USP32-704	0			c.A602C						.						137	119	125					17																	58348812		2203	4300	6503	SO:0001583	missense	84669	exon6			TAGCGTTTCTCAA	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.602A>C	17.37:g.58348812T>G	ENSP00000300896:p.Lys201Thr	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	138	42	NM_032582	0	0	15	28	13	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.820035	0.90873	.	.	ENSG00000170832	ENST00000300896;ENST00000393003	T;T	0.68765	-0.35;-0.35	5.35	5.35	0.76521	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79811	0.4510	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.85130	0.968;0.997	T	0.82137	-0.0606	10	0.87932	D	0	.	15.332	0.74219	0.0:0.0:0.0:1.0	.	201;201	Q7Z5T3;Q8NFA0	.;UBP32_HUMAN	T	201	ENSP00000300896:K201T;ENSP00000376727:K201T	ENSP00000300896:K201T	K	-	2	0	USP32	55703594	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.983000	0.88140	2.014000	0.59158	0.460000	0.39030	AAA	.		0.398	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		G	58348812	T	G	58348812	3	3	61	1	0	0	0	0	1	0	0	0	17096	1841	64	5	4328	5	USP32	17	58348812	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	13542548	58348812	22846398	84	5962											
SPHK1	8877	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74383269	74383269	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctctcactggacagtggtgCccgacgaggactttgtgcta	7	10	12	12	2	1	0	1	0	1	0	2	4	1	2	2	3	2	1	2	3	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:74383269C>G	ENST00000545180.1	+	8	1566	c.757C>G	c.(757-759)Ccc>Gcc	p.P253A	SPHK1_ENST00000590959.1_Missense_Mutation_p.P267A|SPHK1_ENST00000592299.1_Missense_Mutation_p.P253A|SPHK1_ENST00000323374.4_Missense_Mutation_p.P339A|SPHK1_ENST00000392496.3_Missense_Mutation_p.P253A			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	253					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	GACAGTGGTGCCCGACGAGGA	0.627																																					p.P339A	GBM(90;966 1307 27369 33775 44498)	.											.	SPHK1-1107	0			c.C1015G						.						57	43	48					17																	74383269		2203	4300	6503	SO:0001583	missense	8877	exon6			GTGGTGCCCGACG	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.757C>G	17.37:g.74383269C>G	ENSP00000440970:p.Pro253Ala	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	37	8	NM_182965	0	0	13	17	4	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	37	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.373733	0.61624	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.13778	2.56;2.56;2.56	5.08	5.08	0.68730	.	0.252689	0.40144	N	0.001161	T	0.17746	0.0426	M	0.70595	2.14	0.37430	D	0.914003	B;P;P	0.51351	0.175;0.756;0.944	B;B;P	0.45343	0.088;0.374;0.477	T	0.10497	-1.0627	10	0.06236	T	0.91	-5.9695	13.4531	0.61182	0.1567:0.8433:0.0:0.0	.	339;267;253	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	A	253;339;253;252	ENSP00000440970:P253A;ENSP00000313681:P339A;ENSP00000376285:P253A	ENSP00000313681:P339A	P	+	1	0	SPHK1	71894864	0.949000	0.32298	0.993000	0.49108	0.818000	0.46254	2.111000	0.41883	2.346000	0.79739	0.563000	0.77884	CCC	.		0.627	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		G	74383269	C	G	74383269	3	3	61	1	0	0	0	0	1	0	0	0	15078	739	26	4	1079	4	SPHK1	17	74383269	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	16034457	74383269	6811941	85	5963											
DCC	1630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	51025752	51025752	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagcagcgaggaggcaccaaGcagaaccatccccacagctt	13	4	10	14	1	0	1	0	0	0	1	1	3	1	2	4	2	5	4	4	2	3	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr18:51025752G>T	ENST00000442544.2	+	27	4599	c.3983G>T	c.(3982-3984)aGc>aTc	p.S1328I	DCC_ENST00000581580.1_Missense_Mutation_p.S961I|RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1328					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GAGGCACCAAGCAGAACCATC	0.537																																					p.S1328I		.											.	DCC-225	0			c.G3983T						.						232	178	196					18																	51025752		2203	4300	6503	SO:0001583	missense	1630	exon27			CACCAAGCAGAAC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3983G>T	18.37:g.51025752G>T	ENSP00000389140:p.Ser1328Ile	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	96	53	NM_005215	0	0	0	0	0		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454949	0.43634	.	.	ENSG00000187323	ENST00000442544	T	0.46819	0.86	6.17	6.17	0.99709	Neogenin, C-terminal (1);	0.168925	0.51477	D	0.000094	T	0.53802	0.1819	L	0.47716	1.5	0.54753	D	0.999981	P	0.49696	0.927	P	0.48952	0.596	T	0.46133	-0.9213	10	0.44086	T	0.13	-9.5941	19.6509	0.95805	0.0:0.0:1.0:0.0	.	1328	P43146	DCC_HUMAN	I	1328	ENSP00000389140:S1328I	ENSP00000389140:S1328I	S	+	2	0	DCC	49279750	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	7.871000	0.87180	2.941000	0.99782	0.655000	0.94253	AGC	.		0.537	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	51025752	G	T	51025752	3	4	61	1	0	0	0	0	1	0	0	0	4288	971	34	4	4089	4	DCC	18	51025752	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		51025752	27051496	86	5964											
SHC2	25759	hgsc.bcm.edu	37	chr19	438830	438830	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggacggacgccagggccttgTtgggggcctgagttgggggc	4	7	21	9	2	0	1	0	1	0	0	0	3	0	3	3	7	0	2	3	7	0	3	rs140148508	byFrequency	TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:438830T>C	ENST00000264554.6	-	4	607	c.608A>G	c.(607-609)aAc>aGc	p.N203S		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	203	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGGCCTTGTTGGGGGCCTG	0.682													T|||	39	0.00778754	0.0287	0.0014	5008	,	,		10768	0		0	False		,,,				2504	0				p.N203S		.											.	SHC2-392	0			c.A608G						.	T	SER/ASN	78,3948		0,78,1935	25	29	28		608	3.7	1	19	dbSNP_134	28	1,8257		0,1,4128	yes	missense	SHC2	NM_012435.2	46	0,79,6063	CC,CT,TT		0.0121,1.9374,0.6431	benign	203/583	438830	79,12205	2013	4129	6142	SO:0001583	missense	25759	exon4			GCCTTGTTGGGGG	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.608A>G	19.37:g.438830T>C	ENSP00000264554:p.Asn203Ser	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	7	5	NM_012435	0	0	0	0	0	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	T	2.476	-0.320733	0.05386	0.019374	1.21E-4	ENSG00000129946	ENST00000264554	T	0.13538	2.58	3.67	3.67	0.42095	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.047852	0.85682	D	0.000000	T	0.01156	0.0038	N	0.11064	0.09	0.47153	D	0.999335	B	0.24963	0.115	B	0.24701	0.055	T	0.23048	-1.0199	10	0.02654	T	1	-52.872	8.7866	0.34825	0.0:0.0989:0.0:0.9011	.	203	P98077	SHC2_HUMAN	S	203	ENSP00000264554:N203S	ENSP00000264554:N203S	N	-	2	0	SHC2	389830	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	2.390000	0.44416	1.632000	0.50472	0.402000	0.26972	AAC	T|0.990;C|0.010		0.682	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			C	438830	T	C	438830	3	2	61	1	0	0	0	0	1	0	0	0	14303	1725	60	3	1176	3	SHC2	19	438830	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		438830	58690153	87	5965											
ARID3A	1820	hgsc.bcm.edu	37	chr19	971962	971962	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggcggcggcagcagcagcaAcgcaggcggccggggaggaa	9	0	20	12	6	0	0	0	0	0	0	0	2	0	2	1	8	4	5	1	8	2	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:971962A>G	ENST00000263620.3	+	9	2006	c.1679A>G	c.(1678-1680)aAc>aGc	p.N560S		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	560	Gly-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		agcagcagcAACGCAGGCGGC	0.662																																					p.N560S	Pancreas(29;54 1022 32760 50921)	.											.	ARID3A-90	0			c.A1679G						.						25	30	28					19																	971962		2200	4292	6492	SO:0001583	missense	1820	exon9			GCAGCAACGCAGG	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1679A>G	19.37:g.971962A>G	ENSP00000263620:p.Asn560Ser	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_005224	0	0	0	0	0	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	37	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.446385	0.00178	.	.	ENSG00000116017	ENST00000263620	T	0.34667	1.35	2.91	-2.46	0.06461	.	3.447310	0.01123	N	0.005824	T	0.20700	0.0498	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08229	-1.0732	10	0.09843	T	0.71	-5.2858	3.9526	0.09375	0.257:0.2085:0.5345:0.0	.	560	Q99856	ARI3A_HUMAN	S	560	ENSP00000263620:N560S	ENSP00000263620:N560S	N	+	2	0	ARID3A	922962	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	-0.806000	0.04525	-0.772000	0.04602	0.418000	0.28097	AAC	.		0.662	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		G	971962	A	G	971962	3	3	61	1	0	0	0	0	1	0	0	0	916	43	2	3	1709	3	ARID3A	19	971962	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	533132	971962	58157021	88	5966											
BTBD2	55643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1986877	1986877	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgttgggcagcacctccacCggctccttgaacatgacgcg	8	7	11	15	4	0	2	0	2	0	0	2	2	2	2	4	2	2	4	4	2	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:1986877C>G	ENST00000255608.4	-	8	1384	c.1368G>C	c.(1366-1368)ccG>ccC	p.P456P	AC005306.3_ENST00000587498.1_RNA	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	456						cytoplasmic mRNA processing body (GO:0000932)				endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCACCTCCACCGGCTCCTTGA	0.632																																					p.P456P		.											.	BTBD2-92	0			c.G1368C						.						52	54	53					19																	1986877		2203	4300	6503	SO:0001819	synonymous_variant	55643	exon8			CTCCACCGGCTCC	AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"BTB/POZ domain containing"	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.1368G>C	19.37:g.1986877C>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	62	12	NM_017797	1	0	114	172	57	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Silent	SNP	ENST00000255608.4	37	CCDS12078.1																																																																																			.		0.632	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2			G	1986877	C	G	1986877	2	3	61	1	0	0	0	0	0	0	0	1	1546	639	23	4		4	BTBD2	19	1986877	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	1014915	1986877	57142106	89	5967											
SLC44A2	57153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10745556	10745556	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacttacggcagacctggttGgcctttagtgagtcacagtc	8	11	11	11	1	1	2	1	1	0	1	2	2	1	2	2	3	1	2	2	3	2	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:10745556G>C	ENST00000335757.5	+	11	1324	c.948G>C	c.(946-948)ttG>ttC	p.L316F	SLC44A2_ENST00000407327.4_Missense_Mutation_p.L314F|SLC44A2_ENST00000586078.1_Missense_Mutation_p.L316F			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	316					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	AGACCTGGTTGGCCTTTAGTG	0.597																																					p.L316F		.											.	SLC44A2-91	0			c.G948C						.						151	140	144					19																	10745556		2203	4300	6503	SO:0001583	missense	57153	exon11			CTGGTTGGCCTTT	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"Solute carriers"	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.948G>C	19.37:g.10745556G>C	ENSP00000336888:p.Leu316Phe	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	206	58	NM_020428	0	0	0	0	0	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	37	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177297	0.38413	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.14266	2.52;2.53	5.46	3.27	0.37495	.	0.532611	0.23295	N	0.049756	T	0.17534	0.0421	L	0.58101	1.795	0.45161	D	0.998171	B;B;B	0.20887	0.049;0.013;0.014	B;B;B	0.35727	0.209;0.04;0.16	T	0.03175	-1.1064	10	0.30854	T	0.27	-23.7844	9.2861	0.37758	0.0773:0.0:0.7775:0.1453	.	316;316;314	Q8IWA5-2;Q8IWA5;Q8IWA5-3	.;CTL2_HUMAN;.	F	314;316;316	ENSP00000385135:L314F;ENSP00000336888:L316F	ENSP00000336888:L316F	L	+	3	2	SLC44A2	10606556	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.740000	0.62087	0.641000	0.30601	0.557000	0.71058	TTG	.		0.597	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			C	10745556	G	C	10745556	3	2	61	1	0	0	0	0	1	0	0	0	14668	1339	47	4	1025	4	SLC44A2	19	10745556	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	8758679	10745556	48383427	90	5968											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11326077	11326077	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctacttgtccacgcggtcTgaggtttgcttccagtgtgt	5	14	11	11	2	1	1	0	1	1	0	3	1	3	1	3	2	2	2	3	2	1	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:11326077T>C	ENST00000294618.7	-	32	4103	c.4092A>G	c.(4090-4092)tcA>tcG	p.S1364S	DOCK6_ENST00000319867.7_Silent_p.S703S|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1364					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						CCACGCGGTCTGAGGTTTGCT	0.587																																					p.S1364S		.											.	DOCK6-93	0			c.A4092G						.						59	61	60					19																	11326077		2074	4199	6273	SO:0001819	synonymous_variant	57572	exon32			GCGGTCTGAGGTT		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.4092A>G	19.37:g.11326077T>C		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_020812	0	0	9	9	0	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			.		0.587	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		C	11326077	T	C	11326077	2	2	61	1	0	0	0	0	0	0	0	1	4702	1567	55	3		3	DOCK6	19	11326077	Silent	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	580521	11326077	47802906	91	5969											
ZNF823	55552	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11833231	11833231	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcatgtgacttcgaaagctcGagctatgagataacactttc	12	12	8	9	2	1	2	1	2	0	1	4	5	1	2	0	0	3	2	0	0	3	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:11833231G>C	ENST00000341191.6	-	4	1271	c.1118C>G	c.(1117-1119)tCg>tGg	p.S373W	ZNF823_ENST00000545749.1_Missense_Mutation_p.S191W	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	373					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(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						TCGAAAGCTCGAGCTATGAGA	0.423										HNSCC(68;0.2)																											p.S373W		.											.	ZNF823-24	0			c.C1118G						.						109	114	112					19																	11833231		2203	4300	6503	SO:0001583	missense	55552	exon4			AAGCTCGAGCTAT	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.1118C>G	19.37:g.11833231G>C	ENSP00000340683:p.Ser373Trp	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	154	47	NM_001080493	0	0	1	7	6	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	37	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	N	11.84	1.757736	0.31137	.	.	ENSG00000197933	ENST00000545749;ENST00000341191;ENST00000431998	T;T;T	0.08282	3.11;3.11;3.11	0.632	0.632	0.17705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30293	0.0760	M	0.90425	3.115	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.03384	-1.1042	9	0.87932	D	0	.	7.1241	0.25461	1.0E-4:0.0:0.9999:0.0	.	373	P16415	ZN823_HUMAN	W	191;373;329	ENSP00000440162:S191W;ENSP00000340683:S373W;ENSP00000410654:S329W	ENSP00000340683:S373W	S	-	2	0	ZNF823	11694231	0.000000	0.05858	0.001000	0.08648	0.423000	0.31445	-0.236000	0.09003	0.618000	0.30179	0.298000	0.19748	TCG	.		0.423	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		C	11833231	G	C	11833231	3	2	61	1	0	0	0	0	1	0	0	0	18211	1059	37	4	718	4	ZNF823	19	11833231	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	507154	11833231	47295752	92	5970											
PODNL1	79883	hgsc.bcm.edu	37	chr19	14044017	14044017	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggcacgcggtccagcccaTtgccatagaggtgcagcgtg	8	6	15	12	3	0	1	0	0	0	1	1	2	1	1	3	3	4	2	3	3	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:14044017T>C	ENST00000339560.5	-	8	1313	c.1040A>G	c.(1039-1041)aAt>aGt	p.N347S	PODNL1_ENST00000254320.3_Missense_Mutation_p.N265S|PODNL1_ENST00000538517.2_Missense_Mutation_p.N256S|PODNL1_ENST00000538371.2_Missense_Mutation_p.N345S	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	347	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			GTCCAGCCCATTGCCATAGAG	0.726																																					p.N347S		.											.	PODNL1-90	0			c.A1040G						.						4	6	5					19																	14044017		1952	3807	5759	SO:0001583	missense	79883	exon8			AGCCCATTGCCAT	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1040A>G	19.37:g.14044017T>C	ENSP00000345175:p.Asn347Ser	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	5	3	NM_024825	0	0	1	2	1	B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	CCDS12300.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.256351	0.39896	.	.	ENSG00000132000	ENST00000538371;ENST00000538517;ENST00000339560;ENST00000545071;ENST00000254320	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	4.58	2.44	0.29823	.	0.141451	0.31936	U	0.006840	D	0.84479	0.5481	H	0.94222	3.51	0.25906	N	0.983291	B;P;D;D	0.64830	0.286;0.883;0.994;0.969	B;P;D;P	0.63877	0.28;0.531;0.919;0.725	T	0.75897	-0.3155	10	0.72032	D	0.01	.	7.2206	0.25985	0.0:0.1948:0.0:0.8052	.	345;265;256;347	F5H7F9;B7Z3M0;G3V1J6;Q6PEZ8	.;.;.;PONL1_HUMAN	S	345;256;347;197;265	ENSP00000442553:N345S;ENSP00000440080:N256S;ENSP00000345175:N347S;ENSP00000254320:N265S	ENSP00000254320:N265S	N	-	2	0	PODNL1	13905017	1.000000	0.71417	0.729000	0.30791	0.099000	0.18886	4.215000	0.58534	0.613000	0.30089	-0.371000	0.07208	AAT	.		0.726	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		C	14044017	T	C	14044017	3	2	61	1	0	0	0	0	1	0	0	0	12205	1493	52	3	502	3	PODNL1	19	14044017	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	2210786	14044017	45084966	93	5971											
GRAMD1A	57655	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	35500801	35500802	+	Frame_Shift_Ins	INS	-	-	CA																															acttcctcagatgctgagccINSccacttataagcagcgtaat																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:35500801_35500802insCA	ENST00000317991.5	+	4	442_443	c.250_251insCA	c.(250-252)cccfs	p.P84fs	GRAMD1A_ENST00000424536.2_Frame_Shift_Ins_p.P84fs|GRAMD1A_ENST00000411896.2_Frame_Shift_Ins_p.P77fs|GRAMD1A_ENST00000504615.2_5'UTR|GRAMD1A_ENST00000598073.1_3'UTR|GRAMD1A_ENST00000599564.1_Frame_Shift_Ins_p.P171fs	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	84						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GATGCTGAGCCCCACTTATAAG	0.559																																					p.P84fs		.											.	GRAMD1A-90	0			c.250_251insCA						.																																			SO:0001589	frameshift_variant	57655	exon4			.	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		Exception_encountered	19.37:g.35500801_35500802insCA	ENSP00000441032:p.Pro84fs	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	147	50	NM_020895	0	0	0	0	0	A6NKY7|Q8NC77|Q9P1Z5	Frame_Shift_Ins	INS	ENST00000317991.5	37	CCDS42546.1																																																																																			.		0.559	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		CA	35500802	-	CA	35500801	7	5	61	1	0	1	1	0	0	0	0	0	6768	623	22	0	264	0	GRAMD1A	19	35500801	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	21456784	35500801	23628182	94	5972											
ZFP82	284406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36883897	36883897	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acattccttacatttataagGtttctcaccaatatgaatac	14	15	3	9	0	1	1	1	1	1	0	3	1	2	1	2	1	2	1	2	1	7	8	rs143115887		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:36883897G>T	ENST00000392161.3	-	5	1587	c.1345C>A	c.(1345-1347)Cct>Act	p.P449T	ZFP82_ENST00000392171.1_Missense_Mutation_p.P449T	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P449S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CATTTATAAGGTTTCTCACCA	0.413																																					p.P449T		.											.	ZFP82-91	1	Substitution - Missense(1)	skin(1)	c.C1345A						.						92	90	91					19																	36883897		2203	4300	6503	SO:0001583	missense	284406	exon5			TATAAGGTTTCTC	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"Zinc fingers, C2H2-type", "-"	28682	protein-coding gene	gene with protein product			"zinc finger protein 545", "zinc finger protein 82 homolog (mouse)", "zinc finger protein 82"	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1345C>A	19.37:g.36883897G>T	ENSP00000431265:p.Pro449Thr	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	170	54	NM_133466	0	0	3	4	1	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	37	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536339	0.65085	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.16897	2.31;2.31	4.2	4.2	0.49525	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41294	D	0.000902	T	0.42698	0.1214	M	0.79343	2.45	0.49915	D	0.999832	D	0.89917	1.0	D	0.97110	1.0	T	0.44003	-0.9356	10	0.72032	D	0.01	.	14.447	0.67359	0.0:0.0:1.0:0.0	.	449	Q8N141	ZFP82_HUMAN	T	449	ENSP00000431265:P449T;ENSP00000446080:P449T	ENSP00000431265:P449T	P	-	1	0	ZFP82	41575737	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.542000	0.82095	2.352000	0.79861	0.591000	0.81541	CCT	.		0.413	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		T	36883897	G	T	36883897	3	4	61	1	0	0	0	0	1	0	0	0	17685	1261	44	4	257	4	ZFP82	19	36883897	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	1383096	36883897	22245086	95	5973											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41018832	41018832	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgagctgggcgggcggcgAgcgttgctgcagcaggccct	4	5	20	12	5	0	0	0	0	0	0	0	2	0	0	1	5	5	5	1	5	0	1	rs814533	byFrequency	TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:41018832A>G	ENST00000352632.3	+	14	2222	c.2136A>G	c.(2134-2136)cgA>cgG	p.R712R	SPTBN4_ENST00000344104.3_Silent_p.R712R|SPTBN4_ENST00000338932.3_Silent_p.R712R|SPTBN4_ENST00000598249.1_Silent_p.R712R|SPTBN4_ENST00000595535.1_Silent_p.R712R			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	712					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGGGCGGCGAGCGTTGCTGC	0.751													G|||	1110	0.221645	0.4758	0.1239	5008	,	,		9743	0.1052		0.1372	False		,,,				2504	0.1544				p.R712R		.											.	SPTBN4-94	0			c.A2136G						.	G		502,1916		17,468,724	1	2	2		2136	3.2	1	19	dbSNP_86	2	282,4934		4,274,2330	no	coding-synonymous	SPTBN4	NM_020971.2		21,742,3054	GG,GA,AA		5.4064,20.761,10.2698		712/2565	41018832	784,6850	1209	2608	3817	SO:0001819	synonymous_variant	57731	exon14			GCGGCGAGCGTTG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.2136A>G	19.37:g.41018832A>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_020971	0	0	0	0	0	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			A|0.806;G|0.194		0.751	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			G	41018832	A	G	41018832	2	3	61	1	0	0	0	0	0	0	0	1	15153	291	11	3		3	SPTBN4	19	41018832	Silent	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	4134935	41018832	18110151	96	5974											
CPT1C	126129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50200612	50200612	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccggtgtgtttcctgcCagccccctcagttggctttt	3	14	9	15	1	2	0	2	0	0	0	3	0	3	0	5	2	2	3	5	2	0	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:50200612C>A	ENST00000392518.4	+	4	543	c.171C>A	c.(169-171)gcC>gcA	p.A57A	CPT1C_ENST00000354199.5_Silent_p.A57A|CPT1C_ENST00000323446.5_Silent_p.A57A|CPT1C_ENST00000405931.2_Silent_p.A57A|CPT1C_ENST00000598293.1_Silent_p.A57A	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	57					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		TGTTTCCTGCCAGCCCCCTCA	0.542																																					p.A57A		.											.	CPT1C-92	0			c.C171A						.						194	139	158					19																	50200612		2203	4300	6503	SO:0001819	synonymous_variant	126129	exon4			TCCTGCCAGCCCC	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.171C>A	19.37:g.50200612C>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	101	27	NM_001199752	0	0	4	4	0	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	37	CCDS12779.1																																																																																			.		0.542	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		A	50200612	C	A	50200612	2	1	61	1	0	0	0	0	0	0	0	1	3839	581	21	4		4	CPT1C	19	50200612	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	9181780	50200612	8928371	97	5975											
ZNF613	79898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52447643	52447643	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttccttcatgccaagcaTgaacaatttcataatgaaat	14	13	4	10	0	2	2	2	2	0	0	4	2	4	2	3	0	3	1	3	0	5	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:52447643T>A	ENST00000293471.6	+	6	1186	c.507T>A	c.(505-507)caT>caA	p.H169Q	ZNF613_ENST00000391794.4_Missense_Mutation_p.H133Q	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	169					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(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		ATGCCAAGCATGAACAATTTC	0.348																																					p.H169Q		.											.	ZNF613-91	0			c.T507A						.						94	102	99					19																	52447643		2203	4300	6503	SO:0001583	missense	79898	exon6			CAAGCATGAACAA	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.507T>A	19.37:g.52447643T>A	ENSP00000293471:p.His169Gln	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	196	77	NM_001031721	0	0	7	10	3	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	37	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	T	10.57	1.386951	0.25031	.	.	ENSG00000176024	ENST00000293471;ENST00000391794	T;T	0.28454	1.61;1.61	2.9	1.88	0.25563	.	0.429945	0.17365	N	0.176876	T	0.18882	0.0453	N	0.24115	0.695	0.25401	N	0.988446	P	0.51791	0.948	B	0.42555	0.391	T	0.08973	-1.0696	10	0.62326	D	0.03	.	6.0884	0.19980	0.0:0.1332:0.0:0.8668	.	169	Q6PF04	ZN613_HUMAN	Q	169;133	ENSP00000293471:H169Q;ENSP00000375671:H133Q	ENSP00000293471:H169Q	H	+	3	2	ZNF613	57139455	0.003000	0.15002	0.186000	0.23195	0.107000	0.19398	0.002000	0.13061	0.531000	0.28639	0.528000	0.53228	CAT	.		0.348	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		A	52447643	T	A	52447643	3	1	61	1	0	0	0	0	1	0	0	0	18070	1461	51	5	521	5	ZNF613	19	52447643	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	2247031	52447643	6681340	98	5976											
MZF1	7593	hgsc.bcm.edu;broad.mit.edu	37	chr19	59082617	59082617	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatagcggaagcaccggAaacgcaggcgtgcagcttca	11	5	12	13	4	2	0	2	0	0	0	2	2	2	2	2	3	5	4	2	3	3	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:59082617A>G	ENST00000215057.2	-	2	700	c.140T>C	c.(139-141)tTc>tCc	p.F47S	MZF1_ENST00000599369.1_Missense_Mutation_p.F47S|MZF1_ENST00000594234.1_Missense_Mutation_p.F47S|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594108.1_Missense_Mutation_p.F47S	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	47	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		GAAGCACCGGAAACGCAGGCG	0.642																																					p.F47S		.											.	MZF1-91	0			c.T140C						.						22	25	24					19																	59082617		2203	4299	6502	SO:0001583	missense	7593	exon2			CACCGGAAACGCA	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.140T>C	19.37:g.59082617A>G	ENSP00000215057:p.Phe47Ser	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	38	3	NM_198055	0	0	7	7	0	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.955202	0.53293	.	.	ENSG00000099326	ENST00000215057	T	0.12984	2.63	4.35	4.35	0.52113	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.000000	0.42420	D	0.000720	T	0.47248	0.1435	H	0.96943	3.91	0.09310	N	0.999996	D;B	0.76494	0.999;0.261	D;B	0.67231	0.95;0.247	T	0.54622	-0.8266	9	.	.	.	-23.3828	10.1266	0.42654	1.0:0.0:0.0:0.0	.	47;47	Q7Z729;P28698	.;MZF1_HUMAN	S	47	ENSP00000215057:F47S	.	F	-	2	0	MZF1	63774429	0.001000	0.12720	0.022000	0.16811	0.835000	0.47333	1.122000	0.31295	1.959000	0.56917	0.460000	0.39030	TTC	.		0.642	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		G	59082617	A	G	59082617	3	3	61	1	0	0	0	0	1	0	0	0	10133	246	9	3	2084	3	MZF1	19	59082617	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	6634974	59082617	46366	99	5977											
CPXM1	56265	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	2775062	2775063	+	Frame_Shift_Ins	INS	-	-	A																															tggggtcagcagacgccaatINSaatccccgccccacgctgag																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr20:2775062_2775063insA	ENST00000380605.2	-	14	2042_2043	c.1978_1979insT	c.(1978-1980)tatfs	p.Y660fs		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	660					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CAGACGCCAATAATCCCCGCCC	0.599																																					p.Y660fs		.											.	CPXM1-94	0			c.1979_1980insT						.																																			SO:0001589	frameshift_variant	56265	exon14			.	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.1979dupT	20.37:g.2775064_2775064dupA	ENSP00000369979:p.Tyr660fs	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	73	28	NM_019609	0	0	0	0	0	Q6P4G8|Q6UW65|Q9NUB5	Frame_Shift_Ins	INS	ENST00000380605.2	37	CCDS13033.1																																																																																			.		0.599	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		A	2775063	-	A	2775062	7	5	61	1	0	1	1	0	0	0	0	0	3843	1406	49	0	229	0	CPXM1	20	2775062	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08		2775062	60250458	100	5978											
ZNF341	84905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	32357951	32357951	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctcgacacatttctggAgcacatcaagagccaccagg	14	6	9	12	1	2	1	1	0	1	1	3	3	2	2	2	2	3	2	2	2	2	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr20:32357951A>C	ENST00000375200.1	+	10	1840	c.1475A>C	c.(1474-1476)gAg>gCg	p.E492A	ZNF341_ENST00000342427.2_Missense_Mutation_p.E485A	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	492					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						ACATTTCTGGAGCACATCAAG	0.597																																					p.E485A		.											.	ZNF341-92	0			c.A1454C						.						69	58	61					20																	32357951		2203	4300	6503	SO:0001583	missense	84905	exon10			TTCTGGAGCACAT	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"Zinc fingers, C2H2-type"	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1475A>C	20.37:g.32357951A>C	ENSP00000364346:p.Glu492Ala	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	43	15	NM_032819	0	0	4	5	1	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	37		.	.	.	.	.	.	.	.	.	.	A	25.6	4.651504	0.88056	.	.	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.31247	1.5;1.5	5.35	5.35	0.76521	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.051359	0.85682	D	0.000000	T	0.30696	0.0773	N	0.17872	0.535	0.53005	D	0.999962	P;P;P	0.50819	0.792;0.939;0.925	B;P;P	0.53809	0.257;0.735;0.616	T	0.03608	-1.1020	10	0.13470	T	0.59	-36.6794	15.6282	0.76878	1.0:0.0:0.0:0.0	.	433;492;485	Q504V9;Q9BYN7;Q9BYN7-2	.;ZN341_HUMAN;.	A	485;492	ENSP00000344308:E485A;ENSP00000364346:E492A	ENSP00000344308:E485A	E	+	2	0	ZNF341	31821612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.898000	0.92538	2.152000	0.67230	0.443000	0.29094	GAG	.		0.597	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				C	32357951	A	C	32357951	3	2	61	1	0	0	0	0	1	0	0	0	17889	304	11	5	1492	5	ZNF341	20	32357951	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	29582889	32357951	30667569	101	5979											
MORC3	23515	hgsc.bcm.edu	37	chr21	37692578	37692578	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaagatggcggcgcagccaCcccgcgggatacgcctcagc	8	4	13	16	5	2	1	2	0	0	1	2	2	2	2	4	3	3	1	4	3	2	1	rs202025634	byFrequency	TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr21:37692578C>A	ENST00000400485.1	+	1	92	c.16C>A	c.(16-18)Ccc>Acc	p.P6T	AP000692.10_ENST00000608391.1_RNA|MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	6					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						GGCGCAGCCACCCCGCGGGAT	0.726													C|||	3	0.000599042	0.0023	0	5008	,	,		9802	0		0	False		,,,				2504	0				p.P6T		.											.	MORC3-92	0			c.C16A						.						8	10	9					21																	37692578		1849	4043	5892	SO:0001583	missense	23515	exon1			CAGCCACCCCGCG	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"zinc finger, CW-type with coiled-coil domain 3", "zinc finger, CW type with coiled-coil domain 3"	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.16C>A	21.37:g.37692578C>A	ENSP00000383333:p.Pro6Thr	Somatic	6	1		WXS	Illumina HiSeq	Phase_I	8	5	NM_015358	0	0	0	0	0	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	C	12.61	1.990603	0.35131	.	.	ENSG00000159256	ENST00000400485	T	0.13778	2.56	4.65	2.84	0.33178	.	0.737086	0.13416	N	0.389504	T	0.06781	0.0173	N	0.14661	0.345	0.27815	N	0.941991	B	0.06786	0.001	B	0.06405	0.002	T	0.41034	-0.9531	10	0.07990	T	0.79	-2.4018	8.1544	0.31160	0.0:0.8113:0.0:0.1887	.	6	Q14149	MORC3_HUMAN	T	6	ENSP00000383333:P6T	ENSP00000383333:P6T	P	+	1	0	MORC3	36614448	0.999000	0.42202	1.000000	0.80357	0.985000	0.73830	1.816000	0.38992	0.561000	0.29186	0.563000	0.77884	CCC	.		0.726	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37692578	C	A	37692578	3	1	61	1	0	0	0	0	1	0	0	0	9728	507	18	4	18	4	MORC3	21	37692578	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		37692578	10437317	102	5980											
CECR6	27439	hgsc.bcm.edu	37	chr22	17600589	17600589	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgccagcaagggcacgtccaCcaggcagccgcccagcaggc	9	1	13	18	3	0	0	0	0	0	0	1	0	1	0	5	3	3	4	5	3	1	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:17600589C>G	ENST00000331437.3	-	1	1554	c.1429G>C	c.(1429-1431)Gtg>Ctg	p.V477L	CECR6_ENST00000399875.1_Missense_Mutation_p.V122L|AC006946.15_ENST00000441544.1_5'Flank	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	477										haematopoietic_and_lymphoid_tissue(1)	1		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)		GGCACGTCCACCAGGCAGCCG	0.697																																					p.V477L		.											.	CECR6-90	0			c.G1429C						.						4	4	4					22																	17600589		2023	4042	6065	SO:0001583	missense	27439	exon1			CGTCCACCAGGCA	AF307451	CCDS13740.1, CCDS54494.1	22q11.2	2008-06-12			ENSG00000183307	ENSG00000183307			1844	protein-coding gene	gene with protein product						11381032	Standard	NM_031890		Approved		uc002zmb.2	Q9BXQ6	OTTHUMG00000030471	ENST00000331437.3:c.1429G>C	22.37:g.17600589C>G	ENSP00000329318:p.Val477Leu	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_031890	0	0	0	0	0	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	37	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.137885	0.37728	.	.	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.32	4.32	0.51571	.	0.000000	0.53938	U	0.000050	T	0.47820	0.1466	N	0.20986	0.625	0.40994	D	0.984875	P	0.35745	0.518	B	0.39531	0.302	T	0.56571	-0.7957	9	0.59425	D	0.04	.	14.668	0.68924	0.0:1.0:0.0:0.0	.	477	Q9BXQ6	CECR6_HUMAN	L	122;477	.	ENSP00000329318:V477L	V	-	1	0	CECR6	15980589	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	4.385000	0.59613	2.116000	0.64780	0.462000	0.41574	GTG	.		0.697	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890		G	17600589	C	G	17600589	3	3	61	1	0	0	0	0	1	0	0	0	3214	507	18	4	311	4	CECR6	22	17600589	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		17600589	33703977	103	5981											
PPM1F	9647	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	22285579	22285579	+	Frame_Shift_Del	DEL	T	T	-																															ctgtccctgctgtaccaaaaTgacctgggaatccccgagcc																								rs376795506		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:22285579delT	ENST00000263212.5	-	6	937	c.832delA	c.(832-834)attfs	p.I278fs	PPM1F_ENST00000538191.1_Frame_Shift_Del_p.I174fs|PPM1F_ENST00000397495.4_Frame_Shift_Del_p.I278fs|PPM1F_ENST00000407142.1_Frame_Shift_Del_p.I110fs	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	278					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		TGTACCAAAATGACCTGGGAA	0.637																																					p.I278fs		.											.	PPM1F-292	0			c.832delA						.						124	98	107					22																	22285579		2203	4300	6503	SO:0001589	frameshift_variant	9647	exon6			.	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.832delA	22.37:g.22285579delT	ENSP00000263212:p.Ile278fs	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	90	41	NM_014634	0	0	0	0	0	A8K6G3|B7Z2C3|Q96PM2	Frame_Shift_Del	DEL	ENST00000263212.5	37	CCDS13796.1																																																																																			.		0.637	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		-	22285579	T	-	22285579	7	5	61	1	0	1	0	1	0	0	0	0	12368	1464	51	0	544	0	PPM1F	22	22285579	Frame_Shift_Del	DEL	T	TCGA-BQ-5877-01A-11D-1589-08	4684990	22285579	29018987	104	5982											
CABIN1	23523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24447376	24447376	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgcgaaaaaagaggcaagCgctgattgtgcgggagaagg	13	5	17	6	3	0	3	0	1	0	2	0	5	0	3	0	3	3	3	0	3	5	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:24447376C>T	ENST00000398319.2	+	8	1131	c.746C>T	c.(745-747)gCg>gTg	p.A249V	CABIN1_ENST00000263119.5_Missense_Mutation_p.A249V|CABIN1_ENST00000405822.2_Intron	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	249					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AAGAGGCAAGCGCTGATTGTG	0.542																																					p.A249V		.											.	CABIN1-94	0			c.C746T						.						117	102	107					22																	24447376		2203	4300	6503	SO:0001583	missense	23523	exon8			GGCAAGCGCTGAT	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.746C>T	22.37:g.24447376C>T	ENSP00000381364:p.Ala249Val	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	58	25	NM_001199281	0	0	3	9	6	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679191	0.68042	.	.	ENSG00000099991	ENST00000454754;ENST00000263119;ENST00000445422;ENST00000398319;ENST00000536026	T;T;T;T	0.63096	0.33;-0.02;0.33;-0.02	5.32	5.32	0.75619	.	0.105434	0.64402	D	0.000006	T	0.73969	0.3655	L	0.56769	1.78	0.80722	D	1	D;D;D	0.71674	0.986;0.963;0.998	P;B;P	0.61132	0.457;0.373;0.884	T	0.72418	-0.4300	10	0.40728	T	0.16	.	18.4214	0.90591	0.0:1.0:0.0:0.0	.	204;249;249	C9J068;F5H5W5;Q9Y6J0	.;.;CABIN_HUMAN	V	204;249;204;249;249	ENSP00000394209:A204V;ENSP00000263119:A249V;ENSP00000412389:A204V;ENSP00000381364:A249V	ENSP00000263119:A249V	A	+	2	0	CABIN1	22777376	1.000000	0.71417	0.979000	0.43373	0.279000	0.26890	6.486000	0.73629	2.666000	0.90696	0.551000	0.68910	GCG	.		0.542	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24447376	C	T	24447376	3	4	61	1	0	0	0	0	1	0	0	0	2534	768	27	1	772	1	CABIN1	22	24447376	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	2161797	24447376	26857190	105	5983											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30050709	30050709	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccaagaggaattgcttccaAaaagggtaagagattaaatt	17	9	9	6	0	0	2	0	0	0	2	1	4	1	3	2	2	1	2	2	2	7	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:30050709A>T	ENST00000338641.4	+	5	952	c.511A>T	c.(511-513)Aaa>Taa	p.K171*	NF2_ENST00000413209.2_Intron|NF2_ENST00000347330.5_Intron|NF2_ENST00000403435.1_Nonsense_Mutation_p.K171*|NF2_ENST00000361452.4_Nonsense_Mutation_p.K130*|NF2_ENST00000353887.4_Nonsense_Mutation_p.K88*|NF2_ENST00000334961.7_Nonsense_Mutation_p.K88*|NF2_ENST00000403999.3_Nonsense_Mutation_p.K171*|NF2_ENST00000361676.4_Nonsense_Mutation_p.K129*|NF2_ENST00000361166.4_Nonsense_Mutation_p.K171*|NF2_ENST00000397789.3_Nonsense_Mutation_p.K171*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	171	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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.?(3)		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						ATTGCTTCCAAAAAGGGTAAG	0.423			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.K171X		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	3	Unknown(3)	large_intestine(1)|stomach(1)|central_nervous_system(1)	c.A511T						.						113	114	114					22																	30050709		2203	4300	6503	SO:0001587	stop_gained	4771	exon5	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	CTTCCAAAAAGGG	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.511A>T	22.37:g.30050709A>T	ENSP00000344666:p.Lys171*	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	145	73	NM_000268	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	A	41	8.773705	0.98948	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.99	5.99	0.97316	.	0.049049	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	.	.	.	X	171;171;130;171;171;88;88;171;129;171	.	.	K	+	1	0	NF2	28380709	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.185000	0.94900	2.291000	0.77112	0.533000	0.62120	AAA	.		0.423	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		T	30050709	A	T	30050709	4	4	61	1	0	0	0	0	0	1	0	0	10383	15	1	5	529	5	NF2	22	30050709	Nonsense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	5603333	30050709	21253857	106	5984											
USP9Y	8287	hgsc.bcm.edu	37	chrY	14847584	14847584	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcaataaatttggcacattAaatgggttccagattttgca	14	14	7	6	0	1	1	1	0	0	1	2	1	2	1	1	2	1	3	1	2	5	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chrY:14847584A>G	ENST00000338981.3	+	8	1641	c.696A>G	c.(694-696)ttA>ttG	p.L232L	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	232					BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TTGGCACATTAAATGGGTTCC	0.289																																					p.L232L		.											.	USP9Y-136	0			c.A696G						.						51	52	52					Y																	14847584		591	1915	2506	SO:0001819	synonymous_variant	8287	exon8			CACATTAAATGGG	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.696A>G	Y.37:g.14847584A>G		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_004654	0	0	2	2	0	O14601	Silent	SNP	ENST00000338981.3	37	CCDS14781.1																																																																																			.		0.289	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		G	14847584	A	G	14847584	2	3	61	1	0	0	0	0	0	0	0	1	17124	359	13	3		3	USP9Y	24	14847584	Silent	SNP	A	TCGA-BQ-5877-01A-11D-1589-08		14847584	44525982	107	5985											
USP9Y	8287	hgsc.bcm.edu	37	chrY	14847619	14847619	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgcatgatcgtttttttaAtggatcagcattaaatattc	11	19	6	5	1	1	1	1	1	0	0	3	2	1	2	0	1	2	3	0	1	4	8			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chrY:14847619A>C	ENST00000338981.3	+	8	1676	c.731A>C	c.(730-732)aAt>aCt	p.N244T	USP9Y_ENST00000426564.2_3'UTR	NM_004654.3	NP_004645.2	O00507	USP9Y_HUMAN	ubiquitin specific peptidase 9, Y-linked	244					BMP signaling pathway (GO:0030509)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)	co-SMAD binding (GO:0070410)|cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(8)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CGTTTTTTTAATGGATCAGCA	0.274																																					p.N244T		.											.	USP9Y-136	0			c.A731C						.						46	46	46					Y																	14847619		590	1912	2502	SO:0001583	missense	8287	exon8			TTTTTAATGGATC	Y13618	CCDS14781.1	Yq11.2	2010-04-09	2009-03-17		ENSG00000114374	ENSG00000114374		"Ubiquitin-specific peptidases"	12633	protein-coding gene	gene with protein product	"fat facets-like homolog (Drosophila)"	400005	"ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)"			8922996, 9384609, 19246359	Standard	NM_004654		Approved	DFFRY	uc004fst.1	O00507	OTTHUMG00000036469	ENST00000338981.3:c.731A>C	Y.37:g.14847619A>C	ENSP00000342812:p.Asn244Thr	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_004654	0	0	0	0	0	O14601	Missense_Mutation	SNP	ENST00000338981.3	37	CCDS14781.1																																																																																			.		0.274	USP9Y-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088703.2	NM_004654		C	14847619	A	C	14847619	3	2	61	1	0	0	0	0	1	0	0	0	17124	101	4	5	753	5	USP9Y	24	14847619	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	35	14847619	44525947	108	5986											
CHD5	26038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6204188	6204188	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggtctttccacttgatcagGtagtgcacatcccccttctt	7	14	7	13	0	3	1	1	1	2	0	5	1	5	1	3	2	1	2	3	2	1	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:6204188G>A	ENST00000262450.3	-	12	1929	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		ACTTGATCAGGTAGTGCACAT	0.567																																					p.Y610Y		.											.	CHD5-719	0			c.C1830T						.						245	196	213					1																	6204188		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon12			GATCAGGTAGTGC	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"Zinc fingers, PHD-type"	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.1830C>T	1.37:g.6204188G>A		Somatic	187	0		WXS	Illumina HiSeq	Phase_I	169	82	NM_015557	0	0	0	0	0	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			.		0.567	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6204188	G	A	6204188	2	1	62	1	0	0	0	0	0	0	0	1	3334	1256	44	2		2	CHD5	1	6204188	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		6204188	243046433	1	5987											
PTCHD2	57540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11562884	11562884	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actcagtagatgaccgctggGaggaacaacgggctaagttt	12	8	13	8	2	1	2	1	1	0	1	1	4	1	4	1	3	2	4	1	3	4	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:11562884G>T	ENST00000294484.6	+	3	1384	c.1246G>T	c.(1246-1248)Gag>Tag	p.E416*	PTCHD2_ENST00000389575.3_Nonsense_Mutation_p.E416*	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	416					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		TGACCGCTGGGAGGAACAACG	0.567																																					p.E416X		.											.	PTCHD2-209	0			c.G1246T						.						92	94	93					1																	11562884		2002	4177	6179	SO:0001587	stop_gained	57540	exon3			CGCTGGGAGGAAC	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1246G>T	1.37:g.11562884G>T	ENSP00000294484:p.Glu416*	Somatic	87	1		WXS	Illumina HiSeq	Phase_I	80	8	NM_020780	0	0	0	0	0	Q5VTU9|Q9UJD6	Nonsense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	G	39	7.696786	0.98438	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	.	.	.	6.08	6.08	0.98989	.	0.376195	0.29185	N	0.012886	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-34.0868	19.2272	0.93822	0.0:0.0:1.0:0.0	.	.	.	.	X	416	.	ENSP00000294484:E416X	E	+	1	0	PTCHD2	11485471	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.420000	0.52735	2.894000	0.99253	0.655000	0.94253	GAG	.		0.567	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11562884	G	T	11562884	4	4	62	1	0	0	0	0	0	1	0	0	12762	1175	41	4	1252	4	PTCHD2	1	11562884	Nonsense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	5358696	11562884	237687737	2	5988											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27057775	27057775	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaccaccgtcccagacccctCatgcccaaccttcgtatcag	10	7	5	19	2	2	1	2	0	0	1	4	1	3	1	7	0	3	1	7	0	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:27057775C>T	ENST00000324856.7	+	3	1854	c.1483C>T	c.(1483-1485)Cat>Tat	p.H495Y	ARID1A_ENST00000457599.2_Missense_Mutation_p.H495Y|ARID1A_ENST00000374152.2_Missense_Mutation_p.H112Y	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	495					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCAGACCCCTCATGCCCAACC	0.582			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.H495Y		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.C1483T						.						347	315	326					1																	27057775		2203	4300	6503	SO:0001583	missense	8289	exon3			ACCCCTCATGCCC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1483C>T	1.37:g.27057775C>T	ENSP00000320485:p.His495Tyr	Somatic	443	0		WXS	Illumina HiSeq	Phase_I	446	61	NM_006015	0	0	73	83	10	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.935864	0.34189	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	T;T;T;T	0.43688	4.5;4.28;0.94;4.29	5.33	5.33	0.75918	.	0.344170	0.34046	N	0.004318	T	0.22437	0.0541	N	0.08118	0	0.80722	D	1	B;B;B	0.29988	0.068;0.264;0.068	B;B;B	0.24701	0.014;0.055;0.014	T	0.12993	-1.0526	10	0.02654	T	1	-11.5851	19.2116	0.93757	0.0:1.0:0.0:0.0	.	495;495;149	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	Y	495;495;112;112	ENSP00000320485:H495Y;ENSP00000387636:H495Y;ENSP00000432473:H112Y;ENSP00000363267:H112Y	ENSP00000320485:H495Y	H	+	1	0	ARID1A	26930362	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	3.260000	0.51523	2.766000	0.95052	0.655000	0.94253	CAT	.		0.582	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27057775	C	T	27057775	3	4	62	1	0	0	0	0	1	0	0	0	913	826	29	2	1493	2	ARID1A	1	27057775	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	15494891	27057775	222192846	3	5989											
POMGNT1	55624	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	46662703	46662704	+	Frame_Shift_Del	DEL	GA	GA	-																															atggctcgccgagtgtccagGatcaacttgatattgacaat																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:46662703_46662704delGA	ENST00000371984.3	-	3	330_331	c.173_174delTC	c.(172-174)atcfs	p.I58fs	POMGNT1_ENST00000535522.1_Frame_Shift_Del_p.I36fs|POMGNT1_ENST00000396420.3_Frame_Shift_Del_p.I58fs|POMGNT1_ENST00000371992.1_Frame_Shift_Del_p.I58fs|POMGNT1_ENST00000371986.3_Frame_Shift_Del_p.I58fs	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)	58					protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)			breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(166;0.155)					GAGTGTCCAGGATCAACTTGAT	0.55																																					p.58_58del		.											.	POMGNT1-91	0			c.173_174del						.																																			SO:0001589	frameshift_variant	55624	exon3			.		CCDS531.1, CCDS57995.1	1p34.1	2014-09-17	2013-07-31		ENSG00000085998	ENSG00000085998	2.4.1.-	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	19139	protein-coding gene	gene with protein product	"protein O-mannose beta-1,2-N-acetylglucosaminyltransferase"	606822	"muscle-eye-brain disease", "protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase"	MEB		11742540, 12788071	Standard	NM_017739		Approved	FLJ20277, MGAT1.2, LGMD2O	uc001cpg.3	Q8WZA1	OTTHUMG00000007604	ENST00000371984.3:c.173_174delTC	1.37:g.46662703_46662704delGA	ENSP00000361052:p.Ile58fs	Somatic	312	0		WXS	Illumina HiSeq	Phase_I	257	97	NM_017739	0	0	0	0	0	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Frame_Shift_Del	DEL	ENST00000371984.3	37	CCDS531.1																																																																																			.		0.55	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739		-	46662704	GA	-	46662703	7	5	62	1	0	1	0	1	0	0	0	0	12269	1164	41	0	1888	0	POMGNT1	1	46662703	Frame_Shift_Del	DEL	GA	TCGA-BQ-5878-01A-11D-1589-08	19604928	46662703	202587918	4	5990											
C1orf177	163747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	55272686	55272686	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggtttgacatctctgctgTttatcccaactggaagaagt	10	14	9	8	0	1	2	0	1	1	1	3	3	2	3	1	2	2	3	1	2	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:55272686T>C	ENST00000371273.3	+	2	137	c.122T>C	c.(121-123)gTt>gCt	p.V41A	C1orf177_ENST00000358193.3_Missense_Mutation_p.V41A	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	41										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						ATCTCTGCTGTTTATCCCAAC	0.582																																					p.V41A		.											.	C1orf177-90	0			c.T122C						.						230	214	219					1																	55272686		2203	4300	6503	SO:0001583	missense	163747	exon2			CTGCTGTTTATCC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.122T>C	1.37:g.55272686T>C	ENSP00000360320:p.Val41Ala	Somatic	304	0		WXS	Illumina HiSeq	Phase_I	240	97	NM_001110533	0	0	0	0	0	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.241605	0.39598	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26518	1.73;1.73	3.72	3.72	0.42706	.	0.129282	0.31821	N	0.007008	T	0.36138	0.0956	L	0.59436	1.845	0.36448	D	0.865922	D;D	0.56035	0.974;0.974	P;P	0.54499	0.754;0.754	T	0.43589	-0.9382	10	0.48119	T	0.1	-2.4596	10.7545	0.46228	0.0:0.0:0.0:1.0	.	41;41	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	A	41	ENSP00000350924:V41A;ENSP00000360320:V41A	ENSP00000350924:V41A	V	+	2	0	C1orf177	55045274	0.977000	0.34250	0.832000	0.32986	0.687000	0.40016	2.492000	0.45311	1.929000	0.55896	0.379000	0.24179	GTT	.		0.582	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		C	55272686	T	C	55272686	3	2	62	1	0	0	0	0	1	0	0	0	2023	1725	60	3	128	3	C1orf177	1	55272686	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	8609983	55272686	193977935	5	5991											
L1TD1	54596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	62672679	62672679	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggagaaaactctaaaataGgtgatgataatgaaaattta	21	10	8	2	0	1	4	0	3	1	1	1	5	1	4	0	2	1	0	0	2	10	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:62672679G>C	ENST00000498273.1	+	3	674	c.379G>C	c.(379-381)Ggt>Cgt	p.G127R		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	127										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						ctctaaaataggtgatgataa	0.308																																					p.G127R		.											.	L1TD1-92	0			c.G379C						.						59	70	66					1																	62672679		2194	4294	6488	SO:0001583	missense	54596	exon4			AAAATAGGTGATG	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.379G>C	1.37:g.62672679G>C	ENSP00000419901:p.Gly127Arg	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	96	46	NM_001164835	0	0	0	0	0	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	6.882	0.532168	0.13127	.	.	ENSG00000240563	ENST00000498273	T	0.11277	2.79	2.07	1.1	0.20463	.	.	.	.	.	T	0.06142	0.0159	N	0.14661	0.345	0.09310	N	1	B	0.27594	0.182	B	0.25291	0.059	T	0.36504	-0.9745	9	0.54805	T	0.06	.	6.423	0.21754	0.0:0.3091:0.6909:0.0	.	127	Q5T7N2	LITD1_HUMAN	R	127	ENSP00000419901:G127R	ENSP00000419901:G127R	G	+	1	0	L1TD1	62445267	0.034000	0.19679	0.001000	0.08648	0.024000	0.10985	1.838000	0.39211	0.419000	0.25927	0.313000	0.20887	GGT	.		0.308	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		C	62672679	G	C	62672679	3	2	62	1	0	0	0	0	1	0	0	0	8610	1000	35	4	381	4	L1TD1	1	62672679	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	7399993	62672679	186577942	6	5992											
VANGL1	81839	broad.mit.edu;bcgsc.ca	37	chr1	116202267	116202267	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attgttgtttttcagggaaaGaactagagagagacacaagt	15	11	11	4	0	1	3	1	0	0	3	1	6	1	4	0	1	1	2	0	1	4	5	rs143990097		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:116202267G>C	ENST00000355485.2	+	3	348	c.77G>C	c.(76-78)aGa>aCa	p.R26T	VANGL1_ENST00000369510.4_Missense_Mutation_p.R26T|VANGL1_ENST00000310260.3_Missense_Mutation_p.R26T|VANGL1_ENST00000369509.1_Missense_Mutation_p.R26T	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	26					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTCAGGGAAAGAACTAGAGAG	0.413																																					p.R26T													.	VANGL1-226	0			c.G77C						.						127	138	134					1																	116202267		2203	4300	6503	SO:0001583	missense	81839	exon3			GGGAAAGAACTAG	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.77G>C	1.37:g.116202267G>C	ENSP00000347672:p.Arg26Thr	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	190	8	NM_001172412	0	0	0	0	0	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.572304	0.86542	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.88381	0.6421	M	0.70595	2.14	0.58432	D	0.999999	P;P	0.48998	0.9;0.918	P;P	0.50378	0.506;0.639	D	0.89451	0.3730	10	0.62326	D	0.03	-9.9475	17.453	0.87597	0.0:0.0:1.0:0.0	.	26;26	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	T	26	ENSP00000347672:R26T;ENSP00000358523:R26T;ENSP00000310800:R26T;ENSP00000358522:R26T	ENSP00000310800:R26T	R	+	2	0	VANGL1	116003790	1.000000	0.71417	0.995000	0.50966	0.934000	0.57294	7.940000	0.87693	2.561000	0.86390	0.563000	0.77884	AGA	G|1.000;A|0.000		0.413	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			C	116202267	G	C	116202267	3	2	62	1	0	0	0	0	1	0	0	0	17152	942	33	4	83	4	VANGL1	1	116202267	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	53529588	116202267	133048354	7	5993											
NTRK1	4914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156849153	156849153	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacagcaccgactattaccGtgtaagggtcctttgtcccc	8	11	8	14	2	0	0	0	0	0	0	2	1	2	0	5	1	3	2	5	1	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:156849153G>A	ENST00000524377.1	+	15	2086	c.2045G>A	c.(2044-2046)cGt>cAt	p.R682H	NTRK1_ENST00000392302.2_Splice_Site_p.R646H|NTRK1_ENST00000358660.3_Splice_Site_p.R679H|NTRK1_ENST00000368196.3_Splice_Site_p.R676H	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	682	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GACTATTACCGTGTAAGGGTC	0.562			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.R682H		.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1-1393	0			c.G2045A						.						84	75	78					1																	156849153		2203	4300	6503	SO:0001630	splice_region_variant	4914	exon15			ATTACCGTGTAAG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.2046+1G>A	1.37:g.156849153G>A		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	79	42	NM_002529	0	0	0	0	0	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953656	0.73902	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	4.13	4.13	0.48395	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Tyrosine-protein kinase, receptor class II, conserved site (1);Protein kinase, catalytic domain (1);	0.000000	0.45126	D	0.000390	D	0.86764	0.6011	L	0.56280	1.765	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.987;0.938;0.99	D	0.88394	0.3010	10	0.87932	D	0	.	15.4596	0.75342	0.0:0.0:1.0:0.0	.	679;676;682;646	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	H	646;676;682;679	ENSP00000376120:R646H;ENSP00000357179:R676H;ENSP00000431418:R682H;ENSP00000351486:R679H	ENSP00000351486:R679H	R	+	2	0	NTRK1	155115777	1.000000	0.71417	0.930000	0.37139	0.719000	0.41307	7.703000	0.84585	2.315000	0.78130	0.561000	0.74099	CGT	.		0.562	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	Missense_Mutation	A	156849153	G	A	156849153	5	1	62	1	0	0	0	0	0	0	1	0	10732	1159	40	1	2233	1	NTRK1	1	156849153	Splice_Site	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	40646886	156849153	92401468	8	5994											
GLRX2	51022	hgsc.bcm.edu;bcgsc.ca	37	chr1	193074704	193074704	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgctggattccagcgagtGccacccacgtgtaaacatcc	10	7	10	14	3	0	0	0	0	0	0	2	2	2	1	4	1	4	2	4	1	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:193074704G>A	ENST00000367439.3	-	0	0				GLRX2_ENST00000367440.3_Missense_Mutation_p.A22V|GLRX2_ENST00000472197.1_Intron	NM_197962.2	NP_932066.1	Q9NS18	GLRX2_HUMAN	glutaredoxin 2						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|DNA protection (GO:0042262)|glutathione metabolic process (GO:0006749)|protein folding (GO:0006457)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|response to hydrogen peroxide (GO:0042542)|response to organic substance (GO:0010033)|response to redox state (GO:0051775)|response to temperature stimulus (GO:0009266)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|arsenate reductase (glutaredoxin) activity (GO:0008794)|electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|metal ion binding (GO:0046872)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|large_intestine(1)|lung(3)	5					Glutathione(DB00143)	TCCAGCGAGTGCCACCCACGT	0.652																																					p.A22V		.											.	GLRX2-186	0			c.C65T						.						41	44	43					1																	193074704		2203	4300	6503	SO:0001631	upstream_gene_variant	51022	exon1			GCGAGTGCCACCC	AF132495	CCDS1380.1, CCDS1381.1	1q31.2	2012-09-20			ENSG00000023572	ENSG00000023572			16065	protein-coding gene	gene with protein product	"bA101E13.1 (GRX2 glutaredoxin (thioltransferase) 2)"	606820				11297543	Standard	NM_016066		Approved	GRX2, bA101E13.1	uc001gsz.2	Q9NS18	OTTHUMG00000035677		1.37:g.193074704G>A	Exception_encountered	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	31	14	NM_016066	0	0	0	0	0	Q3LR69|Q7L1N7|Q96JC0|Q9Y3D4	Missense_Mutation	SNP	ENST00000367439.3	37	CCDS1381.1	.	.	.	.	.	.	.	.	.	.	G	9.608	1.130447	0.21041	.	.	ENSG00000023572	ENST00000367440	T	0.35236	1.32	2.13	-4.26	0.03755	.	595.624000	0.00166	N	0.000000	T	0.23171	0.0560	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.11421	-1.0588	9	0.33940	T	0.23	2.0784	2.9471	0.05849	0.1273:0.3676:0.3584:0.1468	.	22	Q9NS18-2	.	V	22	ENSP00000356410:A22V	ENSP00000356410:A22V	A	-	2	0	GLRX2	191341327	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-1.156000	0.03160	-3.466000	0.00158	-0.687000	0.03738	GCA	.		0.652	GLRX2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086699.1	NM_016066		A	193074704	G	A	193074704	1	1	62	0	1	0	0	0	0	0	0	0	6480	1319	46	2		2	GLRX2	1	193074704	5'Flank	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	36225551	193074704	56175917	9	5995											
NEK7	140609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	198266319	198266319	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttatactcactgtgtaagaaGatagaacagtgtgactaccc	14	11	8	8	0	1	4	1	1	0	3	1	4	1	4	1	0	3	1	1	0	7	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:198266319G>C	ENST00000367385.4	+	9	1089	c.747G>C	c.(745-747)aaG>aaC	p.K249N	NEK7_ENST00000538004.1_Missense_Mutation_p.K249N	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						TGTGTAAGAAGATAGAACAGT	0.378																																					p.K249N		.											.	NEK7-358	0			c.G747C						.						150	150	150					1																	198266319		2203	4300	6503	SO:0001583	missense	140609	exon9			TAAGAAGATAGAA	AB062450	CCDS1394.1	1q31.3	2012-11-15	2012-11-15		ENSG00000151414	ENSG00000151414			13386	protein-coding gene	gene with protein product		606848	"NIMA (never in mitosis gene a)-related kinase 7"			11701951	Standard	NM_133494		Approved		uc001gun.4	Q8TDX7	OTTHUMG00000035658	ENST00000367385.4:c.747G>C	1.37:g.198266319G>C	ENSP00000356355:p.Lys249Asn	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	188	84	NM_133494	0	0	22	25	3	A6NGT8	Missense_Mutation	SNP	ENST00000367385.4	37	CCDS1394.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279186	0.80692	.	.	ENSG00000151414	ENST00000367385;ENST00000538004	T;T	0.66460	-0.21;-0.21	5.98	5.06	0.68205	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.69700	0.3140	L	0.42744	1.35	0.80722	D	1	P	0.39737	0.685	P	0.50049	0.629	T	0.70777	-0.4780	10	0.59425	D	0.04	.	14.6335	0.68673	0.0693:0.0:0.9307:0.0	.	249	Q8TDX7	NEK7_HUMAN	N	249	ENSP00000356355:K249N;ENSP00000444621:K249N	ENSP00000356355:K249N	K	+	3	2	NEK7	196532942	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.580000	0.60942	2.838000	0.97847	0.655000	0.94253	AAG	.		0.378	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		C	198266319	G	C	198266319	3	2	62	1	0	0	0	0	1	0	0	0	10355	933	33	4	777	4	NEK7	1	198266319	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	5191615	198266319	50984302	10	5996											
GDF7	151449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	20871056	20871056	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaactccatggcaccagaCgcggcgccggcctcctgctg	6	6	11	18	4	1	1	1	0	0	1	3	1	3	1	5	3	2	2	5	3	1	0	rs376857749		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:20871056C>T	ENST00000272224.3	+	2	1800	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D		NM_182828.2	NP_878248.2	Q7Z4P5	GDF7_HUMAN	growth differentiation factor 7	408					activin receptor signaling pathway (GO:0032924)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching morphogenesis of an epithelial tube (GO:0048754)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|forebrain morphogenesis (GO:0048853)|gland morphogenesis (GO:0022612)|growth (GO:0040007)|midbrain development (GO:0030901)|morphogenesis of an epithelial fold (GO:0060571)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of tendon cell differentiation (GO:2001051)|positive regulation of transcription, DNA-templated (GO:0045893)|reproductive structure development (GO:0048608)|roof plate formation (GO:0021509)|spinal cord association neuron differentiation (GO:0021527)	extracellular space (GO:0005615)				breast(1)|cervix(1)|endometrium(2)|lung(1)|prostate(1)|skin(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCACCAGACGCGGCGCCGG	0.612																																					p.D408D		.											.	GDF7-226	0			c.C1224T						.						69	60	63					2																	20871056		2203	4300	6503	SO:0001819	synonymous_variant	151449	exon2			ACCAGACGCGGCG	AF522369	CCDS1701.1	2p24.1	2008-05-22			ENSG00000143869	ENSG00000143869			4222	protein-coding gene	gene with protein product		604651				10022976, 9808626	Standard	NM_182828		Approved	BMP12	uc002rdz.1	Q7Z4P5	OTTHUMG00000090781	ENST00000272224.3:c.1224C>T	2.37:g.20871056C>T		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	15	11	NM_182828	0	0	0	2	2		Silent	SNP	ENST00000272224.3	37	CCDS1701.1																																																																																			.		0.612	GDF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207563.2	NM_182828		T	20871056	C	T	20871056	2	4	62	1	0	0	0	0	0	0	0	1	6338	535	19	1		1	GDF7	2	20871056	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		20871056	222328317	11	5997											
AUP1	27429	hgsc.bcm.edu	37	chr2	74756587	74756587	+	5'UTR	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagaacccgactggcgcgtaGagcagcagcacgagcagtag	12	3	14	12	4	0	2	0	0	0	2	0	4	0	2	1	1	5	6	1	1	3	2	rs376231592		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:74756587G>C	ENST00000258080.3	+	0	84				HTRA2_ENST00000352222.3_5'Flank|AUP1_ENST00000377526.3_Silent_p.L30L	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2						adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						CTGGCGCGTAGAGCAGCAGCA	0.667													G|||	1	0.000199681	0	0	5008	,	,		17159	0		0.001	False		,,,				2504	0				p.L30L		.											.	AUP1-90	0			c.C90G						.	G	,,	0,4280		0,0,2140	25	38	33		,,90	4.7	1	2		33	1,8483		0,1,4241	no	utr-5,utr-5,coding-synonymous	AUP1,HTRA2	NM_013247.4,NM_145074.2,NM_181575.3	,,	0,1,6381	CC,CG,GG		0.0118,0.0,0.0078	,,	,,30/411	74756587	1,12763	2140	4242	6382	SO:0001623	5_prime_UTR_variant	550	exon2			CGCGTAGAGCAGC		CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"Serine peptidases / Serine peptidases", "Parkinson disease"	14348	protein-coding gene	gene with protein product		606441	"protease, serine, 25"	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957	ENST00000258080.3:c.-547G>C	2.37:g.74756587G>C		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	10	6	NM_181575	0	0	124	211	87	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	37	CCDS1951.1																																																																																			.		0.667	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		C	74756587	G	C	74756587	1	2	62	0	1	0	0	0	0	0	0	0	1221	929	33	4		4	AUP1	2	74756587	5'UTR	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	53885531	74756587	168442786	12	5998											
HOXD8	3234	hgsc.bcm.edu	37	chr2	176995295	176995295	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcccgcacgcgcccccgcaGgcgcacgcgcacccgcaccc	5	2	10	24	8	0	0	0	0	0	0	1	0	1	0	5	1	0	5	5	1	0	1	rs564911040	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:176995295G>C	ENST00000313173.4	+	1	828	c.201G>C	c.(199-201)caG>caC	p.Q67H	HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000548663.1_Intron|HOXD8_ENST00000429017.1_Intron|HOXD8_ENST00000544999.1_Missense_Mutation_p.Q67H|HOXD8_ENST00000450510.2_Missense_Mutation_p.Q67H	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8	67					anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		CGCCCCCGCAGGCGCACGCGC	0.786																																					p.Q67H		.											.	HOXD8-90	0			c.G201C						.						2	2	2					2																	176995295		839	1924	2763	SO:0001583	missense	3234	exon1			CCCGCAGGCGCAC		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"Homeoboxes / ANTP class : HOXL subclass"	5139	protein-coding gene	gene with protein product		142985	"homeo box D8"	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.201G>C	2.37:g.176995295G>C	ENSP00000315949:p.Gln67His	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	6	3	NM_001199746	0	0	0	0	0	F8WBG7|Q5BL00|Q8IXZ1	Missense_Mutation	SNP	ENST00000313173.4	37	CCDS2268.1	.	.	.	.	.	.	.	.	.	.	G	7.325	0.617776	0.14129	.	.	ENSG00000175879	ENST00000313173;ENST00000544999;ENST00000450510	D;D;D	0.91237	-2.81;-2.71;-2.71	3.11	3.11	0.35812	.	1.271540	0.05917	N	0.632694	T	0.81240	0.4781	N	0.08118	0	0.21822	N	0.999524	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.66874	-0.5813	10	0.23891	T	0.37	.	10.1671	0.42886	0.0:0.0:1.0:0.0	.	67;67	Q8IXZ1;P13378	.;HXD8_HUMAN	H	67	ENSP00000315949:Q67H;ENSP00000437431:Q67H;ENSP00000409026:Q67H	ENSP00000315949:Q67H	Q	+	3	2	HOXD8	176703541	0.992000	0.36948	0.993000	0.49108	0.612000	0.37316	-0.177000	0.09796	1.473000	0.48159	0.442000	0.29010	CAG	.		0.786	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1			C	176995295	G	C	176995295	3	2	62	1	0	0	0	0	1	0	0	0	7346	991	35	4	203	4	HOXD8	2	176995295	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	102238708	176995295	66204078	13	5999											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179401833	179401833	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caattgccattcagccccctCcttggcctcacatttttcca	7	13	4	17	0	2	0	2	0	0	0	4	0	4	0	6	1	2	0	6	1	1	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:179401833C>T	ENST00000591111.1	-	306	95304	c.95080G>A	c.(95080-95082)Gag>Aag	p.E31694K	TTN_ENST00000342992.6_Missense_Mutation_p.E30767K|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E24462K|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E24270K|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E24395K|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E33335K|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592836.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31694	Fibronectin type-III 130. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAGCCCCCTCCTTGGCCTCA	0.502																																					p.E33335K		.											.	TTN-636	0			c.G100003A						.						67	66	66					2																	179401833		1941	4126	6067	SO:0001583	missense	7273	exon356			CCCCCTCCTTGGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.95080G>A	2.37:g.179401833C>T	ENSP00000465570:p.Glu31694Lys	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	79	15	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	22.5	4.293637	0.80914	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.41	5.41	0.78517	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56731	0.2005	N	0.05554	-0.025	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.67806	-0.5575	9	0.87932	D	0	.	19.1973	0.93695	0.0:1.0:0.0:0.0	.	24270;24395;24462;31694	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	30767;24270;24462;24395;24267	ENSP00000343764:E30767K;ENSP00000434586:E24270K;ENSP00000340554:E24462K;ENSP00000352154:E24395K	ENSP00000340554:E24462K	E	-	1	0	TTN	179110079	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.544000	0.85801	0.462000	0.41574	GAG	.		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179401833	C	T	179401833	3	4	62	1	0	0	0	0	1	0	0	0	16768	864	30	2	8004	2	TTN	2	179401833	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2406538	179401833	63797540	14	6000											
TTN	7273	hgsc.bcm.edu;broad.mit.edu	37	chr2	179452053	179452053	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atataatgtgtcacttggctCccaccgtcgttttcaggagg	8	13	10	10	2	2	0	2	0	0	0	4	1	3	1	2	3	0	2	2	3	2	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:179452053C>T	ENST00000591111.1	-	257	59186	c.58962G>A	c.(58960-58962)ggG>ggA	p.G19654G	TTN_ENST00000342992.6_Silent_p.G18727G|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.G12422G|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.G12230G|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000359218.5_Silent_p.G12355G|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Silent_p.G21295G			Q8WZ42	TITIN_HUMAN	titin	19654	Fibronectin type-III 42. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCACTTGGCTCCCACCGTCGT	0.468																																					p.G21295G		.											.	TTN-636	0			c.G63885A						.						69	65	66					2																	179452053		1909	4130	6039	SO:0001819	synonymous_variant	7273	exon307			TTGGCTCCCACCG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.58962G>A	2.37:g.179452053C>T		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	92	6	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179452053	C	T	179452053	2	4	62	1	0	0	0	0	0	0	0	1	16768	842	30	2		2	TTN	2	179452053	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	50220	179452053	63747320	15	6001											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179458757	179458757	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaccacacagtatttgcCggaatctgaacgtttggcct	11	10	8	12	2	1	1	0	1	1	0	1	2	1	2	3	2	3	2	3	2	4	3	rs191927501		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:179458757C>T	ENST00000591111.1	-	247	53664	c.53440G>A	c.(53440-53442)Ggc>Agc	p.G17814S	TTN_ENST00000342992.6_Missense_Mutation_p.G16887S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G10582S|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G10390S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G10515S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G19455S			Q8WZ42	TITIN_HUMAN	titin	17814	Ig-like 104.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGTATTTGCCGGAATCTGAA	0.408													C|||	1	0.000199681	0	0	5008	,	,		22120	0		0.001	False		,,,				2504	0				p.G19455S		.											.	TTN-636	0			c.G58363A						.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4040		0,0,2020	177	176	176		31168,50659,31543,31744	6.2	1	2		176	5,8383		0,5,4189	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	56,56,56,56	0,5,6209	TT,TC,CC		0.0596,0.0,0.0402	probably-damaging,probably-damaging,probably-damaging,probably-damaging	10390/26927,16887/33424,10515/27052,10582/27119	179458757	5,12423	2020	4194	6214	SO:0001583	missense	7273	exon297			ATTTGCCGGAATC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.53440G>A	2.37:g.179458757C>T	ENSP00000465570:p.Gly17814Ser	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	424	62	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	20.4	3.978176	0.74360	0.0	5.96E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.92469	0.7609	H	0.95402	3.665	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.93386	0.6747	9	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	10390;10515;10582;17814	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	16887;10390;10582;10515;10388	ENSP00000343764:G16887S;ENSP00000434586:G10390S;ENSP00000340554:G10582S;ENSP00000352154:G10515S	ENSP00000340554:G10582S	G	-	1	0	TTN	179167003	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.760000	0.85248	2.941000	0.99782	0.655000	0.94253	GGC	C|0.999;T|0.000		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179458757	C	T	179458757	3	4	62	1	0	0	0	0	1	0	0	0	16768	652	23	1	49880	1	TTN	2	179458757	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	6704	179458757	63740616	16	6002											
FSIP2	401024	broad.mit.edu	37	chr2	186671552	186671552	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcactgttaaaggagttctCagatgctcaaattaaggttt	12	15	8	6	0	3	1	3	0	1	1	4	2	3	2	0	2	1	4	0	2	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:186671552C>G	ENST00000424728.1	+	17	17519	c.17519C>G	c.(17518-17520)tCa>tGa	p.S5840*	FSIP2_ENST00000343098.5_Nonsense_Mutation_p.S5929*			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5840										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AAGGAGTTCTCAGATGCTCAA	0.383																																					p.S5929X													.	FSIP2-90	0			c.C17786G						.						96	88	90					2																	186671552		1848	4087	5935	SO:0001587	stop_gained	401024	exon17			AGTTCTCAGATGC	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17519C>G	2.37:g.186671552C>G	ENSP00000401306:p.Ser5840*	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	188	3	NM_173651	0	0	0	0	0	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Nonsense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	C	56	27.166061	0.99970	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	13.377	0.60745	0.0:1.0:0.0:0.0	.	.	.	.	X	5929;5840	.	ENSP00000344403:S5929X	S	+	2	0	FSIP2	186379797	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	3.643000	0.54374	2.515000	0.84797	0.591000	0.81541	TCA	.		0.383	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		G	186671552	C	G	186671552	4	3	62	1	0	0	0	0	0	1	0	0	6094	838	29	4	17852	4	FSIP2	2	186671552	Nonsense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	7212795	186671552	56527821	17	6003											
CPO	130749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	207833968	207833968	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttctcatatacgtttgagctGagggacagtggaacatatgg	11	12	12	6	1	1	2	1	2	1	0	2	4	1	4	0	3	3	2	0	3	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:207833968G>C	ENST00000272852.3	+	9	979	c.933G>C	c.(931-933)ctG>ctC	p.L311L		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	311						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		CGTTTGAGCTGAGGGACAGTG	0.512																																					p.L311L		.											.	CPO-154	0			c.G933C						.						147	133	138					2																	207833968		2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGAGCTGAGGGAC		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"metallocarboxypeptidase O", "metallocarboxypeptidase C"	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.933G>C	2.37:g.207833968G>C		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	81	36	NM_173077	0	0	0	0	0	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			.		0.512	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		C	207833968	G	C	207833968	2	2	62	1	0	0	0	0	0	0	0	1	3826	1277	45	4		4	CPO	2	207833968	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	21162416	207833968	35365405	18	6004											
ABCA12	26154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	215840568	215840568	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggagatctgaatctctggAtaactgttgctggaatttct	9	14	12	6	0	3	2	0	1	3	1	4	5	3	4	0	4	2	2	0	4	3	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:215840568A>G	ENST00000272895.7	-	34	5541	c.5322T>C	c.(5320-5322)taT>taC	p.Y1774Y	ABCA12_ENST00000389661.4_Silent_p.Y1456Y	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1774					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GAATCTCTGGATAACTGTTGC	0.453																																					p.Y1774Y	Ovarian(66;664 1488 5121 34295)	.											.	ABCA12-99	0			c.T5322C						.						147	142	144					2																	215840568		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon34			CTCTGGATAACTG	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.5322T>C	2.37:g.215840568A>G		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	87	31	NM_173076	0	0	3	6	3	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			.		0.453	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215840568	A	G	215840568	2	3	62	1	0	0	0	0	0	0	0	1	30	340	12	3		3	ABCA12	2	215840568	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	8006600	215840568	27358805	19	6005											
TMPPE	643853	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	33135655	33135655	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acagcagccagggtggccttCgcgcctagggacagctgcct	7	6	14	14	2	0	0	0	0	0	0	1	1	0	1	4	3	4	2	4	3	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:33135655C>T	ENST00000342462.4	-	2	223	c.33G>A	c.(31-33)gcG>gcA	p.A11A	GLB1_ENST00000307377.8_Intron|GLB1_ENST00000307363.5_Intron|TMPPE_ENST00000416695.2_Intron|GLB1_ENST00000445488.2_Intron|GLB1_ENST00000399402.3_Intron	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain	11						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.A11A(1)		breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						GGGTGGCCTTCGCGCCTAGGG	0.587																																					p.A11A		.											.	TMPPE-90	1	Substitution - coding silent(1)	lung(1)	c.G33A						.																																			SO:0001819	synonymous_variant	643853	exon2			GGCCTTCGCGCCT	AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779	ENST00000342462.4:c.33G>A	3.37:g.33135655C>T		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	82	8	NM_001039770	0	0	1	1	0	B2RNG5|Q6ZRG1	Silent	SNP	ENST00000342462.4	37	CCDS33732.1																																																																																			.		0.587	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770		T	33135655	C	T	33135655	2	4	62	1	0	0	0	0	0	0	0	1	16270	871	31	1		1	TMPPE	3	33135655	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		33135655	164886775	20	6006											
CTNNB1	1499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	41274905	41274905	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaactgtctttggactctCaggaatctttcagatgctgc	9	13	9	10	0	4	2	2	0	3	2	5	4	4	4	0	2	3	1	0	2	2	2	rs74692094	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:41274905C>T	ENST00000349496.5	+	8	1435	c.1155C>T	c.(1153-1155)ctC>ctT	p.L385L	CTNNB1_ENST00000405570.1_Silent_p.L385L|CTNNB1_ENST00000396183.3_Silent_p.L385L|CTNNB1_ENST00000453024.1_Silent_p.L378L|CTNNB1_ENST00000396185.3_Silent_p.L385L	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	385					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTTGGACTCTCAGGAATCTTT	0.413		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.L385L	Colon(6;3 56 14213 18255)	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1-24361	0			c.C1155T						.						102	93	96					3																	41274905		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GACTCTCAGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1155C>T	3.37:g.41274905C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	126	47	NM_001098209	0	0	201	349	148	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																			C|0.999;A|0.001		0.413	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41274905	C	T	41274905	2	4	62	1	0	0	0	0	0	0	0	1	4022	813	29	2		2	CTNNB1	3	41274905	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	8139250	41274905	156747525	21	6007											
RAD54L2	23132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	51697406	51697406	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgatgatgaggataaagaCgatgatgtgatagaggtcac	16	9	13	3	1	1	7	1	5	0	2	1	9	1	8	0	2	0	0	0	2	4	2	rs192987707	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:51697406C>T	ENST00000409535.2	+	22	4499	c.4374C>T	c.(4372-4374)gaC>gaT	p.D1458D	RAD54L2_ENST00000296477.3_Silent_p.D1152D	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1458						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		AGGATAAAGACGATGATGTGA	0.562													C|||	2	0.000399361	0	0.0014	5008	,	,		16861	0.001		0	False		,,,				2504	0				p.D1458D		.											.	RAD54L2-93	0			c.C4374T						.	C		0,4406		0,0,2203	43	43	43		4374	-4.3	0.5	3		43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RAD54L2	NM_015106.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1458/1468	51697406	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23132	exon22			TAAAGACGATGAT	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.4374C>T	3.37:g.51697406C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	54	24	NM_015106	0	0	7	9	2	Q8TB57|Q9BV54	Silent	SNP	ENST00000409535.2	37	CCDS33765.2	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.471	-0.321889	0.05386	0.0	1.16E-4	ENSG00000164080	ENST00000432863	.	.	.	5.56	-4.31	0.03698	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.211	14.0112	0.64498	0.0:0.3295:0.0:0.6705	.	.	.	.	X	1287	.	.	R	+	1	2	RAD54L2	51672446	0.091000	0.21658	0.532000	0.27989	0.945000	0.59286	-0.754000	0.04787	-1.554000	0.01700	-0.736000	0.03550	CGA	C|0.999;T|0.001		0.562	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		T	51697406	C	T	51697406	2	4	62	1	0	0	0	0	0	0	0	1	13026	535	19	1		1	RAD54L2	3	51697406	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	10422501	51697406	146325024	22	6008											
TMF1	7110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	69101211	69101211	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcctgcttagcgaagctggaGagctgggaggcgttgaacca	9	7	16	9	2	0	2	0	1	0	1	0	5	0	3	2	3	5	4	2	3	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:69101211G>A	ENST00000398559.2	-	1	243	c.27C>T	c.(25-27)ctC>ctT	p.L9L	TMF1_ENST00000543976.1_Silent_p.L9L|CTD-2013N24.2_ENST00000595925.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	9					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CGAAGCTGGAGAGCTGGGAGG	0.642																																					p.L9L		.											.	TMF1-90	0			c.C27T						.						62	65	64					3																	69101211		1931	4151	6082	SO:0001819	synonymous_variant	7110	exon1			GCTGGAGAGCTGG		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.27C>T	3.37:g.69101211G>A		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	133	57	NM_007114	0	0	23	37	14	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	37	CCDS43105.1																																																																																			.		0.642	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69101211	G	A	69101211	2	1	62	1	0	0	0	0	0	0	0	1	16260	929	33	2		2	TMF1	3	69101211	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	17403805	69101211	128921219	23	6009											
MAPK10	5602	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	86950416	86950416	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgaattcattacttcctTgtagataagttctgtaagaa	12	17	6	6	0	3	3	1	1	2	2	4	3	4	3	1	0	1	3	1	0	6	9			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:86950416T>C	ENST00000359221.3	-	13	1712	c.1186A>G	c.(1186-1188)Aag>Gag	p.K396E	MAPK10_ENST00000395169.3_Missense_Mutation_p.K358E|MAPK10_ENST00000395166.1_Missense_Mutation_p.K358E|MAPK10_ENST00000361569.2_Missense_Mutation_p.K396E|MAPK10_ENST00000395157.3_Missense_Mutation_p.K251E|MAPK10_ENST00000395161.2_Missense_Mutation_p.K396E|MAPK10_ENST00000449047.2_Missense_Mutation_p.K251E|MAPK10_ENST00000395160.3_Missense_Mutation_p.K251E			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	396					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		ATTACTTCCTTGTAGATAAGT	0.328																																					p.K396E		.											.	MAPK10-1402	0			c.A1186G						.						172	162	166					4																	86950416		2203	4300	6503	SO:0001583	missense	5602	exon13			CTTCCTTGTAGAT	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.1186A>G	4.37:g.86950416T>C	ENSP00000352157:p.Lys396Glu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	79	41	NM_002753	0	0	0	0	0	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Missense_Mutation	SNP	ENST00000359221.3	37	CCDS34026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.80|15.80	2.940106|2.940106	0.52972|0.52972	.|.	.|.	ENSG00000109339|ENSG00000109339	ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161|ENST00000515400	T;T;T;T;T;T;T;T|.	0.59083|.	0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29|.	5.96|5.96	5.96|5.96	0.96718|0.96718	Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68696|0.68696	0.3029|0.3029	L|L	0.52206|0.52206	1.635|1.635	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.08055|.	0.0;0.002;0.003;0.002;0.001|.	T|T	0.66023|0.66023	-0.6026|-0.6026	10|5	0.33141|.	T|.	0.24|.	-19.5226|-19.5226	16.0984|16.0984	0.81148|0.81148	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	282;251;358;396;396|.	B7Z1Z1;Q499Y8;P53779-3;P53779-2;P53779|.	.;.;.;.;MK10_HUMAN|.	E|R	358;396;251;396;358;251;251;396|308	ENSP00000378598:K358E;ENSP00000352157:K396E;ENSP00000378586:K251E;ENSP00000355297:K396E;ENSP00000378595:K358E;ENSP00000378589:K251E;ENSP00000414469:K251E;ENSP00000378590:K396E|.	ENSP00000352157:K396E|.	K|Q	-|-	1|2	0|0	MAPK10|MAPK10	87169440|87169440	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.935000|6.935000	0.75886|0.75886	2.278000|2.278000	0.76064|0.76064	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.		0.328	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			C	86950416	T	C	86950416	3	2	62	1	0	0	0	0	1	0	0	0	9297	1821	63	3	221	3	MAPK10	4	86950416	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08		86950416	104203860	24	6010											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	151827110	151827110	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaatgcaaggcaaagttcAagtactgctctgctaacatg	15	9	9	8	0	2	0	1	0	1	0	2	1	2	0	0	1	5	6	0	1	7	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:151827110A>T	ENST00000357115.3	-	13	1878	c.1635T>A	c.(1633-1635)ctT>ctA	p.L545L	LRBA_ENST00000510413.1_Silent_p.L545L|LRBA_ENST00000535741.1_Silent_p.L545L|LRBA_ENST00000507224.1_Silent_p.L545L	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	545						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GGCAAAGTTCAAGTACTGCTC	0.388																																					p.L545L		.											.	LRBA-157	0			c.T1635A						.						83	81	82					4																	151827110		2203	4300	6503	SO:0001819	synonymous_variant	987	exon13			AAGTTCAAGTACT	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1635T>A	4.37:g.151827110A>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	82	37	NM_006726	0	0	10	20	10	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1																																																																																			.		0.388	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151827110	A	T	151827110	2	4	62	1	0	0	0	0	0	0	0	1	8956	117	5	5		5	LRBA	4	151827110	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	64876694	151827110	39327166	25	6011											
ACCN5	51802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	156763435	156763436	+	Missense_Mutation	DNP	GC	GC	AT																															tccttcaagcaaccagaagtGctgtagctgctaaaattctg																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:156763435_156763436GC>AT	ENST00000537611.2	-	6	978_979	c.932_933GC>AT	c.(931-933)aGC>aAT	p.S311N		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	311					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										AACCAGAAGTGCTGTAGCTGCT	0.416																																					p.S311N		.											.	.	0			c.G932A						.																																			SO:0001583	missense	51802	exon6			GAAGTGCTGTAGC	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.932_933delinsAT	4.37:g.156763435_156763436delinsAT	ENSP00000442477:p.Ser311Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	112	64		0	0	0	0	0		Missense_Mutation	DNP	ENST00000537611.2	37	CCDS3793.1																																																																																			.		0.416	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			AT	156763436	GC	AT	156763435	3	1	62	1	0	0	0	0	1	0	0	0	132	1310	46	2	604	2	ACCN5	4	156763435	Missense_Mutation	DNP	GC	TCGA-BQ-5878-01A-11D-1589-08	4936325	156763435	34390841	26	6012											
HMGB2	3148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	174254775	174254775	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgaggacattttgccccgcGgcttgttggggtctccttta	5	13	12	11	3	1	0	0	0	1	0	2	2	1	1	3	4	1	2	3	4	1	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:174254775G>A	ENST00000296503.5	-	2	899	c.26C>T	c.(25-27)cCg>cTg	p.P9L	HMGB2_ENST00000446922.2_Missense_Mutation_p.P9L|HMGB2_ENST00000438704.2_Missense_Mutation_p.P9L			P26583	HMGB2_HUMAN	high mobility group box 2	9					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cell chemotaxis (GO:0060326)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to lipopolysaccharide (GO:0071222)|chromatin organization (GO:0006325)|DNA ligation involved in DNA repair (GO:0051103)|DNA topological change (GO:0006265)|male gonad development (GO:0008584)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive chemotaxis (GO:0050918)|positive regulation of DNA binding (GO:0043388)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of nuclease activity (GO:0032075)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to steroid hormone (GO:0048545)|spermatid nucleus differentiation (GO:0007289)|V(D)J recombination (GO:0033151)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	chemoattractant activity (GO:0042056)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		TTTGCCCCGCGGCTTGTTGGG	0.627																																					p.P9L		.											.	HMGB2-650	0			c.C26T						.						68	71	70					4																	174254775		2203	4300	6503	SO:0001583	missense	3148	exon1			CCCCGCGGCTTGT		CCDS3816.1	4q31	2011-07-01	2011-04-05	2002-08-16	ENSG00000164104	ENSG00000164104		"High-mobility group / Canonical"	5000	protein-coding gene	gene with protein product		163906	"high-mobility group (nonhistone chromosomal) protein 2", "high-mobility group box 2"	HMG2		1754403	Standard	NM_002129		Approved		uc011ckc.1	P26583	OTTHUMG00000160799	ENST00000296503.5:c.26C>T	4.37:g.174254775G>A	ENSP00000296503:p.Pro9Leu	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	87	43	NM_001130689	0	0	41	71	30	B2R4K8|D3DP37|Q5U072	Missense_Mutation	SNP	ENST00000296503.5	37	CCDS3816.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673983	0.67928	.	.	ENSG00000164104	ENST00000296503;ENST00000446922;ENST00000438704;ENST00000506267	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	5.45	4.61	0.57282	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (3);	0.088329	0.48767	D	0.000173	T	0.35128	0.0921	M	0.86097	2.795	0.80722	D	1	B	0.29481	0.245	B	0.28709	0.093	T	0.21621	-1.0240	10	0.42905	T	0.14	.	13.8749	0.63647	0.0744:0.0:0.9256:0.0	.	9	P26583	HMGB2_HUMAN	L	9	ENSP00000296503:P9L;ENSP00000393448:P9L;ENSP00000404912:P9L;ENSP00000423001:P9L	ENSP00000296503:P9L	P	-	2	0	HMGB2	174491350	1.000000	0.71417	0.938000	0.37757	0.038000	0.13279	9.505000	0.97989	1.313000	0.45069	0.563000	0.77884	CCG	.		0.627	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		A	174254775	G	A	174254775	3	1	62	1	0	0	0	0	1	0	0	0	7247	1116	39	1	619	1	HMGB2	4	174254775	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	17491340	174254775	16899501	27	6013											
ODZ3	55714	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	183664509	183664515	+	Frame_Shift_Del	DEL	GCGATTT	GCGATTT	-																															cgatggcagtctgtacgtagGcgatttcaactatgtgcggc																								rs189480567		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	GCGATTT	GCGATTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:183664509_183664515delGCGATTT	ENST00000511685.1	+	19	3689_3695	c.3566_3572delGCGATTT	c.(3565-3573)ggcgatttcfs	p.GDF1189fs	TENM3_ENST00000406950.2_Frame_Shift_Del_p.GDF1189fs|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1189					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1189G(1)									CTGTACGTAGGCGATTTCAACTATGTG	0.473																																					p.1189_1191del		.											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.3566_3572del						.																																			SO:0001589	frameshift_variant	55714	exon18			.	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"odz, odd Oz/ten-m homolog 3 (Drosophila)"	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3566_3572delGCGATTT	4.37:g.183664509_183664515delGCGATTT	ENSP00000424226:p.Gly1189fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_001080477	0	0	0	0	0	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Frame_Shift_Del	DEL	ENST00000511685.1	37	CCDS47165.1																																																																																			.		0.473	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			-	183664515	GCGATTT	-	183664509	7	5	62	1	0	1	0	1	0	0	0	0	10862	1203	42	0	3636	0	ODZ3	4	183664509	Frame_Shift_Del	DEL	GCGATTT	TCGA-BQ-5878-01A-11D-1589-08	9409734	183664509	7489767	28	6014											
EXOC3	11336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	446365	446365	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gttgcgacagcagtgcaaagGgttgctgggatgctccagcg	8	8	16	9	2	0	0	0	0	0	0	1	2	1	1	1	2	6	6	1	2	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:446365G>A	ENST00000512944.1	+	2	234	c.45G>A	c.(43-45)agG>agA	p.R15R	EXOC3_ENST00000510441.1_3'UTR|EXOC3_ENST00000315013.5_Silent_p.R15R	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	26					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CAGTGCAAAGGGTTGCTGGGA	0.587																																					p.R15R		.											.	EXOC3-90	0			c.G45A						.						74	77	76					5																	446365		2000	4166	6166	SO:0001819	synonymous_variant	11336	exon2			GCAAAGGGTTGCT	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"SEC6-like 1 (S. cerevisiae)"	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.45G>A	5.37:g.446365G>A		Somatic	97	1		WXS	Illumina HiSeq	Phase_I	100	45	NM_007277	0	0	36	82	46	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Silent	SNP	ENST00000512944.1	37	CCDS54830.1																																																																																			.		0.587	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277		A	446365	G	A	446365	2	1	62	1	0	0	0	0	0	0	0	1	5316	1223	43	2		2	EXOC3	5	446365	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		446365	180468895	29	6015											
SLC45A2	51151	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	33984558	33984558	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccgcgtagcagaactctcttCcgaacatggccatgctgtgc	8	9	10	14	3	1	1	0	0	1	1	3	2	2	1	3	1	5	3	3	1	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:33984558C>T	ENST00000296589.4	-	1	277	c.131G>A	c.(130-132)gGa>gAa	p.G44E	SLC45A2_ENST00000509381.1_Missense_Mutation_p.G44E|SLC45A2_ENST00000382102.3_Missense_Mutation_p.G44E|SLC45A2_ENST00000342059.3_Missense_Mutation_p.G44E|SLC45A2_ENST00000345083.5_Missense_Mutation_p.G44E	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	44					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						GAACTCTCTTCCGAACATGGC	0.557																																					p.G44E	Ovarian(31;380 859 8490 22203 49048)	.											.	SLC45A2-93	0			c.G131A						.						58	52	54					5																	33984558		2203	4300	6503	SO:0001583	missense	51151	exon1			TCTCTTCCGAACA	AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"Solute carriers"	16472	protein-coding gene	gene with protein product		606202	"membrane associated transporter"	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.131G>A	5.37:g.33984558C>T	ENSP00000296589:p.Gly44Glu	Somatic	33	1		WXS	Illumina HiSeq	Phase_I	32	12	NM_016180	0	0	0	0	0	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	37	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.757106	0.89843	.	.	ENSG00000164175	ENST00000296589;ENST00000342059;ENST00000382102;ENST00000509381;ENST00000345083	D;D;D;D;D	0.96967	-4.19;-4.19;-4.19;-4.19;-4.19	5.62	5.62	0.85841	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.98601	0.9532	M	0.91300	3.195	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99357	1.0916	10	0.87932	D	0	-21.1585	19.6584	0.95853	0.0:1.0:0.0:0.0	.	44;44;44	D6RGY6;Q9UMX9-4;Q9UMX9	.;.;S45A2_HUMAN	E	44	ENSP00000296589:G44E;ENSP00000341014:G44E;ENSP00000371534:G44E;ENSP00000421100:G44E;ENSP00000340444:G44E	ENSP00000296589:G44E	G	-	2	0	SLC45A2	34020315	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	7.569000	0.82380	2.645000	0.89757	0.551000	0.68910	GGA	.		0.557	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		T	33984558	C	T	33984558	3	4	62	1	0	0	0	0	1	0	0	0	14673	855	30	2	1504	2	SLC45A2	5	33984558	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	33538193	33984558	146930702	30	6016											
PRLR	5618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	35070231	35070231	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agccaagacgctcaccactaGgtatctgaatgaaggtcgct	12	8	10	11	2	2	3	1	2	1	1	3	3	2	3	2	2	1	3	2	2	5	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:35070231G>C	ENST00000382002.5	-	7	1106	c.680C>G	c.(679-681)cCt>cGt	p.P227R	PRLR_ENST00000513753.1_Missense_Mutation_p.P227R|PRLR_ENST00000231423.3_Missense_Mutation_p.P227R|PRLR_ENST00000348262.3_Missense_Mutation_p.P227R|PRLR_ENST00000542609.1_Missense_Mutation_p.P227R|PRLR_ENST00000397391.3_Missense_Mutation_p.P156R|PRLR_ENST00000310101.5_Missense_Mutation_p.P227R|PRLR_ENST00000511486.1_Missense_Mutation_p.P126R|PRLR_ENST00000509934.1_5'UTR|PRLR_ENST00000342362.5_Missense_Mutation_p.P126R	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	227	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	CTCACCACTAGGTATCTGAAT	0.418																																					p.P227R		.											.	PRLR-93	0			c.C680G						.						105	89	94					5																	35070231		2203	4300	6503	SO:0001583	missense	5618	exon7			CCACTAGGTATCT		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.680C>G	5.37:g.35070231G>C	ENSP00000371432:p.Pro227Arg	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	49	19	NM_000949	0	0	0	0	0	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	37	CCDS3909.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620133	0.46736	.	.	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000348262;ENST00000397391;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101	T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.65	5.65	0.86999	Fibronectin, type III (2);	0.000000	0.85682	D	0.000000	T	0.74382	0.3709	M	0.90542	3.125	0.58432	D	0.999993	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.999;1.0;0.998;0.997;0.996;0.994	T	0.79629	-0.1724	10	0.87932	D	0	-15.5927	15.3486	0.74363	0.0:0.0:0.8598:0.1401	.	227;227;126;156;227;227;227	P16471-3;P16471;P16471-2;Q8TD76;P16471-7;P16471-6;P16471-4	.;PRLR_HUMAN;.;.;.;.;.	R	227;227;227;156;227;126;227;126;227	ENSP00000231423:P227R;ENSP00000424841:P227R;ENSP00000311613:P227R;ENSP00000380546:P156R;ENSP00000441813:P227R;ENSP00000339213:P126R;ENSP00000371432:P227R;ENSP00000422556:P126R;ENSP00000309008:P227R	ENSP00000231423:P227R	P	-	2	0	PRLR	35105988	1.000000	0.71417	0.986000	0.45419	0.092000	0.18411	6.868000	0.75516	2.668000	0.90789	0.655000	0.94253	CCT	.		0.418	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2			C	35070231	G	C	35070231	3	2	62	1	0	0	0	0	1	0	0	0	12560	1000	35	4	1204	4	PRLR	5	35070231	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1085673	35070231	145845029	31	6017											
SEPP1	100129792	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	42801313	42801313	+	3'UTR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgaaagctcactgctgcCaaggtgctgatgtccatgat	9	11	10	11	0	2	3	1	3	1	0	3	3	3	3	2	1	4	3	2	1	2	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:42801313C>G	ENST00000361970.5	+	0	2282				SEPP1_ENST00000509276.1_5'UTR|SEPP1_ENST00000507920.1_Missense_Mutation_p.L108F|SEPP1_ENST00000506577.1_Missense_Mutation_p.G219R|SEPP1_ENST00000514985.1_Missense_Mutation_p.G219R|SEPP1_ENST00000511224.1_Missense_Mutation_p.G219R	NM_001134848.1	NP_001128320.1	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152											endometrium(1)	1						TCACTGCTGCCAAGGTGCTGA	0.473																																					.													.	SEPP1-68	0			.						.						169	171	170					5																	42801313		2151	4263	6414	SO:0001624	3_prime_UTR_variant	6414	.			TGCTGCCAAGGTG		CCDS47203.1	5p12	2008-07-14			ENSG00000198865	ENSG00000198865			34438	protein-coding gene	gene with protein product							Standard	NM_001134848		Approved	LOC100129792	uc003jmx.3	Q4G0S7	OTTHUMG00000162141	ENST00000361970.5:c.*1430C>G	5.37:g.42801313C>G		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	108	44	.	0	0	148	228	80	B3KXI4|B4E0P7|Q5BLP6	Missense_Mutation	SNP	ENST00000361970.5	37	CCDS47203.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.420055	0.62622	.	.	ENSG00000250722	ENST00000514985;ENST00000511224;ENST00000506577;ENST00000514218	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.74	2.87	0.33458	.	0.494897	0.16929	N	0.193779	T	0.30417	0.0764	L	0.54323	1.7	0.09310	N	0.999995	.	.	.	.	.	.	T	0.11012	-1.0605	8	0.22109	T	0.4	.	7.4306	0.27126	0.0:0.6606:0.1357:0.2037	.	.	.	.	R	219	ENSP00000420939:G219R;ENSP00000427671:G219R;ENSP00000425915:G219R;ENSP00000421626:G219R	ENSP00000425915:G219R	G	-	1	0	SEPP1	42837070	0.000000	0.05858	0.020000	0.16555	0.954000	0.61252	0.082000	0.14847	1.429000	0.47314	0.591000	0.81541	GGC	.		0.473	CCDC152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367497.1	XM_001717416		G	42801313	C	G	42801313	1	3	62	0	1	0	0	0	0	0	0	0	14089	594	21	4		4	SEPP1	5	42801313	3'UTR	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	7731082	42801313	138113947	32	6018											
GCNT4	51301	broad.mit.edu	37	chr5	74325475	74325475	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaataggctattgggaagcTtttctcctcctttgagacaa	11	13	9	8	0	1	2	0	1	1	2	3	4	2	3	2	2	1	2	2	2	5	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:74325475T>C	ENST00000322348.4	-	1	1249	c.388A>G	c.(388-390)Agc>Ggc	p.S130G		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	130					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		ATTGGGAAGCTTTTCTCCTCC	0.398																																					p.S130G													.	GCNT4-93	0			c.A388G						.						137	132	133					5																	74325475		2203	4300	6503	SO:0001583	missense	51301	exon1			GGAAGCTTTTCTC	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	17973	protein-coding gene	gene with protein product	"core 2 beta-1,6-N-acetylglucosaminyltransferase 3", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"		"glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.388A>G	5.37:g.74325475T>C	ENSP00000317027:p.Ser130Gly	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	248	5	NM_016591	0	0	5	5	0		Missense_Mutation	SNP	ENST00000322348.4	37	CCDS4026.1	.	.	.	.	.	.	.	.	.	.	.	7.707	0.694395	0.15039	.	.	ENSG00000176928	ENST00000322348	T	0.40476	1.03	5.91	-4.4	0.03600	.	1.139620	0.05953	N	0.639154	T	0.25938	0.0632	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20009	-1.0288	10	0.27082	T	0.32	-10.8422	7.199	0.25871	0.0:0.3198:0.3621:0.3181	.	130	Q9P109	GCNT4_HUMAN	G	130	ENSP00000317027:S130G	ENSP00000317027:S130G	S	-	1	0	GCNT4	74361231	0.000000	0.05858	0.003000	0.11579	0.856000	0.48823	0.302000	0.19192	-1.082000	0.03101	-0.290000	0.09829	AGC	.		0.398	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591		C	74325475	T	C	74325475	3	2	62	1	0	0	0	0	1	0	0	0	6323	1609	56	3	977	3	GCNT4	5	74325475	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	31524162	74325475	106589785	33	6019											
SPOCK1	6695	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	136328174	136328174	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atatttaaaatggtcttactGccttgggctgtgttggagct	8	16	11	6	0	1	0	0	0	1	0	1	1	1	1	1	3	3	3	1	3	4	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:136328174G>A	ENST00000394945.1	-	7	874	c.705C>T	c.(703-705)ggC>ggT	p.G235G	SPOCK1_ENST00000282223.7_Splice_Site_p.G235G	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	235					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGTCTTACTGCCTTGGGCTG	0.438																																					p.G235G		.											.	SPOCK1-91	0			c.C705T						.						161	152	155					5																	136328174		2203	4300	6503	SO:0001630	splice_region_variant	6695	exon7			CTTACTGCCTTGG	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.706+1C>T	5.37:g.136328174G>A		Somatic	163	0		WXS	Illumina HiSeq	Phase_I	122	48	NM_004598	0	0	0	0	0	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	37	CCDS4191.1																																																																																			.		0.438	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	Silent	A	136328174	G	A	136328174	5	1	62	1	0	0	0	0	0	0	1	0	15111	1333	46	2	634	2	SPOCK1	5	136328174	Splice_Site	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	62002699	136328174	44587086	34	6020											
KDM3B	51780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	137715373	137715373	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaggactccatcactcgTcttatggaggtgtctgtaac	9	12	9	11	1	4	0	2	0	2	0	6	2	5	2	1	3	1	1	1	3	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:137715373T>C	ENST00000314358.5	+	5	881	c.681T>C	c.(679-681)cgT>cgC	p.R227R		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	227					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						CCATCACTCGTCTTATGGAGG	0.483																																					p.R227R		.											.	KDM3B-542	0			c.T681C						.						174	148	157					5																	137715373		2203	4300	6503	SO:0001819	synonymous_variant	51780	exon5			CACTCGTCTTATG	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.681T>C	5.37:g.137715373T>C		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	103	37	NM_016604	0	0	26	52	26	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			.		0.483	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137715373	T	C	137715373	2	2	62	1	0	0	0	0	0	0	0	1	8148	1654	58	3		3	KDM3B	5	137715373	Silent	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	1387199	137715373	43199887	35	6021											
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138715041	138715067	+	Splice_Site	DEL	GACCTGTGCTCGGAGGGAGACAGGATG	GACCTGTGCTCGGAGGGAGACAGGATG	-																															caccgtgggcaggccccactGacctgtgctcggagggagac																								rs376791961|rs541083735|rs369734824|rs576828926	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	GACCTGTGCTCGGAGGGAGACAGGATG	GACCTGTGCTCGGAGGGAGACAGGATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:138715041_138715067delGACCTGTGCTCGGAGGGAGACAGGATG	ENST00000348729.3	-	9	972_974	c.926_928delCATCCTGTCTCCCTCCGAGCACAGGTC	c.(925-930)tcatcc>tcc	p.309_310SS>S	SLC23A1_ENST00000503919.1_5'Flank|SLC23A1_ENST00000353963.3_Splice_Site_p.313_314SS>S	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	309					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	AGGCCCCACTGACCTGTGCTCGGAGGGAGACAGGATGGTGGCTACAG	0.581																																					p.313_314del		.											.	SLC23A1-90	0			c.938_940del						.																																			SO:0001630	splice_region_variant	9963	exon9			.	AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"Solute carriers"	10974	protein-coding gene	gene with protein product		603790	"solute carrier family 23 (nucleobase transporters), member 2"	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.926-1CATCCTGTCTCCCTCCGAGCACAGGTC>-	5.37:g.138715041_138715067delGACCTGTGCTCGGAGGGAGACAGGATG		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	32	11	NM_152685	0	0	0	0	0	O95191|Q8WWB6|Q9UGH4|Q9UI39	In_Frame_Del	DEL	ENST00000348729.3	37	CCDS4212.1																																																																																			.		0.581	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685	In_Frame_Del	-	138715067	GACCTGTGCTCGGAGGGAGACAGGATG	-	138715041	8	5	62	1	0	1	0	1	0	0	1	0	14494	1299	45	0	892	0	SLC23A1	5	138715041	Splice_Site	DEL	GACCTGTGCTCGGAGGGAGACAGGATG	TCGA-BQ-5878-01A-11D-1589-08	999668	138715041	42200219	36	6022											
PSD2	84249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	139197069	139197069	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatactctcctggcagcaaCgagtttagcaggctggtggc	8	9	12	12	1	1	0	0	0	1	0	2	1	1	0	2	4	4	5	2	4	3	3	rs142589356		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:139197069C>T	ENST00000274710.3	+	5	1225	c.1020C>T	c.(1018-1020)aaC>aaT	p.N340N		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	340	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCAGCAACGAGTTTAGCA	0.592																																					p.N340N		.											.	PSD2-91	0			c.C1020T						.	C		0,4406		0,0,2203	81	76	78		1020	-0.2	1	5	dbSNP_134	78	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	PSD2	NM_032289.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		340/772	139197069	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	84249	exon5			CAGCAACGAGTTT	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1020C>T	5.37:g.139197069C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	62	21	NM_032289	0	0	0	0	0	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	37	CCDS4216.1																																																																																			C|1.000;T|0.000		0.592	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139197069	C	T	139197069	2	4	62	1	0	0	0	0	0	0	0	1	12676	535	19	1		1	PSD2	5	139197069	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	482028	139197069	41718191	37	6023											
PCDHB15	56121	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140625417	140625417	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgatattaaatgagaagctgGaccgggagaagctgtgtggc	12	9	15	5	1	0	3	0	2	0	2	0	6	0	4	1	3	2	2	1	3	5	2	rs564192004		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:140625417G>C	ENST00000231173.3	+	1	271	c.271G>C	c.(271-273)Gac>Cac	p.D91H		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	91	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGAAGCTGGACCGGGAGAA	0.498													G|||	1	0.000199681	8e-04	0	5008	,	,		17009	0		0	False		,,,				2504	0				p.D91H		.											.	PCDHB15-156	0			c.G271C						.						54	61	59					5																	140625417		2203	4300	6503	SO:0001583	missense	56121	exon1			AAGCTGGACCGGG	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.271G>C	5.37:g.140625417G>C	ENSP00000231173:p.Asp91His	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	99	8	NM_018935	0	0	3	3	0	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964851	0.74131	.	.	ENSG00000113248	ENST00000231173	T	0.53640	0.61	4.92	4.92	0.64577	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.82121	0.4968	H	0.98849	4.35	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.89982	0.4101	9	0.87932	D	0	.	18.0878	0.89463	0.0:0.0:1.0:0.0	.	91	Q9Y5E8	PCDBF_HUMAN	H	91	ENSP00000231173:D91H	ENSP00000231173:D91H	D	+	1	0	PCDHB15	140605601	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	9.804000	0.99143	2.442000	0.82660	0.491000	0.48974	GAC	.		0.498	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		C	140625417	G	C	140625417	3	2	62	1	0	0	0	0	1	0	0	0	11566	1174	41	4	273	4	PCDHB15	5	140625417	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1428348	140625417	40289843	38	6024											
FAT2	2196	broad.mit.edu	37	chr5	150892049	150892049	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcaggcgaatggaagcgTccatctcctccaccaggatg	10	7	10	14	2	2	0	1	0	1	0	5	3	4	2	5	3	1	0	5	3	2	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:150892049T>C	ENST00000261800.5	-	20	11594	c.11582A>G	c.(11581-11583)gAc>gGc	p.D3861G	CTC-251D13.1_ENST00000606930.1_RNA	NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3861	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATGGAAGCGTCCATCTCCTC	0.577																																					p.D3861G													.	FAT2-96	0			c.A11582G						.						89	76	81					5																	150892049		2203	4300	6503	SO:0001583	missense	2196	exon20			GAAGCGTCCATCT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.11582A>G	5.37:g.150892049T>C	ENSP00000261800:p.Asp3861Gly	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	89	4	NM_001447	0	0	0	0	0	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	T	0.078	-1.189237	0.01607	.	.	ENSG00000086570	ENST00000261800	T	0.74842	-0.88	5.02	-0.613	0.11594	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.955911	0.08702	N	0.906338	T	0.52075	0.1712	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30822	-0.9965	9	.	.	.	.	5.8894	0.18899	0.0:0.3066:0.3552:0.3383	.	3861	Q9NYQ8	FAT2_HUMAN	G	3861	ENSP00000261800:D3861G	.	D	-	2	0	FAT2	150872242	0.000000	0.05858	0.000000	0.03702	0.607000	0.37147	0.212000	0.17497	0.048000	0.15891	0.459000	0.35465	GAC	.		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150892049	T	C	150892049	3	2	62	1	0	0	0	0	1	0	0	0	5709	1667	58	3	1483	3	FAT2	5	150892049	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	10266632	150892049	30023211	39	6025											
RPL26L1	51121	hgsc.bcm.edu;broad.mit.edu	37	chr5	172396527	172396527	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatataaagaagaacttattGagaaaatgcaggaataaata	23	9	7	2	0	0	3	0	1	0	3	0	5	0	4	0	1	2	1	0	1	13	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:172396527G>A	ENST00000521476.1	+	4	545	c.421G>A	c.(421-423)Gag>Aag	p.E141K	RPL26L1_ENST00000519974.1_Missense_Mutation_p.E141K|RPL26L1_ENST00000265100.2_Missense_Mutation_p.E141K|RPL26L1_ENST00000519239.1_Missense_Mutation_p.E141K			Q9UNX3	RL26L_HUMAN	ribosomal protein L26-like 1	141					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|large ribosomal subunit (GO:0015934)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|lung(2)|prostate(1)|urinary_tract(1)	7	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGAACTTATTGAGAAAATGCA	0.398																																					p.E141K		.											.	RPL26L1-90	0			c.G421A						.						75	84	81					5																	172396527		2203	4298	6501	SO:0001583	missense	51121	exon4			CTTATTGAGAAAA	AF083248	CCDS4382.1	5q35.2	2008-03-14	2001-12-07	2001-12-14	ENSG00000037241	ENSG00000037241		"L ribosomal proteins"	17050	protein-coding gene	gene with protein product			"ribosomal protein L26 pseudogene 1"	RPL26P1		11042152	Standard	NM_016093		Approved		uc003mcc.3	Q9UNX3	OTTHUMG00000130517	ENST00000521476.1:c.421G>A	5.37:g.172396527G>A	ENSP00000428223:p.Glu141Lys	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	114	8	NM_016093	0	0	70	79	9	B3KY82|D3DQM0	Missense_Mutation	SNP	ENST00000521476.1	37	CCDS4382.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.836364	0.71373	.	.	ENSG00000037241	ENST00000519974;ENST00000521476;ENST00000265100;ENST00000519239	.	.	.	4.58	4.58	0.56647	.	0.051784	0.85682	D	0.000000	T	0.57932	0.2087	L	0.60455	1.87	0.58432	D	0.999997	B	0.06786	0.001	B	0.06405	0.002	T	0.55354	-0.8154	9	0.13853	T	0.58	.	17.9134	0.88942	0.0:0.0:1.0:0.0	.	141	Q9UNX3	RL26L_HUMAN	K	141	.	ENSP00000265100:E141K	E	+	1	0	RPL26L1	172329133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.184000	0.94893	2.522000	0.85027	0.650000	0.86243	GAG	.		0.398	RPL26L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372559.1	NM_016093		A	172396527	G	A	172396527	3	1	62	1	0	0	0	0	1	0	0	0	13606	1291	45	2	431	2	RPL26L1	5	172396527	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	21504478	172396527	8518733	40	6026											
F13A1	2162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	6196094	6196094	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgtgcttgatggcttgaaccGaggcggggccacaccgatac	8	7	14	12	4	0	2	0	2	0	0	0	4	0	2	3	4	3	2	3	4	2	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:6196094G>A	ENST00000264870.3	-	10	1506	c.1241C>T	c.(1240-1242)tCg>tTg	p.S414L		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	414					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GGCTTGAACCGAGGCGGGGCC	0.502																																					p.S414L		.											.	F13A1-519	0			c.C1241T	GRCh37	CM023371|CM993150	F13A1	M		.						96	77	84					6																	6196094		2203	4300	6503	SO:0001583	missense	2162	exon10			TGAACCGAGGCGG	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1241C>T	6.37:g.6196094G>A	ENSP00000264870:p.Ser414Leu	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_000129	0	0	13	13	0	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831865	0.71258	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.55234	0.53	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.71400	0.3335	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.989;0.999	T	0.74621	-0.3604	10	0.87932	D	0	.	18.7232	0.91703	0.0:0.0:1.0:0.0	.	351;414	F5H080;P00488	.;F13A_HUMAN	L	414;351	ENSP00000264870:S414L	ENSP00000264870:S414L	S	-	2	0	F13A1	6141093	1.000000	0.71417	0.928000	0.36995	0.036000	0.12997	9.131000	0.94446	2.728000	0.93425	0.655000	0.94253	TCG	.		0.502	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		A	6196094	G	A	6196094	3	1	62	1	0	0	0	0	1	0	0	0	5353	1059	37	1	981	1	F13A1	6	6196094	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		6196094	164918973	41	6027											
HMGA1	3159	broad.mit.edu	37	chr6	34210572	34210572	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aagggtgctgccaagacccgGgtgagacttgagatgggact	10	7	16	8	1	0	3	0	2	0	3	0	6	0	4	2	3	2	1	2	3	2	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:34210572G>A	ENST00000447654.1	+	3	708	c.219G>A	c.(217-219)cgG>cgA	p.R73R	HMGA1_ENST00000395004.3_Intron|HMGA1_ENST00000347617.6_Splice_Site_p.R62R|HMGA1_ENST00000311487.5_Splice_Site_p.R73R|HMGA1_ENST00000401473.3_Splice_Site_p.R62R|HMGA1_ENST00000478214.1_3'UTR|HMGA1_ENST00000374116.3_Splice_Site_p.R62R	NM_145901.2|NM_145902.2	NP_665908.1|NP_665909.1	P17096	HMGA1_HUMAN	high mobility group AT-hook 1	73	Interaction with HIPK2. {ECO:0000250}.				base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA unwinding involved in DNA replication (GO:0006268)|establishment of integrated proviral latency (GO:0075713)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chromatin silencing (GO:0031936)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|oncogene-induced cell senescence (GO:0090402)|positive regulation of cellular senescence (GO:2000774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|senescence-associated heterochromatin focus assembly (GO:0035986)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|AT DNA binding (GO:0003680)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			lung(1)	1						CCAAGACCCGGGTGAGACTTG	0.592			T	?	"microfollicular thyroid adenoma,  various benign mesenchymal tumors,"																																p.R73R				Dom	yes		6	6p21	3159	high mobility group AT-hook 1		"E, M"	.	HMGA1-650	0			c.G219A						.						57	50	52					6																	34210572		2196	4291	6487	SO:0001630	splice_region_variant	3159	exon3			GACCCGGGTGAGA	AF176039	CCDS4788.1, CCDS4789.1	6p21	2011-07-01	2002-07-25	2002-07-26	ENSG00000137309	ENSG00000137309		"High-mobility group / Canonical"	5010	protein-coding gene	gene with protein product		600701	"high-mobility group (nonhistone chromosomal) protein isoforms I and Y"	HMGIY		8414980, 11406267	Standard	NM_145903		Approved		uc011dso.2	P17096	OTTHUMG00000014539	ENST00000447654.1:c.219+1G>A	6.37:g.34210572G>A		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	12	3	NM_145901	0	0	0	0	0	P10910|Q5T6U9|Q9UKB0	Silent	SNP	ENST00000447654.1	37	CCDS4789.1																																																																																			.		0.592	HMGA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040214.2	NM_145899	Silent	A	34210572	G	A	34210572	5	1	62	1	0	0	0	0	0	0	1	0	7244	1246	43	2	225	2	HMGA1	6	34210572	Splice_Site	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	28014478	34210572	136904495	42	6028											
ZNF318	24149	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43320114	43320114	+	Splice_Site	DEL	C	C	-																															gtcatgcaaagcagctgataCcttgttgtttatgaagccgc																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:43320114delC	ENST00000361428.2	-	5	2848		c.e5+1		ZNF318_ENST00000318149.3_Splice_Site	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318						meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			GCAGCTGATACCTTGTTGTTT	0.418																																					.		.											.	ZNF318-157	0			c.2770+1G>-						.						110	97	102					6																	43320114		2203	4300	6503	SO:0001630	splice_region_variant	24149	exon6			.	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.2770+1G>-	6.37:g.43320114delC		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	68	30	NM_014345	0	0	0	0	0	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Splice_Site	DEL	ENST00000361428.2	37	CCDS4895.2																																																																																			.		0.418	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	Intron	-	43320114	C	-	43320114	8	5	62	1	0	1	0	1	0	0	1	0	17868	521	18	0	4092	0	ZNF318	6	43320114	Splice_Site	DEL	C	TCGA-BQ-5878-01A-11D-1589-08	9109542	43320114	127794953	43	6029											
GFRAL	389400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	55223928	55223928	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcacatgcttcatagaaaatCatgtttcagtaagttcccca	13	12	6	10	0	3	1	3	0	0	1	4	1	4	1	2	0	1	5	2	0	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:55223928C>T	ENST00000340465.2	+	6	1030	c.944C>T	c.(943-945)tCa>tTa	p.S315L		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	315					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S315L(1)		NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CATAGAAAATCATGTTTCAGT	0.343																																					p.S315L		.											.	GFRAL-154	1	Substitution - Missense(1)	lung(1)	c.C944T						.						62	61	61					6																	55223928		2203	4299	6502	SO:0001583	missense	389400	exon6			GAAAATCATGTTT	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.944C>T	6.37:g.55223928C>T	ENSP00000343636:p.Ser315Leu	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	85	9	NM_207410	0	0	0	0	0	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	37	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941217	0.73557	.	.	ENSG00000187871	ENST00000340465	T	0.63417	-0.04	5.52	4.66	0.58398	GDNF/GAS1 (2);	0.157695	0.42682	D	0.000663	T	0.70193	0.3196	M	0.65498	2.005	0.39285	D	0.964639	D	0.89917	1.0	D	0.97110	1.0	T	0.74589	-0.3615	10	0.54805	T	0.06	-7.1541	14.1925	0.65646	0.0:0.9283:0.0:0.0717	.	315	Q6UXV0	GFRAL_HUMAN	L	315	ENSP00000343636:S315L	ENSP00000343636:S315L	S	+	2	0	GFRAL	55331887	1.000000	0.71417	0.682000	0.30024	0.971000	0.66376	5.350000	0.66016	1.327000	0.45338	0.557000	0.71058	TCA	.		0.343	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		T	55223928	C	T	55223928	3	4	62	1	0	0	0	0	1	0	0	0	6371	838	29	2	966	2	GFRAL	6	55223928	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	11903814	55223928	115891139	44	6030											
AIM1	202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	106968949	106968949	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtcacagcccacgactgAgggtgccccgccctgtggtt	6	8	13	14	2	1	1	1	1	0	0	1	2	1	1	4	2	2	1	4	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:106968949A>T	ENST00000369066.3	+	2	3129	c.2642A>T	c.(2641-2643)gAg>gTg	p.E881V		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CCCACGACTGAGGGTGCCCCG	0.478																																					p.E881V		.											.	AIM1-139	0			c.A2642T						.						70	75	73					6																	106968949		2203	4300	6503	SO:0001583	missense	202	exon2			CGACTGAGGGTGC	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2642A>T	6.37:g.106968949A>T	ENSP00000358062:p.Glu881Val	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	142	62	NM_001624	0	0	7	15	8	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.105028	0.37145	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.73047	-0.71	5.99	4.82	0.62117	.	1.203230	0.05682	N	0.590607	T	0.57770	0.2076	M	0.68317	2.08	0.48830	D	0.999719	B	0.26672	0.156	B	0.21917	0.037	T	0.57277	-0.7839	10	0.72032	D	0.01	.	10.8946	0.47015	0.9291:0.0:0.0709:0.0	.	881	Q9Y4K1	AIM1_HUMAN	V	1289;881	ENSP00000358062:E881V	ENSP00000285105:E1289V	E	+	2	0	AIM1	107075642	1.000000	0.71417	0.609000	0.28983	0.728000	0.41692	4.089000	0.57685	1.079000	0.41038	0.533000	0.62120	GAG	.		0.478	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			T	106968949	A	T	106968949	3	4	62	1	0	0	0	0	1	0	0	0	430	304	11	5	2648	5	AIM1	6	106968949	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	51745021	106968949	64146118	45	6031											
LAMA4	3910	broad.mit.edu	37	chr6	112457351	112457351	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtattttgcatcattaatttGagctttctttaacgtatctt	9	21	5	6	1	3	1	1	1	2	0	3	1	3	1	0	0	3	4	0	0	4	10			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:112457351G>A	ENST00000230538.7	-	25	3785	c.3388C>T	c.(3388-3390)Caa>Taa	p.Q1130*	LAMA4_ENST00000522006.1_Nonsense_Mutation_p.Q1123*|LAMA4_ENST00000389463.4_Nonsense_Mutation_p.Q1123*|LAMA4_ENST00000424408.2_Nonsense_Mutation_p.Q1123*	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1130	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TCATTAATTTGAGCTTTCTTT	0.368																																					p.Q1130X													.	LAMA4-140	0			c.C3388T						.						143	127	133					6																	112457351		2203	4300	6503	SO:0001587	stop_gained	3910	exon25			TAATTTGAGCTTT		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.3388C>T	6.37:g.112457351G>A	ENSP00000230538:p.Gln1130*	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	81	4	NM_001105206	0	0	43	43	0	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Nonsense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	G	44	11.263825	0.99539	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	.	.	.	5.93	5.04	0.67666	.	0.284634	0.40554	N	0.001061	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	15.2455	0.73504	0.0:0.0:0.7447:0.2553	.	.	.	.	X	1130;1123;1123;1123	.	ENSP00000230538:Q1130X	Q	-	1	0	LAMA4	112564044	0.893000	0.30496	0.980000	0.43619	0.958000	0.62258	3.972000	0.56838	1.465000	0.48006	0.655000	0.94253	CAA	.		0.368	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112457351	G	A	112457351	4	1	62	1	0	0	0	0	0	1	0	0	8629	1299	45	2	2143	2	LAMA4	6	112457351	Nonsense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	5488402	112457351	58657716	46	6032											
CTGF	1490	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	132271489	132271489	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcgtcacacacccactcctCgcagcatttcccgggcagct	7	8	7	19	3	1	0	1	0	0	0	5	0	3	0	3	1	2	4	3	1	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:132271489C>T	ENST00000367976.3	-	3	684	c.484G>A	c.(484-486)Gag>Aag	p.E162K	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	162	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|chondrocyte proliferation (GO:0035988)|cytosolic calcium ion transport (GO:0060401)|DNA replication (GO:0006260)|epidermis development (GO:0008544)|extracellular matrix constituent secretion (GO:0070278)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of gene expression (GO:0010629)|organ senescence (GO:0010260)|ossification (GO:0001503)|positive regulation of cardiac muscle contraction (GO:0060452)|positive regulation of cell activation (GO:0050867)|positive regulation of cell death (GO:0010942)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of chondrocyte differentiation (GO:0032330)|response to amino acid (GO:0043200)|response to anoxia (GO:0034059)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to mineralocorticoid (GO:0051385)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell cortex (GO:0005938)|cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|insulin-like growth factor binding (GO:0005520)			breast(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	13	Breast(56;0.0602)			GBM - Glioblastoma multiforme(226;0.015)|OV - Ovarian serous cystadenocarcinoma(155;0.0169)		ACCCACTCCTCGCAGCATTTC	0.652											OREG0017666	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E162K	Esophageal Squamous(127;510 1660 12817 24400 38449)	.											.	CTGF-90	0			c.G484A						.						90	91	91					6																	132271489		2203	4300	6503	SO:0001583	missense	1490	exon3			ACTCCTCGCAGCA	X78947	CCDS5151.1	6q23.2	2008-02-05			ENSG00000118523	ENSG00000118523			2500	protein-coding gene	gene with protein product		121009				1654338	Standard	NM_001901		Approved	IGFBP8, CCN2	uc003qcz.3	P29279	OTTHUMG00000015573	ENST00000367976.3:c.484G>A	6.37:g.132271489C>T	ENSP00000356954:p.Glu162Lys	Somatic	170	0	1594	WXS	Illumina HiSeq	Phase_I	185	79	NM_001901	0	0	42	88	46	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Missense_Mutation	SNP	ENST00000367976.3	37	CCDS5151.1	.	.	.	.	.	.	.	.	.	.	C	37	5.984351	0.97173	.	.	ENSG00000118523	ENST00000367976	T	0.71579	-0.58	5.57	5.57	0.84162	von Willebrand factor, type C (4);	0.049682	0.85682	D	0.000000	T	0.80732	0.4679	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80946	-0.1155	10	0.59425	D	0.04	.	19.5503	0.95314	0.0:1.0:0.0:0.0	.	162	P29279	CTGF_HUMAN	K	162	ENSP00000356954:E162K	ENSP00000356954:E162K	E	-	1	0	CTGF	132313182	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.818000	0.86416	2.619000	0.88677	0.561000	0.74099	GAG	.		0.652	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901		T	132271489	C	T	132271489	3	4	62	1	0	0	0	0	1	0	0	0	4014	893	31	1	577	1	CTGF	6	132271489	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	19814138	132271489	38843578	47	6033											
SASH1	23328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	148808752	148808752	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	catttcttcttgttacagctCaaggaatacgaggcccagca	11	11	8	11	1	3	0	1	0	2	0	3	2	3	1	1	2	4	3	1	2	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:148808752C>G	ENST00000367467.3	+	8	1105	c.630C>G	c.(628-630)ctC>ctG	p.L210L		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	210					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TGTTACAGCTCAAGGAATACG	0.488																																					p.L210L		.											.	SASH1-90	0			c.C630G						.						93	99	97					6																	148808752		2203	4300	6503	SO:0001819	synonymous_variant	23328	exon8			ACAGCTCAAGGAA	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.630C>G	6.37:g.148808752C>G		Somatic	221	0		WXS	Illumina HiSeq	Phase_I	194	68	NM_015278	0	0	0	0	0	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																			.		0.488	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		G	148808752	C	G	148808752	2	3	62	1	0	0	0	0	0	0	0	1	13880	813	29	4		4	SASH1	6	148808752	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	16537263	148808752	22306315	48	6034											
RMND1	55005	ucsc.edu	37	chr6	151751272	151751272	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacatttttatttacacttaCagttttgtctttcacattcc	9	20	2	10	0	2	0	1	0	1	0	3	0	3	0	1	0	2	1	1	0	3	10			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:151751272C>T	ENST00000367303.4	-	5	852		c.e5+1		RMND1_ENST00000336451.3_Splice_Site	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)						translation (GO:0006412)	mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		TTTACACTTACAGTTTTGTCT	0.279																																					.													.	RMND1-90	0			c.729+1G>A						.						54	57	56					6																	151751272		2201	4288	6489	SO:0001630	splice_region_variant	55005	exon6			CACTTACAGTTTT	AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"chromosome 6 open reading frame 96"	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.729+1G>A	6.37:g.151751272C>T		Somatic	102	0		WXS	Illumina HiSeq		100	1	NM_017909	0	0	0	0	0	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Splice_Site	SNP	ENST00000367303.4	37	CCDS5232.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.610767	0.66558	.	.	ENSG00000155906	ENST00000336451;ENST00000367303;ENST00000444024	.	.	.	4.17	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6062	0.84830	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RMND1	151792965	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	5.504000	0.66968	2.308000	0.77769	0.313000	0.20887	.	.		0.279	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	Intron	T	151751272	C	T	151751272	5	4	62	1	0	0	0	0	0	0	1	0	13428	492	17	2	651	2	RMND1	6	151751272	Splice_Site	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2942520	151751272	19363795	49	6035											
TNRC18	84629	hgsc.bcm.edu;broad.mit.edu	37	chr7	5352384	5352384	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcttgcctggggagtgggccGagggccgcgccttgccggcc	2	7	18	14	4	1	0	0	0	1	0	1	2	1	1	6	5	2	0	6	5	0	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:5352384G>A	ENST00000430969.1	-	27	8486	c.8138C>T	c.(8137-8139)tCg>tTg	p.S2713L	TNRC18_ENST00000399537.4_Missense_Mutation_p.S2713L	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2713							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGAGTGGGCCGAGGGCCGCGC	0.761																																					p.S2713L		.											.	TNRC18-46	0			c.C8138T						.						4	6	6					7																	5352384		1215	2847	4062	SO:0001583	missense	84629	exon27			TGGGCCGAGGGCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8138C>T	7.37:g.5352384G>A	ENSP00000395538:p.Ser2713Leu	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	38	7	NM_001080495	0	0	31	49	18	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	6.791|6.791	0.514848|0.514848	0.12944|0.12944	.|.	.|.	ENSG00000182095|ENSG00000182095	ENST00000399544|ENST00000399537;ENST00000430969	.|T;T	.|0.05258	.|3.47;3.47	4.31|4.31	2.46|2.46	0.29980|0.29980	.|.	.|.	.|.	.|.	.|.	T|T	0.06280|0.06280	0.0162|0.0162	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	.|B	.|0.12013	.|0.005	.|B	.|0.06405	.|0.002	T|T	0.45026|0.45026	-0.9289|-0.9289	6|9	0.87932|0.09590	D|T	0|0.72	.|.	10.6731|10.6731	0.45770|0.45770	0.1532:0.0:0.8468:0.0|0.1532:0.0:0.8468:0.0	.|.	.|2713	.|O15417	.|TNC18_HUMAN	W|L	1226|2713	.|ENSP00000382452:S2713L;ENSP00000395538:S2713L	ENSP00000382459:R1226W|ENSP00000382452:S2713L	R|S	-|-	1|2	2|0	TNRC18|TNRC18	5318910|5318910	0.746000|0.746000	0.28272|0.28272	0.001000|0.001000	0.08648|0.08648	0.012000|0.012000	0.07955|0.07955	2.496000|2.496000	0.45346|0.45346	0.246000|0.246000	0.21394|0.21394	0.484000|0.484000	0.47621|0.47621	CGG|TCG	.		0.761	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5352384	G	A	5352384	3	1	62	1	0	0	0	0	1	0	0	0	16371	1059	37	1	784	1	TNRC18	7	5352384	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		5352384	153786279	50	6036											
TNS3	64759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	47440438	47440438	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccgtagccctgcacaGccccagtgtgaaactgcagg	9	5	11	16	1	0	1	0	1	0	0	0	1	0	1	5	1	6	3	5	1	2	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:47440438G>A	ENST00000398879.1	-	14	1163	c.797C>T	c.(796-798)gCt>gTt	p.A266V	TNS3_ENST00000311160.9_Missense_Mutation_p.A266V|TNS3_ENST00000355730.3_Intron			Q68CZ2	TENS3_HUMAN	tensin 3	266	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						GCCCTGCACAGCCCCAGTGTG	0.577																																					p.A266V		.											.	TNS3-94	0			c.C797T						.						78	98	91					7																	47440438		2047	4182	6229	SO:0001583	missense	64759	exon14			TGCACAGCCCCAG	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"SH2 domain containing"	21616	protein-coding gene	gene with protein product	"tumor endothelial marker 6"	606825	"tensin-like SH2 domain-containing 1"	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.797C>T	7.37:g.47440438G>A	ENSP00000381854:p.Ala266Val	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	92	38	NM_022748	0	0	25	52	27	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643525	0.87859	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000457718;ENST00000450444	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.99	4.99	0.66335	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.86793	0.6018	M	0.74546	2.27	0.80722	D	1	P	0.46859	0.885	P	0.45753	0.492	D	0.87020	0.2128	10	0.39692	T	0.17	-16.8831	15.8183	0.78621	0.0:0.0:1.0:0.0	.	266	Q68CZ2	TENS3_HUMAN	V	266;376;266;369;355	ENSP00000312143:A266V;ENSP00000381854:A266V;ENSP00000414358:A369V;ENSP00000396914:A355V	ENSP00000312143:A266V	A	-	2	0	TNS3	47406963	1.000000	0.71417	0.436000	0.26797	0.965000	0.64279	7.322000	0.79097	2.337000	0.79520	0.456000	0.33151	GCT	.		0.577	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		A	47440438	G	A	47440438	3	1	62	1	0	0	0	0	1	0	0	0	16376	971	34	2	3612	2	TNS3	7	47440438	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	42088054	47440438	111698225	51	6037											
POM121	9883	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	72412723	72412723	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcccatgttcaagcccAttttcacggctccacccaag	9	9	5	18	1	2	0	2	0	0	0	4	0	4	0	5	1	1	2	5	1	2	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:72412723A>G	ENST00000434423.2	+	11	2191	c.2191A>G	c.(2191-2193)Att>Gtt	p.I731V	POM121_ENST00000358357.3_Missense_Mutation_p.I466V|POM121_ENST00000446813.1_Missense_Mutation_p.I466V|POM121_ENST00000395270.1_Missense_Mutation_p.I466V|POM121_ENST00000257622.4_Missense_Mutation_p.I466V			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	731	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				GTTCAAGCCCATTTTCACGGC	0.627																																					p.I466V		.											.	POM121-226	0			c.A1396G						.						41	50	47					7																	72412723		2176	4299	6475	SO:0001583	missense	9883	exon11			AAGCCCATTTTCA	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"-"	19702	protein-coding gene	gene with protein product		615753	"POM121 membrane glycoprotein (rat)", "POM121 membrane glycoprotein"			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2191A>G	7.37:g.72412723A>G	ENSP00000405562:p.Ile731Val	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	87	30	NM_172020	1	0	98	126	27	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	A	12.33	1.906382	0.33628	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.09630	2.96;3.0;2.96;3.0;3.24	2.4	2.4	0.29515	.	0.356190	0.20092	N	0.099437	T	0.10121	0.0248	L	0.52573	1.65	0.28363	N	0.920368	B;B	0.24721	0.11;0.029	B;B	0.20184	0.028;0.017	T	0.10776	-1.0615	10	0.46703	T	0.11	.	8.227	0.31575	1.0:0.0:0.0:0.0	.	466;731	A8MXF9;Q96HA1	.;P121A_HUMAN	V	466;466;466;466;731	ENSP00000393020:I466V;ENSP00000257622:I466V;ENSP00000378687:I466V;ENSP00000351124:I466V;ENSP00000405562:I731V	ENSP00000257622:I466V	I	+	1	0	POM121	72050659	1.000000	0.71417	0.875000	0.34327	0.190000	0.23558	2.934000	0.48956	1.097000	0.41459	0.145000	0.16022	ATT	.		0.627	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			G	72412723	A	G	72412723	3	3	62	1	0	0	0	0	1	0	0	0	12265	217	8	3	1434	3	POM121	7	72412723	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	24972285	72412723	86725940	52	6038											
GATAD1	57798	broad.mit.edu	37	chr7	92078080	92078080	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taacagagtaagcaggaaatTcacaggaggtctgctcggct	13	8	12	8	1	2	1	1	0	1	1	3	3	2	3	0	4	3	4	0	4	3	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:92078080T>A	ENST00000287957.3	+	2	541	c.264T>A	c.(262-264)atT>atA	p.I88I		NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	88						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGCAGGAAATTCACAGGAGGT	0.383											OREG0018163	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I88I													.	GATAD1-514	0			c.T264A						.						112	119	117					7																	92078080		2203	4300	6503	SO:0001819	synonymous_variant	57798	exon2			GGAAATTCACAGG		CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259		"GATA zinc finger domain containing"	29941	protein-coding gene	gene with protein product	"ocular development associated gene"	614518				12062807	Standard	NM_021167		Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.264T>A	7.37:g.92078080T>A		Somatic	139	0	1287	WXS	Illumina HiSeq	Phase_I	161	4	NM_021167	0	0	35	37	2	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	Silent	SNP	ENST00000287957.3	37	CCDS5625.1																																																																																			.		0.383	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253929.2	NM_021167		A	92078080	T	A	92078080	2	1	62	1	0	0	0	0	0	0	0	1	6279	1771	62	5		5	GATAD1	7	92078080	Silent	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	19665357	92078080	67060583	53	6039											
PPP1R9A	55607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	94915545	94915545	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccttcaatgatgacttcagtCccagcagtaccagttcagca	11	10	7	13	0	3	2	3	2	0	0	4	2	4	2	3	0	3	4	3	0	2	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:94915545C>A	ENST00000433881.1	+	13	3317	c.2785C>A	c.(2785-2787)Ccc>Acc	p.P929T	PPP1R9A_ENST00000289495.5_Missense_Mutation_p.P1135T|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.P1153T|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.P1213T|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.P929T|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.P1153T			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	929	Interacts with TGN38. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			TGACTTCAGTCCCAGCAGTAC	0.453										HNSCC(28;0.073)																											p.P1213T		.											.	PPP1R9A-208	0			c.C3637A						.						94	84	87					7																	94915545		2203	4300	6503	SO:0001583	missense	55607	exon18			TTCAGTCCCAGCA	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.2785C>A	7.37:g.94915545C>A	ENSP00000398870:p.Pro929Thr	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	64	23	NM_001166160	0	0	16	35	19	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	37	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022533	0.75275	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.19669	2.14;2.32;2.18;2.32;2.13;2.18	4.99	4.99	0.66335	.	0.219511	0.40728	N	0.001031	T	0.37183	0.0994	L	0.34521	1.04	0.35638	D	0.810778	D;D;D;D;D;P	0.89917	0.979;1.0;0.999;1.0;0.999;0.682	P;D;D;D;D;B	0.79108	0.525;0.992;0.973;0.972;0.941;0.096	T	0.31888	-0.9927	10	0.45353	T	0.12	.	18.8526	0.92238	0.0:1.0:0.0:0.0	.	929;1135;1213;1153;1153;929	B7ZLX4;F8W7J9;E9PDX1;D6W5R0;E9PCK6;Q9ULJ8	.;.;.;.;.;NEB1_HUMAN	T	1213;929;1153;929;1135;1153	ENSP00000405514:P1213T;ENSP00000344524:P929T;ENSP00000411342:P1153T;ENSP00000398870:P929T;ENSP00000289495:P1135T;ENSP00000402893:P1153T	ENSP00000289495:P1135T	P	+	1	0	PPP1R9A	94753481	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.886000	0.48578	2.758000	0.94735	0.655000	0.94253	CCC	.		0.453	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		A	94915545	C	A	94915545	3	1	62	1	0	0	0	0	1	0	0	0	12407	855	30	4	3703	4	PPP1R9A	7	94915545	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2837465	94915545	64223118	54	6040											
AMAC1L2	83650	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	11188670	11188670	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	actccacacacccatcgccgCcctccgctccacccagcctc	7	5	4	25	3	0	0	0	0	0	0	5	0	3	0	8	0	1	1	8	0	0	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr8:11188670C>T	ENST00000382435.4	+	1	274	c.55C>T	c.(55-57)Ccc>Tcc	p.P19S		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	19						integral component of membrane (GO:0016021)											CCCATCGCCGCCCTCCGCTCC	0.677																																					p.P19S		.											.	.	0			c.C55T						.						54	56	55					8																	11188670		2203	4300	6503	SO:0001583	missense	83650	exon1			TCGCCGCCCTCCG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"Solute carriers"	15546	protein-coding gene	gene with protein product		615199	"acyl-malonyl condensing enzyme 1-like 2"	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.55C>T	8.37:g.11188670C>T	ENSP00000371872:p.Pro19Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	72	28	NM_054028	0	0	0	0	0	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.250440	0.22880	.	.	ENSG00000177710	ENST00000382435	T	0.27256	1.68	0.34	0.34	0.15985	.	0.159640	0.29321	N	0.012484	T	0.28797	0.0714	N	0.24115	0.695	0.09310	N	0.999993	D	0.89917	1.0	D	0.80764	0.994	T	0.08310	-1.0728	9	0.35671	T	0.21	-11.4858	.	.	.	.	19	Q96KT7	S35G5_HUMAN	S	19	ENSP00000371872:P19S	ENSP00000371872:P19S	P	+	1	0	SLC35G5	11226080	0.007000	0.16637	0.221000	0.23827	0.172000	0.22775	0.166000	0.16583	0.426000	0.26116	0.089000	0.15464	CCC	.		0.677	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028		T	11188670	C	T	11188670	3	4	62	1	0	0	0	0	1	0	0	0	560	739	26	2	57	2	AMAC1L2	8	11188670	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		11188670	135175352	55	6041											
ANK1	286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	41577342	41577342	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggacacagtcgaggtggtctCcctgagccgccatgtgaatt	8	9	13	11	2	1	2	0	2	1	0	3	4	1	3	3	3	1	0	3	3	1	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr8:41577342C>T	ENST00000347528.4	-	10	1027	c.944G>A	c.(943-945)gGa>gAa	p.G315E	ANK1_ENST00000352337.4_Missense_Mutation_p.G315E|ANK1_ENST00000396945.1_Missense_Mutation_p.G315E|ANK1_ENST00000396942.1_Missense_Mutation_p.G315E|ANK1_ENST00000379758.2_Missense_Mutation_p.G315E|ANK1_ENST00000289734.7_Missense_Mutation_p.G315E|ANK1_ENST00000265709.8_Missense_Mutation_p.G348E	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	315	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GAGGTGGTCTCCCTGAGCCGC	0.567																																					p.G348E		.											.	ANK1-716	0			c.G1043A						.						178	151	160					8																	41577342		2203	4300	6503	SO:0001583	missense	286	exon10			TGGTCTCCCTGAG	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.944G>A	8.37:g.41577342C>T	ENSP00000339620:p.Gly315Glu	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	142	57	NM_001142446	0	0	6	13	7	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	32	5.138021	0.94517	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04;0.04	5.91	5.91	0.95273	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	N	0.17345	0.48	0.80722	D	1	D;D;P;D;D	0.89917	1.0;1.0;0.744;1.0;1.0	D;D;B;D;D	0.97110	1.0;1.0;0.414;0.988;1.0	T	0.71728	-0.4505	10	0.54805	T	0.06	.	20.2963	0.98556	0.0:1.0:0.0:0.0	.	348;315;315;315;315	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	E	315;315;315;315;315;315;348;315	ENSP00000339620:G315E;ENSP00000289734:G315E;ENSP00000369082:G315E;ENSP00000380149:G315E;ENSP00000380147:G315E;ENSP00000309131:G315E;ENSP00000265709:G348E	ENSP00000265709:G348E	G	-	2	0	ANK1	41696499	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.757000	0.85209	2.813000	0.96785	0.655000	0.94253	GGA	.		0.567	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41577342	C	T	41577342	3	4	62	1	0	0	0	0	1	0	0	0	620	855	30	2	5187	2	ANK1	8	41577342	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	30388672	41577342	104786680	56	6042											
GDAP1	54332	broad.mit.edu	37	chr8	75263599	75263599	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaatgagccttggtttatgCgtttgaactcaactggagaa	12	12	10	7	1	1	3	1	2	0	1	1	4	1	3	1	2	4	2	1	2	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr8:75263599C>T	ENST00000220822.7	+	2	288	c.208C>T	c.(208-210)Cgt>Tgt	p.R70C	GDAP1_ENST00000521096.1_Intron|CTD-2320G14.2_ENST00000521872.1_RNA|GDAP1_ENST00000434412.2_Missense_Mutation_p.R2C	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	70	GST N-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R70C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			TTGGTTTATGCGTTTGAACTC	0.453																																					p.R70C													.	GDAP1-90	1	Substitution - Missense(1)	kidney(1)	c.C208T						.						343	291	309					8																	75263599		2203	4300	6503	SO:0001583	missense	54332	exon2			TTTATGCGTTTGA		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.208C>T	8.37:g.75263599C>T	ENSP00000220822:p.Arg70Cys	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	324	5	NM_018972	0	0	30	30	0	A8K957|E7FJF3|E7FJF4	Missense_Mutation	SNP	ENST00000220822.7	37	CCDS34911.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.407363	0.83230	.	.	ENSG00000104381	ENST00000220822;ENST00000434412	T;T	0.48201	1.66;0.82	5.17	5.17	0.71159	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.119635	0.64402	D	0.000015	T	0.77811	0.4186	M	0.93420	3.415	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.83650	0.0155	10	0.72032	D	0.01	-26.7646	18.8518	0.92235	0.0:1.0:0.0:0.0	.	70	Q8TB36	GDAP1_HUMAN	C	70;2	ENSP00000220822:R70C;ENSP00000417006:R2C	ENSP00000220822:R70C	R	+	1	0	GDAP1	75426154	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.570000	0.53834	2.678000	0.91216	0.655000	0.94253	CGT	.		0.453	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		T	75263599	C	T	75263599	3	4	62	1	0	0	0	0	1	0	0	0	6327	768	27	1	214	1	GDAP1	8	75263599	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	33686257	75263599	71100423	57	6043											
SPIN1	10927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	91083448	91083448	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttacattacctatgagaaaGaccctgtcttgtacatgtac	12	14	6	9	0	1	2	0	1	1	2	1	3	1	2	2	0	4	2	2	0	6	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr9:91083448G>C	ENST00000375859.3	+	5	795	c.517G>C	c.(517-519)Gac>Cac	p.D173H	SPIN1_ENST00000469017.2_3'UTR|SPIN1_ENST00000541629.1_Missense_Mutation_p.D173H	NM_006717.2	NP_006708.2	Q9Y657	SPIN1_HUMAN	spindlin 1	173	Tudor-like domain 2.				chromatin modification (GO:0016568)|gamete generation (GO:0007276)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of Wnt signaling pathway (GO:0030177)|rRNA transcription (GO:0009303)|Wnt signaling pathway (GO:0016055)	nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle (GO:0005819)	methylated histone binding (GO:0035064)			endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						CTATGAGAAAGACCCTGTCTT	0.403																																					p.D173H		.											.	SPIN1-44	0			c.G517C						.						188	182	184					9																	91083448		2158	4287	6445	SO:0001583	missense	10927	exon5			GAGAAAGACCCTG	AF317228	CCDS43843.1	9q22.1	2008-02-05	2007-01-03	2007-01-03	ENSG00000106723	ENSG00000106723			11243	protein-coding gene	gene with protein product		609936	"spindlin"	SPIN		16098913	Standard	NM_006717		Approved		uc004apy.3	Q9Y657	OTTHUMG00000020168	ENST00000375859.3:c.517G>C	9.37:g.91083448G>C	ENSP00000365019:p.Asp173His	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	132	11	NM_006717	0	0	71	84	13	A8K0X6|B3KRQ4|Q7KZJ8|Q9GZT2|Q9H0N7	Missense_Mutation	SNP	ENST00000375859.3	37	CCDS43843.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.466930	0.84425	.	.	ENSG00000106723	ENST00000375859;ENST00000541629	T;T	0.55588	0.51;0.51	5.12	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.73353	-0.4009	10	0.87932	D	0	-20.5419	14.8406	0.70220	0.0:0.0:0.8552:0.1448	.	173	Q9Y657	SPIN1_HUMAN	H	173	ENSP00000365019:D173H;ENSP00000441864:D173H	ENSP00000365019:D173H	D	+	1	0	SPIN1	90273268	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.155000	0.94700	1.327000	0.45338	0.655000	0.94253	GAC	.		0.403	SPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052967.1	NM_006717		C	91083448	G	C	91083448	3	2	62	1	0	0	0	0	1	0	0	0	15084	942	33	4	531	4	SPIN1	9	91083448	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		91083448	50129983	58	6044											
RXRA	6256	ucsc.edu	37	chr9	137300036	137300036	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtcagcagcagcgaggacatCaagccccccctgggcctcaa	10	4	11	16	1	3	0	3	0	0	0	3	2	3	1	4	2	4	2	4	2	2	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr9:137300036C>T	ENST00000481739.1	+	3	373	c.321C>T	c.(319-321)atC>atT	p.I107I	RXRA_ENST00000356384.4_3'UTR|RXRA_ENST00000540193.1_Silent_p.I10I	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	107	Modulating. {ECO:0000250}.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)	p.I107I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	GCGAGGACATCAAGCCCCCCC	0.637																																					p.I107I													.	RXRA-188	1	Substitution - coding silent(1)	lung(1)	c.C321T						.						60	47	52					9																	137300036		2203	4299	6502	SO:0001819	synonymous_variant	6256	exon3			GGACATCAAGCCC	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"Nuclear hormone receptors"	10477	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 1"	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.321C>T	9.37:g.137300036C>T		Somatic	51	0		WXS	Illumina HiSeq		42	2	NM_002957	0	0	12	13	1	B3KY83|Q2NL52|Q2V504	Silent	SNP	ENST00000481739.1	37	CCDS35172.1																																																																																			.		0.637	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957		T	137300036	C	T	137300036	2	4	62	1	0	0	0	0	0	0	0	1	13795	816	29	2		2	RXRA	9	137300036	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	46216588	137300036	3913395	59	6045											
LCN1	3933	broad.mit.edu	37	chr9	138415819	138415819	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgcacgggaagccggtccGaggggtgaagctcgtgggtg	6	6	20	9	4	0	1	0	1	0	0	2	3	1	2	2	5	3	3	2	5	2	0	rs199573452		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr9:138415819G>A	ENST00000263598.2	+	4	446	c.386G>A	c.(385-387)cGa>cAa	p.R129Q	LCN1_ENST00000371781.3_Missense_Mutation_p.R129Q	NM_001252617.1|NM_001252618.1|NM_001252619.1|NM_002297.3	NP_001239546.1|NP_001239547.1|NP_001239548.1|NP_002288.1	P31025	LCN1_HUMAN	lipocalin 1	129					negative regulation of endopeptidase activity (GO:0010951)|proteolysis (GO:0006508)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|sensory perception of taste (GO:0050909)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)	13		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.54e-08)|Epithelial(140;5.25e-08)|all cancers(34;9.27e-07)|READ - Rectum adenocarcinoma(205;0.155)		AAGCCGGTCCGAGGGGTGAAG	0.642																																					p.R129Q													.	LCN1-90	0			c.G386A						.						75	63	67					9																	138415819		2203	4300	6503	SO:0001583	missense	3933	exon4			CGGTCCGAGGGGT		CCDS6991.1	9q34	2011-11-14	2011-11-01		ENSG00000160349	ENSG00000160349		"Lipocalins"	6525	protein-coding gene	gene with protein product	"Von Ebner gland protein", "tear lipocalin", "lipocalin 1-like 2", "tear prealbumin"	151675	"lipocalin 1 (protein migrating faster than albumin, tear prealbumin)", "lipocalin 1 (tear prealbumin)"			8276406	Standard	NM_002297		Approved	VEGP, TP, PMFA, MGC71975, TLC	uc022bpk.1	P31025	OTTHUMG00000020908	ENST00000263598.2:c.386G>A	9.37:g.138415819G>A	ENSP00000263598:p.Arg129Gln	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	50	4	NM_001252617	0	0	0	0	0	Q5T8A1	Missense_Mutation	SNP	ENST00000263598.2	37	CCDS6991.1	.	.	.	.	.	.	.	.	.	.	G	8.074	0.770937	0.15983	.	.	ENSG00000160349	ENST00000263598;ENST00000371781	T;T	0.08008	3.14;3.14	3.11	-2.31	0.06765	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.672980	0.04586	N	0.395796	T	0.06416	0.0165	L	0.51422	1.61	0.09310	N	1	B	0.32604	0.377	B	0.17722	0.019	T	0.35724	-0.9777	10	0.21014	T	0.42	.	3.6261	0.08113	0.4476:0.0:0.3785:0.174	.	129	P31025	LCN1_HUMAN	Q	129	ENSP00000263598:R129Q;ENSP00000360846:R129Q	ENSP00000263598:R129Q	R	+	2	0	LCN1	137555640	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.719000	0.04974	-0.590000	0.05866	-1.534000	0.00916	CGA	G|0.999;A|0.001		0.642	LCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054992.1	NM_002297		A	138415819	G	A	138415819	3	1	62	1	0	0	0	0	1	0	0	0	8701	1058	37	1	400	1	LCN1	9	138415819	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1115783	138415819	2797612	60	6046											
SPAG6	9576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	22676767	22676767	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacagcatcagatcctttcaGctctcagtcaggtttcaaaa	12	11	6	12	0	5	1	5	0	1	1	7	1	6	1	1	1	2	3	1	1	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:22676767G>T	ENST00000376624.3	+	6	836	c.694G>T	c.(694-696)Gct>Tct	p.A232S	SPAG6_ENST00000376603.2_Missense_Mutation_p.A308S|SPAG6_ENST00000313311.6_Missense_Mutation_p.A232S|SPAG6_ENST00000538630.1_Missense_Mutation_p.A207S|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000376601.1_Intron	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	232					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						GATCCTTTCAGCTCTCAGTCA	0.373																																					p.A232S		.											.	SPAG6-153	0			c.G694T						.						78	77	77					10																	22676767		2203	4300	6503	SO:0001583	missense	9576	exon6			CTTTCAGCTCTCA	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.694G>T	10.37:g.22676767G>T	ENSP00000365811:p.Ala232Ser	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	80	27	NM_172242	0	0	0	0	0	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	37	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620704	0.46736	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.64	3.8	0.43715	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86936	0.6053	M	0.83953	2.67	0.58432	D	0.999999	P;P;P;P	0.49783	0.795;0.928;0.866;0.74	P;P;P;P	0.55222	0.714;0.771;0.508;0.588	D	0.87333	0.2326	10	0.66056	D	0.02	-21.9001	12.0263	0.53373	0.1391:0.0:0.8609:0.0	.	207;308;232;232	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	S	232;308;207;232	ENSP00000365811:A232S;ENSP00000365788:A308S;ENSP00000441325:A207S;ENSP00000323599:A232S	ENSP00000323599:A232S	A	+	1	0	SPAG6	22716773	1.000000	0.71417	0.582000	0.28627	0.580000	0.36256	6.587000	0.74071	0.744000	0.32741	0.655000	0.94253	GCT	.		0.373	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			T	22676767	G	T	22676767	3	4	62	1	0	0	0	0	1	0	0	0	15014	971	34	4	716	4	SPAG6	10	22676767	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		22676767	112857980	61	6047											
PIP4K2A	5305	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	23003187	23003187	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcttcactttctgcgctacGaagtgcttcttcttggtctt	5	17	8	11	2	5	0	1	0	4	0	5	1	5	0	0	1	4	3	0	1	2	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:23003187G>A	ENST00000376573.4	-	1	297	c.69C>T	c.(67-69)ttC>ttT	p.F23F	PIP4K2A_ENST00000545335.1_5'Flank	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	23					megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						TCTGCGCTACGAAGTGCTTCT	0.647																																					p.F23F		.											.	PIP4K2A-665	0			c.C69T						.						94	85	88					10																	23003187		2203	4300	6503	SO:0001819	synonymous_variant	5305	exon1			CGCTACGAAGTGC	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.69C>T	10.37:g.23003187G>A		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	48	23	NM_005028	0	0	8	20	12	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	37	CCDS7141.1																																																																																			.		0.647	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		A	23003187	G	A	23003187	2	1	62	1	0	0	0	0	0	0	0	1	11962	1049	37	1		1	PIP4K2A	10	23003187	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	326420	23003187	112531560	62	6048											
ZNF485	220992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	44112496	44112496	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtaaatgtggaaaatctttCaggtatagctcatcctttgc	12	14	8	7	0	3	0	2	0	1	0	4	1	4	1	1	2	2	3	1	2	6	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:44112496C>T	ENST00000361807.3	+	5	1199	c.1005C>T	c.(1003-1005)ttC>ttT	p.F335F	ZNF485_ENST00000374435.3_Silent_p.F335F|ZNF485_ENST00000374437.2_Silent_p.F244F	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	335					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(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GAAAATCTTTCAGGTATAGCT	0.428																																					p.F335F		.											.	ZNF485-90	0			c.C1005T						.						117	117	117					10																	44112496		2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			ATCTTTCAGGTAT	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"Zinc fingers, C2H2-type", "-"	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.1005C>T	10.37:g.44112496C>T		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	119	46	NM_145312	0	0	1	2	1	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																			.		0.428	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312		T	44112496	C	T	44112496	2	4	62	1	0	0	0	0	0	0	0	1	17970	825	29	2		2	ZNF485	10	44112496	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	21109309	44112496	91422251	63	6049											
PCDH15	65217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	55583106	55583106	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgctttgttgaaaatggtaGagaaggaaaagacttgaaag	16	10	12	3	0	0	4	0	2	0	2	0	6	0	5	0	2	1	3	0	2	7	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:55583106G>C	ENST00000320301.6	-	33	4774	c.4380C>G	c.(4378-4380)ctC>ctG	p.L1460L	PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000361849.3_Silent_p.L1462L|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000437009.1_Silent_p.L1391L|PCDH15_ENST00000395433.1_Silent_p.L1437L|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395432.2_Silent_p.L1420L|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395430.1_Silent_p.L1457L|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373965.2_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1460					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GAAAATGGTAGAGAAGGAAAA	0.363										HNSCC(58;0.16)																											p.L1467L		.											.	PCDH15-193	0			c.C4401G						.						94	97	96					10																	55583106		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon35			ATGGTAGAGAAGG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4380C>G	10.37:g.55583106G>C		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	79	12	NM_001142763	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.		0.363	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55583106	G	C	55583106	2	2	62	1	0	0	0	0	0	0	0	1	11537	929	33	4		4	PCDH15	10	55583106	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	11470610	55583106	79951641	64	6050											
AGAP5	729092	broad.mit.edu	37	chr10	75457454	75457454	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagggacacaccgacccctgTtgctggtcaaactcgaggct	9	7	12	13	2	1	0	1	0	0	0	2	4	1	1	3	3	2	3	3	3	1	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:75457454T>C	ENST00000374094.4	-	1	100	c.60A>G	c.(58-60)caA>caG	p.Q20Q	AGAP5_ENST00000443782.2_Silent_p.Q20Q|RP11-464F9.1_ENST00000399449.3_RNA|RP11-574K11.28_ENST00000580790.1_RNA	NM_001144000.1	NP_001137472.1	A6NIR3	AGAP5_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 5	20					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.Q20Q(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(5)|skin(1)	12						CCGACCCCTGTTGCTGGTCAA	0.607																																					p.Q20Q													.	AGAP5-68	1	Substitution - coding silent(1)	lung(1)	c.A60G						.						59	62	61					10																	75457454		692	1591	2283	SO:0001819	synonymous_variant	729092	exon1			CCCCTGTTGCTGG		CCDS44439.1	10q22.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000172650	ENSG00000172650		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	23467	protein-coding gene	gene with protein product			"centaurin, gamma-like family, member 2"	CTGLF2			Standard	NM_001144000		Approved	Em:AC073389.1	uc009xri.3	A6NIR3	OTTHUMG00000018473	ENST00000374094.4:c.60A>G	10.37:g.75457454T>C		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	89	5	NM_001144000	0	0	5	23	18	A8MSN5	Silent	SNP	ENST00000374094.4	37	CCDS44439.1																																																																																			.		0.607	AGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_001132585		C	75457454	T	C	75457454	2	2	62	1	0	0	0	0	0	0	0	1	371	1722	60	3		3	AGAP5	10	75457454	Silent	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	19874348	75457454	60077293	65	6051											
DLG5	9231	broad.mit.edu;bcgsc.ca	37	chr10	79686110	79686110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttggccaagagcagcttgaGcagcagctccgccttggcgc	7	7	13	14	2	0	2	0	1	0	1	1	2	1	2	3	2	5	5	3	2	1	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:79686110G>A	ENST00000372391.2	-	1	174	c.169C>T	c.(169-171)Ctc>Ttc	p.L57F	DLG5-AS1_ENST00000449852.1_RNA|DLG5_ENST00000372388.2_Missense_Mutation_p.L57F	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	57					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			AGCAGCTTGAGCAGCAGCTCC	0.706																																					p.L57F													.	DLG5-98	0			c.C169T						.						13	19	17					10																	79686110		2045	4173	6218	SO:0001583	missense	9231	exon1			GCTTGAGCAGCAG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"discs, large (Drosophila) homolog 5"			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.169C>T	10.37:g.79686110G>A	ENSP00000361467:p.Leu57Phe	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	11	4	NM_004747	0	0	5	15	10	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	g	21.7	4.190028	0.78789	.	.	ENSG00000151208	ENST00000372391;ENST00000372388;ENST00000372392	T;T	0.08984	3.03;3.04	4.38	3.46	0.39613	DEATH-like (1);Caspase Recruitment (1);	.	.	.	.	T	0.11623	0.0283	L	0.55481	1.735	0.31378	N	0.679355	D	0.54047	0.964	P	0.47118	0.538	T	0.07233	-1.0783	9	0.87932	D	0	.	6.5907	0.22646	0.0995:0.0:0.7195:0.1809	.	57	Q8TDM6	DLG5_HUMAN	F	57	ENSP00000361467:L57F;ENSP00000361464:L57F	ENSP00000361464:L57F	L	-	1	0	DLG5	79356116	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.958000	0.40402	1.995000	0.58328	0.531000	0.56144	CTC	.		0.706	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			A	79686110	G	A	79686110	3	1	62	1	0	0	0	0	1	0	0	0	4569	971	34	2	5718	2	DLG5	10	79686110	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	4228656	79686110	55848637	66	6052											
RPS24	6229	hgsc.bcm.edu;broad.mit.edu	37	chr10	79796974	79796974	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggcctgtatgagaagaaaaAgacctcaagaaagcaacgaa	19	5	10	7	1	1	4	1	1	0	4	1	6	1	4	2	1	2	2	2	1	8	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:79796974A>G	ENST00000372360.3	+	4	339	c.302A>G	c.(301-303)aAg>aGg	p.K101R	RPS24_ENST00000435275.1_Missense_Mutation_p.K101R|RPS24_ENST00000476545.1_3'UTR|RPS24_ENST00000360830.4_Missense_Mutation_p.K101R|RPS24_ENST00000440692.1_Missense_Mutation_p.K101R	NM_001026.4	NP_001017.1	P62847	RS24_HUMAN	ribosomal protein S24	101					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			GAGAAGAAAAAGACCTCAAGA	0.428																																					p.K101R		.											.	RPS24-91	0			c.A302G						.						46	44	45					10																	79796974		2203	4300	6503	SO:0001583	missense	6229	exon4			AGAAAAAGACCTC	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"S ribosomal proteins"	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000372360.3:c.302A>G	10.37:g.79796974A>G	ENSP00000361435:p.Lys101Arg	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	17	3	NM_001142283	0	1	2743	2745	1	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Missense_Mutation	SNP	ENST00000372360.3	37	CCDS7355.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.192792	0.78902	.	.	ENSG00000138326	ENST00000440692;ENST00000435275;ENST00000372360;ENST00000401656;ENST00000360830	.	.	.	4.97	4.97	0.65823	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.61198	0.2328	L	0.37800	1.135	0.80722	D	1	B;B;B	0.30851	0.056;0.297;0.243	B;B;B	0.43623	0.129;0.425;0.294	T	0.57900	-0.7731	8	.	.	.	.	14.9427	0.71006	1.0:0.0:0.0:0.0	.	101;101;101	P62847-3;E7EPK6;P62847	.;.;RS24_HUMAN	R	101	.	.	K	+	2	0	RPS24	79466980	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.057000	0.93889	1.977000	0.57605	0.533000	0.62120	AAG	.		0.428	RPS24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048910.1	NM_001026		G	79796974	A	G	79796974	3	3	62	1	0	0	0	0	1	0	0	0	13667	72	3	3	316	3	RPS24	10	79796974	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	110864	79796974	55737773	67	6053											
FAM178A	55719	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102683799	102683799	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggactcagatctgaaaagCacaagagaatctatgatacc	16	8	9	8	0	3	4	1	2	2	2	3	6	3	5	1	1	2	1	1	1	6	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:102683799C>T	ENST00000238961.4	+	5	1583	c.1041C>T	c.(1039-1041)agC>agT	p.S347S	FAM178A_ENST00000370269.3_Silent_p.S347S|FAM178A_ENST00000370271.3_Silent_p.S347S	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	347						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											ATCTGAAAAGCACAAGAGAAT	0.343																																					p.S347S		.											.	.	0			c.C1041T						.						44	43	43					10																	102683799		2203	4300	6503	SO:0001819	synonymous_variant	55719	exon5			GAAAAGCACAAGA	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.1041C>T	10.37:g.102683799C>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	50	22	NM_001136123	0	0	8	12	4	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Silent	SNP	ENST00000238961.4	37	CCDS7500.1																																																																																			.		0.343	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102683799	C	T	102683799	2	4	62	1	0	0	0	0	0	0	0	1	5519	709	25	2		2	FAM178A	10	102683799	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	22886825	102683799	32850948	68	6054											
NFKB2	4791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104161522	104161522	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggccgggactgtcacttggtGatacagctctgcagaacctg	8	9	13	11	1	2	2	1	1	1	1	2	3	2	3	2	3	4	2	2	3	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:104161522G>C	ENST00000369966.3	+	21	2564	c.2314G>C	c.(2314-2316)Gat>Cat	p.D772H	NFKB2_ENST00000428099.1_Missense_Mutation_p.D772H|NFKB2_ENST00000189444.6_Missense_Mutation_p.D772H	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	772	Death.		Missing (in truncated form EB308).|Missing (in truncated form LB40).|Missing (in truncated form p80HT).		extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	GTCACTTGGTGATACAGCTCT	0.597			T	IGH@	B-NHL																																p.D772H		.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2-522	0			c.G2314C						.						47	47	47					10																	104161522		1987	4164	6151	SO:0001583	missense	4791	exon21			CTTGGTGATACAG	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"Ankyrin repeat domain containing"	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.2314G>C	10.37:g.104161522G>C	ENSP00000358983:p.Asp772His	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	43	9	NM_001077494	0	0	81	88	7	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	g	15.85	2.954405	0.53293	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.21543	2.0;2.0;2.0	3.79	3.79	0.43588	Death (1);DEATH-like (2);	0.428788	0.25052	N	0.033513	T	0.17109	0.0411	L	0.36672	1.1	0.20403	N	0.999908	P;P	0.50943	0.94;0.94	P;P	0.44732	0.459;0.459	T	0.11397	-1.0589	10	0.59425	D	0.04	.	6.0921	0.20001	0.1804:0.0:0.8196:0.0	.	772;772	Q00653;A8K9D9	NFKB2_HUMAN;.	H	772	ENSP00000410256:D772H;ENSP00000358983:D772H;ENSP00000189444:D772H	ENSP00000189444:D772H	D	+	1	0	NFKB2	104151512	1.000000	0.71417	0.127000	0.21898	0.959000	0.62525	4.901000	0.63259	2.105000	0.64084	0.556000	0.70494	GAT	.		0.597	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			C	104161522	G	C	104161522	3	2	62	1	0	0	0	0	1	0	0	0	10402	1290	45	4	2392	4	NFKB2	10	104161522	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1477723	104161522	31373225	69	6055											
BRSK2	9024	broad.mit.edu	37	chr11	1466527	1466527	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgtcctgtgtccacagaggGggcaagaatgagcccgaacc	10	5	13	13	2	0	3	0	1	0	2	2	4	2	3	5	2	2	1	5	2	3	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:1466527G>C	ENST00000528841.1	+	10	1200	c.816G>C	c.(814-816)ggG>ggC	p.G272G	BRSK2_ENST00000382179.1_Silent_p.G318G|BRSK2_ENST00000544817.1_5'UTR|BRSK2_ENST00000526678.1_Silent_p.G272G|BRSK2_ENST00000528710.1_Silent_p.G212G|BRSK2_ENST00000308230.5_Silent_p.G272G|BRSK2_ENST00000531197.1_Silent_p.G272G|BRSK2_ENST00000308219.9_Silent_p.G272G			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	272					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		TCCACAGAGGGGGCAAGAATG	0.692																																					p.G318G													.	BRSK2-333	0			c.G954C						.						29	37	35					11																	1466527		2124	4227	6351	SO:0001819	synonymous_variant	9024	exon10			CAGAGGGGGCAAG	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.816G>C	11.37:g.1466527G>C		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_001256630	0	0	0	0	0	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Silent	SNP	ENST00000528841.1	37	CCDS58107.1																																																																																			.		0.692	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		C	1466527	G	C	1466527	2	2	62	1	0	0	0	0	0	0	0	1	1527	1219	43	4		4	BRSK2	11	1466527	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		1466527	133539989	70	6056											
OR52J3	119679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	5068082	5068082	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgtttctgatccatgccttCactggcatggaggctgaggt	7	13	12	9	0	2	2	1	2	1	0	3	3	3	3	2	4	1	3	2	4	0	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:5068082C>T	ENST00000380370.1	+	1	327	c.327C>T	c.(325-327)ttC>ttT	p.F109F		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCATGCCTTCACTGGCATGG	0.502																																					p.F109F		.											.	OR52J3-71	0			c.C327T						.						135	106	116					11																	5068082		2201	4298	6499	SO:0001819	synonymous_variant	119679	exon1			TGCCTTCACTGGC	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"GPCR / Class A : Olfactory receptors"	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.327C>T	11.37:g.5068082C>T		Somatic	65	1		WXS	Illumina HiSeq	Phase_I	93	12	NM_001001916	0	0	0	0	0	Q6IFE4	Silent	SNP	ENST00000380370.1	37	CCDS31370.1																																																																																			.		0.502	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916		T	5068082	C	T	5068082	2	4	62	1	0	0	0	0	0	0	0	1	11148	825	29	2		2	OR52J3	11	5068082	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	3601555	5068082	129938434	71	6057											
OR51B6	390058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	5373545	5373545	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaagcatgttcctcatgtcGttcacatcacaatgagctac	12	11	7	11	1	3	1	3	1	0	0	5	2	4	1	1	0	3	4	1	0	3	3	rs138981931		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:5373545G>T	ENST00000380219.1	+	1	808	c.808G>T	c.(808-810)Gtt>Ttt	p.V270F	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	270					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCTCATGTCGTTCACATCAC	0.398																																					p.V270F		.											.	OR51B6-70	0			c.G808T						.						215	193	200					11																	5373545		2201	4297	6498	SO:0001583	missense	390058	exon1			CATGTCGTTCACA		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"GPCR / Class A : Olfactory receptors"	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.808G>T	11.37:g.5373545G>T	ENSP00000369568:p.Val270Phe	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	195	83	NM_001004750	0	0	0	0	0		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.618023	0.46736	.	.	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00130	8.69	5.13	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	0.136091	0.33127	N	0.005251	T	0.00412	0.0013	M	0.76838	2.35	0.09310	N	1	D	0.71674	0.998	D	0.74674	0.984	T	0.38222	-0.9671	10	0.87932	D	0	.	8.1363	0.31056	0.0849:0.1595:0.7556:0.0	.	270	Q9H340	O51B6_HUMAN	F	269;270	ENSP00000369568:V270F	ENSP00000369568:V270F	V	+	1	0	OR51B6	5330121	0.114000	0.22134	0.847000	0.33407	0.957000	0.61999	0.805000	0.27112	1.379000	0.46325	0.650000	0.86243	GTT	G|1.000;A|0.000		0.398	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750		T	5373545	G	T	5373545	3	4	62	1	0	0	0	0	1	0	0	0	11118	1145	40	4	810	4	OR51B6	11	5373545	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	305463	5373545	129632971	72	6058											
TUB	7275	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	8120419	8120419	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggagctggcagctgtgtgCtacgtgagtcctaggttcgg	6	10	16	9	2	0	1	0	1	0	0	2	2	1	2	1	4	4	5	1	4	2	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:8120419C>G	ENST00000299506.2	+	9	1262	c.1113C>G	c.(1111-1113)tgC>tgG	p.C371W	TUB_ENST00000534099.1_Missense_Mutation_p.C377W|TUB_ENST00000305253.4_Missense_Mutation_p.C426W	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	371					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		CAGCTGTGTGCTACGTGAGTC	0.502											OREG0020732	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C426W		.											.	TUB-91	0			c.C1278G						.						114	108	110					11																	8120419		2201	4296	6497	SO:0001583	missense	7275	exon10			TGTGTGCTACGTG	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"tubby (mouse) homolog", "tubby homolog (mouse)"			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.1113C>G	11.37:g.8120419C>G	ENSP00000299506:p.Cys371Trp	Somatic	99	0	646	WXS	Illumina HiSeq	Phase_I	101	37	NM_003320	0	0	0	0	0	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.122978	0.56613	.	.	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.96300	-3.97;-3.97;-3.97	5.27	3.41	0.39046	Tubby, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.97473	0.9173	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.992;0.995;0.987	D	0.96862	0.9633	10	0.62326	D	0.03	0.2328	10.0609	0.42275	0.0:0.7635:0.0:0.2365	.	377;371;426	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	W	377;426;371	ENSP00000434400:C377W;ENSP00000305426:C426W;ENSP00000299506:C371W	ENSP00000299506:C371W	C	+	3	2	TUB	8076995	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	2.369000	0.44231	0.723000	0.32274	0.555000	0.69702	TGC	.		0.502	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		G	8120419	C	G	8120419	3	3	62	1	0	0	0	0	1	0	0	0	16775	805	28	4	1358	4	TUB	11	8120419	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2746874	8120419	126886097	73	6059											
ELP4	26610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	31561263	31561263	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaagtatttcctggcagAaggaattgtcaatgggcata	12	12	10	7	0	2	1	2	0	0	1	3	2	3	2	1	3	0	3	1	3	6	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:31561263A>G	ENST00000350638.5	+	3	349	c.314A>G	c.(313-315)gAa>gGa	p.E105G	ELP4_ENST00000379163.5_Missense_Mutation_p.E105G|ELP4_ENST00000395934.2_Missense_Mutation_p.E105G	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	105					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					TTCCTGGCAGAAGGAATTGTC	0.338																																					p.E105G		.											.	ELP4-948	0			c.A314G						.						192	161	170					11																	31561263		1821	4080	5901	SO:0001583	missense	26610	exon3			TGGCAGAAGGAAT	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"Elongator acetyltransferase complex subunits"	1171	protein-coding gene	gene with protein product		606985	"chromosome 11 open reading frame 19", "elongation protein 4 homolog (S. cerevisiae)"	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.314A>G	11.37:g.31561263A>G	ENSP00000298937:p.Glu105Gly	Somatic	271	1		WXS	Illumina HiSeq	Phase_I	211	85	NM_019040	0	0	13	22	9	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	37	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	A	22.2	4.257149	0.80246	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.57595	0.39;0.39;0.39	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.77491	0.4138	M	0.90309	3.105	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.82748	-0.0304	10	0.72032	D	0.01	-12.448	15.207	0.73186	1.0:0.0:0.0:0.0	.	105;105;105	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	G	105	ENSP00000298937:E105G;ENSP00000368461:E105G;ENSP00000379267:E105G	ENSP00000298937:E105G	E	+	2	0	ELP4	31517839	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	7.890000	0.87313	2.124000	0.65301	0.383000	0.25322	GAA	.		0.338	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040		G	31561263	A	G	31561263	3	3	62	1	0	0	0	0	1	0	0	0	5095	246	9	3	324	3	ELP4	11	31561263	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	23440844	31561263	103445253	74	6060											
OR4A16	81327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55111508	55111508	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttttattcaattatcacaCtcatgttgaatcctttaata	12	19	3	7	0	3	1	3	1	0	0	4	1	4	1	1	0	0	2	1	0	6	8			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:55111508C>A	ENST00000314721.2	+	1	882	c.832C>A	c.(832-834)Ctc>Atc	p.L278I		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						AATTATCACACTCATGTTGAA	0.323																																					p.L278I		.											.	OR4A16-69	0			c.C832A						.						89	85	86					11																	55111508		2201	4296	6497	SO:0001583	missense	81327	exon1			ATCACACTCATGT	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.832C>A	11.37:g.55111508C>A	ENSP00000325128:p.Leu278Ile	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	93	28	NM_001005274	0	0	0	0	0	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	c	10.38	1.333574	0.24167	.	.	ENSG00000181961	ENST00000314721	T	0.37058	1.22	2.86	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.26304	0.0642	N	0.08118	0	0.21802	N	0.999535	B	0.31599	0.33	B	0.40602	0.334	T	0.37126	-0.9719	9	0.87932	D	0	.	11.4549	0.50176	0.0:1.0:0.0:0.0	.	278	Q8NH70	O4A16_HUMAN	I	278	ENSP00000325128:L278I	ENSP00000325128:L278I	L	+	1	0	OR4A16	54868084	0.438000	0.25602	0.986000	0.45419	0.221000	0.24807	6.035000	0.70940	1.606000	0.50161	0.423000	0.28283	CTC	.		0.323	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		A	55111508	C	A	55111508	3	1	62	1	0	0	0	0	1	0	0	0	11067	565	20	4	834	4	OR4A16	11	55111508	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	23550245	55111508	79895008	75	6061											
BSCL2	26580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62458109	62458109	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcctcaggctctagctcCtcttctccgctcaggggctg	3	11	11	16	1	5	0	2	0	3	0	7	0	6	0	3	4	1	4	3	4	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:62458109C>T	ENST00000403550.1	-	10	1440	c.1017G>A	c.(1015-1017)gaG>gaA	p.E339E	BSCL2_ENST00000407022.3_Silent_p.E339E|BSCL2_ENST00000433053.1_Silent_p.E403E|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR|BSCL2_ENST00000405837.1_Silent_p.E405E|LRRN4CL_ENST00000317449.4_5'Flank|BSCL2_ENST00000421906.1_Silent_p.E339E|BSCL2_ENST00000360796.5_Silent_p.E403E|BSCL2_ENST00000278893.7_3'UTR			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	339					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						GCTCTAGCTCCTCTTCTCCGC	0.567																																					p.E403E		.											.	BSCL2-514	0			c.G1209A						.						82	80	81					11																	62458109		2202	4299	6501	SO:0001819	synonymous_variant	26580	exon10			TAGCTCCTCTTCT		CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"spastic paraplegia 17 (Silver syndrome)"	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.1017G>A	11.37:g.62458109C>T		Somatic	180	1		WXS	Illumina HiSeq	Phase_I	161	72	NM_001122955	1	0	89	176	86	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Silent	SNP	ENST00000403550.1	37	CCDS8031.1																																																																																			.		0.567	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667		T	62458109	C	T	62458109	2	4	62	1	0	0	0	0	0	0	0	1	1530	680	24	2		2	BSCL2	11	62458109	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	7346601	62458109	72548407	76	6062											
RAB6A	5870	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	73418504	73418504	+	Frame_Shift_Del	DEL	A	A	-																															gcttttgcactagtttcaatAaacataacattcagctcttt																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:73418504delA	ENST00000336083.3	-	6	911	c.456delT	c.(454-456)tttfs	p.F152fs	RAB6A_ENST00000310653.6_Frame_Shift_Del_p.F152fs|RAB6A_ENST00000541588.1_Intron|RAB6A_ENST00000536566.1_Frame_Shift_Del_p.F119fs	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	152					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						TAGTTTCAATAAACATAACAT	0.348																																					p.F152fs		.											.	RAB6A-227	0			c.456delT						.						189	175	180					11																	73418504		2200	4293	6493	SO:0001589	frameshift_variant	5870	exon6			.	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"RAB, member RAS oncogene"	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.456delT	11.37:g.73418504delA	ENSP00000336850:p.Phe152fs	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	121	51	NM_002869	0	0	0	0	0	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Frame_Shift_Del	DEL	ENST00000336083.3	37	CCDS8224.1																																																																																			.		0.348	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2			-	73418504	A	-	73418504	7	5	62	1	0	1	0	1	0	0	0	0	12983	359	13	0	182	0	RAB6A	11	73418504	Frame_Shift_Del	DEL	A	TCGA-BQ-5878-01A-11D-1589-08	10960395	73418504	61588012	77	6063											
USP28	57646	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	113679118	113679119	+	Frame_Shift_Ins	INS	-	-	TG																															acaatcacagcatgctcagaINScgacaagcagcgaaccccat																								rs2465647	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:113679118_113679119insTG	ENST00000003302.4	-	18	2273_2274	c.2205_2206insCA	c.(2203-2208)tcgtctfs	p.S736fs	USP28_ENST00000545540.1_Frame_Shift_Ins_p.S611fs|USP28_ENST00000544967.1_Frame_Shift_Ins_p.S444fs|USP28_ENST00000260188.5_Frame_Shift_Ins_p.S736fs	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	736					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		GCATGCTCAGACGACAAGCAGC	0.47																																					p.S736fs	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	.											.	USP28-706	0			c.2206_2207insCA						.																																			SO:0001589	frameshift_variant	57646	exon18			.	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2205_2206insCA	11.37:g.113679118_113679119insTG	ENSP00000003302:p.Ser736fs	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	142	54	NM_020886	0	0	0	0	0	B0YJC0|B0YJC1|Q9P213	Frame_Shift_Ins	INS	ENST00000003302.4	37	CCDS31680.1																																																																																			.		0.47	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			TG	113679119	-	TG	113679118	7	5	62	1	0	1	1	0	0	0	0	0	17091	275	10	0	1059	0	USP28	11	113679118	Frame_Shift_Ins	INS	-	TCGA-BQ-5878-01A-11D-1589-08	40260614	113679118	21327398	78	6064	69	2									
USP28	57646	hgsc.bcm.edu	37	chr11	113679119	113679119	+	Frame_Shift_Del	DEL	C	C	-																															acaatcacagcatgctcagaCgacaagcagcgaaccccatg																								rs2465647	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:113679119delC	ENST00000003302.4	-	18	2273	c.2205delG	c.(2203-2205)tcgfs	p.S736fs	USP28_ENST00000545540.1_Frame_Shift_Del_p.S611fs|USP28_ENST00000544967.1_Frame_Shift_Del_p.S444fs|USP28_ENST00000260188.5_Frame_Shift_Del_p.S736fs	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	736					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		CATGCTCAGACGACAAGCAGC	0.473																																					p.S735fs	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	.											.	USP28-706	0			c.2205delG						.						129	120	123					11																	113679119		2201	4296	6497	SO:0001589	frameshift_variant	57646	exon18			.	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2205delG	11.37:g.113679119delC	ENSP00000003302:p.Ser736fs	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	143	39	NM_020886	0	0	0	0	0	B0YJC0|B0YJC1|Q9P213	Frame_Shift_Del	DEL	ENST00000003302.4	37	CCDS31680.1																																																																																			.		0.473	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			-	113679119	C	-	113679119	7	5	62	1	0	1	0	1	0	0	0	0	17091	523	19	0	1060	0	USP28	11	113679119	Frame_Shift_Del	DEL	C	TCGA-BQ-5878-01A-11D-1589-08	1	113679119	21327397	79	6065	69	2									
NANOG	79923	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7942255	7942255	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagcttgccttgctttgaAgcatccgactgtaaagaatc	12	11	8	10	1	0	2	0	1	0	1	2	3	1	2	2	0	4	4	2	0	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:7942255A>C	ENST00000229307.4	+	1	264	c.45A>C	c.(43-45)gaA>gaC	p.E15D	NANOG_ENST00000526286.1_Missense_Mutation_p.E15D	NM_024865.2	NP_079141.2	Q9H9S0	NANOG_HUMAN	Nanog homeobox	15					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|embryo development (GO:0009790)|embryonic pattern specification (GO:0009880)|endodermal cell fate specification (GO:0001714)|gonad development (GO:0008406)|mesodermal cell fate commitment (GO:0001710)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to retinoic acid (GO:0032526)|somatic stem cell maintenance (GO:0035019)|stem cell division (GO:0017145)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14				Kidney(36;0.0872)		CTTGCTTTGAAGCATCCGACT	0.443																																					p.E15D		.											.	NANOG-90	0			c.A45C						.						172	157	162					12																	7942255		2203	4300	6503	SO:0001583	missense	79923	exon1			CTTTGAAGCATCC	AB093576	CCDS31736.1, CCDS73436.1	12p13.31	2011-06-20			ENSG00000111704	ENSG00000111704		"Homeoboxes / ANTP class : NKL subclass"	20857	protein-coding gene	gene with protein product		607937				12787505, 12787504	Standard	XM_005253484		Approved	FLJ12581, FLJ40451	uc009zfy.1	Q9H9S0		ENST00000229307.4:c.45A>C	12.37:g.7942255A>C	ENSP00000229307:p.Glu15Asp	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	190	30	NM_024865	0	0	0	0	0	D3DUU4|Q2TTG0|Q6JZS5	Missense_Mutation	SNP	ENST00000229307.4	37	CCDS31736.1	.	.	.	.	.	.	.	.	.	.	.	14.22	2.469400	0.43839	.	.	ENSG00000111704	ENST00000229307;ENST00000526286	D;D	0.91686	-2.89;-2.86	3.24	3.24	0.37175	.	0.322217	0.25060	N	0.033452	D	0.88797	0.6534	L	0.54323	1.7	0.09310	N	1	P	0.50066	0.931	P	0.44772	0.46	T	0.80759	-0.1239	10	0.32370	T	0.25	-6.5459	8.2396	0.31652	1.0:0.0:0.0:0.0	.	15	Q9H9S0	NANOG_HUMAN	D	15	ENSP00000229307:E15D;ENSP00000435288:E15D	ENSP00000229307:E15D	E	+	3	2	NANOG	7833522	0.000000	0.05858	0.015000	0.15790	0.011000	0.07611	0.369000	0.20416	1.714000	0.51371	0.379000	0.24179	GAA	.		0.443	NANOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387480.2	NM_024865		C	7942255	A	C	7942255	3	2	62	1	0	0	0	0	1	0	0	0	10175	69	3	5	47	5	NANOG	12	7942255	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08		7942255	125909640	80	6066											
MAGOHB	55110	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	10766047	10766047	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcttctcaccgtccggccGaaattcgaactccagaaact	10	9	6	16	4	2	1	1	0	2	1	6	3	4	1	5	1	2	0	5	1	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:10766047G>T	ENST00000320756.2	-	1	175	c.85C>A	c.(85-87)Cgg>Agg	p.R29R	MAGOHB_ENST00000539554.1_Intron|MAGOHB_ENST00000381881.2_Silent_p.R29R	NM_018048.3	NP_060518.1	Q96A72	MGN2_HUMAN	mago-nashi homolog B (Drosophila)	29					mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|large_intestine(2)	4						CCGTCCGGCCGAAATTCGAAC	0.617																																					p.R29R		.											.	MAGOHB-153	0			c.C85A						.						97	98	97					12																	10766047		2203	4300	6503	SO:0001819	synonymous_variant	55110	exon1			CCGGCCGAAATTC		CCDS8628.1	12p13.2	2014-02-12	2008-01-24		ENSG00000111196	ENSG00000111196			25504	protein-coding gene	gene with protein product							Standard	NM_018048		Approved	FLJ10292, MGN2	uc001qyq.2	Q96A72	OTTHUMG00000168407	ENST00000320756.2:c.85C>A	12.37:g.10766047G>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	110	9	NM_018048	0	0	3	3	0		Silent	SNP	ENST00000320756.2	37	CCDS8628.1																																																																																			.		0.617	MAGOHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399616.1	NM_018048		T	10766047	G	T	10766047	2	4	62	1	0	0	0	0	0	0	0	1	9220	1057	37	4		4	MAGOHB	12	10766047	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	2823792	10766047	123085848	81	6067											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49434210	49434210	+	Frame_Shift_Del	DEL	T	T	-																															agggtgggcgagaataagggTcaggggactggaagcgaggg																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:49434210delT	ENST00000301067.7	-	31	7342	c.7343delA	c.(7342-7344)gacfs	p.D2448fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2448	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGAATAAGGGTCAGGGGACTG	0.612																																					p.D2448fs		.											.	MLL2-612	0			c.7343delA						.						43	49	47					12																	49434210		2063	4194	6257	SO:0001589	frameshift_variant	8085	exon31			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7343delA	12.37:g.49434210delT	ENSP00000301067:p.Asp2448fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	76	31	NM_003482	0	0	0	0	0	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.612	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49434210	T	-	49434210	7	5	62	1	0	1	0	1	0	0	0	0	9646	1667	58	0	9366	0	MLL2	12	49434210	Frame_Shift_Del	DEL	T	TCGA-BQ-5878-01A-11D-1589-08	38668163	49434210	84417685	82	6068											
CIT	11113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120173153	120173153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtttagctgctcctccaggtCtgtgattacctaaaagagga	10	12	10	9	0	1	2	0	1	1	1	3	3	3	3	3	2	3	3	3	2	4	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:120173153C>T	ENST00000261833.7	-	24	2894	c.2842G>A	c.(2842-2844)Gac>Aac	p.D948N	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Missense_Mutation_p.D990N	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	948					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TCCTCCAGGTCTGTGATTACC	0.458																																					p.D990N		.											.	CIT-399	0			c.G2968A						.						190	170	177					12																	120173153		2203	4300	6503	SO:0001583	missense	11113	exon25			CCAGGTCTGTGAT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.2842G>A	12.37:g.120173153C>T	ENSP00000261833:p.Asp948Asn	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	110	43	NM_001206999	0	0	0	0	0	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553919	0.86231	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.65178	-0.08;-0.14	5.06	5.06	0.68205	.	0.054479	0.64402	D	0.000001	T	0.58104	0.2099	N	0.24115	0.695	0.80722	D	1	D;P;B	0.56035	0.974;0.805;0.447	P;B;B	0.47981	0.563;0.346;0.223	T	0.65059	-0.6260	10	0.72032	D	0.01	.	18.797	0.91999	0.0:1.0:0.0:0.0	.	990;948;481	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	N	990;948	ENSP00000376306:D990N;ENSP00000261833:D948N	ENSP00000261833:D948N	D	-	1	0	CIT	118657536	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.505000	0.84491	0.655000	0.94253	GAC	.		0.458	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120173153	C	T	120173153	3	4	62	1	0	0	0	0	1	0	0	0	3444	913	32	2	3337	2	CIT	12	120173153	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	70738943	120173153	13678742	83	6069											
OASL	8638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	121465530	121465530	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacatgaaattctcgtcttCttcagtacccatttcccagg	10	13	5	13	1	4	1	1	1	3	0	6	1	5	1	2	1	2	1	2	1	3	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:121465530C>A	ENST00000257570.5	-	4	1018	c.748G>T	c.(748-750)Gaa>Taa	p.E250*	OASL_ENST00000339275.5_Intron	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	250					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTCTCGTCTTCTTCAGTACCC	0.478																																					p.E250X	Colon(192;517 2041 31392 31913 39966)	.											.	OASL-69	0			c.G748T						.						142	116	125					12																	121465530		2203	4300	6503	SO:0001587	stop_gained	8638	exon4			CGTCTTCTTCAGT	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.748G>T	12.37:g.121465530C>A	ENSP00000257570:p.Glu250*	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	73	26	NM_003733	0	0	2	2	0	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Nonsense_Mutation	SNP	ENST00000257570.5	37	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434616	0.83885	.	.	ENSG00000135114	ENST00000257570	.	.	.	5.58	-2.54	0.06307	.	3.081050	0.00951	N	0.002969	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-20.7634	0.3898	0.00408	0.2468:0.2802:0.242:0.231	.	.	.	.	X	250	.	ENSP00000257570:E250X	E	-	1	0	OASL	119949913	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.430000	0.02434	-0.099000	0.12263	-0.302000	0.09304	GAA	.		0.478	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		A	121465530	C	A	121465530	4	1	62	1	0	0	0	0	0	1	0	0	10828	922	32	4	808	4	OASL	12	121465530	Nonsense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	1292377	121465530	12386365	84	6070											
C14orf93	60686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23467861	23467861	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactttccttgagaggcccAggctcctcaggtggggaact	7	9	14	11	0	1	1	1	1	0	1	3	4	3	3	3	6	1	1	3	6	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:23467861A>C	ENST00000299088.6	-	2	801	c.372T>G	c.(370-372)ccT>ccG	p.P124P	C14orf93_ENST00000397379.3_Silent_p.P124P|RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000557513.1_5'Flank|C14orf93_ENST00000397382.4_Silent_p.P124P|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000406429.2_Silent_p.P124P|C14orf93_ENST00000397377.1_5'UTR|C14orf93_ENST00000341470.4_Silent_p.P124P	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	124						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		TGAGAGGCCCAGGCTCCTCAG	0.597																																					p.P124P		.											.	C14orf93-91	0			c.T372G						.						58	60	59					14																	23467861		2203	4300	6503	SO:0001819	synonymous_variant	60686	exon2			AGGCCCAGGCTCC	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.372T>G	14.37:g.23467861A>C		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	53	23	NM_021944	0	0	20	33	13	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Silent	SNP	ENST00000299088.6	37	CCDS9583.1																																																																																			.		0.597	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		C	23467861	A	C	23467861	2	2	62	1	0	0	0	0	0	0	0	1	1786	175	7	5		5	C14orf93	14	23467861	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08		23467861	83881679	85	6071											
SOS2	6655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	50605361	50605361	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttctatccgtaaacagtaaGgctgattctgatactgctga	11	13	9	8	1	2	3	0	3	2	0	3	3	3	3	1	1	3	5	1	1	5	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:50605361G>A	ENST00000216373.5	-	18	3201	c.2927C>T	c.(2926-2928)cCt>cTt	p.P976L	SOS2_ENST00000543680.1_Missense_Mutation_p.P943L	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	976	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					TAAACAGTAAGGCTGATTCTG	0.308																																					p.P976L		.											.	SOS2-849	0			c.C2927T						.						92	92	92					14																	50605361		2201	4299	6500	SO:0001583	missense	6655	exon18			CAGTAAGGCTGAT	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11188	protein-coding gene	gene with protein product		601247	"son of sevenless (Drosophilia) homolog 2"			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.2927C>T	14.37:g.50605361G>A	ENSP00000216373:p.Pro976Leu	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	110	46	NM_006939	0	0	12	35	23	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	G	33	5.254361	0.95336	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.35048	1.33;1.33	5.6	5.6	0.85130	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.61862	0.2381	M	0.87381	2.88	0.80722	D	1	D;D	0.58620	0.983;0.965	P;P	0.55087	0.768;0.708	T	0.69198	-0.5208	10	0.87932	D	0	.	19.6046	0.95575	0.0:0.0:1.0:0.0	.	943;976	B7ZKT6;Q07890	.;SOS2_HUMAN	L	976;943	ENSP00000216373:P976L;ENSP00000445328:P943L	ENSP00000216373:P976L	P	-	2	0	SOS2	49675111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.405000	0.97313	2.640000	0.89533	0.655000	0.94253	CCT	.		0.308	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			A	50605361	G	A	50605361	3	1	62	1	0	0	0	0	1	0	0	0	14969	1000	35	2	1095	2	SOS2	14	50605361	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	27137500	50605361	56744179	86	6072											
FBXO34	55030	broad.mit.edu	37	chr14	55818482	55818482	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaatctttgtgcattagtatCactgtgtccaaggtagacaa	12	13	9	7	0	2	1	1	0	1	1	3	2	3	1	1	1	1	3	1	1	6	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:55818482C>T	ENST00000313833.4	+	2	1619	c.1374C>T	c.(1372-1374)atC>atT	p.I458I	FBXO34_ENST00000440021.1_Silent_p.I458I	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	458										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GCATTAGTATCACTGTGTCCA	0.438																																					p.I458I													.	FBXO34-228	0			c.C1374T						.						131	124	126					14																	55818482		2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			TAGTATCACTGTG	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1374C>T	14.37:g.55818482C>T		Somatic	229	0		WXS	Illumina HiSeq	Phase_I	174	4	NM_017943	0	0	86	88	2	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			.		0.438	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			T	55818482	C	T	55818482	2	4	62	1	0	0	0	0	0	0	0	1	5763	816	29	2		2	FBXO34	14	55818482	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	5213121	55818482	51531058	87	6073											
AK7	122481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	96917831	96917831	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaggagaattttaatattcGatgggctgcccaaacaggat	14	10	11	6	1	0	1	0	0	0	1	1	5	0	2	1	3	2	1	1	3	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:96917831G>A	ENST00000267584.4	+	10	1066	c.1022G>A	c.(1021-1023)cGa>cAa	p.R341Q		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	341					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		TTTAATATTCGATGGGCTGCC	0.393																																					p.R341Q		.											.	AK7-228	0			c.G1022A						.						94	90	91					14																	96917831		2203	4300	6503	SO:0001583	missense	122481	exon10			ATATTCGATGGGC	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1022G>A	14.37:g.96917831G>A	ENSP00000267584:p.Arg341Gln	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	78	29	NM_152327	0	0	2	7	5	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	37	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	9.591	1.126082	0.20959	.	.	ENSG00000140057	ENST00000267584	T	0.61040	0.14	5.72	5.72	0.89469	.	0.354917	0.31772	N	0.007090	T	0.47948	0.1473	L	0.60455	1.87	0.54753	D	0.999986	P	0.35527	0.507	B	0.19666	0.026	T	0.46830	-0.9163	10	0.30078	T	0.28	-17.9477	12.7326	0.57206	0.0789:0.0:0.9211:0.0	.	341	Q96M32	KAD7_HUMAN	Q	341	ENSP00000267584:R341Q	ENSP00000267584:R341Q	R	+	2	0	AK7	95987584	0.290000	0.24343	0.621000	0.29145	0.004000	0.04260	2.176000	0.42500	2.711000	0.92665	0.655000	0.94253	CGA	.		0.393	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			A	96917831	G	A	96917831	3	1	62	1	0	0	0	0	1	0	0	0	444	1058	37	1	1060	1	AK7	14	96917831	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	41099349	96917831	10431709	88	6074											
ARHGAP11A	9824	broad.mit.edu;bcgsc.ca	37	chr15	32929514	32929514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtccgtcagaagaattaattCtttgttggagtatagcagac	12	13	10	6	1	2	3	1	0	1	3	3	4	3	4	1	1	1	3	1	1	5	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr15:32929514C>T	ENST00000361627.3	+	12	3262	c.2540C>T	c.(2539-2541)tCt>tTt	p.S847F	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.S658F|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.S658F	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	847					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AGAATTAATTCTTTGTTGGAG	0.408																																					p.S847F	Colon(45;757 1134 30003 36652)												.	ARHGAP11A-292	0			c.C2540T						.						121	128	125					15																	32929514		2201	4300	6501	SO:0001583	missense	9824	exon12			TTAATTCTTTGTT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.2540C>T	15.37:g.32929514C>T	ENSP00000355090:p.Ser847Phe	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	145	6	NM_014783	0	0	0	0	0	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.331080	0.81690	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.34667	1.35	5.67	5.67	0.87782	.	0.000000	0.56097	D	0.000025	T	0.65450	0.2692	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68655	-0.5351	10	0.87932	D	0	.	19.7686	0.96352	0.0:1.0:0.0:0.0	.	847	Q6P4F7	RHGBA_HUMAN	F	847;658	ENSP00000355090:S847F	ENSP00000355090:S847F	S	+	2	0	ARHGAP11A	30716806	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.951000	0.75983	2.665000	0.90641	0.591000	0.81541	TCT	.		0.408	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32929514	C	T	32929514	3	4	62	1	0	0	0	0	1	0	0	0	863	913	32	2	2609	2	ARHGAP11A	15	32929514	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		32929514	69601878	89	6075											
MAP2K5	5607	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	67956981	67956981	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gagtttaaagattttacataGaggtatgtgctgggcttata	12	15	11	3	0	0	2	0	0	0	2	0	3	0	2	0	2	2	4	0	2	7	8			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr15:67956981G>C	ENST00000178640.5	+	13	1472	c.845G>C	c.(844-846)aGa>aCa	p.R282T	MAP2K5_ENST00000395476.2_Missense_Mutation_p.R282T|MAP2K5_ENST00000354498.5_Missense_Mutation_p.R246T|MAP2K5_ENST00000340972.4_Missense_Mutation_p.R92T	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R282T(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						ATTTTACATAGAGGTATGTGC	0.333																																					p.R282T		.											.	MAP2K5-546	2	Substitution - Missense(2)	endometrium(2)	c.G845C						.						112	114	113					15																	67956981		2199	4297	6496	SO:0001583	missense	5607	exon13			TACATAGAGGTAT	U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.845G>C	15.37:g.67956981G>C	ENSP00000178640:p.Arg282Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	93	8	NM_145160	0	0	0	0	0	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	37	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501730	0.85176	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.19105	2.17;2.17;2.17;2.17	6.04	6.04	0.98038	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65616	0.2708	H	0.98048	4.135	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.78226	-0.2286	10	0.87932	D	0	-21.9076	18.7754	0.91910	0.0:0.0:1.0:0.0	.	92;282;282	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	T	282;282;282;246;92	ENSP00000378859:R282T;ENSP00000178640:R282T;ENSP00000346493:R246T;ENSP00000342101:R92T	ENSP00000178640:R282T	R	+	2	0	MAP2K5	65744035	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.843000	0.86859	2.873000	0.98535	0.563000	0.77884	AGA	.		0.333	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162		C	67956981	G	C	67956981	3	2	62	1	0	0	0	0	1	0	0	0	9265	942	33	4	895	4	MAP2K5	15	67956981	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	35027467	67956981	34574411	90	6076											
AGBL1	123624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	87217502	87217502	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgctttgtttaactggcAgggtctacagtttggtacca	9	15	10	7	0	1	0	0	0	1	0	1	0	1	0	1	3	4	5	1	3	4	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr15:87217502A>G	ENST00000441037.2	+	22	3014		c.e22-1		AGBL1_ENST00000389298.3_Splice_Site|AGBL1_ENST00000421325.2_Splice_Site	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.?(1)		NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TTTAACTGGCAGGGTCTACAG	0.478																																					.		.											.	.	1	Unknown(1)	lung(1)	c.2920-2A>G						.						52	49	50					15																	87217502		1970	4174	6144	SO:0001630	splice_region_variant	123624	exon22			ACTGGCAGGGTCT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 4"	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2920-1A>G	15.37:g.87217502A>G		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	18	8	NM_152336	0	0	0	0	0	A1A4X5|A6NJH6|C9JHL5	Splice_Site	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.744859	0.69418	.	.	ENSG00000166748	ENST00000421325;ENST00000389298	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.967	0.58490	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGBL1	85018506	1.000000	0.71417	0.987000	0.45799	0.840000	0.47671	5.346000	0.65992	2.068000	0.61886	0.460000	0.39030	.	.		0.478	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	Intron	G	87217502	A	G	87217502	5	3	62	1	0	0	0	0	0	0	1	0	375	202	7	3	3000	3	AGBL1	15	87217502	Splice_Site	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	19260521	87217502	15313890	91	6077											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2816146	2816146	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcgagcctctccagccactCaccggcgatccaggtccaga	8	6	9	18	3	2	1	1	0	1	1	6	3	4	1	6	2	2	0	6	2	0	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:2816146C>G	ENST00000301740.8	+	11	6166	c.5617C>G	c.(5617-5619)Cac>Gac	p.H1873D		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1873	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TCCAGCCACTCACCGGCGATC	0.612																																					p.H1873D		.											.	SRRM2-93	0			c.C5617G						.						80	77	78					16																	2816146		2198	4300	6498	SO:0001583	missense	23524	exon11			GCCACTCACCGGC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.5617C>G	16.37:g.2816146C>G	ENSP00000301740:p.His1873Asp	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	73	22	NM_016333	0	0	145	242	97	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	2.782	-0.253191	0.05829	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24538	1.85	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000006	T	0.27489	0.0675	N	0.08118	0	0.35745	D	0.819014	D	0.65815	0.995	P	0.57911	0.829	T	0.42189	-0.9466	10	0.52906	T	0.07	-12.2072	16.5384	0.84377	0.0:1.0:0.0:0.0	.	1873	Q9UQ35	SRRM2_HUMAN	D	1873;1873;1125	ENSP00000301740:H1873D	ENSP00000301740:H1873D	H	+	1	0	SRRM2	2756147	0.881000	0.30235	1.000000	0.80357	0.997000	0.91878	1.956000	0.40382	2.492000	0.84095	0.650000	0.86243	CAC	.		0.612	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2816146	C	G	2816146	3	3	62	1	0	0	0	0	1	0	0	0	15201	826	29	4	5655	4	SRRM2	16	2816146	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		2816146	87538607	92	6078											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2818196	2818196	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtcgtcgtcctcctcctcctCtggctccagttctagtgact	3	14	8	16	2	2	1	0	1	2	0	9	1	7	1	5	1	0	2	5	1	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:2818196C>G	ENST00000301740.8	+	11	8216	c.7667C>G	c.(7666-7668)tCt>tGt	p.S2556C	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2556	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						tcctcctcctcTGGCTCCAGT	0.572																																					p.S2556C		.											.	SRRM2-93	0			c.C7667G						.						56	51	53					16																	2818196		2198	4300	6498	SO:0001583	missense	23524	exon11			CCTCCTCTGGCTC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7667C>G	16.37:g.2818196C>G	ENSP00000301740:p.Ser2556Cys	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	42	15	NM_016333	0	0	76	124	48	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951695	0.73787	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.77877	-1.13	5.91	5.91	0.95273	.	0.000000	0.51477	D	0.000098	D	0.82586	0.5069	L	0.32530	0.975	0.36253	D	0.854052	D	0.76494	0.999	D	0.77557	0.99	D	0.85933	0.1453	10	0.62326	D	0.03	-5.5072	15.8054	0.78501	0.0:1.0:0.0:0.0	.	2556	Q9UQ35	SRRM2_HUMAN	C	2556;2138;1808	ENSP00000301740:S2556C	ENSP00000301740:S2556C	S	+	2	0	SRRM2	2758197	0.998000	0.40836	1.000000	0.80357	0.886000	0.51366	4.236000	0.58675	2.808000	0.96608	0.655000	0.94253	TCT	.		0.572	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2818196	C	G	2818196	3	3	62	1	0	0	0	0	1	0	0	0	15201	913	32	4	7705	4	SRRM2	16	2818196	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2050	2818196	87536557	93	6079											
LONP2	83752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	48385617	48385617	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacgacaggatttaagtttTgtcacagcaagctgcctgga	11	11	11	8	1	1	0	1	0	0	0	1	3	1	2	1	2	4	4	1	2	3	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:48385617T>C	ENST00000285737.4	+	15	2556	c.2463T>C	c.(2461-2463)ttT>ttC	p.F821F	LONP2_ENST00000564259.1_3'UTR|LONP2_ENST00000535754.1_Silent_p.F777F	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						ATTTAAGTTTTGTCACAGCAA	0.473																																					p.F821F		.											.	LONP2-90	0			c.T2463C						.						89	85	86					16																	48385617		2200	4300	6500	SO:0001819	synonymous_variant	83752	exon15			AAGTTTTGTCACA	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.2463T>C	16.37:g.48385617T>C		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	89	34	NM_031490	0	0	27	59	32		Silent	SNP	ENST00000285737.4	37	CCDS10734.1																																																																																			.		0.473	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		C	48385617	T	C	48385617	2	2	62	1	0	0	0	0	0	0	0	1	8918	1809	63	3		3	LONP2	16	48385617	Silent	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	45567421	48385617	41969136	94	6080											
HP	3240	hgsc.bcm.edu	37	chr16	72094682	72094682	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggacacctggtatgcgActgggatcttaagctttgat	10	11	13	7	1	1	1	0	1	1	0	1	5	1	4	1	4	2	2	1	4	2	3	rs470428	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:72094682A>G	ENST00000355906.5	+	7	1172	c.1114A>G	c.(1114-1116)Act>Gct	p.T372A	HP_ENST00000570083.1_Missense_Mutation_p.T313A|HPR_ENST00000540303.2_5'Flank|HP_ENST00000565574.1_Missense_Mutation_p.T313A|HPR_ENST00000356967.5_Intron|HP_ENST00000357763.4_Missense_Mutation_p.T408A|HPR_ENST00000561690.1_5'Flank|HP_ENST00000398131.2_Missense_Mutation_p.T313A|HP_ENST00000562526.1_3'UTR	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	372	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		CTGGTATGCGACTGGGATCTT	0.522													G|||	3	0.000599042	0.0015	0.0014	5008	,	,		21936	0		0	False		,,,				2504	0				p.T372A		.											.	HP-22	0			c.A1114G						.						225	219	221					16																	72094682		2127	4236	6363	SO:0001583	missense	3240	exon7			TATGCGACTGGGA		CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.1114A>G	16.37:g.72094682A>G	ENSP00000348170:p.Thr372Ala	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	96	21	NM_005143	0	0	0	0	0	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Missense_Mutation	SNP	ENST00000355906.5	37	CCDS45524.1	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	G	4.630	0.117074	0.08881	.	.	ENSG00000257017	ENST00000355906;ENST00000398131;ENST00000405951;ENST00000357763	D;D	0.88277	-2.36;-2.36	5.21	5.21	0.72293	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.063724	0.64402	N	0.000010	T	0.60170	0.2248	N	0.01202	-0.96	0.36005	D	0.837667	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.65364	-0.6186	10	0.02654	T	1	.	11.2306	0.48910	0.0848:0.0:0.9152:0.0	rs470428;rs470428	194;247;313;372	Q6PEJ8;Q6NSB4;Q0VAC5;P00738	.;.;.;HPT_HUMAN	A	372;313;247;348	ENSP00000348170:T372A;ENSP00000381199:T313A	ENSP00000348170:T372A	T	+	1	0	HP	70652183	0.979000	0.34478	0.007000	0.13788	0.021000	0.10359	2.798000	0.47884	1.449000	0.47699	-0.124000	0.14976	ACT	T|0.840;C|0.001		0.522	HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143		G	72094682	A	G	72094682	3	3	62	1	0	0	0	0	1	0	0	0	7348	275	10	3	1140	3	HP	16	72094682	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	23709065	72094682	18260071	95	6081											
HPR	3250	hgsc.bcm.edu	37	chr16	72110800	72110800	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcggcatgtctaagtaccaGgaagacacctgctatggcga	11	8	12	10	2	1	1	0	0	1	1	2	3	1	2	2	3	2	3	2	3	4	3	rs371896670		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:72110800G>A	ENST00000540303.2	+	5	899	c.867G>A	c.(865-867)caG>caA	p.Q289Q	HPR_ENST00000356967.5_Silent_p.Q289Q|HPR_ENST00000228226.8_Silent_p.Q326Q|HPR_ENST00000561690.1_Intron	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	289	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CTAAGTACCAGGAAGACACCT	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		26704	0		0	False		,,,				2504	0				p.Q289Q		.											.	HPR-515	0			c.G867A						.	G		5,4151		0,5,2073	216	145	168		867	1.7	1	16		168	1,8393		0,1,4196	no	coding-synonymous	HPR	NM_020995.3		0,6,6269	AA,AG,GG		0.0119,0.1203,0.0478		289/349	72110800	6,12544	2078	4197	6275	SO:0001819	synonymous_variant	3250	exon5			GTACCAGGAAGAC	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.867G>A	16.37:g.72110800G>A		Somatic	108	1		WXS	Illumina HiSeq	Phase_I	123	7	NM_020995	0	0	0	0	0	Q7LE20|Q92658|Q92659|Q9ULB0	Silent	SNP	ENST00000540303.2	37	CCDS42193.1																																																																																			.		0.567	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995		A	72110800	G	A	72110800	2	1	62	1	0	0	0	0	0	0	0	1	7358	991	35	2		2	HPR	16	72110800	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	16118	72110800	18243953	96	6082											
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72828734	72828734	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccttttcctccagcttcCtcttgagagtgttcattgtg	4	17	9	11	0	2	1	1	1	1	1	5	2	5	1	4	1	1	2	4	1	0	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:72828734C>T	ENST00000268489.5	-	9	8519	c.7847G>A	c.(7846-7848)aGg>aAg	p.R2616K	ZFHX3_ENST00000397992.5_Missense_Mutation_p.R1702K	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2616					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTCCAGCTTCCTCTTGAGAGT	0.547																																					p.R2616K		.											.	ZFHX3-72	0			c.G7847A						.						207	212	210					16																	72828734		2198	4300	6498	SO:0001583	missense	463	exon9			AGCTTCCTCTTGA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.7847G>A	16.37:g.72828734C>T	ENSP00000268489:p.Arg2616Lys	Somatic	533	1		WXS	Illumina HiSeq	Phase_I	461	188	NM_006885	0	0	4	6	2	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.362208	0.41902	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.74737	-0.87;-0.86	5.64	5.64	0.86602	.	0.000000	0.56097	D	0.000033	D	0.84014	0.5379	L	0.56199	1.76	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	D	0.83807	0.0239	10	0.54805	T	0.06	.	19.683	0.95971	0.0:1.0:0.0:0.0	.	2616	Q15911	ZFHX3_HUMAN	K	2616;1702	ENSP00000268489:R2616K;ENSP00000438926:R1702K	ENSP00000268489:R2616K	R	-	2	0	ZFHX3	71386235	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.653000	0.90120	0.561000	0.74099	AGG	.		0.547	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72828734	C	T	72828734	3	4	62	1	0	0	0	0	1	0	0	0	17666	681	24	2	3272	2	ZFHX3	16	72828734	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	717934	72828734	17526019	97	6083											
GEMIN4	50628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	649344	649344	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcagcacctcgtctggctCaagaagagcagccactggaa	11	7	10	13	1	3	2	2	0	1	2	4	3	3	3	2	2	3	3	2	2	3	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:649344C>G	ENST00000319004.5	-	2	2057	c.1939G>C	c.(1939-1941)Gag>Cag	p.E647Q	GEMIN4_ENST00000576778.1_Missense_Mutation_p.E636Q	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	647					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCGTCTGGCTCAAGAAGAGCA	0.488																																					p.E647Q		.											.	GEMIN4-206	0			c.G1939C						.						64	67	66					17																	649344		1893	4118	6011	SO:0001583	missense	50628	exon2			CTGGCTCAAGAAG	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1939G>C	17.37:g.649344C>G	ENSP00000321706:p.Glu647Gln	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	84	10	NM_015721	0	0	12	19	7	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	.	.	.	.	.	.	.	.	.	.	C	4.186	0.033188	0.08101	.	.	ENSG00000179409	ENST00000319004	T	0.05786	3.39	5.57	4.6	0.57074	.	0.448686	0.24490	N	0.038075	T	0.05456	0.0144	L	0.41236	1.265	0.22378	N	0.999157	B	0.21225	0.053	B	0.17722	0.019	T	0.35076	-0.9803	10	0.30078	T	0.28	-12.805	5.0874	0.14691	0.1555:0.6319:0.1337:0.0789	.	647	P57678	GEMI4_HUMAN	Q	647	ENSP00000321706:E647Q	ENSP00000321706:E647Q	E	-	1	0	GEMIN4	596094	0.185000	0.23213	0.959000	0.39883	0.826000	0.46750	0.956000	0.29202	1.358000	0.45922	0.655000	0.94253	GAG	.		0.488	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		G	649344	C	G	649344	3	3	62	1	0	0	0	0	1	0	0	0	6350	835	29	4	1241	4	GEMIN4	17	649344	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		649344	80545866	98	6084											
C17orf48	56985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10608559	10608559	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcttaaagttccagttcatCatacatggggaaaccatgaa	14	10	9	8	0	2	1	2	1	0	0	3	2	3	2	2	3	2	3	2	3	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:10608559C>T	ENST00000379774.4	+	2	407	c.316C>T	c.(316-318)Cat>Tat	p.H106Y	ADPRM_ENST00000609540.1_Missense_Mutation_p.H106Y	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	106							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										TCCAGTTCATCATACATGGGG	0.353																																					p.H106Y		.											.	.	0			c.C316T						.						88	82	84					17																	10608559		2203	4300	6503	SO:0001583	missense	56985	exon2			GTTCATCATACAT	BC070155	CCDS11159.2	17p13.1	2012-07-20	2012-07-20	2012-07-20	ENSG00000170222	ENSG00000170222	3.6.1.13, 3.6.1.16, 3.6.1.53		30925	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 48"	C17orf48		18352857	Standard	XM_005256738		Approved	MDS006	uc002gmt.3	Q3LIE5	OTTHUMG00000130366	ENST00000379774.4:c.316C>T	17.37:g.10608559C>T	ENSP00000369099:p.His106Tyr	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	115	18	NM_020233	0	0	10	10	0	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	37	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565615	0.86439	.	.	ENSG00000170222	ENST00000379774	D	0.84660	-1.88	5.64	5.64	0.86602	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.89949	0.6863	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83803	0.0237	10	0.02654	T	1	-8.9416	19.5025	0.95103	0.0:1.0:0.0:0.0	.	106	Q3LIE5	ADPRM_HUMAN	Y	106	ENSP00000369099:H106Y	ENSP00000369099:H106Y	H	+	1	0	C17orf48	10549284	1.000000	0.71417	0.964000	0.40570	0.988000	0.76386	6.987000	0.76206	2.937000	0.99478	0.650000	0.86243	CAT	.		0.353	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		T	10608559	C	T	10608559	3	4	62	1	0	0	0	0	1	0	0	0	1864	826	29	2	318	2	C17orf48	17	10608559	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	9959215	10608559	70586651	99	6085											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y	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	265	268					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	490	85		WXS	Illumina HiSeq		465	69	NM_145301	0	0	25	76	51	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		T	15457087	C	T	15457087	3	4	62	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	4848528	15457087	65738123	100	6086											
MYO18A	399687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27430634	27430634	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccggctcaggcccatgcAgcagctgctcttctccagat	7	8	9	17	1	3	1	1	0	2	1	4	1	3	1	3	2	4	5	3	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:27430634A>T	ENST00000527372.1	-	21	3670	c.3490T>A	c.(3490-3492)Tgc>Agc	p.C1164S	MYO18A_ENST00000533112.1_Missense_Mutation_p.C1164S|MYO18A_ENST00000354329.4_Missense_Mutation_p.C1164S|MYO18A_ENST00000531253.1_Missense_Mutation_p.C1164S	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1164	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AGGCCCATGCAGCAGCTGCTC	0.657																																					p.C1164S	Esophageal Squamous(182;472 2015 7001 15270 22562)	.											.	MYO18A-22	0			c.T3490A						.						47	54	52					17																	27430634		2074	4207	6281	SO:0001583	missense	399687	exon21			CCATGCAGCAGCT	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.3490T>A	17.37:g.27430634A>T	ENSP00000437073:p.Cys1164Ser	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	32	16	NM_078471	0	0	16	28	12	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887500	0.33348	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428	D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11	5.44	3.22	0.36961	Myosin head, motor domain (2);	0.313479	0.39544	N	0.001332	T	0.74680	0.3748	N	0.25890	0.77	0.37666	D	0.922943	B;B;B;B;B	0.22346	0.006;0.009;0.009;0.009;0.068	B;B;B;B;B	0.21708	0.003;0.015;0.009;0.009;0.036	T	0.66392	-0.5935	10	0.32370	T	0.25	.	3.1069	0.06345	0.6565:0.0:0.1571:0.1864	.	833;776;1164;1164;1164	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	S	1164;1164;1164;1164;1164;60;60;776	ENSP00000346291:C1164S;ENSP00000435932:C1164S;ENSP00000434228:C1164S;ENSP00000437073:C1164S	ENSP00000346291:C1164S	C	-	1	0	MYO18A	24454760	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.734000	0.47368	0.878000	0.35920	0.459000	0.35465	TGC	.		0.657	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27430634	A	T	27430634	3	4	62	1	0	0	0	0	1	0	0	0	10090	188	7	5	2762	5	MYO18A	17	27430634	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	11973547	27430634	53764576	101	6087											
KCNJ16	3773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	68129360	68129360	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggtcatttagtgcagttGccattgtcagcagctgtgaa	10	12	12	7	0	2	1	2	1	0	0	2	2	2	1	1	1	4	4	1	1	3	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:68129360G>A	ENST00000589377.1	+	2	1295	c.1132G>A	c.(1132-1134)Gcc>Acc	p.A378T	KCNJ16_ENST00000585558.1_Missense_Mutation_p.A413T|KCNJ16_ENST00000392671.1_Missense_Mutation_p.A378T|KCNJ16_ENST00000283936.1_Missense_Mutation_p.A378T|KCNJ16_ENST00000586462.1_Missense_Mutation_p.A417T|KCNJ16_ENST00000392670.1_Missense_Mutation_p.A378T	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	378					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					TAGTGCAGTTGCCATTGTCAG	0.498																																					p.A378T		.											.	KCNJ16-516	0			c.G1132A						.						109	92	98					17																	68129360		2203	4300	6503	SO:0001583	missense	3773	exon6			GCAGTTGCCATTG	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.1132G>A	17.37:g.68129360G>A	ENSP00000465967:p.Ala378Thr	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	84	43	NM_001270422	0	0	68	162	94		Missense_Mutation	SNP	ENST00000589377.1	37	CCDS11687.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.058214	0.36277	.	.	ENSG00000153822	ENST00000283936;ENST00000392671;ENST00000392670	D;D;D	0.89270	-2.49;-2.49;-2.49	5.8	5.8	0.92144	.	1.758860	0.02733	N	0.115373	D	0.84584	0.5504	L	0.27053	0.805	0.36349	D	0.859948	B;B	0.29909	0.261;0.01	B;B	0.21546	0.035;0.007	T	0.60910	-0.7169	9	.	.	.	.	13.9035	0.63819	0.0735:0.0:0.9265:0.0	.	378;378	A8K434;Q9NPI9	.;IRK16_HUMAN	T	378	ENSP00000283936:A378T;ENSP00000376439:A378T;ENSP00000376438:A378T	.	A	+	1	0	KCNJ16	65640955	0.999000	0.42202	0.952000	0.39060	0.454000	0.32378	6.073000	0.71245	2.736000	0.93811	0.591000	0.81541	GCC	.		0.498	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		A	68129360	G	A	68129360	3	1	62	1	0	0	0	0	1	0	0	0	8071	1319	46	2	1134	2	KCNJ16	17	68129360	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	40698726	68129360	13065850	102	6088											
FOXK2	3607	broad.mit.edu	37	chr17	80525990	80525990	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcttcagggtacaaggtgggCcgagtgatgccatctgacct	8	10	13	10	1	3	2	1	2	2	0	3	3	3	2	3	3	2	1	3	3	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:80525990C>T	ENST00000335255.5	+	3	849	c.675C>T	c.(673-675)ggC>ggT	p.G225G		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	225					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ACAAGGTGGGCCGAGTGATGC	0.522																																					p.G225G													.	FOXK2-226	0			c.C675T						.						54	53	53					17																	80525990		2203	4300	6503	SO:0001819	synonymous_variant	3607	exon3			GGTGGGCCGAGTG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.675C>T	17.37:g.80525990C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_004514	0	0	39	39	0	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			.		0.522	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		T	80525990	C	T	80525990	2	4	62	1	0	0	0	0	0	0	0	1	6034	726	26	2		2	FOXK2	17	80525990	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	12396630	80525990	669220	103	6089											
YES1	7525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	756694	756694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgctgttccctttgctgaaGatgacggacatggtgacact	8	12	11	10	1	0	4	0	3	0	1	1	5	1	5	1	2	2	3	1	2	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr18:756694G>A	ENST00000584307.1	-	2	304	c.134C>T	c.(133-135)tCt>tTt	p.S45F	YES1_ENST00000577611.1_5'UTR|YES1_ENST00000577961.1_Missense_Mutation_p.S50F|YES1_ENST00000314574.4_Missense_Mutation_p.S45F			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	45					blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	CTTTGCTGAAGATGACGGACA	0.468																																					p.S45F		.											.	YES1-547	0			c.C134T						.						248	208	222					18																	756694		2203	4300	6503	SO:0001583	missense	7525	exon2			GCTGAAGATGACG	M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"SH2 domain containing"	12841	protein-coding gene	gene with protein product		164880	"v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.134C>T	18.37:g.756694G>A	ENSP00000462468:p.Ser45Phe	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	235	33	NM_005433	0	0	55	64	9	A6NLB3|D3DUH1	Missense_Mutation	SNP	ENST00000584307.1	37	CCDS11824.1	.	.	.	.	.	.	.	.	.	.	G	6.428	0.447146	0.12223	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	T	0.75050	-0.9	4.66	4.66	0.58398	.	0.822602	0.09557	U	0.786109	T	0.66297	0.2775	L	0.29908	0.895	0.45366	D	0.998353	B	0.02656	0.0	B	0.08055	0.003	T	0.53851	-0.8380	10	0.16420	T	0.52	.	17.9046	0.88914	0.0:0.0:1.0:0.0	.	45	P07947	YES_HUMAN	F	45	ENSP00000324740:S45F	ENSP00000324740:S45F	S	-	2	0	YES1	746694	1.000000	0.71417	0.017000	0.16124	0.934000	0.57294	6.760000	0.74939	2.299000	0.77371	0.313000	0.20887	TCT	.		0.468	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		A	756694	G	A	756694	3	1	62	1	0	0	0	0	1	0	0	0	17507	942	33	2	1541	2	YES1	18	756694	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		756694	77320554	104	6090											
DSC3	1825	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	28576918	28576918	+	Frame_Shift_Del	DEL	T	T	-																															tcctttcatcatttcaatggTttcctgccctccatttttca																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr18:28576918delT	ENST00000360428.4	-	15	2412	c.2332delA	c.(2332-2334)accfs	p.T778fs	DSC3_ENST00000434452.1_Frame_Shift_Del_p.T778fs	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	778					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			ATTTCAATGGTTTCCTGCCCT	0.502																																					p.T778fs		.											.	DSC3-94	0			c.2332delA						.						119	96	104					18																	28576918		2203	4300	6503	SO:0001589	frameshift_variant	1825	exon15			.	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.2332delA	18.37:g.28576918delT	ENSP00000353608:p.Thr778fs	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	60	22	NM_024423	0	0	0	0	0	A6NN35|Q14200|Q9HAZ9	Frame_Shift_Del	DEL	ENST00000360428.4	37	CCDS32810.1																																																																																			.		0.502	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		-	28576918	T	-	28576918	7	5	62	1	0	1	0	1	0	0	0	0	4778	1725	60	0	397	0	DSC3	18	28576918	Frame_Shift_Del	DEL	T	TCGA-BQ-5878-01A-11D-1589-08	27820224	28576918	49500330	105	6091											
KIAA1012	22878	broad.mit.edu	37	chr18	29496396	29496396	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcagcttcactagatgaCgctaccaacataccttgtaa	12	11	7	11	1	2	2	2	1	0	1	2	2	2	2	2	1	4	4	2	1	5	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr18:29496396C>T	ENST00000283351.4	-	4	791	c.456G>A	c.(454-456)gcG>gcA	p.A152A	TRAPPC8_ENST00000582539.1_Silent_p.A98A|TRAPPC8_ENST00000582513.1_Silent_p.A152A	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	152					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CACTAGATGACGCTACCAACA	0.363																																					p.A152A													.	TRAPPC8-159	0			c.G456A						.						105	86	92					18																	29496396		2203	4300	6503	SO:0001819	synonymous_variant	22878	exon4			AGATGACGCTACC	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.456G>A	18.37:g.29496396C>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_014939	0	0	0	0	0	A0JP15|B3KME5|Q9H0L2	Silent	SNP	ENST00000283351.4	37	CCDS11901.1																																																																																			.		0.363	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		T	29496396	C	T	29496396	2	4	62	1	0	0	0	0	0	0	0	1	8225	523	19	1		1	KIAA1012	18	29496396	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	919478	29496396	48580852	106	6092											
PCSK4	92840	broad.mit.edu	37	chr19	1489873	1489873	+	5'Flank	DEL	A	A	-																															acgccccggtgccgcaggtgAaagtactgcccgtcagggaa																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:1489873delA	ENST00000233596.3	+	0	0				PCSK4_ENST00000587784.1_Intron|PCSK4_ENST00000300954.5_Frame_Shift_Del_p.F71fs	NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6						regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCGCAGGTGAAAGTACTGCC	0.692																																					p.F71fs													.	PCSK4-90	0			c.213delT						.						17	19	18					19																	1489873		2198	4297	6495	SO:0001631	upstream_gene_variant	54760	exon2			CAGGTGAAAGTAC	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"Receptor accessory proteins"	30078	protein-coding gene	gene with protein product	"polyposis locus protein 1-like 1", "deleted in polyposis 1-like 1"	609346	"chromosome 19 open reading frame 32"	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072		19.37:g.1489873delA	Exception_encountered	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_017573	0	0	0	0	0	B2RE01|D6W5Z0|Q96LM0	Frame_Shift_Del	DEL	ENST00000233596.3	37	CCDS12070.1																																																																																			.		0.692	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393		-	1489873	A	-	1489873	6	5	62	0	1	1	0	1	0	0	0	0	11628	243	9	0		0	PCSK4	19	1489873	5'Flank	DEL	A	TCGA-BQ-5878-01A-11D-1589-08		1489873	57639110	107	6093											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	9087506	9087506	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caggggttcccctgggacatCagaagttagttccaatgtgc	9	10	12	10	0	1	1	1	0	0	1	3	2	3	2	3	3	1	3	3	3	3	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:9087506C>T	ENST00000397910.4	-	1	4512	c.4309G>A	c.(4309-4311)Gat>Aat	p.D1437N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1437	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTGGGACATCAGAAGTTAGT	0.512																																					p.D1437N		.											.	MUC16-566	0			c.G4309A						.						118	114	116					19																	9087506		1966	4148	6114	SO:0001583	missense	94025	exon1			GGACATCAGAAGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4309G>A	19.37:g.9087506C>T	ENSP00000381008:p.Asp1437Asn	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	149	12	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	3.824	-0.037221	0.07497	.	.	ENSG00000181143	ENST00000397910	T	0.02944	4.1	1.0	-0.286	0.12862	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.26845	0.161	B	0.18263	0.021	T	0.44190	-0.9344	8	0.87932	D	0	.	3.1617	0.06522	0.0:0.617:0.0:0.383	.	1437	B5ME49	.	N	1437	ENSP00000381008:D1437N	ENSP00000381008:D1437N	D	-	1	0	MUC16	8948506	0.001000	0.12720	0.002000	0.10522	0.042000	0.13812	-0.052000	0.11865	-0.065000	0.13021	0.305000	0.20034	GAT	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9087506	C	T	9087506	3	4	62	1	0	0	0	0	1	0	0	0	9998	826	29	2	39550	2	MUC16	19	9087506	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	7597633	9087506	50041477	108	6094											
ECSIT	51295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11618829	11618829	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgtggggctgggggggaTctgctgcacctgttgagtct	4	11	18	8	1	2	1	0	1	2	0	2	3	2	2	1	5	2	4	1	5	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:11618829T>C	ENST00000270517.7	-	5	908	c.773A>G	c.(772-774)gAt>gGt	p.D258G	ZNF653_ENST00000593191.1_5'Flank|ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000417981.2_Missense_Mutation_p.D44G|ECSIT_ENST00000591104.1_Missense_Mutation_p.D258G|ECSIT_ENST00000591352.1_5'UTR|ECSIT_ENST00000592312.1_Missense_Mutation_p.D142G|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000588998.1_Missense_Mutation_p.D44G|ECSIT_ENST00000252440.7_Missense_Mutation_p.D258G	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	258					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CTGGGGGGGATCTGCTGCACC	0.577																																					p.D258G		.											.	ECSIT-91	0			c.A773G						.						99	108	105					19																	11618829		2203	4300	6503	SO:0001583	missense	51295	exon5			GGGGGATCTGCTG	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"Mitochondrial respiratory chain complex assembly factors"	29548	protein-coding gene	gene with protein product	"signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"	608388	"ECSIT homolog (Drosophila)"			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.773A>G	19.37:g.11618829T>C	ENSP00000270517:p.Asp258Gly	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	117	39	NM_001142464	0	0	49	87	38	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.901102	0.52227	.	.	ENSG00000130159	ENST00000270517;ENST00000417981;ENST00000252440	T;T;T	0.80480	-1.38;1.22;-1.38	3.81	2.67	0.31697	.	0.528567	0.19970	N	0.102018	T	0.77343	0.4116	M	0.73598	2.24	0.09310	N	1	P;P;P	0.44139	0.827;0.557;0.485	B;B;B	0.41510	0.359;0.178;0.248	T	0.71646	-0.4530	10	0.66056	D	0.02	-5.0804	6.5677	0.22521	0.0:0.0:0.2477:0.7523	.	44;258;258	E9PAN9;Q9BQ95-2;Q9BQ95	.;.;ECSIT_HUMAN	G	258;44;258	ENSP00000270517:D258G;ENSP00000412712:D44G;ENSP00000252440:D258G	ENSP00000252440:D258G	D	-	2	0	ECSIT	11479829	0.181000	0.23161	0.007000	0.13788	0.266000	0.26442	2.000000	0.40816	1.671000	0.50874	0.459000	0.35465	GAT	.		0.577	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581		C	11618829	T	C	11618829	3	2	62	1	0	0	0	0	1	0	0	0	4911	1435	50	3	538	3	ECSIT	19	11618829	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	2531323	11618829	47510154	109	6095											
ZNF844	284391	broad.mit.edu	37	chr19	12187704	12187704	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgcctatgaatgtaaagaGtgtgacaaagcattcatatc	16	11	8	6	0	1	3	1	2	0	1	2	3	1	3	1	0	2	2	1	0	7	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:12187704G>A	ENST00000439326.3	+	4	1944	c.1769G>A	c.(1768-1770)aGt>aAt	p.S590N	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	590					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AATGTAAAGAGTGTGACAAAG	0.398																																					p.S590N													.	.	0			c.G1769A						.						124	109	114					19																	12187704		692	1591	2283	SO:0001583	missense	284391	exon4			TAAAGAGTGTGAC	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"Zinc fingers, C2H2-type", "-"	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1769G>A	19.37:g.12187704G>A	ENSP00000392024:p.Ser590Asn	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_001136501	0	0	8	14	6	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427784	0.25726	.	.	ENSG00000223547	ENST00000439326	T	0.04917	3.53	2.2	-4.4	0.03600	.	.	.	.	.	T	0.02083	0.0065	N	0.02916	-0.46	0.50813	D	0.999895	B	0.20780	0.048	B	0.19666	0.026	T	0.45862	-0.9232	9	0.30078	T	0.28	.	4.5323	0.12011	0.3711:0.0:0.4564:0.1725	.	590	Q08AG5	ZN844_HUMAN	N	590	ENSP00000392024:S590N	ENSP00000392024:S590N	S	+	2	0	ZNF844	12048704	0.000000	0.05858	0.006000	0.13384	0.440000	0.31957	-5.708000	0.00103	-1.106000	0.03008	0.205000	0.17691	AGT	.		0.398	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			A	12187704	G	A	12187704	3	1	62	1	0	0	0	0	1	0	0	0	18222	1029	36	2	1783	2	ZNF844	19	12187704	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	568875	12187704	46941279	110	6096											
HOOK2	29911	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	12875721	12875721	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttatgctgcagctcctcgatCcgccgggctgctggcggaag	5	9	14	13	4	0	0	0	0	0	0	3	2	2	1	3	3	4	5	3	3	2	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:12875721C>T	ENST00000397668.3	-	20	1807	c.1734G>A	c.(1732-1734)cgG>cgA	p.R578R	HOOK2_ENST00000264827.5_Silent_p.R576R|HOOK2_ENST00000589965.1_5'Flank	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	578	Required for localization to the centrosome and induction of aggresome formation.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						GCTCCTCGATCCGCCGGGCTG	0.632											OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R578R		.											.	HOOK2-92	0			c.G1734A						.						67	73	71					19																	12875721		2018	4169	6187	SO:0001819	synonymous_variant	29911	exon20			CTCGATCCGCCGG	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1734G>A	19.37:g.12875721C>T		Somatic	108	0	683	WXS	Illumina HiSeq	Phase_I	145	9	NM_013312	0	0	1	1	0	O60562	Silent	SNP	ENST00000397668.3	37	CCDS42508.1																																																																																			.		0.632	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		T	12875721	C	T	12875721	2	4	62	1	0	0	0	0	0	0	0	1	7304	842	30	2		2	HOOK2	19	12875721	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	688017	12875721	46253262	111	6097											
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15288375	15288375	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caccggcgtggcagtcgaagTtgtcgtagaggcaggcgggc	7	6	18	10	5	0	1	0	0	0	1	2	2	0	1	1	5	0	4	1	5	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:15288375T>C	ENST00000263388.2	-	24	4439	c.4364A>G	c.(4363-4365)aAc>aGc	p.N1455S		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1455					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GCAGTCGAAGTTGTCGTAGAG	0.657																																					p.N1455S		.											.	NOTCH3-855	0			c.A4364G						.						14	13	13					19																	15288375		2111	4180	6291	SO:0001583	missense	4854	exon24			TCGAAGTTGTCGT	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.4364A>G	19.37:g.15288375T>C	ENSP00000263388:p.Asn1455Ser	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	15	4	NM_000435	0	0	306	581	275	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816967	0.70912	.	.	ENSG00000074181	ENST00000263388	T	0.63913	-0.07	4.66	4.66	0.58398	Notch domain (5);	.	.	.	.	T	0.56746	0.2006	L	0.47016	1.485	0.45883	D	0.998736	B	0.31968	0.349	B	0.33799	0.17	T	0.60255	-0.7299	9	0.56958	D	0.05	.	13.0613	0.59008	0.0:0.0:0.0:1.0	.	1455	Q9UM47	NOTC3_HUMAN	S	1455	ENSP00000263388:N1455S	ENSP00000263388:N1455S	N	-	2	0	NOTCH3	15149375	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	1.398000	0.34554	1.728000	0.51552	0.260000	0.18958	AAC	.		0.657	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		C	15288375	T	C	15288375	3	2	62	1	0	0	0	0	1	0	0	0	10576	1725	60	3	2641	3	NOTCH3	19	15288375	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	2412654	15288375	43840608	112	6098											
UNC13A	23025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	17750273	17750273	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagaaggtgatgctggtgAgaaggtccacagtggatttg	12	9	16	4	0	0	3	0	2	0	2	1	6	1	4	1	4	1	1	1	4	3	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:17750273A>T	ENST00000519716.2	-	24	2917	c.2918T>A	c.(2917-2919)cTc>cAc	p.L973H	UNC13A_ENST00000428389.2_Missense_Mutation_p.L1061H|UNC13A_ENST00000550896.1_Missense_Mutation_p.L971H|UNC13A_ENST00000551649.1_Missense_Mutation_p.L973H|UNC13A_ENST00000252773.7_Missense_Mutation_p.L973H|UNC13A_ENST00000552293.1_Missense_Mutation_p.L973H	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	973					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GATGCTGGTGAGAAGGTCCAC	0.532																																					p.L973H		.											.	UNC13A-25	0			c.T2918A						.						79	78	79					19																	17750273		1967	4144	6111	SO:0001583	missense	23025	exon23			CTGGTGAGAAGGT	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2918T>A	19.37:g.17750273A>T	ENSP00000429562:p.Leu973His	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	32	8	NM_001080421	0	0	0	0	0	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	A	20.4	3.975812	0.74360	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.87729	-2.28;-2.29;-2.27;-2.12;-2.16;-2.29	3.95	3.95	0.45737	.	0.179999	0.36303	U	0.002675	D	0.92619	0.7655	M	0.80183	2.485	0.52501	D	0.999952	D	0.89917	1.0	D	0.83275	0.996	D	0.93099	0.6507	10	0.87932	D	0	-16.3271	11.1266	0.48322	1.0:0.0:0.0:0.0	.	973	Q9UPW8	UN13A_HUMAN	H	973;1061;973;973;973;971	ENSP00000429562:L973H;ENSP00000400409:L1061H;ENSP00000252773:L973H;ENSP00000447236:L973H;ENSP00000447572:L973H;ENSP00000446831:L971H	ENSP00000252773:L973H	L	-	2	0	UNC13A	17611273	1.000000	0.71417	0.892000	0.35008	0.984000	0.73092	9.105000	0.94246	1.568000	0.49683	0.248000	0.18094	CTC	.		0.532	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17750273	A	T	17750273	3	4	62	1	0	0	0	0	1	0	0	0	17017	304	11	5	2273	5	UNC13A	19	17750273	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	2461898	17750273	41378710	113	6099											
ZNF85	7639	broad.mit.edu	37	chr19	21131687	21131687	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaggctgtgaaagtatggatGagtgtaagatgcacaaagga	16	8	14	3	0	0	3	0	2	0	1	0	5	0	5	0	3	1	4	0	3	5	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:21131687G>C	ENST00000328178.8	+	4	480	c.367G>C	c.(367-369)Gag>Cag	p.E123Q	ZNF85_ENST00000597314.1_3'UTR|ZNF85_ENST00000601023.1_Missense_Mutation_p.E64Q|ZNF85_ENST00000345030.6_Missense_Mutation_p.E90Q	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	123					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						AAGTATGGATGAGTGTAAGAT	0.338																																					p.E153Q													.	ZNF85-514	0			c.G457C						.						62	64	63					19																	21131687		2203	4299	6502	SO:0001583	missense	7639	exon5			ATGGATGAGTGTA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.367G>C	19.37:g.21131687G>C	ENSP00000329793:p.Glu123Gln	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	80	3	NM_001256171	0	0	5	5	0	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	9.761	1.170185	0.21621	.	.	ENSG00000105750	ENST00000328178;ENST00000345030	T;T	0.06218	3.45;3.33	1.04	-0.843	0.10744	.	.	.	.	.	T	0.16214	0.0390	M	0.85041	2.73	0.09310	N	1	D;B;P	0.58620	0.983;0.442;0.756	P;B;B	0.58454	0.839;0.076;0.398	T	0.14615	-1.0466	9	0.38643	T	0.18	.	2.2708	0.04090	0.2803:0.3367:0.3829:0.0	.	90;64;123	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	Q	123;90	ENSP00000329793:E123Q;ENSP00000342340:E90Q	ENSP00000329793:E123Q	E	+	1	0	ZNF85	20923527	0.002000	0.14202	0.063000	0.19743	0.061000	0.15899	0.242000	0.18087	0.452000	0.26830	0.455000	0.32223	GAG	.		0.338	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		C	21131687	G	C	21131687	3	2	62	1	0	0	0	0	1	0	0	0	18225	1291	45	4	381	4	ZNF85	19	21131687	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	3381414	21131687	37997296	114	6100											
CYP2A13	1553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41596079	41596079	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gaggaggcgggcttcctcatCgacgccctccggggcacgca	6	5	15	15	5	1	0	1	0	0	0	4	3	3	1	3	5	0	3	3	5	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:41596079C>G	ENST00000330436.3	+	3	471	c.471C>G	c.(469-471)atC>atG	p.I157M		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	157					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	GCTTCCTCATCGACGCCCTCC	0.687																																					p.I157M		.											.	CYP2A13-93	0			c.C471G						.						31	32	31					19																	41596079		2202	4300	6502	SO:0001583	missense	1553	exon3			CCTCATCGACGCC	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.471C>G	19.37:g.41596079C>G	ENSP00000332679:p.Ile157Met	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	75	46	NM_000766	0	0	0	0	0	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	11.11	1.542221	0.27563	.	.	ENSG00000197838	ENST00000330436	T	0.01379	4.96	3.43	-3.64	0.04515	.	0.840898	0.10215	U	0.701698	T	0.01353	0.0044	L	0.45285	1.41	0.09310	N	1	B	0.25667	0.131	B	0.30029	0.11	T	0.47623	-0.9103	10	0.49607	T	0.09	.	1.1459	0.01775	0.1312:0.246:0.2879:0.3349	.	157	Q16696	CP2AD_HUMAN	M	157	ENSP00000332679:I157M	ENSP00000332679:I157M	I	+	3	3	CYP2A13	46287919	0.000000	0.05858	0.053000	0.19242	0.011000	0.07611	-2.752000	0.00791	-0.321000	0.08627	0.305000	0.20034	ATC	.		0.687	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		G	41596079	C	G	41596079	3	3	62	1	0	0	0	0	1	0	0	0	4167	874	31	4	481	4	CYP2A13	19	41596079	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	20464392	41596079	17532904	115	6101											
DMWD	1762	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	46289265	46289265	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcccccgccagctgggtgcgGgagactgttggagcgggaca	6	5	18	12	3	0	1	0	0	0	1	0	4	0	3	3	4	3	2	3	4	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:46289265G>A	ENST00000270223.6	-	3	1534	c.1489C>T	c.(1489-1491)Ccg>Tcg	p.P497S	DMWD_ENST00000601370.1_5'Flank|DMWD_ENST00000377735.3_Missense_Mutation_p.P497S|AC011530.4_ENST00000593999.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	497										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GCTGGGTGCGGGAGACTGTTG	0.731																																					p.P497S		.											.	DMWD-90	0			c.C1489T						.						6	7	7					19																	46289265		1846	3685	5531	SO:0001583	missense	1762	exon3			GGTGCGGGAGACT	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"WD repeat domain containing"	2936	protein-coding gene	gene with protein product		609857	"dystrophia myotonica-containing WD repeat motif"			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1489C>T	19.37:g.46289265G>A	ENSP00000270223:p.Pro497Ser	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	19	7	NM_004943	0	0	20	36	16		Missense_Mutation	SNP	ENST00000270223.6	37	CCDS33054.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533457	0.64972	.	.	ENSG00000185800	ENST00000377735;ENST00000270223	T;T	0.59906	0.25;0.23	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.64516	0.2605	L	0.49126	1.545	0.58432	D	0.99999	D;D;D	0.71674	0.997;0.998;0.997	P;D;P	0.64776	0.888;0.929;0.888	T	0.58549	-0.7617	10	0.09084	T	0.74	-15.5092	14.4428	0.67330	0.0:0.0:1.0:0.0	.	182;497;497	Q8WUW6;G5E9A7;Q09019	.;.;DMWD_HUMAN	S	497	ENSP00000366964:P497S;ENSP00000270223:P497S	ENSP00000270223:P497S	P	-	1	0	DMWD	50981105	1.000000	0.71417	0.939000	0.37840	0.356000	0.29392	9.141000	0.94612	2.365000	0.80145	0.462000	0.41574	CCG	.		0.731	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943		A	46289265	G	A	46289265	3	1	62	1	0	0	0	0	1	0	0	0	4604	1232	43	2	547	2	DMWD	19	46289265	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	4693186	46289265	12839718	116	6102											
HRC	3270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49658341	49658341	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcgaagctctgctgatgcctCctcggagagcccggcgactc	6	7	13	15	4	1	2	0	1	1	1	4	5	2	2	3	2	4	2	3	2	1	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:49658341C>T	ENST00000252825.4	-	1	340	c.154G>A	c.(154-156)Gag>Aag	p.E52K	TRPM4_ENST00000427978.2_5'Flank|TRPM4_ENST00000252826.5_5'Flank|TRPM4_ENST00000355712.5_5'Flank|HRC_ENST00000595625.1_Missense_Mutation_p.E52K	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	52					cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GCTGATGCCTCCTCGGAGAGC	0.597																																					p.E52K	Melanoma(37;75 1097 24567 25669 30645)	.											.	HRC-91	0			c.G154A						.						168	147	154					19																	49658341		2203	4300	6503	SO:0001583	missense	3270	exon1			ATGCCTCCTCGGA		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.154G>A	19.37:g.49658341C>T	ENSP00000252825:p.Glu52Lys	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	173	24	NM_002152	0	0	0	0	0	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.921389	0.73213	.	.	ENSG00000130528	ENST00000252825	T	0.06687	3.27	3.26	3.26	0.37387	.	.	.	.	.	T	0.08802	0.0218	L	0.47716	1.5	0.09310	N	0.999997	B	0.33694	0.421	B	0.24701	0.055	T	0.16188	-1.0411	9	0.66056	D	0.02	-4.7962	12.7671	0.57399	0.0:1.0:0.0:0.0	.	52	P23327	SRCH_HUMAN	K	52	ENSP00000252825:E52K	ENSP00000252825:E52K	E	-	1	0	HRC	54350153	0.554000	0.26522	0.204000	0.23530	0.009000	0.06853	1.738000	0.38207	2.104000	0.64026	0.561000	0.74099	GAG	.		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49658341	C	T	49658341	3	4	62	1	0	0	0	0	1	0	0	0	7373	864	30	2	1969	2	HRC	19	49658341	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	3369076	49658341	9470642	117	6103											
NAPSA	9476	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	50862007	50862007	+	Frame_Shift_Del	DEL	A	A	-																															atccagggcctggaaaccggAcaagcagaggcggacgccat																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:50862007delA	ENST00000253719.2	-	9	1274	c.1066delT	c.(1066-1068)tccfs	p.S356fs	NR1H2_ENST00000542413.1_Intron|NR1H2_ENST00000600978.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	356					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		TGGAAACCGGACAAGCAGAGG	0.632																																					p.S356fs		.											.	NAPSA-90	0			c.1066delT						.						24	26	25					19																	50862007		2200	4299	6499	SO:0001589	frameshift_variant	9476	exon9			.	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"kidney-derived aspartic protease-like protein"	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.1066delT	19.37:g.50862007delA	ENSP00000253719:p.Ser356fs	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	22	11	NM_004851	0	0	0	0	0	Q8WWD9	Frame_Shift_Del	DEL	ENST00000253719.2	37	CCDS12794.1																																																																																			.		0.632	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851		-	50862007	A	-	50862007	7	5	62	1	0	1	0	1	0	0	0	0	10191	275	10	0	200	0	NAPSA	19	50862007	Frame_Shift_Del	DEL	A	TCGA-BQ-5878-01A-11D-1589-08	1203666	50862007	8266976	118	6104											
FPR2	2358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52272650	52272650	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tacgggtcctcactgctgtgGtggcttctttcttcatctgt	3	17	10	11	1	5	0	2	0	3	0	6	0	6	0	1	3	2	2	1	3	1	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:52272650G>C	ENST00000598776.1	+	2	1511	c.739G>C	c.(739-741)Gtg>Ctg	p.V247L	FPR2_ENST00000598953.1_Missense_Mutation_p.V247L|FPR2_ENST00000340023.6_Missense_Mutation_p.V247L	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	247					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)			endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						CACTGCTGTGGTGGCTTCTTT	0.483																																					p.V247L		.											.	FPR2-501	0			c.G739C						.						162	129	140					19																	52272650		2203	4300	6503	SO:0001583	missense	2358	exon2			GCTGTGGTGGCTT	M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"GPCR / Class A : Formyl peptide receptors", "GPCR / Class A : Leukotriene receptors"	3827	protein-coding gene	gene with protein product		136538	"formyl peptide receptor-like 1"	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.739G>C	19.37:g.52272650G>C	ENSP00000468897:p.Val247Leu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	63	28	NM_001005738	0	0	0	0	0	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	37	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	17.61	3.432553	0.62844	.	.	ENSG00000171049	ENST00000340023	T	0.72051	-0.62	3.79	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	0.083720	0.47455	U	0.000226	T	0.81659	0.4869	M	0.85777	2.775	0.31492	N	0.66581	D	0.55800	0.973	D	0.64506	0.926	T	0.81373	-0.0962	10	0.54805	T	0.06	.	8.5694	0.33561	0.1273:0.0:0.8727:0.0	.	247	P25090	FPR2_HUMAN	L	247	ENSP00000340191:V247L	ENSP00000340191:V247L	V	+	1	0	FPR2	56964462	0.210000	0.23517	0.680000	0.29994	0.976000	0.68499	1.340000	0.33896	0.909000	0.36697	0.484000	0.47621	GTG	.		0.483	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738		C	52272650	G	C	52272650	3	2	62	1	0	0	0	0	1	0	0	0	6058	1261	44	4	741	4	FPR2	19	52272650	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1410643	52272650	6856333	119	6105											
LAIR2	3904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55019129	55019129	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttcccagaccctccatcTcggctgagccaggcactgtg	6	8	9	18	1	1	2	0	1	1	1	4	2	3	2	5	2	1	2	5	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:55019129T>A	ENST00000301202.2	+	3	216	c.94T>A	c.(94-96)Tcg>Acg	p.S32T	LAIR2_ENST00000351841.2_Missense_Mutation_p.S32T	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	32	Ig-like C2-type.					extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		ACCCTCCATCTCGGCTGAGCC	0.577																																					p.S32T		.											.	LAIR2-91	0			c.T94A						.						116	129	124					19																	55019129		2203	4300	6503	SO:0001583	missense	3904	exon3			TCCATCTCGGCTG	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6478	protein-coding gene	gene with protein product		602993	"leukocyte-associated Ig-like receptor 2"			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.94T>A	19.37:g.55019129T>A	ENSP00000301202:p.Ser32Thr	Somatic	259	0		WXS	Illumina HiSeq	Phase_I	222	79	NM_002288	0	0	18	18	0	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.675150	0.29783	.	.	ENSG00000167618	ENST00000412608;ENST00000452094;ENST00000301202;ENST00000351841	T;T;T	0.23147	1.92;2.69;2.69	3.39	0.919	0.19392	Immunoglobulin-like fold (1);	2.380980	0.01840	N	0.035242	T	0.39064	0.1064	M	0.69358	2.11	0.09310	N	1	P;P;P	0.48589	0.911;0.873;0.912	P;B;P	0.50708	0.648;0.275;0.597	T	0.16512	-1.0400	10	0.72032	D	0.01	.	5.5099	0.16874	0.4585:0.0:0.0:0.5414	.	26;32;32	C9JFQ0;Q6ISS4-2;Q6ISS4	.;.;LAIR2_HUMAN	T	26;14;32;32	ENSP00000390729:S26T;ENSP00000301202:S32T;ENSP00000301203:S32T	ENSP00000301202:S32T	S	+	1	0	LAIR2	59710941	0.002000	0.14202	0.041000	0.18516	0.736000	0.42039	-0.423000	0.07034	0.452000	0.26830	0.260000	0.18958	TCG	.		0.577	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1			A	55019129	T	A	55019129	3	1	62	1	0	0	0	0	1	0	0	0	8624	1551	54	5	104	5	LAIR2	19	55019129	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	2746479	55019129	4109854	120	6106											
ZNF417	147687	broad.mit.edu	37	chr19	58420138	58420138	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gaacatgaagcgcagagctgGaaagaaatgatttcccacat	16	7	10	8	1	0	4	0	2	0	2	1	6	1	5	1	1	3	2	1	1	4	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:58420138G>C	ENST00000312026.5	-	3	1672	c.1508C>G	c.(1507-1509)tCc>tGc	p.S503C	CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000595559.1_Missense_Mutation_p.S502C|ZNF417_ENST00000536263.1_Missense_Mutation_p.S304C	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CGCAGAGCTGGAAAGAAATGA	0.393																																					p.S503C													.	ZNF417-90	0			c.C1508G						.						97	81	86					19																	58420138		2203	4295	6498	SO:0001583	missense	147687	exon3			GAGCTGGAAAGAA	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"Zinc fingers, C2H2-type", "-"	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1508C>G	19.37:g.58420138G>C	ENSP00000311319:p.Ser503Cys	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	179	4	NM_152475	0	0	12	12	0	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	.	.	.	.	.	.	.	.	.	.	.	10.38	1.335184	0.24253	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.08008	3.14;3.14	2.2	-4.4	0.03600	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06325	0.0163	L	0.31420	0.93	0.09310	N	1	P;P	0.47604	0.876;0.898	B;P	0.45343	0.345;0.477	T	0.08493	-1.0719	9	0.36615	T	0.2	.	5.1532	0.15021	0.2754:0.0:0.4268:0.2977	.	503;503	F5H0M9;Q8TAU3	.;ZN417_HUMAN	C	503;304	ENSP00000311319:S503C;ENSP00000442760:S304C	ENSP00000311319:S503C	S	-	2	0	ZNF417	63111950	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.803000	0.04540	-1.697000	0.01420	-0.864000	0.03007	TCC	.		0.393	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475		C	58420138	G	C	58420138	3	2	62	1	0	0	0	0	1	0	0	0	17926	1174	41	4	223	4	ZNF417	19	58420138	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	3401009	58420138	708845	121	6107											
PROCR	10544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33762617	33762617	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcacgtgctggaaggcccAgacaccaacaccacgatcat	13	4	9	15	3	1	1	1	0	0	1	1	3	1	2	3	2	2	2	3	2	2	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:33762617A>T	ENST00000216968.4	+	2	265	c.183A>T	c.(181-183)ccA>ccT	p.P61P	EDEM2_ENST00000540582.1_Intron	NM_006404.3	NP_006395.2	Q9UNN8	EPCR_HUMAN	protein C receptor, endothelial	61					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|immune response (GO:0006955)|negative regulation of coagulation (GO:0050819)	cell surface (GO:0009986)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10			BRCA - Breast invasive adenocarcinoma(18;0.0152)		Drotrecogin alfa(DB00055)	TGGAAGGCCCAGACACCAACA	0.622																																					p.P61P		.											.	PROCR-226	0			c.A183T						.						93	70	78					20																	33762617		2203	4300	6503	SO:0001819	synonymous_variant	10544	exon2			AGGCCCAGACACC	L35545	CCDS13248.1	20q11.2	2010-05-04	2010-05-04		ENSG00000101000	ENSG00000101000		"CD molecules"	9452	protein-coding gene	gene with protein product		600646				7929370, 10518938	Standard	NM_006404		Approved	EPCR, CCD41, CD201	uc002xbt.3	Q9UNN8	OTTHUMG00000032323	ENST00000216968.4:c.183A>T	20.37:g.33762617A>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	75	30	NM_006404	0	0	18	42	24	B2RC04|Q14218|Q6IB56|Q96CB3|Q9ULX1	Silent	SNP	ENST00000216968.4	37	CCDS13248.1																																																																																			.		0.622	PROCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078843.3			T	33762617	A	T	33762617	2	4	62	1	0	0	0	0	0	0	0	1	12576	175	7	5		5	PROCR	20	33762617	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08		33762617	29262903	122	6108											
SLC13A3	64849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	45204227	45204227	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacctcacagcctttggcCatggcgaagccccctcccag	7	8	8	18	1	1	0	1	0	0	0	2	1	2	0	6	2	3	0	6	2	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:45204227C>A	ENST00000279027.4	-	10	1335	c.1317G>T	c.(1315-1317)atG>atT	p.M439I	SLC13A3_ENST00000435032.1_Intron|SLC13A3_ENST00000413164.2_Missense_Mutation_p.M389I|SLC13A3_ENST00000290317.5_Missense_Mutation_p.M392I|SLC13A3_ENST00000495082.1_Missense_Mutation_p.M392I|SLC13A3_ENST00000472148.1_Missense_Mutation_p.M357I|SLC13A3_ENST00000396360.1_Missense_Mutation_p.M357I	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	439					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	AGCCTTTGGCCATGGCGAAGC	0.632																																					p.M439I		.											.	SLC13A3-91	0			c.G1317T						.						63	49	54					20																	45204227		2203	4300	6503	SO:0001583	missense	64849	exon10			TTTGGCCATGGCG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1317G>T	20.37:g.45204227C>A	ENSP00000279027:p.Met439Ile	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_022829	0	0	2	4	2	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.386648	0.82902	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915	T;T;T;T;T;T;T	0.03386	3.95;3.95;3.95;3.95;3.95;3.95;3.95	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.06690	0.0171	N	0.25031	0.7	0.80722	D	1	P;P;P;P	0.46020	0.775;0.843;0.746;0.871	P;P;P;P	0.49799	0.507;0.544;0.487;0.622	T	0.36866	-0.9730	10	0.72032	D	0.01	-34.8403	17.6296	0.88103	0.0:1.0:0.0:0.0	.	389;357;392;439	B4DIR8;Q8WWT9-3;F6WI18;Q8WWT9	.;.;.;S13A3_HUMAN	I	392;357;439;357;389;392;392	ENSP00000290317:M392I;ENSP00000379648:M357I;ENSP00000279027:M439I;ENSP00000420177:M357I;ENSP00000415852:M389I;ENSP00000419621:M392I;ENSP00000417784:M392I	ENSP00000279027:M439I	M	-	3	0	SLC13A3	44637634	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.897000	0.69831	2.399000	0.81585	0.655000	0.94253	ATG	.		0.632	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			A	45204227	C	A	45204227	3	1	62	1	0	0	0	0	1	0	0	0	14425	594	21	4	507	4	SLC13A3	20	45204227	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	11441610	45204227	17821293	123	6109											
ZNF831	128611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	57766279	57766279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtaccacacggtgcctcccGggggcctccagccccgcgcc	4	5	12	20	4	0	0	0	0	0	0	2	0	2	0	8	3	3	1	8	3	1	1	rs375833789		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:57766279G>A	ENST00000371030.2	+	1	205	c.205G>A	c.(205-207)Ggg>Agg	p.G69R		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	69	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GGTGCCTCCCGGGGGCCTCCA	0.706																																					p.G69R		.											.	ZNF831-126	0			c.G205A						.	G	ARG/GLY	1,3705		0,1,1852	9	11	10		205	5.6	0.9	20		10	0,8092		0,0,4046	no	missense	ZNF831	NM_178457.1	125	0,1,5898	AA,AG,GG		0.0,0.027,0.0085	probably-damaging	69/1678	57766279	1,11797	1853	4046	5899	SO:0001583	missense	128611	exon1			CCTCCCGGGGGCC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.205G>A	20.37:g.57766279G>A	ENSP00000360069:p.Gly69Arg	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	25	11	NM_178457	0	0	0	0	0	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011024	0.75046	2.7E-4	0.0	ENSG00000124203	ENST00000371030	T	0.05081	3.5	5.55	5.55	0.83447	.	.	.	.	.	T	0.16854	0.0405	L	0.27053	0.805	0.33846	D	0.632	D	0.89917	1.0	D	0.91635	0.999	T	0.05146	-1.0903	9	0.87932	D	0	-18.5525	18.4859	0.90828	0.0:0.0:1.0:0.0	.	69	Q5JPB2	ZN831_HUMAN	R	69	ENSP00000360069:G69R	ENSP00000360069:G69R	G	+	1	0	ZNF831	57199674	0.950000	0.32346	0.917000	0.36280	0.949000	0.60115	2.282000	0.43461	2.608000	0.88229	0.462000	0.41574	GGG	.		0.706	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57766279	G	A	57766279	3	1	62	1	0	0	0	0	1	0	0	0	18217	1116	39	1	207	1	ZNF831	20	57766279	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	12562052	57766279	5259241	124	6110											
DIDO1	11083	broad.mit.edu	37	chr20	61510808	61510808	+	Frame_Shift_Del	DEL	T	T	-																															cccggctgcggtcccactccTtgccccggtcggcctcgcgc																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:61510808delT	ENST00000266070.4	-	16	6825	c.6500delA	c.(6499-6501)aagfs	p.K2167fs	DIDO1_ENST00000395343.1_Frame_Shift_Del_p.K2167fs	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2167	Arg-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					gtcccactccttgccccgGTC	0.726																																					p.K2167fs	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)												.	DIDO1-96	0			c.6500delA						.						14	11	12					20																	61510808		2074	4074	6148	SO:0001589	frameshift_variant	11083	exon16			CACTCCTTGCCCC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.6500delA	20.37:g.61510808delT	ENSP00000266070:p.Lys2167fs	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_001193369	0	0	0	0	0	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Frame_Shift_Del	DEL	ENST00000266070.4	37	CCDS33506.1																																																																																			.		0.726	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		-	61510808	T	-	61510808	7	5	62	1	0	1	0	1	0	0	0	0	4533	1609	56	0	226	0	DIDO1	20	61510808	Frame_Shift_Del	DEL	T	TCGA-BQ-5878-01A-11D-1589-08	3744529	61510808	1514712	125	6111											
LIPI	149998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	15554081	15554081	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaatcctgatttgttaccaTtggagtcagaatggatgaca	13	13	9	6	0	1	3	1	2	0	1	2	5	2	5	2	2	1	1	2	2	4	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr21:15554081T>C	ENST00000536861.1	-	4	640	c.641A>G	c.(640-642)aAt>aGt	p.N214S	LIPI_ENST00000344577.2_Missense_Mutation_p.N235S			Q6XZB0	LIPI_HUMAN	lipase, member I	214					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TTTGTTACCATTGGAGTCAGA	0.398																																					p.N235S		.											.	LIPI-70	0			c.A704G						.						76	71	73					21																	15554081		2203	4300	6503	SO:0001583	missense	149998	exon4			TTACCATTGGAGT	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.641A>G	21.37:g.15554081T>C	ENSP00000440381:p.Asn214Ser	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	45	22	NM_198996	0	0	0	0	0	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	37		.	.	.	.	.	.	.	.	.	.	T	9.157	1.017856	0.19355	.	.	ENSG00000188992	ENST00000344577;ENST00000536861;ENST00000382981	D;D	0.90069	-2.61;-2.61	5.46	4.31	0.51392	.	0.306919	0.38548	N	0.001658	T	0.77177	0.4092	N	0.13235	0.315	0.28263	N	0.924755	B;B	0.18741	0.03;0.03	B;B	0.21151	0.033;0.02	T	0.60172	-0.7315	10	0.08381	T	0.77	.	11.4777	0.50308	0.0:0.0716:0.0:0.9284	.	214;235	G1JSG6;Q6XZB0-2	.;.	S	235;214;109	ENSP00000343331:N235S;ENSP00000440381:N214S	ENSP00000343331:N235S	N	-	2	0	LIPI	14475952	1.000000	0.71417	0.643000	0.29450	0.055000	0.15305	5.357000	0.66058	1.007000	0.39238	0.533000	0.62120	AAT	.		0.398	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		C	15554081	T	C	15554081	3	2	62	1	0	0	0	0	1	0	0	0	8848	1493	52	3	769	3	LIPI	21	15554081	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08		15554081	32575814	126	6112											
DEPDC5	9681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	32301997	32301997	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtacaagataaatattcTgcctctgcttttaacttccc	10	17	4	10	0	2	1	0	0	2	1	3	1	3	1	2	0	4	2	2	0	6	8			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr22:32301997T>G	ENST00000382111.2	+	40	4463	c.4403T>G	c.(4402-4404)cTg>cGg	p.L1468R	DEPDC5_ENST00000400246.1_Missense_Mutation_p.L1468R|DEPDC5_ENST00000539165.1_Silent_p.S305S|DEPDC5_ENST00000382105.2_3'UTR|DEPDC5_ENST00000400248.2_Silent_p.S1457S|DEPDC5_ENST00000400249.2_Silent_p.S1457S|DEPDC5_ENST00000535622.1_Silent_p.S1388S|DEPDC5_ENST00000266091.3_Silent_p.S1466S|DEPDC5_ENST00000382112.3_Silent_p.S1479S			O75140	DEPD5_HUMAN	DEP domain containing 5	0					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ATAAATATTCTGCCTCTGCTT	0.488																																					p.S1488S		.											.	DEPDC5-519	0			c.T4464G						.						89	85	86					22																	32301997		1943	4137	6080	SO:0001583	missense	9681	exon42			ATATTCTGCCTCT	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382111.2:c.4403T>G	22.37:g.32301997T>G	ENSP00000371545:p.Leu1468Arg	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	39	20	NM_001242896	0	0	3	6	3	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.81|11.81	1.751165|1.751165	0.31046|0.31046	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000400246;ENST00000382111	.|T;T	.|0.29655	.|1.56;1.56	5.01|5.01	-1.17|-1.17	0.09648|0.09648	.|.	.|.	.|.	.|.	.|.	T|T	0.29389|0.29389	0.0732|0.0732	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29761|0.29761	-1.0001|-1.0001	4|6	.|0.72032	.|D	.|0.01	.|.	0.9017|0.9017	0.01275|0.01275	0.3175:0.289:0.1114:0.2822|0.3175:0.289:0.1114:0.2822	.|.	.|.	.|.	.|.	G|R	864|1468	.|ENSP00000383105:L1468R;ENSP00000371545:L1468R	.|ENSP00000371545:L1468R	C|L	+|+	1|2	0|0	DEPDC5|DEPDC5	30631997|30631997	0.011000|0.011000	0.17503|0.17503	0.969000|0.969000	0.41365|0.41365	0.990000|0.990000	0.78478|0.78478	-1.295000|-1.295000	0.02764|0.02764	-0.538000|-0.538000	0.06281|0.06281	0.459000|0.459000	0.35465|0.35465	TGC|CTG	.		0.488	DEPDC5-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000129085.1	NM_014662		G	32301997	T	G	32301997	3	3	62	1	0	0	0	0	1	0	0	0	4453	1567	55	5	4617	5	DEPDC5	22	32301997	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08		32301997	19002569	127	6113											
PLXNB2	23654	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	50719301	50719302	+	Frame_Shift_Ins	INS	-	-	T																															tccttgtcgccgtccttggaINSgggcaggaagaagacgcggt																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr22:50719301_50719302insT	ENST00000449103.1	-	24	4004_4005	c.3864_3865insA	c.(3862-3867)ccctccfs	p.S1289fs	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Frame_Shift_Ins_p.S1289fs			O15031	PLXB2_HUMAN	plexin B2	1289					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCGTCCTTGGAGGGCAGGAAGA	0.629																																					p.S1289fs		.											.	PLXNB2-211	0			c.3865_3866insA						.																																			SO:0001589	frameshift_variant	23654	exon24			.		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3864_3865insA	22.37:g.50719301_50719302insT	ENSP00000409171:p.Ser1289fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	42	13	NM_012401	0	0	0	0	0	A6QRH0|Q7KZU3|Q9BSU7	Frame_Shift_Ins	INS	ENST00000449103.1	37	CCDS43035.1																																																																																			.		0.629	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		T	50719302	-	T	50719301	7	5	62	1	0	1	1	0	0	0	0	0	12150	304	11	0	1707	0	PLXNB2	22	50719301	Frame_Shift_Ins	INS	-	TCGA-BQ-5878-01A-11D-1589-08	18417304	50719301	585265	128	6114											
GPKOW	27238	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	48979068	48979068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgggctggtggctgcctgcGatggccattctggatcaaag	6	9	15	11	2	2	0	1	0	1	0	2	2	2	1	3	5	2	2	3	5	1	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:48979068G>A	ENST00000156109.5	-	2	313	c.235C>T	c.(235-237)Cgc>Tgc	p.R79C		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	79						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						GGCTGCCTGCGATGGCCATTC	0.637																																					p.R79C		.											.	GPKOW-132	0			c.C235T						.						37	39	38					X																	48979068		2203	4300	6503	SO:0001583	missense	27238	exon2			GCCTGCGATGGCC	U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"G patch domain containing"	30677	protein-coding gene	gene with protein product	"G patch domain containing 5"					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.235C>T	X.37:g.48979068G>A	ENSP00000156109:p.Arg79Cys	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	35	17	NM_015698	0	0	35	36	1	Q59EK5|Q9BQA8	Missense_Mutation	SNP	ENST00000156109.5	37	CCDS35251.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571866	0.28003	.	.	ENSG00000068394	ENST00000156109	.	.	.	4.73	0.739	0.18324	.	0.440958	0.26038	N	0.026709	T	0.28366	0.0701	L	0.51422	1.61	0.09310	N	0.999999	D	0.65815	0.995	B	0.44315	0.446	T	0.18209	-1.0344	9	0.59425	D	0.04	-3.2051	3.9276	0.09270	0.4817:0.1829:0.3353:0.0	.	79	Q92917	GPKOW_HUMAN	C	79	.	ENSP00000156109:R79C	R	-	1	0	GPKOW	48866012	0.070000	0.21116	0.006000	0.13384	0.580000	0.36256	2.429000	0.44758	0.398000	0.25338	-0.300000	0.09419	CGC	.		0.637	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		A	48979068	G	A	48979068	3	1	62	1	0	0	0	0	1	0	0	0	6633	1058	37	1	1235	1	GPKOW	23	48979068	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		48979068	106291492	129	6115											
ESX1	80712	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	103499100	103499100	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcctgctgttgctccggctCgtggccgccgccaccctcac	2	9	10	20	4	1	0	1	0	0	0	4	0	3	0	6	2	2	4	6	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:103499100C>T	ENST00000372588.4	-	2	324	c.241G>A	c.(241-243)Gag>Aag	p.E81K		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	81					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						TGCTCCGGCTCGTGGCCGCCG	0.662																																					p.E81K	Pancreas(200;1705 2227 25194 28471 45274)	.											.	ESX1-131	0			c.G241A						.						62	70	67					X																	103499100		2200	4276	6476	SO:0001583	missense	80712	exon2			CCGGCTCGTGGCC	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"Homeoboxes / PRD class"	14865	protein-coding gene	gene with protein product		300154	"extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.241G>A	X.37:g.103499100C>T	ENSP00000361669:p.Glu81Lys	Somatic	283	0		WXS	Illumina HiSeq	Phase_I	274	33	NM_153448	0	0	0	0	0	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	c	9.690	1.151579	0.21371	.	.	ENSG00000123576	ENST00000372588	D	0.91521	-2.86	3.13	-6.25	0.02039	.	.	.	.	.	T	0.77011	0.4068	N	0.24115	0.695	0.09310	N	1	P	0.35011	0.48	B	0.18561	0.022	T	0.63902	-0.6532	9	0.13853	T	0.58	-2.0978	12.3476	0.55130	0.0:0.1335:0.6842:0.1822	.	81	Q8N693	ESX1_HUMAN	K	81	ENSP00000361669:E81K	ENSP00000361669:E81K	E	-	1	0	ESX1	103385756	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.657000	0.05335	-2.111000	0.00836	-0.560000	0.04181	GAG	.		0.662	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		T	103499100	C	T	103499100	3	4	62	1	0	0	0	0	1	0	0	0	5276	893	31	1	991	1	ESX1	23	103499100	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	54520032	103499100	51771460	130	6116											
AMOT	154796	hgsc.bcm.edu	37	chrX	112022638	112022638	+	Missense_Mutation	SNP	A	A	G																															ctggagcagcagcagcagcaAcagcaactggagcagcagct																								rs201619225		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:112022638A>G	ENST00000524145.1	-	11	2818	c.2744T>C	c.(2743-2745)gTt>gCt	p.V915A	AMOT_ENST00000371959.3_Missense_Mutation_p.V915A|MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371962.1_Missense_Mutation_p.V683A|AMOT_ENST00000304758.1_Missense_Mutation_p.V506A			Q4VCS5	AMOT_HUMAN	angiomotin	915					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						agcagcagcaacagcaactgg	0.622													A|||	29	0.00768212	0.0045	0.0144	3775	,	,		10189	0		0.0129	False		,,,				2504	0				p.V915A		.											.	AMOT-131	0			c.T2744C						.																																			SO:0001583	missense	154796	exon10			GCAGCAACAGCAA	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.2744T>C	X.37:g.112022638A>G	ENSP00000429013:p.Val915Ala	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_001113490	0	0	0	0	0	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	A	0.688	-0.795435	0.02862	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145	T;T;T;T	0.42131	0.98;2.25;2.49;2.25	4.96	-2.2	0.06994	.	0.976476	0.08375	N	0.955449	T	0.27384	0.0672	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	10	0.05620	T	0.96	-0.1055	8.0184	0.30395	0.2213:0.1649:0.6139:0.0	.	915	Q4VCS5	AMOT_HUMAN	A	506;915;683;915	ENSP00000305557:V506A;ENSP00000361027:V915A;ENSP00000361030:V683A;ENSP00000429013:V915A	ENSP00000305557:V506A	V	-	2	0	AMOT	111909294	0.000000	0.05858	0.017000	0.16124	0.214000	0.24535	-0.372000	0.07504	-0.428000	0.07339	-1.737000	0.00689	GTT	.		0.622	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		G	112022638	A	G	112022638	3	3	62	1	0	0	0	0	1	0	0	0	582	43	2	3	518	3	AMOT	23	112022638	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	8523538	112022638	43247922	131	6117	70	2									
AMOT	154796	hgsc.bcm.edu;broad.mit.edu	37	chrX	112022644	112022644	+	Missense_Mutation	SNP	A	A	G																															cagcagcagcagcaacagcaActggagcagcagctaccatg																								rs200107563		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:112022644A>G	ENST00000524145.1	-	11	2812	c.2738T>C	c.(2737-2739)gTt>gCt	p.V913A	AMOT_ENST00000371959.3_Missense_Mutation_p.V913A|MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371962.1_Missense_Mutation_p.V681A|AMOT_ENST00000304758.1_Missense_Mutation_p.V504A			Q4VCS5	AMOT_HUMAN	angiomotin	913					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						agcaacagcaactggagcagc	0.632													A|||	29	0.00768212	0.0045	0.0144	3775	,	,		10414	0		0.0129	False		,,,				2504	0				p.V913A		.											.	AMOT-131	0			c.T2738C						.	A	ALA/VAL,ALA/VAL	4,3793		0,1,3,1627,538	33	21	25		1511,2738	2.3	1	X		25	21,6642		1,3,16,2416,1807	no	missense,missense	AMOT	NM_133265.2,NM_001113490.1	64,64	1,4,19,4043,2345	GG,GA,G,AA,A		0.3152,0.1053,0.239	benign,benign	504/676,913/1085	112022644	25,10435	2169	4243	6412	SO:0001583	missense	154796	exon10			ACAGCAACTGGAG	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.2738T>C	X.37:g.112022644A>G	ENSP00000429013:p.Val913Ala	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	5	2	NM_001113490	0	0	0	0	0	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	A	3.777	-0.046481	0.07407	0.001053	0.003152	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145	T;T;T;T	0.38240	1.15;2.1;2.35;2.1	4.77	2.27	0.28462	.	0.445107	0.19223	N	0.119612	T	0.23014	0.0556	L	0.44542	1.39	0.25129	N	0.990581	B	0.02656	0.0	B	0.01281	0.0	T	0.26189	-1.0110	10	0.08381	T	0.77	-1.1747	5.9925	0.19474	0.6585:0.0:0.3415:0.0	.	913	Q4VCS5	AMOT_HUMAN	A	504;913;681;913	ENSP00000305557:V504A;ENSP00000361027:V913A;ENSP00000361030:V681A;ENSP00000429013:V913A	ENSP00000305557:V504A	V	-	2	0	AMOT	111909300	0.000000	0.05858	0.988000	0.46212	0.463000	0.32649	-0.139000	0.10358	0.659000	0.30945	0.430000	0.28490	GTT	.		0.632	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		G	112022644	A	G	112022644	3	3	62	1	0	0	0	0	1	0	0	0	582	43	2	3	524	3	AMOT	23	112022644	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	6	112022644	43247916	132	6118	70	2									
GLUD2	2747	ucsc.edu	37	chrX	120182123	120182123	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcccaagaactataccgaAaatgaattggaaaagatcac	20	7	6	8	1	1	3	1	1	0	2	2	5	2	4	2	1	2	0	2	1	10	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:120182123A>T	ENST00000328078.1	+	1	662	c.585A>T	c.(583-585)gaA>gaT	p.E195D		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	195					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						ACTATACCGAAAATGAATTGG	0.463																																					p.E195D													.	GLUD2-131	0			c.A585T						.						123	97	105					X																	120182123		2203	4300	6503	SO:0001583	missense	2747	exon1			TACCGAAAATGAA	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.585A>T	X.37:g.120182123A>T	ENSP00000327589:p.Glu195Asp	Somatic	242	0		WXS	Illumina HiSeq		248	1	NM_012084	0	0	7	7	0	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.880088	0.00537	.	.	ENSG00000182890	ENST00000328078	D	0.95949	-3.86	1.35	-2.62	0.06152	Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain (1);	0.146062	0.64402	N	0.000012	D	0.83677	0.5306	N	0.16066	0.365	0.20489	N	0.999893	B	0.02656	0.0	B	0.09377	0.004	T	0.72880	-0.4158	10	0.12103	T	0.63	-3.7222	1.5316	0.02536	0.3112:0.2241:0.0:0.4648	.	195	P49448	DHE4_HUMAN	D	195	ENSP00000327589:E195D	ENSP00000327589:E195D	E	+	3	2	GLUD2	120009804	0.070000	0.21116	0.003000	0.11579	0.173000	0.22820	-1.826000	0.01705	-0.537000	0.06290	-1.901000	0.00528	GAA	.		0.463	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		T	120182123	A	T	120182123	3	4	62	1	0	0	0	0	1	0	0	0	6497	11	1	5	587	5	GLUD2	23	120182123	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	8159479	120182123	35088437	133	6119											
HS6ST2	90161	hgsc.bcm.edu;broad.mit.edu	37	chrX	132091225	132091225	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggtccggcaccggggagctGaacgcctgcaggcggaggag	7	3	20	11	4	0	1	0	1	0	0	1	4	1	4	3	7	3	3	3	7	1	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:132091225G>C	ENST00000370836.2	-	3	973	c.558C>G	c.(556-558)ttC>ttG	p.F186L	HS6ST2_ENST00000521489.1_Missense_Mutation_p.F186L|HS6ST2_ENST00000370833.2_Missense_Mutation_p.F40L	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2	186					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9	Acute lymphoblastic leukemia(192;0.000127)					CCGGGGAGCTGAACGCCTGCA	0.632																																					p.F186L		.											.	HS6ST2-130	0			c.C558G						.						37	40	39					X																	132091225		2056	4162	6218	SO:0001583	missense	90161	exon3			GGAGCTGAACGCC	AB067776	CCDS48169.1, CCDS48170.1	Xq26.2	2008-02-05			ENSG00000171004	ENSG00000171004		"Sulfotransferases, membrane-bound"	19133	protein-coding gene	gene with protein product		300545				10644753	Standard	NM_147175		Approved		uc011mvd.1	Q96MM7	OTTHUMG00000022430	ENST00000370836.2:c.558C>G	X.37:g.132091225G>C	ENSP00000359873:p.Phe186Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	51	4	NM_001077188	0	0	10	10	0	B9WRT4|B9WRT5|E9PDY5|Q2TB13|Q4VC07|Q6PIC4|Q86SM9|Q8N3T4|Q8NBN4|Q96SJ4	Missense_Mutation	SNP	ENST00000370836.2	37	CCDS48169.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295781	0.40594	.	.	ENSG00000171004	ENST00000370837;ENST00000370836;ENST00000521489;ENST00000370833;ENST00000319809	T;T;T;T	0.75704	-0.96;-0.44;-0.44;-0.95	5.31	5.31	0.75309	.	0.450883	0.25011	N	0.033837	T	0.55033	0.1895	N	0.08118	0	0.80722	D	1	B;B	0.18166	0.026;0.026	B;B	0.12156	0.007;0.004	T	0.52268	-0.8598	10	0.17832	T	0.49	-10.915	15.3384	0.74277	0.0:0.0:1.0:0.0	.	186;186	Q96MM7;E9PDY5	H6ST2_HUMAN;.	L	40;186;186;40;27	ENSP00000359874:F40L;ENSP00000359873:F186L;ENSP00000429473:F186L;ENSP00000359870:F40L	ENSP00000324617:F27L	F	-	3	2	HS6ST2	131918907	0.047000	0.20315	1.000000	0.80357	0.982000	0.71751	1.571000	0.36450	2.212000	0.71576	0.529000	0.55759	TTC	.		0.632	HS6ST2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058332.3	NM_147174		C	132091225	G	C	132091225	3	2	62	1	0	0	0	0	1	0	0	0	7392	1281	45	4	1395	4	HS6ST2	23	132091225	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	11909102	132091225	23179335	134	6120											
F8	2157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	154130375	154130375	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccagcatgtagatgctcGccaataaggcattccacccg	11	8	8	14	2	0	1	0	0	0	1	3	1	2	1	4	1	2	4	4	1	3	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:154130375G>T	ENST00000360256.4	-	19	6266	c.6066C>A	c.(6064-6066)ggC>ggA	p.G2022G		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	2022	F5/8 type A 3.|Plastocyanin-like 6.		G -> D (in HEMA; severe). {ECO:0000269|PubMed:9886318}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GTAGATGCTCGCCAATAAGGC	0.433																																					p.G2022G		.											.	F8-182	0			c.C6066A						.						127	107	114					X																	154130375		2203	4300	6503	SO:0001819	synonymous_variant	2157	exon19			ATGCTCGCCAATA	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.6066C>A	X.37:g.154130375G>T		Somatic	122	1		WXS	Illumina HiSeq	Phase_I	126	65	NM_000132	0	0	8	8	0	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																			.		0.433	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154130375	G	T	154130375	2	4	62	1	0	0	0	0	0	0	0	1	5363	1074	38	4		4	F8	23	154130375	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	22039150	154130375	1140185	135	6121											
ELTD1	64123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	79386001	79386001	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agaaggtaaaaatgcatatgGcaagacaaatcagtgaaata	21	7	9	4	0	1	3	1	1	0	2	1	3	1	3	0	2	1	3	0	2	9	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr1:79386001G>A	ENST00000370742.3	-	10	1391	c.1328C>T	c.(1327-1329)gCc>gTc	p.A443V		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	443					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AATGCATATGGCAAGACAAAT	0.313																																					p.A443V		.											.	ELTD1-24	0			c.C1328T						.						103	97	99					1																	79386001		1812	4078	5890	SO:0001583	missense	64123	exon10			CATATGGCAAGAC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1328C>T	1.37:g.79386001G>A	ENSP00000359778:p.Ala443Val	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	135	37	NM_022159	0	0	37	37	0	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.768298	0.49680	.	.	ENSG00000162618	ENST00000370742	T	0.41065	1.01	5.0	5.0	0.66597	GPCR, family 2-like (1);	0.175937	0.50627	D	0.000111	T	0.21921	0.0528	L	0.45422	1.42	0.40567	D	0.981269	B	0.10296	0.003	B	0.23018	0.043	T	0.04537	-1.0944	9	.	.	.	.	14.2963	0.66316	0.0:0.1486:0.8513:0.0	.	443	Q9HBW9	ELTD1_HUMAN	V	443	ENSP00000359778:A443V	.	A	-	2	0	ELTD1	79158589	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	5.598000	0.67585	2.469000	0.83416	0.650000	0.86243	GCC	.		0.313	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		A	79386001	G	A	79386001	3	1	63	1	0	0	0	0	1	0	0	0	5097	1203	42	2	768	2	ELTD1	1	79386001	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		79386001	169864620	1	6122											
LMNA	4000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156105085	156105085	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacagcctctctgcccagctCagccagctccagaagcaggt	9	6	10	16	0	2	1	1	0	1	1	4	2	3	1	4	1	6	3	4	1	1	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr1:156105085C>T	ENST00000368300.4	+	5	1130	c.918C>T	c.(916-918)ctC>ctT	p.L306L	LMNA_ENST00000448611.2_Silent_p.L194L|LMNA_ENST00000392353.3_Silent_p.L225L|LMNA_ENST00000368297.1_Silent_p.L225L|LMNA_ENST00000368301.2_Silent_p.L306L|LMNA_ENST00000347559.2_Silent_p.L306L|LMNA_ENST00000361308.4_Silent_p.L306L|LMNA_ENST00000368299.3_Silent_p.L306L|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Silent_p.L207L	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	306	Coil 2.|Rod.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CTGCCCAGCTCAGCCAGCTCC	0.662									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.L306L		.											.	LMNA-228	0			c.C918T						.						25	28	27					1																	156105085		2202	4299	6501	SO:0001819	synonymous_variant	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	CCAGCTCAGCCAG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.918C>T	1.37:g.156105085C>T		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	35	10	NM_170707	0	0	212	400	188	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			.		0.662	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		T	156105085	C	T	156105085	2	4	63	1	0	0	0	0	0	0	0	1	8871	813	29	2		2	LMNA	1	156105085	Silent	SNP	C	TCGA-BQ-5879-01A-11D-1589-08	76719084	156105085	93145536	2	6123											
SUSD4	55061	hgsc.bcm.edu	37	chr1	223401081	223401081	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggtgctgggccacgtttgctCtgcatgagggagaacaaagc	9	8	15	9	1	1	2	0	1	1	1	1	3	1	2	1	3	5	4	1	3	2	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr1:223401081C>G	ENST00000343846.3	-	6	1550		c.e6-1		SUSD4_ENST00000484758.2_Splice_Site|SUSD4_ENST00000478605.1_Intron|SUSD4_ENST00000366878.4_Splice_Site|SUSD4_ENST00000454695.2_Splice_Site|SUSD4_ENST00000494793.2_Splice_Site			Q5VX71	SUSD4_HUMAN	sushi domain containing 4							integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		CACGTTTGCTCTGCATGAGGG	0.577																																					.		.											.	SUSD4-68	0			c.917-1G>C						.						60	64	63					1																	223401081		2148	4258	6406	SO:0001630	splice_region_variant	55061	exon8			TTTGCTCTGCATG	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.917-1G>C	1.37:g.223401081C>G		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_017982	0	0	0	0	0	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Splice_Site	SNP	ENST00000343846.3	37	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.236471	0.79800	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000454695	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4353	0.99089	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SUSD4	221467704	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.156000	0.71840	2.836000	0.97738	0.655000	0.94253	.	.		0.577	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982	Intron	G	223401081	C	G	223401081	5	3	63	1	0	0	0	0	0	0	1	0	15442	927	32	4	568	4	SUSD4	1	223401081	Splice_Site	SNP	C	TCGA-BQ-5879-01A-11D-1589-08	67295996	223401081	25849540	3	6124											
SLC5A6	8884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27427384	27427384	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatactcctggtaatacGcgaacatgaccaggccaatg	12	8	11	10	2	0	1	0	1	0	0	1	3	1	2	3	3	3	1	3	3	5	3	rs199587675		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:27427384G>A	ENST00000310574.3	-	9	1423	c.950C>T	c.(949-951)gCg>gTg	p.A317V	SLC5A6_ENST00000408041.1_Missense_Mutation_p.A317V|SLC5A6_ENST00000461319.1_5'Flank	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	317					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.A317V(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CTGGTAATACGCGAACATGAC	0.597																																					p.A317V		.											.	SLC5A6-92	1	Substitution - Missense(1)	large_intestine(1)	c.C950T						.						99	95	96					2																	27427384		2203	4300	6503	SO:0001583	missense	8884	exon9			TAATACGCGAACA	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.950C>T	2.37:g.27427384G>A	ENSP00000310208:p.Ala317Val	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	107	33	NM_021095	0	0	7	14	7	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	37	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.513536	0.27123	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.88586	-2.4;-2.4	4.93	2.04	0.26737	.	0.604283	0.16756	N	0.200821	D	0.85733	0.5765	M	0.67569	2.06	0.39947	D	0.974481	B	0.33345	0.409	B	0.34242	0.178	T	0.82370	-0.0491	10	0.52906	T	0.07	.	7.2906	0.26364	0.1706:0.1441:0.6852:0.0	.	317	Q9Y289	SC5A6_HUMAN	V	317	ENSP00000310208:A317V;ENSP00000384853:A317V	ENSP00000310208:A317V	A	-	2	0	SLC5A6	27280888	0.999000	0.42202	0.226000	0.23910	0.215000	0.24574	3.539000	0.53604	0.585000	0.29608	0.655000	0.94253	GCG	.		0.597	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		A	27427384	G	A	27427384	3	1	63	1	0	0	0	0	1	0	0	0	14701	1087	38	1	993	1	SLC5A6	2	27427384	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		27427384	215771989	4	6125											
ACTR1B	10120	broad.mit.edu;bcgsc.ca	37	chr2	98275011	98275014	+	Frame_Shift_Del	DEL	GAGT	GAGT	-																															caatgtccacccgcatgatgGagtgaggcatggcaaagccc																								rs200965492		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	GAGT	GAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:98275011_98275014delGAGT	ENST00000289228.5	-	6	749_752	c.533_536delACTC	c.(532-537)cactccfs	p.HS178fs		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	178					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						CCGCATGATGGAGTGAGGCATGGC	0.603																																					p.178_179del													.	ACTR1B-91	0			c.533_536del						.																																			SO:0001589	frameshift_variant	10120	exon6			ATGATGGAGTGAG	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.533_536delACTC	2.37:g.98275011_98275014delGAGT	ENSP00000289228:p.His178fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	67	10	NM_005735	0	0	0	0	0	D3DVH2|Q53SK5|Q9BRB7	Frame_Shift_Del	DEL	ENST00000289228.5	37	CCDS2033.1																																																																																			.		0.603	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735		-	98275014	GAGT	-	98275011	7	5	63	1	0	1	0	1	0	0	0	0	210	1174	41	0	618	0	ACTR1B	2	98275011	Frame_Shift_Del	DEL	GAGT	TCGA-BQ-5879-01A-11D-1589-08	70847627	98275011	144924362	5	6126											
RAB3GAP1	22930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	135815628	135815628	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaatgactggaaactgattgGaaactctttgggaaagccac	14	9	11	7	0	1	2	0	2	1	0	1	6	1	5	1	3	3	0	1	3	4	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:135815628G>A	ENST00000264158.8	+	3	165	c.122G>A	c.(121-123)gGa>gAa	p.G41E	RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.G41E|RAB3GAP1_ENST00000425393.1_Missense_Mutation_p.G41E|RAB3GAP1_ENST00000539493.1_5'UTR	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	41					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		AAACTGATTGGAAACTCTTTG	0.383																																					p.G41E		.											.	RAB3GAP1-92	0			c.G122A						.						91	86	88					2																	135815628		2203	4300	6503	SO:0001583	missense	22930	exon3			TGATTGGAAACTC	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.122G>A	2.37:g.135815628G>A	ENSP00000264158:p.Gly41Glu	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	76	27	NM_001172435	0	0	37	62	25	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.554169	0.86231	.	.	ENSG00000115839	ENST00000264158;ENST00000442034;ENST00000425393	T;T	0.48201	0.84;0.82	5.62	5.62	0.85841	.	0.174050	0.52532	D	0.000076	T	0.66268	0.2772	M	0.69823	2.125	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.70227	0.927;0.968	T	0.61466	-0.7057	10	0.25751	T	0.34	-20.0075	16.5774	0.84705	0.0:0.0:1.0:0.0	.	41;41	C9J837;Q15042	.;RB3GP_HUMAN	E	41	ENSP00000264158:G41E;ENSP00000411418:G41E	ENSP00000264158:G41E	G	+	2	0	RAB3GAP1	135532098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.478000	0.81082	2.642000	0.89623	0.655000	0.94253	GGA	.		0.383	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		A	135815628	G	A	135815628	3	1	63	1	0	0	0	0	1	0	0	0	12967	1174	41	2	132	2	RAB3GAP1	2	135815628	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	37540617	135815628	107383745	6	6127											
NEB	4703	hgsc.bcm.edu	37	chr2	152372972	152372972	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggtgtggtttttttgacttaCcccactctgcatctgctgag	5	16	10	10	0	2	2	0	2	2	0	2	2	2	2	2	2	3	3	2	2	1	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:152372972C>A	ENST00000172853.10	-	129	17950		c.e129+1		NEB_ENST00000397345.3_Splice_Site|NEB_ENST00000427231.2_Splice_Site|NEB_ENST00000603639.1_Splice_Site|NEB_ENST00000604864.1_Splice_Site|NEB_ENST00000409198.1_Splice_Site			P20929	NEBU_HUMAN	nebulin						muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTTTGACTTACCCCACTCTGC	0.443																																					.		.											.	NEB-145	0			c.22905+1G>T						.						241	219	226					2																	152372972		2014	4177	6191	SO:0001630	splice_region_variant	4703	exon158			GACTTACCCCACT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17802+1G>T	2.37:g.152372972C>A		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_001164507	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Splice_Site	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	17.45	3.393102	0.62066	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000434685	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5748	0.95438	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEB	152081218	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	7.817000	0.86213	2.622000	0.88805	0.557000	0.71058	.	.		0.443	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	Intron	A	152372972	C	A	152372972	5	1	63	1	0	0	0	0	0	0	1	0	10328	521	18	4	2775	4	NEB	2	152372972	Splice_Site	SNP	C	TCGA-BQ-5879-01A-11D-1589-08	16557344	152372972	90826401	7	6128											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179429062	179429062	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgcatcaatttcatctcttGcagtaatggcaccactacta	11	13	6	11	0	3	0	2	0	1	0	4	0	3	0	1	1	3	4	1	1	4	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:179429062G>T	ENST00000591111.1	-	276	77098	c.76874C>A	c.(76873-76875)gCa>gAa	p.A25625E	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A24698E|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A18393E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A18326E|TTN_ENST00000460472.2_Missense_Mutation_p.A18201E|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A27266E			Q8WZ42	TITIN_HUMAN	titin	25625	Fibronectin type-III 86. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCATCTCTTGCAGTAATGGC	0.393																																					p.A27266E		.											.	TTN-636	0			c.C81797A						.						106	104	105					2																	179429062		1912	4119	6031	SO:0001583	missense	7273	exon326			TCTCTTGCAGTAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76874C>A	2.37:g.179429062G>T	ENSP00000465570:p.Ala25625Glu	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	135	31	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	15.43	2.830143	0.50845	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	6.07	6.07	0.98685	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79287	0.4420	M	0.89478	3.035	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.81406	-0.0947	9	0.87932	D	0	.	20.6452	0.99591	0.0:0.0:1.0:0.0	.	18201;18326;18393;25625	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	24698;18201;18393;18326;18199	ENSP00000343764:A24698E;ENSP00000434586:A18201E;ENSP00000340554:A18393E;ENSP00000352154:A18326E	ENSP00000340554:A18393E	A	-	2	0	TTN	179137308	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.030000	0.88816	2.885000	0.99019	0.650000	0.86243	GCA	.		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179429062	G	T	179429062	3	4	63	1	0	0	0	0	1	0	0	0	16768	1319	46	4	26330	4	TTN	2	179429062	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	27056090	179429062	63770311	8	6129											
PDCD1	5133	hgsc.bcm.edu	37	chr2	242794400	242794400	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacccagactagcagcaccAggctgcccagcaggccgccc	9	2	12	18	1	0	1	0	0	0	1	0	2	0	2	5	3	4	4	5	3	1	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:242794400A>G	ENST00000334409.5	-	3	611	c.542T>C	c.(541-543)cTg>cCg	p.L181P		NM_005018.2	NP_005009.2	Q15116	PDCD1_HUMAN	programmed cell death 1	181					apoptotic process (GO:0006915)|humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			endometrium(1)|lung(2)|ovary(1)|prostate(3)|skin(1)	8		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)		TAGCAGCACCAGGCTGCCCAG	0.701																																					p.L181P		.											.	PDCD1-69	0			c.T542C						.						21	25	24					2																	242794400		2201	4294	6495	SO:0001583	missense	5133	exon3			AGCACCAGGCTGC	AY206416	CCDS33428.1	2q37.3	2014-01-29			ENSG00000188389	ENSG00000188389		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	8760	protein-coding gene	gene with protein product		600244	"systemic lupus erythematosus susceptibility 2"	SLEB2		7851902, 12402038	Standard	NM_005018		Approved	CD279, PD1, hSLE1	uc002wcq.4	Q15116	OTTHUMG00000151342	ENST00000334409.5:c.542T>C	2.37:g.242794400A>G	ENSP00000335062:p.Leu181Pro	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_005018	0	0	0	0	0	O00517|Q8IX89	Missense_Mutation	SNP	ENST00000334409.5	37	CCDS33428.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.847285	0.32606	.	.	ENSG00000188389	ENST00000334409	T	0.75050	-0.9	3.28	3.28	0.37604	.	0.710921	0.11710	N	0.536986	T	0.66819	0.2828	N	0.04724	-0.175	0.49213	D	0.999765	D	0.71674	0.998	P	0.60117	0.869	T	0.65265	-0.6210	10	0.48119	T	0.1	-8.6103	8.2856	0.31926	1.0:0.0:0.0:0.0	.	181	Q15116	PDCD1_HUMAN	P	181	ENSP00000335062:L181P	ENSP00000335062:L181P	L	-	2	0	PDCD1	242443073	0.531000	0.26338	0.866000	0.34008	0.103000	0.19146	1.255000	0.32909	1.732000	0.51606	0.254000	0.18369	CTG	.		0.701	PDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322313.1	NM_005018		G	242794400	A	G	242794400	3	3	63	1	0	0	0	0	1	0	0	0	11641	188	7	3	336	3	PDCD1	2	242794400	Missense_Mutation	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	63365338	242794400	404973	9	6130											
ITIH1	3697	hgsc.bcm.edu;broad.mit.edu	37	chr3	52813483	52813483	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggagcaattcaccatccAcctcaccgtcaatccccaga	12	8	5	16	1	3	1	3	0	0	1	5	2	5	2	6	1	1	1	6	1	3	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr3:52813483A>G	ENST00000273283.2	+	5	470	c.446A>G	c.(445-447)cAc>cGc	p.H149R	ITIH1_ENST00000537050.1_5'Flank|ITIH1_ENST00000542827.1_Missense_Mutation_p.H149R|ITIH1_ENST00000540715.1_Missense_Mutation_p.H7R	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	149	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		TTCACCATCCACCTCACCGTC	0.493																																					p.H149R		.											.	ITIH1-93	0			c.A446G						.						148	134	139					3																	52813483		2203	4300	6503	SO:0001583	missense	3697	exon5			CCATCCACCTCAC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"inter-alpha (globulin) inhibitor, H1 polypeptide"			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.446A>G	3.37:g.52813483A>G	ENSP00000273283:p.His149Arg	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	99	5	NM_002215	0	0	0	0	0	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.526324	0.64860	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715	T;T;T	0.20738	2.05;2.05;4.85	5.48	4.38	0.52667	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.227351	0.47093	D	0.000253	T	0.28764	0.0713	M	0.63428	1.95	0.80722	D	1	P	0.34699	0.464	B	0.42692	0.395	T	0.07635	-1.0762	10	0.59425	D	0.04	-23.1872	10.4273	0.44387	0.5985:0.4015:0.0:0.0	.	149	P19827	ITIH1_HUMAN	R	149;149;7	ENSP00000442584:H149R;ENSP00000273283:H149R;ENSP00000443973:H7R	ENSP00000273283:H149R	H	+	2	0	ITIH1	52788523	1.000000	0.71417	0.906000	0.35671	0.663000	0.39108	4.658000	0.61497	2.094000	0.63399	0.459000	0.35465	CAC	.		0.493	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		G	52813483	A	G	52813483	3	3	63	1	0	0	0	0	1	0	0	0	7924	159	6	3	464	3	ITIH1	3	52813483	Missense_Mutation	SNP	A	TCGA-BQ-5879-01A-11D-1589-08		52813483	145208947	10	6131											
SR140	23350	hgsc.bcm.edu	37	chr3	142747194	142747194	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtgtaggttcttatttgaAaaccagacaccagcccatgt	11	13	8	9	0	1	2	0	1	1	1	1	2	1	2	3	1	2	2	3	1	4	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr3:142747194A>C	ENST00000473835.2	+	15	1482	c.1392A>C	c.(1390-1392)gaA>gaC	p.E464D	U2SURP_ENST00000397933.2_Missense_Mutation_p.E55D|U2SURP_ENST00000493598.2_Missense_Mutation_p.E463D	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	464					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						TCTTATTTGAAAACCAGACAC	0.284																																					p.E464D		.											.	U2SURP-71	0			c.A1392C						.						63	59	60					3																	142747194		1795	4056	5851	SO:0001583	missense	23350	exon15			ATTTGAAAACCAG	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1392A>C	3.37:g.142747194A>C	ENSP00000418563:p.Glu464Asp	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_001080415	0	0	0	0	0	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Missense_Mutation	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	A	6.794	0.515419	0.12944	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000397933;ENST00000493598;ENST00000480029	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.88	5.88	0.94601	SWAP/Surp (3);	0.000000	0.85682	D	0.000000	T	0.12817	0.0311	N	0.01576	-0.805	0.58432	D	0.999999	B;B;B	0.22080	0.052;0.052;0.064	B;B;B	0.23852	0.049;0.013;0.023	T	0.20840	-1.0263	10	0.02654	T	1	-22.1851	11.3358	0.49503	0.9297:0.0:0.0703:0.0	.	463;55;464	O15042-2;O15042-3;O15042	.;.;SR140_HUMAN	D	464;464;55;463;31	ENSP00000418563:E464D;ENSP00000381027:E55D;ENSP00000422011:E463D;ENSP00000417441:E31D	ENSP00000322376:E464D	E	+	3	2	U2SURP	144229884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.367000	0.52350	2.243000	0.73865	0.533000	0.62120	GAA	.		0.284	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		C	142747194	A	C	142747194	3	2	63	1	0	0	0	0	1	0	0	0	15163	11	1	5	1450	5	SR140	3	142747194	Missense_Mutation	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	89933711	142747194	55275236	11	6132											
CP	1356	hgsc.bcm.edu;broad.mit.edu	37	chr3	148916162	148916162	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agttggacttacctgtctccCatttgcatgtaaacttcctt	8	16	6	11	0	1	0	0	0	1	0	3	1	2	1	3	1	3	3	3	1	3	6			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr3:148916162C>A	ENST00000264613.6	-	9	1967	c.1705G>T	c.(1705-1707)Ggg>Tgg	p.G569W	CP_ENST00000462336.1_5'UTR	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	569	F5/8 type A 2.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	ACCTGTCTCCCATTTGCATGT	0.348																																					p.G569W		.											.	CP-515	0			c.G1705T						.						94	88	90					3																	148916162		2203	4300	6503	SO:0001583	missense	1356	exon9			GTCTCCCATTTGC	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1705G>T	3.37:g.148916162C>A	ENSP00000264613:p.Gly569Trp	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	93	15	NM_000096	0	0	0	0	0	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.264268	0.80358	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98926	-5.24;-5.24	5.46	5.46	0.80206	Cupredoxin (2);	0.052731	0.85682	D	0.000000	D	0.99426	0.9797	H	0.95294	3.65	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98548	1.0635	10	0.87932	D	0	-24.5002	17.4968	0.87719	0.0:1.0:0.0:0.0	.	569;569;569;569	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	W	569;352	ENSP00000264613:G569W;ENSP00000420545:G352W	ENSP00000264613:G569W	G	-	1	0	CP	150398852	0.114000	0.22134	1.000000	0.80357	0.965000	0.64279	1.720000	0.38022	2.573000	0.86826	0.650000	0.86243	GGG	.		0.348	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		A	148916162	C	A	148916162	3	1	63	1	0	0	0	0	1	0	0	0	3793	594	21	4	1536	4	CP	3	148916162	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08	6168968	148916162	49106268	12	6133											
ECT2	1894	hgsc.bcm.edu	37	chr3	172520417	172520417	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttcaggcatattaatgAggataagagaaaaacagaag	19	10	9	3	0	1	3	1	1	0	2	1	5	1	4	0	2	1	1	0	2	6	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr3:172520417A>G	ENST00000392692.3	+	19	2095	c.1919A>G	c.(1918-1920)gAg>gGg	p.E640G	ECT2_ENST00000417960.1_Missense_Mutation_p.E608G|ECT2_ENST00000441497.2_Missense_Mutation_p.E609G|ECT2_ENST00000427830.1_Missense_Mutation_p.E609G|ECT2_ENST00000232458.5_Missense_Mutation_p.E609G|ECT2_ENST00000540509.1_Missense_Mutation_p.E640G	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	640	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			CATATTAATGAGGATAAGAGA	0.269																																					p.E640G		.											.	ECT2-724	0			c.A1919G						.						44	48	47					3																	172520417		2188	4283	6471	SO:0001583	missense	1894	exon19			TTAATGAGGATAA	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"Rho guanine nucleotide exchange factors"	3155	protein-coding gene	gene with protein product		600586	"epithelial cell transforming sequence 2 oncogene"			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.1919A>G	3.37:g.172520417A>G	ENSP00000376457:p.Glu640Gly	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_001258315	0	0	0	0	0	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	37	CCDS58860.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.712870	0.89112	.	.	ENSG00000114346	ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.090181	0.85682	D	0.000000	T	0.71728	0.3374	H	0.96175	3.78	0.80722	D	1	P;D;D;D;D	0.67145	0.929;0.966;0.996;0.983;0.991	P;D;D;D;D	0.72075	0.732;0.948;0.976;0.959;0.915	T	0.82123	-0.0613	10	0.87932	D	0	-6.4325	15.3834	0.74679	1.0:0.0:0.0:0.0	.	640;85;640;609;608	Q9H8V3;Q96SJ9;Q9H8V3-3;G5E9L8;Q9H8V3-2	ECT2_HUMAN;.;.;.;.	G	609;640;609;608;609;640	ENSP00000232458:E609G;ENSP00000376457:E640G;ENSP00000401910:E609G;ENSP00000415876:E608G;ENSP00000412259:E609G;ENSP00000443160:E640G	ENSP00000232458:E609G	E	+	2	0	ECT2	174003111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.825000	0.92029	2.036000	0.60181	0.533000	0.62120	GAG	.		0.269	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098		G	172520417	A	G	172520417	3	3	63	1	0	0	0	0	1	0	0	0	4912	304	11	3	1892	3	ECT2	3	172520417	Missense_Mutation	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	23604255	172520417	25502013	13	6134											
FYTTD1	84248	broad.mit.edu;bcgsc.ca	37	chr3	197501076	197501076	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtagtagcaaagagaacTcgtcagtaagtttccatttg	13	12	10	6	1	1	1	1	0	0	1	3	3	2	1	1	0	2	5	1	0	5	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr3:197501076T>C	ENST00000241502.4	+	6	873	c.651T>C	c.(649-651)acT>acC	p.T217T	FYTTD1_ENST00000415708.2_Silent_p.T191T|FYTTD1_ENST00000428395.2_Silent_p.T126T|FYTTD1_ENST00000424384.2_Silent_p.T150T	NM_032288.6	NP_115664.2	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1	217					mRNA export from nucleus (GO:0006406)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		CAAAGAGAACTCGTCAGTAAG	0.378																																					p.T217T													.	FYTTD1-90	0			c.T651C						.						171	168	169					3																	197501076		2203	4300	6503	SO:0001819	synonymous_variant	84248	exon6			GAGAACTCGTCAG	AJ344094	CCDS3329.1, CCDS43196.1, CCDS43196.2	3q29	2011-03-03			ENSG00000122068	ENSG00000122068			25407	protein-coding gene	gene with protein product	"UAP56-interacting factor"					19836239	Standard	NM_001011537		Approved	DKFZp761B1514, UIF	uc003fyi.2	Q96QD9	OTTHUMG00000155453	ENST00000241502.4:c.651T>C	3.37:g.197501076T>C		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	127	5	NM_032288	0	0	0	0	0	A8MY74|B2RCB2|B7Z3R4|B7Z7V1|B7Z8I0|B7ZAJ3|C9J7P6|C9JNG6|C9JTH3|C9JY50|Q96SL9|Q9BQI8	Silent	SNP	ENST00000241502.4	37	CCDS3329.1																																																																																			.		0.378	FYTTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340185.3	NM_032288		C	197501076	T	C	197501076	2	2	63	1	0	0	0	0	0	0	0	1	6146	1538	54	3		3	FYTTD1	3	197501076	Silent	SNP	T	TCGA-BQ-5879-01A-11D-1589-08	24980659	197501076	521354	14	6135											
ADH4	127	bcgsc.ca	37	chr4	100052684	100052684	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatccacctgcacagtcaaGggcaaaatccacacctccct	13	6	6	16	0	1	1	1	0	0	1	4	1	4	1	5	1	1	2	5	1	3	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr4:100052684G>T	ENST00000265512.7	-	6	888	c.814C>A	c.(814-816)Ctt>Att	p.L272I	RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000505590.1_Missense_Mutation_p.L291I|ADH4_ENST00000508393.1_Missense_Mutation_p.L291I|ADH4_ENST00000423445.1_Missense_Mutation_p.L291I	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	272					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		GCACAGTCAAGGGCAAAATCC	0.418																																					p.L272I													.	ADH4-228	0			c.C814A						.						117	116	116					4																	100052684		2203	4300	6503	SO:0001583	missense	127	exon6			AGTCAAGGGCAAA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.814C>A	4.37:g.100052684G>T	ENSP00000265512:p.Leu272Ile	Somatic	104	0		WXS	Illumina HiSeq	Phase_1	96	5	NM_000670	0	0	2	2	0	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	37	CCDS34032.1	.	.	.	.	.	.	.	.	.	.	G	5.819	0.335351	0.11013	.	.	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.09817	2.94;2.94;2.94;2.94	4.39	-8.79	0.00820	Alcohol dehydrogenase, C-terminal (1);	0.732597	0.12061	N	0.503188	T	0.04907	0.0132	N	0.17631	0.505	0.24104	N	0.995862	B;B	0.02656	0.0;0.0	B;B	0.16722	0.016;0.01	T	0.31833	-0.9929	10	0.59425	D	0.04	0.0764	5.4296	0.16446	0.4364:0.0:0.2042:0.3594	.	291;272	P08319-2;P08319	.;ADH4_HUMAN	I	291;272;291;291	ENSP00000424630:L291I;ENSP00000265512:L272I;ENSP00000397939:L291I;ENSP00000425416:L291I	ENSP00000265512:L272I	L	-	1	0	ADH4	100271707	0.067000	0.21026	0.009000	0.14445	0.005000	0.04900	-0.609000	0.05635	-2.142000	0.00804	-0.912000	0.02778	CTT	.		0.418	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		T	100052684	G	T	100052684	3	4	63	1	0	0	0	0	1	0	0	0	310	1000	35	4	344	4	ADH4	4	100052684	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		100052684	91101592	15	6136											
PRSS12	8492	hgsc.bcm.edu	37	chr4	119273492	119273492	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcgctgtcctcgcagctgAgcccagctcgctgggggcga	4	7	16	14	4	0	1	0	1	0	0	3	2	1	1	2	3	3	5	2	3	0	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr4:119273492A>T	ENST00000296498.3	-	1	666	c.384T>A	c.(382-384)gcT>gcA	p.A128A		NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	128	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						CTCGCAGCTGAGCCCAGCTCG	0.706																																					p.A128A		.											.	PRSS12-91	0			c.T384A						.						9	10	10					4																	119273492		2194	4283	6477	SO:0001819	synonymous_variant	8492	exon1			CAGCTGAGCCCAG	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"Serine peptidases / Serine peptidases"	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.384T>A	4.37:g.119273492A>T		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_003619	0	0	0	0	0	Q9UP16	Silent	SNP	ENST00000296498.3	37	CCDS3709.1																																																																																			.		0.706	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2			T	119273492	A	T	119273492	2	4	63	1	0	0	0	0	0	0	0	1	12644	291	11	5		5	PRSS12	4	119273492	Silent	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	19220808	119273492	71880784	16	6137											
SLC12A7	10723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1094290	1094290	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcgaaaagtgccatgttcttCccttcaaagaagctctcttg	10	13	7	11	1	3	1	1	0	2	1	6	2	4	1	2	0	2	2	2	0	4	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr5:1094290C>T	ENST00000264930.5	-	2	241	c.198G>A	c.(196-198)ggG>ggA	p.G66G		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	66					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CCATGTTCTTCCCTTCAAAGA	0.468																																					p.G66G		.											.	SLC12A7-138	0			c.G198A						.						128	120	123					5																	1094290		2203	4300	6503	SO:0001819	synonymous_variant	10723	exon2			GTTCTTCCCTTCA	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.198G>A	5.37:g.1094290C>T		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	87	49	NM_006598	0	0	3	23	20	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1																																																																																			.		0.468	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		T	1094290	C	T	1094290	2	4	63	1	0	0	0	0	0	0	0	1	14420	842	30	2		2	SLC12A7	5	1094290	Silent	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		1094290	179820970	17	6138											
SPOCK1	6695	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	136314458	136314458	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcctttggtcccagctccCgttcatattctaggtcatcc	5	15	7	14	1	3	0	2	0	1	0	7	0	7	0	4	2	1	2	4	2	2	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr5:136314458C>T	ENST00000394945.1	-	11	1374	c.1205G>A	c.(1204-1206)cGg>cAg	p.R402Q	SPOCK1_ENST00000282223.7_Missense_Mutation_p.R402Q|SPOCK1_ENST00000509978.1_5'Flank	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	402					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCCCAGCTCCCGTTCATATTC	0.517																																					p.R402Q		.											.	SPOCK1-91	0			c.G1205A						.						152	131	138					5																	136314458		2203	4300	6503	SO:0001583	missense	6695	exon11			AGCTCCCGTTCAT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.1205G>A	5.37:g.136314458C>T	ENSP00000378401:p.Arg402Gln	Somatic	194	2		WXS	Illumina HiSeq	Phase_I	101	62	NM_004598	0	0	49	267	218	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	C	9.870	1.198629	0.22121	.	.	ENSG00000152377	ENST00000394945;ENST00000282223	T;T	0.43294	0.95;0.95	5.16	0.792	0.18625	.	0.370343	0.27622	N	0.018560	T	0.18002	0.0432	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.13442	-1.0509	10	0.28530	T	0.3	.	5.6023	0.17361	0.0:0.4801:0.1521:0.3678	.	402	Q08629	TICN1_HUMAN	Q	402	ENSP00000378401:R402Q;ENSP00000282223:R402Q	ENSP00000282223:R402Q	R	-	2	0	SPOCK1	136342357	0.125000	0.22332	0.376000	0.26042	0.889000	0.51656	-0.031000	0.12287	0.202000	0.20498	0.557000	0.71058	CGG	.		0.517	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		T	136314458	C	T	136314458	3	4	63	1	0	0	0	0	1	0	0	0	15111	652	23	1	118	1	SPOCK1	5	136314458	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08	135220168	136314458	44600802	18	6139											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140257068	140257068	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cggtgctggtgtcgctggtgGagaacggccaggccccaaag	7	6	17	11	3	0	1	0	0	0	1	1	2	0	1	3	6	2	2	3	6	2	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr5:140257068G>C	ENST00000398631.2	+	1	2011	c.2011G>C	c.(2011-2013)Gag>Cag	p.E671Q	PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	671	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCGCTGGTGGAGAACGGCCA	0.667																																					p.E671Q	Pancreas(113;759 1672 13322 24104 50104)	.											.	.	0			c.G2011C						.						49	54	52					5																	140257068		2203	4299	6502	SO:0001583	missense	56137	exon1			CTGGTGGAGAACG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"Cadherins / Protocadherins : Clustered"	8666	other	complex locus constituent	"KIAA0345-like 2"	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.2011G>C	5.37:g.140257068G>C	ENSP00000381628:p.Glu671Gln	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_018903	0	0	8	8	0	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.342860	0.24339	.	.	ENSG00000251664	ENST00000398631	T	0.51574	0.7	4.81	3.94	0.45596	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.59362	0.2188	M	0.78456	2.415	0.09310	N	1	D;D	0.58620	0.982;0.983	P;P	0.53722	0.733;0.714	T	0.53208	-0.8471	9	0.87932	D	0	.	8.6707	0.34147	0.1783:0.0:0.8217:0.0	.	671;671	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	Q	671	ENSP00000381628:E671Q	ENSP00000381628:E671Q	E	+	1	0	PCDHA12	140237252	1.000000	0.71417	0.084000	0.20598	0.073000	0.16967	8.767000	0.91732	1.014000	0.39417	0.561000	0.74099	GAG	.		0.667	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		C	140257068	G	C	140257068	3	2	63	1	0	0	0	0	1	0	0	0	11548	1175	41	4	2013	4	PCDHA12	5	140257068	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	3942610	140257068	40658192	19	6140											
C7orf51	222950	broad.mit.edu;bcgsc.ca	37	chr7	100086267	100086267	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcccagcttcagccctccCgagccggagggacgggacgc	6	3	14	18	5	1	0	1	0	0	0	2	4	2	3	5	3	3	1	5	3	0	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr7:100086267C>T	ENST00000300179.2	+	4	1082	c.923C>T	c.(922-924)cCg>cTg	p.P308L	NYAP1_ENST00000454988.1_Missense_Mutation_p.P251L|NYAP1_ENST00000423930.1_Missense_Mutation_p.P308L	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	308	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												TCAGCCCTCCCGAGCCGGAGG	0.697																																					p.P308L													.	.	0			c.C923T						.						49	52	51					7																	100086267		2203	4295	6498	SO:0001583	missense	222950	exon4			CCCTCCCGAGCCG	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.923C>T	7.37:g.100086267C>T	ENSP00000300179:p.Pro308Leu	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	148	6	NM_173564	0	0	0	0	0	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	C	3.964	-0.009763	0.07727	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.41758	0.99;0.99;0.99	4.66	2.56	0.30785	.	0.313567	0.23234	N	0.050440	T	0.23210	0.0561	L	0.36672	1.1	0.46396	D	0.999022	P;P	0.40332	0.661;0.713	B;B	0.24541	0.054;0.047	T	0.07443	-1.0772	10	0.66056	D	0.02	-3.7091	5.9193	0.19073	0.2826:0.543:0.1744:0.0	.	251;308	C9JS30;Q6ZVC0	.;CG051_HUMAN	L	308;308;251	ENSP00000300179:P308L;ENSP00000411861:P308L;ENSP00000394424:P251L	ENSP00000300179:P308L	P	+	2	0	C7orf51	99924203	0.003000	0.15002	0.900000	0.35374	0.035000	0.12851	0.636000	0.24644	0.934000	0.37316	0.407000	0.27541	CCG	.		0.697	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100086267	C	T	100086267	3	4	63	1	0	0	0	0	1	0	0	0	2406	652	23	1	933	1	C7orf51	7	100086267	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		100086267	59052396	20	6141											
POP1	10940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	99142345	99142345	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agaaactcacatctggcacgCcaagcggtttcatatggtca	12	9	9	11	2	4	1	3	0	1	1	4	1	4	1	1	3	2	2	1	3	3	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr8:99142345C>T	ENST00000401707.2	+	5	707	c.626C>T	c.(625-627)gCc>gTc	p.A209V	POP1_ENST00000349693.3_Missense_Mutation_p.A209V	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	209					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)	p.A209V(1)		autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			ATCTGGCACGCCAAGCGGTTT	0.488																																					p.A209V		.											.	POP1-154	1	Substitution - Missense(1)	lung(1)	c.C626T						.						75	72	73					8																	99142345		2203	4300	6503	SO:0001583	missense	10940	exon5			GGCACGCCAAGCG	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.626C>T	8.37:g.99142345C>T	ENSP00000385787:p.Ala209Val	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	115	45	NM_001145860	0	0	3	5	2	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	C	36	5.647996	0.96714	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.61980	0.06;0.06	5.81	5.81	0.92471	Ribonuclease P/MRP, subunit POP1 (1);	0.139825	0.47093	D	0.000247	T	0.76905	0.4053	M	0.66378	2.025	0.80722	D	1	D	0.56287	0.975	D	0.65323	0.934	T	0.75004	-0.3470	9	.	.	.	-3.0517	17.8794	0.88835	0.0:1.0:0.0:0.0	.	209	Q99575	POP1_HUMAN	V	209	ENSP00000385787:A209V;ENSP00000339529:A209V	.	A	+	2	0	POP1	99211521	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.731000	0.84895	2.746000	0.94184	0.591000	0.81541	GCC	.		0.488	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		T	99142345	C	T	99142345	3	4	63	1	0	0	0	0	1	0	0	0	12277	739	26	2	640	2	POP1	8	99142345	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		99142345	47221677	21	6142											
PUF60	22827	broad.mit.edu	37	chr8	144898885	144898885	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcttggtagatgatgacGcggttcacggccccgaactt	7	12	11	11	4	2	3	1	2	1	1	3	4	2	3	2	3	1	2	2	3	2	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr8:144898885G>A	ENST00000526683.1	-	12	2040	c.1485C>T	c.(1483-1485)cgC>cgT	p.R495R	SCRIB_ENST00000320476.3_5'Flank|PUF60_ENST00000527197.1_Silent_p.R449R|PUF60_ENST00000349157.6_Silent_p.R478R|PUF60_ENST00000313352.7_Silent_p.R435R|PUF60_ENST00000456095.2_Silent_p.R466R|PUF60_ENST00000524570.1_5'Flank|PUF60_ENST00000453551.2_Silent_p.R452R|SCRIB_ENST00000377533.3_5'Flank|SCRIB_ENST00000356994.2_5'Flank	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	495	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.|RRM 3; atypical. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			AGATGATGACGCGGTTCACGG	0.522																																					p.R495R													.	.	0			c.C1485T						.						269	288	282					8																	144898885		2120	4219	6339	SO:0001819	synonymous_variant	22827	exon12			GATGACGCGGTTC	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.1485C>T	8.37:g.144898885G>A		Somatic	286	0		WXS	Illumina HiSeq	Phase_I	247	7	NM_078480	0	0	227	238	11	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Silent	SNP	ENST00000526683.1	37	CCDS47934.1																																																																																			.		0.522	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		A	144898885	G	A	144898885	2	1	63	1	0	0	0	0	0	0	0	1	12856	1074	38	1		1	PUF60	8	144898885	Silent	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	45756540	144898885	1465137	22	6143											
C9orf66	157983	hgsc.bcm.edu	37	chr9	215109	215109	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcttcgctgcaggggccGaggccggacgagtccattcg	6	6	17	12	5	0	0	0	0	0	0	3	4	1	2	3	5	2	3	3	5	0	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr9:215109G>T	ENST00000382387.2	-	1	784	c.288C>A	c.(286-288)ctC>ctA	p.L96L	DOCK8_ENST00000432829.2_Intron|DOCK8_ENST00000453981.1_Intron	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	96										central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		TGCAGGGGCCGAGGCCGGACG	0.751																																					p.L96L		.											.	C9orf66-514	0			c.C288A						.						2	2	2					9																	215109		1347	3061	4408	SO:0001819	synonymous_variant	157983	exon1			GGGGCCGAGGCCG	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.288C>A	9.37:g.215109G>T		Somatic	4	2		WXS	Illumina HiSeq	Phase_I	6	6	NM_152569	0	0	0	0	0	Q96NB0	Silent	SNP	ENST00000382387.2	37	CCDS6439.1																																																																																			.		0.751	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569		T	215109	G	T	215109	2	4	63	1	0	0	0	0	0	0	0	1	2496	1045	37	4		4	C9orf66	9	215109	Silent	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		215109	140998322	23	6144											
ST8SIA6	338596	broad.mit.edu	37	chr10	17401582	17401582	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatctgtgataatctgaaggTagtcgttctctgaataccta	11	15	8	7	1	3	3	0	3	3	0	5	3	3	3	1	1	1	2	1	1	7	6			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr10:17401582T>A	ENST00000377602.4	-	4	382	c.308A>T	c.(307-309)tAc>tTc	p.Y103F		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	103					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						AATCTGAAGGTAGTCGTTCTC	0.284																																					p.Y103F													.	ST8SIA6-91	0			c.A308T						.						47	46	47					10																	17401582		2203	4297	6500	SO:0001583	missense	338596	exon4			TGAAGGTAGTCGT		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.308A>T	10.37:g.17401582T>A	ENSP00000366827:p.Tyr103Phe	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_001004470	0	0	0	0	0	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.013208	0.54468	.	.	ENSG00000148488	ENST00000377602	T	0.22945	1.93	5.26	4.1	0.47936	.	0.365154	0.28538	N	0.014993	T	0.23249	0.0562	M	0.63843	1.955	0.38539	D	0.949177	B	0.15473	0.013	B	0.12837	0.008	T	0.08207	-1.0733	10	0.17369	T	0.5	-12.1516	8.235	0.31620	0.1766:0.0:0.0:0.8234	.	103	P61647	SIA8F_HUMAN	F	103	ENSP00000366827:Y103F	ENSP00000366827:Y103F	Y	-	2	0	ST8SIA6	17441588	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	2.641000	0.46587	0.989000	0.38761	0.454000	0.30748	TAC	.		0.284	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		A	17401582	T	A	17401582	3	1	63	1	0	0	0	0	1	0	0	0	15268	1638	57	5	908	5	ST8SIA6	10	17401582	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08		17401582	118133165	24	6145											
NELL2	4753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	45097517	45097517	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacaaggattaccttcacagTaggcattatcctctcgaaga	13	11	7	10	1	2	1	1	0	1	1	4	3	3	2	2	2	2	2	2	2	6	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr12:45097517T>C	ENST00000429094.2	-	12	1814	c.1310A>G	c.(1309-1311)tAc>tGc	p.Y437C	NELL2_ENST00000437801.2_Missense_Mutation_p.Y487C|NELL2_ENST00000549027.1_Missense_Mutation_p.Y436C|NELL2_ENST00000551601.1_Missense_Mutation_p.Y436C|NELL2_ENST00000452445.2_Missense_Mutation_p.Y437C|NELL2_ENST00000395487.2_Missense_Mutation_p.Y436C|NELL2_ENST00000333837.4_Missense_Mutation_p.Y460C	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	437	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		ACCTTCACAGTAGGCATTATC	0.403																																					p.Y487C		.											.	NELL2-517	0			c.A1460G						.						97	89	92					12																	45097517		2203	4300	6503	SO:0001583	missense	4753	exon13			TCACAGTAGGCAT	D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"nel (chicken)-like 2"			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.1310A>G	12.37:g.45097517T>C	ENSP00000390680:p.Tyr437Cys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	104	32	NM_001145107	0	0	0	0	0	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.07|19.07	3.756435|3.756435	0.69648|0.69648	.|.	.|.	ENSG00000184613|ENSG00000184613	ENST00000550313|ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684	.|D;D;T;D;D;D;D	.|0.95622	.|-1.56;-1.56;-0.63;-1.56;-1.56;-2.26;-3.76	5.6|5.6	5.6|5.6	0.85130|0.85130	.|Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97396|0.97396	0.9148|0.9148	M|M	0.77616|0.77616	2.38|2.38	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999;1.0;1.0	.|D;D;D;D;D;D	.|0.80764	.|0.956;0.984;0.986;0.994;0.968;0.993	D|D	0.97098|0.97098	0.9795|0.9795	5|10	.|0.36615	.|T	.|0.2	-30.8204|-30.8204	15.7975|15.7975	0.78423|0.78423	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|460;487;436;437;437;436	.|B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2	.|.;.;.;.;NELL2_HUMAN;.	A|C	181|436;437;436;437;436;460;487;436	.|ENSP00000378866:Y436C;ENSP00000390680:Y437C;ENSP00000449332:Y436C;ENSP00000394612:Y437C;ENSP00000447927:Y436C;ENSP00000327988:Y460C;ENSP00000416341:Y487C	.|ENSP00000327988:Y460C	T|Y	-|-	1|2	0|0	NELL2|NELL2	43383784|43383784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.089000|7.089000	0.76909|0.76909	2.135000|2.135000	0.66039|0.66039	0.528000|0.528000	0.53228|0.53228	ACT|TAC	.		0.403	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		C	45097517	T	C	45097517	3	2	63	1	0	0	0	0	1	0	0	0	10360	1638	57	3	1176	3	NELL2	12	45097517	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08		45097517	88754378	25	6146											
PABPC3	5042	ucsc.edu	37	chr13	25672007	25672007	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaagcaaaagcaaatgttAggtgaacggctctttcctct	14	10	8	9	1	2	1	0	1	2	0	3	1	3	1	1	2	3	4	1	2	7	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr13:25672007A>G	ENST00000281589.3	+	1	1708	c.1671A>G	c.(1669-1671)ttA>ttG	p.L557L		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	557	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AGCAAATGTTAGGTGAACGGC	0.433																																					p.L557L													.	PABPC3-72	0			c.A1671G						.						118	107	110					13																	25672007		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			AATGTTAGGTGAA	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1671A>G	13.37:g.25672007A>G		Somatic	156	0		WXS	Illumina HiSeq		90	1	NM_030979	0	0	0	0	0	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																			.		0.433	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		G	25672007	A	G	25672007	2	3	63	1	0	0	0	0	0	0	0	1	11391	417	15	3		3	PABPC3	13	25672007	Silent	SNP	A	TCGA-BQ-5879-01A-11D-1589-08		25672007	89497871	26	6147											
C14orf43	91748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	74196477	74196477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggatggggggcggcgtgTagggaggtagctcaaagctc	8	7	20	6	2	1	1	1	1	0	0	2	3	1	3	0	7	2	4	0	7	3	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr14:74196477T>C	ENST00000286523.5	-	4	2743	c.1961A>G	c.(1960-1962)tAc>tGc	p.Y654C	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.Y654C	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	654					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GGGCGGCGTGTAGGGAGGTAG	0.627																																					p.Y654C		.											.	.	0			c.A1961G						.						69	63	65					14																	74196477		2203	4300	6503	SO:0001583	missense	91748	exon4			GGCGTGTAGGGAG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1961A>G	14.37:g.74196477T>C	ENSP00000286523:p.Tyr654Cys	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	78	23	NM_194278	0	0	52	77	25	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429427	0.83776	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.51071	0.72;0.72;0.72;0.74	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000018	T	0.70404	0.3220	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.75608	-0.3259	10	0.87932	D	0	-12.2873	15.1835	0.72978	0.0:0.0:0.0:1.0	.	654;654	A0PJD3;Q6PJG2	.;CN043_HUMAN	C	654	ENSP00000377634:Y654C;ENSP00000286523:Y654C;ENSP00000407767:Y654C;ENSP00000402380:Y654C	ENSP00000286523:Y654C	Y	-	2	0	C14orf43	73266230	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	8.032000	0.88838	1.977000	0.57605	0.391000	0.25812	TAC	.		0.627	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		C	74196477	T	C	74196477	3	2	63	1	0	0	0	0	1	0	0	0	1778	1638	57	3	1212	3	C14orf43	14	74196477	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08		74196477	33153063	27	6148											
RYR3	6263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	33905537	33905537	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgagaacttcaacacagacgGgctcttcttccctgtgatga	10	11	9	11	1	3	4	1	3	2	2	4	5	4	4	1	1	2	1	1	1	2	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr15:33905537G>T	ENST00000389232.4	+	19	2388	c.2318G>T	c.(2317-2319)gGg>gTg	p.G773V	RYR3_ENST00000415757.3_Missense_Mutation_p.G773V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	773	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AACACAGACGGGCTCTTCTTC	0.552																																					p.G773V		.											.	RYR3-520	0			c.G2318T						.						50	54	53					15																	33905537		2107	4260	6367	SO:0001583	missense	6263	exon19			CAGACGGGCTCTT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2318G>T	15.37:g.33905537G>T	ENSP00000373884:p.Gly773Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	32	18	NM_001243996	0	0	0	0	0	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821891	0.90873	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.70869	-0.52;-0.52	5.4	5.4	0.78164	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.80944	0.4721	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.96	T	0.79305	-0.1858	10	0.45353	T	0.12	.	19.4159	0.94700	0.0:0.0:1.0:0.0	.	773;773	Q15413-2;Q15413	.;RYR3_HUMAN	V	773	ENSP00000373884:G773V;ENSP00000399610:G773V	ENSP00000354735:G773V	G	+	2	0	RYR3	31692829	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.715000	0.84713	2.821000	0.97095	0.650000	0.86243	GGG	.		0.552	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33905537	G	T	33905537	3	4	63	1	0	0	0	0	1	0	0	0	13802	1232	43	4	2392	4	RYR3	15	33905537	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		33905537	68625855	28	6149											
SF3B3	23450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	70595650	70595650	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttttgcctcggaacagtgtCccgagggcattgtggccatc	6	11	13	11	2	0	0	0	0	0	0	3	2	1	1	3	3	2	2	3	3	1	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr16:70595650C>T	ENST00000302516.5	+	17	2462	c.2251C>T	c.(2251-2253)Ccc>Tcc	p.P751S		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	751					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				GGAACAGTGTCCCGAGGGCAT	0.532																																					p.P751S		.											.	SF3B3-91	0			c.C2251T						.						151	123	133					16																	70595650		2198	4300	6498	SO:0001583	missense	23450	exon17			CAGTGTCCCGAGG	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2251C>T	16.37:g.70595650C>T	ENSP00000305790:p.Pro751Ser	Somatic	157	1		WXS	Illumina HiSeq	Phase_I	155	60	NM_012426	0	0	199	302	103	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	37	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	C	19.63	3.863326	0.71949	.	.	ENSG00000189091	ENST00000302516	T	0.35605	1.3	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.39253	0.1071	L	0.49256	1.55	0.80722	D	1	B	0.23490	0.086	B	0.23419	0.046	T	0.11767	-1.0574	10	0.48119	T	0.1	-16.0376	20.2982	0.98569	0.0:1.0:0.0:0.0	.	751	Q15393	SF3B3_HUMAN	S	751	ENSP00000305790:P751S	ENSP00000305790:P751S	P	+	1	0	SF3B3	69153151	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.729000	0.84864	2.873000	0.98535	0.563000	0.77884	CCC	.		0.532	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		T	70595650	C	T	70595650	3	4	63	1	0	0	0	0	1	0	0	0	14184	855	30	2	2313	2	SF3B3	16	70595650	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		70595650	19759103	29	6150											
NUP88	4927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	5314095	5314095	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtgggtgtctgcggctcaCgtagtgagtaaattctagca	9	12	13	7	2	3	1	1	1	2	0	3	1	3	1	0	2	2	4	0	2	5	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:5314095C>T	ENST00000573584.1	-	4	1117	c.608G>A	c.(607-609)cGt>cAt	p.R203H		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	203					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CTGCGGCTCACGTAGTGAGTA	0.388																																					p.R203H		.											.	NUP88-204	0			c.G608A						.						107	114	112					17																	5314095		2203	4300	6503	SO:0001583	missense	4927	exon4			GGCTCACGTAGTG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.608G>A	17.37:g.5314095C>T	ENSP00000458954:p.Arg203His	Somatic	254	0		WXS	Illumina HiSeq	Phase_I	240	84	NM_002532	0	0	23	39	16	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	C	11.84	1.757883	0.31137	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	5.47	3.46	0.39613	.	0.364516	0.30126	N	0.010346	T	0.36936	0.0985	L	0.44542	1.39	0.28618	N	0.908315	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.002;0.002;0.003	T	0.28776	-1.0033	9	0.45353	T	0.12	-6.739	8.1438	0.31100	0.0:0.6984:0.0:0.3016	.	203;72;203	B7Z5I6;B4DP20;Q99567	.;.;NUP88_HUMAN	H	203;72	.	ENSP00000225696:R203H	R	-	2	0	NUP88	5254819	0.997000	0.39634	0.947000	0.38551	0.620000	0.37586	1.229000	0.32600	0.794000	0.33899	0.561000	0.74099	CGT	.		0.388	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		T	5314095	C	T	5314095	3	4	63	1	0	0	0	0	1	0	0	0	10797	536	19	1	1673	1	NUP88	17	5314095	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		5314095	75881115	30	6151											
MYH3	4621	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10554908	10554908	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcgctttttgcctcggtaGccttccaccacctcggggtt	3	13	11	14	3	0	0	0	0	0	0	3	0	1	0	5	4	2	3	5	4	1	5	rs577513442		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:10554908G>A	ENST00000583535.1	-	5	513	c.426C>T	c.(424-426)ggC>ggT	p.G142G	MYH3_ENST00000226209.7_Silent_p.G142G	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	142	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TGCCTCGGTAGCCTTCCACCA	0.557													G|||	1	0.000199681	0	0	5008	,	,		14358	0.001		0	False		,,,				2504	0				p.G142G		.											.	MYH3-95	0			c.C426T						.						137	137	137					17																	10554908		2203	4300	6503	SO:0001819	synonymous_variant	4621	exon5			TCGGTAGCCTTCC		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.426C>T	17.37:g.10554908G>A		Somatic	243	0		WXS	Illumina HiSeq	Phase_I	232	68	NM_002470	0	0	0	0	0	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																			.		0.557	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10554908	G	A	10554908	2	1	63	1	0	0	0	0	0	0	0	1	10061	958	34	2		2	MYH3	17	10554908	Silent	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	5240813	10554908	70640302	31	6152											
DCAF7	10238	broad.mit.edu;bcgsc.ca	37	chr17	61628109	61628109	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacagtctacgcgatgaactGgagtgtgcggcccgataagc	10	7	14	10	4	1	1	0	1	1	0	1	5	1	2	1	2	4	0	1	2	3	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:61628109G>T	ENST00000310827.4	+	1	288	c.71G>T	c.(70-72)tGg>tTg	p.W24L	DCAF7_ENST00000577702.1_3'UTR|DCAF7_ENST00000415273.2_Missense_Mutation_p.W24L|DCAF7_ENST00000431926.1_Missense_Mutation_p.W24L	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	24					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						GCGATGAACTGGAGTGTGCGG	0.642																																					p.W24L													.	DCAF7-91	0			c.G71T						.						62	69	67					17																	61628109		1996	4163	6159	SO:0001583	missense	10238	exon1			TGAACTGGAGTGT	U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30915	protein-coding gene	gene with protein product	"seven-WD-repeat protein of the AN11 family-1", "human anthocyanin"	605973	"WD repeat domain 68"	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.71G>T	17.37:g.61628109G>T	ENSP00000308344:p.Trp24Leu	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	47	4	NM_005828	0	0	108	108	0	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	ENST00000310827.4	37		.	.	.	.	.	.	.	.	.	.	G	26.9	4.783717	0.90282	.	.	ENSG00000136485	ENST00000310827;ENST00000431926;ENST00000415273	T;T;T	0.64085	-0.06;-0.08;1.51	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71056	0.3295	M	0.85710	2.77	0.80722	D	1	P;B	0.39094	0.659;0.416	B;B	0.39706	0.307;0.179	T	0.75396	-0.3332	10	0.54805	T	0.06	-17.3123	19.6415	0.95760	0.0:0.0:1.0:0.0	.	24;24	B4E039;P61962	.;DCAF7_HUMAN	L	24	ENSP00000308344:W24L;ENSP00000402312:W24L;ENSP00000403920:W24L	ENSP00000308344:W24L	W	+	2	0	DCAF7	58981841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.115000	0.94336	2.651000	0.90000	0.561000	0.74099	TGG	.		0.642	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828		T	61628109	G	T	61628109	3	4	63	1	0	0	0	0	1	0	0	0	4281	1357	47	4	73	4	DCAF7	17	61628109	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	51073201	61628109	19567101	32	6153											
GH1	2688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61995168	61995168	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcctttaggaggtcataGacgttgctgtcagaggcgcc	8	10	14	9	2	2	2	2	0	0	2	3	3	3	3	2	4	1	2	2	4	2	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:61995168G>T	ENST00000323322.5	-	4	450	c.408C>A	c.(406-408)gtC>gtA	p.V136V	GH1_ENST00000458650.2_Silent_p.V121V|GH1_ENST00000342364.4_Intron|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Silent_p.V96V	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	136			V -> I (in dbSNP:rs5388). {ECO:0000269|PubMed:12655557, ECO:0000269|PubMed:15001589}.		bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						GGAGGTCATAGACGTTGCTGT	0.607																																					p.V136V		.											.	GH1-522	0			c.C408A						.						68	68	68					17																	61995168		2203	4300	6503	SO:0001819	synonymous_variant	2688	exon4			GTCATAGACGTTG	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"Endogenous ligands"	4261	protein-coding gene	gene with protein product	"pituitary growth hormone", "somatotropin"	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.408C>A	17.37:g.61995168G>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	131	57	NM_000515	0	0	0	0	0	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Silent	SNP	ENST00000323322.5	37	CCDS11653.1																																																																																			.		0.607	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		T	61995168	G	T	61995168	2	4	63	1	0	0	0	0	0	0	0	1	6387	929	33	4		4	GH1	17	61995168	Silent	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	367059	61995168	19200042	33	6154											
LSM14A	26065	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	34710448	34710449	+	Frame_Shift_Del	DEL	AG	AG	-																															tcaacaaggaagagattgacAgagagtttcataataaactt																								rs372366966		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr19:34710448_34710449delAG	ENST00000433627.5	+	7	1009_1010	c.934_935delAG	c.(934-936)agafs	p.R312fs	LSM14A_ENST00000540746.2_Frame_Shift_Del_p.R271fs|LSM14A_ENST00000544216.3_Frame_Shift_Del_p.R312fs	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	312	DFDF. {ECO:0000255|PROSITE- ProRule:PRU00845}.				cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.R312K(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					AGAGATTGACAGAGAGTTTCAT	0.327																																					p.312_312del		.											.	LSM14A-91	1	Substitution - Missense(1)	large_intestine(1)	c.934_935del						.																																			SO:0001589	frameshift_variant	26065	exon7			.	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.934_935delAG	19.37:g.34710452_34710453delAG	ENSP00000413964:p.Arg312fs	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	142	59	NM_001114093	0	0	0	0	0	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Frame_Shift_Del	DEL	ENST00000433627.5	37	CCDS46040.1																																																																																			.		0.327	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		-	34710449	AG	-	34710448	7	5	63	1	0	1	0	1	0	0	0	0	9079	180	7	0	960	0	LSM14A	19	34710448	Frame_Shift_Del	DEL	AG	TCGA-BQ-5879-01A-11D-1589-08		34710448	24418535	34	6155											
RYR1	6261	broad.mit.edu;bcgsc.ca	37	chr19	38948197	38948197	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgtacgctccaaccaaGatcttattactgagaacttg	11	12	8	10	1	1	2	0	1	1	2	2	3	2	2	2	1	4	3	2	1	6	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr19:38948197G>T	ENST00000359596.3	+	17	1852	c.1852G>T	c.(1852-1854)Gat>Tat	p.D618Y	RYR1_ENST00000355481.4_Missense_Mutation_p.D618Y|RYR1_ENST00000360985.3_Missense_Mutation_p.D618Y			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	618	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTCCAACCAAGATCTTATTAC	0.522																																					p.D618Y													.	RYR1-100	0			c.G1852T						.						341	275	297					19																	38948197		2203	4300	6503	SO:0001583	missense	6261	exon17			AACCAAGATCTTA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1852G>T	19.37:g.38948197G>T	ENSP00000352608:p.Asp618Tyr	Somatic	278	0		WXS	Illumina HiSeq	Phase_I	291	10	NM_001042723	0	0	0	0	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521791	0.44866	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97089	-4.24;-4.24;-4.24	3.76	3.76	0.43208	Intracellular calcium-release channel (1);B30.2/SPRY domain (1);	0.075267	0.49916	U	0.000125	D	0.95912	0.8669	L	0.36672	1.1	0.42899	D	0.99422	D;D	0.64830	0.994;0.98	P;P	0.61722	0.862;0.893	D	0.94764	0.7939	10	0.87932	D	0	.	5.1222	0.14865	0.2768:0.0:0.7232:0.0	.	618;618	P21817-2;P21817	.;RYR1_HUMAN	Y	618	ENSP00000352608:D618Y;ENSP00000347667:D618Y;ENSP00000354254:D618Y	ENSP00000347667:D618Y	D	+	1	0	RYR1	43640037	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.680000	0.54641	2.113000	0.64589	0.555000	0.69702	GAT	.		0.522	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38948197	G	T	38948197	3	4	63	1	0	0	0	0	1	0	0	0	13800	942	33	4	1918	4	RYR1	19	38948197	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	4237749	38948197	20180786	35	6156											
ZNF175	7728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52091521	52091521	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagaaaccctatgaatgccTtgactgtgggaaatcgttca	13	10	10	8	1	1	3	1	2	0	1	2	5	1	4	2	1	2	1	2	1	4	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr19:52091521T>C	ENST00000262259.2	+	5	2295	c.1937T>C	c.(1936-1938)cTt>cCt	p.L646P	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	646					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TATGAATGCCTTGACTGTGGG	0.443																																					p.L646P		.											.	ZNF175-90	0			c.T1937C						.						86	84	85					19																	52091521		2203	4300	6503	SO:0001583	missense	7728	exon5			AATGCCTTGACTG	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"Zinc fingers, C2H2-type", "-"	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.1937T>C	19.37:g.52091521T>C	ENSP00000262259:p.Leu646Pro	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	156	50	NM_007147	0	0	3	5	2	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	T	1.034	-0.680825	0.03353	.	.	ENSG00000105497	ENST00000262259	T	0.10763	2.84	2.14	-2.05	0.07321	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.00707	-1.245	0.09310	N	1	B	0.28324	0.207	B	0.29663	0.105	T	0.37009	-0.9724	9	0.48119	T	0.1	.	0.6964	0.00900	0.1625:0.18:0.2558:0.4017	.	646	Q9Y473	ZN175_HUMAN	P	646	ENSP00000262259:L646P	ENSP00000262259:L646P	L	+	2	0	ZNF175	56783333	0.000000	0.05858	0.066000	0.19879	0.247000	0.25773	-3.014000	0.00646	-0.395000	0.07715	-1.142000	0.01873	CTT	.		0.443	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		C	52091521	T	C	52091521	3	2	63	1	0	0	0	0	1	0	0	0	17777	1609	56	3	1951	3	ZNF175	19	52091521	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08	13143324	52091521	7037462	36	6157											
PTPRA	5786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	2998529	2998529	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaaacacagccaccatcgtCatggttaccaacctgaagga	15	6	7	13	1	1	1	1	1	0	0	2	2	1	2	4	2	4	1	4	2	5	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr20:2998529C>T	ENST00000216877.6	+	12	1384	c.984C>T	c.(982-984)gtC>gtT	p.V328V	PTPRA_ENST00000399903.2_Silent_p.V337V|PTPRA_ENST00000358719.4_Silent_p.V193V|PTPRA_ENST00000318266.5_Silent_p.V328V|PTPRA_ENST00000356147.3_Silent_p.V328V|PTPRA_ENST00000380393.3_Silent_p.V337V|PTPRA_ENST00000425918.2_Silent_p.V348V	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	337	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CCACCATCGTCATGGTTACCA	0.433																																					p.V337V		.											.	PTPRA-227	0			c.C1011T						.						114	105	108					20																	2998529		2203	4300	6503	SO:0001819	synonymous_variant	5786	exon17			CATCGTCATGGTT		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.984C>T	20.37:g.2998529C>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	57	27	NM_002836	0	0	88	181	93	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																			.		0.433	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			T	2998529	C	T	2998529	2	4	63	1	0	0	0	0	0	0	0	1	12827	813	29	2		2	PTPRA	20	2998529	Silent	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		2998529	60026991	37	6158											
ASXL1	171023	bcgsc.ca	37	chr20	31024236	31024236	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttctcttcctttagttgtGaagatcagaaggaagtccgt	10	14	10	7	1	2	3	1	1	1	2	5	4	4	4	2	1	0	2	2	1	4	5	rs372409311		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr20:31024236G>T	ENST00000375687.4	+	13	4145	c.3721G>T	c.(3721-3723)Gaa>Taa	p.E1241*	ASXL1_ENST00000306058.5_Nonsense_Mutation_p.E1236*	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1241					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CTTTAGTTGTGAAGATCAGAA	0.453			"F, N, Mis"		"MDS, CMML"																																p.E1241X				Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1-2057	0			c.G3721T						.						89	89	89					20																	31024236		2203	4300	6503	SO:0001587	stop_gained	171023	exon12			AGTTGTGAAGATC	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"additional sex combs like 1 (Drosophila)"			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3721G>T	20.37:g.31024236G>T	ENSP00000364839:p.Glu1241*	Somatic	109	0		WXS	Illumina HiSeq	Phase_1	137	6	NM_015338	0	0	77	78	1	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Nonsense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	G	41	9.093882	0.99064	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	.	.	.	4.56	4.56	0.56223	.	0.356029	0.29775	N	0.011234	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-3.7842	11.2047	0.48762	0.0858:0.0:0.9142:0.0	.	.	.	.	X	1241;1241;1241;1162;1236	.	ENSP00000305119:E1236X	E	+	1	0	ASXL1	30487897	1.000000	0.71417	0.798000	0.32154	0.307000	0.27823	3.450000	0.52957	2.826000	0.97356	0.561000	0.74099	GAA	.		0.453	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		T	31024236	G	T	31024236	4	4	63	1	0	0	0	0	0	1	0	0	1067	1291	45	4	3777	4	ASXL1	20	31024236	Nonsense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	28025707	31024236	32001284	38	6159											
R3HDML	140902	hgsc.bcm.edu	37	chr20	42969909	42969909	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcacatgggccttcacAgctgatgagatacgtgggcc	8	8	14	11	1	1	2	1	2	0	1	1	3	1	2	2	3	2	2	2	3	1	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr20:42969909A>G	ENST00000217043.2	+	2	507	c.335A>G	c.(334-336)cAg>cGg	p.Q112R		NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	112	SCP.					extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			GGGCCTTCACAGCTGATGAGA	0.557																																					p.Q112R		.											.	R3HDML-90	0			c.A335G						.						69	65	66					20																	42969909		2203	4300	6503	SO:0001583	missense	140902	exon2			CTTCACAGCTGAT	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"R3H domain (binds single-stranded nucleic acids) containing-like"				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.335A>G	20.37:g.42969909A>G	ENSP00000217043:p.Gln112Arg	Somatic	85	1		WXS	Illumina HiSeq	Phase_I	76	4	NM_178491	0	0	0	0	0		Missense_Mutation	SNP	ENST00000217043.2	37	CCDS13329.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610007	0.46527	.	.	ENSG00000101074	ENST00000217043	T	0.09073	3.02	5.71	3.38	0.38709	CAP domain (3);	0.127041	0.53938	D	0.000046	T	0.08133	0.0203	N	0.21194	0.64	0.41211	D	0.986442	P	0.47191	0.891	P	0.48598	0.583	T	0.29971	-0.9994	10	0.10636	T	0.68	.	12.3952	0.55380	0.7421:0.2579:0.0:0.0	.	112	Q9H3Y0	CRSPL_HUMAN	R	112	ENSP00000217043:Q112R	ENSP00000217043:Q112R	Q	+	2	0	R3HDML	42403323	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.367000	0.66127	0.389000	0.25086	0.533000	0.62120	CAG	.		0.557	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491		G	42969909	A	G	42969909	3	3	63	1	0	0	0	0	1	0	0	0	12921	188	7	3	341	3	R3HDML	20	42969909	Missense_Mutation	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	11945673	42969909	20055611	39	6160											
SCO2	9997	broad.mit.edu	37	chr22	50962803	50962803	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcttgagctgagagagcCtgtgccaagctgtggggctc	7	8	17	9	0	0	3	0	2	0	1	1	5	0	3	2	3	4	4	2	3	1	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr22:50962803C>G	ENST00000543927.1	-	2	244	c.38G>C	c.(37-39)aGg>aCg	p.R13T	SCO2_ENST00000395693.3_Missense_Mutation_p.R13T|CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000252785.3_Missense_Mutation_p.R13T|SCO2_ENST00000535425.1_Missense_Mutation_p.R13T	NM_001169109.1	NP_001162580.1	O43819	SCO2_HUMAN	SCO2 cytochrome c oxidase assembly protein	13					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|eye development (GO:0001654)|in utero embryonic development (GO:0001701)|muscle system process (GO:0003012)|oxidation-reduction process (GO:0055114)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			endometrium(1)|lung(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTGAGAGAGCCTGTGCCAAGC	0.627																																					p.R13T													.	SCO2-226	0			c.G38C						.						20	22	22					22																	50962803		2199	4291	6490	SO:0001583	missense	9997	exon2			GAGAGCCTGTGCC	AL021683	CCDS14095.1	22q13.33	2014-01-30	2012-10-15		ENSG00000130489	ENSG00000130489		"Mitochondrial respiratory chain complex assembly factors"	10604	protein-coding gene	gene with protein product		604272	"SCO (cytochrome oxidase deficient, yeast) homolog 2", "SCO cytochrome oxidase deficient homolog 2 (yeast)", "myopia 6"	MYP6		10218584, 16091356, 23643385	Standard	NM_005138		Approved	SCO1L	uc003bma.3	O43819	OTTHUMG00000150251	ENST00000543927.1:c.38G>C	22.37:g.50962803C>G	ENSP00000444433:p.Arg13Thr	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	66	3	NM_001169111	0	0	67	69	2	Q3T1B5|Q9UK87	Missense_Mutation	SNP	ENST00000543927.1	37	CCDS14095.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.277703	0.40294	.	.	ENSG00000130489	ENST00000395693;ENST00000543927;ENST00000535425;ENST00000252785;ENST00000439934;ENST00000423348	D;D;D;D;T;T	0.84589	-1.87;-1.87;-1.87;-1.87;-0.76;-0.76	3.58	2.55	0.30701	.	0.842278	0.09589	N	0.781814	T	0.73024	0.3534	L	0.27053	0.805	0.27181	N	0.960674	P	0.38195	0.622	B	0.36666	0.23	T	0.60772	-0.7197	10	0.17832	T	0.49	-1.3951	6.2448	0.20811	0.0:0.8594:0.0:0.1406	.	13	O43819	SCO2_HUMAN	T	13	ENSP00000379046:R13T;ENSP00000444433:R13T;ENSP00000444242:R13T;ENSP00000252785:R13T;ENSP00000415642:R13T;ENSP00000403570:R13T	ENSP00000252785:R13T	R	-	2	0	SCO2	49309669	0.005000	0.15991	0.532000	0.27989	0.049000	0.14656	1.115000	0.31209	1.062000	0.40625	0.655000	0.94253	AGG	.		0.627	SCO2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317091.1	NM_005138		G	50962803	C	G	50962803	3	3	63	1	0	0	0	0	1	0	0	0	13964	681	24	4	766	4	SCO2	22	50962803	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		50962803	341763	40	6161											
SSX1	6756	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	48123289	48123289	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagcatctggcccacaaaacGatgggaaacaactgcacccc	15	4	8	14	1	1	0	0	0	1	0	1	2	1	1	3	2	5	2	3	2	5	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chrX:48123289G>A	ENST00000376919.3	+	6	539	c.403G>A	c.(403-405)Gat>Aat	p.D135N		NM_001278691.1|NM_005635.2	NP_001265620.1|NP_005626.1	Q16384	SSX1_HUMAN	synovial sarcoma, X breakpoint 1	135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		SS18/SSX1(1169)|SS18L1/SSX1(2)	endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						CCCACAAAACGATGGGAAACA	0.423			T	SS18	synovial sarcoma																																p.D135N	Esophageal Squamous(175;994 1982 2214 6527 18857)	.		Dom	yes		X	Xp11.23-p11.22	6756	"synovial sarcoma, X breakpoint 1"		M	.	SSX1-522	0			c.G403A						.						153	141	145					X																	48123289		2203	4299	6502	SO:0001583	missense	6756	exon6			CAAAACGATGGGA	BC001003	CCDS14290.1	Xp11.23	2009-03-12			ENSG00000126752	ENSG00000126752			11335	protein-coding gene	gene with protein product	"cancer/testis antigen family 5, member 1"	312820				7655467	Standard	NM_005635		Approved	CT5.1	uc004djb.1	Q16384	OTTHUMG00000021488	ENST00000376919.3:c.403G>A	X.37:g.48123289G>A	ENSP00000366118:p.Asp135Asn	Somatic	334	0		WXS	Illumina HiSeq	Phase_I	345	19	NM_005635	0	0	0	0	0	A3KN76|Q08AJ2|Q5JQ64	Missense_Mutation	SNP	ENST00000376919.3	37	CCDS14290.1	.	.	.	.	.	.	.	.	.	.	N	0.021	-1.430282	0.01117	.	.	ENSG00000126752	ENST00000376919	T	0.07327	3.2	2.1	1.21	0.21127	.	1.694760	0.03640	N	0.239416	T	0.04318	0.0119	L	0.38175	1.15	0.09310	N	1	P	0.47545	0.897	B	0.29524	0.103	T	0.32903	-0.9889	10	0.02654	T	1	.	4.011	0.09623	0.2273:0.0:0.7727:0.0	.	135	Q16384	SSX1_HUMAN	N	135	ENSP00000366118:D135N	ENSP00000366118:D135N	D	+	1	0	SSX1	48008233	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.159000	0.10056	0.336000	0.23639	0.380000	0.24917	GAT	.		0.423	SSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056485.1	NM_005635		A	48123289	G	A	48123289	3	1	63	1	0	0	0	0	1	0	0	0	15235	1058	37	1	421	1	SSX1	23	48123289	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		48123289	107147271	41	6162											
RGAG1	57529	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	109694572	109694572	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagacaccgaagcaatgTccaaagtgctaatgactgct	15	8	9	9	1	0	3	0	2	0	1	1	4	1	3	2	0	3	3	2	0	5	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chrX:109694572T>C	ENST00000465301.2	+	3	973	c.727T>C	c.(727-729)Tcc>Ccc	p.S243P	RGAG1_ENST00000540313.1_Missense_Mutation_p.S243P	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	243										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CGAAGCAATGTCCAAAGTGCT	0.478																																					p.S243P		.											.	RGAG1-132	0			c.T727C						.						117	106	110					X																	109694572		2203	4300	6503	SO:0001583	missense	57529	exon3			GCAATGTCCAAAG	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.727T>C	X.37:g.109694572T>C	ENSP00000419786:p.Ser243Pro	Somatic	195	2		WXS	Illumina HiSeq	Phase_I	180	55	NM_020769	0	0	0	0	0	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142250	0.57044	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.59772	0.24;0.24	4.02	4.02	0.46733	.	0.000000	0.35805	N	0.002961	T	0.55257	0.1909	N	0.19112	0.55	0.37148	D	0.902013	D	0.89917	1.0	D	0.85130	0.997	T	0.59026	-0.7531	9	.	.	.	-7.523	5.2635	0.15586	0.0:0.127:0.0:0.873	.	243	Q8NET4	RGAG1_HUMAN	P	243	ENSP00000419786:S243P;ENSP00000441452:S243P	.	S	+	1	0	RGAG1	109581228	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.808000	0.38912	1.792000	0.52537	0.486000	0.48141	TCC	.		0.478	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		C	109694572	T	C	109694572	3	2	63	1	0	0	0	0	1	0	0	0	13306	1667	58	3	729	3	RGAG1	23	109694572	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08	61571283	109694572	45575988	42	6163											
USP26	83844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	132160221	132160221	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgcctgggctgctggcAggtttacctccagctttgtg	3	13	15	10	0	0	0	0	0	0	0	1	0	1	0	3	4	4	5	3	4	1	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chrX:132160221A>C	ENST00000511190.1	-	6	2497	c.2028T>G	c.(2026-2028)ccT>ccG	p.P676P	USP26_ENST00000370832.1_Silent_p.P676P|USP26_ENST00000406273.1_Silent_p.P676P	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	676	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GGCTGCTGGCAGGTTTACCTC	0.428																																					p.P676P	NSCLC(104;342 1621 36940 47097 52632)	.											.	USP26-661	0			c.T2028G						.						83	79	81					X																	132160221		2203	4299	6502	SO:0001819	synonymous_variant	83844	exon1			GCTGGCAGGTTTA	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"Ubiquitin-specific peptidases"	13485	protein-coding gene	gene with protein product		300309	"ubiquitin specific protease 26"			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2028T>G	X.37:g.132160221A>C		Somatic	215	0		WXS	Illumina HiSeq	Phase_I	196	41	NM_031907	0	0	0	0	0	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	37	CCDS14635.1																																																																																			.		0.428	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		C	132160221	A	C	132160221	2	2	63	1	0	0	0	0	0	0	0	1	17090	175	7	5		5	USP26	23	132160221	Silent	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	22465649	132160221	23110339	43	6164											
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16952767	16952767	+	3'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcctcaacatcttagcCtttgcggcgctgtactacaa	8	13	6	14	2	3	0	1	0	2	0	4	0	4	0	2	1	5	2	2	1	5	5	rs373089425		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chrY:16952767C>T	ENST00000476359.1	+	0	2621							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.A692A(1)		large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						ACATCTTAGCCTTTGCGGCGC	0.502																																					p.A692A		.											.	.	1	Substitution - coding silent(1)	prostate(1)	c.C2076T						.	C	,	0,571		0,571	53	72	66		1572,2076	-3.8	0	Y		66	1,1871		1,1871	no	coding-synonymous,coding-synonymous	NLGN4Y	NM_001206850.1,NM_014893.4	,	1,2442	T,C		0.0534,0.0,0.0409	,	524/649,692/817	16952767	1,2442	974	2291	3265	SO:0001624	3_prime_UTR_variant	22829	exon6			CTTAGCCTTTGCG		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*2618C>T	Y.37:g.16952767C>T		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	5	4	NM_014893	0	0	0	0	0	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Silent	SNP	ENST00000476359.1	37																																																																																				.		0.502	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		T	16952767	C	T	16952767	1	4	63	0	1	0	0	0	0	0	0	0	10491	668	24	2		2	NLGN4Y	24	16952767	3'UTR	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		16952767	42420799	44	6165											
AGRN	375790	hgsc.bcm.edu	37	chr1	984366	984366	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgctggagcctcaggggctgCtgctgtacaatggcaacgcc	7	7	14	13	2	1	0	1	0	0	0	1	1	1	1	2	4	5	6	2	4	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:984366C>T	ENST00000379370.2	+	24	4275	c.4225C>T	c.(4225-4227)Ctg>Ttg	p.L1409L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1409	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TCAGGGGCTGCTGCTGTACAA	0.706																																					p.L1409L		.											.	AGRN-136	0			c.C4225T						.						8	8	8					1																	984366		2162	4262	6424	SO:0001819	synonymous_variant	375790	exon24			GGGCTGCTGCTGT	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"Proteoglycans / Extracellular Matrix : Other"	329	protein-coding gene	gene with protein product	"agrin proteoglycan"	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.4225C>T	1.37:g.984366C>T		Somatic	6	2		WXS	Illumina HiSeq	Phase_I	12	11	NM_198576	0	0	19	36	17	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			.		0.706	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		T	984366	C	T	984366	2	4	64	1	0	0	0	0	0	0	0	1	397	796	28	2		2	AGRN	1	984366	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		984366	248266255	1	6166											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27106982	27106982	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcggcaacctcctgggctTcctagaggacagccttgccg	7	9	11	14	2	0	1	0	0	0	1	3	2	2	2	5	3	3	2	5	3	3	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:27106982T>C	ENST00000324856.7	+	20	6964	c.6593T>C	c.(6592-6594)tTc>tCc	p.F2198S	ARID1A_ENST00000540690.1_Missense_Mutation_p.F526S|ARID1A_ENST00000457599.2_Missense_Mutation_p.F1981S|ARID1A_ENST00000374152.2_Missense_Mutation_p.F1815S	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2198					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CTCCTGGGCTTCCTAGAGGAC	0.607			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.F2198S		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.T6593C						.						72	69	70					1																	27106982		2203	4300	6503	SO:0001583	missense	8289	exon20			TGGGCTTCCTAGA	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6593T>C	1.37:g.27106982T>C	ENSP00000320485:p.Phe2198Ser	Somatic	96	1		WXS	Illumina HiSeq	Phase_I	108	14	NM_006015	0	0	15	18	3	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149005	0.57151	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.01	5.01	0.66863	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	T	0.77464	-0.2578	10	0.87932	D	0	-7.6982	15.1629	0.72798	0.0:0.0:0.0:1.0	.	1815;2198;1981	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	S	2198;1981;1815;526	ENSP00000320485:F2198S;ENSP00000387636:F1981S;ENSP00000363267:F1815S;ENSP00000442437:F526S	ENSP00000320485:F2198S	F	+	2	0	ARID1A	26979569	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.627000	0.83176	2.236000	0.73375	0.482000	0.46254	TTC	.		0.607	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27106982	T	C	27106982	3	2	64	1	0	0	0	0	1	0	0	0	913	1783	62	3	6671	3	ARID1A	1	27106982	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	26122616	27106982	222143639	2	6167											
MACF1	23499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	39775962	39775962	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatcagattatgaagaacCttcaggcccactatgaagac	14	8	8	11	0	2	5	2	2	0	3	2	5	2	5	3	1	1	0	3	1	5	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:39775962C>A	ENST00000372915.3	+	24	3064	c.2977C>A	c.(2977-2979)Ctt>Att	p.L993I	MACF1_ENST00000545844.1_Missense_Mutation_p.L993I|MACF1_ENST00000567887.1_Missense_Mutation_p.L1025I|MACF1_ENST00000564288.1_Missense_Mutation_p.L988I|MACF1_ENST00000317713.7_Missense_Mutation_p.L993I|MACF1_ENST00000361689.2_Missense_Mutation_p.L993I|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000539005.1_Missense_Mutation_p.L993I			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	993					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TATGAAGAACCTTCAGGCCCA	0.463																																					p.L993I		.											.	MACF1-165	0			c.C2977A						.						114	94	101					1																	39775962		2203	4300	6503	SO:0001583	missense	23499	exon26			AAGAACCTTCAGG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.2977C>A	1.37:g.39775962C>A	ENSP00000362006:p.Leu993Ile	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	53	12	NM_012090	0	0	1	1	0	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.6|20.6	4.013512|4.013512	0.75161|0.75161	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262|ENST00000372925	D;D;D;D;D;D;D|.	0.95035|.	-1.71;-1.73;-1.71;-1.74;-1.62;-3.08;-3.59|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	.|.	.|.	.|.	.|.	T|T	0.77987|0.77987	0.4213|0.4213	M|M	0.87456|0.87456	2.885|2.885	0.80722|0.80722	D|D	1|1	P;D;D|.	0.89917|.	0.524;0.997;1.0|.	B;P;D|.	0.78314|.	0.3;0.839;0.991|.	T|T	0.80953|0.80953	-0.1152|-0.1152	9|5	0.72032|.	D|.	0.01|.	.|.	12.1581|12.1581	0.54089|0.54089	0.0:0.9218:0.0:0.0782|0.0:0.9218:0.0:0.0782	.|.	993;993;958|.	F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	.;.;.|.	I|H	993;993;993;993;993;951;1142|126	ENSP00000439537:L993I;ENSP00000362006:L993I;ENSP00000354573:L993I;ENSP00000313438:L993I;ENSP00000444364:L993I;ENSP00000435070:L951I;ENSP00000437059:L1142I|.	ENSP00000313438:L993I|.	L|P	+|+	1|2	0|0	MACF1|MACF1	39548549|39548549	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.721000|0.721000	0.41392|0.41392	3.237000|3.237000	0.51344|0.51344	2.430000|2.430000	0.82344|0.82344	0.655000|0.655000	0.94253|0.94253	CTT|CCT	.		0.463	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39775962	C	A	39775962	3	1	64	1	0	0	0	0	1	0	0	0	9169	681	24	4	3071	4	MACF1	1	39775962	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	12668980	39775962	209474659	3	6168											
HIVEP3	59269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	41976755	41976755	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accatctggatcccaccgatGggaatcaagggacatggggc	11	6	13	11	1	2	0	1	0	1	0	3	4	3	3	3	5	0	0	3	5	2	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:41976755G>C	ENST00000372583.1	-	9	7473	c.6588C>G	c.(6586-6588)ccC>ccG	p.P2196P	HIVEP3_ENST00000372584.1_Silent_p.P2195P|HIVEP3_ENST00000429157.2_Silent_p.P2195P|HIVEP3_ENST00000247584.5_Silent_p.P2196P|HIVEP3_ENST00000460604.1_5'UTR	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2196					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TCCCACCGATGGGAATCAAGG	0.667																																					p.P2196P		.											.	HIVEP3-157	0			c.C6588G						.						101	103	102					1																	41976755		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon9			ACCGATGGGAATC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.6588C>G	1.37:g.41976755G>C		Somatic	149	0		WXS	Illumina HiSeq	Phase_I	122	22	NM_024503	0	0	1	1	0	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			.		0.667	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		C	41976755	G	C	41976755	2	2	64	1	0	0	0	0	0	0	0	1	7209	1335	47	4		4	HIVEP3	1	41976755	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	2200793	41976755	207273866	4	6169											
HECTD3	79654	hgsc.bcm.edu	37	chr1	45476719	45476719	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcccacacgcagccccaGgccctctgcctcccacaccg	6	3	9	23	3	1	0	0	0	1	0	2	0	2	0	7	2	2	1	7	2	0	0	rs375165079		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:45476719G>A	ENST00000372172.4	-	1	282	c.211C>T	c.(211-213)Ctg>Ttg	p.L71L	UROD_ENST00000246337.4_5'Flank|HECTD3_ENST00000372168.3_5'Flank	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	71					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CGCAGCCCCAGGCCCTCTGCC	0.736													G|||	1	0.000199681	0	0	5008	,	,		10970	0		0.001	False		,,,				2504	0				p.L71L		.											.	HECTD3-658	0			c.C211T						.	G		0,2960		0,0,1480	2	3	3		211	2.6	1	1		3	4,6714		0,4,3355	no	coding-synonymous	HECTD3	NM_024602.5		0,4,4835	AA,AG,GG		0.0595,0.0,0.0413		71/862	45476719	4,9674	1480	3359	4839	SO:0001819	synonymous_variant	79654	exon1			GCCCCAGGCCCTC	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"HECT domain containing 3"			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.211C>T	1.37:g.45476719G>A		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_024602	0	0	0	0	0	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	37	CCDS41318.1																																																																																			.		0.736	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602		A	45476719	G	A	45476719	2	1	64	1	0	0	0	0	0	0	0	1	7062	991	35	2		2	HECTD3	1	45476719	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	3499964	45476719	203773902	5	6170											
NTNG1	22854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	107937850	107937850	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcgaatgtgagcacaacaCtacaggtccagactgtggga	13	7	12	9	1	0	2	0	1	0	1	1	4	1	3	1	2	4	1	1	2	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:107937850C>A	ENST00000370068.1	+	4	1808	c.962C>A	c.(961-963)aCt>aAt	p.T321N	NTNG1_ENST00000370066.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370071.2_Missense_Mutation_p.T321N|NTNG1_ENST00000370073.2_Missense_Mutation_p.T321N|NTNG1_ENST00000370072.3_Missense_Mutation_p.T321N|NTNG1_ENST00000370065.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370074.4_Missense_Mutation_p.T321N|NTNG1_ENST00000370067.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370061.3_Missense_Mutation_p.T321N|NTNG1_ENST00000370070.2_Missense_Mutation_p.T321N|NTNG1_ENST00000542803.1_Missense_Mutation_p.T321N			Q9Y2I2	NTNG1_HUMAN	netrin G1	321	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		GAGCACAACACTACAGGTCCA	0.493																																					p.T321N		.											.	NTNG1-140	0			c.C962A						.						203	192	196					1																	107937850		2203	4300	6503	SO:0001583	missense	22854	exon4			ACAACACTACAGG	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.962C>A	1.37:g.107937850C>A	ENSP00000359085:p.Thr321Asn	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	199	35	NM_001113228	0	0	0	0	0	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	37	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127060	0.94429	.	.	ENSG00000162631	ENST00000370076;ENST00000370073;ENST00000370071;ENST00000542803;ENST00000370061;ENST00000370072;ENST00000370070;ENST00000535584;ENST00000370064;ENST00000370062;ENST00000370074;ENST00000370068;ENST00000294649;ENST00000370067;ENST00000370066;ENST00000370065	T;T;T;T;T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.8	5.8	0.92144	EGF-like, laminin (3);EGF-like region, conserved site (1);	0.000000	0.64402	D	0.000006	D	0.87366	0.6159	H	0.98487	4.245	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.98;1.0	D;D;D;D;D	0.91635	0.997;0.994;0.999;0.912;0.998	D	0.91580	0.5278	10	0.87932	D	0	.	20.0637	0.97700	0.0:1.0:0.0:0.0	.	321;321;321;321;321	B4DKF0;Q9Y2I2;Q9Y2I2-4;Q9Y2I2-2;Q9Y2I2-1	.;NTNG1_HUMAN;.;.;.	N	321;321;321;321;321;321;321;321;82;82;321;321;321;321;321;321	ENSP00000359090:T321N;ENSP00000359088:T321N;ENSP00000440561:T321N;ENSP00000359078:T321N;ENSP00000359089:T321N;ENSP00000359087:T321N;ENSP00000359091:T321N;ENSP00000359085:T321N;ENSP00000359084:T321N;ENSP00000359083:T321N;ENSP00000359082:T321N	ENSP00000294649:T321N	T	+	2	0	NTNG1	107739373	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	7.818000	0.86416	2.751000	0.94390	0.650000	0.86243	ACT	.		0.493	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		A	107937850	C	A	107937850	3	1	64	1	0	0	0	0	1	0	0	0	10730	565	20	4	972	4	NTNG1	1	107937850	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	62461131	107937850	141312771	6	6171											
IGSF3	3321	hgsc.bcm.edu;broad.mit.edu	37	chr1	117131439	117131439	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgccgctgtcgctgacctCggctctctggacggtgaggc	3	9	15	14	4	1	2	0	2	1	0	4	3	1	3	2	4	1	4	2	4	0	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:117131439C>T	ENST00000369486.3	-	8	3082	c.2317G>A	c.(2317-2319)Gag>Aag	p.E773K	IGSF3_ENST00000318837.6_Missense_Mutation_p.E793K|IGSF3_ENST00000369483.1_Missense_Mutation_p.E793K	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	773	Ig-like C2-type 6.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TCGCTGACCTCGGCTCTCTGG	0.627																																					p.E793K		.											.	IGSF3-92	0			c.G2377A						.						29	29	29					1																	117131439		2201	4295	6496	SO:0001583	missense	3321	exon9			TGACCTCGGCTCT	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.2317G>A	1.37:g.117131439C>T	ENSP00000358498:p.Glu773Lys	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	56	12	NM_001542	0	0	1	1	0	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152472	0.57259	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.64438	-0.1;-0.1;-0.1	3.98	3.01	0.34805	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.410465	0.24846	N	0.035140	T	0.43634	0.1256	M	0.66939	2.045	0.49483	D	0.999798	P;P;P	0.45212	0.604;0.853;0.656	B;B;B	0.38106	0.073;0.265;0.12	T	0.50285	-0.8846	10	0.41790	T	0.15	-28.9037	10.5216	0.44922	0.0:0.6523:0.3476:0.0	.	793;773;793	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	K	773;793;793	ENSP00000358498:E773K;ENSP00000358495:E793K;ENSP00000321184:E793K	ENSP00000321184:E793K	E	-	1	0	IGSF3	116932962	0.956000	0.32656	0.994000	0.49952	0.981000	0.71138	2.102000	0.41796	2.050000	0.60909	0.462000	0.41574	GAG	.		0.627	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117131439	C	T	117131439	3	4	64	1	0	0	0	0	1	0	0	0	7622	893	31	1	1283	1	IGSF3	1	117131439	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	9193589	117131439	132119182	7	6172											
SELL	6402	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169677647	169677647	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgatatagatctccacgCagtcctccttgttcttcttg	6	17	6	12	1	4	2	0	1	4	1	7	2	6	2	3	0	0	2	3	0	2	7			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:169677647C>T	ENST00000236147.4	-	3	582	c.422G>A	c.(421-423)tGc>tAc	p.C141Y	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	128	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					GATCTCCACGCAGTCCTCCTT	0.488																																					p.C141Y		.											.	SELL-90	0			c.G422A						.						99	98	98					1																	169677647		2057	4216	6273	SO:0001583	missense	6402	exon3			TCCACGCAGTCCT	M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"CD molecules"	10720	protein-coding gene	gene with protein product		153240	"lymphocyte adhesion molecule 1"	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.422G>A	1.37:g.169677647C>T	ENSP00000236147:p.Cys141Tyr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	86	23	NM_000655	0	0	1	1	0	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	37	CCDS53427.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592012	0.86953	.	.	ENSG00000188404	ENST00000236147	T	0.61980	0.06	5.71	5.71	0.89125	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.56097	D	0.000024	D	0.84279	0.5437	H	0.95539	3.685	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88376	0.2998	10	0.87932	D	0	-22.4594	18.4088	0.90543	0.0:1.0:0.0:0.0	.	141;128	Q8WW79;P14151	.;LYAM1_HUMAN	Y	141	ENSP00000236147:C141Y	ENSP00000236147:C141Y	C	-	2	0	SELL	167944271	1.000000	0.71417	0.997000	0.53966	0.938000	0.57974	7.487000	0.81328	2.698000	0.92095	0.650000	0.86243	TGC	.		0.488	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		T	169677647	C	T	169677647	3	4	64	1	0	0	0	0	1	0	0	0	14048	710	25	2	763	2	SELL	1	169677647	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	52546208	169677647	79572974	8	6173											
CAD	790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27459639	27459639	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctaggccagatcgggccagCccctcctttgaaggtgcatg	7	8	12	14	1	0	2	0	1	0	1	2	2	1	2	6	3	2	1	6	3	2	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:27459639C>A	ENST00000403525.1	+	26	4292	c.4148C>A	c.(4147-4149)gCc>gAc	p.A1383D	CAD_ENST00000264705.4_Missense_Mutation_p.A1446D			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATCGGGCCAGCCCCTCCTTTG	0.537																																					p.A1446D		.											.	CAD-295	0			c.C4337A						.						121	117	118					2																	27459639		2203	4300	6503	SO:0001583	missense	790	exon27			GGCCAGCCCCTCC	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.4148C>A	2.37:g.27459639C>A	ENSP00000384510:p.Ala1383Asp	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	189	42	NM_004341	0	0	4	7	3	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.962670|3.962670	0.74016|0.74016	.|.	.|.	ENSG00000084774|ENSG00000084774	ENST00000264705;ENST00000403525|ENST00000458503	D;D|.	0.86694|.	-2.16;-2.16|.	5.58|5.58	5.58|5.58	0.84498|0.84498	Methylglyoxal synthase-like domain (1);|.	0.092996|.	0.85682|.	D|.	0.000000|.	T|T	0.69931|0.69931	0.3166|0.3166	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	P;D|.	0.71674|.	0.919;0.998|.	P;D|.	0.80764|.	0.587;0.994|.	T|T	0.66064|0.66064	-0.6016|-0.6016	10|5	0.12103|.	T|.	0.63|.	-6.9253|-6.9253	18.128|18.128	0.89592|0.89592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1383;1446|.	F8VPD4;P27708|.	.;PYR1_HUMAN|.	D|T	1446;1383|98	ENSP00000264705:A1446D;ENSP00000384510:A1383D|.	ENSP00000264705:A1446D|.	A|P	+|+	2|1	0|0	CAD|CAD	27313143|27313143	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.966000|0.966000	0.64601|0.64601	4.299000|4.299000	0.59073|0.59073	2.622000|2.622000	0.88805|0.88805	0.561000|0.561000	0.74099|0.74099	GCC|CCC	.		0.537	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27459639	C	A	27459639	3	1	64	1	0	0	0	0	1	0	0	0	2571	739	26	4	4443	4	CAD	2	27459639	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		27459639	215739734	9	6174											
VWA3B	200403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	98744846	98744846	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcactatagcttttctaaagGatctgagtgccaagacccac	12	10	8	11	0	2	2	0	1	2	1	2	3	2	3	2	1	2	2	2	1	5	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:98744846G>T	ENST00000477737.1	+	6	1051	c.847G>T	c.(847-849)Gat>Tat	p.D283Y	VWA3B_ENST00000451075.2_Missense_Mutation_p.D133Y|VWA3B_ENST00000435344.1_Missense_Mutation_p.D283Y	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	283										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTTTCTAAAGGATCTGAGTGC	0.527																																					p.D283Y		.											.	VWA3B-139	0			c.G847T						.						96	96	96					2																	98744846		2002	4172	6174	SO:0001583	missense	200403	exon6			CTAAAGGATCTGA	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.847G>T	2.37:g.98744846G>T	ENSP00000417955:p.Asp283Tyr	Somatic	78	1		WXS	Illumina HiSeq	Phase_I	74	15	NM_144992	0	0	0	0	0	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598190	0.66332	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.15718	7.36;7.36;2.4	5.24	3.39	0.38822	.	0.502898	0.19634	N	0.109604	T	0.36413	0.0966	M	0.65975	2.015	0.26308	N	0.977864	D;D;D	0.76494	0.991;0.999;0.998	P;D;D	0.71656	0.844;0.974;0.946	T	0.07083	-1.0791	10	0.87932	D	0	.	10.7231	0.46052	0.0773:0.1356:0.7872:0.0	.	133;283;283	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	Y	283;283;133	ENSP00000401959:D283Y;ENSP00000417955:D283Y;ENSP00000389463:D133Y	ENSP00000411168:D283Y	D	+	1	0	VWA3B	98111278	1.000000	0.71417	0.950000	0.38849	0.861000	0.49209	2.541000	0.45735	1.324000	0.45282	-0.175000	0.13238	GAT	.		0.527	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98744846	G	T	98744846	3	4	64	1	0	0	0	0	1	0	0	0	17274	1174	41	4	865	4	VWA3B	2	98744846	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	71285207	98744846	144454527	10	6175											
BUB1	699	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	111399713	111399713	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacctttaaaacaaatttctGtttatttttagcatcattca	13	19	2	7	0	3	0	2	0	1	0	3	0	3	0	1	0	3	2	1	0	6	10			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:111399713G>A	ENST00000302759.6	-	20	2564	c.2446C>T	c.(2446-2448)Cag>Tag	p.Q816*	BUB1_ENST00000535254.1_Nonsense_Mutation_p.Q796*|BUB1_ENST00000478175.1_5'UTR|BUB1_ENST00000409311.1_Nonsense_Mutation_p.Q816*	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	816	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		ACAAATTTCTGTTTATTTTTA	0.358																																					p.Q816X													.	BUB1-1060	0			c.C2446T						.						74	72	73					2																	111399713		2203	4300	6503	SO:0001587	stop_gained	699	exon20			ATTTCTGTTTATT	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"budding uninhibited by benzimidazoles 1 (yeast homolog)", "budding uninhibited by benzimidazoles 1 homolog (yeast)"	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.2446C>T	2.37:g.111399713G>A	ENSP00000302530:p.Gln816*	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	43	5	NM_004336	0	0	1	1	0	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Nonsense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	G	38	7.285827	0.98186	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	.	.	.	5.32	4.43	0.53597	.	0.181589	0.49305	D	0.000155	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-8.3351	14.7158	0.69269	0.0:0.1458:0.8542:0.0	.	.	.	.	X	796;816;816;816	.	ENSP00000302530:Q816X	Q	-	1	0	BUB1	111116185	1.000000	0.71417	0.989000	0.46669	0.988000	0.76386	2.831000	0.48144	1.223000	0.43536	0.563000	0.77884	CAG	.		0.358	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		A	111399713	G	A	111399713	4	1	64	1	0	0	0	0	0	1	0	0	1573	1386	48	2	835	2	BUB1	2	111399713	Nonsense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	12654867	111399713	131799660	11	6176											
THSD7B	80731	broad.mit.edu	37	chr2	138208579	138208579	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gacgaccatgtcccaaactgGatctcaagaatcaggtaaag	15	7	9	10	1	2	1	2	0	1	1	4	4	3	2	2	2	1	1	2	2	5	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:138208579G>T	ENST00000409968.1	+	15	3302	c.3124G>T	c.(3124-3126)Gat>Tat	p.D1042Y	THSD7B_ENST00000272643.3_Missense_Mutation_p.D1042Y|THSD7B_ENST00000413152.2_Missense_Mutation_p.D1011Y|THSD7B_ENST00000543459.1_Intron			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	1042	TSP type-1 13. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		TCCCAAACTGGATCTCAAGAA	0.368																																					.													.	THSD7B-75	0			.						.						55	51	52					2																	138208579		1859	4100	5959	SO:0001583	missense	80731	.			AAACTGGATCTCA			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3124G>T	2.37:g.138208579G>T	ENSP00000387145:p.Asp1042Tyr	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	19	4	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	G	25.7	4.666848	0.88251	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.60672	0.58;0.17;0.17	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.80417	0.4619	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81609	-0.0855	10	0.62326	D	0.03	.	20.2191	0.98319	0.0:0.0:1.0:0.0	.	1011	C9JKN6	.	Y	1042;1042;1011	ENSP00000387145:D1042Y;ENSP00000272643:D1042Y;ENSP00000413841:D1011Y	ENSP00000272643:D1042Y	D	+	1	0	THSD7B	137925049	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.780000	0.95670	0.655000	0.94253	GAT	.		0.368	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	138208579	G	T	138208579	3	4	64	1	0	0	0	0	1	0	0	0	15912	1174	41	4	3085	4	THSD7B	2	138208579	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	26808866	138208579	104990794	12	6177											
PECR	55825	ucsc.edu	37	chr2	216908665	216908665	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagtatagagactccggcccCcatccacatccaccgactgt	10	7	8	16	2	0	1	0	0	0	1	3	4	3	1	6	1	0	1	6	1	2	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:216908665C>A	ENST00000265322.7	-	7	862	c.788G>T	c.(787-789)gGg>gTg	p.G263V		NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	263					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	ACTCCGGCCCCCATCCACATC	0.507																																					p.G263V													.	PECR-90	0			c.G788T						.						69	65	66					2																	216908665		2203	4300	6503	SO:0001583	missense	55825	exon7			CGGCCCCCATCCA	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18281	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 29C, member 1"	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.788G>T	2.37:g.216908665C>A	ENSP00000265322:p.Gly263Val	Somatic	36	0		WXS	Illumina HiSeq		43	5	NM_018441	0	0	15	15	0	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Missense_Mutation	SNP	ENST00000265322.7	37	CCDS33375.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.803695	0.70682	.	.	ENSG00000115425	ENST00000265322	T	0.44083	0.93	5.55	5.55	0.83447	NAD(P)-binding domain (1);	0.049612	0.85682	D	0.000000	T	0.77665	0.4164	H	0.98866	4.355	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.991	D	0.85601	0.1252	10	0.87932	D	0	.	12.6996	0.57024	0.0:0.8343:0.1657:0.0	.	263;117	Q9BY49;Q9BY49-2	PECR_HUMAN;.	V	263	ENSP00000265322:G263V	ENSP00000265322:G263V	G	-	2	0	PECR	216616910	0.985000	0.35326	1.000000	0.80357	0.866000	0.49608	2.467000	0.45093	2.607000	0.88179	0.591000	0.81541	GGG	.		0.507	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441		A	216908665	C	A	216908665	3	1	64	1	0	0	0	0	1	0	0	0	11743	623	22	4	131	4	PECR	2	216908665	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	78700086	216908665	26290708	13	6178											
ACAA1	30	broad.mit.edu;bcgsc.ca	37	chr3	38167081	38167092	+	In_Frame_Del	DEL	TGAGCAGCGTGA	TGAGCAGCGTGA	-																															cccacggcgcttcagctcatTgagcagcgtgatgacctgtc																								rs138308587		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	TGAGCAGCGTGA	TGAGCAGCGTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:38167081_38167092delTGAGCAGCGTGA	ENST00000333167.8	-	11	1335_1346	c.1163_1174delTCACGCTGCTCA	c.(1162-1176)atcacgctgctcaat>aat	p.ITLL388del	ACAA1_ENST00000450296.1_In_Frame_Del_p.ITLL347del|ACAA1_ENST00000301810.7_In_Frame_Del_p.ITLL295del|ACAA1_ENST00000480865.1_5'UTR|Y_RNA_ENST00000365095.1_RNA	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	388					alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		TTCAGCTCATTGAGCAGCGTGATGACCTGTCG	0.618																																					p.388_392del													.	ACAA1-91	0			c.1163_1174del						.																																			SO:0001651	inframe_deletion	30	exon11			GCTCATTGAGCAG	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.1163_1174delTCACGCTGCTCA	3.37:g.38167081_38167092delTGAGCAGCGTGA	ENSP00000333664:p.Ile388_Leu391del	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	90	12	NM_001607	0	0	0	0	0	G5E935|Q96CA6	In_Frame_Del	DEL	ENST00000333167.8	37	CCDS2673.1																																																																																			.		0.618	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		-	38167092	TGAGCAGCGTGA	-	38167081	7	5	64	1	0	1	0	1	0	0	0	0	104	1812	63	0	108	0	ACAA1	3	38167081	In_Frame_Del	DEL	TGAGCAGCGTGA	TCGA-BQ-5880-01A-11D-1589-08		38167081	159855349	14	6179											
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52398951	52398951	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccgacctgtttcccaccAtcaaggaggaggacacggac	10	7	11	13	2	1	0	1	0	0	0	3	5	3	4	4	4	0	1	4	4	1	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:52398951A>G	ENST00000420323.2	+	34	5695	c.5434A>G	c.(5434-5436)Atc>Gtc	p.I1812V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1812					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTTTCCCACCATCAAGGAGGA	0.612																																					p.I1812V		.											.	DNAH1-67	0			c.A5434G						.						86	89	88					3																	52398951		2137	4249	6386	SO:0001583	missense	25981	exon34			CCCACCATCAAGG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.5434A>G	3.37:g.52398951A>G	ENSP00000401514:p.Ile1812Val	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	100	30	NM_015512	0	0	0	0	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	4.931	0.172935	0.09391	.	.	ENSG00000114841	ENST00000420323	T	0.37411	1.2	4.49	4.49	0.54785	.	0.143268	0.31358	N	0.007794	T	0.17704	0.0425	N	0.10945	0.07	0.46774	D	0.999194	B	0.12013	0.005	B	0.09377	0.004	T	0.08597	-1.0714	10	0.02654	T	1	.	13.8185	0.63306	1.0:0.0:0.0:0.0	.	1812	C9JXH6	.	V	1812	ENSP00000401514:I1812V	ENSP00000401514:I1812V	I	+	1	0	DNAH1	52373991	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	5.138000	0.64795	1.682000	0.51000	0.383000	0.25322	ATC	.		0.612	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52398951	A	G	52398951	3	3	64	1	0	0	0	0	1	0	0	0	4608	217	8	3	5564	3	DNAH1	3	52398951	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	14231870	52398951	145623479	15	6180											
SLMAP	7871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	57898917	57898917	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agttgagaaaggaatggaatGcattggaaaccgaatgccat	16	8	12	5	1	0	1	0	1	0	1	0	6	0	4	2	3	3	2	2	3	5	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:57898917G>T	ENST00000428312.1	+	19	2096	c.2002G>T	c.(2002-2004)Gca>Tca	p.A668S	SLMAP_ENST00000442599.2_Missense_Mutation_p.A136S|SLMAP_ENST00000295952.3_Missense_Mutation_p.A651S|SLMAP_ENST00000295951.3_Missense_Mutation_p.A651S|SLMAP_ENST00000449503.2_Missense_Mutation_p.A630S|SLMAP_ENST00000416870.1_Missense_Mutation_p.A161S|SLMAP_ENST00000495364.1_Missense_Mutation_p.A202S|SLMAP_ENST00000494088.1_Missense_Mutation_p.A161S			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	668					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GGAATGGAATGCATTGGAAAC	0.338																																					p.A651S		.											.	SLMAP-90	0			c.G1951T						.						78	79	79					3																	57898917		2203	4300	6503	SO:0001583	missense	7871	exon18			TGGAATGCATTGG	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.2002G>T	3.37:g.57898917G>T	ENSP00000398661:p.Ala668Ser	Somatic	107	1		WXS	Illumina HiSeq	Phase_I	98	18	NM_007159	0	0	4	5	1	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Missense_Mutation	SNP	ENST00000428312.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	8.475|8.475|8.475	0.858490|0.858490|0.858490	0.17178|0.17178|0.17178	.|.|.	.|.|.	ENSG00000163681|ENSG00000163681|ENSG00000163681	ENST00000295951;ENST00000295952;ENST00000416870;ENST00000428312;ENST00000449503;ENST00000537224;ENST00000442599;ENST00000495364;ENST00000494088|ENST00000416658;ENST00000438794|ENST00000417128	T;T;T;T;T;T;T;D|.|.	0.82526|.|.	-1.05;-1.05;-1.05;1.64;1.64;1.51;-1.05;-1.62|.|.	6.06|6.06|6.06	3.31|3.31|3.31	0.37934|0.37934|0.37934	.|.|.	0.597033|.|.	0.18857|.|.	N|.|.	0.129230|.|.	T|T|T	0.08802|0.08802|0.08802	0.0218|0.0218|0.0218	N|N|N	0.01048|0.01048|0.01048	-1.04|-1.04|-1.04	0.22571|0.22571|0.22571	N|N|N	0.99897|0.99897|0.99897	B;B;B;B;B;B;B;B|.|.	0.15719|.|.	0.001;0.013;0.006;0.014;0.01;0.0;0.0;0.003|.|.	B;B;B;B;B;B;B;B|.|.	0.17979|.|.	0.002;0.02;0.007;0.019;0.009;0.001;0.001;0.002|.|.	T|T|T	0.30149|0.30149|0.30149	-0.9988|-0.9988|-0.9988	10|5|5	0.07990|.|.	T|.|.	0.79|.|.	-0.555|-0.555|-0.555	6.3828|6.3828|6.3828	0.21544|0.21544|0.21544	0.2:0.0:0.6678:0.1323|0.2:0.0:0.6678:0.1323|0.2:0.0:0.6678:0.1323	.|.|.	161;136;202;161;262;630;668;651|.|.	B7Z863;C9JPE6;Q14BN4-5;Q14BN4-8;Q14BN4-4;Q14BN4-2;Q14BN4;Q14BN4-3|.|.	.;.;.;.;.;.;SLMAP_HUMAN;.|.|.	S|F|I	651;651;161;668;630;262;136;202;161|275;205|251	ENSP00000295951:A651S;ENSP00000295952:A651S;ENSP00000412342:A161S;ENSP00000398661:A668S;ENSP00000412945:A630S;ENSP00000388978:A136S;ENSP00000419543:A202S;ENSP00000418218:A161S|.|.	ENSP00000295951:A651S|.|.	A|C|M	+|+|+	1|2|3	0|0|0	SLMAP|SLMAP|SLMAP	57873957|57873957|57873957	0.533000|0.533000|0.533000	0.26354|0.26354|0.26354	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.948000|0.948000|0.948000	0.59901|0.59901|0.59901	1.039000|1.039000|1.039000	0.30266|0.30266|0.30266	0.881000|0.881000|0.881000	0.35993|0.35993|0.35993	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	GCA|TGC|ATG	.		0.338	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		T	57898917	G	T	57898917	3	4	64	1	0	0	0	0	1	0	0	0	14781	1319	46	4	2021	4	SLMAP	3	57898917	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	5499966	57898917	140123513	16	6181											
GXYLT2	727936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	72957696	72957696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgaagactctctgaagcccGagtttgataagcaggtgaat	12	10	11	8	1	1	5	0	4	1	1	2	6	1	5	1	1	2	2	1	1	4	2	rs142024018		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:72957696G>A	ENST00000389617.4	+	2	615	c.454G>A	c.(454-456)Gag>Aag	p.E152K		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	152					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						TCTGAAGCCCGAGTTTGATAA	0.418													G|||	1	0.000199681	0	0	5008	,	,		20488	0		0.001	False		,,,				2504	0				p.E152K		.											.	.	0			c.G454A						.						67	68	68					3																	72957696		1933	4133	6066	SO:0001583	missense	727936	exon2			AAGCCCGAGTTTG	AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"Glycosyltransferase family 8 domain containing"	33383	protein-coding gene	gene with protein product		613322	"glycosyltransferase 8 domain containing 4"	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.454G>A	3.37:g.72957696G>A	ENSP00000374268:p.Glu152Lys	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	50	11	NM_001080393	0	0	0	0	0		Missense_Mutation	SNP	ENST00000389617.4	37	CCDS46870.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	8.743	0.919451	0.17982	.	.	ENSG00000172986	ENST00000389617;ENST00000498315	T;T	0.49139	0.79;1.79	5.71	5.71	0.89125	.	0.170913	0.51477	D	0.000086	T	0.31670	0.0804	L	0.28115	0.83	0.49582	D	0.999804	P	0.35628	0.513	B	0.26416	0.069	T	0.22661	-1.0210	10	0.06099	T	0.92	.	19.8442	0.96702	0.0:0.0:1.0:0.0	.	152	A0PJZ3	GXLT2_HUMAN	K	152;26	ENSP00000374268:E152K;ENSP00000417239:E26K	ENSP00000374268:E152K	E	+	1	0	GXYLT2	73040386	1.000000	0.71417	0.959000	0.39883	0.811000	0.45836	4.503000	0.60407	2.696000	0.92011	0.655000	0.94253	GAG	G|0.999;A|0.000		0.418	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393		A	72957696	G	A	72957696	3	1	64	1	0	0	0	0	1	0	0	0	6925	1059	37	1	460	1	GXYLT2	3	72957696	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	15058779	72957696	125064734	17	6182											
GBE1	2632	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	81698998	81698998	+	Frame_Shift_Del	DEL	A	A	-																															caatcataattcacattatcAccttcacgaaccacatactt																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:81698998delA	ENST00000429644.2	-	4	1147	c.504delT	c.(502-504)ggtfs	p.G168fs	GBE1_ENST00000489715.1_Frame_Shift_Del_p.G127fs	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	168					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		TCACATTATCACCTTCACGAA	0.348									Glycogen Storage Disease, type IV																												p.G168fs		.											.	GBE1-25	0			c.504delT						.						102	101	101					3																	81698998		1874	4119	5993	SO:0001589	frameshift_variant	2632	exon4	Familial Cancer Database	Andersen Disease, Brancher deficiency	.		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"glycogen branching enzyme", "Andersen disease", "glycogen storage disease type IV"	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.504delT	3.37:g.81698998delA	ENSP00000410833:p.Gly168fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	60	11	NM_000158	0	0	0	0	0	B3KWV3|Q96EN0	Frame_Shift_Del	DEL	ENST00000429644.2	37	CCDS54612.1																																																																																			.		0.348	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2			-	81698998	A	-	81698998	7	5	64	1	0	1	0	1	0	0	0	0	6290	146	6	0	1656	0	GBE1	3	81698998	Frame_Shift_Del	DEL	A	TCGA-BQ-5880-01A-11D-1589-08	8741302	81698998	116323432	18	6183											
COL6A5	256076	broad.mit.edu	37	chr3	130174495	130174495	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcaaaaatctgcagaaattGcaagtctcacttctggtaag	15	11	7	8	0	4	1	2	0	3	1	5	1	4	1	0	1	2	3	0	1	5	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:130174495G>A	ENST00000432398.2	+	37	7269	c.6775G>A	c.(6775-6777)Gca>Aca	p.A2259T	COL6A5_ENST00000265379.6_Missense_Mutation_p.A2259T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2259	Nonhelical 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 region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						TGCAGAAATTGCAAGTCTCAC	0.308																																					p.A2259T													.	.	0			c.G6775A						.						42	41	41					3																	130174495		1805	4070	5875	SO:0001583	missense	256076	exon37			GAAATTGCAAGTC	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6775G>A	3.37:g.130174495G>A	ENSP00000390895:p.Ala2259Thr	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	54	4	NM_153264	0	0	0	0	0	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.865|6.865	0.528920|0.528920	0.13127|0.13127	.|.	.|.	ENSG00000172752|ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157;ENST00000512482|ENST00000512836	D;D;T;T|.	0.90563|.	-2.56;-2.69;-1.08;-1.12|.	4.38|4.38	-0.972|-0.972	0.10300|0.10300	.|.	1.433800|.	0.04946|.	N|.	0.459465|.	T|T	0.27313|0.27313	0.0670|0.0670	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	B;B|.	0.16603|.	0.01;0.018|.	B;B|.	0.16722|.	0.007;0.016|.	T|T	0.29212|0.29212	-1.0019|-1.0019	10|5	0.15066|.	T|.	0.55|.	.|.	0.7455|0.7455	0.00981|0.00981	0.2971:0.1642:0.3706:0.1681|0.2971:0.1642:0.3706:0.1681	.|.	2259;2259|.	A8TX70;A8TX70-2|.	CO6A5_HUMAN;.|.	T|Y	2259;2259;202;94|510	ENSP00000390895:A2259T;ENSP00000265379:A2259T;ENSP00000362250:A202T;ENSP00000424968:A94T|.	ENSP00000265379:A2259T|.	A|C	+|+	1|2	0|0	COL6A5|COL6A5	131657185|131657185	0.009000|0.009000	0.17119|0.17119	0.085000|0.085000	0.20634|0.20634	0.012000|0.012000	0.07955|0.07955	-0.299000|-0.299000	0.08254|0.08254	-0.077000|-0.077000	0.12752|0.12752	0.650000|0.650000	0.86243|0.86243	GCA|TGC	.		0.308	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130174495	G	A	130174495	3	1	64	1	0	0	0	0	1	0	0	0	3708	1319	46	2	6917	2	COL6A5	3	130174495	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	48475497	130174495	67847935	19	6184											
HTT	3064	broad.mit.edu	37	chr4	3124641	3124641	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggttcctcatgcagcccTgtcctttcaagaaaacaaaa	12	9	9	11	0	2	1	2	0	0	1	4	1	4	1	3	2	3	2	3	2	5	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr4:3124641T>C	ENST00000355072.5	+	10	1444	c.1299T>C	c.(1297-1299)ccT>ccC	p.P433P		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	433					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CATGCAGCCCTGTCCTTTCAA	0.348																																					p.P433P													.	HTT-281	0			c.T1299C						.						116	117	117					4																	3124641		1853	4089	5942	SO:0001819	synonymous_variant	3064	exon10			CAGCCCTGTCCTT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1299T>C	4.37:g.3124641T>C		Somatic	201	0		WXS	Illumina HiSeq	Phase_I	163	3	NM_002111	0	0	1	1	0	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			.		0.348	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		C	3124641	T	C	3124641	2	2	64	1	0	0	0	0	0	0	0	1	7478	1567	55	3		3	HTT	4	3124641	Silent	SNP	T	TCGA-BQ-5880-01A-11D-1589-08		3124641	188029635	20	6185											
NFXL1	152518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	47901107	47901107	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttacagtaacaagtagttGtgaccatctttggacaagga	13	12	9	7	0	2	1	0	1	2	0	2	3	2	3	1	2	2	3	1	2	5	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr4:47901107G>A	ENST00000507489.1	-	7	1033	c.857C>T	c.(856-858)aCa>aTa	p.T286I	NFXL1_ENST00000381538.3_Missense_Mutation_p.T286I|NFXL1_ENST00000329043.3_Missense_Mutation_p.T286I	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	286						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						ACAAGTAGTTGTGACCATCTT	0.388																																					p.T286I		.											.	NFXL1-524	0			c.C857T						.						85	79	81					4																	47901107		2203	4300	6503	SO:0001583	missense	152518	exon7			GTAGTTGTGACCA	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.857C>T	4.37:g.47901107G>A	ENSP00000422037:p.Thr286Ile	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	54	10	NM_152995	0	0	0	0	0	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	37	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	G	11.50	1.656404	0.29425	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.42131	0.98;0.98;0.98	4.85	4.85	0.62838	.	0.275863	0.32918	N	0.005484	T	0.46151	0.1378	M	0.62723	1.935	0.43126	D	0.994855	P	0.36683	0.565	B	0.37888	0.26	T	0.53201	-0.8472	10	0.56958	D	0.05	-8.3899	17.9625	0.89090	0.0:0.0:1.0:0.0	.	286	Q6ZNB6	NFXL1_HUMAN	I	286	ENSP00000370949:T286I;ENSP00000422037:T286I;ENSP00000333113:T286I	ENSP00000333113:T286I	T	-	2	0	NFXL1	47595864	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	5.916000	0.69981	2.215000	0.71742	0.655000	0.94253	ACA	.		0.388	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		A	47901107	G	A	47901107	3	1	64	1	0	0	0	0	1	0	0	0	10414	1377	48	2	1946	2	NFXL1	4	47901107	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	44776466	47901107	143253169	21	6186											
SLC4A4	8671	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	72429512	72429512	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtacatttttttcacagtcTgactgcccatactcagaaaa	12	14	5	10	0	3	2	2	1	1	1	3	2	3	2	1	0	3	1	1	0	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr4:72429512T>A	ENST00000264485.5	+	24	3219	c.3102T>A	c.(3100-3102)tcT>tcA	p.S1034S	SLC4A4_ENST00000351898.6_Silent_p.S950S|SLC4A4_ENST00000425175.1_Intron|SLC4A4_ENST00000340595.3_Silent_p.S990S	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	1034					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TTTCACAGTCTGACTGCCCAT	0.363																																					p.S1034S		.											.	SLC4A4-95	0			c.T3102A						.						124	135	131					4																	72429512		2203	4300	6503	SO:0001819	synonymous_variant	8671	exon24			ACAGTCTGACTGC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.3102T>A	4.37:g.72429512T>A		Somatic	199	0		WXS	Illumina HiSeq	Phase_I	195	35	NM_001098484	0	0	0	0	0	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	37	CCDS43236.1																																																																																			.		0.363	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72429512	T	A	72429512	2	1	64	1	0	0	0	0	0	0	0	1	14688	1567	55	5		5	SLC4A4	4	72429512	Silent	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	24528405	72429512	118724764	22	6187											
TBCK	93627	broad.mit.edu	37	chr4	107163639	107163639	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tttcttacatttcttagctgGcataacgacaatgtcacagt	11	15	6	9	1	3	0	1	0	2	0	3	1	3	0	0	1	3	2	0	1	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr4:107163639G>A	ENST00000273980.5	-	13	1605	c.1158C>T	c.(1156-1158)tgC>tgT	p.C386C	TBCK_ENST00000394708.2_Silent_p.C386C|TBCK_ENST00000361687.4_Silent_p.C323C|TBCK_ENST00000432496.2_Silent_p.C386C|TBCK_ENST00000394706.3_Silent_p.C347C					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTCTTAGCTGGCATAACGACA	0.343																																					p.C386C													.	TBCK-336	0			c.C1158T						.						76	72	73					4																	107163639		2203	4300	6503	SO:0001819	synonymous_variant	93627	exon12			TAGCTGGCATAAC		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1158C>T	4.37:g.107163639G>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	87	3	NM_001163436	0	0	0	0	0		Silent	SNP	ENST00000273980.5	37	CCDS54788.1																																																																																			.		0.343	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		A	107163639	G	A	107163639	2	1	64	1	0	0	0	0	0	0	0	1	15668	1195	42	2		2	TBCK	4	107163639	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	34734127	107163639	83990637	23	6188											
PSD2	84249	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	139193812	139193812	+	Frame_Shift_Del	DEL	G	G	-																															tctgagctcagcagctcggaGgggttggagcctggtagtgc																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr5:139193812delG	ENST00000274710.3	+	4	1084	c.879delG	c.(877-879)gagfs	p.E293fs		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	293	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCTCGGAGGGGTTGGAGC	0.632																																					p.E293fs		.											.	PSD2-91	0			c.879delG						.						89	81	84					5																	139193812		2203	4300	6503	SO:0001589	frameshift_variant	84249	exon4			.	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.879delG	5.37:g.139193812delG	ENSP00000274710:p.Glu293fs	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	170	27	NM_032289	0	0	0	0	0	D3DQD3|Q8N3J8	Frame_Shift_Del	DEL	ENST00000274710.3	37	CCDS4216.1																																																																																			.		0.632	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		-	139193812	G	-	139193812	7	5	64	1	0	1	0	1	0	0	0	0	12676	991	35	0	889	0	PSD2	5	139193812	Frame_Shift_Del	DEL	G	TCGA-BQ-5880-01A-11D-1589-08		139193812	41721448	24	6189											
SLC26A8	116369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35949921	35949921	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taaggaatcatgtcaataagCgtctggctggtttctgtggc	9	13	12	7	1	4	0	2	0	2	0	4	1	4	1	0	4	1	2	0	4	4	3	rs547194034		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr6:35949921C>T	ENST00000490799.1	-	8	1355	c.1002G>A	c.(1000-1002)acG>acA	p.T334T	SLC26A8_ENST00000355574.2_Silent_p.T334T|SLC26A8_ENST00000394602.2_Silent_p.T229T	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						TGTCAATAAGCGTCTGGCTGG	0.423													C|||	1	0.000199681	0	0.0014	5008	,	,		20134	0		0	False		,,,				2504	0				p.T334T		.											.	SLC26A8-92	0			c.G1002A						.						123	113	116					6																	35949921		2203	4300	6503	SO:0001819	synonymous_variant	116369	exon8			AATAAGCGTCTGG	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.1002G>A	6.37:g.35949921C>T		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	125	19	NM_052961	0	0	0	0	0		Silent	SNP	ENST00000490799.1	37	CCDS4813.1																																																																																			.		0.423	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			T	35949921	C	T	35949921	2	4	64	1	0	0	0	0	0	0	0	1	14555	755	27	1		1	SLC26A8	6	35949921	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		35949921	135165146	25	6190											
C6orf150	115004	hgsc.bcm.edu	37	chr6	74161604	74161604	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctccagcccctctgcccCaggggcgctggtggcgtcag	4	6	15	16	2	2	0	1	0	1	0	3	0	3	0	5	5	2	2	5	5	0	0	rs141133909	byFrequency	TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr6:74161604C>T	ENST00000370315.3	-	1	395	c.301G>A	c.(301-303)Ggg>Agg	p.G101R	MB21D1_ENST00000370318.1_Missense_Mutation_p.G101R	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	101					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						CCCTCTGCCCCAGGGGCGCTG	0.736													C|||	34	0.00678914	0.0015	0.013	5008	,	,		13030	0		0.0179	False		,,,				2504	0.0051				p.G101R		.											.	MB21D1-90	0			c.G301A						.	C	ARG/GLY	8,3082		0,8,1537	2	3	2		301	-5.3	0	6	dbSNP_134	2	100,6482		0,100,3191	no	missense	MB21D1	NM_138441.2	125	0,108,4728	TT,TC,CC		1.5193,0.2589,1.1166	probably-damaging	101/523	74161604	108,9564	1545	3291	4836	SO:0001583	missense	115004	exon1			CTGCCCCAGGGGC	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.301G>A	6.37:g.74161604C>T	ENSP00000359339:p.Gly101Arg	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_138441	0	0	0	0	0	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	37	CCDS4978.1	28	0.01282051282051282	10	0.02032520325203252	6	0.016574585635359115	1	0.0017482517482517483	11	0.014511873350923483	C	7.159	0.585275	0.13749	0.002589	0.015193	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.30182	1.54;1.94	2.63	-5.26	0.02772	.	.	.	.	.	T	0.07324	0.0185	L	0.40543	1.245	0.09310	N	1	P	0.50617	0.937	B	0.39706	0.307	T	0.04693	-1.0933	9	0.52906	T	0.07	18.0729	5.7516	0.18150	0.3087:0.3523:0.339:0.0	.	101	Q8N884	M21D1_HUMAN	R	101	ENSP00000359342:G101R;ENSP00000359339:G101R	ENSP00000296913:G101R	G	-	1	0	MB21D1	74218325	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.086000	0.14935	-1.736000	0.01352	0.491000	0.48974	GGG	C|0.987;T|0.013		0.736	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		T	74161604	C	T	74161604	3	4	64	1	0	0	0	0	1	0	0	0	2343	594	21	2	1287	2	C6orf150	6	74161604	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	38211683	74161604	96953463	26	6191											
RBAK	57786	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr7	5104736	5104736	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtggaaagttattcaatgAgttgtcatactatactgaac	14	14	8	5	0	2	2	2	2	0	0	2	3	2	3	0	1	3	2	0	1	7	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:5104736A>T	ENST00000353796.3	+	6	1973	c.1649A>T	c.(1648-1650)gAg>gTg	p.E550V	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.E550V	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	550	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TTATTCAATGAGTTGTCATAC	0.393																																					p.E550V		.											.	RBAK-653	0			c.A1649T						.						63	63	63					7																	5104736		2203	4299	6502	SO:0001583	missense	57786	exon6			TCAATGAGTTGTC	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1649A>T	7.37:g.5104736A>T	ENSP00000275423:p.Glu550Val	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	107	35	NM_001204456	0	0	0	0	0	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	37	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187436	0.38609	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.14516	2.5;2.5	3.76	3.76	0.43208	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.572849	0.15837	N	0.242235	T	0.15003	0.0362	L	0.33753	1.03	0.26673	N	0.971686	P	0.42123	0.771	P	0.46885	0.53	T	0.13872	-1.0493	8	.	.	.	.	11.0559	0.47918	1.0:0.0:0.0:0.0	.	550	Q9NYW8	RBAK_HUMAN	V	550	ENSP00000275423:E550V;ENSP00000380120:E550V	.	E	+	2	0	RBAK	5071262	0.000000	0.05858	0.706000	0.30403	0.897000	0.52465	0.042000	0.13949	1.931000	0.55961	0.454000	0.30748	GAG	.		0.393	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		T	5104736	A	T	5104736	3	4	64	1	0	0	0	0	1	0	0	0	13132	304	11	5	1663	5	RBAK	7	5104736	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		5104736	154033927	27	6192											
SP4	6671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	21468915	21468915	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattttgggtaggactctcaGccctctcctctggctttact	5	15	8	13	0	3	0	1	0	3	0	5	1	3	1	2	3	2	2	2	3	2	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:21468915G>A	ENST00000222584.3	+	3	350	c.132G>A	c.(130-132)caG>caA	p.Q44Q		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	44					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						AGGACTCTCAGCCCTCTCCTC	0.483																																					p.Q44Q		.											.	SP4-95	0			c.G132A						.						34	37	36					7																	21468915		2201	4300	6501	SO:0001819	synonymous_variant	6671	exon3			CTCTCAGCCCTCT		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.132G>A	7.37:g.21468915G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	71	9	NM_003112	0	0	0	0	0	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																			.		0.483	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		A	21468915	G	A	21468915	2	1	64	1	0	0	0	0	0	0	0	1	14998	962	34	2		2	SP4	7	21468915	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	16364179	21468915	137669748	28	6193											
SAMD9L	219285	broad.mit.edu	37	chr7	92761639	92761639	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcattttctttgtggaaaaAgggagtgagctgaagaatct	12	14	11	4	0	3	3	1	2	2	1	3	5	3	5	0	2	1	1	0	2	4	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:92761639A>G	ENST00000318238.4	-	5	4862	c.3646T>C	c.(3646-3648)Ttt>Ctt	p.F1216L	SAMD9L_ENST00000411955.1_Missense_Mutation_p.F1216L|SAMD9L_ENST00000437805.1_Missense_Mutation_p.F1216L	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1216					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTGTGGAAAAAGGGAGTGAGC	0.378																																					p.F1216L													.	SAMD9L-94	0			c.T3646C						.						105	100	101					7																	92761639		2203	4299	6502	SO:0001583	missense	219285	exon5			GGAAAAAGGGAGT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.3646T>C	7.37:g.92761639A>G	ENSP00000326247:p.Phe1216Leu	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	211	3	NM_152703	0	0	4	4	0	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	A	0.131	-1.113678	0.01799	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.20598	2.06;2.06;2.06	4.77	0.449	0.16619	.	0.919380	0.09292	N	0.822145	T	0.06735	0.0172	N	0.02202	-0.64	0.09310	N	0.99999	B	0.02656	0.0	B	0.04013	0.001	T	0.38329	-0.9666	10	0.05721	T	0.95	-0.1325	7.8979	0.29717	0.6565:0.0:0.3435:0.0	.	1216	Q8IVG5	SAM9L_HUMAN	L	1216	ENSP00000326247:F1216L;ENSP00000405760:F1216L;ENSP00000408796:F1216L	ENSP00000326247:F1216L	F	-	1	0	SAMD9L	92599575	0.000000	0.05858	0.218000	0.23776	0.607000	0.37147	0.079000	0.14782	-0.005000	0.14395	0.383000	0.25322	TTT	.		0.378	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		G	92761639	A	G	92761639	3	3	64	1	0	0	0	0	1	0	0	0	13859	72	3	3	1112	3	SAMD9L	7	92761639	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	71292724	92761639	66377024	29	6194											
CCDC132	55610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92932848	92932848	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttaagtcaaatttcagcAtcttgcaacttcatgtaagt	12	15	6	8	0	4	0	3	0	1	0	4	0	4	0	0	0	3	4	0	0	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:92932848A>G	ENST00000305866.5	+	17	1566	c.1438A>G	c.(1438-1440)Atc>Gtc	p.I480V	CCDC132_ENST00000535481.1_Missense_Mutation_p.I200V|CCDC132_ENST00000541136.1_Missense_Mutation_p.I291V|CCDC132_ENST00000544910.1_Missense_Mutation_p.I450V|CCDC132_ENST00000317751.6_Missense_Mutation_p.I211V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	480						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			AAATTTCAGCATCTTGCAACT	0.308																																					p.I480V		.											.	CCDC132-90	0			c.A1438G						.						138	134	135					7																	92932848		1818	4077	5895	SO:0001583	missense	55610	exon17			TTCAGCATCTTGC	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1438A>G	7.37:g.92932848A>G	ENSP00000307666:p.Ile480Val	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	254	48	NM_017667	0	0	1	2	1	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.801621	0.31869	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.39229	1.09	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.44829	0.1312	L	0.27053	0.805	0.80722	D	1	P;P;P	0.38863	0.518;0.65;0.518	P;P;P	0.54140	0.558;0.743;0.558	T	0.19257	-1.0311	10	0.14252	T	0.57	-8.589	15.0541	0.71897	1.0:0.0:0.0:0.0	.	200;450;480	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	V	480;450;291;200;211	ENSP00000325582:I211V	ENSP00000307666:I480V	I	+	1	0	CCDC132	92770784	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.051000	0.93849	2.200000	0.70718	0.460000	0.39030	ATC	.		0.308	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92932848	A	G	92932848	3	3	64	1	0	0	0	0	1	0	0	0	2773	217	8	3	1546	3	CCDC132	7	92932848	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	171209	92932848	66205815	30	6195											
STAG3	10734	broad.mit.edu;bcgsc.ca	37	chr7	99779767	99779767	+	Frame_Shift_Del	DEL	T	T	-																															gactttgaagacagcttgaaTcgcaatgtgaagaagagagc																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:99779767delT	ENST00000426455.1	+	3	578	c.171delT	c.(169-171)aatfs	p.N57fs	STAG3_ENST00000394018.2_Frame_Shift_Del_p.N57fs|STAG3_ENST00000317296.5_Frame_Shift_Del_p.N57fs	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	57					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACAGCTTGAATCGCAATGTGA	0.438																																					p.N57fs													.	STAG3-543	0			c.171delT						.						122	112	115					7																	99779767		2203	4300	6503	SO:0001589	frameshift_variant	10734	exon3			CTTGAATCGCAAT	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.171delT	7.37:g.99779767delT	ENSP00000400359:p.Asn57fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	67	10	NM_012447	0	0	0	0	0	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Frame_Shift_Del	DEL	ENST00000426455.1	37	CCDS34703.1																																																																																			.		0.438	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		-	99779767	T	-	99779767	7	5	64	1	0	1	0	1	0	0	0	0	15276	1432	50	0	177	0	STAG3	7	99779767	Frame_Shift_Del	DEL	T	TCGA-BQ-5880-01A-11D-1589-08	6846919	99779767	59358896	31	6196											
SH2B2	10603	broad.mit.edu	37	chr7	101943829	101943829	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caggtggctgcgatgggacgGaagccatgaatggtgccggc	8	6	18	9	3	0	1	0	1	0	0	0	4	0	3	2	6	3	1	2	6	2	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:101943829G>A	ENST00000536178.1	+	2	169	c.124G>A	c.(124-126)Gaa>Aaa	p.E42K	SH2B2_ENST00000306803.8_5'Flank			O14492	SH2B2_HUMAN	SH2B adaptor protein 2	0					actin cytoskeleton organization (GO:0030036)|antigen receptor-mediated signaling pathway (GO:0050851)|B-1 B cell homeostasis (GO:0001922)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cytokine-mediated signaling pathway (GO:0019221)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|regulation of JAK-STAT cascade (GO:0046425)|regulation of metabolic process (GO:0019222)|regulation of Ras protein signal transduction (GO:0046578)|signal transduction (GO:0007165)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stress fiber (GO:0001725)	JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	9						CGATGGGACGGAAGCCATGAA	0.701																																					.													.	.	0			.						.						9	11	10					7																	101943829		1767	3673	5440	SO:0001583	missense	10603	.			GGGACGGAAGCCA	AB000520		7q22.1	2013-02-14			ENSG00000160999	ENSG00000160999		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	17381	protein-coding gene	gene with protein product	"adaptor protein with pleckstrin homology and src"	605300				9233773	Standard	XM_005276976		Approved	APS	uc011kko.2	O14492	OTTHUMG00000150652	ENST00000536178.1:c.124G>A	7.37:g.101943829G>A	ENSP00000440273:p.Glu42Lys	Somatic	47	1		WXS	Illumina HiSeq	Phase_I	55	13	.	0	0	0	0	0	A6ND74	Missense_Mutation	SNP	ENST00000536178.1	37		.	.	.	.	.	.	.	.	.	.	G	13.40	2.225853	0.39300	.	.	ENSG00000160999	ENST00000536178	T	0.42513	0.97	3.51	1.35	0.21983	.	.	.	.	.	T	0.19805	0.0476	N	0.08118	0	.	.	.	.	.	.	.	.	.	T	0.27157	-1.0082	6	0.22706	T	0.39	.	5.0789	0.14646	0.1359:0.0:0.6453:0.2188	.	.	.	.	K	42	ENSP00000440273:E42K	ENSP00000440273:E42K	E	+	1	0	SH2B2	101730549	1.000000	0.71417	0.991000	0.47740	0.922000	0.55478	3.601000	0.54059	0.642000	0.30620	0.462000	0.41574	GAA	.		0.701	SH2B2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_020979		A	101943829	G	A	101943829	3	1	64	1	0	0	0	0	1	0	0	0	14260	1175	41	2	130	2	SH2B2	7	101943829	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	2164062	101943829	57194834	32	6197											
AKR1B1	231	broad.mit.edu	37	chr7	134133231	134133231	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttctcctgagtgagataTgggtggcactcaatctgcaa	11	11	10	9	0	3	2	1	2	2	1	4	3	3	2	1	2	2	2	1	2	4	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:134133231T>C	ENST00000285930.4	-	6	646	c.567A>G	c.(565-567)ccA>ccG	p.P189P	AKR1B1_ENST00000489022.1_5'Flank	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	189					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)			kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	GAGTGAGATATGGGTGGCACT	0.532																																					p.P189P													.	AKR1B1-93	0			c.A567G						.						103	96	98					7																	134133231		2203	4300	6503	SO:0001819	synonymous_variant	231	exon6			GAGATATGGGTGG	J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"Aldo-keto reductases"	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.567A>G	7.37:g.134133231T>C		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	37	7	NM_001628	0	1	124	223	98	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Silent	SNP	ENST00000285930.4	37	CCDS5831.1																																																																																			.		0.532	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628		C	134133231	T	C	134133231	2	2	64	1	0	0	0	0	0	0	0	1	466	1451	51	3		3	AKR1B1	7	134133231	Silent	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	32189402	134133231	25005432	33	6198											
GPR124	25960	hgsc.bcm.edu	37	chr8	37698794	37698794	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggggttccaccaggctcAggggcagcggccccctcctg	5	6	15	15	1	1	1	1	1	0	0	3	1	3	1	5	6	1	3	5	6	0	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr8:37698794A>G	ENST00000412232.2	+	19	2951	c.2938A>G	c.(2938-2940)Agg>Ggg	p.R980G	GPR124_ENST00000315215.7_Missense_Mutation_p.R763G	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	980					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CACCAGGCTCAGGGGCAGCGG	0.692																																					p.R980G		.											.	GPR124-157	0			c.A2938G						.						23	28	26					8																	37698794		2202	4299	6501	SO:0001583	missense	25960	exon19			AGGCTCAGGGGCA	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.2938A>G	8.37:g.37698794A>G	ENSP00000406367:p.Arg980Gly	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_032777	0	0	3	3	0	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	A	9.090	1.001376	0.19121	.	.	ENSG00000020181	ENST00000416514;ENST00000315215;ENST00000412232	T;T	0.57752	0.38;0.49	4.96	-0.371	0.12525	.	0.390573	0.26297	N	0.025188	T	0.31167	0.0788	N	0.24115	0.695	0.26959	N	0.965857	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20107	-1.0285	10	0.15066	T	0.55	-29.167	9.6756	0.40039	0.1983:0.6935:0.1082:0.0	.	763;980	Q96PE1-2;Q96PE1	.;GP124_HUMAN	G	973;763;980	ENSP00000323508:R763G;ENSP00000406367:R980G	ENSP00000323508:R763G	R	+	1	2	GPR124	37817952	1.000000	0.71417	0.998000	0.56505	0.812000	0.45895	2.462000	0.45049	-0.059000	0.13154	-0.213000	0.12676	AGG	.		0.692	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			G	37698794	A	G	37698794	3	3	64	1	0	0	0	0	1	0	0	0	6658	179	7	3	2991	3	GPR124	8	37698794	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		37698794	108665228	34	6199											
PREX2	80243	broad.mit.edu;bcgsc.ca	37	chr8	69046477	69046477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatagcgaatgcaggtgttcTttttcactttcagtcacttc	8	16	8	9	1	4	0	3	0	1	0	5	2	4	0	0	1	2	2	0	1	2	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr8:69046477T>C	ENST00000288368.4	+	32	4227	c.3950T>C	c.(3949-3951)cTt>cCt	p.L1317P		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1317					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GCAGGTGTTCTTTTTCACTTT	0.458																																					p.L1317P													.	PREX2-390	0			c.T3950C						.						112	95	101					8																	69046477		2203	4300	6503	SO:0001583	missense	80243	exon32			GTGTTCTTTTTCA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"Rho guanine nucleotide exchange factors"	22950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 129"	612139	"DEP domain containing 2"	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3950T>C	8.37:g.69046477T>C	ENSP00000288368:p.Leu1317Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	115	6	NM_024870	0	0	1	1	0	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.303488	0.81136	.	.	ENSG00000046889	ENST00000288368	T	0.49432	0.78	5.58	5.58	0.84498	.	0.152410	0.44902	D	0.000414	T	0.70351	0.3214	M	0.80982	2.52	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.75297	-0.3367	10	0.87932	D	0	.	15.7584	0.78054	0.0:0.0:0.0:1.0	.	1317	Q70Z35	PREX2_HUMAN	P	1317	ENSP00000288368:L1317P	ENSP00000288368:L1317P	L	+	2	0	PREX2	69209031	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	7.698000	0.84413	2.135000	0.66039	0.533000	0.62120	CTT	.		0.458	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		C	69046477	T	C	69046477	3	2	64	1	0	0	0	0	1	0	0	0	12506	1609	56	3	4305	3	PREX2	8	69046477	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	31347683	69046477	77317545	35	6200											
FAM135B	51059	broad.mit.edu	37	chr8	139164987	139164987	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttatctctagagctcctactCtcatgctgagcattgaaggc	9	13	8	11	0	2	3	1	2	2	1	5	3	3	3	1	1	4	3	1	1	4	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr8:139164987C>G	ENST00000395297.1	-	13	1901	c.1731G>C	c.(1729-1731)gaG>gaC	p.E577D		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	577										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AGCTCCTACTCTCATGCTGAG	0.483										HNSCC(54;0.14)																											p.E577D													.	FAM135B-31	0			c.G1731C						.						136	130	132					8																	139164987		1895	4120	6015	SO:0001583	missense	51059	exon13			CCTACTCTCATGC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1731G>C	8.37:g.139164987C>G	ENSP00000378710:p.Glu577Asp	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	263	6	NM_015912	0	0	0	0	0	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	10.74	1.436809	0.25900	.	.	ENSG00000147724	ENST00000395297	T	0.23754	1.89	5.45	0.776	0.18532	.	0.348795	0.30593	N	0.009285	T	0.37571	0.1008	M	0.63428	1.95	0.09310	N	1	D;D;D	0.65815	0.995;0.986;0.976	D;P;P	0.64237	0.923;0.783;0.53	T	0.22521	-1.0214	10	0.24483	T	0.36	-8.3513	8.5303	0.33331	0.0:0.5159:0.0:0.4841	.	577;577;577	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	D	577	ENSP00000378710:E577D	ENSP00000276737:E577D	E	-	3	2	FAM135B	139234169	0.006000	0.16342	0.000000	0.03702	0.010000	0.07245	-0.007000	0.12810	-0.072000	0.12864	-0.768000	0.03414	GAG	.		0.483	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		G	139164987	C	G	139164987	3	3	64	1	0	0	0	0	1	0	0	0	5465	912	32	4	2521	4	FAM135B	8	139164987	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	70118510	139164987	7199035	36	6201											
UBE2R2	54926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	33900238	33900238	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagagtggagaactgcctTctgaaaggtggaatcctact	12	9	11	9	0	1	3	0	1	1	2	2	5	2	4	2	3	3	0	2	3	4	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr9:33900238T>A	ENST00000263228.3	+	3	522	c.331T>A	c.(331-333)Tct>Act	p.S111T		NM_017811.3	NP_060281.2	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme E2R 2	111					protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		AGAACTGCCTTCTGAAAGGTG	0.383																																					p.S111T		.											.	UBE2R2-226	0			c.T331A						.						152	143	146					9																	33900238		2203	4300	6503	SO:0001583	missense	54926	exon3			CTGCCTTCTGAAA	AK000426	CCDS6546.1	9p11.2	2008-02-05			ENSG00000107341	ENSG00000107341		"Ubiquitin-conjugating enzymes E2"	19907	protein-coding gene	gene with protein product		612506				12037680	Standard	XM_005251496		Approved	UBC3B, CDC34B, FLJ20419, MGC10481	uc003ztm.3	Q712K3	OTTHUMG00000019797	ENST00000263228.3:c.331T>A	9.37:g.33900238T>A	ENSP00000263228:p.Ser111Thr	Somatic	134	2		WXS	Illumina HiSeq	Phase_I	150	36	NM_017811	0	0	20	33	13	D3DRL5|Q9NX64	Missense_Mutation	SNP	ENST00000263228.3	37	CCDS6546.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.990741	0.93106	.	.	ENSG00000107341	ENST00000263228	T	0.37752	1.18	5.61	5.61	0.85477	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.46386	0.1390	L	0.38733	1.17	0.80722	D	1	D	0.60575	0.988	P	0.59221	0.854	T	0.38564	-0.9655	10	0.48119	T	0.1	-6.062	15.45	0.75265	0.0:0.0:0.0:1.0	.	111	Q712K3	UB2R2_HUMAN	T	111	ENSP00000263228:S111T	ENSP00000263228:S111T	S	+	1	0	UBE2R2	33890238	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.569000	0.82380	2.127000	0.65507	0.455000	0.32223	TCT	.		0.383	UBE2R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052118.1	NM_017811		A	33900238	T	A	33900238	3	1	64	1	0	0	0	0	1	0	0	0	16904	1783	62	5	341	5	UBE2R2	9	33900238	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08		33900238	107313193	37	6202											
RGP1	57704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35751270	35751270	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attctttctctaggccttcaGgatgtccggtttccccagga	6	14	9	12	1	3	0	1	0	2	0	6	2	5	2	4	4	0	1	4	4	1	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr9:35751270G>A	ENST00000378103.3	-	0	0				GBA2_ENST00000545786.1_5'Flank|RGP1_ENST00000456972.2_Silent_p.Q205Q|MSMP_ENST00000414286.1_5'Flank|GBA2_ENST00000378094.4_5'Flank|RGP1_ENST00000378078.4_Silent_p.Q165Q	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TAGGCCTTCAGGATGTCCGGT	0.498																																					p.Q165Q		.											.	RGP1-23	0			c.G495A						.						226	221	222					9																	35751270		1947	4138	6085	SO:0001631	upstream_gene_variant	9827	exon6			CCTTCAGGATGTC	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		9.37:g.35751270G>A	Exception_encountered	Somatic	404	0		WXS	Illumina HiSeq	Phase_I	410	87	NM_001080496	0	0	0	0	0	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Silent	SNP	ENST00000378103.3	37	CCDS6589.1																																																																																			.		0.498	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		A	35751270	G	A	35751270	1	1	64	0	1	0	0	0	0	0	0	0	13316	991	35	2		2	RGP1	9	35751270	5'Flank	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	1851032	35751270	105462161	38	6203											
NUP214	8021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134020018	134020018	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agctgcttcattctcctttgGatcatctggttttaagccta	7	17	7	10	0	4	0	2	0	2	0	5	1	4	1	2	2	3	3	2	2	2	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr9:134020018G>T	ENST00000359428.5	+	12	1790	c.1646G>T	c.(1645-1647)gGa>gTa	p.G549V	RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.G549V|RP11-544A12.4_ENST00000588378.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.G549V|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	549	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCTCCTTTGGATCATCTGGT	0.537			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.G549V	Pancreas(4;24 48 25510 30394 32571)	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214-1131	0			c.G1646T						.						82	78	79					9																	134020018		2203	4300	6503	SO:0001583	missense	8021	exon12			CCTTTGGATCATC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1646G>T	9.37:g.134020018G>T	ENSP00000352400:p.Gly549Val	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	107	24	NM_005085	0	0	0	0	0	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.7|21.7	4.184253|4.184253	0.78677|0.78677	.|.	.|.	ENSG00000126883|ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899|ENST00000530863	T;T;T|.	0.40756|.	1.24;1.02;1.25|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.000000|.	0.42172|.	D|.	0.000758|.	T|T	0.45935|0.45935	0.1367|0.1367	N|N	0.08118|0.08118	0|0	0.58432|0.58432	D|D	0.999998|0.999998	D;D|.	0.63046|.	0.992;0.992|.	P;P|.	0.59357|.	0.856;0.856|.	T|T	0.41034|0.41034	-0.9531|-0.9531	10|5	0.51188|.	T|.	0.08|.	-8.3011|-8.3011	17.3793|17.3793	0.87400|0.87400	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	549;549|.	P35658-4;P35658|.	.;NU214_HUMAN|.	V|C	549;549;549;549;142|124	ENSP00000352400:G549V;ENSP00000396576:G549V;ENSP00000405014:G549V|.	ENSP00000352400:G549V|.	G|W	+|+	2|3	0|0	NUP214|NUP214	133009839|133009839	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.875000|0.875000	0.50365|0.50365	5.666000|5.666000	0.68059|0.68059	2.778000|2.778000	0.95560|0.95560	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134020018	G	T	134020018	3	4	64	1	0	0	0	0	1	0	0	0	10788	1174	41	4	1692	4	NUP214	9	134020018	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	98268748	134020018	7193413	39	6204											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16918967	16918967	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtagaagttaagcagaaccGgcccagcgatggtgagggga	13	5	16	7	2	0	3	0	1	0	2	0	5	0	4	2	4	3	3	2	4	4	2	rs143741363		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr10:16918967G>A	ENST00000377833.4	-	57	9100	c.9035C>T	c.(9034-9036)cCg>cTg	p.P3012L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3012	CUB 22. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAGCAGAACCGGCCCAGCGAT	0.483													G|||	1	0.000199681	0	0	5008	,	,		17695	0.001		0	False		,,,				2504	0				p.P3012L		.											.	CUBN-166	0			c.C9035T						.	G	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	124	108	114		9035	5.8	0.3	10	dbSNP_134	114	1,8599	1.2+/-3.3	0,1,4299	no	missense	CUBN	NM_001081.3	98	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	probably-damaging	3012/3624	16918967	3,13003	2203	4300	6503	SO:0001583	missense	8029	exon57			AGAACCGGCCCAG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.9035C>T	10.37:g.16918967G>A	ENSP00000367064:p.Pro3012Leu	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	119	18	NM_001081	0	0	21	41	20	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015130	0.75161	4.54E-4	1.16E-4	ENSG00000107611	ENST00000377833	T	0.16897	2.31	5.8	5.8	0.92144	CUB (5);	0.000000	0.46758	D	0.000275	T	0.22781	0.0550	L	0.48362	1.52	0.80722	D	1	D	0.55800	0.973	P	0.44897	0.463	T	0.00402	-1.1762	10	0.54805	T	0.06	.	18.8345	0.92155	0.0:0.0:1.0:0.0	.	3012	O60494	CUBN_HUMAN	L	3012	ENSP00000367064:P3012L	ENSP00000367064:P3012L	P	-	2	0	CUBN	16958973	1.000000	0.71417	0.339000	0.25562	0.006000	0.05464	7.336000	0.79245	2.735000	0.93741	0.655000	0.94253	CCG	G|1.000;A|0.000		0.483	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16918967	G	A	16918967	3	1	64	1	0	0	0	0	1	0	0	0	4057	1116	39	1	1880	1	CUBN	10	16918967	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		16918967	118615780	40	6205											
ACADSB	36	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	124793900	124793900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaatttcctgacttgtttgtCttcttggaagattcctcctc	7	18	6	10	0	2	2	0	1	2	1	6	3	5	3	3	1	0	1	3	1	2	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr10:124793900C>T	ENST00000358776.4	+	2	85	c.71C>T	c.(70-72)tCt>tTt	p.S24F	ACADSB_ENST00000496730.2_3'UTR|ACADSB_ENST00000368869.4_5'UTR	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	24					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	ACTTGTTTGTCTTCTTGGAAG	0.363																																					p.S24F		.											.	ACADSB-92	0			c.C71T						.						143	141	142					10																	124793900		2203	4300	6503	SO:0001583	missense	36	exon2			GTTTGTCTTCTTG	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"acyl-Coenzyme A dehydrogenase, short/branched chain"			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.71C>T	10.37:g.124793900C>T	ENSP00000357873:p.Ser24Phe	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	168	37	NM_001609	0	0	1	2	1	B4DQ51|Q5SQN6|Q96CX7	Missense_Mutation	SNP	ENST00000358776.4	37	CCDS7634.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.85|16.85	3.235388|3.235388	0.58886|0.58886	.|.	.|.	ENSG00000196177|ENSG00000196177	ENST00000411816|ENST00000358776	.|D	.|0.97430	.|-4.38	4.95|4.95	4.02|4.02	0.46733|0.46733	.|.	.|0.689788	.|0.14097	.|N	.|0.341677	D|D	0.93792|0.93792	0.8015|0.8015	L|L	0.27053|0.27053	0.805|0.805	0.26364|0.26364	N|N	0.976999|0.976999	.|P	.|0.45283	.|0.855	.|B	.|0.41510	.|0.359	D|D	0.87882|0.87882	0.2678|0.2678	5|10	.|0.49607	.|T	.|0.09	.|.	12.9162|12.9162	0.58207|0.58207	0.0:0.6883:0.3117:0.0|0.0:0.6883:0.3117:0.0	.|.	.|24	.|P45954	.|ACDSB_HUMAN	F|F	30|24	.|ENSP00000357873:S24F	.|ENSP00000357873:S24F	L|S	+|+	1|2	0|0	ACADSB|ACADSB	124783890|124783890	0.776000|0.776000	0.28616|0.28616	0.955000|0.955000	0.39395|0.39395	0.812000|0.812000	0.45895|0.45895	1.477000|1.477000	0.35431|0.35431	1.167000|1.167000	0.42706|0.42706	0.591000|0.591000	0.81541|0.81541	CTT|TCT	.		0.363	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609		T	124793900	C	T	124793900	3	4	64	1	0	0	0	0	1	0	0	0	115	913	32	2	77	2	ACADSB	10	124793900	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	107874933	124793900	10740847	41	6206											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092643	1092643	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaccactcccagccctccaAcaaccaccacaaccacccct	12	3	1	25	0	0	0	0	0	0	0	2	0	2	0	10	0	4	0	10	0	3	0	rs149562922		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:1092643A>C	ENST00000441003.2	+	30	4489	c.4462A>C	c.(4462-4464)Aca>Cca	p.T1488P	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1489P|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4223	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caGCCCTCCAACAaccaccac	0.627																																					p.T1488P		.											.	MUC2-90	0			c.A4462C						.						302	443	394					11																	1092643		1680	3118	4798	SO:0001583	missense	4583	exon30			CCTCCAACAACCA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4462A>C	11.37:g.1092643A>C	ENSP00000415183:p.Thr1488Pro	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	-	3.842	-0.033557	0.07543	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15952	2.41;2.38	1.28	1.28	0.21552	.	0.642730	0.11935	U	0.515356	T	0.27063	0.0663	.	.	.	0.09310	N	0.999998	D	0.64830	0.994	P	0.62885	0.908	T	0.12344	-1.0551	9	0.30078	T	0.28	.	6.6385	0.22897	1.0:0.0:0.0:0.0	.	1488	E7EUV1	.	P	1488;1489	ENSP00000415183:T1488P;ENSP00000351956:T1489P	ENSP00000351956:T1489P	T	+	1	0	MUC2	1082643	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-2.044000	0.01411	0.654000	0.30846	0.000000	0.15137	ACA	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1092643	A	C	1092643	3	2	64	1	0	0	0	0	1	0	0	0	10000	43	2	5	4580	5	MUC2	11	1092643	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		1092643	133913873	42	6207			1	18		4	4	768	N	T_C_A	1.339896e-09
MUC2	4583	hgsc.bcm.edu	37	chr11	1092795	1092795	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctccaccaaccaccacTcccatcaccaccaccaccac	12	3	0	26	0	1	0	1	0	0	0	3	0	3	0	11	0	1	0	11	0	1	0	rs12786761		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:1092795T>A	ENST00000441003.2	+	30	4641	c.4614T>A	c.(4612-4614)acT>acA	p.T1538T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1539T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caaccaccactcccatcacca	0.627																																					p.T1538T		.											.	MUC2-90	0			c.T4614A						.						126	251	206					11																	1092795		1606	2836	4442	SO:0001819	synonymous_variant	4583	exon30			CACCACTCCCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4614T>A	11.37:g.1092795T>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	11	9	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092795	T	A	1092795	2	1	64	1	0	0	0	0	0	0	0	1	10000	1538	54	5		5	MUC2	11	1092795	Silent	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	152	1092795	133913721	43	6208			1	18		4	4	768	N	T_C_A	1.339896e-09
MUC2	4583	hgsc.bcm.edu	37	chr11	1092813	1092813	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcccatcaccaccaccacCacggtgaccccaaccccaac	12	3	3	23	1	1	1	1	1	0	0	2	1	2	1	9	1	2	0	9	1	2	0	rs12577898|rs199900755		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:1092813C>T	ENST00000441003.2	+	30	4659	c.4632C>T	c.(4630-4632)acC>acT	p.T1544T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1545T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccaccacGGTGACCC	0.637																																					p.T1544T		.											.	MUC2-90	0			c.C4632T						.						47	95	78					11																	1092813		1759	3190	4949	SO:0001819	synonymous_variant	4583	exon30			CACCACCACGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4632C>T	11.37:g.1092813C>T		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	27	6	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092813	C	T	1092813	2	4	64	1	0	0	0	0	0	0	0	1	10000	581	21	2		2	MUC2	11	1092813	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	18	1092813	133913703	44	6209			1	18		4	4	768	N	T_C_A	1.339896e-09
MUC2	4583	hgsc.bcm.edu	37	chr11	1093410	1093410	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accggcacacagaccccaacCacgacacccatcaccaccac	14	1	4	22	2	1	1	1	0	0	1	1	2	1	1	7	1	1	1	7	1	1	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:1093410C>A	ENST00000441003.2	+	30	5256	c.5229C>A	c.(5227-5229)acC>acA	p.T1743T	MUC2_ENST00000333592.6_Silent_p.T31T|MUC2_ENST00000359061.5_Silent_p.T1710T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1743T(1)|p.T1710T(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	agaccccaaccacgacaccca	0.642																																					p.T1743T		.											.	MUC2-90	2	Substitution - coding silent(2)	prostate(2)	c.C5229A						.						209	243	231					11																	1093410		2021	3936	5957	SO:0001819	synonymous_variant	4583	exon30			CCCAACCACGACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5229C>A	11.37:g.1093410C>A		Somatic	4	0		WXS	Illumina HiSeq	Phase_I	62	12	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093410	C	A	1093410	2	1	64	1	0	0	0	0	0	0	0	1	10000	581	21	4		4	MUC2	11	1093410	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	597	1093410	133913106	45	6210			1	18		4	4	768	N	T_C_A	1.339896e-09
LGR4	55366	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	27390335	27390336	+	Frame_Shift_Ins	INS	-	-	A																															tcattatatcttttgcagatINSaagcttctttcgacagttgc																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:27390335_27390336insA	ENST00000379214.4	-	18	2377_2378	c.1934_1935insT	c.(1933-1935)ttafs	p.L645fs	LGR4_ENST00000389858.4_Frame_Shift_Ins_p.L621fs	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	645					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CTTTTGCAGATAAGCTTCTTTC	0.431																																					p.L645fs		.											.	LGR4-91	0			c.1935_1936insT						.																																			SO:0001589	frameshift_variant	55366	exon18			.	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1935dupT	11.37:g.27390337_27390337dupA	ENSP00000368516:p.Leu645fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	112	21	NM_018490	0	0	0	0	0	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Frame_Shift_Ins	INS	ENST00000379214.4	37	CCDS31449.1																																																																																			.		0.431	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		A	27390336	-	A	27390335	7	5	64	1	0	1	1	0	0	0	0	0	8778	1403	49	0	924	0	LGR4	11	27390335	Frame_Shift_Ins	INS	-	TCGA-BQ-5880-01A-11D-1589-08	26296925	27390335	107616181	46	6211											
OR8J3	81168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55904466	55904466	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accgtgactgctatcatatgCgaagcgcaggtggaaaaggc	12	7	13	9	3	1	1	1	1	0	0	1	3	1	2	1	3	3	2	1	3	5	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:55904466C>T	ENST00000301529.1	-	1	728	c.729G>A	c.(727-729)tcG>tcA	p.S243S		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S243S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					CTATCATATGCGAAGCGCAGG	0.403																																					p.S243S		.											.	OR8J3-70	1	Substitution - coding silent(1)	endometrium(1)	c.G729A						.						122	113	116					11																	55904466		2201	4296	6497	SO:0001819	synonymous_variant	81168	exon1			CATATGCGAAGCG		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"GPCR / Class A : Olfactory receptors"	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.729G>A	11.37:g.55904466C>T		Somatic	119	1		WXS	Illumina HiSeq	Phase_I	117	25	NM_001004064	0	0	0	0	0	Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	37	CCDS31520.1																																																																																			.		0.403	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		T	55904466	C	T	55904466	2	4	64	1	0	0	0	0	0	0	0	1	11268	755	27	1		1	OR8J3	11	55904466	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	28514131	55904466	79102050	47	6212											
DPAGT1	1798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118971040	118971040	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgactggccagcctctaggCcgttaattcctgctaggata	8	11	11	11	1	1	1	0	1	1	0	2	2	2	2	4	3	2	2	4	3	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:118971040C>T	ENST00000409993.2	-	6	2126	c.575G>A	c.(574-576)gGc>gAc	p.G192D	DPAGT1_ENST00000432443.2_Missense_Mutation_p.G85D|DPAGT1_ENST00000354202.4_Missense_Mutation_p.G192D|DPAGT1_ENST00000445653.1_5'Flank			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	192			G -> S (in CMSTA2). {ECO:0000269|PubMed:22742743}.		cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		AGCCTCTAGGCCGTTAATTCC	0.507											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G192D		.											.	DPAGT1-221	0			c.G575A						.						107	104	105					11																	118971040		2200	4295	6495	SO:0001583	missense	1798	exon4			TCTAGGCCGTTAA	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.575G>A	11.37:g.118971040C>T	ENSP00000386597:p.Gly192Asp	Somatic	153	0	1492	WXS	Illumina HiSeq	Phase_I	166	28	NM_001382	0	0	8	12	4	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	37	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	C	34	5.350440	0.95830	.	.	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.98914	-5.23;-5.23;-5.23	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.99554	0.9840	H	0.98487	4.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97880	1.0291	10	0.87932	D	0	-21.1374	18.6978	0.91607	0.0:1.0:0.0:0.0	.	85;192	E7EW40;Q9H3H5	.;GPT_HUMAN	D	192;192;85	ENSP00000386597:G192D;ENSP00000346142:G192D;ENSP00000404036:G85D	ENSP00000346142:G192D	G	-	2	0	DPAGT1	118476250	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.652000	0.90054	0.655000	0.94253	GGC	.		0.507	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		T	118971040	C	T	118971040	3	4	64	1	0	0	0	0	1	0	0	0	4721	739	26	2	675	2	DPAGT1	11	118971040	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	63066574	118971040	16035476	48	6213											
PRB4	5545	broad.mit.edu;bcgsc.ca	37	chr12	11461597	11461597	+	Frame_Shift_Del	DEL	C	C	-																															gggtaccttgggactggtttCctccttgtgggggtggtctt																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:11461597delC	ENST00000535904.1	-	3	353	c.320delG	c.(319-321)ggafs	p.G107fs	PRB4_ENST00000445719.2_Frame_Shift_Del_p.G107fs|PRB4_ENST00000279575.1_Frame_Shift_Del_p.G107fs			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	128	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.					extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGACTGGTTTCCTCCTTGTGG	0.612										HNSCC(22;0.051)																											p.G107fs													.	PRB4-91	0			c.320delG						.						190	200	197					12																	11461597		2203	4299	6502	SO:0001589	frameshift_variant	5545	exon3			TGGTTTCCTCCTT		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.320delG	12.37:g.11461597delC	ENSP00000442834:p.Gly107fs	Somatic	589	0		WXS	Illumina HiSeq	Phase_I	731	106	NM_001261399	0	0	0	0	0	A1L439|O00600|P02813|P10161|P10162|P81489	Frame_Shift_Del	DEL	ENST00000535904.1	37	CCDS8641.1																																																																																			.		0.612	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		-	11461597	C	-	11461597	7	5	64	1	0	1	0	1	0	0	0	0	12474	855	30	0	427	0	PRB4	12	11461597	Frame_Shift_Del	DEL	C	TCGA-BQ-5880-01A-11D-1589-08		11461597	122390298	49	6214											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49443557	49443558	+	Frame_Shift_Del	DEL	AT	AT	-																															agctgtcccagcatcgcacaAtagtgagtcatcagtctctg																								rs201794205		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:49443557_49443558delAT	ENST00000301067.7	-	11	3812_3813	c.3813_3814delAT	c.(3811-3816)ctattgfs	p.LL1271fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1271					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GCATCGCACAATAGTGAGTCAT	0.609																																					p.1271_1272del		.											.	MLL2-612	0			c.3813_3814del						.																																			SO:0001589	frameshift_variant	8085	exon11			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.3813_3814delAT	12.37:g.49443557_49443558delAT	ENSP00000301067:p.Leu1271fs	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	158	24	NM_003482	0	0	0	0	0	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.609	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49443558	AT	-	49443557	7	5	64	1	0	1	0	1	0	0	0	0	9646	98	4	0	12975	0	MLL2	12	49443557	Frame_Shift_Del	DEL	AT	TCGA-BQ-5880-01A-11D-1589-08	37981960	49443557	84408338	50	6215											
DGKA	1606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56346149	56346149	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aagaacaagctatggtacttCgaatttgccacatctgaatc	14	11	7	9	1	1	2	0	1	1	1	3	3	1	2	1	1	4	2	1	1	7	4	rs546159503		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:56346149C>G	ENST00000331886.5	+	20	2131	c.1677C>G	c.(1675-1677)ttC>ttG	p.F559L	DGKA_ENST00000551156.1_Missense_Mutation_p.F559L|DGKA_ENST00000394147.1_Missense_Mutation_p.F559L|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	559					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	TATGGTACTTCGAATTTGCCA	0.478																																					p.F559L		.											.	DGKA-255	0			c.C1677G						.						163	139	147					12																	56346149		2203	4300	6503	SO:0001583	missense	1606	exon20			GTACTTCGAATTT	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"EF-hand domain containing"	2849	protein-coding gene	gene with protein product		125855	"diacylglycerol kinase, alpha (80kD)"	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.1677C>G	12.37:g.56346149C>G	ENSP00000328405:p.Phe559Leu	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	172	57	NM_201554	0	0	3	4	1	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	37	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.404771	0.42613	.	.	ENSG00000065357	ENST00000331886;ENST00000555218;ENST00000394147;ENST00000551156;ENST00000552903	T;T;T;T;T	0.39229	1.09;1.67;1.09;1.09;1.67	5.02	-9.21	0.00678	Diacylglycerol kinase, accessory domain (2);	0.053094	0.85682	N	0.000000	T	0.34600	0.0903	L	0.43923	1.385	0.45914	D	0.998757	B;B	0.29378	0.01;0.243	B;B	0.42214	0.054;0.38	T	0.43294	-0.9400	10	0.49607	T	0.09	.	11.684	0.51474	0.0:0.1096:0.2082:0.6822	.	478;559	G3V4E1;P23743	.;DGKA_HUMAN	L	559;478;559;559;169	ENSP00000328405:F559L;ENSP00000451743:F478L;ENSP00000377703:F559L;ENSP00000450359:F559L;ENSP00000451518:F169L	ENSP00000328405:F559L	F	+	3	2	DGKA	54632416	0.169000	0.23002	0.857000	0.33713	0.979000	0.70002	-0.687000	0.05156	-1.471000	0.01886	-0.339000	0.08088	TTC	.		0.478	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			G	56346149	C	G	56346149	3	3	64	1	0	0	0	0	1	0	0	0	4476	883	31	4	1751	4	DGKA	12	56346149	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	6902592	56346149	77505746	51	6216											
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76424647	76424647	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttctgccgcgtggatttgAccgccaggatggcctgacga	6	9	14	12	4	1	2	0	2	1	0	1	5	1	4	4	3	1	1	4	3	0	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:76424647A>G	ENST00000266671.5	-	1	3065	c.875T>C	c.(874-876)gTc>gCc	p.V292A	RP11-290L1.3_ENST00000552367.1_RNA|PHLDA1_ENST00000602540.1_Missense_Mutation_p.V151A|RP11-290L1.2_ENST00000547721.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	292					apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				CGTGGATTTGACCGCCAGGAT	0.657																																					p.V292A		.											.	PHLDA1-90	0			c.T875C						.						55	50	52					12																	76424647		2203	4300	6503	SO:0001583	missense	22822	exon1			GATTTGACCGCCA	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.875T>C	12.37:g.76424647A>G	ENSP00000266671:p.Val292Ala	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_007350	0	0	10	10	0	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Missense_Mutation	SNP	ENST00000266671.5	37	CCDS31861.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.583687	0.86748	.	.	ENSG00000139289	ENST00000266671;ENST00000421361	T	0.78126	-1.15	4.73	4.73	0.59995	.	0.000000	0.64402	D	0.000002	T	0.77818	0.4187	L	0.46157	1.445	0.48901	D	0.99972	P	0.40970	0.734	P	0.46510	0.519	T	0.80953	-0.1152	10	0.87932	D	0	-20.3063	14.3863	0.66947	1.0:0.0:0.0:0.0	.	292	Q8WV24	PHLA1_HUMAN	A	292;151	ENSP00000266671:V292A	ENSP00000266671:V292A	V	-	2	0	PHLDA1	74710914	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.851000	0.69481	1.995000	0.58328	0.459000	0.35465	GTC	.		0.657	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		G	76424647	A	G	76424647	3	3	64	1	0	0	0	0	1	0	0	0	11874	275	10	3	334	3	PHLDA1	12	76424647	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	20078498	76424647	57427248	52	6217											
FGD6	55785	broad.mit.edu	37	chr12	95479666	95479666	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtagccactcatagaagaatCctctgtgtttgctgatacct	10	13	8	10	0	2	3	1	1	1	2	3	3	3	3	3	0	3	3	3	0	5	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:95479666C>A	ENST00000343958.4	-	19	4220	c.3997G>T	c.(3997-3999)Gat>Tat	p.D1333Y	FGD6_ENST00000546711.1_Missense_Mutation_p.D1333Y	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1333	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						ATAGAAGAATCCTCTGTGTTT	0.333																																					p.D1333Y													.	FGD6-137	0			c.G3997T						.						103	115	111					12																	95479666		2202	4299	6501	SO:0001583	missense	55785	exon19			AAGAATCCTCTGT	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.3997G>T	12.37:g.95479666C>A	ENSP00000344446:p.Asp1333Tyr	Somatic	260	0		WXS	Illumina HiSeq	Phase_I	253	4	NM_018351	0	0	1	1	0	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.66|19.66	3.869742|3.869742	0.72065|0.72065	.|.	.|.	ENSG00000180263|ENSG00000180263	ENST00000343958;ENST00000546711|ENST00000548069	T;T|.	0.71579|.	2.59;-0.58|.	5.54|5.54	5.54|5.54	0.83059|0.83059	Pleckstrin homology-type (1);Pleckstrin homology domain (1);|.	0.000000|.	0.47852|.	D|.	0.000202|.	T|T	0.70727|0.70727	0.3257|0.3257	L|L	0.51422|0.51422	1.61|1.61	0.58432|0.58432	D|D	0.999992|0.999992	D;D|.	0.89917|.	0.998;1.0|.	D;D|.	0.76071|.	0.964;0.987|.	T|T	0.66630|0.66630	-0.5875|-0.5875	10|5	0.87932|.	D|.	0|.	-22.0153|-22.0153	19.4712|19.4712	0.94963|0.94963	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1333;1333|.	Q6ZV73-2;Q6ZV73|.	.;FGD6_HUMAN|.	Y|S	1333|76	ENSP00000344446:D1333Y;ENSP00000450342:D1333Y|.	ENSP00000344446:D1333Y|.	D|R	-|-	1|3	0|2	FGD6|FGD6	94003797|94003797	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.596000|4.596000	0.61055|0.61055	2.597000|2.597000	0.87782|0.87782	0.561000|0.561000	0.74099|0.74099	GAT|AGG	.		0.333	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		A	95479666	C	A	95479666	3	1	64	1	0	0	0	0	1	0	0	0	5856	855	30	4	307	4	FGD6	12	95479666	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	19055019	95479666	38372229	53	6218											
WSCD2	9671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	108589975	108589975	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaggggagggttgtccgggaGaaggaggaagagcgaggtaa	13	4	21	3	2	0	2	0	0	0	2	1	7	1	5	1	7	1	2	1	7	4	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:108589975G>C	ENST00000332082.4	+	3	1184	c.366G>C	c.(364-366)gaG>gaC	p.E122D	WSCD2_ENST00000547525.1_Missense_Mutation_p.E122D|WSCD2_ENST00000549903.1_Missense_Mutation_p.E122D|WSCD2_ENST00000261400.3_Missense_Mutation_p.E122D			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	122						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						TTGTCCGGGAGAAGGAGGAAG	0.562																																					p.E122D		.											.	WSCD2-136	0			c.G366C						.						31	33	32					12																	108589975		1980	4147	6127	SO:0001583	missense	9671	exon2			CCGGGAGAAGGAG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.366G>C	12.37:g.108589975G>C	ENSP00000331933:p.Glu122Asp	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	59	22	NM_014653	0	0	0	0	0	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	G	9.938	1.216827	0.22373	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.32023	1.48;1.47;1.48;1.47	5.07	5.07	0.68467	.	0.333232	0.34386	N	0.004017	T	0.22551	0.0544	L	0.28740	0.885	0.40278	D	0.978364	B	0.09022	0.002	B	0.06405	0.002	T	0.06110	-1.0845	10	0.15066	T	0.55	-14.9021	14.9014	0.70681	0.0:0.1436:0.8564:0.0	.	122	Q2TBF2	WSCD2_HUMAN	D	122	ENSP00000448047:E122D;ENSP00000261400:E122D;ENSP00000331933:E122D;ENSP00000447272:E122D	ENSP00000261400:E122D	E	+	3	2	WSCD2	107114105	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	2.741000	0.47426	2.617000	0.88574	0.655000	0.94253	GAG	.		0.562	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		C	108589975	G	C	108589975	3	2	64	1	0	0	0	0	1	0	0	0	17440	933	33	4	368	4	WSCD2	12	108589975	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	13110309	108589975	25261920	54	6219											
ZC3H13	23091	broad.mit.edu;ucsc.edu	37	chr13	46549686	46549686	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctttcccgctctcgatCgtggtctcggtctctatccc	2	15	7	17	4	4	0	0	0	4	0	11	1	6	0	2	2	0	1	2	2	1	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr13:46549686C>A	ENST00000242848.4	-	12	2548	c.2200G>T	c.(2200-2202)Gat>Tat	p.D734Y	ZC3H13_ENST00000282007.3_Missense_Mutation_p.D734Y			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	734	Arg/Glu-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		cgctctcGATCGTGGTCTCGG	0.498																																					p.D734Y	Esophageal Squamous(187;747 2077 11056 31291 44172)												.	ZC3H13-92	0			c.G2200T						.						137	118	125					13																	46549686		2199	4292	6491	SO:0001583	missense	23091	exon12			CTCGATCGTGGTC	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.2200G>T	13.37:g.46549686C>A	ENSP00000242848:p.Asp734Tyr	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	17	3	NM_015070	0	0	9	16	7	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	C	11.81	1.748494	0.30955	.	.	ENSG00000123200	ENST00000242848;ENST00000282007	T;T	0.37584	2.19;1.19	5.19	5.19	0.71726	.	0.000000	0.56097	D	0.000028	T	0.54287	0.1849	.	.	.	0.80722	D	1	P;D	0.63046	0.91;0.992	P;P	0.61397	0.578;0.888	T	0.47005	-0.9150	9	0.30854	T	0.27	.	17.6464	0.88149	0.0:1.0:0.0:0.0	.	734;734	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	Y	734	ENSP00000242848:D734Y;ENSP00000282007:D734Y	ENSP00000242848:D734Y	D	-	1	0	ZC3H13	45447687	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.314000	0.65804	2.567000	0.86603	0.557000	0.71058	GAT	.		0.498	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46549686	C	A	46549686	3	1	64	1	0	0	0	0	1	0	0	0	17597	884	31	4	2518	4	ZC3H13	13	46549686	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		46549686	68620192	55	6220											
SOX1	6656	hgsc.bcm.edu	37	chr13	112722435	112722435	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcggcgcggctgtggccAtgggcgtgggcgtgggcgtg	1	6	24	10	7	0	0	0	0	0	0	0	0	0	0	1	7	0	1	1	7	0	0	rs554658976|rs577675384	byFrequency	TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr13:112722435A>G	ENST00000330949.1	+	1	523	c.463A>G	c.(463-465)Atg>Gtg	p.M155V		NM_005986.2	NP_005977.2	O00570	SOX1_HUMAN	SRY (sex determining region Y)-box 1	155					chromatin organization (GO:0006325)|forebrain neuron development (GO:0021884)|lens morphogenesis in camera-type eye (GO:0002089)|neuron migration (GO:0001764)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4	all_lung(23;0.000652)|Lung NSC(43;0.017)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	all_cancers(25;0.000331)|Lung NSC(25;0.0496)|all_lung(25;0.0831)|all_epithelial(44;0.0868)|Breast(118;0.231)		OV - Ovarian serous cystadenocarcinoma(48;0.132)		ggcTGTGGCCATGGGCGTGGG	0.791																																					p.M155V		.											.	SOX1-468	0			c.A463G						.						2	2	2					13																	112722435		1223	2659	3882	SO:0001583	missense	6656	exon1			GTGGCCATGGGCG		CCDS9523.1	13q34	2008-07-18			ENSG00000182968	ENSG00000182968		"SRY (sex determining region Y)-boxes"	11189	protein-coding gene	gene with protein product	"SRY-related HMG-box gene 1"	602148				9337405	Standard	NM_005986		Approved		uc001vsb.1	O00570	OTTHUMG00000017362	ENST00000330949.1:c.463A>G	13.37:g.112722435A>G	ENSP00000330218:p.Met155Val	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	3	NM_005986	0	0	0	0	0	Q5W0Q1	Missense_Mutation	SNP	ENST00000330949.1	37	CCDS9523.1	.	.	.	.	.	.	.	.	.	.	A	4.148	0.025808	0.08054	.	.	ENSG00000182968	ENST00000330949	T	0.37058	1.22	2.55	-1.05	0.10036	.	0.625334	0.14156	U	0.337708	T	0.10852	0.0265	N	0.02775	-0.495	0.21416	N	0.999691	B	0.16802	0.019	B	0.15052	0.012	T	0.19095	-1.0316	10	0.22706	T	0.39	.	0.6394	0.00808	0.2264:0.214:0.3477:0.2119	.	155	O00570	SOX1_HUMAN	V	155	ENSP00000330218:M155V	ENSP00000330218:M155V	M	+	1	0	SOX1	111770436	0.043000	0.20138	0.997000	0.53966	0.788000	0.44548	0.826000	0.27407	-0.260000	0.09418	-0.731000	0.03576	ATG	.		0.791	SOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045817.3	NM_005986		G	112722435	A	G	112722435	3	3	64	1	0	0	0	0	1	0	0	0	14972	217	8	3	465	3	SOX1	13	112722435	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	66172749	112722435	2447443	56	6221											
MGAT2	4247	broad.mit.edu	37	chr14	50089217	50089220	+	Frame_Shift_Del	DEL	CTAA	CTAA	-																															aatacatgtttccagaaactCtaactatcagtgaaaagttt																								rs563513161	byFrequency	TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	CTAA	CTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr14:50089217_50089220delCTAA	ENST00000305386.2	+	1	1729_1732	c.1231_1234delCTAA	c.(1231-1236)ctaactfs	p.LT411fs	RP11-649E7.5_ENST00000555043.1_RNA|RPL36AL_ENST00000298289.6_5'Flank	NM_002408.3	NP_002399.1	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	411					cellular protein metabolic process (GO:0044267)|oligosaccharide biosynthetic process (GO:0009312)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0008455)|carbohydrate binding (GO:0030246)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)	11	all_epithelial(31;0.0021)|Breast(41;0.0124)					TCCAGAAACTCTAACTATCAGTGA	0.392																																					p.411_412del													.	MGAT2-90	0			c.1231_1234del						.			13,4251		6,1,2125						2.3	1			53	36,8218		18,0,4109	no	frameshift	MGAT2	NM_002408.3		24,1,6234	A1A1,A1R,RR		0.4362,0.3049,0.3914				49,12469				SO:0001589	frameshift_variant	4247	exon1			GAAACTCTAACTA	U15128	CCDS9690.1	14q21	2013-02-25			ENSG00000168282	ENSG00000168282	2.4.1.143	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7045	protein-coding gene	gene with protein product		602616				7635144	Standard	NM_002408		Approved	GNT-II	uc001wwr.3	Q10469	OTTHUMG00000140271	ENST00000305386.2:c.1231_1234delCTAA	14.37:g.50089217_50089220delCTAA	ENSP00000307423:p.Leu411fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	100	8	NM_002408	0	0	0	0	0	B3KPC5|B3KQM0	Frame_Shift_Del	DEL	ENST00000305386.2	37	CCDS9690.1																																																																																			.		0.392	MGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276807.1	NM_002408		-	50089220	CTAA	-	50089217	7	5	64	1	0	1	0	1	0	0	0	0	9568	912	32	0	1233	0	MGAT2	14	50089217	Frame_Shift_Del	DEL	CTAA	TCGA-BQ-5880-01A-11D-1589-08		50089217	57260323	57	6222											
RDH11	51109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	68157017	68157017	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcattgtagaatttctcGccctgcaggttatggaagtg	8	13	11	9	1	1	1	0	0	1	1	2	2	1	2	2	2	2	4	2	2	4	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr14:68157017G>A	ENST00000381346.4	-	5	686	c.576C>T	c.(574-576)ggC>ggT	p.G192G	RP11-1012A1.4_ENST00000553306.1_Missense_Mutation_p.A23V|RP11-1012A1.4_ENST00000554493.1_5'Flank|RDH11_ENST00000428130.2_Intron|RDH11_ENST00000553384.1_Silent_p.G179G	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	192					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	AGAATTTCTCGCCCTGCAGGT	0.517																																					p.G192G		.											.	RDH11-91	0			c.C576T						.						186	159	168					14																	68157017		2203	4300	6503	SO:0001819	synonymous_variant	51109	exon5			TTTCTCGCCCTGC	AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	17964	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 1", "androgen-regulated short-chain dehydrogenase/reductase 1"	607849	"retinol dehydrogenase 11 (all-trans and 9-cis)"			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.576C>T	14.37:g.68157017G>A		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	90	26	NM_016026	0	0	7	27	20	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Silent	SNP	ENST00000381346.4	37	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	G	9.466	1.094486	0.20471	.	.	ENSG00000258466	ENST00000557564	.	.	.	5.67	-11.3	0.00108	.	.	.	.	.	T	0.33440	0.0863	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41124	-0.9526	4	.	.	.	.	3.1001	0.06323	0.2592:0.1913:0.4203:0.1292	.	.	.	.	V	23	.	.	A	-	2	0	RP11-1012A1.4	67226770	0.000000	0.05858	0.230000	0.23976	0.971000	0.66376	-1.633000	0.02022	-2.268000	0.00685	-0.150000	0.13652	GCG	.		0.517	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			A	68157017	G	A	68157017	2	1	64	1	0	0	0	0	0	0	0	1	13222	1074	38	1		1	RDH11	14	68157017	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	18067800	68157017	39192523	58	6223											
CYFIP1	23191	broad.mit.edu	37	chr15	22929873	22929873	+	Frame_Shift_Del	DEL	A	A	-																															acatgaagtgcagtgtgaagAacgaccactcagcgtacaag																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr15:22929873delA	ENST00000313077.7	+	6	672	c.547delA	c.(547-549)aacfs	p.N183fs	CYFIP1_ENST00000560848.1_Frame_Shift_Del_p.N183fs	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		CAGTGTGAAGAACGACCACTC	0.572																																					p.N183fs													.	CYFIP1-99	0			c.547delA						.						128	96	107					15																	22929873		2203	4300	6503	SO:0001589	frameshift_variant	23191	exon6			GTGAAGAACGACC	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.547delA	15.37:g.22929873delA	ENSP00000324549:p.Asn183fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	49	8	NM_014608	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000313077.7	37	CCDS10009.1																																																																																			.		0.572	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		-	22929873	A	-	22929873	7	5	64	1	0	1	0	1	0	0	0	0	4143	246	9	0	565	0	CYFIP1	15	22929873	Frame_Shift_Del	DEL	A	TCGA-BQ-5880-01A-11D-1589-08		22929873	79601519	59	6224											
RFX7	64864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	56387238	56387238	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaattgttcattgacatttgCtgctccataagcaccagctc	10	13	7	11	0	1	1	1	1	0	0	3	2	2	1	2	0	4	5	2	0	2	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr15:56387238C>G	ENST00000559447.2	-	9	2668	c.2397G>C	c.(2395-2397)caG>caC	p.Q799H	RFX7_ENST00000422057.1_Missense_Mutation_p.Q799H|RFX7_ENST00000423270.1_Missense_Mutation_p.Q896H|RFX7_ENST00000317318.6_Missense_Mutation_p.Q896H			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	799					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TTGACATTTGCTGCTCCATAA	0.418																																					p.Q896H		.											.	RFX7-90	0			c.G2688C						.						105	103	103					15																	56387238		1983	4164	6147	SO:0001583	missense	64864	exon9			CATTTGCTGCTCC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"regulatory factor X domain containing 2"	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2397G>C	15.37:g.56387238C>G	ENSP00000453281:p.Gln799His	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	81	15	NM_022841	0	0	2	2	0	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	C	12.40	1.925982	0.34002	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.53423	0.62;0.62;0.62	5.57	4.46	0.54185	.	0.069338	0.51477	D	0.000090	T	0.33614	0.0869	N	0.14661	0.345	0.38957	D	0.95847	P;P	0.49961	0.855;0.93	B;P	0.44732	0.359;0.459	T	0.34304	-0.9834	10	0.87932	D	0	-7.1862	10.8605	0.46823	0.0:0.8402:0.0:0.1598	.	799;799	Q2KHR2;C9JU50	RFX7_HUMAN;.	H	799;896;896	ENSP00000387504:Q799H;ENSP00000313299:Q896H;ENSP00000397644:Q896H	ENSP00000313299:Q896H	Q	-	3	2	RFX7	54174530	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	0.596000	0.24044	2.602000	0.87976	0.514000	0.50259	CAG	.		0.418	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		G	56387238	C	G	56387238	3	3	64	1	0	0	0	0	1	0	0	0	13300	796	28	4	1698	4	RFX7	15	56387238	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	33457365	56387238	46144154	60	6225											
HERC1	8925	hgsc.bcm.edu	37	chr15	63947971	63947971	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacttctgacttatcatagtTaggtcttagtttggcccctt	8	17	7	9	0	3	1	1	1	2	0	3	1	3	1	2	2	1	2	2	2	5	7	rs202195874		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr15:63947971T>C	ENST00000443617.2	-	50	10141	c.10054A>G	c.(10054-10056)Aac>Gac	p.N3352D		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3352					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TTATCATAGTTAGGTCTTAGT	0.368																																					p.N3352D		.											.	HERC1-666	0			c.A10054G						.	T	ASP/ASN	0,3672		0,0,1836	61	54	56		10054	5.1	1	15		56	5,8169		0,5,4082	yes	missense	HERC1	NM_003922.3	23	0,5,5918	CC,CT,TT		0.0612,0.0,0.0422	benign	3352/4862	63947971	5,11841	1836	4087	5923	SO:0001583	missense	8925	exon50			CATAGTTAGGTCT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.10054A>G	15.37:g.63947971T>C	ENSP00000390158:p.Asn3352Asp	Somatic	8	1		WXS	Illumina HiSeq	Phase_I	11	7	NM_003922	0	0	2	2	0	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.715248	0.30413	0.0	6.12E-4	ENSG00000103657	ENST00000443617	T	0.24538	1.85	5.06	5.06	0.68205	.	0.202896	0.41396	D	0.000882	T	0.16085	0.0387	N	0.14661	0.345	0.43145	D	0.994906	B	0.26002	0.139	B	0.24006	0.05	T	0.09228	-1.0684	10	0.21014	T	0.42	.	15.1223	0.72453	0.0:0.0:0.0:1.0	.	3352	Q15751	HERC1_HUMAN	D	3352	ENSP00000390158:N3352D	ENSP00000390158:N3352D	N	-	1	0	HERC1	61735024	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.922000	0.63404	2.040000	0.60383	0.533000	0.62120	AAC	.		0.368	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	63947971	T	C	63947971	3	2	64	1	0	0	0	0	1	0	0	0	7078	1754	61	3	4647	3	HERC1	15	63947971	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	7560733	63947971	38583421	61	6226											
RPGRIP1L	23322	broad.mit.edu	37	chr16	53730090	53730090	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttttatcctcctgcttgcggGcatgctgtttaagtaaaatg	8	16	9	8	1	0	0	0	0	0	0	2	0	2	0	2	1	3	5	2	1	4	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr16:53730090G>A	ENST00000379925.3	-	3	253	c.203C>T	c.(202-204)gCc>gTc	p.A68V	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.A68V|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.A68V|RPGRIP1L_ENST00000568653.3_Missense_Mutation_p.A68V|RPGRIP1L_ENST00000566096.1_Missense_Mutation_p.A68V|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.A68V	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	68					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CTGCTTGCGGGCATGCTGTTT	0.373																																					p.A68V													.	RPGRIP1L-91	0			c.C203T						.						129	132	131					16																	53730090		2198	4300	6498	SO:0001583	missense	23322	exon3			TTGCGGGCATGCT		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.203C>T	16.37:g.53730090G>A	ENSP00000369257:p.Ala68Val	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	253	5	NM_001127897	0	0	2	2	0	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.960376	0.92791	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	D;D	0.82893	-1.66;-1.66	5.73	5.73	0.89815	.	0.121316	0.56097	D	0.000032	D	0.90466	0.7014	M	0.68952	2.095	0.44798	D	0.9978	D;D;D;D	0.76494	0.97;0.97;0.998;0.999	P;P;D;D	0.72075	0.78;0.78;0.948;0.976	D	0.89417	0.3707	10	0.46703	T	0.11	-8.6039	19.8956	0.96956	0.0:0.0:1.0:0.0	.	68;68;68;68	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	V	68	ENSP00000369257:A68V;ENSP00000262135:A68V	ENSP00000262135:A68V	A	-	2	0	RPGRIP1L	52287591	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.063000	0.71162	2.708000	0.92522	0.563000	0.77884	GCC	.		0.373	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		A	53730090	G	A	53730090	3	1	64	1	0	0	0	0	1	0	0	0	13582	1203	42	2	3844	2	RPGRIP1L	16	53730090	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		53730090	36624663	62	6227											
CES1	1066	hgsc.bcm.edu	37	chr16	55866949	55866949	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcagagagagtggccaggaTaaaggcacggagccacatcg	14	3	15	9	2	0	2	0	0	0	2	1	5	0	4	2	4	2	2	2	4	2	1	rs114788146	byFrequency	TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr16:55866949T>C	ENST00000361503.4	-	1	149	c.19A>G	c.(19-21)Atc>Gtc	p.I7V	CES1_ENST00000360526.3_Missense_Mutation_p.I7V|CES1_ENST00000422046.2_Missense_Mutation_p.I7V			P23141	EST1_HUMAN	carboxylesterase 1	7				RAFI -> PALV (in Ref. 3; BAA04650, 8; BAC87749/BAC87751, 9; BAF83312/BAF84898 and 11; AAH12418). {ECO:0000305}.	epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GTGGCCAGGATAAAGGCACGG	0.602													.|||	194	0.038738	0.0234	0.0259	5008	,	,		14138	0.0556		0.0348	False		,,,				2504	0.0552				p.I7V	NSCLC(162;1801 2756 42904 52896)	.											.	CES1-68	0			c.A19G						.																																			SO:0001583	missense	1066	exon1			CCAGGATAAAGGC	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.19A>G	16.37:g.55866949T>C	ENSP00000355193:p.Ile7Val	Somatic	51	1		WXS	Illumina HiSeq	Phase_I	53	5	NM_001025195	0	0	1	1	0	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	0.011	-1.740567	0.00675	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.66638	-0.22;-0.22;-0.22	3.81	-3.67	0.04476	Carboxylesterase, type B (1);	1.757160	0.03836	N	0.269883	T	0.26048	0.0635	N	0.01086	-1.025	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.36672	-0.9738	10	0.02654	T	1	.	0.8085	0.01089	0.2777:0.2688:0.2726:0.1809	.	7;7;7	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	V	7	ENSP00000353720:I7V;ENSP00000355193:I7V;ENSP00000390492:I7V	ENSP00000353720:I7V	I	-	1	0	CES1	54424450	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.671000	0.01954	-0.669000	0.05289	-2.067000	0.00394	ATC	T|1.000;C|0.000		0.602	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		C	55866949	T	C	55866949	3	2	64	1	0	0	0	0	1	0	0	0	3275	1406	49	3	1743	3	CES1	16	55866949	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	2136859	55866949	34487804	63	6228											
DNAH2	146754	broad.mit.edu	37	chr17	7696416	7696416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttatggatgacctaaatatgCccgctaaggacatgtttggg	11	12	11	7	1	0	1	0	1	0	0	0	3	0	3	2	3	1	2	2	3	5	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr17:7696416C>T	ENST00000572933.1	+	48	8922	c.7462C>T	c.(7462-7464)Ccc>Tcc	p.P2488S	DNAH2_ENST00000389173.2_Missense_Mutation_p.P2488S			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2488	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CCTAAATATGCCCGCTAAGGA	0.522																																					p.P2488S													.	DNAH2-102	0			c.C7462T						.						123	107	113					17																	7696416		2203	4300	6503	SO:0001583	missense	146754	exon47			AATATGCCCGCTA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.7462C>T	17.37:g.7696416C>T	ENSP00000458355:p.Pro2488Ser	Somatic	78	2		WXS	Illumina HiSeq	Phase_I	116	4	NM_020877	0	0	0	0	0	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.830320	0.71258	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.63417	-0.04	4.39	3.41	0.39046	ATPase, AAA+ type, core (1);	0.204155	0.41823	N	0.000820	T	0.80088	0.4559	H	0.95187	3.635	0.80722	D	1	B	0.31077	0.307	P	0.46718	0.525	T	0.82246	-0.0552	10	0.72032	D	0.01	.	11.2081	0.48782	0.0:0.9077:0.0:0.0922	.	2488	Q9P225	DYH2_HUMAN	S	2488	ENSP00000373825:P2488S	ENSP00000353818:P2488S	P	+	1	0	DNAH2	7637141	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.293000	0.78740	1.070000	0.40811	0.632000	0.83419	CCC	.		0.522	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7696416	C	T	7696416	3	4	64	1	0	0	0	0	1	0	0	0	4613	739	26	2	7648	2	DNAH2	17	7696416	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		7696416	73498794	64	6229											
FASN	2194	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	80041413	80041413	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgagcgggtggttctgagaaAggtcgaatttgccaatttcc	9	11	13	8	3	1	1	0	1	1	1	3	4	2	1	2	3	2	1	2	3	3	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr17:80041413A>C	ENST00000306749.2	-	31	5539	c.5321T>G	c.(5320-5322)cTt>cGt	p.L1774R	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1774	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GTTCTGAGAAAGGTCGAATTT	0.637																																					p.L1774R	Colon(59;314 1043 11189 28578 32273)	.											.	FASN-90	0			c.T5321G						.						54	53	54					17																	80041413		2199	4298	6497	SO:0001583	missense	2194	exon31			TGAGAAAGGTCGA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5321T>G	17.37:g.80041413A>C	ENSP00000304592:p.Leu1774Arg	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	100	11	NM_004104	0	0	4	6	2	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.846071	0.51164	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.04083	3.71	4.77	3.69	0.42338	Alcohol dehydrogenase, C-terminal (1);Polyketide synthase, enoylreductase (1);NAD(P)-binding domain (1);	0.076785	0.56097	D	0.000039	T	0.24236	0.0587	M	0.90252	3.1	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	T	0.01127	-1.1443	10	0.87932	D	0	-12.1836	9.8571	0.41092	0.9181:0.0:0.0819:0.0	.	1774	P49327	FAS_HUMAN	R	1774;739	ENSP00000304592:L1774R	ENSP00000304592:L1774R	L	-	2	0	FASN	77634702	1.000000	0.71417	0.518000	0.27811	0.128000	0.20619	8.901000	0.92560	0.675000	0.31264	0.459000	0.35465	CTT	.		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		C	80041413	A	C	80041413	3	2	64	1	0	0	0	0	1	0	0	0	5702	72	3	5	2266	5	FASN	17	80041413	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	72344997	80041413	1153797	65	6230											
LAMA1	284217	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr18	7025998	7025998	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttggaggctatggtgagAgggcaggcgcagggctggca	7	8	20	6	1	0	1	0	1	0	1	0	3	0	2	0	7	0	6	0	7	1	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr18:7025998A>G	ENST00000389658.3	-	17	2475	c.2382T>C	c.(2380-2382)ccT>ccC	p.P794P		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	794	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTATGGTGAGAGGGCAGGCGC	0.622																																					p.P794P		.											.	LAMA1-149	0			c.T2382C						.						51	42	45					18																	7025998		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon17			GGTGAGAGGGCAG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"Laminins"	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2382T>C	18.37:g.7025998A>G		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	21	4	NM_005559	0	0	0	0	0		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			.		0.622	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	7025998	A	G	7025998	2	3	64	1	0	0	0	0	0	0	0	1	8626	291	11	3		3	LAMA1	18	7025998	Silent	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		7025998	71051250	66	6231											
ZNF236	7776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	74622686	74622686	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caacagctacaggattccagCacacttgagtctcaggccct	11	8	8	14	0	1	1	1	1	1	0	3	2	2	2	2	2	4	2	2	2	2	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr18:74622686C>T	ENST00000253159.8	+	16	2916	c.2718C>T	c.(2716-2718)agC>agT	p.S906S	ZNF236_ENST00000320610.9_Silent_p.S908S	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	906					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		AGGATTCCAGCACACTTGAGT	0.493																																					p.S906S		.											.	ZNF236-94	0			c.C2718T						.						73	72	72					18																	74622686		2000	4185	6185	SO:0001819	synonymous_variant	7776	exon16			TTCCAGCACACTT	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.2718C>T	18.37:g.74622686C>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	132	29	NM_007345	0	0	0	0	0	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			.		0.493	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			T	74622686	C	T	74622686	2	4	64	1	0	0	0	0	0	0	0	1	17821	709	25	2		2	ZNF236	18	74622686	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	67596688	74622686	3454562	67	6232											
ZNF266	10781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9524367	9524367	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaaggctttcccacattTgacacattcaaaaggcttct	13	11	6	11	0	2	1	1	1	1	0	3	1	3	1	1	2	1	3	1	2	3	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr19:9524367T>G	ENST00000592904.1	-	5	3310	c.1234A>C	c.(1234-1236)Aaa>Caa	p.K412Q	ZNF266_ENST00000588933.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000588221.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000361451.2_Missense_Mutation_p.K412Q|ZNF266_ENST00000592292.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000361151.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000590306.1_Missense_Mutation_p.K412Q			Q14584	ZN266_HUMAN	zinc finger protein 266	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						TTCCCACATTTGACACATTCA	0.433																																					p.K412Q		.											.	ZNF266-91	0			c.A1234C						.						72	72	72					19																	9524367		2203	4300	6503	SO:0001583	missense	10781	exon11			CACATTTGACACA	X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"Zinc fingers, C2H2-type"	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1234A>C	19.37:g.9524367T>G	ENSP00000466714:p.Lys412Gln	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	75	22	NM_001271314	0	0	3	4	1	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	37	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.259791	0.39995	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.07444	3.19;3.19	2.76	-5.41	0.02648	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02533	0.0077	N	0.03029	-0.43	0.09310	N	1	B	0.22604	0.072	B	0.17098	0.017	T	0.45848	-0.9233	9	0.21014	T	0.42	.	5.5147	0.16900	0.0:0.411:0.2893:0.2997	.	412	Q14584	ZN266_HUMAN	Q	412	ENSP00000354680:K412Q;ENSP00000355047:K412Q	ENSP00000355047:K412Q	K	-	1	0	ZNF266	9385367	0.000000	0.05858	0.000000	0.03702	0.998000	0.95712	-1.671000	0.01954	-1.372000	0.02137	0.454000	0.30748	AAA	.		0.433	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			G	9524367	T	G	9524367	3	3	64	1	0	0	0	0	1	0	0	0	17837	1821	63	5	419	5	ZNF266	19	9524367	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08		9524367	49604616	68	6233											
ZNF561	93134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9721627	9721627	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacactgctttaggtgtgaaGaagctgtgacagctctccca	10	10	10	11	0	1	3	0	2	1	1	2	3	1	3	1	1	3	3	1	1	3	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr19:9721627G>A	ENST00000302851.3	-	6	1073	c.710C>T	c.(709-711)tCt>tTt	p.S237F	ZNF561_ENST00000495503.1_5'UTR|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000354661.4_Missense_Mutation_p.S101F|ZNF561_ENST00000424629.1_Missense_Mutation_p.S168F	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	237					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(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						TAGGTGTGAAGAAGCTGTGAC	0.373																																					p.S237F		.											.	ZNF561-91	0			c.C710T						.						65	63	63					19																	9721627		2203	4300	6503	SO:0001583	missense	93134	exon6			TGTGAAGAAGCTG	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"Zinc fingers, C2H2-type", "-"	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.710C>T	19.37:g.9721627G>A	ENSP00000303915:p.Ser237Phe	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	113	24	NM_152289	0	0	1	1	0	B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	37	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	G	11.49	1.655669	0.29425	.	.	ENSG00000171469	ENST00000424629;ENST00000302851;ENST00000354661;ENST00000444611	T;T;T;T	0.29917	1.55;1.55;1.55;2.36	1.1	1.1	0.20463	.	.	.	.	.	T	0.48223	0.1488	M	0.77486	2.375	0.09310	N	1	D	0.61697	0.99	D	0.71656	0.974	T	0.22312	-1.0220	9	0.37606	T	0.19	.	5.1359	0.14934	0.0:0.3792:0.6208:0.0	.	237	Q8N587	ZN561_HUMAN	F	168;237;101;243	ENSP00000393074:S168F;ENSP00000303915:S237F;ENSP00000346687:S101F;ENSP00000392013:S243F	ENSP00000303915:S237F	S	-	2	0	ZNF561	9582627	0.019000	0.18553	0.002000	0.10522	0.033000	0.12548	2.273000	0.43381	0.905000	0.36596	0.298000	0.19748	TCT	.		0.373	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		A	9721627	G	A	9721627	3	1	64	1	0	0	0	0	1	0	0	0	18024	942	33	2	754	2	ZNF561	19	9721627	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	197260	9721627	49407356	69	6234											
MYO9B	4650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17311587	17311587	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggaatcggtgttccgccaGatcaccaacgccaatgagct	10	7	11	13	4	1	2	1	1	0	1	3	3	2	3	4	2	2	2	4	2	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr19:17311587G>T	ENST00000594824.1	+	26	4659	c.4512G>T	c.(4510-4512)caG>caT	p.Q1504H	MYO9B_ENST00000397274.2_Missense_Mutation_p.Q1504H|MYO9B_ENST00000595618.1_Missense_Mutation_p.Q1504H			Q13459	MYO9B_HUMAN	myosin IXB	1504	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						TGTTCCGCCAGATCACCAACG	0.577																																					p.Q1504H		.											.	MYO9B-67	0			c.G4512T						.						127	138	135					19																	17311587		2113	4228	6341	SO:0001583	missense	4650	exon26			CCGCCAGATCACC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.4512G>T	19.37:g.17311587G>T	ENSP00000471367:p.Gln1504His	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	96	25	NM_001130065	0	0	9	9	0	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		.	.	.	.	.	.	.	.	.	.	G	12.57	1.977073	0.34848	.	.	ENSG00000099331	ENST00000397274	D	0.84223	-1.82	4.75	2.43	0.29744	.	0.446964	0.20636	N	0.088489	T	0.68137	0.2968	N	0.08118	0	0.29597	N	0.848014	P;P;P;P	0.37708	0.472;0.606;0.472;0.472	B;B;B;B	0.37422	0.116;0.249;0.116;0.126	T	0.65508	-0.6151	10	0.44086	T	0.13	.	7.4385	0.27169	0.2708:0.0:0.7292:0.0	.	1504;1504;1504;1510	Q13459;Q13459-2;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.;.	H	1504	ENSP00000380444:Q1504H	ENSP00000380444:Q1504H	Q	+	3	2	MYO9B	17172587	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	1.332000	0.33805	1.006000	0.39211	0.491000	0.48974	CAG	.		0.577	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			T	17311587	G	T	17311587	3	4	64	1	0	0	0	0	1	0	0	0	10110	933	33	4	4610	4	MYO9B	19	17311587	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	7589960	17311587	41817396	70	6235											
KIAA0406	9675	hgsc.bcm.edu;broad.mit.edu	37	chr20	36612011	36612011	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggaaccaggtggagtcTgggtccaccttcatcaagtg	10	8	14	9	0	3	0	2	0	1	0	4	3	4	3	3	5	1	0	3	5	2	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr20:36612011T>A	ENST00000373448.2	-	9	3355	c.3117A>T	c.(3115-3117)ccA>ccT	p.P1039P	TTI1_ENST00000449821.1_Silent_p.P1039P|TTI1_ENST00000373447.3_Silent_p.P1039P	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	1039					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						AGGTGGAGTCTGGGTCCACCT	0.617																																					p.P1039P		.											.	TTI1-94	0			c.A3117T						.						63	49	54					20																	36612011		2203	4300	6503	SO:0001819	synonymous_variant	9675	exon9			GGAGTCTGGGTCC	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"	614425	"KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)"	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.3117A>T	20.37:g.36612011T>A		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	50	5	NM_014657	0	0	8	17	9	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Silent	SNP	ENST00000373448.2	37	CCDS13300.1																																																																																			.		0.617	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		A	36612011	T	A	36612011	2	1	64	1	0	0	0	0	0	0	0	1	8194	1567	55	5		5	KIAA0406	20	36612011	Silent	SNP	T	TCGA-BQ-5880-01A-11D-1589-08		36612011	26413509	71	6236											
EMILIN3	90187	broad.mit.edu	37	chr20	39993715	39993715	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcccccatctacactgccGgtattcagcctttacgtagc	7	10	9	15	2	2	0	1	0	1	0	2	0	2	0	4	2	5	2	4	2	4	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr20:39993715G>A	ENST00000332312.3	-	2	442	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	84	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CTACACTGCCGGTATTCAGCC	0.577																																					p.R84W													.	EMILIN3-91	0			c.C250T						.						206	159	175					20																	39993715		2203	4300	6503	SO:0001583	missense	90187	exon2			ACTGCCGGTATTC	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.250C>T	20.37:g.39993715G>A	ENSP00000332806:p.Arg84Trp	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	120	4	NM_052846	0	0	0	0	0	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	37	CCDS13316.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.476057	0.84640	.	.	ENSG00000183798	ENST00000332312	T	0.44482	0.92	4.48	4.48	0.54585	EMI domain (2);	0.374349	0.27311	N	0.019942	T	0.56292	0.1975	L	0.44542	1.39	0.41724	D	0.989522	D	0.89917	1.0	D	0.73708	0.981	T	0.54655	-0.8261	9	.	.	.	-20.5859	17.3473	0.87313	0.0:0.0:1.0:0.0	.	84	Q9NT22	EMIL3_HUMAN	W	84	ENSP00000332806:R84W	.	R	-	1	2	EMILIN3	39427129	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.645000	0.91049	2.308000	0.77769	0.655000	0.94253	CGG	.		0.577	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		A	39993715	G	A	39993715	3	1	64	1	0	0	0	0	1	0	0	0	5108	1115	39	1	2062	1	EMILIN3	20	39993715	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	3381704	39993715	23031805	72	6237											
PREX1	57580	ucsc.edu;bcgsc.ca	37	chr20	47271873	47271873	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggcagctccacgaatctGgaagcacagtgtgtccggct	8	8	14	11	2	1	0	0	0	1	0	3	2	3	1	2	4	2	4	2	4	2	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr20:47271873G>A	ENST00000371941.3	-	19	2186	c.2164C>T	c.(2164-2166)Cag>Tag	p.Q722*	PREX1_ENST00000396220.1_Nonsense_Mutation_p.Q722*	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	722					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CCACGAATCTGGAAGCACAGT	0.552																																					p.Q722X													.	PREX1-231	0			c.C2164T						.						132	93	106					20																	47271873		2203	4300	6503	SO:0001587	stop_gained	57580	exon19			GAATCTGGAAGCA	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2164C>T	20.37:g.47271873G>A	ENSP00000361009:p.Gln722*	Somatic	16	0		WXS	Illumina HiSeq		19	4	NM_020820	0	0	1	1	0	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Nonsense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	40	8.093210	0.98651	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	.	.	.	4.85	4.85	0.62838	.	0.000000	0.52532	U	0.000074	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.991	0.89169	0.0:0.0:1.0:0.0	.	.	.	.	X	722	.	ENSP00000361009:Q722X	Q	-	1	0	PREX1	46705280	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	4.759000	0.62227	2.228000	0.72767	0.655000	0.94253	CAG	.		0.552	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47271873	G	A	47271873	4	1	64	1	0	0	0	0	0	1	0	0	12505	1357	47	2	2903	2	PREX1	20	47271873	Nonsense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	7278158	47271873	15753647	73	6238											
KCNQ2	3785	broad.mit.edu	37	chr20	62073832	62073832	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctgccaagtacaccaggAacgaggccaggatgagacaa	14	5	11	11	1	1	1	0	1	1	1	2	5	1	3	3	3	3	1	3	3	4	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr20:62073832A>G	ENST00000359125.2	-	5	917	c.743T>C	c.(742-744)tTc>tCc	p.F248S	KCNQ2_ENST00000359689.1_Missense_Mutation_p.F248S|KCNQ2_ENST00000360480.3_Missense_Mutation_p.F248S|KCNQ2_ENST00000344425.5_Missense_Mutation_p.F248S|KCNQ2_ENST00000370224.1_Missense_Mutation_p.F248S|KCNQ2_ENST00000357249.2_Missense_Mutation_p.F248S|KCNQ2_ENST00000344462.4_Missense_Mutation_p.F248S|KCNQ2_ENST00000354587.3_Missense_Mutation_p.F248S	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	248					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTACACCAGGAACGAGGCCAG	0.567																																					p.F248S													.	KCNQ2-92	0			c.T743C						.						335	261	286					20																	62073832		2203	4300	6503	SO:0001583	missense	3785	exon5			ACCAGGAACGAGG	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.743T>C	20.37:g.62073832A>G	ENSP00000352035:p.Phe248Ser	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	272	5	NM_172106	0	0	0	0	0	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.022082	0.54576	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222;ENST00000370221;ENST00000344425	D;D;D;D;D;D;D;D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98	3.25	3.25	0.37280	Ion transport (1);	0.150137	0.45126	D	0.000395	D	0.95050	0.8397	N	0.21097	0.63	0.58432	D	0.999996	B;B;B;B;B;B	0.26445	0.149;0.012;0.004;0.004;0.006;0.004	B;B;B;B;B;B	0.29267	0.1;0.042;0.009;0.009;0.009;0.027	D	0.93475	0.6822	10	0.87932	D	0	-3.9255	11.9223	0.52799	1.0:0.0:0.0:0.0	.	248;248;248;248;248;248	B4DEP4;Q53Y30;O43526-3;O43526-2;O43526-4;O43526	.;.;.;.;.;KCNQ2_HUMAN	S	248	ENSP00000349789:F248S;ENSP00000352035:F248S;ENSP00000359246:F248S;ENSP00000346601:F248S;ENSP00000352718:F248S;ENSP00000399612:F248S;ENSP00000353668:F248S;ENSP00000339611:F248S;ENSP00000359244:F248S;ENSP00000359242:F248S;ENSP00000359241:F248S;ENSP00000345523:F248S	ENSP00000345523:F248S	F	-	2	0	KCNQ2	61544276	1.000000	0.71417	0.988000	0.46212	0.896000	0.52359	9.073000	0.93992	1.259000	0.44117	0.254000	0.18369	TTC	.		0.567	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		G	62073832	A	G	62073832	3	3	64	1	0	0	0	0	1	0	0	0	8104	246	9	3	1991	3	KCNQ2	20	62073832	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	14801959	62073832	951688	74	6239											
BAGE	85319	hgsc.bcm.edu;broad.mit.edu	37	chr21	11097627	11097627	+	RNA	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcctggcttggagcagctggGcagacaatgccagaaaaacc	12	5	13	11	0	0	2	0	0	0	2	0	3	0	3	3	3	4	4	3	3	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr21:11097627G>C	ENST00000470054.1	-	0	242							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gagcagctgggcagacaatgc	0.557																																					p.A12G		.											.	.	0			c.C35G						.						61	79	73					21																	11097627		1445	2599	4044			85318	exon2			AGCTGGGCAGACA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"cancer/testis antigen family 2, member 2"					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11097627G>C		Somatic	66	2		WXS	Illumina HiSeq	Phase_I	84	8	NM_182481	0	0	0	0	0	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				.		0.557	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		C	11097627	G	C	11097627	1	2	64	0	1	0	0	0	0	0	0	0	1292	1203	42	4		4	BAGE	21	11097627	RNA	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		11097627	37032268	75	6240											
UMODL1	89766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43505425	43505425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agagagggaccctgtgggctCctggtacaacgtcaccatac	10	7	12	12	1	1	1	1	0	0	1	2	3	2	2	3	3	3	2	3	3	3	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr21:43505425C>T	ENST00000408910.2	+	4	506	c.506C>T	c.(505-507)tCc>tTc	p.S169F	UMODL1_ENST00000400424.2_Missense_Mutation_p.S97F|UMODL1_ENST00000400427.1_Missense_Mutation_p.S97F|UMODL1_ENST00000408989.2_Missense_Mutation_p.S169F	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	169					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CCTGTGGGCTCCTGGTACAAC	0.537																																					p.S169F	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	.											.	UMODL1-93	0			c.C506T						.						113	117	116					21																	43505425		1912	4141	6053	SO:0001583	missense	89766	exon4			TGGGCTCCTGGTA		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.506C>T	21.37:g.43505425C>T	ENSP00000386147:p.Ser169Phe	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	181	34	NM_173568	0	0	0	0	0	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	8.956	0.969471	0.18659	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000380462;ENST00000400417;ENST00000423139	T;T;T;T	0.72394	-0.65;-0.63;-0.65;-0.63	3.02	-6.05	0.02172	.	0.899723	0.09081	N	0.851345	T	0.29423	0.0733	N	0.00823	-1.155	0.20703	N	0.999862	B;B	0.20261	0.043;0.0	B;B	0.15052	0.012;0.0	T	0.18178	-1.0345	10	0.32370	T	0.25	-0.4883	1.9738	0.03412	0.1682:0.5079:0.1126:0.2114	.	169;169	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	F	97;97;169;169;15;15;4	ENSP00000383279:S97F;ENSP00000383276:S97F;ENSP00000386126:S169F;ENSP00000386147:S169F	ENSP00000369829:S15F	S	+	2	0	UMODL1	42378494	0.020000	0.18652	0.030000	0.17652	0.492000	0.33523	-1.121000	0.03270	-1.577000	0.01650	-0.253000	0.11424	TCC	.		0.537	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43505425	C	T	43505425	3	4	64	1	0	0	0	0	1	0	0	0	17013	855	30	2	520	2	UMODL1	21	43505425	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	32407798	43505425	4624470	76	6241											
MYO18B	84700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	26400727	26400727	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccagccagagggcagcctgCagtcctggttgagctgtact	7	8	13	13	0	0	2	0	1	0	1	1	2	1	2	4	2	5	5	4	2	1	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr22:26400727C>T	ENST00000407587.2	+	42	6548	c.6379C>T	c.(6379-6381)Cag>Tag	p.Q2127*	MYO18B_ENST00000536101.1_Nonsense_Mutation_p.Q2126*|MYO18B_ENST00000335473.7_Nonsense_Mutation_p.Q2126*			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2126						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GGGCAGCCTGCAGTCCTGGTT	0.532																																					p.Q2126X		.											.	MYO18B-142	0			c.C6376T						.						79	83	81					22																	26400727		2115	4248	6363	SO:0001587	stop_gained	84700	exon42			AGCCTGCAGTCCT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.6379C>T	22.37:g.26400727C>T	ENSP00000386096:p.Gln2127*	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	102	13	NM_032608	0	0	0	0	0	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Nonsense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	C	48	14.649130	0.99804	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	.	.	.	4.33	3.25	0.37280	.	1.244550	0.05893	N	0.628605	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	8.5131	0.33229	0.2492:0.7508:0.0:0.0	.	.	.	.	X	2126;2126;2127	.	ENSP00000334563:Q2126X	Q	+	1	0	MYO18B	24730727	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.482000	0.45224	2.246000	0.74042	0.650000	0.86243	CAG	.		0.532	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26400727	C	T	26400727	4	4	64	1	0	0	0	0	0	1	0	0	10091	711	25	2	6538	2	MYO18B	22	26400727	Nonsense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		26400727	24903839	77	6242											
MKL1	57591	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	40814880	40814880	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcatctggtccttgtcgCgcccctctagctccgcccgc	3	9	10	19	4	2	0	0	0	2	0	5	0	4	0	5	1	2	3	5	1	1	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr22:40814880C>T	ENST00000355630.3	-	12	2152	c.1562G>A	c.(1561-1563)cGc>cAc	p.R521H	MKL1_ENST00000402042.1_Missense_Mutation_p.R471H|MKL1_ENST00000407029.1_Missense_Mutation_p.R521H|MKL1_ENST00000396617.3_Missense_Mutation_p.R521H	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	521					negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GTCCTTGTCGCGCCCCTCTAG	0.682			T	RBM15	acute megakaryocytic leukemia																																p.R521H		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	0			c.G1562A						.						28	33	31					22																	40814880		2203	4297	6500	SO:0001583	missense	57591	exon12			TTGTCGCGCCCCT	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1562G>A	22.37:g.40814880C>T	ENSP00000347847:p.Arg521His	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	98	21	NM_020831	0	0	2	2	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.039005	0.35989	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.44482	0.93;0.92;0.93;0.93	4.89	3.86	0.44501	.	0.428770	0.23016	N	0.052902	T	0.30230	0.0758	N	0.04959	-0.14	0.09310	N	0.999999	D;D;D	0.67145	0.968;0.996;0.993	B;P;P	0.53185	0.374;0.72;0.609	T	0.05852	-1.0860	10	0.45353	T	0.12	-4.7852	8.2012	0.31426	0.1863:0.7301:0.0:0.0835	.	471;521;521	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	H	521;521;471;521	ENSP00000347847:R521H;ENSP00000379861:R521H;ENSP00000385584:R471H;ENSP00000385835:R521H	ENSP00000347847:R521H	R	-	2	0	MKL1	39144826	0.227000	0.23707	0.758000	0.31321	0.866000	0.49608	0.691000	0.25467	1.165000	0.42670	0.591000	0.81541	CGC	.		0.682	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		T	40814880	C	T	40814880	3	4	64	1	0	0	0	0	1	0	0	0	9626	768	27	1	1249	1	MKL1	22	40814880	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	14414153	40814880	10489686	78	6243											
CLCN4	1183	broad.mit.edu	37	chrX	10162970	10162970	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggcaccttggctggggtcatCgatctcgccgtggactggat	5	10	15	11	3	2	0	1	0	1	0	4	3	2	2	2	6	0	2	2	6	0	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chrX:10162970C>G	ENST00000380833.4	+	5	655	c.264C>G	c.(262-264)atC>atG	p.I88M	CLCN4_ENST00000380829.1_Missense_Mutation_p.I88M|CLCN4_ENST00000421085.2_5'UTR	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	88					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CTGGGGTCATCGATCTCGCCG	0.572																																					p.I88M	Melanoma(74;1050 1296 1576 30544 38374)												.	CLCN4-134	0			c.C264G						.						134	102	113					X																	10162970		2203	4300	6503	SO:0001583	missense	1183	exon5			GGTCATCGATCTC	X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"Ion channels / Chloride channels : Voltage-sensitive"	2022	protein-coding gene	gene with protein product		302910	"chloride channel 4"			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.264C>G	X.37:g.10162970C>G	ENSP00000370213:p.Ile88Met	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	85	3	NM_001830	0	0	1	1	0	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637149	0.47049	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000454850	D;D;D	0.93076	-3.16;-3.16;-3.16	4.84	-4.86	0.03132	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.95567	0.8559	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.92175	0.5747	10	0.87932	D	0	-28.7158	5.9732	0.19363	0.3863:0.154:0.0:0.4597	.	88	P51793	CLCN4_HUMAN	M	88	ENSP00000370213:I88M;ENSP00000370209:I88M;ENSP00000403064:I88M	ENSP00000370209:I88M	I	+	3	3	CLCN4	10122970	0.372000	0.25064	0.280000	0.24747	0.576000	0.36127	-0.275000	0.08525	-1.006000	0.03412	-0.374000	0.07098	ATC	.		0.572	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			G	10162970	C	G	10162970	3	3	64	1	0	0	0	0	1	0	0	0	3471	874	31	4	274	4	CLCN4	23	10162970	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		10162970	145107590	79	6244											
MAOB	4129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	43702915	43702915	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tccggattcttaatgccttaCcctaagagtgtaagtcctgc	9	13	8	11	1	1	1	0	0	1	1	3	2	3	2	4	1	3	1	4	1	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chrX:43702915C>G	ENST00000378069.4	-	2	289		c.e2+1		MAOB_ENST00000487544.1_Splice_Site|MAOB_ENST00000536181.1_Splice_Site|MAOB_ENST00000538942.1_Splice_Site	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B						negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TAATGCCTTACCCTAAGAGTG	0.478																																					.		.											.	MAOB-555	0			c.141+1G>C						.						83	67	73					X																	43702915		2203	4300	6503	SO:0001630	splice_region_variant	4129	exon3			GCCTTACCCTAAG		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.141+1G>C	X.37:g.43702915C>G		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	30	14	NM_000898	0	0	0	0	0	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Splice_Site	SNP	ENST00000378069.4	37	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440115	0.83993	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5321	0.90996	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAOB	43587859	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.391000	0.66266	2.318000	0.78349	0.600000	0.82982	.	.		0.478	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898	Intron	G	43702915	C	G	43702915	5	3	64	1	0	0	0	0	0	0	1	0	9251	521	18	4	1476	4	MAOB	23	43702915	Splice_Site	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	33539945	43702915	111567645	80	6245											
SMC1A	8243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53407985	53407985	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcatcaatctcatccaggAcgaagaagggggctggcttg	11	7	13	10	1	2	1	2	0	1	1	4	3	3	2	1	4	1	3	1	4	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chrX:53407985A>T	ENST00000322213.4	-	23	3588	c.3461T>A	c.(3460-3462)gTc>gAc	p.V1154D	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1154	Ala/Asp-rich (DA-box).				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CTCATCCAGGACGAAGAAGGG	0.632																																					p.V1154D		.											.	SMC1A-232	0			c.T3461A						.						69	60	63					X																	53407985		2203	4300	6503	SO:0001583	missense	8243	exon23			TCCAGGACGAAGA	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3461T>A	X.37:g.53407985A>T	ENSP00000323421:p.Val1154Asp	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	67	27	NM_006306	0	0	1	6	5	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	37	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943345	0.73672	.	.	ENSG00000072501	ENST00000322213	D	0.92099	-2.97	5.29	5.29	0.74685	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.96901	0.8988	M	0.93150	3.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97755	1.0217	10	0.87932	D	0	.	13.4304	0.61051	1.0:0.0:0.0:0.0	.	1154	Q14683	SMC1A_HUMAN	D	1154	ENSP00000323421:V1154D	ENSP00000323421:V1154D	V	-	2	0	SMC1A	53424710	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.113000	0.94321	1.882000	0.54519	0.481000	0.45027	GTC	.		0.632	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		T	53407985	A	T	53407985	3	4	64	1	0	0	0	0	1	0	0	0	14813	275	10	5	252	5	SMC1A	23	53407985	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	9705070	53407985	101862575	81	6246											
C1orf86	199990	broad.mit.edu	37	chr1	2125303	2125303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtgtccaggaaaaggtcttgGgtccgacagtgaagacttca	11	9	13	8	1	2	2	1	1	1	1	4	4	4	3	2	3	0	0	2	3	3	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:2125303G>A	ENST00000378546.4	-	3	269	c.245C>T	c.(244-246)cCc>cTc	p.P82L	C1orf86_ENST00000378545.3_Missense_Mutation_p.P185L|C1orf86_ENST00000487186.1_5'UTR|C1orf86_ENST00000400919.3_5'UTR	NM_182533.2	NP_872339	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	82					cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		AAAGGTCTTGGGTCCGACAGT	0.672																																					p.P82L													.	C1orf86-90	0			c.C245T						.						48	58	55					1																	2125303		2202	4300	6502	SO:0001583	missense	199990	exon3			GTCTTGGGTCCGA	AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378546.4:c.245C>T	1.37:g.2125303G>A	ENSP00000367808:p.Pro82Leu	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	91	3	NM_001256946	0	0	212	223	11	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	Missense_Mutation	SNP	ENST00000378546.4	37	CCDS38.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.405|9.405	1.079136|1.079136	0.20227|0.20227	.|.	.|.	ENSG00000162585|ENSG00000162585	ENST00000400918;ENST00000378546;ENST00000378545|ENST00000378543;ENST00000420515	T;T;T|T	0.50001|0.37411	0.91;0.84;0.76|1.2	3.75|3.75	0.437|0.437	0.16555|0.16555	.|.	2.940440|2.940440	0.01281|0.01281	N|N	0.009732|0.009732	T|T	0.36413|0.36413	0.0966|0.0966	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	B|P	0.33103|0.50819	0.397|0.939	B|P	0.31547|0.47941	0.132|0.562	T|T	0.20672|0.20672	-1.0268|-1.0268	10|10	0.72032|0.87932	D|D	0.01|0	-0.007|-0.007	3.4021|3.4021	0.07327|0.07327	0.1055:0.3392:0.4118:0.1435|0.1055:0.3392:0.4118:0.1435	.|.	82|78	Q6NZ36|Q6ZRT9	CA086_HUMAN|.	L|S	82;82;185|37;82	ENSP00000383709:P82L;ENSP00000367808:P82L;ENSP00000367807:P185L|ENSP00000409721:P82S	ENSP00000367807:P185L|ENSP00000367804:P37S	P|P	-|-	2|1	0|0	C1orf86|C1orf86	2115163|2115163	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.051000|0.051000	0.14879|0.14879	0.217000|0.217000	0.17603|0.17603	0.278000|0.278000	0.22164|0.22164	0.462000|0.462000	0.41574|0.41574	CCC|CCA	.		0.672	C1orf86-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316541.1	NM_182533		A	2125303	G	A	2125303	3	1	65	1	0	0	0	0	1	0	0	0	2069	1232	43	2	545	2	C1orf86	1	2125303	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		2125303	247125318	1	6247											
ACOT7	11332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6399500	6399500	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcccagaagtacctgtgagGatgttttcggacatcacgtt	9	12	10	10	2	1	2	1	1	0	1	3	4	2	4	2	2	1	3	2	2	2	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:6399500G>T	ENST00000377855.2	-	3	587	c.441C>A	c.(439-441)atC>atA	p.I147I	ACOT7_ENST00000541130.1_Silent_p.I117I|ACOT7_ENST00000545482.1_Silent_p.I32I|ACOT7_ENST00000608083.1_Silent_p.I105I|ACOT7_ENST00000377845.3_Silent_p.I117I|ACOT7_ENST00000377842.3_Silent_p.I96I|ACOT7_ENST00000361521.4_Silent_p.I137I	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	147	Acyl coenzyme A hydrolase 1.				coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TACCTGTGAGGATGTTTTCGG	0.597																																					p.I147I	GBM(74;673 1226 4974 11850 13190)	.											.	ACOT7-514	0			c.C441A						.						96	73	81					1																	6399500		2203	4300	6503	SO:0001819	synonymous_variant	11332	exon3			TGTGAGGATGTTT	AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"Acyl CoA thioesterases"	24157	protein-coding gene	gene with protein product	"brain acyl CoA hydrolase"	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.441C>A	1.37:g.6399500G>T		Somatic	86	1		WXS	Illumina HiSeq	Phase_I	78	18	NM_181864	0	0	0	0	0	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Silent	SNP	ENST00000377855.2	37	CCDS65.1																																																																																			.		0.597	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274		T	6399500	G	T	6399500	2	4	65	1	0	0	0	0	0	0	0	1	155	1164	41	4		4	ACOT7	1	6399500	Silent	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	4274197	6399500	242851121	2	6248											
HES2	54626	hgsc.bcm.edu	37	chr1	6479040	6479040	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgctggggcgggggcagacgGgccactggaatccccagcgc	6	3	18	14	4	0	1	0	0	0	1	1	2	1	2	3	6	1	2	3	6	1	0	rs2235687	byFrequency	TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:6479040G>A	ENST00000377834.4	-	4	513	c.415C>T	c.(415-417)Ccg>Tcg	p.P139S	HES2_ENST00000377836.4_Intron|HES2_ENST00000471190.1_5'Flank|HES2_ENST00000487437.1_3'UTR|HES2_ENST00000489730.1_3'UTR|HES2_ENST00000377837.1_Intron	NM_019089.4	NP_061962.2	Q9Y543	HES2_HUMAN	hes family bHLH transcription factor 2	139	Pro-rich.		P -> S (in dbSNP:rs2235687).		negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|transcription factor binding (GO:0008134)			lung(1)|ovary(1)	2	Ovarian(185;0.0634)|all_lung(157;0.154)	all_cancers(23;1.05e-30)|all_epithelial(116;1.37e-17)|all_hematologic(16;1.81e-05)|all_lung(118;2.27e-05)|Acute lymphoblastic leukemia(12;4.98e-05)|Lung NSC(185;9.97e-05)|Colorectal(325;0.0002)|all_neural(13;0.000531)|Renal(390;0.00188)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.02e-35)|GBM - Glioblastoma multiforme(13;1.75e-28)|Colorectal(212;6.1e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000888)|BRCA - Breast invasive adenocarcinoma(365;0.00106)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		ggggcagACGGGCCACTGGAA	0.791													.|||	391	0.0780751	0.1384	0.0346	5008	,	,		9585	0.13		0.0239	False		,,,				2504	0.0297				p.P139S		.											.	HES2-650	0			c.C415T						.						1	1	1					1																	6479040		770	1901	2671	SO:0001583	missense	54626	exon4			CAGACGGGCCACT	AL031848	CCDS30574.1	1p36.31	2013-10-17	2013-10-17		ENSG00000069812	ENSG00000069812		"Basic helix-loop-helix proteins"	16005	protein-coding gene	gene with protein product		609970	"hairy and enhancer of split 2 (Drosophila)"			15254753	Standard	NM_019089		Approved	bHLHb40	uc001amx.3	Q9Y543	OTTHUMG00000000752	ENST00000377834.4:c.415C>T	1.37:g.6479040G>A	ENSP00000367065:p.Pro139Ser	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_019089	0	0	0	0	0	A2RTZ9|Q96EN4|Q9Y542	Missense_Mutation	SNP	ENST00000377834.4	37	CCDS30574.1	182	0.08333333333333333	56	0.11382113821138211	12	0.03314917127071823	94	0.16433566433566432	20	0.026385224274406333	G	12.21	1.869614	0.33069	.	.	ENSG00000069812	ENST00000377834	T	0.58797	0.31	3.36	0.264	0.15607	.	3.233610	0.00892	N	0.002254	T	0.00144	0.0004	N	0.08118	0	0.58432	P	4.000000000004E-6	B	0.14438	0.01	B	0.06405	0.002	T	0.03933	-1.0991	9	0.27785	T	0.31	-9.2319	6.1626	0.20372	0.3543:0.0:0.6457:0.0	rs2235687	139	Q9Y543	HES2_HUMAN	S	139	ENSP00000367065:P139S	ENSP00000367065:P139S	P	-	1	0	HES2	6401627	0.013000	0.17824	0.000000	0.03702	0.036000	0.12997	0.444000	0.21661	0.071000	0.16664	0.462000	0.41574	CCG	G|0.916;A|0.084		0.791	HES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001881.1	NM_019089		A	6479040	G	A	6479040	3	1	65	1	0	0	0	0	1	0	0	0	7087	1232	43	2	110	2	HES2	1	6479040	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	79540	6479040	242771581	3	6249											
SSX2IP	117178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	85124036	85124036	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctacatgacttttcaaaAttctccactgttttctgatg	9	19	4	9	0	4	2	1	2	3	0	5	2	4	2	1	0	1	1	1	0	3	7			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:85124036A>T	ENST00000342203.3	-	9	1306	c.1043T>A	c.(1042-1044)aTt>aAt	p.I348N	SSX2IP_ENST00000370612.4_Missense_Mutation_p.I348N|SSX2IP_ENST00000437941.2_Missense_Mutation_p.I321N|SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000605755.1_Missense_Mutation_p.I321N	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	348					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		ACTTTTCAAAATTCTCCACTG	0.408																																					p.I348N		.											.	SSX2IP-92	0			c.T1043A						.						152	139	143					1																	85124036		2203	4300	6503	SO:0001583	missense	117178	exon9			TTCAAAATTCTCC		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1043T>A	1.37:g.85124036A>T	ENSP00000340279:p.Ile348Asn	Somatic	87	1		WXS	Illumina HiSeq	Phase_I	92	27	NM_001166293	0	0	0	1	1	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	CCDS699.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.583160	0.28268	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.43688	0.94;0.94	5.81	5.81	0.92471	.	0.216387	0.50627	D	0.000111	T	0.30293	0.0760	L	0.57536	1.79	0.44117	D	0.996895	B;B;B	0.20887	0.049;0.012;0.012	B;B;B	0.20384	0.029;0.013;0.013	T	0.19257	-1.0311	10	0.72032	D	0.01	-1.5242	16.1637	0.81739	1.0:0.0:0.0:0.0	.	344;348;321	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	N	348;321;344;348	ENSP00000340279:I348N;ENSP00000412781:I321N	ENSP00000340279:I348N	I	-	2	0	SSX2IP	84896624	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.209000	0.58493	2.216000	0.71823	0.533000	0.62120	ATT	.		0.408	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		T	85124036	A	T	85124036	3	4	65	1	0	0	0	0	1	0	0	0	15236	101	4	5	825	5	SSX2IP	1	85124036	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	78644996	85124036	164126585	4	6250											
MYBPHL	343263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109839700	109839700	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgtcagccttctgcaccGtgtatcccagaagtgctgta	7	13	10	11	1	2	1	1	0	1	1	3	1	3	1	3	0	3	4	3	0	3	4	rs200935635		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:109839700G>C	ENST00000357155.1	-	4	591	c.542C>G	c.(541-543)aCg>aGg	p.T181R	MYBPHL_ENST00000477962.1_Intron	NM_001010985.2|NM_001265613.1	NP_001010985.2|NP_001252542.1	A2RUH7	MBPHL_HUMAN	myosin binding protein H-like	181	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.									central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(2)	14		all_lung(203;0.00519)|all_epithelial(167;0.00575)|Lung NSC(277;0.00822)		Colorectal(144;0.0306)|Lung(183;0.0681)|COAD - Colon adenocarcinoma(174;0.117)|Epithelial(280;0.197)|all cancers(265;0.225)		CTTCTGCACCGTGTATCCCAG	0.577																																					p.T181R		.											.	MYBPHL-92	0			c.C542G						.						169	169	169					1																	109839700		2203	4300	6503	SO:0001583	missense	343263	exon4			TGCACCGTGTATC	AK129834	CCDS30793.1	1p13	2013-02-11			ENSG00000221986	ENSG00000221986		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	30434	protein-coding gene	gene with protein product							Standard	NM_001010985		Approved		uc001dxk.1	A2RUH7	OTTHUMG00000012002	ENST00000357155.1:c.542C>G	1.37:g.109839700G>C	ENSP00000349678:p.Thr181Arg	Somatic	217	2		WXS	Illumina HiSeq	Phase_I	183	64	NM_001010985	0	0	0	0	0	B7ZME5|Q5T2Z7	Missense_Mutation	SNP	ENST00000357155.1	37	CCDS30793.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769751	0.69992	.	.	ENSG00000221986	ENST00000357155	D	0.87729	-2.29	4.15	3.24	0.37175	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	D	0.88945	0.6575	M	0.66560	2.04	0.45930	D	0.99876	D;D	0.89917	1.0;0.967	D;P	0.87578	0.998;0.858	D	0.87804	0.2627	9	0.40728	T	0.16	.	10.551	0.45087	0.0964:0.0:0.9036:0.0	.	158;181	B7ZME5;A2RUH7	.;MBPHL_HUMAN	R	181	ENSP00000349678:T181R	ENSP00000349678:T181R	T	-	2	0	MYBPHL	109641223	0.999000	0.42202	0.964000	0.40570	0.995000	0.86356	2.769000	0.47654	1.355000	0.45865	0.561000	0.74099	ACG	G|0.999;A|0.001		0.577	MYBPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033197.1	NM_001010985		C	109839700	G	C	109839700	3	2	65	1	0	0	0	0	1	0	0	0	10040	1145	40	4	542	4	MYBPHL	1	109839700	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	24715664	109839700	139410921	5	6251											
SMG5	23381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156236156	156236156	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctctttctccacaggttccTtggactctggttcatctgcg	4	15	8	14	1	5	0	1	0	4	0	7	1	6	1	3	3	1	2	3	3	0	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:156236156T>C	ENST00000361813.5	-	12	1415	c.1271A>G	c.(1270-1272)aAg>aGg	p.K424R	SMG5_ENST00000368267.5_Intron|SMG5_ENST00000489907.2_5'UTR	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	424					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					CACAGGTTCCTTGGACTCTGG	0.582																																					p.K424R		.											.	SMG5-231	0			c.A1271G						.						40	42	41					1																	156236156		2203	4300	6503	SO:0001583	missense	23381	exon12			GGTTCCTTGGACT	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"EST1 telomerase component homolog B (S. cerevisiae)"	610962	"smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.1271A>G	1.37:g.156236156T>C	ENSP00000355261:p.Lys424Arg	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	89	31	NM_015327	0	0	3	5	2	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	37	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185549	0.21870	.	.	ENSG00000198952	ENST00000361813	T	0.29142	1.58	5.28	1.67	0.24075	.	0.436632	0.25777	N	0.028378	T	0.04048	0.0113	N	0.12182	0.205	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.33266	-0.9875	10	0.09843	T	0.71	-8.5258	5.1542	0.15027	0.0:0.2355:0.1441:0.6204	.	424	Q9UPR3	SMG5_HUMAN	R	424	ENSP00000355261:K424R	ENSP00000355261:K424R	K	-	2	0	SMG5	154502780	1.000000	0.71417	0.364000	0.25888	0.638000	0.38207	0.547000	0.23299	0.030000	0.15379	0.460000	0.39030	AAG	.		0.582	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		C	156236156	T	C	156236156	3	2	65	1	0	0	0	0	1	0	0	0	14828	1609	56	3	1823	3	SMG5	1	156236156	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	46396456	156236156	93014465	6	6252											
POMC	5443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	25387619	25387619	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagcaacagggcccccgagCggctgcagcacgatctcggc	8	3	13	17	4	1	0	0	0	1	0	2	2	1	0	3	3	5	4	3	3	1	0	rs146551109		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:25387619C>T	ENST00000405623.1	-	2	478	c.23G>A	c.(22-24)cGc>cAc	p.R8H	POMC_ENST00000395826.2_Missense_Mutation_p.R8H|POMC_ENST00000380794.1_Missense_Mutation_p.R8H|POMC_ENST00000264708.3_Missense_Mutation_p.R8H			P01189	COLI_HUMAN	proopiomelanocortin	8					cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)	p.R8H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	GGCCCCCGAGCGGCTGCAGCA	0.612																																					p.R8H	Colon(110;1515 1566 8452 10082 43216)	.											.	POMC-91	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G23A						.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	41	44	43		23,23	3.8	0	2	dbSNP_134	43	0,8598		0,0,4299	no	missense,missense	POMC	NM_000939.2,NM_001035256.1	29,29	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	8/268,8/268	25387619	1,13003	2203	4299	6502	SO:0001583	missense	5443	exon3			CCCGAGCGGCTGC		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"Endogenous ligands"	9201	protein-coding gene	gene with protein product	"adrenocorticotropin", "beta-lipotropin", "alpha-melanocyte stimulating hormone", "beta-melanocyte stimulating hormone", "beta-endorphin", "adrenocorticotropic hormone", "opiomelanocortin prepropeptide"	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.23G>A	2.37:g.25387619C>T	ENSP00000384092:p.Arg8His	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	98	27	NM_001035256	0	0	0	0	0	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	37	CCDS1717.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485311	0.26598	2.27E-4	0.0	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.64	3.82	0.43975	.	0.809526	0.10655	N	0.649411	T	0.64800	0.2631	L	0.33485	1.01	0.09310	N	1	D	0.60575	0.988	B	0.43916	0.436	T	0.52011	-0.8632	10	0.15952	T	0.53	-24.4143	4.8248	0.13410	0.1512:0.6107:0.0:0.2382	.	8	P01189	COLI_HUMAN	H	8	ENSP00000370171:R8H;ENSP00000384092:R8H;ENSP00000264708:R8H;ENSP00000379170:R8H;ENSP00000387993:R8H	ENSP00000264708:R8H	R	-	2	0	POMC	25241123	0.278000	0.24230	0.019000	0.16419	0.096000	0.18686	0.717000	0.25851	1.381000	0.46364	0.462000	0.41574	CGC	C|1.000;T|0.000		0.612	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256		T	25387619	C	T	25387619	3	4	65	1	0	0	0	0	1	0	0	0	12268	768	27	1	788	1	POMC	2	25387619	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		25387619	217811754	7	6253											
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32656054	32656054	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcctccatgctgggtagaAgttcaacaagaacagcagca	13	8	10	10	0	1	2	1	0	0	2	3	2	3	2	2	1	5	6	2	1	5	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:32656054A>C	ENST00000421745.2	+	12	3278	c.3144A>C	c.(3142-3144)gaA>gaC	p.E1048D		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1048					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GCTGGGTAGAAGTTCAACAAG	0.483																																					p.E1048D	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.A3144C						.						92	80	84					2																	32656054		2203	4300	6503	SO:0001583	missense	57448	exon12			GGTAGAAGTTCAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.3144A>C	2.37:g.32656054A>C	ENSP00000393596:p.Glu1048Asp	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	63	20	NM_016252	0	0	0	0	0	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	17.67	3.447198	0.63178	.	.	ENSG00000115760	ENST00000421745	D	0.84070	-1.8	5.62	0.657	0.17850	.	0.000000	0.85682	D	0.000000	D	0.83894	0.5353	L	0.36672	1.1	0.45541	D	0.998494	D	0.58970	0.984	D	0.68192	0.956	T	0.81510	-0.0900	10	0.87932	D	0	.	9.7011	0.40187	0.6633:0.0:0.3367:0.0	.	1048	Q9NR09	BIRC6_HUMAN	D	1048	ENSP00000393596:E1048D	ENSP00000393596:E1048D	E	+	3	2	BIRC6	32509558	1.000000	0.71417	0.985000	0.45067	0.974000	0.67602	1.623000	0.37008	-0.105000	0.12132	0.533000	0.62120	GAA	.		0.483	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32656054	A	C	32656054	3	2	65	1	0	0	0	0	1	0	0	0	1439	69	3	5	3190	5	BIRC6	2	32656054	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	7268435	32656054	210543319	8	6254											
NFE2L2	4780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178098956	178098956	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atacttctcgacttactccaAgatctatatcttgcctccaa	11	14	3	13	1	3	1	0	0	3	1	6	2	5	1	3	0	3	0	3	0	6	6			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:178098956A>C	ENST00000397062.3	-	2	643	c.89T>G	c.(88-90)cTt>cGt	p.L30R	NFE2L2_ENST00000423513.1_Missense_Mutation_p.L14R|NFE2L2_ENST00000397063.4_Missense_Mutation_p.L14R|NFE2L2_ENST00000446151.2_Missense_Mutation_p.L14R|NFE2L2_ENST00000464747.1_Missense_Mutation_p.L14R	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	30					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L30R(2)|p.L30H(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTTACTCCAAGATCTATATC	0.363			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.L30R		.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2-90	3	Substitution - Missense(3)	endometrium(2)|kidney(1)	c.T89G						.						68	61	63					2																	178098956		1839	4101	5940	SO:0001583	missense	4780	exon2			ACTCCAAGATCTA		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.89T>G	2.37:g.178098956A>C	ENSP00000380252:p.Leu30Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	66	7	NM_006164	0	0	1	1	0	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.849301	0.71603	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1;1.1	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.69931	0.3166	M	0.86953	2.85	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.998	T	0.76061	-0.3097	10	0.87932	D	0	.	16.098	0.81144	1.0:0.0:0.0:0.0	.	14;14;14;30	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	R	14;30;14;14;14;14;14	ENSP00000380253:L14R;ENSP00000380252:L30R;ENSP00000411575:L14R;ENSP00000391590:L14R;ENSP00000400073:L14R;ENSP00000412191:L14R;ENSP00000410015:L14R	ENSP00000380252:L30R	L	-	2	0	NFE2L2	177807202	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.210000	0.71456	0.460000	0.39030	CTT	.		0.363	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098956	A	C	178098956	3	2	65	1	0	0	0	0	1	0	0	0	10394	72	3	5	1744	5	NFE2L2	2	178098956	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	145442902	178098956	65100417	9	6255											
AGPS	8540	hgsc.bcm.edu;broad.mit.edu	37	chr2	178301498	178301498	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttattttctaggcatccTtaaatcctagtgatacacct	11	17	4	9	0	1	1	0	1	1	0	3	1	3	1	3	1	1	1	3	1	6	8			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:178301498T>G	ENST00000264167.4	+	4	594	c.448T>G	c.(448-450)Tta>Gta	p.L150V	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	150					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			CTAGGCATCCTTAAATCCTAG	0.303																																					p.L150V		.											.	AGPS-92	0			c.T448G						.						71	74	73					2																	178301498		2202	4292	6494	SO:0001583	missense	8540	exon4			GCATCCTTAAATC	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.448T>G	2.37:g.178301498T>G	ENSP00000264167:p.Leu150Val	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	115	7	NM_003659	0	0	0	0	0	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	37	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	T	9.464	1.093816	0.20471	.	.	ENSG00000018510	ENST00000264167;ENST00000536686	D	0.97575	-4.44	5.62	1.71	0.24356	.	0.148425	0.46758	D	0.000266	D	0.93979	0.8072	M	0.65975	2.015	0.80722	D	1	B	0.20887	0.049	B	0.14578	0.011	D	0.86266	0.1658	10	0.22109	T	0.4	.	6.0179	0.19613	0.2548:0.0693:0.0:0.6759	.	150	O00116	ADAS_HUMAN	V	150;20	ENSP00000264167:L150V	ENSP00000264167:L150V	L	+	1	2	AGPS	178009744	0.994000	0.37717	0.991000	0.47740	0.999000	0.98932	1.525000	0.35953	0.036000	0.15547	0.533000	0.62120	TTA	.		0.303	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			G	178301498	T	G	178301498	3	3	65	1	0	0	0	0	1	0	0	0	394	1606	56	5	462	5	AGPS	2	178301498	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	202542	178301498	64897875	10	6256											
SSFA2	6744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	182786760	182786760	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gggatttgaaattcctcctgGagaaagctcagaatctgttt	11	13	10	7	0	2	3	1	1	1	2	4	5	4	4	2	2	1	2	2	2	3	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:182786760G>C	ENST00000431877.2	+	16	3475	c.3296G>C	c.(3295-3297)gGa>gCa	p.G1099A	SSFA2_ENST00000409136.1_Missense_Mutation_p.G608A|SSFA2_ENST00000409001.1_Missense_Mutation_p.G1077A|SSFA2_ENST00000320370.7_Missense_Mutation_p.G1099A|SSFA2_ENST00000467172.2_3'UTR|SSFA2_ENST00000428267.2_Missense_Mutation_p.G924A	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	1099						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			ATTCCTCCTGGAGAAAGCTCA	0.438																																					p.G1099A		.											.	SSFA2-153	0			c.G3296C						.						86	89	88					2																	182786760		2203	4300	6503	SO:0001583	missense	6744	exon16			CTCCTGGAGAAAG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.3296G>C	2.37:g.182786760G>C	ENSP00000388731:p.Gly1099Ala	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	134	30	NM_001130445	0	0	3	7	4	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536228	0.27475	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136;ENST00000451836	T;T;T;T;T	0.13420	2.84;2.59;2.81;2.81;2.6	5.81	3.98	0.46160	.	0.255590	0.34156	N	0.004205	T	0.09512	0.0234	L	0.31120	0.905	0.33216	D	0.554017	B;B;B;B;B	0.20261	0.043;0.043;0.043;0.043;0.043	B;B;B;B;B	0.19148	0.024;0.024;0.024;0.024;0.024	T	0.10847	-1.0612	10	0.29301	T	0.29	-16.5272	8.2067	0.31458	0.1663:0.1882:0.6455:0.0	.	924;608;1077;1099;1099	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	A	1099;1099;1077;924;608;44	ENSP00000388731:G1099A;ENSP00000314669:G1099A;ENSP00000387319:G1077A;ENSP00000409867:G924A;ENSP00000386916:G608A	ENSP00000314669:G1099A	G	+	2	0	SSFA2	182495005	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.480000	0.45206	1.461000	0.47929	0.563000	0.77884	GGA	.		0.438	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		C	182786760	G	C	182786760	3	2	65	1	0	0	0	0	1	0	0	0	15215	1174	41	4	3358	4	SSFA2	2	182786760	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	4485262	182786760	60412613	11	6257											
ZFAND2B	130617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220072989	220072989	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctacagacttgctgccaTctccagagcacaagctgtgg	9	9	9	14	0	1	2	0	0	1	2	3	2	2	2	3	1	5	3	3	1	2	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:220072989T>G	ENST00000289528.5	+	5	641	c.446T>G	c.(445-447)aTc>aGc	p.I149S	ZFAND2B_ENST00000409097.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000444522.2_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409206.1_Missense_Mutation_p.I149S	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	149						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)	p.I149T(1)		endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTGCTGCCATCTCCAGAGCA	0.532																																					p.I149S		.											.	ZFAND2B-68	1	Substitution - Missense(1)	kidney(1)	c.T446G						.						75	62	66					2																	220072989		2203	4300	6503	SO:0001583	missense	130617	exon5			CTGCCATCTCCAG	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"Zinc fingers, AN1-type domain containing"	25206	protein-coding gene	gene with protein product	"arsenite inducible RNA associated protein-like"	613474	"zinc finger, AN1-type 2B"			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.446T>G	2.37:g.220072989T>G	ENSP00000289528:p.Ile149Ser	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	54	18	NM_138802	0	0	0	0	0	Q8NB98	Missense_Mutation	SNP	ENST00000289528.5	37	CCDS2435.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088523	0.55968	.	.	ENSG00000158552	ENST00000409206;ENST00000409594;ENST00000289528;ENST00000422255;ENST00000409097;ENST00000409336;ENST00000409217;ENST00000444522	T;T;T;T;T;T;T;T	0.44881	0.96;0.96;0.92;0.92;0.91;0.92;0.92;0.91	5.32	5.32	0.75619	Zinc finger, AN1-type (1);	0.400654	0.26646	N	0.023223	T	0.48241	0.1489	L	0.54323	1.7	0.40724	D	0.982682	D;B;B	0.57571	0.98;0.329;0.069	P;B;B	0.51550	0.673;0.116;0.053	T	0.52230	-0.8603	10	0.59425	D	0.04	-15.7601	11.5973	0.50981	0.0:0.0:0.0:1.0	.	40;149;149	B3KQB0;Q8WV99;B4DEN4	.;ZFN2B_HUMAN;.	S	149	ENSP00000386824:I149S;ENSP00000386399:I149S;ENSP00000289528:I149S;ENSP00000409931:I149S;ENSP00000387179:I149S;ENSP00000386898:I149S;ENSP00000386370:I149S;ENSP00000411334:I149S	ENSP00000289528:I149S	I	+	2	0	ZFAND2B	219781233	0.998000	0.40836	1.000000	0.80357	0.961000	0.63080	3.720000	0.54933	2.233000	0.73108	0.533000	0.62120	ATC	.		0.532	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		G	220072989	T	G	220072989	3	3	65	1	0	0	0	0	1	0	0	0	17660	1435	50	5	464	5	ZFAND2B	2	220072989	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	37286229	220072989	23126384	12	6258											
UGT1A3	54659	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	234637943	234637943	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccatgccagaggccaccaGgcagtggtcctcaccccaga	9	5	10	17	0	1	2	1	0	0	2	3	2	3	2	7	3	1	1	7	3	0	0	rs374045195		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:234637943G>A	ENST00000482026.1	+	1	190	c.171G>A	c.(169-171)caG>caA	p.Q57Q	UGT1A1_ENST00000608381.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000609767.1_Silent_p.Q57Q|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000373424.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	57					cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194)			breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	46		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)	Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313)	GAGGCCACCAGGCAGTGGTCC	0.552																																					p.Q57Q		.											.	UGT1A3-24	0			c.G171A						.	G	,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	78	79	78		,,,,,,171,,	-2.3	0	2		78	0,8600		0,0,4300	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,,,	,,,,,,57/535,,	234637943	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	54659	exon1			CCACCAGGCAGTG	M84127	CCDS2509.1	2q37	2010-03-05	2005-07-20		ENSG00000243135	ENSG00000243135		"UDP glucuronosyltransferases"	12535	other	complex locus constituent		606428	"UDP glycosyltransferase 1 family, polypeptide A3"			9295054, 1339448, 11434514	Standard	NM_019093		Approved	UGT1C		P35503	OTTHUMG00000059118	ENST00000482026.1:c.171G>A	2.37:g.234637943G>A		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	76	21	NM_019093	0	0	0	0	0	B8K287	Silent	SNP	ENST00000482026.1	37	CCDS2509.1																																																																																			.		0.552	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		A	234637943	G	A	234637943	2	1	65	1	0	0	0	0	0	0	0	1	16979	991	35	2		2	UGT1A3	2	234637943	Silent	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	14564954	234637943	8561430	13	6259											
ASB1	51665	broad.mit.edu	37	chr2	239344354	239344354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttgtgttcctcctgcagccGcatcaacgagaagtctgtct	7	12	9	13	2	3	1	1	0	2	1	5	2	5	1	3	0	3	3	3	0	2	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:239344354G>A	ENST00000264607.4	+	3	441	c.194G>A	c.(193-195)cGc>cAc	p.R65H	ASB1_ENST00000469885.1_3'UTR|ASB1_ENST00000409297.1_Intron	NM_001040445.1	NP_001035535.1	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box containing 1	65					intracellular signal transduction (GO:0035556)|male genitalia development (GO:0030539)|negative regulation of cytokine biosynthetic process (GO:0042036)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				breast(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		TCCTGCAGCCGCATCAACGAG	0.652																																					p.R65H													.	ASB1-226	0			c.G194A						.						29	26	27					2																	239344354		2203	4300	6503	SO:0001583	missense	51665	exon3			GCAGCCGCATCAA	AF156777	CCDS33416.1	2q37	2013-01-10	2011-01-25		ENSG00000065802	ENSG00000065802		"Ankyrin repeat domain containing"	16011	protein-coding gene	gene with protein product		605758	"ankyrin repeat and SOCS box-containing 1"				Standard	XR_241235		Approved	ASB-1	uc002vyg.3	Q9Y576	OTTHUMG00000152866	ENST00000264607.4:c.194G>A	2.37:g.239344354G>A	ENSP00000264607:p.Arg65His	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_001040445	0	0	0	0	0	A6NL50|Q4ZG29|Q9ULS4	Missense_Mutation	SNP	ENST00000264607.4	37	CCDS33416.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559986	0.65538	.	.	ENSG00000065802	ENST00000264607	T	0.53206	0.63	5.48	5.48	0.80851	Ankyrin repeat-containing domain (3);	0.051919	0.85682	D	0.000000	T	0.60843	0.2300	L	0.46885	1.475	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.51379	-0.8713	10	0.15066	T	0.55	-34.7392	19.3512	0.94387	0.0:0.0:1.0:0.0	.	65	Q9Y576	ASB1_HUMAN	H	65	ENSP00000264607:R65H	ENSP00000264607:R65H	R	+	2	0	ASB1	239009093	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	8.925000	0.92832	2.581000	0.87130	0.650000	0.86243	CGC	.		0.652	ASB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328294.1	NM_001040445		A	239344354	G	A	239344354	3	1	65	1	0	0	0	0	1	0	0	0	1014	1087	38	1	204	1	ASB1	2	239344354	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	4706411	239344354	3855019	14	6260											
TOP2B	7155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	25651158	25651158	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctactggtgctccactgaAttcttcatcaaattccactt	9	16	4	12	0	4	1	2	1	2	0	6	1	6	1	2	1	2	1	2	1	3	6			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:25651158A>C	ENST00000264331.4	-	29	3831	c.3832T>G	c.(3832-3834)Ttc>Gtc	p.F1278V	TOP2B_ENST00000475717.1_5'Flank|TOP2B_ENST00000435706.2_Missense_Mutation_p.F1273V|TOP2B_ENST00000542520.1_Missense_Mutation_p.F130V|TOP2B_ENST00000540199.1_Missense_Mutation_p.F130V	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1278					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	GCTCCACTGAATTCTTCATCA	0.393																																					p.F1273V		.											.	TOP2B-273	0			c.T3817G						.						66	56	59					3																	25651158		1855	4094	5949	SO:0001583	missense	7155	exon29			CACTGAATTCTTC	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.3832T>G	3.37:g.25651158A>C	ENSP00000264331:p.Phe1278Val	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_001068	0	0	8	10	2	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	A	12.12	1.841924	0.32513	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.42131	0.98;1.02;1.02;0.98	5.72	4.56	0.56223	.	0.376224	0.33650	N	0.004681	T	0.27205	0.0667	N	0.19112	0.55	0.48341	D	0.99963	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.04400	-1.0954	10	0.25106	T	0.35	-0.2287	11.3624	0.49651	0.9285:0.0:0.0715:0.0	.	1278;1273	Q02880;Q02880-2	TOP2B_HUMAN;.	V	130;1273;1278;130	ENSP00000446023:F130V;ENSP00000396704:F1273V;ENSP00000264331:F1278V;ENSP00000437352:F130V	ENSP00000264331:F1278V	F	-	1	0	TOP2B	25626162	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.672000	0.54583	1.001000	0.39076	0.477000	0.44152	TTC	.		0.393	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				C	25651158	A	C	25651158	3	2	65	1	0	0	0	0	1	0	0	0	16399	101	4	5	1080	5	TOP2B	3	25651158	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08		25651158	172371272	15	6261											
C3orf23	285343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	44438258	44438258	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaatcatatttacagacCgttctggcatgagtgcagtg	11	12	10	8	1	2	2	1	1	1	1	2	2	2	2	1	1	3	4	1	1	4	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:44438258C>T	ENST00000342649.4	+	8	1244	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TCAIM_ENST00000417237.1_Missense_Mutation_p.R273C	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	273						mitochondrion (GO:0005739)		p.R273G(1)									ATTTACAGACCGTTCTGGCAT	0.408																																					p.R273C		.											.	.	1	Substitution - Missense(1)	lung(1)	c.C817T						.						135	124	128					3																	44438258		2203	4300	6503	SO:0001583	missense	285343	exon8			ACAGACCGTTCTG		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.817C>T	3.37:g.44438258C>T	ENSP00000341539:p.Arg273Cys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	128	55	NM_173826	0	0	1	1	0	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	37	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.396479	0.62177	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.48201	0.82;0.82	5.6	3.8	0.43715	.	0.255107	0.43747	N	0.000534	T	0.56046	0.1959	L	0.51422	1.61	0.46396	D	0.999026	D	0.89917	1.0	P	0.60682	0.878	T	0.56007	-0.8050	10	0.66056	D	0.02	.	9.6854	0.40096	0.0:0.6626:0.267:0.0703	.	273	Q8N3R3	CC023_HUMAN	C	273	ENSP00000402581:R273C;ENSP00000341539:R273C	ENSP00000341539:R273C	R	+	1	0	C3orf23	44413262	1.000000	0.71417	0.930000	0.37139	0.684000	0.39900	2.565000	0.45939	0.718000	0.32166	0.655000	0.94253	CGT	.		0.408	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		T	44438258	C	T	44438258	3	4	65	1	0	0	0	0	1	0	0	0	2222	652	23	1	895	1	C3orf23	3	44438258	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	18787100	44438258	153584172	16	6262											
CCDC58	131076	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122102042	122102042	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaactcggcgaactcctcAcagttcacaccgccactggg	9	7	10	15	3	2	0	2	0	0	0	4	2	3	1	3	3	2	1	3	3	2	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:122102042A>G	ENST00000291458.5	-	1	36	c.30T>C	c.(28-30)tgT>tgC	p.C10C	FAM162A_ENST00000232125.5_5'Flank|FAM162A_ENST00000469967.1_5'Flank|CCDC58_ENST00000479899.1_5'UTR|FAM162A_ENST00000477892.1_5'Flank|CCDC58_ENST00000497726.1_Silent_p.C10C	NM_001017928.2	NP_001017928.1	Q4VC31	CCD58_HUMAN	coiled-coil domain containing 58	10						mitochondrion (GO:0005739)				large_intestine(1)|lung(1)	2				GBM - Glioblastoma multiforme(114;0.148)		CGAACTCCTCACAGTTCACAC	0.602																																					p.C10C		.											.	CCDC58-90	0			c.T30C						.						83	73	76					3																	122102042		2203	4300	6503	SO:0001819	synonymous_variant	131076	exon1			CTCCTCACAGTTC	AK090592	CCDS33838.1	3q21.1	2006-01-17			ENSG00000160124	ENSG00000160124			31136	protein-coding gene	gene with protein product							Standard	XM_005247108		Approved	FLJ33273	uc003eey.3	Q4VC31	OTTHUMG00000159490	ENST00000291458.5:c.30T>C	3.37:g.122102042A>G		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	125	14	NM_001017928	0	0	36	38	2	Q32LY6	Silent	SNP	ENST00000291458.5	37	CCDS33838.1																																																																																			.		0.602	CCDC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355754.1	NM_001017928		G	122102042	A	G	122102042	2	3	65	1	0	0	0	0	0	0	0	1	2834	157	6	3		3	CCDC58	3	122102042	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	77663784	122102042	75920388	17	6263											
PIK3CB	5291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	138409857	138409857	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttacctaagatgccaaaatAgaaactgccctatcctccga	14	9	5	13	1	0	2	0	0	0	2	2	3	2	2	5	0	4	0	5	0	7	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:138409857A>G	ENST00000477593.1	-	14	2094	c.2021T>C	c.(2020-2022)cTa>cCa	p.L674P	PIK3CB_ENST00000544716.1_Missense_Mutation_p.L120P|PIK3CB_ENST00000289153.2_Missense_Mutation_p.L674P			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	674	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	ATGCCAAAATAGAAACTGCCC	0.353																																					p.L674P		.											.	PIK3CB-1311	0			c.T2021C						.						135	140	138					3																	138409857		2203	4300	6503	SO:0001583	missense	5291	exon13			CAAAATAGAAACT		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2021T>C	3.37:g.138409857A>G	ENSP00000418143:p.Leu674Pro	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	269	63	NM_006219	0	0	3	3	0	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	37	CCDS3104.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.8|21.8	4.204435|4.204435	0.79127|0.79127	.|.	.|.	ENSG00000051382|ENSG00000051382	ENST00000477593;ENST00000544716;ENST00000289153|ENST00000493568	T;T;T|.	0.77358|.	-1.09;-1.09;-1.09|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86142|0.86142	0.5862|0.5862	M|M	0.93420|0.93420	3.415|3.415	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.998;0.997;1.0|.	D|D	0.89873|0.89873	0.4024|0.4024	10|5	0.87932|.	D|.	0|.	-9.4984|-9.4984	15.8807|15.8807	0.79201|0.79201	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	674;261;120|.	P42338;B4DZI3;Q68DL0|.	PK3CB_HUMAN;.;.|.	P|H	674;120;674|306	ENSP00000418143:L674P;ENSP00000438259:L120P;ENSP00000289153:L674P|.	ENSP00000289153:L674P|.	L|Y	-|-	2|1	0|0	PIK3CB|PIK3CB	139892547|139892547	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.983000|0.983000	0.72400|0.72400	9.339000|9.339000	0.96797|0.96797	2.151000|2.151000	0.67156|0.67156	0.533000|0.533000	0.62120|0.62120	CTA|TAT	.		0.353	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			G	138409857	A	G	138409857	3	3	65	1	0	0	0	0	1	0	0	0	11940	420	15	3	1229	3	PIK3CB	3	138409857	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	16307815	138409857	59612573	18	6264											
PDE6B	5158	hgsc.bcm.edu;broad.mit.edu	37	chr4	619837	619837	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacatcggggtcgtgggccAcgtggctcagaccaaaaaga	11	5	15	10	3	1	2	1	0	0	2	3	3	1	3	2	5	0	1	2	5	2	0			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr4:619837A>C	ENST00000496514.1	+	1	443	c.422A>C	c.(421-423)cAc>cCc	p.H141P	PDE6B_ENST00000255622.6_Missense_Mutation_p.H141P			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	141	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	GTCGTGGGCCACGTGGCTCAG	0.642																																					p.H141P	GBM(71;463 1194 9848 25922 46834)	.											.	PDE6B-90	0			c.A422C						.						22	16	18					4																	619837		2193	4298	6491	SO:0001583	missense	5158	exon1			TGGGCCACGTGGC	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.422A>C	4.37:g.619837A>C	ENSP00000420295:p.His141Pro	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	9	5	NM_001145291	0	0	0	0	0	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	37	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.877195	0.72294	.	.	ENSG00000133256	ENST00000255622;ENST00000496514	T;T	0.67523	-0.27;-0.27	4.88	4.88	0.63580	GAF (2);	0.103854	0.64402	D	0.000005	T	0.81418	0.4818	M	0.91406	3.205	0.80722	D	1	D;D	0.55385	0.971;0.964	P;P	0.56865	0.808;0.709	D	0.84544	0.0640	10	0.49607	T	0.09	.	12.4206	0.55518	1.0:0.0:0.0:0.0	.	141;141	P35913;P35913-2	PDE6B_HUMAN;.	P	141	ENSP00000255622:H141P;ENSP00000420295:H141P	ENSP00000255622:H141P	H	+	2	0	PDE6B	609837	0.663000	0.27448	1.000000	0.80357	0.862000	0.49288	5.590000	0.67530	1.845000	0.53610	0.459000	0.35465	CAC	.		0.642	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		C	619837	A	C	619837	3	2	65	1	0	0	0	0	1	0	0	0	11672	159	6	5	424	5	PDE6B	4	619837	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08		619837	190534439	19	6265											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79032748	79032748	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagttttggtggagaaaacTaagactttcctgccagtggt	12	12	11	6	0	0	2	0	0	0	2	1	3	1	2	2	3	2	1	2	3	4	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr5:79032748T>C	ENST00000446378.2	+	2	8191	c.8160T>C	c.(8158-8160)acT>acC	p.T2720T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2720					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TGGAGAAAACTAAGACTTTCC	0.378																																					p.T2720T		.											.	CMYA5-77	0			c.T8160C						.						41	41	41					5																	79032748		1825	4074	5899	SO:0001819	synonymous_variant	202333	exon2			GAAAACTAAGACT	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.8160T>C	5.37:g.79032748T>C		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	26	3	NM_153610	0	0	0	0	0	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.		0.378	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79032748	T	C	79032748	2	2	65	1	0	0	0	0	0	0	0	1	3596	1509	53	3		3	CMYA5	5	79032748	Silent	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		79032748	101882512	20	6266											
CYFIP2	26999	broad.mit.edu	37	chr5	156819902	156819902	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttgaacaatgaggtttttgCcatcctgaacaaatacatga	14	12	7	8	0	0	4	0	4	0	0	1	4	1	4	2	1	4	1	2	1	5	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr5:156819902C>T	ENST00000521420.1	+	30	3669	c.3578C>T	c.(3577-3579)gCc>gTc	p.A1193V	CYFIP2_ENST00000377576.3_Missense_Mutation_p.A1219V|CYFIP2_ENST00000347377.6_Missense_Mutation_p.A1219V|CYFIP2_ENST00000435847.2_Missense_Mutation_p.A918V|CYFIP2_ENST00000522463.1_Missense_Mutation_p.A1023V|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000541131.1_Missense_Mutation_p.A1144V|CYFIP2_ENST00000318218.6_Missense_Mutation_p.A1244V					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAGGTTTTTGCCATCCTGAAC	0.517																																					p.A1219V													.	CYFIP2-22	0			c.C3656T						.						107	113	111					5																	156819902		2134	4256	6390	SO:0001583	missense	26999	exon31			TTTTTGCCATCCT	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"p53 inducible protein"	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3578C>T	5.37:g.156819902C>T	ENSP00000430904:p.Ala1193Val	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	115	4	NM_001037332	0	0	112	112	0		Missense_Mutation	SNP	ENST00000521420.1	37		.	.	.	.	.	.	.	.	.	.	C	24.6	4.550606	0.86127	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86;1.86;1.86	5.38	5.38	0.77491	.	0.102104	0.64402	D	0.000002	T	0.51176	0.1659	M	0.66939	2.045	0.80722	D	1	B;B;B;P;B;D	0.53885	0.072;0.086;0.018;0.565;0.046;0.963	B;B;B;B;B;D	0.67231	0.045;0.145;0.049;0.305;0.055;0.95	T	0.48364	-0.9042	10	0.59425	D	0.04	-30.2542	19.5107	0.95140	0.0:1.0:0.0:0.0	.	1083;1023;1193;1219;1219;1244	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	V	1244;1023;1193;1219;1219;1144;918	ENSP00000325817:A1244V;ENSP00000428009:A1023V;ENSP00000430904:A1193V;ENSP00000313567:A1219V;ENSP00000366799:A1219V;ENSP00000444645:A1144V;ENSP00000403793:A918V	ENSP00000325817:A1244V	A	+	2	0	CYFIP2	156752480	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.679000	0.91253	0.655000	0.94253	GCC	.		0.517	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156819902	C	T	156819902	3	4	65	1	0	0	0	0	1	0	0	0	4144	739	26	2	3774	2	CYFIP2	5	156819902	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	77787154	156819902	24095358	21	6267											
SCAND3	114821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	28543371	28543371	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacttggcatcttgaactaaCttccttaattgattttgatg	10	18	6	7	0	1	3	0	3	1	0	2	3	2	3	1	1	3	1	1	1	4	9			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr6:28543371C>A	ENST00000452236.2	-	3	1728	c.1111G>T	c.(1111-1113)Gtt>Ttt	p.V371F	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						CTTGAACTAACTTCCTTAATT	0.343																																					p.V371F		.											.	SCAND3-91	0			c.G1111T						.						122	124	124					6																	28543371		2203	4300	6503	SO:0001583	missense	114821	exon3			AACTAACTTCCTT																												ENST00000452236.2:c.1111G>T	6.37:g.28543371C>A	ENSP00000395259:p.Val371Phe	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	199	63	NM_052923	0	0	0	0	0		Missense_Mutation	SNP	ENST00000452236.2	37	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.208100	0.58343	.	.	ENSG00000232040	ENST00000452236	T	0.01474	4.85	3.45	2.58	0.30949	Integrase, catalytic core (1);Ribonuclease H-like (1);	.	.	.	.	T	0.01320	0.0043	L	0.29908	0.895	0.27530	N	0.951136	D	0.69078	0.997	D	0.63488	0.915	T	0.54337	-0.8309	9	0.23891	T	0.37	.	6.9505	0.24542	0.0:0.8705:0.0:0.1295	.	371	Q6R2W3	SCND3_HUMAN	F	371	ENSP00000395259:V371F	ENSP00000395259:V371F	V	-	1	0	SCAND3	28651350	0.993000	0.37304	0.998000	0.56505	0.998000	0.95712	0.080000	0.14802	0.789000	0.33779	0.655000	0.94253	GTT	.		0.343	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			A	28543371	C	A	28543371	3	1	65	1	0	0	0	0	1	0	0	0	13908	565	20	4	2874	4	SCAND3	6	28543371	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		28543371	142571696	22	6268											
BAT5	7920	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31655645	31655646	+	Frame_Shift_Ins	INS	-	-	G																															caaccactgcctcaccactcINSgaagaccctcctctgccatc																										TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr6:31655645_31655646insG	ENST00000395952.3	-	17	1564_1565	c.1402_1403insC	c.(1402-1404)cgafs	p.R468fs	XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000440843.2_Frame_Shift_Ins_p.R435fs|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000375842.4_Frame_Shift_Ins_p.R249fs	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	468						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						CCTCACCACTCGAAGACCCTCC	0.594																																					p.R468fs		.											.	ABHD16A-91	0			c.1403_1404insC						.																																			SO:0001589	frameshift_variant	7920	exon17			.	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.1403dupC	6.37:g.31655646_31655646dupG	ENSP00000379282:p.Arg468fs	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	118	21	NM_021160	0	0	0	0	0	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Frame_Shift_Ins	INS	ENST00000395952.3	37	CCDS4713.1																																																																																			.		0.594	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			G	31655646	-	G	31655645	7	5	65	1	0	1	1	0	0	0	0	0	1325	884	31	0	289	0	BAT5	6	31655645	Frame_Shift_Ins	INS	-	TCGA-BQ-5881-01A-11D-1589-08	3112274	31655645	139459422	23	6269											
ZNF451	26036	hgsc.bcm.edu	37	chr6	56989646	56989646	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcagaaagaagagaagaatAgagcattcagagtatgtgct	18	7	12	4	0	1	6	1	0	0	6	1	7	1	6	0	0	3	4	0	0	6	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr6:56989646A>G	ENST00000370706.4	+	4	545	c.301A>G	c.(301-303)Aga>Gga	p.R101G	RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.R101G|RP11-203B9.4_ENST00000416069.2_RNA|ZNF451_ENST00000491832.2_Missense_Mutation_p.R101G|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGAGAAGAATAGAGCATTCAG	0.299																																					p.R101G		.											.	ZNF451-93	0			c.A301G						.						43	41	41					6																	56989646		2203	4299	6502	SO:0001583	missense	26036	exon4			AAGAATAGAGCAT	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.301A>G	6.37:g.56989646A>G	ENSP00000359740:p.Arg101Gly	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_001031623	0	0	0	0	0	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	37	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.396743	0.62177	.	.	ENSG00000112200	ENST00000510483;ENST00000370706;ENST00000357489;ENST00000491832	T;T;T;T	0.06449	3.3;3.3;3.3;3.3	5.37	5.37	0.77165	.	0.109018	0.64402	D	0.000012	T	0.03220	0.0094	L	0.36672	1.1	0.80722	D	1	P;P;P;P	0.41848	0.763;0.561;0.736;0.561	B;B;B;B	0.36845	0.234;0.157;0.159;0.157	T	0.41680	-0.9495	10	0.72032	D	0.01	-15.9926	15.3546	0.74418	1.0:0.0:0.0:0.0	.	101;101;101;101	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	G	73;101;101;101	ENSP00000427558:R73G;ENSP00000359740:R101G;ENSP00000350083:R101G;ENSP00000421645:R101G	ENSP00000350083:R101G	R	+	1	2	ZNF451	57097605	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	6.483000	0.73617	2.153000	0.67306	0.533000	0.62120	AGA	.		0.299	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		G	56989646	A	G	56989646	3	3	65	1	0	0	0	0	1	0	0	0	17954	412	15	3	315	3	ZNF451	6	56989646	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	25334001	56989646	114125421	24	6270											
INTS1	26173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	1535858	1535858	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgtgatgcccagcatcaTggacacggccaggacgtcgg	8	6	14	13	4	1	1	1	1	0	0	2	3	1	3	2	4	2	2	2	4	0	0			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr7:1535858T>C	ENST00000404767.3	-	12	1730	c.1645A>G	c.(1645-1647)Atg>Gtg	p.M549V	INTS1_ENST00000389470.4_Missense_Mutation_p.M677V	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	549					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CCCAGCATCATGGACACGGCC	0.632																																					p.M549V		.											.	.	0			c.A1645G						.						84	95	91					7																	1535858		2106	4225	6331	SO:0001583	missense	26173	exon12			GCATCATGGACAC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1645A>G	7.37:g.1535858T>C	ENSP00000385722:p.Met549Val	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	136	35	NM_001080453	0	0	5	6	1	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	37	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	T	18.94	3.730230	0.69074	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.47528	0.84;0.85	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	L	0.52011	1.625	0.80722	D	1	P	0.39044	0.656	B	0.42361	0.385	T	0.47509	-0.9112	10	0.41790	T	0.15	.	14.7485	0.69508	0.0:0.0:0.0:1.0	.	549	Q8N201	INT1_HUMAN	V	549;677	ENSP00000385722:M549V;ENSP00000374121:M677V	ENSP00000374121:M677V	M	-	1	0	INTS1	1502384	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.866000	0.87056	1.897000	0.54924	0.533000	0.62120	ATG	.		0.632	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			C	1535858	T	C	1535858	3	2	65	1	0	0	0	0	1	0	0	0	7796	1464	51	3	5075	3	INTS1	7	1535858	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		1535858	157602805	25	6271											
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	121668665	121668665	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tacatcccctagagttatatCcacacctccaacacctatct	12	11	2	16	0	1	1	0	0	1	1	4	1	4	1	6	0	2	1	6	0	6	5	rs368834797		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr7:121668665C>A	ENST00000393386.2	+	14	5459	c.5048C>A	c.(5047-5049)tCc>tAc	p.S1683Y	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.S823Y	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1683					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AGAGTTATATCCACACCTCCA	0.383																																					p.S1683Y		.											.	PTPRZ1-699	0			c.C5048A						.						184	155	165					7																	121668665		2203	4300	6503	SO:0001583	missense	5803	exon14			TTATATCCACACC	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5048C>A	7.37:g.121668665C>A	ENSP00000377047:p.Ser1683Tyr	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	173	11	NM_002851	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480370	0.84747	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.79141	0.76;-1.24	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000002	D	0.84880	0.5570	L	0.46157	1.445	0.53688	D	0.999977	D;D;P	0.67145	0.996;0.97;0.95	D;P;P	0.65874	0.939;0.682;0.736	D	0.84173	0.0435	10	0.51188	T	0.08	.	20.0637	0.97700	0.0:1.0:0.0:0.0	.	822;823;1683	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	Y	1683;823	ENSP00000377047:S1683Y;ENSP00000410000:S823Y	ENSP00000377047:S1683Y	S	+	2	0	PTPRZ1	121455901	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.356000	0.79445	2.751000	0.94390	0.650000	0.86243	TCC	.		0.383	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121668665	C	A	121668665	3	1	65	1	0	0	0	0	1	0	0	0	12846	855	30	4	5102	4	PTPRZ1	7	121668665	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	120132807	121668665	37469998	26	6272											
KIAA0146	23514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	48308957	48308957	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caagttctatagaaattttaGagtattcatcagatagtgaa	16	14	7	4	0	3	4	2	1	1	3	3	4	3	4	0	0	0	2	0	0	8	8			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr8:48308957G>C	ENST00000297423.4	+	6	931	c.547G>C	c.(547-549)Gag>Cag	p.E183Q	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.E113Q|SPIDR_ENST00000518074.1_Missense_Mutation_p.E123Q	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	183	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											AGAAATTTTAGAGTATTCATC	0.313																																					p.E183Q		.											.	KIAA0146-68	0			c.G547C						.						40	39	39					8																	48308957		1801	4064	5865	SO:0001583	missense	23514	exon6			ATTTTAGAGTATT	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.547G>C	8.37:g.48308957G>C	ENSP00000297423:p.Glu183Gln	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	64	22	NM_001080394	0	0	0	0	0	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.132560	0.56828	.	.	ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342	.	.	.	5.7	4.83	0.62350	.	0.082508	0.50627	D	0.000116	T	0.68577	0.3016	M	0.66939	2.045	0.32160	N	0.583101	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.77004	0.989;0.989;0.989;0.989	T	0.76460	-0.2951	9	0.72032	D	0.01	.	11.6736	0.51417	0.0828:0.0:0.9172:0.0	.	123;113;183;183	B4E0Y6;B4DFV2;B4DEV5;Q14159	.;.;.;K0146_HUMAN	Q	183;123;113	.	ENSP00000297423:E183Q	E	+	1	0	KIAA0146	48471510	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.069000	0.64370	1.414000	0.47017	0.655000	0.94253	GAG	.		0.313	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		C	48308957	G	C	48308957	3	2	65	1	0	0	0	0	1	0	0	0	8178	943	33	4	569	4	KIAA0146	8	48308957	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		48308957	98055065	27	6273											
FER1L6	654463	ucsc.edu;bcgsc.ca	37	chr8	125074167	125074167	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggagagcttttgggaggagTacccttgtgggcacctacac	8	10	14	9	0	0	1	0	0	0	1	0	4	0	3	2	4	3	3	2	4	2	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr8:125074167T>A	ENST00000522917.1	+	25	3428	c.3222T>A	c.(3220-3222)agT>agA	p.S1074R	FER1L6-AS2_ENST00000601180.1_RNA|FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.S1074R	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1074	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TTGGGAGGAGTACCCTTGTGG	0.542																																					p.S1074R													.	FER1L6-100	0			c.T3222A						.						101	104	103					8																	125074167		2015	4219	6234	SO:0001583	missense	654463	exon25			GAGGAGTACCCTT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"fer-1-like 6 (C. elegans)"				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.3222T>A	8.37:g.125074167T>A	ENSP00000428280:p.Ser1074Arg	Somatic	165	2		WXS	Illumina HiSeq		141	46	NM_001039112	0	0	0	0	0		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	T	19.83	3.900796	0.72754	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.84944	-1.92;-1.92	5.51	4.63	0.57726	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	D	0.84986	0.5594	L	0.33668	1.02	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	T	0.80308	-0.1437	10	0.10902	T	0.67	-11.0157	9.245	0.37520	0.0:0.7852:0.0:0.2148	.	1074	Q2WGJ9	FR1L6_HUMAN	R	1074	ENSP00000428280:S1074R;ENSP00000381982:S1074R	ENSP00000381982:S1074R	S	+	3	2	FER1L6	125143348	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	1.585000	0.36600	1.426000	0.47256	-0.242000	0.12053	AGT	.		0.542	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	125074167	T	A	125074167	3	1	65	1	0	0	0	0	1	0	0	0	5834	1635	57	5	3316	5	FER1L6	8	125074167	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	76765210	125074167	21289855	28	6274											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113259109	113259109	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttaccttttcaccagagtTgtctttagctgttggaatct	7	17	7	10	0	3	1	1	0	2	1	3	2	3	2	3	1	2	3	3	1	3	7			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr9:113259109T>C	ENST00000401783.2	-	8	2122	c.1786A>G	c.(1786-1788)Aac>Gac	p.N596D	SVEP1_ENST00000302728.8_Missense_Mutation_p.N596D|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.N573D|SVEP1_ENST00000374461.1_Missense_Mutation_p.N573D	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	596	HYR 1. {ECO:0000255|PROSITE- ProRule:PRU00113}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TCACCAGAGTTGTCTTTAGCT	0.398																																					p.N596D		.											.	SVEP1-75	0			c.A1786G						.						115	107	109					9																	113259109		1881	4083	5964	SO:0001583	missense	79987	exon8			CAGAGTTGTCTTT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1786A>G	9.37:g.113259109T>C	ENSP00000384917:p.Asn596Asp	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_153366	0	0	0	0	0	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505631	0.85282	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.71	5.71	0.89125	Hyalin (2);	0.000000	0.85682	D	0.000000	T	0.59088	0.2168	M	0.90759	3.145	0.38327	D	0.943687	D;D;D	0.89917	0.999;1.0;0.996	D;D;D	0.87578	0.995;0.998;0.99	T	0.71155	-0.4675	10	0.72032	D	0.01	.	14.9529	0.71088	0.0:0.0:0.0:1.0	.	596;596;596	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	D	596;573;596;573	ENSP00000384917:N596D;ENSP00000363593:N573D;ENSP00000304118:N596D;ENSP00000363585:N573D	ENSP00000304118:N596D	N	-	1	0	SVEP1	112298930	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.259000	0.72494	2.181000	0.69327	0.477000	0.44152	AAC	.		0.398	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113259109	T	C	113259109	3	2	65	1	0	0	0	0	1	0	0	0	15452	1812	63	3	9093	3	SVEP1	9	113259109	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		113259109	27954322	29	6275											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092795	1092795	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctccaccaaccaccacTcccatcaccaccaccaccac	12	3	0	26	0	1	0	1	0	0	0	3	0	3	0	11	0	1	0	11	0	1	0	rs12786761		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:1092795T>A	ENST00000441003.2	+	30	4641	c.4614T>A	c.(4612-4614)acT>acA	p.T1538T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1539T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caaccaccactcccatcacca	0.627																																					p.T1538T		.											.	MUC2-90	0			c.T4614A						.						126	251	206					11																	1092795		1606	2836	4442	SO:0001819	synonymous_variant	4583	exon30			CACCACTCCCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4614T>A	11.37:g.1092795T>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092795	T	A	1092795	2	1	65	1	0	0	0	0	0	0	0	1	10000	1538	54	5		5	MUC2	11	1092795	Silent	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		1092795	133913721	30	6276			1	19		3	3	598	N	T_C	6.2404e-07
MUC2	4583	hgsc.bcm.edu	37	chr11	1092813	1092813	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcccatcaccaccaccacCacggtgaccccaaccccaac	12	3	3	23	1	1	1	1	1	0	0	2	1	2	1	9	1	2	0	9	1	2	0	rs12577898|rs199900755		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:1092813C>T	ENST00000441003.2	+	30	4659	c.4632C>T	c.(4630-4632)acC>acT	p.T1544T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1545T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccaccacGGTGACCC	0.637																																					p.T1544T		.											.	MUC2-90	0			c.C4632T						.						47	95	78					11																	1092813		1759	3190	4949	SO:0001819	synonymous_variant	4583	exon30			CACCACCACGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4632C>T	11.37:g.1092813C>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092813	C	T	1092813	2	4	65	1	0	0	0	0	0	0	0	1	10000	581	21	2		2	MUC2	11	1092813	Silent	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	18	1092813	133913703	31	6277			1	19		3	3	598	N	T_C	6.2404e-07
MUC2	4583	hgsc.bcm.edu	37	chr11	1093392	1093392	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accccaaccccaacacccacCggcacacagaccccaaccac	14	0	3	24	1	0	1	0	0	0	1	0	1	0	1	9	1	3	1	9	1	3	0	rs55912427		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:1093392C>T	ENST00000441003.2	+	30	5238	c.5211C>T	c.(5209-5211)acC>acT	p.T1737T	MUC2_ENST00000333592.6_Silent_p.T25T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1704T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caacacccaccggcacacaga	0.647																																					p.T1737T		.											.	MUC2-90	0			c.C5211T						.						163	215	197					11																	1093392		1996	3874	5870	SO:0001819	synonymous_variant	4583	exon30			ACCCACCGGCACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5211C>T	11.37:g.1093392C>T		Somatic	6	1		WXS	Illumina HiSeq	Phase_I	75	4	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093392	C	T	1093392	2	4	65	1	0	0	0	0	0	0	0	1	10000	639	23	1		1	MUC2	11	1093392	Silent	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	579	1093392	133913124	32	6278			1	19		3	3	598	N	T_C	6.2404e-07
INTS5	80789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62417117	62417117	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaggtcaatggaccatgcActaatcacaggtgcccaggc	12	7	11	11	0	2	1	2	1	0	0	2	2	2	2	2	4	2	1	2	4	2	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:62417117A>G	ENST00000330574.2	-	2	487	c.435T>C	c.(433-435)agT>agC	p.S145S		NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	145					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						TGGACCATGCACTAATCACAG	0.572																																					p.S145S		.											.	INTS5-92	0			c.T435C						.						108	107	107					11																	62417117		2202	4299	6501	SO:0001819	synonymous_variant	80789	exon2			CCATGCACTAATC	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"KIAA1698"	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.435T>C	11.37:g.62417117A>G		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	111	44	NM_030628	0	0	1	3	2	Q8N6W5|Q9C0G5	Silent	SNP	ENST00000330574.2	37	CCDS8027.1																																																																																			.		0.572	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		G	62417117	A	G	62417117	2	3	65	1	0	0	0	0	0	0	0	1	7802	156	6	3		3	INTS5	11	62417117	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	61323725	62417117	72589399	33	6279											
ARAP1	116985	hgsc.bcm.edu;broad.mit.edu	37	chr11	72423355	72423355	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctattgtgctgggcaaggacAagctcaggctgctggtatgc	8	10	14	9	0	1	0	1	0	0	0	1	1	1	1	0	4	4	6	0	4	4	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:72423355A>G	ENST00000393609.3	-	7	1110	c.908T>C	c.(907-909)tTg>tCg	p.L303S	ARAP1_ENST00000393605.3_Missense_Mutation_p.L63S|ARAP1_ENST00000426523.1_Missense_Mutation_p.L58S|ARAP1_ENST00000359373.5_Missense_Mutation_p.L303S|ARAP1_ENST00000455638.2_Missense_Mutation_p.L303S|ARAP1_ENST00000429686.1_Missense_Mutation_p.L58S|ARAP1_ENST00000334211.8_Missense_Mutation_p.L58S	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	303					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GGGCAAGGACAAGCTCAGGCT	0.672																																					p.L303S	Ovarian(102;1198 1520 13195 17913 37529)	.											.	ARAP1-91	0			c.T908C						.						28	28	28					11																	72423355		2200	4293	6493	SO:0001583	missense	116985	exon7			AAGGACAAGCTCA	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.908T>C	11.37:g.72423355A>G	ENSP00000377233:p.Leu303Ser	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	23	6	NM_001040118	0	0	2	2	0	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	A	0.304	-0.971901	0.02215	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58;2.58	4.44	2.14	0.27477	.	0.724250	0.11919	N	0.516857	T	0.05135	0.0137	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.43621	-0.9380	10	0.07990	T	0.79	.	8.6422	0.33983	0.16:0.0:0.84:0.0	.	58;58;303;303;63	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	S	303;303;63;58;303;58;58;92	ENSP00000352332:L303S;ENSP00000390461:L303S;ENSP00000377230:L63S;ENSP00000335506:L58S;ENSP00000377233:L303S;ENSP00000392264:L58S;ENSP00000403127:L58S	ENSP00000335506:L58S	L	-	2	0	ARAP1	72101003	0.145000	0.22656	0.008000	0.14137	0.081000	0.17604	0.839000	0.27586	0.330000	0.23485	0.459000	0.35465	TTG	.		0.672	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		G	72423355	A	G	72423355	3	3	65	1	0	0	0	0	1	0	0	0	838	131	5	3	3560	3	ARAP1	11	72423355	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	10006238	72423355	62583161	34	6280											
PGR	5241	broad.mit.edu	37	chr11	100933334	100933334	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cattaacaggttgatcagtgGtggaatcaactgtatgtctt	11	14	10	6	0	3	1	2	1	1	0	3	2	3	2	0	3	2	2	0	3	4	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:100933334G>A	ENST00000325455.5	-	4	3509	c.2056C>T	c.(2056-2058)Cca>Tca	p.P686S	PGR_ENST00000534013.1_Missense_Mutation_p.P92S|PGR_ENST00000263463.5_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	686	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	TTGATCAGTGGTGGAATCAAC	0.458																																					p.P686S	Pancreas(124;2271 2354 21954 22882)												.	PGR-652	0			c.C2056T						.						257	231	240					11																	100933334		2203	4300	6503	SO:0001583	missense	5241	exon4			TCAGTGGTGGAAT	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"Nuclear hormone receptors"	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2056C>T	11.37:g.100933334G>A	ENSP00000325120:p.Pro686Ser	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	258	6	NM_000926	0	0	0	0	0	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.713456	0.30413	.	.	ENSG00000082175	ENST00000325455;ENST00000534013	T;T	0.34859	1.34;1.34	5.86	-2.06	0.07298	Nuclear hormone receptor, ligand-binding (1);	0.307621	0.36101	N	0.002795	T	0.20373	0.0490	L	0.52126	1.63	0.80722	D	1	B;B	0.17667	0.023;0.001	B;B	0.19666	0.026;0.001	T	0.20840	-1.0263	10	0.10636	T	0.68	.	0.9072	0.01287	0.3248:0.1098:0.3401:0.2254	.	686;67	P06401;A7LQ08	PRGR_HUMAN;.	S	686;92	ENSP00000325120:P686S;ENSP00000436561:P92S	ENSP00000325120:P686S	P	-	1	0	PGR	100438544	0.996000	0.38824	0.097000	0.21041	0.737000	0.42083	1.371000	0.34250	-0.722000	0.04922	-0.182000	0.12963	CCA	.		0.458	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			A	100933334	G	A	100933334	3	1	65	1	0	0	0	0	1	0	0	0	11831	1261	44	2	765	2	PGR	11	100933334	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	28509979	100933334	34073182	35	6281											
ZW10	9183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113628545	113628545	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggatgggcaagatgccagcGgcctaaggatatacttcagc	11	7	14	9	1	1	1	1	0	0	1	1	3	1	3	2	4	4	1	2	4	4	4	rs377079908		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:113628545G>A	ENST00000200135.3	-	7	908	c.764C>T	c.(763-765)cCg>cTg	p.P255L		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	255	Interaction with RINT1.				ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		AGATGCCAGCGGCCTAAGGAT	0.403													G|||	1	0.000199681	8e-04	0	5008	,	,		18410	0		0	False		,,,				2504	0				p.P255L		.											.	ZW10-228	0			c.C764T						.	G	LEU/PRO	0,4402		0,0,2201	66	69	68		764	5.5	1	11		68	1,8591	1.2+/-3.3	0,1,4295	no	missense	ZW10	NM_004724.3	98	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	255/780	113628545	1,12993	2201	4296	6497	SO:0001583	missense	9183	exon7			GCCAGCGGCCTAA	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.764C>T	11.37:g.113628545G>A	ENSP00000200135:p.Pro255Leu	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	65	19	NM_004724	0	0	1	1	0	A1A528	Missense_Mutation	SNP	ENST00000200135.3	37	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921357	0.73213	0.0	1.16E-4	ENSG00000086827	ENST00000200135	T	0.64438	-0.1	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.62392	0.2424	L	0.53249	1.67	0.80722	D	1	P	0.43857	0.819	B	0.41374	0.355	T	0.68330	-0.5437	10	0.87932	D	0	-10.4182	18.3058	0.90180	0.0:0.0:1.0:0.0	.	255	O43264	ZW10_HUMAN	L	255	ENSP00000200135:P255L	ENSP00000200135:P255L	P	-	2	0	ZW10	113133755	1.000000	0.71417	0.999000	0.59377	0.869000	0.49853	8.079000	0.89508	2.571000	0.86741	0.650000	0.86243	CCG	.		0.403	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		A	113628545	G	A	113628545	3	1	65	1	0	0	0	0	1	0	0	0	18279	1116	39	1	1615	1	ZW10	11	113628545	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	12695211	113628545	21377971	36	6282											
H3F3C	440093	ucsc.edu	37	chr12	31944972	31944972	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgaagcgccacggtcccAggcctgtagcgatgaggctt	7	8	13	13	4	1	1	0	1	1	0	3	3	2	1	3	3	2	2	3	3	2	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr12:31944972A>G	ENST00000340398.3	-	1	203	c.129T>C	c.(127-129)ccT>ccC	p.P43P		NM_001013699.2	NP_001013721.2	Q6NXT2	H3C_HUMAN	H3 histone, family 3C	43					positive regulation of cell growth (GO:0030307)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	nucleosomal DNA binding (GO:0031492)	p.P43P(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	18						CCACGGTCCCAGGCCTGTAGC	0.617										HNSCC(67;0.2)																											p.P43P													.	H3F3C-68	1	Substitution - coding silent(1)	lung(1)	c.T129C						.						62	60	61					12																	31944972		2203	4300	6503	SO:0001819	synonymous_variant	440093	exon1			GGTCCCAGGCCTG	BC066906	CCDS31769.1	12p11.21	2012-02-15			ENSG00000188375	ENSG00000188375		"Histones / Replication-independent"	33164	protein-coding gene	gene with protein product						21274551	Standard	NM_001013699		Approved	H3.5	uc001rkr.3	Q6NXT2	OTTHUMG00000157811	ENST00000340398.3:c.129T>C	12.37:g.31944972A>G		Somatic	75	0		WXS	Illumina HiSeq		80	1	NM_001013699	0	0	0	668	668	E9P281	Silent	SNP	ENST00000340398.3	37	CCDS31769.1																																																																																			.		0.617	H3F3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349653.1	NM_001013699		G	31944972	A	G	31944972	2	3	65	1	0	0	0	0	0	0	0	1	6956	175	7	3		3	H3F3C	12	31944972	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08		31944972	101906923	37	6283											
SKA3	221150	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	21732196	21732196	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgaatttaaaaccaacgaAgtacgatcttcaacttccaa	16	11	4	10	2	3	1	1	1	2	0	4	3	4	1	2	0	4	1	2	0	8	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr13:21732196A>G	ENST00000314759.5	-	7	1108	c.984T>C	c.(982-984)acT>acC	p.T328T	SKA3_ENST00000400018.3_Silent_p.T328T	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	328					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AAACCAACGAAGTACGATCTT	0.333																																					p.T328T		.											.	SKA3-90	0			c.T984C						.						111	119	116					13																	21732196		2203	4300	6503	SO:0001819	synonymous_variant	221150	exon7			CAACGAAGTACGA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 3"	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.984T>C	13.37:g.21732196A>G		Somatic	174	1		WXS	Illumina HiSeq	Phase_I	182	40	NM_145061	0	0	0	0	0	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Silent	SNP	ENST00000314759.5	37	CCDS31946.1																																																																																			.		0.333	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061		G	21732196	A	G	21732196	2	3	65	1	0	0	0	0	0	0	0	1	14386	59	3	3		3	SKA3	13	21732196	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08		21732196	93437682	38	6284											
ITGBL1	9358	ucsc.edu;bcgsc.ca	37	chr13	102235670	102235670	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgatgagagggactgtagaGctgtctatgaccgatattct	10	12	13	6	1	2	4	0	3	2	2	2	7	2	5	1	1	1	2	1	1	3	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr13:102235670G>C	ENST00000376180.3	+	6	1051	c.832G>C	c.(832-834)Gct>Cct	p.A278P	ITGBL1_ENST00000376162.3_Missense_Mutation_p.A185P|ITGBL1_ENST00000545560.2_Missense_Mutation_p.A137P	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	278	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGACTGTAGAGCTGTCTATGA	0.473																																					p.A278P													.	ITGBL1-92	0			c.G832C						.						247	236	240					13																	102235670		2203	4300	6503	SO:0001583	missense	9358	exon6			TGTAGAGCTGTCT	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"ten integrin EGF-like repeat domains protein", "ITGBL1, integrin beta-like 1"	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.832G>C	13.37:g.102235670G>C	ENSP00000365351:p.Ala278Pro	Somatic	242	2		WXS	Illumina HiSeq		246	83	NM_004791	0	0	1	1	0	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Missense_Mutation	SNP	ENST00000376180.3	37	CCDS9499.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.174126	0.38413	.	.	ENSG00000198542	ENST00000376180;ENST00000537118;ENST00000539955;ENST00000545560;ENST00000376162	D;T;D	0.84944	-1.92;-0.97;-1.71	5.11	0.959	0.19624	Epidermal growth factor-like (1);	0.309269	0.39210	N	0.001434	D	0.85961	0.5819	L	0.51422	1.61	0.54753	D	0.999981	D;P	0.65815	0.995;0.589	D;P	0.79784	0.993;0.632	T	0.80266	-0.1454	10	0.27785	T	0.31	.	4.8497	0.13531	0.0715:0.12:0.4414:0.3671	.	137;278	B3KTP1;O95965	.;ITGBL_HUMAN	P	278;186;137;137;185	ENSP00000365351:A278P;ENSP00000439903:A137P;ENSP00000365332:A185P	ENSP00000365332:A185P	A	+	1	0	ITGBL1	101033671	1.000000	0.71417	0.240000	0.24138	0.005000	0.04900	2.055000	0.41345	0.220000	0.20860	-0.218000	0.12543	GCT	.		0.473	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791		C	102235670	G	C	102235670	3	2	65	1	0	0	0	0	1	0	0	0	7923	971	34	4	854	4	ITGBL1	13	102235670	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	80503474	102235670	12934208	39	6285											
AKAP6	9472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	33204952	33204952	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcctgaaagtggaagccTggtaaggcagctggaggtca	10	8	14	9	0	2	1	1	1	1	0	3	3	2	3	2	5	2	3	2	5	3	1	rs201928179		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr14:33204952T>A	ENST00000280979.4	+	11	3406	c.3236T>A	c.(3235-3237)cTg>cAg	p.L1079Q	AKAP6_ENST00000557272.1_Missense_Mutation_p.L1079Q	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1079					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		AGTGGAAGCCTGGTAAGGCAG	0.488																																					p.L1079Q	Melanoma(49;821 1200 7288 13647 42351)	.											.	AKAP6-733	0			c.T3236A						.						70	72	71					14																	33204952		2203	4300	6503	SO:0001583	missense	9472	exon11			GAAGCCTGGTAAG	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"A-kinase anchor proteins"	376	protein-coding gene	gene with protein product	"protein kinase A anchoring protein 6"	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.3236T>A	14.37:g.33204952T>A	ENSP00000280979:p.Leu1079Gln	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	77	26	NM_004274	0	0	0	0	0	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.981383	0.74474	.	.	ENSG00000151320	ENST00000280979;ENST00000557272	T;T	0.22539	3.18;1.95	5.7	4.54	0.55810	.	0.118007	0.37809	N	0.001926	T	0.26629	0.0651	N	0.14661	0.345	0.44000	D	0.996707	D	0.71674	0.998	D	0.63488	0.915	T	0.07385	-1.0775	10	0.62326	D	0.03	-5.2892	12.8687	0.57953	0.0:0.0:0.1363:0.8637	.	1079	Q13023	AKAP6_HUMAN	Q	1079	ENSP00000280979:L1079Q;ENSP00000451247:L1079Q	ENSP00000280979:L1079Q	L	+	2	0	AKAP6	32274703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.041000	0.76558	0.961000	0.38030	0.477000	0.44152	CTG	T|0.999;C|0.000		0.488	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		A	33204952	T	A	33204952	3	1	65	1	0	0	0	0	1	0	0	0	455	1580	55	5	3274	5	AKAP6	14	33204952	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		33204952	74144588	40	6286											
DAAM1	23002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	59791109	59791109	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcttcgctatgaatttcTgatgttaggaattcaacctg	10	16	7	8	1	4	2	2	2	2	0	5	3	4	3	1	1	1	2	1	1	5	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr14:59791109T>A	ENST00000395125.1	+	7	949	c.926T>A	c.(925-927)cTg>cAg	p.L309Q	DAAM1_ENST00000360909.3_Missense_Mutation_p.L309Q|DAAM1_ENST00000351081.1_Missense_Mutation_p.L309Q	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	309	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		TATGAATTTCTGATGTTAGGA	0.308																																					p.L309Q		.											.	DAAM1-227	0			c.T926A						.						87	91	90					14																	59791109		2203	4300	6503	SO:0001583	missense	23002	exon8			AATTTCTGATGTT	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.926T>A	14.37:g.59791109T>A	ENSP00000378557:p.Leu309Gln	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	117	35	NM_001270520	0	0	0	0	0	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	37	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.330005	0.60743	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125	D;D;D	0.84516	-1.86;-1.86;-1.86	5.17	4.01	0.46588	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.80508	2.5	0.80722	D	1	P;P	0.45634	0.835;0.863	P;P	0.49140	0.466;0.601	D	0.88524	0.3098	10	0.62326	D	0.03	.	12.2246	0.54453	0.0:0.0:0.1426:0.8574	.	309;309	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	Q	309	ENSP00000354162:L309Q;ENSP00000247170:L309Q;ENSP00000378557:L309Q	ENSP00000247170:L309Q	L	+	2	0	DAAM1	58860862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.841000	0.86834	0.965000	0.38133	0.533000	0.62120	CTG	.		0.308	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59791109	T	A	59791109	3	1	65	1	0	0	0	0	1	0	0	0	4221	1580	55	5	952	5	DAAM1	14	59791109	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	26586157	59791109	47558431	41	6287											
MGA	23269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42005411	42005411	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagcccctccctgcaacaaTgacttctgtcgactgggttg	7	10	10	14	2	1	1	0	1	1	0	3	3	2	1	3	1	3	2	3	1	2	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr15:42005411T>A	ENST00000570161.1	+	8	3147	c.3147T>A	c.(3145-3147)aaT>aaA	p.N1049K	MGA_ENST00000566586.1_Missense_Mutation_p.N1049K|MGA_ENST00000545763.1_Missense_Mutation_p.N1049K|MGA_ENST00000389936.4_Missense_Mutation_p.N1049K|MGA_ENST00000219905.7_Missense_Mutation_p.N1049K			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCTGCAACAATGACTTCTGTC	0.463																																					p.N1049K		.											.	MGA-522	0			c.T3147A						.						156	153	154					15																	42005411		1992	4139	6131	SO:0001583	missense	23269	exon9			CAACAATGACTTC	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.3147T>A	15.37:g.42005411T>A	ENSP00000457035:p.Asn1049Lys	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	117	32	NM_001080541	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762234	0.49468	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.16457	2.34;2.34;2.34	5.75	3.24	0.37175	.	0.270326	0.40144	N	0.001172	T	0.15739	0.0379	N	0.14661	0.345	0.36995	D	0.894984	P;P	0.50272	0.933;0.533	P;B	0.56865	0.808;0.305	T	0.15983	-1.0418	10	0.44086	T	0.13	.	4.9526	0.14023	0.1341:0.1556:0.0:0.7103	.	1049;1049	F5H7K2;E7ENI0	.;.	K	1049	ENSP00000219905:N1049K;ENSP00000374586:N1049K;ENSP00000442467:N1049K	ENSP00000219905:N1049K	N	+	3	2	MGA	39792703	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.237000	0.17985	0.882000	0.36016	0.533000	0.62120	AAT	.		0.463	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42005411	T	A	42005411	3	1	65	1	0	0	0	0	1	0	0	0	9565	1461	51	5	3177	5	MGA	15	42005411	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		42005411	60525981	42	6288											
VPS13C	54832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	62167108	62167108	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagaggcttctcactccaaTcactaacccctctgcaaatt	13	10	4	14	0	3	1	2	0	2	1	5	1	4	1	3	1	2	2	3	1	4	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr15:62167108T>A	ENST00000261517.5	-	77	10454	c.10381A>T	c.(10381-10383)Att>Ttt	p.I3461F	VPS13C_ENST00000395898.3_Missense_Mutation_p.I3418F|VPS13C_ENST00000395896.4_Missense_Mutation_p.I3461F|VPS13C_ENST00000558919.1_5'Flank|VPS13C_ENST00000249837.3_Missense_Mutation_p.I3418F	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CTCACTCCAATCACTAACCCC	0.303																																					p.I3461F		.											.	VPS13C-92	0			c.A10381T						.						104	104	104					15																	62167108		2203	4300	6503	SO:0001583	missense	54832	exon77			CTCCAATCACTAA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10381A>T	15.37:g.62167108T>A	ENSP00000261517:p.Ile3461Phe	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	173	60	NM_020821	0	0	0	0	0		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.404605	0.83230	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.43294	0.95;0.95;1.12	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.56108	0.1963	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.69078	0.978;0.995;0.997;0.997	D;D;D;D	0.71656	0.923;0.962;0.974;0.92	T	0.56511	-0.7967	10	0.54805	T	0.06	.	16.1946	0.82018	0.0:0.0:0.0:1.0	.	3418;3461;3418;3461	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	F	3418;3461;3461;3461	ENSP00000249837:I3418F;ENSP00000261517:I3461F;ENSP00000379233:I3461F	ENSP00000249837:I3418F	I	-	1	0	VPS13C	59954400	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.402000	0.59722	2.228000	0.72767	0.528000	0.53228	ATT	.		0.303	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62167108	T	A	62167108	3	1	65	1	0	0	0	0	1	0	0	0	17224	1435	50	5	944	5	VPS13C	15	62167108	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	20161697	62167108	40364284	43	6289											
PRR25	388199	hgsc.bcm.edu	37	chr16	863367	863367	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccggcaaggacgccggacCgacacggcctccccatccct	8	3	11	19	5	0	0	0	0	0	0	2	4	2	2	7	4	0	1	7	4	1	0	rs367751056|rs371962006|rs138733834	byFrequency	TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr16:863367C>T	ENST00000301698.1	+	3	715	c.715C>T	c.(715-717)Cga>Tga	p.R239*		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	239										large_intestine(1)|lung(1)|skin(1)	3						GACGCCGGACCGACACGGCCT	0.711													-|||	5	0.000998403	0	0	5008	,	,		12233	0		0	False		,,,				2504	0.0051				p.R239X		.											.	PRR25-135	0			c.C715T						.	-	stop/ARG	0,3270		0,0,1635	10	18	16		715	-0.3	0	16		16	7,8213		0,7,4103	no	stop-gained	PRR25	NM_001013638.1		0,7,5738	TT,TC,CC		0.0852,0.0,0.0609		239/403	863367	7,11483	1635	4110	5745	SO:0001587	stop_gained	388199	exon3			CCGGACCGACACG	BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.715C>T	16.37:g.863367C>T	ENSP00000301698:p.Arg239*	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	12	6	NM_001013638	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000301698.1	37	CCDS45372.1	.	.	.	.	.	.	.	.	.	.	-	7.788	0.710968	0.15239	0.0	8.52E-4	ENSG00000167945	ENST00000301698	.	.	.	0.13	-0.261	0.12963	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	.	.	.	.	.	.	.	X	239	.	ENSP00000301698:R239X	R	+	1	2	PRR25	803368	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.233000	0.01204	-2.944000	0.00296	-2.980000	0.00080	CGA	.		0.711	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638		T	863367	C	T	863367	4	4	65	1	0	0	0	0	0	1	0	0	12626	644	23	1	725	1	PRR25	16	863367	Nonsense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		863367	89491386	44	6290											
ZZEF1	23140	broad.mit.edu	37	chr17	3977517	3977517	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacgaggagctgtaaatcCagcccccaagacacggcaac	14	3	11	13	2	0	2	0	0	0	2	1	5	1	3	3	2	3	3	3	2	4	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr17:3977517C>T	ENST00000381638.2	-	24	3736	c.3612G>A	c.(3610-3612)ctG>ctA	p.L1204L	ZZEF1_ENST00000574474.1_5'Flank	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1204							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GCTGTAAATCCAGCCCCCAAG	0.577																																					p.L1204L													.	ZZEF1-93	0			c.G3612A						.						173	165	167					17																	3977517		2203	4300	6503	SO:0001819	synonymous_variant	23140	exon24			TAAATCCAGCCCC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.3612G>A	17.37:g.3977517C>T		Somatic	301	0		WXS	Illumina HiSeq	Phase_I	364	6	NM_015113	0	0	0	0	0	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			.		0.577	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3977517	C	T	3977517	2	4	65	1	0	0	0	0	0	0	0	1	18287	581	21	2		2	ZZEF1	17	3977517	Silent	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		3977517	77217693	45	6291											
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7578190	7578190	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagacctcaggcggctcaTagggcaccaccacactatgt	11	6	9	15	1	2	1	2	0	0	1	2	1	2	1	4	3	0	2	4	3	2	2	rs121912666		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr17:7578190T>G	ENST00000269305.4	-	6	848	c.659A>C	c.(658-660)tAt>tCt	p.Y220S	TP53_ENST00000455263.2_Missense_Mutation_p.Y220S|TP53_ENST00000420246.2_Missense_Mutation_p.Y220S|TP53_ENST00000413465.2_Missense_Mutation_p.Y220S|TP53_ENST00000445888.2_Missense_Mutation_p.Y220S|TP53_ENST00000359597.4_Missense_Mutation_p.Y220S|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGCGGCTCATAGGGCACCAC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y220S	Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	.	TP53-70225	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	c.A659C	GRCh37	CM015378|CM951227	TP53	M	rs121912666	.						102	94	97					17																	7578190		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCTCATAGGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.659A>C	17.37:g.7578190T>G	ENSP00000269305:p.Tyr220Ser	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	61	9	NM_000546	0	0	4	4	0	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.447753	0.84101	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99833	-7.03;-7.03;-7.03;-7.03;-7.03;-7.03;-7.03;-7.03	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	A	1	D;D;D;D;D;D;D	0.89917	1.0;0.994;0.997;1.0;0.995;0.968;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.921;0.963;1.0;0.977;0.926;1.0	D	0.96735	0.9542	9	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220S;ENSP00000352610:Y220S;ENSP00000269305:Y220S;ENSP00000398846:Y220S;ENSP00000391127:Y220S;ENSP00000391478:Y220S;ENSP00000425104:Y88S;ENSP00000423862:Y127S	ENSP00000269305:Y220S	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578190	T	G	7578190	3	3	65	1	0	0	0	0	1	0	0	0	16414	1406	49	5	635	5	TP53	17	7578190	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	3600673	7578190	73617020	46	6292											
SLC47A1	55244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	19451346	19451346	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcgtgatcctgcagcggAgtgcgctcgtcctgctcctc	3	10	14	14	4	0	1	0	1	0	0	5	2	3	2	3	2	4	3	3	2	0	0			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr17:19451346A>G	ENST00000270570.4	+	4	441	c.355A>G	c.(355-357)Agt>Ggt	p.S119G	SLC47A1_ENST00000571335.1_5'UTR|SLC47A1_ENST00000436810.2_Missense_Mutation_p.S96G|SLC47A1_ENST00000457293.1_Missense_Mutation_p.S119G|SLC47A1_ENST00000395585.1_Missense_Mutation_p.S119G|SLC47A1_ENST00000575023.1_Missense_Mutation_p.S119G|SLC47A1_ENST00000542886.1_Missense_Mutation_p.S119G|SLC47A1_ENST00000584348.1_3'UTR	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	119					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	CCTGCAGCGGAGTGCGCTCGT	0.612																																					p.S119G		.											.	SLC47A1-90	0			c.A355G						.						144	120	128					17																	19451346		2203	4300	6503	SO:0001583	missense	55244	exon4			CAGCGGAGTGCGC		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.355A>G	17.37:g.19451346A>G	ENSP00000270570:p.Ser119Gly	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	110	59	NM_018242	0	0	7	18	11	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.623256	0.00820	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	4.99	2.98	0.34508	.	0.272209	0.40385	N	0.001106	T	0.09512	0.0234	N	0.01751	-0.74	0.09310	N	1	B;B;B;B	0.09022	0.001;0.002;0.001;0.0	B;B;B;B	0.09377	0.002;0.004;0.004;0.002	T	0.37079	-0.9721	10	0.02654	T	1	-24.9116	9.8375	0.40977	0.1719:0.0:0.8281:0.0	.	96;119;119;119	E7EX57;B4DYV3;Q96FL8;Q96FL8-3	.;.;S47A1_HUMAN;.	G	96;119;119;119;119	ENSP00000407155:S96G;ENSP00000270570:S119G;ENSP00000415586:S119G;ENSP00000440435:S119G;ENSP00000378951:S119G	ENSP00000270570:S119G	S	+	1	0	SLC47A1	19391938	0.956000	0.32656	0.005000	0.12908	0.001000	0.01503	5.014000	0.64029	0.494000	0.27859	-0.464000	0.05259	AGT	.		0.612	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		G	19451346	A	G	19451346	3	3	65	1	0	0	0	0	1	0	0	0	14679	304	11	3	369	3	SLC47A1	17	19451346	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	11873156	19451346	61743864	47	6293											
CHAD	1101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48546019	48546019	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtaggttgagcagcttggtCttctctgacaccttggggat	6	14	13	8	0	2	2	0	2	2	0	3	3	2	3	1	4	2	4	1	4	1	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr17:48546019C>A	ENST00000508540.1	-	1	308	c.156G>T	c.(154-156)aaG>aaT	p.K52N	ACSF2_ENST00000506085.1_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000300441.4_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.K52N|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000504392.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	52	LRRNT.				bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GCAGCTTGGTCTTCTCTGACA	0.622																																					p.K52N		.											.	CHAD-92	0			c.G156T						.						92	77	82					17																	48546019		2203	4300	6503	SO:0001583	missense	1101	exon1			CTTGGTCTTCTCT	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	1909	protein-coding gene	gene with protein product	"chondroadherin proteoglycan"	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.156G>T	17.37:g.48546019C>A	ENSP00000423812:p.Lys52Asn	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	86	17	NM_001267	0	0	0	1	1	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	.	.	.	.	.	.	.	.	.	.	C	9.129	1.010904	0.19277	.	.	ENSG00000136457	ENST00000508540;ENST00000258969	T;T	0.04015	3.73;3.73	4.31	2.29	0.28610	Leucine-rich repeat-containing N-terminal (1);	0.490348	0.23123	N	0.051679	T	0.01835	0.0058	N	0.04018	-0.295	0.28724	N	0.902844	B	0.17465	0.022	B	0.14578	0.011	T	0.45086	-0.9285	10	0.09084	T	0.74	.	4.7213	0.12920	0.1537:0.601:0.0:0.2453	.	52	O15335	CHAD_HUMAN	N	52	ENSP00000423812:K52N;ENSP00000258969:K52N	ENSP00000258969:K52N	K	-	3	2	CHAD	45901018	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	1.268000	0.33062	0.442000	0.26555	0.462000	0.41574	AAG	.		0.622	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		A	48546019	C	A	48546019	3	1	65	1	0	0	0	0	1	0	0	0	3316	912	32	4	935	4	CHAD	17	48546019	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	29094673	48546019	32649191	48	6294											
ZNF559	84527	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	9452840	9452840	+	Frame_Shift_Del	DEL	A	A	-																															catgcaaactcaagatggagAaaaattctatgaatgtaaag																										TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr19:9452840delA	ENST00000393883.2	+	6	1361	c.713delA	c.(712-714)gaafs	p.E238fs	ZNF559_ENST00000603380.1_Frame_Shift_Del_p.E238fs|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000587557.1_Frame_Shift_Del_p.E302fs|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000317221.7_3'UTR|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000592896.1_3'UTR|ZNF177_ENST00000446085.4_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000538743.1_Frame_Shift_Del_p.E158fs	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						CAAGATGGAGAAAAATTCTAT	0.363																																					p.E302fs		.											.	ZNF559-91	0			c.905delA						.						77	79	79					19																	9452840		2201	4300	6501	SO:0001589	frameshift_variant	84527	exon6			.	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.713delA	19.37:g.9452840delA	ENSP00000377461:p.Glu238fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	110	38	NM_001202406	0	0	0	0	0	K7EMG6	Frame_Shift_Del	DEL	ENST00000393883.2	37	CCDS12211.1																																																																																			.		0.363	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		-	9452840	A	-	9452840	7	5	65	1	0	1	0	1	0	0	0	0	18022	246	9	0	727	0	ZNF559	19	9452840	Frame_Shift_Del	DEL	A	TCGA-BQ-5881-01A-11D-1589-08		9452840	49676143	49	6295											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31770237	31770237	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacagctgctgctgctgctActgctgctgctgctgctgcc	3	11	11	16	0	0	0	0	0	0	0	0	0	0	0	2	0	12	10	2	0	1	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr19:31770237A>G	ENST00000240587.4	-	2	789	c.462T>C	c.(460-462)agT>agC	p.S154S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	154	Ser-rich.				in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					tgctgctgctactgctgctgc	0.607																																					p.S154S		.											.	TSHZ3-232	0			c.T462C						.						39	44	42					19																	31770237		2184	4294	6478	SO:0001819	synonymous_variant	57616	exon2			GCTGCTACTGCTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.462T>C	19.37:g.31770237A>G		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_020856	7	5	3	7274	7259	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			.		0.607	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31770237	A	G	31770237	2	3	65	1	0	0	0	0	0	0	0	1	16658	388	14	3		3	TSHZ3	19	31770237	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	22317397	31770237	27358746	50	6296											
CAPNS1	826	hgsc.bcm.edu	37	chr19	36631958	36631958	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggcggcggcggcggcggCgggggaggcgggggcctggg	3	1	28	9	7	0	0	0	0	0	0	0	1	0	1	1	12	0	0	1	12	1	0	rs567500165		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr19:36631958C>G	ENST00000246533.3	+	2	643	c.45C>G	c.(43-45)ggC>ggG	p.G15G	CAPNS1_ENST00000588815.1_Silent_p.G15G|CAPNS1_ENST00000590874.1_Silent_p.G15G|CAPNS1_ENST00000587718.1_Silent_p.G15G|CAPNS1_ENST00000588780.1_Silent_p.G15G|CAPNS1_ENST00000589146.1_Silent_p.G15G	NM_001003962.1|NM_001749.2	NP_001003962.1|NP_001740.1	P04632	CPNS1_HUMAN	calpain, small subunit 1	15	Gly-rich (hydrophobic).|Poly-Gly.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			gcggcggcggcgggggaggcg	0.736													C|||	1	0.000199681	0	0	5008	,	,		3971	0.001		0	False		,,,				2504	0				p.G15G	Esophageal Squamous(129;1541 1691 5780 18353 34150)	.											.	CAPNS1-90	0			c.C45G						.						6	7	7					19																	36631958		1958	3947	5905	SO:0001819	synonymous_variant	826	exon2			CGGCGGCGGGGGA	X04106	CCDS12489.1	19q13.1	2013-01-10		2001-08-10	ENSG00000126247	ENSG00000126247	3.4.22.52	"EF-hand domain containing"	1481	protein-coding gene	gene with protein product		114170		CAPN4		3024120, 3016651	Standard	NM_001003962		Approved	CANP, CANPS, 30K, CDPS	uc002odj.3	P04632		ENST00000246533.3:c.45C>G	19.37:g.36631958C>G		Somatic	9	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_001749	0	0	0	0	0	A8K0P1|Q8WTX3|Q96EW0	Silent	SNP	ENST00000246533.3	37	CCDS12489.1																																																																																			.		0.736	CAPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457411.2			G	36631958	C	G	36631958	2	3	65	1	0	0	0	0	0	0	0	1	2639	755	27	4		4	CAPNS1	19	36631958	Silent	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	4861721	36631958	22497025	51	6297											
LILRB4	11006	broad.mit.edu	37	chr19	55175654	55175654	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggagcctacagtaaacccAccctttcagccctgccgagt	10	8	8	15	1	1	0	1	0	0	0	1	2	1	1	5	1	5	1	5	1	4	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr19:55175654A>C	ENST00000391736.1	+	6	688	c.373A>C	c.(373-375)Acc>Ccc	p.T125P	LILRB4_ENST00000391734.3_Missense_Mutation_p.T125P|LILRB4_ENST00000430952.2_Missense_Mutation_p.T125P|LILRB4_ENST00000270452.2_Missense_Mutation_p.T125P|LILRB4_ENST00000391733.3_Missense_Mutation_p.T125P	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	125	Ig-like C2-type 2.				immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CAGTAAACCCACCCTTTCAGC	0.572																																					p.T125P													.	LILRB4-93	0			c.A373C						.						92	95	94					19																	55175654		2203	4300	6503	SO:0001583	missense	11006	exon4			AAACCCACCCTTT	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.373A>C	19.37:g.55175654A>C	ENSP00000375616:p.Thr125Pro	Somatic	110	12		WXS	Illumina HiSeq	Phase_I	119	10	NM_006847	0	0	9	10	1	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	A	12.51	1.959220	0.34565	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.03124	4.04;4.04;4.04;4.04;4.04;4.04	2.72	-3.96	0.04106	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.11495	0.0280	M	0.83012	2.62	0.09310	N	1	D;D;D;P;P	0.58268	0.967;0.982;0.978;0.94;0.952	P;P;P;P;P	0.57152	0.814;0.8;0.699;0.653;0.765	T	0.02813	-1.1107	9	0.87932	D	0	.	7.4436	0.27198	0.2671:0.0:0.0:0.7329	.	125;125;125;125;125	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	P	125	ENSP00000375616:T125P;ENSP00000270452:T125P;ENSP00000408995:T125P;ENSP00000375614:T125P;ENSP00000375613:T125P;ENSP00000401962:T125P	ENSP00000270452:T125P	T	+	1	0	LILRB4	59867466	0.000000	0.05858	0.033000	0.17914	0.008000	0.06430	-2.611000	0.00885	-0.668000	0.05296	0.329000	0.21502	ACC	.		0.572	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			C	55175654	A	C	55175654	3	2	65	1	0	0	0	0	1	0	0	0	8815	159	6	5	387	5	LILRB4	19	55175654	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	18543696	55175654	3953329	52	6298											
ZNF628	89887	hgsc.bcm.edu	37	chr19	55993790	55993790	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcagcagtgccacgtggaAgaggccgcggccgggcgccc	7	3	16	15	5	1	1	1	0	0	1	1	2	1	2	4	4	2	1	4	4	1	0	rs7254184	byFrequency	TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr19:55993790A>G	ENST00000598519.1	+	3	1783	c.1230A>G	c.(1228-1230)gaA>gaG	p.E410E	NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000591590.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.E406E|NAT14_ENST00000587400.1_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	410					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)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		GCCACGTGGAAGAggccgcgg	0.786													N|||	3011	0.601238	0.5847	0.6254	5008	,	,		4864	0.3274		0.7306	False		,,,				2504	0.7556				p.E410E		.											.	ZNF628-22	0			c.A1230G						.						1	1	1					19																	55993790		599	1269	1868	SO:0001819	synonymous_variant	89887	exon3			CGTGGAAGAGGCC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.1230A>G	19.37:g.55993790A>G		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_033113	0	0	0	0	0	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			A|0.440;G|0.560		0.786	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		G	55993790	A	G	55993790	2	3	65	1	0	0	0	0	0	0	0	1	18084	69	3	3		3	ZNF628	19	55993790	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	818136	55993790	3135193	53	6299											
RBPJL	11317	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	43940944	43940944	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgcggctggtgctgcgCgggggccgggagctgggtac	2	7	22	10	4	0	0	0	0	0	0	0	1	0	1	1	6	6	5	1	6	1	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr20:43940944C>T	ENST00000343694.3	+	6	600	c.528C>T	c.(526-528)cgC>cgT	p.R176R	RBPJL_ENST00000372741.3_Silent_p.R176R|RBPJL_ENST00000372743.1_Silent_p.R176R	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	176					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				tggtgctgcgCGGGGGCCGGG	0.602																																					p.R176R		.											.	RBPJL-227	0			c.C528T						.						28	31	30					20																	43940944		2203	4300	6503	SO:0001819	synonymous_variant	11317	exon6			GCTGCGCGGGGGC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.528C>T	20.37:g.43940944C>T		Somatic	39	1		WXS	Illumina HiSeq	Phase_I	44	14	NM_014276	0	0	0	0	0	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	37	CCDS13349.1																																																																																			.		0.602	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		T	43940944	C	T	43940944	2	4	65	1	0	0	0	0	0	0	0	1	13194	755	27	1		1	RBPJL	20	43940944	Silent	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		43940944	19084576	54	6300											
BRWD1	54014	bcgsc.ca	37	chr21	40608669	40608669	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaggaggctgcaaattgatgCccgcatcagctgtccaatcg	11	8	11	11	2	1	1	1	1	0	0	3	2	2	2	2	2	3	4	2	2	3	1	rs370519269		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr21:40608669C>T	ENST00000333229.2	-	23	2945	c.2618G>A	c.(2617-2619)gGc>gAc	p.G873D	BRWD1_ENST00000380800.3_Missense_Mutation_p.G873D|BRWD1_ENST00000342449.3_Missense_Mutation_p.G873D	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	873					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				CAAATTGATGCCCGCATCAGC	0.403																																					p.G873D	Melanoma(170;988 1986 4794 16843 39731)												.	BRWD1-94	0			c.G2618A						.						109	104	106					21																	40608669		2203	4300	6503	SO:0001583	missense	54014	exon23			TTGATGCCCGCAT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.2618G>A	21.37:g.40608669C>T	ENSP00000330753:p.Gly873Asp	Somatic	64	0		WXS	Illumina HiSeq	Phase_1	68	5	NM_018963	0	0	0	0	0	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.871459	0.91587	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.69040	-0.37;-0.37;-0.37	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	D	0.84866	0.5567	M	0.86420	2.815	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	D	0.87449	0.2400	10	0.87932	D	0	-5.9368	18.9924	0.92798	0.0:1.0:0.0:0.0	.	540;873;873	Q5R2U6;Q9NSI6-2;Q9NSI6	.;.;BRWD1_HUMAN	D	873	ENSP00000330753:G873D;ENSP00000344333:G873D;ENSP00000370178:G873D	ENSP00000330753:G873D	G	-	2	0	BRWD1	39530539	1.000000	0.71417	0.995000	0.50966	0.677000	0.39632	7.321000	0.79088	2.498000	0.84270	0.650000	0.86243	GGC	.		0.403	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40608669	C	T	40608669	3	4	65	1	0	0	0	0	1	0	0	0	1528	739	26	2	4663	2	BRWD1	21	40608669	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		40608669	7521226	55	6301											
TOP3B	8940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	22327036	22327036	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tagcttctttcttctccgtgGgagcttggctgaacagttct	5	16	10	10	1	4	1	0	1	4	0	5	2	4	2	1	2	3	4	1	2	2	6			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr22:22327036G>T	ENST00000398793.2	-	4	691	c.257C>A	c.(256-258)cCc>cAc	p.P86H	TOP3B_ENST00000413067.2_5'UTR|TOP3B_ENST00000357179.5_Missense_Mutation_p.P86H	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	86	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CTTCTCCGTGGGAGCTTGGCT	0.562											OREG0026347	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P86H		.											.	TOP3B-538	0			c.C257A						.						155	123	134					22																	22327036		2203	4300	6503	SO:0001583	missense	8940	exon4			TCCGTGGGAGCTT	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.257C>A	22.37:g.22327036G>T	ENSP00000381773:p.Pro86His	Somatic	65	0	755	WXS	Illumina HiSeq	Phase_I	69	29	NM_003935	0	0	0	2	2	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	37	CCDS13797.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372315	0.82573	.	.	ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000449517;ENST00000424393;ENST00000437929;ENST00000430142	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.0	3.97	0.46021	DNA topoisomerase, type IA, core domain (1);Toprim domain (2);	0.052237	0.85682	D	0.000000	T	0.47563	0.1452	H	0.94620	3.56	0.80722	D	1	P	0.41848	0.763	P	0.48030	0.564	T	0.65166	-0.6234	10	0.87932	D	0	-8.5874	15.6079	0.76689	0.0:0.1378:0.8622:0.0	.	86	O95985	TOP3B_HUMAN	H	86	ENSP00000349705:P86H;ENSP00000381773:P86H;ENSP00000390977:P86H;ENSP00000402622:P86H;ENSP00000414538:P86H	ENSP00000349705:P86H	P	-	2	0	TOP3B	20657036	1.000000	0.71417	0.432000	0.26747	0.906000	0.53458	9.361000	0.97122	1.317000	0.45149	0.563000	0.77884	CCC	.		0.562	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		T	22327036	G	T	22327036	3	4	65	1	0	0	0	0	1	0	0	0	16401	1232	43	4	2391	4	TOP3B	22	22327036	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		22327036	28977530	56	6302											
CABIN1	23523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24483456	24483456	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggccagccgcattcaggaCaagctgaactccaatgagct	11	6	11	13	2	1	2	1	2	0	0	2	3	2	3	3	2	4	3	3	2	3	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr22:24483456C>A	ENST00000398319.2	+	23	3700	c.3315C>A	c.(3313-3315)gaC>gaA	p.D1105E	CABIN1_ENST00000263119.5_Missense_Mutation_p.D1105E|CABIN1_ENST00000405822.2_Missense_Mutation_p.D1055E	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1105					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GCATTCAGGACAAGCTGAACT	0.547																																					p.D1105E		.											.	CABIN1-94	0			c.C3315A						.						70	64	66					22																	24483456		2203	4300	6503	SO:0001583	missense	23523	exon23			TCAGGACAAGCTG	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.3315C>A	22.37:g.24483456C>A	ENSP00000381364:p.Asp1105Glu	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	61	15	NM_001199281	0	0	0	1	1	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149010	0.57151	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.75477	-0.94;-0.94;-0.94	5.1	1.91	0.25777	Tetratricopeptide-like helical (1);	0.055118	0.64402	D	0.000001	T	0.54111	0.1838	L	0.27053	0.805	0.80722	D	1	P;P	0.40619	0.724;0.603	B;B	0.34452	0.183;0.089	T	0.42899	-0.9424	10	0.23302	T	0.38	.	9.3964	0.38406	0.0:0.7705:0.0:0.2295	.	1055;1105	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	E	1105;1055;1105	ENSP00000263119:D1105E;ENSP00000384694:D1055E;ENSP00000381364:D1105E	ENSP00000263119:D1105E	D	+	3	2	CABIN1	22813456	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.242000	0.32755	0.299000	0.22661	0.650000	0.86243	GAC	.		0.547	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24483456	C	A	24483456	3	1	65	1	0	0	0	0	1	0	0	0	2534	477	17	4	3401	4	CABIN1	22	24483456	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	2156420	24483456	26821110	57	6303											
DDX53	168400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	23019108	23019108	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagagagttggctcttcacGtggaagctgaatgttcaaag	11	11	12	7	1	3	2	2	1	1	1	3	4	3	3	0	2	1	4	0	2	4	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chrX:23019108G>A	ENST00000327968.5	+	1	1022	c.934G>A	c.(934-936)Gtg>Atg	p.V312M	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	312	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						GGCTCTTCACGTGGAAGCTGA	0.408													G|||	1	0.000264901	8e-04	0	3775	,	,		16112	0		0	False		,,,				2504	0				p.V312M		.											.	DDX53-228	0			c.G934A						.						74	73	73					X																	23019108		2203	4300	6503	SO:0001583	missense	168400	exon1			CTTCACGTGGAAG	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"DEAD-boxes"	20083	protein-coding gene	gene with protein product	"cancer associated gene", "cancer/testis antigen 26"						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.934G>A	X.37:g.23019108G>A	ENSP00000368667:p.Val312Met	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	64	36	NM_182699	0	0	0	0	0	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	37	CCDS35214.1	.	.	.	.	.	.	.	.	.	.	G	9.356	1.066739	0.20067	.	.	ENSG00000184735	ENST00000327968	T	0.05139	3.49	4.3	1.28	0.21552	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.300009	0.31370	N	0.007767	T	0.24586	0.0596	M	0.91920	3.255	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02877	-1.1099	10	0.87932	D	0	-6.7638	4.8973	0.13757	0.2269:0.1801:0.593:0.0	.	312	Q86TM3	DDX53_HUMAN	M	312	ENSP00000368667:V312M	ENSP00000368667:V312M	V	+	1	0	DDX53	22929029	1.000000	0.71417	0.029000	0.17559	0.023000	0.10783	2.224000	0.42945	0.759000	0.33084	0.600000	0.82982	GTG	.		0.408	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699		A	23019108	G	A	23019108	3	1	65	1	0	0	0	0	1	0	0	0	4377	1145	40	1	936	1	DDX53	23	23019108	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		23019108	132251452	58	6304											
ZBTB8OS	339487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	33099257	33099257	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgcttacccggggtatgaAgaattcatcagcactgaact	11	12	9	9	1	2	3	2	2	0	1	2	3	2	3	1	2	4	3	1	2	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:33099257A>C	ENST00000468695.1	-	4	370	c.352T>G	c.(352-354)Ttc>Gtc	p.F118V	ZBTB8OS_ENST00000492007.1_Intron|ZBTB8OS_ENST00000373501.2_Missense_Mutation_p.F106V|ZBTB8OS_ENST00000341885.5_Intron	NM_178547.2	NP_848642.1	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite strand	106					tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	extracellular vesicular exosome (GO:0070062)|tRNA-splicing ligase complex (GO:0072669)	metal ion binding (GO:0046872)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CGGGGTATGAAGAATTCATCA	0.313																																					p.F118V		.											.	ZBTB8OS-90	0			c.T352G						.						52	56	55					1																	33099257		2203	4296	6499	SO:0001583	missense	339487	exon4			GTATGAAGAATTC	AY151084	CCDS365.1	1p35.1	2010-09-30			ENSG00000176261	ENSG00000176261			24094	protein-coding gene	gene with protein product	"archease"	615891				12477932	Standard	NM_178547		Approved	ARCH	uc001bvp.3	Q8IWT0	OTTHUMG00000007856	ENST00000468695.1:c.352T>G	1.37:g.33099257A>C	ENSP00000417677:p.Phe118Val	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	70	40	NM_178547	0	0	0	0	0	Q5TGK5|Q6PDA1|Q8IWS9|Q8NEV6|Q8NEV7	Missense_Mutation	SNP	ENST00000468695.1	37	CCDS365.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.225490|4.225490	0.79576|0.79576	.|.	.|.	ENSG00000176261|ENSG00000176261	ENST00000468695;ENST00000373501|ENST00000436661	.|.	.|.	.|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72431|0.72431	0.3459|0.3459	M|M	0.77820|0.77820	2.39|2.39	0.80722|0.80722	D|D	1|1	P;D|.	0.89917|.	0.712;1.0|.	P;D|.	0.87578|.	0.525;0.998|.	T|T	0.73855|0.73855	-0.3851|-0.3851	9|5	0.07990|.	T|.	0.79|.	-14.6218|-14.6218	10.1989|10.1989	0.43071|0.43071	0.8518:0.0:0.0:0.1482|0.8518:0.0:0.0:0.1482	.|.	106;118|.	Q8IWT0-2;A8K0B5|.	.;.|.	V|R	118;106|116	.|.	ENSP00000362600:F106V|.	F|L	-|-	1|2	0|0	ZBTB8OS|ZBTB8OS	32871844|32871844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.227000|7.227000	0.78070|0.78070	2.180000|2.180000	0.69256|0.69256	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.		0.313	ZBTB8OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021669.3	NM_178547		C	33099257	A	C	33099257	3	2	66	1	0	0	0	0	1	0	0	0	17589	72	3	5	203	5	ZBTB8OS	1	33099257	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08		33099257	216151364	1	6305											
RLF	6018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40701983	40701983	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcagcataaggagaaaagaGacaaaaaacctattggctct	19	7	8	7	0	2	2	1	0	1	2	2	4	2	2	1	2	2	2	1	2	7	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:40701983G>A	ENST00000372771.4	+	8	1636	c.1609G>A	c.(1609-1611)Gac>Aac	p.D537N		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	537					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			GGAGAAAAGAGACAAAAAACC	0.358																																					p.D537N		.											.	RLF-93	0			c.G1609A						.						65	70	68					1																	40701983		2199	4298	6497	SO:0001583	missense	6018	exon8			AAAAGAGACAAAA		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1609G>A	1.37:g.40701983G>A	ENSP00000361857:p.Asp537Asn	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	101	34	NM_012421	0	0	0	1	1	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.710822	0.48517	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.36699	1.24	6.07	6.07	0.98685	.	0.378317	0.33144	N	0.005225	T	0.42877	0.1222	L	0.40543	1.245	0.37876	D	0.930215	B;D	0.67145	0.23;0.996	B;P	0.56216	0.064;0.794	T	0.15983	-1.0418	10	0.18710	T	0.47	-14.4249	14.7663	0.69642	0.0684:0.0:0.9316:0.0	.	230;537	F5H2M5;Q13129	.;RLF_HUMAN	N	537;230	ENSP00000361857:D537N	ENSP00000361857:D537N	D	+	1	0	RLF	40474570	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.802000	0.47916	2.885000	0.99019	0.655000	0.94253	GAC	.		0.358	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40701983	G	A	40701983	3	1	66	1	0	0	0	0	1	0	0	0	13421	942	33	2	1639	2	RLF	1	40701983	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	7602726	40701983	208548638	2	6306											
TMEM53	79639	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45120714	45120714	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacgtagcggtacagcatGacgccaccgttgctgaagac	11	6	12	12	4	0	3	0	2	0	1	0	3	0	3	2	1	5	6	2	1	3	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:45120714G>T	ENST00000372237.3	-	3	514	c.351C>A	c.(349-351)gtC>gtA	p.V117V	TMEM53_ENST00000372235.3_Silent_p.V87V|TMEM53_ENST00000372243.3_Intron|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372242.3_Silent_p.V117V|TMEM53_ENST00000476724.1_5'UTR	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	117						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					GGTACAGCATGACGCCACCGT	0.577											OREG0013446	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V117V		.											.	TMEM53-92	0			c.C351A						.						60	62	62					1																	45120714		2203	4300	6503	SO:0001819	synonymous_variant	79639	exon3			CAGCATGACGCCA		CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.351C>A	1.37:g.45120714G>T		Somatic	82	0	929	WXS	Illumina HiSeq	Phase_I	46	26	NM_024587	0	0	2	18	16	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Silent	SNP	ENST00000372237.3	37	CCDS511.1																																																																																			.		0.577	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587		T	45120714	G	T	45120714	2	4	66	1	0	0	0	0	0	0	0	1	16211	1277	45	4		4	TMEM53	1	45120714	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	4418731	45120714	204129907	3	6307											
DAP3	7818	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	155695184	155695185	+	Frame_Shift_Ins	INS	-	-	A																															tttatcaggtgaagacattcINSagtgaagcttgcctgatggt																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:155695184_155695185insA	ENST00000368336.5	+	5	406_407	c.282_283insA	c.(283-285)agtfs	p.S95fs	DAP3_ENST00000471642.2_Frame_Shift_Ins_p.S54fs|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000496863.1_3'UTR|DAP3_ENST00000343043.3_Frame_Shift_Ins_p.S95fs|DAP3_ENST00000535183.1_Frame_Shift_Ins_p.S54fs|DAP3_ENST00000421487.2_Frame_Shift_Ins_p.S61fs|MSTO1_ENST00000538143.1_Intron	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	95					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TGAAGACATTCAGTGAAGCTTG	0.45																																					p.F94fs		.											.	DAP3-228	0			c.282_283insA						.																																			SO:0001589	frameshift_variant	7818	exon5			.	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"Mitochondrial ribosomal proteins / small subunits"	2673	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S29"	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.283dupA	1.37:g.155695185_155695185dupA	ENSP00000357320:p.Ser95fs	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	178	63	NM_033657	0	0	0	0	0	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Frame_Shift_Ins	INS	ENST00000368336.5	37	CCDS1120.1																																																																																			.		0.45	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632		A	155695185	-	A	155695184	7	5	66	1	0	1	1	0	0	0	0	0	4240	825	29	0	296	0	DAP3	1	155695184	Frame_Shift_Ins	INS	-	TCGA-BQ-5882-01A-11D-1589-08	110574470	155695184	93555437	4	6308	71	2									
DAP3	7818	hgsc.bcm.edu;bcgsc.ca	37	chr1	155695186	155695186	+	Missense_Mutation	SNP	G	G	A																															ttatcaggtgaagacattcaGtgaagcttgcctgatggtaa																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:155695186G>A	ENST00000368336.5	+	5	408	c.284G>A	c.(283-285)aGt>aAt	p.S95N	DAP3_ENST00000471642.2_Missense_Mutation_p.S54N|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000496863.1_3'UTR|DAP3_ENST00000343043.3_Missense_Mutation_p.S95N|DAP3_ENST00000535183.1_Missense_Mutation_p.S54N|DAP3_ENST00000421487.2_Missense_Mutation_p.S61N|MSTO1_ENST00000538143.1_Intron	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	95					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					AAGACATTCAGTGAAGCTTGC	0.453																																					p.S95N		.											.	DAP3-228	0			c.G284A						.						187	174	178					1																	155695186		2203	4300	6503	SO:0001583	missense	7818	exon5			CATTCAGTGAAGC	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"Mitochondrial ribosomal proteins / small subunits"	2673	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S29"	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.284G>A	1.37:g.155695186G>A	ENSP00000357320:p.Ser95Asn	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	182	66	NM_033657	0	0	91	91	0	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Missense_Mutation	SNP	ENST00000368336.5	37	CCDS1120.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.629646	0.00813	.	.	ENSG00000132676	ENST00000368336;ENST00000343043;ENST00000421487;ENST00000535183	T;T;T;T	0.40756	1.03;1.03;1.06;1.02	5.65	-2.53	0.06326	.	0.680865	0.15179	N	0.276217	T	0.01835	0.0058	N	0.00114	-2.085	0.09310	N	0.999999	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.46665	-0.9175	10	0.02654	T	1	0.0	11.3623	0.49651	0.6267:0.0:0.3733:0.0	.	54;61;61;95	B4DP59;B4DY62;E7EM60;P51398	.;.;.;RT29_HUMAN	N	95;95;61;54	ENSP00000357320:S95N;ENSP00000341692:S95N;ENSP00000412605:S61N;ENSP00000445003:S54N	ENSP00000341692:S95N	S	+	2	0	DAP3	153961810	0.928000	0.31464	0.005000	0.12908	0.078000	0.17371	1.904000	0.39868	-0.315000	0.08703	-0.136000	0.14681	AGT	.		0.453	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632		A	155695186	G	A	155695186	3	1	66	1	0	0	0	0	1	0	0	0	4240	1029	36	2	298	2	DAP3	1	155695186	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	2	155695186	93555435	5	6309	71	2									
TIPRL	261726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	168168189	168168189	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatgttacgagaatatacGtcacgagaaagcaaaatttc	17	10	7	7	3	1	2	1	0	0	2	2	4	1	2	0	0	4	2	0	0	8	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:168168189G>A	ENST00000367833.2	+	6	790	c.645G>A	c.(643-645)acG>acA	p.T215T		NM_152902.3	NP_690866.1	O75663	TIPRL_HUMAN	TOR signaling pathway regulator	215	Interaction with PPP2CA.				DNA damage checkpoint (GO:0000077)|negative regulation of protein phosphatase type 2A activity (GO:0034048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|kidney(1)|large_intestine(1)|ovary(2)|skin(1)	6	all_hematologic(923;0.215)					GAGAATATACGTCACGAGAAA	0.259																																					p.T215T		.											.	TIPRL-91	0			c.G645A						.						56	60	59					1																	168168189		2200	4299	6499	SO:0001819	synonymous_variant	261726	exon6			ATATACGTCACGA	AB097034	CCDS1270.1, CCDS30935.1	1q23.2	2014-03-07	2014-03-07		ENSG00000143155	ENSG00000143155			30231	protein-coding gene	gene with protein product		611807	"TIP41, TOR signaling pathway regulator-like (S. cerevisiae)"			12761501	Standard	NM_001031800		Approved	MGC3794, dJ69E11.3, TIP41	uc001gfg.3	O75663	OTTHUMG00000034646	ENST00000367833.2:c.645G>A	1.37:g.168168189G>A		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	51	11	NM_152902	0	0	28	53	24	B2R8V3|Q5HYB2|Q8IZ86	Silent	SNP	ENST00000367833.2	37	CCDS1270.1																																																																																			.		0.259	TIPRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083822.1	NM_152902		A	168168189	G	A	168168189	2	1	66	1	0	0	0	0	0	0	0	1	15958	1132	40	1		1	TIPRL	1	168168189	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	12473003	168168189	81082432	6	6310											
RFWD2	64326	hgsc.bcm.edu	37	chr1	175914297	175914297	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgagttaacccttcataccaAttctagcacctaattggggg	11	12	8	10	0	2	1	1	1	1	0	2	1	2	1	3	2	3	2	3	2	5	7			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:175914297A>G	ENST00000367669.3	-	20	2702	c.2188T>C	c.(2188-2190)Ttg>Ctg	p.L730L	RFWD2_ENST00000308769.8_Silent_p.L706L	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	730					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTTCATACCAATTCTAGCACC	0.318																																					p.L730L	Ovarian(134;1413 1765 5706 35534 51541)	.											.	RFWD2-659	0			c.T2188C						.						49	44	46					1																	175914297		2203	4300	6503	SO:0001819	synonymous_variant	64326	exon20			ATACCAATTCTAG	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.2188T>C	1.37:g.175914297A>G		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_022457	0	0	0	0	0	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Silent	SNP	ENST00000367669.3	37	CCDS30944.1																																																																																			.		0.318	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		G	175914297	A	G	175914297	2	3	66	1	0	0	0	0	0	0	0	1	13292	98	4	3		3	RFWD2	1	175914297	Silent	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	7746108	175914297	73336324	7	6311											
KLHDC8A	55220	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	205312513	205312513	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcttccccagggcggtgaCggccacccccgcccgggctg	3	4	14	20	5	0	1	0	1	0	0	1	1	1	1	7	4	0	2	7	4	0	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:205312513C>T	ENST00000367156.3	-	5	1036	c.220G>A	c.(220-222)Gtc>Atc	p.V74I	KLHDC8A_ENST00000460687.1_Intron|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.V74I|KLHDC8A_ENST00000537168.1_Intron|KLHDC8A_ENST00000606529.1_5'Flank|KLHDC8A_ENST00000367155.3_Missense_Mutation_p.V74I	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	74										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGGGCGGTGACGGCCACCCCC	0.672																																					p.V74I		.											.	KLHDC8A-91	0			c.G220A						.						61	64	63					1																	205312513		2203	4300	6503	SO:0001583	missense	55220	exon2			CGGTGACGGCCAC		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.220G>A	1.37:g.205312513C>T	ENSP00000356124:p.Val74Ile	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	174	52	NM_018203	0	0	0	0	0	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	37	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.040035	0.55003	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253	T;T;T	0.80304	-1.36;-1.36;-1.36	5.65	4.73	0.59995	Kelch-type beta propeller (1);	0.190308	0.45361	N	0.000376	T	0.78065	0.4225	M	0.72576	2.205	0.31222	N	0.697307	B	0.13594	0.008	B	0.08055	0.003	T	0.76753	-0.2843	10	0.51188	T	0.08	-18.7937	10.6433	0.45604	0.0:0.8425:0.0:0.1575	.	74	Q8IYD2	KLD8A_HUMAN	I	74	ENSP00000356123:V74I;ENSP00000356124:V74I;ENSP00000442229:V74I	ENSP00000356123:V74I	V	-	1	0	KLHDC8A	203579136	0.981000	0.34729	0.230000	0.23976	0.980000	0.70556	2.591000	0.46163	1.346000	0.45694	0.655000	0.94253	GTC	.		0.672	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		T	205312513	C	T	205312513	3	4	66	1	0	0	0	0	1	0	0	0	8383	536	19	1	852	1	KLHDC8A	1	205312513	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	29398216	205312513	43938108	8	6312											
GPR113	165082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	26534291	26534291	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgagtcagcagcgccagagCgggttcttccggaacagtgt	8	9	14	10	3	2	2	1	1	1	1	3	3	3	3	2	2	4	2	2	2	1	3	rs199709313		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:26534291C>A	ENST00000311519.1	-	11	2304	c.2305G>T	c.(2305-2307)Gct>Tct	p.A769S	GPR113_ENST00000541401.1_Missense_Mutation_p.A372S|GPR113_ENST00000333478.6_Missense_Mutation_p.A570S|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000421160.2_Missense_Mutation_p.A700S	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	769					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)					AGCGCCAGAGCGGGTTCTTCC	0.627																																					p.A769S		.											.	GPR113-94	0			c.G2305T						.						100	110	106					2																	26534291		2203	4300	6503	SO:0001583	missense	165082	exon11			CCAGAGCGGGTTC	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.2305G>T	2.37:g.26534291C>A	ENSP00000307831:p.Ala769Ser	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	132	8	NM_001145168	0	0	1	1	0	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	0.611	-0.825017	0.02755	.	.	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.31247	1.5;1.5;1.54;1.5	5.85	-11.7	0.00046	.	.	.	.	.	T	0.14356	0.0347	L	0.28344	0.845	0.09310	N	1	B;B;B;B	0.32968	0.239;0.34;0.392;0.201	B;B;B;B	0.36808	0.167;0.208;0.233;0.148	T	0.15521	-1.0434	9	0.35671	T	0.21	-1.2208	2.2094	0.03944	0.1583:0.2911:0.3173:0.2333	.	700;570;769;372	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	S	372;570;700;769	ENSP00000445729:A372S;ENSP00000327396:A570S;ENSP00000388537:A700S;ENSP00000307831:A769S	ENSP00000307831:A769S	A	-	1	0	GPR113	26387795	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.755000	0.01814	-1.746000	0.01335	-0.187000	0.12897	GCT	C|1.000;A|0.000		0.627	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		A	26534291	C	A	26534291	3	1	66	1	0	0	0	0	1	0	0	0	6650	768	27	4	1035	4	GPR113	2	26534291	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		26534291	216665082	9	6313											
HEATR5B	54497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37267620	37267620	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagccacgatacatcggaccActagaatccactatcaaagc	15	7	6	13	2	1	1	1	0	0	1	3	3	2	2	3	1	3	0	3	1	6	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:37267620A>T	ENST00000233099.5	-	20	2993	c.2898T>A	c.(2896-2898)agT>agA	p.S966R	HEATR5B_ENST00000354531.2_Missense_Mutation_p.S966R	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	966						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ACATCGGACCACTAGAATCCA	0.373																																					p.S966R		.											.	HEATR5B-142	0			c.T2898A						.						107	92	97					2																	37267620		2203	4300	6503	SO:0001583	missense	54497	exon20			CGGACCACTAGAA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2898T>A	2.37:g.37267620A>T	ENSP00000233099:p.Ser966Arg	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	125	38	NM_019024	0	0	8	16	8	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.686846	0.48097	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.06528	3.29;3.29	5.5	1.75	0.24633	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.06096	0.0158	L	0.38175	1.15	0.51767	D	0.999939	B	0.32425	0.371	B	0.32149	0.141	T	0.35599	-0.9782	10	0.52906	T	0.07	-15.7822	11.2928	0.49261	0.805:0.0:0.195:0.0	.	966	Q9P2D3	HTR5B_HUMAN	R	966	ENSP00000233099:S966R;ENSP00000346531:S966R	ENSP00000233099:S966R	S	-	3	2	HEATR5B	37121124	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	1.659000	0.37387	0.035000	0.15519	-1.139000	0.01908	AGT	.		0.373	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		T	37267620	A	T	37267620	3	4	66	1	0	0	0	0	1	0	0	0	7053	156	6	5	3385	5	HEATR5B	2	37267620	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	10733329	37267620	205931753	10	6314											
UGGT1	56886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	128918714	128918714	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttctctccttcacagatCattgggccactggaggatag	8	12	9	12	0	4	1	2	0	2	1	6	3	5	3	2	3	0	0	2	3	1	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:128918714C>A	ENST00000259253.6	+	25	2744	c.2697C>A	c.(2695-2697)atC>atA	p.I899I	UGGT1_ENST00000375990.3_Silent_p.I875I	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	899					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CTTCACAGATCATTGGGCCAC	0.478																																					p.I899I		.											.	UGGT1-91	0			c.C2697A						.						96	95	95					2																	128918714		2203	4300	6503	SO:0001819	synonymous_variant	56886	exon25			ACAGATCATTGGG	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.2697C>A	2.37:g.128918714C>A		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	139	45	NM_020120	0	0	0	0	0	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			.		0.478	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		A	128918714	C	A	128918714	2	1	66	1	0	0	0	0	0	0	0	1	16974	816	29	4		4	UGGT1	2	128918714	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	91651094	128918714	114280659	11	6315											
MGAT5	4249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	135206357	135206357	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcccaccccaggcaccagaGggtctgcccctgccgggact	6	4	12	19	2	1	1	0	0	1	1	1	2	1	2	7	3	2	1	7	3	0	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:135206357G>A	ENST00000409645.1	+	17	2417	c.2165G>A	c.(2164-2166)aGg>aAg	p.R722K	MGAT5_ENST00000281923.2_Missense_Mutation_p.R722K			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	722					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		AGGCACCAGAGGGTCTGCCCC	0.597																																					p.R722K		.											.	MGAT5-93	0			c.G2165A						.						66	66	66					2																	135206357		2203	4300	6503	SO:0001583	missense	4249	exon16			ACCAGAGGGTCTG	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.2165G>A	2.37:g.135206357G>A	ENSP00000386377:p.Arg722Lys	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	113	36	NM_002410	0	0	4	7	3	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	37	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389249	0.95988	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.82958	0.5150	M	0.81341	2.54	0.80722	D	1	D	0.56035	0.974	D	0.70487	0.969	D	0.85213	0.1022	9	0.72032	D	0.01	-17.0654	18.7668	0.91876	0.0:0.0:1.0:0.0	.	722	Q09328	MGT5A_HUMAN	K	722	.	ENSP00000281923:R722K	R	+	2	0	MGAT5	134922827	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	9.702000	0.98712	2.523000	0.85059	0.655000	0.94253	AGG	.		0.597	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		A	135206357	G	A	135206357	3	1	66	1	0	0	0	0	1	0	0	0	9573	1000	35	2	2227	2	MGAT5	2	135206357	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	6287643	135206357	107993016	12	6316											
FMNL2	114793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	153471511	153471511	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactggaagaaaacatttcTcatgtaactatatctcagaa	17	11	6	7	0	2	2	2	0	2	2	4	4	2	3	0	1	3	1	0	1	8	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:153471511T>A	ENST00000288670.9	+	12	1576	c.1209T>A	c.(1207-1209)tcT>tcA	p.S403S		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	403	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						AAAACATTTCTCATGTAACTA	0.378																																					p.S403S		.											.	FMNL2-516	0			c.T1209A						.						84	84	84					2																	153471511		1882	4124	6006	SO:0001819	synonymous_variant	114793	exon12			CATTTCTCATGTA	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"formin homology 2 domain containing 2"	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1209T>A	2.37:g.153471511T>A		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	106	38	NM_052905	0	0	0	0	0	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			.		0.378	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		A	153471511	T	A	153471511	2	1	66	1	0	0	0	0	0	0	0	1	5971	1538	54	5		5	FMNL2	2	153471511	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	18265154	153471511	89727862	13	6317											
GPD2	2820	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	157367411	157367411	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agatatctgcagaaggccatCatgaagttggatattgagca	14	10	11	6	0	2	4	1	2	1	2	2	5	2	5	1	2	2	3	1	2	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:157367411C>T	ENST00000310454.6	+	4	750	c.378C>T	c.(376-378)atC>atT	p.I126I	GPD2_ENST00000409674.1_Silent_p.I126I|GPD2_ENST00000438166.2_Silent_p.I126I|GPD2_ENST00000540309.1_Silent_p.I126I|GPD2_ENST00000409125.4_Intron	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	126					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						AGAAGGCCATCATGAAGTTGG	0.378																																					p.I126I		.											.	GPD2-91	0			c.C378T						.						178	177	178					2																	157367411		2203	4300	6503	SO:0001819	synonymous_variant	2820	exon4			GGCCATCATGAAG		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"EF-hand domain containing"	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.378C>T	2.37:g.157367411C>T		Somatic	256	0		WXS	Illumina HiSeq	Phase_I	277	76	NM_001083112	0	0	5	13	7	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Silent	SNP	ENST00000310454.6	37	CCDS2202.1																																																																																			.		0.378	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			T	157367411	C	T	157367411	2	4	66	1	0	0	0	0	0	0	0	1	6626	816	29	2		2	GPD2	2	157367411	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	3895900	157367411	85831962	14	6318											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179575504	179575504	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taactaatctggtactttccGccacttcgtatttctctgct	7	17	5	12	2	2	0	0	0	2	0	5	0	3	0	2	1	3	3	2	1	4	7	rs375083775		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:179575504G>A	ENST00000591111.1	-	96	27593	c.27369C>T	c.(27367-27369)ggC>ggT	p.G9123G	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.G9440G|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.G8196G			Q8WZ42	TITIN_HUMAN	titin	13254	Ig-like 74.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G8196G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTACTTTCCGCCACTTCGTA	0.488																																					p.G9440G		.											.	TTN-636	1	Substitution - coding silent(1)	large_intestine(1)	c.C28320T						.	G	,,,	1,3979		0,1,1989	148	143	144		,24588,,	-12.3	0.4	2		144	0,8340		0,0,4170	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6159	AA,AG,GG		0.0,0.0251,0.0081	,,,	,8196/33424,,	179575504	1,12319	1990	4170	6160	SO:0001819	synonymous_variant	7273	exon98			CTTTCCGCCACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27369C>T	2.37:g.179575504G>A		Somatic	144	2		WXS	Illumina HiSeq	Phase_I	182	52	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179575504	G	A	179575504	2	1	66	1	0	0	0	0	0	0	0	1	16768	1074	38	1		1	TTN	2	179575504	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	22208093	179575504	63623869	15	6319											
CTLA4	1493	broad.mit.edu	37	chr2	204735458	204735458	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggtgactgaagtctgtgcgGcaacctacatgatggggaat	11	9	14	7	1	1	3	0	3	1	0	1	4	1	4	1	4	3	1	1	4	4	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:204735458G>A	ENST00000302823.3	+	2	416	c.259G>A	c.(259-261)Gca>Aca	p.A87T	CTLA4_ENST00000427473.2_Missense_Mutation_p.A50T|CTLA4_ENST00000472206.1_Intron|CTLA4_ENST00000295854.6_Missense_Mutation_p.A87T|CTLA4_ENST00000487393.1_Intron	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	87	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	AGTCTGTGCGGCAACCTACAT	0.542																																					p.A87T													.	CTLA4-90	0			c.G259A						.						148	131	137					2																	204735458		2203	4300	6503	SO:0001583	missense	1493	exon2			TGTGCGGCAACCT		CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	2505	protein-coding gene	gene with protein product		123890	"celiac disease 3", "insulin-dependent diabetes mellitus 12"	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.259G>A	2.37:g.204735458G>A	ENSP00000303939:p.Ala87Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	123	4	NM_005214	0	0	1	1	0	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Missense_Mutation	SNP	ENST00000302823.3	37	CCDS2362.1	.	.	.	.	.	.	.	.	.	.	G	0.022	-1.411045	0.01145	.	.	ENSG00000163599	ENST00000302823;ENST00000295854;ENST00000427473	T;T;T	0.41758	0.99;0.99;0.99	5.25	-4.65	0.03339	Immunoglobulin V-set (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	1.353580	0.04504	N	0.381715	T	0.17704	0.0425	N	0.03324	-0.35	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.006	T	0.19614	-1.0300	10	0.15952	T	0.53	-7.9033	7.3794	0.26847	0.6341:0.0:0.1496:0.2163	.	87;87	Q8TDA6;P16410	.;CTLA4_HUMAN	T	87;87;50	ENSP00000303939:A87T;ENSP00000295854:A87T;ENSP00000409707:A50T	ENSP00000295854:A87T	A	+	1	0	CTLA4	204443703	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.612000	0.24283	-1.349000	0.02202	-0.229000	0.12294	GCA	.		0.542	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214		A	204735458	G	A	204735458	3	1	66	1	0	0	0	0	1	0	0	0	4017	1203	42	2	265	2	CTLA4	2	204735458	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	25159954	204735458	38463915	16	6320											
ACADL	33	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	211081192	211081192	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatataggacatgacaatacCtgaatgaatactaaaacctg	19	9	6	7	0	0	3	0	3	0	0	0	4	0	4	2	1	3	0	2	1	10	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:211081192C>T	ENST00000233710.3	-	4	642	c.415G>A	c.(415-417)Ggt>Agt	p.G139S	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	139					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		ATGACAATACCTGAATGAATA	0.338																																					p.G139S		.											.	ACADL-90	0			c.G415A						.						107	101	103					2																	211081192		2202	4300	6502	SO:0001583	missense	33	exon4			CAATACCTGAATG	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.415G>A	2.37:g.211081192C>T	ENSP00000233710:p.Gly139Ser	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	112	44	NM_001608	0	0	8	33	23	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679212	0.68042	.	.	ENSG00000115361	ENST00000233710	D	0.99683	-6.39	5.77	4.9	0.64082	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.179938	0.64402	D	0.000017	D	0.98469	0.9490	N	0.16266	0.395	0.30365	N	0.783448	B	0.26445	0.149	B	0.34038	0.174	D	0.99899	1.1157	10	0.66056	D	0.02	.	15.4418	0.75190	0.0:0.933:0.0:0.067	.	139	P28330	ACADL_HUMAN	S	139	ENSP00000233710:G139S	ENSP00000233710:G139S	G	-	1	0	ACADL	210789437	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	5.531000	0.67148	1.578000	0.49821	0.655000	0.94253	GGT	.		0.338	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		T	211081192	C	T	211081192	3	4	66	1	0	0	0	0	1	0	0	0	112	681	24	2	909	2	ACADL	2	211081192	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	6345734	211081192	32118181	17	6321											
DGKD	8527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234363455	234363455	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaacaactattttggcattGgcctggatgcgaagatatcc	11	12	10	8	1	0	2	0	1	0	1	1	4	1	3	2	3	3	1	2	3	5	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:234363455G>T	ENST00000264057.2	+	19	2323	c.2311G>T	c.(2311-2313)Ggc>Tgc	p.G771C	DGKD_ENST00000409813.3_Missense_Mutation_p.G727C	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	771					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TTTTGGCATTGGCCTGGATGC	0.453																																					p.G771C		.											.	DGKD-676	0			c.G2311T						.						168	145	153					2																	234363455		2203	4300	6503	SO:0001583	missense	8527	exon19			GGCATTGGCCTGG	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2311G>T	2.37:g.234363455G>T	ENSP00000264057:p.Gly771Cys	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	148	41	NM_152879	0	0	10	41	31	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.405390	0.83230	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	D;D	0.89270	-2.49;-2.49	3.57	3.57	0.40892	Diacylglycerol kinase, accessory domain (2);	0.000000	0.64402	D	0.000004	D	0.96324	0.8801	H	0.97077	3.935	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97837	1.0266	10	0.87932	D	0	.	16.4941	0.84223	0.0:0.0:1.0:0.0	.	655;727;771	Q53SE4;Q16760-2;Q16760	.;.;DGKD_HUMAN	C	771;727	ENSP00000264057:G771C;ENSP00000386455:G727C	ENSP00000264057:G771C	G	+	1	0	DGKD	234028194	1.000000	0.71417	0.973000	0.42090	0.987000	0.75469	9.627000	0.98412	2.305000	0.77605	0.643000	0.83706	GGC	.		0.453	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234363455	G	T	234363455	3	4	66	1	0	0	0	0	1	0	0	0	4478	1348	47	4	2409	4	DGKD	2	234363455	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	23282263	234363455	8835918	18	6322											
SATB1	6304	broad.mit.edu;ucsc.edu	37	chr3	18391172	18391172	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttgctgttgctgctgctgTtgctgcaaagaaacaaggag	9	12	13	7	0	0	1	0	0	0	1	0	2	0	2	0	1	7	9	0	1	3	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:18391172T>A	ENST00000338745.6	-	11	3516	c.1782A>T	c.(1780-1782)caA>caT	p.Q594H	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.Q594H|SATB1_ENST00000417717.2_Missense_Mutation_p.Q626H	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	594	Poly-Gln.				activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						gctgctgctgttgctgcAAAG	0.582																																					p.Q626H													.	SATB1-228	0			c.A1878T						.						8	10	9					3																	18391172		2168	4252	6420	SO:0001583	missense	6304	exon12			CTGCTGTTGCTGC		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1782A>T	3.37:g.18391172T>A	ENSP00000341024:p.Gln594His	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	15	5	NM_001195470	0	0	0	0	0	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	37	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	0.454	-0.892361	0.02491	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	T;T;T	0.25749	1.78;1.78;1.84	3.08	1.14	0.20703	.	0.839327	0.10778	N	0.635150	T	0.10852	0.0265	N	0.14661	0.345	0.80722	D	1	P;B	0.39782	0.688;0.003	B;B	0.25987	0.065;0.001	T	0.09487	-1.0672	10	0.59425	D	0.04	-4.561	5.2867	0.15706	0.0:0.6668:0.2077:0.1255	.	626;594	Q01826-2;Q01826	.;SATB1_HUMAN	H	594;594;626	ENSP00000341024:Q594H;ENSP00000399708:Q594H;ENSP00000399518:Q626H	ENSP00000341024:Q594H	Q	-	3	2	SATB1	18366176	0.997000	0.39634	0.385000	0.26158	0.633000	0.38033	0.960000	0.29253	0.022000	0.15160	-0.464000	0.05259	CAA	.		0.582	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		A	18391172	T	A	18391172	3	1	66	1	0	0	0	0	1	0	0	0	13885	1722	60	5	513	5	SATB1	3	18391172	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		18391172	179631258	19	6323											
CCDC13	152206	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	42793437	42793438	+	Frame_Shift_Ins	INS	-	-	TC																															gaattcataccaatgctctgINStctcccatctgggccctcgg																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:42793437_42793438insTC	ENST00000310232.6	-	5	676_677	c.593_594insGA	c.(592-594)gacfs	p.D198fs	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	198										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CCAATGCTCTGTCTCCCATCTG	0.609																																					p.D198fs		.											.	CCDC13-91	0			c.594_595insGA						.																																			SO:0001589	frameshift_variant	152206	exon5			.	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.592_593dupGA	3.37:g.42793440_42793441dupTC	ENSP00000309836:p.Asp198fs	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	83	25	NM_144719	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000310232.6	37	CCDS2705.1																																																																																			.		0.609	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		TC	42793438	-	TC	42793437	7	5	66	1	0	1	1	0	0	0	0	0	2771	1368	48	0	1601	0	CCDC13	3	42793437	Frame_Shift_Ins	INS	-	TCGA-BQ-5882-01A-11D-1589-08	24402265	42793437	155228993	20	6324	72	2									
CCDC13	152206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	42793447	42793447	+	Missense_Mutation	SNP	T	T	G																															ccaatgctctgtctcccatcTgggccctcggtggcttggct																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:42793447T>G	ENST00000310232.6	-	5	667	c.584A>C	c.(583-585)cAg>cCg	p.Q195P	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	195										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GTCTCCCATCTGGGCCCTCGG	0.592																																					p.Q195P		.											.	CCDC13-91	0			c.A584C						.						84	77	79					3																	42793447		2203	4300	6503	SO:0001583	missense	152206	exon5			CCCATCTGGGCCC	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.584A>C	3.37:g.42793447T>G	ENSP00000309836:p.Gln195Pro	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	94	33	NM_144719	0	0	0	0	0		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	4.532	0.098801	0.08681	.	.	ENSG00000244607	ENST00000310232	T	0.24723	1.84	4.01	1.44	0.22558	.	0.735360	0.13594	N	0.376366	T	0.23451	0.0567	L	0.55103	1.725	0.20403	N	0.999901	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.21586	-1.0241	10	0.56958	D	0.05	.	8.5317	0.33337	0.0:0.0:0.4318:0.5682	.	195;195;195	B4DZD2;Q96LI1;Q8IYE1	.;.;CCD13_HUMAN	P	195	ENSP00000309836:Q195P	ENSP00000309836:Q195P	Q	-	2	0	CCDC13	42768451	0.092000	0.21681	0.182000	0.23118	0.423000	0.31445	-0.078000	0.11375	0.286000	0.22352	0.533000	0.62120	CAG	.		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		G	42793447	T	G	42793447	3	3	66	1	0	0	0	0	1	0	0	0	2771	1580	55	5	1611	5	CCDC13	3	42793447	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	10	42793447	155228983	21	6325	72	2									
STAB1	23166	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52544437	52544437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggagtggggatggccgcGtctgtgtggctattgacgag	5	10	19	7	3	1	1	0	1	1	0	1	4	1	3	1	5	0	2	1	5	1	2	rs569908210		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:52544437G>A	ENST00000321725.6	+	25	2777	c.2701G>A	c.(2701-2703)Gtc>Atc	p.V901I		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	901	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GGATGGCCGCGTCTGTGTGGC	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		18485	0		0	False		,,,				2504	0				p.V901I		.											.	STAB1-139	0			c.G2701A						.						95	86	89					3																	52544437		2203	4300	6503	SO:0001583	missense	23166	exon25			GGCCGCGTCTGTG	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2701G>A	3.37:g.52544437G>A	ENSP00000312946:p.Val901Ile	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	70	37	NM_015136	0	0	4	4	0	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.637778	0.29157	.	.	ENSG00000010327	ENST00000321725	T	0.42131	0.98	5.86	1.84	0.25277	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.431461	0.22025	N	0.065676	T	0.29850	0.0746	L	0.37697	1.125	0.19575	N	0.999963	B	0.20988	0.05	B	0.12837	0.008	T	0.16719	-1.0393	10	0.36615	T	0.2	.	9.6284	0.39765	0.3064:0.0:0.6936:0.0	.	901	Q9NY15	STAB1_HUMAN	I	901	ENSP00000312946:V901I	ENSP00000312946:V901I	V	+	1	0	STAB1	52519477	0.886000	0.30341	0.825000	0.32803	0.923000	0.55619	1.548000	0.36201	0.322000	0.23283	-0.345000	0.07892	GTC	.		0.612	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52544437	G	A	52544437	3	1	66	1	0	0	0	0	1	0	0	0	15269	1145	40	1	2799	1	STAB1	3	52544437	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	9750990	52544437	145477993	22	6326											
EPHB1	2047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	134670526	134670526	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgctgcagatgagagctTctcccaggtggactttgggg	7	11	14	9	0	1	2	0	1	1	2	2	4	1	3	1	4	3	3	1	4	0	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:134670526T>A	ENST00000398015.3	+	3	807	c.437T>A	c.(436-438)tTc>tAc	p.F146Y	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	146	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GATGAGAGCTTCTCCCAGGTG	0.493																																					p.F146Y		.											.	EPHB1-1492	0			c.T437A						.						154	151	152					3																	134670526		1972	4204	6176	SO:0001583	missense	2047	exon3			AGAGCTTCTCCCA	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.437T>A	3.37:g.134670526T>A	ENSP00000381097:p.Phe146Tyr	Somatic	273	0		WXS	Illumina HiSeq	Phase_I	222	112	NM_004441	0	0	0	1	1	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644684	0.87859	.	.	ENSG00000154928	ENST00000398015;ENST00000474732	T;T	0.04234	3.67;3.67	5.49	5.49	0.81192	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	M	0.86097	2.795	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.91635	0.999;0.991	T	0.01725	-1.1287	9	.	.	.	.	15.6027	0.76636	0.0:0.0:0.0:1.0	.	146;146	B5A969;P54762	.;EPHB1_HUMAN	Y	146;124	ENSP00000381097:F146Y;ENSP00000418352:F124Y	.	F	+	2	0	EPHB1	136153216	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.085000	0.62840	0.533000	0.62120	TTC	.		0.493	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134670526	T	A	134670526	3	1	66	1	0	0	0	0	1	0	0	0	5187	1783	62	5	447	5	EPHB1	3	134670526	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	82126089	134670526	63351904	23	6327											
RBP2	5948	broad.mit.edu	37	chr3	139195248	139195248	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagggccttcatgtagccCtcaaagttttcattactctc	8	13	6	14	0	4	0	3	0	1	0	5	0	4	0	3	1	2	2	3	1	3	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:139195248C>A	ENST00000232217.2	-	1	110	c.54G>T	c.(52-54)gaG>gaT	p.E18D	RP11-319G6.1_ENST00000515247.1_RNA	NM_004164.2	NP_004155.2	P50120	RET2_HUMAN	retinol binding protein 2, cellular	18					epidermis development (GO:0008544)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12					Vitamin A(DB00162)	TCATGTAGCCCTCAAAGTTTT	0.557																																					p.E18D													.	RBP2-91	0			c.G54T						.						228	187	201					3																	139195248		2203	4300	6503	SO:0001583	missense	5948	exon1			GTAGCCCTCAAAG	U13831	CCDS3109.1	3q23	2013-03-01	2001-11-28		ENSG00000114113	ENSG00000114113		"Fatty acid binding protein family"	9920	protein-coding gene	gene with protein product		180280	"retinol-binding protein 2, cellular"			7657783, 10072590	Standard	NM_004164		Approved	CRBP2, RBPC2, CRBPII, CRABP-II	uc003eth.3	P50120	OTTHUMG00000159956	ENST00000232217.2:c.54G>T	3.37:g.139195248C>A	ENSP00000232217:p.Glu18Asp	Somatic	111	1		WXS	Illumina HiSeq	Phase_I	83	4	NM_004164	0	0	0	0	0	A8K7G3|Q6ISQ9|Q6ISS7	Missense_Mutation	SNP	ENST00000232217.2	37	CCDS3109.1	.	.	.	.	.	.	.	.	.	.	C	5.699	0.313507	0.10789	.	.	ENSG00000114113	ENST00000232217;ENST00000511956;ENST00000506825	T;T	0.08546	3.08;3.08	5.44	-10.9	0.00192	Calycin-like (1);Cytosolic fatty-acid binding (2);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.348037	0.36101	N	0.002797	T	0.01870	0.0059	N	0.11789	0.175	0.50467	D	0.99987	B	0.09022	0.002	B	0.12837	0.008	T	0.51172	-0.8739	10	0.06099	T	0.92	.	1.2537	0.01987	0.3373:0.3044:0.105:0.2534	.	18	P50120	RET2_HUMAN	D	18	ENSP00000232217:E18D;ENSP00000424333:E18D	ENSP00000232217:E18D	E	-	3	2	RBP2	140677938	0.542000	0.26426	0.617000	0.29091	0.606000	0.37113	-0.735000	0.04888	-2.133000	0.00813	-1.461000	0.01025	GAG	.		0.557	RBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358490.1	NM_004164		A	139195248	C	A	139195248	3	1	66	1	0	0	0	0	1	0	0	0	13188	680	24	4	366	4	RBP2	3	139195248	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	4524722	139195248	58827182	24	6328											
MED12L	116931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151078359	151078359	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgatctctatgtgtcatgtAgccacctcagaagtaaattt	12	14	7	8	0	3	2	2	1	1	1	4	2	3	2	2	0	1	2	2	0	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:151078359A>G	ENST00000474524.1	+	19	2856	c.2818A>G	c.(2818-2820)Agc>Ggc	p.S940G	P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000273432.4_Missense_Mutation_p.S800G	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	940						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGTGTCATGTAGCCACCTCAG	0.438																																					p.S940G		.											.	MED12L-576	0			c.A2818G						.						211	195	201					3																	151078359		2203	4300	6503	SO:0001583	missense	116931	exon19			TCATGTAGCCACC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2818A>G	3.37:g.151078359A>G	ENSP00000417235:p.Ser940Gly	Somatic	280	0		WXS	Illumina HiSeq	Phase_I	239	125	NM_053002	0	0	0	0	0	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133418	0.77662	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.79653	-1.29;-1.29	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.85660	0.5748	L	0.45228	1.405	0.80722	D	1	P;D;P	0.56035	0.48;0.974;0.956	B;D;D	0.67725	0.412;0.953;0.931	D	0.87163	0.2216	10	0.87932	D	0	-22.6472	15.5111	0.75782	1.0:0.0:0.0:0.0	.	800;940;940	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	G	940;800	ENSP00000417235:S940G;ENSP00000273432:S800G	ENSP00000273432:S800G	S	+	1	0	MED12L	152561049	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.649000	0.91067	2.199000	0.70637	0.533000	0.62120	AGC	.		0.438	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	151078359	A	G	151078359	3	3	66	1	0	0	0	0	1	0	0	0	9454	420	15	3	2892	3	MED12L	3	151078359	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	11883111	151078359	46944071	25	6329											
NAF1	92345	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	164050121	164050121	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcagtggtggagggggaggGggtgggggtagggagtatgg	6	6	28	1	0	0	0	0	0	0	0	0	3	0	3	0	11	0	3	0	11	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr4:164050121G>A	ENST00000274054.2	-	8	1606	c.1413C>T	c.(1411-1413)ccC>ccT	p.P471P	NAF1_ENST00000422287.2_Intron|NAF1_ENST00000509434.1_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	471	Pro-rich.				pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				gagggggagggggtgggggta	0.517																																					p.P471P		.											.	NAF1-70	0			c.C1413T						.						10	11	10					4																	164050121		2191	4274	6465	SO:0001819	synonymous_variant	92345	exon8			GGGAGGGGGTGGG		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.1413C>T	4.37:g.164050121G>A		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	22	16	NM_138386	0	0	0	2	2	D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	37	CCDS3803.1																																																																																			.		0.517	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		A	164050121	G	A	164050121	2	1	66	1	0	0	0	0	0	0	0	1	10165	1219	43	2		2	NAF1	4	164050121	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		164050121	27104155	26	6330											
TERT	7015	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	1255515	1255515	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgggagctgcagcacaCatgcgtgaaacctgagagga	14	5	14	8	1	0	2	0	2	0	1	0	6	0	4	1	2	5	3	1	2	2	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:1255515C>A	ENST00000310581.5	-	14	3101	c.3044G>T	c.(3043-3045)tGt>tTt	p.C1015F	TERT_ENST00000296820.5_3'UTR|TERT_ENST00000334602.6_Missense_Mutation_p.C952F	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1015	CTE.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CTGCAGCACACATGCGTGAAA	0.572									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.C1015F		.											.	TERT-1272	0			c.G3044T						.						76	82	80					5																	1255515		2161	4266	6427	SO:0001583	missense	7015	exon14	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AGCACACATGCGT	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3044G>T	5.37:g.1255515C>A	ENSP00000309572:p.Cys1015Phe	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	51	14	NM_198253	0	0	0	0	0	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	c	14.17	2.454152	0.43634	.	.	ENSG00000164362	ENST00000310581;ENST00000334602	T;T	0.66815	-0.23;-0.23	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.83622	0.5294	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.83650	0.0155	10	0.27082	T	0.32	-0.9462	16.718	0.85402	0.0:1.0:0.0:0.0	.	952;1015	O14746-3;O14746	.;TERT_HUMAN	F	1015;952	ENSP00000309572:C1015F;ENSP00000334346:C952F	ENSP00000309572:C1015F	C	-	2	0	TERT	1308515	1.000000	0.71417	0.180000	0.23079	0.008000	0.06430	6.534000	0.73833	2.237000	0.73441	0.655000	0.94253	TGT	.		0.572	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			A	1255515	C	A	1255515	3	1	66	1	0	0	0	0	1	0	0	0	15796	478	17	4	366	4	TERT	5	1255515	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		1255515	179659745	27	6331											
CCNI2	645121	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	132084160	132084160	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggccgcctcctgatttCagtgaaggtagggaggcctc	6	11	13	11	1	1	2	1	2	0	0	3	3	2	3	4	4	0	1	4	4	2	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:132084160C>A	ENST00000378731.1	+	2	602	c.551C>A	c.(550-552)tCa>tAa	p.S184*	SEPT8_ENST00000481030.1_5'Flank	NM_001039780.2	NP_001034869.1	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2	184					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCCTGATTTCAGTGAAGGTA	0.542																																					p.S184X		.											.	CCNI2-68	0			c.C551A						.						78	76	77					5																	132084160		2203	4300	6503	SO:0001587	stop_gained	645121	exon2			TGATTTCAGTGAA	BC132837	CCDS34236.1, CCDS75297.1	5q31.1	2014-07-03			ENSG00000205089	ENSG00000205089			33869	protein-coding gene	gene with protein product						23707792	Standard	NM_001287252		Approved	FLJ16793	uc003kxq.1	Q6ZMN8	OTTHUMG00000059737	ENST00000378731.1:c.551C>A	5.37:g.132084160C>A	ENSP00000368005:p.Ser184*	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	163	47	NM_001039780	0	0	0	0	0	B2RNE2|B7ZMB7|B7ZMB8	Nonsense_Mutation	SNP	ENST00000378731.1	37	CCDS34236.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374680	0.61735	.	.	ENSG00000205089	ENST00000378731	.	.	.	4.74	2.95	0.34219	.	0.352786	0.29699	N	0.011430	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	10.896	0.47023	0.0:0.8799:0.0:0.1201	.	.	.	.	X	184	.	ENSP00000368005:S184X	S	+	2	0	CCNI2	132112059	0.186000	0.23225	0.002000	0.10522	0.016000	0.09150	2.489000	0.45285	0.667000	0.31107	0.651000	0.88453	TCA	.		0.542	CCNI2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132833.1	NM_001039780		A	132084160	C	A	132084160	4	1	66	1	0	0	0	0	0	1	0	0	2933	838	29	4	557	4	CCNI2	5	132084160	Nonsense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	130828645	132084160	48831100	28	6332											
PCDHB16	57717	hgsc.bcm.edu;broad.mit.edu	37	chr5	140563807	140563807	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggacgccaacgacaactCgcccttcgtgctgtacccgc	7	7	10	17	5	0	0	0	0	0	0	2	2	0	1	3	1	4	3	3	1	3	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:140563807C>A	ENST00000361016.2	+	1	2828	c.1673C>A	c.(1672-1674)tCg>tAg	p.S558*		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	558	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACGACAACTCGCCCTTCGTG	0.711																																					p.S558X		.											.	PCDHB16-92	0			c.C1673A						.						11	12	12					5																	140563807		1879	3737	5616	SO:0001587	stop_gained	57717	exon1			ACAACTCGCCCTT	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1673C>A	5.37:g.140563807C>A	ENSP00000354293:p.Ser558*	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	98	33	NM_020957	0	0	80	80	0	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Nonsense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	c	48	13.975717	0.99773	.	.	ENSG00000196963	ENST00000361016	.	.	.	4.12	3.17	0.36434	.	1.688500	0.04202	N	0.330215	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	6.9564	0.24574	0.0:0.7253:0.1781:0.0966	.	.	.	.	X	558	.	ENSP00000354293:S558X	S	+	2	0	PCDHB16	140543991	0.000000	0.05858	0.992000	0.48379	0.997000	0.91878	1.063000	0.30567	1.860000	0.53959	0.479000	0.44913	TCG	.		0.711	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563807	C	A	140563807	4	1	66	1	0	0	0	0	0	1	0	0	11567	893	31	4	1675	4	PCDHB16	5	140563807	Nonsense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	8479647	140563807	40351453	29	6333											
OR5V1	81696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	29323498	29323498	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagaatgtcaacactgtatGcaccactgagttaaggaaac	15	8	9	9	0	1	2	1	1	0	1	1	3	1	3	1	1	3	4	1	1	5	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:29323498G>C	ENST00000377154.1	-	4	774	c.475C>G	c.(475-477)Cat>Gat	p.H159D	OR5V1_ENST00000543825.1_Missense_Mutation_p.H159D			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AACACTGTATGCACCACTGAG	0.438																																					p.H159D	Ovarian(32;43 883 21137 32120 42650)	.											.	OR5V1-72	0			c.C475G						.						88	85	86					6																	29323498		2203	4299	6502	SO:0001583	missense	81696	exon1			CTGTATGCACCAC		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.475C>G	6.37:g.29323498G>C	ENSP00000366359:p.His159Asp	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	67	37	NM_030876	0	0	0	0	0	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420539	0.25639	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.00262	8.4;8.4	4.28	4.28	0.50868	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34484	N	0.003929	T	0.00328	0.0010	M	0.88512	2.96	0.26396	N	0.976491	D	0.89917	1.0	D	0.91635	0.999	T	0.37291	-0.9712	10	0.51188	T	0.08	-51.5055	12.8107	0.57637	0.0:0.0:0.8357:0.1643	.	159	Q9UGF6	OR5V1_HUMAN	D	159	ENSP00000366359:H159D;ENSP00000443309:H159D	ENSP00000366356:H159D	H	-	1	0	OR5V1	29431477	0.000000	0.05858	0.876000	0.34364	0.772000	0.43724	-0.032000	0.12266	2.374000	0.81015	0.543000	0.68304	CAT	.		0.438	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			C	29323498	G	C	29323498	3	2	66	1	0	0	0	0	1	0	0	0	11210	1319	46	4	493	4	OR5V1	6	29323498	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		29323498	141791569	30	6334											
C6orf222	389384	broad.mit.edu	37	chr6	36294406	36294406	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccccctcttggcctcctcgGagccgtgtttcttggggttt	1	14	11	15	2	2	0	0	0	2	0	4	1	3	1	6	4	1	2	6	4	0	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:36294406G>T	ENST00000437635.2	-	5	1094	c.917C>A	c.(916-918)tCc>tAc	p.S306Y		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	306										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						GGCCTCCTCGGAGCCGTGTTT	0.572																																					p.S306Y													.	C6orf222-93	0			c.C917A						.						147	158	154					6																	36294406		2203	4300	6503	SO:0001583	missense	389384	exon5			TCCTCGGAGCCGT		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.917C>A	6.37:g.36294406G>T	ENSP00000418983:p.Ser306Tyr	Somatic	337	0		WXS	Illumina HiSeq	Phase_I	224	4	NM_001010903	0	0	0	0	0	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	37	CCDS34439.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.076782	0.36662	.	.	ENSG00000189325	ENST00000437635	T	0.52526	0.66	3.42	1.61	0.23674	.	0.342640	0.21652	N	0.071173	T	0.34629	0.0904	M	0.62723	1.935	0.09310	N	1	D	0.53462	0.96	P	0.52217	0.693	T	0.13872	-1.0493	10	0.87932	D	0	-19.7313	5.9357	0.19165	0.2456:0.0:0.7544:0.0	.	306	P0C671	CF222_HUMAN	Y	306	ENSP00000418983:S306Y	ENSP00000418983:S306Y	S	-	2	0	C6orf222	36402384	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	0.583000	0.23849	0.447000	0.26695	0.462000	0.41574	TCC	.		0.572	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		T	36294406	G	T	36294406	3	4	66	1	0	0	0	0	1	0	0	0	2362	1174	41	4	1073	4	C6orf222	6	36294406	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	6970908	36294406	134820661	31	6335											
RIMS1	22999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	73108662	73108662	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatacctttgtttagctccaTatgtcaaagtatatcttttg	10	19	5	7	0	2	0	1	0	1	0	3	0	3	0	2	0	2	3	2	0	7	10			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:73108662T>G	ENST00000521978.1	+	33	4726	c.4726T>G	c.(4726-4728)Tat>Gat	p.Y1576D	RIMS1_ENST00000348717.5_Missense_Mutation_p.Y1359D|RIMS1_ENST00000517960.1_Missense_Mutation_p.Y1359D|RIMS1_ENST00000518273.1_Missense_Mutation_p.Y1255D|RIMS1_ENST00000414192.2_Missense_Mutation_p.Y103D|RIMS1_ENST00000517827.1_Missense_Mutation_p.Y710D|RIMS1_ENST00000425662.2_Missense_Mutation_p.Y644D|RIMS1_ENST00000401910.3_Missense_Mutation_p.Y896D|RIMS1_ENST00000264839.7_Missense_Mutation_p.Y1425D|RIMS1_ENST00000522291.1_Missense_Mutation_p.Y1175D|RIMS1_ENST00000523963.1_Missense_Mutation_p.Y701D|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000520567.1_Missense_Mutation_p.Y1226D|RIMS1_ENST00000491071.2_Missense_Mutation_p.Y1365D|RIMS1_ENST00000538414.1_Missense_Mutation_p.Y382D	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1576	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				TTTAGCTCCATATGTCAAAGT	0.318																																					p.Y1576D		.											.	RIMS1-144	0			c.T4726G						.						66	62	63					6																	73108662		1796	4064	5860	SO:0001583	missense	22999	exon33			GCTCCATATGTCA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"Rab3-interacting molecule"	606629	"RAB3 interacting protein 2"	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4726T>G	6.37:g.73108662T>G	ENSP00000428417:p.Tyr1576Asp	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	39	15	NM_014989	0	0	0	0	0	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	23.1|23.1|23.1	4.374106|4.374106|4.374106	0.82573|0.82573|0.82573	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|.|0.80033	.|.|-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;0.34;-1.33;-1.33;-1.33;-1.33	5.37|5.37|5.37	5.37|5.37|5.37	0.77165|0.77165|0.77165	.|.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|.|0.000000	.|.|0.56097	.|.|D	.|.|0.000022	D|D|D	0.93953|0.93953|0.93953	0.8064|0.8064|0.8064	H|H|H	0.99516|0.99516|0.99516	4.605|4.605|4.605	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0	.|.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|.|0.97110	.|.|1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;0.999;0.999;0.999;0.994;0.999	D|D|D	0.96600|0.96600|0.96600	0.9444|0.9444|0.9444	5|5|10	.|.|0.87932	.|.|D	.|.|0	-24.6441|-24.6441|-24.6441	15.6587|15.6587|15.6587	0.77165|0.77165|0.77165	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|.|200;382;710;701;1425;896;1175;479;1255;1359;652;1365;1576	.|.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	Q|R|D	493|921|1365;1425;1365;1359;1255;1175;1425;1359;1255;1226;1175;1576;896;701;644;741;710;624;382;103	.|.|ENSP00000430101:Y1365D;ENSP00000275037:Y1359D;ENSP00000264839:Y1425D;ENSP00000429959:Y1359D;ENSP00000430408:Y1255D;ENSP00000430502:Y1226D;ENSP00000430932:Y1175D;ENSP00000428417:Y1576D;ENSP00000385649:Y896D;ENSP00000428328:Y701D;ENSP00000411235:Y644D;ENSP00000389503:Y741D;ENSP00000428367:Y710D;ENSP00000359448:Y624D;ENSP00000439730:Y382D;ENSP00000402273:Y103D	.|.|ENSP00000264839:Y1425D	H|I|Y	+|+|+	3|2|1	2|0|0	RIMS1|RIMS1|RIMS1	73165383|73165383|73165383	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.987000|0.987000|0.987000	0.45799|0.45799|0.45799	0.938000|0.938000|0.938000	0.57974|0.57974|0.57974	7.934000|7.934000|7.934000	0.87649|0.87649|0.87649	2.157000|2.157000|2.157000	0.67596|0.67596|0.67596	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	CAT|ATA|TAT	.		0.318	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	73108662	T	G	73108662	3	3	66	1	0	0	0	0	1	0	0	0	13399	1406	49	5	5019	5	RIMS1	6	73108662	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	36814256	73108662	98006405	32	6336											
ANLN	54443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	36445953	36445953	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgggaagatgatgtaaaTcactcatttgcaaaacaaaa	17	10	7	7	0	2	2	2	1	0	1	3	3	3	3	1	1	2	2	1	1	7	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:36445953T>C	ENST00000265748.2	+	4	872	c.651T>C	c.(649-651)aaT>aaC	p.N217N	ANLN_ENST00000396068.2_Silent_p.N217N	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	217	Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						ATGATGTAAATCACTCATTTG	0.468																																					p.N217N		.											.	ANLN-517	0			c.T651C						.						108	105	106					7																	36445953		2203	4300	6503	SO:0001819	synonymous_variant	54443	exon4			TGTAAATCACTCA	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.651T>C	7.37:g.36445953T>C		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	143	48	NM_018685	0	0	5	8	3	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	37	CCDS5447.1																																																																																			.		0.468	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		C	36445953	T	C	36445953	2	2	66	1	0	0	0	0	0	0	0	1	694	1432	50	3		3	ANLN	7	36445953	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		36445953	122692710	33	6337											
POM121	9883	hgsc.bcm.edu	37	chr7	72416149	72416149	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccacccccacctttggtcTgaacacccctgcgcctggag	6	7	9	19	2	1	1	0	1	1	0	1	2	1	2	7	2	2	0	7	2	1	1	rs17406301		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:72416149T>A	ENST00000434423.2	+	12	3554	c.3554T>A	c.(3553-3555)cTg>cAg	p.L1185Q	POM121_ENST00000446813.1_Missense_Mutation_p.L920Q|POM121_ENST00000358357.3_Missense_Mutation_p.L920Q|POM121_ENST00000257622.4_Missense_Mutation_p.L920Q|POM121_ENST00000395270.1_Missense_Mutation_p.L920Q|NSUN5P2_ENST00000388955.4_RNA			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1185	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				ACCTTTGGTCTGAACACCCCT	0.632																																					p.L920Q		.											.	POM121-226	0			c.T2759A						.						24	26	25					7																	72416149		2203	4297	6500	SO:0001583	missense	9883	exon12			TTGGTCTGAACAC	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"-"	19702	protein-coding gene	gene with protein product		615753	"POM121 membrane glycoprotein (rat)", "POM121 membrane glycoprotein"			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3554T>A	7.37:g.72416149T>A	ENSP00000405562:p.Leu1185Gln	Somatic	72	2		WXS	Illumina HiSeq	Phase_I	65	4	NM_172020	0	0	41	96	55	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	A	0.005	-2.172827	0.00312	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.03689	3.84;3.9;3.84;3.9;4.16	3.16	1.97	0.26223	.	0.212871	0.23674	N	0.045695	T	0.00608	0.0020	N	0.00040	-2.495	0.18873	N	0.999988	B	0.02656	0.0	B	0.01281	0.0	T	0.45818	-0.9235	10	0.02654	T	1	.	7.0701	0.25173	0.7989:0.0:0.0:0.2011	rs17406301	920	A8MXF9	.	Q	920;920;920;920;1185	ENSP00000393020:L920Q;ENSP00000257622:L920Q;ENSP00000378687:L920Q;ENSP00000351124:L920Q;ENSP00000405562:L1185Q	ENSP00000257622:L920Q	L	+	2	0	POM121	72054085	1.000000	0.71417	0.867000	0.34043	0.067000	0.16453	3.491000	0.53252	0.400000	0.25396	-1.791000	0.00627	CTG	.		0.632	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			A	72416149	T	A	72416149	3	1	66	1	0	0	0	0	1	0	0	0	12265	1580	55	5	2801	5	POM121	7	72416149	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	35970196	72416149	86722514	34	6338											
MUC17	140453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100681165	100681165	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcatgcaaacctcaacttaTagtgacagaagaactccttt	15	10	6	10	0	1	3	1	1	0	2	2	3	2	3	2	0	5	2	2	0	6	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:100681165T>C	ENST00000306151.4	+	3	6532	c.6468T>C	c.(6466-6468)taT>taC	p.Y2156Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2156	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTCAACTTATAGTGACAGAA	0.463																																					p.Y2156Y		.											.	MUC17-95	0			c.T6468C						.						221	219	220					7																	100681165		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6468T>C	7.37:g.100681165T>C		Somatic	335	0		WXS	Illumina HiSeq	Phase_I	383	130	NM_001040105	0	0	0	0	0	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100681165	T	C	100681165	2	2	66	1	0	0	0	0	0	0	0	1	9999	1413	49	3		3	MUC17	7	100681165	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	28265016	100681165	58457498	35	6339											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116340025	116340025	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctacatggaaatgcctcTggagtgtattctcacagaaa	12	12	8	9	0	2	1	1	0	2	1	4	3	3	3	2	2	2	1	2	2	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:116340025T>C	ENST00000318493.6	+	2	1074	c.887T>C	c.(886-888)cTg>cCg	p.L296P	MET_ENST00000397752.3_Missense_Mutation_p.L296P|MET_ENST00000436117.2_Missense_Mutation_p.L296P			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GAAATGCCTCTGGAGTGTATT	0.428			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.L296P		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.T887C						.						81	77	78					7																	116340025		1839	4092	5931	SO:0001583	missense	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TGCCTCTGGAGTG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.887T>C	7.37:g.116340025T>C	ENSP00000317272:p.Leu296Pro	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	199	57	NM_000245	0	0	30	55	25	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.978979	0.34942	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.17691	2.26;2.26;2.26	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.068376	0.64402	D	0.000011	T	0.51601	0.1684	M	0.90595	3.13	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.999;1.0;0.999;0.999;0.999;0.999;0.999;1.0;0.996;0.999;1.0;1.0	T	0.60895	-0.7172	10	0.87932	D	0	-8.4229	16.8222	0.85835	0.0:0.0:0.0:1.0	.	296;296;296;296;296;296;296;296;296;296;296;296;296	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	P	296	ENSP00000380860:L296P;ENSP00000317272:L296P;ENSP00000410980:L296P	ENSP00000317272:L296P	L	+	2	0	MET	116127261	1.000000	0.71417	1.000000	0.80357	0.010000	0.07245	7.636000	0.83301	2.371000	0.80710	0.533000	0.62120	CTG	.		0.428	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116340025	T	C	116340025	3	2	66	1	0	0	0	0	1	0	0	0	9510	1580	55	3	889	3	MET	7	116340025	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	15658860	116340025	42798638	36	6340											
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121651531	121651531	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgtcatttgaatccatcCtgtcttcctatgatggtgca	8	16	8	9	0	2	2	1	2	1	0	5	2	5	2	3	1	1	1	3	1	2	3	rs143422308		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:121651531C>T	ENST00000393386.2	+	12	2842	c.2431C>T	c.(2431-2433)Ctg>Ttg	p.L811L	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	811					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TGAATCCATCCTGTCTTCCTA	0.458																																					p.L811L		.											.	PTPRZ1-699	0			c.C2431T						.						281	232	249					7																	121651531		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			TCCATCCTGTCTT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.2431C>T	7.37:g.121651531C>T		Somatic	344	0		WXS	Illumina HiSeq	Phase_I	398	114	NM_002851	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			C|1.000;G|0.000		0.458	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121651531	C	T	121651531	2	4	66	1	0	0	0	0	0	0	0	1	12846	680	24	2		2	PTPRZ1	7	121651531	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	5311506	121651531	37487132	37	6341											
WRN	7486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	30938567	30938567	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacatgaagttttaattcacGttgaagatgaaacatgggac	16	11	9	5	1	1	4	1	3	0	1	1	5	1	5	0	1	2	2	0	1	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:30938567G>A	ENST00000298139.5	+	9	1273	c.1024G>A	c.(1024-1026)Gtt>Att	p.V342I		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	342					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTTAATTCACGTTGAAGATGA	0.353			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.V342I	Ovarian(18;161 598 2706 14834 27543)	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"L, E, M, O"	.	WRN-1036	0			c.G1024A						.						105	101	103					8																	30938567		2203	4300	6503	SO:0001583	missense	7486	exon9	Familial Cancer Database	WS, Adult Progeria	ATTCACGTTGAAG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"Werner syndrome"			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1024G>A	8.37:g.30938567G>A	ENSP00000298139:p.Val342Ile	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	142	31	NM_000553	0	0	4	8	4	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	4.269	0.049074	0.08243	.	.	ENSG00000165392	ENST00000298139	T	0.41758	0.99	5.27	-3.21	0.05140	.	0.909998	0.09395	N	0.807993	T	0.17534	0.0421	N	0.20401	0.57	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28427	-1.0044	10	0.10111	T	0.7	-0.4055	0.2738	0.00235	0.3113:0.1387:0.2652:0.2848	.	342	Q14191	WRN_HUMAN	I	342	ENSP00000298139:V342I	ENSP00000298139:V342I	V	+	1	0	WRN	31058109	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.336000	0.07863	-0.260000	0.09418	-0.143000	0.13931	GTT	.		0.353	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			A	30938567	G	A	30938567	3	1	66	1	0	0	0	0	1	0	0	0	17435	1145	40	1	1054	1	WRN	8	30938567	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		30938567	115425455	38	6342											
HTRA4	203100	broad.mit.edu;bcgsc.ca	37	chr8	38831823	38831823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccgcggggctgggacgatGcctcctgccggggctgctgc	3	6	18	14	4	0	0	0	0	0	0	1	3	1	1	4	5	4	3	4	5	0	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:38831823G>A	ENST00000302495.4	+	1	141	c.41G>A	c.(40-42)tGc>tAc	p.C14Y	CTD-2544N14.3_ENST00000520863.1_RNA	NM_153692.3	NP_710159.1	P83105	HTRA4_HUMAN	HtrA serine peptidase 4	14					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)	11		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			CTGGGACGATGCCTCCTGCCG	0.642																																					p.C14Y													.	HTRA4-90	0			c.G41A						.						28	26	27					8																	38831823		2200	4295	6495	SO:0001583	missense	203100	exon1			GACGATGCCTCCT	AK075205	CCDS6110.1	8p11.23	2008-02-05			ENSG00000169495	ENSG00000169495			26909	protein-coding gene	gene with protein product		610700					Standard	NM_153692		Approved	FLJ90724	uc003xmj.3	P83105	OTTHUMG00000164070	ENST00000302495.4:c.41G>A	8.37:g.38831823G>A	ENSP00000305919:p.Cys14Tyr	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_153692	0	0	0	0	0	Q542Z4|Q6PF13	Missense_Mutation	SNP	ENST00000302495.4	37	CCDS6110.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.588054	0.46110	.	.	ENSG00000169495	ENST00000302495	D	0.83992	-1.79	4.02	-1.43	0.08884	.	1.588980	0.04207	N	0.331058	T	0.73822	0.3636	L	0.36672	1.1	0.09310	N	1	B	0.19706	0.038	B	0.16722	0.016	T	0.58515	-0.7623	10	0.54805	T	0.06	-0.0836	4.3765	0.11272	0.0:0.2103:0.3614:0.4283	.	14	P83105	HTRA4_HUMAN	Y	14	ENSP00000305919:C14Y	ENSP00000305919:C14Y	C	+	2	0	HTRA4	38950980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.190000	0.17057	-0.125000	0.11703	-0.262000	0.10625	TGC	.		0.642	HTRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377077.1	NM_153692		A	38831823	G	A	38831823	3	1	66	1	0	0	0	0	1	0	0	0	7477	1319	46	2	43	2	HTRA4	8	38831823	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	7893256	38831823	107532199	39	6343											
TTC35	9694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	109489022	109489022	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttttaacaggttaagtatacCcaaggtggacttgaaaacct	14	12	8	7	0	0	1	0	1	0	0	0	2	0	2	2	3	3	2	2	3	7	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:109489022C>T	ENST00000220853.3	+	9	638	c.603C>T	c.(601-603)acC>acT	p.T201T	EMC2_ENST00000520294.1_3'UTR	NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	201						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											TTAAGTATACCCAAGGTGGAC	0.338																																					p.T201T		.											.	.	0			c.C603T						.						100	100	100					8																	109489022		2203	4300	6503	SO:0001819	synonymous_variant	9694	exon9			GTATACCCAAGGT	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.603C>T	8.37:g.109489022C>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	85	27	NM_014673	0	0	1	1	0	Q8WUE1	Silent	SNP	ENST00000220853.3	37	CCDS6309.1																																																																																			.		0.338	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		T	109489022	C	T	109489022	2	4	66	1	0	0	0	0	0	0	0	1	16736	610	22	2		2	TTC35	8	109489022	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	70657199	109489022	36875000	40	6344											
FAM49B	51571	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	130883632	130883632	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgctttacctctcgtatttCgtggccagctcctctgtatg	4	15	9	13	3	2	0	0	0	2	0	5	0	3	0	3	1	2	4	3	1	3	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:130883632C>A	ENST00000519824.2	-	4	457	c.184G>T	c.(184-186)Gaa>Taa	p.E62*	FAM49B_ENST00000522250.1_5'UTR|FAM49B_ENST00000401979.2_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522746.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522941.1_5'UTR|FAM49B_ENST00000518879.1_Intron|SNORA25_ENST00000363205.1_RNA|FAM49B_ENST00000519110.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000523509.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000517654.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000519540.1_Nonsense_Mutation_p.E62*	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	62						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)		p.E62K(1)		kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			TCTCGTATTTCGTGGCCAGCT	0.378																																					p.E62X		.											.	FAM49B-90	1	Substitution - Missense(1)	large_intestine(1)	c.G184T						.						110	106	108					8																	130883632		2203	4300	6503	SO:0001587	stop_gained	51571	exon4			GTATTTCGTGGCC	AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.184G>T	8.37:g.130883632C>A	ENSP00000429150:p.Glu62*	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	153	56	NM_016623	0	0	0	0	0	Q96AZ5|Q9NW21|Q9NZE7	Nonsense_Mutation	SNP	ENST00000519824.2	37	CCDS6361.1	.	.	.	.	.	.	.	.	.	.	C	37	6.228266	0.97394	.	.	ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000519142;ENST00000520204;ENST00000518283;ENST00000523993;ENST00000520254;ENST00000519020;ENST00000518167;ENST00000517672	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-18.5272	19.0946	0.93244	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000384880:E62X	E	-	1	0	FAM49B	130952814	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.745000	0.94114	0.650000	0.86243	GAA	.		0.378	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623		A	130883632	C	A	130883632	4	1	66	1	0	0	0	0	0	1	0	0	5595	893	31	4	826	4	FAM49B	8	130883632	Nonsense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	21394610	130883632	15480390	41	6345											
PHF20L1	51105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133816926	133816926	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcacattatcaaacaagaGgaaaaataatcaaggcaact	21	6	7	7	0	2	1	2	0	0	1	2	3	2	2	0	2	3	2	0	2	8	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:133816926G>C	ENST00000395386.2	+	8	1087	c.788G>C	c.(787-789)aGg>aCg	p.R263T	PHF20L1_ENST00000395390.2_Missense_Mutation_p.R238T|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395379.1_Missense_Mutation_p.R263T|PHF20L1_ENST00000395376.1_Missense_Mutation_p.R268T|PHF20L1_ENST00000337920.4_Missense_Mutation_p.R237T	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	263							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TCAAACAAGAGGAAAAATAAT	0.378																																					p.R263T		.											.	PHF20L1-92	0			c.G788C						.						106	100	102					8																	133816926		2203	4300	6503	SO:0001583	missense	51105	exon8			ACAAGAGGAAAAA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.788G>C	8.37:g.133816926G>C	ENSP00000378784:p.Arg263Thr	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	164	48	NM_016018	0	0	25	41	16	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365266	0.82463	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000395382;ENST00000395390;ENST00000395374	T;T;T;T;T;T;T;T	0.69685	-0.35;-0.18;0.1;0.49;-0.42;0.23;-0.16;0.92	5.5	5.5	0.81552	.	0.189440	0.56097	D	0.000032	T	0.75213	0.3819	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D	0.89917	0.996;0.997;0.999;1.0;0.996	D;D;D;D;D	0.87578	0.99;0.993;0.997;0.998;0.99	T	0.75590	-0.3265	10	0.49607	T	0.09	-16.2918	18.372	0.90409	0.0:0.0:1.0:0.0	.	238;102;263;263;237	F8W9L8;G5E9D0;A8MW92;A8MW92-4;A8MW92-2	.;.;P20L1_HUMAN;.;.	T	267;263;238;263;263;237;268;133;238;102	ENSP00000378781:R267T;ENSP00000378777:R263T;ENSP00000355301:R238T;ENSP00000378784:R263T;ENSP00000324519:R263T;ENSP00000338269:R237T;ENSP00000378775:R268T;ENSP00000378788:R238T	ENSP00000324519:R263T	R	+	2	0	PHF20L1	133886108	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.969000	0.70422	2.596000	0.87737	0.585000	0.79938	AGG	.		0.378	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		C	133816926	G	C	133816926	3	2	66	1	0	0	0	0	1	0	0	0	11858	1000	35	4	814	4	PHF20L1	8	133816926	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	2933294	133816926	12547096	42	6346											
CA9	768	broad.mit.edu;ucsc.edu	37	chr9	35676109	35676109	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggctctgggtcccgggcGggagtaccgggctctgcagc	4	7	18	12	3	2	0	0	0	2	0	3	2	3	1	2	5	3	4	2	5	1	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr9:35676109G>T	ENST00000378357.4	+	4	757	c.653G>T	c.(652-654)cGg>cTg	p.R218L		NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	218	Catalytic.				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GGTCCCGGGCGGGAGTACCGG	0.692																																					p.R218L													.	CA9-95	0			c.G653T						.						15	19	18					9																	35676109		2198	4297	6495	SO:0001583	missense	768	exon4			CCGGGCGGGAGTA	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"Carbonic anhydrases"	1383	protein-coding gene	gene with protein product	"carbonic dehydratase", "RCC-associated protein G250"	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.653G>T	9.37:g.35676109G>T	ENSP00000367608:p.Arg218Leu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	34	4	NM_001216	0	0	12	12	0	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	37	CCDS6585.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.476813	0.26511	.	.	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.66280	-0.2	4.96	-3.15	0.05233	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.795232	0.10999	N	0.610736	T	0.41003	0.1140	L	0.41906	1.305	0.31010	N	0.719311	P;P	0.40931	0.733;0.562	B;B	0.31946	0.071;0.138	T	0.42932	-0.9422	10	0.31617	T	0.26	.	6.2742	0.20971	0.5689:0.1454:0.2858:0.0	.	218;218	F5H404;Q16790	.;CAH9_HUMAN	L	218	ENSP00000367608:R218L	ENSP00000367608:R218L	R	+	2	0	CA9	35666109	0.021000	0.18746	0.923000	0.36655	0.062000	0.15995	-0.145000	0.10265	-0.377000	0.07930	-0.812000	0.03155	CGG	.		0.692	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		T	35676109	G	T	35676109	3	4	66	1	0	0	0	0	1	0	0	0	2530	1116	39	4	667	4	CA9	9	35676109	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		35676109	105537322	43	6347											
FBXO10	26267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	37537307	37537307	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctgctgcagtgagttcaGcactaggcagctgggcagct	7	9	13	12	0	1	1	1	1	0	0	2	1	2	1	1	2	5	8	1	2	1	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr9:37537307G>T	ENST00000432825.2	-	3	1267	c.1219C>A	c.(1219-1221)Ctg>Atg	p.L407M	FBXO10_ENST00000543968.1_5'Flank|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	407					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		AGTGAGTTCAGCACTAGGCAG	0.612																																					p.L407M		.											.	FBXO10-637	0			c.C1219A						.						22	24	23					9																	37537307		2000	4176	6176	SO:0001583	missense	26267	exon3			AGTTCAGCACTAG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1219C>A	9.37:g.37537307G>T	ENSP00000403802:p.Leu407Met	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	32	11	NM_012166	0	0	2	6	4	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.044290	0.55110	.	.	ENSG00000147912	ENST00000432825	T	0.51071	0.72	5.46	3.59	0.41128	Carbohydrate-binding/sugar hydrolysis domain (1);	0.084546	0.50627	D	0.000114	T	0.45657	0.1353	L	0.29908	0.895	0.80722	D	1	D	0.64830	0.994	P	0.56343	0.796	T	0.42413	-0.9453	10	0.72032	D	0.01	-14.4477	7.4587	0.27283	0.1335:0.1507:0.7157:0.0	.	407	Q9UK96	FBX10_HUMAN	M	407	ENSP00000403802:L407M	ENSP00000276960:L407M	L	-	1	2	FBXO10	37527307	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.365000	0.59486	2.543000	0.85770	0.655000	0.94253	CTG	.		0.612	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			T	37537307	G	T	37537307	3	4	66	1	0	0	0	0	1	0	0	0	5745	962	34	4	1687	4	FBXO10	9	37537307	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	1861198	37537307	103676124	44	6348											
ASPN	54829	hgsc.bcm.edu	37	chr9	95237070	95237070	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcatcatcatcatcatctGtgtcttccatatccttcagc	9	15	3	14	0	8	0	6	0	2	0	10	0	10	0	2	0	1	0	2	0	1	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr9:95237070G>C	ENST00000375544.3	-	2	353	c.110C>G	c.(109-111)aCa>aGa	p.T37R	ASPN_ENST00000450139.2_Missense_Mutation_p.T9R|ASPN_ENST00000375543.1_Missense_Mutation_p.T37R|CENPP_ENST00000375587.3_Intron|ASPN_ENST00000395538.3_Missense_Mutation_p.T37R	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	37	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						atcatcatcTGTGTCTTCCAT	0.403																																					p.T37R		.											.	ASPN-514	0			c.C110G						.						96	94	95					9																	95237070		2203	4300	6503	SO:0001583	missense	54829	exon2			TCATCTGTGTCTT	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.110C>G	9.37:g.95237070G>C	ENSP00000364694:p.Thr37Arg	Somatic	44	1		WXS	Illumina HiSeq	Phase_I	52	4	NM_001193335	0	0	1	1	0	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	37		.	.	.	.	.	.	.	.	.	.	G	12.69	2.013068	0.35511	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538;ENST00000450139	T;T;T	0.54071	0.59;1.0;1.0	5.02	1.98	0.26296	.	0.794353	0.11537	N	0.554171	T	0.29652	0.0740	N	0.22421	0.69	0.09310	N	1	B;B	0.25521	0.128;0.055	B;B	0.16289	0.015;0.015	T	0.16394	-1.0404	10	0.22706	T	0.39	.	1.3393	0.02151	0.1757:0.125:0.3536:0.3457	.	37;37	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	R	37;37;37;9	ENSP00000364694:T37R;ENSP00000364693:T37R;ENSP00000378909:T37R	ENSP00000364693:T37R	T	-	2	0	ASPN	94276891	0.000000	0.05858	0.006000	0.13384	0.928000	0.56348	-0.149000	0.10204	0.177000	0.19895	0.655000	0.94253	ACA	.		0.403	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		C	95237070	G	C	95237070	3	2	66	1	0	0	0	0	1	0	0	0	1058	1377	48	4	1060	4	ASPN	9	95237070	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	57699763	95237070	45976361	45	6349											
CAMSAP1	157922	broad.mit.edu	37	chr9	138714243	138714243	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaaaccacaggatgggccTcacccatgaaatcgtgctcg	12	7	10	12	2	1	2	1	2	0	0	3	3	1	3	3	2	2	1	3	2	3	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr9:138714243T>C	ENST00000389532.4	-	11	2328	c.2264A>G	c.(2263-2265)gAg>gGg	p.E755G	CAMSAP1_ENST00000409386.3_Missense_Mutation_p.E766G|CAMSAP1_ENST00000483991.1_5'UTR|CAMSAP1_ENST00000312405.6_Missense_Mutation_p.E477G	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	755					cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		AGGATGGGCCTCACCCATGAA	0.542																																					p.E755G													.	CAMSAP1-92	0			c.A2264G						.						89	89	89					9																	138714243		2203	4300	6503	SO:0001583	missense	157922	exon11			TGGGCCTCACCCA	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.2264A>G	9.37:g.138714243T>C	ENSP00000374183:p.Glu755Gly	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	97	3	NM_015447	0	0	23	23	0	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Missense_Mutation	SNP	ENST00000389532.4	37	CCDS35176.2	.	.	.	.	.	.	.	.	.	.	T	16.43	3.121608	0.56613	.	.	ENSG00000130559	ENST00000389532;ENST00000312405;ENST00000409386	T;T;T	0.16196	2.36;2.36;2.36	4.76	4.76	0.60689	.	0.775970	0.12701	N	0.446337	T	0.23806	0.0576	M	0.72894	2.215	0.49483	D	0.999795	B;B	0.12013	0.001;0.005	B;B	0.09377	0.002;0.004	T	0.04268	-1.0964	10	0.87932	D	0	-2.0545	13.1355	0.59407	0.0:0.0:0.0:1.0	.	755;766	Q5T5Y3;Q5T5Y3-3	CAMP1_HUMAN;.	G	755;477;766	ENSP00000374183:E755G;ENSP00000312463:E477G;ENSP00000386420:E766G	ENSP00000312463:E477G	E	-	2	0	CAMSAP1	137854064	0.999000	0.42202	0.781000	0.31783	0.057000	0.15508	2.212000	0.42835	1.903000	0.55091	0.533000	0.62120	GAG	.		0.542	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857		C	138714243	T	C	138714243	3	2	66	1	0	0	0	0	1	0	0	0	2617	1551	54	3	2572	3	CAMSAP1	9	138714243	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	43477173	138714243	2499188	46	6350											
RBM17	84991	broad.mit.edu;bcgsc.ca	37	chr10	6157412	6157414	+	Splice_Site	DEL	TCA	TCA	-																															aactgtcttttgtttgccttTcagcggttgttgacttgaat																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:6157412_6157414delTCA	ENST00000446108.1	+	12	1746		c.e12-1		RBM17_ENST00000476706.1_Splice_Site|RBM17_ENST00000379888.4_Splice_Site	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17						alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						TGTTTGCCTTTCAGCGGTTGTTG	0.355																																					.													.	RBM17-90	0			.						.																																			SO:0001630	splice_region_variant	84991	.			TGCCTTTCAGCGG	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"RNA binding motif (RRM) containing", "G patch domain containing"	16944	protein-coding gene	gene with protein product	"splicing factor 45kDa"	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.1103-1TCA>-	10.37:g.6157412_6157414delTCA		Somatic	198	0		WXS	Illumina HiSeq	Phase_I	256	119	.	0	0	0	0	0	Q96GY6	Splice_Site	DEL	ENST00000446108.1	37	CCDS7077.1																																																																																			.		0.355	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905	Intron	-	6157414	TCA	-	6157412	8	5	66	1	0	1	0	1	0	0	1	0	13151	1798	62	0		0	RBM17	10	6157412	Splice_Site	DEL	TCA	TCGA-BQ-5882-01A-11D-1589-08		6157412	129377335	47	6351											
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	24508666	24508666	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcagtttccaagtcttcccGcaatatcccaaggagacaca	12	10	6	13	1	2	1	1	0	1	1	5	2	5	1	3	1	0	2	3	1	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:24508666G>T	ENST00000376454.3	+	2	212	c.182G>T	c.(181-183)cGc>cTc	p.R61L	KIAA1217_ENST00000376462.1_5'UTR|KIAA1217_ENST00000376452.3_Missense_Mutation_p.R61L|KIAA1217_ENST00000458595.1_Missense_Mutation_p.R61L	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	61					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AAGTCTTCCCGCAATATCCCA	0.498																																					p.R61L		.											.	KIAA1217-98	0			c.G182T						.						71	69	70					10																	24508666		2203	4300	6503	SO:0001583	missense	56243	exon2			CTTCCCGCAATAT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.182G>T	10.37:g.24508666G>T	ENSP00000365637:p.Arg61Leu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	106	25	NM_019590	0	0	3	4	1	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029194	0.93518	.	.	ENSG00000120549	ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.77	5.77	0.91146	.	0.093558	0.39985	N	0.001204	T	0.74981	0.3788	L	0.43923	1.385	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.998	T	0.73588	-0.3935	10	0.49607	T	0.09	.	19.9927	0.97374	0.0:0.0:1.0:0.0	.	61;61;61;61	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	L	61	ENSP00000365639:R61L;ENSP00000392625:R61L;ENSP00000365637:R61L;ENSP00000365635:R61L	ENSP00000365635:R61L	R	+	2	0	KIAA1217	24548672	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	6.115000	0.71566	2.745000	0.94114	0.655000	0.94253	CGC	.		0.498	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24508666	G	T	24508666	3	4	66	1	0	0	0	0	1	0	0	0	8237	1087	38	4	188	4	KIAA1217	10	24508666	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	18351254	24508666	111026081	48	6352											
EPC1	80314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	32580239	32580239	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgatctctccattgtagtcgCccaaattatacctaaaatta	13	14	4	10	1	1	1	0	1	1	0	4	1	2	1	3	0	1	1	3	0	7	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:32580239C>G	ENST00000263062.8	-	6	1096	c.827G>C	c.(826-828)gGc>gCc	p.G276A	EPC1_ENST00000319778.6_Missense_Mutation_p.G276A|EPC1_ENST00000375110.2_Missense_Mutation_p.G226A	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	276					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				ATTGTAGTCGCCCAAATTATA	0.313																																					p.G276A		.											.	EPC1-93	0			c.G827C						.						75	73	74					10																	32580239		2203	4300	6503	SO:0001583	missense	80314	exon6			TAGTCGCCCAAAT	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.827G>C	10.37:g.32580239C>G	ENSP00000263062:p.Gly276Ala	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	176	31	NM_025209	0	0	0	0	0	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	37	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170633	0.38315	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.66099	-0.19;-0.19;-0.19	4.89	4.89	0.63831	.	0.214139	0.49305	D	0.000142	T	0.55497	0.1924	L	0.39245	1.2	0.45594	D	0.99853	B;B;B;B	0.25667	0.048;0.131;0.097;0.059	B;B;B;B	0.27380	0.015;0.019;0.079;0.008	T	0.51124	-0.8745	10	0.22109	T	0.4	-15.0295	18.3946	0.90494	0.0:1.0:0.0:0.0	.	276;226;276;276	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	A	226;276;276	ENSP00000364251:G226A;ENSP00000318559:G276A;ENSP00000263062:G276A	ENSP00000263062:G276A	G	-	2	0	EPC1	32620245	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	3.929000	0.56514	2.419000	0.82065	0.467000	0.42956	GGC	.		0.313	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			G	32580239	C	G	32580239	3	3	66	1	0	0	0	0	1	0	0	0	5173	739	26	4	1723	4	EPC1	10	32580239	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	8071573	32580239	102954508	49	6353											
OSBPL5	114879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	3141834	3141834	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acgcaccacagcttggtccaGctcttcagggtgccgcggat	7	8	12	14	3	2	0	1	0	1	0	3	1	3	1	3	3	3	3	3	3	0	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:3141834G>C	ENST00000263650.7	-	6	582	c.423C>G	c.(421-423)agC>agG	p.S141R	OSBPL5_ENST00000389989.3_Intron|OSBPL5_ENST00000525498.1_Missense_Mutation_p.S93R|OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000348039.5_Intron	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCTTGGTCCAGCTCTTCAGGG	0.677																																					p.S141R		.											.	OSBPL5-113	0			c.C423G						.						53	49	51					11																	3141834		2202	4298	6500	SO:0001583	missense	114879	exon6			GGTCCAGCTCTTC	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.423C>G	11.37:g.3141834G>C	ENSP00000263650:p.Ser141Arg	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	64	36	NM_020896	0	0	5	6	1	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	37	CCDS31344.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.763077	0.49574	.	.	ENSG00000021762	ENST00000263650;ENST00000525498	T;T	0.76186	-1.0;2.64	4.38	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.115051	0.64402	D	0.000020	T	0.74786	0.3762	L	0.54323	1.7	0.80722	D	1	P;B;B	0.36753	0.568;0.056;0.425	B;B;B	0.44278	0.175;0.149;0.445	T	0.78091	-0.2339	10	0.72032	D	0.01	-34.5207	12.7278	0.57180	0.0829:0.0:0.9171:0.0	.	93;102;141	B4DVB0;E7EP03;Q9H0X9	.;.;OSBL5_HUMAN	R	141;93	ENSP00000263650:S141R;ENSP00000433342:S93R	ENSP00000263650:S141R	S	-	3	2	OSBPL5	3098410	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.883000	0.28200	2.285000	0.76669	0.555000	0.69702	AGC	.		0.677	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			C	3141834	G	C	3141834	3	2	66	1	0	0	0	0	1	0	0	0	11306	962	34	4	2284	4	OSBPL5	11	3141834	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		3141834	131864682	50	6354											
OR8H3	390152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55890629	55890629	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatgatttttacttacttaAagccaagaaagtcttattcc	13	16	4	8	0	1	2	0	1	1	1	2	2	2	2	2	0	3	0	2	0	8	8			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:55890629A>G	ENST00000313472.3	+	1	781	c.781A>G	c.(781-783)Aag>Gag	p.K261E		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TACTTACTTAAAGCCAAGAAA	0.373																																					p.K261E		.											.	OR8H3-70	0			c.A781G						.						102	101	101					11																	55890629		2201	4296	6497	SO:0001583	missense	390152	exon1			TACTTAAAGCCAA	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"GPCR / Class A : Olfactory receptors"	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.781A>G	11.37:g.55890629A>G	ENSP00000323928:p.Lys261Glu	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	121	58	NM_001005201	0	0	0	0	0	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.276100	0.23307	.	.	ENSG00000181761	ENST00000313472	T	0.37411	1.2	3.62	2.35	0.29111	GPCR, rhodopsin-like superfamily (1);	0.222186	0.32134	N	0.006528	T	0.54822	0.1882	M	0.83774	2.66	0.09310	N	1	D	0.76494	0.999	D	0.71414	0.973	T	0.40194	-0.9576	10	0.87932	D	0	.	5.4761	0.16695	0.5957:0.3026:0.1016:0.0	.	261	Q8N146	OR8H3_HUMAN	E	261	ENSP00000323928:K261E	ENSP00000323928:K261E	K	+	1	0	OR8H3	55647205	0.000000	0.05858	0.804000	0.32291	0.121000	0.20230	-0.491000	0.06474	1.415000	0.47037	0.145000	0.16022	AAG	.		0.373	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		G	55890629	A	G	55890629	3	3	66	1	0	0	0	0	1	0	0	0	11265	15	1	3	783	3	OR8H3	11	55890629	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	52748795	55890629	79115887	51	6355											
IFLTD1	160492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	25702289	25702289	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttccactctggaacagctaCctacagtagctttagaagtc	11	12	7	11	0	1	1	0	0	1	1	3	2	2	2	2	1	5	3	2	1	6	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:25702289C>A	ENST00000282881.6	-	2	367	c.218G>T	c.(217-219)gGt>gTt	p.G73V	IFLTD1_ENST00000539744.1_5'UTR|IFLTD1_ENST00000445693.1_Intron|IFLTD1_ENST00000413632.2_Missense_Mutation_p.G94V|IFLTD1_ENST00000458174.2_Missense_Mutation_p.G94V	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		73					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGAACAGCTACCTACAGTAGC	0.353																																					p.G94V		.											.	IFLTD1-92	0			c.G281T						.						55	50	52					12																	25702289		2203	4300	6503	SO:0001583	missense	160492	exon3			CAGCTACCTACAG																												ENST00000282881.6:c.218G>T	12.37:g.25702289C>A	ENSP00000282881:p.Gly73Val	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_001145728	0	0	0	0	0	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	.	.	.	.	.	.	.	.	.	.	C	4.838	0.155802	0.09236	.	.	ENSG00000152936	ENST00000282881;ENST00000458174;ENST00000413632;ENST00000538178;ENST00000540106;ENST00000542224	T;T;T	0.13538	2.74;2.77;2.58	3.4	-6.81	0.01704	.	.	.	.	.	T	0.03305	0.0096	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.09377	0.004;0.002;0.001	T	0.36915	-0.9728	9	0.06625	T	0.88	-7.9674	1.5985	0.02669	0.1745:0.4041:0.1887:0.2328	.	94;94;73	Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9	.;.;ILFT1_HUMAN	V	73;94;94;48;48;48	ENSP00000282881:G73V;ENSP00000407353:G94V;ENSP00000393150:G94V	ENSP00000282881:G73V	G	-	2	0	IFLTD1	25593556	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.175000	0.01263	-1.982000	0.00988	0.460000	0.39030	GGT	.		0.353	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			A	25702289	C	A	25702289	3	1	66	1	0	0	0	0	1	0	0	0	7551	507	18	4	976	4	IFLTD1	12	25702289	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		25702289	108149606	52	6356											
ALG10B	144245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	38714192	38714192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttctgtgcagggaatgTcattgcacaaaagttaactg	11	13	10	7	0	3	0	1	0	2	0	3	1	3	1	0	1	3	3	0	1	4	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:38714192T>C	ENST00000308742.4	+	3	915	c.599T>C	c.(598-600)gTc>gCc	p.V200A	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	200					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				GCAGGGAATGTCATTGCACAA	0.388																																					p.V200A		.											.	ALG10B-93	0			c.T599C						.						167	169	168					12																	38714192		2203	4300	6503	SO:0001583	missense	144245	exon3			GGAATGTCATTGC	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.599T>C	12.37:g.38714192T>C	ENSP00000310120:p.Val200Ala	Somatic	418	0		WXS	Illumina HiSeq	Phase_I	442	140	NM_001013620	0	0	3	10	7	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	37	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	N	7.218	0.596709	0.13875	.	.	ENSG00000175548	ENST00000308742	T	0.55760	0.5	3.24	3.24	0.37175	.	0.332405	0.30771	N	0.008920	T	0.35219	0.0924	L	0.31420	0.93	0.80722	D	1	B	0.15719	0.014	B	0.10450	0.005	T	0.10941	-1.0608	10	0.12103	T	0.63	.	10.1623	0.42860	0.0:0.0:0.0:1.0	.	200	Q5I7T1	AG10B_HUMAN	A	200	ENSP00000310120:V200A	ENSP00000310120:V200A	V	+	2	0	ALG10B	37000459	0.999000	0.42202	0.009000	0.14445	0.383000	0.30230	5.798000	0.69095	1.719000	0.51432	0.448000	0.29417	GTC	.		0.388	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		C	38714192	T	C	38714192	3	2	66	1	0	0	0	0	1	0	0	0	512	1667	58	3	609	3	ALG10B	12	38714192	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	13011903	38714192	95137703	53	6357											
MLL2	8085	hgsc.bcm.edu	37	chr12	49427714	49427714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgttccgatattctgccaTgagattagtgtgctccttct	6	17	8	10	1	2	1	0	1	2	1	4	3	4	1	3	0	2	2	3	0	2	6	rs372758101		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:49427714T>C	ENST00000301067.7	-	39	10773	c.10774A>G	c.(10774-10776)Atg>Gtg	p.M3592V	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3592	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TATTCTGCCATGAGATTAGTG	0.582																																					p.M3592V		.											.	MLL2-612	0			c.A10774G						.	T	VAL/MET	1,4325		0,1,2162	14	13	14		10774	5.4	1	12		14	0,8464		0,0,4232	no	missense	MLL2	NM_003482.3	21	0,1,6394	CC,CT,TT		0.0,0.0231,0.0078	benign	3592/5538	49427714	1,12789	2163	4232	6395	SO:0001583	missense	8085	exon39			CTGCCATGAGATT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10774A>G	12.37:g.49427714T>C	ENSP00000301067:p.Met3592Val	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	9	5	NM_003482	0	0	5	15	10	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	9.346	1.064224	0.20067	2.31E-4	0.0	ENSG00000167548	ENST00000301067	T	0.39056	1.1	5.38	5.38	0.77491	.	0.000000	0.44688	D	0.000428	T	0.25791	0.0628	N	0.08118	0	0.31092	N	0.71073	B	0.26483	0.15	B	0.19946	0.027	T	0.30563	-0.9974	10	0.87932	D	0	.	14.6888	0.69068	0.0:0.0:0.0:1.0	.	3592	O14686	MLL2_HUMAN	V	3592	ENSP00000301067:M3592V	ENSP00000301067:M3592V	M	-	1	0	MLL2	47713981	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.118000	0.71583	2.189000	0.69895	0.460000	0.39030	ATG	.		0.582	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49427714	T	C	49427714	3	2	66	1	0	0	0	0	1	0	0	0	9646	1464	51	3	5903	3	MLL2	12	49427714	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	10713522	49427714	84424181	54	6358											
GCN1L1	10985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120582190	120582190	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtctcagcgtacatggaGataacccgctggcccgcgcg	7	7	13	14	5	1	1	1	0	1	1	2	2	1	1	2	2	3	3	2	2	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:120582190G>T	ENST00000300648.6	-	42	5427	c.5415C>A	c.(5413-5415)atC>atA	p.I1805I		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1805					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGTACATGGAGATAACCCGCT	0.597																																					p.I1805I		.											.	GCN1L1-94	0			c.C5415A						.						58	63	61					12																	120582190		2058	4197	6255	SO:0001819	synonymous_variant	10985	exon42			CATGGAGATAACC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5415C>A	12.37:g.120582190G>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	93	29	NM_006836	0	0	38	57	19	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			.		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120582190	G	T	120582190	2	4	66	1	0	0	0	0	0	0	0	1	6319	932	33	4		4	GCN1L1	12	120582190	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	71154476	120582190	13269705	55	6359											
HPD	3242	broad.mit.edu	37	chr12	122292680	122292680	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctcccgcatgattttggCgccccgttcccgtgctttct	2	13	11	15	4	1	1	0	1	1	0	3	1	3	1	4	2	1	4	4	2	0	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:122292680C>T	ENST00000289004.4	-	7	378	c.343G>A	c.(343-345)Gcc>Acc	p.A115T	HPD_ENST00000543163.1_Missense_Mutation_p.A76T|RP11-7M8.2_ENST00000543848.1_RNA	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	115					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	ATGATTTTGGCGCCCCGTTCC	0.602																																					p.A115T													.	HPD-90	0			c.G343A						.						149	128	135					12																	122292680		2203	4300	6503	SO:0001583	missense	3242	exon7			TTTTGGCGCCCCG	BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"glyoxalase domain containing 3"	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.343G>A	12.37:g.122292680C>T	ENSP00000289004:p.Ala115Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	114	4	NM_002150	0	0	0	0	0	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	37	CCDS9224.1	.	.	.	.	.	.	.	.	.	.	C	31	5.098737	0.94197	.	.	ENSG00000158104	ENST00000289004;ENST00000545969;ENST00000543163	T;T	0.66815	-0.23;-0.23	5.29	5.29	0.74685	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.000000	0.85682	D	0.000000	T	0.79293	0.4421	M	0.85777	2.775	0.80722	D	1	D	0.59357	0.985	P	0.52267	0.694	D	0.83576	0.0115	10	0.72032	D	0.01	-26.0275	17.9063	0.88919	0.0:1.0:0.0:0.0	.	115	P32754	HPPD_HUMAN	T	115;112;76	ENSP00000289004:A115T;ENSP00000441677:A76T	ENSP00000289004:A115T	A	-	1	0	HPD	120777063	1.000000	0.71417	0.986000	0.45419	0.984000	0.73092	7.276000	0.78559	2.478000	0.83669	0.467000	0.42956	GCC	.		0.602	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150		T	122292680	C	T	122292680	3	4	66	1	0	0	0	0	1	0	0	0	7353	768	27	1	870	1	HPD	12	122292680	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	1710490	122292680	11559215	56	6360											
ATP12A	479	bcgsc.ca	37	chr13	25265156	25265156	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggttatcaacacgggtgaccGcaccatcattggccatattg	10	10	10	11	2	2	1	2	1	0	0	2	1	2	1	3	3	1	2	3	3	3	4	rs565225438		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr13:25265156G>A	ENST00000381946.3	+	8	1003	c.836G>A	c.(835-837)cGc>cAc	p.R279H	ATP12A_ENST00000218548.6_Missense_Mutation_p.R285H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	279					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		ACGGGTGACCGCACCATCATT	0.537													G|||	1	0.000199681	8e-04	0	5008	,	,		22507	0		0	False		,,,				2504	0				p.R285H	Pancreas(156;1582 1935 18898 22665 26498)												.	ATP12A-137	0			c.G854A						.						176	154	161					13																	25265156		2203	4300	6503	SO:0001583	missense	479	exon8			GTGACCGCACCAT	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.836G>A	13.37:g.25265156G>A	ENSP00000371372:p.Arg279His	Somatic	132	0		WXS	Illumina HiSeq	Phase_1	96	5	NM_001185085	0	0	0	0	0	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.817425	0.32145	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.88124	-2.34;-2.34	5.02	4.18	0.49190	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.074956	0.56097	N	0.000025	T	0.79347	0.4430	L	0.33093	0.98	0.52501	D	0.999955	B;B	0.26845	0.161;0.013	B;B	0.19946	0.027;0.003	T	0.75221	-0.3394	10	0.37606	T	0.19	.	11.3177	0.49401	0.0884:0.0:0.9116:0.0	.	285;279	P54707-2;P54707	.;AT12A_HUMAN	H	285;279	ENSP00000218548:R285H;ENSP00000371372:R279H	ENSP00000218548:R285H	R	+	2	0	ATP12A	24163156	0.998000	0.40836	1.000000	0.80357	0.539000	0.34962	2.576000	0.46033	1.338000	0.45544	0.462000	0.41574	CGC	G|1.000;A|0.000		0.537	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		A	25265156	G	A	25265156	3	1	66	1	0	0	0	0	1	0	0	0	1123	1087	38	1	884	1	ATP12A	13	25265156	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		25265156	89904722	57	6361											
C13orf23	80209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	39596542	39596542	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtaccagacctgcattgttAtaagcacctaaaataaaaac	17	9	6	9	0	0	1	0	0	0	1	0	1	0	1	3	1	4	4	3	1	8	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr13:39596542A>T	ENST00000352251.3	-	9	1484	c.651T>A	c.(649-651)taT>taA	p.Y217*	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Nonsense_Mutation_p.Y195*	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	217	Pro-rich.																CTGCATTGTTATAAGCACCTA	0.378																																					p.Y217X		.											.	.	0			c.T651A						.						132	130	131					13																	39596542		2203	4300	6503	SO:0001587	stop_gained	80209	exon9			ATTGTTATAAGCA	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.651T>A	13.37:g.39596542A>T	ENSP00000332034:p.Tyr217*	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	145	72	NM_025138	0	0	0	0	0	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Nonsense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	A	44	11.133907	0.99521	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	.	.	.	5.69	-5.32	0.02722	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.1752	17.3861	0.87416	0.267:0.0:0.733:0.0	.	.	.	.	X	217;195	.	.	Y	-	3	2	PROSER1	38494542	0.996000	0.38824	0.817000	0.32601	0.961000	0.63080	0.263000	0.18478	-1.201000	0.02659	-0.250000	0.11733	TAT	.		0.378	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		T	39596542	A	T	39596542	4	4	66	1	0	0	0	0	0	1	0	0	1725	456	16	5	2203	5	C13orf23	13	39596542	Nonsense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	14331386	39596542	75573336	58	6362											
TRIM9	114088	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	51475908	51475908	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgtgcctttaccccacTgatcctcagtcaggtgcact	7	12	9	13	0	2	2	2	2	0	0	3	2	3	2	4	1	3	1	4	1	1	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:51475908T>C	ENST00000298355.3	-	5	2317	c.1196A>G	c.(1195-1197)cAg>cGg	p.Q399R	TRIM9_ENST00000338969.5_Missense_Mutation_p.Q399R|TRIM9_ENST00000360392.4_Missense_Mutation_p.Q399R	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	399	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TTTACCCCACTGATCCTCAGT	0.488																																					p.Q399R		.											.	TRIM9-227	0			c.A1196G						.						179	132	148					14																	51475908		2203	4300	6503	SO:0001583	missense	114088	exon5			CCCCACTGATCCT	AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16288	protein-coding gene	gene with protein product		606555	"tripartite motif-containing 9"			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1196A>G	14.37:g.51475908T>C	ENSP00000298355:p.Gln399Arg	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	149	49	NM_052978	0	0	4	9	5	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.412686	0.83340	.	.	ENSG00000100505	ENST00000298355;ENST00000338969;ENST00000360392	T;T;T	0.70986	-0.37;-0.53;0.54	5.94	5.94	0.96194	B-box, C-terminal (1);COS domain (1);	0.000000	0.85682	D	0.000000	T	0.80722	0.4677	M	0.62723	1.935	0.54753	D	0.99998	D;D;P	0.61697	0.986;0.99;0.901	D;D;P	0.67382	0.951;0.941;0.482	T	0.77872	-0.2426	10	0.26408	T	0.33	.	15.5887	0.76506	0.0:0.0:0.0:1.0	.	399;399;399	Q9C026-5;Q9C026-4;Q9C026	.;.;TRIM9_HUMAN	R	399	ENSP00000298355:Q399R;ENSP00000342970:Q399R;ENSP00000353561:Q399R	ENSP00000298355:Q399R	Q	-	2	0	TRIM9	50545658	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.997000	0.88414	2.275000	0.75901	0.528000	0.53228	CAG	.		0.488	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163		C	51475908	T	C	51475908	3	2	66	1	0	0	0	0	1	0	0	0	16582	1580	55	3	1010	3	TRIM9	14	51475908	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		51475908	55873632	59	6363											
SPTLC2	9517	broad.mit.edu	37	chr14	77984506	77984506	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttcagcatctcccgtccaaAggcgctgcaaaggggaaaac	12	6	10	13	2	2	0	1	0	1	0	4	1	3	1	2	3	3	3	2	3	4	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:77984506A>T	ENST00000216484.2	-	11	1637	c.1444T>A	c.(1444-1446)Ttt>Att	p.F482I		NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	482					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	TCCCGTCCAAAGGCGCTGCAA	0.498																																					p.F482I													.	SPTLC2-92	0			c.T1444A						.						65	58	61					14																	77984506		2203	4300	6503	SO:0001583	missense	9517	exon11			GTCCAAAGGCGCT	AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.1444T>A	14.37:g.77984506A>T	ENSP00000216484:p.Phe482Ile	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	71	3	NM_004863	0	0	1	1	0	Q16685	Missense_Mutation	SNP	ENST00000216484.2	37	CCDS9865.1	.	.	.	.	.	.	.	.	.	.	A	34	5.366067	0.95900	.	.	ENSG00000100596	ENST00000216484	D	0.91631	-2.88	5.79	5.79	0.91817	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	M	0.62209	1.925	0.80722	D	1	P	0.45078	0.85	P	0.53722	0.733	D	0.94554	0.7756	10	0.87932	D	0	-18.6843	16.1267	0.81400	1.0:0.0:0.0:0.0	.	482	O15270	SPTC2_HUMAN	I	482	ENSP00000216484:F482I	ENSP00000216484:F482I	F	-	1	0	SPTLC2	77054259	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.339000	0.96797	2.205000	0.71048	0.455000	0.32223	TTT	.		0.498	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863		T	77984506	A	T	77984506	3	4	66	1	0	0	0	0	1	0	0	0	15156	72	3	5	252	5	SPTLC2	14	77984506	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	26508598	77984506	29365034	60	6364											
RTL1	388015	broad.mit.edu;bcgsc.ca	37	chr14	101348358	101348358	+	Frame_Shift_Del	DEL	T	T	-																															cagcccgtattggaagaatcTtcatctccgcttgagagtac																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:101348358delT	ENST00000534062.1	-	1	2826	c.2768delA	c.(2767-2769)aagfs	p.K923fs	MIR127_ENST00000384876.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	923					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TGGAAGAATCTTCATCTCCGC	0.537																																					p.K923fs													.	RTL1-46	0			c.2768delA						.						38	37	37					14																	101348358		1568	3582	5150	SO:0001589	frameshift_variant	388015	exon1			AGAATCTTCATCT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.2768delA	14.37:g.101348358delT	ENSP00000435342:p.Lys923fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	53	17	NM_001134888	0	0	0	0	0	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	37	CCDS53910.1																																																																																			.		0.537	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		-	101348358	T	-	101348358	7	5	66	1	0	1	0	1	0	0	0	0	13756	1609	56	0	1312	0	RTL1	14	101348358	Frame_Shift_Del	DEL	T	TCGA-BQ-5882-01A-11D-1589-08	23363852	101348358	6001182	61	6365											
AHNAK2	113146	broad.mit.edu	37	chr14	105413526	105413526	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggtccacgttggggccCttaacatctatctgggggcc	6	11	12	12	1	3	0	1	0	2	0	4	0	4	0	3	5	1	1	3	5	2	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:105413526C>A	ENST00000333244.5	-	7	8381	c.8262G>T	c.(8260-8262)aaG>aaT	p.K2754N	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2754						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CGTTGGGGCCCTTAACATCTA	0.612																																					p.K2754N													.	AHNAK2-47	0			c.G8262T						.						125	138	134					14																	105413526		1851	4080	5931	SO:0001583	missense	113146	exon7			GGGGCCCTTAACA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.8262G>T	14.37:g.105413526C>A	ENSP00000353114:p.Lys2754Asn	Somatic	308	1		WXS	Illumina HiSeq	Phase_I	374	5	NM_138420	0	0	29	29	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	1.648	-0.514652	0.04200	.	.	ENSG00000185567	ENST00000333244	T	0.02280	4.36	2.49	-3.11	0.05299	.	.	.	.	.	T	0.01800	0.0057	L	0.49513	1.565	0.09310	N	1	P	0.41784	0.762	B	0.37304	0.246	T	0.41574	-0.9501	9	0.17832	T	0.49	.	1.259	0.01997	0.1242:0.2674:0.2385:0.3699	.	2754	Q8IVF2	AHNK2_HUMAN	N	2754	ENSP00000353114:K2754N	ENSP00000353114:K2754N	K	-	3	2	AHNAK2	104484571	0.000000	0.05858	0.007000	0.13788	0.009000	0.06853	-1.520000	0.02241	-0.433000	0.07286	-0.683000	0.03753	AAG	.		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105413526	C	A	105413526	3	1	66	1	0	0	0	0	1	0	0	0	415	680	24	4	9129	4	AHNAK2	14	105413526	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	4065168	105413526	1936014	62	6366											
USP50	373509	broad.mit.edu	37	chr15	50835960	50835960	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacatgtctgtcatcagataGgcaaaagcagtggcaacttc	13	9	9	10	0	3	1	2	0	1	1	4	1	3	1	0	2	2	3	0	2	4	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr15:50835960G>A	ENST00000532404.1	-	3	452	c.279C>T	c.(277-279)gcC>gcT	p.A93A	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	98	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		TCATCAGATAGGCAAAAGCAG	0.453																																					p.A93A													.	USP50-658	0			c.C279T						.						49	47	47					15																	50835960		1919	4142	6061	SO:0001819	synonymous_variant	373509	exon3			CAGATAGGCAAAA	AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"Ubiquitin-specific peptidases"	20079	protein-coding gene	gene with protein product			"ubiquitin specific protease 50"			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.279C>T	15.37:g.50835960G>A		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_203494	0	0	0	0	0	E9PP86	Silent	SNP	ENST00000532404.1	37	CCDS53944.1																																																																																			.		0.453	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			A	50835960	G	A	50835960	2	1	66	1	0	0	0	0	0	0	0	1	17115	987	35	2		2	USP50	15	50835960	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		50835960	51695432	63	6367											
ADAMTS7	11173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	79064138	79064138	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggatgcggatctcgcgtGcgcccgctgggatcagcccc	4	8	14	15	5	2	0	1	0	1	0	3	3	2	3	3	3	3	1	3	3	0	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr15:79064138G>A	ENST00000388820.4	-	15	2375	c.2165C>T	c.(2164-2166)gCa>gTa	p.A722V	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	722	Spacer.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GATCTCGCGTGCGCCCGCTGG	0.622																																					p.A722V		.											.	ADAMTS7-226	0			c.C2165T						.						53	39	43					15																	79064138		2196	4293	6489	SO:0001583	missense	11173	exon15			TCGCGTGCGCCCG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"ADAM metallopeptidases with thrombospondin type 1 motif"	223	protein-coding gene	gene with protein product	"COMPase", "a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"	605009	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.2165C>T	15.37:g.79064138G>A	ENSP00000373472:p.Ala722Val	Somatic	35	2		WXS	Illumina HiSeq	Phase_I	39	20	NM_014272	0	0	0	0	0	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587457	0.66105	.	.	ENSG00000136378	ENST00000388820	T	0.69926	-0.44	4.03	4.03	0.46877	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	D	0.87724	0.6249	H	0.97491	4.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.92218	0.5782	10	0.87932	D	0	.	15.0564	0.71917	0.0:0.0:1.0:0.0	.	722;722	A8MQ00;Q9UKP4	.;ATS7_HUMAN	V	722	ENSP00000373472:A722V	ENSP00000373472:A722V	A	-	2	0	ADAMTS7	76851193	1.000000	0.71417	0.080000	0.20451	0.142000	0.21351	9.398000	0.97281	2.106000	0.64143	0.433000	0.28618	GCA	.		0.622	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		A	79064138	G	A	79064138	3	1	66	1	0	0	0	0	1	0	0	0	271	1319	46	2	2935	2	ADAMTS7	15	79064138	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	28228178	79064138	23467254	64	6368											
IL16	3603	broad.mit.edu	37	chr15	81598328	81598328	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgaggttctttccatcaacgGcaagtctctcaaggggacca	10	10	10	11	1	4	1	2	1	2	0	6	2	5	2	2	4	1	2	2	4	3	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr15:81598328G>A	ENST00000302987.4	+	16	3500	c.3500G>A	c.(3499-3501)gGc>gAc	p.G1167D	RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394660.2_Missense_Mutation_p.G1167D|IL16_ENST00000394652.2_Missense_Mutation_p.G466D			Q14005	IL16_HUMAN	interleukin 16	1167	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TCCATCAACGGCAAGTCTCTC	0.542																																					p.G1167D													.	IL16-653	0			c.G3500A						.						167	172	170					15																	81598328		2203	4300	6503	SO:0001583	missense	3603	exon17			TCAACGGCAAGTC	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"Interleukins and interleukin receptors"	5980	protein-coding gene	gene with protein product	"prointerleukin 16", "lymphocyte chemoattractant factor"	603035	"interleukin 16 (lymphocyte chemoattractant factor)"			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3500G>A	15.37:g.81598328G>A	ENSP00000302935:p.Gly1167Asp	Somatic	270	1		WXS	Illumina HiSeq	Phase_I	206	6	NM_001172128	0	0	20	20	0	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.424887	0.62733	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.41400	1.0;1.0;1.0	4.64	4.64	0.57946	PDZ/DHR/GLGF (4);	0.000000	0.47852	D	0.000214	T	0.68146	0.2969	M	0.83312	2.635	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	T	0.73515	-0.3958	10	0.59425	D	0.04	.	17.6977	0.88286	0.0:0.0:1.0:0.0	.	999;660;704;557;1167;1167	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	D	1167;999;1167;704;557;466;466	ENSP00000378155:G1167D;ENSP00000302935:G1167D;ENSP00000378147:G466D	ENSP00000302935:G1167D	G	+	2	0	IL16	79385383	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	8.841000	0.92131	2.386000	0.81285	0.655000	0.94253	GGC	.		0.542	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		A	81598328	G	A	81598328	3	1	66	1	0	0	0	0	1	0	0	0	7654	1203	42	2	3562	2	IL16	15	81598328	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	2534190	81598328	20933064	65	6369											
EARS2	124454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23540828	23540828	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgcgggtactcaccccagCacacgcttggcaatcacatc	9	7	8	17	2	2	0	2	0	0	0	3	0	2	0	3	2	3	4	3	2	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:23540828C>T	ENST00000563459.1	-	7	1353	c.1347G>A	c.(1345-1347)gtG>gtA	p.V449V	EARS2_ENST00000563232.1_Silent_p.V449V|EARS2_ENST00000564501.1_Silent_p.V449V|EARS2_ENST00000449606.1_Silent_p.V449V|EARS2_ENST00000564987.1_5'UTR			Q5JPH6	SYEM_HUMAN	glutamyl-tRNA synthetase 2, mitochondrial	449					gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|tRNA aminoacylation for mitochondrial protein translation (GO:0070127)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|glutamate-tRNA(Gln) ligase activity (GO:0050561)|tRNA binding (GO:0000049)			central_nervous_system(1)|endometrium(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8				GBM - Glioblastoma multiforme(48;0.0353)		CTCACCCCAGCACACGCTTGG	0.607																																					p.V449V		.											.	EARS2-90	0			c.G1347A						.						38	42	41					16																	23540828		2124	4249	6373	SO:0001819	synonymous_variant	124454	exon7			CCCCAGCACACGC	AB075850	CCDS42132.1	16p12.2	2014-05-06	2012-10-26		ENSG00000103356	ENSG00000103356	6.1.1.17	"Aminoacyl tRNA synthetases / Class I"	29419	protein-coding gene	gene with protein product	"glutamate tRNA ligase 2, mitochondrial"	612799	"glutamyl-tRNA synthetase 2, mitochondrial (putative)"			15779907, 19805282, 22492562	Standard	NM_001083614		Approved	KIAA1970, MSE1	uc002dlt.4	Q5JPH6	OTTHUMG00000177018	ENST00000563459.1:c.1347G>A	16.37:g.23540828C>T		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	46	13	NM_001083614	0	0	0	0	0	B3KTT2|D3DWF1|Q86YH3|Q8TF31	Silent	SNP	ENST00000563459.1	37	CCDS42132.1																																																																																			.		0.607	EARS2-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434844.1	NM_133451		T	23540828	C	T	23540828	2	4	66	1	0	0	0	0	0	0	0	1	4889	697	25	2		2	EARS2	16	23540828	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		23540828	66813925	66	6370											
STX4	6810	broad.mit.edu	37	chr16	31050905	31050905	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaagaacatcctgagctcagCggactacgtggaacgtgggc	11	6	14	10	3	1	2	1	1	0	1	2	5	2	4	1	3	5	1	1	3	4	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:31050905C>T	ENST00000313843.3	+	9	1061	c.746C>T	c.(745-747)gCg>gTg	p.A249V	STX4_ENST00000394998.1_Missense_Mutation_p.A247V|STX4_ENST00000493902.1_3'UTR	NM_004604.3	NP_004595.2	Q12846	STX4_HUMAN	syntaxin 4	249	Interaction with CENPF. {ECO:0000250}.|t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|neurotransmitter transport (GO:0006836)|platelet activation (GO:0030168)|post-Golgi vesicle-mediated transport (GO:0006892)|SNARE complex assembly (GO:0035493)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|membrane (GO:0016020)|myelin sheath adaxonal region (GO:0035749)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)				NS(2)|breast(1)|large_intestine(3)|lung(3)	9						CTGAGCTCAGCGGACTACGTG	0.622																																					p.A249V													.	STX4-90	0			c.C746T						.						139	124	129					16																	31050905		2197	4300	6497	SO:0001583	missense	6810	exon9			GCTCAGCGGACTA	AF026007	CCDS10700.1, CCDS61916.1	16p11.2	2008-02-05	2006-04-25	2006-04-25	ENSG00000103496	ENSG00000103496			11439	protein-coding gene	gene with protein product		186591	"syntaxin 4A (placental)"	STX4A		8206394, 16339081	Standard	NM_001272095		Approved	p35-2	uc002eak.4	Q12846	OTTHUMG00000132404	ENST00000313843.3:c.746C>T	16.37:g.31050905C>T	ENSP00000317714:p.Ala249Val	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	159	5	NM_004604	0	2	256	258	0	A8MXY0|Q15525|Q6FHE8	Missense_Mutation	SNP	ENST00000313843.3	37	CCDS10700.1	.	.	.	.	.	.	.	.	.	.	C	9.222	1.033546	0.19590	.	.	ENSG00000103496	ENST00000394998;ENST00000313843	T;T	0.20881	2.04;2.04	6.08	5.13	0.70059	t-SNARE (1);Target SNARE coiled-coil domain (3);	0.313701	0.35207	N	0.003372	T	0.09512	0.0234	N	0.05467	-0.045	0.09310	N	0.999999	D;D	0.54397	0.966;0.966	P;B	0.45660	0.489;0.362	T	0.18085	-1.0348	10	0.02654	T	1	.	6.6274	0.22837	0.0:0.6976:0.1487:0.1537	.	249;247	Q12846;A8MXY0	STX4_HUMAN;.	V	247;249	ENSP00000378447:A247V;ENSP00000317714:A249V	ENSP00000317714:A249V	A	+	2	0	STX4	30958406	0.000000	0.05858	0.989000	0.46669	0.953000	0.61014	-0.083000	0.11286	1.590000	0.49995	0.655000	0.94253	GCG	.		0.622	STX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255538.3	NM_004604		T	31050905	C	T	31050905	3	4	66	1	0	0	0	0	1	0	0	0	15379	768	27	1	780	1	STX4	16	31050905	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	7510077	31050905	59303848	67	6371											
ZNF646	9726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31089679	31089679	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcggcatcggaagcgggcTggcggtgccagcggtgggag	6	4	22	9	5	0	0	0	0	0	0	1	2	0	2	1	8	3	2	1	8	1	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:31089679T>C	ENST00000394979.2	+	1	2457	c.2034T>C	c.(2032-2034)gcT>gcC	p.A678A	ZNF646_ENST00000300850.5_Silent_p.A678A			O15015	ZN646_HUMAN	zinc finger protein 646	678					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						GGAAGCGGGCTGGCGGTGCCA	0.647																																					p.A678A		.											.	ZNF646-153	0			c.T2034C						.						26	33	30					16																	31089679		2192	4291	6483	SO:0001819	synonymous_variant	9726	exon2			GCGGGCTGGCGGT	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"Zinc fingers, C2H2-type"	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.2034T>C	16.37:g.31089679T>C		Somatic	74	2		WXS	Illumina HiSeq	Phase_I	89	33	NM_014699	0	0	6	8	2	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				.		0.647	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		C	31089679	T	C	31089679	2	2	66	1	0	0	0	0	0	0	0	1	18094	1567	55	3		3	ZNF646	16	31089679	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	38774	31089679	59265074	68	6372											
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85690000	85690000	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggagcgcgagcgcgagcgCgagcgtgagcgtgaggctga	8	3	21	9	8	0	3	0	3	0	0	0	7	0	4	0	2	5	1	0	2	0	0	rs145522531|rs376902954		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:85690000C>T	ENST00000253458.7	+	7	1217	c.1041C>T	c.(1039-1041)cgC>cgT	p.R347R	GSE1_ENST00000393243.1_Silent_p.R274R|GSE1_ENST00000405402.2_Silent_p.R243R|RN7SL381P_ENST00000577658.1_RNA	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	347																	agcgcgagcgcgagcgtgagc	0.647																																					p.R347R		.											.	.	0			c.C1041T						.						11	13	12					16																	85690000		2130	4144	6274	SO:0001819	synonymous_variant	23199	exon7			CGAGCGCGAGCGT	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1041C>T	16.37:g.85690000C>T		Somatic	19	1		WXS	Illumina HiSeq	Phase_I	22	7	NM_014615	0	0	0	0	0	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	N	7.137	0.580957	0.13686	.	.	ENSG00000131149	ENST00000412692	.	.	.	2.49	-4.98	0.03019	.	.	.	.	.	T	0.50411	0.1614	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49969	-0.8882	4	.	.	.	-12.1141	7.7571	0.28930	0.0:0.2532:0.5643:0.1824	rs62643366	.	.	.	V	154	.	.	A	+	2	0	KIAA0182	84247501	0.399000	0.25287	0.668000	0.29813	0.590000	0.36582	0.000000	0.12993	-2.629000	0.00435	-1.063000	0.02288	GCG	.		0.647	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		T	85690000	C	T	85690000	2	4	66	1	0	0	0	0	0	0	0	1	8180	755	27	1		1	KIAA0182	16	85690000	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	54600321	85690000	4664753	69	6373											
RNF166	115992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	88765421	88765421	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctttccacacagtgcttCaccagctcctgctggtccag	6	11	9	15	0	1	0	1	0	0	0	4	0	4	0	4	2	3	4	4	2	0	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:88765421C>A	ENST00000312838.4	-	4	593	c.498G>T	c.(496-498)gtG>gtT	p.V166V	RNF166_ENST00000567844.1_Silent_p.V85V|RNF166_ENST00000537718.2_Silent_p.V57V|RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000562499.1_5'Flank|RNF166_ENST00000541206.2_Silent_p.V57V|RNF166_ENST00000568683.1_Silent_p.V57V	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	166							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CACAGTGCTTCACCAGCTCCT	0.677																																					p.V166V		.											.	RNF166-226	0			c.G498T						.						52	49	50					16																	88765421		2191	4293	6484	SO:0001819	synonymous_variant	115992	exon4			GTGCTTCACCAGC	AK057106	CCDS10969.1, CCDS54056.1, CCDS54057.1	16q24.3	2013-01-09			ENSG00000158717	ENSG00000158717		"RING-type (C3HC4) zinc fingers"	28856	protein-coding gene	gene with protein product						12477932	Standard	NM_178841		Approved	MGC2647, MGC14381	uc002flk.3	Q96A37	OTTHUMG00000137863	ENST00000312838.4:c.498G>T	16.37:g.88765421C>A		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	14	8	NM_178841	0	0	24	39	15	B3KQ03|D3DX75|H3BTU8|Q96DM0	Silent	SNP	ENST00000312838.4	37	CCDS10969.1																																																																																			.		0.677	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841		A	88765421	C	A	88765421	2	1	66	1	0	0	0	0	0	0	0	1	13489	813	29	4		4	RNF166	16	88765421	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	3075421	88765421	1589332	70	6374											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_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	265	268					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	527	67		WXS	Illumina HiSeq		605	89	NM_145301	0	0	8	88	80	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		T	15457087	C	T	15457087	3	4	66	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		15457087	65738123	71	6375											
MED1	5469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37579984	37579984	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtttctgaacaaatgctctAgatactgggattggctgggg	10	12	13	6	0	2	2	0	1	2	1	2	3	2	3	0	4	3	3	0	4	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:37579984A>T	ENST00000394287.3	-	12	1147	c.942T>A	c.(940-942)tcT>tcA	p.S314S	MED1_ENST00000300651.6_Silent_p.S314S			O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		CAAATGCTCTAGATACTGGGA	0.413										HNSCC(31;0.082)																											p.S314S	Pancreas(21;279 768 2492 4877 24026)	.											.	MED1-620	0			c.T942A						.						101	102	101					17																	37579984		2203	4300	6503	SO:0001819	synonymous_variant	5469	exon12			TGCTCTAGATACT	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.942T>A	17.37:g.37579984A>T		Somatic	108	1		WXS	Illumina HiSeq	Phase_I	123	49	NM_004774	0	0	10	18	8	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Silent	SNP	ENST00000394287.3	37																																																																																				.		0.413	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	NM_004774		T	37579984	A	T	37579984	2	4	66	1	0	0	0	0	0	0	0	1	9450	407	15	5		5	MED1	17	37579984	Silent	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	22122897	37579984	43615226	72	6376											
UNC13D	201294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73837041	73837041	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccaggtcactcaccacAtgtccagatgaaagctcgca	12	6	9	14	1	2	2	2	1	0	1	4	2	3	2	3	2	1	2	3	2	1	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:73837041A>T	ENST00000207549.4	-	7	990	c.611T>A	c.(610-612)aTg>aAg	p.M204K	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Missense_Mutation_p.M204K	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	204	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CACTCACCACATGTCCAGATG	0.592									Familial Hemophagocytic Lymphohistiocytosis																												p.M204K		.											.	UNC13D-92	0			c.T611A						.						250	240	243					17																	73837041		2203	4300	6503	SO:0001583	missense	201294	exon7	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACCACATGTCCA	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.611T>A	17.37:g.73837041A>T	ENSP00000207549:p.Met204Lys	Somatic	451	0		WXS	Illumina HiSeq	Phase_I	474	146	NM_199242	0	0	0	0	0	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830248	0.71258	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.39406	1.08;1.08	4.44	4.44	0.53790	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.059897	0.64402	D	0.000004	T	0.61887	0.2383	M	0.82323	2.585	0.80722	D	1	D;B	0.53312	0.959;0.132	P;B	0.57244	0.816;0.207	T	0.69544	-0.5117	10	0.87932	D	0	.	13.7049	0.62631	1.0:0.0:0.0:0.0	.	204;204	B4DTQ6;Q70J99	.;UN13D_HUMAN	K	204	ENSP00000207549:M204K;ENSP00000388093:M204K	ENSP00000207549:M204K	M	-	2	0	UNC13D	71348636	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.339000	0.90041	1.650000	0.50662	0.460000	0.39030	ATG	.		0.592	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73837041	A	T	73837041	3	4	66	1	0	0	0	0	1	0	0	0	17020	217	8	5	2765	5	UNC13D	17	73837041	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	36257057	73837041	7358169	73	6377											
QRICH2	84074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74288035	74288035	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caggccatgtggatctgcctGaggttgcaccataccttgct	7	11	11	12	0	1	1	0	1	1	0	1	2	1	2	4	3	4	3	4	3	1	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:74288035G>A	ENST00000262765.5	-	4	2454	c.2275C>T	c.(2275-2277)Cag>Tag	p.Q759*		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	759	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GGATCTGCCTGAGGTTGCACC	0.522																																					p.Q759X		.											.	QRICH2-94	0			c.C2275T						.						181	166	171					17																	74288035		2203	4300	6503	SO:0001587	stop_gained	84074	exon4			CTGCCTGAGGTTG	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.2275C>T	17.37:g.74288035G>A	ENSP00000262765:p.Gln759*	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	219	74	NM_032134	0	0	0	2	2	A2RRE1|Q96LM3	Nonsense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	g	38	6.650945	0.97734	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	.	.	.	4.21	0.735	0.18300	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-0.4735	11.7828	0.52023	0.0:0.4377:0.5623:0.0	.	.	.	.	X	759	.	ENSP00000262765:Q759X	Q	-	1	0	QRICH2	71799630	0.000000	0.05858	0.003000	0.11579	0.066000	0.16364	-1.577000	0.02127	0.500000	0.27991	-0.537000	0.04273	CAG	.		0.522	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74288035	G	A	74288035	4	1	66	1	0	0	0	0	0	1	0	0	12912	1299	45	2	2780	2	QRICH2	17	74288035	Nonsense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	450994	74288035	6907175	74	6378											
TAF4B	6875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	23865865	23865865	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaaagcgtggttgccttacGacaacttctgcctaactccc	10	10	8	13	2	1	0	0	0	1	0	2	2	2	0	3	1	6	1	3	1	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr18:23865865G>A	ENST00000269142.5	+	7	1990	c.992G>A	c.(991-993)cGa>cAa	p.R331Q	TAF4B_ENST00000578121.1_Missense_Mutation_p.R331Q|TAF4B_ENST00000400466.2_Missense_Mutation_p.R331Q	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	331	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GTTGCCTTACGACAACTTCTG	0.408																																					p.R331Q		.											.	TAF4B-71	0			c.G992A						.						117	105	108					18																	23865865		1933	4147	6080	SO:0001583	missense	6875	exon7			CCTTACGACAACT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.992G>A	18.37:g.23865865G>A	ENSP00000269142:p.Arg331Gln	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	197	104	NM_005640	0	0	1	7	6	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	g	15.30	2.793145	0.50102	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.49720	0.77;0.77;0.77	5.72	4.83	0.62350	TAFH/NHR1 (3);	0.124363	0.56097	D	0.000033	T	0.62768	0.2455	L	0.58428	1.81	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.961	T	0.58907	-0.7553	10	0.16420	T	0.52	-9.2264	15.6095	0.76704	0.0:0.0:0.861:0.139	.	331;331	Q92750;A4PBF7	TAF4B_HUMAN;.	Q	331	ENSP00000389365:R331Q;ENSP00000269142:R331Q;ENSP00000383314:R331Q	ENSP00000269142:R331Q	R	+	2	0	TAF4B	22119863	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.418000	0.80167	1.388000	0.46506	0.558000	0.71614	CGA	.		0.408	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		A	23865865	G	A	23865865	3	1	66	1	0	0	0	0	1	0	0	0	15559	1058	37	1	1018	1	TAF4B	18	23865865	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		23865865	54211383	75	6379											
SERPINB5	5268	hgsc.bcm.edu	37	chr18	61170566	61170566	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcatttttgtccttcagattGaaaaacaactcaactcagag	14	13	5	9	0	4	3	4	1	0	2	5	3	5	3	1	0	3	0	1	0	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr18:61170566G>C	ENST00000382771.4	+	7	1031	c.739G>C	c.(739-741)Gaa>Caa	p.E247Q	SERPINB5_ENST00000464346.1_3'UTR	NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	247					cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						CCTTCAGATTGAAAAACAACT	0.368																																					p.E247Q		.											.	SERPINB5-651	0			c.G739C						.						34	32	33					18																	61170566		2203	4300	6503	SO:0001583	missense	5268	exon7			CAGATTGAAAAAC	U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"Serine (or cysteine) peptidase inhibitors"	8949	protein-coding gene	gene with protein product	"protease inhibitor 5 (maspin)"	154790	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.739G>C	18.37:g.61170566G>C	ENSP00000372221:p.Glu247Gln	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_002639	0	0	0	0	0	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181715	0.78677	.	.	ENSG00000206075	ENST00000382771	T	0.21932	1.98	6.05	4.26	0.50523	Serpin domain (3);	0.000000	0.85682	D	0.000000	T	0.37320	0.0999	H	0.94620	3.56	0.80722	D	1	P	0.45827	0.867	B	0.39904	0.313	T	0.58797	-0.7573	10	0.87932	D	0	.	13.4186	0.60982	0.1292:0.0:0.8708:0.0	.	247	P36952	SPB5_HUMAN	Q	247	ENSP00000372221:E247Q	ENSP00000372221:E247Q	E	+	1	0	SERPINB5	59321546	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.860000	0.75473	1.573000	0.49748	0.655000	0.94253	GAA	.		0.368	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639		C	61170566	G	C	61170566	3	2	66	1	0	0	0	0	1	0	0	0	14136	1291	45	4	761	4	SERPINB5	18	61170566	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	37304701	61170566	16906682	76	6380											
LPPR3	79948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	814747	814747	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtgctgggacgggaaggtcTtcctgtaagaggcgtccagc	7	8	16	10	3	1	1	0	0	1	1	3	3	3	3	2	4	2	2	2	4	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:814747T>C	ENST00000520876.3	-	6	680	c.602A>G	c.(601-603)aAg>aGg	p.K201R	LPPR3_ENST00000359894.2_Missense_Mutation_p.K201R|MIR3187_ENST00000583431.1_RNA	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		201						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										CGGGAAGGTCTTCCTGTAAGA	0.667																																					p.K201R		.											.	.	0			c.A602G						.						40	33	35					19																	814747		2187	4296	6483	SO:0001583	missense	0	exon6			AAGGTCTTCCTGT																												ENST00000520876.3:c.602A>G	19.37:g.814747T>C	ENSP00000430297:p.Lys201Arg	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	36	11	NM_001270366	0	0	0	0	0	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	37	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.010930	0.75046	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876	T;T	0.48201	0.82;0.82	4.77	4.77	0.60923	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.53110	0.1776	L	0.46567	1.45	0.39303	D	0.964943	P;P;D	0.56746	0.918;0.933;0.977	P;P;P	0.55871	0.596;0.718;0.786	T	0.54370	-0.8304	10	0.35671	T	0.21	-24.8006	12.0107	0.53286	0.0:0.0:0.0:1.0	.	202;201;201	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	R	202;201;201	ENSP00000352962:K201R;ENSP00000430297:K201R	ENSP00000300947:K202R	K	-	2	0	AC006273.1	765747	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.722000	0.61958	1.780000	0.52325	0.454000	0.30748	AAG	.		0.667	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			C	814747	T	C	814747	3	2	66	1	0	0	0	0	1	0	0	0	8951	1609	56	3	1646	3	LPPR3	19	814747	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		814747	58314236	77	6381											
ARID3A	1820	bcgsc.ca	37	chr19	972016	972016	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggcggccaggctgggccagCggggctgtccacaccctcca	5	4	15	17	3	0	0	0	0	0	0	2	0	2	0	5	6	1	2	5	6	0	0	rs150609955		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:972016C>T	ENST00000263620.3	+	9	2060	c.1733C>T	c.(1732-1734)gCg>gTg	p.A578V		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	578	Gly-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGGGCCAGCGGGGCTGTCC	0.697																																					p.A578V	Pancreas(29;54 1022 32760 50921)												.	ARID3A-90	0			c.C1733T						.	C	VAL/ALA	1,4357		0,1,2178	28	30	29		1733	5	0	19	dbSNP_134	29	0,8454		0,0,4227	no	missense	ARID3A	NM_005224.2	64	0,1,6405	TT,TC,CC		0.0,0.0229,0.0078	possibly-damaging	578/594	972016	1,12811	2179	4227	6406	SO:0001583	missense	1820	exon9			GGCCAGCGGGGCT	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1733C>T	19.37:g.972016C>T	ENSP00000263620:p.Ala578Val	Somatic	25	0		WXS	Illumina HiSeq	Phase_1	24	4	NM_005224	0	0	5	5	0	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	37	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495803	0.26774	2.29E-4	0.0	ENSG00000116017	ENST00000263620	T	0.39787	1.06	5.03	5.03	0.67393	.	2.957760	0.01861	N	0.036628	T	0.40645	0.1125	L	0.44542	1.39	0.09310	N	1	P	0.35844	0.524	B	0.25884	0.064	T	0.47005	-0.9150	10	0.59425	D	0.04	7.9711	13.8475	0.63477	0.0:1.0:0.0:0.0	.	578	Q99856	ARI3A_HUMAN	V	578	ENSP00000263620:A578V	ENSP00000263620:A578V	A	+	2	0	ARID3A	923016	0.186000	0.23225	0.008000	0.14137	0.054000	0.15201	4.458000	0.60095	2.328000	0.79073	0.561000	0.74099	GCG	C|1.000;T|0.000		0.697	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		T	972016	C	T	972016	3	4	66	1	0	0	0	0	1	0	0	0	916	768	27	1	1763	1	ARID3A	19	972016	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	157269	972016	58156967	78	6382											
ABCA7	10347	broad.mit.edu	37	chr19	1062275	1062275	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgagcacctggagctgcttgCgcgcctgcgcggtgtcccgg	3	7	16	15	6	0	0	0	0	0	0	1	2	1	1	3	3	5	3	3	3	0	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:1062275C>T	ENST00000263094.6	+	42	5906	c.5675C>T	c.(5674-5676)gCg>gTg	p.A1892V	ABCA7_ENST00000433129.1_Missense_Mutation_p.A1892V|ABCA7_ENST00000435683.2_Missense_Mutation_p.A1754V	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1892	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGCTGCTTGCGCGCCTGCGC	0.692																																					p.A1892V													.	ABCA7-98	0			c.C5675T						.						90	98	95					19																	1062275		2203	4298	6501	SO:0001583	missense	10347	exon42			TGCTTGCGCGCCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5675C>T	19.37:g.1062275C>T	ENSP00000263094:p.Ala1892Val	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	304	5	NM_019112	0	0	6	6	0	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	C	19.25	3.792252	0.70452	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.96459	-4.02;-4.02	3.61	2.55	0.30701	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.97523	0.9189	M	0.86097	2.795	0.30577	N	0.762881	D;D	0.76494	0.999;0.998	D;D	0.67231	0.95;0.937	D	0.94100	0.7361	9	0.87932	D	0	.	7.0336	0.24980	0.0:0.7206:0.1747:0.1046	.	1017;1892	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	V	1892	ENSP00000263094:A1892V;ENSP00000414062:A1892V	ENSP00000263094:A1892V	A	+	2	0	ABCA7	1013275	0.007000	0.16637	0.735000	0.30896	0.759000	0.43091	1.406000	0.34646	0.718000	0.32166	0.555000	0.69702	GCG	.		0.692	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1062275	C	T	1062275	3	4	66	1	0	0	0	0	1	0	0	0	37	768	27	1	5837	1	ABCA7	19	1062275	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	90259	1062275	58066708	79	6383											
JSRP1	126306	hgsc.bcm.edu	37	chr19	2253780	2253780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccttcttgcgcgcggggAcgctccgagggcctgcgggg	2	6	19	14	7	1	0	0	0	1	0	2	2	2	1	3	5	2	1	3	5	0	2	rs10426549	byFrequency	TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:2253780A>G	ENST00000300961.6	-	5	339	c.275T>C	c.(274-276)gTc>gCc	p.V92A	JSRP1_ENST00000586471.2_Missense_Mutation_p.V92A	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	92			V -> A (in dbSNP:rs10426549).		protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGCGCGGGGACGCTCCGAGG	0.761													G|||	1026	0.204872	0.5219	0.072	5008	,	,		11441	0.0734		0.0845	False		,,,				2504	0.1299				p.V92A		.											.	JSRP1-91	0			c.T275C						.	G	ALA/VAL	495,1775		30,435,670	2	4	3		275	0.1	0.4	19	dbSNP_119	3	248,4804		5,238,2283	no	missense	JSRP1	NM_144616.3	64	35,673,2953	GG,GA,AA		4.9089,21.8062,10.1475	benign	92/332	2253780	743,6579	1135	2526	3661	SO:0001583	missense	126306	exon5			GCGGGGACGCTCC	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.275T>C	19.37:g.2253780A>G	ENSP00000300961:p.Val92Ala	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_144616	0	0	0	0	0		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	362	0.16575091575091574	231	0.4695121951219512	21	0.058011049723756904	48	0.08391608391608392	62	0.08179419525065963	a	0.017	-1.492342	0.01009	0.218062	0.049089	ENSG00000167476	ENST00000300961	T	0.18657	2.2	3.74	0.0998	0.14504	.	1.682840	0.03947	N	0.287865	T	0.00012	0.0000	N	0.04508	-0.205	0.46927	P	7.479999999999709E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47560	-0.9108	9	0.18710	T	0.47	0.0096	4.6604	0.12639	0.3093:0.1591:0.5316:0.0	rs10426549;rs58800051	92	Q96MG2	JSPR1_HUMAN	A	92	ENSP00000300961:V92A	ENSP00000300961:V92A	V	-	2	0	JSRP1	2204780	0.001000	0.12720	0.427000	0.26684	0.036000	0.12997	-0.186000	0.09670	-0.634000	0.05538	-0.930000	0.02707	GTC	A|0.832;G|0.168		0.761	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		G	2253780	A	G	2253780	3	3	66	1	0	0	0	0	1	0	0	0	7987	275	10	3	732	3	JSRP1	19	2253780	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	1191505	2253780	56875203	80	6384											
ZNF607	84775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38190209	38190209	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtggcttctctccagtatGaatactctgatgtactttaa	10	16	7	8	0	2	2	0	2	2	0	4	2	3	2	1	1	2	3	1	1	5	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:38190209G>T	ENST00000355202.4	-	5	1418	c.823C>A	c.(823-825)Cat>Aat	p.H275N	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.H274N	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	275					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)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			TCTCCAGTATGAATACTCTGA	0.423																																					p.H275N		.											.	ZNF607-90	0			c.C823A						.						48	48	48					19																	38190209		2203	4300	6503	SO:0001583	missense	84775	exon5			CAGTATGAATACT	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"Zinc fingers, C2H2-type", "-"	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.823C>A	19.37:g.38190209G>T	ENSP00000347338:p.His275Asn	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	119	49	NM_032689	0	0	0	0	0	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708084	0.48412	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.67345	-0.26;-0.26	2.27	2.27	0.28462	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84005	0.5377	M	0.92923	3.36	0.33659	D	0.609455	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.88981	0.3408	9	0.87932	D	0	.	11.6009	0.51001	0.0:0.0:1.0:0.0	.	275;274	Q96SK3;F5H141	ZN607_HUMAN;.	N	275;274	ENSP00000347338:H275N;ENSP00000438015:H274N	ENSP00000347338:H275N	H	-	1	0	ZNF607	42882049	1.000000	0.71417	0.991000	0.47740	0.731000	0.41821	7.908000	0.87438	1.255000	0.44051	0.561000	0.74099	CAT	.		0.423	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		T	38190209	G	T	38190209	3	4	66	1	0	0	0	0	1	0	0	0	18065	1290	45	4	1271	4	ZNF607	19	38190209	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	35936429	38190209	20938774	81	6385											
SIPA1L3	23094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38621370	38621370	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgcacctctgtcactgtgaAggtggtcatcatcccgcctt	6	11	10	14	2	4	1	3	1	1	0	5	1	5	1	3	2	0	1	3	2	1	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:38621370A>C	ENST00000222345.6	+	10	3610	c.3101A>C	c.(3100-3102)aAg>aCg	p.K1034T		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1034	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GTCACTGTGAAGGTGGTCATC	0.627																																					p.K1034T		.											.	SIPA1L3-91	0			c.A3101C						.						67	60	62					19																	38621370		2203	4300	6503	SO:0001583	missense	23094	exon10			CTGTGAAGGTGGT	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3101A>C	19.37:g.38621370A>C	ENSP00000222345:p.Lys1034Thr	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	92	28	NM_015073	0	0	6	20	14	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.437903	0.62955	.	.	ENSG00000105738	ENST00000222345	T	0.62788	0.0	5.33	5.33	0.75918	PDZ/DHR/GLGF (2);	0.108901	0.64402	D	0.000008	T	0.33673	0.0871	N	0.00972	-1.085	0.58432	D	0.999992	B	0.33212	0.402	B	0.33846	0.171	T	0.42999	-0.9418	10	0.28530	T	0.3	-40.8953	14.5799	0.68282	1.0:0.0:0.0:0.0	.	1034	O60292	SI1L3_HUMAN	T	1034	ENSP00000222345:K1034T	ENSP00000222345:K1034T	K	+	2	0	SIPA1L3	43313210	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.751000	0.55165	2.148000	0.66965	0.533000	0.62120	AAG	.		0.627	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		C	38621370	A	C	38621370	3	2	66	1	0	0	0	0	1	0	0	0	14363	72	3	5	3131	5	SIPA1L3	19	38621370	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	431161	38621370	20507613	82	6386											
ZNF780B	163131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40540344	40540344	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacatttcttacattcaaagGgtttctcacctgtacaagtt	11	15	5	10	0	3	0	2	0	2	0	4	0	3	0	1	1	2	3	1	1	4	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:40540344G>A	ENST00000434248.1	-	5	2487	c.2422C>T	c.(2422-2424)Cct>Tct	p.P808S	ZNF780B_ENST00000221355.6_Missense_Mutation_p.P660S	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	808					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)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					ACATTCAAAGGGTTTCTCACC	0.393																																					p.P808S		.											.	ZNF780B-47	0			c.C2422T						.						59	64	62					19																	40540344		2188	4297	6485	SO:0001583	missense	163131	exon5			TCAAAGGGTTTCT	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.2422C>T	19.37:g.40540344G>A	ENSP00000391641:p.Pro808Ser	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	100	38	NM_001005851	0	0	3	3	0	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400412	0.25291	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.06142	3.55;3.34	2.24	1.16	0.20824	Zinc finger, C2H2 (1);	.	.	.	.	T	0.06050	0.0157	L	0.41906	1.305	0.20926	N	0.999822	B	0.02656	0.0	B	0.04013	0.001	T	0.34153	-0.9840	9	0.59425	D	0.04	.	6.6373	0.22889	0.1624:0.0:0.8376:0.0	.	808	Q9Y6R6	Z780B_HUMAN	S	808;660	ENSP00000391641:P808S;ENSP00000221355:P660S	ENSP00000221355:P660S	P	-	1	0	ZNF780B	45232184	0.008000	0.16893	0.148000	0.22405	0.135000	0.20990	0.773000	0.26661	0.135000	0.18707	-0.448000	0.05591	CCT	.		0.393	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		A	40540344	G	A	40540344	3	1	66	1	0	0	0	0	1	0	0	0	18185	1232	43	2	83	2	ZNF780B	19	40540344	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	1918974	40540344	18588639	83	6387											
CLPTM1	1209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45495628	45495628	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctttgtcatcaagatgcccGttatgtaccggatcggctgc	7	12	10	12	3	2	1	2	0	0	1	3	2	2	2	3	2	3	3	3	2	3	3	rs369873479		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:45495628G>A	ENST00000337392.5	+	13	1843	c.1693G>A	c.(1693-1695)Gtt>Att	p.V565I	CLPTM1_ENST00000541297.2_Missense_Mutation_p.V551I|CLPTM1_ENST00000546079.1_Missense_Mutation_p.V463I	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	565					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CAAGATGCCCGTTATGTACCG	0.627																																					p.V565I		.											.	CLPTM1-91	0			c.G1693A						.	G	ILE/VAL	0,4406		0,0,2203	203	182	190		1693	4.2	0.4	19		190	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLPTM1	NM_001294.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	565/670	45495628	1,13005	2203	4300	6503	SO:0001583	missense	1209	exon13			ATGCCCGTTATGT	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1693G>A	19.37:g.45495628G>A	ENSP00000336994:p.Val565Ile	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	261	100	NM_001294	0	0	231	454	222	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	37	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.191286	0.38707	0.0	1.16E-4	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.21	4.17	0.49024	.	0.186290	0.46758	D	0.000276	T	0.11836	0.0288	N	0.02916	-0.46	0.31931	N	0.612128	P;P	0.40602	0.723;0.602	B;B	0.30316	0.114;0.053	T	0.10636	-1.0621	9	0.17369	T	0.5	-31.7339	9.7828	0.40658	0.0929:0.0:0.9071:0.0	.	551;565	F5H8J3;O96005	.;CLPT1_HUMAN	I	463;551;565;565	.	ENSP00000336994:V565I	V	+	1	0	CLPTM1	50187468	1.000000	0.71417	0.352000	0.25734	0.978000	0.69477	6.750000	0.74888	1.443000	0.47586	0.650000	0.86243	GTT	.		0.627	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		A	45495628	G	A	45495628	3	1	66	1	0	0	0	0	1	0	0	0	3560	1145	40	1	1743	1	CLPTM1	19	45495628	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	4955284	45495628	13633355	84	6388											
NLRP2	55655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55493701	55493701	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcatacacggtggtgctgtAtggtcctgcaggccttggga	6	11	14	10	1	1	0	1	0	0	0	2	1	2	1	2	5	3	3	2	5	2	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:55493701A>T	ENST00000543010.1	+	6	778	c.635A>T	c.(634-636)tAt>tTt	p.Y212F	NLRP2_ENST00000448584.2_Missense_Mutation_p.Y212F|NLRP2_ENST00000537859.1_Missense_Mutation_p.Y190F|NLRP2_ENST00000538819.1_Missense_Mutation_p.Y188F|NLRP2_ENST00000263437.6_Missense_Mutation_p.Y209F|NLRP2_ENST00000339757.7_Missense_Mutation_p.Y190F|NLRP2_ENST00000391721.4_Missense_Mutation_p.Y188F|NLRP2_ENST00000427260.2_Missense_Mutation_p.Y189F	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	212	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GTGGTGCTGTATGGTCCTGCA	0.527																																					p.Y212F		.											.	NLRP2-120	0			c.A635T						.						78	79	79					19																	55493701		2203	4300	6503	SO:0001583	missense	55655	exon6			TGCTGTATGGTCC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.635A>T	19.37:g.55493701A>T	ENSP00000445135:p.Tyr212Phe	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	135	53	NM_017852	0	0	0	0	0	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	A	9.855	1.194818	0.22037	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	D;D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	1.62	0.524	0.17066	NACHT nucleoside triphosphatase (1);	1.825070	0.03631	N	0.237909	T	0.71913	0.3396	N	0.10972	0.075	0.09310	N	1	B;B;B;B;P	0.35433	0.213;0.284;0.332;0.284;0.501	B;B;B;B;B	0.41412	0.356;0.128;0.295;0.195;0.295	T	0.63193	-0.6692	10	0.48119	T	0.1	.	4.2437	0.10662	0.6116:0.0:0.3884:0.0	.	189;190;209;188;212	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	F	212;188;190;212;190;189;188;209	ENSP00000445135:Y212F;ENSP00000375601:Y188F;ENSP00000344074:Y190F;ENSP00000409370:Y212F;ENSP00000440601:Y190F;ENSP00000402474:Y189F;ENSP00000441133:Y188F;ENSP00000263437:Y209F	ENSP00000263437:Y209F	Y	+	2	0	NLRP2	60185513	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	0.117000	0.15583	0.085000	0.17107	0.402000	0.26972	TAT	.		0.527	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55493701	A	T	55493701	3	4	66	1	0	0	0	0	1	0	0	0	10503	449	16	5	653	5	NLRP2	19	55493701	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	9998073	55493701	3635282	85	6389											
AHCY	191	ucsc.edu	37	chr20	32880315	32880315	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcccttccaggcatacacTggagggtgagtggcacatca	9	8	12	12	1	1	1	1	1	0	0	3	2	2	2	2	4	1	2	2	4	1	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr20:32880315T>C	ENST00000217426.2	-	4	373		c.e4-2		AHCY_ENST00000468908.1_Splice_Site|AHCY_ENST00000538132.1_Splice_Site	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase						cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGGCATACACTGGAGGGTGAG	0.572																																					.													.	AHCY-91	0			c.212-2A>G						.						110	84	93					20																	32880315		2203	4300	6503	SO:0001630	splice_region_variant	191	exon5			ATACACTGGAGGG	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.296-2A>G	20.37:g.32880315T>C		Somatic	88	0		WXS	Illumina HiSeq		137	1	NM_001161766	0	0	2	2	0	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Splice_Site	SNP	ENST00000217426.2	37	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.982756	0.74474	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0795	0.72103	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AHCY	32343976	1.000000	0.71417	0.970000	0.41538	0.799000	0.45148	6.293000	0.72731	2.035000	0.60131	0.459000	0.35465	.	.		0.572	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687	Intron	C	32880315	T	C	32880315	5	2	66	1	0	0	0	0	0	0	1	0	409	1594	55	3	1032	3	AHCY	20	32880315	Splice_Site	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		32880315	30145205	86	6390											
RPL3	6122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	39714484	39714484	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggctgtgaggtggaccggCttggacgggtcatccttagg	7	9	17	8	2	1	1	1	1	0	0	2	3	2	3	2	7	0	2	2	7	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr22:39714484C>A	ENST00000216146.4	-	2	290	c.117G>T	c.(115-117)aaG>aaT	p.K39N	RPL3_ENST00000465618.1_5'UTR|RPL3_ENST00000401609.1_5'UTR|SNORD43_ENST00000583861.1_RNA	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	39					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	GGTGGACCGGCTTGGACGGGT	0.592																																					p.K39N		.											.	RPL3-154	0			c.G117T						.						58	54	55					22																	39714484		2203	4298	6501	SO:0001583	missense	6122	exon2			GACCGGCTTGGAC	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"L ribosomal proteins"	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.117G>T	22.37:g.39714484C>A	ENSP00000346001:p.Lys39Asn	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	55	13	NM_001033853	0	2	158	2108	1940	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	37	CCDS13988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.63|16.63	3.175374|3.175374	0.57692|0.57692	.|.	.|.	ENSG00000100316|ENSG00000100316	ENST00000427905|ENST00000216146;ENST00000453303	.|T;T	.|0.49720	.|1.38;0.77	4.5|4.5	3.48|3.48	0.39840|0.39840	.|Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61123|0.61123	0.2322|0.2322	M|M	0.88842|0.88842	2.985|2.985	0.80722|0.80722	D|D	1|1	.|D;P	.|0.57899	.|0.981;0.715	.|P;P	.|0.48982	.|0.597;0.477	T|T	0.69982|0.69982	-0.4997|-0.4997	5|10	.|0.72032	.|D	.|0.01	.|.	12.3136|12.3136	0.54942|0.54942	0.0:0.9173:0.0:0.0827|0.0:0.9173:0.0:0.0827	.|.	.|39;39	.|P39023;B3KS36	.|RL3_HUMAN;.	S|N	71|39;66	.|ENSP00000346001:K39N;ENSP00000415198:K66N	.|ENSP00000346001:K39N	A|K	-|-	1|3	0|2	RPL3|RPL3	38044430|38044430	1.000000|1.000000	0.71417|0.71417	0.787000|0.787000	0.31911|0.31911	0.431000|0.431000	0.31685|0.31685	2.393000|2.393000	0.44442|0.44442	0.884000|0.884000	0.36064|0.36064	0.455000|0.455000	0.32223|0.32223	GCC|AAG	.		0.592	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967		A	39714484	C	A	39714484	3	1	66	1	0	0	0	0	1	0	0	0	13611	796	28	4	1130	4	RPL3	22	39714484	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		39714484	11590082	87	6391											
EFCAB6	64800	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	44107398	44107399	+	Frame_Shift_Ins	INS	-	-	A																															cttcttggtatttggtatacINSaaaagtgtcgaggacaatct																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr22:44107398_44107399insA	ENST00000262726.7	-	10	1240_1241	c.987_988insT	c.(985-990)tttgtafs	p.V330fs	EFCAB6_ENST00000396231.2_Frame_Shift_Ins_p.V178fs|EFCAB6_ENST00000358439.4_Frame_Shift_Ins_p.V224fs	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	330	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATTTGGTATACAAAAGTGTCGA	0.381																																					p.V330fs		.											.	EFCAB6-97	0			c.988_989insT						.																																			SO:0001589	frameshift_variant	64800	exon10			.	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.988dupT	22.37:g.44107402_44107402dupA	ENSP00000262726:p.Val330fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	88	25	NM_022785	0	0	0	0	0	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Frame_Shift_Ins	INS	ENST00000262726.7	37	CCDS14049.1																																																																																			.		0.381	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	44107399	-	A	44107398	7	5	66	1	0	1	1	0	0	0	0	0	4950	478	17	0	3609	0	EFCAB6	22	44107398	Frame_Shift_Ins	INS	-	TCGA-BQ-5882-01A-11D-1589-08	4392914	44107398	7197168	88	6392											
YY2	404281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	21875588	21875588	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcccttgatttcaatttgcGcacacacttgcgcatccaca	9	13	5	14	2	1	1	1	1	0	0	3	1	3	1	2	0	2	2	2	0	1	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chrX:21875588G>A	ENST00000429584.2	+	1	1484	c.986G>A	c.(985-987)cGc>cAc	p.R329H	MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000465888.1_3'UTR|MBTPS2_ENST00000365779.2_Intron	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	329	Mediates transcriptional repression.				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(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						TTCAATTTGCGCACACACTTG	0.532																																					p.R329H		.											.	YY2-193	0			c.G986A						.						182	181	181					X																	21875588		2203	4300	6503	SO:0001583	missense	404281	exon1			ATTTGCGCACACA	AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.986G>A	X.37:g.21875588G>A	ENSP00000389381:p.Arg329His	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	289	203	NM_206923	0	0	0	5	5	B2RP10|Q6Q1S4	Missense_Mutation	SNP	ENST00000429584.2	37	CCDS14202.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787837	0.90367	.	.	ENSG00000230797	ENST00000429584	T	0.41400	1.0	4.6	4.6	0.57074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.52273	0.1724	L	0.35288	1.05	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.53222	-0.8469	10	0.52906	T	0.07	.	14.034	0.64634	0.0:0.0:1.0:0.0	.	329	O15391	TYY2_HUMAN	H	329	ENSP00000389381:R329H	ENSP00000389381:R329H	R	+	2	0	YY2	21785509	1.000000	0.71417	0.992000	0.48379	0.757000	0.42996	7.776000	0.85560	2.276000	0.75962	0.544000	0.68410	CGC	.		0.532	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		A	21875588	G	A	21875588	3	1	66	1	0	0	0	0	1	0	0	0	17542	1087	38	1	988	1	YY2	23	21875588	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		21875588	133394972	89	6393											
CLCNKA	1187	ucsc.edu	37	chr1	16356252	16356253	+	Missense_Mutation	DNP	CA	CA	TG																															atgctgattctggccaccacCatccccatgcctgccgggta																								rs201976704|rs200828311		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr1:16356252_16356253CA>TG	ENST00000331433.4	+	13	1273_1274	c.1254_1255CA>TG	c.(1252-1257)acCAtc>acTGtc	p.I419V	CLCNKA_ENST00000439316.2_Missense_Mutation_p.I376V|CLCNKA_ENST00000375692.1_Missense_Mutation_p.I419V|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Missense_Mutation_p.I419V			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	419					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TGGCCACCACCATCCCCATGCC	0.589																																					p.I419V													.	CLCNKA-91	0			c.A1255G						.																																			SO:0001583	missense	1187	exon13			ACCACCATCCCCA		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"Ion channels / Chloride channels : Voltage-sensitive"	2026	protein-coding gene	gene with protein product		602024	"chloride channel Ka"			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	Exception_encountered	1.37:g.16356252_16356253delinsTG	ENSP00000332771:p.Ile419Val	Somatic	250	3		WXS	Illumina HiSeq		253	2	NM_004070	0	0	0	0	0	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	DNP	ENST00000331433.4	37	CCDS167.1																																																																																			A|0.999;G|0.001		0.589	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1			TG	16356253	CA	TG	16356252	3	4	67	1	0	0	0	0	1	0	0	0	3475	581	21	2	1300	2	CLCNKA	1	16356252	Missense_Mutation	DNP	CA	TCGA-BQ-5883-01A-11D-1589-08		16356252	232894369	1	6394											
KIAA0090	23065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	19545821	19545821	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgccaggcccgattcaggagCttcacctgtgccagtctctt	6	10	10	15	2	3	0	2	0	1	0	4	2	3	1	4	2	2	1	4	2	0	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr1:19545821C>T	ENST00000477853.1	-	23	3000	c.2958G>A	c.(2956-2958)aaG>aaA	p.K986K	EMC1_ENST00000375208.3_Silent_p.K964K|EMC1_ENST00000480380.1_5'UTR|EMC1_ENST00000375199.3_Silent_p.K985K|RP1-43E13.2_ENST00000437898.1_RNA	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	986						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											GATTCAGGAGCTTCACCTGTG	0.502																																					p.K986K		.											.	.	0			c.G2958A						.						76	71	72					1																	19545821		2203	4300	6503	SO:0001819	synonymous_variant	23065	exon23			CAGGAGCTTCACC		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"KIAA0090"	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.2958G>A	1.37:g.19545821C>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	75	4	NM_015047	0	0	69	80	11	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	37	CCDS190.1	.	.	.	.	.	.	.	.	.	.	C	9.326	1.059255	0.19987	.	.	ENSG00000127463	ENST00000375197	.	.	.	6.06	-0.986	0.10252	.	.	.	.	.	T	0.58977	0.2160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56153	-0.8026	4	.	.	.	.	12.1403	0.53994	0.0:0.5935:0.0:0.4065	.	.	.	.	T	611	.	.	A	-	1	0	KIAA0090	19418408	0.934000	0.31675	0.995000	0.50966	0.993000	0.82548	0.012000	0.13287	-0.119000	0.11830	-0.312000	0.09012	GCT	.		0.502	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		T	19545821	C	T	19545821	2	4	67	1	0	0	0	0	0	0	0	1	8174	796	28	2		2	KIAA0090	1	19545821	Silent	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	3189569	19545821	229704800	2	6395											
MSH4	4438	broad.mit.edu	37	chr1	76282197	76282197	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagattcatcatcagcccaaAaccttgaattgttaattaat	15	14	4	8	0	3	2	3	1	0	1	3	2	3	2	2	0	2	1	2	0	6	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr1:76282197A>C	ENST00000263187.3	+	6	1059	c.955A>C	c.(955-957)Aac>Cac	p.N319H		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	319					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						ATCAGCCCAAAACCTTGAATT	0.284								Mismatch excision repair (MMR)																													p.N319H													.	MSH4-660	0			c.A955C						.						59	61	60					1																	76282197		2203	4300	6503	SO:0001583	missense	4438	exon6			GCCCAAAACCTTG	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.955A>C	1.37:g.76282197A>C	ENSP00000263187:p.Asn319His	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_002440	0	0	0	0	0	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.413507	0.42817	.	.	ENSG00000057468	ENST00000263187	D	0.93604	-3.25	5.44	5.44	0.79542	DNA mismatch repair protein MutS, connector (1);DNA mismatch repair protein MutS, core (2);	0.098954	0.64402	D	0.000003	D	0.90679	0.7076	M	0.76002	2.32	0.44352	D	0.997241	B	0.22276	0.067	B	0.25759	0.063	D	0.90061	0.4156	10	0.87932	D	0	-14.4209	15.5023	0.75709	1.0:0.0:0.0:0.0	.	319	O15457	MSH4_HUMAN	H	319	ENSP00000263187:N319H	ENSP00000263187:N319H	N	+	1	0	MSH4	76054785	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.970000	0.76099	2.080000	0.62538	0.533000	0.62120	AAC	.		0.284	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		C	76282197	A	C	76282197	3	2	67	1	0	0	0	0	1	0	0	0	9897	14	1	5	977	5	MSH4	1	76282197	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	56736376	76282197	172968424	3	6396											
ZNF687	57592	bcgsc.ca	37	chr1	151260133	151260133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgcctaaggctgacgggcggGcagggctggggactggggga	6	5	22	8	2	0	1	0	1	0	0	0	3	0	3	1	8	1	3	1	8	1	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr1:151260133G>A	ENST00000368879.2	+	2	1464	c.1366G>A	c.(1366-1368)Gca>Aca	p.A456T		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGACGGGCGGGCAGGGCTGGG	0.632																																					p.A456T													.	ZNF687-92	0			c.G1366A						.						42	50	47					1																	151260133		2203	4300	6503	SO:0001583	missense	57592	exon2			GGGCGGGCAGGGC		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.1366G>A	1.37:g.151260133G>A	ENSP00000357874:p.Ala456Thr	Somatic	70	0		WXS	Illumina HiSeq	Phase_1	86	5	NM_020832	0	0	24	24	0	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	37		.	.	.	.	.	.	.	.	.	.	G	7.725	0.698029	0.15106	.	.	ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.00856	5.61;5.61;5.95	5.16	-1.35	0.09114	.	1.827670	0.03593	N	0.232244	T	0.00271	0.0008	L	0.27053	0.805	0.18873	N	0.999988	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.45425	-0.9262	10	0.22109	T	0.4	.	2.5477	0.04741	0.2143:0.3408:0.3288:0.1161	.	456;456;456	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	T	456	ENSP00000336620:A456T;ENSP00000319829:A456T;ENSP00000357874:A456T	ENSP00000319829:A456T	A	+	1	0	ZNF687	149526757	0.228000	0.23718	0.033000	0.17914	0.952000	0.60782	0.703000	0.25646	-0.424000	0.07382	0.561000	0.74099	GCA	.		0.632	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		A	151260133	G	A	151260133	3	1	67	1	0	0	0	0	1	0	0	0	18124	1203	42	2	1368	2	ZNF687	1	151260133	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	74977936	151260133	97990488	4	6397											
AQP10	89872	broad.mit.edu	37	chr1	154294468	154294468	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggagaaaccaaaggcaacttCttcaccatgtttctggctgg	11	10	10	10	0	3	1	1	0	2	1	3	2	3	1	2	4	2	3	2	4	3	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr1:154294468C>T	ENST00000324978.3	+	2	205	c.165C>T	c.(163-165)ttC>ttT	p.F55F	AQP10_ENST00000484864.1_Silent_p.F55F|AQP10_ENST00000355197.4_Intron	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	55					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AAGGCAACTTCTTCACCATGT	0.577																																					p.F55F													.	AQP10-90	0			c.C165T						.						71	60	64					1																	154294468		2202	4279	6481	SO:0001819	synonymous_variant	89872	exon2			CAACTTCTTCACC	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"Ion channels / Aquaporins"	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.165C>T	1.37:g.154294468C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	93	3	NM_080429	0	0	0	0	0	Q5VYD3|Q5VYD4|Q8NG70	Silent	SNP	ENST00000324978.3	37	CCDS1065.1																																																																																			.		0.577	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429		T	154294468	C	T	154294468	2	4	67	1	0	0	0	0	0	0	0	1	822	912	32	2		2	AQP10	1	154294468	Silent	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	3034335	154294468	94956153	5	6398											
KIF3C	3797	broad.mit.edu;bcgsc.ca	37	chr2	26203576	26203576	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgcggctgctcttcctccggGgccgcttccccagcatcccc	2	9	10	20	3	1	0	0	0	1	0	5	0	5	0	7	3	3	4	7	3	0	2			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:26203576G>A	ENST00000264712.3	-	1	1790	c.1211C>T	c.(1210-1212)cCc>cTc	p.P404L	KIF3C_ENST00000405914.1_Missense_Mutation_p.P404L	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	404					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCCTCCGGGGCCGCTTCCC	0.652																																					p.P404L													.	KIF3C-94	0			c.C1211T						.						46	48	47					2																	26203576		2203	4300	6503	SO:0001583	missense	3797	exon1			CTCCGGGGCCGCT		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"Kinesins"	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1211C>T	2.37:g.26203576G>A	ENSP00000264712:p.Pro404Leu	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	109	5	NM_002254	0	0	6	6	0	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	37	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	G	8.691	0.907521	0.17833	.	.	ENSG00000084731	ENST00000264712;ENST00000542511;ENST00000405914	T;T	0.73258	-0.73;-0.73	5.0	4.04	0.47022	Kinesin, motor domain (1);	0.465840	0.23937	N	0.043100	T	0.46580	0.1400	N	0.12182	0.205	0.40162	D	0.977078	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34453	-0.9828	10	0.27082	T	0.32	.	4.7743	0.13171	0.2331:0.0:0.7669:0.0	.	404;404	B7ZM25;O14782	.;KIF3C_HUMAN	L	404;210;404	ENSP00000264712:P404L;ENSP00000385030:P404L	ENSP00000264712:P404L	P	-	2	0	KIF3C	26057080	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.612000	0.46343	1.249000	0.43950	0.655000	0.94253	CCC	.		0.652	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			A	26203576	G	A	26203576	3	1	67	1	0	0	0	0	1	0	0	0	8323	1232	43	2	1202	2	KIF3C	2	26203576	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		26203576	216995797	6	6399											
VWA3B	200403	broad.mit.edu	37	chr2	98736133	98736133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catagtgctggattttggcgGcattctggagggggagcttg	6	12	17	6	1	1	0	0	0	1	0	1	3	1	3	0	6	2	3	0	6	1	5	rs200875707		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:98736133G>A	ENST00000477737.1	+	4	653	c.449G>A	c.(448-450)gGc>gAc	p.G150D	VWA3B_ENST00000451075.2_Intron|VWA3B_ENST00000435344.1_Missense_Mutation_p.G150D	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	150										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GATTTTGGCGGCATTCTGGAG	0.522																																					p.G150D													.	VWA3B-139	0			c.G449A						.						192	187	189					2																	98736133		1991	4149	6140	SO:0001583	missense	200403	exon4			TTGGCGGCATTCT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.449G>A	2.37:g.98736133G>A	ENSP00000417955:p.Gly150Asp	Somatic	319	0		WXS	Illumina HiSeq	Phase_I	388	7	NM_144992	0	0	0	0	0	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	1.464	-0.561569	0.03939	.	.	ENSG00000168658	ENST00000435344;ENST00000477737	T;T	0.35973	1.28;1.28	6.02	-3.25	0.05079	.	1.332560	0.04551	N	0.389819	T	0.19967	0.0480	N	0.17474	0.49	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.13407	0.009;0.002	T	0.17501	-1.0367	10	0.32370	T	0.25	.	4.4567	0.11647	0.553:0.1139:0.2439:0.0893	.	150;150	Q502W6;Q502W6-8	VWA3B_HUMAN;.	D	150	ENSP00000401959:G150D;ENSP00000417955:G150D	ENSP00000411168:G150D	G	+	2	0	VWA3B	98102565	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	0.140000	0.16056	-0.462000	0.06984	-0.150000	0.13652	GGC	G|0.999;C|0.001		0.522	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98736133	G	A	98736133	3	1	67	1	0	0	0	0	1	0	0	0	17274	1203	42	2	459	2	VWA3B	2	98736133	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	72532557	98736133	144463240	7	6400											
SMPD4	55627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	130931124	130931124	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcacgatgctgtactccaCaggattcacgcgcccctgta	9	9	8	15	3	2	0	2	0	0	0	3	2	3	1	3	1	2	3	3	1	2	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:130931124C>T	ENST00000409031.1	-	4	1497	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	SMPD4_ENST00000452225.2_Intron|SMPD4_ENST00000351288.6_Missense_Mutation_p.V117M|SMPD4_ENST00000453750.1_Intron|SMPD4_ENST00000431183.2_Intron|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000443958.2_Intron|SMPD4_ENST00000339679.7_Missense_Mutation_p.C29Y	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	78					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	CTGTACTCCACAGGATTCACG	0.542																																					p.V117M		.											.	SMPD4-90	0			c.G349A						.						59	54	56					2																	130931124		2203	4300	6503	SO:0001583	missense	55627	exon4			ACTCCACAGGATT	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.349G>A	2.37:g.130931124C>T	ENSP00000386531:p.Val117Met	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	50	7	NM_017751	0	0	24	33	9	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.864|0.864	-0.734336|-0.734336	0.03111|0.03111	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000339679|ENST00000351288;ENST00000409031;ENST00000441135	.|.	.|.	.|.	3.74|3.74	0.579|0.579	0.17397|0.17397	.|.	.|0.842482	.|0.10004	.|N	.|0.728107	T|T	0.30230|0.30230	0.0758|0.0758	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	1|1	B|B;B	0.02656|0.15719	0.0|0.014;0.007	B|B;B	0.01281|0.17098	0.0|0.017;0.008	T|T	0.27640|0.27640	-1.0068|-1.0068	8|9	0.22109|0.36615	T|T	0.4|0.2	.|.	3.3119|3.3119	0.07020|0.07020	0.0:0.4028:0.2084:0.3888|0.0:0.4028:0.2084:0.3888	.|.	29|78;117	B4E0T5|Q9NXE4;B1PBA3	.|NSMA3_HUMAN;.	Y|M	29|117;117;78	.|.	ENSP00000339721:C29Y|ENSP00000259217:V117M	C|V	-|-	2|1	0|0	SMPD4|SMPD4	130647594|130647594	0.367000|0.367000	0.25023|0.25023	0.045000|0.045000	0.18777|0.18777	0.188000|0.188000	0.23474|0.23474	1.298000|1.298000	0.33412|0.33412	0.248000|0.248000	0.21435|0.21435	0.455000|0.455000	0.32223|0.32223	TGT|GTG	.		0.542	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		T	130931124	C	T	130931124	3	4	67	1	0	0	0	0	1	0	0	0	14839	478	17	2	2319	2	SMPD4	2	130931124	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	32194991	130931124	112268249	8	6401											
THSD7B	80731	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	137852688	137852688	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agaacttctgcagcaatgtcCcaggtattacgcctttatgc	10	12	8	11	1	1	1	0	0	1	1	2	1	2	1	2	1	5	3	2	1	5	5			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:137852688C>T	ENST00000409968.1	+	4	1374	c.1196C>T	c.(1195-1197)cCc>cTc	p.P399L	THSD7B_ENST00000413152.2_Missense_Mutation_p.P368L|THSD7B_ENST00000272643.3_Missense_Mutation_p.P399L|THSD7B_ENST00000543459.1_Missense_Mutation_p.P258L			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	399	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CAGCAATGTCCCAGGTATTAC	0.418																																					.													.	THSD7B-75	0			.						.						74	82	79					2																	137852688		1962	4159	6121	SO:0001583	missense	80731	.			AATGTCCCAGGTA			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.1196C>T	2.37:g.137852688C>T	ENSP00000387145:p.Pro399Leu	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	70	7	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	18.53	3.644315	0.67244	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152;ENST00000543459	T;T;T;T	0.60040	0.22;0.22;0.22;1.83	5.84	4.96	0.65561	.	0.047672	0.85682	D	0.000000	T	0.68769	0.3037	M	0.63843	1.955	0.80722	D	1	D;P	0.55385	0.971;0.929	P;P	0.57468	0.821;0.821	T	0.68307	-0.5443	10	0.35671	T	0.21	.	15.9247	0.79606	0.1365:0.8635:0.0:0.0	.	399;368	Q9C0I4;C9JKN6	THS7B_HUMAN;.	L	399;399;368;258	ENSP00000387145:P399L;ENSP00000272643:P399L;ENSP00000413841:P368L;ENSP00000443370:P258L	ENSP00000272643:P399L	P	+	2	0	THSD7B	137569158	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	5.698000	0.68302	1.446000	0.47643	0.650000	0.86243	CCC	.		0.418	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		T	137852688	C	T	137852688	3	4	67	1	0	0	0	0	1	0	0	0	15912	623	22	2	1113	2	THSD7B	2	137852688	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	6921564	137852688	105346685	9	6402											
PER2	8864	hgsc.bcm.edu	37	chr2	239162113	239162113	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcagtgaataagctgctgGcactggggcgggaaagggca	10	5	19	7	1	0	1	0	1	0	0	0	2	0	2	0	6	2	5	0	6	3	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:239162113G>C	ENST00000254657.3	-	19	2830	c.2551C>G	c.(2551-2553)Cca>Gca	p.P851A	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	851	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TAAGCTGCTGGCACTGGGGCG	0.692																																					p.P851A		.											.	PER2-154	0			c.C2551G						.						22	22	22					2																	239162113		2203	4300	6503	SO:0001583	missense	8864	exon19			CTGCTGGCACTGG	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2551C>G	2.37:g.239162113G>C	ENSP00000254657:p.Pro851Ala	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_022817	0	0	9	9	0	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	G	6.080	0.383145	0.11524	.	.	ENSG00000132326	ENST00000254657	T	0.12147	2.71	3.66	2.77	0.32553	.	0.344461	0.21397	U	0.075216	T	0.16041	0.0386	M	0.76574	2.34	0.80722	D	1	B;B	0.14012	0.009;0.009	B;B	0.12156	0.007;0.007	T	0.03175	-1.1064	10	0.27082	T	0.32	-5.6874	9.3435	0.38093	0.1134:0.0:0.8866:0.0	.	851;851	B4DH14;O15055	.;PER2_HUMAN	A	851	ENSP00000254657:P851A	ENSP00000254657:P851A	P	-	1	0	PER2	238826852	1.000000	0.71417	0.174000	0.22961	0.062000	0.15995	4.714000	0.61902	0.829000	0.34733	0.491000	0.48974	CCA	.		0.692	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		C	239162113	G	C	239162113	3	2	67	1	0	0	0	0	1	0	0	0	11756	1203	42	4	1236	4	PER2	2	239162113	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	101309425	239162113	4037260	10	6403											
ENTPD3	956	hgsc.bcm.edu;broad.mit.edu	37	chr3	40465427	40465427	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacaaattcacagaggagacTtggccccaaatacactttga	15	9	7	10	0	1	3	1	1	0	2	1	4	1	3	2	2	2	0	2	2	4	5			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr3:40465427T>A	ENST00000301825.3	+	10	1444	c.1326T>A	c.(1324-1326)acT>acA	p.T442T	ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3_ENST00000445129.1_Silent_p.T442T|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3_ENST00000456402.1_Silent_p.T442T	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	442					nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		CAGAGGAGACTTGGCCCCAAA	0.408																																					p.T442T		.											.	ENTPD3-91	0			c.T1326A						.						118	109	112					3																	40465427		2203	4300	6503	SO:0001819	synonymous_variant	956	exon10			GGAGACTTGGCCC	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.1326T>A	3.37:g.40465427T>A		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	179	9	NM_001248	0	0	1	1	0	B2R8D0|G5E9N0|O60495|Q8N6K2	Silent	SNP	ENST00000301825.3	37	CCDS2691.1																																																																																			.		0.408	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248		A	40465427	T	A	40465427	2	1	67	1	0	0	0	0	0	0	0	1	5153	1596	56	5		5	ENTPD3	3	40465427	Silent	SNP	T	TCGA-BQ-5883-01A-11D-1589-08		40465427	157557003	11	6404											
LTF	4057	broad.mit.edu	37	chr3	46492033	46492033	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatcctccttgccattcacActtcgtgccacaacggcatg	8	10	7	16	2	1	0	1	0	0	0	4	0	3	0	4	1	3	2	4	1	1	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr3:46492033A>G	ENST00000231751.4	-	7	1129	c.834T>C	c.(832-834)agT>agC	p.S278S	LTF_ENST00000417439.1_Silent_p.S278S|LTF_ENST00000426532.2_Silent_p.S234S	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	278	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		TGCCATTCACACTTCGTGCCA	0.567																																					p.S278S													.	LTF-703	0			c.T834C						.						99	86	90					3																	46492033		2203	4296	6499	SO:0001819	synonymous_variant	4057	exon7			ATTCACACTTCGT		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.834T>C	3.37:g.46492033A>G		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	77	5	NM_002343	0	0	57	63	6	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			.		0.567	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		G	46492033	A	G	46492033	2	3	67	1	0	0	0	0	0	0	0	1	9104	156	6	3		3	LTF	3	46492033	Silent	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	6026606	46492033	151530397	12	6405											
ZIC4	84107	hgsc.bcm.edu	37	chr3	147109013	147109013	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctcgcagccctcgaactCgcatctgaagggcttctcgc	6	8	10	17	5	2	1	0	1	2	0	6	2	2	1	2	1	2	4	2	1	2	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr3:147109013C>A	ENST00000383075.3	-	4	1221	c.709G>T	c.(709-711)Gag>Tag	p.E237*	ZIC4_ENST00000473123.1_Nonsense_Mutation_p.E237*|ZIC4_ENST00000425731.3_Nonsense_Mutation_p.E275*|ZIC4_ENST00000525172.2_Nonsense_Mutation_p.E287*|ZIC4_ENST00000472749.2_5'UTR|ZIC4_ENST00000491672.1_Nonsense_Mutation_p.E31*|ZIC4_ENST00000484399.1_Nonsense_Mutation_p.E237*	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	237						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						CCCTCGAACTCGCATCTGAAG	0.617																																					p.E287X		.											.	ZIC4-91	0			c.G859T						.						26	28	28					3																	147109013		2202	4299	6501	SO:0001587	stop_gained	84107	exon4			CGAACTCGCATCT	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"Zinc fingers, C2H2-type"	20393	protein-coding gene	gene with protein product		608948	"zinc finger protein of the cerebellum 4"				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.709G>T	3.37:g.147109013C>A	ENSP00000372553:p.Glu237*	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_001168378	0	0	0	0	0	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Nonsense_Mutation	SNP	ENST00000383075.3	37	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	37	6.016150	0.97205	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000491672	.	.	.	4.83	4.83	0.62350	.	0.000000	0.46758	D	0.000280	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.2835	0.90105	0.0:1.0:0.0:0.0	.	.	.	.	X	237;275;287;237;237;31	.	ENSP00000372553:E237X	E	-	1	0	ZIC4	148591703	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.901000	0.69861	2.381000	0.81170	0.462000	0.41574	GAG	.		0.617	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1			A	147109013	C	A	147109013	4	1	67	1	0	0	0	0	0	1	0	0	17713	893	31	4	303	4	ZIC4	3	147109013	Nonsense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	100616980	147109013	50913417	13	6406											
IDUA	3425	hgsc.bcm.edu	37	chr4	980971	980971	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccccgcacctggtgcaTgtggacgcggcccgcgcgct	4	5	16	16	6	0	0	0	0	0	0	0	2	0	1	4	4	1	3	4	4	0	0	rs10794537	byFrequency	TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr4:980971T>G	ENST00000247933.4	+	1	187	c.99T>G	c.(97-99)caT>caG	p.H33Q	IDUA_ENST00000453894.1_Missense_Mutation_p.H33Q|SLC26A1_ENST00000398520.2_Intron	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	33			H -> Q (in dbSNP:rs10794537). {ECO:0000269|PubMed:1362562, ECO:0000269|PubMed:1505961, ECO:0000269|PubMed:1946389, ECO:0000269|PubMed:21394825}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			ACCTGGTGCATGTGGACGCGG	0.801													G|||	4467	0.891973	0.9826	0.8386	5008	,	,		8604	0.8472		0.8042	False		,,,				2504	0.9438				p.H33Q		.											.	IDUA-91	0			c.T99G						.						1	1	1					4																	980971		552	1375	1927	SO:0001583	missense	3425	exon1			GGTGCATGTGGAC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.99T>G	4.37:g.980971T>G	ENSP00000247933:p.His33Gln	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_000203	0	0	0	11	11	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	1801|1801	0.8246336996336996|0.8246336996336996	464|464	0.943089430894309|0.943089430894309	294|294	0.8121546961325967|0.8121546961325967	448|448	0.7832167832167832|0.7832167832167832	595|595	0.7849604221635884|0.7849604221635884	G|G	3.726|3.726	-0.056533|-0.056533	0.07362|0.07362	.|.	.|.	ENSG00000127415|ENSG00000127415	ENST00000504568|ENST00000247933;ENST00000453894;ENST00000502910	.|D;D;D	.|0.93247	.|-3.18;-3.19;-3.03	3.62|3.62	-0.897|-0.897	0.10553|0.10553	.|.	.|0.728933	.|0.12190	.|N	.|0.491278	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.36817|0.36817	-0.9732|-0.9732	4|9	.|0.10111	.|T	.|0.7	.|.	1.2904|1.2904	0.02059|0.02059	0.1461:0.2669:0.3485:0.2385|0.1461:0.2669:0.3485:0.2385	rs10794537|rs10794537	.|33;33	.|B3KWK6;P35475	.|.;IDUA_HUMAN	G|Q	33|33	.|ENSP00000247933:H33Q;ENSP00000396458:H33Q;ENSP00000422952:H33Q	.|ENSP00000247933:H33Q	C|H	+|+	1|3	0|2	IDUA|IDUA	970971|970971	0.000000|0.000000	0.05858|0.05858	0.992000|0.992000	0.48379|0.48379	0.012000|0.012000	0.07955|0.07955	-2.547000|-2.547000	0.00931|0.00931	-0.253000|-0.253000	0.09514|0.09514	-1.482000|-1.482000	0.00985|0.00985	TGT|CAT	T|0.175;G|0.825		0.801	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203		G	980971	T	G	980971	3	3	67	1	0	0	0	0	1	0	0	0	7525	1461	51	5	101	5	IDUA	4	980971	Missense_Mutation	SNP	T	TCGA-BQ-5883-01A-11D-1589-08		980971	190173305	14	6407											
CENPC1	1060	hgsc.bcm.edu	37	chr4	68338326	68338326	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaggttggttgatctttcaTctttttatctgagtaaaaag	11	18	8	4	0	4	2	1	2	3	0	4	2	4	2	0	2	0	3	0	2	5	8			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr4:68338326T>A	ENST00000273853.6	-	19	3079	c.2829A>T	c.(2827-2829)agA>agT	p.R943S		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	943	MIF2 homology domain III.				chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										TGATCTTTCATCTTTTTATCT	0.249																																					p.R943S		.											.	CENPC1-205	0			c.A2829T						.						25	23	24					4																	68338326		1675	3879	5554	SO:0001583	missense	1060	exon19			CTTTCATCTTTTT	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.2829A>T	4.37:g.68338326T>A	ENSP00000273853:p.Arg943Ser	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	9	8	NM_001812	0	0	1	2	1	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	37	CCDS47063.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126153	0.56721	.	.	ENSG00000145241	ENST00000273853	.	.	.	3.59	-2.03	0.07365	.	0.474882	0.18938	N	0.127023	T	0.15478	0.0373	N	0.12182	0.205	0.27738	N	0.944564	B	0.19445	0.036	B	0.12837	0.008	T	0.07693	-1.0759	9	0.72032	D	0.01	.	3.7757	0.08659	0.5677:0.1197:0.0:0.3126	.	943	Q03188	CENPC_HUMAN	S	943	.	ENSP00000273853:R943S	R	-	3	2	CENPC1	68020921	0.998000	0.40836	0.995000	0.50966	0.790000	0.44656	0.133000	0.15912	-0.350000	0.08262	0.402000	0.26972	AGA	.		0.249	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			A	68338326	T	A	68338326	3	1	67	1	0	0	0	0	1	0	0	0	3235	1432	50	5	6	5	CENPC1	4	68338326	Missense_Mutation	SNP	T	TCGA-BQ-5883-01A-11D-1589-08	67357355	68338326	122815950	15	6408											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	123264653	123264653	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcagtagttcatctggCttgagcttcactgcatgcat	8	13	9	11	0	3	1	2	1	1	0	4	1	4	1	1	1	4	7	1	1	1	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr4:123264653C>G	ENST00000264501.4	+	73	12814	c.12441C>G	c.(12439-12441)ggC>ggG	p.G4147G	KIAA1109_ENST00000388738.3_Silent_p.G4147G			Q2LD37	K1109_HUMAN	KIAA1109	4147	Ser-rich.				regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTTCATCTGGCTTGAGCTTCA	0.478																																					p.G4147G		.											.	KIAA1109-80	0			c.C12441G						.						121	111	114					4																	123264653		1972	4163	6135	SO:0001819	synonymous_variant	84162	exon71			ATCTGGCTTGAGC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12441C>G	4.37:g.123264653C>G		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	91	7	NM_015312	0	0	25	27	2	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.957|8.957	0.969706|0.969706	0.18659|0.18659	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000442707	.|.	.|.	.|.	5.78|5.78	-3.62|-3.62	0.04543|0.04543	.|.	.|.	.|.	.|.	.|.	T|T	0.40767|0.40767	0.1130|0.1130	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.37337|0.37337	-0.9710|-0.9710	4|4	.|.	.|.	.|.	.|.	4.0748|4.0748	0.09899|0.09899	0.0995:0.2869:0.4148:0.1987|0.0995:0.2869:0.4148:0.1987	.|.	.|.	.|.	.|.	G|V	523|93	.|.	.|.	A|L	+|+	2|1	0|0	KIAA1109|KIAA1109	123484103|123484103	0.019000|0.019000	0.18553|0.18553	0.092000|0.092000	0.20876|0.20876	0.981000|0.981000	0.71138|0.71138	-0.715000|-0.715000	0.04997|0.04997	-0.295000|-0.295000	0.08960|0.08960	0.591000|0.591000	0.81541|0.81541	GCT|CTT	.		0.478	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123264653	C	G	123264653	2	3	67	1	0	0	0	0	0	0	0	1	8229	784	28	4		4	KIAA1109	4	123264653	Silent	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	54926327	123264653	67889623	16	6409											
TPPP	11076	hgsc.bcm.edu	37	chr5	678087	678087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccgattccagcgacagcCtcttggctgcccggtccttc	4	10	9	18	3	1	0	0	0	1	0	5	2	4	0	6	2	3	1	6	2	0	3	rs570878136	byFrequency	TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr5:678087C>T	ENST00000360578.5	-	2	210	c.89G>A	c.(88-90)aGg>aAg	p.R30K	CTD-2589H19.6_ENST00000607068.1_RNA	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	30	Mediates interaction with LIMK1.				microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.R30K(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CAGCGACAGCCTCTTGGCTGC	0.677													C|||	15	0.00299521	0.0061	0	5008	,	,		16462	0.0069		0	False		,,,				2504	0				p.R30K		.											.	TPPP-90	1	Substitution - Missense(1)	prostate(1)	c.G89A						.						14	17	16					5																	678087		2199	4295	6494	SO:0001583	missense	11076	exon2			GACAGCCTCTTGG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"brain specific protein p25 alpha"	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.89G>A	5.37:g.678087C>T	ENSP00000353785:p.Arg30Lys	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_007030	0	0	4	4	0		Missense_Mutation	SNP	ENST00000360578.5	37	CCDS3856.1	.	.	.	.	.	.	.	.	.	.	c	14.67	2.605282	0.46423	.	.	ENSG00000171368	ENST00000360578	T	0.45276	0.9	5.23	5.23	0.72850	.	0.149935	0.44902	D	0.000407	T	0.29588	0.0738	L	0.29908	0.895	0.44635	D	0.997618	B	0.15141	0.012	B	0.13407	0.009	T	0.11867	-1.0570	10	0.05436	T	0.98	-54.1656	16.5545	0.84482	0.0:1.0:0.0:0.0	.	30	O94811	TPPP_HUMAN	K	30	ENSP00000353785:R30K	ENSP00000353785:R30K	R	-	2	0	TPPP	731087	1.000000	0.71417	0.998000	0.56505	0.405000	0.30901	4.081000	0.57627	2.437000	0.82529	0.491000	0.48974	AGG	.		0.677	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030		T	678087	C	T	678087	3	4	67	1	0	0	0	0	1	0	0	0	16446	681	24	2	582	2	TPPP	5	678087	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		678087	180237173	17	6410											
MAST4	375449	broad.mit.edu	37	chr5	66432487	66432487	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaatcccctggagaggctggGaacaggttagagcccatgtg	10	7	15	9	0	0	2	0	0	0	2	1	5	1	3	3	4	2	2	3	4	3	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr5:66432487G>A	ENST00000403625.2	+	19	2784	c.2489G>A	c.(2488-2490)gGa>gAa	p.G830E	MAST4_ENST00000403666.1_Missense_Mutation_p.G641E|MAST4_ENST00000261569.7_Missense_Mutation_p.G636E|MAST4_ENST00000404260.3_Missense_Mutation_p.G833E|MAST4_ENST00000405643.1_Missense_Mutation_p.G651E	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	833	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GAGAGGCTGGGAACAGGTTAG	0.453																																					p.G830E													.	MAST4-647	0			c.G2489A						.						43	42	42					5																	66432487		1851	4099	5950	SO:0001583	missense	375449	exon19			GGCTGGGAACAGG	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2489G>A	5.37:g.66432487G>A	ENSP00000385727:p.Gly830Glu	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	16	3	NM_001164664	0	0	0	0	0	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	34	5.313789	0.95655	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8	5.81	5.81	0.92471	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64875	0.2638	M	0.93808	3.46	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.998	T	0.73649	-0.3916	10	0.87932	D	0	-20.4931	20.0784	0.97758	0.0:0.0:1.0:0.0	.	651;833;636;641	E7EWQ5;O15021;O15021-2;O15021-3	.;MAST4_HUMAN;.;.	E	833;830;641;651;651;636;636	ENSP00000385048:G833E;ENSP00000385727:G830E;ENSP00000384313:G641E;ENSP00000384099:G651E;ENSP00000261569:G636E	ENSP00000261569:G636E	G	+	2	0	MAST4	66468243	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.756000	0.98918	2.736000	0.93811	0.655000	0.94253	GGA	.		0.453	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66432487	G	A	66432487	3	1	67	1	0	0	0	0	1	0	0	0	9352	1174	41	2	2693	2	MAST4	5	66432487	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	65754400	66432487	114482773	18	6411											
GPR98	84059	broad.mit.edu	37	chr5	90136585	90136585	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccagattgtcctttttgAcccaaaaggtggtgccagaa	10	12	9	10	0	0	3	0	1	0	2	2	3	2	3	4	2	1	0	4	2	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr5:90136585A>G	ENST00000405460.2	+	78	16898	c.16802A>G	c.(16801-16803)gAc>gGc	p.D5601G	GPR98_ENST00000425867.2_Missense_Mutation_p.D1262G	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5601					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTCCTTTTTGACCCAAAAGGT	0.458																																					p.D5601G													.	GPR98-103	0			c.A16802G						.						149	145	146					5																	90136585		1880	4129	6009	SO:0001583	missense	84059	exon78			TTTTTGACCCAAA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.16802A>G	5.37:g.90136585A>G	ENSP00000384582:p.Asp5601Gly	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	220	3	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.449278	0.43531	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.27557	1.66;1.66	6.16	3.76	0.43208	.	0.279017	0.45606	N	0.000341	T	0.26085	0.0636	M	0.62723	1.935	0.37331	D	0.909999	P;B;P	0.40794	0.61;0.003;0.729	B;B;B	0.35770	0.104;0.002;0.21	T	0.12811	-1.0533	9	.	.	.	.	6.9375	0.24474	0.7429:0.1272:0.1299:0.0	.	1262;5601;1262	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	G	5601;5601;1262	ENSP00000384582:D5601G;ENSP00000392618:D1262G	.	D	+	2	0	GPR98	90172341	0.984000	0.35163	0.988000	0.46212	0.993000	0.82548	1.951000	0.40333	0.548000	0.28955	0.528000	0.53228	GAC	.		0.458	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90136585	A	G	90136585	3	3	67	1	0	0	0	0	1	0	0	0	6742	275	10	3	17112	3	GPR98	5	90136585	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	23704098	90136585	90778675	19	6412											
PCDHA9	9752	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140229899	140229899	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcgggctacaacgcgtggCtttcatacgagctgcagcca	9	8	11	13	4	1	0	1	0	0	0	2	1	1	0	1	2	6	4	1	2	3	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr5:140229899C>T	ENST00000532602.1	+	1	2852	c.1819C>T	c.(1819-1821)Ctt>Ttt	p.L607F	PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.L607F	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	607	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAACGCGTGGCTTTCATACGA	0.672																																					p.L607F	Melanoma(55;1800 1972 14909)	.											.	PCDHA9-138	0			c.C1819T						.						64	70	68					5																	140229899		2196	4268	6464	SO:0001583	missense	9752	exon1			GCGTGGCTTTCAT	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1819C>T	5.37:g.140229899C>T	ENSP00000436042:p.Leu607Phe	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	110	9	NM_031857	0	0	1	1	0	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518012	0.44763	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53640	0.61;0.61	3.36	3.36	0.38483	Cadherin (4);Cadherin-like (1);	0.000000	0.26156	U	0.026019	T	0.70544	0.3236	M	0.89478	3.035	0.28601	N	0.909177	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.66756	-0.5843	10	0.87932	D	0	.	11.3375	0.49513	0.0:0.8154:0.1846:0.0	.	607;607	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	F	607	ENSP00000436042:L607F;ENSP00000367362:L607F	ENSP00000367362:L607F	L	+	1	0	PCDHA9	140210083	0.962000	0.33011	1.000000	0.80357	0.276000	0.26787	0.080000	0.14802	1.839000	0.53478	0.313000	0.20887	CTT	.		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140229899	C	T	140229899	3	4	67	1	0	0	0	0	1	0	0	0	11557	797	28	2	1821	2	PCDHA9	5	140229899	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	50093314	140229899	40685361	20	6413											
MICB	4277	broad.mit.edu	37	chr6	31473399	31473399	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcctcttccccagagcccCacagtcttcgttacaacctc	7	12	4	18	1	2	1	0	0	2	1	6	1	4	1	6	0	3	1	6	0	2	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr6:31473399C>T	ENST00000252229.6	+	2	155	c.76C>T	c.(76-78)Cac>Tac	p.H26Y	MICB_ENST00000538442.1_5'UTR|MICB_ENST00000399150.3_Missense_Mutation_p.H26Y	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CCCAGAGCCCCACAGTCTTCG	0.522																																					p.H26Y													.	MICB-90	0			c.C76T						.						80	82	81					6																	31473399		1254	2547	3801	SO:0001583	missense	4277	exon2			GAGCCCCACAGTC		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"Immunoglobulin superfamily / C1-set domain containing"	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.76C>T	6.37:g.31473399C>T	ENSP00000252229:p.His26Tyr	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	88	3	NM_005931	0	0	0	0	0		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	.	.	.	.	.	.	.	.	.	.	N	12.80	2.046132	0.36085	.	.	ENSG00000204516	ENST00000399150;ENST00000252229	T;T	0.10099	2.91;2.91	2.68	1.79	0.24919	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.416002	0.17505	U	0.171837	T	0.22044	0.0531	M	0.92923	3.36	0.09310	N	0.999995	D;D	0.89917	0.998;1.0	D;D	0.87578	0.997;0.998	T	0.04281	-1.0963	10	0.87932	D	0	.	5.4307	0.16452	0.0:0.8319:0.0:0.168	.	26;26	A2AC57;Q29980	.;MICB_HUMAN	Y	26	ENSP00000382103:H26Y;ENSP00000252229:H26Y	ENSP00000252229:H26Y	H	+	1	0	MICB	31581378	0.001000	0.12720	0.001000	0.08648	0.053000	0.15095	1.117000	0.31234	0.462000	0.27095	0.305000	0.20034	CAC	.		0.522	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931		T	31473399	C	T	31473399	3	4	67	1	0	0	0	0	1	0	0	0	9600	594	21	2	82	2	MICB	6	31473399	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		31473399	139641668	21	6414											
SAMD9L	219285	broad.mit.edu;bcgsc.ca	37	chr7	92763422	92763422	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtcaccgattttagtttaagGatagtgctgtttaccagttc	9	16	9	7	1	1	0	1	0	0	0	2	2	1	1	2	1	2	4	2	1	4	8			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr7:92763422G>A	ENST00000318238.4	-	5	3079	c.1863C>T	c.(1861-1863)atC>atT	p.I621I	SAMD9L_ENST00000437805.1_Silent_p.I621I|SAMD9L_ENST00000411955.1_Silent_p.I621I	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	621					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTAGTTTAAGGATAGTGCTGT	0.383																																					p.I621I													.	SAMD9L-94	0			c.C1863T						.						102	104	104					7																	92763422		2203	4300	6503	SO:0001819	synonymous_variant	219285	exon5			TTTAAGGATAGTG	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1863C>T	7.37:g.92763422G>A		Somatic	268	0		WXS	Illumina HiSeq	Phase_I	314	10	NM_152703	0	0	4	4	0	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Silent	SNP	ENST00000318238.4	37	CCDS34681.1																																																																																			.		0.383	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		A	92763422	G	A	92763422	2	1	67	1	0	0	0	0	0	0	0	1	13859	1164	41	2		2	SAMD9L	7	92763422	Silent	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		92763422	66375241	22	6415											
CFTR	1080	broad.mit.edu	37	chr7	117235098	117235098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgctaatttggtgcttagtaAtttttctggcagaggtaaga	10	16	11	4	0	1	2	0	0	1	2	1	2	1	2	0	3	2	5	0	3	4	7			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr7:117235098A>G	ENST00000003084.6	+	15	2737	c.2605A>G	c.(2605-2607)Att>Gtt	p.I869V	CFTR_ENST00000454343.1_Missense_Mutation_p.I808V	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	869	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GTGCTTAGTAATTTTTCTGGC	0.333									Cystic Fibrosis																												p.I869V													.	CFTR-518	0			c.A2605G						.						123	115	118					7																	117235098		2203	4300	6503	SO:0001583	missense	1080	exon15	Familial Cancer Database	CF	TTAGTAATTTTTC	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2605A>G	7.37:g.117235098A>G	ENSP00000003084:p.Ile869Val	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	133	4	NM_000492	0	0	21	25	4	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	A	4.036	0.004297	0.07866	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.94537	-3.45;-3.45;-3.45	5.58	-7.53	0.01336	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.336013	0.35436	N	0.003211	D	0.85557	0.5724	N	0.21373	0.66	0.21105	N	0.999783	B	0.06786	0.001	B	0.12156	0.007	T	0.66838	-0.5822	10	0.07813	T	0.8	-3.3811	16.9272	0.86179	0.4584:0.0:0.5416:0.0	.	869	P13569	CFTR_HUMAN	V	869;808;839	ENSP00000003084:I869V;ENSP00000403677:I808V;ENSP00000389119:I839V	ENSP00000003084:I869V	I	+	1	0	CFTR	117022334	0.001000	0.12720	0.001000	0.08648	0.622000	0.37654	-0.007000	0.12810	-1.600000	0.01603	0.482000	0.46254	ATT	.		0.333	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		G	117235098	A	G	117235098	3	3	67	1	0	0	0	0	1	0	0	0	3300	101	4	3	2663	3	CFTR	7	117235098	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	24471676	117235098	41903565	23	6416											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150763663	150763663	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggccagtggcactgcaggggGtgacgacgggggtgcctcgg	5	5	21	10	3	0	1	0	1	0	0	1	2	0	1	2	7	2	2	2	7	0	0	rs201747636	byFrequency	TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr7:150763663G>C	ENST00000485713.1	+	6	1678	c.638G>C	c.(637-639)gGt>gCt	p.G213A	SLC4A2_ENST00000310317.5_Missense_Mutation_p.G131A|SLC4A2_ENST00000392826.2_Missense_Mutation_p.G204A|SLC4A2_ENST00000413384.2_Missense_Mutation_p.G213A|SLC4A2_ENST00000461735.1_Missense_Mutation_p.G199A	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	213	Pro-rich.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACTGCAGGGGGTGACGACGGG	0.697													G|||	10	0.00199681	0.0076	0	5008	,	,		13416	0		0	False		,,,				2504	0				p.G213A		.											.	SLC4A2-90	0			c.G638C						.						7	8	8					7																	150763663		1967	3832	5799	SO:0001583	missense	6522	exon6			CAGGGGGTGACGA		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.638G>C	7.37:g.150763663G>C	ENSP00000419412:p.Gly213Ala	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_003040	0	0	0	18	18	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	4.212	0.038073	0.08148	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.74842	-0.86;-0.86;-0.88;-0.85;-0.85	5.01	5.01	0.66863	.	0.393001	0.25777	N	0.028380	T	0.53222	0.1783	N	0.12182	0.205	0.25695	N	0.985641	P;P;P	0.45044	0.849;0.849;0.765	B;B;B	0.39465	0.3;0.3;0.157	T	0.48647	-0.9017	10	0.08837	T	0.75	.	13.7564	0.62940	0.0:0.0:1.0:0.0	.	204;199;213	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	A	213;213;131;204;199	ENSP00000419412:G213A;ENSP00000405600:G213A;ENSP00000311402:G131A;ENSP00000376571:G204A;ENSP00000419164:G199A	ENSP00000311402:G131A	G	+	2	0	SLC4A2	150394596	0.735000	0.28153	0.465000	0.27155	0.473000	0.32948	0.923000	0.28757	2.615000	0.88500	0.558000	0.71614	GGT	.		0.697	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		C	150763663	G	C	150763663	3	2	67	1	0	0	0	0	1	0	0	0	14686	1261	44	4	656	4	SLC4A2	7	150763663	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	33528565	150763663	8375000	24	6417											
ADCY8	114	broad.mit.edu;bcgsc.ca	37	chr8	131916171	131916174	+	Frame_Shift_Del	DEL	TAAG	TAAG	-																															ctgtcctcaggctgcttaatTaagtaagtttcgatattatg																										TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	TAAG	TAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr8:131916171_131916174delTAAG	ENST00000286355.5	-	7	3847_3850	c.1755_1758delCTTA	c.(1753-1758)tacttafs	p.YL585fs	ADCY8_ENST00000377928.3_Frame_Shift_Del_p.YL585fs	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	585					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCTGCTTAATTAAGTAAGTTTCGA	0.49										HNSCC(32;0.087)																											p.585_586del													.	ADCY8-157	0			c.1755_1758del						.																																			SO:0001589	frameshift_variant	114	exon7			CTTAATTAAGTAA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1755_1758delCTTA	8.37:g.131916175_131916178delTAAG	ENSP00000286355:p.Tyr585fs	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	205	22	NM_001115	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000286355.5	37	CCDS6363.1																																																																																			.		0.49	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			-	131916174	TAAG	-	131916171	7	5	67	1	0	1	0	1	0	0	0	0	300	1751	61	0	2045	0	ADCY8	8	131916171	Frame_Shift_Del	DEL	TAAG	TCGA-BQ-5883-01A-11D-1589-08		131916171	14447851	25	6418											
TMEM2	23670	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	74300679	74300679	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtcataaagatgagctGgtttggctaatcccagaggt	10	13	11	7	0	1	3	1	1	0	2	2	3	2	3	1	3	1	3	1	3	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr9:74300679G>C	ENST00000377044.4	-	23	4474	c.3935C>G	c.(3934-3936)cCa>cGa	p.P1312R	TMEM2_ENST00000377066.5_Missense_Mutation_p.P1249R|TMEM2_ENST00000396272.3_Missense_Mutation_p.P305R	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1312					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AAGATGAGCTGGTTTGGCTAA	0.373																																					p.P1312R		.											.	TMEM2-92	0			c.C3935G						.						115	107	110					9																	74300679		2203	4300	6503	SO:0001583	missense	23670	exon23			TGAGCTGGTTTGG		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.3935C>G	9.37:g.74300679G>C	ENSP00000366243:p.Pro1312Arg	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	106	8	NM_013390	0	0	30	32	2	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553987	0.65425	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272	T;T;T	0.73469	-0.75;-0.68;2.49	5.78	5.78	0.91487	.	0.109175	0.64402	D	0.000005	T	0.78842	0.4347	M	0.61703	1.905	0.48087	D	0.999587	P;P	0.47604	0.836;0.898	B;P	0.47299	0.342;0.543	T	0.79548	-0.1758	10	0.52906	T	0.07	.	19.6126	0.95616	0.0:0.0:1.0:0.0	.	1312;1249	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	R	1312;1249;305	ENSP00000366243:P1312R;ENSP00000366266:P1249R;ENSP00000379569:P305R	ENSP00000366243:P1312R	P	-	2	0	TMEM2	73490499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.685000	0.74543	2.730000	0.93505	0.650000	0.86243	CCA	.		0.373	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		C	74300679	G	C	74300679	3	2	67	1	0	0	0	0	1	0	0	0	16153	1348	47	4	224	4	TMEM2	9	74300679	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		74300679	66912752	26	6419											
CORO2A	7464	broad.mit.edu	37	chr9	100899870	100899870	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcactgtggcatcttcagaaCaggaggcgatctcaaaatca	13	9	9	10	1	5	1	4	0	2	1	6	3	5	2	0	3	1	1	0	3	3	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr9:100899870C>A	ENST00000343933.5	-	3	559	c.302G>T	c.(301-303)tGt>tTt	p.C101F	CORO2A_ENST00000375077.4_Missense_Mutation_p.C101F	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	101					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				ATCTTCAGAACAGGAGGCGAT	0.542																																					p.C101F													.	CORO2A-230	0			c.G302T						.						134	132	133					9																	100899870		2203	4300	6503	SO:0001583	missense	7464	exon3			TCAGAACAGGAGG	U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"Coronins", "WD repeat domain containing"	2255	protein-coding gene	gene with protein product	"coronin 2A", "coronin-like protein B", "WD protein IR10", "WD-repeat protein 2"	602159	"coronin, actin-binding protein, 2A"			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.302G>T	9.37:g.100899870C>A	ENSP00000343746:p.Cys101Phe	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	222	4	NM_003389	0	0	13	13	0	Q5TBR5|Q92829|Q9BWS5	Missense_Mutation	SNP	ENST00000343933.5	37	CCDS6735.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.418670	0.62622	.	.	ENSG00000106789	ENST00000343933;ENST00000375077	T;T	0.61274	0.12;0.12	4.58	3.67	0.42095	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.092083	0.85682	D	0.000000	T	0.73659	0.3615	M	0.76574	2.34	0.80722	D	1	P	0.52577	0.954	D	0.67900	0.954	T	0.77550	-0.2546	10	0.72032	D	0.01	-0.9345	13.889	0.63726	0.0:0.8456:0.1544:0.0	.	101	Q92828	COR2A_HUMAN	F	101	ENSP00000343746:C101F;ENSP00000364218:C101F	ENSP00000343746:C101F	C	-	2	0	CORO2A	99939691	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	5.740000	0.68629	1.254000	0.44035	0.561000	0.74099	TGT	.		0.542	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389		A	100899870	C	A	100899870	3	1	67	1	0	0	0	0	1	0	0	0	3762	478	17	4	1315	4	CORO2A	9	100899870	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	26599191	100899870	40313561	27	6420											
TDRD1	56165	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	115978231	115978231	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaccaaatggacatgttaaAgtacattttgtggattatgg	13	15	9	4	0	0	0	0	0	0	0	0	2	0	2	1	3	2	2	1	3	6	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr10:115978231A>T	ENST00000369280.1	+	18	2842	c.2382A>T	c.(2380-2382)aaA>aaT	p.K794N	TDRD1_ENST00000251864.2_Missense_Mutation_p.K794N|TDRD1_ENST00000369281.2_Intron|TDRD1_ENST00000369282.1_Missense_Mutation_p.K794N|TDRD1_ENST00000422662.1_Missense_Mutation_p.K398N			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	794	Tudor 3. {ECO:0000255|PROSITE- ProRule:PRU00211}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		GACATGTTAAAGTACATTTTG	0.373																																					p.K794N		.											.	TDRD1-90	0			c.A2382T						.						202	183	190					10																	115978231		2203	4300	6503	SO:0001583	missense	56165	exon18			TGTTAAAGTACAT	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.2382A>T	10.37:g.115978231A>T	ENSP00000358286:p.Lys794Asn	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	195	13	NM_198795	0	0	0	0	0	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	37		.	.	.	.	.	.	.	.	.	.	A	16.91	3.252942	0.59212	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000422662;ENST00000369280	T;T;T;T	0.10192	2.9;2.9;2.9;2.9	5.93	4.8	0.61643	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.542996	0.21329	N	0.076323	T	0.28466	0.0704	M	0.63843	1.955	0.38193	D	0.939969	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.95;0.998;0.999	T	0.03981	-1.0987	10	0.62326	D	0.03	-24.3657	10.4344	0.44426	0.9269:0.0:0.0731:0.0	.	398;794;794	Q9BXT4-4;Q9BXT4;Q9BXT4-3	.;TDRD1_HUMAN;.	N	794;794;398;794	ENSP00000358288:K794N;ENSP00000251864:K794N;ENSP00000402794:K398N;ENSP00000358286:K794N	ENSP00000251864:K794N	K	+	3	2	TDRD1	115968221	0.923000	0.31300	0.942000	0.38095	0.647000	0.38526	1.723000	0.38053	1.082000	0.41137	0.533000	0.62120	AAA	.		0.373	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			T	115978231	A	T	115978231	3	4	67	1	0	0	0	0	1	0	0	0	15762	69	3	5	2448	5	TDRD1	10	115978231	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08		115978231	19556516	28	6421											
MMP21	118856	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	127459092	127459092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtgctaaatctcaccatcaCctctccatattggtttctct	8	16	4	13	0	4	0	2	0	3	0	7	0	4	0	3	1	1	2	3	1	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr10:127459092C>T	ENST00000368808.3	-	5	1047	c.1048G>A	c.(1048-1050)Gtg>Atg	p.V350M		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	350					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	CTCACCATCACCTCTCCATAT	0.413																																					p.V350M		.											.	MMP21-228	0			c.G1048A						.						191	172	178					10																	127459092		2203	4300	6503	SO:0001583	missense	118856	exon5			CCATCACCTCTCC	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1048G>A	10.37:g.127459092C>T	ENSP00000357798:p.Val350Met	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	148	8	NM_147191	0	0	0	0	0	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	37	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165493	0.38217	.	.	ENSG00000154485	ENST00000368808	T	0.20332	2.08	5.62	-0.228	0.13098	Hemopexin/matrixin (2);	0.651830	0.14795	N	0.297980	T	0.12987	0.0315	N	0.22421	0.69	0.09310	N	1	B	0.19935	0.04	B	0.15484	0.013	T	0.21793	-1.0235	10	0.59425	D	0.04	-28.7392	9.267	0.37647	0.0:0.2518:0.5805:0.1677	.	350	Q8N119	MMP21_HUMAN	M	350	ENSP00000357798:V350M	ENSP00000357798:V350M	V	-	1	0	MMP21	127449082	0.001000	0.12720	0.000000	0.03702	0.638000	0.38207	-0.056000	0.11787	-0.027000	0.13873	-0.150000	0.13652	GTG	.		0.413	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			T	127459092	C	T	127459092	3	4	67	1	0	0	0	0	1	0	0	0	9685	507	18	2	673	2	MMP21	10	127459092	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	11480861	127459092	8075655	29	6422											
AP2A2	161	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	984672	984672	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctgcatccacagatctcCaggattacacttactatttt	10	14	5	12	1	2	1	0	0	2	1	4	2	3	2	2	1	3	1	2	1	3	5			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:984672C>T	ENST00000448903.2	+	7	874	c.733C>T	c.(733-735)Cag>Tag	p.Q245*	AP2A2_ENST00000534328.1_Nonsense_Mutation_p.Q245*|AP2A2_ENST00000332231.5_Nonsense_Mutation_p.Q245*	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	245					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CACAGATCTCCAGGATTACAC	0.582																																					p.Q245X		.											.	AP2A2-90	0			c.C733T						.						160	173	169					11																	984672		2066	4224	6290	SO:0001587	stop_gained	161	exon7			GATCTCCAGGATT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.733C>T	11.37:g.984672C>T	ENSP00000413234:p.Gln245*	Somatic	257	1		WXS	Illumina HiSeq	Phase_I	271	20	NM_012305	0	0	187	193	6	O75403|Q53ET1|Q96SI8	Nonsense_Mutation	SNP	ENST00000448903.2	37	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.907592	0.92107	.	.	ENSG00000183020	ENST00000525796;ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000329626	.	.	.	3.84	3.84	0.44239	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	-45.2751	16.1239	0.81380	0.0:1.0:0.0:0.0	.	.	.	.	X	85;245;245;245;245;245;118	.	ENSP00000328024:Q118X	Q	+	1	0	AP2A2	974672	1.000000	0.71417	0.912000	0.35992	0.283000	0.27025	7.675000	0.84002	1.870000	0.54199	0.591000	0.81541	CAG	.		0.582	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	984672	C	T	984672	4	4	67	1	0	0	0	0	0	1	0	0	740	595	21	2	759	2	AP2A2	11	984672	Nonsense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		984672	134021844	30	6423											
SYT9	143425	broad.mit.edu	37	chr11	7334870	7334870	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttcacaaagctgtcaatttgCccgccaaggacttttctggg	9	12	9	11	1	3	0	2	0	1	0	3	1	3	1	2	2	2	1	2	2	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:7334870C>T	ENST00000318881.6	+	3	979	c.742C>T	c.(742-744)Ccc>Tcc	p.P248S	SYT9_ENST00000396716.2_Missense_Mutation_p.P216S	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	248	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TGTCAATTTGCCCGCCAAGGA	0.413																																					p.P248S													.	SYT9-155	0			c.C742T						.						116	117	116					11																	7334870		2201	4296	6497	SO:0001583	missense	143425	exon3			AATTTGCCCGCCA	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"Synaptotagmins"	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.742C>T	11.37:g.7334870C>T	ENSP00000324419:p.Pro248Ser	Somatic	162	1		WXS	Illumina HiSeq	Phase_I	160	4	NM_175733	0	0	5	5	0		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.576914	0.86645	.	.	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.70986	-0.53;-0.53	5.87	5.87	0.94306	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.64402	D	0.000001	D	0.83695	0.5310	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.84279	0.0493	10	0.87932	D	0	.	18.0718	0.89410	0.0:1.0:0.0:0.0	.	248	Q86SS6	SYT9_HUMAN	S	216;248	ENSP00000379944:P216S;ENSP00000324419:P248S	ENSP00000324419:P248S	P	+	1	0	SYT9	7291446	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	CCC	.		0.413	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733		T	7334870	C	T	7334870	3	4	67	1	0	0	0	0	1	0	0	0	15513	739	26	2	752	2	SYT9	11	7334870	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	6350198	7334870	127671646	31	6424											
STX5	6811	bcgsc.ca	37	chr11	62592562	62592562	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcccgggagaactgctCtctccggctcctctgctgct	4	10	12	15	2	2	1	0	0	2	1	5	2	4	1	3	3	5	4	3	3	1	0			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:62592562C>A	ENST00000294179.3	-	8	778	c.625G>T	c.(625-627)Gag>Tag	p.E209*	STX5_ENST00000541317.1_Nonsense_Mutation_p.E113*|STX5_ENST00000394690.1_Nonsense_Mutation_p.E155*|STX5_ENST00000377897.4_Nonsense_Mutation_p.E209*	NM_001244666.1|NM_003164.4	NP_001231595.1|NP_003155.2	Q13190	STX5_HUMAN	syntaxin 5	209					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle targeting (GO:0006903)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|SNARE complex (GO:0031201)	protein N-terminus binding (GO:0047485)|SNAP receptor activity (GO:0005484)			breast(2)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	18						GAGAACTGCTCTCTCCGGCTC	0.562																																					p.E209X													.	STX5-154	0			c.G625T						.						45	52	50					11																	62592562		2201	4299	6500	SO:0001587	stop_gained	6811	exon8			ACTGCTCTCTCCG	U26648	CCDS8038.2, CCDS58140.1	11q12.3	2008-02-05	2006-04-25	2006-04-25	ENSG00000162236	ENSG00000162236			11440	protein-coding gene	gene with protein product		603189	"syntaxin 5A"	STX5A		9188044, 11959998	Standard	NM_003164		Approved	SED5	uc001nvh.3	Q13190	OTTHUMG00000143864	ENST00000294179.3:c.625G>T	11.37:g.62592562C>A	ENSP00000294179:p.Glu209*	Somatic	87	0		WXS	Illumina HiSeq	Phase_1	76	5	NM_003164	0	0	76	76	0	B2R8T2|F8W8Q9|Q5U0D4|Q7Z3T6|Q9BUG1	Nonsense_Mutation	SNP	ENST00000294179.3	37	CCDS8038.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.551595|5.551595	0.96501|0.96501	.|.	.|.	ENSG00000162236|ENSG00000162236	ENST00000431400|ENST00000377897;ENST00000294179;ENST00000394690;ENST00000541317	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.045290|0.045290	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.69305|.	0.3096|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.66834|.	-0.5823|.	4|.	.|0.29301	.|T	.|0.29	-1.1359|-1.1359	16.7371|16.7371	0.85449|0.85449	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|X	63|209;209;155;113	.|.	.|ENSP00000294179:E209X	E|E	-|-	3|1	2|0	STX5|STX5	62349138|62349138	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.260000|7.260000	0.78391|0.78391	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAG|GAG	.		0.562	STX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290113.1	NM_003164		A	62592562	C	A	62592562	4	1	67	1	0	0	0	0	0	1	0	0	15380	922	32	4	458	4	STX5	11	62592562	Nonsense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	55257692	62592562	72413954	32	6425											
ARHGAP20	57569	broad.mit.edu	37	chr11	110450663	110450663	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgccctgatgagggacCgggcattccggaaacatggc	9	6	14	12	2	0	2	0	2	0	0	1	4	1	4	4	4	3	1	4	4	1	1	rs202001398		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:110450663C>T	ENST00000260283.4	-	16	3291	c.3007G>A	c.(3007-3009)Ggt>Agt	p.G1003S	ARHGAP20_ENST00000529591.1_Missense_Mutation_p.G546S|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.G977S|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.G977S|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.G967S|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.G980S|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.G967S	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	1003					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.G1003S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GATGAGGGACCGGGCATTCCG	0.507													C|||	1	0.000199681	0	0	5008	,	,		20149	0.001		0	False		,,,				2504	0				p.G1003S													.	ARHGAP20-230	1	Substitution - Missense(1)	large_intestine(1)	c.G3007A						.						62	61	61					11																	110450663		2201	4298	6499	SO:0001583	missense	57569	exon16			AGGGACCGGGCAT	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"Rho GTPase activating proteins"	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.3007G>A	11.37:g.110450663C>T	ENSP00000260283:p.Gly1003Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	101	4	NM_020809	0	0	1	1	0	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.893	-0.724850	0.03158	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.07908	3.15;3.15;3.18;3.15;3.15;3.15;3.15	5.9	0.311	0.15831	.	0.363057	0.27181	N	0.020541	T	0.05547	0.0146	L	0.36672	1.1	0.09310	N	1	B;B;B	0.22346	0.004;0.041;0.068	B;B;B	0.17722	0.003;0.009;0.019	T	0.39057	-0.9632	10	0.23302	T	0.38	.	5.9856	0.19432	0.1254:0.4172:0.0:0.4573	.	977;1003;980	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	S	1003;977;546;980;967;977;967	ENSP00000260283:G1003S;ENSP00000349660:G977S;ENSP00000437905:G546S;ENSP00000432076:G980S;ENSP00000436319:G967S;ENSP00000436522:G977S;ENSP00000431399:G967S	ENSP00000260283:G1003S	G	-	1	0	ARHGAP20	109955873	0.000000	0.05858	0.038000	0.18304	0.136000	0.21042	-0.447000	0.06828	0.056000	0.16144	-0.809000	0.03173	GGT	C|0.999;T|0.000		0.507	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		T	110450663	C	T	110450663	3	4	67	1	0	0	0	0	1	0	0	0	870	652	23	1	572	1	ARHGAP20	11	110450663	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	47858101	110450663	24555853	33	6426											
DCPS	28960	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	126201299	126201299	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgctgtatcattgcaGatgtaaagacgaccgtggtt	9	12	13	7	2	1	2	1	0	0	2	1	3	1	2	1	2	2	6	1	2	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:126201299G>T	ENST00000263579.4	+	3	705		c.e3-1		DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger						cellular response to menadione (GO:0036245)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		TATCATTGCAGATGTAAAGAC	0.567																																					.		.											.	DCPS-90	0			c.377-1G>T						.						137	131	133					11																	126201299		2201	4298	6499	SO:0001630	splice_region_variant	28960	exon3			ATTGCAGATGTAA	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.377-1G>T	11.37:g.126201299G>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	200	12	NM_014026	0	0	1	1	0	Q8NHL8|Q9Y2S5	Splice_Site	SNP	ENST00000263579.4	37	CCDS8473.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.584618	0.46110	.	.	ENSG00000110063	ENST00000263579	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9226	0.92530	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DCPS	125706509	1.000000	0.71417	0.996000	0.52242	0.450000	0.32258	8.744000	0.91596	2.778000	0.95560	0.655000	0.94253	.	.		0.567	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	Intron	T	126201299	G	T	126201299	5	4	67	1	0	0	0	0	0	0	1	0	4307	956	33	4	386	4	DCPS	11	126201299	Splice_Site	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	15750636	126201299	8805217	34	6427											
PRDM10	56980	broad.mit.edu	37	chr11	129814751	129814751	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actgggtgcgcttggggatgCgccgcttggagaacaccccg	6	7	16	12	4	0	1	0	0	0	1	0	3	0	2	3	4	3	2	3	4	1	2			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:129814751C>T	ENST00000360871.3	-	6	908	c.677G>A	c.(676-678)cGc>cAc	p.R226H	PRDM10_ENST00000423662.2_Missense_Mutation_p.R140H|PRDM10_ENST00000528746.1_Missense_Mutation_p.R200H|PRDM10_ENST00000358825.5_Missense_Mutation_p.R226H|PRDM10_ENST00000304538.6_Missense_Mutation_p.R140H|PRDM10_ENST00000526082.1_Missense_Mutation_p.R140H	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	226	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		CTTGGGGATGCGCCGCTTGGA	0.627																																					p.R226H													.	PRDM10-91	0			c.G677A						.						55	59	58					11																	129814751		2201	4297	6498	SO:0001583	missense	56980	exon6			GGGATGCGCCGCT	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.677G>A	11.37:g.129814751C>T	ENSP00000354118:p.Arg226His	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	114	4	NM_020228	0	0	1	1	0	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668188	0.88348	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	5.25	5.25	0.73442	.	0.066838	0.64402	D	0.000016	T	0.67915	0.2944	M	0.64404	1.975	0.53688	D	0.999973	D;D;D;D;D;D;D	0.89917	1.0;0.965;1.0;0.99;1.0;1.0;1.0	D;B;D;B;D;D;D	0.79784	0.983;0.21;0.989;0.328;0.993;0.989;0.989	T	0.69953	-0.5005	10	0.72032	D	0.01	-17.5432	19.2892	0.94092	0.0:1.0:0.0:0.0	.	140;226;226;226;140;140;140	B7ZL72;Q9NQV6-4;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;.;PRD10_HUMAN;.;.;.	H	226;140;226;140;200;140	ENSP00000351686:R226H;ENSP00000302669:R140H;ENSP00000354118:R226H;ENSP00000398431:R140H;ENSP00000431262:R200H;ENSP00000432237:R140H	ENSP00000302669:R140H	R	-	2	0	PRDM10	129319961	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.445000	0.80570	2.627000	0.88993	0.644000	0.83932	CGC	.		0.627	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		T	129814751	C	T	129814751	3	4	67	1	0	0	0	0	1	0	0	0	12480	768	27	1	2873	1	PRDM10	11	129814751	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	3613452	129814751	5191765	35	6428											
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	11	7	6	17	1	1	0	0	0	1	0	2	0	2	0	5	1	5	2	5	1	4	3	rs121913529		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	.	KRAS-92875	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						.						91	81	85					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog", "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	40	13	NM_004985	0	0	13	29	16	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	67	1	0	0	0	0	1	0	0	0	8459	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		25398284	108453611	36	6429											
OR10AD1	121275	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48596939	48596939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtccaggaggtgataaagAtgatgaggccattcatggcc	11	9	13	8	0	1	4	1	3	0	1	2	5	2	5	3	4	0	0	3	4	2	2			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr12:48596939A>G	ENST00000310248.2	-	1	231	c.137T>C	c.(136-138)aTc>aCc	p.I46T		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	46						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GGTGATAAAGATGATGAGGCC	0.542																																					p.I46T		.											.	OR10AD1-69	0			c.T137C						.						96	81	86					12																	48596939		2203	4300	6503	SO:0001583	missense	121275	exon1			ATAAAGATGATGA		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"GPCR / Class A : Olfactory receptors"	14819	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily AD, member 1 pseudogene"	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.137T>C	12.37:g.48596939A>G	ENSP00000308689:p.Ile46Thr	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	53	5	NM_001004134	0	0	0	0	0	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.762337	0.49468	.	.	ENSG00000172640	ENST00000310248	T	0.00531	6.76	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.189939	0.25929	N	0.027383	T	0.01061	0.0035	M	0.79475	2.455	0.33098	D	0.53878	D	0.59357	0.985	P	0.50537	0.643	T	0.47586	-0.9106	10	0.72032	D	0.01	-30.4283	12.9182	0.58216	1.0:0.0:0.0:0.0	.	46	Q8NGE0	O10AD_HUMAN	T	46	ENSP00000308689:I46T	ENSP00000308689:I46T	I	-	2	0	OR10AD1	46883206	0.910000	0.30920	1.000000	0.80357	0.519000	0.34347	6.493000	0.73658	2.213000	0.71641	0.533000	0.62120	ATC	.		0.542	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1			G	48596939	A	G	48596939	3	3	67	1	0	0	0	0	1	0	0	0	10922	333	12	3	820	3	OR10AD1	12	48596939	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	23198655	48596939	85254956	37	6430											
ATP5B	506	ucsc.edu	37	chr12	57036240	57036240	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatctatgtaatttttcttAcctgtacagaggtgatagat	11	17	7	6	0	3	3	1	1	2	2	3	3	3	3	1	1	2	2	1	1	5	7			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr12:57036240A>G	ENST00000262030.3	-	7	1125		c.e7+1		ATP5B_ENST00000550162.1_Splice_Site|ATP5B_ENST00000552919.1_Splice_Site|SNORD59A_ENST00000384304.1_RNA	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide						angiogenesis (GO:0001525)|ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|osteoblast differentiation (GO:0001649)|proton transport (GO:0015992)|regulation of intracellular pH (GO:0051453)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial nucleoid (GO:0042645)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AATTTTTCTTACCTGTACAGA	0.478																																					.													.	ATP5B-91	0			c.1074+2T>C						.						75	78	77					12																	57036240		2203	4300	6503	SO:0001630	splice_region_variant	506	exon8			TTTCTTACCTGTA	M27132	CCDS8924.1	12p13.3	2012-10-12			ENSG00000110955	ENSG00000110955	3.6.3.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	830	protein-coding gene	gene with protein product		102910		ATPSB		2687158	Standard	NM_001686		Approved		uc001slr.3	P06576	OTTHUMG00000170291	ENST00000262030.3:c.1074+1T>C	12.37:g.57036240A>G		Somatic	79	0		WXS	Illumina HiSeq		95	1	NM_001686	0	0	0	0	0	A8K4X0|Q14283	Splice_Site	SNP	ENST00000262030.3	37	CCDS8924.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.204126	0.79127	.	.	ENSG00000110955	ENST00000262030;ENST00000552919;ENST00000551020;ENST00000552959;ENST00000551570	.	.	.	6.01	6.01	0.97437	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5038	0.75722	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP5B	55322507	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	7.275000	0.78548	2.306000	0.77630	0.496000	0.49642	.	.		0.478	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	NM_001686	Intron	G	57036240	A	G	57036240	5	3	67	1	0	0	0	0	0	0	1	0	1149	405	14	3	529	3	ATP5B	12	57036240	Splice_Site	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	8439301	57036240	76815655	38	6431											
STON2	85439	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	81862455	81862455	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cctccatccaccacatggttCtccccggaggagctctcgga	7	8	9	17	2	2	0	0	0	2	0	6	3	4	3	6	4	1	2	6	4	0	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr14:81862455C>G	ENST00000267540.2	-	2	356	c.156G>C	c.(154-156)gaG>gaC	p.E52D	STON2_ENST00000555447.1_Missense_Mutation_p.E52D	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	52					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		CCACATGGTTCTCCCCGGAGG	0.577																																					p.E52D		.											.	STON2-95	0			c.G156C						.						71	64	66					14																	81862455		2203	4300	6503	SO:0001583	missense	85439	exon4			ATGGTTCTCCCCG	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.156G>C	14.37:g.81862455C>G	ENSP00000267540:p.Glu52Asp	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	82	7	NM_001256430	0	0	4	4	0	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	37	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938177	0.52972	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.54866	0.55;0.55	5.8	1.95	0.26073	Stonin-2, N-terminal (1);	0.362161	0.29040	N	0.013335	T	0.44456	0.1294	L	0.59436	1.845	0.23309	N	0.997936	P;B;P	0.35714	0.517;0.334;0.461	B;B;B	0.36504	0.226;0.122;0.145	T	0.43702	-0.9375	10	0.87932	D	0	-12.0903	5.4312	0.16454	0.0:0.4999:0.2873:0.2127	.	52;52;52	Q8WXE9;Q17R23;G3V2T7	STON2_HUMAN;.;.	D	52;64;52	ENSP00000450857:E52D;ENSP00000267540:E52D	ENSP00000267540:E52D	E	-	3	2	STON2	80932208	0.910000	0.30920	0.991000	0.47740	0.836000	0.47400	-0.309000	0.08145	0.801000	0.34066	-0.179000	0.13096	GAG	.		0.577	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		G	81862455	C	G	81862455	3	3	67	1	0	0	0	0	1	0	0	0	15350	912	32	4	2575	4	STON2	14	81862455	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		81862455	25487085	39	6432											
MFAP1	4236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	44109600	44109600	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcatagtctggccttttTccggacacataacgctttac	8	12	10	11	2	1	0	0	0	1	0	2	1	2	1	2	4	2	2	2	4	3	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr15:44109600T>G	ENST00000267812.3	-	2	358	c.126A>C	c.(124-126)ggA>ggC	p.G42G		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	42					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		CTGGCCTTTTTCCGGACACAT	0.433																																					p.G42G		.											.	MFAP1-226	0			c.A126C						.						128	118	121					15																	44109600		2198	4298	6496	SO:0001819	synonymous_variant	4236	exon2			CCTTTTTCCGGAC		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.126A>C	15.37:g.44109600T>G		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	214	12	NM_005926	0	0	53	58	5	Q86TG6	Silent	SNP	ENST00000267812.3	37	CCDS10105.1																																																																																			.		0.433	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		G	44109600	T	G	44109600	2	3	67	1	0	0	0	0	0	0	0	1	9538	1770	62	5		5	MFAP1	15	44109600	Silent	SNP	T	TCGA-BQ-5883-01A-11D-1589-08		44109600	58421792	40	6433											
LASS3	204219	broad.mit.edu;bcgsc.ca	37	chr15	101013174	101013174	+	Frame_Shift_Del	DEL	C	C	-																															tgtacaatcatcacgagggtCccactgcgaatataattagc																										TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr15:101013174delC	ENST00000394113.1	-	11	1383	c.693delG	c.(691-693)gggfs	p.G231fs	CERS3_ENST00000538112.2_Frame_Shift_Del_p.G231fs|CERS3_ENST00000560944.1_Intron|CERS3_ENST00000284382.4_Frame_Shift_Del_p.G231fs			Q8IU89	CERS3_HUMAN	ceramide synthase 3	231	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										TCACGAGGGTCCCACTGCGAA	0.433																																					p.G231fs													.	.	0			c.693delG						.						118	101	107					15																	101013174		2203	4300	6503	SO:0001589	frameshift_variant	204219	exon10			GAGGGTCCCACTG		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.693delG	15.37:g.101013174delC	ENSP00000377672:p.Gly231fs	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	124	17	NM_178842	0	0	0	0	0	Q8NE64|Q8NEN6	Frame_Shift_Del	DEL	ENST00000394113.1	37	CCDS10384.1																																																																																			.		0.433	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		-	101013174	C	-	101013174	7	5	67	1	0	1	0	1	0	0	0	0	8661	842	30	0	474	0	LASS3	15	101013174	Frame_Shift_Del	DEL	C	TCGA-BQ-5883-01A-11D-1589-08	56903574	101013174	1518218	41	6434											
CYB5D2	124936	bcgsc.ca	37	chr17	4058011	4058021	+	Frame_Shift_Del	DEL	CCCGGCACTGA	CCCGGCACTGA	-																															ggagaggatgggctgcccacCccggcactgacccaggtaga																								rs367926129		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	CCCGGCACTGA	CCCGGCACTGA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr17:4058011_4058021delCCCGGCACTGA	ENST00000301391.3	+	3	935_945	c.435_445delCCCGGCACTGA	c.(433-447)accccggcactgaccfs	p.TPALT145fs	CYB5D2_ENST00000573984.1_Frame_Shift_Del_p.TPALT33fs|CYB5D2_ENST00000575411.2_3'UTR|CYB5D2_ENST00000575251.1_Frame_Shift_Del_p.TPALT33fs	NM_144611.3	NP_653212.1	Q8WUJ1	NEUFC_HUMAN	cytochrome b5 domain containing 2	145					nervous system development (GO:0007399)	extracellular region (GO:0005576)	heme binding (GO:0020037)			breast(1)|large_intestine(3)|liver(2)|ovary(1)	7						GGCTGCCCACCCCGGCACTGACCCAGGTAGA	0.592																																					p.145_149del													.	CYB5D2-155	0			c.435_445del						.																																			SO:0001589	frameshift_variant	124936	exon3			GCCCACCCCGGCA	AK172844	CCDS11044.1, CCDS58501.1	17p13.2	2006-03-10							28471	protein-coding gene	gene with protein product							Standard	NM_144611		Approved	MGC32124	uc002fxm.4	Q8WUJ1		ENST00000301391.3:c.435_445delCCCGGCACTGA	17.37:g.4058011_4058021delCCCGGCACTGA	ENSP00000301391:p.Thr145fs	Somatic	80	0		WXS	Illumina HiSeq	Phase_1	77	3	NM_144611	0	0	0	0	0	B2R7R6|D3DTJ9|I3L1K2	Frame_Shift_Del	DEL	ENST00000301391.3	37	CCDS11044.1																																																																																			.		0.592	CYB5D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438698.1	NM_144611		-	4058021	CCCGGCACTGA	-	4058011	7	5	67	1	0	1	0	1	0	0	0	0	4131	610	22	0	445	0	CYB5D2	17	4058011	Frame_Shift_Del	DEL	CCCGGCACTGA	TCGA-BQ-5883-01A-11D-1589-08		4058011	77137199	42	6435											
AURKB	9212	broad.mit.edu	37	chr17	8108544	8108544	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccctcccaccttgacgatgCggcgataggtctcgttgtgt	5	11	12	13	4	1	1	0	1	1	0	3	3	2	1	3	2	1	1	3	2	1	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr17:8108544C>T	ENST00000585124.1	-	8	944	c.851G>A	c.(850-852)cGc>cAc	p.R284H	AURKB_ENST00000316199.6_Missense_Mutation_p.R285H|AURKB_ENST00000535053.1_3'UTR|AURKB_ENST00000534871.1_Missense_Mutation_p.R243H|AURKB_ENST00000578549.1_Missense_Mutation_p.R252H	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	284	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|central_nervous_system(1)|lung(2)	4						CTTGACGATGCGGCGATAGGT	0.592																																					p.R284H	NSCLC(134;1161 2470 43664 51568)												.	AURKB-1508	0			c.G851A						.						99	73	82					17																	8108544		2203	4300	6503	SO:0001583	missense	9212	exon8			ACGATGCGGCGAT	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11390	protein-coding gene	gene with protein product	"aurora-B", "aurora-1", "protein phosphatase 1, regulatory subunit 48"	604970	"serine/threonine kinase 12"	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.851G>A	17.37:g.8108544C>T	ENSP00000463999:p.Arg284His	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	31	3	NM_004217	0	0	0	0	0	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Missense_Mutation	SNP	ENST00000585124.1	37	CCDS11134.1	.	.	.	.	.	.	.	.	.	.	C	34	5.356147	0.95854	.	.	ENSG00000178999	ENST00000316199;ENST00000534871	T;T	0.66815	-0.23;-0.23	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.71660	0.3366	L	0.47016	1.485	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.54100	0.742;0.742	T	0.74523	-0.3637	10	0.87932	D	0	-19.9451	16.5723	0.84622	0.0:1.0:0.0:0.0	.	284;284	C7G533;Q96GD4	.;AURKB_HUMAN	H	284;243	ENSP00000313950:R284H;ENSP00000443869:R243H	ENSP00000313950:R284H	R	-	2	0	AURKB	8049269	0.376000	0.25098	0.991000	0.47740	0.910000	0.53928	3.226000	0.51254	2.787000	0.95880	0.650000	0.86243	CGC	.		0.592	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217		T	8108544	C	T	8108544	3	4	67	1	0	0	0	0	1	0	0	0	1224	768	27	1	191	1	AURKB	17	8108544	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	4050533	8108544	73086666	43	6436											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y	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	265	268					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	465	64		WXS	Illumina HiSeq		643	96	NM_145301	0	0	15	85	70	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		T	15457087	C	T	15457087	3	4	67	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	7348543	15457087	65738123	44	6437											
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288532	74288532	+	Missense_Mutation	SNP	C	C	T																															caccaggttggaccaaaccaCgctgatctgcaccaggtggg																										TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr17:74288532C>T	ENST00000262765.5	-	4	1957	c.1778G>A	c.(1777-1779)cGt>cAt	p.R593H		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	593	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GACCAAACCACGCTGATCTGC	0.537																																					p.R593H		.											.	QRICH2-94	0			c.G1778A						.						165	136	146					17																	74288532		2203	4300	6503	SO:0001583	missense	84074	exon4			AAACCACGCTGAT	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1778G>A	17.37:g.74288532C>T	ENSP00000262765:p.Arg593His	Somatic	74	2		WXS	Illumina HiSeq	Phase_I	68	6	NM_032134	0	0	0	1	1	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	C	7.632	0.679114	0.14907	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.22743	1.94	4.41	-8.82	0.00810	.	.	.	.	.	T	0.17408	0.0418	L	0.40543	1.245	0.09310	N	1	D;P	0.69078	0.997;0.945	P;B	0.54499	0.754;0.36	T	0.02009	-1.1230	9	0.23891	T	0.37	0.8777	2.711	0.05174	0.132:0.3548:0.2026:0.3106	.	593;593	B5MD94;Q9H0J4	.;QRIC2_HUMAN	H	593	ENSP00000262765:R593H	ENSP00000262765:R593H	R	-	2	0	QRICH2	71800127	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-14.214000	0.00000	-2.005000	0.00959	-0.798000	0.03219	CGT	C|1.000;T|0.000		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		T	74288532	C	T	74288532	3	4	67	1	0	0	0	0	1	0	0	0	12912	536	19	1	3277	1	QRICH2	17	74288532	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	58831445	74288532	6906678	45	6438	73	2									
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288538	74288538	+	Missense_Mutation	SNP	T	T	A																															gttggaccaaaccacgctgaTctgcaccaggtgggaccaaa																								rs142871405		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr17:74288538T>A	ENST00000262765.5	-	4	1951	c.1772A>T	c.(1771-1773)gAt>gTt	p.D591V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	591	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						ACCACGCTGATCTGCACCAGG	0.542																																					p.D591V		.											.	QRICH2-94	0			c.A1772T						.						168	139	149					17																	74288538		2203	4300	6503	SO:0001583	missense	84074	exon4			CGCTGATCTGCAC	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1772A>T	17.37:g.74288538T>A	ENSP00000262765:p.Asp591Val	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	73	5	NM_032134	0	0	0	0	0	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	T	0.110	-1.140197	0.01728	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.09350	2.99	5.05	-10.1	0.00402	.	.	.	.	.	T	0.06005	0.0156	L	0.36672	1.1	0.09310	N	1	B;B	0.21147	0.001;0.052	B;B	0.15052	0.001;0.012	T	0.15521	-1.0434	9	0.25751	T	0.34	-0.0073	5.5216	0.16936	0.4711:0.3571:0.0862:0.0856	.	591;591	B5MD94;Q9H0J4	.;QRIC2_HUMAN	V	591	ENSP00000262765:D591V	ENSP00000262765:D591V	D	-	2	0	QRICH2	71800133	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-12.362000	0.00002	-4.878000	0.00028	-5.321000	0.00001	GAT	T|1.000;C|0.000		0.542	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74288538	T	A	74288538	3	1	67	1	0	0	0	0	1	0	0	0	12912	1435	50	5	3283	5	QRICH2	17	74288538	Missense_Mutation	SNP	T	TCGA-BQ-5883-01A-11D-1589-08	6	74288538	6906672	46	6439	73	2									
RBBP8	5932	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	20573491	20573491	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcagcccttgaataaatgCtctccagacaataaaccatc	14	10	4	13	0	2	2	1	1	1	1	4	2	2	2	3	0	3	1	3	0	6	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr18:20573491C>G	ENST00000399722.2	+	11	2052	c.1701C>G	c.(1699-1701)tgC>tgG	p.C567W	RBBP8_ENST00000399725.2_Missense_Mutation_p.C567W|RBBP8_ENST00000360790.5_Missense_Mutation_p.C567W|RBBP8_ENST00000327155.5_Missense_Mutation_p.C567W	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	567					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			TGAATAAATGCTCTCCAGACA	0.438								Homologous recombination																													p.C567W		.											.	RBBP8-659	0			c.C1701G						.						42	43	43					18																	20573491		2203	4300	6503	SO:0001583	missense	5932	exon11			TAAATGCTCTCCA	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1701C>G	18.37:g.20573491C>G	ENSP00000382628:p.Cys567Trp	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	87	5	NM_203292	0	0	88	93	5	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	37	CCDS11875.1	.	.	.	.	.	.	.	.	.	.	C	8.135	0.783853	0.16189	.	.	ENSG00000101773	ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790	T;T;T;T;T	0.30182	1.56;1.54;1.56;1.56;1.56	5.47	-1.84	0.07809	.	0.955160	0.08781	N	0.894641	T	0.13713	0.0332	N	0.08118	0	0.80722	D	1	B;B;B	0.26845	0.161;0.161;0.05	B;B;B	0.27262	0.078;0.078;0.078	T	0.11348	-1.0591	10	0.42905	T	0.14	2.5577	4.5073	0.11894	0.398:0.2625:0.0:0.3395	.	567;567;567	E7ETY1;A6NKN2;Q99708	.;.;COM1_HUMAN	W	567	ENSP00000323050:C567W;ENSP00000382630:C567W;ENSP00000382628:C567W;ENSP00000382627:C567W;ENSP00000354024:C567W	ENSP00000323050:C567W	C	+	3	2	RBBP8	18827489	0.237000	0.23815	0.580000	0.28601	0.726000	0.41606	-0.151000	0.10175	-0.215000	0.10063	-0.150000	0.13652	TGC	.		0.438	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		G	20573491	C	G	20573491	3	3	67	1	0	0	0	0	1	0	0	0	13137	805	28	4	1739	4	RBBP8	18	20573491	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		20573491	57503757	47	6440											
ACSBG2	81616	broad.mit.edu	37	chr19	6147661	6147661	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagtactatgaggcttgtcGgaaggctgcaaaatccttga	11	10	11	9	1	0	2	0	2	0	0	2	3	1	3	2	3	2	4	2	3	5	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr19:6147661G>A	ENST00000586696.1	+	3	548	c.272G>A	c.(271-273)cGg>cAg	p.R91Q	ACSBG2_ENST00000591403.1_Missense_Mutation_p.R91Q|ACSBG2_ENST00000588485.1_5'UTR|ACSBG2_ENST00000252669.5_Missense_Mutation_p.R91Q|ACSBG2_ENST00000588304.1_Missense_Mutation_p.R41Q			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	91					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GAGGCTTGTCGGAAGGCTGCA	0.408																																					p.R91Q													.	ACSBG2-23	0			c.G272A						.						108	113	112					19																	6147661		2203	4300	6503	SO:0001583	missense	81616	exon3			CTTGTCGGAAGGC		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.272G>A	19.37:g.6147661G>A	ENSP00000465589:p.Arg91Gln	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	166	4	NM_030924	0	0	0	0	0	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.751591	0.49257	.	.	ENSG00000130377	ENST00000252669	T	0.41758	0.99	5.79	4.76	0.60689	AMP-dependent synthetase/ligase (1);	0.359807	0.20545	N	0.090240	T	0.62648	0.2445	M	0.78285	2.405	0.46774	D	0.999191	B;D	0.64830	0.325;0.994	B;D	0.64776	0.228;0.929	T	0.65236	-0.6217	10	0.52906	T	0.07	-45.6197	12.9332	0.58299	0.0782:0.0:0.9218:0.0	.	91;91	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	Q	91	ENSP00000252669:R91Q	ENSP00000252669:R91Q	R	+	2	0	ACSBG2	6098661	1.000000	0.71417	0.795000	0.32087	0.079000	0.17450	5.538000	0.67193	1.462000	0.47948	-0.126000	0.14955	CGG	.		0.408	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		A	6147661	G	A	6147661	3	1	67	1	0	0	0	0	1	0	0	0	174	1116	39	1	278	1	ACSBG2	19	6147661	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		6147661	52981322	48	6441											
ZFP30	22835	broad.mit.edu	37	chr19	38126264	38126264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgaaataagttctgagtaaCgacgaaagaacttctgacat	16	10	9	6	2	2	4	0	3	2	1	2	6	2	4	0	0	2	2	0	0	5	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr19:38126264C>T	ENST00000351218.2	-	6	1735	c.1178G>A	c.(1177-1179)cGt>cAt	p.R393H	ZFP30_ENST00000514101.2_Missense_Mutation_p.R393H|ZFP30_ENST00000392144.1_Missense_Mutation_p.R393H|ZFP30_ENST00000589018.1_Intron	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	393					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)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTCTGAGTAACGACGAAAGAA	0.408																																					p.R393H													.	ZFP30-90	0			c.G1178A						.						69	72	71					19																	38126264		2203	4300	6503	SO:0001583	missense	22835	exon6			GAGTAACGACGAA	AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"Zinc fingers, C2H2-type", "-"	29555	protein-coding gene	gene with protein product			"zinc finger protein 30 homolog (mouse)"			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.1178G>A	19.37:g.38126264C>T	ENSP00000343581:p.Arg393His	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	106	5	NM_014898	0	0	3	3	0	Q58EY8	Missense_Mutation	SNP	ENST00000351218.2	37	CCDS33005.1	.	.	.	.	.	.	.	.	.	.	C	8.628	0.893085	0.17613	.	.	ENSG00000120784	ENST00000351218;ENST00000514101;ENST00000392144;ENST00000440715	T;T;T	0.36340	1.26;1.26;1.26	3.9	2.86	0.33363	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35262	N	0.003340	T	0.34716	0.0907	L	0.27975	0.815	0.23851	N	0.996661	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.33059	-0.9883	10	0.11485	T	0.65	.	3.6934	0.08354	0.0:0.5686:0.2232:0.2082	.	393;393	D3Y2A0;Q9Y2G7	.;ZFP30_HUMAN	H	393;393;393;308	ENSP00000343581:R393H;ENSP00000422930:R393H;ENSP00000375988:R393H	ENSP00000343581:R393H	R	-	2	0	ZFP30	42818104	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.122000	0.10627	2.175000	0.68902	0.591000	0.81541	CGT	.		0.408	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898		T	38126264	C	T	38126264	3	4	67	1	0	0	0	0	1	0	0	0	17676	536	19	1	385	1	ZFP30	19	38126264	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	31978603	38126264	21002719	49	6442											
ARFGEF2	10564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47632919	47632919	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgaagttcttctttctgatGtatttgcacaattgcagtgg	9	17	9	6	0	3	2	0	2	3	0	3	2	3	2	0	1	2	4	0	1	3	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr20:47632919G>A	ENST00000371917.4	+	31	4282	c.4282G>A	c.(4282-4284)Gta>Ata	p.V1428I		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1428					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TCTTTCTGATGTATTTGCACA	0.353																																					p.V1428I	Esophageal Squamous(176;1738 1974 26285 33069 35354)	.											.	ARFGEF2-358	0			c.G4282A						.						208	185	193					20																	47632919		2203	4300	6503	SO:0001583	missense	10564	exon31			TCTGATGTATTTG	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.4282G>A	20.37:g.47632919G>A	ENSP00000360985:p.Val1428Ile	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	147	43	NM_006420	0	0	21	51	30	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	37	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	G	7.760	0.705132	0.15172	.	.	ENSG00000124198	ENST00000371917	T	0.38722	1.12	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.054023	0.64402	D	0.000002	T	0.11580	0.0282	N	0.00841	-1.15	0.43069	D	0.994705	B	0.02656	0.0	B	0.01281	0.0	T	0.33189	-0.9878	10	0.02654	T	1	.	7.2277	0.26024	0.206:0.0:0.794:0.0	.	1428	Q9Y6D5	BIG2_HUMAN	I	1428	ENSP00000360985:V1428I	ENSP00000360985:V1428I	V	+	1	0	ARFGEF2	47066326	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	5.353000	0.66034	2.587000	0.87381	0.591000	0.81541	GTA	.		0.353	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47632919	G	A	47632919	3	1	67	1	0	0	0	0	1	0	0	0	853	1377	48	2	4404	2	ARFGEF2	20	47632919	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		47632919	15392601	50	6443											
CLIC6	54102	hgsc.bcm.edu	37	chr21	36042941	36042941	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcagcaaccacctggcCgaggagggccccgccgaggg	8	2	15	16	3	1	0	1	0	0	0	1	3	1	1	6	4	3	2	6	4	1	0	rs367854236	byFrequency	TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr21:36042941C>T	ENST00000360731.3	+	1	1254	c.1254C>T	c.(1252-1254)gcC>gcT	p.A418A	CLIC6_ENST00000349499.2_Silent_p.A418A			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	418						chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						ACCACCTGGCCGAGGAGGGCC	0.766													C|||	4	0.000798722	0.003	0	5008	,	,		9996	0		0	False		,,,				2504	0				p.A418A		.											.	CLIC6-91	0			c.C1254T						.	C		3,3783		0,3,1890	4	7	6		1254	-5.6	0.2	21		6	0,7312		0,0,3656	no	coding-synonymous	CLIC6	NM_053277.1		0,3,5546	TT,TC,CC		0.0,0.0792,0.027		418/687	36042941	3,11095	1893	3656	5549	SO:0001819	synonymous_variant	54102	exon1			CCTGGCCGAGGAG	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"Ion channels / Chloride channels : Intracellular"	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.1254C>T	21.37:g.36042941C>T		Somatic	5	2		WXS	Illumina HiSeq	Phase_I	12	8	NM_053277	0	0	0	5	5	A8K0U8|Q8IX31	Silent	SNP	ENST00000360731.3	37																																																																																				.		0.766	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			T	36042941	C	T	36042941	2	4	67	1	0	0	0	0	0	0	0	1	3536	639	23	1		1	CLIC6	21	36042941	Silent	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		36042941	12086954	51	6444											
MMP11	4320	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	24123480	24123480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctttgtgtggcgcctccGtgggggccagctgcagcccg	2	8	18	13	3	0	0	0	0	0	0	1	0	1	0	4	4	3	3	4	4	0	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr22:24123480G>A	ENST00000215743.3	+	6	1011	c.959G>A	c.(958-960)cGt>cAt	p.R320H		NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	320					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	TGGCGCCTCCGTGGGGGCCAG	0.672																																					p.R320H		.											.	MMP11-291	0			c.G959A						.						41	43	43					22																	24123480		2203	4300	6503	SO:0001583	missense	4320	exon6			GCCTCCGTGGGGG		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.959G>A	22.37:g.24123480G>A	ENSP00000215743:p.Arg320His	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	77	21	NM_005940	0	0	18	20	2	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546617	0.86022	.	.	ENSG00000099953	ENST00000215743	T	0.02421	4.3	4.73	4.73	0.59995	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.08891	0.0220	L	0.41124	1.26	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.18840	-1.0324	10	0.38643	T	0.18	.	12.7499	0.57302	0.0822:0.0:0.9178:0.0	.	320	P24347	MMP11_HUMAN	H	320	ENSP00000215743:R320H	ENSP00000215743:R320H	R	+	2	0	MMP11	22453480	0.998000	0.40836	0.968000	0.41197	0.986000	0.74619	8.987000	0.93497	2.649000	0.89929	0.650000	0.86243	CGT	.		0.672	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		A	24123480	G	A	24123480	3	1	67	1	0	0	0	0	1	0	0	0	9675	1145	40	1	981	1	MMP11	22	24123480	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		24123480	27181086	52	6445											
XBP1	7494	broad.mit.edu	37	chr22	29196498	29196499	+	In_Frame_Ins	INS	-	-	GCC																															cggccgggttcggcgcggctINSgccaccaccaccatagctcc																								rs528996789	byFrequency	TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr22:29196498_29196499insGCC	ENST00000216037.6	-	1	86_87	c.14_15insGGC	c.(13-15)gca>gcGGCa	p.5_5A>AA	XBP1_ENST00000344347.5_In_Frame_Ins_p.5_5A>AA|XBP1_ENST00000405219.3_5'Flank|CTA-292E10.6_ENST00000451486.1_RNA|CTA-292E10.6_ENST00000458080.1_RNA|CTA-292E10.6_ENST00000418292.1_RNA|CTA-292E10.6_ENST00000585003.1_RNA|XBP1_ENST00000403532.3_In_Frame_Ins_p.5_5A>AA	NM_001079539.1|NM_005080.3	NP_001073007.1|NP_005071.2	P17861	XBP1_HUMAN	X-box binding protein 1	5					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial cell maturation involved in salivary gland development (GO:0060691)|exocrine pancreas development (GO:0031017)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|serotonin secretion, neurotransmission (GO:0060096)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(1)|lung(1)	5						TCGGCGCGGCTGCCACCACCAC	0.762																																					p.A5delinsAA													.	XBP1-290	0			c.15_16insGGC						.		,	24,1974		9,6,984					,	1.1	1			2	13,4915		3,7,2454	no	coding,coding	XBP1	NM_005080.3,NM_001079539.1	,	12,13,3438	A1A1,A1R,RR		0.2638,1.2012,0.5342	,	,		37,6889				SO:0001652	inframe_insertion	7494	exon1			CGCGGCTGCCACC	M31627	CCDS13847.1	22q12.1	2013-01-10			ENSG00000100219	ENSG00000100219		"basic leucine zipper proteins"	12801	protein-coding gene	gene with protein product		194355		XBP2		1718857, 2196176	Standard	NM_001079539		Approved		uc003aec.3	P17861	OTTHUMG00000151094	ENST00000216037.6:c.12_14dupGGC	22.37:g.29196499_29196501dupGCC	ENSP00000216037:p.Ala7dup	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001079539	0	0	0	0	0	Q8WYK6|Q969P1|Q96BD7	In_Frame_Ins	INS	ENST00000216037.6	37	CCDS13847.1																																																																																			.		0.762	XBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321274.1	NM_005080		GCC	29196499	-	GCC	29196498	7	5	67	1	0	1	1	0	0	0	0	0	17455	1567	55	0	1161	0	XBP1	22	29196498	In_Frame_Ins	INS	-	TCGA-BQ-5883-01A-11D-1589-08	5073018	29196498	22108068	53	6446											
MEI1	150365	hgsc.bcm.edu	37	chr22	42189857	42189857	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctctattgtcccaggccTgtgttggctgcctggaggcc	4	11	12	14	0	1	0	0	0	1	0	2	1	2	1	5	4	1	2	5	4	1	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr22:42189857T>C	ENST00000401548.3	+	27	3410	c.3370T>C	c.(3370-3372)Tgt>Cgt	p.C1124R	MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000400107.1_Missense_Mutation_p.C457R|MEI1_ENST00000300398.4_Missense_Mutation_p.C132R	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GTCCCAGGCCTGTGTTGGCTG	0.458																																					p.C1124R		.											.	MEI1-70	0			c.T3370C						.						41	41	41					22																	42189857		1863	4101	5964	SO:0001583	missense	150365	exon27			CAGGCCTGTGTTG	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3370T>C	22.37:g.42189857T>C	ENSP00000384115:p.Cys1124Arg	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_152513	0	0	0	0	0		Missense_Mutation	SNP	ENST00000401548.3	37	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.162039	0.78226	.	.	ENSG00000167077	ENST00000401548;ENST00000400107;ENST00000300398;ENST00000419798;ENST00000403492	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.66	4.6	0.57074	.	0.342116	0.31010	N	0.008427	T	0.73946	0.3652	L	0.54323	1.7	0.48975	D	0.999734	D;D;D;D;D;D	0.65815	0.993;0.967;0.985;0.985;0.995;0.993	D;P;P;P;P;P	0.65010	0.931;0.6;0.838;0.838;0.838;0.865	T	0.75895	-0.3156	10	0.72032	D	0.01	-18.1438	9.3129	0.37917	0.0:0.0:0.2784:0.7216	.	138;457;234;367;492;1124	B7Z735;Q5TIA1-3;E9PB79;Q5TIA1-5;Q5TIA1-2;Q5TIA1	.;.;.;.;.;MEI1_HUMAN	R	1124;457;132;234;132	ENSP00000384115:C1124R;ENSP00000382978:C457R;ENSP00000300398:C132R;ENSP00000385298:C132R	ENSP00000300398:C132R	C	+	1	0	MEI1	40519803	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	2.126000	0.42026	2.153000	0.67306	0.459000	0.35465	TGT	.		0.458	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		C	42189857	T	C	42189857	3	2	67	1	0	0	0	0	1	0	0	0	9490	1580	55	3	3476	3	MEI1	22	42189857	Missense_Mutation	SNP	T	TCGA-BQ-5883-01A-11D-1589-08	12993359	42189857	9114709	54	6447											
AR	367	hgsc.bcm.edu	37	chrX	66765195	66765196	+	Missense_Mutation	DNP	GC	GC	AG																															cagcagcagcagcagcagcaGcagcagcagcagcagcagca																										TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chrX:66765195_66765196GC>AG	ENST00000374690.3	+	1	731_732	c.207_208GC>AG	c.(205-210)caGCag>caAGag	p.Q70E	AR_ENST00000504326.1_Missense_Mutation_p.Q70E|AR_ENST00000396044.3_Missense_Mutation_p.Q70E|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	70	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcagcagcagcagca	0.678									Androgen Insensitivity Syndrome																												p.Q70E		.											.	AR	0			c.C208G						.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CAGCAGCAGCAGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	X.37:g.66765195_66765196delinsAG	ENSP00000363822:p.Gln70Glu	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	19	4		0	0	0	0	0	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	DNP	ENST00000374690.3	37	CCDS14387.1																																																																																			.		0.678	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		AG	66765196	GC	AG	66765195	3	1	67	1	0	0	0	0	1	0	0	0	836	962	34	2	209	2	AR	23	66765195	Missense_Mutation	DNP	GC	TCGA-BQ-5883-01A-11D-1589-08		66765195	88505365	55	6448											
CNGA2	1260	broad.mit.edu	37	chrX	150911739	150911739	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgcctgctgcactttgcccGcatgtttgagttctttgacc	4	14	9	14	2	1	2	0	2	1	0	1	2	1	2	4	0	3	5	4	0	0	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chrX:150911739G>A	ENST00000329903.4	+	6	797	c.764G>A	c.(763-765)cGc>cAc	p.R255H		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	255					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.R255H(1)		breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					CACTTTGCCCGCATGTTTGAG	0.527																																					p.R255H													.	CNGA2-193	1	Substitution - Missense(1)	endometrium(1)	c.G764A						.						179	137	151					X																	150911739		2203	4300	6503	SO:0001583	missense	1260	exon7			TTGCCCGCATGTT	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.764G>A	X.37:g.150911739G>A	ENSP00000328478:p.Arg255His	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	206	5	NM_005140	0	0	0	0	0	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260930	0.80246	.	.	ENSG00000183862	ENST00000329903	D	0.99519	-6.07	5.49	5.49	0.81192	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99739	0.9897	H	0.98005	4.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97103	0.9799	10	0.87932	D	0	.	15.6554	0.77129	0.0:0.0:1.0:0.0	.	255	Q16280	CNGA2_HUMAN	H	255	ENSP00000328478:R255H	ENSP00000328478:R255H	R	+	2	0	CNGA2	150662395	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.644000	0.83416	2.293000	0.77203	0.600000	0.82982	CGC	.		0.527	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		A	150911739	G	A	150911739	3	1	67	1	0	0	0	0	1	0	0	0	3603	1087	38	1	786	1	CNGA2	23	150911739	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08	84146544	150911739	4358821	56	6449											
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16952767	16952767	+	3'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcctcaacatcttagcCtttgcggcgctgtactacaa	8	13	6	14	2	3	0	1	0	2	0	4	0	4	0	2	1	5	2	2	1	5	5	rs373089425		TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chrY:16952767C>T	ENST00000476359.1	+	0	2621							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.A692A(1)		large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						ACATCTTAGCCTTTGCGGCGC	0.502																																					p.A692A		.											.	.	1	Substitution - coding silent(1)	prostate(1)	c.C2076T						.	C	,	0,571		0,571	53	72	66		1572,2076	-3.8	0	Y		66	1,1871		1,1871	no	coding-synonymous,coding-synonymous	NLGN4Y	NM_001206850.1,NM_014893.4	,	1,2442	T,C		0.0534,0.0,0.0409	,	524/649,692/817	16952767	1,2442	974	2291	3265	SO:0001624	3_prime_UTR_variant	22829	exon6			CTTAGCCTTTGCG		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"neuroligin 4, Y linked"			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*2618C>T	Y.37:g.16952767C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	5	5	NM_014893	0	0	0	0	0	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Silent	SNP	ENST00000476359.1	37																																																																																				.		0.502	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		T	16952767	C	T	16952767	1	4	67	0	1	0	0	0	0	0	0	0	10491	668	24	2		2	NLGN4Y	24	16952767	3'UTR	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		16952767	42420799	57	6450											
SKI	6497	hgsc.bcm.edu	37	chr1	2160390	2160390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgcggccgcggtgccggCgccggtgcccgcagccaccg	2	2	19	18	9	0	0	0	0	0	0	0	0	0	0	6	5	3	1	6	5	0	0	rs28384811	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:2160390C>G	ENST00000378536.4	+	1	257	c.185C>G	c.(184-186)gCg>gGg	p.A62G		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	62					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		gcggtgccggcgccggTGCCC	0.776													C|||	229	0.0457268	0.0234	0.0576	5008	,	,		4535	0.0079		0.0706	False		,,,				2504	0.0808				p.A62G	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.C185G						.						1	1	1					1																	2160390		788	1840	2628	SO:0001583	missense	6497	exon1			TGCCGGCGCCGGT	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.185C>G	1.37:g.2160390C>G	ENSP00000367797:p.Ala62Gly	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	3	2	NM_003036	0	0	0	0	0	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	37	CCDS39.1	102	0.046703296703296704	20	0.04065040650406504	28	0.07734806629834254	3	0.005244755244755245	51	0.06728232189973615	C	9.688	1.151208	0.21371	.	.	ENSG00000157933	ENST00000378536	D	0.95821	-3.82	2.3	2.3	0.28687	.	.	.	.	.	T	0.47857	0.1468	N	0.08118	0	0.45733	P	0.001363000000000003	D	0.57899	0.981	P	0.58520	0.84	T	0.76271	-0.3020	8	0.20519	T	0.43	-11.9718	7.7374	0.28823	0.0:1.0:0.0:0.0	rs28384811	62	P12755	SKI_HUMAN	G	62	ENSP00000367797:A62G	ENSP00000367797:A62G	A	+	2	0	SKI	2150250	0.994000	0.37717	0.998000	0.56505	0.971000	0.66376	0.878000	0.28126	1.104000	0.41587	0.185000	0.17295	GCG	C|0.953;G|0.047		0.776	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		G	2160390	C	G	2160390	3	3	68	1	0	0	0	0	1	0	0	0	14389	768	27	4	187	4	SKI	1	2160390	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		2160390	247090231	1	6451											
SRRM1	10250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24979017	24979017	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaagaaaaggagaaggagaAgacccgaccacgatctcggt	18	3	12	8	3	1	4	0	0	1	4	2	8	1	4	2	3	0	0	2	3	6	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:24979017A>T	ENST00000323848.9	+	7	1133	c.818A>T	c.(817-819)aAg>aTg	p.K273M	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.K273M|SRRM1_ENST00000537199.1_Missense_Mutation_p.K142M|SRRM1_ENST00000447431.2_Missense_Mutation_p.K273M	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	273	Arg-rich.|Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GAGAAGGAGAAGACCCGACCA	0.502																																					p.K273M	Ovarian(68;897 1494 3282 17478)	.											.	SRRM1-93	0			c.A818T						.						34	36	36					1																	24979017		2203	4300	6503	SO:0001583	missense	10250	exon7			AGGAGAAGACCCG	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.818A>T	1.37:g.24979017A>T	ENSP00000326261:p.Lys273Met	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	25	7	NM_005839	0	0	39	68	29	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093181	0.56075	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389;ENST00000537199	T;T;T;T	0.52754	0.76;0.76;0.76;0.65	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000003	T	0.46347	0.1388	N	0.19112	0.55	0.45791	D	0.998673	D;D	0.58620	0.983;0.971	P;P	0.55824	0.785;0.615	T	0.50233	-0.8852	10	0.66056	D	0.02	-2.6317	10.596	0.45338	0.9281:0.0:0.0719:0.0	.	273;273	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	M	273;273;273;142	ENSP00000326261:K273M;ENSP00000391430:K273M;ENSP00000363510:K273M;ENSP00000441776:K142M	ENSP00000326261:K273M	K	+	2	0	SRRM1	24851604	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	3.872000	0.56085	2.320000	0.78422	0.528000	0.53228	AAG	.		0.502	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24979017	A	T	24979017	3	4	68	1	0	0	0	0	1	0	0	0	15200	72	3	5	844	5	SRRM1	1	24979017	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	22818627	24979017	224271604	2	6452											
SRRM1	10250	hgsc.bcm.edu	37	chr1	24993412	24993412	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccacaccaccaccacgaCgaaggtactttgtcaaatat	13	8	5	15	2	1	0	1	0	0	0	2	2	2	0	4	1	1	1	4	1	4	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:24993412C>G	ENST00000323848.9	+	13	2050	c.1735C>G	c.(1735-1737)Cga>Gga	p.R579G	snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.R588G|SRRM1_ENST00000447431.2_Missense_Mutation_p.R591G	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	579	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		ACCACCACGACGAAGGTACTT	0.577																																					p.R579G	Ovarian(68;897 1494 3282 17478)	.											.	SRRM1-93	0			c.C1735G						.						52	43	46					1																	24993412		2203	4300	6503	SO:0001583	missense	10250	exon13			CCACGACGAAGGT	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1735C>G	1.37:g.24993412C>G	ENSP00000326261:p.Arg579Gly	Somatic	54	2		WXS	Illumina HiSeq	Phase_I	42	3	NM_005839	0	0	0	0	0	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.306626	0.81247	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.36699	1.24;1.24;1.24	5.66	5.66	0.87406	.	0.000000	0.52532	D	0.000077	T	0.60090	0.2242	M	0.62723	1.935	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.76575	0.988;0.972	T	0.60016	-0.7345	10	0.62326	D	0.03	-1.8915	19.3453	0.94361	0.0:1.0:0.0:0.0	.	591;579	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	G	579;591;588	ENSP00000326261:R579G;ENSP00000391430:R591G;ENSP00000363510:R588G	ENSP00000326261:R579G	R	+	1	2	SRRM1	24865999	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	4.350000	0.59392	2.654000	0.90174	0.650000	0.86243	CGA	.		0.577	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		G	24993412	C	G	24993412	3	3	68	1	0	0	0	0	1	0	0	0	15200	528	19	4	1785	4	SRRM1	1	24993412	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	14395	24993412	224257209	3	6453											
PEF1	553115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	32100869	32100869	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccgtaggaacttggaggTggctgaccataggggccccc	8	6	15	12	1	0	1	0	1	0	0	0	3	0	3	4	6	1	3	4	6	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:32100869T>C	ENST00000373703.4	-	2	301	c.279A>G	c.(277-279)ccA>ccG	p.P93P	PEF1_ENST00000440872.2_Silent_p.P93P|PEF1_ENST00000492061.1_5'UTR	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	93	9 X 9 AA approximate tandem repeat of [AP]-P-G-G-P-Y-G-G-P-P.				proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		AACTTGGAGGTGGCTGACCAT	0.587																																					p.P93P		.											.	PEF1-68	0			c.A279G						.						49	51	50					1																	32100869		2203	4300	6503	SO:0001819	synonymous_variant	553115	exon2			TGGAGGTGGCTGA		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"EF-hand domain containing"	30009	protein-coding gene	gene with protein product	"peflin"	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.279A>G	1.37:g.32100869T>C		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	93	21	NM_012392	0	1	43	88	44		Silent	SNP	ENST00000373703.4	37	CCDS345.1																																																																																			.		0.587	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392		C	32100869	T	C	32100869	2	2	68	1	0	0	0	0	0	0	0	1	11744	1683	59	3		3	PEF1	1	32100869	Silent	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	7107457	32100869	217149752	4	6454											
AKR1A1	10327	ucsc.edu	37	chr1	46032694	46032694	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggccttatgcctttgagTgagccttgccagagcctcat	7	12	10	12	0	1	3	1	2	0	1	1	3	1	3	5	1	4	0	5	1	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:46032694T>C	ENST00000372070.3	+	5	1103		c.e5+2		AKR1A1_ENST00000351829.4_Splice_Site|AKR1A1_ENST00000471651.1_Nonstop_Mutation_p.*120R	NM_001202413.1|NM_001202414.1|NM_006066.3	NP_001189342.1|NP_001189343.1|NP_006057.1	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1 (aldehyde reductase)						aldehyde catabolic process (GO:0046185)|cellular aldehyde metabolic process (GO:0006081)|D-glucuronate catabolic process (GO:0042840)|glucose metabolic process (GO:0006006)|L-ascorbic acid biosynthetic process (GO:0019853)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|L-glucuronate reductase activity (GO:0047939)			lung(3)|prostate(1)|urinary_tract(1)	5	Acute lymphoblastic leukemia(166;0.155)				Doxorubicin(DB00997)	TGCCTTTGAGTGAGCCTTGCC	0.552																																					.													.	AKR1A1-226	0			c.356+2T>C						.						110	96	101					1																	46032694		2203	4300	6503	SO:0001630	splice_region_variant	10327	exon5			TTTGAGTGAGCCT	J04794	CCDS523.1	1p33-p32	2010-04-08			ENSG00000117448	ENSG00000117448	1.1.1.2	"Aldo-keto reductases"	380	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 3"	103830				2498333, 10393438	Standard	NM_001202414		Approved	ALR, DD3	uc001coe.3	P14550	OTTHUMG00000007740	ENST00000372070.3:c.356+2T>C	1.37:g.46032694T>C		Somatic	113	0		WXS	Illumina HiSeq		92	2	NM_001202413	0	0	6	6	0	A8KAL8|D3DQ04|Q6IAZ4	Splice_Site	SNP	ENST00000372070.3	37	CCDS523.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.924867	0.52759	.	.	ENSG00000117448	ENST00000372070;ENST00000434299;ENST00000351829	.	.	.	5.83	3.48	0.39840	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1397	0.31076	0.1203:0.0654:0.0:0.8143	.	.	.	.	.	-1	.	.	.	+	.	.	AKR1A1	45805281	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	7.965000	0.87945	0.454000	0.26884	-0.352000	0.07741	.	.		0.552	AKR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020851.1	NM_006066	Intron	C	46032694	T	C	46032694	5	2	68	1	0	0	0	0	0	0	1	0	465	1710	59	3	368	3	AKR1A1	1	46032694	Splice_Site	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	13931825	46032694	203217927	5	6455											
SLC1A7	6512	broad.mit.edu	37	chr1	53555558	53555558	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgaccatggtgacgaggccGgcctgggggatgccagctgc	7	6	17	11	2	0	2	0	2	0	0	0	4	0	3	4	5	3	1	4	5	0	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:53555558G>A	ENST00000371494.4	-	9	1402	c.1275C>T	c.(1273-1275)gcC>gcT	p.A425A	SLC1A7_ENST00000488036.1_5'UTR	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	425					dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.A425A(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		TGACGAGGCCGGCCTGGGGGA	0.627																																					p.A425A	NSCLC(128;80 1811 21245 38490 51715)												.	SLC1A7-155	1	Substitution - coding silent(1)	lung(1)	c.C1275T						.						73	66	69					1																	53555558		2203	4300	6503	SO:0001819	synonymous_variant	6512	exon9			GAGGCCGGCCTGG	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"Solute carriers"	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.1275C>T	1.37:g.53555558G>A		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	70	3	NM_006671	0	0	0	0	0	Q5VVZ0|Q969Z8|Q9BW45	Silent	SNP	ENST00000371494.4	37	CCDS574.1																																																																																			.		0.627	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671		A	53555558	G	A	53555558	2	1	68	1	0	0	0	0	0	0	0	1	14469	1103	39	1		1	SLC1A7	1	53555558	Silent	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	7522864	53555558	195695063	6	6456											
SIPA1L2	57568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	232650793	232650793	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgagaccggctttcccacAgtgccttgcatgttagctcc	6	12	9	14	1	1	1	0	1	1	1	3	2	3	1	4	1	3	4	4	1	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:232650793A>C	ENST00000366630.1	-	2	651	c.293T>G	c.(292-294)cTg>cGg	p.L98R	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.L98R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	98					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GCTTTCCCACAGTGCCTTGCA	0.517																																					p.L98R		.											.	SIPA1L2-95	0			c.T293G						.						156	154	155					1																	232650793		2020	4187	6207	SO:0001583	missense	57568	exon1			TCCCACAGTGCCT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.293T>G	1.37:g.232650793A>C	ENSP00000355589:p.Leu98Arg	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	177	39	NM_020808	0	0	3	4	1	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	A	0.689	-0.795281	0.02862	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.78816	-1.21;-1.21	5.19	4.02	0.46733	.	0.630597	0.14001	N	0.348152	T	0.50171	0.1600	N	0.08118	0	0.09310	N	1	P	0.39216	0.664	B	0.32289	0.143	T	0.35325	-0.9793	10	0.14252	T	0.57	-9.9849	5.5611	0.17144	0.6384:0.0:0.3616:0.0	.	98	Q9P2F8	SI1L2_HUMAN	R	98	ENSP00000355589:L98R;ENSP00000262861:L98R	ENSP00000262861:L98R	L	-	2	0	SIPA1L2	230717416	0.005000	0.15991	0.062000	0.19696	0.262000	0.26303	1.251000	0.32862	0.942000	0.37525	0.528000	0.53228	CTG	.		0.517	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		C	232650793	A	C	232650793	3	2	68	1	0	0	0	0	1	0	0	0	14362	188	7	5	4959	5	SIPA1L2	1	232650793	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	179095235	232650793	16599828	7	6457											
DNMT3A	1788	broad.mit.edu	37	chr2	25469548	25469548	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccccccagggcccattcaAtcatgggcttgttctgcacc	7	9	9	16	0	3	0	2	0	1	0	3	0	3	0	5	2	2	3	5	2	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:25469548A>G	ENST00000264709.3	-	10	1557	c.1220T>C	c.(1219-1221)aTt>aCt	p.I407T	DNMT3A_ENST00000380746.4_Missense_Mutation_p.I218T|DNMT3A_ENST00000402667.1_Missense_Mutation_p.I184T|DNMT3A_ENST00000321117.5_Missense_Mutation_p.I407T|DNMT3A_ENST00000474887.1_5'Flank	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	407					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.I407S(1)|p.I407T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCCCATTCAATCATGGGCTT	0.647			"Mis, F, N, S"		AML																																p.I407T				Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A-1924	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1220C						.						67	66	66					2																	25469548		2203	4298	6501	SO:0001583	missense	1788	exon10			CATTCAATCATGG		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1220T>C	2.37:g.25469548A>G	ENSP00000264709:p.Ile407Thr	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	123	3	NM_175629	0	0	14	14	0	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	37	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184390	0.78677	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.80470	0.4629	M	0.61703	1.905	0.80722	D	1	D;D	0.63880	0.993;0.99	D;P	0.68192	0.956;0.852	T	0.82352	-0.0500	10	0.72032	D	0.01	-7.9615	12.4658	0.55757	1.0:0.0:0.0:0.0	.	407;218	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	T	218;407;407;184	ENSP00000370122:I218T;ENSP00000324375:I407T;ENSP00000264709:I407T;ENSP00000384237:I184T	ENSP00000264709:I407T	I	-	2	0	DNMT3A	25323052	1.000000	0.71417	0.998000	0.56505	0.770000	0.43624	8.987000	0.93497	2.050000	0.60909	0.533000	0.62120	ATT	.		0.647	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		G	25469548	A	G	25469548	3	3	68	1	0	0	0	0	1	0	0	0	4687	101	4	3	1574	3	DNMT3A	2	25469548	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		25469548	217729825	8	6458											
SOS1	6654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	39285904	39285904	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gattgggcatcagctattgcCcatttatcaattggatgagg	10	13	11	7	0	2	1	2	1	0	0	2	3	2	2	1	3	2	2	1	3	3	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:39285904C>T	ENST00000426016.1	-	4	341	c.255G>A	c.(253-255)tgG>tgA	p.W85*	SOS1_ENST00000402219.2_Nonsense_Mutation_p.W85*|SOS1_ENST00000395038.2_Nonsense_Mutation_p.W85*|SOS1_ENST00000428721.2_Nonsense_Mutation_p.W28*			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	85					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				CAGCTATTGCCCATTTATCAA	0.338									Noonan syndrome																												p.W85X		.											.	SOS1-851	0			c.G255A						.						75	76	76					2																	39285904		2202	4300	6502	SO:0001587	stop_gained	6654	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TATTGCCCATTTA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.255G>A	2.37:g.39285904C>T	ENSP00000387784:p.Trp85*	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	109	33	NM_005633	0	0	11	16	5	A8K2G3|B4DXG2	Nonsense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005675	0.93287	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721;ENST00000451331	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.9598	0.97242	0.0:1.0:0.0:0.0	.	.	.	.	X	85;85;85;85;28;28	.	ENSP00000263879:W85X	W	-	3	0	SOS1	39139408	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.711000	0.84669	2.716000	0.92895	0.655000	0.94253	TGG	.		0.338	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39285904	C	T	39285904	4	4	68	1	0	0	0	0	0	1	0	0	14968	624	22	2	3830	2	SOS1	2	39285904	Nonsense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	13816356	39285904	203913469	9	6459											
TANC1	85461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160086335	160086335	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gaagaggaagaaacttctccCcaggaagaatctgtttcccc	13	8	9	11	0	2	3	0	0	2	3	4	6	3	5	4	2	1	1	4	2	5	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:160086335C>A	ENST00000263635.6	+	27	4635	c.4398C>A	c.(4396-4398)ccC>ccA	p.P1466P	TANC1_ENST00000454300.1_Silent_p.P1360P	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1466					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						AAACTTCTCCCCAGGAAGAAT	0.517																																					p.P1466P		.											.	TANC1-92	0			c.C4398A						.						94	104	101					2																	160086335		1964	4133	6097	SO:0001819	synonymous_variant	85461	exon27			TTCTCCCCAGGAA	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.4398C>A	2.37:g.160086335C>A		Somatic	146	1		WXS	Illumina HiSeq	Phase_I	144	36	NM_033394	0	0	7	9	2	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			.		0.517	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			A	160086335	C	A	160086335	2	1	68	1	0	0	0	0	0	0	0	1	15576	610	22	4		4	TANC1	2	160086335	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	120800431	160086335	83113038	10	6460											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	170034511	170034513	+	In_Frame_Del	DEL	GAT	GAT	-																															cccatcatacaccgtgtgtcGatggtggccctccaaatcag																								rs80338752		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:170034511_170034513delGAT	ENST00000263816.3	-	53	10478_10480	c.10193_10195delATC	c.(10192-10197)catcga>cga	p.H3398del	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3398					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.R3399*(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	ACCGTGTGTCGATGGTGGCCCTC	0.424																																					p.3398_3399del		.											.	LRP2-175	1	Substitution - Nonsense(1)	large_intestine(1)	c.10193_10195del	GRCh37	CM073183	LRP2	M	rs80338752	.																																			SO:0001651	inframe_deletion	4036	exon53			.		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10193_10195delATC	2.37:g.170034511_170034513delGAT	ENSP00000263816:p.His3398del	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	58	12	NM_004525	0	0	0	0	0	O00711|Q16215	In_Frame_Del	DEL	ENST00000263816.3	37	CCDS2232.1																																																																																			.		0.424	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170034513	GAT	-	170034511	7	5	68	1	0	1	0	1	0	0	0	0	8981	1066	37	0	3880	0	LRP2	2	170034511	In_Frame_Del	DEL	GAT	TCGA-BQ-5884-01A-11D-1589-08	9948176	170034511	73164862	11	6461											
IRS1	3667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	227662872	227662872	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctccgagttcagcttcaCgaagctgatggtcttgctgg	6	12	12	11	2	3	1	2	1	1	0	4	3	4	1	2	2	4	4	2	2	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:227662872C>T	ENST00000305123.5	-	1	1603	c.583G>A	c.(583-585)Gtg>Atg	p.V195M	IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	195	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TTCAGCTTCACGAAGCTGATG	0.567											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V195M		.											.	IRS1-1272	0			c.G583A						.						57	55	56					2																	227662872		2203	4300	6503	SO:0001583	missense	3667	exon1			GCTTCACGAAGCT		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"Pleckstrin homology (PH) domain containing"	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.583G>A	2.37:g.227662872C>T	ENSP00000304895:p.Val195Met	Somatic	86	0	2321	WXS	Illumina HiSeq	Phase_I	93	23	NM_005544	0	0	7	10	3		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366266	0.82463	.	.	ENSG00000169047	ENST00000305123	T	0.74526	-0.85	5.79	5.79	0.91817	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4);	0.000000	0.64402	D	0.000017	D	0.87661	0.6233	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87579	0.2483	10	0.56958	D	0.05	-29.8384	20.0212	0.97504	0.0:1.0:0.0:0.0	.	195	P35568	IRS1_HUMAN	M	195	ENSP00000304895:V195M	ENSP00000304895:V195M	V	-	1	0	IRS1	227371116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.735000	0.93741	0.561000	0.74099	GTG	.		0.567	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		T	227662872	C	T	227662872	3	4	68	1	0	0	0	0	1	0	0	0	7861	536	19	1	3149	1	IRS1	2	227662872	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	57628361	227662872	15536501	12	6462											
ALS2CL	259173	broad.mit.edu	37	chr3	46725271	46725271	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacagctcacccacactcaCctggccctgggagtccttgg	7	8	9	17	0	3	0	3	0	0	0	4	1	4	1	4	3	1	1	4	3	0	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr3:46725271C>T	ENST00000318962.4	-	9	996		c.e9+1		ALS2CL_ENST00000415953.1_Splice_Site	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like						endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCCACACTCACCTGGCCCTGG	0.617																																					.													.	ALS2CL-155	0			c.912+1G>A						.						139	141	140					3																	46725271		2203	4300	6503	SO:0001630	splice_region_variant	259173	exon10			CACTCACCTGGCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.912+1G>A	3.37:g.46725271C>T		Somatic	327	0		WXS	Illumina HiSeq	Phase_I	235	7	NM_001190707	0	0	0	0	0	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Splice_Site	SNP	ENST00000318962.4	37	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764058	0.69878	.	.	ENSG00000178038	ENST00000318962;ENST00000415953	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8568	0.78983	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ALS2CL	46700275	1.000000	0.71417	0.988000	0.46212	0.799000	0.45148	4.474000	0.60203	2.609000	0.88269	0.655000	0.94253	.	.		0.617	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	Intron	T	46725271	C	T	46725271	5	4	68	1	0	0	0	0	0	0	1	0	551	521	18	2	2020	2	ALS2CL	3	46725271	Splice_Site	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		46725271	151297159	13	6463											
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122632248	122632248	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgcacttcggggcagccCtcggggttgcacgtcttgaa	5	8	14	14	5	1	1	0	1	1	0	3	1	1	1	2	4	2	4	2	4	1	3	rs183401039	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr3:122632248C>G	ENST00000357599.3	-	17	2690	c.2304G>C	c.(2302-2304)gaG>gaC	p.E768D	SEMA5B_ENST00000451055.2_Missense_Mutation_p.E822D|SEMA5B_ENST00000195173.4_Missense_Mutation_p.E767D	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	768	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CGGGGCAGCCCTCGGGGTTGC	0.701													C|||	39	0.00778754	0.028	0.0029	5008	,	,		12549	0		0	False		,,,				2504	0				p.E822D		.											.	SEMA5B-157	0			c.G2466C						.	C	ASP/GLU	67,4271		0,67,2102	8	10	9		2304	-1.4	0.5	3		9	0,8524		0,0,4262	yes	missense	SEMA5B	NM_001031702.2	45	0,67,6364	GG,GC,CC		0.0,1.5445,0.5209	benign	768/1152	122632248	67,12795	2169	4262	6431	SO:0001583	missense	54437	exon17			GCAGCCCTCGGGG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"Semaphorins"	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2304G>C	3.37:g.122632248C>G	ENSP00000350215:p.Glu768Asp	Somatic	10	1		WXS	Illumina HiSeq	Phase_I	17	3	NM_001256347	0	0	0	0	0	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	9.118	1.008295	0.19199	0.015445	0.0	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	4.21	-1.36	0.09085	.	0.290114	0.36444	N	0.002595	T	0.11410	0.0278	N	0.20986	0.625	0.33813	D	0.628111	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.15052	0.007;0.012;0.012	T	0.11792	-1.0573	10	0.27082	T	0.32	.	12.3916	0.55362	0.0:0.4912:0.4387:0.07	.	710;768;768	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	D	768;767;710;822;768	ENSP00000350215:E768D;ENSP00000195173:E767D;ENSP00000389588:E822D;ENSP00000377208:E768D	ENSP00000195173:E767D	E	-	3	2	SEMA5B	124114938	0.655000	0.27376	0.474000	0.27266	0.617000	0.37484	0.231000	0.17872	-0.948000	0.03668	-1.268000	0.01426	GAG	C|0.993;G|0.007		0.701	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		G	122632248	C	G	122632248	3	3	68	1	0	0	0	0	1	0	0	0	14070	680	24	4	1179	4	SEMA5B	3	122632248	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	75906977	122632248	75390182	14	6464											
CPNE4	131034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	131254172	131254172	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccagggcagctggagatGcctgcagggaagaagaaatc	12	6	15	8	0	0	3	0	0	0	3	1	5	0	4	2	3	4	3	2	3	3	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr3:131254172G>A	ENST00000512055.1	-	20	3667	c.1541C>T	c.(1540-1542)gCa>gTa	p.A514V	CPNE4_ENST00000511604.1_Splice_Site_p.A514V|CPNE4_ENST00000502818.1_Splice_Site_p.A532V|CPNE4_ENST00000503204.1_5'UTR|CPNE4_ENST00000429747.1_Splice_Site_p.A514V|CPNE4_ENST00000512332.1_Splice_Site_p.A532V			Q96A23	CPNE4_HUMAN	copine IV	514						extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						AGCTGGAGATGCCTGCAGGGA	0.453																																					p.A514V		.											.	CPNE4-92	0			c.C1541T						.						97	91	93					3																	131254172		2203	4300	6503	SO:0001630	splice_region_variant	131034	exon16			GGAGATGCCTGCA	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1540-1C>T	3.37:g.131254172G>A		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	114	25	NM_130808	0	0	0	0	0	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	37	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766296	0.69878	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.70996	0.3288	M	0.76838	2.35	0.80722	D	1	P;B	0.44627	0.839;0.361	P;B	0.56563	0.801;0.134	T	0.72050	-0.4407	10	0.48119	T	0.1	-15.9346	18.8677	0.92300	0.0:0.0:1.0:0.0	.	532;514	Q96A23-2;Q96A23	.;CPNE4_HUMAN	V	514;514;532;514;532	ENSP00000421705:A514V;ENSP00000411904:A514V;ENSP00000424853:A532V;ENSP00000423811:A514V;ENSP00000421646:A532V	ENSP00000411904:A514V	A	-	2	0	CPNE4	132736862	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	9.476000	0.97823	2.460000	0.83146	0.557000	0.71058	GCA	.		0.453	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	Missense_Mutation	A	131254172	G	A	131254172	5	1	68	1	0	0	0	0	0	0	1	0	3820	1333	46	2	136	2	CPNE4	3	131254172	Splice_Site	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	8621924	131254172	66768258	15	6465											
SUCNR1	56670	broad.mit.edu	37	chr3	151599109	151599110	+	Frame_Shift_Ins	INS	-	-	T																															tgtgaggatcgcttcacgccINStggggagttggaagcagtat																								rs368899419		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr3:151599109_151599110insT	ENST00000362032.5	+	3	883_884	c.778_779insT	c.(778-780)ctgfs	p.L260fs	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	260						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	CGCTTCACGCCTGGGGAGTTGG	0.49																																					p.L260fs													.	SUCNR1-711	0			c.778_779insT						.																																			SO:0001589	frameshift_variant	56670	exon3			TCACGCCTGGGGA	AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"GPCR / Class A : Orphans"	4542	protein-coding gene	gene with protein product		606381	"G protein-coupled receptor 91"	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.779dupT	3.37:g.151599110_151599110dupT	ENSP00000355156:p.Leu260fs	Somatic	286	0		WXS	Illumina HiSeq	Phase_I	244	13	NM_033050	0	0	0	0	0	A8K305|Q8TDQ8	Frame_Shift_Ins	INS	ENST00000362032.5	37	CCDS3162.1																																																																																			.		0.49	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		T	151599110	-	T	151599109	7	5	68	1	0	1	1	0	0	0	0	0	15398	680	24	0	784	0	SUCNR1	3	151599109	Frame_Shift_Ins	INS	-	TCGA-BQ-5884-01A-11D-1589-08	20344937	151599109	46423321	16	6466											
TIFA	92610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	113199250	113199250	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctgtatggcaggtccattTtatttaggtagcccagctct	8	14	9	10	0	1	0	0	0	1	0	2	0	2	0	3	3	2	4	3	3	4	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr4:113199250T>G	ENST00000361717.3	-	2	604	c.323A>C	c.(322-324)aAa>aCa	p.K108T	TIFA_ENST00000500655.2_Missense_Mutation_p.K108T	NM_052864.2	NP_443096.1	Q96CG3	TIFA_HUMAN	TRAF-interacting protein with forkhead-associated domain	108					I-kappaB kinase/NF-kappaB signaling (GO:0007249)					breast(2)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)	6		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00172)		CAGGTCCATTTTATTTAGGTA	0.388																																					p.K108T		.											.	TIFA-90	0			c.A323C						.						45	42	43					4																	113199250		2203	4300	6503	SO:0001583	missense	92610	exon2			TCCATTTTATTTA	BC008294	CCDS34051.1	4q25	2008-03-17				ENSG00000145365			19075	protein-coding gene	gene with protein product	"TRAF2 binding protein", "TRAF6 binding protein"	609028				1179819	Standard	NM_052864		Approved	MGC20791, T2BP, T6BP, TIFAA	uc003ial.3	Q96CG3		ENST00000361717.3:c.323A>C	4.37:g.113199250T>G	ENSP00000354911:p.Lys108Thr	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	56	16	NM_052864	0	1	8	16	7		Missense_Mutation	SNP	ENST00000361717.3	37	CCDS34051.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.382639	0.82792	.	.	ENSG00000145365	ENST00000361717;ENST00000500655	D;D	0.86694	-2.16;-2.16	5.79	5.79	0.91817	Forkhead-associated (FHA) domain (2);	0.092657	0.64402	D	0.000001	D	0.92916	0.7746	M	0.71581	2.175	0.50813	D	0.999896	D	0.89917	1.0	D	0.91635	0.999	D	0.93532	0.6870	10	0.72032	D	0.01	-34.6044	16.1303	0.81428	0.0:0.0:0.0:1.0	.	108	Q96CG3	TIFA_HUMAN	T	108	ENSP00000354911:K108T;ENSP00000424231:K108T	ENSP00000354911:K108T	K	-	2	0	TIFA	113418699	1.000000	0.71417	0.077000	0.20336	0.992000	0.81027	3.462000	0.53042	2.218000	0.71995	0.533000	0.62120	AAA	.		0.388	TIFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363647.2	NM_052864		G	113199250	T	G	113199250	3	3	68	1	0	0	0	0	1	0	0	0	15926	1841	64	5	235	5	TIFA	4	113199250	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08		113199250	77955026	17	6467											
METTL14	57721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	119631350	119631350	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaggaagaggtggaactTctgctggccgtggacgagaa	10	7	18	6	2	1	2	0	0	1	2	1	7	1	6	1	6	2	1	1	6	3	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr4:119631350T>A	ENST00000388822.5	+	11	1431	c.1264T>A	c.(1264-1266)Tct>Act	p.S422T	METTL14_ENST00000506780.1_Missense_Mutation_p.S384T			Q9HCE5	MET14_HUMAN	methyltransferase like 14	422	Gly-rich.				mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						AGGTGGAACTTCTGCTGGCCG	0.527																																					p.S422T		.											.	METTL14-90	0			c.T1264A						.						56	58	58					4																	119631350		2203	4300	6503	SO:0001583	missense	57721	exon11			GGAACTTCTGCTG	AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.1264T>A	4.37:g.119631350T>A	ENSP00000373474:p.Ser422Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	93	16	NM_020961	0	0	13	22	9	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	37	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.469312	0.43839	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.62	4.42	0.53409	.	0.215770	0.49305	D	0.000149	T	0.30448	0.0765	N	0.14661	0.345	0.38962	D	0.958572	B;B	0.29037	0.231;0.139	B;B	0.19946	0.027;0.027	T	0.11916	-1.0568	9	0.08381	T	0.77	-2.7465	12.8488	0.57846	0.0:0.0:0.1363:0.8637	.	384;422	D6RBL4;Q9HCE5	.;MTL14_HUMAN	T	422;384	.	ENSP00000373474:S422T	S	+	1	0	METTL14	119850798	1.000000	0.71417	0.961000	0.40146	0.958000	0.62258	4.909000	0.63314	0.937000	0.37394	0.528000	0.53228	TCT	.		0.527	METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961		A	119631350	T	A	119631350	3	1	68	1	0	0	0	0	1	0	0	0	9523	1783	62	5	1306	5	METTL14	4	119631350	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	6432100	119631350	71522926	18	6468											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123161284	123161284	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tagaacatctatatattgtaGaaggtgagaaaacagtggag	17	10	11	3	0	1	3	0	1	1	3	1	5	1	4	0	2	2	1	0	2	9	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr4:123161284G>C	ENST00000264501.4	+	29	4820	c.4447G>C	c.(4447-4449)Gaa>Caa	p.E1483Q	KIAA1109_ENST00000455637.1_Missense_Mutation_p.E1483Q|KIAA1109_ENST00000388738.3_Missense_Mutation_p.E1483Q			Q2LD37	K1109_HUMAN	KIAA1109	1483					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATATATTGTAGAAGGTGAGAA	0.398																																					p.E1483Q		.											.	KIAA1109-80	0			c.G4447C						.						118	113	114					4																	123161284		1871	4109	5980	SO:0001583	missense	84162	exon27			ATTGTAGAAGGTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.4447G>C	4.37:g.123161284G>C	ENSP00000264501:p.Glu1483Gln	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	103	23	NM_015312	0	0	13	28	15	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.16|17.16	3.318796|3.318796	0.60524|0.60524	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.24908|.	2.42;2.42;1.83|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.000000|.	0.44285|.	U|.	0.000466|.	T|.	0.57125|.	0.2032|.	N|N	0.24115|0.24115	0.695|0.695	0.49798|0.49798	D|D	0.999822|0.999822	B;B|.	0.32245|.	0.361;0.247|.	B;B|.	0.42343|.	0.384;0.214|.	T|.	0.49184|.	-0.8966|.	10|.	0.66056|.	D|.	0.02|.	.|.	20.2885|20.2885	0.98538|0.98538	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1482;1483|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	Q|Y	1483|55	ENSP00000264501:E1483Q;ENSP00000373390:E1483Q;ENSP00000389925:E1483Q|.	ENSP00000264501:E1483Q|.	E|X	+|+	1|3	0|2	KIAA1109|KIAA1109	123380734|123380734	1.000000|1.000000	0.71417|0.71417	0.874000|0.874000	0.34290|0.34290	0.951000|0.951000	0.60555|0.60555	8.632000|8.632000	0.90995|0.90995	2.791000|2.791000	0.96007|0.96007	0.650000|0.650000	0.86243|0.86243	GAA|TAG	.		0.398	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123161284	G	C	123161284	3	2	68	1	0	0	0	0	1	0	0	0	8229	943	33	4	4553	4	KIAA1109	4	123161284	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	3529934	123161284	67992992	19	6469											
ATG10	83734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	81474374	81474374	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgctataagatgcgactgCtacagggaccatgggacact	12	8	12	9	1	0	1	0	0	0	1	0	4	0	3	1	2	4	2	1	2	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:81474374C>A	ENST00000282185.3	+	5	715	c.421C>A	c.(421-423)Cta>Ata	p.L141I	ATG10_ENST00000458350.3_Missense_Mutation_p.L141I|ATG10_ENST00000513634.1_Missense_Mutation_p.L141I|ATG10_ENST00000514253.2_3'UTR	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	141					autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		GATGCGACTGCTACAGGGACC	0.418																																					p.L141I		.											.	ATG10-90	0			c.C421A						.						209	180	190					5																	81474374		2203	4300	6503	SO:0001583	missense	83734	exon6			CGACTGCTACAGG	AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"APG10 autophagy 10-like (S. cerevisiae)", "ATG10 autophagy related 10 homolog (S. cerevisiae)"	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.421C>A	5.37:g.81474374C>A	ENSP00000282185:p.Leu141Ile	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	69	15	NM_001131028	0	0	15	25	10	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	37	CCDS4057.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.413463	0.62511	.	.	ENSG00000152348	ENST00000282185;ENST00000458350;ENST00000513634	T;T;T	0.45276	1.9;1.9;0.9	5.37	3.56	0.40772	Autophagy-related protein 3 (1);	0.380233	0.27105	N	0.020920	T	0.43344	0.1243	L	0.55990	1.75	0.28013	N	0.934837	B;P	0.42620	0.175;0.785	B;P	0.46419	0.174;0.516	T	0.32161	-0.9917	10	0.37606	T	0.19	-3.2788	10.6892	0.45860	0.0:0.8444:0.0:0.1556	.	141;141	D6RDX3;Q9H0Y0	.;ATG10_HUMAN	I	141	ENSP00000282185:L141I;ENSP00000404938:L141I;ENSP00000425225:L141I	ENSP00000282185:L141I	L	+	1	2	ATG10	81510130	0.946000	0.32159	0.933000	0.37362	0.790000	0.44656	0.765000	0.26546	1.392000	0.46585	0.305000	0.20034	CTA	.		0.418	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028		A	81474374	C	A	81474374	3	1	68	1	0	0	0	0	1	0	0	0	1090	796	28	4	435	4	ATG10	5	81474374	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		81474374	99440886	20	6470											
WDR36	134430	broad.mit.edu	37	chr5	110428267	110428267	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggttcagcgcgctcaagcGccggttctatgtaacaacct	8	9	11	13	5	3	0	2	0	1	0	3	0	3	0	2	2	4	4	2	2	4	4			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:110428267G>T	ENST00000513710.2	+	1	285	c.281G>T	c.(280-282)cGc>cTc	p.R94L	WDR36_ENST00000506538.2_Missense_Mutation_p.R94L|CTC-551A13.2_ENST00000507269.3_RNA|WDR36_ENST00000505303.1_Missense_Mutation_p.R38L			Q8NI36	WDR36_HUMAN	WD repeat domain 36	94					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GCGCTCAAGCGCCGGTTCTAT	0.567																																					p.R94L													.	WDR36-92	0			c.G281T						.						37	37	37					5																	110428267		2202	4300	6502	SO:0001583	missense	134430	exon1			TCAAGCGCCGGTT	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"WD repeat domain containing"	30696	protein-coding gene	gene with protein product		609669	"glaucoma 1, open angle, G"	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.281G>T	5.37:g.110428267G>T	ENSP00000424628:p.Arg94Leu	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	38	5	NM_139281	0	0	11	12	1	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	37	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789609	0.70337	.	.	ENSG00000134987	ENST00000506538;ENST00000513710;ENST00000505303	T;T;T	0.28454	1.61;1.61;3.28	5.98	5.11	0.69529	WD40 repeat-like-containing domain (1);	0.108665	0.64402	D	0.000010	T	0.28599	0.0708	M	0.67397	2.05	0.58432	D	0.999996	P	0.38767	0.646	B	0.30855	0.121	T	0.15206	-1.0445	10	0.87932	D	0	-5.4709	9.7297	0.40352	0.0738:0.1425:0.7836:0.0	.	94	Q8NI36	WDR36_HUMAN	L	94;94;38	ENSP00000423067:R94L;ENSP00000424628:R94L;ENSP00000422158:R38L	ENSP00000422158:R38L	R	+	2	0	WDR36	110456166	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.469000	0.60169	1.520000	0.48965	0.650000	0.86243	CGC	.		0.567	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		T	110428267	G	T	110428267	3	4	68	1	0	0	0	0	1	0	0	0	17323	1087	38	4	283	4	WDR36	5	110428267	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	28953893	110428267	70486993	21	6471											
ARHGAP26	23092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	142283206	142283206	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accatcagtccctacaccatGgagggatacctctacgtgca	11	8	8	14	1	2	0	1	0	1	0	3	2	3	2	4	2	4	1	4	2	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:142283206G>C	ENST00000274498.4	+	8	1182	c.804G>C	c.(802-804)atG>atC	p.M268I	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.M268I	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	268	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTACACCATGGAGGGATACC	0.473																																					p.M268I		.											.	ARHGAP26-660	0			c.G804C						.						97	84	88					5																	142283206		2203	4300	6503	SO:0001583	missense	23092	exon8			CACCATGGAGGGA	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.804G>C	5.37:g.142283206G>C	ENSP00000274498:p.Met268Ile	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	54	11	NM_015071	0	0	24	37	13	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018359	0.35606	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.04317	3.65;3.65	5.49	5.49	0.81192	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.09379	0.0231	L	0.38953	1.18	0.80722	D	1	P;P	0.37548	0.481;0.599	B;P	0.46076	0.186;0.503	T	0.39231	-0.9624	10	0.25751	T	0.34	.	19.3843	0.94550	0.0:0.0:1.0:0.0	.	268;268	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	I	268	ENSP00000274498:M268I;ENSP00000367243:M268I	ENSP00000274498:M268I	M	+	3	0	ARHGAP26	142263390	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	6.162000	0.71874	2.574000	0.86865	0.563000	0.77884	ATG	.		0.473	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		C	142283206	G	C	142283206	3	2	68	1	0	0	0	0	1	0	0	0	875	1348	47	4	834	4	ARHGAP26	5	142283206	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	31854939	142283206	38632054	22	6472											
GABRB2	2561	broad.mit.edu	37	chr5	160753381	160753381	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actggctatctaaccgtataCagagagaaatcgtaattggt	14	11	9	7	2	1	2	0	0	1	2	2	3	1	2	1	2	2	3	1	2	6	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:160753381C>G	ENST00000393959.1	-	9	1184	c.1185G>C	c.(1183-1185)ctG>ctC	p.L395L	GABRB2_ENST00000353437.6_Intron|GABRB2_ENST00000274547.2_Silent_p.L395L|GABRB2_ENST00000517547.1_Intron|GABRB2_ENST00000520240.1_Intron|GABRB2_ENST00000517901.1_Intron			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	395					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)	p.L395L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		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)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|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)	TAACCGTATACAGAGAGAAAT	0.388																																					p.L395L													.	GABRB2-91	1	Substitution - coding silent(1)	endometrium(1)	c.G1185C						.						110	107	108					5																	160753381		2203	4299	6502	SO:0001819	synonymous_variant	2561	exon10			CGTATACAGAGAG		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1185G>C	5.37:g.160753381C>G		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	113	4	NM_021911	0	0	0	0	0	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Silent	SNP	ENST00000393959.1	37	CCDS4355.1																																																																																			.		0.388	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			G	160753381	C	G	160753381	2	3	68	1	0	0	0	0	0	0	0	1	6186	465	17	4		4	GABRB2	5	160753381	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	18470175	160753381	20161879	23	6473											
DOCK2	1794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	169477372	169477372	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gaacaccacctctgccccggGagatgatgtgaagaatgccc	11	6	11	13	1	1	4	0	2	1	2	1	6	1	4	5	1	3	0	5	1	3	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:169477372G>C	ENST00000256935.8	+	41	4264	c.4184G>C	c.(4183-4185)gGa>gCa	p.G1395A	DOCK2_ENST00000540750.1_Missense_Mutation_p.G456A|DOCK2_ENST00000520908.1_Missense_Mutation_p.G887A|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1395	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTGCCCCGGGAGATGATGTG	0.562																																					p.G1395A		.											.	DOCK2-97	0			c.G4184C						.						119	111	114					5																	169477372		2203	4300	6503	SO:0001583	missense	1794	exon41			CCCCGGGAGATGA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"dedicator of cyto-kinesis 2"				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4184G>C	5.37:g.169477372G>C	ENSP00000256935:p.Gly1395Ala	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	137	32	NM_004946	0	0	49	49	0	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658712	0.47467	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.08896	3.7;3.33;3.04	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	M	0.63428	1.95	0.58432	D	0.999999	D;D	0.71674	0.998;0.994	D;P	0.72075	0.976;0.839	T	0.00320	-1.1820	10	0.30854	T	0.27	.	19.427	0.94746	0.0:0.0:1.0:0.0	.	887;1395	E7ERW7;Q92608	.;DOCK2_HUMAN	A	1395;887;456	ENSP00000256935:G1395A;ENSP00000429283:G887A;ENSP00000438827:G456A	ENSP00000256935:G1395A	G	+	2	0	DOCK2	169409950	1.000000	0.71417	0.332000	0.25469	0.198000	0.23893	7.884000	0.87274	2.603000	0.88011	0.655000	0.94253	GGA	.		0.562	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169477372	G	C	169477372	3	2	68	1	0	0	0	0	1	0	0	0	4698	1174	41	4	4346	4	DOCK2	5	169477372	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	8723991	169477372	11437888	24	6474											
F12	2161	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176831305	176831305	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctaggggacaccggggtcgGaggcgccgcctgggttgggg	4	5	21	11	4	0	0	0	0	0	0	1	2	0	2	4	9	0	1	4	9	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:176831305G>A	ENST00000253496.3	-	9	958	c.910C>T	c.(910-912)Ccg>Tcg	p.P304S	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	304	Pro-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	ACCGGGGTCGGAGGCGCCGCC	0.701									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P304S		.											.	F12-90	0			c.C910T						.						16	21	19					5																	176831305		2200	4295	6495	SO:0001583	missense	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GGGTCGGAGGCGC	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.910C>T	5.37:g.176831305G>A	ENSP00000253496:p.Pro304Ser	Somatic	38	0	1934	WXS	Illumina HiSeq	Phase_I	30	7	NM_000505	0	0	5	10	5	P78339	Missense_Mutation	SNP	ENST00000253496.3	37	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068656	0.36470	.	.	ENSG00000131187	ENST00000253496	T	0.62364	0.03	3.94	1.0	0.19881	Kringle-like fold (1);	0.463200	0.16155	N	0.227071	T	0.32912	0.0845	N	0.14661	0.345	0.19300	N	0.999975	B	0.34103	0.437	B	0.27500	0.08	T	0.22103	-1.0226	10	0.09084	T	0.74	.	6.3798	0.21527	0.0:0.1784:0.4636:0.358	.	304	P00748	FA12_HUMAN	S	304	ENSP00000253496:P304S	ENSP00000253496:P304S	P	-	1	0	F12	176763911	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.786000	0.04623	0.206000	0.20587	0.561000	0.74099	CCG	.		0.701	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176831305	G	A	176831305	3	1	68	1	0	0	0	0	1	0	0	0	5352	1174	41	2	961	2	F12	5	176831305	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	7353933	176831305	4083955	25	6475											
MAML1	9794	broad.mit.edu;bcgsc.ca	37	chr5	179193285	179193285	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caccccggcaccagccccggGccagatgtccacatggcagc	8	3	11	19	2	0	1	0	0	0	1	1	1	1	1	7	3	2	2	7	3	0	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:179193285G>T	ENST00000292599.3	+	2	1537	c.1274G>T	c.(1273-1275)gGc>gTc	p.G425V	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCAGCCCCGGGCCAGATGTCC	0.637																																					p.G425V													.	MAML1-848	0			c.G1274T						.						70	84	79					5																	179193285		2203	4300	6503	SO:0001583	missense	9794	exon2			CCCCGGGCCAGAT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1274G>T	5.37:g.179193285G>T	ENSP00000292599:p.Gly425Val	Somatic	255	0		WXS	Illumina HiSeq	Phase_I	204	8	NM_014757	0	0	31	33	2		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	G	9.410	1.080166	0.20309	.	.	ENSG00000161021	ENST00000292599;ENST00000376951	T	0.23147	1.92	4.74	3.86	0.44501	.	0.282061	0.31884	N	0.006919	T	0.26412	0.0645	L	0.40543	1.245	0.31149	N	0.705712	D;P	0.55385	0.971;0.855	P;B	0.51999	0.687;0.282	T	0.24941	-1.0146	10	0.56958	D	0.05	-12.2642	4.2806	0.10831	0.2122:0.2049:0.5829:0.0	.	462;425	Q59GH4;Q92585	.;MAML1_HUMAN	V	425;462	ENSP00000292599:G425V	ENSP00000292599:G425V	G	+	2	0	MAML1	179125891	0.002000	0.14202	0.998000	0.56505	0.572000	0.35998	0.082000	0.14847	0.963000	0.38082	0.313000	0.20887	GGC	.		0.637	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		T	179193285	G	T	179193285	3	4	68	1	0	0	0	0	1	0	0	0	9230	1203	42	4	1280	4	MAML1	5	179193285	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	2361980	179193285	1721975	26	6476											
ZBTB9	221504	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33423041	33423041	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgtgtccctcctggtgcAgggccgggaacttagggctc	5	10	15	11	1	0	1	0	1	0	0	3	2	2	2	3	4	2	2	3	4	2	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:33423041A>G	ENST00000395064.2	+	2	432	c.164A>G	c.(163-165)cAg>cGg	p.Q55R		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	55	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						CTCCTGGTGCAGGGCCGGGAA	0.552																																					p.Q55R		.											.	ZBTB9-90	0			c.A164G						.						173	168	170					6																	33423041		2203	4300	6503	SO:0001583	missense	221504	exon2			TGGTGCAGGGCCG	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.164A>G	6.37:g.33423041A>G	ENSP00000378503:p.Gln55Arg	Somatic	296	2		WXS	Illumina HiSeq	Phase_I	247	65	NM_152735	0	0	9	16	7	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	37	CCDS4780.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.251348	0.80135	.	.	ENSG00000213588	ENST00000395064	T	0.21932	1.98	4.97	4.97	0.65823	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.113982	0.34460	U	0.003959	T	0.30166	0.0756	L	0.55743	1.74	0.46774	D	0.999196	D	0.89917	1.0	D	0.87578	0.998	T	0.02942	-1.1091	10	0.51188	T	0.08	.	12.6511	0.56761	1.0:0.0:0.0:0.0	.	55	Q96C00	ZBTB9_HUMAN	R	55	ENSP00000378503:Q55R	ENSP00000378503:Q55R	Q	+	2	0	ZBTB9	33531019	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.599000	0.74127	2.070000	0.61991	0.460000	0.39030	CAG	.		0.552	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		G	33423041	A	G	33423041	3	3	68	1	0	0	0	0	1	0	0	0	17590	188	7	3	166	3	ZBTB9	6	33423041	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		33423041	137692026	27	6477											
ZNF318	24149	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43333130	43333130	+	Frame_Shift_Del	DEL	T	T	-																															gtggtcattgccaacagtgaTccttaagctcttttccaaag																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:43333130delT	ENST00000361428.2	-	2	525	c.448delA	c.(448-450)atcfs	p.I150fs	ZNF318_ENST00000318149.3_Frame_Shift_Del_p.I150fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	150					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CCAACAGTGATCCTTAAGCTC	0.473																																					p.I150fs		.											.	ZNF318-157	0			c.448delA						.						104	99	101					6																	43333130		2203	4300	6503	SO:0001589	frameshift_variant	24149	exon2			.	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"Zinc fingers, C2H2-type"	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.448delA	6.37:g.43333130delT	ENSP00000354964:p.Ile150fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	73	25	NM_014345	0	0	0	0	0	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	37	CCDS4895.2																																																																																			.		0.473	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		-	43333130	T	-	43333130	7	5	68	1	0	1	0	1	0	0	0	0	17868	1435	50	0	6427	0	ZNF318	6	43333130	Frame_Shift_Del	DEL	T	TCGA-BQ-5884-01A-11D-1589-08	9910089	43333130	127781937	28	6478											
EEF1A1	1915	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	74229620	74229620	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatacctcagcagcctcctTctcaaatttttcaatggttc	10	14	4	13	0	3	0	3	0	1	0	6	0	4	0	3	1	3	2	3	1	3	5			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:74229620T>C	ENST00000316292.9	-	1	1121	c.130A>G	c.(130-132)Aag>Gag	p.K44E	EEF1A1_ENST00000491404.1_5'Flank|EEF1A1_ENST00000331523.2_Missense_Mutation_p.K44E|EEF1A1_ENST00000309268.6_Missense_Mutation_p.K44E	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	44	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GCAGCCTCCTTCTCAAATTTT	0.423																																					p.K44E		.											.	EEF1A1-226	0			c.A130G						.						127	129	128					6																	74229620		2203	4300	6503	SO:0001583	missense	1915	exon2			CCTCCTTCTCAAA	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.130A>G	6.37:g.74229620T>C	ENSP00000339063:p.Lys44Glu	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	162	13	NM_001402	0	0	24	26	2	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380554	0.42207	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977;ENST00000456206;ENST00000356303;ENST00000455918	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.15	4.15	0.48705	Protein synthesis factor, GTP-binding (2);	0.000000	0.85682	U	0.000000	T	0.23965	0.0580	L	0.39326	1.205	0.80722	D	1	B;B;B;B;B	0.14012	0.002;0.009;0.009;0.009;0.009	B;B;B;B;B	0.26416	0.013;0.069;0.069;0.069;0.069	T	0.21999	-1.0229	10	0.87932	D	0	.	13.6597	0.62359	0.0:0.0:0.0:1.0	.	44;44;44;44;44	A6PW80;P68104;Q53HR5;Q6IPS9;Q5VTE0	.;EF1A1_HUMAN;.;.;EF1A3_HUMAN	E	44	ENSP00000339063:K44E;ENSP00000339053:K44E;ENSP00000330054:K44E;ENSP00000348651:K44E;ENSP00000392366:K44E	ENSP00000339053:K44E	K	-	1	0	EEF1A1	74286341	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.669000	0.83911	1.874000	0.54306	0.454000	0.30748	AAG	.		0.423	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		C	74229620	T	C	74229620	3	2	68	1	0	0	0	0	1	0	0	0	4934	1792	62	3	1286	3	EEF1A1	6	74229620	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	30896490	74229620	96885447	29	6479											
ZNF292	23036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	87964665	87964665	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttgtattgaaaactcaaTggccctttgatccagaattc	12	14	6	9	0	1	3	1	2	0	1	3	3	2	3	2	1	2	1	2	1	6	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:87964665T>C	ENST00000369577.3	+	8	1361	c.1318T>C	c.(1318-1320)Tgg>Cgg	p.W440R	ZNF292_ENST00000339907.4_Missense_Mutation_p.W435R	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	440						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GAAAACTCAATGGCCCTTTGA	0.378																																					p.W440R		.											.	ZNF292-72	0			c.T1318C						.						75	69	71					6																	87964665		1844	4086	5930	SO:0001583	missense	23036	exon8			ACTCAATGGCCCT	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1318T>C	6.37:g.87964665T>C	ENSP00000358590:p.Trp440Arg	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	38	5	NM_015021	0	0	5	9	4	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241783	0.58995	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.39787	1.06;1.06	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	M	0.72894	2.215	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.63435	-0.6638	10	0.87932	D	0	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	440	O60281	ZN292_HUMAN	R	440;435	ENSP00000358590:W440R;ENSP00000342847:W435R	ENSP00000342847:W435R	W	+	1	0	ZNF292	88021384	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	8.040000	0.89188	2.323000	0.78572	0.528000	0.53228	TGG	.		0.378	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		C	87964665	T	C	87964665	3	2	68	1	0	0	0	0	1	0	0	0	17858	1464	51	3	1348	3	ZNF292	6	87964665	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	13735045	87964665	83150402	30	6480											
HOXA4	3201	hgsc.bcm.edu	37	chr7	27169876	27169876	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcctggggtggcgggggcCgcctcgcagcgccgcggggc	2	3	21	15	7	0	0	0	0	0	0	1	0	0	0	4	7	1	1	4	7	0	0	rs112274824	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:27169876C>A	ENST00000360046.5	-	1	542	c.477G>T	c.(475-477)gcG>gcT	p.A159A	HOXA-AS3_ENST00000518848.1_RNA|HOXA4_ENST00000428284.2_Silent_p.A159A|HOXA-AS2_ENST00000517550.1_RNA|HOXA-AS2_ENST00000521687.1_RNA|HOXA-AS2_ENST00000521159.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA3_ENST00000521401.1_Intron	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	159	Pro-rich (part of the transcriptional activation domain).				anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						tggcgggggccgcctcgcagc	0.801													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		4363	0		0	False		,,,				2504	0				p.A159A		.											.	HOXA4-153	0			c.G477T						.						1	2	1					7																	27169876		1066	2267	3333	SO:0001819	synonymous_variant	3201	exon1			GGGGGCCGCCTCG		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"Homeoboxes / ANTP class : HOXL subclass"	5105	protein-coding gene	gene with protein product		142953	"homeo box A4"	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.477G>T	7.37:g.27169876C>A		Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_002141	0	0	0	0	0	A4D180|O43366	Silent	SNP	ENST00000360046.5	37	CCDS5405.1																																																																																			C|0.500;A|0.500		0.801	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4			A	27169876	C	A	27169876	2	1	68	1	0	0	0	0	0	0	0	1	7315	639	23	4		4	HOXA4	7	27169876	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		27169876	131968787	31	6481											
CHN2	1124	broad.mit.edu	37	chr7	29440319	29440319	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcaaaaatgacaactaacCccatctatgaacacattgga	17	10	4	10	0	2	2	1	2	1	0	2	3	2	3	2	1	3	0	2	1	6	4			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:29440319C>A	ENST00000222792.6	+	6	981	c.451C>A	c.(451-453)Ccc>Acc	p.P151T	CHN2_ENST00000495789.2_Missense_Mutation_p.P164T|CHN2_ENST00000546235.1_Missense_Mutation_p.P136T|CHN2_ENST00000539389.1_Intron|CHN2_ENST00000539406.1_Missense_Mutation_p.P226T|CHN2_ENST00000435288.2_Intron	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	151					positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						GACAACTAACCCCATCTATGA	0.403																																					p.P151T	Ovarian(1;44 48 13232 18918 31480)												.	CHN2-229	0			c.C451A						.						99	92	95					7																	29440319		2203	4300	6503	SO:0001583	missense	1124	exon6			ACTAACCCCATCT	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"Rho GTPase activating proteins", "SH2 domain containing"	1944	protein-coding gene	gene with protein product	"beta chimerin", "chimaerin 2"	602857	"chimerin (chimaerin) 2"			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.451C>A	7.37:g.29440319C>A	ENSP00000222792:p.Pro151Thr	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	116	4	NM_004067	0	0	38	38	0	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	37	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048036	0.93740	.	.	ENSG00000106069	ENST00000539406;ENST00000222792;ENST00000409350;ENST00000495789;ENST00000546235;ENST00000446446	T;T;T;T;T;D	0.89343	-0.02;-0.02;-0.02;-0.02;-0.02;-2.5	6.17	6.17	0.99709	.	0.200984	0.53938	D	0.000046	D	0.92893	0.7739	L	0.50333	1.59	0.80722	D	1	D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.937;0.996;0.999;0.994;0.991	D	0.89325	0.3643	10	0.22706	T	0.39	.	20.4745	0.99168	0.0:1.0:0.0:0.0	.	136;164;226;151;151	B7Z1W9;B7Z1V0;F5H003;A4D1A2;P52757	.;.;.;.;CHIO_HUMAN	T	226;151;164;164;136;2	ENSP00000444063:P226T;ENSP00000222792:P151T;ENSP00000386968:P164T;ENSP00000438587:P164T;ENSP00000442812:P136T;ENSP00000396867:P2T	ENSP00000222792:P151T	P	+	1	0	CHN2	29406844	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.538000	0.82048	2.941000	0.99782	0.655000	0.94253	CCC	.		0.403	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067		A	29440319	C	A	29440319	3	1	68	1	0	0	0	0	1	0	0	0	3369	623	22	4	473	4	CHN2	7	29440319	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	2270443	29440319	129698344	32	6482											
SEMA3A	10371	broad.mit.edu	37	chr7	83636753	83636753	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctgtgggcatatggaccaagGaacacccttctcacatcact	11	9	8	13	0	2	0	2	0	1	0	3	2	2	2	2	3	1	1	2	3	3	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:83636753G>C	ENST00000265362.4	-	10	1370	c.1056C>G	c.(1054-1056)ttC>ttG	p.F352L	SEMA3A_ENST00000436949.1_Missense_Mutation_p.F352L	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	352	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						ATGGACCAAGGAACACCCTTC	0.453																																					p.F352L													.	SEMA3A-156	0			c.C1056G						.						152	122	132					7																	83636753		2203	4300	6503	SO:0001583	missense	10371	exon10			ACCAAGGAACACC	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1056C>G	7.37:g.83636753G>C	ENSP00000265362:p.Phe352Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	99	3	NM_006080	0	0	0	0	0		Missense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829227	0.71258	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.49432	0.78;0.78	4.72	2.86	0.33363	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.66386	0.2784	M	0.82716	2.605	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.68530	-0.5384	10	0.87932	D	0	.	8.1244	0.30990	0.3363:0.0:0.6637:0.0	.	352	Q14563	SEM3A_HUMAN	L	352	ENSP00000265362:F352L;ENSP00000415260:F352L	ENSP00000265362:F352L	F	-	3	2	SEMA3A	83474689	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.144000	0.31565	1.109000	0.41680	0.561000	0.74099	TTC	.		0.453	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		C	83636753	G	C	83636753	3	2	68	1	0	0	0	0	1	0	0	0	14056	1165	41	4	1291	4	SEMA3A	7	83636753	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	54196434	83636753	75501910	33	6483											
ANKIB1	54467	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92019370	92019370	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcattctcaagtgttcttaTccatatggatttttcttgga	8	18	7	8	1	3	0	1	0	3	0	5	2	4	2	1	2	0	2	1	2	3	7			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:92019370T>C	ENST00000265742.3	+	15	2368	c.1992T>C	c.(1990-1992)taT>taC	p.Y664Y		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	664							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTGTTCTTATCCATATGGAT	0.333																																					p.Y664Y		.											.	ANKIB1-432	0			c.T1992C						.						107	102	103					7																	92019370		1828	4082	5910	SO:0001819	synonymous_variant	54467	exon15			TTCTTATCCATAT	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"Ankyrin repeat domain containing"	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1992T>C	7.37:g.92019370T>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	120	29	NM_019004	0	0	100	160	60	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																			.		0.333	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			C	92019370	T	C	92019370	2	2	68	1	0	0	0	0	0	0	0	1	630	1442	50	3		3	ANKIB1	7	92019370	Silent	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	8382617	92019370	67119293	34	6484											
SLC26A5	375611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	103019735	103019735	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtcgctatttgcatagtaAattggtgcatttatttgaaa	13	16	8	4	1	0	1	0	1	0	0	1	1	0	1	0	1	2	4	0	1	7	8			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:103019735A>C	ENST00000306312.3	-	16	1893	c.1632T>G	c.(1630-1632)atT>atG	p.I544M	SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393723.1_Missense_Mutation_p.I512M|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000393730.1_Missense_Mutation_p.I512M|SLC26A5_ENST00000354356.4_De_novo_Start_InFrame|SLC26A5_ENST00000393729.1_Missense_Mutation_p.I507M|SLC26A5_ENST00000432958.2_Missense_Mutation_p.I512M|SLC26A5_ENST00000339444.6_Missense_Mutation_p.I544M|SLC26A5_ENST00000393727.1_Missense_Mutation_p.I544M	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	544	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TTGCATAGTAAATTGGTGCAT	0.318																																					p.I544M		.											.	SLC26A5-91	0			c.T1632G						.						112	107	109					7																	103019735		2203	4299	6502	SO:0001583	missense	375611	exon16			ATAGTAAATTGGT	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1632T>G	7.37:g.103019735A>C	ENSP00000304783:p.Ile544Met	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	100	34	NM_206883	0	0	0	0	0	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	37	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.052577	0.55218	.	.	ENSG00000170615	ENST00000339444;ENST00000306312;ENST00000393730;ENST00000432958;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D	0.94862	-3.54;-3.54;-3.54;-3.54;-3.54;-3.54;-3.54	6.13	4.99	0.66335	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.151455	0.56097	D	0.000021	D	0.96288	0.8789	M	0.82056	2.57	0.80722	D	1	P;D;D	0.67145	0.645;0.996;0.995	P;D;D	0.67382	0.643;0.951;0.918	D	0.95580	0.8645	10	0.49607	T	0.09	.	8.2331	0.31610	0.8582:0.0:0.1418:0.0	.	544;512;544	P58743;Q496J2;P58743-2	S26A5_HUMAN;.;.	M	544;544;512;512;507;544;512	ENSP00000342396:I544M;ENSP00000304783:I544M;ENSP00000377331:I512M;ENSP00000389733:I512M;ENSP00000377330:I507M;ENSP00000377328:I544M;ENSP00000377324:I512M	ENSP00000304783:I544M	I	-	3	3	SLC26A5	102806971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.023000	0.30065	2.364000	0.80123	0.524000	0.50904	ATT	.		0.318	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		C	103019735	A	C	103019735	3	2	68	1	0	0	0	0	1	0	0	0	14552	10	1	5	663	5	SLC26A5	7	103019735	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	11000365	103019735	56118928	35	6485											
UBE3C	9690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	157046775	157046775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactgcctggctttccgccAgggccttgccaatgtcgtca	5	10	11	15	2	1	0	1	0	0	0	3	0	2	0	5	2	2	2	5	2	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:157046775A>G	ENST00000348165.5	+	20	3182	c.2822A>G	c.(2821-2823)cAg>cGg	p.Q941R		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	941	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GCTTTCCGCCAGGGCCTTGCC	0.567																																					p.Q941R		.											.	UBE3C-704	0			c.A2822G						.						56	53	54					7																	157046775		2203	4300	6503	SO:0001583	missense	9690	exon20			TCCGCCAGGGCCT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.2822A>G	7.37:g.157046775A>G	ENSP00000309198:p.Gln941Arg	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	60	21	NM_014671	0	0	34	83	49	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	37	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.268398	0.80469	.	.	ENSG00000009335	ENST00000348165	T	0.56103	0.48	5.31	5.31	0.75309	HECT (4);	0.000000	0.85682	D	0.000000	T	0.45115	0.1326	N	0.20610	0.595	0.80722	D	1	B;P	0.38677	0.437;0.642	P;P	0.48334	0.475;0.574	T	0.30357	-0.9981	10	0.05833	T	0.94	.	15.5565	0.76200	1.0:0.0:0.0:0.0	.	941;794	Q15386;B4DHJ9	UBE3C_HUMAN;.	R	941	ENSP00000309198:Q941R	ENSP00000309198:Q941R	Q	+	2	0	UBE3C	156739536	1.000000	0.71417	0.996000	0.52242	0.769000	0.43574	8.946000	0.92992	2.143000	0.66587	0.533000	0.62120	CAG	.		0.567	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		G	157046775	A	G	157046775	3	3	68	1	0	0	0	0	1	0	0	0	16914	188	7	3	2900	3	UBE3C	7	157046775	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	54027040	157046775	2091888	36	6486											
PDLIM2	64236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	22452077	22452077	+	IGR	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatggagggaatgagattgtCactggaagctttggagggga	11	10	17	3	0	1	1	1	1	0	1	1	7	1	6	0	6	1	1	0	6	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:22452077C>T	ENST00000397760.4	+	0	1837				AC037459.4_ENST00000430850.2_Intron|PDLIM2_ENST00000265810.4_Missense_Mutation_p.S339L			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		ATGAGATTGTCACTGGAAGCT	0.527																																					p.S339L		.											.	PDLIM2-90	0			c.C1016T						.						167	167	167					8																	22452077		2203	4300	6503	SO:0001628	intergenic_variant	64236	exon10			GATTGTCACTGGA	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270		8.37:g.22452077C>T		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	167	11	NM_176871	0	0	0	0	0	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		.	.	.	.	.	.	.	.	.	.	C	13.63	2.293984	0.40594	.	.	ENSG00000120913	ENST00000265810	T	0.13538	2.58	1.84	0.907	0.19321	.	.	.	.	.	T	0.08582	0.0213	.	.	.	0.09310	N	0.999999	B	0.23185	0.081	B	0.15052	0.012	T	0.31971	-0.9924	8	0.49607	T	0.09	.	3.5437	0.07820	0.0:0.7384:0.0:0.2616	.	339	Q96JY6-3	.	L	339	ENSP00000265810:S339L	ENSP00000265810:S339L	S	+	2	0	PDLIM2	22508022	0.004000	0.15560	0.006000	0.13384	0.019000	0.09904	0.023000	0.13533	0.318000	0.23185	0.491000	0.48974	TCA	.		0.527	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			T	22452077	C	T	22452077	1	4	68	0	1	0	0	0	0	0	0	0	11706	838	29	2		2	PDLIM2	8	22452077	IGR	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		22452077	123911945	37	6487											
SLC7A13	157724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	87226722	87226722	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctcaaaccaagccaatcTtattttaaaatgtattaaag	16	14	3	8	0	2	0	1	0	2	0	3	0	2	0	2	0	2	1	2	0	9	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:87226722T>A	ENST00000297524.3	-	4	1436	c.1333A>T	c.(1333-1335)Aga>Tga	p.R445*	SLC7A13_ENST00000419776.2_3'UTR|CTD-3118D11.3_ENST00000523112.1_RNA	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	445						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)	p.R445*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CAAGCCAATCTTATTTTAAAA	0.348																																					p.R445X		.											.	SLC7A13-90	1	Substitution - Nonsense(1)	large_intestine(1)	c.A1333T						.						56	61	60					8																	87226722		2203	4300	6503	SO:0001587	stop_gained	157724	exon4			CCAATCTTATTTT	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1333A>T	8.37:g.87226722T>A	ENSP00000297524:p.Arg445*	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	53	17	NM_138817	0	0	0	0	0	Q05C37|Q08AH9|Q96N84	Nonsense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030925	0.35797	.	.	ENSG00000164893	ENST00000297524	.	.	.	4.13	-0.155	0.13395	.	0.844613	0.10208	N	0.702444	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	5.8345	0.18599	0.0:0.1058:0.4904:0.4039	.	.	.	.	X	445	.	ENSP00000297524:R445X	R	-	1	2	SLC7A13	87295838	0.001000	0.12720	0.000000	0.03702	0.068000	0.16541	1.079000	0.30766	0.195000	0.20347	0.533000	0.62120	AGA	.		0.348	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		A	87226722	T	A	87226722	4	1	68	1	0	0	0	0	0	1	0	0	14727	1617	56	5	83	5	SLC7A13	8	87226722	Nonsense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	64774645	87226722	59137300	38	6488											
ZHX2	22882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	123965936	123965936	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggggtgatgtggttccacAatattacaaggaccccaaaa	13	8	11	9	1	0	1	0	1	0	0	1	2	1	2	3	4	1	1	3	4	6	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:123965936A>C	ENST00000314393.4	+	3	3021	c.2186A>C	c.(2185-2187)cAa>cCa	p.Q729P		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	729					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			GTGGTTCCACAATATTACAAG	0.527																																					p.Q729P	Esophageal Squamous(94;1056 1388 11767 13799 49639)	.											.	ZHX2-227	0			c.A2186C						.						96	101	100					8																	123965936		2203	4300	6503	SO:0001583	missense	22882	exon3			TTCCACAATATTA	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.2186A>C	8.37:g.123965936A>C	ENSP00000314709:p.Gln729Pro	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	107	27	NM_014943	0	0	12	36	24		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	A	4.171	0.030196	0.08101	.	.	ENSG00000178764	ENST00000314393	T	0.18502	2.21	5.94	0.233	0.15386	.	0.814635	0.11109	N	0.598853	T	0.09202	0.0227	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33085	-0.9882	10	0.36615	T	0.2	-0.5406	4.2111	0.10512	0.4285:0.383:0.0659:0.1227	.	729	Q9Y6X8	ZHX2_HUMAN	P	729	ENSP00000314709:Q729P	ENSP00000314709:Q729P	Q	+	2	0	ZHX2	124035117	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	0.379000	0.20585	0.099000	0.17552	-0.466000	0.05196	CAA	.		0.527	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		C	123965936	A	C	123965936	3	2	68	1	0	0	0	0	1	0	0	0	17708	130	5	5	2188	5	ZHX2	8	123965936	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	36739214	123965936	22398086	39	6489											
FLJ43860	389690	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	142477599	142477599	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccaggccgtcgatggccGtccagatgaggtcgctcaac	8	6	13	14	4	1	2	1	1	0	1	4	3	2	2	4	3	2	1	4	3	1	0	rs567666900	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:142477599G>A	ENST00000430863.1	-	0	2302					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GTCGATGGCCGTCCAGATGAG	0.662																																					.													.	.	0			.						.						56	65	62					8																	142477599		2100	4222	6322			389690	.			ATGGCCGTCCAGA			8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"maestro heat-like repeat containing"	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142477599G>A		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	31	7	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000430863.1	37																																																																																				.		0.662	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414		A	142477599	G	A	142477599	1	1	68	0	1	0	0	0	0	0	0	0	5949	1145	40	1		1	FLJ43860	8	142477599	RNA	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	18511663	142477599	3886423	40	6490											
FAM83H	286077	hgsc.bcm.edu	37	chr8	144810122	144810122	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtccagccgctggtgcccGtcgggtccgagctccgggaa	5	7	15	14	5	0	0	0	0	0	0	4	2	3	1	5	3	3	2	5	3	2	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:144810122G>A	ENST00000388913.3	-	5	1634	c.1509C>T	c.(1507-1509)gaC>gaT	p.D503D		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	503					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCTGGTGCCCGTCGGGTCCGA	0.761																																					p.D503D		.											.	FAM83H-92	0			c.C1509T						.						3	5	4					8																	144810122		1410	3264	4674	SO:0001819	synonymous_variant	286077	exon5			GTGCCCGTCGGGT	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1509C>T	8.37:g.144810122G>A		Somatic	4	1		WXS	Illumina HiSeq	Phase_I	5	4	NM_198488	0	0	2	7	5	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	37	CCDS6410.2																																																																																			.		0.761	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		A	144810122	G	A	144810122	2	1	68	1	0	0	0	0	0	0	0	1	5659	1136	40	1		1	FAM83H	8	144810122	Silent	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	2332523	144810122	1553900	41	6491											
VCP	7415	ucsc.edu	37	chr9	35062136	35062136	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgctccacctcgccatgagtCtgccagaacaggatgtctgg	8	8	11	14	2	2	2	0	1	2	1	4	3	3	3	4	2	2	1	4	2	1	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr9:35062136C>T	ENST00000358901.6	-	9	1841		c.e9-1			NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CGCCATGAGTCTGCCAGAACA	0.527																																					.													.	VCP-228	0			c.946-1G>A						.						181	158	166					9																	35062136		2203	4300	6503	SO:0001630	splice_region_variant	7415	exon10			ATGAGTCTGCCAG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.946-1G>A	9.37:g.35062136C>T		Somatic	129	0		WXS	Illumina HiSeq		101	1	NM_007126	0	0	3	3	0	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Splice_Site	SNP	ENST00000358901.6	37	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.079345	0.76528	.	.	ENSG00000165280	ENST00000358901	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VCP	35052136	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	.	.		0.527	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126	Intron	T	35062136	C	T	35062136	5	4	68	1	0	0	0	0	0	0	1	0	17173	927	32	2	1511	2	VCP	9	35062136	Splice_Site	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		35062136	106151295	42	6492											
KIAA0368	23392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	114178598	114178598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggacagtggtcccggtcAtgtacttgactggagttttc	8	12	13	8	1	1	1	1	1	0	0	3	4	2	3	1	4	1	2	1	4	2	4			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr9:114178598A>G	ENST00000338205.5	-	17	1937	c.1718T>C	c.(1717-1719)aTg>aCg	p.M573T	KIAA0368_ENST00000259335.4_Missense_Mutation_p.M751T			Q5VYK3	ECM29_HUMAN	KIAA0368	579					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GGTCCCGGTCATGTACTTGAC	0.383																																					p.M751T		.											.	KIAA0368-68	0			c.T2252C						.						96	93	94					9																	114178598		1848	4097	5945	SO:0001583	missense	23392	exon19			CCGGTCATGTACT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1718T>C	9.37:g.114178598A>G	ENSP00000339889:p.Met573Thr	Somatic	58	1		WXS	Illumina HiSeq	Phase_I	54	13	NM_001080398	0	0	59	115	56	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	A	3.455	-0.111276	0.06881	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.42513	0.97	5.44	5.44	0.79542	Armadillo-type fold (1);	0.192897	0.56097	D	0.000038	T	0.29389	0.0732	N	0.19112	0.55	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.07290	-1.0780	10	0.20519	T	0.43	-4.3236	15.4926	0.75619	1.0:0.0:0.0:0.0	.	579;48	Q5VYK3;B3KXF2	ECM29_HUMAN;.	T	573;751;48	ENSP00000259335:M751T	ENSP00000259335:M751T	M	-	2	0	KIAA0368	113218419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.946000	0.70234	2.058000	0.61347	0.528000	0.53228	ATG	.		0.383	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		G	114178598	A	G	114178598	3	3	68	1	0	0	0	0	1	0	0	0	8192	217	8	3	3933	3	KIAA0368	9	114178598	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	79116462	114178598	27034833	43	6493											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139410162	139410162	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctcgcagtgcgtccccGtgtaccctggaccgtgggag	5	7	13	16	4	0	0	0	0	0	0	2	2	1	2	6	2	2	2	6	2	1	1	rs376055493		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr9:139410162G>A	ENST00000277541.6	-	11	1751	c.1676C>T	c.(1675-1677)aCg>aTg	p.T559M		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	559	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTGCGTCCCCGTGTACCCTGG	0.682			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.T559M		.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1-5459	0			c.C1676T						.	G	MET/THR	1,4033		0,1,2016	9	13	12		1676	5.1	1	9		12	0,8174		0,0,4087	no	missense	NOTCH1	NM_017617.3	81	0,1,6103	AA,AG,GG		0.0,0.0248,0.0082	probably-damaging	559/2556	139410162	1,12207	2017	4087	6104	SO:0001583	missense	4851	exon11			GTCCCCGTGTACC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.1676C>T	9.37:g.139410162G>A	ENSP00000277541:p.Thr559Met	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	6	5	NM_017617	0	0	0	0	0	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868363	0.72065	2.48E-4	0.0	ENSG00000148400	ENST00000277541	D	0.91843	-2.92	5.05	5.05	0.67936	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.266386	0.34750	N	0.003702	D	0.95658	0.8588	M	0.77616	2.38	0.58432	D	0.999999	D	0.65815	0.995	D	0.64595	0.927	D	0.96151	0.9108	10	0.72032	D	0.01	.	17.3792	0.87400	0.0:0.0:1.0:0.0	.	559	P46531	NOTC1_HUMAN	M	559	ENSP00000277541:T559M	ENSP00000277541:T559M	T	-	2	0	NOTCH1	138529983	1.000000	0.71417	0.996000	0.52242	0.326000	0.28443	6.414000	0.73318	2.327000	0.79052	0.557000	0.71058	ACG	.		0.682	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139410162	G	A	139410162	3	1	68	1	0	0	0	0	1	0	0	0	10573	1145	40	1	6087	1	NOTCH1	9	139410162	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	25231564	139410162	1803269	44	6494											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu	37	chr10	16871011	16871011	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggctggtgaatgagccTctgtctccataaagagttcc	8	10	12	11	1	2	3	0	2	2	1	4	3	3	3	4	3	1	2	4	3	3	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:16871011T>A	ENST00000377833.4	-	66	10622	c.10557A>T	c.(10555-10557)agA>agT	p.R3519S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3519	CUB 27. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGAATGAGCCTCTGTCTCCAT	0.502																																					p.R3519S		.											.	CUBN-166	0			c.A10557T						.						88	61	70					10																	16871011		2203	4300	6503	SO:0001583	missense	8029	exon66			TGAGCCTCTGTCT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.10557A>T	10.37:g.16871011T>A	ENSP00000367064:p.Arg3519Ser	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	40	10	NM_001081	0	0	0	0	0	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	1.506	-0.550649	0.03996	.	.	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.15603	2.41	5.94	-11.9	0.00025	CUB (5);	2.229840	0.01788	N	0.032161	T	0.03915	0.0110	N	0.02275	-0.615	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.40308	-0.9570	10	0.08599	T	0.76	.	2.155	0.03810	0.4694:0.1443:0.1281:0.2582	.	3519	O60494	CUBN_HUMAN	S	3519;360	ENSP00000367064:R3519S	ENSP00000367064:R3519S	R	-	3	2	CUBN	16911017	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.866000	0.00723	-2.526000	0.00494	-0.366000	0.07423	AGA	.		0.502	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16871011	T	A	16871011	3	1	68	1	0	0	0	0	1	0	0	0	4057	1548	54	5	322	5	CUBN	10	16871011	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08		16871011	118663736	45	6495											
EPC1	80314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	32582651	32582651	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcataatcaggctgttcagCatccaaactaaaagctgaca	16	9	6	10	0	3	1	3	1	0	0	4	1	4	1	1	1	3	4	1	1	4	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:32582651C>A	ENST00000263062.8	-	3	597	c.328G>T	c.(328-330)Gct>Tct	p.A110S	EPC1_ENST00000375110.2_Missense_Mutation_p.A60S|EPC1_ENST00000319778.6_Missense_Mutation_p.A110S	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	110					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GGCTGTTCAGCATCCAAACTA	0.368																																					p.A110S		.											.	EPC1-93	0			c.G328T						.						51	46	48					10																	32582651		2203	4300	6503	SO:0001583	missense	80314	exon3			GTTCAGCATCCAA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.328G>T	10.37:g.32582651C>A	ENSP00000263062:p.Ala110Ser	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	37	11	NM_025209	0	0	0	0	0	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	37	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501195	0.26861	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.40476	1.03;1.03;1.03	5.67	4.76	0.60689	Enhancer of polycomb-like, N-terminal (1);	0.091656	0.85682	D	0.000000	T	0.17959	0.0431	N	0.04508	-0.205	0.42849	D	0.994075	B;P;B;B	0.39022	0.073;0.655;0.02;0.073	B;B;B;B	0.30855	0.105;0.121;0.037;0.105	T	0.09509	-1.0671	10	0.10902	T	0.67	-6.3339	14.4806	0.67579	0.0:0.9292:0.0:0.0708	.	110;60;110;110	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	S	60;110;110	ENSP00000364251:A60S;ENSP00000318559:A110S;ENSP00000263062:A110S	ENSP00000263062:A110S	A	-	1	0	EPC1	32622657	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.957000	0.56730	1.389000	0.46526	0.467000	0.42956	GCT	.		0.368	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			A	32582651	C	A	32582651	3	1	68	1	0	0	0	0	1	0	0	0	5173	710	25	4	2234	4	EPC1	10	32582651	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	15711640	32582651	102952096	46	6496											
ZNF33B	7582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	43088537	43088537	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctgagtgagttgtgactTctggcagaaggtttttccac	8	14	12	7	0	1	4	0	3	1	1	2	4	2	4	1	2	1	4	1	2	1	4			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:43088537T>G	ENST00000359467.3	-	5	1975	c.1861A>C	c.(1861-1863)Aag>Cag	p.K621Q	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	621					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)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						AGTTGTGACTTCTGGCAGAAG	0.363																																					p.K621Q	Melanoma(137;1247 1767 16772 25727 43810)	.											.	ZNF33B-90	0			c.A1861C						.						96	96	96					10																	43088537		2203	4300	6503	SO:0001583	missense	7582	exon5			GTGACTTCTGGCA	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1861A>C	10.37:g.43088537T>G	ENSP00000352444:p.Lys621Gln	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	183	42	NM_006955	0	0	24	48	24	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	T	9.434	1.086178	0.20390	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.01015	5.44	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35646	N	0.003071	T	0.02807	0.0084	L	0.56124	1.755	0.09310	N	1	D	0.71674	0.998	D	0.68621	0.959	T	0.40021	-0.9585	10	0.38643	T	0.18	.	9.025	0.36224	0.0:0.0:0.0:1.0	.	621	Q06732	ZN33B_HUMAN	Q	621;587	ENSP00000352444:K621Q	ENSP00000352444:K621Q	K	-	1	0	ZNF33B	42408543	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.848000	0.27710	1.446000	0.47643	0.336000	0.21669	AAG	.		0.363	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		G	43088537	T	G	43088537	3	3	68	1	0	0	0	0	1	0	0	0	17887	1792	62	5	479	5	ZNF33B	10	43088537	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	10505886	43088537	92446210	47	6497											
CBARA1	10367	hgsc.bcm.edu	37	chr10	74322781	74322781	+	Missense_Mutation	SNP	T	T	G																															ccctttatcaccgatgtcacTttttaggttgtctacacatg																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:74322781T>G	ENST00000361114.5	-	3	298	c.202A>C	c.(202-204)Agt>Cgt	p.S68R	MICU1_ENST00000604025.1_5'UTR|MICU1_ENST00000401998.3_Missense_Mutation_p.S68R|MICU1_ENST00000398761.4_Missense_Mutation_p.S68R	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	68					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										CCGATGTCACTTTTTAGGTTG	0.393																																					p.S68R		.											.	.	0			c.A202C						.						161	136	143					10																	74322781		1859	4107	5966	SO:0001583	missense	10367	exon3			TGTCACTTTTTAG	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"EF-hand domain containing"	1530	protein-coding gene	gene with protein product		605084	"calcium binding atopy-related autoantigen 1"	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.202A>C	10.37:g.74322781T>G	ENSP00000354415:p.Ser68Arg	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	40	5	NM_001195518	0	0	144	144	0	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Missense_Mutation	SNP	ENST00000361114.5	37	CCDS55715.1	.	.	.	.	.	.	.	.	.	.	T	8.049	0.765559	0.15914	.	.	ENSG00000107745	ENST00000361114;ENST00000398761;ENST00000401998	T;T;T	0.79247	-1.25;-1.25;-1.25	5.5	0.333	0.15943	.	1.158280	0.05998	N	0.647136	T	0.61426	0.2346	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54403	-0.8299	10	0.16896	T	0.51	.	0.8372	0.01142	0.1531:0.2187:0.1588:0.4694	.	68	Q9BPX6	MICU1_HUMAN	R	68	ENSP00000354415:S68R;ENSP00000381745:S68R;ENSP00000384068:S68R	ENSP00000354415:S68R	S	-	1	0	MICU1	73992787	0.952000	0.32445	0.979000	0.43373	0.067000	0.16453	0.143000	0.16115	0.086000	0.17137	-0.371000	0.07208	AGT	.		0.393	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		G	74322781	T	G	74322781	3	3	68	1	0	0	0	0	1	0	0	0	2702	1609	56	5	1274	5	CBARA1	10	74322781	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	31234244	74322781	61211966	48	6498	74	2									
CBARA1	10367	broad.mit.edu	37	chr10	74322786	74322786	+	Frame_Shift_Del	DEL	A	A	-																															tatcaccgatgtcactttttAggttgtctacacatggtgga																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:74322786delA	ENST00000361114.5	-	3	293	c.197delT	c.(196-198)ctafs	p.L66fs	MICU1_ENST00000604025.1_5'UTR|MICU1_ENST00000401998.3_Frame_Shift_Del_p.L66fs|MICU1_ENST00000398761.4_Frame_Shift_Del_p.L66fs	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	66					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										GTCACTTTTTAGGTTGTCTAC	0.398																																					p.L66fs													.	.	0			c.197delT						.						154	130	137					10																	74322786		1861	4104	5965	SO:0001589	frameshift_variant	10367	exon3			CTTTTTAGGTTGT	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"EF-hand domain containing"	1530	protein-coding gene	gene with protein product		605084	"calcium binding atopy-related autoantigen 1"	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.197delT	10.37:g.74322786delA	ENSP00000354415:p.Leu66fs	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_001195518	0	0	0	0	0	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Frame_Shift_Del	DEL	ENST00000361114.5	37	CCDS55715.1																																																																																			.		0.398	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		-	74322786	A	-	74322786	7	5	68	1	0	1	0	1	0	0	0	0	2702	420	15	0	1279	0	CBARA1	10	74322786	Frame_Shift_Del	DEL	A	TCGA-BQ-5884-01A-11D-1589-08	5	74322786	61211961	49	6499	74	2									
IFIT3	3437	broad.mit.edu	37	chr10	91098669	91098669	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttaatccagcaagaacatgCtgaccaagcagaaatcagaa	18	6	8	9	0	1	4	1	1	0	3	2	4	2	4	2	0	4	4	2	0	6	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:91098669C>A	ENST00000371818.4	+	2	437	c.257C>A	c.(256-258)gCt>gAt	p.A86D	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron|IFIT3_ENST00000371811.4_Missense_Mutation_p.A86D	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	86					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						CAAGAACATGCTGACCAAGCA	0.453																																					p.A86D													.	IFIT3-90	0			c.C257A						.						97	98	97					10																	91098669		2203	4300	6503	SO:0001583	missense	3437	exon2			AACATGCTGACCA	U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"Tetratricopeptide (TTC) repeat domain containing"	5411	protein-coding gene	gene with protein product		604650	"interferon-induced protein with tetratricopeptide repeats 4"	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.257C>A	10.37:g.91098669C>A	ENSP00000360883:p.Ala86Asp	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	66	3	NM_001549	0	0	42	42	0	Q99634|Q9BSK7	Missense_Mutation	SNP	ENST00000371818.4	37	CCDS7402.1	.	.	.	.	.	.	.	.	.	.	C	4.933	0.173346	0.09391	.	.	ENSG00000119917	ENST00000371818;ENST00000371811	D;D	0.92858	-3.12;-3.12	4.57	-1.1	0.09872	Tetratricopeptide-like helical (1);	1.363970	0.04700	N	0.415647	D	0.89319	0.6681	L	0.50333	1.59	0.09310	N	1	B	0.19583	0.037	B	0.27608	0.081	T	0.74529	-0.3635	10	0.29301	T	0.29	0.4225	9.4267	0.38583	0.3562:0.4198:0.224:0.0	.	86	O14879	IFIT3_HUMAN	D	86	ENSP00000360883:A86D;ENSP00000360876:A86D	ENSP00000360876:A86D	A	+	2	0	IFIT3	91088649	0.000000	0.05858	0.000000	0.03702	0.277000	0.26821	-0.095000	0.11077	-0.170000	0.10816	0.650000	0.86243	GCT	.		0.453	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049294.1	NM_001549		A	91098669	C	A	91098669	3	1	68	1	0	0	0	0	1	0	0	0	7545	797	28	4	272	4	IFIT3	10	91098669	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	16775883	91098669	44436078	50	6500											
IFIT5	24138	broad.mit.edu;bcgsc.ca	37	chr10	91178386	91178387	+	Frame_Shift_Ins	INS	-	-	GCTC																															ttcctgactgctctctgtgaINSgctccgactttccatttaaa																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:91178386_91178387insGCTC	ENST00000371795.4	+	2	1643_1644	c.1430_1431insGCTC	c.(1429-1434)gagctcfs	p.-478fs	IFIT5_ENST00000416601.1_Frame_Shift_Ins_p.-430fs	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5						defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						GCTCTCTGTGAGCTCCGACTTT	0.371																																					p.E477fs													.	IFIT5-90	0			c.1430_1431insGCTC						.																																			SO:0001589	frameshift_variant	24138	exon2			TCTGTGAGCTCCG	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.1431_1434dupGCTC	10.37:g.91178387_91178390dupGCTC	ENSP00000360860:p.Leu478fs	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	106	11	NM_012420	0	0	0	0	0	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Frame_Shift_Ins	INS	ENST00000371795.4	37	CCDS7403.1																																																																																			.		0.371	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		GCTC	91178387	-	GCTC	91178386	7	5	68	1	0	1	1	0	0	0	0	0	7546	304	11	0	1436	0	IFIT5	10	91178386	Frame_Shift_Ins	INS	-	TCGA-BQ-5884-01A-11D-1589-08	79717	91178386	44356361	51	6501											
PDE6C	5146	broad.mit.edu;bcgsc.ca	37	chr10	95400272	95400272	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtcacttaccacaattggcgGcatgggttcaacgtggggca	9	9	13	10	2	2	0	2	0	0	0	2	0	2	0	1	5	2	3	1	5	3	3	rs200781437		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:95400272G>A	ENST00000371447.3	+	13	1833	c.1695G>A	c.(1693-1695)cgG>cgA	p.R565R		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	565				R -> Q (in Ref. 1; AAA96392 and 2; AAA92886). {ECO:0000305}.	phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ACAATTGGCGGCATGGGTTCA	0.453													G|||	1	0.000199681	0	0.0014	5008	,	,		18596	0		0	False		,,,				2504	0				p.R565R													.	PDE6C-94	0			c.G1695A						.						181	162	169					10																	95400272		2203	4300	6503	SO:0001819	synonymous_variant	5146	exon13			TTGGCGGCATGGG	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"Phosphodiesterases"	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1695G>A	10.37:g.95400272G>A		Somatic	235	0		WXS	Illumina HiSeq	Phase_I	192	7	NM_006204	0	0	0	0	0	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			G|1.000;A|0.000		0.453	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		A	95400272	G	A	95400272	2	1	68	1	0	0	0	0	0	0	0	1	11673	1190	42	2		2	PDE6C	10	95400272	Silent	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	4221886	95400272	40134475	52	6502											
PGM2L1	283209	hgsc.bcm.edu	37	chr11	74085550	74085550	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcagtcccaaaagtcattcgGcaacaaagacgatctcgcag	14	6	9	12	3	2	1	1	0	1	1	5	2	3	1	1	1	1	3	1	1	4	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr11:74085550G>A	ENST00000298198.4	-	2	500	c.189C>T	c.(187-189)tgC>tgT	p.C63C		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	63					glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					AAGTCATTCGGCAACAAAGAC	0.403																																					p.C63C		.											.	PGM2L1-91	0			c.C189T						.						142	118	126					11																	74085550		2200	4293	6493	SO:0001819	synonymous_variant	283209	exon2			CATTCGGCAACAA	AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"glucose-1,6-bisphosphate synthase"	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.189C>T	11.37:g.74085550G>A		Somatic	96	1		WXS	Illumina HiSeq	Phase_I	87	5	NM_173582	0	0	24	24	0	Q96MQ7|Q9UIK3	Silent	SNP	ENST00000298198.4	37	CCDS8231.1																																																																																			.		0.403	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582		A	74085550	G	A	74085550	2	1	68	1	0	0	0	0	0	0	0	1	11825	1195	42	2		2	PGM2L1	11	74085550	Silent	SNP	G	TCGA-BQ-5884-01A-11D-1589-08		74085550	60920966	53	6503											
AMOTL1	154810	broad.mit.edu	37	chr11	94602565	94602565	+	Frame_Shift_Del	DEL	C	C	-																															gcctcccttcccagccgcggCcggctgagcacgacccctgc																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr11:94602565delC	ENST00000433060.2	+	12	2832	c.2691delC	c.(2689-2691)ggcfs	p.G897fs	AMOTL1_ENST00000317829.8_Frame_Shift_Del_p.G847fs|AMOTL1_ENST00000317837.9_Frame_Shift_Del_p.G484fs	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	897					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CCAGCCGCGGCCGGCTGAGCA	0.647																																					p.G897fs													.	AMOTL1-91	0			c.2691delC						.						23	29	27					11																	94602565		2105	4230	6335	SO:0001589	frameshift_variant	154810	exon12			CCGCGGCCGGCTG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2691delC	11.37:g.94602565delC	ENSP00000387739:p.Gly897fs	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	7	3	NM_130847	0	0	0	0	0	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Frame_Shift_Del	DEL	ENST00000433060.2	37	CCDS44712.1																																																																																			.		0.647	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		-	94602565	C	-	94602565	7	5	68	1	0	1	0	1	0	0	0	0	583	726	26	0	2737	0	AMOTL1	11	94602565	Frame_Shift_Del	DEL	C	TCGA-BQ-5884-01A-11D-1589-08	20517015	94602565	40403951	54	6504											
ZC3H12C	85463	broad.mit.edu;ucsc.edu	37	chr11	110036283	110036283	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctggcggatcccatacTgtggaatgccgcaagatccc	9	7	11	14	2	0	1	0	0	0	1	2	3	2	3	4	3	3	1	4	3	3	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr11:110036283T>A	ENST00000278590.3	+	6	2524	c.2473T>A	c.(2473-2475)Tgt>Agt	p.C825S	ZC3H12C_ENST00000453089.2_Missense_Mutation_p.C794S|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.C826S	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	825							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GATCCCATACTGTGGAATGCC	0.502																																					p.C825S													.	ZC3H12C-68	0			c.T2473A						.						34	37	36					11																	110036283		1901	4119	6020	SO:0001583	missense	85463	exon6			CCATACTGTGGAA		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"Zinc fingers, CCCH-type domain containing"	29362	protein-coding gene	gene with protein product	"MCP induced protein 3"	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.2473T>A	11.37:g.110036283T>A	ENSP00000278590:p.Cys825Ser	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	24	4	NM_033390	0	0	14	29	15	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	37	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.055314	0.36277	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.28666	1.61;1.6;1.61	6.03	6.03	0.97812	.	0.448650	0.27936	N	0.017258	T	0.45236	0.1332	L	0.43152	1.355	0.38492	D	0.948009	D;D;D	0.63880	0.993;0.993;0.993	P;D;P	0.72338	0.777;0.977;0.777	T	0.28332	-1.0047	10	0.09843	T	0.71	-20.173	16.5582	0.84512	0.0:0.0:0.0:1.0	.	826;825;825	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	S	825;826;794	ENSP00000278590:C825S;ENSP00000431821:C826S;ENSP00000413094:C794S	ENSP00000278590:C825S	C	+	1	0	ZC3H12C	109541493	0.995000	0.38212	0.997000	0.53966	0.088000	0.18126	1.600000	0.36762	2.308000	0.77769	0.533000	0.62120	TGT	.		0.502	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		A	110036283	T	A	110036283	3	1	68	1	0	0	0	0	1	0	0	0	17595	1580	55	5	2495	5	ZC3H12C	11	110036283	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	15433718	110036283	24970233	55	6505											
CD27	939	hgsc.bcm.edu	37	chr12	6554354	6554354	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagctgcccagagaggcaCtactgggctcagggaaagct	12	5	14	10	0	1	2	1	0	0	2	1	4	1	3	1	3	4	4	1	3	3	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:6554354C>A	ENST00000266557.3	+	1	322	c.93C>A	c.(91-93)caC>caA	p.H31Q	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	31					cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						CAGAGAGGCACTACTGGGCTC	0.632																																					p.H31Q		.											.	CD27-659	0			c.C93A						.						27	29	29					12																	6554354		2203	4300	6503	SO:0001583	missense	939	exon1			GAGGCACTACTGG	M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"Tumor necrosis factor receptor superfamily", "CD molecules"	11922	protein-coding gene	gene with protein product		186711	"tumor necrosis factor receptor superfamily, member 7"	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.93C>A	12.37:g.6554354C>A	ENSP00000266557:p.His31Gln	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_001242	0	0	6	6	0	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.381098	0.42207	.	.	ENSG00000139193	ENST00000266557	D	0.90676	-2.71	4.91	-0.44	0.12261	TNFR/CD27/30/40/95 cysteine-rich region (2);	0.313247	0.24409	N	0.038774	T	0.77226	0.4099	L	0.34521	1.04	0.29291	N	0.869361	B	0.27013	0.166	B	0.25759	0.063	T	0.61153	-0.7120	10	0.08381	T	0.77	-12.4844	1.0852	0.01651	0.302:0.3719:0.1473:0.1789	.	31	P26842	CD27_HUMAN	Q	31	ENSP00000266557:H31Q	ENSP00000266557:H31Q	H	+	3	2	CD27	6424615	0.060000	0.20803	0.879000	0.34478	0.789000	0.44602	-0.784000	0.04633	0.244000	0.21351	0.557000	0.71058	CAC	.		0.632	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1			A	6554354	C	A	6554354	3	1	68	1	0	0	0	0	1	0	0	0	2996	564	20	4	95	4	CD27	12	6554354	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		6554354	127297541	56	6506											
ESPL1	9700	broad.mit.edu	37	chr12	53687097	53687097	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgggatgtgactgaccgcGacattgaccgctacacggaa	10	8	12	11	4	1	3	0	3	1	0	1	6	1	5	2	2	1	1	2	2	2	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:53687097G>A	ENST00000257934.4	+	31	6293	c.6202G>A	c.(6202-6204)Gac>Aac	p.D2068N	PFDN5_ENST00000351500.3_5'Flank|PFDN5_ENST00000550846.1_5'Flank|PFDN5_ENST00000551018.1_5'Flank|PFDN5_ENST00000334478.4_5'Flank|ESPL1_ENST00000552462.1_Missense_Mutation_p.D2068N	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	2068					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						GACTGACCGCGACATTGACCG	0.532																																					p.D2068N	Colon(53;1069 1201 2587 5382)												.	ESPL1-228	0			c.G6202A						.						58	59	59					12																	53687097		2203	4300	6503	SO:0001583	missense	9700	exon31			GACCGCGACATTG	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.6202G>A	12.37:g.53687097G>A	ENSP00000257934:p.Asp2068Asn	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	63	3	NM_012291	0	0	7	7	0		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410077	0.83340	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.39229	1.09;1.09	4.6	4.6	0.57074	.	0.054909	0.64402	D	0.000001	T	0.72819	0.3508	M	0.93197	3.39	0.52501	D	0.999956	D	0.89917	1.0	D	0.72625	0.978	T	0.81040	-0.1113	10	0.72032	D	0.01	.	16.7111	0.85385	0.0:0.0:1.0:0.0	.	2068	Q14674	ESPL1_HUMAN	N	2068;1743;2068	ENSP00000257934:D2068N;ENSP00000449831:D2068N	ENSP00000257934:D2068N	D	+	1	0	ESPL1	51973364	1.000000	0.71417	1.000000	0.80357	0.628000	0.37860	9.207000	0.95064	2.576000	0.86940	0.563000	0.77884	GAC	.		0.532	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		A	53687097	G	A	53687097	3	1	68	1	0	0	0	0	1	0	0	0	5266	1058	37	1	6320	1	ESPL1	12	53687097	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	47132743	53687097	80164798	57	6507											
SLC39A5	283375	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	56630209	56630209	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aggcgaaaacgaaggaatctCgaaacacgcaacttggatcc	16	5	10	10	4	1	0	0	0	1	0	3	5	2	2	1	3	3	1	1	3	6	1	rs139155884	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:56630209C>G	ENST00000266980.4	+	7	1268	c.975C>G	c.(973-975)ctC>ctG	p.L325L	ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Silent_p.L325L	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	325					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GAAGGAATCTCGAAACACGCA	0.557																																					p.L325L		.											.	SLC39A5-92	0			c.C975G						.						134	129	131					12																	56630209		2203	4300	6503	SO:0001819	synonymous_variant	283375	exon9			GAATCTCGAAACA		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"Solute carriers"	20502	protein-coding gene	gene with protein product		608730	"solute carrier family 39 (metal ion transporter), member 5"				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.975C>G	12.37:g.56630209C>G		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	100	27	NM_173596	0	0	4	6	2	B2R808|Q8N6Y3	Silent	SNP	ENST00000266980.4	37	CCDS8912.2																																																																																			C|0.999;T|0.001		0.557	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		G	56630209	C	G	56630209	2	3	68	1	0	0	0	0	0	0	0	1	14653	871	31	4		4	SLC39A5	12	56630209	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	2943112	56630209	77221686	58	6508											
STAT2	6773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56742947	56742947	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcggccccactcccctacCtgaaggtttgggctgagcaa	7	9	11	14	1	0	2	0	2	0	0	2	2	1	2	5	3	2	3	5	3	3	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:56742947C>T	ENST00000314128.4	-	16	1463	c.1440G>A	c.(1438-1440)caG>caA	p.Q480Q	STAT2_ENST00000556539.1_5'UTR|STAT2_ENST00000418572.2_Intron|STAT2_ENST00000557235.1_Splice_Site_p.Q476Q			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	480					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						ACTCCCCTACCTGAAGGTTTG	0.562																																					p.Q480Q		.											.	STAT2-847	0			c.G1440A						.						93	93	93					12																	56742947		2203	4300	6503	SO:0001630	splice_region_variant	6773	exon16			CCCTACCTGAAGG	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"SH2 domain containing"	11363	protein-coding gene	gene with protein product		600556	"signal transducer and activator of transcription 2, 113kD"			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1440+1G>A	12.37:g.56742947C>T		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	160	41	NM_005419	0	0	0	0	0	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Silent	SNP	ENST00000314128.4	37	CCDS8917.1																																																																																			.		0.562	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	Silent	T	56742947	C	T	56742947	5	4	68	1	0	0	0	0	0	0	1	0	15297	695	24	2	1151	2	STAT2	12	56742947	Splice_Site	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	112738	56742947	77108948	59	6509											
DENR	8562	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	123253468	123253468	+	Splice_Site	DEL	G	G	-																															attcaggaaaaatggccagaGgtgagtgcatggaacacata																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:123253468delG	ENST00000280557.6	+	7	738	c.552delG	c.(550-552)gag>ga	p.E184fs	DENR_ENST00000455982.2_Intron|Y_RNA_ENST00000384187.1_RNA	NM_003677.3	NP_003668.2	O43583	DENR_HUMAN	density-regulated protein	184					formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)		translation initiation factor activity (GO:0003743)			kidney(1)|large_intestine(1)|urinary_tract(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.28e-05)|Epithelial(86;6.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.199)		AATGGCCAGAGGTGAGTGCAT	0.363																																					p.E184fs		.											.	.	0			c.552delG						.						70	67	68					12																	123253468		1874	4097	5971	SO:0001630	splice_region_variant	8562	exon7			.	AF038554	CCDS45003.1	12q24.31	1999-06-17			ENSG00000139726	ENSG00000139726			2769	protein-coding gene	gene with protein product		604550				9628587	Standard	NM_003677		Approved	DRP, DRP1, SMAP-3	uc001uda.3	O43583	OTTHUMG00000168844	ENST00000280557.6:c.552+1G>-	12.37:g.123253468delG		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	54	16	NM_003677	0	0	0	0	0	Q9H3U6|Q9UKZ0	Frame_Shift_Del	DEL	ENST00000280557.6	37	CCDS45003.1																																																																																			.		0.363	DENR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401336.1	NM_003677	Frame_Shift_Del	-	123253468	G	-	123253468	8	5	68	1	0	1	0	1	0	0	1	0	4449	1014	35	0	574	0	DENR	12	123253468	Splice_Site	DEL	G	TCGA-BQ-5884-01A-11D-1589-08	66510521	123253468	10598427	60	6510											
FREM2	341640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	39265553	39265553	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattacagagacgaaaacctActggtgcctttgaaaatatc	15	11	7	8	1	0	2	0	1	0	1	1	4	0	2	2	1	4	0	2	1	8	5			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr13:39265553A>G	ENST00000280481.7	+	1	4288	c.4072A>G	c.(4072-4074)Act>Gct	p.T1358A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1358					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)		ACGAAAACCTACTGGTGCCTT	0.383																																					p.T1358A		.											.	FREM2-100	0			c.A4072G						.						64	65	64					13																	39265553		2203	4300	6503	SO:0001583	missense	341640	exon1			AAACCTACTGGTG	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.4072A>G	13.37:g.39265553A>G	ENSP00000280481:p.Thr1358Ala	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	98	23	NM_207361	0	0	2	3	1	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.720360	0.00700	.	.	ENSG00000150893	ENST00000280481	T	0.40756	1.02	5.81	-0.554	0.11811	.	1.289890	0.04720	N	0.419174	T	0.13927	0.0337	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19063	-1.0317	10	0.08837	T	0.75	.	1.7548	0.02980	0.3096:0.2411:0.3249:0.1243	.	1358	Q5SZK8	FREM2_HUMAN	A	1358	ENSP00000280481:T1358A	ENSP00000280481:T1358A	T	+	1	0	FREM2	38163553	0.000000	0.05858	0.001000	0.08648	0.731000	0.41821	0.004000	0.13106	0.122000	0.18314	0.533000	0.62120	ACT	.		0.383	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39265553	A	G	39265553	3	3	68	1	0	0	0	0	1	0	0	0	6064	391	14	3	4074	3	FREM2	13	39265553	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		39265553	75904325	61	6511											
TPT1	7178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	45913688	45913688	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgttctgcagcccctgtcaTaaaaggttttactctttctg	7	17	7	10	0	4	0	1	0	3	0	4	0	4	0	2	1	3	3	2	1	3	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr13:45913688T>A	ENST00000530705.1	-	4	643	c.343A>T	c.(343-345)Atg>Ttg	p.M115L	TPT1-AS1_ENST00000523506.1_RNA|TPT1-AS1_ENST00000520590.1_RNA|TPT1-AS1_ENST00000521336.1_RNA|TPT1_ENST00000309246.5_Missense_Mutation_p.M115L|TPT1-AS1_ENST00000517509.1_RNA|TPT1-AS1_ENST00000520310.1_RNA|TPT1_ENST00000529421.1_5'UTR|TPT1_ENST00000379060.4_Missense_Mutation_p.M103L|TPT1-AS1_ENST00000412946.2_RNA|SNORA31_ENST00000362607.1_RNA|TPT1_ENST00000379055.1_Missense_Mutation_p.M81L|RP11-290D2.6_ENST00000610057.1_RNA|TPT1_ENST00000379056.1_Missense_Mutation_p.M81L|TPT1-AS1_ENST00000520622.1_RNA			P13693	TCTP_HUMAN	tumor protein, translationally-controlled 1	115					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ectoderm development (GO:2000384)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|regulation of apoptotic process (GO:0042981)|response to virus (GO:0009615)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|multivesicular body (GO:0005771)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			lung(1)	1		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)		GCCCCTGTCATAAAAGGTTTT	0.328																																					p.M115L		.											.	TPT1-90	0			c.A343T						.						110	112	111					13																	45913688		2203	4299	6502	SO:0001583	missense	7178	exon4			CTGTCATAAAAGG	X16064	CCDS9397.1, CCDS66538.1, CCDS73566.1	13q14	2010-08-18			ENSG00000133112	ENSG00000133112			12022	protein-coding gene	gene with protein product		600763				2813067, 10343127	Standard	NM_001286273		Approved	TCTP, fortilin	uc001uzy.1	P13693	OTTHUMG00000016845	ENST00000530705.1:c.343A>T	13.37:g.45913688T>A	ENSP00000431872:p.Met115Leu	Somatic	204	1		WXS	Illumina HiSeq	Phase_I	196	44	NM_003295	1	1	4056	5590	1532	B2R7E5|Q6YLS2|Q7Z4J4|Q8TBK7|Q96EE2|Q9UC70	Missense_Mutation	SNP	ENST00000530705.1	37	CCDS9397.1	.	.	.	.	.	.	.	.	.	.	.	16.97	3.267590	0.59540	.	.	ENSG00000133112	ENST00000379056;ENST00000530705;ENST00000379060;ENST00000379055;ENST00000309246;ENST00000527226	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	4.79	4.79	0.61399	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.037685	0.85682	D	0.000000	T	0.43122	0.1233	M	0.83774	2.66	0.80722	D	1	B	0.02656	0.0	B	0.17433	0.018	T	0.47142	-0.9140	10	0.02654	T	1	.	13.8369	0.63415	0.0:0.0:0.0:1.0	.	115	P13693	TCTP_HUMAN	L	81;115;103;81;115;114	ENSP00000368345:M81L;ENSP00000431872:M115L;ENSP00000368350:M103L;ENSP00000368344:M81L;ENSP00000339051:M115L;ENSP00000433738:M114L	ENSP00000339051:M115L	M	-	1	0	TPT1	44811688	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.581000	0.67471	1.931000	0.55961	0.533000	0.62120	ATG	.		0.328	TPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044758.3			A	45913688	T	A	45913688	3	1	68	1	0	0	0	0	1	0	0	0	16462	1406	49	5	187	5	TPT1	13	45913688	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	6648135	45913688	69256190	62	6512											
MLNR	2862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	49796387	49796387	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gcggcctttaaactgctgctCgcaaggaagtccaggccgag	9	7	13	12	3	0	0	0	0	0	0	2	2	1	1	3	3	3	3	3	3	4	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr13:49796387C>G	ENST00000218721.1	+	2	1113	c.1113C>G	c.(1111-1113)ctC>ctG	p.L371L	MLNR_ENST00000398307.1_3'UTR	NM_001507.1	NP_001498.1	O43193	MTLR_HUMAN	motilin receptor	371					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone-releasing hormone receptor activity (GO:0016520)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)	14		all_lung(13;8.31e-06)|Lung NSC(96;0.000251)|Breast(56;0.0008)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;6.1e-09)		AACTGCTGCTCGCAAGGAAGT	0.547																																					p.L371L		.											.	MLNR-90	0			c.C1113G						.						81	81	81					13																	49796387		2203	4300	6503	SO:0001819	synonymous_variant	2862	exon2			GCTGCTCGCAAGG	AF034632	CCDS9414.1	13q14-q21	2012-08-08	2004-05-27	2004-05-28	ENSG00000102539	ENSG00000102539		"GPCR / Class A : Motilin receptors"	4495	protein-coding gene	gene with protein product		602885	"G protein-coupled receptor 38"	GPR38		9441746	Standard	NM_001507		Approved		uc010tgj.2	O43193	OTTHUMG00000016909	ENST00000218721.1:c.1113C>G	13.37:g.49796387C>G		Somatic	119	1		WXS	Illumina HiSeq	Phase_I	85	24	NM_001507	0	0	3	4	1		Silent	SNP	ENST00000218721.1	37	CCDS9414.1																																																																																			.		0.547	MLNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044897.1	NM_001507		G	49796387	C	G	49796387	2	3	68	1	0	0	0	0	0	0	0	1	9657	871	31	4		4	MLNR	13	49796387	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	3882699	49796387	65373491	63	6513											
OR4N5	390437	bcgsc.ca	37	chr14	20612342	20612343	+	Frame_Shift_Ins	INS	-	-	T																															attatcgttggttctgtggcINSttgggggctttatccattcc																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr14:20612342_20612343insT	ENST00000333629.1	+	1	448_449	c.448_449insT	c.(448-450)cttfs	p.L150fs	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		GGTTCTGTGGCTTGGGGGCTTT	0.49																																					p.L150fs													.	OR4N5-69	0			c.448_449insT						.																																			SO:0001589	frameshift_variant	390437	exon1			CTGTGGCTTGGGG		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.450dupT	14.37:g.20612344_20612344dupT	ENSP00000332110:p.Leu150fs	Somatic	326	28		WXS	Illumina HiSeq	Phase_1	265	29	NM_001004724	0	0	0	0	0	Q6IF11	Frame_Shift_Ins	INS	ENST00000333629.1	37	CCDS32031.1																																																																																			.		0.49	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			T	20612343	-	T	20612342	7	5	68	1	0	1	1	0	0	0	0	0	11105	797	28	0	450	0	OR4N5	14	20612342	Frame_Shift_Ins	INS	-	TCGA-BQ-5884-01A-11D-1589-08		20612342	86737198	64	6514											
APEX1	328	ucsc.edu	37	chr14	20925021	20925021	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtttcttacggcataggTgagaccctattgatgcctaa	12	12	9	8	1	1	2	0	2	1	1	1	3	1	2	2	2	2	2	2	2	5	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr14:20925021T>C	ENST00000216714.3	+	4	707		c.e4+2		OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557054.1_Intron|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000398030.4_Splice_Site|APEX1_ENST00000557365.1_Splice_Site|APEX1_ENST00000555414.1_Splice_Site	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1						aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)			breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	ACGGCATAGGTGAGACCCTAT	0.473								Other BER factors																													.													.	APEX1-661	0			c.439+2T>C						.						35	34	34					14																	20925021		2203	4300	6503	SO:0001630	splice_region_variant	328	exon4			CATAGGTGAGACC	X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"APEX nuclease (multifunctional DNA repair enzyme)"	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.439+2T>C	14.37:g.20925021T>C		Somatic	39	0		WXS	Illumina HiSeq		28	1	NM_001641	0	0	0	0	0	Q969L5|Q99775	Splice_Site	SNP	ENST00000216714.3	37	CCDS9550.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.666222	0.67814	.	.	ENSG00000100823	ENST00000555414;ENST00000216714;ENST00000553681;ENST00000398030;ENST00000555839;ENST00000556054;ENST00000557592;ENST00000557150;ENST00000438886	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.118	0.72419	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	APEX1	19994861	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.152000	0.77419	2.207000	0.71202	0.533000	0.62120	.	.		0.473	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641	Intron	C	20925021	T	C	20925021	5	2	68	1	0	0	0	0	0	0	1	0	769	1710	59	3	451	3	APEX1	14	20925021	Splice_Site	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	312679	20925021	86424519	65	6515											
TSC2	7249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2122849	2122849	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgcctggatttggtcatcaGctttcaggcccaaagacact	10	11	9	11	0	3	1	3	0	0	1	3	2	3	2	2	3	2	1	2	3	1	2	rs45517218		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr16:2122849G>A	ENST00000219476.3	+	21	2850		c.e21-1		TSC2_ENST00000350773.4_Splice_Site|TSC2_ENST00000439673.2_Splice_Site|TSC2_ENST00000401874.2_Splice_Site|TSC2_ENST00000382538.6_Splice_Site|TSC2_ENST00000568454.1_Splice_Site|TSC2_ENST00000353929.4_Splice_Site	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2						acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				TTGGTCATCAGCTTTCAGGCC	0.627			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												.		.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2-1908	0			c.2221-1G>A						.						53	58	56					16																	2122849		2198	4300	6498	SO:0001630	splice_region_variant	7249	exon21	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCATCAGCTTTCA	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2221-1G>A	16.37:g.2122849G>A		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	60	29	NM_000548	0	0	0	0	0	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Splice_Site	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.269512	0.40095	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3044	0.94155	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TSC2	2062850	1.000000	0.71417	0.996000	0.52242	0.714000	0.41099	7.284000	0.78650	2.551000	0.86045	0.655000	0.94253	.	.		0.627	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	Intron	A	2122849	G	A	2122849	5	1	68	1	0	0	0	0	0	0	1	0	16639	985	34	2	2298	2	TSC2	16	2122849	Splice_Site	SNP	G	TCGA-BQ-5884-01A-11D-1589-08		2122849	88231904	66	6516											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3598164	3598164	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgaggctcctgttgagctgTagtgcttgtcccagggcctg	4	12	15	10	0	0	2	0	2	0	0	2	2	2	2	3	2	2	5	3	2	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr16:3598164T>C	ENST00000301749.7	-	0	3147				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|LA16c-390H2.4_ENST00000573820.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGTTGAGCTGTAGTGCTTGTC	0.587																																					p.L914L		.											.	NLRC3-96	0			c.A2742G						.						33	35	34					16																	3598164		1962	4132	6094			197358	exon16			GAGCTGTAGTGCT	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3598164T>C		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	9	8	NM_178844	0	0	3	3	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				.		0.587	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		C	3598164	T	C	3598164	1	2	68	0	1	0	0	0	0	0	0	0	10494	1625	57	3		3	NLRC3	16	3598164	RNA	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	1475315	3598164	86756589	67	6517											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	506	50		WXS	Illumina HiSeq		444	67	NM_145301	0	0	13	59	46	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		T	15457087	C	T	15457087	3	4	68	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		15457087	65738123	68	6518											
KRTAP4-9	100132386	broad.mit.edu	37	chr17	39261742	39261742	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctgctgtgagaccacctgCtgcaggaccacctgctgccg	7	7	12	15	1	0	1	0	1	0	1	0	3	0	2	5	1	6	5	5	1	0	0	rs549296843	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:39261742C>T	ENST00000391415.1	+	1	159	c.102C>T	c.(100-102)tgC>tgT	p.C34C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	34	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						AGACCACCTGCTGCAGGACCA	0.652													C|||	9	0.00179712	0.003	0	5008	,	,		17191	0		0	False		,,,				2504	0.0051				p.C34C													.	.	0			c.C102T						.						16	21	20					17																	39261742		692	1591	2283	SO:0001819	synonymous_variant	100132386	exon1			CACCTGCTGCAGG	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"Keratin associated proteins"	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.102C>T	17.37:g.39261742C>T		Somatic	41	1		WXS	Illumina HiSeq	Phase_I	56	4	NM_001146041	0	0	0	0	0		Silent	SNP	ENST00000391415.1	37	CCDS54124.1																																																																																			.		0.652	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		T	39261742	C	T	39261742	2	4	68	1	0	0	0	0	0	0	0	1	8578	805	28	2		2	KRTAP4-9	17	39261742	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	23804655	39261742	41933468	69	6519											
RSAD1	55316	broad.mit.edu	37	chr17	48559512	48559512	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actcggcctgcgatgctctgCggacgctggcagaggcccgg	5	6	16	14	5	1	1	0	0	1	1	2	3	1	2	2	5	3	3	2	5	0	0	rs373296180		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:48559512C>A	ENST00000258955.2	+	4	620	c.535C>A	c.(535-537)Cgg>Agg	p.R179R		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	179					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CGATGCTCTGCGGACGCTGGC	0.657											OREG0024567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R179R													.	RSAD1-90	0			c.C535A						.						63	71	69					17																	48559512		2201	4297	6498	SO:0001819	synonymous_variant	55316	exon4			GCTCTGCGGACGC	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.535C>A	17.37:g.48559512C>A		Somatic	167	0	955	WXS	Illumina HiSeq	Phase_I	131	4	NM_018346	0	0	51	51	0	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Silent	SNP	ENST00000258955.2	37	CCDS11569.1																																																																																			.		0.657	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346		A	48559512	C	A	48559512	2	1	68	1	0	0	0	0	0	0	0	1	13726	759	27	4		4	RSAD1	17	48559512	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	9297770	48559512	32635698	70	6520											
TBC1D16	125058	bcgsc.ca	37	chr17	77915895	77915895	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccgttcatgtgcatggcCaggtttccgaagtgcaggag	7	10	13	11	2	1	0	1	0	0	0	3	2	3	1	4	3	2	4	4	3	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:77915895C>A	ENST00000310924.2	-	11	2134	c.2019G>T	c.(2017-2019)ctG>ctT	p.L673L	TBC1D16_ENST00000340848.7_Silent_p.L311L|TBC1D16_ENST00000576768.1_Silent_p.L298L	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	673							Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			TGTGCATGGCCAGGTTTCCGA	0.652																																					p.L673L	Ovarian(14;397 562 4850 31922 49378)												.	TBC1D16-90	0			c.G2019T						.						70	48	55					17																	77915895		2202	4300	6502	SO:0001819	synonymous_variant	125058	exon11			CATGGCCAGGTTT	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.2019G>T	17.37:g.77915895C>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_1	30	4	NM_019020	0	0	75	75	0	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	CCDS11766.1																																																																																			.		0.652	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		A	77915895	C	A	77915895	2	1	68	1	0	0	0	0	0	0	0	1	15637	581	21	4		4	TBC1D16	17	77915895	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	29356383	77915895	3279315	71	6521											
SLC38A10	124565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79220316	79220316	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagtgctccagggagcgCtggttaaggtcctgggatgg	7	9	17	8	1	1	1	1	0	0	1	3	3	3	3	2	5	2	3	2	5	1	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:79220316C>T	ENST00000374759.3	-	16	2783	c.2400G>A	c.(2398-2400)caG>caA	p.Q800Q		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	800					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCAGGGAGCGCTGGTTAAGGT	0.682																																					p.Q800Q		.											.	SLC38A10-70	0			c.G2400A						.						18	20	19					17																	79220316		1869	4067	5936	SO:0001819	synonymous_variant	124565	exon16			GGAGCGCTGGTTA	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2400G>A	17.37:g.79220316C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	45	13	NM_001037984	0	0	60	146	86	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																			.		0.682	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79220316	C	T	79220316	2	4	68	1	0	0	0	0	0	0	0	1	14634	796	28	2		2	SLC38A10	17	79220316	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	1304421	79220316	1974894	72	6522											
ZNF532	55205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	56587630	56587630	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttccacttcaacttccaCtcttcagagccctgtgggag	8	12	7	14	0	3	1	2	0	1	1	5	2	5	2	3	1	3	0	3	1	2	5			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr18:56587630C>T	ENST00000336078.4	+	4	2887	c.2111C>T	c.(2110-2112)aCt>aTt	p.T704I	ZNF532_ENST00000591808.1_Missense_Mutation_p.T704I|ZNF532_ENST00000591083.1_Missense_Mutation_p.T704I|ZNF532_ENST00000589288.1_Missense_Mutation_p.T704I|ZNF532_ENST00000591230.1_Missense_Mutation_p.T704I	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	704					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(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TCAACTTCCACTCTTCAGAGC	0.473																																					p.T704I		.											.	ZNF532-154	0			c.C2111T						.						63	67	65					18																	56587630		2203	4300	6503	SO:0001583	missense	55205	exon4			CTTCCACTCTTCA	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.2111C>T	18.37:g.56587630C>T	ENSP00000338217:p.Thr704Ile	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	80	18	NM_018181	0	0	12	20	8	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	c	2.772	-0.255447	0.05829	.	.	ENSG00000074657	ENST00000336078	T	0.32515	1.45	5.43	4.55	0.56014	.	0.394325	0.27526	N	0.018974	T	0.17023	0.0409	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13845	-1.0494	10	0.35671	T	0.21	-5.4027	8.1333	0.31039	0.0:0.7358:0.1536:0.1107	.	704	Q9HCE3	ZN532_HUMAN	I	704	ENSP00000338217:T704I	ENSP00000338217:T704I	T	+	2	0	ZNF532	54738610	0.026000	0.19158	0.014000	0.15608	0.567000	0.35839	2.740000	0.47418	1.298000	0.44778	0.544000	0.68410	ACT	.		0.473	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56587630	C	T	56587630	3	4	68	1	0	0	0	0	1	0	0	0	18004	565	20	2	2113	2	ZNF532	18	56587630	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		56587630	21489618	73	6523											
CCNE1	898	hgsc.bcm.edu;broad.mit.edu	37	chr19	30308341	30308341	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atagagaggaagtctggaaaAtcatgttaaacaaggaaaag	20	7	11	3	0	2	1	1	0	1	1	2	5	2	4	0	3	1	1	0	3	9	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr19:30308341A>G	ENST00000262643.3	+	6	634	c.355A>G	c.(355-357)Atc>Gtc	p.I119V	CCNE1_ENST00000357943.5_Missense_Mutation_p.I119V|CCNE1_ENST00000444983.2_Missense_Mutation_p.I104V	NM_001238.2	NP_001229.1	P24864	CCNE1_HUMAN	cyclin E1	119					androgen receptor signaling pathway (GO:0030521)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|Wnt signaling pathway (GO:0016055)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|skin(1)	20	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			AGTCTGGAAAATCATGTTAAA	0.423			A		serous ovarian																																p.I119V		.		Dom	yes		19	19q12	898	cyclin E1		E	.	CCNE1-1270	0			c.A355G						.						135	126	129					19																	30308341		2203	4300	6503	SO:0001583	missense	898	exon6			TGGAAAATCATGT	M73812	CCDS12419.1	19q12	2014-07-03			ENSG00000105173	ENSG00000105173			1589	protein-coding gene	gene with protein product	"cyclin Es", "cyclin Et"	123837		CCNE		1833066	Standard	NM_001238		Approved		uc002nsn.3	P24864	OTTHUMG00000177626	ENST00000262643.3:c.355A>G	19.37:g.30308341A>G	ENSP00000262643:p.Ile119Val	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	108	6	NM_001238	0	0	8	9	1	A8K684|Q14091|Q8NFG1|Q92501|Q9UD21	Missense_Mutation	SNP	ENST00000262643.3	37	CCDS12419.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.663508	0.29515	.	.	ENSG00000105173	ENST00000262643;ENST00000357943;ENST00000444983	T;T;T	0.10960	2.82;2.82;2.82	6.06	5.02	0.67125	Cyclin, N-terminal (1);Cyclin-like (1);	0.091237	0.64402	D	0.000001	T	0.07234	0.0183	N	0.12569	0.235	0.39397	D	0.966517	P	0.44380	0.834	B	0.41723	0.365	T	0.45279	-0.9272	10	0.23891	T	0.37	.	12.6906	0.56972	0.8623:0.1377:0.0:0.0	.	119	P24864	CCNE1_HUMAN	V	119;119;104	ENSP00000262643:I119V;ENSP00000350625:I119V;ENSP00000410179:I104V	ENSP00000262643:I119V	I	+	1	0	CCNE1	35000181	1.000000	0.71417	0.955000	0.39395	0.625000	0.37756	6.248000	0.72418	1.071000	0.40834	0.533000	0.62120	ATC	.		0.423	CCNE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438138.1	NM_001238		G	30308341	A	G	30308341	3	3	68	1	0	0	0	0	1	0	0	0	2926	101	4	3	373	3	CCNE1	19	30308341	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		30308341	28820642	74	6524											
HNRNPUL1	11100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41800265	41800265	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatgatggtgggcctgcCtgctgctggcaagaccacat	7	10	13	11	0	1	3	0	2	1	1	1	3	1	3	3	3	3	3	3	3	1	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr19:41800265C>G	ENST00000392006.3	+	9	1462	c.1289C>G	c.(1288-1290)cCt>cGt	p.P430R	HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.P330R|HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.P330R|HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.P316R|HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.P341R|HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.P430R|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.P330R	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	430	Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						GTGGGCCTGCCTGCTGCTGGC	0.537																																					p.P430R		.											.	HNRNPUL1-69	0			c.C1289G						.						166	120	135					19																	41800265		2203	4300	6503	SO:0001583	missense	11100	exon9			GCCTGCCTGCTGC	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1289C>G	19.37:g.41800265C>G	ENSP00000375863:p.Pro430Arg	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	69	15	NM_007040	0	0	94	147	53	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	37	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717475	0.89205	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.46	5.46	0.80206	.	0.105015	0.64402	D	0.000003	T	0.78685	0.4322	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.973;1.0;1.0	D;D;D;P;D;D	0.97110	0.999;0.999;0.999;0.816;1.0;0.999	T	0.82489	-0.0432	10	0.87932	D	0	-7.8178	18.2528	0.90009	0.0:1.0:0.0:0.0	.	341;330;430;316;430;330	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;HNRL1_HUMAN;.	R	330;430;316;341	ENSP00000340857:P330R;ENSP00000375863:P430R;ENSP00000367460:P316R;ENSP00000263367:P341R	ENSP00000263367:P341R	P	+	2	0	HNRNPUL1	46492105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.557000	0.82243	2.840000	0.97914	0.655000	0.94253	CCT	.		0.537	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		G	41800265	C	G	41800265	3	3	68	1	0	0	0	0	1	0	0	0	7295	681	24	4	1323	4	HNRNPUL1	19	41800265	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	11491924	41800265	17328718	75	6525											
ZFP64	55734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	50769885	50769885	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttgaaaggcttctccccCgagtgcacccgcatgtgcct	7	9	9	16	2	1	1	0	1	1	0	2	2	1	1	4	1	2	3	4	1	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr20:50769885C>T	ENST00000216923.4	-	6	1195	c.846G>A	c.(844-846)tcG>tcA	p.S282S	ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Silent_p.S280S|ZFP64_ENST00000346617.4_Silent_p.S228S	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	282					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(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GCTTCTCCCCCGAGTGCACCC	0.552																																					p.S282S		.											.	ZFP64-155	0			c.G846A						.						80	72	75					20																	50769885		2203	4300	6503	SO:0001819	synonymous_variant	55734	exon6			CTCCCCCGAGTGC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.846G>A	20.37:g.50769885C>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	46	16	NM_018197	0	0	6	11	5	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			.		0.552	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		T	50769885	C	T	50769885	2	4	68	1	0	0	0	0	0	0	0	1	17684	639	23	1		1	ZFP64	20	50769885	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		50769885	12255635	76	6526											
IFNGR2	3460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34799207	34799207	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagtgactgtcgggcctccAgaaaacattgaggtgacccc	10	8	11	12	1	1	4	1	3	0	1	3	4	2	4	4	2	1	0	4	2	2	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr21:34799207A>T	ENST00000290219.6	+	4	1077	c.429A>T	c.(427-429)ccA>ccT	p.P143P	IFNGR2_ENST00000381995.1_Silent_p.P162P|IFNGR2_ENST00000405436.1_Silent_p.P64P	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	143	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	TCGGGCCTCCAGAAAACATTG	0.388																																					p.P143P		.											.	IFNGR2-186	0			c.A429T						.						162	158	159					21																	34799207		2203	4300	6503	SO:0001819	synonymous_variant	3460	exon4			GCCTCCAGAAAAC		CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128		"Interferons", "Fibronectin type III domain containing"	5440	protein-coding gene	gene with protein product		147569		IFNGT1		3136170	Standard	NM_005534		Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.429A>T	21.37:g.34799207A>T		Somatic	372	1		WXS	Illumina HiSeq	Phase_I	297	78	NM_005534	0	0	104	165	61	Q9BTL5	Silent	SNP	ENST00000290219.6	37	CCDS33544.1																																																																																			.		0.388	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139916.1			T	34799207	A	T	34799207	2	4	68	1	0	0	0	0	0	0	0	1	7571	175	7	5		5	IFNGR2	21	34799207	Silent	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		34799207	13330688	77	6527											
MKL1	57591	broad.mit.edu	37	chr22	40813489	40813489	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcgctggagagccaggctgGgacgagggctggacaggaga	9	3	21	8	2	0	2	0	0	0	2	0	7	0	4	1	7	1	3	1	7	0	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr22:40813489G>A	ENST00000355630.3	-	13	2663	c.2073C>T	c.(2071-2073)tcC>tcT	p.S691S	MKL1_ENST00000396617.3_Silent_p.S691S|MKL1_ENST00000402042.1_Silent_p.S641S|RP5-1042K10.13_ENST00000609279.1_RNA|MKL1_ENST00000407029.1_Silent_p.S691S	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	691	Pro-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						AGCCAGGCTGGGACGAGGGCT	0.692			T	RBM15	acute megakaryocytic leukemia																																p.S691S				Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	0			c.C2073T						.						10	11	11					22																	40813489		2200	4296	6496	SO:0001819	synonymous_variant	57591	exon13			AGGCTGGGACGAG	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.2073C>T	22.37:g.40813489G>A		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_020831	0	0	1	1	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	37	CCDS14003.1																																																																																			.		0.692	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		A	40813489	G	A	40813489	2	1	68	1	0	0	0	0	0	0	0	1	9626	1219	43	2		2	MKL1	22	40813489	Silent	SNP	G	TCGA-BQ-5884-01A-11D-1589-08		40813489	10491077	78	6528											
SFRS17A	8227	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	1718090	1718090	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgttccacacaggaaacAaaaggagctggaagagctgg	14	6	14	7	0	0	1	0	0	0	1	1	4	1	4	1	4	3	3	1	4	4	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chrX:1718090A>T	ENST00000313871.3	+	4	1113	c.917A>T	c.(916-918)cAa>cTa	p.Q306L	AKAP17A_ENST00000381261.3_Missense_Mutation_p.Q306L	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	306					B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						CACAGGAAACAAAAGGAGCTG	0.577																																					p.Q306L													.	AKAP17A-40	0			c.A917T						.						62	70	67					X																	1718090		2203	4296	6499	SO:0001583	missense	8227	exon4			GGAAACAAAAGGA	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.917A>T	X.37:g.1718090A>T	ENSP00000324827:p.Gln306Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	30	5	NM_005088	0	0	0	1	1	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	37	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	a	3.057	-0.194055	0.06259	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.27890	1.64;3.24	1.58	1.58	0.23477	.	0.086316	0.48767	U	0.000170	T	0.24044	0.0582	.	.	.	0.80722	D	1	B;B	0.22211	0.001;0.066	B;B	0.25987	0.0;0.065	T	0.06844	-1.0804	9	0.51188	T	0.08	.	9.1449	0.36925	1.0:0.0:0.0:0.0	.	306;306	Q02040-3;Q02040	.;AK17A_HUMAN	L	306	ENSP00000324827:Q306L;ENSP00000370660:Q306L	ENSP00000324827:Q306L	Q	+	2	0	AKAP17A	1678090	1.000000	0.71417	0.598000	0.28837	0.160000	0.22226	3.143000	0.50608	0.442000	0.26555	0.084000	0.15446	CAA	.		0.577	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		T	1718090	A	T	1718090	3	4	68	1	0	0	0	0	1	0	0	0	14205	130	5	5	927	5	SFRS17A	23	1718090	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		1718090	153552470	79	6529											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcctcctcctcctcctGttgcttctgctgctgctgtt	0	17	6	18	0	1	0	0	0	1	0	7	0	7	0	6	0	4	6	6	0	0	3	rs201290098		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E|SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		.											.	SHROOM4-131	0			c.C3391G						.						15	14	15					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3391C>G	X.37:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_020717	0	0	6	6	0	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50350751	G	C	50350751	3	2	68	1	0	0	0	0	1	0	0	0	14328	1386	48	4	1106	4	SHROOM4	23	50350751	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	48632661	50350751	104919809	80	6530											
CCDC21	64793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	26603078	26603078	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatctgacactccaggaacAcctgcgccaggcccaaccag	12	4	9	16	1	1	1	0	1	1	0	2	3	2	2	5	2	3	0	5	2	3	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:26603078A>T	ENST00000252992.4	+	13	2086	c.1955A>T	c.(1954-1956)cAc>cTc	p.H652L	CEP85_ENST00000469609.1_3'UTR|CEP85_ENST00000451429.2_Missense_Mutation_p.H601L|SH3BGRL3_ENST00000270792.5_5'Flank	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	652						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						CTCCAGGAACACCTGCGCCAG	0.557																																					p.H652L		.											.	CEP85-90	0			c.A1955T						.						66	63	64					1																	26603078		2203	4300	6503	SO:0001583	missense	64793	exon13			AGGAACACCTGCG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"coiled-coil domain containing 21"	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1955A>T	1.37:g.26603078A>T	ENSP00000252992:p.His652Leu	Somatic	73	2		WXS	Illumina HiSeq	Phase_I	38	23	NM_022778	0	0	0	4	4	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.29|14.29	2.491684|2.491684	0.44249|0.44249	.|.	.|.	ENSG00000130695|ENSG00000130695	ENST00000451429;ENST00000252992|ENST00000453146	T;T|.	0.11712|.	2.75;2.75|.	5.51|5.51	4.39|4.39	0.52855|0.52855	.|.	0.164015|.	0.53938|.	D|.	0.000043|.	T|T	0.41419|0.41419	0.1158|0.1158	N|N	0.25647|0.25647	0.755|0.755	0.35482|0.35482	D|D	0.798211|0.798211	B;B;P|.	0.39696|.	0.048;0.098;0.683|.	B;B;B|.	0.39465|.	0.032;0.049;0.3|.	T|T	0.48479|0.48479	-0.9032|-0.9032	10|5	0.16896|.	T|.	0.51|.	-6.2062|-6.2062	6.6738|6.6738	0.23083|0.23083	0.7771:0.0:0.2229:0.0|0.7771:0.0:0.2229:0.0	.|.	601;652;652|.	F8W7K4;Q6P2H3;Q6P2H3-2|.	.;CEP85_HUMAN;.|.	L|S	601;652|326	ENSP00000417002:H601L;ENSP00000252992:H652L|.	ENSP00000252992:H652L|.	H|T	+|+	2|1	0|0	CEP85|CEP85	26475665|26475665	0.963000|0.963000	0.33076|0.33076	1.000000|1.000000	0.80357|0.80357	0.633000|0.633000	0.38033|0.38033	1.767000|1.767000	0.38501|0.38501	2.105000|2.105000	0.64084|0.64084	0.454000|0.454000	0.30748|0.30748	CAC|ACC	.		0.557	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		T	26603078	A	T	26603078	3	4	69	1	0	0	0	0	1	0	0	0	2802	159	6	5	2001	5	CCDC21	1	26603078	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08		26603078	222647543	1	6531											
OSCP1	127700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36915923	36915923	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggtcgaggatgtaaagcatCtccccgcccaagttcaagaa	12	8	10	11	2	2	1	1	0	1	1	4	3	2	2	3	2	1	3	3	2	5	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:36915923C>T	ENST00000356637.5	-	1	111	c.48G>A	c.(46-48)gaG>gaA	p.E16E	OSCP1_ENST00000235532.5_Silent_p.E16E|OSCP1_ENST00000354267.3_Silent_p.E16E|OSCP1_ENST00000315643.9_Silent_p.E16E			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	16					transport (GO:0006810)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						TGTAAAGCATCTCCCCGCCCA	0.652																																					p.E16E		.											.	OSCP1-4	0			c.G48A						.						46	46	46					1																	36915923		2203	4300	6503	SO:0001819	synonymous_variant	127700	exon1			AAGCATCTCCCCG		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"oxidored nitro domain containing protein"	608854	"chromosome 1 open reading frame 102"	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.48G>A	1.37:g.36915923C>T		Somatic	88	1		WXS	Illumina HiSeq	Phase_I	93	35	NM_145047	0	0	3	5	2	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Silent	SNP	ENST00000356637.5	37																																																																																				.		0.652	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047		T	36915923	C	T	36915923	2	4	69	1	0	0	0	0	0	0	0	1	11312	912	32	2		2	OSCP1	1	36915923	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	10312845	36915923	212334698	2	6532											
LRRC41	10489	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	46751890	46751890	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgcaacagctgccgaagTgactgctgagcagccacatc	11	7	11	12	1	0	3	0	3	0	0	1	4	0	3	2	0	7	4	2	0	2	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:46751890T>G	ENST00000343304.6	-	4	924	c.639A>C	c.(637-639)tcA>tcC	p.S213S	LRRC41_ENST00000472710.1_5'UTR	NM_006369.4	NP_006360.3	Q15345	LRC41_HUMAN	leucine rich repeat containing 41	213					protein ubiquitination (GO:0016567)	membrane (GO:0016020)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GCTGCCGAAGTGACTGCTGAG	0.572																																					p.S213S		.											.	LRRC41-156	0			c.A639C						.						49	48	49					1																	46751890		2203	4300	6503	SO:0001819	synonymous_variant	10489	exon4			CCGAAGTGACTGC	AK024051	CCDS533.1	1p34.1	2008-02-05			ENSG00000132128	ENSG00000132128			16917	protein-coding gene	gene with protein product						11384984	Standard	XM_005270376		Approved	MUF1	uc001cpn.3	Q15345	OTTHUMG00000007810	ENST00000343304.6:c.639A>C	1.37:g.46751890T>G		Somatic	69	1		WXS	Illumina HiSeq	Phase_I	62	20	NM_006369	0	0	12	19	7	A8K5G8|Q3MJ96|Q5TDF5|Q71RA8|Q9BSM0	Silent	SNP	ENST00000343304.6	37	CCDS533.1																																																																																			.		0.572	LRRC41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021438.1	NM_006369		G	46751890	T	G	46751890	2	3	69	1	0	0	0	0	0	0	0	1	9024	1683	59	5		5	LRRC41	1	46751890	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	9835967	46751890	202498731	3	6533											
CYB5RL	606495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	54640395	54640395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaccagtgcgaatggctttCtccgacagcagctgaccagc	10	7	11	13	2	1	2	0	1	1	1	2	4	1	2	3	1	4	3	3	1	1	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:54640395C>T	ENST00000534324.1	-	6	844	c.845G>A	c.(844-846)aGa>aAa	p.R282K	CYB5RL_ENST00000287899.8_Missense_Mutation_p.R214K|RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000419823.2_Missense_Mutation_p.R282K|CYB5RL_ENST00000537208.1_Missense_Mutation_p.R214K|CYB5RL_ENST00000401046.3_Missense_Mutation_p.R134K|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R282K|RP11-446E24.4_ENST00000525949.1_5'Flank|AL357673.1_ENST00000536061.1_5'Flank			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	282							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						GAATGGCTTTCTCCGACAGCA	0.547																																					p.R282K		.											.	.	0			c.G845A						.						42	44	43					1																	54640395		1944	4162	6106	SO:0001583	missense	606495	exon8			GGCTTTCTCCGAC		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.845G>A	1.37:g.54640395C>T	ENSP00000434343:p.Arg282Lys	Somatic	53	1		WXS	Illumina HiSeq	Phase_I	42	17	NM_001031672	0	0	1	1	0	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	37	CCDS44151.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.249230	0.39797	.	.	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208	D;D;D;D;D;D	0.89552	-2.11;-2.11;-2.11;-2.53;-2.11;-2.53	5.14	3.27	0.37495	Oxidoreductase FAD/NAD(P)-binding (1);	0.000000	0.42682	U	0.000678	D	0.83459	0.5259	L	0.39633	1.23	0.34427	D	0.698071	P;P	0.48162	0.906;0.813	P;B	0.46659	0.523;0.391	T	0.81773	-0.0779	10	0.09084	T	0.74	-15.2588	9.7602	0.40528	0.0:0.8418:0.0:0.1582	.	282;134	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	K	282;134;282;214;282;214	ENSP00000409075:R282K;ENSP00000383825:R134K;ENSP00000434343:R282K;ENSP00000287899:R214K;ENSP00000438151:R282K;ENSP00000443797:R214K	ENSP00000287899:R214K	R	-	2	0	CYB5RL	54412983	1.000000	0.71417	0.999000	0.59377	0.640000	0.38277	2.675000	0.46875	0.750000	0.32877	0.555000	0.69702	AGA	.		0.547	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672		T	54640395	C	T	54640395	3	4	69	1	0	0	0	0	1	0	0	0	4136	913	32	2	106	2	CYB5RL	1	54640395	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	7888505	54640395	194610226	4	6534											
KIAA1324	57535	broad.mit.edu;bcgsc.ca	37	chr1	109735396	109735396	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctatattgaccgagattcagGaacctgccactcctgcccca	10	9	7	15	1	1	2	1	1	0	1	2	4	2	3	6	1	3	0	6	1	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:109735396G>T	ENST00000369939.3	+	14	2030	c.1847G>T	c.(1846-1848)gGa>gTa	p.G616V	KIAA1324_ENST00000529753.1_Missense_Mutation_p.G529V|KIAA1324_ENST00000369938.1_3'UTR	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	616					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		CGAGATTCAGGAACCTGCCAC	0.567																																					p.G616V													.	KIAA1324-157	0			c.G1847T						.						145	137	140					1																	109735396		2203	4300	6503	SO:0001583	missense	57535	exon14			ATTCAGGAACCTG	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"estrogen induced gene 121"	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.1847G>T	1.37:g.109735396G>T	ENSP00000358955:p.Gly616Val	Somatic	256	1		WXS	Illumina HiSeq	Phase_I	192	74	NM_020775	0	0	0	0	0	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	37	CCDS794.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283430	0.80803	.	.	ENSG00000116299	ENST00000369939;ENST00000457623;ENST00000529753	T;T;T	0.62941	-0.01;-0.01;-0.01	4.81	4.81	0.61882	Growth factor, receptor (1);	0.052875	0.85682	D	0.000000	T	0.68146	0.2969	L	0.47716	1.5	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.988;0.993;0.988;0.988	T	0.67043	-0.5770	10	0.45353	T	0.12	-15.0032	17.1659	0.86816	0.0:0.0:1.0:0.0	.	616;529;616;616	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	V	616;566;529	ENSP00000358955:G616V;ENSP00000393964:G566V;ENSP00000434595:G529V	ENSP00000358955:G616V	G	+	2	0	KIAA1324	109536919	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	6.541000	0.73865	2.659000	0.90383	0.650000	0.86243	GGA	.		0.567	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		T	109735396	G	T	109735396	3	4	69	1	0	0	0	0	1	0	0	0	8244	1174	41	4	1901	4	KIAA1324	1	109735396	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	55095001	109735396	139515225	5	6535											
ARNT	405	bcgsc.ca	37	chr1	150804346	150804346	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggaccaccacgaagtgAggttccccatcctttacaga	11	8	9	13	1	0	2	0	1	0	1	2	4	2	3	5	2	1	1	5	2	2	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:150804346A>G	ENST00000358595.5	-	10	1103	c.903T>C	c.(901-903)ccT>ccC	p.P301P	ARNT_ENST00000354396.2_Silent_p.P301P|ARNT_ENST00000468970.1_5'UTR|ARNT_ENST00000515192.1_Silent_p.P292P|ARNT_ENST00000505755.1_Silent_p.P286P	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	301					cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCACGAAGTGAGGTTCCCCAT	0.443			T	ETV6	AML																																p.P301P				Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT-1085	0			c.T903C						.						70	71	70					1																	150804346		2203	4300	6503	SO:0001819	synonymous_variant	405	exon10			GAAGTGAGGTTCC	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"Basic helix-loop-helix proteins"	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.903T>C	1.37:g.150804346A>G		Somatic	99	2		WXS	Illumina HiSeq	Phase_1	96	5	NM_001668	0	0	2	2	0	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Silent	SNP	ENST00000358595.5	37	CCDS970.1																																																																																			.		0.443	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2			G	150804346	A	G	150804346	2	3	69	1	0	0	0	0	0	0	0	1	966	291	11	3		3	ARNT	1	150804346	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	41068950	150804346	98446275	6	6536											
NCSTN	23385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160326495	160326495	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggcacagtggtcaacctcaCccgagagcagtgccaggatc	10	6	12	13	1	2	1	2	0	0	1	3	3	2	2	3	3	3	2	3	3	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:160326495C>T	ENST00000294785.5	+	15	1870	c.1745C>T	c.(1744-1746)aCc>aTc	p.T582I	NCSTN_ENST00000368065.4_Missense_Mutation_p.T324I|NCSTN_ENST00000368063.1_Missense_Mutation_p.T562I|NCSTN_ENST00000535857.1_Missense_Mutation_p.T444I|NCSTN_ENST00000392212.4_Missense_Mutation_p.T562I	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	582					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GTCAACCTCACCCGAGAGCAG	0.532																																					p.T582I		.											.	NCSTN-658	0			c.C1745T						.						150	138	142					1																	160326495		2203	4300	6503	SO:0001583	missense	23385	exon15			ACCTCACCCGAGA	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.1745C>T	1.37:g.160326495C>T	ENSP00000294785:p.Thr582Ile	Somatic	118	2		WXS	Illumina HiSeq	Phase_I	119	32	NM_015331	0	0	40	67	27	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	ENST00000294785.5	37	CCDS1203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.7|25.7	4.666363|4.666363	0.88251|0.88251	.|.	.|.	ENSG00000162736|ENSG00000162736	ENST00000435149|ENST00000294785;ENST00000368063;ENST00000535857;ENST00000368067;ENST00000392212;ENST00000368065	.|T;T;T;T	.|0.79141	.|-1.24;-1.23;-0.25;-1.23	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.046265	.|0.85682	.|D	.|0.000000	T|T	0.82167|0.82167	0.4978|0.4978	L|L	0.59436|0.59436	1.845|1.845	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D	.|0.67145	.|0.991;0.994;0.996	.|P;P;P	.|0.60236	.|0.86;0.827;0.871	T|T	0.82508|0.82508	-0.0422|-0.0422	5|10	.|0.56958	.|D	.|0.05	-16.0093|-16.0093	18.4423|18.4423	0.90671|0.90671	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|444;562;582	.|F6Y097;Q92542-2;Q92542	.|.;.;NICA_HUMAN	S|I	259|582;562;444;289;562;324	.|ENSP00000294785:T582I;ENSP00000357042:T562I;ENSP00000442605:T444I;ENSP00000376047:T562I	.|ENSP00000294785:T582I	P|T	+|+	1|2	0|0	NCSTN|NCSTN	158593119|158593119	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.750000|0.750000	0.42670|0.42670	4.757000|4.757000	0.62213|0.62213	2.699000|2.699000	0.92147|0.92147	0.650000|0.650000	0.86243|0.86243	CCC|ACC	.		0.532	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331		T	160326495	C	T	160326495	3	4	69	1	0	0	0	0	1	0	0	0	10267	507	18	2	1803	2	NCSTN	1	160326495	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	9522149	160326495	88924126	7	6537											
FMO4	2329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171303821	171303822	+	Missense_Mutation	DNP	AT	AT	GC																															tagagagagcgacattagccAtcatcggccttatcggcctt																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:171303821_171303822AT>GC	ENST00000367749.3	+	8	1429_1430	c.1099_1100AT>GC	c.(1099-1101)ATc>GCc	p.I367A		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	367					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GACATTAGCCATCATCGGCCTT	0.411																																					p.I367A	Pancreas(24;816 862 7754 7993 32832)	.											.	FMO4	0			c.T1100C						.																																			SO:0001583	missense	2329	exon8			TAGCCATCATCGG	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	Exception_encountered	1.37:g.171303821_171303822delinsGC	ENSP00000356723:p.Ile367Ala	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	136	43		0	0	0	0	0	Q53XR0	Missense_Mutation	DNP	ENST00000367749.3	37	CCDS1295.1																																																																																			.		0.411	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		GC	171303822	AT	GC	171303821	3	3	69	1	0	0	0	0	1	0	0	0	5976	217	8	3	1121	3	FMO4	1	171303821	Missense_Mutation	DNP	AT	TCGA-BQ-5885-01A-11D-1589-08	10977326	171303821	77946800	8	6538											
FAM129A	116496	broad.mit.edu	37	chr1	184943459	184943459	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtaagcgcacttgccctcGtccagctggctggaggctga	7	9	13	12	2	0	1	0	1	0	0	2	2	1	2	2	3	3	5	2	3	1	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:184943459G>T	ENST00000367511.3	-	1	223	c.30C>A	c.(28-30)gaC>gaA	p.D10E		NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	10					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						ACTTGCCCTCGTCCAGCTGGC	0.726																																					p.D10E													.	FAM129A-94	0			c.C30A						.						16	19	18					1																	184943459		2172	4242	6414	SO:0001583	missense	116496	exon1			GCCCTCGTCCAGC	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.30C>A	1.37:g.184943459G>T	ENSP00000356481:p.Asp10Glu	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	11	4	NM_052966	0	0	0	0	0	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310008	0.81247	.	.	ENSG00000135842	ENST00000367511	T	0.18960	2.18	4.24	2.26	0.28386	.	0.161083	0.37623	N	0.002020	T	0.31167	0.0788	L	0.41492	1.28	0.34448	D	0.700335	D	0.89917	1.0	D	0.81914	0.995	T	0.40021	-0.9585	10	0.72032	D	0.01	-12.5229	7.1527	0.25620	0.2189:0.0:0.7811:0.0	.	10	Q9BZQ8	NIBAN_HUMAN	E	10	ENSP00000356481:D10E	ENSP00000356481:D10E	D	-	3	2	FAM129A	183210082	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.089000	0.41672	0.979000	0.38497	0.491000	0.48974	GAC	.		0.726	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			T	184943459	G	T	184943459	3	4	69	1	0	0	0	0	1	0	0	0	5452	1136	40	4	2812	4	FAM129A	1	184943459	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	13639638	184943459	64307162	9	6539											
HEATR1	55127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	236738095	236738095	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgaaaattcattatactttcCcagagtgagatgcagaacca	15	11	7	8	0	1	4	1	2	0	3	2	5	2	4	2	0	3	1	2	0	5	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:236738095C>T	ENST00000366582.3	-	23	3307	c.3193G>A	c.(3193-3195)Gga>Aga	p.G1065R	HEATR1_ENST00000366581.2_Intron	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1065					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TTATACTTTCCCAGAGTGAGA	0.423																																					p.G1065R		.											.	HEATR1-93	0			c.G3193A						.						72	72	72					1																	236738095		2203	4300	6503	SO:0001583	missense	55127	exon23			ACTTTCCCAGAGT	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.3193G>A	1.37:g.236738095C>T	ENSP00000355541:p.Gly1065Arg	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	108	43	NM_018072	0	0	1	1	0	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.659073	0.67586	.	.	ENSG00000119285	ENST00000366582	T	0.66099	-0.19	5.73	5.73	0.89815	Armadillo-type fold (2);	0.167388	0.52532	D	0.000065	T	0.65059	0.2655	M	0.62723	1.935	0.80722	D	1	P	0.42735	0.788	B	0.42495	0.389	T	0.62334	-0.6876	10	0.28530	T	0.3	.	19.904	0.97001	0.0:1.0:0.0:0.0	.	1065	Q9H583	HEAT1_HUMAN	R	1065	ENSP00000355541:G1065R	ENSP00000355541:G1065R	G	-	1	0	HEATR1	234804718	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	2.615000	0.46368	2.689000	0.91719	0.655000	0.94253	GGA	.		0.423	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236738095	C	T	236738095	3	4	69	1	0	0	0	0	1	0	0	0	7048	632	22	2	3333	2	HEATR1	1	236738095	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	51794636	236738095	12512526	10	6540											
HEATR1	55127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	236749736	236749736	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattaatatgtcagcggctaTcttaagtacctcgtacctaa	13	13	6	9	2	2	0	1	0	1	0	3	0	2	0	2	1	3	3	2	1	8	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:236749736T>C	ENST00000366582.3	-	15	1846	c.1732A>G	c.(1732-1734)Ata>Gta	p.I578V	HEATR1_ENST00000366581.2_Missense_Mutation_p.I578V	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	578					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCAGCGGCTATCTTAAGTACC	0.368																																					p.I578V		.											.	HEATR1-93	0			c.A1732G						.																																			SO:0001583	missense	55127	exon15			CGGCTATCTTAAG	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1732A>G	1.37:g.236749736T>C	ENSP00000355541:p.Ile578Val	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	156	50	NM_018072	0	0	0	0	0	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.926731	0.00493	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.42900	0.96;0.96	5.28	-2.98	0.05513	Armadillo-like helical (1);Armadillo-type fold (1);	0.667620	0.15450	N	0.261734	T	0.13157	0.0319	N	0.03115	-0.41	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.13019	-1.0525	10	0.26408	T	0.33	.	1.7301	0.02930	0.1285:0.3195:0.2162:0.3358	.	578	Q9H583	HEAT1_HUMAN	V	578	ENSP00000355541:I578V;ENSP00000355540:I578V	ENSP00000355540:I578V	I	-	1	0	HEATR1	234816359	0.001000	0.12720	0.931000	0.37212	0.129000	0.20672	-0.294000	0.08309	-0.174000	0.10743	0.460000	0.39030	ATA	T|1.000;C|0.000		0.368	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		C	236749736	T	C	236749736	3	2	69	1	0	0	0	0	1	0	0	0	7048	1435	50	3	4826	3	HEATR1	1	236749736	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	11641	236749736	12500885	11	6541											
FMN2	56776	hgsc.bcm.edu	37	chr1	240256171	240256171	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcctggaccggttcctgctGgggccgagcggcggggctgg	2	6	21	12	4	0	0	0	0	0	0	1	2	1	1	4	9	2	3	4	9	0	1	rs142232913	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:240256171G>A	ENST00000319653.9	+	1	992	c.762G>A	c.(760-762)ctG>ctA	p.L254L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	254					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGTTCCTGCTGGGGCCGAGCG	0.776													G|||	32	0.00638978	0	0.0058	5008	,	,		10259	0		0.0139	False		,,,				2504	0.0143				p.L254L		.											.	FMN2-145	0			c.G762A						.	G		3,3203		0,3,1600	2	3	2		762	2.5	1	1	dbSNP_134	2	38,6696		0,38,3329	no	coding-synonymous	FMN2	NM_020066.4		0,41,4929	AA,AG,GG		0.5643,0.0936,0.4125		254/1723	240256171	41,9899	1603	3367	4970	SO:0001819	synonymous_variant	56776	exon1			CCTGCTGGGGCCG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.762G>A	1.37:g.240256171G>A		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	5	3	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			G|0.994;A|0.006		0.776	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240256171	G	A	240256171	2	1	69	1	0	0	0	0	0	0	0	1	5969	1335	47	2		2	FMN2	1	240256171	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	3506435	240256171	8994450	12	6542											
OR2M3	127062	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	248366486	248366486	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatcttttcagtggccttCatgggaaactctgtcatggt	7	14	10	10	0	5	0	3	0	2	0	5	1	5	1	2	3	1	0	2	3	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:248366486C>A	ENST00000456743.1	+	1	155	c.117C>A	c.(115-117)ttC>ttA	p.F39L		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F39L(1)		endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CAGTGGCCTTCATGGGAAACT	0.547																																					p.F39L		.											.	OR2M3-70	1	Substitution - Missense(1)	lung(1)	c.C117A						.						231	228	229					1																	248366486		2203	4297	6500	SO:0001583	missense	127062	exon1			GGCCTTCATGGGA		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"GPCR / Class A : Olfactory receptors"	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.117C>A	1.37:g.248366486C>A	ENSP00000389625:p.Phe39Leu	Somatic	634	0		WXS	Illumina HiSeq	Phase_I	639	61	NM_001004689	0	0	0	0	0	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.658172	0.00779	.	.	ENSG00000228198	ENST00000456743	T	0.01647	4.71	2.43	-1.17	0.09648	.	1.333000	0.05812	N	0.614187	T	0.00356	0.0011	N	0.00020	-2.77	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.51036	-0.8756	10	0.02654	T	1	.	2.0514	0.03571	0.287:0.3225:0.2842:0.1063	.	39	Q8NG83	OR2M3_HUMAN	L	39	ENSP00000389625:F39L	ENSP00000389625:F39L	F	+	3	2	OR2M3	246433109	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-2.442000	0.01014	-0.082000	0.12640	0.398000	0.26397	TTC	.		0.547	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		A	248366486	C	A	248366486	3	1	69	1	0	0	0	0	1	0	0	0	11037	825	29	4	119	4	OR2M3	1	248366486	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	8110315	248366486	884135	13	6543											
CAD	51374	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27440797	27440797	+	IGR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccctcaccgatccctcctaCaaggcacagatcttagtgct	9	9	7	16	1	2	1	1	0	1	1	4	2	4	1	4	1	2	2	4	1	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:27440797C>A	ENST00000606999.1	+	0	956				CAD_ENST00000403525.1_Nonsense_Mutation_p.Y45*|CAD_ENST00000264705.4_Nonsense_Mutation_p.Y45*	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor						cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)											ATCCCTCCTACAAGGCACAGA	0.572																																					p.Y45X		.											.	CAD-295	0			c.C135A						.						124	115	118					2																	27440797		2203	4300	6503	SO:0001628	intergenic_variant	790	exon2			CTCCTACAAGGCA	BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"apoptosis-related protein 3"		"chromosome 2 open reading frame 28"	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405		2.37:g.27440797C>A		Somatic	189	0		WXS	Illumina HiSeq	Phase_I	143	54	NM_004341	0	0	0	0	0	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Nonsense_Mutation	SNP	ENST00000606999.1	37		.	.	.	.	.	.	.	.	.	.	C	31	5.075282	0.94000	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	.	.	.	5.05	4.17	0.49024	.	0.070247	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0623	12.2333	0.54500	0.0:0.917:0.0:0.083	.	.	.	.	X	45	.	ENSP00000264705:Y45X	Y	+	3	2	CAD	27294301	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	2.602000	0.46257	1.351000	0.45789	0.484000	0.47621	TAC	.		0.572	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085		A	27440797	C	A	27440797	1	1	69	0	1	0	0	0	0	0	0	0	2571	489	17	4		4	CAD	2	27440797	IGR	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		27440797	215758576	14	6544											
MAP4K3	8491	bcgsc.ca	37	chr2	39526944	39526944	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catattccagttgcagatccTaatagtacaaaataaaatat	18	12	4	7	0	0	1	0	0	0	1	2	1	2	1	2	0	2	3	2	0	9	8			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:39526944T>C	ENST00000263881.3	-	16	1444		c.e16-2		MAP4K3_ENST00000437545.1_Splice_Site|MAP4K3_ENST00000536018.1_Splice_Site|MAP4K3_ENST00000341681.5_Splice_Site	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3						intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				TTGCAGATCCTAATAGTACAA	0.269																																					.													.	MAP4K3-550	0			c.1120-2A>G						.						34	37	36					2																	39526944		2199	4277	6476	SO:0001630	splice_region_variant	8491	exon17			AGATCCTAATAGT	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1120-2A>G	2.37:g.39526944T>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_1	42	4	NM_003618	0	0	0	0	0	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Splice_Site	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	T	14.00	2.404335	0.42613	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5697	0.76323	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAP4K3	39380448	1.000000	0.71417	0.998000	0.56505	0.572000	0.35998	6.382000	0.73167	2.084000	0.62774	0.260000	0.18958	.	.		0.269	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	Intron	C	39526944	T	C	39526944	5	2	69	1	0	0	0	0	0	0	1	0	9286	1536	53	3	1642	3	MAP4K3	2	39526944	Splice_Site	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	12086147	39526944	203672429	15	6545											
RTN4	57142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55253513	55253514	+	Missense_Mutation	DNP	TT	TT	AG																															tgaaccaagtccatttttgtTtcataagcaatctttgtacc																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:55253513_55253514TT>AG	ENST00000337526.6	-	3	1964_1965	c.1721_1722AA>CT	c.(1720-1722)gAA>gCT	p.E574A	RTN4_ENST00000317610.7_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.E368A|RTN4_ENST00000394611.2_Missense_Mutation_p.E368A|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000354474.6_Missense_Mutation_p.E342A|RTN4_ENST00000404909.1_Missense_Mutation_p.E368A|RTN4_ENST00000405240.1_Missense_Mutation_p.E368A	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	574					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						CCATTTTTGTTTCATAAGCAAT	0.416																																					p.E574A		.											.	RTN4	0			c.A1721C						.																																			SO:0001583	missense	57142	exon3			TTTGTTTCATAAG	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1721_1722delinsAG	2.37:g.55253513_55253514delinsAG	ENSP00000337838:p.Glu574Ala	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	132	33		0	0	0	0	0	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	DNP	ENST00000337526.6	37	CCDS42684.1																																																																																			.		0.416	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			AG	55253514	TT	AG	55253513	3	1	69	1	0	0	0	0	1	0	0	0	13760	1838	64	5	1922	5	RTN4	2	55253513	Missense_Mutation	DNP	TT	TCGA-BQ-5885-01A-11D-1589-08	15726569	55253513	187945860	16	6546											
USP34	9736	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	61505306	61505306	+	Frame_Shift_Del	DEL	T	T	-																															atcttaacacttacctgtccTtcccttgaaaatttaaaggg																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:61505306delT	ENST00000398571.2	-	41	5503	c.5427delA	c.(5425-5427)gaafs	p.E1809fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1809					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTACCTGTCCTTCCCTTGAAA	0.343																																					p.E1809fs		.											.	USP34-579	0			c.5427delA						.						92	79	84					2																	61505306		1864	4092	5956	SO:0001589	frameshift_variant	9736	exon41			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5427delA	2.37:g.61505306delT	ENSP00000381577:p.Glu1809fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	38	12	NM_014709	0	0	0	0	0	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	37	CCDS42686.1																																																																																			.		0.343	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			-	61505306	T	-	61505306	7	5	69	1	0	1	0	1	0	0	0	0	17098	1606	56	0	5373	0	USP34	2	61505306	Frame_Shift_Del	DEL	T	TCGA-BQ-5885-01A-11D-1589-08	6251793	61505306	181694067	17	6547											
ALMS1	7840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	73680677	73680677	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatattggcacacagacgaaTttgaaatgccggagaggcat	14	8	12	7	2	0	3	0	1	0	2	0	6	0	3	1	3	1	2	1	3	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:73680677T>C	ENST00000264448.6	+	8	7131	c.7020T>C	c.(7018-7020)aaT>aaC	p.N2340N	ALMS1_ENST00000377715.1_Silent_p.N2340N|ALMS1_ENST00000409009.1_Silent_p.N2298N	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2340					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CACAGACGAATTTGAAATGCC	0.448																																					p.N2340N		.											.	ALMS1-142	0			c.T7020C						.						56	53	54					2																	73680677		1872	4112	5984	SO:0001819	synonymous_variant	7840	exon8			GACGAATTTGAAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7020T>C	2.37:g.73680677T>C		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	71	14	NM_015120	0	0	1	1	0	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			.		0.448	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73680677	T	C	73680677	2	2	69	1	0	0	0	0	0	0	0	1	535	1490	52	3		3	ALMS1	2	73680677	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	12175371	73680677	169518696	18	6548											
SEMA4F	10505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74902749	74902749	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccacagccagttgagaacatGaaattgtaccacgtgagttg	13	9	10	9	1	0	3	0	3	0	1	0	4	0	3	3	0	3	3	3	0	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:74902749G>A	ENST00000357877.2	+	11	1619	c.1470G>A	c.(1468-1470)atG>atA	p.M490I	SEMA4F_ENST00000473350.1_3'UTR|SEMA4F_ENST00000339773.5_Missense_Mutation_p.M335I	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	490	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)	p.M490I(1)		biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						TTGAGAACATGAAATTGTACC	0.512																																					p.M490I		.											.	SEMA4F-93	1	Substitution - Missense(1)	large_intestine(1)	c.G1470A						.						102	91	95					2																	74902749		2203	4300	6503	SO:0001583	missense	10505	exon11			GAACATGAAATTG	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"Semaphorins"	10734	protein-coding gene	gene with protein product	"m-Sema M"	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.1470G>A	2.37:g.74902749G>A	ENSP00000350547:p.Met490Ile	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	134	40	NM_004263	0	0	0	0	0	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.818592	0.32145	.	.	ENSG00000135622	ENST00000357877;ENST00000339773	T;T	0.32023	1.47;1.47	4.5	3.58	0.41010	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.129054	0.51477	D	0.000093	T	0.17916	0.0430	N	0.12887	0.27	0.34285	D	0.682588	B;B	0.14012	0.003;0.009	B;B	0.15052	0.007;0.012	T	0.15983	-1.0418	10	0.46703	T	0.11	.	12.2822	0.54771	0.0:0.1859:0.814:0.0	.	335;490	O95754-2;O95754	.;SEM4F_HUMAN	I	490;335	ENSP00000350547:M490I;ENSP00000342675:M335I	ENSP00000342675:M335I	M	+	3	0	SEMA4F	74756257	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.936000	0.40183	2.333000	0.79357	0.467000	0.42956	ATG	.		0.512	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74902749	G	A	74902749	3	1	69	1	0	0	0	0	1	0	0	0	14067	1290	45	2	1512	2	SEMA4F	2	74902749	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1222072	74902749	168296624	19	6549											
TBC1D8	11138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	101670697	101670697	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	accagcttctccgcctcgggGaagttgaacctggcctcgaa	8	8	11	14	3	1	1	0	1	1	0	4	3	1	2	5	3	2	2	5	3	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:101670697G>A	ENST00000376840.4	-	4	458	c.459C>T	c.(457-459)ttC>ttT	p.F153F	TBC1D8_ENST00000409318.1_Silent_p.F168F			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	153	GRAM 1.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CCGCCTCGGGGAAGTTGAACC	0.617																																					p.F153F		.											.	TBC1D8-25	0			c.C459T						.						35	41	39					2																	101670697		2066	4231	6297	SO:0001819	synonymous_variant	11138	exon4			CTCGGGGAAGTTG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.459C>T	2.37:g.101670697G>A		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	18	12	NM_001102426	0	0	0	5	5	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	37	CCDS46375.1																																																																																			.		0.617	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		A	101670697	G	A	101670697	2	1	69	1	0	0	0	0	0	0	0	1	15657	1165	41	2		2	TBC1D8	2	101670697	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	26767948	101670697	141528676	20	6550											
TMEM177	80775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	120439354	120439354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagggggatgctcaatccgGgccgctcctgatgggctcat	6	8	16	11	2	2	1	2	1	0	0	4	3	4	3	3	5	1	3	3	5	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:120439354G>A	ENST00000424086.1	+	2	1398	c.925G>A	c.(925-927)Ggc>Agc	p.G309S	TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000272521.6_Missense_Mutation_p.G309S|TMEM177_ENST00000401466.1_Missense_Mutation_p.G309S|TMEM177_ENST00000409951.1_Intron	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	309						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	13	Colorectal(110;0.196)					GCTCAATCCGGGCCGCTCCTG	0.577																																					p.G309S		.											.	TMEM177-91	0			c.G925A						.						43	47	46					2																	120439354		2201	4299	6500	SO:0001583	missense	80775	exon2			AATCCGGGCCGCT	BC004404	CCDS2128.1	2q14.2	2008-02-05			ENSG00000144120	ENSG00000144120			28143	protein-coding gene	gene with protein product						12477932	Standard	NM_001105198		Approved	MGC10993	uc002tmc.1	Q53S58	OTTHUMG00000153312	ENST00000424086.1:c.925G>A	2.37:g.120439354G>A	ENSP00000402661:p.Gly309Ser	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	129	44	NM_030577	0	0	11	15	4	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	37	CCDS2128.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928205	0.34002	.	.	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000415646	T;T;T	0.31510	1.49;1.49;1.49	4.44	2.51	0.30379	.	0.000000	0.53938	D	0.000044	T	0.16041	0.0386	N	0.17674	0.51	0.09310	N	1	B	0.14012	0.009	B	0.15052	0.012	T	0.18085	-1.0348	10	0.25751	T	0.34	-4.387	5.7699	0.18247	0.1213:0.1952:0.6835:0.0	.	309	Q53S58	TM177_HUMAN	S	309;309;309;248	ENSP00000385966:G309S;ENSP00000402661:G309S;ENSP00000272521:G309S	ENSP00000272521:G309S	G	+	1	0	TMEM177	120155824	0.003000	0.15002	0.010000	0.14722	0.097000	0.18754	0.068000	0.14531	0.514000	0.28300	0.549000	0.68633	GGC	.		0.577	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577		A	120439354	G	A	120439354	3	1	69	1	0	0	0	0	1	0	0	0	16126	1232	43	2	927	2	TMEM177	2	120439354	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	18768657	120439354	122760019	21	6551											
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141819633	141819633	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacttacttgtctgccttgaAtgacagtgtgtctatttttt	7	20	7	7	0	2	2	0	2	2	0	2	2	2	2	1	0	3	0	1	0	4	8			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:141819633A>T	ENST00000389484.3	-	8	2194	c.1223T>A	c.(1222-1224)aTt>aAt	p.I408N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	408					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCTGCCTTGAATGACAGTGTG	0.358										TSP Lung(27;0.18)																											p.I408N	Colon(99;50 2074 2507 20106)	.											.	LRP1B-311	0			c.T1223A						.						217	197	204					2																	141819633		2203	4300	6503	SO:0001583	missense	53353	exon8			CCTTGAATGACAG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1223T>A	2.37:g.141819633A>T	ENSP00000374135:p.Ile408Asn	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	212	76	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.491685	0.44249	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91686	-2.89	5.63	4.48	0.54585	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.371653	0.26734	N	0.022764	D	0.92047	0.7480	M	0.85630	2.765	0.23260	N	0.99803	B	0.27192	0.171	B	0.28849	0.095	D	0.86417	0.1752	10	0.72032	D	0.01	.	10.4218	0.44354	0.8641:0.0:0.1359:0.0	.	408	Q9NZR2	LRP1B_HUMAN	N	408;346	ENSP00000374135:I408N	ENSP00000374135:I408N	I	-	2	0	LRP1B	141536103	1.000000	0.71417	0.763000	0.31416	0.516000	0.34256	5.279000	0.65597	1.070000	0.40811	0.533000	0.62120	ATT	.		0.358	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141819633	A	T	141819633	3	4	69	1	0	0	0	0	1	0	0	0	8980	101	4	5	12912	5	LRP1B	2	141819633	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	21380279	141819633	101379740	22	6552											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170083080	170083080	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatatgttgccttacagttAttaagaaaggttgatcatct	12	17	7	5	0	2	2	1	1	1	1	2	2	2	2	1	1	2	3	1	1	6	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:170083080A>G	ENST00000263816.3	-	32	5531	c.5246T>C	c.(5245-5247)aTa>aCa	p.I1749T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1749					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CCTTACAGTTATTAAGAAAGG	0.368																																					p.I1749T		.											.	LRP2-175	0			c.T5246C						.						79	76	77					2																	170083080		2203	4300	6503	SO:0001583	missense	4036	exon32			ACAGTTATTAAGA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5246T>C	2.37:g.170083080A>G	ENSP00000263816:p.Ile1749Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	119	26	NM_004525	0	0	3	4	1	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	18.57	3.652915	0.67472	.	.	ENSG00000081479	ENST00000263816	D	0.90900	-2.75	5.83	5.83	0.93111	Six-bladed beta-propeller, TolB-like (1);	0.111411	0.64402	D	0.000005	D	0.90943	0.7153	M	0.83223	2.63	0.80722	D	1	P	0.40144	0.704	B	0.35971	0.215	D	0.92052	0.5649	10	0.87932	D	0	.	16.2041	0.82108	1.0:0.0:0.0:0.0	.	1749	P98164	LRP2_HUMAN	T	1749	ENSP00000263816:I1749T	ENSP00000263816:I1749T	I	-	2	0	LRP2	169791326	1.000000	0.71417	0.916000	0.36221	0.996000	0.88848	9.310000	0.96267	2.219000	0.72066	0.533000	0.62120	ATA	.		0.368	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170083080	A	G	170083080	3	3	69	1	0	0	0	0	1	0	0	0	8981	449	16	3	8913	3	LRP2	2	170083080	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	28263447	170083080	73116293	23	6553											
EPHA4	2043	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	222365873	222365873	+	Frame_Shift_Del	DEL	G	G	-																															gcatccgtggagagagccttGtaatatccaattttgcaagc																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:222365873delG	ENST00000281821.2	-	4	884	c.843delC	c.(841-843)tacfs	p.Y281fs	EPHA4_ENST00000409938.1_Frame_Shift_Del_p.Y281fs|EPHA4_ENST00000392071.4_Frame_Shift_Del_p.Y230fs|EPHA4_ENST00000409854.1_Frame_Shift_Del_p.Y281fs	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	281	Cys-rich.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		AGAGAGCCTTGTAATATCCAA	0.483																																					p.Y281X		.											.	EPHA4-1441	0			c.843delC						.						59	57	57					2																	222365873		2203	4300	6503	SO:0001589	frameshift_variant	2043	exon4			.	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3388	protein-coding gene	gene with protein product		602188	"EphA4"	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.843delC	2.37:g.222365873delG	ENSP00000281821:p.Tyr281fs	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	92	57	NM_004438	0	0	0	0	0	A8K2P1|B2R601|B7Z6Q8|Q2M380	Nonsense_Mutation	DEL	ENST00000281821.2	37	CCDS2447.1																																																																																			.		0.483	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			-	222365873	G	-	222365873	7	5	69	1	0	1	0	1	0	0	0	0	5182	1372	48	0	2173	0	EPHA4	2	222365873	Frame_Shift_Del	DEL	G	TCGA-BQ-5885-01A-11D-1589-08	52282793	222365873	20833500	24	6554											
CUL3	8452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	225422516	225422516	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attcttacgctggatttcttGaattgcatttttcagaaggt	9	18	8	6	1	3	2	1	1	2	1	3	3	3	3	0	2	2	2	0	2	3	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:225422516G>A	ENST00000264414.4	-	2	462	c.124C>T	c.(124-126)Caa>Taa	p.Q42*	CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409096.1_Nonsense_Mutation_p.Q18*|CUL3_ENST00000409777.1_Nonsense_Mutation_p.Q18*|CUL3_ENST00000344951.4_Intron	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	42					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TGGATTTCTTGAATTGCATTT	0.333																																					p.Q48X		.											.	CUL3-229	0			c.C142T						.						88	85	86					2																	225422516		2201	4298	6499	SO:0001587	stop_gained	8452	exon2			TTTCTTGAATTGC	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.124C>T	2.37:g.225422516G>A	ENSP00000264414:p.Gln42*	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	99	53	NM_001257198	0	0	0	4	4	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Nonsense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	8.780125|8.780125	0.98952|0.98952	.|.	.|.	ENSG00000036257|ENSG00000036257	ENST00000264414;ENST00000409096;ENST00000409777|ENST00000436172	.|.	.|.	.|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76941	.|0.4058	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74262	.|-0.3722	.|4	0.07030|.	T|.	0.85|.	.|.	20.1731|20.1731	0.98165|0.98165	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	42;18;18|62	.|.	ENSP00000264414:Q42X|.	Q|S	-|-	1|2	0|0	CUL3|CUL3	225130760|225130760	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.714000|9.714000	0.98744|0.98744	2.768000|2.768000	0.95171|0.95171	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.		0.333	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			A	225422516	G	A	225422516	4	1	69	1	0	0	0	0	0	1	0	0	4062	1299	45	2	2242	2	CUL3	2	225422516	Nonsense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	3056643	225422516	17776857	25	6555											
USP40	55230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234449396	234449396	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctggcccagctgatcaacaGgaattagattattctcctcc	10	12	7	12	0	3	2	1	1	2	1	5	3	4	3	3	2	2	1	3	2	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:234449396G>T	ENST00000427112.2	-	9	1114	c.1079C>A	c.(1078-1080)cCt>cAt	p.P360H	USP40_ENST00000251722.6_Missense_Mutation_p.P360H|USP40_ENST00000450966.1_Missense_Mutation_p.P372H			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	360	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.P372R(2)		breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CTGATCAACAGGAATTAGATT	0.378																																					p.P372H		.											.	USP40-455	2	Substitution - Missense(2)	lung(2)	c.C1115A						.						169	157	160					2																	234449396		1838	4092	5930	SO:0001583	missense	55230	exon9			TCAACAGGAATTA	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1079C>A	2.37:g.234449396G>T	ENSP00000387898:p.Pro360His	Somatic	254	2		WXS	Illumina HiSeq	Phase_I	248	111	NM_018218	0	0	0	3	3	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544257	0.65198	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.05258	3.47;3.48;3.48	5.31	3.39	0.38822	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.336030	0.05934	U	0.635709	T	0.18718	0.0449	L	0.55481	1.735	0.30283	N	0.791122	D;D	0.57899	0.981;0.976	P;P	0.60068	0.868;0.792	T	0.07214	-1.0784	10	0.72032	D	0.01	.	9.7296	0.40352	0.0745:0.0:0.7855:0.1401	.	360;372	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	H	372;360;360	ENSP00000415434:P372H;ENSP00000251722:P360H;ENSP00000387898:P360H	ENSP00000251722:P360H	P	-	2	0	USP40	234114135	1.000000	0.71417	0.952000	0.39060	0.980000	0.70556	2.988000	0.49386	1.373000	0.46208	0.561000	0.74099	CCT	.		0.378	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		T	234449396	G	T	234449396	3	4	69	1	0	0	0	0	1	0	0	0	17105	1000	35	4	2720	4	USP40	2	234449396	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	9026880	234449396	8749977	26	6556											
TRPM8	79054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234847784	234847784	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccgcgcatgcgcaagaTcttcagccggctcatctaca	10	7	10	14	4	4	1	2	0	2	1	4	2	4	1	2	1	4	3	2	1	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:234847784T>A	ENST00000324695.4	+	5	531	c.491T>A	c.(490-492)aTc>aAc	p.I164N	TRPM8_ENST00000409625.1_Missense_Mutation_p.I87N|TRPM8_ENST00000433712.2_5'UTR|TRPM8_ENST00000355722.4_Missense_Mutation_p.I114N	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	164					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	ATGCGCAAGATCTTCAGCCGG	0.607																																					p.I164N		.											.	TRPM8-94	0			c.T491A						.						36	38	37					2																	234847784		2203	4300	6503	SO:0001583	missense	79054	exon5			GCAAGATCTTCAG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.491T>A	2.37:g.234847784T>A	ENSP00000323926:p.Ile164Asn	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	82	32	NM_024080	0	0	0	0	0	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.109476	0.77096	.	.	ENSG00000144481	ENST00000324695;ENST00000355722;ENST00000409625	T;T;T	0.81163	-1.46;-1.46;-1.46	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000001	D	0.90181	0.6931	M	0.84585	2.705	0.80722	D	1	P;D	0.71674	0.567;0.998	B;D	0.74023	0.343;0.982	D	0.91731	0.5396	10	0.87932	D	0	-40.7179	14.6612	0.68873	0.0:0.0:0.0:1.0	.	114;164	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	N	164;114;87	ENSP00000323926:I164N;ENSP00000347956:I114N;ENSP00000386771:I87N	ENSP00000323926:I164N	I	+	2	0	TRPM8	234512523	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.795000	0.62489	2.154000	0.67381	0.478000	0.44815	ATC	.		0.607	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234847784	T	A	234847784	3	1	69	1	0	0	0	0	1	0	0	0	16625	1435	50	5	505	5	TRPM8	2	234847784	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	398388	234847784	8351589	27	6557											
ATP2B2	491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	10387742	10387742	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagcccacgtcggccttcttGagtgcaggcccgtcgttggt	5	10	13	13	4	1	1	0	1	1	0	3	1	1	1	3	3	2	2	3	3	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:10387742G>A	ENST00000352432.4	-	16	2553	c.2484C>T	c.(2482-2484)ctC>ctT	p.L828L	ATP2B2_ENST00000397077.1_Silent_p.L783L|ATP2B2_ENST00000383800.4_Silent_p.L783L|ATP2B2_ENST00000360273.2_Silent_p.L828L|ATP2B2_ENST00000343816.4_Silent_p.L814L			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	828					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						CGGCCTTCTTGAGTGCAGGCC	0.652																																					p.L828L	Ovarian(125;1619 1709 15675 19819 38835)	.											.	ATP2B2-95	0			c.C2484T						.						62	56	58					3																	10387742		2203	4300	6503	SO:0001819	synonymous_variant	491	exon17			CTTCTTGAGTGCA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.2484C>T	3.37:g.10387742G>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	67	17	NM_001001331	0	0	0	0	0	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			.		0.652	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10387742	G	A	10387742	2	1	69	1	0	0	0	0	0	0	0	1	1141	1277	45	2		2	ATP2B2	3	10387742	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08		10387742	187634688	28	6558											
CCBP2	1238	broad.mit.edu	37	chr3	42906259	42906259	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agatctatctgctgaatctgGccatctccaaccttctgttt	8	15	6	12	0	5	2	0	1	5	1	6	2	5	2	3	1	2	2	3	1	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:42906259G>A	ENST00000422265.1	+	3	440	c.265G>A	c.(265-267)Gcc>Acc	p.A89T	RP11-141M3.5_ENST00000471537.1_RNA|ACKR2_ENST00000273145.2_Missense_Mutation_p.A89T|ACKR2_ENST00000442925.1_Missense_Mutation_p.A89T|KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Intron	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	89					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										GCTGAATCTGGCCATCTCCAA	0.547																																					p.A89T													.	CCBP2-659	0			c.G265A						.						173	157	163					3																	42906259		2203	4300	6503	SO:0001583	missense	1238	exon3			AATCTGGCCATCT	U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"GPCR / Class A : Chemokine receptors : Atypical"	1565	protein-coding gene	gene with protein product		602648	"chemokine binding protein 2"	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.265G>A	3.37:g.42906259G>A	ENSP00000416996:p.Ala89Thr	Somatic	316	2		WXS	Illumina HiSeq	Phase_I	266	4	NM_001296	0	0	0	0	0	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607829	0.66558	.	.	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.56103	0.48;0.48;0.48	5.28	5.28	0.74379	GPCR, rhodopsin-like superfamily (1);	0.135021	0.33127	N	0.005242	T	0.68284	0.2984	M	0.68728	2.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.977	T	0.68477	-0.5398	9	.	.	.	.	12.5775	0.56371	0.0:0.0:0.8338:0.1662	.	89;89	O00590;Q7Z7I1	CCBP2_HUMAN;.	T	89	ENSP00000396150:A89T;ENSP00000416996:A89T;ENSP00000273145:A89T	.	A	+	1	0	CCBP2	42881263	0.983000	0.35010	1.000000	0.80357	0.886000	0.51366	1.846000	0.39289	2.477000	0.83638	0.563000	0.77884	GCC	.		0.547	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296		A	42906259	G	A	42906259	3	1	69	1	0	0	0	0	1	0	0	0	2740	1203	42	2	267	2	CCBP2	3	42906259	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	32518517	42906259	155116171	29	6559											
ZNF502	91392	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	44762384	44762384	+	Frame_Shift_Del	DEL	G	G	-																															ggctgggtaaacaagaacaaGcctgctctggagcaggatgt																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:44762384delG	ENST00000296091.4	+	4	331	c.75delG	c.(73-75)aagfs	p.K25fs	ZNF502_ENST00000449836.1_Frame_Shift_Del_p.K25fs|ZNF502_ENST00000436624.2_Frame_Shift_Del_p.K25fs	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	25					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		ACAAGAACAAGCCTGCTCTGG	0.418																																					p.K25fs		.											.	ZNF502-90	0			c.75delG						.						59	63	61					3																	44762384		2203	4300	6503	SO:0001589	frameshift_variant	91392	exon4			.	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.75delG	3.37:g.44762384delG	ENSP00000296091:p.Lys25fs	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	115	33	NM_001134440	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000296091.4	37	CCDS2719.1																																																																																			.		0.418	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		-	44762384	G	-	44762384	7	5	69	1	0	1	0	1	0	0	0	0	17982	962	34	0	81	0	ZNF502	3	44762384	Frame_Shift_Del	DEL	G	TCGA-BQ-5885-01A-11D-1589-08	1856125	44762384	153260046	30	6560											
FYCO1	79443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46009968	46009968	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtgaggcgaacgttgtcCtccgctgcagtgcgccccct	6	8	12	15	4	0	1	0	1	0	0	2	2	2	1	4	1	3	3	4	1	2	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:46009968C>T	ENST00000296137.2	-	8	1063	c.858G>A	c.(856-858)gaG>gaA	p.E286E	FYCO1_ENST00000535325.1_Silent_p.E286E	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	286					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		GAACGTTGTCCTCCGCTGCAG	0.617																																					p.E286E		.											.	FYCO1-91	0			c.G858A						.						102	85	91					3																	46009968		2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			GTTGTCCTCCGCT	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.858G>A	3.37:g.46009968C>T		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	91	20	NM_024513	0	0	1	1	0	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			.		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46009968	C	T	46009968	2	4	69	1	0	0	0	0	0	0	0	1	6144	680	24	2		2	FYCO1	3	46009968	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	1247584	46009968	152012462	31	6561											
CCR5	1234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46415150	46415150	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctgggctccctacaacAttgtccttctcctgaacacc	7	13	5	16	0	3	1	0	1	3	0	6	1	5	1	4	1	3	1	4	1	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:46415150A>T	ENST00000292303.4	+	2	903	c.757A>T	c.(757-759)Att>Ttt	p.I253F	RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000343801.4_Missense_Mutation_p.I253F|CCR5_ENST00000445772.1_Missense_Mutation_p.I253F	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	253					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TCCCTACAACATTGTCCTTCT	0.463																																					p.I253F		.											.	CCR5-993	0			c.A757T						.						227	243	237					3																	46415150		2203	4296	6499	SO:0001583	missense	1234	exon3			TACAACATTGTCC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.757A>T	3.37:g.46415150A>T	ENSP00000292303:p.Ile253Phe	Somatic	688	0		WXS	Illumina HiSeq	Phase_I	556	164	NM_000579	0	0	0	0	0	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	37	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.923708	0.73213	.	.	ENSG00000160791	ENST00000343801;ENST00000400886;ENST00000292303;ENST00000445772	T;T;T	0.76060	-0.99;-0.99;-0.99	5.69	-3.74	0.04385	GPCR, rhodopsin-like superfamily (1);	0.268702	0.24301	U	0.039739	D	0.85128	0.5626	H	0.96691	3.865	0.49687	D	0.999818	D	0.53885	0.963	P	0.59889	0.865	D	0.83665	0.0163	10	0.87932	D	0	.	6.5629	0.22495	0.4959:0.3178:0.1864:0.0	.	253	P51681	CCR5_HUMAN	F	253;233;253;253	ENSP00000343985:I253F;ENSP00000292303:I253F;ENSP00000404881:I253F	ENSP00000292303:I253F	I	+	1	0	CCR5	46390154	0.942000	0.31987	0.996000	0.52242	0.849000	0.48306	0.234000	0.17930	-0.152000	0.11156	0.459000	0.35465	ATT	.		0.463	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		T	46415150	A	T	46415150	3	4	69	1	0	0	0	0	1	0	0	0	2950	217	8	5	759	5	CCR5	3	46415150	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	405182	46415150	151607280	32	6562											
MST1	63891	broad.mit.edu	37	chr3	49726048	49726048	+	5'Flank	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccagggacccctaagcatTgagtcagaagcagcaggagt	13	6	12	10	0	1	2	1	1	0	1	1	4	1	4	3	2	4	3	3	2	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:49726048T>A	ENST00000327697.6	+	0	0				MST1_ENST00000494828.2_5'UTR|MST1_ENST00000545762.1_Missense_Mutation_p.Q12L|RNF123_ENST00000432042.1_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.Q26L|MST1_ENST00000383728.3_5'UTR	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		CCCTAAGCATTGAGTCAGAAG	0.582																																					p.Q26L													.	MST1-278	0			c.A77T						.						29	30	29					3																	49726048		2202	4299	6501	SO:0001631	upstream_gene_variant	4485	exon1			AAGCATTGAGTCA	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891		3.37:g.49726048T>A	Exception_encountered	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	36	3	NM_020998	0	0	28	28	0	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	T	3.258	-0.151898	0.06585	.	.	ENSG00000173531	ENST00000449682;ENST00000545762	D;T	0.87179	-2.22;0.9	3.75	0.0309	0.14168	.	1.155600	0.06675	N	0.766915	T	0.75451	0.3851	N	0.25647	0.755	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.56571	-0.7957	10	0.09338	T	0.73	.	5.9284	0.19124	0.0:0.452:0.0:0.548	.	12;26	B7Z538;G3XAK1	.;.	L	26;12	ENSP00000414287:Q26L;ENSP00000437535:Q12L	ENSP00000411117:Q26L	Q	-	2	0	MST1	49701052	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.046000	0.11983	0.008000	0.14787	0.459000	0.35465	CAA	.		0.582	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49726048	T	A	49726048	1	1	69	0	1	0	0	0	0	0	0	0	9915	1812	63	5		5	MST1	3	49726048	5'Flank	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	3310898	49726048	148296382	33	6563											
QTRTD1	79691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113798773	113798773	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcatatctggtgttagtcGgccagatgaggtgctcgagt	7	12	14	8	2	2	2	1	1	1	1	4	3	2	2	1	3	1	3	1	3	2	2	rs199551955		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:113798773G>A	ENST00000493014.1	+	4	517	c.449G>A	c.(448-450)cGg>cAg	p.R150Q	QTRTD1_ENST00000479882.1_Missense_Mutation_p.R133Q|QTRTD1_ENST00000281273.4_Missense_Mutation_p.R256Q|QTRTD1_ENST00000485050.1_Missense_Mutation_p.R268Q	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						GGTGTTAGTCGGCCAGATGAG	0.423													G|||	1	0.000199681	0	0.0014	5008	,	,		19554	0		0	False		,,,				2504	0				p.R268Q		.											.	QTRTD1-91	0			c.G803A						.						180	174	176					3																	113798773		2203	4300	6503	SO:0001583	missense	79691	exon7			TTAGTCGGCCAGA	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.449G>A	3.37:g.113798773G>A	ENSP00000419169:p.Arg150Gln	Somatic	320	0		WXS	Illumina HiSeq	Phase_I	280	111	NM_001256835	0	0	1	4	3		Missense_Mutation	SNP	ENST00000493014.1	37	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.505730	0.26949	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	5.58	-1.43	0.08884	.	0.364818	0.28760	N	0.014230	T	0.33702	0.0872	L	0.40543	1.245	0.34875	D	0.744043	B;B	0.29590	0.25;0.015	B;B	0.20384	0.029;0.006	T	0.13098	-1.0522	9	0.44086	T	0.13	-0.6577	6.1058	0.20073	0.3234:0.0:0.4693:0.2072	.	150;256	B7Z472;Q9H974	.;QTRD1_HUMAN	Q	268;256;133;150	.	ENSP00000281273:R256Q	R	+	2	0	QTRTD1	115281463	0.996000	0.38824	0.856000	0.33681	0.200000	0.23975	1.800000	0.38833	-0.186000	0.10533	0.555000	0.69702	CGG	.		0.423	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638		A	113798773	G	A	113798773	3	1	69	1	0	0	0	0	1	0	0	0	12918	1116	39	1	789	1	QTRTD1	3	113798773	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	64072725	113798773	84223657	34	6564											
ZBBX	79740	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	167083714	167083714	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtgacatcatatatgatTgattgaccaatttgcccact	11	16	6	8	0	1	4	1	4	0	0	1	4	1	4	2	0	1	0	2	0	3	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:167083714T>G	ENST00000392766.2	-	6	573	c.233A>C	c.(232-234)cAa>cCa	p.Q78P	ZBBX_ENST00000392767.2_Missense_Mutation_p.Q78P|ZBBX_ENST00000455345.2_Missense_Mutation_p.Q78P|ZBBX_ENST00000307529.5_Missense_Mutation_p.Q78P|ZBBX_ENST00000392764.1_Missense_Mutation_p.Q49P|ZBBX_ENST00000469220.1_Intron	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	78						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CATATATGATTGATTGACCAA	0.289																																					p.Q78P		.											.	ZBBX-92	0			c.A233C						.						116	108	111					3																	167083714		1824	4071	5895	SO:0001583	missense	79740	exon6			TATGATTGATTGA	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.233A>C	3.37:g.167083714T>G	ENSP00000376519:p.Gln78Pro	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	108	39	NM_024687	0	0	0	0	0	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	T	5.789	0.329827	0.10956	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764;ENST00000474464	T;T;T;T;T;T	0.32988	2.92;2.92;2.92;2.92;2.74;1.43	5.26	-1.63	0.08345	.	.	.	.	.	T	0.20047	0.0482	L	0.44542	1.39	0.09310	N	0.999994	B;B	0.12630	0.006;0.003	B;B	0.16289	0.015;0.004	T	0.31530	-0.9940	9	0.52906	T	0.07	-2.1505	1.0522	0.01582	0.1499:0.2902:0.1547:0.4052	.	78;78	A8MT70-2;A8MT70	.;ZBBX_HUMAN	P	78;78;78;78;49;78	ENSP00000376519:Q78P;ENSP00000376520:Q78P;ENSP00000390232:Q78P;ENSP00000305065:Q78P;ENSP00000376517:Q49P;ENSP00000419307:Q78P	ENSP00000305065:Q78P	Q	-	2	0	ZBBX	168566408	0.486000	0.25980	0.013000	0.15412	0.018000	0.09664	0.353000	0.20130	-0.448000	0.07128	-0.386000	0.06593	CAA	.		0.289	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		G	167083714	T	G	167083714	3	3	69	1	0	0	0	0	1	0	0	0	17549	1812	63	5	2233	5	ZBBX	3	167083714	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	53284941	167083714	30938716	35	6565											
TNFSF10	8743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	172224404	172224404	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatattcccccttgatagaTggaatagagtccatattctg	13	13	7	8	0	1	3	0	1	1	2	3	4	3	4	3	1	0	0	3	1	6	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:172224404T>A	ENST00000241261.2	-	5	846	c.724A>T	c.(724-726)Atc>Ttc	p.I242F	TNFSF10_ENST00000420541.2_3'UTR	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	242					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CCTTGATAGATGGAATAGAGT	0.333																																					p.I242F		.											.	TNFSF10-662	0			c.A724T						.						168	163	165					3																	172224404		2203	4300	6503	SO:0001583	missense	8743	exon5			GATAGATGGAATA	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.724A>T	3.37:g.172224404T>A	ENSP00000241261:p.Ile242Phe	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	176	60	NM_003810	0	0	13	44	31	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	37	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.600378	0.46423	.	.	ENSG00000121858	ENST00000241261	D	0.95412	-3.7	5.68	4.5	0.54988	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.323500	0.37530	N	0.002051	D	0.97604	0.9215	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.97812	1.0251	10	0.72032	D	0.01	-18.1925	13.2187	0.59875	0.0:0.0:0.1329:0.8671	.	242	P50591	TNF10_HUMAN	F	242	ENSP00000241261:I242F	ENSP00000241261:I242F	I	-	1	0	TNFSF10	173707098	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	3.882000	0.56160	1.065000	0.40693	0.482000	0.46254	ATC	.		0.333	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			A	172224404	T	A	172224404	3	1	69	1	0	0	0	0	1	0	0	0	16333	1464	51	5	125	5	TNFSF10	3	172224404	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	5140690	172224404	25798026	36	6566											
OTOP1	133060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	4199006	4199007	+	Missense_Mutation	DNP	TC	TC	CT																															tgggctccctccccagctgcTctcctcctgcttctcctcct																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:4199006_4199007TC>CT	ENST00000296358.4	-	5	1578_1579	c.1554_1555GA>AG	c.(1552-1557)gaGAgc>gaAGgc	p.S519G		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	519					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCCCAGCTGCTCTCCTCCTGCT	0.564																																					p.S519G		.											.	OTOP1	0			c.G1554A						.																																			SO:0001583	missense	133060	exon5			GCTGCTCTCCTCC	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1554_1555delinsCT	4.37:g.4199006_4199007delinsCT	ENSP00000296358:p.Ser519Gly	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	96	27		0	0	0	0	0	A1L476	Missense_Mutation	DNP	ENST00000296358.4	37	CCDS3372.1																																																																																			.		0.564	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		CT	4199007	TC	CT	4199006	3	2	69	1	0	0	0	0	1	0	0	0	11331	1551	54	3	291	3	OTOP1	4	4199006	Missense_Mutation	DNP	TC	TCGA-BQ-5885-01A-11D-1589-08		4199006	186955270	37	6567											
SDAD1	55153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76877179	76877179	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaccggacattctggctataCcgcatcatcataaagttctt	11	12	7	11	2	4	0	2	0	2	0	4	2	4	1	2	2	1	3	2	2	4	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:76877179C>T	ENST00000356260.5	-	21	2083	c.1965G>A	c.(1963-1965)cgG>cgA	p.R655R	SDAD1_ENST00000395711.4_Silent_p.R618R|AC110615.1_ENST00000599764.1_Silent_p.Y41Y	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	655					actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCTGGCTATACCGCATCATCA	0.393																																					p.R655R		.											.	SDAD1-91	0			c.G1965A						.						242	227	232					4																	76877179		2203	4300	6503	SO:0001819	synonymous_variant	55153	exon21			GCTATACCGCATC	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.1965G>A	4.37:g.76877179C>T		Somatic	392	0		WXS	Illumina HiSeq	Phase_I	311	101	NM_018115	0	0	18	42	24	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Silent	SNP	ENST00000356260.5	37	CCDS3573.2																																																																																			.		0.393	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115		T	76877179	C	T	76877179	2	4	69	1	0	0	0	0	0	0	0	1	13982	494	18	2		2	SDAD1	4	76877179	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	72678173	76877179	114277097	38	6568											
ADAD1	132612	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	123336554	123336554	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgatgggaattgcagtgatAccagaggcttagaaatcgct	12	10	13	6	1	0	4	0	2	0	2	1	5	0	5	1	2	2	3	1	2	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:123336554A>G	ENST00000296513.2	+	11	1455	c.1270A>G	c.(1270-1272)Acc>Gcc	p.T424A	ADAD1_ENST00000388724.2_Missense_Mutation_p.T413A|ADAD1_ENST00000388725.2_Missense_Mutation_p.T406A	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	424	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTGCAGTGATACCAGAGGCTT	0.333																																					p.T424A		.											.	ADAD1-90	0			c.A1270G						.						103	100	101					4																	123336554		2203	4300	6503	SO:0001583	missense	132612	exon11			AGTGATACCAGAG	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.1270A>G	4.37:g.123336554A>G	ENSP00000296513:p.Thr424Ala	Somatic	171	1		WXS	Illumina HiSeq	Phase_I	125	10	NM_139243	0	0	0	0	0	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	37	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.169474	0.38315	.	.	ENSG00000164113	ENST00000296513;ENST00000388724;ENST00000388725	D;D;D	0.93133	-3.17;-3.17;-3.17	5.12	3.94	0.45596	Adenosine deaminase/editase (3);	0.310779	0.32987	N	0.005405	D	0.91375	0.7279	L	0.39020	1.185	0.31646	N	0.64739	P;D	0.58620	0.745;0.983	B;P	0.60286	0.382;0.872	D	0.86329	0.1697	10	0.08599	T	0.76	-14.2059	7.0801	0.25227	0.7952:0.0:0.0737:0.1312	.	413;424	Q96M93-2;Q96M93	.;ADAD1_HUMAN	A	424;413;406	ENSP00000296513:T424A;ENSP00000373376:T413A;ENSP00000373377:T406A	ENSP00000296513:T424A	T	+	1	0	ADAD1	123556004	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.208000	0.58486	0.800000	0.34041	0.528000	0.53228	ACC	.		0.333	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		G	123336554	A	G	123336554	3	3	69	1	0	0	0	0	1	0	0	0	231	391	14	3	1304	3	ADAD1	4	123336554	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	46459375	123336554	67817722	39	6569											
ANKRD50	57182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	125592787	125592787	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actatatgcagcattagccaAtaatgttctcccatttgaat	13	14	5	9	0	1	1	0	1	1	0	2	1	1	1	2	0	3	3	2	0	6	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:125592787A>G	ENST00000504087.1	-	4	2682	c.1645T>C	c.(1645-1647)Ttg>Ctg	p.L549L	ANKRD50_ENST00000515641.1_Silent_p.L370L	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	549										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						GCATTAGCCAATAATGTTCTC	0.393																																					p.L549L		.											.	ANKRD50-90	0			c.T1645C						.						122	117	119					4																	125592787		2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			TAGCCAATAATGT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1645T>C	4.37:g.125592787A>G		Somatic	248	1		WXS	Illumina HiSeq	Phase_I	214	22	NM_020337	0	0	1	1	0	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			.		0.393	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		G	125592787	A	G	125592787	2	3	69	1	0	0	0	0	0	0	0	1	677	98	4	3		3	ANKRD50	4	125592787	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	2256233	125592787	65561489	40	6570											
PLK4	10733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	128804442	128804442	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taagaaagccatgtacaaagCaggaatggtacagagagtcc	17	6	11	7	0	0	2	0	0	0	2	1	4	1	3	2	2	4	3	2	2	6	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:128804442C>T	ENST00000270861.5	+	3	426	c.152C>T	c.(151-153)gCa>gTa	p.A51V	PLK4_ENST00000514379.1_Missense_Mutation_p.A10V|PLK4_ENST00000507249.1_Missense_Mutation_p.A51V|PLK4_ENST00000515069.1_Missense_Mutation_p.A51V|PLK4_ENST00000513090.1_Intron|PLK4_ENST00000511942.1_3'UTR	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						ATGTACAAAGCAGGAATGGTA	0.308																																					p.A51V	Colon(135;508 1718 19061 31832 42879)	.											.	PLK4-333	0			c.C152T						.						71	71	71					4																	128804442		2203	4299	6502	SO:0001583	missense	10733	exon3			ACAAAGCAGGAAT	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.152C>T	4.37:g.128804442C>T	ENSP00000270861:p.Ala51Val	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	48	13	NM_014264	0	0	0	0	0	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815330	0.50527	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000507249;ENST00000514379	T;T;T;T	0.65732	-0.17;-0.17;-0.17;1.83	5.39	5.39	0.77823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.110302	0.64402	D	0.000009	T	0.49218	0.1544	L	0.36672	1.1	0.48901	D	0.999727	B	0.23128	0.08	B	0.27608	0.081	T	0.46105	-0.9215	10	0.31617	T	0.26	-8.6513	7.0116	0.24865	0.0:0.79:0.0:0.21	.	51	O00444	PLK4_HUMAN	V	51;51;51;10	ENSP00000270861:A51V;ENSP00000421774:A51V;ENSP00000423412:A51V;ENSP00000423582:A10V	ENSP00000270861:A51V	A	+	2	0	PLK4	129023892	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.422000	0.52749	2.520000	0.84964	0.655000	0.94253	GCA	.		0.308	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			T	128804442	C	T	128804442	3	4	69	1	0	0	0	0	1	0	0	0	12124	710	25	2	162	2	PLK4	4	128804442	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	3211655	128804442	62349834	41	6571											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	151829520	151829520	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctcatcagacaaatattGcctgtaatccaactgtgcaa	15	11	5	10	0	2	1	2	0	1	1	4	1	3	1	2	0	3	2	2	0	6	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:151829520G>A	ENST00000357115.3	-	11	1702	c.1459C>T	c.(1459-1461)Caa>Taa	p.Q487*	LRBA_ENST00000510413.1_Nonsense_Mutation_p.Q487*|LRBA_ENST00000507224.1_Nonsense_Mutation_p.Q487*|LRBA_ENST00000535741.1_Nonsense_Mutation_p.Q487*	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	487						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GACAAATATTGCCTGTAATCC	0.363																																					p.Q487X		.											.	LRBA-157	0			c.C1459T						.						126	121	122					4																	151829520		2203	4300	6503	SO:0001587	stop_gained	987	exon11			AATATTGCCTGTA	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1459C>T	4.37:g.151829520G>A	ENSP00000349629:p.Gln487*	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	93	31	NM_006726	0	0	0	0	0	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Nonsense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	G	43	9.887563	0.99288	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	.	.	.	5.63	5.63	0.86233	.	0.000000	0.48286	U	0.000186	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	20.047	0.97613	0.0:0.0:1.0:0.0	.	.	.	.	X	487	.	ENSP00000349629:Q487X	Q	-	1	0	LRBA	152048970	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	9.120000	0.94369	2.802000	0.96397	0.563000	0.77884	CAA	.		0.363	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151829520	G	A	151829520	4	1	69	1	0	0	0	0	0	1	0	0	8956	1328	46	2	7324	2	LRBA	4	151829520	Nonsense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	23025078	151829520	39324756	42	6572											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	187540288	187540291	+	Frame_Shift_Del	DEL	TCCA	TCCA	-																															gcaggactgtgcaaattgccTccaattacagttacatgaac																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	TCCA	TCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:187540288_187540291delTCCA	ENST00000441802.2	-	10	7658_7661	c.7449_7452delTGGA	c.(7447-7452)attggafs	p.IG2483fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2483	Cadherin 22. {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						GCAAATTGCCTCCAATTACAGTTA	0.471										HNSCC(5;0.00058)																											p.2483_2484del	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.7449_7452del						.																																			SO:0001589	frameshift_variant	2195	exon10			.	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.7449_7452delTGGA	4.37:g.187540288_187540291delTCCA	ENSP00000406229:p.Ile2483fs	Somatic	443	0		WXS	Illumina HiSeq	Phase_I	385	90	NM_005245	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.471	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187540291	TCCA	-	187540288	7	5	69	1	0	1	0	1	0	0	0	0	5708	1538	54	0	6386	0	FAT1	4	187540288	Frame_Shift_Del	DEL	TCCA	TCGA-BQ-5885-01A-11D-1589-08	35710768	187540288	3613988	43	6573											
GOLPH3	64083	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	32126417	32126417	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgagaagctgccgcactctCttggtagccaaatcatactg	10	10	9	12	2	2	1	1	0	1	1	4	2	2	1	2	1	4	3	2	1	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:32126417C>A	ENST00000265070.6	-	4	1113	c.798G>T	c.(796-798)aaG>aaT	p.K266N	GOLPH3_ENST00000512668.1_5'Flank	NM_022130.3	NP_071413.1	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3 (coat-protein)	266					cell adhesion molecule production (GO:0060352)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|gene expression (GO:0010467)|glycoprotein biosynthetic process (GO:0009101)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi vesicle budding (GO:0048194)|lamellipodium assembly (GO:0030032)|leukocyte tethering or rolling (GO:0050901)|positive regulation of protein secretion (GO:0050714)|positive regulation of TOR signaling (GO:0032008)|protein retention in Golgi apparatus (GO:0045053)|protein secretion (GO:0009306)|regulation of mitochondrion organization (GO:0010821)	cytosol (GO:0005829)|endosome (GO:0005768)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	enzyme binding (GO:0019899)|phosphatidylinositol-4-phosphate binding (GO:0070273)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11						GCCGCACTCTCTTGGTAGCCA	0.552																																					p.K266N		.											.	GOLPH3-227	0			c.G798T						.						94	80	85					5																	32126417		2203	4300	6503	SO:0001583	missense	64083	exon4			CACTCTCTTGGTA	AK075156	CCDS3896.1	5p13.2	2008-07-18			ENSG00000113384	ENSG00000113384			15452	protein-coding gene	gene with protein product	"golgi peripheral membrane protein 1, 34 kDa", "golgi protein", "coat-protein", "golgi-associated protein"	612207				11042173, 16263763	Standard	NM_022130		Approved	GPP34, GOPP1, MIDAS	uc003jhp.1	Q9H4A6	OTTHUMG00000090679	ENST00000265070.6:c.798G>T	5.37:g.32126417C>A	ENSP00000265070:p.Lys266Asn	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	142	33	NM_022130	0	0	14	15	1	Q9UIW5	Missense_Mutation	SNP	ENST00000265070.6	37	CCDS3896.1	.	.	.	.	.	.	.	.	.	.	C	8.954	0.968949	0.18659	.	.	ENSG00000113384	ENST00000265070;ENST00000542582	.	.	.	6.17	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.63745	0.2537	L	0.60845	1.875	0.80722	D	1	D	0.63046	0.992	P	0.61328	0.887	T	0.60944	-0.7162	9	0.23302	T	0.38	.	7.4739	0.27365	0.1395:0.7289:0.0:0.1316	.	266	Q9H4A6	GOLP3_HUMAN	N	266;249	.	ENSP00000265070:K266N	K	-	3	2	GOLPH3	32162174	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	2.589000	0.46145	1.606000	0.50161	-0.182000	0.12963	AAG	.		0.552	GOLPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207363.2	NM_022130		A	32126417	C	A	32126417	3	1	69	1	0	0	0	0	1	0	0	0	6588	912	32	4	102	4	GOLPH3	5	32126417	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		32126417	148788843	44	6574											
GPBP1	65056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	56545332	56545332	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcactgataagaagagtgaaTttttgaaagcattgaaaaga	18	10	10	3	0	0	7	0	4	0	3	0	7	0	7	0	0	1	2	0	0	6	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:56545332T>G	ENST00000506184.2	+	9	2006	c.901T>G	c.(901-903)Ttt>Gtt	p.F301V	GPBP1_ENST00000514387.2_Missense_Mutation_p.F130V|GPBP1_ENST00000424459.3_Missense_Mutation_p.F321V|GPBP1_ENST00000454432.2_Missense_Mutation_p.F321V|GPBP1_ENST00000511209.1_Missense_Mutation_p.F293V|GPBP1_ENST00000264779.6_Missense_Mutation_p.F308V|GPBP1_ENST00000538707.1_Missense_Mutation_p.F308V			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	301					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		GAAGAGTGAATTTTTGAAAGC	0.388																																					p.F308V		.											.	GPBP1-135	0			c.T922G						.						107	104	105					5																	56545332		2203	4299	6502	SO:0001583	missense	65056	exon8			AGTGAATTTTTGA		CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.901T>G	5.37:g.56545332T>G	ENSP00000421202:p.Phe301Val	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	107	32	NM_001127236	0	0	21	35	14	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Missense_Mutation	SNP	ENST00000506184.2	37	CCDS34162.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987062	0.74589	.	.	ENSG00000062194	ENST00000424459;ENST00000514387;ENST00000506184;ENST00000454432;ENST00000511209;ENST00000264779;ENST00000538707	T;T;T;T;T;T;T	0.59364	1.24;0.27;1.3;1.24;1.24;1.3;1.3	6.16	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.55970	0.1954	M	0.62723	1.935	0.46701	D	0.999164	P;P;P;P	0.47545	0.897;0.728;0.728;0.728	B;B;B;B	0.42214	0.38;0.294;0.23;0.294	T	0.60632	-0.7225	10	0.87932	D	0	-10.4	11.4966	0.50413	0.1338:0.0:0.0:0.8662	.	321;308;293;301	D4PHA4;Q86WP2-2;Q86WP2-3;Q86WP2	.;.;.;GPBP1_HUMAN	V	321;130;301;321;293;308;308	ENSP00000401596:F321V;ENSP00000421709:F130V;ENSP00000421202:F301V;ENSP00000403522:F321V;ENSP00000422337:F293V;ENSP00000264779:F308V;ENSP00000440090:F308V	ENSP00000264779:F308V	F	+	1	0	GPBP1	56581089	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.480000	0.66820	1.110000	0.41699	0.528000	0.53228	TTT	.		0.388	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913		G	56545332	T	G	56545332	3	3	69	1	0	0	0	0	1	0	0	0	6615	1493	52	5	952	5	GPBP1	5	56545332	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	24418915	56545332	124369928	45	6575											
TRIM23	373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	64905230	64905230	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacgacacagagtttcatgtAgatcataaaaataagctcga	17	9	8	7	2	2	2	2	0	0	2	3	5	2	2	0	0	1	3	0	0	5	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:64905230A>T	ENST00000231524.9	-	6	1255	c.884T>A	c.(883-885)cTa>cAa	p.L295Q	TRIM23_ENST00000274327.7_Missense_Mutation_p.L295Q|TRIM23_ENST00000381018.3_Missense_Mutation_p.L295Q|TRIM23_ENST00000508808.1_5'UTR	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	295					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		AGTTTCATGTAGATCATAAAA	0.363																																					p.L295Q		.											.	TRIM23-230	0			c.T884A						.						91	85	87					5																	64905230		2203	4300	6503	SO:0001583	missense	373	exon6			TCATGTAGATCAT	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.884T>A	5.37:g.64905230A>T	ENSP00000231524:p.Leu295Gln	Somatic	113	1		WXS	Illumina HiSeq	Phase_I	75	25	NM_033228	0	0	0	0	0	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.588606	0.86851	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.77229	-1.01;-1.02;-1.08	5.39	5.39	0.77823	B-box, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85869	0.5797	L	0.58101	1.795	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.996	D;D;D	0.75484	0.922;0.986;0.964	D	0.87366	0.2347	10	0.87932	D	0	.	15.7008	0.77541	1.0:0.0:0.0:0.0	.	295;295;295	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	Q	295	ENSP00000231524:L295Q;ENSP00000370406:L295Q;ENSP00000274327:L295Q	ENSP00000231524:L295Q	L	-	2	0	TRIM23	64940986	1.000000	0.71417	0.897000	0.35233	0.987000	0.75469	8.910000	0.92685	2.169000	0.68431	0.533000	0.62120	CTA	.		0.363	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		T	64905230	A	T	64905230	3	4	69	1	0	0	0	0	1	0	0	0	16530	420	15	5	931	5	TRIM23	5	64905230	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	8359898	64905230	116010030	46	6576											
CD180	4064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	66478708	66478708	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgtgttggtatttccaccTgagaaggtatttaactgcaa	12	14	9	6	0	0	1	0	1	0	1	1	2	1	1	2	2	2	4	2	2	6	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:66478708T>G	ENST00000256447.4	-	3	2120	c.1963A>C	c.(1963-1965)Agg>Cgg	p.R655R	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	655					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TATTTCCACCTGAGAAGGTAT	0.373																																					p.R655R		.											.	CD180-91	0			c.A1963C						.						36	39	38					5																	66478708		2203	4300	6503	SO:0001819	synonymous_variant	4064	exon3			TCCACCTGAGAAG	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1963A>C	5.37:g.66478708T>G		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_005582	0	0	0	0	0	B2R7Z7|Q32MM5	Silent	SNP	ENST00000256447.4	37	CCDS3992.1																																																																																			.		0.373	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		G	66478708	T	G	66478708	2	3	69	1	0	0	0	0	0	0	0	1	2978	1579	55	5		5	CD180	5	66478708	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	1573478	66478708	114436552	47	6577											
LNPEP	4012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	96328816	96328816	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcaaaactactttgaaaTtcagtacccacttaagaaat	16	14	3	8	0	2	2	2	1	0	1	2	2	2	2	1	0	3	1	1	0	7	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:96328816T>A	ENST00000231368.5	+	5	1921	c.1229T>A	c.(1228-1230)aTt>aAt	p.I410N	LNPEP_ENST00000395770.3_Missense_Mutation_p.I396N	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	410					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-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		TACTTTGAAATTCAGTACCCA	0.303																																					p.I410N		.											.	LNPEP-229	0			c.T1229A						.						66	67	67					5																	96328816		2202	4299	6501	SO:0001583	missense	4012	exon5			TTGAAATTCAGTA	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"cystinyl aminopeptidase", "placental leucine aminopeptidase"	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.1229T>A	5.37:g.96328816T>A	ENSP00000231368:p.Ile410Asn	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	112	46	NM_005575	0	0	0	2	2	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.278587	0.80692	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.03035	4.07;4.07	4.94	4.94	0.65067	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.25082	0.0609	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.16100	-1.0414	10	0.87932	D	0	.	14.5573	0.68109	0.0:0.0:0.0:1.0	.	410	Q9UIQ6	LCAP_HUMAN	N	410;396	ENSP00000231368:I410N;ENSP00000379117:I396N	ENSP00000231368:I410N	I	+	2	0	LNPEP	96354572	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.757000	0.68766	1.964000	0.57103	0.455000	0.32223	ATT	.		0.303	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		A	96328816	T	A	96328816	3	1	69	1	0	0	0	0	1	0	0	0	8887	1493	52	5	1247	5	LNPEP	5	96328816	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	29850108	96328816	84586444	48	6578											
TRIM36	55521	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	114469835	114469835	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcctcattgatctctggcAcgtctatgcctgaaagaatt	9	14	8	10	1	3	3	1	2	2	1	5	3	4	3	2	1	1	2	2	1	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:114469835A>G	ENST00000282369.3	-	8	1377	c.1256T>C	c.(1255-1257)gTg>gCg	p.V419A	TRIM36_ENST00000514154.1_Missense_Mutation_p.V264A|TRIM36_ENST00000513154.1_Missense_Mutation_p.V407A	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	419	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		GATCTCTGGCACGTCTATGCC	0.313																																					p.V419A		.											.	TRIM36-725	0			c.T1256C						.						70	65	67					5																	114469835		2202	4300	6502	SO:0001583	missense	55521	exon8			TCTGGCACGTCTA	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16280	protein-coding gene	gene with protein product	"zinc-binding protein Rbcc728", "tripartite motif protein 36", "RING finger protein 98"	609317	"tripartite motif-containing 36"			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.1256T>C	5.37:g.114469835A>G	ENSP00000282369:p.Val419Ala	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	41	12	NM_018700	0	0	0	0	0	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	A	2.258	-0.370008	0.05069	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.59638	0.91;1.03;0.25	5.28	5.28	0.74379	Fibronectin, type III (3);	0.387682	0.31507	N	0.007529	T	0.35913	0.0948	N	0.12569	0.235	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29274	-1.0017	10	0.02654	T	1	.	15.2106	0.73222	1.0:0.0:0.0:0.0	.	407;419	E9PFI8;Q9NQ86	.;TRI36_HUMAN	A	419;407;264	ENSP00000282369:V419A;ENSP00000423934:V407A;ENSP00000424259:V264A	ENSP00000282369:V419A	V	-	2	0	TRIM36	114497734	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	3.363000	0.52321	1.997000	0.58415	0.460000	0.39030	GTG	.		0.313	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		G	114469835	A	G	114469835	3	3	69	1	0	0	0	0	1	0	0	0	16543	159	6	3	942	3	TRIM36	5	114469835	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	18141019	114469835	66445425	49	6579											
PCDHA9	9752	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140228538	140228538	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcttgactctcggtttcCactagagggcgcgtccgatg	5	10	13	13	5	1	2	0	1	1	1	4	3	3	2	3	2	0	2	3	2	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:140228538C>A	ENST00000532602.1	+	1	1491	c.458C>A	c.(457-459)cCa>cAa	p.P153Q	PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.P153Q|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	153	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCGGTTTCCACTAGAGGGC	0.547																																					p.P153Q	Melanoma(55;1800 1972 14909)	.											.	PCDHA9-138	0			c.C458A						.						54	51	52					5																	140228538		2202	4292	6494	SO:0001583	missense	9752	exon1			GGTTTCCACTAGA	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"Cadherins / Protocadherins : Clustered"	8675	other	complex locus constituent	"KIAA0345-like 5"	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.458C>A	5.37:g.140228538C>A	ENSP00000436042:p.Pro153Gln	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	194	45	NM_031857	0	0	0	0	0	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352609	0.82132	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.48201	0.82;0.82	4.13	4.13	0.48395	Cadherin (3);Cadherin-like (1);	0.000000	0.31697	U	0.007216	T	0.67552	0.2905	M	0.83384	2.64	0.28140	N	0.929845	D;D	0.62365	0.986;0.991	D;P	0.64877	0.93;0.894	T	0.64719	-0.6341	10	0.87932	D	0	.	12.8791	0.58008	0.1634:0.8366:0.0:0.0	.	153;153	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	Q	153	ENSP00000436042:P153Q;ENSP00000367362:P153Q	ENSP00000367362:P153Q	P	+	2	0	PCDHA9	140208722	0.000000	0.05858	0.994000	0.49952	0.994000	0.84299	1.041000	0.30291	2.263000	0.75096	0.591000	0.81541	CCA	.		0.547	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140228538	C	A	140228538	3	1	69	1	0	0	0	0	1	0	0	0	11557	594	21	4	460	4	PCDHA9	5	140228538	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	25758703	140228538	40686722	50	6580											
PCDHGA9	56107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140784720	140784720	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	taccagtgatgggttggctgGtgtgcccacctcacactttg	6	12	12	11	0	1	1	1	1	0	0	1	1	1	1	3	3	2	2	3	3	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:140784720G>C	ENST00000573521.1	+	1	2201	c.2201G>C	c.(2200-2202)gGt>gCt	p.G734A	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	734					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGTTGGCTGGTGTGCCCACC	0.572																																					p.G734A		.											.	.	0			c.G2201C						.						68	76	73					5																	140784720		2178	4290	6468	SO:0001583	missense	56107	exon1			TGGCTGGTGTGCC	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.2201G>C	5.37:g.140784720G>C	ENSP00000460274:p.Gly734Ala	Somatic	91	1		WXS	Illumina HiSeq	Phase_I	79	24	NM_032089	0	0	0	0	0	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			.		0.572	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		C	140784720	G	C	140784720	3	2	69	1	0	0	0	0	1	0	0	0	11587	1261	44	4	2203	4	PCDHGA9	5	140784720	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	556182	140784720	40130540	51	6581											
PCDHGC3	5098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140856636	140856636	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcgaggacaccaaactccAtgagatttacatccaggcca	13	8	7	13	1	0	1	0	1	0	1	3	4	2	2	4	2	2	0	4	2	2	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:140856636A>G	ENST00000308177.3	+	1	1057	c.953A>G	c.(952-954)cAt>cGt	p.H318R	PCDHGA12_ENST00000252085.3_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|RN7SL68P_ENST00000488078.2_RNA	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	318	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAAACTCCATGAGATTTAC	0.557																																					p.H318R		.											.	PCDHGC3-24	0			c.A953G						.						85	79	81					5																	140856636		2203	4300	6503	SO:0001583	missense	5098	exon1			AACTCCATGAGAT	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.953A>G	5.37:g.140856636A>G	ENSP00000312070:p.His318Arg	Somatic	104	1		WXS	Illumina HiSeq	Phase_I	102	35	NM_032402	0	0	0	0	0	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	37	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.214694	0.39102	.	.	ENSG00000240184	ENST00000308177	T	0.52295	0.67	5.38	5.38	0.77491	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.56396	0.1982	M	0.82323	2.585	0.24048	N	0.996054	P;P	0.49559	0.523;0.925	B;B	0.42422	0.287;0.387	T	0.60586	-0.7234	9	0.87932	D	0	.	15.5494	0.76137	1.0:0.0:0.0:0.0	.	318;318	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	R	318	ENSP00000312070:H318R	ENSP00000312070:H318R	H	+	2	0	PCDHGC3	140836820	0.237000	0.23815	0.999000	0.59377	0.987000	0.75469	3.449000	0.52950	2.264000	0.75181	0.533000	0.62120	CAT	.		0.557	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		G	140856636	A	G	140856636	3	3	69	1	0	0	0	0	1	0	0	0	11595	217	8	3	955	3	PCDHGC3	5	140856636	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	71916	140856636	40058624	52	6582											
BAT1	7919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31507042	31507042	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatggcctgagggatgcacTcatgctggactaaaagttgg	11	9	14	7	0	1	1	1	1	0	0	1	4	1	3	1	4	2	3	1	4	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:31507042T>C	ENST00000396172.1	-	3	851	c.221A>G	c.(220-222)gAg>gGg	p.E74G	DDX39B_ENST00000449074.2_Missense_Mutation_p.E74G|SNORD117_ENST00000364915.1_RNA|DDX39B_ENST00000453105.2_Intron|DDX39B_ENST00000458640.1_Missense_Mutation_p.E74G|DDX39B_ENST00000415382.2_Intron|ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank|SNORD84_ENST00000584275.1_RNA|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000417556.2_Missense_Mutation_p.E74G|DDX39B_ENST00000376177.2_Missense_Mutation_p.E74G	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	74					ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						AGGGATGCACTCATGCTGGAC	0.507																																					p.E74G		.											.	DDX39B-92	0			c.A221G						.						100	108	105					6																	31507042		1511	2709	4220	SO:0001583	missense	7919	exon3			ATGCACTCATGCT	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"DEAD-boxes"	13917	protein-coding gene	gene with protein product	"U2AF65-associated protein 56"	142560	"HLA-B associated transcript 1"	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.221A>G	6.37:g.31507042T>C	ENSP00000379475:p.Glu74Gly	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	114	48	NM_004640	0	0	0	0	0	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	37	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869256	0.72065	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000427214;ENST00000428098;ENST00000419338;ENST00000456662;ENST00000449074;ENST00000428450;ENST00000449757;ENST00000456976;ENST00000418897;ENST00000419020;ENST00000458215	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.53	5.53	0.82687	DEAD-like helicase (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	L	0.50993	1.605	0.80722	D	1	D;D;P	0.58970	0.984;0.972;0.897	P;P;P	0.57371	0.735;0.819;0.635	T	0.54221	-0.8326	10	0.72032	D	0.01	-22.5551	13.6077	0.62056	0.0:0.0:0.0:1.0	.	94;74;74	Q59G92;Q13838;Q5STU3	.;DX39B_HUMAN;.	G	74;74;74;74;74;74;74;74;74;74;97;74;89;74;74	ENSP00000365347:E74G;ENSP00000416269:E74G;ENSP00000379475:E74G;ENSP00000412582:E74G;ENSP00000399371:E74G;ENSP00000392672:E74G;ENSP00000410313:E74G;ENSP00000416350:E74G;ENSP00000391946:E74G;ENSP00000405707:E74G;ENSP00000409426:E97G;ENSP00000393984:E74G;ENSP00000399841:E89G;ENSP00000405245:E74G	ENSP00000365347:E74G	E	-	2	0	DDX39B	31615021	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.568000	0.82369	2.095000	0.63458	0.460000	0.39030	GAG	.		0.507	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		C	31507042	T	C	31507042	3	2	69	1	0	0	0	0	1	0	0	0	1319	1551	54	3	1101	3	BAT1	6	31507042	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		31507042	139608025	53	6583											
NOTCH4	4855	broad.mit.edu	37	chr6	32188966	32188966	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgggtcctggaagcactcGttgacatcacgttcacaggc	8	9	11	13	2	2	1	2	1	0	0	4	2	3	2	2	3	1	3	2	3	1	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:32188966G>A	ENST00000375023.3	-	4	726	c.588C>T	c.(586-588)aaC>aaT	p.N196N		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	196	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGAAGCACTCGTTGACATCAC	0.627																																					p.N196N													.	NOTCH4-1321	0			c.C588T						.						68	63	65					6																	32188966		1510	2708	4218	SO:0001819	synonymous_variant	4855	exon4			GCACTCGTTGACA		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.588C>T	6.37:g.32188966G>A		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	80	4	NM_004557	0	0	0	0	0	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			.		0.627	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			A	32188966	G	A	32188966	2	1	69	1	0	0	0	0	0	0	0	1	10577	1136	40	1		1	NOTCH4	6	32188966	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	681924	32188966	138926101	54	6584											
DST	667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	56347659	56347659	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgctggtcctcttccccAactctttttggaaggcctaa	7	13	7	14	0	2	0	0	0	2	0	4	1	4	1	4	3	2	1	4	3	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:56347659A>G	ENST00000361203.3	-	84	20271	c.20264T>C	c.(20263-20265)tTg>tCg	p.L6755S	DST_ENST00000244364.6_Missense_Mutation_p.L4452S|DST_ENST00000421834.2_Missense_Mutation_p.L4778S|DST_ENST00000446842.2_Missense_Mutation_p.L6540S|DST_ENST00000370769.4_Missense_Mutation_p.L6866S|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Missense_Mutation_p.L4669S|DST_ENST00000370754.5_Missense_Mutation_p.L7044S			Q03001	DYST_HUMAN	dystonin	6754					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CCTCTTCCCCAACTCTTTTTG	0.448																																					p.L4452S		.											.	DST-523	0			c.T13355C						.						53	52	52					6																	56347659		1871	4102	5973	SO:0001583	missense	667	exon70			TTCCCCAACTCTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.20264T>C	6.37:g.56347659A>G	ENSP00000354508:p.Leu6755Ser	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	63	22	NM_015548	0	0	4	4	0	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	A	18.68	3.676124	0.67928	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.65	5.65	0.86999	.	0.000000	0.41396	D	0.000891	T	0.75671	0.3881	M	0.87682	2.9	0.32532	N	0.534844	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.999	T	0.81079	-0.1095	9	0.87932	D	0	.	16.1657	0.81754	1.0:0.0:0.0:0.0	.	4778;6866;7044;6864;4452	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	S	4452;7044;6866;4778;6540;4669;6755	ENSP00000244364:L4452S;ENSP00000359790:L7044S;ENSP00000359805:L6866S;ENSP00000400883:L4778S;ENSP00000393645:L6540S;ENSP00000359824:L4669S;ENSP00000354508:L6755S	ENSP00000244364:L4452S	L	-	2	0	DST	56455618	1.000000	0.71417	0.987000	0.45799	0.992000	0.81027	9.307000	0.96226	2.276000	0.75962	0.528000	0.53228	TTG	.		0.448	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56347659	A	G	56347659	3	3	69	1	0	0	0	0	1	0	0	0	4794	131	5	3	2220	3	DST	6	56347659	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	24158693	56347659	114767408	55	6585											
AIM1	202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	106992678	106992678	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataggatttttcaaatgctCacatgataatgtacagtgaa	16	13	7	5	0	2	2	2	2	0	0	2	3	2	3	0	1	2	2	0	1	6	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:106992678C>A	ENST00000369066.3	+	11	4445	c.3958C>A	c.(3958-3960)Cac>Aac	p.H1320N	AIM1_ENST00000535438.1_Missense_Mutation_p.H139N|AIM1_ENST00000487681.1_3'UTR	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TTCAAATGCTCACATGATAAT	0.323																																					p.H1320N		.											.	AIM1-139	0			c.C3958A						.						87	89	88					6																	106992678		2203	4300	6503	SO:0001583	missense	202	exon11			AATGCTCACATGA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3958C>A	6.37:g.106992678C>A	ENSP00000358062:p.His1320Asn	Somatic	92	1		WXS	Illumina HiSeq	Phase_I	88	28	NM_001624	0	0	0	0	0	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324079	0.60634	.	.	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	T;T;T	0.74315	-0.83;-0.83;-0.83	5.72	5.72	0.89469	Beta/gamma crystallin (3);Gamma-crystallin-related (1);	0.087070	0.85682	D	0.000000	D	0.82618	0.5076	M	0.68317	2.08	0.58432	D	0.999996	D;P	0.67145	0.996;0.629	D;P	0.65323	0.934;0.498	D	0.83503	0.0076	10	0.72032	D	0.01	.	19.4664	0.94945	0.0:1.0:0.0:0.0	.	139;1320	B4DU04;Q9Y4K1	.;AIM1_HUMAN	N	1320;139;139	ENSP00000358062:H1320N;ENSP00000391419:H139N;ENSP00000439183:H139N	ENSP00000358062:H1320N	H	+	1	0	AIM1	107099371	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.865000	0.62998	2.703000	0.92315	0.561000	0.74099	CAC	.		0.323	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106992678	C	A	106992678	3	1	69	1	0	0	0	0	1	0	0	0	430	826	29	4	4000	4	AIM1	6	106992678	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	50645019	106992678	64122389	56	6586											
SLC35D3	340146	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	137243696	137243696	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agttctccttcctgaccctgGtgcagtgcctgaccagctcc	5	11	9	16	0	1	2	0	2	1	0	4	2	3	2	6	1	3	3	6	1	0	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:137243696G>C	ENST00000331858.4	+	1	295	c.130G>C	c.(130-132)Gtg>Ctg	p.V44L		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	44					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		CCTGACCCTGGTGCAGTGCCT	0.677																																					p.V44L		.											.	SLC35D3-91	0			c.G130C						.						41	37	38					6																	137243696		2202	4298	6500	SO:0001583	missense	340146	exon1			ACCCTGGTGCAGT		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.130G>C	6.37:g.137243696G>C	ENSP00000333591:p.Val44Leu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	50	17	NM_001008783	0	0	0	0	0	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	.	.	.	.	.	.	.	.	.	.	G	6.901	0.535701	0.13188	.	.	ENSG00000182747	ENST00000331858	T	0.50277	0.75	4.53	4.53	0.55603	.	0.154256	0.43110	D	0.000610	T	0.09642	0.0237	N	0.04880	-0.145	0.43608	D	0.995972	B	0.09022	0.002	B	0.06405	0.002	T	0.16928	-1.0386	10	0.02654	T	1	-17.4101	13.2101	0.59819	0.0:0.213:0.787:0.0	.	44	Q5M8T2	S35D3_HUMAN	L	44	ENSP00000333591:V44L	ENSP00000333591:V44L	V	+	1	0	SLC35D3	137285389	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.017000	0.57167	2.074000	0.62210	0.491000	0.48974	GTG	.		0.677	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		C	137243696	G	C	137243696	3	2	69	1	0	0	0	0	1	0	0	0	14615	1261	44	4	132	4	SLC35D3	6	137243696	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	30251018	137243696	33871371	57	6587											
TAX1BP1	8887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	27856087	27856087	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgttctcacattgtcaaaTgcacaaccagttctgcaata	13	13	5	10	0	3	0	2	0	2	0	4	0	3	0	1	0	3	4	1	0	5	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:27856087T>C	ENST00000396319.2	+	14	1972	c.1884T>C	c.(1882-1884)aaT>aaC	p.N628N	TAX1BP1_ENST00000409980.1_Silent_p.N652N|TAX1BP1_ENST00000265393.6_Intron|TAX1BP1_ENST00000433216.2_Intron|TAX1BP1_ENST00000543117.1_Intron	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	628					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			CATTGTCAAATGCACAACCAG	0.378																																					p.N628N		.											.	TAX1BP1-153	0			c.T1884C						.						160	156	157					7																	27856087		2203	4300	6503	SO:0001819	synonymous_variant	8887	exon14			GTCAAATGCACAA	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1884T>C	7.37:g.27856087T>C		Somatic	347	0		WXS	Illumina HiSeq	Phase_I	298	100	NM_006024	0	0	13	27	14	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Silent	SNP	ENST00000396319.2	37	CCDS5415.1																																																																																			.		0.378	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		C	27856087	T	C	27856087	2	2	69	1	0	0	0	0	0	0	0	1	15626	1461	51	3		3	TAX1BP1	7	27856087	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		27856087	131282576	58	6588											
ZNF679	168417	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	63721262	63721262	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgtctggagcaaaataaaGagccttggaatataaagaga	17	8	10	6	0	1	2	0	0	1	2	1	5	1	4	2	2	2	1	2	2	8	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:63721262G>A	ENST00000421025.1	+	4	486	c.217G>A	c.(217-219)Gag>Aag	p.E73K	ZNF679_ENST00000255746.4_Missense_Mutation_p.E73K	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	73	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						GCAAAATAAAGAGCCTTGGAA	0.378																																					p.E73K													.	ZNF679-1	0			c.G217A						.						121	109	113					7																	63721262		692	1591	2283	SO:0001583	missense	168417	exon4			AATAAAGAGCCTT	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.217G>A	7.37:g.63721262G>A	ENSP00000416809:p.Glu73Lys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	56	24	NM_153363	0	0	0	0	0		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	G	5.786	0.329447	0.10956	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.07800	3.16;3.16	0.235	0.235	0.15431	Krueppel-associated box (2);	.	.	.	.	T	0.07818	0.0196	L	0.47716	1.5	0.09310	N	1	B	0.14012	0.009	B	0.15052	0.012	T	0.32241	-0.9914	8	0.46703	T	0.11	.	.	.	.	.	73	Q8IYX0	ZN679_HUMAN	K	73	ENSP00000416809:E73K;ENSP00000255746:E73K	ENSP00000255746:E73K	E	+	1	0	ZNF679	63358697	0.303000	0.24463	0.027000	0.17364	0.031000	0.12232	1.500000	0.35682	0.308000	0.22923	0.313000	0.20887	GAG	.		0.378	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		A	63721262	G	A	63721262	3	1	69	1	0	0	0	0	1	0	0	0	18118	943	33	2	227	2	ZNF679	7	63721262	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	35865175	63721262	95417401	59	6589											
TPST1	8460	hgsc.bcm.edu	37	chr7	65705943	65705943	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaggttattccccaatgcCaaatttctcctgatggtccg	8	14	7	12	1	2	1	0	1	2	0	5	1	4	1	5	2	1	1	5	2	4	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:65705943C>G	ENST00000304842.5	+	2	956	c.531C>G	c.(529-531)gcC>gcG	p.A177A	TPST1_ENST00000480281.1_Intron	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	177					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						TCCCCAATGCCAAATTTCTCC	0.403																																					p.A177A		.											.	TPST1-90	0			c.C531G						.						53	55	54					7																	65705943		2203	4300	6503	SO:0001819	synonymous_variant	8460	exon2			CAATGCCAAATTT	AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"Sulfotransferases, membrane-bound"	12020	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog A (Drosophila)"	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.531C>G	7.37:g.65705943C>G		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	82	10	NM_003596	0	0	3	3	0	A4D2M0|Q6FGM7	Silent	SNP	ENST00000304842.5	37	CCDS5533.1																																																																																			.		0.403	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2	NM_003596		G	65705943	C	G	65705943	2	3	69	1	0	0	0	0	0	0	0	1	16460	581	21	4		4	TPST1	7	65705943	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	1984681	65705943	93432720	60	6590											
DMTF1	9988	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	86802963	86802966	+	Splice_Site	DEL	AAGG	AAGG	-																															taaggattctctgactaataAaggtaagataacactgtgaa																								rs138809401		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	AAGG	AAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:86802963_86802966delAAGG	ENST00000394703.5	+	8	1003_1005	c.440_442delAAGG	c.(439-444)aaaggg>agg	p.KG147fs	DMTF1_ENST00000411766.2_Splice_Site_p.KG106fs|DMTF1_ENST00000432937.2_Splice_Site_p.KG59fs|DMTF1_ENST00000413276.2_Splice_Site_p.KG147fs|DMTF1_ENST00000331242.7_Splice_Site_p.KG147fs|DMTF1_ENST00000414194.2_5'UTR|DMTF1_ENST00000394702.3_Splice_Site_p.KG147fs	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	147	Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.|Required for transcriptional activation. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CTGACTAATAAAGGTAAGATAACA	0.382																																					p.147_148del		.											.	DMTF1-91	0			c.440_442del						.																																			SO:0001630	splice_region_variant	9988	exon6			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.442+1AAGG>-	7.37:g.86802963_86802966delAAGG		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	53	12	NM_001142327	0	0	0	0	0	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	In_Frame_Del	DEL	ENST00000394703.5	37	CCDS5601.1																																																																																			.		0.382	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	Frame_Shift_Del	-	86802966	AAGG	-	86802963	8	5	69	1	0	1	0	1	0	0	1	0	4603	14	1	0	454	0	DMTF1	7	86802963	Splice_Site	DEL	AAGG	TCGA-BQ-5885-01A-11D-1589-08	21097020	86802963	72335700	61	6591											
AKAP9	10142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	91631868	91631868	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagtaaaagatgatttagaAgacagtaaaaataaacagga	24	7	8	2	0	0	4	0	1	0	3	0	5	0	5	0	1	1	2	0	1	10	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:91631868A>G	ENST00000359028.2	+	9	2898	c.2673A>G	c.(2671-2673)gaA>gaG	p.E891E	AKAP9_ENST00000356239.3_Silent_p.E879E|AKAP9_ENST00000358100.2_Silent_p.E891E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	891	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ATGATTTAGAAGACAGTAAAA	0.294			T	BRAF	papillary thyroid																																p.E879E		.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9-755	0			c.A2637G						.						45	50	48					7																	91631868		2199	4289	6488	SO:0001819	synonymous_variant	10142	exon8			TTTAGAAGACAGT	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.2673A>G	7.37:g.91631868A>G		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	75	21	NM_005751	0	0	2	2	0	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.		0.294	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91631868	A	G	91631868	2	3	69	1	0	0	0	0	0	0	0	1	459	69	3	3		3	AKAP9	7	91631868	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	4828905	91631868	67506795	62	6592											
PEX1	5189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92119227	92119227	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagagacattgtgagctcTgcatggtaaattgtagtaat	13	12	11	5	0	1	3	0	1	1	2	1	4	1	3	0	1	2	5	0	1	4	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:92119227T>C	ENST00000248633.4	-	22	3534		c.e22-2		PEX1_ENST00000438045.1_Splice_Site|PEX1_ENST00000428214.1_Splice_Site|AC007566.10_ENST00000427458.1_RNA|AC007566.10_ENST00000441539.1_RNA	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1						ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTGTGAGCTCTGCATGGTAAA	0.393																																					.		.											.	PEX1-91	0			c.3439-2A>G						.						48	44	45					7																	92119227		2203	4300	6503	SO:0001630	splice_region_variant	5189	exon23			GAGCTCTGCATGG	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"ATPases / AAA-type"	8850	protein-coding gene	gene with protein product		602136	"peroxisome biogenesis factor 1", "Zellweger syndrome 1", "Zellweger syndrome"	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3439-2A>G	7.37:g.92119227T>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	48	21	NM_000466	0	0	1	5	4	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Splice_Site	SNP	ENST00000248633.4	37	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.023778	0.54683	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2209	0.65826	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PEX1	91957163	1.000000	0.71417	0.995000	0.50966	0.747000	0.42532	6.048000	0.71046	2.230000	0.72887	0.528000	0.53228	.	.		0.393	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	Intron	C	92119227	T	C	92119227	5	2	69	1	0	0	0	0	0	0	1	0	11761	1594	55	3	426	3	PEX1	7	92119227	Splice_Site	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	487359	92119227	67019436	63	6593											
LMTK2	22853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	97823720	97823720	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccgagtcggaggacgagaccGagcaccccgtgcccatcatc	9	4	12	16	5	1	1	1	0	0	1	3	6	1	3	5	2	2	1	5	2	0	0	rs199600469		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:97823720G>C	ENST00000297293.5	+	11	4236	c.3943G>C	c.(3943-3945)Gag>Cag	p.E1315Q		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1315					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GGACGAGACCGAGCACCCCGT	0.642																																					p.E1315Q		.											.	LMTK2-1381	0			c.G3943C						.						116	109	112					7																	97823720		2203	4300	6503	SO:0001583	missense	22853	exon11			GAGACCGAGCACC	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 100"	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3943G>C	7.37:g.97823720G>C	ENSP00000297293:p.Glu1315Gln	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	145	47	NM_014916	0	0	0	0	0	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.79	3.892758	0.72524	.	.	ENSG00000164715	ENST00000297293	T	0.78126	-1.15	6.08	6.08	0.98989	.	0.267216	0.42682	D	0.000673	T	0.80899	0.4712	L	0.54323	1.7	0.36996	D	0.895043	D	0.61697	0.99	P	0.49361	0.608	T	0.82568	-0.0392	10	0.46703	T	0.11	.	19.6516	0.95815	0.0:0.0:1.0:0.0	.	1315	Q8IWU2	LMTK2_HUMAN	Q	1315	ENSP00000297293:E1315Q	ENSP00000297293:E1315Q	E	+	1	0	LMTK2	97661656	1.000000	0.71417	0.961000	0.40146	0.339000	0.28857	6.316000	0.72857	2.894000	0.99253	0.655000	0.94253	GAG	G|0.999;C|0.000		0.642	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		C	97823720	G	C	97823720	3	2	69	1	0	0	0	0	1	0	0	0	8882	1059	37	4	3985	4	LMTK2	7	97823720	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	5704493	97823720	61314943	64	6594											
MGAM	8972	hgsc.bcm.edu	37	chr7	141759733	141759733	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggatgacgtcttcatcaaAtacccaaatgatggagacat	15	9	9	8	1	3	3	2	2	1	1	3	6	3	4	1	2	1	0	1	2	3	2	rs73740235		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:141759733A>G	ENST00000549489.2	+	33	4121	c.4026A>G	c.(4024-4026)aaA>aaG	p.K1342K	MGAM_ENST00000475668.2_Silent_p.K1342K	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1342	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCTTCATCAAATACCCAAATG	0.498																																					p.K1342K		.											.	MGAM-70	0			c.A4026G						.						44	38	40					7																	141759733		1935	4143	6078	SO:0001819	synonymous_variant	8972	exon33			CATCAAATACCCA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4026A>G	7.37:g.141759733A>G		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_004668	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			A|0.500;G|0.500		0.498	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141759733	A	G	141759733	2	3	69	1	0	0	0	0	0	0	0	1	9566	98	4	3		3	MGAM	7	141759733	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	43936013	141759733	17378930	65	6595											
SLC7A2	6542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	17401959	17401959	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctgttctgttttgggaaGgtacatcaagtgttgcaaga	9	15	11	6	0	3	1	1	0	2	1	4	2	3	2	0	2	2	5	0	2	4	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:17401959G>T	ENST00000494857.1	+	4	594		c.e4-1		SLC7A2_ENST00000004531.10_Splice_Site|SLC7A2_ENST00000398090.3_Splice_Site|SLC7A2_ENST00000522656.1_Splice_Site|SLC7A2_ENST00000470360.1_Splice_Site	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2						amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	GTTTTGGGAAGGTACATCAAG	0.388																																					.		.											.	SLC7A2-93	0			c.377-1G>T						.						120	121	121					8																	17401959		2203	4300	6503	SO:0001630	splice_region_variant	6542	exon3			TGGGAAGGTACAT	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"Solute carriers"	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.377-1G>T	8.37:g.17401959G>T		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	127	41	NM_001008539	0	0	0	0	0	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Splice_Site	SNP	ENST00000494857.1	37	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437083	0.62955	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8219	0.96602	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC7A2	17446335	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	9.823000	0.99369	2.767000	0.95098	0.563000	0.77884	.	.		0.388	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	Intron	T	17401959	G	T	17401959	5	4	69	1	0	0	0	0	0	0	1	0	14729	1014	35	4	506	4	SLC7A2	8	17401959	Splice_Site	SNP	G	TCGA-BQ-5885-01A-11D-1589-08		17401959	128962063	66	6596											
ADAMDEC1	27299	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	24256052	24256052	+	Frame_Shift_Del	DEL	C	C	-																															tttgtgtttgatgtgatgaaCctactcaatgtggtaagaca																								rs2291576	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:24256052delC	ENST00000256412.4	+	8	970	c.750delC	c.(748-750)aacfs	p.N250fs	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Frame_Shift_Del_p.N171fs|ADAMDEC1_ENST00000538205.1_Frame_Shift_Del_p.N171fs|RP11-624C23.1_ENST00000523578.1_RNA	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	250	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		ATGTGATGAACCTACTCAATG	0.338																																					p.N250fs	Ovarian(147;687 1849 3699 25981 31337)	.											.	ADAMDEC1-228	0			c.750delC						.						190	182	185					8																	24256052		2203	4300	6503	SO:0001589	frameshift_variant	27299	exon8			.	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.750delC	8.37:g.24256052delC	ENSP00000256412:p.Asn250fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	165	55	NM_014479	0	0	0	0	0	B7ZAK5	Frame_Shift_Del	DEL	ENST00000256412.4	37	CCDS6044.1																																																																																			.		0.338	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		-	24256052	C	-	24256052	7	5	69	1	0	1	0	1	0	0	0	0	254	506	18	0	780	0	ADAMDEC1	8	24256052	Frame_Shift_Del	DEL	C	TCGA-BQ-5885-01A-11D-1589-08	6854093	24256052	122107970	67	6597											
EBF2	64641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	25715868	25715868	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccggtgggtgagccatttaGaaatcctggtgaacctggaa	10	9	14	8	1	0	3	0	2	0	1	1	4	1	4	4	4	2	0	4	4	4	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:25715868G>A	ENST00000520164.1	-	14	2032	c.1495C>T	c.(1495-1497)Cta>Tta	p.L499L	EBF2_ENST00000408929.3_Silent_p.L351L|EBF2_ENST00000535548.1_Silent_p.L230L	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	499	Pro/Ser/Thr-rich.				adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GAGCCATTTAGAAATCCTGGT	0.483																																					p.L499L	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	.											.	EBF2-26	0			c.C1495T						.						125	125	125					8																	25715868		1950	4140	6090	SO:0001819	synonymous_variant	64641	exon14			CATTTAGAAATCC	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.1495C>T	8.37:g.25715868G>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	74	24	NM_022659	0	0	0	0	0	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Silent	SNP	ENST00000520164.1	37	CCDS43726.1																																																																																			.		0.483	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		A	25715868	G	A	25715868	2	1	69	1	0	0	0	0	0	0	0	1	4892	933	33	2		2	EBF2	8	25715868	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1459816	25715868	120648154	68	6598											
PRKDC	5591	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	48826505	48826505	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagcgctaattctgtgactcGaggcaggaacacatccagga	12	7	12	10	2	1	1	0	1	1	0	3	5	2	3	1	3	2	2	1	3	2	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:48826505G>A	ENST00000314191.2	-	24	2793	c.2737C>T	c.(2737-2739)Cga>Tga	p.R913*	PRKDC_ENST00000338368.3_Nonsense_Mutation_p.R913*|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	913					B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.V909_L917delVFLPRVTEL(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	TCTGTGACTCGAGGCAGGAAC	0.428								Non-homologous end-joining																													.	Esophageal Squamous(79;1091 1253 12329 31680 40677)												.	PRKDC-1515	1	Deletion - In frame(1)	NS(1)	.						.						118	122	121					8																	48826505		1962	4142	6104	SO:0001587	stop_gained	5591	.			TGACTCGAGGCAG		CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.2737C>T	8.37:g.48826505G>A	ENSP00000313420:p.Arg913*	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	187	58	.	0	0	0	0	0	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Nonsense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	G	41	8.534688	0.98852	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	.	.	.	4.7	4.7	0.59300	.	0.071778	0.56097	D	0.000028	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.9989	0.89193	0.0:0.0:1.0:0.0	.	.	.	.	X	913	.	ENSP00000313420:R913X	R	-	1	2	PRKDC	48989058	1.000000	0.71417	0.988000	0.46212	0.673000	0.39480	7.364000	0.79526	2.291000	0.77112	0.563000	0.77884	CGA	.		0.428	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640		A	48826505	G	A	48826505	4	1	69	1	0	0	0	0	0	1	0	0	12550	1066	37	1	9900	1	PRKDC	8	48826505	Nonsense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	23110637	48826505	97537517	69	6599											
NCOA2	10499	hgsc.bcm.edu;broad.mit.edu	37	chr8	71126196	71126196	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaagattgcacatttgtcAggtttgaagttaaagttgtc	11	17	9	4	0	1	2	1	1	0	1	2	2	1	2	0	1	1	4	0	1	4	7	rs557435092		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:71126196A>C	ENST00000452400.2	-	4	382	c.201T>G	c.(199-201)ccT>ccG	p.P67P		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	67	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CACATTTGTCAGGTTTGAAGT	0.303			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P67P		.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2-639	0			c.T201G						.						97	84	88					8																	71126196		1788	4071	5859	SO:0001819	synonymous_variant	10499	exon4			TTTGTCAGGTTTG	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.201T>G	8.37:g.71126196A>C		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	46	15	NM_006540	0	0	0	3	3	Q14CD2	Silent	SNP	ENST00000452400.2	37	CCDS47872.1																																																																																			.		0.303	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			C	71126196	A	C	71126196	2	2	69	1	0	0	0	0	0	0	0	1	10255	175	7	5		5	NCOA2	8	71126196	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	22299691	71126196	75237826	70	6600											
SYBU	55638	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	110587763	110587763	+	Frame_Shift_Del	DEL	T	T	-																															tggaatgcacaagctccaggTcaccagattctgtggtggtg																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:110587763delT	ENST00000422135.1	-	8	1879	c.1364delA	c.(1363-1365)gacfs	p.D455fs	SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000528331.1_Frame_Shift_Del_p.D336fs|SYBU_ENST00000440310.1_Frame_Shift_Del_p.D455fs|SYBU_ENST00000446070.2_Frame_Shift_Del_p.D454fs|SYBU_ENST00000529175.1_Frame_Shift_Del_p.D249fs|SYBU_ENST00000408908.2_Frame_Shift_Del_p.D455fs|SYBU_ENST00000399066.3_Frame_Shift_Del_p.D452fs|SYBU_ENST00000532779.1_Frame_Shift_Del_p.D387fs|SYBU_ENST00000424158.2_Frame_Shift_Del_p.D460fs|SYBU_ENST00000533065.1_Frame_Shift_Del_p.D336fs|SYBU_ENST00000276646.9_Frame_Shift_Del_p.D455fs|SYBU_ENST00000533895.1_Frame_Shift_Del_p.D454fs|SYBU_ENST00000533171.1_Frame_Shift_Del_p.D455fs|SYBU_ENST00000408889.3_Frame_Shift_Del_p.D336fs|SYBU_ENST00000419099.1_Frame_Shift_Del_p.D454fs|SYBU_ENST00000433638.1_Frame_Shift_Del_p.D455fs|SYBU_ENST00000528647.1_Frame_Shift_Del_p.D454fs|SYBU_ENST00000529690.1_Frame_Shift_Del_p.D325fs	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	455					regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						AAGCTCCAGGTCACCAGATTC	0.577																																					p.D455fs		.											.	SYBU-227	0			c.1364delA						.						133	137	136					8																	110587763		2102	4215	6317	SO:0001589	frameshift_variant	55638	exon8			.	AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"syntaphilin-like"	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.1364delA	8.37:g.110587763delT	ENSP00000407118:p.Asp455fs	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	122	40	NM_001099752	0	0	0	0	0	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Frame_Shift_Del	DEL	ENST00000422135.1	37	CCDS47912.1																																																																																			.		0.577	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786		-	110587763	T	-	110587763	7	5	69	1	0	1	0	1	0	0	0	0	15459	1667	58	0	631	0	SYBU	8	110587763	Frame_Shift_Del	DEL	T	TCGA-BQ-5885-01A-11D-1589-08	39461567	110587763	35776259	71	6601											
PHF20L1	51105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133854952	133854952	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaacttatataacaagtgaGcatagctatcaaaagccaca	18	8	7	8	0	1	1	1	1	0	0	1	2	1	2	1	1	5	2	1	1	9	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:133854952G>C	ENST00000395386.2	+	19	2879	c.2580G>C	c.(2578-2580)gaG>gaC	p.E860D	AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000220847.7_Missense_Mutation_p.E247D|AF230666.2_ENST00000429151.1_RNA|PHF20L1_ENST00000395390.2_Missense_Mutation_p.E835D	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	860							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TAACAAGTGAGCATAGCTATC	0.398																																					p.E860D		.											.	PHF20L1-92	0			c.G2580C						.						74	70	71					8																	133854952		1849	4099	5948	SO:0001583	missense	51105	exon19			AAGTGAGCATAGC	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2580G>C	8.37:g.133854952G>C	ENSP00000378784:p.Glu860Asp	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	104	49	NM_016018	0	0	5	10	5	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803425	0.70682	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	T;T	0.54479	0.61;0.57	5.11	1.23	0.21249	.	0.365573	0.21339	U	0.076161	T	0.66655	0.2811	M	0.76574	2.34	0.33710	D	0.6156	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.967	T	0.71424	-0.4597	10	0.39692	T	0.17	-4.2073	9.4695	0.38833	0.2956:0.0:0.7044:0.0	.	835;860	F8W9L8;A8MW92	.;P20L1_HUMAN	D	860;247;835	ENSP00000378784:E860D;ENSP00000378788:E835D	ENSP00000220847:E247D	E	+	3	2	PHF20L1	133924134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.184000	0.32053	0.261000	0.21753	0.650000	0.86243	GAG	.		0.398	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		C	133854952	G	C	133854952	3	2	69	1	0	0	0	0	1	0	0	0	11858	962	34	4	2746	4	PHF20L1	8	133854952	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	23267189	133854952	12509070	72	6602											
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144944250	144944250	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatggccactggcatggggaGgtggtggtggctggtggggt	5	9	22	5	0	0	0	0	0	0	0	0	1	0	1	1	11	0	2	1	11	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:144944250G>T	ENST00000525985.1	-	2	3243	c.3172C>A	c.(3172-3174)Ctc>Atc	p.L1058I				P58107	EPIPL_HUMAN	epiplakin 1	1058						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGCATGGGGAGGTGGTGGTGG	0.622																																					p.L1058I		.											.	EPPK1-25	0			c.C3172A						.						33	38	36					8																	144944250		2118	4239	6357	SO:0001583	missense	83481	exon1			TGGGGAGGTGGTG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.3172C>A	8.37:g.144944250G>T	ENSP00000436337:p.Leu1058Ile	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	22	6	NM_031308	0	0	0	1	1	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	G	12.43	1.936941	0.34189	.	.	ENSG00000227184	ENST00000525985	T	0.79247	-1.25	4.4	2.49	0.30216	.	.	.	.	.	T	0.61813	0.2377	L	0.31207	0.915	0.25590	N	0.98671	B	0.27700	0.186	B	0.24701	0.055	T	0.46034	-0.9220	9	0.19590	T	0.45	.	7.0089	0.24851	0.0:0.32:0.5041:0.1759	.	1058	E9PPU0	.	I	1058	ENSP00000436337:L1058I	ENSP00000436337:L1058I	L	-	1	0	EPPK1	145016238	0.002000	0.14202	0.982000	0.44146	0.140000	0.21249	-0.269000	0.08596	2.242000	0.73789	0.563000	0.77884	CTC	.		0.622	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144944250	G	T	144944250	3	4	69	1	0	0	0	0	1	0	0	0	5203	1000	35	4	4094	4	EPPK1	8	144944250	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	11089298	144944250	1419772	73	6603											
ARHGAP39	80728	hgsc.bcm.edu;broad.mit.edu	37	chr8	145806407	145806407	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggcgcgcggggactccgtgTtctgcttcagcgtctgcagc	4	9	15	13	5	3	0	1	0	2	0	4	1	4	1	1	3	4	3	1	3	0	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:145806407T>C	ENST00000276826.5	-	2	536	c.335A>G	c.(334-336)aAc>aGc	p.N112S	ARHGAP39_ENST00000377307.2_Missense_Mutation_p.N112S|ARHGAP39_ENST00000540274.1_Missense_Mutation_p.N112S			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	112					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						GGACTCCGTGTTCTGCTTCAG	0.706																																					p.N112S		.											.	ARHGAP39-90	0			c.A335G						.						14	15	15					8																	145806407		2190	4288	6478	SO:0001583	missense	80728	exon4			TCCGTGTTCTGCT		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.335A>G	8.37:g.145806407T>C	ENSP00000276826:p.Asn112Ser	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_025251	0	0	0	0	0	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	37		.	.	.	.	.	.	.	.	.	.	T	14.91	2.676795	0.47886	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.14022	2.54;2.54;2.54	5.4	4.25	0.50352	.	0.385486	0.28865	N	0.013896	T	0.10680	0.0261	N	0.20574	0.59	0.33264	D	0.560137	B;B	0.28512	0.111;0.214	B;B	0.37239	0.074;0.244	T	0.17930	-1.0353	10	0.37606	T	0.19	-3.2953	7.9013	0.29736	0.0:0.0945:0.0:0.9055	.	112;112	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	S	112	ENSP00000276826:N112S;ENSP00000366522:N112S;ENSP00000445075:N112S	ENSP00000276826:N112S	N	-	2	0	ARHGAP39	145777215	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	0.946000	0.29069	0.882000	0.36016	0.445000	0.29226	AAC	.		0.706	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			C	145806407	T	C	145806407	3	2	69	1	0	0	0	0	1	0	0	0	884	1725	60	3	3049	3	ARHGAP39	8	145806407	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	862157	145806407	557615	74	6604											
SMC5	23137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	72901129	72901129	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttacaggcaacagatattaAggaggcatctcaaaaatgca	17	9	8	7	0	1	1	1	0	1	1	2	2	1	2	0	3	3	3	0	3	6	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr9:72901129A>T	ENST00000361138.5	+	8	1053	c.995A>T	c.(994-996)aAg>aTg	p.K332M		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	332					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						ACAGATATTAAGGAGGCATCT	0.353																																					p.K332M		.											.	SMC5-229	0			c.A995T						.						65	74	71					9																	72901129		2203	4300	6503	SO:0001583	missense	23137	exon8			ATATTAAGGAGGC	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"Structural maintenance of chromosomes proteins"	20465	protein-coding gene	gene with protein product		609386	"SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.995A>T	9.37:g.72901129A>T	ENSP00000354957:p.Lys332Met	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	104	37	NM_015110	0	0	1	4	3	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.450498	0.63290	.	.	ENSG00000198887	ENST00000361138	T	0.20598	2.06	5.34	2.93	0.34026	RecF/RecN/SMC (1);	0.052632	0.64402	D	0.000001	T	0.37999	0.1024	M	0.66939	2.045	0.54753	D	0.999983	D	0.89917	1.0	D	0.81914	0.995	T	0.10382	-1.0632	10	0.54805	T	0.06	-18.9526	6.4737	0.22024	0.7458:0.0:0.1261:0.1282	.	332	Q8IY18	SMC5_HUMAN	M	332	ENSP00000354957:K332M	ENSP00000354957:K332M	K	+	2	0	SMC5	72090949	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.657000	0.37366	0.949000	0.37715	0.402000	0.26972	AAG	.		0.353	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		T	72901129	A	T	72901129	3	4	69	1	0	0	0	0	1	0	0	0	14818	72	3	5	1025	5	SMC5	9	72901129	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08		72901129	68312302	75	6605											
PAPPA	5069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	118997553	118997553	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgagctggagttcctctaccCcttggtccctgagtctctga	5	12	10	14	1	2	2	0	2	2	0	5	4	4	3	4	2	2	2	4	2	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr9:118997553C>G	ENST00000328252.3	+	7	2738	c.2369C>G	c.(2368-2370)cCc>cGc	p.P790R	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	790					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TTCCTCTACCCCTTGGTCCCT	0.567																																					p.P790R		.											.	PAPPA-77	0			c.C2369G						.						116	93	101					9																	118997553		2203	4300	6503	SO:0001583	missense	5069	exon7			TCTACCCCTTGGT		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2369C>G	9.37:g.118997553C>G	ENSP00000330658:p.Pro790Arg	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	85	31	NM_002581	0	0	0	0	0	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446744	0.63178	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.01947	4.54	6.04	6.04	0.98038	.	0.148253	0.64402	D	0.000007	T	0.14184	0.0343	M	0.74881	2.28	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.921	T	0.00005	-1.2530	10	0.87932	D	0	-8.2519	20.5948	0.99439	0.0:1.0:0.0:0.0	.	234;790	E7EMD3;Q13219	.;PAPP1_HUMAN	R	790;234	ENSP00000330658:P790R	ENSP00000330658:P790R	P	+	2	0	PAPPA	118037374	1.000000	0.71417	0.819000	0.32651	0.753000	0.42808	7.779000	0.85648	2.873000	0.98535	0.563000	0.77884	CCC	.		0.567	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		G	118997553	C	G	118997553	3	3	69	1	0	0	0	0	1	0	0	0	11458	623	22	4	2395	4	PAPPA	9	118997553	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	46096424	118997553	22215878	76	6606											
ITGA8	8516	broad.mit.edu	37	chr10	15713632	15713632	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atccccagtaaactccccagCagcaactgagtatcctgttt	11	10	6	14	0	0	1	0	1	0	0	3	1	3	1	5	0	4	5	5	0	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:15713632C>A	ENST00000378076.3	-	8	1170	c.817G>T	c.(817-819)Gct>Tct	p.A273S		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	273					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						AACTCCCCAGCAGCAACTGAG	0.363																																					p.A273S													.	ITGA8-230	0			c.G817T						.						83	76	79					10																	15713632		2203	4300	6503	SO:0001583	missense	8516	exon8			CCCCAGCAGCAAC	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.817G>T	10.37:g.15713632C>A	ENSP00000367316:p.Ala273Ser	Somatic	98	1		WXS	Illumina HiSeq	Phase_I	69	3	NM_003638	0	0	0	0	0	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.209167	0.79240	.	.	ENSG00000077943	ENST00000378076	T	0.24350	1.86	5.69	5.69	0.88448	.	0.161832	0.56097	D	0.000026	T	0.23210	0.0561	N	0.21142	0.635	0.39281	D	0.964556	D	0.52996	0.957	P	0.46026	0.501	T	0.02975	-1.1087	10	0.14252	T	0.57	.	19.4142	0.94688	0.0:1.0:0.0:0.0	.	273	P53708	ITA8_HUMAN	S	273	ENSP00000367316:A273S	ENSP00000367316:A273S	A	-	1	0	ITGA8	15753638	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	4.353000	0.59411	2.673000	0.90976	0.455000	0.32223	GCT	.		0.363	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		A	15713632	C	A	15713632	3	1	69	1	0	0	0	0	1	0	0	0	7903	710	25	4	2466	4	ITGA8	10	15713632	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		15713632	119821115	77	6607											
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	64960365	64960365	+	Frame_Shift_Del	DEL	A	A	-																															cacagcaggagtcatcctgtAaaaaggattccccagtttgc																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:64960365delA	ENST00000399262.2	-	11	5365	c.5147delT	c.(5146-5148)ttafs	p.L1716fs	JMJD1C_ENST00000399251.1_Intron|JMJD1C_ENST00000542921.1_Frame_Shift_Del_p.L1534fs|JMJD1C_ENST00000402544.1_Frame_Shift_Del_p.L1497fs	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1716					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					GTCATCCTGTAAAAAGGATTC	0.413																																					p.L1716fs		.											.	JMJD1C-275	0			c.5147delT						.						83	76	78					10																	64960365		1855	4105	5960	SO:0001589	frameshift_variant	221037	exon11			.	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.5147delT	10.37:g.64960365delA	ENSP00000382204:p.Leu1716fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	89	32	NM_032776	0	0	0	0	0	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Frame_Shift_Del	DEL	ENST00000399262.2	37	CCDS41532.1																																																																																			.		0.413	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		-	64960365	A	-	64960365	7	5	69	1	0	1	0	1	0	0	0	0	7971	372	13	0	2539	0	JMJD1C	10	64960365	Frame_Shift_Del	DEL	A	TCGA-BQ-5885-01A-11D-1589-08	49246733	64960365	70574382	78	6608											
C10orf27	219793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	72537063	72537063	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagtactttgccccctgcTcccgcagaggctcctccttc	4	11	8	18	1	0	2	0	1	0	1	4	2	3	2	5	1	3	4	5	1	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:72537063T>C	ENST00000299290.1	-	7	925	c.536A>G	c.(535-537)gAg>gGg	p.E179G	TBATA_ENST00000456372.2_Missense_Mutation_p.E179G	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	179					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											TGCCCCCTGCTCCCGCAGAGG	0.637																																					p.E179G		.											.	.	0			c.A536G						.						46	51	49					10																	72537063		2203	4300	6503	SO:0001583	missense	219793	exon7			CCCTGCTCCCGCA	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"chromosome 10 open reading frame 27"	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.536A>G	10.37:g.72537063T>C	ENSP00000299290:p.Glu179Gly	Somatic	91	2		WXS	Illumina HiSeq	Phase_I	76	22	NM_152710	0	0	0	0	0	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	37	CCDS7308.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.088180	0.36855	.	.	ENSG00000166220	ENST00000299290;ENST00000536955;ENST00000456372	T;T	0.24908	1.83;1.83	5.05	2.45	0.29901	.	0.384397	0.22553	N	0.058572	T	0.43344	0.1243	M	0.72479	2.2	0.31044	N	0.716002	D;D;D;D	0.65815	0.995;0.972;0.972;0.972	D;P;P;P	0.65323	0.934;0.797;0.797;0.797	T	0.47209	-0.9135	10	0.59425	D	0.04	-17.1833	8.8124	0.34976	0.0:0.0:0.3731:0.6269	.	199;178;180;179	B7Z8G0;B7ZMN4;B7ZMN5;Q96M53	.;.;.;SPATL_HUMAN	G	179;197;179	ENSP00000299290:E179G;ENSP00000400224:E179G	ENSP00000299290:E179G	E	-	2	0	C10orf27	72207069	0.991000	0.36638	0.462000	0.27118	0.219000	0.24729	2.535000	0.45685	0.834000	0.34852	0.397000	0.26171	GAG	.		0.637	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710		C	72537063	T	C	72537063	3	2	69	1	0	0	0	0	1	0	0	0	1604	1551	54	3	539	3	C10orf27	10	72537063	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	7576698	72537063	62997684	79	6609											
USP54	159195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	75294429	75294429	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtcccctgagaatcagaaGagaagtgactgaccacagac	14	6	10	11	0	1	6	1	3	0	4	2	8	2	6	3	0	0	0	3	0	3	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:75294429G>A	ENST00000339859.4	-	11	1344	c.1244C>T	c.(1243-1245)tCt>tTt	p.S415F	USP54_ENST00000497106.1_Intron|USP54_ENST00000319786.7_Missense_Mutation_p.S415F|USP54_ENST00000408019.1_Missense_Mutation_p.S415F|USP54_ENST00000394811.2_5'UTR|USP54_ENST00000428547.1_Missense_Mutation_p.S265F			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	415					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					AGAATCAGAAGAGAAGTGACT	0.498																																					p.S415F	Colon(195;880 2046 8854 25025 38456)	.											.	USP54-721	0			c.C1244T						.						134	130	131					10																	75294429		1925	4124	6049	SO:0001583	missense	159195	exon10			TCAGAAGAGAAGT	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"Ubiquitin-specific peptidases"	23513	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 29", "ubiquitin specific protease 54"	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.1244C>T	10.37:g.75294429G>A	ENSP00000345216:p.Ser415Phe	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	89	31	NM_152586	0	0	0	0	0	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	ENST00000339859.4	37	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915589	0.92178	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000319786	T;T;T	0.38240	1.25;1.25;1.15	5.54	5.54	0.83059	.	0.801566	0.09945	U	0.735488	T	0.56411	0.1983	L	0.38175	1.15	0.46774	D	0.999197	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.996;0.996;0.997	T	0.54029	-0.8354	10	0.72032	D	0.01	-5.8858	19.5024	0.95100	0.0:0.0:1.0:0.0	.	415;415;415	B7Z7X1;Q70EL1-6;Q70EL1	.;.;UBP54_HUMAN	F	415;415;265;415	ENSP00000345216:S415F;ENSP00000386080:S415F;ENSP00000408714:S265F	ENSP00000326547:S415F	S	-	2	0	USP54	74964435	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.017000	0.93651	2.607000	0.88179	0.655000	0.94253	TCT	.		0.498	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		A	75294429	G	A	75294429	3	1	69	1	0	0	0	0	1	0	0	0	17118	942	33	2	3862	2	USP54	10	75294429	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	2757366	75294429	60240318	80	6610											
PI4K2A	55361	hgsc.bcm.edu;broad.mit.edu	37	chr10	99400806	99400806	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggcccaccgcgagcggaacGagttcccggaggatcctgag	9	4	15	13	5	0	1	0	1	0	0	2	6	2	4	4	4	2	1	4	4	1	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:99400806G>A	ENST00000370631.3	+	1	364	c.307G>A	c.(307-309)Gag>Aag	p.E103K	PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	103					basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		CGAGCGGAACGAGTTCCCGGA	0.731																																					p.E103K		.											.	PI4K2A-226	0			c.G307A						.																																			SO:0001583	missense	55361	exon1			CGGAACGAGTTCC	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.307G>A	10.37:g.99400806G>A	ENSP00000359665:p.Glu103Lys	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	17	6	NM_018425	0	0	0	0	0	D3DR59|Q9NSG8	Missense_Mutation	SNP	ENST00000370631.3	37	CCDS7469.1	.	.	.	.	.	.	.	.	.	.	G	8.587	0.883606	0.17467	.	.	ENSG00000155252	ENST00000370631	.	.	.	3.53	3.53	0.40419	.	0.171047	0.51477	D	0.000098	T	0.25938	0.0632	N	0.11427	0.14	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.10359	-1.0633	9	0.06891	T	0.86	-7.6782	7.9672	0.30107	0.1963:0.0:0.8037:0.0	.	103	Q9BTU6	P4K2A_HUMAN	K	103	.	ENSP00000359665:E103K	E	+	1	0	PI4K2A	99390796	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	2.327000	0.43858	1.808000	0.52836	0.313000	0.20887	GAG	.		0.731	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425		A	99400806	G	A	99400806	3	1	69	1	0	0	0	0	1	0	0	0	11897	1059	37	1	309	1	PI4K2A	10	99400806	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	24106377	99400806	36133941	81	6611											
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104130513	104130513	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgagaccatctataccacCtctgtgttcaggcacaagat	11	11	7	12	1	3	2	1	0	2	2	4	3	3	2	3	1	1	2	3	1	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:104130513C>A	ENST00000369983.3	+	29	3813	c.3553C>A	c.(3553-3555)Ctc>Atc	p.L1185I		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1185					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TCTATACCACCTCTGTGTTCA	0.552																																					p.L1186I		.											.	GBF1-91	0			c.C3556A						.						225	181	196					10																	104130513		2203	4300	6503	SO:0001583	missense	8729	exon29			TACCACCTCTGTG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.3553C>A	10.37:g.104130513C>A	ENSP00000359000:p.Leu1185Ile	Somatic	239	0		WXS	Illumina HiSeq	Phase_I	179	62	NM_001199378	0	0	3	4	1	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541954	0.65198	.	.	ENSG00000107862	ENST00000369983	T	0.10573	2.86	5.36	2.53	0.30540	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.29908	0.895	0.53005	D	0.999965	D;D;D	0.63880	0.985;0.968;0.993	P;P;D	0.70016	0.614;0.53;0.967	T	0.09862	-1.0655	10	0.12766	T	0.61	-10.2271	9.4682	0.38826	0.0:0.7169:0.0:0.2831	.	1185;1185;1185	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	I	1185	ENSP00000359000:L1185I	ENSP00000359000:L1185I	L	+	1	0	GBF1	104120503	0.999000	0.42202	0.991000	0.47740	0.997000	0.91878	2.530000	0.45641	0.402000	0.25451	0.655000	0.94253	CTC	.		0.552	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			A	104130513	C	A	104130513	3	1	69	1	0	0	0	0	1	0	0	0	6291	681	24	4	3663	4	GBF1	10	104130513	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	4729707	104130513	31404234	82	6612											
CNNM2	54805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104679308	104679308	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtatcgtcatcttcggagaGatcgtgccccaggccatctg	7	10	12	12	3	3	1	1	0	2	1	6	3	3	2	3	3	1	1	3	3	1	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:104679308G>T	ENST00000369878.4	+	1	1259	c.1071G>T	c.(1069-1071)gaG>gaT	p.E357D	CNNM2_ENST00000369875.3_Missense_Mutation_p.E357D|CNNM2_ENST00000433628.2_Missense_Mutation_p.E357D	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	357	DUF21.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TCTTCGGAGAGATCGTGCCCC	0.607																																					p.E357D		.											.	CNNM2-515	0			c.G1071T						.						76	75	75					10																	104679308		2203	4300	6503	SO:0001583	missense	54805	exon1			CGGAGAGATCGTG	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"cyclin M2"	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1071G>T	10.37:g.104679308G>T	ENSP00000358894:p.Glu357Asp	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	125	42	NM_199076	0	0	0	0	0	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.594054	0.46214	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	D;D;D	0.94576	-3.46;-3.46;-3.46	4.32	2.42	0.29668	Domain of unknown function DUF21 (1);	0.112531	0.64402	D	0.000007	D	0.97642	0.9227	H	0.95950	3.745	0.80722	D	1	D;D;D	0.89917	0.985;0.988;1.0	D;D;D	0.91635	0.972;0.984;0.999	D	0.96198	0.9143	10	0.87932	D	0	.	8.1171	0.30950	0.2718:0.0:0.7282:0.0	.	357;357;357	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	D	357	ENSP00000392875:E357D;ENSP00000358891:E357D;ENSP00000358894:E357D	ENSP00000286899:E357D	E	+	3	2	CNNM2	104669298	1.000000	0.71417	0.998000	0.56505	0.690000	0.40134	2.046000	0.41260	0.262000	0.21774	0.561000	0.74099	GAG	.		0.607	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104679308	G	T	104679308	3	4	69	1	0	0	0	0	1	0	0	0	3619	933	33	4	1073	4	CNNM2	10	104679308	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	548795	104679308	30855439	83	6613											
SORCS1	114815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	108412294	108412294	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cgccatcagtgcaattattgGaaaccaccttcctgtaccta	11	11	6	13	1	1	0	1	0	0	0	2	1	2	1	5	1	3	2	5	1	5	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:108412294G>A	ENST00000263054.6	-	18	2328	c.2321C>T	c.(2320-2322)tCc>tTc	p.S774F	SORCS1_ENST00000369698.1_Missense_Mutation_p.S309F|SORCS1_ENST00000344440.6_Missense_Mutation_p.S774F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	774					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GCAATTATTGGAAACCACCTT	0.468																																					p.S774F		.											.	SORCS1-153	0			c.C2321T						.						112	106	108					10																	108412294		2203	4300	6503	SO:0001583	missense	114815	exon18			TTATTGGAAACCA	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2321C>T	10.37:g.108412294G>A	ENSP00000263054:p.Ser774Phe	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	116	37	NM_001206572	0	0	0	0	0	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482881	0.84747	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.67523	-0.27;-0.27;-0.27	5.74	5.74	0.90152	VPS10 (1);PKD domain (1);	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	M	0.75777	2.31	0.45979	D	0.998792	D;D;D;D;D	0.58620	0.972;0.983;0.983;0.972;0.983	P;D;D;P;D	0.65684	0.825;0.937;0.915;0.866;0.937	T	0.80571	-0.1323	9	.	.	.	-16.8758	19.9145	0.97053	0.0:0.0:1.0:0.0	.	774;774;774;774;774	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	F	309;774;774	ENSP00000358712:S309F;ENSP00000263054:S774F;ENSP00000345964:S774F	.	S	-	2	0	SORCS1	108402284	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.448000	0.80631	2.709000	0.92574	0.655000	0.94253	TCC	.		0.468	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108412294	G	A	108412294	3	1	69	1	0	0	0	0	1	0	0	0	14962	1174	41	2	1455	2	SORCS1	10	108412294	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	3732986	108412294	27122453	84	6614											
MMP21	118856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	127455494	127455494	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatcctctttggataagaatTaagtactcgatttctgttga	12	16	7	6	1	2	2	0	1	2	1	4	4	3	3	1	1	1	2	1	1	5	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:127455494T>G	ENST00000368808.3	-	7	1446	c.1447A>C	c.(1447-1449)Aat>Cat	p.N483H		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	483					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	GGATAAGAATTAAGTACTCGA	0.303																																					p.N483H		.											.	MMP21-228	0			c.A1447C						.						67	70	69					10																	127455494		2203	4300	6503	SO:0001583	missense	118856	exon7			AAGAATTAAGTAC	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1447A>C	10.37:g.127455494T>G	ENSP00000357798:p.Asn483His	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	98	27	NM_147191	0	0	0	0	0	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	37	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.271658	0.59649	.	.	ENSG00000154485	ENST00000368808	T	0.02446	4.29	5.95	-4.11	0.03928	Hemopexin/matrixin (2);	0.904543	0.09772	N	0.757825	T	0.02688	0.0081	N	0.19112	0.55	0.09310	N	1	P	0.40282	0.711	P	0.47528	0.549	T	0.38607	-0.9653	10	0.56958	D	0.05	-10.6851	3.1826	0.06589	0.1141:0.3438:0.3474:0.1948	.	483	Q8N119	MMP21_HUMAN	H	483	ENSP00000357798:N483H	ENSP00000357798:N483H	N	-	1	0	MMP21	127445484	0.000000	0.05858	0.000000	0.03702	0.422000	0.31414	-0.140000	0.10342	-0.647000	0.05444	-0.274000	0.10170	AAT	.		0.303	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			G	127455494	T	G	127455494	3	3	69	1	0	0	0	0	1	0	0	0	9685	1754	61	5	266	5	MMP21	10	127455494	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	19043200	127455494	8079253	85	6615											
PHRF1	57661	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	601639	601639	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccgcaaaaagtaagagcTcagcgacaagatctaagaaa	19	5	8	9	2	2	3	1	0	1	3	3	4	3	3	1	0	2	3	1	0	6	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:601639T>C	ENST00000264555.5	+	10	1218	c.1090T>C	c.(1090-1092)Tca>Cca	p.S364P	PHRF1_ENST00000413872.2_Missense_Mutation_p.S363P|PHRF1_ENST00000533464.1_Missense_Mutation_p.S360P|PHRF1_ENST00000416188.2_Missense_Mutation_p.S364P	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	364	Arg-rich.				mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						AAGTAAGAGCTCAGCGACAAG	0.507																																					p.S364P		.											.	PHRF1-22	0			c.T1090C						.						85	94	91					11																	601639		1969	4145	6114	SO:0001583	missense	57661	exon10			AAGAGCTCAGCGA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.1090T>C	11.37:g.601639T>C	ENSP00000264555:p.Ser364Pro	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	59	29	NM_020901	0	0	4	6	2	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	37		.	.	.	.	.	.	.	.	.	.	T	13.18	2.160816	0.38119	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	4.37	0.796	0.18648	.	0.956972	0.08463	N	0.942121	T	0.29652	0.0740	L	0.35414	1.06	0.09310	N	1	B;B;B;B	0.11235	0.002;0.004;0.004;0.002	B;B;B;B	0.14578	0.005;0.011;0.011;0.005	T	0.26155	-1.0111	10	0.33940	T	0.23	-5.4809	5.8681	0.18789	0.0:0.1006:0.4218:0.4776	.	360;363;364;364	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	P	364;363;364;360	ENSP00000264555:S364P;ENSP00000388589:S363P;ENSP00000410626:S364P;ENSP00000431870:S360P	ENSP00000264555:S364P	S	+	1	0	PHRF1	591639	0.001000	0.12720	0.002000	0.10522	0.005000	0.04900	0.583000	0.23849	-0.016000	0.14127	-1.252000	0.01501	TCA	.		0.507	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		C	601639	T	C	601639	3	2	69	1	0	0	0	0	1	0	0	0	11887	1551	54	3	1124	3	PHRF1	11	601639	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		601639	134404877	86	6616											
MUC6	4588	broad.mit.edu	37	chr11	1027279	1027279	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtccctcaccaggtgatgccGttgatgacagtggactgctc	7	10	12	12	1	1	3	1	3	0	0	3	4	2	4	3	2	2	2	3	2	0	1	rs376692745		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:1027279G>A	ENST00000421673.2	-	17	2270	c.2220C>T	c.(2218-2220)aaC>aaT	p.N740N		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	740					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGGTGATGCCGTTGATGACAG	0.642																																					p.N740N													.	MUC6-23	0			c.C2220T						.			1,4189		0,1,2094	115	134	128		2220	-6.9	0	11		128	2,8394		0,2,4196	no	coding-synonymous	MUC6	NM_005961.2		0,3,6290	AA,AG,GG		0.0238,0.0239,0.0238		740/2440	1027279	3,12583	2095	4198	6293	SO:0001819	synonymous_variant	4588	exon17			GATGCCGTTGATG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.2220C>T	11.37:g.1027279G>A		Somatic	254	0		WXS	Illumina HiSeq	Phase_I	247	6	NM_005961	0	0	0	0	0	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.		0.642	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1027279	G	A	1027279	2	1	69	1	0	0	0	0	0	0	0	1	10005	1136	40	1		1	MUC6	11	1027279	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	425640	1027279	133979237	87	6617											
FAU	740	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64888258	64888258	+	5'Flank	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgacctgtcttcttcttCttcttctcctgtttggccac	2	17	6	16	1	6	0	0	0	6	0	7	1	6	0	4	1	0	1	4	1	0	6	rs3202210		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:64888258C>A	ENST00000279242.2	+	0	0				MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000529639.1_Missense_Mutation_p.K99N|FAU_ENST00000531743.1_Missense_Mutation_p.K99N|FAU_ENST00000279259.3_Nonsense_Mutation_p.E81*|MRPL49_ENST00000526171.1_5'Flank|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000529259.1_3'UTR|FAU_ENST00000527548.1_Missense_Mutation_p.K99N|FAU_ENST00000525297.1_Missense_Mutation_p.K64N	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						TCTTCTTCTTCTTCTTCTCCT	0.557																																					p.K99N		.											.	FAU-90	0			c.G297T						.						82	88	86					11																	64888258		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon5			CTTCTTCTTCTTC		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		11.37:g.64888258C>A	Exception_encountered	Somatic	254	0		WXS	Illumina HiSeq	Phase_I	220	80	NM_001997	1	1	1975	3553	1570	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	37	CCDS8096.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.0|21.0	4.082357|4.082357	0.76528|0.76528	.|.	.|.	ENSG00000149806|ENSG00000149806	ENST00000279259|ENST00000529639;ENST00000531743;ENST00000525297;ENST00000527548;ENST00000526555	.|T;T;T;T;T	.|0.50277	.|0.75;0.75;0.75;0.75;0.75	5.7|5.7	4.79|4.79	0.61399|0.61399	.|.	.|0.045214	.|0.85682	.|D	.|0.000000	.|T	.|0.72503	.|0.3468	M|M	0.93016|0.93016	3.37|3.37	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.79541	.|-0.1761	.|8	0.25106|0.72032	T|D	0.35|0.01	.|.	12.7196|12.7196	0.57134|0.57134	0.0:0.9196:0.0:0.0804|0.0:0.9196:0.0:0.0804	.|.	.|.	.|.	.|.	X|N	81|99;99;64;99;99	.|ENSP00000435370:K99N;ENSP00000431822:K99N;ENSP00000436110:K64N;ENSP00000434440:K99N;ENSP00000433139:K99N	ENSP00000279259:E81X|ENSP00000436110:K64N	E|K	-|-	1|3	0|2	FAU|FAU	64644834|64644834	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	2.548000|2.548000	0.45794|0.45794	1.411000|1.411000	0.46957|0.46957	0.655000|0.655000	0.94253|0.94253	GAA|AAG	.		0.557	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		A	64888258	C	A	64888258	1	1	69	0	1	0	0	0	0	0	0	0	5713	912	32	4		4	FAU	11	64888258	5'Flank	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	63860979	64888258	70118258	88	6618											
DPP3	10072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66260242	66260242	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagtttgagcggctggtggcGagcgcagagcagctgctgaa	9	7	17	8	3	0	3	0	2	0	1	0	4	0	3	0	3	5	6	0	3	2	1	rs200674271		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:66260242G>A	ENST00000360510.2	+	10	1109	c.1044G>A	c.(1042-1044)gcG>gcA	p.A348A	DPP3_ENST00000453114.1_Silent_p.A348A|DPP3_ENST00000531863.1_Silent_p.A368A|DPP3_ENST00000530165.1_Silent_p.A318A|DPP3_ENST00000532677.1_Silent_p.A367A|DPP3_ENST00000533799.1_3'UTR|DPP3_ENST00000541961.1_Silent_p.A348A			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	348					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						GGCTGGTGGCGAGCGCAGAGC	0.602																																					p.A348A		.											.	DPP3-46	0			c.G1044A						.						95	89	91					11																	66260242		2200	4295	6495	SO:0001819	synonymous_variant	10072	exon10			GGTGGCGAGCGCA	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.1044G>A	11.37:g.66260242G>A		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	149	64	NM_130443	0	0	1	4	3	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Silent	SNP	ENST00000360510.2	37	CCDS8141.1																																																																																			.		0.602	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			A	66260242	G	A	66260242	2	1	69	1	0	0	0	0	0	0	0	1	4739	1045	37	1		1	DPP3	11	66260242	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1371984	66260242	68746274	89	6619											
FOLR2	2350	hgsc.bcm.edu	37	chr11	71932098	71932098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctggggccctggatccAgcaggtagggtgtctccccc	6	7	13	15	0	1	0	0	0	1	0	3	1	2	1	5	5	2	2	5	5	2	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:71932098A>G	ENST00000298223.6	+	3	522	c.335A>G	c.(334-336)cAg>cGg	p.Q112R	FOLR2_ENST00000454954.2_Missense_Mutation_p.Q71R|FOLR2_ENST00000449475.2_Missense_Mutation_p.Q129R	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	112				IQ -> VR (in Ref. 6; AA sequence). {ECO:0000305}.	folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)			breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	CCCTGGATCCAGCAGGTAGGG	0.637																																					p.Q112R		.											.	FOLR2-290	0			c.A335G						.						17	18	18					11																	71932098		2200	4291	6491	SO:0001583	missense	2350	exon3			GGATCCAGCAGGT	AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.335A>G	11.37:g.71932098A>G	ENSP00000298223:p.Gln112Arg	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_001113535	0	0	0	0	0	Q05CA5|Q6GTE8	Missense_Mutation	SNP	ENST00000298223.6	37	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	N	8.068	0.769589	0.15983	.	.	ENSG00000165457	ENST00000449475;ENST00000298223;ENST00000454954;ENST00000539412;ENST00000536778;ENST00000535625;ENST00000321324;ENST00000538353	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	4.37	-0.643	0.11482	Folate receptor-like (1);	0.224016	0.38005	N	0.001858	T	0.68824	0.3043	L	0.53249	1.67	0.23023	N	0.998413	B	0.17038	0.02	B	0.25405	0.06	T	0.54450	-0.8292	10	0.25106	T	0.35	.	9.9831	0.41826	0.6851:0.0:0.3149:0.0	.	112	P14207	FOLR2_HUMAN	R	129;112;71;123;127;112;125;112	ENSP00000405638:Q129R;ENSP00000298223:Q112R;ENSP00000414094:Q71R;ENSP00000441547:Q123R;ENSP00000438568:Q127R;ENSP00000444794:Q112R;ENSP00000321957:Q125R;ENSP00000440337:Q112R	ENSP00000298223:Q112R	Q	+	2	0	FOLR2	71609746	0.010000	0.17322	0.901000	0.35422	0.462000	0.32619	0.950000	0.29122	-0.662000	0.05338	-1.815000	0.00603	CAG	.		0.637	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		G	71932098	A	G	71932098	3	3	69	1	0	0	0	0	1	0	0	0	6001	188	7	3	341	3	FOLR2	11	71932098	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	5671856	71932098	63074418	90	6620											
DGAT2	84649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	75509461	75509461	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtgccctactccaagccCatcaccactgttggtaagcc	8	9	8	16	0	1	0	1	0	0	0	2	0	2	0	5	2	4	2	5	2	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:75509461C>T	ENST00000228027.7	+	7	1259	c.999C>T	c.(997-999)ccC>ccT	p.P333P	DGAT2_ENST00000376262.3_Silent_p.P290P|RP11-535A19.1_ENST00000534354.1_RNA	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	333					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					ACTCCAAGCCCATCACCACTG	0.552																																					p.P333P	Melanoma(35;811 1096 8354 24009 39363)	.											.	DGAT2-226	0			c.C999T						.						48	43	45					11																	75509461		2200	4293	6493	SO:0001819	synonymous_variant	84649	exon7			CAAGCCCATCACC		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"diacylglycerol O-acyltransferase homolog 2 (mouse)"			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.999C>T	11.37:g.75509461C>T		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	51	17	NM_032564	0	0	0	0	0	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Silent	SNP	ENST00000228027.7	37	CCDS31642.1																																																																																			.		0.552	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		T	75509461	C	T	75509461	2	4	69	1	0	0	0	0	0	0	0	1	4469	581	21	2		2	DGAT2	11	75509461	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	3577363	75509461	59497055	91	6621											
CNTN5	53942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	99690367	99690367	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catctctctttggttccaaaAccagaccacgatacagcagc	12	9	6	14	1	2	1	0	0	2	1	4	2	3	1	3	1	4	2	3	1	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:99690367A>C	ENST00000524871.1	+	4	438	c.148A>C	c.(148-150)Acc>Ccc	p.T50P	CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000279463.3_Missense_Mutation_p.T50P|CNTN5_ENST00000527185.1_Missense_Mutation_p.T50P|CNTN5_ENST00000528682.1_Missense_Mutation_p.T50P	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	50					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TGGTTCCAAAACCAGACCACG	0.423																																					p.T50P		.											.	CNTN5-366	0			c.A148C						.						115	117	116					11																	99690367		1906	4138	6044	SO:0001583	missense	53942	exon3			TCCAAAACCAGAC	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.148A>C	11.37:g.99690367A>C	ENSP00000435637:p.Thr50Pro	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	107	13	NM_001243270	0	0	0	0	0	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.642177	0.29157	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	T;T;T;T	0.56941	0.43;0.5;0.5;0.5	5.06	-2.19	0.07015	.	1.005590	0.08006	N	0.989611	T	0.28699	0.0711	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23583	-1.0184	10	0.62326	D	0.03	.	1.2696	0.02018	0.5048:0.1176:0.1378:0.2399	.	50;50	E9PKE8;O94779	.;CNTN5_HUMAN	P	50	ENSP00000433575:T50P;ENSP00000436185:T50P;ENSP00000435637:T50P;ENSP00000279463:T50P	ENSP00000279463:T50P	T	+	1	0	CNTN5	99195577	0.217000	0.23597	0.017000	0.16124	0.764000	0.43329	0.669000	0.25142	-0.145000	0.11294	0.528000	0.53228	ACC	.		0.423	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		C	99690367	A	C	99690367	3	2	69	1	0	0	0	0	1	0	0	0	3650	43	2	5	154	5	CNTN5	11	99690367	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	24180906	99690367	35316149	92	6622											
BCL9L	283149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118771686	118771686	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcccggtgagcccatctgAttaatactgatggtgaggtc	9	11	12	9	1	1	4	0	4	1	0	2	4	1	4	2	3	3	0	2	3	2	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:118771686A>C	ENST00000334801.3	-	6	3730	c.2766T>G	c.(2764-2766)aaT>aaG	p.N922K	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	922	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		AGCCCATCTGATTAATACTGA	0.632																																					p.N922K		.											.	BCL9L-229	0			c.T2766G						.						62	60	61					11																	118771686		2200	4295	6495	SO:0001583	missense	283149	exon6			CATCTGATTAATA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2766T>G	11.37:g.118771686A>C	ENSP00000335320:p.Asn922Lys	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_182557	0	0	3	6	3	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.982733	0.34942	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	T	0.66280	-0.2	4.48	-0.626	0.11544	.	0.114359	0.38663	N	0.001612	T	0.39009	0.1062	N	0.19112	0.55	0.45129	D	0.998148	P;P	0.44734	0.728;0.842	B;B	0.39217	0.294;0.236	T	0.14090	-1.0485	10	0.54805	T	0.06	-7.3556	6.4799	0.22057	0.2778:0.1784:0.5439:0.0	.	917;922	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	K	922;885;215;922;922	ENSP00000335320:N922K	ENSP00000335320:N922K	N	-	3	2	BCL9L	118276896	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.052000	0.30429	-0.032000	0.13758	0.533000	0.62120	AAT	.		0.632	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		C	118771686	A	C	118771686	3	2	69	1	0	0	0	0	1	0	0	0	1383	330	12	5	1745	5	BCL9L	11	118771686	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	19081319	118771686	16234830	93	6623											
OR8D1	283159	broad.mit.edu	37	chr11	124179984	124179984	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctctgaggagcggatgtGaaggatgctgtagaggatga	10	8	17	6	1	1	4	0	3	1	1	1	8	1	8	1	4	2	2	1	4	2	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:124179984G>T	ENST00000357821.2	-	1	749	c.679C>A	c.(679-681)Cac>Aac	p.H227N		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	227						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GAGCGGATGTGAAGGATGCTG	0.488																																					p.H227N													.	OR8D1-71	0			c.C679A						.						65	54	58					11																	124179984		2201	4299	6500	SO:0001583	missense	283159	exon1			GGATGTGAAGGAT	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.679C>A	11.37:g.124179984G>T	ENSP00000350474:p.His227Asn	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	40	3	NM_001002917	0	0	0	0	0	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	37	CCDS31706.1	.	.	.	.	.	.	.	.	.	.	g	10.44	1.352111	0.24512	.	.	ENSG00000196341	ENST00000357821	T	0.00069	8.77	4.29	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	0.990146	0.08180	U	0.985687	T	0.00178	0.0005	L	0.43923	1.385	0.09310	N	1	B	0.27264	0.173	B	0.32022	0.139	T	0.18147	-1.0346	10	0.62326	D	0.03	.	8.1084	0.30900	0.0:0.1281:0.3546:0.5173	.	227	Q8WZ84	OR8D1_HUMAN	N	227	ENSP00000350474:H227N	ENSP00000350474:H227N	H	-	1	0	OR8D1	123685194	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	-0.284000	0.08422	0.409000	0.25649	0.508000	0.49915	CAC	.		0.488	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		T	124179984	G	T	124179984	3	4	69	1	0	0	0	0	1	0	0	0	11257	1290	45	4	250	4	OR8D1	11	124179984	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	5408298	124179984	10826532	94	6624											
OR8B8	26493	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	124310919	124310919	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagggggatctggactccCggttggtcagttaagcctgc	8	9	15	9	1	2	1	1	0	1	1	3	3	3	3	2	5	2	2	2	5	2	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:124310919C>T	ENST00000328064.2	-	1	135	c.63G>A	c.(61-63)ccG>ccA	p.P21P		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	21					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TCTGGACTCCCGGTTGGTCAG	0.502																																					p.P21P		.											.	OR8B8-69	0			c.G63A						.						62	61	61					11																	124310919		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GACTCCCGGTTGG	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.63G>A	11.37:g.124310919C>T		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	76	28	NM_012378	0	0	0	0	0	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	37	CCDS8446.1																																																																																			.		0.502	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310919	C	T	124310919	2	4	69	1	0	0	0	0	0	0	0	1	11256	639	23	1		1	OR8B8	11	124310919	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	130935	124310919	10695597	95	6625											
C3AR1	719	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	8212439	8212439	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcgatccaggctaatggCagtaagcaggaagacactgg	14	5	13	9	1	0	1	0	0	0	1	1	3	1	2	1	4	2	4	1	4	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:8212439C>T	ENST00000307637.4	-	2	546	c.343G>A	c.(343-345)Gcc>Acc	p.A115T		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	115					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		AGGCTAATGGCAGTAAGCAGG	0.517																																					p.A115T		.											.	C3AR1-227	0			c.G343A						.						186	151	163					12																	8212439		2203	4300	6503	SO:0001583	missense	719	exon2			TAATGGCAGTAAG	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.343G>A	12.37:g.8212439C>T	ENSP00000302079:p.Ala115Thr	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	80	22	NM_004054	0	0	4	4	0	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	37	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059489	0.55325	.	.	ENSG00000171860	ENST00000307637;ENST00000546241	T;T	0.44482	0.92;0.92	5.64	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.379197	0.23680	N	0.045625	T	0.39835	0.1093	L	0.54965	1.715	0.40028	D	0.975498	P	0.41475	0.751	B	0.40375	0.327	T	0.26643	-1.0097	10	0.33141	T	0.24	.	12.4036	0.55426	0.0:0.9187:0.0:0.0813	.	115	Q16581	C3AR_HUMAN	T	115	ENSP00000302079:A115T;ENSP00000444500:A115T	ENSP00000302079:A115T	A	-	1	0	C3AR1	8103706	0.993000	0.37304	0.990000	0.47175	0.984000	0.73092	3.119000	0.50422	1.388000	0.46506	0.655000	0.94253	GCC	.		0.517	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			T	8212439	C	T	8212439	3	4	69	1	0	0	0	0	1	0	0	0	2211	710	25	2	1109	2	C3AR1	12	8212439	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		8212439	125639456	96	6626											
DENND5B	160518	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	31586129	31586130	+	In_Frame_Ins	INS	-	-	GGCGAA																															cccaacatgctcagaatgctINSggcgaaggcgttctttcctg																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:31586129_31586130insGGCGAA	ENST00000389082.5	-	8	2329_2330	c.2065_2066insTTCGCC	c.(2065-2067)cag>cTTCGCCag	p.688_689insLR	DENND5B_ENST00000536562.1_In_Frame_Ins_p.723_724insLR|DENND5B_ENST00000354285.4_In_Frame_Ins_p.710_711insLR|DENND5B_ENST00000306833.6_In_Frame_Ins_p.723_724insLR	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	688					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CTCAGAATGCTGGCGAAGGCGT	0.48																																					p.Q689delinsLRQ		.											.	DENND5B-24	0			c.2066_2067insTTCGCC						.																																			SO:0001652	inframe_insertion	160518	exon8			.	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2060_2065dupTTCGCC	12.37:g.31586130_31586135dupGGCGAA	ENSP00000373734:p.Leu687_Arg688dup	Somatic	254	0		WXS	Illumina HiSeq	Phase_I	195	33	NM_144973	0	0	0	0	0	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	In_Frame_Ins	INS	ENST00000389082.5	37	CCDS44857.1																																																																																			.		0.48	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		GGCGAA	31586130	-	GGCGAA	31586129	7	5	69	1	0	1	1	0	0	0	0	0	4448	1580	55	0	1814	0	DENND5B	12	31586129	In_Frame_Ins	INS	-	TCGA-BQ-5885-01A-11D-1589-08	23373690	31586129	102265766	97	6627			1	20		2	2	17	N	T_-	7.183969e-05
DENND5B	160518	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	31586145	31586145	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctggcgaaggcgttcttTcctgcgctgtgcagtggcac	5	11	14	11	3	1	0	0	0	1	0	2	1	2	0	1	3	3	5	1	3	1	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:31586145T>C	ENST00000389082.5	-	8	2314	c.2050A>G	c.(2050-2052)Aaa>Gaa	p.K684E	DENND5B_ENST00000536562.1_Missense_Mutation_p.K719E|DENND5B_ENST00000354285.4_Missense_Mutation_p.K706E|DENND5B_ENST00000306833.6_Missense_Mutation_p.K719E	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	684					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						AGGCGTTCTTTCCTGCGCTGT	0.473																																					p.K684E		.											.	DENND5B-24	0			c.A2050G						.						171	179	177					12																	31586145		2136	4248	6384	SO:0001583	missense	160518	exon8			GTTCTTTCCTGCG	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2050A>G	12.37:g.31586145T>C	ENSP00000373734:p.Lys684Glu	Somatic	240	1		WXS	Illumina HiSeq	Phase_I	190	50	NM_144973	0	0	0	1	1	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.899329	0.52227	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.08008	3.62;3.7;3.7;3.14	4.13	4.13	0.48395	.	0.066714	0.64402	D	0.000015	T	0.09423	0.0232	L	0.41236	1.265	0.42120	D	0.991421	B;B;B	0.25955	0.128;0.017;0.138	B;B;B	0.29663	0.06;0.015;0.105	T	0.13124	-1.0521	10	0.48119	T	0.1	-10.0012	13.3308	0.60485	0.0:0.0:0.0:1.0	.	706;684;719	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	E	684;719;719;706	ENSP00000373734:K684E;ENSP00000306482:K719E;ENSP00000444889:K719E;ENSP00000346238:K706E	ENSP00000306482:K719E	K	-	1	0	DENND5B	31477412	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	5.492000	0.66893	1.732000	0.51606	0.533000	0.62120	AAA	.		0.473	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		C	31586145	T	C	31586145	3	2	69	1	0	0	0	0	1	0	0	0	4448	1792	62	3	1830	3	DENND5B	12	31586145	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	16	31586145	102265750	98	6628			1	20		2	2	17	N	T_-	7.183969e-05
KRT77	374454	hgsc.bcm.edu	37	chr12	53086340	53086341	+	Missense_Mutation	DNP	AG	AG	CA																															actgctgcagggcctcctccAggtcctgcagcttctgccac																								rs150981240|rs200694410	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:53086340_53086341AG>CA	ENST00000341809.3	-	7	1319_1320	c.1291_1292CT>TG	c.(1291-1293)CTg>TGg	p.L431W	KRT77_ENST00000537195.1_Missense_Mutation_p.L198W|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	431	Coil 2.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.Q429fs*17(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						GGCCTCCTCCAGGTCCTGCAGC	0.619																																					p.L431W		.											.	KRT77	1	Deletion - Frameshift(1)	ovary(1)	c.C1291T						.																																			SO:0001583	missense	374454	exon7			CCTCCAGGTCCTG	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"-", "Intermediate filaments type II, keratins (basic)"	20411	protein-coding gene	gene with protein product		611158	"keratin 1B"	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1291_1292delinsCA	12.37:g.53086340_53086341delinsCA	ENSP00000342710:p.Leu431Trp	Somatic	40	1		WXS	Illumina HiSeq	Phase_I	44	4		0	0	0	0	0	Q7RTS8	Missense_Mutation	DNP	ENST00000341809.3	37	CCDS8837.1																																																																																			G|0.996;T|0.004		0.619	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		CA	53086341	AG	CA	53086340	3	2	69	1	0	0	0	0	1	0	0	0	8511	188	7	5	456	5	KRT77	12	53086340	Missense_Mutation	DNP	AG	TCGA-BQ-5885-01A-11D-1589-08	21500195	53086340	80765555	99	6629											
ATF7	11016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53931334	53931334	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtcaaggggcccagcagcAgcctgttgtgaaagaaaaat	14	7	12	8	0	1	2	1	1	0	1	1	2	1	2	2	2	3	3	2	2	4	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:53931334A>T	ENST00000548446.2	-	5	412	c.300T>A	c.(298-300)gcT>gcA	p.A100A	ATF7_ENST00000456903.4_Silent_p.A89A|RP11-793H13.10_ENST00000591834.1_Silent_p.A89A|ATF7_ENST00000420353.2_Silent_p.A89A|ATF7_ENST00000415113.1_Silent_p.A89A|ATF7_ENST00000328463.7_Silent_p.A100A			P17544	ATF7_HUMAN	activating transcription factor 7	100	Transactivation domain.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	GCCCAGCAGCAGCCTGTTGTG	0.443																																					p.A89A		.											.	ATF7-455	0			c.T267A						.						68	70	69					12																	53931334		1903	4133	6036	SO:0001819	synonymous_variant	11016	exon5			AGCAGCAGCCTGT	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"basic leucine zipper proteins"	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.300T>A	12.37:g.53931334A>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	49	16	NM_001130060	0	0	0	0	0	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	37																																																																																				.		0.443	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		T	53931334	A	T	53931334	2	4	69	1	0	0	0	0	0	0	0	1	1087	175	7	5		5	ATF7	12	53931334	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	844994	53931334	79920561	100	6630											
PRIM1	5557	hgsc.bcm.edu	37	chr12	57135252	57135252	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacactaaaagggctcttcaGtagatgattgattcctttgc	12	13	8	8	0	2	3	1	2	1	1	3	3	3	3	1	1	2	2	1	1	4	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:57135252G>C	ENST00000338193.6	-	9	985	c.949C>G	c.(949-951)Ctg>Gtg	p.L317V		NM_000946.2	NP_000937.1	P49642	PRI1_HUMAN	primase, DNA, polypeptide 1 (49kDa)	317					DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			kidney(1)|lung(6)|prostate(1)	8						GGGCTCTTCAGTAGATGATTG	0.398																																					p.L317V		.											.	.	0			c.C949G						.						70	64	66					12																	57135252		1837	4104	5941	SO:0001583	missense	5557	exon9			TCTTCAGTAGATG	BC005266	CCDS44926.1	12q13.3	2007-06-19	2007-06-19			ENSG00000198056			9369	protein-coding gene	gene with protein product		176635				8530050	Standard	NM_000946		Approved		uc001smd.3	P49642	OTTHUMG00000170034	ENST00000338193.6:c.949C>G	12.37:g.57135252G>C	ENSP00000350491:p.Leu317Val	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_000946	0	0	3	3	0		Missense_Mutation	SNP	ENST00000338193.6	37	CCDS44926.1	.	.	.	.	.	.	.	.	.	.	G	18.27	3.587509	0.66105	.	.	ENSG00000198056	ENST00000537418;ENST00000338193;ENST00000549549;ENST00000550770	T;T;T	0.56103	0.48;0.48;0.48	4.92	1.05	0.20165	.	0.000000	0.64402	D	0.000001	T	0.72684	0.3491	M	0.90309	3.105	0.54753	D	0.99998	D	0.89917	1.0	D	0.87578	0.998	T	0.72606	-0.4242	10	0.87932	D	0	-1.1101	8.6788	0.34196	0.3902:0.0:0.6098:0.0	.	317	P49642	PRI1_HUMAN	V	324;317;98;320	ENSP00000350491:L317V;ENSP00000449806:L98V;ENSP00000450185:L320V	ENSP00000350491:L317V	L	-	1	2	PRIM1	55421519	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	3.107000	0.50329	0.076000	0.16826	0.655000	0.94253	CTG	.		0.398	PRIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406956.1	NM_000946		C	57135252	G	C	57135252	3	2	69	1	0	0	0	0	1	0	0	0	12519	1020	36	4	333	4	PRIM1	12	57135252	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	3203918	57135252	76716643	101	6631											
SRGAP1	57522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64521913	64521913	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagccctcccattagaaggtCcacgtcatcagggcaataca	12	7	8	14	1	2	1	2	0	0	1	4	1	4	1	3	2	2	1	3	2	4	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:64521913C>A	ENST00000355086.3	+	21	3337	c.2813C>A	c.(2812-2814)tCc>tAc	p.S938Y	SRGAP1_ENST00000543397.1_Missense_Mutation_p.S875Y|SRGAP1_ENST00000357825.3_Missense_Mutation_p.S915Y	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	938					axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.S938C(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		ATTAGAAGGTCCACGTCATCA	0.532																																					p.S938Y		.											.	SRGAP1-653	1	Substitution - Missense(1)	ovary(1)	c.C2813A						.						53	49	50					12																	64521913		2203	4300	6503	SO:0001583	missense	57522	exon21			GAAGGTCCACGTC	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2813C>A	12.37:g.64521913C>A	ENSP00000347198:p.Ser938Tyr	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	43	12	NM_020762	0	0	1	5	4	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781515	0.90282	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.21191	3.02;2.6;2.02	5.65	5.65	0.86999	.	0.000000	0.34986	U	0.003527	T	0.42449	0.1203	L	0.58101	1.795	0.80722	D	1	D;D	0.60160	0.987;0.98	P;P	0.61592	0.851;0.891	T	0.02553	-1.1142	9	.	.	.	.	20.1057	0.97893	0.0:1.0:0.0:0.0	.	938;875	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	Y	938;915;875	ENSP00000347198:S938Y;ENSP00000350480:S915Y;ENSP00000437948:S875Y	.	S	+	2	0	SRGAP1	62808180	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	7.695000	0.84257	2.827000	0.97445	0.650000	0.86243	TCC	.		0.532	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			A	64521913	C	A	64521913	3	1	69	1	0	0	0	0	1	0	0	0	15177	855	30	4	2895	4	SRGAP1	12	64521913	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	7386661	64521913	69329982	102	6632											
EID3	493861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	104698219	104698219	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaaaagctgagacattccaTtttgtttttggttcattcaa	11	17	7	6	0	2	1	2	1	0	1	3	2	3	1	1	1	1	4	1	1	3	8			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:104698219T>A	ENST00000527879.1	+	1	703	c.507T>A	c.(505-507)caT>caA	p.H169Q	TXNRD1_ENST00000354940.6_Intron|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000529546.1_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3											large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						AGACATTCCATTTTGTTTTTG	0.418																																					p.H169Q		.											.	.	0			c.T507A						.						188	184	185					12																	104698219		1919	4136	6055	SO:0001583	missense	493861	exon1			ATTCCATTTTGTT	BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.507T>A	12.37:g.104698219T>A	ENSP00000435619:p.His169Gln	Somatic	355	0		WXS	Illumina HiSeq	Phase_I	282	113	NM_001008394	0	0	4	6	2		Missense_Mutation	SNP	ENST00000527879.1	37	CCDS53822.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.228683	0.39399	.	.	ENSG00000255150	ENST00000527879	T	0.43688	0.94	4.94	0.971	0.19698	.	.	.	.	.	T	0.53546	0.1803	M	0.72118	2.19	0.30872	N	0.732351	D	0.76494	0.999	D	0.77557	0.99	T	0.54139	-0.8338	9	0.10636	T	0.68	.	7.1994	0.25873	0.0:0.6158:0.0:0.3842	.	169	Q8N140	EID3_HUMAN	Q	169	ENSP00000435619:H169Q	ENSP00000435619:H169Q	H	+	3	2	EID3	103222349	0.586000	0.26782	0.839000	0.33178	0.046000	0.14306	-0.290000	0.08354	0.077000	0.16863	-0.375000	0.07067	CAT	.		0.418	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394		A	104698219	T	A	104698219	3	1	69	1	0	0	0	0	1	0	0	0	5000	1490	52	5	509	5	EID3	12	104698219	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	40176306	104698219	29153676	103	6633											
DTX1	1840	hgsc.bcm.edu	37	chr12	113515832	113515832	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcccccggcggagcgcgcaCcccggggcagaacaacctca	8	1	13	19	6	1	1	1	0	0	1	1	2	1	2	5	4	3	2	5	4	2	0	rs190645916	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:113515832C>A	ENST00000257600.3	+	2	1366	c.863C>A	c.(862-864)aCc>aAc	p.T288N		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	288	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						ggagcgcgcaccccggggcAG	0.841													C|||	58	0.0115815	8e-04	0.0216	5008	,	,		5386	0		0.0129	False		,,,				2504	0.0297				p.T288N		.											.	DTX1-659	0			c.C863A						.						1	1	1					12																	113515832		426	929	1355	SO:0001583	missense	1840	exon2			CGCGCACCCCGGG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.863C>A	12.37:g.113515832C>A	ENSP00000257600:p.Thr288Asn	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	3	NM_004416	0	0	0	0	0	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	17	0.007783882783882784	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	10	0.013192612137203167	C	11.15	1.554245	0.27739	.	.	ENSG00000135144	ENST00000257600	T	0.11604	2.76	3.36	0.862	0.19056	.	0.934666	0.09014	N	0.861063	T	0.03305	0.0096	N	0.14661	0.345	0.24759	N	0.992931	B	0.16166	0.016	B	0.10450	0.005	T	0.45440	-0.9261	10	0.18276	T	0.48	-2.7661	2.0747	0.03622	0.2506:0.3155:0.0:0.4339	.	288	Q86Y01	DTX1_HUMAN	N	288	ENSP00000257600:T288N	ENSP00000257600:T288N	T	+	2	0	DTX1	112000215	0.076000	0.21285	0.999000	0.59377	0.982000	0.71751	0.766000	0.26560	0.515000	0.28320	0.505000	0.49811	ACC	C|0.992;A|0.008		0.841	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			A	113515832	C	A	113515832	3	1	69	1	0	0	0	0	1	0	0	0	4804	507	18	4	869	4	DTX1	12	113515832	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	8817613	113515832	20336063	104	6634											
SLC15A4	121260	bcgsc.ca	37	chr12	129278885	129278885	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaaagtaatagttcaaataGcagccgttaatattacctgg	17	11	7	6	1	1	0	1	0	0	0	1	0	1	0	2	1	3	4	2	1	9	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:129278885G>C	ENST00000266771.5	-	8	1629	c.1590C>G	c.(1588-1590)tgC>tgG	p.C530W	SLC15A4_ENST00000545031.1_Missense_Mutation_p.C47W|SLC15A4_ENST00000544112.1_Missense_Mutation_p.C193W	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	530					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		AGTTCAAATAGCAGCCGTTAA	0.398																																					p.C530W													.	SLC15A4-90	0			c.C1590G						.						51	64	60					12																	129278885		2203	4300	6503	SO:0001583	missense	121260	exon8			CAAATAGCAGCCG	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"Solute carriers"	23090	protein-coding gene	gene with protein product		615806	"solute carrier family 15, member 4"			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1590C>G	12.37:g.129278885G>C	ENSP00000266771:p.Cys530Trp	Somatic	94	9		WXS	Illumina HiSeq	Phase_1	67	19	NM_145648	0	0	19	19	0	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Missense_Mutation	SNP	ENST00000266771.5	37	CCDS9264.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.569829	0.45798	.	.	ENSG00000139370	ENST00000266771;ENST00000545031;ENST00000544112	T;T	0.12255	3.97;2.7	5.68	3.81	0.43845	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.36193	0.0958	M	0.80746	2.51	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.11470	-1.0586	10	0.72032	D	0.01	.	10.7816	0.46382	0.068:0.0:0.8012:0.1307	.	530	Q8N697	S15A4_HUMAN	W	530;47;193	ENSP00000266771:C530W;ENSP00000439946:C193W	ENSP00000266771:C530W	C	-	3	2	SLC15A4	127844838	1.000000	0.71417	0.630000	0.29268	0.288000	0.27193	5.102000	0.64572	0.702000	0.31825	0.655000	0.94253	TGC	.		0.398	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648		C	129278885	G	C	129278885	3	2	69	1	0	0	0	0	1	0	0	0	14433	963	34	4	147	4	SLC15A4	12	129278885	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	15763053	129278885	4573010	105	6635											
FLT1	2321	broad.mit.edu;bcgsc.ca	37	chr13	29001983	29001983	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcatcctcttcagttacGtccttgataattaacgagta	10	14	6	11	2	2	1	1	1	1	0	4	2	4	1	3	0	3	3	3	0	4	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr13:29001983G>A	ENST00000282397.4	-	9	1433	c.1182C>T	c.(1180-1182)gaC>gaT	p.D394D	FLT1_ENST00000539099.1_Silent_p.D394D|FLT1_ENST00000541932.1_Silent_p.D394D	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	394	Ig-like C2-type 4.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTTCAGTTACGTCCTTGATAA	0.388																																					p.D394D													.	FLT1-1406	0			c.C1182T						.						141	126	131					13																	29001983		2203	4300	6503	SO:0001819	synonymous_variant	2321	exon9			AGTTACGTCCTTG	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1182C>T	13.37:g.29001983G>A		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	147	6	NM_002019	0	0	0	0	0	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																			.		0.388	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			A	29001983	G	A	29001983	2	1	69	1	0	0	0	0	0	0	0	1	5960	1136	40	1		1	FLT1	13	29001983	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08		29001983	86167895	106	6636											
ARHGEF7	8874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	111885553	111885553	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttacattttcatttcagaGaagcctgtgtctcccaaatc	10	15	6	10	0	3	1	2	0	1	1	5	2	3	1	2	0	2	1	2	0	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr13:111885553G>A	ENST00000375741.2	+	7	985	c.735G>A	c.(733-735)gaG>gaA	p.E245E	ARHGEF7_ENST00000544132.1_5'UTR|ARHGEF7_ENST00000317133.5_Splice_Site_p.E224E|ARHGEF7_ENST00000370623.3_Splice_Site_p.E152E|ARHGEF7_ENST00000375736.4_Splice_Site_p.E67E|ARHGEF7_ENST00000375737.5_Splice_Site_p.E142E|ARHGEF7_ENST00000375723.1_Splice_Site_p.E67E|ARHGEF7_ENST00000218789.5_Splice_Site_p.E67E|ARHGEF7_ENST00000375739.2_Splice_Site_p.E195E|ARHGEF7_ENST00000426073.2_Splice_Site_p.E67E	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	245					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TCATTTCAGAGAAGCCTGTGT	0.428																																					p.E245E		.											.	ARHGEF7-232	0			c.G735A						.						102	103	103					13																	111885553		2203	4300	6503	SO:0001630	splice_region_variant	8874	exon7			TTCAGAGAAGCCT	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.734-1G>A	13.37:g.111885553G>A		Somatic	192	1		WXS	Illumina HiSeq	Phase_I	132	76	NM_001113511	0	0	0	0	0	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	37	CCDS45068.1																																																																																			.		0.428	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	Silent	A	111885553	G	A	111885553	5	1	69	1	0	0	0	0	0	0	1	0	911	956	33	2	761	2	ARHGEF7	13	111885553	Splice_Site	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	82883570	111885553	3284325	107	6637											
SAV1	60485	hgsc.bcm.edu	37	chr14	51131903	51131903	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taatgttaagctacctgaagCatgcctcccctgattctgtg	9	13	8	11	0	1	2	0	2	1	0	2	2	2	2	4	0	4	3	4	0	4	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr14:51131903C>T	ENST00000324679.4	-	2	892	c.529G>A	c.(529-531)Gct>Act	p.A177T	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	177					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					CTACCTGAAGCATGCCTCCCC	0.358																																					p.A177T		.											.	SAV1-658	0			c.G529A						.						18	18	18					14																	51131903		2170	4247	6417	SO:0001583	missense	60485	exon2			CTGAAGCATGCCT	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.529G>A	14.37:g.51131903C>T	ENSP00000324729:p.Ala177Thr	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	128	54	NM_021818	0	0	0	2	2	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Missense_Mutation	SNP	ENST00000324679.4	37	CCDS9701.1	.	.	.	.	.	.	.	.	.	.	C	3.839	-0.034114	0.07543	.	.	ENSG00000151748	ENST00000555720;ENST00000324679;ENST00000535862;ENST00000553731	T;T	0.44083	0.93;0.94	4.65	1.82	0.25136	.	0.308244	0.35970	N	0.002863	T	0.12944	0.0314	N	0.02539	-0.55	0.20926	N	0.999822	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	10	0.09084	T	0.74	-2.4379	4.115	0.10077	0.0:0.4329:0.1722:0.3949	.	177	Q9H4B6	SAV1_HUMAN	T	109;177;144;61	ENSP00000451492:A109T;ENSP00000324729:A177T	ENSP00000324729:A177T	A	-	1	0	SAV1	50201653	0.962000	0.33011	0.997000	0.53966	0.955000	0.61496	0.134000	0.15932	0.194000	0.20326	0.563000	0.77884	GCT	.		0.358	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			T	51131903	C	T	51131903	3	4	69	1	0	0	0	0	1	0	0	0	13888	710	25	2	638	2	SAV1	14	51131903	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		51131903	56217637	108	6638											
YLPM1	56252	bcgsc.ca	37	chr14	75230946	75230947	+	Frame_Shift_Ins	INS	-	-	C																															agctccaccaccaccgtccgINSccccccctggaaataagaca																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr14:75230946_75230947insC	ENST00000552421.1	+	1	878_879	c.754_755insC	c.(754-756)gccfs	p.A252fs	YLPM1_ENST00000325680.7_Frame_Shift_Ins_p.A252fs|YLPM1_ENST00000238571.3_Frame_Shift_Ins_p.A252fs			P49750	YLPM1_HUMAN	YLP motif containing 1	252					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ACCACCGTCCGCCCCCCCTGGA	0.579																																					p.A252fs													.	YLPM1-71	0			c.754_755insC						.																																			SO:0001589	frameshift_variant	56252	exon1			CCGTCCGCCCCCC	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.761dupC	14.37:g.75230953_75230953dupC	ENSP00000447921:p.Ala252fs	Somatic	56	1		WXS	Illumina HiSeq	Phase_1	27	7	NM_019589	0	0	0	0	0	P49752|Q96I64|Q9P1V7	Frame_Shift_Ins	INS	ENST00000552421.1	37																																																																																				.		0.579	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		C	75230947	-	C	75230946	7	5	69	1	0	1	1	0	0	0	0	0	17519	1087	38	0	756	0	YLPM1	14	75230946	Frame_Shift_Ins	INS	-	TCGA-BQ-5885-01A-11D-1589-08	24099043	75230946	32118594	109	6639											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	18841596	18841597	+	Missense_Mutation	DNP	GC	GC	TT																															gagcaaacatgccatcgaatGctaccaaaagcatctggcca																								rs371226711		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr16:18841596_18841597GC>TT	ENST00000446231.2	-	52	9299_9300	c.8887_8888GC>AA	c.(8887-8889)GCa>AAa	p.A2963K	SMG1_ENST00000389467.3_Missense_Mutation_p.A2963K			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2963					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GCCATCGAATGCTACCAAAAGC	0.391																																					p.A2963K		.											.	SMG1	0			c.G8887A						.																																			SO:0001583	missense	23049	exon52			CGAATGCTACCAA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.8887_8888delinsTT	16.37:g.18841596_18841597delinsTT	ENSP00000402515:p.Ala2963Lys	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	47	21		0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	DNP	ENST00000446231.2	37	CCDS45430.1																																																																																			.		0.391	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		TT	18841597	GC	TT	18841596	3	4	69	1	0	0	0	0	1	0	0	0	14827	1319	46	4	2145	4	SMG1	16	18841596	Missense_Mutation	DNP	GC	TCGA-BQ-5885-01A-11D-1589-08		18841596	71513157	110	6640											
IL4R	3566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27374876	27374876	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggccaggaggatggtggcCagacccctgtcatggccagt	8	7	15	11	0	1	1	1	0	0	1	1	3	1	3	5	6	0	0	5	6	0	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr16:27374876C>T	ENST00000395762.2	+	11	2462	c.2203C>T	c.(2203-2205)Cag>Tag	p.Q735*	IL4R_ENST00000170630.2_Nonsense_Mutation_p.Q735*|IL4R_ENST00000380922.3_Nonsense_Mutation_p.Q720*|IL4R_ENST00000543915.2_Nonsense_Mutation_p.Q735*	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	735					defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GGATGGTGGCCAGACCCCTGT	0.647																																					p.Q735X		.											.	IL4R-227	0			c.C2203T						.						54	54	54					16																	27374876		2197	4300	6497	SO:0001587	stop_gained	3566	exon11			GGTGGCCAGACCC	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"Interleukins and interleukin receptors", "CD molecules"	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.2203C>T	16.37:g.27374876C>T	ENSP00000379111:p.Gln735*	Somatic	130	1		WXS	Illumina HiSeq	Phase_I	137	35	NM_000418	0	0	3	7	4	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Nonsense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	C	38	7.243394	0.98161	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	.	.	.	5.33	-4.85	0.03142	.	0.724527	0.12583	N	0.456238	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-14.1539	3.6218	0.08099	0.2032:0.3204:0.383:0.0935	.	.	.	.	X	735;735;720;735	.	ENSP00000170630:Q735X	Q	+	1	0	IL4R	27282377	0.000000	0.05858	0.105000	0.21289	0.192000	0.23643	-1.099000	0.03343	-0.670000	0.05282	0.655000	0.94253	CAG	.		0.647	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			T	27374876	C	T	27374876	4	4	69	1	0	0	0	0	0	1	0	0	7719	595	21	2	2255	2	IL4R	16	27374876	Nonsense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	8533280	27374876	62979877	111	6641											
TMEM188	255919	broad.mit.edu	37	chr16	50059600	50059600	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgattcctgcggtggtttccGgtaactgccaaggttaggaa	8	12	13	8	2	0	1	0	1	0	0	2	2	2	2	3	5	3	3	3	5	4	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr16:50059600G>A	ENST00000427478.2	+	1	79				CNEP1R1_ENST00000458059.3_Missense_Mutation_p.G22S|CNEP1R1_ENST00000562576.1_Intron|CNEP1R1_ENST00000565556.1_5'UTR|CNEP1R1_ENST00000567712.1_3'UTR	NM_001281789.1	NP_001268718.1	Q8N9A8	NEPR1_HUMAN	CTD nuclear envelope phosphatase 1 regulatory subunit 1						lipid metabolic process (GO:0006629)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear membrane (GO:0031965)											GGTGGTTTCCGGTAACTGCCA	0.512																																					p.G22S													.	.	0			c.G64A						.						91	89	89					16																	50059600		1891	4121	6012	SO:0001627	intron_variant	255919	exon2			GTTTCCGGTAACT	AK095420	CCDS45480.1, CCDS61931.1	16q12.1	2012-02-01	2012-02-01	2012-02-01	ENSG00000205423	ENSG00000205423			26759	protein-coding gene	gene with protein product	"nuclear envelope phosphatase 1-regulatory subunit 1"		"chromosome 16 open reading frame 69", "transmembrane protein 188"	C16orf69, TMEM188		22134922	Standard	NM_153261		Approved	FLJ38101, NEP1-R1	uc002eft.3	Q8N9A8		ENST00000427478.2:c.25+349G>A	16.37:g.50059600G>A		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	65	4	NM_153261	0	0	1	1	0	Q4G1A9|Q5H9V0|Q8NE06	Missense_Mutation	SNP	ENST00000427478.2	37		.	.	.	.	.	.	.	.	.	.	G	24.1	4.494115	0.85069	.	.	ENSG00000205423	ENST00000458059	.	.	.	3.79	0.659	0.17861	.	.	.	.	.	T	0.12135	0.0295	N	0.03608	-0.345	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.32877	-0.9890	8	0.08179	T	0.78	.	3.9992	0.09572	0.2125:0.0:0.5915:0.196	.	22	Q8N9A8-2	.	S	22	.	ENSP00000405635:G22S	G	+	1	0	TMEM188	48617101	0.179000	0.23135	0.000000	0.03702	0.747000	0.42532	1.751000	0.38339	0.177000	0.19895	0.462000	0.41574	GGT	.		0.512	CNEP1R1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153261		A	50059600	G	A	50059600	1	1	69	0	1	0	0	0	0	0	0	0	16142	1116	39	1		1	TMEM188	16	50059600	Intron	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	22684724	50059600	40295153	112	6642											
NKD1	85407	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	50667463	50667463	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggccctcctcccctccctagCccccctcgggcacaagaagc	6	5	8	22	1	0	1	0	0	0	1	4	1	3	1	8	2	2	1	8	2	3	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr16:50667463C>G	ENST00000268459.3	+	10	1408	c.1184C>G	c.(1183-1185)gCc>gGc	p.A395G		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	395					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		CCCTCCCTAGCCCCCCTCGGG	0.721																																					p.A395G		.											.	NKD1-226	0			c.C1184G						.						9	12	11					16																	50667463		2160	4247	6407	SO:0001583	missense	85407	exon10			CCCTAGCCCCCCT	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"EF-hand domain containing"	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.1184C>G	16.37:g.50667463C>G	ENSP00000268459:p.Ala395Gly	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	32	11	NM_033119	0	0	0	0	0	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	37	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	C	9.960	1.222465	0.22457	.	.	ENSG00000140807	ENST00000268459	T	0.65364	-0.15	4.05	4.05	0.47172	.	0.262951	0.37178	N	0.002203	T	0.57681	0.2070	L	0.51422	1.61	0.09310	N	0.999994	P	0.37330	0.59	B	0.40410	0.328	T	0.50792	-0.8786	10	0.21014	T	0.42	-8.4212	14.5612	0.68136	0.0:1.0:0.0:0.0	.	395	Q969G9	NKD1_HUMAN	G	395	ENSP00000268459:A395G	ENSP00000268459:A395G	A	+	2	0	NKD1	49224964	0.004000	0.15560	0.909000	0.35828	0.607000	0.37147	1.081000	0.30791	2.092000	0.63282	0.305000	0.20034	GCC	.		0.721	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			G	50667463	C	G	50667463	3	3	69	1	0	0	0	0	1	0	0	0	10467	739	26	4	1222	4	NKD1	16	50667463	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	607863	50667463	39687290	113	6643											
TRPV3	162514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3458126	3458126	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcccatgagaggcaccatctCcttggggtgggctttcatgg	6	10	14	11	0	2	1	1	1	1	1	3	2	2	1	3	5	0	2	3	5	0	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:3458126C>T	ENST00000576742.1	-	2	340	c.19G>A	c.(19-21)Gag>Aag	p.E7K	TRPV3_ENST00000301365.4_Missense_Mutation_p.E7K|TRPV3_ENST00000572519.1_Missense_Mutation_p.E7K	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	7					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GGCACCATCTCCTTGGGGTGG	0.622																																					p.E7K		.											.	TRPV3-94	0			c.G19A						.						39	40	39					17																	3458126		2203	4300	6503	SO:0001583	missense	162514	exon2			CCATCTCCTTGGG	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.19G>A	17.37:g.3458126C>T	ENSP00000461518:p.Glu7Lys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	80	25	NM_001258205	0	0	0	0	0	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812560	0.70912	.	.	ENSG00000167723	ENST00000381913;ENST00000301365	T	0.42131	0.98	4.79	4.79	0.61399	.	0.098779	0.43747	D	0.000525	T	0.33323	0.0859	N	0.24115	0.695	0.35360	D	0.788099	P;P;P	0.40534	0.59;0.598;0.72	B;B;B	0.41202	0.111;0.19;0.35	T	0.51988	-0.8635	10	0.87932	D	0	-16.4794	13.7071	0.62646	0.0:1.0:0.0:0.0	.	7;7;7	Q8NET8-3;Q8NET8;Q8NET8-2	.;TRPV3_HUMAN;.	K	7	ENSP00000301365:E7K	ENSP00000301365:E7K	E	-	1	0	TRPV3	3404876	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.073000	0.57570	2.399000	0.81585	0.462000	0.41574	GAG	.		0.622	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		T	3458126	C	T	3458126	3	4	69	1	0	0	0	0	1	0	0	0	16630	864	30	2	2421	2	TRPV3	17	3458126	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		3458126	77737084	114	6644											
COX10	1352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	13977738	13977738	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatgtcaataagcagtggAttacatttcagcactttagc	13	12	9	7	0	2	0	2	0	0	0	2	2	2	2	0	2	4	2	0	2	5	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:13977738A>C	ENST00000261643.3	+	2	219	c.142A>C	c.(142-144)Att>Ctt	p.I48L	COX10_ENST00000537334.1_5'UTR|COX10_ENST00000536205.1_5'UTR|COX10_ENST00000429152.2_Missense_Mutation_p.I48L	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	48					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TAAGCAGTGGATTACATTTCA	0.408																																					p.I48L		.											.	COX10-226	0			c.A142C						.						187	183	185					17																	13977738		2203	4300	6503	SO:0001583	missense	1352	exon2			CAGTGGATTACAT	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.142A>C	17.37:g.13977738A>C	ENSP00000261643:p.Ile48Leu	Somatic	383	1		WXS	Illumina HiSeq	Phase_I	324	115	NM_001303	0	0	8	14	6	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.45|12.45	1.940770|1.940770	0.34283|0.34283	.|.	.|.	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	.|T	.|0.37915	.|1.17	5.03|5.03	-3.34|-3.34	0.04943|0.04943	.|.	.|0.618238	.|0.17063	.|N	.|0.188488	T|T	0.24699|0.24699	0.0599|0.0599	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	T|T	0.02037|0.02037	-1.1225|-1.1225	5|10	.|0.45353	.|T	.|0.12	-18.4175|-18.4175	8.3088|8.3088	0.32058|0.32058	0.3998:0.1258:0.4744:0.0|0.3998:0.1258:0.4744:0.0	.|.	.|48	.|Q12887	.|COX10_HUMAN	A|L	8|48	.|ENSP00000261643:I48L	.|ENSP00000261643:I48L	D|I	+|+	2|1	0|0	COX10|COX10	13918463|13918463	0.992000|0.992000	0.36948|0.36948	0.409000|0.409000	0.26459|0.26459	0.912000|0.912000	0.54170|0.54170	0.470000|0.470000	0.22084|0.22084	-0.785000|-0.785000	0.04522|0.04522	0.528000|0.528000	0.53228|0.53228	GAT|ATT	.		0.408	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		C	13977738	A	C	13977738	3	2	69	1	0	0	0	0	1	0	0	0	3768	333	12	5	148	5	COX10	17	13977738	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	10519612	13977738	67217472	115	6645											
KRT13	3860	broad.mit.edu	37	chr17	39658760	39658760	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctcgctcagctgggcctcGatgctgctgatgagtccctg	5	10	13	13	2	1	2	1	2	0	0	4	3	2	2	2	1	4	5	2	1	0	0	rs147022064		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:39658760G>A	ENST00000246635.3	-	6	1156	c.1110C>T	c.(1108-1110)atC>atT	p.I370I	KRT13_ENST00000587544.1_Silent_p.I370I|KRT13_ENST00000336861.3_Silent_p.I370I|KRT13_ENST00000587118.1_5'Flank|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	370	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.I370I(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				GCTGGGCCTCGATGCTGCTGA	0.602																																					p.I370I													.	KRT13-95	1	Substitution - coding silent(1)	lung(1)	c.C1110T						.						152	128	136					17																	39658760		2203	4300	6503	SO:0001819	synonymous_variant	3860	exon6			GGCCTCGATGCTG		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.1110C>T	17.37:g.39658760G>A		Somatic	307	0		WXS	Illumina HiSeq	Phase_I	307	6	NM_002274	0	0	0	0	0	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	37	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	G	9.837	1.190118	0.21954	.	.	ENSG00000171401	ENST00000157775	.	.	.	4.45	-1.25	0.09405	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	7.4566	0.27270	0.2321:0.4076:0.3603:0.0	.	.	.	.	X	347	.	ENSP00000157775:R347X	R	-	1	2	KRT13	36912286	0.002000	0.14202	0.994000	0.49952	0.935000	0.57460	-1.284000	0.02793	-0.035000	0.13691	0.478000	0.44815	CGA	G|1.000;T|0.000		0.602	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39658760	G	A	39658760	2	1	69	1	0	0	0	0	0	0	0	1	8471	1048	37	1		1	KRT13	17	39658760	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	25681022	39658760	41536450	116	6646											
TBX4	9496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	59544913	59544913	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagccatgccaggaaggctGtatgtccacccggattctcc	8	8	10	15	1	1	0	0	0	1	0	3	2	2	2	6	3	2	2	6	3	2	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:59544913G>C	ENST00000240335.1	+	4	489	c.444G>C	c.(442-444)ctG>ctC	p.L148L	TBX4_ENST00000393853.4_Silent_p.L148L	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	148					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CAGGAAGGCTGTATGTCCACC	0.587																																					p.L148L		.											.	TBX4-227	0			c.G444C						.						46	47	47					17																	59544913		2203	4300	6503	SO:0001819	synonymous_variant	9496	exon4			AAGGCTGTATGTC	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"T-boxes"	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.444G>C	17.37:g.59544913G>C		Somatic	89	1		WXS	Illumina HiSeq	Phase_I	78	25	NM_018488	0	0	0	0	0	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			.		0.587	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		C	59544913	G	C	59544913	2	2	69	1	0	0	0	0	0	0	0	1	15692	1364	48	4		4	TBX4	17	59544913	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	19886153	59544913	21650297	117	6647											
TEX19	400629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80320426	80320426	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggctgtgcccctgggcCtgggccttgaggatgctgac	5	8	17	11	0	0	2	0	2	0	0	0	4	0	4	4	5	2	2	4	5	0	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:80320426C>A	ENST00000333437.4	+	2	710	c.400C>A	c.(400-402)Ctg>Atg	p.L134M		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	134					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6						GCCCCTGGGCCTGGGCCTTGA	0.597																																					p.L134M		.											.	TEX19-90	0			c.C400A						.						68	68	68					17																	80320426		2203	4300	6503	SO:0001583	missense	400629	exon2			CTGGGCCTGGGCC	BC016939	CCDS11809.1	17q25.3	2009-04-14			ENSG00000182459	ENSG00000182459			33802	protein-coding gene	gene with protein product		615647					Standard	NM_207459		Approved	FLJ35767	uc002keq.3	Q8NA77	OTTHUMG00000132857	ENST00000333437.4:c.400C>A	17.37:g.80320426C>A	ENSP00000331500:p.Leu134Met	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	202	78	NM_207459	0	0	0	0	0		Missense_Mutation	SNP	ENST00000333437.4	37	CCDS11809.1	.	.	.	.	.	.	.	.	.	.	C	8.539	0.872893	0.17322	.	.	ENSG00000182459	ENST00000333437	.	.	.	3.79	-0.753	0.11068	.	.	.	.	.	T	0.40297	0.1111	L	0.34521	1.04	0.09310	N	0.999999	D	0.76494	0.999	D	0.68943	0.961	T	0.23583	-1.0184	8	0.87932	D	0	-8.5728	4.373	0.11256	0.0:0.4173:0.3653:0.2174	.	134	Q8NA77	TEX19_HUMAN	M	134	.	ENSP00000331500:L134M	L	+	1	2	TEX19	77913715	0.093000	0.21703	0.021000	0.16686	0.007000	0.05969	0.763000	0.26517	-0.070000	0.12908	-0.251000	0.11542	CTG	.		0.597	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459		A	80320426	C	A	80320426	3	1	69	1	0	0	0	0	1	0	0	0	15812	680	24	4	402	4	TEX19	17	80320426	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	20775513	80320426	874784	118	6648											
PSMA8	143471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	23731852	23731852	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgctagagtagtaataaAcagagcccgtgtggagtgcc	12	9	13	7	1	0	3	0	1	0	2	0	4	0	4	2	1	4	3	2	1	5	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr18:23731852A>G	ENST00000308268.6	+	3	367	c.278A>G	c.(277-279)aAc>aGc	p.N93S	PSMA8_ENST00000415576.2_Missense_Mutation_p.N87S|PSMA8_ENST00000343848.6_Missense_Mutation_p.N49S	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	93					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			GTAGTAATAAACAGAGCCCGT	0.378																																					p.N93S		.											.	PSMA8-91	0			c.A278G						.						104	103	104					18																	23731852		2203	4300	6503	SO:0001583	missense	143471	exon3			TAATAAACAGAGC	BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"Proteasome (prosome, macropain) subunits"	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.278A>G	18.37:g.23731852A>G	ENSP00000311121:p.Asn93Ser	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	116	39	NM_144662	0	0	0	0	0	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Missense_Mutation	SNP	ENST00000308268.6	37	CCDS32808.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.518879	0.44763	.	.	ENSG00000154611	ENST00000308268;ENST00000415576;ENST00000343848;ENST00000538664;ENST00000536423	T;T;T	0.21361	2.01;2.01;2.01	5.34	2.96	0.34315	.	0.096815	0.64402	N	0.000002	T	0.20251	0.0487	L	0.60012	1.86	0.44579	D	0.997548	B;B;B;B	0.30193	0.052;0.041;0.214;0.272	B;B;B;B	0.33750	0.019;0.083;0.079;0.169	T	0.03306	-1.1050	10	0.42905	T	0.14	-9.0093	6.0378	0.19718	0.7464:0.1656:0.088:0.0	.	61;93;87;49	F5GY34;Q8TAA3;Q8TAA3-5;Q8TAA3-2	.;PSA7L_HUMAN;.;.	S	93;87;49;61;49	ENSP00000311121:N93S;ENSP00000409284:N87S;ENSP00000345584:N49S	ENSP00000311121:N93S	N	+	2	0	PSMA8	21985850	1.000000	0.71417	0.988000	0.46212	0.969000	0.65631	5.075000	0.64407	0.479000	0.27511	0.533000	0.62120	AAC	.		0.378	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1	NM_144662		G	23731852	A	G	23731852	3	3	69	1	0	0	0	0	1	0	0	0	12702	43	2	3	288	3	PSMA8	18	23731852	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08		23731852	54345396	119	6649											
ZNF57	126295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2917763	2917763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtcctcaacgtttagagaaCatgtgagaattcacacgcaa	14	9	9	9	2	2	2	2	1	0	2	3	4	3	2	1	1	2	2	1	1	5	3	rs549800352	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:2917763C>T	ENST00000306908.5	+	4	1292	c.1144C>T	c.(1144-1146)Cat>Tat	p.H382Y	ZNF57_ENST00000523428.1_Missense_Mutation_p.H350Y|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GTTTAGAGAACATGTGAGAAT	0.448																																					p.H382Y	NSCLC(150;910 1964 4303 10464 26498)	.											.	ZNF57-71	0			c.C1144T						.						90	82	84					19																	2917763		2203	4300	6503	SO:0001583	missense	126295	exon4			AGAGAACATGTGA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"Zinc fingers, C2H2-type", "-"	13125	protein-coding gene	gene with protein product			"zinc finger protein 424"	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1144C>T	19.37:g.2917763C>T	ENSP00000303696:p.His382Tyr	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	134	52	NM_173480	0	0	2	6	4	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.084453	0.36758	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	D;D	0.86769	-2.17;-2.17	2.25	2.25	0.28309	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94693	0.8288	H	0.96175	3.78	0.09310	N	0.999999	D	0.89917	1.0	D	0.69479	0.964	D	0.86081	0.1544	9	0.87932	D	0	.	10.1544	0.42814	0.0:1.0:0.0:0.0	.	382	Q68EA5	ZNF57_HUMAN	Y	382;384;350	ENSP00000303696:H382Y;ENSP00000430223:H350Y	ENSP00000303696:H382Y	H	+	1	0	ZNF57	2868763	0.980000	0.34600	0.002000	0.10522	0.002000	0.02628	2.918000	0.48829	1.259000	0.44117	0.511000	0.50034	CAT	.		0.448	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		T	2917763	C	T	2917763	3	4	69	1	0	0	0	0	1	0	0	0	18033	478	17	2	1158	2	ZNF57	19	2917763	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		2917763	56211220	120	6650											
ZNF846	162993	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9868191	9868191	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagttcttagatgtttagcaAgtgctgaagattgagtgaag	12	14	12	3	0	1	5	0	3	1	2	1	5	1	5	0	0	2	4	0	0	6	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:9868191A>G	ENST00000397902.2	-	6	1975	c.1562T>C	c.(1561-1563)cTt>cCt	p.L521P	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000592859.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						ATGTTTAGCAAGTGCTGAAGA	0.368																																					p.L521P		.											.	ZNF846-23	0			c.T1562C						.						150	158	155					19																	9868191		2050	4222	6272	SO:0001583	missense	162993	exon6			TTAGCAAGTGCTG	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1562T>C	19.37:g.9868191A>G	ENSP00000380999:p.Leu521Pro	Somatic	317	0		WXS	Illumina HiSeq	Phase_I	279	100	NM_001077624	0	0	2	7	5	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	18.50	3.637264	0.67130	.	.	ENSG00000196605	ENST00000397902	T	0.14266	2.52	1.74	1.74	0.24563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41119	0.1145	M	0.91717	3.235	0.21579	N	0.999631	D	0.89917	1.0	D	0.91635	0.999	T	0.09465	-1.0673	9	0.87932	D	0	.	7.5297	0.27677	1.0:0.0:0.0:0.0	.	521	Q147U1	ZN846_HUMAN	P	521	ENSP00000380999:L521P	ENSP00000380999:L521P	L	-	2	0	ZNF846	9729191	0.712000	0.27916	0.008000	0.14137	0.897000	0.52465	5.067000	0.64357	1.067000	0.40740	0.374000	0.22700	CTT	.		0.368	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		G	9868191	A	G	9868191	3	3	69	1	0	0	0	0	1	0	0	0	18224	72	3	3	43	3	ZNF846	19	9868191	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	6950428	9868191	49260792	121	6651											
UNC13A	23025	broad.mit.edu	37	chr19	17778940	17778940	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcacttcatcctggtcccGcatagcattgagctgctcca	8	11	7	15	1	2	1	2	1	0	0	5	1	5	1	3	1	3	4	3	1	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:17778940G>A	ENST00000519716.2	-	6	453	c.454C>T	c.(454-456)Cgg>Tgg	p.R152W	UNC13A_ENST00000252773.7_Missense_Mutation_p.R152W|UNC13A_ENST00000550896.1_Missense_Mutation_p.R152W|UNC13A_ENST00000552293.1_Missense_Mutation_p.R152W|UNC13A_ENST00000428389.2_Missense_Mutation_p.R240W|UNC13A_ENST00000551649.1_Missense_Mutation_p.R152W	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	152					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						TCCTGGTCCCGCATAGCATTG	0.537																																					p.R152W													.	UNC13A-25	0			c.C454T						.						87	92	91					19																	17778940		2024	4188	6212	SO:0001583	missense	23025	exon6			GGTCCCGCATAGC	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.454C>T	19.37:g.17778940G>A	ENSP00000429562:p.Arg152Trp	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_001080421	0	0	0	0	0	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	16.86	3.240295	0.58995	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;T;T;D	0.81579	-1.5;-1.51;-1.5;-1.37;-1.37;-1.5	4.37	-1.71	0.08133	.	0.000000	0.85682	U	0.000000	D	0.83312	0.5227	L	0.56769	1.78	0.36191	D	0.850098	D	0.76494	0.999	P	0.60609	0.877	D	0.85399	0.1130	10	0.66056	D	0.02	-13.6272	12.7879	0.57516	0.0:0.0:0.3681:0.6319	.	152	Q9UPW8	UN13A_HUMAN	W	152;240;152;152;152;152	ENSP00000429562:R152W;ENSP00000400409:R240W;ENSP00000252773:R152W;ENSP00000447236:R152W;ENSP00000447572:R152W;ENSP00000446831:R152W	ENSP00000252773:R152W	R	-	1	2	UNC13A	17639940	0.941000	0.31946	0.992000	0.48379	0.908000	0.53690	0.121000	0.15667	-0.020000	0.14032	-0.324000	0.08512	CGG	.		0.537	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17778940	G	A	17778940	3	1	69	1	0	0	0	0	1	0	0	0	17017	1086	38	1	4805	1	UNC13A	19	17778940	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	7910749	17778940	41350043	122	6652											
GATAD2A	54815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	19603133	19603133	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agtgacatgaagtccgagagGagacccccctcacctgacgt	11	6	11	13	2	1	5	1	3	0	2	2	7	2	5	5	1	0	0	5	1	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:19603133G>T	ENST00000360315.3	+	3	600	c.288G>T	c.(286-288)agG>agT	p.R96S	GATAD2A_ENST00000358713.3_Missense_Mutation_p.R96S|GATAD2A_ENST00000429563.2_Intron|GATAD2A_ENST00000252577.5_Missense_Mutation_p.R96S|GATAD2A_ENST00000473184.1_3'UTR|GATAD2A_ENST00000537887.1_Intron|GATAD2A_ENST00000404158.1_Missense_Mutation_p.R96S	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	96					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						AGTCCGAGAGGAGACCCCCCT	0.617																																					p.R96S		.											.	GATAD2A-90	0			c.G288T						.						48	48	48					19																	19603133		1568	3582	5150	SO:0001583	missense	54815	exon3			CGAGAGGAGACCC	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.288G>T	19.37:g.19603133G>T	ENSP00000353463:p.Arg96Ser	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_017660	0	0	1	4	3	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	G	14.79	2.640385	0.47153	.	.	ENSG00000167491	ENST00000417582;ENST00000360315;ENST00000252577;ENST00000457895;ENST00000432704;ENST00000404158;ENST00000429242;ENST00000358713	T;T;T;T;T;T;T	0.56444	0.49;0.98;1.01;0.46;0.53;0.55;0.98	5.61	5.61	0.85477	.	0.219648	0.47093	D	0.000252	T	0.48519	0.1504	L	0.38175	1.15	0.80722	D	1	B;B	0.25351	0.124;0.124	B;B	0.27500	0.08;0.074	T	0.47446	-0.9117	10	0.87932	D	0	-15.9509	18.201	0.89838	0.0:0.0:1.0:0.0	.	115;96	B5MC40;Q86YP4	.;P66A_HUMAN	S	96;96;96;96;96;115;96;96	ENSP00000403703:R96S;ENSP00000353463:R96S;ENSP00000252577:R96S;ENSP00000404212:R96S;ENSP00000390495:R96S;ENSP00000414252:R96S;ENSP00000351552:R96S	ENSP00000252577:R96S	R	+	3	2	GATAD2A	19464133	1.000000	0.71417	0.997000	0.53966	0.494000	0.33585	1.747000	0.38298	2.642000	0.89623	0.561000	0.74099	AGG	.		0.617	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		T	19603133	G	T	19603133	3	4	69	1	0	0	0	0	1	0	0	0	6280	1165	41	4	294	4	GATAD2A	19	19603133	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1824193	19603133	39525850	123	6653											
C19orf40	91442	broad.mit.edu	37	chr19	33467343	33467343	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcattgtggttcaggttcaaGagcaaaccaaagagcccagt	13	9	10	9	0	3	2	3	0	0	2	3	2	3	2	2	2	3	3	2	2	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:33467343G>C	ENST00000588258.1	+	5	513	c.403G>C	c.(403-405)Gag>Cag	p.E135Q	C19orf40_ENST00000590179.1_Missense_Mutation_p.E40Q|C19orf40_ENST00000590281.1_Missense_Mutation_p.E135Q|C19orf40_ENST00000589646.1_Missense_Mutation_p.E40Q	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	135					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					TCAGGTTCAAGAGCAAACCAA	0.502								Direct reversal of damage			OREG0025408	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E135Q													.	C19orf40-90	0			c.G403C						.						64	66	65					19																	33467343		2203	4300	6503	SO:0001583	missense	91442	exon5			GTTCAAGAGCAAA	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 24kDa"	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.403G>C	19.37:g.33467343G>C	ENSP00000466121:p.Glu135Gln	Somatic	160	0	840	WXS	Illumina HiSeq	Phase_I	150	3	NM_152266	0	0	0	0	0	B3KY46|Q8WUJ7|Q96FX6	Missense_Mutation	SNP	ENST00000588258.1	37	CCDS12426.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.658620	0.67586	.	.	ENSG00000131944	ENST00000254262	.	.	.	5.29	5.29	0.74685	.	0.221552	0.45867	D	0.000339	T	0.74711	0.3752	L	0.56769	1.78	0.41062	D	0.98538	D	0.76494	0.999	D	0.63488	0.915	T	0.71705	-0.4512	9	0.32370	T	0.25	-26.4895	18.9478	0.92628	0.0:0.0:1.0:0.0	.	135	Q9BTP7	FAP24_HUMAN	Q	135	.	ENSP00000254262:E135Q	E	+	1	0	C19orf40	38159183	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	8.198000	0.89729	2.643000	0.89663	0.579000	0.79373	GAG	.		0.502	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266		C	33467343	G	C	33467343	3	2	69	1	0	0	0	0	1	0	0	0	1929	943	33	4	417	4	C19orf40	19	33467343	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	13864210	33467343	25661640	124	6654											
PAK4	10298	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39667267	39667267	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggttctgcgcccaggtgaGcaaggaagtgccccgaagga	9	6	16	10	2	1	1	0	1	1	0	1	4	1	3	3	4	3	2	3	4	3	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:39667267G>T	ENST00000593690.1	+	9	1824	c.1397G>T	c.(1396-1398)aGc>aTc	p.S466I	PAK4_ENST00000599470.1_Missense_Mutation_p.S313I|PAK4_ENST00000358301.3_Missense_Mutation_p.S466I|PAK4_ENST00000360442.3_Missense_Mutation_p.S466I|PAK4_ENST00000435673.2_Missense_Mutation_p.S466I|PAK4_ENST00000599386.1_Missense_Mutation_p.S313I|PAK4_ENST00000321944.4_Missense_Mutation_p.S376I	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	466	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			GCCCAGGTGAGCAAGGAAGTG	0.672																																					p.S466I		.											.	PAK4-957	0			c.G1397T						.						134	138	136					19																	39667267		2203	4300	6503	SO:0001583	missense	10298	exon7			AGGTGAGCAAGGA	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"p21(CDKN1A)-activated kinase 4"			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.1397G>T	19.37:g.39667267G>T	ENSP00000469413:p.Ser466Ile	Somatic	367	0		WXS	Illumina HiSeq	Phase_I	225	94	NM_001014832	0	0	12	34	22	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310361	0.81358	.	.	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.65549	-0.16;-0.16;-0.16	4.87	3.79	0.43588	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.174438	0.51477	D	0.000092	T	0.62816	0.2459	L	0.35249	1.045	0.49213	D	0.999762	P;P;D	0.54964	0.927;0.946;0.969	P;P;D	0.63703	0.479;0.807;0.917	T	0.64462	-0.6402	10	0.87932	D	0	.	5.7648	0.18221	0.2083:0.0:0.7917:0.0	.	376;313;466	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	I	466;313;270;222;466;466	ENSP00000351049:S466I;ENSP00000392753:S466I;ENSP00000353625:S466I	ENSP00000326864:S313I	S	+	2	0	PAK4	44359107	0.904000	0.30761	1.000000	0.80357	0.989000	0.77384	1.132000	0.31418	2.525000	0.85131	0.655000	0.94253	AGC	.		0.672	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			T	39667267	G	T	39667267	3	4	69	1	0	0	0	0	1	0	0	0	11429	971	34	4	1419	4	PAK4	19	39667267	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	6199924	39667267	19461716	125	6655											
SIRPB1	10326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	1551504	1551504	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgctgagatctccagggcaTagcttttgctgactgcttgc	6	12	12	11	1	1	2	0	2	1	1	2	3	1	2	1	1	4	5	1	1	1	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr20:1551504T>A	ENST00000381605.4	-	4	1095	c.1031A>T	c.(1030-1032)tAt>tTt	p.Y344F	RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000262929.5_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	344	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CTCCAGGGCATAGCTTTTGCT	0.507																																					p.Y344F		.											.	SIRPB1-91	0			c.A1031T						.						191	178	183					20																	1551504		2203	4300	6503	SO:0001583	missense	10326	exon4			AGGGCATAGCTTT	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.1031A>T	20.37:g.1551504T>A	ENSP00000371018:p.Tyr344Phe	Somatic	274	0		WXS	Illumina HiSeq	Phase_I	201	78	NM_006065	0	0	0	0	0	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	0.112	-1.137007	0.01742	.	.	ENSG00000101307	ENST00000381605	T	0.02015	4.5	1.96	-3.91	0.04168	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.801060	0.02558	N	0.096430	T	0.01156	0.0038	N	0.04959	-0.14	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44907	-0.9297	10	0.10636	T	0.68	.	3.3438	0.07128	0.5823:0.1453:0.0:0.2723	.	344	O00241	SIRB1_HUMAN	F	344	ENSP00000371018:Y344F	ENSP00000371018:Y344F	Y	-	2	0	SIRPB1	1499504	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.905000	0.04075	-1.342000	0.02222	-0.728000	0.03583	TAT	.		0.507	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		A	1551504	T	A	1551504	3	1	69	1	0	0	0	0	1	0	0	0	14365	1406	49	5	173	5	SIRPB1	20	1551504	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		1551504	61474016	126	6656											
ProSAPiP1	9762	broad.mit.edu	37	chr20	3146663	3146663	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccccaggtcctggtagcccGaccccccaccgctgctgccg	4	6	10	21	3	0	0	0	0	0	0	2	1	2	0	9	2	3	3	9	2	1	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr20:3146663G>A	ENST00000329152.3	-	2	2200	c.803C>T	c.(802-804)tCg>tTg	p.S268L	LZTS3_ENST00000360342.3_Missense_Mutation_p.S268L|LZTS3_ENST00000337576.5_Missense_Mutation_p.S268L			O60299	LZTS3_HUMAN		268						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											CTGGTAGCCCGACCCCCCACC	0.662																																					p.S268L													.	.	0			c.C803T						.						32	30	31					20																	3146663		2203	4300	6503	SO:0001583	missense	0	exon2			TAGCCCGACCCCC																												ENST00000329152.3:c.803C>T	20.37:g.3146663G>A	ENSP00000332123:p.Ser268Leu	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	51	4	NM_014731	0	0	13	13	0	A2A2Q7|D3DVX6|Q8IXX8	Missense_Mutation	SNP	ENST00000329152.3	37	CCDS13049.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.509731	0.44660	.	.	ENSG00000088899	ENST00000329152;ENST00000360342;ENST00000337576	T;T;T	0.39787	1.06;1.5;1.5	5.46	4.51	0.55191	.	5.061020	0.00166	N	0.000008	T	0.19927	0.0479	N	0.01352	-0.895	0.09310	N	1	B;B	0.19935	0.04;0.024	B;B	0.08055	0.003;0.002	T	0.19160	-1.0314	10	0.27082	T	0.32	-2.4182	7.31	0.26469	0.2318:0.0:0.7682:0.0	.	268;268	O60299-2;O60299	.;PRIP1_HUMAN	L	268	ENSP00000332123:S268L;ENSP00000353496:S268L;ENSP00000338166:S268L	ENSP00000332123:S268L	S	-	2	0	RP5-1187M17.10	3094663	0.996000	0.38824	0.977000	0.42913	0.962000	0.63368	4.192000	0.58378	1.297000	0.44761	0.561000	0.74099	TCG	.		0.662	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2			A	3146663	G	A	3146663	3	1	69	1	0	0	0	0	1	0	0	0	12902	1059	37	1	1226	1	ProSAPiP1	20	3146663	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1595159	3146663	59878857	127	6657											
GFRA4	64096	hgsc.bcm.edu	37	chr20	3641291	3641291	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcacgttgtccacgtagttAggggtgacggcggtgcctgc	5	10	15	11	4	1	1	1	1	0	0	2	1	2	1	2	4	2	3	2	4	2	3	rs367771398		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr20:3641291A>C	ENST00000319242.3	-	3	608	c.609T>G	c.(607-609)ccT>ccG	p.P203P	GFRA4_ENST00000290417.2_Silent_p.P173P			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	203					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						CCACGTAGTTAGGGGTGACGG	0.711																																					p.P203P		.											.	GFRA4-90	0			c.T609G						.	A	,	0,4208		0,0,2104	7	8	8		519,609	-0.8	1	20		8	4,8228		0,4,4112	no	coding-synonymous,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	0,4,6216	CC,CA,AA		0.0486,0.0,0.0322	,	173/270,203/300	3641291	4,12436	2104	4116	6220	SO:0001819	synonymous_variant	64096	exon3			GTAGTTAGGGGTG	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"persephin receptor"					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.609T>G	20.37:g.3641291A>C		Somatic	3	2		WXS	Illumina HiSeq	Phase_I	7	5	NM_145762	0	0	0	0	0	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			.		0.711	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762		C	3641291	A	C	3641291	2	2	69	1	0	0	0	0	0	0	0	1	6370	407	15	5		5	GFRA4	20	3641291	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	494628	3641291	59384229	128	6658											
PLCG1	5335	hgsc.bcm.edu	37	chr20	39796566	39796566	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaaaccctatgccaactttCaaggtacagctcaggcctct	11	9	7	14	0	3	0	2	0	1	0	3	0	3	0	3	2	5	3	3	2	5	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr20:39796566C>G	ENST00000373271.1	+	20	2781	c.2376C>G	c.(2374-2376)ttC>ttG	p.F792L	PLCG1_ENST00000373272.2_Missense_Mutation_p.F792L|PLCG1_ENST00000244007.3_Missense_Mutation_p.F792L	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	792	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TGCCAACTTTCAAGGTACAGC	0.557																																					p.F792L		.											.	PLCG1-911	0			c.C2376G						.						65	58	61					20																	39796566		2203	4300	6503	SO:0001583	missense	5335	exon20			AACTTTCAAGGTA	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing"	9065	protein-coding gene	gene with protein product		172420	"phospholipase C, gamma 1 (formerly subtype 148)"	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2376C>G	20.37:g.39796566C>G	ENSP00000362368:p.Phe792Leu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_182811	0	0	0	0	0	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	C	7.615	0.675542	0.14841	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.27890	1.64;1.64;1.64	5.25	0.965	0.19661	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);Src homology-3 domain (2);	0.151131	0.64402	D	0.000011	T	0.09291	0.0229	N	0.01874	-0.695	0.80722	D	1	B;B;B	0.24368	0.102;0.036;0.062	B;B;B	0.20384	0.029;0.013;0.013	T	0.13872	-1.0493	10	0.21540	T	0.41	.	5.9894	0.19452	0.1267:0.5726:0.0:0.3007	.	792;792;792	P19174-2;P19174;A2A284	.;PLCG1_HUMAN;.	L	792	ENSP00000244007:F792L;ENSP00000362368:F792L;ENSP00000362369:F792L	ENSP00000244007:F792L	F	+	3	2	PLCG1	39229980	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.811000	0.27198	0.379000	0.24794	-0.136000	0.14681	TTC	.		0.557	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		G	39796566	C	G	39796566	3	3	69	1	0	0	0	0	1	0	0	0	12061	825	29	4	2454	4	PLCG1	20	39796566	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	36155275	39796566	23228954	129	6659											
SLMO2	51012	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	57613690	57613690	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taacagtttcccacgggtggCtgccgatgtgaaccaaaaaa	13	8	10	10	2	0	1	0	1	0	0	1	2	1	1	3	2	3	2	3	2	5	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr20:57613690C>T	ENST00000355937.4	-	2	211		c.e2-1		SLMO2_ENST00000371033.5_Splice_Site	NM_016045.2	NP_057129.2	Q9Y3B1	SLMO2_HUMAN	slowmo homolog 2 (Drosophila)						phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(1)|lung(2)|skin(2)	5	all_lung(29;0.00711)		Colorectal(105;0.109)			CCACGGGTGGCTGCCGATGTG	0.338																																					.													.	SLMO2-45	0			c.33-1G>A						.						74	68	70					20																	57613690		1851	4088	5939	SO:0001630	splice_region_variant	51012	exon3			GGGTGGCTGCCGA	AF151865	CCDS42893.1, CCDS58783.1	20q13.32	2008-10-22	2007-02-06	2007-02-06	ENSG00000101166	ENSG00000101166			15892	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 45"	C20orf45			Standard	NM_016045		Approved	dJ543J19.5, PRELID3B	uc002yam.3	Q9Y3B1	OTTHUMG00000032856	ENST00000355937.4:c.33-1G>A	20.37:g.57613690C>T		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	137	54	NM_016045	0	0	0	1	1	E1P5I8|Q5JX17|Q9NUL0	Splice_Site	SNP	ENST00000355937.4	37	CCDS42893.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.006397	0.54361	.	.	ENSG00000101166	ENST00000355937;ENST00000371033	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9075	0.88923	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLMO2	57047085	1.000000	0.71417	0.998000	0.56505	0.573000	0.36030	7.299000	0.78831	2.530000	0.85305	0.655000	0.94253	.	.		0.338	SLMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079897.2	NM_016045	Intron	T	57613690	C	T	57613690	5	4	69	1	0	0	0	0	0	0	1	0	14783	811	28	2	572	2	SLMO2	20	57613690	Splice_Site	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	17817124	57613690	5411830	130	6660											
SF3A1	10291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30737847	30737847	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggattcgggcccccagctccTctggcgtggtggggggaggg	3	7	20	11	2	1	0	0	0	1	0	3	2	2	2	3	8	1	1	3	8	0	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:30737847T>A	ENST00000215793.8	-	7	1059	c.905A>T	c.(904-906)gAg>gTg	p.E302V	SF3A1_ENST00000439242.1_Missense_Mutation_p.E237V	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	302					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						CCCCAGCTCCTCTGGCGTGGT	0.547																																					p.E302V		.											.	SF3A1-157	0			c.A905T						.						60	57	58					22																	30737847		2203	4300	6503	SO:0001583	missense	10291	exon7			AGCTCCTCTGGCG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.905A>T	22.37:g.30737847T>A	ENSP00000215793:p.Glu302Val	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	104	31	NM_005877	0	0	6	9	3	E9PAW1	Missense_Mutation	SNP	ENST00000215793.8	37	CCDS13875.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.058118	0.55325	.	.	ENSG00000099995	ENST00000439242;ENST00000215793;ENST00000536049	T;T	0.34667	1.37;1.35	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.61311	0.2337	M	0.73598	2.24	0.80722	D	1	D	0.62365	0.991	D	0.76071	0.987	T	0.61987	-0.6949	10	0.48119	T	0.1	-28.8415	16.4504	0.83984	0.0:0.0:0.0:1.0	.	302	Q15459	SF3A1_HUMAN	V	237;302;199	ENSP00000390336:E237V;ENSP00000215793:E302V	ENSP00000215793:E302V	E	-	2	0	SF3A1	29067847	1.000000	0.71417	0.996000	0.52242	0.359000	0.29487	7.958000	0.87877	2.288000	0.76882	0.533000	0.62120	GAG	.		0.547	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		A	30737847	T	A	30737847	3	1	69	1	0	0	0	0	1	0	0	0	14178	1551	54	5	1516	5	SF3A1	22	30737847	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		30737847	20566719	131	6661											
APOBEC3G	60489	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	39482535	39482535	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggggctgcgcaccctggcCgaggctggggccaaaatttc	7	6	16	12	2	0	0	0	0	0	0	1	2	0	0	3	6	1	3	3	6	2	1	rs138907659		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:39482535C>G	ENST00000407997.3	+	6	1344	c.987C>G	c.(985-987)gcC>gcG	p.A329A	APOBEC3G_ENST00000452957.2_Silent_p.A329A	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	329	Necessary for homooligomerization.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					GCACCCTGGCCGAGGCTGGGG	0.522																																					p.A329A		.											.	APOBEC3G-227	0			c.C987G						.						101	112	108					22																	39482535		2203	4300	6503	SO:0001819	synonymous_variant	60489	exon6			CCTGGCCGAGGCT	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.987C>G	22.37:g.39482535C>G		Somatic	319	0		WXS	Illumina HiSeq	Phase_I	206	59	NM_021822	0	0	27	40	13	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	37	CCDS13984.1																																																																																			C|1.000;T|0.000		0.522	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		G	39482535	C	G	39482535	2	3	69	1	0	0	0	0	0	0	0	1	794	639	23	4		4	APOBEC3G	22	39482535	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	8744688	39482535	11822031	132	6662											
L3MBTL2	83746	ucsc.edu	37	chr22	41621938	41621938	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgacattgagctcacaccGccaaaaggtaagactagaga	17	6	9	9	1	1	4	1	2	0	2	1	5	1	4	2	1	1	2	2	1	5	3	rs376552822		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:41621938G>A	ENST00000216237.5	+	12	1655	c.1497G>A	c.(1495-1497)ccG>ccA	p.P499P		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	499					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGCTCACACCGCCAAAAGGTA	0.582																																					p.P499P													.	L3MBTL2-92	0			c.G1497A						.						77	58	64					22																	41621938		2203	4300	6503	SO:0001819	synonymous_variant	83746	exon12			CACACCGCCAAAA	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.1497G>A	22.37:g.41621938G>A		Somatic	59	1		WXS	Illumina HiSeq		41	4	NM_031488	0	0	0	0	0	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Silent	SNP	ENST00000216237.5	37	CCDS14011.1																																																																																			.		0.582	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		A	41621938	G	A	41621938	2	1	69	1	0	0	0	0	0	0	0	1	8613	1074	38	1		1	L3MBTL2	22	41621938	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	2139403	41621938	9682628	133	6663											
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	46804928	46804928	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgggcccaccactggtggCctccatcagaacgctgtcct	6	8	12	15	1	1	1	1	0	0	1	3	1	3	1	5	4	1	1	5	4	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:46804928C>T	ENST00000262738.3	-	9	5190	c.5191G>A	c.(5191-5193)Gcc>Acc	p.A1731T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1731	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CCACTGGTGGCCTCCATCAGA	0.657																																					p.A1731T		.											.	CELSR1-525	0			c.G5191A						.						55	49	51					22																	46804928		2203	4300	6503	SO:0001583	missense	9620	exon9			TGGTGGCCTCCAT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5191G>A	22.37:g.46804928C>T	ENSP00000262738:p.Ala1731Thr	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	33	9	NM_014246	0	0	1	6	5	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.522920	0.64747	.	.	ENSG00000075275	ENST00000262738	T	0.77877	-1.13	4.56	4.56	0.56223	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.079373	0.49305	U	0.000152	D	0.86690	0.5993	M	0.72118	2.19	0.34714	D	0.728064	D;P	0.76494	0.999;0.949	D;P	0.76575	0.988;0.881	D	0.89745	0.3936	10	0.36615	T	0.2	.	16.9316	0.86191	0.0:1.0:0.0:0.0	.	44;1731	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	T	1731	ENSP00000262738:A1731T	ENSP00000262738:A1731T	A	-	1	0	CELSR1	45183592	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	2.775000	0.47702	2.090000	0.63153	0.561000	0.74099	GCC	.		0.657	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46804928	C	T	46804928	3	4	69	1	0	0	0	0	1	0	0	0	3227	739	26	2	3961	2	CELSR1	22	46804928	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	5182990	46804928	4499638	134	6664											
KLHDC7B	113730	hgsc.bcm.edu	37	chr22	50987534	50987534	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcctcctgcggcggccccTgtgtccctgcctctacctgc	2	9	11	19	2	1	0	0	0	1	0	3	1	3	0	7	2	5	0	7	2	1	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:50987534T>C	ENST00000395676.2	+	1	1073	c.939T>C	c.(937-939)ccT>ccC	p.P313P	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	313										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CGGCGGCCCCTGTGTCCCTGC	0.736																																					p.P313P		.											.	KLHDC7B-90	0			c.T939C						.						20	26	24					22																	50987534		1802	3717	5519	SO:0001819	synonymous_variant	113730	exon1			GGCCCCTGTGTCC	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.939T>C	22.37:g.50987534T>C		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	96	5	NM_138433	0	0	0	0	0		Silent	SNP	ENST00000395676.2	37	CCDS14097.2																																																																																			.		0.736	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433		C	50987534	T	C	50987534	2	2	69	1	0	0	0	0	0	0	0	1	8382	1567	55	3		3	KLHDC7B	22	50987534	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	4182606	50987534	317032	135	6665											
RLIM	51132	bcgsc.ca	37	chrX	73811737	73811737	+	Silent	SNP	T	T	A																															ctaggactggaactggaactTgaactggaactggaactcga																								rs113198776		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chrX:73811737T>A	ENST00000332687.6	-	4	1631	c.1413A>T	c.(1411-1413)tcA>tcT	p.S471S	RLIM_ENST00000349225.2_Silent_p.S471S	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	471	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						aactggaacttgaactggaac	0.478																																					p.S471S	Esophageal Squamous(169;1899 1923 14997 18818 32118)												.	RLIM-228	0			c.A1413T						.						38	38	38					X																	73811737		2203	4300	6503	SO:0001819	synonymous_variant	51132	exon5			GGAACTTGAACTG	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1413A>T	X.37:g.73811737T>A		Somatic	40	2		WXS	Illumina HiSeq	Phase_1	35	12	NM_183353	1	0	1	2	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Silent	SNP	ENST00000332687.6	37	CCDS14427.1																																																																																			.		0.478	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		A	73811737	T	A	73811737	2	1	69	1	0	0	0	0	0	0	0	1	13422	1799	63	5		5	RLIM	23	73811737	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		73811737	81458823	136	6666	75	2									
RLIM	51132	bcgsc.ca	37	chrX	73811739	73811739	+	Missense_Mutation	SNP	A	A	G																															aggactggaactggaacttgAactggaactggaactcgaac																								rs201164156		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chrX:73811739A>G	ENST00000332687.6	-	4	1629	c.1411T>C	c.(1411-1413)Tca>Cca	p.S471P	RLIM_ENST00000349225.2_Missense_Mutation_p.S471P	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	471	Poly-Ser.|Ser-rich.				negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						ctggaacttgaactggaactg	0.483																																					p.S471P	Esophageal Squamous(169;1899 1923 14997 18818 32118)												.	RLIM-228	0			c.T1411C						.																																			SO:0001583	missense	51132	exon5			AACTTGAACTGGA	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1411T>C	X.37:g.73811739A>G	ENSP00000328059:p.Ser471Pro	Somatic	37	2		WXS	Illumina HiSeq	Phase_1	35	12	NM_183353	0	0	1	1	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.619369	0.00118	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	D;D	0.85258	-1.96;-1.96	1.66	0.0881	0.14453	.	0.638142	0.11946	U	0.514165	T	0.59032	0.2164	N	0.08118	0	0.09310	N	1	P	0.44734	0.842	B	0.29267	0.1	T	0.56607	-0.7951	10	0.34782	T	0.22	-0.2213	3.7245	0.08469	0.5962:0.4038:0.0:0.0	.	471	Q9NVW2	RNF12_HUMAN	P	471	ENSP00000328059:S471P;ENSP00000253571:S471P	ENSP00000328059:S471P	S	-	1	0	RLIM	73728464	0.991000	0.36638	0.012000	0.15200	0.011000	0.07611	0.068000	0.14531	0.675000	0.31264	0.441000	0.28932	TCA	.		0.483	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		G	73811739	A	G	73811739	3	3	69	1	0	0	0	0	1	0	0	0	13422	246	9	3	467	3	RLIM	23	73811739	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	2	73811739	81458821	137	6667	75	2									
KLHL4	56062	broad.mit.edu;bcgsc.ca	37	chrX	86887393	86887404	+	In_Frame_Del	DEL	GGACTGTGATGC	GGACTGTGATGC	-																															taatccagttggcaaaatctGgactgtgatgcctcccatgt																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	GGACTGTGATGC	GGACTGTGATGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chrX:86887393_86887404delGGACTGTGATGC	ENST00000373119.4	+	7	1653_1664	c.1508_1519delGGACTGTGATGC	c.(1507-1521)tggactgtgatgcct>tct	p.503_507WTVMP>S	KLHL4_ENST00000373114.4_In_Frame_Del_p.503_507WTVMP>S	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	503						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GGCAAAATCTGGACTGTGATGCCTCCCATGTC	0.373																																					p.503_507del													.	KLHL4-133	0			c.1508_1519del						.																																			SO:0001651	inframe_deletion	56062	exon7			AAATCTGGACTGT	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1508_1519delGGACTGTGATGC	X.37:g.86887393_86887404delGGACTGTGATGC	ENSP00000362211:p.Trp503_Pro507delinsSer	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	15	6	NM_019117	0	0	0	0	0	B2RTW2|Q9Y3J5	In_Frame_Del	DEL	ENST00000373119.4	37	CCDS14457.1																																																																																			.		0.373	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			-	86887404	GGACTGTGATGC	-	86887393	7	5	69	1	0	1	0	1	0	0	0	0	8412	1357	47	0	1534	0	KLHL4	23	86887393	In_Frame_Del	DEL	GGACTGTGATGC	TCGA-BQ-5885-01A-11D-1589-08	13075654	86887393	68383167	138	6668			2	21		2	2	18	N	GGACTGTGATGC_A	7.63295e-05
KLHL4	56062	bcgsc.ca	37	chrX	86887410	86887410	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggactgtgatgcctcccAtgtcaacacatcggcacggc	8	9	10	14	2	2	1	1	1	1	0	4	2	3	2	2	3	2	1	2	3	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chrX:86887410A>G	ENST00000373119.4	+	7	1670	c.1525A>G	c.(1525-1527)Atg>Gtg	p.M509V	KLHL4_ENST00000373114.4_Missense_Mutation_p.M509V	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	509						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GATGCCTCCCATGTCAACACA	0.368																																					p.M509V													.	KLHL4-133	0			c.A1525G						.						96	84	88					X																	86887410		2203	4300	6503	SO:0001583	missense	56062	exon7			CCTCCCATGTCAA	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1525A>G	X.37:g.86887410A>G	ENSP00000362211:p.Met509Val	Somatic	25	0		WXS	Illumina HiSeq	Phase_1	14	8	NM_019117	0	0	0	0	0	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.757884	0.69648	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	D;D	0.84146	-1.81;-1.81	5.33	5.33	0.75918	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.90783	0.7106	M	0.90759	3.145	0.80722	D	1	P;P	0.45569	0.861;0.707	P;P	0.50049	0.629;0.495	D	0.92172	0.5744	10	0.66056	D	0.02	.	13.4632	0.61239	1.0:0.0:0.0:0.0	.	509;509	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	V	509	ENSP00000362211:M509V;ENSP00000362206:M509V	ENSP00000362206:M509V	M	+	1	0	KLHL4	86774066	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.734000	0.91543	1.774000	0.52232	0.417000	0.27973	ATG	.		0.368	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			G	86887410	A	G	86887410	3	3	69	1	0	0	0	0	1	0	0	0	8412	217	8	3	1551	3	KLHL4	23	86887410	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	17	86887410	68383150	139	6669			2	21		2	2	18	N	GGACTGTGATGC_A	7.63295e-05
AGTR2	186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	115303624	115303624	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatctctggcaacaatgagTctaccttgaactgttcacag	12	11	7	11	0	3	2	1	2	2	0	4	2	3	2	1	1	3	2	1	1	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chrX:115303624T>G	ENST00000371906.4	+	3	281	c.91T>G	c.(91-93)Tct>Gct	p.S31A		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	31					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	CAACAATGAGTCTACCTTGAA	0.383																																					p.S31A		.											.	AGTR2-565	0			c.T91G						.						125	107	113					X																	115303624		2203	4300	6503	SO:0001583	missense	186	exon3			AATGAGTCTACCT	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.91T>G	X.37:g.115303624T>G	ENSP00000360973:p.Ser31Ala	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	98	63	NM_000686	0	0	0	0	0	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	T	7.505	0.653477	0.14580	.	.	ENSG00000180772	ENST00000371906	T	0.37752	1.18	4.14	4.14	0.48551	.	0.844018	0.10647	N	0.650365	T	0.24353	0.0590	N	0.19112	0.55	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.13019	-1.0525	10	0.39692	T	0.17	-5.3221	8.5784	0.33612	0.0:0.0:0.0:1.0	.	31	P50052	AGTR2_HUMAN	A	31	ENSP00000360973:S31A	ENSP00000360973:S31A	S	+	1	0	AGTR2	115217652	0.012000	0.17670	0.098000	0.21074	0.802000	0.45316	1.925000	0.40074	1.537000	0.49254	0.412000	0.27726	TCT	.		0.383	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		G	115303624	T	G	115303624	3	3	69	1	0	0	0	0	1	0	0	0	402	1667	58	5	93	5	AGTR2	23	115303624	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	28416214	115303624	39966936	140	6670											
RERE	473	broad.mit.edu;bcgsc.ca	37	chr1	8420197	8420197	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgactggctggcgtgactggGggtgtccaccacagtgggct	5	9	17	10	1	0	2	0	2	0	0	1	2	1	2	2	5	0	2	2	5	0	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:8420197G>C	ENST00000337907.3	-	19	4004	c.3370C>G	c.(3370-3372)Ccc>Gcc	p.P1124A	RERE_ENST00000400908.2_Missense_Mutation_p.P1124A|RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_Missense_Mutation_p.P856A|RERE_ENST00000476556.1_Missense_Mutation_p.P570A	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1124					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GCGTGACTGGGGGTGTCCACC	0.682																																					p.P1124A													.	RERE-515	0			c.C3370G						.						8	9	9					1																	8420197		2152	4188	6340	SO:0001583	missense	473	exon19			GACTGGGGGTGTC	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.3370C>G	1.37:g.8420197G>C	ENSP00000338629:p.Pro1124Ala	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	18	5	NM_012102	0	0	0	0	0	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124291	0.56613	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T;T	0.48836	0.8;0.81;0.99;0.8	5.56	5.56	0.83823	.	.	.	.	.	T	0.59770	0.2218	M	0.62016	1.91	0.80722	D	1	P;P	0.39883	0.693;0.56	P;P	0.49561	0.615;0.615	T	0.58211	-0.7676	9	0.46703	T	0.11	-25.6856	18.0981	0.89497	0.0:0.0:1.0:0.0	.	856;1124	B1AKN3;Q9P2R6	.;RERE_HUMAN	A	1124;856;570;1124	ENSP00000338629:P1124A;ENSP00000366684:P856A;ENSP00000422246:P570A;ENSP00000383700:P1124A	ENSP00000338629:P1124A	P	-	1	0	RERE	8342784	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	9.718000	0.98758	2.601000	0.87937	0.655000	0.94253	CCC	.		0.682	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			C	8420197	G	C	8420197	3	2	70	1	0	0	0	0	1	0	0	0	13263	1232	43	4	1354	4	RERE	1	8420197	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		8420197	240830424	1	6671											
COL11A1	1301	broad.mit.edu	37	chr1	103428308	103428308	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctattggaccagtctcaccGgttggtccctaaattagata	10	12	8	11	1	1	1	1	0	1	1	3	2	2	2	4	3	0	1	4	3	5	6	rs369136682		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:103428308G>A	ENST00000370096.3	-	39	3237	c.2925C>T	c.(2923-2925)acC>acT	p.T975T	COL11A1_ENST00000353414.4_Silent_p.T936T|COL11A1_ENST00000358392.2_Silent_p.T987T|COL11A1_ENST00000512756.1_Silent_p.T859T	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	975	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CAGTCTCACCGGTTGGTCCCT	0.438																																					p.T987T													.	COL11A1-586	0			c.C2961T						.	G	,,,	0,4406		0,0,2203	77	75	75		2808,2925,2961,2577	1.8	1	1		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL11A1	NM_001190709.1,NM_001854.3,NM_080629.2,NM_080630.3	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	936/1768,975/1807,987/1819,859/1691	103428308	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1301	exon39			CTCACCGGTTGGT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2925C>T	1.37:g.103428308G>A		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	129	4	NM_080629	0	0	0	0	0	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	37	CCDS778.1																																																																																			.		0.438	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103428308	G	A	103428308	2	1	70	1	0	0	0	0	0	0	0	1	3673	1103	39	1		1	COL11A1	1	103428308	Silent	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	95008111	103428308	145822313	2	6672											
SLC6A17	388662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110709565	110709565	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcatcaatgccgaagaacaGcaaagtgacccagcgtgagc	14	4	12	11	2	1	3	1	2	0	1	1	4	1	3	2	1	5	2	2	1	4	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:110709565G>A	ENST00000331565.4	+	2	499	c.14G>A	c.(13-15)aGc>aAc	p.S5N	RP5-1028L10.1_ENST00000418579.1_RNA|RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	5					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CCGAAGAACAGCAAAGTGACC	0.577																																					p.S5N		.											.	SLC6A17-92	0			c.G14A						.						54	49	51					1																	110709565		2203	4300	6503	SO:0001583	missense	388662	exon2			AGAACAGCAAAGT		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.14G>A	1.37:g.110709565G>A	ENSP00000330199:p.Ser5Asn	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	45	11	NM_001010898	0	0	0	0	0	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201454	0.79015	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.75938	-0.98	4.31	4.31	0.51392	.	0.091130	0.64402	D	0.000001	T	0.71921	0.3397	M	0.67397	2.05	0.44834	D	0.997843	P	0.42203	0.773	P	0.46208	0.507	T	0.76203	-0.3045	10	0.51188	T	0.08	.	16.9598	0.86269	0.0:0.0:1.0:0.0	.	5	Q9H1V8	S6A17_HUMAN	N	5	ENSP00000330199:S5N	ENSP00000330199:S5N	S	+	2	0	SLC6A17	110511088	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.350000	0.59392	2.221000	0.72209	0.563000	0.77884	AGC	.		0.577	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110709565	G	A	110709565	3	1	70	1	0	0	0	0	1	0	0	0	14712	971	34	2	16	2	SLC6A17	1	110709565	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	7281257	110709565	138541056	3	6673											
ELF3	1999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201984378	201984378	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctggaacgggtggatggccGgcgactcgtctacaagtttg	7	9	15	10	4	1	0	0	0	1	0	2	3	1	2	2	5	2	1	2	5	3	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:201984378G>C	ENST00000359651.3	+	8	4235	c.1043G>C	c.(1042-1044)cGg>cCg	p.R348P	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.R348P|ELF3_ENST00000367284.5_Missense_Mutation_p.R348P					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						GTGGATGGCCGGCGACTCGTC	0.557																																					p.R348P		.											.	ELF3-226	0			c.G1043C						.						84	86	85					1																	201984378		2203	4300	6503	SO:0001583	missense	1999	exon9			ATGGCCGGCGACT	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.1043G>C	1.37:g.201984378G>C	ENSP00000352673:p.Arg348Pro	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	69	15	NM_001114309	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.878405	0.91740	.	.	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044	T;T;T	0.15372	2.43;2.43;2.43	4.61	4.61	0.57282	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.64402	D	0.000001	T	0.48241	0.1489	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57877	-0.7735	10	0.87932	D	0	.	16.4352	0.83873	0.0:0.0:1.0:0.0	.	348	P78545	ELF3_HUMAN	P	348;348;348;325	ENSP00000352673:R348P;ENSP00000356253:R348P;ENSP00000356252:R348P	ENSP00000311348:R325P	R	+	2	0	ELF3	200251001	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.616000	0.98359	2.421000	0.82119	0.555000	0.69702	CGG	.		0.557	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		C	201984378	G	C	201984378	3	2	70	1	0	0	0	0	1	0	0	0	5068	1116	39	4	1073	4	ELF3	1	201984378	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	91274813	201984378	47266243	4	6674											
CAPN9	10753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	230883264	230883264	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccttacctctaccgggccCcagggcctcaggcacacccg	6	6	10	19	2	2	0	1	0	1	0	2	0	2	0	7	3	3	1	7	3	2	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:230883264C>G	ENST00000271971.2	+	1	135	c.22C>G	c.(22-24)Cca>Gca	p.P8A	CAPN9_ENST00000354537.1_Missense_Mutation_p.P8A|RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Missense_Mutation_p.P8A	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	8					digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				CTACCGGGCCCCAGGGCCTCA	0.622																																					p.P8A		.											.	CAPN9-91	0			c.C22G						.						57	64	62					1																	230883264		2203	4300	6503	SO:0001583	missense	10753	exon1			CGGGCCCCAGGGC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"EF-hand domain containing"	1486	protein-coding gene	gene with protein product	"novel calpain large subunit-4"	606401	"calpain 9 (nCL-4)"			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.22C>G	1.37:g.230883264C>G	ENSP00000271971:p.Pro8Ala	Somatic	151	1		WXS	Illumina HiSeq	Phase_I	150	45	NM_006615	0	0	0	0	0	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	.	.	.	.	.	.	.	.	.	.	C	6.007	0.369759	0.11352	.	.	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	T;T;T	0.48201	0.82;0.82;0.82	5.29	-0.727	0.11166	.	0.460979	0.25055	N	0.033497	T	0.21427	0.0516	N	0.24115	0.695	0.09310	N	1	B;B;B	0.10296	0.0;0.003;0.002	B;B;B	0.12837	0.001;0.008;0.004	T	0.17961	-1.0352	10	0.07175	T	0.84	.	2.0222	0.03511	0.1248:0.3314:0.123:0.4207	.	8;8;8	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	A	8	ENSP00000271971:P8A;ENSP00000346538:P8A;ENSP00000355626:P8A	ENSP00000271971:P8A	P	+	1	0	CAPN9	228949887	0.006000	0.16342	0.000000	0.03702	0.121000	0.20230	-0.053000	0.11846	-0.465000	0.06953	0.655000	0.94253	CCA	.		0.622	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		G	230883264	C	G	230883264	3	3	70	1	0	0	0	0	1	0	0	0	2638	623	22	4	24	4	CAPN9	1	230883264	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	28898886	230883264	18367357	5	6675											
FAM161A	84140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	62066806	62066806	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taagagttttggagacttgtGttctgagaggtgtttctggt	7	17	14	3	0	2	3	0	1	2	3	2	5	2	3	0	3	0	3	0	3	1	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:62066806G>A	ENST00000405894.3	-	3	1434	c.1333C>T	c.(1333-1335)Cac>Tac	p.H445Y	FAM161A_ENST00000404929.1_Missense_Mutation_p.H445Y	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	445					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GGAGACTTGTGTTCTGAGAGG	0.408																																					p.H445Y		.											.	FAM161A-136	0			c.C1333T						.						122	110	114					2																	62066806		1874	4103	5977	SO:0001583	missense	84140	exon3			ACTTGTGTTCTGA		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1333C>T	2.37:g.62066806G>A	ENSP00000385893:p.His445Tyr	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	170	52	NM_032180	0	0	0	0	0	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	G	7.735	0.700095	0.15106	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.21734	1.99;1.99	5.19	-0.0571	0.13803	.	0.977729	0.08450	N	0.943967	T	0.08980	0.0222	N	0.08118	0	0.09310	N	1	B;B	0.17268	0.003;0.021	B;B	0.17098	0.013;0.017	T	0.36841	-0.9731	10	0.28530	T	0.3	-13.5655	2.5423	0.04729	0.1324:0.2247:0.4122:0.2308	.	445;445	Q3B820;Q3B820-3	F161A_HUMAN;.	Y	445	ENSP00000385158:H445Y;ENSP00000385893:H445Y	ENSP00000385158:H445Y	H	-	1	0	FAM161A	61920310	0.001000	0.12720	0.001000	0.08648	0.044000	0.14063	0.602000	0.24134	-0.235000	0.09767	-0.185000	0.12909	CAC	.		0.408	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62066806	G	A	62066806	3	1	70	1	0	0	0	0	1	0	0	0	5488	1377	48	2	665	2	FAM161A	2	62066806	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		62066806	181132567	6	6676											
LMAN2L	81562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97373520	97373520	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcttttcctcttctggggTtctctccactgtcagttcaa	5	16	8	12	0	5	0	2	0	3	0	8	1	7	0	2	2	1	3	2	2	1	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:97373520T>C	ENST00000264963.4	-	7	857	c.835A>G	c.(835-837)Acc>Gcc	p.T279A	LMAN2L_ENST00000537039.1_Missense_Mutation_p.T141A|LMAN2L_ENST00000426463.2_Missense_Mutation_p.T145A|FER1L5_ENST00000457909.1_RNA|LMAN2L_ENST00000377079.4_Missense_Mutation_p.T290A|LMAN2L_ENST00000534882.1_Missense_Mutation_p.T134A	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like	279					ER to Golgi vesicle-mediated transport (GO:0006888)|protein folding (GO:0006457)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|lung(2)|skin(1)|urinary_tract(1)	7						TCTTCTGGGGTTCTCTCCACT	0.468																																					p.T290A		.											.	LMAN2L-90	0			c.A868G						.						111	111	111					2																	97373520		2203	4300	6503	SO:0001583	missense	81562	exon8			CTGGGGTTCTCTC	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453	ENST00000264963.4:c.835A>G	2.37:g.97373520T>C	ENSP00000264963:p.Thr279Ala	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	154	37	NM_001142292	0	0	0	0	0	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	37	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544490	0.65198	.	.	ENSG00000114988	ENST00000264963;ENST00000377079;ENST00000426463;ENST00000537039;ENST00000534882	T;T;T;T;T	0.77358	0.91;0.9;-1.09;-1.04;-1.08	5.62	5.62	0.85841	Concanavalin A-like lectin/glucanase, subgroup (1);	0.095537	0.64402	D	0.000001	T	0.69106	0.3074	L	0.46157	1.445	0.51482	D	0.999927	B;B;B;B;B	0.26081	0.141;0.031;0.141;0.004;0.065	B;B;B;B;B	0.20955	0.021;0.023;0.021;0.002;0.032	T	0.64846	-0.6311	10	0.09590	T	0.72	.	14.8095	0.69982	0.0:0.0:0.0:1.0	.	134;152;145;290;279	B4DVH1;B4DI83;B4DSH3;Q9H0V9-2;Q9H0V9	.;.;.;.;LMA2L_HUMAN	A	279;290;145;141;134	ENSP00000264963:T279A;ENSP00000366280:T290A;ENSP00000396391:T145A;ENSP00000441701:T141A;ENSP00000438501:T134A	ENSP00000264963:T279A	T	-	1	0	LMAN2L	96737247	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.930000	0.70104	2.129000	0.65627	0.533000	0.62120	ACC	.		0.468	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		C	97373520	T	C	97373520	3	2	70	1	0	0	0	0	1	0	0	0	8862	1725	60	3	219	3	LMAN2L	2	97373520	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	35306714	97373520	145825853	7	6677											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170072853	170072853	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaggttcccagtaaagagAgttttcacagatgtgccatc	11	11	10	9	1	1	2	1	0	0	2	4	4	2	2	2	1	1	3	2	1	2	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:170072853A>G	ENST00000263816.3	-	35	6021	c.5736T>C	c.(5734-5736)acT>acC	p.T1912T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1912					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CAGTAAAGAGAGTTTTCACAG	0.502																																					p.T1912T		.											.	LRP2-175	0			c.T5736C						.						150	136	141					2																	170072853		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon35			AAAGAGAGTTTTC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5736T>C	2.37:g.170072853A>G		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	105	41	NM_004525	0	0	0	0	0	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			.		0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170072853	A	G	170072853	2	3	70	1	0	0	0	0	0	0	0	1	8981	291	11	3		3	LRP2	2	170072853	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	72699333	170072853	73126520	8	6678											
SATB2	23314	hgsc.bcm.edu	37	chr2	200320598	200320598	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgggctgttacctcccaCggccttggccacggcgccgt	3	8	12	18	5	0	0	0	0	0	0	2	0	2	0	6	4	1	2	6	4	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:200320598C>G	ENST00000417098.1	-	2	979	c.163G>C	c.(163-165)Gtg>Ctg	p.V55L	SATB2_ENST00000260926.5_Missense_Mutation_p.V55L|SATB2_ENST00000457245.1_Missense_Mutation_p.V55L|SATB2-AS1_ENST00000442967.1_RNA|SATB2_ENST00000428695.1_Missense_Mutation_p.V55L|SATB2-AS1_ENST00000441234.1_RNA|SATB2_ENST00000443023.1_Missense_Mutation_p.V55L	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	55					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTACCTCCCACGGCCTTGGCC	0.706																																					p.V55L	Colon(30;262 767 11040 24421 36230)	.											.	SATB2-91	0			c.G163C						.						2	3	3					2																	200320598		1726	3685	5411	SO:0001583	missense	23314	exon3			CTCCCACGGCCTT	AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.163G>C	2.37:g.200320598C>G	ENSP00000401112:p.Val55Leu	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	7	5	NM_015265	0	0	0	0	0	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	9.937	1.216494	0.22373	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5	5.76	4.83	0.62350	.	0.188172	0.36519	N	0.002542	T	0.23451	0.0567	N	0.02011	-0.69	0.31777	N	0.631404	B;B	0.20261	0.043;0.012	B;B	0.15870	0.014;0.01	T	0.18241	-1.0343	10	0.21540	T	0.41	-4.8194	9.7471	0.40453	0.0:0.7856:0.1416:0.0728	.	55;55	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	L	55	ENSP00000401112:V55L;ENSP00000388764:V55L;ENSP00000260926:V55L;ENSP00000388581:V55L;ENSP00000405420:V55L	ENSP00000260926:V55L	V	-	1	0	SATB2	200028843	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.018000	0.30002	2.724000	0.93272	0.462000	0.41574	GTG	.		0.706	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		G	200320598	C	G	200320598	3	3	70	1	0	0	0	0	1	0	0	0	13886	536	19	4	2078	4	SATB2	2	200320598	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	30247745	200320598	42878775	9	6679											
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	37340849	37340849	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaacttaattgaacagcTtgaacaagataaggtaaaac	21	8	7	5	0	0	4	0	2	0	2	0	4	0	4	0	1	5	2	0	1	9	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr3:37340849T>C	ENST00000361924.2	+	9	1447	c.1073T>C	c.(1072-1074)cTt>cCt	p.L358P	GOLGA4_ENST00000356847.4_Missense_Mutation_p.L380P|GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	358	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ATTGAACAGCTTGAACAAGAT	0.333																																					p.L380P		.											.	GOLGA4-93	0			c.T1139C						.						44	44	44					3																	37340849		2203	4297	6500	SO:0001583	missense	2803	exon10			AACAGCTTGAACA	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1073T>C	3.37:g.37340849T>C	ENSP00000354486:p.Leu358Pro	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	78	41	NM_001172713	0	0	0	0	0	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388371	0.82902	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000450863;ENST00000437131	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.45	5.45	0.79879	.	0.000000	0.29830	N	0.011099	T	0.61825	0.2378	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.64939	-0.6289	10	0.52906	T	0.07	.	15.519	0.75851	0.0:0.0:0.0:1.0	.	358;380;358	Q13439-4;F8W8Q7;Q13439	.;.;GOGA4_HUMAN	P	358;380;363;229	ENSP00000354486:L358P;ENSP00000349305:L380P;ENSP00000387633:L363P;ENSP00000405842:L229P	ENSP00000349305:L380P	L	+	2	0	GOLGA4	37315853	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.923000	0.87546	2.077000	0.62373	0.372000	0.22366	CTT	.		0.333	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		C	37340849	T	C	37340849	3	2	70	1	0	0	0	0	1	0	0	0	6575	1609	56	3	1177	3	GOLGA4	3	37340849	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		37340849	160681581	10	6680											
MORC1	27136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	108788509	108788509	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggcaatagcaaagatgtTtagttttaactctcttggct	12	14	9	6	0	1	2	0	0	1	2	2	2	1	2	0	2	2	5	0	2	5	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr3:108788509T>A	ENST00000483760.1	-	9	828	c.785A>T	c.(784-786)aAa>aTa	p.K262I	MORC1_ENST00000232603.5_Missense_Mutation_p.K262I					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GCAAAGATGTTTAGTTTTAAC	0.373																																					p.K262I		.											.	MORC1-98	0			c.A785T						.						113	113	113					3																	108788509		2203	4300	6503	SO:0001583	missense	27136	exon9			AGATGTTTAGTTT	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"cancer/testis antigen 33"	603205	"microrchidia (mouse) homolog", "microrchidia homolog (mouse)"	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.785A>T	3.37:g.108788509T>A	ENSP00000417282:p.Lys262Ile	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	156	42	NM_014429	0	0	0	0	0		Missense_Mutation	SNP	ENST00000483760.1	37		.	.	.	.	.	.	.	.	.	.	T	20.8	4.054789	0.75960	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.74106	-0.81;-0.81	4.84	3.68	0.42216	ATPase-like, ATP-binding domain (1);	0.128321	0.35708	N	0.003033	D	0.82365	0.5021	M	0.69185	2.1	0.46298	D	0.998976	D;P	0.89917	1.0;0.892	D;P	0.87578	0.998;0.54	T	0.81984	-0.0682	10	0.62326	D	0.03	-23.3217	8.914	0.35570	0.0:0.0897:0.0:0.9103	.	262;262	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	262	ENSP00000232603:K262I;ENSP00000417282:K262I	ENSP00000232603:K262I	K	-	2	0	MORC1	110271199	1.000000	0.71417	0.933000	0.37362	0.947000	0.59692	3.950000	0.56676	0.972000	0.38314	0.482000	0.46254	AAA	.		0.373	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108788509	T	A	108788509	3	1	70	1	0	0	0	0	1	0	0	0	9726	1841	64	5	2249	5	MORC1	3	108788509	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	71447660	108788509	89233921	11	6681											
PODXL2	50512	broad.mit.edu	37	chr3	127379564	127379564	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccggggaccaggcctcatcAggtgtggaggtggagagcag	8	6	18	9	1	2	1	2	0	0	1	3	4	3	3	3	7	1	1	3	7	0	0	rs368660055		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr3:127379564A>G	ENST00000342480.6	+	3	732	c.693A>G	c.(691-693)tcA>tcG	p.S231S		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	231					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						AGGCCTCATCAGGTGTGGAGG	0.622																																					p.S231S													.	PODXL2-91	0			c.A693G						.						64	72	69					3																	127379564		2203	4300	6503	SO:0001819	synonymous_variant	50512	exon3			CTCATCAGGTGTG	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.693A>G	3.37:g.127379564A>G		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	173	3	NM_015720	0	0	0	0	0	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	37	CCDS3044.1																																																																																			.		0.622	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		G	127379564	A	G	127379564	2	3	70	1	0	0	0	0	0	0	0	1	12207	175	7	3		3	PODXL2	3	127379564	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	18591055	127379564	70642866	12	6682											
TACC3	10460	hgsc.bcm.edu	37	chr4	1741439	1741439	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgagcaggtaaaggcgaCacaggaggagaaccgggagc	13	2	17	9	2	0	2	0	1	0	1	0	6	0	4	2	5	3	2	2	5	3	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr4:1741439C>G	ENST00000313288.4	+	11	2058	c.1952C>G	c.(1951-1953)aCa>aGa	p.T651R		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	651					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GTAAAGGCGACACAGGAGGAG	0.672																																					p.T651R	Ovarian(120;482 2294 11894 35824)	.											.	TACC3-91	0			c.C1952G						.						83	62	69					4																	1741439		2183	4284	6467	SO:0001583	missense	10460	exon11			AGGCGACACAGGA	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.1952C>G	4.37:g.1741439C>G	ENSP00000326550:p.Thr651Arg	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	9	2	NM_006342	0	0	0	0	0	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243156	0.39697	.	.	ENSG00000013810	ENST00000313288	T	0.42900	0.96	4.17	-2.21	0.06973	.	1.447700	0.04587	N	0.396027	T	0.47021	0.1423	L	0.57536	1.79	0.09310	N	1	B;P	0.49696	0.095;0.927	B;P	0.52109	0.099;0.69	T	0.45338	-0.9268	10	0.62326	D	0.03	1.2548	4.1637	0.10296	0.2362:0.2398:0.0:0.5239	.	651;651	Q2NKK4;Q9Y6A5	.;TACC3_HUMAN	R	651	ENSP00000326550:T651R	ENSP00000326550:T651R	T	+	2	0	TACC3	1711237	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	0.085000	0.14912	-0.244000	0.09639	-0.142000	0.14014	ACA	.		0.672	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			G	1741439	C	G	1741439	3	3	70	1	0	0	0	0	1	0	0	0	15535	478	17	4	1990	4	TACC3	4	1741439	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08		1741439	189412837	13	6683											
DAPP1	27071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100787280	100787280	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatattacgctggaaattggTgagaatttttaagccttcag	12	14	10	5	1	1	1	1	1	0	1	1	4	1	2	1	2	2	1	1	2	5	7			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr4:100787280T>G	ENST00000512369.1	+	8	842		c.e8+2		DAPP1_ENST00000296414.7_Splice_Site	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides						protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		TGGAAATTGGTGAGAATTTTT	0.358																																					.		.											.	DAPP1-93	0			c.774+2T>G						.						81	74	77					4																	100787280		1864	4095	5959	SO:0001630	splice_region_variant	27071	exon8			AATTGGTGAGAAT	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.774+2T>G	4.37:g.100787280T>G		Somatic	35	1		WXS	Illumina HiSeq	Phase_I	31	8	NM_014395	0	0	0	0	0	Q8TCK5|Q9UHF2	Splice_Site	SNP	ENST00000512369.1	37	CCDS47112.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869368	0.72065	.	.	ENSG00000070190	ENST00000296414;ENST00000512369	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6232	0.76824	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	DAPP1	101006303	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	6.692000	0.74578	2.326000	0.78906	0.533000	0.62120	.	.		0.358	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1		Intron	G	100787280	T	G	100787280	5	3	70	1	0	0	0	0	0	0	1	0	4245	1710	59	5	806	5	DAPP1	4	100787280	Splice_Site	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	99045841	100787280	90366996	14	6684											
SLC30A5	64924	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr5	68399835	68399835	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagaaaagaatttaaagacaAaaagttaaatgatcctagga	22	9	7	3	0	0	4	0	1	0	3	1	5	1	5	1	1	0	1	1	1	11	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:68399835A>G	ENST00000396591.3	+	4	883				SLC30A5_ENST00000502979.1_Missense_Mutation_p.K66R|SLC30A5_ENST00000380860.4_Missense_Mutation_p.K107R	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5						cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TTTAAAGACAAAAAGTTAAAT	0.284																																					p.K107R		.											.	SLC30A5-226	0			c.A320G						.						22	23	23					5																	68399835		2178	4287	6465	SO:0001627	intron_variant	64924	exon4			AAGACAAAAAGTT	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.274-623A>G	5.37:g.68399835A>G		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	30	10	NM_024055	0	0	0	0	0	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	37	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.950224	0.34377	.	.	ENSG00000145740	ENST00000380860;ENST00000502979	.	.	.	2.74	2.74	0.32292	.	.	.	.	.	T	0.42832	0.1220	.	.	.	0.19300	N	0.99998	P	0.37398	0.593	P	0.45577	0.486	T	0.36696	-0.9737	7	0.87932	D	0	.	7.3651	0.26768	1.0:0.0:0.0:0.0	.	107	Q9BVY8	.	R	107;66	.	ENSP00000370241:K107R	K	+	2	0	SLC30A5	68435591	0.144000	0.22641	0.636000	0.29352	0.015000	0.08874	1.174000	0.31932	1.510000	0.48803	0.459000	0.35465	AAA	.		0.284	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			G	68399835	A	G	68399835	1	3	70	0	1	0	0	0	0	0	0	0	14590	14	1	3		3	SLC30A5	5	68399835	Intron	SNP	A	TCGA-BQ-5886-01A-11D-1589-08		68399835	112515425	15	6685											
F2RL2	2151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	75913735	75913735	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagaatccaaagaatgccAaggagatgaagtaatagagt	19	8	10	4	0	0	5	0	1	0	4	1	6	1	5	2	1	1	1	2	1	8	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:75913735A>G	ENST00000296641.4	-	2	1000	c.797T>C	c.(796-798)tTg>tCg	p.L266S	IQGAP2_ENST00000379730.3_Intron|IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000502745.1_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.L244S|IQGAP2_ENST00000396234.3_Intron	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	266					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		AAAGAATGCCAAGGAGATGAA	0.423																																					p.L266S		.											.	F2RL2-228	0			c.T797C						.						76	72	73					5																	75913735		2203	4300	6503	SO:0001583	missense	2151	exon2			AATGCCAAGGAGA	U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"GPCR / Class A : Protease activated receptors"	3539	protein-coding gene	gene with protein product	"proteinase-activated receptor-3"	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.797T>C	5.37:g.75913735A>G	ENSP00000296641:p.Leu266Ser	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	59	14	NM_004101	0	0	0	0	0	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	CCDS4031.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155954	0.78114	.	.	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.70045	-0.45;-0.45	5.3	5.3	0.74995	GPCR, rhodopsin-like superfamily (1);	0.152354	0.43579	D	0.000549	T	0.76695	0.4023	L	0.56340	1.77	0.46678	D	0.999155	D	0.89917	1.0	D	0.80764	0.994	T	0.73272	-0.4035	10	0.22706	T	0.39	-8.0196	15.2748	0.73734	1.0:0.0:0.0:0.0	.	266	O00254	PAR3_HUMAN	S	266;244	ENSP00000296641:L266S;ENSP00000426703:L244S	ENSP00000296641:L266S	L	-	2	0	F2RL2	75949491	1.000000	0.71417	0.860000	0.33809	0.967000	0.64934	8.850000	0.92190	2.006000	0.58801	0.460000	0.39030	TTG	.		0.423	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3			G	75913735	A	G	75913735	3	3	70	1	0	0	0	0	1	0	0	0	5358	131	5	3	331	3	F2RL2	5	75913735	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	7513900	75913735	105001525	16	6686											
BHMT	635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	78415082	78415082	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcctcattcactctcccagTtcgccagcttcatcgagagt	7	13	6	15	2	4	1	3	0	1	1	8	2	5	1	3	0	1	2	3	0	0	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:78415082T>C	ENST00000274353.5	+	3	274	c.167T>C	c.(166-168)gTt>gCt	p.V56A	BHMT_ENST00000524080.1_Intron|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	56	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				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)	ACTCTCCCAGTTCGCCAGCTT	0.433																																					p.V56A		.											.	BHMT-91	0			c.T167C						.						92	87	89					5																	78415082		2203	4300	6503	SO:0001630	splice_region_variant	635	exon3			TCCCAGTTCGCCA	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.167-1T>C	5.37:g.78415082T>C		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	125	41	NM_001713	0	0	0	0	0	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388243	0.82902	.	.	ENSG00000145692	ENST00000274353	T	0.45276	0.9	5.6	5.6	0.85130	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.73249	0.3563	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.81360	-0.0968	9	.	.	.	.	16.0786	0.80985	0.0:0.0:0.0:1.0	.	56	Q93088	BHMT1_HUMAN	A	56	ENSP00000274353:V56A	.	V	+	2	0	BHMT	78450838	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	7.669000	0.83911	2.254000	0.74563	0.460000	0.39030	GTT	.		0.433	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713	Missense_Mutation	C	78415082	T	C	78415082	5	2	70	1	0	0	0	0	0	0	1	0	1426	1739	60	3	177	3	BHMT	5	78415082	Splice_Site	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	2501347	78415082	102500178	17	6687											
PCDHB3	56132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140481178	140481178	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgaagcgattaatagttaTgaagtcgacatcgaggccaa	14	11	10	6	3	0	2	0	2	0	0	2	5	0	2	1	1	1	1	1	1	6	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:140481178T>C	ENST00000231130.2	+	1	945	c.945T>C	c.(943-945)taT>taC	p.Y315Y	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	315	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTAATAGTTATGAAGTCGACA	0.428																																					p.Y315Y		.											.	PCDHB3-92	0			c.T945C						.						54	58	56					5																	140481178		2203	4300	6503	SO:0001819	synonymous_variant	56132	exon1			TAGTTATGAAGTC	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.945T>C	5.37:g.140481178T>C		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	86	32	NM_018937	0	0	0	0	0	B2R8P2	Silent	SNP	ENST00000231130.2	37	CCDS4245.1																																																																																			.		0.428	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		C	140481178	T	C	140481178	2	2	70	1	0	0	0	0	0	0	0	1	11569	1471	51	3		3	PCDHB3	5	140481178	Silent	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	62066096	140481178	40434082	18	6688											
ODZ2	57451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	167674296	167674296	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctccccgttgacctctacCgctatgatgagatttctggc	6	12	8	15	2	2	3	0	3	2	1	3	4	3	3	5	1	1	2	5	1	2	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:167674296C>A	ENST00000518659.1	+	27	6391	c.6352C>A	c.(6352-6354)Cgc>Agc	p.R2118S	TENM2_ENST00000403607.2_Missense_Mutation_p.R1942S|TENM2_ENST00000520394.1_Missense_Mutation_p.R1879S|TENM2_ENST00000519204.1_Missense_Mutation_p.R1997S|TENM2_ENST00000545108.1_Missense_Mutation_p.R2117S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2118					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGACCTCTACCGCTATGATGA	0.493																																					p.R2109S		.											.	.	0			c.C6325A						.						167	167	167					5																	167674296		2016	4172	6188	SO:0001583	missense	57451	exon27			CTCTACCGCTATG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"odz, odd Oz/ten-m homolog 2 (Drosophila)"	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6352C>A	5.37:g.167674296C>A	ENSP00000429430:p.Arg2118Ser	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	185	57	NM_001122679	0	0	0	0	0	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	18.69	3.678710	0.68042	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89123	-1.99;-1.98;-2.09;-2.44;-2.47	5.44	5.44	0.79542	.	0.103671	0.64402	D	0.000001	D	0.93861	0.8036	M	0.71581	2.175	0.54753	D	0.999989	D;P;D	0.69078	0.974;0.899;0.997	P;B;D	0.75484	0.807;0.44;0.986	D	0.92184	0.5754	10	0.30854	T	0.27	.	19.2461	0.93902	0.0:1.0:0.0:0.0	.	2117;2118;1879	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2118;2117;1997;1879;1942	ENSP00000429430:R2118S;ENSP00000438635:R2117S;ENSP00000428964:R1997S;ENSP00000427874:R1879S;ENSP00000384905:R1942S	ENSP00000384905:R1942S	R	+	1	0	ODZ2	167606874	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.906000	0.56340	2.560000	0.86352	0.561000	0.74099	CGC	.		0.493	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167674296	C	A	167674296	3	1	70	1	0	0	0	0	1	0	0	0	10861	652	23	4	6431	4	ODZ2	5	167674296	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	27193118	167674296	13240964	19	6689											
PFN3	345456	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176827191	176827191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctgcatgcgcagcccgcgTatgagttcgtgcaccgtctt	5	10	11	15	5	1	1	0	1	1	0	2	1	1	1	3	0	4	5	3	0	1	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:176827191T>C	ENST00000358571.2	-	1	446	c.387A>G	c.(385-387)atA>atG	p.I129M	F12_ENST00000514943.1_5'Flank	NM_001029886.2	NP_001025057.1	P60673	PROF3_HUMAN	profilin 3	129					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	lipid binding (GO:0008289)			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAGCCCGCGTATGAGTTCGT	0.706																																					p.I129M		.											.	PFN3-90	0			c.A387G						.						18	19	19					5																	176827191		2099	4229	6328	SO:0001583	missense	345456	exon1			CCCGCGTATGAGT	AC090063	CCDS34301.1	5q35.2	2008-08-26			ENSG00000196570	ENSG00000196570			18627	protein-coding gene	gene with protein product		612812				11867228	Standard	NM_001029886		Approved		uc003mgl.2	P60673	OTTHUMG00000163408	ENST00000358571.2:c.387A>G	5.37:g.176827191T>C	ENSP00000351379:p.Ile129Met	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	52	14	NM_001029886	0	0	0	0	0	A2RUL3	Missense_Mutation	SNP	ENST00000358571.2	37	CCDS34301.1	.	.	.	.	.	.	.	.	.	.	T	11.75	1.732218	0.30684	.	.	ENSG00000196570	ENST00000358571	D	0.85861	-2.04	4.76	2.91	0.33838	.	0.294068	0.29459	N	0.012099	D	0.86167	0.5868	L	0.44542	1.39	0.21652	N	0.999609	D	0.71674	0.998	D	0.79108	0.992	T	0.74847	-0.3525	10	0.39692	T	0.17	.	5.3821	0.16197	0.1086:0.0:0.6881:0.2033	.	129	P60673	PROF3_HUMAN	M	129	ENSP00000351379:I129M	ENSP00000351379:I129M	I	-	3	3	PFN3	176759797	0.015000	0.18098	0.596000	0.28811	0.168000	0.22595	-0.004000	0.12878	0.415000	0.25817	-0.724000	0.03597	ATA	.		0.706	PFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373234.1	NM_001029886		C	176827191	T	C	176827191	3	2	70	1	0	0	0	0	1	0	0	0	11795	1628	57	3	30	3	PFN3	5	176827191	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	9152895	176827191	4088069	20	6690											
VARS2	57176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30893383	30893383	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggccttcttggagcccctgGgcaccctgggctactgtggg	4	9	15	13	0	1	0	0	0	1	0	1	1	1	1	4	5	2	2	4	5	1	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:30893383G>C	ENST00000321897.5	+	27	3480	c.2848G>C	c.(2848-2850)Ggc>Cgc	p.G950R	VARS2_ENST00000416670.2_Missense_Mutation_p.G950R|VARS2_ENST00000541562.1_Missense_Mutation_p.G980R|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Missense_Mutation_p.G810R			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	950					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						GGAGCCCCTGGGCACCCTGGG	0.647																																					p.G980R		.											.	VARS2-26	0			c.G2938C						.						19	22	21					6																	30893383		1493	2701	4194	SO:0001583	missense	57176	exon28			CCCCTGGGCACCC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2848G>C	6.37:g.30893383G>C	ENSP00000316092:p.Gly950Arg	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	41	9	NM_001167734	0	0	0	0	0	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	G	5.589	0.293519	0.10567	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.62	3.84	0.44239	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.708730	0.14077	N	0.342996	T	0.13628	0.0330	L	0.44542	1.39	0.30330	N	0.78675	B;B;B;B	0.29988	0.264;0.001;0.002;0.0	B;B;B;B	0.26094	0.066;0.001;0.001;0.0	T	0.15378	-1.0439	10	0.15952	T	0.53	-9.346	8.9906	0.36022	0.1719:0.0:0.8281:0.0	.	388;948;980;950	Q5ST30-2;B7ZL25;F5GXJ0;Q5ST30	.;.;.;SYVM_HUMAN	R	950;950;810;980	ENSP00000316092:G950R;ENSP00000394802:G950R;ENSP00000438200:G810R;ENSP00000441000:G980R	ENSP00000316092:G950R	G	+	1	0	VARS2	31001362	0.997000	0.39634	1.000000	0.80357	0.153000	0.21895	0.990000	0.29642	0.737000	0.32582	-0.140000	0.14226	GGC	.		0.647	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		C	30893383	G	C	30893383	3	2	70	1	0	0	0	0	1	0	0	0	17157	1232	43	4	3048	4	VARS2	6	30893383	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		30893383	140221684	21	6691											
TTBK1	84630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43226956	43226956	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggggtcctgaggctgaagtCtgggaggagacagatgtcaa	10	7	18	6	0	2	4	1	2	1	2	3	6	3	5	1	5	0	1	1	5	2	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:43226956C>G	ENST00000259750.4	+	11	1280	c.1197C>G	c.(1195-1197)gtC>gtG	p.V399V	TTBK1_ENST00000304139.5_Silent_p.V348V	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	399					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			AGGCTGAAGTCTGGGAGGAGA	0.642																																					p.V399V		.											.	TTBK1-353	0			c.C1197G						.						51	58	56					6																	43226956		2203	4300	6503	SO:0001819	synonymous_variant	84630	exon11			TGAAGTCTGGGAG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.1197C>G	6.37:g.43226956C>G		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	104	26	NM_032538	0	0	0	0	0	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	37	CCDS34455.1																																																																																			.		0.642	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			G	43226956	C	G	43226956	2	3	70	1	0	0	0	0	0	0	0	1	16709	900	32	4		4	TTBK1	6	43226956	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	12333573	43226956	127888111	22	6692											
GPR110	266977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	46977043	46977043	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aatgacagatataatgagagGgcacccataacccaggcaaa	18	5	9	9	0	0	3	0	2	0	2	0	4	0	3	2	2	1	2	2	2	5	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:46977043G>A	ENST00000371253.2	-	11	2343	c.2128C>T	c.(2128-2130)Cct>Tct	p.P710S	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.P513S	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	710					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						ATAATGAGAGGGCACCCATAA	0.478																																					p.P710S		.											.	GPR110-71	0			c.C2128T						.						88	80	83					6																	46977043		2203	4300	6503	SO:0001583	missense	266977	exon11			TGAGAGGGCACCC	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"-", "GPCR / Class B : Orphans"	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2128C>T	6.37:g.46977043G>A	ENSP00000360299:p.Pro710Ser	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	56	16	NM_153840	0	0	0	0	0	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.576276	0.86645	.	.	ENSG00000153292	ENST00000371253;ENST00000283297	D;D	0.84516	-1.86;-1.86	5.9	5.9	0.94986	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000013	D	0.93572	0.7948	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93726	0.7037	10	0.87932	D	0	-22.4263	20.2789	0.98501	0.0:0.0:1.0:0.0	.	710	Q5T601	GP110_HUMAN	S	710;513	ENSP00000360299:P710S;ENSP00000283297:P513S	ENSP00000283297:P513S	P	-	1	0	GPR110	47085002	1.000000	0.71417	0.995000	0.50966	0.855000	0.48748	9.861000	0.99562	2.788000	0.95919	0.650000	0.86243	CCT	.		0.478	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46977043	G	A	46977043	3	1	70	1	0	0	0	0	1	0	0	0	6647	1232	43	2	624	2	GPR110	6	46977043	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	3750087	46977043	124138024	23	6693											
AIM1	202	hgsc.bcm.edu	37	chr6	106960432	106960432	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgacgggggcgttgcctcCgctgcgagcccagagtccaa	6	6	14	15	5	0	1	0	0	0	1	3	3	2	1	4	2	3	2	4	2	1	1	rs146137130	byFrequency	TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:106960432C>G	ENST00000369066.3	+	1	703	c.216C>G	c.(214-216)tcC>tcG	p.S72S		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GCGTTGCCTCCGCTGCGAGCC	0.677																																					p.S72S		.											.	AIM1-139	0			c.C216G						.						11	11	11					6																	106960432		2153	4219	6372	SO:0001819	synonymous_variant	202	exon1			TGCCTCCGCTGCG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.216C>G	6.37:g.106960432C>G		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	14	4	NM_001624	0	0	0	0	0	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	37	CCDS34506.1																																																																																			C|0.995;A|0.005		0.677	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			G	106960432	C	G	106960432	2	3	70	1	0	0	0	0	0	0	0	1	430	639	23	4		4	AIM1	6	106960432	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	59983389	106960432	64154635	24	6694											
C6orf170	221322	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	121576521	121576521	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaacagaatcagaaccctcTactggagtaggaattctttc	14	10	8	9	0	3	2	1	0	2	2	4	5	3	4	1	2	3	1	1	2	6	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:121576521T>A	ENST00000398212.2	-	17	2020	c.1971A>T	c.(1969-1971)gtA>gtT	p.V657V	TBC1D32_ENST00000275159.6_Silent_p.V657V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	657					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										CAGAACCCTCTACTGGAGTAG	0.289																																					p.V657V		.											.	C6orf170-92	0			c.A1971T						.						55	55	55					6																	121576521		1794	4047	5841	SO:0001819	synonymous_variant	221322	exon17			ACCCTCTACTGGA	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"broad-minded homolog"	615867	"chromosome 6 open reading frame 171", "chromosome 6 open reading frame 170"	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1971A>T	6.37:g.121576521T>A		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	116	43	NM_152730	0	0	0	0	0	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			.		0.289	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121576521	T	A	121576521	2	1	70	1	0	0	0	0	0	0	0	1	2350	1509	53	5		5	C6orf170	6	121576521	Silent	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	14616089	121576521	49538546	25	6695											
HIVEP2	3097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	143091819	143091819	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccaagtatctgagaaaTgcttgtgtacatgacacttc	11	12	8	10	0	1	2	0	2	1	1	2	3	1	2	1	0	3	3	1	0	4	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:143091819T>C	ENST00000367604.1	-	4	4696	c.4057A>G	c.(4057-4059)Att>Gtt	p.I1353V	HIVEP2_ENST00000367603.2_Missense_Mutation_p.I1353V|HIVEP2_ENST00000012134.2_Missense_Mutation_p.I1353V			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ATCTGAGAAATGCTTGTGTAC	0.507																																					p.I1353V	Esophageal Squamous(107;843 1510 13293 16805 42198)	.											.	HIVEP2-95	0			c.A4057G						.						81	80	80					6																	143091819		2007	4178	6185	SO:0001583	missense	3097	exon5			GAGAAATGCTTGT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.4057A>G	6.37:g.143091819T>C	ENSP00000356576:p.Ile1353Val	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	96	29	NM_006734	0	0	0	0	0	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	T	9.819	1.185356	0.21870	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02121	4.44;4.44;4.44	6.08	6.08	0.98989	.	0.046170	0.85682	D	0.000000	T	0.01092	0.0036	L	0.38953	1.18	0.46927	D	0.999254	B	0.30236	0.274	B	0.19666	0.026	T	0.62296	-0.6884	10	0.23891	T	0.37	-16.7632	16.6438	0.85155	0.0:0.0:0.0:1.0	.	1353	P31629	ZEP2_HUMAN	V	1353	ENSP00000356576:I1353V;ENSP00000356575:I1353V;ENSP00000012134:I1353V	ENSP00000012134:I1353V	I	-	1	0	HIVEP2	143133512	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.593000	0.61034	2.333000	0.79357	0.533000	0.62120	ATT	.		0.507	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			C	143091819	T	C	143091819	3	2	70	1	0	0	0	0	1	0	0	0	7208	1464	51	3	3307	3	HIVEP2	6	143091819	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	21515298	143091819	28023248	26	6696											
CADPS2	93664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	122269335	122269335	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgccaattgcagccggccAtcaagttcccttctgatctg	7	12	8	14	1	4	1	1	1	3	0	5	1	5	1	4	1	3	2	4	1	2	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr7:122269335A>G	ENST00000449022.2	-	4	853	c.834T>C	c.(832-834)gaT>gaC	p.D278D	CADPS2_ENST00000334010.7_Silent_p.D278D|CADPS2_ENST00000313070.7_Silent_p.D278D|CADPS2_ENST00000412584.2_Silent_p.D278D	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	278					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GCAGCCGGCCATCAAGTTCCC	0.358																																					p.D278D		.											.	CADPS2-94	0			c.T834C						.						67	64	65					7																	122269335		1866	4095	5961	SO:0001819	synonymous_variant	93664	exon4			CCGGCCATCAAGT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.834T>C	7.37:g.122269335A>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	33	6	NM_001167940	0	0	0	0	0	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	37	CCDS55158.1																																																																																			.		0.358	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		G	122269335	A	G	122269335	2	3	70	1	0	0	0	0	0	0	0	1	2577	214	8	3		3	CADPS2	7	122269335	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08		122269335	36869328	27	6697											
NUP205	23165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	135276257	135276257	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcctccaactatttatatTccttatttgaagatgctcca	10	17	4	10	0	0	2	0	1	0	1	3	2	3	2	4	0	3	1	4	0	6	8			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr7:135276257T>G	ENST00000285968.6	+	11	1559	c.1533T>G	c.(1531-1533)atT>atG	p.I511M	NUP205_ENST00000440390.2_Intron	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	511					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CTATTTATATTCCTTATTTGA	0.403																																					p.I511M		.											.	NUP205-207	0			c.T1533G						.						122	115	117					7																	135276257		2203	4300	6503	SO:0001583	missense	23165	exon11			TTATATTCCTTAT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1533T>G	7.37:g.135276257T>G	ENSP00000285968:p.Ile511Met	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	130	46	NM_015135	0	0	0	0	0	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806891	0.70797	.	.	ENSG00000155561	ENST00000285968	T	0.32023	1.47	5.96	3.3	0.37823	.	0.043164	0.85682	D	0.000000	T	0.32615	0.0835	L	0.55481	1.735	0.80722	D	1	P	0.51653	0.947	P	0.50231	0.635	T	0.06427	-1.0827	10	0.46703	T	0.11	-10.0959	4.1716	0.10332	0.1437:0.2942:0.0:0.5621	.	511	Q92621	NU205_HUMAN	M	511	ENSP00000285968:I511M	ENSP00000285968:I511M	I	+	3	3	NUP205	134926797	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.569000	0.23638	0.394000	0.25230	0.533000	0.62120	ATT	.		0.403	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			G	135276257	T	G	135276257	3	3	70	1	0	0	0	0	1	0	0	0	10785	1771	62	5	1575	5	NUP205	7	135276257	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	13006922	135276257	23862406	28	6698											
RGS20	8601	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	54764571	54764572	+	Frame_Shift_Del	DEL	AT	AT	-																															ctcagagatataatacagacAttcaccaaatcacagaaaat																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr8:54764571_54764572delAT	ENST00000297313.3	+	1	204_205	c.112_113delAT	c.(112-114)attfs	p.I38fs	RGS20_ENST00000344277.6_Frame_Shift_Del_p.I38fs	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	38					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			TAATACAGACATTCACCAAATC	0.455																																					p.38_38del		.											.	RGS20-227	0			c.112_113del						.																																			SO:0001589	frameshift_variant	8601	exon1			.	AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.112_113delAT	8.37:g.54764571_54764572delAT	ENSP00000297313:p.Ile38fs	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	119	38	NM_170587	0	0	0	0	0	Q96BG9	Frame_Shift_Del	DEL	ENST00000297313.3	37	CCDS6155.1																																																																																			.		0.455	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			-	54764572	AT	-	54764571	7	5	70	1	0	1	0	1	0	0	0	0	13335	217	8	0	114	0	RGS20	8	54764571	Frame_Shift_Del	DEL	AT	TCGA-BQ-5886-01A-11D-1589-08		54764571	91599451	29	6699	76	2									
RGS20	8601	bcgsc.ca	37	chr8	54764573	54764573	+	Silent	SNP	T	T	C																															cagagatataatacagacatTcaccaaatcacagaaaatga																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr8:54764573T>C	ENST00000297313.3	+	1	206	c.114T>C	c.(112-114)atT>atC	p.I38I	RGS20_ENST00000344277.6_Silent_p.I38I	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	38					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			ATACAGACATTCACCAAATCA	0.458																																					p.I38I													.	RGS20-227	0			c.T114C						.						109	110	110					8																	54764573		2203	4300	6503	SO:0001819	synonymous_variant	8601	exon1			AGACATTCACCAA	AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.114T>C	8.37:g.54764573T>C		Somatic	121	0		WXS	Illumina HiSeq	Phase_1	109	34	NM_170587	0	0	0	0	0	Q96BG9	Silent	SNP	ENST00000297313.3	37	CCDS6155.1																																																																																			.		0.458	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			C	54764573	T	C	54764573	2	2	70	1	0	0	0	0	0	0	0	1	13335	1771	62	3		3	RGS20	8	54764573	Silent	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	2	54764573	91599449	30	6700	76	2									
PPAPDC2	403313	hgsc.bcm.edu	37	chr9	4662477	4662477	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccatggcggcggtggcggCggcagcaggtttgagttcca	5	7	18	11	4	0	1	0	1	0	0	1	1	1	1	2	7	1	4	2	7	0	2	rs369535277		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:4662477C>A	ENST00000381883.2	+	1	180	c.102C>A	c.(100-102)ggC>ggA	p.G34G	SPATA6L_ENST00000223517.5_Intron|SPATA6L_ENST00000381895.5_Intron|SPATA6L_ENST00000381890.5_Intron|SPATA6L_ENST00000454239.2_Intron|SPATA6L_ENST00000475086.1_Intron	NM_203453.3	NP_982278.3	Q8IY26	PPAC2_HUMAN	phosphatidic acid phosphatase type 2 domain containing 2	34						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(2)|lung(1)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.026)		GCGGTGGCGGCGGCAGCAGGT	0.731											OREG0019084	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0	0	5008	,	,		11652	0		0.001	False		,,,				2504	0				p.G34G	Melanoma(187;1057 3809 8526)	.											.	PPAPDC2-90	0			c.C102A						.	C	,	0,2856		0,0,1428	2	3	3		,102	2.9	0.2	9		3	3,6207		0,3,3102	no	intron,coding-synonymous	C9orf68,PPAPDC2	NM_001039395.3,NM_203453.2	,	0,3,4530	AA,AC,CC		0.0483,0.0,0.0331	,	,34/296	4662477	3,9063	1428	3105	4533	SO:0001819	synonymous_variant	403313	exon1			TGGCGGCGGCAGC	AK128369	CCDS34981.1	9p24	2010-04-23			ENSG00000205808	ENSG00000205808			23682	protein-coding gene	gene with protein product	"polyisoprenoid diphosphate phosphatase type 1"	611666				16464866	Standard	NM_203453		Approved	FLJ90191, FLJ46512, PDP1	uc003zin.4	Q8IY26	OTTHUMG00000019466	ENST00000381883.2:c.102C>A	9.37:g.4662477C>A		Somatic	4	1	620	WXS	Illumina HiSeq	Phase_I	10	7	NM_203453	0	0	0	0	0	B3KY05|Q5JVJ6|Q8NCK9	Silent	SNP	ENST00000381883.2	37	CCDS34981.1																																																																																			.		0.731	PPAPDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051567.1	NM_203453		A	4662477	C	A	4662477	2	1	70	1	0	0	0	0	0	0	0	1	12321	755	27	4		4	PPAPDC2	9	4662477	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08		4662477	136550954	31	6701											
FANCG	2189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35077002	35077002	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaccccagtgctgtgtacAcctggaccaacacaggccgt	10	6	11	14	1	0	0	0	0	0	0	0	2	0	2	5	3	3	2	5	3	2	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:35077002A>G	ENST00000378643.3	-	6	1234	c.743T>C	c.(742-744)gTg>gCg	p.V248A	FANCG_ENST00000476212.1_5'Flank	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	248					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|mitochondrion organization (GO:0007005)|ovarian follicle development (GO:0001541)|response to radiation (GO:0009314)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	damaged DNA binding (GO:0003684)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|stomach(1)	28			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TGCTGTGTACACCTGGACCAA	0.527			"Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks																													p.V248A		.	yes	Rec		Fanconi anaemia G	9	9p13	2189	"Fanconi anemia, complementation group G"		L	.	FANCG-724	0			c.T743C						.						90	94	93					9																	35077002		2203	4300	6503	SO:0001583	missense	2189	exon6			GTGTACACCTGGA	AJ007669	CCDS6574.1	9p13	2014-09-17			ENSG00000221829	ENSG00000221829		"Fanconi anemia, complementation groups"	3588	protein-coding gene	gene with protein product	"DNA repair protein XRCC9", "X-ray repair, complementing defective, in Chinese hamster, 9", "X-ray repair complementing defective repair in Chinese hamster cells 9"	602956		XRCC9		9256465, 9382107	Standard	NM_004629		Approved	FAG	uc003zwb.1	O15287	OTTHUMG00000019850	ENST00000378643.3:c.743T>C	9.37:g.35077002A>G	ENSP00000367910:p.Val248Ala	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	106	28	NM_004629	0	0	0	0	0		Missense_Mutation	SNP	ENST00000378643.3	37	CCDS6574.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.227799	0.79576	.	.	ENSG00000221829	ENST00000378643;ENST00000543657	T	0.32272	1.46	6.07	6.07	0.98685	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.50292	0.1607	L	0.60455	1.87	0.34793	D	0.735929	D	0.76494	0.999	D	0.69654	0.965	T	0.64179	-0.6468	9	0.72032	D	0.01	-23.4289	13.0206	0.58784	1.0:0.0:0.0:0.0	.	248	O15287	FANCG_HUMAN	A	248	ENSP00000367910:V248A	ENSP00000367910:V248A	V	-	2	0	FANCG	35067002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.582000	0.60957	2.326000	0.78906	0.533000	0.62120	GTG	.		0.527	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629		G	35077002	A	G	35077002	3	3	70	1	0	0	0	0	1	0	0	0	5687	159	6	3	1161	3	FANCG	9	35077002	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	30414525	35077002	106136429	32	6702											
TLE4	7091	broad.mit.edu	37	chr9	82267584	82267584	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacacccttcagggctccAgccccctgccattccaccca	7	7	5	22	0	1	0	1	0	0	0	4	0	4	0	8	1	2	1	8	1	0	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:82267584A>G	ENST00000376552.2	+	7	1485	c.467A>G	c.(466-468)cAg>cGg	p.Q156R	TLE4_ENST00000376537.4_Missense_Mutation_p.Q156R|TLE4_ENST00000376534.4_5'UTR|TLE4_ENST00000455913.1_3'UTR|TLE4_ENST00000376520.4_Missense_Mutation_p.Q156R|TLE4_ENST00000265284.6_Missense_Mutation_p.Q131R|TLE4_ENST00000376544.3_Missense_Mutation_p.Q156R	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	156	Gly/Pro-rich (GP domain).				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TCAGGGCTCCAGCCCCCTGCC	0.537																																					p.Q156R													.	TLE4-524	0			c.A467G						.						89	97	95					9																	82267584		1998	4152	6150	SO:0001583	missense	7091	exon7			GGCTCCAGCCCCC	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"WD repeat domain containing"	11840	protein-coding gene	gene with protein product		605132	"transducin-like enhancer of split 4, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.467A>G	9.37:g.82267584A>G	ENSP00000365735:p.Gln156Arg	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	145	4	NM_007005	0	0	0	0	0	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.184277	0.57800	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000399288;ENST00000435650;ENST00000376537;ENST00000265284;ENST00000425506;ENST00000428713;ENST00000490347	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.83;0.91;0.88;0.91;0.89;0.88;1.47;1.83	6.04	4.89	0.63831	.	0.055536	0.64402	D	0.000001	T	0.53642	0.1809	M	0.79475	2.455	0.80722	D	1	B;B;B;B	0.29571	0.249;0.027;0.042;0.028	B;B;B;B	0.35813	0.211;0.009;0.028;0.082	T	0.52823	-0.8524	10	0.42905	T	0.14	-13.7371	13.4934	0.61408	0.8695:0.1305:0.0:0.0	.	131;156;156;156	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	R	156;156;156;170;170;156;131;154;141;26	ENSP00000365735:Q156R;ENSP00000365727:Q156R;ENSP00000365703:Q156R;ENSP00000415423:Q170R;ENSP00000365720:Q156R;ENSP00000265284:Q131R;ENSP00000412567:Q154R;ENSP00000409313:Q141R;ENSP00000417844:Q26R	ENSP00000265284:Q131R	Q	+	2	0	TLE4	81457404	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	5.401000	0.66326	1.079000	0.41038	0.460000	0.39030	CAG	.		0.537	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		G	82267584	A	G	82267584	3	3	70	1	0	0	0	0	1	0	0	0	15973	188	7	3	493	3	TLE4	9	82267584	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	47190582	82267584	58945847	33	6703											
SMC2	10592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	106862707	106862707	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactccaaccattcaaaaatTaaaagaggtatattctgtat	17	13	4	7	0	2	1	1	0	1	1	3	1	3	1	2	1	2	2	2	1	9	7			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:106862707T>C	ENST00000286398.7	+	7	917	c.629T>C	c.(628-630)tTa>tCa	p.L210S	SMC2_ENST00000303219.8_Missense_Mutation_p.L210S|SMC2_ENST00000374793.3_Missense_Mutation_p.L210S|SMC2_ENST00000374787.3_Missense_Mutation_p.L210S	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	210					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						ATTCAAAAATTAAAAGAGGTA	0.274																																					p.L210S		.											.	SMC2-210	0			c.T629C						.						37	45	42					9																	106862707		2179	4270	6449	SO:0001583	missense	10592	exon7			AAAAATTAAAAGA	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"Structural maintenance of chromosomes proteins"	14011	protein-coding gene	gene with protein product		605576	"SMC2 (structural maintenance of chromosomes 2, yeast)-like 1", "SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.629T>C	9.37:g.106862707T>C	ENSP00000286398:p.Leu210Ser	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	118	35	NM_006444	0	0	0	0	0	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465044	0.84425	.	.	ENSG00000136824	ENST00000286398;ENST00000440179;ENST00000374793;ENST00000303219;ENST00000536893;ENST00000374787	T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78	5.57	5.57	0.84162	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.44095	0.1277	M	0.93898	3.47	0.52501	D	0.999959	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.57940	-0.7724	10	0.87932	D	0	-5.7921	14.5587	0.68120	0.0:0.0:0.0:1.0	.	210;210;210	A8K984;O95347;Q2KQ72	.;SMC2_HUMAN;.	S	210;65;210;210;210;210	ENSP00000286398:L210S;ENSP00000414999:L65S;ENSP00000363925:L210S;ENSP00000306152:L210S;ENSP00000363919:L210S	ENSP00000286398:L210S	L	+	2	0	SMC2	105902528	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.677000	0.84024	2.109000	0.64355	0.528000	0.53228	TTA	.		0.274	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			C	106862707	T	C	106862707	3	2	70	1	0	0	0	0	1	0	0	0	14815	1764	61	3	651	3	SMC2	9	106862707	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	24595123	106862707	34350724	34	6704											
PTGR1	22949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	114359672	114359672	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatagccaacaaagtgctTcttcagggtccatgtcttag	11	11	10	9	0	3	0	1	0	2	0	4	1	4	1	2	2	3	1	2	2	4	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:114359672T>G	ENST00000407693.2	-	2	293	c.31A>C	c.(31-33)Aag>Cag	p.K11Q	PTGR1_ENST00000538962.1_Missense_Mutation_p.K11Q|PTGR1_ENST00000309195.5_Missense_Mutation_p.K11Q|PTGR1_ENST00000238248.3_5'UTR	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	11					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						ACAAAGTGCTTCTTCAGGGTC	0.403																																					p.K11Q	Ovarian(200;132 2151 7551 19220 46064)	.											.	PTGR1-90	0			c.A31C						.						109	95	100					9																	114359672		2203	4300	6503	SO:0001583	missense	22949	exon2			AGTGCTTCTTCAG	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.31A>C	9.37:g.114359672T>G	ENSP00000385763:p.Lys11Gln	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	35	15	NM_001146108	0	0	0	0	0	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Missense_Mutation	SNP	ENST00000407693.2	37	CCDS6779.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483746	0.26598	.	.	ENSG00000106853	ENST00000538962;ENST00000309195;ENST00000407693;ENST00000333580;ENST00000422125;ENST00000374313;ENST00000374308	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	4.62	4.62	0.57501	GroES-like (1);	0.092047	0.85682	D	0.000000	T	0.43656	0.1257	M	0.62154	1.92	0.80722	D	1	B;B;B	0.33171	0.4;0.278;0.077	B;B;B	0.29440	0.102;0.061;0.015	T	0.46665	-0.9175	10	0.48119	T	0.1	2.0981	12.2191	0.54423	0.0:0.0:0.0:1.0	.	11;11;11	F5GY50;B4DPK3;Q14914	.;.;PTGR1_HUMAN	Q	11	ENSP00000440281:K11Q;ENSP00000311572:K11Q;ENSP00000385763:K11Q;ENSP00000395965:K11Q	ENSP00000311572:K11Q	K	-	1	0	PTGR1	113399493	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	2.756000	0.47549	2.020000	0.59435	0.374000	0.22700	AAG	.		0.403	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			G	114359672	T	G	114359672	3	3	70	1	0	0	0	0	1	0	0	0	12783	1792	62	5	1025	5	PTGR1	9	114359672	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	7496965	114359672	26853759	35	6705											
GAPVD1	26130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	128064468	128064468	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacaaagtgttatttacaCagtttttacctccctgtatg	11	15	5	10	0	0	0	0	0	0	0	1	0	1	0	2	0	2	3	2	0	5	7	rs139510593		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:128064468C>T	ENST00000495955.1	+	5	682	c.392C>T	c.(391-393)aCa>aTa	p.T131I	GAPVD1_ENST00000265956.4_Missense_Mutation_p.T131I|GAPVD1_ENST00000394105.2_Missense_Mutation_p.T131I|GAPVD1_ENST00000470056.1_Missense_Mutation_p.T131I|GAPVD1_ENST00000312123.9_Missense_Mutation_p.T131I|RNU6-1020P_ENST00000363684.1_RNA|GAPVD1_ENST00000394084.1_Missense_Mutation_p.T131I|GAPVD1_ENST00000297933.6_Missense_Mutation_p.T131I|GAPVD1_ENST00000394104.2_Missense_Mutation_p.T131I|GAPVD1_ENST00000394083.2_Missense_Mutation_p.T131I			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	131	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						GTTATTTACACAGTTTTTACC	0.388																																					p.T131I		.											.	GAPVD1-93	0			c.C392T						.						144	144	144					9																	128064468		2203	4300	6503	SO:0001583	missense	26130	exon3			TTTACACAGTTTT		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.392C>T	9.37:g.128064468C>T	ENSP00000419063:p.Thr131Ile	Somatic	260	1		WXS	Illumina HiSeq	Phase_I	243	75	NM_015635	0	0	0	0	0	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	C	18.27	3.585977	0.66105	.	.	ENSG00000165219	ENST00000394084;ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123	D;D;D;D;D;D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5;-1.5;-1.5;-1.5;-1.5;-1.5	5.84	5.84	0.93424	Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	D	0.86900	0.6044	L	0.44542	1.39	0.80722	D	1	P;P;P;P;D;B	0.69078	0.649;0.762;0.762;0.762;0.997;0.226	B;B;B;B;D;B	0.78314	0.219;0.391;0.391;0.391;0.991;0.103	D	0.86666	0.1907	10	0.56958	D	0.05	.	19.1433	0.93455	0.0:1.0:0.0:0.0	.	131;131;131;131;131;131	Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6;B0QZ65	GAPD1_HUMAN;.;.;.;.;.	I	131	ENSP00000377646:T131I;ENSP00000419767:T131I;ENSP00000377665:T131I;ENSP00000377664:T131I;ENSP00000265956:T131I;ENSP00000377645:T131I;ENSP00000419063:T131I;ENSP00000418747:T131I;ENSP00000297933:T131I;ENSP00000309582:T131I	ENSP00000265956:T131I	T	+	2	0	GAPVD1	127104289	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.516000	0.67055	2.760000	0.94817	0.655000	0.94253	ACA	C|1.000;G|0.000		0.388	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			T	128064468	C	T	128064468	3	4	70	1	0	0	0	0	1	0	0	0	6259	478	17	2	398	2	GAPVD1	9	128064468	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	13704796	128064468	13148963	36	6706											
DNM1	1759	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131010868	131010868	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gttctccatggcaggccagcGagaccgaggagaatggctcc	9	6	14	12	2	1	2	0	0	1	2	3	5	2	2	4	4	1	3	4	4	1	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:131010868G>A	ENST00000372923.3	+	19	2004	c.1912G>A	c.(1912-1914)Gag>Aag	p.E638K	DNM1_ENST00000475805.1_Missense_Mutation_p.E638K|DNM1_ENST00000486160.1_Missense_Mutation_p.E638K|DNM1_ENST00000341179.7_Missense_Mutation_p.E638K|DNM1_ENST00000393594.3_Missense_Mutation_p.E638K	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	638					endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						GCAGGCCAGCGAGACCGAGGA	0.597																																					.	GBM(113;146 1575 2722 28670 29921)												.	DNM1-228	0			.						.						84	71	76					9																	131010868		2203	4300	6503	SO:0001583	missense	1759	.			GCCAGCGAGACCG	L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"Pleckstrin homology (PH) domain containing"	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.1912G>A	9.37:g.131010868G>A	ENSP00000362014:p.Glu638Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	84	26	.	0	0	0	0	0	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Missense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.269545	0.40095	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393594;ENST00000486160;ENST00000543158	D;D;D;D;D	0.92858	-3.12;-3.12;-3.11;-3.12;-3.11	4.67	4.67	0.58626	.	0.211412	0.41605	N	0.000846	T	0.80829	0.4698	N	0.08118	0	0.58432	D	0.999999	B;B;B	0.32382	0.118;0.188;0.368	B;B;B	0.19148	0.011;0.024;0.017	T	0.80139	-0.1507	10	0.10111	T	0.7	-4.3209	17.7725	0.88497	0.0:0.0:1.0:0.0	.	638;638;577	Q05193;Q05193-3;B4DHH5	DYN1_HUMAN;.;.	K	638;638;638;638;638;183	ENSP00000419225:E638K;ENSP00000345680:E638K;ENSP00000362014:E638K;ENSP00000377219:E638K;ENSP00000420045:E638K	ENSP00000345680:E638K	E	+	1	0	DNM1	130050689	1.000000	0.71417	0.972000	0.41901	0.505000	0.33919	5.485000	0.66850	2.439000	0.82584	0.650000	0.86243	GAG	.		0.597	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408		A	131010868	G	A	131010868	3	1	70	1	0	0	0	0	1	0	0	0	4681	1059	37	1	1981	1	DNM1	9	131010868	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	2946400	131010868	10202563	37	6707											
CERCAM	51148	broad.mit.edu	37	chr9	131196837	131196837	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctggcctcacagcctctgCgccgcatgctgcccgtggac	4	8	12	17	3	2	0	1	0	1	0	2	1	2	1	4	2	5	3	4	2	0	0	rs372372318		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:131196837C>T	ENST00000372838.4	+	11	1878	c.1480C>T	c.(1480-1482)Cgc>Tgc	p.R494C	CERCAM_ENST00000372842.1_Missense_Mutation_p.R416C|RP11-339B21.10_ENST00000610052.1_RNA	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	494					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						ACAGCCTCTGCGCCGCATGCT	0.697																																					p.R494C													.	CERCAM-69	0			c.C1480T						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	45	46	46		1480	3.3	0.8	9		46	0,8598		0,0,4299	no	missense	CERCAM	NM_016174.4	180	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	494/596	131196837	1,13003	2203	4299	6502	SO:0001583	missense	51148	exon11			CCTCTGCGCCGCA	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"glycosyltransferase 25 domain containing 3"		"cerebral cell adhesion molecule"	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.1480C>T	9.37:g.131196837C>T	ENSP00000361929:p.Arg494Cys	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	76	3	NM_016174	0	0	0	0	0	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Missense_Mutation	SNP	ENST00000372838.4	37	CCDS6901.2	.	.	.	.	.	.	.	.	.	.	C	17.14	3.312444	0.60414	2.27E-4	0.0	ENSG00000167123	ENST00000372842;ENST00000372838;ENST00000413863	T;T	0.78481	-1.17;-1.18	5.25	3.27	0.37495	.	0.508491	0.20924	N	0.083222	T	0.67183	0.2866	N	0.25485	0.75	0.22034	N	0.999409	P	0.50272	0.933	P	0.50109	0.631	T	0.60078	-0.7333	10	0.56958	D	0.05	-18.147	1.5153	0.02504	0.1665:0.4399:0.2147:0.1788	.	494	Q5T4B2	GT253_HUMAN	C	416;494;447	ENSP00000361933:R416C;ENSP00000361929:R494C	ENSP00000361929:R494C	R	+	1	0	CERCAM	130236658	0.000000	0.05858	0.795000	0.32087	0.602000	0.36980	0.315000	0.19451	1.118000	0.41863	0.549000	0.68633	CGC	.		0.697	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174		T	131196837	C	T	131196837	3	4	70	1	0	0	0	0	1	0	0	0	3272	768	27	1	1522	1	CERCAM	9	131196837	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	185969	131196837	10016594	38	6708											
C10orf54	64115	broad.mit.edu	37	chr10	73521465	73521465	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatccagcagggtcaggttgCgcatggtgatggagaagttg	9	10	16	6	1	1	2	1	1	0	1	2	3	2	2	1	4	2	4	1	4	2	3	rs200235042	byFrequency	TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr10:73521465C>T	ENST00000394957.3	-	2	459	c.401G>A	c.(400-402)cGc>cAc	p.R134H	C10orf54_ENST00000481568.2_5'UTR|CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	134	Ig-like.				BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GGTCAGGTTGCGCATGGTGAT	0.647													C|||	2	0.000399361	0	0	5008	,	,		22472	0.002		0	False		,,,				2504	0				p.R134H													.	C10orf54-515	0			c.G401A						.						73	69	71					10																	73521465		2203	4300	6503	SO:0001583	missense	64115	exon2			AGGTTGCGCATGG	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"Immunoglobulin superfamily / V-set domain containing"	30085	protein-coding gene	gene with protein product	"stress induced secreted protein 1"	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.401G>A	10.37:g.73521465C>T	ENSP00000378409:p.Arg134His	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_022153	0	0	0	0	0	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	37	CCDS31218.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	14.53	2.562276	0.45694	.	.	ENSG00000107738	ENST00000394957;ENST00000263569	T	0.66280	-0.2	5.75	-6.8	0.01709	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.040480	0.07437	N	0.896600	T	0.35128	0.0921	N	0.17674	0.51	0.19300	N	0.999974	B;B	0.18013	0.025;0.002	B;B	0.09377	0.004;0.003	T	0.18461	-1.0336	10	0.48119	T	0.1	-0.7654	0.3776	0.00390	0.3311:0.2135:0.1402:0.3152	.	130;134	Q2TA85;Q9H7M9	.;GI24_HUMAN	H	134;130	ENSP00000378409:R134H	ENSP00000263569:R130H	R	-	2	0	C10orf54	73191471	0.000000	0.05858	0.542000	0.28115	0.970000	0.65996	-1.375000	0.02563	-1.017000	0.03367	0.655000	0.94253	CGC	C|0.999;T|0.000		0.647	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		T	73521465	C	T	73521465	3	4	70	1	0	0	0	0	1	0	0	0	1611	768	27	1	558	1	C10orf54	10	73521465	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08		73521465	62013282	39	6709											
C10orf62	414157	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	99349694	99349694	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggagaagaaaggaaaccTctgagtgtccatcagacaag	17	5	12	7	0	2	5	1	1	1	4	3	7	3	6	2	2	1	0	2	2	4	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr10:99349694T>A	ENST00000370640.3	+	1	245	c.40T>A	c.(40-42)Tct>Act	p.S14T	PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron|HOGA1_ENST00000370647.4_Intron|HOGA1_ENST00000370646.4_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	14										endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		AAAGGAAACCTCTGAGTGTCC	0.502																																					p.S14T		.											.	C10orf62-90	0			c.T40A						.						100	100	100					10																	99349694		2203	4300	6503	SO:0001583	missense	414157	exon1			GAAACCTCTGAGT		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.40T>A	10.37:g.99349694T>A	ENSP00000359674:p.Ser14Thr	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	97	7	NM_001009997	0	0	0	0	0	Q49A70|Q8N3Y6	Missense_Mutation	SNP	ENST00000370640.3	37	CCDS31261.1	.	.	.	.	.	.	.	.	.	.	T	4.766	0.142421	0.09083	.	.	ENSG00000203942	ENST00000370640	T	0.42513	0.97	5.27	-10.5	0.00291	.	3.688920	0.00929	N	0.002686	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.18777	-1.0326	10	0.14656	T	0.56	.	1.8333	0.03134	0.3493:0.094:0.1283:0.4284	.	14	Q5T681	CJ062_HUMAN	T	14	ENSP00000359674:S14T	ENSP00000359674:S14T	S	+	1	0	C10orf62	99339684	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.585000	0.00903	-2.847000	0.00332	-1.294000	0.01345	TCT	.		0.502	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997		A	99349694	T	A	99349694	3	1	70	1	0	0	0	0	1	0	0	0	1615	1551	54	5	42	5	C10orf62	10	99349694	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	25828229	99349694	36185053	40	6710											
NPS	594857	broad.mit.edu;bcgsc.ca	37	chr10	129350829	129350829	+	Frame_Shift_Del	DEL	T	T	-																															agccaattttggagaagatgTttgtgaaaaggtcctttcgc																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr10:129350829delT	ENST00000398023.1	+	3	216	c.196delT	c.(196-198)tttfs	p.F66fs		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	66					neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						GGAGAAGATGTTTGTGAAAAG	0.413																																					p.F66fs													.	NPS-22	0			c.196delT						.						204	199	201					10																	129350829		1843	4101	5944	SO:0001589	frameshift_variant	594857	exon3			AAGATGTTTGTGA	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"Endogenous ligands"	33940	protein-coding gene	gene with protein product	"prepro-neuropeptide S"	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.196delT	10.37:g.129350829delT	ENSP00000381105:p.Phe66fs	Somatic	413	0		WXS	Illumina HiSeq	Phase_I	339	47	NM_001030013	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000398023.1	37	CCDS41577.1																																																																																			.		0.413	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013		-	129350829	T	-	129350829	7	5	70	1	0	1	0	1	0	0	0	0	10625	1725	60	0	206	0	NPS	10	129350829	Frame_Shift_Del	DEL	T	TCGA-BQ-5886-01A-11D-1589-08	30001135	129350829	6183918	41	6711											
ST5	6764	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	8751785	8751785	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cactgccttccctctctgggGgtgggcccgcctcccccgca	2	8	11	20	2	1	0	0	0	1	0	4	0	3	0	6	3	1	1	6	3	0	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:8751785G>A	ENST00000534127.1	-	6	1437	c.1052C>T	c.(1051-1053)cCc>cTc	p.P351L	ST5_ENST00000313726.6_Missense_Mutation_p.P351L|ST5_ENST00000526757.1_Intron|ST5_ENST00000357665.1_Missense_Mutation_p.P351L|ST5_ENST00000530438.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	351	Pro-rich.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CCTCTCTGGGGGTGGGCCCGC	0.687																																					p.P351L		.											.	ST5-227	0			c.C1052T						.						41	47	45					11																	8751785		2201	4296	6497	SO:0001583	missense	6764	exon6			TCTGGGGGTGGGC	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"DENN/MADD domain containing"	11350	protein-coding gene	gene with protein product	"DENN/MADD domain containing 2B"	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1052C>T	11.37:g.8751785G>A	ENSP00000433528:p.Pro351Leu	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	109	25	NM_005418	0	0	0	0	0	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.487492	0.44249	.	.	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.04809	3.55;3.55;3.55	6.17	5.27	0.74061	.	0.340768	0.28409	N	0.015455	T	0.06325	0.0163	L	0.41236	1.265	0.46798	D	0.999205	B	0.06786	0.001	B	0.06405	0.002	T	0.28808	-1.0032	10	0.33940	T	0.23	-18.7575	15.9068	0.79436	0.0643:0.0:0.9357:0.0	.	351	P78524	ST5_HUMAN	L	351	ENSP00000433528:P351L;ENSP00000319678:P351L;ENSP00000350294:P351L	ENSP00000319678:P351L	P	-	2	0	ST5	8708361	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.667000	0.61561	1.642000	0.50584	-0.123000	0.14984	CCC	.		0.687	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		A	8751785	G	A	8751785	3	1	70	1	0	0	0	0	1	0	0	0	15252	1232	43	2	2433	2	ST5	11	8751785	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		8751785	126254731	42	6712											
ZNF143	7702	hgsc.bcm.edu;broad.mit.edu	37	chr11	9519236	9519236	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaaaggttatggattaaaaAgtcacgtcagaactcataca	17	11	7	6	1	3	1	3	0	0	1	3	2	3	2	0	2	2	1	0	2	8	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:9519236A>C	ENST00000396602.2	+	10	975	c.856A>C	c.(856-858)Agt>Cgt	p.S286R	ZNF143_ENST00000299606.2_Missense_Mutation_p.S258R|ZNF143_ENST00000530463.1_Missense_Mutation_p.S285R|ZNF143_ENST00000396597.3_Missense_Mutation_p.S255R|ZNF143_ENST00000396604.1_Missense_Mutation_p.S285R	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	286					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		TGGATTAAAAAGTCACGTCAG	0.318																																					p.S286R		.											.	ZNF143-90	0			c.A856C						.						53	55	54					11																	9519236		2201	4294	6495	SO:0001583	missense	7702	exon10			TTAAAAAGTCACG	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.856A>C	11.37:g.9519236A>C	ENSP00000379847:p.Ser286Arg	Somatic	93	2		WXS	Illumina HiSeq	Phase_I	79	6	NM_003442	0	0	0	0	0	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Missense_Mutation	SNP	ENST00000396602.2	37	CCDS7799.2	.	.	.	.	.	.	.	.	.	.	A	22.0	4.227654	0.79576	.	.	ENSG00000166478	ENST00000396604;ENST00000396602;ENST00000530463;ENST00000396597;ENST00000299606	T;T;T;T;T	0.11821	2.74;2.74;2.74;2.74;2.74	5.32	5.32	0.75619	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.10551	0.0258	N	0.03967	-0.31	0.80722	D	1	P;P;P	0.48998	0.899;0.918;0.918	P;P;P	0.49387	0.571;0.609;0.609	T	0.41484	-0.9506	10	0.33940	T	0.23	.	15.2911	0.73868	1.0:0.0:0.0:0.0	.	255;285;286	P52747-2;E7ER34;P52747	.;.;ZN143_HUMAN	R	285;286;285;255;258	ENSP00000379849:S285R;ENSP00000379847:S286R;ENSP00000432154:S285R;ENSP00000379843:S255R;ENSP00000299606:S258R	ENSP00000299606:S258R	S	+	1	0	ZNF143	9475812	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.295000	0.96095	2.016000	0.59253	0.528000	0.53228	AGT	.		0.318	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		C	9519236	A	C	9519236	3	2	70	1	0	0	0	0	1	0	0	0	17764	72	3	5	890	5	ZNF143	11	9519236	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	767451	9519236	125487280	43	6713											
OR8H3	390152	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	55890388	55890388	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcatcactttttctgtgaCacttccccaattttagctct	8	18	3	12	0	4	1	2	1	2	0	5	1	5	1	2	0	1	1	2	0	2	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:55890388C>A	ENST00000313472.3	+	1	540	c.540C>A	c.(538-540)gaC>gaA	p.D180E		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	180						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TTTTCTGTGACACTTCCCCAA	0.423																																					p.D180E		.											.	OR8H3-70	0			c.C540A						.						247	224	232					11																	55890388		2201	4296	6497	SO:0001583	missense	390152	exon1			CTGTGACACTTCC	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"GPCR / Class A : Olfactory receptors"	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.540C>A	11.37:g.55890388C>A	ENSP00000323928:p.Asp180Glu	Somatic	377	1		WXS	Illumina HiSeq	Phase_I	340	19	NM_001005201	0	0	0	0	0	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504092	0.26949	.	.	ENSG00000181761	ENST00000313472	T	0.00048	8.82	3.62	0.503	0.16940	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000030	T	0.00271	0.0008	L	0.46885	1.475	0.09310	N	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.52147	-0.8614	10	0.59425	D	0.04	.	4.7151	0.12891	0.1409:0.4302:0.0:0.4289	.	180	Q8N146	OR8H3_HUMAN	E	180	ENSP00000323928:D180E	ENSP00000323928:D180E	D	+	3	2	OR8H3	55646964	0.000000	0.05858	0.153000	0.22517	0.346000	0.29079	-2.727000	0.00807	-0.121000	0.11787	0.173000	0.16961	GAC	.		0.423	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		A	55890388	C	A	55890388	3	1	70	1	0	0	0	0	1	0	0	0	11265	477	17	4	542	4	OR8H3	11	55890388	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	46371152	55890388	79116128	44	6714											
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	62290316	62290316	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caggcatcttgaatttgggaCctttcaactttccctctggg	7	14	9	11	0	3	1	1	1	2	0	4	2	4	2	2	3	1	1	2	3	2	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:62290316C>T	ENST00000378024.4	-	5	11847	c.11573G>A	c.(11572-11574)gGt>gAt	p.G3858D	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3858					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GAATTTGGGACCTTTCAACTT	0.478																																					p.G3858D		.											.	AHNAK-109	0			c.G11573A						.						196	202	200					11																	62290316		2202	4299	6501	SO:0001583	missense	79026	exon5			TTGGGACCTTTCA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11573G>A	11.37:g.62290316C>T	ENSP00000367263:p.Gly3858Asp	Somatic	422	0		WXS	Illumina HiSeq	Phase_I	412	35	NM_001620	0	0	0	0	0	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	12.21	1.869769	0.33069	.	.	ENSG00000124942	ENST00000378024	T	0.03496	3.91	4.51	4.51	0.55191	.	0.000000	0.42053	D	0.000767	T	0.21227	0.0511	M	0.93594	3.435	0.46678	D	0.999153	D	0.65815	0.995	P	0.61201	0.885	T	0.41106	-0.9527	10	0.15499	T	0.54	.	17.021	0.86433	0.0:1.0:0.0:0.0	.	3858	Q09666	AHNK_HUMAN	D	3858	ENSP00000367263:G3858D	ENSP00000367263:G3858D	G	-	2	0	AHNAK	62046892	0.954000	0.32549	0.066000	0.19879	0.046000	0.14306	4.583000	0.60964	2.350000	0.79820	0.543000	0.68304	GGT	.		0.478	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62290316	C	T	62290316	3	4	70	1	0	0	0	0	1	0	0	0	414	507	18	2	6219	2	AHNAK	11	62290316	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	6399928	62290316	72716200	45	6715											
TUT1	64852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62346405	62346405	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaagcaggaggttgtgaaTctggaggggaagctggggtg	10	7	21	3	0	1	2	0	1	1	1	1	6	1	5	0	7	2	3	0	7	3	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:62346405T>C	ENST00000476907.1	-	5	1479	c.788A>G	c.(787-789)gAt>gGt	p.D263G	MIR3654_ENST00000496634.2_Missense_Mutation_p.D263G|TUT1_ENST00000308436.7_Missense_Mutation_p.D301G			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	263	Pro-rich.				mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AGGTTGTGAATCTGGAGGGGA	0.627																																					p.D301G		.											.	TUT1-91	0			c.A902G						.						38	45	43					11																	62346405		2202	4299	6501	SO:0001583	missense	64852	exon5			TGTGAATCTGGAG	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.788A>G	11.37:g.62346405T>C	ENSP00000419607:p.Asp263Gly	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_022830	0	0	0	0	0	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	37		.	.	.	.	.	.	.	.	.	.	T	10.15	1.271130	0.23221	.	.	ENSG00000149016	ENST00000308436;ENST00000476907;ENST00000278279	T;T	0.40476	1.03;1.05	4.91	2.58	0.30949	.	0.311232	0.25590	N	0.029624	T	0.29256	0.0728	L	0.36672	1.1	0.24619	N	0.993685	B	0.12013	0.005	B	0.12156	0.007	T	0.20940	-1.0260	10	0.54805	T	0.06	1.3697	5.9223	0.19088	0.0:0.2193:0.0:0.7807	.	301	F5H0R1	.	G	301;263;124	ENSP00000308000:D301G;ENSP00000419607:D263G	ENSP00000441670:D263G	D	-	2	0	TUT1	62102981	1.000000	0.71417	0.932000	0.37286	0.144000	0.21451	1.147000	0.31602	0.370000	0.24538	0.460000	0.39030	GAT	.		0.627	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		C	62346405	T	C	62346405	3	2	70	1	0	0	0	0	1	0	0	0	16813	1435	50	3	1856	3	TUT1	11	62346405	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	56089	62346405	72660111	46	6716											
PC	5091	broad.mit.edu	37	chr11	66636400	66636400	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgccgtgcctgtccacCaggaactccacggtgcctgc	5	9	11	16	2	0	0	0	0	0	0	2	1	2	1	6	2	6	1	6	2	1	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:66636400C>A	ENST00000393958.2	-	9	1032	c.939G>T	c.(937-939)ctG>ctT	p.L313L	PC_ENST00000393955.2_Silent_p.L313L|PC_ENST00000524491.1_Silent_p.L273L|PC_ENST00000355677.3_Silent_p.L313L|PC_ENST00000393960.1_Silent_p.L313L	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	313	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GCCTGTCCACCAGGAACTCCA	0.647																																					p.L313L													.	PC-228	0			c.G939T						.						94	82	86					11																	66636400		2200	4295	6495	SO:0001819	synonymous_variant	5091	exon9			GTCCACCAGGAAC	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.939G>T	11.37:g.66636400C>A		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	108	4	NM_000920	0	0	0	0	0	B4DN00|Q16705	Silent	SNP	ENST00000393958.2	37	CCDS8152.1																																																																																			.		0.647	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		A	66636400	C	A	66636400	2	1	70	1	0	0	0	0	0	0	0	1	11523	581	21	4		4	PC	11	66636400	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	4289995	66636400	68370116	47	6717											
ARHGEF12	23365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	120336044	120336044	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcaaatctcgtcagaaaaaGgattctcgatttcagacttt	14	13	6	8	2	5	2	3	0	2	2	7	4	5	3	0	1	0	0	0	1	3	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:120336044G>T	ENST00000397843.2	+	28	2878	c.2712G>T	c.(2710-2712)aaG>aaT	p.K904N	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.K801N|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.K885N	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	904	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GTCAGAAAAAGGATTCTCGAT	0.393			T	MLL	AML																																p.K904N		.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12-661	0			c.G2712T						.						94	89	91					11																	120336044		1863	4111	5974	SO:0001583	missense	23365	exon28			GAAAAAGGATTCT	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.2712G>T	11.37:g.120336044G>T	ENSP00000380942:p.Lys904Asn	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	101	30	NM_015313	0	0	0	0	0	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.000713	0.74818	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.70282	-0.47;-0.47;-0.47	5.69	4.78	0.61160	Dbl homology (DH) domain (5);	0.000000	0.51477	D	0.000085	D	0.82577	0.5067	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.83981	0.0332	10	0.66056	D	0.02	-17.5309	10.7839	0.46395	0.1444:0.0:0.8556:0.0	.	801;885;904	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	N	904;885;801	ENSP00000380942:K904N;ENSP00000349056:K885N;ENSP00000432984:K801N	ENSP00000349056:K885N	K	+	3	2	ARHGEF12	119841254	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.679000	0.46909	1.424000	0.47217	0.650000	0.86243	AAG	.		0.393	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120336044	G	T	120336044	3	4	70	1	0	0	0	0	1	0	0	0	897	991	35	4	2822	4	ARHGEF12	11	120336044	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	53699644	120336044	14670472	48	6718											
ESAM	90952	hgsc.bcm.edu	37	chr11	124623757	124623757	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggagggccatggggtggccGgagggctcgtgcggaggtga	5	5	24	7	3	0	1	0	1	0	0	1	4	0	4	2	9	1	1	2	9	0	0	rs200154876		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:124623757G>A	ENST00000278927.5	-	7	1087	c.958C>T	c.(958-960)Cgg>Tgg	p.R320W	VSIG2_ENST00000326621.5_5'Flank|VSIG2_ENST00000403470.1_5'Flank|ESAM_ENST00000442070.2_Intron	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	320					blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		TGGGGTGGCCGGAGGGCTCGT	0.662																																					p.R320W		.											.	ESAM-90	0			c.C958T						.						63	73	70					11																	124623757		2201	4299	6500	SO:0001583	missense	90952	exon7			GTGGCCGGAGGGC	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.958C>T	11.37:g.124623757G>A	ENSP00000278927:p.Arg320Trp	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	58	3	NM_138961	0	0	0	0	0	B4DVN8|Q96T50	Missense_Mutation	SNP	ENST00000278927.5	37	CCDS8453.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.718138	0.68844	.	.	ENSG00000149564	ENST00000278927	T	0.33216	1.42	5.28	3.33	0.38152	.	0.221063	0.40222	N	0.001144	T	0.41073	0.1143	L	0.46157	1.445	0.43292	D	0.995272	D	0.76494	0.999	P	0.57720	0.826	T	0.22977	-1.0201	10	0.66056	D	0.02	.	11.5605	0.50774	0.0:0.0:0.5312:0.4688	.	320	Q96AP7	ESAM_HUMAN	W	320	ENSP00000278927:R320W	ENSP00000278927:R320W	R	-	1	2	ESAM	124128967	0.992000	0.36948	0.220000	0.23810	0.918000	0.54935	3.110000	0.50352	0.645000	0.30675	0.655000	0.94253	CGG	G|0.999;C|0.000		0.662	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961		A	124623757	G	A	124623757	3	1	70	1	0	0	0	0	1	0	0	0	5260	1115	39	1	218	1	ESAM	11	124623757	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	4287713	124623757	10382759	49	6719											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu	37	chr12	49431830	49431830	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggttcagaggcatcagcAgcagggggagggcgctcctc	7	5	18	11	2	2	1	2	0	0	1	4	2	3	2	1	6	2	5	1	6	0	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:49431830A>T	ENST00000301067.7	-	34	9308	c.9309T>A	c.(9307-9309)gcT>gcA	p.A3103A	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3103					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGGCATCAGCAGCAGGGGGAG	0.642																																					p.A3103A		.											.	MLL2-612	0			c.T9309A						.						21	22	22					12																	49431830		1971	4145	6116	SO:0001819	synonymous_variant	8085	exon34			ATCAGCAGCAGGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.9309T>A	12.37:g.49431830A>T		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_003482	0	0	0	0	0	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.642	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49431830	A	T	49431830	2	4	70	1	0	0	0	0	0	0	0	1	9646	175	7	5		5	MLL2	12	49431830	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08		49431830	84420065	50	6720											
MCRS1	10445	hgsc.bcm.edu	37	chr12	49956786	49956786	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcctggggcgttacctGtctggtcctccagcaggtaa	6	10	12	13	1	1	0	0	0	1	0	4	0	4	0	4	4	3	4	4	4	2	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:49956786G>C	ENST00000550165.1	-	9	1069	c.803C>G	c.(802-804)aCa>aGa	p.T268R	MCRS1_ENST00000357123.4_Missense_Mutation_p.T281R|MCRS1_ENST00000547182.1_5'UTR|MCRS1_ENST00000546244.1_Missense_Mutation_p.T77R|MCRS1_ENST00000343810.4_Missense_Mutation_p.T268R			Q96EZ8	MCRS1_HUMAN	microspherule protein 1	268					cellular protein modification process (GO:0006464)|chromatin organization (GO:0006325)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23						GGCGTTACCTGTCTGGTCCTC	0.587																																					p.T281R		.											.	MCRS1-289	0			c.C842G						.						45	36	39					12																	49956786		2203	4298	6501	SO:0001583	missense	10445	exon7			TTACCTGTCTGGT	BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778		"INO80 complex subunits"	6960	protein-coding gene	gene with protein product	"INO80 complex subunit Q"	609504				9765390, 9654073	Standard	NM_006337		Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.803C>G	12.37:g.49956786G>C	ENSP00000448056:p.Thr268Arg	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_001012300	0	0	0	0	0	O14742|O75497|Q6VN53|Q7Z372	Missense_Mutation	SNP	ENST00000550165.1	37	CCDS8787.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848843	0.71603	.	.	ENSG00000187778	ENST00000546244;ENST00000343810;ENST00000550165;ENST00000357123;ENST00000553173	.	.	.	5.64	5.64	0.86602	.	0.086145	0.85682	D	0.000000	T	0.66723	0.2818	L	0.47716	1.5	0.53005	D	0.999967	P;P;P	0.51351	0.944;0.642;0.887	P;B;P	0.56042	0.79;0.305;0.668	T	0.68372	-0.5426	9	0.72032	D	0.01	-8.7582	17.2003	0.86904	0.0:0.0:1.0:0.0	.	255;268;281	F8W126;Q96EZ8;Q96EZ8-2	.;MCRS1_HUMAN;.	R	77;268;268;281;255	.	ENSP00000345358:T268R	T	-	2	0	MCRS1	48243053	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.847000	0.69451	2.662000	0.90505	0.555000	0.69702	ACA	.		0.587	MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	NM_006337		C	49956786	G	C	49956786	3	2	70	1	0	0	0	0	1	0	0	0	9424	1377	48	4	617	4	MCRS1	12	49956786	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	524956	49956786	83895109	51	6721											
ERBB3	2065	hgsc.bcm.edu;broad.mit.edu	37	chr12	56495577	56495577	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccactgcaggcacaactcCagatgaagactatgaatata	15	7	8	11	0	0	4	0	2	0	2	1	4	1	4	2	1	2	2	2	1	6	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:56495577C>T	ENST00000267101.3	+	28	4207	c.3767C>T	c.(3766-3768)cCa>cTa	p.P1256L	ERBB3_ENST00000450146.2_Missense_Mutation_p.P613L|ERBB3_ENST00000415288.2_Missense_Mutation_p.P1197L|PA2G4_ENST00000303305.6_5'Flank|RP11-603J24.17_ENST00000548595.1_RNA|ERBB3_ENST00000553131.1_Missense_Mutation_p.P497L|PA2G4_ENST00000552766.1_5'Flank|ERBB3_ENST00000549832.1_Missense_Mutation_p.P376L|RP11-603J24.9_ENST00000548861.1_Intron	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1256					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			GGCACAACTCCAGATGAAGAC	0.557																																					p.P1256L		.											.	ERBB3-1403	0			c.C3767T						.						79	70	73					12																	56495577		2203	4300	6503	SO:0001583	missense	2065	exon28			CAACTCCAGATGA	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3767C>T	12.37:g.56495577C>T	ENSP00000267101:p.Pro1256Leu	Somatic	91	1		WXS	Illumina HiSeq	Phase_I	126	9	NM_001982	0	0	0	0	0	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.408715	0.42715	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.78126	-1.01;-0.93;-1.0;-1.15;-0.89	5.82	5.82	0.92795	.	0.000000	0.56097	D	0.000031	T	0.65123	0.2661	N	0.19112	0.55	0.80722	D	1	P;B;B	0.36535	0.557;0.361;0.118	B;B;B	0.33620	0.167;0.081;0.037	T	0.69427	-0.5148	10	0.62326	D	0.03	.	14.3848	0.66938	0.1484:0.8516:0.0:0.0	.	1197;376;1256	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	L	1256;613;1197;379;497;376	ENSP00000267101:P1256L;ENSP00000399178:P613L;ENSP00000408340:P1197L;ENSP00000449129:P497L;ENSP00000448729:P376L	ENSP00000267101:P1256L	P	+	2	0	ERBB3	54781844	0.985000	0.35326	0.997000	0.53966	0.907000	0.53573	3.316000	0.51960	2.752000	0.94435	0.655000	0.94253	CCA	.		0.557	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56495577	C	T	56495577	3	4	70	1	0	0	0	0	1	0	0	0	5221	594	21	2	4008	2	ERBB3	12	56495577	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	6538791	56495577	77356318	52	6722											
MON2	23041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	62972277	62972277	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcaaagaaatgaaaatattGatgtcgaggtaaggaggcta	17	10	11	3	1	1	3	1	2	0	1	2	5	1	4	0	3	0	2	0	3	7	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:62972277G>A	ENST00000393632.2	+	31	4958	c.4567G>A	c.(4567-4569)Gat>Aat	p.D1523N	MON2_ENST00000552738.1_Missense_Mutation_p.D1494N|MON2_ENST00000393630.3_Missense_Mutation_p.D1524N|MON2_ENST00000546600.1_Missense_Mutation_p.D1523N|MON2_ENST00000393629.2_Missense_Mutation_p.D1517N|MON2_ENST00000280379.6_Missense_Mutation_p.D1524N	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1523					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TGAAAATATTGATGTCGAGGT	0.284																																					p.D1523N		.											.	MON2-514	0			c.G4567A						.						30	30	30					12																	62972277		2200	4284	6484	SO:0001583	missense	23041	exon31			AATATTGATGTCG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4567G>A	12.37:g.62972277G>A	ENSP00000377252:p.Asp1523Asn	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	47	9	NM_015026	0	0	0	0	0	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	32	5.188128	0.94923	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09;0.09	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.76506	0.3997	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.97110	0.993;0.997;0.982;0.992;1.0	T	0.74993	-0.3474	9	.	.	.	-19.6244	19.7297	0.96177	0.0:0.0:1.0:0.0	.	1517;1494;1523;392;1523	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	N	1523;1524;1524;1523;1494;1517	ENSP00000377252:D1523N;ENSP00000377250:D1524N;ENSP00000280379:D1524N;ENSP00000447407:D1523N;ENSP00000449215:D1494N;ENSP00000377249:D1517N	.	D	+	1	0	MON2	61258544	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.471000	0.97696	2.658000	0.90341	0.650000	0.86243	GAT	.		0.284	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		A	62972277	G	A	62972277	3	1	70	1	0	0	0	0	1	0	0	0	9725	1290	45	2	4689	2	MON2	12	62972277	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	6476700	62972277	70879618	53	6723											
NAP1L1	4673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	76444427	76444427	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcaaggatagcttcagcatCatcatcctatttttaaagga	14	12	7	8	0	3	0	3	0	0	0	4	2	4	2	1	2	3	3	1	2	5	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:76444427C>T	ENST00000261182.8	-	12	1429	c.943G>A	c.(943-945)Gat>Aat	p.D315N	NAP1L1_ENST00000549596.1_Missense_Mutation_p.D315N|NAP1L1_ENST00000535020.2_Missense_Mutation_p.D315N|NAP1L1_ENST00000393263.3_Missense_Mutation_p.D315N|NAP1L1_ENST00000548044.1_Missense_Mutation_p.D274N|NAP1L1_ENST00000431879.3_Missense_Mutation_p.D247N|NAP1L1_ENST00000552342.1_Missense_Mutation_p.D326N|NAP1L1_ENST00000547773.1_Missense_Mutation_p.D252N|NAP1L1_ENST00000544816.1_Missense_Mutation_p.D132N|NAP1L1_ENST00000547993.1_Missense_Mutation_p.D132N|NAP1L1_ENST00000542344.1_Missense_Mutation_p.D273N	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	315					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				GCTTCAGCATCATCATCCTAT	0.373																																					p.D315N		.											.	NAP1L1-92	0			c.G943A						.						63	60	61					12																	76444427		2203	4300	6503	SO:0001583	missense	4673	exon12			CAGCATCATCATC		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.943G>A	12.37:g.76444427C>T	ENSP00000261182:p.Asp315Asn	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	82	27	NM_004537	0	0	0	0	0	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	37	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682803	0.88542	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000544816;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000547993;ENST00000552342;ENST00000548044	T;T;T;T;T;T;T;T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	M	0.68952	2.095	0.80722	D	1	B;B;B;B;B;B;B	0.34226	0.389;0.18;0.389;0.443;0.18;0.162;0.202	B;B;B;B;B;B;B	0.42163	0.274;0.378;0.274;0.196;0.285;0.135;0.196	T	0.40701	-0.9549	10	0.66056	D	0.02	.	19.7712	0.96366	0.0:1.0:0.0:0.0	.	315;273;326;315;247;252;315	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	N	315;309;315;247;252;132;273;315;315;132;326;274	ENSP00000261182:D315N;ENSP00000450236:D309N;ENSP00000376947:D315N;ENSP00000409795:D247N;ENSP00000448167:D252N;ENSP00000437507:D132N;ENSP00000444759:D273N;ENSP00000445008:D315N;ENSP00000447793:D315N;ENSP00000448007:D132N;ENSP00000447196:D326N;ENSP00000449649:D274N	ENSP00000261182:D315N	D	-	1	0	NAP1L1	74730694	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.677000	0.91161	0.585000	0.79938	GAT	.		0.373	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207		T	76444427	C	T	76444427	3	4	70	1	0	0	0	0	1	0	0	0	10181	826	29	2	248	2	NAP1L1	12	76444427	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	13472150	76444427	57407468	54	6724											
HMGB1	3146	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	31036826	31036826	+	Missense_Mutation	SNP	G	G	A																															tgatttttgggcgatactcaGagcagaagaggaagaaggcc																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:31036826G>A	ENST00000405805.1	-	4	1260	c.320C>T	c.(319-321)tCt>tTt	p.S107F	HMGB1_ENST00000399489.1_Missense_Mutation_p.S107F|HMGB1_ENST00000326004.4_Missense_Mutation_p.S107F|HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000339872.4_Missense_Mutation_p.S107F|HMGB1_ENST00000399494.1_Missense_Mutation_p.S107F|HMGB1_ENST00000341423.5_Missense_Mutation_p.S107F			P09429	HMGB1_HUMAN	high mobility group box 1	107					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		GCGATACTCAGAGCAGAAGAG	0.393																																					p.S107F		.											.	HMGB1-227	0			c.C320T						.						45	46	46					13																	31036826		2187	4290	6477	SO:0001583	missense	3146	exon4			TACTCAGAGCAGA	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.320C>T	13.37:g.31036826G>A	ENSP00000384678:p.Ser107Phe	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	99	23	NM_002128	0	0	0	0	0	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Missense_Mutation	SNP	ENST00000405805.1	37	CCDS9335.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868452	0.72065	.	.	ENSG00000189403	ENST00000405805;ENST00000339872;ENST00000341423;ENST00000399489;ENST00000399494;ENST00000426225;ENST00000326004	D;D;D;D;D;D	0.98150	-4.75;-4.75;-4.75;-4.75;-4.75;-4.75	5.5	3.76	0.43208	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.53938	D	0.000050	D	0.97977	0.9334	M	0.85373	2.75	0.80722	D	1	B;P;B;B	0.37176	0.099;0.586;0.314;0.204	B;P;P;B	0.49047	0.2;0.599;0.498;0.264	D	0.97456	1.0031	10	0.87932	D	0	.	10.4698	0.44629	0.0694:0.0:0.7963:0.1343	.	107;68;107;107	B7Z965;B3KQ05;P09429;Q5T7C4	.;.;HMGB1_HUMAN;.	F	107	ENSP00000384678:S107F;ENSP00000343040:S107F;ENSP00000345347:S107F;ENSP00000382412:S107F;ENSP00000382417:S107F;ENSP00000369904:S107F	ENSP00000369904:S107F	S	-	2	0	HMGB1	29934826	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.536000	0.82023	0.683000	0.31428	-0.148000	0.13756	TCT	.		0.393	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		A	31036826	G	A	31036826	3	1	70	1	0	0	0	0	1	0	0	0	7246	942	33	2	335	2	HMGB1	13	31036826	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		31036826	84133052	55	6725	77	2									
HMGB1	3146	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	31036836	31036836	+	Frame_Shift_Del	DEL	G	G	-																															gcgatactcagagcagaagaGgaagaaggccgaactaaaaa																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:31036836delG	ENST00000405805.1	-	4	1250	c.310delC	c.(310-312)ctcfs	p.L104fs	HMGB1_ENST00000399489.1_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000326004.4_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000339872.4_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000399494.1_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000341423.5_Frame_Shift_Del_p.L104fs			P09429	HMGB1_HUMAN	high mobility group box 1	104					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		GAGCAGAAGAGGAAGAAGGCC	0.378																																					p.L104fs		.											.	HMGB1-227	0			c.310delC						.						42	43	43					13																	31036836		2183	4287	6470	SO:0001589	frameshift_variant	3146	exon4			.	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.310delC	13.37:g.31036836delG	ENSP00000384678:p.Leu104fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	82	19	NM_002128	0	0	0	0	0	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Frame_Shift_Del	DEL	ENST00000405805.1	37	CCDS9335.1																																																																																			.		0.378	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		-	31036836	G	-	31036836	7	5	70	1	0	1	0	1	0	0	0	0	7246	1000	35	0	345	0	HMGB1	13	31036836	Frame_Shift_Del	DEL	G	TCGA-BQ-5886-01A-11D-1589-08	10	31036836	84133042	56	6726	77	2									
POSTN	10631	bcgsc.ca	37	chr13	38154768	38154768	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgatgatctcgcggaataTgtgaatcgcaccgtttctcc	8	13	9	11	4	2	3	0	3	2	0	5	4	2	4	2	1	0	2	2	1	3	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:38154768T>C	ENST00000379747.4	-	11	1576	c.1459A>G	c.(1459-1461)Ata>Gta	p.I487V	POSTN_ENST00000379749.4_Missense_Mutation_p.I487V|POSTN_ENST00000379743.4_Missense_Mutation_p.I487V|POSTN_ENST00000541179.1_Missense_Mutation_p.I487V|POSTN_ENST00000541481.1_Missense_Mutation_p.I487V|POSTN_ENST00000379742.4_Missense_Mutation_p.I487V	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	487	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TCGCGGAATATGTGAATCGCA	0.443																																					p.I487V													.	POSTN-516	0			c.A1459G						.						318	291	300					13																	38154768		2203	4300	6503	SO:0001583	missense	10631	exon11			GGAATATGTGAAT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1459A>G	13.37:g.38154768T>C	ENSP00000369071:p.Ile487Val	Somatic	309	2		WXS	Illumina HiSeq	Phase_1	287	9	NM_006475	0	0	0	0	0	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	T	0.807	-0.753251	0.03041	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38;-2.38;-2.38	5.03	0.973	0.19710	FAS1 domain (6);	0.283388	0.40554	N	0.001070	T	0.75064	0.3799	N	0.16743	0.435	0.26793	N	0.969361	B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.001;0.0;0.0	B;B;B;B;B;B;B	0.12156	0.007;0.002;0.006;0.002;0.003;0.002;0.006	T	0.57294	-0.7836	10	0.10111	T	0.7	-8.6758	8.6825	0.34218	0.0:0.4161:0.0:0.5839	.	487;487;487;487;487;487;487	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	V	487	ENSP00000437959:I487V;ENSP00000369073:I487V;ENSP00000369071:I487V;ENSP00000369067:I487V;ENSP00000369066:I487V;ENSP00000437953:I487V	ENSP00000369066:I487V	I	-	1	0	POSTN	37052768	0.892000	0.30473	0.999000	0.59377	0.661000	0.39034	0.428000	0.21395	0.324000	0.23333	0.460000	0.39030	ATA	.		0.443	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		C	38154768	T	C	38154768	3	2	70	1	0	0	0	0	1	0	0	0	12285	1464	51	3	1103	3	POSTN	13	38154768	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	7117932	38154768	77015110	57	6727											
ELF1	1997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41515309	41515309	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggctcctccttttacccctGgacttgaagatactctcgac	7	13	7	14	1	1	2	0	1	1	1	4	4	3	3	4	2	2	1	4	2	3	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:41515309G>A	ENST00000239882.3	-	8	1318	c.1004C>T	c.(1003-1005)cCa>cTa	p.P335L	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.P311L	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	335					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TTTTACCCCTGGACTTGAAGA	0.453																																					p.P335L		.											.	ELF1-227	0			c.C1004T						.						131	134	133					13																	41515309		2203	4300	6503	SO:0001583	missense	1997	exon8			ACCCCTGGACTTG	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1004C>T	13.37:g.41515309G>A	ENSP00000239882:p.Pro335Leu	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	211	46	NM_172373	0	0	0	0	0	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460748	0.43736	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.55413	0.52;0.52	5.47	5.47	0.80525	.	0.503265	0.21383	N	0.075437	T	0.43612	0.1255	L	0.29908	0.895	0.38663	D	0.952122	B;B	0.25235	0.059;0.121	B;B	0.18263	0.015;0.021	T	0.41752	-0.9491	10	0.54805	T	0.06	.	16.6683	0.85259	0.0:0.1294:0.8706:0.0	.	311;335	E9PDQ9;P32519	.;ELF1_HUMAN	L	311;77;335	ENSP00000405580:P311L;ENSP00000239882:P335L	ENSP00000239882:P335L	P	-	2	0	ELF1	40413309	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	4.056000	0.57448	2.729000	0.93468	0.655000	0.94253	CCA	.		0.453	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		A	41515309	G	A	41515309	3	1	70	1	0	0	0	0	1	0	0	0	5066	1348	47	2	863	2	ELF1	13	41515309	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	3360541	41515309	73654569	58	6728											
GPHN	10243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	67389425	67389425	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagctctacctcatgccattGaccttttacgtgatgccatt	8	14	6	13	1	2	2	1	2	1	0	2	2	2	2	4	0	5	1	4	0	2	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr14:67389425G>C	ENST00000315266.5	+	7	1620	c.499G>C	c.(499-501)Gac>Cac	p.D167H	GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000459628.1_Missense_Mutation_p.D149H|GPHN_ENST00000543237.1_Missense_Mutation_p.D180H|GPHN_ENST00000478722.1_Missense_Mutation_p.D167H|GPHN_ENST00000305960.9_Missense_Mutation_p.D136H	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	167	Interaction with GABARAP. {ECO:0000250}.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TCATGCCATTGACCTTTTACG	0.403			T	MLL	AL																																p.D167H		.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN-228	0			c.G499C						.						187	164	172					14																	67389425		2203	4300	6503	SO:0001583	missense	10243	exon7			GCCATTGACCTTT	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.499G>C	14.37:g.67389425G>C	ENSP00000312771:p.Asp167His	Somatic	255	0		WXS	Illumina HiSeq	Phase_I	221	63	NM_001024218	0	0	0	0	0	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999756	0.74818	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960;ENST00000555456	.	.	.	5.02	4.12	0.48240	Molybdopterin binding (2);	0.000000	0.85682	D	0.000000	T	0.52386	0.1731	N	0.08118	0	0.58432	D	0.999994	B;D;B;D;D	0.89917	0.343;1.0;0.047;0.999;0.999	B;D;B;D;D	0.91635	0.281;0.999;0.052;0.993;0.989	T	0.62946	-0.6746	9	0.87932	D	0	-6.4813	13.7767	0.63057	0.0761:0.0:0.9239:0.0	.	136;180;167;167;149	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	H	167;167;149;180;136;100	.	ENSP00000303019:D136H	D	+	1	0	GPHN	66459178	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.550000	0.98110	2.321000	0.78463	0.655000	0.94253	GAC	.		0.403	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67389425	G	C	67389425	3	2	70	1	0	0	0	0	1	0	0	0	6630	1290	45	4	525	4	GPHN	14	67389425	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		67389425	39960115	59	6729											
ATG2B	55102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	96761860	96761860	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagctctacttctgcagaaAgacttgtgaagaaatccttc	13	11	8	9	0	2	4	0	1	2	3	4	5	3	4	1	0	3	2	1	0	5	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr14:96761860A>T	ENST00000359933.4	-	35	6070	c.5177T>A	c.(5176-5178)cTt>cAt	p.L1726H	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1726					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TTCTGCAGAAAGACTTGTGAA	0.308																																					p.L1726H		.											.	ATG2B-93	0			c.T5177A						.						55	54	55					14																	96761860		2203	4290	6493	SO:0001583	missense	55102	exon35			GCAGAAAGACTTG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.5177T>A	14.37:g.96761860A>T	ENSP00000353010:p.Leu1726His	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	112	36	NM_018036	0	0	0	0	0	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	26.0	4.697600	0.88830	.	.	ENSG00000066739	ENST00000359933	T	0.13657	2.57	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.40886	0.1135	M	0.80332	2.49	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.31613	-0.9937	10	0.54805	T	0.06	.	15.8864	0.79251	1.0:0.0:0.0:0.0	.	1726	Q96BY7	ATG2B_HUMAN	H	1726	ENSP00000353010:L1726H	ENSP00000261834:L370H	L	-	2	0	ATG2B	95831613	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.539000	0.90637	2.223000	0.72356	0.454000	0.30748	CTT	.		0.308	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96761860	A	T	96761860	3	4	70	1	0	0	0	0	1	0	0	0	1095	72	3	5	1091	5	ATG2B	14	96761860	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	29372435	96761860	10587680	60	6730											
NOMO2	283820	hgsc.bcm.edu	37	chr16	18532277	18532277	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agacttcagagggcctaagaCcaaggcgggttcactgtcga	11	7	13	10	2	2	3	2	0	0	3	3	4	2	3	2	3	0	1	2	3	2	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr16:18532277C>T	ENST00000381474.3	-	19	2148	c.2083G>A	c.(2083-2085)Gtc>Atc	p.V695I	NOMO2_ENST00000543392.1_Missense_Mutation_p.V528I|NOMO2_ENST00000330537.6_Missense_Mutation_p.V695I	NM_001004060.1	NP_001004060.1	Q5JPE7	NOMO2_HUMAN	NODAL modulator 2	695						endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(4)|kidney(1)|large_intestine(2)|liver(3)|lung(5)|ovary(3)|prostate(1)|skin(1)	20						GGGCCTAAGACCAAGGCGGGT	0.567																																					p.V695I		.											.	NOMO2-23	0			c.G2083A						.						7	8	8					16																	18532277		1997	4088	6085	SO:0001583	missense	283820	exon19			CTAAGACCAAGGC	AL512687	CCDS10570.1, CCDS32394.1	16p12.3	2008-02-05			ENSG00000185164	ENSG00000185164			22652	protein-coding gene	gene with protein product		609158				15257293	Standard	NM_001004060		Approved	NOMO, PM5	uc002dfe.3	Q5JPE7	OTTHUMG00000131366	ENST00000381474.3:c.2083G>A	16.37:g.18532277C>T	ENSP00000370883:p.Val695Ile	Somatic	271	0		WXS	Illumina HiSeq	Phase_I	337	82	NM_173614	0	0	0	0	0	Q4G177	Missense_Mutation	SNP	ENST00000381474.3	37	CCDS32394.1	.	.	.	.	.	.	.	.	.	.	.	18.89	3.720080	0.68844	.	.	ENSG00000185164	ENST00000330537;ENST00000381474;ENST00000543392	T;T;T	0.04706	3.61;3.59;3.57	3.37	3.37	0.38596	.	0.000000	0.85682	D	0.000000	T	0.10380	0.0254	L	0.47716	1.5	0.80722	D	1	D;D	0.62365	0.991;0.985	P;P	0.57425	0.82;0.643	T	0.37842	-0.9688	10	0.14656	T	0.56	-27.7224	14.2293	0.65879	0.0:1.0:0.0:0.0	.	528;695	Q4G177;Q5JPE7	.;NOMO2_HUMAN	I	695;695;528	ENSP00000331851:V695I;ENSP00000370883:V695I;ENSP00000439970:V528I	ENSP00000331851:V695I	V	-	1	0	NOMO2	18439778	1.000000	0.71417	0.274000	0.24659	0.987000	0.75469	6.873000	0.75541	1.845000	0.53610	0.455000	0.32223	GTC	.		0.567	NOMO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435858.1	NM_001004060		T	18532277	C	T	18532277	3	4	70	1	0	0	0	0	1	0	0	0	10558	507	18	2	1780	2	NOMO2	16	18532277	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08		18532277	71822476	61	6731											
ITGAX	3687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31371300	31371300	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcactttcgaggaattcagGcgcagctcaaaccccctcag	10	9	8	14	2	4	0	4	0	0	0	5	2	4	1	2	2	2	2	2	2	2	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr16:31371300G>A	ENST00000268296.4	+	7	742	c.621G>A	c.(619-621)agG>agA	p.R207R	ITGAX_ENST00000562522.1_Silent_p.R207R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	207	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						AGGAATTCAGGCGCAGCTCAA	0.522																																					p.R207R		.											.	ITGAX-229	0			c.G621A						.						103	105	104					16																	31371300		2197	4300	6497	SO:0001819	synonymous_variant	3687	exon7			ATTCAGGCGCAGC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.621G>A	16.37:g.31371300G>A		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	223	108	NM_000887	0	0	0	0	0	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			.		0.522	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31371300	G	A	31371300	2	1	70	1	0	0	0	0	0	0	0	1	7910	1194	42	2		2	ITGAX	16	31371300	Silent	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	12839023	31371300	58983453	62	6732											
TK2	7084	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	66547680	66547680	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcctttgatgagccacTcctcatggagatggtgaatt	8	12	12	9	0	1	4	1	3	0	1	2	5	2	4	3	3	2	1	3	3	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr16:66547680T>A	ENST00000451102.2	-	9	1003	c.653A>T	c.(652-654)gAg>gTg	p.E218V	TK2_ENST00000563369.2_Missense_Mutation_p.E121V|TK2_ENST00000527800.1_Missense_Mutation_p.E121V|TK2_ENST00000417693.3_Missense_Mutation_p.E200V|TK2_ENST00000568170.1_5'Flank|TK2_ENST00000544898.1_Missense_Mutation_p.E169V|TK2_ENST00000525974.1_Missense_Mutation_p.E121V|TK2_ENST00000564917.1_Missense_Mutation_p.E235V|TK2_ENST00000545043.2_Missense_Mutation_p.E193V|TK2_ENST00000527284.1_Missense_Mutation_p.E187V|TK2_ENST00000299697.7_Missense_Mutation_p.E260V|RP11-403P17.5_ENST00000561728.1_Silent_p.G34G			O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	218					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|DNA replication (GO:0006260)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|thymidine kinase activity (GO:0004797)			large_intestine(1)|lung(2)|urinary_tract(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)		GATGAGCCACTCCTCATGGAG	0.537																																					p.E218V													.	TK2-115	0			c.A653T						.						81	66	71					16																	66547680		2201	4300	6501	SO:0001583	missense	7084	exon9			AGCCACTCCTCAT		CCDS10805.1, CCDS10805.2, CCDS54016.1, CCDS54017.1, CCDS54018.1, CCDS61955.1	16q22-q23.1	2012-10-02			ENSG00000166548	ENSG00000166548	2.7.1.21		11831	protein-coding gene	gene with protein product		188250					Standard	NM_004614		Approved		uc002eos.3	O00142	OTTHUMG00000137499	ENST00000451102.2:c.653A>T	16.37:g.66547680T>A	ENSP00000414334:p.Glu218Val	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	87	7	NM_004614	0	0	0	0	0	B4DGJ7|B4DZK7|B7ZAB1|E9PH08|O15238	Missense_Mutation	SNP	ENST00000451102.2	37	CCDS10805.2	.	.	.	.	.	.	.	.	.	.	T	18.75	3.691358	0.68271	.	.	ENSG00000166548	ENST00000299697;ENST00000417693;ENST00000545043;ENST00000451102;ENST00000527800;ENST00000527284;ENST00000544898;ENST00000525974	D;D;D;D;D;D;D;D	0.94376	-3.41;-3.41;-3.41;-3.41;-3.41;-3.41;-3.41;-3.41	4.89	4.89	0.63831	.	0.098662	0.64402	D	0.000001	D	0.95095	0.8411	M	0.70595	2.14	0.51482	D	0.999929	D;P;B;D;B	0.56968	0.978;0.922;0.064;0.978;0.185	P;P;B;P;B	0.58577	0.841;0.782;0.209;0.841;0.205	D	0.95195	0.8311	10	0.62326	D	0.03	-31.3551	12.5335	0.56128	0.0:0.0:0.0:1.0	.	260;218;169;260;187	Q8IZR3;O00142;F5GYK4;E5KNQ5;O00142-2	.;KITM_HUMAN;.;.;.	V	260;200;193;218;121;187;169;121	ENSP00000299697:E260V;ENSP00000407469:E200V;ENSP00000438143:E193V;ENSP00000414334:E218V;ENSP00000433770:E121V;ENSP00000435312:E187V;ENSP00000440898:E169V;ENSP00000434594:E121V	ENSP00000299697:E260V	E	-	2	0	TK2	65105181	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	5.787000	0.69013	2.058000	0.61347	0.528000	0.53228	GAG	.		0.537	TK2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268806.4			A	66547680	T	A	66547680	3	1	70	1	0	0	0	0	1	0	0	0	15965	1551	54	5	152	5	TK2	16	66547680	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	35176380	66547680	23807073	63	6733											
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85690103	85690103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtgagcgtgagaaggagcgcGagcgcgagctggagcgccag	9	3	20	9	6	0	2	0	2	0	1	0	7	0	4	1	2	5	1	1	2	1	0	rs532185802		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr16:85690103G>A	ENST00000253458.7	+	7	1320	c.1144G>A	c.(1144-1146)Gag>Aag	p.E382K	GSE1_ENST00000393243.1_Missense_Mutation_p.E309K|GSE1_ENST00000405402.2_Missense_Mutation_p.E278K|RN7SL381P_ENST00000577658.1_RNA	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	382																	gaaggagcgcgagcgcgagct	0.706													G|||	1	0.000199681	0	0	5008	,	,		13649	0		0.001	False		,,,				2504	0				p.E382K		.											.	.	0			c.G1144A						.						5	6	6					16																	85690103		1947	3842	5789	SO:0001583	missense	23199	exon7			GAGCGCGAGCGCG	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"genetic suppressor element 1"		"KIAA0182", "Gse1 coiled-coil protein homolog (mouse)"	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1144G>A	16.37:g.85690103G>A	ENSP00000253458:p.Glu382Lys	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	6	5	NM_014615	0	0	0	0	0	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853813	0.32791	.	.	ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243	T;T;T	0.10477	2.87;2.87;2.87	4.87	4.87	0.63330	.	0.225508	0.44483	D	0.000446	T	0.22205	0.0535	M	0.64404	1.975	0.80722	D	1	D;D	0.69078	0.997;0.99	P;P	0.58454	0.839;0.548	T	0.05194	-1.0900	10	0.07175	T	0.84	-12.1607	16.1523	0.81632	0.0:0.0:1.0:0.0	.	309;382	Q14687-3;Q14687	.;GSE1_HUMAN	K	278;382;309	ENSP00000384839:E278K;ENSP00000253458:E382K;ENSP00000376934:E309K	ENSP00000253458:E382K	E	+	1	0	KIAA0182	84247604	1.000000	0.71417	0.993000	0.49108	0.165000	0.22458	8.347000	0.90062	2.425000	0.82216	0.561000	0.74099	GAG	.		0.706	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		A	85690103	G	A	85690103	3	1	70	1	0	0	0	0	1	0	0	0	8180	1059	37	1	1170	1	KIAA0182	16	85690103	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	19142423	85690103	4664650	64	6734											
SLC13A5	284111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	6606332	6606332	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgttgggtcccgtcccggTcagggtggcggtgcccccga	3	7	16	15	5	1	0	1	0	0	0	3	1	3	0	4	5	1	1	4	5	0	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:6606332T>G	ENST00000433363.2	-	5	906	c.673A>C	c.(673-675)Acc>Ccc	p.T225P	SLC13A5_ENST00000573648.1_Missense_Mutation_p.T225P|SLC13A5_ENST00000381074.4_Missense_Mutation_p.T182P|SLC13A5_ENST00000293800.6_Missense_Mutation_p.T208P	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	225					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						CCCGTCCCGGTCAGGGTGGCG	0.642																																					p.T225P		.											.	SLC13A5-90	0			c.A673C						.						117	98	105					17																	6606332		2203	4300	6503	SO:0001583	missense	284111	exon5			TCCCGGTCAGGGT	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"Solute carriers"	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.673A>C	17.37:g.6606332T>G	ENSP00000406220:p.Thr225Pro	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	141	39	NM_001143838	0	0	0	0	0	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Missense_Mutation	SNP	ENST00000433363.2	37	CCDS11079.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384652	0.82792	.	.	ENSG00000141485	ENST00000293800;ENST00000433363;ENST00000381074	T;T	0.11169	2.8;2.8	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.40473	0.1118	M	0.89715	3.055	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.996;0.994;0.994;1.0	D;D;D;D;D	0.97110	0.967;0.945;0.967;0.967;1.0	T	0.48364	-0.9042	10	0.87932	D	0	.	13.806	0.63233	0.0:0.0:0.0:1.0	.	225;182;182;208;225	B7ZLB4;F8W7N2;B7Z4P2;B3KXR0;Q86YT5	.;.;.;.;S13A5_HUMAN	P	225;225;182	ENSP00000406220:T225P;ENSP00000370464:T182P	ENSP00000293800:T225P	T	-	1	0	SLC13A5	6547056	1.000000	0.71417	0.991000	0.47740	0.674000	0.39518	5.844000	0.69430	2.216000	0.71823	0.459000	0.35465	ACC	.		0.642	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550		G	6606332	T	G	6606332	3	3	70	1	0	0	0	0	1	0	0	0	14427	1667	58	5	1065	5	SLC13A5	17	6606332	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		6606332	74588878	65	6735											
PIK3R5	23533	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	8812455	8812455	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccgggtccctgctgaccAgctcctgcaggctccagcag	5	6	13	17	1	0	1	0	1	0	0	3	1	3	1	5	3	4	5	5	3	0	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:8812455A>G	ENST00000447110.1	-	3	264	c.140T>C	c.(139-141)cTg>cCg	p.L47P	PIK3R5_ENST00000584803.1_Missense_Mutation_p.L47P|PIK3R5_ENST00000581552.1_Missense_Mutation_p.L47P	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	47	Heterodimerization. {ECO:0000250}.			L -> Q (in Ref. 6; AAW63122). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CCTGCTGACCAGCTCCTGCAG	0.597																																					p.L47P	NSCLC(18;589 615 7696 20311 50332)	.											.	PIK3R5-1146	0			c.T140C						.						29	25	27					17																	8812455		2203	4300	6503	SO:0001583	missense	23533	exon3			CTGACCAGCTCCT	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.140T>C	17.37:g.8812455A>G	ENSP00000392812:p.Leu47Pro	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	26	4	NM_001142633	0	0	0	0	0	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Missense_Mutation	SNP	ENST00000447110.1	37	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.433132	0.43224	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T;T	0.80123	-1.34;-1.34	5.22	5.22	0.72569	.	0.076071	0.53938	D	0.000052	D	0.83459	0.5259	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85017	0.0909	10	0.59425	D	0.04	-7.8781	13.6276	0.62176	1.0:0.0:0.0:0.0	.	47	Q8WYR1	PI3R5_HUMAN	P	47	ENSP00000269300:L47P;ENSP00000392812:L47P	ENSP00000269300:L47P	L	-	2	0	PIK3R5	8753180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.181000	0.77682	2.100000	0.63781	0.528000	0.53228	CTG	.		0.597	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308		G	8812455	A	G	8812455	3	3	70	1	0	0	0	0	1	0	0	0	11948	188	7	3	2570	3	PIK3R5	17	8812455	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	2206123	8812455	72382755	66	6736											
KIAA0100	9703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26948415	26948415	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaggagggggagggctgAcctgtggttgtggtaaccat	8	8	19	6	0	0	2	0	1	0	1	0	4	0	4	2	6	1	4	2	6	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:26948415A>G	ENST00000528896.2	-	27	5134		c.e27+1		KIAA0100_ENST00000389003.3_Splice_Site|KIAA0100_ENST00000579924.2_5'Flank|KIAA0100_ENST00000544884.1_Splice_Site	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100							extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GGGAGGGCTGACCTGTGGTTG	0.542																																					.		.											.	KIAA0100-93	0			c.5059+2T>C						.						113	103	106					17																	26948415		2203	4300	6503	SO:0001630	splice_region_variant	9703	exon28			GGGCTGACCTGTG	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5059+1T>C	17.37:g.26948415A>G		Somatic	252	0		WXS	Illumina HiSeq	Phase_I	283	62	NM_014680	0	0	0	0	0	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Splice_Site	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.779355	0.70107	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4732	0.67531	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0100	23972542	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	8.702000	0.91338	2.211000	0.71520	0.402000	0.26972	.	.		0.542	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	Intron	G	26948415	A	G	26948415	5	3	70	1	0	0	0	0	0	0	1	0	8175	289	10	3	1698	3	KIAA0100	17	26948415	Splice_Site	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	18135960	26948415	54246795	67	6737											
MPO	4353	hgsc.bcm.edu	37	chr17	56356475	56356475	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgaagtcgaggtcgtggTccaacagctggccccattgc	7	8	15	11	2	0	1	0	1	0	0	3	2	1	1	3	4	3	1	3	4	2	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:56356475T>C	ENST00000225275.3	-	6	955	c.779A>G	c.(778-780)gAc>gGc	p.D260G	MPO_ENST00000578493.1_5'Flank|MPO_ENST00000340482.3_Missense_Mutation_p.D292G	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	260					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)	GAGGTCGTGGTCCAACAGCTG	0.657																																					p.D260G		.											.	MPO-156	0			c.A779G						.						56	55	56					17																	56356475		2203	4300	6503	SO:0001583	missense	4353	exon6			TCGTGGTCCAACA		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.779A>G	17.37:g.56356475T>C	ENSP00000225275:p.Asp260Gly	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	27	3	NM_000250	0	0	0	0	0	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566371	0.86439	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.71103	-0.54;-0.54	5.51	4.4	0.53042	.	0.134476	0.53938	D	0.000044	D	0.85665	0.5749	M	0.91249	3.19	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	D	0.87073	0.2161	10	0.87932	D	0	-44.0613	10.9432	0.47285	0.1403:0.0:0.0:0.8597	.	260	P05164	PERM_HUMAN	G	292;260	ENSP00000344419:D292G;ENSP00000225275:D260G	ENSP00000225275:D260G	D	-	2	0	MPO	53711474	1.000000	0.71417	0.951000	0.38953	0.952000	0.60782	6.177000	0.71961	0.879000	0.35944	0.460000	0.39030	GAC	.		0.657	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			C	56356475	T	C	56356475	3	2	70	1	0	0	0	0	1	0	0	0	9757	1667	58	3	1486	3	MPO	17	56356475	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	29408060	56356475	24838735	68	6738											
NACA2	342538	ucsc.edu	37	chr17	59668318	59668318	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacatagccttccgtgccCtcttttcactccgactctgt	5	14	7	15	2	3	0	1	0	2	0	5	2	5	1	4	1	2	0	4	1	1	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:59668318C>T	ENST00000521764.1	-	1	245	c.224G>A	c.(223-225)aGg>aAg	p.R75K		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	75	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					CTTCCGTGCCCTCTTTTCACT	0.458																																					p.R75K													.	NACA2-91	0			c.G224A						.						246	229	234					17																	59668318		2203	4300	6503	SO:0001583	missense	342538	exon1			CGTGCCCTCTTTT	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.224G>A	17.37:g.59668318C>T	ENSP00000427802:p.Arg75Lys	Somatic	390	1		WXS	Illumina HiSeq		532	1	NM_199290	0	0	0	0	0	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976583	0.34848	.	.	ENSG00000253506	ENST00000521764	T	0.17528	2.27	0.753	-0.748	0.11087	Nascent polypeptide-associated complex NAC (2);	0.072360	0.50627	N	0.000118	T	0.01489	0.0048	N	0.00010	-3.04	0.23577	N	0.997375	B	0.02656	0.0	B	0.01281	0.0	T	0.46076	-0.9217	9	.	.	.	.	4.0866	0.09950	0.0:0.257:0.0:0.743	.	75	Q9H009	NACA2_HUMAN	K	75	ENSP00000427802:R75K	.	R	-	2	0	NACA2	57023100	1.000000	0.71417	0.973000	0.42090	0.773000	0.43773	3.300000	0.51834	-0.188000	0.10499	-0.624000	0.04008	AGG	.		0.458	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		T	59668318	C	T	59668318	3	4	70	1	0	0	0	0	1	0	0	0	10159	681	24	2	427	2	NACA2	17	59668318	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	3311843	59668318	21526892	69	6739											
C17orf28	283987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72954436	72954436	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctcaccacaatgagcaggtCggcgtgggtccctgtgaaga	9	7	13	12	2	1	3	1	2	0	1	3	3	2	3	3	3	1	1	3	3	2	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:72954436C>G	ENST00000425042.2	-	11	1455	c.1378G>C	c.(1378-1380)Gac>Cac	p.D460H		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	460					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											ATGAGCAGGTCGGCGTGGGTC	0.667											OREG0024721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D460H		.											.	.	0			c.G1378C						.						55	43	47					17																	72954436		2203	4300	6503	SO:0001583	missense	283987	exon11			GCAGGTCGGCGTG		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.1378G>C	17.37:g.72954436C>G	ENSP00000413520:p.Asp460His	Somatic	28	0	1141	WXS	Illumina HiSeq	Phase_I	48	5	NM_030630	0	0	0	0	0	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	37	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918325	0.92249	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.86732	0.6003	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90618	0.4557	9	0.87932	D	0	-29.5566	18.1326	0.89606	0.0:1.0:0.0:0.0	.	460	Q8IV36	CQ028_HUMAN	H	232;460;232	.	ENSP00000317795:D232H	D	-	1	0	C17orf28	70466031	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.550000	0.82173	2.284000	0.76573	0.561000	0.74099	GAC	.		0.667	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		G	72954436	C	G	72954436	3	3	70	1	0	0	0	0	1	0	0	0	1858	884	31	4	1024	4	C17orf28	17	72954436	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	13286118	72954436	8240774	70	6740											
ITGB4	3691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73752809	73752809	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgccttcactttgagcactcCcagtgccccaggcccgctgg	5	8	10	18	2	1	1	1	1	0	0	2	1	2	1	5	2	2	2	5	2	0	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:73752809C>T	ENST00000200181.3	+	37	5109	c.4922C>T	c.(4921-4923)cCc>cTc	p.P1641L	ITGB4_ENST00000339591.3_Missense_Mutation_p.P1624L|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Missense_Mutation_p.P1571L|ITGB4_ENST00000579662.1_Missense_Mutation_p.P1571L|ITGB4_ENST00000449880.2_Missense_Mutation_p.P1624L	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1641					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTGAGCACTCCCAGTGCCCCA	0.667																																					p.P1641L		.											.	ITGB4-227	0			c.C4922T						.						53	55	54					17																	73752809		2203	4299	6502	SO:0001583	missense	3691	exon37			GCACTCCCAGTGC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4922C>T	17.37:g.73752809C>T	ENSP00000200181:p.Pro1641Leu	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	124	29	NM_000213	0	0	0	0	0	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.644502	0.47258	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.61627	0.09;0.09;0.09	5.04	5.04	0.67666	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.82802	0.5116	M	0.93978	3.48	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.87598	0.2495	10	0.87932	D	0	.	18.7536	0.91823	0.0:1.0:0.0:0.0	.	1624;1571;1641	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	L	1641;1624;1624	ENSP00000200181:P1641L;ENSP00000344079:P1624L;ENSP00000400217:P1624L	ENSP00000200181:P1641L	P	+	2	0	ITGB4	71264404	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	7.776000	0.85560	2.518000	0.84900	0.462000	0.41574	CCC	.		0.667	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			T	73752809	C	T	73752809	3	4	70	1	0	0	0	0	1	0	0	0	7918	623	22	2	5227	2	ITGB4	17	73752809	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	798373	73752809	7442401	71	6741											
GADD45B	4616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2477582	2477582	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagtgggtcccctacatcTctcttcaggaacgctgaggc	8	9	10	14	1	3	1	1	1	2	0	5	2	4	2	3	3	2	1	3	3	2	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:2477582T>A	ENST00000215631.4	+	4	698	c.466T>A	c.(466-468)Tct>Act	p.S156T		NM_015675.3	NP_056490.2	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta	156					activation of MAPKK activity (GO:0000186)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of cell cycle (GO:0051726)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|lung(1)|ovary(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCTACATCTCTCTTCAGGA	0.552																																					p.S156T		.											.	GADD45B-90	0			c.T466A						.						39	40	40					19																	2477582		2203	4300	6503	SO:0001583	missense	4616	exon4			TACATCTCTCTTC	AF090950	CCDS32868.1	19p13.3	2012-10-02			ENSG00000099860	ENSG00000099860			4096	protein-coding gene	gene with protein product	"myeloid differentiation primary response", "growth arrest and DNA-damage-inducible beta"	604948		MYD118		1899477, 9827804	Standard	NM_015675		Approved	GADD45BETA, DKFZP566B133	uc002lwb.2	O75293	OTTHUMG00000180434	ENST00000215631.4:c.466T>A	19.37:g.2477582T>A	ENSP00000215631:p.Ser156Thr	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	39	13	NM_015675	0	0	0	0	0	A8KAM2|O75960|Q17R46	Missense_Mutation	SNP	ENST00000215631.4	37	CCDS32868.1	.	.	.	.	.	.	.	.	.	.	T	2.003	-0.428988	0.04701	.	.	ENSG00000099860	ENST00000215631	T	0.40756	1.02	4.66	-0.362	0.12560	.	0.260085	0.37012	N	0.002300	T	0.15522	0.0374	N	0.24115	0.695	0.58432	D	0.999999	B	0.29716	0.255	B	0.21917	0.037	T	0.29971	-0.9994	10	0.02654	T	1	.	1.0667	0.01612	0.1464:0.2718:0.1505:0.4313	.	156	O75293	GA45B_HUMAN	T	156	ENSP00000215631:S156T	ENSP00000215631:S156T	S	+	1	0	GADD45B	2428582	0.000000	0.05858	0.307000	0.25127	0.709000	0.40893	-1.720000	0.01871	-0.128000	0.11641	0.443000	0.29094	TCT	.		0.552	GADD45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451337.1	NM_015675		A	2477582	T	A	2477582	3	1	70	1	0	0	0	0	1	0	0	0	6201	1551	54	5	480	5	GADD45B	19	2477582	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		2477582	56651401	72	6742											
S1PR4	8698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	3179456	3179456	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggccaccatcatgggcctCtatggggccatcttccgcct	5	10	10	16	1	3	0	1	0	2	0	4	0	4	0	6	4	0	0	6	4	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:3179456C>T	ENST00000246115.3	+	1	721	c.666C>T	c.(664-666)ctC>ctT	p.L222L	S1PR4_ENST00000591346.1_3'UTR	NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	222					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						TCATGGGCCTCTATGGGGCCA	0.672																																					p.L222L	GBM(82;318 1638 33279 49708)	.											.	S1PR4-591	0			c.C666T						.						86	93	91					19																	3179456		2203	4300	6503	SO:0001819	synonymous_variant	8698	exon1			GGGCCTCTATGGG	AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3170	protein-coding gene	gene with protein product		603751	"endothelial differentiation, G-protein-coupled receptor 6", "endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.666C>T	19.37:g.3179456C>T		Somatic	245	0		WXS	Illumina HiSeq	Phase_I	263	85	NM_003775	0	0	0	0	0	D6W612	Silent	SNP	ENST00000246115.3	37	CCDS12105.1																																																																																			.		0.672	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775		T	3179456	C	T	3179456	2	4	70	1	0	0	0	0	0	0	0	1	13828	900	32	2		2	S1PR4	19	3179456	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	701874	3179456	55949527	73	6743											
SLC7A10	56301	hgsc.bcm.edu	37	chr19	33706864	33706864	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgggcgagatgaagatgcccGagccgatgatgttccctgca	9	8	14	10	3	0	4	0	2	0	2	1	7	1	4	3	1	3	2	3	1	1	1	rs370231027		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:33706864G>C	ENST00000253188.4	-	2	313	c.167C>G	c.(166-168)tCg>tGg	p.S56W	CTD-2540B15.6_ENST00000590492.1_RNA	NM_019849.2	NP_062823.1	Q9NS82	AAA1_HUMAN	solute carrier family 7 (neutral amino acid transporter light chain, asc system), member 10	56					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|D-alanine transport (GO:0042941)|D-serine transport (GO:0042942)|ion transport (GO:0006811)|L-serine transport (GO:0015825)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	18	Esophageal squamous(110;0.137)					GAAGATGCCCGAGCCGATGAT	0.682																																					p.S56W		.											.	SLC7A10-91	0			c.C167G						.						22	21	21					19																	33706864		2200	4297	6497	SO:0001583	missense	56301	exon2			ATGCCCGAGCCGA	AB037670	CCDS12431.1	19q13.11	2013-05-28	2011-07-12		ENSG00000130876	ENSG00000130876		"Solute carriers"	11058	protein-coding gene	gene with protein product		607959				10734121, 10863037	Standard	NM_019849		Approved	asc-1	uc002num.2	Q9NS82	OTTHUMG00000180344	ENST00000253188.4:c.167C>G	19.37:g.33706864G>C	ENSP00000253188:p.Ser56Trp	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_019849	0	0	0	0	0	B2RE84	Missense_Mutation	SNP	ENST00000253188.4	37	CCDS12431.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630872	0.87660	.	.	ENSG00000130876	ENST00000253188	D	0.91237	-2.81	4.98	4.98	0.66077	Amino acid permease domain (1);	0.063353	0.64402	D	0.000003	D	0.96962	0.9008	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98358	1.0547	10	0.87932	D	0	.	17.3072	0.87198	0.0:0.0:1.0:0.0	.	56	Q9NS82	AAA1_HUMAN	W	56	ENSP00000253188:S56W	ENSP00000253188:S56W	S	-	2	0	SLC7A10	38398704	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	9.869000	0.99810	2.347000	0.79759	0.456000	0.33151	TCG	.		0.682	SLC7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450846.2	NM_019849		C	33706864	G	C	33706864	3	2	70	1	0	0	0	0	1	0	0	0	14725	1059	37	4	1444	4	SLC7A10	19	33706864	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	30527408	33706864	25422119	74	6744											
ZFP14	57677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36831480	36831481	+	Missense_Mutation	DNP	GC	GC	AT																															ggtctctcaccaatatgaatGctctggtgtgaaataagctg																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:36831480_36831481GC>AT	ENST00000270001.7	-	5	1362_1363	c.1247_1248GC>AT	c.(1246-1248)aGC>aAT	p.S416N		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	416					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)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					CAATATGAATGCTCTGGTGTGA	0.416																																					p.S416N		.											.	ZFP14	0			c.G1247A						.																																			SO:0001583	missense	57677	exon5			TGAATGCTCTGGT	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.1247_1248delinsAT	19.37:g.36831480_36831481delinsAT	ENSP00000270001:p.Ser416Asn	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	164	53		0	0	0	0	0	A7MD23	Missense_Mutation	DNP	ENST00000270001.7	37	CCDS33002.1																																																																																			.		0.416	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		AT	36831481	GC	AT	36831480	3	1	70	1	0	0	0	0	1	0	0	0	17671	1310	46	2	357	2	ZFP14	19	36831480	Missense_Mutation	DNP	GC	TCGA-BQ-5886-01A-11D-1589-08	3124616	36831480	22297503	75	6745											
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	40395905	40395906	+	Missense_Mutation	DNP	TC	TC	GT																															cccattaccccaggccacgtTctcctgcaggacggcaaacc																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:40395905_40395906TC>GT	ENST00000221347.6	-	15	7498_7499	c.7491_7492GA>AC	c.(7489-7494)gaGAac>gaACac	p.N2498H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2498	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CAGGCCACGTTCTCCTGCAGGA	0.629																																					p.N2498H		.											.	FCGBP	0			c.G7491A						.																																			SO:0001583	missense	8857	exon15			CACGTTCTCCTGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.7491_7492delinsGT	19.37:g.40395905_40395906delinsGT	ENSP00000221347:p.Asn2498His	Somatic	397	1		WXS	Illumina HiSeq	Phase_I	414	50		0	0	0	0	0	O95784	Missense_Mutation	DNP	ENST00000221347.6	37	CCDS12546.1																																																																																			.		0.629	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		GT	40395906	TC	GT	40395905	3	3	70	1	0	0	0	0	1	0	0	0	5797	1783	62	5	8813	5	FCGBP	19	40395905	Missense_Mutation	DNP	TC	TCGA-BQ-5886-01A-11D-1589-08	3564425	40395905	18733078	76	6746											
BCAM	4059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45322968	45322968	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccctgctgccgccagcggcGggagaagggggctccgtgag	5	4	18	14	4	0	2	0	1	0	1	1	3	1	2	5	4	3	2	5	4	1	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:45322968G>T	ENST00000270233.6	+	13	1770	c.1748G>T	c.(1747-1749)cGg>cTg	p.R583L	BCAM_ENST00000589651.1_Missense_Mutation_p.R583L	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	583					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CGCCAGCGGCGGGAGAAGGGG	0.637																																					p.R583L		.											.	BCAM-91	0			c.G1748T						.						14	17	16					19																	45322968		2183	4244	6427	SO:0001583	missense	4059	exon13			AGCGGCGGGAGAA	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1748G>T	19.37:g.45322968G>T	ENSP00000270233:p.Arg583Leu	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	39	18	NM_001013257	0	0	0	0	0	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	4.697	0.129623	0.08981	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.59772	0.24;0.34	4.08	1.68	0.24146	.	.	.	.	.	T	0.33904	0.0879	N	0.08118	0	0.09310	N	1	B	0.24092	0.097	B	0.15870	0.014	T	0.15521	-1.0434	9	0.30078	T	0.28	-5.8905	10.1318	0.42682	0.0:0.4182:0.5817:0.0	.	583	P50895	BCAM_HUMAN	L	583	ENSP00000270233:R583L;ENSP00000375817:R583L	ENSP00000270233:R583L	R	+	2	0	BCAM	50014808	0.003000	0.15002	0.037000	0.18230	0.042000	0.13812	1.344000	0.33941	0.242000	0.21303	0.531000	0.56144	CGG	.		0.637	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45322968	G	T	45322968	3	4	70	1	0	0	0	0	1	0	0	0	1345	1116	39	4	1798	4	BCAM	19	45322968	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	4927063	45322968	13806015	77	6747											
CCDC114	93233	broad.mit.edu	37	chr19	48800292	48800292	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgctggaggcagggccggTgctggagacgtggtctctgc	5	8	19	9	2	1	1	0	0	1	1	2	3	1	2	1	6	3	3	1	6	0	0	rs190723331		TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:48800292T>G	ENST00000315396.7	-	14	2636	c.1954A>C	c.(1954-1956)Acc>Ccc	p.T652P		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	652	Ser-rich.				outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		GCAGGGCCGGTGCTGGAGACG	0.682																																					p.T652P													.	CCDC114-91	0			c.A1954C						.						39	40	40					19																	48800292		2203	4299	6502	SO:0001583	missense	93233	exon14			GGCCGGTGCTGGA	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.1954A>C	19.37:g.48800292T>G	ENSP00000318429:p.Thr652Pro	Somatic	77	2		WXS	Illumina HiSeq	Phase_I	83	4	NM_144577	0	0	0	0	0	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	.	.	.	.	.	.	.	.	.	.	T	2.053	-0.417249	0.04766	.	.	ENSG00000105479	ENST00000315396	T	0.24723	1.84	3.45	-6.89	0.01660	.	.	.	.	.	T	0.07908	0.0198	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44832	-0.9302	9	0.30854	T	0.27	1.9698	11.5423	0.50673	0.0:0.1068:0.6637:0.2295	.	652	Q96M63	CC114_HUMAN	P	652	ENSP00000318429:T652P	ENSP00000318429:T652P	T	-	1	0	CCDC114	53492104	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.767000	0.00782	-3.288000	0.00195	-1.286000	0.01371	ACC	T|0.999;C|0.000		0.682	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577		G	48800292	T	G	48800292	3	3	70	1	0	0	0	0	1	0	0	0	2757	1696	59	5	62	5	CCDC114	19	48800292	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	3477324	48800292	10328691	78	6748											
HRC	3270	hgsc.bcm.edu	37	chr19	49657763	49657763	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatcatcatcgtcatcttcTtcatggccttggtgcctgtg	5	16	8	12	1	7	0	5	0	2	0	8	0	7	0	2	2	1	0	2	2	0	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:49657763T>A	ENST00000252825.4	-	1	918	c.732A>T	c.(730-732)gaA>gaT	p.E244D	HRC_ENST00000595625.1_Missense_Mutation_p.E244D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	244	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)	p.E244E(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cgtcatcttcttcatGGCCTT	0.522																																					p.E244D	Melanoma(37;75 1097 24567 25669 30645)	.											.	HRC-91	1	Substitution - coding silent(1)	lung(1)	c.A732T						.						118	85	96					19																	49657763		2203	4300	6503	SO:0001583	missense	3270	exon1			ATCTTCTTCATGG		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"histidine-rich calcium-binding protein"			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.732A>T	19.37:g.49657763T>A	ENSP00000252825:p.Glu244Asp	Somatic	30	1		WXS	Illumina HiSeq	Phase_I	33	2	NM_002152	0	0	0	0	0	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	t	8.405	0.842850	0.16963	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.06294	3.32	3.24	2.17	0.27698	.	.	.	.	.	T	0.07593	0.0191	L	0.57536	1.79	0.09310	N	0.999998	B	0.28820	0.224	B	0.33846	0.171	T	0.37641	-0.9697	9	0.13853	T	0.58	0.3786	7.0233	0.24926	0.0:0.1288:0.0:0.8712	.	244	P23327	SRCH_HUMAN	D	244;214	ENSP00000252825:E244D	ENSP00000252825:E244D	E	-	3	2	HRC	54349575	0.001000	0.12720	0.040000	0.18447	0.049000	0.14656	0.298000	0.19120	1.251000	0.43983	0.375000	0.23000	GAA	.		0.522	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		A	49657763	T	A	49657763	3	1	70	1	0	0	0	0	1	0	0	0	7373	1606	56	5	1391	5	HRC	19	49657763	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	857471	49657763	9471220	79	6749											
ZNF543	125919	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	57839185	57839185	+	Frame_Shift_Del	DEL	G	G	-																															cctcaaagaactcccaattaGggcaatccaaggatcaggat																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:57839185delG	ENST00000321545.4	+	4	700	c.355delG	c.(355-357)gggfs	p.G119fs		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	119					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)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CTCCCAATTAGGGCAATCCAA	0.512																																					p.G119fs		.											.	ZNF543-92	0			c.355delG						.						64	67	66					19																	57839185		2203	4300	6503	SO:0001589	frameshift_variant	125919	exon4			.	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.355delG	19.37:g.57839185delG	ENSP00000322545:p.Gly119fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	69	15	NM_213598	0	0	0	0	0	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Frame_Shift_Del	DEL	ENST00000321545.4	37	CCDS33130.1																																																																																			.		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		-	57839185	G	-	57839185	7	5	70	1	0	1	0	1	0	0	0	0	18008	1000	35	0	369	0	ZNF543	19	57839185	Frame_Shift_Del	DEL	G	TCGA-BQ-5886-01A-11D-1589-08	8181422	57839185	1289798	80	6750											
PTPRA	5786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	3016279	3016279	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggactggtgtcctatggaGatattacagtggaactgaag	12	11	13	5	0	0	2	0	1	0	1	1	5	1	4	1	4	2	0	1	4	5	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr20:3016279G>T	ENST00000216877.6	+	20	2342	c.1942G>T	c.(1942-1944)Gat>Tat	p.D648Y	PTPRA_ENST00000358719.4_Missense_Mutation_p.D513Y|PTPRA_ENST00000380393.3_Missense_Mutation_p.D657Y|PTPRA_ENST00000399903.2_Missense_Mutation_p.D657Y|PTPRA_ENST00000318266.5_Missense_Mutation_p.D648Y|PTPRA_ENST00000356147.3_Missense_Mutation_p.D648Y|PTPRA_ENST00000425918.2_Missense_Mutation_p.D668Y	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	657	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GTCCTATGGAGATATTACAGT	0.532																																					p.D657Y		.											.	PTPRA-227	0			c.G1969T						.						106	94	98					20																	3016279		2203	4300	6503	SO:0001583	missense	5786	exon25			TATGGAGATATTA		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1942G>T	20.37:g.3016279G>T	ENSP00000216877:p.Asp648Tyr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	26	12	NM_002836	0	0	0	0	0	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860550	0.32884	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	5.57	5.57	0.84162	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	U	0.000000	D	0.90597	0.7052	M	0.72353	2.195	0.80722	D	1	P;D;D	0.89917	0.49;1.0;1.0	B;D;D	0.91635	0.143;0.999;0.963	D	0.85912	0.1441	10	0.02654	T	1	.	19.5578	0.95358	0.0:0.0:1.0:0.0	.	668;657;648	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	Y	657;648;657;513;267;668;648;648	ENSP00000369756:D657Y;ENSP00000216877:D648Y;ENSP00000382787:D657Y;ENSP00000351559:D513Y;ENSP00000393553:D668Y;ENSP00000314568:D648Y;ENSP00000348468:D648Y	ENSP00000216877:D648Y	D	+	1	0	PTPRA	2964279	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	9.869000	0.99810	2.604000	0.88044	0.563000	0.77884	GAT	.		0.532	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			T	3016279	G	T	3016279	3	4	70	1	0	0	0	0	1	0	0	0	12827	942	33	4	2039	4	PTPRA	20	3016279	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		3016279	60009241	81	6751											
GFRA4	64096	hgsc.bcm.edu	37	chr20	3641542	3641542	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggagggcggtgagccggagaGaggccccgtccccaccctcg	6	3	17	15	4	0	2	0	1	0	1	2	5	1	4	6	5	1	0	6	5	0	0	rs58634535	byFrequency	TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr20:3641542G>A	ENST00000319242.3	-	2	440	c.441C>T	c.(439-441)ctC>ctT	p.L147L	GFRA4_ENST00000290417.2_Intron			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	147					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						GAGCCGGAGAGAGGCCCCGTC	0.761													G|||	1080	0.215655	0.2897	0.2075	5008	,	,		6888	0.2163		0.16	False		,,,				2504	0.1779				p.L147L		.											.	GFRA4-90	0			c.C441T						.	G	,	373,1901		10,353,774	1	2	2		,441	1	0	20	dbSNP_129	2	558,4460		15,528,1966	no	intron,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	25,881,2740	AA,AG,GG		11.12,16.4028,12.7674	,	,147/300	3641542	931,6361	1137	2509	3646	SO:0001819	synonymous_variant	64096	exon2			CGGAGAGAGGCCC	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"persephin receptor"					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.441C>T	20.37:g.3641542G>A		Somatic	2	2		WXS	Illumina HiSeq	Phase_I	7	7	NM_145762	0	0	0	0	0	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			G|0.788;A|0.212		0.761	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762		A	3641542	G	A	3641542	2	1	70	1	0	0	0	0	0	0	0	1	6370	929	33	2		2	GFRA4	20	3641542	Silent	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	625263	3641542	59383978	82	6752											
PARD6B	84612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49366607	49366607	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgatcaagtaacagacaTgatgattgcaaatagccgta	15	10	8	8	1	1	4	1	3	0	1	1	4	1	4	2	0	3	3	2	0	5	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr20:49366607T>C	ENST00000371610.2	+	3	944	c.701T>C	c.(700-702)aTg>aCg	p.M234T	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	234	Interaction with PARD3 and CDC42. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						GTAACAGACATGATGATTGCA	0.433																																					p.M234T		.											.	PARD6B-91	0			c.T701C						.						124	117	120					20																	49366607		2203	4300	6503	SO:0001583	missense	84612	exon3			CAGACATGATGAT	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"par-6 (partitioning defective 6, C.elegans) homolog beta", "par-6 partitioning defective 6 homolog beta (C. elegans)"			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.701T>C	20.37:g.49366607T>C	ENSP00000360672:p.Met234Thr	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	156	52	NM_032521	0	0	0	0	0	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	37	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.659758	0.67586	.	.	ENSG00000124171	ENST00000371610	T	0.27402	1.67	6.02	6.02	0.97574	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.54727	0.1876	M	0.63169	1.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56456	-0.7976	10	0.87932	D	0	-60.5095	16.5446	0.84426	0.0:0.0:0.0:1.0	.	234	Q9BYG5	PAR6B_HUMAN	T	234	ENSP00000360672:M234T	ENSP00000360672:M234T	M	+	2	0	PARD6B	48800014	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	5.917000	0.69989	2.311000	0.77944	0.533000	0.62120	ATG	.		0.433	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		C	49366607	T	C	49366607	3	2	70	1	0	0	0	0	1	0	0	0	11472	1464	51	3	711	3	PARD6B	20	49366607	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	45725065	49366607	13658913	83	6753											
KRTAP10-11	386678	broad.mit.edu	37	chr21	46067216	46067216	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtccctcctctgccgccccGcaagctcccgcctggcctgc	2	8	9	22	3	1	0	0	0	1	0	4	0	4	0	8	1	3	2	8	1	1	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr21:46067216G>A	ENST00000334670.8	+	1	886	c.841G>A	c.(841-843)Gca>Aca	p.A281T	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	281						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CTGCCGCCCCGCAAGCTCCCG	0.657																																					p.A281T													.	KRTAP10-11-91	0			c.G841A						.						35	44	41					21																	46067216		2189	4278	6467	SO:0001583	missense	386678	exon1			CGCCCCGCAAGCT	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"Keratin associated proteins"	20528	protein-coding gene	gene with protein product			"keratin associated protein 10-11"	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.841G>A	21.37:g.46067216G>A	ENSP00000334197:p.Ala281Thr	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	70	4	NM_198692	0	0	0	0	0	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	g	1.731	-0.494073	0.04322	.	.	ENSG00000243489	ENST00000334670	T	0.00682	5.86	3.93	-0.303	0.12792	.	.	.	.	.	T	0.00496	0.0016	N	0.14661	0.345	0.09310	N	1	P	0.39250	0.665	B	0.30646	0.118	T	0.51624	-0.8682	9	0.23891	T	0.37	.	7.4188	0.27061	0.5633:0.0:0.4367:0.0	.	281	P60412	KR10B_HUMAN	T	281	ENSP00000334197:A281T	ENSP00000334197:A281T	A	+	1	0	KRTAP10-11	44891644	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.804000	0.04535	-0.119000	0.11830	-0.379000	0.06801	GCA	.		0.657	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		A	46067216	G	A	46067216	3	1	70	1	0	0	0	0	1	0	0	0	8528	1087	38	1	843	1	KRTAP10-11	21	46067216	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		46067216	2062679	84	6754											
EMID1	129080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	29627008	29627008	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccctgtcttcctcttcaGatgaccatgctgactgtcat	6	14	7	14	1	4	3	2	2	2	1	6	3	6	3	3	0	1	1	3	0	0	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr22:29627008G>T	ENST00000404820.3	+	6	592		c.e6-1		EMID1_ENST00000484039.1_Splice_Site|EMID1_ENST00000404755.3_Splice_Site|EMID1_ENST00000334018.6_Splice_Site			Q96A84	EMID1_HUMAN	EMI domain containing 1							collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						TTCCTCTTCAGATGACCATGC	0.587																																					.		.											.	EMID1-90	0			c.466-1G>T						.						68	65	66					22																	29627008		2203	4300	6503	SO:0001630	splice_region_variant	129080	exon6			TCTTCAGATGACC	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"EMI domain containing"	18036	protein-coding gene	gene with protein product	"emilin and multimerin-domain containing protein 1", "putative emu1"	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.466-1G>T	22.37:g.29627008G>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	103	27	NM_133455	0	0	0	0	0	B0QYK6|Q6ICG1|Q86SS7	Splice_Site	SNP	ENST00000404820.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.15|10.15	1.270790|1.270790	0.23221|0.23221	.|.	.|.	ENSG00000186998|ENSG00000186998	ENST00000334018;ENST00000429226;ENST00000404755;ENST00000404820;ENST00000430127|ENST00000433143	.|.	.|.	.|.	4.64|4.64	4.64|4.64	0.57946|0.57946	.|.	.|.	.|.	.|.	.|.	.|T	.|0.64735	.|0.2625	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.63537	.|-0.6615	.|4	.|.	.|.	.|.	.|.	13.3293|13.3293	0.60477|0.60477	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	.|I	-1|1	.|.	.|.	.|R	+|+	.|2	.|0	EMID1|EMID1	27957008|27957008	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.024000|0.024000	0.10985|0.10985	4.969000|4.969000	0.63735|0.63735	2.293000|2.293000	0.77203|0.77203	0.591000|0.591000	0.81541|0.81541	.|AGA	.		0.587	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455	Intron	T	29627008	G	T	29627008	5	4	70	1	0	0	0	0	0	0	1	0	5104	956	33	4	487	4	EMID1	22	29627008	Splice_Site	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		29627008	21677558	85	6755											
SBF1	6305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50885659	50885659	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaagttgtaaacgcgacgcGttgtcttcacctggggaagg	10	9	14	8	4	2	1	1	0	1	1	2	3	2	2	1	3	1	3	1	3	4	4	rs375012426	byFrequency	TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr22:50885659G>C	ENST00000390679.3	-	40	5700	c.5516C>G	c.(5515-5517)aCg>aGg	p.T1839R	SBF1_ENST00000380817.3_Missense_Mutation_p.T1865R|SBF1_ENST00000348911.6_Missense_Mutation_p.T1840R			O95248	MTMR5_HUMAN	SET binding factor 1	1839	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		AACGCGACGCGTTGTCTTCAC	0.667																																					p.T1865R		.											.	SBF1-90	0			c.C5594G						.						48	59	55					22																	50885659		2096	4202	6298	SO:0001583	missense	6305	exon41			CGACGCGTTGTCT	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	10542	protein-coding gene	gene with protein product	"myotubularin related 5", "DENN/MADD domain containing 7A"	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.5516C>G	22.37:g.50885659G>C	ENSP00000375097:p.Thr1839Arg	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	56	13	NM_002972	0	0	0	0	0	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.51|17.51	3.408090|3.408090	0.62399|0.62399	.|.	.|.	ENSG00000100241|ENSG00000100241	ENST00000418590|ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	.|T;T;T	.|0.12255	.|2.7;2.7;2.7	3.51|3.51	3.51|3.51	0.40186|0.40186	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.26448|0.26448	0.0646|0.0646	L|L	0.31845|0.31845	0.965|0.965	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D	.|0.89917	.|0.959;1.0;0.979	.|P;D;D	.|0.91635	.|0.85;0.999;0.913	T|T	0.06058|0.06058	-1.0848|-1.0848	5|10	.|0.66056	.|D	.|0.02	.|.	15.1872|15.1872	0.73012|0.73012	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1839;1865;386	.|O95248;O95248-4;A6PVG7	.|MTMR5_HUMAN;.;.	K|R	386|1865;1840;1875;1839	.|ENSP00000370196:T1865R;ENSP00000252027:T1840R;ENSP00000375097:T1839R	.|ENSP00000336522:T1875R	N|T	-|-	3|2	2|0	SBF1|SBF1	49232525|49232525	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.777000|0.777000	0.43975|0.43975	2.406000|2.406000	0.44557|0.44557	1.989000|1.989000	0.58080|0.58080	0.462000|0.462000	0.41574|0.41574	AAC|ACG	.		0.667	SBF1-201	KNOWN	basic	protein_coding	protein_coding				C	50885659	G	C	50885659	3	2	70	1	0	0	0	0	1	0	0	0	13890	1145	40	4	91	4	SBF1	22	50885659	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	21258651	50885659	418907	86	6756											
EIF2S3	1968	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	24089815	24089815	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttagacggcttctaggtgtaCgcactgaaggagacaagaaa	14	8	12	7	2	1	4	0	1	1	3	1	5	1	4	0	3	1	3	0	3	6	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chrX:24089815C>T	ENST00000253039.4	+	10	1406	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	385					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						TCTAGGTGTACGCACTGAAGG	0.403																																					p.R385C		.											.	EIF2S3-130	0			c.C1153T						.						37	37	37					X																	24089815		2203	4298	6501	SO:0001583	missense	1968	exon10			GGTGTACGCACTG	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"eukaryotic translation initiation factor 2G"	300161	"eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.1153C>T	X.37:g.24089815C>T	ENSP00000253039:p.Arg385Cys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	46	30	NM_001415	0	0	0	0	0	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	37	CCDS14210.1	.	.	.	.	.	.	.	.	.	.	c	27.8	4.868409	0.91587	.	.	ENSG00000130741	ENST00000253039	T	0.65549	-0.16	4.95	4.95	0.65309	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation initiation factor 2, gamma subunit, C-terminal (1);	0.052313	0.85682	D	0.000000	T	0.78830	0.4345	M	0.91972	3.26	0.80722	D	1	D	0.56746	0.977	P	0.52109	0.69	D	0.85370	0.1113	10	0.87932	D	0	.	17.6111	0.88053	0.0:1.0:0.0:0.0	.	385	P41091	IF2G_HUMAN	C	385	ENSP00000253039:R385C	ENSP00000253039:R385C	R	+	1	0	EIF2S3	23999736	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.363000	0.79516	2.175000	0.68902	0.597000	0.82753	CGC	.		0.403	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415		T	24089815	C	T	24089815	3	4	70	1	0	0	0	0	1	0	0	0	5022	536	19	1	1191	1	EIF2S3	23	24089815	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08		24089815	131180745	87	6757											
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	44949021	44949021	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcctaatgggttcttggtgGcccaatcttgaagatcttta	8	16	9	8	0	3	2	0	1	3	1	4	2	4	2	2	3	0	1	2	3	4	7			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chrX:44949021G>A	ENST00000377967.4	+	25	3623	c.3582G>A	c.(3580-3582)tgG>tgA	p.W1194*	KDM6A_ENST00000382899.4_Nonsense_Mutation_p.W1201*|KDM6A_ENST00000536777.1_Nonsense_Mutation_p.W1149*|KDM6A_ENST00000543216.1_Nonsense_Mutation_p.W1115*	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1194	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.W1194*(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						GTTCTTGGTGGCCCAATCTTG	0.368			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.W1194X	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	7	Whole gene deletion(6)|Substitution - Nonsense(1)	oesophagus(2)|breast(2)|pancreas(2)|urinary_tract(1)	c.G3582A						.						115	98	103					X																	44949021		2203	4300	6503	SO:0001587	stop_gained	7403	exon25			TTGGTGGCCCAAT	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.3582G>A	X.37:g.44949021G>A	ENSP00000367203:p.Trp1194*	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	37	29	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Nonsense_Mutation	SNP	ENST00000377967.4	37	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.566749|7.566749	0.98361|0.98361	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000414389;ENST00000433797|ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	.|.	.|.	.|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.45538|.	0.1347|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42258|.	-0.9462|.	3|.	.|0.02654	.|T	.|1	-5.5328|-5.5328	17.8727|17.8727	0.88815|0.88815	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	T|X	792;837|891;1194;1149;1201;1115	.|.	.|ENSP00000334340:W891X	A|W	+|+	1|3	0|0	KDM6A|KDM6A	44833965|44833965	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.358000|9.358000	0.97109|0.97109	2.153000|2.153000	0.67306|0.67306	0.468000|0.468000	0.43344|0.43344	GCC|TGG	.		0.368	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		A	44949021	G	A	44949021	4	1	70	1	0	0	0	0	0	1	0	0	8158	1212	42	2	3680	2	KDM6A	23	44949021	Nonsense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	20859206	44949021	110321539	88	6758											
ELF4	2000	hgsc.bcm.edu	37	chrX	129201251	129201251	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccactgagaatcagtggAgcccctggggctgccacctg	8	6	14	13	0	1	1	1	1	0	1	1	3	1	2	5	4	2	1	5	4	1	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chrX:129201251A>G	ENST00000308167.5	-	9	1816	c.1437T>C	c.(1435-1437)gcT>gcC	p.A479A	ELF4_ENST00000335997.7_Silent_p.A479A	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GAATCAGTGGAGCCCCTGGGG	0.642			T	ERG	AML																																p.A479A		.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4-659	0			c.T1437C						.						28	31	30					X																	129201251		2202	4298	6500	SO:0001819	synonymous_variant	2000	exon9			CAGTGGAGCCCCT	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1437T>C	X.37:g.129201251A>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_001421	0	0	0	0	0		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																			.		0.642	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		G	129201251	A	G	129201251	2	3	70	1	0	0	0	0	0	0	0	1	5069	291	11	3		3	ELF4	23	129201251	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	84252230	129201251	26069309	89	6759											
IL9R	3581	hgsc.bcm.edu	37	chrX	155239602	155239602	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcacttgtggcccagcgcGtccttggaaatctgtggccc	5	10	12	14	2	2	0	1	0	1	0	3	1	3	1	3	3	1	1	3	3	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chrX:155239602G>A	ENST00000244174.5	+	9	1273	c.1094G>A	c.(1093-1095)cGt>cAt	p.R365H	IL9R_ENST00000540897.1_3'UTR|IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000424344.3_Missense_Mutation_p.R344H	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	365			R -> H (in dbSNP:rs2228650).		cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GGCCCAGCGCGTCCTTGGAAA	0.662																																					p.R365H		.											.	IL9R-40	0			c.G1094A						.						42	70	62					X																	155239602		1941	4257	6198	SO:0001583	missense	3581	exon9			CAGCGCGTCCTTG	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1094G>A	X.37:g.155239602G>A	ENSP00000244174:p.Arg365His	Somatic	76	2		WXS	Illumina HiSeq	Phase_I	76	5	NM_002186	0	0	0	0	0	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	37	CCDS14771.4	130	0.05952380952380952	42	0.08536585365853659	11	0.03038674033149171	50	0.08741258741258741	27	0.03562005277044855	N	0.057	-1.234707	0.01505	.	.	ENSG00000124334	ENST00000244174;ENST00000424344	T;T	0.10099	2.91;2.91	1.44	0.201	0.15186	.	5.140280	0.00520	N	0.000181	T	0.00241	0.0007	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32481	-0.9905	9	0.13470	T	0.59	-9.2578	3.2156	0.06697	0.7419:0.0:0.2581:0.0	.	365	Q01113	IL9R_HUMAN	H	365;344	ENSP00000244174:R365H;ENSP00000388918:R344H	ENSP00000244174:R365H	R	+	2	0	IL9R	154892796	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.579000	0.05834	-0.003000	0.14444	-1.144000	0.01866	CGT	G|1.000;|0.000		0.662	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		A	155239602	G	A	155239602	3	1	70	1	0	0	0	0	1	0	0	0	7729	1145	40	1	1128	1	IL9R	23	155239602	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	26038351	155239602	30958	90	6760											
PTPRF	5792	hgsc.bcm.edu	37	chr1	44084813	44084813	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaactcccatcctggcctTcctacgacgggtcaaggcct	7	8	8	18	2	1	0	1	0	0	0	4	1	4	0	6	3	2	0	6	3	3	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr1:44084813T>C	ENST00000359947.4	+	27	4926	c.4586T>C	c.(4585-4587)tTc>tCc	p.F1529S	PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Missense_Mutation_p.F1520S|PTPRF_ENST00000422171.2_Missense_Mutation_p.F888S|PTPRF_ENST00000372413.3_Missense_Mutation_p.F1520S|PTPRF_ENST00000372414.3_Missense_Mutation_p.F1529S	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1529	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATCCTGGCCTTCCTACGACGG	0.632																																					p.F1529S		.											.	PTPRF-232	0			c.T4586C						.						57	51	53					1																	44084813		2203	4300	6503	SO:0001583	missense	5792	exon27			TGGCCTTCCTACG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4586T>C	1.37:g.44084813T>C	ENSP00000353030:p.Phe1529Ser	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_002840	0	0	36	36	0	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.04|17.04	3.286754|3.286754	0.59867|0.59867	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407|ENST00000429895	T;T;T;T;T;T|.	0.39406|.	1.08;1.08;1.08;1.08;1.08;1.08|.	5.42|5.42	4.3|4.3	0.51218|0.51218	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);|.	0.000000|.	0.35936|.	N|.	0.002893|.	D|D	0.89238|0.89238	0.6658|0.6658	H|H	0.99752|0.99752	4.75|4.75	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.996;1.0|.	D;D;D;P;D|.	0.97110|.	1.0;1.0;1.0;0.771;1.0|.	D|D	0.91544|0.91544	0.5252|0.5252	10|5	0.87932|.	D|.	0|.	.|.	11.2154|11.2154	0.48823|0.48823	0.0:0.0719:0.0:0.9281|0.0:0.0719:0.0:0.9281	.|.	1174;888;1106;1520;1529|.	Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586|.	.;.;.;.;PTPRF_HUMAN|.	S|P	1529;1520;1529;1520;888;601|1175	ENSP00000353030:F1529S;ENSP00000398822:F1520S;ENSP00000361491:F1529S;ENSP00000361490:F1520S;ENSP00000387885:F888S;ENSP00000361484:F601S|.	ENSP00000353030:F1529S|.	F|S	+|+	2|1	0|0	PTPRF|PTPRF	43857400|43857400	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.520000|0.520000	0.34377|0.34377	7.991000|7.991000	0.88244|0.88244	1.013000|1.013000	0.39391|0.39391	0.459000|0.459000	0.35465|0.35465	TTC|TCC	.		0.632	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			C	44084813	T	C	44084813	3	2	71	1	0	0	0	0	1	0	0	0	12833	1783	62	3	4684	3	PTPRF	1	44084813	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		44084813	205165808	1	6761											
OR2G2	81470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247751788	247751788	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgtatttactaactattTtggggaataccaccatcatt	11	17	5	8	0	2	0	1	0	1	0	2	1	2	1	2	2	3	1	2	2	6	10			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr1:247751788T>C	ENST00000320065.1	+	1	127	c.127T>C	c.(127-129)Ttg>Ctg	p.L43L	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ACTAACTATTTTGGGGAATAC	0.408																																					p.L43L		.											.	OR2G2-68	0			c.T127C						.						227	217	220					1																	247751788		2203	4300	6503	SO:0001819	synonymous_variant	81470	exon1			ACTATTTTGGGGA	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"GPCR / Class A : Olfactory receptors"	15007	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily G, member 2", "olfactory receptor, family 2, subfamily G, member 2 pseudogene"				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.127T>C	1.37:g.247751788T>C		Somatic	178	0		WXS	Illumina HiSeq	Phase_I	319	87	NM_001001915	0	0	0	0	0	Q5JQT2|Q6IEZ0	Silent	SNP	ENST00000320065.1	37	CCDS31092.1																																																																																			.		0.408	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			C	247751788	T	C	247751788	2	2	71	1	0	0	0	0	0	0	0	1	11024	1838	64	3		3	OR2G2	1	247751788	Silent	SNP	T	TCGA-BQ-5887-01A-11D-1961-08	203666975	247751788	1498833	2	6762											
CCT4	10575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	62115531	62115531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatacctttggcggcggaaaTgttgctgaagcggatctggg	8	10	16	7	3	1	1	0	1	1	0	1	4	1	3	1	5	3	2	1	5	3	3	rs199542002		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:62115531T>C	ENST00000394440.3	-	1	408	c.112A>G	c.(112-114)Att>Gtt	p.I38V	CCT4_ENST00000544185.1_5'UTR|CCT4_ENST00000538252.1_5'UTR|CCT4_ENST00000544079.1_Missense_Mutation_p.I38V|AC107081.5_ENST00000425779.1_RNA	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	38					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			GCGGCGGAAATGTTGCTGAAG	0.677																																					p.I38V		.											.	CCT4-92	0			c.A112G						.	T	VAL/ILE	0,4404		0,0,2202	47	43	45		112	3.3	0.8	2		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	CCT4	NM_006430.2	29	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	38/540	62115531	1,13003	2202	4300	6502	SO:0001583	missense	10575	exon1			CGGAAATGTTGCT		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"Heat Shock Proteins / Chaperonins"	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.112A>G	2.37:g.62115531T>C	ENSP00000377958:p.Ile38Val	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	50	23	NM_001256721	0	0	21	86	65	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	37	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513788	0.64522	0.0	1.16E-4	ENSG00000115484	ENST00000394440;ENST00000544079	T;T	0.12984	2.63;2.63	4.44	3.27	0.37495	.	0.053328	0.64402	D	0.000001	T	0.14570	0.0352	L	0.36672	1.1	0.80722	D	1	P;P	0.48834	0.916;0.847	P;B	0.47134	0.539;0.399	T	0.01520	-1.1334	10	0.87932	D	0	-12.7568	9.5232	0.39149	0.1581:0.0:0.0:0.8419	.	38;38	F5H5W3;P50991	.;TCPD_HUMAN	V	38	ENSP00000377958:I38V;ENSP00000443061:I38V	ENSP00000377958:I38V	I	-	1	0	CCT4	61969035	1.000000	0.71417	0.823000	0.32752	0.746000	0.42486	5.484000	0.66844	0.722000	0.32252	0.529000	0.55759	ATT	T|0.998;C|0.002		0.677	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62115531	T	C	62115531	3	2	71	1	0	0	0	0	1	0	0	0	2961	1464	51	3	1563	3	CCT4	2	62115531	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		62115531	181083842	3	6763											
ZSWIM2	151112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	187693177	187693177	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cataggttaatttttttgaaTttgaattatctaatttgata	13	21	5	2	0	1	3	0	3	1	0	1	3	1	3	0	1	0	1	0	1	7	10			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:187693177T>A	ENST00000295131.2	-	9	1475	c.1436A>T	c.(1435-1437)aAt>aTt	p.N479I		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	479					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TTTTTTTGAATTTGAATTATC	0.299																																					p.N479I		.											.	ZSWIM2-93	0			c.A1436T						.						36	42	40					2																	187693177		2202	4298	6500	SO:0001583	missense	151112	exon9			TTTGAATTTGAAT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1436A>T	2.37:g.187693177T>A	ENSP00000295131:p.Asn479Ile	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	43	7	NM_182521	0	0	0	0	0	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	6.741	0.505511	0.12822	.	.	ENSG00000163012	ENST00000295131	T	0.28895	1.59	5.6	1.83	0.25207	.	1.004620	0.08011	N	0.990290	T	0.21186	0.0510	L	0.32530	0.975	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.36890	-0.9729	10	0.87932	D	0	0.0079	1.3043	0.02085	0.1451:0.1617:0.1507:0.5425	.	479	Q8NEG5	ZSWM2_HUMAN	I	479	ENSP00000295131:N479I	ENSP00000295131:N479I	N	-	2	0	ZSWIM2	187401422	0.045000	0.20229	0.035000	0.18076	0.220000	0.24768	0.733000	0.26087	0.070000	0.16634	-0.376000	0.06991	AAT	.		0.299	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		A	187693177	T	A	187693177	3	1	71	1	0	0	0	0	1	0	0	0	18273	1493	52	5	469	5	ZSWIM2	2	187693177	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08	125577646	187693177	55506196	4	6764											
PRRT3	285368	hgsc.bcm.edu	37	chr3	9989480	9989480	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgccgaagggggccccaGcgtagcgggggtgcagtggc	6	3	19	13	4	0	0	0	0	0	0	0	1	0	0	4	5	3	2	4	5	2	1	rs543324498		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr3:9989480G>C	ENST00000412055.1	-	4	1506	c.1377C>G	c.(1375-1377)cgC>cgG	p.R459R	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	459	Pro-rich.					integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						GGGGGCCCCAGCGTAGCGGGG	0.721													g|||	1	0.000199681	0	0	5008	,	,		11573	0		0.001	False		,,,				2504	0				p.R459R		.											.	PRRT3-90	0			c.C1377G						.						4	6	5					3																	9989480		1778	3849	5627	SO:0001819	synonymous_variant	285368	exon4			GCCCCAGCGTAGC	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"Proline-rich transmembrane proteins"	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.1377C>G	3.37:g.9989480G>C		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	8	8	NM_207351	0	0	1	2	1	Q49AD0|Q6UXY6|Q8NBC9	Silent	SNP	ENST00000412055.1	37	CCDS43049.1																																																																																			.		0.721	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		C	9989480	G	C	9989480	2	2	71	1	0	0	0	0	0	0	0	1	12640	958	34	4		4	PRRT3	3	9989480	Silent	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		9989480	188032950	5	6765											
CHST2	9435	hgsc.bcm.edu	37	chr3	142839977	142839977	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggcagctgggggcgcccaGggccgcctccggccgggccg	3	2	20	16	5	0	0	0	0	0	0	1	1	1	0	6	6	1	2	6	6	0	0	rs185111962	byFrequency	TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr3:142839977G>A	ENST00000309575.3	+	2	1703	c.319G>A	c.(319-321)Ggg>Agg	p.G107R		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	107					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						ggggcgcccagggccgcctcc	0.761													G|||	32	0.00638978	8e-04	0.0115	5008	,	,		9166	0		0.0179	False		,,,				2504	0.0051				p.G107R		.											.	CHST2-93	0			c.G319A						.	G	ARG/GLY	6,3188		0,6,1591	2	2	2		319	2.4	0.8	3		2	29,6187		0,29,3079	no	missense	CHST2	NM_004267.4	125	0,35,4670	AA,AG,GG		0.4665,0.1879,0.3719	benign	107/531	142839977	35,9375	1597	3108	4705	SO:0001583	missense	9435	exon2			CGCCCAGGGCCGC	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"Sulfotransferases, membrane-bound"	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.319G>A	3.37:g.142839977G>A	ENSP00000307911:p.Gly107Arg	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	6	5	NM_004267	0	0	0	1	1	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	CCDS3129.1	22	0.010073260073260074	6	0.012195121951219513	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	4.642	0.119345	0.08881	0.001879	0.004665	ENSG00000175040	ENST00000309575	D	0.97041	-4.22	3.3	2.42	0.29668	.	.	.	.	.	D	0.85225	0.5648	N	0.14661	0.345	0.27986	N	0.935857	B	0.06786	0.001	B	0.08055	0.003	T	0.82478	-0.0437	9	0.51188	T	0.08	-12.4417	4.825	0.13412	0.1239:0.2213:0.6548:0.0	.	107	Q9Y4C5	CHST2_HUMAN	R	107	ENSP00000307911:G107R	ENSP00000307911:G107R	G	+	1	0	CHST2	144322667	0.000000	0.05858	0.845000	0.33349	0.137000	0.21094	-0.018000	0.12568	0.947000	0.37659	0.407000	0.27541	GGG	G|0.990;A|0.010		0.761	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		A	142839977	G	A	142839977	3	1	71	1	0	0	0	0	1	0	0	0	3410	1000	35	2	321	2	CHST2	3	142839977	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08	132850497	142839977	55182453	6	6766											
SULT1E1	6783	broad.mit.edu	37	chr4	70713465	70713465	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtacacgtggactctttcccTtttcccaccaagattttaca	9	14	5	13	1	1	1	0	0	1	1	3	2	3	2	3	1	2	1	3	1	3	6			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr4:70713465T>C	ENST00000226444.3	-	6	654	c.542A>G	c.(541-543)aAg>aGg	p.K181R		NM_005420.2	NP_005411.1	P49888	ST1E1_HUMAN	sulfotransferase family 1E, estrogen-preferring, member 1	181					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	estrone sulfotransferase activity (GO:0004304)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid binding (GO:0005496)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10					Acetaminophen(DB00316)|Cyclizine(DB01176)	ACTCTTTCCCTTTTCCCACCA	0.373																																					p.K181R													.	SULT1E1-91	0			c.A542G						.						101	101	101					4																	70713465		2203	4299	6502	SO:0001583	missense	6783	exon6			TTTCCCTTTTCCC	BC027956	CCDS3531.1	4q13.1	2008-02-05	2004-02-06	2004-02-04	ENSG00000109193	ENSG00000109193	2.8.2.4	"Sulfotransferases, cytosolic"	11377	protein-coding gene	gene with protein product		600043	"sulfotransferase, estrogen-preferring"	STE		7961757	Standard	NM_005420		Approved	EST	uc003heo.3	P49888	OTTHUMG00000129403	ENST00000226444.3:c.542A>G	4.37:g.70713465T>C	ENSP00000226444:p.Lys181Arg	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	126	3	NM_005420	0	0	0	0	0	Q8N6X5	Missense_Mutation	SNP	ENST00000226444.3	37	CCDS3531.1	.	.	.	.	.	.	.	.	.	.	T	6.523	0.464767	0.12402	.	.	ENSG00000109193	ENST00000226444	D	0.81996	-1.56	4.21	1.61	0.23674	Sulfotransferase domain (1);	0.213134	0.41194	D	0.000932	T	0.67655	0.2916	L	0.35341	1.055	0.34216	D	0.674848	B	0.09022	0.002	B	0.16289	0.015	T	0.56866	-0.7908	10	0.21014	T	0.42	.	3.4375	0.07452	0.4064:0.0991:0.0:0.4945	.	181	P49888	ST1E1_HUMAN	R	181	ENSP00000226444:K181R	ENSP00000226444:K181R	K	-	2	0	SULT1E1	70748054	1.000000	0.71417	0.824000	0.32777	0.522000	0.34438	2.559000	0.45888	0.341000	0.23771	0.528000	0.53228	AAG	.		0.373	SULT1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251559.1	NM_005420		C	70713465	T	C	70713465	3	2	71	1	0	0	0	0	1	0	0	0	15412	1609	56	3	354	3	SULT1E1	4	70713465	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		70713465	120440811	7	6767											
RCHY1	25898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76439476	76439476	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgaccgctggcgccatcTtcccgggccgtcgccgccat	3	9	11	18	6	2	1	0	1	2	0	4	1	3	1	6	2	0	1	6	2	0	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr4:76439476T>C	ENST00000324439.5	-	1	419	c.21A>G	c.(19-21)gaA>gaG	p.E7E	THAP6_ENST00000507885.1_5'Flank|THAP6_ENST00000514480.1_5'Flank|THAP6_ENST00000380837.3_5'Flank|THAP6_ENST00000507556.1_5'Flank|THAP6_ENST00000311638.3_5'Flank|RCHY1_ENST00000512706.1_5'UTR|RCHY1_ENST00000451788.1_Silent_p.E7E|THAP6_ENST00000508105.1_5'Flank|RCHY1_ENST00000514021.1_Intron|THAP6_ENST00000502620.1_5'Flank|RCHY1_ENST00000513257.1_Silent_p.E7E|THAP6_ENST00000504190.1_5'Flank|RCHY1_ENST00000380840.2_Silent_p.E7E|THAP6_ENST00000507557.1_5'Flank	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	7					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TGGCGCCATCTTCCCGGGCCG	0.602																																					p.E7E		.											.	RCHY1-228	0			c.A21G						.						78	69	72					4																	76439476		2203	4300	6503	SO:0001819	synonymous_variant	25898	exon1			GCCATCTTCCCGG	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.21A>G	4.37:g.76439476T>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	74	12	NM_001008925	0	0	1	1	0	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Silent	SNP	ENST00000324439.5	37	CCDS3567.1																																																																																			.		0.602	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		C	76439476	T	C	76439476	2	2	71	1	0	0	0	0	0	0	0	1	13209	1606	56	3		3	RCHY1	4	76439476	Silent	SNP	T	TCGA-BQ-5887-01A-11D-1961-08	5726011	76439476	114714800	8	6768											
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	90052799	90052799	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atattctttacttaaagggcGctggggaagttattactgcc	10	14	10	7	1	1	0	0	0	1	0	1	1	1	1	1	3	3	2	1	3	7	7	rs200576500	byFrequency	TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:90052799G>A	ENST00000405460.2	+	57	11857	c.11761G>A	c.(11761-11763)Gct>Act	p.A3921T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3921	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTTAAAGGGCGCTGGGGAAGT	0.388													G|||	2	0.000399361	0.0015	0	5008	,	,		16046	0		0	False		,,,				2504	0				p.A3921T		.											.	GPR98-103	0			c.G11761A						.	G	THR/ALA	5,3673		0,5,1834	77	75	76		11761	2.3	0.1	5		76	0,8158		0,0,4079	yes	missense	GPR98	NM_032119.3	58	0,5,5913	AA,AG,GG		0.0,0.1359,0.0422	benign	3921/6307	90052799	5,11831	1839	4079	5918	SO:0001583	missense	84059	exon57			AAGGGCGCTGGGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11761G>A	5.37:g.90052799G>A	ENSP00000384582:p.Ala3921Thr	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	109	26	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	0.526	-0.860029	0.02610	0.001359	0.0	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27256	1.68	5.3	2.27	0.28462	Na-Ca exchanger/integrin-beta4 (1);	0.732108	0.13525	N	0.381387	T	0.11879	0.0289	N	0.14661	0.345	0.22050	N	0.999396	B;B	0.23058	0.079;0.013	B;B	0.10450	0.005;0.002	T	0.25012	-1.0144	10	0.25751	T	0.34	.	4.1082	0.10047	0.2731:0.3558:0.3711:0.0	.	3921;3921	E7ETI5;Q8WXG9	.;GPR98_HUMAN	T	3921	ENSP00000384582:A3921T	ENSP00000296619:A3921T	A	+	1	0	GPR98	90088555	0.001000	0.12720	0.090000	0.20809	0.015000	0.08874	-0.111000	0.10807	0.694000	0.31654	0.467000	0.42956	GCT	.		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90052799	G	A	90052799	3	1	71	1	0	0	0	0	1	0	0	0	6742	1087	38	1	11987	1	GPR98	5	90052799	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		90052799	90862461	9	6769											
KDM3B	51780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	137766032	137766032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaccctccgtaagcgactctAtgaggagtatggcgtgcaag	10	8	13	10	3	1	1	0	1	1	0	2	4	2	2	2	2	2	3	2	2	4	3			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:137766032A>G	ENST00000314358.5	+	22	5188	c.4988A>G	c.(4987-4989)tAt>tGt	p.Y1663C	KDM3B_ENST00000394866.1_Missense_Mutation_p.Y1319C|KDM3B_ENST00000542866.1_Missense_Mutation_p.Y695C	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1663	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						AAGCGACTCTATGAGGAGTAT	0.542																																					p.Y1663C		.											.	KDM3B-542	0			c.A4988G						.						146	136	140					5																	137766032		2203	4300	6503	SO:0001583	missense	51780	exon22			GACTCTATGAGGA	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.4988A>G	5.37:g.137766032A>G	ENSP00000326563:p.Tyr1663Cys	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	191	27	NM_016604	0	0	13	21	8	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178274	0.78564	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.70631	-0.5;-0.5;-0.5	5.71	4.51	0.55191	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.056809	0.64402	D	0.000001	T	0.72550	0.3474	L	0.41824	1.3	0.58432	D	0.999997	P;P	0.46457	0.878;0.786	P;P	0.54544	0.575;0.755	T	0.72181	-0.4368	10	0.51188	T	0.08	-12.6174	11.8878	0.52613	0.8691:0.0:0.0:0.1309	.	1319;1663	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	C	1663;1453;1319;695	ENSP00000326563:Y1663C;ENSP00000378335:Y1319C;ENSP00000439462:Y695C	ENSP00000326563:Y1663C	Y	+	2	0	KDM3B	137793931	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.941000	0.63540	0.939000	0.37446	0.533000	0.62120	TAT	.		0.542	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		G	137766032	A	G	137766032	3	3	71	1	0	0	0	0	1	0	0	0	8148	449	16	3	5074	3	KDM3B	5	137766032	Missense_Mutation	SNP	A	TCGA-BQ-5887-01A-11D-1961-08	47713233	137766032	43149228	10	6770											
C6orf211	79624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	151789725	151789725	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaatattagccgacttctTgttgtcctctgaactggcta	8	17	7	9	1	2	1	0	1	2	0	3	2	3	1	2	1	2	2	2	1	5	8			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr6:151789725T>G	ENST00000367294.3	+	5	1065	c.806T>G	c.(805-807)tTg>tGg	p.L269W	C6orf211_ENST00000545879.1_Missense_Mutation_p.L150W	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	269										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GCCGACTTCTTGTTGTCCTCT	0.328																																					p.L269W		.											.	C6orf211-90	0			c.T806G						.						132	138	136					6																	151789725		2203	4300	6503	SO:0001583	missense	79624	exon5			ACTTCTTGTTGTC	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.806T>G	6.37:g.151789725T>G	ENSP00000356263:p.Leu269Trp	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	141	12	NM_024573	0	0	32	45	13	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.593869	0.86953	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.23552	1.9;1.9	6.02	6.02	0.97574	Domain of unknown function DUF89 (2);	0.141422	0.45126	D	0.000394	T	0.59959	0.2232	H	0.95884	3.735	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.74682	-0.3583	10	0.87932	D	0	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	269	Q9H993	CF211_HUMAN	W	269;150	ENSP00000356263:L269W;ENSP00000444121:L150W	ENSP00000356263:L269W	L	+	2	0	C6orf211	151831418	1.000000	0.71417	0.087000	0.20705	0.990000	0.78478	7.963000	0.87922	2.299000	0.77371	0.528000	0.53228	TTG	.		0.328	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		G	151789725	T	G	151789725	3	3	71	1	0	0	0	0	1	0	0	0	2360	1821	63	5	824	5	C6orf211	6	151789725	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		151789725	19325342	11	6771											
COL28A1	340267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	7412962	7412963	+	Missense_Mutation	DNP	CC	CC	AT																															cacagccaacttgaagtcatCcttgctggagaactgcttca																										TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr7:7412962_7412963CC>AT	ENST00000399429.3	-	32	2714_2715	c.2574_2575GG>AT	c.(2572-2577)aaGGat>aaATat	p.D859Y		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	859	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTGAAGTCATCCTTGCTGGAGA	0.515																																					p.D859Y		.											.	COL28A1	0			c.G2574A						.																																			SO:0001583	missense	340267	exon32			GTCATCCTTGCTG	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"Collagens"	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2574_2575delinsAT	7.37:g.7412962_7412963delinsAT	ENSP00000382356:p.Asp859Tyr	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	116	25		0	0	0	0	0	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	DNP	ENST00000399429.3	37	CCDS43553.1																																																																																			.		0.515	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		AT	7412963	CC	AT	7412962	3	1	71	1	0	0	0	0	1	0	0	0	3692	855	30	4	818	4	COL28A1	7	7412962	Missense_Mutation	DNP	CC	TCGA-BQ-5887-01A-11D-1961-08		7412962	151725701	12	6772											
AKAP3	10566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	4736579	4736579	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaggttgccaatatcttcagGgtactcaaaggaaatgtctg	12	11	11	7	0	4	0	2	0	2	0	4	2	4	1	1	3	2	2	1	3	5	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:4736579G>C	ENST00000545990.2	-	5	2013	c.1489C>G	c.(1489-1491)Cct>Gct	p.P497A	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.P497A	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	497					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ATATCTTCAGGGTACTCAAAG	0.463																																					p.P497A		.											.	AKAP3-292	0			c.C1489G						.						67	64	65					12																	4736579		2203	4300	6503	SO:0001583	missense	10566	exon4			CTTCAGGGTACTC	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"A-kinase anchor proteins"	373	protein-coding gene	gene with protein product	"Fibrous Sheath Protein of 95 kDa", "cancer/testis antigen 82"	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1489C>G	12.37:g.4736579G>C	ENSP00000440994:p.Pro497Ala	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	47	10	NM_006422	0	0	0	0	0	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	0.811	-0.752022	0.03041	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.11821	2.74;2.74	4.5	-1.34	0.09143	A-kinase anchor 110kDa, C-terminal (1);	0.887861	0.09758	N	0.759675	T	0.13457	0.0326	M	0.68317	2.08	0.09310	N	1	B	0.29481	0.245	B	0.32090	0.14	T	0.40194	-0.9576	10	0.72032	D	0.01	0.0048	1.207	0.01896	0.1864:0.1329:0.362:0.3187	.	497	O75969	AKAP3_HUMAN	A	497	ENSP00000228850:P497A;ENSP00000440994:P497A	ENSP00000228850:P497A	P	-	1	0	AKAP3	4606840	0.215000	0.23574	0.000000	0.03702	0.001000	0.01503	1.832000	0.39151	-0.187000	0.10516	-0.136000	0.14681	CCT	.		0.463	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		C	4736579	G	C	4736579	3	2	71	1	0	0	0	0	1	0	0	0	452	1232	43	4	1080	4	AKAP3	12	4736579	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		4736579	129115316	13	6773											
ARID2	196528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46244916	46244916	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggaccacctcctactgtcAgtcaaatgttatctgtgaaa	12	11	8	10	0	3	1	2	1	1	0	4	2	4	2	3	1	1	1	3	1	4	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:46244916A>T	ENST00000334344.6	+	15	3182	c.3010A>T	c.(3010-3012)Agt>Tgt	p.S1004C	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Missense_Mutation_p.S614C|ARID2_ENST00000422737.1_Missense_Mutation_p.S855C|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1004	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCCTACTGTCAGTCAAATGTT	0.502			"N, S, F"		hepatocellular carcinoma																																p.S1004C		.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2-100	0			c.A3010T						.						212	175	188					12																	46244916		2203	4300	6503	SO:0001583	missense	196528	exon15			ACTGTCAGTCAAA		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.3010A>T	12.37:g.46244916A>T	ENSP00000335044:p.Ser1004Cys	Somatic	91	1		WXS	Illumina HiSeq	Phase_I	148	26	NM_152641	0	0	3	4	1	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.710443	0.48517	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.49720	0.77	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.58075	0.2097	L	0.29908	0.895	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.81914	0.995;0.995;0.99	T	0.62105	-0.6924	10	0.72032	D	0.01	-11.3288	15.7664	0.78128	1.0:0.0:0.0:0.0	.	1004;614;1004	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	C	1004;121;121;855;614	ENSP00000335044:S1004C	ENSP00000335044:S1004C	S	+	1	0	ARID2	44531183	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.623000	0.67757	2.137000	0.66172	0.379000	0.24179	AGT	.		0.502	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46244916	A	T	46244916	3	4	71	1	0	0	0	0	1	0	0	0	915	188	7	5	3068	5	ARID2	12	46244916	Missense_Mutation	SNP	A	TCGA-BQ-5887-01A-11D-1961-08	41508337	46244916	87606979	14	6774											
COL4A1	1282	ucsc.edu	37	chr13	110827563	110827563	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccacgcagagcgctggttAccttttcacctcgcagccct	6	11	8	16	3	1	1	1	0	0	1	3	1	2	1	4	1	3	4	4	1	1	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr13:110827563A>C	ENST00000375820.4	-	37	3320		c.e37+1			NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1						axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			AGCGCTGGTTACCTTTTCACC	0.547																																					.													.	COL4A1-654	0			c.3198+2T>G						.						147	113	125					13																	110827563		2203	4300	6503	SO:0001630	splice_region_variant	1282	exon38			CTGGTTACCTTTT	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"Collagens"	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.3198+1T>G	13.37:g.110827563A>C		Somatic	73	0		WXS	Illumina HiSeq		75	2	NM_001845	0	0	0	0	0	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Splice_Site	SNP	ENST00000375820.4	37	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103563	0.37145	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7145	0.77658	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL4A1	109625564	1.000000	0.71417	0.996000	0.52242	0.171000	0.22731	7.681000	0.84073	2.168000	0.68352	0.528000	0.53228	.	.		0.547	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		Intron	C	110827563	A	C	110827563	5	2	71	1	0	0	0	0	0	0	1	0	3695	405	14	5	1873	5	COL4A1	13	110827563	Splice_Site	SNP	A	TCGA-BQ-5887-01A-11D-1961-08		110827563	4342315	15	6775											
HERC2	8924	broad.mit.edu	37	chr15	28370205	28370205	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggtcgaccaggcgagggTatgtgctgagccacaggcca	8	6	16	11	2	0	1	0	1	0	0	1	3	0	1	3	4	2	3	3	4	1	1			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr15:28370205T>G	ENST00000261609.7	-	84	13045	c.12937A>C	c.(12937-12939)Acc>Ccc	p.T4313P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAGGCGAGGGTATGTGCTGAG	0.622																																					p.T4313P													.	HERC2-234	0			c.A12937C						.						136	125	129					15																	28370205		2203	4300	6503	SO:0001583	missense	8924	exon84			CGAGGGTATGTGC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.12937A>C	15.37:g.28370205T>G	ENSP00000261609:p.Thr4313Pro	Somatic	131	22		WXS	Illumina HiSeq	Phase_I	186	26	NM_004667	0	0	24	24	0		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.869602	0.91587	.	.	ENSG00000128731	ENST00000261609	D	0.88664	-2.41	5.19	5.19	0.71726	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.96349	0.8809	H	0.96805	3.885	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.97752	1.0215	10	0.87932	D	0	.	15.0549	0.71908	0.0:0.0:0.0:1.0	.	4313	O95714	HERC2_HUMAN	P	4313	ENSP00000261609:T4313P	ENSP00000261609:T4313P	T	-	1	0	HERC2	26043800	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	8.030000	0.88816	1.951000	0.56629	0.533000	0.62120	ACC	.		0.622	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28370205	T	G	28370205	3	3	71	1	0	0	0	0	1	0	0	0	7079	1638	57	5	1607	5	HERC2	15	28370205	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		28370205	74161187	16	6776											
RYR3	6263	broad.mit.edu	37	chr15	33954438	33954438	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggctctacagcgcggtgtgCgccctgggaaacagccgcgt	7	6	15	13	5	1	0	0	0	1	0	1	1	1	1	2	3	5	1	2	3	2	1	rs372058994		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr15:33954438C>T	ENST00000389232.4	+	35	4777	c.4707C>T	c.(4705-4707)tgC>tgT	p.C1569C	RYR3_ENST00000415757.3_Silent_p.C1569C	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1569	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GCGCGGTGTGCGCCCTGGGAA	0.612																																					p.C1569C													.	RYR3-520	0			c.C4707T						.	C		1,4157		0,1,2078	55	54	55		4707	-9.4	0.6	15		55	1,8441		0,1,4220	no	coding-synonymous	RYR3	NM_001036.3		0,2,6298	TT,TC,CC		0.0118,0.0241,0.0159		1569/4871	33954438	2,12598	2079	4221	6300	SO:0001819	synonymous_variant	6263	exon35			GGTGTGCGCCCTG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.4707C>T	15.37:g.33954438C>T		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	23	3	NM_001243996	0	0	0	0	0	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			.		0.612	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33954438	C	T	33954438	2	4	71	1	0	0	0	0	0	0	0	1	13802	776	27	1		1	RYR3	15	33954438	Silent	SNP	C	TCGA-BQ-5887-01A-11D-1961-08	5584233	33954438	68576954	17	6777											
HERPUD1	9709	broad.mit.edu	37	chr16	56974154	56974154	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggggccaccgttgttatgtAcctgtaagcagatggtttct	7	13	13	8	1	1	1	0	0	1	1	1	1	1	1	3	3	2	6	3	3	3	5			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr16:56974154A>G	ENST00000439977.2	+	6	1099	c.902A>G	c.(901-903)tAc>tGc	p.Y301C	HERPUD1_ENST00000344114.4_Intron|HERPUD1_ENST00000379792.2_Missense_Mutation_p.Y276C|HERPUD1_ENST00000570273.1_Intron|RP11-325K4.2_ENST00000570210.1_RNA|RP11-325K4.3_ENST00000565861.1_RNA|HERPUD1_ENST00000300302.5_Missense_Mutation_p.Y300C	NM_001010989.1|NM_014685.2	NP_001010989.1|NP_055500.1	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	301					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of protein binding (GO:0032092)|regulation of protein ubiquitination (GO:0031396)|response to unfolded protein (GO:0006986)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	11						GTTGTTATGTACCTGTAAGCA	0.398			T	ERG	prostate																																p.Y301C				Dom	yes		16	16q12.2-q13	9709	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"		E	.	HERPUD1-90	0			c.A902G						.						122	117	119					16																	56974154		2198	4300	6498	SO:0001583	missense	9709	exon6			TTATGTACCTGTA	AB034989	CCDS10771.1, CCDS45492.1	16q13	2008-05-14			ENSG00000051108	ENSG00000051108			13744	protein-coding gene	gene with protein product		608070				10922362, 10708769	Standard	NM_001010989		Approved	KIAA0025, Mif1, HERP, SUP	uc002eke.2	Q15011	OTTHUMG00000133276	ENST00000439977.2:c.902A>G	16.37:g.56974154A>G	ENSP00000409555:p.Tyr301Cys	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	197	5	NM_014685	0	0	0	0	0	E9PGD1|O60644|Q6IAN8|Q96D92	Missense_Mutation	SNP	ENST00000439977.2	37	CCDS10771.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.254051	0.80135	.	.	ENSG00000051108	ENST00000439977;ENST00000379792;ENST00000300302	T	0.21543	2.0	5.74	5.74	0.90152	.	0.053782	0.85682	N	0.000000	T	0.49830	0.1580	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.54931	-0.8219	10	0.87932	D	0	-10.6095	15.2162	0.73267	1.0:0.0:0.0:0.0	.	276;300;301	E9PGD1;Q15011-2;Q15011	.;.;HERP1_HUMAN	C	300;276;301	ENSP00000369118:Y276C	ENSP00000300302:Y301C	Y	+	2	0	HERPUD1	55531655	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.050000	0.93843	2.186000	0.69663	0.533000	0.62120	TAC	.		0.398	HERPUD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257056.5			G	56974154	A	G	56974154	3	3	71	1	0	0	0	0	1	0	0	0	7084	391	14	3	924	3	HERPUD1	16	56974154	Missense_Mutation	SNP	A	TCGA-BQ-5887-01A-11D-1961-08		56974154	33380599	18	6778											
FLII	2314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18149935	18149935	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttcccagggaagaggctctcGaacttcttttgcaggctgaa	9	11	11	10	1	2	2	0	1	2	1	4	4	3	3	1	3	2	3	1	3	3	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:18149935G>A	ENST00000327031.4	-	23	3249	c.3024C>T	c.(3022-3024)ttC>ttT	p.F1008F	FLII_ENST00000579294.1_Silent_p.F997F|FLII_ENST00000379450.4_Silent_p.F922F|FLII_ENST00000578558.1_Intron|FLII_ENST00000545457.2_Silent_p.F953F	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1008					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					AGAGGCTCTCGAACTTCTTTT	0.627																																					p.F1008F		.											.	FLII-91	0			c.C3024T						.						60	53	56					17																	18149935		2203	4300	6503	SO:0001819	synonymous_variant	2314	exon23			GCTCTCGAACTTC	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3024C>T	17.37:g.18149935G>A		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	52	13	NM_002018	0	0	139	215	76	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			.		0.627	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		A	18149935	G	A	18149935	2	1	71	1	0	0	0	0	0	0	0	1	5944	1049	37	1		1	FLII	17	18149935	Silent	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		18149935	63045275	19	6779											
FDXR	2232	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	72860612	72860612	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccctcacccttgatcttGtcctggagacccaagaaatc	9	9	8	15	0	2	3	1	1	1	2	4	4	3	3	5	2	0	0	5	2	2	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:72860612G>C	ENST00000293195.5	-	8	870	c.792C>G	c.(790-792)gaC>gaG	p.D264E	FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000544854.1_Missense_Mutation_p.D212E|FDXR_ENST00000583917.1_Intron|FDXR_ENST00000413947.2_Missense_Mutation_p.D295E|GRIN2C_ENST00000578159.1_5'Flank|FDXR_ENST00000581530.1_Missense_Mutation_p.D270E|FDXR_ENST00000582944.1_Missense_Mutation_p.D256E|FDXR_ENST00000420580.2_Missense_Mutation_p.D224E|FDXR_ENST00000442102.2_Missense_Mutation_p.D307E|FDXR_ENST00000455107.2_Missense_Mutation_p.D220E	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	264					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	CCTTGATCTTGTCCTGGAGAC	0.612											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D307E		.											.	FDXR-226	0			c.C921G						.						42	47	45					17																	72860612		2203	4300	6503	SO:0001583	missense	2232	exon8			GATCTTGTCCTGG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.792C>G	17.37:g.72860612G>C	ENSP00000293195:p.Asp264Glu	Somatic	50	0	1140	WXS	Illumina HiSeq	Phase_I	88	7	NM_001258012	0	0	0	0	0	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	37	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.556819	0.00910	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35	4.65	2.43	0.29744	.	0.279368	0.40554	N	0.001071	T	0.04724	0.0128	N	0.04162	-0.26	0.33484	D	0.587776	B;B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.09377	0.004;0.003;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.31613	-0.9937	10	0.05351	T	0.99	-16.3668	2.2561	0.04055	0.1249:0.3442:0.3522:0.1788	.	224;307;295;262;212;264;256;264;270	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;ADRO_HUMAN;.	E	224;212;270;220;307;295	ENSP00000414172:D224E;ENSP00000445432:D212E;ENSP00000390875:D220E;ENSP00000416515:D307E;ENSP00000408595:D295E	ENSP00000293195:D270E	D	-	3	2	FDXR	70372207	0.964000	0.33143	1.000000	0.80357	0.295000	0.27426	0.151000	0.16283	0.910000	0.36722	0.561000	0.74099	GAC	.		0.612	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		C	72860612	G	C	72860612	3	2	71	1	0	0	0	0	1	0	0	0	5826	1368	48	4	703	4	FDXR	17	72860612	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08	54710677	72860612	8334598	20	6780											
RNMT	8731	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	13731629	13731630	+	Frame_Shift_Ins	INS	-	-	T																															attaatgaaaacacaacagcINSttctgggactgggctttctg																										TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr18:13731629_13731630insT	ENST00000383314.2	+	3	353_354	c.113_114insT	c.(112-117)gcttctfs	p.S39fs	RNMT_ENST00000592764.1_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000535051.1_Intron|RNMT_ENST00000589866.1_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000262173.3_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000543302.2_Frame_Shift_Ins_p.S39fs			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	39					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						AACACAACAGCTTCTGGGACTG	0.371																																					p.A38fs	GBM(29;474 594 19092 36647 41529)	.											.	RNMT-90	0			c.113_114insT						.																																			SO:0001589	frameshift_variant	8731	exon3			.	AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.115dupT	18.37:g.13731631_13731631dupT	ENSP00000372804:p.Ser39fs	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	140	31	NM_003799	0	0	0	0	0	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Frame_Shift_Ins	INS	ENST00000383314.2	37	CCDS11867.1																																																																																			.		0.371	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799		T	13731630	-	T	13731629	7	5	71	1	0	1	1	0	0	0	0	0	13538	797	28	0	115	0	RNMT	18	13731629	Frame_Shift_Ins	INS	-	TCGA-BQ-5887-01A-11D-1961-08		13731629	64345619	21	6781											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	137	1		WXS	Illumina HiSeq		122	1	NM_031203	0	0	0	0	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	71	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		8527467	50601516	22	6782											
NANOS3	342977	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	13988494	13988494	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctacagccacaccacccgAaactcggcaggcaagaagct	13	4	9	15	2	1	1	0	0	1	1	2	2	1	1	3	2	4	3	3	2	4	1			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:13988494A>G	ENST00000397555.2	+	2	375	c.375A>G	c.(373-375)cgA>cgG	p.R125R	NANOS3_ENST00000339133.5_Silent_p.R144R|NANOS3_ENST00000591727.1_Intron|MIR181C_ENST00000384881.1_RNA|MIR181D_ENST00000384853.1_RNA	NM_001098622.2	NP_001092092.1	P60323	NANO3_HUMAN	nanos homolog 3 (Drosophila)	125					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	7			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			ACACCACCCGAAACTCGGCAG	0.662																																					p.R144R		.											.	NANOS3-69	0			c.A432G						.						13	17	16					19																	13988494		2065	4127	6192	SO:0001819	synonymous_variant	342977	exon1			CACCCGAAACTCG	BM702754	CCDS42511.1	19p13.13	2003-12-01				ENSG00000187556			22048	protein-coding gene	gene with protein product		608229					Standard	NM_001098622		Approved	NANOS1L, NOS3	uc002mxj.4	P60323		ENST00000397555.2:c.375A>G	19.37:g.13988494A>G		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	36	8	NM_001098622	0	0	0	0	0	Q495E5	Silent	SNP	ENST00000397555.2	37																																																																																				.		0.662	NANOS3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_292819		G	13988494	A	G	13988494	2	3	71	1	0	0	0	0	0	0	0	1	10178	233	9	3		3	NANOS3	19	13988494	Silent	SNP	A	TCGA-BQ-5887-01A-11D-1961-08	5461027	13988494	45140489	23	6783											
NLRP7	199713	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55452315	55452315	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctggctttgctaactcCgagtcttcttctgcatctcc	5	14	6	16	1	4	0	0	0	4	0	6	1	5	0	4	1	3	3	4	1	1	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:55452315C>T	ENST00000590030.1	-	2	376	c.336G>A	c.(334-336)tcG>tcA	p.S112S	NLRP7_ENST00000588756.1_Silent_p.S112S|NLRP7_ENST00000592784.1_Silent_p.S112S|NLRP7_ENST00000340844.2_Silent_p.S112S|NLRP7_ENST00000448121.2_Silent_p.S112S|NLRP7_ENST00000446217.1_Silent_p.S140S|NLRP7_ENST00000328092.5_Silent_p.S112S			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	112							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TTGCTAACTCCGAGTCTTCTT	0.433																																					p.S112S		.											.	NLRP7-291	0			c.G336A						.						239	189	206					19																	55452315		2203	4300	6503	SO:0001819	synonymous_variant	199713	exon3			TAACTCCGAGTCT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.336G>A	19.37:g.55452315C>T		Somatic	215	0		WXS	Illumina HiSeq	Phase_I	255	60	NM_001127255	0	0	0	0	0	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			.		0.433	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55452315	C	T	55452315	2	4	71	1	0	0	0	0	0	0	0	1	10508	639	23	1		1	NLRP7	19	55452315	Silent	SNP	C	TCGA-BQ-5887-01A-11D-1961-08	41463821	55452315	3676668	24	6784											
TMC2	117532	broad.mit.edu;bcgsc.ca	37	chr20	2621849	2621849	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagggccctgggacctccaAttctgccagcaggaccacac	9	5	11	16	0	1	0	0	0	1	0	2	2	2	2	5	3	2	2	5	3	1	1			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:2621849A>G	ENST00000358864.1	+	20	2588	c.2573A>G	c.(2572-2574)aAt>aGt	p.N858S		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	858					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GGGACCTCCAATTCTGCCAGC	0.582																																					p.N858S													.	TMC2-93	0			c.A2573G						.						86	88	87					20																	2621849		2203	4300	6503	SO:0001583	missense	117532	exon20			CCTCCAATTCTGC	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.2573A>G	20.37:g.2621849A>G	ENSP00000351732:p.Asn858Ser	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	199	6	NM_080751	0	0	0	0	0	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	A	0.040	-1.286909	0.01387	.	.	ENSG00000149488	ENST00000358864	T	0.62498	0.02	4.89	0.764	0.18465	.	1.617550	0.03411	N	0.204850	T	0.24431	0.0592	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46176	-0.9210	10	0.02654	T	1	4.0E-4	6.2652	0.20922	0.4255:0.0:0.5745:0.0	.	858	Q8TDI7	TMC2_HUMAN	S	858	ENSP00000351732:N858S	ENSP00000351732:N858S	N	+	2	0	TMC2	2569849	0.005000	0.15991	0.005000	0.12908	0.028000	0.11728	0.914000	0.28624	0.313000	0.23062	-0.462000	0.05337	AAT	.		0.582	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			G	2621849	A	G	2621849	3	3	71	1	0	0	0	0	1	0	0	0	16017	101	4	3	2651	3	TMC2	20	2621849	Missense_Mutation	SNP	A	TCGA-BQ-5887-01A-11D-1961-08		2621849	60403671	25	6785											
CHD6	84181	broad.mit.edu	37	chr20	40033696	40033696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtcttttcagtcactgccGtaccacttttcgttgtgctt	5	17	7	12	2	3	0	2	0	1	0	4	0	3	0	2	0	3	3	2	0	1	7	rs375040457		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:40033696G>A	ENST00000373233.3	-	37	7862	c.7685C>T	c.(7684-7686)aCg>aTg	p.T2562M	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2562					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AGTCACTGCCGTACCACTTTT	0.527																																					p.T2562M													.	CHD6-238	0			c.C7685T						.	G	MET/THR	0,4406		0,0,2203	131	129	129		7685	3.7	0	20		129	1,8599	1.2+/-3.3	0,1,4299	no	missense	CHD6	NM_032221.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	2562/2716	40033696	1,13005	2203	4300	6503	SO:0001583	missense	84181	exon37			ACTGCCGTACCAC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.7685C>T	20.37:g.40033696G>A	ENSP00000362330:p.Thr2562Met	Somatic	186	2		WXS	Illumina HiSeq	Phase_I	237	5	NM_032221	0	0	15	15	0	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	G	8.202	0.798281	0.16397	0.0	1.16E-4	ENSG00000124177	ENST00000373233	D	0.86497	-2.13	5.65	3.73	0.42828	.	0.604983	0.15766	N	0.245699	T	0.79311	0.4424	L	0.48642	1.525	0.46203	D	0.998922	P	0.39131	0.661	B	0.29663	0.105	T	0.77130	-0.2701	10	0.66056	D	0.02	0.0011	7.825	0.29309	0.1395:0.1329:0.7276:0.0	.	2562	Q8TD26	CHD6_HUMAN	M	2562	ENSP00000362330:T2562M	ENSP00000362330:T2562M	T	-	2	0	CHD6	39467110	0.004000	0.15560	0.001000	0.08648	0.252000	0.25951	1.505000	0.35736	0.953000	0.37825	0.655000	0.94253	ACG	.		0.527	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40033696	G	A	40033696	3	1	71	1	0	0	0	0	1	0	0	0	3335	1145	40	1	466	1	CHD6	20	40033696	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08	37411847	40033696	22991824	26	6786											
PRIC285	85441	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	62198513	62198513	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagaccaggcggctctgcCgcgccacctcgtgagtctcc	6	6	13	16	4	2	2	0	1	2	1	4	3	2	3	5	3	1	1	5	3	1	0			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:62198513C>T	ENST00000467148.1	-	6	2267	c.2198G>A	c.(2197-2199)cGg>cAg	p.R733Q	HELZ2_ENST00000427522.2_Missense_Mutation_p.R164Q|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	733	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCGGCTCTGCCGCGCCACCTC	0.662																																					p.R733Q		.											.	.	0			c.G2198A						.						42	45	44					20																	62198513		2201	4296	6497	SO:0001583	missense	85441	exon7			CTCTGCCGCGCCA	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.2198G>A	20.37:g.62198513C>T	ENSP00000417401:p.Arg733Gln	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	156	9	NM_001037335	0	0	3	3	0	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.354760	0.01256	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.92199	-2.99;-2.99	5.06	-10.1	0.00402	.	1.876900	0.02583	N	0.099118	T	0.75027	0.3794	N	0.04880	-0.145	0.09310	N	1	B;B	0.16603	0.018;0.014	B;B	0.06405	0.002;0.001	T	0.70296	-0.4911	10	0.05959	T	0.93	-12.0678	6.0815	0.19944	0.1162:0.2139:0.0711:0.5987	.	733;164	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	Q	164;733	ENSP00000393257:R164Q;ENSP00000417401:R733Q	ENSP00000393257:R164Q	R	-	2	0	RP4-697K14.7	61668957	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.789000	0.04609	-1.726000	0.01370	-1.028000	0.02416	CGG	.		0.662	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62198513	C	T	62198513	3	4	71	1	0	0	0	0	1	0	0	0	12514	652	23	1	5807	1	PRIC285	20	62198513	Missense_Mutation	SNP	C	TCGA-BQ-5887-01A-11D-1961-08	22164817	62198513	827007	27	6787											
INPP5J	27124	hgsc.bcm.edu;broad.mit.edu	37	chr22	31529986	31529986	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggatgacagcacactggagCtccttgcacccaagtcccgc	10	6	10	15	1	0	1	0	1	0	0	2	3	2	3	3	2	3	3	3	2	1	1			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr22:31529986C>T	ENST00000331075.5	+	13	2651	c.2602C>T	c.(2602-2604)Ctc>Ttc	p.L868F	INPP5J_ENST00000404453.1_Missense_Mutation_p.L233F|INPP5J_ENST00000405300.1_Missense_Mutation_p.L501F|INPP5J_ENST00000402238.1_Missense_Mutation_p.L207F|INPP5J_ENST00000404390.3_Missense_Mutation_p.L500F|INPP5J_ENST00000412277.2_Missense_Mutation_p.L801F|INPP5J_ENST00000401755.1_Missense_Mutation_p.L233F|INPP5J_ENST00000400294.2_Missense_Mutation_p.L501F	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	868	Ser-rich.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						CACACTGGAGCTCCTTGCACC	0.657																																					p.L500F		.											.	INPP5J-205	0			c.C1498T						.						21	26	24					22																	31529986		2173	4270	6443	SO:0001583	missense	27124	exon13			CTGGAGCTCCTTG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.2602C>T	22.37:g.31529986C>T	ENSP00000333262:p.Leu868Phe	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	35	7	NM_001002837	0	0	3	6	3	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Missense_Mutation	SNP	ENST00000331075.5	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.204521	0.79127	.	.	ENSG00000185133	ENST00000331075;ENST00000412277;ENST00000400294;ENST00000405300;ENST00000404390;ENST00000402238;ENST00000404453;ENST00000401755	D;D;D;D;D;D;D;D	0.99319	-5.26;-5.24;-5.3;-5.3;-5.29;-5.74;-4.51;-4.51	5.54	5.54	0.83059	.	0.142348	0.32134	N	0.006526	D	0.98776	0.9588	L	0.29908	0.895	0.45129	D	0.998142	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.74674	0.984;0.963;0.963;0.962	D	0.99486	1.0949	10	0.49607	T	0.09	.	15.7279	0.77777	0.0:0.8631:0.1369:0.0	.	501;207;868;500	Q15735-2;B5MCL8;Q15735;Q15735-3	.;.;PI5PA_HUMAN;.	F	868;801;501;501;500;207;233;233	ENSP00000333262:L868F;ENSP00000392924:L801F;ENSP00000383150:L501F;ENSP00000384596:L501F;ENSP00000384534:L500F;ENSP00000385264:L207F;ENSP00000385343:L233F;ENSP00000384540:L233F	ENSP00000333262:L868F	L	+	1	0	INPP5J	29859986	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.528000	0.60580	2.610000	0.88304	0.655000	0.94253	CTC	.		0.657	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837		T	31529986	C	T	31529986	3	4	71	1	0	0	0	0	1	0	0	0	7780	797	28	2	1548	2	INPP5J	22	31529986	Missense_Mutation	SNP	C	TCGA-BQ-5887-01A-11D-1961-08		31529986	19774580	28	6788											
ALAS2	212	hgsc.bcm.edu	37	chrX	55046923	55046923	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccagctccagcaccatgaCgctgcagggtctccctggcc	7	6	10	18	1	1	1	0	1	1	0	3	1	2	1	5	2	3	4	5	2	0	0	rs185504937		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chrX:55046923C>T	ENST00000330807.5	-	6	790	c.653G>A	c.(652-654)cGt>cAt	p.R218H	ALAS2_ENST00000498636.1_5'Flank|ALAS2_ENST00000396198.3_Missense_Mutation_p.R205H|ALAS2_ENST00000335854.4_Missense_Mutation_p.R181H	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	218			R -> H (in XLSA; significantly increased thermosensitivity; dbSNP:rs185504937). {ECO:0000269|PubMed:21309041}.		cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	AGCACCATGACGCTGCAGGGT	0.542													c|||	2	0.000529801	0	0.0014	3775	,	,		16485	0		0.001	False		,,,				2504	0				p.R218H		.											.	ALAS2-131	0			c.G653A						.		HIS/ARG,HIS/ARG,HIS/ARG	0,3825		0,0,0,1632,561	24	19	21		653,542,614	-0.3	1	X		21	4,6706		0,3,1,2423,1857	yes	missense,missense,missense	ALAS2	NM_000032.4,NM_001037967.3,NM_001037968.3	29,29,29	0,3,1,4055,2418	TT,TC,T,CC,C		0.0596,0.0,0.038	possibly-damaging,possibly-damaging,possibly-damaging	218/588,181/551,205/575	55046923	4,10531	2193	4284	6477	SO:0001583	missense	212	exon6			CCATGACGCTGCA		CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"sideroblastic/hypochromic anemia"	301300	"aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.653G>A	X.37:g.55046923C>T	ENSP00000332369:p.Arg218His	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	10	10	NM_000032	0	0	0	0	0	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Missense_Mutation	SNP	ENST00000330807.5	37	CCDS14366.1	2|2	0.0012055455093429777|0.0012055455093429777	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	c|c	17.63|17.63	3.438420|3.438420	0.62955|0.62955	0.0|0.0	5.96E-4|5.96E-4	ENSG00000158578|ENSG00000158578	ENST00000330807;ENST00000396198;ENST00000335854|ENST00000455688	D;D;D|.	0.95447|.	-3.71;-3.71;-3.71|.	5.01|5.01	-0.267|-0.267	0.12938|0.12938	Aminotransferase, class I/classII (1);Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.517064|.	0.22034|.	N|.	0.065549|.	T|T	0.43853|0.43853	0.1266|0.1266	L|L	0.58925|0.58925	1.835|1.835	0.32536|0.32536	N|N	0.534315|0.534315	P;P;P|.	0.42993|.	0.52;0.797;0.653|.	B;P;P|.	0.47645|.	0.425;0.553;0.553|.	T|T	0.51260|0.51260	-0.8728|-0.8728	10|5	0.49607|.	T|.	0.09|.	-0.0054|-0.0054	3.4364|3.4364	0.07448|0.07448	0.3175:0.2067:0.0:0.4758|0.3175:0.2067:0.0:0.4758	.|.	181;205;218|.	A8K6C4;Q5JZF5;P22557|.	.;.;HEM0_HUMAN|.	H|I	218;205;181|170	ENSP00000332369:R218H;ENSP00000379501:R205H;ENSP00000337131:R181H|.	ENSP00000332369:R218H|.	R|V	-|-	2|1	0|0	ALAS2|ALAS2	55063648|55063648	0.915000|0.915000	0.31059|0.31059	0.992000|0.992000	0.48379|0.48379	0.923000|0.923000	0.55619|0.55619	0.333000|0.333000	0.19768|0.19768	-0.009000|-0.009000	0.14296|0.14296	0.519000|0.519000	0.50382|0.50382	CGT|GTC	C|0.999;T|0.001		0.542	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032		T	55046923	C	T	55046923	3	4	71	1	0	0	0	0	1	0	0	0	485	536	19	1	1134	1	ALAS2	23	55046923	Missense_Mutation	SNP	C	TCGA-BQ-5887-01A-11D-1961-08		55046923	100223637	29	6789											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22190695	22190695	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcccggtgcgcgtgtagccGggggcacagtcctaggggca	5	6	17	13	4	0	0	0	0	0	0	2	0	2	0	3	5	2	3	3	5	2	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:22190695G>A	ENST00000374695.3	-	37	4717	c.4638C>T	c.(4636-4638)ccC>ccT	p.P1546P		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1546	Laminin EGF-like 9; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCGTGTAGCCGGGGGCACAGT	0.652																																					p.P1546P		.											.	HSPG2-141	0			c.C4638T						.						36	31	33					1																	22190695		2163	4218	6381	SO:0001819	synonymous_variant	3339	exon37			GTAGCCGGGGGCA	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.4638C>T	1.37:g.22190695G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_005529	0	0	1	1	0	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			.		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22190695	G	A	22190695	2	1	72	1	0	0	0	0	0	0	0	1	7451	1103	39	1		1	HSPG2	1	22190695	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		22190695	227059926	1	6790											
KHDRBS1	10657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	32508212	32508212	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcatacagagagcacccatAtggacgttattaaaaacaaa	19	7	7	8	1	0	1	0	0	0	1	0	3	0	2	1	1	4	3	1	1	7	4			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:32508212A>G	ENST00000327300.7	+	9	1486	c.1319A>G	c.(1318-1320)tAt>tGt	p.Y440C	KHDRBS1_ENST00000492989.1_Missense_Mutation_p.Y401C|KHDRBS1_ENST00000307714.8_3'UTR	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1											endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GAGCACCCATATGGACGTTAT	0.483																																					p.Y440C	Ovarian(173;401 1982 12359 31110 42403)	.											.	KHDRBS1-227	0			c.A1319G						.						59	57	58					1																	32508212		2203	4300	6503	SO:0001583	missense	10657	exon9			ACCCATATGGACG	U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"GAP-associated tyrosine phosphoprotein p62 (Sam68)"	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.1319A>G	1.37:g.32508212A>G	ENSP00000313829:p.Tyr440Cys	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	58	13	NM_006559	0	0	40	74	34		Missense_Mutation	SNP	ENST00000327300.7	37	CCDS350.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.382684	0.42207	.	.	ENSG00000121774	ENST00000327300;ENST00000492989;ENST00000355201	T;T	0.71103	-0.54;-0.51	5.85	4.72	0.59763	.	0.057453	0.64402	D	0.000001	T	0.81735	0.4885	M	0.78456	2.415	0.80722	D	1	D;D	0.69078	0.996;0.997	P;D	0.63192	0.819;0.912	D	0.83637	0.0148	10	0.87932	D	0	.	12.1125	0.53848	0.9331:0.0:0.0668:0.0	.	440;401	Q07666;Q07666-3	KHDR1_HUMAN;.	C	440;401;416	ENSP00000313829:Y440C;ENSP00000417731:Y401C	ENSP00000313829:Y440C	Y	+	2	0	KHDRBS1	32280799	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.716000	0.91420	1.156000	0.42514	-0.256000	0.11100	TAT	.		0.483	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		G	32508212	A	G	32508212	3	3	72	1	0	0	0	0	1	0	0	0	8167	449	16	3	1353	3	KHDRBS1	1	32508212	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08	10317517	32508212	216742409	2	6791											
TTLL7	79739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	84348653	84348653	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgaacaagtacctggaatTaccccagtcaggaccaatgc	13	8	9	11	0	1	1	1	1	0	0	1	3	1	3	4	2	4	1	4	2	6	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:84348653T>C	ENST00000260505.8	-	20	2913	c.2536A>G	c.(2536-2538)Aat>Gat	p.N846D	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	846					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		TACCTGGAATTACCCCAGTCA	0.398																																					p.N846D		.											.	TTLL7-91	0			c.A2536G						.						156	150	152					1																	84348653		2203	4300	6503	SO:0001583	missense	79739	exon20			TGGAATTACCCCA	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.2536A>G	1.37:g.84348653T>C	ENSP00000260505:p.Asn846Asp	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	162	21	NM_024686	0	0	0	0	0	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	ENST00000260505.8	37	CCDS690.2	.	.	.	.	.	.	.	.	.	.	T	11.08	1.532905	0.27387	.	.	ENSG00000137941	ENST00000260505	T	0.03004	4.08	5.5	1.79	0.24919	.	0.504331	0.23351	N	0.049127	T	0.00468	0.0015	N	0.04880	-0.145	0.28908	N	0.892872	B	0.06786	0.001	B	0.04013	0.001	T	0.44711	-0.9310	10	0.12766	T	0.61	.	3.8611	0.08996	0.0:0.188:0.414:0.398	.	846	Q6ZT98	TTLL7_HUMAN	D	846	ENSP00000260505:N846D	ENSP00000260505:N846D	N	-	1	0	TTLL7	84121241	1.000000	0.71417	0.971000	0.41717	0.928000	0.56348	3.636000	0.54317	0.417000	0.25871	-0.321000	0.08615	AAT	.		0.398	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686		C	84348653	T	C	84348653	3	2	72	1	0	0	0	0	1	0	0	0	16765	1754	61	3	135	3	TTLL7	1	84348653	Missense_Mutation	SNP	T	TCGA-BQ-5888-01A-11D-1589-08	51840441	84348653	164901968	3	6792											
HSD17B7	51478	broad.mit.edu	37	chr1	162769622	162769622	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgcaaggaaatctaatttCagcctcgaggacttccagca	13	9	9	10	1	2	0	1	0	1	0	4	3	3	2	2	2	3	2	2	2	3	3			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:162769622C>A	ENST00000254521.3	+	5	592	c.537C>A	c.(535-537)ttC>ttA	p.F179L	HSD17B7_ENST00000367917.3_Missense_Mutation_p.F179L|HSD17B7_ENST00000485405.1_3'UTR	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	179					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					AATCTAATTTCAGCCTCGAGG	0.493																																					p.F179L													.	HSD17B7-91	0			c.C537A						.						68	62	64					1																	162769622		2203	4300	6503	SO:0001583	missense	51478	exon5			TAATTTCAGCCTC	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5215	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 37C, member 1"	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.537C>A	1.37:g.162769622C>A	ENSP00000254521:p.Phe179Leu	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	63	3	NM_016371	0	0	17	17	0	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Missense_Mutation	SNP	ENST00000254521.3	37	CCDS1242.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241919	0.39598	.	.	ENSG00000132196	ENST00000367917;ENST00000254521;ENST00000413934	T;T;T	0.75477	3.05;-0.94;3.05	4.44	2.56	0.30785	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.41971	0.1182	N	0.16266	0.395	0.37031	D	0.896675	P	0.37038	0.579	B	0.41988	0.372	T	0.30475	-0.9977	9	0.40728	T	0.16	-15.6945	6.7317	0.23387	0.0:0.7057:0.0:0.2943	.	179	P56937	DHB7_HUMAN	L	179;179;32	ENSP00000356894:F179L;ENSP00000254521:F179L;ENSP00000412146:F32L	ENSP00000254521:F179L	F	+	3	2	HSD17B7	161036246	1.000000	0.71417	0.969000	0.41365	0.955000	0.61496	1.007000	0.29860	0.488000	0.27723	0.650000	0.86243	TTC	.		0.493	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371		A	162769622	C	A	162769622	3	1	72	1	0	0	0	0	1	0	0	0	7409	825	29	4	555	4	HSD17B7	1	162769622	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08	78420969	162769622	86480999	4	6793											
CFH	3075	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	196706023	196706023	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatatgacaaccacactgaAttatcgggatggagaaaaag	18	7	9	7	1	0	3	0	2	0	1	1	5	0	4	1	2	1	0	1	2	7	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:196706023A>T	ENST00000367429.4	+	16	2723	c.2483A>T	c.(2482-2484)aAt>aTt	p.N828I		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	828	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ACCACACTGAATTATCGGGAT	0.333																																					p.N828I		.											.	CFH-566	0			c.A2483T						.						65	62	63					1																	196706023		2203	4300	6503	SO:0001583	missense	3075	exon16			CACTGAATTATCG	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2483A>T	1.37:g.196706023A>T	ENSP00000356399:p.Asn828Ile	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	61	6	NM_000186	0	0	1	1	0	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	12.36	1.913921	0.33815	.	.	ENSG00000000971	ENST00000367429	T	0.65732	-0.17	5.91	3.6	0.41247	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.69735	0.3144	M	0.73372	2.23	0.80722	D	1	D	0.60160	0.987	P	0.59357	0.856	T	0.68217	-0.5467	9	0.42905	T	0.14	.	6.5067	0.22198	0.7623:0.1583:0.0794:0.0	.	828	P08603	CFAH_HUMAN	I	828	ENSP00000356399:N828I	ENSP00000356399:N828I	N	+	2	0	CFH	194972646	0.999000	0.42202	0.929000	0.37066	0.092000	0.18411	1.560000	0.36331	1.049000	0.40321	0.454000	0.30748	AAT	.		0.333	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		T	196706023	A	T	196706023	3	4	72	1	0	0	0	0	1	0	0	0	3289	101	4	5	2563	5	CFH	1	196706023	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08	33936401	196706023	52544598	5	6794											
PPP1R15B	84919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204379183	204379183	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actatcaaaaccatcatcctCagcttcctcatcccaatcct	12	11	1	17	0	4	0	4	0	0	0	8	0	8	0	5	0	2	1	5	0	4	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:204379183C>A	ENST00000367188.4	-	1	1736	c.1357G>T	c.(1357-1359)Gag>Tag	p.E453*	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	453					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			CCATCATCCTCAGCTTCCTCA	0.448																																					p.E453X		.											.	PPP1R15B-652	0			c.G1357T						.						132	133	133					1																	204379183		2203	4300	6503	SO:0001587	stop_gained	84919	exon1			CATCCTCAGCTTC	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1357G>T	1.37:g.204379183C>A	ENSP00000356156:p.Glu453*	Somatic	300	1		WXS	Illumina HiSeq	Phase_I	269	61	NM_032833	0	0	0	0	0	Q53GQ4|Q658M2|Q6P156|Q96SN1	Nonsense_Mutation	SNP	ENST00000367188.4	37	CCDS1445.1	.	.	.	.	.	.	.	.	.	.	C	42	9.816625	0.99271	.	.	ENSG00000158615	ENST00000367188;ENST00000543650	.	.	.	4.95	4.95	0.65309	.	0.314427	0.31051	N	0.008354	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-17.5764	16.3288	0.82997	0.0:1.0:0.0:0.0	.	.	.	.	X	453;363	.	ENSP00000356156:E453X	E	-	1	0	PPP1R15B	202645806	1.000000	0.71417	0.826000	0.32828	0.997000	0.91878	6.493000	0.73658	2.423000	0.82170	0.655000	0.94253	GAG	.		0.448	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		A	204379183	C	A	204379183	4	1	72	1	0	0	0	0	0	1	0	0	12393	835	29	4	792	4	PPP1R15B	1	204379183	Nonsense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08	7673160	204379183	44871438	6	6795											
BATF3	55509	hgsc.bcm.edu	37	chr1	212873074	212873074	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgacgctcctctgcaggaCgctgccggcggccgggagcc	4	4	16	17	7	1	0	0	0	1	0	2	3	2	2	4	4	3	3	4	4	0	0	rs2202683	byFrequency	TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:212873074C>T	ENST00000243440.1	-	1	253	c.31G>A	c.(31-33)Gtc>Atc	p.V11I	BATF3_ENST00000478275.1_5'Flank	NM_018664.2	NP_061134.1	Q9NR55	BATF3_HUMAN	basic leucine zipper transcription factor, ATF-like 3	11			V -> I (in dbSNP:rs2202683).		dendritic cell differentiation (GO:0097028)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to virus (GO:0009615)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0046)|all cancers(67;0.00785)|GBM - Glioblastoma multiforme(131;0.0731)|Epithelial(68;0.0781)		CTCTGCAGGACGCTGCCGGCG	0.806													c|||	1011	0.201877	0.2239	0.1052	5008	,	,		4637	0.1875		0.1233	False		,,,				2504	0.3364				p.V11I		.											.	BATF3-68	0			c.G31A						.						1	1	1					1																	212873074		797	2005	2802	SO:0001583	missense	55509	exon1			GCAGGACGCTGCC	AF255346	CCDS1508.1	1q32.3	2013-01-10			ENSG00000123685	ENSG00000123685		"basic leucine zipper proteins"	28915	protein-coding gene	gene with protein product	"Jun dimerization protein 1"	612470				10878360, 12087103	Standard	NM_018664		Approved	JUNDM1, SNFT, JDP1	uc001hjl.2	Q9NR55	OTTHUMG00000036807	ENST00000243440.1:c.31G>A	1.37:g.212873074C>T	ENSP00000243440:p.Val11Ile	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_018664	0	0	0	0	0		Missense_Mutation	SNP	ENST00000243440.1	37	CCDS1508.1	369	0.16895604395604397	110	0.22357723577235772	53	0.1464088397790055	109	0.19055944055944055	97	0.1279683377308707	c	15.18	2.756149	0.49362	.	.	ENSG00000123685	ENST00000243440	T	0.57107	0.42	3.94	3.94	0.45596	.	0.397991	0.20707	U	0.087161	T	0.00039	0.0001	L	0.29908	0.895	0.42635	P	0.006601999999999997	D	0.52996	0.957	B	0.36719	0.231	T	0.11203	-1.0597	9	0.35671	T	0.21	-0.8671	11.5076	0.50476	0.0:1.0:0.0:0.0	rs2202683	11	Q9NR55	BATF3_HUMAN	I	11	ENSP00000243440:V11I	ENSP00000243440:V11I	V	-	1	0	BATF3	210939697	1.000000	0.71417	0.957000	0.39632	0.662000	0.39071	1.053000	0.30442	1.720000	0.51447	0.424000	0.28305	GTC	C|0.001;G|0.830		0.806	BATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089403.1	NM_018664		T	212873074	C	T	212873074	3	4	72	1	0	0	0	0	1	0	0	0	1328	536	19	1	364	1	BATF3	1	212873074	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08	8493891	212873074	36377547	7	6796											
DIS3L2	129563	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	233075106	233075106	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgccctctcctgcaagccaCtcgctgacggtaggatggaa	9	8	11	13	2	1	1	0	1	1	0	3	3	1	3	3	3	3	3	3	3	3	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr2:233075106C>G	ENST00000409307.1	+	9	1195	c.1195C>G	c.(1195-1197)Ctc>Gtc	p.L399V	DIS3L2_ENST00000325385.7_Missense_Mutation_p.L399V|DIS3L2_ENST00000273009.6_Missense_Mutation_p.L399V					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CTGCAAGCCACTCGCTGACGG	0.512																																					p.L399V		.											.	DIS3L2-136	0			c.C1195G						.						97	98	98					2																	233075106		2074	4234	6308	SO:0001583	missense	129563	exon10			AAGCCACTCGCTG	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.1195C>G	2.37:g.233075106C>G	ENSP00000386799:p.Leu399Val	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	79	9	NM_152383	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.954379	0.73902	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307;ENST00000424049	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	5.16	5.16	0.70880	Ribonuclease II/R (2);	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	M	0.79693	2.465	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	T	0.67409	-0.5678	10	0.72032	D	0.01	-16.4035	15.5539	0.76177	0.0:1.0:0.0:0.0	.	399	Q8IYB7	DI3L2_HUMAN	V	399;399;399;399;399;34	ENSP00000273009:L399V;ENSP00000315569:L399V;ENSP00000386799:L399V;ENSP00000415419:L34V	ENSP00000273009:L399V	L	+	1	0	DIS3L2	232783350	0.994000	0.37717	0.445000	0.26908	0.945000	0.59286	3.829000	0.55760	2.381000	0.81170	0.455000	0.32223	CTC	.		0.512	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		G	233075106	C	G	233075106	3	3	72	1	0	0	0	0	1	0	0	0	4548	565	20	4	1229	4	DIS3L2	2	233075106	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		233075106	10124267	8	6797											
AMIGO3	29925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49755505	49755505	+	3'UTR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgccagctgcacgcggccaTtgaggcccctccggcctggc	4	6	13	18	3	0	1	0	1	0	0	1	1	1	1	6	4	3	2	6	4	0	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr3:49755505T>C	ENST00000480687.1	-	0	4879				RNF123_ENST00000433785.1_Intron|RNF123_ENST00000327697.6_Intron|AMIGO3_ENST00000535833.1_Missense_Mutation_p.N465S|AMIGO3_ENST00000320431.7_Missense_Mutation_p.N465S			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CACGCGGCCATTGAGGCCCCT	0.632																																					p.N465S		.											.	AMIGO3-91	0			c.A1394G						.						72	71	71					3																	49755505		2203	4300	6503	SO:0001624	3_prime_UTR_variant	386724	exon1			CGGCCATTGAGGC	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.*3680A>G	3.37:g.49755505T>C		Somatic	142	1		WXS	Illumina HiSeq	Phase_I	127	22	NM_198722	0	0	2	3	1	A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	37	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.096839	0.76870	.	.	ENSG00000176020	ENST00000320431;ENST00000535833	T;T	0.66460	-0.21;-0.21	5.45	5.45	0.79879	.	0.114778	0.64402	D	0.000020	T	0.76814	0.4040	M	0.75777	2.31	0.80722	D	1	D	0.67145	0.996	P	0.60609	0.877	T	0.79640	-0.1719	10	0.87932	D	0	-14.8242	8.9474	0.35767	0.0:0.0836:0.0:0.9164	.	465	Q86WK7	AMGO3_HUMAN	S	465	ENSP00000323096:N465S;ENSP00000439268:N465S	ENSP00000323096:N465S	N	-	2	0	AMIGO3	49730509	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.856000	0.69518	2.080000	0.62538	0.459000	0.35465	AAT	.		0.632	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		C	49755505	T	C	49755505	1	2	72	0	1	0	0	0	0	0	0	0	577	1493	52	3		3	AMIGO3	3	49755505	3'UTR	SNP	T	TCGA-BQ-5888-01A-11D-1589-08		49755505	148266925	9	6798											
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221062	161221062	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggggaggaaaaggacagAaaggtgaggggggtatgaaa	17	3	20	1	0	0	4	0	2	0	2	0	7	0	7	0	8	0	1	0	8	5	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr3:161221062A>G	ENST00000327928.4	+	4	766	c.766A>G	c.(766-768)Aaa>Gaa	p.K256E		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	256	Collagen-like 2.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						AAAAGGACAGAAAGGTGAGGG	0.582																																					p.K256E		.											.	.	0			c.A766G						.						6	6	6					3																	161221062		1882	4058	5940	SO:0001583	missense	131149	exon4			GGACAGAAAGGTG		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"C1q and tumor necrosis factor related protein 15"		"otolin 1 homolog (zebrafish)"			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.766A>G	3.37:g.161221062A>G	ENSP00000330808:p.Lys256Glu	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_001080440	0	0	0	0	0		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.600002	0.46318	.	.	ENSG00000182447	ENST00000327928	D	0.93247	-3.19	4.79	3.6	0.41247	.	0.260709	0.36519	N	0.002555	D	0.93713	0.7991	M	0.74546	2.27	0.09310	N	1	D	0.53619	0.961	P	0.52957	0.714	D	0.86251	0.1649	10	0.22109	T	0.4	.	10.4489	0.44509	0.836:0.164:0.0:0.0	.	256	A6NHN0	OTOL1_HUMAN	E	256	ENSP00000330808:K256E	ENSP00000330808:K256E	K	+	1	0	OTOL1	162703756	0.044000	0.20184	0.039000	0.18376	0.750000	0.42670	2.908000	0.48750	0.649000	0.30751	0.455000	0.32223	AAA	.		0.582	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		G	161221062	A	G	161221062	3	3	72	1	0	0	0	0	1	0	0	0	11330	247	9	3	780	3	OTOL1	3	161221062	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08	111465557	161221062	36801368	10	6799											
OTOP1	133060	hgsc.bcm.edu	37	chr4	4228410	4228410	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcccatactggctgctcAgcatctcggccagtttctgt	6	12	9	14	1	4	0	2	0	2	0	5	0	4	0	2	2	4	4	2	2	1	2	rs201691469		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr4:4228410A>G	ENST00000296358.4	-	1	206	c.182T>C	c.(181-183)cTg>cCg	p.L61P		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	61					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTGGCTGCTCAGCATCTCGGC	0.726																																					p.L61P		.											.	OTOP1-92	0			c.T182C						.						9	10	9					4																	4228410		2137	4171	6308	SO:0001583	missense	133060	exon1			CTGCTCAGCATCT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.182T>C	4.37:g.4228410A>G	ENSP00000296358:p.Leu61Pro	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_177998	0	0	0	0	0	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.095183	0.56075	.	.	ENSG00000163982	ENST00000296358	T	0.17691	2.26	4.08	1.58	0.23477	.	0.182461	0.36628	U	0.002487	T	0.23289	0.0563	L	0.39245	1.2	0.80722	D	1	D	0.64830	0.994	P	0.60789	0.879	T	0.01720	-1.1288	10	0.87932	D	0	.	6.1537	0.20326	0.749:0.1634:0.0876:0.0	.	61	Q7RTM1	OTOP1_HUMAN	P	61	ENSP00000296358:L61P	ENSP00000296358:L61P	L	-	2	0	OTOP1	4279311	1.000000	0.71417	0.999000	0.59377	0.643000	0.38383	3.369000	0.52365	0.426000	0.26116	0.352000	0.21897	CTG	A|0.993;G|0.007		0.726	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		G	4228410	A	G	4228410	3	3	72	1	0	0	0	0	1	0	0	0	11331	188	7	3	1680	3	OTOP1	4	4228410	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08		4228410	186925866	11	6800											
CDH10	1008	broad.mit.edu	37	chr5	24492973	24492973	+	Frame_Shift_Del	DEL	A	A	-																															gattgacagcagctaaactgAaaaaaaatttctgtccacct																										TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr5:24492973delA	ENST00000264463.4	-	10	2084	c.1577delT	c.(1576-1578)ttcfs	p.F526fs	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	526	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		AGCTAAACTGAAAAAAAATTT	0.313										HNSCC(23;0.051)																											p.F526fs													.	CDH10-253	0			c.1577delT						.						170	183	179					5																	24492973		2203	4298	6501	SO:0001589	frameshift_variant	1008	exon10			AAACTGAAAAAAA	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"Cadherins / Major cadherins"	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1577delT	5.37:g.24492973delA	ENSP00000264463:p.Phe526fs	Somatic	351	0		WXS	Illumina HiSeq	Phase_I	348	7	NM_006727	0	0	0	0	0	Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	37	CCDS3892.1																																																																																			.		0.313	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		-	24492973	A	-	24492973	7	5	72	1	0	1	0	1	0	0	0	0	3102	246	9	0	801	0	CDH10	5	24492973	Frame_Shift_Del	DEL	A	TCGA-BQ-5888-01A-11D-1589-08		24492973	156422287	12	6801											
EBF1	1879	bcgsc.ca	37	chr5	158158101	158158101	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaaacgctcagggtcaccAgggtgccgaggaatgacctt	10	6	14	11	2	2	1	2	1	0	0	2	3	2	2	3	4	2	2	3	4	2	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr5:158158101A>G	ENST00000313708.6	-	11	1383	c.1101T>C	c.(1099-1101)ccT>ccC	p.P367P	EBF1_ENST00000517373.1_Silent_p.P359P|EBF1_ENST00000380654.4_Silent_p.P336P|EBF1_ENST00000518836.1_5'UTR	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	367					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|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)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGGGTCACCAGGGTGCCGAG	0.438			T	HMGA2	lipoma																																p.P367P				Dom	yes		5	5q34	1879	early B-cell factor 1		M	.	EBF1-92	0			c.T1101C						.						68	68	68					5																	158158101		2203	4300	6503	SO:0001819	synonymous_variant	1879	exon11			GTCACCAGGGTGC	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"early B-cell factor"	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1101T>C	5.37:g.158158101A>G		Somatic	38	0		WXS	Illumina HiSeq	Phase_1	63	4	NM_024007	0	0	0	0	0	Q8IW11	Silent	SNP	ENST00000313708.6	37	CCDS4343.1																																																																																			.		0.438	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		G	158158101	A	G	158158101	2	3	72	1	0	0	0	0	0	0	0	1	4891	175	7	3		3	EBF1	5	158158101	Silent	SNP	A	TCGA-BQ-5888-01A-11D-1589-08	133665128	158158101	22757159	13	6802											
ABCC10	89845	broad.mit.edu	37	chr6	43412937	43412937	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctacctcaccgtgtatgCgaccattgctggtgtaaatt	8	15	8	10	2	2	0	1	0	1	0	2	1	2	0	3	1	3	3	3	1	4	6			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr6:43412937C>T	ENST00000372530.4	+	14	3130	c.2915C>T	c.(2914-2916)gCg>gTg	p.A972V	ABCC10_ENST00000244533.3_Missense_Mutation_p.A944V	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	972	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	ACCGTGTATGCGACCATTGCT	0.607																																					p.A972V													.	ABCC10-96	0			c.C2915T						.						130	100	110					6																	43412937		2203	4300	6503	SO:0001583	missense	89845	exon14			TGTATGCGACCAT	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2915C>T	6.37:g.43412937C>T	ENSP00000361608:p.Ala972Val	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	92	4	NM_001198934	0	0	12	12	0	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.775586	0.70107	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	D;D	0.89196	-2.48;-2.48	4.56	3.65	0.41850	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.261486	0.36409	N	0.002602	T	0.78780	0.4337	L	0.44542	1.39	0.39035	D	0.960021	P;P	0.52316	0.936;0.952	B;B	0.42462	0.388;0.348	T	0.79001	-0.1981	10	0.36615	T	0.2	-11.8221	11.6154	0.51086	0.0:0.5948:0.4051:0.0	.	944;972	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	V	972;944	ENSP00000361608:A972V;ENSP00000244533:A944V	ENSP00000244533:A944V	A	+	2	0	ABCC10	43520915	1.000000	0.71417	0.719000	0.30619	0.914000	0.54420	3.693000	0.54735	2.359000	0.80004	0.462000	0.41574	GCG	.		0.607	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43412937	C	T	43412937	3	4	72	1	0	0	0	0	1	0	0	0	50	768	27	1	2877	1	ABCC10	6	43412937	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		43412937	127702130	14	6803											
WASF1	8936	hgsc.bcm.edu	37	chr6	110424747	110424747	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatccatccatatgatccaCgtatgtctgaggtctaaaag	13	11	8	9	1	2	3	0	2	2	1	5	3	5	3	3	1	0	1	3	1	4	3			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr6:110424747C>A	ENST00000392589.1	-	9	1563	c.727G>T	c.(727-729)Gtg>Ttg	p.V243L	WASF1_ENST00000392586.1_Missense_Mutation_p.V243L|WASF1_ENST00000359451.2_Missense_Mutation_p.V243L|WASF1_ENST00000392587.2_Missense_Mutation_p.V243L|WASF1_ENST00000392588.1_Missense_Mutation_p.V243L	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	243					actin filament polymerization (GO:0030041)|cellular component movement (GO:0006928)|lamellipodium morphogenesis (GO:0072673)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|Rac protein signal transduction (GO:0016601)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|lamellipodium (GO:0030027)|mitochondrial outer membrane (GO:0005741)|SCAR complex (GO:0031209)|synapse (GO:0045202)	protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		ATATGATCCACGTATGTCTGA	0.358																																					p.V243L		.											.	WASF1-90	0			c.G727T						.						100	92	95					6																	110424747		2203	4300	6503	SO:0001583	missense	8936	exon8			GATCCACGTATGT	D87459	CCDS5080.1	6q21	2010-08-20			ENSG00000112290	ENSG00000112290		"A-kinase anchor proteins"	12732	protein-coding gene	gene with protein product		605035				9843499, 9889097	Standard	XM_005267204		Approved	WAVE1, SCAR1, KIAA0269, WAVE	uc003pty.1	Q92558	OTTHUMG00000015357	ENST00000392589.1:c.727G>T	6.37:g.110424747C>A	ENSP00000376368:p.Val243Leu	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	70	4	NM_001024935	0	0	1	1	0	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	37	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612405	0.46631	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.51	5.51	0.81932	.	0.213000	0.48286	D	0.000185	T	0.12263	0.0298	N	0.08118	0	0.34639	D	0.720416	B	0.14012	0.009	B	0.09377	0.004	T	0.07366	-1.0776	10	0.10902	T	0.67	.	19.7791	0.96410	0.0:1.0:0.0:0.0	.	243	Q92558	WASF1_HUMAN	L	243	ENSP00000376365:V243L;ENSP00000376366:V243L;ENSP00000376368:V243L;ENSP00000376367:V243L;ENSP00000352425:V243L	ENSP00000352425:V243L	V	-	1	0	WASF1	110531440	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.456000	0.60081	2.763000	0.94921	0.650000	0.86243	GTG	.		0.358	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		A	110424747	C	A	110424747	3	1	72	1	0	0	0	0	1	0	0	0	17285	536	19	4	964	4	WASF1	6	110424747	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08	67011810	110424747	60690320	15	6804											
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121681010	121681010	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatgccaagcgccatgcagtGgggcctgttgtcgtccactg	6	10	13	12	2	0	0	0	0	0	0	2	0	1	0	4	2	3	2	4	2	2	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr7:121681010G>A	ENST00000393386.2	+	21	6189	c.5778G>A	c.(5776-5778)gtG>gtA	p.V1926V	PTPRZ1_ENST00000449182.1_Silent_p.V1059V	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1926	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GCCATGCAGTGGGGCCTGTTG	0.498																																					p.V1926V		.											.	PTPRZ1-699	0			c.G5778A						.						74	66	69					7																	121681010		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon21			TGCAGTGGGGCCT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5778G>A	7.37:g.121681010G>A		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	108	18	NM_002851	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			.		0.498	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121681010	G	A	121681010	2	1	72	1	0	0	0	0	0	0	0	1	12846	1335	47	2		2	PTPRZ1	7	121681010	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		121681010	37457653	16	6805											
MTBP	27085	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	121518998	121518998	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgctgggccacaaagagggtCctcgggactcaatcacattg	10	8	12	11	1	2	1	2	0	0	1	4	2	3	2	2	3	1	1	2	3	2	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr8:121518998C>T	ENST00000305949.1	+	16	1825	c.1780C>T	c.(1780-1782)Cct>Tct	p.P594S		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	594	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			CAAAGAGGGTCCTCGGGACTC	0.398																																					p.P594S		.											.	MTBP-228	0			c.C1780T						.						83	79	80					8																	121518998		2203	4300	6503	SO:0001583	missense	27085	exon16			GAGGGTCCTCGGG		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"MDM2 (mouse double minute 2)-binding protein, 104kD", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.1780C>T	8.37:g.121518998C>T	ENSP00000303398:p.Pro594Ser	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	84	6	NM_022045	0	0	4	4	0	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	37	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.586138	0.28268	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.44	4.55	0.56014	.	0.197586	0.44902	D	0.000417	T	0.49047	0.1534	L	0.60455	1.87	0.32183	N	0.58014	P	0.38078	0.617	B	0.33960	0.173	T	0.61978	-0.6951	9	0.46703	T	0.11	-8.4215	15.931	0.79659	0.0:0.8506:0.1494:0.0	.	594	Q96DY7	MTBP_HUMAN	S	594	.	ENSP00000303398:P594S	P	+	1	0	MTBP	121588179	1.000000	0.71417	0.997000	0.53966	0.864000	0.49448	2.735000	0.47377	1.267000	0.44247	0.563000	0.77884	CCT	.		0.398	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		T	121518998	C	T	121518998	3	4	72	1	0	0	0	0	1	0	0	0	9937	855	30	2	1842	2	MTBP	8	121518998	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		121518998	24845024	17	6806											
SLC35D2	11046	hgsc.bcm.edu	37	chr9	99122448	99122448	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactctaccttaatttacttGtgcttgataatccacttatg	10	18	4	9	0	1	1	0	1	1	0	2	1	2	1	2	0	4	1	2	0	6	9			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr9:99122448G>C	ENST00000253270.7	-	4	397	c.335C>G	c.(334-336)aCa>aGa	p.T112R	SLC35D2_ENST00000375259.4_Missense_Mutation_p.T112R|SLC35D2_ENST00000375257.1_Missense_Mutation_p.T112R|SLC35D2_ENST00000482643.1_5'UTR	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	112					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				TAATTTACTTGTGCTTGATAA	0.383																																					p.T112R		.											.	SLC35D2-90	0			c.C335G						.						114	102	106					9																	99122448		2203	4300	6503	SO:0001583	missense	11046	exon4			TTACTTGTGCTTG	AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.335C>G	9.37:g.99122448G>C	ENSP00000253270:p.Thr112Arg	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_007001	0	0	1	1	0	O95454|Q498C1|Q75W21|Q7Z5X5	Missense_Mutation	SNP	ENST00000253270.7	37	CCDS6717.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.955964	0.73902	.	.	ENSG00000130958	ENST00000253270;ENST00000375259;ENST00000375257	T;T;T	0.65549	0.48;-0.16;-0.15	4.81	4.81	0.61882	.	0.338511	0.29529	N	0.011888	T	0.80243	0.4587	M	0.82823	2.61	0.48901	D	0.999722	D;D	0.76494	0.999;0.991	D;D	0.83275	0.996;0.954	T	0.83281	-0.0038	10	0.87932	D	0	.	14.9045	0.70709	0.0:0.0:1.0:0.0	.	112;112	Q76EJ3-2;Q76EJ3	.;S35D2_HUMAN	R	112	ENSP00000253270:T112R;ENSP00000364408:T112R;ENSP00000364406:T112R	ENSP00000253270:T112R	T	-	2	0	SLC35D2	98162269	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.627000	0.61276	2.502000	0.84385	0.655000	0.94253	ACA	.		0.383	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			C	99122448	G	C	99122448	3	2	72	1	0	0	0	0	1	0	0	0	14614	1377	48	4	714	4	SLC35D2	9	99122448	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		99122448	42090983	18	6807											
CAMK1D	57118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	12811756	12811756	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtcaaaaatggagggcaaaGgagatgtgatgtccactgcc	13	8	13	7	0	1	2	1	1	0	1	2	4	2	3	2	3	1	1	2	3	3	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr10:12811756G>A	ENST00000378847.3	+	5	860	c.523G>A	c.(523-525)Gga>Aga	p.G175R	CAMK1D_ENST00000378845.1_Missense_Mutation_p.G175R	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		GGAGGGCAAAGGAGATGTGAT	0.458																																					p.G175R		.											.	CAMK1D-334	0			c.G523A						.						177	140	153					10																	12811756		2203	4300	6503	SO:0001583	missense	57118	exon5			GGCAAAGGAGATG	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.523G>A	10.37:g.12811756G>A	ENSP00000368124:p.Gly175Arg	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	92	17	NM_153498	0	0	0	0	0	B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	37	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892484	0.91889	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.65364	-0.15;-0.15	5.2	5.2	0.72013	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.115496	0.64402	D	0.000017	T	0.68796	0.3040	N	0.25060	0.705	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.79784	0.993;0.987	T	0.71912	-0.4449	10	0.52906	T	0.07	-14.2799	17.7041	0.88303	0.0:0.0:1.0:0.0	.	175;175	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	R	175	ENSP00000368124:G175R;ENSP00000368122:G175R	ENSP00000368122:G175R	G	+	1	0	CAMK1D	12851762	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.950000	0.87804	2.403000	0.81681	0.561000	0.74099	GGA	.		0.458	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		A	12811756	G	A	12811756	3	1	72	1	0	0	0	0	1	0	0	0	2603	1001	35	2	541	2	CAMK1D	10	12811756	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		12811756	122722991	19	6808											
MUC5B	727897	hgsc.bcm.edu;ucsc.edu	37	chr11	1253260	1253260	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaccagaaccaggctgaCgacttcacggccctcagcgg	10	6	10	15	3	3	2	3	1	0	1	3	3	3	2	3	3	3	1	3	3	2	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr11:1253260C>A	ENST00000529681.1	+	15	1771	c.1713C>A	c.(1711-1713)gaC>gaA	p.D571E	MUC5B_ENST00000447027.1_Missense_Mutation_p.D574E	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	571	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACCAGGCTGACGACTTCACGG	0.672																																					p.D571E		.											.	.	0			c.C1713A						.						42	50	48					11																	1253260		2049	4192	6241	SO:0001583	missense	727897	exon15			GGCTGACGACTTC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1713C>A	11.37:g.1253260C>A	ENSP00000436812:p.Asp571Glu	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254981	0.22965	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.65364	-0.15;-0.15	3.77	-5.54	0.02544	von Willebrand factor, type D domain (3);	.	.	.	.	D	0.83982	0.5372	H	0.98314	4.2	0.36992	D	0.894823	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.984;0.996;0.996	D	0.86512	0.1810	9	0.87932	D	0	.	12.6531	0.56772	0.0:0.2249:0.0:0.7751	.	571;1230;574	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	E	571;574;572;607	ENSP00000436812:D571E;ENSP00000415793:D574E	ENSP00000343037:D572E	D	+	3	2	MUC5B	1209836	0.027000	0.19231	0.934000	0.37439	0.455000	0.32408	-1.078000	0.03413	-1.179000	0.02737	-0.369000	0.07265	GAC	.		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1253260	C	A	1253260	3	1	72	1	0	0	0	0	1	0	0	0	10004	535	19	4	1780	4	MUC5B	11	1253260	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		1253260	133753256	20	6809											
OR5T2	219464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	56000140	56000140	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtagactctgggtgacatGctcactgaatacaggagagg	12	9	13	7	0	2	4	1	2	1	2	2	5	2	4	0	3	2	2	0	3	3	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr11:56000140G>T	ENST00000313264.4	-	1	597	c.522C>A	c.(520-522)agC>agA	p.S174R		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TGGGTGACATGCTCACTGAAT	0.433																																					p.S174R		.											.	OR5T2-70	0			c.C522A						.						201	169	180					11																	56000140		2201	4296	6497	SO:0001583	missense	219464	exon1			TGACATGCTCACT	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.522C>A	11.37:g.56000140G>T	ENSP00000323688:p.Ser174Arg	Somatic	194	1		WXS	Illumina HiSeq	Phase_I	217	50	NM_001004746	0	0	0	0	0	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	.	.	.	.	.	.	.	.	.	.	G	2.242	-0.373512	0.05034	.	.	ENSG00000181718	ENST00000313264	T	0.00446	7.39	5.07	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.718686	0.11856	N	0.522814	T	0.00210	0.0006	N	0.11651	0.15	0.18873	N	0.999985	B	0.09022	0.002	B	0.08055	0.003	T	0.35674	-0.9779	10	0.38643	T	0.18	.	3.4272	0.07414	0.1451:0.1394:0.5715:0.144	.	174	Q8NGG2	OR5T2_HUMAN	R	174	ENSP00000323688:S174R	ENSP00000323688:S174R	S	-	3	2	OR5T2	55756716	0.018000	0.18449	0.544000	0.28141	0.303000	0.27691	0.074000	0.14662	0.617000	0.30160	0.471000	0.43371	AGC	.		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		T	56000140	G	T	56000140	3	4	72	1	0	0	0	0	1	0	0	0	11208	1310	46	4	556	4	OR5T2	11	56000140	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	54746880	56000140	79006376	21	6810											
C11orf9	745	broad.mit.edu;bcgsc.ca	37	chr11	61544792	61544798	+	Frame_Shift_Del	DEL	GGTGCCC	GGTGCCC	-																															gtgttgtggcagcgggcacaGgtgcccgacaccgtcttcca																										TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	GGTGCCC	GGTGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr11:61544792_61544798delGGTGCCC	ENST00000278836.5	+	12	1743_1749	c.1647_1653delGGTGCCC	c.(1645-1653)caggtgcccfs	p.QVP549fs	MYRF_ENST00000389602.4_5'Flank|TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Frame_Shift_Del_p.QVP540fs|MYRF_ENST00000327797.1_Frame_Shift_Del_p.QVP174fs	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	549					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGCGGGCACAGGTGCCCGACACCGTCT	0.647																																					p.549_551del													.	.	0			c.1647_1653del						.																																			SO:0001589	frameshift_variant	745	exon12			GGCACAGGTGCCC		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"myelin gene regulatory factor"	608329	"chromosome 11 open reading frame 9"	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.1647_1653delGGTGCCC	11.37:g.61544792_61544798delGGTGCCC	ENSP00000278836:p.Gln549fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	60	6	NM_001127392	0	0	0	0	0	O43582|Q9P1Q6	Frame_Shift_Del	DEL	ENST00000278836.5	37	CCDS44622.1																																																																																			.		0.647	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		-	61544798	GGTGCCC	-	61544792	7	5	72	1	0	1	0	1	0	0	0	0	1675	991	35	0	1716	0	C11orf9	11	61544792	Frame_Shift_Del	DEL	GGTGCCC	TCGA-BQ-5888-01A-11D-1589-08	5544652	61544792	73461724	22	6811											
SLCO1B3	28234	broad.mit.edu	37	chr12	21030825	21030825	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cttacgtctttaaatatatgGagcaacagtacggtcagtct	12	13	8	8	2	3	0	1	0	2	0	3	1	3	1	0	2	4	2	0	2	7	6			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr12:21030825G>C	ENST00000381545.3	+	10	1309	c.1090G>C	c.(1090-1092)Gag>Cag	p.E364Q	LST3_ENST00000540229.1_Missense_Mutation_p.E364Q|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000381541.3_Intron|SLCO1B3_ENST00000553473.1_Missense_Mutation_p.E364Q|SLCO1B3_ENST00000261196.2_Missense_Mutation_p.E364Q	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	364					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TAAATATATGGAGCAACAGTA	0.353																																					p.E364Q													.	SLCO1B3-155	0			c.G1090C						.						136	136	136					12																	21030825		2203	4299	6502	SO:0001583	missense	28234	exon10			TATATGGAGCAAC		CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"Solute carriers"	10961	protein-coding gene	gene with protein product		605495	"solute carrier family 21 (organic anion transporter), member 8"	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1090G>C	12.37:g.21030825G>C	ENSP00000370956:p.Glu364Gln	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	168	4	NM_019844	0	0	0	0	0	E7EMT8|Q5JAR4	Missense_Mutation	SNP	ENST00000381545.3	37	CCDS8684.1	.	.	.	.	.	.	.	.	.	.	.	17.94	3.511137	0.64522	.	.	ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000111700;ENSG00000257046	ENST00000261196;ENST00000381545;ENST00000553473;ENST00000544370;ENST00000540229	T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56	3.13	3.13	0.36017	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83700	0.5311	M	0.84948	2.725	0.80722	D	1	D;D;D	0.89917	1.0;0.996;0.996	D;D;D	0.79108	0.992;0.989;0.974	D	0.86364	0.1719	10	0.87932	D	0	.	12.1271	0.53922	0.0:0.0:1.0:0.0	.	364;364;364	Q5JAR4;B3KP78;Q9NPD5	.;.;SO1B3_HUMAN	Q	364;364;364;188;364	ENSP00000261196:E364Q;ENSP00000370956:E364Q;ENSP00000451758:E364Q;ENSP00000443225:E188Q;ENSP00000441269:E364Q	ENSP00000441269:E364Q	E	+	1	0	SLCO1B3;RP11-545J16.1	20922092	1.000000	0.71417	0.180000	0.23079	0.187000	0.23431	7.557000	0.82243	1.585000	0.49928	0.305000	0.20034	GAG	.		0.353	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1	NM_019844		C	21030825	G	C	21030825	3	2	72	1	0	0	0	0	1	0	0	0	14756	1175	41	4	1120	4	SLCO1B3	12	21030825	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		21030825	112821070	23	6812											
CELA1	1990	hgsc.bcm.edu	37	chr12	51740415	51740415	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atatccacttaccataaaggAccagcatgttgccgatggag	13	9	9	10	1	0	0	0	0	0	0	1	3	1	2	4	2	3	2	4	2	4	4	rs370927847|rs386762976|rs55827519	byFrequency	TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr12:51740415A>C	ENST00000293636.1	-	1	48	c.8T>G	c.(7-9)gTc>gGc	p.V3G		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ACCATAAAGGACCAGCATGTT	0.512																																					p.V3G		.											.	CELA1-153	1	Deletion - Frameshift(1)	large_intestine(1)	c.T8G						.						198	125	149					12																	51740415		2199	4290	6489	SO:0001583	missense	1990	exon1			TAAAGGACCAGCA		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"elastase 1, pancreatic"	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.8T>G	12.37:g.51740415A>C	ENSP00000293636:p.Val3Gly	Somatic	81	1		WXS	Illumina HiSeq	Phase_I	80	4	NM_001971	0	0	0	0	0	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	37	CCDS8812.1	.	.	.	.	.	.	.	.	.	.	-	10.50	1.368338	0.24771	.	.	ENSG00000139610	ENST00000293636	D	0.89552	-2.53	3.61	0.701	0.18104	.	0.180867	0.43747	D	0.000529	T	0.82121	0.4968	L	0.55990	1.75	0.28932	N	0.891491	B	0.27823	0.19	B	0.26517	0.07	T	0.73855	-0.3851	10	0.87932	D	0	-1.5222	3.134	0.06433	0.3198:0.0:0.4933:0.1868	.	3	Q9UNI1	CELA1_HUMAN	G	3	ENSP00000293636:V3G	ENSP00000293636:V3G	V	-	2	0	CELA1	50026682	0.009000	0.17119	0.433000	0.26760	0.045000	0.14185	0.204000	0.17335	-0.043000	0.13513	-0.633000	0.03987	GTC	.		0.512	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		C	51740415	A	C	51740415	3	2	72	1	0	0	0	0	1	0	0	0	3216	275	10	5	800	5	CELA1	12	51740415	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08	30709590	51740415	82111480	24	6813											
TPCN1	53373	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113704162	113704162	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactccggcttggcatctatGtgagcgcacatgctcctcat	7	11	9	14	2	2	1	1	1	1	0	4	1	4	1	2	2	2	4	2	2	1	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr12:113704162G>T	ENST00000335509.6	+	4	728		c.e4+1		TPCN1_ENST00000550785.1_Splice_Site|TPCN1_ENST00000392569.4_Splice_Site|TPCN1_ENST00000541517.1_Splice_Site	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1						calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						TGGCATCTATGTGAGCGCACA	0.622																																					.													.	TPCN1-93	0			c.414+1G>T						.						112	127	122					12																	113704162		2203	4300	6503	SO:0001630	splice_region_variant	53373	exon4			ATCTATGTGAGCG	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.414+1G>T	12.37:g.113704162G>T		Somatic	353	2		WXS	Illumina HiSeq	Phase_I	384	73	NM_017901	0	0	0	1	1	A7E258|Q86XS9|Q8NC20	Splice_Site	SNP	ENST00000335509.6	37	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152622	0.38021	.	.	ENSG00000186815	ENST00000552642;ENST00000335509;ENST00000552897;ENST00000550785;ENST00000541517;ENST00000392569;ENST00000552542;ENST00000548465	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1947	0.93682	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TPCN1	112188545	1.000000	0.71417	0.989000	0.46669	0.005000	0.04900	9.428000	0.97476	2.532000	0.85374	0.561000	0.74099	.	.		0.622	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	Intron	T	113704162	G	T	113704162	5	4	72	1	0	0	0	0	0	0	1	0	16428	1391	48	4	645	4	TPCN1	12	113704162	Splice_Site	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	61963747	113704162	20147733	25	6814											
HERC1	8925	hgsc.bcm.edu	37	chr15	63929810	63929810	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aacactgtgccattggcctgGatgacaaaggtacaattctg	12	10	10	9	0	1	1	0	1	1	0	1	2	1	2	2	3	3	1	2	3	4	3	rs368460721		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr15:63929810G>C	ENST00000443617.2	-	64	12213	c.12126C>G	c.(12124-12126)atC>atG	p.I4042M		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4042					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CATTGGCCTGGATGACAAAGG	0.373																																					p.I4042M		.											.	HERC1-666	0			c.C12126G						.	G	MET/ILE	0,3740		0,0,1870	57	51	53		12126	1.8	1	15		53	1,8159		0,1,4079	no	missense	HERC1	NM_003922.3	10	0,1,5949	CC,CG,GG		0.0123,0.0,0.0084	probably-damaging	4042/4862	63929810	1,11899	1870	4080	5950	SO:0001583	missense	8925	exon64			GGCCTGGATGACA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12126C>G	15.37:g.63929810G>C	ENSP00000390158:p.Ile4042Met	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	8	3	NM_003922	0	0	0	1	1	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.214505	0.58452	0.0	1.23E-4	ENSG00000103657	ENST00000443617	D	0.87029	-2.2	4.92	1.77	0.24775	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.64402	U	0.000001	D	0.88800	0.6535	L	0.61218	1.895	0.52501	D	0.999954	D	0.59767	0.986	D	0.63283	0.913	D	0.86234	0.1639	10	0.87932	D	0	.	4.5728	0.12217	0.2168:0.0:0.5167:0.2665	.	4042	Q15751	HERC1_HUMAN	M	4042	ENSP00000390158:I4042M	ENSP00000390158:I4042M	I	-	3	3	HERC1	61716863	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.893000	0.28336	0.596000	0.29794	0.655000	0.94253	ATC	.		0.373	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	63929810	G	C	63929810	3	2	72	1	0	0	0	0	1	0	0	0	7078	1164	41	4	2519	4	HERC1	15	63929810	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		63929810	38601582	26	6815											
SNX1	6642	hgsc.bcm.edu	37	chr15	64426982	64426982	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacaagcctgataagctgcaGcaggccaaggacgagatcct	14	5	11	11	1	0	2	0	1	0	1	1	4	1	3	3	2	5	3	3	2	4	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr15:64426982G>A	ENST00000559844.1	+	12	1355	c.1341G>A	c.(1339-1341)caG>caA	p.Q447Q	SNX1_ENST00000561026.1_Silent_p.Q382Q|SNX1_ENST00000560829.1_Silent_p.Q229Q|SNX1_ENST00000353874.4_Intron|SNX1_ENST00000261889.5_Silent_p.Q447Q			Q13596	SNX1_HUMAN	sorting nexin 1	447	BAR.				early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						ATAAGCTGCAGCAGGCCAAGG	0.627																																					p.Q447Q		.											.	SNX1-226	0			c.G1341A						.						34	32	33					15																	64426982		2203	4300	6503	SO:0001819	synonymous_variant	6642	exon12			GCTGCAGCAGGCC	BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.1341G>A	15.37:g.64426982G>A		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_003099	0	0	52	52	0	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Silent	SNP	ENST00000559844.1	37	CCDS32266.1																																																																																			.		0.627	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		A	64426982	G	A	64426982	2	1	72	1	0	0	0	0	0	0	0	1	14912	962	34	2		2	SNX1	15	64426982	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	497172	64426982	38104410	27	6816											
METTL9	51108	hgsc.bcm.edu	37	chr16	21611192	21611192	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggtgggccggcggcggcCgcgggcggcaggaaggagaa	6	1	23	11	7	0	1	0	0	0	1	0	3	0	2	3	9	0	1	3	9	2	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr16:21611192C>G	ENST00000358154.3	+	1	396	c.138C>G	c.(136-138)gcC>gcG	p.A46A	METTL9_ENST00000396014.4_Silent_p.A46A	NM_001077180.1|NM_016025.3	NP_001070648.1|NP_057109.3	Q9H1A3	METL9_HUMAN	methyltransferase like 9	46	Poly-Ala.									endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	7				GBM - Glioblastoma multiforme(48;0.0759)		cggcggcggccgcgggcggcA	0.771																																					p.A46A		.											.	METTL9-91	0			c.C138G						.						3	4	3					16																	21611192		1579	3397	4976	SO:0001819	synonymous_variant	51108	exon1			GGCGGCCGCGGGC	NM_016025, AF151839	CCDS10598.2, CCDS45440.1	16p12.2	2008-11-06			ENSG00000197006	ENSG00000197006			24586	protein-coding gene	gene with protein product	"DORA reverse strand protein 1"	609388				10810093, 11132146	Standard	NM_001077180		Approved	DREV1	uc002dje.3	Q9H1A3	OTTHUMG00000131584	ENST00000358154.3:c.138C>G	16.37:g.21611192C>G		Somatic	4	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_016025	0	0	12	32	20	Q8NBT8|Q9BWJ7|Q9H1A2|Q9Y390	Silent	SNP	ENST00000358154.3	37	CCDS10598.2																																																																																			.		0.771	METTL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254465.1	NM_016025		G	21611192	C	G	21611192	2	3	72	1	0	0	0	0	0	0	0	1	9533	639	23	4		4	METTL9	16	21611192	Silent	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		21611192	68743561	28	6817											
ANKRD11	29123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89345492	89345492	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcactcaccacggggatgtgGagcttgctgagcggcttgcc	6	8	15	12	2	1	1	1	1	0	0	1	3	1	3	2	4	4	4	2	4	0	2	rs569755271		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr16:89345492G>A	ENST00000301030.4	-	9	7918	c.7458C>T	c.(7456-7458)ctC>ctT	p.L2486L	ANKRD11_ENST00000378330.2_Silent_p.L2486L	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2486					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CGGGGATGTGGAGCTTGCTGA	0.657																																					p.L2486L		.											.	ANKRD11-139	0			c.C7458T						.						25	22	23					16																	89345492		2197	4298	6495	SO:0001819	synonymous_variant	29123	exon9			GATGTGGAGCTTG	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7458C>T	16.37:g.89345492G>A		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	50	11	NM_001256183	0	0	0	0	0	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																			.		0.657	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89345492	G	A	89345492	2	1	72	1	0	0	0	0	0	0	0	1	639	1161	41	2		2	ANKRD11	16	89345492	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	67734300	89345492	1009261	29	6818											
SLFN11	91607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33679780	33679780	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaacaccctgggaccattcGgcttcaggaaatacctcgag	11	8	10	12	2	1	1	1	1	0	0	3	4	1	3	3	3	2	1	3	3	3	3	rs377363363		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr17:33679780G>A	ENST00000394566.1	-	7	2573	c.2301C>T	c.(2299-2301)gcC>gcT	p.A767A	SLFN11_ENST00000308377.4_Silent_p.A767A	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	767					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGGACCATTCGGCTTCAGGAA	0.443																																					p.A767A		.											.	SLFN11-159	0			c.C2301T						.	G	,,,,	0,4406		0,0,2203	65	61	62		2301,2301,2301,2301,2301	1.7	0	17		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	767/902,767/902,767/902,767/902,767/902	33679780	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	91607	exon5			CCATTCGGCTTCA	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2301C>T	17.37:g.33679780G>A		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	94	21	NM_152270	0	0	18	21	3	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	37	CCDS11294.1																																																																																			.		0.443	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33679780	G	A	33679780	2	1	72	1	0	0	0	0	0	0	0	1	14765	1103	39	1		1	SLFN11	17	33679780	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		33679780	47515430	30	6819											
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39191011	39191011	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggctggcagcagctggaGccgcatgtcccactggtgga	6	8	15	12	1	0	0	0	0	0	0	1	2	1	2	2	5	3	5	2	5	0	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr17:39191011G>C	ENST00000344363.5	-	1	96	c.63C>G	c.(61-63)ggC>ggG	p.G21G		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	21						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCAGCTGGAGCCGCATGTCC	0.587																																					p.G21G		.											.	.	0			c.C63G						.						42	50	47					17																	39191011		1973	4168	6141	SO:0001819	synonymous_variant	81850	exon1			GCTGGAGCCGCAT	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.63C>G	17.37:g.39191011G>C		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	65	5	NM_030966	0	0	0	0	0	Q07628|Q8IUG0|Q9BYS2	Silent	SNP	ENST00000344363.5	37	CCDS42323.1																																																																																			.		0.587	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			C	39191011	G	C	39191011	2	2	72	1	0	0	0	0	0	0	0	1	8524	958	34	4		4	KRTAP1-3	17	39191011	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	5511231	39191011	42004199	31	6820											
PTPRM	5797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	8379245	8379245	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggaaccatgagaaaaaccgGtgcatggacatcctgccccc	12	5	10	14	2	0	1	0	1	0	1	1	4	1	3	5	3	4	1	5	3	3	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr18:8379245G>A	ENST00000332175.8	+	26	4691	c.3654G>A	c.(3652-3654)cgG>cgA	p.R1218R	PTPRM_ENST00000400053.4_Silent_p.R1156R|PTPRM_ENST00000444013.1_Silent_p.R1005R|PTPRM_ENST00000400060.4_Silent_p.R1232R|PTPRM_ENST00000580170.1_Silent_p.R1231R	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1218	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AGAAAAACCGGTGCATGGACA	0.562																																					p.R1231R		.											.	PTPRM-228	0			c.G3693A						.						138	108	118					18																	8379245		2203	4300	6503	SO:0001819	synonymous_variant	5797	exon28			AAACCGGTGCATG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3654G>A	18.37:g.8379245G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	107	22	NM_001105244	0	0	23	38	15	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	37	CCDS11840.1																																																																																			.		0.562	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	8379245	G	A	8379245	2	1	72	1	0	0	0	0	0	0	0	1	12838	1248	44	2		2	PTPRM	18	8379245	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		8379245	69698003	32	6821											
PRTN3	5657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	841048	841048	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccctgccctggcgtccgtgCtgctggccttgctgctgagc	1	10	14	16	2	0	1	0	1	0	0	1	1	1	1	4	2	6	4	4	2	0	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:841048C>T	ENST00000234347.5	+	1	86	c.40C>T	c.(40-42)Ctg>Ttg	p.L14L	PRTN3_ENST00000544537.2_5'Flank	NM_002777.3	NP_002768.3	P24158	PRTN3_HUMAN	proteinase 3	14					collagen catabolic process (GO:0030574)|mature dendritic cell differentiation (GO:0097029)|negative regulation of phagocytosis (GO:0050765)|positive regulation of cell proliferation (GO:0008284)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|ovary(2)|urinary_tract(1)	4		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGTCCGTGCTGCTGGCCTT	0.657																																					p.L14L		.											.	PRTN3-91	0			c.C40T						.						32	30	31					19																	841048		2202	4300	6502	SO:0001819	synonymous_variant	5657	exon1			TCCGTGCTGCTGG		CCDS32860.1	19p13.3	2008-07-31	2008-07-31			ENSG00000196415			9495	protein-coding gene	gene with protein product	"myeloblastin", "serine proteinase, neutrophil", "Wegener granulomatosis autoantigen"	177020				2258701	Standard	NM_002777		Approved	PR-3, ACPA, C-ANCA, AGP7, MBT, P29	uc002lqa.1	P24158		ENST00000234347.5:c.40C>T	19.37:g.841048C>T		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	49	12	NM_002777	0	0	0	0	0	P15637|P18078|Q4VB08|Q4VB09|Q6LBM7|Q6LBN2|Q9UD25|Q9UQD8	Silent	SNP	ENST00000234347.5	37	CCDS32860.1																																																																																			.		0.657	PRTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457888.2	NM_002777		T	841048	C	T	841048	2	4	72	1	0	0	0	0	0	0	0	1	12668	796	28	2		2	PRTN3	19	841048	Silent	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		841048	58287935	33	6822											
NDUFA11	126328	ucsc.edu	37	chr19	5897010	5897010	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggcagcggcggtcaggccTgcgagacagaggagggaggc	9	3	20	9	3	1	2	1	0	0	2	1	5	1	4	1	7	2	1	1	7	1	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:5897010T>A	ENST00000308961.4	-	2	145		c.e2-2		AC104532.3_ENST00000589277.1_RNA|AC104532.3_ENST00000590441.1_RNA|NDUFA11_ENST00000592634.1_Splice_Site|AC024592.12_ENST00000586349.1_Splice_Site|NDUFA11_ENST00000418389.2_Splice_Site|FUT5_ENST00000252675.5_Splice_Site	NM_175614.4	NP_783313.1	Q86Y39	NDUAB_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 11, 14.7kDa						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)				central_nervous_system(1)|lung(1)	2						CGGTCAGGCCTGCGAGACAGA	0.612																																					.													.	NDUFA11-90	0			c.98-2A>T						.						118	102	108					19																	5897010		2203	4300	6503	SO:0001630	splice_region_variant	126328	exon3			CAGGCCTGCGAGA	AJ539081	CCDS12155.1, CCDS54203.1	19p13.3	2011-07-04				ENSG00000174886		"Mitochondrial respiratory chain complex / Complex I"	20371	protein-coding gene	gene with protein product	"complex I B14.7 subunit"	612638				12381726	Standard	NM_001193375		Approved	B14.7	uc002mdp.2	Q86Y39		ENST00000308961.4:c.98-2A>T	19.37:g.5897010T>A		Somatic	81	1		WXS	Illumina HiSeq		102	1	NM_001193375	0	0	2	2	0	C9JT23|Q6ZS66	Splice_Site	SNP	ENST00000308961.4	37	CCDS12155.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.620763	0.46736	.	.	ENSG00000174886	ENST00000418389;ENST00000308961	.	.	.	3.96	3.96	0.45880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5079	0.39058	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NDUFA11	5848010	0.976000	0.34144	0.906000	0.35671	0.227000	0.25037	2.368000	0.44222	1.583000	0.49898	0.334000	0.21626	.	.		0.612	NDUFA11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452218.1	NM_175614	Intron	A	5897010	T	A	5897010	5	1	72	1	0	0	0	0	0	0	1	0	10287	1594	55	5	341	5	NDUFA11	19	5897010	Splice_Site	SNP	T	TCGA-BQ-5888-01A-11D-1589-08	5055962	5897010	53231973	34	6823											
HNRNPL	3191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39336576	39336576	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcatccgagtccccagggcGggagatcttctggctggtag	6	9	15	11	2	3	1	1	0	2	1	5	3	5	1	3	4	0	2	3	4	1	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:39336576G>C	ENST00000221419.5	-	3	907	c.541C>G	c.(541-543)Cgc>Ggc	p.R181G	HNRNPL_ENST00000600873.1_Missense_Mutation_p.R48G|AC008982.2_ENST00000600473.1_RNA	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	181					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TCCCCAGGGCGGGAGATCTTC	0.542																																					p.R181G		.											.	HNRNPL-22	0			c.C541G						.						117	115	115					19																	39336576		2203	4300	6503	SO:0001583	missense	3191	exon3			CAGGGCGGGAGAT	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"RNA binding motif (RRM) containing"	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.541C>G	19.37:g.39336576G>C	ENSP00000221419:p.Arg181Gly	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	227	31	NM_001533	0	0	37	82	45	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	37	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.004874	0.54254	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750;ENST00000423415;ENST00000536292	.	.	.	5.39	5.39	0.77823	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.69655	0.3135	M	0.74258	2.255	0.58432	D	0.999995	B	0.18461	0.028	B	0.20767	0.031	T	0.68812	-0.5310	9	0.66056	D	0.02	.	17.9088	0.88928	0.0:0.0:1.0:0.0	.	181	P14866	HNRPL_HUMAN	G	181;48;48;48;109	.	ENSP00000221419:R181G	R	-	1	0	HNRNPL	44028416	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	5.035000	0.64158	2.541000	0.85698	0.462000	0.41574	CGC	.		0.542	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			C	39336576	G	C	39336576	3	2	72	1	0	0	0	0	1	0	0	0	7291	1116	39	4	1272	4	HNRNPL	19	39336576	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	33439566	39336576	19792407	35	6824											
TRPM4	54795	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	49703680	49703680	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcccaagatcgtcatcgtGagcaagatggtgaggcaggg	10	6	17	8	2	1	4	1	2	0	2	3	4	1	4	1	4	1	2	1	4	2	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:49703680G>T	ENST00000252826.5	+	18	2895	c.2769G>T	c.(2767-2769)gtG>gtT	p.V923V	TRPM4_ENST00000427978.2_Silent_p.V778V|TRPM4_ENST00000355712.5_Silent_p.V569V	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	923					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		TCGTCATCGTGAGCAAGATGG	0.612																																					p.V923V		.											.	TRPM4-91	0			c.G2769T						.						35	33	34					19																	49703680		2203	4300	6503	SO:0001819	synonymous_variant	54795	exon18			CATCGTGAGCAAG	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.2769G>T	19.37:g.49703680G>T		Somatic	41	1		WXS	Illumina HiSeq	Phase_I	43	10	NM_017636	0	0	0	0	0	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	37	CCDS33073.1																																																																																			.		0.612	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49703680	G	T	49703680	2	4	72	1	0	0	0	0	0	0	0	1	16621	1277	45	4		4	TRPM4	19	49703680	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	10367104	49703680	9425303	36	6825											
LILRA6	79168	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	54745734	54745734	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggctgggcagggctgagaGggtgggtttgttgtagaatc	7	10	20	4	0	0	2	0	1	0	2	1	3	0	2	0	5	0	6	0	5	2	3			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:54745734G>T	ENST00000396365.2	-	4	415	c.376C>A	c.(376-378)Ctc>Atc	p.L126I	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.L126I|LILRA6_ENST00000440558.2_Missense_Mutation_p.L126I|LILRA6_ENST00000245621.5_Missense_Mutation_p.L126I|LILRA6_ENST00000391735.3_Missense_Mutation_p.L126I|LILRA6_ENST00000270464.5_Missense_Mutation_p.L126I	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	126					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.L126F(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGGGCTGAGAGGGTGGGTTTG	0.567																																					p.L126I		.											.	LILRA6-24	2	Substitution - Missense(2)	lung(2)	c.C376A						.						62	102	89					19																	54745734		2108	4294	6402	SO:0001583	missense	79168	exon4			CTGAGAGGGTGGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15495	protein-coding gene	gene with protein product			"leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.376C>A	19.37:g.54745734G>T	ENSP00000379651:p.Leu126Ile	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	64	23	NM_024318	0	0	1	1	0		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212570	0.58452	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.01981	5.38;5.38;5.38;4.52;5.38;5.38	3.4	3.4	0.38934	Immunoglobulin-like fold (1);	0.278862	0.25747	N	0.028562	T	0.11153	0.0272	M	0.81942	2.565	0.23546	N	0.997443	D;P;D;D;D;D	0.76494	0.995;0.947;0.982;0.997;0.997;0.999	D;D;D;D;D;D	0.81914	0.986;0.959;0.949;0.987;0.995;0.995	T	0.00984	-1.1491	10	0.87932	D	0	.	10.5189	0.44907	0.0:0.0:1.0:0.0	.	126;126;126;126;126;126	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	I	126	ENSP00000390120:L126I;ENSP00000270464:L126I;ENSP00000411227:L126I;ENSP00000375615:L126I;ENSP00000379651:L126I;ENSP00000245621:L126I	ENSP00000245621:L126I	L	-	1	0	LILRA6	59437546	0.011000	0.17503	0.553000	0.28255	0.078000	0.17371	1.276000	0.33156	1.936000	0.56123	0.184000	0.17185	CTC	.		0.567	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		T	54745734	G	T	54745734	3	4	72	1	0	0	0	0	1	0	0	0	8811	1000	35	4	1089	4	LILRA6	19	54745734	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	5042054	54745734	4383249	37	6826											
ZNF446	55663	hgsc.bcm.edu	37	chr19	58991385	58991385	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcagaagcctgcgctcGggtgagtgccccacaccatc	7	7	12	15	2	1	2	0	1	1	1	3	2	1	2	4	1	4	2	4	1	1	0	rs372496370	byFrequency	TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:58991385G>A	ENST00000594369.1	+	6	1182	c.801G>A	c.(799-801)tcG>tcA	p.S267S	ZNF446_ENST00000335841.4_Splice_Site_p.R239Q|ZNF446_ENST00000596341.1_Splice_Site_p.S267S	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	267					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GCCTGCGCTCGGGTGAGTGCC	0.677													G|||	5	0.000998403	0.003	0	5008	,	,		14880	0		0	False		,,,				2504	0.001				p.S267S		.											.	ZNF446-91	0			c.G801A						.	G		3,4347		0,3,2172	9	11	10		801	-5.9	0.1	19		10	0,8546		0,0,4273	no	coding-synonymous-near-splice	ZNF446	NM_017908.2		0,3,6445	AA,AG,GG		0.0,0.069,0.0233		267/451	58991385	3,12893	2175	4273	6448	SO:0001630	splice_region_variant	55663	exon6			GCGCTCGGGTGAG		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"Zinc fingers, C2H2-type", "-", "-", "-"	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.802+1G>A	19.37:g.58991385G>A		Somatic	12	1		WXS	Illumina HiSeq	Phase_I	11	7	NM_017908	0	0	2	2	0		Silent	SNP	ENST00000594369.1	37	CCDS12982.1																																																																																			.		0.677	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	Silent	A	58991385	G	A	58991385	5	1	72	1	0	0	0	0	0	0	1	0	17951	1130	39	1	819	1	ZNF446	19	58991385	Splice_Site	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	4245651	58991385	137598	38	6827											
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981411	61981411	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcctgggtgccgtggggcGggcggcagggtccaggcgag	3	5	23	10	4	0	0	0	0	0	0	1	1	1	0	3	7	2	1	3	7	0	0	rs55915440	byFrequency	TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr20:61981411G>A	ENST00000370263.4	-	5	1573	c.1352C>T	c.(1351-1353)cCg>cTg	p.P451L	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	451					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCCGTGGGGCGGGCGGCAGGG	0.711													G|||	9	0.00179712	0	0.0029	5008	,	,		12301	0		0.004	False		,,,				2504	0.0031				p.P451L		.											.	CHRNA4-91	0			c.C1352T						.	G	LEU/PRO	1,4185		0,1,2092	6	6	6		1352	2.6	0	20	dbSNP_129	6	20,8254		0,20,4117	no	missense	CHRNA4	NM_000744.5	98	0,21,6209	AA,AG,GG		0.2417,0.0239,0.1685	benign	451/628	61981411	21,12439	2093	4137	6230	SO:0001583	missense	1137	exon5			TGGGGCGGGCGGC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.1352C>T	20.37:g.61981411G>A	ENSP00000359285:p.Pro451Leu	Somatic	9	1		WXS	Illumina HiSeq	Phase_I	10	6	NM_000744	0	0	0	0	0	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	37	CCDS13517.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	3.039	-0.197981	0.06219	2.39E-4	0.002417	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.76578	-1.03	4.65	2.6	0.31112	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.565980	0.03236	N	0.179688	T	0.72669	0.3489	L	0.47716	1.5	0.20703	N	0.999863	B;B	0.11235	0.004;0.004	B;B	0.10450	0.005;0.001	T	0.53556	-0.8422	10	0.48119	T	0.1	.	5.8657	0.18773	0.1788:0.1724:0.6487:0.0	rs55915440	380;451	Q4VAQ5;P43681	.;ACHA4_HUMAN	L	357;451;380	ENSP00000359285:P451L	ENSP00000359280:P357L	P	-	2	0	CHRNA4	61451855	0.640000	0.27243	0.001000	0.08648	0.001000	0.01503	1.128000	0.31369	0.354000	0.24105	-0.211000	0.12701	CCG	G|0.999;A|0.001		0.711	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			A	61981411	G	A	61981411	3	1	72	1	0	0	0	0	1	0	0	0	3391	1116	39	1	539	1	CHRNA4	20	61981411	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		61981411	1044109	39	6828											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43298959	43298959	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggggccgcgggccggggCggcgaagaccctgcgccgcg	3	1	21	16	10	0	1	0	0	0	1	0	2	0	1	4	6	1	0	4	6	1	0	rs375565529		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr21:43298959C>G	ENST00000269844.3	-	3	368	c.258G>C	c.(256-258)ccG>ccC	p.P86P	PRDM15_ENST00000398548.1_Intron|PRDM15_ENST00000538201.1_Intron|AP001619.2_ENST00000432411.1_RNA|PRDM15_ENST00000422911.1_Intron	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	86					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						cgggccggggcggcgaagacc	0.861																																					p.P86P		.											.	PRDM15-90	0			c.G258C						.						1	1	1					21																	43298959		34	112	146	SO:0001819	synonymous_variant	63977	exon3			CCGGGGCGGCGAA	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.258G>C	21.37:g.43298959C>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_022115	0	0	0	0	0	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			.		0.861	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		G	43298959	C	G	43298959	2	3	72	1	0	0	0	0	0	0	0	1	12485	755	27	4		4	PRDM15	21	43298959	Silent	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		43298959	4830936	40	6829											
KRTAP10-3	386682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45978127	45978127	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcggcagaggagggacaCggaggaggagggtctgcagc	9	2	23	7	2	1	1	0	0	1	1	1	6	1	6	0	9	2	2	0	9	0	0	rs369545090		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr21:45978127C>T	ENST00000391620.1	-	1	516	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	158	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						AGGAGGGACACGGAGGAGGAG	0.692																																					p.V158M		.											.	KRTAP10-3-91	0			c.G472A						.	C	MET/VAL,	1,4405	2.1+/-5.4	0,1,2202	89	96	93		472,	2.6	0.6	21		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	TSPEAR,KRTAP10-3	NM_198696.2,NM_144991.2	21,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,	158/222,	45978127	2,13004	2203	4300	6503	SO:0001583	missense	386682	exon1			GGGACACGGAGGA	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"Keratin associated proteins"	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.472G>A	21.37:g.45978127C>T	ENSP00000375478:p.Val158Met	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	152	31	NM_198696	0	0	0	0	0	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	.	.	.	.	.	.	.	.	.	.	c	3.276	-0.148013	0.06627	2.27E-4	1.16E-4	ENSG00000212935	ENST00000391620	T	0.01438	4.89	3.53	2.61	0.31194	.	.	.	.	.	T	0.05823	0.0152	M	0.84948	2.725	0.09310	N	1	D	0.59357	0.985	P	0.53593	0.73	T	0.14144	-1.0483	9	0.59425	D	0.04	.	9.6661	0.39986	0.0:0.5593:0.4407:0.0	.	158	P60369	KR103_HUMAN	M	158	ENSP00000375478:V158M	ENSP00000375478:V158M	V	-	1	0	KRTAP10-3	44802555	0.060000	0.20803	0.577000	0.28562	0.005000	0.04900	0.116000	0.15561	0.772000	0.33382	0.561000	0.74099	GTG	.		0.692	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			T	45978127	C	T	45978127	3	4	72	1	0	0	0	0	1	0	0	0	8531	536	19	1	197	1	KRTAP10-3	21	45978127	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08	2679168	45978127	2151768	41	6830											
GTSE1	51512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46724721	46724721	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagcgattctactttctccAaaagtactgccacagaagta	15	10	6	10	1	2	1	0	0	2	1	3	2	2	1	2	0	4	2	2	0	7	5			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr22:46724721A>C	ENST00000454366.1	+	10	2073	c.1861A>C	c.(1861-1863)Aaa>Caa	p.K621Q		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	602					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TACTTTCTCCAAAAGTACTGC	0.567																																					p.K621Q	GBM(153;542 1915 12487 29016 50495)	.											.	GTSE1-187	0			c.A1861C						.						88	95	93					22																	46724721		2203	4300	6503	SO:0001583	missense	51512	exon10			TTCTCCAAAAGTA	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1861A>C	22.37:g.46724721A>C	ENSP00000415430:p.Lys621Gln	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	255	43	NM_016426	0	0	0	1	1	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	7.057	0.565524	0.13560	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07021	3.23	4.41	-0.765	0.11023	.	0.925293	0.09363	N	0.812463	T	0.03871	0.0109	N	0.12471	0.22	0.09310	N	1	B;B	0.25312	0.123;0.123	B;B	0.21360	0.023;0.034	T	0.45687	-0.9244	10	0.25751	T	0.34	-5.7757	4.1358	0.10170	0.3102:0.4118:0.278:0.0	.	602;581	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	Q	621;581	ENSP00000415430:K621Q	ENSP00000354634:K581Q	K	+	1	0	GTSE1	45103385	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.240000	0.08952	-0.032000	0.13758	0.533000	0.62120	AAA	.		0.567	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		C	46724721	A	C	46724721	3	2	72	1	0	0	0	0	1	0	0	0	6906	131	5	5	1895	5	GTSE1	22	46724721	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08		46724721	4579845	42	6831											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350698	50350698	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctctgcctcctcctcCtcctcttcctcttcctcttc	0	17	1	23	0	4	0	0	0	4	0	13	0	12	0	9	0	1	0	9	0	0	3			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chrX:50350698C>T	ENST00000289292.7	-	6	3727	c.3444G>A	c.(3442-3444)gaG>gaA	p.E1148E	SHROOM4_ENST00000460112.3_Silent_p.E1032E|SHROOM4_ENST00000376020.2_Silent_p.E1148E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1148	Glu-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctcctcctcctcctcttcct	0.557													C|||	1	0.000264901	0	0.0014	3775	,	,		12007	0		0	False		,,,				2504	0				p.E1148E		.											.	SHROOM4-131	0			c.G3444A						.						22	20	21					X																	50350698		2203	4298	6501	SO:0001819	synonymous_variant	57477	exon6			CTCCTCCTCCTCT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3444G>A	X.37:g.50350698C>T		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_020717	0	0	0	0	0	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																			.		0.557	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50350698	C	T	50350698	2	4	72	1	0	0	0	0	0	0	0	1	14328	680	24	2		2	SHROOM4	23	50350698	Silent	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		50350698	104919862	43	6832											
IRS4	8471	broad.mit.edu	37	chrX	107978243	107978243	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttcggggcttctgcagggtgCcggggacgtgctgggctggg	2	9	21	9	3	1	0	0	0	1	0	2	1	1	1	1	7	3	4	1	7	0	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chrX:107978243C>T	ENST00000372129.2	-	1	1408	c.1332G>A	c.(1330-1332)cgG>cgA	p.R444R	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	444					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CTGCAGGGTGCCGGGGACGTG	0.617																																					p.R444R													.	IRS4-623	0			c.G1332A						.						65	63	64					X																	107978243		2203	4300	6503	SO:0001819	synonymous_variant	8471	exon1			AGGGTGCCGGGGA	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1332G>A	X.37:g.107978243C>T		Somatic	194	0		WXS	Illumina HiSeq	Phase_I	197	5	NM_003604	0	0	0	0	0		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			.		0.617	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107978243	C	T	107978243	2	4	72	1	0	0	0	0	0	0	0	1	7863	726	26	2		2	IRS4	23	107978243	Silent	SNP	C	TCGA-BQ-5888-01A-11D-1589-08	57627545	107978243	47292317	44	6833											
MIIP	60672	hgsc.bcm.edu	37	chr1	12089880	12089880	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgcctgtggatcccggtacCccctgccgcctgtgcaggac	4	8	13	16	2	0	0	0	0	0	0	1	2	1	2	6	3	4	2	6	3	1	1			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:12089880C>T	ENST00000235332.4	+	7	943	c.774C>T	c.(772-774)acC>acT	p.T258T	MIIP_ENST00000436478.2_Silent_p.T258T|MIIP_ENST00000466860.1_3'UTR	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	258	Interaction with IGFBP2.									autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						ATCCCGGTACCCCCTGCCGCC	0.662																																					p.T258T		.											.	MIIP-91	0			c.C774T						.						47	44	45					1																	12089880		2203	4299	6502	SO:0001819	synonymous_variant	60672	exon7			CGGTACCCCCTGC	AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"invasion inhibitory protein 45"	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.774C>T	1.37:g.12089880C>T		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_021933	0	0	33	33	0	C0KL22|Q96HU6|Q9H839|Q9HA00	Silent	SNP	ENST00000235332.4	37	CCDS143.1																																																																																			.		0.662	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933		T	12089880	C	T	12089880	2	4	73	1	0	0	0	0	0	0	0	1	9610	610	22	2		2	MIIP	1	12089880	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08		12089880	237160741	1	6834											
PHACTR4	65979	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	28800653	28800653	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcttcccatcactattgaaAtgctaaaagtgtaagtgcct	12	13	6	10	0	2	1	1	1	1	0	3	1	3	1	2	0	2	2	2	0	5	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:28800653A>T	ENST00000373839.3	+	7	1672	c.1411A>T	c.(1411-1413)Atg>Ttg	p.M471L	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.M481L	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	471					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		CACTATTGAAATGCTAAAAGT	0.413																																					p.M481L		.											.	PHACTR4-90	0			c.A1441T						.						102	103	103					1																	28800653		1898	4120	6018	SO:0001583	missense	65979	exon6			ATTGAAATGCTAA	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1411A>T	1.37:g.28800653A>T	ENSP00000362945:p.Met471Leu	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	214	19	NM_023923	0	0	0	0	0	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	A	4.322	0.059030	0.08339	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.21191	2.02;2.02	5.75	4.55	0.56014	.	0.347042	0.36134	N	0.002762	T	0.13286	0.0322	N	0.20401	0.57	0.30856	N	0.734034	B;B	0.19073	0.033;0.009	B;B	0.18871	0.023;0.004	T	0.06972	-1.0797	10	0.27785	T	0.31	-6.0179	10.959	0.47374	0.7173:0.2827:0.0:0.0	.	481;471	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	L	471;481;470	ENSP00000362945:M471L;ENSP00000362942:M481L	ENSP00000362942:M481L	M	+	1	0	PHACTR4	28673240	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.932000	0.56537	2.190000	0.69967	0.533000	0.62120	ATG	.		0.413	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		T	28800653	A	T	28800653	3	4	73	1	0	0	0	0	1	0	0	0	11838	101	4	5	1483	5	PHACTR4	1	28800653	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	16710773	28800653	220449968	2	6835											
FAM151A	338094	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	55077293	55077293	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttacaggccagctgcttgAactgtgacaggagaggctca	10	8	12	11	0	1	3	1	2	0	1	1	4	1	3	2	3	4	3	2	3	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:55077293A>C	ENST00000302250.2	-	6	1086	c.926T>G	c.(925-927)tTc>tGc	p.F309C	FAM151A_ENST00000371304.2_Intron|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	309						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CAGCTGCTTGAACTGTGACAG	0.567																																					p.F309C		.											.	FAM151A-90	0			c.T926G						.						127	111	116					1																	55077293		2203	4300	6503	SO:0001583	missense	338094	exon6			TGCTTGAACTGTG	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 179"	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.926T>G	1.37:g.55077293A>C	ENSP00000306888:p.Phe309Cys	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	157	9	NM_176782	0	0	0	0	0	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	37	CCDS594.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.560447	0.65538	.	.	ENSG00000162391	ENST00000302250	T	0.15017	2.46	4.59	4.59	0.56863	.	0.064498	0.64402	D	0.000009	T	0.30198	0.0757	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.68192	0.956	T	0.03413	-1.1039	10	0.87932	D	0	-31.1715	13.3708	0.60711	1.0:0.0:0.0:0.0	.	309	Q8WW52	F151A_HUMAN	C	309	ENSP00000306888:F309C	ENSP00000306888:F309C	F	-	2	0	FAM151A	54849881	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	6.952000	0.75989	2.039000	0.60335	0.533000	0.62120	TTC	.		0.567	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782		C	55077293	A	C	55077293	3	2	73	1	0	0	0	0	1	0	0	0	5474	246	9	5	843	5	FAM151A	1	55077293	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	26276640	55077293	194173328	3	6836											
SSX2IP	117178	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	85121610	85121610	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagggaccattcttctttgaGacgttccttttcttccaaca	9	15	6	11	1	3	1	0	1	3	1	5	3	5	2	3	1	1	1	3	1	2	7			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:85121610G>A	ENST00000342203.3	-	11	1557	c.1294C>T	c.(1294-1296)Ctc>Ttc	p.L432F	SSX2IP_ENST00000437941.2_Missense_Mutation_p.L405F|SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000370612.4_Missense_Mutation_p.L432F|SSX2IP_ENST00000605755.1_Missense_Mutation_p.L405F	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	432					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TCTTCTTTGAGACGTTCCTTT	0.388																																					p.L432F		.											.	SSX2IP-92	0			c.C1294T						.						86	85	86					1																	85121610		2203	4300	6503	SO:0001583	missense	117178	exon11			CTTTGAGACGTTC		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1294C>T	1.37:g.85121610G>A	ENSP00000340279:p.Leu432Phe	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	82	6	NM_001166293	0	0	13	13	0	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	CCDS699.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495910	0.85069	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.67345	-0.21;-0.26	5.07	5.07	0.68467	.	0.116998	0.64402	D	0.000014	T	0.71392	0.3334	M	0.62723	1.935	0.49798	D	0.999822	D;D;D	0.67145	0.996;0.987;0.987	P;P;P	0.56474	0.799;0.635;0.635	T	0.72064	-0.4403	10	0.49607	T	0.09	-20.4465	18.6376	0.91384	0.0:0.0:1.0:0.0	.	428;432;405	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	F	432;405;428;432	ENSP00000340279:L432F;ENSP00000412781:L405F	ENSP00000340279:L432F	L	-	1	0	SSX2IP	84894198	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.237000	0.65360	2.648000	0.89879	0.591000	0.81541	CTC	.		0.388	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		A	85121610	G	A	85121610	3	1	73	1	0	0	0	0	1	0	0	0	15236	942	33	2	566	2	SSX2IP	1	85121610	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	30044317	85121610	164129011	4	6837											
TXNIP	10628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145439917	145439917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggtggatgtcaatacccctGatttaatggtgagatccatt	10	14	10	7	0	1	2	1	2	0	1	2	4	2	3	3	3	1	0	3	3	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:145439917G>A	ENST00000369317.4	+	3	797	c.463G>A	c.(463-465)Gat>Aat	p.D155N	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	155					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAATACCCCTGATTTAATGGT	0.428																																					p.D155N		.											.	TXNIP-92	0			c.G463A						.						86	92	90					1																	145439917		2202	4299	6501	SO:0001583	missense	10628	exon3			ACCCCTGATTTAA	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"upregulated by 1,25-dihydroxyvitamin D-3", "thioredoxin binding protein 2"	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.463G>A	1.37:g.145439917G>A	ENSP00000358323:p.Asp155Asn	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	171	19	NM_006472	0	0	4	6	2	B4E3D3|Q16226|Q6PML0|Q9BXG9	Missense_Mutation	SNP	ENST00000369317.4	37	CCDS913.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529556	0.64860	.	.	ENSG00000117289	ENST00000369317;ENST00000425134	T;T	0.11169	3.17;2.8	5.27	5.27	0.74061	Immunoglobulin E-set (1);	0.048081	0.85682	D	0.000000	T	0.06371	0.0164	N	0.25485	0.75	0.80722	D	1	P;P	0.51791	0.938;0.948	P;P	0.49528	0.532;0.614	T	0.46034	-0.9220	10	0.15499	T	0.54	-0.5065	16.4254	0.83813	0.0:0.0:1.0:0.0	.	100;155	B4E3D3;Q9H3M7	.;TXNIP_HUMAN	N	155;100	ENSP00000358323:D155N;ENSP00000396322:D100N	ENSP00000358323:D155N	D	+	1	0	TXNIP	144151274	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.243000	0.78219	2.753000	0.94483	0.651000	0.88453	GAT	.		0.428	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		A	145439917	G	A	145439917	3	1	73	1	0	0	0	0	1	0	0	0	16836	1290	45	2	473	2	TXNIP	1	145439917	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	60318307	145439917	103810704	5	6838											
INSRR	3645	broad.mit.edu	37	chr1	156816378	156816378	+	Frame_Shift_Del	DEL	G	G	-																															tgagggctgtcctcctcagtGgttagcgtgatggcccgcac																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:156816378delG	ENST00000368195.3	-	8	2139	c.1743delC	c.(1741-1743)accfs	p.T582fs	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	582	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTCCTCAGTGGTTAGCGTGA	0.607																																					p.T581fs													.	INSRR-1403	0			c.1743delC						.						131	96	108					1																	156816378		2203	4300	6503	SO:0001589	frameshift_variant	3645	exon8			CTCAGTGGTTAGC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.1743delC	1.37:g.156816378delG	ENSP00000357178:p.Thr582fs	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	68	6	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Frame_Shift_Del	DEL	ENST00000368195.3	37	CCDS1160.1																																																																																			.		0.607	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		-	156816378	G	-	156816378	7	5	73	1	0	1	0	1	0	0	0	0	7795	1335	47	0	2209	0	INSRR	1	156816378	Frame_Shift_Del	DEL	G	TCGA-BQ-5889-01A-11D-1589-08	11376461	156816378	92434243	6	6839											
PYHIN1	149628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158912063	158912063	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcttctgtatctgaagcTggtcctgaccaaacgtttga	8	13	9	11	1	3	3	0	3	3	0	4	3	4	3	3	1	2	3	3	1	3	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:158912063T>G	ENST00000368140.1	+	5	1121	c.876T>G	c.(874-876)gcT>gcG	p.A292A	PYHIN1_ENST00000392254.2_Silent_p.A292A|PYHIN1_ENST00000392252.3_Silent_p.A283A|PYHIN1_ENST00000368138.3_Silent_p.A283A|PYHIN1_ENST00000485134.1_3'UTR	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	292	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					TATCTGAAGCTGGTCCTGACC	0.353																																					p.A292A		.											.	PYHIN1-94	0			c.T876G						.						49	50	50					1																	158912063		2203	4298	6501	SO:0001819	synonymous_variant	149628	exon5			TGAAGCTGGTCCT	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.876T>G	1.37:g.158912063T>G		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	72	8	NM_152501	0	0	5	5	0	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Silent	SNP	ENST00000368140.1	37	CCDS1178.1																																																																																			.		0.353	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		G	158912063	T	G	158912063	2	3	73	1	0	0	0	0	0	0	0	1	12897	1567	55	5		5	PYHIN1	1	158912063	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	2095685	158912063	90338558	7	6840											
CACNA1S	779	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	201017795	201017795	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgtcgctgttcaggggcatGttcatgcccaccagccgctg	5	9	12	15	3	2	0	2	0	0	0	3	0	2	0	4	2	2	5	4	2	0	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:201017795G>T	ENST00000362061.3	-	36	4582	c.4356C>A	c.(4354-4356)aaC>aaA	p.N1452K	CACNA1S_ENST00000367338.3_Missense_Mutation_p.N1433K	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1452					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCAGGGGCATGTTCATGCCCA	0.617																																					p.N1452K		.											.	CACNA1S-94	0			c.C4356A						.						80	61	67					1																	201017795		2203	4300	6503	SO:0001583	missense	779	exon36			GGGCATGTTCATG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.4356C>A	1.37:g.201017795G>T	ENSP00000355192:p.Asn1452Lys	Somatic	46	2		WXS	Illumina HiSeq	Phase_I	83	7	NM_000069	0	0	2	2	0	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	21.3	4.127572	0.77549	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.09255	3.0;3.0	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.41789	0.1174	M	0.92923	3.36	0.53005	D	0.99996	D	0.89917	1.0	D	0.87578	0.998	T	0.51434	-0.8706	10	0.87932	D	0	.	13.3252	0.60454	0.0766:0.0:0.9234:0.0	.	1452	Q13698	CAC1S_HUMAN	K	1452;1433	ENSP00000355192:N1452K;ENSP00000356307:N1433K	ENSP00000355192:N1452K	N	-	3	2	CACNA1S	199284418	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.680000	0.68168	2.549000	0.85964	0.557000	0.71058	AAC	.		0.617	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201017795	G	T	201017795	3	4	73	1	0	0	0	0	1	0	0	0	2553	1368	48	4	1301	4	CACNA1S	1	201017795	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	42105732	201017795	48232826	8	6841											
ZP4	57829	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	238053765	238053765	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtcatcaaacttaccccaAgctattagtacaggaggaga	16	8	8	9	0	2	1	2	0	0	1	2	3	2	2	2	2	4	2	2	2	7	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:238053765A>T	ENST00000366570.4	-	1	329	c.171T>A	c.(169-171)gcT>gcA	p.A57A	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	57					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACTTACCCCAAGCTATTAGTA	0.478																																					p.A57A	NSCLC(166;160 2029 11600 18754 19936)	.											.	ZP4-93	0			c.T171A						.						68	67	67					1																	238053765		2203	4300	6503	SO:0001819	synonymous_variant	57829	exon1			ACCCCAAGCTATT	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"Zona pellucida glycoproteins"	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.171T>A	1.37:g.238053765A>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	89	9	NM_021186	0	0	0	0	0	B2RAE1	Silent	SNP	ENST00000366570.4	37	CCDS1615.1																																																																																			.		0.478	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238053765	A	T	238053765	2	4	73	1	0	0	0	0	0	0	0	1	18250	59	3	5		5	ZP4	1	238053765	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	37035970	238053765	11196856	9	6842											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112762	248112763	+	Frame_Shift_Del	DEL	TG	TG	-																															gagggcacagtgtttttgagTgccaccatctttctcgtgtt																								rs34851853|rs4925790|rs4925789	byFrequency	TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:248112762_248112763delTG	ENST00000357191.3	+	1	603_604	c.603_604delTG	c.(601-606)agtgccfs	p.A202fs	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	202			A -> T (in dbSNP:rs4925790).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TGTTTTTGAGTGCCACCATCTT	0.49																																					p.201_202del		.											.	OR2L8-70	0			c.603_604del						.																																			SO:0001589	frameshift_variant	391190	exon1			.	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.603_604delTG	1.37:g.248112762_248112763delTG	ENSP00000349719:p.Ala202fs	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	64	17	NM_001001963	0	0	0	0	0	Q6IF03	Frame_Shift_Del	DEL	ENST00000357191.3	37	CCDS31101.1																																																																																			.		0.49	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			-	248112763	TG	-	248112762	7	5	73	1	0	1	0	1	0	0	0	0	11035	1693	59	0	605	0	OR2L8	1	248112762	Frame_Shift_Del	DEL	TG	TCGA-BQ-5889-01A-11D-1589-08	10058997	248112762	1137859	10	6843											
OR2T12	127064	broad.mit.edu	37	chr1	248458256	248458256	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaggacaggatgagggaaaAggggaccaggagcattaaca	16	3	17	5	0	0	1	0	1	0	0	0	7	0	7	1	7	2	1	1	7	3	1			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:248458256A>G	ENST00000317996.1	-	1	624	c.625T>C	c.(625-627)Ttt>Ctt	p.F209L		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F209L(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			ATGAGGGAAAAGGGGACCAGG	0.547																																					p.F209L													.	OR2T12-71	1	Substitution - Missense(1)	prostate(1)	c.T625C						.						49	43	45					1																	248458256		2202	4282	6484	SO:0001583	missense	127064	exon1			GGGAAAAGGGGAC	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.625T>C	1.37:g.248458256A>G	ENSP00000324583:p.Phe209Leu	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	111	3	NM_001004692	0	0	0	0	0		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	a	0.425	-0.906199	0.02453	.	.	ENSG00000177201	ENST00000317996	T	0.32988	1.43	1.55	-0.261	0.12963	GPCR, rhodopsin-like superfamily (1);	0.858771	0.09453	N	0.800195	T	0.14960	0.0361	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.29397	-1.0013	10	0.25751	T	0.34	.	6.739	0.23424	0.772:0.0:0.0:0.228	.	209	Q8NG77	O2T12_HUMAN	L	209	ENSP00000324583:F209L	ENSP00000324583:F209L	F	-	1	0	OR2T12	246524879	0.000000	0.05858	0.023000	0.16930	0.191000	0.23601	-1.313000	0.02718	0.540000	0.28808	0.147000	0.16070	TTT	.		0.547	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		G	248458256	A	G	248458256	3	3	73	1	0	0	0	0	1	0	0	0	11045	72	3	3	340	3	OR2T12	1	248458256	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	345494	248458256	792365	11	6844											
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458380	248458380	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgatcgatctcgtgtgcaccGcaatatgggaagctcagggt	9	10	13	9	3	2	1	1	1	1	0	4	3	2	2	1	2	2	3	1	2	3	1	rs144239623		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:248458380G>A	ENST00000317996.1	-	1	500	c.501C>T	c.(499-501)tgC>tgT	p.C167C		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	167						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			CGTGTGCACCGCAATATGGGA	0.577																																					p.C167C		.											.	OR2T12-71	0			c.C501T						.	G		3,4399	2.1+/-5.4	0,3,2198	94	87	89		501	-1.1	0	1	dbSNP_134	89	0,8596		0,0,4298	no	coding-synonymous	OR2T12	NM_001004692.1		0,3,6496	AA,AG,GG		0.0,0.0682,0.0231		167/321	248458380	3,12995	2201	4298	6499	SO:0001819	synonymous_variant	127064	exon1			TGCACCGCAATAT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"GPCR / Class A : Olfactory receptors"	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.501C>T	1.37:g.248458380G>A		Somatic	134	1		WXS	Illumina HiSeq	Phase_I	154	8	NM_001004692	0	0	0	0	0		Silent	SNP	ENST00000317996.1	37	CCDS31110.1																																																																																			G|1.000;A|0.000		0.577	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		A	248458380	G	A	248458380	2	1	73	1	0	0	0	0	0	0	0	1	11045	1079	38	1		1	OR2T12	1	248458380	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	124	248458380	792241	12	6845											
CRIM1	51232	hgsc.bcm.edu;bcgsc.ca	37	chr2	36583678	36583678	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcggcaccttcgggatttaCggaacctgcgaccgggggct	6	7	16	12	5	0	0	0	0	0	0	1	3	0	2	3	6	3	2	3	6	2	3	rs369487866		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:36583678C>G	ENST00000280527.2	+	1	610	c.243C>G	c.(241-243)taC>taG	p.Y81*	RP11-490M8.1_ENST00000565283.1_lincRNA	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	81	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TCGGGATTTACGGAACCTGCG	0.682																																					p.Y81X		.											.	CRIM1-118	0			c.C243G						.						40	42	41					2																	36583678		2202	4298	6500	SO:0001587	stop_gained	51232	exon1			GATTTACGGAACC	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.243C>G	2.37:g.36583678C>G	ENSP00000280527:p.Tyr81*	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	72	8	NM_016441	0	0	44	44	0	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Nonsense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	36|36	5.673833|5.673833	0.96764|0.96764	.|.	.|.	ENSG00000150938|ENSG00000150938	ENST00000428774|ENST00000280527;ENST00000426856	.|.	.|.	.|.	3.26|3.26	-0.383|-0.383	0.12477|0.12477	.|.	.|0.313844	.|0.28790	.|N	.|0.014130	T|.	0.13157|.	0.0319|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34527|.	-0.9825|.	3|.	.|0.02654	.|T	.|1	-0.0216|-0.0216	4.367|4.367	0.11228|0.11228	0.0:0.4434:0.1693:0.3873|0.0:0.4434:0.1693:0.3873	.|.	.|.	.|.	.|.	R|X	22|81;31	.|.	.|ENSP00000280527:Y81X	T|Y	+|+	2|3	0|2	CRIM1|CRIM1	36437182|36437182	0.988000|0.988000	0.35896|0.35896	0.948000|0.948000	0.38648|0.38648	0.105000|0.105000	0.19272|0.19272	0.433000|0.433000	0.21477|0.21477	-0.053000|-0.053000	0.13289|0.13289	-0.132000|-0.132000	0.14878|0.14878	ACG|TAC	.		0.682	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		G	36583678	C	G	36583678	4	3	73	1	0	0	0	0	0	1	0	0	3879	547	19	4	245	4	CRIM1	2	36583678	Nonsense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08		36583678	206615695	13	6846											
SRBD1	55133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	45647009	45647009	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacactgtccagtgttgcctTgagtaaagtctgggatacgt	10	12	11	8	1	1	1	0	1	1	0	2	2	2	2	2	1	3	2	2	1	4	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:45647009T>C	ENST00000263736.4	-	17	2136	c.2074A>G	c.(2074-2076)Aag>Gag	p.K692E	SRBD1_ENST00000535761.1_Missense_Mutation_p.K211E|SRBD1_ENST00000490133.1_5'UTR	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	692					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			AGTGTTGCCTTGAGTAAAGTC	0.383																																					p.K692E		.											.	SRBD1-90	0			c.A2074G						.						151	136	141					2																	45647009		2203	4300	6503	SO:0001583	missense	55133	exon17			TTGCCTTGAGTAA	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2074A>G	2.37:g.45647009T>C	ENSP00000263736:p.Lys692Glu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	170	19	NM_018079	0	0	6	6	0	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	37	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029717	0.54790	.	.	ENSG00000068784	ENST00000263736;ENST00000535761	T;T	0.32272	1.83;1.46	5.74	5.74	0.90152	Tex-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40372	0.1114	L	0.39020	1.185	0.46336	D	0.998999	D	0.67145	0.996	P	0.60609	0.877	T	0.08994	-1.0695	10	0.14656	T	0.56	.	16.0363	0.80631	0.0:0.0:0.0:1.0	.	692	Q8N5C6	SRBD1_HUMAN	E	692;211	ENSP00000263736:K692E;ENSP00000441272:K211E	ENSP00000263736:K692E	K	-	1	0	SRBD1	45500513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.193000	0.70182	0.460000	0.39030	AAG	.		0.383	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		C	45647009	T	C	45647009	3	2	73	1	0	0	0	0	1	0	0	0	15165	1821	63	3	933	3	SRBD1	2	45647009	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	9063331	45647009	197552364	14	6847											
EIF5B	9669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	99978207	99978207	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatttgaagaagaaactgtAaaatccaaagtgactgttga	19	10	8	4	0	0	5	0	3	0	2	1	5	1	5	1	0	1	2	1	0	7	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:99978207A>T	ENST00000289371.6	+	4	1045	c.843A>T	c.(841-843)gtA>gtT	p.V281V		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	281					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAGAAACTGTAAAATCCAAAG	0.388																																					p.V281V	Colon(162;2388 2567 2705 3444)	.											.	EIF5B-93	0			c.A843T						.						98	97	97					2																	99978207		1836	4081	5917	SO:0001819	synonymous_variant	9669	exon4			AACTGTAAAATCC	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.843A>T	2.37:g.99978207A>T		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	187	15	NM_015904	0	0	101	138	37	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			.		0.388	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		T	99978207	A	T	99978207	2	4	73	1	0	0	0	0	0	0	0	1	5057	349	13	5		5	EIF5B	2	99978207	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	54331198	99978207	143221166	15	6848											
SLC20A1	6574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	113404533	113404533	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctccgtgggagccaatgAtgtagcaaattcttttggta	10	14	10	7	1	2	1	0	1	2	0	3	2	2	2	2	2	2	3	2	2	4	6			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:113404533A>T	ENST00000272542.3	+	2	667	c.128A>T	c.(127-129)gAt>gTt	p.D43V	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	43					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						GGAGCCAATGATGTAGCAAAT	0.502																																					p.D43V		.											.	SLC20A1-92	0			c.A128T						.						110	104	106					2																	113404533		2203	4300	6503	SO:0001583	missense	6574	exon2			CCAATGATGTAGC		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.128A>T	2.37:g.113404533A>T	ENSP00000272542:p.Asp43Val	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	97	10	NM_005415	0	0	6	6	0	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	37	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542663	0.85917	.	.	ENSG00000144136	ENST00000272542	D	0.95412	-3.7	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.98557	0.9518	H	0.97918	4.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99372	1.0920	10	0.87932	D	0	3.1498	13.0754	0.59083	1.0:0.0:0.0:0.0	.	43	Q8WUM9	S20A1_HUMAN	V	43	ENSP00000272542:D43V	ENSP00000272542:D43V	D	+	2	0	SLC20A1	113121004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.283000	0.95860	2.036000	0.60181	0.482000	0.46254	GAT	.		0.502	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		T	113404533	A	T	113404533	3	4	73	1	0	0	0	0	1	0	0	0	14470	333	12	5	130	5	SLC20A1	2	113404533	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	13426326	113404533	129794840	16	6849											
SLC20A1	6574	hgsc.bcm.edu;broad.mit.edu	37	chr2	113404573	113404573	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagctgtgggctcaggtgtAgtgaccctgaagcaagcctg	9	8	14	10	0	1	2	1	2	0	0	1	2	1	2	2	2	3	4	2	2	3	1			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:113404573A>G	ENST00000272542.3	+	2	707	c.168A>G	c.(166-168)gtA>gtG	p.V56V	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	56					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						GCTCAGGTGTAGTGACCCTGA	0.507																																					p.V56V		.											.	SLC20A1-92	0			c.A168G						.						111	104	106					2																	113404573		2203	4300	6503	SO:0001819	synonymous_variant	6574	exon2			AGGTGTAGTGACC		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.168A>G	2.37:g.113404573A>G		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	77	5	NM_005415	0	0	4	4	0	Q08344|Q6DHX8|Q9UQ82	Silent	SNP	ENST00000272542.3	37	CCDS2099.1																																																																																			.		0.507	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		G	113404573	A	G	113404573	2	3	73	1	0	0	0	0	0	0	0	1	14470	407	15	3		3	SLC20A1	2	113404573	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	40	113404573	129794800	17	6850											
ERCC3	2071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	128050232	128050232	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggactccagtcttgctgagcTtcctgaggtactcggtgatg	6	12	13	10	1	1	3	0	3	1	0	4	4	3	4	2	3	3	3	2	3	1	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:128050232T>A	ENST00000285398.2	-	3	519	c.425A>T	c.(424-426)aAg>aTg	p.K142M	ERCC3_ENST00000493187.2_Missense_Mutation_p.K78M	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	142					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGCTGAGCTTCCTGAGGTA	0.493			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.K142M		.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3-723	0			c.A425T						.						102	92	95					2																	128050232		2203	4300	6503	SO:0001583	missense	2071	exon3	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTGAGCTTCCTGA	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.425A>T	2.37:g.128050232T>A	ENSP00000285398:p.Lys142Met	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	116	12	NM_000122	0	0	10	10	0	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	37	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485972	0.84854	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.73363	-0.74;-0.74	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	L	0.57536	1.79	0.80722	D	1	B	0.24576	0.106	P	0.46208	0.507	T	0.81722	-0.0803	10	0.72032	D	0.01	-32.2621	14.8747	0.70485	0.0:0.0:0.0:1.0	.	142	P19447	ERCC3_HUMAN	M	142;78	ENSP00000285398:K142M;ENSP00000444796:K78M	ENSP00000285398:K142M	K	-	2	0	ERCC3	127766702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.916000	0.55485	0.528000	0.53228	AAG	.		0.493	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		A	128050232	T	A	128050232	3	1	73	1	0	0	0	0	1	0	0	0	5227	1609	56	5	1975	5	ERCC3	2	128050232	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	14645659	128050232	115149141	18	6851											
UGT1A1	54658	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	234669022	234669022	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgtcccatgctgggaagaTactgttgatcccagtggatg	8	11	14	8	0	0	2	0	1	0	1	2	4	2	4	2	3	2	2	2	3	2	2	rs375204962		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:234669022T>C	ENST00000608383.1	+	1	89	c.89T>C	c.(88-90)aTa>aCa	p.I30T	UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000360418.3_Missense_Mutation_p.I30T|UGT1A6_ENST00000406651.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A8_ENST00000305208.5_Missense_Mutation_p.I30T|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	30					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	GCTGGGAAGATACTGTTGATC	0.612																																					p.I30T		.											.	UGT1A1-24	0			c.T89C						.	T	THR/ILE,,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	66	52	57		89,,,,,,,,,	6.1	0.1	2		57	0,8600		0,0,4300	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A1,UGT1A3	NM_000463.2,NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	89,,,,,,,,,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,,,,,,,,,	30/534,,,,,,,,,	234669022	1,13005	2203	4300	6503	SO:0001583	missense	54658	exon1			GGAAGATACTGTT	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"UDP glucuronosyltransferases"	12530	other	complex locus constituent		191740	"UDP glycosyltransferase 1 family, polypeptide A1"	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000608383.1:c.89T>C	2.37:g.234669022T>C	ENSP00000476741:p.Ile30Thr	Somatic	44	1		WXS	Illumina HiSeq	Phase_I	52	5	NM_000463	0	0	0	0	0	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000608383.1	37	CCDS2510.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425296	0.62733	2.27E-4	0.0	ENSG00000241635	ENST00000305208;ENST00000360418	T;T	0.71103	-0.54;-0.54	6.07	6.07	0.98685	.	.	.	.	.	T	0.80076	0.4557	L	0.55990	1.75	0.31696	N	0.641215	P;P	0.46952	0.887;0.537	P;B	0.58266	0.836;0.158	T	0.82948	-0.0204	9	0.87932	D	0	.	16.6277	0.84984	0.0:0.0:0.0:1.0	.	30;30	A6NJC3;P22309	.;UD11_HUMAN	T	30	ENSP00000304845:I30T;ENSP00000353593:I30T	ENSP00000304845:I30T	I	+	2	0	UGT1A1	234333761	0.998000	0.40836	0.056000	0.19401	0.047000	0.14425	8.001000	0.88508	2.330000	0.79161	0.528000	0.53228	ATA	.		0.612	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding				C	234669022	T	C	234669022	3	2	73	1	0	0	0	0	1	0	0	0	16977	1406	49	3	91	3	UGT1A1	2	234669022	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	106618790	234669022	8530351	19	6852											
IL5RA	3568	hgsc.bcm.edu;broad.mit.edu	37	chr3	3143448	3143448	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgttctgcaggatggtccGcacacttgctgaaaagcctt	8	11	11	11	2	1	1	0	1	1	0	3	2	2	2	2	2	3	4	2	2	2	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr3:3143448G>A	ENST00000446632.2	-	5	869	c.295C>T	c.(295-297)Cgg>Tgg	p.R99W	IL5RA_ENST00000445864.2_Missense_Mutation_p.R99W|IL5RA_ENST00000256452.3_Missense_Mutation_p.R99W|IL5RA_ENST00000438560.1_Missense_Mutation_p.R99W|IL5RA_ENST00000311981.8_Missense_Mutation_p.R99W|IL5RA_ENST00000383846.1_Missense_Mutation_p.R99W|IL5RA_ENST00000418488.2_Missense_Mutation_p.R99W|IL5RA_ENST00000430514.2_Missense_Mutation_p.R99W|SNORA43_ENST00000517240.1_RNA|IL5RA_ENST00000456302.1_Missense_Mutation_p.R99W	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	99	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		AGGATGGTCCGCACACTTGCT	0.463																																					p.R99W	GBM(169;430 2801 24955 28528)	.											.	IL5RA-91	0			c.C295T						.						119	109	112					3																	3143448		2203	4300	6503	SO:0001583	missense	3568	exon5			TGGTCCGCACACT	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"Interleukins and interleukin receptors", "CD molecules"	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.295C>T	3.37:g.3143448G>A	ENSP00000412209:p.Arg99Trp	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_001243099	0	0	1	1	0	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848333	0.51164	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000445864;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302;ENST00000445701;ENST00000427088	D;D;D;T;T;T;T;T;T;T	0.89270	-2.49;-2.39;-2.49;0.96;1.08;1.04;1.04;1.04;1.04;1.01	5.19	2.3	0.28687	Immunoglobulin-like fold (1);	0.815981	0.11006	N	0.609943	D	0.92074	0.7488	M	0.63843	1.955	0.21915	N	0.999473	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;P;D;D;D	0.77004	0.962;0.977;0.897;0.945;0.989;0.936	T	0.81116	-0.1079	10	0.72032	D	0.01	-6.1948	6.7086	0.23264	0.0845:0.0:0.5918:0.3237	.	99;99;99;99;99;99	B4E2G0;Q01344-3;Q01344-2;Q01344;B3IU77;E7ERY4	.;.;.;IL5RA_HUMAN;.;.	W	99	ENSP00000412209:R99W;ENSP00000390753:R99W;ENSP00000256452:R99W;ENSP00000388858:R99W;ENSP00000402598:R99W;ENSP00000373358:R99W;ENSP00000309196:R99W;ENSP00000400400:R99W;ENSP00000392059:R99W;ENSP00000398117:R99W	ENSP00000256452:R99W	R	-	1	2	IL5RA	3118448	0.968000	0.33430	0.006000	0.13384	0.002000	0.02628	2.882000	0.48546	0.162000	0.19483	-0.142000	0.14014	CGG	.		0.463	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			A	3143448	G	A	3143448	3	1	73	1	0	0	0	0	1	0	0	0	7721	1086	38	1	1025	1	IL5RA	3	3143448	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08		3143448	194878982	20	6853											
FILIP1L	11259	broad.mit.edu	37	chr3	99648841	99648841	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagccaggtccattttttcAgcctttaaaatgcctatgac	12	13	6	10	0	1	1	1	1	0	0	2	1	2	1	4	1	3	0	4	1	4	6			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr3:99648841A>G	ENST00000354552.3	-	3	755	c.285T>C	c.(283-285)gcT>gcC	p.A95A	CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000398326.2_Silent_p.A95A|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000331335.5_Silent_p.A95A	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	95						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						CCATTTTTTCAGCCTTTAAAA	0.433																																					p.A95A													.	FILIP1L-45	0			c.T285C						.						146	133	137					3																	99648841		1855	4099	5954	SO:0001819	synonymous_variant	11259	exon3			TTTTTCAGCCTTT		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"downregulated in ovarian cancer 1", "GPBP-interacting protein of 130 kDa"	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.285T>C	3.37:g.99648841A>G		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	159	4	NM_182909	0	0	0	0	0	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Silent	SNP	ENST00000354552.3	37	CCDS43117.1																																																																																			.		0.433	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890		G	99648841	A	G	99648841	2	3	73	1	0	0	0	0	0	0	0	1	5914	175	7	3		3	FILIP1L	3	99648841	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	96505393	99648841	98373589	21	6854											
PLCXD2	257068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	111432757	111432757	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttattttctaccactgtccCttctacaagcagtacccctt	8	15	3	15	0	2	0	0	0	2	0	3	0	3	0	4	0	4	2	4	0	5	8	rs372815872		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr3:111432757C>T	ENST00000477665.1	+	3	972	c.648C>T	c.(646-648)ccC>ccT	p.P216P	PLCXD2_ENST00000393934.3_Silent_p.P216P	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	216					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)	p.P216P(1)		endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						ACCACTGTCCCTTCTACAAGC	0.443																																					p.P216P		.											.	PLCXD2-227	1	Substitution - coding silent(1)	lung(1)	c.C648T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	83	82	82		648,648	3.5	1	3		82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLCXD2	NM_001185106.1,NM_153268.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	216/306,216/305	111432757	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	257068	exon3			CTGTCCCTTCTAC	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.648C>T	3.37:g.111432757C>T		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	111	13	NM_001185106	0	0	0	0	0	Q96N12	Silent	SNP	ENST00000477665.1	37	CCDS54619.1																																																																																			.		0.443	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		T	111432757	C	T	111432757	2	4	73	1	0	0	0	0	0	0	0	1	12068	668	24	2		2	PLCXD2	3	111432757	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	11783916	111432757	86589673	22	6855											
LYAR	55646	broad.mit.edu;bcgsc.ca	37	chr4	4276371	4276375	+	Frame_Shift_Del	DEL	CTTCA	CTTCA	-																															tttctttctcttttattcttCttcacctccccttgctgttc																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	CTTCA	CTTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr4:4276371_4276375delCTTCA	ENST00000343470.4	-	7	791_795	c.551_555delTGAAG	c.(550-555)gtgaagfs	p.VK184fs	LYAR_ENST00000452476.1_Frame_Shift_Del_p.VK184fs	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	184	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ttttATTCTTCTTCACCTCCCCTTG	0.449																																					p.184_185del													.	LYAR-90	0			c.551_555del						.																																			SO:0001589	frameshift_variant	55646	exon7			ATTCTTCTTCACC	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.551_555delTGAAG	4.37:g.4276371_4276375delCTTCA	ENSP00000345917:p.Val184fs	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	168	13	NM_017816	0	0	0	0	0	D3DVS4|Q6FI78|Q9NYS1	Frame_Shift_Del	DEL	ENST00000343470.4	37	CCDS3374.1																																																																																			.		0.449	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		-	4276375	CTTCA	-	4276371	7	5	73	1	0	1	0	1	0	0	0	0	9128	912	32	0	600	0	LYAR	4	4276371	Frame_Shift_Del	DEL	CTTCA	TCGA-BQ-5889-01A-11D-1589-08		4276371	186877905	23	6856											
DRD5	1816	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	9784079	9784079	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtggaccgctactgggccatCtccaggcccttccgctacaa	7	8	10	16	2	1	0	0	0	1	0	3	1	2	1	5	3	2	2	5	3	3	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr4:9784079C>G	ENST00000304374.2	+	1	822	c.426C>G	c.(424-426)atC>atG	p.I142M		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	142					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	ACTGGGCCATCTCCAGGCCCT	0.597																																					p.I142M		.											.	DRD5-91	0			c.C426G						.						38	37	37					4																	9784079		2203	4300	6503	SO:0001583	missense	1816	exon1			GGCCATCTCCAGG	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.426C>G	4.37:g.9784079C>G	ENSP00000306129:p.Ile142Met	Somatic	45	1		WXS	Illumina HiSeq	Phase_I	57	5	NM_000798	0	0	0	0	0	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	c	14.45	2.537998	0.45176	.	.	ENSG00000169676	ENST00000304374	D	0.81908	-1.55	4.35	0.628	0.17681	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.92961	0.7760	H	0.98199	4.17	0.44985	D	0.998009	D	0.89917	1.0	D	0.80764	0.994	D	0.90969	0.4818	10	0.87932	D	0	.	8.8431	0.35153	0.0:0.575:0.0:0.425	.	142	P21918	DRD5_HUMAN	M	142	ENSP00000306129:I142M	ENSP00000306129:I142M	I	+	3	3	DRD5	9393177	0.997000	0.39634	0.997000	0.53966	0.970000	0.65996	0.504000	0.22626	-0.106000	0.12110	0.305000	0.20034	ATC	.		0.597	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			G	9784079	C	G	9784079	3	3	73	1	0	0	0	0	1	0	0	0	4771	903	32	4	428	4	DRD5	4	9784079	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	5507708	9784079	181370197	24	6857											
C4orf14	84273	broad.mit.edu;bcgsc.ca	37	chr4	57842784	57842784	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagagatcaactcttccactCcatagccggtcttggcgctg	8	10	9	14	2	3	1	1	0	2	1	5	2	5	1	3	2	2	1	3	2	2	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr4:57842784C>A	ENST00000264230.4	-	1	2205	c.968G>T	c.(967-969)gGa>gTa	p.G323V	POLR2B_ENST00000431623.2_5'Flank|POLR2B_ENST00000441246.2_5'Flank|POLR2B_ENST00000381227.1_5'Flank|POLR2B_ENST00000314595.5_5'Flank	NM_032313.2	NP_115689.1	Q8NC60	NOA1_HUMAN	nitric oxide associated 1	323	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				apoptotic process (GO:0006915)|GTP catabolic process (GO:0006184)|mitochondrial translation (GO:0032543)|regulation of cell death (GO:0010941)|regulation of cellular respiration (GO:0043457)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)										CTCTTCCACTCCATAGCCGGT	0.612																																					p.G323V													.	.	0			c.G968T						.						73	67	69					4																	57842784		2203	4300	6503	SO:0001583	missense	84273	exon1			TCCACTCCATAGC	AK098215	CCDS3510.1	4q12	2013-05-24	2011-10-19	2011-10-19	ENSG00000084092	ENSG00000084092			28473	protein-coding gene	gene with protein product	"nitric oxide synthase, mitochondrial (putative)", "mitochondrial GTPase 3 homolog (S. cerevisiae)"	614919	"chromosome 4 open reading frame 14"	C4orf14		16380119, 2118999, 21771794, 22447445	Standard	NM_032313		Approved	MGC3232, hAtNOS1, hNOA1, MTG3	uc003hck.3	Q8NC60	OTTHUMG00000128773	ENST00000264230.4:c.968G>T	4.37:g.57842784C>A	ENSP00000264230:p.Gly323Val	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	144	8	NM_032313	0	0	12	13	1	Q8N7L6|Q9BSQ9	Missense_Mutation	SNP	ENST00000264230.4	37	CCDS3510.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553057	0.86127	.	.	ENSG00000084092	ENST00000264230	T	0.18016	2.24	5.89	5.02	0.67125	.	0.051645	0.85682	D	0.000000	T	0.57725	0.2073	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74896	-0.3508	10	0.87932	D	0	.	16.1738	0.81836	0.1343:0.8657:0.0:0.0	.	323	Q8NC60	CD014_HUMAN	V	323	ENSP00000264230:G323V	ENSP00000264230:G323V	G	-	2	0	C4orf14	57537541	1.000000	0.71417	0.532000	0.27989	0.862000	0.49288	7.386000	0.79775	1.424000	0.47217	0.555000	0.69702	GGA	.		0.612	NOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250694.2	NM_032313		A	57842784	C	A	57842784	3	1	73	1	0	0	0	0	1	0	0	0	2257	855	30	4	1156	4	C4orf14	4	57842784	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	48058705	57842784	133311492	25	6858											
OTUD4	54726	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	146076795	146076795	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgacttaagaacctttCtagacaaaggcaggctagta	14	10	10	7	0	1	4	0	2	1	2	1	4	1	4	1	2	1	3	1	2	6	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr4:146076795C>A	ENST00000447906.2	-	9	921	c.734G>T	c.(733-735)aGa>aTa	p.R245I	OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Missense_Mutation_p.R180I			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	245					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					AAGAACCTTTCTAGACAAAGG	0.358																																					p.R180I		.											.	OTUD4-565	0			c.G539T						.						106	105	105					4																	146076795		2203	4300	6503	SO:0001583	missense	54726	exon9			ACCTTTCTAGACA		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"OTU domain containing"	24949	protein-coding gene	gene with protein product		611744	"OTU domain containing 4"			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.734G>T	4.37:g.146076795C>A	ENSP00000395487:p.Arg245Ile	Somatic	212	0		WXS	Illumina HiSeq	Phase_I	176	11	NM_001102653	0	0	4	4	0	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	C	16.36	3.101779	0.56183	.	.	ENSG00000164164	ENST00000454497;ENST00000447906;ENST00000514973	T;T;T	0.32753	1.44;1.44;1.45	5.37	5.37	0.77165	.	0.077530	0.56097	D	0.000034	T	0.40448	0.1117	L	0.60455	1.87	0.80722	D	1	D;D	0.65815	0.995;0.985	P;P	0.52217	0.693;0.578	T	0.18777	-1.0326	10	0.54805	T	0.06	-19.7161	11.4953	0.50404	0.0:0.9095:0.0:0.0905	.	245;244	G3V0I6;Q01804	.;OTUD4_HUMAN	I	180;245;179	ENSP00000409279:R180I;ENSP00000395487:R245I;ENSP00000425972:R179I	ENSP00000395487:R245I	R	-	2	0	OTUD4	146296245	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	0.964000	0.29306	2.669000	0.90835	0.655000	0.94253	AGA	.		0.358	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		A	146076795	C	A	146076795	3	1	73	1	0	0	0	0	1	0	0	0	11340	913	32	4	2662	4	OTUD4	4	146076795	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	88234011	146076795	45077481	26	6859											
CCT5	22948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	10261751	10261751	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagctgggctttgctggtcTtgtacaggagatctcatttg	7	14	13	7	0	2	1	1	0	2	1	3	3	2	1	0	3	3	4	0	3	2	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:10261751T>G	ENST00000280326.4	+	8	1493	c.1073T>G	c.(1072-1074)cTt>cGt	p.L358R	CCT5_ENST00000506600.1_Missense_Mutation_p.L265R|CCT5_ENST00000515390.1_Missense_Mutation_p.L303R|CCT5_ENST00000515676.1_Missense_Mutation_p.L320R|CCT5_ENST00000503026.1_Missense_Mutation_p.L337R|CTD-2256P15.4_ENST00000606194.1_RNA	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	358					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TTTGCTGGTCTTGTACAGGAG	0.498																																					p.L358R		.											.	CCT5-92	0			c.T1073G						.						155	163	160					5																	10261751		2203	4300	6503	SO:0001583	missense	22948	exon8			CTGGTCTTGTACA	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"Heat Shock Proteins / Chaperonins"	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1073T>G	5.37:g.10261751T>G	ENSP00000280326:p.Leu358Arg	Somatic	330	1		WXS	Illumina HiSeq	Phase_I	375	36	NM_012073	0	0	170	180	10	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	37	CCDS3877.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.658564	0.47467	.	.	ENSG00000150753	ENST00000280326;ENST00000503026;ENST00000515390;ENST00000440011;ENST00000515676;ENST00000506600	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.39	5.39	0.77823	.	0.213452	0.41823	D	0.000808	T	0.74891	0.3776	L	0.51422	1.61	0.32706	N	0.512183	B;B;B;B;B;B	0.19445	0.036;0.003;0.021;0.003;0.003;0.003	B;B;B;B;B;B	0.29176	0.099;0.039;0.025;0.016;0.027;0.016	T	0.77606	-0.2525	10	0.41790	T	0.15	-5.3569	14.6511	0.68797	0.0:0.0:0.0:1.0	.	265;303;207;356;358;358	B4DYD8;E7ENZ3;B4DZY9;Q9BU08;A8K2X8;P48643	.;.;.;.;.;TCPE_HUMAN	R	358;337;303;331;320;265	ENSP00000280326:L358R;ENSP00000423318:L337R;ENSP00000426923:L303R;ENSP00000427297:L320R;ENSP00000423052:L265R	ENSP00000280326:L358R	L	+	2	0	CCT5	10314751	0.974000	0.33945	0.007000	0.13788	0.973000	0.67179	7.554000	0.82212	2.045000	0.60652	0.456000	0.33151	CTT	.		0.498	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			G	10261751	T	G	10261751	3	3	73	1	0	0	0	0	1	0	0	0	2962	1609	56	5	1103	5	CCT5	5	10261751	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		10261751	170653509	27	6860											
GPR98	84059	hgsc.bcm.edu;broad.mit.edu	37	chr5	90052965	90052965	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctcatgggattcttgaatTtgcagataaacaggtatgcc	12	13	9	7	0	2	2	1	1	2	1	3	3	2	3	1	2	3	2	1	2	4	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:90052965T>A	ENST00000405460.2	+	57	12023	c.11927T>A	c.(11926-11928)tTt>tAt	p.F3976Y		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3976	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATTCTTGAATTTGCAGATAAA	0.413																																					p.F3976Y		.											.	GPR98-103	0			c.T11927A						.						76	78	77					5																	90052965		1871	4114	5985	SO:0001583	missense	84059	exon57			TTGAATTTGCAGA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11927T>A	5.37:g.90052965T>A	ENSP00000384582:p.Phe3976Tyr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	51	4	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.1|25.1	4.606868|4.606868	0.87157|0.87157	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.61627|.	0.09|.	5.08|5.08	5.08|5.08	0.68730|0.68730	Na-Ca exchanger/integrin-beta4 (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85630|0.85630	0.5741|0.5741	M|M	0.93507|0.93507	3.425|3.425	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.996;0.999|.	D;D|.	0.72338|.	0.974;0.977|.	D|D	0.89683|0.89683	0.3892|0.3892	10|5	0.48119|.	T|.	0.1|.	.|.	15.1356|15.1356	0.72562|0.72562	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	3976;3976|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	Y|M	3976|1542	ENSP00000384582:F3976Y|.	ENSP00000296619:F3976Y|.	F|L	+|+	2|1	0|2	GPR98|GPR98	90088721|90088721	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.768000|0.768000	0.43524|0.43524	7.117000|7.117000	0.77129|0.77129	2.041000|2.041000	0.60428|0.60428	0.383000|0.383000	0.25322|0.25322	TTT|TTG	.		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90052965	T	A	90052965	3	1	73	1	0	0	0	0	1	0	0	0	6742	1841	64	5	12153	5	GPR98	5	90052965	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	79791214	90052965	90862295	28	6861											
KIF20A	10112	bcgsc.ca	37	chr5	137518908	137518908	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgccccactacctgtcccgGcaaacattcgcttctccatc	7	10	5	19	2	1	0	0	0	1	0	5	0	2	0	5	1	3	2	5	1	2	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:137518908G>T	ENST00000394894.3	+	8	1109	c.883G>T	c.(883-885)Gca>Tca	p.A295S	KIF20A_ENST00000508792.1_Missense_Mutation_p.A277S	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	295	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ACCTGTCCCGGCAAACATTCG	0.498																																					p.A295S													.	KIF20A-90	0			c.G883T						.						72	69	70					5																	137518908		2203	4300	6503	SO:0001583	missense	10112	exon8			GTCCCGGCAAACA	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"Kinesins"	9787	protein-coding gene	gene with protein product		605664	"RAB6 interacting, kinesin-like (rabkinesin6)"	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.883G>T	5.37:g.137518908G>T	ENSP00000378356:p.Ala295Ser	Somatic	111	0		WXS	Illumina HiSeq	Phase_1	95	5	NM_005733	0	0	3	3	0	B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	37	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	G	6.006	0.369587	0.11352	.	.	ENSG00000112984	ENST00000394894;ENST00000508792	T;T	0.41758	0.99;0.99	4.88	3.1	0.35709	Kinesin, motor domain (4);	0.155388	0.30068	N	0.010491	T	0.23014	0.0556	N	0.05592	-0.015	0.28431	N	0.917255	B;B	0.27286	0.003;0.174	B;B	0.33846	0.027;0.171	T	0.24835	-1.0149	10	0.12430	T	0.62	-1.6083	11.0739	0.48019	0.1383:0.0:0.8617:0.0	.	277;295	B4DL79;O95235	.;KI20A_HUMAN	S	295;277	ENSP00000378356:A295S;ENSP00000420880:A277S	ENSP00000378356:A295S	A	+	1	0	KIF20A	137546807	0.827000	0.29292	0.996000	0.52242	0.773000	0.43773	2.525000	0.45598	0.671000	0.31185	0.655000	0.94253	GCA	.		0.498	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		T	137518908	G	T	137518908	3	4	73	1	0	0	0	0	1	0	0	0	8307	1203	42	4	909	4	KIF20A	5	137518908	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	47465943	137518908	43396352	29	6862											
ARAP3	64411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141033934	141033934	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctacttcctcatacacTggctcctcgtacacaggctc	7	10	6	18	1	1	0	1	0	0	0	5	0	3	0	4	2	3	3	4	2	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:141033934T>C	ENST00000239440.4	-	33	4283	c.4218A>G	c.(4216-4218)ccA>ccG	p.P1406P	ARAP3_ENST00000513878.1_Silent_p.P1055P|FCHSD1_ENST00000435817.2_5'Flank|ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000522783.1_5'Flank|FCHSD1_ENST00000519800.1_5'Flank|ARAP3_ENST00000508305.1_Silent_p.P1237P	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1406					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CCTCATACACTGGCTCCTCGT	0.577																																					p.P1406P		.											.	ARAP3-291	0			c.A4218G						.						106	105	105					5																	141033934		2203	4300	6503	SO:0001819	synonymous_variant	64411	exon33			ATACACTGGCTCC	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	24097	protein-coding gene	gene with protein product		606647	"centaurin, delta 3"	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4218A>G	5.37:g.141033934T>C		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	144	15	NM_022481	0	0	18	23	5	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			.		0.577	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		C	141033934	T	C	141033934	2	2	73	1	0	0	0	0	0	0	0	1	840	1567	55	3		3	ARAP3	5	141033934	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	3515026	141033934	39881326	30	6863											
FBXO38	81545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	147781650	147781650	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgaagagtaaggggccAtgaggcttttagcattccag	11	8	15	7	1	0	2	0	1	0	1	1	4	1	2	2	4	1	3	2	4	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:147781650A>G	ENST00000340253.5	+	4	536	c.368A>G	c.(367-369)cAt>cGt	p.H123R	FBXO38_ENST00000509699.2_3'UTR|FBXO38_ENST00000394370.3_Missense_Mutation_p.H123R|FBXO38_ENST00000296701.6_Missense_Mutation_p.H123R|FBXO38_ENST00000513826.1_Missense_Mutation_p.H123R			Q6PIJ6	FBX38_HUMAN	F-box protein 38	123					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAAGGGGCCATGAGGCTTTT	0.458																																					p.H123R		.											.	FBXO38-231	0			c.A368G						.						143	136	139					5																	147781650		2203	4299	6502	SO:0001583	missense	81545	exon4			GGGGCCATGAGGC	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"F-boxes /  "other""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.368A>G	5.37:g.147781650A>G	ENSP00000342023:p.His123Arg	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	143	19	NM_001271723	0	0	2	2	0	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	37		.	.	.	.	.	.	.	.	.	.	A	15.58	2.876042	0.51695	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.29917	1.55;1.56;1.55;1.56	5.77	5.77	0.91146	F-box domain, Skp2-like (1);	0.152919	0.64402	D	0.000014	T	0.20373	0.0490	L	0.27053	0.805	0.42393	D	0.992538	B;B;P	0.47677	0.038;0.053;0.899	B;B;B	0.41036	0.023;0.022;0.346	T	0.05683	-1.0870	10	0.02654	T	1	-12.0661	15.2058	0.73177	1.0:0.0:0.0:0.0	.	123;123;123	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	R	123	ENSP00000342023:H123R;ENSP00000296701:H123R;ENSP00000377895:H123R;ENSP00000426410:H123R	ENSP00000296701:H123R	H	+	2	0	FBXO38	147761843	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.793000	0.69060	2.326000	0.78906	0.533000	0.62120	CAT	.		0.458	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		G	147781650	A	G	147781650	3	3	73	1	0	0	0	0	1	0	0	0	5765	217	8	3	378	3	FBXO38	5	147781650	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	6747716	147781650	33133610	31	6864											
RFX6	222546	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	117241541	117241541	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgatattgaaagggttgaTttgaacagcattggctctca	11	14	10	6	0	2	4	1	4	2	0	3	4	2	4	0	2	2	3	0	2	3	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr6:117241541T>C	ENST00000332958.2	+	12	1267	c.1251T>C	c.(1249-1251)gaT>gaC	p.D417D		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	417					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AAAGGGTTGATTTGAACAGCA	0.418																																					p.D417D		.											.	RFX6-93	0			c.T1251C						.						221	197	205					6																	117241541		2203	4300	6503	SO:0001819	synonymous_variant	222546	exon12			GGTTGATTTGAAC	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1251T>C	6.37:g.117241541T>C		Somatic	236	0		WXS	Illumina HiSeq	Phase_I	264	22	NM_173560	0	0	0	0	0	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			.		0.418	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		C	117241541	T	C	117241541	2	2	73	1	0	0	0	0	0	0	0	1	13299	1490	52	3		3	RFX6	6	117241541	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		117241541	53873526	32	6865											
MAD1L1	8379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	1855740	1855740	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcggctgaagagctcgaggGtgagcgagctgaggaaggca	10	4	20	7	3	0	4	0	3	0	1	1	7	0	5	0	5	3	4	0	5	2	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:1855740G>A	ENST00000406869.1	-	19	2680	c.2123C>T	c.(2122-2124)aCc>aTc	p.T708I	MAD1L1_ENST00000265854.7_Missense_Mutation_p.T708I|MAD1L1_ENST00000399654.2_Missense_Mutation_p.T708I|MAD1L1_ENST00000402746.1_Missense_Mutation_p.T616I			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	708					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GAGCTCGAGGGTGAGCGAGCT	0.667																																					p.T708I		.											.	MAD1L1-1083	0			c.C2123T						.						28	35	33					7																	1855740		2040	4207	6247	SO:0001583	missense	8379	exon19			TCGAGGGTGAGCG	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.2123C>T	7.37:g.1855740G>A	ENSP00000385334:p.Thr708Ile	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	81	15	NM_003550	0	1	74	99	24	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679536	0.88542	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	3.98	3.98	0.46160	.	.	.	.	.	T	0.73628	0.3611	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79671	-0.1706	9	0.87932	D	0	-6.9772	16.1426	0.81536	0.0:0.0:1.0:0.0	.	616;708	B3KR41;Q9Y6D9	.;MD1L1_HUMAN	I	616;708;708;259;708;259	ENSP00000384155:T616I;ENSP00000382562:T708I;ENSP00000385334:T708I;ENSP00000265854:T708I;ENSP00000394886:T259I	ENSP00000265854:T708I	T	-	2	0	MAD1L1	1822266	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.338000	0.90038	1.787000	0.52448	0.456000	0.33151	ACC	.		0.667	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		A	1855740	G	A	1855740	3	1	73	1	0	0	0	0	1	0	0	0	9172	1261	44	2	37	2	MAD1L1	7	1855740	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08		1855740	157282923	33	6866											
GLI3	2737	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	42004728	42004728	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccctgtcccactgggtcctGgttctgcatgccattcacca	5	11	8	17	0	2	0	1	0	1	0	4	0	4	0	6	2	2	2	6	2	0	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:42004728G>T	ENST00000395925.3	-	15	4027	c.3943C>A	c.(3943-3945)Cag>Aag	p.Q1315K	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1315					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						ACTGGGTCCTGGTTCTGCATG	0.652									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.Q1315K		.											.	GLI3-1149	0			c.C3943A						.						37	36	36					7																	42004728		2203	4300	6503	SO:0001583	missense	2737	exon15	Familial Cancer Database	;	GGTCCTGGTTCTG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"Zinc fingers, C2H2-type"	4319	protein-coding gene	gene with protein product	"zinc finger protein GLI3", "oncogene GLI3", "DNA-binding protein"	165240	"Greig cephalopolysyndactyly syndrome", "GLI-Kruppel family member GLI3", "glioma-associated oncogene family zinc finger 3"	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3943C>A	7.37:g.42004728G>T	ENSP00000379258:p.Gln1315Lys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	89	5	NM_000168	0	0	2	2	0	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681803	0.47991	.	.	ENSG00000106571	ENST00000395925	T	0.12569	2.67	5.65	5.65	0.86999	.	0.741669	0.13841	N	0.359041	T	0.09024	0.0223	N	0.22421	0.69	0.23150	N	0.998213	B	0.13145	0.007	B	0.10450	0.005	T	0.34900	-0.9810	10	0.10377	T	0.69	.	9.7991	0.40753	0.0:0.1247:0.6842:0.1911	.	1315	P10071	GLI3_HUMAN	K	1315	ENSP00000379258:Q1315K	ENSP00000379258:Q1315K	Q	-	1	0	GLI3	41971253	0.977000	0.34250	0.012000	0.15200	0.777000	0.43975	2.070000	0.41491	2.655000	0.90218	0.655000	0.94253	CAG	.		0.652	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42004728	G	T	42004728	3	4	73	1	0	0	0	0	1	0	0	0	6459	1357	47	4	803	4	GLI3	7	42004728	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	40148988	42004728	117133935	34	6867											
CALCR	799	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	93055856	93055856	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccccaacgctggttccActgaattttgaattgggccc	7	11	8	15	1	0	2	0	2	0	0	2	2	2	2	5	2	1	2	5	2	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:93055856A>G	ENST00000394441.1	-	13	1552	c.1237T>C	c.(1237-1239)Tgg>Cgg	p.W413R	CALCR_ENST00000421592.1_Missense_Mutation_p.W429R|CALCR_ENST00000426151.1_Missense_Mutation_p.W413R|CALCR_ENST00000360249.4_Missense_Mutation_p.W429R|CALCR_ENST00000359558.2_Missense_Mutation_p.W447R	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	447					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CGCTGGTTCCACTGAATTTTG	0.542																																					p.W447R		.											.	CALCR-664	0			c.T1339C						.						46	51	50					7																	93055856		2203	4300	6503	SO:0001583	missense	799	exon16			GGTTCCACTGAAT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"GPCR / Class B : Calcitonin receptors"	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1237T>C	7.37:g.93055856A>G	ENSP00000377959:p.Trp413Arg	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	142	15	NM_001164737	0	0	0	0	0	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823645	0.71143	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	4.57	4.57	0.56435	.	.	.	.	.	T	0.68659	0.3025	L	0.45228	1.405	0.51482	D	0.999925	D;P	0.71674	0.998;0.613	D;B	0.72075	0.976;0.248	T	0.66106	-0.6006	9	0.33141	T	0.24	.	10.4932	0.44762	1.0:0.0:0.0:0.0	.	447;413	F5H605;A4D1G6	.;.	R	447;429;429;413;413	ENSP00000352561:W447R;ENSP00000353385:W429R;ENSP00000399552:W429R;ENSP00000377959:W413R;ENSP00000389295:W413R	ENSP00000352561:W447R	W	-	1	0	CALCR	92893792	1.000000	0.71417	0.495000	0.27527	0.014000	0.08584	6.514000	0.73746	2.055000	0.61198	0.477000	0.44152	TGG	.		0.542	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		G	93055856	A	G	93055856	3	3	73	1	0	0	0	0	1	0	0	0	2585	159	6	3	191	3	CALCR	7	93055856	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	51051128	93055856	66082807	35	6868											
EPHB6	2051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142562311	142562311	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acgcaggccagtggggctggGggggcctccctggtggcagc	4	5	20	12	1	0	0	0	0	0	0	1	0	1	0	3	8	1	3	3	8	0	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:142562311G>T	ENST00000392957.2	+	7	1540	c.753G>T	c.(751-753)ggG>ggT	p.G251G	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Silent_p.G251G	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	251	Cys-rich.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GTGGGGCTGGGGGGGCCTCCC	0.682																																					p.G251G		.											.	EPHB6-1489	0			c.G753T						.						47	59	55					7																	142562311		2184	4281	6465	SO:0001819	synonymous_variant	2051	exon7			GGCTGGGGGGGCC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.753G>T	7.37:g.142562311G>T		Somatic	212	0		WXS	Illumina HiSeq	Phase_I	233	37	NM_004445	0	0	4	4	0	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			.		0.682	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562311	G	T	142562311	2	4	73	1	0	0	0	0	0	0	0	1	5191	1219	43	4		4	EPHB6	7	142562311	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	49506455	142562311	16576352	36	6869											
FBXO16	157574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	28321296	28321296	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcgctccaacaggcctgTgaggattcttcttctttgag	7	12	11	11	1	3	2	0	2	3	0	4	3	4	3	2	2	2	2	2	2	1	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr8:28321296T>G	ENST00000380254.2	-	4	323	c.175A>C	c.(175-177)Aca>Cca	p.T59P	FBXO16_ENST00000518734.1_Missense_Mutation_p.T47P|FBXO16_ENST00000517436.1_5'UTR|FBXO16_ENST00000346498.2_Missense_Mutation_p.T47P	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	59										large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		AACAGGCCTGTGAGGATTCTT	0.443																																					p.T59P		.											.	FBXO16-227	0			c.A175C						.						49	49	49					8																	28321296		2203	4300	6503	SO:0001583	missense	157574	exon4			GGCCTGTGAGGAT	AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050		"F-boxes /  "other""	13618	protein-coding gene	gene with protein product		608519	"F-box only protein 16"			12243353	Standard	NM_172366		Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000380254.2:c.175A>C	8.37:g.28321296T>G	ENSP00000369604:p.Thr59Pro	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	91	9	NM_172366	0	0	4	4	0	Q3T1B2|Q3T1B3|Q3T1B4	Missense_Mutation	SNP	ENST00000380254.2	37	CCDS6068.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.777109	0.31411	.	.	ENSG00000214050	ENST00000380254;ENST00000346498;ENST00000518734;ENST00000517673	T;T;T;T	0.44083	2.46;2.49;2.5;0.93	5.78	3.22	0.36961	.	0.330602	0.27366	U	0.019690	T	0.28267	0.0698	L	0.47716	1.5	0.46260	D	0.99895	P;P;P	0.37176	0.454;0.586;0.586	B;B;B	0.31337	0.128;0.128;0.128	T	0.04191	-1.0970	10	0.30854	T	0.27	-19.474	5.3812	0.16192	0.0:0.26:0.1382:0.6017	.	47;47;59	Q3T1B3;Q3T1B2;Q8IX29	.;.;FBX16_HUMAN	P	59;47;47;59	ENSP00000369604:T59P;ENSP00000341416:T47P;ENSP00000429687:T47P;ENSP00000429390:T59P	ENSP00000341416:T47P	T	-	1	0	FBXO16	28377215	0.126000	0.22350	0.865000	0.33974	0.984000	0.73092	0.580000	0.23803	0.447000	0.26695	0.482000	0.46254	ACA	.		0.443	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366		G	28321296	T	G	28321296	3	3	73	1	0	0	0	0	1	0	0	0	5748	1696	59	5	727	5	FBXO16	8	28321296	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		28321296	118042726	37	6870											
PDP1	54704	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	94935503	94935503	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagaggtaacttaccaccgaTtaaggccacaggataagttt	14	9	9	9	1	0	1	0	0	0	1	0	3	0	2	3	3	2	2	3	3	4	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr8:94935503T>A	ENST00000297598.4	+	2	1485	c.1216T>A	c.(1216-1218)Tta>Ata	p.L406I	PDP1_ENST00000396200.3_Missense_Mutation_p.L431I|PDP1_ENST00000517764.1_Missense_Mutation_p.L406I|PDP1_ENST00000520728.1_Missense_Mutation_p.L406I	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	406					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TTACCACCGATTAAGGCCACA	0.458																																					p.L431I		.											.	PDP1-229	0			c.T1291A						.						124	120	121					8																	94935503		2203	4300	6503	SO:0001583	missense	54704	exon3			CACCGATTAAGGC	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9279	protein-coding gene	gene with protein product		605993	"protein phosphatase 2C, magnesium-dependent, catalytic subunit"	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.1216T>A	8.37:g.94935503T>A	ENSP00000297598:p.Leu406Ile	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	171	13	NM_001161780	0	0	2	2	0	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.847623	0.32606	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.16897	2.31;2.31;2.31;2.31	6.03	2.5	0.30297	Protein phosphatase 2C-like (5);	0.072136	0.56097	D	0.000026	T	0.20129	0.0484	L	0.28608	0.87	0.58432	D	0.999998	D;P	0.56287	0.975;0.932	P;P	0.57502	0.822;0.725	T	0.02004	-1.1231	10	0.27082	T	0.32	-7.6451	9.7831	0.40660	0.0:0.1882:0.0:0.8118	.	457;406	B4DYX8;Q9P0J1	.;PDP1_HUMAN	I	406;406;431;406	ENSP00000297598:L406I;ENSP00000428317:L406I;ENSP00000379503:L431I;ENSP00000430380:L406I	ENSP00000297598:L406I	L	+	1	2	PDP1	95004679	0.732000	0.28121	1.000000	0.80357	0.993000	0.82548	1.160000	0.31761	1.108000	0.41662	0.533000	0.62120	TTA	.		0.458	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		A	94935503	T	A	94935503	3	1	73	1	0	0	0	0	1	0	0	0	11711	1490	52	5	1399	5	PDP1	8	94935503	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	66614207	94935503	51428519	38	6871											
NFIB	4781	hgsc.bcm.edu;broad.mit.edu	37	chr9	14307404	14307404	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctttcttcatcctttgacAttcgcttctcatgcttttta	5	21	3	12	1	4	1	2	1	3	0	7	1	5	1	1	0	1	2	1	0	1	8			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr9:14307404A>T	ENST00000380959.3	-	2	619	c.146T>A	c.(145-147)aTg>aAg	p.M49K	NFIB_ENST00000380934.4_Missense_Mutation_p.M75K|NFIB_ENST00000380953.1_Missense_Mutation_p.M49K|NFIB_ENST00000397579.2_Missense_Mutation_p.M49K|NFIB_ENST00000397575.3_Missense_Mutation_p.M49K|NFIB_ENST00000397581.2_Missense_Mutation_p.M49K|NFIB_ENST00000380921.3_Missense_Mutation_p.M49K	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	49					anterior commissure morphogenesis (GO:0021960)|chondrocyte differentiation (GO:0002062)|Clara cell differentiation (GO:0060486)|commissural neuron axon guidance (GO:0071679)|DNA replication (GO:0006260)|glial cell differentiation (GO:0010001)|hindbrain development (GO:0030902)|lung ciliated cell differentiation (GO:0061141)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000795)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|principal sensory nucleus of trigeminal nerve development (GO:0021740)|transcription from RNA polymerase II promoter (GO:0006366)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)	cerebellar mossy fiber (GO:0044300)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		ATCCTTTGACATTCGCTTCTC	0.453			T	"MYB, HGMA2"	"adenoid cystic carcinoma, lipoma"																																p.M75K	Esophageal Squamous(132;921 1730 14828 40753 46471)	.		Dom	yes		9	9p24.1	4781	nuclear factor I/B		E	.	NFIB-226	0			c.T224A						.						148	136	140					9																	14307404		2203	4300	6503	SO:0001583	missense	4781	exon2			TTTGACATTCGCT	U07810	CCDS6474.1, CCDS55291.1, CCDS55292.1, CCDS65007.1	9p24.1	2008-02-05			ENSG00000147862	ENSG00000147862			7785	protein-coding gene	gene with protein product		600728				7590749	Standard	NM_001190737		Approved	NFI-RED, NFIB2, NFIB3	uc003zlf.3	O00712	OTTHUMG00000021027	ENST00000380959.3:c.146T>A	9.37:g.14307404A>T	ENSP00000370346:p.Met49Lys	Somatic	81	1		WXS	Illumina HiSeq	Phase_I	96	8	NM_001190738	0	0	3	5	2	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	37	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.664854	0.67700	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000380921	T;T;T;T;T;T	0.59364	0.33;0.38;0.36;0.29;0.27;0.4	5.71	5.71	0.89125	CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.70343	0.3213	M	0.72118	2.19	0.80722	D	1	P;P;P	0.40431	0.717;0.717;0.717	P;P;P	0.52189	0.599;0.692;0.599	T	0.71076	-0.4697	10	0.48119	T	0.1	.	16.0042	0.80349	1.0:0.0:0.0:0.0	.	49;49;49	Q5VW27;Q5VW29;O00712	.;.;NFIB_HUMAN	K	75;49;49;49;49;49;49	ENSP00000370321:M75K;ENSP00000370346:M49K;ENSP00000370340:M49K;ENSP00000380705:M49K;ENSP00000380711:M49K;ENSP00000380709:M49K	ENSP00000370308:M49K	M	-	2	0	NFIB	14297404	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.171000	0.68590	0.528000	0.53228	ATG	.		0.453	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596		T	14307404	A	T	14307404	3	4	73	1	0	0	0	0	1	0	0	0	10397	217	8	5	1148	5	NFIB	9	14307404	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08		14307404	126906027	39	6872											
SNX30	401548	broad.mit.edu	37	chr9	115567070	115567071	+	Frame_Shift_Ins	INS	-	-	A																															tttaggatctcattttgcccINSaacggtggtactccagcagg																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr9:115567070_115567071insA	ENST00000374232.3	+	2	335_336	c.171_172insA	c.(172-174)aacfs	p.N58fs		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	58					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TCATTTTGCCCAACGGTGGTAC	0.401																																					p.P57fs													.	SNX30-68	0			c.171_172insA						.																																			SO:0001589	frameshift_variant	401548	exon2			TTTGCCCAACGGT	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"Sorting nexins"	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.173dupA	9.37:g.115567072_115567072dupA	ENSP00000363349:p.Asn58fs	Somatic	234	0		WXS	Illumina HiSeq	Phase_I	248	24	NM_001012994	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000374232.3	37	CCDS43865.1																																																																																			.		0.401	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1			A	115567071	-	A	115567070	7	5	73	1	0	1	1	0	0	0	0	0	14932	581	21	0	177	0	SNX30	9	115567070	Frame_Shift_Ins	INS	-	TCGA-BQ-5889-01A-11D-1589-08	101259666	115567070	25646361	40	6873											
GAPVD1	26130	broad.mit.edu;bcgsc.ca	37	chr9	128117986	128117986	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaagattttctgcagtttcTttatggtgcaatggcccagg	9	14	11	7	0	2	2	0	0	2	2	2	2	2	2	1	3	2	3	1	3	3	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr9:128117986T>A	ENST00000495955.1	+	25	4165	c.3875T>A	c.(3874-3876)cTt>cAt	p.L1292H	GAPVD1_ENST00000394083.2_Missense_Mutation_p.L1226H|GAPVD1_ENST00000297933.6_Missense_Mutation_p.L1274H|GAPVD1_ENST00000470056.1_Missense_Mutation_p.L1247H|GAPVD1_ENST00000312123.9_Missense_Mutation_p.L1253H|GAPVD1_ENST00000265956.4_Missense_Mutation_p.L1266H|GAPVD1_ENST00000394105.2_Missense_Mutation_p.L1301H|GAPVD1_ENST00000394104.2_Missense_Mutation_p.L1292H			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1292					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CTGCAGTTTCTTTATGGTGCA	0.413																																					p.L1301H													.	GAPVD1-93	0			c.T3902A						.						57	58	58					9																	128117986		2203	4300	6503	SO:0001583	missense	26130	exon24			AGTTTCTTTATGG		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.3875T>A	9.37:g.128117986T>A	ENSP00000419063:p.Leu1292His	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	65	7	NM_015635	0	0	8	9	1	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	T	28.7	4.941646	0.92526	.	.	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123	T;T;T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42;1.42;1.42	6.1	6.1	0.99115	.	0.000000	0.85682	D	0.000000	T	0.54351	0.1853	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.99;0.993;0.994;0.997;0.997;0.998	T	0.55952	-0.8059	10	0.87932	D	0	.	15.8671	0.79074	0.0:0.0:0.0:1.0	.	1292;307;1247;1253;1274;1301	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	H	1247;1301;1292;1266;1226;1292;1274;1253	ENSP00000419767:L1247H;ENSP00000377665:L1301H;ENSP00000377664:L1292H;ENSP00000265956:L1266H;ENSP00000377645:L1226H;ENSP00000419063:L1292H;ENSP00000297933:L1274H;ENSP00000309582:L1253H	ENSP00000265956:L1266H	L	+	2	0	GAPVD1	127157807	1.000000	0.71417	0.956000	0.39512	0.991000	0.79684	7.698000	0.84413	2.340000	0.79590	0.528000	0.53228	CTT	.		0.413	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128117986	T	A	128117986	3	1	73	1	0	0	0	0	1	0	0	0	6259	1609	56	5	3992	5	GAPVD1	9	128117986	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	12550916	128117986	13095445	41	6874											
RPL7A	6130	ucsc.edu	37	chr9	136216909	136216909	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctgtccttcgagcaggTgagtaggccccaccttaggg	7	8	12	14	1	0	1	0	1	0	0	2	2	1	1	6	3	1	2	6	3	2	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr9:136216909T>A	ENST00000323345.6	+	4	445		c.e4+2		SNORD24_ENST00000383884.1_RNA|MED22_ENST00000471524.1_5'Flank|SNORD36B_ENST00000363961.1_RNA|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000371999.1_5'Flank|SNORD36A_ENST00000362874.1_RNA|MED22_ENST00000344469.5_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000463740.1_Splice_Site|MED22_ENST00000476080.1_5'Flank|RPL7A_ENST00000315731.4_Splice_Site|MED22_ENST00000343730.5_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		TTCGAGCAGGTGAGTAGGCCC	0.532																																					.													.	RPL7A-90	0			c.415+2T>A						.						56	60	59					9																	136216909		2203	4300	6503	SO:0001630	splice_region_variant	6130	exon4			AGCAGGTGAGTAG	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.415+2T>A	9.37:g.136216909T>A		Somatic	95	1		WXS	Illumina HiSeq		80	2	NM_000972	0	0	1	1	0	P11518|Q5T8U4	Splice_Site	SNP	ENST00000323345.6	37	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.574485	0.65878	.	.	ENSG00000148303	ENST00000323345;ENST00000426651;ENST00000315731	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0455	0.64702	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPL7A	135206730	1.000000	0.71417	0.983000	0.44433	0.667000	0.39255	7.104000	0.77024	1.911000	0.55334	0.482000	0.46254	.	.		0.532	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	Intron	A	136216909	T	A	136216909	5	1	73	1	0	0	0	0	0	0	1	0	13632	1710	59	5	431	5	RPL7A	9	136216909	Splice_Site	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	8098923	136216909	4996522	42	6875											
STAM	8027	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	17735224	17735225	+	Missense_Mutation	DNP	GC	GC	AA																															ttcctcttttttgttaggctGcagaacaagcaaaagcaagc																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr10:17735224_17735225GC>AA	ENST00000377524.3	+	6	663_664	c.448_449GC>AA	c.(448-450)GCa>AAa	p.A150K	STAM_ENST00000540523.1_Missense_Mutation_p.A39K|RP11-390B4.3_ENST00000445235.1_RNA	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	150					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						TTGTTAGGCTGCAGAACAAGCA	0.406																																					p.A150K		.											.	STAM	0			c.C449A						.																																			SO:0001583	missense	8027	exon6			AGGCTGCAGAACA	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	Exception_encountered	10.37:g.17735224_17735225delinsAA	ENSP00000366746:p.Ala150Lys	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	122	10		0	0	0	0	0	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	DNP	ENST00000377524.3	37	CCDS7122.1																																																																																			.		0.406	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		AA	17735225	GC	AA	17735224	3	1	73	1	0	0	0	0	1	0	0	0	15280	1319	46	2	470	2	STAM	10	17735224	Missense_Mutation	DNP	GC	TCGA-BQ-5889-01A-11D-1589-08		17735224	117799523	43	6876											
BMS1	9790	hgsc.bcm.edu	37	chr10	43312105	43312105	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgtgcacaagggaaaatcAggccccaatactcaggtatg	14	6	11	10	1	2	0	2	0	0	0	2	2	2	1	2	3	2	2	2	3	6	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr10:43312105A>G	ENST00000374518.5	+	14	2451	c.2388A>G	c.(2386-2388)tcA>tcG	p.S796S		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	796					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AGGGAAAATCAGGCCCCAATA	0.483																																					p.S796S		.											.	BMS1-93	0			c.A2388G						.						110	115	113					10																	43312105		2203	4300	6503	SO:0001819	synonymous_variant	9790	exon14			AAAATCAGGCCCC	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2388A>G	10.37:g.43312105A>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_014753	0	0	10	10	0	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			.		0.483	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		G	43312105	A	G	43312105	2	3	73	1	0	0	0	0	0	0	0	1	1473	175	7	3		3	BMS1	10	43312105	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	25576881	43312105	92222642	44	6877											
AGAP7	653268	hgsc.bcm.edu;broad.mit.edu	37	chr10	51465326	51465326	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcttctttaggtgtttcTttttattggcatgaggagag	6	21	10	4	0	3	2	0	1	3	1	3	3	3	2	0	3	0	2	0	3	2	10			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr10:51465326T>G	ENST00000374095.5	-	7	1255	c.1130A>C	c.(1129-1131)aAg>aCg	p.K377T		NM_001077685.1	NP_001071153.1	Q5VUJ5	AGAP7_HUMAN		377	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	11						TAGGTGTTTCTTTTTATTGGC	0.522																																					p.K377T		.											.	.	0			c.A1130C						.						29	37	35					10																	51465326		1960	4050	6010	SO:0001583	missense	653268	exon7			TGTTTCTTTTTAT																												ENST00000374095.5:c.1130A>C	10.37:g.51465326T>G	ENSP00000363208:p.Lys377Thr	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	250	14	NM_001077685	0	0	37	37	0	A6NGH4	Missense_Mutation	SNP	ENST00000374095.5	37	CCDS41524.1	.	.	.	.	.	.	.	.	.	.	.	13.53	2.263837	0.39995	.	.	ENSG00000204169	ENST00000374095	T	0.58358	0.34	.	.	.	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.116826	0.56097	D	0.000029	T	0.67942	0.2947	M	0.86178	2.8	0.50632	D	0.999883	D	0.76494	0.999	D	0.80764	0.994	T	0.65063	-0.6259	9	0.87932	D	0	.	4.6093	0.12395	0.0:5.0E-4:0.0:0.9995	.	377	Q5VUJ5	AGAP7_HUMAN	T	377	ENSP00000363208:K377T	ENSP00000363208:K377T	K	-	2	0	AGAP7	51135332	1.000000	0.71417	0.026000	0.17262	0.026000	0.11368	2.111000	0.41883	0.149000	0.19098	0.147000	0.16070	AAG	.		0.522	AGAP7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048033.1			G	51465326	T	G	51465326	3	3	73	1	0	0	0	0	1	0	0	0	373	1609	56	5	865	5	AGAP7	10	51465326	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	8153221	51465326	84069421	45	6878											
KIAA1279	26128	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	70775391	70775391	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaaagcattcggaaaaaagCtgtgcagtttggaaccggtg	13	8	14	6	2	0	0	0	0	0	0	1	3	0	3	1	4	4	4	1	4	5	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr10:70775391C>T	ENST00000361983.4	+	7	1187	c.1085C>T	c.(1084-1086)gCt>gTt	p.A362V		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	362					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						CGGAAAAAAGCTGTGCAGTTT	0.413																																					p.A362V		.											.	KIAA1279-91	0			c.C1085T						.						104	102	103					10																	70775391		2203	4300	6503	SO:0001583	missense	26128	exon7			AAAAAGCTGTGCA	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1085C>T	10.37:g.70775391C>T	ENSP00000354848:p.Ala362Val	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	133	10	NM_015634	0	0	22	22	0	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	37	CCDS7284.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.816067	0.32145	.	.	ENSG00000198954	ENST00000361983	T	0.47528	0.84	5.51	4.59	0.56863	.	0.045642	0.85682	D	0.000000	T	0.44201	0.1282	M	0.62723	1.935	0.80722	D	1	B	0.21071	0.051	B	0.19946	0.027	T	0.30475	-0.9977	10	0.13470	T	0.59	-31.2821	15.2395	0.73458	0.0:0.9292:0.0:0.0708	.	362	Q96EK5	KBP_HUMAN	V	362	ENSP00000354848:A362V	ENSP00000354848:A362V	A	+	2	0	KIAA1279	70445397	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.856000	0.48341	2.763000	0.94921	0.650000	0.86243	GCT	.		0.413	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		T	70775391	C	T	70775391	3	4	73	1	0	0	0	0	1	0	0	0	8242	797	28	2	1111	2	KIAA1279	10	70775391	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	19310065	70775391	64759356	46	6879											
ZCCHC24	219654	ucsc.edu	37	chr10	81146146	81146146	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccaggaccttgcacttctcGcagaggtgctgcgggtgctc	5	9	13	14	2	1	1	0	0	1	1	3	2	1	2	2	3	4	4	2	3	0	2	rs145739202	byFrequency	TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr10:81146146G>A	ENST00000372336.3	-	4	867	c.681C>T	c.(679-681)tgC>tgT	p.C227C	ZCCHC24_ENST00000372333.3_Nonsense_Mutation_p.R168*|RP11-342M3.5_ENST00000438554.2_RNA	NM_153367.3	NP_699198.2	Q8N2G6	ZCH24_HUMAN	zinc finger, CCHC domain containing 24	227							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)	9						TGCACTTCTCGCAGAGGTGCT	0.692													G|||	2	0.000399361	0	0	5008	,	,		15598	0		0	False		,,,				2504	0.002				p.C227C													.	ZCCHC24-153	0			c.C681T						.	G		1,4405	2.1+/-5.4	0,1,2202	47	42	44		681	-4.6	1	10	dbSNP_134	44	0,8600		0,0,4300	no	coding-synonymous	ZCCHC24	NM_153367.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		227/242	81146146	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	219654	exon4			CTTCTCGCAGAGG	AK075279	CCDS7359.1	10q22.3	2014-02-20	2008-06-23	2008-06-23	ENSG00000165424	ENSG00000165424		"Zinc fingers, CCHC domain containing"	26911	protein-coding gene	gene with protein product	"zinc finger, 3CxxC-type 8"		"chromosome 10 open reading frame 56"	C10orf56		12477932	Standard	NM_153367		Approved	FLJ90798, Z3CXXC8	uc010qlr.2	Q8N2G6	OTTHUMG00000018561	ENST00000372336.3:c.681C>T	10.37:g.81146146G>A		Somatic	32	0		WXS	Illumina HiSeq		41	4	NM_153367	0	0	2	2	0	Q5U5T9|Q8TAG0	Silent	SNP	ENST00000372336.3	37	CCDS7359.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834625	0.91036	2.27E-4	0.0	ENSG00000165424	ENST00000372333	.	.	.	5.63	-4.64	0.03349	.	.	.	.	.	.	.	.	.	.	.	0.50632	D	0.999889	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-21.6282	15.151	0.72700	0.848:0.0:0.152:0.0	.	.	.	.	X	168	.	ENSP00000361408:R168X	R	-	1	2	ZCCHC24	80816152	0.132000	0.22450	0.965000	0.40720	0.980000	0.70556	-0.288000	0.08377	-0.667000	0.05303	-0.345000	0.07892	CGA	G|1.000;A|0.000		0.692	ZCCHC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048947.1	NM_153367		A	81146146	G	A	81146146	2	1	73	1	0	0	0	0	0	0	0	1	17620	1079	38	1		1	ZCCHC24	10	81146146	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	10370755	81146146	54388601	47	6880											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092643	1092643	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaccactcccagccctccaAcaaccaccacaaccacccct	12	3	1	25	0	0	0	0	0	0	0	2	0	2	0	10	0	4	0	10	0	3	0	rs149562922		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:1092643A>C	ENST00000441003.2	+	30	4489	c.4462A>C	c.(4462-4464)Aca>Cca	p.T1488P	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1489P|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4223	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caGCCCTCCAACAaccaccac	0.627																																					p.T1488P		.											.	MUC2-90	0			c.A4462C						.						302	443	394					11																	1092643		1680	3118	4798	SO:0001583	missense	4583	exon30			CCTCCAACAACCA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4462A>C	11.37:g.1092643A>C	ENSP00000415183:p.Thr1488Pro	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	18	5	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	-	3.842	-0.033557	0.07543	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15952	2.41;2.38	1.28	1.28	0.21552	.	0.642730	0.11935	U	0.515356	T	0.27063	0.0663	.	.	.	0.09310	N	0.999998	D	0.64830	0.994	P	0.62885	0.908	T	0.12344	-1.0551	9	0.30078	T	0.28	.	6.6385	0.22897	1.0:0.0:0.0:0.0	.	1488	E7EUV1	.	P	1488;1489	ENSP00000415183:T1488P;ENSP00000351956:T1489P	ENSP00000351956:T1489P	T	+	1	0	MUC2	1082643	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-2.044000	0.01411	0.654000	0.30846	0.000000	0.15137	ACA	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1092643	A	C	1092643	3	2	73	1	0	0	0	0	1	0	0	0	10000	43	2	5	4580	5	MUC2	11	1092643	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08		1092643	133913873	48	6881			1	22		6	6	493	N	T_C_A	4.883282e-17
MUC2	4583	hgsc.bcm.edu	37	chr11	1092795	1092795	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctccaccaaccaccacTcccatcaccaccaccaccac	12	3	0	26	0	1	0	1	0	0	0	3	0	3	0	11	0	1	0	11	0	1	0	rs12786761		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:1092795T>A	ENST00000441003.2	+	30	4641	c.4614T>A	c.(4612-4614)acT>acA	p.T1538T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1539T|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caaccaccactcccatcacca	0.627																																					p.T1538T		.											.	MUC2-90	0			c.T4614A						.						126	251	206					11																	1092795		1606	2836	4442	SO:0001819	synonymous_variant	4583	exon30			CACCACTCCCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4614T>A	11.37:g.1092795T>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092795	T	A	1092795	2	1	73	1	0	0	0	0	0	0	0	1	10000	1538	54	5		5	MUC2	11	1092795	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	152	1092795	133913721	49	6882			1	22		6	6	493	N	T_C_A	4.883282e-17
MUC2	4583	hgsc.bcm.edu	37	chr11	1092813	1092813	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcccatcaccaccaccacCacggtgaccccaaccccaac	12	3	3	23	1	1	1	1	1	0	0	2	1	2	1	9	1	2	0	9	1	2	0	rs12577898|rs199900755		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:1092813C>T	ENST00000441003.2	+	30	4659	c.4632C>T	c.(4630-4632)acC>acT	p.T1544T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1545T|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccaccacGGTGACCC	0.637																																					p.T1544T		.											.	MUC2-90	0			c.C4632T						.						47	95	78					11																	1092813		1759	3190	4949	SO:0001819	synonymous_variant	4583	exon30			CACCACCACGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4632C>T	11.37:g.1092813C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	49	7	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092813	C	T	1092813	2	4	73	1	0	0	0	0	0	0	0	1	10000	581	21	2		2	MUC2	11	1092813	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	18	1092813	133913703	50	6883			1	22		6	6	493	N	T_C_A	4.883282e-17
MUC2	4583	hgsc.bcm.edu	37	chr11	1093091	1093091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccatcaccaccaccactaCggtgaccccaaccccaacac	13	3	4	21	1	1	1	1	1	0	0	1	1	1	1	8	1	4	0	8	1	3	1			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:1093091C>T	ENST00000441003.2	+	30	4937	c.4910C>T	c.(4909-4911)aCg>aTg	p.T1637M	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1604M|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccactacggtgacccca	0.627																																					p.T1637M		.											.	MUC2-90	0			c.C4910T						.																																			SO:0001583	missense	4583	exon30			CCACTACGGTGAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4910C>T	11.37:g.1093091C>T	ENSP00000415183:p.Thr1637Met	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	76	7	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.843	-0.033403	0.07543	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15372	2.43;2.73	1.75	0.773	0.18516	.	76.623900	0.01155	U	0.006513	T	0.15825	0.0381	.	.	.	0.09310	N	1	D	0.63046	0.992	P	0.45428	0.48	T	0.19745	-1.0296	9	0.44086	T	0.13	.	3.5968	0.08009	0.0:0.744:0.0:0.256	.	1637	E7EUV1	.	M	1637;1604	ENSP00000415183:T1637M;ENSP00000351956:T1604M	ENSP00000351956:T1604M	T	+	2	0	MUC2	1083091	0.002000	0.14202	0.012000	0.15200	0.183000	0.23260	0.515000	0.22801	1.016000	0.39470	0.121000	0.15741	ACG	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093091	C	T	1093091	3	4	73	1	0	0	0	0	1	0	0	0	10000	536	19	1	5028	1	MUC2	11	1093091	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	278	1093091	133913425	51	6884			1	22		6	6	493	N	T_C_A	4.883282e-17
MUC2	4583	hgsc.bcm.edu	37	chr11	1093116	1093116	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accccaaccccaacacccacCggcacacagaccccaaccac	14	0	3	24	1	0	1	0	0	0	1	0	1	0	1	9	1	3	1	9	1	3	0	rs111163724		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:1093116C>T	ENST00000441003.2	+	30	4962	c.4935C>T	c.(4933-4935)acC>acT	p.T1645T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1612T|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caacacccaccggcacacaga	0.627																																					p.T1645T		.											.	MUC2-90	0			c.C4935T						.						68	124	105					11																	1093116		1783	3351	5134	SO:0001819	synonymous_variant	4583	exon30			ACCCACCGGCACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4935C>T	11.37:g.1093116C>T		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	85	11	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093116	C	T	1093116	2	4	73	1	0	0	0	0	0	0	0	1	10000	639	23	1		1	MUC2	11	1093116	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	25	1093116	133913400	52	6885			1	22		6	6	493	N	T_C_A	4.883282e-17
MUC2	4583	hgsc.bcm.edu	37	chr11	1093135	1093135	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcacacagaccccaaccAcgacacccatcaccaccacc	13	1	4	23	2	1	1	1	0	0	1	1	2	1	1	8	1	1	1	8	1	1	0	rs56080332		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:1093135A>C	ENST00000441003.2	+	30	4981	c.4954A>C	c.(4954-4956)Acg>Ccg	p.T1652P	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1619P|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaaccacgacacccat	0.627																																					p.T1652P		.											.	MUC2-90	0			c.A4954C						.						104	167	145					11																	1093135		1799	3362	5161	SO:0001583	missense	4583	exon30			CCAACCACGACAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4954A>C	11.37:g.1093135A>C	ENSP00000415183:p.Thr1652Pro	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	86	19	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	1.105	-0.659880	0.03454	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.08370	3.1;3.14	1.75	-3.51	0.04696	.	7739.210000	0.00166	N	0.000003	T	0.05914	0.0154	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34304	-0.9834	9	0.46703	T	0.11	.	3.4472	0.07484	0.5097:0.3224:0.0:0.1679	rs56080332	1652	E7EUV1	.	P	1652;1619	ENSP00000415183:T1652P;ENSP00000351956:T1619P	ENSP00000351956:T1619P	T	+	1	0	MUC2	1083135	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.830000	0.00744	-1.075000	0.03129	-1.890000	0.00535	ACG	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1093135	A	C	1093135	3	2	73	1	0	0	0	0	1	0	0	0	10000	159	6	5	5072	5	MUC2	11	1093135	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	19	1093135	133913381	53	6886			1	22		6	6	493	N	T_C_A	4.883282e-17
PTPRJ	5795	hgsc.bcm.edu;broad.mit.edu	37	chr11	48152110	48152110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatcatttcagatgcataTcacacaggagggagctggca	14	8	11	8	0	3	2	3	0	0	2	3	4	3	4	0	3	2	3	0	3	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:48152110T>C	ENST00000418331.2	+	8	1809	c.1457T>C	c.(1456-1458)aTc>aCc	p.I486T	PTPRJ_ENST00000440289.2_Missense_Mutation_p.I486T	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	486	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CAGATGCATATCACACAGGAG	0.478																																					p.I486T		.											.	PTPRJ-541	0			c.T1457C						.						99	90	93					11																	48152110		2201	4298	6499	SO:0001583	missense	5795	exon8			TGCATATCACACA	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1457T>C	11.37:g.48152110T>C	ENSP00000400010:p.Ile486Thr	Somatic	50	1		WXS	Illumina HiSeq	Phase_I	53	6	NM_001098503	0	0	22	24	2	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	9.901	1.207011	0.22205	.	.	ENSG00000149177	ENST00000418331;ENST00000440289	T;T	0.54479	0.57;0.57	5.71	-6.38	0.01957	Fibronectin, type III (3);Immunoglobulin-like fold (1);	.	.	.	.	T	0.33789	0.0875	N	0.20986	0.625	0.09310	N	1	B;B	0.23490	0.007;0.086	B;B	0.21360	0.006;0.034	T	0.24048	-1.0171	9	0.21014	T	0.42	.	14.7241	0.69329	0.0:0.1541:0.0:0.8459	.	486;486	Q12913;Q6P4H4	PTPRJ_HUMAN;.	T	486	ENSP00000400010:I486T;ENSP00000409733:I486T	ENSP00000400010:I486T	I	+	2	0	PTPRJ	48108686	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.726000	0.04936	-0.899000	0.03901	0.533000	0.62120	ATC	.		0.478	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			C	48152110	T	C	48152110	3	2	73	1	0	0	0	0	1	0	0	0	12836	1435	50	3	1487	3	PTPRJ	11	48152110	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	47058975	48152110	86854406	54	6887											
KAT5	10524	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	65480307	65480307	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgtccattacattgactgTgagttctgggcctgaggtgg	7	13	13	8	1	1	3	0	3	1	0	2	3	2	3	2	3	2	1	2	3	2	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:65480307T>A	ENST00000377046.3	+	3	420		c.e3+2		KAT5_ENST00000530446.1_Splice_Site|KAT5_ENST00000341318.4_Splice_Site|KAT5_ENST00000525204.1_Splice_Site|KAT5_ENST00000352980.4_Splice_Site|KAT5_ENST00000534650.1_Splice_Site	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5						androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						ACATTGACTGTGAGTTCTGGG	0.547																																					.		.											.	KAT5-90	0			c.247+2T>A						.						123	117	119					11																	65480307		2201	4297	6498	SO:0001630	splice_region_variant	10524	exon2			TGACTGTGAGTTC	U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.148+2T>A	11.37:g.65480307T>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	117	8	NM_001206833	0	0	0	0	0	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Splice_Site	SNP	ENST00000377046.3	37	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	t	17.79	3.475097	0.63737	.	.	ENSG00000172977	ENST00000377046;ENST00000352980;ENST00000341318;ENST00000530446;ENST00000530605;ENST00000528198;ENST00000531880	.	.	.	4.3	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4329	0.50052	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KAT5	65236883	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.458000	0.66679	1.822000	0.53115	0.459000	0.35465	.	.		0.547	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388	Intron	A	65480307	T	A	65480307	5	1	73	1	0	0	0	0	0	0	1	0	8004	1710	59	5	255	5	KAT5	11	65480307	Splice_Site	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	17328197	65480307	69526209	55	6888											
NDUFV1	4723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67379406	67379406	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgcccgcctcattgagttCtataagcacgagagctgtgg	9	10	11	11	3	2	2	1	1	1	1	3	3	2	2	2	1	2	3	2	1	2	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:67379406C>A	ENST00000322776.6	+	8	1272	c.1119C>A	c.(1117-1119)ttC>ttA	p.F373L	NDUFV1_ENST00000415352.2_Missense_Mutation_p.F366L|NDUFV1_ENST00000526169.1_3'UTR|DOC2GP_ENST00000495263.1_RNA|NDUFV1_ENST00000532303.1_Missense_Mutation_p.F272L|NDUFV1_ENST00000529927.1_Missense_Mutation_p.F364L	NM_001166102.1|NM_007103.3	NP_001159574.1|NP_009034.2	P49821	NDUV1_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa	373					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(3)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	16						TCATTGAGTTCTATAAGCACG	0.612																																					p.F373L		.											.	NDUFV1-91	0			c.C1119A						.						130	117	122					11																	67379406		2200	4294	6494	SO:0001583	missense	4723	exon8			TGAGTTCTATAAG	AF092131	CCDS8173.1, CCDS53669.1	11q13	2011-07-04	2002-08-29		ENSG00000167792	ENSG00000167792	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7716	protein-coding gene	gene with protein product	"complex I 51kDa subunit", "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial"	161015	"NADH dehydrogenase (ubiquinone) flavoprotein 1 (51kD)"			1478657	Standard	NM_007103		Approved	CI-51K	uc001omj.2	P49821	OTTHUMG00000166215	ENST00000322776.6:c.1119C>A	11.37:g.67379406C>A	ENSP00000322450:p.Phe373Leu	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	124	12	NM_007103	1	0	260	287	26	O60924|O60940|Q16104|Q6IBR3|Q96BF8|Q96HS7	Missense_Mutation	SNP	ENST00000322776.6	37	CCDS8173.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834500	0.91036	.	.	ENSG00000167792	ENST00000322776;ENST00000532303;ENST00000529927;ENST00000415352;ENST00000453836	D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08	4.89	3.98	0.46160	NADH ubiquinone oxidoreductase, F subunit, iron sulphur binding (2);	0.000000	0.85682	D	0.000000	D	0.97495	0.9180	H	0.98370	4.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.999	D	0.97852	1.0275	10	0.87932	D	0	-20.1332	12.1898	0.54264	0.0:0.9151:0.0:0.0849	.	366;364;373	G3V0I5;P49821-2;P49821	.;.;NDUV1_HUMAN	L	373;272;364;366;244	ENSP00000322450:F373L;ENSP00000432015:F272L;ENSP00000436766:F364L;ENSP00000395368:F366L	ENSP00000322450:F373L	F	+	3	2	NDUFV1	67135982	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.801000	0.55545	1.189000	0.43028	0.491000	0.48974	TTC	.		0.612	NDUFV1-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388406.1	NM_007103		A	67379406	C	A	67379406	3	1	73	1	0	0	0	0	1	0	0	0	10325	912	32	4	1149	4	NDUFV1	11	67379406	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	1899099	67379406	67627110	56	6889											
HYLS1	219844	hgsc.bcm.edu	37	chr11	125769383	125769383	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagggtgaaggagatgtcagGagagaagcccaatctatcca	14	6	13	8	0	2	3	1	1	1	2	3	6	3	4	2	3	1	0	2	3	4	1			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:125769383G>T	ENST00000425380.2	+	3	901	c.120G>T	c.(118-120)agG>agT	p.R40S	HYLS1_ENST00000526028.1_Missense_Mutation_p.R40S|HYLS1_ENST00000356438.3_Missense_Mutation_p.R40S|PUS3_ENST00000227474.3_Intron	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	40						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		GAGATGTCAGGAGAGAAGCCC	0.488																																					p.R40S	Esophageal Squamous(172;2590 2636 8884 10471)	.											.	HYLS1-91	0			c.G120T						.						88	79	82					11																	125769383		2201	4299	6500	SO:0001583	missense	219844	exon3			TGTCAGGAGAGAA	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.120G>T	11.37:g.125769383G>T	ENSP00000414884:p.Arg40Ser	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	81	5	NM_001134793	0	0	2	4	2	B3KXI8|Q96BX9	Missense_Mutation	SNP	ENST00000425380.2	37	CCDS8467.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.446536	0.25987	.	.	ENSG00000198331	ENST00000356438;ENST00000425380;ENST00000526028	T;T;T	0.63580	-0.05;-0.05;-0.05	6.17	1.81	0.25067	.	0.207432	0.29501	N	0.011979	T	0.42854	0.1221	L	0.44542	1.39	0.29443	N	0.859016	P	0.41848	0.763	B	0.31101	0.124	T	0.40905	-0.9538	10	0.40728	T	0.16	.	6.3201	0.21213	0.3191:0.162:0.5189:0.0	.	40	Q96M11	HYLS1_HUMAN	S	40	ENSP00000348815:R40S;ENSP00000414884:R40S;ENSP00000436833:R40S	ENSP00000348815:R40S	R	+	3	2	HYLS1	125274593	0.982000	0.34865	0.982000	0.44146	0.989000	0.77384	0.896000	0.28377	0.507000	0.28148	0.655000	0.94253	AGG	.		0.488	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014		T	125769383	G	T	125769383	3	4	73	1	0	0	0	0	1	0	0	0	7490	1165	41	4	122	4	HYLS1	11	125769383	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	58389977	125769383	9237133	57	6890											
PEX5	5830	bcgsc.ca	37	chr12	7362624	7362624	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttccttacagggaggcTgtggagcactttctggaggc	6	12	13	10	0	2	0	0	0	2	0	3	3	3	3	1	5	2	2	1	5	1	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr12:7362624T>G	ENST00000455147.2	+	17	2305	c.1725T>G	c.(1723-1725)gcT>gcG	p.A575A	PEX5_ENST00000266564.3_Silent_p.A567A|PEX5_ENST00000420616.2_Silent_p.A575A|PEX5_ENST00000266563.5_Silent_p.A538A|PEX5_ENST00000434354.2_Silent_p.A590A|PEX5_ENST00000412720.2_Silent_p.A596A	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	575					cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						ACAGGGAGGCTGTGGAGCACT	0.567																																					p.A590A													.	PEX5-91	0			c.T1770G						.						40	41	41					12																	7362624		2203	4300	6503	SO:0001819	synonymous_variant	5830	exon16			GGAGGCTGTGGAG	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"Tetratricopeptide (TTC) repeat domain containing"	9719	protein-coding gene	gene with protein product		600414	"peroxisome receptor 1"	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.1725T>G	12.37:g.7362624T>G		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	51	5	NM_001131023	0	0	0	0	0	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	37	CCDS44823.1																																																																																			.		0.567	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319		G	7362624	T	G	7362624	2	3	73	1	0	0	0	0	0	0	0	1	11774	1567	55	5		5	PEX5	12	7362624	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		7362624	126489271	58	6891											
SLC26A10	65012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	58016635	58016635	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctggctgactcgctgcccaTtgcactggttagttttgcgg	4	14	12	11	2	1	1	0	1	1	0	2	1	1	1	1	3	3	5	1	3	1	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr12:58016635T>C	ENST00000320442.4	+	6	1168	c.857T>C	c.(856-858)aTt>aCt	p.I286T	SLC26A10_ENST00000379218.2_Missense_Mutation_p.I286T	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	286						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					TCGCTGCCCATTGCACTGGTT	0.572																																					p.I286T		.											.	SLC26A10-531	0			c.T857C						.						110	91	98					12																	58016635		2203	4300	6503	SO:0001583	missense	65012	exon6			TGCCCATTGCACT		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"Solute carriers"	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.857T>C	12.37:g.58016635T>C	ENSP00000320217:p.Ile286Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	114	15	NM_133489	0	0	0	0	0	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	.	14.38	2.518982	0.44866	.	.	ENSG00000135502	ENST00000320442;ENST00000379218	D;D	0.93547	-3.24;-3.24	3.76	3.76	0.43208	Sulphate transporter (1);	.	.	.	.	D	0.94850	0.8336	M	0.91090	3.175	0.42787	D	0.993885	P	0.45283	0.855	P	0.46685	0.524	D	0.94723	0.7902	9	0.45353	T	0.12	.	11.1297	0.48339	0.0:0.0:0.0:1.0	.	286	Q8NG04	S2610_HUMAN	T	286	ENSP00000320217:I286T;ENSP00000368520:I286T	ENSP00000320217:I286T	I	+	2	0	SLC26A10	56302902	0.996000	0.38824	0.902000	0.35471	0.457000	0.32468	6.621000	0.74228	1.941000	0.56285	0.523000	0.50628	ATT	.		0.572	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			C	58016635	T	C	58016635	3	2	73	1	0	0	0	0	1	0	0	0	14547	1493	52	3	879	3	SLC26A10	12	58016635	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	50654011	58016635	75835260	59	6892											
YEATS4	8089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	69759615	69759615	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgaaacaggatggggtgAattcgaaataatcatcaaaa	18	9	9	5	1	2	2	2	2	0	0	3	4	2	3	0	3	2	0	0	3	7	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr12:69759615A>C	ENST00000247843.2	+	4	554	c.284A>C	c.(283-285)gAa>gCa	p.E95A	YEATS4_ENST00000548020.1_Intron	NM_006530.2	NP_006521.1	O95619	YETS4_HUMAN	YEATS domain containing 4	95	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding transcription factor activity (GO:0003700)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(1)	5	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			GGATGGGGTGAATTCGAAATA	0.279																																					p.E95A		.											.	YEATS4-226	0			c.A284C						.						74	78	76					12																	69759615		2203	4292	6495	SO:0001583	missense	8089	exon4			GGGGTGAATTCGA	AJ245746	CCDS8990.1, CCDS73495.1	12q13-q15	2008-02-05				ENSG00000127337			24859	protein-coding gene	gene with protein product		602116				9302258, 11903063	Standard	XM_005269163		Approved	NuBI-1, GAS41, YAF9	uc001sux.3	O95619	OTTHUMG00000169358	ENST00000247843.2:c.284A>C	12.37:g.69759615A>C	ENSP00000247843:p.Glu95Ala	Somatic	173	1		WXS	Illumina HiSeq	Phase_I	190	33	NM_006530	0	0	8	9	1	Q9NQD0	Missense_Mutation	SNP	ENST00000247843.2	37	CCDS8990.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.784664	0.90282	.	.	ENSG00000127337	ENST00000247843;ENST00000549685;ENST00000552955	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.88411	0.6429	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92459	0.5976	8	.	.	.	-26.0432	16.1327	0.81454	1.0:0.0:0.0:0.0	.	95	O95619	YETS4_HUMAN	A	95;37;136	.	.	E	+	2	0	YEATS4	68045882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.653000	0.91088	2.269000	0.75478	0.454000	0.30748	GAA	.		0.279	YEATS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403663.1	NM_006530		C	69759615	A	C	69759615	3	2	73	1	0	0	0	0	1	0	0	0	17506	246	9	5	298	5	YEATS4	12	69759615	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	11742980	69759615	64092280	60	6893											
KCNC2	3747	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	75436984	75436984	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagagcattgcctgccaaGcccgctatgttgtttaagct	8	12	9	12	1	1	1	1	0	0	1	1	1	1	1	3	0	5	5	3	0	3	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr12:75436984G>T	ENST00000549446.1	-	5	2498	c.1818C>A	c.(1816-1818)ggC>ggA	p.G606G	KCNC2_ENST00000298972.1_Intron|KCNC2_ENST00000550433.1_Intron|KCNC2_ENST00000548513.1_Intron|KCNC2_ENST00000350228.2_Intron|KCNC2_ENST00000540018.1_Silent_p.G551G|RP11-81K13.1_ENST00000550049.1_RNA|RP11-81K13.1_ENST00000547040.1_RNA|RP11-81K13.1_ENST00000549762.1_RNA|KCNC2_ENST00000341669.3_Intron	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	606					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	TGCCTGCCAAGCCCGCTATGT	0.423																																					p.G606G		.											.	KCNC2-224	0			c.C1818A						.						144	137	139					12																	75436984		2203	4300	6503	SO:0001819	synonymous_variant	3747	exon5			TGCCAAGCCCGCT	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.1818C>A	12.37:g.75436984G>T		Somatic	86	1		WXS	Illumina HiSeq	Phase_I	97	7	NM_139137	0	0	0	0	0	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	37	CCDS9007.1																																																																																			.		0.423	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		T	75436984	G	T	75436984	2	4	73	1	0	0	0	0	0	0	0	1	8036	958	34	4		4	KCNC2	12	75436984	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	5677369	75436984	58414911	61	6894											
UBE3B	89910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	109939240	109939240	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggggggtgcctctgatcCggatcttcttctgtgacatc	4	14	13	10	1	4	2	0	2	4	0	6	3	5	3	2	4	1	0	2	4	0	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr12:109939240C>T	ENST00000342494.3	+	13	1778	c.1183C>T	c.(1183-1185)Cgg>Tgg	p.R395W	UBE3B_ENST00000434735.2_Missense_Mutation_p.R395W|UBE3B_ENST00000535900.1_3'UTR|UBE3B_ENST00000280774.5_Missense_Mutation_p.R395W	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	395					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GCCTCTGATCCGGATCTTCTT	0.552																																					p.R395W		.											.	UBE3B-660	0			c.C1183T						.						151	140	144					12																	109939240		2203	4300	6503	SO:0001583	missense	89910	exon13			CTGATCCGGATCT	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1183C>T	12.37:g.109939240C>T	ENSP00000340596:p.Arg395Trp	Somatic	158	1		WXS	Illumina HiSeq	Phase_I	218	33	NM_130466	0	0	0	0	0	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.688603	0.88639	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494	T;T;T;T	0.49720	1.11;0.77;1.37;1.11	5.55	4.65	0.58169	.	0.153047	0.64402	D	0.000013	T	0.50650	0.1628	L	0.59436	1.845	0.80722	D	1	D	0.69078	0.997	P	0.46452	0.517	T	0.57768	-0.7754	10	0.87932	D	0	-2.6712	14.5289	0.67909	0.1478:0.8522:0.0:0.0	.	395	Q7Z3V4	UBE3B_HUMAN	W	395	ENSP00000391529:R395W;ENSP00000280774:R395W;ENSP00000443131:R395W;ENSP00000340596:R395W	ENSP00000280774:R395W	R	+	1	2	UBE3B	108423623	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.837000	0.55820	1.314000	0.45095	0.655000	0.94253	CGG	.		0.552	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		T	109939240	C	T	109939240	3	4	73	1	0	0	0	0	1	0	0	0	16913	643	23	1	1225	1	UBE3B	12	109939240	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	34502256	109939240	23912655	62	6895											
ZMYM5	9205	hgsc.bcm.edu;ucsc.edu	37	chr13	20398872	20398872	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatagacaaaacacagaatcTtttgaggttgaataaagtaa	19	11	7	4	0	1	4	0	2	1	2	1	4	1	4	0	1	1	2	0	1	9	7			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr13:20398872T>C	ENST00000337963.4	-	8	2019	c.1755A>G	c.(1753-1755)aaA>aaG	p.K585K		NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	585						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		acacagaatcttttgaggttg	0.333																																					p.K585K		.											.	ZMYM5-90	0			c.A1755G						.						27	23	24					13																	20398872		1567	3581	5148	SO:0001819	synonymous_variant	9205	exon8			AGAATCTTTTGAG	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.1755A>G	13.37:g.20398872T>C		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	35	4	NM_001142684	0	0	3	3	0	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Silent	SNP	ENST00000337963.4	37																																																																																				.		0.333	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		C	20398872	T	C	20398872	2	2	73	1	0	0	0	0	0	0	0	1	17735	1606	56	3		3	ZMYM5	13	20398872	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		20398872	94771006	63	6896											
TNFRSF19	55504	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	24243093	24243093	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtccagtctcattctgaaAactttacagcagctactgat	12	12	6	11	0	2	2	1	2	2	0	4	2	3	2	1	0	5	2	1	0	4	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr13:24243093A>C	ENST00000382258.4	+	9	1306	c.1102A>C	c.(1102-1104)Aac>Cac	p.N368H	TNFRSF19_ENST00000382263.3_Missense_Mutation_p.N368H|TNFRSF19_ENST00000248484.4_Missense_Mutation_p.N368H|TNFRSF19_ENST00000403372.2_Missense_Mutation_p.N236H	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	368					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		TCATTCTGAAAACTTTACAGC	0.413																																					p.N368H		.											.	TNFRSF19-228	0			c.A1102C						.						113	115	114					13																	24243093		2203	4300	6503	SO:0001583	missense	55504	exon9			TCTGAAAACTTTA	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"Tumor necrosis factor receptor superfamily"	11915	protein-coding gene	gene with protein product	"toxicity and JNK inducer"	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.1102A>C	13.37:g.24243093A>C	ENSP00000371693:p.Asn368His	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	160	14	NM_018647	0	0	5	5	0	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.042549	0.55003	.	.	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.79749	-1.29;1.32;-1.3;-1.29	5.71	3.22	0.36961	.	0.505867	0.20968	N	0.082460	T	0.78892	0.4355	L	0.27053	0.805	0.09310	N	1	D;D;D	0.63880	0.986;0.993;0.993	P;P;P	0.58873	0.794;0.847;0.847	T	0.69176	-0.5214	10	0.66056	D	0.02	-3.4156	8.9366	0.35704	0.853:0.0:0.147:0.0	.	236;368;368	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	H	368;236;368;368	ENSP00000248484:N368H;ENSP00000385408:N236H;ENSP00000371693:N368H;ENSP00000371698:N368H	ENSP00000248484:N368H	N	+	1	0	TNFRSF19	23141093	0.007000	0.16637	0.000000	0.03702	0.006000	0.05464	0.827000	0.27421	0.422000	0.26005	0.533000	0.62120	AAC	.		0.413	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647		C	24243093	A	C	24243093	3	2	73	1	0	0	0	0	1	0	0	0	16324	14	1	5	1132	5	TNFRSF19	13	24243093	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	3844221	24243093	90926785	64	6897											
CKAP2	26586	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	53042426	53042426	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattaagcctattgaagagaTgcgacacacgattgtagata	16	10	9	6	2	0	3	0	1	0	2	0	6	0	3	1	0	2	1	1	0	6	6			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr13:53042426T>A	ENST00000378037.5	+	7	1583	c.1493T>A	c.(1492-1494)aTg>aAg	p.M498K	CKAP2_ENST00000258607.5_Missense_Mutation_p.M497K|CKAP2_ENST00000490903.1_Missense_Mutation_p.M449K	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		ATTGAAGAGATGCGACACACG	0.299																																					p.M498K		.											.	CKAP2-92	0			c.T1493A						.						97	100	99					13																	53042426		2203	4300	6503	SO:0001583	missense	26586	exon7			AAGAGATGCGACA	AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1493T>A	13.37:g.53042426T>A	ENSP00000367276:p.Met498Lys	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	44	4	NM_001098525	0	0	8	8	0		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	.	.	.	.	.	.	.	.	.	.	.	16.76	3.211433	0.58343	.	.	ENSG00000136108	ENST00000258607;ENST00000378037;ENST00000490903	T;T;T	0.26373	1.74;1.74;1.74	5.53	5.53	0.82687	.	0.149392	0.47093	D	0.000251	T	0.32941	0.0846	M	0.74881	2.28	0.43959	D	0.99663	P;P;P	0.42409	0.61;0.61;0.779	B;B;B	0.41036	0.346;0.346;0.346	T	0.23904	-1.0175	10	0.87932	D	0	-5.2435	12.0802	0.53667	0.0:0.0:0.0:1.0	.	449;498;497	E9PD90;Q8WWK9;B2RMQ4	.;CKAP2_HUMAN;.	K	497;498;449	ENSP00000258607:M497K;ENSP00000367276:M498K;ENSP00000417830:M449K	ENSP00000258607:M497K	M	+	2	0	CKAP2	51940427	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.810000	0.55613	2.100000	0.63781	0.533000	0.62120	ATG	.		0.299	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2			A	53042426	T	A	53042426	3	1	73	1	0	0	0	0	1	0	0	0	3448	1464	51	5	1519	5	CKAP2	13	53042426	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	28799333	53042426	62127452	65	6898											
AP1G2	8906	ucsc.edu	37	chr14	24032631	24032631	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcattgtagaggcggcgcacAgagtaggcatgtagctcctg	9	8	15	9	2	0	2	0	0	0	2	1	2	1	2	1	3	1	7	1	3	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr14:24032631A>T	ENST00000308724.5	-	13	2123	c.1368T>A	c.(1366-1368)tcT>tcA	p.S456S	RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000397120.3_Silent_p.S456S|RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000556277.1_5'Flank	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	456					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		GGCGGCGCACAGAGTAGGCAT	0.632											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S456S													.	AP1G2-45	0			c.T1368A						.						62	51	54					14																	24032631		2203	4300	6503	SO:0001819	synonymous_variant	8906	exon14			GCGCACAGAGTAG	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1368T>A	14.37:g.24032631A>T		Somatic	17	0	768	WXS	Illumina HiSeq		24	1	NM_003917	0	0	42	47	5	D3DS51|O75504	Silent	SNP	ENST00000308724.5	37	CCDS9602.1																																																																																			.		0.632	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		T	24032631	A	T	24032631	2	4	73	1	0	0	0	0	0	0	0	1	733	175	7	5		5	AP1G2	14	24032631	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08		24032631	83316909	66	6899											
CLEC14A	161198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	38723829	38723829	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccgcagatcacagtcccCgactttcaccccattgtttg	7	11	7	16	2	2	1	2	0	0	1	4	2	4	1	5	0	0	2	5	0	0	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr14:38723829C>T	ENST00000342213.2	-	1	1745	c.1399G>A	c.(1399-1401)Ggg>Agg	p.G467R		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	467						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		TCACAGTCCCCGACTTTCACC	0.597																																					p.G467R		.											.	CLEC14A-94	0			c.G1399A						.						75	77	76					14																	38723829		2203	4300	6503	SO:0001583	missense	161198	exon1			AGTCCCCGACTTT		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.1399G>A	14.37:g.38723829C>T	ENSP00000353013:p.Gly467Arg	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	160	22	NM_175060	0	0	79	79	0	Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	37	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	C	8.642	0.896202	0.17686	.	.	ENSG00000176435	ENST00000342213	T	0.73681	-0.77	4.19	-6.15	0.02105	.	0.640736	0.12966	N	0.424617	T	0.50343	0.1610	L	0.27053	0.805	0.09310	N	1	B	0.20459	0.045	B	0.09377	0.004	T	0.33624	-0.9861	10	0.87932	D	0	-0.4303	2.5087	0.04652	0.1371:0.2062:0.1279:0.5287	.	467	Q86T13	CLC14_HUMAN	R	467	ENSP00000353013:G467R	ENSP00000353013:G467R	G	-	1	0	CLEC14A	37793580	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	0.081000	0.14823	-1.071000	0.03145	-0.253000	0.11424	GGG	.		0.597	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		T	38723829	C	T	38723829	3	4	73	1	0	0	0	0	1	0	0	0	3505	652	23	1	77	1	CLEC14A	14	38723829	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	14691198	38723829	68625711	67	6900											
C14orf73	91828	hgsc.bcm.edu	37	chr14	103569064	103569064	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcgacgcccgcggctgcgAgcagctctatatcctgctgg	5	7	14	15	6	1	0	0	0	1	0	2	2	2	0	2	2	4	4	2	2	2	2	rs200540457	byFrequency	TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr14:103569064A>G	ENST00000380069.3	+	2	1080	c.1004A>G	c.(1003-1005)gAg>gGg	p.E335G		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	335					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						CGCGGCTGCGAGCAGCTCTAT	0.721													A|||	5	0.000998403	0	0	5008	,	,		13331	0		0.003	False		,,,				2504	0.002				p.E335G		.											.	EXOC3L4-23	0			c.A1004G						.	A	GLY/GLU	3,3927		0,3,1962	3	5	4		1004	4.1	1	14		4	16,7720		0,16,3852	yes	missense	EXOC3L4	NM_001077594.1	98	0,19,5814	GG,GA,AA		0.2068,0.0763,0.1629	probably-damaging	335/723	103569064	19,11647	1965	3868	5833	SO:0001583	missense	91828	exon2			GCTGCGAGCAGCT	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 73"	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.1004A>G	14.37:g.103569064A>G	ENSP00000369409:p.Glu335Gly	Somatic	7	1		WXS	Illumina HiSeq	Phase_I	5	4	NM_001077594	0	0	0	2	2	Q14CR2	Missense_Mutation	SNP	ENST00000380069.3	37	CCDS32163.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.008818	0.54361	7.63E-4	0.002068	ENSG00000205436	ENST00000380069	T	0.07444	3.19	4.09	4.09	0.47781	.	0.167420	0.38897	N	0.001524	T	0.22205	0.0535	M	0.65975	2.015	0.33684	D	0.612504	D	0.57257	0.979	P	0.62885	0.908	T	0.24977	-1.0145	10	0.52906	T	0.07	-28.7086	11.0792	0.48049	1.0:0.0:0.0:0.0	.	335	Q17RC7	EX3L4_HUMAN	G	335	ENSP00000369409:E335G	ENSP00000369409:E335G	E	+	2	0	EXOC3L4	102638817	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	2.142000	0.42177	1.726000	0.51525	0.402000	0.26972	GAG	.		0.721	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093		G	103569064	A	G	103569064	3	3	73	1	0	0	0	0	1	0	0	0	1783	304	11	3	1010	3	C14orf73	14	103569064	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	64845235	103569064	3780476	68	6901											
C15orf2	23742	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	24923231	24923231	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacaacccagcggcaacacTgcctcagtccaaggctccac	12	4	7	18	1	1	0	1	0	0	0	3	0	3	0	4	2	4	2	4	2	3	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:24923231T>A	ENST00000329468.2	+	1	2691	c.2217T>A	c.(2215-2217)acT>acA	p.T739T		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	739					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GCGGCAACACTGCCTCAGTCC	0.557																																					p.T739T		.											.	.	0			c.T2217A						.						108	110	109					15																	24923231		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			CAACACTGCCTCA	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2217T>A	15.37:g.24923231T>A		Somatic	239	0		WXS	Illumina HiSeq	Phase_I	231	22	NM_018958	0	0	0	0	0		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.		0.557	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923231	T	A	24923231	2	1	73	1	0	0	0	0	0	0	0	1	1788	1567	55	5		5	C15orf2	15	24923231	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		24923231	77608161	69	6902											
HERC2	8924	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	28510872	28510872	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaatggcctcgtcctcacTggagccttcaaacagatagg	10	8	11	12	2	2	1	2	0	0	1	4	3	3	3	3	4	2	0	3	4	3	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:28510872T>A	ENST00000261609.7	-	14	1870	c.1762A>T	c.(1762-1764)Agt>Tgt	p.S588C		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCGTCCTCACTGGAGCCTTCA	0.577																																					p.S588C		.											.	HERC2-234	0			c.A1762T						.						123	92	102					15																	28510872		2203	4300	6503	SO:0001583	missense	8924	exon14			CCTCACTGGAGCC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.1762A>T	15.37:g.28510872T>A	ENSP00000261609:p.Ser588Cys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	84	10	NM_004667	0	0	0	0	0		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	31	5.104071	0.94245	.	.	ENSG00000128731	ENST00000261609	D	0.85411	-1.98	5.83	5.83	0.93111	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.90202	0.6937	L	0.48986	1.54	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.90297	0.4327	10	0.52906	T	0.07	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	588	O95714	HERC2_HUMAN	C	588	ENSP00000261609:S588C	ENSP00000261609:S588C	S	-	1	0	HERC2	26184467	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.629000	0.83207	2.367000	0.80283	0.529000	0.55759	AGT	.		0.577	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28510872	T	A	28510872	3	1	73	1	0	0	0	0	1	0	0	0	7079	1580	55	5	13062	5	HERC2	15	28510872	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	3587641	28510872	74020520	70	6903											
TMEM62	80021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43426530	43426530	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaattctgttctgaaactAttgacatcattcaaccagct	14	13	5	9	0	4	3	2	2	2	1	4	3	4	3	1	0	3	2	1	0	4	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:43426530A>G	ENST00000260403.2	+	2	535	c.256A>G	c.(256-258)Att>Gtt	p.I86V		NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	86						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		TTCTGAAACTATTGACATCAT	0.507																																					p.I86V		.											.	TMEM62-136	0			c.A256G						.						110	93	99					15																	43426530		2203	4299	6502	SO:0001583	missense	80021	exon2			GAAACTATTGACA	BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.256A>G	15.37:g.43426530A>G	ENSP00000260403:p.Ile86Val	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	83	10	NM_024956	0	0	3	3	0	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	37	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	A	7.057	0.565544	0.13560	.	.	ENSG00000137842	ENST00000260403	T	0.22945	1.93	4.97	2.62	0.31277	.	0.161216	0.53938	D	0.000050	T	0.09379	0.0231	N	0.05259	-0.085	0.43708	D	0.996176	B	0.12630	0.006	B	0.15484	0.013	T	0.18209	-1.0344	10	0.05833	T	0.94	-8.7407	8.1815	0.31313	0.8138:0.0:0.1862:0.0	.	86	Q0P6H9	TMM62_HUMAN	V	86	ENSP00000260403:I86V	ENSP00000260403:I86V	I	+	1	0	TMEM62	41213822	0.969000	0.33509	1.000000	0.80357	0.998000	0.95712	1.160000	0.31761	0.912000	0.36772	0.533000	0.62120	ATT	.		0.507	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		G	43426530	A	G	43426530	3	3	73	1	0	0	0	0	1	0	0	0	16221	449	16	3	262	3	TMEM62	15	43426530	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	14915658	43426530	59104862	71	6904											
FES	2242	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	91438758	91438758	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcagcaccatctaccaggaGctgcagagcatccgaaagcg	12	6	10	13	2	2	1	1	0	1	1	3	3	3	2	3	1	6	4	3	1	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:91438758G>T	ENST00000328850.3	+	19	2581	c.2439G>T	c.(2437-2439)gaG>gaT	p.E813D	FES_ENST00000394300.3_Missense_Mutation_p.E755D|FES_ENST00000394302.1_Missense_Mutation_p.E672D|FES_ENST00000450438.2_Missense_Mutation_p.E685D|FES_ENST00000414248.2_Missense_Mutation_p.E685D|FES_ENST00000444422.2_Missense_Mutation_p.E743D	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	813	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			TCTACCAGGAGCTGCAGAGCA	0.642																																					p.E813D		.											.	FES-546	0			c.G2439T						.						60	60	60					15																	91438758		2198	4298	6496	SO:0001583	missense	2242	exon19			CCAGGAGCTGCAG	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"SH2 domain containing"	3657	protein-coding gene	gene with protein product	"Oncogene FES, feline sarcoma virus", "c-fes/fps protein"	190030	"feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog", "feline sarcoma oncogene"			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.2439G>T	15.37:g.91438758G>T	ENSP00000331504:p.Glu813Asp	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	108	8	NM_002005	0	0	182	192	10	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	37	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789274	0.31685	.	.	ENSG00000182511	ENST00000328850;ENST00000414248;ENST00000394302;ENST00000444422;ENST00000394300;ENST00000450438	T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08	4.18	3.25	0.37280	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.164239	0.53938	D	0.000058	T	0.37999	0.1024	N	0.25031	0.7	0.44780	D	0.997783	B;B;B;B;B;B	0.13594	0.001;0.008;0.001;0.001;0.008;0.001	B;B;B;B;B;B	0.14023	0.004;0.01;0.003;0.002;0.01;0.004	T	0.16394	-1.0404	10	0.19147	T	0.46	-35.8073	9.2926	0.37795	0.0886:0.1513:0.7602:0.0	.	795;685;672;755;743;813	B4DUD9;P07332-2;E7ENM8;P07332-3;P07332-4;P07332	.;.;.;.;.;FES_HUMAN	D	813;685;672;743;755;685	ENSP00000331504:E813D;ENSP00000414629:E685D;ENSP00000377839:E672D;ENSP00000400868:E743D;ENSP00000377837:E755D;ENSP00000409915:E685D	ENSP00000331504:E813D	E	+	3	2	FES	89239762	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.776000	0.26704	2.339000	0.79563	0.555000	0.69702	GAG	.		0.642	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		T	91438758	G	T	91438758	3	4	73	1	0	0	0	0	1	0	0	0	5839	962	34	4	2509	4	FES	15	91438758	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	48012228	91438758	11092634	72	6905											
DECR2	26063	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	457438	457438	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctaggccgccaggaagcTggctggggccaccggccggc	5	5	16	15	3	1	0	0	0	1	0	1	1	1	1	5	7	1	2	5	7	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr16:457438T>G	ENST00000219481.5	+	4	353	c.215T>G	c.(214-216)cTg>cGg	p.L72R	DECR2_ENST00000424398.2_Missense_Mutation_p.L60R|DECR2_ENST00000461947.1_Intron|DECR2_ENST00000397710.1_Missense_Mutation_p.L123R	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	72					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				GCCAGGAAGCTGGCTGGGGCC	0.652																																					p.L72R		.											.	DECR2-90	0			c.T215G						.						26	31	29					16																	457438		2201	4299	6500	SO:0001583	missense	26063	exon4			GGAAGCTGGCTGG	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2754	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 17C, member 1"	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.215T>G	16.37:g.457438T>G	ENSP00000219481:p.Leu72Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	109	9	NM_020664	0	0	2	2	0	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	37	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.096100	0.56075	.	.	ENSG00000242612	ENST00000219481;ENST00000397710;ENST00000424398	T;T	0.54071	0.59;0.59	4.89	4.89	0.63831	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.75332	0.3835	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80446	-0.1379	10	0.87932	D	0	.	12.2476	0.54578	0.0:0.0:0.0:1.0	.	72	Q9NUI1	DECR2_HUMAN	R	72;123;60	ENSP00000219481:L72R;ENSP00000400374:L60R	ENSP00000219481:L72R	L	+	2	0	DECR2	397439	1.000000	0.71417	0.987000	0.45799	0.506000	0.33950	7.499000	0.81566	1.831000	0.53308	0.459000	0.35465	CTG	.		0.652	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		G	457438	T	G	457438	3	3	73	1	0	0	0	0	1	0	0	0	4389	1580	55	5	229	5	DECR2	16	457438	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		457438	89897315	73	6906											
PIGQ	9091	hgsc.bcm.edu	37	chr16	624548	624548	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctggagccaccactgccagCacggggggcctggctgccgt	5	5	16	15	2	0	0	0	0	0	0	0	1	0	1	5	5	4	3	5	5	0	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr16:624548C>T	ENST00000026218.5	+	2	562	c.474C>T	c.(472-474)agC>agT	p.S158S	PIGQ_ENST00000409527.2_Silent_p.S158S|PIGQ_ENST00000321878.5_Silent_p.S158S|PIGQ_ENST00000470411.2_Silent_p.S158S	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	158					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				CCACTGCCAGCACGGGGGGCC	0.657																																					p.S158S		.											.	PIGQ-226	0			c.C474T						.						12	11	11					16																	624548		2157	4255	6412	SO:0001819	synonymous_variant	9091	exon2			TGCCAGCACGGGG	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"Phosphatidylinositol glycan anchor biosynthesis"	14135	protein-coding gene	gene with protein product		605754	"phosphatidylinositol glycan, class Q"			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.474C>T	16.37:g.624548C>T		Somatic	14	2		WXS	Illumina HiSeq	Phase_I	29	23	NM_148920	0	0	9	19	10	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Silent	SNP	ENST00000026218.5	37	CCDS10411.1																																																																																			.		0.657	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204		T	624548	C	T	624548	2	4	73	1	0	0	0	0	0	0	0	1	11922	709	25	2		2	PIGQ	16	624548	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	167110	624548	89730205	74	6907											
TSC2	7249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2126139	2126139	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatcaggtgccgcctgcccTtccggaaggattttgtccct	5	12	10	14	2	2	0	2	0	0	0	4	2	4	2	5	3	2	0	5	3	1	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr16:2126139T>C	ENST00000219476.3	+	24	3340	c.2710T>C	c.(2710-2712)Ttc>Ctc	p.F904L	TSC2_ENST00000568454.1_Missense_Mutation_p.F915L|TSC2_ENST00000382538.6_Missense_Mutation_p.F855L|TSC2_ENST00000439673.2_Missense_Mutation_p.F867L|TSC2_ENST00000353929.4_Missense_Mutation_p.F904L|TSC2_ENST00000401874.2_Missense_Mutation_p.F904L|TSC2_ENST00000350773.4_Missense_Mutation_p.F904L	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	904					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CCGCCTGCCCTTCCGGAAGGA	0.567			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.F904L		.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2-1908	0			c.T2710C						.						117	94	102					16																	2126139		2198	4300	6498	SO:0001583	missense	7249	exon24	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTGCCCTTCCGGA	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.2710T>C	16.37:g.2126139T>C	ENSP00000219476:p.Phe904Leu	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	104	13	NM_001114382	0	0	8	9	1	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.281054	0.59758	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95;-1.95	5.09	5.09	0.68999	Tuberin-type domain (1);	0.056979	0.64402	D	0.000001	T	0.81221	0.4777	N	0.14661	0.345	0.51012	D	0.999905	B;B;B;B;B;D	0.59357	0.101;0.313;0.176;0.021;0.082;0.985	B;B;B;B;B;D	0.72338	0.147;0.174;0.091;0.132;0.103;0.977	T	0.77351	-0.2620	10	0.02654	T	1	-38.9999	9.422	0.38557	0.0:0.0795:0.0:0.9205	.	855;867;904;904;904;904	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	L	904;904;904;867;855;904	ENSP00000219476:F904L;ENSP00000384468:F904L;ENSP00000248099:F904L;ENSP00000399232:F867L;ENSP00000371978:F855L;ENSP00000344383:F904L	ENSP00000219476:F904L	F	+	1	0	TSC2	2066140	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.116000	0.64661	1.919000	0.55581	0.459000	0.35465	TTC	.		0.567	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		C	2126139	T	C	2126139	3	2	73	1	0	0	0	0	1	0	0	0	16639	1609	56	3	2800	3	TSC2	16	2126139	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	1501591	2126139	88228614	75	6908											
PRPF8	10594	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	1564455	1564455	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaacggattctgcttcaaaAcctagatggcaaggcaggca	14	7	11	9	1	2	2	1	0	1	2	2	3	2	3	1	4	3	4	1	4	5	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:1564455A>T	ENST00000572621.1	-	27	4605	c.4340T>A	c.(4339-4341)gTt>gAt	p.V1447D	PRPF8_ENST00000304992.6_Splice_Site_p.V1447D			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1447	Linker.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CTGCTTCAAAACCTAGATGGC	0.547																																					p.V1447D		.											.	PRPF8-525	0			c.T4340A						.						82	73	76					17																	1564455		2203	4300	6503	SO:0001630	splice_region_variant	10594	exon28			TTCAAAACCTAGA	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.4339-1T>A	17.37:g.1564455A>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	79	9	NM_006445	0	0	0	0	0	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	a	12.99	2.102694	0.37145	.	.	ENSG00000174231	ENST00000304992	T	0.80994	-1.44	6.17	6.17	0.99709	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.80999	0.4732	L	0.47716	1.5	0.80722	D	1	P	0.42620	0.785	P	0.45794	0.493	T	0.82474	-0.0439	10	0.66056	D	0.02	-2.8406	16.8222	0.85835	1.0:0.0:0.0:0.0	.	1447	Q6P2Q9	PRP8_HUMAN	D	1447	ENSP00000304350:V1447D	ENSP00000304350:V1447D	V	-	2	0	PRPF8	1511205	1.000000	0.71417	1.000000	0.80357	0.193000	0.23685	9.307000	0.96226	2.371000	0.80710	0.533000	0.62120	GTT	.		0.547	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		Missense_Mutation	T	1564455	A	T	1564455	5	4	73	1	0	0	0	0	0	0	1	0	12604	57	2	5	2731	5	PRPF8	17	1564455	Splice_Site	SNP	A	TCGA-BQ-5889-01A-11D-1589-08		1564455	79630755	76	6909											
NEURL4	84461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7220554	7220554	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggccagggtctccgccccaGcatattgaagggagggggaa	10	5	16	10	1	1	1	0	1	1	0	2	3	1	3	4	5	1	1	4	5	3	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:7220554G>A	ENST00000399464.2	-	28	4469	c.4454C>T	c.(4453-4455)gCt>gTt	p.A1485V	RP11-542C16.2_ENST00000575474.1_Silent_p.L299L|GPS2_ENST00000380728.2_5'Flank|NEURL4_ENST00000315614.7_Missense_Mutation_p.A1483V|GPS2_ENST00000391950.3_5'Flank|NEURL4_ENST00000574120.1_5'Flank|GPS2_ENST00000389167.5_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.A1461V	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1485						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTCCGCCCCAGCATATTGAAG	0.647																																					p.A1485V		.											.	NEURL4-46	0			c.C4454T						.						27	29	28					17																	7220554		1909	4108	6017	SO:0001583	missense	84461	exon28			GCCCCAGCATATT		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"neuralized homolog 4 (Drosophila)"			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.4454C>T	17.37:g.7220554G>A	ENSP00000382390:p.Ala1485Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	50	5	NM_032442	0	0	27	27	0	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	37	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522700	0.85600	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.38722	1.12;1.12	5.02	5.02	0.67125	.	0.068616	0.64402	D	0.000017	T	0.49575	0.1565	M	0.71581	2.175	0.40718	D	0.982632	P;P	0.44139	0.827;0.734	B;B	0.43386	0.418;0.239	T	0.59747	-0.7396	10	0.72032	D	0.01	-10.282	17.1077	0.86668	0.0:0.0:1.0:0.0	.	1483;1485	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	V	1483;1485	ENSP00000319826:A1483V;ENSP00000382390:A1485V	ENSP00000319826:A1483V	A	-	2	0	NEURL4	7161278	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.975000	0.70475	2.325000	0.78763	0.462000	0.41574	GCT	.		0.647	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7220554	G	A	7220554	3	1	73	1	0	0	0	0	1	0	0	0	10373	971	34	2	242	2	NEURL4	17	7220554	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	5656099	7220554	73974656	77	6910											
MYH10	4628	broad.mit.edu	37	chr17	8452026	8452026	+	Frame_Shift_Del	DEL	T	T	-																															atggtctcctggaaattatcTttgtcttgctgtcccggaat																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:8452026delT	ENST00000269243.4	-	9	1107	c.969delA	c.(967-969)aaafs	p.K323fs	RN7SL129P_ENST00000479993.2_RNA|MYH10_ENST00000360416.3_Frame_Shift_Del_p.K333fs|MYH10_ENST00000396239.1_Frame_Shift_Del_p.K323fs|MYH10_ENST00000379980.4_Frame_Shift_Del_p.K339fs	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	323	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GGAAATTATCTTTGTCTTGCT	0.383																																					p.K333fs													.	MYH10-92	0			c.999delA						.						163	160	161					17																	8452026		2203	4300	6503	SO:0001589	frameshift_variant	4628	exon10			ATTATCTTTGTCT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.969delA	17.37:g.8452026delT	ENSP00000269243:p.Lys323fs	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	204	19	NM_001256012	0	0	0	0	0	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Frame_Shift_Del	DEL	ENST00000269243.4	37	CCDS11144.1																																																																																			.		0.383	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			-	8452026	T	-	8452026	7	5	73	1	0	1	0	1	0	0	0	0	10055	1606	56	0	5093	0	MYH10	17	8452026	Frame_Shift_Del	DEL	T	TCGA-BQ-5889-01A-11D-1589-08	1231472	8452026	72743184	78	6911											
SCRN2	90507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45915217	45915217	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagctatgaagcttacgcaTaagcctggctctccctcttc	9	11	8	13	1	2	1	0	1	2	0	4	2	2	1	2	1	4	4	2	1	5	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:45915217T>C	ENST00000290216.9	-	8	1396	c.1271A>G	c.(1270-1272)tAt>tGt	p.Y424C	SCRN2_ENST00000584123.1_Missense_Mutation_p.Y432C|SCRN2_ENST00000407215.3_3'UTR	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	424						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						AGCTTACGCATAAGCCTGGCT	0.657																																					p.Y424C		.											.	SCRN2-91	0			c.A1271G						.						24	26	25					17																	45915217		2203	4300	6503	SO:0001583	missense	90507	exon8			TACGCATAAGCCT	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.1271A>G	17.37:g.45915217T>C	ENSP00000290216:p.Tyr424Cys	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	45	8	NM_138355	0	0	31	36	5	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	37	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.631333	0.28978	.	.	ENSG00000141295	ENST00000290216	T	0.09817	2.94	5.72	5.72	0.89469	.	0.114320	0.64402	D	0.000008	T	0.37237	0.0996	M	0.83953	2.67	0.53688	D	0.999977	D	0.89917	1.0	D	0.85130	0.997	T	0.26538	-1.0100	10	0.87932	D	0	-1.5376	14.9863	0.71351	0.0:0.0:0.0:1.0	.	424	Q96FV2	SCRN2_HUMAN	C	424	ENSP00000290216:Y424C	ENSP00000290216:Y424C	Y	-	2	0	SCRN2	43270216	1.000000	0.71417	0.037000	0.18230	0.025000	0.11179	5.686000	0.68211	2.184000	0.69523	0.533000	0.62120	TAT	.		0.657	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		C	45915217	T	C	45915217	3	2	73	1	0	0	0	0	1	0	0	0	13971	1406	49	3	10	3	SCRN2	17	45915217	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	37463191	45915217	35279993	79	6912											
TEX2	55852	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	62290509	62290509	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggaatcacttccgtagcCatccccctcagaatcacact	10	10	6	15	1	3	1	3	0	0	1	5	2	5	2	4	1	1	2	4	1	3	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:62290509C>T	ENST00000583097.1	-	2	1241	c.1069G>A	c.(1069-1071)Ggc>Agc	p.G357S	TEX2_ENST00000258991.3_Missense_Mutation_p.G357S|TEX2_ENST00000584379.1_Missense_Mutation_p.G357S			Q8IWB9	TEX2_HUMAN	testis expressed 2	357					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		CTTCCGTAGCCATCCCCCTCA	0.498																																					p.G357S		.											.	TEX2-91	0			c.G1069A						.						85	76	79					17																	62290509		2203	4300	6503	SO:0001583	missense	55852	exon2			CGTAGCCATCCCC	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"transmembrane protein 96"		"testis expressed sequence 2"			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.1069G>A	17.37:g.62290509C>T	ENSP00000462665:p.Gly357Ser	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	115	12	NM_018469	0	0	4	4	0	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	37		.	.	.	.	.	.	.	.	.	.	C	5.664	0.307054	0.10733	.	.	ENSG00000136478	ENST00000258991	T	0.42513	0.97	6.03	3.96	0.45880	.	0.773939	0.13084	N	0.415036	T	0.20820	0.0501	N	0.08118	0	0.09310	N	1	B;B	0.20261	0.043;0.025	B;B	0.20577	0.03;0.013	T	0.27191	-1.0081	10	0.11485	T	0.65	-0.2203	8.1607	0.31196	0.5291:0.374:0.0969:0.0	.	357;357	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	S	357	ENSP00000258991:G357S	ENSP00000258991:G357S	G	-	1	0	TEX2	59644241	0.137000	0.22531	0.007000	0.13788	0.465000	0.32709	1.751000	0.38339	0.809000	0.34255	0.655000	0.94253	GGC	.		0.498	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		T	62290509	C	T	62290509	3	4	73	1	0	0	0	0	1	0	0	0	15813	594	21	2	2379	2	TEX2	17	62290509	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	16375292	62290509	18904701	80	6913											
PRPSAP1	5635	broad.mit.edu	37	chr17	74307703	74307703	+	Frame_Shift_Del	DEL	T	T	-																															ccgaatggcttcagaaagaaTcaaactgatatccacagtct																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:74307703delT	ENST00000446526.3	-	10	1523	c.1078delA	c.(1078-1080)attfs	p.I360fs	PRPSAP1_ENST00000324684.4_Frame_Shift_Del_p.I257fs|PRPSAP1_ENST00000588364.1_5'UTR	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	331					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						TCAGAAAGAATCAAACTGATA	0.468																																					p.I360fs													.	PRPSAP1-116	0			c.1078delA						.						154	120	131					17																	74307703		2203	4300	6503	SO:0001589	frameshift_variant	5635	exon10			AAAGAATCAAACT	D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.1078delA	17.37:g.74307703delT	ENSP00000414624:p.Ile360fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	93	10	NM_002766	0	0	0	0	0	B2R6M4|Q96H06	Frame_Shift_Del	DEL	ENST00000446526.3	37	CCDS11743.2																																																																																			.		0.468	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766		-	74307703	T	-	74307703	7	5	73	1	0	1	0	1	0	0	0	0	12610	1435	50	0	83	0	PRPSAP1	17	74307703	Frame_Shift_Del	DEL	T	TCGA-BQ-5889-01A-11D-1589-08	12017194	74307703	6887507	81	6914											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2226655	2226655	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggacggcctggctgggCtgaagggcgagggcagccgc	6	4	20	11	3	0	1	0	1	0	0	0	3	0	2	2	6	2	4	2	6	1	0	rs113164803	byFrequency	TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:2226655C>A	ENST00000398665.3	+	27	4171	c.4135C>A	c.(4135-4137)Ctg>Atg	p.L1379M		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1379					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGCTGGGCTGAAGGGCGA	0.721													C|||	25	0.00499201	0	0.0101	5008	,	,		10782	0		0.0129	False		,,,				2504	0.0051				p.L1379M		.											.	DOT1L-132	0			c.C4135A						.	C	MET/LEU	8,3926		0,8,1959	5	8	7		4135	-0.8	0.4	19	dbSNP_132	7	110,7998		0,110,3944	yes	missense	DOT1L	NM_032482.2	15	0,118,5903	AA,AC,CC		1.3567,0.2034,0.9799	benign	1379/1538	2226655	118,11924	1967	4054	6021	SO:0001583	missense	84444	exon27			GCTGGGCTGAAGG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.4135C>A	19.37:g.2226655C>A	ENSP00000381657:p.Leu1379Met	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	13	6	NM_032482	0	0	5	12	7	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	18	0.008241758241758242	0	0.0	3	0.008287292817679558	0	0.0	15	0.01978891820580475	C	4.901	0.167515	0.09339	0.002034	0.013567	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000457590	T;T	0.33438	1.84;1.41	4.53	-0.833	0.10782	.	0.433127	0.16897	N	0.195045	T	0.07052	0.0179	N	0.19112	0.55	0.09310	N	1	B;B	0.18461	0.028;0.015	B;B	0.16289	0.01;0.015	T	0.15150	-1.0447	10	0.87932	D	0	-2.4127	1.7907	0.03051	0.185:0.4435:0.1107:0.2607	.	1379;1379	Q8TEK3;Q8TEK3-2	DOT1L_HUMAN;.	M	1379;1379;259	ENSP00000381657:L1379M;ENSP00000407411:L259M	ENSP00000221482:L1379M	L	+	1	2	DOT1L	2177655	0.145000	0.22656	0.388000	0.26195	0.167000	0.22549	0.312000	0.19397	0.335000	0.23614	0.561000	0.74099	CTG	C|0.992;A|0.008		0.721	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		A	2226655	C	A	2226655	3	1	73	1	0	0	0	0	1	0	0	0	4720	796	28	4	4241	4	DOT1L	19	2226655	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08		2226655	56902328	82	6915											
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7533867	7533867	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaaccggctggccaagagcGatgtgcccatccagctgctc	9	6	12	14	2	0	2	0	0	0	2	2	3	1	2	4	2	5	3	4	2	2	0	rs374597663		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:7533867G>A	ENST00000359920.6	+	17	3326	c.3073G>A	c.(3073-3075)Gat>Aat	p.D1025N	ARHGEF18_ENST00000319670.9_Missense_Mutation_p.D867N|CTD-2207O23.3_ENST00000593531.1_Silent_p.A982A	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	1025					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GGCCAAGAGCGATGTGCCCAT	0.697																																					p.D1025N		.											.	ARHGEF18-228	0			c.G3073A						.	G	ASN/ASP,ASN/ASP	0,4358		0,0,2179	19	18	18		3073,2599	5.1	1	19		18	1,8561		0,1,4280	no	missense,missense	ARHGEF18	NM_001130955.1,NM_015318.3	23,23	0,1,6459	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging,probably-damaging	1025/1174,867/1016	7533867	1,12919	2179	4281	6460	SO:0001583	missense	23370	exon17			AAGAGCGATGTGC	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.3073G>A	19.37:g.7533867G>A	ENSP00000352995:p.Asp1025Asn	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	16	6	NM_001130955	0	0	10	24	14	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	G	33	5.258442	0.95368	0.0	1.17E-4	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.42900	0.96;0.96	5.11	5.11	0.69529	.	0.376195	0.22116	N	0.064410	T	0.49795	0.1578	L	0.50333	1.59	0.44918	D	0.997935	D;D	0.58970	0.98;0.984	P;P	0.52066	0.689;0.544	T	0.45848	-0.9233	10	0.41790	T	0.15	-20.5858	16.0301	0.80572	0.0:0.0:1.0:0.0	.	867;1025	Q6ZSZ5-2;Q6ZSZ5	.;ARHGI_HUMAN	N	867;1025	ENSP00000319200:D867N;ENSP00000352995:D1025N	ENSP00000319200:D867N	D	+	1	0	ARHGEF18	7439867	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	9.129000	0.94430	2.388000	0.81334	0.563000	0.77884	GAT	.		0.697	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		A	7533867	G	A	7533867	3	1	73	1	0	0	0	0	1	0	0	0	901	1058	37	1	3139	1	ARHGEF18	19	7533867	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	5307212	7533867	51595116	83	6916											
MYO1F	4542	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	8604865	8604865	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggcggtgctggggcgccccTtcttgtctccatccagcttc	2	11	12	16	3	2	0	0	0	2	0	5	0	3	0	4	4	2	2	4	4	0	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:8604865T>G	ENST00000338257.8	-	16	1925	c.1658A>C	c.(1657-1659)aAg>aCg	p.K553T		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	553	Myosin motor.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						GGGGCGCCCCTTCTTGTCTCC	0.632																																					p.K553T		.											.	MYO1F-93	0			c.A1658C						.						40	43	42					19																	8604865		1904	4113	6017	SO:0001583	missense	4542	exon16			CGCCCCTTCTTGT	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"Myosins / Myosin superfamily : Class I"	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.1658A>C	19.37:g.8604865T>G	ENSP00000344871:p.Lys553Thr	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	87	6	NM_012335	0	0	32	32	0	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577175	0.86645	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.88201	-2.35	5.01	5.01	0.66863	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93249	0.7849	M	0.73217	2.22	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.93407	0.6765	10	0.52906	T	0.07	.	13.55	0.61726	0.0:0.0:0.0:1.0	.	553	O00160	MYO1F_HUMAN	T	598;553	ENSP00000344871:K553T	ENSP00000304899:K598T	K	-	2	0	MYO1F	8510865	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.902000	0.69869	1.891000	0.54761	0.482000	0.46254	AAG	.		0.632	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			G	8604865	T	G	8604865	3	3	73	1	0	0	0	0	1	0	0	0	10098	1609	56	5	1690	5	MYO1F	19	8604865	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	1070998	8604865	50524118	84	6917											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11312613	11312613	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttgatgtaggggaaggcGtggtcggtgctgagcagcgt	6	10	19	6	3	1	2	0	2	1	0	2	3	1	3	0	5	3	3	0	5	2	2	rs200959822	byFrequency	TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:11312613G>A	ENST00000294618.7	-	44	5651	c.5640C>T	c.(5638-5640)caC>caT	p.H1880H	DOCK6_ENST00000319867.7_Silent_p.H1219H|CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000586702.1_5'UTR	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1880	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						AGGGGAAGGCGTGGTCGGTGC	0.657													G|||	2	0.000399361	0.0015	0	5008	,	,		11923	0		0	False		,,,				2504	0				p.H1880H		.											.	DOCK6-93	0			c.C5640T						.	G		2,4260		0,2,2129	69	73	72		5640	-0.1	1	19		72	12,8428		0,12,4208	no	coding-synonymous	DOCK6	NM_020812.2		0,14,6337	AA,AG,GG		0.1422,0.0469,0.1102		1880/2048	11312613	14,12688	2131	4220	6351	SO:0001819	synonymous_variant	57572	exon44			GAAGGCGTGGTCG		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.5640C>T	19.37:g.11312613G>A		Somatic	7	2		WXS	Illumina HiSeq	Phase_I	14	10	NM_020812	0	0	22	53	31	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			G|0.996;A|0.004		0.657	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11312613	G	A	11312613	2	1	73	1	0	0	0	0	0	0	0	1	4702	1136	40	1		1	DOCK6	19	11312613	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	2707748	11312613	47816370	85	6918											
PSG9	5678	broad.mit.edu	37	chr19	43773527	43773527	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttctctcctcacctgtgagCaggagccccttccaggtgat	6	11	10	14	0	2	2	1	2	1	0	5	3	4	3	5	2	2	2	5	2	0	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:43773527C>A	ENST00000270077.3	-	1	153	c.57G>T	c.(55-57)ctG>ctT	p.L19L	PSG9_ENST00000596730.1_Silent_p.L19L|PSG9_ENST00000244293.7_Silent_p.L19L|PSG9_ENST00000593948.1_Silent_p.L19L|PSG9_ENST00000443718.3_Silent_p.L19L|PSG9_ENST00000291752.5_Silent_p.L19L|PSG9_ENST00000418820.2_Silent_p.L19L	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	19					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				CACCTGTGAGCAGGAGCCCCT	0.592																																					p.L19L													.	PSG9-92	0			c.G57T						.						93	92	92					19																	43773527		2203	4300	6503	SO:0001819	synonymous_variant	5678	exon1			TGTGAGCAGGAGC	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.57G>T	19.37:g.43773527C>A		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	191	4	NM_002784	0	0	0	0	0	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000270077.3	37	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	c	8.208	0.799687	0.16397	.	.	ENSG00000183668	ENST00000418820	.	.	.	2.17	1.03	0.20045	.	.	.	.	.	T	0.53514	0.1801	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42682	-0.9437	4	.	.	.	.	6.4778	0.22045	0.0:0.6917:0.3083:0.0	.	.	.	.	F	6	.	.	C	-	2	0	PSG9	48465367	0.918000	0.31147	0.348000	0.25681	0.383000	0.30230	0.701000	0.25616	0.229000	0.21039	0.298000	0.19748	TGC	.		0.592	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		A	43773527	C	A	43773527	2	1	73	1	0	0	0	0	0	0	0	1	12691	697	25	4		4	PSG9	19	43773527	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	32460914	43773527	15355456	86	6919											
PHLDB3	653583	hgsc.bcm.edu	37	chr19	43983649	43983649	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcacccagacacctgcaCatgtgggcagttttccgggt	8	8	12	13	1	0	1	0	0	0	1	1	1	1	1	3	2	2	5	3	2	0	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:43983649C>G	ENST00000292140.5	-	14	1942	c.1582G>C	c.(1582-1584)Gtg>Ctg	p.V528L		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	528							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GACACCTGCACATGTGGGCAG	0.657																																					p.V528L		.											.	PHLDB3-68	0			c.G1582C						.						11	14	13					19																	43983649		1984	4106	6090	SO:0001583	missense	653583	exon14			CCTGCACATGTGG		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"Pleckstrin homology (PH) domain containing"	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1582G>C	19.37:g.43983649C>G	ENSP00000292140:p.Val528Leu	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	4	3	NM_198850	0	0	3	6	3	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	C	3.207	-0.162514	0.06502	.	.	ENSG00000176531	ENST00000292140	T	0.46451	0.87	4.59	-2.83	0.05769	Pleckstrin homology-type (1);	0.459815	0.19359	N	0.116188	T	0.20088	0.0483	N	0.20986	0.625	0.09310	N	0.999996	B	0.09022	0.002	B	0.06405	0.002	T	0.07139	-1.0788	10	0.31617	T	0.26	.	3.5787	0.07943	0.2598:0.3586:0.3007:0.0809	.	528	Q6NSJ2	PHLB3_HUMAN	L	528	ENSP00000292140:V528L	ENSP00000292140:V528L	V	-	1	0	PHLDB3	48675489	0.006000	0.16342	0.000000	0.03702	0.005000	0.04900	0.143000	0.16115	-0.391000	0.07763	-0.282000	0.10007	GTG	.		0.657	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			G	43983649	C	G	43983649	3	3	73	1	0	0	0	0	1	0	0	0	11879	478	17	4	352	4	PHLDB3	19	43983649	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	210122	43983649	15145334	87	6920											
TIMM17B	10245	hgsc.bcm.edu	37	chrX	48751202	48751202	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttcggaactgctgggcTgtgtagcgagtgaggaggat	8	10	16	7	2	0	1	0	1	0	0	1	5	0	4	1	4	3	3	1	4	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chrX:48751202T>C	ENST00000376582.3	-	6	559	c.411A>G	c.(409-411)acA>acG	p.T137T	TIMM17B_ENST00000465150.2_Silent_p.T187T|TIMM17B_ENST00000495490.2_Silent_p.T157T|TIMM17B_ENST00000396779.3_Silent_p.T187T|TIMM17B_ENST00000472645.1_5'UTR	NM_005834.3	NP_005825.1	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17 homolog B (yeast)	137					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)	6						ACTGCTGGGCTGTGTAGCGAG	0.597																																					p.T187T		.											.	TIMM17B-131	0			c.A561G						.						52	42	45					X																	48751202		2203	4299	6502	SO:0001819	synonymous_variant	10245	exon7			CTGGGCTGTGTAG	AF034790	CCDS14308.1, CCDS55411.1	Xp11.23	2008-02-05			ENSG00000126768	ENSG00000126768			17310	protein-coding gene	gene with protein product		300249				10339406	Standard	NM_001167947		Approved	DXS9822, JM3	uc004dla.2	O60830	OTTHUMG00000034498	ENST00000376582.3:c.411A>G	X.37:g.48751202T>C		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_001167947	1	0	134	135	0	A8K2E2|J3KPV3|Q9UJV0	Silent	SNP	ENST00000376582.3	37	CCDS14308.1																																																																																			.		0.597	TIMM17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083411.2	NM_005834		C	48751202	T	C	48751202	2	2	73	1	0	0	0	0	0	0	0	1	15941	1567	55	3		3	TIMM17B	23	48751202	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		48751202	106519358	88	6921											
GPRASP1	9737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	101910683	101910683	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaggaggagcccattattggGtcctggttttggaccagagt	8	11	15	7	0	0	1	0	0	0	1	1	5	1	4	3	5	1	1	3	5	1	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chrX:101910683G>C	ENST00000361600.5	+	5	2643	c.1842G>C	c.(1840-1842)ggG>ggC	p.G614G	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000444152.1_Silent_p.G614G|GPRASP1_ENST00000537097.1_Silent_p.G614G|GPRASP1_ENST00000415986.1_Silent_p.G614G	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	614	Glu-rich.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						CCATTATTGGGTCCTGGTTTT	0.512																																					p.G614G		.											.	GPRASP1-131	0			c.G1842C						.						104	103	103					X																	101910683		2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			TATTGGGTCCTGG	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.1842G>C	X.37:g.101910683G>C		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	160	24	NM_001099411	0	0	3	3	0	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	37	CCDS35352.1																																																																																			.		0.512	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		C	101910683	G	C	101910683	2	2	73	1	0	0	0	0	0	0	0	1	6743	1248	44	4		4	GPRASP1	23	101910683	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	53159481	101910683	53359877	89	6922											
F8	2157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	154157883	154157883	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgagggatgctatgactcctCgtaaggcaatctgataaggg	11	10	13	7	1	1	3	0	3	1	0	3	4	2	4	1	3	1	3	1	3	4	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chrX:154157883C>T	ENST00000360256.4	-	14	4382	c.4182G>A	c.(4180-4182)acG>acA	p.T1394T		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1394	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TATGACTCCTCGTAAGGCAAT	0.428																																					p.T1394T		.											.	F8-182	0			c.G4182A						.						166	149	154					X																	154157883		2203	4300	6503	SO:0001819	synonymous_variant	2157	exon14			ACTCCTCGTAAGG	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"Factor VIIIF8B", "hemophilia A"	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.4182G>A	X.37:g.154157883C>T		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	137	25	NM_000132	0	0	0	0	0	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																			.		0.428	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154157883	C	T	154157883	2	4	73	1	0	0	0	0	0	0	0	1	5363	871	31	1		1	F8	23	154157883	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	52247200	154157883	1112677	90	6923											
NOC2L	26155	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	891312	891312	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccctcttacctgctgctaTcctttgccacctttccaaac	6	14	3	18	0	1	0	0	0	1	0	4	0	4	0	7	0	5	2	7	0	3	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:891312T>G	ENST00000327044.6	-	6	738	c.689A>C	c.(688-690)gAt>gCt	p.D230A	NOC2L_ENST00000487214.1_5'UTR	NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	230					apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		CCTGCTGCTATCCTTTGCCAC	0.562																																					p.D230A		.											.	NOC2L-92	0			c.A689C						.						97	84	88					1																	891312		2201	4300	6501	SO:0001583	missense	26155	exon6			CTGCTATCCTTTG	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"novel INHAT repressor", "protein phosphatase 1, regulatory subunit 12"	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.689A>C	1.37:g.891312T>G	ENSP00000317992:p.Asp230Ala	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	29	20	NM_015658	0	0	0	0	0	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.549380	0.45383	.	.	ENSG00000188976	ENST00000327044	T	0.68479	-0.33	4.31	4.31	0.51392	.	0.170398	0.51477	D	0.000100	T	0.64327	0.2588	M	0.78049	2.395	0.49798	D	0.999825	P;P	0.41624	0.757;0.757	B;B	0.36186	0.219;0.219	T	0.70901	-0.4746	10	0.62326	D	0.03	-20.7265	11.3195	0.49412	0.0:0.0:0.0:1.0	.	230;230	B3KNC3;Q9Y3T9	.;NOC2L_HUMAN	A	230	ENSP00000317992:D230A	ENSP00000317992:D230A	D	-	2	0	NOC2L	881175	1.000000	0.71417	0.011000	0.14972	0.030000	0.12068	3.716000	0.54904	1.820000	0.53075	0.334000	0.21626	GAT	.		0.562	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658		G	891312	T	G	891312	3	3	74	1	0	0	0	0	1	0	0	0	10539	1435	50	5	1616	5	NOC2L	1	891312	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		891312	248359309	1	6924											
MMEL1	79258	broad.mit.edu	37	chr1	2540842	2540842	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccggccggtccttggcagtCgaattctccagcaccgctgt	5	9	12	15	4	1	0	0	0	1	0	4	1	2	0	5	3	1	3	5	3	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:2540842C>T	ENST00000378412.3	-	6	632	c.471G>A	c.(469-471)tcG>tcA	p.S157S	MMEL1_ENST00000288709.6_Silent_p.S148S|MMEL1_ENST00000502556.1_Silent_p.S157S			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	157						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		CCTTGGCAGTCGAATTCTCCA	0.657																																					p.S157S													.	MMEL1-90	0			c.G471A						.						35	26	29					1																	2540842		2203	4299	6502	SO:0001819	synonymous_variant	79258	exon6			GGCAGTCGAATTC	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"membrane metallo-endopeptidase-like 2"	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.471G>A	1.37:g.2540842C>T		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	19	3	NM_033467	0	0	0	0	0	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2																																																																																			.		0.657	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		T	2540842	C	T	2540842	2	4	74	1	0	0	0	0	0	0	0	1	9671	871	31	1		1	MMEL1	1	2540842	Silent	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	1649530	2540842	246709779	2	6925											
ATP13A2	23400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	17322884	17322884	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagggggccactcacccaGgacagagagggcagccacaa	12	2	14	13	0	1	1	1	0	0	1	1	3	1	2	3	4	2	2	3	4	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:17322884G>T	ENST00000326735.8	-	13	1336	c.1303C>A	c.(1303-1305)Ctg>Atg	p.L435M	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000452699.1_Missense_Mutation_p.L430M|ATP13A2_ENST00000341676.5_Missense_Mutation_p.L430M|ATP13A2_ENST00000502860.1_Intron			Q9NQ11	AT132_HUMAN	ATPase type 13A2	435					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CACTCACCCAGGACAGAGAGG	0.612																																					p.L435M		.											.	ATP13A2-93	0			c.C1303A						.						69	78	75					1																	17322884		2203	4300	6503	SO:0001583	missense	23400	exon13			CACCCAGGACAGA	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.1303C>A	1.37:g.17322884G>T	ENSP00000327214:p.Leu435Met	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	90	35	NM_022089	0	0	0	0	0	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879903	0.51801	.	.	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000506174	D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98	4.69	2.76	0.32466	ATPase, P-type, ATPase-associated domain (1);	0.545880	0.17421	N	0.174829	D	0.93462	0.7914	M	0.71871	2.18	0.40886	D	0.984039	P;P;D;P	0.53745	0.489;0.898;0.962;0.656	B;P;P;P	0.62491	0.314;0.672;0.903;0.579	D	0.90678	0.4603	10	0.59425	D	0.04	.	4.3183	0.11003	0.2691:0.1732:0.5577:0.0	.	148;430;430;435	Q6ZP48;Q5JXY1;Q6S9Z9;Q9NQ11	.;.;.;AT132_HUMAN	M	435;430;430;149	ENSP00000327214:L435M;ENSP00000341115:L430M;ENSP00000413307:L430M;ENSP00000424393:L149M	ENSP00000327214:L435M	L	-	1	2	ATP13A2	17195471	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	1.657000	0.37366	0.383000	0.24910	-0.258000	0.10820	CTG	.		0.612	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17322884	G	T	17322884	3	4	74	1	0	0	0	0	1	0	0	0	1125	991	35	4	2543	4	ATP13A2	1	17322884	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	14782042	17322884	231927737	3	6926											
MRPL9	65005	broad.mit.edu	37	chr1	151735832	151735832	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agaaaggctgaagttgcaggCcaggtcaggggcgttccctt	9	8	15	9	1	1	2	1	1	0	1	2	2	2	2	2	5	1	4	2	5	2	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:151735832C>T	ENST00000368830.3	-	1	208	c.124G>A	c.(124-126)Gcc>Acc	p.A42T	OAZ3_ENST00000453029.2_5'Flank|OAZ3_ENST00000321531.5_Intron|OAZ3_ENST00000315067.8_Intron|RP11-98D18.3_ENST00000512280.1_RNA|OAZ3_ENST00000479764.1_5'Flank|MRPL9_ENST00000368829.3_Missense_Mutation_p.A42T|RP11-98D18.2_ENST00000420382.1_RNA|MRPL9_ENST00000467306.1_5'UTR	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	42					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AAGTTGCAGGCCAGGTCAGGG	0.647																																					p.A42T													.	MRPL9-91	0			c.G124A						.						24	24	24					1																	151735832		2203	4298	6501	SO:0001583	missense	65005	exon1			TGCAGGCCAGGTC	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"Mitochondrial ribosomal proteins / large subunits"	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.124G>A	1.37:g.151735832C>T	ENSP00000357823:p.Ala42Thr	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_031420	0	0	27	62	35	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.389211	0.25118	.	.	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.32515	1.45;1.45	4.93	1.83	0.25207	.	0.927468	0.08934	N	0.872606	T	0.04952	0.0133	N	0.14661	0.345	0.09310	N	1	B;B;B	0.26672	0.156;0.039;0.039	B;B;B	0.23852	0.049;0.023;0.014	T	0.44143	-0.9347	10	0.17369	T	0.5	-0.4622	6.0132	0.19588	0.0:0.5216:0.3693:0.1091	.	42;42;42	B4DDZ7;B4DUJ1;Q9BYD2	.;.;RM09_HUMAN	T	42	ENSP00000357823:A42T;ENSP00000357822:A42T	ENSP00000357822:A42T	A	-	1	0	MRPL9	150002456	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.691000	0.25467	0.199000	0.20427	-0.176000	0.13171	GCC	.		0.647	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420		T	151735832	C	T	151735832	3	4	74	1	0	0	0	0	1	0	0	0	9845	739	26	2	707	2	MRPL9	1	151735832	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	134412948	151735832	97514789	4	6927											
FCER1G	2207	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161185157	161185157	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tactccttttggttgaacaaGcaggtaagagggtttggtga	10	13	13	5	0	0	3	0	2	0	1	1	3	1	3	1	4	3	4	1	4	4	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:161185157G>T	ENST00000289902.1	+	1	71	c.46G>T	c.(46-48)Gca>Tca	p.A16S	FCER1G_ENST00000367992.3_Missense_Mutation_p.A16S|FCER1G_ENST00000490414.1_3'UTR	NM_004106.1	NP_004097.1	P30273	FCERG_HUMAN	Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide	16					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 II (GO:0019886)|blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|negative regulation of mast cell apoptotic process (GO:0033026)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|phagocytosis, engulfment (GO:0006911)|platelet activation (GO:0030168)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I hypersensitivity (GO:0001812)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|protein localization to plasma membrane (GO:0072659)|regulation of platelet activation (GO:0010543)|serotonin secretion by platelet (GO:0002554)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)			endometrium(1)|lung(5)	6	all_cancers(52;1.35e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Benzylpenicilloyl Polylysine(DB00895)	GGTTGAACAAGCAGGTAAGAG	0.552																																					p.A16S		.											.	FCER1G-90	0			c.G46T						.						191	170	177					1																	161185157		2203	4300	6503	SO:0001583	missense	2207	exon1			GAACAAGCAGGTA		CCDS1225.1	1q23	2008-02-05			ENSG00000158869	ENSG00000158869			3611	protein-coding gene	gene with protein product		147139				2138619	Standard	NM_004106		Approved		uc001fyz.1	P30273	OTTHUMG00000034343	ENST00000289902.1:c.46G>T	1.37:g.161185157G>T	ENSP00000289902:p.Ala16Ser	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	147	45	NM_004106	0	0	0	0	0	Q5VTW4	Missense_Mutation	SNP	ENST00000289902.1	37	CCDS1225.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.433722	0.43224	.	.	ENSG00000158869	ENST00000367992;ENST00000289902	T	0.30714	1.52	5.17	4.26	0.50523	.	0.296828	0.26903	N	0.021920	T	0.38532	0.1044	.	.	.	0.27667	N	0.94689	D;D	0.63880	0.993;0.993	D;D	0.70227	0.968;0.968	T	0.38908	-0.9639	8	0.44086	T	0.13	.	9.7959	0.40735	0.0925:0.0:0.9075:0.0	.	16;16	A6NCQ8;P30273	.;FCERG_HUMAN	S	16	ENSP00000356971:A16S	ENSP00000289902:A16S	A	+	1	0	FCER1G	159451781	1.000000	0.71417	1.000000	0.80357	0.215000	0.24574	1.939000	0.40213	1.419000	0.47118	-0.133000	0.14855	GCA	.		0.552	FCER1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083012.1	NM_004106		T	161185157	G	T	161185157	3	4	74	1	0	0	0	0	1	0	0	0	5794	971	34	4	48	4	FCER1G	1	161185157	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	9449325	161185157	88065464	5	6928											
FCGR2A	2212	hgsc.bcm.edu;broad.mit.edu	37	chr1	161487871	161487871	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactctgaaccccagggcacCtactgacgatgataaaaaca	15	6	8	12	1	1	3	0	3	1	0	1	5	1	3	3	1	3	1	3	1	5	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:161487871C>A	ENST00000271450.6	+	7	925	c.887C>A	c.(886-888)cCt>cAt	p.P296H	FCGR2A_ENST00000367972.4_Missense_Mutation_p.P295H|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000486608.1_3'UTR	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	296					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCCAGGGCACCTACTGACGAT	0.443																																					p.P296H		.											.	FCGR2A-91	0			c.C887A						.						72	72	72					1																	161487871		2203	4297	6500	SO:0001583	missense	2212	exon7			GGGCACCTACTGA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3616	protein-coding gene	gene with protein product	"Immunoglobulin G Fc receptor II"	146790	"Fc fragment of IgG, low affinity IIa, receptor for (CD32)"	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.887C>A	1.37:g.161487871C>A	ENSP00000271450:p.Pro296His	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	111	35	NM_001136219	0	0	38	38	0	Q8WUN1|Q8WW64	Missense_Mutation	SNP	ENST00000271450.6	37	CCDS44264.1	.	.	.	.	.	.	.	.	.	.	.	10.12	1.264122	0.23136	.	.	ENSG00000143226	ENST00000367972;ENST00000271450;ENST00000537821;ENST00000461298	T;T	0.02763	4.18;4.17	0.565	0.565	0.17309	.	4.463590	0.00639	N	0.000515	T	0.02083	0.0065	N	0.08118	0	0.29664	N	0.842961	D;D	0.76494	0.998;0.999	D;D	0.83275	0.99;0.996	T	0.51188	-0.8737	8	0.56958	D	0.05	.	.	.	.	.	296;295	P12318;P12318-2	FCG2A_HUMAN;.	H	295;296;31;31	ENSP00000356949:P295H;ENSP00000271450:P296H	ENSP00000271450:P296H	P	+	2	0	FCGR2A	159754495	0.002000	0.14202	0.006000	0.13384	0.006000	0.05464	0.646000	0.24797	0.556000	0.29098	0.563000	0.77884	CCT	.		0.443	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642		A	161487871	C	A	161487871	3	1	74	1	0	0	0	0	1	0	0	0	5800	681	24	4	913	4	FCGR2A	1	161487871	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	302714	161487871	87762750	6	6929											
CACNA1S	779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201030589	201030589	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attggagtctatggccttgtAcagcagcctgggggtgggca	7	10	16	8	0	1	0	0	0	1	0	1	1	1	1	2	5	3	3	2	5	2	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:201030589A>G	ENST00000362061.3	-	25	3287	c.3061T>C	c.(3061-3063)Tac>Cac	p.Y1021H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.Y1021H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1021	Dihydropyridine binding. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGGCCTTGTACAGCAGCCTG	0.557																																					p.Y1021H		.											.	CACNA1S-94	0			c.T3061C						.						99	91	94					1																	201030589		2203	4300	6503	SO:0001583	missense	779	exon25			CCTTGTACAGCAG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.3061T>C	1.37:g.201030589A>G	ENSP00000355192:p.Tyr1021His	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	83	17	NM_000069	0	0	0	0	0	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507446	0.85282	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97529	-4.42;-4.42	5.21	5.21	0.72293	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98639	0.9544	M	0.89968	3.075	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	D	0.99751	1.1018	10	0.72032	D	0.01	.	15.3483	0.74359	1.0:0.0:0.0:0.0	.	1021	Q13698	CAC1S_HUMAN	H	1021	ENSP00000355192:Y1021H;ENSP00000356307:Y1021H	ENSP00000355192:Y1021H	Y	-	1	0	CACNA1S	199297212	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	8.889000	0.92470	2.087000	0.62958	0.459000	0.35465	TAC	.		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		G	201030589	A	G	201030589	3	3	74	1	0	0	0	0	1	0	0	0	2553	391	14	3	2640	3	CACNA1S	1	201030589	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	39542718	201030589	48220032	7	6930											
NAV1	89796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201781618	201781618	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaccttctccaacaacgtgGagccagccaatggcttcctg	9	9	9	14	1	1	1	0	1	1	0	3	2	2	2	5	2	4	1	5	2	3	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:201781618G>T	ENST00000367296.4	+	27	5470	c.5050G>T	c.(5050-5052)Gag>Tag	p.E1684*	NAV1_ENST00000367300.3_Nonsense_Mutation_p.E1624*|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367295.1_Nonsense_Mutation_p.E1290*|NAV1_ENST00000367297.4_Nonsense_Mutation_p.E1676*|NAV1_ENST00000367302.1_Nonsense_Mutation_p.E1637*|NAV1_ENST00000295624.6_Nonsense_Mutation_p.E1681*	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1684					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						CAACAACGTGGAGCCAGCCAA	0.562																																					p.E1684X		.											.	NAV1-228	0			c.G5050T						.						131	108	116					1																	201781618		2203	4300	6503	SO:0001587	stop_gained	89796	exon27			AACGTGGAGCCAG	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.5050G>T	1.37:g.201781618G>T	ENSP00000356265:p.Glu1684*	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	182	84	NM_020443	0	0	0	0	0	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Nonsense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	G	48	14.566335	0.99801	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295;ENST00000367301	.	.	.	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-33.9888	20.2191	0.98319	0.0:0.0:1.0:0.0	.	.	.	.	X	1637;1684;1681;1676;1624;1290;93	.	ENSP00000295624:E1681X	E	+	1	0	NAV1	200048241	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.753000	0.98904	2.866000	0.98385	0.650000	0.86243	GAG	.		0.562	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		T	201781618	G	T	201781618	4	4	74	1	0	0	0	0	0	1	0	0	10208	1175	41	4	5213	4	NAV1	1	201781618	Nonsense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	751029	201781618	47469003	8	6931											
PLEKHA6	22874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204236626	204236626	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatagtagaagaggcagcgaTccaccaggacgaaccagcgc	14	4	12	11	3	0	2	0	0	0	2	1	5	1	3	3	2	3	2	3	2	5	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:204236626T>A	ENST00000272203.3	-	5	573	c.257A>T	c.(256-258)gAt>gTt	p.D86V	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.D86V	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	86	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GAGGCAGCGATCCACCAGGAC	0.592																																					p.D86V		.											.	PLEKHA6-654	0			c.A257T						.						114	85	95					1																	204236626		2203	4300	6503	SO:0001583	missense	22874	exon5			CAGCGATCCACCA	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.257A>T	1.37:g.204236626T>A	ENSP00000272203:p.Asp86Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	125	40	NM_014935	0	0	12	16	4	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554500	0.86231	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.15017	2.46;2.46	5.51	5.51	0.81932	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.86573	2.825	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	T	0.56962	-0.7892	10	0.87932	D	0	-24.5699	15.2951	0.73898	0.0:0.0:0.0:1.0	.	86	Q9Y2H5	PKHA6_HUMAN	V	86	ENSP00000272203:D86V;ENSP00000402046:D86V	ENSP00000272203:D86V	D	-	2	0	PLEKHA6	202503249	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	6.511000	0.73733	2.086000	0.62901	0.448000	0.29417	GAT	.		0.592	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204236626	T	A	204236626	3	1	74	1	0	0	0	0	1	0	0	0	12086	1435	50	5	2961	5	PLEKHA6	1	204236626	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	2455008	204236626	45013995	9	6932											
KIAA1804	84451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	233518317	233518317	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattcctcgctgccaaggagAgaactaaatcccatgtgcct	12	9	8	12	1	0	1	0	0	0	1	3	3	2	2	4	1	3	1	4	1	5	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:233518317A>G	ENST00000366624.3	+	10	3232	c.2971A>G	c.(2971-2973)Aga>Gga	p.R991G	MLK4_ENST00000366622.1_Missense_Mutation_p.R437G	NM_032435.2	NP_115811.2																					TGCCAAGGAGAGAACTAAATC	0.557																																					p.R991G		.											.	KIAA1804-523	0			c.A2971G						.						118	102	108					1																	233518317		2203	4300	6503	SO:0001583	missense	0	exon10			AAGGAGAGAACTA																												ENST00000366624.3:c.2971A>G	1.37:g.233518317A>G	ENSP00000355583:p.Arg991Gly	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	149	39	NM_032435	0	0	10	15	5		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.760485	0.49468	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.74947	-0.89;3.17	4.55	4.55	0.56014	.	0.160789	0.30428	U	0.009649	T	0.61236	0.2331	N	0.22421	0.69	0.33546	D	0.59548	P;B	0.40619	0.724;0.029	B;B	0.38500	0.275;0.023	T	0.73569	-0.3941	10	0.48119	T	0.1	.	12.6166	0.56580	1.0:0.0:0.0:0.0	.	438;991	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	G	991;437	ENSP00000355583:R991G;ENSP00000355581:R437G	ENSP00000355581:R437G	R	+	1	2	RP5-862P8.2	231584940	0.995000	0.38212	0.055000	0.19348	0.009000	0.06853	2.656000	0.46716	1.908000	0.55244	0.460000	0.39030	AGA	.		0.557	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			G	233518317	A	G	233518317	3	3	74	1	0	0	0	0	1	0	0	0	8280	296	11	3	3009	3	KIAA1804	1	233518317	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	29281691	233518317	15732304	10	6933											
TBCE	6905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	235599915	235599915	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtagtaaacgacaatcagAtatcacaagtaagagctgct	16	9	9	7	1	2	2	2	0	0	2	2	3	2	2	0	1	3	5	0	1	7	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:235599915A>C	ENST00000366601.3	+	11	1131	c.955A>C	c.(955-957)Ata>Cta	p.I319L	TBCE_ENST00000406207.1_Missense_Mutation_p.I319L|TBCE_ENST00000543662.1_Missense_Mutation_p.I370L|TBCE_ENST00000472011.1_3'UTR			Q15813	TBCE_HUMAN	tubulin folding cofactor E	319					'de novo' posttranslational protein folding (GO:0051084)|adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|microtubule cytoskeleton organization (GO:0000226)|muscle atrophy (GO:0014889)|peripheral nervous system neuron axonogenesis (GO:0048936)|post-chaperonin tubulin folding pathway (GO:0007023)|post-embryonic development (GO:0009791)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	chaperone binding (GO:0051087)			NS(1)|endometrium(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	14	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)			CGACAATCAGATATCACAAGT	0.428																																					p.I319L		.											.	TBCE-90	0			c.A955C						.						127	121	123					1																	235599915		2203	4300	6503	SO:0001583	missense	6905	exon11			AATCAGATATCAC	U61232	CCDS1605.1, CCDS73052.1	1q42.3	2014-02-04	2006-11-21		ENSG00000116957	ENSG00000116957			11582	protein-coding gene	gene with protein product		604934	"tubulin-specific chaperone e", "Kenny-Caffey syndrome", "hypoparathyroidism, growth and mental retardation, and dysmorphism"	KCS, HRD		8706133, 9806825, 12389028	Standard	NM_001079515		Approved	KCS1, pac2	uc001hxa.1	Q15813	OTTHUMG00000039987	ENST00000366601.3:c.955A>C	1.37:g.235599915A>C	ENSP00000355560:p.Ile319Leu	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	158	34	NM_003193	0	0	0	0	0	A8K8C2|B7Z3P1	Missense_Mutation	SNP	ENST00000366601.3	37	CCDS1605.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163199	0.78226	.	.	ENSG00000116957	ENST00000366601;ENST00000406207;ENST00000543662	T;T;T	0.25414	1.8;1.8;1.8	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.32466	0.0830	L	0.52823	1.66	0.58432	D	0.999993	D;B;P	0.60575	0.988;0.391;0.538	P;B;P	0.52309	0.695;0.194;0.545	T	0.04723	-1.0931	10	0.15952	T	0.53	-23.5139	12.9072	0.58160	1.0:0.0:0.0:0.0	.	370;319;319	B7Z3P1;A8K8C2;Q15813	.;.;TBCE_HUMAN	L	319;319;370	ENSP00000355560:I319L;ENSP00000384571:I319L;ENSP00000439170:I370L	ENSP00000355560:I319L	I	+	1	0	TBCE	233666538	1.000000	0.71417	0.946000	0.38457	0.879000	0.50718	5.808000	0.69165	2.053000	0.61076	0.533000	0.62120	ATA	.		0.428	TBCE-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096458.3	NM_003193		C	235599915	A	C	235599915	3	2	74	1	0	0	0	0	1	0	0	0	15666	333	12	5	993	5	TBCE	1	235599915	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	2081598	235599915	13650706	11	6934											
PLB1	151056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	28847964	28847964	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacctggtagagcgaatgAaaaacagccccgtgagtaca	14	5	13	9	2	0	3	0	2	0	1	0	5	0	4	3	2	4	2	3	2	5	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:28847964A>C	ENST00000327757.5	+	50	3612	c.3568A>C	c.(3568-3570)Aaa>Caa	p.K1190Q	PLB1_ENST00000422425.2_Missense_Mutation_p.K1179Q|PLB1_ENST00000541605.1_Missense_Mutation_p.K155Q	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1190	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					AGAGCGAATGAAAAACAGCCC	0.642																																					p.K1190Q		.											.	PLB1-141	0			c.A3568C						.						78	83	81					2																	28847964		2203	4300	6503	SO:0001583	missense	151056	exon50			CGAATGAAAAACA		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3568A>C	2.37:g.28847964A>C	ENSP00000330442:p.Lys1190Gln	Somatic	117	1		WXS	Illumina HiSeq	Phase_I	128	38	NM_153021	0	0	0	0	0	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.53|18.53	3.644515|3.644515	0.67358|0.67358	.|.	.|.	ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000541605|ENST00000404858	T;T;T|.	0.13901|.	2.55;2.55;2.55|.	5.69|5.69	5.69|5.69	0.88448|0.88448	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);|.	0.215792|.	0.37577|.	N|.	0.002030|.	T|.	0.64616|.	0.2614|.	L|L	0.58428|0.58428	1.81|1.81	0.43982|0.43982	D|D	0.996678|0.996678	D;D|.	0.63880|.	0.985;0.993|.	P;D|.	0.62955|.	0.853;0.909|.	T|.	0.63497|.	-0.6624|.	10|.	0.17369|.	T|.	0.5|.	-10.8195|-10.8195	12.3323|12.3323	0.55046|0.55046	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1179;1190|.	Q6P1J6-3;Q6P1J6|.	.;PLB1_HUMAN|.	Q|C	1190;1179;155|1177	ENSP00000330442:K1190Q;ENSP00000416440:K1179Q;ENSP00000437426:K155Q|.	ENSP00000330442:K1190Q|.	K|X	+|+	1|3	0|0	PLB1|PLB1	28701468|28701468	0.992000|0.992000	0.36948|0.36948	0.936000|0.936000	0.37596|0.37596	0.607000|0.607000	0.37147|0.37147	2.562000|2.562000	0.45914|0.45914	2.171000|2.171000	0.68590|0.68590	0.459000|0.459000	0.35465|0.35465	AAA|TGA	.		0.642	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2			C	28847964	A	C	28847964	3	2	74	1	0	0	0	0	1	0	0	0	12050	247	9	5	3799	5	PLB1	2	28847964	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08		28847964	214351409	12	6935											
TFCP2L1	29842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	121991738	121991738	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattctgctccagctcctgaCagacataaatggtcatcttt	10	13	7	11	0	3	2	1	1	2	1	5	3	5	2	2	1	2	2	2	1	2	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:121991738C>T	ENST00000263707.5	-	12	1224	c.1127G>A	c.(1126-1128)tGt>tAt	p.C376Y		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	376					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CAGCTCCTGACAGACATAAAT	0.532																																					p.C376Y		.											.	TFCP2L1-93	0			c.G1127A						.						103	91	95					2																	121991738		2203	4300	6503	SO:0001583	missense	29842	exon12			TCCTGACAGACAT	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1127G>A	2.37:g.121991738C>T	ENSP00000263707:p.Cys376Tyr	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	87	32	NM_014553	0	0	1	1	0	Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	37	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941307	0.73557	.	.	ENSG00000115112	ENST00000263707	T	0.26067	1.76	5.7	4.83	0.62350	.	0.152997	0.64402	D	0.000010	T	0.49677	0.1571	M	0.81942	2.565	0.80722	D	1	D	0.61080	0.989	P	0.60886	0.88	T	0.55730	-0.8095	10	0.56958	D	0.05	.	14.5903	0.68359	0.0:0.93:0.0:0.07	.	376	Q9NZI6	TF2L1_HUMAN	Y	376	ENSP00000263707:C376Y	ENSP00000263707:C376Y	C	-	2	0	TFCP2L1	121708208	1.000000	0.71417	0.994000	0.49952	0.818000	0.46254	6.831000	0.75324	1.426000	0.47256	0.549000	0.68633	TGT	.		0.532	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		T	121991738	C	T	121991738	3	4	74	1	0	0	0	0	1	0	0	0	15828	478	17	2	328	2	TFCP2L1	2	121991738	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	93143774	121991738	121207635	13	6936											
ABCA12	26154	broad.mit.edu	37	chr2	215880304	215880304	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctctgaaagagacaggttGcagaattctttcattgcatc	11	13	8	9	0	3	3	1	1	2	2	5	4	3	3	0	1	2	3	0	1	2	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:215880304G>T	ENST00000272895.7	-	15	2085	c.1866C>A	c.(1864-1866)tgC>tgA	p.C622*	ABCA12_ENST00000389661.4_Nonsense_Mutation_p.C304*	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	622					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GAGACAGGTTGCAGAATTCTT	0.428																																					p.C622X	Ovarian(66;664 1488 5121 34295)												.	ABCA12-99	0			c.C1866A						.						109	104	106					2																	215880304		2203	4300	6503	SO:0001587	stop_gained	26154	exon15			CAGGTTGCAGAAT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.1866C>A	2.37:g.215880304G>T	ENSP00000272895:p.Cys622*	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_173076	0	0	0	0	0	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Nonsense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.439121	0.83885	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	.	.	.	5.65	1.82	0.25136	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6521	0.34040	0.3031:0.0:0.6969:0.0	.	.	.	.	X	622;304	.	ENSP00000272895:C622X	C	-	3	2	ABCA12	215588549	0.998000	0.40836	0.960000	0.40013	0.083000	0.17756	1.111000	0.31159	0.417000	0.25871	-0.136000	0.14681	TGC	.		0.428	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		T	215880304	G	T	215880304	4	4	74	1	0	0	0	0	0	1	0	0	30	1311	46	4	6077	4	ABCA12	2	215880304	Nonsense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	93888566	215880304	27319069	14	6937											
C2orf24	27013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220039577	220039577	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagctccccattcgtcgtTgaagacctcctcctcctccc	6	10	6	19	2	0	2	0	1	0	1	7	2	5	2	7	0	2	3	7	0	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:220039577T>G	ENST00000409789.1	-	6	860	c.433A>C	c.(433-435)Aac>Cac	p.N145H	CNPPD1_ENST00000360507.5_Missense_Mutation_p.N145H			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	145					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						CATTCGTCGTTGAAGACCTCC	0.577																																					p.N145H		.											.	CNPPD1-90	0			c.A433C						.						86	80	82					2																	220039577		2203	4300	6503	SO:0001583	missense	27013	exon5			CGTCGTTGAAGAC	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 24"	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.433A>C	2.37:g.220039577T>G	ENSP00000386277:p.Asn145His	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	91	31	NM_015680	0	0	55	100	45	B2RC77|O75548|Q9H4N0|Q9UQN0	Missense_Mutation	SNP	ENST00000409789.1	37	CCDS2433.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250866	0.80135	.	.	ENSG00000115649	ENST00000360507;ENST00000409789;ENST00000453038;ENST00000451647	T;T;T	0.58940	0.3;0.3;0.3	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.81192	0.4771	M	0.93638	3.44	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.86432	0.1761	10	0.87932	D	0	-21.9189	13.8616	0.63564	0.0:0.0:0.0:1.0	.	145	Q9BV87	CNPD1_HUMAN	H	145;145;145;172	ENSP00000353698:N145H;ENSP00000386277:N145H;ENSP00000410109:N145H	ENSP00000353698:N145H	N	-	1	0	CNPPD1	219747821	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.766000	0.85320	1.873000	0.54277	0.459000	0.35465	AAC	.		0.577	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680		G	220039577	T	G	220039577	3	3	74	1	0	0	0	0	1	0	0	0	2165	1812	63	5	815	5	C2orf24	2	220039577	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	4159273	220039577	23159796	15	6938											
AGXT	189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	241808770	241808770	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agcgagccgtggacatcgggGagcgcataggtaagggagag	11	4	19	7	4	0	1	0	0	0	1	1	5	0	3	1	5	3	2	1	5	2	2	rs180177208		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:241808770G>A	ENST00000307503.3	+	2	736	c.349G>A	c.(349-351)Gag>Aag	p.E117K		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	117					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	GGACATCGGGGAGCGCATAGG	0.657																																					p.E117K		.											.	AGXT-90	0			c.G349A						.						51	52	52					2																	241808770		2203	4300	6503	SO:0001583	missense	189	exon2			ATCGGGGAGCGCA	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"oxalosis I", "primary hyperoxaluria type 1", "L-alanine: glyoxylate aminotransferase 1", "serine:pyruvate aminotransferase", "glycolicaciduria"	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.349G>A	2.37:g.241808770G>A	ENSP00000302620:p.Glu117Lys	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	87	32	NM_000030	0	0	0	0	0	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	37	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	G	6.004	0.369211	0.11352	.	.	ENSG00000172482	ENST00000307503	D	0.85702	-2.02	4.12	4.12	0.48240	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.160335	0.53938	D	0.000048	T	0.80681	0.4669	L	0.60067	1.865	0.49915	D	0.999836	B;B	0.14012	0.004;0.009	B;B	0.17979	0.012;0.02	T	0.75516	-0.3290	10	0.27785	T	0.31	-32.4358	10.2905	0.43592	0.151:0.0:0.849:0.0	.	117;117	B7Z548;P21549	.;SPYA_HUMAN	K	117	ENSP00000302620:E117K	ENSP00000302620:E117K	E	+	1	0	AGXT	241457443	1.000000	0.71417	0.826000	0.32828	0.290000	0.27261	4.798000	0.62510	2.007000	0.58848	0.591000	0.81541	GAG	.		0.657	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030		A	241808770	G	A	241808770	3	1	74	1	0	0	0	0	1	0	0	0	404	1175	41	2	355	2	AGXT	2	241808770	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	21769193	241808770	1390603	16	6939											
PASK	23178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242065794	242065794	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccaacgtggaaggaacgtGtcctgggctttctctgtcgc	7	11	12	11	3	1	0	0	0	1	0	5	2	3	2	2	3	2	1	2	3	3	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:242065794G>A	ENST00000405260.1	-	10	3234	c.2536C>T	c.(2536-2538)Cac>Tac	p.H846Y	PASK_ENST00000358649.4_Missense_Mutation_p.H846Y|PASK_ENST00000544142.1_Missense_Mutation_p.H660Y|PASK_ENST00000234040.4_Missense_Mutation_p.H846Y|PASK_ENST00000403638.3_Missense_Mutation_p.H846Y|PASK_ENST00000539818.1_Missense_Mutation_p.H630Y	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	846					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GAAGGAACGTGTCCTGGGCTT	0.572																																					p.H846Y		.											.	PASK-536	0			c.C2536T						.						159	149	152					2																	242065794		2203	4300	6503	SO:0001583	missense	23178	exon10			GAACGTGTCCTGG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2536C>T	2.37:g.242065794G>A	ENSP00000384016:p.His846Tyr	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	165	59	NM_015148	0	0	1	4	3	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.619945	0.00828	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.66280	-0.2;-0.19;-0.2;-0.15;-0.19;0.81	3.24	-6.48	0.01896	.	1.203440	0.06016	N	0.650378	T	0.35856	0.0946	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.32365	0.367;0.011;0.032;0.031;0.09	B;B;B;B;B	0.28385	0.089;0.036;0.009;0.024;0.023	T	0.20773	-1.0265	10	0.31617	T	0.26	.	6.1419	0.20265	0.3709:0.0:0.4891:0.14	.	811;660;846;846;846	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	Y	846;660;846;846;630;846	ENSP00000234040:H846Y;ENSP00000441374:H660Y;ENSP00000384016:H846Y;ENSP00000351475:H846Y;ENSP00000443083:H630Y;ENSP00000384438:H846Y	ENSP00000234040:H846Y	H	-	1	0	PASK	241714467	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.416000	0.02467	-1.226000	0.02574	-1.169000	0.01745	CAC	.		0.572	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		A	242065794	G	A	242065794	3	1	74	1	0	0	0	0	1	0	0	0	11498	1377	48	2	1471	2	PASK	2	242065794	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	257024	242065794	1133579	17	6940											
SYN2	7079	broad.mit.edu;bcgsc.ca	37	chr3	12192767	12192767	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcgctatctataagacaCtgggaggagaaaagttccct	12	10	11	8	1	1	2	0	0	1	2	3	4	2	3	1	3	0	2	1	3	5	4	rs371670872		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:12192767C>T	ENST00000287814.4	-	0	1650				SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4						central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						CTATAAGACACTGGGAGGAGA	0.418																																					.	Melanoma(199;1446 2144 30617 38794 51714)												.	SYN2-24	0			.						.						84	76	79					3																	12192767		1873	4104	5977	SO:0001628	intergenic_variant	6854	.			AAGACACTGGGAG	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"tissue inhibitor of metalloproteinase 4"			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763		3.37:g.12192767C>T		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	8	5	.	0	0	0	0	0	B2R7K6	Silent	SNP	ENST00000287814.4	37	CCDS2608.1																																																																																			.		0.418	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		T	12192767	C	T	12192767	1	4	74	0	1	0	0	0	0	0	0	0	15473	564	20	2		2	SYN2	3	12192767	IGR	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		12192767	185829663	18	6941											
ZNF502	91392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	44763320	44763320	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	actttccaaacaaaggcaaaCctctctcagcatcagagaat	16	8	5	12	0	3	1	2	0	1	1	5	2	4	1	2	1	3	2	2	1	4	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:44763320C>G	ENST00000296091.4	+	4	1267	c.1011C>G	c.(1009-1011)aaC>aaG	p.N337K	ZNF502_ENST00000436624.2_Missense_Mutation_p.N337K|ZNF502_ENST00000449836.1_Missense_Mutation_p.N337K	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		CAAAGGCAAACCTCTCTCAGC	0.403																																					p.N337K		.											.	ZNF502-90	0			c.C1011G						.						57	61	60					3																	44763320		2203	4300	6503	SO:0001583	missense	91392	exon4			GGCAAACCTCTCT	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"Zinc fingers, C2H2-type"	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.1011C>G	3.37:g.44763320C>G	ENSP00000296091:p.Asn337Lys	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	117	79	NM_001134440	0	0	0	0	0		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.31|11.31	1.599882|1.599882	0.28534|0.28534	.|.	.|.	ENSG00000196653|ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624|ENST00000427783	T;T;T|.	0.07021|.	3.23;3.23;3.23|.	4.27|4.27	-1.17|-1.17	0.09648|0.09648	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|.	.|.	.|.	.|.	T|T	0.14700|0.14700	0.0355|0.0355	N|N	0.20986|0.20986	0.625|0.625	0.09310|0.09310	N|N	1|1	P|.	0.35982|.	0.531|.	B|.	0.24155|.	0.051|.	T|T	0.29119|0.29119	-1.0022|-1.0022	9|6	0.10377|0.02654	T|T	0.69|1	.|.	1.6891|1.6891	0.02848|0.02848	0.1337:0.367:0.1313:0.368|0.1337:0.367:0.1313:0.368	.|.	337|.	Q8TBZ5|.	ZN502_HUMAN|.	K|S	337|337	ENSP00000397390:N337K;ENSP00000296091:N337K;ENSP00000406469:N337K|.	ENSP00000296091:N337K|ENSP00000397812:T337S	N|T	+|+	3|2	2|0	ZNF502|ZNF502	44738324|44738324	0.000000|0.000000	0.05858|0.05858	0.859000|0.859000	0.33776|0.33776	0.997000|0.997000	0.91878|0.91878	-1.664000|-1.664000	0.01966|0.01966	-0.114000|-0.114000	0.11936|0.11936	0.655000|0.655000	0.94253|0.94253	AAC|ACC	.		0.403	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		G	44763320	C	G	44763320	3	3	74	1	0	0	0	0	1	0	0	0	17982	506	18	4	1017	4	ZNF502	3	44763320	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	32570553	44763320	153259110	19	6942											
NBEAL2	23218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47032943	47032943	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctgtgaagggcctgctGagtgtggtgcggggctggag	4	9	21	7	1	1	2	0	2	1	0	1	3	1	3	1	6	2	3	1	6	1	0	rs181297174		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:47032943G>T	ENST00000450053.3	+	8	869	c.690G>T	c.(688-690)ctG>ctT	p.L230L	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Silent_p.L230L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	230					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		AGGGCCTGCTGAGTGTGGTGC	0.637																																					p.L230L		.											.	NBEAL2-69	0			c.G690T						.						31	33	32					3																	47032943		2012	4187	6199	SO:0001819	synonymous_variant	23218	exon8			CCTGCTGAGTGTG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.690G>T	3.37:g.47032943G>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	29	22	NM_015175	0	0	0	0	0	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1																																																																																			G|0.999;C|0.000		0.637	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47032943	G	T	47032943	2	4	74	1	0	0	0	0	0	0	0	1	10214	1277	45	4		4	NBEAL2	3	47032943	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	2269623	47032943	150989487	20	6943											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47143047	47143047	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtccgttcacagtccacTgagatgatgtttgaaaacaa	12	12	9	8	1	1	3	1	3	0	1	3	4	3	3	2	0	1	3	2	0	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:47143047T>C	ENST00000409792.3	-	8	4960		c.e8-2			NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2						angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.?(2)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CACAGTCCACTGAGATGATGT	0.408			"N, F, S, Mis"		clear cell renal carcinoma																																.		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	2	Unknown(2)	kidney(2)	c.4918-2A>G						.						109	108	108					3																	47143047		2203	4300	6503	SO:0001630	splice_region_variant	29072	exon9			GTCCACTGAGATG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4918-2A>G	3.37:g.47143047T>C		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	139	102	NM_014159	0	0	0	18	18	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Splice_Site	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	27.7	4.856990	0.91433	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2291	0.82321	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD2	47118051	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.955000	0.87856	2.238000	0.73509	0.528000	0.53228	.	.		0.408	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	Intron	C	47143047	T	C	47143047	5	2	74	1	0	0	0	0	0	0	1	0	14163	1594	55	3	2834	3	SETD2	3	47143047	Splice_Site	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	110104	47143047	150879383	21	6944											
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	52696272	52696272	+	Frame_Shift_Del	DEL	T	T	-																															tcccagagtttgcaagcggcTttatattcaggagaatctgg																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:52696272delT	ENST00000296302.7	-	4	406	c.405delA	c.(403-405)aaafs	p.K135fs	PBRM1_ENST00000394830.3_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.K135fs			Q86U86	PB1_HUMAN	polybromo 1	135					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGCAAGCGGCTTTATATTCAG	0.368			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.K135fs		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.405delA						.						110	106	107					3																	52696272		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon5			.	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.405delA	3.37:g.52696272delT	ENSP00000296302:p.Lys135fs	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	91	61	NM_018313	0	0	0	0	0	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																				.		0.368	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		-	52696272	T	-	52696272	7	5	74	1	0	1	0	1	0	0	0	0	11517	1606	56	0	4603	0	PBRM1	3	52696272	Frame_Shift_Del	DEL	T	TCGA-BQ-5890-01A-11D-1589-08	5553225	52696272	145326158	22	6945											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129324250	129324250	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accgccaccacgtcgggcgcCggttccacgaagcaggcggt	7	4	14	16	7	0	0	0	0	0	0	2	1	1	0	5	4	1	2	5	4	1	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:129324250C>G	ENST00000324093.4	-	1	1411	c.1233G>C	c.(1231-1233)ccG>ccC	p.P411P	PLXND1_ENST00000393239.1_Silent_p.P411P	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	411	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CGTCGGGCGCCGGTTCCACGA	0.751																																					p.P411P	Ovarian(97;366 1484 3738 22084 39045)	.											.	PLXND1-90	0			c.G1233C						.						2	2	2					3																	129324250		1394	3019	4413	SO:0001819	synonymous_variant	23129	exon1			GGGCGCCGGTTCC	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.1233G>C	3.37:g.129324250C>G		Somatic	8	2		WXS	Illumina HiSeq	Phase_I	5	5	NM_015103	0	0	1	1	0	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			.		0.751	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		G	129324250	C	G	129324250	2	3	74	1	0	0	0	0	0	0	0	1	12153	639	23	4		4	PLXND1	3	129324250	Silent	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	76627978	129324250	68698180	23	6946											
NPHP3	27031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132410108	132410108	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggggccttccaggtacTccaatctcactgtttcccaa	8	11	8	14	0	1	0	1	0	1	0	5	0	4	0	4	3	1	2	4	3	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:132410108T>C	ENST00000337331.5	-	18	2584	c.2498A>G	c.(2497-2499)gAg>gGg	p.E833G	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	833					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TTCCAGGTACTCCAATCTCAC	0.388																																					p.E833G		.											.	NPHP3-91	0			c.A2498G						.						163	169	167					3																	132410108		2203	4300	6503	SO:0001583	missense	27031	exon18			AGGTACTCCAATC	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.2498A>G	3.37:g.132410108T>C	ENSP00000338766:p.Glu833Gly	Somatic	251	0		WXS	Illumina HiSeq	Phase_I	308	175	NM_153240	0	0	3	5	2	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	37	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.525698	0.27299	.	.	ENSG00000113971	ENST00000393144;ENST00000337331	D	0.91577	-2.87	4.55	3.35	0.38373	.	0.108809	0.64402	D	0.000011	D	0.87977	0.6314	M	0.61703	1.905	0.80722	D	1	B	0.24258	0.1	B	0.24541	0.054	D	0.83643	0.0151	10	0.49607	T	0.09	-10.5568	10.9157	0.47135	0.0:0.0:0.1571:0.8429	.	833	Q7Z494	NPHP3_HUMAN	G	113;833	ENSP00000338766:E833G	ENSP00000338766:E833G	E	-	2	0	NPHP3	133892798	1.000000	0.71417	0.291000	0.24904	0.151000	0.21798	5.118000	0.64673	0.661000	0.30985	0.460000	0.39030	GAG	.		0.388	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		C	132410108	T	C	132410108	3	2	74	1	0	0	0	0	1	0	0	0	10606	1551	54	3	1534	3	NPHP3	3	132410108	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	3085858	132410108	65612322	24	6947											
AMOTL2	51421	hgsc.bcm.edu	37	chr3	134080584	134080584	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacgccgccgctggtcctCgatggcgccgcgcagcagtg	4	5	16	16	7	0	0	0	0	0	0	2	1	1	0	4	3	1	4	4	3	0	0	rs377093098		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:134080584C>A	ENST00000422605.2	-	6	1511	c.1345G>T	c.(1345-1347)Gag>Tag	p.E449*	AMOTL2_ENST00000514516.1_Nonsense_Mutation_p.E507*|AMOTL2_ENST00000249883.5_Nonsense_Mutation_p.E449*|AMOTL2_ENST00000513145.1_Nonsense_Mutation_p.E449*			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	449					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CGCTGGTCCTCGATGGCGCCG	0.642																																					p.E449X		.											.	AMOTL2-135	0			c.G1345T						.						10	12	11					3																	134080584		2189	4278	6467	SO:0001587	stop_gained	51421	exon6			GGTCCTCGATGGC	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"Leman coiled-coil protein", "angiomotin-like protein 2"	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1345G>T	3.37:g.134080584C>A	ENSP00000409999:p.Glu449*	Somatic	13	1		WXS	Illumina HiSeq	Phase_I	31	2	NM_016201	0	0	71	71	0	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Nonsense_Mutation	SNP	ENST00000422605.2	37		.	.	.	.	.	.	.	.	.	.	C	41	8.966426	0.99019	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-31.3381	19.1782	0.93612	0.0:1.0:0.0:0.0	.	.	.	.	X	449;449;507;449	.	ENSP00000249883:E449X	E	-	1	0	AMOTL2	135563274	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.527000	0.81931	2.769000	0.95229	0.563000	0.77884	GAG	.		0.642	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		A	134080584	C	A	134080584	4	1	74	1	0	0	0	0	0	1	0	0	584	893	31	4	1017	4	AMOTL2	3	134080584	Nonsense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	1670476	134080584	63941846	25	6948											
STX18	53407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	4436571	4436571	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcccaattcaggttgtgtttCagccaaaattttttctgtta	9	18	6	8	0	3	0	2	0	1	0	4	0	4	0	2	1	1	3	2	1	4	7			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:4436571C>T	ENST00000306200.2	-	7	691	c.628G>A	c.(628-630)Gaa>Aaa	p.E210K	STX18_ENST00000505286.1_Missense_Mutation_p.E210K	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	210					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		GGTTGTGTTTCAGCCAAAATT	0.353																																					p.E210K		.											.	STX18-90	0			c.G628A						.						80	81	81					4																	4436571		2203	4300	6503	SO:0001583	missense	53407	exon7			GTGTTTCAGCCAA	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.628G>A	4.37:g.4436571C>T	ENSP00000305810:p.Glu210Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	71	18	NM_016930	0	0	21	35	14	Q596L3|Q5TZP5	Missense_Mutation	SNP	ENST00000306200.2	37	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	C	9.694	1.152643	0.21371	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.19	2.55	0.30701	.	0.372946	0.28388	N	0.015531	T	0.35828	0.0945	L	0.55103	1.725	0.09310	N	0.999999	B	0.06786	0.001	B	0.09377	0.004	T	0.30563	-0.9974	10	0.09338	T	0.73	-1.7145	8.2654	0.31810	0.0:0.7549:0.0:0.2451	.	210	Q9P2W9	STX18_HUMAN	K	210;210;129;129	ENSP00000426648:E210K;ENSP00000305810:E210K;ENSP00000425483:E129K;ENSP00000422376:E129K	ENSP00000305810:E210K	E	-	1	0	STX18	4487472	0.834000	0.29399	0.008000	0.14137	0.804000	0.45430	2.929000	0.48916	0.225000	0.20959	0.655000	0.94253	GAA	.		0.353	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			T	4436571	C	T	4436571	3	4	74	1	0	0	0	0	1	0	0	0	15373	835	29	2	399	2	STX18	4	4436571	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		4436571	186717705	26	6949											
YTHDC1	91746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	69185877	69185877	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcagggggatagtcaatccTtggtttctttctgctgttat	6	17	10	8	0	4	0	2	0	2	0	5	1	5	1	1	3	1	3	1	3	3	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:69185877T>C	ENST00000344157.4	-	12	1983	c.1648A>G	c.(1648-1650)Agg>Ggg	p.R550G	YTHDC1_ENST00000355665.3_Missense_Mutation_p.R532G|YTHDC1_ENST00000579690.1_Missense_Mutation_p.R550G	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	550	Arg-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TAGTCAATCCTTGGTTTCTTT	0.323																																					p.R550G		.											.	YTHDC1-92	0			c.A1648G						.						66	68	67					4																	69185877		2203	4300	6503	SO:0001583	missense	91746	exon12			CAATCCTTGGTTT	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1648A>G	4.37:g.69185877T>C	ENSP00000339245:p.Arg550Gly	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	81	25	NM_001031732	0	0	20	25	5	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	37	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.013953	0.54468	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.27557	1.68;1.66	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.44519	0.1297	L	0.27053	0.805	0.58432	D	0.999999	D;D	0.67145	0.989;0.996	D;P	0.75020	0.985;0.867	T	0.41805	-0.9488	10	0.72032	D	0.01	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	532;550	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	G	550;532	ENSP00000339245:R550G;ENSP00000347888:R532G	ENSP00000339245:R550G	R	-	1	2	YTHDC1	68868472	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.886000	0.69743	2.371000	0.80710	0.533000	0.62120	AGG	.		0.323	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		C	69185877	T	C	69185877	3	2	74	1	0	0	0	0	1	0	0	0	17529	1608	56	3	559	3	YTHDC1	4	69185877	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	64749306	69185877	121968399	27	6950											
ELOVL6	79071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	111119479	111119479	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattcttgtaaagtcaacaCtgacatgttcattggggctg	11	14	9	7	0	3	1	2	1	1	0	3	1	3	1	0	2	1	3	0	2	4	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:111119479C>A	ENST00000394607.3	-	2	176	c.13G>T	c.(13-15)Gtg>Ttg	p.V5L	ELOVL6_ENST00000506461.1_5'UTR|ELOVL6_ENST00000302274.3_Missense_Mutation_p.V5L			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	5					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		AAAGTCAACACTGACATGTTC	0.418																																					p.V5L		.											.	ELOVL6-91	0			c.G13T						.						210	182	191					4																	111119479		2203	4300	6503	SO:0001583	missense	79071	exon2			TCAACACTGACAT	AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.13G>T	4.37:g.111119479C>A	ENSP00000378105:p.Val5Leu	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	147	45	NM_001130721	0	0	5	6	1	Q4W5L0|Q8NCD1	Missense_Mutation	SNP	ENST00000394607.3	37	CCDS3690.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.761175	0.69763	.	.	ENSG00000170522	ENST00000394607;ENST00000302274;ENST00000506625;ENST00000503885	T;T	0.21932	1.98;1.98	5.68	5.68	0.88126	.	0.204024	0.41712	D	0.000835	T	0.16981	0.0408	N	0.22421	0.69	0.48511	D	0.999667	B	0.02656	0.0	B	0.04013	0.001	T	0.06110	-1.0845	10	0.23302	T	0.38	-10.017	18.5758	0.91154	0.0:1.0:0.0:0.0	.	5	Q9H5J4	ELOV6_HUMAN	L	5	ENSP00000378105:V5L;ENSP00000304736:V5L	ENSP00000304736:V5L	V	-	1	0	ELOVL6	111338928	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.795000	0.75140	2.683000	0.91414	0.655000	0.94253	GTG	.		0.418	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090		A	111119479	C	A	111119479	3	1	74	1	0	0	0	0	1	0	0	0	5091	565	20	4	800	4	ELOVL6	4	111119479	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	41933602	111119479	80034797	28	6951											
INPP4B	8821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	143181690	143181690	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttttccgctcacactttccgGggctgtacattcacatacca	8	13	6	14	2	2	0	2	0	0	0	4	0	4	0	3	2	2	3	3	2	2	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:143181690G>T	ENST00000513000.1	-	12	1076	c.643C>A	c.(643-645)Ccg>Acg	p.P215T	INPP4B_ENST00000508116.1_Missense_Mutation_p.P215T|INPP4B_ENST00000262992.4_Missense_Mutation_p.P215T|INPP4B_ENST00000308502.4_Missense_Mutation_p.P215T|INPP4B_ENST00000509777.1_Missense_Mutation_p.P215T	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	215					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.P215S(2)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					ACACTTTCCGGGGCTGTACAT	0.279																																					p.P215T		.											.	INPP4B-228	2	Substitution - Missense(2)	lung(2)	c.C643A						.						53	53	53					4																	143181690		2203	4300	6503	SO:0001583	missense	8821	exon12			TTTCCGGGGCTGT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"inositol polyphosphate-4-phosphatase, type II, 105kD"			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.643C>A	4.37:g.143181690G>T	ENSP00000425487:p.Pro215Thr	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	52	16	NM_003866	0	0	2	2	0	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.349424	0.41599	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.52	3.78	0.43462	.	0.221687	0.37219	N	0.002193	T	0.18551	0.0445	N	0.14661	0.345	0.32366	N	0.556496	P;P	0.45531	0.86;0.767	P;B	0.47075	0.536;0.359	T	0.12604	-1.0541	10	0.09843	T	0.71	.	6.5521	0.22440	0.1539:0.0:0.6999:0.1463	.	86;215	B7Z6T2;O15327	.;INP4B_HUMAN	T	215;215;215;86;215;215;30;30;215;86	ENSP00000425487:P215T;ENSP00000262992:P215T;ENSP00000308441:P215T;ENSP00000423954:P215T;ENSP00000422793:P215T;ENSP00000426207:P30T;ENSP00000427250:P215T;ENSP00000421065:P86T	ENSP00000262992:P215T	P	-	1	0	INPP4B	143401140	0.996000	0.38824	0.954000	0.39281	0.988000	0.76386	1.385000	0.34408	0.674000	0.31244	0.655000	0.94253	CCG	.		0.279	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		T	143181690	G	T	143181690	3	4	74	1	0	0	0	0	1	0	0	0	7774	1232	43	4	2195	4	INPP4B	4	143181690	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	32062211	143181690	47972586	29	6952											
TIGD4	201798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	153691640	153691640	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacatttttaggatgataatCatttaaataataaggaagta	19	14	6	2	0	1	1	1	1	0	0	1	3	1	3	0	2	1	1	0	2	9	9			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:153691640C>T	ENST00000304337.2	-	2	1337	c.517G>A	c.(517-519)Gat>Aat	p.D173N		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	173						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					GGATGATAATCATTTAAATAA	0.353																																					p.D173N		.											.	TIGD4-91	0			c.G517A						.						35	38	37					4																	153691640		2172	4288	6460	SO:0001583	missense	201798	exon2			GATAATCATTTAA	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.517G>A	4.37:g.153691640C>T	ENSP00000355162:p.Asp173Asn	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	56	18	NM_145720	0	0	1	1	0	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341226	0.41498	.	.	ENSG00000169989	ENST00000304337	T	0.14893	2.47	5.7	5.7	0.88788	.	0.000000	0.46145	D	0.000301	T	0.16854	0.0405	L	0.35723	1.085	0.38647	D	0.951745	B	0.26744	0.158	B	0.26864	0.074	T	0.09100	-1.0690	10	0.17369	T	0.5	-28.5772	19.8349	0.96652	0.0:1.0:0.0:0.0	.	173	Q8IY51	TIGD4_HUMAN	N	173	ENSP00000355162:D173N	ENSP00000355162:D173N	D	-	1	0	TIGD4	153911090	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.463000	0.66712	2.861000	0.98227	0.655000	0.94253	GAT	.		0.353	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		T	153691640	C	T	153691640	3	4	74	1	0	0	0	0	1	0	0	0	15930	826	29	2	1025	2	TIGD4	4	153691640	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	10509950	153691640	37462636	30	6953											
SORBS2	8470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	186545113	186545114	+	Missense_Mutation	DNP	GT	GT	AG																															caggcgcgcagcaggtccttGtgctgctgctcgctctcgta																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:186545113_186545114GT>AG	ENST00000284776.7	-	13	1966_1967	c.1457_1458AC>CT	c.(1456-1458)cAC>cCT	p.H486P	SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.H390P|SORBS2_ENST00000355634.5_Missense_Mutation_p.H586P|SORBS2_ENST00000431808.1_Missense_Mutation_p.H486P|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000319471.9_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	486					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCAGGTCCTTGTGCTGCTGCTC	0.579																																					p.H586P	Esophageal Squamous(153;41 2433 9491 36028)	.											.	SORBS2	0			c.A1757C						.																																			SO:0001583	missense	8470	exon16			TCCTTGTGCTGCT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"Arg/Abl interacting protein"					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1457_1458delinsAG	4.37:g.186545113_186545114delinsAG	ENSP00000284776:p.His486Pro	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	114	49		0	0	0	0	0	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	DNP	ENST00000284776.7	37	CCDS3845.1																																																																																			.		0.579	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		AG	186545114	GT	AG	186545113	3	1	74	1	0	0	0	0	1	0	0	0	14960	1368	48	2	1880	2	SORBS2	4	186545113	Missense_Mutation	DNP	GT	TCGA-BQ-5890-01A-11D-1589-08	32853473	186545113	4609163	31	6954											
HEATR7B2	133558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	41048530	41048530	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaagccctattgcaccagccCcacgtaactcccctaaactg	12	7	5	17	1	0	0	0	0	0	0	1	0	1	0	6	0	5	2	6	0	5	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:41048530C>T	ENST00000399564.4	-	16	2030	c.1580G>A	c.(1579-1581)gGg>gAg	p.G527E	MROH2B_ENST00000506092.2_Missense_Mutation_p.G82E	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	527																	TGCACCAGCCCCACGTAACTC	0.448																																					p.G527E		.											.	.	0			c.G1580A						.						92	85	87					5																	41048530		1879	4102	5981	SO:0001583	missense	133558	exon16			CCAGCCCCACGTA		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1580G>A	5.37:g.41048530C>T	ENSP00000382476:p.Gly527Glu	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	58	31	NM_173489	0	0	0	0	0	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.522411	0.44866	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.07908	3.15;3.15	4.87	4.87	0.63330	Armadillo-type fold (1);	0.218754	0.32593	N	0.005895	T	0.28167	0.0695	M	0.74647	2.275	0.30027	N	0.813842	D	0.89917	1.0	D	0.97110	1.0	T	0.03202	-1.1061	10	0.66056	D	0.02	.	13.7123	0.62675	0.0:1.0:0.0:0.0	.	527	Q7Z745	HTRB2_HUMAN	E	82;231;527	ENSP00000441504:G82E;ENSP00000382476:G527E	ENSP00000296803:G231E	G	-	2	0	HEATR7B2	41084287	0.914000	0.31030	0.274000	0.24659	0.058000	0.15608	3.303000	0.51858	2.683000	0.91414	0.655000	0.94253	GGG	.		0.448	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41048530	C	T	41048530	3	4	74	1	0	0	0	0	1	0	0	0	7056	623	22	2	3285	2	HEATR7B2	5	41048530	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		41048530	139866730	32	6955											
FOXD1	2297	broad.mit.edu	37	chr5	72743507	72743507	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcggccgcggcgttgggtggGagcagcggctgccgcttgaa	4	6	20	11	6	0	1	0	1	0	0	0	2	0	2	2	5	3	4	2	5	1	2	rs367705300	byFrequency	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:72743507G>A	ENST00000499003.3	-	1	845	c.681C>T	c.(679-681)ctC>ctT	p.L227L	RP11-79P5.2_ENST00000514661.1_lincRNA|FOXD1_ENST00000513595.1_5'Flank	NM_004472.2	NP_004463.1	Q16676	FOXD1_HUMAN	forkhead box D1	227					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in ureteric bud branching (GO:0060678)|metanephric capsule development (GO:0072213)|metanephric capsule specification (GO:0072267)|metanephric nephron development (GO:0072210)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme development (GO:0072076)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of gene expression (GO:0010628)|positive regulation of kidney development (GO:0090184)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|lung(2)	4		Lung NSC(167;0.00327)|Ovarian(174;0.0175)|Prostate(461;0.151)		OV - Ovarian serous cystadenocarcinoma(47;1.07e-54)		cgttgggtgggagcagcggcT	0.751																																					.													.	.	0			.						.						8	12	11					5																	72743507		1866	3729	5595	SO:0001819	synonymous_variant	2297	.			GGGTGGGAGCAGC	U59831	CCDS75259.1	5q13.2	2014-06-04			ENSG00000251493	ENSG00000251493		"Forkhead boxes"	3802	protein-coding gene	gene with protein product		601091		FKHL8		7957066, 8825632	Standard	NM_004472		Approved	FREAC4	uc003kcp.3	Q16676	OTTHUMG00000162495	ENST00000499003.3:c.681C>T	5.37:g.72743507G>A		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	29	4	.	0	0	0	0	0	Q12949	Silent	SNP	ENST00000499003.3	37																																																																																				.		0.751	FOXD1-001	KNOWN	sequence_error|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000369154.2	NM_004472		A	72743507	G	A	72743507	2	1	74	1	0	0	0	0	0	0	0	1	6015	1161	41	2		2	FOXD1	5	72743507	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	31694977	72743507	108171753	33	6956											
KLHL3	26249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	136975648	136975648	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gattgccttgggtgcctggcCgccaaccacaatcatgacct	8	9	10	14	1	1	1	1	1	0	0	1	2	1	1	6	2	3	0	6	2	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:136975648C>T	ENST00000309755.4	-	9	1365	c.922G>A	c.(922-924)Ggc>Agc	p.G308S	KLHL3_ENST00000506491.1_Missense_Mutation_p.G226S|KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000508657.1_Missense_Mutation_p.G276S	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	308					distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GGTGCCTGGCCGCCAACCACA	0.542																																					p.G308S		.											.	KLHL3-90	0			c.G922A						.						94	88	90					5																	136975648		2203	4300	6503	SO:0001583	missense	26249	exon9			CCTGGCCGCCAAC	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"Kelch-like", "BTB/POZ domain containing"	6354	protein-coding gene	gene with protein product		605775	"kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)"			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.922G>A	5.37:g.136975648C>T	ENSP00000312397:p.Gly308Ser	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	90	20	NM_017415	0	0	0	0	0	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Missense_Mutation	SNP	ENST00000309755.4	37	CCDS4192.1	.	.	.	.	.	.	.	.	.	.	C	35	5.522061	0.96416	.	.	ENSG00000146021	ENST00000506491;ENST00000508657;ENST00000309755;ENST00000505853	D;D;D;D	0.99494	-6.01;-6.01;-6.01;-6.01	4.54	4.54	0.55810	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.99701	0.9886	H	0.96048	3.76	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.989;0.999	D	0.97261	0.9904	10	0.87932	D	0	.	17.8383	0.88707	0.0:1.0:0.0:0.0	.	77;268;276;308	B7Z6E2;D6RH21;Q9UH77-2;Q9UH77	.;.;.;KLHL3_HUMAN	S	226;276;308;268	ENSP00000424828:G226S;ENSP00000422099:G276S;ENSP00000312397:G308S;ENSP00000426173:G268S	ENSP00000312397:G308S	G	-	1	0	KLHL3	137003547	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	7.416000	0.80143	2.535000	0.85469	0.655000	0.94253	GGC	.		0.542	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			T	136975648	C	T	136975648	3	4	74	1	0	0	0	0	1	0	0	0	8404	652	23	1	869	1	KLHL3	5	136975648	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	64232141	136975648	43939612	34	6957											
FAM13B	51306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	137289855	137289855	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtacataaaaatcatatacCtagtaaaagacagtgcttta	19	11	5	6	0	1	1	1	0	0	1	1	1	1	1	1	0	3	3	1	0	10	8			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:137289855C>G	ENST00000033079.3	-	14	2103	c.1652G>C	c.(1651-1653)aGa>aCa	p.R551T	FAM13B_ENST00000425075.2_Splice_Site_p.R455T|FAM13B_ENST00000420893.2_Splice_Site_p.R551T	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	551					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						AATCATATACCTAGTAAAAGA	0.388																																					p.R551T		.											.	.	0			c.G1652C						.						67	65	66					5																	137289855		2203	4300	6503	SO:0001630	splice_region_variant	51306	exon14			ATATACCTAGTAA	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.1652+1G>C	5.37:g.137289855C>G		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	77	17	NM_001101800	0	0	0	0	0	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148430	0.78001	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.27104	2.85;1.69;2.85	5.49	5.49	0.81192	.	0.083341	0.64402	D	0.000002	T	0.51550	0.1681	M	0.73217	2.22	0.54753	D	0.999983	D;D;D	0.89917	1.0;0.981;1.0	D;D;D	0.74023	0.982;0.962;0.959	T	0.46978	-0.9152	9	.	.	.	-6.7113	18.3606	0.90372	0.0:1.0:0.0:0.0	.	455;551;551	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	T	551;455;551	ENSP00000033079:R551T;ENSP00000394669:R455T;ENSP00000388521:R551T	.	R	-	2	0	FAM13B	137317754	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	6.298000	0.72763	2.576000	0.86940	0.585000	0.79938	AGA	.		0.388	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		Missense_Mutation	G	137289855	C	G	137289855	5	3	74	1	0	0	0	0	0	0	1	0	5469	695	24	4	1135	4	FAM13B	5	137289855	Splice_Site	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	314207	137289855	43625405	35	6958											
PCDHB9	57717	broad.mit.edu;bcgsc.ca	37	chr5	140567235	140567235	+	IGR	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttttaatggatgatccctttCagatttaccgggctgagctg	8	15	10	8	1	1	3	1	2	0	1	2	4	2	4	2	2	2	2	2	2	2	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:140567235C>G	ENST00000361016.2	+	0	4814					NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16						calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGATCCCTTTCAGATTTACCG	0.433																																					.													.	.	0			.						.						46	49	48					5																	140567235		2173	4281	6454	SO:0001628	intergenic_variant	56127	.			CCCTTTCAGATTT	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"Cadherins / Protocadherins : Clustered"	14546	other	protocadherin	"cadherin ME1", "protocadherin-3x", "PCDHbeta 16"	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325		5.37:g.140567235C>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	114	27	.	0	0	3	3	0	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			.		0.433	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		G	140567235	C	G	140567235	1	3	74	0	1	0	0	0	0	0	0	0	11575	827	29	4		4	PCDHB9	5	140567235	IGR	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	3277380	140567235	40348025	36	6959											
GABRA1	2554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	161281260	161281260	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatggttatgacaatcgcctGagaccaggattgggaggtag	11	9	15	6	1	0	2	0	2	0	1	1	6	0	4	2	4	0	2	2	4	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:161281260G>A	ENST00000428797.2	+	4	526	c.171G>A	c.(169-171)ctG>ctA	p.L57L	GABRA1_ENST00000444819.1_Silent_p.L57L|GABRA1_ENST00000437025.2_Silent_p.L57L|GABRA1_ENST00000023897.6_Silent_p.L57L|GABRA1_ENST00000420560.1_Silent_p.L57L|GABRA1_ENST00000393943.4_Silent_p.L57L	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	57					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|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)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	ACAATCGCCTGAGACCAGGAT	0.383																																					p.L57L		.											.	GABRA1-93	0			c.G171A						.						92	95	94					5																	161281260		2203	4299	6502	SO:0001819	synonymous_variant	2554	exon4			TCGCCTGAGACCA		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4075	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 1"	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.171G>A	5.37:g.161281260G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	112	23	NM_001127643	0	0	0	0	0	D3DQK6|Q8N629	Silent	SNP	ENST00000428797.2	37	CCDS4357.1																																																																																			.		0.383	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161281260	G	A	161281260	2	1	74	1	0	0	0	0	0	0	0	1	6179	1277	45	2		2	GABRA1	5	161281260	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	20714025	161281260	19634000	37	6960											
TNXB	7148	hgsc.bcm.edu	37	chr6	32049190	32049190	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccccacacgctgcctgccacGaagcccgtagaggttcatct	8	7	9	17	3	2	1	1	0	1	1	2	2	2	1	5	1	3	3	5	1	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:32049190G>A	ENST00000375244.3	-	10	4198	c.3997C>T	c.(3997-3999)Cgt>Tgt	p.R1333C	RNA5SP206_ENST00000516703.1_RNA|TNXB_ENST00000375247.2_Missense_Mutation_p.R1333C			P22105	TENX_HUMAN	tenascin XB	1420	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TGCCTGCCACGAAGCCCGTAG	0.647																																					p.R1333C		.											.	TNXB-90	0			c.C3997T						.						23	30	28					6																	32049190		2123	4220	6343	SO:0001583	missense	7148	exon10			TGCCACGAAGCCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.3997C>T	6.37:g.32049190G>A	ENSP00000364393:p.Arg1333Cys	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	8	5	NM_019105	0	0	1	1	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	G	17.37	3.372666	0.61624	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.57595	0.39;0.39	5.23	5.23	0.72850	.	0.950594	0.08613	N	0.919605	T	0.53286	0.1787	M	0.69823	2.125	0.09310	N	1	D	0.53312	0.959	P	0.54924	0.764	T	0.46638	-0.9177	10	0.49607	T	0.09	.	10.2526	0.43377	0.0912:0.0:0.9088:0.0	.	1333	P22105-3	.	C	1333	ENSP00000364393:R1333C;ENSP00000364396:R1333C	ENSP00000364393:R1333C	R	-	1	0	TNXB	32157168	0.365000	0.25006	0.021000	0.16686	0.986000	0.74619	1.552000	0.36244	2.610000	0.88304	0.407000	0.27541	CGT	.		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32049190	G	A	32049190	3	1	74	1	0	0	0	0	1	0	0	0	16378	1058	37	1	10856	1	TNXB	6	32049190	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		32049190	139065877	38	6961											
SCUBE3	222663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35213120	35213120	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatcaaccccccacccaaGcgcaagatccttatcgtggt	12	7	6	16	2	1	1	1	0	0	1	3	1	2	1	5	1	3	1	5	1	5	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:35213120G>A	ENST00000274938.7	+	19	2517	c.2517G>A	c.(2515-2517)aaG>aaA	p.K839K	SCUBE3_ENST00000394681.1_Silent_p.K855K	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CCCCACCCAAGCGCAAGATCC	0.562																																					p.K839K		.											.	SCUBE3-91	0			c.G2517A						.						111	102	105					6																	35213120		2203	4300	6503	SO:0001819	synonymous_variant	222663	exon19			ACCCAAGCGCAAG	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2517G>A	6.37:g.35213120G>A		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	122	39	NM_152753	0	0	0	0	0		Silent	SNP	ENST00000274938.7	37	CCDS4800.1																																																																																			.		0.562	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		A	35213120	G	A	35213120	2	1	74	1	0	0	0	0	0	0	0	1	13978	962	34	2		2	SCUBE3	6	35213120	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	3163930	35213120	135901947	39	6962											
PEX6	5190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42932546	42932546	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	accttcctccaggtcatgaaCcctgcgtttgagggcagctg	7	10	11	13	1	1	2	1	2	0	0	3	2	3	2	4	2	3	3	4	2	1	2	rs61753232		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:42932546C>T	ENST00000304611.8	-	16	2857	c.2788G>A	c.(2788-2790)Gtt>Att	p.V930I	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	930					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			AGGTCATGAACCCTGCGTTTG	0.587																																					p.V930I		.											.	PEX6-91	0			c.G2788A						.						112	98	103					6																	42932546		2203	4300	6503	SO:0001583	missense	5190	exon16			CATGAACCCTGCG	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"ATPases / AAA-type"	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2788G>A	6.37:g.42932546C>T	ENSP00000303511:p.Val930Ile	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	148	54	NM_000287	0	0	54	102	48	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.765700	0.31228	.	.	ENSG00000124587	ENST00000304611	D	0.94723	-3.5	5.78	4.92	0.64577	.	0.159370	0.56097	D	0.000024	T	0.79616	0.4476	N	0.13272	0.32	0.80722	D	1	B	0.25667	0.131	B	0.29942	0.109	T	0.76016	-0.3113	10	0.02654	T	1	-14.3262	14.7217	0.69311	0.0:0.9297:0.0:0.0703	.	930	Q13608	PEX6_HUMAN	I	930	ENSP00000303511:V930I	ENSP00000303511:V930I	V	-	1	0	PEX6	43040524	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.850000	0.48294	1.453000	0.47775	-0.143000	0.13931	GTT	.		0.587	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		T	42932546	C	T	42932546	3	4	74	1	0	0	0	0	1	0	0	0	11776	507	18	2	162	2	PEX6	6	42932546	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	7719426	42932546	128182521	40	6963											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51882414	51882414	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcacgcttcaggccacacagGaaggccaaggacactgcagg	12	4	12	13	1	2	0	2	0	0	0	2	2	2	2	2	5	1	2	2	5	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:51882414G>A	ENST00000371117.3	-	34	5669	c.5394C>T	c.(5392-5394)ttC>ttT	p.F1798F	PKHD1_ENST00000340994.4_Silent_p.F1798F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1798					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGCCACACAGGAAGGCCAAGG	0.522																																					p.F1798F		.											.	PKHD1-603	0			c.C5394T						.						101	89	93					6																	51882414		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon34			ACACAGGAAGGCC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5394C>T	6.37:g.51882414G>A		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	103	42	NM_170724	0	0	0	0	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			.		0.522	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51882414	G	A	51882414	2	1	74	1	0	0	0	0	0	0	0	1	11997	1165	41	2		2	PKHD1	6	51882414	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	8949868	51882414	119232653	41	6964											
SYNCRIP	10492	hgsc.bcm.edu;bcgsc.ca	37	chr6	86332353	86332354	+	Frame_Shift_Ins	INS	-	-	T																															caagaaagcaaaagcctctgINSttttttttcttgtcatccgg																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:86332353_86332354insT	ENST00000369622.3	-	8	1354_1355	c.854_855insA	c.(853-855)aacfs	p.N285fs	SYNCRIP_ENST00000355238.6_Frame_Shift_Ins_p.N285fs	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	285	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		AAAAGCCTCTGTTTTTTTTCTT	0.411																																					p.N285fs		.											.	SYNCRIP-92	0			c.855_856insA						.																																			SO:0001589	frameshift_variant	10492	exon8			.	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"RNA binding motif (RRM) containing"	16918	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein Q"					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.855dupA	6.37:g.86332361_86332361dupT	ENSP00000358635:p.Asn285fs	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	191	33	NM_006372	0	0	0	0	0	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Frame_Shift_Ins	INS	ENST00000369622.3	37	CCDS5005.1																																																																																			.		0.411	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		T	86332354	-	T	86332353	7	5	74	1	0	1	1	0	0	0	0	0	15476	1368	48	0	1078	0	SYNCRIP	6	86332353	Frame_Shift_Ins	INS	-	TCGA-BQ-5890-01A-11D-1589-08	34449939	86332353	84782714	42	6965											
ENPP1	5167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	132206107	132206107	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatgacaccctactgcgaaAgtatgctgaagaaagaaatg	16	8	9	8	1	1	4	1	2	0	2	1	5	1	4	1	0	3	2	1	0	6	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:132206107A>C	ENST00000360971.2	+	23	2368	c.2348A>C	c.(2347-2349)aAg>aCg	p.K783T		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	783	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	CTACTGCGAAAGTATGCTGAA	0.408																																					p.K783T	Colon(104;336 1535 5856 11019 33782)	.											.	ENPP1-95	0			c.A2348C						.						228	208	215					6																	132206107		2203	4300	6503	SO:0001583	missense	5167	exon23			TGCGAAAGTATGC	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2348A>C	6.37:g.132206107A>C	ENSP00000354238:p.Lys783Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	96	34	NM_006208	0	0	16	30	14	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	37	CCDS5150.2	.	.	.	.	.	.	.	.	.	.	A	12.63	1.996697	0.35226	.	.	ENSG00000197594	ENST00000360971	T	0.69561	-0.41	5.91	-0.54	0.11861	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.445357	0.26013	N	0.026870	T	0.46405	0.1391	L	0.61036	1.89	0.22940	N	0.998539	B	0.24920	0.114	B	0.37833	0.259	T	0.54180	-0.8332	10	0.45353	T	0.12	-2.7243	8.0938	0.30816	0.6341:0.1292:0.2367:0.0	.	783	P22413	ENPP1_HUMAN	T	783	ENSP00000354238:K783T	ENSP00000354238:K783T	K	+	2	0	ENPP1	132247800	1.000000	0.71417	0.005000	0.12908	0.829000	0.46940	1.859000	0.39418	-0.182000	0.10602	-0.242000	0.12053	AAG	.		0.408	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			C	132206107	A	C	132206107	3	2	74	1	0	0	0	0	1	0	0	0	5142	72	3	5	2438	5	ENPP1	6	132206107	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	45873754	132206107	38908960	43	6966											
TNFAIP3	7128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	138200458	138200458	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaacaagggcttttgcacaCtgtgtttcatcgagtacaga	13	11	9	8	1	1	1	1	0	0	1	2	2	1	1	0	1	3	4	0	1	4	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:138200458C>A	ENST00000237289.4	+	7	1942	c.1876C>A	c.(1876-1878)Ctg>Atg	p.L626M		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	626	Interaction with TNIP1. {ECO:0000250}.|Required for proteosomal degradation of UBE2N and UBE2D3, TRAF6 deubiquitination, and TAX1BP1 interaction with UBE2N. {ECO:0000250}.|Sufficient for inhibitory activity of TNF-induced NF-kappa-B activity. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.L626fs*45(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CTTTTGCACACTGTGTTTCAT	0.512			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.L626M	GBM(130;153 1739 22295 28918 47987)	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3-1498	26	Whole gene deletion(25)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(26)	c.C1876A						.						71	77	75					6																	138200458		2203	4300	6503	SO:0001583	missense	7128	exon7			TGCACACTGTGTT	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1876C>A	6.37:g.138200458C>A	ENSP00000237289:p.Leu626Met	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	52	32	NM_001270507	0	0	2	2	0	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552844	0.65425	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.43688	0.94	5.82	4.96	0.65561	Zinc finger, A20-type (3);	0.066315	0.64402	D	0.000008	T	0.49406	0.1555	M	0.67953	2.075	0.45837	D	0.9987	D	0.76494	0.999	D	0.75484	0.986	T	0.51934	-0.8642	10	0.41790	T	0.15	-20.5642	11.1227	0.48300	0.0:0.8531:0.0:0.1469	.	626	P21580	TNAP3_HUMAN	M	626	ENSP00000237289:L626M	ENSP00000237289:L626M	L	+	1	2	TNFAIP3	138242151	0.881000	0.30235	0.909000	0.35828	0.972000	0.66771	1.756000	0.38390	1.472000	0.48140	0.655000	0.94253	CTG	.		0.512	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			A	138200458	C	A	138200458	3	1	74	1	0	0	0	0	1	0	0	0	16306	564	20	4	1898	4	TNFAIP3	6	138200458	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	5994351	138200458	32914609	44	6967											
HOXA2	3199	broad.mit.edu;bcgsc.ca	37	chr7	27140389	27140390	+	Frame_Shift_Ins	INS	-	-	A																															attgtggtgagtgtgtctgtINSaaaaaagtctaagctgtcag																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr7:27140389_27140390insA	ENST00000222718.5	-	2	1396_1397	c.1086_1087insT	c.(1084-1089)tttacafs	p.T363fs	HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000428939.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	363					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						AGTGTGTCTGTAAAAAAGTCTA	0.436																																					p.T363fs													.	HOXA2-92	0			c.1087_1088insT						.																																			SO:0001589	frameshift_variant	3199	exon2			TGTCTGTAAAAAA		CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.1087dupT	7.37:g.27140395_27140395dupA	ENSP00000222718:p.Thr363fs	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	165	23	NM_006735	0	0	0	0	0	A1L4K3|B2RMW3	Frame_Shift_Ins	INS	ENST00000222718.5	37	CCDS5403.1																																																																																			.		0.436	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			A	27140390	-	A	27140389	7	5	74	1	0	1	1	0	0	0	0	0	7313	1638	57	0	47	0	HOXA2	7	27140389	Frame_Shift_Ins	INS	-	TCGA-BQ-5890-01A-11D-1589-08		27140389	131998274	45	6968											
LRWD1	222229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	102110042	102110043	+	Missense_Mutation	DNP	TC	TC	GA																															ggcctcctatgacaagcggaTcatcctctgggacatcgggg																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr7:102110042_102110043TC>GA	ENST00000292616.5	+	10	1402_1403	c.1250_1251TC>GA	c.(1249-1251)aTC>aGA	p.I417R	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	417					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						GACAAGCGGATCATCCTCTGGG	0.644																																					p.I417R		.											.	LRWD1	0			c.C1251A						.																																			SO:0001583	missense	222229	exon10			GCGGATCATCCTC	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"WD repeat domain containing"	21769	protein-coding gene	gene with protein product	"origin recognition complex associated", "centromere protein 33"	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	Exception_encountered	7.37:g.102110042_102110043delinsGA	ENSP00000292616:p.Ile417Arg	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	127	27		0	0	0	0	0	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	DNP	ENST00000292616.5	37	CCDS34715.1																																																																																			.		0.644	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		GA	102110043	TC	GA	102110042	3	3	74	1	0	0	0	0	1	0	0	0	9072	1435	50	5	1288	5	LRWD1	7	102110042	Missense_Mutation	DNP	TC	TCGA-BQ-5890-01A-11D-1589-08	74969653	102110042	57028621	46	6969											
CSMD1	64478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	3216707	3216707	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaggtgcactccacacacGgcggcccccacccaggcagg	9	2	12	18	2	0	1	0	0	0	1	1	1	1	1	4	5	1	2	4	5	0	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr8:3216707G>A	ENST00000520002.1	-	22	3829	c.3274C>T	c.(3274-3276)Cgt>Tgt	p.R1092C	CSMD1_ENST00000400186.3_Missense_Mutation_p.R1092C|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1091C|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1092C|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1091C|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1092C|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1091C			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1092	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTCCACACACGGCGGCCCCCA	0.557																																					p.R1091C		.											.	CSMD1-86	0			c.C3271T						.						70	74	73					8																	3216707		2203	4300	6503	SO:0001583	missense	64478	exon21			ACACACGGCGGCC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3274C>T	8.37:g.3216707G>A	ENSP00000430733:p.Arg1092Cys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	120	33	NM_033225	0	0	0	0	0	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.9|20.9	4.074273|4.074273	0.76415|0.76415	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.|T;T;T;T;T	.|0.64991	.|-0.13;-0.13;-0.13;-0.13;-0.13	5.34|5.34	5.34|5.34	0.76211|0.76211	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.83096|0.83096	0.5180|0.5180	M|M	0.92268|0.92268	3.29|3.29	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.998;0.999;0.998	D|D	0.86677|0.86677	0.1914|0.1914	5|10	.|0.66056	.|D	.|0.02	.|.	13.9698|13.9698	0.64233|0.64233	0.0:0.0:0.8484:0.1516|0.0:0.0:0.8484:0.1516	.|.	.|1092;1092;1092	.|E5RIG2;Q96PZ7;Q96PZ7-4	.|.;CSMD1_HUMAN;.	L|C	571|1092;1092;954;1091;1091;1091	.|ENSP00000383047:R1092C;ENSP00000430733:R1092C;ENSP00000441462:R1091C;ENSP00000446243:R1091C;ENSP00000441675:R1091C	.|ENSP00000320445:R954C	P|R	-|-	2|1	0|0	CSMD1|CSMD1	3204114|3204114	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.283000|4.283000	0.58977|0.58977	2.489000|2.489000	0.83994|0.83994	0.550000|0.550000	0.68814|0.68814	CCG|CGT	.		0.557	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3216707	G	A	3216707	3	1	74	1	0	0	0	0	1	0	0	0	3950	1116	39	1	7623	1	CSMD1	8	3216707	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		3216707	143147315	47	6970											
ADAM7	8756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	24357759	24357760	+	Missense_Mutation	DNP	AC	AC	CA																															gtagcctgtgaagaaaccttAcatgttaccagtgagcatcc																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr8:24357759_24357760AC>CA	ENST00000175238.6	+	18	2075_2076	c.1992_1993AC>CA	c.(1990-1995)ttACat>ttCAat	p.664_665LH>FN	ADAM7_ENST00000520720.1_Missense_Mutation_p.436_437LH>FN|RP11-624C23.1_ENST00000519689.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.664_665LH>FN	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	664	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AAGAAACCTTACATGTTACCAG	0.411																																					p.LH664FN		.											.	ADAM7	0			c.C1993A						.																																			SO:0001583	missense	8756	exon18			ACCTTACATGTTA	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"ADAM metallopeptidase domain containing"	214	protein-coding gene	gene with protein product		607310	"a disintegrin and metalloproteinase domain 7"				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	Exception_encountered	8.37:g.24357759_24357760delinsCA	ENSP00000175238:p.L664_H665delinsFN	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	68	26		0	0	0	0	0	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	DNP	ENST00000175238.6	37	CCDS6045.1																																																																																			.		0.411	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		CA	24357760	AC	CA	24357759	3	2	74	1	0	0	0	0	1	0	0	0	251	388	14	5	2062	5	ADAM7	8	24357759	Missense_Mutation	DNP	AC	TCGA-BQ-5890-01A-11D-1589-08	21141052	24357759	122006263	48	6971											
COL14A1	7373	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	121219275	121219276	+	Frame_Shift_Ins	INS	-	-	A																															aactggactcatgccccaggINSaaatgtggaaaaatacagag																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr8:121219275_121219276insA	ENST00000297848.3	+	10	1403_1404	c.1133_1134insA	c.(1132-1137)ggaaatfs	p.N379fs	COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_Frame_Shift_Ins_p.N379fs|COL14A1_ENST00000247781.3_Frame_Shift_Ins_p.N284fs|COL14A1_ENST00000309791.4_Frame_Shift_Ins_p.N379fs	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CATGCCCCAGGAAATGTGGAAA	0.436																																					p.G378fs		.											.	COL14A1-543	0			c.1133_1134insA						.																																			SO:0001589	frameshift_variant	7373	exon10			.		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1136dupA	8.37:g.121219278_121219278dupA	ENSP00000297848:p.Asn379fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_021110	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000297848.3	37	CCDS34938.1																																																																																			.		0.436	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121219276	-	A	121219275	7	5	74	1	0	1	1	0	0	0	0	0	3677	1174	41	0	1167	0	COL14A1	8	121219275	Frame_Shift_Ins	INS	-	TCGA-BQ-5890-01A-11D-1589-08	96861516	121219275	25144747	49	6972											
IFNA16	3449	broad.mit.edu	37	chr9	21216839	21216839	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acaagggctgtatttcttccCcatcagataaagagtgattc	12	12	8	9	0	2	3	1	1	1	2	4	3	3	3	2	1	0	2	2	1	4	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:21216839C>T	ENST00000380216.1	-	1	471	c.466G>A	c.(466-468)Ggg>Agg	p.G156R		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	156					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TATTTCTTCCCCATCAGATAA	0.443																																					p.G156R													.	IFNA16-91	0			c.G466A						.						253	244	247					9																	21216839		2203	4300	6503	SO:0001583	missense	3449	exon1			TCTTCCCCATCAG		CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"Interferons"	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.466G>A	9.37:g.21216839C>T	ENSP00000369564:p.Gly156Arg	Somatic	545	0		WXS	Illumina HiSeq	Phase_I	582	7	NM_002173	0	0	0	0	0	Q5VV12	Missense_Mutation	SNP	ENST00000380216.1	37	CCDS34996.1	.	.	.	.	.	.	.	.	.	.	-	8.342	0.828869	0.16749	.	.	ENSG00000147885	ENST00000380216	T	0.05513	3.43	2.62	1.67	0.24075	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.361767	0.28834	N	0.014000	T	0.05456	0.0144	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32295	-0.9912	10	0.87932	D	0	.	8.8612	0.35258	0.0:0.7688:0.2312:0.0	.	156	P05015	IFN16_HUMAN	R	156	ENSP00000369564:G156R	ENSP00000369564:G156R	G	-	1	0	IFNA16	21206839	0.000000	0.05858	0.011000	0.14972	0.023000	0.10783	0.304000	0.19228	0.403000	0.25479	0.184000	0.17185	GGG	.		0.443	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173		T	21216839	C	T	21216839	3	4	74	1	0	0	0	0	1	0	0	0	7556	623	22	2	107	2	IFNA16	9	21216839	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		21216839	119996592	50	6973											
CBWD6	644019	hgsc.bcm.edu	37	chr9	69206734	69206734	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaacagtaaactgtacCttcagccttatgacctccat	11	12	5	13	0	2	1	1	1	1	0	3	1	3	1	4	0	5	3	4	0	5	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:69206734C>T	ENST00000377457.5	-	13	1056	c.951G>A	c.(949-951)aaG>aaA	p.K317K	CBWD6_ENST00000468061.1_5'UTR|CBWD6_ENST00000377449.1_Splice_Site_p.K281K|CBWD6_ENST00000382399.4_Splice_Site_p.K297K	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	317	CobW C-terminal.						ATP binding (GO:0005524)			lung(4)	4						TAAACTGTACCTTCAGCCTTA	0.353																																					p.K317K		.											.	.	0			c.G951A						.						1	1	1					9																	69206734		203	351	554	SO:0001630	splice_region_variant	644019	exon13			CTGTACCTTCAGC		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.951+1G>A	9.37:g.69206734C>T		Somatic	582	2		WXS	Illumina HiSeq	Phase_I	626	99	NM_001085457	0	0	5	5	0		Silent	SNP	ENST00000377457.5	37	CCDS43827.1	.	.	.	.	.	.	.	.	.	.	.	8.138	0.784534	0.16189	.	.	ENSG00000204790	ENST00000416428	.	.	.	2.65	2.65	0.31530	.	.	.	.	.	T	0.60130	0.2245	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	4	.	.	.	-5.4011	10.7283	0.46081	0.0:1.0:0.0:0.0	.	.	.	.	S	76	.	.	G	-	1	0	CBWD6	68496554	1.000000	0.71417	0.675000	0.29917	0.675000	0.39556	6.081000	0.71309	1.313000	0.45069	0.184000	0.17185	GGT	.		0.353	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	Silent	T	69206734	C	T	69206734	5	4	74	1	0	0	0	0	0	0	1	0	2722	695	24	2	248	2	CBWD6	9	69206734	Splice_Site	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	47989895	69206734	72006697	51	6974											
FLJ46321	389763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	84608073	84608073	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggaaatttccttccttagTtccaacaaacaaaagatgtt	15	12	5	9	0	0	1	0	0	0	1	3	2	3	2	3	1	2	2	3	1	6	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:84608073T>G	ENST00000344803.2	+	4	2735	c.2688T>G	c.(2686-2688)agT>agG	p.S896R		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	896					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTTCCTTAGTTCCAACAAAC	0.428																																					p.S896R		.											.	.	0			c.T2688G						.						74	65	68					9																	84608073		1843	4100	5943	SO:0001583	missense	389763	exon4			CCTTAGTTCCAAC		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2688T>G	9.37:g.84608073T>G	ENSP00000341988:p.Ser896Arg	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	66	26	NM_001001670	0	0	0	0	0		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	6.930	0.541227	0.13250	.	.	ENSG00000214929	ENST00000344803	T	0.44482	0.92	3.45	-0.949	0.10376	.	2.375910	0.01543	N	0.019319	T	0.28499	0.0705	L	0.34521	1.04	0.09310	N	1	B	0.29085	0.232	B	0.30251	0.113	T	0.03910	-1.0993	10	0.21540	T	0.41	1.1122	0.6148	0.00767	0.1883:0.1384:0.2367:0.4366	.	896	Q6ZQQ2	F75D1_HUMAN	R	896	ENSP00000341988:S896R	ENSP00000341988:S896R	S	+	3	2	FAM75D1	83797893	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.406000	0.07187	-0.259000	0.09432	-0.417000	0.06048	AGT	.		0.428	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		G	84608073	T	G	84608073	3	3	74	1	0	0	0	0	1	0	0	0	5951	1722	60	5	2702	5	FLJ46321	9	84608073	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	15401339	84608073	56605358	52	6975											
TXN	7295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	113013695	113013695	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacgtggctgagaagtcaacTactacaagtttatcacctgc	12	10	8	11	1	2	1	2	1	0	1	2	2	2	1	1	1	4	2	1	1	6	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:113013695T>C	ENST00000374517.5	-	2	276	c.72A>G	c.(70-72)gtA>gtG	p.V24V	TXN_ENST00000374515.5_Silent_p.V24V	NM_003329.3	NP_003320.2	P10599	THIO_HUMAN	thioredoxin	24	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|glycerol ether metabolic process (GO:0006662)|innate immune response (GO:0045087)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oxidation-reduction process (GO:0055114)|positive regulation of DNA binding (GO:0043388)|regulation of protein import into nucleus, translocation (GO:0033158)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	peptide disulfide oxidoreductase activity (GO:0015037)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			kidney(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(323;7.36e-07)		AGAAGTCAACTACTACAAGTT	0.363																																					p.V24V		.											.	TXN-90	0			c.A72G						.						60	60	60					9																	113013695		2203	4300	6503	SO:0001819	synonymous_variant	7295	exon2			GTCAACTACTACA	X77584	CCDS35103.1, CCDS59139.1	9q31	2008-02-05			ENSG00000136810	ENSG00000136810			12435	protein-coding gene	gene with protein product		187700					Standard	NM_003329		Approved	TRX	uc004bep.2	P10599	OTTHUMG00000020480	ENST00000374517.5:c.72A>G	9.37:g.113013695T>C		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_001244938	0	0	811	1767	956	B1ALW1|O60744|Q53X69|Q96KI3|Q9UDG5	Silent	SNP	ENST00000374517.5	37	CCDS35103.1																																																																																			.		0.363	TXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053614.1			C	113013695	T	C	113013695	2	2	74	1	0	0	0	0	0	0	0	1	16823	1509	53	3		3	TXN	9	113013695	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	28405622	113013695	28199736	53	6976											
FAM125B	89853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	129143362	129143362	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggttgcacagacagcagatgGtgtggatgctgacctctgga	9	9	15	8	0	1	3	0	1	1	2	1	5	1	5	1	4	3	4	1	4	0	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:129143362G>C	ENST00000361171.3	+	3	305	c.224G>C	c.(223-225)gGt>gCt	p.G75A	MVB12B_ENST00000545391.1_Missense_Mutation_p.G75A|MVB12B_ENST00000535766.1_Missense_Mutation_p.G68A|MVB12B_ENST00000436593.3_Missense_Mutation_p.G60A	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	75	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										ACAGCAGATGGTGTGGATGCT	0.478																																					p.G75A		.											.	.	0			c.G224C						.						131	113	119					9																	129143362		2203	4300	6503	SO:0001583	missense	89853	exon3			CAGATGGTGTGGA	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 28", "family with sequence similarity 125, member B"	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.224G>C	9.37:g.129143362G>C	ENSP00000354772:p.Gly75Ala	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	93	28	NM_001011703	0	0	0	1	1	Q8N6S7	Missense_Mutation	SNP	ENST00000361171.3	37	CCDS35142.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625105	0.66901	.	.	ENSG00000196814	ENST00000361171;ENST00000545391;ENST00000402437;ENST00000436593;ENST00000535766	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	5.15	5.15	0.70609	MABP domain (1);	0.101991	0.64402	D	0.000002	T	0.71937	0.3399	M	0.81497	2.545	0.58432	D	0.999999	D;P;P	0.89917	1.0;0.841;0.675	D;P;B	0.91635	0.999;0.46;0.337	T	0.76542	-0.2921	10	0.87932	D	0	-9.369	18.6946	0.91596	0.0:0.0:1.0:0.0	.	68;60;75	B7Z4X0;B7Z1P9;Q9H7P6	.;.;F125B_HUMAN	A	75;75;60;60;68	ENSP00000354772:G75A;ENSP00000441988:G75A;ENSP00000384751:G60A;ENSP00000401379:G60A;ENSP00000442846:G68A	ENSP00000354772:G75A	G	+	2	0	FAM125B	128183183	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.359000	0.97115	2.418000	0.82041	0.650000	0.86243	GGT	.		0.478	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525		C	129143362	G	C	129143362	3	2	74	1	0	0	0	0	1	0	0	0	5444	1261	44	4	234	4	FAM125B	9	129143362	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	16129667	129143362	12070069	54	6977											
ARID5B	84159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	63699986	63699986	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggtgattgtgaagcttgaAgacctggtcaagtgggtaca	12	10	14	5	0	1	4	1	3	0	1	1	4	1	4	1	3	2	2	1	3	5	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr10:63699986A>G	ENST00000279873.7	+	3	731	c.321A>G	c.(319-321)gaA>gaG	p.E107E		NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	107					adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					TGAAGCTTGAAGACCTGGTCA	0.453																																					p.E107E		.											.	ARID5B-94	0			c.A321G						.						156	145	148					10																	63699986		2203	4300	6503	SO:0001819	synonymous_variant	84159	exon3			GCTTGAAGACCTG	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"-"	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.321A>G	10.37:g.63699986A>G		Somatic	140	1		WXS	Illumina HiSeq	Phase_I	118	39	NM_032199	0	0	0	0	0	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	37	CCDS31208.1																																																																																			.		0.453	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63699986	A	G	63699986	2	3	74	1	0	0	0	0	0	0	0	1	922	69	3	3		3	ARID5B	10	63699986	Silent	SNP	A	TCGA-BQ-5890-01A-11D-1589-08		63699986	71834761	55	6978											
DMBT1	1755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	124351862	124351862	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgagtagaggtcctatacCgaggctcctggggcaccgtg	7	7	15	12	3	0	1	0	0	0	1	2	3	2	1	5	4	1	3	5	4	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr10:124351862C>A	ENST00000338354.3	+	20	2357	c.2251C>A	c.(2251-2253)Cga>Aga	p.R751R	DMBT1_ENST00000368955.3_Silent_p.R741R|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Silent_p.R741R|DMBT1_ENST00000368909.3_Silent_p.R751R|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	751	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)	p.R751R(3)		breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGTCCTATACCGAGGCTCCTG	0.582																																					p.R751R	Ovarian(182;93 2026 18125 22222 38972)	.											.	DMBT1-494	3	Substitution - coding silent(3)	lung(3)	c.C2251A						.						322	237	265					10																	124351862		2025	4157	6182	SO:0001819	synonymous_variant	1755	exon20			CTATACCGAGGCT		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2251C>A	10.37:g.124351862C>A		Somatic	397	1		WXS	Illumina HiSeq	Phase_I	437	141	NM_007329	0	0	0	0	0	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				.		0.582	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124351862	C	A	124351862	2	1	74	1	0	0	0	0	0	0	0	1	4588	644	23	4		4	DMBT1	10	124351862	Silent	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	60651876	124351862	11182885	56	6979											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092622	1092622	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaccactcccagccctccaAccaccactcccagccctcca	9	4	2	26	0	0	0	0	0	0	0	4	0	4	0	10	0	3	0	10	0	1	0	rs568697007	byFrequency	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:1092622A>G	ENST00000441003.2	+	30	4468	c.4441A>G	c.(4441-4443)Acc>Gcc	p.T1481A	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1482A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4216	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1481P(1)|p.T1482P(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cagccctccaaccaccactcc	0.637													a|||	4	0.000798722	0	0	5008	,	,		18372	0		0.002	False		,,,				2504	0.002				p.T1481A		.											.	MUC2-90	2	Substitution - Missense(2)	skin(2)	c.A4441G						.						217	326	288					11																	1092622		1539	2902	4441	SO:0001583	missense	4583	exon30			CCTCCAACCACCA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4441A>G	11.37:g.1092622A>G	ENSP00000415183:p.Thr1481Ala	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	a	1.472	-0.559630	0.03967	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15256	2.5;2.44	1.44	-2.88	0.05682	.	2.511670	0.03361	U	0.197566	T	0.07188	0.0182	.	.	.	0.09310	N	1	B	0.17667	0.023	B	0.06405	0.002	T	0.26710	-1.0095	9	0.09590	T	0.72	.	4.9543	0.14031	0.3953:0.4467:0.158:0.0	.	1481	E7EUV1	.	A	1481;1482	ENSP00000415183:T1481A;ENSP00000351956:T1482A	ENSP00000351956:T1482A	T	+	1	0	MUC2	1082622	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-0.257000	0.08745	-0.714000	0.04975	0.000000	0.15137	ACC	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1092622	A	G	1092622	3	3	74	1	0	0	0	0	1	0	0	0	10000	43	2	3	4559	3	MUC2	11	1092622	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08		1092622	133913894	57	6980			1	23		4	4	910	N	T_C_A	4.720058e-09
MUC2	4583	hgsc.bcm.edu	37	chr11	1092795	1092795	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctccaccaaccaccacTcccatcaccaccaccaccac	12	3	0	26	0	1	0	1	0	0	0	3	0	3	0	11	0	1	0	11	0	1	0	rs12786761		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:1092795T>A	ENST00000441003.2	+	30	4641	c.4614T>A	c.(4612-4614)acT>acA	p.T1538T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1539T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caaccaccactcccatcacca	0.627																																					p.T1538T		.											.	MUC2-90	0			c.T4614A						.						126	251	206					11																	1092795		1606	2836	4442	SO:0001819	synonymous_variant	4583	exon30			CACCACTCCCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4614T>A	11.37:g.1092795T>A		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	11	8	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092795	T	A	1092795	2	1	74	1	0	0	0	0	0	0	0	1	10000	1538	54	5		5	MUC2	11	1092795	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	173	1092795	133913721	58	6981			1	23		4	4	910	N	T_C_A	4.720058e-09
MUC2	4583	hgsc.bcm.edu	37	chr11	1093254	1093254	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accccaaccccaacacccacCggcacacagaccccaacatc	14	1	3	23	1	0	1	0	0	0	1	1	1	0	1	8	1	3	1	8	1	3	0	rs111164664		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:1093254C>T	ENST00000441003.2	+	30	5100	c.5073C>T	c.(5071-5073)acC>acT	p.T1691T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1658T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caacacccaccggcacacaga	0.632																																					p.T1691T		.											.	MUC2-90	0			c.C5073T						.						100	145	129					11																	1093254		1824	3303	5127	SO:0001819	synonymous_variant	4583	exon30			ACCCACCGGCACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5073C>T	11.37:g.1093254C>T		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093254	C	T	1093254	2	4	74	1	0	0	0	0	0	0	0	1	10000	639	23	1		1	MUC2	11	1093254	Silent	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	459	1093254	133913262	59	6982			1	23		4	4	910	N	T_C_A	4.720058e-09
MUC2	4583	hgsc.bcm.edu	37	chr11	1093531	1093531	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaaccccaacacccaccAgcacaaagagtacaaccgtg	15	2	5	19	1	0	1	0	0	0	1	0	1	0	1	7	0	5	2	7	0	5	1	rs56104295		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:1093531A>G	ENST00000441003.2	+	30	5377	c.5350A>G	c.(5350-5352)Agc>Ggc	p.S1784G	MUC2_ENST00000333592.6_Missense_Mutation_p.S72G|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.S1740G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccagcacaaagag	0.602																																					p.S1784G		.											.	MUC2-90	0			c.A5350G						.						104	125	118					11																	1093531		2178	4256	6434	SO:0001583	missense	4583	exon30			CCCACCAGCACAA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5350A>G	11.37:g.1093531A>G	ENSP00000415183:p.Ser1784Gly	Somatic	14	1		WXS	Illumina HiSeq	Phase_I	31	7	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	8.370	0.835151	0.16820	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.08458	3.09;3.33;3.73	1.65	-3.28	0.05033	.	0.455035	0.14693	U	0.304033	T	0.03827	0.0108	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39461	-0.9613	9	0.20519	T	0.43	.	4.3192	0.11009	0.6479:0.1915:0.1606:0.0	rs56104295	1784	E7EUV1	.	G	1784;1740;72	ENSP00000415183:S1784G;ENSP00000351956:S1740G;ENSP00000331373:S72G	ENSP00000331373:S72G	S	+	1	0	MUC2	1083531	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.963000	0.00671	-1.605000	0.01593	-2.632000	0.00153	AGC	.		0.602	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093531	A	G	1093531	3	3	74	1	0	0	0	0	1	0	0	0	10000	188	7	3	5468	3	MUC2	11	1093531	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	277	1093531	133912985	60	6983			1	23		4	4	910	N	T_C_A	4.720058e-09
CD81	975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	2417109	2417109	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctgcagcttgactgctGtggctccagcacactgactg	6	11	10	14	0	1	2	0	2	1	0	3	2	2	2	1	1	4	5	1	1	0	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:2417109G>T	ENST00000263645.5	+	6	726	c.470G>T	c.(469-471)tGt>tTt	p.C157F	CD81_ENST00000481687.1_Missense_Mutation_p.C163F|CD81_ENST00000381036.3_Missense_Mutation_p.C195F|CD81_ENST00000492627.1_Missense_Mutation_p.C86F|CD81_ENST00000524805.1_3'UTR|CD81_ENST00000526072.1_Missense_Mutation_p.C86F	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	157					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		CTTGACTGCTGTGGCTCCAGC	0.602																																					p.C157F		.											.	CD81-650	0			c.G470T						.						94	73	80					11																	2417109		2202	4299	6501	SO:0001583	missense	975	exon6			ACTGCTGTGGCTC		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"CD molecules", "Tetraspanins"	1701	protein-coding gene	gene with protein product		186845	"CD81 antigen (target of antiproliferative antibody 1)"	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.470G>T	11.37:g.2417109G>T	ENSP00000263645:p.Cys157Phe	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	75	32	NM_004356	0	0	0	0	0	P18582|Q5U0J6	Missense_Mutation	SNP	ENST00000263645.5	37	CCDS7734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.61|11.61	1.691270|1.691270	0.30052|0.30052	.|.	.|.	ENSG00000110651|ENSG00000110651	ENST00000475945;ENST00000263645;ENST00000492627;ENST00000527343;ENST00000381036;ENST00000492252;ENST00000526072;ENST00000481687|ENST00000464784	D;D;D;D;D;D;D;D|.	0.99881|.	-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47|.	3.56|3.56	3.56|3.56	0.40772|0.40772	Tetraspanin, EC2 domain (1);CD81 extracellular domain (1);|.	0.106944|.	0.64402|.	D|.	0.000003|.	D|D	0.85999|0.85999	0.5828|0.5828	H|H	0.96662|0.96662	3.86|3.86	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.89124|0.89124	0.3505|0.3505	10|5	0.87932|.	D|.	0|.	.|.	10.8427|10.8427	0.46726|0.46726	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	195;157|.	A6NMH8;P60033|.	.;CD81_HUMAN|.	F|L	86;157;86;146;195;150;86;163|142	ENSP00000433178:C86F;ENSP00000263645:C157F;ENSP00000437242:C86F;ENSP00000433767:C146F;ENSP00000370424:C195F;ENSP00000432249:C150F;ENSP00000431780:C86F;ENSP00000432033:C163F|.	ENSP00000263645:C157F|.	C|V	+|+	2|1	0|0	CD81|CD81	2373685|2373685	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.035000|0.035000	0.12851|0.12851	3.056000|3.056000	0.49923|0.49923	2.011000|2.011000	0.59026|0.59026	0.491000|0.491000	0.48974|0.48974	TGT|GTG	.		0.602	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356		T	2417109	G	T	2417109	3	4	74	1	0	0	0	0	1	0	0	0	3045	1377	48	4	492	4	CD81	11	2417109	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	1323578	2417109	132589407	61	6984											
NELL1	4745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	21581738	21581738	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcttcctatattgcagacaTtgatgaatgtgccttaagaa	12	14	8	7	0	0	4	0	2	0	2	1	4	1	4	2	0	3	2	2	0	5	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:21581738T>G	ENST00000357134.5	+	17	1942	c.1790T>G	c.(1789-1791)aTt>aGt	p.I597S	NELL1_ENST00000532434.1_Missense_Mutation_p.I550S|NELL1_ENST00000298925.5_Missense_Mutation_p.I625S|NELL1_ENST00000325319.5_Missense_Mutation_p.I540S|NELL1_ENST00000529218.1_Intron	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	597	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						ATTGCAGACATTGATGAATGT	0.478																																					p.I597S		.											.	NELL1-155	0			c.T1790G						.						132	122	125					11																	21581738		2203	4300	6503	SO:0001583	missense	4745	exon17			CAGACATTGATGA	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"nel (chicken)-like 1"			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1790T>G	11.37:g.21581738T>G	ENSP00000349654:p.Ile597Ser	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	144	60	NM_006157	0	0	0	0	0	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.603633	0.66445	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	5.9	5.9	0.94986	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.067178	0.64402	D	0.000016	D	0.96898	0.8987	M	0.88570	2.965	0.51767	D	0.999934	D;D;D;D	0.64830	0.993;0.994;0.986;0.994	P;D;P;D	0.63192	0.857;0.912;0.885;0.912	D	0.97543	1.0087	10	0.87932	D	0	-6.8617	16.3275	0.82990	0.0:0.0:0.0:1.0	.	540;625;550;597	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	S	625;597;540;550	ENSP00000298925:I625S;ENSP00000349654:I597S;ENSP00000317837:I540S;ENSP00000437170:I550S	ENSP00000298925:I625S	I	+	2	0	NELL1	21538314	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	8.040000	0.89188	2.266000	0.75297	0.528000	0.53228	ATT	.		0.478	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		G	21581738	T	G	21581738	3	3	74	1	0	0	0	0	1	0	0	0	10359	1493	52	5	1856	5	NELL1	11	21581738	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	19164629	21581738	113424778	62	6985											
SLC5A12	159963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	26742996	26742996	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgttaagaggatgacaaatAggtaagcaatgaagaagact	19	8	11	3	0	0	5	0	2	0	3	0	6	0	6	0	2	1	3	0	2	7	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:26742996A>T	ENST00000396005.3	-	1	575	c.266T>A	c.(265-267)cTa>cAa	p.L89Q	SLC5A12_ENST00000280467.6_Missense_Mutation_p.L89Q	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	89					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GATGACAAATAGGTAAGCAAT	0.468																																					p.L89Q		.											.	SLC5A12-92	0			c.T266A						.						94	95	95					11																	26742996		2203	4299	6502	SO:0001583	missense	159963	exon1			ACAAATAGGTAAG	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.266T>A	11.37:g.26742996A>T	ENSP00000379326:p.Leu89Gln	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	66	28	NM_178498	0	0	2	8	6	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	9.586	1.124947	0.20959	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.91686	-2.89;-2.89	5.83	1.3	0.21679	.	1.064190	0.07282	N	0.870876	D	0.91740	0.7388	L	0.58583	1.82	0.09310	N	1	B;P	0.37176	0.204;0.586	P;B	0.45856	0.495;0.436	T	0.81684	-0.0821	10	0.59425	D	0.04	.	6.9268	0.24419	0.1679:0.2534:0.5788:0.0	.	89;89	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	Q	89	ENSP00000379326:L89Q;ENSP00000280467:L89Q	ENSP00000280467:L89Q	L	-	2	0	SLC5A12	26699572	0.018000	0.18449	0.000000	0.03702	0.042000	0.13812	1.941000	0.40233	-0.023000	0.13963	-0.472000	0.04984	CTA	.		0.468	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		T	26742996	A	T	26742996	3	4	74	1	0	0	0	0	1	0	0	0	14696	420	15	5	1650	5	SLC5A12	11	26742996	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	5161258	26742996	108263520	63	6986											
FLRT1	28992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63884401	63884401	+	Intron	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcatgccttcaagggccTcaacagcctgcggcgcctgg	6	7	13	15	2	2	0	2	0	0	0	2	0	2	0	4	3	5	2	4	3	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:63884401T>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Missense_Mutation_p.L221H	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TTCAAGGGCCTCAACAGCCTG	0.657																																					p.L221H		.											.	FLRT1-90	0			c.T662A						.						37	33	34					11																	63884401		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AGGGCCTCAACAG	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34309A>T	11.37:g.63884401T>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_013280	0	0	0	0	0	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	37	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012781	0.75161	.	.	ENSG00000126500	ENST00000246841	T	0.71222	-0.55	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000007	D	0.88966	0.6581	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92298	0.5847	10	0.87932	D	0	-26.892	14.697	0.69129	0.0:0.0:0.0:1.0	.	193	Q9NZU1	FLRT1_HUMAN	H	221	ENSP00000246841:L221H	ENSP00000246841:L221H	L	+	2	0	FLRT1	63640977	0.997000	0.39634	0.940000	0.37924	0.996000	0.88848	5.163000	0.64948	2.114000	0.64651	0.454000	0.30748	CTC	.		0.657	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63884401	T	A	63884401	1	1	74	0	1	0	0	0	0	0	0	0	5957	1551	54	5		5	FLRT1	11	63884401	Intron	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	37141405	63884401	71122115	64	6987											
PITPNM1	9600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67265787	67265787	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccccatcgtggctgtaaggGctcaggctgtaggaggggga	7	8	17	9	1	1	0	1	0	0	0	3	2	2	2	2	6	0	5	2	6	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:67265787G>A	ENST00000534749.1	-	10	1679	c.1491C>T	c.(1489-1491)agC>agT	p.S497S	PITPNM1_ENST00000436757.2_Silent_p.S497S|PITPNM1_ENST00000356404.3_Silent_p.S497S			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	497					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						GGCTGTAAGGGCTCAGGCTGT	0.657																																					p.S497S	GBM(28;144 709 4607 5525)	.											.	PITPNM1-227	0			c.C1491T						.						56	55	55					11																	67265787		2196	4291	6487	SO:0001819	synonymous_variant	9600	exon11			GTAAGGGCTCAGG	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1"	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.1491C>T	11.37:g.67265787G>A		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	23	8	NM_001130848	0	0	0	1	1	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	37	CCDS31620.1																																																																																			.		0.657	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		A	67265787	G	A	67265787	2	1	74	1	0	0	0	0	0	0	0	1	11976	1194	42	2		2	PITPNM1	11	67265787	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	3381386	67265787	67740729	65	6988											
KDM5A	5927	broad.mit.edu	37	chr12	472130	472130	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcccaagacattgataccTgagtcttcacacgtcttgtt	11	12	7	11	1	3	3	1	2	2	1	3	3	3	3	2	0	2	1	2	0	3	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:472130T>C	ENST00000399788.2	-	5	1033	c.671A>G	c.(670-672)cAg>cGg	p.Q224R	KDM5A_ENST00000382815.4_Splice_Site_p.Q224R	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	224					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CATTGATACCTGAGTCTTCAC	0.453			T	NUP98	AML																																p.Q224R				Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A-227	0			c.A671G						.						130	123	125					12																	472130		1865	4113	5978	SO:0001630	splice_region_variant	5927	exon5			GATACCTGAGTCT		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.672+1A>G	12.37:g.472130T>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	117	3	NM_001042603	0	0	0	0	0	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.823461	0.50739	.	.	ENSG00000073614	ENST00000399787;ENST00000399788;ENST00000382815	D;D	0.84589	-1.87;-1.68	5.45	5.45	0.79879	.	0.067638	0.64402	D	0.000010	T	0.80747	0.4682	L	0.47716	1.5	0.45452	D	0.998429	B;B;P	0.35139	0.217;0.354;0.486	B;B;B	0.31946	0.138;0.065;0.138	T	0.81577	-0.0869	10	0.54805	T	0.06	-15.5519	14.3786	0.66897	0.0:0.0:0.0:1.0	.	224;224;224	F5H1F7;P29375;P29375-2	.;KDM5A_HUMAN;.	R	183;224;224	ENSP00000382688:Q224R;ENSP00000372265:Q224R	ENSP00000372265:Q224R	Q	-	2	0	KDM5A	342391	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	5.128000	0.64733	2.193000	0.70182	0.533000	0.62120	CAG	.		0.453	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	Missense_Mutation	C	472130	T	C	472130	5	2	74	1	0	0	0	0	0	0	1	0	8154	1594	55	3	4497	3	KDM5A	12	472130	Splice_Site	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		472130	133379765	66	6989											
WNK1	65125	broad.mit.edu;bcgsc.ca	37	chr12	977170	977170	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtagccatttcccagcggCgtaagagcacctccttcctg	9	9	9	14	2	0	1	0	0	0	1	3	1	3	1	5	1	3	3	5	1	3	4	rs200794710		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:977170C>T	ENST00000315939.6	+	9	2782				WNK1_ENST00000537687.1_Missense_Mutation_p.R760C|WNK1_ENST00000530271.2_Missense_Mutation_p.R845C|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000340908.4_Intron|WNK1_ENST00000574564.1_Missense_Mutation_p.R59C	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTCCCAGCGGCGTAAGAGCAC	0.512																																					p.R845C	Colon(19;451 567 6672 12618 28860)												.	WNK1-916	0			c.C2533T						.	C	CYS/ARG,CYS/ARG,,	0,3850		0,0,1925	104	105	105		2278,2533,,	5.7	1	12		105	1,8271		0,1,4135	yes	missense,missense,intron,intron	WNK1	NM_001184985.1,NM_213655.4,NM_014823.2,NM_018979.3	180,180,,	0,1,6060	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging,probably-damaging,,	760/2643,845/2635,,	977170	1,12121	1925	4136	6061	SO:0001627	intron_variant	65125	exon10			CAGCGGCGTAAGA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 167"	605232	"protein kinase, lysine deficient 1", "hereditary sensory neuropathy, type II"	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2140-3261C>T	12.37:g.977170C>T		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	134	7	NM_213655	0	0	0	0	0	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.984466	0.53934	0.0	1.21E-4	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.15603	2.41;2.41	5.67	5.67	0.87782	.	.	.	.	.	T	0.46795	0.1411	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.39522	-0.9610	8	0.56958	D	0.05	.	19.7725	0.96373	0.0:1.0:0.0:0.0	.	845	F5H2M7	.	C	760;845	ENSP00000444465:R760C;ENSP00000433548:R845C	ENSP00000433548:R845C	R	+	1	0	WNK1	847431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.673000	0.90976	0.467000	0.42956	CGT	.		0.512	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		T	977170	C	T	977170	1	4	74	0	1	0	0	0	0	0	0	0	17410	768	27	1		1	WNK1	12	977170	Intron	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	505040	977170	132874725	67	6990											
KCNC2	3747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	75441966	75441966	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccatcagaagcacacgtgtAatcacctgtcgtcagtagga	12	9	9	11	2	3	1	3	0	0	1	5	2	4	2	2	1	1	3	2	1	3	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:75441966A>C	ENST00000549446.1	-	4	2427	c.1747T>G	c.(1747-1749)Tac>Gac	p.Y583D	KCNC2_ENST00000548513.1_Missense_Mutation_p.Y583D|KCNC2_ENST00000550433.1_Missense_Mutation_p.Y583D|KCNC2_ENST00000298972.1_Missense_Mutation_p.Y583D|KCNC2_ENST00000350228.2_Intron|KCNC2_ENST00000548243.1_5'Flank|KCNC2_ENST00000540018.1_Intron|KCNC2_ENST00000341669.3_Missense_Mutation_p.Y583D|KCNC2_ENST00000393288.2_Missense_Mutation_p.Y583D	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	583					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GCACACGTGTAATCACCTGTC	0.463																																					p.Y583D		.											.	KCNC2-224	0			c.T1747G						.						322	257	279					12																	75441966		2203	4300	6503	SO:0001583	missense	3747	exon4			ACGTGTAATCACC	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.1747T>G	12.37:g.75441966A>C	ENSP00000449253:p.Tyr583Asp	Somatic	284	0		WXS	Illumina HiSeq	Phase_I	286	108	NM_139137	0	0	0	0	0	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	37	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.589934	0.86851	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000393288	D;D;D;D;D;D	0.97959	-4.52;-4.57;-4.63;-4.52;-4.57;-4.61	5.55	5.55	0.83447	.	1.098430	0.06893	N	0.804679	D	0.98052	0.9358	L	0.55990	1.75	0.58432	D	0.999996	D;P;D	0.57899	0.981;0.895;0.964	P;B;P	0.55871	0.786;0.389;0.745	D	0.93970	0.7248	10	0.72032	D	0.01	.	15.683	0.77388	1.0:0.0:0.0:0.0	.	583;583;583	Q96PR1-2;Q96PR1;Q96PR1-3	.;KCNC2_HUMAN;.	D	583	ENSP00000448301:Y583D;ENSP00000449941:Y583D;ENSP00000449253:Y583D;ENSP00000340121:Y583D;ENSP00000298972:Y583D;ENSP00000376966:Y583D	ENSP00000298972:Y583D	Y	-	1	0	KCNC2	73728233	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.855000	0.75445	2.104000	0.64026	0.477000	0.44152	TAC	.		0.463	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		C	75441966	A	C	75441966	3	2	74	1	0	0	0	0	1	0	0	0	8036	362	13	5	243	5	KCNC2	12	75441966	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	74464796	75441966	58409929	68	6991											
NUAK1	9891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	106460987	106460987	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgctgagtatttgctgctgtGtttcaagatgcccttcctcc	5	15	9	12	1	1	2	1	1	0	1	3	2	3	2	3	0	3	5	3	0	2	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:106460987G>T	ENST00000261402.2	-	7	2958	c.1579C>A	c.(1579-1581)Cac>Aac	p.H527N		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	527					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						TTGCTGCTGTGTTTCAAGATG	0.627																																					p.H527N		.											.	NUAK1-359	0			c.C1579A						.						68	75	72					12																	106460987		2203	4300	6503	SO:0001583	missense	9891	exon7			TGCTGTGTTTCAA	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"AMP-activated protein kinase family member 5"	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.1579C>A	12.37:g.106460987G>T	ENSP00000261402:p.His527Asn	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	121	53	NM_014840	0	0	1	1	0	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692745	0.68271	.	.	ENSG00000074590	ENST00000261402	T	0.73258	-0.73	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000008	T	0.77239	0.4101	M	0.61703	1.905	0.54753	D	0.999988	P	0.47910	0.902	P	0.50082	0.63	T	0.78411	-0.2214	10	0.51188	T	0.08	.	19.0535	0.93054	0.0:0.0:1.0:0.0	.	527	O60285	NUAK1_HUMAN	N	527	ENSP00000261402:H527N	ENSP00000261402:H527N	H	-	1	0	NUAK1	104985117	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	9.476000	0.97823	2.493000	0.84123	0.462000	0.41574	CAC	.		0.627	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		T	106460987	G	T	106460987	3	4	74	1	0	0	0	0	1	0	0	0	10738	1377	48	4	410	4	NUAK1	12	106460987	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	31019021	106460987	27390908	69	6992											
TBX3	6926	broad.mit.edu	37	chr12	115120983	115120983	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgtcccaggaatgaccGgatctctcatggagaggctc	8	10	12	11	1	2	2	1	1	1	1	5	5	3	4	2	4	1	2	2	4	1	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:115120983G>A	ENST00000257566.3	-	1	412	c.23C>T	c.(22-24)cCg>cTg	p.P8L	TBX3_ENST00000349155.2_Missense_Mutation_p.P8L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	8					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AGGAATGACCGGATCTCTCAT	0.607											OREG0022153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P8L													.	TBX3-93	0			c.C23T						.						40	42	41					12																	115120983		2128	4187	6315	SO:0001583	missense	6926	exon1			ATGACCGGATCTC	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.23C>T	12.37:g.115120983G>A	ENSP00000257566:p.Pro8Leu	Somatic	87	0	1463	WXS	Illumina HiSeq	Phase_I	103	3	NM_005996	0	0	0	0	0	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	G	31	5.075268	0.94000	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.88975	-2.43;-2.45	5.1	5.1	0.69264	.	0.054754	0.85682	D	0.000000	D	0.93703	0.7988	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.991;0.998	D	0.94336	0.7566	10	0.87932	D	0	.	18.5226	0.90959	0.0:0.0:1.0:0.0	.	8;8;8	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	L	8	ENSP00000257567:P8L;ENSP00000257566:P8L	ENSP00000257566:P8L	P	-	2	0	TBX3	113605366	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.192000	0.94947	2.384000	0.81235	0.655000	0.94253	CCG	.		0.607	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115120983	G	A	115120983	3	1	74	1	0	0	0	0	1	0	0	0	15691	1116	39	1	2240	1	TBX3	12	115120983	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	8659996	115120983	18730912	70	6993											
FZD10	11211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	130648407	130648407	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggagggactggagagcaCcggctgcacgctggtcttcc	7	6	15	13	2	1	1	0	0	1	1	2	4	2	3	3	5	2	4	3	5	0	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:130648407C>A	ENST00000229030.4	+	1	1404	c.920C>A	c.(919-921)aCc>aAc	p.T307N	FZD10_ENST00000539839.1_Missense_Mutation_p.H274Q|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	307					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		CTGGAGAGCACCGGCTGCACG	0.667																																					p.T307N		.											.	FZD10-658	0			c.C920A						.						68	65	66					12																	130648407		2203	4300	6503	SO:0001583	missense	11211	exon1			AGAGCACCGGCTG	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.920C>A	12.37:g.130648407C>A	ENSP00000229030:p.Thr307Asn	Somatic	95	1		WXS	Illumina HiSeq	Phase_I	89	27	NM_007197	0	0	0	0	0		Missense_Mutation	SNP	ENST00000229030.4	37	CCDS9267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.41|12.41	1.928557|1.928557	0.34002|0.34002	.|.	.|.	ENSG00000111432|ENSG00000111432	ENST00000539839|ENST00000229030	.|T	.|0.48836	.|0.8	5.1|5.1	5.1|5.1	0.69264|0.69264	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.69949|0.69949	0.3168|0.3168	M|M	0.76328|0.76328	2.33|2.33	0.58432|0.58432	D|D	0.999994|0.999994	.|D	.|0.89917	.|1.0	.|D	.|0.79108	.|0.992	T|T	0.74016|0.74016	-0.3800|-0.3800	6|10	0.87932|0.72032	D|D	0|0.01	.|.	18.5184|18.5184	0.90943|0.90943	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|307	.|Q9ULW2	.|FZD10_HUMAN	Q|N	274|307	.|ENSP00000229030:T307N	ENSP00000438460:H274Q|ENSP00000229030:T307N	H|T	+|+	3|2	2|0	FZD10|FZD10	129214360|129214360	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.954000|0.954000	0.61252|0.61252	5.756000|5.756000	0.68757|0.68757	2.374000|2.374000	0.81015|0.81015	0.561000|0.561000	0.74099|0.74099	CAC|ACC	.		0.667	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	130648407	C	A	130648407	3	1	74	1	0	0	0	0	1	0	0	0	6148	507	18	4	922	4	FZD10	12	130648407	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	15527424	130648407	3203488	71	6994											
RNF17	56163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	25352542	25352542	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaactcatcagctgtaatgTtggtatgaaacatattggtc	12	14	9	6	0	2	2	2	2	0	0	3	2	2	2	0	2	3	4	0	2	5	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr13:25352542T>C	ENST00000255324.5	+	4	479	c.427T>C	c.(427-429)Ttg>Ctg	p.L143L	RNF17_ENST00000381921.1_Silent_p.L143L|RNF17_ENST00000255325.6_Silent_p.L143L|RNF17_ENST00000255326.4_3'UTR	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	143					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		AGCTGTAATGTTGGTATGAAA	0.383																																					p.L143L		.											.	RNF17-228	0			c.T427C						.						158	141	147					13																	25352542		2203	4300	6503	SO:0001819	synonymous_variant	56163	exon4			GTAATGTTGGTAT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"RING-type (C3HC4) zinc fingers", "Tudor domain containing"	10060	protein-coding gene	gene with protein product	"spermatogenesis associated 23"	605793	"tudor domain containing 4"	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.427T>C	13.37:g.25352542T>C		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	197	60	NM_001184993	0	0	0	0	0	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	37	CCDS9308.2																																																																																			.		0.383	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		C	25352542	T	C	25352542	2	2	74	1	0	0	0	0	0	0	0	1	13493	1722	60	3		3	RNF17	13	25352542	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		25352542	89817336	72	6995											
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671451	25671451	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctttagctcagcgcaaagAagagcgccaggcttacctca	12	7	10	12	2	2	2	2	0	0	2	2	2	2	2	2	1	5	4	2	1	4	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr13:25671451A>G	ENST00000281589.3	+	1	1152	c.1115A>G	c.(1114-1116)gAa>gGa	p.E372G		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	372					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CAGCGCAAAGAAGAGCGCCAG	0.483																																					p.E372G		.											.	PABPC3-72	0			c.A1115G						.						148	135	139					13																	25671451		2203	4300	6503	SO:0001583	missense	5042	exon1			GCAAAGAAGAGCG	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1115A>G	13.37:g.25671451A>G	ENSP00000281589:p.Glu372Gly	Somatic	133	2		WXS	Illumina HiSeq	Phase_I	143	11	NM_030979	0	0	1	1	0	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.913192	0.52439	.	.	ENSG00000151846	ENST00000281589	T	0.06068	3.35	1.41	1.41	0.22369	.	0.127984	0.32134	N	0.006539	T	0.25195	0.0612	M	0.91818	3.245	0.50813	D	0.999894	D	0.89917	1.0	D	0.73708	0.981	T	0.01604	-1.1314	10	0.87932	D	0	.	6.5323	0.22334	1.0:0.0:0.0:0.0	.	372	Q9H361	PABP3_HUMAN	G	372	ENSP00000281589:E372G	ENSP00000281589:E372G	E	+	2	0	PABPC3	24569451	1.000000	0.71417	0.917000	0.36280	0.690000	0.40134	6.256000	0.72473	0.632000	0.30432	0.260000	0.18958	GAA	.		0.483	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		G	25671451	A	G	25671451	3	3	74	1	0	0	0	0	1	0	0	0	11391	246	9	3	1117	3	PABPC3	13	25671451	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	318909	25671451	89498427	73	6996											
SYNE2	23224	broad.mit.edu	37	chr14	64669634	64669634	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttccaagcctgttgtttatGatgtctgcgatgatcaagag	9	15	10	7	1	2	3	1	2	1	1	3	4	3	3	2	0	2	2	2	0	3	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr14:64669634G>C	ENST00000344113.4	+	100	18366	c.18154G>C	c.(18154-18156)Gat>Cat	p.D6052H	SYNE2_ENST00000554584.1_Missense_Mutation_p.D6014H|SYNE2_ENST00000358025.3_Missense_Mutation_p.D6052H|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.D2686H|SYNE2_ENST00000357395.3_Missense_Mutation_p.D2437H|SYNE2_ENST00000394768.2_Missense_Mutation_p.D2437H|SYNE2_ENST00000555022.1_5'Flank	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6052					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGTTGTTTATGATGTCTGCGA	0.488																																					p.D6052H													.	SYNE2-164	0			c.G18154C						.						134	117	123					14																	64669634		2203	4300	6503	SO:0001583	missense	23224	exon100			GTTTATGATGTCT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.18154G>C	14.37:g.64669634G>C	ENSP00000341781:p.Asp6052His	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_182914	0	0	21	21	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628212	0.46944	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000556906	T;T;T;T;T;T;T	0.50813	1.07;1.07;1.07;0.73;1.07;1.07;1.58	5.93	5.93	0.95920	.	0.110360	0.39146	N	0.001453	T	0.63628	0.2527	L	0.56769	1.78	0.80722	D	1	D;D;D;D;D	0.69078	0.993;0.978;0.99;0.994;0.997	D;D;P;D;D	0.69479	0.914;0.93;0.824;0.964;0.922	T	0.64799	-0.6322	10	0.87932	D	0	.	13.5281	0.61607	0.0709:0.0:0.9291:0.0	.	2437;440;6014;6052;6052	Q8WXH0-7;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;.;SYNE2_HUMAN;.	H	6052;2437;6052;6014;6020;2686;2437;22	ENSP00000350719:D6052H;ENSP00000349969:D2437H;ENSP00000341781:D6052H;ENSP00000452570:D6014H;ENSP00000450831:D2686H;ENSP00000378249:D2437H;ENSP00000452298:D22H	ENSP00000261678:D6020H	D	+	1	0	SYNE2	63739387	1.000000	0.71417	0.969000	0.41365	0.070000	0.16714	3.358000	0.52284	2.814000	0.96858	0.655000	0.94253	GAT	.		0.488	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64669634	G	C	64669634	3	2	74	1	0	0	0	0	1	0	0	0	15478	1290	45	4	18548	4	SYNE2	14	64669634	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		64669634	42679906	74	6997											
CSPG4	1464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75981607	75981607	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcggcgctccacggggaggCcagaggaggtgccaaggacc	8	3	17	13	3	0	1	0	0	0	1	2	4	1	4	4	7	1	1	4	7	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr15:75981607C>T	ENST00000308508.5	-	3	1891	c.1799G>A	c.(1798-1800)gGc>gAc	p.G600D		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	600	Globular or compact configuration stabilized by disulfide bonds.|Interaction with COL6A2. {ECO:0000250}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CACGGGGAGGCCAGAGGAGGT	0.672																																					p.G600D		.											.	CSPG4-229	0			c.G1799A						.						19	23	21					15																	75981607		2192	4287	6479	SO:0001583	missense	1464	exon3			GGGAGGCCAGAGG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1799G>A	15.37:g.75981607C>T	ENSP00000312506:p.Gly600Asp	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	49	23	NM_001897	0	0	1	1	0	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	2.636	-0.285218	0.05605	.	.	ENSG00000173546	ENST00000308508	T	0.19938	2.11	5.35	4.4	0.53042	.	0.186703	0.37955	N	0.001879	T	0.15522	0.0374	L	0.53249	1.67	0.09310	N	1	B	0.33583	0.418	B	0.24541	0.054	T	0.18272	-1.0342	10	0.24483	T	0.36	.	6.6414	0.22911	0.1799:0.7302:0.0:0.0899	.	600	Q6UVK1	CSPG4_HUMAN	D	600	ENSP00000312506:G600D	ENSP00000312506:G600D	G	-	2	0	CSPG4	73768662	.	.	0.001000	0.08648	0.417000	0.31264	.	.	1.194000	0.43101	0.555000	0.69702	GGC	.		0.672	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75981607	C	T	75981607	3	4	74	1	0	0	0	0	1	0	0	0	3966	739	26	2	5201	2	CSPG4	15	75981607	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		75981607	26549785	75	6998											
MCTP2	55784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	94884070	94884070	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatattttaaaactggaaGatccaaacagtttagaagat	19	11	6	5	0	0	3	0	0	0	3	1	4	1	4	1	1	3	1	1	1	8	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr15:94884070G>T	ENST00000357742.4	+	6	886	c.886G>T	c.(886-888)Gat>Tat	p.D296Y	MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Missense_Mutation_p.D296Y|MCTP2_ENST00000543482.1_Missense_Mutation_p.D296Y	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	296					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			AAAACTGGAAGATCCAAACAG	0.388																																					p.D296Y		.											.	MCTP2-93	0			c.G886T						.						84	82	83					15																	94884070		2197	4298	6495	SO:0001583	missense	55784	exon6			CTGGAAGATCCAA	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.886G>T	15.37:g.94884070G>T	ENSP00000350377:p.Asp296Tyr	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	56	25	NM_001159643	0	0	1	2	1	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.148823	0.78001	.	.	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.10573	2.86;2.86;2.86	5.77	4.86	0.63082	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.29652	0.0740	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.99;0.994;0.997;0.999	T	0.02053	-1.1222	10	0.87932	D	0	.	14.4552	0.67411	0.0712:0.0:0.9288:0.0	.	296;296;296;296;296	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	Y	296	ENSP00000438521:D296Y;ENSP00000395109:D296Y;ENSP00000350377:D296Y	ENSP00000350377:D296Y	D	+	1	0	MCTP2	92685074	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.178000	0.94855	1.442000	0.47568	-0.136000	0.14681	GAT	.		0.388	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94884070	G	T	94884070	3	4	74	1	0	0	0	0	1	0	0	0	9426	942	33	4	908	4	MCTP2	15	94884070	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	18902463	94884070	7647322	76	6999											
PRSS21	10942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2868724	2868724	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggatggtccagtttggcCagctgacttccatgccatcc	6	11	12	12	0	0	1	0	1	0	0	3	2	3	2	5	4	2	2	5	4	0	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:2868724C>G	ENST00000005995.3	+	4	346	c.304C>G	c.(304-306)Cag>Gag	p.Q102E	PRSS21_ENST00000455114.1_Missense_Mutation_p.Q100E|PRSS21_ENST00000450020.3_Missense_Mutation_p.Q102E			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	102	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						CCAGTTTGGCCAGCTGACTTC	0.562																																					p.Q102E		.											.	PRSS21-92	0			c.C304G						.						126	101	109					16																	2868724		2198	4300	6498	SO:0001583	missense	10942	exon4			TTTGGCCAGCTGA	AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"Serine peptidases / Serine peptidases"	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.304C>G	16.37:g.2868724C>G	ENSP00000005995:p.Gln102Glu	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	184	35	NM_144957	0	0	0	0	0	Q9NS34|Q9P2V6	Missense_Mutation	SNP	ENST00000005995.3	37	CCDS10478.1	.	.	.	.	.	.	.	.	.	.	c	0.406	-0.915839	0.02415	.	.	ENSG00000007038	ENST00000455114;ENST00000450020;ENST00000005995	D;D;D	0.87412	-2.25;-2.25;-2.25	4.9	0.325	0.15903	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.253065	0.20623	N	0.088727	T	0.57636	0.2067	N	0.00670	-1.27	0.09310	N	1	B;B;B	0.15930	0.015;0.012;0.012	B;B;B	0.12837	0.008;0.005;0.005	T	0.56220	-0.8015	10	0.02654	T	1	.	10.9331	0.47230	0.0:0.6074:0.267:0.1256	.	102;100;102	Q9Y6M0;Q9Y6M0-2;Q9Y6M0-3	TEST_HUMAN;.;.	E	100;102;102	ENSP00000400632:Q100E;ENSP00000407741:Q102E;ENSP00000005995:Q102E	ENSP00000005995:Q102E	Q	+	1	0	PRSS21	2808725	0.201000	0.23410	0.726000	0.30738	0.199000	0.23934	0.700000	0.25601	0.575000	0.29434	-0.299000	0.09455	CAG	.		0.562	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799		G	2868724	C	G	2868724	3	3	74	1	0	0	0	0	1	0	0	0	12647	595	21	4	318	4	PRSS21	16	2868724	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		2868724	87486029	77	7000											
ZNF597	146434	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	3487524	3487524	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	taactgctgattaatctcagGcttgccttcctctcctgttg	6	16	7	12	0	2	1	1	1	2	0	5	1	3	1	3	1	3	3	3	1	2	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:3487524G>C	ENST00000301744.4	-	4	410	c.175C>G	c.(175-177)Cct>Gct	p.P59A		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	59	KRAB.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						TTAATCTCAGGCTTGCCTTCC	0.413																																					p.P59A		.											.	ZNF597-90	0			c.C175G						.						49	50	50					16																	3487524		2197	4300	6497	SO:0001583	missense	146434	exon4			TCTCAGGCTTGCC	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"Zinc fingers, C2H2-type", "-"	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.175C>G	16.37:g.3487524G>C	ENSP00000301744:p.Pro59Ala	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	145	91	NM_152457	0	0	4	4	0		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.351852	0.00217	.	.	ENSG00000167981	ENST00000301744	T	0.08458	3.09	4.91	-1.26	0.09376	Krueppel-associated box (1);	0.486115	0.17564	N	0.169702	T	0.04227	0.0117	N	0.25201	0.72	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33929	-0.9849	10	0.62326	D	0.03	-0.9659	1.0959	0.01673	0.1461:0.1764:0.3287:0.3488	.	59	Q96LX8	ZN597_HUMAN	A	59	ENSP00000301744:P59A	ENSP00000301744:P59A	P	-	1	0	ZNF597	3427525	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	0.183000	0.16919	-0.121000	0.11787	-0.262000	0.10625	CCT	.		0.413	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		C	3487524	G	C	3487524	3	2	74	1	0	0	0	0	1	0	0	0	18059	1203	42	4	1103	4	ZNF597	16	3487524	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	618800	3487524	86867229	78	7001											
USP31	57478	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	23083424	23083424	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagagagcgacgccagggaGgtgcgtctggaggaagctgc	9	5	18	9	3	2	1	1	0	1	1	2	6	2	4	1	4	4	1	1	4	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:23083424G>T	ENST00000219689.7	-	15	2429	c.2430C>A	c.(2428-2430)acC>acA	p.T810T	USP31_ENST00000567975.1_Silent_p.T103T	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		ACGCCAGGGAGGTGCGTCTGG	0.577																																					p.T810T		.											.	USP31-663	0			c.C2430A						.						122	120	121					16																	23083424		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon15			CAGGGAGGTGCGT	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2430C>A	16.37:g.23083424G>T		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	232	20	NM_020718	0	0	2	4	2	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	37	CCDS10607.1																																																																																			.		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		T	23083424	G	T	23083424	2	4	74	1	0	0	0	0	0	0	0	1	17095	987	35	4		4	USP31	16	23083424	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	19595900	23083424	67271329	79	7002											
NUP93	9688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56792502	56792502	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcccacatctcccagcgaTtggagagtctgagtgcagcc	9	9	10	13	1	2	2	0	1	2	1	4	4	3	2	3	1	3	1	3	1	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:56792502T>C	ENST00000308159.5	+	3	353	c.232T>C	c.(232-234)Ttg>Ctg	p.L78L	NUP93_ENST00000569842.1_Silent_p.L78L	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	78					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						CTCCCAGCGATTGGAGAGTCT	0.512																																					p.L78L	Colon(33;610 796 1305 1705 38917)	.											.	NUP93-205	0			c.T232C						.						108	94	98					16																	56792502		2198	4300	6498	SO:0001819	synonymous_variant	9688	exon3			CAGCGATTGGAGA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.232T>C	16.37:g.56792502T>C		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	98	37	NM_014669	0	0	17	25	8	B3KPQ8|Q14705	Silent	SNP	ENST00000308159.5	37	CCDS10769.1																																																																																			.		0.512	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		C	56792502	T	C	56792502	2	2	74	1	0	0	0	0	0	0	0	1	10798	1490	52	3		3	NUP93	16	56792502	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	33709078	56792502	33562251	80	7003											
COG8	84342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	69368791	69368791	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggacagcccaaagtacatgCactggcccagcagagagtcc	13	4	11	13	0	0	1	0	0	0	1	1	3	1	2	3	2	4	3	3	2	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:69368791C>G	ENST00000306875.4	-	3	1160	c.1046G>C	c.(1045-1047)tGc>tCc	p.C349S	RP11-343C2.12_ENST00000562949.1_5'Flank|COG8_ENST00000562081.1_Missense_Mutation_p.C349S	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	349					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						AAAGTACATGCACTGGCCCAG	0.592																																					p.C349S		.											.	COG8-91	0			c.G1046C						.						57	60	59					16																	69368791		2198	4300	6498	SO:0001583	missense	84342	exon3			TACATGCACTGGC	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.1046G>C	16.37:g.69368791C>G	ENSP00000305459:p.Cys349Ser	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	93	34	NM_032382	0	0	13	20	7	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	ENST00000306875.4	37	CCDS10876.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460053	0.84317	.	.	ENSG00000213380	ENST00000306875	T	0.47528	0.84	5.93	5.93	0.95920	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61489	0.2351	L	0.61218	1.895	0.80722	D	1	B;B	0.33379	0.41;0.41	P;P	0.46917	0.531;0.531	T	0.54330	-0.8310	10	0.35671	T	0.21	-0.7999	20.3363	0.98740	0.0:1.0:0.0:0.0	.	376;349	B4DYU2;Q96MW5	.;COG8_HUMAN	S	349	ENSP00000305459:C349S	ENSP00000305459:C349S	C	-	2	0	COG8	67926292	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.441000	0.80485	2.814000	0.96858	0.563000	0.77884	TGC	.		0.592	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		G	69368791	C	G	69368791	3	3	74	1	0	0	0	0	1	0	0	0	3670	710	25	4	804	4	COG8	16	69368791	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	12576289	69368791	20985962	81	7004											
ZNF778	197320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89294017	89294017	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggccttactagacacgtaCgaacacacacgggcgagaag	13	5	12	11	4	0	2	0	0	0	2	0	4	0	2	1	2	3	1	1	2	5	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:89294017C>T	ENST00000433976.2	+	6	1569	c.1237C>T	c.(1237-1239)Cga>Tga	p.R413*	ZNF778_ENST00000306502.6_Nonsense_Mutation_p.R371*|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		TAGACACGTACGAACACACAC	0.498																																					p.R441X		.											.	.	0			c.C1321T						.						92	96	94					16																	89294017		2154	4282	6436	SO:0001587	stop_gained	197320	exon7			CACGTACGAACAC	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1237C>T	16.37:g.89294017C>T	ENSP00000405289:p.Arg413*	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	80	23	NM_001201407	0	0	2	3	1	Q08AG0	Nonsense_Mutation	SNP	ENST00000433976.2	37	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	C	35	5.468936	0.96274	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	.	.	.	1.13	-0.119	0.13543	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1288	0.14899	0.6032:0.3967:0.0:0.0	.	.	.	.	X	413;371	.	ENSP00000305203:R371X	R	+	1	2	ZNF778	87821518	0.000000	0.05858	0.002000	0.10522	0.104000	0.19210	-0.846000	0.04336	-0.009000	0.14296	0.558000	0.71614	CGA	.		0.498	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		T	89294017	C	T	89294017	4	4	74	1	0	0	0	0	0	1	0	0	18183	528	19	1	1255	1	ZNF778	16	89294017	Nonsense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	19925226	89294017	1060736	82	7005											
DEF8	54849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	90015887	90015887	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tagaggaatggccatcctgtCcctgcgagcccctgggccct	6	8	12	15	1	0	1	0	0	0	1	2	3	2	2	6	3	2	0	6	3	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:90015887C>A	ENST00000268676.7	+	2	103	c.14C>A	c.(13-15)tCc>tAc	p.S5Y	DEF8_ENST00000418391.2_5'UTR|DEF8_ENST00000563795.1_5'UTR|DEF8_ENST00000567874.1_5'UTR|DEF8_ENST00000570182.1_5'UTR|DEF8_ENST00000569453.1_5'UTR|DEF8_ENST00000563594.1_5'UTR	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	5					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		GCCATCCTGTCCCTGCGAGCC	0.672																																					p.S5Y		.											.	DEF8-68	0			c.C14A						.						46	47	47					16																	90015887		2198	4300	6498	SO:0001583	missense	54849	exon2			TCCTGTCCCTGCG	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.14C>A	16.37:g.90015887C>A	ENSP00000268676:p.Ser5Tyr	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	90	31	NM_207514	0	0	4	11	7	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Missense_Mutation	SNP	ENST00000268676.7	37	CCDS10989.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417522	0.42918	.	.	ENSG00000140995	ENST00000268676	T	0.50001	0.76	2.59	-0.8	0.10897	.	.	.	.	.	T	0.23014	0.0556	N	0.08118	0	0.09310	N	0.999994	B	0.16166	0.016	B	0.16289	0.015	T	0.18745	-1.0327	9	0.87932	D	0	.	3.1996	0.06645	0.0:0.4875:0.226:0.2865	.	5	Q6ZN54	DEFI8_HUMAN	Y	5	ENSP00000268676:S5Y	ENSP00000268676:S5Y	S	+	2	0	DEF8	88543388	0.007000	0.16637	0.000000	0.03702	0.020000	0.10135	1.378000	0.34328	-0.124000	0.11724	0.511000	0.50034	TCC	.		0.672	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		A	90015887	C	A	90015887	3	1	74	1	0	0	0	0	1	0	0	0	4393	855	30	4	16	4	DEF8	16	90015887	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	721870	90015887	338866	83	7006											
AMAC1L3	643664	broad.mit.edu	37	chr17	7385463	7385463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcctgcctgctggcttcGtgggccccctttctcatatg	2	12	13	14	1	1	0	1	0	1	0	3	0	1	0	4	4	2	2	4	4	1	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:7385463G>A	ENST00000412468.2	+	2	275	c.160G>A	c.(160-162)Gtg>Atg	p.V54M	ZBTB4_ENST00000380599.4_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	54	EamA 1.					integral component of membrane (GO:0016021)											TGCTGGCTTCGTGGGCCCCCT	0.647																																					p.V54M													.	.	0			c.G160A						.						69	74	73					17																	7385463		2203	4300	6503	SO:0001583	missense	643664	exon2			GGCTTCGTGGGCC		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.160G>A	17.37:g.7385463G>A	ENSP00000396523:p.Val54Met	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	163	6	NM_001102614	0	0	0	0	0		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.965819	0.34659	.	.	ENSG00000181222	ENST00000412468	T	0.32988	1.43	4.04	4.04	0.47022	.	.	.	.	.	T	0.44052	0.1275	L	0.36672	1.1	0.44595	D	0.997561	D	0.89917	1.0	D	0.72982	0.979	T	0.31138	-0.9954	9	0.38643	T	0.18	-6.0135	15.3126	0.74045	0.0:0.0:1.0:0.0	.	54	P0C7Q6	S35G6_HUMAN	M	54	ENSP00000396523:V54M	ENSP00000396523:V54M	V	+	1	0	SLC35G6	7326187	1.000000	0.71417	1.000000	0.80357	0.064000	0.16182	3.428000	0.52792	1.959000	0.56917	0.462000	0.41574	GTG	.		0.647	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		A	7385463	G	A	7385463	3	1	74	1	0	0	0	0	1	0	0	0	561	1145	40	1	166	1	AMAC1L3	17	7385463	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		7385463	73809747	84	7007											
KDM6B	23135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7755372	7755372	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactgggagaccatcagcgcTttctgtgatcggtgcgtgcc	6	11	13	11	3	2	2	1	1	1	1	3	3	2	2	2	2	4	1	2	2	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:7755372T>G	ENST00000448097.2	+	18	4600	c.4269T>G	c.(4267-4269)gcT>gcG	p.A1423A	KDM6B_ENST00000254846.5_Silent_p.A1423A			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1423	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CCATCAGCGCTTTCTGTGATC	0.632											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A1423A		.											.	KDM6B-205	0			c.T4269G						.						95	82	86					17																	7755372		2203	4300	6503	SO:0001819	synonymous_variant	23135	exon18			CAGCGCTTTCTGT	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.4269T>G	17.37:g.7755372T>G		Somatic	57	0	644	WXS	Illumina HiSeq	Phase_I	63	19	NM_001080424	0	0	0	0	0	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				.		0.632	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		G	7755372	T	G	7755372	2	3	74	1	0	0	0	0	0	0	0	1	8159	1596	56	5		5	KDM6B	17	7755372	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	369909	7755372	73439838	85	7008											
KPNB1	3837	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45753779	45753779	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttatttcattacagtgttGggtggtgaattcctcaagta	9	16	10	6	0	2	1	2	1	0	0	3	1	3	1	1	2	1	3	1	2	5	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:45753779G>T	ENST00000290158.4	+	16	2324	c.1917G>T	c.(1915-1917)ttG>ttT	p.L639F	KPNB1_ENST00000535458.2_Missense_Mutation_p.L494F|KPNB1_ENST00000537679.1_Missense_Mutation_p.L423F|KPNB1_ENST00000540627.1_Missense_Mutation_p.L494F	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	639					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						TTACAGTGTTGGGTGGTGAAT	0.428																																					p.X639C		.											.	KPNB1-229	0			c.A1917T						.						166	160	162					17																	45753779		2203	4300	6503	SO:0001583	missense	3837	exon16			AGTGTTGGGTGGT	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"Importins", "Armadillo repeat containing"	6400	protein-coding gene	gene with protein product	"importin 1"	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.1917G>T	17.37:g.45753779G>T	ENSP00000290158:p.Leu639Phe	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	114	32	NM_002265	0	0	0	1	1	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Missense_Mutation	SNP	ENST00000290158.4	37	CCDS11513.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.176879	0.38413	.	.	ENSG00000108424	ENST00000535458;ENST00000290158;ENST00000540627;ENST00000537679	T;T;T;T	0.60672	0.17;0.17;0.17;0.17	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72350	0.3449	M	0.84511	2.7	0.45390	D	0.998372	D;D	0.63046	0.992;0.978	P;P	0.61397	0.888;0.838	T	0.80728	-0.1253	9	0.46703	T	0.11	-22.0495	7.5951	0.28044	0.0759:0.0:0.6449:0.2792	.	423;639	F5H4R7;Q14974	.;IMB1_HUMAN	F	494;639;494;423	ENSP00000438253:L494F;ENSP00000290158:L639F;ENSP00000438964:L494F;ENSP00000445006:L423F	ENSP00000290158:L639F	L	+	3	2	KPNB1	43108778	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.514000	0.45503	2.785000	0.95823	0.655000	0.94253	TTG	.		0.428	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265		T	45753779	G	T	45753779	3	4	74	1	0	0	0	0	1	0	0	0	8456	1339	47	4	1979	4	KPNB1	17	45753779	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	37998407	45753779	35441431	86	7009											
ERN1	2081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62121548	62121548	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacctctgcaggcagctcccGgtagtggtgcttctgcaaag	7	9	12	13	1	2	0	0	0	2	0	3	0	3	0	2	3	4	6	2	3	2	2	rs185854736		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:62121548G>A	ENST00000433197.3	-	22	2829	c.2734C>T	c.(2734-2736)Cgg>Tgg	p.R912W		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GGCAGCTCCCGGTAGTGGTGC	0.552													G|||	1	0.000199681	8e-04	0	5008	,	,		16731	0		0	False		,,,				2504	0				p.R912W		.											.	ERN1-784	0			c.C2734T						.						23	25	24					17																	62121548		1922	4134	6056	SO:0001583	missense	2081	exon22			GCTCCCGGTAGTG	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.2734C>T	17.37:g.62121548G>A	ENSP00000401445:p.Arg912Trp	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	58	20	NM_001433	0	0	0	0	0		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.33	2.503786	0.44558	.	.	ENSG00000178607	ENST00000433197	T	0.32753	1.44	5.22	3.14	0.36123	PUG domain (1);KEN domain, ribonuclease activator (2);	0.000000	0.64402	D	0.000001	T	0.59959	0.2232	M	0.90759	3.145	0.53688	D	0.999979	D	0.89917	1.0	D	0.66716	0.946	T	0.71424	-0.4597	10	0.87932	D	0	-26.8746	14.1183	0.65169	0.0:0.0:0.5827:0.4172	.	912	O75460	ERN1_HUMAN	W	912	ENSP00000401445:R912W	ENSP00000401445:R912W	R	-	1	2	ERN1	59475280	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	1.669000	0.37492	1.194000	0.43101	-0.268000	0.10319	CGG	G|0.999;A|0.000		0.552	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		A	62121548	G	A	62121548	3	1	74	1	0	0	0	0	1	0	0	0	5250	1115	39	1	203	1	ERN1	17	62121548	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	16367769	62121548	19073662	87	7010											
ABCA9	10350	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	66981100	66981100	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	accactgacgggttccccagGatgctcagcacaaagcacag	12	5	10	14	1	1	1	1	1	0	0	2	2	2	2	3	2	3	4	3	2	1	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:66981100G>A	ENST00000340001.4	-	34	4516	c.4305C>T	c.(4303-4305)atC>atT	p.I1435I	ABCA9_ENST00000453985.2_Silent_p.I1397I|ABCA9_ENST00000370732.2_Intron|ABCA9_ENST00000482072.1_5'Flank	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1435	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GGTTCCCCAGGATGCTCAGCA	0.597																																					p.I1435I		.											.	ABCA9-95	0			c.C4305T						.						132	116	121					17																	66981100		2203	4300	6503	SO:0001819	synonymous_variant	10350	exon34			CCCCAGGATGCTC	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"ATP binding cassette transporters / subfamily A"	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.4305C>T	17.37:g.66981100G>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	174	31	NM_080283	0	0	0	0	0	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	37	CCDS11681.1																																																																																			.		0.597	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		A	66981100	G	A	66981100	2	1	74	1	0	0	0	0	0	0	0	1	39	1164	41	2		2	ABCA9	17	66981100	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	4859552	66981100	14214110	88	7011											
ABCA10	10349	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	67170778	67170778	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atgagttcccatgaaagctgGaatcccagaaatatgaagta	16	9	9	7	0	0	4	0	3	0	1	2	5	2	5	2	1	1	3	2	1	6	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:67170778G>T	ENST00000269081.4	-	25	3927	c.3018C>A	c.(3016-3018)ttC>ttA	p.F1006L	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_Intron	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1006					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					ATGAAAGCTGGAATCCCAGAA	0.333																																					p.F1006L		.											.	ABCA10-93	0			c.C3018A						.						78	86	83					17																	67170778		2202	4296	6498	SO:0001583	missense	10349	exon25			AAGCTGGAATCCC	AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"ATP binding cassette transporters / subfamily A"	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.3018C>A	17.37:g.67170778G>T	ENSP00000269081:p.Phe1006Leu	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	231	71	NM_080282	0	0	0	0	0	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	2.023	-0.424331	0.04734	.	.	ENSG00000154263	ENST00000269081	D	0.84944	-1.92	3.1	2.05	0.26809	.	.	.	.	.	T	0.67277	0.2876	N	0.17474	0.49	0.09310	N	1	B	0.25351	0.124	B	0.26614	0.071	T	0.51942	-0.8641	9	0.11485	T	0.65	.	1.6357	0.02741	0.1265:0.2031:0.4424:0.2279	.	1006	Q8WWZ4	ABCAA_HUMAN	L	1006	ENSP00000269081:F1006L	ENSP00000269081:F1006L	F	-	3	2	ABCA10	64682373	0.000000	0.05858	0.001000	0.08648	0.086000	0.17979	-0.664000	0.05292	0.551000	0.29008	0.407000	0.27541	TTC	.		0.333	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67170778	G	T	67170778	3	4	74	1	0	0	0	0	1	0	0	0	29	1165	41	4	1677	4	ABCA10	17	67170778	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	189678	67170778	14024432	89	7012											
FASN	2194	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	80050833	80050833	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggtggcgtacacccgccGggccagggacttcttggtca	6	8	15	12	3	2	0	1	0	1	0	2	2	2	1	3	5	1	1	3	5	1	3	rs200752265		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:80050833G>A	ENST00000306749.2	-	6	936	c.718C>T	c.(718-720)Cgg>Tgg	p.R240W		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	240	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TACACCCGCCGGGCCAGGGAC	0.682																																					p.R240W	Colon(59;314 1043 11189 28578 32273)	.											.	FASN-90	0			c.C718T						.						30	31	31					17																	80050833		2183	4296	6479	SO:0001583	missense	2194	exon6			CCCGCCGGGCCAG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.718C>T	17.37:g.80050833G>A	ENSP00000304592:p.Arg240Trp	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	37	12	NM_004104	0	0	5	8	3	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841387	0.71488	.	.	ENSG00000169710	ENST00000306749	T	0.32988	1.43	4.64	2.47	0.30058	Thiolase-like, subgroup (1);Thiolase-like (1);	0.239450	0.32401	N	0.006145	T	0.51873	0.1700	M	0.86028	2.79	0.34231	D	0.676504	D	0.89917	1.0	D	0.66351	0.943	T	0.63350	-0.6657	10	0.87932	D	0	-32.0916	6.8759	0.24147	0.1029:0.0:0.2594:0.6378	.	240	P49327	FAS_HUMAN	W	240	ENSP00000304592:R240W	ENSP00000304592:R240W	R	-	1	2	FASN	77644122	0.246000	0.23909	0.993000	0.49108	0.893000	0.52053	1.570000	0.36439	0.338000	0.23692	0.313000	0.20887	CGG	G|0.998;T|0.002		0.682	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80050833	G	A	80050833	3	1	74	1	0	0	0	0	1	0	0	0	5702	1115	39	1	6969	1	FASN	17	80050833	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	12880055	80050833	1144377	90	7013											
MED16	10025	hgsc.bcm.edu	37	chr19	879943	879943	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcagctcaccttcccGtggctgtcaatccccaccag	7	7	7	20	1	2	0	2	0	0	0	4	0	4	0	7	1	2	3	7	1	1	1	rs201392672|rs76403059	byFrequency	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000395808.3_Missense_Mutation_p.H449Q|MED16_ENST00000606828.1_Intron|MED16_ENST00000269814.4_Missense_Mutation_p.H449Q|MED16_ENST00000312090.6_Missense_Mutation_p.H449Q|MED16_ENST00000325464.1_Missense_Mutation_p.H449Q			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	449					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACCTTCCCGTGGCTGTCAA	0.672																																					p.H449Q		.											.	MED16-186	0			c.C1347G						.						13	11	12					19																	879943		2152	4247	6399	SO:0001583	missense	10025	exon8			CTTCCCGTGGCTG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1347C>G	19.37:g.879943G>C	ENSP00000464810:p.His449Gln	Somatic	15	1		WXS	Illumina HiSeq	Phase_I	19	2	NM_005481	0	0	0	0	0	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	3.376	-0.127462	0.06753	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000424039	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.21	-7.89	0.01174	WD40 repeat-like-containing domain (1);	0.323237	0.32357	N	0.006220	T	0.21307	0.0513	L	0.37850	1.14	0.37741	D	0.925623	B;B;B;B;B	0.13145	0.006;0.007;0.002;0.001;0.001	B;B;B;B;B	0.14023	0.006;0.006;0.003;0.006;0.01	T	0.20009	-1.0288	10	0.15066	T	0.55	-14.2411	8.1092	0.30905	0.4704:0.1904:0.3392:0.0	.	449;449;449;449;449	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	Q	449;449;449;449;449;305;210;208;449	ENSP00000325612:H449Q;ENSP00000308528:H449Q;ENSP00000379153:H449Q;ENSP00000269814:H449Q	ENSP00000269814:H449Q	H	-	3	2	MED16	830943	0.000000	0.05858	0.886000	0.34754	0.057000	0.15508	-3.404000	0.00482	-1.779000	0.01280	-2.326000	0.00250	CAC	.		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		C	879943	G	C	879943	3	2	74	1	0	0	0	0	1	0	0	0	9459	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		879943	58249040	91	7014											
MOBKL2A	126308	ucsc.edu	37	chr19	2076916	2076916	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggagcccatctgcgcgatgCggtcaaagtggtggatgtag	8	8	16	9	4	2	0	1	0	1	0	2	3	2	2	1	4	3	1	1	4	2	1	rs534131418	byFrequency	TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:2076916C>T	ENST00000357066.3	-	4	897	c.518G>A	c.(517-519)cGc>cAc	p.R173H	MOB3A_ENST00000592280.1_Missense_Mutation_p.R173H|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	173						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CTGCGCGATGCGGTCAAAGTG	0.582													C|||	2	0.000399361	0	0	5008	,	,		18570	0.002		0	False		,,,				2504	0				p.R173H													.	.	0			c.G518A						.						89	73	79					19																	2076916		2203	4300	6503	SO:0001583	missense	126308	exon4			GCGATGCGGTCAA	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"MOB kinase activators"	29802	protein-coding gene	gene with protein product	"MOB LAK"		"MOB1, Mps One Binder kinase activator-like 2A (yeast)"	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.518G>A	19.37:g.2076916C>T	ENSP00000349575:p.Arg173His	Somatic	36	0		WXS	Illumina HiSeq		33	4	NM_130807	0	0	3	3	0	B3KTF1|O75249|Q8TF69	Missense_Mutation	SNP	ENST00000357066.3	37	CCDS12081.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.264098	0.59431	.	.	ENSG00000172081	ENST00000357066	.	.	.	3.74	3.74	0.42951	.	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	L	0.47716	1.5	0.80722	D	1	B	0.14012	0.009	B	0.20955	0.032	T	0.54892	-0.8225	9	0.35671	T	0.21	-48.1009	14.2648	0.66110	0.0:1.0:0.0:0.0	.	173	Q96BX8	MOB3A_HUMAN	H	173	.	ENSP00000349575:R173H	R	-	2	0	MOBKL2A	2027916	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.608000	0.67654	1.937000	0.56155	0.491000	0.48974	CGC	.		0.582	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807		T	2076916	C	T	2076916	3	4	74	1	0	0	0	0	1	0	0	0	9709	768	27	1	143	1	MOBKL2A	19	2076916	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	1196973	2076916	57052067	92	7015											
ZNF558	148156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8922351	8922351	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagaggaccttgtgctgaaaGcttttccacactgattacat	11	12	9	9	0	0	3	0	2	0	1	1	5	1	4	2	1	3	2	2	1	2	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:8922351G>C	ENST00000601372.1	-	10	1526	c.815C>G	c.(814-816)gCt>gGt	p.A272G	ZNF558_ENST00000301475.1_Missense_Mutation_p.A272G|ZNF558_ENST00000444186.2_Missense_Mutation_p.A201G			Q96NG5	ZN558_HUMAN	zinc finger protein 558	272					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15						TGTGCTGAAAGCTTTTCCACA	0.463																																					p.A272G		.											.	ZNF558-90	0			c.C815G						.						154	142	146					19																	8922351		2203	4300	6503	SO:0001583	missense	148156	exon6			CTGAAAGCTTTTC	AK055494	CCDS12208.1	19p13.2	2013-09-20			ENSG00000167785	ENSG00000167785		"Zinc fingers, C2H2-type", "-"	26422	protein-coding gene	gene with protein product							Standard	NM_144693		Approved	FLJ30932	uc002mkn.1	Q96NG5	OTTHUMG00000182196	ENST00000601372.1:c.815C>G	19.37:g.8922351G>C	ENSP00000471277:p.Ala272Gly	Somatic	188	1		WXS	Illumina HiSeq	Phase_I	214	73	NM_144693	0	0	1	1	0	A8K5F0|B7Z798	Missense_Mutation	SNP	ENST00000601372.1	37	CCDS12208.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.726843	0.69074	.	.	ENSG00000167785	ENST00000301475;ENST00000444186	T;T	0.01043	5.41;5.41	5.07	5.07	0.68467	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43416	D	0.000563	T	0.01592	0.0051	N	0.21324	0.655	0.30401	N	0.779985	P	0.40931	0.733	B	0.42112	0.376	T	0.42430	-0.9452	10	0.87932	D	0	-11.7496	15.9729	0.80034	0.0:0.0:1.0:0.0	.	272	Q96NG5	ZN558_HUMAN	G	272;201	ENSP00000301475:A272G;ENSP00000410703:A201G	ENSP00000301475:A272G	A	-	2	0	ZNF558	8783351	0.000000	0.05858	1.000000	0.80357	0.961000	0.63080	0.257000	0.18369	2.636000	0.89361	0.591000	0.81541	GCT	.		0.463	ZNF558-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459955.2	NM_144693		C	8922351	G	C	8922351	3	2	74	1	0	0	0	0	1	0	0	0	18021	971	34	4	397	4	ZNF558	19	8922351	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	6845435	8922351	50206632	93	7016											
PPP1R15A	23645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49379135	49379135	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgtcccttcgtccccaGtccagaccacgcccttgagc	5	9	7	20	2	1	2	0	1	1	1	5	2	4	2	7	0	1	0	7	0	0	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:49379135G>A	ENST00000200453.5	+	3	2199	c.1930G>A	c.(1930-1932)Gtc>Atc	p.V644I		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	644					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		TTCGTCCCCAGTCCAGACCAC	0.672																																					p.V644I		.											.	PPP1R15A-226	0			c.G1930A						.						122	120	121					19																	49379135		2203	4300	6503	SO:0001583	missense	23645	exon3			TCCCCAGTCCAGA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1930G>A	19.37:g.49379135G>A	ENSP00000200453:p.Val644Ile	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	284	91	NM_014330	0	0	69	117	48	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	7.302	0.613292	0.14066	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05081	3.5	2.9	-5.81	0.02340	.	2.513440	0.01909	N	0.039689	T	0.01905	0.0060	N	0.02916	-0.46	0.09310	N	1	B	0.22346	0.068	B	0.18263	0.021	T	0.35325	-0.9793	10	0.07030	T	0.85	0.3665	0.7652	0.01014	0.2207:0.1394:0.1939:0.446	.	644	O75807	PR15A_HUMAN	I	644;484;602	ENSP00000200453:V644I	ENSP00000200453:V644I	V	+	1	0	PPP1R15A	54070947	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	-0.505000	0.06367	-1.336000	0.02238	-0.274000	0.10170	GTC	.		0.672	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		A	49379135	G	A	49379135	3	1	74	1	0	0	0	0	1	0	0	0	12392	1029	36	2	1936	2	PPP1R15A	19	49379135	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	40456784	49379135	9749848	94	7017											
ZNF773	374928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58018434	58018434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcatgaaacatcagagagTtcacactggagaaagacctt	15	8	8	10	0	3	4	3	1	0	3	3	6	3	4	2	1	1	1	2	1	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:58018434T>C	ENST00000282292.4	+	4	1111	c.971T>C	c.(970-972)gTt>gCt	p.V324A	ZNF773_ENST00000598770.1_Missense_Mutation_p.V323A|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	324					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(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)		CATCAGAGAGTTCACACTGGA	0.428																																					p.V324A		.											.	ZNF773-91	0			c.T971C						.						128	130	130					19																	58018434		2203	4300	6503	SO:0001583	missense	374928	exon4			AGAGAGTTCACAC	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.971T>C	19.37:g.58018434T>C	ENSP00000282292:p.Val324Ala	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	200	47	NM_198542	0	0	2	2	0	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	37	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.418764	0.25552	.	.	ENSG00000152439	ENST00000282292	T	0.00976	5.48	1.17	1.17	0.20885	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00906	0.0030	L	0.37850	1.14	0.09310	N	0.999999	P;B	0.39903	0.694;0.429	B;B	0.34652	0.133;0.187	T	0.51521	-0.8695	9	0.87932	D	0	.	5.4406	0.16507	0.0:0.0:0.2844:0.7155	.	323;324	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	A	324	ENSP00000282292:V324A	ENSP00000282292:V324A	V	+	2	0	ZNF773	62710246	0.000000	0.05858	0.990000	0.47175	0.939000	0.58152	0.440000	0.21592	0.785000	0.33685	0.254000	0.18369	GTT	.		0.428	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		C	58018434	T	C	58018434	3	2	74	1	0	0	0	0	1	0	0	0	18178	1725	60	3	985	3	ZNF773	19	58018434	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	8639299	58018434	1110549	95	7018											
ZNF418	147686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58437999	58437999	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacagctttgaggaaatgacTtcccacattcactacactca	14	10	5	12	0	2	2	2	2	0	0	3	3	3	3	1	1	3	1	1	1	3	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:58437999T>C	ENST00000396147.1	-	4	1841	c.1550A>G	c.(1549-1551)aAg>aGg	p.K517R	ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000425570.3_Missense_Mutation_p.K538R|ZNF418_ENST00000599852.1_Missense_Mutation_p.K432R|ZNF418_ENST00000595830.1_Missense_Mutation_p.K517R	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		AGGAAATGACTTCCCACATTC	0.433																																					p.K517R		.											.	ZNF418-90	0			c.A1550G						.						115	117	116					19																	58437999		2193	4293	6486	SO:0001583	missense	147686	exon4			AATGACTTCCCAC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1550A>G	19.37:g.58437999T>C	ENSP00000379451:p.Lys517Arg	Somatic	185	1		WXS	Illumina HiSeq	Phase_I	165	65	NM_133460	0	0	0	0	0	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	37	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	17.02	3.282436	0.59867	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.26223	1.75;1.75	2.41	2.41	0.29592	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31702	0.0805	L	0.52206	1.635	0.21967	N	0.999442	P	0.45044	0.849	P	0.49637	0.617	T	0.08046	-1.0741	9	0.49607	T	0.09	.	9.453	0.38739	0.0:0.0:0.0:1.0	.	517	Q8TF45	ZN418_HUMAN	R	517;538;483	ENSP00000379451:K517R;ENSP00000407039:K538R	ENSP00000379451:K517R	K	-	2	0	ZNF418	63129811	1.000000	0.71417	0.030000	0.17652	0.345000	0.29048	4.043000	0.57354	1.107000	0.41642	0.260000	0.18958	AAG	.		0.433	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		C	58437999	T	C	58437999	3	2	74	1	0	0	0	0	1	0	0	0	17927	1609	56	3	484	3	ZNF418	19	58437999	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	419565	58437999	690984	96	7019											
PLCB1	23236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	8741054	8741054	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttttatcttttatattacagGttctgtaaaggcacctgcca	10	17	6	8	0	2	0	0	0	2	0	2	0	2	0	2	2	2	3	2	2	6	8			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:8741054G>T	ENST00000338037.6	+	25	2684	c.2657G>T	c.(2656-2658)gGt>gTt	p.G886V	PLCB1_ENST00000378641.3_Splice_Site_p.G886V|PLCB1_ENST00000378637.2_Splice_Site_p.G886V|PLCB1_ENST00000494924.1_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	886					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TATATTACAGGTTCTGTAAAG	0.348																																					p.Q886L		.											.	PLCB1-297	0			c.A2657T						.						42	42	42					20																	8741054		2203	4300	6503	SO:0001630	splice_region_variant	23236	exon25			TTACAGGTTCTGT	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2657-1G>T	20.37:g.8741054G>T		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	69	21	NM_015192	0	0	0	0	0	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.522308	0.64747	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.19250	2.17;2.16;2.17	6.07	6.07	0.98685	.	0.168672	0.52532	D	0.000067	T	0.39384	0.1076	L	0.44542	1.39	0.80722	D	1	D;D	0.65815	0.988;0.995	P;D	0.63113	0.676;0.911	T	0.00559	-1.1671	9	.	.	.	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	886;886	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	V	886;886;886;806;806	ENSP00000367908:G886V;ENSP00000338185:G886V;ENSP00000367904:G886V	.	G	+	2	0	PLCB1	8689054	1.000000	0.71417	0.996000	0.52242	0.929000	0.56500	8.960000	0.93117	2.885000	0.99019	0.655000	0.94253	GGT	.		0.348	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Missense_Mutation	T	8741054	G	T	8741054	5	4	74	1	0	0	0	0	0	0	1	0	12053	1275	44	4	2755	4	PLCB1	20	8741054	Splice_Site	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		8741054	54284466	97	7020											
KCNS1	3787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	43726464	43726464	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accagccagcagcgtgagatAgaagggcagcacagacacaa	16	2	12	11	1	0	3	0	1	0	3	0	4	0	3	2	1	4	3	2	1	3	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:43726464A>T	ENST00000306117.1	-	4	1345	c.949T>A	c.(949-951)Tat>Aat	p.Y317N	KCNS1_ENST00000537075.1_Missense_Mutation_p.Y317N	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	317					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				AGCGTGAGATAGAAGGGCAGC	0.632																																					p.Y317N		.											.	KCNS1-90	0			c.T949A						.						74	57	62					20																	43726464		2203	4300	6503	SO:0001583	missense	3787	exon4			TGAGATAGAAGGG	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.949T>A	20.37:g.43726464A>T	ENSP00000307694:p.Tyr317Asn	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	29	16	NM_002251	0	0	0	0	0	A2RUL9|B7ZM31|O43652|Q6DJU6	Missense_Mutation	SNP	ENST00000306117.1	37	CCDS13342.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403414	0.83230	.	.	ENSG00000124134	ENST00000306117;ENST00000537075	D;D	0.98701	-5.08;-5.08	5.31	5.31	0.75309	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99336	0.9767	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98784	1.0733	10	0.87932	D	0	.	15.2726	0.73717	1.0:0.0:0.0:0.0	.	317	Q96KK3	KCNS1_HUMAN	N	317	ENSP00000307694:Y317N;ENSP00000445595:Y317N	ENSP00000307694:Y317N	Y	-	1	0	KCNS1	43159878	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.220000	0.95180	2.015000	0.59207	0.459000	0.35465	TAT	.		0.632	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251		T	43726464	A	T	43726464	3	4	74	1	0	0	0	0	1	0	0	0	8109	420	15	5	639	5	KCNS1	20	43726464	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	34985410	43726464	19299056	98	7021											
WFDC2	10406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44108666	44108666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccaggtggacagccagtGtcctggccagatgaaatgct	9	8	14	10	0	0	2	0	1	0	1	1	3	1	3	4	3	3	1	4	3	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:44108666G>A	ENST00000372676.3	+	3	384	c.308G>A	c.(307-309)tGt>tAt	p.C103Y	AL031663.1_ENST00000599747.1_5'Flank|WFDC2_ENST00000488143.1_3'UTR|WFDC2_ENST00000342873.3_Missense_Mutation_p.C52Y|WFDC2_ENST00000339946.3_Missense_Mutation_p.C55Y	NM_006103.3	NP_006094.3	Q14508	WFDC2_HUMAN	WAP four-disulfide core domain 2	103	WAP 2. {ECO:0000255|PROSITE- ProRule:PRU00722}.				negative regulation of endopeptidase activity (GO:0010951)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase inhibitor activity (GO:0019828)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1		Myeloproliferative disorder(115;0.0122)				GACAGCCAGTGTCCTGGCCAG	0.537																																					p.C103Y		.											.	WFDC2-90	0			c.G308A						.						107	112	110					20																	44108666		2203	4300	6503	SO:0001583	missense	10406	exon3			GCCAGTGTCCTGG	X63187	CCDS35501.1	20q13.12	2013-01-21			ENSG00000101443	ENSG00000101443		"WAP four-disulfide core domain containing"	15939	protein-coding gene	gene with protein product	"epididymal protein 4"					1686187, 10570965	Standard	NM_006103		Approved	HE4, WAP5, dJ461P17.6, EDDM4	uc002xoo.3	Q14508	OTTHUMG00000032594	ENST00000372676.3:c.308G>A	20.37:g.44108666G>A	ENSP00000361761:p.Cys103Tyr	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	181	74	NM_006103	0	0	2476	5142	2666	A2A2A5|A2A2A6|A6PVD5|Q6IB27|Q8WXV9|Q8WXW0|Q8WXW1|Q8WXW2|Q96KJ1	Missense_Mutation	SNP	ENST00000372676.3	37	CCDS35501.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620538	0.46736	.	.	ENSG00000101443	ENST00000372676;ENST00000339946;ENST00000342873	D;D;D	0.99239	-5.61;-5.61;-5.61	5.26	5.26	0.73747	Whey acidic protein, 4-disulphide core (5);	0.000000	0.64402	D	0.000017	D	0.99670	0.9877	H	0.98276	4.19	0.43947	D	0.996613	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.97440	1.0021	10	0.87932	D	0	-13.7907	14.7141	0.69254	0.0:0.0:1.0:0.0	.	52;55;103	Q14508-2;Q14508-3;Q14508	.;.;WFDC2_HUMAN	Y	103;55;52	ENSP00000361761:C103Y;ENSP00000340215:C55Y;ENSP00000342890:C52Y	ENSP00000340215:C55Y	C	+	2	0	WFDC2	43542080	0.997000	0.39634	0.953000	0.39169	0.096000	0.18686	3.179000	0.50887	2.598000	0.87819	0.655000	0.94253	TGT	.		0.537	WFDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079476.3			A	44108666	G	A	44108666	3	1	74	1	0	0	0	0	1	0	0	0	17385	1377	48	2	318	2	WFDC2	20	44108666	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	382202	44108666	18916854	99	7022											
DNTTIP1	116092	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	44424050	44424050	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggacgcagagcagctgAtccaggaagcctgtcggagc	10	5	16	10	2	0	2	0	1	0	1	2	5	1	5	2	4	4	3	2	4	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:44424050A>G	ENST00000372622.3	+	4	408	c.340A>G	c.(340-342)Atc>Gtc	p.I114V		NM_052951.2	NP_443183.1	Q9H147	TDIF1_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 1	114						nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9		Myeloproliferative disorder(115;0.0122)				AGAGCAGCTGATCCAGGAAGC	0.557																																					p.I114V		.											.	DNTTIP1-91	0			c.A340G						.						48	32	38					20																	44424050		2203	4300	6503	SO:0001583	missense	116092	exon4			CAGCTGATCCAGG	AB035676	CCDS13369.1	20q13.12	2003-09-10	2003-09-10	2003-09-12	ENSG00000101457	ENSG00000101457			16160	protein-coding gene	gene with protein product	"novel protein similar to synaptotagmin 1 (SYT1, P65) (isoform 1)", "TdT binding protein"	611388	"chromosome 20 open reading frame 167"	C20orf167		11473582	Standard	NM_052951		Approved	dJ447F3.4, Tdif1	uc002xpk.3	Q9H147	OTTHUMG00000032610	ENST00000372622.3:c.340A>G	20.37:g.44424050A>G	ENSP00000361705:p.Ile114Val	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	18	7	NM_052951	0	0	27	46	19	B2RA18|Q96DE3|Q9BQP2|Q9H148	Missense_Mutation	SNP	ENST00000372622.3	37	CCDS13369.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	17.46|17.46	3.396221|3.396221	0.62177|0.62177	.|.	.|.	ENSG00000101457|ENSG00000101457	ENST00000372622;ENST00000449078;ENST00000415790|ENST00000435014	T;T|.	0.48201|.	0.92;0.82|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.045638|.	0.85682|.	D|.	0.000000|.	T|.	0.60715|.	0.2290|.	L|L	0.42686|0.42686	1.345|1.345	0.44711|0.44711	D|D	0.997702|0.997702	B|.	0.28850|.	0.225|.	B|.	0.30316|.	0.114|.	T|.	0.57551|.	-0.7792|.	10|.	0.35671|.	T|.	0.21|.	-18.7653|-18.7653	14.5366|14.5366	0.67966|0.67966	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	114|.	Q9H147|.	TDIF1_HUMAN|.	V|W	114;109;74|40	ENSP00000361705:I114V;ENSP00000392509:I74V|.	ENSP00000361705:I114V|.	I|X	+|+	1|3	0|0	DNTTIP1|DNTTIP1	43857457|43857457	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.264000|7.264000	0.78432|0.78432	2.304000|2.304000	0.77564|0.77564	0.524000|0.524000	0.50904|0.50904	ATC|TGA	.		0.557	DNTTIP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079502.1	NM_052951		G	44424050	A	G	44424050	3	3	74	1	0	0	0	0	1	0	0	0	4692	333	12	3	354	3	DNTTIP1	20	44424050	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	315384	44424050	18601470	100	7023											
PSMA7	5688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	60714841	60714841	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgggcaggcacccacctgcTtcagactggcgatgtagcgg	7	6	15	13	3	1	1	1	0	0	1	1	2	1	1	2	4	2	4	2	4	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:60714841T>G	ENST00000370873.4	-	3	470	c.344A>C	c.(343-345)aAg>aCg	p.K115T	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370858.3_Missense_Mutation_p.K115T|PSMA7_ENST00000370861.1_Missense_Mutation_p.K45T	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	115					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			ACCCACCTGCTTCAGACTGGC	0.617																																					p.K115T		.											.	PSMA7-90	0			c.A344C						.						67	55	59					20																	60714841		2203	4300	6503	SO:0001583	missense	5688	exon3			ACCTGCTTCAGAC	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"Proteasome (prosome, macropain) subunits"	9536	protein-coding gene	gene with protein product	"proteasome subunit XAPC7", "proteasome subunit RC6-1"	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.344A>C	20.37:g.60714841T>G	ENSP00000359910:p.Lys115Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	64	21	NM_002792	0	0	1	2	1	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Missense_Mutation	SNP	ENST00000370873.4	37	CCDS13489.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	19.47|19.47	3.834596|3.834596	0.71373|0.71373	.|.	.|.	ENSG00000101182|ENSG00000101182	ENST00000370873;ENST00000370861;ENST00000370858|ENST00000442551	T;T;T|.	0.21191|.	2.02;2.02;2.02|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80110|0.80110	0.4563|0.4563	M|M	0.88512|0.88512	2.96|2.96	0.80722|0.80722	D|D	1|1	P|.	0.46578|.	0.88|.	P|.	0.55391|.	0.775|.	D|D	0.83890|0.83890	0.0284|0.0284	10|5	0.87932|.	D|.	0|.	.|.	14.9125|14.9125	0.70770|0.70770	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	115|.	O14818|.	PSA7_HUMAN|.	T|R	115;45;115|41	ENSP00000359910:K115T;ENSP00000359898:K45T;ENSP00000359895:K115T|.	ENSP00000359895:K115T|.	K|S	-|-	2|1	0|0	PSMA7|PSMA7	60148236|60148236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.264000|0.264000	0.26372|0.26372	7.469000|7.469000	0.80959|0.80959	1.974000|1.974000	0.57490|0.57490	0.460000|0.460000	0.39030|0.39030	AAG|AGC	.		0.617	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		G	60714841	T	G	60714841	3	3	74	1	0	0	0	0	1	0	0	0	12701	1609	56	5	422	5	PSMA7	20	60714841	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	16290791	60714841	2310679	101	7024											
PRPF6	57473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62642772	62642772	+	Intron	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggaagccaatgggaacacGcagatggtggagaagatcat	15	5	15	6	1	1	3	1	0	0	3	1	7	1	5	1	4	2	1	1	4	4	0	rs199552405		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:62642772G>C	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.T480T			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					ATGGGAACACGCAGATGGTGG	0.587																																					p.T480T		.											.	PRPF6-70	0			c.G1440C						.						94	77	83					20																	62642772		2203	4300	6503	SO:0001627	intron_variant	24148	exon11			GAACACGCAGATG	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.4+37285C>G	20.37:g.62642772G>C		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_012469	0	0	47	90	43	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			G|0.999;A|0.000		0.587	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62642772	G	C	62642772	1	2	74	0	1	0	0	0	0	0	0	0	12603	1074	38	4		4	PRPF6	20	62642772	Intron	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	1927931	62642772	382748	102	7025											
SON	6651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34925625	34925625	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tatggctgtcctggagtcttCggctgtgaccgtcctggagt	4	13	14	10	2	1	1	0	1	1	0	4	3	3	3	3	4	0	2	3	4	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr21:34925625C>T	ENST00000356577.4	+	3	4563	c.4088C>T	c.(4087-4089)tCg>tTg	p.S1363L	SON_ENST00000381679.4_Missense_Mutation_p.S1363L|SON_ENST00000300278.4_Missense_Mutation_p.S1363L|SON_ENST00000381692.2_Intron|SON_ENST00000290239.6_Missense_Mutation_p.S1363L	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1363	4 X 8 AA tandem repeats of V-L-E-SS- [AVT]-VT.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CTGGAGTCTTCGGCTGTGACC	0.577																																					p.S1363L		.											.	SON-97	0			c.C4088T						.						52	45	48					21																	34925625		2203	4300	6503	SO:0001583	missense	6651	exon3			AGTCTTCGGCTGT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.4088C>T	21.37:g.34925625C>T	ENSP00000348984:p.Ser1363Leu	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	68	17	NM_032195	0	0	15	25	10	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.86|11.86	1.765064|1.765064	0.31228|0.31228	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	.|T;T;T;T	.|0.11930	.|2.93;2.93;2.92;2.73	5.08|5.08	4.2|4.2	0.49525|0.49525	.|.	.|0.972270	.|0.08431	.|N	.|0.946875	T|T	0.10035|0.10035	0.0246|0.0246	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.20780	.|0.048;0.004;0.019;0.007;0.019	.|B;B;B;B;B	.|0.09377	.|0.004;0.001;0.004;0.004;0.004	T|T	0.26360|0.26360	-1.0105|-1.0105	5|10	.|0.36615	.|T	.|0.2	.|.	9.0913|9.0913	0.36612|0.36612	0.0:0.9012:0.0:0.0988|0.0:0.9012:0.0:0.0988	.|.	.|1363;1363;1044;1363;1363	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	W|L	358|1363	.|ENSP00000348984:S1363L;ENSP00000290239:S1363L;ENSP00000300278:S1363L;ENSP00000371095:S1363L	.|ENSP00000290239:S1363L	R|S	+|+	1|2	2|0	SON|SON	33847495|33847495	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.011000|0.011000	0.07611|0.07611	0.354000|0.354000	0.20146|0.20146	1.362000|1.362000	0.46000|0.46000	0.514000|0.514000	0.50259|0.50259	CGG|TCG	.		0.577	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34925625	C	T	34925625	3	4	74	1	0	0	0	0	1	0	0	0	14958	893	31	1	4098	1	SON	21	34925625	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		34925625	13204270	103	7026											
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123200037	123200037	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttacagtgcccatgacctTtcaaagtgggatttatttgc	9	16	8	8	0	1	1	1	1	0	0	1	2	1	2	2	1	3	0	2	1	3	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chrX:123200037T>C	ENST00000371160.1	+	22	2399	c.2109T>C	c.(2107-2109)ctT>ctC	p.L703L	STAG2_ENST00000371144.3_Silent_p.L703L|STAG2_ENST00000371145.3_Silent_p.L703L|STAG2_ENST00000354548.5_Silent_p.L634L|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371157.3_Silent_p.L703L|STAG2_ENST00000218089.9_Silent_p.L703L	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	703					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						CCCATGACCTTTCAAAGTGGG	0.294																																					p.L703L		.											.	STAG2-134	0			c.T2109C						.						60	61	61					X																	123200037		2202	4298	6500	SO:0001819	synonymous_variant	10735	exon22			TGACCTTTCAAAG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2109T>C	X.37:g.123200037T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	65	44	NM_001042749	0	0	0	0	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	37	CCDS14607.1																																																																																			.		0.294	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		C	123200037	T	C	123200037	2	2	74	1	0	0	0	0	0	0	0	1	15275	1828	64	3		3	STAG2	23	123200037	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		123200037	32070523	104	7027											
RER1	11079	broad.mit.edu	37	chr1	2332308	2332308	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccttacagatgacggtccttCgctacccaccaaacagaacg	12	7	7	15	3	0	3	0	1	0	2	2	3	1	3	4	1	4	1	4	1	4	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr1:2332308C>G	ENST00000605895.1	+	5	432	c.299C>G	c.(298-300)tCg>tGg	p.S100W	RER1_ENST00000488353.1_Missense_Mutation_p.S100W|RER1_ENST00000378512.1_Missense_Mutation_p.S100W|RER1_ENST00000378518.1_Missense_Mutation_p.R67G|RER1_ENST00000378513.3_Missense_Mutation_p.R67G	NM_007033.4	NP_008964.3	O15258	RER1_HUMAN	retention in endoplasmic reticulum sorting receptor 1	100					positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)	cell surface (GO:0009986)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)				endometrium(3)|kidney(1)	4	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.28e-37)|OV - Ovarian serous cystadenocarcinoma(86;8.29e-23)|GBM - Glioblastoma multiforme(42;4.71e-08)|Colorectal(212;4.73e-05)|COAD - Colon adenocarcinoma(227;0.00021)|Kidney(185;0.00116)|BRCA - Breast invasive adenocarcinoma(365;0.00459)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0182)|Lung(427;0.204)		GACGGTCCTTCGCTACCCACC	0.478																																					p.S100W													.	RER1-90	0			c.C299G						.						182	181	182					1																	2332308		1923	4127	6050	SO:0001583	missense	11079	exon5			GTCCTTCGCTACC	AF157324	CCDS41232.1	1p36	2013-10-18	2013-10-18		ENSG00000157916	ENSG00000157916			30309	protein-coding gene	gene with protein product			"RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae)"			9309388, 17668005	Standard	NM_007033		Approved		uc001aje.2	O15258	OTTHUMG00000001403	ENST00000605895.1:c.299C>G	1.37:g.2332308C>G	ENSP00000475168:p.Ser100Trp	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	183	4	NM_007033	0	0	354	354	0	O95322	Missense_Mutation	SNP	ENST00000605895.1	37	CCDS41232.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.29|12.29	1.893876|1.893876	0.33442|0.33442	.|.	.|.	ENSG00000157916|ENSG00000157916	ENST00000378518;ENST00000378513|ENST00000306256;ENST00000434662;ENST00000378512;ENST00000443438	.|.	.|.	.|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.352313	.|0.30003	.|N	.|0.010644	T|T	0.77110|0.77110	0.4082|0.4082	M|M	0.75884|0.75884	2.315|2.315	0.32657|0.32657	N|N	0.51866|0.51866	.|D;D	.|0.76494	.|0.999;0.983	.|D;P	.|0.75484	.|0.986;0.881	T|T	0.81965|0.81965	-0.0691|-0.0691	6|9	0.14656|0.72032	T|D	0.56|0.01	.|.	18.7441|18.7441	0.91785|0.91785	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|100;100	.|Q5T091;O15258	.|.;RER1_HUMAN	G|W	67|100	.|.	ENSP00000367774:R67G|ENSP00000302088:S100W	R|S	+|+	1|2	0|0	RER1|RER1	2322168|2322168	1.000000|1.000000	0.71417|0.71417	0.354000|0.354000	0.25760|0.25760	0.011000|0.011000	0.07611|0.07611	6.983000|6.983000	0.76180|0.76180	2.661000|2.661000	0.90470|0.90470	0.643000|0.643000	0.83706|0.83706	CGC|TCG	.		0.478	RER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004061.2			G	2332308	C	G	2332308	3	3	75	1	0	0	0	0	1	0	0	0	13262	893	31	4	313	4	RER1	1	2332308	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		2332308	246918313	1	7028											
NFIA	4774	broad.mit.edu	37	chr1	61554264	61554264	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaaagtccccacaatgctcTaatccagggctctgtgtcca	10	10	8	13	0	2	0	0	0	2	0	5	0	5	0	4	1	1	3	4	1	4	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr1:61554264T>C	ENST00000403491.3	+	2	955	c.471T>C	c.(469-471)tcT>tcC	p.S157S	NFIA_ENST00000485903.2_Silent_p.S157S|NFIA_ENST00000407417.3_Silent_p.S149S|NFIA_ENST00000371191.1_Silent_p.S180S|NFIA_ENST00000371187.3_Silent_p.S157S|NFIA_ENST00000371189.4_Silent_p.S202S|NFIA_ENST00000371185.2_Silent_p.S157S|NFIA_ENST00000479364.1_Intron|NFIA_ENST00000371184.2_Silent_p.S157S	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	157					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						CACAATGCTCTAATCCAGGGC	0.453																																					p.S202S													.	NFIA-92	0			c.T606C						.						79	86	84					1																	61554264		2203	4300	6503	SO:0001819	synonymous_variant	4774	exon3			ATGCTCTAATCCA	U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.471T>C	1.37:g.61554264T>C		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	108	3	NM_001145512	0	0	17	17	0	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Silent	SNP	ENST00000403491.3	37	CCDS44156.1																																																																																			.		0.453	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595		C	61554264	T	C	61554264	2	2	75	1	0	0	0	0	0	0	0	1	10396	1509	53	3		3	NFIA	1	61554264	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	59221956	61554264	187696357	2	7029											
TMED5	50999	ucsc.edu	37	chr1	93620447	93620447	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgctgttgatggattccTggagataaataaaataattt	14	15	9	3	0	0	3	0	2	0	1	1	5	1	4	1	2	1	2	1	2	5	6			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr1:93620447T>A	ENST00000370282.3	-	4	957		c.e4-2		TMED5_ENST00000483033.1_Splice_Site|TMED5_ENST00000479918.1_Splice_Site	NM_016040.4	NP_057124.3	Q9Y3A6	TMED5_HUMAN	transmembrane emp24 protein transport domain containing 5						Golgi ribbon formation (GO:0090161)|protein transport (GO:0015031)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)		GATGGATTCCTGGAGataaat	0.363																																					.													.	TMED5-91	0			c.472-2A>T						.						89	85	86					1																	93620447		2203	4300	6503	SO:0001630	splice_region_variant	50999	exon5			GATTCCTGGAGAT	BC070051	CCDS743.1, CCDS53342.1	1p22.1	2013-09-19			ENSG00000117500	ENSG00000117500			24251	protein-coding gene	gene with protein product						10810093	Standard	NM_016040		Approved	CGI-100	uc001dpn.3	Q9Y3A6	OTTHUMG00000010162	ENST00000370282.3:c.472-2A>T	1.37:g.93620447T>A		Somatic	165	0		WXS	Illumina HiSeq		123	1	NM_016040	0	0	0	0	0	B1AKT4|B2R703|D3DT38|Q96AX8	Splice_Site	SNP	ENST00000370282.3	37	CCDS743.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.001138	0.74818	.	.	ENSG00000117500	ENST00000370282;ENST00000479918;ENST00000535517	.	.	.	5.92	4.78	0.61160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5287	0.56102	0.125:0.0:0.0:0.875	.	.	.	.	.	-1	.	.	.	-	.	.	TMED5	93393035	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	7.977000	0.88081	1.044000	0.40200	0.533000	0.62120	.	.		0.363	TMED5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028076.3	NM_016040	Intron	A	93620447	T	A	93620447	5	1	75	1	0	0	0	0	0	0	1	0	16039	1594	55	5	223	5	TMED5	1	93620447	Splice_Site	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	32066183	93620447	155630174	3	7030											
ANKRD35	148741	bcgsc.ca	37	chr1	145555716	145555716	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagatggaaccgccatgatCagaagctgctggaggcagtg	12	6	15	8	1	1	3	1	1	0	2	1	6	1	5	2	3	3	3	2	3	2	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr1:145555716C>A	ENST00000355594.4	+	2	151	c.64C>A	c.(64-66)Cag>Aag	p.Q22K	ANKRD35_ENST00000544626.1_Missense_Mutation_p.Q22K	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	22										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCGCCATGATCAGAAGCTGCT	0.577																																					p.Q22K	Melanoma(9;127 754 22988 51047)												.	ANKRD35-95	0			c.C64A						.						63	61	61					1																	145555716		2203	4300	6503	SO:0001583	missense	148741	exon2			CATGATCAGAAGC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.64C>A	1.37:g.145555716C>A	ENSP00000347802:p.Gln22Lys	Somatic	62	0		WXS	Illumina HiSeq	Phase_1	102	6	NM_144698	0	0	0	0	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.620476	0.66787	.	.	ENSG00000198483	ENST00000355594;ENST00000544626	T;T	0.52295	0.67;1.44	5.99	5.99	0.97316	Ankyrin repeat-containing domain (2);	0.000000	0.46758	D	0.000272	T	0.23846	0.0577	L	0.29908	0.895	0.35906	D	0.830723	P	0.39665	0.682	B	0.35182	0.197	T	0.09997	-1.0649	10	0.38643	T	0.18	-27.8271	15.9778	0.80083	0.0:1.0:0.0:0.0	.	22	Q8N283	ANR35_HUMAN	K	22	ENSP00000347802:Q22K;ENSP00000442671:Q22K	ENSP00000347802:Q22K	Q	+	1	0	ANKRD35	144267073	0.997000	0.39634	0.997000	0.53966	0.938000	0.57974	2.958000	0.49145	2.840000	0.97914	0.655000	0.94253	CAG	.		0.577	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145555716	C	A	145555716	3	1	75	1	0	0	0	0	1	0	0	0	664	827	29	4	70	4	ANKRD35	1	145555716	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	51935269	145555716	103694905	4	7031											
XPO1	7514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	61709536	61709536	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttgtaggtgagggaaggccGacttaaggagattagccaca	12	8	14	7	1	0	2	0	1	0	1	0	5	0	3	2	4	1	1	2	4	4	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:61709536G>A	ENST00000401558.2	-	23	3678	c.2951C>T	c.(2950-2952)tCg>tTg	p.S984L	XPO1_ENST00000404992.2_Missense_Mutation_p.S984L|XPO1_ENST00000406957.1_Missense_Mutation_p.S984L|RP11-355B11.2_ENST00000603199.1_RNA|RP11-355B11.2_ENST00000605437.1_RNA|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000603652.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	984					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			AGGGAAGGCCGACTTAAGGAG	0.398			Mis		CLL																																p.S984L		.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1-229	0			c.C2951T						.						129	130	129					2																	61709536		2203	4300	6503	SO:0001583	missense	7514	exon23			AAGGCCGACTTAA	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.2951C>T	2.37:g.61709536G>A	ENSP00000384863:p.Ser984Leu	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	128	12	NM_003400	0	0	107	123	16	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953001	0.73902	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.68025	-0.3;-0.3;-0.3	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (2);Exportin 1, C-terminal (1);	0.055426	0.85682	D	0.000000	T	0.68366	0.2993	M	0.75615	2.305	0.58432	D	0.999998	B;B	0.31752	0.338;0.233	B;B	0.24848	0.034;0.056	T	0.70883	-0.4751	10	0.66056	D	0.02	-16.6961	19.6691	0.95903	0.0:0.0:1.0:0.0	.	631;984	B3KWD0;O14980	.;XPO1_HUMAN	L	984	ENSP00000384863:S984L;ENSP00000385942:S984L;ENSP00000385559:S984L	ENSP00000384863:S984L	S	-	2	0	XPO1	61563040	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.529000	0.81952	2.721000	0.93114	0.591000	0.81541	TCG	.		0.398	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		A	61709536	G	A	61709536	3	1	75	1	0	0	0	0	1	0	0	0	17478	1059	37	1	276	1	XPO1	2	61709536	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		61709536	181489837	5	7032											
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141643776	141643776	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtccaataaagtaaactttGattgaagtgaaaatcaagtg	17	12	8	4	0	1	3	1	3	0	0	2	3	2	3	1	0	1	1	1	0	9	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:141643776G>C	ENST00000389484.3	-	24	4866	c.3895C>G	c.(3895-3897)Caa>Gaa	p.Q1299E		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1299					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.Q1299K(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGTAAACTTTGATTGAAGTGA	0.328										TSP Lung(27;0.18)																											p.Q1299E	Colon(99;50 2074 2507 20106)	.											.	LRP1B-311	1	Substitution - Missense(1)	endometrium(1)	c.C3895G						.						77	79	78					2																	141643776		2202	4299	6501	SO:0001583	missense	53353	exon24			AACTTTGATTGAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3895C>G	2.37:g.141643776G>C	ENSP00000374135:p.Gln1299Glu	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	97	80	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144239	0.57044	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90620	-2.7;-2.7	5.68	5.68	0.88126	Six-bladed beta-propeller, TolB-like (1);	0.140025	0.48767	D	0.000173	T	0.81597	0.4856	N	0.13043	0.29	0.42707	D	0.993639	B;B	0.34015	0.009;0.435	B;B	0.24974	0.009;0.057	T	0.79825	-0.1640	10	0.12430	T	0.62	.	19.7974	0.96491	0.0:0.0:1.0:0.0	.	482;1299	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	E	1299;1237;444	ENSP00000374135:Q1299E;ENSP00000413239:Q444E	ENSP00000374135:Q1299E	Q	-	1	0	LRP1B	141360246	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.640000	0.98453	2.673000	0.90976	0.650000	0.86243	CAA	.		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141643776	G	C	141643776	3	2	75	1	0	0	0	0	1	0	0	0	8980	1299	45	4	10176	4	LRP1B	2	141643776	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	79934240	141643776	101555597	6	7033											
ARL6IP6	151188	broad.mit.edu	37	chr2	153591621	153591621	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaatgtttcctcctactcctCtttcacctgccaggttcaag	7	14	6	14	0	3	0	2	0	1	0	6	1	6	0	5	1	2	2	5	1	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:153591621C>T	ENST00000326446.5	+	3	1279	c.568C>T	c.(568-570)Ctt>Ttt	p.L190F	ARL6IP6_ENST00000463690.1_3'UTR	NM_152522.5	NP_689735.1	Q8N6S5	AR6P6_HUMAN	ADP-ribosylation factor-like 6 interacting protein 6	190						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	5						TCCTACTCCTCTTTCACCTGC	0.378																																					p.L190F													.	ARL6IP6-90	0			c.C568T						.						121	117	118					2																	153591621		2202	4300	6502	SO:0001583	missense	151188	exon3			ACTCCTCTTTCAC	AK023109	CCDS2197.1	2q23	2014-05-12	2014-05-12		ENSG00000177917	ENSG00000177917			24048	protein-coding gene	gene with protein product							Standard	NM_152522		Approved	MGC33864	uc002tyn.3	Q8N6S5	OTTHUMG00000131901	ENST00000326446.5:c.568C>T	2.37:g.153591621C>T	ENSP00000315357:p.Leu190Phe	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	134	5	NM_152522	0	0	33	34	1	B2RDS6|Q7Z4G7	Missense_Mutation	SNP	ENST00000326446.5	37	CCDS2197.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996919	0.74818	.	.	ENSG00000177917	ENST00000326446	.	.	.	5.87	5.0	0.66597	.	0.180871	0.36134	N	0.002768	T	0.64216	0.2578	M	0.69823	2.125	0.54753	D	0.999986	B;P	0.50272	0.197;0.933	B;P	0.47786	0.09;0.557	T	0.69935	-0.5010	9	0.87932	D	0	-18.2762	13.9229	0.63942	0.0:0.9261:0.0:0.0739	.	190;190	B3KMZ5;Q8N6S5	.;AR6P6_HUMAN	F	190	.	ENSP00000315357:L190F	L	+	1	0	ARL6IP6	153299867	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.883000	0.69721	1.498000	0.48600	-0.136000	0.14681	CTT	.		0.378	ARL6IP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254852.3	NM_152522		T	153591621	C	T	153591621	3	4	75	1	0	0	0	0	1	0	0	0	946	913	32	2	578	2	ARL6IP6	2	153591621	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	11947845	153591621	89607752	7	7034											
FSIP2	401024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	186671400	186671400	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgctaagtttttagaagaTgttattactgagatggttaa	12	15	9	5	1	0	3	0	1	0	3	0	4	0	3	1	1	1	4	1	1	6	7			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:186671400T>C	ENST00000424728.1	+	17	17367	c.17367T>C	c.(17365-17367)gaT>gaC	p.D5789D	FSIP2_ENST00000343098.5_Silent_p.D5878D			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5789										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TTTTAGAAGATGTTATTACTG	0.333																																					p.D5878D		.											.	FSIP2-90	0			c.T17634C						.						74	70	71					2																	186671400		1805	4076	5881	SO:0001819	synonymous_variant	401024	exon17			AGAAGATGTTATT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.17367T>C	2.37:g.186671400T>C		Somatic	89	1		WXS	Illumina HiSeq	Phase_I	62	60	NM_173651	0	0	0	0	0	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				.		0.333	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		C	186671400	T	C	186671400	2	2	75	1	0	0	0	0	0	0	0	1	6094	1461	51	3		3	FSIP2	2	186671400	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	33079779	186671400	56527973	8	7035											
ACADL	33	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	211057526	211057526	+	Splice_Site	DEL	A	A	-																															tgtatcagaaaactatacttActttgcaattgggtactccc																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:211057526delA	ENST00000233710.3	-	10	1427		c.e10+1		AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain						carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AACTATACTTACTTTGCAATT	0.383																																					.		.											.	ACADL-90	0			c.1199+2T>-						.						77	72	74					2																	211057526		2203	4300	6503	SO:0001630	splice_region_variant	33	exon11			.	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.1199+1T>-	2.37:g.211057526delA		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	66	63	NM_001608	0	0	0	0	0	B2R8T3|Q8IUN8	Splice_Site	DEL	ENST00000233710.3	37	CCDS2389.1																																																																																			.		0.383	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	Intron	-	211057526	A	-	211057526	8	5	75	1	0	1	0	1	0	0	1	0	112	405	14	0	99	0	ACADL	2	211057526	Splice_Site	DEL	A	TCGA-BQ-5891-01A-11D-1589-08	24386126	211057526	32141847	9	7036	78	2									
ACADL	33	bcgsc.ca	37	chr2	211057527	211057527	+	Splice_Site	SNP	C	C	G																															gtatcagaaaactatacttaCtttgcaattgggtactccca																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:211057527C>G	ENST00000233710.3	-	10	1427		c.e10+1		AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain						carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		ACTATACTTACTTTGCAATTG	0.383																																					.													.	ACADL-90	0			c.1199+1G>C						.						78	73	74					2																	211057527		2203	4300	6503	SO:0001630	splice_region_variant	33	exon11			TACTTACTTTGCA	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.1199+1G>C	2.37:g.211057527C>G		Somatic	63	0		WXS	Illumina HiSeq	Phase_1	67	63	NM_001608	0	0	0	0	0	B2R8T3|Q8IUN8	Splice_Site	SNP	ENST00000233710.3	37	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767632	0.69878	.	.	ENSG00000115361	ENST00000233710	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1672	0.98154	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ACADL	210765772	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	6.963000	0.76055	2.861000	0.98227	0.655000	0.94253	.	.		0.383	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	Intron	G	211057527	C	G	211057527	5	3	75	1	0	0	0	0	0	0	1	0	112	579	20	4	100	4	ACADL	2	211057527	Splice_Site	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	1	211057527	32141846	10	7037	78	2									
OXTR	5021	ucsc.edu;bcgsc.ca	37	chr3	8809676	8809676	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcgagtgcttctggcgtgtGgtgcgcagcgccagcagcac	5	7	16	13	5	1	0	0	0	1	0	1	1	1	0	1	2	5	4	1	2	0	1	rs534029823		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:8809676G>A	ENST00000316793.3	-	3	822	c.198C>T	c.(196-198)acC>acT	p.T66T	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	66					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	TCTGGCGTGTGGTGCGCAGCG	0.657																																					p.T66T													.	OXTR-68	0			c.C198T						.						35	32	33					3																	8809676		2197	4295	6492	SO:0001819	synonymous_variant	5021	exon3			GCGTGTGGTGCGC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"GPCR / Class A : Vasopressin and oxytocin receptors"	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.198C>T	3.37:g.8809676G>A		Somatic	22	0		WXS	Illumina HiSeq		20	4	NM_000916	0	0	0	0	0	Q15071	Silent	SNP	ENST00000316793.3	37	CCDS2570.1																																																																																			.		0.657	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2			A	8809676	G	A	8809676	2	1	75	1	0	0	0	0	0	0	0	1	11364	1335	47	2		2	OXTR	3	8809676	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		8809676	189212754	11	7038											
CCR5	1234	broad.mit.edu;bcgsc.ca	37	chr3	46415326	46415326	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaaactacctcttagtcttCttccaaaagcacattgccaa	14	11	4	12	0	3	1	0	0	3	1	4	1	4	1	3	0	4	1	3	0	6	5			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:46415326C>T	ENST00000292303.4	+	2	1079	c.933C>T	c.(931-933)ttC>ttT	p.F311F	CCR5_ENST00000445772.1_Silent_p.F311F|RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000343801.4_Silent_p.F311F	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	311					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TCTTAGTCTTCTTCCAAAAGC	0.502																																					p.F311F													.	CCR5-993	0			c.C933T						.						168	163	164					3																	46415326		2203	4296	6499	SO:0001819	synonymous_variant	1234	exon3			AGTCTTCTTCCAA		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.933C>T	3.37:g.46415326C>T		Somatic	300	0		WXS	Illumina HiSeq	Phase_I	283	8	NM_000579	0	0	3	3	0	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Silent	SNP	ENST00000292303.4	37	CCDS2739.1																																																																																			.		0.502	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		T	46415326	C	T	46415326	2	4	75	1	0	0	0	0	0	0	0	1	2950	912	32	2		2	CCR5	3	46415326	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	37605650	46415326	151607104	12	7039											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	47162849	47162850	+	Frame_Shift_Del	DEL	TT	TT	-																															gtcagaatagtgtctataacTttgactgctccgagaagaac																								rs114327122		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:47162849_47162850delTT	ENST00000409792.3	-	3	3318_3319	c.3276_3277delAA	c.(3274-3279)caaagtfs	p.S1093fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1093					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.S1093R(1)|p.S590R(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTCTATAACTTTGACTGCTCC	0.416			"N, F, S, Mis"		clear cell renal carcinoma																																p.1092_1093del		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	2	Substitution - Missense(2)	large_intestine(2)	c.3276_3277del						.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3276_3277delAA	3.37:g.47162849_47162850delTT	ENSP00000386759:p.Ser1093fs	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	141	121	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.416	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47162850	TT	-	47162849	7	5	75	1	0	1	0	1	0	0	0	0	14163	1609	56	0	4493	0	SETD2	3	47162849	Frame_Shift_Del	DEL	TT	TCGA-BQ-5891-01A-11D-1589-08	747523	47162849	150859581	13	7040											
ACTL6A	86	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179304341	179304341	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcttctatttcagagtatgcGgttgaaattgattgcaaata	12	16	8	5	1	3	3	1	2	2	1	3	3	3	3	0	1	2	3	0	1	5	8			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:179304341G>A	ENST00000429709.2	+	13	1343	c.1130G>A	c.(1129-1131)cGg>cAg	p.R377Q	RP11-15L13.4_ENST00000608818.1_RNA|ACTL6A_ENST00000450518.2_Missense_Mutation_p.R335Q|ACTL6A_ENST00000392662.1_Missense_Mutation_p.R335Q|RP11-145M9.6_ENST00000610007.1_RNA	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	377					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			CAGAGTATGCGGTTGAAATTG	0.348																																					p.R377Q		.											.	ACTL6A-91	0			c.G1130A						.						88	88	88					3																	179304341		2203	4300	6503	SO:0001583	missense	86	exon13			GTATGCGGTTGAA	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1130G>A	3.37:g.179304341G>A	ENSP00000397552:p.Arg377Gln	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	61	53	NM_004301	0	0	0	2	2	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	37	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140591	0.94560	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.94687	-3.49;-3.49;-3.49	5.91	4.07	0.47477	.	0.049963	0.85682	D	0.000000	D	0.95984	0.8692	L	0.59436	1.845	0.58432	D	0.999997	D	0.76494	0.999	D	0.64321	0.924	D	0.95826	0.8854	10	0.87932	D	0	.	15.2754	0.73737	0.0:0.0:0.7438:0.2562	.	377	O96019	ACL6A_HUMAN	Q	377;335;335	ENSP00000397552:R377Q;ENSP00000394014:R335Q;ENSP00000376430:R335Q	ENSP00000376430:R335Q	R	+	2	0	ACTL6A	180787035	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.371000	0.97162	0.789000	0.33779	0.655000	0.94253	CGG	.		0.348	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		A	179304341	G	A	179304341	3	1	75	1	0	0	0	0	1	0	0	0	198	1116	39	1	1180	1	ACTL6A	3	179304341	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	132141492	179304341	18718089	14	7041											
SH3BP2	6452	hgsc.bcm.edu	37	chr4	2824707	2824707	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaacgctgcgtctactactTcaagagtagcacctctgcct	10	10	7	14	2	3	1	1	0	2	1	3	1	3	1	2	0	6	3	2	0	5	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr4:2824707T>C	ENST00000356331.5	+	3	443	c.182T>C	c.(181-183)tTc>tCc	p.F61S	SH3BP2_ENST00000442312.2_Missense_Mutation_p.F89S|SH3BP2_ENST00000503393.2_Missense_Mutation_p.F118S|SH3BP2_ENST00000511747.1_Missense_Mutation_p.F61S|SH3BP2_ENST00000389838.2_Missense_Mutation_p.F61S|SH3BP2_ENST00000452765.2_Missense_Mutation_p.F61S|SH3BP2_ENST00000435136.2_Missense_Mutation_p.F61S	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	61	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GTCTACTACTTCAAGAGTAGC	0.637									Cherubism																												p.F118S		.											.	SH3BP2-514	0			c.T353C						.						76	65	69					4																	2824707		2203	4300	6503	SO:0001583	missense	6452	exon3	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	ACTACTTCAAGAG	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	10825	protein-coding gene	gene with protein product		602104	"Cherubism"			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.182T>C	4.37:g.2824707T>C	ENSP00000348685:p.Phe61Ser	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001145856	0	0	5	5	0	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	37	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.538605	0.65085	.	.	ENSG00000087266	ENST00000452765;ENST00000389838;ENST00000503219;ENST00000504294;ENST00000508385;ENST00000512014;ENST00000513095;ENST00000442312;ENST00000502260;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	T;T;T;T;T;T;T;T;T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49;2.49	4.24	4.24	0.50183	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.34250	0.0891	M	0.70108	2.13	0.53005	D	0.999965	D;D;P;P	0.69078	0.99;0.997;0.93;0.939	D;D;P;P	0.68621	0.932;0.959;0.462;0.697	T	0.13926	-1.0491	10	0.87932	D	0	-16.0505	12.9914	0.58620	0.0:0.0:0.0:1.0	.	89;89;118;61	B4DT04;B7Z9B6;D6R919;P78314	.;.;.;3BP2_HUMAN	S	61;61;61;61;61;61;61;89;61;61;61;118;61	ENSP00000409746:F61S;ENSP00000374488:F61S;ENSP00000422796:F61S;ENSP00000423275:F61S;ENSP00000424917:F61S;ENSP00000424105:F61S;ENSP00000423823:F61S;ENSP00000388152:F89S;ENSP00000425537:F61S;ENSP00000403231:F61S;ENSP00000424846:F61S;ENSP00000422168:F118S;ENSP00000348685:F61S	ENSP00000348685:F61S	F	+	2	0	SH3BP2	2794505	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	7.106000	0.77039	1.568000	0.49683	0.402000	0.26972	TTC	.		0.637	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		C	2824707	T	C	2824707	3	2	75	1	0	0	0	0	1	0	0	0	14277	1783	62	3	447	3	SH3BP2	4	2824707	Missense_Mutation	SNP	T	TCGA-BQ-5891-01A-11D-1589-08		2824707	188329569	15	7042											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811129	140811129	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgttgctgTtgctgtttctgctgcatgag	2	17	13	9	0	1	1	0	1	1	0	1	1	1	1	0	0	8	11	0	0	0	3	rs62344941		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr4:140811129T>C	ENST00000509479.2	-	2	2317	c.1461A>G	c.(1459-1461)caA>caG	p.Q487Q	MAML3_ENST00000398940.1_Silent_p.Q26Q|MAML3_ENST00000327122.5_Silent_p.Q331Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgttgctgttgctgtttct	0.552																																					p.Q487Q		.											.	MAML3-455	0			c.A1461G						.						18	21	20					4																	140811129		2197	4294	6491	SO:0001819	synonymous_variant	55534	exon2			TTGCTGTTGCTGT	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1461A>G	4.37:g.140811129T>C		Somatic	27	1		WXS	Illumina HiSeq	Phase_I	18	3	NM_018717	0	0	2	2	0		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.		0.552	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			C	140811129	T	C	140811129	2	2	75	1	0	0	0	0	0	0	0	1	9232	1722	60	3		3	MAML3	4	140811129	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	137986422	140811129	50343147	16	7043											
HAND2	9464	broad.mit.edu	37	chr4	174449979	174449979	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctggtcgtccttggccagCaggtccatgaggtaggcgat	6	11	14	10	2	1	1	0	1	1	0	4	2	3	1	3	5	1	2	3	5	1	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr4:174449979C>T	ENST00000359562.4	-	1	1401	c.462G>A	c.(460-462)ctG>ctA	p.L154L	HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000503474.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000502896.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2_ENST00000505300.1_5'UTR	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	154					adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		CCTTGGCCAGCAGGTCCATGA	0.577																																					p.L154L													.	HAND2-91	0			c.G462A						.						145	128	134					4																	174449979		2203	4300	6503	SO:0001819	synonymous_variant	9464	exon1			GGCCAGCAGGTCC	AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.462G>A	4.37:g.174449979C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	86	4	NM_021973	0	0	0	0	0	B6ECG9|O95300|O95301|P97833|Q494T1	Silent	SNP	ENST00000359562.4	37	CCDS3819.1																																																																																			.		0.577	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			T	174449979	C	T	174449979	2	4	75	1	0	0	0	0	0	0	0	1	6971	697	25	2		2	HAND2	4	174449979	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	33638850	174449979	16704297	17	7044											
KLHL3	26249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	136963990	136963990	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagagcagtcattacctgcGttgcgccggcacatgttcat	9	10	11	11	3	2	1	2	0	0	1	2	2	2	1	2	1	4	4	2	1	1	3	rs562736621		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:136963990G>A	ENST00000309755.4	-	13	2030	c.1587C>T	c.(1585-1587)aaC>aaT	p.N529N	KLHL3_ENST00000541417.1_3'UTR|KLHL3_ENST00000508657.1_Silent_p.N497N|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000506491.1_Silent_p.N447N	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	529			N -> K (in PHA2D; impaired interaction with WNK1). {ECO:0000269|PubMed:22406640}.		distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		CATTACCTGCGTTGCGCCGGC	0.537																																					p.N529N		.											.	KLHL3-90	0			c.C1587T						.						219	189	199					5																	136963990		2203	4300	6503	SO:0001819	synonymous_variant	26249	exon13			ACCTGCGTTGCGC	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"Kelch-like", "BTB/POZ domain containing"	6354	protein-coding gene	gene with protein product		605775	"kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)"			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1587C>T	5.37:g.136963990G>A		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	260	90	NM_017415	0	0	0	0	0	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																			.		0.537	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			A	136963990	G	A	136963990	2	1	75	1	0	0	0	0	0	0	0	1	8404	1136	40	1		1	KLHL3	5	136963990	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		136963990	43951270	18	7045											
PCDHGA1	56114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140711928	140711928	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaccagaacgacaacgcGcccgagatcctgtaccccgc	10	4	10	17	5	0	2	0	0	0	2	1	5	1	3	5	1	3	1	5	1	3	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:140711928G>A	ENST00000517417.1	+	1	1677	c.1677G>A	c.(1675-1677)gcG>gcA	p.A559A	PCDHGA1_ENST00000378105.3_Silent_p.A559A	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	559	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGACAACGCGCCCGAGATCC	0.647																																					p.A559A		.											.	PCDHGA1-137	0			c.G1677A						.						130	144	140					5																	140711928		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			CAACGCGCCCGAG	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1677G>A	5.37:g.140711928G>A		Somatic	320	0		WXS	Illumina HiSeq	Phase_I	431	204	NM_018912	0	0	4	6	2	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																			.		0.647	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140711928	G	A	140711928	2	1	75	1	0	0	0	0	0	0	0	1	11576	1074	38	1		1	PCDHGA1	5	140711928	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	3747938	140711928	40203332	19	7046											
DRD1	1812	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	174870046	174870046	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaggatacgaacagagaaGtccctctccaccaccagccc	12	5	9	15	1	1	2	0	1	1	1	3	5	2	3	5	1	3	0	5	1	3	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:174870046G>A	ENST00000393752.2	-	2	1049	c.57C>T	c.(55-57)gaC>gaT	p.D19D		NM_000794.3	NP_000785.1	P21728	DRD1_HUMAN	dopamine receptor D1	19					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult walking behavior (GO:0007628)|astrocyte development (GO:0014002)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|cellular response to catecholamine stimulus (GO:0071870)|cerebral cortex GABAergic interneuron migration (GO:0021853)|conditioned taste aversion (GO:0001661)|dentate gyrus development (GO:0021542)|dopamine metabolic process (GO:0042417)|dopamine transport (GO:0015872)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose import (GO:0046323)|grooming behavior (GO:0007625)|habituation (GO:0046959)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|maternal behavior (GO:0042711)|mating behavior (GO:0007617)|memory (GO:0007613)|neuronal action potential (GO:0019228)|operant conditioning (GO:0035106)|peristalsis (GO:0030432)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|prepulse inhibition (GO:0060134)|protein import into nucleus (GO:0006606)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|sensitization (GO:0046960)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|transmission of nerve impulse (GO:0019226)|vasodilation (GO:0042311)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GAACAGAGAAGTCCCTCTCCA	0.572																																					p.D19D		.											.	DRD1-93	0			c.C57T						.						106	108	107					5																	174870046		2203	4300	6503	SO:0001819	synonymous_variant	1812	exon2			AGAGAAGTCCCTC	X55760	CCDS4393.1	5q34-q35	2012-08-08			ENSG00000184845	ENSG00000184845		"GPCR / Class A : Dopamine receptors"	3020	protein-coding gene	gene with protein product		126449					Standard	NM_000794		Approved		uc003mcz.3	P21728	OTTHUMG00000130557	ENST00000393752.2:c.57C>T	5.37:g.174870046G>A		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	190	77	NM_000794	0	0	0	0	0	B2RA44|Q4QRJ0	Silent	SNP	ENST00000393752.2	37	CCDS4393.1																																																																																			.		0.572	DRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252982.2	NM_000794		A	174870046	G	A	174870046	2	1	75	1	0	0	0	0	0	0	0	1	4767	1020	36	2		2	DRD1	5	174870046	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	34158118	174870046	6045214	20	7047											
UBR2	23304	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42657391	42657391	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taccttgatgactatggggaGaccgaccagggactcaggta	11	8	13	9	1	1	3	1	2	0	1	1	6	1	4	3	4	1	1	3	4	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:42657391G>A	ENST00000372899.1	+	46	5367	c.5109G>A	c.(5107-5109)gaG>gaA	p.E1703E	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Silent_p.E1703E	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1703					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			ACTATGGGGAGACCGACCAGG	0.517																																					p.E1703E		.											.	UBR2-94	0			c.G5109A						.						254	259	257					6																	42657391		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon46			TGGGGAGACCGAC	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.5109G>A	6.37:g.42657391G>A		Somatic	495	0		WXS	Illumina HiSeq	Phase_I	393	351	NM_015255	0	0	0	48	48	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			.		0.517	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		A	42657391	G	A	42657391	2	1	75	1	0	0	0	0	0	0	0	1	16935	933	33	2		2	UBR2	6	42657391	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		42657391	128457676	21	7048											
DOPEY1	23033	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	83862077	83862077	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgtccatgcattgacattActctctgaggtaaatattaa	13	14	7	7	0	1	2	0	2	1	0	3	2	2	2	1	1	2	2	1	1	5	5			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:83862077A>G	ENST00000349129.2	+	30	6380	c.6120A>G	c.(6118-6120)ttA>ttG	p.L2040L	DOPEY1_ENST00000369739.3_Silent_p.L2031L|DOPEY1_ENST00000237163.5_Intron|DOPEY1_ENST00000484282.1_3'UTR	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2040					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CATTGACATTACTCTCTGAGG	0.294																																					p.L2040L		.											.	DOPEY1-155	0			c.A6120G						.						62	63	63					6																	83862077		2203	4291	6494	SO:0001819	synonymous_variant	23033	exon30			GACATTACTCTCT	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6120A>G	6.37:g.83862077A>G		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	66	4	NM_015018	0	0	0	0	0	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																			.		0.294	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83862077	A	G	83862077	2	3	75	1	0	0	0	0	0	0	0	1	4718	388	14	3		3	DOPEY1	6	83862077	Silent	SNP	A	TCGA-BQ-5891-01A-11D-1589-08	41204686	83862077	87252990	22	7049											
USP45	85015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	99930682	99930682	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagtggtcctttttcagtCtccttcatgctgtgaagaaa	10	14	9	8	0	3	2	2	1	1	1	5	3	4	2	2	1	1	1	2	1	3	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:99930682C>A	ENST00000327681.6	-	8	1324	c.792G>T	c.(790-792)gaG>gaT	p.E264D	USP45_ENST00000500704.2_Missense_Mutation_p.E264D|USP45_ENST00000369233.2_Missense_Mutation_p.E264D|USP45_ENST00000329966.6_Missense_Mutation_p.E264D|USP45_ENST00000392738.2_Intron|USP45_ENST00000472914.2_Missense_Mutation_p.E264D	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	264	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTTTTCAGTCTCCTTCATGC	0.383																																					p.E264D		.											.	USP45-637	0			c.G792T						.						82	85	84					6																	99930682		2203	4300	6503	SO:0001583	missense	85015	exon8			TTCAGTCTCCTTC	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.792G>T	6.37:g.99930682C>A	ENSP00000333376:p.Glu264Asp	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	86	80	NM_001080481	0	0	0	2	2	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.164251	0.38217	.	.	ENSG00000123552	ENST00000500704;ENST00000327681;ENST00000369233;ENST00000511403;ENST00000329966;ENST00000472914	T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47	5.32	3.4	0.38934	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.16257	0.0391	L	0.41961	1.31	0.80722	D	1	B;B	0.30482	0.039;0.281	B;B	0.39185	0.039;0.293	T	0.03630	-1.1018	10	0.42905	T	0.14	.	9.9212	0.41466	0.0:0.7614:0.0:0.2386	.	264;264	D6RBV3;Q70EL2	.;UBP45_HUMAN	D	264;264;264;20;264;264	ENSP00000424372:E264D;ENSP00000333376:E264D;ENSP00000358236:E264D;ENSP00000423374:E20D;ENSP00000330540:E264D;ENSP00000423993:E264D	ENSP00000333376:E264D	E	-	3	2	USP45	100037403	0.155000	0.22806	0.998000	0.56505	0.743000	0.42351	-0.128000	0.10531	0.616000	0.30141	0.557000	0.71058	GAG	.		0.383	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		A	99930682	C	A	99930682	3	1	75	1	0	0	0	0	1	0	0	0	17109	912	32	4	1696	4	USP45	6	99930682	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	16068605	99930682	71184385	23	7050											
HOXA5	3202	broad.mit.edu	37	chr7	27182685	27182685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgacttatgtgcagcttgCgcatccaggggtagatctgg	8	11	13	9	1	1	2	0	1	1	1	2	2	2	2	1	3	3	4	1	3	2	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr7:27182685C>T	ENST00000222726.3	-	1	602	c.542G>A	c.(541-543)cGc>cAc	p.R181H	HOXA5_ENST00000520854.1_5'Flank|HOXA3_ENST00000521401.1_5'Flank|HOXA6_ENST00000521478.1_5'Flank|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000518848.1_RNA	NM_019102.3	NP_061975.2	P20719	HXA5_HUMAN	homeobox A5	181					anterior/posterior pattern specification (GO:0009952)|bronchiole development (GO:0060435)|cell migration (GO:0016477)|cell-cell signaling involved in mammary gland development (GO:0060764)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|intestinal epithelial cell maturation (GO:0060574)|lung alveolus development (GO:0048286)|lung goblet cell differentiation (GO:0060480)|lung-associated mesenchyme development (GO:0060484)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal-epithelial cell signaling (GO:0060638)|multicellular organism growth (GO:0035264)|negative regulation of angiogenesis (GO:0016525)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of apoptotic process (GO:0043065)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|respiratory system process (GO:0003016)|thyroid gland development (GO:0030878)|trachea cartilage morphogenesis (GO:0060535)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(12)|skin(1)	16						GTGCAGCTTGCGCATCCAGGG	0.677																																					p.R181H	Colon(119;75 2200 7557 42868)												.	HOXA5-514	0			c.G542A						.						92	114	107					7																	27182685		2203	4300	6503	SO:0001583	missense	3202	exon1			AGCTTGCGCATCC		CCDS5406.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106004	ENSG00000106004		"Homeoboxes / ANTP class : HOXL subclass"	5106	protein-coding gene	gene with protein product		142952	"homeo box A5"	HOX1C, HOX1		1973146, 1358459	Standard	NM_019102		Approved		uc003syn.2	P20719	OTTHUMG00000023214	ENST00000222726.3:c.542G>A	7.37:g.27182685C>T	ENSP00000222726:p.Arg181His	Somatic	275	0		WXS	Illumina HiSeq	Phase_I	459	5	NM_019102	0	0	18	18	0	A4D179|O43367|Q96CY6	Missense_Mutation	SNP	ENST00000222726.3	37	CCDS5406.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948206	0.73787	.	.	ENSG00000106004	ENST00000222726	D	0.95656	-3.77	5.53	5.53	0.82687	Homeodomain-like (1);Homeobox protein, antennapedia type, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97898	0.9309	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	D	0.98528	1.0626	10	0.87932	D	0	.	19.0547	0.93058	0.0:1.0:0.0:0.0	.	181	P20719	HXA5_HUMAN	H	181	ENSP00000222726:R181H	ENSP00000222726:R181H	R	-	2	0	HOXA5	27149210	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.448000	0.80631	2.606000	0.88127	0.591000	0.81541	CGC	.		0.677	HOXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358705.1			T	27182685	C	T	27182685	3	4	75	1	0	0	0	0	1	0	0	0	7316	768	27	1	278	1	HOXA5	7	27182685	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		27182685	131955978	24	7051											
C7orf41	222166	broad.mit.edu	37	chr7	30197075	30197075	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tactggggcttccggatgcaGatgacgatgcgtttgaagag	9	10	15	7	3	0	4	0	2	0	2	1	6	1	5	1	3	3	3	1	3	2	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr7:30197075G>A	ENST00000324453.8	+	3	634	c.307G>A	c.(307-309)Gat>Aat	p.D103N	C7orf41_ENST00000455738.1_Missense_Mutation_p.D70N|C7orf41_ENST00000409688.1_Missense_Mutation_p.D62N|C7orf41_ENST00000324489.5_Missense_Mutation_p.D70N|C7orf41_ENST00000415604.1_Missense_Mutation_p.D103N|AC007036.5_ENST00000511893.1_RNA	NM_152793.2	NP_690006.2	Q8N3F0	MTURN_HUMAN		103					multicellular organismal development (GO:0007275)					NS(1)|large_intestine(2)	3						TCCGGATGCAGATGACGATGC	0.562																																					p.D103N													.	C7orf41-90	0			c.G307A						.						157	167	163					7																	30197075		2203	4300	6503	SO:0001583	missense	222166	exon3			GATGCAGATGACG																												ENST00000324453.8:c.307G>A	7.37:g.30197075G>A	ENSP00000324204:p.Asp103Asn	Somatic	297	0		WXS	Illumina HiSeq	Phase_I	492	7	NM_152793	0	1	38	39	0	B8ZZW9|Q8N791|Q8N8M4|Q8NEX2	Missense_Mutation	SNP	ENST00000324453.8	37	CCDS5425.2	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860130	0.71834	.	.	ENSG00000180354	ENST00000324453;ENST00000409688;ENST00000415604;ENST00000324489;ENST00000455738	.	.	.	6.17	6.17	0.99709	.	0.119080	0.56097	D	0.000038	T	0.55609	0.1931	N	0.24115	0.695	0.49299	D	0.999771	B	0.25809	0.135	B	0.30855	0.121	T	0.53085	-0.8488	9	0.66056	D	0.02	-9.1856	19.8676	0.96824	0.0:0.0:1.0:0.0	.	103	Q8N3F0	CG041_HUMAN	N	103;62;103;70;70	.	ENSP00000324204:D103N	D	+	1	0	C7orf41	30163600	1.000000	0.71417	0.985000	0.45067	0.614000	0.37383	8.028000	0.88798	2.941000	0.99782	0.655000	0.94253	GAT	.		0.562	C7orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250409.1			A	30197075	G	A	30197075	3	1	75	1	0	0	0	0	1	0	0	0	2397	942	33	2	317	2	C7orf41	7	30197075	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	3014390	30197075	128941588	25	7052											
IRF5	3663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	128587532	128587532	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggcccctgcctgccagcctgCcccctgcaggcgaacagctc	5	5	11	20	1	0	0	0	0	0	0	1	1	0	0	7	2	7	2	7	2	1	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr7:128587532C>T	ENST00000402030.2	+	6	754	c.682C>T	c.(682-684)Ccc>Tcc	p.P228S	IRF5_ENST00000477535.1_Intron|IRF5_ENST00000357234.5_Missense_Mutation_p.P244S|IRF5_ENST00000473745.1_Missense_Mutation_p.P228S|IRF5_ENST00000249375.4_Missense_Mutation_p.P228S	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	228					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						TGCCAGCCTGCCCCCTGCAGG	0.682																																					p.P244S		.											.	IRF5-226	0			c.C730T						.						15	18	17					7																	128587532		2120	4170	6290	SO:0001583	missense	3663	exon6			AGCCTGCCCCCTG		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.682C>T	7.37:g.128587532C>T	ENSP00000385352:p.Pro228Ser	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	54	23	NM_001098629	0	0	47	84	37	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	37	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630932	0.67015	.	.	ENSG00000128604	ENST00000357234;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D	0.97529	-4.4;-4.42;-4.42;-4.42	5.26	2.02	0.26589	.	0.848323	0.10423	N	0.676477	D	0.95175	0.8436	L	0.53249	1.67	0.36808	D	0.885713	B;B	0.30634	0.043;0.288	B;B	0.35413	0.027;0.202	D	0.93066	0.6478	10	0.56958	D	0.05	-11.2851	8.0991	0.30846	0.1597:0.4338:0.4065:0.0	.	228;244	Q13568;Q13568-2	IRF5_HUMAN;.	S	244;228;228;228;218	ENSP00000349770:P244S;ENSP00000385352:P228S;ENSP00000249375:P228S;ENSP00000419149:P228S	ENSP00000249375:P228S	P	+	1	0	IRF5	128374768	0.309000	0.24518	0.269000	0.24586	0.935000	0.57460	0.974000	0.29436	0.667000	0.31107	0.561000	0.74099	CCC	.		0.682	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627		T	128587532	C	T	128587532	3	4	75	1	0	0	0	0	1	0	0	0	7854	739	26	2	748	2	IRF5	7	128587532	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	98390457	128587532	30551131	26	7053											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccactcaccattctgggaGggcgacggcgacggcgacgg	7	4	17	13	6	2	0	1	0	1	0	2	4	2	1	2	6	0	0	2	6	0	1	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		.											.	PODXL-136	0			c.C90G						.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	7.37:g.131241029G>C		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	7	3	NM_001018111	0	0	0	0	0	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	75	1	0	0	0	0	0	0	0	1	12206	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	2653497	131241029	27897634	27	7054											
KIAA1429	25962	broad.mit.edu	37	chr8	95503873	95503873	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgtcctcctctattgccTgaaaacccaccacgggaaga	10	7	7	17	2	1	2	0	1	1	1	3	3	3	3	7	1	2	0	7	1	4	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr8:95503873T>C	ENST00000297591.5	-	22	5148	c.5073A>G	c.(5071-5073)tcA>tcG	p.S1691S	KIAA1429_ENST00000437199.1_3'UTR	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1691					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CTCTATTGCCTGAAAACCCAC	0.428																																					p.S1691S													.	KIAA1429-92	0			c.A5073G						.						135	126	129					8																	95503873		2203	4300	6503	SO:0001819	synonymous_variant	25962	exon22			ATTGCCTGAAAAC	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.5073A>G	8.37:g.95503873T>C		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	142	3	NM_015496	0	0	38	39	1	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			.		0.428	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		C	95503873	T	C	95503873	2	2	75	1	0	0	0	0	0	0	0	1	8252	1567	55	3		3	KIAA1429	8	95503873	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08		95503873	50860149	28	7055											
BAAT	570	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	104125282	104125282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatacagagactaccccaaCgcctgagccaaagacctgaa	16	4	7	14	1	0	4	0	2	0	2	0	5	0	4	5	0	4	0	5	0	5	2	rs141722672	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr9:104125282C>T	ENST00000395051.3	-	3	755	c.685G>A	c.(685-687)Gtt>Att	p.V229I	BAAT_ENST00000259407.2_Missense_Mutation_p.V229I			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	229					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	ACTACCCCAACGCCTGAGCCA	0.388													C|||	4	0.000798722	0.0015	0	5008	,	,		18562	0.002		0	False		,,,				2504	0				p.V229I		.											.	BAAT-228	0			c.G685A						.	C	ILE/VAL,ILE/VAL	7,4393	11.4+/-27.6	0,7,2193	61	63	62		685,685	-0.3	0.5	9	dbSNP_134	62	0,8598		0,0,4299	yes	missense,missense	BAAT	NM_001127610.1,NM_001701.3	29,29	0,7,6492	TT,TC,CC		0.0,0.1591,0.0539	benign,benign	229/419,229/419	104125282	7,12991	2200	4299	6499	SO:0001583	missense	570	exon4			CCCCAACGCCTGA	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"glycine N-choloyltransferase"	602938	"bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)", "bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.685G>A	9.37:g.104125282C>T	ENSP00000378491:p.Val229Ile	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	71	26	NM_001127610	0	0	1	1	0	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	37	CCDS6752.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	0	0.0	C	0.007	-1.950142	0.00475	0.001591	0.0	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.21734	1.99;1.99	4.96	-0.299	0.12808	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.391226	0.24879	N	0.034863	T	0.06416	0.0165	N	0.03238	-0.38	0.27280	N	0.95812	B	0.15930	0.015	B	0.14578	0.011	T	0.41610	-0.9499	10	0.02654	T	1	-10.6106	8.7705	0.34728	0.0:0.4737:0.0:0.5263	.	229	Q14032	BAAT_HUMAN	I	229	ENSP00000259407:V229I;ENSP00000378491:V229I	ENSP00000259407:V229I	V	-	1	0	BAAT	103165103	0.000000	0.05858	0.529000	0.27951	0.057000	0.15508	-1.997000	0.01470	-0.160000	0.11002	-0.290000	0.09829	GTT	C|0.999;T|0.001		0.388	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1			T	104125282	C	T	104125282	3	4	75	1	0	0	0	0	1	0	0	0	1281	536	19	1	575	1	BAAT	9	104125282	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		104125282	37088149	29	7056											
ADAMTSL2	9719	hgsc.bcm.edu	37	chr9	136419613	136419613	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccagggcctggacggggcCgggctgatgggcttcgtccc	4	6	18	13	3	0	1	0	1	0	0	2	2	1	2	4	6	1	2	4	6	0	1	rs370480318	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr9:136419613C>T	ENST00000354484.4	+	10	1631	c.1074C>T	c.(1072-1074)gcC>gcT	p.A358A	ADAMTSL2_ENST00000393061.3_Silent_p.A467A|ADAMTSL2_ENST00000393060.1_Silent_p.A358A	NM_001145320.1	NP_001138792.1	Q86TH1	ATL2_HUMAN	ADAMTS-like 2	358					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)		TGGACGGGGCCGGGCTGATGG	0.701																																					p.A358A		.											.	ADAMTSL2-91	0			c.C1074T						.	C	,	0,3798		0,0,1899	6	7	7		1074,1074	-8.1	0	9		7	2,7310		0,2,3654	no	coding-synonymous,coding-synonymous	ADAMTSL2	NM_001145320.1,NM_014694.3	,	0,2,5553	TT,TC,CC		0.0274,0.0,0.018	,	358/952,358/952	136419613	2,11108	1899	3656	5555	SO:0001819	synonymous_variant	9719	exon10			CGGGGCCGGGCTG	AB011177	CCDS6976.1	9q34.3	2005-01-12			ENSG00000197859	ENSG00000197859			14631	protein-coding gene	gene with protein product		612277				9628581, 14667842	Standard	NM_014694		Approved	KIAA0605	uc004cei.3	Q86TH1	OTTHUMG00000131706	ENST00000354484.4:c.1074C>T	9.37:g.136419613C>T		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_014694	0	0	0	2	2	B1B0D5|O60345	Silent	SNP	ENST00000354484.4	37	CCDS6976.1																																																																																			.		0.701	ADAMTSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254619.1	NM_014694		T	136419613	C	T	136419613	2	4	75	1	0	0	0	0	0	0	0	1	275	639	23	1		1	ADAMTSL2	9	136419613	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	32294331	136419613	4793818	30	7057											
SORCS1	114815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	108427534	108427534	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgccggcaggcactggccaTtgctgtgtcgctcataacca	8	9	11	13	2	1	0	1	0	0	0	2	0	1	0	3	3	3	4	3	3	1	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr10:108427534T>C	ENST00000263054.6	-	17	2223	c.2216A>G	c.(2215-2217)aAt>aGt	p.N739S	SORCS1_ENST00000369698.1_Missense_Mutation_p.N274S|SORCS1_ENST00000344440.6_Missense_Mutation_p.N739S	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	739					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GCACTGGCCATTGCTGTGTCG	0.458																																					p.N739S		.											.	SORCS1-153	0			c.A2216G						.						69	62	65					10																	108427534		2203	4300	6503	SO:0001583	missense	114815	exon17			TGGCCATTGCTGT	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2216A>G	10.37:g.108427534T>C	ENSP00000263054:p.Asn739Ser	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	34	31	NM_001206572	0	0	0	0	0	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	T	7.105	0.574795	0.13623	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.23348	1.91;2.47;2.47	5.49	4.33	0.51752	VPS10 (1);	0.111999	0.64402	N	0.000012	T	0.12433	0.0302	N	0.05031	-0.125	0.39169	D	0.962557	B;B;B;B;B	0.25206	0.073;0.054;0.12;0.073;0.007	B;B;B;B;B	0.25506	0.028;0.061;0.061;0.028;0.02	T	0.13548	-1.0505	9	.	.	.	-18.7721	11.8351	0.52319	0.0:0.0698:0.0:0.9302	.	739;739;739;739;739	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	S	274;739;739	ENSP00000358712:N274S;ENSP00000263054:N739S;ENSP00000345964:N739S	.	N	-	2	0	SORCS1	108417524	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	3.928000	0.56506	0.982000	0.38575	0.379000	0.24179	AAT	.		0.458	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		C	108427534	T	C	108427534	3	2	75	1	0	0	0	0	1	0	0	0	14962	1493	52	3	1564	3	SORCS1	10	108427534	Missense_Mutation	SNP	T	TCGA-BQ-5891-01A-11D-1589-08		108427534	27107213	31	7058											
OR52J3	119679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	5068288	5068288	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggctcacataatagcccAttcctactgtgagcacatgg	11	10	8	12	0	2	1	2	1	0	0	3	1	3	1	2	2	3	2	2	2	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr11:5068288A>T	ENST00000380370.1	+	1	533	c.533A>T	c.(532-534)cAt>cTt	p.H178L		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATAATAGCCCATTCCTACTGT	0.418																																					p.H178L		.											.	OR52J3-71	0			c.A533T						.						191	162	172					11																	5068288		2201	4298	6499	SO:0001583	missense	119679	exon1			TAGCCCATTCCTA	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"GPCR / Class A : Olfactory receptors"	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.533A>T	11.37:g.5068288A>T	ENSP00000369728:p.His178Leu	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	117	112	NM_001001916	0	0	0	0	0	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.387131	0.61956	.	.	ENSG00000205495	ENST00000380370	T	0.00183	8.6	3.89	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000183	T	0.01061	0.0035	H	0.98769	4.325	0.37287	D	0.908099	D	0.89917	1.0	D	0.97110	1.0	T	0.13019	-1.0525	10	0.87932	D	0	.	11.9816	0.53123	1.0:0.0:0.0:0.0	.	178	Q8NH60	O52J3_HUMAN	L	178	ENSP00000369728:H178L	ENSP00000369728:H178L	H	+	2	0	OR52J3	5024864	0.235000	0.23794	0.989000	0.46669	0.817000	0.46193	3.921000	0.56454	1.742000	0.51746	0.533000	0.62120	CAT	.		0.418	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916		T	5068288	A	T	5068288	3	4	75	1	0	0	0	0	1	0	0	0	11148	217	8	5	535	5	OR52J3	11	5068288	Missense_Mutation	SNP	A	TCGA-BQ-5891-01A-11D-1589-08		5068288	129938228	32	7059											
IL10RA	3587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117866403	117866403	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccagctgtatgtgcggcgccGaaagaagctacccagtgtcc	9	7	12	13	3	0	1	0	0	0	1	1	2	1	1	4	1	4	3	4	1	4	2	rs145975996		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr11:117866403G>A	ENST00000227752.3	+	6	908	c.788G>A	c.(787-789)cGa>cAa	p.R263Q	IL10RA_ENST00000545409.1_Missense_Mutation_p.R114Q|IL10RA_ENST00000541785.1_Missense_Mutation_p.R243Q|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	263					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		GTGCGGCGCCGAAAGAAGCTA	0.602																																					p.R263Q		.											.	IL10RA-91	0			c.G788A						.	G	GLN/ARG	0,4400		0,0,2200	96	76	83		788	-1.2	0	11	dbSNP_134	83	2,8590	2.2+/-6.3	0,2,4294	yes	missense	IL10RA	NM_001558.3	43	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	263/579	117866403	2,12990	2200	4296	6496	SO:0001583	missense	3587	exon6			GGCGCCGAAAGAA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.788G>A	11.37:g.117866403G>A	ENSP00000227752:p.Arg263Gln	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	42	20	NM_001558	0	0	9	9	0	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066789	0.55539	0.0	2.33E-4	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.56941	0.43;0.43;1.15	5.16	-1.2	0.09554	.	0.427526	0.16007	N	0.233988	T	0.52757	0.1754	M	0.63428	1.95	0.09310	N	1	D;D	0.69078	0.997;0.995	P;P	0.51945	0.685;0.639	T	0.47420	-0.9119	10	0.45353	T	0.12	-4.5989	7.1947	0.25845	0.1825:0.5157:0.3019:0.0	.	243;263	F5GYV8;Q13651	.;I10R1_HUMAN	Q	263;243;114;243	ENSP00000227752:R263Q;ENSP00000441397:R243Q;ENSP00000443019:R114Q	ENSP00000227752:R263Q	R	+	2	0	IL10RA	117371613	0.000000	0.05858	0.024000	0.17045	0.667000	0.39255	-0.002000	0.12924	0.003000	0.14656	0.563000	0.77884	CGA	G|1.000;A|0.000		0.602	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			A	117866403	G	A	117866403	3	1	75	1	0	0	0	0	1	0	0	0	7641	1058	37	1	810	1	IL10RA	11	117866403	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	112798115	117866403	17140113	33	7060											
ART4	420	broad.mit.edu	37	chr12	14993941	14993941	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caggctaagtgggctttttgCcacatcctaaaataattctt	11	14	7	9	0	1	0	0	0	1	0	2	0	2	0	2	2	1	2	2	2	4	7			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr12:14993941C>T	ENST00000228936.4	-	2	672	c.291G>A	c.(289-291)tgG>tgA	p.W97*	RP11-233G1.4_ENST00000444324.2_RNA|C12orf60_ENST00000527783.1_Intron	NM_021071.2	NP_066549.2	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 (Dombrock blood group)	97					arginine metabolic process (GO:0006525)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)			large_intestine(5)|liver(1)|lung(3)|prostate(1)|skin(2)|stomach(3)	15						GGGCTTTTTGCCACATCCTAA	0.408																																					p.W97X													.	ART4-90	0			c.G291A						.						136	132	133					12																	14993941		2203	4300	6503	SO:0001587	stop_gained	420	exon2			TTTTTGCCACATC	X95826	CCDS8668.1	12q13.2-q13.3	2014-07-18	2014-01-02	2006-01-12	ENSG00000111339	ENSG00000111339		"CD molecules", "Blood group antigens"	726	protein-coding gene	gene with protein product		110600	"Dombrock blood group", "ADP-ribosyltransferase 4 (DO blood group)", "ADP-ribosyltransferase 4"	DO		9119374	Standard	NM_021071		Approved	DOK1, CD297	uc001rcl.1	Q93070	OTTHUMG00000168738	ENST00000228936.4:c.291G>A	12.37:g.14993941C>T	ENSP00000228936:p.Trp97*	Somatic	311	1		WXS	Illumina HiSeq	Phase_I	439	6	NM_021071	0	0	0	0	0	Q9BZ50|Q9BZ51|Q9HB06	Nonsense_Mutation	SNP	ENST00000228936.4	37	CCDS8668.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504628	0.44558	.	.	ENSG00000111339	ENST00000228936;ENST00000420600	.	.	.	4.35	4.35	0.52113	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0835	15.1953	0.73081	0.0:1.0:0.0:0.0	.	.	.	.	X	97;80	.	ENSP00000228936:W97X	W	-	3	0	ART4	14885208	1.000000	0.71417	0.761000	0.31378	0.138000	0.21146	4.059000	0.57470	2.716000	0.92895	0.563000	0.77884	TGG	.		0.408	ART4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400859.1	NM_021071		T	14993941	C	T	14993941	4	4	75	1	0	0	0	0	0	1	0	0	1000	740	26	2	661	2	ART4	12	14993941	Nonsense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		14993941	118857954	34	7061											
TDG	6996	hgsc.bcm.edu	37	chr12	104378526	104378526	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tataaaatgttgtgattctaGctctgctatgttatgccatc	10	17	7	7	0	2	1	0	1	2	0	3	1	2	1	1	0	3	4	1	0	6	7			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr12:104378526G>T	ENST00000392872.3	+	8	1026		c.e8-1		TDG_ENST00000266775.9_Splice_Site|TDG_ENST00000544861.1_Splice_Site|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Splice_Site	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase						base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		TGTGATTCTAGCTCTGCTATG	0.323								Base excision repair (BER), DNA glycosylases																													.		.											.	TDG-661	0			c.793-1G>T						.						45	42	43					12																	104378526		2203	4300	6503	SO:0001630	splice_region_variant	6996	exon8			ATTCTAGCTCTGC	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.793-1G>T	12.37:g.104378526G>T		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	76	4	NM_003211	0	0	0	0	0	Q8IUZ6|Q8IZM3	Splice_Site	SNP	ENST00000392872.3	37	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099218	0.76983	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TDG	102902656	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	9.869000	0.99810	2.840000	0.97914	0.655000	0.94253	.	.		0.323	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		Intron	T	104378526	G	T	104378526	5	4	75	1	0	0	0	0	0	0	1	0	15757	985	34	4	822	4	TDG	12	104378526	Splice_Site	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	89384585	104378526	29473369	35	7062											
ATXN2	6311	hgsc.bcm.edu	37	chr12	112036797	112036797	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgttgctgctgctgctgCtgctgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1	rs4098854	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr12:112036797C>T	ENST00000377617.3	-	1	683	c.522G>A	c.(520-522)caG>caA	p.Q174Q	ATXN2_ENST00000549455.1_5'UTR|ATXN2_ENST00000608853.1_Silent_p.Q14Q|ATXN2_ENST00000389153.4_5'Flank|ATXN2_ENST00000542287.2_Intron|ATXN2_ENST00000550104.1_Silent_p.Q174Q|RP11-686G8.2_ENST00000547021.1_RNA|ATXN2_ENST00000535949.1_Intron	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	174	Poly-Gln.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						gctgctgctgctgctgctgct	0.731													C|||	3289	0.656749	0.5734	0.6787	5008	,	,		4944	0.622		0.7167	False		,,,				2504	0.728				p.Q174Q		.											.	ATXN2-136	0			c.G522A						.						1	1	1					12																	112036797		720	1770	2490	SO:0001819	synonymous_variant	6311	exon1			CTGCTGCTGCTGC	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.522G>A	12.37:g.112036797C>T		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	5	3	NM_002973	1	0	379	421	41	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	37	CCDS31902.1																																																																																			C|0.429;T|0.571		0.731	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	112036797	C	T	112036797	2	4	75	1	0	0	0	0	0	0	0	1	1212	796	28	2		2	ATXN2	12	112036797	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	7658271	112036797	21815098	36	7063											
EFHA1	221154	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	22088516	22088516	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatccagtttcattagttttCactgtcatcaagtcatcttg	9	18	5	9	0	6	0	5	0	1	0	7	0	7	0	1	0	0	2	1	0	3	6			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:22088516C>T	ENST00000382374.4	-	7	704	c.639G>A	c.(637-639)gtG>gtA	p.V213V		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	213					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										CATTAGTTTTCACTGTCATCA	0.318																																					p.V213V		.											.	EFHA1-90	0			c.G639A						.						184	177	179					13																	22088516		2202	4300	6502	SO:0001819	synonymous_variant	221154	exon7			AGTTTTCACTGTC	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.639G>A	13.37:g.22088516C>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	93	9	NM_152726	0	0	94	97	3	Q8N0T6|Q8NAX8	Silent	SNP	ENST00000382374.4	37	CCDS9297.1																																																																																			.		0.318	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726		T	22088516	C	T	22088516	2	4	75	1	0	0	0	0	0	0	0	1	4954	813	29	2		2	EFHA1	13	22088516	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		22088516	93081362	37	7064											
KL	9365	hgsc.bcm.edu;broad.mit.edu	37	chr13	33591068	33591068	+	Missense_Mutation	SNP	G	G	C																															tccccaatggcagcgcgggcGtccccaaccgcgaggggctg																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:33591068G>C	ENST00000380099.3	+	1	498	c.490G>C	c.(490-492)Gtc>Ctc	p.V164L	KL_ENST00000426690.2_Intron|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	164	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CAGCGCGGGCGTCCCCAACCG	0.711																																					p.V164L		.											.	KL-155	0			c.G490C						.						12	12	12					13																	33591068		2147	4218	6365	SO:0001583	missense	9365	exon1			GCGGGCGTCCCCA	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.490G>C	13.37:g.33591068G>C	ENSP00000369442:p.Val164Leu	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	24	10	NM_004795	0	0	1	53	52	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.183306	0.38511	.	.	ENSG00000133116	ENST00000380099	T	0.29397	1.57	4.05	1.25	0.21368	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.545315	0.20635	N	0.088517	T	0.23727	0.0574	L	0.38175	1.15	0.25597	N	0.98663	B	0.21606	0.058	B	0.30401	0.115	T	0.22138	-1.0225	10	0.39692	T	0.17	-7.2429	8.2462	0.31691	0.2774:0.0:0.7226:0.0	.	164	Q9UEF7	KLOT_HUMAN	L	164	ENSP00000369442:V164L	ENSP00000369442:V164L	V	+	1	0	KL	32489068	0.000000	0.05858	0.989000	0.46669	0.909000	0.53808	0.077000	0.14738	0.029000	0.15352	0.462000	0.41574	GTC	.		0.711	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			C	33591068	G	C	33591068	3	2	75	1	0	0	0	0	1	0	0	0	8352	1145	40	4	492	4	KL	13	33591068	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	11502552	33591068	81578810	38	7065	79	2									
KL	9365	bcgsc.ca	37	chr13	33591076	33591077	+	Missense_Mutation	DNP	CC	CC	TG																															ggcagcgcgggcgtccccaaCcgcgaggggctgcgctacta																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	CC	CC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:33591076_33591077CC>TG	ENST00000380099.3	+	1	506_507	c.498_499CC>TG	c.(496-501)aaCCgc>aaTGgc	p.R167G	KL_ENST00000426690.2_Intron|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	167	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GCGTCCCCAACCGCGAGGGGCT	0.723																																					p.R167G													.	KL-155	0			c.C499G						.																																			SO:0001583	missense	9365	exon1			CCCAACCGCGAGG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	Exception_encountered	13.37:g.33591076_33591077delinsTG	ENSP00000369442:p.Arg167Gly	Somatic	21	0		WXS	Illumina HiSeq	Phase_1	15	4	NM_004795	0	0	0	0	0	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	DNP	ENST00000380099.3	37	CCDS9347.1																																																																																			.		0.723	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			TG	33591077	CC	TG	33591076	3	4	75	1	0	0	0	0	1	0	0	0	8352	506	18	2	500	2	KL	13	33591076	Missense_Mutation	DNP	CC	TCGA-BQ-5891-01A-11D-1589-08	8	33591076	81578802	39	7066	79	2									
COX8C	341947	hgsc.bcm.edu	37	chr14	93813725	93813725	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcggggcccccgcgccagcgGcccctgtctgccgcggtgag	2	5	16	18	6	1	1	0	1	1	0	2	1	1	1	6	4	2	0	6	4	0	0	rs201840112	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr14:93813725G>T	ENST00000342144.2	+	1	189	c.111G>T	c.(109-111)cgG>cgT	p.R37R	UNC79_ENST00000256339.4_Intron	NM_182971.2	NP_892016.1	Q7Z4L0	COX8C_HUMAN	cytochrome c oxidase subunit VIIIC	37						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			large_intestine(1)|lung(1)|prostate(2)|skin(1)	5		all_cancers(154;0.083)		Epithelial(152;0.176)|all cancers(159;0.197)|COAD - Colon adenocarcinoma(157;0.202)		CGCGCCAGCGGCCCCTGTCTG	0.771													G|||	28	0.00559105	0.0061	0	5008	,	,		9861	0		0.004	False		,,,				2504	0.0164				p.R37R	GBM(134;630 1800 8342 13106 15419)	.											.	COX8C-226	0			c.G111T						.						4	5	5					14																	93813725		1483	3126	4609	SO:0001819	synonymous_variant	341947	exon1			CCAGCGGCCCCTG	AY161004	CCDS9910.1	14q32.13	2011-07-04	2011-05-25			ENSG00000187581		"Mitochondrial respiratory chain complex / Complex IV"	24382	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit VIII isoform 3"		"cytochrome c oxidase subunit 8C"			12909344	Standard	NM_182971		Approved	COX8-3	uc001ybt.1	Q7Z4L0		ENST00000342144.2:c.111G>T	14.37:g.93813725G>T		Somatic	4	2		WXS	Illumina HiSeq	Phase_I	13	12	NM_182971	0	0	0	0	0	Q495K7	Silent	SNP	ENST00000342144.2	37	CCDS9910.1																																																																																			G|0.996;T|0.004		0.771	COX8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412769.1	NM_182971		T	93813725	G	T	93813725	2	4	75	1	0	0	0	0	0	0	0	1	3792	1190	42	4		4	COX8C	14	93813725	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		93813725	13535815	40	7067											
AKT1	207	hgsc.bcm.edu	37	chr14	105237141	105237141	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actcctcatcaaaatacctgGtgtcagtctccgacgtgacc	10	10	7	14	2	4	1	3	1	1	0	6	2	5	1	4	1	1	0	4	1	3	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr14:105237141G>C	ENST00000554581.1	-	12	2784	c.1304C>G	c.(1303-1305)aCc>aGc	p.T435S	RP11-982M15.2_ENST00000557223.1_RNA|AKT1_ENST00000555458.1_Missense_Mutation_p.T130S|AKT1_ENST00000544168.1_Missense_Mutation_p.T373S|AKT1_ENST00000349310.3_Missense_Mutation_p.T435S|AKT1_ENST00000554585.1_5'UTR|AKT1_ENST00000402615.2_Missense_Mutation_p.T435S|AKT1_ENST00000554192.1_Missense_Mutation_p.T122S|AKT1_ENST00000554848.1_Missense_Mutation_p.T435S|AKT1_ENST00000407796.2_Missense_Mutation_p.T435S|AKT1_ENST00000555528.1_Missense_Mutation_p.T435S			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	435	AGC-kinase C-terminal.		T -> P (in CWD6). {ECO:0000269|PubMed:23246288}.		activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	AAAATACCTGGTGTCAGTCTC	0.612		1	Mis		"breast, colorectal, ovarian, NSCLC"						OREG0022961	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T435S		.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1-9189	0			c.C1304G						.						123	103	110					14																	105237141		2203	4300	6503	SO:0001583	missense	207	exon13			TACCTGGTGTCAG	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"Pleckstrin homology (PH) domain containing"	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.1304C>G	14.37:g.105237141G>C	ENSP00000451828:p.Thr435Ser	Somatic	44	0	1387	WXS	Illumina HiSeq	Phase_I	36	2	NM_005163	0	0	144	144	0	B2RAM5|B7Z5R1|Q9BWB6	Missense_Mutation	SNP	ENST00000554581.1	37	CCDS9994.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.732571	0.89482	.	.	ENSG00000142208	ENST00000554581;ENST00000407796;ENST00000349310;ENST00000402615;ENST00000555528;ENST00000555458;ENST00000554192;ENST00000544168;ENST00000554848	T;T;T;T;T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36	4.01	4.01	0.46588	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.84615	0.5511	M	0.93062	3.375	0.80722	D	1	D	0.65815	0.995	D	0.67382	0.951	D	0.89048	0.3453	10	0.87932	D	0	.	15.4048	0.74868	0.0:0.0:1.0:0.0	.	435	P31749	AKT1_HUMAN	S	435;435;435;435;435;130;122;373;435	ENSP00000451828:T435S;ENSP00000384293:T435S;ENSP00000270202:T435S;ENSP00000385326:T435S;ENSP00000450688:T435S;ENSP00000451470:T130S;ENSP00000450681:T122S;ENSP00000443897:T373S;ENSP00000451166:T435S	ENSP00000270202:T435S	T	-	2	0	AKT1	104308186	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	5.101000	0.64566	2.215000	0.71742	0.467000	0.42956	ACC	.		0.612	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163		C	105237141	G	C	105237141	3	2	75	1	0	0	0	0	1	0	0	0	478	1261	44	4	146	4	AKT1	14	105237141	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	11423416	105237141	2112399	41	7068											
PKD1	5310	hgsc.bcm.edu	37	chr16	2168405	2168405	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttcgtgggcagctgaaaaGgacactgctgccacggtgcc	8	7	13	13	2	0	1	0	1	0	0	1	2	0	2	3	3	4	3	3	3	2	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr16:2168405G>A	ENST00000262304.4	-	5	796	c.588C>T	c.(586-588)tcC>tcT	p.S196S	PKD1_ENST00000423118.1_Silent_p.S196S|RP11-304L19.2_ENST00000562027.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	196	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CAGCTGAAAAGGACACTGCTG	0.652																																					p.S196S		.											.	PKD1-91	0			c.C588T						.						1	2	2					16																	2168405		867	1809	2676	SO:0001819	synonymous_variant	5310	exon5			TGAAAAGGACACT	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.588C>T	16.37:g.2168405G>A		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	37	8	NM_000296	0	0	48	51	3	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2168405	G	A	2168405	2	1	75	1	0	0	0	0	0	0	0	1	11989	987	35	2		2	PKD1	16	2168405	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		2168405	88186348	42	7069											
RANBP10	57610	hgsc.bcm.edu;broad.mit.edu	37	chr16	67840335	67840335	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcgctgcaagcgccggctCagctcctgctccccagggga	6	5	14	16	3	1	0	1	0	0	0	3	1	3	1	4	4	4	5	4	4	1	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr16:67840335C>T	ENST00000317506.3	-	1	220	c.105G>A	c.(103-105)ctG>ctA	p.L35L	TSNAXIP1_ENST00000388833.3_5'Flank|RANBP10_ENST00000536251.1_5'UTR|RANBP10_ENST00000602677.1_Silent_p.L35L|RANBP10_ENST00000425512.2_5'UTR|TSNAXIP1_ENST00000561639.1_5'Flank|TSNAXIP1_ENST00000415766.3_5'Flank|RANBP10_ENST00000448631.2_Silent_p.L35L|RANBP10_ENST00000602887.1_5'UTR|RANBP10_ENST00000411657.2_5'UTR	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	35	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		AGCGCCGGCTCAGCTCCTGCT	0.701																																					p.L35L		.											.	RANBP10-227	0			c.G105A						.						14	15	15					16																	67840335		2183	4253	6436	SO:0001819	synonymous_variant	57610	exon1			CCGGCTCAGCTCC	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.105G>A	16.37:g.67840335C>T		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	18	6	NM_020850	0	0	9	15	6	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Silent	SNP	ENST00000317506.3	37	CCDS32469.1																																																																																			.		0.701	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		T	67840335	C	T	67840335	2	4	75	1	0	0	0	0	0	0	0	1	13058	813	29	2		2	RANBP10	16	67840335	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	65671930	67840335	22514418	43	7070											
ZFHX3	463	broad.mit.edu	37	chr16	72984648	72984648	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggtatgagtcccccatcAccgccttccactcgtcctcc	6	10	6	19	2	1	1	1	1	0	0	6	1	5	1	7	1	0	1	7	1	1	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr16:72984648A>C	ENST00000268489.5	-	3	3608	c.2936T>G	c.(2935-2937)gTg>gGg	p.V979G	ZFHX3_ENST00000397992.5_Missense_Mutation_p.V65G	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	979					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				GTCCCCCATCACCGCCTTCCA	0.592																																					p.V979G													.	ZFHX3-72	0			c.T2936G						.						128	112	117					16																	72984648		2198	4300	6498	SO:0001583	missense	463	exon3			CCCATCACCGCCT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2936T>G	16.37:g.72984648A>C	ENSP00000268489:p.Val979Gly	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	113	8	NM_006885	0	1	6	7	0	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.908930	0.33721	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.53857	0.6;0.6	5.22	5.22	0.72569	.	0.000000	0.45126	D	0.000397	T	0.61986	0.2391	M	0.70595	2.14	0.80722	D	1	P	0.52316	0.952	P	0.52957	0.714	T	0.66972	-0.5788	10	0.87932	D	0	.	10.3495	0.43927	0.9231:0.0:0.0769:0.0	.	979	Q15911	ZFHX3_HUMAN	G	979;65	ENSP00000268489:V979G;ENSP00000438926:V65G	ENSP00000268489:V979G	V	-	2	0	ZFHX3	71542149	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.334000	0.72944	1.959000	0.56917	0.533000	0.62120	GTG	.		0.592	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72984648	A	C	72984648	3	2	75	1	0	0	0	0	1	0	0	0	17666	159	6	5	8207	5	ZFHX3	16	72984648	Missense_Mutation	SNP	A	TCGA-BQ-5891-01A-11D-1589-08	5144313	72984648	17370105	44	7071											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	496	71		WXS	Illumina HiSeq		793	114	NM_145301	0	0	12	97	85	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		T	15457087	C	T	15457087	3	4	75	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		15457087	65738123	45	7072											
AKAP10	11216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	19861611	19861611	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatcaagagaatcagttaaaAaagacgctgtagtttcatgc	16	11	8	6	1	3	2	3	0	0	2	3	3	3	2	0	0	1	4	0	0	7	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr17:19861611A>G	ENST00000225737.6	-	4	750	c.593T>C	c.(592-594)tTt>tCt	p.F198S	AKAP10_ENST00000572155.1_5'Flank|AKAP10_ENST00000395536.3_Missense_Mutation_p.F198S	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	198	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					ATCAGTTAAAAAAGACGCTGT	0.418																																					p.F198S		.											.	AKAP10-226	0			c.T593C						.						65	65	65					17																	19861611		2203	4300	6503	SO:0001583	missense	11216	exon4			GTTAAAAAAGACG	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"A-kinase anchor proteins"	368	protein-coding gene	gene with protein product	"dual-specificity A-kinase anchoring protein 2", "protein kinase A anchoring protein 10", "mitochondrial A kinase PPKA anchor protein 10"	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.593T>C	17.37:g.19861611A>G	ENSP00000225737:p.Phe198Ser	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	99	49	NM_007202	0	0	17	26	9	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	.	.	.	.	.	.	.	.	.	.	A	5.074	0.199347	0.09652	.	.	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.17054	2.3	5.98	3.72	0.42706	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.607188	0.19356	N	0.116264	T	0.05914	0.0154	N	0.03115	-0.41	0.24009	N	0.996183	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.42068	-0.9473	10	0.06236	T	0.91	-3.1154	7.7403	0.28837	0.6869:0.0:0.3131:0.0	.	198;198;198	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	S	198	ENSP00000225737:F198S	ENSP00000225737:F198S	F	-	2	0	AKAP10	19802203	1.000000	0.71417	0.995000	0.50966	0.345000	0.29048	1.891000	0.39738	0.471000	0.27319	0.482000	0.46254	TTT	.		0.418	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		G	19861611	A	G	19861611	3	3	75	1	0	0	0	0	1	0	0	0	446	14	1	3	1443	3	AKAP10	17	19861611	Missense_Mutation	SNP	A	TCGA-BQ-5891-01A-11D-1589-08	4404524	19861611	61333599	46	7073											
SLC14A1	6563	bcgsc.ca	37	chr18	43319599	43319599	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgttcatggcgctcacctgGcaaacccacctcctggctct	7	10	8	16	1	3	0	2	0	1	0	4	0	4	0	4	3	1	4	4	3	1	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr18:43319599G>A	ENST00000321925.4	+	8	1150	c.918G>A	c.(916-918)tgG>tgA	p.W306*	SLC14A1_ENST00000586142.1_Nonsense_Mutation_p.W306*|SLC14A1_ENST00000436407.3_Nonsense_Mutation_p.W362*|SLC14A1_ENST00000535474.1_Nonsense_Mutation_p.W174*|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000502059.2_Nonsense_Mutation_p.W198*|SLC14A1_ENST00000589700.1_Missense_Mutation_p.G257D|SLC14A1_ENST00000591541.1_Nonsense_Mutation_p.W10*|SLC14A1_ENST00000402943.2_Nonsense_Mutation_p.W201*|SLC14A1_ENST00000415427.3_Nonsense_Mutation_p.W362*|RP11-116O18.3_ENST00000586213.1_RNA	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	306					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						CGCTCACCTGGCAAACCCACC	0.537																																					p.W362X													.	SLC14A1-515	0			c.G1086A						.						100	86	91					18																	43319599		2203	4300	6503	SO:0001587	stop_gained	6563	exon7			CACCTGGCAAACC	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.918G>A	18.37:g.43319599G>A	ENSP00000318546:p.Trp306*	Somatic	124	0		WXS	Illumina HiSeq	Phase_1	91	5	NM_001146037	0	0	0	0	0	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Nonsense_Mutation	SNP	ENST00000321925.4	37	CCDS11925.1	.	.	.	.	.	.	.	.	.	.	G	41	8.740906	0.98935	.	.	ENSG00000141469	ENST00000321925;ENST00000415427;ENST00000502059;ENST00000402943;ENST00000535474;ENST00000436407	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.6308	18.6387	0.91387	0.0:0.0:1.0:0.0	.	.	.	.	X	306;362;198;201;174;362	.	ENSP00000318546:W306X	W	+	3	0	SLC14A1	41573597	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.159000	0.94728	2.640000	0.89533	0.591000	0.81541	TGG	.		0.537	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		A	43319599	G	A	43319599	4	1	75	1	0	0	0	0	0	1	0	0	14428	1212	42	2	1112	2	SLC14A1	18	43319599	Nonsense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		43319599	34757649	47	7074											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	9065718	9065718	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccctcaatttagggctcaggGaggaaattgactctttctga	10	12	10	9	0	4	2	2	2	2	0	4	4	4	4	1	3	0	1	1	3	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:9065718G>T	ENST00000397910.4	-	3	21931	c.21728C>A	c.(21727-21729)tCc>tAc	p.S7243Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7245	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGCTCAGGGAGGAAATTGA	0.468																																					p.S7243Y		.											.	MUC16-566	0			c.C21728A						.						169	161	164					19																	9065718		1979	4157	6136	SO:0001583	missense	94025	exon3			CTCAGGGAGGAAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21728C>A	19.37:g.9065718G>T	ENSP00000381008:p.Ser7243Tyr	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	220	16	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.932	-0.016036	0.07681	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	2.75	-0.661	0.11417	.	.	.	.	.	T	0.06962	0.0177	L	0.42245	1.32	.	.	.	D	0.65815	0.995	D	0.68943	0.961	T	0.29274	-1.0017	8	0.87932	D	0	.	5.0419	0.14463	0.4634:0.0:0.5366:0.0	.	7243	B5ME49	.	Y	7243	ENSP00000381008:S7243Y	ENSP00000381008:S7243Y	S	-	2	0	MUC16	8926718	0.015000	0.18098	0.000000	0.03702	0.007000	0.05969	2.004000	0.40854	-0.046000	0.13446	0.195000	0.17529	TCC	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9065718	G	T	9065718	3	4	75	1	0	0	0	0	1	0	0	0	9998	1174	41	4	22123	4	MUC16	19	9065718	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		9065718	50063265	48	7075											
ZNF761	388561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53958709	53958709	+	RNA	SNP	T	T	A																															aaatcaatacttgaaagacaTaggataattcatactgaaga																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:53958709T>A	ENST00000454407.1	+	0	1401							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TTGAAAGACATAGGATAATTC	0.383																																					p.H316Q		.											.	ZNF761-91	0			c.T948A						.						83	85	85					19																	53958709		2203	4300	6503			388561	exon7			AAGACATAGGATA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958709T>A		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	114	97	NM_001008401	0	0	0	0	0	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				.		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		A	53958709	T	A	53958709	1	1	75	0	1	0	0	0	0	0	0	0	18168	1403	49	5		5	ZNF761	19	53958709	RNA	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	44892991	53958709	5170274	49	7076	80	2									
ZNF761	388561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53958711	53958711	+	RNA	SNP	G	G	A																															atcaatacttgaaagacataGgataattcatactgaagaga																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:53958711G>A	ENST00000454407.1	+	0	1403							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GAAAGACATAGGATAATTCAT	0.383																																					p.R317K		.											.	ZNF761-91	0			c.G950A						.						84	85	85					19																	53958711		2203	4300	6503			388561	exon7			GACATAGGATAAT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958711G>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	114	98	NM_001008401	0	0	0	0	0	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				.		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		A	53958711	G	A	53958711	1	1	75	0	1	0	0	0	0	0	0	0	18168	1000	35	2		2	ZNF761	19	53958711	RNA	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	2	53958711	5170272	50	7077	80	2									
GGTLC1	92086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	23967129	23967129	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtcctctgcgaccacagaCaggtgagcagtgcccccgtc	7	6	11	17	3	1	2	0	1	1	1	3	3	2	2	5	1	3	1	5	1	0	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr20:23967129C>T	ENST00000335694.4	-	2	324	c.120G>A	c.(118-120)ctG>ctA	p.L40L	GGTLC1_ENST00000278765.4_Silent_p.L40L|GGTLC1_ENST00000286890.4_Silent_p.L40L	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	40					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						CGACCACAGACAGGTGAGCAG	0.647																																					p.L40L		.											.	GGTLC1-23	0			c.G120A						.						51	45	47					20																	23967129		2203	4300	6503	SO:0001819	synonymous_variant	92086	exon2			CACAGACAGGTGA	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"Gamma-glutamyltransferases"	16437	protein-coding gene	gene with protein product		612338	"gamma-glutamyltransferase-like activity 4", "gamma-glutamyltransferase-like activity 3"	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.120G>A	20.37:g.23967129C>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	101	56	NM_178311	0	0	0	0	0	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	37	CCDS13163.1																																																																																			.		0.647	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		T	23967129	C	T	23967129	2	4	75	1	0	0	0	0	0	0	0	1	6385	465	17	2		2	GGTLC1	20	23967129	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		23967129	39058391	51	7078											
MATN4	8785	broad.mit.edu	37	chr20	43927153	43927153	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgaagcgcttcactagctcGaagttttgtggacgcacgct	9	10	11	11	5	1	0	1	0	0	0	2	3	1	1	0	1	2	5	0	1	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr20:43927153G>A	ENST00000372754.1	-	7	1214	c.1206C>T	c.(1204-1206)ttC>ttT	p.F402F	MATN4_ENST00000353917.5_Silent_p.F279F|MATN4_ENST00000360607.6_Silent_p.F320F|MATN4_ENST00000372756.1_Silent_p.F361F|MATN4_ENST00000342716.4_Silent_p.F361F|MATN4_ENST00000537548.1_Silent_p.F361F|MATN4_ENST00000372751.4_Silent_p.F212F			O95460	MATN4_HUMAN	matrilin 4	402	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				TCACTAGCTCGAAGTTTTGTG	0.597																																					p.F361F													.	MATN4-90	0			c.C1083T						.						82	69	73					20																	43927153		2203	4300	6503	SO:0001819	synonymous_variant	8785	exon7			TAGCTCGAAGTTT	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.1206C>T	20.37:g.43927153G>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	236	7	NM_003833	0	0	0	0	0	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																				.		0.597	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1			A	43927153	G	A	43927153	2	1	75	1	0	0	0	0	0	0	0	1	9361	1049	37	1		1	MATN4	20	43927153	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	19960024	43927153	19098367	52	7079											
OGFR	11054	hgsc.bcm.edu	37	chr20	61443716	61443716	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgggagctgccgggggtgcGgcagagtgccctggactact	5	6	19	11	3	0	1	0	0	0	1	0	3	0	3	2	5	5	2	2	5	1	1	rs41309371	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr20:61443716G>A	ENST00000290291.6	+	7	774	c.749G>A	c.(748-750)cGg>cAg	p.R250Q	OGFR_ENST00000370461.1_Missense_Mutation_p.R198Q	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	250					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CCGGGGGTGCGGCAGAGTGCC	0.697													G|||	77	0.0153754	0	0.0072	5008	,	,		10012	0.0099		0.0109	False		,,,				2504	0.0521				p.R250Q		.											.	OGFR-68	0			c.G749A						.	G	GLN/ARG	13,4267		0,13,2127	12	12	12		749	3.5	1	20	dbSNP_127	12	167,8295		0,167,4064	yes	missense	OGFR	NM_007346.2	43	0,180,6191	AA,AG,GG		1.9735,0.3037,1.4127	probably-damaging	250/678	61443716	180,12562	2140	4231	6371	SO:0001583	missense	11054	exon7			GGGTGCGGCAGAG	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.749G>A	20.37:g.61443716G>A	ENSP00000290291:p.Arg250Gln	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	18	10	NM_007346	0	0	76	112	36	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	23	0.010531135531135532	2	0.0040650406504065045	3	0.008287292817679558	9	0.015734265734265736	9	0.011873350923482849	G	23.7	4.446822	0.84101	0.003037	0.019735	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.50001	1.69;0.76;1.15	4.57	3.5	0.40072	Opioid growth factor receptor (OGFr) conserved domain (1);	0.311886	0.29059	N	0.013267	T	0.36138	0.0956	L	0.52206	1.635	0.25470	N	0.987836	D;D;D	0.89917	1.0;0.999;0.999	D;P;P	0.63957	0.92;0.875;0.875	T	0.31943	-0.9925	10	0.51188	T	0.08	-25.1591	3.8836	0.09088	0.182:0.0:0.5777:0.2402	rs41309371	250;233;250	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	Q	250;250;250;105;198	ENSP00000290291:R250Q;ENSP00000359499:R250Q;ENSP00000359491:R198Q	ENSP00000290291:R250Q	R	+	2	0	OGFR	60914161	1.000000	0.71417	0.966000	0.40874	0.818000	0.46254	4.169000	0.58223	2.047000	0.60756	0.561000	0.74099	CGG	G|0.989;A|0.011		0.697	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			A	61443716	G	A	61443716	3	1	75	1	0	0	0	0	1	0	0	0	10869	1116	39	1	775	1	OGFR	20	61443716	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	17516563	61443716	1581804	53	7080											
TMPRSS15	5651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	19685347	19685347	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgccatatgctctggattcTgaaccgcactaaaccattgt	11	12	7	11	1	2	1	0	1	2	0	2	2	2	2	3	1	4	2	3	1	4	4	rs111276490		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr21:19685347T>G	ENST00000284885.3	-	18	2113	c.2080A>C	c.(2080-2082)Aga>Cga	p.R694R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	694	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTCTGGATTCTGAACCGCACT	0.443																																					p.R694R		.											.	TMPRSS15-160	0			c.A2080C						.						149	133	138					21																	19685347		2203	4300	6503	SO:0001819	synonymous_variant	5651	exon18			GGATTCTGAACCG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"Serine peptidases / Transmembrane"	9490	protein-coding gene	gene with protein product	"proenterokinase", "enteropeptidase"	606635	"protease, serine, 7 (enterokinase)"	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2080A>C	21.37:g.19685347T>G		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	114	107	NM_002772	0	0	0	0	0	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																			T|0.500;C|0.500		0.443	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		G	19685347	T	G	19685347	2	3	75	1	0	0	0	0	0	0	0	1	16278	1588	55	5		5	TMPRSS15	21	19685347	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08		19685347	28444548	54	7081											
TXNRD2	10587	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	19870863	19870863	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtacctccaccacgtcaccAatggcgtagatgtggggcac	9	7	11	14	3	1	1	1	0	0	1	2	1	2	1	4	3	1	3	4	3	3	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr22:19870863A>T	ENST00000400521.1	-	12	1077	c.1071T>A	c.(1069-1071)atT>atA	p.I357I	TXNRD2_ENST00000400518.1_Silent_p.I327I|TXNRD2_ENST00000400519.1_Silent_p.I356I|TXNRD2_ENST00000542719.1_Silent_p.I327I|TXNRD2_ENST00000535882.1_Silent_p.I356I	NM_006440.3	NP_006431.2	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2	357					cell redox homeostasis (GO:0045454)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|response to oxygen radical (GO:0000305)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|urinary_tract(2)	30	Colorectal(54;0.0993)					CCACGTCACCAATGGCGTAGA	0.652																																					.													.	TXNRD2-92	0			.						.						90	102	98					22																	19870863		2059	4207	6266	SO:0001819	synonymous_variant	10587	.			GTCACCAATGGCG	AF106697	CCDS42981.1, CCDS63402.1	22q11.21	2014-09-17			ENSG00000184470	ENSG00000184470			18155	protein-coding gene	gene with protein product	"thioredoxin reductase beta", "selenoprotein Z"	606448				9923614, 10215850, 11012661	Standard	NM_006440		Approved	TR, TRXR2, TR3	uc021wlj.1	Q9NNW7	OTTHUMG00000149975	ENST00000400521.1:c.1071T>A	22.37:g.19870863A>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	85	74	.	0	0	1	52	51	O95840|Q96IJ2|Q9H2Z5|Q9NZV3|Q9NZV4|Q9P2Y0|Q9P2Y1|Q9UQU8	Silent	SNP	ENST00000400521.1	37	CCDS42981.1																																																																																			.		0.652	TXNRD2-003	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000314903.3	NM_006440		T	19870863	A	T	19870863	2	4	75	1	0	0	0	0	0	0	0	1	16841	126	5	5		5	TXNRD2	22	19870863	Silent	SNP	A	TCGA-BQ-5891-01A-11D-1589-08		19870863	31433703	55	7082											
CCDC116	164592	broad.mit.edu;bcgsc.ca	37	chr22	21989095	21989095	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttctcagggctgctgggctCaagctctggcgtgcctgaag	5	10	15	11	1	3	1	2	1	2	0	4	1	3	1	1	3	3	5	1	3	2	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr22:21989095C>G	ENST00000292779.3	+	4	904	c.743C>G	c.(742-744)tCa>tGa	p.S248*	CCDC116_ENST00000607942.1_Nonsense_Mutation_p.S248*	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	248										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					CTGCTGGGCTCAAGCTCTGGC	0.577																																					p.S248X													.	CCDC116-92	0			c.C743G						.						85	90	88					22																	21989095		2203	4300	6503	SO:0001587	stop_gained	164592	exon4			TGGGCTCAAGCTC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.743C>G	22.37:g.21989095C>G	ENSP00000292779:p.Ser248*	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	165	7	NM_152612	0	0	0	0	0	Q8N9Y9	Nonsense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.687235	0.68157	.	.	ENSG00000161180	ENST00000292779	.	.	.	4.56	4.56	0.56223	.	0.269330	0.27035	N	0.021260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-55.3163	13.0826	0.59121	0.0:1.0:0.0:0.0	.	.	.	.	X	248	.	ENSP00000292779:S248X	S	+	2	0	CCDC116	20319095	0.644000	0.27277	0.178000	0.23040	0.062000	0.15995	3.279000	0.51670	2.554000	0.86153	0.485000	0.47835	TCA	.		0.577	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		G	21989095	C	G	21989095	4	3	75	1	0	0	0	0	0	1	0	0	2759	838	29	4	753	4	CCDC116	22	21989095	Nonsense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	2118232	21989095	29315471	56	7083											
SH3BP1	23616	hgsc.bcm.edu	37	chr22	38051328	38051328	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgccgcccccccaggtctcCggctcccgctcctcccctcc	2	7	7	25	3	1	0	0	0	1	0	6	0	5	0	10	2	1	2	10	2	0	0	rs61678571	byFrequency	TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr22:38051328C>A	ENST00000357436.4	+	18	2056	c.1743C>A	c.(1741-1743)tcC>tcA	p.S581S	SH3BP1_ENST00000599616.1_Intron|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	581					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					CCCAGGTCTCCGGCTCCCGCT	0.736																																					p.S581S		.											.	SH3BP1-90	0			c.C1743A						.						5	7	6					22																	38051328		1747	3534	5281	SO:0001819	synonymous_variant	23616	exon18			GGTCTCCGGCTCC		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"Rho GTPase activating proteins"	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1743C>A	22.37:g.38051328C>A		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_018957	0	0	3	3	0	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			C|0.984;T|0.016		0.736	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		A	38051328	C	A	38051328	2	1	75	1	0	0	0	0	0	0	0	1	14276	639	23	4		4	SH3BP1	22	38051328	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	16062233	38051328	13253238	57	7084											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350698	50350698	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctctgcctcctcctcCtcctcttcctcttcctcttc	0	17	1	23	0	4	0	0	0	4	0	13	0	12	0	9	0	1	0	9	0	0	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chrX:50350698C>T	ENST00000289292.7	-	6	3727	c.3444G>A	c.(3442-3444)gaG>gaA	p.E1148E	SHROOM4_ENST00000376020.2_Silent_p.E1148E|SHROOM4_ENST00000460112.3_Silent_p.E1032E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1148	Glu-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctcctcctcctcctcttcct	0.557													C|||	1	0.000264901	0	0.0014	3775	,	,		12007	0		0	False		,,,				2504	0				p.E1148E		.											.	SHROOM4-131	0			c.G3444A						.						22	20	21					X																	50350698		2203	4298	6501	SO:0001819	synonymous_variant	57477	exon6			CTCCTCCTCCTCT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3444G>A	X.37:g.50350698C>T		Somatic	15	1		WXS	Illumina HiSeq	Phase_I	23	6	NM_020717	0	0	11	11	0	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																			.		0.557	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		T	50350698	C	T	50350698	2	4	75	1	0	0	0	0	0	0	0	1	14328	680	24	2		2	SHROOM4	23	50350698	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		50350698	104919862	58	7085											
COL4A6	1288	broad.mit.edu	37	chrX	107434729	107434729	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttggtcccccttcagcccTggaaatccctgaggccctag	6	9	9	17	0	1	1	1	1	0	0	3	2	3	2	6	3	1	0	6	3	2	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chrX:107434729T>C	ENST00000372216.4	-	19	1318	c.1218A>G	c.(1216-1218)ccA>ccG	p.P406P	COL4A6_ENST00000538570.1_Silent_p.P405P|COL4A6_ENST00000334504.7_Silent_p.P405P|COL4A6_ENST00000545689.1_Silent_p.P405P|COL4A6_ENST00000394872.2_Silent_p.P406P	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	406	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						CCTTCAGCCCTGGAAATCCCT	0.567									Alport syndrome with Diffuse Leiomyomatosis																												p.P406P	Melanoma(87;1895 1945 2589 7165)												.	COL4A6-199	0			c.A1218G						.						112	106	108					X																	107434729		2203	4300	6503	SO:0001819	synonymous_variant	1288	exon19	Familial Cancer Database		CAGCCCTGGAAAT	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.1218A>G	X.37:g.107434729T>C		Somatic	242	0		WXS	Illumina HiSeq	Phase_I	218	5	NM_001847	0	0	0	0	0	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Silent	SNP	ENST00000372216.4	37	CCDS14541.1																																																																																			.		0.567	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			C	107434729	T	C	107434729	2	2	75	1	0	0	0	0	0	0	0	1	3701	1567	55	3		3	COL4A6	23	107434729	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	57084031	107434729	47835831	59	7086											
RCAN3	11123	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	24840967	24840967	+	Frame_Shift_Del	DEL	T	T	-																															tttggtgaaaatgaagatgaTttggatgagatgatggattt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:24840967delT	ENST00000374395.4	+	2	418	c.105delT	c.(103-105)gatfs	p.D35fs	RCAN3_ENST00000436717.2_Frame_Shift_Del_p.D35fs|RCAN3_ENST00000412742.2_Frame_Shift_Del_p.D35fs|RCAN3_ENST00000538532.1_Frame_Shift_Del_p.D35fs|RCAN3_ENST00000374393.2_Frame_Shift_Del_p.D35fs	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	35					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		ATGAAGATGATTTGGATGAGA	0.433																																					p.D35fs		.											.	RCAN3-90	0			c.105delT						.						206	186	193					1																	24840967		2203	4300	6503	SO:0001589	frameshift_variant	11123	exon1			.		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"Down syndrome critical region gene 1-like 2"	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.105delT	1.37:g.24840967delT	ENSP00000363516:p.Asp35fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	101	21	NM_001251980	0	0	0	0	0	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Frame_Shift_Del	DEL	ENST00000374395.4	37	CCDS254.1																																																																																			.		0.433	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2			-	24840967	T	-	24840967	7	5	76	1	0	1	0	1	0	0	0	0	13202	1490	52	0	107	0	RCAN3	1	24840967	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08		24840967	224409654	1	7087											
SFRS4	6429	hgsc.bcm.edu;broad.mit.edu	37	chr1	29475685	29475685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttttctctttcttgctcCggctccgactctggctccgg	1	16	9	15	3	3	0	0	0	3	0	7	1	6	0	3	3	2	4	3	3	0	4	rs368357249		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:29475685C>T	ENST00000373795.4	-	6	956	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	RP11-242O24.3_ENST00000413004.1_lincRNA|SRSF4_ENST00000546138.1_Silent_p.P139P|SRSF4_ENST00000466448.1_5'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	241	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						TTTCTTgctccggctccgact	0.592																																					p.R241Q		.											.	SRSF4-226	0			c.G722A						.	C	GLN/ARG	2,4398		0,2,2198	50	60	57		722	5.8	1	1		57	0,8596		0,0,4298	no	missense	SRSF4	NM_005626.4	43	0,2,6496	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	241/495	29475685	2,12994	2200	4298	6498	SO:0001583	missense	6429	exon6			TTGCTCCGGCTCC	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10786	protein-coding gene	gene with protein product	"SR splicing factor 4"	601940	"splicing factor, arginine/serine-rich 4"	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.722G>A	1.37:g.29475685C>T	ENSP00000362900:p.Arg241Gln	Somatic	200	1		WXS	Illumina HiSeq	Phase_I	162	15	NM_005626	0	0	50	61	11	Q5VXP1|Q9BUA4|Q9UEB5	Missense_Mutation	SNP	ENST00000373795.4	37	CCDS333.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.131145	0.56828	4.55E-4	0.0	ENSG00000116350	ENST00000373795;ENST00000434636	T	0.38401	1.14	5.77	5.77	0.91146	.	0.201011	0.34932	N	0.003572	T	0.35189	0.0923	L	0.52573	1.65	0.80722	D	1	D	0.61080	0.989	B	0.42087	0.375	T	0.19778	-1.0295	10	0.59425	D	0.04	.	13.8822	0.63688	0.1522:0.8478:0.0:0.0	.	241	Q08170	SRSF4_HUMAN	Q	241	ENSP00000362900:R241Q	ENSP00000362900:R241Q	R	-	2	0	SRSF4	29348272	0.993000	0.37304	0.999000	0.59377	0.988000	0.76386	3.219000	0.51200	2.723000	0.93209	0.655000	0.94253	CGG	.		0.592	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626		T	29475685	C	T	29475685	3	4	76	1	0	0	0	0	1	0	0	0	14211	652	23	1	766	1	SFRS4	1	29475685	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	4634718	29475685	219774936	2	7088											
GJB5	2709	broad.mit.edu	37	chr1	35223072	35223072	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagcgtgtgtggagtgatgaCcacaaggacttcgactgcaa	11	8	14	8	2	0	2	0	2	0	0	1	6	0	4	1	2	2	1	1	2	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:35223072C>A	ENST00000338513.1	+	2	314	c.141C>A	c.(139-141)gaC>gaA	p.D47E	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	47					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				GGAGTGATGACCACAAGGACT	0.592																																					p.D47E													.	GJB5-91	0			c.C141A						.						142	120	128					1																	35223072		2203	4300	6503	SO:0001583	missense	2709	exon2			TGATGACCACAAG	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"Ion channels / Gap junction proteins (connexins)"	4287	protein-coding gene	gene with protein product	"connexin 31.1"	604493	"gap junction protein, beta 5 (connexin 31.1)", "gap junction protein, beta 5"			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.141C>A	1.37:g.35223072C>A	ENSP00000340811:p.Asp47Glu	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_005268	0	0	1	1	0	Q9UPA3	Missense_Mutation	SNP	ENST00000338513.1	37	CCDS382.1	.	.	.	.	.	.	.	.	.	.	C	4.945	0.175507	0.09391	.	.	ENSG00000189280	ENST00000338513	D	0.98150	-4.75	5.89	4.03	0.46877	Connexin, N-terminal (2);	0.052219	0.85682	D	0.000000	D	0.88340	0.6410	N	0.01289	-0.905	0.36678	D	0.87886	B	0.14805	0.011	B	0.21360	0.034	D	0.83549	0.0100	10	0.02654	T	1	.	9.8486	0.41043	0.0:0.757:0.115:0.128	.	47	O95377	CXB5_HUMAN	E	47	ENSP00000340811:D47E	ENSP00000340811:D47E	D	+	3	2	GJB5	34995659	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	0.341000	0.19909	0.840000	0.34995	0.561000	0.74099	GAC	.		0.592	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268		A	35223072	C	A	35223072	3	1	76	1	0	0	0	0	1	0	0	0	6431	506	18	4	143	4	GJB5	1	35223072	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	5747387	35223072	214027549	3	7089											
ZNF691	51058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	43317094	43317094	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcggcggcgctcagacctCaccacgcaccagcaagatca	10	6	9	16	4	3	2	3	0	0	2	4	2	3	2	3	2	1	3	3	2	1	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:43317094C>A	ENST00000372506.1	+	4	805	c.465C>A	c.(463-465)ctC>ctA	p.L155L	ZNF691_ENST00000372508.3_Silent_p.L155L|ZNF691_ENST00000372504.1_Silent_p.L177L|ZNF691_ENST00000372502.1_Silent_p.L177L|ZNF691_ENST00000397044.3_Silent_p.L186L|ZNF691_ENST00000372507.1_Silent_p.L155L	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	186						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|ovary(2)|prostate(1)	7	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GCTCAGACCTCACCACGCACC	0.597																																					p.L186L		.											.	ZNF691-24	0			c.C558A						.						61	56	58					1																	43317094		2203	4300	6503	SO:0001819	synonymous_variant	51058	exon4			AGACCTCACCACG		CCDS476.1, CCDS55595.1	1p34.2	2013-01-08			ENSG00000164011	ENSG00000164011		"Zinc fingers, C2H2-type"	28028	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001242739		Approved	Zfp691	uc021omh.1	Q5VV52	OTTHUMG00000007623	ENST00000372506.1:c.465C>A	1.37:g.43317094C>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	78	17	NM_001242739	0	0	10	11	1	A8MXP6|B4DJR7|O95878|Q9NWE8	Silent	SNP	ENST00000372506.1	37	CCDS476.1																																																																																			.		0.597	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		A	43317094	C	A	43317094	2	1	76	1	0	0	0	0	0	0	0	1	18128	813	29	4		4	ZNF691	1	43317094	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	8094022	43317094	205933527	4	7090											
FGGY	55277	hgsc.bcm.edu	37	chr1	60139806	60139806	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggatttcgcttctgtacagGtatgtgaagaccagggggtg	8	11	16	6	1	1	2	0	1	1	1	2	3	1	3	1	4	1	3	1	4	3	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:60139806G>C	ENST00000303721.7	+	14	1686		c.e14+1		FGGY_ENST00000371218.4_Splice_Site|FGGY_ENST00000371212.1_Splice_Site|FGGY_ENST00000371210.1_Splice_Site	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing						carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					TTCTGTACAGGTATGTGAAGA	0.557																																					.		.											.	FGGY-69	0			c.1584+1G>C						.						161	106	124					1																	60139806		2203	4300	6503	SO:0001630	splice_region_variant	55277	exon15			GTACAGGTATGTG		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1512+1G>C	1.37:g.60139806G>C		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_001113411	0	0	0	0	0	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Splice_Site	SNP	ENST00000303721.7	37	CCDS611.2	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146268	0.77888	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212;ENST00000371210	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6873	0.95984	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FGGY	59912394	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.760000	0.91671	2.890000	0.99128	0.585000	0.79938	.	.		0.557	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	Intron	C	60139806	G	C	60139806	5	2	76	1	0	0	0	0	0	0	1	0	5890	1275	44	4	1639	4	FGGY	1	60139806	Splice_Site	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	16822712	60139806	189110815	5	7091											
CACHD1	57685	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	65143946	65143946	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccagaaagaatgcttcggggGgattgtgggagccaaaagtc	12	7	15	7	1	0	2	0	0	0	2	2	4	0	4	2	4	2	1	2	4	4	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:65143946G>A	ENST00000371073.2	+	23	3197	c.3197G>A	c.(3196-3198)gGg>gAg	p.G1066E	CACHD1_ENST00000290039.5_Missense_Mutation_p.G1015E|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1066					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						TGCTTCGGGGGGATTGTGGGA	0.473																																					p.G1015E		.											.	CACHD1-92	0			c.G3044A						.						94	95	95					1																	65143946		2203	4300	6503	SO:0001583	missense	57685	exon23			TCGGGGGGATTGT	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"von Willebrand factor type A and cache domain containing 1"	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3197G>A	1.37:g.65143946G>A	ENSP00000360113:p.Gly1066Glu	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	84	6	NM_020925	0	0	6	7	1	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	G	33	5.284715	0.95517	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.58210	0.35;0.4	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.66839	0.2830	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66056	-0.6018	10	0.87932	D	0	-25.7352	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1066	Q5VU97	CAHD1_HUMAN	E	1066;1015	ENSP00000360113:G1066E;ENSP00000290039:G1015E	ENSP00000290039:G1015E	G	+	2	0	CACHD1	64916534	1.000000	0.71417	0.941000	0.38009	0.996000	0.88848	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GGG	.		0.473	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		A	65143946	G	A	65143946	3	1	76	1	0	0	0	0	1	0	0	0	2543	1232	43	2	3134	2	CACHD1	1	65143946	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	5004140	65143946	184106675	6	7092											
FMO1	2326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171247924	171247924	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcaatataagcatccagatAtatttaaggacaagagagtc	17	9	9	6	0	0	2	0	0	0	2	2	4	1	3	1	2	1	2	1	2	7	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:171247924A>T	ENST00000354841.4	+	4	672	c.541A>T	c.(541-543)Ata>Tta	p.I181L	FMO1_ENST00000402921.2_Missense_Mutation_p.I118L|FMO1_ENST00000367750.3_Missense_Mutation_p.I181L|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	181					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GCATCCAGATATATTTAAGGA	0.418																																					p.I181L		.											.	FMO1-515	0			c.A541T						.						74	77	76					1																	171247924		2203	4300	6503	SO:0001583	missense	2326	exon5			CCAGATATATTTA	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.541A>T	1.37:g.171247924A>T	ENSP00000346901:p.Ile181Leu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	137	44	NM_002021	0	0	71	167	96	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	37	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131021	0.37630	.	.	ENSG00000010932	ENST00000367750;ENST00000433267;ENST00000402921;ENST00000354841	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.66	1.85	0.25348	.	0.462268	0.24947	N	0.034331	T	0.13243	0.0321	N	0.20610	0.595	0.09310	N	0.999994	B;B;B	0.13145	0.007;0.001;0.002	B;B;B	0.16289	0.015;0.001;0.01	T	0.21621	-1.0240	10	0.31617	T	0.26	-0.8266	5.0708	0.14606	0.5496:0.1475:0.3029:0.0	.	118;181;181	B7Z3P4;B2RCG5;Q01740	.;.;FMO1_HUMAN	L	181;181;118;181	ENSP00000356724:I181L;ENSP00000406982:I181L;ENSP00000385543:I118L;ENSP00000346901:I181L	ENSP00000346901:I181L	I	+	1	0	FMO1	169514548	0.000000	0.05858	0.998000	0.56505	0.998000	0.95712	0.351000	0.20096	0.401000	0.25424	0.460000	0.39030	ATA	.		0.418	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		T	171247924	A	T	171247924	3	4	76	1	0	0	0	0	1	0	0	0	5973	449	16	5	555	5	FMO1	1	171247924	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	106103978	171247924	78002697	7	7093											
C1orf9	51430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	172558217	172558217	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagtaaaggaaaagattatcTtgtgttagctcaaccaccct	14	11	8	8	0	2	1	1	0	1	1	2	3	2	2	2	1	2	3	2	1	7	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:172558217T>G	ENST00000263688.3	+	18	2195	c.1976T>G	c.(1975-1977)cTt>cGt	p.L659R	SUCO_ENST00000367723.4_Missense_Mutation_p.L810R|SUCO_ENST00000608151.1_Missense_Mutation_p.L811R|SUCO_ENST00000610051.1_Intron	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	659					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											AAAGATTATCTTGTGTTAGCT	0.383																																					p.L659R		.											.	.	0			c.T1976G						.						79	81	81					1																	172558217		2203	4299	6502	SO:0001583	missense	51430	exon18			ATTATCTTGTGTT	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1976T>G	1.37:g.172558217T>G	ENSP00000263688:p.Leu659Arg	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	88	30	NM_014283	0	0	7	13	6	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	37	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	T	3.471	-0.108011	0.06924	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	4.95	2.51	0.30379	.	0.913904	0.09394	N	0.808213	T	0.11324	0.0276	L	0.43152	1.355	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.06405	0.001;0.002;0.001	T	0.28170	-1.0052	9	0.18276	T	0.48	-0.0114	2.1827	0.03879	0.4718:0.1619:0.0:0.3663	.	659;811;659	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	R	811;659	.	ENSP00000263688:L659R	L	+	2	0	C1orf9	170824840	0.000000	0.05858	0.002000	0.10522	0.610000	0.37248	-0.219000	0.09228	0.693000	0.31634	0.460000	0.39030	CTT	.		0.383	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		G	172558217	T	G	172558217	3	3	76	1	0	0	0	0	1	0	0	0	2073	1609	56	5	2046	5	C1orf9	1	172558217	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	1310293	172558217	76692404	8	7094											
C1orf14	81626	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	182921876	182921876	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgctcaccttacagtcctgCagcacttcgtcgcaatacag	9	9	7	16	3	1	0	1	0	0	0	4	0	2	0	3	0	4	4	3	0	3	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:182921876C>T	ENST00000367547.3	-	1	629	c.393G>A	c.(391-393)ctG>ctA	p.L131L	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_5'Flank	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	203										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						TACAGTCCTGCAGCACTTCGT	0.627																																					p.L131L													.	SHCBP1L-91	0			c.G393A						.						40	37	38					1																	182921876		2203	4300	6503	SO:0001819	synonymous_variant	81626	exon1			GTCCTGCAGCACT	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 14"	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.393G>A	1.37:g.182921876C>T		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	30	7	NM_030933	0	0	0	0	0	Q4G195|Q9BZQ3|Q9H2B6	Silent	SNP	ENST00000367547.3	37	CCDS30955.1																																																																																			.		0.627	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182921876	C	T	182921876	2	4	76	1	0	0	0	0	0	0	0	1	2006	697	25	2		2	C1orf14	1	182921876	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	10363659	182921876	66328745	9	7095											
KIF21B	23046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	200973948	200973948	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctcgccagtagcccctgtCcgcttcagccgctctgagcc	4	8	10	19	4	2	1	1	1	1	0	4	1	3	1	6	0	3	4	6	0	1	2	rs140945427		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:200973948C>A	ENST00000422435.2	-	6	1162	c.846G>T	c.(844-846)cgG>cgT	p.R282R	KIF21B_ENST00000332129.2_Silent_p.R282R|KIF21B_ENST00000461742.2_Silent_p.R282R|KIF21B_ENST00000360529.5_Silent_p.R282R	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	282	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TAGCCCCTGTCCGCTTCAGCC	0.597																																					p.R282R		.											.	KIF21B-96	0			c.G846T						.						52	49	50					1																	200973948		2203	4300	6503	SO:0001819	synonymous_variant	23046	exon6			CCCTGTCCGCTTC	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"Kinesins", "WD repeat domain containing"	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.846G>T	1.37:g.200973948C>A		Somatic	68	2		WXS	Illumina HiSeq	Phase_I	84	26	NM_017596	0	0	3	3	0	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			C|1.000;T|0.000		0.597	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200973948	C	A	200973948	2	1	76	1	0	0	0	0	0	0	0	1	8310	842	30	4		4	KIF21B	1	200973948	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	18052072	200973948	48276673	10	7096											
TMEM81	388730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205053045	205053045	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttggcttgaaagggtttgAagacctcatcgtcagtggag	10	11	14	6	1	2	3	2	2	0	1	3	4	2	4	1	3	0	3	1	3	2	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:205053045A>C	ENST00000367167.3	-	1	600	c.404T>G	c.(403-405)tTc>tGc	p.F135C		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	135	Ig-like.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			AAAGGGTTTGAAGACCTCATC	0.468																																					p.F135C		.											.	TMEM81-68	0			c.T404G						.						87	92	90					1																	205053045		2203	4300	6503	SO:0001583	missense	388730	exon1			GGTTTGAAGACCT	BC061592	CCDS1450.1	1q32.1	2013-01-11			ENSG00000174529	ENSG00000174529		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32349	protein-coding gene	gene with protein product							Standard	NM_203376		Approved	UNQ2788, MGC75217, HC3107, KVLA2788	uc001hbt.3	Q6P7N7	OTTHUMG00000037103	ENST00000367167.3:c.404T>G	1.37:g.205053045A>C	ENSP00000356135:p.Phe135Cys	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	139	32	NM_203376	0	0	2	3	1	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	37	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.853325	0.51270	.	.	ENSG00000174529	ENST00000367167	T	0.42900	0.96	5.93	5.93	0.95920	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.64216	0.2578	M	0.72894	2.215	0.47245	D	0.999365	D	0.89917	1.0	D	0.91635	0.999	T	0.67562	-0.5639	10	0.87932	D	0	-6.5281	14.6242	0.68608	1.0:0.0:0.0:0.0	.	135	Q6P7N7	TMM81_HUMAN	C	135	ENSP00000356135:F135C	ENSP00000356135:F135C	F	-	2	0	TMEM81	203319668	1.000000	0.71417	0.999000	0.59377	0.171000	0.22731	5.953000	0.70290	2.281000	0.76405	0.533000	0.62120	TTC	.		0.468	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		C	205053045	A	C	205053045	3	2	76	1	0	0	0	0	1	0	0	0	16237	246	9	5	367	5	TMEM81	1	205053045	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	4079097	205053045	44197576	11	7097											
NT5C1B	93034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	18767651	18767651	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccgcagtgatgattcttGtgatccctgtgatggaaaga	9	13	11	8	1	1	5	0	4	1	1	3	6	3	6	2	1	0	1	2	1	1	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr2:18767651G>C	ENST00000359846.2	-	4	384	c.307C>G	c.(307-309)Caa>Gaa	p.Q103E	NT5C1B_ENST00000460052.1_5'UTR|NT5C1B_ENST00000600945.1_Missense_Mutation_p.Q103E|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.Q103E|NT5C1B_ENST00000304081.4_Missense_Mutation_p.Q43E|RNU6-1215P_ENST00000384441.1_RNA	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	103	Ser-rich.				nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GATGATTCTTGTGATCCCTGT	0.488																																					p.Q120E		.											.	NT5C1B-47	0			c.C358G						.						97	86	89					2																	18767651		2203	4300	6503	SO:0001583	missense	93034	exon4			ATTCTTGTGATCC	AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.307C>G	2.37:g.18767651G>C	ENSP00000352904:p.Gln103Glu	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	104	11	NM_001199087	0	0	0	0	0	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	37	CCDS33150.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.655456	0.29425	.	.	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846;ENST00000416783	D	0.91124	-2.79	4.79	4.79	0.61399	.	0.287423	0.25604	N	0.029528	D	0.84723	0.5535	L	0.29908	0.895	0.26210	N	0.979313	B;B;B;P;B;B;B;B	0.35745	0.366;0.366;0.278;0.518;0.39;0.264;0.209;0.313	B;B;B;B;B;B;B;B	0.35931	0.156;0.156;0.079;0.156;0.068;0.164;0.106;0.214	T	0.77930	-0.2403	10	0.37606	T	0.19	-30.2005	13.6483	0.62294	0.0:0.0:1.0:0.0	.	86;120;43;86;43;43;103;103	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-2;Q96P26;Q96P26-4	.;.;.;.;.;.;5NT1B_HUMAN;.	E	103;43;43;103;120	ENSP00000412639:Q43E	ENSP00000305979:Q43E	Q	-	1	0	NT5C1B-RDH14;NT5C1B	18631132	0.991000	0.36638	0.985000	0.45067	0.092000	0.18411	2.396000	0.44468	2.941000	0.99782	0.655000	0.94253	CAA	.		0.488	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			C	18767651	G	C	18767651	3	2	76	1	0	0	0	0	1	0	0	0	10712	1386	48	4	1553	4	NT5C1B	2	18767651	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		18767651	224431722	12	7098											
GPR155	151556	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	175346653	175346657	+	Frame_Shift_Del	DEL	GTTAA	GTTAA	-																															tggtcatattgactgcaatgGttaagttctctgcaggtaaa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	GTTAA	GTTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr2:175346653_175346657delGTTAA	ENST00000392552.2	-	2	266_270	c.28_32delTTAAC	c.(28-33)ttaaccfs	p.LT10fs	GPR155_ENST00000392551.2_Frame_Shift_Del_p.LT10fs|GPR155_ENST00000295500.4_Frame_Shift_Del_p.LT10fs	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	10					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						GACTGCAATGGTTAAGTTCTCTGCA	0.4																																					p.10_11del		.											.	GPR155-91	0			c.28_32del						.																																			SO:0001589	frameshift_variant	151556	exon2			.	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.28_32delTTAAC	2.37:g.175346653_175346657delGTTAA	ENSP00000376335:p.Leu10fs	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	162	45	NM_001267051	0	0	0	0	0	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Frame_Shift_Del	DEL	ENST00000392552.2	37	CCDS2259.1																																																																																			.		0.4	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		-	175346657	GTTAA	-	175346653	7	5	76	1	0	1	0	1	0	0	0	0	6680	1261	44	0	2640	0	GPR155	2	175346653	Frame_Shift_Del	DEL	GTTAA	TCGA-BQ-5892-01A-11D-1589-08	156579002	175346653	67852720	13	7099											
CPO	130749	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	207827299	207827299	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagttaattctcacaccttaCggctacaccaaaaataaatc	16	10	3	12	1	1	0	1	0	1	0	3	0	1	0	2	1	2	2	2	1	7	5			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr2:207827299C>T	ENST00000272852.3	+	7	784	c.738C>T	c.(736-738)taC>taT	p.Y246Y		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	246						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		TCACACCTTACGGCTACACCA	0.448																																					p.Y246Y		.											.	CPO-154	0			c.C738T						.						170	160	164					2																	207827299		2203	4300	6503	SO:0001819	synonymous_variant	130749	exon7			ACCTTACGGCTAC		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"metallocarboxypeptidase O", "metallocarboxypeptidase C"	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.738C>T	2.37:g.207827299C>T		Somatic	179	0		WXS	Illumina HiSeq	Phase_I	255	15	NM_173077	0	0	0	0	0	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			.		0.448	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		T	207827299	C	T	207827299	2	4	76	1	0	0	0	0	0	0	0	1	3826	547	19	1		1	CPO	2	207827299	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	32480646	207827299	35372074	14	7100											
VHL	7428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	10191506	10191506	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgatgcctccaggttgtcCggagcctagtcaagcctgag	8	8	13	12	2	1	1	1	1	0	0	3	3	3	2	5	2	4	1	5	2	2	2	rs5030820		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr3:10191506C>G	ENST00000256474.2	+	3	1339	c.499C>G	c.(499-501)Cgg>Ggg	p.R167G	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Missense_Mutation_p.R126G	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	167			R -> G (in VHLD; type I-II). {ECO:0000269|PubMed:9829911}.|R -> Q (in pheochromocytoma and VHLD; type II; common mutation; dbSNP:rs5030821). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.|R -> W (in pheochromocytoma and VHLD; type II; common mutation; dbSNP:rs5030820). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8592333, ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.R167W(8)|p.R167G(2)|p.R167fs*1(1)|p.V166fs*6(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCAGGTTGTCCGGAGCCTAGT	0.512		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																												p.R167G		.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	.	VHL-6694	12	Substitution - Missense(10)|Deletion - Frameshift(1)|Insertion - Frameshift(1)	kidney(8)|adrenal_gland(2)|large_intestine(1)|endometrium(1)	c.C499G	GRCh37	CM941383|CM941384|HX040002	VHL	M|X	rs5030820	.						92	84	87					3																	10191506		2203	4300	6503	SO:0001583	missense	7428	exon3	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	GTTGTCCGGAGCC	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.499C>G	3.37:g.10191506C>G	ENSP00000256474:p.Arg167Gly	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	58	24	NM_000551	0	0	5	11	6	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548531	0.65311	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99830	-7.01;-7.01	4.86	3.97	0.46021	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.85682	D	0.000000	D	0.99664	0.9875	M	0.68952	2.095	0.42468	D	0.992812	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97794	1.0240	10	0.54805	T	0.06	-6.8035	10.4067	0.44260	0.3559:0.6441:0.0:0.0	.	126;167	P40337-2;P40337	.;VHL_HUMAN	G	167;126;85	ENSP00000256474:R167G;ENSP00000344757:R126G	ENSP00000256474:R167G	R	+	1	2	VHL	10166506	0.999000	0.42202	0.908000	0.35775	0.831000	0.47069	2.914000	0.48797	1.375000	0.46248	0.655000	0.94253	CGG	C|1.000		0.512	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10191506	C	G	10191506	3	3	76	1	0	0	0	0	1	0	0	0	17195	643	23	4	509	4	VHL	3	10191506	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		10191506	187830924	15	7101											
BAP1	51533	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	52443866	52443866	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccctcctcacctgggtcgCtctccagctccagccagccc	4	8	7	22	1	2	0	1	0	1	0	7	0	5	0	8	1	3	2	8	1	0	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr3:52443866C>T	ENST00000327906.3	+	0	0				BAP1_ENST00000296288.5_Missense_Mutation_p.S10N|PHF7_ENST00000347025.2_5'Flank|BAP1_ENST00000460680.1_Missense_Mutation_p.S10N	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.S10T(1)|p.E7_S10delELES(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		ACCTGGGTCGCTCTCCAGCTC	0.746																																					p.S10N		.											.	BAP1-1032	2	Substitution - Missense(1)|Deletion - In frame(1)	kidney(2)	c.G29A						.						24	30	28					3																	52443866		2203	4298	6501	SO:0001631	upstream_gene_variant	8314	exon1			GGGTCGCTCTCCA	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		3.37:g.52443866C>T	Exception_encountered	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	48	24	NM_004656	0	0	0	0	0	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	37	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	C	35	5.450733	0.96205	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.61627	0.09;0.09	4.93	4.93	0.64822	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	0.000000	0.85682	D	0.000000	T	0.79131	0.4394	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83154	-0.0102	10	0.66056	D	0.02	-4.1481	15.9287	0.79644	0.0:1.0:0.0:0.0	.	10	Q92560	BAP1_HUMAN	N	10	ENSP00000417132:S10N;ENSP00000296288:S10N	ENSP00000296288:S10N	S	-	2	0	BAP1	52418906	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.832000	0.62759	2.289000	0.77006	0.561000	0.74099	AGC	.		0.746	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		T	52443866	C	T	52443866	1	4	76	0	1	0	0	0	0	0	0	0	1312	797	28	2		2	BAP1	3	52443866	5'Flank	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	42252360	52443866	145578564	16	7102											
HAUS3	79441	hgsc.bcm.edu	37	chr4	2242527	2242530	+	Frame_Shift_Del	DEL	TTCA	TTCA	-																															ctttcagacaacacgttctgTtcattcacattcccacaaaa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	TTCA	TTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:2242527_2242530delTTCA	ENST00000243706.4	-	2	373_376	c.144_147delTGAA	c.(142-147)aatgaafs	p.NE48fs	POLN_ENST00000511885.2_Intron|POLN_ENST00000515357.1_Intron|HAUS3_ENST00000506763.1_Frame_Shift_Del_p.NE48fs|HAUS3_ENST00000443786.2_Frame_Shift_Del_p.NE48fs	NM_024511.5	NP_078787.2	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	48					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						ACACGTTCTGTTCATTCACATTCC	0.407																																					p.48_49del		.											.	HAUS3-138	0			c.144_147del						.																																			SO:0001589	frameshift_variant	79441	exon2			.	AF040964	CCDS33941.1	4p16.3	2013-10-11	2009-04-20	2009-04-20	ENSG00000214367	ENSG00000214367		"HAUS augmin-like complex subunits"	28719	protein-coding gene	gene with protein product		613430	"chromosome 4 open reading frame 15"	C4orf15		19427217, 19812674	Standard	NM_024511		Approved	MGC4701, IT1, dgt3	uc003ges.1	Q68CZ6		ENST00000243706.4:c.144_147delTGAA	4.37:g.2242531_2242534delTTCA	ENSP00000243706:p.Asn48fs	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	148	39	NM_024511	0	0	0	0	0	B4DF64|O43606|Q8TAZ5|Q9BTJ9	Frame_Shift_Del	DEL	ENST00000243706.4	37	CCDS33941.1																																																																																			.		0.407	HAUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357446.1	NM_024511		-	2242530	TTCA	-	2242527	7	5	76	1	0	1	0	1	0	0	0	0	6988	1722	60	0	1680	0	HAUS3	4	2242527	Frame_Shift_Del	DEL	TTCA	TCGA-BQ-5892-01A-11D-1589-08		2242527	188911749	17	7103	81	2									
HAUS3	79441	hgsc.bcm.edu;bcgsc.ca	37	chr4	2242534	2242534	+	Missense_Mutation	SNP	A	A	C																															acaacacgttctgttcattcAcattcccacaaaaccacttc																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:2242534A>C	ENST00000243706.4	-	2	369	c.140T>G	c.(139-141)gTg>gGg	p.V47G	POLN_ENST00000511885.2_Intron|POLN_ENST00000515357.1_Intron|HAUS3_ENST00000506763.1_Missense_Mutation_p.V47G|HAUS3_ENST00000443786.2_Missense_Mutation_p.V47G	NM_024511.5	NP_078787.2	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	47					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CTGTTCATTCACATTCCCACA	0.413																																					p.V47G		.											.	HAUS3-138	0			c.T140G						.						121	110	114					4																	2242534		2203	4300	6503	SO:0001583	missense	79441	exon2			TCATTCACATTCC	AF040964	CCDS33941.1	4p16.3	2013-10-11	2009-04-20	2009-04-20	ENSG00000214367	ENSG00000214367		"HAUS augmin-like complex subunits"	28719	protein-coding gene	gene with protein product		613430	"chromosome 4 open reading frame 15"	C4orf15		19427217, 19812674	Standard	NM_024511		Approved	MGC4701, IT1, dgt3	uc003ges.1	Q68CZ6		ENST00000243706.4:c.140T>G	4.37:g.2242534A>C	ENSP00000243706:p.Val47Gly	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	153	13	NM_024511	0	0	5	5	0	B4DF64|O43606|Q8TAZ5|Q9BTJ9	Missense_Mutation	SNP	ENST00000243706.4	37	CCDS33941.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101593	0.76983	.	.	ENSG00000214367	ENST00000506763;ENST00000243706;ENST00000443786	T;T	0.59638	0.25;0.25	4.68	4.68	0.58851	.	0.084524	0.49305	U	0.000154	T	0.70596	0.3242	M	0.78049	2.395	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.62089	0.898;0.898	T	0.74222	-0.3735	10	0.87932	D	0	-17.236	8.3587	0.32346	0.9107:0.0:0.0893:0.0	.	47;47	B4DF64;Q68CZ6	.;HAUS3_HUMAN	G	47	ENSP00000243706:V47G;ENSP00000392903:V47G	ENSP00000243706:V47G	V	-	2	0	HAUS3	2212332	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.993000	0.70616	1.850000	0.53721	0.459000	0.35465	GTG	.		0.413	HAUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357446.1	NM_024511		C	2242534	A	C	2242534	3	2	76	1	0	0	0	0	1	0	0	0	6988	159	6	5	1687	5	HAUS3	4	2242534	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	7	2242534	188911742	18	7104	81	2									
APBB2	323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	41015603	41015603	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccttccccaggggtacctgTttcatccggggagctgggtg	4	10	15	12	1	1	0	1	0	0	0	3	1	3	1	5	5	2	3	5	5	1	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:41015603T>A	ENST00000295974.8	-	6	1461	c.832A>T	c.(832-834)Aca>Tca	p.T278S	APBB2_ENST00000506352.1_Missense_Mutation_p.T278S|APBB2_ENST00000508593.1_Missense_Mutation_p.T278S|APBB2_ENST00000513140.1_Missense_Mutation_p.T278S	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	278					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						GGGGTACCTGTTTCATCCGGG	0.507																																					p.T278S	Ovarian(3;20 75 16686 49997)	.											.	APBB2-92	0			c.A832T						.						123	121	122					4																	41015603		1967	4143	6110	SO:0001583	missense	323	exon6			TACCTGTTTCATC	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.832A>T	4.37:g.41015603T>A	ENSP00000295974:p.Thr278Ser	Somatic	299	2		WXS	Illumina HiSeq	Phase_I	327	89	NM_173075	0	0	0	0	0	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	37	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.609|9.609	1.130697|1.130697	0.21041|0.21041	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000513611|ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352	.|T;T;T;T	.|0.16073	.|2.38;2.38;2.38;2.37	6.03|6.03	-1.64|-1.64	0.08318|0.08318	.|.	.|0.353536	.|0.31484	.|N	.|0.007572	T|T	0.09512|0.09512	0.0234|0.0234	L|L	0.31065|0.31065	0.9|0.9	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.26602	.|0.016;0.002;0.005;0.154	.|B;B;B;B	.|0.25759	.|0.022;0.005;0.007;0.063	T|T	0.30001|0.30001	-0.9993|-0.9993	5|10	.|0.09338	.|T	.|0.73	.|.	11.3558|11.3558	0.49615|0.49615	0.0:0.369:0.0:0.631|0.0:0.369:0.0:0.631	.|.	.|261;278;278;278	.|B4DJ88;E9PG87;Q92870-2;Q92870	.|.;.;.;APBB2_HUMAN	I|S	267|278;277;278;278;278	.|ENSP00000295974:T278S;ENSP00000426018:T278S;ENSP00000427211:T278S;ENSP00000421539:T278S	.|ENSP00000295974:T278S	N|T	-|-	2|1	0|0	APBB2|APBB2	40710360|40710360	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.071000|0.071000	0.16799|0.16799	1.642000|1.642000	0.37207|0.37207	-0.038000|-0.038000	0.13624|0.13624	0.455000|0.455000	0.32223|0.32223	AAC|ACA	.		0.507	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		A	41015603	T	A	41015603	3	1	76	1	0	0	0	0	1	0	0	0	761	1725	60	5	1499	5	APBB2	4	41015603	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	38773069	41015603	150138673	19	7105											
TMPRSS11A	339967	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	68777129	68777129	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtagactccaggcttgtcCttttgaccacagttatctcc	7	14	8	12	0	1	2	0	1	1	1	4	2	3	2	4	1	0	3	4	1	2	5	rs376494815		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:68777129C>T	ENST00000334830.7	-	10	1943	c.1197G>A	c.(1195-1197)aaG>aaA	p.K399K	TMPRSS11A_ENST00000396188.2_Silent_p.K396K|TMPRSS11A_ENST00000508048.1_Silent_p.K395K|UBA6-AS1_ENST00000500538.2_RNA			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	399	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						CAGGCTTGTCCTTTTGACCAC	0.403																																					p.K399K	NSCLC(26;2 894 10941 14480 22546)	.											.	TMPRSS11A-69	0			c.G1197A						.	C	,	0,4406		0,0,2203	181	170	174		1188,1197	3.8	1	4		174	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMPRSS11A	NM_001114387.1,NM_182606.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	396/419,399/422	68777129	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	339967	exon10			CTTGTCCTTTTGA	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1197G>A	4.37:g.68777129C>T		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	176	9	NM_182606	0	0	0	0	0	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Silent	SNP	ENST00000334830.7	37	CCDS3519.1																																																																																			.		0.403	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		T	68777129	C	T	68777129	2	4	76	1	0	0	0	0	0	0	0	1	16271	680	24	2		2	TMPRSS11A	4	68777129	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	27761526	68777129	122377147	20	7106											
ALPK1	80216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	113333046	113333046	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggcggctattgtgttcttgGtggaccggttcctgtatggg	3	14	16	8	3	1	0	0	0	1	0	2	1	2	1	2	6	0	4	2	6	2	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:113333046G>A	ENST00000458497.1	+	5	619	c.340G>A	c.(340-342)Gtg>Atg	p.V114M	ALPK1_ENST00000505912.1_3'UTR|ALPK1_ENST00000177648.9_Missense_Mutation_p.V114M|ALPK1_ENST00000504176.2_Missense_Mutation_p.V36M	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	114							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TGTGTTCTTGGTGGACCGGTT	0.622																																					p.V114M		.											.	ALPK1-337	0			c.G340A						.						54	51	52					4																	113333046		2203	4300	6503	SO:0001583	missense	80216	exon5			TTCTTGGTGGACC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.340G>A	4.37:g.113333046G>A	ENSP00000398048:p.Val114Met	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	39	7	NM_001102406	0	0	2	6	4	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	5.078	0.200114	0.09652	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000309610;ENST00000504176	T;T;T	0.24151	1.87;1.87;1.87	5.34	-1.67	0.08238	.	0.652897	0.16722	N	0.202210	T	0.05364	0.0142	N	0.00538	-1.39	0.20873	N	0.999835	B;B;B;B	0.18610	0.029;0.023;0.006;0.009	B;B;B;B	0.12837	0.008;0.008;0.005;0.004	T	0.39231	-0.9624	10	0.18276	T	0.48	0.8551	6.1882	0.20510	0.448:0.3512:0.2008:0.0	.	36;89;89;114	F5H138;Q9H623;E7EX13;Q96QP1	.;.;.;ALPK1_HUMAN	M	114;114;89;36	ENSP00000398048:V114M;ENSP00000177648:V114M;ENSP00000426044:V36M	ENSP00000177648:V114M	V	+	1	0	ALPK1	113552495	1.000000	0.71417	0.016000	0.15963	0.097000	0.18754	2.098000	0.41757	-0.525000	0.06391	-0.502000	0.04539	GTG	.		0.622	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		A	113333046	G	A	113333046	3	1	76	1	0	0	0	0	1	0	0	0	544	1261	44	2	350	2	ALPK1	4	113333046	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	44555917	113333046	77821230	21	7107											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123128292	123128292	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagactggtctagtgacaGtcctccagacattttttcat	10	14	7	10	0	3	3	2	1	1	2	5	3	5	3	2	1	0	0	2	1	2	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:123128292G>C	ENST00000264501.4	+	16	1899	c.1526G>C	c.(1525-1527)aGt>aCt	p.S509T	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Missense_Mutation_p.S509T|KIAA1109_ENST00000388738.3_Missense_Mutation_p.S509T			Q2LD37	K1109_HUMAN	KIAA1109	509					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TCTAGTGACAGTCCTCCAGAC	0.313																																					p.S509T		.											.	KIAA1109-80	0			c.G1526C						.						117	112	114					4																	123128292		1798	4073	5871	SO:0001583	missense	84162	exon14			GTGACAGTCCTCC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1526G>C	4.37:g.123128292G>C	ENSP00000264501:p.Ser509Thr	Somatic	300	0		WXS	Illumina HiSeq	Phase_I	276	65	NM_015312	0	0	1	3	2	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.47|11.47	1.647458|1.647458	0.29246|0.29246	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.23147	.|2.51;2.51;1.92	5.67|5.67	4.81|4.81	0.61882|0.61882	.|.	.|0.580238	.|0.15339	.|N	.|0.267600	T|T	0.38983|0.38983	0.1061|0.1061	L|L	0.33485|0.33485	1.01|1.01	0.42164|0.42164	D|D	0.991613|0.991613	.|D	.|0.58268	.|0.982	.|D	.|0.67548	.|0.952	T|T	0.08848|0.08848	-1.0702|-1.0702	5|10	.|0.45353	.|T	.|0.12	.|.	13.7177|13.7177	0.62708|0.62708	0.0749:0.0:0.9251:0.0|0.0749:0.0:0.9251:0.0	.|.	.|509	.|Q2LD37	.|K1109_HUMAN	H|T	341|509	.|ENSP00000264501:S509T;ENSP00000373390:S509T;ENSP00000389925:S509T	.|ENSP00000264501:S509T	Q|S	+|+	3|2	2|0	KIAA1109|KIAA1109	123347742|123347742	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.198000|3.198000	0.51035|0.51035	1.349000|1.349000	0.45751|0.45751	0.655000|0.655000	0.94253|0.94253	CAG|AGT	.		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123128292	G	C	123128292	3	2	76	1	0	0	0	0	1	0	0	0	8229	1029	36	4	1580	4	KIAA1109	4	123128292	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	9795246	123128292	68025984	22	7108											
MGC42105	167359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	43280172	43280172	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgggcgattttggattcAgcacagtaagcaaaaaaggt	14	9	13	5	1	1	0	1	0	0	0	1	2	1	1	0	4	2	3	0	4	4	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:43280172A>G	ENST00000512796.1	+	4	2151	c.652A>G	c.(652-654)Agc>Ggc	p.S218G	NIM1_ENST00000326035.2_Missense_Mutation_p.S218G			Q8IY84	NIM1_HUMAN		218	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TTTTGGATTCAGCACAGTAAG	0.433																																					p.S218G		.											.	.	0			c.A652G						.						93	87	89					5																	43280172		2203	4300	6503	SO:0001583	missense	0	exon4			GGATTCAGCACAG																												ENST00000512796.1:c.652A>G	5.37:g.43280172A>G	ENSP00000420849:p.Ser218Gly	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	120	40	NM_153361	0	0	1	2	1	B3KVM1	Missense_Mutation	SNP	ENST00000512796.1	37	CCDS3943.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.726016	0.89298	.	.	ENSG00000177453	ENST00000326035;ENST00000512796	T;T	0.30448	1.53;1.53	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56819	0.2011	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.56062	-0.8041	10	0.33940	T	0.23	.	15.9442	0.79782	1.0:0.0:0.0:0.0	.	218	Q8IY84	NIM1_HUMAN	G	218	ENSP00000313572:S218G;ENSP00000420849:S218G	ENSP00000313572:S218G	S	+	1	0	AC114947.1	43315929	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.166000	0.68216	0.533000	0.62120	AGC	.		0.433	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			G	43280172	A	G	43280172	3	3	76	1	0	0	0	0	1	0	0	0	9577	188	7	3	662	3	MGC42105	5	43280172	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08		43280172	137635088	23	7109											
HTR1A	3350	broad.mit.edu	37	chr5	63257393	63257393	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccacgcacgcattgcccaGcaccgcgcagaagatgagcg	11	3	11	16	5	0	3	0	1	0	2	0	3	0	3	3	0	3	4	3	0	1	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:63257393G>A	ENST00000323865.3	-	1	387	c.154C>T	c.(154-156)Ctg>Ttg	p.L52L	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	52					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GCATTGCCCAGCACCGCGCAG	0.592																																					p.L52L													.	HTR1A-94	0			c.C154T						.						78	79	78					5																	63257393		2203	4300	6503	SO:0001819	synonymous_variant	3350	exon1			TGCCCAGCACCGC	AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5286	protein-coding gene	gene with protein product		109760	"5-hydroxytryptamine (serotonin) receptor 1A"	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.154C>T	5.37:g.63257393G>A		Somatic	85	1		WXS	Illumina HiSeq	Phase_I	82	3	NM_000524	0	0	0	0	0	Q6LAE7	Silent	SNP	ENST00000323865.3	37	CCDS34168.1																																																																																			.		0.592	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		A	63257393	G	A	63257393	2	1	76	1	0	0	0	0	0	0	0	1	7457	962	34	2		2	HTR1A	5	63257393	Silent	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	19977221	63257393	117657867	24	7110											
BDP1	55814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	70800508	70800508	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaggaagatgtcatattaCagcctgagaaaaatgattct	17	10	9	5	0	2	4	1	2	1	3	2	6	2	5	1	1	2	0	1	1	6	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:70800508C>T	ENST00000358731.4	+	16	2565	c.2302C>T	c.(2302-2304)Cag>Tag	p.Q768*	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	768					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGTCATATTACAGCCTGAGAA	0.328																																					p.Q768X		.											.	BDP1-92	0			c.C2302T						.						94	86	88					5																	70800508		1839	4090	5929	SO:0001587	stop_gained	55814	exon16			ATATTACAGCCTG	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.2302C>T	5.37:g.70800508C>T	ENSP00000351575:p.Gln768*	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	143	42	NM_018429	0	0	2	3	1	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Nonsense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	C	38	7.211890	0.98139	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	.	.	.	4.86	1.8	0.24995	.	0.592434	0.16073	N	0.230909	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9453	0.29982	0.165:0.4911:0.3439:0.0	.	.	.	.	X	768;768;348;768	.	ENSP00000351575:Q768X	Q	+	1	0	BDP1	70836264	0.007000	0.16637	0.008000	0.14137	0.007000	0.05969	0.576000	0.23744	0.600000	0.29862	0.603000	0.83216	CAG	.		0.328	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70800508	C	T	70800508	4	4	76	1	0	0	0	0	0	1	0	0	1396	479	17	2	2364	2	BDP1	5	70800508	Nonsense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	7543115	70800508	110114752	25	7111											
SAR1B	51128	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	133956720	133956720	+	Frame_Shift_Del	DEL	T	T	-																															tccaatccaagaaataccagTttaccagttttcttatataa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:133956720delT	ENST00000402673.2	-	3	359	c.81delA	c.(79-81)aaafs	p.K27fs	SAR1B_ENST00000439578.1_Frame_Shift_Del_p.K27fs|SAR1B_ENST00000507419.1_Intron	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	27					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAAATACCAGTTTACCAGTTT	0.343																																					p.K27fs		.											.	SAR1B-227	0			c.81delA						.						179	162	168					5																	133956720		2202	4300	6502	SO:0001589	frameshift_variant	51128	exon4			.	AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700			10535	protein-coding gene	gene with protein product		607690	"SAR1a gene homolog (S. cerevisiae) 2", "SAR1a gene homolog 2 (S. cerevisiae)", "SAR1 homolog B (S. cerevisiae)"	SARA2			Standard	NM_001033503		Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	ENST00000402673.2:c.81delA	5.37:g.133956720delT	ENSP00000385432:p.Lys27fs	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	170	41	NM_001033503	0	0	0	0	0	D3DQA4|Q567T4	Frame_Shift_Del	DEL	ENST00000402673.2	37	CCDS4177.1																																																																																			.		0.343	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103		-	133956720	T	-	133956720	7	5	76	1	0	1	0	1	0	0	0	0	13872	1722	60	0	535	0	SAR1B	5	133956720	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	63156212	133956720	46958540	26	7112											
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	179192969	179192987	+	Frame_Shift_Del	DEL	GGGTCTGCAGGGCAGACCT	GGGTCTGCAGGGCAGACCT	-																															gctctccacaagtgagggccGggtctgcagggcagaccttt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	GGGTCTGCAGGGCAGACCT	GGGTCTGCAGGGCAGACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:179192969_179192987delGGGTCTGCAGGGCAGACCT	ENST00000292599.3	+	2	1221_1239	c.958_976delGGGTCTGCAGGGCAGACCT	c.(958-978)gggtctgcagggcagacctttfs	p.GSAGQTF320fs	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTGAGGGCCGGGTCTGCAGGGCAGACCTTTCTGGGGCC	0.571																																					p.320_326del		.											.	MAML1-848	0			c.958_976del						.																																			SO:0001589	frameshift_variant	9794	exon2			.	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.958_976delGGGTCTGCAGGGCAGACCT	5.37:g.179192969_179192987delGGGTCTGCAGGGCAGACCT	ENSP00000292599:p.Gly320fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	89	21	NM_014757	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000292599.3	37	CCDS34315.1																																																																																			.		0.571	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		-	179192987	GGGTCTGCAGGGCAGACCT	-	179192969	7	5	76	1	0	1	0	1	0	0	0	0	9230	1116	39	0	964	0	MAML1	5	179192969	Frame_Shift_Del	DEL	GGGTCTGCAGGGCAGACCT	TCGA-BQ-5892-01A-11D-1589-08	45236249	179192969	1722291	27	7113											
PECI	10455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	4128067	4128067	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcataatttcatgatacatcTgtgtaatgggaagacaagga	15	11	10	5	0	2	2	1	1	1	1	2	4	2	4	0	2	1	2	0	2	5	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr6:4128067T>A	ENST00000380118.3	-	5	538		c.e5-2		ECI2_ENST00000465828.1_Splice_Site|C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000413766.2_Splice_Site|ECI2_ENST00000361538.2_Splice_Site|C6orf201_ENST00000333388.5_Intron|ECI2_ENST00000380125.2_Splice_Site			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2						fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						ATGATACATCTGTGTAATGGG	0.398																																					.		.											.	ECI2-90	0			c.412-2A>T						.						116	118	117					6																	4128067		2203	4300	6503	SO:0001630	splice_region_variant	10455	exon6			TACATCTGTGTAA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"acyl-Coenzyme A binding domain containing 2", " Hepatocellular carcinoma-associated antigen 88"	608024	"peroxisomal D3,D2-enoyl-CoA isomerase"	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.502-2A>T	6.37:g.4128067T>A		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	194	53	NM_006117	0	0	0	0	0	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Splice_Site	SNP	ENST00000380118.3	37	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	T	12.53	1.966691	0.34659	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000361538;ENST00000465828;ENST00000495548	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6923	0.69096	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ECI2	4073066	1.000000	0.71417	0.918000	0.36340	0.109000	0.19521	6.484000	0.73621	2.148000	0.66965	0.533000	0.62120	.	.		0.398	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	Intron	A	4128067	T	A	4128067	5	1	76	1	0	0	0	0	0	0	1	0	11742	1594	55	5	708	5	PECI	6	4128067	Splice_Site	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		4128067	166987000	28	7114											
SCGN	10590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	25701539	25701539	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtctgagctggctttgtgTcttgggctgaaaatcaaccc	9	12	11	9	0	3	2	1	2	2	0	3	2	3	2	1	2	2	3	1	2	4	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr6:25701539T>C	ENST00000377961.2	+	11	975	c.807T>C	c.(805-807)tgT>tgC	p.C269C	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	269	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						TGGCTTTGTGTCTTGGGCTGA	0.463																																					p.C269C		.											.	SCGN-93	0			c.T807C						.						146	132	137					6																	25701539		2203	4300	6503	SO:0001819	synonymous_variant	10590	exon11			TTTGTGTCTTGGG	BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"EF-hand domain containing"	16941	protein-coding gene	gene with protein product	"calbindin-like"	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.807T>C	6.37:g.25701539T>C		Somatic	145	1		WXS	Illumina HiSeq	Phase_I	197	57	NM_006998	0	0	4	14	10	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Silent	SNP	ENST00000377961.2	37	CCDS4561.1																																																																																			.		0.463	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			C	25701539	T	C	25701539	2	2	76	1	0	0	0	0	0	0	0	1	13935	1673	58	3		3	SCGN	6	25701539	Silent	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	21573472	25701539	145413528	29	7115											
SKIV2L	6499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31937328	31937328	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagggctctcagggacccctGagggcctggtggtccgctgc	4	7	16	14	1	1	1	1	1	1	0	3	2	2	2	4	5	1	2	4	5	0	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr6:31937328G>A	ENST00000375394.2	+	28	3690	c.3577G>A	c.(3577-3579)Gag>Aag	p.E1193K	STK19_ENST00000375333.2_5'Flank|SKIV2L_ENST00000544581.1_Missense_Mutation_p.E1000K|STK19_ENST00000375331.2_5'Flank|DXO_ENST00000478221.1_5'Flank	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	1193					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						AGGGACCCCTGAGGGCCTGGT	0.662																																					p.E1193K		.											.	SKIV2L-290	0			c.G3577A						.						64	77	72					6																	31937328		1511	2709	4220	SO:0001583	missense	6499	exon28			ACCCCTGAGGGCC		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.3577G>A	6.37:g.31937328G>A	ENSP00000364543:p.Glu1193Lys	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	160	41	NM_006929	0	0	30	41	11	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	37	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946649	0.92593	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.39229	1.09;1.09	5.38	5.38	0.77491	DSH, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71221	0.3314	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80353	-0.1418	10	0.87932	D	0	-26.0112	17.9328	0.89004	0.0:0.0:1.0:0.0	.	1193	Q15477	SKIV2_HUMAN	K	1193;1035;1000	ENSP00000364543:E1193K;ENSP00000442645:E1000K	ENSP00000364543:E1193K	E	+	1	0	SKIV2L	32045307	1.000000	0.71417	0.476000	0.27291	0.947000	0.59692	8.247000	0.89830	2.507000	0.84556	0.655000	0.94253	GAG	.		0.662	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31937328	G	A	31937328	3	1	76	1	0	0	0	0	1	0	0	0	14391	1291	45	2	3687	2	SKIV2L	6	31937328	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	6235789	31937328	139177739	30	7116											
C7orf51	222950	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	100087003	100087003	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctgtggacctacccagcCacagcagctgggctcaagag	9	5	12	15	1	1	1	1	0	0	1	1	2	1	2	4	2	4	4	4	2	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr7:100087003C>T	ENST00000300179.2	+	4	1818	c.1659C>T	c.(1657-1659)gcC>gcT	p.A553A	NYAP1_ENST00000454988.1_Silent_p.A496A|NYAP1_ENST00000423930.1_Silent_p.A553A	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	553					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CCTACCCAGCCACAGCAGCTG	0.682																																					p.A553A		.											.	.	0			c.C1659T						.						16	19	18					7																	100087003		2157	4234	6391	SO:0001819	synonymous_variant	222950	exon4			CCCAGCCACAGCA	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"chromosome 7 open reading frame 51", "KIAA1486-like"	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.1659C>T	7.37:g.100087003C>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	81	19	NM_173564	0	0	0	0	0	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	37	CCDS5696.1																																																																																			.		0.682	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100087003	C	T	100087003	2	4	76	1	0	0	0	0	0	0	0	1	2406	581	21	2		2	C7orf51	7	100087003	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		100087003	59051660	31	7117											
LAMB1	3912	broad.mit.edu	37	chr7	107580801	107580801	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctggggtcacagtcacAggctagaagggaataagcaa	13	5	13	10	0	2	1	2	0	0	1	2	2	2	2	2	4	1	2	2	4	5	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr7:107580801A>G	ENST00000222399.6	-	25	3624	c.3394T>C	c.(3394-3396)Tgt>Cgt	p.C1132R	CTB-13F3.1_ENST00000608515.1_RNA|LAMB1_ENST00000393561.1_Missense_Mutation_p.C1156R	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1132	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TCACAGTCACAGGCTAGAAGG	0.502																																					p.C1132R													.	LAMB1-97	0			c.T3394C						.						56	50	52					7																	107580801		2203	4300	6503	SO:0001583	missense	3912	exon25			AGTCACAGGCTAG	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3394T>C	7.37:g.107580801A>G	ENSP00000222399:p.Cys1132Arg	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	63	3	NM_002291	0	0	1	1	0	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.187734	0.78789	.	.	ENSG00000091136	ENST00000393561;ENST00000222399	D;D	0.94330	-3.4;-3.4	5.3	5.3	0.74995	EGF-like, laminin (4);	.	.	.	.	D	0.98406	0.9470	H	0.99764	4.76	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99620	1.0983	9	0.87932	D	0	.	15.3999	0.74830	1.0:0.0:0.0:0.0	.	1132;1156	P07942;G3XAI2	LAMB1_HUMAN;.	R	1156;1132	ENSP00000377191:C1156R;ENSP00000222399:C1132R	ENSP00000222399:C1132R	C	-	1	0	LAMB1	107368037	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.761000	0.91691	2.225000	0.72522	0.460000	0.39030	TGT	.		0.502	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		G	107580801	A	G	107580801	3	3	76	1	0	0	0	0	1	0	0	0	8631	188	7	3	2006	3	LAMB1	7	107580801	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	7493798	107580801	51557862	32	7118											
CADPS2	93664	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	122130209	122130210	+	Frame_Shift_Ins	INS	-	-	A																															aattgcaggaactggtttatINSatgattgacctgtggcccta																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr7:122130209_122130210insA	ENST00000449022.2	-	11	1796_1797	c.1777_1778insT	c.(1777-1779)tatfs	p.Y593fs	CADPS2_ENST00000313070.7_Frame_Shift_Ins_p.Y593fs|CADPS2_ENST00000334010.7_Frame_Shift_Ins_p.Y593fs|CADPS2_ENST00000412584.2_Frame_Shift_Ins_p.Y593fs|CADPS2_ENST00000476131.1_5'Flank	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	593					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						AACTGGTTTATATGATTGACCT	0.376																																					p.Y593fs		.											.	CADPS2-94	0			c.1778_1779insT						.																																			SO:0001589	frameshift_variant	93664	exon11			.		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.1778dupT	7.37:g.122130210_122130210dupA	ENSP00000398481:p.Tyr593fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	145	39	NM_001167940	0	0	0	0	0	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Frame_Shift_Ins	INS	ENST00000449022.2	37	CCDS55158.1																																																																																			.		0.376	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		A	122130210	-	A	122130209	7	5	76	1	0	1	1	0	0	0	0	0	2577	1406	49	0	2236	0	CADPS2	7	122130209	Frame_Shift_Ins	INS	-	TCGA-BQ-5892-01A-11D-1589-08	14549408	122130209	37008454	33	7119											
KIAA1967	57805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	22473664	22473664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggaggcggccaaggaagaagCcaccaaggaggaagaagcca	16	0	16	9	1	0	2	0	0	0	2	0	6	0	6	4	6	2	0	4	6	6	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr8:22473664C>T	ENST00000308511.4	+	14	1997	c.1748C>T	c.(1747-1749)gCc>gTc	p.A583V	CCAR2_ENST00000389279.3_Missense_Mutation_p.A583V|CCAR2_ENST00000520861.1_Missense_Mutation_p.A258V|RP11-582J16.5_ENST00000521025.1_RNA			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	583					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										AAGGAAGAAGCCACCAAGGAG	0.552																																					p.A583V		.											.	KIAA1967-92	0			c.C1748T						.						94	92	93					8																	22473664		2203	4300	6503	SO:0001583	missense	57805	exon14			AAGAAGCCACCAA	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1748C>T	8.37:g.22473664C>T	ENSP00000310670:p.Ala583Val	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	133	39	NM_021174	0	0	32	61	29	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.012|2.012	-0.426830|-0.426830	0.04701|0.04701	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861|ENST00000520738	T;T;T|.	0.31769|.	1.48;1.48;1.48|.	3.18|3.18	0.0872|0.0872	0.14449|0.14449	.|.	0.654422|.	0.13268|.	N|.	0.400758|.	T|T	0.14313|0.14313	0.0346|0.0346	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.04013|.	0.001;0.0|.	T|T	0.24404|0.24404	-1.0161|-1.0161	10|5	0.28530|.	T|.	0.3|.	-1.6537|-1.6537	3.0601|3.0601	0.06197|0.06197	0.1906:0.4477:0.0:0.3617|0.1906:0.4477:0.0:0.3617	.|.	258;583|.	G3V119;Q8N163|.	.;K1967_HUMAN|.	V|S	583;583;258|275	ENSP00000310670:A583V;ENSP00000373930:A583V;ENSP00000429773:A258V|.	ENSP00000310670:A583V|.	A|P	+|+	2|1	0|0	KIAA1967|KIAA1967	22529609|22529609	0.001000|0.001000	0.12720|0.12720	0.050000|0.050000	0.19076|0.19076	0.319000|0.319000	0.28217|0.28217	-0.315000|-0.315000	0.08081|0.08081	-0.013000|-0.013000	0.14199|0.14199	-0.323000|-0.323000	0.08544|0.08544	GCC|CCA	.		0.552	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		T	22473664	C	T	22473664	3	4	76	1	0	0	0	0	1	0	0	0	8286	739	26	2	1798	2	KIAA1967	8	22473664	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		22473664	123890358	34	7120											
KCTD9	54793	broad.mit.edu	37	chr8	25293942	25293942	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaacaggcttacctttattgCcacttctaggtgttcaatca	11	14	6	10	0	3	0	2	0	1	0	3	0	3	0	2	2	3	2	2	2	5	7			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr8:25293942C>T	ENST00000221200.4	-	7	779	c.559G>A	c.(559-561)Gca>Aca	p.A187T	KCTD9_ENST00000518067.1_5'Flank	NM_017634.3	NP_060104.2	Q7L273	KCTD9_HUMAN	potassium channel tetramerization domain containing 9	187					protein homooligomerization (GO:0051260)					breast(1)|endometrium(2)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	12		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Epithelial(17;2.39e-12)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0438)		ACCTTTATTGCCACTTCTAGG	0.323																																					p.A187T													.	KCTD9-90	0			c.G559A						.						96	101	99					8																	25293942		2203	4300	6503	SO:0001583	missense	54793	exon7			TTATTGCCACTTC	BC021216	CCDS6048.1	8p21.1	2013-06-20	2013-06-20		ENSG00000104756	ENSG00000104756		"BTB/POZ domain containing"	22401	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 9"			11483580	Standard	NM_017634		Approved	FLJ20038, BTBD27	uc003xeo.3	Q7L273	OTTHUMG00000099428	ENST00000221200.4:c.559G>A	8.37:g.25293942C>T	ENSP00000221200:p.Ala187Thr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	80	4	NM_017634	0	0	0	0	0	Q6NUM8|Q9NXV4	Missense_Mutation	SNP	ENST00000221200.4	37	CCDS6048.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467383	0.43839	.	.	ENSG00000104756	ENST00000221200	T	0.44083	0.93	5.58	5.58	0.84498	BTB/POZ-like (1);BTB/POZ fold (2);	0.298399	0.30830	U	0.008781	T	0.26195	0.0639	N	0.08118	0	0.53005	D	0.999966	B	0.06786	0.001	B	0.06405	0.002	T	0.11084	-1.0602	10	0.13108	T	0.6	.	19.9348	0.97133	0.0:1.0:0.0:0.0	.	187	Q7L273	KCTD9_HUMAN	T	187	ENSP00000221200:A187T	ENSP00000221200:A187T	A	-	1	0	KCTD9	25349859	0.995000	0.38212	0.998000	0.56505	0.863000	0.49368	3.248000	0.51430	2.789000	0.95967	0.591000	0.81541	GCA	.		0.323	KCTD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216890.1	NM_017634		T	25293942	C	T	25293942	3	4	76	1	0	0	0	0	1	0	0	0	8137	739	26	2	634	2	KCTD9	8	25293942	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	2820278	25293942	121070080	35	7121											
TEX15	56154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	30704070	30704070	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaaaaggctgggaataaaTgtcaaatcctagaatttctc	16	10	7	8	0	2	1	1	0	1	1	4	2	3	2	2	2	0	1	2	2	8	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr8:30704070T>C	ENST00000256246.2	-	1	2538	c.2464A>G	c.(2464-2466)Att>Gtt	p.I822V	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	822					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGGGAATAAATGTCAAATCCT	0.373																																					p.I822V		.											.	TEX15-97	0			c.A2464G						.						55	51	53					8																	30704070		2203	4298	6501	SO:0001583	missense	56154	exon1			AATAAATGTCAAA	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2464A>G	8.37:g.30704070T>C	ENSP00000256246:p.Ile822Val	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	101	10	NM_031271	0	0	0	0	0		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.665157	0.00765	.	.	ENSG00000133863	ENST00000256246	T	0.09911	2.93	6.03	3.73	0.42828	.	0.872782	0.10069	N	0.719942	T	0.08846	0.0219	L	0.27053	0.805	0.09310	N	1	B	0.33171	0.4	B	0.33960	0.173	T	0.19224	-1.0312	10	0.87932	D	0	.	7.3269	0.26560	0.0:0.1436:0.0:0.8564	.	822	Q9BXT5	TEX15_HUMAN	V	822	ENSP00000256246:I822V	ENSP00000256246:I822V	I	-	1	0	TEX15	30823612	0.000000	0.05858	0.032000	0.17829	0.027000	0.11550	0.328000	0.19681	2.302000	0.77476	0.533000	0.62120	ATT	.		0.373	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30704070	T	C	30704070	3	2	76	1	0	0	0	0	1	0	0	0	15811	1464	51	3	5921	3	TEX15	8	30704070	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	5410128	30704070	115659952	36	7122											
FAM75A3	727830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	40705657	40705657	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagccaaaggccaatgtttcCccctattcacaagagtgaga	13	8	9	11	0	1	2	1	1	0	2	2	4	2	2	4	1	1	1	4	1	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr9:40705657C>T	ENST00000356699.5	+	4	3343	c.3314C>T	c.(3313-3315)cCc>cTc	p.P1105L	RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	1105					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCAATGTTTCCCCCTATTCAC	0.478																																					p.P1105L		.											.	.	0			c.C3314T						.						125	111	116					9																	40705657		1582	3157	4739	SO:0001583	missense	727830	exon4			TGTTTCCCCCTAT			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A3"	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.3314C>T	9.37:g.40705657C>T	ENSP00000349132:p.Pro1105Leu	Somatic	315	0		WXS	Illumina HiSeq	Phase_I	322	168	NM_001083124	0	0	0	0	0		Missense_Mutation	SNP	ENST00000356699.5	37	CCDS47969.1	.	.	.	.	.	.	.	.	.	.	C	5.075	0.199434	0.09652	.	.	ENSG00000147926	ENST00000356699	T	0.03860	3.78	2.79	-3.16	0.05217	.	1.572250	0.03917	N	0.282808	T	0.05960	0.0155	L	0.38175	1.15	0.09310	N	1	D	0.61697	0.99	P	0.52481	0.7	T	0.27872	-1.0061	10	0.19590	T	0.45	.	0.5688	0.00692	0.1756:0.2945:0.1729:0.357	.	1105	Q5VYP0	F75A3_HUMAN	L	1105	ENSP00000349132:P1105L	ENSP00000349132:P1105L	P	+	2	0	FAM75A3	40695657	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.642000	0.05427	-0.776000	0.04578	0.398000	0.26397	CCC	.		0.478	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124		T	40705657	C	T	40705657	3	4	76	1	0	0	0	0	1	0	0	0	5640	623	22	2	3328	2	FAM75A3	9	40705657	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		40705657	100507774	37	7123											
RORB	6096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	77286722	77286722	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaccgagcctggcttataGaaccaaggaaagtccagaag	15	5	11	10	1	0	3	0	0	0	3	1	5	1	4	4	2	2	1	4	2	6	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr9:77286722G>A	ENST00000396204.2	+	9	1162	c.1162G>A	c.(1162-1164)Gaa>Aaa	p.E388K	RORB_ENST00000376896.3_Missense_Mutation_p.E377K			Q92753	RORB_HUMAN	RAR-related orphan receptor B	388	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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)	p.E377Q(2)|p.E377*(1)		breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	CTGGCTTATAGAACCAAGGAA	0.428																																					p.E377K		.											.	RORB-229	3	Substitution - Missense(2)|Substitution - Nonsense(1)	breast(2)|ovary(1)	c.G1129A						.						73	69	70					9																	77286722		2203	4300	6503	SO:0001583	missense	6096	exon9			CTTATAGAACCAA	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.1162G>A	9.37:g.77286722G>A	ENSP00000379507:p.Glu388Lys	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	96	33	NM_006914	0	0	0	0	0	Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	37		.	.	.	.	.	.	.	.	.	.	G	22.2	4.255074	0.80135	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.96967	-4.19;-4.19	5.73	5.73	0.89815	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.95834	0.8644	L	0.56280	1.765	0.80722	D	1	B;B	0.27594	0.182;0.01	B;B	0.35813	0.211;0.04	D	0.93462	0.6811	10	0.52906	T	0.07	.	20.2602	0.98440	0.0:0.0:1.0:0.0	.	388;377	Q92753;Q58EY0	RORB_HUMAN;.	K	377;388	ENSP00000366093:E377K;ENSP00000379507:E388K	ENSP00000366093:E377K	E	+	1	0	RORB	76476542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.807000	0.99171	2.861000	0.98227	0.655000	0.94253	GAA	.		0.428	RORB-201	KNOWN	basic	protein_coding	protein_coding				A	77286722	G	A	77286722	3	1	76	1	0	0	0	0	1	0	0	0	13561	943	33	2	1163	2	RORB	9	77286722	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	36581065	77286722	63926709	38	7124											
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	113265327	113265327	+	Frame_Shift_Del	DEL	G	G	-																															tagaaacttacccacacaccGgggttctggcccatcccact																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr9:113265327delG	ENST00000401783.2	-	6	1810	c.1474delC	c.(1474-1476)cggfs	p.R492fs	SVEP1_ENST00000302728.8_Frame_Shift_Del_p.R492fs|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Frame_Shift_Del_p.R469fs|SVEP1_ENST00000374461.1_Frame_Shift_Del_p.R469fs	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	492	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CCCACACACCGGGGTTCTGGC	0.443																																					p.R492fs		.											.	SVEP1-75	0			c.1474delC						.						133	135	134					9																	113265327		1926	4129	6055	SO:0001589	frameshift_variant	79987	exon6			.	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1474delC	9.37:g.113265327delG	ENSP00000384917:p.Arg492fs	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	110	29	NM_153366	0	0	0	0	0	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Frame_Shift_Del	DEL	ENST00000401783.2	37	CCDS48004.1																																																																																			.		0.443	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	113265327	G	-	113265327	7	5	76	1	0	1	0	1	0	0	0	0	15452	1115	39	0	9413	0	SVEP1	9	113265327	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08	35978605	113265327	27948104	39	7125											
CDK5RAP2	55755	broad.mit.edu	37	chr9	123313163	123313163	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaggttaaagttttctttCttcaattcagtgatttgctg	8	21	7	5	0	4	1	2	1	2	0	4	1	4	1	0	1	1	3	0	1	4	9			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr9:123313163C>A	ENST00000349780.4	-	4	392	c.213G>T	c.(211-213)aaG>aaT	p.K71N	CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.K71N|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.K71N|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.K71N	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	71					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGTTTTCTTTCTTCAATTCAG	0.383																																					p.K71N													.	CDK5RAP2-229	0			c.G213T						.						90	93	92					9																	123313163		2203	4300	6503	SO:0001583	missense	55755	exon4			TTCTTTCTTCAAT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.213G>T	9.37:g.123313163C>A	ENSP00000343818:p.Lys71Asn	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	138	5	NM_018249	0	0	12	12	0	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.776470	0.70107	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000345313	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	6.08	5.19	0.71726	Spindle associated (1);	0.000000	0.64402	D	0.000007	T	0.49270	0.1547	M	0.76574	2.34	0.47862	D	0.999531	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.997	T	0.52697	-0.8541	10	0.87932	D	0	.	10.6118	0.45425	0.0:0.8517:0.0:0.1483	.	71;71;71	Q96SN8-2;Q96SN8-4;Q96SN8	.;.;CK5P2_HUMAN	N	71	ENSP00000354065:K71N;ENSP00000352258:K71N;ENSP00000343818:K71N;ENSP00000353317:K71N	ENSP00000341695:K71N	K	-	3	2	CDK5RAP2	122352984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.387000	0.34430	1.589000	0.49982	0.591000	0.81541	AAG	.		0.383	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		A	123313163	C	A	123313163	3	1	76	1	0	0	0	0	1	0	0	0	3152	912	32	4	5608	4	CDK5RAP2	9	123313163	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	10047836	123313163	17900268	40	7126											
C10orf90	118611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	128193076	128193076	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtgtctggagaaaaactggtCtctttgtcgtctgcatgggt	7	14	13	7	1	3	1	0	0	3	1	5	2	3	1	0	3	2	1	0	3	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr10:128193076C>G	ENST00000284694.7	-	3	813	c.693G>C	c.(691-693)gaG>gaC	p.E231D	C10orf90_ENST00000544758.1_Missense_Mutation_p.E328D|C10orf90_ENST00000392694.1_Missense_Mutation_p.E184D|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000454341.1_Missense_Mutation_p.E231D|C10orf90_ENST00000356858.3_Missense_Mutation_p.E184D	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	231					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		AAAAACTGGTCTCTTTGTCGT	0.557											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E231D		.											.	C10orf90-92	0			c.G693C						.						73	78	76					10																	128193076		2203	4300	6503	SO:0001583	missense	118611	exon3			ACTGGTCTCTTTG	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"fragile-site associated tumor suppressor"					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.693G>C	10.37:g.128193076C>G	ENSP00000284694:p.Glu231Asp	Somatic	96	0	1563	WXS	Illumina HiSeq	Phase_I	98	24	NM_001004298	0	0	0	0	0	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.944946	0.34283	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.28255	1.91;1.9;1.94;1.92;1.62	5.27	3.38	0.38709	.	0.457153	0.20722	N	0.086884	T	0.28863	0.0716	L	0.58101	1.795	0.09310	N	1	B;B;B;B;B	0.13594	0.001;0.001;0.008;0.001;0.001	B;B;B;B;B	0.19148	0.003;0.01;0.024;0.01;0.007	T	0.25641	-1.0126	10	0.59425	D	0.04	-3.5758	8.1384	0.31069	0.3227:0.5212:0.1561:0.0	.	328;328;184;231;231	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	D	184;231;231;328;231;184;184	ENSP00000284694:E231D;ENSP00000398786:E231D;ENSP00000444369:E328D;ENSP00000405995:E231D;ENSP00000376459:E184D	ENSP00000284694:E231D	E	-	3	2	C10orf90	128183066	0.000000	0.05858	0.001000	0.08648	0.061000	0.15899	0.565000	0.23578	0.756000	0.33013	0.655000	0.94253	GAG	.		0.557	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		G	128193076	C	G	128193076	3	3	76	1	0	0	0	0	1	0	0	0	1627	912	32	4	1434	4	C10orf90	10	128193076	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		128193076	7341671	41	7127											
OR52B2	255725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6190974	6190974	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccataccaaatgttaacagTgatgtcagcacaggctaaac	15	8	8	10	0	1	1	1	1	0	0	1	1	1	1	2	1	4	3	2	1	5	3	rs35364339		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:6190974T>A	ENST00000530810.1	-	1	664	c.583A>T	c.(583-585)Act>Tct	p.T195S	RP11-290F24.3_ENST00000529961.1_RNA	NM_001004052.1	NP_001004052.1	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B, member 2	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(15)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGTTAACAGTGATGTCAGCA	0.478																																					p.T195S	NSCLC(5;186 261 1778 7098 14207)	.											.	.	0			c.A583T						.						51	51	51					11																	6190974		2072	4218	6290	SO:0001583	missense	255725	exon1			TAACAGTGATGTC	AB065763	CCDS53598.1	11p15.4	2012-08-09				ENSG00000255307		"GPCR / Class A : Olfactory receptors"	15207	protein-coding gene	gene with protein product							Standard	NM_001004052		Approved		uc010qzy.2	Q96RD2		ENST00000530810.1:c.583A>T	11.37:g.6190974T>A	ENSP00000432011:p.Thr195Ser	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	43	11	NM_001004052	0	0	0	0	0	Q8NGM7	Missense_Mutation	SNP	ENST00000530810.1	37	CCDS53598.1	.	.	.	.	.	.	.	.	.	.	T	9.208	1.030275	0.19512	.	.	ENSG00000255307	ENST00000530810	T	0.00042	8.84	5.32	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00144	0.0004	N	0.03881	-0.34	0.09310	N	1	D	0.76494	0.999	D	0.83275	0.996	T	0.64347	-0.6429	9	0.26408	T	0.33	.	7.1804	0.25770	0.146:0.0:0.1526:0.7014	.	195	Q96RD2	O52B2_HUMAN	S	195	ENSP00000432011:T195S	ENSP00000432011:T195S	T	-	1	0	OR52B2	6147550	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.367000	0.20382	1.007000	0.39238	0.450000	0.29827	ACT	.		0.478	OR52B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385977.1	NM_001004052		A	6190974	T	A	6190974	3	1	76	1	0	0	0	0	1	0	0	0	11137	1696	59	5	391	5	OR52B2	11	6190974	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		6190974	128815542	42	7128											
MTCH2	23788	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	47653227	47653227	+	Frame_Shift_Del	DEL	G	G	-																															atggaagggatgtgtgatgaGggtagcagcagaacgagcga																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:47653227delG	ENST00000302503.3	-	6	563	c.406delC	c.(406-408)ctcfs	p.L136fs	MTCH2_ENST00000534074.1_5'Flank|MTCH2_ENST00000542981.1_Intron	NM_014342.3	NP_055157.1	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2	136					protein localization to mitochondrion (GO:0070585)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11						TGTGTGATGAGGGTAGCAGCA	0.433																																					p.L136fs		.											.	MTCH2-90	0			c.406delC						.						170	137	148					11																	47653227		2201	4298	6499	SO:0001589	frameshift_variant	23788	exon6			.	AF085361	CCDS7943.1	11p11.2	2013-05-22	2011-05-19		ENSG00000109919	ENSG00000109919		"Solute carriers"	17587	protein-coding gene	gene with protein product	"solute carrier family 25, member 50"	613221	"mitochondrial carrier homolog 2 (C. elegans)"				Standard	NM_014342		Approved	SLC25A50	uc010rho.2	Q9Y6C9	OTTHUMG00000166926	ENST00000302503.3:c.406delC	11.37:g.47653227delG	ENSP00000303222:p.Leu136fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	66	23	NM_014342	0	0	0	0	0	B2R7L8	Frame_Shift_Del	DEL	ENST00000302503.3	37	CCDS7943.1																																																																																			.		0.433	MTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391921.2	NM_014342		-	47653227	G	-	47653227	7	5	76	1	0	1	0	1	0	0	0	0	9939	1000	35	0	537	0	MTCH2	11	47653227	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08	41462253	47653227	87353289	43	7129											
NUP160	23279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47819410	47819410	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcataaggtccacagctctAgcacgtgactcaattattcc	11	11	7	12	1	3	1	2	1	1	0	5	1	5	1	2	1	2	2	2	1	4	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:47819410A>C	ENST00000378460.2	-	27	3256	c.3210T>G	c.(3208-3210)gcT>gcG	p.A1070A	NUP160_ENST00000530326.1_Silent_p.A956A|NUP160_ENST00000528071.1_Silent_p.A956A	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	1070					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						CCACAGCTCTAGCACGTGACT	0.443																																					p.A1070A		.											.	NUP160-209	0			c.T3210G						.						152	129	137					11																	47819410		2201	4298	6499	SO:0001819	synonymous_variant	23279	exon27			AGCTCTAGCACGT	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.3210T>G	11.37:g.47819410A>C		Somatic	114	1		WXS	Illumina HiSeq	Phase_I	144	34	NM_015231	0	0	20	31	11	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	37	CCDS31484.1																																																																																			.		0.443	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231		C	47819410	A	C	47819410	2	2	76	1	0	0	0	0	0	0	0	1	10783	407	15	5		5	NUP160	11	47819410	Silent	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	166183	47819410	87187106	44	7130											
OR4C11	219429	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	55371448	55371448	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgcagacctgctggctCatgatggttgggtaacgcaa	10	10	13	8	1	1	3	1	2	0	1	1	3	1	3	1	3	3	6	1	3	2	2	rs373760102		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:55371448C>A	ENST00000302231.4	-	1	426	c.402G>T	c.(400-402)atG>atT	p.M134I		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	134						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						CCTGCTGGCTCATGATGGTTG	0.463																																					p.M134I		.											.	OR4C11-69	0			c.G402T						.						88	72	78					11																	55371448		2177	4010	6187	SO:0001583	missense	219429	exon1			CTGGCTCATGATG	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.402G>T	11.37:g.55371448C>A	ENSP00000306651:p.Met134Ile	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	110	6	NM_001004700	0	0	0	0	0	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319072	0.41096	.	.	ENSG00000172188	ENST00000302231	T	0.00551	6.65	4.34	3.42	0.39159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000014	T	0.02047	0.0064	M	0.82923	2.615	0.27993	N	0.935588	D	0.69078	0.997	D	0.75020	0.985	T	0.08027	-1.0742	10	0.72032	D	0.01	.	10.4812	0.44695	0.0:0.9023:0.0:0.0977	.	134	Q6IEV9	OR4CB_HUMAN	I	134	ENSP00000306651:M134I	ENSP00000306651:M134I	M	-	3	0	OR4C11	55128024	0.991000	0.36638	0.963000	0.40424	0.237000	0.25408	2.968000	0.49224	1.187000	0.43000	0.478000	0.44815	ATG	.		0.463	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		A	55371448	C	A	55371448	3	1	76	1	0	0	0	0	1	0	0	0	11071	826	29	4	532	4	OR4C11	11	55371448	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	7552038	55371448	79635068	45	7131											
DDX47	51202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12974592	12974592	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttttttctctgtagctgTgattgtaggtggaattgatt	6	21	10	4	0	2	2	0	2	2	0	3	3	2	3	0	2	1	3	0	2	3	8			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr12:12974592T>C	ENST00000358007.3	+	4	396	c.374T>C	c.(373-375)gTg>gCg	p.V125A	DDX47_ENST00000352940.4_Missense_Mutation_p.V125A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	125	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		TCTGTAGCTGTGATTGTAGGT	0.358																																					p.V125A		.											.	DDX47-226	0			c.T374C						.						137	139	139					12																	12974592		2203	4300	6503	SO:0001583	missense	51202	exon4			TAGCTGTGATTGT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"DEAD-boxes"	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.374T>C	12.37:g.12974592T>C	ENSP00000350698:p.Val125Ala	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	102	35	NM_201224	0	0	0	0	0	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.143646	0.77888	.	.	ENSG00000213782	ENST00000352940;ENST00000358007;ENST00000544400	T;T;T	0.15017	2.46;2.46;2.46	4.87	4.87	0.63330	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	N	0.13299	0.325	0.80722	D	1	B;B;D	0.55385	0.398;0.186;0.971	B;B;P	0.59703	0.379;0.121;0.862	T	0.05517	-1.0880	10	0.46703	T	0.11	-19.7359	14.3028	0.66364	0.0:0.0:0.0:1.0	.	125;125;125	Q9H4E3;G5E955;Q9H0S4	.;.;DDX47_HUMAN	A	125;125;62	ENSP00000319578:V125A;ENSP00000350698:V125A;ENSP00000444000:V62A	ENSP00000319578:V125A	V	+	2	0	DDX47	12865859	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	4.293000	0.59037	2.051000	0.60960	0.454000	0.30748	GTG	.		0.358	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		C	12974592	T	C	12974592	3	2	76	1	0	0	0	0	1	0	0	0	4371	1696	59	3	388	3	DDX47	12	12974592	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		12974592	120877303	46	7132											
ANP32D	23519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48866684	48866684	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agtaacagagcctcagtgggCctagaagtattggcagaaaa	15	7	12	7	0	1	3	1	0	0	3	1	3	1	3	2	2	2	3	2	2	6	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr12:48866684C>T	ENST00000266594.1	+	1	237	c.237C>T	c.(235-237)ggC>ggT	p.G79G		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	79						nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						CCTCAGTGGGCCTAGAAGTAT	0.378																																					p.G79G		.											.	ANP32D-227	0			c.C237T						.						91	91	91					12																	48866684		2203	4300	6503	SO:0001819	synonymous_variant	23519	exon1			AGTGGGCCTAGAA	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"ANP32 acidic nuclear phosphoproteins"	16676	protein-coding gene	gene with protein product	"pp32 related 2"	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.237C>T	12.37:g.48866684C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	112	38	NM_012404	0	0	0	0	0	Q6NTC4	Silent	SNP	ENST00000266594.1	37	CCDS31788.1																																																																																			.		0.378	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404		T	48866684	C	T	48866684	2	4	76	1	0	0	0	0	0	0	0	1	708	726	26	2		2	ANP32D	12	48866684	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	35892092	48866684	84985211	47	7133											
TDG	6996	broad.mit.edu	37	chr12	104380795	104380795	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggcagtggatgacccagtCatttacagaccaaattcctt	11	11	9	10	0	1	2	1	1	0	1	2	3	2	3	3	2	1	1	3	2	2	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr12:104380795C>T	ENST00000392872.3	+	10	1394	c.1160C>T	c.(1159-1161)tCa>tTa	p.S387L	TDG_ENST00000536395.1_3'UTR|TDG_ENST00000544861.1_Missense_Mutation_p.S244L|TDG_ENST00000266775.9_Missense_Mutation_p.S383L|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.S183L	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	387					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		ATGACCCAGTCATTTACAGAC	0.413								Base excision repair (BER), DNA glycosylases																													p.S387L													.	TDG-661	0			c.C1160T						.						168	133	145					12																	104380795		2203	4300	6503	SO:0001583	missense	6996	exon10			CCCAGTCATTTAC	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.1160C>T	12.37:g.104380795C>T	ENSP00000376611:p.Ser387Leu	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	166	6	NM_003211	0	0	12	14	2	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723998	0.68959	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	T;T;T;T	0.31769	1.78;1.78;1.86;1.48	5.95	5.06	0.68205	.	0.444493	0.26556	N	0.023704	T	0.33760	0.0874	L	0.56769	1.78	0.58432	D	0.999992	B;B;B	0.14438	0.01;0.002;0.002	B;B;B	0.11329	0.004;0.006;0.006	T	0.10683	-1.0619	10	0.59425	D	0.04	0.0634	15.4557	0.75311	0.0:0.9335:0.0:0.0665	.	183;387;387	B4DI29;B2R848;Q13569	.;.;TDG_HUMAN	L	387;383;244;183	ENSP00000376611:S387L;ENSP00000266775:S383L;ENSP00000445899:S244L;ENSP00000439054:S183L	ENSP00000266775:S383L	S	+	2	0	TDG	102904925	1.000000	0.71417	0.784000	0.31847	0.985000	0.73830	4.673000	0.61604	1.526000	0.49068	0.655000	0.94253	TCA	.		0.413	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2			T	104380795	C	T	104380795	3	4	76	1	0	0	0	0	1	0	0	0	15757	838	29	2	1198	2	TDG	12	104380795	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	55514111	104380795	29471100	48	7134											
KLF12	11278	hgsc.bcm.edu	37	chr13	74420188	74420188	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacaccagatgcagaggccAcaaggggccctggagttaat	13	5	12	11	0	0	2	0	0	0	2	0	3	0	3	3	4	2	2	3	4	3	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr13:74420188A>G	ENST00000377669.2	-	3	472	c.446T>C	c.(445-447)gTg>gCg	p.V149A	KLF12_ENST00000472022.1_5'UTR|KLF12_ENST00000377666.4_Missense_Mutation_p.V149A	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	149					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		TGCAGAGGCCACAAGGGGCCC	0.473																																					p.V149A		.											.	KLF12-91	0			c.T446C						.						81	70	74					13																	74420188		2203	4300	6503	SO:0001583	missense	11278	exon4			GAGGCCACAAGGG	AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6346	protein-coding gene	gene with protein product	"KLF12 zinc finger transcriptional repressor", "AP-2rep transcription factor", "AP-2 repressor"	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.446T>C	13.37:g.74420188A>G	ENSP00000366897:p.Val149Ala	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_007249	0	0	7	7	0	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	37	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.879334	0.72294	.	.	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.29142	1.58;1.58	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.47930	0.1472	L	0.53249	1.67	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	T	0.29336	-1.0015	10	0.38643	T	0.18	.	15.7258	0.77756	1.0:0.0:0.0:0.0	.	149	Q9Y4X4	KLF12_HUMAN	A	149	ENSP00000366897:V149A;ENSP00000366894:V149A	ENSP00000344057:V149A	V	-	2	0	KLF12	73318189	1.000000	0.71417	0.997000	0.53966	0.849000	0.48306	7.161000	0.77505	2.311000	0.77944	0.533000	0.62120	GTG	.		0.473	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249		G	74420188	A	G	74420188	3	3	76	1	0	0	0	0	1	0	0	0	8361	159	6	3	782	3	KLF12	13	74420188	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08		74420188	40749690	49	7135											
CHD8	57680	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	21862522	21862522	+	Frame_Shift_Del	DEL	T	T	-																															tggtaaggctttcatctgtcTttttgtctagtcgagcaaaa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:21862522delT	ENST00000557364.1	-	31	5776	c.5513delA	c.(5512-5514)aagfs	p.K1838fs	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Frame_Shift_Del_p.K1559fs|CHD8_ENST00000399982.2_Frame_Shift_Del_p.K1838fs|SNORD8_ENST00000363915.1_RNA|SNORD9_ENST00000362566.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1838					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		TTCATCTGTCTTTTTGTCTAG	0.498																																					p.K1838fs		.											.	CHD8-277	0			c.5513delA						.						76	78	77					14																	21862522		2011	4188	6199	SO:0001589	frameshift_variant	57680	exon30			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.5513delA	14.37:g.21862522delT	ENSP00000451601:p.Lys1838fs	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	83	24	NM_001170629	0	0	0	0	0	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	37	CCDS53885.1																																																																																			.		0.498	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21862522	T	-	21862522	7	5	76	1	0	1	0	1	0	0	0	0	3337	1609	56	0	2264	0	CHD8	14	21862522	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08		21862522	85487018	50	7136											
FBXO34	55030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55818351	55818351	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagatgaactcgttgggttaCctttttcctctcatacctat	8	16	6	11	1	1	2	1	1	1	1	4	2	2	2	3	1	3	2	3	1	4	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:55818351C>G	ENST00000313833.4	+	2	1488	c.1243C>G	c.(1243-1245)Cct>Gct	p.P415A	FBXO34_ENST00000440021.1_Missense_Mutation_p.P415A	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	415										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CGTTGGGTTACCTTTTTCCTC	0.458																																					p.P415A		.											.	FBXO34-228	0			c.C1243G						.						149	132	138					14																	55818351		2203	4300	6503	SO:0001583	missense	55030	exon2			GGGTTACCTTTTT	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1243C>G	14.37:g.55818351C>G	ENSP00000313159:p.Pro415Ala	Somatic	238	0		WXS	Illumina HiSeq	Phase_I	210	57	NM_017943	0	0	12	18	6	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.215359	0.01542	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.16897	2.31;2.31	5.48	1.31	0.21738	.	0.732971	0.11730	U	0.535077	T	0.12305	0.0299	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.33599	-0.9862	10	0.40728	T	0.16	-21.5592	0.8915	0.01255	0.1775:0.4073:0.173:0.2422	.	415	Q9NWN3	FBX34_HUMAN	A	415	ENSP00000313159:P415A;ENSP00000394117:P415A	ENSP00000313159:P415A	P	+	1	0	FBXO34	54888104	.	.	0.001000	0.08648	0.123000	0.20343	.	.	0.409000	0.25649	-0.156000	0.13503	CCT	.		0.458	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			G	55818351	C	G	55818351	3	3	76	1	0	0	0	0	1	0	0	0	5763	507	18	4	1245	4	FBXO34	14	55818351	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	33955829	55818351	51531189	51	7137											
SFRS5	6430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	70238167	70238167	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggtccagatcagttgacAgtggcaattaaactgtaaat	15	10	9	7	0	1	2	1	1	0	1	2	2	2	2	1	2	1	3	1	2	6	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:70238167A>G	ENST00000553521.1	+	9	2261	c.808A>G	c.(808-810)Agt>Ggt	p.S270G	SRSF5_ENST00000557154.1_Missense_Mutation_p.S270G|SRSF5_ENST00000394366.2_Missense_Mutation_p.S270G|SRSF5_ENST00000553635.1_Missense_Mutation_p.S267G|SRSF5_ENST00000556587.1_3'UTR			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	270					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						ATCAGTTGACAGTGGCAATTA	0.428																																					p.S270G		.											.	SRSF5-226	0			c.A808G						.						98	106	104					14																	70238167		2203	4300	6503	SO:0001583	missense	6430	exon8			GTTGACAGTGGCA	AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10787	protein-coding gene	gene with protein product	"SR splicing factor 5"	600914	"splicing factor, arginine/serine-rich 5"	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.808A>G	14.37:g.70238167A>G	ENSP00000452123:p.Ser270Gly	Somatic	212	1		WXS	Illumina HiSeq	Phase_I	226	35	NM_001039465	0	0	47	70	23	O14797|Q16662|Q49AD6|Q6FGE0	Missense_Mutation	SNP	ENST00000553521.1	37	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	A	16.10	3.027850	0.54790	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000557154;ENST00000553635	T;T;T;T	0.15256	3.19;3.19;3.19;2.44	5.65	5.65	0.86999	.	0.483083	0.26711	N	0.022894	T	0.19406	0.0466	N	0.14661	0.345	0.80722	D	1	P;P	0.46395	0.877;0.805	P;P	0.51866	0.682;0.483	T	0.04005	-1.0985	10	0.49607	T	0.09	.	15.882	0.79211	1.0:0.0:0.0:0.0	.	267;270	Q13243-3;Q13243	.;SRSF5_HUMAN	G	270;270;270;267	ENSP00000452123:S270G;ENSP00000377892:S270G;ENSP00000451088:S270G;ENSP00000451391:S267G	ENSP00000377892:S270G	S	+	1	0	SRSF5	69307920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.860000	0.75473	2.155000	0.67459	0.533000	0.62120	AGT	.		0.428	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465		G	70238167	A	G	70238167	3	3	76	1	0	0	0	0	1	0	0	0	14212	188	7	3	834	3	SFRS5	14	70238167	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	14419816	70238167	37111373	52	7138											
DICER1	23405	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	95562982	95562982	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccctccacatcaggctCtcctcctcctcatcctcctc	5	10	5	21	0	3	0	2	0	1	0	10	1	8	1	7	2	1	1	7	2	0	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:95562982C>A	ENST00000526495.1	-	25	4566	c.4275G>T	c.(4273-4275)gaG>gaT	p.E1425D	DICER1_ENST00000527414.1_Missense_Mutation_p.E1425D|DICER1_ENST00000393063.1_Missense_Mutation_p.E1425D|DICER1_ENST00000343455.3_Missense_Mutation_p.E1425D|DICER1_ENST00000541352.1_Missense_Mutation_p.E1425D|DICER1_ENST00000556045.1_Missense_Mutation_p.E323D			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1425					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		ACATCAGGCTctcctcctcct	0.478			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.E1425D		.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1-961	0			c.G4275T						.						60	56	57					14																	95562982		2203	4300	6503	SO:0001583	missense	23405	exon24	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	CAGGCTCTCCTCC	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"dicer 1, double-stranded RNA-specific endoribonuclease"	606241	"Dicer1, Dcr-1 homolog (Drosophila)", "multinodular goitre 1"	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.4275G>T	14.37:g.95562982C>A	ENSP00000437256:p.Glu1425Asp	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	61	24	NM_030621	0	0	10	13	3	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	37	CCDS9931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.70|11.70	1.715346|1.715346	0.30413|0.30413	.|.	.|.	ENSG00000100697|ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045;ENST00000541352|ENST00000532939	T;T;T;T;D;T|.	0.87103|.	0.36;0.36;0.36;0.36;-2.21;0.67|.	5.32|5.32	1.91|1.91	0.25777|0.25777	Ribonuclease III (3);|.	0.391869|0.391869	0.24366|0.24366	N|N	0.039146|0.039146	T|.	0.38746|.	0.1052|.	L|L	0.38175|0.38175	1.15|1.15	0.39976|0.39976	D|D	0.974854|0.974854	B;B;B|.	0.13594|.	0.008;0.001;0.0|.	B;B;B|.	0.14578|.	0.009;0.011;0.004|.	T|.	0.21075|.	-1.0256|.	10|.	0.30854|.	T|.	0.27|.	-10.9506|-10.9506	0.6205|0.6205	0.00777|0.00777	0.405:0.2239:0.2011:0.17|0.405:0.2239:0.2011:0.17	.|.	323;1425;1425|.	B3KRG4;E0AD28;Q9UPY3|.	.;.;DICER_HUMAN|.	D|X	1425;1425;1425;1425;323;1425|104	ENSP00000343745:E1425D;ENSP00000437256:E1425D;ENSP00000376783:E1425D;ENSP00000435681:E1425D;ENSP00000451041:E323D;ENSP00000444719:E1425D|.	ENSP00000343745:E1425D|.	E|E	-|-	3|1	2|0	DICER1|DICER1	94632735|94632735	0.946000|0.946000	0.32159|0.32159	0.825000|0.825000	0.32803|0.32803	0.882000|0.882000	0.50991|0.50991	0.405000|0.405000	0.21015|0.21015	0.561000|0.561000	0.29186|0.29186	0.561000|0.561000	0.74099|0.74099	GAG|GAG	.		0.478	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			A	95562982	C	A	95562982	3	1	76	1	0	0	0	0	1	0	0	0	4532	912	32	4	1513	4	DICER1	14	95562982	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	25324815	95562982	11786558	53	7139											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95916297	95916297	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcaggaaggtgtgaagggAaggcaggtccggcaggctgg	9	4	22	6	1	0	1	0	1	0	0	1	3	1	3	1	9	0	4	1	9	3	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:95916297A>G	ENST00000334258.5	-	7	1434	c.1420T>C	c.(1420-1422)Tcc>Ccc	p.S474P	SYNE3_ENST00000554873.1_Missense_Mutation_p.S231P|SYNE3_ENST00000553340.1_Missense_Mutation_p.S474P|SYNE3_ENST00000557275.1_Missense_Mutation_p.S474P	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	474					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						GTGTGAAGGGAAGGCAGGTCC	0.652																																					p.S474P		.											.	.	0			c.T1420C						.						32	32	32					14																	95916297		2170	4249	6419	SO:0001583	missense	161176	exon7			GAAGGGAAGGCAG	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1420T>C	14.37:g.95916297A>G	ENSP00000334308:p.Ser474Pro	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_152592	0	0	2	2	0	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.989367	0.53934	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.15487	3.42;2.42;3.42;2.85	5.17	2.57	0.30868	.	0.000000	0.41712	D	0.000834	T	0.28830	0.0715	M	0.68317	2.08	0.27326	N	0.956905	D;D;D	0.67145	0.996;0.996;0.993	P;P;P	0.60682	0.878;0.878;0.759	T	0.04915	-1.0918	10	0.34782	T	0.22	-19.7633	6.0538	0.19800	0.6679:0.1694:0.0:0.1627	.	474;474;474	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	P	474;231;474;474	ENSP00000334308:S474P;ENSP00000452154:S231P;ENSP00000450562:S474P;ENSP00000450774:S474P	ENSP00000334308:S474P	S	-	1	0	C14orf49	94986050	0.963000	0.33076	0.998000	0.56505	0.802000	0.45316	0.686000	0.25392	0.754000	0.32968	0.482000	0.46254	TCC	.		0.652	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		G	95916297	A	G	95916297	3	3	76	1	0	0	0	0	1	0	0	0	1780	246	9	3	1551	3	C14orf49	14	95916297	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	353315	95916297	11433243	54	7140											
TELO2	9894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1552985	1552985	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaactacagcctccggcaGcgcatggacatcctggatgt	9	8	10	14	2	1	0	1	0	0	0	3	2	3	2	3	3	4	2	3	3	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:1552985G>T	ENST00000262319.6	+	15	2103	c.1824G>T	c.(1822-1824)caG>caT	p.Q608H	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	608					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				GCCTCCGGCAGCGCATGGACA	0.622																																					p.Q608H		.											.	TELO2-90	0			c.G1824T						.						143	133	137					16																	1552985		2199	4300	6499	SO:0001583	missense	9894	exon15			CCGGCAGCGCATG	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"TEL2, telomere maintenance 2, homolog (S. cerevisiae)"			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1824G>T	16.37:g.1552985G>T	ENSP00000262319:p.Gln608His	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	166	19	NM_016111	0	0	16	25	9	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.772621	0.69992	.	.	ENSG00000100726	ENST00000262319	T	0.26518	1.73	5.09	5.09	0.68999	Telomere length regulation protein, conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.49660	0.1570	M	0.76938	2.355	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.50734	-0.8793	10	0.54805	T	0.06	-37.6041	10.8668	0.46860	0.0882:0.0:0.9118:0.0	.	608	Q9Y4R8	TELO2_HUMAN	H	608	ENSP00000262319:Q608H	ENSP00000262319:Q608H	Q	+	3	2	TELO2	1492986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.437000	0.52863	2.391000	0.81399	0.462000	0.41574	CAG	.		0.622	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		T	1552985	G	T	1552985	3	4	76	1	0	0	0	0	1	0	0	0	15789	962	34	4	1878	4	TELO2	16	1552985	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		1552985	88801768	55	7141											
CNOT1	23019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	58580300	58580300	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagagttgctcatctaaatTcttcaggcgatctttatcct	10	15	7	9	1	5	1	2	0	3	1	6	3	6	1	1	1	1	2	1	1	3	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:58580300T>G	ENST00000317147.5	-	29	4263	c.3931A>C	c.(3931-3933)Aat>Cat	p.N1311H	CNOT1_ENST00000245138.4_Missense_Mutation_p.N162H|SNORA46_ENST00000384762.1_RNA|CNOT1_ENST00000441024.2_Missense_Mutation_p.N1311H|CNOT1_ENST00000569240.1_Missense_Mutation_p.N1306H	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1311	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TCATCTAAATTCTTCAGGCGA	0.413																																					p.N1311H		.											.	CNOT1-95	0			c.A3931C						.						142	128	133					16																	58580300		2198	4300	6498	SO:0001583	missense	23019	exon29			CTAAATTCTTCAG	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3931A>C	16.37:g.58580300T>G	ENSP00000320949:p.Asn1311His	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	159	43	NM_206999	0	0	28	48	20	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.719378	0.48728	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.49432	0.81;0.78	5.39	5.39	0.77823	.	0.219192	0.53938	D	0.000042	T	0.35335	0.0928	N	0.24115	0.695	0.45541	D	0.998496	B;B;B;B	0.31351	0.0;0.32;0.0;0.003	B;B;B;B	0.34138	0.003;0.176;0.001;0.004	T	0.26258	-1.0108	10	0.48119	T	0.1	.	10.6062	0.45396	0.0:0.0753:0.0:0.9247	.	162;1311;1311;1306	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	H	1311;162;1306;1311	ENSP00000320949:N1311H;ENSP00000413113:N1311H	ENSP00000245138:N162H	N	-	1	0	CNOT1	57137801	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.289000	0.72696	2.043000	0.60533	0.528000	0.53228	AAT	.		0.413	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		G	58580300	T	G	58580300	3	3	76	1	0	0	0	0	1	0	0	0	3623	1783	62	5	3505	5	CNOT1	16	58580300	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	57027315	58580300	31774453	56	7142											
NFATC3	4775	broad.mit.edu	37	chr16	68200904	68200904	+	Frame_Shift_Del	DEL	T	T	-																															ttctctgcagatagcctctaTacccgttgagtgctgtaagt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:68200904delT	ENST00000346183.3	+	5	1784	c.1760delT	c.(1759-1761)atafs	p.I587fs	NFATC3_ENST00000575270.1_Frame_Shift_Del_p.I587fs|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000329524.4_Frame_Shift_Del_p.I587fs|NFATC3_ENST00000349223.5_Frame_Shift_Del_p.I587fs	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	587	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		ATAGCCTCTATACCCGTTGAG	0.383																																					p.I587fs													.	NFATC3-92	0			c.1760delT						.						223	215	218					16																	68200904		2198	4300	6498	SO:0001589	frameshift_variant	4775	exon5			CCTCTATACCCGT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"Nuclear factor of activated T-cells"	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1760delT	16.37:g.68200904delT	ENSP00000300659:p.Ile587fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	157	10	NM_173163	0	0	0	0	0	O75211|Q14516|Q99840|Q99841|Q99842	Frame_Shift_Del	DEL	ENST00000346183.3	37	CCDS10860.1																																																																																			.		0.383	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		-	68200904	T	-	68200904	7	5	76	1	0	1	0	1	0	0	0	0	10390	1406	49	0	1778	0	NFATC3	16	68200904	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	9620604	68200904	22153849	57	7143											
SF3B3	23450	broad.mit.edu	37	chr16	70563043	70563043	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggcaagagtggatgccGtcgcatcgttcctggccagt	6	11	13	11	3	0	1	0	0	0	1	3	2	1	2	3	3	1	3	3	3	1	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:70563043G>A	ENST00000302516.5	+	3	549	c.338G>A	c.(337-339)cGt>cAt	p.R113H	SNORD111B_ENST00000408587.1_RNA	NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	113					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				AGTGGATGCCGTCGCATCGTT	0.443																																					p.R113H													.	SF3B3-91	0			c.G338A						.						81	77	79					16																	70563043		2198	4300	6498	SO:0001583	missense	23450	exon3			GATGCCGTCGCAT	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.338G>A	16.37:g.70563043G>A	ENSP00000305790:p.Arg113His	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	119	4	NM_012426	0	0	32	32	0	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Missense_Mutation	SNP	ENST00000302516.5	37	CCDS10894.1	.	.	.	.	.	.	.	.	.	.	G	34	5.293119	0.95546	.	.	ENSG00000189091	ENST00000302516;ENST00000310750	T	0.50001	0.76	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.80253	0.4589	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86338	0.1703	10	0.87932	D	0	.	19.5928	0.95522	0.0:0.0:1.0:0.0	.	113	Q15393	SF3B3_HUMAN	H	113	ENSP00000305790:R113H	ENSP00000305790:R113H	R	+	2	0	SF3B3	69120544	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	9.847000	0.99503	2.624000	0.88883	0.561000	0.74099	CGT	.		0.443	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		A	70563043	G	A	70563043	3	1	76	1	0	0	0	0	1	0	0	0	14184	1145	40	1	344	1	SF3B3	16	70563043	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	2362139	70563043	19791710	58	7144											
MLKL	197259	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	74729257	74729257	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcctgctgatcttcctgtgcCcaggacgctccttggcttat	4	14	9	14	1	1	1	0	1	1	0	4	2	4	2	4	2	2	3	4	2	1	3	rs376500500		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:74729257C>G	ENST00000308807.7	-	2	862	c.399G>C	c.(397-399)tgG>tgC	p.W133C	MLKL_ENST00000306247.7_Missense_Mutation_p.W133C	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						CTTCCTGTGCCCAGGACGCTC	0.542																																					p.W133C													.	MLKL-561	0			c.G399C						.						171	134	147					16																	74729257		2198	4300	6498	SO:0001583	missense	197259	exon2			CTGTGCCCAGGAC	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.399G>C	16.37:g.74729257C>G	ENSP00000308351:p.Trp133Cys	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	194	35	NM_152649	0	0	6	7	1		Missense_Mutation	SNP	ENST00000308807.7	37	CCDS32487.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.442978	0.25987	.	.	ENSG00000168404	ENST00000308807;ENST00000306247	T;T	0.78595	-1.19;2.72	4.15	3.08	0.35506	.	0.298558	0.30959	N	0.008526	T	0.79076	0.4385	L	0.34521	1.04	0.48087	D	0.999588	D;B	0.89917	1.0;0.152	D;B	0.78314	0.991;0.087	T	0.77991	-0.2379	10	0.49607	T	0.09	-10.8226	9.0746	0.36513	0.0:0.7742:0.2258:0.0	.	133;133	Q8NB16-2;Q8NB16	.;MLKL_HUMAN	C	133	ENSP00000308351:W133C;ENSP00000303118:W133C	ENSP00000303118:W133C	W	-	3	0	MLKL	73286758	0.880000	0.30214	0.792000	0.32020	0.055000	0.15305	1.805000	0.38883	2.243000	0.73865	0.555000	0.69702	TGG	.		0.542	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649		G	74729257	C	G	74729257	3	3	76	1	0	0	0	0	1	0	0	0	9644	624	22	4	1087	4	MLKL	16	74729257	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	4166214	74729257	15625496	59	7145											
ZNF778	197320	broad.mit.edu	37	chr16	89288533	89288533	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggactcagtctgccttcAtgaagaacagacacaggcag	13	7	11	10	0	3	3	2	1	1	2	3	4	3	4	1	2	2	1	1	2	3	2	rs547595021		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:89288533A>T	ENST00000433976.2	+	3	391	c.59A>T	c.(58-60)cAt>cTt	p.H20L	ZNF778_ENST00000306502.6_Intron	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	20					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		GTCTGCCTTCATGAAGAACAG	0.443																																					p.H20L													.	.	0			c.A59T						.						108	102	104					16																	89288533		1961	4168	6129	SO:0001583	missense	197320	exon3			GCCTTCATGAAGA	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.59A>T	16.37:g.89288533A>T	ENSP00000405289:p.His20Leu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	103	4	NM_182531	0	0	0	0	0	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	37	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	A	10.40	1.338506	0.24253	.	.	ENSG00000170100	ENST00000433976	T	0.05649	3.41	1.17	-2.12	0.07165	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.25678	N	0.985829	P	0.36647	0.563	B	0.26094	0.066	T	0.44847	-0.9301	9	0.09590	T	0.72	.	4.7794	0.13195	0.4168:0.5831:0.0:0.0	.	20	Q96MU6	ZN778_HUMAN	L	20	ENSP00000405289:H20L	ENSP00000405289:H20L	H	+	2	0	ZNF778	87816034	0.000000	0.05858	0.249000	0.24280	0.277000	0.26821	-0.446000	0.06837	-0.453000	0.07076	0.369000	0.22263	CAT	.		0.443	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		T	89288533	A	T	89288533	3	4	76	1	0	0	0	0	1	0	0	0	18183	217	8	5	65	5	ZNF778	16	89288533	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	14559276	89288533	1066220	60	7146											
SERPINF1	5176	broad.mit.edu	37	chr17	1673260	1673260	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcggctatgacctgtacCgggtgcgatccagcacgagc	8	8	12	13	4	0	1	0	1	0	0	2	3	1	1	3	2	4	3	3	2	2	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:1673260C>A	ENST00000254722.4	+	3	362	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	SERPINF1_ENST00000571870.1_3'UTR	NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	67					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						TGACCTGTACCGGGTGCGATC	0.632																																					p.R67R													.	SERPINF1-227	0			c.C199A						.						92	85	88					17																	1673260		2203	4300	6503	SO:0001819	synonymous_variant	5176	exon3			CTGTACCGGGTGC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.199C>A	17.37:g.1673260C>A		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	182	6	NM_002615	0	0	36	36	0	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Silent	SNP	ENST00000254722.4	37	CCDS11012.1																																																																																			.		0.632	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		A	1673260	C	A	1673260	2	1	76	1	0	0	0	0	0	0	0	1	14146	643	23	4		4	SERPINF1	17	1673260	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		1673260	79521950	61	7147											
SLC13A5	284111	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	6597517	6597517	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggcatcggagacatacCtaggtggggaaaagcacagc	13	5	14	9	1	0	1	0	0	0	1	1	3	0	2	1	5	3	2	1	5	4	2	rs113208940		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:6597517C>G	ENST00000433363.2	-	8	1289		c.e8-1		SLC13A5_ENST00000381074.4_Splice_Site|SLC13A5_ENST00000573648.1_Splice_Site|SLC13A5_ENST00000293800.6_Splice_Site	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5						transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						GGAGACATACCTAGGTGGGGA	0.502																																					.		.											.	SLC13A5-90	0			c.1056-1G>C						.						74	62	66					17																	6597517		2203	4300	6503	SO:0001630	splice_region_variant	284111	exon9			ACATACCTAGGTG	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"Solute carriers"	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1056-1G>C	17.37:g.6597517C>G		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	66	17	NM_001143838	0	0	0	0	0	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Splice_Site	SNP	ENST00000433363.2	37	CCDS11079.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.969840	0.34754	.	.	ENSG00000141485	ENST00000293800;ENST00000433363;ENST00000381074	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5007	0.87731	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC13A5	6538241	1.000000	0.71417	0.947000	0.38551	0.090000	0.18270	6.842000	0.75379	2.815000	0.96918	0.561000	0.74099	.	G|1.000		0.502	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	Intron	G	6597517	C	G	6597517	5	3	76	1	0	0	0	0	0	0	1	0	14427	695	24	4	671	4	SLC13A5	17	6597517	Splice_Site	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	4924257	6597517	74597693	62	7148											
GAS7	8522	broad.mit.edu;bcgsc.ca	37	chr17	9846496	9846496	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgcccttcagctgtttctGgagcagtagttcaaacccag	8	13	9	11	0	3	0	2	0	1	0	3	1	3	1	2	1	4	5	2	1	2	5			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:9846496G>A	ENST00000432992.2	-	7	833	c.673C>T	c.(673-675)Cag>Tag	p.Q225*	GAS7_ENST00000542249.1_Nonsense_Mutation_p.Q161*|GAS7_ENST00000437099.2_Nonsense_Mutation_p.Q161*|GAS7_ENST00000585266.1_Nonsense_Mutation_p.Q165*|GAS7_ENST00000580865.1_Nonsense_Mutation_p.Q85*|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000323816.4_Nonsense_Mutation_p.Q165*|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000578655.1_5'Flank|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000579158.1_Nonsense_Mutation_p.Q161*	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	225	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						AGCTGTTTCTGGAGCAGTAGT	0.552			T	MLL	AML*																																p.Q225X				Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7-1083	0			c.C673T						.						182	164	170					17																	9846496		2203	4300	6503	SO:0001587	stop_gained	8522	exon7			GTTTCTGGAGCAG	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.673C>T	17.37:g.9846496G>A	ENSP00000407552:p.Gln225*	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	334	16	NM_201433	0	0	4	4	0	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Nonsense_Mutation	SNP	ENST00000432992.2	37	CCDS11152.1	.	.	.	.	.	.	.	.	.	.	G	38	6.925348	0.97940	.	.	ENSG00000007237	ENST00000323816;ENST00000396115;ENST00000437099;ENST00000432992;ENST00000537970;ENST00000541114	.	.	.	5.36	5.36	0.76844	.	0.081859	0.51477	D	0.000091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6746	18.2231	0.89907	0.0:0.0:1.0:0.0	.	.	.	.	X	225;165;164;85;165;39	.	.	Q	-	1	0	GAS7	9787221	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	8.955000	0.93058	2.676000	0.91093	0.655000	0.94253	CAG	.		0.552	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433		A	9846496	G	A	9846496	4	1	76	1	0	0	0	0	0	1	0	0	6270	1357	47	2	789	2	GAS7	17	9846496	Nonsense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	3248979	9846496	71348714	63	7149											
MYO1D	4642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	30932193	30932193	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagaggcagacaatgaggtCtttgttgtctttcgtatgga	10	13	13	5	1	2	3	0	1	2	2	3	5	2	4	0	3	0	3	0	3	3	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:30932193C>T	ENST00000318217.5	-	21	3080	c.2776G>A	c.(2776-2778)Gac>Aac	p.D926N	MYO1D_ENST00000394649.4_Missense_Mutation_p.D838N|MYO1D_ENST00000579584.1_Missense_Mutation_p.D926N	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	926	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			ACAATGAGGTCTTTGTTGTCT	0.423																																					p.D926N		.											.	MYO1D-137	0			c.G2776A						.						131	112	119					17																	30932193		2203	4300	6503	SO:0001583	missense	4642	exon21			TGAGGTCTTTGTT	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"Myosins / Myosin superfamily : Class I"	7598	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 108"	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2776G>A	17.37:g.30932193C>T	ENSP00000324527:p.Asp926Asn	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	108	19	NM_015194	0	0	51	70	19	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	C	32	5.168518	0.94768	.	.	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.61158	0.13	4.88	4.88	0.63580	Myosin tail 2 (1);	0.000000	0.41294	U	0.000917	T	0.77579	0.4151	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.99;0.994	T	0.81355	-0.0970	10	0.72032	D	0.01	.	15.8776	0.79178	0.0:1.0:0.0:0.0	.	837;926	Q7Z3N6;O94832	.;MYO1D_HUMAN	N	926;118	ENSP00000324527:D926N	ENSP00000324527:D926N	D	-	1	0	MYO1D	27956306	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.421000	0.82119	0.655000	0.94253	GAC	.		0.423	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			T	30932193	C	T	30932193	3	4	76	1	0	0	0	0	1	0	0	0	10096	913	32	2	252	2	MYO1D	17	30932193	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	21085697	30932193	50263017	64	7150											
ERBB2	2064	broad.mit.edu	37	chr17	37883164	37883164	+	Frame_Shift_Del	DEL	T	T	-																															acctggtggatgctgaggagTatctggtaccccagcagggc																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:37883164delT	ENST00000269571.5	+	25	3226	c.3067delT	c.(3067-3069)tatfs	p.Y1023fs	ERBB2_ENST00000541774.1_Frame_Shift_Del_p.Y1008fs|ERBB2_ENST00000445658.2_Frame_Shift_Del_p.Y747fs|ERBB2_ENST00000540147.1_Frame_Shift_Del_p.Y993fs|ERBB2_ENST00000584601.1_Frame_Shift_Del_p.Y993fs|ERBB2_ENST00000406381.2_Frame_Shift_Del_p.Y993fs|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584450.1_Frame_Shift_Del_p.Y1023fs|MIEN1_ENST00000474210.1_5'Flank			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	1023					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	TGCTGAGGAGTATCTGGTACC	0.627		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.Y1023fs				Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2-9959	0			c.3067delT						.						106	109	108					17																	37883164		2203	4300	6503	SO:0001589	frameshift_variant	2064	exon25			GAGGAGTATCTGG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.3067delT	17.37:g.37883164delT	ENSP00000269571:p.Tyr1023fs	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	333	7	NM_004448	0	0	0	0	0	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Frame_Shift_Del	DEL	ENST00000269571.5	37	CCDS32642.1																																																																																			.		0.627	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			-	37883164	T	-	37883164	7	5	76	1	0	1	0	1	0	0	0	0	5219	1638	57	0	3165	0	ERBB2	17	37883164	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	6950971	37883164	43312046	65	7151											
UBTF	7343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	42289818	42289818	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccttcacctccttcgtaGtggcctgcaaaccaaaagcc	10	9	7	15	1	1	0	1	0	0	0	4	0	3	0	6	1	3	2	6	1	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:42289818G>C	ENST00000302904.4	-	8	1157	c.665C>G	c.(664-666)aCt>aGt	p.T222S	UBTF_ENST00000343638.5_Intron|UBTF_ENST00000436088.1_Missense_Mutation_p.T222S|UBTF_ENST00000393606.3_Intron|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000527034.1_Intron|UBTF_ENST00000526094.1_Intron|UBTF_ENST00000529383.1_Missense_Mutation_p.T222S|UBTF_ENST00000533177.1_Intron|UBTF_ENST00000537550.1_5'Flank			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	222					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CTCCTTCGTAGTGGCCTGCAA	0.637																																					p.T222S		.											.	UBTF-90	0			c.C665G						.						78	73	75					17																	42289818		2203	4300	6503	SO:0001583	missense	7343	exon8			TTCGTAGTGGCCT	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.665C>G	17.37:g.42289818G>C	ENSP00000302640:p.Thr222Ser	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	179	44	NM_014233	0	0	0	0	0	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	g	2.112	-0.403562	0.04832	.	.	ENSG00000108312	ENST00000302904;ENST00000436088;ENST00000529383	D;D;D	0.97791	-4.54;-4.54;-4.54	4.9	3.89	0.44902	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.171589	0.50627	N	0.000119	D	0.89853	0.6835	N	0.03050	-0.425	0.33275	D	0.561518	B	0.12630	0.006	B	0.23716	0.048	D	0.84792	0.0779	10	0.02654	T	1	-4.647	10.1054	0.42530	0.0:0.1493:0.696:0.1547	.	222	P17480	UBF1_HUMAN	S	222	ENSP00000302640:T222S;ENSP00000390669:T222S;ENSP00000435708:T222S	ENSP00000302640:T222S	T	-	2	0	UBTF	39645344	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.273000	0.65564	1.135000	0.42183	0.442000	0.29010	ACT	.		0.637	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		C	42289818	G	C	42289818	3	2	76	1	0	0	0	0	1	0	0	0	16942	1029	36	4	1685	4	UBTF	17	42289818	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	4406654	42289818	38905392	66	7152											
MRPL10	124995	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45901623	45901623	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcccattggccgacatgacaGaatccttctcgcgttgctct	7	12	8	14	3	2	2	0	1	2	1	5	3	4	2	3	1	1	2	3	1	1	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:45901623G>A	ENST00000351111.2	-	5	739	c.734C>T	c.(733-735)tCt>tTt	p.S245F	MRPL10_ENST00000290208.7_Missense_Mutation_p.S255F|OSBPL7_ENST00000007414.3_5'Flank|OSBPL7_ENST00000392507.3_5'Flank|MRPL10_ENST00000414011.1_Missense_Mutation_p.S255F	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	245					ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						CGACATGACAGAATCCTTCTC	0.577																																					p.S255F		.											.	MRPL10-91	0			c.C764T						.						119	104	109					17																	45901623		2203	4300	6503	SO:0001583	missense	124995	exon6			ATGACAGAATCCT	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"Mitochondrial ribosomal proteins / large subunits"	14055	protein-coding gene	gene with protein product	"39S ribosomal protein L10, mitochondrial"	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.734C>T	17.37:g.45901623G>A	ENSP00000324100:p.Ser245Phe	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	179	87	NM_148887	0	0	44	104	60	A6NGJ4|Q96B80|Q96Q55	Missense_Mutation	SNP	ENST00000351111.2	37	CCDS11516.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.809636	0.50421	.	.	ENSG00000159111	ENST00000351111;ENST00000290208;ENST00000414011	T;T;T	0.50813	0.73;1.76;1.76	4.76	2.49	0.30216	.	1.038680	0.07593	N	0.922261	T	0.57286	0.2043	L	0.59436	1.845	0.09310	N	1	P;D	0.56521	0.8;0.976	B;P	0.51016	0.347;0.656	T	0.53034	-0.8495	10	0.72032	D	0.01	-2.0384	13.9408	0.64054	0.0:0.3197:0.6803:0.0	.	245;255	Q7Z7H8;A6NGJ4	RM10_HUMAN;.	F	245;255;255	ENSP00000324100:S245F;ENSP00000290208:S255F;ENSP00000395870:S255F	ENSP00000290208:S255F	S	-	2	0	MRPL10	43256622	0.009000	0.17119	0.001000	0.08648	0.056000	0.15407	1.692000	0.37731	0.954000	0.37851	0.491000	0.48974	TCT	.		0.577	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255		A	45901623	G	A	45901623	3	1	76	1	0	0	0	0	1	0	0	0	9800	942	33	2	55	2	MRPL10	17	45901623	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	3611805	45901623	35293587	67	7153											
GGA3	23163	broad.mit.edu	37	chr17	73237524	73237524	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccacctcgccattgatGacctgcccttcaataattgt	9	12	7	13	1	1	2	1	2	0	0	2	2	1	2	5	0	2	1	5	0	3	5			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:73237524G>T	ENST00000245541.6	-	10	1119	c.903C>A	c.(901-903)gtC>gtA	p.V301V	GGA3_ENST00000351904.7_Silent_p.V268V|GGA3_ENST00000537686.1_3'UTR|GGA3_ENST00000582486.1_Silent_p.V229V|GGA3_ENST00000538886.1_Silent_p.V179V|GGA3_ENST00000578348.1_Silent_p.V179V|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000582717.1_Silent_p.V229V	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	301	Binds to ARF1 (in long isoform).|Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			CGCCATTGATGACCTGCCCTT	0.547																																					p.V301V													.	GGA3-154	0			c.C903A						.						160	142	148					17																	73237524		2203	4300	6503	SO:0001819	synonymous_variant	23163	exon10			ATTGATGACCTGC	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.903C>A	17.37:g.73237524G>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	156	4	NM_138619	0	0	14	14	0	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Silent	SNP	ENST00000245541.6	37	CCDS11717.1																																																																																			.		0.547	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619		T	73237524	G	T	73237524	2	4	76	1	0	0	0	0	0	0	0	1	6374	1277	45	4		4	GGA3	17	73237524	Silent	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	27335901	73237524	7957686	68	7154											
SERPINB10	5273	broad.mit.edu	37	chr18	61584738	61584739	+	Frame_Shift_Ins	INS	-	-	A																															caaatgtgaccctgaaagtgINSaaaaaaaaaggaaaatggta																								rs201620640		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr18:61584738_61584739insA	ENST00000238508.3	+	3	276_277	c.217_218insA	c.(217-219)gaafs	p.E73fs		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	73					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R76fs*7(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				CCCTGAAAGTGAAAAAAAAAGG	0.282																																					p.E73fs													.	SERPINB10-227	1	Deletion - Frameshift(1)	large_intestine(1)	c.217_218insA						.																																			SO:0001589	frameshift_variant	5273	exon2			GAAAGTGAAAAAA	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.226dupA	18.37:g.61584747_61584747dupA	ENSP00000238508:p.Glu73fs	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	42	7	NM_005024	0	0	0	0	0	Q4VAX4|Q4VAX7	Frame_Shift_Ins	INS	ENST00000238508.3	37	CCDS11990.1																																																																																			-|0.985;A|0.015		0.282	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		A	61584739	-	A	61584738	7	5	76	1	0	1	1	0	0	0	0	0	14129	1291	45	0	223	0	SERPINB10	18	61584738	Frame_Shift_Ins	INS	-	TCGA-BQ-5892-01A-11D-1589-08		61584738	16492510	69	7155											
SHC2	25759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	422226	422226	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatactgcccggggttggTgacgctgtctcgcacaagga	8	8	14	11	3	1	1	0	1	1	0	2	3	1	2	1	4	2	3	1	4	2	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:422226T>C	ENST00000264554.6	-	11	1539	c.1540A>G	c.(1540-1542)Acc>Gcc	p.T514A		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	514	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGGGTTGGTGACGCTGTCT	0.677																																					p.T514A		.											.	SHC2-392	0			c.A1540G						.						23	28	27					19																	422226		2196	4298	6494	SO:0001583	missense	25759	exon11			GGTTGGTGACGCT	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"SH2 domain containing"	29869	protein-coding gene	gene with protein product	"neuronal Shc adaptor homolog"	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1540A>G	19.37:g.422226T>C	ENSP00000264554:p.Thr514Ala	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	31	9	NM_012435	0	0	3	3	0	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.738320	0.69304	.	.	ENSG00000129946	ENST00000264554	T	0.65178	-0.14	4.76	4.76	0.60689	SH2 motif (5);	0.000000	0.85682	D	0.000000	T	0.67401	0.2889	M	0.65975	2.015	0.54753	D	0.999983	P	0.36495	0.556	P	0.44561	0.453	T	0.71563	-0.4555	10	0.62326	D	0.03	-60.9323	13.7837	0.63097	0.0:0.0:0.0:1.0	.	514	P98077	SHC2_HUMAN	A	514	ENSP00000264554:T514A	ENSP00000264554:T514A	T	-	1	0	SHC2	373226	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	7.409000	0.80053	2.084000	0.62774	0.533000	0.62120	ACC	.		0.677	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			C	422226	T	C	422226	3	2	76	1	0	0	0	0	1	0	0	0	14303	1696	59	3	216	3	SHC2	19	422226	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		422226	58706757	70	7156											
LRRC8E	80131	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	7960603	7960603	+	Frame_Shift_Del	DEL	G	G	-																															ccgtggccatgctcatgattGgggtctttggctgcaccctc																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:7960603delG	ENST00000306708.6	+	2	216	c.115delG	c.(115-117)gggfs	p.G39fs		NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	39					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						GCTCATGATTGGGGTCTTTGG	0.627																																					p.G39fs		.											.	LRRC8E-92	0			c.115delG						.						120	90	100					19																	7960603		2203	4300	6503	SO:0001589	frameshift_variant	80131	exon3			.		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.115delG	19.37:g.7960603delG	ENSP00000306524:p.Gly39fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	68	17	NM_001268284	0	0	0	0	0	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Frame_Shift_Del	DEL	ENST00000306708.6	37	CCDS12189.1																																																																																			.		0.627	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		-	7960603	G	-	7960603	7	5	76	1	0	1	0	1	0	0	0	0	9050	1348	47	0	117	0	LRRC8E	19	7960603	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08	7538377	7960603	51168380	71	7157											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9046479	9046479	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctaggactggtggccattaCaggtgtggcatctggactac	8	10	13	10	0	1	0	0	0	1	0	1	2	1	2	2	6	2	1	2	6	3	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:9046479C>G	ENST00000397910.4	-	5	35355	c.35152G>C	c.(35152-35154)Gta>Cta	p.V11718L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11720	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGCCATTACAGGTGTGGCA	0.502																																					p.V11718L		.											.	MUC16-566	0			c.G35152C						.						125	120	121					19																	9046479		1975	4155	6130	SO:0001583	missense	94025	exon5			CCATTACAGGTGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.35152G>C	19.37:g.9046479C>G	ENSP00000381008:p.Val11718Leu	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	158	44	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	6.049	0.377322	0.11466	.	.	ENSG00000181143	ENST00000397910	T	0.01998	4.51	3.09	-1.82	0.07857	.	.	.	.	.	T	0.00845	0.0028	N	0.01352	-0.895	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47032	-0.9148	8	0.87932	D	0	.	1.1809	0.01845	0.2598:0.1629:0.1061:0.4712	.	11718	B5ME49	.	L	11718	ENSP00000381008:V11718L	ENSP00000381008:V11718L	V	-	1	0	MUC16	8907479	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.203000	0.09438	-0.527000	0.06374	-0.373000	0.07131	GTA	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9046479	C	G	9046479	3	3	76	1	0	0	0	0	1	0	0	0	9998	478	17	4	8691	4	MUC16	19	9046479	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	1085876	9046479	50082504	72	7158											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	9085838	9085838	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgcacagaaactttttCtgaagaaactgcatgtagtg	12	13	9	7	0	2	3	0	1	2	2	2	3	2	3	0	0	4	3	0	0	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:9085838C>A	ENST00000397910.4	-	1	6180	c.5977G>T	c.(5977-5979)Gaa>Taa	p.E1993*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1993	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAAACTTTTTCTGAAGAAACT	0.473																																					p.E1993X		.											.	MUC16-566	0			c.G5977T						.						139	135	136					19																	9085838		1983	4158	6141	SO:0001587	stop_gained	94025	exon1			CTTTTTCTGAAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5977G>T	19.37:g.9085838C>A	ENSP00000381008:p.Glu1993*	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	126	9	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	46	12.553061	0.99677	.	.	ENSG00000181143	ENST00000397910	.	.	.	0.235	0.235	0.15431	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	.	.	.	.	.	.	.	X	1993	.	ENSP00000381008:E1993X	E	-	1	0	MUC16	8946838	0.001000	0.12720	0.291000	0.24904	0.292000	0.27327	0.223000	0.17719	0.308000	0.22923	0.313000	0.20887	GAA	.		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9085838	C	A	9085838	4	1	76	1	0	0	0	0	0	1	0	0	9998	922	32	4	37882	4	MUC16	19	9085838	Nonsense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	39359	9085838	50043145	73	7159											
ZNF44	51710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12384693	12384693	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcccggtgtttgtgtccaGtatcaactctgatgtagcaa	9	13	9	10	1	2	1	1	1	1	0	4	1	4	1	2	1	2	4	2	1	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:12384693G>C	ENST00000356109.5	-	5	639	c.521C>G	c.(520-522)aCt>aGt	p.T174S	ZNF44_ENST00000355684.5_Missense_Mutation_p.T126S	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	174					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		TTTGTGTCCAGTATCAACTCT	0.438																																					p.T174S		.											.	ZNF44-23	0			c.C521G						.						158	157	158					19																	12384693		2179	4293	6472	SO:0001583	missense	51710	exon5			TGTCCAGTATCAA	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"Zinc fingers, C2H2-type", "-"	13110	protein-coding gene	gene with protein product		194542	"zinc finger protein 58", "zinc finger protein 44 (KOX 7)", "zinc finger protein 55"	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.521C>G	19.37:g.12384693G>C	ENSP00000348419:p.Thr174Ser	Somatic	145	1		WXS	Illumina HiSeq	Phase_I	171	48	NM_001164276	0	0	7	14	7	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Missense_Mutation	SNP	ENST00000356109.5	37	CCDS54223.1	.	.	.	.	.	.	.	.	.	.	G	4.481	0.089108	0.08583	.	.	ENSG00000197857	ENST00000393337;ENST00000356109;ENST00000457673;ENST00000355684	T;T;T	0.07114	3.29;3.22;3.28	1.28	0.0261	0.14148	.	.	.	.	.	T	0.07324	0.0185	L	0.39692	1.235	.	.	.	B;B	0.24368	0.102;0.048	B;B	0.22753	0.018;0.041	T	0.15065	-1.0450	8	0.46703	T	0.11	.	8.1694	0.31245	0.0:0.2536:0.7464:0.0	.	174;126	P15621;F8W7T7	ZNF44_HUMAN;.	S	174;174;126;126	ENSP00000377008:T174S;ENSP00000348419:T174S;ENSP00000347910:T126S	ENSP00000347910:T126S	T	-	2	0	ZNF44	12245693	0.000000	0.05858	0.002000	0.10522	0.361000	0.29550	-0.136000	0.10405	0.070000	0.16634	0.313000	0.20887	ACT	.		0.438	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264		C	12384693	G	C	12384693	3	2	76	1	0	0	0	0	1	0	0	0	17944	1029	36	4	1474	4	ZNF44	19	12384693	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	3298855	12384693	46744290	74	7160											
CALR	811	broad.mit.edu	37	chr19	13054650	13054658	+	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-																															aggatgatgaggacaaagatGaggatgaggaggatgaggag																								rs374121178|rs550353351	byFrequency	TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	GAGGATGAG	GAGGATGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:13054650_13054658delGAGGATGAG	ENST00000316448.5	+	9	1250_1258	c.1177_1185delGAGGATGAG	c.(1177-1185)gaggatgagdel	p.EDE396del	RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000592268.1_5'Flank|RAD23A_ENST00000586534.1_5'Flank|CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000541222.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	396	Asp/Glu/Lys-rich.|C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|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)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	ggacaaagatgaggatgaggaggatgagg	0.569														16	0.00319489	0.0113	0.0014	5008	,	,		17189	0		0	False		,,,				2504	0				p.393_395del													.	CALR-91	0			c.1177_1185del						.			197,4061		72,53,2004						-3	0.8			229	266,7976		129,8,3984	no	coding	CALR	NM_004343.3		201,61,5988	A1A1,A1R,RR		3.2274,4.6266,3.704				463,12037				SO:0001651	inframe_deletion	811	exon9			AAAGATGAGGATG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1177_1185delGAGGATGAG	19.37:g.13054659_13054667delGAGGATGAG	ENSP00000320866:p.Glu396_Glu398del	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	5	3	NM_004343	0	0	0	0	0	Q6IAT4|Q9UDG2	In_Frame_Del	DEL	ENST00000316448.5	37	CCDS12288.1																																																																																			.		0.569	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		-	13054658	GAGGATGAG	-	13054650	7	5	76	1	0	1	0	1	0	0	0	0	2598	1291	45	0	1211	0	CALR	19	13054650	In_Frame_Del	DEL	GAGGATGAG	TCGA-BQ-5892-01A-11D-1589-08	669957	13054650	46074333	75	7161											
ZNF208	7757	broad.mit.edu;bcgsc.ca	37	chr19	22157487	22157487	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acactcatccacattggtatAaccaatttttaagtgtaaat	15	14	4	8	0	1	0	1	0	0	0	2	0	2	0	2	1	1	2	2	1	6	7			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:22157487A>T	ENST00000397126.4	-	4	497	c.349T>A	c.(349-351)Tat>Aat	p.Y117N	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	117					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				ACATTGGTATAACCAATTTTT	0.353																																					p.Y117N													.	ZNF208-7	0			c.T349A						.						90	90	90					19																	22157487		2038	4232	6270	SO:0001583	missense	7757	exon4			TGGTATAACCAAT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"Zinc fingers, C2H2-type", "-"	12999	protein-coding gene	gene with protein product	"zinc finger protein 95"	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.349T>A	19.37:g.22157487A>T	ENSP00000380315:p.Tyr117Asn	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	182	7	NM_007153	0	0	0	0	0		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	A	7.551	0.662680	0.14645	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.06449	3.3	1.62	-1.2	0.09554	.	.	.	.	.	T	0.06826	0.0174	.	.	.	0.09310	N	1	D	0.54047	0.964	P	0.50136	0.632	T	0.27536	-1.0071	8	0.28530	T	0.3	.	2.3589	0.04302	0.491:0.3012:0.2078:0.0	.	117	O43345	ZN208_HUMAN	N	117	ENSP00000380315:Y117N	ENSP00000380315:Y117N	Y	-	1	0	ZNF208	21949327	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.308000	0.08156	-0.342000	0.08363	0.240000	0.17902	TAT	.		0.353	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22157487	A	T	22157487	3	4	76	1	0	0	0	0	1	0	0	0	17798	362	13	5	3497	5	ZNF208	19	22157487	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	9102837	22157487	36971496	76	7162											
MAP4K1	11184	hgsc.bcm.edu	37	chr19	39096057	39096057	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaacctcacctttctctTcatcttttccttcttggggg	4	17	7	13	0	5	1	2	1	3	0	7	1	6	1	3	2	1	1	3	2	1	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:39096057T>C	ENST00000591517.1	-	19	1466	c.1438A>G	c.(1438-1440)Aag>Gag	p.K480E	MAP4K1_ENST00000423454.2_Missense_Mutation_p.K142E|MAP4K1_ENST00000589130.1_Missense_Mutation_p.K476E|MAP4K1_ENST00000589002.1_5'Flank|MAP4K1_ENST00000396857.2_Missense_Mutation_p.K480E|MAP4K1_ENST00000586296.1_Intron	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	480					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ACCTTTCTCTTCATCTTTTCC	0.587																																					p.K480E		.											.	MAP4K1-980	0			c.A1438G						.						21	21	21					19																	39096057		1807	4060	5867	SO:0001583	missense	11184	exon19			TTCTCTTCATCTT	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.1438A>G	19.37:g.39096057T>C	ENSP00000465039:p.Lys480Glu	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	17	2	NM_007181	0	0	0	0	0		Missense_Mutation	SNP	ENST00000591517.1	37	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	.	1.988	-0.432397	0.04669	.	.	ENSG00000104814	ENST00000396857;ENST00000221409;ENST00000423454	T;T	0.72394	-0.65;2.9	4.72	4.72	0.59763	.	1.847090	0.02398	N	0.080338	T	0.58163	0.2103	N	0.22421	0.69	0.22656	N	0.998888	P;B;B	0.38195	0.622;0.143;0.162	B;B;B	0.32762	0.152;0.075;0.055	T	0.53585	-0.8418	10	0.52906	T	0.07	.	6.9512	0.24546	0.0:0.1009:0.0:0.8991	.	142;480;480	B4E087;Q92918-2;Q92918	.;.;M4K1_HUMAN	E	480;480;142	ENSP00000380066:K480E;ENSP00000396383:K142E	ENSP00000221409:K480E	K	-	1	0	MAP4K1	43787897	0.899000	0.30636	0.992000	0.48379	0.788000	0.44548	0.992000	0.29667	1.989000	0.58080	0.334000	0.21626	AAG	.		0.587	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		C	39096057	T	C	39096057	3	2	76	1	0	0	0	0	1	0	0	0	9284	1792	62	3	1181	3	MAP4K1	19	39096057	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	16938570	39096057	20032926	77	7163											
ZNF225	7768	broad.mit.edu	37	chr19	44636328	44636328	+	Frame_Shift_Del	DEL	T	T	-																															gtgaagagtgtgggaaaagaTttactcagaattcacaactt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:44636328delT	ENST00000262894.6	+	5	1841	c.1561delT	c.(1561-1563)tttfs	p.F521fs	ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_Frame_Shift_Del_p.F521fs	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				TGGGAAAAGATTTACTCAGAA	0.388																																					p.F521fs													.	.	0			c.1561delT						.						83	92	89					19																	44636328		2200	4296	6496	SO:0001589	frameshift_variant	7768	exon5			AAAAGATTTACTC	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.1561delT	19.37:g.44636328delT	ENSP00000262894:p.Phe521fs	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	125	12	NM_013362	0	0	0	0	0	A8K8S2|Q53F12|Q9NS46|Q9UID8	Frame_Shift_Del	DEL	ENST00000262894.6	37	CCDS46100.1																																																																																			.		0.388	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			-	44636328	T	-	44636328	7	5	76	1	0	1	0	1	0	0	0	0	17811	1493	52	0	1575	0	ZNF225	19	44636328	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	5540271	44636328	14492655	78	7164											
ZNF544	27300	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58774085	58774085	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcaatctcaacttgtaGtgcatcggcggacacatact	11	9	10	11	2	1	0	1	0	1	0	3	1	1	1	0	3	4	4	0	3	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:58774085G>A	ENST00000596652.1	+	6	2347	c.2113G>A	c.(2113-2115)Gtg>Atg	p.V705M	ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000415203.2_Missense_Mutation_p.V677M|ZNF544_ENST00000600044.1_Missense_Mutation_p.V677M|CTD-3138B18.5_ENST00000597230.1_RNA|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000600220.1_Missense_Mutation_p.V677M|ZNF544_ENST00000599953.1_Missense_Mutation_p.V563M|ZNF544_ENST00000269829.4_Missense_Mutation_p.V705M			Q6NX49	ZN544_HUMAN	zinc finger protein 544	705					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)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		TCAACTTGTAGTGCATCGGCG	0.488																																					p.V705M		.											.	ZNF544-91	0			c.G2113A						.						143	146	145					19																	58774085		2203	4300	6503	SO:0001583	missense	27300	exon7			CTTGTAGTGCATC	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.2113G>A	19.37:g.58774085G>A	ENSP00000469635:p.Val705Met	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	327	85	NM_014480	0	0	17	17	0	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	G	7.249	0.602782	0.13939	.	.	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.36340	1.26;1.26	3.46	-0.182	0.13287	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24661	0.0598	L	0.49126	1.545	0.09310	N	1	B;B;P	0.39480	0.061;0.235;0.675	B;B;B	0.32677	0.018;0.019;0.15	T	0.12734	-1.0536	9	0.48119	T	0.1	.	4.3215	0.11020	0.411:0.1657:0.4233:0.0	.	677;677;705	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	M	705;677;257	ENSP00000269829:V705M;ENSP00000394341:V677M	ENSP00000269829:V705M	V	+	1	0	ZNF544	63465897	0.000000	0.05858	0.000000	0.03702	0.507000	0.33981	-0.746000	0.04829	-0.024000	0.13941	0.563000	0.77884	GTG	.		0.488	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		A	58774085	G	A	58774085	3	1	76	1	0	0	0	0	1	0	0	0	18009	1029	36	2	2127	2	ZNF544	19	58774085	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	14137757	58774085	354898	79	7165											
JAG1	182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	10625851	10625851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcacttaaaagcatccccctCatcatagcaggtgccaccgt	11	8	7	15	1	2	0	2	0	0	0	3	0	3	0	4	1	3	3	4	1	3	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr20:10625851C>T	ENST00000254958.5	-	17	2682	c.2167G>A	c.(2167-2169)Gag>Aag	p.E723K	JAG1_ENST00000488480.1_RNA|JAG1_ENST00000423891.2_Missense_Mutation_p.E564K	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	723	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)	p.E723fs*6(1)		biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GCATCCCCCTCATCATAGCAG	0.547									Alagille Syndrome																												p.E723K		.											.	JAG1-1273	1	Insertion - Frameshift(1)	lung(1)	c.G2167A						.						122	99	107					20																	10625851		2203	4300	6503	SO:0001583	missense	182	exon17	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCCCCTCATCATA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2167G>A	20.37:g.10625851C>T	ENSP00000254958:p.Glu723Lys	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	142	43	NM_000214	0	0	36	41	5	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.224010	0.39300	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.85629	-2.01;-2.01	5.85	5.85	0.93711	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.74238	0.3690	N	0.12569	0.235	0.58432	D	0.999995	B	0.02656	0.0	B	0.06405	0.002	T	0.68777	-0.5319	10	0.10377	T	0.69	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	723	P78504	JAG1_HUMAN	K	723;564	ENSP00000254958:E723K;ENSP00000389519:E564K	ENSP00000254958:E723K	E	-	1	0	JAG1	10573851	1.000000	0.71417	0.989000	0.46669	0.978000	0.69477	4.891000	0.63185	2.767000	0.95098	0.655000	0.94253	GAG	.		0.547	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10625851	C	T	10625851	3	4	76	1	0	0	0	0	1	0	0	0	7955	835	29	2	1529	2	JAG1	20	10625851	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		10625851	52399669	80	7166											
CEP250	11190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	34064377	34064378	+	Frame_Shift_Ins	INS	-	-	T																															ctcagtgccttaaatgaggcINStttggcgttagataaagttg																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr20:34064377_34064378insT	ENST00000397527.1	+	16	2540_2541	c.1820_1821insT	c.(1819-1824)gctttgfs	p.L608fs	RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Frame_Shift_Ins_p.L608fs|RP3-477O4.14_ENST00000444933.1_RNA	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	608	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			TTAAATGAGGCTTTGGCGTTAG	0.515																																					p.A607fs		.											.	CEP250-27	0			c.1820_1821insT						.																																			SO:0001589	frameshift_variant	11190	exon16			.	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.1823dupT	20.37:g.34064380_34064380dupT	ENSP00000380661:p.Leu608fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	74	23	NM_007186	0	0	0	0	0	E1P5Q3|O14812|O60588|Q9H450	Frame_Shift_Ins	INS	ENST00000397527.1	37	CCDS13255.1																																																																																			.		0.515	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34064378	-	T	34064377	7	5	76	1	0	1	1	0	0	0	0	0	3258	797	28	0	1870	0	CEP250	20	34064377	Frame_Shift_Ins	INS	-	TCGA-BQ-5892-01A-11D-1589-08	23438526	34064377	28961143	81	7167											
SON	6651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34918555	34918555	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagctgaatggtgaaacaaaTacacccattgaaggaaacca	18	6	8	9	0	0	3	0	3	0	0	0	4	0	4	2	2	4	1	2	2	6	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr21:34918555T>G	ENST00000356577.4	+	2	589	c.114T>G	c.(112-114)aaT>aaG	p.N38K	SON_ENST00000381679.4_Missense_Mutation_p.N38K|SON_ENST00000300278.4_Missense_Mutation_p.N38K|SON_ENST00000290239.6_Missense_Mutation_p.N38K|SON_ENST00000381692.2_Missense_Mutation_p.N38K	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	38					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GTGAAACAAATACACCCATTG	0.393																																					p.N38K		.											.	SON-97	0			c.T114G						.						75	76	76					21																	34918555		2203	4300	6503	SO:0001583	missense	6651	exon2			AACAAATACACCC	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.114T>G	21.37:g.34918555T>G	ENSP00000348984:p.Asn38Lys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	65	23	NM_032195	0	0	28	43	15	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678619	0.68042	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000381692;ENST00000300278;ENST00000381679	T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45	5.68	-2.68	0.06041	.	0.232218	0.30244	N	0.010080	T	0.15003	0.0362	L	0.27053	0.805	0.22639	N	0.998909	B;D;D;D	0.58970	0.003;0.984;0.967;0.967	B;P;P;P	0.50860	0.001;0.449;0.652;0.652	T	0.20571	-1.0271	10	0.66056	D	0.02	.	10.9891	0.47539	0.0:0.578:0.0:0.422	.	38;38;38;38	Q6ZRV7;P18583;P18583-3;P18583-6	.;SON_HUMAN;.;.	K	38	ENSP00000348984:N38K;ENSP00000290239:N38K;ENSP00000371111:N38K;ENSP00000300278:N38K;ENSP00000371095:N38K	ENSP00000290239:N38K	N	+	3	2	SON	33840425	0.995000	0.38212	0.896000	0.35187	0.659000	0.38960	0.152000	0.16302	-0.281000	0.09141	-0.359000	0.07587	AAT	.		0.393	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34918555	T	G	34918555	3	3	76	1	0	0	0	0	1	0	0	0	14958	1403	49	5	120	5	SON	21	34918555	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		34918555	13211340	82	7168											
SON	6651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34922861	34922861	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgagttgccagggcccTctgtgacaccagtgccacag	7	8	12	14	0	1	2	0	2	1	0	1	2	1	2	5	1	3	1	5	1	0	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr21:34922861T>G	ENST00000356577.4	+	3	1799	c.1324T>G	c.(1324-1326)Tct>Gct	p.S442A	SON_ENST00000381679.4_Missense_Mutation_p.S442A|SON_ENST00000300278.4_Missense_Mutation_p.S442A|SON_ENST00000290239.6_Missense_Mutation_p.S442A|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	442					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GCCAGGGCCCTCTGTGACACC	0.632																																					p.S442A		.											.	SON-97	0			c.T1324G						.						34	37	36					21																	34922861		2202	4299	6501	SO:0001583	missense	6651	exon3			GGGCCCTCTGTGA	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.1324T>G	21.37:g.34922861T>G	ENSP00000348984:p.Ser442Ala	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	87	23	NM_032195	0	0	30	48	18	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937742	0.52972	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.14893	2.65;2.66;2.66;2.47	4.92	1.26	0.21427	.	0.404453	0.21839	N	0.068355	T	0.13713	0.0332	N	0.19112	0.55	0.24219	N	0.995448	P;P;P	0.47962	0.844;0.903;0.903	B;P;P	0.50270	0.432;0.636;0.636	T	0.09975	-1.0650	10	0.38643	T	0.18	.	6.7013	0.23227	0.0:0.3711:0.0:0.6289	.	442;442;442	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	A	442	ENSP00000348984:S442A;ENSP00000290239:S442A;ENSP00000300278:S442A;ENSP00000371095:S442A	ENSP00000290239:S442A	S	+	1	0	SON	33844731	.	.	1.000000	0.80357	0.966000	0.64601	.	.	0.427000	0.26145	0.402000	0.26972	TCT	.		0.632	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34922861	T	G	34922861	3	3	76	1	0	0	0	0	1	0	0	0	14958	1551	54	5	1334	5	SON	21	34922861	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	4306	34922861	13207034	83	7169											
PRMT2	3275	hgsc.bcm.edu;broad.mit.edu	37	chr21	48056904	48056905	+	Splice_Site	INS	-	-	AA																															cccagaagtgaatcgcaggtINSaatttccgttccacttccta																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr21:48056904_48056905insAA	ENST00000397637.1	+	2	993		c.e2+2		PRMT2_ENST00000458387.2_Splice_Site|PRMT2_ENST00000451211.2_Splice_Site|PRMT2_ENST00000334494.4_Splice_Site|PRMT2_ENST00000397628.1_Splice_Site|PRMT2_ENST00000397638.2_Splice_Site|PRMT2_ENST00000291705.6_Splice_Site|PRMT2_ENST00000440086.1_Splice_Site|PRMT2_ENST00000355680.3_Splice_Site			P55345	ANM2_HUMAN	protein arginine methyltransferase 2						developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		GAATCGCAGGTAATTTCCGTTC	0.421																																					.		.											.	PRMT2-91	0			c.39+2->AA						.																																			SO:0001630	splice_region_variant	3275	exon2			.	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"Protein arginine methyltransferases"	5186	protein-coding gene	gene with protein product		601961	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1", "HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.39+2->AA	21.37:g.48056905_48056906dupAA		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	55	12	NM_001535	0	0	0	0	0	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Splice_Site	INS	ENST00000397637.1	37	CCDS13737.1																																																																																			.		0.421	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	Intron	AA	48056905	-	AA	48056904	8	5	76	1	0	1	1	0	0	0	1	0	12566	1652	57	0	43	0	PRMT2	21	48056904	Splice_Site	INS	-	TCGA-BQ-5892-01A-11D-1589-08	13134043	48056904	72991	84	7170											
UBE2L3	7332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	21975858	21975858	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagcctgagcacccgcttcGggctgacctagctgaagaat	9	7	11	14	2	0	4	0	3	0	1	1	4	0	4	4	1	3	4	4	1	3	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr22:21975858G>C	ENST00000342192.4	+	4	563	c.365G>C	c.(364-366)cGg>cCg	p.R122P	UBE2L3_ENST00000545681.1_Missense_Mutation_p.R90P|UBE2L3_ENST00000458578.2_Missense_Mutation_p.R180P	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	122					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)		UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					CACCCGCTTCGGGCTGACCTA	0.478																																					p.R180P		.											.	UBE2L3-414	0			c.G539C						.						34	34	34					22																	21975858		2203	4300	6503	SO:0001583	missense	7332	exon4			CGCTTCGGGCTGA	AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651		"Ubiquitin-conjugating enzymes E2"	12488	protein-coding gene	gene with protein product		603721				8672131, 9693040	Standard	NM_001256356		Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000342192.4:c.365G>C	22.37:g.21975858G>C	ENSP00000344259:p.Arg122Pro	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	62	20	NM_001256355	0	0	188	276	88	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Missense_Mutation	SNP	ENST00000342192.4	37	CCDS13790.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.485144	0.84854	.	.	ENSG00000185651	ENST00000458578;ENST00000342192;ENST00000545681	T;T;T	0.71934	-0.61;-0.61;1.16	5.66	5.66	0.87406	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.070661	0.53938	D	0.000050	D	0.87103	0.6094	M	0.90814	3.15	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75484	0.986;0.977	D	0.89031	0.3442	10	0.66056	D	0.02	.	17.2403	0.87011	0.0:0.0:1.0:0.0	.	90;122	B4DDG1;P68036	.;UB2L3_HUMAN	P	180;122;90	ENSP00000400906:R180P;ENSP00000344259:R122P;ENSP00000445931:R90P	ENSP00000344259:R122P	R	+	2	0	UBE2L3	20305858	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	9.848000	0.99507	2.680000	0.91292	0.561000	0.74099	CGG	.		0.478	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157		C	21975858	G	C	21975858	3	2	76	1	0	0	0	0	1	0	0	0	16896	1116	39	4	379	4	UBE2L3	22	21975858	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		21975858	29328708	85	7171											
LIMK2	3985	broad.mit.edu	37	chr22	31667152	31667152	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actctatgtgcatcatccacCgggatctgaactcgcacaac	11	9	7	14	2	3	1	1	1	2	0	5	2	4	2	2	1	3	2	2	1	3	1	rs530553008		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr22:31667152C>T	ENST00000331728.4	+	12	1462	c.1348C>T	c.(1348-1350)Cgg>Tgg	p.R450W	LIMK2_ENST00000340552.4_Missense_Mutation_p.R429W|LIMK2_ENST00000333611.4_Missense_Mutation_p.R429W|LIMK2_ENST00000444929.2_Missense_Mutation_p.R204W|LIMK2_ENST00000406516.1_Missense_Mutation_p.R372W	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	450	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						CATCATCCACCGGGATCTGAA	0.537																																					p.R450W													.	LIMK2-548	0			c.C1348T						.						186	142	157					22																	31667152		2203	4300	6503	SO:0001583	missense	3985	exon12			ATCCACCGGGATC	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1348C>T	22.37:g.31667152C>T	ENSP00000332687:p.Arg450Trp	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	174	5	NM_005569	0	0	38	39	1	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Missense_Mutation	SNP	ENST00000331728.4	37	CCDS13891.1	.	.	.	.	.	.	.	.	.	.	.	19.32	3.805918	0.70682	.	.	ENSG00000182541	ENST00000406516;ENST00000444929;ENST00000331728;ENST00000436394;ENST00000333611;ENST00000340552	D;D;D;D;D	0.94138	-3.36;-2.43;-2.43;-2.43;-3.36	5.28	4.25	0.50352	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98068	0.9363	H	0.99261	4.49	0.54753	D	0.999987	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.999;0.999;0.998;0.971	D	0.98141	1.0436	10	0.87932	D	0	-17.07	11.9007	0.52682	0.4439:0.5561:0.0:0.0	.	482;429;204;450;372	F5GY29;Q7L3H5;E7EUC1;P53671;B5MC51	.;.;.;LIMK2_HUMAN;.	W	372;204;450;482;429;429	ENSP00000384602:R372W;ENSP00000409522:R204W;ENSP00000332687:R450W;ENSP00000330470:R429W;ENSP00000339916:R429W	ENSP00000332687:R450W	R	+	1	2	LIMK2	29997152	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	1.785000	0.38684	1.204000	0.43247	0.460000	0.39030	CGG	.		0.537	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733		T	31667152	C	T	31667152	3	4	76	1	0	0	0	0	1	0	0	0	8824	643	23	1	1451	1	LIMK2	22	31667152	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	9691294	31667152	19637414	86	7172											
NUP50	10762	hgsc.bcm.edu	37	chr22	45574342	45574342	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatctgacacctatctttaaAgactatgagaaatatttagc	15	13	6	7	0	2	3	0	2	2	2	2	5	2	3	1	0	1	0	1	0	7	7			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr22:45574342A>G	ENST00000347635.4	+	5	1030	c.564A>G	c.(562-564)aaA>aaG	p.K188K	NUP50_ENST00000407019.2_Silent_p.K160K|NUP50_ENST00000396096.2_Silent_p.K160K|CTA-268H5.12_ENST00000610217.1_RNA|NUP50_ENST00000425733.2_5'UTR	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	188	5 X 2 AA repeats of F-G.|Binding to CDKN1B. {ECO:0000250}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTATCTTTAAAGACTATGAGA	0.453																																					p.K188K		.											.	NUP50-68	0			c.A564G						.						42	42	42					22																	45574342		2202	4296	6498	SO:0001819	synonymous_variant	10762	exon5			CTTTAAAGACTAT	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"nucleoporin 50kD"	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.564A>G	22.37:g.45574342A>G		Somatic	87	2		WXS	Illumina HiSeq	Phase_I	113	12	NM_007172	0	0	17	17	0	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Silent	SNP	ENST00000347635.4	37	CCDS14062.1																																																																																			.		0.453	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2			G	45574342	A	G	45574342	2	3	76	1	0	0	0	0	0	0	0	1	10792	69	3	3		3	NUP50	22	45574342	Silent	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	13907190	45574342	5730224	87	7173											
ATXN3L	92552	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	13337247	13337248	+	Frame_Shift_Del	DEL	TG	TG	-																															gaagcaggagttacacatgaTgtctttggaagatcttgcga																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chrX:13337247_13337248delTG	ENST00000380622.2	-	1	1270_1271	c.806_807delCA	c.(805-807)acafs	p.T269fs	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	269					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TTACACATGATGTCTTTGGAAG	0.426																																					p.269_269del		.											.	ATXN3L-542	0			c.806_807del						.																																			SO:0001589	frameshift_variant	92552	exon1			.		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.806_807delCA	X.37:g.13337247_13337248delTG	ENSP00000369996:p.Thr269fs	Somatic	338	0		WXS	Illumina HiSeq	Phase_I	360	205	NM_001135995	0	0	0	0	0	B2RNY8	Frame_Shift_Del	DEL	ENST00000380622.2	37	CCDS48080.1																																																																																			.		0.426	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		-	13337248	TG	-	13337247	7	5	76	1	0	1	0	1	0	0	0	0	1215	1451	51	0	264	0	ATXN3L	23	13337247	Frame_Shift_Del	DEL	TG	TCGA-BQ-5892-01A-11D-1589-08		13337247	141933313	88	7174											
UTP14A	10813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	129045744	129045744	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atgccttgcctgcttcagatCcacagagaagtagcattcaa	12	10	8	11	0	2	2	2	0	0	2	3	3	3	2	3	0	4	3	3	0	3	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chrX:129045744C>T	ENST00000394422.3	+	6	412	c.384C>T	c.(382-384)atC>atT	p.I128I	UTP14A_ENST00000371042.3_5'Flank|UTP14A_ENST00000371051.5_Silent_p.I74I|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000425117.2_Intron	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	128					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						TGCTTCAGATCCACAGAGAAG	0.473																																					p.I128I		.											.	UTP14A-132	0			c.C384T						.						139	133	135					X																	129045744		2203	4300	6503	SO:0001819	synonymous_variant	10813	exon6			TCAGATCCACAGA	AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"serologically defined colon cancer antigen 16"	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.384C>T	X.37:g.129045744C>T		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	180	109	NM_006649	0	0	0	0	0	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Silent	SNP	ENST00000394422.3	37	CCDS14615.1																																																																																			.		0.473	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		T	129045744	C	T	129045744	2	4	76	1	0	0	0	0	0	0	0	1	17128	845	30	2		2	UTP14A	23	129045744	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	115708497	129045744	26224816	89	7175											
JAK1	3716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	65344759	65344759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtcatcaacggtgatggtgCgatttggagcataccagagc	10	10	13	8	2	2	2	2	1	0	1	2	4	2	3	1	3	5	1	1	3	2	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:65344759C>T	ENST00000342505.4	-	4	526	c.278G>A	c.(277-279)cGc>cAc	p.R93H		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	93	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGTGATGGTGCGATTTGGAGC	0.507			Mis		ALL																																p.R93H		.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1-3900	0			c.G278A						.						134	132	133					1																	65344759		2051	4200	6251	SO:0001583	missense	3716	exon4			ATGGTGCGATTTG	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.278G>A	1.37:g.65344759C>T	ENSP00000343204:p.Arg93His	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	45	25	NM_002227	0	0	95	137	42	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.643910	0.00792	.	.	ENSG00000162434	ENST00000342505	T	0.60797	0.16	5.17	-4.45	0.03546	Band 4.1 domain (1);FERM domain (1);	.	.	.	.	T	0.03564	0.0102	N	0.00044	-2.46	0.20926	N	0.999829	B	0.02656	0.0	B	0.01281	0.0	T	0.48091	-0.9065	9	0.02654	T	1	-0.1135	14.8839	0.70553	0.0:0.2045:0.0:0.7955	.	93	P23458	JAK1_HUMAN	H	93	ENSP00000343204:R93H	ENSP00000343204:R93H	R	-	2	0	JAK1	65117347	0.002000	0.14202	0.069000	0.20011	0.073000	0.16967	-0.194000	0.09559	-0.765000	0.04645	-0.794000	0.03295	CGC	.		0.507	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65344759	C	T	65344759	3	4	77	1	0	0	0	0	1	0	0	0	7958	768	27	1	3274	1	JAK1	1	65344759	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		65344759	183905862	1	7176											
ARHGAP29	9411	bcgsc.ca	37	chr1	94696978	94696978	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaacctgaaaatatggcttCtttcaaatatagtaacatgt	16	13	5	7	0	2	1	1	1	1	0	2	1	2	1	1	1	2	2	1	1	8	6	rs200189126		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:94696978C>T	ENST00000260526.6	-	2	372	c.190G>A	c.(190-192)Gaa>Aaa	p.E64K	ARHGAP29_ENST00000370217.3_Missense_Mutation_p.E64K	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	64					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		AATATGGCTTCTTTCAAATAT	0.363																																					p.E64K													.	ARHGAP29-296	0			c.G190A						.						74	73	74					1																	94696978		2203	4300	6503	SO:0001583	missense	9411	exon2			TGGCTTCTTTCAA		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.190G>A	1.37:g.94696978C>T	ENSP00000260526:p.Glu64Lys	Somatic	90	1		WXS	Illumina HiSeq	Phase_1	74	18	NM_004815	0	0	21	21	0	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826469	0.90955	.	.	ENSG00000137962	ENST00000260526;ENST00000370217	T;T	0.27720	1.65;1.68	5.83	5.83	0.93111	.	0.000000	0.37219	N	0.002196	T	0.36358	0.0964	L	0.55990	1.75	0.48632	D	0.999685	D;P	0.56035	0.974;0.521	P;B	0.54499	0.754;0.443	T	0.08269	-1.0730	10	0.72032	D	0.01	-21.095	17.0506	0.86517	0.0:1.0:0.0:0.0	.	64;64	Q52LW3-2;Q52LW3	.;RHG29_HUMAN	K	64	ENSP00000260526:E64K;ENSP00000359237:E64K	ENSP00000260526:E64K	E	-	1	0	ARHGAP29	94469566	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.413000	0.59795	2.770000	0.95276	0.655000	0.94253	GAA	.		0.363	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		T	94696978	C	T	94696978	3	4	77	1	0	0	0	0	1	0	0	0	878	922	32	2	3683	2	ARHGAP29	1	94696978	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	29352219	94696978	154553643	2	7177											
SNX7	51375	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	99150445	99150445	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgttttatttcttaggatgCctcattgatggacatgaact	10	17	8	6	0	2	2	1	2	1	0	2	4	2	4	1	2	2	1	1	2	3	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:99150445C>A	ENST00000306121.3	+	2	194	c.185C>A	c.(184-186)gCc>gAc	p.A62D	SNX7_ENST00000529992.1_Missense_Mutation_p.A62D|SNX7_ENST00000370189.5_5'UTR	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	200	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TCTTAGGATGCCTCATTGATG	0.303																																					p.A62D													.	SNX7-229	0			c.C185A						.						97	88	91					1																	99150445		2203	4300	6503	SO:0001583	missense	51375	exon2			AGGATGCCTCATT	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"Sorting nexins"	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.185C>A	1.37:g.99150445C>A	ENSP00000304429:p.Ala62Asp	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	104	37	NM_015976	0	0	0	0	0	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624884	0.66901	.	.	ENSG00000162627	ENST00000529992;ENST00000306121	T;T	0.32753	2.12;1.44	5.29	4.36	0.52297	.	.	.	.	.	T	0.15522	0.0374	N	0.19112	0.55	0.80722	D	1	B;D	0.53462	0.003;0.96	B;P	0.51229	0.003;0.663	T	0.03221	-1.1059	9	0.16896	T	0.51	.	15.2016	0.73142	0.142:0.858:0.0:0.0	.	62;62	E9PNL2;Q9UNH6-3	.;.	D	62	ENSP00000434731:A62D;ENSP00000304429:A62D	ENSP00000304429:A62D	A	+	2	0	SNX7	98923033	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	3.677000	0.54619	1.212000	0.43366	0.650000	0.86243	GCC	.		0.303	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			A	99150445	C	A	99150445	3	1	77	1	0	0	0	0	1	0	0	0	14939	739	26	4	191	4	SNX7	1	99150445	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	4453467	99150445	150100176	3	7178											
ANKRD35	148741	bcgsc.ca	37	chr1	145560900	145560900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttataggtcagaggctaGtccagcacccagatctcgca	10	10	9	12	1	3	2	1	0	2	2	5	2	4	2	2	2	1	3	2	2	3	4	rs202165652		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:145560900G>A	ENST00000355594.4	+	9	844	c.757G>A	c.(757-759)Gtc>Atc	p.V253I	ANKRD35_ENST00000544626.1_3'UTR	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	253										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCAGAGGCTAGTCCAGCACCC	0.473																																					p.V253I	Melanoma(9;127 754 22988 51047)												.	ANKRD35-95	0			c.G757A						.						130	128	129					1																	145560900		2203	4300	6503	SO:0001583	missense	148741	exon9			AGGCTAGTCCAGC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.757G>A	1.37:g.145560900G>A	ENSP00000347802:p.Val253Ile	Somatic	134	0		WXS	Illumina HiSeq	Phase_1	101	21	NM_144698	0	0	0	0	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919305	0.33908	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.65364	-0.15	5.39	5.39	0.77823	.	0.274245	0.26013	N	0.026876	T	0.37183	0.0994	L	0.34521	1.04	0.80722	D	1	P	0.37955	0.612	B	0.34536	0.185	T	0.32693	-0.9897	10	0.34782	T	0.22	-6.4309	14.5188	0.67838	0.0:0.0:1.0:0.0	.	253	Q8N283	ANR35_HUMAN	I	162;253	ENSP00000347802:V253I	ENSP00000347802:V253I	V	+	1	0	ANKRD35	144272257	0.999000	0.42202	0.923000	0.36655	0.658000	0.38924	4.107000	0.57811	2.808000	0.96608	0.655000	0.94253	GTC	.		0.473	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145560900	G	A	145560900	3	1	77	1	0	0	0	0	1	0	0	0	664	1029	36	2	791	2	ANKRD35	1	145560900	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	46410455	145560900	103689721	4	7179											
NTRK1	4914	broad.mit.edu	37	chr1	156837966	156837966	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgctgggaggaggagggaCtgggcggagtgcctgaacag	9	4	21	7	2	0	1	0	1	0	0	0	6	0	6	1	6	3	1	1	6	1	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:156837966C>A	ENST00000524377.1	+	5	540	c.499C>A	c.(499-501)Ctg>Atg	p.L167M	NTRK1_ENST00000392302.2_Missense_Mutation_p.L137M|NTRK1_ENST00000368196.3_Missense_Mutation_p.L167M|NTRK1_ENST00000358660.3_Missense_Mutation_p.L167M	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	167	LRRCT.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GGAGGAGGGACTGGGCGGAGT	0.657			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.L167M				Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1-1393	0			c.C499A						.						61	63	62					1																	156837966		2203	4300	6503	SO:0001583	missense	4914	exon5			GAGGGACTGGGCG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.499C>A	1.37:g.156837966C>A	ENSP00000431418:p.Leu167Met	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	154	4	NM_001012331	0	0	0	0	0	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.105615	0.56291	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67	5.21	3.22	0.36961	Cysteine-rich flanking region, C-terminal (1);	1.036150	0.07713	N	0.942312	T	0.79299	0.4422	L	0.47716	1.5	0.09310	N	1	B;P;P;B	0.35745	0.142;0.518;0.51;0.383	B;B;B;B	0.36030	0.133;0.216;0.143;0.155	T	0.69483	-0.5133	10	0.32370	T	0.25	.	9.2994	0.37835	0.1431:0.7786:0.0:0.0783	.	167;167;167;137	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	M	137;167;167;167	ENSP00000376120:L137M;ENSP00000357179:L167M;ENSP00000431418:L167M;ENSP00000351486:L167M	ENSP00000351486:L167M	L	+	1	2	NTRK1	155104590	0.058000	0.20735	0.176000	0.23000	0.933000	0.57130	0.782000	0.26788	1.166000	0.42689	0.462000	0.41574	CTG	.		0.657	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		A	156837966	C	A	156837966	3	1	77	1	0	0	0	0	1	0	0	0	10732	564	20	4	647	4	NTRK1	1	156837966	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	11277066	156837966	92412655	5	7180											
FCGR2A	2212	bcgsc.ca	37	chr1	161480669	161480669	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggggatcattgtggctgTggtcattgcgactgctgtag	7	13	15	6	1	2	0	2	0	0	0	2	2	2	1	0	4	2	3	0	4	2	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:161480669T>G	ENST00000271450.6	+	5	703	c.665T>G	c.(664-666)gTg>gGg	p.V222G	RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000367972.4_Missense_Mutation_p.V221G	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	222					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	ATTGTGGCTGTGGTCATTGCG	0.512																																					p.V222G													.	FCGR2A-91	0			c.T665G						.						232	230	231					1																	161480669		2203	4300	6503	SO:0001583	missense	2212	exon5			TGGCTGTGGTCAT	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3616	protein-coding gene	gene with protein product	"Immunoglobulin G Fc receptor II"	146790	"Fc fragment of IgG, low affinity IIa, receptor for (CD32)"	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.665T>G	1.37:g.161480669T>G	ENSP00000271450:p.Val222Gly	Somatic	238	1		WXS	Illumina HiSeq	Phase_1	260	35	NM_001136219	0	0	2	2	0	Q8WUN1|Q8WW64	Missense_Mutation	SNP	ENST00000271450.6	37	CCDS44264.1	.	.	.	.	.	.	.	.	.	.	.	12.98	2.101851	0.37048	.	.	ENSG00000143226	ENST00000367972;ENST00000271450	T;T	0.01998	4.51;4.51	2.27	-0.676	0.11361	.	2.881450	0.01271	N	0.009457	T	0.01695	0.0054	L	0.60455	1.87	0.25785	N	0.984687	D;P	0.54601	0.967;0.955	P;P	0.48454	0.576;0.578	T	0.35176	-0.9799	9	0.87932	D	0	.	5.0419	0.14463	0.0:0.5402:0.0:0.4598	.	222;221	P12318;P12318-2	FCG2A_HUMAN;.	G	221;222	ENSP00000356949:V221G;ENSP00000271450:V222G	ENSP00000271450:V222G	V	+	2	0	FCGR2A	159747293	0.000000	0.05858	0.006000	0.13384	0.027000	0.11550	-0.017000	0.12590	-0.155000	0.11098	0.459000	0.35465	GTG	.		0.512	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642		G	161480669	T	G	161480669	3	3	77	1	0	0	0	0	1	0	0	0	5800	1696	59	5	683	5	FCGR2A	1	161480669	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	4642703	161480669	87769952	6	7181											
BAT2L2	23215	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	171501662	171501662	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcgaagaatggaagaacaaAggaaggcagcttgtgcggag	16	4	16	5	2	0	2	0	0	0	2	0	6	0	5	0	4	4	2	0	4	6	1	rs14798|rs11546357		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:171501662A>C	ENST00000338920.4	+	12	1666	c.1429A>C	c.(1429-1431)Agg>Cgg	p.R477R	PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000392078.3_Silent_p.R479R|PRRC2C_ENST00000426496.2_Silent_p.R477R|PRRC2C_ENST00000367742.3_Silent_p.R479R	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	477	Glu-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GGAAGAACAAAGGAAGGCAGC	0.458																																					p.R477R		.											.	.	0			c.A1429C						.						81	72	75					1																	171501662		2203	4298	6501	SO:0001819	synonymous_variant	23215	exon12			GAACAAAGGAAGG	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.1429A>C	1.37:g.171501662A>C		Somatic	21	1		WXS	Illumina HiSeq	Phase_I	14	14	NM_015172	0	1	8	128	119	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2																																																																																			A|1.000;T|0.000		0.458	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171501662	A	C	171501662	2	2	77	1	0	0	0	0	0	0	0	1	1322	63	3	5		5	BAT2L2	1	171501662	Silent	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	10020993	171501662	77748959	7	7182											
SLC9A11	284525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	173505010	173505010	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctatacaatattccaaGaaagttaaaacatttttaaa	18	16	2	5	0	1	1	0	0	1	1	2	1	2	1	1	0	2	1	1	0	10	10			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:173505010G>T	ENST00000367714.3	-	15	2156	c.1734C>A	c.(1732-1734)ttC>ttA	p.F578L	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Intron	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	578					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.F578L(1)									AATATTCCAAGAAAGTTAAAA	0.259																																					p.F578L		.											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1734A						.						30	36	34					1																	173505010		2143	4195	6338	SO:0001583	missense	284525	exon15			TTCCAAGAAAGTT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"Solute carriers"	28664	protein-coding gene	gene with protein product			"solute carrier family 9, isoform 11", "solute carrier family 9, member 11", "solute carrier family 9, member C2"	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1734C>A	1.37:g.173505010G>T	ENSP00000356687:p.Phe578Leu	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	113	29	NM_178527	0	0	0	0	0	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	G	1.013	-0.687321	0.03328	.	.	ENSG00000162753	ENST00000367714	T	0.04275	3.66	5.81	2.48	0.30137	.	0.605739	0.15672	N	0.250356	T	0.00967	0.0032	L	0.36672	1.1	0.09310	N	1	B	0.22346	0.068	B	0.15484	0.013	T	0.47898	-0.9081	10	0.11485	T	0.65	-5.8685	3.7288	0.08485	0.2435:0.2051:0.5513:0.0	.	578	Q5TAH2	S9A11_HUMAN	L	578	ENSP00000356687:F578L	ENSP00000356687:F578L	F	-	3	2	SLC9A11	171771633	0.739000	0.28196	0.234000	0.24042	0.083000	0.17756	1.040000	0.30278	0.747000	0.32809	0.603000	0.83216	TTC	.		0.259	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173505010	G	T	173505010	3	4	77	1	0	0	0	0	1	0	0	0	14743	933	33	4	1696	4	SLC9A11	1	173505010	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	2003348	173505010	75745611	8	7183											
PTGS2	5743	hgsc.bcm.edu	37	chr1	186649374	186649374	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggcgccaggtactcacctgTatggctgagcgccaggaccg	7	6	14	14	4	1	1	1	1	0	0	1	2	1	2	4	4	2	3	4	4	2	2	rs199946406		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:186649374T>C	ENST00000367468.5	-	1	185	c.49A>G	c.(49-51)Aca>Gca	p.T17A	PTGS2_ENST00000490885.2_5'UTR|RP5-973M2.2_ENST00000608917.1_lincRNA	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	17					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	TACTCACCTGTATGGCTGAGC	0.706											OREG0014057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T17A		.											.	PTGS2-227	0			c.A49G						.						5	8	7					1																	186649374		1841	3707	5548	SO:0001583	missense	5743	exon1			CACCTGTATGGCT	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.49A>G	1.37:g.186649374T>C	ENSP00000356438:p.Thr17Ala	Somatic	6	1	2009	WXS	Illumina HiSeq	Phase_I	6	6	NM_000963	0	0	0	0	0	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	37	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	T	0.215	-1.033430	0.02029	.	.	ENSG00000073756	ENST00000367468	T	0.62232	0.04	4.37	3.46	0.39613	Epidermal growth factor-like, type 3 (1);	0.546358	0.18770	N	0.131621	T	0.29190	0.0726	N	0.02286	-0.61	0.20703	N	0.999861	B	0.02656	0.0	B	0.04013	0.001	T	0.22591	-1.0212	10	0.02654	T	1	.	9.1985	0.37242	0.0:0.8948:0.0:0.1052	.	17	P35354	PGH2_HUMAN	A	17	ENSP00000356438:T17A	ENSP00000356438:T17A	T	-	1	0	PTGS2	184915997	0.849000	0.29639	0.819000	0.32651	0.031000	0.12232	1.317000	0.33631	1.137000	0.42214	-0.220000	0.12472	ACA	.		0.706	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		C	186649374	T	C	186649374	3	2	77	1	0	0	0	0	1	0	0	0	12786	1638	57	3	1805	3	PTGS2	1	186649374	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	13144364	186649374	62601247	9	7184											
AKT3	10000	hgsc.bcm.edu	37	chr1	243668589	243668589	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagtaggaaaattgagggaAatgcggccgcctctcattgt	12	9	13	7	2	1	2	1	1	1	1	2	4	1	4	2	3	1	1	2	3	4	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:243668589A>G	ENST00000366539.1	-	14	1602	c.1402T>C	c.(1402-1404)Ttc>Ctc	p.F468L	AKT3_ENST00000263826.5_Missense_Mutation_p.F468L|AKT3_ENST00000336199.5_Intron|AKT3_ENST00000366540.1_Intron			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	468	AGC-kinase C-terminal.				mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			AATTGAGGGAAATGCGGCCGC	0.393																																					p.F468L		.											.	AKT3-1423	0			c.T1402C						.						108	105	106					1																	243668589		2203	4300	6503	SO:0001583	missense	10000	exon13			GAGGGAAATGCGG	AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"Pleckstrin homology (PH) domain containing"	393	protein-coding gene	gene with protein product	"protein kinase B, gamma"	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.1402T>C	1.37:g.243668589A>G	ENSP00000355497:p.Phe468Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_005465	0	0	35	35	0	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Missense_Mutation	SNP	ENST00000366539.1	37	CCDS31077.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.676997	0.88445	.	.	ENSG00000117020	ENST00000366539;ENST00000263826	D;D	0.91464	-2.85;-2.85	5.4	5.4	0.78164	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.95893	0.8663	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.96629	0.9465	10	0.87932	D	0	.	15.5974	0.76595	1.0:0.0:0.0:0.0	.	468	Q9Y243	AKT3_HUMAN	L	468	ENSP00000355497:F468L;ENSP00000263826:F468L	ENSP00000263826:F468L	F	-	1	0	AKT3	241735212	1.000000	0.71417	0.994000	0.49952	0.906000	0.53458	9.139000	0.94554	2.271000	0.75665	0.533000	0.62120	TTC	.		0.393	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690		G	243668589	A	G	243668589	3	3	77	1	0	0	0	0	1	0	0	0	481	14	1	3	89	3	AKT3	1	243668589	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	57019215	243668589	5582032	10	7185											
OR13G1	441933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247835611	247835611	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggagaatagtaaagggtcaCcactgtgagatgagatgagc	15	7	14	5	0	1	4	1	3	0	3	1	7	1	4	1	2	1	1	1	2	4	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:247835611C>G	ENST00000359688.2	-	1	754	c.733G>C	c.(733-735)Gtg>Ctg	p.V245L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TAAAGGGTCACCACTGTGAGA	0.448																																					p.V245L		.											.	OR13G1-69	0			c.G733C						.						162	139	147					1																	247835611		2203	4300	6503	SO:0001583	missense	441933	exon1			GGGTCACCACTGT	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"GPCR / Class A : Olfactory receptors"	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.733G>C	1.37:g.247835611C>G	ENSP00000352717:p.Val245Leu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	122	32	NM_001005487	0	0	0	0	0	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.373546	0.24857	.	.	ENSG00000197437	ENST00000359688	T	0.00355	7.91	4.2	3.29	0.37713	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	N	0.001320	T	0.00815	0.0027	M	0.86740	2.835	0.09310	N	1	D	0.76494	0.999	D	0.77557	0.99	T	0.26258	-1.0108	10	0.66056	D	0.02	-60.5376	10.2821	0.43545	0.0:0.9016:0.0:0.0984	.	245	Q8NGZ3	O13G1_HUMAN	L	245	ENSP00000352717:V245L	ENSP00000352717:V245L	V	-	1	0	OR13G1	245902234	0.021000	0.18746	0.037000	0.18230	0.096000	0.18686	0.139000	0.16036	1.126000	0.42016	-0.214000	0.12660	GTG	.		0.448	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		G	247835611	C	G	247835611	3	3	77	1	0	0	0	0	1	0	0	0	10968	507	18	4	194	4	OR13G1	1	247835611	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	4167022	247835611	1415010	11	7186											
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu	37	chr3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcctctctctgaaatcactGagcaggagaaagattttcta	13	12	7	9	0	4	4	1	2	3	2	6	5	5	4	1	1	1	1	1	1	3	3	rs104886003		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E545K	Colon(199;1504 1750 3362 26421 31210 32040)	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA-27752	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)	c.G1633A						.						61	60	60					3																	178936091		1813	4072	5885	SO:0001583	missense	5290	exon10			ATCACTGAGCAGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_006218	0	0	12	12	0	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	.		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936091	G	A	178936091	3	1	77	1	0	0	0	0	1	0	0	0	11939	1291	45	2	1667	2	PIK3CA	3	178936091	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		178936091	19086339	12	7187											
ANXA3	306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	79531260	79531260	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttaaaaatctgtggtggAgatgactgaaccaagaagat	15	10	10	6	0	2	5	0	2	2	3	2	6	2	5	1	2	1	0	1	2	6	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr4:79531260A>T	ENST00000264908.6	+	13	1342	c.963A>T	c.(961-963)ggA>ggT	p.G321G	ANXA3_ENST00000503570.2_Silent_p.G282G|ANXA3_ENST00000512884.1_Silent_p.G282G	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	321					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						TCTGTGGTGGAGATGACTGAA	0.373																																					p.G321G	GBM(2;126 157 27790 28920 42492)	.											.	ANXA3-90	0			c.A963T						.						90	89	89					4																	79531260		2203	4300	6503	SO:0001819	synonymous_variant	306	exon13			TGGTGGAGATGAC	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.963A>T	4.37:g.79531260A>T		Somatic	94	1		WXS	Illumina HiSeq	Phase_I	78	39	NM_005139	0	0	71	111	40	B2R9W6|Q6LET2	Silent	SNP	ENST00000264908.6	37	CCDS3584.1																																																																																			.		0.373	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		T	79531260	A	T	79531260	2	4	77	1	0	0	0	0	0	0	0	1	719	291	11	5		5	ANXA3	4	79531260	Silent	SNP	A	TCGA-BQ-5893-01A-11D-1589-08		79531260	111623016	13	7188											
GAB1	2549	hgsc.bcm.edu	37	chr4	144354854	144354854	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcaactgtcaaagcaagaAgcccgaacccaccaggtaaa	17	4	7	13	1	2	1	2	0	0	1	2	2	2	1	3	1	4	2	3	1	7	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr4:144354854A>G	ENST00000262994.4	+	3	880	c.578A>G	c.(577-579)aAg>aGg	p.K193R	GAB1_ENST00000262995.4_Missense_Mutation_p.K193R|GAB1_ENST00000505913.1_Missense_Mutation_p.K90R	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	193					activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					CAAAGCAAGAAGCCCGAACCC	0.438																																					p.K193R		.											.	GAB1-1146	0			c.A578G						.						70	69	69					4																	144354854		2203	4300	6503	SO:0001583	missense	2549	exon3			GCAAGAAGCCCGA	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"Pleckstrin homology (PH) domain containing"	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.578A>G	4.37:g.144354854A>G	ENSP00000262994:p.Lys193Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_207123	0	0	13	13	0	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	37	CCDS3759.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.9|28.9	4.960201|4.960201	0.92791|0.92791	.|.	.|.	ENSG00000109458|ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000514639;ENST00000505913;ENST00000509992|ENST00000512843	T;T;T;T;T|.	0.37235|.	2.51;2.52;1.21;2.07;1.29|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69904|0.69904	0.3163|0.3163	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.996;0.999|.	D;D|.	0.78314|.	0.955;0.991|.	T|T	0.67518|0.67518	-0.5650|-0.5650	10|5	0.10111|.	T|.	0.7|.	-8.8266|-8.8266	16.3483|16.3483	0.83171|0.83171	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	193;193|.	Q13480;Q13480-2|.	GAB1_HUMAN;.|.	R|G	193;193;193;90;172|71	ENSP00000262995:K193R;ENSP00000262994:K193R;ENSP00000427435:K193R;ENSP00000424554:K90R;ENSP00000425921:K172R|.	ENSP00000262994:K193R|.	K|S	+|+	2|1	0|0	GAB1|GAB1	144574304|144574304	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	5.129000|5.129000	0.64739|0.64739	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.		0.438	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		G	144354854	A	G	144354854	3	3	77	1	0	0	0	0	1	0	0	0	6167	72	3	3	588	3	GAB1	4	144354854	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	64823594	144354854	46799422	14	7189											
CCNB1	891	bcgsc.ca	37	chr5	68470159	68470159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatcctaattgactggctaGtacaggttcaaatgaaattc	13	12	7	9	0	1	2	1	2	0	0	3	2	2	2	2	2	1	3	2	2	5	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:68470159G>A	ENST00000256442.5	+	5	881	c.628G>A	c.(628-630)Gta>Ata	p.V210I	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	210					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TGACTGGCTAGTACAGGTTCA	0.433																																					p.V210I													.	CCNB1-650	0			c.G628A						.						181	171	175					5																	68470159		2203	4300	6503	SO:0001583	missense	891	exon5			TGGCTAGTACAGG	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"G2/mitotic-specific cyclin B1"	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.628G>A	5.37:g.68470159G>A	ENSP00000256442:p.Val210Ile	Somatic	193	1		WXS	Illumina HiSeq	Phase_1	150	19	NM_031966	0	0	45	45	0	A8K066|Q5TZP9	Missense_Mutation	SNP	ENST00000256442.5	37	CCDS3997.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493419	0.44352	.	.	ENSG00000134057	ENST00000256442;ENST00000506572;ENST00000505500;ENST00000507798	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	6.16	3.43	0.39272	Cyclin, N-terminal (2);Cyclin-like (3);	0.063186	0.64402	N	0.000004	T	0.08133	0.0203	N	0.25957	0.775	0.58432	D	0.999993	B;B;B	0.14012	0.006;0.009;0.002	B;B;B	0.27170	0.029;0.077;0.016	T	0.24440	-1.0160	10	0.14656	T	0.56	.	10.5457	0.45058	0.2071:0.0:0.7929:0.0	.	210;210;210	E9PC90;Q5TZP9;P14635	.;.;CCNB1_HUMAN	I	210;210;210;26	ENSP00000256442:V210I;ENSP00000423387:V210I;ENSP00000424588:V210I;ENSP00000426230:V26I	ENSP00000256442:V210I	V	+	1	0	CCNB1	68505915	1.000000	0.71417	0.898000	0.35279	0.993000	0.82548	3.423000	0.52756	0.474000	0.27392	0.650000	0.86243	GTA	.		0.433	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966		A	68470159	G	A	68470159	3	1	77	1	0	0	0	0	1	0	0	0	2917	1029	36	2	646	2	CCNB1	5	68470159	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		68470159	112445101	15	7190											
COL4A3BP	10087	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	74712823	74712828	+	In_Frame_Del	DEL	TACCAT	TACCAT	-																															cgcttcccctttaaagtctaTaccattaattccttttggtg																										TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	TACCAT	TACCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:74712823_74712828delTACCAT	ENST00000405807.4	-	7	1131_1136	c.710_715delATGGTA	c.(709-717)aatggtata>ata	p.NG237del	COL4A3BP_ENST00000261415.7_In_Frame_Del_p.NG237del|COL4A3BP_ENST00000380494.5_In_Frame_Del_p.NG365del	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	237					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TTAAAGTCTATACCATTAATTCCTTT	0.32																																					p.365_367del		.											.	COL4A3BP-226	0			c.1094_1099del						.																																			SO:0001651	inframe_deletion	10087	exon8			.	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.710_715delATGGTA	5.37:g.74712823_74712828delTACCAT	ENSP00000383996:p.Asn237_Gly238del	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	73	26	NM_001130105	0	0	0	0	0	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	In_Frame_Del	DEL	ENST00000405807.4	37	CCDS4028.1																																																																																			.		0.32	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713		-	74712828	TACCAT	-	74712823	7	5	77	1	0	1	0	1	0	0	0	0	3698	1406	49	0	1203	0	COL4A3BP	5	74712823	In_Frame_Del	DEL	TACCAT	TCGA-BQ-5893-01A-11D-1589-08	6242664	74712823	106202437	16	7191											
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140476195	140476195	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgcctggctgtcgtaccaGctgctcaaggccacggagcc	8	6	12	15	3	1	0	1	0	0	0	2	1	1	1	4	3	5	4	4	3	3	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:140476195G>T	ENST00000194155.4	+	1	1969	c.1821G>T	c.(1819-1821)caG>caT	p.Q607H		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	607	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTCGTACCAGCTGCTCAAGG	0.721																																					p.Q607H		.											.	PCDHB2-96	0			c.G1821T						.						15	17	16					5																	140476195		1966	3871	5837	SO:0001583	missense	56133	exon1			GTACCAGCTGCTC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"Cadherins / Protocadherins : Clustered"	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1821G>T	5.37:g.140476195G>T	ENSP00000194155:p.Gln607His	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	181	23	NM_018936	0	0	14	14	0	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.080942	0.36758	.	.	ENSG00000112852	ENST00000194155	T	0.52983	0.64	4.39	3.5	0.40072	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.29524	0.0736	N	0.11201	0.11	0.31320	N	0.686092	P	0.40032	0.699	B	0.43155	0.41	T	0.19224	-1.0312	9	0.48119	T	0.1	.	4.967	0.14096	0.1693:0.0:0.6498:0.1808	.	607	Q9Y5E7	PCDB2_HUMAN	H	607	ENSP00000194155:Q607H	ENSP00000194155:Q607H	Q	+	3	2	PCDHB2	140456379	0.001000	0.12720	1.000000	0.80357	0.997000	0.91878	-0.515000	0.06290	2.151000	0.67156	0.556000	0.70494	CAG	.		0.721	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		T	140476195	G	T	140476195	3	4	77	1	0	0	0	0	1	0	0	0	11568	962	34	4	1823	4	PCDHB2	5	140476195	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	65763372	140476195	40439065	17	7192											
PCDHB3	56132	bcgsc.ca	37	chr5	140481333	140481333	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggagagactgtactggctgTtttcagtgtttctgatctag	7	15	13	6	0	3	2	1	1	2	1	3	4	3	3	0	2	1	4	0	2	2	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:140481333T>G	ENST00000231130.2	+	1	1100	c.1100T>G	c.(1099-1101)gTt>gGt	p.V367G	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	367	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTACTGGCTGTTTTCAGTGTT	0.458																																					p.V367G													.	PCDHB3-92	0			c.T1100G						.						85	81	82					5																	140481333		2203	4300	6503	SO:0001583	missense	56132	exon1			TGGCTGTTTTCAG	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1100T>G	5.37:g.140481333T>G	ENSP00000231130:p.Val367Gly	Somatic	110	0		WXS	Illumina HiSeq	Phase_1	105	23	NM_018937	0	0	1	1	0	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375104	0.61735	.	.	ENSG00000113205	ENST00000231130	T	0.52526	0.66	4.93	4.93	0.64822	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.77260	0.4104	H	0.95328	3.655	0.44123	D	0.996906	D	0.63880	0.993	D	0.72075	0.976	D	0.84871	0.0825	9	0.87932	D	0	.	14.9009	0.70678	0.0:0.0:0.0:1.0	.	367	Q9Y5E6	PCDB3_HUMAN	G	367	ENSP00000231130:V367G	ENSP00000231130:V367G	V	+	2	0	PCDHB3	140461517	0.922000	0.31269	0.997000	0.53966	0.993000	0.82548	6.057000	0.71119	1.975000	0.57531	0.533000	0.62120	GTT	.		0.458	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		G	140481333	T	G	140481333	3	3	77	1	0	0	0	0	1	0	0	0	11569	1725	60	5	1102	5	PCDHB3	5	140481333	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	5138	140481333	40433927	18	7193											
PCDHB5	26167	broad.mit.edu	37	chr5	140517124	140517124	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gtcgtcgctcttcctcttttCggtgctcctgttcgtggcag	1	16	11	13	4	2	0	0	0	2	0	8	0	4	0	2	2	1	4	2	2	0	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:140517124C>G	ENST00000231134.5	+	1	2325	c.2108C>G	c.(2107-2109)tCg>tGg	p.S703W		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	703					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCCTCTTTTCGGTGCTCCTG	0.701																																					p.S703W													.	PCDHB5-95	0			c.C2108G						.						88	93	92					5																	140517124		2201	4296	6497	SO:0001583	missense	26167	exon1			TCTTTTCGGTGCT	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2108C>G	5.37:g.140517124C>G	ENSP00000231134:p.Ser703Trp	Somatic	311	0		WXS	Illumina HiSeq	Phase_I	211	6	NM_015669	0	0	8	8	0	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.790762	0.31685	.	.	ENSG00000113209	ENST00000231134	T	0.20738	2.05	4.56	1.56	0.23342	.	.	.	.	.	T	0.40448	0.1117	H	0.96080	3.765	0.09310	N	0.999999	P	0.36110	0.537	B	0.34722	0.188	T	0.47355	-0.9124	9	0.66056	D	0.02	.	15.094	0.72220	0.0:0.5961:0.4039:0.0	.	703	Q9Y5E4	PCDB5_HUMAN	W	703	ENSP00000231134:S703W	ENSP00000231134:S703W	S	+	2	0	PCDHB5	140497308	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.034000	0.12225	0.075000	0.16796	0.505000	0.49811	TCG	.		0.701	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		G	140517124	C	G	140517124	3	3	77	1	0	0	0	0	1	0	0	0	11571	893	31	4	2110	4	PCDHB5	5	140517124	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	35791	140517124	40398136	19	7194											
LARS	51520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	145533344	145533344	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcaatatcatcaggggagtCggaaggaacacttgtaacca	15	7	11	8	1	2	0	2	0	0	0	3	3	2	3	1	4	3	2	1	4	5	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:145533344C>T	ENST00000394434.2	-	12	1349	c.1183G>A	c.(1183-1185)Gac>Aac	p.D395N	LARS_ENST00000274562.9_Missense_Mutation_p.D368N|LARS_ENST00000545646.1_Missense_Mutation_p.D349N|LARS_ENST00000510191.1_Missense_Mutation_p.D341N	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	395	Editing domain.				gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TCAGGGGAGTCGGAAGGAACA	0.363																																					p.D395N		.											.	LARS-90	0			c.G1183A						.						128	121	123					5																	145533344		2203	4300	6503	SO:0001583	missense	51520	exon12			GGGAGTCGGAAGG	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"Aminoacyl tRNA synthetases / Class I"	6512	protein-coding gene	gene with protein product	"leucine tRNA ligase 1, cytoplasmic"	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.1183G>A	5.37:g.145533344C>T	ENSP00000377954:p.Asp395Asn	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	67	31	NM_020117	0	0	23	49	26	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	37	CCDS34265.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346551	0.95807	.	.	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000510191;ENST00000274562	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.59	5.59	0.84812	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.996;0.948	T	0.70536	-0.4845	10	0.54805	T	0.06	-7.3038	19.956	0.97218	0.0:1.0:0.0:0.0	.	368;349;395	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	N	395;349;341;368	ENSP00000377954:D395N;ENSP00000437791:D349N;ENSP00000426005:D341N;ENSP00000274562:D368N	ENSP00000274562:D368N	D	-	1	0	LARS	145513537	1.000000	0.71417	0.998000	0.56505	0.887000	0.51463	5.851000	0.69481	2.788000	0.95919	0.557000	0.71058	GAC	.		0.363	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		T	145533344	C	T	145533344	3	4	77	1	0	0	0	0	1	0	0	0	8655	884	31	1	2431	1	LARS	5	145533344	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	5016220	145533344	35381916	20	7195											
GRPEL2	134266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	148730749	148730749	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggggtgcagcctggcacCgtggcattagtaagacaaga	10	8	15	8	1	0	2	0	0	0	2	0	2	0	2	2	4	2	5	2	4	3	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:148730749C>T	ENST00000329271.3	+	4	692	c.582C>T	c.(580-582)acC>acT	p.T194T	GRPEL2_ENST00000507562.1_3'UTR|GRPEL2_ENST00000416916.2_3'UTR|GRPEL2-AS1_ENST00000521295.1_RNA	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	194					cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	adenyl-nucleotide exchange factor activity (GO:0000774)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCTGGCACCGTGGCATTAG	0.527																																					p.T194T		.											.	GRPEL2-91	0			c.C582T						.						119	111	114					5																	148730749		2203	4300	6503	SO:0001819	synonymous_variant	134266	exon4			TGGCACCGTGGCA	AL832325	CCDS4295.1	5q33.1	2008-02-05			ENSG00000164284	ENSG00000164284			21060	protein-coding gene	gene with protein product							Standard	NM_152407		Approved	DKFZp451C205, Mt-GrpE#2, FLJ23713	uc003lqj.3	Q8TAA5	OTTHUMG00000130048	ENST00000329271.3:c.582C>T	5.37:g.148730749C>T		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	105	37	NM_152407	0	0	9	11	2	B4DFA6|Q49AJ6	Silent	SNP	ENST00000329271.3	37	CCDS4295.1																																																																																			.		0.527	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		T	148730749	C	T	148730749	2	4	77	1	0	0	0	0	0	0	0	1	6828	639	23	1		1	GRPEL2	5	148730749	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	3197405	148730749	32184511	21	7196											
HLA-G	3135	ucsc.edu	37	chr6	29797247	29797247	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtctttgactatgaggccacCctgaggtgctgggccctggg	5	10	15	11	0	1	3	0	3	1	0	1	3	1	3	3	4	1	1	3	4	1	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr6:29797247C>T	ENST00000360323.6	+	4	696	c.672C>T	c.(670-672)acC>acT	p.T224T	HLA-G_ENST00000376828.2_Silent_p.T229T|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.T224T|HLA-G_ENST00000376818.3_Silent_p.T132T			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	224	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						ATGAGGCCACCCTGAGGTGCT	0.582																																					p.T224T													.	HLA-G-517	0			c.C672T						.						95	99	98					6																	29797247		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			GGCCACCCTGAGG		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.672C>T	6.37:g.29797247C>T		Somatic	158	0		WXS	Illumina HiSeq		288	1	NM_002127	0	0	0	0	0		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			.		0.582	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797247	C	T	29797247	2	4	77	1	0	0	0	0	0	0	0	1	7233	610	22	2		2	HLA-G	6	29797247	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		29797247	141317820	22	7197											
CCDC28A	25901	bcgsc.ca	37	chr6	139106480	139106480	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcctgaggataagagaaaaAcagccagtgactccaatctg	15	8	9	9	0	1	3	0	2	1	1	3	5	3	4	3	1	2	0	3	1	4	2	rs147073588|rs77141562		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr6:139106480A>C	ENST00000332797.6	+	4	864	c.709A>C	c.(709-711)Aca>Cca	p.T237P		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	237										autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		TAAGAGAAAAACAGCCAGTGA	0.383																																					p.T237P													.	CCDC28A-90	0			c.A709C						.						95	103	100					6																	139106480		2203	4300	6503	SO:0001583	missense	25901	exon4			AGAAAAACAGCCA	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"chromosome 6 open reading frame 80"	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.709A>C	6.37:g.139106480A>C	ENSP00000332716:p.Thr237Pro	Somatic	177	0		WXS	Illumina HiSeq	Phase_1	150	31	NM_015439	1	0	94	95	0	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Missense_Mutation	SNP	ENST00000332797.6	37	CCDS5192.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172686	0.38413	.	.	ENSG00000024862	ENST00000332797;ENST00000026464	T	0.25579	1.79	5.43	-1.13	0.09775	.	1.035910	0.07517	N	0.909962	T	0.11836	0.0288	L	0.59436	1.845	0.09310	N	0.999997	P	0.35821	0.523	B	0.39617	0.305	T	0.35325	-0.9793	10	0.40728	T	0.16	-4.0052	8.2322	0.31605	0.4315:0.1281:0.4404:0.0	.	237	Q8IWP9	CC28A_HUMAN	P	237;124	ENSP00000332716:T237P	ENSP00000026464:T124P	T	+	1	0	CCDC28A	139148173	0.133000	0.22466	0.985000	0.45067	0.993000	0.82548	0.068000	0.14531	-0.445000	0.07159	-0.290000	0.09829	ACA	.		0.383	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439		C	139106480	A	C	139106480	3	2	77	1	0	0	0	0	1	0	0	0	2808	43	2	5	723	5	CCDC28A	6	139106480	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	109309233	139106480	32008587	23	7198											
HIVEP2	3097	broad.mit.edu	37	chr6	143090729	143090729	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacttgatgatgtaagcttgCcggttccaggcctatgcata	9	12	10	10	1	0	2	0	2	0	0	1	2	1	2	3	2	3	4	3	2	3	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr6:143090729C>T	ENST00000367604.1	-	4	5786	c.5147G>A	c.(5146-5148)gGc>gAc	p.G1716D	HIVEP2_ENST00000367603.2_Missense_Mutation_p.G1716D|HIVEP2_ENST00000012134.2_Missense_Mutation_p.G1716D			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1716					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TGTAAGCTTGCCGGTTCCAGG	0.433																																					p.G1716D	Esophageal Squamous(107;843 1510 13293 16805 42198)												.	HIVEP2-95	0			c.G5147A						.						113	104	107					6																	143090729		1867	4120	5987	SO:0001583	missense	3097	exon5			AGCTTGCCGGTTC	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5147G>A	6.37:g.143090729C>T	ENSP00000356576:p.Gly1716Asp	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	129	4	NM_006734	0	0	8	8	0	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474421	0.63737	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02737	4.18;4.18;4.18	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.04318	0.0119	L	0.31578	0.945	0.80722	D	1	D	0.62365	0.991	P	0.57101	0.813	T	0.56559	-0.7959	10	0.49607	T	0.09	-20.3273	20.031	0.97536	0.0:1.0:0.0:0.0	.	1716	P31629	ZEP2_HUMAN	D	1716	ENSP00000356576:G1716D;ENSP00000356575:G1716D;ENSP00000012134:G1716D	ENSP00000012134:G1716D	G	-	2	0	HIVEP2	143132422	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	4.903000	0.63272	2.735000	0.93741	0.655000	0.94253	GGC	.		0.433	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			T	143090729	C	T	143090729	3	4	77	1	0	0	0	0	1	0	0	0	7208	739	26	2	2217	2	HIVEP2	6	143090729	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	3984249	143090729	28024338	24	7199											
SAMD5	389432	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	147830100	147830100	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtttacgagtggctcaaagcGctgcagcttccgcagtacgc	8	9	12	12	4	1	0	1	0	0	0	2	1	2	0	1	1	5	7	1	1	3	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr6:147830100G>A	ENST00000367474.1	+	1	38	c.36G>A	c.(34-36)gcG>gcA	p.A12A		NM_001030060.2	NP_001025231.1	Q5TGI4	SAMD5_HUMAN	sterile alpha motif domain containing 5	12	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.												Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)		GGCTCAAAGCGCTGCAGCTTC	0.637																																					p.A12A		.											.	SAMD5-68	0			c.G36A						.						53	49	50					6																	147830100		2203	4300	6503	SO:0001819	synonymous_variant	389432	exon1			CAAAGCGCTGCAG	AL354880	CCDS34548.1	6q24.3	2013-01-10			ENSG00000203727	ENSG00000203727		"Sterile alpha motif (SAM) domain containing"	21180	protein-coding gene	gene with protein product							Standard	NM_001030060		Approved	dJ875H10.1	uc003qmc.2	Q5TGI4	OTTHUMG00000015767	ENST00000367474.1:c.36G>A	6.37:g.147830100G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	55	12	NM_001030060	0	0	1	4	3		Silent	SNP	ENST00000367474.1	37	CCDS34548.1																																																																																			.		0.637	SAMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042610.1	NM_001030060		A	147830100	G	A	147830100	2	1	77	1	0	0	0	0	0	0	0	1	13855	1074	38	1		1	SAMD5	6	147830100	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	4739371	147830100	23284967	25	7200											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4820940	4820940	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcagccacgaagtacagccGgaggtgagtgtggcgacggc	9	5	16	11	4	1	1	1	1	0	0	1	4	1	2	2	4	3	1	2	4	2	1	rs200423282		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:4820940G>A	ENST00000348624.4	+	2	270	c.176G>A	c.(175-177)cGg>cAg	p.R59Q	AP5Z1_ENST00000401897.1_Missense_Mutation_p.R59Q	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	59					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											AAGTACAGCCGGAGGTGAGTG	0.647																																					p.R59Q		.											.	.	0			c.G176A						.	G	GLN/ARG	0,4246		0,0,2123	37	43	41		176	5.6	0.8	7		41	1,8497		0,1,4248	yes	missense	KIAA0415	NM_014855.2	43	0,1,6371	AA,AG,GG		0.0118,0.0,0.0078	probably-damaging	59/808	4820940	1,12743	2123	4249	6372	SO:0001583	missense	9907	exon2			ACAGCCGGAGGTG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"KIAA0415"	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.176G>A	7.37:g.4820940G>A	ENSP00000297562:p.Arg59Gln	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_014855	0	0	0	0	0	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.209170	0.79240	0.0	1.18E-4	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.63744	-0.06;0.52	5.58	5.58	0.84498	.	0.122597	0.47093	D	0.000252	T	0.79981	0.4540	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81881	-0.0729	10	0.72032	D	0.01	.	16.7325	0.85439	0.0:0.0:1.0:0.0	.	59	O43299	K0415_HUMAN	Q	59	ENSP00000297562:R59Q;ENSP00000384980:R59Q	ENSP00000297562:R59Q	R	+	2	0	KIAA0415	4787466	1.000000	0.71417	0.799000	0.32177	0.033000	0.12548	8.511000	0.90535	2.627000	0.88993	0.655000	0.94253	CGG	.		0.647	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			A	4820940	G	A	4820940	3	1	77	1	0	0	0	0	1	0	0	0	8196	1116	39	1	182	1	KIAA0415	7	4820940	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		4820940	154317723	26	7201											
PKD1L1	168507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	47970797	47970797	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttggtgggggtctccatcGtgacagtcccaggaagcagc	7	8	14	12	1	1	1	0	1	1	0	4	2	2	2	3	4	2	1	3	4	1	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:47970797G>A	ENST00000289672.2	-	6	691	c.641C>T	c.(640-642)aCg>aTg	p.T214M		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	214					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGTCTCCATCGTGACAGTCCC	0.617																																					p.T214M		.											.	PKD1L1-145	0			c.C641T						.						67	68	68					7																	47970797		2203	4300	6503	SO:0001583	missense	168507	exon6			TCCATCGTGACAG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.641C>T	7.37:g.47970797G>A	ENSP00000289672:p.Thr214Met	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	85	27	NM_138295	0	0	0	0	0	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.481	0.859718	0.17178	.	.	ENSG00000158683	ENST00000289672	T	0.23147	1.92	3.26	-2.9	0.05648	.	6.156550	0.00725	N	0.000901	T	0.12817	0.0311	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.08055	0.003	T	0.20505	-1.0273	10	0.46703	T	0.11	.	4.4996	0.11858	0.4273:0.1738:0.3989:0.0	.	214	Q8TDX9	PK1L1_HUMAN	M	214	ENSP00000289672:T214M	ENSP00000289672:T214M	T	-	2	0	PKD1L1	47937322	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.622000	0.02042	-0.610000	0.05716	-0.225000	0.12378	ACG	.		0.617	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47970797	G	A	47970797	3	1	77	1	0	0	0	0	1	0	0	0	11990	1145	40	1	8116	1	PKD1L1	7	47970797	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	43149857	47970797	111167866	27	7202											
TPK1	27010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	144245631	144245631	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taacctgcatacaaggctgtCcaacaggaataaggccacac	15	6	8	12	0	0	0	0	0	0	0	1	1	1	1	3	3	4	2	3	3	6	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:144245631C>A	ENST00000360057.3	-	8	668	c.566G>T	c.(565-567)gGa>gTa	p.G189V	TPK1_ENST00000538212.2_Missense_Mutation_p.G135V|TPK1_ENST00000549981.1_Missense_Mutation_p.G72V|TPK1_ENST00000378099.3_Missense_Mutation_p.G140V|TPK1_ENST00000547966.1_5'UTR	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	189					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	ACAAGGCTGTCCAACAGGAAT	0.418																																					p.G189V	Ovarian(45;88 1034 2073 5829 28455)	.											.	TPK1-188	0			c.G566T						.						200	167	178					7																	144245631		2203	4300	6503	SO:0001583	missense	27010	exon8			GGCTGTCCAACAG	AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.566G>T	7.37:g.144245631C>A	ENSP00000353165:p.Gly189Val	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	145	65	NM_022445	0	0	8	11	3	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	37	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524985	0.64747	.	.	ENSG00000196511	ENST00000360057;ENST00000538212;ENST00000378099;ENST00000549981	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.95	5.95	0.96441	Thiamin pyrophosphokinase, vitamin B1-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.91402	0.7287	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.993;1.0;0.999	D	0.92101	0.5688	10	0.59425	D	0.04	-17.4306	15.8749	0.79154	0.0:1.0:0.0:0.0	.	140;189;135	F5GZG6;Q9H3S4;Q6ZQX6	.;TPK1_HUMAN;.	V	189;135;140;72	ENSP00000353165:G189V;ENSP00000438813:G135V;ENSP00000367339:G140V;ENSP00000448698:G72V	ENSP00000353165:G189V	G	-	2	0	TPK1	143876564	1.000000	0.71417	1.000000	0.80357	0.467000	0.32768	5.315000	0.65810	2.817000	0.96982	0.563000	0.77884	GGA	.		0.418	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		A	144245631	C	A	144245631	3	1	77	1	0	0	0	0	1	0	0	0	16437	855	30	4	173	4	TPK1	7	144245631	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	96274834	144245631	14893032	28	7203											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151845739	151845739	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gttcaagtggacccacagatCcaagtcaaggttgagtagcc	12	8	11	10	0	2	2	2	1	0	1	3	3	3	3	3	2	1	3	3	2	4	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:151845739C>A	ENST00000262189.6	-	52	13491	c.13273G>T	c.(13273-13275)Gat>Tat	p.D4425Y	KMT2C_ENST00000355193.2_Missense_Mutation_p.D4482Y	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4425					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										ACCCACAGATCCAAGTCAAGG	0.502																																					p.D4425Y		.											.	MLL3-1398	0			c.G13273T						.						97	89	92					7																	151845739		2203	4300	6503	SO:0001583	missense	58508	exon52			ACAGATCCAAGTC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13273G>T	7.37:g.151845739C>A	ENSP00000262189:p.Asp4425Tyr	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	102	45	NM_170606	0	0	20	27	7	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.05|17.05	3.290706|3.290706	0.59976|0.59976	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.90385|.	-2.0;-1.98;-2.66|.	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	0.000000|.	0.44285|.	U|.	0.000480|.	T|T	0.78123|0.78123	0.4234|0.4234	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.997;0.999;0.999|.	T|T	0.78221|0.78221	-0.2288|-0.2288	10|5	0.49607|.	T|.	0.09|.	.|.	19.1777|19.1777	0.93609|0.93609	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4425;3543;4482|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	Y|V	4425;4482;1042|1985	ENSP00000262189:D4425Y;ENSP00000347325:D4482Y;ENSP00000410411:D1042Y|.	ENSP00000262189:D4425Y|.	D|G	-|-	1|2	0|0	MLL3|MLL3	151476672|151476672	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.957000|0.957000	0.61999|0.61999	7.776000|7.776000	0.85560|0.85560	2.602000|2.602000	0.87976|0.87976	0.557000|0.557000	0.71058|0.71058	GAT|GGA	.		0.502	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151845739	C	A	151845739	3	1	77	1	0	0	0	0	1	0	0	0	9647	855	30	4	1494	4	MLL3	7	151845739	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	7600108	151845739	7292924	29	7204											
MYOM2	9172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	2044224	2044224	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaagcgtgaagttcaccatAaaaactggcacgaggtcaat	16	7	9	9	2	2	1	2	1	0	0	2	2	2	1	1	2	2	2	1	2	6	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:2044224A>G	ENST00000262113.4	+	18	2404	c.2263A>G	c.(2263-2265)Aaa>Gaa	p.K755E	MYOM2_ENST00000523438.1_Missense_Mutation_p.K180E	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	755	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		AGTTCACCATAAAAACTGGCA	0.517																																					p.K755E		.											.	MYOM2-95	0			c.A2263G						.						104	92	96					8																	2044224		2203	4300	6503	SO:0001583	missense	9172	exon18			CACCATAAAAACT		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2263A>G	8.37:g.2044224A>G	ENSP00000262113:p.Lys755Glu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	73	23	NM_003970	0	0	1	1	0	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.135743	0.00335	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.54675	0.56;0.56	5.46	0.23	0.15372	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.912312	0.09530	N	0.789730	T	0.32315	0.0825	N	0.25201	0.72	0.09310	N	1	B	0.23540	0.087	B	0.30943	0.122	T	0.31166	-0.9953	10	0.02654	T	1	.	6.2231	0.20693	0.4732:0.3775:0.0689:0.0804	.	755	P54296	MYOM2_HUMAN	E	755;180	ENSP00000262113:K755E;ENSP00000428396:K180E	ENSP00000262113:K755E	K	+	1	0	MYOM2	2031631	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.150000	0.16263	-0.212000	0.10109	-1.477000	0.00996	AAA	.		0.517	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		G	2044224	A	G	2044224	3	3	77	1	0	0	0	0	1	0	0	0	10117	363	13	3	2329	3	MYOM2	8	2044224	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08		2044224	144319798	30	7205											
EBF2	64641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	25766022	25766022	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgtcccttgggtttcctgCtgttttcaaacaattctgat	7	17	7	10	0	2	1	1	1	1	0	4	1	4	1	2	1	2	3	2	1	2	5	rs200594181		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:25766022C>A	ENST00000520164.1	-	7	1138	c.601G>T	c.(601-603)Gca>Tca	p.A201S	EBF2_ENST00000408929.3_Missense_Mutation_p.A53S	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	201	Interaction with DNA. {ECO:0000250}.				adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GGGTTTCCTGCTGTTTTCAAA	0.378													C|||	1	0.000199681	8e-04	0	5008	,	,		16876	0		0	False		,,,				2504	0				p.A201S	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	.											.	EBF2-26	0			c.G601T						.	C	SER/ALA	1,3657		0,1,1828	83	83	83		601	5.8	1	8		83	0,8198		0,0,4099	no	missense	EBF2	NM_022659.2	99	0,1,5927	AA,AC,CC		0.0,0.0273,0.0084	benign	201/576	25766022	1,11855	1829	4099	5928	SO:0001583	missense	64641	exon7			TTCCTGCTGTTTT	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.601G>T	8.37:g.25766022C>A	ENSP00000430241:p.Ala201Ser	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	53	25	NM_022659	0	0	0	0	0	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	29.7	5.026717	0.93518	2.73E-4	0.0	ENSG00000221818	ENST00000520164;ENST00000408929	T;T	0.62232	0.14;0.04	5.77	5.77	0.91146	.	0.000000	0.85682	U	0.000000	T	0.78483	0.4290	M	0.85373	2.75	0.80722	D	1	P	0.39940	0.696	P	0.50136	0.632	T	0.80061	-0.1540	10	0.87932	D	0	-0.8376	20.3473	0.98799	0.0:1.0:0.0:0.0	.	201	Q9HAK2	COE2_HUMAN	S	201;53	ENSP00000430241:A201S;ENSP00000386178:A53S	ENSP00000386178:A53S	A	-	1	0	EBF2	25821939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.884000	0.98904	0.655000	0.94253	GCA	C|0.999;A|0.000		0.378	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		A	25766022	C	A	25766022	3	1	77	1	0	0	0	0	1	0	0	0	4892	797	28	4	1166	4	EBF2	8	25766022	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	23721798	25766022	120598000	31	7206											
FAM110B	90362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	59059734	59059734	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcagcgcaagcatgatcagCtcagactgtgaacagtctca	12	7	10	12	2	3	3	3	2	1	1	4	3	3	3	0	0	4	4	0	0	2	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:59059734C>T	ENST00000361488.3	+	5	1825	c.945C>T	c.(943-945)agC>agT	p.S315S	FAM110B_ENST00000520369.1_Intron	NM_147189.2	NP_671722.1	Q8TC76	F110B_HUMAN	family with sequence similarity 110, member B	315						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)	26		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				GCATGATCAGCTCAGACTGTG	0.483																																					p.S315S		.											.	FAM110B-153	0			c.C945T						.						79	75	76					8																	59059734		2203	4300	6503	SO:0001819	synonymous_variant	90362	exon5			GATCAGCTCAGAC	U79298	CCDS6170.1	8q12.1	2007-06-21	2007-03-21	2007-03-21		ENSG00000169122			28587	protein-coding gene	gene with protein product		611394	"chromosome 8 open reading frame 72"	C8orf72		8619474, 9110174, 17499476	Standard	XM_005251324		Approved	MGC39325	uc003xtj.1	Q8TC76		ENST00000361488.3:c.945C>T	8.37:g.59059734C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	45	19	NM_147189	0	1	16	48	31	Q5BM08|Q9Y4K2	Silent	SNP	ENST00000361488.3	37	CCDS6170.1																																																																																			.		0.483	FAM110B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378095.2	NM_147189		T	59059734	C	T	59059734	2	4	77	1	0	0	0	0	0	0	0	1	5413	796	28	2		2	FAM110B	8	59059734	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	33293712	59059734	87304288	32	7207											
MYBL1	4603	broad.mit.edu;bcgsc.ca	37	chr8	67477040	67477040	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtcttcccataaaccacTgtttcccattcacaatttga	10	15	3	13	0	3	1	1	1	2	0	5	1	5	1	3	0	1	1	3	0	3	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:67477040T>A	ENST00000522677.3	-	16	2561	c.2151A>T	c.(2149-2151)acA>acT	p.T717T	MYBL1_ENST00000522419.1_5'Flank|MYBL1_ENST00000524176.2_Silent_p.T657T|MYBL1_ENST00000517885.1_Silent_p.T375T	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	717					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			CATAAACCACTGTTTCCCATT	0.328																																					p.T717T													.	MYBL1-395	0			c.A2151T						.						108	100	103					8																	67477040		1855	4083	5938	SO:0001819	synonymous_variant	4603	exon16			AACCACTGTTTCC	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.2151A>T	8.37:g.67477040T>A		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	11	4	NM_001080416	0	0	3	5	2	E7EW29|Q495F9	Silent	SNP	ENST00000522677.3	37	CCDS47867.1																																																																																			.		0.328	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		A	67477040	T	A	67477040	2	1	77	1	0	0	0	0	0	0	0	1	10034	1567	55	5		5	MYBL1	8	67477040	Silent	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	8417306	67477040	78886982	33	7208											
CSMD3	114788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	113249531	113249531	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtttccttcctttgaaattGtaagagcctttccatatata	10	18	5	8	0	0	2	0	1	0	1	3	2	3	2	4	0	1	2	4	0	5	9			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:113249531G>T	ENST00000297405.5	-	67	10759	c.10515C>A	c.(10513-10515)taC>taA	p.Y3505*	CSMD3_ENST00000455883.2_Nonsense_Mutation_p.Y3336*|CSMD3_ENST00000352409.3_Nonsense_Mutation_p.Y3435*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.Y3465*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3505						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTTTGAAATTGTAAGAGCCTT	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.Y3505X		.											.	CSMD3-1132	0			c.C10515A						.						157	144	148					8																	113249531		2203	4300	6503	SO:0001587	stop_gained	114788	exon67			GAAATTGTAAGAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10515C>A	8.37:g.113249531G>T	ENSP00000297405:p.Tyr3505*	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	104	38	NM_198123	0	0	0	0	0	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	51	17.550337	0.99888	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.77	-1.61	0.08399	.	0.090578	0.46442	D	0.000299	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.6815	0.23123	0.3366:0.1118:0.5516:0.0	.	.	.	.	X	3465;3505;2775;3336;3435	.	ENSP00000297405:Y3505X	Y	-	3	2	CSMD3	113318707	0.982000	0.34865	0.993000	0.49108	0.533000	0.34776	0.213000	0.17521	-0.254000	0.09500	-0.499000	0.04595	TAC	.		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113249531	G	T	113249531	4	4	77	1	0	0	0	0	0	1	0	0	3952	1372	48	4	628	4	CSMD3	8	113249531	Nonsense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	45772491	113249531	33114491	34	7209			1	24		2	2	36	N	G_C	9.383625e-05
CSMD3	114788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	113249566	113249566	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatataattttgggcaaataCatcatcaggaactgtgaata	16	13	7	5	0	2	1	2	1	0	0	2	2	2	2	0	2	2	1	0	2	8	7			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:113249566C>A	ENST00000297405.5	-	67	10724	c.10480G>T	c.(10480-10482)Gta>Tta	p.V3494L	CSMD3_ENST00000455883.2_Missense_Mutation_p.V3325L|CSMD3_ENST00000352409.3_Missense_Mutation_p.V3424L|CSMD3_ENST00000343508.3_Missense_Mutation_p.V3454L	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3494						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGGGCAAATACATCATCAGGA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V3494L		.											.	CSMD3-1132	0			c.G10480T						.						110	103	105					8																	113249566		2203	4300	6503	SO:0001583	missense	114788	exon67			CAAATACATCATC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10480G>T	8.37:g.113249566C>A	ENSP00000297405:p.Val3494Leu	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	80	25	NM_198123	0	0	0	0	0	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563747	0.45694	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.33865	1.71;1.7;1.78;1.39;1.76	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000010	T	0.55417	0.1919	M	0.71206	2.165	0.48087	D	0.999581	D;D;B	0.61080	0.989;0.961;0.038	D;P;B	0.63033	0.91;0.741;0.07	T	0.50432	-0.8829	10	0.16896	T	0.51	.	17.9788	0.89134	0.0:1.0:0.0:0.0	.	3325;3494;3454	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	L	3454;3494;2764;3325;3424	ENSP00000345799:V3454L;ENSP00000297405:V3494L;ENSP00000341558:V2764L;ENSP00000412263:V3325L;ENSP00000343124:V3424L	ENSP00000297405:V3494L	V	-	1	0	CSMD3	113318742	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	7.627000	0.83176	2.467000	0.83353	0.467000	0.42956	GTA	.		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113249566	C	A	113249566	3	1	77	1	0	0	0	0	1	0	0	0	3952	478	17	4	663	4	CSMD3	8	113249566	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	35	113249566	33114456	35	7210			1	24		2	2	36	N	G_C	9.383625e-05
DENND3	22898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	142186773	142186773	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgtccaagaaagaagtcttCgaagccaacctgaaaaccga	16	5	9	11	3	1	3	0	1	1	2	3	5	2	3	4	0	3	0	4	0	7	1	rs374490803		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:142186773C>T	ENST00000262585.2	+	15	2657	c.2379C>T	c.(2377-2379)ttC>ttT	p.F793F	DENND3_ENST00000424248.1_Silent_p.F741F|DENND3_ENST00000519811.1_Silent_p.F873F	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	793					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			AAGAAGTCTTCGAAGCCAACC	0.512																																					p.F793F		.											.	DENND3-91	0			c.C2379T						.	C		0,4406		0,0,2203	117	105	109		2379	-8	0.4	8		109	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DENND3	NM_014957.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		793/1199	142186773	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	22898	exon15			AGTCTTCGAAGCC	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"DENN/MADD domain containing", "WD repeat domain containing"	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.2379C>T	8.37:g.142186773C>T		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	91	40	NM_014957	0	0	7	8	1	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	C	9.548	1.115101	0.20795	0.0	2.33E-4	ENSG00000105339	ENST00000518668	.	.	.	5.37	-7.98	0.01135	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.7694	14.5506	0.68065	0.0:0.5424:0.0:0.4576	.	.	.	.	X	798	.	.	R	+	1	2	DENND3	142255955	0.831000	0.29352	0.363000	0.25875	0.894000	0.52154	-0.115000	0.10741	-1.794000	0.01256	-1.124000	0.02001	CGA	.		0.512	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		T	142186773	C	T	142186773	2	4	77	1	0	0	0	0	0	0	0	1	4443	883	31	1		1	DENND3	8	142186773	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	28937207	142186773	4177249	36	7211											
FAM83H	286077	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	144809117	144809117	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggggacgttgagtggctctgGgcagagaggaagcgggaagg	9	5	22	5	2	1	2	0	1	1	1	1	6	1	5	0	7	1	3	0	7	2	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:144809117G>C	ENST00000388913.3	-	5	2639	c.2514C>G	c.(2512-2514)gcC>gcG	p.A838A		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	838					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			AGTGGCTCTGGGCAGAGAGGA	0.701																																					p.A838A		.											.	FAM83H-92	0			c.C2514G						.						10	11	11					8																	144809117		1984	4151	6135	SO:0001819	synonymous_variant	286077	exon5			GCTCTGGGCAGAG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.2514C>G	8.37:g.144809117G>C		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	22	8	NM_198488	0	0	10	17	7	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	37	CCDS6410.2																																																																																			.		0.701	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		C	144809117	G	C	144809117	2	2	77	1	0	0	0	0	0	0	0	1	5659	1219	43	4		4	FAM83H	8	144809117	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	2622344	144809117	1554905	37	7212											
SMARCA2	6595	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	2110312	2110312	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaattcaatgaacctggatcCcagtatttcattttcttgct	11	16	5	9	0	3	1	2	1	1	0	4	2	4	2	2	1	2	2	2	1	4	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:2110312C>T	ENST00000382203.1	+	24	3560	c.3351C>T	c.(3349-3351)tcC>tcT	p.S1117S	SMARCA2_ENST00000357248.2_Silent_p.S1117S|SMARCA2_ENST00000382194.1_Silent_p.S1117S|SMARCA2_ENST00000349721.2_Silent_p.S1117S			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1117	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		AACCTGGATCCCAGTATTTCA	0.453																																					p.S1117S		.											.	SMARCA2-653	0			c.C3351T						.						94	88	90					9																	2110312		2203	4300	6503	SO:0001819	synonymous_variant	6595	exon24			TGGATCCCAGTAT	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.3351C>T	9.37:g.2110312C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	102	32	NM_139045	0	0	16	20	4	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			.		0.453	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		T	2110312	C	T	2110312	2	4	77	1	0	0	0	0	0	0	0	1	14801	610	22	2		2	SMARCA2	9	2110312	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		2110312	139103119	38	7213											
MELK	9833	bcgsc.ca	37	chr9	36651842	36651842	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcttctttctcctgtggaCaagccagtgctaccccattc	6	15	6	14	0	3	0	0	0	3	0	5	1	3	1	4	1	3	1	4	1	2	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:36651842C>A	ENST00000298048.2	+	12	1205	c.1021C>A	c.(1021-1023)Caa>Aaa	p.Q341K	MELK_ENST00000536329.1_Missense_Mutation_p.Q270K|MELK_ENST00000536987.1_Missense_Mutation_p.Q210K|MELK_ENST00000536860.1_Missense_Mutation_p.Q293K|MELK_ENST00000545008.1_Missense_Mutation_p.Q270K|MELK_ENST00000538311.1_Missense_Mutation_p.Q147K|MELK_ENST00000543751.1_Missense_Mutation_p.Q309K|MELK_ENST00000541717.1_Missense_Mutation_p.Q341K	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	341	Autoinhibitory region.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			CTCCTGTGGACAAGCCAGTGC	0.507																																					p.Q341K	Ovarian(82;980 1317 7225 14391 18624)												.	MELK-760	0			c.C1021A						.						216	200	205					9																	36651842		2203	4300	6503	SO:0001583	missense	9833	exon12			TGTGGACAAGCCA	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1021C>A	9.37:g.36651842C>A	ENSP00000298048:p.Gln341Lys	Somatic	293	5		WXS	Illumina HiSeq	Phase_1	312	43	NM_014791	0	0	6	6	0	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Missense_Mutation	SNP	ENST00000298048.2	37	CCDS6606.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.612920	0.28712	.	.	ENSG00000165304	ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751	T;T;T;T;T;T;T;T	0.70164	-0.28;0.72;0.5;1.04;0.41;-0.46;-0.28;-0.28	5.63	2.62	0.31277	.	0.927532	0.09315	N	0.819067	T	0.51907	0.1702	L	0.44542	1.39	0.09310	N	1	B;B;B;B;B;B;B	0.18863	0.031;0.015;0.001;0.0;0.031;0.001;0.001	B;B;B;B;B;B;B	0.21360	0.021;0.02;0.003;0.003;0.034;0.002;0.001	T	0.38478	-0.9659	10	0.09084	T	0.74	2.8432	4.2728	0.10794	0.1851:0.6187:0.0:0.1962	.	261;270;293;341;270;309;341	B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680	.;.;.;.;.;.;MELK_HUMAN	K	341;147;210;270;293;270;341;309	ENSP00000298048:Q341K;ENSP00000438226:Q147K;ENSP00000439184:Q210K;ENSP00000445452:Q270K;ENSP00000439792:Q293K;ENSP00000443550:Q270K;ENSP00000437804:Q341K;ENSP00000441596:Q309K	ENSP00000298048:Q341K	Q	+	1	0	MELK	36641842	0.000000	0.05858	0.005000	0.12908	0.936000	0.57629	-0.116000	0.10724	0.245000	0.21373	0.655000	0.94253	CAA	.		0.507	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		A	36651842	C	A	36651842	3	1	77	1	0	0	0	0	1	0	0	0	9495	479	17	4	1063	4	MELK	9	36651842	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	34541530	36651842	104561589	39	7214											
FLJ46321	389763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	84607771	84607771	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggagacttcttcagacaagGatctgaggtctaactctgag	11	10	11	9	1	5	4	1	2	4	2	5	6	5	5	0	3	1	0	0	3	2	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:84607771G>T	ENST00000344803.2	+	4	2433	c.2386G>T	c.(2386-2388)Gat>Tat	p.D796Y		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	796					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTCAGACAAGGATCTGAGGTC	0.463																																					p.D796Y		.											.	.	0			c.G2386T						.						102	99	100					9																	84607771		1908	4112	6020	SO:0001583	missense	389763	exon4			GACAAGGATCTGA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2386G>T	9.37:g.84607771G>T	ENSP00000341988:p.Asp796Tyr	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	102	37	NM_001001670	0	0	0	0	0		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.664689	0.29604	.	.	ENSG00000214929	ENST00000344803	T	0.07114	3.22	2.85	1.93	0.25924	.	3.256700	0.00687	N	0.000704	T	0.16896	0.0406	L	0.54323	1.7	0.09310	N	1	D	0.57571	0.98	P	0.60012	0.867	T	0.48234	-0.9053	10	0.02654	T	1	1.3602	5.6289	0.17499	0.1558:0.0:0.8442:0.0	.	796	Q6ZQQ2	F75D1_HUMAN	Y	796	ENSP00000341988:D796Y	ENSP00000341988:D796Y	D	+	1	0	FAM75D1	83797591	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.442000	0.21628	0.762000	0.33152	0.462000	0.41574	GAT	.		0.463	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84607771	G	T	84607771	3	4	77	1	0	0	0	0	1	0	0	0	5951	1174	41	4	2400	4	FLJ46321	9	84607771	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	47955929	84607771	56605660	40	7215											
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	113141740	113141740	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatcatgtctccatattgaTaatgtacgcctcgagcaatt	11	14	7	9	2	2	2	1	2	1	0	4	3	2	2	2	0	2	2	2	0	4	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:113141740T>C	ENST00000401783.2	-	44	10631	c.10295A>G	c.(10294-10296)tAt>tGt	p.Y3432C	SVEP1_ENST00000297826.5_Missense_Mutation_p.Y1358C|SVEP1_ENST00000374469.1_Missense_Mutation_p.Y3409C	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3432	Sushi 34. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TCCATATTGATAATGTACGCC	0.403																																					p.Y3432C		.											.	SVEP1-75	0			c.A10295G						.						112	100	104					9																	113141740		1940	4146	6086	SO:0001583	missense	79987	exon44			TATTGATAATGTA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10295A>G	9.37:g.113141740T>C	ENSP00000384917:p.Tyr3432Cys	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	71	33	NM_153366	0	0	6	6	0	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.394554	0.62066	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.69926	-0.44;-0.44;-0.44	5.87	5.87	0.94306	Complement control module (2);Sushi/SCR/CCP (3);	0.240647	0.43416	D	0.000575	D	0.83912	0.5357	M	0.93720	3.45	0.80722	D	1	D	0.69078	0.997	D	0.63113	0.911	D	0.86941	0.2079	10	0.52906	T	0.07	.	11.9508	0.52954	0.1299:0.0:0.0:0.8701	.	3432	Q4LDE5	SVEP1_HUMAN	C	3432;3409;1358	ENSP00000384917:Y3432C;ENSP00000363593:Y3409C;ENSP00000297826:Y1358C	ENSP00000297826:Y1358C	Y	-	2	0	SVEP1	112181561	1.000000	0.71417	0.989000	0.46669	0.666000	0.39218	4.371000	0.59523	2.248000	0.74166	0.533000	0.62120	TAT	.		0.403	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113141740	T	C	113141740	3	2	77	1	0	0	0	0	1	0	0	0	15452	1406	49	3	440	3	SVEP1	9	113141740	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	28533969	113141740	28071691	41	7216											
OR1B1	347169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125391500	125391500	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtaaccccaaatgcatagaaGaaaaagaactgagccaagca	20	4	8	9	0	0	4	0	1	0	3	0	4	0	4	3	0	5	3	3	0	8	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:125391500G>A	ENST00000304833.3	-	1	352	c.315C>T	c.(313-315)ttC>ttT	p.F105F	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						ATGCATAGAAGAAAAAGAACT	0.502																																					p.F105F		.											.	OR1B1-68	0			c.C315T						.						85	77	79					9																	125391500		2203	4300	6503	SO:0001819	synonymous_variant	347169	exon1			ATAGAAGAAAAAG	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"GPCR / Class A : Olfactory receptors"	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.315C>T	9.37:g.125391500G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	55	21	NM_001004450	0	0	0	0	0	Q6IFN3	Silent	SNP	ENST00000304833.3	37	CCDS35126.1																																																																																			.		0.502	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450		A	125391500	G	A	125391500	2	1	77	1	0	0	0	0	0	0	0	1	10977	933	33	2		2	OR1B1	9	125391500	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	12249760	125391500	15821931	42	7217											
PIP4K2A	5305	bcgsc.ca	37	chr10	22856802	22856802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttctttgtcactagcttctCtagccactgtagagccctga	7	15	7	12	0	3	2	1	1	2	1	4	2	3	2	2	0	3	2	2	0	3	6	rs201266267		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr10:22856802C>T	ENST00000376573.4	-	6	884	c.656G>A	c.(655-657)aGa>aAa	p.R219K	PIP4K2A_ENST00000422321.1_5'UTR|PIP4K2A_ENST00000323883.7_Missense_Mutation_p.R79K|PIP4K2A_ENST00000545335.1_Missense_Mutation_p.R160K	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	219	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						ACTAGCTTCTCTAGCCACTGT	0.453																																					p.R219K													.	PIP4K2A-665	0			c.G656A						.						140	123	129					10																	22856802		2203	4300	6503	SO:0001583	missense	5305	exon6			GCTTCTCTAGCCA	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.656G>A	10.37:g.22856802C>T	ENSP00000365757:p.Arg219Lys	Somatic	177	1		WXS	Illumina HiSeq	Phase_1	115	20	NM_005028	0	0	36	36	0	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	37	CCDS7141.1	.	.	.	.	.	.	.	.	.	.	C	35	5.513277	0.96402	.	.	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335;ENST00000422321;ENST00000376565	T;T;T	0.69306	-0.39;-0.39;-0.39	5.36	5.36	0.76844	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.88130	0.6354	H	0.96301	3.8	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.80764	0.994;0.971	D	0.91774	0.5430	10	0.87932	D	0	-22.5481	19.0839	0.93194	0.0:1.0:0.0:0.0	.	79;219	B4DH09;P48426	.;PI42A_HUMAN	K	219;79;160;171;178	ENSP00000365757:R219K;ENSP00000326294:R79K;ENSP00000442098:R160K	ENSP00000326294:R79K	R	-	2	0	PIP4K2A	22896808	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.252000	0.78309	2.530000	0.85305	0.650000	0.86243	AGA	.		0.453	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		T	22856802	C	T	22856802	3	4	77	1	0	0	0	0	1	0	0	0	11962	913	32	2	584	2	PIP4K2A	10	22856802	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		22856802	112677945	43	7218											
SVIL	6840	bcgsc.ca	37	chr10	29813511	29813511	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttttgagactggctgggAcaatttgttaaacaaggcca	11	11	11	8	1	0	1	0	1	0	1	0	3	0	2	1	3	1	3	1	3	4	4	rs201719880		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr10:29813511A>G	ENST00000355867.4	-	14	3228	c.2476T>C	c.(2476-2478)Tcc>Ccc	p.S826P	SVIL_ENST00000375398.2_Missense_Mutation_p.S826P|SVIL_ENST00000375400.3_Missense_Mutation_p.S400P|SVIL_ENST00000535393.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	826					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACTGGCTGGGACAATTTGTTA	0.488																																					p.S826P													.	SVIL-96	0			c.T2476C						.						157	146	149					10																	29813511		2203	4300	6503	SO:0001583	missense	6840	exon14			GCTGGGACAATTT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2476T>C	10.37:g.29813511A>G	ENSP00000348128:p.Ser826Pro	Somatic	157	8		WXS	Illumina HiSeq	Phase_1	138	32	NM_021738	0	0	30	30	0	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.266428	0.80358	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.48522	0.81;0.81;0.81	5.82	1.87	0.25490	.	0.199679	0.53938	D	0.000048	T	0.59555	0.2202	M	0.71581	2.175	0.80722	D	1	D;D	0.67145	0.996;0.987	D;P	0.63703	0.917;0.719	T	0.57046	-0.7878	9	.	.	.	-16.6333	8.422	0.32707	0.6211:0.2563:0.0:0.1226	.	400;826	O95425-2;O95425	.;SVIL_HUMAN	P	400;826;826	ENSP00000364549:S400P;ENSP00000364547:S826P;ENSP00000348128:S826P	.	S	-	1	0	SVIL	29853517	0.999000	0.42202	0.982000	0.44146	0.936000	0.57629	1.744000	0.38268	0.418000	0.25898	0.459000	0.35465	TCC	.		0.488	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29813511	A	G	29813511	3	3	77	1	0	0	0	0	1	0	0	0	15453	275	10	3	4268	3	SVIL	10	29813511	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	6956709	29813511	105721236	44	7219											
OR13A1	79290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	45799786	45799786	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaagccctgcaggatgaactCggttaccaacgtctggttac	11	9	10	11	2	1	1	0	1	1	0	2	2	1	2	2	3	6	3	2	3	5	2	rs200530280		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr10:45799786C>T	ENST00000553795.1	-	4	393	c.85G>A	c.(85-87)Gag>Aag	p.E29K	OR13A1_ENST00000536058.1_Missense_Mutation_p.E29K|OR13A1_ENST00000374401.2_Missense_Mutation_p.E29K	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E29K(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						AGGATGAACTCGGTTACCAAC	0.517																																					p.E29K		.											.	OR13A1-68	1	Substitution - Missense(1)	skin(1)	c.G85A						.						70	81	77					10																	45799786		2203	4300	6503	SO:0001583	missense	79290	exon4			TGAACTCGGTTAC	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"GPCR / Class A : Olfactory receptors"	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.85G>A	10.37:g.45799786C>T	ENSP00000451950:p.Glu29Lys	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	84	38	NM_001004297	0	0	0	0	0	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Missense_Mutation	SNP	ENST00000553795.1	37	CCDS31188.1	.	.	.	.	.	.	.	.	.	.	c	10.75	1.438543	0.25900	.	.	ENSG00000256574	ENST00000553795;ENST00000536058;ENST00000374401	T;T;T	0.01119	5.31;5.31;5.31	5.09	3.18	0.36537	.	0.350510	0.20650	N	0.088225	T	0.02380	0.0073	M	0.80028	2.48	0.29732	N	0.837839	B	0.25743	0.133	B	0.27715	0.082	T	0.04678	-1.0934	10	0.72032	D	0.01	-21.4609	8.6395	0.33968	0.0:0.7602:0.1539:0.0858	.	29	Q8NGR1	O13A1_HUMAN	K	29	ENSP00000451950:E29K;ENSP00000438657:E29K;ENSP00000363522:E29K	ENSP00000311379:E29K	E	-	1	0	OR13A1	45119792	0.008000	0.16893	0.368000	0.25939	0.065000	0.16274	0.141000	0.16076	0.625000	0.30304	0.603000	0.83216	GAG	C|0.999;A|0.001		0.517	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297		T	45799786	C	T	45799786	3	4	77	1	0	0	0	0	1	0	0	0	10959	893	31	1	905	1	OR13A1	10	45799786	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	15986275	45799786	89734961	45	7220											
ADAMTS14	140766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	72517740	72517740	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctgccacctgtggagaggGcatccagcagcggcaggtgg	7	6	16	12	1	1	1	0	0	1	1	2	2	2	1	3	5	3	3	3	5	0	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr10:72517740G>T	ENST00000373207.1	+	20	2960	c.2960G>T	c.(2959-2961)gGc>gTc	p.G987V	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.G990V	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	987	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						TGTGGAGAGGGCATCCAGCAG	0.652																																					p.G990V		.											.	ADAMTS14-232	0			c.G2969T						.						55	56	56					10																	72517740		2201	4298	6499	SO:0001583	missense	140766	exon20			GAGAGGGCATCCA	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2960G>T	10.37:g.72517740G>T	ENSP00000362303:p.Gly987Val	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	138	46	NM_139155	0	0	0	0	0	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964690	0.74131	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	D;D	0.83755	-1.76;-1.76	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	D	0.95623	0.8577	H	0.99842	4.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98126	1.0428	10	0.87932	D	0	.	16.6601	0.85238	0.0:0.0:1.0:0.0	.	987;990	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	V	990;987	ENSP00000362304:G990V;ENSP00000362303:G987V	ENSP00000362303:G987V	G	+	2	0	ADAMTS14	72187746	1.000000	0.71417	0.979000	0.43373	0.585000	0.36419	7.829000	0.86735	2.250000	0.74265	0.561000	0.74099	GGC	.		0.652	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72517740	G	T	72517740	3	4	77	1	0	0	0	0	1	0	0	0	259	1203	42	4	3047	4	ADAMTS14	10	72517740	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	26717954	72517740	63017007	46	7221											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092966	1092966	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	accactacggtgaccccaacCccaacacccaccggcacaca	13	2	5	21	2	0	1	0	1	0	0	0	1	0	1	7	2	3	1	7	2	3	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:1092966C>A	ENST00000441003.2	+	30	4812	c.4785C>A	c.(4783-4785)acC>acA	p.T1595T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tgaccccaaccccaacaccca	0.637																																					p.T1595T		.											.	MUC2-90	0			c.C4785A						.						48	83	71					11																	1092966		1785	3239	5024	SO:0001819	synonymous_variant	4583	exon30			CCCAACCCCAACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4785C>A	11.37:g.1092966C>A		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	30	5	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1092966	C	A	1092966	2	1	77	1	0	0	0	0	0	0	0	1	10000	610	22	4		4	MUC2	11	1092966	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		1092966	133913550	47	7222											
PPFIBP2	8495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	7618800	7618800	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggaacaggtgagtgtcCtcacagaccaagtagaagcc	12	7	11	11	0	1	3	1	1	0	2	3	4	3	4	4	2	2	1	4	2	4	1	rs17851928		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:7618800C>G	ENST00000299492.4	+	5	770	c.382C>G	c.(382-384)Ctc>Gtc	p.L128V	PPFIBP2_ENST00000533792.1_5'UTR|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.L16V	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	128				L -> I (in Ref. 2; AAH21714). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GGTGAGTGTCCTCACAGACCA	0.512																																					p.L128V		.											.	PPFIBP2-273	0			c.C382G						.						63	58	60					11																	7618800		2201	4296	6497	SO:0001583	missense	8495	exon5			AGTGTCCTCACAG	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.382C>G	11.37:g.7618800C>G	ENSP00000299492:p.Leu128Val	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_003621	0	0	0	0	0	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.718828	0.89205	.	.	ENSG00000166387	ENST00000299492;ENST00000527790;ENST00000541115;ENST00000528883	T;T;T	0.49720	2.55;2.55;0.77	5.5	5.5	0.81552	.	0.000000	0.53938	D	0.000044	T	0.70202	0.3197	M	0.78344	2.41	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;1.0;1.0	D;D;D;D	0.91635	0.999;0.929;0.999;0.997	T	0.72626	-0.4236	10	0.59425	D	0.04	-6.6607	16.8778	0.86056	0.0:1.0:0.0:0.0	.	16;16;51;128	E9PK77;B7Z433;F5GWB0;Q8ND30	.;.;.;LIPB2_HUMAN	V	128;128;51;16	ENSP00000299492:L128V;ENSP00000434981:L128V;ENSP00000435469:L16V	ENSP00000299492:L128V	L	+	1	0	PPFIBP2	7575376	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.639000	0.61361	2.600000	0.87896	0.655000	0.94253	CTC	.		0.512	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		G	7618800	C	G	7618800	3	3	77	1	0	0	0	0	1	0	0	0	12340	681	24	4	396	4	PPFIBP2	11	7618800	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	6525834	7618800	127387716	48	7223											
TTC17	55761	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	43380551	43380551	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccggtacgagctgccgccttGctccggcccaggctggctcc	3	7	13	18	4	0	0	0	0	0	0	2	1	2	0	6	4	4	5	6	4	1	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:43380551G>A	ENST00000039989.4	+	1	61	c.47G>A	c.(46-48)tGc>tAc	p.C16Y	RP11-484D2.2_ENST00000526220.1_RNA|TTC17_ENST00000299240.6_Missense_Mutation_p.C16Y	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	16					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						CTGCCGCCTTGCTCCGGCCCA	0.711																																					p.C16Y		.											.	TTC17-95	0			c.G47A						.						10	13	12					11																	43380551		2188	4280	6468	SO:0001583	missense	55761	exon1			CGCCTTGCTCCGG	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"Tetratricopeptide (TTC) repeat domain containing"	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.47G>A	11.37:g.43380551G>A	ENSP00000039989:p.Cys16Tyr	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	20	10	NM_018259	0	0	1	2	1	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759055	0.49468	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.30981	1.51;1.52	5.5	5.5	0.81552	.	0.471757	0.22070	N	0.065056	T	0.13114	0.0318	N	0.08118	0	0.23611	N	0.99729	B;B	0.33379	0.41;0.021	B;B	0.26094	0.066;0.037	T	0.17623	-1.0363	10	0.17832	T	0.49	-0.8355	9.4046	0.38453	0.0:0.1538:0.6866:0.1596	.	16;16	Q96AE7;G3XAB3	TTC17_HUMAN;.	Y	16	ENSP00000299240:C16Y;ENSP00000039989:C16Y	ENSP00000039989:C16Y	C	+	2	0	TTC17	43337127	0.979000	0.34478	0.972000	0.41901	0.951000	0.60555	3.441000	0.52893	2.868000	0.98415	0.555000	0.69702	TGC	.		0.711	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		A	43380551	G	A	43380551	3	1	77	1	0	0	0	0	1	0	0	0	16717	1319	46	2	49	2	TTC17	11	43380551	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	35761751	43380551	91625965	49	7224											
PICALM	8301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	85714416	85714416	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaatgatatacctgcttgCagctgtagaatctttgattt	12	15	8	6	0	1	4	0	2	1	2	1	4	1	4	1	0	4	4	1	0	6	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:85714416C>A	ENST00000393346.3	-	9	1034	c.886G>T	c.(886-888)Gca>Tca	p.A296S	PICALM_ENST00000356360.5_Missense_Mutation_p.A296S|PICALM_ENST00000526033.1_Missense_Mutation_p.A296S|PICALM_ENST00000532317.1_Missense_Mutation_p.A296S|PICALM_ENST00000528398.1_Missense_Mutation_p.A245S			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	296					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				TACCTGCTTGCAGCTGTAGAA	0.388			T	"MLLT10, MLL"	"TALL, AML, "																																p.A296S		.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM-659	0			c.G886T						.						97	93	94					11																	85714416		2203	4299	6502	SO:0001583	missense	8301	exon9			TGCTTGCAGCTGT	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.886G>T	11.37:g.85714416C>A	ENSP00000377015:p.Ala296Ser	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	99	27	NM_007166	0	0	0	0	0	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Missense_Mutation	SNP	ENST00000393346.3	37	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559328	0.86335	.	.	ENSG00000073921	ENST00000532317;ENST00000526033;ENST00000447890;ENST00000393346;ENST00000528398;ENST00000356360	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.72574	0.3477	M	0.71036	2.16	0.80722	D	1	D;D;B;P	0.69078	0.997;0.968;0.356;0.95	D;P;B;P	0.75020	0.985;0.854;0.178;0.716	T	0.71533	-0.4564	9	.	.	.	-9.5668	19.5037	0.95106	0.0:1.0:0.0:0.0	.	245;296;296;296	E9PN05;F8VPG7;Q13492;Q13492-3	.;.;PICAL_HUMAN;.	S	296;296;296;296;245;296	ENSP00000436958:A296S;ENSP00000433846:A296S;ENSP00000377015:A296S;ENSP00000434884:A245S;ENSP00000348718:A296S	.	A	-	1	0	PICALM	85392064	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.596000	0.87737	0.655000	0.94253	GCA	.		0.388	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		A	85714416	C	A	85714416	3	1	77	1	0	0	0	0	1	0	0	0	11906	710	25	4	1148	4	PICALM	11	85714416	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	42333865	85714416	49292100	50	7225											
USP28	57646	broad.mit.edu	37	chr11	113679909	113679909	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccagttatcctcctgaatGtaatgcttgagttccacaga	10	12	8	11	1	0	3	0	2	0	1	3	3	3	3	4	0	1	4	4	0	3	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:113679909G>T	ENST00000003302.4	-	17	2108	c.2040C>A	c.(2038-2040)taC>taA	p.Y680*	USP28_ENST00000260188.5_Nonsense_Mutation_p.Y680*|USP28_ENST00000545540.1_Nonsense_Mutation_p.Y555*|USP28_ENST00000544967.1_Nonsense_Mutation_p.Y388*	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	680					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		CCTCCTGAATGTAATGCTTGA	0.463																																					p.Y680X	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)												.	USP28-706	0			c.C2040A						.						363	369	367					11																	113679909		2201	4296	6497	SO:0001587	stop_gained	57646	exon17			CTGAATGTAATGC	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2040C>A	11.37:g.113679909G>T	ENSP00000003302:p.Tyr680*	Somatic	591	0		WXS	Illumina HiSeq	Phase_I	568	7	NM_020886	0	0	12	12	0	B0YJC0|B0YJC1|Q9P213	Nonsense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	41	9.146417	0.99080	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540	.	.	.	5.56	1.87	0.25490	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.1715	10.5421	0.45039	0.3142:0.0:0.6858:0.0	.	.	.	.	X	680;680;388;555	.	ENSP00000003302:Y680X	Y	-	3	2	USP28	113185119	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.477000	0.35431	0.584000	0.29591	0.563000	0.77884	TAC	.		0.463	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			T	113679909	G	T	113679909	4	4	77	1	0	0	0	0	0	1	0	0	17091	1372	48	4	1229	4	USP28	11	113679909	Nonsense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	27965493	113679909	21326607	51	7226											
OR8G2	0	broad.mit.edu	37	chr11	124095997	124095997	+	IGR	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttccctctcttggggctCtcctgctccagcacctacat	4	13	6	18	0	3	0	0	0	3	0	7	0	5	0	4	2	3	3	4	2	1	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:124095997C>A								OR10D3 (39045 upstream) : OR8G1 (24425 downstream)																							TCTTGGGGCTCTCCTGCTCCA	0.418																																					p.L200L													.	.	0			c.C600A						.						153	158	157					11																	124095997		1963	4182	6145	SO:0001628	intergenic_variant	26492	exon1			GGGGCTCTCCTGC																													11.37:g.124095997C>A		Somatic	268	0		WXS	Illumina HiSeq	Phase_I	249	5	NM_001007249	0	0	0	0	0		Silent	SNP		37																																																																																				.	0	0.418									A	124095997	C	A	124095997	1	1	77	0	1	0	0	0	0	0	0	0	11261	900	32	4		4	OR8G2	11	124095997	IGR	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	10416088	124095997	10910519	52	7227											
TXNRD1	7296	broad.mit.edu;bcgsc.ca	37	chr12	104721450	104721453	+	Splice_Site	DEL	GTGA	GTGA	-																															atgcaggttccactgtcaagGtgagtgttgtgcttgttgcc																										TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	GTGA	GTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr12:104721450_104721453delGTGA	ENST00000529546.1	+	10	1203		c.e10+1		TXNRD1_ENST00000526691.1_Splice_Site|TXNRD1_ENST00000542918.1_Splice_Site|TXNRD1_ENST00000503506.2_Splice_Site|TXNRD1_ENST00000525566.1_Splice_Site|TXNRD1_ENST00000524698.1_Splice_Site|TXNRD1_ENST00000354940.6_Splice_Site|TXNRD1_ENST00000427956.1_Splice_Site|TXNRD1_ENST00000526950.1_Splice_Site|TXNRD1_ENST00000397736.2_Splice_Site|TXNRD1_ENST00000540716.1_Splice_Site|TXNRD1_ENST00000378070.4_Splice_Site|TXNRD1_ENST00000388854.3_Splice_Site|TXNRD1_ENST00000429002.2_Splice_Site|TXNRD1_ENST00000526390.1_Splice_Site			Q16881	TRXR1_HUMAN	thioredoxin reductase 1						cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cellular lipid metabolic process (GO:0044255)|mesoderm formation (GO:0001707)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	16					Arsenic trioxide(DB01169)|Flavin adenine dinucleotide(DB03147)	CACTGTCAAGGTGAGTGTTGTGCT	0.466																																					.	Ovarian(139;555 1836 9186 9946 10884)												.	TXNRD1-90	0			.						.																																			SO:0001630	splice_region_variant	7296	.			GTCAAGGTGAGTG		CCDS53820.1, CCDS53821.1, CCDS53823.1, CCDS58274.1	12q23-q24.1	2012-03-01							12437	protein-coding gene	gene with protein product		601112				7589432	Standard	NM_001093771		Approved	TXNR, GRIM-12, Trxr1	uc021rcx.2	Q16881		ENST00000529546.1:c.978+1GTGA>-	12.37:g.104721450_104721453delGTGA		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	21	9	.	0	0	0	0	0	B7Z1F4|B7Z3Y8|B7Z904|E9PMY9|F5H780|Q6FI31|Q6VB40|Q6VB41|Q6VB42|Q6VBP2|Q6VBP3|Q6VBP4|Q6VBP5|Q6VBP9|Q6VBQ0|Q6YNQ1|Q76P53|Q7LA96|Q8WVC8|Q99475|Q9UES8|Q9UH79	Splice_Site	DEL	ENST00000529546.1	37	CCDS58274.1																																																																																			.		0.466	TXNRD1-004	PUTATIVE	basic|exp_conf|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000389969.1	NM_003330	Intron	-	104721453	GTGA	-	104721450	8	5	77	1	0	1	0	1	0	0	1	0	16840	1275	44	0	1607	0	TXNRD1	12	104721450	Splice_Site	DEL	GTGA	TCGA-BQ-5893-01A-11D-1589-08		104721450	29130445	53	7228											
ZCCHC8	55596	bcgsc.ca	37	chr12	122958214	122958214	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctatgaattttagtggccgTtgaaggactggtgtctgcag	8	13	14	6	1	1	2	0	2	1	0	1	3	1	3	1	3	1	3	1	3	4	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr12:122958214T>G	ENST00000336229.4	-	14	2084	c.1954A>C	c.(1954-1956)Acg>Ccg	p.T652P	ZCCHC8_ENST00000543897.1_Missense_Mutation_p.T414P|ZCCHC8_ENST00000536306.1_Missense_Mutation_p.T414P|ZCCHC8_ENST00000538116.1_Missense_Mutation_p.T263P	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	652					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		TTAGTGGCCGTTGAAGGACTG	0.458																																					p.T652P													.	ZCCHC8-90	0			c.A1954C						.						161	162	161					12																	122958214		1914	4125	6039	SO:0001583	missense	55596	exon14			TGGCCGTTGAAGG	BC017704		12q24.31	2014-04-14				ENSG00000033030		"Zinc fingers, CCHC domain containing"	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.1954A>C	12.37:g.122958214T>G	ENSP00000337313:p.Thr652Pro	Somatic	313	2		WXS	Illumina HiSeq	Phase_1	208	29	NM_017612	0	0	36	36	0	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	T	12.63	1.996555	0.35226	.	.	ENSG00000033030	ENST00000536306;ENST00000543897;ENST00000336229;ENST00000538116	T;T;T;T	0.45276	0.93;0.93;0.92;0.9	5.88	-11.8	0.00035	.	1.320320	0.04424	N	0.368136	T	0.23806	0.0576	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09796	-1.0658	10	0.30078	T	0.28	1.7467	2.1097	0.03700	0.2227:0.3696:0.1514:0.2563	.	652	Q6NZY4	ZCHC8_HUMAN	P	414;414;652;263	ENSP00000441423:T414P;ENSP00000438993:T414P;ENSP00000337313:T652P;ENSP00000440028:T263P	ENSP00000337313:T652P	T	-	1	0	ZCCHC8	121524167	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.508000	0.00960	-1.689000	0.01434	-2.007000	0.00441	ACG	.		0.458	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		G	122958214	T	G	122958214	3	3	77	1	0	0	0	0	1	0	0	0	17626	1725	60	5	173	5	ZCCHC8	12	122958214	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	18236764	122958214	10893681	54	7229											
SPATA13	221178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	24825881	24825881	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccaggccgcccatgcctgCtcaccaggtgccaccctaca	7	7	8	19	1	1	0	1	0	0	0	2	0	2	0	7	2	4	1	7	2	1	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr13:24825881C>A	ENST00000382095.4	+	3	577	c.170C>A	c.(169-171)gCt>gAt	p.A57D	SPATA13-AS1_ENST00000430733.1_RNA|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.A560D|SPATA13_ENST00000382108.3_Missense_Mutation_p.A682D|SPATA13_ENST00000424834.2_Missense_Mutation_p.A682D	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	57					cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CCCATGCCTGCTCACCAGGTG	0.622																																					p.A682D		.											.	SPATA13-229	0			c.C2045A						.						60	65	63					13																	24825881		2203	4300	6503	SO:0001583	missense	221178	exon4			TGCCTGCTCACCA	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.170C>A	13.37:g.24825881C>A	ENSP00000371527:p.Ala57Asp	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	118	49	NM_001166271	0	0	3	4	1	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.7|25.7	4.662502|4.662502	0.88251|0.88251	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000382108;ENST00000382095;ENST00000434675;ENST00000438694|ENST00000424834	T;T;T|.	0.35789|.	1.29;1.29;1.29|.	5.97|5.97	5.13|5.13	0.70059|0.70059	.|.	0.125113|.	0.56097|.	D|.	0.000034|.	T|.	0.61173|.	0.2326|.	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	P;D;B|.	0.53462|.	0.634;0.96;0.361|.	B;P;B|.	0.48795|.	0.3;0.59;0.074|.	T|.	0.55866|.	-0.8073|.	10|.	0.46703|.	T|.	0.11|.	.|.	13.7166|13.7166	0.62700|0.62700	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	3;3;57|.	Q96N96-5;Q96N96-4;Q96N96|.	.;.;SPT13_HUMAN|.	D|X	682;57;17;3|719	ENSP00000371542:A682D;ENSP00000371527:A57D;ENSP00000401605:A17D|.	ENSP00000371527:A57D|.	A|C	+|+	2|3	0|2	SPATA13|SPATA13	23723881|23723881	1.000000|1.000000	0.71417|0.71417	0.636000|0.636000	0.29352|0.29352	0.775000|0.775000	0.43874|0.43874	5.552000|5.552000	0.67281|0.67281	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	GCT|TGC	.		0.622	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		A	24825881	C	A	24825881	3	1	77	1	0	0	0	0	1	0	0	0	15032	797	28	4	2055	4	SPATA13	13	24825881	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		24825881	90343997	55	7230											
SHISA2	387914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	26620708	26620708	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtgtgagggaagggggaCtgaatctgcctgtagccagg	8	9	18	6	0	1	2	0	2	1	0	1	4	1	4	2	5	2	1	2	5	3	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr13:26620708C>G	ENST00000319420.3	-	2	886	c.831G>C	c.(829-831)caG>caC	p.Q277H		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	277					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						GGAAGGGGGACTGAATCTGCC	0.567																																					p.Q277H		.											.	SHISA2-69	0			c.G831C						.						104	91	96					13																	26620708		2203	4300	6503	SO:0001583	missense	387914	exon2			GGGGGACTGAATC		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.831G>C	13.37:g.26620708C>G	ENSP00000313079:p.Gln277His	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	85	30	NM_001007538	0	0	1	1	0	B9EH70|Q5W0G8	Missense_Mutation	SNP	ENST00000319420.3	37	CCDS31951.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.599692	0.66332	.	.	ENSG00000180730	ENST00000319420	T	0.52057	0.68	5.58	4.74	0.60224	.	0.149265	0.46758	D	0.000272	T	0.55924	0.1951	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	T	0.60530	-0.7245	10	0.66056	D	0.02	-21.8958	14.6091	0.68504	0.0:0.9296:0.0:0.0704	.	277	Q6UWI4	SHSA2_HUMAN	H	277	ENSP00000313079:Q277H	ENSP00000313079:Q277H	Q	-	3	2	SHISA2	25518708	1.000000	0.71417	0.996000	0.52242	0.854000	0.48673	2.473000	0.45145	1.364000	0.46038	0.650000	0.86243	CAG	.		0.567	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		G	26620708	C	G	26620708	3	3	77	1	0	0	0	0	1	0	0	0	14312	564	20	4	60	4	SHISA2	13	26620708	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	1794827	26620708	88549170	56	7231											
TTBK2	146057	bcgsc.ca	37	chr15	43132600	43132600	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaatcgatcattcctcccAcagccaataaatctacaaac	15	10	3	13	1	2	1	1	1	1	0	5	2	4	1	3	0	3	0	3	0	6	4	rs141523080		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr15:43132600A>C	ENST00000267890.6	-	4	357	c.249T>G	c.(247-249)tgT>tgG	p.C83W	TTBK2_ENST00000567274.1_Missense_Mutation_p.C83W|TTBK2_ENST00000567840.1_Missense_Mutation_p.C83W	NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	83	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CATTCCTCCCACAGCCAATAA	0.318																																					p.C83W													.	TTBK2-338	0			c.T249G						.						133	126	128					15																	43132600		1820	4084	5904	SO:0001583	missense	146057	exon4			CCTCCCACAGCCA	AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"spinocerebellar ataxia 11"	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.249T>G	15.37:g.43132600A>C	ENSP00000267890:p.Cys83Trp	Somatic	187	0		WXS	Illumina HiSeq	Phase_1	132	26	NM_173500	0	0	1	1	0	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	.	.	.	.	.	.	.	.	.	.	A	11.81	1.750201	0.30955	.	.	ENSG00000128881	ENST00000267890;ENST00000399479;ENST00000263802	T	0.64438	-0.1	5.31	4.18	0.49190	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.082061	0.85682	D	0.000000	T	0.73892	0.3645	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.999	T	0.75193	-0.3404	10	0.87932	D	0	.	11.2089	0.48786	0.9264:0.0:0.0736:0.0	.	63;14;83;83	Q8IWY7;Q6IQ55-2;Q6IQ55-3;Q6IQ55	.;.;.;TTBK2_HUMAN	W	83;13;63	ENSP00000267890:C83W	ENSP00000263802:C63W	C	-	3	2	TTBK2	40919892	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.929000	0.48916	0.955000	0.37878	0.477000	0.44152	TGT	.		0.318	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		C	43132600	A	C	43132600	3	2	77	1	0	0	0	0	1	0	0	0	16710	157	6	5	3533	5	TTBK2	15	43132600	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08		43132600	59398792	57	7232											
DENND4A	10260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65983020	65983020	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttttagatttggtaagtctCactggcttaggagaattagg	10	15	11	5	0	1	2	1	0	1	2	2	3	1	2	0	4	0	2	0	4	5	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr15:65983020C>T	ENST00000431932.2	-	22	3988	c.3780G>A	c.(3778-3780)gtG>gtA	p.V1260V	DENND4A_ENST00000567323.1_5'Flank|DENND4A_ENST00000443035.3_Silent_p.V1303V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1260					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TGGTAAGTCTCACTGGCTTAG	0.413																																					p.V1303V		.											.	DENND4A-229	0			c.G3909A						.						101	104	103					15																	65983020		1893	4107	6000	SO:0001819	synonymous_variant	10260	exon23			AAGTCTCACTGGC	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3780G>A	15.37:g.65983020C>T		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	100	29	NM_001144823	0	0	4	8	4	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			.		0.413	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	65983020	C	T	65983020	2	4	77	1	0	0	0	0	0	0	0	1	4444	813	29	2		2	DENND4A	15	65983020	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	22850420	65983020	36548372	58	7233											
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75692465	75692465	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtagagtcctcagaccaCgaagggaaggaaacccaggt	15	4	13	9	1	1	2	1	0	0	2	2	5	2	4	3	4	1	1	3	4	5	1	rs373830836		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr15:75692465C>T	ENST00000394947.3	-	12	2084	c.1770G>A	c.(1768-1770)tcG>tcA	p.S590S	SIN3A_ENST00000360439.4_Silent_p.S590S|SIN3A_ENST00000394949.4_Silent_p.S590S	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						CCTCAGACCACGAAGGGAAGG	0.393																																					p.S590S		.											.	SIN3A-230	0			c.G1770A						.	C	,,	0,4394		0,0,2197	96	91	93		1770,1770,1770	-12.2	0.2	15		93	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	SIN3A	NM_001145357.1,NM_001145358.1,NM_015477.2	,,	0,1,6490	TT,TC,CC		0.0116,0.0,0.0077	,,	590/1274,590/1274,590/1274	75692465	1,12981	2197	4294	6491	SO:0001819	synonymous_variant	25942	exon12			AGACCACGAAGGG	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1770G>A	15.37:g.75692465C>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	87	32	NM_001145358	0	0	3	7	4		Silent	SNP	ENST00000394947.3	37	CCDS10279.1																																																																																			.		0.393	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		T	75692465	C	T	75692465	2	4	77	1	0	0	0	0	0	0	0	1	14357	523	19	1		1	SIN3A	15	75692465	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	9709445	75692465	26838927	59	7234											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_178167	0	0	0	10	10	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	77	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08		2059674	88295079	60	7235											
PKD1	5310	broad.mit.edu	37	chr16	2142592	2142592	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggccagagctcctcagAcctgccacagcatcagtcac	10	6	8	17	0	3	2	3	0	0	2	4	2	4	2	5	1	3	2	5	1	0	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:2142592A>C	ENST00000262304.4	-	39	11366	c.11158T>G	c.(11158-11160)Tct>Gct	p.S3720A	RP11-304L19.1_ENST00000570072.1_RNA|RP11-304L19.3_ENST00000565937.1_RNA|MIR1225_ENST00000408729.1_RNA|PKD1_ENST00000423118.1_Splice_Site_p.S3719A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3720					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGCTCCTCAGACCTGCCACAG	0.687																																					p.S3720A													.	PKD1-91	0			c.T11158G						.																																			SO:0001630	splice_region_variant	5310	exon39			CCTCAGACCTGCC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.11157-1T>G	16.37:g.2142592A>C		Somatic	38	6		WXS	Illumina HiSeq	Phase_I	27	11	NM_001009944	0	0	4	5	1	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.283947	0.23392	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.70516	-0.49;-0.49	3.74	2.63	0.31362	Polycystin cation channel, PKD1/PKD2 (1);	0.495398	0.20598	N	0.089201	T	0.76040	0.3932	M	0.66939	2.045	0.31441	N	0.671983	D;B	0.69078	0.997;0.374	D;B	0.80764	0.994;0.268	T	0.71087	-0.4694	10	0.16420	T	0.52	.	5.0637	0.14570	0.7478:0.0:0.0904:0.1618	.	3719;3720	P98161-3;P98161	.;PKD1_HUMAN	A	3720;3719;3054	ENSP00000262304:S3720A;ENSP00000399501:S3719A	ENSP00000262304:S3720A	S	-	1	0	PKD1	2082593	0.984000	0.35163	1.000000	0.80357	0.583000	0.36354	1.268000	0.33062	0.492000	0.27815	0.260000	0.18958	TCT	.		0.687	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		Missense_Mutation	C	2142592	A	C	2142592	5	2	77	1	0	0	0	0	0	0	1	0	11989	289	10	5	1785	5	PKD1	16	2142592	Splice_Site	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	82918	2142592	88212161	61	7236											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613197	3613197	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catggcctcctccacgctgcGggccagctcggtgtgctgca	4	8	13	16	3	0	0	0	0	0	0	3	0	2	0	4	3	4	4	4	3	0	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:3613197G>A	ENST00000301749.7	-	0	2146				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCCACGCTGCGGGCCAGCTCG	0.706																																					p.R581C		.											.	NLRC3-96	0			c.C1741T						.																																					197358	exon5			CGCTGCGGGCCAG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613197G>A		Somatic	19	2		WXS	Illumina HiSeq	Phase_I	17	14	NM_178844	0	0	0	0	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	G	2.943	-0.218437	0.06101	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85	4.89	1.09	0.20402	.	0.489205	0.20893	N	0.083782	T	0.72606	0.3481	.	.	.	0.21020	N	0.999808	B	0.21821	0.061	B	0.16289	0.015	T	0.59423	-0.7457	9	0.39692	T	0.17	.	5.1383	0.14947	0.2107:0.0:0.563:0.2263	.	628	C9JLH9	.	C	581;581;581;628;563	ENSP00000301749:R581C;ENSP00000352039:R581C;ENSP00000414415:R628C;ENSP00000323897:R563C	ENSP00000301749:R581C	R	-	1	0	NLRC3	3553198	0.000000	0.05858	0.422000	0.26621	0.013000	0.08279	-0.179000	0.09768	0.380000	0.24823	-0.345000	0.07892	CGC	.		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		A	3613197	G	A	3613197	1	1	77	0	1	0	0	0	0	0	0	0	10494	1116	39	1		1	NLRC3	16	3613197	RNA	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	1470605	3613197	86741556	62	7237											
CIITA	4261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	10992850	10992850	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagttgggcagaaaagtCagaaaagacgtgagtgagcc	16	5	14	6	1	1	6	1	2	0	4	1	6	1	6	1	1	1	2	1	1	5	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:10992850C>A	ENST00000324288.8	+	5	560	c.427C>A	c.(427-429)Cag>Aag	p.Q143K	CIITA_ENST00000381835.5_Missense_Mutation_p.Q143K|CIITA_ENST00000537380.1_3'UTR	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	143					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GCAGAAAAGTCAGAAAAGACG	0.507			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.Q143K		.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA-226	0			c.C427A						.						159	151	154					16																	10992850		2197	4300	6497	SO:0001583	missense	4261	exon5			AAAAGTCAGAAAA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"Nucleotide-binding domain and leucine rich repeat containing"	7067	protein-coding gene	gene with protein product	"NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"	600005	"MHC class II transactivator"	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.427C>A	16.37:g.10992850C>A	ENSP00000316328:p.Gln143Lys	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	137	29	NM_000246	0	0	0	0	0	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446255	0.43429	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.74842	-0.88;1.54	3.81	3.81	0.43845	.	0.428781	0.17282	N	0.179967	T	0.66626	0.2808	L	0.50333	1.59	0.25966	N	0.982563	P;P;B;B;P;B	0.40398	0.649;0.455;0.126;0.126;0.716;0.323	B;B;B;B;B;B	0.36567	0.228;0.094;0.049;0.049;0.228;0.079	T	0.64118	-0.6482	10	0.54805	T	0.06	.	11.3836	0.49771	0.0:1.0:0.0:0.0	.	143;143;143;143;144;143	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	K	143;143;144;143	ENSP00000316328:Q143K;ENSP00000371257:Q143K	ENSP00000316328:Q143K	Q	+	1	0	CIITA	10900351	0.989000	0.36119	0.889000	0.34880	0.900000	0.52787	3.160000	0.50739	2.134000	0.65973	0.557000	0.71058	CAG	.		0.507	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		A	10992850	C	A	10992850	3	1	77	1	0	0	0	0	1	0	0	0	3434	827	29	4	445	4	CIITA	16	10992850	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	7379653	10992850	79361903	63	7238											
B3GNT9	80262	hgsc.bcm.edu	37	chr16	67184342	67184342	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccagggaggcgccaaggAgcagcgtgagcaatgcgtcc	9	3	17	12	3	0	1	0	1	0	0	1	3	1	3	3	4	4	2	3	4	2	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:67184342A>G	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Missense_Mutation_p.L16P	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GGCGCCAAGGAGCAGCGTGAG	0.746																																					p.L16P		.											.	.	0			c.T47C						.						4	4	4					16																	67184342		1947	3941	5888	SO:0001628	intergenic_variant	84752	exon2			CCAAGGAGCAGCG	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		16.37:g.67184342A>G		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	9	2	NM_033309	0	0	0	0	0	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	37	CCDS10828.1	.	.	.	.	.	.	.	.	.	.	a	11.96	1.794201	0.31777	.	.	ENSG00000237172	ENST00000449549	T	0.35789	1.29	4.85	4.85	0.62838	.	.	.	.	.	T	0.32675	0.0837	L	0.48642	1.525	0.52501	D	0.999954	B	0.06786	0.001	B	0.08055	0.003	T	0.13737	-1.0498	9	0.62326	D	0.03	-15.0545	11.8506	0.52410	1.0:0.0:0.0:0.0	.	16	Q6UX72	B3GN9_HUMAN	P	16	ENSP00000400157:L16P	ENSP00000400157:L16P	L	-	2	0	B3GNT9	65741843	0.006000	0.16342	0.876000	0.34364	0.016000	0.09150	1.314000	0.33597	1.828000	0.53243	0.249000	0.18162	CTC	.		0.746	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		G	67184342	A	G	67184342	1	3	77	0	1	0	0	0	0	0	0	0	1265	304	11	3		3	B3GNT9	16	67184342	IGR	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	56191492	67184342	23170411	64	7239											
ANKRD11	29123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89349917	89349917	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccttatcggggccatccttCttctccttctctcgtgctgg	2	16	8	15	2	3	0	0	0	3	0	9	0	5	0	4	3	1	1	4	3	1	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:89349917C>G	ENST00000301030.4	-	9	3493	c.3033G>C	c.(3031-3033)aaG>aaC	p.K1011N	ANKRD11_ENST00000378330.2_Missense_Mutation_p.K1011N	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1011	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GGCCATCCTTCTTCTCCTTCT	0.517																																					p.K1011N		.											.	ANKRD11-139	0			c.G3033C						.						142	139	140					16																	89349917		2198	4300	6498	SO:0001583	missense	29123	exon9			ATCCTTCTTCTCC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3033G>C	16.37:g.89349917C>G	ENSP00000301030:p.Lys1011Asn	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	122	69	NM_001256183	0	0	2	12	10	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.26|16.26	3.072498|3.072498	0.55646|0.55646	.|.	.|.	ENSG00000167522|ENSG00000167522	ENST00000301030;ENST00000378330|ENST00000330736	T;T|.	0.54071|.	0.59;0.59|.	5.5|5.5	3.5|3.5	0.40072|0.40072	.|.	0.059984|.	0.64402|.	D|.	0.000004|.	T|T	0.69324|0.69324	0.3098|0.3098	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D|.	0.59767|.	0.986|.	P|.	0.62435|.	0.902|.	T|T	0.71626|0.71626	-0.4536|-0.4536	10|6	0.51188|0.54805	T|T	0.08|0.06	.|.	12.1739|12.1739	0.54173|0.54173	0.0:0.8519:0.0:0.1481|0.0:0.8519:0.0:0.1481	.|.	1011|.	Q6UB99|.	ANR11_HUMAN|.	N|T	1011|562	ENSP00000301030:K1011N;ENSP00000367581:K1011N|.	ENSP00000301030:K1011N|ENSP00000330815:R562T	K|R	-|-	3|2	2|0	ANKRD11|ANKRD11	87877418|87877418	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.198000|0.198000	0.23893|0.23893	4.656000|4.656000	0.61483|0.61483	1.425000|1.425000	0.47237|0.47237	0.655000|0.655000	0.94253|0.94253	AAG|AGA	.		0.517	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		G	89349917	C	G	89349917	3	3	77	1	0	0	0	0	1	0	0	0	639	912	32	4	4978	4	ANKRD11	16	89349917	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	22165575	89349917	1004836	65	7240											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	308	18		WXS	Illumina HiSeq		647	69	NM_145301	0	0	14	53	39	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		T	15457087	C	T	15457087	3	4	77	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		15457087	65738123	66	7241											
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18082124	18082124	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtggccgtgcacgtggagaaCctgctcagtgcccatgagaa	9	7	14	11	2	1	2	1	1	0	2	1	4	1	2	3	2	4	2	3	2	2	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr17:18082124C>A	ENST00000205890.5	+	66	10871	c.10533C>A	c.(10531-10533)aaC>aaA	p.N3511K	MYO15A_ENST00000418233.3_Missense_Mutation_p.P793T|MYO15A_ENST00000451725.2_3'UTR|RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3511	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					ACGTGGAGAACCTGCTCAGTG	0.617																																					p.N3511K		.											.	MYO15A-97	0			c.C10533A						.						128	144	139					17																	18082124		2148	4261	6409	SO:0001583	missense	51168	exon65			GGAGAACCTGCTC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.10533C>A	17.37:g.18082124C>A	ENSP00000205890:p.Asn3511Lys	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	100	55	NM_016239	0	0	0	0	0	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.080015	0.36662	.	.	ENSG00000091536	ENST00000205890	D	0.87256	-2.23	5.66	4.69	0.59074	FERM domain (1);	.	.	.	.	D	0.82314	0.5010	L	0.57536	1.79	0.80722	D	1	B	0.31680	0.335	B	0.28139	0.086	T	0.80151	-0.1502	9	0.51188	T	0.08	.	7.4648	0.27316	0.0:0.7138:0.1379:0.1483	.	3511	Q9UKN7	MYO15_HUMAN	K	3511	ENSP00000205890:N3511K	ENSP00000205890:N3511K	N	+	3	2	MYO15A	18022849	1.000000	0.71417	0.997000	0.53966	0.947000	0.59692	2.577000	0.46042	1.398000	0.46701	-0.422000	0.05995	AAC	.		0.617	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18082124	C	A	18082124	3	1	77	1	0	0	0	0	1	0	0	0	10088	506	18	4	10787	4	MYO15A	17	18082124	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	2625037	18082124	63113086	67	7242											
ACCN1	40	hgsc.bcm.edu	37	chr17	31618997	31618997	+	Intron	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctggcccctgcagcgccCgctcgccgcctctgccgccc	1	5	10	25	5	1	0	0	0	1	0	2	0	1	0	9	1	3	2	9	1	0	0	rs112647385	byFrequency	TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr17:31618997C>A	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Missense_Mutation_p.R46L	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2						central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	CTGCAGCGCCCGCTCGCCGCC	0.806													C|||	1091	0.217851	0.112	0.1902	5008	,	,		5226	0.3194		0.2664	False		,,,				2504	0.226				p.R46L		.											.	.	0			c.G137T						.						1	2	2					17																	31618997		903	2226	3129	SO:0001627	intron_variant	40	exon1			AGCGCCCGCTCGC	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"Ion channels / Acid-sensing (proton-gated) ion channels"	99	protein-coding gene	gene with protein product	"degenerin"	601784	"amiloride-sensitive cation channel 1, neuronal"	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.556-179912G>T	17.37:g.31618997C>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	5	5	NM_183377	0	0	0	0	0	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	37	CCDS42296.1	567	0.25961538461538464	84	0.17073170731707318	81	0.22375690607734808	197	0.34440559440559443	205	0.2704485488126649	C	13.69	2.313571	0.40996	.	.	ENSG00000108684	ENST00000225823	T	0.65178	-0.14	4.45	-0.0635	0.13776	.	1.386070	0.04769	N	0.427624	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.17038	0.02	B	0.10450	0.005	T	0.17715	-1.0360	9	0.29301	T	0.29	-24.8125	4.0823	0.09932	0.0:0.3667:0.3479:0.2854	.	46	E9PBX2	.	L	46	ENSP00000225823:R46L	ENSP00000225823:R46L	R	-	2	0	ACCN1	28643110	0.458000	0.25760	0.926000	0.36857	0.865000	0.49528	1.119000	0.31258	0.274000	0.22072	0.306000	0.20318	CGG	C|0.740;A|0.260		0.806	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		A	31618997	C	A	31618997	1	1	77	0	1	0	0	0	0	0	0	0	128	652	23	4		4	ACCN1	17	31618997	Intron	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	13536873	31618997	49576213	68	7243											
KIAA1468	57614	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	59888685	59888685	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatttttattgaagaataaCtataagcttacatcaataac	18	14	4	5	0	1	2	1	1	0	1	1	3	1	2	0	0	4	1	0	0	10	9			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr18:59888685C>T	ENST00000398130.2	+	5	1045	c.813C>T	c.(811-813)aaC>aaT	p.N271N	KIAA1468_ENST00000256858.6_Silent_p.N271N	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	271	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.									autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				TGAAGAATAACTATAAGCTTA	0.303																																					p.N271N		.											.	KIAA1468-158	0			c.C813T						.						52	49	50					18																	59888685		1803	4062	5865	SO:0001819	synonymous_variant	57614	exon5			GAATAACTATAAG	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.813C>T	18.37:g.59888685C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	98	28	NM_020854	0	0	0	1	1		Silent	SNP	ENST00000398130.2	37	CCDS11979.2																																																																																			.		0.303	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854		T	59888685	C	T	59888685	2	4	77	1	0	0	0	0	0	0	0	1	8257	564	20	2		2	KIAA1468	18	59888685	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		59888685	18188563	69	7244											
RHPN2	85415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	33503622	33503622	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tcttcactgtaatgttccagGataaaatccttaaagaaaaa	17	12	5	7	0	2	1	1	0	1	1	4	2	4	2	2	1	0	2	2	1	7	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:33503622G>C	ENST00000254260.3	-	5	434	c.399C>G	c.(397-399)atC>atG	p.I133M	RHPN2_ENST00000400226.4_De_novo_Start_InFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	133	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					AATGTTCCAGGATAAAATCCT	0.348																																					p.I133M		.											.	RHPN2-516	0			c.C399G						.						64	63	64					19																	33503622		2203	4300	6503	SO:0001583	missense	85415	exon5			TTCCAGGATAAAA	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.399C>G	19.37:g.33503622G>C	ENSP00000254260:p.Ile133Met	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	54	24	NM_033103	0	0	0	0	0	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.045171	0.36085	.	.	ENSG00000131941	ENST00000254260	T	0.36340	1.26	4.67	-0.356	0.12583	BRO1 domain (3);	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69316	-0.5177	10	0.87932	D	0	4.3606	9.4837	0.38917	0.5257:0.0:0.4743:0.0	.	133	Q8IUC4	RHPN2_HUMAN	M	133	ENSP00000254260:I133M	ENSP00000254260:I133M	I	-	3	3	RHPN2	38195462	1.000000	0.71417	0.998000	0.56505	0.408000	0.30992	0.918000	0.28678	0.003000	0.14656	0.455000	0.32223	ATC	.		0.348	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		C	33503622	G	C	33503622	3	2	77	1	0	0	0	0	1	0	0	0	13383	1164	41	4	1705	4	RHPN2	19	33503622	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		33503622	25625361	70	7245											
KIAA0355	9710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	34832921	34832921	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccacagcagccgtcactGcctgtgccccctccaccacg	8	5	7	21	2	1	0	1	0	0	0	2	0	2	0	7	0	5	1	7	0	1	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:34832921G>A	ENST00000299505.6	+	10	2955	c.2082G>A	c.(2080-2082)ctG>ctA	p.L694L		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	694										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AGCCGTCACTGCCTGTGCCCC	0.632																																					p.L694L		.											.	KIAA0355-91	0			c.G2082A						.						69	72	71					19																	34832921		2203	4299	6502	SO:0001819	synonymous_variant	9710	exon10			GTCACTGCCTGTG		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.2082G>A	19.37:g.34832921G>A		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	111	35	NM_014686	0	0	9	9	0	Q2M3W4	Silent	SNP	ENST00000299505.6	37	CCDS12436.1																																																																																			.		0.632	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		A	34832921	G	A	34832921	2	1	77	1	0	0	0	0	0	0	0	1	8191	1306	46	2		2	KIAA0355	19	34832921	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	1329299	34832921	24296062	71	7246											
TMEM149	79713	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36230750	36230750	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaggatagggataggggtcGgctttctccttgggccagca	7	9	15	10	1	1	0	0	0	1	0	3	2	1	2	3	6	1	2	3	6	2	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:36230750G>C	ENST00000592537.1	-	4	682	c.582C>G	c.(580-582)gcC>gcG	p.A194A	IGFLR1_ENST00000344990.3_Intron|AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000588992.1_Intron|IGFLR1_ENST00000246532.1_Silent_p.A194A|IGFLR1_ENST00000592889.1_Intron|KMT2B_ENST00000607650.1_RNA|IGFLR1_ENST00000587101.1_5'UTR			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						GATAGGGGTCGGCTTTCTCCT	0.617																																					p.A194A		.											.	IGFLR1-90	0			c.C582G						.						88	91	90					19																	36230750		2203	4300	6503	SO:0001819	synonymous_variant	79713	exon4			GGGGTCGGCTTTC	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 4", "transmembrane protein 149"	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.582C>G	19.37:g.36230750G>C		Somatic	197	0		WXS	Illumina HiSeq	Phase_I	159	66	NM_024660	0	0	0	1	1	Q8N5X0	Silent	SNP	ENST00000592537.1	37	CCDS12472.1																																																																																			.		0.617	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660		C	36230750	G	C	36230750	2	2	77	1	0	0	0	0	0	0	0	1	16094	1103	39	4		4	TMEM149	19	36230750	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	1397829	36230750	22898233	72	7247											
CNFN	84518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42893120	42893120	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccgtgagacctgtgtgccAgtcactgagctgggtctggt	5	11	15	10	1	2	2	1	2	1	1	3	3	3	2	3	2	2	1	3	2	0	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:42893120A>G	ENST00000222032.5	-	2	119	c.70T>C	c.(70-72)Tgg>Cgg	p.W24R	CNFN_ENST00000597255.1_Missense_Mutation_p.W24R	NM_032488.3	NP_115877.2	Q9BYD5	CNFN_HUMAN	cornifelin	24					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				lung(1)|prostate(1)	2		Prostate(69;0.00899)				CCTGTGTGCCAGTCACTGAGC	0.617																																					p.W24R		.											.	CNFN-90	0			c.T70C						.						133	99	111					19																	42893120		2203	4300	6503	SO:0001583	missense	84518	exon2			TGTGCCAGTCACT	AB049591	CCDS12606.1	19q13.31	2006-01-11				ENSG00000105427			30183	protein-coding gene	gene with protein product		611764					Standard	NM_032488		Approved	PLAC8L2	uc002otp.4	Q9BYD5		ENST00000222032.5:c.70T>C	19.37:g.42893120A>G	ENSP00000222032:p.Trp24Arg	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	37	22	NM_032488	0	0	1	1	0	B2R569	Missense_Mutation	SNP	ENST00000222032.5	37	CCDS12606.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.244613	0.59103	.	.	ENSG00000105427	ENST00000222032	T	0.29655	1.56	5.0	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.53738	0.1815	M	0.89658	3.05	0.46078	D	0.998858	D	0.56746	0.977	P	0.56612	0.802	T	0.60702	-0.7211	10	0.72032	D	0.01	-18.0017	10.0235	0.42057	0.8298:0.1702:0.0:0.0	.	24	Q9BYD5	CNFN_HUMAN	R	24	ENSP00000222032:W24R	ENSP00000222032:W24R	W	-	1	0	CNFN	47584960	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.707000	0.68370	0.847000	0.35167	-0.471000	0.05019	TGG	.		0.617	CNFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463859.1	NM_032488		G	42893120	A	G	42893120	3	3	77	1	0	0	0	0	1	0	0	0	3601	188	7	3	280	3	CNFN	19	42893120	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	6662370	42893120	16235863	73	7248											
ZNF285	26974	bcgsc.ca	37	chr19	44896602	44896602	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctcttccttggtgaagacaAcagccacatccttgaatgtc	10	11	8	12	0	1	3	0	2	1	1	4	3	3	3	3	1	2	1	3	1	3	3	rs149291798		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:44896602A>C	ENST00000330997.4	-	3	108	c.44T>G	c.(43-45)gTt>gGt	p.V15G	ZNF285_ENST00000544719.2_Missense_Mutation_p.V15G|ZNF285_ENST00000591679.1_Missense_Mutation_p.V22G|CTC-512J12.4_ENST00000588655.1_RNA|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GGTGAAGACAACAGCCACATC	0.448																																					p.V15G													.	ZNF285-94	0			c.T44G						.						126	112	117					19																	44896602		2203	4300	6503	SO:0001583	missense	26974	exon3			AAGACAACAGCCA	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"Zinc fingers, C2H2-type", "-"	13079	protein-coding gene	gene with protein product			"zinc finger protein 285A"	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.44T>G	19.37:g.44896602A>C	ENSP00000333595:p.Val15Gly	Somatic	151	0		WXS	Illumina HiSeq	Phase_1	102	19	NM_152354	0	0	1	1	0	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358004	0.82243	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.04758	3.56	3.07	3.07	0.35406	Krueppel-associated box (4);	.	.	.	.	T	0.32645	0.0836	H	0.99156	4.45	0.43808	D	0.996368	D;D	0.69078	0.997;0.976	D;P	0.64776	0.929;0.906	T	0.50709	-0.8796	9	0.87932	D	0	.	9.5743	0.39447	1.0:0.0:0.0:0.0	.	39;15	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	G	38;15	ENSP00000333595:V15G	ENSP00000333595:V15G	V	-	2	0	ZNF285	49588442	0.949000	0.32298	0.926000	0.36857	0.886000	0.51366	3.679000	0.54634	1.420000	0.47138	0.369000	0.22263	GTT	.		0.448	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		C	44896602	A	C	44896602	3	2	77	1	0	0	0	0	1	0	0	0	17854	43	2	5	1736	5	ZNF285	19	44896602	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	2003482	44896602	14232381	74	7249											
DMPK	1760	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46280763	46280763	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaccccggcccagccgtGtctccgggggacacagcaac	7	4	11	19	3	1	0	0	0	1	0	3	1	2	1	6	3	3	1	6	3	1	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:46280763G>A	ENST00000291270.4	-	8	1093	c.968C>T	c.(967-969)aCa>aTa	p.T323I	DMPK_ENST00000447742.2_Missense_Mutation_p.T323I|DMPK_ENST00000458663.2_Missense_Mutation_p.T323I|DMPK_ENST00000343373.4_Missense_Mutation_p.T333I|DMPK_ENST00000354227.5_Missense_Mutation_p.T323I|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000600757.1_Missense_Mutation_p.T333I	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	323	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		GCCCAGCCGTGTCTCCGGGGG	0.647																																					p.T333I	Esophageal Squamous(35;307 869 9153 24033 28903)	.											.	DMPK-546	0			c.C998T						.						39	41	40					19																	46280763		2203	4300	6503	SO:0001583	missense	1760	exon7			AGCCGTGTCTCCG	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"dystrophia myotonica 1", "DM protein kinase", "myotonin protein kinase A", "myotonic dystrophy associated protein kinase", "thymopoietin homolog"	605377	"dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.968C>T	19.37:g.46280763G>A	ENSP00000291270:p.Thr323Ile	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	76	31	NM_001081563	0	0	27	67	40	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	g	6.239	0.412186	0.11812	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	4.63	-1.42	0.08913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.960065	0.08582	N	0.924432	T	0.47985	0.1475	L	0.48935	1.535	0.09310	N	1	B;B;B;B;B;B;B;B	0.10296	0.001;0.0;0.003;0.001;0.001;0.001;0.001;0.0	B;B;B;B;B;B;B;B	0.12156	0.005;0.002;0.003;0.007;0.007;0.004;0.001;0.001	T	0.31392	-0.9945	10	0.21014	T	0.42	.	4.9214	0.13871	0.5892:0.0:0.2497:0.1611	.	323;323;349;323;323;323;370;333	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	I	323;349;323;323;323;333;333;323	ENSP00000401753:T323I;ENSP00000291270:T323I;ENSP00000413417:T323I;ENSP00000345997:T333I;ENSP00000346168:T323I	ENSP00000291270:T323I	T	-	2	0	DMPK	50972603	0.000000	0.05858	0.091000	0.20842	0.655000	0.38815	-1.221000	0.02968	-0.044000	0.13491	-0.254000	0.11334	ACA	.		0.647	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		A	46280763	G	A	46280763	3	1	77	1	0	0	0	0	1	0	0	0	4595	1377	48	2	960	2	DMPK	19	46280763	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	1384161	46280763	12848220	75	7250											
VN1R2	317701	broad.mit.edu	37	chr19	53762720	53762720	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttttccaactattagcccTtttgttctcatgtgccgtga	6	18	7	10	1	1	1	1	1	1	0	3	1	2	1	3	0	3	2	3	0	3	7			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:53762720T>C	ENST00000341702.3	+	1	1176	c.1092T>C	c.(1090-1092)ccT>ccC	p.P364P	VN1R2_ENST00000598458.1_Intron	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	364					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.P364P(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		CTATTAGCCCTTTTGTTCTCA	0.433																																					p.P364P													.	VN1R2-90	1	Substitution - coding silent(1)	lung(1)	c.T1092C						.						196	182	187					19																	53762720		2203	4300	6503	SO:0001819	synonymous_variant	317701	exon1			TAGCCCTTTTGTT	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.1092T>C	19.37:g.53762720T>C		Somatic	217	1		WXS	Illumina HiSeq	Phase_I	240	3	NM_173856	0	0	0	0	0	A1L411|Q8TDU4	Silent	SNP	ENST00000341702.3	37	CCDS12862.1																																																																																			.		0.433	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		C	53762720	T	C	53762720	2	2	77	1	0	0	0	0	0	0	0	1	17212	1596	56	3		3	VN1R2	19	53762720	Silent	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	7481957	53762720	5366263	76	7251											
PRKCG	5582	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	54385815	54385815	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcccctgttttgcagaaagGgggccctgaggcagaaggtg	8	7	17	9	0	0	3	0	1	0	2	0	3	0	3	3	5	1	3	3	5	2	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:54385815G>T	ENST00000263431.3	+	1	349	c.67G>T	c.(67-69)Ggg>Tgg	p.G23W	PRKCG_ENST00000540413.1_Missense_Mutation_p.G23W|PRKCG_ENST00000536044.1_Missense_Mutation_p.G23W|PRKCG_ENST00000542049.1_5'Flank	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	23					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	TTGCAGAAAGGGGGCCCTGAG	0.627																																					p.G23W		.											.	PRKCG-1367	0			c.G67T						.						66	74	71					19																	54385815		2203	4300	6503	SO:0001583	missense	5582	exon1			AGAAAGGGGGCCC	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.67G>T	19.37:g.54385815G>T	ENSP00000263431:p.Gly23Trp	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	156	72	NM_002739	0	0	0	0	0	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.929442	0.73327	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000419486	D;D;D	0.95069	-3.6;-3.6;-3.6	4.08	4.08	0.47627	.	.	.	.	.	D	0.96830	0.8965	M	0.77820	2.39	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.999	D	0.97398	0.9994	9	0.87932	D	0	.	14.1554	0.65415	0.0:0.0:1.0:0.0	.	23;23;23;23	F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;KPCG_HUMAN	W	23;23;23;46	ENSP00000440541:G23W;ENSP00000443493:G23W;ENSP00000263431:G23W	ENSP00000263431:G23W	G	+	1	0	PRKCG	59077627	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.851000	0.92205	1.996000	0.58369	0.491000	0.48974	GGG	.		0.627	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		T	54385815	G	T	54385815	3	4	77	1	0	0	0	0	1	0	0	0	12541	1232	43	4	69	4	PRKCG	19	54385815	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	623095	54385815	4743168	77	7252											
KIR3DL3	115653	hgsc.bcm.edu	37	chr19	55239373	55239373	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accctctggacatcgtggtcGtaggtgagagaatacagacc	11	8	12	10	2	1	3	0	1	1	2	3	5	1	4	2	3	1	1	2	3	3	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:55239373G>A	ENST00000291860.1	+	4	670	c.652G>A	c.(652-654)Gta>Ata	p.V218I	KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CATCGTGGTCGTAGGTGAGAG	0.542																																					p.V218I		.											.	KIR3DL3-46	0			c.G652A						.						8	8	8					19																	55239373		1846	3121	4967	SO:0001583	missense	115653	exon4			GTGGTCGTAGGTG	AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.652G>A	19.37:g.55239373G>A	ENSP00000291860:p.Val218Ile	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	146	65	NM_153443	0	0	0	0	0	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	.	.	.	.	.	.	.	.	.	.	-	4.693	0.128795	0.08981	.	.	ENSG00000242019	ENST00000291860	T	0.00730	5.77	1.38	0.293	0.15742	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.958988	0.08407	N	0.950530	T	0.00328	0.0010	N	0.00436	-1.5	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44345	-0.9334	10	0.45353	T	0.12	.	4.3253	0.11038	0.5511:0.0:0.4489:0.0	.	218	Q8N743	KI3L3_HUMAN	I	218	ENSP00000291860:V218I	ENSP00000291860:V218I	V	+	1	0	KIR3DL3	59931185	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.697000	0.05098	-0.402000	0.07633	-1.140000	0.01884	GTA	.		0.542	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443		A	55239373	G	A	55239373	3	1	77	1	0	0	0	0	1	0	0	0	8343	1145	40	1	666	1	KIR3DL3	19	55239373	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	853558	55239373	3889610	78	7253											
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35563508	35563508	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcccagctgtttgatgtatcGaagacgttgaaattgaggtg	10	13	12	6	2	0	4	0	3	0	1	2	5	1	4	1	1	1	4	1	1	3	4	rs121434517		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr20:35563508G>C	ENST00000262878.4	-	4	632	c.433C>G	c.(433-435)Cga>Gga	p.R145G	SAMHD1_ENST00000373694.5_5'UTR	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	145			R -> Q (in AGS5). {ECO:0000269|PubMed:19525956}.		dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				TTGATGTATCGAAGACGTTGA	0.433																																					p.R145G		.											.	SAMHD1-90	0			c.C433G						.						135	125	129					20																	35563508		2203	4300	6503	SO:0001583	missense	25939	exon4			TGTATCGAAGACG	AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.433C>G	20.37:g.35563508G>C	ENSP00000262878:p.Arg145Gly	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_015474	0	0	34	34	0	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	37	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.343156	0.82022	.	.	ENSG00000101347	ENST00000262878	D	0.96522	-4.04	6.05	4.04	0.47022	HD domain (1);	0.000000	0.85682	D	0.000000	D	0.98327	0.9445	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98576	1.0648	10	0.87932	D	0	-16.0364	9.3019	0.37851	0.0657:0.0:0.6789:0.2553	.	145	Q9Y3Z3	SAMH1_HUMAN	G	145	ENSP00000262878:R145G	ENSP00000262878:R145G	R	-	1	2	SAMHD1	34996922	1.000000	0.71417	0.967000	0.41034	0.983000	0.72400	3.147000	0.50639	1.571000	0.49722	0.650000	0.86243	CGA	.		0.433	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		C	35563508	G	C	35563508	3	2	77	1	0	0	0	0	1	0	0	0	13860	1066	37	4	1499	4	SAMHD1	20	35563508	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		35563508	27462012	79	7254											
EIF1AX	1964	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	20152121	20152121	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgtccgaggtatttatcCaaacctacaaaagaaaagtc	17	10	6	8	1	0	1	0	0	0	1	3	2	2	1	3	1	2	1	3	1	9	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:20152121C>A	ENST00000379607.5	-	4	412	c.209G>T	c.(208-210)tGg>tTg	p.W70L	EIF1AX_ENST00000379593.1_Missense_Mutation_p.W42L|snoU2_19_ENST00000364722.1_RNA|snoU2-30_ENST00000365012.1_RNA	NM_001412.3	NP_001403.1	P47813	IF1AX_HUMAN	eukaryotic translation initiation factor 1A, X-linked	70	S1-like.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(2)|lung(1)|ovary(1)|prostate(1)	5						GGTATTTATCCAAACCTACAA	0.323																																					p.W70L		.											.	EIF1AX-131	0			c.G209T						.						56	47	50					X																	20152121		2203	4300	6503	SO:0001583	missense	1964	exon4			TTTATCCAAACCT	L18960	CCDS14196.1	Xp22.13	2014-02-19	2002-11-28	2004-05-26	ENSG00000173674	ENSG00000173674			3250	protein-coding gene	gene with protein product		300186	"eukaryotic translation initiation factor 1A, X chromosome"	EIF4C, EIF1A		8106356, 9381176	Standard	NM_001412		Approved	eIF-1A, eIF-4C	uc004czt.3	P47813	OTTHUMG00000022704	ENST00000379607.5:c.209G>T	X.37:g.20152121C>A	ENSP00000368927:p.Trp70Leu	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	33	20	NM_001412	0	0	0	0	0	B2R5U5|Q0VGC2|Q5JPS5|Q5JPS6	Missense_Mutation	SNP	ENST00000379607.5	37	CCDS14196.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803652	0.90623	.	.	ENSG00000173674	ENST00000379607;ENST00000379593	T;T	0.58652	0.32;0.32	5.64	5.64	0.86602	Nucleic acid-binding, OB-fold-like (1);RNA-binding domain, S1, IF1 type (2);Nucleic acid-binding, OB-fold (1);	.	.	.	.	D	0.86653	0.5984	H	0.99090	4.425	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.92362	0.5898	9	0.87932	D	0	-3.1686	16.8722	0.86043	0.0:1.0:0.0:0.0	.	70	P47813	IF1AX_HUMAN	L	70;42	ENSP00000368927:W70L;ENSP00000368912:W42L	ENSP00000368912:W42L	W	-	2	0	EIF1AX	20062042	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.076000	0.76806	2.361000	0.80049	0.600000	0.82982	TGG	.		0.323	EIF1AX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058913.1			A	20152121	C	A	20152121	3	1	77	1	0	0	0	0	1	0	0	0	5003	595	21	4	241	4	EIF1AX	23	20152121	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		20152121	135118439	80	7255											
GPR34	2857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	41555435	41555435	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagtatggatgcttgctctTggtggattcctaactatgat	9	16	10	6	0	1	1	0	1	1	0	2	3	2	3	1	3	3	3	1	3	4	7			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:41555435T>A	ENST00000378142.4	+	3	833	c.549T>A	c.(547-549)ctT>ctA	p.L183L	CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron|GPR34_ENST00000378138.5_Silent_p.L183L|CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378166.4_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	183					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						TGCTTGCTCTTGGTGGATTCC	0.353																																					p.L183L		.											.	GPR34-131	0			c.T549A						.						63	59	60					X																	41555435		2203	4300	6503	SO:0001819	synonymous_variant	2857	exon3			TGCTCTTGGTGGA	AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"GPCR / Class A : Orphans"	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.549T>A	X.37:g.41555435T>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	58	49	NM_001097579	0	0	1	1	0	O95853	Silent	SNP	ENST00000378142.4	37	CCDS14258.1																																																																																			.		0.353	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		A	41555435	T	A	41555435	2	1	77	1	0	0	0	0	0	0	0	1	6709	1799	63	5		5	GPR34	23	41555435	Silent	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	21403314	41555435	113715125	81	7256											
GPRASP1	9737	broad.mit.edu	37	chrX	101908967	101908967	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcagacccaaggttaggacCcaggcccagataatgcctgg	11	6	12	12	0	1	2	1	0	0	2	1	3	1	3	4	4	1	1	4	4	3	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:101908967C>A	ENST00000361600.5	+	5	927	c.126C>A	c.(124-126)acC>acA	p.T42T	GPRASP1_ENST00000537097.1_Silent_p.T42T|GPRASP1_ENST00000415986.1_Silent_p.T42T|GPRASP1_ENST00000444152.1_Silent_p.T42T|RP4-769N13.7_ENST00000602441.1_RNA	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	42					endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AGGTTAGGACCCAGGCCCAGA	0.562																																					p.T42T													.	GPRASP1-131	0			c.C126A						.						130	128	129					X																	101908967		2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			TAGGACCCAGGCC	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.126C>A	X.37:g.101908967C>A		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	125	4	NM_001099411	0	0	0	0	0	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	37	CCDS35352.1																																																																																			.		0.562	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		A	101908967	C	A	101908967	2	1	77	1	0	0	0	0	0	0	0	1	6743	610	22	4		4	GPRASP1	23	101908967	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	60353532	101908967	53361593	82	7257											
BCORL1	63035	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	129173153	129173154	+	Frame_Shift_Ins	INS	-	-	CTGG																															aatgacaacctggagaccatINSctggctcctgctgtcctatg																										TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:129173153_129173154insCTGG	ENST00000218147.7	+	10	4711_4712	c.4514_4515insCTGG	c.(4513-4518)atctggfs	p.-1509fs	BCORL1_ENST00000359304.2_Frame_Shift_Ins_p.-1379fs|BCORL1_ENST00000303743.5_Frame_Shift_Ins_p.-1583fs|BCORL1_ENST00000540052.1_Frame_Shift_Ins_p.-1509fs			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1						chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CTGGAGACCATCTGGCTCCTGC	0.574																																					p.I1505fs		.											.	BCORL1-294	0			c.4514_4515insCTGG						.																																			SO:0001589	frameshift_variant	63035	exon9			.	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4515_4518dupCTGG	X.37:g.129173154_129173157dupCTGG	ENSP00000218147:p.Leu1509fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	38	22	NM_021946	0	0	0	0	0	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Frame_Shift_Ins	INS	ENST00000218147.7	37	CCDS14616.1																																																																																			.		0.574	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		CTGG	129173154	-	CTGG	129173153	7	5	77	1	0	1	1	0	0	0	0	0	1388	1435	50	0	4774	0	BCORL1	23	129173153	Frame_Shift_Ins	INS	-	TCGA-BQ-5893-01A-11D-1589-08	27264186	129173153	26097407	83	7258											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109801211	109801211	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atccaggcggtggccgccacGctggccacgccaccggacca	7	3	13	18	5	0	0	0	0	0	0	1	1	1	1	7	5	0	1	7	5	0	0			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr1:109801211G>C	ENST00000271332.3	+	2	3529	c.3468G>C	c.(3466-3468)acG>acC	p.T1156T		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1156					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGGCCGCCACGCTGGCCACGC	0.672																																					p.T1156T	NSCLC(158;1285 2011 34800 34852 42084)	.											.	CELSR2-526	0			c.G3468C						.						21	21	21					1																	109801211		2196	4293	6489	SO:0001819	synonymous_variant	1952	exon2			CGCCACGCTGGCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.3468G>C	1.37:g.109801211G>C		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	11	2	NM_001408	0	0	16	16	0	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			.		0.672	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		C	109801211	G	C	109801211	2	2	78	1	0	0	0	0	0	0	0	1	3228	1074	38	4		4	CELSR2	1	109801211	Silent	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		109801211	139449410	1	7259											
DUSP12	11266	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	161726704	161726704	+	Frame_Shift_Del	DEL	G	G	-																															gtggatgaaatgaaaatattGcctgttttgggatcacaaac																										TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr1:161726704delG	ENST00000367943.4	+	6	1022	c.990delG	c.(988-990)ttgfs	p.L330fs		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	330					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			TGAAAATATTGCCTGTTTTGG	0.373																																					p.L330fs		.											.	DUSP12-226	0			c.990delG						.																																			SO:0001589	frameshift_variant	11266	exon6			.	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3067	protein-coding gene	gene with protein product	"serine/threonine specific protein phosphatase", "YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.990delG	1.37:g.161726704delG	ENSP00000356920:p.Leu330fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	68	23	NM_007240	0	0	0	0	0	Q5VXA8	Frame_Shift_Del	DEL	ENST00000367943.4	37	CCDS1234.1																																																																																			.		0.373	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240		-	161726704	G	-	161726704	7	5	78	1	0	1	0	1	0	0	0	0	4823	1310	46	0	1012	0	DUSP12	1	161726704	Frame_Shift_Del	DEL	G	TCGA-BQ-5894-01A-11D-1589-08	51925493	161726704	87523917	2	7260											
PLXNA2	5362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	208270156	208270156	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccggacacctgcccctccaCctctgtcaggttcccaaagg	7	7	8	19	1	2	0	1	0	1	0	4	1	4	1	7	3	1	1	7	3	1	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr1:208270156C>A	ENST00000367033.3	-	7	2561	c.1804G>T	c.(1804-1806)Gtg>Ttg	p.V602L		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	602					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TGCCCCTCCACCTCTGTCAGG	0.562																																					p.V602L		.											.	PLXNA2-92	0			c.G1804T						.						76	63	67					1																	208270156		2203	4300	6503	SO:0001583	missense	5362	exon7			CCTCCACCTCTGT	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1804G>T	1.37:g.208270156C>A	ENSP00000356000:p.Val602Leu	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	63	20	NM_025179	0	0	1	2	1	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.764098	0.31228	.	.	ENSG00000076356	ENST00000367033	T	0.00856	5.61	4.92	4.92	0.64577	.	0.309702	0.38837	N	0.001558	T	0.01695	0.0054	L	0.57536	1.79	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.61272	-0.7096	10	0.22109	T	0.4	.	18.3153	0.90218	0.0:1.0:0.0:0.0	.	602	O75051	PLXA2_HUMAN	L	602	ENSP00000356000:V602L	ENSP00000356000:V602L	V	-	1	0	PLXNA2	206336779	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.321000	0.65846	2.563000	0.86464	0.655000	0.94253	GTG	.		0.562	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208270156	C	A	208270156	3	1	78	1	0	0	0	0	1	0	0	0	12146	507	18	4	3984	4	PLXNA2	1	208270156	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	46543452	208270156	40980465	3	7261											
PNPT1	87178	broad.mit.edu	37	chr2	55900121	55900121	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttttaccaactgctgaatgCcctgaattatttgttgggta	9	16	8	8	0	0	2	0	2	0	0	0	2	0	2	2	1	4	3	2	1	6	6			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:55900121C>T	ENST00000447944.2	-	9	859	c.773G>A	c.(772-774)gGc>gAc	p.G258D		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	258					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTGCTGAATGCCCTGAATTAT	0.393																																					p.G258D													.	PNPT1-90	0			c.G773A						.						141	146	145					2																	55900121		2203	4300	6503	SO:0001583	missense	87178	exon9			TGAATGCCCTGAA	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.773G>A	2.37:g.55900121C>T	ENSP00000400646:p.Gly258Asp	Somatic	274	0		WXS	Illumina HiSeq	Phase_I	268	4	NM_033109	0	0	22	22	0	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	37	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432574	0.43224	.	.	ENSG00000138035	ENST00000447944	T	0.42131	0.98	5.67	5.67	0.87782	Exoribonuclease, phosphorolytic domain 2 (1);	0.118776	0.56097	D	0.000023	T	0.28300	0.0699	N	0.08118	0	0.58432	D	0.999993	B	0.19935	0.04	B	0.26094	0.066	T	0.07385	-1.0775	10	0.35671	T	0.21	-2.1503	17.0606	0.86547	0.0:0.8734:0.1266:0.0	.	258	Q8TCS8	PNPT1_HUMAN	D	258	ENSP00000400646:G258D	ENSP00000386075:G258D	G	-	2	0	PNPT1	55753625	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.827000	0.62723	2.828000	0.97474	0.655000	0.94253	GGC	.		0.393	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		T	55900121	C	T	55900121	3	4	78	1	0	0	0	0	1	0	0	0	12199	739	26	2	1658	2	PNPT1	2	55900121	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		55900121	187299252	4	7262											
ANKRD23	200539	hgsc.bcm.edu;broad.mit.edu	37	chr2	97505559	97505559	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgtgcagagccgtgtcccCttcctgctgagaacgcaggc	6	8	12	15	3	0	2	0	1	0	2	3	3	2	2	4	1	4	3	4	1	1	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:97505559C>T	ENST00000318357.4	-	8	768	c.727G>A	c.(727-729)Ggg>Agg	p.G243R	ANKRD23_ENST00000476975.1_Intron|ANKRD23_ENST00000418232.1_Missense_Mutation_p.G243R|ANKRD23_ENST00000331001.2_Missense_Mutation_p.G201R	NM_144994.7	NP_659431.5	Q86SG2	ANR23_HUMAN	ankyrin repeat domain 23	243					fatty acid metabolic process (GO:0006631)|response to mechanical stimulus (GO:0009612)	I band (GO:0031674)|intercalated disc (GO:0014704)|nucleus (GO:0005634)	titin binding (GO:0031432)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)	9						GCCGTGTCCCCTTCCTGCTGA	0.647																																					p.G243R		.											.	ANKRD23-91	0			c.G727A						.						29	26	27					2																	97505559		2203	4300	6503	SO:0001583	missense	200539	exon8			TGTCCCCTTCCTG		CCDS2027.1	2q11.2	2013-01-10			ENSG00000163126	ENSG00000163126		"Ankyrin repeat domain containing"	24470	protein-coding gene	gene with protein product	"diabetes related ankyrin repeat protein"	610736				12456686	Standard	NM_144994		Approved	DARP, FLJ32449, MARP3	uc002sxa.3	Q86SG2	OTTHUMG00000130534	ENST00000318357.4:c.727G>A	2.37:g.97505559C>T	ENSP00000321679:p.Gly243Arg	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	37	7	NM_144994	0	0	0	0	0	Q711K7|Q8NAJ7	Missense_Mutation	SNP	ENST00000318357.4	37	CCDS2027.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.964298	0.92791	.	.	ENSG00000163126	ENST00000318357;ENST00000418232;ENST00000331001	T;T;T	0.65732	-0.17;-0.17;-0.17	5.05	5.05	0.67936	Ankyrin repeat-containing domain (4);	0.000000	0.40064	N	0.001191	T	0.80924	0.4717	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83639	0.0149	10	0.66056	D	0.02	-30.8309	13.7706	0.63021	0.0:1.0:0.0:0.0	.	201;243	Q86SG2-2;Q86SG2	.;ANR23_HUMAN	R	243;243;201	ENSP00000321679:G243R;ENSP00000398987:G243R;ENSP00000333108:G201R	ENSP00000321679:G243R	G	-	1	0	ANKRD23	96869286	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.780000	0.68956	2.623000	0.88846	0.650000	0.86243	GGG	.		0.647	ANKRD23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252956.1	NM_144994		T	97505559	C	T	97505559	3	4	78	1	0	0	0	0	1	0	0	0	652	681	24	2	198	2	ANKRD23	2	97505559	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	41605438	97505559	145693814	5	7263											
MBD5	55777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	149226038	149226038	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttaatgattggatcatcaAatgccatgggaaggctatat	14	12	10	5	0	2	1	2	1	0	0	2	3	2	3	1	3	1	2	1	3	5	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:149226038A>G	ENST00000407073.1	+	9	1523	c.526A>G	c.(526-528)Aat>Gat	p.N176D	MBD5_ENST00000404807.1_Missense_Mutation_p.N176D	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	176					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		TGGATCATCAAATGCCATGGG	0.423																																					p.N176D		.											.	MBD5-95	0			c.A526G						.						77	73	74					2																	149226038		2203	4300	6503	SO:0001583	missense	55777	exon9			TCATCAAATGCCA	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.526A>G	2.37:g.149226038A>G	ENSP00000386049:p.Asn176Asp	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	99	24	NM_018328	0	0	1	2	1	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.227484	0.58668	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.45668	0.89;0.89	5.16	5.16	0.70880	.	0.088275	0.49305	D	0.000155	T	0.30070	0.0753	N	0.08118	0	0.33054	D	0.533103	D	0.56968	0.978	P	0.47528	0.549	T	0.43015	-0.9417	10	0.40728	T	0.16	-3.4654	13.8586	0.63545	1.0:0.0:0.0:0.0	.	176	Q9P267	MBD5_HUMAN	D	176	ENSP00000386049:N176D;ENSP00000384672:N176D	ENSP00000384672:N176D	N	+	1	0	MBD5	148942508	1.000000	0.71417	0.909000	0.35828	0.972000	0.66771	4.483000	0.60264	2.079000	0.62486	0.482000	0.46254	AAT	.		0.423	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			G	149226038	A	G	149226038	3	3	78	1	0	0	0	0	1	0	0	0	9372	14	1	3	540	3	MBD5	2	149226038	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	51720479	149226038	93973335	6	7264											
CYTIP	9595	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	158287080	158287080	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatagttacgttagcaggTttccggacgatctgatcagg	10	11	12	8	3	2	2	1	1	1	1	3	4	3	3	1	3	2	4	1	3	3	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:158287080T>C	ENST00000264192.3	-	5	588	c.467A>G	c.(466-468)aAc>aGc	p.N156S	CYTIP_ENST00000540637.1_Missense_Mutation_p.N50S|CYTIP_ENST00000497432.1_5'Flank	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	156	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						CGTTAGCAGGTTTCCGGACGA	0.428																																					p.N156S		.											.	CYTIP-93	0			c.A467G						.						173	152	159					2																	158287080		2203	4300	6503	SO:0001583	missense	9595	exon5			AGCAGGTTTCCGG	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"cytohesin binding protein HE", "cytohesin binder and regulator"	604448	"pleckstrin homology, Sec7 and coiled-coil domains, binding protein"	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.467A>G	2.37:g.158287080T>C	ENSP00000264192:p.Asn156Ser	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	87	17	NM_004288	0	0	0	0	0	B4DWH9|Q15630|Q8NE32	Missense_Mutation	SNP	ENST00000264192.3	37	CCDS2204.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.427467	0.62733	.	.	ENSG00000115165	ENST00000264192;ENST00000540637;ENST00000418920	T;T;T	0.24908	1.83;1.83;1.83	5.87	4.71	0.59529	PDZ/DHR/GLGF (4);	0.040138	0.85682	N	0.000000	T	0.34366	0.0895	N	0.26162	0.8	0.40568	D	0.981273	D	0.61080	0.989	D	0.77557	0.99	T	0.15838	-1.0423	10	0.59425	D	0.04	-24.1417	8.8383	0.35126	0.0:0.0847:0.0:0.9153	.	156	O60759	CYTIP_HUMAN	S	156;50;50	ENSP00000264192:N156S;ENSP00000440801:N50S;ENSP00000394308:N50S	ENSP00000264192:N156S	N	-	2	0	CYTIP	157995326	1.000000	0.71417	0.994000	0.49952	0.973000	0.67179	2.314000	0.43743	1.149000	0.42402	0.533000	0.62120	AAC	.		0.428	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288		C	158287080	T	C	158287080	3	2	78	1	0	0	0	0	1	0	0	0	4213	1725	60	3	628	3	CYTIP	2	158287080	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08	9061042	158287080	84912293	7	7265											
SCN1A	6323	broad.mit.edu	37	chr2	166866330	166866330	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgagtaacccaaggcatttgCtgttaaactgaccaatgaaa	15	10	8	8	0	0	3	0	3	0	0	0	3	0	3	2	1	3	4	2	1	6	3			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:166866330C>T	ENST00000303395.4	-	20	3900	c.3901G>A	c.(3901-3903)Gca>Aca	p.A1301T	SCN1A_ENST00000409050.1_Missense_Mutation_p.A1273T|SCN1A_ENST00000423058.2_Missense_Mutation_p.A1301T|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.A1290T|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1301					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAGGCATTTGCTGTTAAACTG	0.368																																					p.A1301T													.	SCN1A-147	0			c.G3901A						.						86	85	85					2																	166866330		2203	4300	6503	SO:0001583	missense	6323	exon20			CATTTGCTGTTAA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3901G>A	2.37:g.166866330C>T	ENSP00000303540:p.Ala1301Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	109	4	NM_001165963	0	0	0	0	0	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	34	5.315144	0.95655	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.98550	-4.99;-4.99;-4.99;-4.99	5.46	5.46	0.80206	Ion transport (1);	0.092549	0.47093	D	0.000250	D	0.99137	0.9702	M	0.88570	2.965	0.80722	D	1	D;D;D	0.89917	0.985;1.0;1.0	P;D;D	0.91635	0.801;0.999;0.998	D	0.99609	1.0980	10	0.87932	D	0	.	19.3188	0.94229	0.0:1.0:0.0:0.0	.	1290;1273;1301	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	T	1301;1301;1290;1273	ENSP00000407030:A1301T;ENSP00000303540:A1301T;ENSP00000364554:A1290T;ENSP00000386312:A1273T	ENSP00000303540:A1301T	A	-	1	0	SCN1A	166574576	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.621000	0.83083	2.569000	0.86673	0.650000	0.86243	GCA	.		0.368	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166866330	C	T	166866330	3	4	78	1	0	0	0	0	1	0	0	0	13946	797	28	2	2156	2	SCN1A	2	166866330	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	8579250	166866330	76333043	8	7266											
ARMC8	25852	hgsc.bcm.edu	37	chr3	137986077	137986077	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcttgaattttctccaagCaaagaggttagtattgattt	11	17	7	6	0	2	3	0	2	2	1	3	3	2	3	1	1	1	3	1	1	5	8			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr3:137986077C>G	ENST00000469044.1	+	15	1651	c.1380C>G	c.(1378-1380)agC>agG	p.S460R	ARMC8_ENST00000393058.3_Missense_Mutation_p.S450R|ARMC8_ENST00000461822.1_Missense_Mutation_p.S393R|NME9_ENST00000341790.5_Intron|ARMC8_ENST00000538260.1_Missense_Mutation_p.S429R|NME9_ENST00000317876.4_Intron|ARMC8_ENST00000485396.1_Missense_Mutation_p.S387R|NME9_ENST00000536478.1_Intron|ARMC8_ENST00000491704.1_Missense_Mutation_p.S418R|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000481646.1_Missense_Mutation_p.S446R|NME9_ENST00000383180.2_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	460										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TTTCTCCAAGCAAAGAGGTTA	0.353																																					p.S446R		.											.	ARMC8-90	0			c.C1338G						.						93	81	85					3																	137986077		1818	4076	5894	SO:0001583	missense	25852	exon16			TCCAAGCAAAGAG		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1380C>G	3.37:g.137986077C>G	ENSP00000419413:p.Ser460Arg	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_015396	0	0	0	0	0	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Missense_Mutation	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	C	18.37	3.609677	0.66558	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000491704;ENST00000461822;ENST00000485396;ENST00000538260;ENST00000393058;ENST00000539459	T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;1.29;1.29;1.29;-0.18	5.84	3.09	0.35607	Armadillo-like helical (1);Armadillo-type fold (1);	0.038234	0.85682	N	0.000000	T	0.60104	0.2243	L	0.55481	1.735	0.80722	D	1	P;P;P;B;P	0.51240	0.905;0.651;0.886;0.281;0.943	B;B;P;B;P	0.50570	0.386;0.157;0.59;0.056;0.644	T	0.53457	-0.8436	10	0.25106	T	0.35	-31.5808	7.5339	0.27700	0.0:0.6608:0.0:0.3392	.	387;393;429;460;446	B7Z637;B7Z441;F5GWK4;Q8IUR7;Q8IUR7-2	.;.;.;ARMC8_HUMAN;.	R	446;460;418;393;387;429;450;317	ENSP00000420333:S446R;ENSP00000419413:S460R;ENSP00000417304:S418R;ENSP00000420706:S393R;ENSP00000417049:S387R;ENSP00000441592:S429R;ENSP00000376778:S450R	ENSP00000376778:S450R	S	+	3	2	ARMC8	139468767	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.543000	0.36147	0.382000	0.24878	0.561000	0.74099	AGC	.		0.353	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		G	137986077	C	G	137986077	3	3	78	1	0	0	0	0	1	0	0	0	958	709	25	4	1462	4	ARMC8	3	137986077	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		137986077	60036353	9	7267											
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57180739	57180739	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaggaagatgcgcggaggaGctcaaaaggcaggaggagga	15	2	19	5	2	1	1	1	0	0	1	1	8	1	7	0	7	2	2	0	7	4	0	rs112530577	byFrequency	TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr4:57180739G>C	ENST00000504228.1	+	6	1176	c.1071G>C	c.(1069-1071)gaG>gaC	p.E357D	KIAA1211_ENST00000264229.6_Missense_Mutation_p.E357D|KIAA1211_ENST00000541073.1_Missense_Mutation_p.E350D			Q6ZU35	K1211_HUMAN	KIAA1211	357	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					gcgcggaggagctcaaaaggc	0.697													G|||	102	0.0203674	0.0749	0.0043	5008	,	,		12008	0		0	False		,,,				2504	0				p.E357D		.											.	KIAA1211-70	0			c.G1071C						.	G	ASP/GLU	150,3800		1,148,1826	7	9	9		1071	2.4	0.2	4	dbSNP_132	9	4,7840		0,4,3918	yes	missense	KIAA1211	NM_020722.1	45	1,152,5744	CC,CG,GG		0.051,3.7975,1.3057	probably-damaging	357/1234	57180739	154,11640	1975	3922	5897	SO:0001583	missense	57482	exon8			GGAGGAGCTCAAA	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1071G>C	4.37:g.57180739G>C	ENSP00000423366:p.Glu357Asp	Somatic	5	2		WXS	Illumina HiSeq	Phase_I	4	4	NM_020722	0	0	0	0	0	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	35	0.016025641025641024	35	0.07113821138211382	0	0.0	0	0.0	0	0.0	G	14.25	2.480481	0.44044	0.037975	5.1E-4	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.02050	4.48;4.48;4.48	5.09	2.39	0.29439	.	.	.	.	.	T	0.00328	0.0010	N	0.19112	0.55	0.23869	N	0.996617	D;D;D	0.64830	0.994;0.994;0.971	P;P;P	0.61800	0.894;0.894;0.832	T	0.52771	-0.8531	9	0.44086	T	0.13	-2.2251	7.8321	0.29349	0.4706:0.0:0.5294:0.0	.	350;350;357	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	D	357;357;350;267	ENSP00000264229:E357D;ENSP00000423366:E357D;ENSP00000444006:E350D	ENSP00000264229:E357D	E	+	3	2	KIAA1211	56875496	0.001000	0.12720	0.190000	0.23270	0.075000	0.17131	0.315000	0.19451	0.160000	0.19432	0.462000	0.41574	GAG	G|0.984;C|0.016		0.697	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		C	57180739	G	C	57180739	3	2	78	1	0	0	0	0	1	0	0	0	8236	962	34	4	1089	4	KIAA1211	4	57180739	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		57180739	133973537	10	7268											
FBXW7	55294	broad.mit.edu	37	chr4	153268165	153268165	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttgcccttggccattggCtgctctgaggtccccaaaag	6	12	11	12	0	1	1	0	1	1	0	2	1	2	1	4	3	2	3	4	3	2	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr4:153268165C>T	ENST00000281708.4	-	4	1872	c.643G>A	c.(643-645)Gcc>Acc	p.A215T	FBXW7_ENST00000296555.5_Missense_Mutation_p.A97T|FBXW7_ENST00000603548.1_Missense_Mutation_p.A215T|FBXW7_ENST00000393956.3_Missense_Mutation_p.A39T|FBXW7_ENST00000263981.5_Missense_Mutation_p.A135T|FBXW7_ENST00000603841.1_Missense_Mutation_p.A215T	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	215					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGGCCATTGGCTGCTCTGAGG	0.443			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.A215T				Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7-6296	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.G643A						.						164	151	156					4																	153268165		2203	4300	6503	SO:0001583	missense	55294	exon4			CATTGGCTGCTCT	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.643G>A	4.37:g.153268165C>T	ENSP00000281708:p.Ala215Thr	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	122	3	NM_033632	0	0	5	5	0	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.351810	0.61183	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.58797	0.31;0.36;0.31;0.59	5.83	5.83	0.93111	.	0.053021	0.85682	D	0.000000	T	0.44201	0.1282	N	0.14661	0.345	0.80722	D	1	B;P;B;B	0.34522	0.084;0.455;0.001;0.447	B;B;B;B	0.32342	0.026;0.068;0.001;0.144	T	0.38045	-0.9679	10	0.38643	T	0.18	-12.804	20.1162	0.97934	0.0:1.0:0.0:0.0	.	39;215;97;135	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	T	215;97;135;39	ENSP00000281708:A215T;ENSP00000296555:A97T;ENSP00000263981:A135T;ENSP00000377528:A39T	ENSP00000263981:A135T	A	-	1	0	FBXW7	153487615	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.757000	0.94681	0.563000	0.77884	GCC	.		0.443	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			T	153268165	C	T	153268165	3	4	78	1	0	0	0	0	1	0	0	0	5788	797	28	2	1516	2	FBXW7	4	153268165	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	96087426	153268165	37886111	11	7269											
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	32108131	32108131	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagatgaaattcttgctattAatgggaaacctctggttggg	11	13	12	5	0	2	2	0	1	2	1	2	4	2	3	1	3	2	2	1	3	4	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr5:32108131A>G	ENST00000438447.1	+	25	8798	c.8410A>G	c.(8410-8412)Aat>Gat	p.N2804D	CTD-2152M20.2_ENST00000503441.1_RNA|PDZD2_ENST00000513490.1_3'UTR|PDZD2_ENST00000282493.3_Missense_Mutation_p.N2804D			O15018	PDZD2_HUMAN	PDZ domain containing 2	2804	PDZ 6. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TCTTGCTATTAATGGGAAACC	0.403																																					p.N2804D		.											.	PDZD2-563	0			c.A8410G						.						134	139	137					5																	32108131		2203	4300	6503	SO:0001583	missense	23037	exon24			GCTATTAATGGGA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.8410A>G	5.37:g.32108131A>G	ENSP00000402033:p.Asn2804Asp	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	126	53	NM_178140	0	0	1	1	0	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.233379	0.79688	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.56776	0.44;0.44	5.88	5.88	0.94601	PDZ/DHR/GLGF (4);	0.097034	0.45867	D	0.000337	T	0.59742	0.2216	L	0.41415	1.275	0.35013	D	0.757058	D	0.76494	0.999	D	0.71870	0.975	T	0.68269	-0.5453	10	0.39692	T	0.17	.	8.7229	0.34452	0.9164:0.0:0.0836:0.0	.	2804	O15018	PDZD2_HUMAN	D	2804;2605;2804	ENSP00000402033:N2804D;ENSP00000282493:N2804D	ENSP00000282493:N2804D	N	+	1	0	PDZD2	32143888	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	3.761000	0.55242	2.242000	0.73789	0.533000	0.62120	AAT	.		0.403	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	32108131	A	G	32108131	3	3	78	1	0	0	0	0	1	0	0	0	11727	362	13	3	8504	3	PDZD2	5	32108131	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08		32108131	148807129	12	7270											
SLIT3	6586	hgsc.bcm.edu	37	chr5	168098301	168098301	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgtccttctccacggagcgGcacaggccgtgcttgcacac	6	8	11	16	3	1	0	0	0	1	0	3	1	2	1	3	3	3	3	3	3	0	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr5:168098301G>C	ENST00000519560.1	-	34	4448	c.4029C>G	c.(4027-4029)tgC>tgG	p.C1343W	SLIT3_ENST00000404867.3_Missense_Mutation_p.C1343W|SLIT3_ENST00000332966.8_Missense_Mutation_p.C1350W	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1343	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.C1343*(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCACGGAGCGGCACAGGCCGT	0.677																																					p.C1350W	Ovarian(29;311 847 10864 17279 24903)	.											.	SLIT3-95	1	Substitution - Nonsense(1)	lung(1)	c.C4050G						.						43	35	37					5																	168098301		2203	4300	6503	SO:0001583	missense	6586	exon34			GGAGCGGCACAGG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"slit (Drosophila) homolog 3"	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.4029C>G	5.37:g.168098301G>C	ENSP00000430333:p.Cys1343Trp	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_001271946	0	0	20	20	0	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692168	0.48202	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.82433	-1.6;-1.61;-1.59	5.16	-3.59	0.04583	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.91952	0.7451	H	0.95004	3.61	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	D	0.91550	0.5256	10	0.72032	D	0.01	.	15.2185	0.73288	0.6215:0.0:0.3785:0.0	.	1343	O75094	SLIT3_HUMAN	W	1343;1350;1343	ENSP00000430333:C1343W;ENSP00000332164:C1350W;ENSP00000384890:C1343W	ENSP00000332164:C1350W	C	-	3	2	SLIT3	168030879	0.999000	0.42202	0.356000	0.25785	0.910000	0.53928	0.533000	0.23082	-0.956000	0.03631	-1.598000	0.00824	TGC	.		0.677	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		C	168098301	G	C	168098301	3	2	78	1	0	0	0	0	1	0	0	0	14773	1195	42	4	554	4	SLIT3	5	168098301	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	135990170	168098301	12816959	13	7271											
GMDS	2762	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	1930387	1930387	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcgtttggcatccagatttcCcaaactgaaacattccagtt	11	13	6	11	1	0	2	0	1	0	1	4	2	3	2	3	1	2	3	3	1	2	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:1930387C>T	ENST00000380815.4	-	7	990	c.721G>A	c.(721-723)Gga>Aga	p.G241R	GMDS_ENST00000530927.1_Missense_Mutation_p.G211R	NM_001500.3	NP_001491.1	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	241					'de novo' GDP-L-fucose biosynthetic process (GO:0042351)|GDP-mannose metabolic process (GO:0019673)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	GDP-mannose 4,6-dehydratase activity (GO:0008446)|NADP+ binding (GO:0070401)		GMDS/PDE8B(2)	breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|prostate(1)	21	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		TCCAGATTTCCCAAACTGAAA	0.408																																					p.G241R		.											.	GMDS-90	0			c.G721A						.						143	124	131					6																	1930387		2203	4300	6503	SO:0001583	missense	2762	exon7			GATTTCCCAAACT	AF042377	CCDS4474.1, CCDS58994.1	6p25	2011-09-14			ENSG00000112699	ENSG00000112699	4.2.1.47	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	4369	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 3E, member 1"	602884				9525924, 19027726	Standard	NM_001500		Approved	GMD, SDR3E1	uc003mtq.3	O60547	OTTHUMG00000016143	ENST00000380815.4:c.721G>A	6.37:g.1930387C>T	ENSP00000370194:p.Gly241Arg	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	134	33	NM_001500	0	0	29	72	43	E9PI88|O75357|Q5T954|Q6FH09|Q9UGZ3|Q9UJK9	Missense_Mutation	SNP	ENST00000380815.4	37	CCDS4474.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953109	0.92660	.	.	ENSG00000112699	ENST00000530927;ENST00000380815	D;D	0.95656	-3.77;-3.77	5.63	5.63	0.86233	NAD-dependent epimerase/dehydratase (1);	0.000000	0.85682	D	0.000000	D	0.99042	0.9672	H	0.99415	4.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99198	1.0872	10	0.87932	D	0	-19.5481	19.6914	0.96002	0.0:1.0:0.0:0.0	.	241	O60547	GMDS_HUMAN	R	211;241	ENSP00000436726:G211R;ENSP00000370194:G241R	ENSP00000370194:G241R	G	-	1	0	GMDS	1875386	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.644000	0.89710	0.563000	0.77884	GGA	.		0.408	GMDS-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043380.3			T	1930387	C	T	1930387	3	4	78	1	0	0	0	0	1	0	0	0	6506	632	22	2	417	2	GMDS	6	1930387	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		1930387	169184680	14	7272											
MEP1A	4224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	46801054	46801054	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcgattctacaattcggAgggatatggttttggggtaa	9	13	12	7	2	1	0	0	0	1	0	3	3	1	2	1	5	1	2	1	5	4	7			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:46801054A>G	ENST00000230588.4	+	11	1397	c.1388A>G	c.(1387-1389)gAg>gGg	p.E463G		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	463	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			TACAATTCGGAGGGATATGGT	0.498																																					p.E463G		.											.	MEP1A-183	0			c.A1388G						.						74	76	75					6																	46801054		2203	4300	6503	SO:0001583	missense	4224	exon11			ATTCGGAGGGATA		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.1388A>G	6.37:g.46801054A>G	ENSP00000230588:p.Glu463Gly	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	130	19	NM_005588	0	0	0	0	0	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	15.89	2.965894	0.53507	.	.	ENSG00000112818	ENST00000230588	T	0.42900	0.96	5.72	5.72	0.89469	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73269	-0.4036	10	0.72032	D	0.01	-31.3608	15.9995	0.80280	1.0:0.0:0.0:0.0	.	491;463	B7ZL91;Q16819	.;MEP1A_HUMAN	G	463	ENSP00000230588:E463G	ENSP00000230588:E463G	E	+	2	0	MEP1A	46909013	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	9.339000	0.96797	2.186000	0.69663	0.528000	0.53228	GAG	.		0.498	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		G	46801054	A	G	46801054	3	3	78	1	0	0	0	0	1	0	0	0	9500	304	11	3	1430	3	MEP1A	6	46801054	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	44870667	46801054	124314013	15	7273											
OPN5	221391	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	47754339	47754339	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgctgaaataatgactatCaatttagcagtctgtgatct	12	13	7	9	1	3	3	1	3	2	0	3	3	3	3	1	0	1	2	1	0	5	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:47754339C>A	ENST00000371211.2	+	2	247	c.219C>A	c.(217-219)atC>atA	p.I73I	OPN5_ENST00000489301.2_Silent_p.I73I|OPN5_ENST00000393699.2_Silent_p.I73I	NM_181744.3	NP_859528.1	Q6U736	OPN5_HUMAN	opsin 5	73					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.I73I(1)		endometrium(1)|large_intestine(3)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	29						TAATGACTATCAATTTAGCAG	0.403																																					p.I73I	Melanoma(28;740 973 10870 42660 45347)	.											.	OPN5-69	1	Substitution - coding silent(1)	lung(1)	c.C219A						.						139	128	132					6																	47754339		2203	4300	6503	SO:0001819	synonymous_variant	221391	exon2			GACTATCAATTTA	AY288419	CCDS4923.1	6p12.3	2012-08-08	2004-01-23		ENSG00000124818	ENSG00000124818		"GPCR / Class A : Opsin receptors"	19992	protein-coding gene	gene with protein product	"neuropsin"	609042	"transmembrane protein 13"	TMEM13		14623103, 14623098	Standard	NR_033806		Approved	neuropsin, dJ402H5.1	uc003ozc.3	Q6U736	OTTHUMG00000014803	ENST00000371211.2:c.219C>A	6.37:g.47754339C>A		Somatic	137	1		WXS	Illumina HiSeq	Phase_I	123	43	NM_181744	0	0	0	0	0	A0AV33|Q5T5B9|Q5T886|Q7Z603|Q86SL5	Silent	SNP	ENST00000371211.2	37	CCDS4923.1																																																																																			.		0.403	OPN5-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359451.1	NM_181744		A	47754339	C	A	47754339	2	1	78	1	0	0	0	0	0	0	0	1	10909	816	29	4		4	OPN5	6	47754339	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	953285	47754339	123360728	16	7274											
KLHL31	401265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	53517013	53517013	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcgaggccaggcttccttCtgcgttgcggccgcccgcgg	3	7	15	16	6	1	0	0	0	1	0	2	1	2	0	4	4	3	2	4	4	0	3			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:53517013C>T	ENST00000407079.1	-	2	1287	c.1288G>A	c.(1288-1290)Gaa>Aaa	p.E430K	KLHL31_ENST00000370905.3_Missense_Mutation_p.E430K			Q9H511	KLH31_HUMAN	kelch-like family member 31	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					AGGCTTCCTTCTGCGTTGCGG	0.662																																					p.E430K		.											.	KLHL31-23	0			c.G1288A						.						48	49	49					6																	53517013		2203	4299	6502	SO:0001583	missense	401265	exon3			TTCCTTCTGCGTT		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"Kelch-like", "BTB/POZ domain containing"	21353	protein-coding gene	gene with protein product		610749	"kelch repeat and BTB (POZ) domain containing 1", "kelch-like 31 (Drosophila)"	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1288G>A	6.37:g.53517013C>T	ENSP00000384644:p.Glu430Lys	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	96	35	NM_001003760	0	0	1	1	0	A6N9J2|B2RP49	Missense_Mutation	SNP	ENST00000407079.1	37	CCDS34478.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.636551	0.47049	.	.	ENSG00000124743	ENST00000370905;ENST00000407079	T;T	0.78924	-1.22;-1.22	5.69	4.81	0.61882	Galactose oxidase, beta-propeller (1);	0.045766	0.85682	D	0.000000	T	0.50480	0.1618	L	0.38531	1.155	0.53005	D	0.999961	B	0.17465	0.022	B	0.15870	0.014	T	0.54814	-0.8237	10	0.07030	T	0.85	.	16.5527	0.84476	0.0:0.8693:0.1307:0.0	.	430	Q9H511	KLH31_HUMAN	K	430	ENSP00000359942:E430K;ENSP00000384644:E430K	ENSP00000359942:E430K	E	-	1	0	KLHL31	53624972	0.999000	0.42202	0.077000	0.20336	0.797000	0.45037	7.800000	0.85949	1.367000	0.46095	0.650000	0.86243	GAA	.		0.662	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760		T	53517013	C	T	53517013	3	4	78	1	0	0	0	0	1	0	0	0	8406	922	32	2	620	2	KLHL31	6	53517013	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	5762674	53517013	117598054	17	7275											
COL19A1	1310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	70639518	70639518	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taattgcgaggaggcagactGatgaaaaggacactgtggat	14	8	14	5	1	0	3	0	2	0	1	0	7	0	6	0	4	1	1	0	4	3	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:70639518G>T	ENST00000322773.4	+	6	694	c.592G>T	c.(592-594)Gat>Tat	p.D198Y		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	198	Laminin G-like.				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GAGGCAGACTGATGAAAAGGA	0.423																																					p.D198Y		.											.	COL19A1-156	0			c.G592T						.						111	106	108					6																	70639518		2203	4300	6503	SO:0001583	missense	1310	exon6			CAGACTGATGAAA		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.592G>T	6.37:g.70639518G>T	ENSP00000316030:p.Asp198Tyr	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	93	16	NM_001858	0	0	0	0	0	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	3.418	-0.118699	0.06838	.	.	ENSG00000082293	ENST00000322773	T	0.02525	4.26	5.64	3.86	0.44501	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.564051	0.17635	N	0.167232	T	0.01800	0.0057	L	0.50333	1.59	0.80722	D	1	P	0.52842	0.956	B	0.41723	0.365	T	0.57648	-0.7775	10	0.66056	D	0.02	.	11.8431	0.52366	0.1408:0.0:0.8592:0.0	.	198	Q14993	COJA1_HUMAN	Y	198	ENSP00000316030:D198Y	ENSP00000316030:D198Y	D	+	1	0	COL19A1	70696239	0.997000	0.39634	0.001000	0.08648	0.020000	0.10135	5.263000	0.65507	0.732000	0.32470	0.655000	0.94253	GAT	.		0.423	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			T	70639518	G	T	70639518	3	4	78	1	0	0	0	0	1	0	0	0	3682	1290	45	4	610	4	COL19A1	6	70639518	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	17122505	70639518	100475549	18	7276											
STX11	8676	broad.mit.edu	37	chr6	144507993	144507993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccgcttcctcacgtccatgCggcgcctcagcagcatcaag	7	7	9	18	4	3	0	3	0	0	0	5	0	5	0	4	1	3	3	4	1	1	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:144507993C>T	ENST00000367568.4	+	2	412	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W		NM_003764.3	NP_003755.2	O75558	STX11_HUMAN	syntaxin 11	77					cytotoxic T cell degranulation (GO:0043316)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|natural killer cell degranulation (GO:0043320)|neutrophil degranulation (GO:0043312)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	SNAP receptor activity (GO:0005484)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	12				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		CACGTCCATGCGGCGCCTCAG	0.627									Familial Hemophagocytic Lymphohistiocytosis																												p.R77W													.	STX11-91	0			c.C229T						.						31	30	30					6																	144507993		2203	4300	6503	SO:0001583	missense	8676	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TCCATGCGGCGCC	AF044309	CCDS5205.1	6q24.1	2014-09-17			ENSG00000135604	ENSG00000135604			11429	protein-coding gene	gene with protein product		605014				9553086	Standard	NM_003764		Approved		uc003qks.4	O75558	OTTHUMG00000015739	ENST00000367568.4:c.229C>T	6.37:g.144507993C>T	ENSP00000356540:p.Arg77Trp	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	34	4	NM_003764	0	0	8	8	0	E1P598|O75378|O95148|Q5TCL6	Missense_Mutation	SNP	ENST00000367568.4	37	CCDS5205.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419397	0.62622	.	.	ENSG00000135604	ENST00000367568	T	0.17854	2.25	5.99	3.22	0.36961	t-SNARE (1);Syntaxin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.35595	0.0937	M	0.84433	2.695	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	T	0.46992	-0.9151	10	0.87932	D	0	-35.3942	15.3757	0.74602	0.3632:0.6368:0.0:0.0	.	77	O75558	STX11_HUMAN	W	77	ENSP00000356540:R77W	ENSP00000356540:R77W	R	+	1	2	STX11	144549686	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	1.928000	0.40104	0.400000	0.25396	-0.181000	0.13052	CGG	.		0.627	STX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042544.1			T	144507993	C	T	144507993	3	4	78	1	0	0	0	0	1	0	0	0	15369	759	27	1	231	1	STX11	6	144507993	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	73868475	144507993	26607074	19	7277											
SKAP2	8935	bcgsc.ca	37	chr7	26765601	26765601	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catctttgggagaagctgctGtaaactaatataaaacaaac	17	10	7	7	0	1	1	0	0	1	1	1	2	1	1	0	1	5	3	0	1	8	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr7:26765601G>C	ENST00000345317.2	-	8	912	c.599C>G	c.(598-600)aCa>aGa	p.T200R	SKAP2_ENST00000489977.1_5'UTR|SKAP2_ENST00000539623.1_Missense_Mutation_p.T28R	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	200	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						AGAAGCTGCTGTAAACTAATA	0.318																																					p.T200R													.	SKAP2-91	0			c.C599G						.						68	67	67					7																	26765601		2203	4299	6502	SO:0001583	missense	8935	exon8			GCTGCTGTAAACT		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.599C>G	7.37:g.26765601G>C	ENSP00000005587:p.Thr200Arg	Somatic	57	0		WXS	Illumina HiSeq	Phase_1	75	4	NM_003930	0	0	0	0	0	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	37	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.319068	0.60524	.	.	ENSG00000005020	ENST00000345317;ENST00000539623;ENST00000535331	T;T	0.11277	2.79;2.79	6.03	6.03	0.97812	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.141470	0.64402	D	0.000004	T	0.25158	0.0611	L	0.31804	0.96	0.46586	D	0.999119	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	T	0.00389	-1.1770	10	0.39692	T	0.17	-17.1783	20.5666	0.99351	0.0:0.0:1.0:0.0	.	185;200	B7Z5N4;O75563	.;SKAP2_HUMAN	R	200;28;185	ENSP00000005587:T200R;ENSP00000443593:T28R	ENSP00000005587:T200R	T	-	2	0	SKAP2	26732126	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.778000	0.75043	2.854000	0.98071	0.655000	0.94253	ACA	.		0.318	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			C	26765601	G	C	26765601	3	2	78	1	0	0	0	0	1	0	0	0	14388	1377	48	4	500	4	SKAP2	7	26765601	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		26765601	132373062	20	7278											
TXNDC3	51314	broad.mit.edu	37	chr7	37927910	37927910	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agtttgcgatggacagtttgCcggtcaaccagttgtatggc	8	12	13	8	2	1	0	1	0	0	0	1	2	1	1	2	3	3	4	2	3	2	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr7:37927910C>T	ENST00000199447.4	+	15	1651	c.1279C>T	c.(1279-1281)Ccg>Tcg	p.P427S	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.P427S	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	427	NDK 2.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										GGACAGTTTGCCGGTCAACCA	0.368																																					p.P427S													.	.	0			c.C1279T						.						98	96	96					7																	37927910		2203	4300	6503	SO:0001583	missense	51314	exon15			AGTTTGCCGGTCA	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 2"	607421	"thioredoxin domain containing 3 (spermatozoa)"	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1279C>T	7.37:g.37927910C>T	ENSP00000199447:p.Pro427Ser	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	141	4	NM_016616	0	0	1	1	0	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.001785	0.35320	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.52057	0.68;0.68	4.42	4.42	0.53409	.	0.957326	0.08619	N	0.918683	T	0.55721	0.1938	L	0.43554	1.36	0.32934	D	0.517549	P	0.38677	0.642	P	0.51550	0.673	T	0.54091	-0.8345	10	0.34782	T	0.22	-13.8286	12.7452	0.57278	0.0:0.8337:0.1663:0.0	.	427	Q8N427	TXND3_HUMAN	S	427	ENSP00000199447:P427S;ENSP00000397063:P427S	ENSP00000199447:P427S	P	+	1	0	TXNDC3	37894435	0.562000	0.26586	0.835000	0.33067	0.035000	0.12851	2.365000	0.44196	2.758000	0.94735	0.563000	0.77884	CCG	.		0.368	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		T	37927910	C	T	37927910	3	4	78	1	0	0	0	0	1	0	0	0	16831	739	26	2	1329	2	TXNDC3	7	37927910	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	11162309	37927910	121210753	21	7279											
PTPRZ1	5803	broad.mit.edu	37	chr7	121652844	121652844	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagtttttgatgtgtcgccTacttctcatatgcactctgc	6	16	7	12	1	2	1	1	1	2	0	4	1	2	1	2	0	3	2	2	0	2	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr7:121652844T>C	ENST00000393386.2	+	12	4155	c.3744T>C	c.(3742-3744)ccT>ccC	p.P1248P	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1248					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ATGTGTCGCCTACTTCTCATA	0.368																																					p.P1248P													.	PTPRZ1-699	0			c.T3744C						.						138	138	138					7																	121652844		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			GTCGCCTACTTCT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3744T>C	7.37:g.121652844T>C		Somatic	331	0		WXS	Illumina HiSeq	Phase_I	274	4	NM_002851	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			.		0.368	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121652844	T	C	121652844	2	2	78	1	0	0	0	0	0	0	0	1	12846	1509	53	3		3	PTPRZ1	7	121652844	Silent	SNP	T	TCGA-BQ-5894-01A-11D-1589-08	83724934	121652844	37485819	22	7280											
INSIG1	3638	hgsc.bcm.edu	37	chr7	155090012	155090012	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accgatgcccagattgcacgAccacttctggagctgctcct	8	9	9	15	2	1	1	0	0	1	1	2	4	2	2	4	1	4	3	4	1	0	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr7:155090012A>C	ENST00000340368.4	+	2	228	c.17A>C	c.(16-18)gAc>gCc	p.D6A	INSIG1_ENST00000342407.5_Missense_Mutation_p.D6A|INSIG1_ENST00000344756.4_Missense_Mutation_p.D6A|AC144652.1_ENST00000609974.1_lincRNA	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1	6					cell proliferation (GO:0008283)|cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|metabolic process (GO:0008152)|middle ear morphogenesis (GO:0042474)|negative regulation of cargo loading into COPII-coated vesicle (GO:1901303)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)				endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGATTGCACGACCACTTCTGG	0.652																																					p.D6A		.											.	INSIG1-90	0			c.A17C						.						8	10	9					7																	155090012		2175	4239	6414	SO:0001583	missense	3638	exon2			TGCACGACCACTT		CCDS5938.1, CCDS5939.1	7q36	2008-07-18			ENSG00000186480	ENSG00000186480			6083	protein-coding gene	gene with protein product	"INSIG-1 membrane protein"	602055				9268630	Standard	NM_005542		Approved	CL-6, MGC1405	uc003wly.3	O15503	OTTHUMG00000151330	ENST00000340368.4:c.17A>C	7.37:g.155090012A>C	ENSP00000344741:p.Asp6Ala	Somatic	8	1		WXS	Illumina HiSeq	Phase_I	19	4	NM_198337	0	0	4	5	1	A4D2N1|A8K6L0|Q53XW8|Q9BUV5	Missense_Mutation	SNP	ENST00000340368.4	37	CCDS5938.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.154191	0.57259	.	.	ENSG00000186480	ENST00000340368;ENST00000344756;ENST00000425172;ENST00000342407	T;T;T;T	0.54479	0.64;0.57;0.71;0.67	4.16	3.0	0.34707	.	0.365887	0.29684	N	0.011466	T	0.40619	0.1124	L	0.46157	1.445	0.23747	N	0.996956	B;B;B	0.34103	0.419;0.437;0.075	B;B;B	0.30572	0.117;0.115;0.04	T	0.35525	-0.9785	10	0.66056	D	0.02	.	6.695	0.23193	0.7991:0.0:0.2009:0.0	.	6;6;6	F5H6P3;A4D2N1;O15503	.;.;INSI1_HUMAN	A	6	ENSP00000344741:D6A;ENSP00000340010:D6A;ENSP00000414691:D6A;ENSP00000344035:D6A	ENSP00000344741:D6A	D	+	2	0	INSIG1	154720945	0.986000	0.35501	0.996000	0.52242	0.790000	0.44656	2.698000	0.47068	0.483000	0.27608	0.397000	0.26171	GAC	.		0.652	INSIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322244.3	NM_198336		C	155090012	A	C	155090012	3	2	78	1	0	0	0	0	1	0	0	0	7786	275	10	5	19	5	INSIG1	7	155090012	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	33437168	155090012	4048651	23	7281											
EPPK1	83481	broad.mit.edu	37	chr8	144940741	144940741	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcgggcaccaggacgccCgcgatgcagctggtgccctc	5	6	15	15	4	0	0	0	0	0	0	1	2	0	1	3	4	3	3	3	4	0	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr8:144940741C>T	ENST00000525985.1	-	2	6752	c.6681G>A	c.(6679-6681)gcG>gcA	p.A2227A				P58107	EPIPL_HUMAN	epiplakin 1	2227						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCAGGACGCCCGCGATGCAGC	0.677																																					p.A2227A													.	EPPK1-25	0			c.G6681A						.						76	80	78					8																	144940741		2150	4229	6379	SO:0001819	synonymous_variant	83481	exon1			GACGCCCGCGATG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6681G>A	8.37:g.144940741C>T		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	133	4	NM_031308	0	0	2	2	0	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				.		0.677	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144940741	C	T	144940741	2	4	78	1	0	0	0	0	0	0	0	1	5203	639	23	1		1	EPPK1	8	144940741	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		144940741	1423281	24	7282											
KIAA2026	158358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	5922386	5922386	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcctgcctcactctggcTagtcttaactgatggtgtta	6	17	8	10	0	3	1	1	1	2	0	4	1	4	1	2	2	2	2	2	2	3	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr9:5922386T>G	ENST00000399933.3	-	8	3609	c.3610A>C	c.(3610-3612)Agc>Cgc	p.S1204R	KIAA2026_ENST00000381461.2_Missense_Mutation_p.S1174R	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1204										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TCACTCTGGCTAGTCTTAACT	0.453																																					p.S1204R		.											.	KIAA2026-92	0			c.A3610C						.						115	112	113					9																	5922386		2013	4183	6196	SO:0001583	missense	158358	exon8			TCTGGCTAGTCTT	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3610A>C	9.37:g.5922386T>G	ENSP00000382815:p.Ser1204Arg	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	97	32	NM_001017969	0	0	1	3	2	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	37		.	.	.	.	.	.	.	.	.	.	T	14.67	2.603738	0.46423	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.99	4.99	0.66335	.	0.365571	0.26975	N	0.021550	T	0.30665	0.0772	L	0.27053	0.805	0.28046	N	0.933557	P	0.35908	0.527	B	0.35470	0.203	T	0.32214	-0.9915	9	0.62326	D	0.03	-2.703	11.277	0.49172	0.1362:0.0:0.0:0.8638	.	1204	Q5HYC2	K2026_HUMAN	R	1204;1174	.	ENSP00000370870:S1174R	S	-	1	0	KIAA2026	5912386	0.984000	0.35163	0.997000	0.53966	0.663000	0.39108	3.354000	0.52254	2.102000	0.63906	0.454000	0.30748	AGC	.		0.453	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5922386	T	G	5922386	3	3	78	1	0	0	0	0	1	0	0	0	8291	1522	53	5	2705	5	KIAA2026	9	5922386	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08		5922386	135291045	25	7283											
GTF3C5	9328	broad.mit.edu	37	chr9	135919313	135919313	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgaccagagacccagcaccGgtaaggcccccctccatgca	10	3	9	19	2	0	1	0	0	0	1	1	3	1	1	8	2	2	3	8	2	1	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr9:135919313G>A	ENST00000372097.5	+	3	895	c.572G>A	c.(571-573)cGg>cAg	p.R191Q	GTF3C5_ENST00000342018.8_Splice_Site_p.R191Q|GTF3C5_ENST00000372108.5_Splice_Site_p.R191Q|GTF3C5_ENST00000372099.6_Splice_Site_p.R182Q|GTF3C5_ENST00000485692.1_3'UTR|GTF3C5_ENST00000372095.5_Splice_Site_p.R66Q	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	191					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		ACCCAGCACCGGTAAGGCCCC	0.622																																					p.R191Q													.	GTF3C5-90	0			c.G572A						.						46	51	49					9																	135919313		2203	4300	6503	SO:0001630	splice_region_variant	9328	exon3			AGCACCGGTAAGG	AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"General transcription factors"	4668	protein-coding gene	gene with protein product	"transcription factor IIIC, 63 kD"	604890	"general transcription factor IIIC, polypeptide 5 (63kD)"			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	ENST00000372097.5:c.572+1G>A	9.37:g.135919313G>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	124	3	NM_012087	0	0	1	1	0	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation	SNP	ENST00000372097.5	37	CCDS6958.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707924	0.89018	.	.	ENSG00000148308	ENST00000372097;ENST00000440319;ENST00000372099;ENST00000372095;ENST00000372089;ENST00000372108;ENST00000342018;ENST00000439697	T;T;T;T	0.45668	0.9;0.9;0.89;0.9	4.98	4.98	0.66077	.	0.262185	0.34314	N	0.004064	T	0.60314	0.2259	M	0.62723	1.935	0.47276	D	0.999371	D;D;D	0.76494	0.995;0.997;0.999	P;P;D	0.65874	0.828;0.809;0.939	T	0.58769	-0.7578	10	0.36615	T	0.2	0.7009	17.2419	0.87015	0.0:0.0:1.0:0.0	.	66;191;191	B7Z1V3;Q9Y5Q8-3;Q9Y5Q8	.;.;TF3C5_HUMAN	Q	191;144;182;66;41;191;191;66	ENSP00000361169:R191Q;ENSP00000361171:R182Q;ENSP00000361180:R191Q;ENSP00000339530:R191Q	ENSP00000339530:R191Q	R	+	2	0	GTF3C5	134909134	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	4.436000	0.59948	2.282000	0.76494	0.563000	0.77884	CGG	.		0.622	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823	Missense_Mutation	A	135919313	G	A	135919313	5	1	78	1	0	0	0	0	0	0	1	0	6897	1130	39	1	582	1	GTF3C5	9	135919313	Splice_Site	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	129996927	135919313	5294118	26	7284											
STAM	8027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	17747670	17747670	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttaatgaacgaagatccgaTgtattccatgtatgcaaagt	14	12	9	6	2	0	2	0	1	0	1	2	4	2	2	2	0	2	4	2	0	6	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr10:17747670T>A	ENST00000377524.3	+	12	1354	c.1139T>A	c.(1138-1140)aTg>aAg	p.M380K	STAM_ENST00000540523.1_Missense_Mutation_p.M269K	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	380	ITAM.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						GAAGATCCGATGTATTCCATG	0.368																																					p.M380K		.											.	STAM-154	0			c.T1139A						.						160	153	156					10																	17747670		2203	4300	6503	SO:0001583	missense	8027	exon12			ATCCGATGTATTC	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1139T>A	10.37:g.17747670T>A	ENSP00000366746:p.Met380Lys	Somatic	228	0		WXS	Illumina HiSeq	Phase_I	166	48	NM_003473	0	0	9	17	8	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	37	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.077571	0.55753	.	.	ENSG00000136738	ENST00000377524;ENST00000540523	T;T	0.38722	1.47;1.12	5.64	4.49	0.54785	.	0.132590	0.64402	D	0.000002	T	0.33089	0.0851	L	0.48642	1.525	0.52501	D	0.999957	P;B	0.36048	0.534;0.173	B;B	0.32211	0.142;0.031	T	0.11494	-1.0585	10	0.28530	T	0.3	-5.6897	11.8463	0.52387	0.0:0.0697:0.0:0.9303	.	269;380	B4DZT2;Q92783	.;STAM1_HUMAN	K	380;269	ENSP00000366746:M380K;ENSP00000438073:M269K	ENSP00000366746:M380K	M	+	2	0	STAM	17787676	1.000000	0.71417	0.968000	0.41197	0.992000	0.81027	7.698000	0.84413	2.152000	0.67230	0.533000	0.62120	ATG	.		0.368	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		A	17747670	T	A	17747670	3	1	78	1	0	0	0	0	1	0	0	0	15280	1464	51	5	1185	5	STAM	10	17747670	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08		17747670	117787077	27	7285											
C10orf2	56652	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102750271	102750271	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgacaacctgcagttcatGatgggtcacgagcagctgtc	10	9	11	11	2	2	1	2	1	0	0	4	3	2	1	1	1	4	4	1	1	1	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr10:102750271G>T	ENST00000311916.2	+	3	1748	c.1563G>T	c.(1561-1563)atG>atT	p.M521I	C10orf2_ENST00000473656.1_3'UTR|MRPL43_ENST00000477279.1_5'Flank|MRPL43_ENST00000318364.8_5'Flank|C10orf2_ENST00000370228.1_Missense_Mutation_p.M521I|MRPL43_ENST00000342071.1_5'Flank	NM_001163813.1|NM_021830.4	NP_001157285.1|NP_068602.2	Q96RR1	PEO1_HUMAN	chromosome 10 open reading frame 2	521	SF4 helicase. {ECO:0000255|PROSITE- ProRule:PRU00596}.				cell death (GO:0008219)|DNA unwinding involved in DNA replication (GO:0006268)|mitochondrial DNA replication (GO:0006264)|protein hexamerization (GO:0034214)|protein homooligomerization (GO:0051260)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial nucleoid (GO:0042645)	5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|stomach(1)	24		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TGCAGTTCATGATGGGTCACG	0.493																																					p.M521I		.											.	C10orf2-69	0			c.G1563T						.						215	182	193					10																	102750271		2203	4300	6503	SO:0001583	missense	56652	exon3			GTTCATGATGGGT	AF292004	CCDS7506.1, CCDS53570.1	10q24	2013-05-13			ENSG00000107815	ENSG00000107815			1160	protein-coding gene	gene with protein product	"twinkle", "T7 helicase-related protein with intramitochondrial nucleoid localization"	606075	"infantile onset spinocerebellar ataxia (autosomal recessive)"	IOSCA		11431692, 10645945, 16135556	Standard	NM_021830		Approved	PEO, PEO1, TWINKLE, FLJ21832, TWINL	uc001ksf.2	Q96RR1	OTTHUMG00000018917	ENST00000311916.2:c.1563G>T	10.37:g.102750271G>T	ENSP00000309595:p.Met521Ile	Somatic	250	1		WXS	Illumina HiSeq	Phase_I	230	76	NM_021830	0	0	9	26	17	B2CQL2|Q6MZX2|Q6PJP5|Q96RR0	Missense_Mutation	SNP	ENST00000311916.2	37	CCDS7506.1	.	.	.	.	.	.	.	.	.	.	G	34	5.341268	0.95783	.	.	ENSG00000107815	ENST00000311916;ENST00000370228	D;D	0.93547	-3.24;-3.24	5.73	5.73	0.89815	Circadian clock protein KaiC/DNA repair protein RadA (1);DNA helicase, DnaB-like, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96436	0.8837	M	0.76574	2.34	0.80722	D	1	D;P	0.67145	0.996;0.587	D;P	0.75484	0.986;0.608	D	0.95117	0.8243	10	0.36615	T	0.2	-17.5845	18.8559	0.92252	0.0:0.0:1.0:0.0	.	521;521	Q96RR1-2;Q96RR1	.;PEO1_HUMAN	I	521	ENSP00000309595:M521I;ENSP00000359248:M521I	ENSP00000309595:M521I	M	+	3	0	C10orf2	102740261	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.868000	0.98415	0.557000	0.71058	ATG	.		0.493	C10orf2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049886.1	NM_021830		T	102750271	G	T	102750271	3	4	78	1	0	0	0	0	1	0	0	0	1601	1290	45	4	1573	4	C10orf2	10	102750271	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	85002601	102750271	32784476	28	7286											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092813	1092813	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcccatcaccaccaccacCacggtgaccccaaccccaac	12	3	3	23	1	1	1	1	1	0	0	2	1	2	1	9	1	2	0	9	1	2	0	rs12577898|rs199900755		TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:1092813C>T	ENST00000441003.2	+	30	4659	c.4632C>T	c.(4630-4632)acC>acT	p.T1544T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1545T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccaccacGGTGACCC	0.637																																					p.T1544T		.											.	MUC2-90	0			c.C4632T						.						47	95	78					11																	1092813		1759	3190	4949	SO:0001819	synonymous_variant	4583	exon30			CACCACCACGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4632C>T	11.37:g.1092813C>T		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092813	C	T	1092813	2	4	78	1	0	0	0	0	0	0	0	1	10000	581	21	2		2	MUC2	11	1092813	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		1092813	133913703	29	7287											
OR52N5	390075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	5799428	5799428	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccttggcaatgatagggttgGtgagtgtggtagcataacgc	9	11	15	6	1	0	2	0	2	0	0	0	2	0	2	1	4	2	4	1	4	4	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:5799428G>T	ENST00000317093.2	-	1	469	c.437C>A	c.(436-438)aCc>aAc	p.T146N	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GATAGGGTTGGTGAGTGTGGT	0.507																																					p.T146N		.											.	OR52N5-70	0			c.C437A						.						146	115	126					11																	5799428		2125	4095	6220	SO:0001583	missense	390075	exon1			GGGTTGGTGAGTG	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"GPCR / Class A : Olfactory receptors"	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.437C>A	11.37:g.5799428G>T	ENSP00000322866:p.Thr146Asn	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	34	11	NM_001001922	0	0	0	0	0	B9EH12|Q6IFG2	Missense_Mutation	SNP	ENST00000317093.2	37	CCDS31397.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.245082	0.39697	.	.	ENSG00000181009	ENST00000317093	T	0.01051	5.4	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31697	U	0.007215	T	0.04048	0.0113	L	0.50919	1.6	0.38487	D	0.947868	D	0.62365	0.991	D	0.65010	0.931	T	0.54715	-0.8252	10	0.51188	T	0.08	.	14.1011	0.65056	0.0:0.0:1.0:0.0	.	146	Q8NH56	O52N5_HUMAN	N	146	ENSP00000322866:T146N	ENSP00000322866:T146N	T	-	2	0	OR52N5	5756004	0.994000	0.37717	0.771000	0.31576	0.554000	0.35429	2.842000	0.48230	1.952000	0.56665	0.494000	0.49563	ACC	.		0.507	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922		T	5799428	G	T	5799428	3	4	78	1	0	0	0	0	1	0	0	0	11156	1261	44	4	541	4	OR52N5	11	5799428	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	4706615	5799428	129207088	30	7288											
ACCSL	390110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	44073203	44073203	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctcatgtgttgtcttcagGtggtggttctaaatggctgc	5	16	12	8	0	4	0	2	0	3	0	5	0	4	0	0	4	1	3	0	4	2	4	rs200162550	byFrequency	TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:44073203G>T	ENST00000378832.1	+	5	762	c.706G>T	c.(706-708)Gtg>Ttg	p.V236L		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	236					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						TTGTCTTCAGGTGGTGGTTCT	0.532																																					p.V236L		.											.	ACCSL-95	0			c.G706T						.						318	308	311					11																	44073203		2094	4207	6301	SO:0001630	splice_region_variant	390110	exon5			CTTCAGGTGGTGG		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.706-1G>T	11.37:g.44073203G>T		Somatic	476	1		WXS	Illumina HiSeq	Phase_I	415	54	NM_001031854	0	0	0	0	0		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.624524	0.66901	.	.	ENSG00000205126	ENST00000378832	D	0.92965	-3.14	4.62	4.62	0.57501	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.90710	0.7085	L	0.43554	1.36	0.80722	D	1	P	0.44946	0.846	P	0.47786	0.557	D	0.89650	0.3869	9	.	.	.	-22.261	15.014	0.71570	0.0:0.0:1.0:0.0	.	236	Q4AC99	1A1L2_HUMAN	L	236	ENSP00000368109:V236L	.	V	+	1	0	ACCSL	44029779	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	7.516000	0.81772	2.392000	0.81423	0.563000	0.77884	GTG	G|0.998;A|0.002		0.532	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854	Missense_Mutation	T	44073203	G	T	44073203	5	4	78	1	0	0	0	0	0	0	1	0	134	1275	44	4	724	4	ACCSL	11	44073203	Splice_Site	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	38273775	44073203	90933313	31	7289											
DKFZp761E198	91056	hgsc.bcm.edu	37	chr11	65545368	65545368	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acggaggtagtcccccgccaGgggcagcacggcccagtcat	8	4	14	15	3	1	0	1	0	0	0	2	1	2	1	4	5	1	3	4	5	1	1	rs577605653	byFrequency	TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:65545368G>C	ENST00000532090.2	-	2	2806	c.2596C>G	c.(2596-2598)Ctg>Gtg	p.L866V		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	866					endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						TCCCCCGCCAGGGGCAGCACG	0.721													G|||	7	0.00139776	0	0.0101	5008	,	,		13832	0		0	False		,,,				2504	0				p.L866V		.											.	.	0			c.C2596G						.						6	7	7					11																	65545368		1919	4021	5940	SO:0001583	missense	91056	exon2			CCGCCAGGGGCAG	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.2596C>G	11.37:g.65545368G>C	ENSP00000454303:p.Leu866Val	Somatic	3	2		WXS	Illumina HiSeq	Phase_I	6	4	NM_138368	0	0	3	12	9	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Missense_Mutation	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			.		0.721	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368		C	65545368	G	C	65545368	3	2	78	1	0	0	0	0	1	0	0	0	4554	991	35	4	44	4	DKFZp761E198	11	65545368	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	21472165	65545368	69461148	32	7290											
BUD13	84811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	116633298	116633298	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagctgcttcttgtctccaAaatgggattttgcttgcttt	7	17	8	9	0	2	0	0	0	2	0	3	1	2	1	1	1	4	4	1	1	3	6			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:116633298A>G	ENST00000260210.4	-	4	1030	c.1007T>C	c.(1006-1008)tTt>tCt	p.F336S	BUD13_ENST00000375445.3_Intron	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	336					mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		CTTGTCTCCAAAATGGGATTT	0.443																																					p.F336S		.											.	BUD13-154	0			c.T1007C						.						134	120	125					11																	116633298		2201	4296	6497	SO:0001583	missense	84811	exon4			TCTCCAAAATGGG	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 71"		"BUD13 homolog (yeast)"			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.1007T>C	11.37:g.116633298A>G	ENSP00000260210:p.Phe336Ser	Somatic	267	0		WXS	Illumina HiSeq	Phase_I	213	66	NM_032725	0	0	6	20	14	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	37	CCDS8374.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.503865	0.44558	.	.	ENSG00000137656	ENST00000260210	T	0.16597	2.33	4.83	-1.94	0.07571	.	1.189750	0.05897	N	0.629384	T	0.12008	0.0292	L	0.31926	0.97	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.41502	-0.9505	10	0.87932	D	0	-0.611	3.4276	0.07416	0.4025:0.0:0.1998:0.3978	.	336;336	A8K4Z6;Q9BRD0	.;BUD13_HUMAN	S	336	ENSP00000260210:F336S	ENSP00000260210:F336S	F	-	2	0	BUD13	116138508	0.000000	0.05858	0.276000	0.24689	0.974000	0.67602	0.121000	0.15667	0.010000	0.14839	0.533000	0.62120	TTT	.		0.443	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725		G	116633298	A	G	116633298	3	3	78	1	0	0	0	0	1	0	0	0	1576	14	1	3	880	3	BUD13	11	116633298	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	51087930	116633298	18373218	33	7291											
EMG1	10162	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7084424	7084424	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtatcagatcactttccaGttggatgtatgaaagttggc	11	13	10	7	0	2	2	2	1	0	1	3	3	3	3	1	2	0	4	1	2	3	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr12:7084424G>A	ENST00000261407.4	-	0	2268				EMG1_ENST00000261406.6_Missense_Mutation_p.V168I|LPCAT3_ENST00000535021.1_5'Flank|EMG1_ENST00000546220.1_3'UTR	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						TCACTTTCCAGTTGGATGTAT	0.443																																					.													.	.	0			.						.						94	89	91					12																	7084424		1944	4152	6096	SO:0001628	intergenic_variant	10436	.			TTTCCAGTTGGAT	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"O-acyltransferase (membrane bound) domain containing 5", "membrane bound O-acyltransferase domain containing 5"	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970		12.37:g.7084424G>A		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	53	8	.	0	0	100	147	47	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Missense_Mutation	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																			.		0.443	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768		A	7084424	G	A	7084424	1	1	78	0	1	0	0	0	0	0	0	0	5103	1029	36	2		2	EMG1	12	7084424	IGR	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		7084424	126767471	34	7292											
C12orf51	283450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112694159	112694159	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgcgaagagcatctgctatCaaatctaaggtacaggcagc	13	9	10	9	1	3	1	1	0	2	1	3	2	3	1	0	2	5	4	0	2	5	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr12:112694159C>T	ENST00000430131.2	-	20	3141	c.1996G>A	c.(1996-1998)Gat>Aat	p.D666N	RP3-521E19.2_ENST00000547401.1_RNA|HECTD4_ENST00000550722.1_Missense_Mutation_p.D952N|HECTD4_ENST00000377560.5_Missense_Mutation_p.D916N			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	666					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CATCTGCTATCAAATCTAAGG	0.423																																					p.D954N		.											.	.	0			c.G2860A						.						126	129	128					12																	112694159		2203	4300	6503	SO:0001583	missense	283450	exon21			TGCTATCAAATCT	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.1996G>A	12.37:g.112694159C>T	ENSP00000404379:p.Asp666Asn	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	177	55	NM_001109662	0	0	0	0	0	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	C	36	5.948543	0.97134	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.65178	-0.02;0.0;-0.14	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.70919	0.3279	L	0.27053	0.805	0.58432	D	0.999995	D;D;D	0.67145	0.996;0.993;0.996	D;D;D	0.73708	0.981;0.971;0.981	T	0.73202	-0.4057	10	0.87932	D	0	.	19.4096	0.94665	0.0:1.0:0.0:0.0	.	666;666;666	Q9Y4D8-2;Q9Y4D8;Q9Y4D8-3	.;K0614_HUMAN;.	N	916;666;952	ENSP00000366783:D916N;ENSP00000404379:D666N;ENSP00000449784:D952N	ENSP00000366783:D916N	D	-	1	0	C12orf51	111178542	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.298000	0.78815	2.820000	0.97059	0.655000	0.94253	GAT	.		0.423	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112694159	C	T	112694159	3	4	78	1	0	0	0	0	1	0	0	0	1700	826	29	2	10218	2	C12orf51	12	112694159	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	105609735	112694159	21157736	35	7293											
TDRD3	81550	broad.mit.edu	37	chr13	61102844	61102844	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcagcatagtgatggtgcTtttaaaaaaagagataactc	15	12	8	6	0	1	2	1	1	1	1	3	3	1	2	0	1	3	2	0	1	6	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr13:61102844T>C	ENST00000196169.3	+	11	1994	c.1206T>C	c.(1204-1206)gcT>gcC	p.A402A	TDRD3_ENST00000377881.2_Silent_p.A402A|TDRD3_ENST00000377894.2_Silent_p.A402A|TDRD3_ENST00000535286.1_Silent_p.A495A	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	402					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GTGATGGTGCTTTTAAAAAAA	0.373																																					p.A495A	Colon(36;164 906 35820 50723)												.	TDRD3-516	0			c.T1485C						.						72	79	76					13																	61102844		2203	4300	6503	SO:0001819	synonymous_variant	81550	exon11			TGGTGCTTTTAAA	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.1206T>C	13.37:g.61102844T>C		Somatic	169	0		WXS	Illumina HiSeq	Phase_I	141	4	NM_001146070	0	0	2	2	0	B2MWP9|Q53XA6|Q6P992	Silent	SNP	ENST00000196169.3	37	CCDS9441.1																																																																																			.		0.373	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		C	61102844	T	C	61102844	2	2	78	1	0	0	0	0	0	0	0	1	15764	1596	56	3		3	TDRD3	13	61102844	Silent	SNP	T	TCGA-BQ-5894-01A-11D-1589-08		61102844	54067034	36	7294											
ING1	3621	hgsc.bcm.edu	37	chr13	111371943	111371943	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtccagcaaccacgaccaCgacgacggcgcctcgggcac	9	2	12	18	7	0	0	0	0	0	0	2	3	1	0	4	2	2	2	4	2	1	0			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr13:111371943C>G	ENST00000375774.3	+	2	1395	c.933C>G	c.(931-933)caC>caG	p.H311Q	ING1_ENST00000338450.7_Missense_Mutation_p.H124Q|ING1_ENST00000333219.7_Missense_Mutation_p.H168Q|ING1_ENST00000375775.3_Missense_Mutation_p.H99Q	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	311					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ACCACGACCACGACGACGGCG	0.657																																					p.H311Q		.											.	ING1-515	0			c.C933G						.						63	50	54					13																	111371943		2202	4300	6502	SO:0001583	missense	3621	exon2			CGACCACGACGAC		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"Zinc fingers, PHD-type"	6062	protein-coding gene	gene with protein product	"inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1"	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.933C>G	13.37:g.111371943C>G	ENSP00000364929:p.His311Gln	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_005537	0	0	26	26	0	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	37	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	C	0.059	-1.229151	0.01518	.	.	ENSG00000153487	ENST00000338450;ENST00000333219;ENST00000375775;ENST00000375774	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.26	-5.48	0.02592	.	0.354834	0.32258	N	0.006360	T	0.51244	0.1663	L	0.57536	1.79	0.27600	N	0.948993	D;P;D	0.67145	0.996;0.826;0.994	P;B;D	0.75484	0.826;0.415;0.986	T	0.54364	-0.8305	10	0.14252	T	0.57	-24.524	16.5209	0.84315	0.0:0.4147:0.0:0.5853	.	311;168;124	Q9UK53;Q5T9H0;Q9UK53-4	ING1_HUMAN;.;.	Q	124;168;99;311	ENSP00000345202:H124Q;ENSP00000328436:H168Q;ENSP00000364930:H99Q;ENSP00000364929:H311Q	ENSP00000328436:H168Q	H	+	3	2	ING1	110169944	0.000000	0.05858	0.379000	0.26080	0.180000	0.23129	-2.557000	0.00924	-1.139000	0.02881	0.491000	0.48974	CAC	.		0.657	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		G	111371943	C	G	111371943	3	3	78	1	0	0	0	0	1	0	0	0	7756	535	19	4	1087	4	ING1	13	111371943	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	50269099	111371943	3797935	37	7295											
FITM1	161247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24601751	24601751	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gctgcctgctcatggcagagGaagcagctgtgttcgccaag	8	8	14	11	1	1	1	1	0	0	1	2	2	1	2	2	2	4	6	2	2	2	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr14:24601751G>C	ENST00000267426.5	+	2	887	c.598G>C	c.(598-600)Gaa>Caa	p.E200Q	FITM1_ENST00000559294.1_Missense_Mutation_p.E4Q	NM_203402.2	NP_981947.1	A5D6W6	FITM1_HUMAN	fat storage-inducing transmembrane protein 1	200					lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						CATGGCAGAGGAAGCAGCTGT	0.652																																					p.E200Q		.											.	FITM1-68	0			c.G598C						.						64	56	58					14																	24601751		2203	4300	6503	SO:0001583	missense	161247	exon2			GCAGAGGAAGCAG		CCDS9611.1	14q12	2009-07-09			ENSG00000139914	ENSG00000139914			33714	protein-coding gene	gene with protein product	"fat-inducing transcript 1"	612028				18160536	Standard	NM_203402		Approved	FIT1	uc001wmf.2	A5D6W6	OTTHUMG00000133476	ENST00000267426.5:c.598G>C	14.37:g.24601751G>C	ENSP00000267426:p.Glu200Gln	Somatic	135	1		WXS	Illumina HiSeq	Phase_I	93	37	NM_203402	0	0	0	2	2	Q8IUQ7	Missense_Mutation	SNP	ENST00000267426.5	37	CCDS9611.1	.	.	.	.	.	.	.	.	.	.	g	15.81	2.943666	0.53079	.	.	ENSG00000139914	ENST00000267426	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.79707	0.4492	M	0.80183	2.485	0.54753	D	0.999984	D	0.69078	0.997	D	0.74023	0.982	T	0.82820	-0.0268	9	0.72032	D	0.01	1.4737	15.8474	0.78903	0.0:0.0:1.0:0.0	.	200	A5D6W6	FITM1_HUMAN	Q	200	.	ENSP00000267426:E200Q	E	+	1	0	FITM1	23671591	1.000000	0.71417	0.998000	0.56505	0.817000	0.46193	8.341000	0.90046	2.324000	0.78689	0.462000	0.41574	GAA	.		0.652	FITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257366.1	NM_203402		C	24601751	G	C	24601751	3	2	78	1	0	0	0	0	1	0	0	0	5917	1175	41	4	604	4	FITM1	14	24601751	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		24601751	82747789	38	7296											
ITGAL	3683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30507473	30507473	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccggctacccactcgggcGgtttggagaagccatcactg	7	7	12	15	3	1	1	1	0	0	1	2	2	1	1	4	4	2	2	4	4	2	2	rs199716730		TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr16:30507473G>A	ENST00000356798.6	+	14	1739	c.1559G>A	c.(1558-1560)cGg>cAg	p.R520Q	ITGAL_ENST00000568012.1_3'UTR|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Missense_Mutation_p.R437Q|RP11-297C4.1_ENST00000563751.1_RNA	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	520					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	CCACTCGGGCGGTTTGGAGAA	0.597													G|||	1	0.000199681	8e-04	0	5008	,	,		15112	0		0	False		,,,				2504	0				p.R520Q	NSCLC(110;1462 1641 3311 33990 49495)	.											.	ITGAL-994	0			c.G1559A						.	G	GLN/ARG,GLN/ARG	1,4393	2.1+/-5.4	0,1,2196	78	85	83		1310,1559	2.9	0.2	16		83	0,8600		0,0,4300	no	missense,missense	ITGAL	NM_001114380.1,NM_002209.2	43,43	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging,probably-damaging	437/1087,520/1171	30507473	1,12993	2197	4300	6497	SO:0001583	missense	3683	exon14			TCGGGCGGTTTGG		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"CD molecules", "Integrins"	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1559G>A	16.37:g.30507473G>A	ENSP00000349252:p.Arg520Gln	Somatic	209	1		WXS	Illumina HiSeq	Phase_I	244	31	NM_002209	0	0	7	7	0	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.18	2.159140	0.38119	2.28E-4	0.0	ENSG00000005844	ENST00000356798;ENST00000358164	T;T	0.26067	1.76;1.76	5.94	2.88	0.33553	.	0.401626	0.21542	N	0.072880	T	0.30916	0.0780	M	0.91196	3.185	0.46631	D	0.999137	P;P	0.49559	0.925;0.746	B;B	0.36244	0.22;0.185	T	0.28586	-1.0039	10	0.87932	D	0	.	6.6609	0.23014	0.1387:0.0:0.7177:0.1437	.	437;520	Q96HB1;P20701	.;ITAL_HUMAN	Q	520;437	ENSP00000349252:R520Q;ENSP00000350886:R437Q	ENSP00000349252:R520Q	R	+	2	0	ITGAL	30414974	0.700000	0.27796	0.186000	0.23195	0.007000	0.05969	3.438000	0.52871	0.384000	0.24942	0.563000	0.77884	CGG	G|0.999;A|0.001		0.597	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			A	30507473	G	A	30507473	3	1	78	1	0	0	0	0	1	0	0	0	7907	1116	39	1	1613	1	ITGAL	16	30507473	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		30507473	59847280	39	7297											
SLC12A3	6559	broad.mit.edu	37	chr16	56906659	56906659	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcttcttcccctcggccacAggcatcctggcaggggccaa	7	8	10	16	1	2	0	0	0	2	0	5	0	4	0	5	5	0	2	5	5	1	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr16:56906659A>G	ENST00000563236.1	+	8	1081	c.1056A>G	c.(1054-1056)acA>acG	p.T352T	SLC12A3_ENST00000438926.2_Silent_p.T352T|SLC12A3_ENST00000262502.5_Silent_p.T351T|SLC12A3_ENST00000566786.1_Silent_p.T351T			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	352					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CCTCGGCCACAGGCATCCTGG	0.562																																					p.T352T													.	SLC12A3-155	0			c.A1056G						.						77	69	72					16																	56906659		2198	4300	6498	SO:0001819	synonymous_variant	6559	exon8			GGCCACAGGCATC		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1056A>G	16.37:g.56906659A>G		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	98	3	NM_001126108	0	0	1	1	0	A8MSJ2|C9JNN9	Silent	SNP	ENST00000563236.1	37	CCDS58464.1																																																																																			.		0.562	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			G	56906659	A	G	56906659	2	3	78	1	0	0	0	0	0	0	0	1	14416	175	7	3		3	SLC12A3	16	56906659	Silent	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	26399186	56906659	33448094	40	7298											
PMFBP1	83449	broad.mit.edu	37	chr16	72158703	72158703	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaggttctcttttaaggcgGccatctcctcctggaactcc	6	12	10	13	1	2	0	0	0	2	0	6	2	4	2	4	5	1	1	4	5	2	3			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr16:72158703G>A	ENST00000537792.1	-	1	49	c.50C>T	c.(49-51)gCc>gTc	p.A17V	PMFBP1_ENST00000537465.1_Missense_Mutation_p.A856V|PMFBP1_ENST00000355636.6_Missense_Mutation_p.A706V|PMFBP1_ENST00000237353.10_Missense_Mutation_p.A851V			Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	856						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TTTTAAGGCGGCCATCTCCTC	0.572											OREG0023927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A851V													.	PMFBP1-92	0			c.C2552T						.						161	147	152					16																	72158703		2198	4300	6498	SO:0001583	missense	83449	exon17			AAGGCGGCCATCT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000537792.1:c.50C>T	16.37:g.72158703G>A	ENSP00000443366:p.Ala17Val	Somatic	240	1	1135	WXS	Illumina HiSeq	Phase_I	221	4	NM_031293	0	0	0	0	0	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000537792.1	37		.	.	.	.	.	.	.	.	.	.	G	7.010	0.556590	0.13436	.	.	ENSG00000118557	ENST00000537792;ENST00000537465;ENST00000237353;ENST00000355636	T;T;T;T	0.50277	0.75;2.6;2.59;2.59	5.09	0.423	0.16463	.	1.675920	0.03139	N	0.166374	T	0.37128	0.0992	L	0.34521	1.04	0.09310	N	1	B;B;B	0.32829	0.386;0.253;0.386	B;B;B	0.31337	0.124;0.128;0.124	T	0.23868	-1.0176	10	0.28530	T	0.3	3.1154	8.0291	0.30454	0.0:0.1483:0.3945:0.4571	.	856;851;856	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	V	17;856;851;706	ENSP00000443366:A17V;ENSP00000443817:A856V;ENSP00000237353:A851V;ENSP00000347854:A706V	ENSP00000237353:A851V	A	-	2	0	PMFBP1	70716204	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.551000	0.23361	0.257000	0.21650	0.655000	0.94253	GCC	.		0.572	PMFBP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000396523.1	NM_031293		A	72158703	G	A	72158703	3	1	78	1	0	0	0	0	1	0	0	0	12160	1203	42	2	551	2	PMFBP1	16	72158703	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	15252044	72158703	18196050	41	7299											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y	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	265	268					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	623	94		WXS	Illumina HiSeq		530	91	NM_145301	0	0	4	41	37	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		T	15457087	C	T	15457087	3	4	78	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		15457087	65738123	42	7300											
GPRC5C	55890	broad.mit.edu	37	chr17	72428210	72428210	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtcaacagcaacaaccCacacgccggcagggccagaa	14	1	11	15	2	1	1	1	0	0	1	1	1	1	1	3	3	4	3	3	3	4	0	rs138824950		TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr17:72428210C>G	ENST00000481232.1	+	1	544	c.33C>G	c.(31-33)ccC>ccG	p.P11P	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_5'Flank|GPRC5C_ENST00000392627.1_Silent_p.P11P			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	0					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						AGCAACAACCCACACGCCGGC	0.687																																					p.P11P													.	GPRC5C-525	0			c.C33G						.						42	41	41					17																	72428210		2201	4299	6500	SO:0001819	synonymous_variant	55890	exon1			ACAACCCACACGC	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"GPCR / Class C : Orphans"	13309	protein-coding gene	gene with protein product		605949	"G protein-coupled receptor, family C, group 5, member C"			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000481232.1:c.33C>G	17.37:g.72428210C>G		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_022036	0	0	32	49	17	B5BUN4|Q2NL85|Q9NZG5	Silent	SNP	ENST00000481232.1	37																																																																																				C|1.000;T|0.000		0.687	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000145095.2			G	72428210	C	G	72428210	2	3	78	1	0	0	0	0	0	0	0	1	6747	581	21	4		4	GPRC5C	17	72428210	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	56971123	72428210	8767000	43	7301											
WDR45L	56270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80579499	80579499	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttactttctcggatgcagTtgcaattcttgttccctgca	7	16	7	11	1	2	0	0	0	2	0	4	1	3	1	1	1	4	5	1	1	2	6			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr17:80579499T>C	ENST00000392325.4	-	6	798	c.604A>G	c.(604-606)Act>Gct	p.T202A	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	202																	TCGGATGCAGTTGCAATTCTT	0.542																																					p.T202A		.											.	.	0			c.A604G						.						127	97	107					17																	80579499		2203	4300	6503	SO:0001583	missense	56270	exon6			ATGCAGTTGCAAT	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"WD repeat domain containing"	25072	protein-coding gene	gene with protein product		609226	"WDR45-like"	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.604A>G	17.37:g.80579499T>C	ENSP00000376139:p.Thr202Ala	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	81	11	NM_019613	0	0	47	68	21	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	37	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618375	0.66787	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.57907	0.37	4.82	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81327	0.4799	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87771	0.2605	10	0.72032	D	0.01	-25.7216	14.6708	0.68942	0.0:0.0:0.0:1.0	.	202	Q5MNZ6	WIPI3_HUMAN	A	202;174	ENSP00000376139:T202A	ENSP00000376139:T202A	T	-	1	0	WDR45L	78172788	1.000000	0.71417	0.910000	0.35882	0.534000	0.34807	7.503000	0.81632	1.935000	0.56089	0.460000	0.39030	ACT	.		0.542	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		C	80579499	T	C	80579499	3	2	78	1	0	0	0	0	1	0	0	0	17331	1725	60	3	450	3	WDR45L	17	80579499	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08	8151289	80579499	615711	44	7302											
TRAPPC5	126003	broad.mit.edu	37	chr19	7747477	7747477	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaggccaacgatgacgcgcGcaccttctacatcatcgagc	10	6	10	15	5	2	1	1	1	1	0	3	3	2	1	2	1	3	2	2	1	2	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr19:7747477G>A	ENST00000317378.5	+	2	525	c.338G>A	c.(337-339)cGc>cAc	p.R113H	TRAPPC5_ENST00000596148.1_Missense_Mutation_p.R113H|TRAPPC5_ENST00000595985.1_Missense_Mutation_p.R46H|TRAPPC5_ENST00000426877.2_Missense_Mutation_p.R113H|CTD-3214H19.16_ENST00000597959.1_3'UTR	NM_174894.2	NP_777554.1	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	113					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|TRAPP complex (GO:0030008)		p.R113L(1)		NS(1)|lung(2)	3						GATGACGCGCGCACCTTCTAC	0.627																																					p.R113H													.	TRAPPC5-68	1	Substitution - Missense(1)	lung(1)	c.G338A						.						36	39	38					19																	7747477		2189	4280	6469	SO:0001583	missense	126003	exon2			ACGCGCGCACCTT	BC042161	CCDS42490.1	19p13.3	2011-10-10				ENSG00000181029		"Trafficking protein particle complex"	23067	protein-coding gene	gene with protein product							Standard	NM_001042462		Approved	MGC52424, TRS31	uc002mhj.2	Q8IUR0		ENST00000317378.5:c.338G>A	19.37:g.7747477G>A	ENSP00000316990:p.Arg113His	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	48	3	NM_001042461	0	0	228	228	0	A8K7I6	Missense_Mutation	SNP	ENST00000317378.5	37	CCDS42490.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.795911	0.50208	.	.	ENSG00000181029	ENST00000317378;ENST00000426877	T;T	0.43294	0.95;0.95	4.1	2.97	0.34412	NO signalling/Golgi transport  ligand-binding domain (1);	0.265289	0.28077	U	0.016682	T	0.28400	0.0702	L	0.41027	1.25	0.39601	D	0.969734	B	0.17038	0.02	B	0.12156	0.007	T	0.25293	-1.0136	10	0.48119	T	0.1	-0.0594	3.7045	0.08395	0.3578:0.0:0.6422:0.0	.	113	Q8IUR0	TPPC5_HUMAN	H	113	ENSP00000316990:R113H;ENSP00000399025:R113H	ENSP00000316990:R113H	R	+	2	0	TRAPPC5	7653477	1.000000	0.71417	0.997000	0.53966	0.628000	0.37860	4.743000	0.62110	1.846000	0.53633	0.485000	0.47835	CGC	.		0.627	TRAPPC5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461252.1	XM_058961		A	7747477	G	A	7747477	3	1	78	1	0	0	0	0	1	0	0	0	16495	1087	38	1	340	1	TRAPPC5	19	7747477	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		7747477	51381506	45	7303											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945880	48945880	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacagctgctgcagcgcTgaggccgccccaccgcccgc	6	5	12	18	4	0	1	0	1	0	0	0	1	0	1	5	1	5	5	5	1	1	1	rs62130268	byFrequency	TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr19:48945880T>C	ENST00000263269.3	+	13	2785	c.2697T>C	c.(2695-2697)gcT>gcC	p.A899A		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	899					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTGCAGCGCTGAGGCCGCCC	0.781													c|||	3742	0.747204	0.6188	0.8545	5008	,	,		4716	0.6548		0.8887	False		,,,				2504	0.7945				p.A899A		.											.	GRIN2D-156	0			c.T2697C						.			1689,437		638,413,12	1	1	1		2697	-3.3	1	19	dbSNP_129	1	3712,202		1757,198,2	no	coding-synonymous	GRIN2D	NM_000836.2		2395,611,14	CC,CT,TT		5.161,20.555,10.5795		899/1337	48945880	5401,639	1063	1957	3020	SO:0001819	synonymous_variant	2906	exon13			CAGCGCTGAGGCC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4588	protein-coding gene	gene with protein product	"N-methyl-d-aspartate receptor subunit 2D"	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2697T>C	19.37:g.48945880T>C		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	5	5	NM_000836	0	0	1	1	0		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			T|0.245;C|0.755		0.781	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			C	48945880	T	C	48945880	2	2	78	1	0	0	0	0	0	0	0	1	6803	1567	55	3		3	GRIN2D	19	48945880	Silent	SNP	T	TCGA-BQ-5894-01A-11D-1589-08	41198403	48945880	10183103	46	7304											
NTN5	126147	hgsc.bcm.edu	37	chr19	49174237	49174237	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcaggagggcaaaggtcaCgggcatggtcacagcagagc	12	3	17	9	1	2	1	2	0	0	1	2	3	2	2	0	5	3	4	0	5	1	0			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr19:49174237C>G	ENST00000270235.4	-	2	102	c.7G>C	c.(7-9)Gtg>Ctg	p.V3L	SEC1P_ENST00000430145.2_RNA	NM_145807.1	NP_665806.1	Q8WTR8	NET5_HUMAN	netrin 5	3						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	10						GCAAAGGTCACGGGCATGGTC	0.657																																					p.V3L		.											.	NTN5-136	0			c.G7C						.						9	10	10					19																	49174237		2132	4184	6316	SO:0001583	missense	126147	exon2			AGGTCACGGGCAT		CCDS33068.1	19q13.33	2013-03-01			ENSG00000142233	ENSG00000142233		"Netrins"	25208	protein-coding gene	gene with protein product	"Netrin-5"					12477932	Standard	NM_145807		Approved		uc002pkb.3	Q8WTR8		ENST00000270235.4:c.7G>C	19.37:g.49174237C>G	ENSP00000270235:p.Val3Leu	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_145807	0	0	1	1	0	Q8N4X9|Q8WU63	Missense_Mutation	SNP	ENST00000270235.4	37	CCDS33068.1	.	.	.	.	.	.	.	.	.	.	C	12.25	1.880307	0.33162	.	.	ENSG00000142233	ENST00000270235	T	0.27720	1.65	4.72	-1.6	0.08426	.	0.468333	0.21670	N	0.070883	T	0.15478	0.0373	L	0.41236	1.265	0.09310	N	1	B;P	0.37370	0.005;0.592	B;B	0.32677	0.008;0.15	T	0.09997	-1.0649	10	0.31617	T	0.26	.	2.2736	0.04096	0.3973:0.3507:0.1501:0.1019	.	3;3	Q8WTR8-2;Q8WTR8	.;NET5_HUMAN	L	3	ENSP00000270235:V3L	ENSP00000270235:V3L	V	-	1	0	NTN5	53866049	0.000000	0.05858	0.001000	0.08648	0.662000	0.39071	-0.664000	0.05292	0.091000	0.17302	0.455000	0.32223	GTG	.		0.657	NTN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466176.1	NM_145807		G	49174237	C	G	49174237	3	3	78	1	0	0	0	0	1	0	0	0	10729	536	19	4	1486	4	NTN5	19	49174237	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	228357	49174237	9954746	47	7305											
KLK3	354	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	51359636	51359636	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acccccagtgggtcctcacaGctgcccactgcatcaggaag	9	6	10	16	0	2	0	2	0	0	0	3	1	3	1	4	2	3	2	4	2	1	0			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr19:51359636G>T	ENST00000326003.2	+	2	228	c.187G>T	c.(187-189)Gct>Tct	p.A63S	KLK3_ENST00000597483.1_Missense_Mutation_p.A63S|KLK3_ENST00000593997.1_Missense_Mutation_p.A63S|KLK3_ENST00000595952.1_Missense_Mutation_p.A63S|KLK3_ENST00000360617.3_Missense_Mutation_p.A63S	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	63	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GGTCCTCACAGCTGCCCACTG	0.617																																					p.A63S	Colon(185;1767 2023 13025 30120 37630)	.											.	KLK3-228	0			c.G187T						.						76	77	77					19																	51359636		2203	4300	6503	SO:0001583	missense	354	exon2			CTCACAGCTGCCC	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"Kallikreins"	6364	protein-coding gene	gene with protein product		176820	"kallikrein 3, (prostate specific antigen)"	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.187G>T	19.37:g.51359636G>T	ENSP00000314151:p.Ala63Ser	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	144	42	NM_001030050	0	0	1	1	0	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Missense_Mutation	SNP	ENST00000326003.2	37	CCDS12807.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.281163	0.40394	.	.	ENSG00000142515	ENST00000326003;ENST00000422986;ENST00000360617;ENST00000435152;ENST00000326052	D;D;D	0.95272	-3.66;-3.66;-3.66	2.91	1.81	0.25067	.	0.000000	0.32041	N	0.006661	D	0.96231	0.8771	M	0.77486	2.375	0.27490	N	0.952326	D;D;D;D	0.89917	0.998;0.987;0.999;1.0	D;D;D;D	0.91635	0.951;0.923;0.976;0.999	D	0.90785	0.4682	10	0.87932	D	0	.	8.8252	0.35050	0.0:0.0:0.7734:0.2266	.	63;63;63;63	Q8NCW4;G3XAE3;G3V0H4;C9JXH3	.;.;.;.	S	63	ENSP00000314151:A63S;ENSP00000393628:A63S;ENSP00000353829:A63S	ENSP00000314151:A63S	A	+	1	0	KLK3	56051448	0.999000	0.42202	0.987000	0.45799	0.256000	0.26092	6.780000	0.75063	0.516000	0.28340	0.436000	0.28706	GCT	.		0.617	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864		T	51359636	G	T	51359636	3	4	78	1	0	0	0	0	1	0	0	0	8426	971	34	4	193	4	KLK3	19	51359636	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	2185399	51359636	7769347	48	7306											
JAG1	182	hgsc.bcm.edu	37	chr20	10621489	10621489	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctgcaacggcagcaatcagCgagctgtttccatcacgttt	9	11	9	12	3	3	0	2	0	1	0	4	1	4	0	1	1	5	6	1	1	2	2	rs202075581	byFrequency	TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr20:10621489C>A	ENST00000254958.5	-	25	3656	c.3141G>T	c.(3139-3141)tcG>tcT	p.S1047S	JAG1_ENST00000423891.2_Silent_p.S888S	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1047					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CAGCAATCAGCGAGCTGTTTC	0.448									Alagille Syndrome																												p.S1047S		.											.	JAG1-1273	0			c.G3141T						.						113	100	104					20																	10621489		2203	4300	6503	SO:0001819	synonymous_variant	182	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AATCAGCGAGCTG	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3141G>T	20.37:g.10621489C>A		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	74	5	NM_000214	0	1	16	17	0	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			C|0.999;T|0.001		0.448	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		A	10621489	C	A	10621489	2	1	78	1	0	0	0	0	0	0	0	1	7955	755	27	4		4	JAG1	20	10621489	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		10621489	52404031	49	7307											
MAFB	9935	hgsc.bcm.edu	37	chr20	39316754	39316754	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgtagccccggttcttcAgggtccgccgcttctgcttc	2	11	13	15	4	3	0	1	0	2	0	5	0	4	0	4	3	2	4	4	3	1	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr20:39316754A>G	ENST00000373313.2	-	1	1126	c.737T>C	c.(736-738)cTg>cCg	p.L246P	MAFB_ENST00000396967.1_Missense_Mutation_p.L246P	NM_005461.3	NP_005452.2	Q9Y5Q3	MAFB_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B	246	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				brain segmentation (GO:0035284)|inner ear morphogenesis (GO:0042472)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|respiratory gaseous exchange (GO:0007585)|rhombomere 5 development (GO:0021571)|rhombomere 6 development (GO:0021572)|segment specification (GO:0007379)|sensory organ development (GO:0007423)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(1)	2		Myeloproliferative disorder(115;0.00878)				CCGGTTCTTCAGGGTCCGCCG	0.617			T	IGH@	MM																																p.L246P		.		Dom	yes		20	20q11.2-q13.1	9935	v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian)		L	.	MAFB-846	0			c.T737C						.						26	26	26					20																	39316754		2203	4300	6503	SO:0001583	missense	9935	exon1			TTCTTCAGGGTCC	AF134157	CCDS13311.1	20q11.1-q13.1	2013-07-09	2013-07-09	2001-11-30	ENSG00000204103	ENSG00000204103			6408	protein-coding gene	gene with protein product		608968	"Kreisler (mouse) maf-related leucine zipper homolog"	KRML		10444328	Standard	NM_005461		Approved		uc002xji.3	Q9Y5Q3	OTTHUMG00000033052	ENST00000373313.2:c.737T>C	20.37:g.39316754A>G	ENSP00000362410:p.Leu246Pro	Somatic	34	1		WXS	Illumina HiSeq	Phase_I	33	2	NM_005461	0	0	23	23	0	B3KNE1|Q9H1F1	Missense_Mutation	SNP	ENST00000373313.2	37	CCDS13311.1	.	.	.	.	.	.	.	.	.	.	A	18.48	3.632371	0.67015	.	.	ENSG00000204103	ENST00000373313;ENST00000396967	D;D	0.93953	-3.32;-3.32	4.49	4.49	0.54785	Basic-leucine zipper (bZIP) transcription factor (2);Maf transcription factor (1);Eukaryotic transcription factor, Skn-1-like, DNA-binding (1);	0.000000	0.64402	D	0.000004	D	0.97349	0.9133	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98183	1.0458	10	0.66056	D	0.02	-16.2256	13.9843	0.64324	1.0:0.0:0.0:0.0	.	246	Q9Y5Q3	MAFB_HUMAN	P	246	ENSP00000362410:L246P;ENSP00000380167:L246P	ENSP00000362410:L246P	L	-	2	0	MAFB	38750168	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.139000	0.94554	1.908000	0.55244	0.374000	0.22700	CTG	.		0.617	MAFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080375.2			G	39316754	A	G	39316754	3	3	78	1	0	0	0	0	1	0	0	0	9183	188	7	3	238	3	MAFB	20	39316754	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	28695265	39316754	23708766	50	7308											
PI3	5266	broad.mit.edu	37	chr20	43804649	43804649	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccactaagcctggctcctGccccattatcttgatccggt	6	12	7	16	1	1	1	0	1	1	0	4	1	4	1	6	2	2	1	6	2	2	3			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr20:43804649G>T	ENST00000243924.3	+	2	274	c.227G>T	c.(226-228)tGc>tTc	p.C76F		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	76	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				CCTGGCTCCTGCCCCATTATC	0.498																																					p.C76F													.	PI3-514	0			c.G227T						.						131	113	119					20																	43804649		2203	4300	6503	SO:0001583	missense	5266	exon2			GCTCCTGCCCCAT	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"WAP four-disulfide core domain containing"	8947	protein-coding gene	gene with protein product	"skin-derived antileukoproteinase", "trappin-2"	182257	"protease inhibitor 3, skin-derived (SKALP)"			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.227G>T	20.37:g.43804649G>T	ENSP00000243924:p.Cys76Phe	Somatic	94	2		WXS	Illumina HiSeq	Phase_I	125	6	NM_002638	4	2	3075	3109	28	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	37	CCDS13344.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414861	0.62511	.	.	ENSG00000124102	ENST00000243924	D	0.99239	-5.61	4.49	4.49	0.54785	Whey acidic protein, 4-disulphide core (5);4-disulphide core (1);	0.000000	0.47093	D	0.000255	D	0.99664	0.9875	H	0.98996	4.395	0.42882	D	0.994173	D	0.89917	1.0	D	0.97110	1.0	D	0.97354	0.9965	10	0.87932	D	0	.	13.4053	0.60908	0.0:0.0:1.0:0.0	.	76	P19957	ELAF_HUMAN	F	76	ENSP00000243924:C76F	ENSP00000243924:C76F	C	+	2	0	PI3	43238063	0.998000	0.40836	0.874000	0.34290	0.082000	0.17680	3.612000	0.54142	2.432000	0.82394	0.650000	0.86243	TGC	.		0.498	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638		T	43804649	G	T	43804649	3	4	78	1	0	0	0	0	1	0	0	0	11896	1319	46	4	233	4	PI3	20	43804649	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	4487895	43804649	19220871	51	7309											
C21orf91	54149	broad.mit.edu	37	chr21	19190580	19190580	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttcccagtttacaaacaCtgcaaatgttgtcatcattc	11	14	5	11	0	2	0	2	0	0	0	4	0	3	0	1	0	3	4	1	0	3	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr21:19190580C>T	ENST00000400558.3	-	2	146	c.56G>A	c.(55-57)aGt>aAt	p.S19N	C21orf91_ENST00000284881.4_Missense_Mutation_p.S19N|C21orf91_ENST00000400559.3_Missense_Mutation_p.S19N|C21orf91_ENST00000493464.1_5'UTR	NM_001100421.1	NP_001093891.1			chromosome 21 open reading frame 91											endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		TTTACAAACACTGCAAATGTT	0.353																																					p.S19N													.	C21orf91-91	0			c.G56A						.						202	188	192					21																	19190580		1876	4110	5986	SO:0001583	missense	54149	exon2			CAAACACTGCAAA	AF239726	CCDS42907.1, CCDS42908.1, CCDS42909.1	21q21.1	2011-12-12	2003-07-22		ENSG00000154642	ENSG00000154642			16459	protein-coding gene	gene with protein product	"cold sore susceptibility gene 1", "early undifferentiated retina and lens"		"chromosome 21 open reading frame 38"	C21orf38, C21orf14		22039568	Standard	NM_001100421		Approved	YG81, EURL, CSSG1	uc002yko.4	Q9NYK6	OTTHUMG00000074509	ENST00000400558.3:c.56G>A	21.37:g.19190580C>T	ENSP00000383403:p.Ser19Asn	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	125	5	NM_017447	0	0	2	2	0		Missense_Mutation	SNP	ENST00000400558.3	37	CCDS42909.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011286	0.93346	.	.	ENSG00000154642	ENST00000284881;ENST00000400559;ENST00000400558;ENST00000405964	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.49609	0.1567	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.41645	-0.9497	9	.	.	.	-6.9151	16.4282	0.83831	0.0:1.0:0.0:0.0	.	19;19	Q9NYK6-3;Q9NYK6	.;EURL_HUMAN	N	19	ENSP00000284881:S19N;ENSP00000383404:S19N;ENSP00000383403:S19N;ENSP00000385566:S19N	.	S	-	2	0	C21orf91	18112451	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.845000	0.75394	2.554000	0.86153	0.655000	0.94253	AGT	.		0.353	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447		T	19190580	C	T	19190580	3	4	78	1	0	0	0	0	1	0	0	0	2140	565	20	2	853	2	C21orf91	21	19190580	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		19190580	28939315	52	7310											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43221684	43221684	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacatggcagagccgctgaCggtatcaaaggtcacggtca	12	6	12	11	3	3	2	3	1	0	1	3	2	3	2	1	4	2	3	1	4	3	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr21:43221684C>A	ENST00000269844.3	-	31	4350	c.4240G>T	c.(4240-4242)Gtc>Ttc	p.V1414F	PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Missense_Mutation_p.V1085F|PRDM15_ENST00000447207.2_Missense_Mutation_p.V1048F|PRDM15_ENST00000538201.1_Missense_Mutation_p.V1068F|PRDM15_ENST00000422911.1_Missense_Mutation_p.V1105F	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GAGCCGCTGACGGTATCAAAG	0.572																																					p.V1414F		.											.	PRDM15-90	0			c.G4240T						.						68	60	63					21																	43221684		2203	4300	6503	SO:0001583	missense	63977	exon31			CGCTGACGGTATC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4240G>T	21.37:g.43221684C>A	ENSP00000269844:p.Val1414Phe	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	49	3	NM_022115	0	0	4	4	0	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	c	19.42	3.824556	0.71143	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	4.29	4.29	0.51040	.	.	.	.	.	T	0.56499	0.1989	L	0.27053	0.805	0.58432	D	0.999995	D;D;D	0.89917	1.0;0.999;0.997	D;D;P	0.87578	0.998;0.995;0.902	T	0.63171	-0.6697	9	0.87932	D	0	-33.0293	15.7568	0.78037	0.0:1.0:0.0:0.0	.	1414;1105;1085	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	F	1105;1085;1068;1048;1414	ENSP00000408592:V1105F;ENSP00000381556:V1085F;ENSP00000444044:V1068F;ENSP00000390245:V1048F;ENSP00000269844:V1414F	ENSP00000269844:V1414F	V	-	1	0	PRDM15	42094753	1.000000	0.71417	0.980000	0.43619	0.319000	0.28217	7.206000	0.77891	1.934000	0.56057	0.558000	0.71614	GTC	.		0.572	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43221684	C	A	43221684	3	1	78	1	0	0	0	0	1	0	0	0	12485	536	19	4	287	4	PRDM15	21	43221684	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	24031104	43221684	4908211	53	7311											
NF2	4771	broad.mit.edu	37	chr22	30000023	30000024	+	Frame_Shift_Del	DEL	CT	CT	-																															gcttcccgcatgagcttcagCtctctcaagaggaagcaacc																								rs371800843		TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr22:30000023_30000024delCT	ENST00000338641.4	+	1	477_478	c.36_37delCT	c.(34-39)agctctfs	p.SS12fs	NF2_ENST00000397789.3_Frame_Shift_Del_p.SS12fs|NF2_ENST00000403435.1_Frame_Shift_Del_p.SS12fs|NF2_ENST00000353887.4_Frame_Shift_Del_p.SS12fs|NF2_ENST00000334961.7_Frame_Shift_Del_p.SS12fs|NF2_ENST00000361452.4_Frame_Shift_Del_p.SS12fs|NF2_ENST00000413209.2_Frame_Shift_Del_p.SS12fs|NF2_ENST00000361166.4_Frame_Shift_Del_p.SS12fs|NF2_ENST00000347330.5_Frame_Shift_Del_p.SS12fs|NF2_ENST00000361676.4_Frame_Shift_Del_p.SS12fs|NF2_ENST00000403999.3_Frame_Shift_Del_p.SS12fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	12					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.L14fs*34(2)|p.?(1)|p.S13fs*10(1)		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						TGAGCTTCAGCTCTCTCAAGAG	0.663			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.12_13del			yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	4	Deletion - Frameshift(3)|Unknown(1)	meninges(2)|lung(1)|soft_tissue(1)	c.36_37del						.																																			SO:0001589	frameshift_variant	4771	exon1	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	CTTCAGCTCTCTC	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.36_37delCT	22.37:g.30000027_30000028delCT	ENSP00000344666:p.Ser12fs	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	11	5	NM_181831	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	37	CCDS13861.1																																																																																			.		0.663	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		-	30000024	CT	-	30000023	7	5	78	1	0	1	0	1	0	0	0	0	10383	796	28	0	38	0	NF2	22	30000023	Frame_Shift_Del	DEL	CT	TCGA-BQ-5894-01A-11D-1589-08		30000023	21304543	54	7312											
KCNJ4	3761	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	38823432	38823433	+	In_Frame_Ins	INS	-	-	GGA																															aggtcccgctggtccaggggINScaggtactcgccctcctggg																										TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr22:38823432_38823433insGGA	ENST00000303592.3	-	2	963_964	c.705_706insTCC	c.(703-708)ctgccc>ctgTCCccc	p.235_236LP>LSP	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	235					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					TGGTCCAGGGGCAGGTACTCGC	0.629																																					p.P236delinsSP		.											.	KCNJ4-90	0			c.706_707insTCC						.																																			SO:0001652	inframe_insertion	3761	exon2			.	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.705_706insTCC	22.37:g.38823432_38823433insGGA	ENSP00000306497:p.Leu235_Pro236insSer	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	54	13	NM_004981	0	0	0	0	0	Q14D44	In_Frame_Ins	INS	ENST00000303592.3	37	CCDS13971.1																																																																																			.		0.629	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		GGA	38823433	-	GGA	38823432	7	5	78	1	0	1	1	0	0	0	0	0	8074	1203	42	0	635	0	KCNJ4	22	38823432	In_Frame_Ins	INS	-	TCGA-BQ-5894-01A-11D-1589-08	8823409	38823432	12481134	55	7313											
CSMD2	114784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	34180229	34180229	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctccacaggcgccgtctgcCccccaggcacgtgatgcggg	5	5	14	17	4	1	1	0	1	1	0	2	1	2	1	5	3	2	2	5	3	0	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:34180229C>T	ENST00000373381.4	-	21	3540	c.3364G>A	c.(3364-3366)Ggc>Agc	p.G1122S		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1082	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CGCCGTCTGCCCCCCAGGCAC	0.607																																					p.G1082S		.											.	CSMD2-103	0			c.G3244A						.						120	136	131					1																	34180229		2203	4300	6503	SO:0001583	missense	114784	exon21			GTCTGCCCCCCAG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.3364G>A	1.37:g.34180229C>T	ENSP00000362479:p.Gly1122Ser	Somatic	302	0		WXS	Illumina HiSeq	Phase_I	106	71	NM_052896	0	0	0	0	0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	C	36	5.810255	0.96975	.	.	ENSG00000121904	ENST00000373381	T	0.24151	1.87	5.85	5.85	0.93711	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	0.998;1.0	T	0.21075	-1.0256	10	0.46703	T	0.11	.	19.1531	0.93496	0.0:1.0:0.0:0.0	.	1082;1122	Q7Z408;E7EUA6	CSMD2_HUMAN;.	S	1122	ENSP00000362479:G1122S	ENSP00000241312:G1082S	G	-	1	0	CSMD2	33952816	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.753000	0.94483	0.655000	0.94253	GGC	.		0.607	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34180229	C	T	34180229	3	4	79	1	0	0	0	0	1	0	0	0	3951	623	22	2	7415	2	CSMD2	1	34180229	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		34180229	215070392	1	7314											
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	78444626	78444626	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaactcctccaccaccaccGccgccaccaccgccaccagc	9	4	4	24	3	0	0	0	0	0	0	2	0	2	0	11	0	2	0	11	0	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:78444626G>A	ENST00000370768.2	-	1	144	c.63C>T	c.(61-63)ggC>ggT	p.G21G	FUBP1_ENST00000370767.1_Silent_p.G21G|FUBP1_ENST00000436586.2_Silent_p.G21G	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	21	Gly-rich.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						caccaccaccgccgccaccac	0.602			"F, N"		oligodendroglioma																																p.G21G		.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1-227	0			c.C63T						.						39	46	43					1																	78444626		2203	4300	6503	SO:0001819	synonymous_variant	8880	exon1			ACCACCGCCGCCA	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.63C>T	1.37:g.78444626G>A		Somatic	90	1		WXS	Illumina HiSeq	Phase_I	42	27	NM_003902	0	0	0	0	0	Q12828	Silent	SNP	ENST00000370768.2	37	CCDS683.1																																																																																			.		0.602	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		A	78444626	G	A	78444626	2	1	79	1	0	0	0	0	0	0	0	1	6111	1074	38	1		1	FUBP1	1	78444626	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	44264397	78444626	170805995	2	7315											
ENSA	2029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150601936	150601936	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagggttctcttcttcttgtTtctgggacatggcgggaccg	4	14	13	10	2	4	0	0	0	4	0	5	2	4	2	1	4	0	2	1	4	0	5	rs148754482		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:150601936T>G	ENST00000369014.5	-	1	136	c.11A>C	c.(10-12)aAa>aCa	p.K4T	ENSA_ENST00000369009.3_Missense_Mutation_p.K4T|ENSA_ENST00000356527.5_Missense_Mutation_p.K4T|ENSA_ENST00000354702.3_5'Flank|ENSA_ENST00000361631.5_5'Flank|ENSA_ENST00000513281.1_5'Flank|ENSA_ENST00000503241.1_Missense_Mutation_p.K4T|ENSA_ENST00000362052.7_Missense_Mutation_p.K4T|ENSA_ENST00000503345.1_Missense_Mutation_p.K4T|ENSA_ENST00000271690.8_Missense_Mutation_p.K4T|ENSA_ENST00000369016.4_Missense_Mutation_p.K4T|ENSA_ENST00000339643.5_Missense_Mutation_p.K4T|ENSA_ENST00000361532.5_5'Flank			O43768	ENSA_HUMAN	endosulfine alpha	4					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|regulation of catalytic activity (GO:0050790)|regulation of insulin secretion (GO:0050796)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|transport (GO:0006810)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ion channel inhibitor activity (GO:0008200)|phosphatase inhibitor activity (GO:0019212)|potassium channel inhibitor activity (GO:0019870)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)	4	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			TTCTTCTTGTTTCTGGGACAT	0.662																																					p.K4T	Esophageal Squamous(188;763 2078 3002 3411 26027)	.											.	ENSA-90	0			c.A11C						.						59	61	60					1																	150601936		2203	4300	6503	SO:0001583	missense	2029	exon1			TCTTGTTTCTGGG	X99906	CCDS958.1, CCDS959.1, CCDS960.1, CCDS961.1, CCDS962.1, CCDS963.1, CCDS964.1, CCDS965.1	1q21.3	2010-03-11			ENSG00000143420	ENSG00000143420			3360	protein-coding gene	gene with protein product		603061				9653196	Standard	NM_004436		Approved	MGC4319, MGC8394, MGC78563, ARPP-19e	uc001eve.3	O43768	OTTHUMG00000035004	ENST00000369014.5:c.11A>C	1.37:g.150601936T>G	ENSP00000358010:p.Lys4Thr	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	76	35	NM_207044	1	0	60	122	61	A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	Missense_Mutation	SNP	ENST00000369014.5	37	CCDS958.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543606	0.65198	.	.	ENSG00000143420	ENST00000369016;ENST00000369014;ENST00000369009;ENST00000339643;ENST00000271690;ENST00000356527;ENST00000502246;ENST00000503345;ENST00000503241;ENST00000362052	T	0.46063	0.88	5.78	3.46	0.39613	.	0.177686	0.48286	D	0.000183	T	0.26702	0.0653	L	0.40543	1.245	0.33054	D	0.533083	D;P;D;P;D	0.76494	0.999;0.728;0.982;0.534;0.99	P;B;P;B;P	0.60012	0.867;0.372;0.628;0.154;0.794	T	0.06679	-1.0813	10	0.16420	T	0.52	.	5.8762	0.18830	0.1492:0.0804:0.0:0.7704	.	4;4;4;4;4	A6NMQ3;O43768-8;E9PB69;O43768;O43768-3	.;.;.;ENSA_HUMAN;.	T	4	ENSP00000358012:K4T	ENSP00000271690:K4T	K	-	2	0	ENSA	148868560	1.000000	0.71417	0.998000	0.56505	0.671000	0.39405	3.104000	0.50306	1.004000	0.39156	-0.710000	0.03640	AAA	T|1.000;C|0.000		0.662	ENSA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000084720.2	NM_207042		G	150601936	T	G	150601936	3	3	79	1	0	0	0	0	1	0	0	0	5149	1841	64	5	610	5	ENSA	1	150601936	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	72157310	150601936	98648685	3	7316											
HORMAD1	84072	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150689613	150689613	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttaaaataaatattgtattaCcatctagatatcttgttcca	15	17	3	6	0	2	1	0	0	2	1	3	1	3	1	2	0	1	2	2	0	9	10			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:150689613C>T	ENST00000361824.2	-	3	284		c.e3+1		HORMAD1_ENST00000368993.2_Splice_Site|HORMAD1_ENST00000322343.7_Splice_Site|HORMAD1_ENST00000476530.1_Splice_Site|HORMAD1_ENST00000368995.4_Splice_Site	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1						blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TATTGTATTACCATCTAGATA	0.294																																					.													.	HORMAD1-92	0			c.178+1G>A						.						59	60	59					1																	150689613		2203	4300	6503	SO:0001630	splice_region_variant	84072	exon4			GTATTACCATCTA	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"cancer/testis antigen 46"	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.178+1G>A	1.37:g.150689613C>T		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	71	25	NM_032132	0	0	0	0	0	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Splice_Site	SNP	ENST00000361824.2	37	CCDS967.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354851	0.82243	.	.	ENSG00000143452	ENST00000368995;ENST00000368993;ENST00000368992;ENST00000540570;ENST00000322343;ENST00000361824;ENST00000368987;ENST00000442853	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8768	0.88827	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HORMAD1	148956237	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.100000	0.76989	2.554000	0.86153	0.460000	0.39030	.	.		0.294	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132	Intron	T	150689613	C	T	150689613	5	4	79	1	0	0	0	0	0	0	1	0	7307	521	18	2	1057	2	HORMAD1	1	150689613	Splice_Site	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	87677	150689613	98561008	4	7317											
FMO2	2327	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171174553	171174553	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatggaacagtggaggagaaCattgatgtcatcatttttgc	12	12	12	5	0	2	2	2	1	0	1	2	6	2	4	0	3	3	0	0	3	2	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:171174553C>A	ENST00000209929.7	+	7	1121	c.963C>A	c.(961-963)aaC>aaA	p.N321K	RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.N321K|FMO2_ENST00000529935.1_3'UTR			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	320					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGGAGGAGAACATTGATGTCA	0.398																																					p.N321K													.	FMO2-91	0			c.C963A						.						106	102	104					1																	171174553		2203	4300	6503	SO:0001583	missense	2327	exon7			GGAGAACATTGAT	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"flavin containing monooxygenase 2"			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.963C>A	1.37:g.171174553C>A	ENSP00000209929:p.Asn321Lys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	52	15	NM_001460	0	0	6	7	1	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.277366	0.23307	.	.	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.52754	0.65;0.65	5.67	3.79	0.43588	.	0.506226	0.24781	N	0.035643	T	0.14830	0.0358	L	0.35644	1.08	0.29886	N	0.82557	B	0.10296	0.003	B	0.18263	0.021	T	0.15122	-1.0448	10	0.26408	T	0.33	-8.1593	5.2666	0.15603	0.0:0.6183:0.1527:0.2289	.	321	Q99518	FMO2_HUMAN	K	321	ENSP00000209929:N321K;ENSP00000405905:N321K	ENSP00000209929:N321K	N	+	3	2	FMO2	169441177	0.004000	0.15560	0.900000	0.35374	0.779000	0.44077	-0.206000	0.09398	0.733000	0.32492	-0.137000	0.14449	AAC	.		0.398	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		A	171174553	C	A	171174553	3	1	79	1	0	0	0	0	1	0	0	0	5974	477	17	4	985	4	FMO2	1	171174553	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	20484940	171174553	78076068	5	7318											
LAMB3	3914	hgsc.bcm.edu	37	chr1	209801450	209801450	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cataggtcacagcgctctccCtgcacatgctccttgcacac	8	9	7	17	1	2	0	1	0	1	0	4	0	3	0	2	1	4	4	2	1	1	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:209801450C>G	ENST00000356082.4	-	11	1352	c.1218G>C	c.(1216-1218)caG>caC	p.Q406H	LAMB3_ENST00000391911.1_Missense_Mutation_p.Q406H|LAMB3_ENST00000367030.3_Missense_Mutation_p.Q406H	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	406	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		AGCGCTCTCCCTGCACATGCT	0.642											OREG0014217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q406H		.											.	LAMB3-156	0			c.G1218C						.						64	45	52					1																	209801450		2201	4299	6500	SO:0001583	missense	3914	exon11			CTCTCCCTGCACA	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.1218G>C	1.37:g.209801450C>G	ENSP00000348384:p.Gln406His	Somatic	12	0	2185	WXS	Illumina HiSeq	Phase_I	15	3	NM_000228	0	0	17	17	0	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.816924	0.32145	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.61980	0.06;0.06;0.06	5.12	0.62	0.17637	EGF-like, laminin (4);EGF-like region, conserved site (1);	0.259562	0.39985	N	0.001204	T	0.43612	0.1255	L	0.41356	1.27	0.41635	D	0.989047	B	0.24768	0.111	B	0.20577	0.03	T	0.19549	-1.0302	10	0.42905	T	0.14	.	2.5948	0.04851	0.1375:0.4366:0.2683:0.1575	.	406	Q13751	LAMB3_HUMAN	H	406	ENSP00000375778:Q406H;ENSP00000348384:Q406H;ENSP00000355997:Q406H	ENSP00000348384:Q406H	Q	-	3	2	LAMB3	207868073	0.981000	0.34729	1.000000	0.80357	0.690000	0.40134	0.128000	0.15810	0.231000	0.21079	0.456000	0.33151	CAG	.		0.642	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		G	209801450	C	G	209801450	3	3	79	1	0	0	0	0	1	0	0	0	8633	680	24	4	2352	4	LAMB3	1	209801450	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	38626897	209801450	39449171	6	7319											
ASAP2	8853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	9515020	9515020	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atatttttggattgctccaaGcttatgctgatggtgtggat	8	17	11	5	0	0	1	0	1	0	0	1	3	1	3	1	3	3	3	1	3	3	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:9515020G>C	ENST00000281419.3	+	17	2033	c.1693G>C	c.(1693-1695)Gct>Cct	p.A565P	ASAP2_ENST00000315273.4_Missense_Mutation_p.A565P	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	565					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ATTGCTCCAAGCTTATGCTGA	0.473																																					p.A565P		.											.	ASAP2-90	0			c.G1693C						.						100	100	100					2																	9515020		2203	4300	6503	SO:0001583	missense	8853	exon17			CTCCAAGCTTATG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1693G>C	2.37:g.9515020G>C	ENSP00000281419:p.Ala565Pro	Somatic	191	1		WXS	Illumina HiSeq	Phase_I	158	60	NM_001135191	0	0	5	10	5	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	37	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957409	0.73902	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.60040	0.26;0.22	5.27	5.27	0.74061	Ankyrin repeat-containing domain (1);	0.114641	0.64402	D	0.000015	T	0.62258	0.2413	L	0.43923	1.385	0.44754	D	0.997751	D;P	0.67145	0.996;0.938	P;B	0.54544	0.755;0.182	T	0.65286	-0.6205	10	0.66056	D	0.02	.	13.8057	0.63230	0.0:0.0:0.8468:0.1532	.	565;565	O43150-2;O43150	.;ASAP2_HUMAN	P	565	ENSP00000281419:A565P;ENSP00000316404:A565P	ENSP00000281419:A565P	A	+	1	0	ASAP2	9432471	1.000000	0.71417	0.946000	0.38457	0.972000	0.66771	6.520000	0.73773	2.450000	0.82876	0.655000	0.94253	GCT	.		0.473	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9515020	G	C	9515020	3	2	79	1	0	0	0	0	1	0	0	0	1012	971	34	4	1759	4	ASAP2	2	9515020	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		9515020	233684353	7	7320											
HEATR5B	54497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37235951	37235951	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taattgctctttttggttttGactctgcttcctttttaata	6	23	5	7	0	2	1	0	1	2	0	3	1	3	1	1	1	2	3	1	1	3	11			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:37235951G>A	ENST00000233099.5	-	28	4420	c.4325C>T	c.(4324-4326)tCa>tTa	p.S1442L	HEATR5B_ENST00000354531.2_Missense_Mutation_p.S1442L	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1442						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TTTTGGTTTTGACTCTGCTTC	0.323																																					p.S1442L		.											.	HEATR5B-142	0			c.C4325T						.						275	252	260					2																	37235951		2203	4300	6503	SO:0001583	missense	54497	exon28			GGTTTTGACTCTG	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4325C>T	2.37:g.37235951G>A	ENSP00000233099:p.Ser1442Leu	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	196	83	NM_019024	0	0	8	10	2	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096063	0.56075	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.48201	0.82;0.82	5.75	4.87	0.63330	Armadillo-like helical (1);Armadillo-type fold (1);	0.421246	0.25753	N	0.028524	T	0.31071	0.0785	L	0.29908	0.895	0.35398	D	0.79138	B;B	0.28933	0.228;0.0	B;B	0.21546	0.035;0.002	T	0.33059	-0.9883	10	0.23891	T	0.37	-16.3124	9.1639	0.37038	0.0727:0.0:0.7809:0.1464	.	1442;1442	Q9P2D3-3;Q9P2D3	.;HTR5B_HUMAN	L	1442	ENSP00000233099:S1442L;ENSP00000346531:S1442L	ENSP00000233099:S1442L	S	-	2	0	HEATR5B	37089455	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.382000	0.66213	2.716000	0.92895	0.655000	0.94253	TCA	.		0.323	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37235951	G	A	37235951	3	1	79	1	0	0	0	0	1	0	0	0	7053	1294	45	2	1926	2	HEATR5B	2	37235951	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	27720931	37235951	205963422	8	7321											
CLASP1	23332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	122122716	122122716	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggagcagaatggtcttgAagtgctcctcccagacacca	11	7	11	12	0	1	3	0	1	1	2	3	4	3	4	3	2	2	3	3	2	2	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:122122716A>C	ENST00000263710.4	-	36	4420	c.4031T>G	c.(4030-4032)tTc>tGc	p.F1344C	CLASP1_ENST00000545861.1_Missense_Mutation_p.F1051C|CLASP1_ENST00000455322.2_Missense_Mutation_p.F1300C|CLASP1_ENST00000397587.3_Missense_Mutation_p.F1284C|CLASP1_ENST00000409078.3_Missense_Mutation_p.F1277C|CLASP1_ENST00000541377.1_Missense_Mutation_p.F1283C|CLASP1_ENST00000541859.1_Missense_Mutation_p.F1061C	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1344	Interaction with CLIP2. {ECO:0000250}.|Interaction with PHLDB2 and RSN.|Localization to kinetochores.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					AATGGTCTTGAAGTGCTCCTC	0.557																																					p.F1344C		.											.	CLASP1-91	0			c.T4031G						.						69	75	73					2																	122122716		2086	4216	6302	SO:0001583	missense	23332	exon35			GTCTTGAAGTGCT	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.4031T>G	2.37:g.122122716A>C	ENSP00000263710:p.Phe1344Cys	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	39	20	NM_015282	0	0	8	17	9	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	a	27.0	4.794213	0.90453	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.57	5.57	0.84162	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.82678	0.5089	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.995;0.999;0.997;0.997	D	0.85278	0.1060	10	0.87932	D	0	-10.7425	16.0196	0.80472	1.0:0.0:0.0:0.0	.	1277;1284;1285;1344	E7EUA5;F5GWS0;A2RU21;Q7Z460	.;.;.;CLAP1_HUMAN	C	1344;1300;1284;1283;1061;1277;1051	ENSP00000263710:F1344C;ENSP00000389372:F1300C;ENSP00000380717:F1284C;ENSP00000441625:F1283C;ENSP00000441770:F1061C;ENSP00000386442:F1277C;ENSP00000438620:F1051C	ENSP00000263710:F1344C	F	-	2	0	CLASP1	121839186	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.927000	0.92846	2.249000	0.74217	0.454000	0.30748	TTC	.		0.557	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		C	122122716	A	C	122122716	3	2	79	1	0	0	0	0	1	0	0	0	3460	246	9	5	605	5	CLASP1	2	122122716	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	84886765	122122716	121076657	9	7322											
NFE2L2	4780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178098800	178098800	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctgaattgggagaaatTcacctgtctcttcatctagt	9	14	9	9	0	4	2	2	1	2	1	5	3	4	2	1	2	0	1	1	2	3	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:178098800T>C	ENST00000397062.3	-	2	799	c.245A>G	c.(244-246)gAa>gGa	p.E82G	NFE2L2_ENST00000464747.1_Missense_Mutation_p.E66G|NFE2L2_ENST00000423513.1_Missense_Mutation_p.E66G|NFE2L2_ENST00000446151.2_Missense_Mutation_p.E66G|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E66G	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	82					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E82G(3)|p.G81_F83delGEF(1)|p.E82V(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TGGGAGAAATTCACCTGTCTC	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.E82G		.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2-90	5	Substitution - Missense(4)|Deletion - In frame(1)	liver(3)|lung(1)|oesophagus(1)	c.A245G						.						137	137	137					2																	178098800		1900	4105	6005	SO:0001583	missense	4780	exon2			AGAAATTCACCTG		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.245A>G	2.37:g.178098800T>C	ENSP00000380252:p.Glu82Gly	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	99	41	NM_006164	0	0	38	61	23	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.048793	0.93740	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.38077	1.57;1.57;1.57;1.16;1.16;1.57	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.66287	0.2774	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.997;0.994;0.998;0.997	T	0.72959	-0.4133	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	66;66;66;82	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	G	66;82;66;66;66;66	ENSP00000380253:E66G;ENSP00000380252:E82G;ENSP00000411575:E66G;ENSP00000400073:E66G;ENSP00000412191:E66G;ENSP00000410015:E66G	ENSP00000380252:E82G	E	-	2	0	NFE2L2	177807046	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.503000	0.81632	2.210000	0.71456	0.460000	0.39030	GAA	.		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098800	T	C	178098800	3	2	79	1	0	0	0	0	1	0	0	0	10394	1783	62	3	1588	3	NFE2L2	2	178098800	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	55976084	178098800	65100573	10	7323											
TTN	7273	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179550284	179550284	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cactctcttagaaataatgtGcagcttttcttccacaacat	12	14	4	11	0	2	1	0	0	2	1	4	1	3	1	1	0	3	2	1	0	4	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:179550284G>A	ENST00000591111.1	-	126	31626	c.31402C>T	c.(31402-31404)Cac>Tac	p.H10468Y	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.H9541Y|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.H10785Y|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAAATAATGTGCAGCTTTTCT	0.353																																					p.H10785Y													.	TTN-636	0			c.C32353T						.						113	108	110					2																	179550284		1902	4118	6020	SO:0001583	missense	7273	exon128			TAATGTGCAGCTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.31402C>T	2.37:g.179550284G>A	ENSP00000465570:p.His10468Tyr	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	58	22	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	12.49	1.954726	0.34471	.	.	ENSG00000155657	ENST00000342992	T	0.64991	-0.13	5.95	5.08	0.68730	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.51261	0.1664	L	0.38175	1.15	0.34818	D	0.738351	B	0.02656	0.0	B	0.04013	0.001	T	0.59506	-0.7442	9	0.87932	D	0	.	9.3702	0.38250	0.0786:0.1842:0.7373:0.0	.	10468	Q8WZ42	TITIN_HUMAN	Y	9541	ENSP00000343764:H9541Y	ENSP00000343764:H9541Y	H	-	1	0	TTN	179258529	0.671000	0.27521	0.974000	0.42286	0.991000	0.79684	2.340000	0.43974	1.524000	0.49035	0.655000	0.94253	CAC	.		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179550284	G	A	179550284	3	1	79	1	0	0	0	0	1	0	0	0	16768	1319	46	2	72116	2	TTN	2	179550284	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	1451484	179550284	63649089	11	7324											
FN1	2335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	216289927	216289927	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccacaccactgtctgtgAcacagtggccatagggagga	12	6	12	11	0	1	2	0	1	1	1	1	4	1	4	3	3	0	0	3	3	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:216289927A>C	ENST00000359671.1	-	7	1191	c.926T>G	c.(925-927)gTc>gGc	p.V309G	FN1_ENST00000354785.4_Missense_Mutation_p.V309G|FN1_ENST00000323926.6_Missense_Mutation_p.V309G|FN1_ENST00000432072.2_Missense_Mutation_p.V309G|FN1_ENST00000426059.1_Missense_Mutation_p.V309G|FN1_ENST00000446046.1_Missense_Mutation_p.V309G|FN1_ENST00000356005.4_Missense_Mutation_p.V309G|FN1_ENST00000357009.2_Missense_Mutation_p.V309G|FN1_ENST00000336916.4_Missense_Mutation_p.V309G|FN1_ENST00000346544.3_Missense_Mutation_p.V309G|FN1_ENST00000421182.1_Missense_Mutation_p.V309G|FN1_ENST00000345488.5_Missense_Mutation_p.V309G|FN1_ENST00000357867.4_Missense_Mutation_p.V309G|FN1_ENST00000443816.1_Missense_Mutation_p.V309G			P02751	FINC_HUMAN	fibronectin 1	309	Collagen-binding.|Fibronectin type-I 6. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	ACTGTCTGTGACACAGTGGCC	0.557																																					p.V309G		.											.	FN1-584	0			c.T926G						.						138	138	138					2																	216289927		2203	4300	6503	SO:0001583	missense	2335	exon7			TCTGTGACACAGT		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.926T>G	2.37:g.216289927A>C	ENSP00000352696:p.Val309Gly	Somatic	267	1		WXS	Illumina HiSeq	Phase_I	224	90	NM_212476	0	0	34	58	24	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	A	21.6	4.179602	0.78564	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000426059	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.83	4.69	0.59074	.	0.187265	0.36303	N	0.002672	T	0.52108	0.1714	L	0.36672	1.1	0.80722	D	1	B;D;B;P;B;B;P;D;B;B;P	0.69078	0.055;0.997;0.09;0.891;0.25;0.294;0.593;0.97;0.25;0.25;0.935	B;D;B;P;B;B;B;P;B;B;P	0.80764	0.092;0.994;0.072;0.621;0.092;0.149;0.21;0.839;0.092;0.092;0.736	T	0.54609	-0.8268	10	0.87932	D	0	.	11.3208	0.49421	0.9296:0.0:0.0704:0.0	.	309;309;309;309;309;309;309;309;309;309;309	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	G	309	ENSP00000394423:V309G;ENSP00000323534:V309G;ENSP00000338200:V309G;ENSP00000350534:V309G;ENSP00000346839:V309G;ENSP00000352696:V309G;ENSP00000265312:V309G;ENSP00000273049:V309G;ENSP00000349509:V309G;ENSP00000410422:V309G;ENSP00000415018:V309G;ENSP00000399538:V309G;ENSP00000348285:V309G;ENSP00000398907:V309G	ENSP00000265313:V309G	V	-	2	0	FN1	215998172	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.190000	0.58365	2.231000	0.72958	0.460000	0.39030	GTC	.		0.557	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216289927	A	C	216289927	3	2	79	1	0	0	0	0	1	0	0	0	5981	275	10	5	6700	5	FN1	2	216289927	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	36739643	216289927	26909446	12	7325											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233712220	233712220	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcagcgtcagcagcagcAgctgccacagcagcagcagc	11	2	12	16	1	1	0	1	0	0	0	1	0	1	0	2	0	11	8	2	0	0	0	rs527464858	byFrequency	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:233712220A>C	ENST00000409547.1	+	29	3934	c.3623A>C	c.(3622-3624)cAg>cCg	p.Q1208P	GIGYF2_ENST00000409480.1_Missense_Mutation_p.Q1230P|GIGYF2_ENST00000409451.3_Missense_Mutation_p.Q1229P|GIGYF2_ENST00000373566.3_Missense_Mutation_p.Q1230P|GIGYF2_ENST00000409196.3_Missense_Mutation_p.Q1202P|GIGYF2_ENST00000373563.4_Missense_Mutation_p.Q1208P	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1208	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		cagcagcagcagctgccacag	0.567																																					p.Q1229P		.											.	GIGYF2-28	0			c.A3686C						.						15	17	16					2																	233712220		2188	4274	6462	SO:0001583	missense	26058	exon29			AGCAGCAGCTGCC	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3623A>C	2.37:g.233712220A>C	ENSP00000386537:p.Gln1208Pro	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001103147	0	0	0	0	0	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	A	8.906	0.957519	0.18507	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451	T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.3	4.13	0.48395	.	0.921754	0.09517	N	0.791427	T	0.55673	0.1935	L	0.45137	1.4	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.46345	-0.9198	10	0.59425	D	0.04	-3.325	10.0439	0.42175	0.8304:0.1696:0.0:0.0	.	1229;1208;1202	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	P	1230;1208;1230;1208;1202;1229	ENSP00000362667:Q1230P;ENSP00000362664:Q1208P;ENSP00000386765:Q1230P;ENSP00000386537:Q1208P;ENSP00000387070:Q1202P;ENSP00000387170:Q1229P	ENSP00000362664:Q1208P	Q	+	2	0	GIGYF2	233420464	1.000000	0.71417	0.990000	0.47175	0.144000	0.21451	4.293000	0.59037	0.828000	0.34709	0.533000	0.62120	CAG	.		0.567	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		C	233712220	A	C	233712220	3	2	79	1	0	0	0	0	1	0	0	0	6398	188	7	5	3791	5	GIGYF2	2	233712220	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	17422293	233712220	9487153	13	7326											
SCN5A	6331	hgsc.bcm.edu;bcgsc.ca	37	chr3	38645417	38645417	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagggcaccagcagtgatGtgtggtggctctcgctctcc	5	9	14	13	1	2	1	0	1	2	0	4	1	2	1	3	3	1	4	3	3	0	0	rs199473575		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr3:38645417G>A	ENST00000333535.4	-	12	1825	c.1676C>T	c.(1675-1677)aCa>aTa	p.T559I	SCN5A_ENST00000451551.2_Missense_Mutation_p.T559I|SCN5A_ENST00000413689.1_Missense_Mutation_p.T559I|SCN5A_ENST00000425664.1_Missense_Mutation_p.T559I|SCN5A_ENST00000423572.2_Missense_Mutation_p.T559I|SCN5A_ENST00000455624.2_Missense_Mutation_p.T559I|SCN5A_ENST00000414099.2_Missense_Mutation_p.T559I|SCN5A_ENST00000443581.1_Missense_Mutation_p.T559I|SCN5A_ENST00000450102.2_Missense_Mutation_p.T559I|SCN5A_ENST00000449557.2_Missense_Mutation_p.T559I			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	559					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGCAGTGATGTGTGGTGGCT	0.622																																					p.T559I		.											.	SCN5A-98	0			c.C1676T						.						49	55	53					3																	38645417		2086	4212	6298	SO:0001583	missense	6331	exon12			AGTGATGTGTGGT	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10593	protein-coding gene	gene with protein product	"long QT syndrome 3"	600163	"sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1676C>T	3.37:g.38645417G>A	ENSP00000328968:p.Thr559Ile	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	67	35	NM_001160160	0	0	1	1	0	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780662	0.49891	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	4.27	2.43	0.29744	Domain of unknown function DUF3451 (1);	0.879266	0.09862	N	0.746040	D	0.87014	0.6072	L	0.44542	1.39	0.29849	N	0.828558	B;P;B;B;P;P;P	0.43231	0.259;0.801;0.418;0.259;0.801;0.799;0.763	B;B;B;B;B;B;B	0.43360	0.041;0.417;0.051;0.059;0.192;0.371;0.293	T	0.81636	-0.0843	10	0.72032	D	0.01	.	6.1048	0.20067	0.1921:0.2795:0.5284:0.0	.	559;559;559;559;559;559;559	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	I	559	ENSP00000398962:T559I;ENSP00000398266:T559I;ENSP00000410257:T559I;ENSP00000388797:T559I;ENSP00000397915:T559I;ENSP00000416634:T559I;ENSP00000328968:T559I;ENSP00000399524:T559I;ENSP00000403355:T559I;ENSP00000413996:T559I	ENSP00000328968:T559I	T	-	2	0	SCN5A	38620421	0.911000	0.30947	0.896000	0.35187	0.619000	0.37552	1.714000	0.37961	1.020000	0.39573	-0.224000	0.12420	ACA	.		0.622	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38645417	G	A	38645417	3	1	79	1	0	0	0	0	1	0	0	0	13954	1377	48	2	4442	2	SCN5A	3	38645417	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		38645417	159377013	14	7327											
PDZRN3	23024	broad.mit.edu;bcgsc.ca	37	chr3	73440201	73440201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatcccaatgtcgtcttcatCgtccgtccggtagcacacag	9	10	8	14	4	2	0	1	0	1	0	7	0	5	0	3	1	1	2	3	1	3	2	rs200273452		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr3:73440201C>T	ENST00000263666.4	-	6	1435	c.1321G>A	c.(1321-1323)Gat>Aat	p.D441N	PDZRN3_ENST00000535920.1_Missense_Mutation_p.D163N|PDZRN3_ENST00000462146.2_Missense_Mutation_p.D98N|PDZRN3_ENST00000479530.1_Missense_Mutation_p.D158N|PDZRN3_ENST00000466780.1_Missense_Mutation_p.D98N|PDZRN3_ENST00000466348.1_5'UTR	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	441	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCGTCTTCATCGTCCGTCCGG	0.438													C|||	1	0.000199681	0	0	5008	,	,		18795	0		0.001	False		,,,				2504	0				p.D441N													.	PDZRN3-232	0			c.G1321A						.	C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	271	252	258		1321	5.2	0.6	3		258	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDZRN3	NM_015009.1	23	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	probably-damaging	441/1067	73440201	4,13002	2203	4300	6503	SO:0001583	missense	23024	exon6			CTTCATCGTCCGT	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1321G>A	3.37:g.73440201C>T	ENSP00000263666:p.Asp441Asn	Somatic	417	0		WXS	Illumina HiSeq	Phase_I	386	15	NM_015009	0	0	3	3	0	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	C	33	5.239542	0.95240	2.27E-4	3.49E-4	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000416926;ENST00000492909	T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75	5.18	5.18	0.71444	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	L	0.41632	1.29	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.993;0.999;0.985;0.997	T	0.31392	-0.9945	10	0.52906	T	0.07	.	18.2949	0.90141	0.0:1.0:0.0:0.0	.	163;158;158;441	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	N	441;163;98;98;158;441;139	ENSP00000263666:D441N;ENSP00000442026:D163N;ENSP00000418168:D98N;ENSP00000418484:D98N;ENSP00000418624:D158N;ENSP00000419250:D139N	ENSP00000263666:D441N	D	-	1	0	PDZRN3	73522891	1.000000	0.71417	0.607000	0.28956	0.911000	0.54048	7.638000	0.83328	2.413000	0.81919	0.655000	0.94253	GAT	.		0.438	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73440201	C	T	73440201	3	4	79	1	0	0	0	0	1	0	0	0	11735	884	31	1	1899	1	PDZRN3	3	73440201	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	34794784	73440201	124582229	15	7328											
ATP2C1	27032	broad.mit.edu;bcgsc.ca	37	chr3	130673864	130673864	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttttccccttagggtgttgtCattggaacaggagaaaattc	10	14	10	7	0	1	1	1	0	0	1	3	3	2	2	2	3	1	1	2	3	4	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr3:130673864C>T	ENST00000510168.1	+	10	1246	c.696C>T	c.(694-696)gtC>gtT	p.V232V	ATP2C1_ENST00000328560.8_Silent_p.V232V|ATP2C1_ENST00000507488.2_Silent_p.V216V|ATP2C1_ENST00000513801.1_Silent_p.V216V|ATP2C1_ENST00000422190.2_Silent_p.V232V|ATP2C1_ENST00000393221.4_Silent_p.V266V|ATP2C1_ENST00000533801.2_Silent_p.V227V|ATP2C1_ENST00000504381.1_Silent_p.V177V|ATP2C1_ENST00000428331.2_Silent_p.V232V|ATP2C1_ENST00000359644.3_Silent_p.V232V|ATP2C1_ENST00000504948.1_Silent_p.V216V|ATP2C1_ENST00000505330.1_Silent_p.V216V|ATP2C1_ENST00000508532.1_Silent_p.V232V			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	232					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AGGGTGTTGTCATTGGAACAG	0.343									Hailey-Hailey disease																												p.V266V	Esophageal Squamous(99;456 1443 27647 34099 42636)												.	ATP2C1-91	0			c.C798T						.						103	103	103					3																	130673864		2203	4300	6503	SO:0001819	synonymous_variant	27032	exon9	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	TGTTGTCATTGGA	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.696C>T	3.37:g.130673864C>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	51	16	NM_001199181	0	0	0	0	0	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Silent	SNP	ENST00000510168.1	37	CCDS46914.1	.	.	.	.	.	.	.	.	.	.	C	9.223	1.033964	0.19590	.	.	ENSG00000017260	ENST00000504612	.	.	.	5.28	3.48	0.39840	.	.	.	.	.	T	0.54398	0.1856	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50566	-0.8813	4	.	.	.	.	5.561	0.17144	0.0:0.6103:0.1566:0.2331	.	.	.	.	L	186	.	.	S	+	2	0	ATP2C1	132156554	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.926000	0.28804	1.234000	0.43709	0.650000	0.86243	TCA	.		0.343	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		T	130673864	C	T	130673864	2	4	79	1	0	0	0	0	0	0	0	1	1144	813	29	2		2	ATP2C1	3	130673864	Silent	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	57233663	130673864	67348566	16	7329											
AFAP1	60312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	7857226	7857226	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccggagcttttccggggcTcagcggcacagcttcctcat	5	11	11	14	3	2	0	2	0	0	0	5	1	5	1	3	4	3	4	3	4	0	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr4:7857226T>G	ENST00000360265.4	-	3	535	c.301A>C	c.(301-303)Agc>Cgc	p.S101R	AFAP1_ENST00000382543.3_Missense_Mutation_p.S101R|AFAP1_ENST00000358461.2_Missense_Mutation_p.S101R|AFAP1_ENST00000420658.1_Missense_Mutation_p.S101R			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	101	Pro-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TTTCCGGGGCTCAGCGGCACA	0.562																																					p.S101R		.											.	AFAP1-90	0			c.A301C						.						89	76	81					4																	7857226		2203	4300	6503	SO:0001583	missense	60312	exon4			CGGGGCTCAGCGG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.301A>C	4.37:g.7857226T>G	ENSP00000353402:p.Ser101Arg	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	60	26	NM_001134647	0	0	0	2	2	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793690	0.70452	.	.	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	4.79	4.79	0.61399	.	0.087086	0.85682	D	0.000000	T	0.52403	0.1732	L	0.34521	1.04	0.43326	D	0.995356	D;D	0.67145	0.996;0.99	P;P	0.58577	0.719;0.841	T	0.56347	-0.7994	10	0.66056	D	0.02	-20.9708	13.3262	0.60461	0.0:0.0:0.0:1.0	.	101;101	E9PDT7;Q8N556	.;AFAP1_HUMAN	R	101	ENSP00000353402:S101R;ENSP00000410689:S101R;ENSP00000351245:S101R;ENSP00000371983:S101R	ENSP00000351245:S101R	S	-	1	0	AFAP1	7908126	1.000000	0.71417	0.975000	0.42487	0.988000	0.76386	3.466000	0.53071	1.780000	0.52325	0.459000	0.35465	AGC	.		0.562	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		G	7857226	T	G	7857226	3	3	79	1	0	0	0	0	1	0	0	0	353	1551	54	5	2203	5	AFAP1	4	7857226	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08		7857226	183297050	17	7330											
SLC10A4	201780	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	48490947	48490948	+	Frame_Shift_Ins	INS	-	-	TC																															tgatggaaaccgctcagactINStctctctaaatgtggagata																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr4:48490947_48490948insTC	ENST00000273861.4	+	3	1524_1525	c.1305_1306insTC	c.(1306-1308)tctfs	p.S436fs	ZAR1_ENST00000327939.4_5'Flank	NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	436						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						CCGCTCAGACTTCTCTCTAAAT	0.351																																					p.T435fs		.											.	SLC10A4-90	0			c.1305_1306insTC						.																																			SO:0001589	frameshift_variant	201780	exon3			.	BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"Solute carriers"	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.1310_1311dupTC	4.37:g.48490952_48490953dupTC	ENSP00000273861:p.Ser436fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	67	16	NM_152679	0	0	0	0	0	Q8WUZ2	Frame_Shift_Ins	INS	ENST00000273861.4	37	CCDS3482.1																																																																																			.		0.351	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		TC	48490948	-	TC	48490947	7	5	79	1	0	1	1	0	0	0	0	0	14408	1596	56	0	1315	0	SLC10A4	4	48490947	Frame_Shift_Ins	INS	-	TCGA-BQ-7044-01A-11D-1961-08	40633721	48490947	142663329	18	7331											
SMARCAD1	56916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	95191935	95191935	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggctggcattggtacataAacatggacttaatggcattt	11	14	10	6	0	0	0	0	0	0	0	0	1	0	1	0	5	2	4	0	5	4	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr4:95191935A>G	ENST00000354268.4	+	11	1611	c.1538A>G	c.(1537-1539)aAa>aGa	p.K513R	SMARCAD1_ENST00000457823.2_Missense_Mutation_p.K513R|SMARCAD1_ENST00000509418.1_Missense_Mutation_p.K83R			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	513	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		TTGGTACATAAACATGGACTT	0.343																																					p.K513R		.											.	SMARCAD1-229	0			c.A1538G						.						198	186	190					4																	95191935		2203	4300	6503	SO:0001583	missense	56916	exon11			TACATAAACATGG	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.1538A>G	4.37:g.95191935A>G	ENSP00000346217:p.Lys513Arg	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	123	47	NM_001128429	0	0	9	23	14	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	A	17.84	3.488315	0.64074	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268;ENST00000509418	D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19	5.86	5.86	0.93980	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.46442	D	0.000282	D	0.85660	0.5748	N	0.03294	-0.36	0.54753	D	0.999987	B;B	0.32753	0.256;0.383	B;B	0.37091	0.241;0.155	D	0.84661	0.0706	10	0.23302	T	0.38	-27.7438	16.2652	0.82574	1.0:0.0:0.0:0.0	.	513;513	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	R	513;513;513;83	ENSP00000351947:K513R;ENSP00000415576:K513R;ENSP00000346217:K513R;ENSP00000423286:K83R	ENSP00000346217:K513R	K	+	2	0	SMARCAD1	95410958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.861000	0.75478	2.241000	0.73720	0.528000	0.53228	AAA	.		0.343	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		G	95191935	A	G	95191935	3	3	79	1	0	0	0	0	1	0	0	0	14804	14	1	3	1576	3	SMARCAD1	4	95191935	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	46700988	95191935	95962341	19	7332											
MYO10	4651	ucsc.edu	37	chr5	16701576	16701576	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaagttgggcttctcctcGcatgcgctctcagccagctc	5	12	10	14	2	2	1	1	1	2	0	6	1	2	1	2	1	3	5	2	1	1	3	rs367952629		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:16701576G>A	ENST00000513610.1	-	25	3382	c.2928C>T	c.(2926-2928)tgC>tgT	p.C976C	MYO10_ENST00000505695.1_Silent_p.C315C|MYO10_ENST00000274203.9_Silent_p.C333C|MYO10_ENST00000515803.1_Silent_p.C315C|MYO10_ENST00000427430.2_Silent_p.C333C|MYO10_ENST00000512061.1_5'Flank	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	976					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GCTTCTCCTCGCATGCGCTCT	0.592																																					p.C976C													.	MYO10-3	0			c.C2928T						.						35	39	38					5																	16701576		2105	4231	6336	SO:0001819	synonymous_variant	4651	exon25			CTCCTCGCATGCG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2928C>T	5.37:g.16701576G>A		Somatic	75	0		WXS	Illumina HiSeq		52	5	NM_012334	0	0	27	27	0	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			.		0.592	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16701576	G	A	16701576	2	1	79	1	0	0	0	0	0	0	0	1	10087	1079	38	1		1	MYO10	5	16701576	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		16701576	164213684	20	7333											
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	32108145	32108145	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctattaatgggaaacctctGgttgggctcatgcactttga	9	13	11	8	0	2	1	1	1	1	0	2	2	2	2	1	3	2	4	1	3	3	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:32108145G>A	ENST00000438447.1	+	25	8812	c.8424G>A	c.(8422-8424)ctG>ctA	p.L2808L	PDZD2_ENST00000282493.3_Silent_p.L2808L|PDZD2_ENST00000513490.1_3'UTR|CTD-2152M20.2_ENST00000503441.1_RNA			O15018	PDZD2_HUMAN	PDZ domain containing 2	2808	PDZ 6. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGAAACCTCTGGTTGGGCTCA	0.388																																					p.L2808L		.											.	PDZD2-563	0			c.G8424A						.						129	134	133					5																	32108145		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon24			ACCTCTGGTTGGG	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.8424G>A	5.37:g.32108145G>A		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	125	54	NM_178140	0	0	2	2	0	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			.		0.388	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32108145	G	A	32108145	2	1	79	1	0	0	0	0	0	0	0	1	11727	1335	47	2		2	PDZD2	5	32108145	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	15406569	32108145	148807115	21	7334											
POLK	51426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	74872636	74872636	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttgctgattatgatcccaAttttatggccatgagtcttg	9	16	8	8	0	1	3	0	3	1	0	2	3	2	3	2	1	1	1	2	1	3	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:74872636A>C	ENST00000241436.4	+	6	744	c.572A>C	c.(571-573)aAt>aCt	p.N191T	POLK_ENST00000352007.5_Missense_Mutation_p.N191T|POLK_ENST00000508526.1_Missense_Mutation_p.N191T|POLK_ENST00000380481.3_Missense_Mutation_p.N101T|POLK_ENST00000515295.1_Missense_Mutation_p.N191T|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000504026.1_Missense_Mutation_p.N191T	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	191	UmuC.				DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		TATGATCCCAATTTTATGGCC	0.328								DNA polymerases (catalytic subunits)																													p.N191T		.											.	POLK-229	0			c.A572C						.						72	70	71					5																	74872636		2203	4299	6502	SO:0001583	missense	51426	exon6			ATCCCAATTTTAT	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.572A>C	5.37:g.74872636A>C	ENSP00000241436:p.Asn191Thr	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	54	24	NM_016218	0	0	5	11	6	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	37	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.883355	0.72410	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000515295;ENST00000504026;ENST00000508526;ENST00000380481	T;T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99;-0.99	5.34	5.34	0.76211	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.296696	0.40064	N	0.001200	T	0.77987	0.4213	L	0.38175	1.15	0.42098	D	0.991328	P;P;P;D	0.53885	0.804;0.607;0.597;0.963	P;P;P;P	0.62740	0.663;0.653;0.624;0.906	T	0.80415	-0.1392	10	0.87932	D	0	-10.8466	11.291	0.49250	0.9266:0.0:0.0734:0.0	.	191;191;191;191	Q9UBT6-3;Q5Q9G5;Q9UBT6-2;Q9UBT6	.;.;.;POLK_HUMAN	T	191;191;191;191;191;101	ENSP00000241436:N191T;ENSP00000342256:N191T;ENSP00000424174:N191T;ENSP00000425075:N191T;ENSP00000426853:N191T;ENSP00000369848:N101T	ENSP00000241436:N191T	N	+	2	0	POLK	74908392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.254000	0.65457	2.018000	0.59344	0.460000	0.39030	AAT	.		0.328	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		C	74872636	A	C	74872636	3	2	79	1	0	0	0	0	1	0	0	0	12230	101	4	5	590	5	POLK	5	74872636	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	42764491	74872636	106042624	22	7335											
ZNF608	57507	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	123983889	123983889	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcacttttcagtttagAgaggtttttgtccgttttgc	5	17	11	8	2	1	1	1	0	0	1	2	2	2	1	2	2	1	4	2	2	1	8			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:123983889A>T	ENST00000306315.5	-	4	2623	c.2188T>A	c.(2188-2190)Tct>Act	p.S730T	ZNF608_ENST00000504926.1_Missense_Mutation_p.S303T	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	730							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		TTCAGTTTAGAGAGGTTTTTG	0.483																																					p.S730T		.											.	ZNF608-229	0			c.T2188A						.						29	31	30					5																	123983889		2203	4300	6503	SO:0001583	missense	57507	exon4			GTTTAGAGAGGTT	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.2188T>A	5.37:g.123983889A>T	ENSP00000307746:p.Ser730Thr	Somatic	40	1		WXS	Illumina HiSeq	Phase_I	47	21	NM_020747	0	0	2	3	1	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	A	15.82	2.947262	0.53186	.	.	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.49432	0.78;0.78	6.01	4.84	0.62591	.	0.321088	0.35903	N	0.002902	T	0.44307	0.1287	L	0.56769	1.78	0.38018	D	0.934741	P	0.46142	0.873	B	0.39660	0.306	T	0.48937	-0.8990	10	0.35671	T	0.21	-11.9515	13.5264	0.61597	0.8699:0.1301:0.0:0.0	.	730	Q9ULD9	ZN608_HUMAN	T	303;730	ENSP00000427657:S303T;ENSP00000307746:S730T	ENSP00000307746:S730T	S	-	1	0	ZNF608	124011788	0.997000	0.39634	0.945000	0.38365	0.940000	0.58332	3.554000	0.53720	1.074000	0.40909	0.523000	0.50628	TCT	.		0.483	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		T	123983889	A	T	123983889	3	4	79	1	0	0	0	0	1	0	0	0	18066	304	11	5	2374	5	ZNF608	5	123983889	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	49111253	123983889	56931371	23	7336											
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179192887	179192887	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgccacacaaacccccttGgcacaggacattaatattaa	14	9	5	13	0	1	0	0	0	1	0	1	1	1	1	3	2	2	1	3	2	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:179192887G>A	ENST00000292599.3	+	2	1139	c.876G>A	c.(874-876)ttG>ttA	p.L292L	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAACCCCCTTGGCACAGGACA	0.527																																					p.L292L		.											.	MAML1-848	0			c.G876A						.						63	71	68					5																	179192887		2203	4300	6503	SO:0001819	synonymous_variant	9794	exon2			CCCCTTGGCACAG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.876G>A	5.37:g.179192887G>A		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	146	68	NM_014757	0	0	7	8	1		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																			.		0.527	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		A	179192887	G	A	179192887	2	1	79	1	0	0	0	0	0	0	0	1	9230	1339	47	2		2	MAML1	5	179192887	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	55208998	179192887	1722373	24	7337											
BAT2	7916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31595867	31595867	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agctccacctccagcatcagCcccaacaccagagacagaac	14	3	6	18	0	1	2	1	0	0	2	3	3	3	2	6	0	5	2	6	0	2	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr6:31595867C>T	ENST00000376033.2	+	12	1850	c.1616C>T	c.(1615-1617)gCc>gTc	p.A539V	PRRC2A_ENST00000376007.4_Missense_Mutation_p.A539V	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	539	2 X type B repeats.|4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CCAGCATCAGCCCCAACACCA	0.627																																					p.A539V		.											.	PRRC2A-156	0			c.C1616T						.						127	114	119					6																	31595867		1511	2709	4220	SO:0001583	missense	7916	exon12			CATCAGCCCCAAC	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"HLA-B associated transcript 2"	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.1616C>T	6.37:g.31595867C>T	ENSP00000365201:p.Ala539Val	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	136	55	NM_004638	0	1	52	89	36	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	9.670	1.146580	0.21288	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.08102	3.13;3.13	4.62	0.771	0.18504	.	0.843533	0.10340	N	0.686385	T	0.00967	0.0032	N	0.02011	-0.69	0.24306	N	0.995104	B	0.02656	0.0	B	0.04013	0.001	T	0.48269	-0.9050	10	0.87932	D	0	-0.1078	6.2328	0.20744	0.0:0.5543:0.0:0.4457	.	539	P48634	PRC2A_HUMAN	V	539;528;539;539	ENSP00000365175:A539V;ENSP00000365201:A539V	ENSP00000365175:A539V	A	+	2	0	PRRC2A	31703846	0.098000	0.21812	0.464000	0.27143	0.840000	0.47671	1.319000	0.33655	0.269000	0.21961	0.561000	0.74099	GCC	.		0.627	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31595867	C	T	31595867	3	4	79	1	0	0	0	0	1	0	0	0	1320	739	26	2	1658	2	BAT2	6	31595867	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		31595867	139519200	25	7338											
C6orf226	441150	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42858492	42858492	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgaagctgaggcagaggccGgggccgagcattggggactg	8	4	19	10	3	0	2	0	1	0	1	0	5	0	3	3	6	2	3	3	6	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr6:42858492G>A	ENST00000408925.2	-	1	62	c.35C>T	c.(34-36)cCg>cTg	p.P12L		NM_001008739.1	NP_001008739.1	Q5I0X4	CF226_HUMAN	chromosome 6 open reading frame 226	12										lung(2)	2						GGCAGAGGCCGGGGCCGAGCA	0.672																																					p.P12L		.											.	.	0			c.C35T						.						30	39	36					6																	42858492		1987	4153	6140	SO:0001583	missense	441150	exon1			GAGGCCGGGGCCG	BC051007, BC060325	CCDS43463.1	6p21.1	2009-02-11			ENSG00000221821	ENSG00000221821			34431	protein-coding gene	gene with protein product							Standard	NM_001008739		Approved	LOC441150	uc003osw.3	Q5I0X4	OTTHUMG00000156926	ENST00000408925.2:c.35C>T	6.37:g.42858492G>A	ENSP00000386146:p.Pro12Leu	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	86	30	NM_001008739	0	0	14	29	15		Missense_Mutation	SNP	ENST00000408925.2	37	CCDS43463.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.062387	0.36373	.	.	ENSG00000221821	ENST00000408925	.	.	.	4.44	3.54	0.40534	.	0.508870	0.15438	N	0.262358	T	0.14056	0.0340	N	0.08118	0	0.09310	N	1	D	0.67145	0.996	P	0.52267	0.694	T	0.05370	-1.0889	9	0.49607	T	0.09	-4.2365	10.0913	0.42449	0.0:0.2039:0.7961:0.0	.	12	Q5I0X4	CF226_HUMAN	L	12	.	ENSP00000386146:P12L	P	-	2	0	C6orf226	42966470	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.029000	0.12329	1.056000	0.40484	0.561000	0.74099	CCG	.		0.672	C6orf226-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346635.1	NM_001008739		A	42858492	G	A	42858492	3	1	79	1	0	0	0	0	1	0	0	0	2365	1116	39	1	274	1	C6orf226	6	42858492	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	11262625	42858492	128256575	26	7339											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51917922	51917922	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatccacatagaacaggcCcgtctcctgggccagaggga	10	7	11	13	1	2	2	1	0	1	2	4	3	3	3	4	3	1	0	4	3	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr6:51917922C>T	ENST00000371117.3	-	21	2367	c.2092G>A	c.(2092-2094)Ggc>Agc	p.G698S	PKHD1_ENST00000340994.4_Missense_Mutation_p.G698S	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	698					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TAGAACAGGCCCGTCTCCTGG	0.517																																					p.G698S		.											.	PKHD1-603	0			c.G2092A						.						72	73	73					6																	51917922		2203	4300	6503	SO:0001583	missense	5314	exon21			ACAGGCCCGTCTC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2092G>A	6.37:g.51917922C>T	ENSP00000360158:p.Gly698Ser	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	62	25	NM_170724	0	0	11	14	3	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.511891	0.44660	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.86865	-1.97;-2.18	5.63	3.77	0.43336	.	0.810468	0.11546	N	0.553288	T	0.63141	0.2486	L	0.33485	1.01	0.09310	N	1	B;B	0.20887	0.047;0.049	B;B	0.16289	0.015;0.012	T	0.50734	-0.8793	10	0.13108	T	0.6	.	9.2695	0.37661	0.0:0.7612:0.0:0.2388	.	698;698	P08F94-2;P08F94	.;PKHD1_HUMAN	S	698	ENSP00000360158:G698S;ENSP00000341097:G698S	ENSP00000341097:G698S	G	-	1	0	PKHD1	52025881	0.000000	0.05858	0.012000	0.15200	0.396000	0.30629	0.272000	0.18644	1.462000	0.47948	0.655000	0.94253	GGC	.		0.517	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51917922	C	T	51917922	3	4	79	1	0	0	0	0	1	0	0	0	11997	623	22	2	10359	2	PKHD1	6	51917922	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	9059430	51917922	119197145	27	7340											
CLIP2	7461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	73752800	73752800	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccactgcacaaacagtcAtctggaccctcctcctcccc	8	8	4	21	0	2	0	1	0	1	0	6	1	6	1	7	1	2	1	7	1	1	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:73752800A>T	ENST00000395060.1	+	2	144	c.144A>T	c.(142-144)tcA>tcT	p.S48S	CLIP2_ENST00000361545.5_Silent_p.S48S|CLIP2_ENST00000223398.6_Silent_p.S48S			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	48						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						ACAAACAGTCATCTGGACCCT	0.657																																					p.S48S		.											.	CLIP2-93	0			c.A144T						.						21	17	18					7																	73752800		2195	4292	6487	SO:0001819	synonymous_variant	7461	exon3			ACAGTCATCTGGA	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.144A>T	7.37:g.73752800A>T		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	29	18	NM_032421	0	0	8	37	29	O14527|O43611	Silent	SNP	ENST00000395060.1	37	CCDS5569.1																																																																																			.		0.657	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		T	73752800	A	T	73752800	2	4	79	1	0	0	0	0	0	0	0	1	3539	204	8	5		5	CLIP2	7	73752800	Silent	SNP	A	TCGA-BQ-7044-01A-11D-1961-08		73752800	85385863	28	7341											
UFSP1	402682	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	100486530	100486530	+	Frame_Shift_Del	DEL	G	G	-																															cacaggttgtagaaggagttGgggtcaaaggctgcactcac																								rs372960530		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:100486530delG	ENST00000388761.2	-	1	809	c.363delC	c.(361-363)cccfs	p.P121fs		NM_001015072.3	NP_001015072.2	Q6NVU6	UFSP1_HUMAN	UFM1-specific peptidase 1 (non-functional)	121						extracellular vesicular exosome (GO:0070062)	thiolester hydrolase activity (GO:0016790)|UFM1 hydrolase activity (GO:0071567)			lung(1)|stomach(1)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGAAGGAGTTGGGGTCAAAGG	0.567																																					p.P121fs		.											.	UFSP1-22	0			c.363delC						.						181	154	163					7																	100486530		2203	4300	6503	SO:0001589	frameshift_variant	402682	exon1			.	AF312032	CCDS34710.1	7q22.1	2008-03-25			ENSG00000176125	ENSG00000176125			33821	protein-coding gene	gene with protein product		611481				17182609, 18321862	Standard	NM_001015072		Approved	UFSP	uc003uxc.4	Q6NVU6	OTTHUMG00000159662	ENST00000388761.2:c.363delC	7.37:g.100486530delG	ENSP00000373413:p.Pro121fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	197	106	NM_001015072	0	0	0	0	0	A4D2E4|A8K8V2|B6ZDG6|Q9BXP6	Frame_Shift_Del	DEL	ENST00000388761.2	37	CCDS34710.1																																																																																			.		0.567	UFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356751.1	NM_001015072		-	100486530	G	-	100486530	7	5	79	1	0	1	0	1	0	0	0	0	16970	1335	47	0	69	0	UFSP1	7	100486530	Frame_Shift_Del	DEL	G	TCGA-BQ-7044-01A-11D-1961-08	26733730	100486530	58652133	29	7342											
CHCHD3	54927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	132754922	132754922	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgaggcaccataagcaccaGaataccgctgagacttcgaa	14	6	9	12	2	0	3	0	2	0	2	1	5	0	3	3	1	2	3	3	1	4	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:132754922G>A	ENST00000262570.5	-	2	293	c.149C>T	c.(148-150)tCt>tTt	p.S50F	CHCHD3_ENST00000448878.1_Missense_Mutation_p.S50F|CHCHD3_ENST00000476546.1_Intron|CHCHD3_ENST00000542753.1_Missense_Mutation_p.S50F	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	50					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						ATAAGCACCAGAATACCGCTG	0.353																																					p.S50F		.											.	CHCHD3-90	0			c.C149T						.						79	69	72					7																	132754922		2203	4300	6503	SO:0001583	missense	54927	exon2			GCACCAGAATACC	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21906	protein-coding gene	gene with protein product	"mitochondrial inner membrane organizing system 3", "protein phosphatase 1, regulatory subunit 22"	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.149C>T	7.37:g.132754922G>A	ENSP00000262570:p.Ser50Phe	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	82	17	NM_017812	0	0	62	99	37		Missense_Mutation	SNP	ENST00000262570.5	37	CCDS5828.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.975118	0.34848	.	.	ENSG00000106554	ENST00000262570;ENST00000448878;ENST00000542753	T;T;T	0.46451	0.87;0.87;0.87	6.03	6.03	0.97812	.	0.483083	0.24301	N	0.039727	T	0.55513	0.1925	L	0.43152	1.355	0.23841	N	0.996695	B;D;B	0.65815	0.006;0.995;0.004	B;D;B	0.63283	0.006;0.913;0.007	T	0.51553	-0.8691	10	0.66056	D	0.02	-0.3383	16.0569	0.80812	0.0:0.0:1.0:0.0	.	50;50;50	G3V1K1;C9JRZ6;Q9NX63	.;.;CHCH3_HUMAN	F	50	ENSP00000262570:S50F;ENSP00000389297:S50F;ENSP00000440267:S50F	ENSP00000262570:S50F	S	-	2	0	CHCHD3	132405462	1.000000	0.71417	0.739000	0.30968	0.676000	0.39594	3.255000	0.51484	2.861000	0.98227	0.655000	0.94253	TCT	.		0.353	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		A	132754922	G	A	132754922	3	1	79	1	0	0	0	0	1	0	0	0	3323	942	33	2	562	2	CHCHD3	7	132754922	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	32268392	132754922	26383741	30	7343											
EXOC4	60412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	133692515	133692515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggcatcaagaaaatgtgtAggaacatttttgttcttcag	12	14	9	6	0	3	1	2	0	1	1	3	2	3	2	0	2	1	3	0	2	5	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:133692515A>G	ENST00000253861.4	+	17	2643	c.2614A>G	c.(2614-2616)Agg>Ggg	p.R872G	EXOC4_ENST00000539845.1_Missense_Mutation_p.R771G|EXOC4_ENST00000541309.1_Missense_Mutation_p.R160G|EXOC4_ENST00000545148.1_Missense_Mutation_p.R482G	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	872					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				GAAAATGTGTAGGAACATTTT	0.502																																					p.R872G		.											.	EXOC4-159	0			c.A2614G						.						85	71	76					7																	133692515		2203	4300	6503	SO:0001583	missense	60412	exon17			ATGTGTAGGAACA	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"SEC8-like 1 (S. cerevisiae)"	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2614A>G	7.37:g.133692515A>G	ENSP00000253861:p.Arg872Gly	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	83	36	NM_021807	0	0	50	62	12	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.958834	0.74016	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.45	2.87	0.33458	.	0.000000	0.85682	D	0.000000	T	0.78020	0.4218	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.984;0.998;0.996	T	0.81075	-0.1097	9	0.66056	D	0.02	.	11.6561	0.51320	0.7492:0.2508:0.0:0.0	.	404;482;872	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	G	872;491;771;482;160	.	ENSP00000253861:R872G	R	+	1	2	EXOC4	133343055	0.966000	0.33281	0.990000	0.47175	0.984000	0.73092	1.330000	0.33781	2.078000	0.62432	0.482000	0.46254	AGG	.		0.502	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		G	133692515	A	G	133692515	3	3	79	1	0	0	0	0	1	0	0	0	5319	411	15	3	2689	3	EXOC4	7	133692515	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	937593	133692515	25446148	31	7344											
KIAA1549	57670	broad.mit.edu;ucsc.edu	37	chr7	138595898	138595898	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagctgtctcacctgtttGaacttggaacctggactctg	7	13	10	11	0	2	2	1	2	2	0	3	4	2	4	2	2	3	2	2	2	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:138595898G>T	ENST00000422774.1	-	4	3187	c.3139C>A	c.(3139-3141)Caa>Aaa	p.Q1047K	KIAA1549_ENST00000242365.4_Missense_Mutation_p.Q997K|KIAA1549_ENST00000440172.1_Missense_Mutation_p.Q1047K			Q9HCM3	K1549_HUMAN	KIAA1549	1047						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TCACCTGTTTGAACTTGGAAC	0.328			O	BRAF	pilocytic astrocytoma																																p.Q1047K	NSCLC(119;1534 1718 44213 46230 50068)			Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549-369	0			c.C3139A						.						45	41	42					7																	138595898		1855	4102	5957	SO:0001583	missense	57670	exon4			CTGTTTGAACTTG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.3139C>A	7.37:g.138595898G>T	ENSP00000416040:p.Gln1047Lys	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	28	9	NM_020910	0	0	0	0	0	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.929538	0.52759	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.18960	2.18;2.18;2.21	5.23	5.23	0.72850	.	0.159296	0.42548	D	0.000698	T	0.18923	0.0454	N	0.11560	0.145	0.53005	D	0.999969	P;P	0.50819	0.939;0.925	P;P	0.53988	0.739;0.621	T	0.01874	-1.1256	10	0.06236	T	0.91	.	17.9688	0.89107	0.0:0.0:1.0:0.0	.	1047;1047	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	K	1047;997;1047	ENSP00000406661:Q1047K;ENSP00000242365:Q997K;ENSP00000416040:Q1047K	ENSP00000242365:Q997K	Q	-	1	0	KIAA1549	138246438	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.450000	0.90340	2.721000	0.93114	0.655000	0.94253	CAA	.		0.328	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138595898	G	T	138595898	3	4	79	1	0	0	0	0	1	0	0	0	8265	1299	45	4	2781	4	KIAA1549	7	138595898	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	4903383	138595898	20542765	32	7345											
MGAM	8972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	141750617	141750617	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacagtgaaacacaatggtGtcccaagtcagacttctcct	12	11	7	11	0	2	2	1	1	1	1	4	2	3	2	2	1	2	0	2	1	4	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:141750617G>T	ENST00000549489.2	+	24	2853	c.2758G>T	c.(2758-2760)Gtc>Ttc	p.V920F	MGAM_ENST00000475668.2_Missense_Mutation_p.V920F	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	920					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ACACAATGGTGTCCCAAGTCA	0.388																																					p.V920F		.											.	MGAM-70	0			c.G2758T						.						105	95	98					7																	141750617		1869	4101	5970	SO:0001583	missense	8972	exon24			AATGGTGTCCCAA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.2758G>T	7.37:g.141750617G>T	ENSP00000447378:p.Val920Phe	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	196	41	NM_004668	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.560136	0.27827	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.89681	-2.55	5.81	0.962	0.19643	.	1.575090	0.03884	N	0.277575	D	0.86464	0.5939	M	0.62266	1.93	0.09310	N	1	B	0.27791	0.189	B	0.18561	0.022	T	0.66296	-0.5959	10	0.24483	T	0.36	.	9.7694	0.40580	0.4125:0.0:0.5875:0.0	.	920	O43451	MGA_HUMAN	F	920;920;797	ENSP00000447378:V920F	ENSP00000316431:V797F	V	+	1	0	MGAM	141397086	0.000000	0.05858	0.000000	0.03702	0.389000	0.30415	0.254000	0.18314	-0.105000	0.12132	-0.336000	0.08194	GTC	.		0.388	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141750617	G	T	141750617	3	4	79	1	0	0	0	0	1	0	0	0	9566	1377	48	4	2848	4	MGAM	7	141750617	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	3154719	141750617	17388046	33	7346											
OR2F1	26211	bcgsc.ca	37	chr7	143657509	143657509	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taggttggccatcacatcctGggtcagtggcttcatcagct	7	12	11	11	0	4	0	4	0	0	0	5	0	5	0	2	4	1	3	2	4	1	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:143657509G>T	ENST00000392899.1	+	1	483	c.446G>T	c.(445-447)tGg>tTg	p.W149L	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	149					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					ATCACATCCTGGGTCAGTGGC	0.527																																					p.W149L													.	OR2F1-71	0			c.G446T						.						138	116	124					7																	143657509		2203	4300	6503	SO:0001583	missense	26211	exon1			CATCCTGGGTCAG	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.446G>T	7.37:g.143657509G>T	ENSP00000376633:p.Trp149Leu	Somatic	108	4		WXS	Illumina HiSeq	Phase_1	145	91	NM_012369	0	0	0	0	0	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836523	0.50951	.	.	ENSG00000213215	ENST00000392899	T	0.58210	0.35	5.53	2.74	0.32292	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000128	T	0.63200	0.2491	L	0.43554	1.36	0.37578	D	0.919703	D	0.89917	1.0	D	0.91635	0.999	T	0.67209	-0.5728	10	0.62326	D	0.03	-12.7388	12.892	0.58076	0.0:0.0:0.43:0.57	.	149	Q13607	OR2F1_HUMAN	L	149	ENSP00000376633:W149L	ENSP00000376633:W149L	W	+	2	0	OR2F1	143288442	0.998000	0.40836	0.898000	0.35279	0.599000	0.36880	1.120000	0.31271	0.428000	0.26173	0.655000	0.94253	TGG	.		0.527	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			T	143657509	G	T	143657509	3	4	79	1	0	0	0	0	1	0	0	0	11022	1357	47	4	448	4	OR2F1	7	143657509	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	1906892	143657509	15481154	34	7347											
PTPRN2	5799	broad.mit.edu	37	chr7	157414139	157414139	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgggctccgcctggtaggcGcacagcgcttcccactcctt	4	10	11	16	3	0	0	0	0	0	0	3	0	3	0	4	3	1	4	4	3	1	4	rs77143062		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:157414139G>A	ENST00000389418.4	-	15	2268	c.2259C>T	c.(2257-2259)tgC>tgT	p.C753C	PTPRN2_ENST00000409483.1_Silent_p.C715C|PTPRN2_ENST00000389413.3_Silent_p.C724C|PTPRN2_ENST00000389416.4_Silent_p.C736C|PTPRN2_ENST00000404321.2_Silent_p.C776C	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	753	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCTGGTAGGCGCACAGCGCTT	0.622													g|||	1	0.000199681	8e-04	0	5008	,	,		19599	0		0	False		,,,				2504	0				p.C753C													.	PTPRN2-295	0			c.C2259T						.						196	182	187					7																	157414139		2203	4300	6503	SO:0001819	synonymous_variant	5799	exon15			GTAGGCGCACAGC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9677	protein-coding gene	gene with protein product	"IAR PTPRP"	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2259C>T	7.37:g.157414139G>A		Somatic	287	0		WXS	Illumina HiSeq	Phase_I	395	15	NM_002847	0	0	0	0	0	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.999;A|0.000		0.622	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			A	157414139	G	A	157414139	2	1	79	1	0	0	0	0	0	0	0	1	12840	1079	38	1		1	PTPRN2	7	157414139	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	13756630	157414139	1724524	35	7348											
LZTS1	11178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	20107305	20107305	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaacctccaagggctccccGgcgctgtccccacgtgccag	6	6	10	19	3	1	0	1	0	0	0	4	0	4	0	7	2	2	2	7	2	2	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr8:20107305G>A	ENST00000381569.1	-	4	2076	c.1719C>T	c.(1717-1719)gcC>gcT	p.A573A	LZTS1_ENST00000265801.6_Silent_p.A573A|LZTS1_ENST00000522290.1_Silent_p.A514A			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	573					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		AGGGCTCCCCGGCGCTGTCCC	0.632																																					p.A573A		.											.	LZTS1-91	0			c.C1719T						.						83	82	82					8																	20107305		2203	4300	6503	SO:0001819	synonymous_variant	11178	exon3			CTCCCCGGCGCTG	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"F37/Esophageal cancer-related gene-coding leucine-zipper motif"			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1719C>T	8.37:g.20107305G>A		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	124	56	NM_021020	0	0	1	1	0	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																			.		0.632	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		A	20107305	G	A	20107305	2	1	79	1	0	0	0	0	0	0	0	1	9163	1103	39	1		1	LZTS1	8	20107305	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		20107305	126256717	36	7349											
PPP2R2A	5520	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	26227846	26227849	+	Frame_Shift_Del	DEL	CACA	CACA	-																															acttcaataagaaaatccttCacacagcctggcaccccaag																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CACA	CACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr8:26227846_26227849delCACA	ENST00000380737.3	+	10	1590_1593	c.1261_1264delCACA	c.(1261-1266)cacacafs	p.HT421fs	PPP2R2A_ENST00000315985.7_Frame_Shift_Del_p.HT431fs	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	421					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(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;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GAAAATCCTTCACACAGCCTGGCA	0.426																																					p.431_432del		.											.	PPP2R2A-659	0			c.1291_1294del						.																																			SO:0001589	frameshift_variant	5520	exon10			.	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1261_1264delCACA	8.37:g.26227846_26227849delCACA	ENSP00000370113:p.His421fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	47	12	NM_001177591	0	0	0	0	0	B2RBU8|B4E1T7|P50409|Q00007	Frame_Shift_Del	DEL	ENST00000380737.3	37	CCDS34867.1																																																																																			.		0.426	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		-	26227849	CACA	-	26227846	7	5	79	1	0	1	0	1	0	0	0	0	12413	826	29	0	1340	0	PPP2R2A	8	26227846	Frame_Shift_Del	DEL	CACA	TCGA-BQ-7044-01A-11D-1961-08	6120541	26227846	120136176	37	7350											
PKHD1L1	93035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	110451259	110451259	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attagatgccttttgcccaaGttgtctcctggaaaacatga	11	13	8	9	0	1	2	0	1	1	1	2	3	1	3	3	1	3	1	3	1	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr8:110451259G>A	ENST00000378402.5	+	32	3998	c.3894G>A	c.(3892-3894)aaG>aaA	p.K1298K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1298	IPT/TIG 6.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTTTGCCCAAGTTGTCTCCTG	0.393										HNSCC(38;0.096)																											p.K1298K		.											.	PKHD1L1-145	0			c.G3894A						.						141	137	138					8																	110451259		1844	4085	5929	SO:0001819	synonymous_variant	93035	exon32			GCCCAAGTTGTCT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3894G>A	8.37:g.110451259G>A		Somatic	249	0		WXS	Illumina HiSeq	Phase_I	212	81	NM_177531	0	0	0	0	0	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			.		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110451259	G	A	110451259	2	1	79	1	0	0	0	0	0	0	0	1	11998	1020	36	2		2	PKHD1L1	8	110451259	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	84223413	110451259	35912763	38	7351											
RGS3	5998	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	116269730	116269730	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacccatggggtccaggcaCggcctgagcagcgccacagc	8	3	14	16	2	0	1	0	1	0	0	1	1	1	1	4	4	3	3	4	4	0	0	rs200633658		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr9:116269730C>T	ENST00000374140.2	+	14	1458	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	RGS3_ENST00000374136.1_Missense_Mutation_p.R43W|RGS3_ENST00000350696.5_Missense_Mutation_p.R417W|RGS3_ENST00000343817.5_Missense_Mutation_p.R136W|RGS3_ENST00000317613.6_Missense_Mutation_p.R305W|RGS3_ENST00000394646.3_Missense_Mutation_p.R136W	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	417					inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGTCCAGGCACGGCCTGAGCA	0.672																																					p.R417W													.	RGS3-227	0			c.C1249T						.						35	36	36					9																	116269730		2203	4300	6503	SO:0001583	missense	5998	exon14			CAGGCACGGCCTG	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"Regulators of G-protein signaling"	9999	protein-coding gene	gene with protein product		602189	"regulator of G-protein signalling 3"			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.1249C>T	9.37:g.116269730C>T	ENSP00000363255:p.Arg417Trp	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	47	18	NM_144488	0	0	7	16	9	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.258327	0.80246	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613;ENST00000343817;ENST00000394646;ENST00000374136	T;T;T;T;T	0.67865	0.63;0.63;1.0;0.12;-0.29	5.18	4.26	0.50523	.	0.118165	0.64402	D	0.000015	T	0.71533	0.3351	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D	0.89917	0.993;1.0;1.0;1.0;1.0;1.0	B;D;D;D;D;D	0.75020	0.446;0.95;0.985;0.965;0.979;0.974	T	0.75150	-0.3419	10	0.87932	D	0	.	13.1591	0.59535	0.1603:0.8397:0.0:0.0	.	136;43;136;307;305;417	B3KUB2;Q5VXC0;P49796-4;B3KWG8;P49796-5;P49796	.;.;.;.;.;RGS3_HUMAN	W	417;417;305;136;136;43	ENSP00000363255:R417W;ENSP00000259406:R417W;ENSP00000312844:R305W;ENSP00000340284:R136W;ENSP00000378141:R136W	ENSP00000312844:R305W	R	+	1	2	RGS3	115309551	0.995000	0.38212	0.928000	0.36995	0.816000	0.46133	3.331000	0.52075	1.463000	0.47967	0.655000	0.94253	CGG	C|0.999;A|0.001		0.672	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116269730	C	T	116269730	3	4	79	1	0	0	0	0	1	0	0	0	13338	527	19	1	1440	1	RGS3	9	116269730	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		116269730	24943701	39	7352											
BMS1	9790	ucsc.edu	37	chr10	43315737	43315737	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagccagagttcagtatgaGggttttcgacctgggatgta	10	11	14	6	1	1	2	1	1	0	1	2	5	1	3	2	2	1	4	2	2	3	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:43315737G>T	ENST00000374518.5	+	16	2697	c.2634G>T	c.(2632-2634)gaG>gaT	p.E878D		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	878					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTCAGTATGAGGGTTTTCGAC	0.433																																					p.E878D													.	BMS1-93	0			c.G2634T						.						120	118	118					10																	43315737		2203	4300	6503	SO:0001583	missense	9790	exon16			GTATGAGGGTTTT	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2634G>T	10.37:g.43315737G>T	ENSP00000363642:p.Glu878Asp	Somatic	117	0		WXS	Illumina HiSeq		112	6	NM_014753	0	0	84	128	44	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.115516	0.77323	.	.	ENSG00000165733	ENST00000374518	T	0.17854	2.25	5.05	-4.55	0.03441	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.38506	0.1043	M	0.92122	3.275	0.47778	D	0.999516	D	0.53462	0.96	P	0.58077	0.832	T	0.53995	-0.8359	10	0.39692	T	0.17	.	13.1374	0.59417	0.6341:0.0:0.3659:0.0	.	878	Q14692	BMS1_HUMAN	D	878	ENSP00000363642:E878D	ENSP00000363642:E878D	E	+	3	2	BMS1	42635743	0.998000	0.40836	0.969000	0.41365	0.964000	0.63967	0.474000	0.22148	-0.725000	0.04901	-0.396000	0.06452	GAG	.		0.433	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		T	43315737	G	T	43315737	3	4	79	1	0	0	0	0	1	0	0	0	1473	991	35	4	2692	4	BMS1	10	43315737	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		43315737	92219010	40	7353											
SLC16A9	220963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61413807	61413807	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcttgctacatcttccataAgtaatgaaggtggaaaccct	12	13	7	9	0	2	1	0	1	2	0	3	2	3	2	2	2	3	2	2	2	5	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:61413807A>G	ENST00000395348.3	-	5	1613	c.977T>C	c.(976-978)cTt>cCt	p.L326P	SLC16A9_ENST00000395347.1_Missense_Mutation_p.L326P	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	326					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						ATCTTCCATAAGTAATGAAGG	0.363																																					p.L326P		.											.	SLC16A9-93	0			c.T977C						.						55	52	53					10																	61413807		2203	4300	6503	SO:0001583	missense	220963	exon5			TCCATAAGTAATG	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.977T>C	10.37:g.61413807A>G	ENSP00000378757:p.Leu326Pro	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	77	29	NM_194298	0	0	67	140	73	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.362232	0.61403	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.34472	1.36;1.36	4.73	4.73	0.59995	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.164197	0.56097	D	0.000037	T	0.51534	0.1680	L	0.44542	1.39	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.54186	-0.8331	10	0.66056	D	0.02	.	14.2093	0.65755	1.0:0.0:0.0:0.0	.	326	Q7RTY1	MOT9_HUMAN	P	326	ENSP00000378757:L326P;ENSP00000378756:L326P	ENSP00000378756:L326P	L	-	2	0	SLC16A9	61083813	1.000000	0.71417	0.974000	0.42286	0.984000	0.73092	8.962000	0.93254	1.751000	0.51876	0.482000	0.46254	CTT	.		0.363	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		G	61413807	A	G	61413807	3	3	79	1	0	0	0	0	1	0	0	0	14447	72	3	3	560	3	SLC16A9	10	61413807	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	18098070	61413807	74120940	41	7354											
PDLIM1	9124	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	96998413	96998413	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgacaggagctttaacacTtctgaatcctgagggcttgt	10	12	11	8	0	1	3	0	3	1	0	2	4	2	4	1	2	2	2	1	2	2	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:96998413T>G	ENST00000329399.6	-	6	823	c.715A>C	c.(715-717)Agt>Cgt	p.S239R	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	239					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		GCTTTAACACTTCTGAATCCT	0.468																																					p.S239R		.											.	PDLIM1-90	0			c.A715C						.						94	84	87					10																	96998413		2203	4300	6503	SO:0001583	missense	9124	exon6			TAACACTTCTGAA	U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"carboxyl terminal LIM domain protein 1", "elfin"	605900	"PDZ and LIM domain 1 (elfin)"	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.715A>C	10.37:g.96998413T>G	ENSP00000360305:p.Ser239Arg	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	66	26	NM_020992	0	0	54	133	79	B2RBS6|Q5VZH5|Q9BPZ9	Missense_Mutation	SNP	ENST00000329399.6	37	CCDS7441.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.985379	0.93044	.	.	ENSG00000107438	ENST00000329399	T	0.22134	1.97	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.45337	0.1337	M	0.85859	2.78	0.80722	D	1	D	0.61697	0.99	P	0.57101	0.813	T	0.53578	-0.8419	10	0.66056	D	0.02	-13.9009	14.2967	0.66318	0.0:0.0:0.0:1.0	.	239	O00151	PDLI1_HUMAN	R	239	ENSP00000360305:S239R	ENSP00000360305:S239R	S	-	1	0	PDLIM1	96988403	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.927000	0.87577	1.978000	0.57642	0.454000	0.30748	AGT	.		0.468	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1			G	96998413	T	G	96998413	3	3	79	1	0	0	0	0	1	0	0	0	11705	1609	56	5	282	5	PDLIM1	10	96998413	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	35584606	96998413	38536334	42	7355											
DNMBP	23268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101646325	101646325	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtttctgtaccagcttatggGgccctgtaaacatgctcagt	8	13	10	10	0	2	0	1	0	1	0	2	0	2	0	2	2	4	5	2	2	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:101646325G>C	ENST00000324109.4	-	13	3441	c.3350C>G	c.(3349-3351)cCc>cGc	p.P1117R	DNMBP_ENST00000472036.1_5'UTR|DNMBP_ENST00000342239.3_Missense_Mutation_p.P1141R|DNMBP_ENST00000543621.1_Missense_Mutation_p.P363R|DNMBP_ENST00000540316.1_Missense_Mutation_p.P53R	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1117	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		CAGCTTATGGGGCCCTGTAAA	0.502																																					p.P1117R		.											.	DNMBP-233	0			c.C3350G						.						116	115	115					10																	101646325		2203	4300	6503	SO:0001583	missense	23268	exon13			TTATGGGGCCCTG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.3350C>G	10.37:g.101646325G>C	ENSP00000315659:p.Pro1117Arg	Somatic	256	0		WXS	Illumina HiSeq	Phase_I	236	80	NM_015221	0	0	5	6	1	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.990069	0.93106	.	.	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.82	5.82	0.92795	BAR (3);	0.000000	0.48286	D	0.000199	T	0.82019	0.4946	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.83050	-0.0153	10	0.62326	D	0.03	-22.7596	19.7034	0.96065	0.0:0.0:1.0:0.0	.	1117;363;1141	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	R	1141;1117;363;363;53	ENSP00000344914:P1141R;ENSP00000315659:P1117R;ENSP00000443657:P363R;ENSP00000443573:P53R	ENSP00000315659:P1117R	P	-	2	0	DNMBP	101636315	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.866000	0.99616	2.756000	0.94617	0.561000	0.74099	CCC	.		0.502	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		C	101646325	G	C	101646325	3	2	79	1	0	0	0	0	1	0	0	0	4685	1232	43	4	1403	4	DNMBP	10	101646325	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	4647912	101646325	33888422	43	7356											
SLK	9748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105750528	105750528	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacatggtagagattgacatAttagcatcttgtgatcaccc	12	13	8	8	0	2	3	1	2	1	1	2	4	2	3	1	1	2	2	1	1	4	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:105750528A>G	ENST00000369755.3	+	2	791	c.246A>G	c.(244-246)atA>atG	p.I82M	SLK_ENST00000335753.4_Missense_Mutation_p.I82M	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	82	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AGATTGACATATTAGCATCTT	0.363																																					p.I82M	NSCLC(111;540 1651 1927 4474 17706)	.											.	SLK-549	0			c.A246G						.						132	123	126					10																	105750528		2203	4300	6503	SO:0001583	missense	9748	exon2			TGACATATTAGCA		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.246A>G	10.37:g.105750528A>G	ENSP00000358770:p.Ile82Met	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	69	29	NM_014720	0	0	6	7	1	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.480734	0.63849	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69435	-0.4;-0.4	6.17	-1.34	0.09143	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	L	0.41961	1.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.64067	-0.6494	10	0.42905	T	0.14	.	7.0526	0.25081	0.3492:0.3447:0.0:0.3061	.	82;82	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	M	82	ENSP00000336824:I82M;ENSP00000358770:I82M	ENSP00000336824:I82M	I	+	3	3	SLK	105740518	0.793000	0.28825	0.997000	0.53966	0.966000	0.64601	-0.030000	0.12308	-0.051000	0.13334	-0.313000	0.08912	ATA	.		0.363	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		G	105750528	A	G	105750528	3	3	79	1	0	0	0	0	1	0	0	0	14780	439	16	3	252	3	SLK	10	105750528	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	4104203	105750528	29784219	44	7357											
MUC5B	727897	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	1247945	1247945	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcttccctggcctttgcaaCtacgtgttctctgagcactg	5	13	9	14	2	1	1	0	1	1	0	3	1	2	1	2	1	4	4	2	1	2	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr11:1247945C>G	ENST00000529681.1	+	4	358	c.300C>G	c.(298-300)aaC>aaG	p.N100K	MUC5B_ENST00000447027.1_Missense_Mutation_p.N100K	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	100	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.			FPGLCN -> LPCLCK (in Ref. 2; AAC67545). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCTTTGCAACTACGTGTTCT	0.632																																					p.N100K		.											.	.	0			c.C300G						.						43	45	44					11																	1247945		2150	4262	6412	SO:0001583	missense	727897	exon4			TTGCAACTACGTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.300C>G	11.37:g.1247945C>G	ENSP00000436812:p.Asn100Lys	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708565	0.30322	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.58797	0.31;0.31	3.68	0.662	0.17880	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.67515	0.2901	L	0.59912	1.85	0.36644	D	0.876996	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.79784	0.958;0.993;0.993	T	0.70513	-0.4851	9	0.87932	D	0	.	8.7992	0.34898	0.0:0.6325:0.0:0.3675	.	100;756;100	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	K	100;100;100;133	ENSP00000436812:N100K;ENSP00000415793:N100K	ENSP00000343037:N100K	N	+	3	2	MUC5B	1204521	1.000000	0.71417	0.993000	0.49108	0.927000	0.56198	0.972000	0.29409	0.261000	0.21753	0.561000	0.74099	AAC	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1247945	C	G	1247945	3	3	79	1	0	0	0	0	1	0	0	0	10004	564	20	4	314	4	MUC5B	11	1247945	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		1247945	133758571	45	7358											
PRKRIR	5612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	76063689	76063689	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagaatcaagatttcaaataGagattttaggtattctttgt	14	16	7	4	0	3	3	2	0	1	3	3	4	3	3	0	1	0	1	0	1	6	7			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr11:76063689G>C	ENST00000260045.3	-	5	610	c.505C>G	c.(505-507)Cta>Gta	p.L169V	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	169					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						ATTTCAAATAGAGATTTTAGG	0.413																																					p.L169V		.											.	PRKRIR-93	0			c.C505G						.						44	39	40					11																	76063689		2200	4292	6492	SO:0001583	missense	5612	exon5			CAAATAGAGATTT	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.505C>G	11.37:g.76063689G>C	ENSP00000260045:p.Leu169Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	29	21	NM_004705	0	0	2	9	7	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	37	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.904821	0.33628	.	.	ENSG00000137492	ENST00000260045	.	.	.	4.99	-0.031	0.13911	.	0.157256	0.45606	D	0.000351	T	0.52948	0.1766	M	0.67953	2.075	0.34998	D	0.755717	P	0.46277	0.875	P	0.50082	0.63	T	0.59306	-0.7479	9	0.23302	T	0.38	.	9.0537	0.36392	0.5611:0.0:0.4389:0.0	.	169	O43422	P52K_HUMAN	V	169	.	ENSP00000260045:L169V	L	-	1	2	PRKRIR	75741337	0.470000	0.25854	0.991000	0.47740	0.952000	0.60782	1.098000	0.31000	0.038000	0.15604	0.586000	0.80456	CTA	.		0.413	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		C	76063689	G	C	76063689	3	2	79	1	0	0	0	0	1	0	0	0	12555	933	33	4	1784	4	PRKRIR	11	76063689	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	74815744	76063689	58942827	46	7359											
MLL2	8085	broad.mit.edu	37	chr12	49436618	49436618	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttcagagcccagaacatcCttgaagagctgctgcaggtc	10	8	11	12	1	1	4	1	1	0	3	3	4	2	4	2	1	5	4	2	1	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr12:49436618C>G	ENST00000301067.7	-	26	5687	c.5688G>C	c.(5686-5688)aaG>aaC	p.K1896N		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1896					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCAGAACATCCTTGAAGAGCT	0.537																																					p.K1896N													.	MLL2-612	0			c.G5688C						.						90	88	89					12																	49436618		2007	4171	6178	SO:0001583	missense	8085	exon26			AACATCCTTGAAG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.5688G>C	12.37:g.49436618C>G	ENSP00000301067:p.Lys1896Asn	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	61	3	NM_003482	0	0	8	8	0	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656946	0.29425	.	.	ENSG00000167548	ENST00000301067	D	0.81659	-1.52	5.51	3.69	0.42338	.	0.000000	0.38548	N	0.001657	T	0.79873	0.4521	L	0.34521	1.04	0.28594	N	0.909476	D	0.64830	0.994	P	0.57911	0.829	T	0.73855	-0.3851	10	0.87932	D	0	.	9.1354	0.36870	0.0:0.7627:0.0:0.2373	.	1896	O14686	MLL2_HUMAN	N	1896	ENSP00000301067:K1896N	ENSP00000301067:K1896N	K	-	3	2	MLL2	47722885	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.843000	0.48238	0.697000	0.31718	0.561000	0.74099	AAG	.		0.537	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49436618	C	G	49436618	3	3	79	1	0	0	0	0	1	0	0	0	9646	680	24	4	11041	4	MLL2	12	49436618	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		49436618	84415277	47	7360											
MON2	23041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	62959064	62959064	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagataatgtatccagctatAtttgaccagttgttggcatt	11	15	8	7	0	0	2	0	1	0	1	1	2	1	2	2	1	1	5	2	1	4	8			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr12:62959064A>G	ENST00000393632.2	+	27	4471	c.4080A>G	c.(4078-4080)atA>atG	p.I1360M	MON2_ENST00000393629.2_Missense_Mutation_p.I1360M|MON2_ENST00000552738.1_Missense_Mutation_p.I1337M|MON2_ENST00000280379.6_Missense_Mutation_p.I1361M|MON2_ENST00000393630.3_Missense_Mutation_p.I1361M|MON2_ENST00000546600.1_Missense_Mutation_p.I1360M	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1360					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		ATCCAGCTATATTTGACCAGT	0.348																																					p.I1360M		.											.	MON2-514	0			c.A4080G						.						193	193	193					12																	62959064		2203	4300	6503	SO:0001583	missense	23041	exon27			AGCTATATTTGAC		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4080A>G	12.37:g.62959064A>G	ENSP00000377252:p.Ile1360Met	Somatic	227	1		WXS	Illumina HiSeq	Phase_I	199	91	NM_015026	0	0	6	14	8	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.770800	0.49680	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.44	3.0	0.34707	.	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	L	0.48642	1.525	0.58432	D	0.999998	D;D;D;P;D	0.76494	0.998;0.998;0.998;0.655;0.999	D;D;D;B;D	0.67900	0.919;0.954;0.954;0.295;0.954	T	0.66921	-0.5801	9	.	.	.	-21.3568	8.7848	0.34814	0.4208:0.4646:0.0:0.1146	.	1360;1337;1360;235;1360	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	M	1360;1361;1361;1360;1337;1360	ENSP00000377252:I1360M;ENSP00000377250:I1361M;ENSP00000280379:I1361M;ENSP00000447407:I1360M;ENSP00000449215:I1337M;ENSP00000377249:I1360M	.	I	+	3	3	MON2	61245331	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.341000	0.43983	0.409000	0.25649	-0.316000	0.08728	ATA	.		0.348	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62959064	A	G	62959064	3	3	79	1	0	0	0	0	1	0	0	0	9725	439	16	3	4186	3	MON2	12	62959064	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	13522446	62959064	70892831	48	7361											
EP400	57634	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132472272	132472272	+	Missense_Mutation	SNP	T	T	A																															gaaccaggtgcatcagcgcaTtgcggagctgaggaaagcag																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr12:132472272T>A	ENST00000333577.4	+	8	2463	c.2354T>A	c.(2353-2355)aTt>aAt	p.I785N	EP400_ENST00000332482.4_Missense_Mutation_p.I712N|EP400_ENST00000330386.6_Missense_Mutation_p.I749N|EP400_ENST00000389562.2_Missense_Mutation_p.I748N|EP400_ENST00000389561.2_Missense_Mutation_p.I749N			Q96L91	EP400_HUMAN	E1A binding protein p400	785					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CATCAGCGCATTGCGGAGCTG	0.577																																					p.I749N													.	EP400-520	0			c.T2246A						.						46	44	44					12																	132472272		2203	4300	6503	SO:0001583	missense	57634	exon7			AGCGCATTGCGGA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.2354T>A	12.37:g.132472272T>A	ENSP00000333602:p.Ile785Asn	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	45	12	NM_015409	0	0	9	9	0	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	T	8.644	0.896751	0.17686	.	.	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.93712	-3.24;-3.23;-3.23;-3.27;-3.22	5.3	5.3	0.74995	.	0.136379	0.64402	D	0.000007	D	0.96185	0.8756	M	0.73217	2.22	0.26509	N	0.974622	D;D;D;D;P	0.89917	1.0;0.999;1.0;1.0;0.897	D;D;D;D;P	0.91635	0.988;0.974;0.988;0.999;0.822	D	0.91874	0.5510	10	0.66056	D	0.02	.	15.5437	0.76077	0.0:0.0:0.0:1.0	.	749;749;748;785;712	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	N	712;785;749;748;712;749;785;749;749	ENSP00000333602:I785N;ENSP00000374212:I749N;ENSP00000374213:I748N;ENSP00000331737:I712N;ENSP00000330620:I749N	ENSP00000330620:I749N	I	+	2	0	EP400	131038225	1.000000	0.71417	0.004000	0.12327	0.017000	0.09413	7.997000	0.88414	2.131000	0.65755	0.460000	0.39030	ATT	.		0.577	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132472272	T	A	132472272	3	1	79	1	0	0	0	0	1	0	0	0	5162	1493	52	5	2265	5	EP400	12	132472272	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	69513208	132472272	1379623	49	7362	82	2									
EP400	57634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132472274	132472274	+	Missense_Mutation	SNP	G	G	C																															accaggtgcatcagcgcattGcggagctgaggaaagcaggt																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr12:132472274G>C	ENST00000333577.4	+	8	2465	c.2356G>C	c.(2356-2358)Gcg>Ccg	p.A786P	EP400_ENST00000332482.4_Missense_Mutation_p.A713P|EP400_ENST00000330386.6_Missense_Mutation_p.A750P|EP400_ENST00000389562.2_Missense_Mutation_p.A749P|EP400_ENST00000389561.2_Missense_Mutation_p.A750P			Q96L91	EP400_HUMAN	E1A binding protein p400	786					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TCAGCGCATTGCGGAGCTGAG	0.577																																					p.A750P		.											.	EP400-520	0			c.G2248C						.						46	44	45					12																	132472274		2203	4300	6503	SO:0001583	missense	57634	exon7			CGCATTGCGGAGC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.2356G>C	12.37:g.132472274G>C	ENSP00000333602:p.Ala786Pro	Somatic	82	2		WXS	Illumina HiSeq	Phase_I	47	14	NM_015409	0	0	9	9	0	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	9.373	1.070978	0.20147	.	.	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.91521	-2.84;-2.84;-2.84;-2.86;-2.84	5.3	4.36	0.52297	.	0.168232	0.52532	D	0.000065	D	0.93867	0.8038	M	0.62723	1.935	0.44042	D	0.99677	D;D;D;D;D	0.69078	0.989;0.989;0.989;0.997;0.989	P;P;P;D;P	0.69479	0.885;0.839;0.885;0.964;0.885	D	0.94054	0.7320	10	0.62326	D	0.03	.	15.8677	0.79076	0.0:0.0:0.8643:0.1357	.	750;750;749;786;713	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	P	713;786;750;749;713;750;786;750;750	ENSP00000333602:A786P;ENSP00000374212:A750P;ENSP00000374213:A749P;ENSP00000331737:A713P;ENSP00000330620:A750P	ENSP00000330620:A750P	A	+	1	0	EP400	131038227	1.000000	0.71417	0.760000	0.31359	0.004000	0.04260	5.183000	0.65065	2.637000	0.89404	0.563000	0.77884	GCG	.		0.577	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		C	132472274	G	C	132472274	3	2	79	1	0	0	0	0	1	0	0	0	5162	1319	46	4	2267	4	EP400	12	132472274	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	2	132472274	1379621	50	7363	82	2									
LNX2	222484	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	28136573	28136575	+	In_Frame_Del	DEL	CCG	CCG	-																															aataatctgggcagcaagctCcggagttccatacttcaggt																								rs377695945		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr13:28136573_28136575delCCG	ENST00000316334.3	-	5	1328_1330	c.1199_1201delCGG	c.(1198-1203)ccggag>cag	p.400_401PE>Q		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	400	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		GCAGCAAGCTCCGGAGTTCCATA	0.512																																					p.400_401del		.											.	LNX2-228	0			c.1199_1201del						.																																			SO:0001651	inframe_deletion	222484	exon5			.	AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"RING-type (C3HC4) zinc fingers"	20421	protein-coding gene	gene with protein product		609733	"PDZ domain containing ring finger 1"	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.1199_1201delCGG	13.37:g.28136573_28136575delCCG	ENSP00000325929:p.Pro400_Glu401delinsGln	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	143	58	NM_153371	0	0	0	0	0	Q5W0P0|Q6ZMH2|Q96SH4	In_Frame_Del	DEL	ENST00000316334.3	37	CCDS9323.1																																																																																			.		0.512	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			-	28136575	CCG	-	28136573	7	5	79	1	0	1	0	1	0	0	0	0	8889	864	30	0	895	0	LNX2	13	28136573	In_Frame_Del	DEL	CCG	TCGA-BQ-7044-01A-11D-1961-08		28136573	87033305	51	7364	83	2									
LNX2	222484	bcgsc.ca	37	chr13	28136576	28136576	+	Missense_Mutation	SNP	G	G	A																															aatctgggcagcaagctccgGagttccatacttcaggtcgt																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr13:28136576G>A	ENST00000316334.3	-	5	1327	c.1198C>T	c.(1198-1200)Ccg>Tcg	p.P400S		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	400	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		GCAAGCTCCGGAGTTCCATAC	0.517																																					p.P400S													.	LNX2-228	0			c.C1198T						.						98	101	100					13																	28136576		2203	4300	6503	SO:0001583	missense	222484	exon5			GCTCCGGAGTTCC	AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"RING-type (C3HC4) zinc fingers"	20421	protein-coding gene	gene with protein product		609733	"PDZ domain containing ring finger 1"	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.1198C>T	13.37:g.28136576G>A	ENSP00000325929:p.Pro400Ser	Somatic	174	0		WXS	Illumina HiSeq	Phase_1	134	54	NM_153371	0	0	3	3	0	Q5W0P0|Q6ZMH2|Q96SH4	Missense_Mutation	SNP	ENST00000316334.3	37	CCDS9323.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171568	0.78452	.	.	ENSG00000139517	ENST00000316334	T	0.38240	1.15	5.6	5.6	0.85130	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	L	0.28115	0.83	0.80722	D	1	D	0.54601	0.967	P	0.62014	0.897	T	0.38308	-0.9667	10	0.45353	T	0.12	.	19.6195	0.95650	0.0:0.0:1.0:0.0	.	400	Q8N448	LNX2_HUMAN	S	400	ENSP00000325929:P400S	ENSP00000325929:P400S	P	-	1	0	LNX2	27034576	1.000000	0.71417	0.133000	0.22050	0.651000	0.38670	9.869000	0.99810	2.633000	0.89246	0.561000	0.74099	CCG	.		0.517	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			A	28136576	G	A	28136576	3	1	79	1	0	0	0	0	1	0	0	0	8889	1174	41	2	898	2	LNX2	13	28136576	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	3	28136576	87033302	52	7365	83	2									
KBTBD7	84078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41766948	41766948	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcataaagatagttctgAaccactatgagttcaaagga	17	9	8	7	0	2	3	1	2	1	1	2	4	2	4	1	1	2	3	1	1	6	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr13:41766948A>T	ENST00000379483.3	-	1	1754	c.1446T>A	c.(1444-1446)gtT>gtA	p.V482V		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	482										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		GATAGTTCTGAACCACTATGA	0.433																																					p.V482V		.											.	KBTBD7-91	0			c.T1446A						.						65	59	61					13																	41766948		2203	4300	6503	SO:0001819	synonymous_variant	84078	exon1			GTTCTGAACCACT	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.1446T>A	13.37:g.41766948A>T		Somatic	57	1		WXS	Illumina HiSeq	Phase_I	47	23	NM_032138	0	0	2	4	2	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Silent	SNP	ENST00000379483.3	37	CCDS9377.1																																																																																			.		0.433	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		T	41766948	A	T	41766948	2	4	79	1	0	0	0	0	0	0	0	1	8019	233	9	5		5	KBTBD7	13	41766948	Silent	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	13630372	41766948	73402930	53	7366											
DOCK9	23348	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99540613	99540613	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aacctccatcttcacactcaCcttggcaaaagacttctgac	12	10	4	15	0	4	2	2	1	2	1	5	2	5	2	3	1	1	1	3	1	3	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr13:99540613C>T	ENST00000376460.1	-	17	2058		c.e17+1		DOCK9_ENST00000339416.2_Splice_Site|DOCK9_ENST00000448493.2_Splice_Site|DOCK9_ENST00000442173.1_Splice_Site	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9						blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TTCACACTCACCTTGGCAAAA	0.398																																					.		.											.	DOCK9-90	0			c.1980+1G>A						.						167	158	161					13																	99540613		1931	4118	6049	SO:0001630	splice_region_variant	23348	exon18			CACTCACCTTGGC	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.1977+1G>A	13.37:g.99540613C>T		Somatic	227	0		WXS	Illumina HiSeq	Phase_I	224	24	NM_015296	0	0	0	0	0	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Splice_Site	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.474160	0.84640	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7775	0.96400	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK9	98338614	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.438000	0.80431	2.680000	0.91292	0.655000	0.94253	.	.		0.398	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	Intron	T	99540613	C	T	99540613	5	4	79	1	0	0	0	0	0	0	1	0	4705	521	18	2	4449	2	DOCK9	13	99540613	Splice_Site	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	57773665	99540613	15629265	54	7367											
FAM71D	161142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	67688507	67688507	+	3'UTR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttttacaggagcttgagaaCtgaatcaaacacttcaggta	14	12	8	7	0	2	2	2	2	0	1	2	4	2	3	0	2	4	2	0	2	5	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr14:67688507C>A	ENST00000556046.1	+	0	1713							Q8N9W8	FA71D_HUMAN	family with sequence similarity 71, member D							cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)	13		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		AGCTTGAGAACTGAATCAAAC	0.353																																					p.T391N		.											.	FAM71D-23	0			c.C1172A						.						87	82	84					14																	67688507		2203	4300	6503	SO:0001624	3_prime_UTR_variant	161142	exon7			TGAGAACTGAATC		CCDS9778.1	14q23.3	2007-11-20	2007-11-20	2007-11-20		ENSG00000172717			20101	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 54"	C14orf54			Standard	NM_173526		Approved		uc001xja.2	Q8N9W8		ENST00000556046.1:c.*1228C>A	14.37:g.67688507C>A		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	54	11	NM_173526	0	0	0	0	0	Q86VN4	Missense_Mutation	SNP	ENST00000556046.1	37		.	.	.	.	.	.	.	.	.	.	C	6.948	0.544670	0.13312	.	.	ENSG00000172717	ENST00000556117;ENST00000557671	.	.	.	5.95	1.59	0.23543	.	.	.	.	.	T	0.25306	0.0615	N	0.24115	0.695	.	.	.	.	.	.	.	.	.	T	0.25082	-1.0142	4	.	.	.	0.0	2.5085	0.04651	0.3418:0.4102:0.1494:0.0986	.	.	.	.	M	52;49	.	.	L	+	1	2	FAM71D	66758260	1.000000	0.71417	0.283000	0.24790	0.059000	0.15707	0.853000	0.27777	0.750000	0.32877	-0.345000	0.07892	CTG	.		0.353	FAM71D-009	KNOWN	not_organism_supported|basic|appris_candidate	nonsense_mediated_decay	protein_coding	OTTHUMT00000412390.1	NM_173526		A	67688507	C	A	67688507	1	1	79	0	1	0	0	0	0	0	0	0	5629	565	20	4		4	FAM71D	14	67688507	3'UTR	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		67688507	39661033	55	7368											
DPF3	8110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	73238479	73238479	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctccatccagatgtagcagTtgttctgggccaccccagtc	7	11	9	14	0	2	1	0	0	2	1	5	1	3	1	5	1	1	4	5	1	1	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr14:73238479T>G	ENST00000556509.1	-	2	154	c.155A>C	c.(154-156)aAc>aCc	p.N52T	DPF3_ENST00000541685.1_Missense_Mutation_p.N52T|DPF3_ENST00000546183.1_Missense_Mutation_p.N62T	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	52					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GATGTAGCAGTTGTTCTGGGC	0.622																																					p.N52T		.											.	DPF3-1	0			c.A155C						.						87	95	92					14																	73238479		2195	4299	6494	SO:0001583	missense	8110	exon2			TAGCAGTTGTTCT	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"Zinc fingers, PHD-type"	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.155A>C	14.37:g.73238479T>G	ENSP00000450518:p.Asn52Thr	Somatic	158	1		WXS	Illumina HiSeq	Phase_I	90	38	NM_012074	0	0	0	0	0	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	t	30	5.056952	0.93846	.	.	ENSG00000205683	ENST00000540281;ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.91068	-2.78;-0.26;-0.26	5.54	5.54	0.83059	.	.	.	.	.	D	0.94251	0.8154	M	0.64997	1.995	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.991	D;D;D	0.74023	0.97;0.958;0.982	D	0.94833	0.7998	9	0.87932	D	0	.	15.693	0.77469	0.0:0.0:0.0:1.0	.	62;52;52	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	T	52;52;51;52;62	ENSP00000450518:N52T;ENSP00000441640:N52T;ENSP00000444662:N62T	ENSP00000381791:N107T	N	-	2	0	DPF3	72308232	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.026000	0.88783	2.116000	0.64780	0.529000	0.55759	AAC	.		0.622	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			G	73238479	T	G	73238479	3	3	79	1	0	0	0	0	1	0	0	0	4729	1725	60	5	950	5	DPF3	14	73238479	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	5549972	73238479	34111061	56	7369											
PPP4R4	57718	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	94640864	94640864	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacagcctgttcggttacaTggaggacctgcaggagctca	10	8	13	10	1	1	0	1	0	0	0	2	4	1	3	2	4	5	4	2	4	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr14:94640864T>C	ENST00000304338.3	+	1	216	c.62T>C	c.(61-63)aTg>aCg	p.M21T	PPP4R4_ENST00000328839.3_Missense_Mutation_p.M21T|PPP4R4_ENST00000555690.1_3'UTR	NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	21					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						TTCGGTTACATGGAGGACCTG	0.721																																					p.M21T		.											.	PPP4R4-94	0			c.T62C						.						28	29	29					14																	94640864		2202	4300	6502	SO:0001583	missense	57718	exon1			GTTACATGGAGGA	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.62T>C	14.37:g.94640864T>C	ENSP00000305924:p.Met21Thr	Somatic	88	1		WXS	Illumina HiSeq	Phase_I	49	11	NM_058237	0	0	0	0	0	Q9BUF8|Q9HCF0	Missense_Mutation	SNP	ENST00000304338.3	37	CCDS9921.1	.	.	.	.	.	.	.	.	.	.	t	13.47	2.247193	0.39697	.	.	ENSG00000119698	ENST00000304338;ENST00000328839	.	.	.	2.86	2.86	0.33363	.	0.144296	0.45606	U	0.000349	T	0.32615	0.0835	N	0.22421	0.69	0.32051	N	0.596886	B;B	0.17667	0.001;0.023	B;B	0.22152	0.009;0.038	T	0.40001	-0.9586	9	0.49607	T	0.09	-9.5223	10.1358	0.42706	0.0:0.0:0.0:1.0	.	21;21	Q6NUP7;Q6NUP7-2	PP4R4_HUMAN;.	T	21	.	ENSP00000305924:M21T	M	+	2	0	PPP4R4	93710617	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.072000	0.50049	1.299000	0.44798	0.324000	0.21423	ATG	.		0.721	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		C	94640864	T	C	94640864	3	2	79	1	0	0	0	0	1	0	0	0	12434	1464	51	3	64	3	PPP4R4	14	94640864	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	21402385	94640864	12708676	57	7370											
OCA2	4948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	28090200	28090200	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaatcagtgtcccgttaccTaaagtcaaaatttaaaaaca	17	10	4	10	1	2	0	2	0	0	0	3	0	3	0	3	0	2	1	3	0	9	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:28090200T>A	ENST00000354638.3	-	23	2494		c.e23-2		OCA2_ENST00000353809.5_Splice_Site	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II						cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		TCCCGTTACCTAAAGTCAAAA	0.413									Oculocutaneous Albinism																												.		.											.	OCA2-135	0			c.2339-2A>T						.						47	47	47					15																	28090200		2203	4300	6503	SO:0001630	splice_region_variant	4948	exon24	Familial Cancer Database		GTTACCTAAAGTC		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"melanocyte-specific transporter protein"	611409	"oculocutaneous albinism II (pink-eye dilution (murine) homolog)", "eye color 3 (brown)", "eye color 2 (central brown)", "oculocutaneous albinism II (pink-eye dilution homolog, mouse)"	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.2339-2A>T	15.37:g.28090200T>A		Somatic	74	1		WXS	Illumina HiSeq	Phase_I	59	21	NM_000275	0	0	0	0	0	Q15211|Q15212|Q96EN1|Q9UMI5	Splice_Site	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.314576	0.60524	.	.	ENSG00000104044	ENST00000354638;ENST00000353809	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.845	0.63461	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	OCA2	25763795	1.000000	0.71417	0.954000	0.39281	0.410000	0.31052	7.093000	0.76937	2.143000	0.66587	0.533000	0.62120	.	.		0.413	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	Intron	A	28090200	T	A	28090200	5	1	79	1	0	0	0	0	0	0	1	0	10841	1536	53	5	187	5	OCA2	15	28090200	Splice_Site	SNP	T	TCGA-BQ-7044-01A-11D-1961-08		28090200	74441192	58	7371											
ITPKA	3706	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	41794669	41794670	+	Frame_Shift_Ins	INS	-	-	A																															gcaggtgcttcgcgtctttgINSaagagtttgtgcaaggagat																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:41794669_41794670insA	ENST00000260386.5	+	5	1131_1132	c.1078_1079insA	c.(1078-1080)gaafs	p.E360fs		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	360					actin cytoskeleton organization (GO:0030036)|dendritic spine maintenance (GO:0097062)|inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|positive regulation of dendritic spine morphogenesis (GO:0061003)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendritic spine (GO:0043197)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			kidney(1)|lung(3)|skin(1)	5		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TCGCGTCTTTGAAGAGTTTGTG	0.604																																					p.E360fs		.											.	ITPKA-226	0			c.1078_1079insA						.																																			SO:0001589	frameshift_variant	3706	exon5			.	X54938	CCDS10076.1	15q15.1	2011-04-28	2011-04-28		ENSG00000137825	ENSG00000137825	2.7.1.127		6178	protein-coding gene	gene with protein product		147521	"inositol 1,4,5-trisphosphate 3-kinase A"			1330886, 2175886	Standard	NM_002220		Approved	IP3KA, IP3-3KA	uc001znz.3	P23677	OTTHUMG00000130343	ENST00000260386.5:c.1080dupA	15.37:g.41794671_41794671dupA	ENSP00000260386:p.Glu360fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	80	29	NM_002220	0	0	0	0	0	Q8TAN3	Frame_Shift_Ins	INS	ENST00000260386.5	37	CCDS10076.1																																																																																			.		0.604	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220		A	41794670	-	A	41794669	7	5	79	1	0	1	1	0	0	0	0	0	7938	1291	45	0	1096	0	ITPKA	15	41794669	Frame_Shift_Ins	INS	-	TCGA-BQ-7044-01A-11D-1961-08	13704469	41794669	60736723	59	7372											
C15orf43	145645	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	45270783	45270783	+	Frame_Shift_Del	DEL	A	A	-																															ggcatatcatgttcaaaatgAaattaatatgtctgctataa																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:45270783delA	ENST00000340827.3	+	7	637	c.620delA	c.(619-621)gaafs	p.E207fs		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	207										NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)		GTTCAAAATGAAATTAATATG	0.294																																					p.E207fs		.											.	C15orf43-90	0			c.620delA						.						40	43	42					15																	45270783		2193	4282	6475	SO:0001589	frameshift_variant	145645	exon7			.	BC029537	CCDS10115.1	15q21.1	2006-02-03			ENSG00000167014	ENSG00000167014			28520	protein-coding gene	gene with protein product							Standard	NM_152448		Approved	MGC33951	uc001zuk.4	Q8NHR7	OTTHUMG00000131264	ENST00000340827.3:c.620delA	15.37:g.45270783delA	ENSP00000340644:p.Glu207fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_152448	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000340827.3	37	CCDS10115.1																																																																																			.		0.294	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448		-	45270783	A	-	45270783	7	5	79	1	0	1	0	1	0	0	0	0	1801	246	9	0	646	0	C15orf43	15	45270783	Frame_Shift_Del	DEL	A	TCGA-BQ-7044-01A-11D-1961-08	3476114	45270783	57260609	60	7373											
ZNF609	23060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64966235	64966235	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acagcctctgacagcaaaggGaccagtaacagcagcaaaac	17	3	9	12	0	1	1	0	1	1	0	1	2	1	2	2	1	6	4	2	1	4	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:64966235G>T	ENST00000326648.3	+	4	1310	c.1182G>T	c.(1180-1182)ggG>ggT	p.G394G	RNU6-549P_ENST00000384433.1_RNA|ZNF609_ENST00000559364.1_3'UTR	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	394						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACAGCAAAGGGACCAGTAACA	0.577																																					p.G394G		.											.	ZNF609-92	0			c.G1182T						.						96	97	97					15																	64966235		2203	4299	6502	SO:0001819	synonymous_variant	23060	exon4			CAAAGGGACCAGT	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.1182G>T	15.37:g.64966235G>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	150	55	NM_015042	0	0	7	11	4	Q0D2I2	Silent	SNP	ENST00000326648.3	37	CCDS32270.1																																																																																			.		0.577	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		T	64966235	G	T	64966235	2	4	79	1	0	0	0	0	0	0	0	1	18067	1161	41	4		4	ZNF609	15	64966235	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	19695452	64966235	37565157	61	7374											
THSD4	79875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	72063439	72063439	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agggtggctttcgggtccggGaagtgcggtgtctgtctgat	4	12	18	7	3	2	1	0	1	2	0	4	2	3	2	1	5	1	1	1	5	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:72063439G>C	ENST00000355327.3	+	17	2940	c.2806G>C	c.(2806-2808)Gaa>Caa	p.E936Q	THSD4_ENST00000357769.4_Missense_Mutation_p.E576Q|THSD4_ENST00000261862.6_Missense_Mutation_p.E936Q			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	936	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TCGGGTCCGGGAAGTGCGGTG	0.507																																					p.E936Q		.											.	THSD4-92	0			c.G2806C						.						157	149	151					15																	72063439		1899	4126	6025	SO:0001583	missense	79875	exon16			GTCCGGGAAGTGC	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.2806G>C	15.37:g.72063439G>C	ENSP00000347484:p.Glu936Gln	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	143	63	NM_024817	0	0	3	9	6	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Missense_Mutation	SNP	ENST00000355327.3	37	CCDS10238.2	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724411	0.68959	.	.	ENSG00000187720	ENST00000355327;ENST00000261862;ENST00000357769	T;T;T	0.50813	0.73;0.73;0.73	5.05	5.05	0.67936	.	.	.	.	.	T	0.56761	0.2007	L	0.28649	0.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.54596	-0.8270	9	0.35671	T	0.21	.	15.9236	0.79592	0.0:0.0:1.0:0.0	.	576;936	B4DR13;Q6ZMP0	.;THSD4_HUMAN	Q	936;936;576	ENSP00000347484:E936Q;ENSP00000261862:E936Q;ENSP00000350413:E576Q	ENSP00000261862:E936Q	E	+	1	0	THSD4	69850493	1.000000	0.71417	1.000000	0.80357	0.252000	0.25951	9.638000	0.98445	2.353000	0.79882	0.557000	0.71058	GAA	.		0.507	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		C	72063439	G	C	72063439	3	2	79	1	0	0	0	0	1	0	0	0	15910	1175	41	4	2868	4	THSD4	15	72063439	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	7097204	72063439	30467953	62	7375											
BNC1	646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	83932666	83932666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcctacagtctggggacGtcactgtgaaacctgggcac	9	7	14	11	1	2	1	1	1	1	0	2	3	2	2	2	4	2	1	2	4	2	1	rs377611889		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:83932666G>A	ENST00000345382.2	-	4	1422	c.1337C>T	c.(1336-1338)aCg>aTg	p.T446M	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Missense_Mutation_p.T439M	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	446					chromosome organization (GO:0051276)|epidermis development (GO:0008544)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	56						GTCTGGGGACGTCACTGTGAA	0.527																																					p.T446M		.											.	BNC1-93	0			c.C1337T						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	129	118	122		1337	0.3	0	15		122	0,8600		0,0,4300	no	missense	BNC1	NM_001717.3	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	446/995	83932666	1,13005	2203	4300	6503	SO:0001583	missense	646	exon4			GGGGACGTCACTG	L03427	CCDS10324.1, CCDS73771.1	15q25.1	2013-05-20	2004-04-30	2004-05-04	ENSG00000169594	ENSG00000169594		"Zinc fingers, C2H2-type"	1081	protein-coding gene	gene with protein product		601930	"basonuclin"	BNC		1332044	Standard	NM_001717		Approved	HsT19447	uc002bjt.1	Q01954	OTTHUMG00000147362	ENST00000345382.2:c.1337C>T	15.37:g.83932666G>A	ENSP00000307041:p.Thr446Met	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	71	27	NM_001717	0	0	3	4	1	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	G	0.574	-0.839807	0.02692	2.27E-4	0.0	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.47869	0.83	4.98	0.334	0.15948	.	0.605786	0.17317	N	0.178658	T	0.32376	0.0827	L	0.39397	1.21	0.09310	N	1	B;B	0.23806	0.008;0.091	B;B	0.16289	0.004;0.015	T	0.16958	-1.0385	10	0.51188	T	0.08	-1.7277	5.5626	0.17152	0.2685:0.4447:0.2868:0.0	.	439;446	F5GY04;Q01954	.;BNC1_HUMAN	M	446;439	ENSP00000307041:T446M	ENSP00000307041:T446M	T	-	2	0	BNC1	81723670	0.001000	0.12720	0.001000	0.08648	0.136000	0.21042	0.733000	0.26087	-0.119000	0.11830	0.655000	0.94253	ACG	.		0.527	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		A	83932666	G	A	83932666	3	1	79	1	0	0	0	0	1	0	0	0	1475	1145	40	1	1655	1	BNC1	15	83932666	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	11869227	83932666	18598726	63	7376											
ADAMTS17	170691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	100871170	100871170	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtcaaggaccatttgcgcctGatcagatgttctcgtccact	8	12	9	12	2	3	2	2	1	1	1	5	3	4	3	3	1	1	1	3	1	1	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:100871170G>A	ENST00000268070.4	-	3	645	c.540C>T	c.(538-540)atC>atT	p.I180I		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	180						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		ATTTGCGCCTGATCAGATGTT	0.582																																					p.I180I		.											.	ADAMTS17-228	0			c.C540T						.						129	122	125					15																	100871170		2203	4300	6503	SO:0001819	synonymous_variant	170691	exon3			GCGCCTGATCAGA	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.540C>T	15.37:g.100871170G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	87	47	NM_139057	0	0	0	0	0	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			.		0.582	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		A	100871170	G	A	100871170	2	1	79	1	0	0	0	0	0	0	0	1	262	1280	45	2		2	ADAMTS17	15	100871170	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	16938504	100871170	1660222	64	7377											
PCSK6	5046	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	101933522	101933522	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctcggtggcgctgctgacGgagatggtgtagatgctgtt	5	13	16	7	3	1	3	0	1	1	2	2	4	1	3	0	4	2	5	0	4	1	3	rs376652644		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:101933522G>A	ENST00000348070.1	-	9	1100	c.1101C>T	c.(1099-1101)tcC>tcT	p.S367S	PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000331826.7_Silent_p.S202S|PCSK6_ENST00000358417.3_Silent_p.S367S|PCSK6_ENST00000398181.2_Silent_p.S367S|PCSK6_ENST00000344273.2_Silent_p.S367S	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	368	Peptidase S8.				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)	p.S367S(3)|p.S202S(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CGCTGCTGACGGAGATGGTGT	0.597																																					.													.	PCSK6-46	4	Substitution - coding silent(4)	lung(4)	.						.	G	,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	77	87	83		1102,1102,1102,1102,1102,1102,1102,1102	-6.2	0.8	15		83	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCSK6	NM_002570.3,NM_138319.2,NM_138320.1,NM_138321.1,NM_138322.2,NM_138323.1,NM_138324.1,NM_138325.2	,,,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,,	368/970,368/957,368/976,368/963,368/488,368/624,368/653,368/665	101933522	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5046	.			GCTGACGGAGATG		CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"subtilisin-like protease", "subtilisin-like proprotein convertase 4", "subtilisin/kexin-like protease PACE4"	167405	"paired basic amino acid cleaving system 4"	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.1101C>T	15.37:g.101933522G>A		Somatic	57	1		WXS	Illumina HiSeq	Phase_I	41	18	.	0	0	0	1	1	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Silent	SNP	ENST00000348070.1	37																																																																																				.		0.597	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570		A	101933522	G	A	101933522	2	1	79	1	0	0	0	0	0	0	0	1	11630	1103	39	1		1	PCSK6	15	101933522	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	1062352	101933522	597870	65	7378											
IRX6	79190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	55360382	55360382	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgactgctgggcagtgcGcgaccggagctgggcgccgc	5	5	18	13	6	0	0	0	0	0	0	1	3	0	1	2	3	3	3	2	3	0	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:55360382G>A	ENST00000290552.7	+	2	1512	c.180G>A	c.(178-180)gcG>gcA	p.A60A	RP11-26L20.3_ENST00000558730.2_RNA|IRX6_ENST00000558315.1_3'UTR	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	60					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						TGGGCAGTGCGCGACCGGAGC	0.657																																					p.A60A		.											.	IRX6-174	0			c.G180A						.						26	24	25					16																	55360382		2198	4300	6498	SO:0001819	synonymous_variant	79190	exon2			CAGTGCGCGACCG	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"Homeoboxes / TALE class"	14675	protein-coding gene	gene with protein product		606196	"iroquois homeobox protein 7", "iroquois homeobox protein 6"	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.180G>A	16.37:g.55360382G>A		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	48	28	NM_024335	0	0	4	24	20	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	37	CCDS32449.1																																																																																			.		0.657	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		A	55360382	G	A	55360382	2	1	79	1	0	0	0	0	0	0	0	1	7869	1074	38	1		1	IRX6	16	55360382	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		55360382	34994371	66	7379											
CDH5	1003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	66413245	66413245	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcctcctgggaagatgcAgaggctcatgatgctcctcg	7	11	12	11	1	1	3	1	1	0	2	5	4	4	4	3	2	2	4	3	2	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:66413245A>C	ENST00000341529.3	+	2	153	c.5A>C	c.(4-6)cAg>cCg	p.Q2P	CDH5_ENST00000563425.2_Missense_Mutation_p.Q2P	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	2					adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	GGGAAGATGCAGAGGCTCATG	0.572																																					p.Q2P		.											.	CDH5-525	0			c.A5C						.						79	83	82					16																	66413245		2200	4299	6499	SO:0001583	missense	1003	exon2			AGATGCAGAGGCT	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"CD molecules", "Cadherins / Major cadherins"	1764	protein-coding gene	gene with protein product	"VE-cadherin"	601120	"cadherin 5, type 2, VE-cadherin (vascular epithelium)"			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.5A>C	16.37:g.66413245A>C	ENSP00000344115:p.Gln2Pro	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	268	61	NM_001795	0	0	1	1	0	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	CCDS10804.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791839	0.31685	.	.	ENSG00000179776	ENST00000341529;ENST00000379531	T	0.56103	0.48	4.38	2.03	0.26663	.	.	.	.	.	T	0.27169	0.0666	N	0.08118	0	0.42316	D	0.992239	B	0.11235	0.004	B	0.06405	0.002	T	0.04386	-1.0955	9	0.42905	T	0.14	.	4.3874	0.11323	0.6928:0.2005:0.1067:0.0	.	2	P33151	CADH5_HUMAN	P	2	ENSP00000344115:Q2P	ENSP00000344115:Q2P	Q	+	2	0	CDH5	64970746	0.837000	0.29446	0.481000	0.27354	0.805000	0.45488	1.348000	0.33987	0.204000	0.20548	0.379000	0.24179	CAG	.		0.572	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		C	66413245	A	C	66413245	3	2	79	1	0	0	0	0	1	0	0	0	3119	188	7	5	7	5	CDH5	16	66413245	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	11052863	66413245	23941508	67	7380											
PLCG2	5336	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81922847	81922847	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgatgacaccatgcgtgAaactgctgagcctttcttgt	9	13	9	10	1	1	4	0	4	1	0	1	4	1	4	2	0	4	1	2	0	1	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:81922847A>T	ENST00000359376.3	+	10	1050	c.836A>T	c.(835-837)gAa>gTa	p.E279V		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	279					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						ACCATGCGTGAAACTGCTGAG	0.463																																					p.E279V													.	PLCG2-892	0			c.A836T						.						183	177	179					16																	81922847		2040	4196	6236	SO:0001583	missense	5336	exon10			TGCGTGAAACTGC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"SH2 domain containing"	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.836A>T	16.37:g.81922847A>T	ENSP00000352336:p.Glu279Val	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	34	10	NM_002661	0	0	2	3	1	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	18.61	3.660395	0.67586	.	.	ENSG00000197943	ENST00000359376	T	0.33654	1.4	5.09	5.09	0.68999	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.095942	0.64402	D	0.000001	T	0.52821	0.1758	L	0.55990	1.75	0.53005	D	0.999969	P;D	0.64830	0.797;0.994	P;D	0.63192	0.698;0.912	T	0.56019	-0.8048	10	0.72032	D	0.01	.	14.8381	0.70201	1.0:0.0:0.0:0.0	.	146;279	B4E3H3;P16885	.;PLCG2_HUMAN	V	279	ENSP00000352336:E279V	ENSP00000352336:E279V	E	+	2	0	PLCG2	80480348	1.000000	0.71417	0.837000	0.33122	0.578000	0.36192	6.698000	0.74608	2.046000	0.60703	0.460000	0.39030	GAA	.		0.463	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81922847	A	T	81922847	3	4	79	1	0	0	0	0	1	0	0	0	12062	246	9	5	870	5	PLCG2	16	81922847	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	15509602	81922847	8431906	68	7381											
P2RX5	5026	broad.mit.edu;bcgsc.ca	37	chr17	3583061	3583061	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctcgtcctcggcctcctggGaactgtcttctaggcccctg	3	11	10	17	2	2	0	0	0	2	0	6	1	4	1	6	3	1	0	6	3	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:3583061G>A	ENST00000225328.5	-	11	1480	c.1082C>T	c.(1081-1083)tCc>tTc	p.S361F	P2RX5_ENST00000547178.1_Missense_Mutation_p.S360F|P2RX5_ENST00000552050.1_Missense_Mutation_p.S301F|P2RX5-TAX1BP3_ENST00000550383.1_Missense_Mutation_p.S361F|P2RX5_ENST00000345901.3_Missense_Mutation_p.S337F|P2RX5_ENST00000552276.1_Missense_Mutation_p.S360F|P2RX5_ENST00000435558.1_Missense_Mutation_p.S361F|P2RX5_ENST00000551178.1_Missense_Mutation_p.S336F	NM_001204519.1|NM_002561.3	NP_001191448.1|NP_002552.2	Q93086	P2RX5_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 5	361					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transport (GO:0006810)	integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|ion channel activity (GO:0005216)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						GGCCTCCTGGGAACTGTCTTC	0.647																																					p.S361F													.	P2RX5-22	0			c.C1082T						.						42	40	41					17																	3583061		2203	4300	6503	SO:0001583	missense	5026	exon11			TCCTGGGAACTGT	AF016709	CCDS11034.1, CCDS11035.1, CCDS56014.1, CCDS56015.1	17p13.3	2012-01-17			ENSG00000083454	ENSG00000083454		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8536	protein-coding gene	gene with protein product		602836				9414125	Standard	NM_002561		Approved	P2X5	uc002fwi.3	Q93086	OTTHUMG00000090700	ENST00000225328.5:c.1082C>T	17.37:g.3583061G>A	ENSP00000225328:p.Ser361Phe	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	32	10	NM_002561	0	0	0	1	1	G5E981|O43450|O75540|Q308M5|Q59F38|Q8IXW4|Q93087|Q9NZV0	Missense_Mutation	SNP	ENST00000225328.5	37	CCDS11034.1	.	.	.	.	.	.	.	.	.	.	G	6.998	0.554266	0.13374	.	.	ENSG00000083454	ENST00000435558;ENST00000551178;ENST00000547178;ENST00000225328;ENST00000345901;ENST00000552050	T;T;T;T;T;T	0.04502	3.61;3.61;3.61;3.61;3.61;3.61	3.01	0.971	0.19698	.	13.968400	0.00166	N	0.000000	T	0.03564	0.0102	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B	0.30686	0.29;0.246;0.246;0.246;0.29;0.246	B;B;B;B;B;B	0.25614	0.043;0.037;0.037;0.037;0.062;0.037	T	0.34204	-0.9838	10	0.59425	D	0.04	-16.3435	3.5464	0.07829	0.2514:0.2125:0.5361:0.0	.	301;337;360;336;361;361	B4DEG2;G5E981;Q93086-1;Q93086-2;Q93086;Q93086-4	.;.;.;.;P2RX5_HUMAN;.	F	361;336;360;361;337;301	ENSP00000415370:S361F;ENSP00000447545:S336F;ENSP00000448355:S360F;ENSP00000225328:S361F;ENSP00000342161:S337F;ENSP00000450006:S301F	ENSP00000225328:S361F	S	-	2	0	P2RX5	3529810	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.468000	0.22051	0.193000	0.20303	-0.432000	0.05891	TCC	.		0.647	P2RX5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207388.3	NM_002561, NM_175080, NM_175081		A	3583061	G	A	3583061	3	1	79	1	0	0	0	0	1	0	0	0	11369	1174	41	2	194	2	P2RX5	17	3583061	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		3583061	77612149	69	7382											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	378	24		WXS	Illumina HiSeq		371	32	NM_145301	0	0	5	24	19	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		T	15457087	C	T	15457087	3	4	79	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	11874026	15457087	65738123	70	7383											
SREBF1	6720	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17722461	17722461	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagaggccggggccttgcTgccagctgcgagccggttga	5	6	18	12	3	0	2	0	1	0	1	0	3	0	2	4	5	5	4	4	5	0	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:17722461T>C	ENST00000261646.5	-	5	1118	c.934A>G	c.(934-936)Agc>Ggc	p.S312G	SREBF1_ENST00000583732.1_5'UTR|SREBF1_ENST00000395757.1_Missense_Mutation_p.S58G|SREBF1_ENST00000338854.5_Missense_Mutation_p.S312G|SREBF1_ENST00000435530.2_Missense_Mutation_p.S312G|SREBF1_ENST00000355815.4_Missense_Mutation_p.S342G	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	312	Interaction with LMNA. {ECO:0000250}.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						GGGGCCTTGCTGCCAGCTGCG	0.607																																					p.S342G		.											.	SREBF1-91	0			c.A1024G						.						62	60	60					17																	17722461		2203	4300	6503	SO:0001583	missense	6720	exon6			CCTTGCTGCCAGC	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.934A>G	17.37:g.17722461T>C	ENSP00000261646:p.Ser312Gly	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	83	34	NM_001005291	0	0	13	28	15	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	37	CCDS11189.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.54|11.54	1.668371|1.668371	0.29604|0.29604	.|.	.|.	ENSG00000072310|ENSG00000072310	ENST00000395751|ENST00000338854;ENST00000355815;ENST00000261646;ENST00000395757;ENST00000418712;ENST00000423161;ENST00000435530	.|T;T;T;T;T	.|0.76578	.|0.66;0.65;0.66;1.02;-1.03	4.41|4.41	0.985|0.985	0.19779|0.19779	.|.	.|0.390138	.|0.18906	.|N	.|0.127893	T|T	0.43809|0.43809	0.1264|0.1264	N|N	0.01091|0.01091	-1.02|-1.02	0.27003|0.27003	N|N	0.964868|0.964868	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.001;0.001;0.0;0.001	T|T	0.37150|0.37150	-0.9718|-0.9718	5|10	.|0.14656	.|T	.|0.56	-6.3745|-6.3745	8.5495|8.5495	0.33442|0.33442	0.0:0.7314:0.0:0.2686|0.0:0.7314:0.0:0.2686	.|.	.|312;288;312;342	.|B0I4X3;B0I4X4;P36956;P36956-4	.|.;.;SRBP1_HUMAN;.	R|G	319|312;342;312;58;149;238;312	.|ENSP00000345822:S312G;ENSP00000348069:S342G;ENSP00000261646:S312G;ENSP00000379106:S58G;ENSP00000413389:S312G	.|ENSP00000261646:S312G	Q|S	-|-	2|1	0|0	SREBF1|SREBF1	17663186|17663186	0.654000|0.654000	0.27367|0.27367	0.484000|0.484000	0.27391|0.27391	0.781000|0.781000	0.44180|0.44180	1.287000|1.287000	0.33284|0.33284	-0.124000|-0.124000	0.11724|0.11724	0.459000|0.459000	0.35465|0.35465	CAG|AGC	.		0.607	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		C	17722461	T	C	17722461	3	2	79	1	0	0	0	0	1	0	0	0	15173	1580	55	3	2569	3	SREBF1	17	17722461	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	2265374	17722461	63472749	71	7384											
AKAP10	11216	bcgsc.ca	37	chr17	19845195	19845195	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaacgaaacagttgggatcCacctgtccatcttctccaca	13	9	6	13	1	2	0	0	0	2	0	5	2	4	1	4	1	2	1	4	1	3	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:19845195C>G	ENST00000225737.6	-	6	1162	c.1005G>C	c.(1003-1005)gtG>gtC	p.V335V	AKAP10_ENST00000395536.3_Silent_p.V335V	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	335	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					AGTTGGGATCCACCTGTCCAT	0.368																																					p.V335V													.	AKAP10-226	0			c.G1005C						.						132	101	112					17																	19845195		2203	4300	6503	SO:0001819	synonymous_variant	11216	exon6			GGGATCCACCTGT	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"A-kinase anchor proteins"	368	protein-coding gene	gene with protein product	"dual-specificity A-kinase anchoring protein 2", "protein kinase A anchoring protein 10", "mitochondrial A kinase PPKA anchor protein 10"	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1005G>C	17.37:g.19845195C>G		Somatic	61	0		WXS	Illumina HiSeq	Phase_1	38	4	NM_007202	0	0	15	15	0	B2R650|Q96AJ7	Silent	SNP	ENST00000225737.6	37	CCDS11214.1																																																																																			.		0.368	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		G	19845195	C	G	19845195	2	3	79	1	0	0	0	0	0	0	0	1	446	581	21	4		4	AKAP10	17	19845195	Silent	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	2122734	19845195	61350015	72	7385											
NF1	4763	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	29490388	29490388	+	Frame_Shift_Del	DEL	C	C	-																															tgcagtctttagtcgcatttCtaccaggttagtgtgtaaat																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:29490388delC	ENST00000358273.4	+	4	856	c.473delC	c.(472-474)tctfs	p.S158fs	NF1_ENST00000356175.3_Frame_Shift_Del_p.S158fs|NF1_ENST00000431387.4_Frame_Shift_Del_p.S158fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	158					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGTCGCATTTCTACCAGGTTA	0.368			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.S158fs		.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1-3353	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	c.473delC						.						53	52	52					17																	29490388		2203	4300	6503	SO:0001589	frameshift_variant	4763	exon4	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	.		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.473delC	17.37:g.29490388delC	ENSP00000351015:p.Ser158fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	104	56	NM_001128147	0	0	0	0	0	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	CCDS42292.1																																																																																			.		0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		-	29490388	C	-	29490388	7	5	79	1	0	1	0	1	0	0	0	0	10382	913	32	0	487	0	NF1	17	29490388	Frame_Shift_Del	DEL	C	TCGA-BQ-7044-01A-11D-1961-08	9645193	29490388	51704822	73	7386											
NF1	4763	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	29552188	29552189	+	Frame_Shift_Del	DEL	AG	AG	-																															ttccttctagtggaaataccAgtcaaatgtccatggatcat																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:29552188_29552189delAG	ENST00000358273.4	+	17	2304_2305	c.1921_1922delAG	c.(1921-1923)agtfs	p.S641fs	NF1_ENST00000356175.3_Frame_Shift_Del_p.S641fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	641					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TGGAAATACCAGTCAAATGTCC	0.406			"D, Mis, N, F, S, O"		"neurofibroma, glioma"	"neurofibroma, glioma"			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.641_641del		.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1-3353	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.1921_1922del						.																																			SO:0001589	frameshift_variant	4763	exon17	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	.		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"neurofibromatosis", "von Recklinghausen disease", "Watson disease"	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1921_1922delAG	17.37:g.29552188_29552189delAG	ENSP00000351015:p.Ser641fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	177	70	NM_000267	0	0	0	0	0	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	CCDS42292.1																																																																																			.		0.406	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		-	29552189	AG	-	29552188	7	5	79	1	0	1	0	1	0	0	0	0	10382	188	7	0	2048	0	NF1	17	29552188	Frame_Shift_Del	DEL	AG	TCGA-BQ-7044-01A-11D-1961-08	61800	29552188	51643022	74	7387											
POLG2	11232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62486981	62486981	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcctaggttccacagggtttCtattaactcctttccccagg	7	14	7	13	0	1	0	0	0	1	0	5	0	5	0	5	3	1	2	5	3	3	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:62486981C>G	ENST00000539111.2	-	4	968	c.901G>C	c.(901-903)Gaa>Caa	p.E301Q		NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	301					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			CACAGGGTTTCTATTAACTCC	0.408																																					p.E301Q	Colon(3;18 21 435 17652 48887)	.											.	POLG2-227	0			c.G901C						.						118	105	110					17																	62486981		2203	4300	6503	SO:0001583	missense	11232	exon4			GGGTTTCTATTAA	U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"DNA polymerases"	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.901G>C	17.37:g.62486981C>G	ENSP00000442563:p.Glu301Gln	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	81	39	NM_007215	0	0	6	8	2	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	37	CCDS32706.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.048199	0.75846	.	.	ENSG00000256525	ENST00000539111	T	0.79554	-1.28	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.88194	0.6371	M	0.81341	2.54	0.58432	D	0.999998	D;D	0.71674	0.998;0.998	P;P	0.55713	0.782;0.782	D	0.88758	0.3255	10	0.51188	T	0.08	-11.7483	19.247	0.93906	0.0:1.0:0.0:0.0	.	301;301	E5KS15;Q9UHN1	.;DPOG2_HUMAN	Q	301	ENSP00000442563:E301Q	ENSP00000442563:E301Q	E	-	1	0	POLG2	59917443	1.000000	0.71417	0.997000	0.53966	0.239000	0.25481	6.697000	0.74603	2.516000	0.84829	0.655000	0.94253	GAA	.		0.408	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1	NM_007215		G	62486981	C	G	62486981	3	3	79	1	0	0	0	0	1	0	0	0	12227	922	32	4	576	4	POLG2	17	62486981	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	32934793	62486981	18708229	75	7388											
RNF213	57674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	78293016	78293016	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctctcccagatcactgcCtactgcaatagttgctggga	8	10	8	15	0	2	1	1	0	1	1	3	2	2	2	4	1	4	3	4	1	3	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:78293016C>G	ENST00000582970.1	+	17	3071	c.2928C>G	c.(2926-2928)gcC>gcG	p.A976A	CTD-2047H16.2_ENST00000576808.1_RNA|RNF213_ENST00000508628.2_Silent_p.A1025A|RNF213_ENST00000319921.4_Silent_p.A976A|RNF213_ENST00000456466.1_Silent_p.A976A	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	976					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGATCACTGCCTACTGCAATA	0.522																																					p.A976A		.											.	RNF213-577	0			c.C2928G						.						122	122	122					17																	78293016		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon17			CACTGCCTACTGC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2928C>G	17.37:g.78293016C>G		Somatic	217	0		WXS	Illumina HiSeq	Phase_I	218	79	NM_001256071	0	0	10	15	5	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			.		0.522	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78293016	C	G	78293016	2	3	79	1	0	0	0	0	0	0	0	1	13509	668	24	4		4	RNF213	17	78293016	Silent	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	15806035	78293016	2902194	76	7389											
SIRT7	51547	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79870325	79870325	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcctttttgtgcgttttgtGcagcccctgccaaaccagcc	5	14	8	14	1	0	0	0	0	0	0	1	0	1	0	6	0	6	2	6	0	1	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:79870325G>A	ENST00000328666.6	-	10	1232	c.1170C>T	c.(1168-1170)tgC>tgT	p.C390C	PCYT2_ENST00000570391.1_5'Flank|PCYT2_ENST00000538936.2_5'Flank|PCYT2_ENST00000571105.1_5'Flank|PCYT2_ENST00000570388.1_5'Flank|PCYT2_ENST00000331285.3_5'Flank|PCYT2_ENST00000538721.2_5'Flank	NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	390					histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription on exit from mitosis (GO:0007072)|rRNA transcription (GO:0009303)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleolus organizer region (GO:0005731)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			TGCGTTTTGTGCAGCCCCTGC	0.597																																					p.C390C		.											.	SIRT7-204	0			c.C1170T						.						149	135	140					17																	79870325		2203	4299	6502	SO:0001819	synonymous_variant	51547	exon10			TTTTGTGCAGCCC	AF233395	CCDS11792.1	17q25.3	2010-06-25	2010-06-25			ENSG00000187531			14935	protein-coding gene	gene with protein product		606212	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 7", "sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae)"			10873683, 16618798	Standard	NM_016538		Approved		uc002kcj.2	Q9NRC8		ENST00000328666.6:c.1170C>T	17.37:g.79870325G>A		Somatic	271	2		WXS	Illumina HiSeq	Phase_I	219	107	NM_016538	0	0	12	29	17	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Silent	SNP	ENST00000328666.6	37	CCDS11792.1																																																																																			.		0.597	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538		A	79870325	G	A	79870325	2	1	79	1	0	0	0	0	0	0	0	1	14375	1311	46	2		2	SIRT7	17	79870325	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	1577309	79870325	1324885	77	7390											
USP14	9097	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	163336	163336	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatggggaaaggagaaattTgaaggtgtagaattgaatac	18	9	13	1	0	0	4	0	2	0	2	0	6	0	5	0	4	1	1	0	4	8	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr18:163336T>G	ENST00000261601.7	+	2	136	c.45T>G	c.(43-45)ttT>ttG	p.F15L	USP14_ENST00000383589.2_Missense_Mutation_p.F15L|USP14_ENST00000400266.3_Missense_Mutation_p.F15L|USP14_ENST00000582707.1_Missense_Mutation_p.F15L	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	15	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				AGGAGAAATTTGAAGGTGTAG	0.373																																					p.F15L		.											.	USP14-659	0			c.T45G						.						47	46	46					18																	163336		2203	4300	6503	SO:0001583	missense	9097	exon2			GAAATTTGAAGGT	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"Ubiquitin-specific peptidases"	12612	protein-coding gene	gene with protein product		607274	"ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.45T>G	18.37:g.163336T>G	ENSP00000261601:p.Phe15Leu	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	24	17	NM_001037334	0	0	0	4	4	J3QRZ5|Q53XY5	Missense_Mutation	SNP	ENST00000261601.7	37	CCDS32780.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.171691	0.57584	.	.	ENSG00000101557	ENST00000261601;ENST00000383589;ENST00000400266	T;T;T	0.32023	1.47;1.53;1.52	5.34	4.18	0.49190	Ubiquitin supergroup (1);Ubiquitin (1);	0.000000	0.85682	D	0.000000	T	0.29093	0.0723	L	0.56340	1.77	0.80722	D	1	P;B;B	0.36412	0.552;0.187;0.224	B;B;B	0.38500	0.275;0.105;0.275	T	0.04930	-1.0917	10	0.49607	T	0.09	0.9923	7.3687	0.26790	0.0:0.2181:0.0:0.7819	.	15;15;15	B7Z4N8;A6NJA2;P54578	.;.;UBP14_HUMAN	L	15	ENSP00000261601:F15L;ENSP00000373083:F15L;ENSP00000383125:F15L	ENSP00000261601:F15L	F	+	3	2	USP14	153336	0.996000	0.38824	1.000000	0.80357	0.998000	0.95712	0.344000	0.19962	0.876000	0.35872	0.528000	0.53228	TTT	.		0.373	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151		G	163336	T	G	163336	3	3	79	1	0	0	0	0	1	0	0	0	17078	1809	63	5	51	5	USP14	18	163336	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08		163336	77913912	78	7391											
C19orf45	374877	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	7570473	7570475	+	In_Frame_Del	DEL	CGG	CGG	-																															ggaaattggtgccccggcccCggcagtctggacaccttcat																								rs568541151		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:7570473_7570475delCGG	ENST00000361664.2	+	6	1107_1109	c.966_968delCGG	c.(964-969)cccggc>ccc	p.G323del	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	323										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						GCCCCGGCCCCGGCAGTCTGGAC	0.571																																					p.322_323del		.											.	C19orf45-90	0			c.966_968del						.																																			SO:0001651	inframe_deletion	374877	exon6			.	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.966_968delCGG	19.37:g.7570473_7570475delCGG	ENSP00000355241:p.Gly323del	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	71	25	NM_198534	0	0	0	0	0	Q8N115	In_Frame_Del	DEL	ENST00000361664.2	37	CCDS12179.2																																																																																			.		0.571	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534		-	7570475	CGG	-	7570473	7	5	79	1	0	1	0	1	0	0	0	0	1934	639	23	0	984	0	C19orf45	19	7570473	In_Frame_Del	DEL	CGG	TCGA-BQ-7044-01A-11D-1961-08		7570473	51558510	79	7392											
EPS15L1	58513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	16503123	16503124	+	Missense_Mutation	DNP	GT	GT	AA																															caccccactcaccttcgaagGtaaggaagggtttttcgtga																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:16503123_16503124GT>AA	ENST00000248070.6	-	19	2233_2234	c.2094_2095AC>TT	c.(2092-2097)ttACct>ttTTct	p.698_699LP>FS	EPS15L1_ENST00000455140.2_Missense_Mutation_p.698_699LP>FS|EPS15L1_ENST00000594975.1_Missense_Mutation_p.700_701LP>FS|EPS15L1_ENST00000535753.2_Missense_Mutation_p.698_699LP>FS	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	698	15 X 3 AA repeats of D-P-F.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						ACCTTCGAAGGTAAGGAAGGGT	0.559																																					p.LP698FS		.											.	EPS15L1	0			c.A2094T						.																																			SO:0001583	missense	58513	exon19			CGAAGGTAAGGAA	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.2094_2095delinsAA	19.37:g.16503123_16503124delinsAA	ENSP00000248070:p.L698_P699delinsFS	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	79	43		0	0	0	0	0	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	DNP	ENST00000248070.6	37	CCDS32944.1																																																																																			.		0.559	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		AA	16503124	GT	AA	16503123	3	1	79	1	0	0	0	0	1	0	0	0	5206	1261	44	2	519	2	EPS15L1	19	16503123	Missense_Mutation	DNP	GT	TCGA-BQ-7044-01A-11D-1961-08	8932650	16503123	42625860	80	7393											
EPS15L1	58513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	16551694	16551694	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtttgtccaagaaccctttAccttctggatcggccaagtc	8	13	8	12	1	1	1	0	0	1	1	4	2	2	2	4	2	2	1	4	2	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:16551694A>G	ENST00000248070.6	-	4	331	c.192T>C	c.(190-192)ggT>ggC	p.G64G	EPS15L1_ENST00000455140.2_Silent_p.G64G|EPS15L1_ENST00000594975.1_Silent_p.G64G|CTD-2013N17.4_ENST00000587343.1_RNA|EPS15L1_ENST00000535753.2_Silent_p.G64G|EPS15L1_ENST00000597937.1_Silent_p.G64G	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	64	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						AGAACCCTTTACCTTCTGGAT	0.527																																					p.G64G		.											.	EPS15L1-95	0			c.T192C						.						270	276	274					19																	16551694		2203	4300	6503	SO:0001819	synonymous_variant	58513	exon4			CCCTTTACCTTCT	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.192T>C	19.37:g.16551694A>G		Somatic	541	1		WXS	Illumina HiSeq	Phase_I	503	186	NM_021235	0	0	9	32	23	A2RRF3|A5PL29|B4DKA3	Silent	SNP	ENST00000248070.6	37	CCDS32944.1																																																																																			.		0.527	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		G	16551694	A	G	16551694	2	3	79	1	0	0	0	0	0	0	0	1	5206	378	14	3		3	EPS15L1	19	16551694	Silent	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	48571	16551694	42577289	81	7394											
ELL	8178	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18557590	18557590	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgtctccgacgtggacgtGggaacactggaaacgctgca	9	6	15	11	5	1	0	0	0	1	0	2	4	1	3	1	4	3	2	1	4	2	0	rs200056265		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:18557590G>A	ENST00000262809.4	-	9	1571	c.1500C>T	c.(1498-1500)ccC>ccT	p.P500P	ELL_ENST00000596124.3_Silent_p.P367P	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	500					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		ACGTGGACGTGGGAACACTGG	0.607			T	MLL	AL								g|||	1	0.000199681	0	0.0014	5008	,	,		22196	0		0	False		,,,				2504	0				p.P500P				Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL-1082	0			c.C1500T						.						97	81	87					19																	18557590		2203	4300	6503	SO:0001819	synonymous_variant	8178	exon9			GGACGTGGGAACA	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23114	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 68"	600284	"chromosome 19 open reading frame 17"	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.1500C>T	19.37:g.18557590G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	37	16	NM_006532	0	0	4	9	5		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			G|0.999;A|0.000		0.607	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		A	18557590	G	A	18557590	2	1	79	1	0	0	0	0	0	0	0	1	5075	1335	47	2		2	ELL	19	18557590	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	2005896	18557590	40571393	82	7395											
ZNF708	7562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	21493348	21493348	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctaacatgacattcctatAtaaattctgctgtgctgtgt	10	16	6	9	0	2	1	0	1	2	0	3	1	3	1	1	0	3	2	1	0	5	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:21493348A>G	ENST00000356929.3	-	2	282	c.85T>C	c.(85-87)Tat>Cat	p.Y29H		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	0					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)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						ACATTCCTATATAAATTCTGC	0.333																																					p.Y29H		.											.	ZNF708-516	0			c.T85C						.						62	66	65					19																	21493348		2203	4300	6503	SO:0001583	missense	7562	exon2			TCCTATATAAATT	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"Zinc fingers, C2H2-type", "-"	12945	protein-coding gene	gene with protein product			"zinc finger protein 15-like 1 (KOX 8)", "zinc finger protein 708", "zinc finger protein 708 (KOX8)"	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.85T>C	19.37:g.21493348A>G	ENSP00000349401:p.Tyr29His	Somatic	107	1		WXS	Illumina HiSeq	Phase_I	97	46	NM_021269	0	0	1	1	0	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	.	.	.	.	.	.	.	.	.	.	.	6.938	0.542810	0.13250	.	.	ENSG00000182141	ENST00000356929	T	0.07908	3.15	1.22	1.22	0.21188	Krueppel-associated box (4);	.	.	.	.	T	0.30759	0.0775	M	0.93016	3.37	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.08126	-1.0737	9	0.66056	D	0.02	.	4.192	0.10426	1.0:0.0:0.0:0.0	.	29	P17019	ZN708_HUMAN	H	29	ENSP00000349401:Y29H	ENSP00000349401:Y29H	Y	-	1	0	ZNF708	21285188	0.028000	0.19301	0.234000	0.24042	0.233000	0.25261	1.420000	0.34804	0.257000	0.21650	0.254000	0.18369	TAT	.		0.333	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		G	21493348	A	G	21493348	3	3	79	1	0	0	0	0	1	0	0	0	18144	449	16	3	1618	3	ZNF708	19	21493348	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	2935758	21493348	37635635	83	7396											
ZNF30	90075	hgsc.bcm.edu;broad.mit.edu	37	chr19	35434184	35434184	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgcccacctctgaaaactGtccatcttttgctctacatc	10	13	4	14	0	3	1	0	1	3	0	5	1	4	1	3	0	4	1	3	0	4	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:35434184G>A	ENST00000601142.1	+	5	551	c.314G>A	c.(313-315)tGt>tAt	p.C105Y	ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000303586.7_Missense_Mutation_p.C106Y|ZNF30_ENST00000595818.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.C24Y|ZNF30_ENST00000439785.1_Missense_Mutation_p.C106Y			P17039	ZNF30_HUMAN	zinc finger protein 30	105					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)		TCTGAAAACTGTCCATCTTTT	0.343																																					p.C106Y		.											.	ZNF30-24	0			c.G317A						.						49	47	47					19																	35434184		1840	4081	5921	SO:0001583	missense	90075	exon5			AAAACTGTCCATC	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.314G>A	19.37:g.35434184G>A	ENSP00000469954:p.Cys105Tyr	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	44	22	NM_001099438	0	0	2	2	0	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.858537	0.00065	.	.	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.08458	3.26;3.09	1.35	0.286	0.15710	.	.	.	.	.	T	0.03959	0.0111	N	0.08118	0	0.09310	N	1	B;B	0.20459	0.045;0.006	B;B	0.22386	0.039;0.001	T	0.41627	-0.9498	9	0.48119	T	0.1	.	3.6691	0.08266	0.2555:0.0:0.7445:0.0	.	106;105	P17039-2;P17039	.;ZNF30_HUMAN	Y	106;105;24	ENSP00000403441:C106Y;ENSP00000416457:C24Y	ENSP00000303889:C105Y	C	+	2	0	ZNF30	40126024	0.001000	0.12720	0.142000	0.22268	0.008000	0.06430	0.505000	0.22642	0.141000	0.18875	-0.357000	0.07601	TGT	.		0.343	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325		A	35434184	G	A	35434184	3	1	79	1	0	0	0	0	1	0	0	0	17862	1377	48	2	331	2	ZNF30	19	35434184	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	13940836	35434184	23694799	84	7397											
BCAM	4059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45322619	45322619	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atagcccgcagagccaatccCcggacggcagggttgggtga	9	5	15	12	3	0	2	0	1	0	1	1	3	1	3	4	4	2	3	4	4	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:45322619C>T	ENST00000270233.6	+	12	1512	c.1490C>T	c.(1489-1491)cCc>cTc	p.P497L	BCAM_ENST00000589651.1_Missense_Mutation_p.P497L	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	497	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GAGCCAATCCCCGGACGGCAG	0.662																																					p.P497L		.											.	BCAM-91	0			c.C1490T						.						59	64	62					19																	45322619		2203	4300	6503	SO:0001583	missense	4059	exon12			CAATCCCCGGACG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1490C>T	19.37:g.45322619C>T	ENSP00000270233:p.Pro497Leu	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	46	22	NM_001013257	0	0	214	482	268	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	0.017	-1.487632	0.01018	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.03124	4.04;4.04	4.31	0.796	0.18648	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02533	0.0077	L	0.28694	0.88	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.49532	-0.8930	9	0.13853	T	0.58	-6.5334	3.4865	0.07622	0.1986:0.5733:0.0:0.2281	.	497	P50895	BCAM_HUMAN	L	497	ENSP00000270233:P497L;ENSP00000375817:P497L	ENSP00000270233:P497L	P	+	2	0	BCAM	50014459	0.003000	0.15002	0.001000	0.08648	0.113000	0.19764	-0.023000	0.12456	0.031000	0.15407	0.543000	0.68304	CCC	.		0.662	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45322619	C	T	45322619	3	4	79	1	0	0	0	0	1	0	0	0	1345	623	22	2	1536	2	BCAM	19	45322619	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	9888435	45322619	13806364	85	7398											
ZNF28	7576	ucsc.edu	37	chr19	53304673	53304673	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagatgcgaatgaaagcttAatccaagctgatctttaata	15	11	8	7	1	1	3	0	2	1	1	2	4	2	3	1	0	3	3	1	0	6	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:53304673A>G	ENST00000457749.2	-	4	544	c.425T>C	c.(424-426)tTa>tCa	p.L142S	ZNF28_ENST00000414252.2_Missense_Mutation_p.L89S|ZNF28_ENST00000360272.4_Missense_Mutation_p.L89S|ZNF28_ENST00000438150.2_Missense_Mutation_p.L89S|ZNF28_ENST00000594602.1_3'UTR	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	142					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(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		ATGAAAGCTTAATCCAAGCTG	0.413																																					p.L142S													.	ZNF28-91	0			c.T425C						.						244	229	234					19																	53304673		2203	4300	6503	SO:0001583	missense	7576	exon4			AAGCTTAATCCAA	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.425T>C	19.37:g.53304673A>G	ENSP00000397693:p.Leu142Ser	Somatic	369	5		WXS	Illumina HiSeq		339	14	NM_006969	0	0	18	27	9	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	0.014	-1.584717	0.00872	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.10860	2.83;3.0;2.83;2.83;2.9	1.81	-1.78	0.07957	.	.	.	.	.	T	0.03434	0.0099	N	0.02412	-0.56	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45775	-0.9238	9	0.16420	T	0.52	.	7.0768	0.25209	0.7171:0.0:0.2829:0.0	.	142	P17035	ZNF28_HUMAN	S	89;142;89;89;89	ENSP00000412143:L89S;ENSP00000397693:L142S;ENSP00000353410:L89S;ENSP00000444965:L89S;ENSP00000375661:L89S	ENSP00000353410:L89S	L	-	2	0	ZNF28	57996485	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-2.146000	0.01294	-1.272000	0.02427	-1.924000	0.00514	TTA	.		0.413	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		G	53304673	A	G	53304673	3	3	79	1	0	0	0	0	1	0	0	0	17845	372	13	3	1735	3	ZNF28	19	53304673	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	7982054	53304673	5824310	86	7399											
FCAR	2204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55385758	55385758	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcagcacgatggaccccaaaCagaccaccctcctgtgtctt	10	8	7	16	1	2	1	1	0	1	1	3	3	3	2	5	1	2	1	5	1	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:55385758C>T	ENST00000355524.3	+	1	23	c.13C>T	c.(13-15)Cag>Tag	p.Q5*	FCAR_ENST00000359272.4_Nonsense_Mutation_p.Q5*|FCAR_ENST00000469767.1_Nonsense_Mutation_p.Q5*|FCAR_ENST00000345937.4_Nonsense_Mutation_p.Q5*|FCAR_ENST00000391723.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000353758.4_Nonsense_Mutation_p.Q5*|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000391726.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000391725.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000391724.3_Nonsense_Mutation_p.Q5*	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	5					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		GGACCCCAAACAGACCACCCT	0.483																																					p.Q5X		.											.	FCAR-92	0			c.C13T						.						135	122	127					19																	55385758		2203	4300	6503	SO:0001587	stop_gained	2204	exon1			CCCAAACAGACCA	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.13C>T	19.37:g.55385758C>T	ENSP00000347714:p.Gln5*	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	136	59	NM_133279	0	0	0	0	0	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Nonsense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.549835	0.65311	.	.	ENSG00000186431	ENST00000433231;ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000353758;ENST00000359272;ENST00000391723;ENST00000391724	.	.	.	2.76	1.72	0.24424	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	7.8266	0.29318	0.0:0.2588:0.7412:0.0	.	.	.	.	X	5	.	ENSP00000338257:Q5X	Q	+	1	0	FCAR	60077570	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.054000	0.11826	0.725000	0.32318	-0.226000	0.12346	CAG	.		0.483	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		T	55385758	C	T	55385758	4	4	79	1	0	0	0	0	0	1	0	0	5792	479	17	2	15	2	FCAR	19	55385758	Nonsense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	2081085	55385758	3743225	87	7400											
PARD6B	84612	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	49366983	49366991	+	In_Frame_Del	DEL	TCAAAAACT	TCAAAAACT	-																															tttgaaacacatgctccagaTcaaaaactcttagaagaaga																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	TCAAAAACT	TCAAAAACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr20:49366983_49366991delTCAAAAACT	ENST00000371610.2	+	3	1320_1328	c.1077_1085delTCAAAAACT	c.(1075-1086)gatcaaaaactc>gac	p.QKL360del	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	360					axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						ATGCTCCAGATCAAAAACTCTTAGAAGAA	0.397																																					p.359_362del		.											.	PARD6B-91	0			c.1077_1085del						.																																			SO:0001651	inframe_deletion	84612	exon3			.	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"par-6 (partitioning defective 6, C.elegans) homolog beta", "par-6 partitioning defective 6 homolog beta (C. elegans)"			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.1077_1085delTCAAAAACT	20.37:g.49366983_49366991delTCAAAAACT	ENSP00000360672:p.Gln360_Leu362del	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	74	22	NM_032521	0	0	0	0	0	A2A2A7|Q9Y510	In_Frame_Del	DEL	ENST00000371610.2	37	CCDS33485.1																																																																																			.		0.397	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		-	49366991	TCAAAAACT	-	49366983	7	5	79	1	0	1	0	1	0	0	0	0	11472	1432	50	0	1087	0	PARD6B	20	49366983	In_Frame_Del	DEL	TCAAAAACT	TCGA-BQ-7044-01A-11D-1961-08		49366983	13658537	88	7401											
BMP7	655	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	55777539	55777539	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggggactcaccatccagcGtctccaccgagagctgcagg	8	5	13	15	3	2	1	1	0	1	1	4	3	3	2	4	3	3	2	4	3	0	0	rs112344257		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr20:55777539G>A	ENST00000395863.3	-	3	1257	c.752C>T	c.(751-753)aCg>aTg	p.T251M	BMP7_ENST00000395864.3_Missense_Mutation_p.T251M|BMP7_ENST00000460817.1_5'UTR|BMP7_ENST00000450594.2_Missense_Mutation_p.T251M	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	251					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			ACCATCCAGCGTCTCCACCGA	0.612													G|||	1	0.000199681	0	0	5008	,	,		16001	0		0.001	False		,,,				2504	0				p.T251M													.	BMP7-187	0			c.C752T						.	G	MET/THR	0,4406		0,0,2203	41	36	38		752	3.7	1	20	dbSNP_132	38	2,8598	2.2+/-6.3	0,2,4298	yes	missense	BMP7	NM_001719.2	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	251/432	55777539	2,13004	2203	4300	6503	SO:0001583	missense	655	exon3			TCCAGCGTCTCCA		CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"Bone morphogenetic proteins", "Endogenous ligands"	1074	protein-coding gene	gene with protein product	"osteogenic protein 1"	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.752C>T	20.37:g.55777539G>A	ENSP00000379204:p.Thr251Met	Somatic	41	1		WXS	Illumina HiSeq	Phase_I	22	16	NM_001719	0	0	0	0	0	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	37	CCDS13455.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.92	3.255052	0.59321	0.0	2.33E-4	ENSG00000101144	ENST00000395863;ENST00000395864;ENST00000450594	T;T;T	0.66638	-0.22;-0.22;-0.22	4.78	3.74	0.42951	Transforming growth factor-beta, N-terminal (1);	0.041703	0.85682	D	0.000000	T	0.74336	0.3703	M	0.78916	2.43	0.37592	D	0.920226	D;P;P	0.65815	0.995;0.484;0.846	P;B;B	0.53809	0.735;0.095;0.305	T	0.80286	-0.1446	10	0.54805	T	0.06	.	11.9649	0.53029	0.0:0.4402:0.5598:0.0	.	251;251;251	B1AKZ9;P18075;B1AL00	.;BMP7_HUMAN;.	M	251	ENSP00000379204:T251M;ENSP00000379205:T251M;ENSP00000398687:T251M	ENSP00000379204:T251M	T	-	2	0	BMP7	55210946	0.990000	0.36364	0.967000	0.41034	0.945000	0.59286	2.151000	0.42263	2.369000	0.80426	0.561000	0.74099	ACG	T|0.000;C|0.999		0.612	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			A	55777539	G	A	55777539	3	1	79	1	0	0	0	0	1	0	0	0	1466	1145	40	1	563	1	BMP7	20	55777539	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	6410556	55777539	7247981	89	7402											
NYX	60506	hgsc.bcm.edu	37	chrX	41333524	41333524	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaccgcgtggcgcgcgcctGgttcgctgacctggccgagc	3	6	17	15	7	0	1	0	1	0	0	1	3	0	2	4	4	1	2	4	4	0	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chrX:41333524G>C	ENST00000342595.2	+	2	1274	c.818G>C	c.(817-819)tGg>tCg	p.W273S	NYX_ENST00000378220.1_Missense_Mutation_p.W273S	NM_022567.2	NP_072089.1	Q9GZU5	NYX_HUMAN	nyctalopin	273					response to stimulus (GO:0050896)|visual perception (GO:0007601)	intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(11)|upper_aerodigestive_tract(1)	17						GCGCGCGCCTGGTTCGCTGAC	0.716																																					p.W273S		.											.	NYX-108	0			c.G818C						.						19	19	19					X																	41333524		2200	4292	6492	SO:0001583	missense	60506	exon2			GCGCCTGGTTCGC	AF254868	CCDS14256.1	Xp11.4	2014-01-28			ENSG00000188937	ENSG00000188937			8082	protein-coding gene	gene with protein product		300278		CSNB1, CSNB4		11062471, 11062472	Standard	NM_022567		Approved	CLRP, CSNB1A	uc004dfh.2	Q9GZU5	OTTHUMG00000021370	ENST00000342595.2:c.818G>C	X.37:g.41333524G>C	ENSP00000340328:p.Trp273Ser	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_022567	0	0	0	0	0	D3DWC0|Q2M1S4|Q5H983|Q9H4J0	Missense_Mutation	SNP	ENST00000342595.2	37	CCDS14256.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.159844	0.57368	.	.	ENSG00000188937	ENST00000342595;ENST00000378220	T;T	0.78126	-1.15;-1.15	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.70631	0.3246	N	0.01809	-0.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70539	-0.4844	10	0.08837	T	0.75	.	17.8739	0.88819	0.0:0.0:1.0:0.0	.	273	Q9GZU5	NYX_HUMAN	S	273	ENSP00000340328:W273S;ENSP00000367465:W273S	ENSP00000340328:W273S	W	+	2	0	NYX	41218468	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	7.190000	0.77755	2.154000	0.67381	0.600000	0.82982	TGG	.		0.716	NYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056256.1	NM_022567		C	41333524	G	C	41333524	3	2	79	1	0	0	0	0	1	0	0	0	10823	1357	47	4	824	4	NYX	23	41333524	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		41333524	113937036	90	7403											
PORCN	64840	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	48371012	48371012	+	Frame_Shift_Del	DEL	G	G	-																															cagaaggtggcccggagcctGgcactggccctgctgtgcct																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chrX:48371012delG	ENST00000326194.6	+	5	634	c.591delG	c.(589-591)ctgfs	p.L197fs	PORCN_ENST00000359882.4_Frame_Shift_Del_p.L197fs|PORCN_ENST00000537758.1_Frame_Shift_Del_p.L197fs|PORCN_ENST00000367574.4_Frame_Shift_Del_p.L126fs|PORCN_ENST00000355961.4_Frame_Shift_Del_p.L197fs|PORCN_ENST00000355092.3_Frame_Shift_Del_p.L197fs|PORCN_ENST00000361988.3_Frame_Shift_Del_p.L197fs	NM_203475.1	NP_982301.1	Q9H237	PORCN_HUMAN	porcupine homolog (Drosophila)	197					glycoprotein metabolic process (GO:0009100)|Wnt signaling pathway (GO:0016055)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups (GO:0016746)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCCGGAGCCTGGCACTGGCCC	0.647																																					p.L197fs		.											.	PORCN-133	0			c.591delG						.						54	48	50					X																	48371012		2203	4300	6503	SO:0001589	frameshift_variant	64840	exon5			.	AF317058	CCDS14296.1, CCDS14297.1, CCDS14298.1, CCDS14299.1	Xp11.23	2014-02-05			ENSG00000102312	ENSG00000102312			17652	protein-coding gene	gene with protein product		300651	"dermal hypoplasia, focal"	DHOF		10866835, 12034504, 17546030	Standard	NM_203474		Approved	MG61, PORC, PPN, por	uc004djv.1	Q9H237	OTTHUMG00000024116	ENST00000326194.6:c.591delG	X.37:g.48371012delG	ENSP00000322304:p.Leu197fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	11	11	NM_203475	0	0	0	0	0	B2RBN8|B7ZAR3|Q14829|Q9H234|Q9H235|Q9H236|Q9UJU7	Frame_Shift_Del	DEL	ENST00000326194.6	37	CCDS14299.1																																																																																			.		0.647	PORCN-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356990.1	NM_022825		-	48371012	G	-	48371012	7	5	79	1	0	1	0	1	0	0	0	0	12284	1335	47	0	609	0	PORCN	23	48371012	Frame_Shift_Del	DEL	G	TCGA-BQ-7044-01A-11D-1961-08	7037488	48371012	106899548	91	7404											
KIAA1522	57648	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	33236795	33236795	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcctgcccccttctcccCacctccctccaagcccagga	5	7	7	22	0	1	0	0	0	1	0	4	1	3	1	9	2	3	0	9	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:33236795C>A	ENST00000373480.1	+	6	1941	c.1838C>A	c.(1837-1839)cCa>cAa	p.P613Q	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P672Q|KIAA1522_ENST00000373481.3_Missense_Mutation_p.P624Q	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	613	Pro-rich.									breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CCCTTCTCCCCACCTCCCTCC	0.647																																					p.P672Q		.											.	KIAA1522-90	0			c.C2015A						.						58	64	62					1																	33236795		1901	4107	6008	SO:0001583	missense	57648	exon6			TCTCCCCACCTCC	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.1838C>A	1.37:g.33236795C>A	ENSP00000362579:p.Pro613Gln	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	141	46	NM_020888	0	0	3	13	10	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057475	0.36277	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.18502	2.21;2.21;2.24	4.07	4.07	0.47477	.	0.000000	0.56097	D	0.000038	T	0.33673	0.0871	L	0.56769	1.78	0.38739	D	0.95385	D;D;D	0.76494	0.99;0.99;0.999	P;P;D	0.67548	0.901;0.901;0.952	T	0.16217	-1.0410	10	0.59425	D	0.04	-5.8801	11.0055	0.47631	0.0:0.9058:0.0:0.0942	.	624;613;672	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	Q	672;624;613	ENSP00000383851:P672Q;ENSP00000362580:P624Q;ENSP00000362579:P613Q	ENSP00000362579:P613Q	P	+	2	0	KIAA1522	33009382	0.814000	0.29104	0.958000	0.39756	0.821000	0.46438	3.744000	0.55112	1.954000	0.56735	0.563000	0.77884	CCA	.		0.647	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33236795	C	A	33236795	3	1	80	1	0	0	0	0	1	0	0	0	8259	594	21	4	2037	4	KIAA1522	1	33236795	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		33236795	216013826	1	7405											
SLC5A9	200010	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	48708165	48708165	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggactcggaactgccccCtctctgagctggagaaggag	8	7	15	11	1	1	2	0	1	1	1	3	6	1	5	2	5	3	1	2	5	2	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:48708165C>T	ENST00000438567.2	+	13	1766	c.1714C>T	c.(1714-1716)Ctc>Ttc	p.L572F	SLC5A9_ENST00000533824.1_Missense_Mutation_p.L593F|SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Missense_Mutation_p.L597F	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	572					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						GAACTGCCCCCTCTCTGAGCT	0.597																																					p.L597F		.											.	SLC5A9-93	0			c.C1789T						.						73	73	73					1																	48708165		2203	4300	6503	SO:0001583	missense	200010	exon14			TGCCCCCTCTCTG	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"Solute carriers"	22146	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 9"				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1714C>T	1.37:g.48708165C>T	ENSP00000401730:p.Leu572Phe	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	162	9	NM_001135181	0	0	0	0	0	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	C	2.600	-0.293103	0.05568	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.63255	-0.03;-0.03;-0.03	4.42	2.25	0.28309	.	2.354250	0.01631	N	0.023545	T	0.51381	0.1671	L	0.29908	0.895	0.09310	N	1	B;B;B	0.25521	0.128;0.023;0.112	B;B;B	0.29716	0.04;0.058;0.106	T	0.35649	-0.9780	10	0.44086	T	0.13	.	2.3723	0.04333	0.2782:0.4525:0.1682:0.1011	.	593;572;597	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	F	593;572;597	ENSP00000431900:L593F;ENSP00000401730:L572F;ENSP00000236495:L597F	ENSP00000236495:L597F	L	+	1	0	SLC5A9	48480752	0.000000	0.05858	0.002000	0.10522	0.032000	0.12392	-2.295000	0.01143	0.283000	0.22279	0.655000	0.94253	CTC	.		0.597	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48708165	C	T	48708165	3	4	80	1	0	0	0	0	1	0	0	0	14704	681	24	2	1843	2	SLC5A9	1	48708165	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	15471370	48708165	200542456	2	7406											
CTH	1491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	70895506	70895506	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctctgggagctgatatttcTatgtattctgcaacaaaata	12	14	8	7	0	3	1	0	1	3	0	3	2	3	2	0	1	3	4	0	1	7	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:70895506T>C	ENST00000370938.3	+	6	762	c.618T>C	c.(616-618)tcT>tcC	p.S206S	CTH_ENST00000411986.2_Silent_p.S174S|CTH_ENST00000346806.2_Silent_p.S162S|CTH_ENST00000464926.1_3'UTR	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0	Ig-like C2-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CTGATATTTCTATGTATTCTG	0.353																																					p.S206S		.											.	CTH-91	0			c.T618C						.						103	97	99					1																	70895506		2203	4300	6503	SO:0001819	synonymous_variant	1491	exon6			TATTTCTATGTAT	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.618T>C	1.37:g.70895506T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	79	26	NM_001902	0	0	1	2	1	O95791|Q9NX42	Silent	SNP	ENST00000370938.3	37	CCDS650.1																																																																																			.		0.353	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		C	70895506	T	C	70895506	2	2	80	1	0	0	0	0	0	0	0	1	4015	1509	53	3		3	CTH	1	70895506	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	22187341	70895506	178355115	3	7407											
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94528186	94528186	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaggtagattccaactggAgcctccgcctgcacctggct	7	9	12	13	1	0	1	0	0	0	1	2	3	2	3	5	4	3	3	5	4	2	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:94528186A>T	ENST00000370225.3	-	13	1970	c.1884T>A	c.(1882-1884)gcT>gcA	p.A628A	ABCA4_ENST00000535735.1_Silent_p.A628A	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	628					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TTCCAACTGGAGCCTCCGCCT	0.572																																					p.A628A		.											.	ABCA4-162	0			c.T1884A						.						76	74	75					1																	94528186		2203	4300	6503	SO:0001819	synonymous_variant	24	exon13			AACTGGAGCCTCC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1884T>A	1.37:g.94528186A>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	59	16	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			.		0.572	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94528186	A	T	94528186	2	4	80	1	0	0	0	0	0	0	0	1	34	291	11	5		5	ABCA4	1	94528186	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	23632680	94528186	154722435	4	7408											
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151112138	151112138	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgggcaccagcccctccccTtcttcttcggcttgaagatc	5	12	8	16	1	2	2	0	1	2	1	5	2	3	2	5	2	1	2	5	2	1	5	rs200312578		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:151112138T>C	ENST00000341697.3	-	5	1964	c.273A>G	c.(271-273)gaA>gaG	p.E91E				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	91	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCCCCTCCCCTTCTTCTTCGG	0.582																																					p.E91E		.											.	SEMA6C-92	0			c.A273G						.						55	53	54					1																	151112138		2203	4300	6503	SO:0001819	synonymous_variant	10500	exon5			CTCCCCTTCTTCT	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"Semaphorins"	10740	protein-coding gene	gene with protein product	"m-Sema Y2"	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.273A>G	1.37:g.151112138T>C		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	62	4	NM_001178061	0	0	0	0	0	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Silent	SNP	ENST00000341697.3	37	CCDS984.1																																																																																			T|0.999;G|0.001		0.582	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		C	151112138	T	C	151112138	2	2	80	1	0	0	0	0	0	0	0	1	14073	1606	56	3		3	SEMA6C	1	151112138	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	56583952	151112138	98138483	5	7409											
MRPL9	65005	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	151735603	151735616	+	Frame_Shift_Del	DEL	CGCTCCACGATGAC	CGCTCCACGATGAC	-																															ccagcggtaccttccaccagCgctccacgatgaccgtgccc																								rs567245913|rs199843916		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	CGCTCCACGATGAC	CGCTCCACGATGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:151735603_151735616delCGCTCCACGATGAC	ENST00000368830.3	-	2	244_257	c.160_173delGTCATCGTGGAGCG	c.(160-174)gtcatcgtggagcgcfs	p.VIVER54fs	RP11-98D18.3_ENST00000512280.1_RNA|RP11-98D18.2_ENST00000420382.1_RNA|MRPL9_ENST00000368829.3_Frame_Shift_Del_p.VIVER54fs|OAZ3_ENST00000453029.2_5'Flank|OAZ3_ENST00000315067.8_Start_Codon_Del|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000321531.5_Start_Codon_Del|OAZ3_ENST00000479764.1_5'Flank	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	54					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R58H(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CTTCCACCAGCGCTCCACGATGACCGTGCCCTGG	0.668																																					p.54_58del		.											.	MRPL9-91	1	Substitution - Missense(1)	large_intestine(1)	c.160_173del						.																																			SO:0001589	frameshift_variant	65005	exon2			.	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"Mitochondrial ribosomal proteins / large subunits"	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.160_173delGTCATCGTGGAGCG	1.37:g.151735603_151735616delCGCTCCACGATGAC	ENSP00000357823:p.Val54fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	47	12	NM_031420	0	0	0	0	0	B2RD99|Q5SZR2|Q9BSW8	Frame_Shift_Del	DEL	ENST00000368830.3	37	CCDS1003.1																																																																																			.		0.668	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420		-	151735616	CGCTCCACGATGAC	-	151735603	7	5	80	1	0	1	0	1	0	0	0	0	9845	768	27	0	654	0	MRPL9	1	151735603	Frame_Shift_Del	DEL	CGCTCCACGATGAC	TCGA-BQ-7045-01A-31D-1961-08	623465	151735603	97515018	6	7410											
PROX1	5629	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	214170437	214170438	+	Frame_Shift_Ins	INS	-	-	AT																															cagtgtggcattaaggggcaINSatgaaaatgaaagagagatg																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:214170437_214170438insAT	ENST00000366958.4	+	2	1167_1168	c.559_560insAT	c.(559-561)aatfs	p.N187fs	PROX1_ENST00000498508.2_Frame_Shift_Ins_p.N187fs|PROX1_ENST00000261454.4_Frame_Shift_Ins_p.N187fs|PROX1_ENST00000435016.1_Frame_Shift_Ins_p.N187fs	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	187					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		ATTAAGGGGCAATGAAAATGAA	0.505																																					p.N187fs		.											.	PROX1-654	0			c.559_560insAT						.																																			SO:0001589	frameshift_variant	5629	exon2			.	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.560_561dupAT	1.37:g.214170438_214170439dupAT	ENSP00000355925:p.Asn187fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	74	21	NM_001270616	0	0	0	0	0	A6NK29|A8K2B1|Q5SW76|Q8TB91	Frame_Shift_Ins	INS	ENST00000366958.4	37	CCDS31021.1																																																																																			.		0.505	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		AT	214170438	-	AT	214170437	7	5	80	1	0	1	1	0	0	0	0	0	12589	130	5	0	561	0	PROX1	1	214170437	Frame_Shift_Ins	INS	-	TCGA-BQ-7045-01A-31D-1961-08	62434834	214170437	35080184	7	7411											
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	216373415	216373415	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggtggtctcaatgtaatagGaatatttggtatatggtaac	12	15	11	3	0	1	0	1	0	1	0	2	1	1	1	0	5	1	3	0	5	8	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:216373415G>A	ENST00000307340.3	-	17	3751	c.3365C>T	c.(3364-3366)tCc>tTc	p.S1122F	USH2A_ENST00000366943.2_Missense_Mutation_p.S1122F|USH2A_ENST00000366942.3_Missense_Mutation_p.S1122F|RP5-1099E6.3_ENST00000420867.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1122	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AATGTAATAGGAATATTTGGT	0.363										HNSCC(13;0.011)																											p.S1122F		.											.	USH2A-115	0			c.C3365T						.						66	66	66					1																	216373415		2203	4300	6503	SO:0001583	missense	7399	exon17			TAATAGGAATATT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.3365C>T	1.37:g.216373415G>A	ENSP00000305941:p.Ser1122Phe	Somatic	88	1		WXS	Illumina HiSeq	Phase_I	90	31	NM_007123	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.353632	0.61293	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	D;T;T	0.85258	-1.96;0.55;0.32	6.02	5.06	0.68205	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.162301	0.29093	N	0.013179	D	0.92704	0.7681	M	0.84683	2.71	0.52099	D	0.999947	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.956	D	0.92488	0.5998	10	0.49607	T	0.09	.	16.7932	0.85595	0.0:0.1285:0.8715:0.0	.	1122;1122	O75445-2;O75445	.;USH2A_HUMAN	F	1122	ENSP00000305941:S1122F;ENSP00000355910:S1122F;ENSP00000355909:S1122F	ENSP00000305941:S1122F	S	-	2	0	USH2A	214440038	1.000000	0.71417	0.982000	0.44146	0.319000	0.28217	4.663000	0.61532	2.865000	0.98341	0.655000	0.94253	TCC	.		0.363	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216373415	G	A	216373415	3	1	80	1	0	0	0	0	1	0	0	0	17069	1174	41	2	12481	2	USH2A	1	216373415	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	2202978	216373415	32877206	8	7412											
PLEKHB2	55041	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	131904282	131904282	+	Frame_Shift_Del	DEL	C	C	-																															agacaacgacagcgacctggCactgggcatgctggcaggag																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:131904282delC	ENST00000403716.1	+	8	1165	c.605delC	c.(604-606)gcafs	p.A202fs	PLEKHB2_ENST00000538982.1_Frame_Shift_Del_p.A154fs|PLEKHB2_ENST00000438882.2_Frame_Shift_Del_p.H166fs|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000409279.1_Frame_Shift_Del_p.A202fs|PLEKHB2_ENST00000409158.1_Frame_Shift_Del_p.A210fs|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000439822.2_Frame_Shift_Del_p.H158fs|PLEKHB2_ENST00000409612.1_Frame_Shift_Del_p.A202fs|PLEKHB2_ENST00000234115.6_Frame_Shift_Del_p.A201fs	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	202						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		AGCGACCTGGCACTGGGCATG	0.507																																					p.A216fs		.											.	PLEKHB2-92	0			c.647delC						.						160	166	164					2																	131904282		2203	4300	6503	SO:0001589	frameshift_variant	55041	exon9			.		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.605delC	2.37:g.131904282delC	ENSP00000385892:p.Ala202fs	Somatic	293	0		WXS	Illumina HiSeq	Phase_I	311	83	NM_001267062	0	0	0	0	0	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Frame_Shift_Del	DEL	ENST00000403716.1	37	CCDS46413.1																																																																																			.		0.507	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		-	131904282	C	-	131904282	7	5	80	1	0	1	0	1	0	0	0	0	12091	710	25	0	631	0	PLEKHB2	2	131904282	Frame_Shift_Del	DEL	C	TCGA-BQ-7045-01A-31D-1961-08		131904282	111295091	9	7413	84	2									
PLEKHB2	55041	hgsc.bcm.edu;bcgsc.ca	37	chr2	131904283	131904284	+	Missense_Mutation	DNP	AC	AC	GG																															gacaacgacagcgacctggcActgggcatgctggcaggagc																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:131904283_131904284AC>GG	ENST00000403716.1	+	8	1166_1167	c.606_607AC>GG	c.(604-609)gcACtg>gcGGtg	p.L203V	PLEKHB2_ENST00000538982.1_Missense_Mutation_p.L155V|PLEKHB2_ENST00000438882.2_Missense_Mutation_p.H166R|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000409279.1_Missense_Mutation_p.L203V|PLEKHB2_ENST00000409158.1_Missense_Mutation_p.L211V|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000439822.2_Missense_Mutation_p.H158R|PLEKHB2_ENST00000409612.1_Missense_Mutation_p.L203V|PLEKHB2_ENST00000234115.6_Missense_Mutation_p.L202V	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	203						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		GCGACCTGGCACTGGGCATGCT	0.51																																					p.L211V		.											.	PLEKHB2	0			c.C649G						.																																			SO:0001583	missense	55041	exon9			CTGGCACTGGGCA		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	Exception_encountered	2.37:g.131904283_131904284delinsGG	ENSP00000385892:p.Leu203Val	Somatic	305	0		WXS	Illumina HiSeq	Phase_I	310	84		0	0	0	0	0	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	DNP	ENST00000403716.1	37	CCDS46413.1																																																																																			.		0.51	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		GG	131904284	AC	GG	131904283	3	3	80	1	0	0	0	0	1	0	0	0	12091	146	6	3	632	3	PLEKHB2	2	131904283	Missense_Mutation	DNP	AC	TCGA-BQ-7045-01A-31D-1961-08	1	131904283	111295090	10	7414	84	2									
HTR2B	3357	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	231988374	231988374	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctggtattgattctgtCtgtaatccagaccagttaga	9	15	8	9	0	3	3	0	1	3	2	5	3	5	3	3	1	0	3	3	1	3	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:231988374C>A	ENST00000258400.3	-	2	617	c.105G>T	c.(103-105)caG>caT	p.Q35H	PSMD1_ENST00000308696.6_Intron|PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000409643.1_Intron	NM_000867.4	NP_000858.3	P41595	5HT2B_HUMAN	5-hydroxytryptamine (serotonin) receptor 2B, G protein-coupled	35					activation of phospholipase C activity (GO:0007202)|behavior (GO:0007610)|calcium-mediated signaling (GO:0019722)|cardiac muscle hypertrophy (GO:0003300)|cellular calcium ion homeostasis (GO:0006874)|cellular response to temperature stimulus (GO:0071502)|cGMP biosynthetic process (GO:0006182)|embryonic morphogenesis (GO:0048598)|ERK1 and ERK2 cascade (GO:0070371)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|heart morphogenesis (GO:0003007)|intestine smooth muscle contraction (GO:0014827)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell death (GO:0060548)|neural crest cell differentiation (GO:0014033)|neural crest cell migration (GO:0001755)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphorylation (GO:0016310)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	drug binding (GO:0008144)|G-protein alpha-subunit binding (GO:0001965)|Ras GTPase activator activity (GO:0005099)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	11		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;4.48e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0141)	Amoxapine(DB00543)|Apomorphine(DB00714)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Dihydroergotamine(DB00320)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Lisuride(DB00589)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Ropinirole(DB00268)|Triflupromazine(DB00508)|Yohimbine(DB01392)	TTGATTCTGTCTGTAATCCAG	0.418																																					p.Q35H	Ovarian(155;1331 1891 12853 14038 34991)	.											.	HTR2B-90	0			c.G105T						.						192	179	183					2																	231988374		2203	4300	6503	SO:0001583	missense	3357	exon2			TTCTGTCTGTAAT		CCDS2483.1	2q36.3-q37.1	2012-08-08	2012-02-03		ENSG00000135914	ENSG00000135914		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5294	protein-coding gene	gene with protein product		601122	"5-hydroxytryptamine (serotonin) receptor 2B"			8143856	Standard	NM_000867		Approved	5-HT(2B), 5-HT2B	uc002vro.3	P41595	OTTHUMG00000133222	ENST00000258400.3:c.105G>T	2.37:g.231988374C>A	ENSP00000258400:p.Gln35His	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	144	48	NM_000867	0	0	0	0	0	B2R9D5|Q53TI1|Q62221|Q6P523	Missense_Mutation	SNP	ENST00000258400.3	37	CCDS2483.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121899	0.37436	.	.	ENSG00000135914	ENST00000258400	T	0.36878	1.23	5.52	1.53	0.23141	.	0.500549	0.19422	N	0.114664	T	0.27349	0.0671	L	0.44542	1.39	0.23144	N	0.998224	B	0.33379	0.41	B	0.35510	0.204	T	0.14504	-1.0470	10	0.22706	T	0.39	.	8.4754	0.33009	0.0:0.4476:0.4023:0.1501	.	35	P41595	5HT2B_HUMAN	H	35	ENSP00000258400:Q35H	ENSP00000258400:Q35H	Q	-	3	2	HTR2B	231696618	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	1.887000	0.39698	0.297000	0.22615	-0.237000	0.12165	CAG	.		0.418	HTR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256957.2	NM_000867		A	231988374	C	A	231988374	3	1	80	1	0	0	0	0	1	0	0	0	7463	912	32	4	1352	4	HTR2B	2	231988374	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	100084091	231988374	11210999	11	7415											
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238283616	238283616	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagggaagccgctcctgaCgccctcagagccatcaagca	11	4	11	15	2	2	3	2	1	0	2	3	4	3	4	4	1	3	2	4	1	2	0	rs78427077		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:238283616C>T	ENST00000295550.4	-	8	3570	c.3118G>A	c.(3118-3120)Gtc>Atc	p.V1040I	COL6A3_ENST00000472056.1_Missense_Mutation_p.V433I|COL6A3_ENST00000346358.4_Missense_Mutation_p.V840I|COL6A3_ENST00000409809.1_Missense_Mutation_p.V834I|COL6A3_ENST00000392003.2_Missense_Mutation_p.V633I|COL6A3_ENST00000347401.3_Missense_Mutation_p.V839I|COL6A3_ENST00000353578.4_Missense_Mutation_p.V834I|COL6A3_ENST00000392004.3_Missense_Mutation_p.V834I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1040	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCGCTCCTGACGCCCTCAGAG	0.567													C|||	1	0.000199681	0	0	5008	,	,		19525	0		0.001	False		,,,				2504	0				p.V1040I		.											.	COL6A3-526	0			c.G3118A						.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	46	49	48		3118,1897,2500,1297,2500	5.3	0.5	2	dbSNP_132	48	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense,missense,missense,missense	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	29,29,29,29,29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1040/3178,633/1037,834/1238,433/2571,834/2972	238283616	3,13003	2203	4300	6503	SO:0001583	missense	1293	exon8			TCCTGACGCCCTC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.3118G>A	2.37:g.238283616C>T	ENSP00000295550:p.Val1040Ile	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	76	24	NM_004369	0	0	1	1	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.29	1.894058	0.33442	0.0	3.49E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003	T;T;T;T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47	5.33	5.33	0.75918	von Willebrand factor, type A (3);	0.000000	0.49305	D	0.000154	T	0.79776	0.4504	N	0.16743	0.435	0.46981	D	0.99927	D;D;P;D;D	0.76494	0.998;0.98;0.892;0.999;0.964	D;P;P;P;P	0.66351	0.943;0.709;0.678;0.906;0.489	T	0.77550	-0.2546	10	0.28530	T	0.3	.	13.6833	0.62499	0.0:0.9262:0.0:0.0738	.	433;633;834;834;1040	E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;CO6A3_HUMAN	I	1040;839;834;433;834;840;834;633	ENSP00000295550:V1040I;ENSP00000315609:V839I;ENSP00000315873:V834I;ENSP00000418285:V433I;ENSP00000386844:V834I;ENSP00000295546:V840I;ENSP00000375861:V834I;ENSP00000375860:V633I	ENSP00000295550:V1040I	V	-	1	0	COL6A3	237948355	0.743000	0.28239	0.491000	0.27477	0.042000	0.13812	1.589000	0.36644	2.652000	0.90054	0.655000	0.94253	GTC	C|1.000;T|0.000		0.567	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238283616	C	T	238283616	3	4	80	1	0	0	0	0	1	0	0	0	3707	536	19	1	6610	1	COL6A3	2	238283616	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	6295242	238283616	4915757	12	7416											
AZI2	64343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	28382066	28382066	+	Frame_Shift_Del	DEL	C	C	-																															atctctcttatgggctttttCatgattcagaatacagatat																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:28382066delC	ENST00000479665.1	-	2	574	c.43delG	c.(43-45)gaafs	p.E15fs	AZI2_ENST00000420543.2_Frame_Shift_Del_p.E15fs|AZI2_ENST00000334100.6_Frame_Shift_Del_p.E15fs|AZI2_ENST00000295748.3_5'UTR|AZI2_ENST00000457172.1_Frame_Shift_Del_p.E15fs	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	15	Homodimerization. {ECO:0000250}.				dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						TGGGCTTTTTCATGATTCAGA	0.348																																					p.E15fs		.											.	AZI2-92	0			c.43delG						.						104	107	106					3																	28382066		2203	4300	6503	SO:0001589	frameshift_variant	64343	exon2			.	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.43delG	3.37:g.28382066delC	ENSP00000419371:p.Glu15fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	127	50	NM_001134432	0	0	0	0	0	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Frame_Shift_Del	DEL	ENST00000479665.1	37	CCDS2647.1																																																																																			.		0.348	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326		-	28382066	C	-	28382066	7	5	80	1	0	1	0	1	0	0	0	0	1242	835	29	0	1252	0	AZI2	3	28382066	Frame_Shift_Del	DEL	C	TCGA-BQ-7045-01A-31D-1961-08		28382066	169640364	13	7417											
CRTAP	10491	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	33156008	33156008	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggacttccagcgccgcgagCcctacaagttcctgcagttc	7	8	10	16	4	0	0	0	0	0	0	3	2	2	1	4	1	4	3	4	1	2	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:33156008C>T	ENST00000320954.6	+	1	538	c.439C>T	c.(439-441)Ccc>Tcc	p.P147S	CRTAP_ENST00000449224.1_Missense_Mutation_p.P147S	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	147					chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation to 3-hydroxy-L-proline (GO:0018400)|protein stabilization (GO:0050821)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|macromolecular complex (GO:0032991)|proteinaceous extracellular matrix (GO:0005578)	protein complex binding (GO:0032403)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						GCGCCGCGAGCCCTACAAGTT	0.726																																					p.P147S		.											.	CRTAP-90	0			c.C439T						.						7	8	8					3																	33156008		1469	3247	4716	SO:0001583	missense	10491	exon1			CGCGAGCCCTACA	AJ006470	CCDS2657.1	3p22	2014-09-17			ENSG00000170275	ENSG00000170275			2379	protein-coding gene	gene with protein product	"leprecan-like 3"	605497				9217321, 10429950	Standard	NM_006371		Approved	CASP, LEPREL3	uc003cfl.4	O75718	OTTHUMG00000130746	ENST00000320954.6:c.439C>T	3.37:g.33156008C>T	ENSP00000323696:p.Pro147Ser	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	42	14	NM_006371	0	0	18	53	35	B2RBL6	Missense_Mutation	SNP	ENST00000320954.6	37	CCDS2657.1	.	.	.	.	.	.	.	.	.	.	C	32	5.124174	0.94429	.	.	ENSG00000170275	ENST00000320954;ENST00000509775;ENST00000539684;ENST00000449224;ENST00000423366	T;T	0.78003	-1.14;-1.14	4.31	4.31	0.51392	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.89698	0.6790	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.91955	0.5574	10	0.87932	D	0	-10.8094	16.9301	0.86188	0.0:1.0:0.0:0.0	.	147;147	C9JP16;O75718	.;CRTAP_HUMAN	S	147;147;134;147;147	ENSP00000323696:P147S;ENSP00000409997:P147S	ENSP00000323696:P147S	P	+	1	0	CRTAP	33131012	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.262000	0.78410	2.398000	0.81561	0.467000	0.42956	CCC	.		0.726	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3			T	33156008	C	T	33156008	3	4	80	1	0	0	0	0	1	0	0	0	3904	739	26	2	441	2	CRTAP	3	33156008	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	4773942	33156008	164866422	14	7418											
PTH1R	5745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46939563	46939563	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgacctcccatggacctgcaGgccatgcctaccgacgctgt	7	8	10	16	2	0	1	0	1	0	0	1	3	1	2	6	2	3	2	6	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:46939563G>T	ENST00000313049.5	+	5	627		c.e5-1		PTH1R_ENST00000490109.1_Splice_Site|PTH1R_ENST00000449590.1_Splice_Site|PTH1R_ENST00000418619.1_Splice_Site|PTH1R_ENST00000430002.2_Splice_Site			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor						adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	TGGACCTGCAGGCCATGCCTA	0.617																																					.		.											.	PTH1R-522	0			c.425-1G>T						.						102	103	103					3																	46939563		2203	4300	6503	SO:0001630	splice_region_variant	5745	exon7			CCTGCAGGCCATG		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"GPCR / Class B : Parathyroid hormone receptors"	9608	protein-coding gene	gene with protein product		168468	"parathyroid hormone receptor 1"	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.425-1G>T	3.37:g.46939563G>T		Somatic	125	1		WXS	Illumina HiSeq	Phase_I	183	40	NM_000316	0	0	0	3	3	Q2M1U3	Splice_Site	SNP	ENST00000313049.5	37	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279080	0.80692	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049;ENST00000313063	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7448	0.62868	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTH1R	46914567	1.000000	0.71417	0.999000	0.59377	0.967000	0.64934	9.835000	0.99442	2.379000	0.81126	0.462000	0.41574	.	.		0.617	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	Intron	T	46939563	G	T	46939563	5	4	80	1	0	0	0	0	0	0	1	0	12788	1014	35	4	442	4	PTH1R	3	46939563	Splice_Site	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	13783555	46939563	151082867	15	7419											
USP19	10869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49148708	49148709	+	Missense_Mutation	DNP	TC	TC	AT																															ctttgtcctctagccgctgcTctcggttggatgaatcaatt																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:49148708_49148709TC>AT	ENST00000398888.2	-	21	3316_3317	c.2998_2999GA>AT	c.(2998-3000)GAg>ATg	p.E1000M	USP19_ENST00000434032.2_Missense_Mutation_p.E1101M|USP19_ENST00000453664.1_Missense_Mutation_p.E1091M|USP19_ENST00000398898.2_Missense_Mutation_p.E1040M|USP19_ENST00000398896.1_Missense_Mutation_p.E808M|USP19_ENST00000417901.1_Missense_Mutation_p.E1103M|USP19_ENST00000398892.3_Missense_Mutation_p.E1040M	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1000	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TAGCCGCTGCTCTCGGTTGGAT	0.545																																					p.E1101M		.											.	USP19	0			c.G3307A						.																																			SO:0001583	missense	10869	exon22			GCTGCTCTCGGTT	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2998_2999delinsAT	3.37:g.49148708_49148709delinsAT	ENSP00000381863:p.Glu1000Met	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	115	58		0	0	0	0	0	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	DNP	ENST00000398888.2	37	CCDS43090.1																																																																																			.		0.545	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		AT	49148709	TC	AT	49148708	3	1	80	1	0	0	0	0	1	0	0	0	17083	1551	54	5	981	5	USP19	3	49148708	Missense_Mutation	DNP	TC	TCGA-BQ-7045-01A-31D-1961-08	2209145	49148708	148873722	16	7420											
CISH	1154	broad.mit.edu;bcgsc.ca	37	chr3	50645554	50645554	+	Frame_Shift_Del	DEL	A	A	-																															tgtcgggcctcgctggccgtAatggaaccccaataccagcc																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:50645554delA	ENST00000348721.3	-	3	441	c.261delT	c.(259-261)attfs	p.I87fs	CISH_ENST00000443053.2_Frame_Shift_Del_p.I104fs	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	87	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGCTGGCCGTAATGGAACCCC	0.562																																					p.I104fs													.	CISH-710	0			c.312delT						.						38	38	38					3																	50645554		2203	4300	6503	SO:0001589	frameshift_variant	1154	exon4			GGCCGTAATGGAA	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.261delT	3.37:g.50645554delA	ENSP00000294173:p.Ile87fs	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	69	10	NM_013324	0	0	0	0	0	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Frame_Shift_Del	DEL	ENST00000348721.3	37	CCDS2831.1																																																																																			.		0.562	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		-	50645554	A	-	50645554	7	5	80	1	0	1	0	1	0	0	0	0	3443	358	13	0	519	0	CISH	3	50645554	Frame_Shift_Del	DEL	A	TCGA-BQ-7045-01A-31D-1961-08	1496846	50645554	147376876	17	7421											
MITF	4286	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	69988260	69988261	+	Frame_Shift_Ins	INS	-	-	T																															ttttgcagggattttataagINStttgaagagcaaaacagggc																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:69988260_69988261insT	ENST00000448226.2	+	4	721_722	c.594_595insT	c.(595-597)tttfs	p.F199fs	MITF_ENST00000531774.1_Frame_Shift_Ins_p.F36fs|MITF_ENST00000394351.3_Frame_Shift_Ins_p.F92fs|MITF_ENST00000352241.4_Frame_Shift_Ins_p.F199fs|MITF_ENST00000314589.5_Frame_Shift_Ins_p.F183fs|MITF_ENST00000328528.6_Frame_Shift_Ins_p.F198fs|MITF_ENST00000314557.6_Frame_Shift_Ins_p.F92fs|MITF_ENST00000472437.1_Frame_Shift_Ins_p.F147fs|MITF_ENST00000394355.2_Frame_Shift_Ins_p.F174fs			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	199					bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.K91N(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GATTTTATAAGTTTGAAGAGCA	0.441			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.K198fs	Melanoma(29;269 969 31479 41502 42961)	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	.	MITF-524	1	Substitution - Missense(1)	large_intestine(1)	c.594_595insT						.																																			SO:0001589	frameshift_variant	4286	exon4			.		CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098		"Basic helix-loop-helix proteins"	7105	protein-coding gene	gene with protein product	"homolog of mouse microphthalmia"	156845	"Waardenburg syndrome, type 2A"	WS2A, WS2		8069297, 7874167, 7951321	Standard	NM_198159		Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000448226.2:c.597dupT	3.37:g.69988263_69988263dupT	ENSP00000391803:p.Phe199fs	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	75	38	NM_198159	0	0	0	0	0	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Frame_Shift_Ins	INS	ENST00000448226.2	37																																																																																				.		0.441	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69988261	-	T	69988260	7	5	80	1	0	1	1	0	0	0	0	0	9621	1020	36	0	829	0	MITF	3	69988260	Frame_Shift_Ins	INS	-	TCGA-BQ-7045-01A-31D-1961-08	19342706	69988260	128034170	18	7422											
ATP2C1	27032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	130686204	130686204	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgcaatgatgctgtaattAgaaacaatactctaatgggg	14	12	10	5	0	1	2	0	1	1	1	1	2	1	2	0	2	4	3	0	2	7	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:130686204A>G	ENST00000510168.1	+	16	1799	c.1249A>G	c.(1249-1251)Aga>Gga	p.R417G	ATP2C1_ENST00000533801.2_Missense_Mutation_p.R412G|ATP2C1_ENST00000359644.3_Missense_Mutation_p.R417G|ATP2C1_ENST00000504948.1_Missense_Mutation_p.R401G|ATP2C1_ENST00000507488.2_Missense_Mutation_p.R401G|ATP2C1_ENST00000422190.2_Missense_Mutation_p.R417G|ATP2C1_ENST00000513801.1_Missense_Mutation_p.R401G|ATP2C1_ENST00000393221.4_Missense_Mutation_p.R451G|ATP2C1_ENST00000504381.1_Missense_Mutation_p.R362G|ATP2C1_ENST00000428331.2_Missense_Mutation_p.R417G|ATP2C1_ENST00000505330.1_Missense_Mutation_p.R401G|ATP2C1_ENST00000508532.1_Missense_Mutation_p.R417G|ATP2C1_ENST00000328560.8_Missense_Mutation_p.R417G			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	417					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TGCTGTAATTAGAAACAATAC	0.383									Hailey-Hailey disease																												p.R451G	Esophageal Squamous(99;456 1443 27647 34099 42636)	.											.	ATP2C1-91	0			c.A1351G						.						114	117	116					3																	130686204		2203	4300	6503	SO:0001583	missense	27032	exon15	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	GTAATTAGAAACA	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"ATPases / P-type"	13211	protein-coding gene	gene with protein product	"secretory pathway Ca2+/Mn2+ ATPase 1", "calcium-transporting ATPase type 2C member 1"	604384	"benign chronic pemphigus (Hailey-Hailey disease)"	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.1249A>G	3.37:g.130686204A>G	ENSP00000427461:p.Arg417Gly	Somatic	96	1		WXS	Illumina HiSeq	Phase_I	132	33	NM_001199181	0	0	30	36	6	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Missense_Mutation	SNP	ENST00000510168.1	37	CCDS46914.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.047442	0.36085	.	.	ENSG00000017260	ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421	D;D;D;D;D;D;D;D;D;D;D;D;D	0.92965	-3.01;-3.06;-3.02;-3.02;-3.08;-3.01;-3.01;-3.01;-3.02;-3.14;-3.01;-3.02;-3.02	5.59	4.4	0.53042	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.046259	0.85682	D	0.000000	T	0.79644	0.4481	N	0.01686	-0.76	0.53688	D	0.999978	B;B;B;B;B;B;B	0.18013	0.02;0.025;0.007;0.02;0.007;0.007;0.009	B;B;B;B;B;B;B	0.18263	0.012;0.021;0.021;0.012;0.021;0.007;0.012	T	0.72940	-0.4139	10	0.39692	T	0.17	.	12.0367	0.53429	0.7275:0.2725:0.0:0.0	.	451;412;451;417;451;417;417	G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194	.;.;.;.;.;.;AT2C1_HUMAN	G	401;362;401;451;412;417;417;401;401;417;417;417;417;416	ENSP00000423774:R401G;ENSP00000425320:R362G;ENSP00000421326:R401G;ENSP00000376914:R451G;ENSP00000432956:R412G;ENSP00000427461:R417G;ENSP00000424783:R417G;ENSP00000423330:R401G;ENSP00000422872:R401G;ENSP00000329664:R417G;ENSP00000395809:R417G;ENSP00000352665:R417G;ENSP00000402677:R417G	ENSP00000329664:R417G	R	+	1	2	ATP2C1	132168894	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.143000	0.50608	0.919000	0.36945	0.477000	0.44152	AGA	.		0.383	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		G	130686204	A	G	130686204	3	3	80	1	0	0	0	0	1	0	0	0	1144	412	15	3	1307	3	ATP2C1	3	130686204	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	60697944	130686204	67336226	19	7423											
DZIP1L	199221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	137805834	137805834	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccatgtgctcttcatgcAgttccttcacttttcttttc	5	18	5	13	0	4	0	2	0	2	0	6	0	5	0	2	0	3	3	2	0	0	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:137805834A>G	ENST00000327532.2	-	7	1393	c.1031T>C	c.(1030-1032)cTg>cCg	p.L344P	DZIP1L_ENST00000469243.1_Missense_Mutation_p.L344P|DZIP1L_ENST00000488595.1_5'UTR	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	344					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CTCTTCATGCAGTTCCTTCAC	0.423																																					p.L344P		.											.	DZIP1L-92	0			c.T1031C						.						227	199	209					3																	137805834		2203	4300	6503	SO:0001583	missense	199221	exon8			TCATGCAGTTCCT	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1031T>C	3.37:g.137805834A>G	ENSP00000332148:p.Leu344Pro	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	133	31	NM_001170538	0	0	0	0	0	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607713	0.28623	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.50277	0.75;0.75	5.1	3.92	0.45320	.	0.353745	0.21368	N	0.075699	T	0.61788	0.2375	M	0.65975	2.015	0.44136	D	0.996925	D;D	0.89917	0.999;1.0	D;D	0.73380	0.974;0.98	T	0.58934	-0.7548	10	0.42905	T	0.14	-4.3459	8.3577	0.32340	0.8247:0.0:0.0:0.1753	.	344;344	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	P	344	ENSP00000332148:L344P;ENSP00000419486:L344P	ENSP00000332148:L344P	L	-	2	0	DZIP1L	139288524	0.829000	0.29322	0.156000	0.22583	0.039000	0.13416	4.330000	0.59266	0.859000	0.35456	-0.333000	0.08304	CTG	.		0.423	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		G	137805834	A	G	137805834	3	3	80	1	0	0	0	0	1	0	0	0	4875	188	7	3	1321	3	DZIP1L	3	137805834	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	7119630	137805834	60216596	20	7424											
RASA2	5922	broad.mit.edu;bcgsc.ca	37	chr3	141326509	141326518	+	Splice_Site	DEL	TTATTATTTA	TTATTATTTA	-																															ttaattttgttttactttttTtattatttaggcaaagatgc																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	TTATTATTTA	TTATTATTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:141326509_141326518delTTATTATTTA	ENST00000452898.1	+	20	1971		c.e20-1		RASA2_ENST00000509118.1_Splice_Site|RASA2_ENST00000286364.3_Splice_Site	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2						intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TTTACTTTTTTTATTATTTAGGCAAAGATG	0.305																																					.													.	RASA2-661	0			.						.																																			SO:0001630	splice_region_variant	5922	.			CTTTTTTTATTAT	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"Pleckstrin homology (PH) domain containing"	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.1937-1TTATTATTTA>-	3.37:g.141326509_141326518delTTATTATTTA		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	35	21	.	0	0	0	0	0	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Splice_Site	DEL	ENST00000452898.1	37																																																																																				.		0.305	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	Intron	-	141326518	TTATTATTTA	-	141326509	8	5	80	1	0	1	0	1	0	0	1	0	13093	1856	64	0		0	RASA2	3	141326509	Splice_Site	DEL	TTATTATTTA	TCGA-BQ-7045-01A-31D-1961-08	3520675	141326509	56695921	21	7425											
EIF4G1	1981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	184041746	184041746	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtggcctatgccaacaTgtgccgctgcctcatggcgg	5	10	12	14	2	2	0	1	0	1	0	2	0	2	0	4	3	4	1	4	3	2	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:184041746T>C	ENST00000346169.2	+	16	2724	c.2453T>C	c.(2452-2454)aTg>aCg	p.M818T	EIF4G1_ENST00000441154.1_Missense_Mutation_p.M655T|EIF4G1_ENST00000427845.1_Missense_Mutation_p.M732T|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000352767.3_Missense_Mutation_p.M825T|EIF4G1_ENST00000342981.4_Missense_Mutation_p.M819T|EIF4G1_ENST00000392537.2_Missense_Mutation_p.M731T|EIF4G1_ENST00000350481.5_Missense_Mutation_p.M654T|EIF4G1_ENST00000434061.2_Missense_Mutation_p.M623T|EIF4G1_ENST00000424196.1_Missense_Mutation_p.M825T|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000382330.3_Missense_Mutation_p.M825T|EIF4G1_ENST00000414031.1_Missense_Mutation_p.M778T|EIF4G1_ENST00000435046.2_Missense_Mutation_p.M622T|EIF4G1_ENST00000411531.1_Missense_Mutation_p.M779T|EIF4G1_ENST00000319274.6_Missense_Mutation_p.M818T	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	818	eIF3/EIF4A-binding.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TATGCCAACATGTGCCGCTGC	0.517																																					p.M825T		.											.	EIF4G1-344	0			c.T2474C						.						66	63	64					3																	184041746		2203	4300	6503	SO:0001583	missense	1981	exon17			CCAACATGTGCCG	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"Parkinson disease"	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.2453T>C	3.37:g.184041746T>C	ENSP00000316879:p.Met818Thr	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	124	33	NM_001194946	0	0	26	40	14	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.609064	0.66558	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.92	5.92	0.95590	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.038518	0.85682	D	0.000000	T	0.52517	0.1739	M	0.86805	2.84	0.80722	D	1	P;P;P;P	0.49862	0.929;0.929;0.929;0.929	P;P;P;P	0.56216	0.794;0.794;0.794;0.794	T	0.60692	-0.7213	10	0.87932	D	0	-18.7766	16.3634	0.83296	0.0:0.0:0.0:1.0	.	825;819;818;825	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	T	818;778;731;819;826;825;759;654;825;732;819;818;825;779;654;655;623;622	ENSP00000316879:M818T;ENSP00000391935:M778T;ENSP00000376320:M731T;ENSP00000391412:M819T;ENSP00000413159:M826T;ENSP00000371767:M825T;ENSP00000403269:M759T;ENSP00000317600:M654T;ENSP00000338020:M825T;ENSP00000407682:M732T;ENSP00000343450:M819T;ENSP00000323737:M818T;ENSP00000416255:M825T;ENSP00000395974:M779T;ENSP00000398145:M654T;ENSP00000399858:M655T;ENSP00000411826:M623T;ENSP00000404754:M622T	ENSP00000323737:M818T	M	+	2	0	EIF4G1	185524440	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.270000	0.75569	0.459000	0.35465	ATG	.		0.517	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		C	184041746	T	C	184041746	3	2	80	1	0	0	0	0	1	0	0	0	5049	1464	51	3	2507	3	EIF4G1	3	184041746	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	42715237	184041746	13980684	22	7426											
HGFAC	3083	ucsc.edu	37	chr4	3444828	3444828	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccttccgctacgggggccGcatgctgcatgcctgcactt	4	9	11	17	3	0	0	0	0	0	0	1	0	1	0	5	2	5	5	5	2	1	3	rs554424799		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:3444828G>A	ENST00000382774.3	+	3	465	c.350G>A	c.(349-351)cGc>cAc	p.R117H	HGFAC_ENST00000511533.1_Missense_Mutation_p.R117H	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	117	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TACGGGGGCCGCATGCTGCAT	0.721													G|||	1	0.000199681	0	0	5008	,	,		14389	0.001		0	False		,,,				2504	0				p.R117H													.	HGFAC-514	0			c.G350A						.						17	22	20					4																	3444828		2193	4289	6482	SO:0001583	missense	3083	exon3			GGGGCCGCATGCT	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.350G>A	4.37:g.3444828G>A	ENSP00000372224:p.Arg117His	Somatic	27	0		WXS	Illumina HiSeq		39	4	NM_001528	0	0	0	0	0	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.313041	0.23908	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	T;T	0.50548	0.74;0.74	3.16	2.17	0.27698	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.000000	0.64402	U	0.000005	T	0.36635	0.0974	L	0.52759	1.655	0.31138	N	0.706937	B;B	0.30973	0.302;0.139	B;B	0.29598	0.063;0.104	T	0.46925	-0.9156	10	0.59425	D	0.04	.	6.6572	0.22994	0.0:0.0:0.7172:0.2828	.	117;117	D6RAR4;Q04756	.;HGFA_HUMAN	H	117	ENSP00000372224:R117H;ENSP00000421801:R117H	ENSP00000372224:R117H	R	+	2	0	HGFAC	3414626	0.997000	0.39634	0.988000	0.46212	0.213000	0.24496	1.277000	0.33167	1.709000	0.51313	0.306000	0.20318	CGC	.		0.721	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			A	3444828	G	A	3444828	3	1	80	1	0	0	0	0	1	0	0	0	7107	1087	38	1	360	1	HGFAC	4	3444828	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		3444828	187709448	23	7427											
LAP3	51056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	17590497	17590497	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattcctcagtgtggccaaaGgatctgacgagcccccagtc	9	8	10	14	1	2	1	1	1	1	0	4	3	3	2	4	2	1	0	4	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:17590497G>A	ENST00000226299.4	+	7	1034	c.760G>A	c.(760-762)Gga>Aga	p.G254R	LAP3_ENST00000503467.1_3'UTR|LAP3_ENST00000606142.1_Missense_Mutation_p.G223R|AC006160.5_ENST00000511010.1_RNA	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	254					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						TGTGGCCAAAGGATCTGACGA	0.453																																					p.G254R		.											.	LAP3-90	0			c.G760A						.						110	108	108					4																	17590497		2203	4300	6503	SO:0001583	missense	51056	exon7			GCCAAAGGATCTG	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.760G>A	4.37:g.17590497G>A	ENSP00000226299:p.Gly254Arg	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	134	50	NM_015907	0	0	11	27	16	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	37	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	G	31	5.103254	0.94245	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.58506	0.44;0.33	5.12	5.12	0.69794	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87390	0.6165	H	0.99415	4.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93090	0.6499	10	0.87932	D	0	-22.9866	18.9237	0.92536	0.0:0.0:1.0:0.0	.	254	P28838	AMPL_HUMAN	R	254;88	ENSP00000226299:G254R;ENSP00000424724:G88R	ENSP00000226299:G254R	G	+	1	0	LAP3	17199595	1.000000	0.71417	0.994000	0.49952	0.922000	0.55478	9.673000	0.98631	2.534000	0.85438	0.557000	0.71058	GGA	.		0.453	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			A	17590497	G	A	17590497	3	1	80	1	0	0	0	0	1	0	0	0	8644	1001	35	2	786	2	LAP3	4	17590497	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	14145669	17590497	173563779	24	7428											
TMEM156	80008	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	38990526	38990526	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttgcggatagtgaggatGatcaaaaatataaaaactaa	19	11	8	3	1	1	2	1	2	0	0	1	4	1	4	0	2	2	0	0	2	8	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:38990526G>T	ENST00000381938.3	-	4	791	c.684C>A	c.(682-684)atC>atA	p.I228I		NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	228						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TAGTGAGGATGATCAAAAATA	0.353																																					p.I228I		.											.	TMEM156-91	0			c.C684A						.						120	122	122					4																	38990526		2203	4300	6503	SO:0001819	synonymous_variant	80008	exon4			GAGGATGATCAAA	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.684C>A	4.37:g.38990526G>T		Somatic	160	1		WXS	Illumina HiSeq	Phase_I	121	31	NM_024943	0	0	0	0	0	Q9H5N9	Silent	SNP	ENST00000381938.3	37	CCDS3448.1																																																																																			.		0.353	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943		T	38990526	G	T	38990526	2	4	80	1	0	0	0	0	0	0	0	1	16105	1280	45	4		4	TMEM156	4	38990526	Silent	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	21400029	38990526	152163750	25	7429											
KDR	3791	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	55981041	55981042	+	Splice_Site	INS	-	-	T																															aaaggaaatgtcctcttaccINStacaacgacaactatgtaca																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:55981041_55981042insT	ENST00000263923.4	-	5	952_953	c.657_658insA	c.(655-660)gtaggg>gtaAggg	p.G220fs		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	220					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTCCTCTTACCTACAACGACAA	0.347			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.G220fs		.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR-2298	0			c.658_659insA						.																																			SO:0001630	splice_region_variant	3791	exon5			.	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.658+1->A	4.37:g.55981042_55981042dupT		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	93	27	NM_002253	0	0	0	0	0	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Frame_Shift_Ins	INS	ENST00000263923.4	37	CCDS3497.1																																																																																			.		0.347	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		Frame_Shift_Ins	T	55981042	-	T	55981041	8	5	80	1	0	1	1	0	0	0	1	0	8160	695	24	0	3516	0	KDR	4	55981041	Splice_Site	INS	-	TCGA-BQ-7045-01A-31D-1961-08	16990515	55981041	135173235	26	7430											
KIAA1211	57482	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	57182080	57182080	+	Frame_Shift_Del	DEL	T	T	-																															ttccttgtcccaagccttccTtaccctccgcagaaagtggt																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:57182080delT	ENST00000504228.1	+	6	2517	c.2412delT	c.(2410-2412)cctfs	p.P804fs	KIAA1211_ENST00000541073.1_Frame_Shift_Del_p.P797fs|KIAA1211_ENST00000264229.6_Frame_Shift_Del_p.P804fs			Q6ZU35	K1211_HUMAN	KIAA1211	804										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CAAGCCTTCCTTACCCTCCGC	0.592																																					p.P804fs		.											.	KIAA1211-70	0			c.2412delT						.						81	89	86					4																	57182080		2023	4206	6229	SO:0001589	frameshift_variant	57482	exon8			.	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2412delT	4.37:g.57182080delT	ENSP00000423366:p.Pro804fs	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	65	22	NM_020722	0	0	0	0	0	Q9NTE2|Q9NTP8|Q9ULK9	Frame_Shift_Del	DEL	ENST00000504228.1	37	CCDS43230.1																																																																																			.		0.592	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		-	57182080	T	-	57182080	7	5	80	1	0	1	0	1	0	0	0	0	8236	1596	56	0	2430	0	KIAA1211	4	57182080	Frame_Shift_Del	DEL	T	TCGA-BQ-7045-01A-31D-1961-08	1201039	57182080	133972196	27	7431											
PRKG2	5593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	82074809	82074809	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aatagttacctttccttttgCcaaaatgaaaaaggtacttc	14	14	5	8	0	0	1	0	1	0	0	2	1	1	1	3	1	3	2	3	1	8	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:82074809C>A	ENST00000395578.1	-	7	1095	c.979G>T	c.(979-981)Gca>Tca	p.A327S	PRKG2_ENST00000264399.1_Missense_Mutation_p.A327S|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_5'UTR|PRKG2_ENST00000418486.2_Missense_Mutation_p.A327S			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	327					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TTTCCTTTTGCCAAAATGAAA	0.328																																					p.A327S		.											.	PRKG2-524	0			c.G979T						.						76	73	74					4																	82074809		2203	4300	6503	SO:0001583	missense	5593	exon6			CTTTTGCCAAAAT	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.979G>T	4.37:g.82074809C>A	ENSP00000378945:p.Ala327Ser	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	55	10	NM_006259	0	0	0	0	0	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	37	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	C	6.115	0.389407	0.11581	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	D;D;D	0.92699	-3.09;-3.09;-3.09	6.08	6.08	0.98989	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.049240	0.85682	D	0.000000	D	0.84701	0.5530	L	0.28192	0.835	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.16289	0.015;0.01	T	0.77000	-0.2750	10	0.02654	T	1	-21.5253	14.3009	0.66352	0.1487:0.8513:0.0:0.0	.	327;327	E7EPE6;Q13237	.;KGP2_HUMAN	S	327	ENSP00000378945:A327S;ENSP00000264399:A327S;ENSP00000389038:A327S	ENSP00000264399:A327S	A	-	1	0	PRKG2	82293833	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.691000	0.61738	2.894000	0.99253	0.591000	0.81541	GCA	.		0.328	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82074809	C	A	82074809	3	1	80	1	0	0	0	0	1	0	0	0	12552	739	26	4	1361	4	PRKG2	4	82074809	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	24892729	82074809	109079467	28	7432											
OSTC	58505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	109571838	109571838	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actttgtaccgtgtcccgttCttagtgctcgaatgtcccaa	7	14	8	12	3	1	0	0	0	1	0	4	1	3	0	3	0	2	3	3	0	4	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:109571838C>T	ENST00000361564.4	+	1	99	c.27C>T	c.(25-27)ttC>ttT	p.F9F	OSTC_ENST00000505745.1_3'UTR|OSTC_ENST00000512478.2_Silent_p.F9F|RNU6-431P_ENST00000383874.1_RNA	NM_021227.3	NP_067050.1	Q9NRP0	OSTC_HUMAN	oligosaccharyltransferase complex subunit (non-catalytic)	9			F -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|oligosaccharyltransferase complex (GO:0008250)		p.F9L(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)	6						GTGTCCCGTTCTTAGTGCTCG	0.597																																					p.F9F		.											.	OSTC-131	1	Substitution - Missense(1)	breast(1)	c.C27T						.						74	73	74					4																	109571838		2203	4300	6503	SO:0001819	synonymous_variant	58505	exon1			CCCGTTCTTAGTG	AF201937	CCDS3681.1, CCDS58921.1, CCDS75177.1	4q25	2013-03-06	2013-03-06		ENSG00000198856	ENSG00000198856			24448	protein-coding gene	gene with protein product	"DC2 protein"		"oligosaccharyltransferase complex subunit"			15835887	Standard	NM_021227		Approved	DC2	uc031sgt.1	Q9NRP0	OTTHUMG00000161031	ENST00000361564.4:c.27C>T	4.37:g.109571838C>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	131	42	NM_001267818	0	0	27	37	10	A8MYS2|B2R5H1|D6RH22|Q9P075|Q9P1R4	Silent	SNP	ENST00000361564.4	37	CCDS3681.1																																																																																			.		0.597	OSTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363485.1	NM_021227		T	109571838	C	T	109571838	2	4	80	1	0	0	0	0	0	0	0	1	11322	912	32	2		2	OSTC	4	109571838	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	27497029	109571838	81582438	29	7433											
NDUFS6	4726	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	1801592	1801592	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcgaggcggcgcggagcCtgcccctgggcgccaggtgt	3	5	20	13	5	0	0	0	0	0	0	0	2	0	1	4	6	2	0	4	6	0	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr5:1801592C>A	ENST00000274137.5	+	1	79	c.61C>A	c.(61-63)Ctg>Atg	p.L21M	MRPL36_ENST00000505818.1_5'Flank|NDUFS6_ENST00000510329.1_3'UTR|MRPL36_ENST00000508987.1_5'Flank|MRPL36_ENST00000382647.7_5'Flank|MRPL36_ENST00000505059.2_5'Flank|NDUFS6_ENST00000469176.1_Missense_Mutation_p.L21M	NM_004553.4	NP_004544.1	O75380	NDUS6_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzyme Q reductase)	21					cardiovascular system development (GO:0072358)|cellular metabolic process (GO:0044237)|fatty acid metabolic process (GO:0006631)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrion morphogenesis (GO:0070584)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|muscle contraction (GO:0006936)|reproductive system development (GO:0061458)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	7						GGCGCGGAGCCTGCCCCTGGG	0.701																																					p.L21M		.											.	NDUFS6-226	0			c.C61A						.						13	16	15					5																	1801592		2169	4256	6425	SO:0001583	missense	4726	exon1			CGGAGCCTGCCCC	BC038664	CCDS3866.1	5p15.33	2011-07-04	2002-08-29		ENSG00000145494	ENSG00000145494	1.6.99.3, 1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7713	protein-coding gene	gene with protein product	"complex I 13kDa subunit A", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial"	603848	"NADH dehydrogenase (ubiquinone) Fe-S protein 6 (13kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004553		Approved	CI-13kA	uc003jcy.3	O75380	OTTHUMG00000090372	ENST00000274137.5:c.61C>A	5.37:g.1801592C>A	ENSP00000274137:p.Leu21Met	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	44	21	NM_004553	0	0	21	37	16		Missense_Mutation	SNP	ENST00000274137.5	37	CCDS3866.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.733559	0.30684	.	.	ENSG00000145494	ENST00000274137;ENST00000469176	T	0.77750	-1.12	4.23	0.315	0.15852	.	1.107710	0.06942	N	0.813089	T	0.72676	0.3490	M	0.75447	2.3	0.09310	N	1	P	0.34837	0.472	B	0.33295	0.161	T	0.57676	-0.7770	10	0.33940	T	0.23	-2.3227	3.9905	0.09535	0.0:0.3596:0.377:0.2635	.	21	O75380	NDUS6_HUMAN	M	21	ENSP00000274137:L21M	ENSP00000274137:L21M	L	+	1	2	NDUFS6	1854592	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.256000	0.18351	0.156000	0.19299	-0.171000	0.13296	CTG	.		0.701	NDUFS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206744.2	NM_004553		A	1801592	C	A	1801592	3	1	80	1	0	0	0	0	1	0	0	0	10322	680	24	4	63	4	NDUFS6	5	1801592	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		1801592	179113668	30	7434											
JAKMIP2	9832	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	147010974	147010974	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaaatgaaatatctgcctAccttaacaccttctttcata	16	13	2	10	0	3	1	1	1	2	0	3	1	3	1	3	0	3	0	3	0	8	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr5:147010974A>G	ENST00000265272.5	-	14	2343		c.e14+1		JAKMIP2_ENST00000507386.1_Splice_Site|JAKMIP2_ENST00000333010.6_Splice_Site	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2							Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATATCTGCCTACCTTAACACC	0.388																																					.		.											.	JAKMIP2-154	0			c.1812+2T>C						.						83	77	79					5																	147010974		2203	4300	6503	SO:0001630	splice_region_variant	9832	exon14			CTGCCTACCTTAA	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1875+1T>C	5.37:g.147010974A>G		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	53	13	NM_001270934	0	0	0	0	0	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Splice_Site	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293161	0.80914	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	.	.	.	4.77	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2698	0.66145	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	JAKMIP2	146991167	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.337000	0.90036	1.904000	0.55121	0.533000	0.62120	.	.		0.388	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	Intron	G	147010974	A	G	147010974	5	3	80	1	0	0	0	0	0	0	1	0	7962	405	14	3	587	3	JAKMIP2	5	147010974	Splice_Site	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	145209382	147010974	33904286	31	7435											
C6orf195	154386	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	2623684	2623684	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagagacgtcagaaagcttCattgctaatctccctctgac	11	10	9	11	1	4	3	2	1	2	2	5	5	4	4	1	1	2	2	1	1	2	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:2623684C>A	ENST00000296847.3	-	3	896	c.373G>T	c.(373-375)Gaa>Taa	p.E125*		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	125										cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				CAGAAAGCTTCATTGCTAATC	0.493																																					p.E125X		.											.	C6orf195-90	0			c.G373T						.						65	67	67					6																	2623684		1977	4166	6143	SO:0001587	stop_gained	154386	exon3			AAGCTTCATTGCT	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.373G>T	6.37:g.2623684C>A	ENSP00000296847:p.Glu125*	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	75	27	NM_152554	0	0	0	0	0	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Nonsense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	.	.	.	.	.	.	.	.	.	.	C	36	5.801906	0.96960	.	.	ENSG00000164385	ENST00000296847	.	.	.	4.52	0.877	0.19145	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.3228	0.07056	0.192:0.5359:0.0:0.2721	.	.	.	.	X	125	.	ENSP00000296847:E125X	E	-	1	0	C6orf195	2568683	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	0.349000	0.20055	0.064000	0.16427	-0.136000	0.14681	GAA	.		0.493	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554		A	2623684	C	A	2623684	4	1	80	1	0	0	0	0	0	1	0	0	2356	835	29	4	14	4	C6orf195	6	2623684	Nonsense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		2623684	168491383	32	7436											
C6orf223	221416	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43970795	43970795	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgcaggggcacggctaatgCgctctaattacccaccgccg	8	8	11	14	4	1	0	0	0	1	0	1	0	1	0	3	3	3	4	3	3	3	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:43970795C>T	ENST00000336600.5	+	4	681	c.661C>T	c.(661-663)Cgc>Tgc	p.R221C	C6orf223_ENST00000448947.2_3'UTR|RP5-1120P11.1_ENST00000607590.1_RNA|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000442114.2_Missense_Mutation_p.R201C|C6orf223_ENST00000439969.2_3'UTR	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	221										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			ACGGCTAATGCGCTCTAATTA	0.637																																					p.R221C		.											.	C6orf223-68	0			c.C661T						.						25	31	29					6																	43970795		2202	4295	6497	SO:0001583	missense	221416	exon4			CTAATGCGCTCTA	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.661C>T	6.37:g.43970795C>T	ENSP00000426159:p.Arg221Cys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	88	37	NM_153246	0	0	0	0	0	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	37	CCDS34459.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.973119	0.34848	.	.	ENSG00000181577	ENST00000336600	T	0.40756	1.02	3.26	2.39	0.29439	.	0.205916	0.24638	N	0.036836	T	0.08133	0.0203	N	0.08118	0	0.80722	D	1	P	0.36599	0.56	B	0.27262	0.078	T	0.08722	-1.0708	10	0.87932	D	0	.	6.5098	0.22216	0.0:0.865:0.0:0.135	.	221	Q8N319	CF223_HUMAN	C	221	ENSP00000426159:R221C	ENSP00000426159:R221C	R	+	1	0	C6orf223	44078773	0.337000	0.24766	1.000000	0.80357	0.994000	0.84299	0.280000	0.18790	0.963000	0.38082	0.491000	0.48974	CGC	.		0.637	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246		T	43970795	C	T	43970795	3	4	80	1	0	0	0	0	1	0	0	0	2363	768	27	1	718	1	C6orf223	6	43970795	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	41347111	43970795	127144272	33	7437											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390466	45390466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcagcagcagcagcagcaAcagcagcagcagcagcagga	15	0	13	13	0	0	0	0	0	0	0	0	1	0	1	0	1	12	11	0	1	1	0	rs575896136	byFrequency	TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000541979.1_Silent_p.Q133Q|RUNX2_ENST00000576263.1_Silent_p.Q65Q|RUNX2_ENST00000352853.5_Silent_p.Q133Q|RUNX2_ENST00000465038.2_Silent_p.Q65Q|RUNX2_ENST00000371436.6_Silent_p.Q65Q|RUNX2_ENST00000371432.3_Silent_p.Q51Q|RUNX2_ENST00000359524.5_Silent_p.Q51Q|RP1-244F24.1_ENST00000606796.1_RNA	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0	5008	,	,		7675	0.002		0	False		,,,				2504	0.0031				p.Q65Q		.											.	RUNX2-417	0			c.A195G						.						10	15	14					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	6.37:g.45390466A>G		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_001024630	0	0	33	2812	2779	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	CCDS43467.2																																																																																			.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390466	A	G	45390466	2	3	80	1	0	0	0	0	0	0	0	1	13780	40	2	3		3	RUNX2	6	45390466	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	1419671	45390466	125724601	34	7438											
GFRAL	389400	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	55223709	55223709	+	Frame_Shift_Del	DEL	C	C	-																															gcactatagaacatttcagtCaaaatgctggcagcgtgtga																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:55223709delC	ENST00000340465.2	+	6	811	c.725delC	c.(724-726)tcafs	p.S242fs		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	242					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACATTTCAGTCAAAATGCTGG	0.398																																					p.S242X		.											.	GFRAL-154	0			c.725delC						.						115	106	109					6																	55223709		2203	4300	6503	SO:0001589	frameshift_variant	389400	exon6			.	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.725delC	6.37:g.55223709delC	ENSP00000343636:p.Ser242fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	130	46	NM_207410	0	0	0	0	0	Q5VTF6	Nonsense_Mutation	DEL	ENST00000340465.2	37	CCDS4957.1																																																																																			.		0.398	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		-	55223709	C	-	55223709	7	5	80	1	0	1	0	1	0	0	0	0	6371	838	29	0	747	0	GFRAL	6	55223709	Frame_Shift_Del	DEL	C	TCGA-BQ-7045-01A-31D-1961-08	9833243	55223709	115891358	35	7439											
KIAA1919	91749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	111587895	111587895	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtcattggaattcttcAaggaaaataccctgatttgc	12	13	8	8	0	3	1	2	1	1	0	3	3	3	3	1	2	3	1	1	2	5	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:111587895A>T	ENST00000368847.4	+	4	1483	c.1130A>T	c.(1129-1131)cAa>cTa	p.Q377L		NM_153369.2	NP_699200.2	Q5TF39	NAGT1_HUMAN	KIAA1919	377					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			large_intestine(3)|lung(2)|ovary(4)|skin(3)	12		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		GGAATTCTTCAAGGAAAATAC	0.403																																					p.Q377L		.											.	KIAA1919-93	0			c.A1130T						.						111	115	114					6																	111587895		2203	4300	6503	SO:0001583	missense	91749	exon4			TTCTTCAAGGAAA	BC036115	CCDS5090.1	6q22	2013-10-02			ENSG00000173214	ENSG00000173214			21053	protein-coding gene	gene with protein product							Standard	NM_153369		Approved	MGC33953, MFSD4B	uc003puv.4	Q5TF39	OTTHUMG00000015372	ENST00000368847.4:c.1130A>T	6.37:g.111587895A>T	ENSP00000357840:p.Gln377Leu	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	220	67	NM_153369	0	0	0	1	1	A8K9M0|Q8IYB6|Q96PW9|Q9P0D6	Missense_Mutation	SNP	ENST00000368847.4	37	CCDS5090.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.496996	0.01001	.	.	ENSG00000173214	ENST00000368847	T	0.78481	-1.18	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);	0.239924	0.43110	D	0.000612	T	0.54367	0.1854	L	0.49640	1.575	0.36102	D	0.844223	B	0.28378	0.209	B	0.25987	0.065	T	0.57522	-0.7797	10	0.02654	T	1	-15.1619	16.3615	0.83270	1.0:0.0:0.0:0.0	.	377	Q5TF39	NAGT1_HUMAN	L	377	ENSP00000357840:Q377L	ENSP00000357840:Q377L	Q	+	2	0	KIAA1919	111694588	0.984000	0.35163	0.981000	0.43875	0.149000	0.21700	3.380000	0.52448	2.264000	0.75181	0.450000	0.29827	CAA	.		0.403	KIAA1919-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041827.1	NM_153369		T	111587895	A	T	111587895	3	4	80	1	0	0	0	0	1	0	0	0	8283	130	5	5	1144	5	KIAA1919	6	111587895	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	56364186	111587895	59527172	36	7440											
MLLT4	4301	ucsc.edu;bcgsc.ca	37	chr6	168276027	168276027	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttacagtgaaaattctcgActggctgctgaggtttacaa	11	13	9	8	1	2	2	0	2	2	0	3	3	2	2	0	2	3	3	0	2	5	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:168276027A>C	ENST00000447894.2	+	5	591	c.591A>C	c.(589-591)cgA>cgC	p.R197R	MLLT4_ENST00000392108.3_Silent_p.R197R|MLLT4_ENST00000366806.2_Silent_p.R197R|MLLT4_ENST00000392112.1_Silent_p.R196R|MLLT4_ENST00000351017.4_Silent_p.R197R|MLLT4_ENST00000400822.3_Silent_p.R196R|MLLT4_ENST00000344191.4_Silent_p.R197R			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	197					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		AAAATTCTCGACTGGCTGCTG	0.368			T	MLL	AL																																p.R197R				Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4-685	0			c.A591C						.						111	123	119					6																	168276027		2203	4295	6498	SO:0001819	synonymous_variant	4301	exon5			TTCTCGACTGGCT	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.591A>C	6.37:g.168276027A>C		Somatic	259	2		WXS	Illumina HiSeq		275	87	NM_001040000	0	0	0	0	0	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				.		0.368	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		C	168276027	A	C	168276027	2	2	80	1	0	0	0	0	0	0	0	1	9654	262	10	5		5	MLLT4	6	168276027	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	56688132	168276027	2839040	37	7441											
THBS2	7058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	169622311	169622311	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgccccggcgtgttccccGtgtgccacagcgcgttcctc	2	9	11	19	5	0	0	0	0	0	0	3	0	2	0	7	1	3	2	7	1	0	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:169622311G>T	ENST00000366787.3	-	20	3503	c.3254C>A	c.(3253-3255)aCg>aAg	p.T1085K	THBS2_ENST00000488355.1_5'UTR|XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1085	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.T1085M(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGTGTTCCCCGTGTGCCACAG	0.662																																					p.T1085K	Esophageal Squamous(91;219 1934 18562 44706)	.											.	THBS2-95	1	Substitution - Missense(1)	endometrium(1)	c.C3254A						.						58	58	58					6																	169622311		2203	4300	6503	SO:0001583	missense	7058	exon20			TTCCCCGTGTGCC		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3254C>A	6.37:g.169622311G>T	ENSP00000355751:p.Thr1085Lys	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	102	25	NM_003247	0	0	23	33	10	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290586	0.59976	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.91996	-2.95	4.21	4.21	0.49690	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.42172	U	0.000748	D	0.94453	0.8215	M	0.66939	2.045	0.58432	D	0.999992	D	0.89917	1.0	D	0.72075	0.976	D	0.95110	0.8237	10	0.66056	D	0.02	-24.5393	16.5686	0.84605	0.0:0.0:1.0:0.0	.	1085	P35442	TSP2_HUMAN	K	1085;343	ENSP00000355751:T1085K	ENSP00000355751:T1085K	T	-	2	0	THBS2	169364236	1.000000	0.71417	1.000000	0.80357	0.244000	0.25665	9.166000	0.94766	1.887000	0.54652	0.297000	0.19635	ACG	.		0.662	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169622311	G	T	169622311	3	4	80	1	0	0	0	0	1	0	0	0	15886	1145	40	4	280	4	THBS2	6	169622311	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	1346284	169622311	1492756	38	7442											
CCM2	83605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	45104062	45104062	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccctgtggttccttccagAgagcccaccagcttccggga	6	9	11	15	1	0	1	0	0	0	1	3	3	3	2	6	2	3	2	6	2	0	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:45104062A>G	ENST00000258781.6	+	4	438	c.289A>G	c.(289-291)Aga>Gga	p.R97G	CCM2_ENST00000381112.3_Splice_Site_p.R118G|CCM2_ENST00000541586.1_Splice_Site_p.R39G|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000474617.1_Splice_Site_p.R91G|CCM2_ENST00000475551.1_Splice_Site_p.R91G|CCM2_ENST00000544363.1_Splice_Site_p.R97G	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	97	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TTCCTTCCAGAGAGCCCACCA	0.567																																					p.R118G		.											.	CCM2-90	0			c.A352G						.						43	37	39					7																	45104062		2203	4300	6503	SO:0001630	splice_region_variant	83605	exon4			TTCCAGAGAGCCC	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.289-1A>G	7.37:g.45104062A>G		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	75	11	NM_001029835	0	0	0	0	0	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.058731	0.55325	.	.	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000544363;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	5.32	4.24	0.50183	Phosphotyrosine interaction domain (1);	0.051158	0.85682	D	0.000000	T	0.55130	0.1901	M	0.67953	2.075	0.48901	D	0.999727	B;P;P;P;P;P	0.49559	0.118;0.923;0.925;0.873;0.617;0.873	B;P;P;B;B;P	0.52159	0.075;0.578;0.691;0.385;0.173;0.461	T	0.54476	-0.8288	9	.	.	.	-18.4128	10.5848	0.45275	0.7713:0.2287:0.0:0.0	.	90;60;118;97;39;97	B7Z5A6;B7Z8D5;E9PDJ3;F5H0E1;F5H551;Q9BSQ5	.;.;.;.;.;CCM2_HUMAN	G	97;39;97;91;118;91	ENSP00000258781:R97G;ENSP00000444725:R39G;ENSP00000438035:R97G;ENSP00000417180:R91G;ENSP00000370503:R118G;ENSP00000419474:R91G	.	R	+	1	2	CCM2	45070587	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.295000	0.51794	0.976000	0.38417	0.533000	0.62120	AGA	.		0.567	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	Missense_Mutation	G	45104062	A	G	45104062	5	3	80	1	0	0	0	0	0	0	1	0	2914	318	11	3	400	3	CCM2	7	45104062	Splice_Site	SNP	A	TCGA-BQ-7045-01A-31D-1961-08		45104062	114034601	39	7443											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	82532016	82532016	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttatttttatccttgcgtgAggaaagatgtagtgcatagt	10	16	11	4	1	0	2	0	1	0	1	1	3	1	3	1	1	2	3	1	1	5	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:82532016A>G	ENST00000333891.9	-	9	13816	c.13479T>C	c.(13477-13479)ccT>ccC	p.P4493P	PCLO_ENST00000423517.2_Silent_p.P4493P	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCCTTGCGTGAGGAAAGATGT	0.299																																					p.P4493P		.											.	PCLO-29	0			c.T13479C						.						198	180	186					7																	82532016		1833	4089	5922	SO:0001819	synonymous_variant	27445	exon9			TGCGTGAGGAAAG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13479T>C	7.37:g.82532016A>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	111	63	NM_014510	0	0	0	0	0		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			.		0.299	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82532016	A	G	82532016	2	3	80	1	0	0	0	0	0	0	0	1	11609	291	11	3		3	PCLO	7	82532016	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	37427954	82532016	76606647	40	7444											
AGFG2	3268	hgsc.bcm.edu;broad.mit.edu	37	chr7	100160553	100160553	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccaacccgttccagccCaatggcttggcgccaggtaa	9	7	9	16	2	0	0	0	0	0	0	2	0	2	0	6	3	2	3	6	3	3	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:100160553C>T	ENST00000300176.4	+	9	1277	c.1155C>T	c.(1153-1155)ccC>ccT	p.P385P	AGFG2_ENST00000474713.1_Intron|AGFG2_ENST00000262935.4_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	385	Pro-rich.				regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CGTTCCAGCCCAATGGCTTGG	0.602																																					p.P385P		.											.	AGFG2-90	0			c.C1155T						.						70	59	63					7																	100160553		2203	4300	6503	SO:0001819	synonymous_variant	3268	exon9			CCAGCCCAATGGC	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"ADP-ribosylation factor GTPase activating proteins"	5177	protein-coding gene	gene with protein product		604019	"HIV-1 Rev binding protein-like"	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1155C>T	7.37:g.100160553C>T		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_006076	0	0	12	17	5	O75429|Q96AB9|Q96GL4	Silent	SNP	ENST00000300176.4	37	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	C	9.342	1.063180	0.19987	.	.	ENSG00000106351	ENST00000429987	T	0.47869	0.83	4.67	4.67	0.58626	.	0.466449	0.22090	N	0.064764	T	0.55986	0.1955	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52749	-0.8534	6	.	.	.	-18.2459	13.1309	0.59382	0.0:1.0:0.0:0.0	.	.	.	.	L	127	ENSP00000388594:P127L	.	P	+	2	0	AGFG2	99998489	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.481000	0.35476	2.469000	0.83416	0.549000	0.68633	CCA	.		0.602	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		T	100160553	C	T	100160553	2	4	80	1	0	0	0	0	0	0	0	1	381	581	21	2		2	AGFG2	7	100160553	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	17628537	100160553	58978110	41	7445											
CHCHD3	54927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	132523165	132523165	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattaaaaacttacttgaacTttgcttccacctcttcagca	12	15	3	11	0	2	1	1	1	1	0	3	1	3	1	2	0	5	2	2	0	6	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:132523165T>G	ENST00000262570.5	-	6	662	c.518A>C	c.(517-519)aAg>aCg	p.K173T	CHCHD3_ENST00000476546.1_5'UTR|AC009518.8_ENST00000453078.1_RNA|CHCHD3_ENST00000448878.1_Missense_Mutation_p.K178T	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	173					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						TTACTTGAACTTTGCTTCCAC	0.333																																					p.K173T		.											.	CHCHD3-90	0			c.A518C						.						73	73	73					7																	132523165		2203	4300	6503	SO:0001583	missense	54927	exon6			TTGAACTTTGCTT	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21906	protein-coding gene	gene with protein product	"mitochondrial inner membrane organizing system 3", "protein phosphatase 1, regulatory subunit 22"	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.518A>C	7.37:g.132523165T>G	ENSP00000262570:p.Lys173Thr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	75	39	NM_017812	0	0	0	0	0		Missense_Mutation	SNP	ENST00000262570.5	37	CCDS5828.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.346334	0.61073	.	.	ENSG00000106554	ENST00000262570;ENST00000448878	T;T	0.45668	0.89;0.89	5.97	5.97	0.96955	.	0.165073	0.51477	D	0.000084	T	0.48390	0.1497	L	0.33137	0.985	0.80722	D	1	D;B	0.76494	0.999;0.294	D;B	0.72982	0.979;0.21	T	0.44065	-0.9352	10	0.30078	T	0.28	-29.5969	8.416	0.32672	0.0:0.1479:0.0:0.8521	.	178;173	C9JRZ6;Q9NX63	.;CHCH3_HUMAN	T	173;178	ENSP00000262570:K173T;ENSP00000389297:K178T	ENSP00000262570:K173T	K	-	2	0	CHCHD3	132173705	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.637000	0.46553	2.288000	0.76882	0.533000	0.62120	AAG	.		0.333	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		G	132523165	T	G	132523165	3	3	80	1	0	0	0	0	1	0	0	0	3323	1609	56	5	177	5	CHCHD3	7	132523165	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	32362612	132523165	26615498	42	7446											
TRPV6	55503	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142569741	142569741	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagatcttgcctgtcttccaCcctgtggaatgcgggaggac	7	10	13	11	1	2	1	0	0	2	1	3	5	3	4	3	3	2	0	3	3	1	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:142569741C>A	ENST00000359396.3	-	15	2142	c.1897G>T	c.(1897-1899)Gtg>Ttg	p.V633L		NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	633					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					CTGTCTTCCACCCTGTGGAAT	0.557																																					p.V633L		.											.	TRPV6-92	0			c.G1897T						.						99	90	93					7																	142569741		2203	4300	6503	SO:0001630	splice_region_variant	55503	exon15			CTTCCACCCTGTG	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	14006	protein-coding gene	gene with protein product		606680	"epithelial calcium channel 2"	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1896-1G>T	7.37:g.142569741C>A		Somatic	114	1		WXS	Illumina HiSeq	Phase_I	145	30	NM_018646	0	0	0	0	0	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.513934	0.64522	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	T	0.80304	-1.36	5.55	5.55	0.83447	.	0.067016	0.64402	D	0.000013	T	0.82121	0.4968	M	0.81942	2.565	0.49582	D	0.999807	P	0.40431	0.717	B	0.42827	0.399	T	0.81455	-0.0925	10	0.35671	T	0.21	-16.8766	11.8306	0.52293	0.0:0.9113:0.0:0.0887	.	633	Q9H1D0	TRPV6_HUMAN	L	633;465	ENSP00000352358:V633L	ENSP00000310825:V465L	V	-	1	0	TRPV6	142279863	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	2.661000	0.46758	2.622000	0.88805	0.561000	0.74099	GTG	.		0.557	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	Missense_Mutation	A	142569741	C	A	142569741	5	1	80	1	0	0	0	0	0	0	1	0	16633	521	18	4	284	4	TRPV6	7	142569741	Splice_Site	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	10046576	142569741	16568922	43	7447											
NUB1	51667	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151064971	151064971	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attgtgggaaagagaaggtaCtgtttctaagactctactta	13	13	10	5	0	2	2	0	0	2	2	2	4	2	3	0	2	2	2	0	2	6	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:151064971C>A	ENST00000355851.4	+	10	1089	c.1012C>A	c.(1012-1014)Ctg>Atg	p.L338M	NUB1_ENST00000566856.1_Missense_Mutation_p.L338M|NUB1_ENST00000413040.2_Missense_Mutation_p.L362M|NUB1_ENST00000568733.1_Missense_Mutation_p.L362M	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	338					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		AGAGAAGGTACTGTTTCTAAG	0.323											OREG0018452	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L362M													.	NUB1-226	0			c.C1084A						.						64	59	61					7																	151064971		1821	4091	5912	SO:0001583	missense	51667	exon10			AAGGTACTGTTTC	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"NEDD8 ultimate buster-1"	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1012C>A	7.37:g.151064971C>A	ENSP00000348110:p.Leu338Met	Somatic	26	0	1737	WXS	Illumina HiSeq	Phase_I	25	6	NM_016118	0	0	15	19	4	O95422|Q75MR9|Q8IX22|Q9BXR2	Missense_Mutation	SNP	ENST00000355851.4	37		.	.	.	.	.	.	.	.	.	.	C	12.24	1.879981	0.33162	.	.	ENSG00000013374	ENST00000413040;ENST00000355851	T	0.65178	-0.14	5.63	-2.94	0.05581	.	0.000000	0.64402	D	0.000002	T	0.76695	0.4023	M	0.83312	2.635	0.45035	D	0.998055	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.79045	-0.1964	10	0.87932	D	0	-17.937	14.0566	0.64774	0.0:0.6335:0.0:0.3665	.	338;338	Q9Y5A7;Q9Y5A7-2	NUB1_HUMAN;.	M	338	ENSP00000348110:L338M	ENSP00000348110:L338M	L	+	1	2	NUB1	150695904	0.146000	0.22672	0.438000	0.26821	0.058000	0.15608	0.185000	0.16958	-0.450000	0.07107	-0.345000	0.07892	CTG	.		0.323	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118		A	151064971	C	A	151064971	3	1	80	1	0	0	0	0	1	0	0	0	10740	564	20	4	1046	4	NUB1	7	151064971	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	8495230	151064971	8073692	44	7448											
KCNV1	27012	hgsc.bcm.edu	37	chr8	110986410	110986410	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtaggaagccaccaccaCggccagcttgccaaggcgcg	9	3	14	15	4	0	0	0	0	0	0	0	1	0	1	5	4	3	2	5	4	3	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr8:110986410C>A	ENST00000524391.1	-	2	1240	c.208G>T	c.(208-210)Gtg>Ttg	p.V70L	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Missense_Mutation_p.V70L			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	70					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			GCCACCACCACGGCCAGCTTG	0.692																																					p.V70L		.											.	KCNV1-226	0			c.G208T						.						14	13	13					8																	110986410		2190	4286	6476	SO:0001583	missense	27012	exon1			CCACCACGGCCAG	AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.208G>T	8.37:g.110986410C>A	ENSP00000435954:p.Val70Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_014379	0	0	0	1	1	Q9UHJ4	Missense_Mutation	SNP	ENST00000524391.1	37	CCDS6314.1	.	.	.	.	.	.	.	.	.	.	C	9.543	1.113775	0.20795	.	.	ENSG00000164794	ENST00000524391;ENST00000297404	T;T	0.76448	-1.02;-1.02	4.95	4.07	0.47477	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.406801	0.24251	N	0.040174	T	0.56659	0.2000	N	0.02225	-0.63	0.33369	D	0.573278	B	0.26195	0.144	B	0.30646	0.118	T	0.64816	-0.6318	10	0.45353	T	0.12	.	12.8935	0.58084	0.0:0.8369:0.1631:0.0	.	70	Q6PIU1	KCNV1_HUMAN	L	70	ENSP00000435954:V70L;ENSP00000297404:V70L	ENSP00000297404:V70L	V	-	1	0	KCNV1	111055586	0.764000	0.28473	0.999000	0.59377	0.995000	0.86356	1.510000	0.35790	1.285000	0.44548	0.655000	0.94253	GTG	.		0.692	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379		A	110986410	C	A	110986410	3	1	80	1	0	0	0	0	1	0	0	0	8115	536	19	4	1306	4	KCNV1	8	110986410	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		110986410	35377612	45	7449											
ASTN2	23245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	119202962	119202962	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgagagttgtagtggtgctgGactcggaacagcatcgaggc	9	9	16	7	2	0	1	0	1	0	1	2	5	0	3	0	4	3	4	0	4	2	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:119202962G>T	ENST00000313400.4	-	22	3808	c.3708C>A	c.(3706-3708)gtC>gtA	p.V1236V	ASTN2_ENST00000288520.5_Silent_p.V337V|ASTN2_ENST00000341734.4_Silent_p.V288V|ASTN2_ENST00000361209.2_Silent_p.V1185V|ASTN2_ENST00000361477.3_Silent_p.V288V|ASTN2_ENST00000373996.3_Silent_p.V1232V			O75129	ASTN2_HUMAN	astrotactin 2	1236					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						AGTGGTGCTGGACTCGGAACA	0.502																																					p.V1185V		.											.	ASTN2-161	0			c.C3555A						.						169	135	147					9																	119202962		2203	4300	6503	SO:0001819	synonymous_variant	23245	exon21			GTGCTGGACTCGG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3708C>A	9.37:g.119202962G>T		Somatic	121	1		WXS	Illumina HiSeq	Phase_I	133	50	NM_014010	0	0	4	5	1	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	G	9.467	1.094720	0.20471	.	.	ENSG00000148219	ENST00000417725	.	.	.	5.91	0.931	0.19460	.	.	.	.	.	T	0.50582	0.1624	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33394	-0.9870	4	.	.	.	-31.4992	4.5533	0.12124	0.2258:0.0983:0.5759:0.0999	.	.	.	.	Y	18	.	.	S	-	2	0	ASTN2	118242783	0.999000	0.42202	0.996000	0.52242	0.985000	0.73830	0.491000	0.22419	-0.072000	0.12864	-0.795000	0.03280	TCC	.		0.502	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119202962	G	T	119202962	2	4	80	1	0	0	0	0	0	0	0	1	1066	1161	41	4		4	ASTN2	9	119202962	Silent	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		119202962	22010469	46	7450											
PTRH1	138428	ucsc.edu	37	chr9	130476385	130476385	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catggccactagtgtcacggCcccagtgagggcccctggct	6	7	13	15	1	1	1	1	1	0	0	1	1	1	1	5	4	0	1	5	4	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:130476385C>T	ENST00000419060.1	-	6	2095	c.639G>A	c.(637-639)ggG>ggA	p.G213G	C9orf117_ENST00000373293.5_Intron|PTRH1_ENST00000423807.1_3'UTR|PTRH1_ENST00000429848.1_5'Flank|TTC16_ENST00000393748.4_5'Flank|TTC16_ENST00000373289.3_5'Flank|C9orf117_ENST00000464092.1_3'UTR|PTRH1_ENST00000543175.1_Silent_p.G213G			Q86Y79	PTH_HUMAN	peptidyl-tRNA hydrolase 1 homolog (S. cerevisiae)	213						mitochondrion (GO:0005739)	aminoacyl-tRNA hydrolase activity (GO:0004045)|poly(A) RNA binding (GO:0044822)			NS(1)	1						AGTGTCACGGCCCCAGTGAGG	0.612																																					p.G213G													.	PTRH1-90	0			c.G639A						.						28	28	28					9																	130476385		2202	4299	6501	SO:0001819	synonymous_variant	138428	exon5			TCACGGCCCCAGT	AK090922	CCDS35147.1	9q34.11	2006-02-13	2006-02-13	2006-02-13	ENSG00000187024	ENSG00000187024			27039	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 115"	C9orf115			Standard	NM_001002913		Approved	PTH1	uc004bro.3	Q86Y79	OTTHUMG00000020710	ENST00000419060.1:c.639G>A	9.37:g.130476385C>T		Somatic	29	0		WXS	Illumina HiSeq		21	1	NM_001002913	0	0	11	16	5		Silent	SNP	ENST00000419060.1	37	CCDS35147.1																																																																																			.		0.612	PTRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054219.4	NM_001002913		T	130476385	C	T	130476385	2	4	80	1	0	0	0	0	0	0	0	1	12848	726	26	2		2	PTRH1	9	130476385	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	11273423	130476385	10737046	47	7451											
GOLGA2	2801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131028577	131028577	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcacgttacttcttccaactGatccgtaatttcttggttct	7	18	5	11	2	4	1	1	1	3	0	6	1	6	1	2	1	2	3	2	1	3	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:131028577G>A	ENST00000421699.2	-	8	601	c.589C>T	c.(589-591)Cag>Tag	p.Q197*	GOLGA2_ENST00000609374.1_Nonsense_Mutation_p.Q185*	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	197					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						TCTTCCAACTGATCCGTAATT	0.498																																					p.Q197X		.											.	GOLGA2-91	0			c.C589T						.						133	126	128					9																	131028577		2203	4300	6503	SO:0001587	stop_gained	2801	exon8			CCAACTGATCCGT	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.589C>T	9.37:g.131028577G>A	ENSP00000416097:p.Gln197*	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	107	39	NM_004486	0	0	0	0	0	Q6GRM9|Q9BRB0|Q9NYF9	Nonsense_Mutation	SNP	ENST00000421699.2	37	CCDS6896.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.14|18.14	3.556608|3.556608	0.65425|0.65425	.|.	.|.	ENSG00000167110|ENSG00000167110	ENST00000421699;ENST00000450617|ENST00000458730	.|.	.|.	.|.	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76227	.|0.3958	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74842	.|-0.3527	.|3	0.45353|.	T|.	0.12|.	.|.	19.4623|19.4623	0.94922|0.94922	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	197;224|129	.|.	ENSP00000416097:Q197X|.	Q|S	-|-	1|2	0|0	GOLGA2|GOLGA2	130068398|130068398	1.000000|1.000000	0.71417|0.71417	0.612000|0.612000	0.29024|0.29024	0.034000|0.034000	0.12701|0.12701	6.353000|6.353000	0.73032|0.73032	2.663000|2.663000	0.90544|0.90544	0.558000|0.558000	0.71614|0.71614	CAG|TCA	.		0.498	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		A	131028577	G	A	131028577	4	1	80	1	0	0	0	0	0	1	0	0	6572	1299	45	2	2495	2	GOLGA2	9	131028577	Nonsense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	552192	131028577	10184854	48	7452											
UBAC1	10422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	138839743	138839743	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatctggagctttctggtcTtgttttttctacacagaaac	8	18	7	8	0	4	1	0	0	4	1	4	2	4	2	0	2	3	2	0	2	3	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:138839743T>C	ENST00000371756.3	-	4	559	c.342A>G	c.(340-342)caA>caG	p.Q114Q	UBAC1_ENST00000465873.1_5'Flank	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	114					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CTTTCTGGTCTTGTTTTTTCT	0.517																																					p.Q114Q	NSCLC(78;973 1398 27381 29552 42415)	.											.	UBAC1-92	0			c.A342G						.						82	81	81					9																	138839743		2203	4300	6503	SO:0001819	synonymous_variant	10422	exon4			CTGGTCTTGTTTT	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.342A>G	9.37:g.138839743T>C		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	34	15	NM_016172	0	0	0	0	0	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	37	CCDS35177.1																																																																																			.		0.517	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		C	138839743	T	C	138839743	2	2	80	1	0	0	0	0	0	0	0	1	16867	1606	56	3		3	UBAC1	9	138839743	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	7811166	138839743	2373688	49	7453											
NOTCH1	4851	ucsc.edu	37	chr9	139418248	139418248	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccccgttgcggcaggggttGgtgaggcaggcattgtccag	5	8	17	11	2	0	1	0	1	0	0	1	1	1	1	3	6	1	5	3	6	0	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:139418248G>A	ENST00000277541.6	-	3	399	c.324C>T	c.(322-324)acC>acT	p.T108T	NOTCH1_ENST00000491649.1_5'UTR	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	108	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GGCAGGGGTTGGTGAGGCAGG	0.682			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.T108T				Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1-5459	0			c.C324T						.						18	30	26					9																	139418248		2137	4242	6379	SO:0001819	synonymous_variant	4851	exon3			GGGGTTGGTGAGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.324C>T	9.37:g.139418248G>A		Somatic	38	0		WXS	Illumina HiSeq		42	4	NM_017617	0	0	0	0	0	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			.		0.682	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139418248	G	A	139418248	2	1	80	1	0	0	0	0	0	0	0	1	10573	1335	47	2		2	NOTCH1	9	139418248	Silent	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	578505	139418248	1795183	50	7454											
CDHR1	92211	broad.mit.edu	37	chr10	85968003	85968003	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatcaggattgtggaccTcaacaaccacccgccaacat	13	6	6	16	1	2	0	2	0	0	0	2	2	2	2	5	2	3	0	5	2	3	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr10:85968003T>C	ENST00000372117.3	+	11	1140	c.1037T>C	c.(1036-1038)cTc>cCc	p.L346P	CDHR1_ENST00000332904.3_Missense_Mutation_p.L346P|CDHR1_ENST00000440770.2_Missense_Mutation_p.L105P	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	346	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						ATTGTGGACCTCAACAACCAC	0.602																																					p.L346P													.	CDHR1-91	0			c.T1037C						.						70	69	69					10																	85968003		2203	4300	6503	SO:0001583	missense	92211	exon11			TGGACCTCAACAA	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1037T>C	10.37:g.85968003T>C	ENSP00000361189:p.Leu346Pro	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	84	3	NM_001171971	0	0	2	2	0	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569476	0.86439	.	.	ENSG00000148600	ENST00000332904;ENST00000372117;ENST00000440770	T;T;T	0.61392	0.11;0.11;0.48	5.57	5.57	0.84162	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.79082	0.4386	M	0.86651	2.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.994;0.999	T	0.83148	-0.0105	10	0.87932	D	0	-16.2388	14.7116	0.69238	0.0:0.0:0.0:1.0	.	105;346;346	E7EN47;Q96JP9-2;Q96JP9	.;.;CDHR1_HUMAN	P	346;346;105	ENSP00000331063:L346P;ENSP00000361189:L346P;ENSP00000415980:L105P	ENSP00000331063:L346P	L	+	2	0	CDHR1	85957983	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.698000	0.84413	2.127000	0.65507	0.402000	0.26972	CTC	.		0.602	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		C	85968003	T	C	85968003	3	2	80	1	0	0	0	0	1	0	0	0	3124	1551	54	3	1079	3	CDHR1	10	85968003	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08		85968003	49566744	51	7455											
OR4C15	81309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55322355	55322355	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tactcttctatcatgaacagGaggctctgtggcattctgat	9	14	9	9	0	5	2	1	2	4	0	5	3	5	3	0	3	2	2	0	3	3	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr11:55322355G>C	ENST00000314644.2	+	1	573	c.573G>C	c.(571-573)agG>agC	p.R191S		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						TCATGAACAGGAGGCTCTGTG	0.498										HNSCC(20;0.049)																											p.R191S		.											.	OR4C15-70	0			c.G573C						.						103	99	100					11																	55322355		2201	4296	6497	SO:0001583	missense	81309	exon1			GAACAGGAGGCTC	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"GPCR / Class A : Olfactory receptors"	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.573G>C	11.37:g.55322355G>C	ENSP00000324958:p.Arg191Ser	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	175	53	NM_001001920	0	0	0	0	0	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328725	0.24167	.	.	ENSG00000181939	ENST00000314644	T	0.01347	4.99	5.12	1.75	0.24633	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02083	0.0065	L	0.56769	1.78	0.09310	N	1	B	0.30584	0.286	B	0.32677	0.15	T	0.42068	-0.9473	9	0.87932	D	0	.	4.8871	0.13708	0.2199:0.3168:0.4633:0.0	.	137	Q8NGM1	OR4CF_HUMAN	S	191	ENSP00000324958:R191S	ENSP00000324958:R191S	R	+	3	2	OR4C15	55078931	0.000000	0.05858	0.500000	0.27589	0.181000	0.23173	-1.112000	0.03299	0.549000	0.28973	0.385000	0.25706	AGG	.		0.498	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		C	55322355	G	C	55322355	3	2	80	1	0	0	0	0	1	0	0	0	11074	1165	41	4	575	4	OR4C15	11	55322355	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		55322355	79684161	52	7456											
C2CD3	26005	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	73745646	73745646	+	Intron	DEL	G	G	-																															tcatgcttccagttacttcaGtaactacctatattaaaaat																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr11:73745646delG	ENST00000334126.7	-	31	6108				C2CD3_ENST00000313663.7_Frame_Shift_Del_p.Y1963fs|C2CD3_ENST00000542452.1_5'Flank			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3						brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					AGTTACTTCAGTAACTACCTA	0.368																																					p.Y1963fs		.											.	C2CD3-75	0			c.5889delC						.						74	74	74					11																	73745646		2200	4293	6493	SO:0001627	intron_variant	26005	exon31			.	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5882-323C>-	11.37:g.73745646delG		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	40	10	NM_015531	0	0	0	0	0	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Frame_Shift_Del	DEL	ENST00000334126.7	37																																																																																				.		0.368	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		-	73745646	G	-	73745646	6	5	80	0	1	1	0	1	0	0	0	0	2160	1024	36	0		0	C2CD3	11	73745646	Intron	DEL	G	TCGA-BQ-7045-01A-31D-1961-08	18423291	73745646	61260870	53	7457											
TPI1	7167	broad.mit.edu;bcgsc.ca	37	chr12	6976722	6976722	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaccttcagcgcctcggcTccagcgccatggcgccctcc	4	7	10	20	4	1	1	1	1	0	0	4	1	3	1	6	2	2	1	6	2	0	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr12:6976722T>C	ENST00000229270.4	+	1	440	c.103T>C	c.(103-105)Tcc>Ccc	p.S35P	TPI1_ENST00000535434.1_5'Flank|TPI1_ENST00000488464.2_5'Flank|TPI1_ENST00000396705.5_5'UTR	NM_001159287.1	NP_001152759.1	P60174	TPIS_HUMAN	triosephosphate isomerase 1	35					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glyceraldehyde-3-phosphate metabolic process (GO:0019682)|glycolytic process (GO:0006096)|multicellular organismal development (GO:0007275)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	triose-phosphate isomerase activity (GO:0004807)			endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|skin(2)	19						GCGCCTCGGCTCCAGCGCCAT	0.647																																					p.S35P													.	TPI1-226	0			c.T103C						.						12	16	15					12																	6976722		2193	4295	6488	SO:0001583	missense	7167	exon1			CTCGGCTCCAGCG		CCDS8566.1, CCDS53740.1, CCDS58206.1	12p13.31	2012-10-02			ENSG00000111669	ENSG00000111669	5.3.1.1		12009	protein-coding gene	gene with protein product		190450					Standard	NM_000365		Approved		uc001qrk.4	P60174	OTTHUMG00000133767	ENST00000229270.4:c.103T>C	12.37:g.6976722T>C	ENSP00000229270:p.Ser35Pro	Somatic	28	1		WXS	Illumina HiSeq	Phase_I	34	16	NM_001159287	0	0	36	63	27	B7Z5D8|D3DUS9|P00938|Q6FHP9|Q6IS07|Q8WWD0|Q96AG5	Missense_Mutation	SNP	ENST00000229270.4	37	CCDS53740.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.729886	0.30684	.	.	ENSG00000111669	ENST00000229270	.	.	.	5.22	-10.4	0.00318	.	.	.	.	.	T	0.16557	0.0398	N	0.19112	0.55	0.09310	N	0.999996	.	.	.	.	.	.	T	0.18085	-1.0348	6	0.34782	T	0.22	.	3.3033	0.06990	0.285:0.4093:0.0715:0.2342	.	.	.	.	P	35	.	ENSP00000229270:S35P	S	+	1	0	TPI1	6846983	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-3.323000	0.00512	-2.335000	0.00629	-0.538000	0.04264	TCC	.		0.647	TPI1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258252.1	NM_000365		C	6976722	T	C	6976722	3	2	80	1	0	0	0	0	1	0	0	0	16436	1551	54	3	105	3	TPI1	12	6976722	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08		6976722	126875173	54	7458											
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	59283874	59283874	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtgtgttggccaaattgTcaaaatacccaggttccatt	11	12	10	8	0	1	0	1	0	0	0	2	1	2	1	3	3	1	2	3	3	4	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr12:59283874T>A	ENST00000320743.3	-	5	849	c.563A>T	c.(562-564)gAc>gTc	p.D188V	LRIG3_ENST00000379141.4_Missense_Mutation_p.D128V	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	188					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)			GGCCAAATTGTCAAAATACCC	0.413			T	ROS1	NSCLC																																p.D188V		.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3-229	0			c.A563T						.						247	238	241					12																	59283874		2203	4300	6503	SO:0001583	missense	121227	exon5			AAATTGTCAAAAT	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.563A>T	12.37:g.59283874T>A	ENSP00000326759:p.Asp188Val	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	257	80	NM_153377	0	0	0	0	0	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961782	0.53400	.	.	ENSG00000139263	ENST00000379141;ENST00000320743;ENST00000552267	T;T;T	0.57273	0.41;0.41;0.41	5.55	5.55	0.83447	.	0.000000	0.39020	N	0.001494	T	0.52041	0.1710	L	0.39692	1.235	0.80722	D	1	P;P	0.50528	0.593;0.936	B;P	0.48304	0.406;0.573	T	0.49312	-0.8953	9	.	.	.	.	15.6961	0.77499	0.0:0.0:0.0:1.0	.	128;188	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	V	128;188;95	ENSP00000368436:D128V;ENSP00000326759:D188V;ENSP00000449109:D95V	.	D	-	2	0	LRIG3	57570141	1.000000	0.71417	0.997000	0.53966	0.322000	0.28314	4.225000	0.58600	2.110000	0.64415	0.460000	0.39030	GAC	.		0.413	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59283874	T	A	59283874	3	1	80	1	0	0	0	0	1	0	0	0	8971	1667	58	5	2856	5	LRIG3	12	59283874	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	52307152	59283874	74568021	55	7459											
SLC7A1	6541	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	30096467	30096467	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactcaccagcaacggcaccCgaggctaatgtggcgattat	11	8	10	12	3	1	0	1	0	0	0	1	2	1	0	2	3	3	3	2	3	4	3	rs150705194		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:30096467C>T	ENST00000380752.5	-	8	1562	c.1176G>A	c.(1174-1176)tcG>tcA	p.S392S	SLC7A1_ENST00000473577.1_5'Flank	NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	392					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)	p.S392S(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CAACGGCACCCGAGGCTAATG	0.458																																					p.S392S		.											.	SLC7A1-90	1	Substitution - coding silent(1)	lung(1)	c.G1176A						.	C		0,4406		0,0,2203	286	260	269		1176	-9.8	0.7	13	dbSNP_134	269	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC7A1	NM_003045.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		392/630	30096467	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6541	exon8			GGCACCCGAGGCT	AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"Solute carriers"	11057	protein-coding gene	gene with protein product	"ecotropic retroviral receptor", "amino acid transporter, cationic 1"	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.1176G>A	13.37:g.30096467C>T		Somatic	249	0		WXS	Illumina HiSeq	Phase_I	254	65	NM_003045	0	0	0	0	0	Q5JR50	Silent	SNP	ENST00000380752.5	37	CCDS9333.1																																																																																			C|1.000;T|0.000		0.458	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		T	30096467	C	T	30096467	2	4	80	1	0	0	0	0	0	0	0	1	14724	639	23	1		1	SLC7A1	13	30096467	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		30096467	85073411	56	7460											
GPC6	10082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	94482740	94482740	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tacccgcgccttcattgctgCcaggacctttgtccaggggc	5	10	11	15	2	1	0	1	0	0	0	2	1	2	1	5	3	3	1	5	3	1	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:94482740C>G	ENST00000377047.4	+	3	1268	c.653C>G	c.(652-654)gCc>gGc	p.A218G	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	218					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TTCATTGCTGCCAGGACCTTT	0.498																																					p.A218G		.											.	GPC6-90	0			c.C653G						.						50	49	49					13																	94482740		2203	4300	6503	SO:0001583	missense	10082	exon3			TTGCTGCCAGGAC	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.653C>G	13.37:g.94482740C>G	ENSP00000366246:p.Ala218Gly	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	53	18	NM_005708	0	0	0	7	7	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	C	32	5.161612	0.94727	.	.	ENSG00000183098	ENST00000377047	T	0.57907	0.37	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.77377	0.4121	M	0.87097	2.86	0.53688	D	0.999974	D;D	0.89917	1.0;0.999	D;D	0.81914	0.983;0.995	T	0.78288	-0.2262	10	0.46703	T	0.11	.	19.8022	0.96513	0.0:1.0:0.0:0.0	.	218;218	B4E2M1;Q9Y625	.;GPC6_HUMAN	G	218	ENSP00000366246:A218G	ENSP00000366246:A218G	A	+	2	0	GPC6	93280741	1.000000	0.71417	0.932000	0.37286	0.943000	0.58893	7.442000	0.80503	2.771000	0.95319	0.644000	0.83932	GCC	.		0.498	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		G	94482740	C	G	94482740	3	3	80	1	0	0	0	0	1	0	0	0	6622	739	26	4	663	4	GPC6	13	94482740	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	64386273	94482740	20687138	57	7461											
RAP2A	5911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	98086836	98086836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aatacgaccccaccatcgagGacttctaccgcaaggagatc	13	6	8	14	3	1	1	0	0	1	1	3	5	1	2	4	2	2	1	4	2	4	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:98086836G>A	ENST00000245304.4	+	1	361	c.112G>A	c.(112-114)Gac>Aac	p.D38N		NM_021033.6	NP_066361.1	P10114	RAP2A_HUMAN	RAP2A, member of RAS oncogene family	38					actin cytoskeleton reorganization (GO:0031532)|cellular protein localization (GO:0034613)|establishment of protein localization (GO:0045184)|negative regulation of cell migration (GO:0030336)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of dendrite morphogenesis (GO:0048814)|regulation of JNK cascade (GO:0046328)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.166)			CACCATCGAGGACTTCTACCG	0.627																																					p.D38N		.											.	RAP2A-1271	0			c.G112A						.						114	107	109					13																	98086836		2203	4300	6503	SO:0001583	missense	5911	exon1			ATCGAGGACTTCT	AF205602	CCDS9485.1	13q34	2014-05-09			ENSG00000125249	ENSG00000125249			9861	protein-coding gene	gene with protein product		179540		RAP2			Standard	NM_021033		Approved	K-REV	uc001vnd.3	P10114	OTTHUMG00000017240	ENST00000245304.4:c.112G>A	13.37:g.98086836G>A	ENSP00000245304:p.Asp38Asn	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	174	57	NM_021033	0	0	1	1	0	B2RCJ1|Q5JSC1|Q5JSC2	Missense_Mutation	SNP	ENST00000245304.4	37	CCDS9485.1	.	.	.	.	.	.	.	.	.	.	G	34	5.299548	0.95574	.	.	ENSG00000125249	ENST00000245304	D	0.83335	-1.71	2.95	2.95	0.34219	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89111	0.6622	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90284	0.4317	10	0.66056	D	0.02	.	13.9659	0.64209	0.0:0.0:1.0:0.0	.	38	P10114	RAP2A_HUMAN	N	38	ENSP00000245304:D38N	ENSP00000245304:D38N	D	+	1	0	RAP2A	96884837	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.055000	0.93873	1.673000	0.50895	0.484000	0.47621	GAC	.		0.627	RAP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045528.4			A	98086836	G	A	98086836	3	1	80	1	0	0	0	0	1	0	0	0	13072	1174	41	2	114	2	RAP2A	13	98086836	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	3604096	98086836	17083042	58	7462											
GPR18	2841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99907879	99907879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaatggccattcatcttttGcataataaaacattcgaaag	16	12	5	8	1	2	0	1	0	1	0	3	1	2	0	1	1	2	1	1	1	5	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:99907879G>A	ENST00000340807.3	-	3	804	c.248C>T	c.(247-249)gCa>gTa	p.A83V	UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397470.2_Missense_Mutation_p.A83V|GPR18_ENST00000397473.2_Missense_Mutation_p.A83V|UBAC2_ENST00000376440.2_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	83					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	TTCATCTTTTGCATAATAAAA	0.383																																					p.A83V		.											.	GPR18-90	0			c.C248T						.						71	71	71					13																	99907879		2203	4300	6503	SO:0001583	missense	2841	exon2			TCTTTTGCATAAT	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.248C>T	13.37:g.99907879G>A	ENSP00000343428:p.Ala83Val	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	69	18	NM_001098200	0	0	0	0	0	Q6GTM3|Q96HI6|Q9H2L2	Missense_Mutation	SNP	ENST00000340807.3	37	CCDS9491.1	.	.	.	.	.	.	.	.	.	.	G	5.690	0.311943	0.10789	.	.	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807;ENST00000416594	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	6.07	1.18	0.20946	GPCR, rhodopsin-like superfamily (1);	0.322518	0.32328	N	0.006250	T	0.23054	0.0557	L	0.34521	1.04	0.09310	N	0.999999	B	0.06786	0.001	B	0.08055	0.003	T	0.18555	-1.0333	9	.	.	.	-5.3997	8.9019	0.35499	0.2064:0.3912:0.4024:0.0	.	83	Q14330	GPR18_HUMAN	V	83	ENSP00000380613:A83V;ENSP00000380610:A83V;ENSP00000343428:A83V;ENSP00000401611:A83V	.	A	-	2	0	GPR18	98705880	0.888000	0.30383	0.430000	0.26722	0.894000	0.52154	0.767000	0.26575	0.138000	0.18790	-0.137000	0.14449	GCA	.		0.383	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			A	99907879	G	A	99907879	3	1	80	1	0	0	0	0	1	0	0	0	6695	1319	46	2	751	2	GPR18	13	99907879	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	1821043	99907879	15261999	59	7463											
OR4K2	390431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20345257	20345257	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtctgtgttttataccatCtttactcccactctgaaccc	7	16	4	14	0	3	1	0	1	3	0	4	1	4	1	3	0	3	1	3	0	4	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:20345257C>A	ENST00000298642.2	+	1	867	c.831C>A	c.(829-831)atC>atA	p.I277I		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTATACCATCTTTACTCCCA	0.368																																					p.I277I		.											.	OR4K2-72	0			c.C831A						.						125	129	128					14																	20345257		2203	4300	6503	SO:0001819	synonymous_variant	390431	exon1			TACCATCTTTACT		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.831C>A	14.37:g.20345257C>A		Somatic	188	1		WXS	Illumina HiSeq	Phase_I	151	32	NM_001005501	0	0	0	0	0	B2RNK8|Q6IFA5	Silent	SNP	ENST00000298642.2	37	CCDS32023.1																																																																																			.		0.368	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			A	20345257	C	A	20345257	2	1	80	1	0	0	0	0	0	0	0	1	11098	903	32	4		4	OR4K2	14	20345257	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		20345257	87004283	60	7464											
SNX6	58533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	35062276	35062276	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatcttgtcattctatcAgatttagcagatgcatcctt	9	16	8	8	0	4	2	2	0	2	2	5	3	5	3	1	1	2	2	1	1	2	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:35062276A>T	ENST00000362031.4	-	8	759	c.729T>A	c.(727-729)tcT>tcA	p.S243S	SNX6_ENST00000396534.3_Silent_p.S115S|SNX6_ENST00000355110.5_Silent_p.S119S|SNX6_ENST00000396526.3_Silent_p.S115S	NM_152233.2	NP_689419.2	Q9UNH7	SNX6_HUMAN	sorting nexin 6	231					intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|intracellular (GO:0005622)|nucleus (GO:0005634)	phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			endometrium(4)|lung(1)|ovary(1)	6	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		TCATTCTATCAGATTTAGCAG	0.299																																					p.S243S		.											.	SNX6-226	0			c.T729A						.						73	71	72					14																	35062276		2203	4299	6502	SO:0001819	synonymous_variant	58533	exon8			TCTATCAGATTTA	AF121856	CCDS9648.1, CCDS41942.1	14q13	2010-08-05			ENSG00000129515	ENSG00000129515		"Sorting nexins"	14970	protein-coding gene	gene with protein product		606098				11279102	Standard	XM_006720224		Approved		uc001wsf.1	Q9UNH7	OTTHUMG00000140213	ENST00000362031.4:c.729T>A	14.37:g.35062276A>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	61	18	NM_152233	0	0	9	20	11	C0H5W9|Q9Y449	Silent	SNP	ENST00000362031.4	37	CCDS41942.1																																																																																			.		0.299	SNX6-002	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276642.3			T	35062276	A	T	35062276	2	4	80	1	0	0	0	0	0	0	0	1	14938	175	7	5		5	SNX6	14	35062276	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	14717019	35062276	72287264	61	7465											
CLEC14A	161198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	38724316	38724316	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gttgcagtggccggcgggcgCctggtgggcaccccggtccc	2	6	18	15	4	0	0	0	0	0	0	1	0	1	0	5	6	1	3	5	6	0	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:38724316C>T	ENST00000342213.2	-	1	1258	c.912G>A	c.(910-912)agG>agA	p.R304R		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	304						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		CCGGCGGGCGCCTGGTGGGCA	0.657																																					p.R304R		.											.	CLEC14A-94	0			c.G912A						.						44	48	47					14																	38724316		2198	4289	6487	SO:0001819	synonymous_variant	161198	exon1			CGGGCGCCTGGTG		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"C-type lectin domain containing"	19832	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 27"	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.912G>A	14.37:g.38724316C>T		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	139	50	NM_175060	0	0	0	0	0	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	37	CCDS9667.1																																																																																			.		0.657	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		T	38724316	C	T	38724316	2	4	80	1	0	0	0	0	0	0	0	1	3505	738	26	2		2	CLEC14A	14	38724316	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	3662040	38724316	68625224	62	7466											
PRPF39	55015	hgsc.bcm.edu	37	chr14	45565377	45565377	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccgtattgctatggttactgGaaaaagtatgcagaccttga	12	12	10	7	1	0	2	0	1	0	1	0	3	0	3	2	2	3	5	2	2	6	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:45565377G>C	ENST00000355765.6	+	3	566	c.396G>C	c.(394-396)tgG>tgC	p.W132C		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	132					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						ATGGTTACTGGAAAAAGTATG	0.368																																					p.W132C		.											.	PRPF39-70	0			c.G396C						.						50	46	47					14																	45565377		1879	4114	5993	SO:0001583	missense	55015	exon3			TTACTGGAAAAAG	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"PRP39 pre-mRNA processing factor 39 homolog (yeast)", "PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.396G>C	14.37:g.45565377G>C	ENSP00000348010:p.Trp132Cys	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	19	2	NM_017922	0	0	1	1	0	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	G	18.65	3.668567	0.67814	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T;T	0.63417	-0.04;-0.04	5.87	5.87	0.94306	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.81659	0.4869	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82894	-0.0231	9	0.87932	D	0	-23.913	19.7885	0.96447	0.0:0.0:1.0:0.0	.	132	Q86UA1	PRP39_HUMAN	C	132;122	ENSP00000348010:W132C;ENSP00000452428:W122C	ENSP00000348010:W132C	W	+	3	0	PRPF39	44635127	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.779000	0.95612	0.591000	0.81541	TGG	.		0.368	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			C	45565377	G	C	45565377	3	2	80	1	0	0	0	0	1	0	0	0	12598	1183	41	4	402	4	PRPF39	14	45565377	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	6841061	45565377	61784163	63	7467											
FERMT2	10979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	53386065	53386065	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcatggtcagaccaatctTtttttacatctataaaaaac	15	13	5	8	0	3	1	1	0	2	1	3	2	3	1	1	1	3	1	1	1	6	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:53386065T>A	ENST00000395631.2	-	3	383	c.167A>T	c.(166-168)aAa>aTa	p.K56I	FERMT2_ENST00000343279.4_Missense_Mutation_p.K56I|FERMT2_ENST00000399304.3_Missense_Mutation_p.K56I|FERMT2_ENST00000341590.3_Missense_Mutation_p.K56I|FERMT2_ENST00000553373.1_Missense_Mutation_p.K56I			Q96AC1	FERM2_HUMAN	fermitin family member 2	56	Interaction with membranes containing phosphatidylinositol phosphate.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					AGACCAATCTTTTTTTACATC	0.333																																					p.K56I		.											.	FERMT2-68	0			c.A167T						.						73	72	73					14																	53386065		2203	4300	6503	SO:0001583	missense	10979	exon3			CAATCTTTTTTTA	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.167A>T	14.37:g.53386065T>A	ENSP00000378993:p.Lys56Ile	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	99	27	NM_001135000	0	0	0	0	0	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	37	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478457	0.84747	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000555692;ENST00000554712	T;T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75;2.75	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.22513	0.0543	M	0.62723	1.935	0.80722	D	1	P;B;B	0.35542	0.508;0.375;0.078	P;B;B	0.45998	0.5;0.248;0.042	T	0.00621	-1.1640	10	0.42905	T	0.14	.	16.1966	0.82029	0.0:0.0:0.0:1.0	.	56;56;56	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	I	56;56;56;56;56;12;56	ENSP00000378993:K56I;ENSP00000340391:K56I;ENSP00000342858:K56I;ENSP00000451084:K56I;ENSP00000382243:K56I;ENSP00000452472:K12I;ENSP00000450506:K56I	ENSP00000340391:K56I	K	-	2	0	FERMT2	52455815	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.291000	0.72719	2.232000	0.73038	0.528000	0.53228	AAA	.		0.333	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		A	53386065	T	A	53386065	3	1	80	1	0	0	0	0	1	0	0	0	5837	1841	64	5	1964	5	FERMT2	14	53386065	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	7820688	53386065	53963475	64	7468											
DYNC1H1	1778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102466716	102466716	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agatgaaggagcaaccctggGtttcagtacagcctcgaaag	13	7	12	9	1	1	2	1	1	0	1	2	4	1	3	2	2	4	3	2	2	4	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:102466716G>A	ENST00000360184.4	+	18	4218	c.4054G>A	c.(4054-4056)Gtt>Att	p.V1352I		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1352	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GCAACCCTGGGTTTCAGTACA	0.428																																					p.V1352I		.											.	DYNC1H1-98	0			c.G4054A						.						115	116	116					14																	102466716		2203	4300	6503	SO:0001583	missense	1778	exon18			CCCTGGGTTTCAG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.4054G>A	14.37:g.102466716G>A	ENSP00000348965:p.Val1352Ile	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	87	28	NM_001376	0	0	5	6	1	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.089051	0.55968	.	.	ENSG00000197102	ENST00000360184	T	0.28666	1.6	5.64	5.64	0.86602	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.18635	0.0447	N	0.03983	-0.305	0.80722	D	1	B	0.29646	0.253	B	0.33960	0.173	T	0.14755	-1.0461	10	0.16896	T	0.51	.	20.0769	0.97748	0.0:0.0:1.0:0.0	.	1352	Q14204	DYHC1_HUMAN	I	1352	ENSP00000348965:V1352I	ENSP00000348965:V1352I	V	+	1	0	DYNC1H1	101536469	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	8.001000	0.88508	2.820000	0.97059	0.650000	0.86243	GTT	.		0.428	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102466716	G	A	102466716	3	1	80	1	0	0	0	0	1	0	0	0	4852	1261	44	2	4124	2	DYNC1H1	14	102466716	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	49080651	102466716	4882824	65	7469											
DYNC1H1	1778	broad.mit.edu	37	chr14	102483738	102483738	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatggtggagcacggaggcTtttaccgtacctcagatcaa	11	9	12	9	2	2	2	2	0	0	2	2	4	2	4	2	4	3	3	2	4	3	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:102483738T>C	ENST00000360184.4	+	40	8238	c.8074T>C	c.(8074-8076)Ttt>Ctt	p.F2692L		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2692	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GCACGGAGGCTTTTACCGTAC	0.502																																					p.F2692L													.	DYNC1H1-98	0			c.T8074C						.						138	128	132					14																	102483738		2203	4300	6503	SO:0001583	missense	1778	exon40			GGAGGCTTTTACC	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.8074T>C	14.37:g.102483738T>C	ENSP00000348965:p.Phe2692Leu	Somatic	163	1		WXS	Illumina HiSeq	Phase_I	150	4	NM_001376	0	0	8	8	0	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	30	5.050108	0.93740	.	.	ENSG00000197102	ENST00000360184	T	0.35421	1.31	5.19	5.19	0.71726	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.70482	0.3229	H	0.95260	3.645	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78484	-0.2186	10	0.42905	T	0.14	.	15.0566	0.71917	0.0:0.0:0.0:1.0	.	2692	Q14204	DYHC1_HUMAN	L	2692	ENSP00000348965:F2692L	ENSP00000348965:F2692L	F	+	1	0	DYNC1H1	101553491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.849000	0.86908	1.965000	0.57142	0.459000	0.35465	TTT	.		0.502	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102483738	T	C	102483738	3	2	80	1	0	0	0	0	1	0	0	0	4852	1609	56	3	8232	3	DYNC1H1	14	102483738	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	17022	102483738	4865802	66	7470											
ATP10A	57194	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr15	25924510	25924510	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actgtgaccgccttgaagatGctcctataagtagtctgtgg	9	12	11	9	1	1	3	0	2	1	1	2	3	2	3	3	1	1	2	3	1	4	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr15:25924510G>A	ENST00000356865.6	-	21	4589	c.4478C>T	c.(4477-4479)gCa>gTa	p.A1493V		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1493					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CCTTGAAGATGCTCCTATAAG	0.423																																					p.A1493V		.											.	ATP10A-139	0			c.C4478T						.						57	61	60					15																	25924510		2203	4300	6503	SO:0001583	missense	57194	exon21			GAAGATGCTCCTA	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.4478C>T	15.37:g.25924510G>A	ENSP00000349325:p.Ala1493Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	100	25	NM_024490	0	0	0	0	0	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386201	0.42308	.	.	ENSG00000206190	ENST00000356865	T	0.10477	2.87	4.74	3.76	0.43208	.	10.878000	0.00166	N	0.000006	T	0.07954	0.0199	N	0.08118	0	0.09310	N	1	B	0.30482	0.281	B	0.22601	0.04	T	0.16129	-1.0413	10	0.46703	T	0.11	-3.4971	12.1728	0.54167	0.0:0.0:0.7797:0.2203	.	1493	O60312	AT10A_HUMAN	V	1493	ENSP00000349325:A1493V	ENSP00000349325:A1493V	A	-	2	0	ATP10A	23475603	0.618000	0.27051	0.010000	0.14722	0.250000	0.25880	1.852000	0.39348	2.475000	0.83589	0.655000	0.94253	GCA	.		0.423	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25924510	G	A	25924510	3	1	80	1	0	0	0	0	1	0	0	0	1117	1319	46	2	25	2	ATP10A	15	25924510	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		25924510	76606882	67	7471											
HAPLN3	145864	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	89422488	89422488	+	Frame_Shift_Del	DEL	G	G	-																															gcccgttgggggactggtaaGgaaagaccacacctgcaggg																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr15:89422488delG	ENST00000359595.3	-	4	720	c.506delC	c.(505-507)cctfs	p.P169fs	HAPLN3_ENST00000562889.1_Frame_Shift_Del_p.P231fs	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	169	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	GGACTGGTAAGGAAAGACCAC	0.632											OREG0023445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P169fs		.											.	HAPLN3-90	0			c.506delC						.						36	41	39					15																	89422488		2200	4299	6499	SO:0001589	frameshift_variant	145864	exon4			.	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"Immunoglobulin superfamily / V-set domain containing"	21446	protein-coding gene	gene with protein product			"extracellular link domain containing, 1"	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.506delC	15.37:g.89422488delG	ENSP00000352606:p.Pro169fs	Somatic	68	0	1267	WXS	Illumina HiSeq	Phase_I	65	19	NM_178232	0	0	0	0	0	A8K7P0	Frame_Shift_Del	DEL	ENST00000359595.3	37	CCDS10346.1																																																																																			.		0.632	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232		-	89422488	G	-	89422488	7	5	80	1	0	1	0	1	0	0	0	0	6977	1000	35	0	584	0	HAPLN3	15	89422488	Frame_Shift_Del	DEL	G	TCGA-BQ-7045-01A-31D-1961-08	63497978	89422488	13108904	68	7472											
SYNM	23336	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	99670274	99670274	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaggactcaccgaaggagaAgagcgtgcgagagagagagg	15	2	18	6	3	1	4	1	0	0	4	1	11	1	5	1	3	2	0	1	3	3	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr15:99670274A>T	ENST00000560674.1	+	4	1320	c.851A>T	c.(850-852)aAg>aTg	p.K284M	SYNM_ENST00000328642.7_Missense_Mutation_p.K569M|SYNM_ENST00000336292.6_Missense_Mutation_p.K569M|RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000561323.1_3'UTR			O15061	SYNEM_HUMAN	synemin, intermediate filament protein	570	Coil 2.|Interaction with DMD and UTRN.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						CCGAAGGAGAAGAGCGTGCGA	0.502																																					.	Pancreas(125;1071 1762 21750 40003 40381)												.	SYNM-26	0			.						.						66	70	69					15																	99670274		2050	4195	6245	SO:0001583	missense	23336	.			AGGAGAAGAGCGT	AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"A-kinase anchor proteins", "Intermediate filaments type IV"	24466	protein-coding gene	gene with protein product	"synemin alpha", "synemin beta"	606087	"desmuslin"	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000560674.1:c.851A>T	15.37:g.99670274A>T	ENSP00000453040:p.Lys284Met	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	52	12	.	0	0	0	0	0	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Missense_Mutation	SNP	ENST00000560674.1	37		.	.	.	.	.	.	.	.	.	.	A	17.17	3.320236	0.60634	.	.	ENSG00000182253	ENST00000336292;ENST00000328642	T;T	0.36699	1.24;1.24	5.87	-4.15	0.03881	.	.	.	.	.	T	0.44829	0.1312	.	.	.	0.09310	N	1	D;D	0.69078	0.997;0.993	P;P	0.55667	0.781;0.628	T	0.49890	-0.8891	8	0.87932	D	0	.	10.5138	0.44876	0.4351:0.1047:0.4602:0.0	.	570;569	O15061;C9JIE4	SYNEM_HUMAN;.	M	569	ENSP00000336775:K569M;ENSP00000330469:K569M	ENSP00000330469:K569M	K	+	2	0	SYNM	97487797	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.071000	0.11505	-0.642000	0.05480	-0.290000	0.09829	AAG	.		0.502	SYNM-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000415698.2	NM_145728		T	99670274	A	T	99670274	3	4	80	1	0	0	0	0	1	0	0	0	15487	72	3	5	1722	5	SYNM	15	99670274	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	10247786	99670274	2861118	69	7473											
ZNF598	90850	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	2052644	2052644	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagaacttgcagagcgggtgCccacggtgcgacgtgtcatc	8	7	14	12	4	1	2	1	0	0	2	2	3	1	2	1	2	5	1	1	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr16:2052644C>T	ENST00000563630.1	-	4	632	c.390G>A	c.(388-390)ggG>ggA	p.G130G	ZNF598_ENST00000431526.1_Silent_p.G185G|ZNF598_ENST00000562103.1_Silent_p.G130G			Q86UK7	ZN598_HUMAN	zinc finger protein 598	185							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						AGAGCGGGTGCCCACGGTGCG	0.602																																					p.G185G		.											.	ZNF598-432	0			c.G555A						.						50	58	55					16																	2052644		2169	4266	6435	SO:0001819	synonymous_variant	90850	exon6			CGGGTGCCCACGG	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.390G>A	16.37:g.2052644C>T		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	50	10	NM_178167	0	0	4	5	1	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	37																																																																																				.		0.602	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		T	2052644	C	T	2052644	2	4	80	1	0	0	0	0	0	0	0	1	18060	726	26	2		2	ZNF598	16	2052644	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		2052644	88302109	70	7474											
CLUAP1	23059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3554721	3554721	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatttttccttggacagaTttcacagagatgatgagagc	11	14	10	6	0	1	4	1	2	0	3	2	7	2	5	1	1	1	1	1	1	1	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr16:3554721T>C	ENST00000576634.1	+	2	168	c.24T>C	c.(22-24)aaT>aaC	p.N8N	CLUAP1_ENST00000571025.1_Splice_Site_p.N8N|CLUAP1_ENST00000417763.2_5'UTR|LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000341633.5_Splice_Site_p.N8N	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	8					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						CTTGGACAGATTTCACAGAGA	0.383																																					p.N8N		.											.	CLUAP1-137	0			c.T24C						.						106	103	104					16																	3554721		2197	4300	6497	SO:0001630	splice_region_variant	23059	exon2			GACAGATTTCACA	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.23-1T>C	16.37:g.3554721T>C		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	105	21	NM_015041	0	0	0	0	0	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			.		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	Silent	C	3554721	T	C	3554721	5	2	80	1	0	0	0	0	0	0	1	0	3575	1507	52	3	30	3	CLUAP1	16	3554721	Splice_Site	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	1502077	3554721	86800032	71	7475											
SPG7	6687	broad.mit.edu	37	chr16	89613084	89613084	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaggcgggagatttttGagcagcacctgaagagcctg	11	7	16	7	1	0	5	0	2	0	3	0	7	0	5	2	3	3	2	2	3	1	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr16:89613084G>T	ENST00000268704.2	+	11	1483	c.1468G>T	c.(1468-1470)Gag>Tag	p.E490*		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	490					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GGAGATTTTTGAGCAGCACCT	0.582																																					p.E490X													.	SPG7-226	0			c.G1468T						.						89	93	91					16																	89613084		2198	4300	6498	SO:0001587	stop_gained	6687	exon11			ATTTTTGAGCAGC	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"ATPases / AAA-type"	11237	protein-coding gene	gene with protein product	"paraplegin"	602783	"cell matrix adhesion regulator"	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1468G>T	16.37:g.89613084G>T	ENSP00000268704:p.Glu490*	Somatic	146	16		WXS	Illumina HiSeq	Phase_I	173	33	NM_003119	0	0	16	16	0	O75756|Q2TB70|Q58F00|Q96IB0	Nonsense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	.	.	.	.	.	.	.	.	.	.	G	41	8.594842	0.98877	.	.	ENSG00000197912	ENST00000268704	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	19.2181	0.93786	0.0:0.0:1.0:0.0	.	.	.	.	X	490	.	ENSP00000268704:E490X	E	+	1	0	SPG7	88140585	1.000000	0.71417	0.989000	0.46669	0.932000	0.56968	9.610000	0.98337	2.563000	0.86464	0.561000	0.74099	GAG	.		0.582	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		T	89613084	G	T	89613084	4	4	80	1	0	0	0	0	0	1	0	0	15076	1291	45	4	1660	4	SPG7	16	89613084	Nonsense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	86058363	89613084	741669	72	7476											
TIAF1	9220	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27400954	27400954	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gaggcagtgcttggatcagcCctgaactgctgtagttggaa	9	10	14	8	0	1	1	1	1	0	0	1	4	1	3	1	3	4	5	1	3	3	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:27400954C>G	ENST00000359450.6	-	1	4921	c.264G>C	c.(262-264)agG>agC	p.R88S	MYO18A_ENST00000529578.1_5'UTR|MYO18A_ENST00000531253.1_3'UTR|MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000533112.1_3'UTR|TIAF1_ENST00000408971.2_Missense_Mutation_p.R88S|MYO18A_ENST00000354329.4_3'UTR	NM_004740.3	NP_004731.2	O95411	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1	88					apoptotic process (GO:0006915)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of apoptotic process (GO:0043066)	nucleus (GO:0005634)				kidney(1)|lung(1)|urinary_tract(1)	3	Lung NSC(42;0.015)		Epithelial(11;1.19e-05)|all cancers(11;6.57e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000153)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TTGGATCAGCCCTGAACTGCT	0.532																																					p.R88S		.											.	TIAF1-68	0			c.G264C						.						166	140	149					17																	27400954		2203	4300	6503	SO:0001583	missense	9220	exon1			ATCAGCCCTGAAC	AF105277	CCDS32599.1	17q11.2	2006-08-07				ENSG00000221995			11803	protein-coding gene	gene with protein product		609517				9918798	Standard	NM_004740		Approved		uc002hdv.1	O95411		ENST00000359450.6:c.264G>C	17.37:g.27400954C>G	ENSP00000352424:p.Arg88Ser	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	251	129	NM_004740	0	0	6	23	17	A2RRE2|Q6PEG2	Missense_Mutation	SNP	ENST00000359450.6	37	CCDS32599.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.152934	0.38021	.	.	ENSG00000221995	ENST00000408971;ENST00000511177	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	T	0.22666	0.0547	N	0.08118	0	0.23577	N	0.997377	P	0.35363	0.497	B	0.31016	0.123	T	0.26985	-1.0087	8	0.87932	D	0	.	16.3692	0.83347	0.0:1.0:0.0:0.0	.	88	O95411	TIAF1_HUMAN	S	88	.	ENSP00000386130:R88S	R	-	3	2	TIAF1	24425080	0.786000	0.28738	0.969000	0.41365	0.843000	0.47879	3.603000	0.54074	2.894000	0.99253	0.655000	0.94253	AGG	.		0.532	TIAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372394.2	NM_004740		G	27400954	C	G	27400954	3	3	80	1	0	0	0	0	1	0	0	0	15920	622	22	4	87	4	TIAF1	17	27400954	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		27400954	53794256	73	7477											
TMEM101	84336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42089524	42089524	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgccatacagcacgaagaaCagctggatcatcagctcccc	13	6	8	14	1	2	1	2	0	0	1	3	3	3	2	3	1	6	3	3	1	3	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:42089524C>T	ENST00000589334.1	-	5	861	c.546G>A	c.(544-546)ctG>ctA	p.L182L	TMEM101_ENST00000206380.3_Silent_p.L182L|TMEM101_ENST00000542039.1_Silent_p.L124L			Q96IK0	TM101_HUMAN	transmembrane protein 101	182					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCACGAAGAACAGCTGGATCA	0.587																																					p.L182L		.											.	TMEM101-91	0			c.G546A						.						112	95	100					17																	42089524		2203	4300	6503	SO:0001819	synonymous_variant	84336	exon4			GAAGAACAGCTGG	AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.546G>A	17.37:g.42089524C>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	122	27	NM_032376	0	0	20	27	7	B2R9N6	Silent	SNP	ENST00000589334.1	37	CCDS11474.1																																																																																			.		0.587	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376		T	42089524	C	T	42089524	2	4	80	1	0	0	0	0	0	0	0	1	16048	465	17	2		2	TMEM101	17	42089524	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	14688570	42089524	39105686	74	7478											
TOB1	10140	broad.mit.edu	37	chr17	48941062	48941062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagcaccttcactggtcccTtttcaccaatttggtaagaa	12	12	6	11	0	2	1	2	0	0	1	3	1	3	1	3	2	1	2	3	2	4	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:48941062T>C	ENST00000268957.3	-	3	745	c.317A>G	c.(316-318)aAg>aGg	p.K106R	TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Missense_Mutation_p.K106R|TOB1-AS1_ENST00000416263.3_RNA	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	106					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			CACTGGTCCCTTTTCACCAAT	0.418											OREG0024576	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K106R	NSCLC(144;643 1919 24513 29423 40686)												.	TOB1-226	0			c.A317G						.						140	128	132					17																	48941062		2203	4300	6503	SO:0001583	missense	10140	exon2			GGTCCCTTTTCAC	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.317A>G	17.37:g.48941062T>C	ENSP00000268957:p.Lys106Arg	Somatic	135	0	958	WXS	Illumina HiSeq	Phase_I	150	3	NM_005749	0	0	46	46	0	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	37	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.874040	0.51695	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.52526	0.66;0.66	5.69	4.61	0.57282	Anti-proliferative protein (3);	0.046027	0.85682	N	0.000000	T	0.55497	0.1924	L	0.55017	1.72	0.80722	D	1	P	0.51449	0.945	P	0.54856	0.762	T	0.55457	-0.8138	10	0.52906	T	0.07	.	11.5893	0.50938	0.0:0.0696:0.0:0.9304	.	106	P50616	TOB1_HUMAN	R	106	ENSP00000427695:K106R;ENSP00000268957:K106R	ENSP00000268957:K106R	K	-	2	0	TOB1	46296061	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.698000	0.84413	0.984000	0.38629	-0.256000	0.11100	AAG	.		0.418	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			C	48941062	T	C	48941062	3	2	80	1	0	0	0	0	1	0	0	0	16379	1609	56	3	724	3	TOB1	17	48941062	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	6851538	48941062	32254148	75	7479											
BZRAP1	9256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	56386306	56386306	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctcccgtgtggggcccaGtcgtccagaggcctggggcc	3	7	15	16	2	1	1	0	0	1	1	4	1	2	1	6	5	0	0	6	5	0	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:56386306G>T	ENST00000343736.4	-	22	4490	c.4327C>A	c.(4327-4329)Ctg>Atg	p.L1443M	BZRAP1_ENST00000268893.6_Missense_Mutation_p.L1383M|BZRAP1_ENST00000355701.3_Missense_Mutation_p.L1443M			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1443						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GTGGGGCCCAGTCGTCCAGAG	0.692																																					p.L1443M		.											.	BZRAP1-229	0			c.C4327A						.						27	34	32					17																	56386306		2173	4260	6433	SO:0001583	missense	9256	exon22			GGCCCAGTCGTCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4327C>A	17.37:g.56386306G>T	ENSP00000345824:p.Leu1443Met	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	149	36	NM_004758	0	0	0	1	1	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	G	7.586	0.669756	0.14776	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04758	3.56;3.56;3.56	5.31	2.94	0.34122	.	0.632124	0.16677	N	0.204129	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B;B;B	0.31519	0.327;0.106;0.064	B;B;B	0.28232	0.087;0.015;0.006	T	0.42899	-0.9424	10	0.72032	D	0.01	.	10.1566	0.42827	0.1877:0.0:0.8123:0.0	.	1443;1383;1443	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	M	1443;1443;1383	ENSP00000347929:L1443M;ENSP00000345824:L1443M;ENSP00000268893:L1383M	ENSP00000268893:L1383M	L	-	1	2	BZRAP1	53741305	1.000000	0.71417	0.155000	0.22561	0.518000	0.34316	2.879000	0.48522	1.233000	0.43693	0.563000	0.77884	CTG	.		0.692	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56386306	G	T	56386306	3	4	80	1	0	0	0	0	1	0	0	0	1580	1020	36	4	1286	4	BZRAP1	17	56386306	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	7445244	56386306	24808904	76	7480											
KCNH6	81033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61623123	61623123	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggccacccctagcctcacctCtacatcccctggaagtacaa	10	7	6	18	0	2	0	1	0	1	0	3	1	3	1	7	2	3	1	7	2	5	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:61623123C>T	ENST00000583023.1	+	14	2856	c.2845C>T	c.(2845-2847)Cta>Tta	p.L949L	KCNH6_ENST00000581784.1_Silent_p.L860L|KCNH6_ENST00000314672.5_Silent_p.L913L|KCNH6_ENST00000456941.2_Silent_p.L860L	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	949					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.L949V(1)|p.L949I(1)		breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AGCCTCACCTCTACATCCCCT	0.587																																					p.L949L		.											.	KCNH6-91	2	Substitution - Missense(2)	urinary_tract(1)|lung(1)	c.C2845T						.						122	113	116					17																	61623123		2203	4300	6503	SO:0001819	synonymous_variant	81033	exon14			TCACCTCTACATC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2845C>T	17.37:g.61623123C>T		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	169	33	NM_030779	0	0	0	0	0	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			.		0.587	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		T	61623123	C	T	61623123	2	4	80	1	0	0	0	0	0	0	0	1	8057	912	32	2		2	KCNH6	17	61623123	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	5236817	61623123	19572087	77	7481											
EVPL	2125	broad.mit.edu;bcgsc.ca	37	chr17	74004559	74004559	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcagctcggactcctccCgggaccaggttctccccagc	5	8	10	18	2	2	0	0	0	2	0	6	2	4	2	5	3	3	3	5	3	0	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:74004559C>T	ENST00000301607.3	-	22	4980	c.4727G>A	c.(4726-4728)cGg>cAg	p.R1576Q	TEN1-CDK3_ENST00000567351.1_RNA|EVPL_ENST00000586740.1_Missense_Mutation_p.R1598Q	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1576	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						GGACTCCTCCCGGGACCAGGT	0.731																																					p.R1576Q													.	EVPL-93	0			c.G4727A						.						9	10	10					17																	74004559		2188	4252	6440	SO:0001583	missense	2125	exon22			TCCTCCCGGGACC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4727G>A	17.37:g.74004559C>T	ENSP00000301607:p.Arg1576Gln	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	29	9	NM_001988	0	0	5	6	1	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.897717	0.33535	.	.	ENSG00000167880	ENST00000301607	T	0.65549	-0.16	5.08	3.03	0.35002	.	0.067167	0.64402	D	0.000020	T	0.42291	0.1196	L	0.46741	1.465	0.23787	N	0.996842	B;P	0.37663	0.152;0.604	B;B	0.21546	0.019;0.035	T	0.25606	-1.0127	10	0.10902	T	0.67	-50.0018	8.6707	0.34147	0.0:0.7001:0.0:0.2999	.	1598;1576	B7ZLH8;Q92817	.;EVPL_HUMAN	Q	1576	ENSP00000301607:R1576Q	ENSP00000301607:R1576Q	R	-	2	0	EVPL	71516154	0.004000	0.15560	0.998000	0.56505	0.943000	0.58893	0.201000	0.17276	1.126000	0.42016	0.561000	0.74099	CGG	.		0.731	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74004559	C	T	74004559	3	4	80	1	0	0	0	0	1	0	0	0	5305	652	23	1	1378	1	EVPL	17	74004559	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	12381436	74004559	7190651	78	7482											
ANKRD12	23253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	9257291	9257291	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaactgtgccaggagatacTagtccttctcccaaacctga	11	11	7	12	0	1	2	0	1	1	1	3	3	2	2	4	1	4	0	4	1	4	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:9257291T>C	ENST00000262126.4	+	9	4266	c.4026T>C	c.(4024-4026)acT>acC	p.T1342T	ANKRD12_ENST00000383440.2_Silent_p.T1319T|RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Silent_p.T1319T	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1342						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CAGGAGATACTAGTCCTTCTC	0.398																																					p.T1342T		.											.	ANKRD12-92	0			c.T4026C						.						122	117	119					18																	9257291		2203	4300	6503	SO:0001819	synonymous_variant	23253	exon9			AGATACTAGTCCT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.4026T>C	18.37:g.9257291T>C		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	120	43	NM_015208	0	0	1	3	2	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	37	CCDS11843.1																																																																																			.		0.398	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9257291	T	C	9257291	2	2	80	1	0	0	0	0	0	0	0	1	640	1509	53	3		3	ANKRD12	18	9257291	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08		9257291	68819957	79	7483											
ASXL3	80816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	31263418	31263418	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgacatagaaaccccaggAtctattcttgtcaacactaa	15	11	5	10	0	3	2	1	1	2	1	3	3	3	3	2	1	2	0	2	1	5	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:31263418A>G	ENST00000269197.5	+	8	765	c.765A>G	c.(763-765)ggA>ggG	p.G255G		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	255					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(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AAACCCCAGGATCTATTCTTG	0.418																																					p.G255G		.											.	ASXL3-49	0			c.A765G						.						109	106	107					18																	31263418		1872	4099	5971	SO:0001819	synonymous_variant	80816	exon8			CCCAGGATCTATT	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.765A>G	18.37:g.31263418A>G		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	54	14	NM_030632	0	0	0	0	0	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	37	CCDS45847.1																																																																																			.		0.418	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			G	31263418	A	G	31263418	2	3	80	1	0	0	0	0	0	0	0	1	1069	320	12	3		3	ASXL3	18	31263418	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	22006127	31263418	46813830	80	7484											
ELAC1	55520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	48513160	48513160	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgatggaggagtaaaactgtGctttgaagcagacctgttga	12	11	13	5	0	0	4	0	3	0	1	0	6	0	6	1	2	3	4	1	2	3	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:48513160G>C	ENST00000269466.3	+	4	904	c.797G>C	c.(796-798)tGc>tCc	p.C266S	ELAC1_ENST00000588577.1_3'UTR|RP11-729L2.2_ENST00000590722.2_Intron|RP11-729L2.2_ENST00000588256.1_Intron|SMAD4_ENST00000452201.2_Intron	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	266					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		GTAAAACTGTGCTTTGAAGCA	0.478																																					p.C266S		.											.	ELAC1-90	0			c.G797C						.						96	85	89					18																	48513160		2203	4300	6503	SO:0001583	missense	55520	exon4			AACTGTGCTTTGA	AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"tRNA Z (short form)", "RNaseZ(S)"	608079	"elaC (E. coli) homolog 1", "elaC homolog 1 (E. coli)"			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.797G>C	18.37:g.48513160G>C	ENSP00000269466:p.Cys266Ser	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	48	14	NM_018696	0	0	2	5	3	Q9NS99	Missense_Mutation	SNP	ENST00000269466.3	37	CCDS11949.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725203	0.68959	.	.	ENSG00000141642	ENST00000269466	T	0.76060	-0.99	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.70430	0.3223	L	0.28458	0.855	0.80722	D	1	P	0.37423	0.594	B	0.42959	0.403	T	0.69300	-0.5181	10	0.37606	T	0.19	.	18.233	0.89939	0.0:0.0:1.0:0.0	.	266	Q9H777	RNZ1_HUMAN	S	266	ENSP00000269466:C266S	ENSP00000269466:C266S	C	+	2	0	ELAC1	46767158	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.916000	0.92745	2.597000	0.87782	0.655000	0.94253	TGC	.		0.478	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2			C	48513160	G	C	48513160	3	2	80	1	0	0	0	0	1	0	0	0	5059	1319	46	4	807	4	ELAC1	18	48513160	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	17249742	48513160	29564088	81	7485											
ALPK2	115701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	56196435	56196435	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttccagagtgttcagggaAcatctcagcttggatctttt	9	15	9	8	0	3	1	2	0	2	1	5	3	4	3	1	2	2	2	1	2	1	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:56196435A>G	ENST00000361673.3	-	6	5602	c.5389T>C	c.(5389-5391)Ttc>Ctc	p.F1797L		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1797	Ig-like 2.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGTTCAGGGAACATCTCAGCT	0.358																																					p.F1797L		.											.	ALPK2-765	0			c.T5389C						.						110	106	107					18																	56196435		2203	4300	6503	SO:0001583	missense	115701	exon6			CAGGGAACATCTC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"Immunoglobulin superfamily / I-set domain containing"	20565	protein-coding gene	gene with protein product	"heart alpha-kinase"					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5389T>C	18.37:g.56196435A>G	ENSP00000354991:p.Phe1797Leu	Somatic	123	1		WXS	Illumina HiSeq	Phase_I	104	29	NM_052947	0	0	1	3	2	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	A	22.2	4.252838	0.80135	.	.	ENSG00000198796	ENST00000361673	T	0.48836	0.8	5.59	3.13	0.36017	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.296760	0.29876	N	0.010963	T	0.58308	0.2113	M	0.69823	2.125	0.25484	N	0.98771	P;P	0.52692	0.944;0.955	P;P	0.58660	0.672;0.843	T	0.49781	-0.8903	10	0.39692	T	0.17	-2.3325	8.3914	0.32531	0.7302:0.1421:0.0:0.1278	.	1792;1797	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	L	1797	ENSP00000354991:F1797L	ENSP00000354991:F1797L	F	-	1	0	ALPK2	54347415	1.000000	0.71417	0.966000	0.40874	0.996000	0.88848	3.205000	0.51090	0.367000	0.24454	0.533000	0.62120	TTC	.		0.358	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		G	56196435	A	G	56196435	3	3	80	1	0	0	0	0	1	0	0	0	545	43	2	3	1155	3	ALPK2	18	56196435	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	7683275	56196435	21880813	82	7486											
PLIN4	729359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4512468	4512468	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtgagcccagtggacaCagcatctttagtgccagtca	9	9	10	13	0	2	1	1	1	1	0	2	2	2	2	3	1	3	1	3	1	1	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:4512468C>T	ENST00000301286.3	-	3	1461	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	488	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCAGTGGACACAGCATCTTTA	0.612																																					p.V488M		.											.	PLIN4-68	0			c.G1462A						.						114	124	121					19																	4512468		2000	4164	6164	SO:0001583	missense	729359	exon3			TGGACACAGCATC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1462G>A	19.37:g.4512468C>T	ENSP00000301286:p.Val488Met	Somatic	210	1		WXS	Illumina HiSeq	Phase_I	216	58	NM_001080400	0	0	0	0	0	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.947310	0.34377	.	.	ENSG00000167676	ENST00000301286	T	0.08984	3.03	5.38	2.07	0.26955	.	0.452377	0.18308	N	0.145193	T	0.07143	0.0181	L	0.49640	1.575	0.09310	N	1	P	0.38922	0.651	B	0.34138	0.176	T	0.29212	-1.0019	10	0.31617	T	0.26	-12.8615	6.9595	0.24590	0.0:0.6938:0.1441:0.1621	.	488	Q96Q06	PLIN4_HUMAN	M	488	ENSP00000301286:V488M	ENSP00000301286:V488M	V	-	1	0	PLIN4	4463468	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.519000	0.00952	0.261000	0.21753	0.549000	0.68633	GTG	.		0.612	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		T	4512468	C	T	4512468	3	4	80	1	0	0	0	0	1	0	0	0	12118	478	17	2	2627	2	PLIN4	19	4512468	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		4512468	54616515	83	7487											
ALKBH7	84266	hgsc.bcm.edu	37	chr19	6372879	6372879	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggacgctgccagggcccagCtgggtgcgaggctcgggccc	4	4	18	15	4	0	0	0	0	0	0	1	2	0	1	3	5	3	3	3	5	0	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:6372879C>G	ENST00000245812.3	+	1	436	c.48C>G	c.(46-48)agC>agG	p.S16R	ALKBH7_ENST00000599849.1_5'Flank|ALKBH7_ENST00000596657.1_5'Flank	NM_032306.3	NP_115682.1	Q9BT30	ALKB7_HUMAN	alkB, alkylation repair homolog 7 (E. coli)	16					cellular response to DNA damage stimulus (GO:0006974)|fatty acid metabolic process (GO:0006631)|regulation of lipid storage (GO:0010883)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)	mitochondrial matrix (GO:0005759)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CAGGGCCCAGCTGGGTGCGAG	0.726																																					p.S16R		.											.	ALKBH7-90	0			c.C48G						.						3	4	4					19																	6372879		1984	3943	5927	SO:0001583	missense	84266	exon1			GCCCAGCTGGGTG	AY427650	CCDS12163.1	19p13.3	2008-02-05	2006-02-09	2006-02-09		ENSG00000125652		"Alkylation repair homologs"	21306	protein-coding gene	gene with protein product		613305	"spermatogenesis associated 11"	SPATA11		12477932	Standard	NM_032306		Approved	MGC10974	uc002meo.2	Q9BT30		ENST00000245812.3:c.48C>G	19.37:g.6372879C>G	ENSP00000245812:p.Ser16Arg	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	7	4	NM_032306	0	0	2	5	3	B2R4U9|Q53FF3	Missense_Mutation	SNP	ENST00000245812.3	37	CCDS12163.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.630154	0.46944	.	.	ENSG00000125652	ENST00000245812	T	0.44083	0.93	4.66	4.66	0.58398	.	1.191050	0.05873	N	0.624947	T	0.28928	0.0718	N	0.08118	0	0.31191	N	0.700926	B	0.14438	0.01	B	0.19666	0.026	T	0.03773	-1.1005	10	0.15499	T	0.54	-20.7838	15.3108	0.74031	0.0:1.0:0.0:0.0	.	16	Q9BT30	ALKB7_HUMAN	R	16	ENSP00000245812:S16R	ENSP00000245812:S16R	S	+	3	2	ALKBH7	6323879	0.139000	0.22563	0.954000	0.39281	0.224000	0.24922	0.980000	0.29513	2.529000	0.85273	0.305000	0.20034	AGC	.		0.726	ALKBH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453036.1	NM_032306		G	6372879	C	G	6372879	3	3	80	1	0	0	0	0	1	0	0	0	532	796	28	4	50	4	ALKBH7	19	6372879	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	1860411	6372879	52756104	84	7488											
ZNF763	284390	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12089881	12089881	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaagcattatcttataagtTttcaaacacacctaagaatg	17	12	5	7	0	2	1	1	0	1	1	2	2	2	1	1	0	2	2	1	0	7	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:12089881T>C	ENST00000358987.3	+	4	1269	c.1142T>C	c.(1141-1143)tTt>tCt	p.F381S	ZNF763_ENST00000590798.1_Missense_Mutation_p.F401S|ZNF763_ENST00000343949.5_Missense_Mutation_p.F384S|ZNF763_ENST00000538752.1_Missense_Mutation_p.F401S|ZNF763_ENST00000545530.1_Missense_Mutation_p.F259S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	381					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TCTTATAAGTTTTCAAACACA	0.398																																					p.F384S		.											.	ZNF763-90	0			c.T1151C						.						67	73	71					19																	12089881		2180	4294	6474	SO:0001583	missense	284390	exon4			ATAAGTTTTCAAA	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"Zinc fingers, C2H2-type", "-"	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.1142T>C	19.37:g.12089881T>C	ENSP00000402017:p.Phe381Ser	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	143	55	NM_001012753	0	0	0	0	0	B3KRU3|B4DRE7	Missense_Mutation	SNP	ENST00000358987.3	37		.	.	.	.	.	.	.	.	.	.	t	0	-2.724828	0.00091	.	.	ENSG00000197054	ENST00000538752;ENST00000343949;ENST00000545530;ENST00000358987	T;T;T;T	0.06068	3.45;3.44;3.35;3.45	0.855	-1.71	0.08133	.	.	.	.	.	T	0.01254	0.0041	N	0.00060	-2.34	0.09310	N	1	B;P;B	0.35774	0.018;0.519;0.018	B;P;B	0.45449	0.004;0.481;0.004	T	0.22695	-1.0209	9	0.02654	T	1	.	2.0667	0.03604	0.2548:0.2103:0.0:0.5349	.	401;381;384	F5H0A9;Q0D2J5;Q0D2J5-2	.;ZN763_HUMAN;.	S	401;384;259;381	ENSP00000438117:F401S;ENSP00000369774:F384S;ENSP00000446166:F259S;ENSP00000402017:F381S	ENSP00000369774:F384S	F	+	2	0	ZNF763	11950881	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.148000	0.16224	-1.202000	0.02655	0.155000	0.16302	TTT	.		0.398	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753		C	12089881	T	C	12089881	3	2	80	1	0	0	0	0	1	0	0	0	18169	1841	64	3	1165	3	ZNF763	19	12089881	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	5717002	12089881	47039102	85	7489											
ZSWIM4	65249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13915960	13915960	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccgagatcaacttggtgaAtggtaagggcaccccggggg	9	7	15	10	2	1	2	1	1	0	1	2	3	2	2	3	5	1	2	3	5	3	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:13915960A>G	ENST00000254323.2	+	3	899	c.710A>G	c.(709-711)aAt>aGt	p.N237S	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	237							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			AACTTGGTGAATGGTAAGGGC	0.607											OREG0025298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N237S		.											.	ZSWIM4-90	0			c.A710G						.						35	34	34					19																	13915960		2203	4299	6502	SO:0001583	missense	65249	exon3			TGGTGAATGGTAA	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.710A>G	19.37:g.13915960A>G	ENSP00000254323:p.Asn237Ser	Somatic	73	0	691	WXS	Illumina HiSeq	Phase_I	64	17	NM_023072	0	0	0	0	0		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	A	7.710	0.695019	0.15039	.	.	ENSG00000132003	ENST00000254323	T	0.21191	2.02	4.81	4.81	0.61882	.	0.093972	0.43747	D	0.000522	T	0.10337	0.0253	N	0.05441	-0.05	0.80722	D	1	B	0.16802	0.019	B	0.18561	0.022	T	0.14144	-1.0483	10	0.10377	T	0.69	-33.1503	12.3201	0.54979	1.0:0.0:0.0:0.0	.	237	Q9H7M6	ZSWM4_HUMAN	S	237	ENSP00000254323:N237S	ENSP00000254323:N237S	N	+	2	0	ZSWIM4	13776960	1.000000	0.71417	0.941000	0.38009	0.192000	0.23643	8.632000	0.90995	1.806000	0.52798	0.459000	0.35465	AAT	.		0.607	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		G	13915960	A	G	13915960	3	3	80	1	0	0	0	0	1	0	0	0	18275	101	4	3	720	3	ZSWIM4	19	13915960	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	1826079	13915960	45213023	86	7490											
JAK3	3718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17946018	17946018	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgccatggggcaggccttTgtcctcctaagggggccaga	7	9	14	11	0	0	1	0	0	0	1	2	1	2	1	5	5	1	1	5	5	1	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:17946018T>C	ENST00000527670.1	-	14	1950	c.1921A>G	c.(1921-1923)Aaa>Gaa	p.K641E	JAK3_ENST00000534444.1_Missense_Mutation_p.K641E|JAK3_ENST00000458235.1_Missense_Mutation_p.K641E			P52333	JAK3_HUMAN	Janus kinase 3	641	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGCAGGCCTTTGTCCTCCTAA	0.577		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.K641E		.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3-2418	0			c.A1921G						.						24	27	26					19																	17946018		2203	4300	6503	SO:0001583	missense	3718	exon15			GGCCTTTGTCCTC	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"tyrosine-protein kinase JAK3", "leukocyte Janus kinase"	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1921A>G	19.37:g.17946018T>C	ENSP00000432511:p.Lys641Glu	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	50	13	NM_000215	0	0	0	0	0	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561092	0.65538	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	D;D;D	0.83837	-1.77;-1.77;-1.77	5.32	5.32	0.75619	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.244952	0.39985	N	0.001215	D	0.88998	0.6590	M	0.67569	2.06	0.45439	D	0.998412	D;P	0.65815	0.995;0.931	D;P	0.66497	0.944;0.816	D	0.90111	0.4192	10	0.87932	D	0	-10.7087	13.227	0.59921	0.0:0.0:0.0:1.0	.	641;641	P52333-2;P52333	.;JAK3_HUMAN	E	641	ENSP00000391676:K641E;ENSP00000432511:K641E;ENSP00000436421:K641E	ENSP00000391676:K641E	K	-	1	0	JAK3	17807018	1.000000	0.71417	1.000000	0.80357	0.547000	0.35210	5.606000	0.67641	2.009000	0.58944	0.454000	0.30748	AAA	.		0.577	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		C	17946018	T	C	17946018	3	2	80	1	0	0	0	0	1	0	0	0	7960	1821	63	3	1493	3	JAK3	19	17946018	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	4030058	17946018	41182965	87	7491											
ZNF626	199777	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	20808028	20808028	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtatgaattttcttatGtctagtaaggctacaagagt	12	15	8	6	0	2	2	0	1	2	1	3	2	3	2	1	1	1	3	1	1	7	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:20808028G>A	ENST00000601440.1	-	4	801	c.655C>T	c.(655-657)Cat>Tat	p.H219Y	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	219					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(1)|lung(3)|skin(1)	6						ATTTTCTTATGTCTAGTAAGG	0.383																																					p.H219Y													.	ZNF626-515	0			c.C655T						.						49	52	51					19																	20808028		2149	4275	6424	SO:0001583	missense	199777	exon4			TCTTATGTCTAGT	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"Zinc fingers, C2H2-type", "-"	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.655C>T	19.37:g.20808028G>A	ENSP00000469958:p.His219Tyr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	48	11	NM_001076675	0	0	1	1	0	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	.	.	.	.	.	.	.	.	.	.	N	8.924	0.961677	0.18583	.	.	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	T	0.67523	-0.27	0.798	-0.604	0.11626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.75273	0.3827	H	0.96015	3.755	0.58432	D	0.999998	P	0.40534	0.72	P	0.45071	0.468	T	0.73959	-0.3818	9	0.66056	D	0.02	.	4.4901	0.11810	0.3214:0.0:0.6786:0.0	.	219	Q68DY1	ZN626_HUMAN	Y	219;143;219	ENSP00000445201:H219Y	ENSP00000445201:H219Y	H	-	1	0	ZNF626	20599868	0.997000	0.39634	0.298000	0.25002	0.296000	0.27459	3.378000	0.52432	0.162000	0.19483	0.165000	0.16767	CAT	.		0.383	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		A	20808028	G	A	20808028	3	1	80	1	0	0	0	0	1	0	0	0	18082	1377	48	2	935	2	ZNF626	19	20808028	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	2862010	20808028	38320955	88	7492											
ZNF787	126208	hgsc.bcm.edu	37	chr19	56599455	56599455	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcgtcgtcgtcgtcgtcCtcctcctccccgcccgcgcg	0	9	10	22	9	0	0	0	0	0	0	9	0	4	0	7	0	0	0	7	0	0	0	rs202243737	byFrequency	TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:56599455C>G	ENST00000270459.3	-	3	1204	c.1086G>C	c.(1084-1086)gaG>gaC	p.E362D		NM_001002836.2	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)		CGTCGTCGTCCTCCTCCTCCC	0.786													c|||	31	0.0061901	0.0174	0.0086	5008	,	,		3491	0		0.002	False		,,,				2504	0				p.E362D		.											.	ZNF787-69	0			c.G1086C						.						5	6	6					19																	56599455		1716	3706	5422	SO:0001583	missense	126208	exon3			GTCGTCCTCCTCC	BC077728, AF000560	CCDS42634.1	19q13.42	2013-01-08				ENSG00000142409		"Zinc fingers, C2H2-type"	26998	protein-coding gene	gene with protein product							Standard	NM_001002836		Approved		uc010eth.1	Q6DD87		ENST00000270459.3:c.1086G>C	19.37:g.56599455C>G	ENSP00000270459:p.Glu362Asp	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	26	14	NM_001002836	0	0	0	0	0	O00455	Missense_Mutation	SNP	ENST00000270459.3	37	CCDS42634.1	.	.	.	.	.	.	.	.	.	.	c	2.272	-0.366767	0.05069	.	.	ENSG00000142409	ENST00000270459	T	0.06687	3.27	1.38	0.235	0.15431	.	.	.	.	.	T	0.02688	0.0081	N	0.02539	-0.55	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.48222	-0.9054	9	0.15066	T	0.55	-9.261	5.3742	0.16156	0.0:0.4529:0.5471:0.0	.	362	Q6DD87	ZN787_HUMAN	D	362	ENSP00000270459:E362D	ENSP00000270459:E362D	E	-	3	2	ZNF787	61291267	0.001000	0.12720	0.020000	0.16555	0.393000	0.30537	-0.022000	0.12480	0.167000	0.19631	0.494000	0.49563	GAG	C|0.996;G|0.004		0.786	ZNF787-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457498.1	NM_001002836		G	56599455	C	G	56599455	3	3	80	1	0	0	0	0	1	0	0	0	18191	680	24	4	69	4	ZNF787	19	56599455	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	35791427	56599455	2529528	89	7493											
GDF5	8200	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34025518	34025518	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtggcccccccaccatagCtgtgaccccctggcctgaag	6	7	11	17	0	0	2	0	2	0	0	0	2	0	2	7	3	1	1	7	3	2	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr20:34025518C>T	ENST00000374372.1	-	3	694	c.191G>A	c.(190-192)aGc>aAc	p.S64N	GDF5_ENST00000374369.3_Missense_Mutation_p.S64N			P43026	GDF5_HUMAN	growth differentiation factor 5	64					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			CCCACCATAGCTGTGACCCCC	0.647																																					p.S64N													.	GDF5-226	0			c.G191A						.						24	24	24					20																	34025518		2203	4300	6503	SO:0001583	missense	8200	exon1			CCATAGCTGTGAC	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"cartilage-derived morphogenetic protein-1"	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.191G>A	20.37:g.34025518C>T	ENSP00000363492:p.Ser64Asn	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	22	7	NM_000557	0	0	0	0	0	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.	.	.	.	.	.	.	.	.	.	C	8.655	0.899147	0.17686	.	.	ENSG00000125965	ENST00000374369;ENST00000374372	T;T	0.32023	1.47;1.47	4.28	3.3	0.37823	.	0.974769	0.08453	N	0.943691	T	0.22166	0.0534	N	0.14661	0.345	0.22401	N	0.999132	B;B	0.19583	0.037;0.037	B;B	0.18871	0.023;0.014	T	0.26395	-1.0104	10	0.46703	T	0.11	.	13.148	0.59474	0.1613:0.8387:0.0:0.0	.	64;64	F1T0J1;P43026	.;GDF5_HUMAN	N	64	ENSP00000363489:S64N;ENSP00000363492:S64N	ENSP00000363489:S64N	S	-	2	0	GDF5	33488932	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	2.064000	0.41432	0.937000	0.37394	0.313000	0.20887	AGC	.		0.647	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			T	34025518	C	T	34025518	3	4	80	1	0	0	0	0	1	0	0	0	6336	797	28	2	1322	2	GDF5	20	34025518	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		34025518	29000002	90	7494											
SALL4	57167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	50405586	50405586	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aacaaaggggtcatccctggGgacaatgtcgagggtcccac	11	6	13	11	1	1	0	1	0	0	0	4	2	3	1	2	5	1	0	2	5	3	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr20:50405586G>A	ENST00000217086.4	-	3	2667	c.2556C>T	c.(2554-2556)tcC>tcT	p.S852S	SALL4_ENST00000395997.3_Silent_p.S415S|SALL4_ENST00000371539.3_Silent_p.S75S|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	852					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCATCCCTGGGGACAATGTCG	0.577																																					p.S852S		.											.	SALL4-92	0			c.C2556T						.						57	54	55					20																	50405586		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon3			CCCTGGGGACAAT	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2556C>T	20.37:g.50405586G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_020436	0	0	0	0	0	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			.		0.577	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50405586	G	A	50405586	2	1	80	1	0	0	0	0	0	0	0	1	13845	1219	43	2		2	SALL4	20	50405586	Silent	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	16380068	50405586	12619934	91	7495											
KRTAP13-1	140258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	31768620	31768620	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccagacatcctatgtggaGtccagcccctgccagacctc	8	8	9	16	0	0	2	0	0	0	2	3	3	2	3	7	1	3	0	7	1	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr21:31768620G>T	ENST00000355459.2	+	1	229	c.216G>T	c.(214-216)gaG>gaT	p.E72D		NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	72	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)				endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTATGTGGAGTCCAGCCCCT	0.602																																					p.E72D		.											.	KRTAP13-1-91	0			c.G216T						.						60	61	61					21																	31768620		2203	4300	6503	SO:0001583	missense	140258	exon1			TGTGGAGTCCAGC	AJ457066	CCDS13590.2	21q22.11	2013-06-20			ENSG00000198390	ENSG00000198390		"Keratin associated proteins"	18924	protein-coding gene	gene with protein product		608718				12359730	Standard	NM_181599		Approved	KAP13.1	uc002yoa.3	Q8IUC0	OTTHUMG00000057800	ENST00000355459.2:c.216G>T	21.37:g.31768620G>T	ENSP00000347635:p.Glu72Asp	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_181599	0	0	0	0	0	Q14D20|Q3LI79	Missense_Mutation	SNP	ENST00000355459.2	37	CCDS13590.2	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890413	0.33348	.	.	ENSG00000198390	ENST00000355459	T	0.03982	3.74	4.51	0.568	0.17333	.	1.594350	0.04748	N	0.423995	T	0.09158	0.0226	M	0.68317	2.08	0.09310	N	1	P	0.46784	0.884	P	0.48334	0.574	T	0.32079	-0.9920	10	0.20046	T	0.44	.	3.3017	0.06985	0.2615:0.0:0.4305:0.308	.	72	Q8IUC0	KR131_HUMAN	D	72	ENSP00000347635:E72D	ENSP00000347635:E72D	E	+	3	2	KRTAP13-1	30690491	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	0.172000	0.16704	0.089000	0.17243	0.557000	0.71058	GAG	.		0.602	KRTAP13-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128252.3			T	31768620	G	T	31768620	3	4	80	1	0	0	0	0	1	0	0	0	8543	1020	36	4	218	4	KRTAP13-1	21	31768620	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		31768620	16361275	92	7496											
DNAJC28	54943	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	34861049	34861050	+	Frame_Shift_Ins	INS	-	-	A																															cctttcccactgagattgtcINSaaagtctccttttgccatgg																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr21:34861049_34861050insA	ENST00000314399.3	-	2	1089_1090	c.651_652insT	c.(649-654)tttgacfs	p.D218fs	DNAJC28_ENST00000402202.1_Frame_Shift_Ins_p.D218fs|DNAJC28_ENST00000381947.3_Frame_Shift_Ins_p.D218fs	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	218										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						CTGAGATTGTCAAAGTCTCCTT	0.386																																					p.D218_N219delinsX		.											.	DNAJC28-90	0			c.652_653insT						.																																			SO:0001589	frameshift_variant	54943	exon2			.	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.652dupT	21.37:g.34861052_34861052dupA	ENSP00000320303:p.Asp218fs	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	202	51	NM_017833	0	0	0	0	0	D3DSF2	Nonsense_Mutation	INS	ENST00000314399.3	37	CCDS13626.1																																																																																			.		0.386	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			A	34861050	-	A	34861049	7	5	80	1	0	1	1	0	0	0	0	0	4657	826	29	0	518	0	DNAJC28	21	34861049	Frame_Shift_Ins	INS	-	TCGA-BQ-7045-01A-31D-1961-08	3092429	34861049	13268846	93	7497											
NDUFV3	4731	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	44317078	44317078	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtttcgaggacttgcttcTacggtttctttgtctgcgga	4	17	12	8	3	3	0	0	0	3	0	4	3	3	2	0	3	3	3	0	3	1	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr21:44317078T>C	ENST00000340344.4	+	2	156	c.90T>C	c.(88-90)tcT>tcC	p.S30S	NDUFV3_ENST00000460259.1_3'UTR|NDUFV3_ENST00000354250.2_Silent_p.S30S	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa	30					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		GACTTGCTTCTACGGTTTCTT	0.413																																					p.S30S		.											.	NDUFV3-92	0			c.T90C						.						87	86	86					21																	44317078		2203	4300	6503	SO:0001819	synonymous_variant	4731	exon2			TGCTTCTACGGTT		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.90T>C	21.37:g.44317078T>C		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	94	27	NM_001001503	0	0	7	14	7	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	37	CCDS33573.1																																																																																			.		0.413	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			C	44317078	T	C	44317078	2	2	80	1	0	0	0	0	0	0	0	1	10327	1509	53	3		3	NDUFV3	21	44317078	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	9456029	44317078	3812817	94	7498											
PPM1F	9647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	22287929	22287929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtgaccatcaaacacagcaAagtaggcgcggttcacaggg	13	5	12	11	3	2	1	2	1	0	0	2	1	2	1	1	3	2	3	1	3	3	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:22287929A>G	ENST00000263212.5	-	5	686	c.581T>C	c.(580-582)tTt>tCt	p.F194S	PPM1F_ENST00000538191.1_Missense_Mutation_p.F90S|PPM1F_ENST00000407142.1_Missense_Mutation_p.F26S|PPM1F_ENST00000397495.4_Missense_Mutation_p.F194S	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	194					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		AAACACAGCAAAGTAGGCGCG	0.667																																					p.F194S		.											.	PPM1F-292	0			c.T581C						.						61	52	55					22																	22287929		2203	4300	6503	SO:0001583	missense	9647	exon5			ACAGCAAAGTAGG	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.581T>C	22.37:g.22287929A>G	ENSP00000263212:p.Phe194Ser	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	57	25	NM_014634	0	0	0	1	1	A8K6G3|B7Z2C3|Q96PM2	Missense_Mutation	SNP	ENST00000263212.5	37	CCDS13796.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789526	0.50102	.	.	ENSG00000100034	ENST00000263212;ENST00000407142;ENST00000406981;ENST00000538191;ENST00000397495;ENST00000445205	T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68	4.95	4.95	0.65309	Protein phosphatase 2C-like (5);	0.052935	0.85682	D	0.000000	T	0.46678	0.1405	M	0.92555	3.32	0.48040	D	0.999577	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.995;0.995	T	0.60131	-0.7323	10	0.87932	D	0	-0.6926	14.4382	0.67296	1.0:0.0:0.0:0.0	.	90;194;194	B7Z2C3;A8MX49;P49593	.;.;PPM1F_HUMAN	S	194;26;26;90;194;26	ENSP00000263212:F194S;ENSP00000384930:F26S;ENSP00000439915:F90S;ENSP00000380632:F194S;ENSP00000392372:F26S	ENSP00000263212:F194S	F	-	2	0	PPM1F	20617929	1.000000	0.71417	0.992000	0.48379	0.088000	0.18126	3.605000	0.54088	2.077000	0.62373	0.454000	0.30748	TTT	.		0.667	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		G	22287929	A	G	22287929	3	3	80	1	0	0	0	0	1	0	0	0	12368	14	1	3	799	3	PPM1F	22	22287929	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08		22287929	29016637	95	7499											
SFI1	9814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	31924806	31924806	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtgcagtatcgtggcacaCatacttgtacccgacagggc	10	9	11	11	2	0	0	0	0	0	0	1	1	0	0	1	2	3	4	1	2	4	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:31924806C>T	ENST00000400288.2	+	3	328	c.223C>T	c.(223-225)Cat>Tat	p.H75Y	SFI1_ENST00000414585.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000540643.1_Missense_Mutation_p.H75Y|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000432498.1_Missense_Mutation_p.H75Y	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	75					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						TCGTGGCACACATACTTGTAC	0.483																																					p.H75Y		.											.	SFI1-90	0			c.C223T						.						121	114	116					22																	31924806		1992	4175	6167	SO:0001583	missense	9814	exon3			GGCACACATACTT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.223C>T	22.37:g.31924806C>T	ENSP00000383145:p.His75Tyr	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	130	41	NM_001007467	0	0	0	2	2	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	C	6.278	0.419420	0.11928	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000421060;ENST00000444859;ENST00000400288;ENST00000450787	T;T;T;T;T	0.32515	3.32;3.02;1.45;3.33;2.1	4.26	-0.0926	0.13656	.	0.718935	0.12712	N	0.445472	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22746	0.005;0.012;0.004;0.074	B;B;B;B	0.23018	0.004;0.009;0.006;0.043	T	0.36335	-0.9752	10	0.10377	T	0.69	.	6.4426	0.21859	0.0:0.5881:0.0:0.4119	.	75;75;75;75	A8K8P3-9;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;SFI1_HUMAN;.	Y	75;75;75;75;75;26	ENSP00000402679:H75Y;ENSP00000443025:H75Y;ENSP00000411793:H75Y;ENSP00000383145:H75Y;ENSP00000389364:H26Y	ENSP00000383145:H75Y	H	+	1	0	SFI1	30254806	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	0.236000	0.17967	0.079000	0.16929	-0.237000	0.12165	CAT	.		0.483	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		T	31924806	C	T	31924806	3	4	80	1	0	0	0	0	1	0	0	0	14188	478	17	2	229	2	SFI1	22	31924806	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	9636877	31924806	19379760	96	7500											
APOL1	8542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	36661665	36661665	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggagtttttgggtgagaaCatatccaactttctttcctt	9	16	9	7	0	1	1	0	1	1	1	3	3	3	2	2	2	2	1	2	2	3	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:36661665C>T	ENST00000397278.3	+	6	1012	c.783C>T	c.(781-783)aaC>aaT	p.N261N	APOL1_ENST00000422706.1_Silent_p.N261N|APOL1_ENST00000319136.4_Silent_p.N277N|APOL1_ENST00000426053.1_Silent_p.N243N|APOL1_ENST00000347595.7_Silent_p.N140N|APOL1_ENST00000397279.4_Silent_p.N261N	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	261					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cholesterol metabolic process (GO:0008203)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|intrinsic component of membrane (GO:0031224)|very-low-density lipoprotein particle (GO:0034361)	chloride channel activity (GO:0005254)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	14						TGGGTGAGAACATATCCAACT	0.498																																					p.N277N		.											.	APOL1-221	0			c.C831T						.						123	114	117					22																	36661665		2203	4300	6503	SO:0001819	synonymous_variant	8542	exon7			TGAGAACATATCC	AF019225	CCDS13925.1, CCDS13926.1, CCDS46702.1	22q13.1	2014-09-17			ENSG00000100342	ENSG00000100342		"Apolipoproteins"	618	protein-coding gene	gene with protein product		603743		APOL		9325276, 11374903, 16020735	Standard	NM_003661		Approved		uc011amp.2	O14791	OTTHUMG00000030427	ENST00000397278.3:c.783C>T	22.37:g.36661665C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	60	18	NM_145343	0	0	64	126	62	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Silent	SNP	ENST00000397278.3	37	CCDS13926.1																																																																																			.		0.498	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343		T	36661665	C	T	36661665	2	4	80	1	0	0	0	0	0	0	0	1	805	477	17	2		2	APOL1	22	36661665	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	4736859	36661665	14642901	97	7501											
TNRC6B	23112	hgsc.bcm.edu;broad.mit.edu	37	chr22	40669533	40669533	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggaggagtctggaacaccActggctctcagggcagtgct	9	8	14	10	0	2	0	1	0	2	0	3	3	2	3	1	5	2	3	1	5	1	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:40669533A>G	ENST00000454349.2	+	7	3281	c.3070A>G	c.(3070-3072)Act>Gct	p.T1024A	TNRC6B_ENST00000335727.9_Missense_Mutation_p.T971A|TNRC6B_ENST00000301923.9_Missense_Mutation_p.T277A|TNRC6B_ENST00000402203.1_Missense_Mutation_p.T277A	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1024					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						CTGGAACACCACTGGCTCTCA	0.562																																					p.T1024A		.											.	TNRC6B-22	0			c.A3070G						.						36	42	40					22																	40669533		2031	4171	6202	SO:0001583	missense	23112	exon7			AACACCACTGGCT	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"Trinucleotide (CAG) repeat containing"	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.3070A>G	22.37:g.40669533A>G	ENSP00000401946:p.Thr1024Ala	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	13	5	NM_001162501	0	0	0	1	1	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000454349.2	37	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	G	4.088	0.014360	0.07959	.	.	ENSG00000100354	ENST00000301923;ENST00000402203;ENST00000454349;ENST00000400140;ENST00000335727	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	6.04	0.445	0.16597	.	0.270973	0.41938	N	0.000787	T	0.10680	0.0261	N	0.00583	-1.355	0.20196	N	0.99993	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.001;0.002	T	0.38866	-0.9641	10	0.02654	T	1	0.077	12.1291	0.53932	0.2991:0.0:0.7009:0.0	.	1024;971;971;277	Q9UPQ9;A8MYY3;Q9UPQ9-1;Q9UPQ9-2	TNR6B_HUMAN;.;.;.	A	277;277;1024;971;971	ENSP00000306759:T277A;ENSP00000384795:T277A;ENSP00000401946:T1024A;ENSP00000338371:T971A	ENSP00000306759:T277A	T	+	1	0	TNRC6B	38999479	0.894000	0.30519	0.636000	0.29352	0.958000	0.62258	0.742000	0.26216	-0.246000	0.09611	-0.929000	0.02709	ACT	.		0.562	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				G	40669533	A	G	40669533	3	3	80	1	0	0	0	0	1	0	0	0	16373	159	6	3	3217	3	TNRC6B	22	40669533	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	4007868	40669533	10635033	98	7502											
GLUD2	2747	ucsc.edu	37	chrX	120182805	120182805	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcctggagagaaacattTtggttattccagatctctac	10	15	7	9	0	2	2	0	0	2	2	5	4	4	3	2	2	2	1	2	2	3	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chrX:120182805T>A	ENST00000328078.1	+	1	1344	c.1267T>A	c.(1267-1269)Ttg>Atg	p.L423M		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	423					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						GAGAAACATTTTGGTTATTCC	0.443																																					p.L423M													.	GLUD2-131	0			c.T1267A						.						176	165	169					X																	120182805		2203	4300	6503	SO:0001583	missense	2747	exon1			AACATTTTGGTTA	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1267T>A	X.37:g.120182805T>A	ENSP00000327589:p.Leu423Met	Somatic	121	0		WXS	Illumina HiSeq		124	2	NM_012084	0	0	0	79	79	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	T	0.044	-1.271952	0.01421	.	.	ENSG00000182890	ENST00000328078	D	0.95885	-3.84	1.61	-3.22	0.05125	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (2);NAD(P)-binding domain (1);	0.075950	0.85682	N	0.000000	D	0.93271	0.7856	M	0.80183	2.485	0.24288	N	0.995174	B	0.31893	0.345	B	0.42653	0.394	D	0.84648	0.0699	10	0.25751	T	0.34	.	0.3029	0.00275	0.3391:0.1736:0.1374:0.3499	.	423	P49448	DHE4_HUMAN	M	423	ENSP00000327589:L423M	ENSP00000327589:L423M	L	+	1	2	GLUD2	120010486	1.000000	0.71417	0.003000	0.11579	0.167000	0.22549	0.715000	0.25822	-1.738000	0.01348	-1.616000	0.00795	TTG	.		0.443	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		A	120182805	T	A	120182805	3	1	80	1	0	0	0	0	1	0	0	0	6497	1838	64	5	1269	5	GLUD2	23	120182805	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08		120182805	35087755	99	7503											
RPL10	6134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	153627911	153627911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtggccacatggtgtcagatGaatatgagcagctgtcctct	9	11	12	9	0	2	3	1	2	1	1	3	3	3	3	2	2	2	2	2	2	2	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chrX:153627911G>A	ENST00000369817.2	+	5	742	c.166G>A	c.(166-168)Gaa>Aaa	p.E56K	RPL10_ENST00000406022.2_Missense_Mutation_p.E5K|RPL10_ENST00000424325.2_Missense_Mutation_p.E56K|SNORA70_ENST00000384436.1_RNA			P27635	RL10_HUMAN	ribosomal protein L10	56					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)					GGTGTCAGATGAATATGAGCA	0.507																																					p.E56K		.											.	RPL10-130	0			c.G166A						.						112	110	111					X																	153627911		2203	4300	6503	SO:0001583	missense	6134	exon4			TCAGATGAATATG	AB007170	CCDS14746.1, CCDS76059.1	Xq28	2011-04-06			ENSG00000147403	ENSG00000147403		"L ribosomal proteins"	10298	protein-coding gene	gene with protein product		312173				9582194	Standard	NM_006013		Approved	NOV, QM, DXS648E, DXS648, FLJ23544, L10	uc004fkm.2	P27635	OTTHUMG00000033189	ENST00000369817.2:c.166G>A	X.37:g.153627911G>A	ENSP00000358832:p.Glu56Lys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	89	50	NM_001256577	0	1	187	1065	877	A3KQT0|D3DWW6|Q16470|Q2HXT7|Q53FH7|Q6FGN8|Q8TDA5	Missense_Mutation	SNP	ENST00000369817.2	37	CCDS14746.1	.	.	.	.	.	.	.	.	.	.	G	35	5.435565	0.96150	.	.	ENSG00000147403	ENST00000369817;ENST00000424325;ENST00000436473;ENST00000344746;ENST00000458500;ENST00000406022;ENST00000451365	T;T;T;T	0.79940	-0.98;-0.98;-0.98;-1.32	4.77	4.77	0.60923	Ribosomal protein L10e/L16 (2);	0.150767	0.42420	U	0.000704	D	0.92616	0.7654	H	0.96720	3.87	0.80722	D	1	P;D	0.65815	0.912;0.995	P;D	0.69654	0.876;0.965	D	0.94917	0.8070	10	0.87932	D	0	-16.8236	14.3504	0.66697	0.0:0.0:1.0:0.0	.	56;56	A6QRI9;P27635	.;RL10_HUMAN	K	56;56;56;56;56;5;39	ENSP00000358832:E56K;ENSP00000413436:E56K;ENSP00000341730:E56K;ENSP00000385621:E5K	ENSP00000341730:E56K	E	+	1	0	RPL10	153281105	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	8.919000	0.92770	1.963000	0.57068	0.600000	0.82982	GAA	.		0.507	RPL10-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127774.5	NM_006013		A	153627911	G	A	153627911	3	1	80	1	0	0	0	0	1	0	0	0	13586	1291	45	2	176	2	RPL10	23	153627911	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	33445106	153627911	1642649	100	7504											
CDK11A	728642	broad.mit.edu	37	chr1	1638914	1638914	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaacagggcaggggagtcGggcacatagtcgccctctgt	8	6	16	11	2	1	0	0	0	1	0	3	1	1	1	1	5	1	3	1	5	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:1638914G>T	ENST00000378633.1	-	11	1267	c.1188C>A	c.(1186-1188)ccC>ccA	p.P396P	CDK11A_ENST00000378638.2_Silent_p.P359P|CDK11A_ENST00000378635.3_3'UTR|CDK11A_ENST00000357760.2_Silent_p.P392P|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000356200.3_Silent_p.P359P|CDK11A_ENST00000404249.3_Silent_p.P393P|CDK11A_ENST00000495016.1_5'Flank|CDK11A_ENST00000358779.5_Silent_p.P383P			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	396					apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						CAGGGGAGTCGGGCACATAGT	0.672																																					p.P393P	Pancreas(186;965 2119 30274 40311 50569)												.	CDK11A-14	0			c.C1179A						.						49	62	58					1																	1638914		2019	4148	6167	SO:0001819	synonymous_variant	728642	exon11			GGAGTCGGGCACA	AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"Cyclin-dependent kinases"	1730	protein-coding gene	gene with protein product		116951	"cell division cycle 2-like 2", "cell division cycle 2-like 2 (PITSLRE proteins)"	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.1188C>A	1.37:g.1638914G>T		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	29	15	NM_024011	0	0	23	29	6	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Silent	SNP	ENST00000378633.1	37																																																																																				.		0.672	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		T	1638914	G	T	1638914	2	4	81	1	0	0	0	0	0	0	0	1	3132	1103	39	4		4	CDK11A	1	1638914	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		1638914	247611707	1	7505											
NPHP4	261734	broad.mit.edu	37	chr1	5935029	5935029	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aactcggcgacccccagcgtGgcgtggagcgtgtgctccgt	5	7	15	14	6	0	0	0	0	0	0	2	2	1	1	3	3	4	1	3	3	1	0			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:5935029G>A	ENST00000378156.4	-	21	3214	c.2949C>T	c.(2947-2949)gcC>gcT	p.A983A	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	983					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CCCCCAGCGTGGCGTGGAGCG	0.627																																					p.A983A													.	NPHP4-515	0			c.C2949T						.						74	93	87					1																	5935029		2186	4268	6454	SO:0001819	synonymous_variant	261734	exon21			CAGCGTGGCGTGG	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"nephroretinin", "nephrocystin-4", "POC10 centriolar protein homolog (Chlamydomonas)"	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2949C>T	1.37:g.5935029G>A		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	59	6	NM_015102	0	0	8	9	1	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			.		0.627	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	5935029	G	A	5935029	2	1	81	1	0	0	0	0	0	0	0	1	10607	1335	47	2		2	NPHP4	1	5935029	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	4296115	5935029	243315592	2	7506											
RPS6KA1	6195	broad.mit.edu;bcgsc.ca	37	chr1	26885310	26885310	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtacagattccccaggcaTcccccccagcgctggggccc	6	5	10	20	2	0	1	0	0	0	1	2	1	2	1	7	3	2	3	7	3	1	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:26885310T>C	ENST00000374168.2	+	14	1251	c.1097T>C	c.(1096-1098)aTc>aCc	p.I366T	RPS6KA1_ENST00000374166.4_Missense_Mutation_p.I355T|RPS6KA1_ENST00000374162.2_Missense_Mutation_p.I274T|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.I350T|RPS6KA1_ENST00000526792.1_Missense_Mutation_p.I274T|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.I375T	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	366	AGC-kinase C-terminal.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		TCCCCAGGCATCCCCCCCAGC	0.672																																					p.I375T													.	RPS6KA1-510	0			c.T1124C						.						64	64	64					1																	26885310		2203	4300	6503	SO:0001583	missense	6195	exon13			CAGGCATCCCCCC	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"ribosomal protein S6 kinase, 90kD, polypeptide 1"			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.1097T>C	1.37:g.26885310T>C	ENSP00000363283:p.Ile366Thr	Somatic	105	1		WXS	Illumina HiSeq	Phase_I	97	5	NM_001006665	0	0	0	0	0	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Missense_Mutation	SNP	ENST00000374168.2	37	CCDS284.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.802617	0.31869	.	.	ENSG00000117676	ENST00000374168;ENST00000374166;ENST00000526792;ENST00000374162;ENST00000530003;ENST00000374164;ENST00000531382;ENST00000403732	T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.55	5.55	0.83447	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);	0.101317	0.64402	D	0.000003	T	0.45256	0.1333	L	0.46614	1.455	0.80722	D	1	B;B;B	0.31413	0.003;0.004;0.322	B;B;B	0.32211	0.057;0.008;0.142	T	0.47911	-0.9080	10	0.87932	D	0	.	15.8615	0.79026	0.0:0.0:0.0:1.0	.	350;375;366	B7Z2K7;Q15418-2;Q15418	.;.;KS6A1_HUMAN	T	366;355;274;274;350;86;375;24	ENSP00000363283:I366T;ENSP00000363281:I355T;ENSP00000431651:I274T;ENSP00000363277:I274T;ENSP00000432281:I350T;ENSP00000435412:I375T;ENSP00000383967:I24T	ENSP00000363277:I274T	I	+	2	0	RPS6KA1	26757897	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.778000	0.85637	2.333000	0.79357	0.533000	0.62120	ATC	.		0.672	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953		C	26885310	T	C	26885310	3	2	81	1	0	0	0	0	1	0	0	0	13682	1435	50	3	1290	3	RPS6KA1	1	26885310	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	20950281	26885310	222365311	3	7507											
CGN	57530	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151509762	151509762	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggaattcgacagtgtctaCgatccctcgtccattgcatc	9	11	9	12	3	1	0	0	0	1	0	6	4	3	1	2	1	2	1	2	1	2	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:151509762C>T	ENST00000271636.7	+	21	3685	c.3552C>T	c.(3550-3552)taC>taT	p.Y1184Y		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	1178	Tail.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)	p.Y1184Y(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			ACAGTGTCTACGATCCCTCGT	0.537																																					p.Y1184Y													.	CGN-93	1	Substitution - coding silent(1)	lung(1)	c.C3552T						.						123	92	102					1																	151509762		2203	4300	6503	SO:0001819	synonymous_variant	57530	exon21			TGTCTACGATCCC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.3552C>T	1.37:g.151509762C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	64	18	NM_020770	0	0	10	13	3	A6H8L3|A7MD22|Q5T386|Q9NR25	Silent	SNP	ENST00000271636.7	37	CCDS999.1																																																																																			.		0.537	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151509762	C	T	151509762	2	4	81	1	0	0	0	0	0	0	0	1	3309	547	19	1		1	CGN	1	151509762	Silent	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	124624452	151509762	97740859	4	7508											
ADAR	103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154562826	154562826	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcctgcttgccttgcttcTtgctgtgtgcgcagacggct	2	15	11	13	2	1	1	0	0	1	1	2	1	2	1	2	1	5	5	2	1	0	5			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:154562826T>C	ENST00000368474.4	-	7	2529	c.2330A>G	c.(2329-2331)aAg>aGg	p.K777R	ADAR_ENST00000368471.3_Missense_Mutation_p.K482R|ADAR_ENST00000292205.5_Missense_Mutation_p.K820R	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	777	DRBM 3. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GCCTTGCTTCTTGCTGTGTGC	0.542																																					p.K777R		.											.	ADAR-157	0			c.A2330G						.						99	92	94					1																	154562826		2203	4300	6503	SO:0001583	missense	103	exon7			TGCTTCTTGCTGT	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.2330A>G	1.37:g.154562826T>C	ENSP00000357459:p.Lys777Arg	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	129	22	NM_001111	0	0	49	58	9	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	34	5.404549	0.96051	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.94	5.94	0.96194	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.93038	0.7784	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.997;0.999	D	0.94043	0.7311	10	0.87932	D	0	-29.5181	16.3951	0.83601	0.0:0.0:0.0:1.0	.	758;777;777	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	820;777;482;772	ENSP00000292205:K820R;ENSP00000357459:K777R;ENSP00000357456:K482R;ENSP00000431794:K772R	ENSP00000292205:K820R	K	-	2	0	ADAR	152829450	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.424000	0.80242	2.272000	0.75746	0.460000	0.39030	AAG	.		0.542	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		C	154562826	T	C	154562826	3	2	81	1	0	0	0	0	1	0	0	0	281	1609	56	3	1386	3	ADAR	1	154562826	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	3053064	154562826	94687795	5	7509											
CACNA1S	779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201034981	201034981	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccttgaagagctggacGccgatgcaggcaaacatgaa	13	6	11	11	2	1	3	1	2	0	1	1	5	1	4	2	2	3	3	2	2	3	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:201034981G>T	ENST00000362061.3	-	22	3064	c.2838C>A	c.(2836-2838)ggC>ggA	p.G946G	CACNA1S_ENST00000367338.3_Silent_p.G946G	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	946					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGAGCTGGACGCCGATGCAGG	0.622																																					p.G946G		.											.	CACNA1S-94	0			c.C2838A						.						85	70	75					1																	201034981		2203	4300	6503	SO:0001819	synonymous_variant	779	exon22			CTGGACGCCGATG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.2838C>A	1.37:g.201034981G>T		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	30	10	NM_000069	0	0	0	0	0	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			.		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201034981	G	T	201034981	2	4	81	1	0	0	0	0	0	0	0	1	2553	1074	38	4		4	CACNA1S	1	201034981	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	46472155	201034981	48215640	6	7510											
C2orf44	80304	bcgsc.ca	37	chr2	24261378	24261378	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atagtgacttttctcgtcatGgtaactgccttcttaaaggt	9	16	8	8	1	3	1	1	1	2	0	4	1	3	1	1	2	2	1	1	2	4	6			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr2:24261378G>C	ENST00000295148.4	-	2	1044	c.987C>G	c.(985-987)acC>acG	p.T329T	C2orf44_ENST00000406895.3_Silent_p.T329T	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	329									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTCGTCATGGTAACTGCCT	0.408			T	ALK	NSCLC																																p.T329T				Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44-154	0			c.C987G						.																																			SO:0001819	synonymous_variant	80304	exon2			CGTCATGGTAACT	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.987C>G	2.37:g.24261378G>C		Somatic	75	0		WXS	Illumina HiSeq	Phase_1	89	5	NM_025203	0	0	1	1	0	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	37	CCDS1705.1																																																																																			.		0.408	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		C	24261378	G	C	24261378	2	2	81	1	0	0	0	0	0	0	0	1	2174	1335	47	4		4	C2orf44	2	24261378	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		24261378	218937995	7	7511											
KCNG3	170850	ucsc.edu	37	chr2	42720017	42720017	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccggcggagtacctgctccGgtcatccaggctgcggttgt	4	9	15	13	4	1	0	1	0	0	0	3	1	3	1	4	5	3	4	4	5	1	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr2:42720017G>A	ENST00000306078.1	-	1	1220	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	KCNG3_ENST00000394973.4_Missense_Mutation_p.R209W|MTA3_ENST00000405592.1_5'Flank	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	209					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						TACCTGCTCCGGTCATCCAGG	0.687																																					p.R209W													.	KCNG3-90	0			c.C625T						.						22	17	19					2																	42720017		2167	4259	6426	SO:0001583	missense	170850	exon1			TGCTCCGGTCATC	AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.625C>T	2.37:g.42720017G>A	ENSP00000304127:p.Arg209Trp	Somatic	28	0		WXS	Illumina HiSeq		41	4	NM_172344	0	0	0	0	0	Q53SC1	Missense_Mutation	SNP	ENST00000306078.1	37	CCDS1809.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.797664	0.50208	.	.	ENSG00000171126	ENST00000306078;ENST00000394973	D;D	0.97378	-4.32;-4.36	4.55	4.55	0.56014	.	15.145900	0.00166	N	0.000013	D	0.95611	0.8573	N	0.14661	0.345	0.30668	N	0.753658	B;P	0.44281	0.431;0.831	B;P	0.50231	0.109;0.635	D	0.90095	0.4180	10	0.72032	D	0.01	.	9.2626	0.37621	0.0:0.1576:0.6796:0.1628	.	209;209	Q8TAE7;Q8TAE7-2	KCNG3_HUMAN;.	W	209	ENSP00000304127:R209W;ENSP00000378424:R209W	ENSP00000304127:R209W	R	-	1	2	KCNG3	42573521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.743000	0.47442	2.069000	0.61940	0.563000	0.77884	CGG	.		0.687	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344		A	42720017	G	A	42720017	3	1	81	1	0	0	0	0	1	0	0	0	8050	1115	39	1	693	1	KCNG3	2	42720017	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	18458639	42720017	200479356	8	7512											
DCTN1	1639	broad.mit.edu	37	chr2	74604848	74604848	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctccatcttcaaatacCtggatctgaggccagattca	10	12	7	12	0	5	2	2	1	3	1	6	3	6	3	3	2	2	1	3	2	2	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr2:74604848C>G	ENST00000361874.3	-	3	602	c.285G>C	c.(283-285)caG>caC	p.Q95H	DCTN1_ENST00000409567.3_Missense_Mutation_p.Q95H|DCTN1_ENST00000407639.2_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.Q95H|DCTN1_ENST00000409240.1_Missense_Mutation_p.Q78H|DCTN1_ENST00000409438.1_5'Flank|DCTN1_ENST00000409868.1_Missense_Mutation_p.Q78H	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	95					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CTTCAAATACCTGGATCTGAG	0.458																																					p.Q95H													.	DCTN1-95	0			c.G285C						.						124	126	125					2																	74604848		2203	4300	6503	SO:0001583	missense	1639	exon3			AAATACCTGGATC		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.285G>C	2.37:g.74604848C>G	ENSP00000354791:p.Gln95His	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	121	3	NM_001135040	0	0	0	0	0	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728596	0.69074	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000409240;ENST00000409868;ENST00000409567;ENST00000458655;ENST00000454119;ENST00000417090;ENST00000437375	T;T;T;T;T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88	5.17	2.35	0.29111	Cytoskeleton-associated protein, Gly-rich domain (2);	0.000000	0.41097	D	0.000953	T	0.81413	0.4817	M	0.69523	2.12	0.80722	D	1	D;P;D;D	0.61697	0.99;0.685;0.967;0.987	D;P;D;D	0.64595	0.922;0.685;0.923;0.927	T	0.79790	-0.1655	10	0.45353	T	0.12	-9.9712	9.8164	0.40856	0.0:0.7639:0.0:0.2361	.	95;78;95;95	E9PGE1;E9PFS5;Q14203;A8MY36	.;.;DCTN1_HUMAN;.	H	95;95;78;78;78;95;102;78;99;78	ENSP00000354791:Q95H;ENSP00000377571:Q95H;ENSP00000386406:Q78H;ENSP00000387327:Q78H;ENSP00000386843:Q95H;ENSP00000414315:Q102H;ENSP00000404038:Q78H;ENSP00000402509:Q99H;ENSP00000395312:Q78H	ENSP00000354791:Q95H	Q	-	3	2	DCTN1	74458356	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.967000	0.29344	0.762000	0.33152	0.655000	0.94253	CAG	.		0.458	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		G	74604848	C	G	74604848	3	3	81	1	0	0	0	0	1	0	0	0	4312	680	24	4	3683	4	DCTN1	2	74604848	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	31884831	74604848	168594525	9	7513											
ALS2CR4	65062	broad.mit.edu;bcgsc.ca	37	chr2	202493983	202493983	+	Frame_Shift_Del	DEL	A	A	-																															ctgaaattgtactcagagccAaaagcaagtacagaagactc																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr2:202493983delA	ENST00000409883.2	-	9	955	c.839delT	c.(838-840)ttgfs	p.L280fs	TMEM237_ENST00000466839.1_5'UTR|TMEM237_ENST00000409444.2_Frame_Shift_Del_p.L272fs	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	280					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						ACTCAGAGCCAAAAGCAAGTA	0.428																																					p.L280fs													.	.	0			c.839delT						.						73	68	70					2																	202493983		1902	4131	6033	SO:0001589	frameshift_variant	65062	exon8			AGAGCCAAAAGCA	AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.839delT	2.37:g.202493983delA	ENSP00000386264:p.Leu280fs	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	28	8	NM_001044385	0	0	0	0	0	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Frame_Shift_Del	DEL	ENST00000409883.2	37	CCDS46489.1																																																																																			.		0.428	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388		-	202493983	A	-	202493983	7	5	81	1	0	1	0	1	0	0	0	0	554	131	5	0	407	0	ALS2CR4	2	202493983	Frame_Shift_Del	DEL	A	TCGA-BQ-7046-01A-11D-1961-08	127889135	202493983	40705390	10	7514											
CCR3	1232	broad.mit.edu	37	chr3	46306948	46306948	+	Frame_Shift_Del	DEL	T	T	-																															tgtcagggggcataactgggTttttggccatggcatgtgta																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:46306948delT	ENST00000357422.2	+	4	842	c.299delT	c.(298-300)gttfs	p.V100fs	CCR3_ENST00000395942.2_Frame_Shift_Del_p.V100fs|CCR3_ENST00000545097.1_Frame_Shift_Del_p.V121fs|CCR3_ENST00000395940.2_Frame_Shift_Del_p.V100fs|CCR3_ENST00000541018.1_Frame_Shift_Del_p.V100fs			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	100					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		CATAACTGGGTTTTTGGCCAT	0.488																																					p.V121fs													.	CCR3-660	0			c.362delT						.						181	175	177					3																	46306948		2203	4300	6503	SO:0001589	frameshift_variant	1232	exon3			ACTGGGTTTTTGG	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.299delT	3.37:g.46306948delT	ENSP00000350003:p.Val100fs	Somatic	341	0		WXS	Illumina HiSeq	Phase_I	431	7	NM_178328	0	0	0	0	0	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Frame_Shift_Del	DEL	ENST00000357422.2	37	CCDS2738.1																																																																																			.		0.488	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			-	46306948	T	-	46306948	7	5	81	1	0	1	0	1	0	0	0	0	2948	1725	60	0	368	0	CCR3	3	46306948	Frame_Shift_Del	DEL	T	TCGA-BQ-7046-01A-11D-1961-08		46306948	151715482	11	7515											
KIAA1407	57577	broad.mit.edu	37	chr3	113724781	113724781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactgcttcccaagggaggcTtttcccacaaagggggcaca	10	7	11	13	0	0	0	0	0	0	0	2	1	2	1	2	4	1	3	2	4	2	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:113724781T>C	ENST00000295878.3	-	10	1588	c.1442A>G	c.(1441-1443)aAg>aGg	p.K481R	KIAA1407_ENST00000545063.1_Missense_Mutation_p.K312R	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	481										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CAAGGGAGGCTTTTCCCACAA	0.478																																					p.K481R													.	KIAA1407-92	0			c.A1442G						.						86	89	88					3																	113724781		2203	4300	6503	SO:0001583	missense	57577	exon10			GGAGGCTTTTCCC	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1442A>G	3.37:g.113724781T>C	ENSP00000295878:p.Lys481Arg	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	177	4	NM_020817	0	0	9	9	0	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	T	12.69	2.012114	0.35511	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.47177	1.46;0.85;0.87	5.01	3.81	0.43845	.	0.829403	0.11209	N	0.587888	T	0.32285	0.0824	N	0.22421	0.69	0.80722	D	1	B;B;B	0.17667	0.002;0.023;0.002	B;B;B	0.17098	0.011;0.017;0.011	T	0.04467	-1.0949	10	0.18276	T	0.48	.	9.1934	0.37213	0.0:0.0876:0.0:0.9124	.	468;357;481	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	R	481;312;468	ENSP00000295878:K481R;ENSP00000446381:K312R;ENSP00000418099:K468R	ENSP00000295878:K481R	K	-	2	0	KIAA1407	115207471	0.173000	0.23056	0.775000	0.31657	0.262000	0.26303	0.849000	0.27723	0.877000	0.35895	0.533000	0.62120	AAG	.		0.478	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113724781	T	C	113724781	3	2	81	1	0	0	0	0	1	0	0	0	8250	1609	56	3	1400	3	KIAA1407	3	113724781	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	67417833	113724781	84297649	12	7516											
HPS3	84343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	148872995	148872995	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaccagtgcagctgtacaAagagatggtactcttttcaa	12	11	8	10	0	3	1	2	0	1	1	3	2	3	1	1	1	4	4	1	1	4	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:148872995A>G	ENST00000296051.2	+	8	1642	c.1502A>G	c.(1501-1503)aAa>aGa	p.K501R	HPS3_ENST00000460120.1_Missense_Mutation_p.K336R	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	501					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CAGCTGTACAAAGAGATGGTA	0.348									Hermansky-Pudlak syndrome																												p.K501R		.											.	HPS3-158	0			c.A1502G						.						136	141	140					3																	148872995		2203	4300	6503	SO:0001583	missense	84343	exon8	Familial Cancer Database	HPS, HPS1-8	TGTACAAAGAGAT	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.1502A>G	3.37:g.148872995A>G	ENSP00000296051:p.Lys501Arg	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	96	29	NM_032383	0	0	0	0	0	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	1.459	-0.562938	0.03939	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.64260	-0.09;-0.09	4.89	3.74	0.42951	.	0.205149	0.44902	N	0.000404	T	0.49474	0.1559	L	0.43923	1.385	0.25950	N	0.982762	B;B	0.22746	0.074;0.027	B;B	0.22386	0.039;0.013	T	0.35992	-0.9766	10	0.28530	T	0.3	-8.4607	7.6211	0.28185	0.8276:0.0:0.1724:0.0	.	336;501	G5E9V4;Q969F9	.;HPS3_HUMAN	R	501;336	ENSP00000296051:K501R;ENSP00000418230:K336R	ENSP00000296051:K501R	K	+	2	0	HPS3	150355685	1.000000	0.71417	0.999000	0.59377	0.018000	0.09664	2.513000	0.45494	1.000000	0.39049	-0.250000	0.11733	AAA	.		0.348	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		G	148872995	A	G	148872995	3	3	81	1	0	0	0	0	1	0	0	0	7361	14	1	3	1532	3	HPS3	3	148872995	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08	35148214	148872995	49149435	13	7517											
RBM47	54502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	40440532	40440532	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttgttgagctcacgcactgCgcgcttggcctcgtgcttgt	3	13	13	12	4	1	1	1	1	0	0	2	1	1	1	1	1	3	6	1	1	0	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr4:40440532C>G	ENST00000381793.2	-	3	775	c.379G>C	c.(379-381)Gca>Cca	p.A127P	RBM47_ENST00000295971.7_Missense_Mutation_p.A127P|RBM47_ENST00000381795.6_Missense_Mutation_p.A127P|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000514014.1_Missense_Mutation_p.A89P|RBM47_ENST00000319592.4_Missense_Mutation_p.A127P			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	127	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						TCACGCACTGCGCGCTTGGCC	0.642																																					p.A127P		.											.	RBM47-25	0			c.G379C						.						61	51	55					4																	40440532		2203	4300	6503	SO:0001583	missense	54502	exon4			GCACTGCGCGCTT	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.379G>C	4.37:g.40440532C>G	ENSP00000371212:p.Ala127Pro	Somatic	59	1		WXS	Illumina HiSeq	Phase_I	54	9	NM_001098634	0	0	28	44	16	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	37	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668830	0.88348	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014;ENST00000515053;ENST00000513473;ENST00000505414;ENST00000514782	T;T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.58	5.58	0.84498	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.76343	0.3974	H	0.97940	4.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.85506	0.1194	10	0.87932	D	0	-18.5386	19.5736	0.95432	0.0:1.0:0.0:0.0	.	127;127	A0AV96-2;A0AV96	.;RBM47_HUMAN	P	127;127;127;127;89;127;127;127;127	ENSP00000320108:A127P;ENSP00000371212:A127P;ENSP00000371214:A127P;ENSP00000295971:A127P;ENSP00000423243:A89P;ENSP00000422564:A127P;ENSP00000421589:A127P;ENSP00000423527:A127P;ENSP00000426542:A127P	ENSP00000295971:A127P	A	-	1	0	RBM47	40135289	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	7.813000	0.86123	2.635000	0.89317	0.313000	0.20887	GCA	.		0.642	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		G	40440532	C	G	40440532	3	3	81	1	0	0	0	0	1	0	0	0	13173	768	27	4	1418	4	RBM47	4	40440532	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		40440532	150713744	14	7518											
C4orf37	285555	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	98633942	98633942	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatggggcaagatttccttaAaacaggattgtatgctgcag	12	12	11	6	0	0	1	0	0	0	1	1	2	1	2	1	3	3	4	1	3	5	5			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr4:98633942A>T	ENST00000295268.3	-	10	1317	c.1228T>A	c.(1228-1230)Tta>Ata	p.L410I	STPG2_ENST00000506482.1_5'UTR	NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	410																	GATTTCCTTAAAACAGGATTG	0.348																																					p.L410I		.											.	.	0			c.T1228A						.						98	101	100					4																	98633942		2203	4300	6503	SO:0001583	missense	285555	exon10			TCCTTAAAACAGG	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.1228T>A	4.37:g.98633942A>T	ENSP00000295268:p.Leu410Ile	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	112	39	NM_174952	0	0	0	2	2		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397643	0.25205	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.49139	0.79;2.73	4.85	2.3	0.28687	.	0.854661	0.09752	N	0.760480	T	0.32704	0.0838	L	0.27053	0.805	0.09310	N	0.999998	P	0.38300	0.626	B	0.40782	0.34	T	0.14868	-1.0457	10	0.23302	T	0.38	-8.0438	4.5761	0.12234	0.4933:0.3146:0.192:0.0	.	410	Q8N412	CD037_HUMAN	I	124;410	ENSP00000428346:L124I;ENSP00000295268:L410I	ENSP00000295268:L410I	L	-	1	2	C4orf37	98852965	0.779000	0.28652	0.948000	0.38648	0.774000	0.43823	0.556000	0.23438	1.930000	0.55929	0.528000	0.53228	TTA	.		0.348	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		T	98633942	A	T	98633942	3	4	81	1	0	0	0	0	1	0	0	0	2273	11	1	5	159	5	C4orf37	4	98633942	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08	58193410	98633942	92520334	15	7519											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13727614	13727614	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctttaatatggactttttAcctgggcgatggttctgtca	7	17	9	8	1	3	0	1	0	2	0	3	2	3	1	1	3	1	1	1	3	3	7			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr5:13727614A>G	ENST00000265104.4	-	70	12138		c.e70+1			NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGGACTTTTTACCTGGGCGAT	0.328									Kartagener syndrome																												.		.											.	DNAH5-182	0			c.12033+2T>C						.						54	55	55					5																	13727614		2202	4300	6502	SO:0001630	splice_region_variant	1767	exon71	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTTTTTACCTGGG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12033+1T>C	5.37:g.13727614A>G		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_001369	0	0	0	0	0	Q92860|Q96L74|Q9H5S7|Q9HCG9	Splice_Site	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273400	0.80580	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9744	0.80049	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNAH5	13780614	1.000000	0.71417	0.998000	0.56505	0.858000	0.48976	9.315000	0.96313	2.184000	0.69523	0.528000	0.53228	.	.		0.328	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	Intron	G	13727614	A	G	13727614	5	3	81	1	0	0	0	0	0	0	1	0	4615	405	14	3	1879	3	DNAH5	5	13727614	Splice_Site	SNP	A	TCGA-BQ-7046-01A-11D-1961-08		13727614	167187646	16	7520											
DMXL1	1657	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	118525502	118525502	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgaccccttcctcggcacCagtaagccaggagtcactgg	9	7	10	15	1	1	1	1	1	0	0	3	2	2	2	5	3	1	2	5	3	1	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr5:118525502C>G	ENST00000311085.8	+	29	7315	c.7235C>G	c.(7234-7236)cCa>cGa	p.P2412R	DMXL1_ENST00000539542.1_Missense_Mutation_p.P2412R	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2412										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TCCTCGGCACCAGTAAGCCAG	0.438																																					p.P2412R													.	DMXL1-92	0			c.C7235G						.						107	110	109					5																	118525502		2202	4300	6502	SO:0001583	missense	1657	exon29			CGGCACCAGTAAG	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.7235C>G	5.37:g.118525502C>G	ENSP00000309690:p.Pro2412Arg	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	146	40	NM_005509	0	0	2	9	7		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	5.532	0.283090	0.10458	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.09538	2.97;2.97	6.05	2.08	0.27032	.	0.778290	0.12409	N	0.471491	T	0.08670	0.0215	L	0.42245	1.32	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.35574	-0.9783	10	0.21540	T	0.41	-0.8119	6.1712	0.20418	0.0:0.4786:0.211:0.3104	.	2412;2412	F5H269;Q9Y485	.;DMXL1_HUMAN	R	2412	ENSP00000309690:P2412R;ENSP00000439479:P2412R	ENSP00000309690:P2412R	P	+	2	0	DMXL1	118553401	0.000000	0.05858	0.185000	0.23176	0.361000	0.29550	-0.003000	0.12901	0.903000	0.36546	-0.143000	0.13931	CCA	.		0.438	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118525502	C	G	118525502	3	3	81	1	0	0	0	0	1	0	0	0	4605	594	21	4	7349	4	DMXL1	5	118525502	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	104797888	118525502	62389758	17	7521											
CCNG1	900	bcgsc.ca	37	chr5	162868217	162868217	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atataggtttacggtttcagActtgatgagaatggaaaaga	15	12	11	3	1	1	4	1	2	0	3	1	6	1	5	0	3	1	2	0	3	6	6			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr5:162868217A>G	ENST00000340828.2	+	3	622	c.398A>G	c.(397-399)gAc>gGc	p.D133G	CCNG1_ENST00000512163.1_5'UTR|CCNG1_ENST00000504553.1_5'UTR|CCNG1_ENST00000511683.2_5'UTR|AC112205.1_ENST00000599797.1_Intron|CCNG1_ENST00000510664.1_Splice_Site_p.D5G|CCNG1_ENST00000393929.1_Missense_Mutation_p.D133G	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	133					brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		ACGGTTTCAGACTTGATGAGA	0.373																																					p.D133G													.	CCNG1-725	0			c.A398G						.						127	123	124					5																	162868217		2203	4300	6503	SO:0001583	missense	900	exon4			TTTCAGACTTGAT	D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.398A>G	5.37:g.162868217A>G	ENSP00000344635:p.Asp133Gly	Somatic	85	0		WXS	Illumina HiSeq	Phase_1	72	4	NM_199246	0	0	67	67	0	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Missense_Mutation	SNP	ENST00000340828.2	37	CCDS4360.1	.	.	.	.	.	.	.	.	.	.	A	18.37	3.609937	0.66558	.	.	ENSG00000113328	ENST00000393929;ENST00000340828;ENST00000510097;ENST00000510664	T;T;T;T	0.34667	2.11;2.11;2.11;1.35	5.23	5.23	0.72850	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.42988	0.1227	M	0.78223	2.4	0.80722	D	1	B	0.30482	0.281	B	0.28991	0.097	T	0.48198	-0.9056	10	0.87932	D	0	-3.6381	15.1248	0.72475	1.0:0.0:0.0:0.0	.	133	P51959	CCNG1_HUMAN	G	133;133;133;5	ENSP00000377506:D133G;ENSP00000344635:D133G;ENSP00000423791:D133G;ENSP00000422379:D5G	ENSP00000344635:D133G	D	+	2	0	CCNG1	162800795	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.780000	0.91799	1.979000	0.57680	0.533000	0.62120	GAC	.		0.373	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060		G	162868217	A	G	162868217	3	3	81	1	0	0	0	0	1	0	0	0	2929	275	10	3	404	3	CCNG1	5	162868217	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08	44342715	162868217	18047043	18	7522											
RAB24	53917	broad.mit.edu;bcgsc.ca	37	chr5	176729807	176729807	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtagattctactcatggcctCatagcgctcagagcctgctg	8	11	10	12	1	4	2	3	0	1	2	4	2	4	2	2	1	4	3	2	1	3	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr5:176729807C>G	ENST00000303251.6	-	3	630	c.211G>C	c.(211-213)Gag>Cag	p.E71Q	RAB24_ENST00000303270.6_Missense_Mutation_p.E42Q|PRELID1_ENST00000303204.4_5'Flank|RAB24_ENST00000393611.2_Missense_Mutation_p.E71Q|PRELID1_ENST00000503216.1_5'Flank	NM_001031677.2	NP_001026847.1	Q969Q5	RAB24_HUMAN	RAB24, member RAS oncogene family	71					autophagy (GO:0006914)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	autophagic vacuole (GO:0005776)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCATGGCCTCATAGCGCTCA	0.537																																					p.E71Q													.	RAB24-159	0			c.G211C						.						98	93	95					5																	176729807		2203	4300	6503	SO:0001583	missense	53917	exon3			TGGCCTCATAGCG	AF087904	CCDS34300.1	5q35.3	2009-10-06			ENSG00000169228	ENSG00000169228		"RAB, member RAS oncogene"	9765	protein-coding gene	gene with protein product		612415					Standard	NM_001031677		Approved		uc003mfw.3	Q969Q5	OTTHUMG00000130849	ENST00000303251.6:c.211G>C	5.37:g.176729807C>G	ENSP00000304376:p.Glu71Gln	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	84	4	NM_001031677	0	0	47	47	0	Q7Z4Z7	Missense_Mutation	SNP	ENST00000303251.6	37	CCDS34300.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064810	0.76187	.	.	ENSG00000169228	ENST00000393611;ENST00000303251;ENST00000303270	T;T;T	0.76968	-1.06;-1.06;-1.06	5.49	5.49	0.81192	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	T	0.60637	0.2284	N	0.02765	-0.5	0.80722	D	1	P;P	0.39181	0.536;0.663	B;B	0.37833	0.223;0.259	T	0.70019	-0.4987	10	0.59425	D	0.04	1.7456	18.9659	0.92695	0.0:1.0:0.0:0.0	.	71;42	Q969Q5;F8W8H5	RAB24_HUMAN;.	Q	71;71;42	ENSP00000377235:E71Q;ENSP00000304376:E71Q;ENSP00000302085:E42Q	ENSP00000304376:E71Q	E	-	1	0	RAB24	176662413	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	7.185000	0.77714	2.576000	0.86940	0.555000	0.69702	GAG	.		0.537	RAB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253416.1	NM_130781		G	176729807	C	G	176729807	3	3	81	1	0	0	0	0	1	0	0	0	12943	835	29	4	424	4	RAB24	5	176729807	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	13861590	176729807	4185453	19	7523											
KIAA0319	9856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	24578370	24578370	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaccaggatcaaggttagaCaagcgtaagacgggagagtc	14	7	13	7	2	1	3	1	0	0	3	2	5	1	4	1	3	2	2	1	3	5	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr6:24578370C>G	ENST00000378214.3	-	9	1997	c.1473G>C	c.(1471-1473)ttG>ttC	p.L491F	KIAA0319_ENST00000543707.1_Missense_Mutation_p.L491F|KIAA0319_ENST00000430948.2_Missense_Mutation_p.L446F|KIAA0319_ENST00000535378.1_Missense_Mutation_p.L482F|KIAA0319_ENST00000537886.1_Missense_Mutation_p.L491F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	491	PKD 2. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CAAGGTTAGACAAGCGTAAGA	0.408																																					p.L491F		.											.	KIAA0319-92	0			c.G1473C						.						144	138	140					6																	24578370		2203	4300	6503	SO:0001583	missense	9856	exon9			GTTAGACAAGCGT	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"neuronal migration"	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1473G>C	6.37:g.24578370C>G	ENSP00000367459:p.Leu491Phe	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	131	44	NM_001168377	0	0	1	1	0	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.558223	0.45590	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53	4.12	3.14	0.36123	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD/REJ-like protein (1);PKD domain (2);	0.101129	0.41396	D	0.000885	T	0.20981	0.0505	M	0.64080	1.96	0.43628	D	0.99601	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.00518	-1.1693	10	0.72032	D	0.01	-0.9176	8.9471	0.35764	0.0:0.8102:0.0:0.1898	.	491;482;491	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	F	491;482;446;491;491	ENSP00000439700:L491F;ENSP00000442403:L482F;ENSP00000401086:L446F;ENSP00000367459:L491F;ENSP00000437656:L491F	ENSP00000367459:L491F	L	-	3	2	KIAA0319	24686349	1.000000	0.71417	0.460000	0.27093	0.015000	0.08874	0.975000	0.29449	2.105000	0.64084	0.555000	0.69702	TTG	.		0.408	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		G	24578370	C	G	24578370	3	3	81	1	0	0	0	0	1	0	0	0	8189	477	17	4	1797	4	KIAA0319	6	24578370	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		24578370	146536697	20	7524											
HLA-B	3106	ucsc.edu	37	chr6	31323371	31323371	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtgtgtctttggggggtcTgatgggaagagtcagaaaat	10	11	16	4	1	3	3	1	1	2	2	3	4	3	4	0	4	0	0	0	4	3	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr6:31323371T>C	ENST00000412585.2	-	4	648		c.e4-2			NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TTGGGGGGTCTGATGGGAAGA	0.577									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												.													.	HLA-B-90	0			c.620-2A>G						.						80	83	82					6																	31323371		2203	4300	6503	SO:0001630	splice_region_variant	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	GGGGTCTGATGGG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.620-2A>G	6.37:g.31323371T>C		Somatic	136	0		WXS	Illumina HiSeq		169	1	NM_005514	0	0	9	9	0	Q29764	Splice_Site	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	.	10.61	1.397809	0.25205	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	.	.	.	3.2	3.2	0.36748	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.0844	0.30762	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HLA-B	31431350	0.998000	0.40836	0.599000	0.28851	0.035000	0.12851	3.253000	0.51469	1.476000	0.48215	0.368000	0.22195	.	.		0.577	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	Intron	C	31323371	T	C	31323371	5	2	81	1	0	0	0	0	0	0	1	0	7217	1594	55	3	486	3	HLA-B	6	31323371	Splice_Site	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	6745001	31323371	139791696	21	7525											
RUNX2	860	broad.mit.edu	37	chr6	45390446	45390448	+	In_Frame_Del	DEL	CAG	CAG	-																															agcaacagcagcagcagcaaCagcagcagcagcagcagcaa																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr6:45390446_45390448delCAG	ENST00000371438.1	+	2	533_535	c.175_177delCAG	c.(175-177)cagdel	p.Q71del	RUNX2_ENST00000352853.5_In_Frame_Del_p.Q139del|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000576263.1_In_Frame_Del_p.Q71del|RUNX2_ENST00000359524.5_In_Frame_Del_p.Q57del|RUNX2_ENST00000465038.2_In_Frame_Del_p.Q71del|RUNX2_ENST00000371432.3_In_Frame_Del_p.Q57del|RUNX2_ENST00000371436.6_In_Frame_Del_p.Q71del|RUNX2_ENST00000541979.1_In_Frame_Del_p.Q139del	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						gcagcagcaacagcagcagcagc	0.729																																					p.59_59del													.	RUNX2-417	0			c.175_177del						.																																			SO:0001651	inframe_deletion	860	exon3			CAGCAACAGCAGC	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.175_177delCAG	6.37:g.45390455_45390457delCAG	ENSP00000360493:p.Gln71del	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	80	7	NM_001024630	0	0	0	0	0	O14614|O14615|O95181	In_Frame_Del	DEL	ENST00000371438.1	37	CCDS43467.2																																																																																			.		0.729	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		-	45390448	CAG	-	45390446	7	5	81	1	0	1	0	1	0	0	0	0	13780	479	17	0	197	0	RUNX2	6	45390446	In_Frame_Del	DEL	CAG	TCGA-BQ-7046-01A-11D-1961-08	14067075	45390446	125724621	22	7526											
DNAH11	8701	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	21737744	21737744	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaatctgtgaaatcttgttAgttgctgaaggttttgtgga	9	17	11	4	0	2	2	0	2	2	0	2	3	2	3	0	2	1	4	0	2	4	6			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr7:21737744A>G	ENST00000409508.3	+	36	6124	c.6093A>G	c.(6091-6093)ttA>ttG	p.L2031L	DNAH11_ENST00000328843.6_Silent_p.L2038L	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2038	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						AAATCTTGTTAGTTGCTGAAG	0.423									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						115	105	108					7																	21737744		1948	4162	6110	SO:0001819	synonymous_variant	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTTGTTAGTTGCT	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.6093A>G	7.37:g.21737744A>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	79	38	.	0	0	0	0	0	Q9UJ82	Silent	SNP	ENST00000409508.3	37																																																																																				.		0.423	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		G	21737744	A	G	21737744	2	3	81	1	0	0	0	0	0	0	0	1	4610	417	15	3		3	DNAH11	7	21737744	Silent	SNP	A	TCGA-BQ-7046-01A-11D-1961-08		21737744	137400919	23	7527											
FGL2	10875	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	76828725	76828726	+	Frame_Shift_Ins	INS	-	-	T																															actctctaattctctaactcINStgttatcaccaacctctccc																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr7:76828725_76828726insT	ENST00000248598.5	-	1	417_418	c.385_386insA	c.(385-387)agafs	p.R129fs	CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron|RP11-467H10.2_ENST00000459742.1_RNA	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	129						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						TTCTCTAACTCTGTTATCACCA	0.495																																					p.R129fs		.											.	FGL2-92	0			c.386_387insA						.																																			SO:0001589	frameshift_variant	10875	exon1			.	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.386dupA	7.37:g.76828726_76828726dupT	ENSP00000248598:p.Arg129fs	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	164	33	NM_006682	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000248598.5	37	CCDS5591.1																																																																																			.		0.495	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		T	76828726	-	T	76828725	7	5	81	1	0	1	1	0	0	0	0	0	5892	913	32	0	941	0	FGL2	7	76828725	Frame_Shift_Ins	INS	-	TCGA-BQ-7046-01A-11D-1961-08	55090981	76828725	82309938	24	7528											
MYST3	7994	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	41836161	41836161	+	Splice_Site	DEL	C	C	-																															tgccacaagtacaacttacaCcgtgttttgtttctttaacc																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr8:41836161delC	ENST00000396930.3	-	7	1585	c.1042delG	c.(1042-1044)gta>ta	p.V348fs	KAT6A_ENST00000265713.2_Splice_Site_p.V348fs|KAT6A_ENST00000406337.1_Splice_Site_p.V348fs|KAT6A_ENST00000485568.1_Splice_Site_p.V348fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	348	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ACAACTTACACCGTGTTTTGT	0.383																																					p.V348fs		.											.	.	0			c.1042delG						.						338	340	340					8																	41836161		2203	4300	6503	SO:0001630	splice_region_variant	7994	exon7			.	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1043+1G>-	8.37:g.41836161delC		Somatic	420	0		WXS	Illumina HiSeq	Phase_I	379	105	NM_001099412	0	0	0	0	0	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	37	CCDS6124.1																																																																																			.		0.383	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	Frame_Shift_Del	-	41836161	C	-	41836161	8	5	81	1	0	1	0	1	0	0	1	0	10129	521	18	0	5020	0	MYST3	8	41836161	Splice_Site	DEL	C	TCGA-BQ-7046-01A-11D-1961-08		41836161	104527861	25	7529											
CNTLN	54875	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	17462949	17462949	+	Frame_Shift_Del	DEL	T	T	-																															ctcactaaacagtcatcaaaTgtgaagactttgaaatttga																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr9:17462949delT	ENST00000380647.3	+	20	3426	c.3342delT	c.(3340-3342)aatfs	p.N1114fs	CNTLN_ENST00000425824.1_Frame_Shift_Del_p.N1114fs|CNTLN_ENST00000262360.5_Frame_Shift_Del_p.N1114fs			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	1114					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGTCATCAAATGTGAAGACTT	0.299																																					p.N1114fs		.											.	CNTLN-91	0			c.3342delT						.						83	81	81					9																	17462949		1809	4069	5878	SO:0001589	frameshift_variant	54875	exon20			.	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.3342delT	9.37:g.17462949delT	ENSP00000370021:p.Asn1114fs	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	97	29	NM_017738	0	0	0	0	0	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Frame_Shift_Del	DEL	ENST00000380647.3	37	CCDS43789.1																																																																																			.		0.299	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		-	17462949	T	-	17462949	7	5	81	1	0	1	0	1	0	0	0	0	3645	1461	51	0	3450	0	CNTLN	9	17462949	Frame_Shift_Del	DEL	T	TCGA-BQ-7046-01A-11D-1961-08		17462949	123750482	26	7530											
TLN1	7094	broad.mit.edu	37	chr9	35703618	35703618	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgagtgcctttggtggccTcatcttccacggcttttact	4	14	9	14	2	2	0	1	0	1	0	3	1	3	0	4	3	2	1	4	3	1	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr9:35703618T>C	ENST00000314888.9	-	48	6766	c.6413A>G	c.(6412-6414)gAg>gGg	p.E2138G	TLN1_ENST00000540444.1_Missense_Mutation_p.E2032G|TLN1_ENST00000464379.1_5'UTR	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2138					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTTGGTGGCCTCATCTTCCAC	0.527																																					p.E2138G													.	TLN1-609	0			c.A6413G						.						127	113	118					9																	35703618		2203	4300	6503	SO:0001583	missense	7094	exon48			GTGGCCTCATCTT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6413A>G	9.37:g.35703618T>C	ENSP00000316029:p.Glu2138Gly	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_006289	0	0	146	146	0	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.691071	0.88735	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.72167	-0.63;-0.62	5.24	5.24	0.73138	.	0.052219	0.85682	D	0.000000	T	0.72558	0.3475	M	0.78916	2.43	0.80722	D	1	P	0.40107	0.703	B	0.39027	0.288	T	0.76334	-0.2997	10	0.51188	T	0.08	-25.1672	15.1481	0.72674	0.0:0.0:0.0:1.0	.	2138	Q9Y490	TLN1_HUMAN	G	2138;2032	ENSP00000316029:E2138G;ENSP00000442981:E2032G	ENSP00000316029:E2138G	E	-	2	0	TLN1	35693618	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.158000	0.64917	1.998000	0.58463	0.459000	0.35465	GAG	.		0.527	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		C	35703618	T	C	35703618	3	2	81	1	0	0	0	0	1	0	0	0	15979	1551	54	3	1252	3	TLN1	9	35703618	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	18240669	35703618	105509813	27	7531											
SVIL	6840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	29811367	29811367	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatagacatggttttgctggGtgagtcaagaaggccctccc	10	10	12	9	0	1	3	1	1	0	2	2	3	2	3	2	3	1	2	2	3	4	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:29811367G>C	ENST00000355867.4	-	16	4113	c.3361C>G	c.(3361-3363)Ccc>Gcc	p.P1121A	SVIL_ENST00000375398.2_Missense_Mutation_p.P1121A|SVIL_ENST00000535393.1_Missense_Mutation_p.P19A|SVIL_ENST00000375400.3_Missense_Mutation_p.P695A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1121					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				GTTTTGCTGGGTGAGTCAAGA	0.468																																					p.P1121A		.											.	SVIL-96	0			c.C3361G						.						70	70	70					10																	29811367		2203	4300	6503	SO:0001583	missense	6840	exon16			TGCTGGGTGAGTC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3361C>G	10.37:g.29811367G>C	ENSP00000348128:p.Pro1121Ala	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	86	29	NM_021738	0	0	8	8	0	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	9.477	1.097117	0.20552	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994	T;T;T;T	0.12255	2.79;2.83;2.83;2.7	5.82	2.6	0.31112	.	0.415737	0.28482	N	0.015187	T	0.07863	0.0197	L	0.32530	0.975	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.21827	-1.0234	10	0.12430	T	0.62	-11.1568	4.4588	0.11656	0.2785:0.2093:0.5123:0.0	.	19;695;1121	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	A	695;1121;1121;19;75	ENSP00000364549:P695A;ENSP00000364547:P1121A;ENSP00000348128:P1121A;ENSP00000445472:P19A	ENSP00000348128:P1121A	P	-	1	0	SVIL	29851373	0.955000	0.32602	0.678000	0.29963	0.512000	0.34134	1.769000	0.38522	0.798000	0.33994	0.563000	0.77884	CCC	.		0.468	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			C	29811367	G	C	29811367	3	2	81	1	0	0	0	0	1	0	0	0	15453	1261	44	4	3375	4	SVIL	10	29811367	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		29811367	105723380	28	7532											
PARD3	56288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	34648076	34648076	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttttttgcatttcttaccTcattgcacttgcttattctc	6	21	3	11	0	3	0	1	0	2	0	4	0	3	0	1	0	4	3	1	0	2	9			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:34648076T>C	ENST00000374789.3	-	14	2391	c.2066A>G	c.(2065-2067)gAg>gGg	p.E689G	PARD3_ENST00000545260.1_Splice_Site_p.E632G|PARD3_ENST00000544292.1_Splice_Site_p.E406G|PARD3_ENST00000346874.4_Splice_Site_p.E689G|PARD3_ENST00000340077.5_Splice_Site_p.E689G|PARD3_ENST00000374768.1_Splice_Site_p.E127G|PARD3_ENST00000545693.1_Splice_Site_p.E676G|PARD3_ENST00000374794.3_Splice_Site_p.E632G|PARD3_ENST00000350537.4_Splice_Site_p.E676G|PARD3_ENST00000374790.3_Splice_Site_p.E632G|PARD3_ENST00000374788.3_Splice_Site_p.E689G|PARD3_ENST00000374776.1_Splice_Site_p.E676G|PARD3_ENST00000374773.1_Splice_Site_p.E689G	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	689					apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				ATTTCTTACCTCATTGCACTT	0.378																																					p.E689G		.											.	PARD3-92	0			c.A2066G						.						167	156	160					10																	34648076		2203	4300	6503	SO:0001630	splice_region_variant	56288	exon14			CTTACCTCATTGC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118"	606745	"par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)"			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2067+1A>G	10.37:g.34648076T>C		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	161	47	NM_001184792	0	0	0	0	0	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	37	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328750	0.41197	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292;ENST00000374768	T;T;T;T;T;T;T;T;T;T;T;T;T	0.20332	2.43;2.43;2.49;2.49;2.52;2.45;2.42;2.43;2.1;2.08;2.16;2.12;2.25	5.56	5.56	0.83823	PDZ/DHR/GLGF (1);	0.414096	0.28706	N	0.014403	T	0.30916	0.0780	L	0.50333	1.59	0.80722	D	1	P;P;B;P;B;P;P;B;B;P;P;B;B;P;B	0.46512	0.719;0.879;0.391;0.719;0.391;0.82;0.719;0.236;0.023;0.597;0.825;0.069;0.076;0.506;0.085	B;B;B;B;B;P;B;B;B;B;P;B;B;P;B	0.49502	0.377;0.409;0.304;0.377;0.304;0.613;0.377;0.076;0.013;0.209;0.533;0.113;0.078;0.502;0.113	T	0.01508	-1.1337	10	0.45353	T	0.12	.	15.7055	0.77577	0.0:0.0:0.0:1.0	.	632;632;676;676;676;689;689;689;632;676;689;689;676;689;406	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;.	G	676;632;689;689;689;632;676;632;676;689;689;406;127	ENSP00000443147:E676G;ENSP00000440857:E632G;ENSP00000363921:E689G;ENSP00000363920:E689G;ENSP00000340591:E689G;ENSP00000363926:E632G;ENSP00000311986:E676G;ENSP00000363922:E632G;ENSP00000363908:E676G;ENSP00000341844:E689G;ENSP00000363905:E689G;ENSP00000444429:E406G;ENSP00000363900:E127G	ENSP00000341844:E689G	E	-	2	0	PARD3	34688082	1.000000	0.71417	0.990000	0.47175	0.190000	0.23558	6.186000	0.72026	2.114000	0.64651	0.533000	0.62120	GAG	.		0.378	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	Missense_Mutation	C	34648076	T	C	34648076	5	2	81	1	0	0	0	0	0	0	1	0	11469	1565	54	3	2087	3	PARD3	10	34648076	Splice_Site	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	4836709	34648076	100886671	29	7533											
TMEM26	219623	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	63212836	63212836	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttaaggaagaccagtccctCcatgctggccggagcactct	9	8	11	13	1	1	1	0	0	1	1	3	3	3	3	4	3	2	3	4	3	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:63212836C>T	ENST00000399298.3	-	1	372	c.4G>A	c.(4-6)Gag>Aag	p.E2K	RP11-809M12.1_ENST00000389640.4_RNA|TMEM26_ENST00000399293.1_Missense_Mutation_p.E2K	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	2						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					ACCAGTCCCTCCATGCTGGCC	0.667																																					p.E2K		.											.	TMEM26-90	0			c.G4A						.						45	54	51					10																	63212836		2126	4227	6353	SO:0001583	missense	219623	exon1			GTCCCTCCATGCT	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.4G>A	10.37:g.63212836C>T	ENSP00000382237:p.Glu2Lys	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	75	28	NM_178505	0	0	1	3	2	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	37	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755604	0.49362	.	.	ENSG00000196932	ENST00000399298;ENST00000399293	.	.	.	5.01	4.1	0.47936	.	0.902018	0.09509	N	0.792586	T	0.46132	0.1377	L	0.50333	1.59	0.34559	D	0.71215	P	0.43392	0.805	B	0.34722	0.188	T	0.53373	-0.8448	9	0.24483	T	0.36	-18.3363	14.8814	0.70537	0.1446:0.8554:0.0:0.0	.	2	Q6ZUK4	TMM26_HUMAN	K	2	.	ENSP00000382232:E2K	E	-	1	0	TMEM26	62882842	1.000000	0.71417	1.000000	0.80357	0.204000	0.24138	4.777000	0.62361	1.315000	0.45114	-0.182000	0.12963	GAG	.		0.667	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		T	63212836	C	T	63212836	3	4	81	1	0	0	0	0	1	0	0	0	16183	864	30	2	1126	2	TMEM26	10	63212836	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	28564760	63212836	72321911	30	7534											
DNAJB12	54788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74100871	74100871	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcttgtcatcgccgaacTggtcatactgcttcctcttc	5	14	8	14	2	4	0	2	0	2	0	7	1	5	0	2	2	3	2	2	2	2	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:74100871T>A	ENST00000444643.2	-	4	847	c.515A>T	c.(514-516)cAg>cTg	p.Q172L	DNAJB12_ENST00000338820.3_Missense_Mutation_p.Q206L|DNAJB12_ENST00000394903.2_Missense_Mutation_p.Q206L|DNAJB12_ENST00000461919.1_5'UTR			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	172	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						ATCGCCGAACTGGTCATACTG	0.602																																					p.Q206L		.											.	DNAJB12-226	0			c.A617T						.						75	67	69					10																	74100871		2203	4300	6503	SO:0001583	missense	54788	exon4			CCGAACTGGTCAT	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"Heat shock proteins / DNAJ (HSP40)"	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.515A>T	10.37:g.74100871T>A	ENSP00000403313:p.Gln172Leu	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	69	24	NM_017626	0	0	22	36	14	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	37		.	.	.	.	.	.	.	.	.	.	T	8.916	0.959878	0.18507	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.73258	-0.73;-0.73;-0.73	5.48	5.48	0.80851	Heat shock protein DnaJ, N-terminal (3);	0.122950	0.64402	D	0.000020	T	0.59528	0.2200	N	0.17474	0.49	0.58432	D	0.999999	D;P	0.54207	0.965;0.879	P;B	0.49887	0.625;0.227	T	0.59721	-0.7401	10	0.02654	T	1	-6.3488	15.622	0.76813	0.0:0.0:0.0:1.0	.	172;172	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	L	206;206;172	ENSP00000345575:Q206L;ENSP00000378363:Q206L;ENSP00000403313:Q172L	ENSP00000345575:Q206L	Q	-	2	0	DNAJB12	73770877	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	5.015000	0.64035	2.086000	0.62901	0.529000	0.55759	CAG	.		0.602	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			A	74100871	T	A	74100871	3	1	81	1	0	0	0	0	1	0	0	0	4628	1580	55	5	632	5	DNAJB12	10	74100871	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	10888035	74100871	61433876	31	7535											
CTSD	1509	broad.mit.edu;bcgsc.ca	37	chr11	1776167	1776167	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacctgccagtaggccttgcGggtgacattcaggtaggaca	9	8	14	10	1	1	1	1	1	0	0	1	3	1	2	3	4	2	2	3	4	2	4	rs373621431		TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:1776167G>A	ENST00000236671.2	-	6	928	c.796C>T	c.(796-798)Cgc>Tgc	p.R266C	RP11-295K3.1_ENST00000427721.1_Silent_p.P136P	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	266					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TAGGCCTTGCGGGTGACATTC	0.627																																					p.R266C													.	CTSD-90	0			c.C796T						.	G	CYS/ARG	0,4404		0,0,2202	101	90	93		796	4.2	1	11		93	1,8597	1.2+/-3.3	0,1,4298	no	missense	CTSD	NM_001909.4	180	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	266/413	1776167	1,13001	2202	4299	6501	SO:0001583	missense	1509	exon6			CCTTGCGGGTGAC	M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"Cathepsins"	2529	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 10"	116840	"cathepsin D (lysosomal aspartyl protease)"	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.796C>T	11.37:g.1776167G>A	ENSP00000236671:p.Arg266Cys	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	105	31	NM_001909	0	2	2822	4322	1498	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	37	CCDS7725.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.084397	0.76642	0.0	1.16E-4	ENSG00000117984	ENST00000236671;ENST00000429746;ENST00000438213	T;T;T	0.62788	0.16;0.0;0.32	4.25	4.25	0.50352	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.000000	0.85682	D	0.000000	D	0.85617	0.5738	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90785	0.4682	10	0.87932	D	0	.	17.2114	0.86931	0.0:0.0:1.0:0.0	.	266	P07339	CATD_HUMAN	C	266;4;251	ENSP00000236671:R266C;ENSP00000402586:R4C;ENSP00000415036:R251C	ENSP00000236671:R266C	R	-	1	0	CTSD	1732743	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	5.338000	0.65947	2.373000	0.80994	0.455000	0.32223	CGC	.		0.627	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909		A	1776167	G	A	1776167	3	1	81	1	0	0	0	0	1	0	0	0	4038	1116	39	1	458	1	CTSD	11	1776167	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		1776167	133230349	32	7536											
C11orf84	144097	broad.mit.edu	37	chr11	63594447	63594448	+	Frame_Shift_Del	DEL	GT	GT	-																															tggatctccaggttatccgcGtgcggatggaggagccccca																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:63594447_63594448delGT	ENST00000294244.4	+	6	1281_1282	c.982_983delGT	c.(982-984)gtgfs	p.V328fs		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	328										endometrium(3)|kidney(1)|lung(3)|skin(1)	8						GGTTATCCGCGTGCGGATGGAG	0.683																																					p.328_328del													.	C11orf84-90	0			c.982_983del						.																																			SO:0001589	frameshift_variant	144097	exon6			ATCCGCGTGCGGA	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.982_983delGT	11.37:g.63594447_63594448delGT	ENSP00000294244:p.Val328fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	24	7	NM_138471	0	0	0	0	0	Q68CV7|Q6PHS2|Q96IH0	Frame_Shift_Del	DEL	ENST00000294244.4	37	CCDS31594.1																																																																																			.		0.683	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471		-	63594448	GT	-	63594447	7	5	81	1	0	1	0	1	0	0	0	0	1671	1145	40	0	1004	0	C11orf84	11	63594447	Frame_Shift_Del	DEL	GT	TCGA-BQ-7046-01A-11D-1961-08	61818280	63594447	71412069	33	7537											
NRXN2	9379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64453122	64453122	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcactcctcctacctggCgcaggtttcgggtgacccgg	4	11	11	15	3	1	1	1	1	1	0	5	1	3	1	4	4	1	2	4	4	1	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:64453122C>T	ENST00000377551.1	-	5	1359	c.1148G>A	c.(1147-1149)cGc>cAc	p.R383H	NRXN2_ENST00000377559.3_Missense_Mutation_p.R359H|NRXN2_ENST00000409571.1_Missense_Mutation_p.R383H|NRXN2_ENST00000265459.6_Missense_Mutation_p.R383H			Q9P2S2	NRX2A_HUMAN	neurexin 2	383	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TCCTACCTGGCGCAGGTTTCG	0.602																																					p.R383H		.											.	NRXN2-232	0			c.G1148A						.						86	87	86					11																	64453122		2201	4297	6498	SO:0001583	missense	9379	exon6			ACCTGGCGCAGGT		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1148G>A	11.37:g.64453122C>T	ENSP00000366774:p.Arg383His	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	124	40	NM_015080	0	0	0	0	0	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.9|25.9	4.684359|4.684359	0.88639|0.88639	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000417749|ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300	.|T;T;T;T;T	.|0.78481	.|-1.18;-1.18;-1.18;-1.18;-1.18	4.0|4.0	4.0|4.0	0.46444|0.46444	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.|0.000000	.|0.44097	.|U	.|0.000496	D|D	0.84969|0.84969	0.5590|0.5590	M|M	0.62088|0.62088	1.915|1.915	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.987;0.998	D|D	0.86396|0.86396	0.1739|0.1739	5|10	.|0.87932	.|D	.|0	.|.	11.9853|11.9853	0.53145|0.53145	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|359;383;136	.|Q9P2S2-2;Q9P2S2;E7EV67	.|.;NRX2A_HUMAN;.	T|H	144|383;359;383;359;383;154	.|ENSP00000366774:R383H;ENSP00000366782:R359H;ENSP00000265459:R383H;ENSP00000386416:R383H;ENSP00000388971:R154H	.|ENSP00000265459:R383H	A|R	-|-	1|2	0|0	NRXN2|NRXN2	64209698|64209698	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.814000|7.814000	0.86154|0.86154	1.951000|1.951000	0.56629|0.56629	0.467000|0.467000	0.42956|0.42956	GCC|CGC	.		0.602	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64453122	C	T	64453122	3	4	81	1	0	0	0	0	1	0	0	0	10692	768	27	1	4331	1	NRXN2	11	64453122	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	858675	64453122	70553394	34	7538											
ROBO4	54538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	124765531	124765531	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggcctcccggggcagtctgGgtcctgaacaaggccgtgta	6	8	15	12	2	1	1	0	1	1	0	3	1	3	1	4	5	1	2	4	5	3	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:124765531G>A	ENST00000306534.3	-	6	1343	c.858C>T	c.(856-858)acC>acT	p.T286T	ROBO4_ENST00000533054.1_Silent_p.T141T|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	286	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GGGCAGTCTGGGTCCTGAACA	0.672																																					p.T286T		.											.	ROBO4-92	0			c.C858T						.						36	44	41					11																	124765531		2193	4283	6476	SO:0001819	synonymous_variant	54538	exon6			AGTCTGGGTCCTG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17985	protein-coding gene	gene with protein product	"magic roundabout"	607528	"roundabout homolog 4 (Drosophila)"			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.858C>T	11.37:g.124765531G>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	117	36	NM_019055	0	0	0	0	0	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			.		0.672	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124765531	G	A	124765531	2	1	81	1	0	0	0	0	0	0	0	1	13548	1219	43	2		2	ROBO4	11	124765531	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	60312409	124765531	10240985	35	7539											
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12334210	12334210	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaacggcgtatggccctcacTtcatcatcagtccagtagat	10	10	9	12	2	4	1	4	0	0	1	5	2	5	1	2	2	1	2	2	2	3	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr12:12334210T>G	ENST00000261349.4	-	6	1216	c.1140A>C	c.(1138-1140)gaA>gaC	p.E380D	LRP6_ENST00000543091.1_Missense_Mutation_p.E380D	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	380	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TGGCCCTCACTTCATCATCAG	0.463																																					p.E380D		.											.	LRP6-661	0			c.A1140C						.						216	181	193					12																	12334210		2203	4300	6503	SO:0001583	missense	4040	exon6			CCTCACTTCATCA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1140A>C	12.37:g.12334210T>G	ENSP00000261349:p.Glu380Asp	Somatic	179	1		WXS	Illumina HiSeq	Phase_I	169	59	NM_002336	0	0	0	3	3	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151454	0.38021	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.96200	-3.94;-3.94	5.82	5.82	0.92795	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000006	D	0.92678	0.7673	L	0.60012	1.86	0.49687	D	0.999818	B;B	0.12013	0.001;0.005	B;B	0.17979	0.003;0.02	D	0.88054	0.2789	10	0.28530	T	0.3	.	8.5301	0.33329	0.0:0.1434:0.0:0.8566	.	380;380	F5H7J9;O75581	.;LRP6_HUMAN	D	380	ENSP00000261349:E380D;ENSP00000442472:E380D	ENSP00000261349:E380D	E	-	3	2	LRP6	12225477	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.255000	0.32909	2.222000	0.72286	0.533000	0.62120	GAA	.		0.463	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12334210	T	G	12334210	3	3	81	1	0	0	0	0	1	0	0	0	8987	1606	56	5	3773	5	LRP6	12	12334210	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08		12334210	121517685	36	7540											
CAND1	55832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	67691215	67691215	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gacttcttgttaatttccatCcttcaattctgacctgtcta	8	18	4	11	0	4	1	1	1	3	0	6	2	6	1	3	0	0	1	3	0	3	7			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr12:67691215C>A	ENST00000545606.1	+	5	957	c.520C>A	c.(520-522)Cct>Act	p.P174T		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	174					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAATTTCCATCCTTCAATTCT	0.408																																					p.P174T		.											.	CAND1-516	0			c.C520A						.						119	122	121					12																	67691215		2203	4300	6503	SO:0001583	missense	55832	exon5			TTCCATCCTTCAA		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.520C>A	12.37:g.67691215C>A	ENSP00000442318:p.Pro174Thr	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	154	35	NM_018448	0	0	10	17	7	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	37	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.751582	0.49257	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.66099	-0.19	5.34	5.34	0.76211	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63546	0.2520	M	0.65498	2.005	0.80722	D	1	B	0.25521	0.128	B	0.27380	0.079	T	0.59968	-0.7354	9	.	.	.	-15.7741	19.057	0.93069	0.0:1.0:0.0:0.0	.	174	Q86VP6	CAND1_HUMAN	T	174;174;16	ENSP00000442318:P174T	.	P	+	1	0	CAND1	65977482	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.879000	0.69690	2.508000	0.84585	0.655000	0.94253	CCT	.		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67691215	C	A	67691215	3	1	81	1	0	0	0	0	1	0	0	0	2621	855	30	4	538	4	CAND1	12	67691215	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	55357005	67691215	66160680	37	7541											
TDG	6996	hgsc.bcm.edu	37	chr12	104359839	104359839	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaagcggagaacgcgggcagGtaataccggggccagcgccg	10	2	18	11	6	0	1	0	0	0	1	0	3	0	1	3	5	4	2	3	5	4	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr12:104359839G>C	ENST00000392872.3	+	1	257		c.e1+1		C12orf73_ENST00000553183.1_5'Flank|TDG_ENST00000266775.9_Splice_Site|C12orf73_ENST00000543740.2_5'Flank|TDG_ENST00000544861.1_Splice_Site	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase						base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		ACGCGGGCAGGTAATACCGGG	0.716								Base excision repair (BER), DNA glycosylases																													.		.											.	TDG-661	0			c.23+1G>C						.						9	11	10					12																	104359839		2158	4241	6399	SO:0001630	splice_region_variant	6996	exon1			GGGCAGGTAATAC	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.23+1G>C	12.37:g.104359839G>C		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	17	2	NM_003211	0	0	0	0	0	Q8IUZ6|Q8IZM3	Splice_Site	SNP	ENST00000392872.3	37	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921936	0.33908	.	.	ENSG00000139372	ENST00000392872;ENST00000537100	.	.	.	5.29	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5561	0.39339	0.0968:0.0:0.9032:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TDG	102883969	1.000000	0.71417	1.000000	0.80357	0.205000	0.24178	4.279000	0.58953	1.225000	0.43566	0.491000	0.48974	.	.		0.716	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		Intron	C	104359839	G	C	104359839	5	2	81	1	0	0	0	0	0	0	1	0	15757	1275	44	4	26	4	TDG	12	104359839	Splice_Site	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	36668624	104359839	29492056	38	7542											
CIT	11113	broad.mit.edu	37	chr12	120150415	120150415	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctgctttggctgtatttgcGagttcggaagcaccaacggc	7	11	12	11	3	0	0	0	0	0	0	1	2	0	1	2	3	4	5	2	3	3	4	rs147828404		TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr12:120150415G>C	ENST00000261833.7	-	35	4591	c.4539C>G	c.(4537-4539)ctC>ctG	p.L1513L	CIT_ENST00000392521.2_Silent_p.L1555L|MIR1178_ENST00000408396.1_RNA|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1513	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTGTATTTGCGAGTTCGGAAG	0.607																																					p.L1555L													.	CIT-399	0			c.C4665G						.						66	65	65					12																	120150415		2203	4300	6503	SO:0001819	synonymous_variant	11113	exon36			ATTTGCGAGTTCG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.4539C>G	12.37:g.120150415G>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	84	4	NM_001206999	0	0	1	1	0	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	5.626	0.300157	0.10622	.	.	ENSG00000122966	ENST00000392520	.	.	.	5.92	-4.88	0.03113	.	.	.	.	.	T	0.39358	0.1075	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41342	-0.9514	4	.	.	.	.	3.3781	0.07244	0.536:0.2225:0.1298:0.1118	.	.	.	.	W	1126	.	.	S	-	2	0	CIT	118634798	0.000000	0.05858	0.979000	0.43373	0.980000	0.70556	-0.772000	0.04694	-0.505000	0.06568	-0.738000	0.03535	TCG	G|1.000;A|0.000		0.607	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		C	120150415	G	C	120150415	2	2	81	1	0	0	0	0	0	0	0	1	3444	1045	37	4		4	CIT	12	120150415	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	15790576	120150415	13701480	39	7543											
CHD8	57680	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21862588	21862588	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggtgtcagggtcatatTccacaccaaacgtagacacc	12	8	9	12	1	2	1	2	0	0	1	3	1	3	1	3	2	1	2	3	2	3	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr14:21862588T>A	ENST00000557364.1	-	31	5710	c.5447A>T	c.(5446-5448)gAa>gTa	p.E1816V	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Missense_Mutation_p.E1537V|CHD8_ENST00000399982.2_Missense_Mutation_p.E1816V|SNORD9_ENST00000362566.1_RNA|SNORD8_ENST00000363915.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1816					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		AGGGTCATATTCCACACCAAA	0.438																																					p.E1816V													.	CHD8-277	0			c.A5447T						.						64	64	64					14																	21862588		1999	4184	6183	SO:0001583	missense	57680	exon30			TCATATTCCACAC	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"helicase with SNF2 domain 1"	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.5447A>T	14.37:g.21862588T>A	ENSP00000451601:p.Glu1816Val	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	26	9	NM_001170629	0	0	2	6	4	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.917857	0.33815	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.85258	-1.96;-1.96;-1.96	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.71316	0.3325	N	0.04335	-0.225	0.80722	D	1	B	0.19073	0.033	B	0.24155	0.051	T	0.67542	-0.5644	10	0.32370	T	0.25	-24.4652	14.5778	0.68262	0.0:0.0:0.0:1.0	.	1537	Q9HCK8-2	.	V	1537;1816;1536;1816	ENSP00000406288:E1537V;ENSP00000382863:E1816V;ENSP00000451601:E1816V	ENSP00000262707:E1536V	E	-	2	0	CHD8	20932428	0.917000	0.31117	1.000000	0.80357	0.950000	0.60333	3.169000	0.50809	2.272000	0.75746	0.460000	0.39030	GAA	.		0.438	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		A	21862588	T	A	21862588	3	1	81	1	0	0	0	0	1	0	0	0	3337	1783	62	5	2330	5	CHD8	14	21862588	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08		21862588	85486952	40	7544											
NR2F2	7026	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	96875635	96875635	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacgtgcgagggctgcaagAgcttcttcaagcgcagcgtg	8	8	14	11	4	3	1	2	0	1	1	3	2	3	1	0	1	5	4	0	1	2	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr15:96875635A>G	ENST00000394166.3	+	1	1690	c.301A>G	c.(301-303)Agc>Ggc	p.S101G	NR2F2_ENST00000394171.2_5'Flank|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000421109.2_Intron	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	101					anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			GGGCTGCAAGAGCTTCTTCAA	0.612																																					p.S101G		.											.	NR2F2-228	0			c.A301G						.						66	53	57					15																	96875635		2197	4298	6495	SO:0001583	missense	7026	exon1			TGCAAGAGCTTCT	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.301A>G	15.37:g.96875635A>G	ENSP00000377721:p.Ser101Gly	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	35	14	NM_021005	0	0	45	88	43	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	37	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.468861	0.63625	.	.	ENSG00000185551	ENST00000394166	D	0.96745	-4.11	4.61	4.61	0.57282	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.187668	0.42821	N	0.000656	D	0.91784	0.7401	N	0.01235	-0.94	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.88109	0.2824	10	0.02654	T	1	.	12.8472	0.57837	1.0:0.0:0.0:0.0	.	101	P24468	COT2_HUMAN	G	101	ENSP00000377721:S101G	ENSP00000377721:S101G	S	+	1	0	NR2F2	94676639	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.257000	0.72480	1.705000	0.51264	0.379000	0.24179	AGC	.		0.612	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			G	96875635	A	G	96875635	3	3	81	1	0	0	0	0	1	0	0	0	10654	304	11	3	350	3	NR2F2	15	96875635	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08		96875635	5655757	41	7545											
RSPRY1	89970	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	57261323	57261323	+	Frame_Shift_Del	DEL	A	A	-																															gccggcagctgatttggtacAatgccagaagtaagcctcac																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr16:57261323delA	ENST00000537866.1	+	11	2104	c.1231delA	c.(1231-1233)aatfs	p.N411fs	RSPRY1_ENST00000394420.4_Frame_Shift_Del_p.N411fs|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	411	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						GATTTGGTACAATGCCAGAAG	0.453																																					p.N411fs		.											.	RSPRY1-91	0			c.1231delA						.						122	104	110					16																	57261323		2198	4300	6498	SO:0001589	frameshift_variant	89970	exon11			.	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1231delA	16.37:g.57261323delA	ENSP00000443176:p.Asn411fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	99	54	NM_133368	0	0	0	0	0	Q6UX21|Q8ND53	Frame_Shift_Del	DEL	ENST00000537866.1	37	CCDS10775.1																																																																																			.		0.453	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		-	57261323	A	-	57261323	7	5	81	1	0	1	0	1	0	0	0	0	13745	130	5	0	1269	0	RSPRY1	16	57261323	Frame_Shift_Del	DEL	A	TCGA-BQ-7046-01A-11D-1961-08		57261323	33093430	42	7546											
MYBBP1A	10514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4451584	4451584	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccggtgcctgcttgaactgCgtgctgagggtctgcaacag	6	9	14	12	2	1	2	0	2	1	0	1	2	1	2	2	2	7	3	2	2	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:4451584C>T	ENST00000254718.4	-	12	1884	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	MYBBP1A_ENST00000381556.2_Silent_p.T526T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	526	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GCTTGAACTGCGTGCTGAGGG	0.637																																					p.T526T		.											.	MYBBP1A-92	0			c.G1578A						.						64	64	64					17																	4451584		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon12			GAACTGCGTGCTG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.1578G>A	17.37:g.4451584C>T		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	198	111	NM_014520	0	0	6	27	21	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			.		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4451584	C	T	4451584	2	4	81	1	0	0	0	0	0	0	0	1	10033	755	27	1		1	MYBBP1A	17	4451584	Silent	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		4451584	76743626	43	7547											
KRT40	125115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39140321	39140321	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccccaccaagcagggactatTacaactcccagtaaagtagc	14	6	7	14	0	0	0	0	0	0	0	1	1	1	1	4	1	4	3	4	1	7	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:39140321T>A	ENST00000398486.2	-	3	365	c.205A>T	c.(205-207)Aat>Tat	p.N69Y	KRT40_ENST00000377755.4_Missense_Mutation_p.N69Y	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	69	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CAGGGACTATTACAACTCCCA	0.547																																					p.N69Y		.											.	.	0			c.A205T						.						114	117	116					17																	39140321		2173	4258	6431	SO:0001583	missense	125115	exon3			GACTATTACAACT	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"-", "Intermediate filaments type I, keratins (acidic)"	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.205A>T	17.37:g.39140321T>A	ENSP00000381500:p.Asn69Tyr	Somatic	166	1		WXS	Illumina HiSeq	Phase_I	228	126	NM_182497	0	0	0	0	0	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.253146	0.22965	.	.	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.83419	-1.72;-1.72	4.54	-0.567	0.11763	.	0.221645	0.22876	N	0.054568	T	0.74764	0.3759	M	0.71036	2.16	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.57277	-0.7839	10	0.21014	T	0.42	.	4.4502	0.11617	0.0:0.3063:0.3369:0.3568	.	69	Q6A162	K1C40_HUMAN	Y	69	ENSP00000366984:N69Y;ENSP00000381500:N69Y	ENSP00000366984:N69Y	N	-	1	0	KRT40	36393847	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.054000	0.14205	-0.220000	0.09988	0.482000	0.46254	AAT	.		0.547	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497		A	39140321	T	A	39140321	3	1	81	1	0	0	0	0	1	0	0	0	8499	1754	61	5	1118	5	KRT40	17	39140321	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	34688737	39140321	42054889	44	7548											
ADAM11	4185	broad.mit.edu;bcgsc.ca	37	chr17	42855164	42855164	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggaccatcgctgcctgcCagcttctgccttcaacttca	6	11	7	17	1	3	0	2	0	1	0	4	1	3	1	5	1	5	2	5	1	1	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:42855164C>G	ENST00000200557.6	+	23	2172	c.2003C>G	c.(2002-2004)cCa>cGa	p.P668R	ADAM11_ENST00000535346.1_Missense_Mutation_p.P468R	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	668	Cys-rich.				integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				CGCTGCCTGCCAGCTTCTGCC	0.657																																					p.P668R													.	ADAM11-227	0			c.C2003G						.						43	40	41					17																	42855164		2203	4300	6503	SO:0001583	missense	4185	exon23			GCCTGCCAGCTTC	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"ADAM metallopeptidase domain containing"	189	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, cysteine-rich protein"	155120	"a disintegrin and metalloproteinase domain 11"	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.2003C>G	17.37:g.42855164C>G	ENSP00000200557:p.Pro668Arg	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	72	48	NM_002390	0	0	1	1	0	Q14808|Q14809|Q14810	Missense_Mutation	SNP	ENST00000200557.6	37	CCDS11486.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.260507	0.80246	.	.	ENSG00000073670	ENST00000200557;ENST00000535346	T;T	0.02067	4.47;4.87	4.36	4.36	0.52297	ADAM, cysteine-rich (1);	0.000000	0.85682	D	0.000000	T	0.11879	0.0289	M	0.73430	2.235	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.967;0.998	T	0.01776	-1.1276	10	0.44086	T	0.13	.	15.8196	0.78628	0.0:1.0:0.0:0.0	.	468;668	B4DKD2;O75078	.;ADA11_HUMAN	R	668;468	ENSP00000200557:P668R;ENSP00000443773:P468R	ENSP00000200557:P668R	P	+	2	0	ADAM11	40210690	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.550000	0.82173	2.256000	0.74724	0.561000	0.74099	CCA	.		0.657	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390		G	42855164	C	G	42855164	3	3	81	1	0	0	0	0	1	0	0	0	235	594	21	4	2093	4	ADAM11	17	42855164	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	3714843	42855164	38340046	45	7549											
GPRC5C	55890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72436053	72436053	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacaacctgtgtgaccgctcTggggcgtggggcatcgtcct	5	10	14	12	3	1	1	0	1	1	0	3	1	2	1	3	4	2	2	3	4	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:72436053T>A	ENST00000481232.1	+	2	784	c.273T>A	c.(271-273)tcT>tcA	p.S91S	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Silent_p.S58S|GPRC5C_ENST00000392627.1_Silent_p.S91S			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	46					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						GTGACCGCTCTGGGGCGTGGG	0.662																																					p.S91S		.											.	GPRC5C-525	0			c.T273A						.						62	59	60					17																	72436053		2203	4299	6502	SO:0001819	synonymous_variant	55890	exon2			CCGCTCTGGGGCG	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"GPCR / Class C : Orphans"	13309	protein-coding gene	gene with protein product		605949	"G protein-coupled receptor, family C, group 5, member C"			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000481232.1:c.273T>A	17.37:g.72436053T>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	178	98	NM_022036	0	0	57	250	193	B5BUN4|Q2NL85|Q9NZG5	Silent	SNP	ENST00000481232.1	37																																																																																				.		0.662	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000145095.2			A	72436053	T	A	72436053	2	1	81	1	0	0	0	0	0	0	0	1	6747	1567	55	5		5	GPRC5C	17	72436053	Silent	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	29580889	72436053	8759157	46	7550											
FZR1	51343	broad.mit.edu;bcgsc.ca	37	chr19	3525916	3525916	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagctccccagtgtcctcGcccagcaagcacggagaccg	8	4	11	18	3	0	1	0	0	0	1	3	2	2	1	6	1	3	3	6	1	1	0	rs201664307		TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr19:3525916G>A	ENST00000395095.3	+	2	120	c.120G>A	c.(118-120)tcG>tcA	p.S40S	FZR1_ENST00000441788.2_Silent_p.S40S|FZR1_ENST00000313639.8_Silent_p.S40S	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	40					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGTGTCCTCGCCCAGCAAGC	0.647																																					p.S40S													.	FZR1-227	0			c.G120A						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	38	37	37		120,120,120	-9.3	0.9	19		37	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	FZR1	NM_001136197.1,NM_001136198.1,NM_016263.3	,,	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	,,	40/405,40/497,40/494	3525916	1,12999	2203	4297	6500	SO:0001819	synonymous_variant	51343	exon2			GTCCTCGCCCAGC	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"WD repeat domain containing"	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.120G>A	19.37:g.3525916G>A		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	39	11	NM_001136197	0	0	12	18	6	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Silent	SNP	ENST00000395095.3	37	CCDS45916.1																																																																																			G|0.999;A|0.001		0.647	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3525916	G	A	3525916	2	1	81	1	0	0	0	0	0	0	0	1	6157	1074	38	1		1	FZR1	19	3525916	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		3525916	55603067	47	7551											
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606636	21606636	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttagtattttctcaacccTtactaaacataagataattc	14	16	2	9	0	1	1	1	0	1	1	3	1	1	1	1	0	3	1	1	0	8	10			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr19:21606636T>C	ENST00000355504.4	+	2	1057	c.791T>C	c.(790-792)cTt>cCt	p.L264P	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.L392P	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	264					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)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TTCTCAACCCTTACTAAACAT	0.368																																					p.L392P		.											.	ZNF493-516	0			c.T1175C						.						38	41	40					19																	21606636		2197	4293	6490	SO:0001583	missense	284443	exon4			CAACCCTTACTAA	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"Zinc fingers, C2H2-type", "-"	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.791T>C	19.37:g.21606636T>C	ENSP00000347691:p.Leu264Pro	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_001076678	0	0	5	6	1	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	12.34	1.909058	0.33721	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.53857	0.6;0.6	1.03	1.03	0.20045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.72898	0.3518	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.72327	-0.4327	9	0.87932	D	0	.	6.9938	0.24769	0.0:0.0:0.0:1.0	.	264;392	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	P	392;264	ENSP00000376110:L392P;ENSP00000347691:L264P	ENSP00000347691:L264P	L	+	2	0	ZNF493	21398476	0.172000	0.23043	0.012000	0.15200	0.012000	0.07955	3.865000	0.56033	0.379000	0.24794	0.373000	0.22412	CTT	.		0.368	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		C	21606636	T	C	21606636	3	2	81	1	0	0	0	0	1	0	0	0	17976	1609	56	3	1252	3	ZNF493	19	21606636	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	18080720	21606636	37522347	48	7552											
C20orf3	57136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	24944513	24944513	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagagcccaggtacaggtgcCcatcgtgttcgtgcacctcg	8	8	12	13	3	0	1	0	0	0	1	3	1	0	1	3	2	4	3	3	2	2	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr20:24944513C>T	ENST00000217456.2	-	9	1477	c.1187G>A	c.(1186-1188)gGg>gAg	p.G396E	APMAP_ENST00000447138.1_3'UTR	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	396					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										GTACAGGTGCCCATCGTGTTC	0.627																																					p.G396E		.											.	.	0			c.G1187A						.						103	94	97					20																	24944513		2203	4300	6503	SO:0001583	missense	57136	exon9			AGGTGCCCATCGT	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"chromosome 20 open reading frame 3"	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.1187G>A	20.37:g.24944513C>T	ENSP00000217456:p.Gly396Glu	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	139	24	NM_020531	0	0	109	153	44	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	37	CCDS13166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.06|17.06	3.291373|3.291373	0.59976|0.59976	.|.	.|.	ENSG00000101474|ENSG00000101474	ENST00000217456|ENST00000451442	T|T	0.36520|0.35605	1.25|1.3	4.86|4.86	4.86|4.86	0.63082|0.63082	Six-bladed beta-propeller, TolB-like (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.58708|0.58708	0.2141|0.2141	M|M	0.82132|0.82132	2.575|2.575	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.973|.	D;P|.	0.68192|.	0.956;0.685|.	T|T	0.64643|0.64643	-0.6359|-0.6359	10|8	0.44086|0.62326	T|D	0.13|0.03	-18.3321|-18.3321	15.4972|15.4972	0.75662|0.75662	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	388;396|.	A2A2F9;Q9HDC9|.	.;APMAP_HUMAN|.	E|S	396|389	ENSP00000217456:G396E|ENSP00000395874:G389S	ENSP00000217456:G396E|ENSP00000395874:G389S	G|G	-|-	2|1	0|0	C20orf3|C20orf3	24892513|24892513	1.000000|1.000000	0.71417|0.71417	0.502000|0.502000	0.27614|0.27614	0.164000|0.164000	0.22412|0.22412	7.726000|7.726000	0.84824|0.84824	2.216000|2.216000	0.71823|0.71823	0.561000|0.561000	0.74099|0.74099	GGG|GGC	.		0.627	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		T	24944513	C	T	24944513	3	4	81	1	0	0	0	0	1	0	0	0	2115	623	22	2	67	2	C20orf3	20	24944513	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		24944513	38081007	49	7553											
NCOA3	8202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	46254125	46254125	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accaccttctgtcttttcagGaaaaactatttccaatgatg	12	14	5	10	0	3	1	1	1	2	0	4	2	4	2	3	1	1	0	3	1	4	5			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr20:46254125G>T	ENST00000371998.3	+	5	448	c.257G>T	c.(256-258)gGa>gTa	p.G86V	NCOA3_ENST00000341724.6_Splice_Site_p.G86V|NCOA3_ENST00000372004.3_Splice_Site_p.G86V|NCOA3_ENST00000371997.3_Splice_Site_p.G86V			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	86					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GTCTTTTCAGGAAAAACTATT	0.378																																					p.G86V		.											.	NCOA3-229	0			c.G257T						.						98	89	92					20																	46254125		2203	4300	6503	SO:0001630	splice_region_variant	8202	exon5			TTTCAGGAAAAAC	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.257-1G>T	20.37:g.46254125G>T		Somatic	63	1		WXS	Illumina HiSeq	Phase_I	105	45	NM_181659	0	0	0	0	0	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920015	0.73098	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.02472	4.28;4.43;4.44;4.29	5.62	5.62	0.85841	Helix-loop-helix DNA-binding (3);	0.000000	0.85682	D	0.000000	T	0.12603	0.0306	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.994;0.994;0.995;0.996	D;D;D;D;D	0.97110	1.0;0.922;0.922;0.964;0.943	T	0.01858	-1.1259	9	.	.	.	.	19.6585	0.95853	0.0:0.0:1.0:0.0	.	86;90;86;86;86	Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;NCOA3_HUMAN	V	86	ENSP00000342123:G86V;ENSP00000361073:G86V;ENSP00000361066:G86V;ENSP00000361065:G86V	.	G	+	2	0	NCOA3	45687532	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.062000	0.89475	2.657000	0.90304	0.467000	0.42956	GGA	.		0.378	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	Missense_Mutation	T	46254125	G	T	46254125	5	4	81	1	0	0	0	0	0	0	1	0	10256	1188	41	4	267	4	NCOA3	20	46254125	Splice_Site	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	21309612	46254125	16771395	50	7554											
BACH1	571	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	30698866	30698866	+	Frame_Shift_Del	DEL	A	A	-																															ttggaactgacagagtccgtActggggaatctagtgtcaaa																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr21:30698866delA	ENST00000399921.1	+	3	964	c.721delA	c.(721-723)actfs	p.T241fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.T241fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						CAGAGTCCGTACTGGGGAATC	0.453																																					p.T241fs		.											.	BACH1-92	0			c.721delA						.						57	59	58					21																	30698866		2203	4300	6503	SO:0001589	frameshift_variant	571	exon3			.	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"BTB/POZ domain containing", "basic leucine zipper proteins"	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.721delA	21.37:g.30698866delA	ENSP00000382805:p.Thr241fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	113	38	NM_206866	0	0	0	0	0	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	37	CCDS13585.1																																																																																			.		0.453	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		-	30698866	A	-	30698866	7	5	81	1	0	1	0	1	0	0	0	0	1284	391	14	0	727	0	BACH1	21	30698866	Frame_Shift_Del	DEL	A	TCGA-BQ-7046-01A-11D-1961-08		30698866	17431029	51	7555											
DSCAM	1826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	41459172	41459172	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agacaatgtctttcatccatGgagtagtcactgtcccactg	10	12	8	11	0	3	1	2	0	1	1	5	2	5	2	2	1	0	1	2	1	2	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr21:41459172G>A	ENST00000400454.1	-	22	4370	c.3893C>T	c.(3892-3894)cCa>cTa	p.P1298L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1298	Ig-like C2-type 10.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTTCATCCATGGAGTAGTCAC	0.488																																					p.P1298L	Melanoma(134;970 1778 1785 21664 32388)	.											.	DSCAM-101	0			c.C3893T						.						152	147	149					21																	41459172		1995	4169	6164	SO:0001583	missense	1826	exon22			ATCCATGGAGTAG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.3893C>T	21.37:g.41459172G>A	ENSP00000383303:p.Pro1298Leu	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	137	14	NM_001271534	0	0	0	0	0	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.670051	0.88348	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.25912	1.77;1.77	4.71	4.71	0.59529	Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41488	0.1161	L	0.33339	1.005	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.35226	-0.9797	10	0.59425	D	0.04	.	18.0505	0.89347	0.0:0.0:1.0:0.0	.	1298	O60469	DSCAM_HUMAN	L	1298;1050	ENSP00000383303:P1298L;ENSP00000385342:P1050L	ENSP00000383303:P1298L	P	-	2	0	DSCAM	40381042	1.000000	0.71417	0.262000	0.24481	0.988000	0.76386	9.633000	0.98432	2.316000	0.78162	0.563000	0.77884	CCA	.		0.488	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41459172	G	A	41459172	3	1	81	1	0	0	0	0	1	0	0	0	4779	1348	47	2	2193	2	DSCAM	21	41459172	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	10760306	41459172	6670723	52	7556											
SNAP29	9342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	21237785	21237785	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccagaggggctggttctGccatgagtactgatgcttac	7	11	12	11	0	1	3	0	2	1	1	2	3	2	3	3	3	4	4	3	3	2	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr22:21237785G>C	ENST00000215730.7	+	4	675	c.547G>C	c.(547-549)Gcc>Ccc	p.A183P		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	183					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			GGCTGGTTCTGCCATGAGTAC	0.498																																					p.A183P		.											.	SNAP29-278	0			c.G547C						.						218	198	205					22																	21237785		2203	4300	6503	SO:0001583	missense	9342	exon4			GGTTCTGCCATGA	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"soluble 29 kDa NSF attachment protein"	604202	"synaptosomal-associated protein, 29kD"			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.547G>C	22.37:g.21237785G>C	ENSP00000215730:p.Ala183Pro	Somatic	385	1		WXS	Illumina HiSeq	Phase_I	327	100	NM_004782	0	0	19	42	23		Missense_Mutation	SNP	ENST00000215730.7	37	CCDS13784.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.944634	0.34283	.	.	ENSG00000099940	ENST00000215730;ENST00000439214	.	.	.	4.17	-2.31	0.06765	SNAP-25 (1);	0.598056	0.18243	N	0.147169	T	0.17408	0.0418	N	0.22421	0.69	0.09310	N	1	P	0.41524	0.753	P	0.44921	0.464	T	0.12319	-1.0552	9	0.33141	T	0.24	-0.0293	2.763	0.05312	0.3197:0.0:0.3417:0.3386	.	183	O95721	SNP29_HUMAN	P	183;90	.	ENSP00000215730:A183P	A	+	1	0	SNAP29	19567785	0.014000	0.17966	0.001000	0.08648	0.009000	0.06853	0.143000	0.16115	-0.176000	0.10707	-0.218000	0.12543	GCC	.		0.498	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782		C	21237785	G	C	21237785	3	2	81	1	0	0	0	0	1	0	0	0	14863	1319	46	4	561	4	SNAP29	22	21237785	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		21237785	30066781	53	7557											
HIC2	23119	hgsc.bcm.edu	37	chr22	21799620	21799620	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaagcgagccggcaagcccTttggctctgggagggcgggg	6	6	18	11	3	2	0	1	0	1	0	2	2	2	1	2	6	3	2	2	6	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr22:21799620T>C	ENST00000443632.2	+	2	808	c.436T>C	c.(436-438)Ttt>Ctt	p.F146L	HIC2_ENST00000407598.2_Missense_Mutation_p.F146L|HIC2_ENST00000407464.2_Missense_Mutation_p.F146L			Q96JB3	HIC2_HUMAN	hypermethylated in cancer 2	146					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)				CGGCAAGCCCTTTGGCTCTGG	0.692																																					p.F146L	NSCLC(23;437 858 2282 27947 40366)	.											.	HIC2-703	0			c.T436C						.						11	15	13					22																	21799620		2165	4263	6428	SO:0001583	missense	23119	exon3			AAGCCCTTTGGCT	AB028943	CCDS13789.1	22q11.21	2013-01-09			ENSG00000169635	ENSG00000169635		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18595	protein-coding gene	gene with protein product		607712				11554746	Standard	NM_015094		Approved	KIAA1020, HRG22, ZBTB30, ZNF907	uc002zur.4	Q96JB3	OTTHUMG00000150781	ENST00000443632.2:c.436T>C	22.37:g.21799620T>C	ENSP00000387757:p.Phe146Leu	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_015094	0	0	0	0	0	Q504T6|Q96KR3|Q9NSM9|Q9UPX9	Missense_Mutation	SNP	ENST00000443632.2	37	CCDS13789.1	.	.	.	.	.	.	.	.	.	.	T	9.525	1.109373	0.20714	.	.	ENSG00000169635	ENST00000407464;ENST00000407598;ENST00000443632	T;T;T	0.08634	3.07;3.07;3.07	5.01	5.01	0.66863	.	0.114448	0.64402	N	0.000011	T	0.07007	0.0178	L	0.28556	0.865	0.41520	D	0.98839	B	0.12630	0.006	B	0.12837	0.008	T	0.32561	-0.9902	10	0.18276	T	0.48	.	12.7212	0.57144	0.0:0.0:0.0:1.0	.	146	Q96JB3	HIC2_HUMAN	L	146	ENSP00000385319:F146L;ENSP00000384889:F146L;ENSP00000387757:F146L	ENSP00000385319:F146L	F	+	1	0	HIC2	20129620	0.999000	0.42202	0.997000	0.53966	0.275000	0.26752	2.402000	0.44521	2.098000	0.63641	0.459000	0.35465	TTT	.		0.692	HIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320061.2			C	21799620	T	C	21799620	3	2	81	1	0	0	0	0	1	0	0	0	7123	1609	56	3	442	3	HIC2	22	21799620	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	561835	21799620	29504946	54	7558											
KIAA0090	23065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19566346	19566346	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagcaaactcagcgttccaTaatggtactgcagcagagca	14	8	9	10	1	1	1	1	0	0	1	2	1	2	1	1	1	7	6	1	1	4	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:19566346T>C	ENST00000477853.1	-	8	962	c.920A>G	c.(919-921)tAt>tGt	p.Y307C	EMC1_ENST00000375208.3_Missense_Mutation_p.Y285C|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375199.3_Missense_Mutation_p.Y307C	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	307						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CAGCGTTCCATAATGGTACTG	0.547																																					p.Y307C		.											.	.	0			c.A920G						.						81	83	82					1																	19566346		2203	4300	6503	SO:0001583	missense	23065	exon8			GTTCCATAATGGT		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"KIAA0090"	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.920A>G	1.37:g.19566346T>C	ENSP00000420608:p.Tyr307Cys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	81	28	NM_001271427	0	0	5	12	7	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	.	.	.	.	.	.	.	.	.	.	T	6.476	0.456042	0.12283	.	.	ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208	T;T;T	0.21932	1.98;1.98;1.98	5.63	3.3	0.37823	.	0.510435	0.24343	N	0.039353	T	0.10252	0.0251	N	0.08118	0	0.09310	N	0.999998	B;P;P;B	0.35456	0.218;0.502;0.502;0.369	B;B;B;B	0.36418	0.161;0.161;0.224;0.112	T	0.17653	-1.0362	10	0.36615	T	0.2	-5.9075	8.4851	0.33067	0.1216:0.0:0.1381:0.7404	.	285;307;307;307	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.;.;.;K0090_HUMAN	C	307;307;285	ENSP00000420608:Y307C;ENSP00000364345:Y307C;ENSP00000364354:Y285C	ENSP00000364345:Y307C	Y	-	2	0	KIAA0090	19438933	0.998000	0.40836	0.449000	0.26957	0.158000	0.22134	3.412000	0.52679	2.137000	0.66172	0.533000	0.62120	TAT	.		0.547	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		C	19566346	T	C	19566346	3	2	82	1	0	0	0	0	1	0	0	0	8174	1406	49	3	2125	3	KIAA0090	1	19566346	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		19566346	229684275	1	7559											
LRRC8D	55144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90399759	90399759	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccattatttgtgtttatggcTttatctgcctctacactctc	6	19	5	11	0	3	0	0	0	3	0	4	0	3	0	2	1	2	2	2	1	4	7			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:90399759T>A	ENST00000337338.5	+	3	1539	c.1132T>A	c.(1132-1134)Ttt>Att	p.F378I	LRRC8D_ENST00000394593.3_Missense_Mutation_p.F378I	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	378					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		TGTTTATGGCTTTATCTGCCT	0.373																																					p.F378I		.											.	LRRC8D-92	0			c.T1132A						.						118	117	117					1																	90399759		2203	4300	6503	SO:0001583	missense	55144	exon3			TATGGCTTTATCT	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.1132T>A	1.37:g.90399759T>A	ENSP00000338887:p.Phe378Ile	Somatic	167	1		WXS	Illumina HiSeq	Phase_I	143	49	NM_018103	0	0	9	12	3	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	37	CCDS726.1	.	.	.	.	.	.	.	.	.	.	T	9.959	1.222158	0.22457	.	.	ENSG00000171492	ENST00000337338;ENST00000394593	T;T	0.42513	0.97;0.97	5.86	4.72	0.59763	.	0.393773	0.26919	N	0.021824	T	0.09335	0.0230	N	0.14661	0.345	0.35287	D	0.781816	B	0.10296	0.003	B	0.12156	0.007	T	0.14811	-1.0459	9	.	.	.	.	6.7914	0.23701	0.1355:0.0701:0.0:0.7944	.	378	Q7L1W4	LRC8D_HUMAN	I	378	ENSP00000338887:F378I;ENSP00000378093:F378I	.	F	+	1	0	LRRC8D	90172347	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	2.363000	0.44178	1.004000	0.39156	0.482000	0.46254	TTT	.		0.373	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		A	90399759	T	A	90399759	3	1	82	1	0	0	0	0	1	0	0	0	9049	1609	56	5	1134	5	LRRC8D	1	90399759	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	70833413	90399759	158850862	2	7560											
GFI1	2672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	92948601	92948601	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcctgcatttgaagtgcTgtctgcaaagaggaggcagg	9	8	14	10	1	1	2	0	1	1	1	1	3	1	3	2	3	3	4	2	3	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:92948601T>C	ENST00000370332.1	-	3	436	c.118A>G	c.(118-120)Agc>Ggc	p.S40G	GFI1_ENST00000294702.5_Missense_Mutation_p.S40G|GFI1_ENST00000483490.1_5'UTR|GFI1_ENST00000427103.1_Missense_Mutation_p.S40G	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	40					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		TTTGAAGTGCTGTCTGCAAAG	0.667																																					p.S40G		.											.	GFI1-514	0			c.A118G						.						26	32	30					1																	92948601		2200	4294	6494	SO:0001583	missense	2672	exon3			AAGTGCTGTCTGC	U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"Zinc fingers, C2H2-type"	4237	protein-coding gene	gene with protein product		600871	"growth factor independent 1"	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.118A>G	1.37:g.92948601T>C	ENSP00000359357:p.Ser40Gly	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	55	22	NM_005263	0	0	0	0	0	Q8N564	Missense_Mutation	SNP	ENST00000370332.1	37	CCDS30773.1	.	.	.	.	.	.	.	.	.	.	T	8.861	0.946887	0.18356	.	.	ENSG00000162676	ENST00000370332;ENST00000427103;ENST00000294702	T;T;T	0.09255	3.0;3.0;3.0	5.18	-2.98	0.05513	.	0.726593	0.13857	N	0.357995	T	0.01029	0.0034	N	0.12182	0.205	0.19775	N	0.999954	B	0.02656	0.0	B	0.01281	0.0	T	0.46133	-0.9213	10	0.06891	T	0.86	-6.9644	7.2257	0.26014	0.1163:0.4299:0.0:0.4538	.	40	Q99684	GFI1_HUMAN	G	40	ENSP00000359357:S40G;ENSP00000399719:S40G;ENSP00000294702:S40G	ENSP00000294702:S40G	S	-	1	0	GFI1	92721189	0.003000	0.15002	0.979000	0.43373	0.161000	0.22273	-0.880000	0.04183	-0.481000	0.06792	-0.379000	0.06801	AGC	.		0.667	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263		C	92948601	T	C	92948601	3	2	82	1	0	0	0	0	1	0	0	0	6359	1580	55	3	1170	3	GFI1	1	92948601	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	2548842	92948601	156302020	3	7561											
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94506770	94506770	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcagacacctacctcacTgcctttcctttggctctgga	6	12	9	14	0	2	1	1	0	1	1	3	2	3	2	4	3	2	2	4	3	1	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:94506770T>A	ENST00000370225.3	-	23	3603	c.3517A>T	c.(3517-3519)Agt>Tgt	p.S1173C		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1173					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CCTACCTCACTGCCTTTCCTT	0.567																																					p.S1173C		.											.	ABCA4-162	0			c.A3517T						.						102	94	97					1																	94506770		2203	4300	6503	SO:0001583	missense	24	exon23			CCTCACTGCCTTT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3517A>T	1.37:g.94506770T>A	ENSP00000359245:p.Ser1173Cys	Somatic	83	1		WXS	Illumina HiSeq	Phase_I	60	19	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.445557	0.43429	.	.	ENSG00000198691	ENST00000370225	D	0.91351	-2.83	5.75	-0.546	0.11840	.	1.303050	0.04432	N	0.369442	T	0.43211	0.1237	N	0.00510	-1.415	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45659	-0.9246	10	0.21014	T	0.42	.	0.3843	0.00400	0.2675:0.2846:0.2189:0.229	.	1173	P78363	ABCA4_HUMAN	C	1173	ENSP00000359245:S1173C	ENSP00000359245:S1173C	S	-	1	0	ABCA4	94279358	0.000000	0.05858	0.001000	0.08648	0.795000	0.44927	0.319000	0.19522	-0.113000	0.11958	-0.339000	0.08088	AGT	.		0.567	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94506770	T	A	94506770	3	1	82	1	0	0	0	0	1	0	0	0	34	1580	55	5	3416	5	ABCA4	1	94506770	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	1558169	94506770	154743851	4	7562											
TTF2	8458	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	117633172	117633172	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgatactgccccagcgtAaatttcagttgcaccattta	11	12	8	10	1	1	1	1	1	0	0	1	1	1	1	3	1	4	3	3	1	4	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:117633172A>T	ENST00000369466.4	+	15	2559	c.2515A>T	c.(2515-2517)Aaa>Taa	p.K839*		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	839					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		GCCCCAGCGTAAATTTCAGTT	0.368																																					p.K839X													.	TTF2-91	0			c.A2515T						.						128	121	124					1																	117633172		2203	4300	6503	SO:0001587	stop_gained	8458	exon15			CAGCGTAAATTTC	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 6"	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.2515A>T	1.37:g.117633172A>T	ENSP00000358478:p.Lys839*	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	57	13	NM_003594	0	0	3	3	0	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Nonsense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	.	.	.	.	.	.	.	.	.	.	A	39	7.341644	0.98224	.	.	ENSG00000116830	ENST00000369466	.	.	.	5.1	1.38	0.22167	.	0.596567	0.14006	N	0.347765	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.7907	5.3282	0.15918	0.5193:0.3843:0.0964:0.0	.	.	.	.	X	839	.	ENSP00000358478:K839X	K	+	1	0	TTF2	117434695	0.010000	0.17322	0.403000	0.26384	0.986000	0.74619	0.858000	0.27845	0.413000	0.25759	0.533000	0.62120	AAA	.		0.368	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			T	117633172	A	T	117633172	4	4	82	1	0	0	0	0	0	1	0	0	16752	363	13	5	2573	5	TTF2	1	117633172	Nonsense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	23126402	117633172	131617449	5	7563											
NBPF9	400818	broad.mit.edu	37	chr1	144823878	144823878	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggactcactgtatagatgttAttcaactccttcaggttgtc	9	15	8	9	0	3	1	3	0	0	1	5	2	4	2	1	2	1	3	1	2	4	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:144823878A>C	ENST00000281815.8	+	9	946	c.200A>C	c.(199-201)tAt>tCt	p.Y67S	NBPF9_ENST00000440491.2_Missense_Mutation_p.Y382S|NBPF9_ENST00000338347.4_Missense_Mutation_p.Y382S|NBPF9_ENST00000468645.1_3'UTR			Q3BBW0	NBPF9_HUMAN	neuroblastoma breakpoint family, member 9	715						cytoplasm (GO:0005737)				NS(2)|prostate(1)	3						TATAGATGTTATTCAACTCCT	0.483																																					.													.	.	0			.						.																																			SO:0001583	missense	400818	.			GATGTTATTCAAC		CCDS72895.1, CCDS72896.1	1q21.1	2013-01-17			ENSG00000168614	ENSG00000269713		"neuroblastoma breakpoint family"	31991	protein-coding gene	gene with protein product		613999				16079250	Standard	NM_001037675		Approved	AE01		Q3BBW0	OTTHUMG00000013845	ENST00000281815.8:c.200A>C	1.37:g.144823878A>C	ENSP00000281815:p.Tyr67Ser	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	53	4	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000281815.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	8.138|8.138	0.784620|0.784620	0.16189|0.16189	.|.	.|.	ENSG00000168614|ENSG00000168614	ENST00000375552|ENST00000338347;ENST00000440491;ENST00000281815	.|T;T;T	.|0.08282	.|3.11;3.11;3.11	0.431|0.431	-0.862|-0.862	0.10673|0.10673	.|.	.|.	.|.	.|.	.|.	T|T	0.06325|0.06325	0.0163|0.0163	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.91635	.|0.999	T|T	0.20638|0.20638	-1.0269|-1.0269	3|7	.|0.20046	.|T	.|0.44	.|.	.|.	.|.	.|.	.|.	.|380	.|A2BGT5	.|.	L|S	381|382;382;67	.|ENSP00000342975:Y382S;ENSP00000390934:Y382S;ENSP00000281815:Y67S	.|ENSP00000281815:Y67S	I|Y	+|+	1|2	0|0	NBPF9|NBPF9	143535235|143535235	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.041000|0.041000	0.13682|0.13682	-1.315000|-1.315000	0.02713|0.02713	-0.698000|-0.698000	0.05085|0.05085	0.163000|0.163000	0.16589|0.16589	ATT|TAT	.		0.483	NBPF9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001037675		C	144823878	A	C	144823878	3	2	82	1	0	0	0	0	1	0	0	0	10225	449	16	5	1971	5	NBPF9	1	144823878	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	27190706	144823878	104426743	6	7564											
SCYL3	57147	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169824950	169824950	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctacctgtctgtaaaagAgtattgtagtaatctcgctg	10	16	8	7	1	3	1	0	0	3	1	4	1	3	1	1	0	1	5	1	0	6	7			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:169824950A>T	ENST00000367770.1	-	11	1508	c.1461T>A	c.(1459-1461)acT>acA	p.T487T	SCYL3_ENST00000367772.4_Silent_p.T487T|SCYL3_ENST00000367771.6_Intron			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	487					cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TCTGTAAAAGAGTATTGTAGT	0.378																																					p.T487T													.	SCYL3-361	0			c.T1461A						.						70	71	70					1																	169824950		2203	4300	6503	SO:0001819	synonymous_variant	57147	exon12			TAAAAGAGTATTG	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"ezrin-binding partner PACE-1"	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.1461T>A	1.37:g.169824950A>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	51	20	NM_181093	0	0	0	0	0	A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Silent	SNP	ENST00000367770.1	37	CCDS1287.1																																																																																			.		0.378	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093		T	169824950	A	T	169824950	2	4	82	1	0	0	0	0	0	0	0	1	13981	291	11	5		5	SCYL3	1	169824950	Silent	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	25001072	169824950	79425671	7	7565											
NPL	80896	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	182775301	182775301	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaatggcacaacaggagaagGcctgtccctgagcgtctcag	11	6	13	11	1	1	2	1	1	1	1	3	4	2	2	2	3	2	1	2	3	3	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:182775301G>C	ENST00000367553.1	+	4	208	c.164G>C	c.(163-165)gGc>gCc	p.G55A	NPL_ENST00000367552.2_Missense_Mutation_p.G55A|NPL_ENST00000367550.2_Missense_Mutation_p.G55A|NPL_ENST00000258317.2_Missense_Mutation_p.G55A|NPL_ENST00000367555.1_Missense_Mutation_p.G55A|NPL_ENST00000367554.3_5'UTR|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	55					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						ACAGGAGAAGGCCTGTCCCTG	0.532																																					p.G55A		.											.	NPL-92	0			c.G164C						.						111	109	110					1																	182775301		2203	4300	6503	SO:0001583	missense	80896	exon5			GAGAAGGCCTGTC	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 1 (E. coli)"	611412	"chromosome 1 open reading frame 13"	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.164G>C	1.37:g.182775301G>C	ENSP00000356524:p.Gly55Ala	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	85	13	NM_001200052	0	0	14	19	5	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Missense_Mutation	SNP	ENST00000367553.1	37	CCDS1350.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482498	0.84747	.	.	ENSG00000135838	ENST00000367555;ENST00000367553;ENST00000367552;ENST00000258317;ENST00000367550	D;D;D;D;D	0.94897	-3.55;-1.53;-3.55;-1.53;-3.55	5.26	5.26	0.73747	Aldolase-type TIM barrel (1);	0.050750	0.85682	D	0.000000	D	0.95695	0.8600	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.969	D;D;P	0.74023	0.957;0.982;0.671	D	0.93397	0.6757	10	0.06625	T	0.88	-14.9114	15.7916	0.78369	0.0:0.0:1.0:0.0	.	55;55;55	Q9BXD5-4;Q9BXD5;Q9BXD5-3	.;NPL_HUMAN;.	A	55	ENSP00000356526:G55A;ENSP00000356524:G55A;ENSP00000356523:G55A;ENSP00000258317:G55A;ENSP00000356521:G55A	ENSP00000258317:G55A	G	+	2	0	NPL	181041924	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	6.722000	0.74735	2.451000	0.82905	0.563000	0.77884	GGC	.		0.532	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		C	182775301	G	C	182775301	3	2	82	1	0	0	0	0	1	0	0	0	10611	1203	42	4	174	4	NPL	1	182775301	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	12950351	182775301	66475320	8	7566											
TPR	7175	broad.mit.edu;bcgsc.ca	37	chr1	186324772	186324772	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtgtgatctttacctgttTaagggcagccttagcctcta	8	14	10	9	0	2	1	0	1	2	0	2	1	2	1	3	2	3	2	3	2	4	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:186324772T>A	ENST00000367478.4	-	16	2313	c.2017A>T	c.(2017-2019)Aaa>Taa	p.K673*	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	673					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTTACCTGTTTAAGGGCAGCC	0.408			T	NTRK1	papillary thyroid																																p.K673X				Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR-228	0			c.A2017T						.						128	121	123					1																	186324772		1896	4117	6013	SO:0001587	stop_gained	7175	exon16			CCTGTTTAAGGGC	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2017A>T	1.37:g.186324772T>A	ENSP00000356448:p.Lys673*	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	147	10	NM_003292	0	0	0	0	0	Q15655|Q5SWY0|Q99968	Nonsense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	42	9.615943	0.99220	.	.	ENSG00000047410	ENST00000367478	.	.	.	5.22	5.22	0.72569	.	0.166835	0.51477	D	0.000081	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3973	0.74805	0.0:0.0:0.0:1.0	.	.	.	.	X	673	.	ENSP00000356448:K673X	K	-	1	0	TPR	184591395	1.000000	0.71417	0.996000	0.52242	0.919000	0.55068	3.415000	0.52700	2.106000	0.64143	0.482000	0.46254	AAA	.		0.408	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		A	186324772	T	A	186324772	4	1	82	1	0	0	0	0	0	1	0	0	16449	1763	61	5	5218	5	TPR	1	186324772	Nonsense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	3549471	186324772	62925849	9	7567											
CYP1B1	1545	hgsc.bcm.edu;broad.mit.edu	37	chr2	38302357	38302357	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgccgcgtttccgatcaGtggccacgcaaacgggcccg	6	5	13	17	8	1	0	1	0	0	0	2	1	2	0	5	2	1	2	5	2	1	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:38302357G>C	ENST00000260630.3	-	2	576	c.175C>G	c.(175-177)Ctg>Gtg	p.L59V	CYP1B1_ENST00000494864.1_Intron|CYP1B1_ENST00000407341.1_Missense_Mutation_p.L59V|CYP1B1-AS1_ENST00000431999.1_RNA|CYP1B1-AS1_ENST00000589303.1_RNA	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	59					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	TTTCCGATCAGTGGCCACGCA	0.721																																					p.L59V		.											.	CYP1B1-515	0			c.C175G						.						8	10	9					2																	38302357		2147	4207	6354	SO:0001583	missense	1545	exon2			CGATCAGTGGCCA	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"Cytochrome P450s"	2597	protein-coding gene	gene with protein product		601771	"cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.175C>G	2.37:g.38302357G>C	ENSP00000260630:p.Leu59Val	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_000104	0	0	5	10	5	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	.	.	.	.	.	.	.	.	.	.	G	5.939	0.357214	0.11239	.	.	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.69561	-0.41;-0.41	4.29	2.42	0.29668	.	0.389391	0.24269	N	0.040011	T	0.50292	0.1607	N	0.20574	0.59	0.26804	N	0.969141	B	0.27910	0.193	B	0.38378	0.272	T	0.41627	-0.9498	10	0.14656	T	0.56	.	7.627	0.28218	0.0953:0.1661:0.7386:0.0	.	59	Q53TK1	.	V	59	ENSP00000260630:L59V;ENSP00000384972:L59V	ENSP00000260630:L59V	L	-	1	2	CYP1B1	38155861	0.008000	0.16893	0.990000	0.47175	0.027000	0.11550	0.123000	0.15708	0.415000	0.25817	-0.479000	0.04858	CTG	.		0.721	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104		C	38302357	G	C	38302357	3	2	82	1	0	0	0	0	1	0	0	0	4157	1020	36	4	1464	4	CYP1B1	2	38302357	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		38302357	204897016	10	7568											
BOLA3	388962	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	74362686	74362686	+	3'UTR	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgaagttcatccaaggtCttaagcagcagcatctatgc	12	10	9	10	0	3	1	1	1	2	0	4	1	4	1	1	1	4	4	1	1	4	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:74362686C>A	ENST00000327428.5	-	0	477				BOLA3_ENST00000295326.4_Missense_Mutation_p.R90I	NM_212552.2	NP_997717.2	Q53S33	BOLA3_HUMAN	bolA family member 3							extracellular region (GO:0005576)				large_intestine(1)|lung(1)	2						CATCCAAGGTCTTAAGCAGCA	0.388																																					p.R90I		.											.	BOLA3-90	0			c.G269T						.						190	163	172					2																	74362686		2203	4300	6503	SO:0001624	3_prime_UTR_variant	388962	exon3			CAAGGTCTTAAGC	BC017744	CCDS33224.1, CCDS33225.1	2p13.1	2013-09-02	2013-09-02		ENSG00000163170	ENSG00000163170			24415	protein-coding gene	gene with protein product		613183	"bolA-like 3 (E. coli)", "bolA homolog 3 (E. coli)"			14718656	Standard	NM_001035505		Approved		uc002skc.1	Q53S33	OTTHUMG00000152834	ENST00000327428.5:c.*34G>T	2.37:g.74362686C>A		Somatic	131	1		WXS	Illumina HiSeq	Phase_I	105	33	NM_001035505	0	0	16	32	16	G3XAB0	Missense_Mutation	SNP	ENST00000327428.5	37	CCDS33225.1	.	.	.	.	.	.	.	.	.	.	C	11.64	1.698137	0.30142	.	.	ENSG00000163170	ENST00000295326	.	.	.	4.01	-5.54	0.02544	.	.	.	.	.	T	0.19525	0.0469	N	0.08118	0	0.09310	N	1	B	0.14805	0.011	B	0.13407	0.009	T	0.28808	-1.0032	8	0.87932	D	0	.	7.5135	0.27587	0.0:0.262:0.5237:0.2143	.	90	G3XAB0	.	I	90	.	ENSP00000295326:R90I	R	-	2	0	BOLA3	74216194	0.000000	0.05858	0.000000	0.03702	0.591000	0.36615	-1.560000	0.02160	-0.961000	0.03609	-0.290000	0.09829	AGA	.		0.388	BOLA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328207.2	NM_212552		A	74362686	C	A	74362686	1	1	82	0	1	0	0	0	0	0	0	0	1489	913	32	4		4	BOLA3	2	74362686	3'UTR	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	36060329	74362686	168836687	11	7569											
BCL2L11	10018	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	111921708	111921716	+	Splice_Site	DEL	AGGTATTTT	AGGTATTTT	-																															agctttccttttgttgtttcAggtatttttgaataattacc																								rs142125092		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	AGGTATTTT	AGGTATTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:111921708_111921716delAGGTATTTT	ENST00000393256.3	+	4	771_778	c.498_505delAGGTATTTT	c.(496-507)agaggtattttt>agtt	p.166_169RGIF>S	BCL2L11_ENST00000308659.8_Splice_Site_p.106_109RGIF>S	NM_001204106.1|NM_006538.4|NM_138621.4|NM_138627.3	NP_001191035.1|NP_006529.1|NP_619527.1|NP_619533.1	O43521	B2L11_HUMAN	BCL2-like 11 (apoptosis facilitator)	166					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|brain development (GO:0007420)|cell-matrix adhesion (GO:0007160)|cellular process regulating host cell cycle in response to virus (GO:0060154)|developmental pigmentation (GO:0048066)|ear development (GO:0043583)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|kidney development (GO:0001822)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of cell cycle (GO:0045787)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|post-embryonic organ morphogenesis (GO:0048563)|regulation of developmental pigmentation (GO:0048070)|regulation of organ growth (GO:0046620)|response to endoplasmic reticulum stress (GO:0034976)|spermatogenesis (GO:0007283)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|thymocyte apoptotic process (GO:0070242)|thymus development (GO:0048538)|tube formation (GO:0035148)	BIM-BCL-2 complex (GO:0097141)|BIM-BCL-xl complex (GO:0097140)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|mitochondrial outer membrane (GO:0005741)				endometrium(4)|large_intestine(3)|lung(2)|prostate(2)	11						TTGTTGTTTCAGGTATTTTTGAATAATTA	0.445																																					p.167_169del		.											.	BCL2L11-1083	0			c.499_505del						.																																			SO:0001630	splice_region_variant	10018	exon4			.	AF032458	CCDS2089.1, CCDS2092.1, CCDS42731.1, CCDS56131.1, CCDS56132.1, CCDS56133.1, CCDS56134.1, CCDS56135.1, CCDS56136.1, CCDS74560.1, CCDS74561.1, CCDS74559.1	2q13	2014-09-17			ENSG00000153094	ENSG00000153094			994	protein-coding gene	gene with protein product		603827				9731710, 9430630	Standard	NM_006538		Approved	BOD, BimL, BimEL, BimS, BIM	uc002tgv.1	O43521	OTTHUMG00000131256	ENST00000393256.3:c.499-1AGGTATTTT>-	2.37:g.111921708_111921716delAGGTATTTT		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	58	13	NM_138621	0	0	0	0	0	A8K2W2|O43522|Q0MSE7|Q0MSE8|Q0MSE9|Q53R28|Q6JTU6|Q6T851|Q6TE14|Q6TE15|Q6TE16|Q6V402|Q8WYL6|Q8WYL7|Q8WYL8|Q8WYL9|Q8WYM0|Q8WYM1	Frame_Shift_Del	DEL	ENST00000393256.3	37	CCDS2089.1																																																																																			.		0.445	BCL2L11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254022.3		In_Frame_Del	-	111921716	AGGTATTTT	-	111921708	8	5	82	1	0	1	0	1	0	0	1	0	1370	202	7	0	636	0	BCL2L11	2	111921708	Splice_Site	DEL	AGGTATTTT	TCGA-BQ-7048-01A-11D-1961-08	37559022	111921708	131277665	12	7570											
WDR33	55339	hgsc.bcm.edu	37	chr2	128474756	128474756	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggggccaggtccttgtccggGgttcagagggggaatgcgac	6	7	19	9	2	1	1	1	0	0	1	3	3	3	2	3	7	1	1	3	7	1	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:128474756G>A	ENST00000322313.4	-	17	3000	c.2842C>T	c.(2842-2844)Ccc>Tcc	p.P948S		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	948					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CCTTGTCCGGGGTTCAGAGGG	0.473																																					p.P948S		.											.	WDR33-90	0			c.C2842T						.						41	39	40					2																	128474756		2203	4300	6503	SO:0001583	missense	55339	exon17			GTCCGGGGTTCAG		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2842C>T	2.37:g.128474756G>A	ENSP00000325377:p.Pro948Ser	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	30	11	NM_018383	0	0	9	23	14	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911907	0.52439	.	.	ENSG00000136709	ENST00000322313	D	0.89270	-2.49	5.27	4.33	0.51752	.	0.109084	0.41712	D	0.000831	T	0.77110	0.4082	N	0.08118	0	0.80722	D	1	B	0.14012	0.009	B	0.19666	0.026	T	0.72494	-0.4276	10	0.36615	T	0.2	-6.9429	11.0259	0.47744	0.0:0.188:0.812:0.0	.	948	Q9C0J8	WDR33_HUMAN	S	948	ENSP00000325377:P948S	ENSP00000325377:P948S	P	-	1	0	WDR33	128191226	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.042000	0.41222	2.473000	0.83533	0.563000	0.77884	CCC	.		0.473	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128474756	G	A	128474756	3	1	82	1	0	0	0	0	1	0	0	0	17320	1232	43	2	1192	2	WDR33	2	128474756	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	16553048	128474756	114724617	13	7571											
WDR33	55339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	128526506	128526506	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatgacacatcatgtacttaCatcattgtaataacctgcat	14	14	4	9	0	2	1	2	1	0	0	2	1	2	1	1	0	4	3	1	0	5	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:128526506C>A	ENST00000322313.4	-	3	432		c.e3+1		WDR33_ENST00000409658.3_Splice_Site|WDR33_ENST00000393006.1_Splice_Site	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CATGTACTTACATCATTGTAA	0.323																																					.		.											.	WDR33-90	0			c.273+1G>T						.						138	126	130					2																	128526506		2203	4300	6503	SO:0001630	splice_region_variant	55339	exon4			TACTTACATCATT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"WD repeat domain containing"	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.273+1G>T	2.37:g.128526506C>A		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	126	48	NM_018383	0	0	0	0	0	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Splice_Site	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530432	0.85706	.	.	ENSG00000136709	ENST00000322313;ENST00000436787;ENST00000393006;ENST00000409658;ENST00000408998	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8826	0.92362	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR33	128242976	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.506000	0.81665	2.627000	0.88993	0.655000	0.94253	.	.		0.323	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	Intron	A	128526506	C	A	128526506	5	1	82	1	0	0	0	0	0	0	1	0	17320	492	17	4	4225	4	WDR33	2	128526506	Splice_Site	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	51750	128526506	114672867	14	7572											
RBM45	129831	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178977555	178977555	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccagtgcctcggccccaaCgacaccaagcccatcaaggt	10	4	10	17	2	1	0	1	0	0	0	2	1	1	0	6	3	3	0	6	3	3	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:178977555C>T	ENST00000286070.5	+	1	374	c.282C>T	c.(280-282)aaC>aaT	p.N94N		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	94	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			TCGGCCCCAACGACACCAAGC	0.662																																					p.N94N													.	RBM45-22	0			c.C282T						.						38	39	38					2																	178977555		2203	4300	6503	SO:0001819	synonymous_variant	129831	exon1			CCCCAACGACACC	AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"RNA binding motif (RRM) containing"	24468	protein-coding gene	gene with protein product	"developmentally regulated RNA binding protein 1"	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.282C>T	2.37:g.178977555C>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	55	7	NM_152945	0	0	2	5	3	Q6NYL0|Q8NFC9	Silent	SNP	ENST00000286070.5	37	CCDS33335.1																																																																																			.		0.662	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945		T	178977555	C	T	178977555	2	4	82	1	0	0	0	0	0	0	0	1	13171	535	19	1		1	RBM45	2	178977555	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	50451049	178977555	64221818	15	7573											
TRIP12	9320	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	230701700	230701702	+	Splice_Site	DEL	ACT	ACT	-																															cccaggccagagcctcgccgActacaacagaaaaatgtcat																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	ACT	ACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:230701700_230701702delACT	ENST00000283943.5	-	5	1186	c.1008delAGT	c.(1006-1008)aga>ag	p.R338del	TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000409677.1_Splice_Site_p.R380del|TRIP12_ENST00000389044.4_Splice_Site_p.R380del|TRIP12_ENST00000389045.3_Splice_Site_p.R35del	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	338					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AGCCTCGCCGACTACAACAGAAA	0.483																																					p.336_336del		.											.	TRIP12-572	0			c.1008_1008del						.																																			SO:0001630	splice_region_variant	9320	exon5			.	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1008-1AGT>-	2.37:g.230701700_230701702delACT		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	47	23	NM_004238	0	0	0	0	0	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Frame_Shift_Del	DEL	ENST00000283943.5	37	CCDS33391.1																																																																																			.		0.483	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	In_Frame_Del	-	230701702	ACT	-	230701700	8	5	82	1	0	1	0	1	0	0	1	0	16589	289	10	0	5118	0	TRIP12	2	230701700	Splice_Site	DEL	ACT	TCGA-BQ-7048-01A-11D-1961-08	51724145	230701700	12497673	16	7574											
PRICKLE2	166336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	64084893	64084893	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggatgggttctcctaggAaatagccctcgttgtcagac	8	10	14	9	1	2	1	1	0	1	1	4	3	2	3	2	4	1	2	2	4	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr3:64084893A>G	ENST00000295902.6	-	8	2954	c.2369T>C	c.(2368-2370)tTc>tCc	p.F790S	PRICKLE2_ENST00000564377.1_Missense_Mutation_p.F846S|PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	790					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		TTCTCCTAGGAAATAGCCCTC	0.567																																					p.F790S		.											.	PRICKLE2-95	0			c.T2369C						.						76	77	77					3																	64084893		2203	4300	6503	SO:0001583	missense	166336	exon8			CCTAGGAAATAGC	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"prickle-like 2 (Drosophila)"			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.2369T>C	3.37:g.64084893A>G	ENSP00000295902:p.Phe790Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	84	39	NM_198859	0	0	0	1	1	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.039965	0.75732	.	.	ENSG00000163637	ENST00000295902	D	0.88046	-2.33	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.92004	0.7467	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.63488	0.915	D	0.92874	0.6317	10	0.87932	D	0	-40.9764	15.8395	0.78835	1.0:0.0:0.0:0.0	.	790	Q7Z3G6	PRIC2_HUMAN	S	790	ENSP00000295902:F790S	ENSP00000295902:F790S	F	-	2	0	PRICKLE2	64059933	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.962000	0.93254	2.152000	0.67230	0.533000	0.62120	TTC	.		0.567	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		G	64084893	A	G	64084893	3	3	82	1	0	0	0	0	1	0	0	0	12516	246	9	3	169	3	PRICKLE2	3	64084893	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08		64084893	133937537	17	7575											
DBR1	51163	broad.mit.edu	37	chr3	137892448	137892448	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagcgtgagaactggagccTttttctctccagagtaatac	11	11	10	9	1	1	3	0	1	1	3	3	5	2	4	2	1	4	1	2	1	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr3:137892448T>C	ENST00000260803.4	-	2	371	c.218A>G	c.(217-219)aAg>aGg	p.K73R	DBR1_ENST00000463982.2_5'UTR|DBR1_ENST00000505015.2_5'UTR	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	73					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						AACTGGAGCCTTTTTCTCTCC	0.398																																					p.K73R													.	DBR1-90	0			c.A218G						.						109	112	111					3																	137892448		2203	4300	6503	SO:0001583	missense	51163	exon2			GGAGCCTTTTTCT	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"debranching enzyme (S. Cerevisiae) homolog 1", "debranching enzyme homolog 1 (S. cerevisiae)"			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.218A>G	3.37:g.137892448T>C	ENSP00000260803:p.Lys73Arg	Somatic	194	1		WXS	Illumina HiSeq	Phase_I	170	4	NM_016216	0	0	7	7	0	Q96GH0|Q9NXQ6	Missense_Mutation	SNP	ENST00000260803.4	37	CCDS33863.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.530194	0.45073	.	.	ENSG00000138231	ENST00000260803	T	0.32272	1.46	5.58	5.58	0.84498	Metallophosphoesterase domain (1);	0.105722	0.64402	D	0.000006	T	0.25419	0.0618	L	0.47716	1.5	0.80722	D	1	B	0.25772	0.134	B	0.26416	0.069	T	0.07986	-1.0744	10	0.20046	T	0.44	-4.5131	9.0631	0.36447	0.1638:0.0:0.0:0.8362	.	73	Q9UK59	DBR1_HUMAN	R	73	ENSP00000260803:K73R	ENSP00000260803:K73R	K	-	2	0	DBR1	139375138	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	4.727000	0.61993	2.120000	0.65058	0.533000	0.62120	AAG	.		0.398	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1			C	137892448	T	C	137892448	3	2	82	1	0	0	0	0	1	0	0	0	4263	1609	56	3	1444	3	DBR1	3	137892448	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	73807555	137892448	60129982	18	7576											
SLC2A2	6514	broad.mit.edu;bcgsc.ca	37	chr3	170723087	170723087	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aacttacgccattgattccgGaaaattgctgagccacatgc	12	10	8	11	2	0	2	0	2	0	0	1	3	1	3	3	1	5	1	3	1	4	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr3:170723087G>A	ENST00000314251.3	-	7	1029	c.950C>T	c.(949-951)tCc>tTc	p.S317F	SLC2A2_ENST00000382808.4_Missense_Mutation_p.S198F	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	317	Monosaccharide binding. {ECO:0000250}.				carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	ATTGATTCCGGAAAATTGCTG	0.423																																					p.S317F													.	SLC2A2-515	0			c.C950T						.						172	160	164					3																	170723087		2203	4300	6503	SO:0001583	missense	6514	exon7			ATTCCGGAAAATT	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.950C>T	3.37:g.170723087G>A	ENSP00000323568:p.Ser317Phe	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	151	9	NM_000340	0	0	0	0	0	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.954567	0.53293	.	.	ENSG00000163581	ENST00000314251;ENST00000382808	T;T	0.76578	-1.03;-1.03	5.53	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.93054	0.7789	H	0.99058	4.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95975	0.8973	10	0.87932	D	0	.	16.0903	0.81086	0.0:0.0:0.8649:0.135	.	317	P11168	GTR2_HUMAN	F	317;198	ENSP00000323568:S317F;ENSP00000372258:S198F	ENSP00000323568:S317F	S	-	2	0	SLC2A2	172205781	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	9.434000	0.97515	1.456000	0.47831	0.591000	0.81541	TCC	.		0.423	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		A	170723087	G	A	170723087	3	1	82	1	0	0	0	0	1	0	0	0	14576	1174	41	2	644	2	SLC2A2	3	170723087	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	32830639	170723087	27299343	19	7577											
PLD1	5337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	171394619	171394619	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcgtggagtacctgtcaatGaaatctgcccgggtgcacca	9	8	13	11	2	2	1	1	1	1	0	2	2	2	2	3	3	3	2	3	3	3	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr3:171394619G>A	ENST00000351298.4	-	18	2127	c.2001C>T	c.(1999-2001)ttC>ttT	p.F667F	PLD1_ENST00000340989.4_Silent_p.F667F|PLD1_ENST00000356327.5_Silent_p.F629F|PLD1_ENST00000342215.6_Missense_Mutation_p.S558L	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	667	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ACCTGTCAATGAAATCTGCCC	0.542																																					p.F667F	NSCLC(149;2174 3517 34058)	.											.	PLD1-660	0			c.C2001T						.						52	46	48					3																	171394619		2203	4300	6503	SO:0001819	synonymous_variant	5337	exon18			GTCAATGAAATCT	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.2001C>T	3.37:g.171394619G>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	47	19	NM_002662	0	0	0	0	0		Silent	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505561	0.64410	.	.	ENSG00000075651	ENST00000342215	T	0.34275	1.37	5.81	4.94	0.65067	.	.	.	.	.	T	0.46073	0.1374	.	.	.	0.28598	N	0.90932	.	.	.	.	.	.	T	0.42515	-0.9447	6	0.49607	T	0.09	-20.5851	14.4529	0.67397	0.0699:0.0:0.9301:0.0	.	.	.	.	L	558	ENSP00000339936:S558L	ENSP00000339936:S558L	S	-	2	0	PLD1	172877313	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.889000	0.56212	1.464000	0.47987	0.557000	0.71058	TCA	.		0.542	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171394619	G	A	171394619	2	1	82	1	0	0	0	0	0	0	0	1	12071	1281	45	2		2	PLD1	3	171394619	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	671532	171394619	26627811	20	7578											
SEL1L3	23231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	25806261	25806261	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagctggaatccgtcagaaAggggacgatagagctaattt	13	8	13	7	2	1	2	1	0	0	2	2	5	2	4	1	3	2	3	1	3	4	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr4:25806261A>T	ENST00000399878.3	-	10	1800	c.1678T>A	c.(1678-1680)Ttt>Att	p.F560I	SEL1L3_ENST00000264868.5_Missense_Mutation_p.F525I|SEL1L3_ENST00000502949.1_Missense_Mutation_p.F407I	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	560						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TCCGTCAGAAAGGGGACGATA	0.433																																					p.F560I		.											.	.	0			c.T1678A						.						93	89	90					4																	25806261		1896	4134	6030	SO:0001583	missense	23231	exon10			TCAGAAAGGGGAC	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1678T>A	4.37:g.25806261A>T	ENSP00000382767:p.Phe560Ile	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	55	23	NM_015187	0	0	4	4	0	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.076787	0.36662	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.13538	2.79;2.8;2.58	6.02	2.18	0.27775	Tetratricopeptide-like helical (1);	0.882014	0.10506	N	0.666713	T	0.12732	0.0309	L	0.47716	1.5	0.26551	N	0.973918	B	0.19445	0.036	B	0.12837	0.008	T	0.35375	-0.9791	10	0.20519	T	0.43	-0.7039	10.2524	0.43377	0.7466:0.0:0.2534:0.0	.	560	Q68CR1	SE1L3_HUMAN	I	560;525;407	ENSP00000382767:F560I;ENSP00000264868:F525I;ENSP00000425438:F407I	ENSP00000264868:F525I	F	-	1	0	SEL1L3	25415359	0.998000	0.40836	0.775000	0.31657	0.911000	0.54048	2.508000	0.45450	0.151000	0.19162	0.533000	0.62120	TTT	.		0.433	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25806261	A	T	25806261	3	4	82	1	0	0	0	0	1	0	0	0	14044	72	3	5	1780	5	SEL1L3	4	25806261	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08		25806261	165348015	21	7579											
STOX2	56977	broad.mit.edu	37	chr4	184931856	184931856	+	Frame_Shift_Del	DEL	A	A	-																															acctctgggaaagaataaggAggaccatgacactctgactt																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr4:184931856delA	ENST00000308497.4	+	3	3300	c.1865delA	c.(1864-1866)gagfs	p.E622fs	STOX2_ENST00000438269.1_Frame_Shift_Del_p.E622fs	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	622					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AAGAATAAGGAGGACCATGAC	0.532																																					p.E622fs													.	STOX2-22	0			c.1865delA						.						47	47	47					4																	184931856		1954	4146	6100	SO:0001589	frameshift_variant	56977	exon3			ATAAGGAGGACCA	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.1865delA	4.37:g.184931856delA	ENSP00000311257:p.Glu622fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	70	8	NM_020225	0	0	0	0	0	A6H8U4|Q9NPS8	Frame_Shift_Del	DEL	ENST00000308497.4	37	CCDS47167.1																																																																																			.		0.532	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		-	184931856	A	-	184931856	7	5	82	1	0	1	0	1	0	0	0	0	15352	304	11	0	1875	0	STOX2	4	184931856	Frame_Shift_Del	DEL	A	TCGA-BQ-7048-01A-11D-1961-08	159125595	184931856	6222420	22	7580											
ACSL1	2180	broad.mit.edu;ucsc.edu	37	chr4	185724472	185724472	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggctgggccctccactcAccgccacttccactgactgc	6	7	9	19	1	1	1	1	1	0	0	3	1	3	1	5	2	1	2	5	2	0	1	rs201598489		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr4:185724472A>T	ENST00000515030.1	-	2	521		c.e2+1		ACSL1_ENST00000437665.3_Splice_Site|ACSL1_ENST00000454703.2_Intron|ACSL1_ENST00000504342.1_Splice_Site|ACSL1_ENST00000513317.1_Splice_Site|ACSL1_ENST00000281455.2_Splice_Site|ACSL1_ENST00000507295.1_Splice_Site|ACSL1_ENST00000504900.1_Splice_Site			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1						adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CCCTCCACTCACCGCCACTTC	0.547																																					.													.	ACSL1-92	0			c.195+2T>A						.						48	46	47					4																	185724472		2203	4300	6503	SO:0001630	splice_region_variant	2180	exon3			CCACTCACCGCCA	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"Acyl-CoA synthetase family"	3569	protein-coding gene	gene with protein product	"lignoceroyl-CoA synthase", "long-chain fatty-acid-coenzyme A ligase 1"	152425	"fatty-acid-Coenzyme A ligase, long-chain 2"	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.195+1T>A	4.37:g.185724472A>T		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	12	8	NM_001995	0	0	0	36	36	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Splice_Site	SNP	ENST00000515030.1	37	CCDS3839.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.248886	0.80024	.	.	ENSG00000151726	ENST00000515030;ENST00000281455;ENST00000507295;ENST00000504342;ENST00000513317;ENST00000504900	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9604	0.71153	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ACSL1	185961466	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	8.626000	0.90969	2.114000	0.64651	0.533000	0.62120	.	.		0.547	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	Intron	T	185724472	A	T	185724472	5	4	82	1	0	0	0	0	0	0	1	0	177	173	6	5	1979	5	ACSL1	4	185724472	Splice_Site	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	792616	185724472	5429804	23	7581											
FAM149A	25854	hgsc.bcm.edu	37	chr4	187088232	187088232	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaacggttgtcaaggcccagCacaacccacacgttccgggt	10	6	11	14	3	1	0	1	0	0	0	2	1	2	0	3	3	3	3	3	3	3	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr4:187088232C>G	ENST00000356371.5	+	12	2148	c.2148C>G	c.(2146-2148)agC>agG	p.S716R	FAM149A_ENST00000514153.1_Missense_Mutation_p.S425R|FAM149A_ENST00000502970.1_Missense_Mutation_p.S425R|FAM149A_ENST00000503432.1_Missense_Mutation_p.S425R|FAM149A_ENST00000227065.4_Missense_Mutation_p.S425R|FAM149A_ENST00000389354.5_Missense_Mutation_p.S425R			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	716										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		CAAGGCCCAGCACAACCCACA	0.453																																					p.S425R		.											.	FAM149A-90	0			c.C1275G						.						72	66	68					4																	187088232		2203	4300	6503	SO:0001583	missense	25854	exon11			GCCCAGCACAACC	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2148C>G	4.37:g.187088232C>G	ENSP00000348732:p.Ser716Arg	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001006655	0	0	47	47	0	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	14.29|14.29|14.29	2.492410|2.492410|2.492410	0.44352|0.44352|0.44352	.|.|.	.|.|.	ENSG00000109794|ENSG00000109794|ENSG00000109794	ENST00000510843|ENST00000512271|ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	.|.|T;T;T;T;T;T	.|.|0.13420	.|.|2.68;2.59;2.68;2.68;2.68;2.68	5.72|5.72|5.72	3.68|3.68|3.68	0.42216|0.42216|0.42216	.|.|.	.|.|0.120460	.|.|0.64402	.|.|D	.|.|0.000020	T|T|T	0.31199|0.31199|0.31199	0.0789|0.0789|0.0789	M|M|M	0.70595|0.70595|0.70595	2.14|2.14|2.14	0.27657|0.27657|0.27657	N|N|N	0.947213|0.947213|0.947213	.|.|D;D	.|.|0.76494	.|.|0.999;0.997	.|.|D;D	.|.|0.72075	.|.|0.976;0.91	T|T|T	0.04565|0.04565|0.04565	-1.0942|-1.0942|-1.0942	5|5|10	.|.|0.66056	.|.|D	.|.|0.02	-14.6564|-14.6564|-14.6564	7.8564|7.8564|7.8564	0.29485|0.29485|0.29485	0.0:0.7449:0.0:0.2551|0.0:0.7449:0.0:0.2551|0.0:0.7449:0.0:0.2551	.|.|.	.|.|716;716	.|.|A5PLN7-3;A5PLN7	.|.|.;F149A_HUMAN	G|D|R	103|103|425;716;425;425;425;425	.|.|ENSP00000426835:S425R;ENSP00000348732:S716R;ENSP00000227065:S425R;ENSP00000427155:S425R;ENSP00000424380:S425R;ENSP00000374005:S425R	.|.|ENSP00000227065:S425R	A|H|S	+|+|+	2|1|3	0|0|2	FAM149A|FAM149A|FAM149A	187325226|187325226|187325226	0.995000|0.995000|0.995000	0.38212|0.38212|0.38212	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.151000|0.151000|0.151000	0.21798|0.21798|0.21798	0.130000|0.130000|0.130000	0.15850|0.15850|0.15850	1.434000|1.434000|1.434000	0.47414|0.47414|0.47414	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GCA|CAC|AGC	.		0.453	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		G	187088232	C	G	187088232	3	3	82	1	0	0	0	0	1	0	0	0	5471	709	25	4	1309	4	FAM149A	4	187088232	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	1363760	187088232	4066044	24	7582											
TNPO1	3842	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	72151675	72151675	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actttcagaacttcccaaatGgtgtaacagactttattaaa	15	13	5	8	0	1	2	1	0	0	2	2	2	2	2	1	1	2	1	1	1	6	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:72151675G>A	ENST00000337273.5	+	4	706	c.280G>A	c.(280-282)Ggt>Agt	p.G94S	TNPO1_ENST00000447967.2_Missense_Mutation_p.G86S|TNPO1_ENST00000513944.1_3'UTR|TNPO1_ENST00000506351.2_Missense_Mutation_p.G86S|TNPO1_ENST00000454282.1_Intron|TNPO1_ENST00000523768.1_Intron	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	94	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		CTTCCCAAATGGTGTAACAGA	0.328																																					p.G94S		.											.	TNPO1-228	0			c.G280A						.						62	62	62					5																	72151675		2203	4297	6500	SO:0001583	missense	3842	exon4			CCAAATGGTGTAA	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.280G>A	5.37:g.72151675G>A	ENSP00000336712:p.Gly94Ser	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	81	20	NM_002270	0	0	7	9	2	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.737401	0.49045	.	.	ENSG00000083312	ENST00000337273;ENST00000447967;ENST00000506351	T;T;T	0.65549	-0.16;-0.16;-0.16	4.89	4.89	0.63831	Armadillo-like helical (1);Armadillo-type fold (1);Importin-beta, N-terminal (3);	0.095869	0.64402	D	0.000001	T	0.43255	0.1239	N	0.10685	0.025	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29852	-0.9998	10	0.18276	T	0.48	-2.9577	18.4554	0.90718	0.0:0.0:1.0:0.0	.	94	Q92973	TNPO1_HUMAN	S	94;86;86	ENSP00000336712:G94S;ENSP00000415164:G86S;ENSP00000425118:G86S	ENSP00000336712:G94S	G	+	1	0	TNPO1	72187431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.320000	0.96346	2.430000	0.82344	0.650000	0.86243	GGT	.		0.328	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		A	72151675	G	A	72151675	3	1	82	1	0	0	0	0	1	0	0	0	16367	1348	47	2	294	2	TNPO1	5	72151675	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		72151675	108763585	25	7583											
FNIP1	96459	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	131007378	131007379	+	Frame_Shift_Del	DEL	CT	CT	-																															cagcaatttttttatctgaaCtctctttatccccatggggg																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:131007378_131007379delCT	ENST00000510461.1	-	14	2853_2854	c.2758_2759delAG	c.(2758-2760)agtfs	p.S921fs	CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Frame_Shift_Del_p.S893fs|FNIP1_ENST00000307954.8_Frame_Shift_Del_p.S876fs	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	921					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TTTATCTGAACTCTCTTTATCC	0.416																																					p.920_920del		.											.	FNIP1-92	0			c.2758_2759del						.																																			SO:0001589	frameshift_variant	96459	exon14			.	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2758_2759delAG	5.37:g.131007382_131007383delCT	ENSP00000421985:p.Ser921fs	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	144	61	NM_133372	0	0	0	0	0	D6RJH5|Q86T47|Q9BUT0	Frame_Shift_Del	DEL	ENST00000510461.1	37	CCDS34227.1																																																																																			.		0.416	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		-	131007379	CT	-	131007378	7	5	82	1	0	1	0	1	0	0	0	0	5994	565	20	0	761	0	FNIP1	5	131007378	Frame_Shift_Del	DEL	CT	TCGA-BQ-7048-01A-11D-1961-08	58855703	131007378	49907882	26	7584											
FGF1	2246	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141974869	141974869	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctctttaatcagaagagaCtggcagggggagaaacaaga	16	7	12	6	0	2	4	1	0	1	4	3	6	2	4	0	3	1	1	0	3	4	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:141974869C>A	ENST00000359370.6	-	4	533	c.454G>T	c.(454-456)Gtc>Ttc	p.V152F	FGF1_ENST00000337706.2_Missense_Mutation_p.V152F|FGF1_ENST00000378046.1_Missense_Mutation_p.V152F|AC005592.2_ENST00000443800.1_RNA|FGF1_ENST00000360966.5_3'UTR|FGF1_ENST00000407758.1_3'UTR|AC005592.2_ENST00000414314.1_RNA|FGF1_ENST00000494579.1_5'UTR|FGF1_ENST00000419524.2_Missense_Mutation_p.V152F	NM_000800.4|NM_001144892.2|NM_001144934.1|NM_001144935.1|NM_001257205.1|NM_001257206.1|NM_001257207.1|NM_001257210.1|NM_001257212.1|NM_033137.2	NP_000791.1|NP_001138364.1|NP_001138406.1|NP_001138407.1|NP_001244134.1|NP_001244135.1|NP_001244136.1|NP_001244139.1|NP_001244141.1|NP_149128.1	P05230	FGF1_HUMAN	fibroblast growth factor 1 (acidic)	152					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|branch elongation involved in ureteric bud branching (GO:0060681)|cell differentiation (GO:0030154)|cellular response to heat (GO:0034605)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesonephric epithelium development (GO:0072163)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|S100 protein binding (GO:0044548)			large_intestine(1)|lung(2)	3		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Amlexanox(DB01025)|Pazopanib(DB06589)|Pentosan Polysulfate(DB00686)	TCAGAAGAGACTGGCAGGGGG	0.493																																					p.V152F		.											.	FGF1-947	0			c.G454T						.						65	66	66					5																	141974869		2203	4300	6503	SO:0001583	missense	2246	exon4			AAGAGACTGGCAG	X59065	CCDS4275.1, CCDS4276.1	5q31.3-q33.2	2014-01-30			ENSG00000113578	ENSG00000113578		"Endogenous ligands"	3665	protein-coding gene	gene with protein product	"heparin-binding growth factor 1", "endothelial cell growth factor, alpha", "endothelial cell growth factor, beta"	131220		FGFA		1697263, 3523756	Standard	NM_033137		Approved	AFGF, ECGF, ECGFA, ECGFB, HBGF1, ECGF-beta, FGF-alpha, GLIO703	uc031slo.1	P05230	OTTHUMG00000059703	ENST00000359370.6:c.454G>T	5.37:g.141974869C>A	ENSP00000352329:p.Val152Phe	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	105	36	NM_001257209	0	0	0	0	0	B2R5T0|D3DQF2|P07502|Q16588	Missense_Mutation	SNP	ENST00000359370.6	37	CCDS4275.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.694692	0.68386	.	.	ENSG00000113578	ENST00000359370;ENST00000378046;ENST00000337706;ENST00000441680;ENST00000419524	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.87	5.87	0.94306	.	0.081539	0.51477	D	0.000089	T	0.58133	0.2101	M	0.80982	2.52	0.54753	D	0.999984	P;D	0.53745	0.465;0.962	B;P	0.48189	0.132;0.57	T	0.64495	-0.6394	10	0.87932	D	0	.	20.2084	0.98285	0.0:1.0:0.0:0.0	.	151;152	A8K147;P05230	.;FGF1_HUMAN	F	152	ENSP00000352329:V152F;ENSP00000367285:V152F;ENSP00000338548:V152F;ENSP00000404742:V152F;ENSP00000396195:V152F	ENSP00000338548:V152F	V	-	1	0	FGF1	141955053	0.996000	0.38824	0.940000	0.37924	0.841000	0.47740	4.573000	0.60893	2.774000	0.95407	0.650000	0.86243	GTC	.		0.493	FGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132735.2	NM_000800		A	141974869	C	A	141974869	3	1	82	1	0	0	0	0	1	0	0	0	5857	565	20	4	17	4	FGF1	5	141974869	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	10967491	141974869	38940391	27	7585											
KIF13A	63971	broad.mit.edu;bcgsc.ca	37	chr6	17783900	17783900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaaatcgaggaagagaactGgtatgtgggtttccattcca	12	11	11	7	1	1	1	1	0	0	1	4	4	3	2	2	3	1	2	2	3	4	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:17783900G>A	ENST00000259711.6	-	29	3626	c.3521C>T	c.(3520-3522)cCa>cTa	p.P1174L	KIF13A_ENST00000378814.5_Missense_Mutation_p.P1161L|KIF13A_ENST00000378816.5_Missense_Mutation_p.P1174L|KIF13A_ENST00000378826.2_Missense_Mutation_p.P1174L|KIF13A_ENST00000378843.2_Missense_Mutation_p.P1161L	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1174					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			GAAGAGAACTGGTATGTGGGT	0.318																																					p.P1174L													.	KIF13A-137	0			c.C3521T						.						71	70	70					6																	17783900		1820	4071	5891	SO:0001583	missense	63971	exon29			AGAACTGGTATGT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.3521C>T	6.37:g.17783900G>A	ENSP00000259711:p.Pro1174Leu	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_001105566	0	0	1	3	2	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.135171|5.135171	0.94517|0.94517	.|.	.|.	ENSG00000137177|ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816;ENST00000506044|ENST00000358380	T;T;T;T;T;T|.	0.80994|.	-1.42;0.74;-1.44;-1.4;-1.42;-1.4|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.80706|.	0.4674|.	M|M	0.85299|0.85299	2.745|2.745	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.998;0.999;1.0;0.999|.	T|.	0.81417|.	-0.0942|.	10|.	0.87932|.	D|.	0|.	.|.	19.3733|19.3733	0.94498|0.94498	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1161;1174;1174;1161|.	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3|.	.;.;KI13A_HUMAN;.|.	L|X	1161;178;1174;1174;1161;1174;172|568	ENSP00000368091:P1161L;ENSP00000425616:P178L;ENSP00000259711:P1174L;ENSP00000368103:P1174L;ENSP00000368120:P1161L;ENSP00000368093:P1174L|.	ENSP00000259711:P1174L|.	P|Q	-|-	2|1	0|0	KIF13A|KIF13A	17891879|17891879	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.990000|0.990000	0.78478|0.78478	9.689000|9.689000	0.98673|0.98673	2.667000|2.667000	0.90743|0.90743	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.		0.318	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			A	17783900	G	A	17783900	3	1	82	1	0	0	0	0	1	0	0	0	8295	1348	47	2	1965	2	KIF13A	6	17783900	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		17783900	153331167	28	7586											
UBR2	23304	broad.mit.edu	37	chr6	42611951	42611951	+	Splice_Site	DEL	G	G	-																															aacattaaaaaaaaaaaaaaGacaggtgtctccatgatgga																								rs112519289	byFrequency	TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:42611951delG	ENST00000372899.1	+	19	2355		c.e19-1		UBR2_ENST00000372901.1_Splice_Site|UBR2_ENST00000372883.3_Splice_Site	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2						cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AAAAAAAAAAGACAGGTGTCT	0.373																																					.													.	UBR2-94	0			c.2098-1G>-						.						74	81	79					6																	42611951		2203	4300	6503	SO:0001630	splice_region_variant	23304	exon19			AAAAAAGACAGGT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2098-1G>-	6.37:g.42611951delG		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	1177	6	NM_015255	0	0	0	0	0	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Splice_Site	DEL	ENST00000372899.1	37	CCDS4870.1																																																																																			.		0.373	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	Intron	-	42611951	G	-	42611951	8	5	82	1	0	1	0	1	0	0	1	0	16935	956	33	0	2317	0	UBR2	6	42611951	Splice_Site	DEL	G	TCGA-BQ-7048-01A-11D-1961-08	24828051	42611951	128503116	29	7587											
XPO5	57510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43541219	43541219	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtccaagagctccttacttGacaacgtgttccaggatctg	9	12	9	11	1	1	2	0	1	1	1	4	3	4	3	3	1	3	2	3	1	3	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:43541219G>C	ENST00000265351.7	-	2	435	c.225C>G	c.(223-225)gtC>gtG	p.V75V	POLH_ENST00000372236.4_5'Flank|POLH_ENST00000535400.1_5'Flank|POLH_ENST00000372226.1_5'Flank	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	75	Necessary for interaction with Ran.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			CTCCTTACTTGACAACGTGTT	0.433																																					p.V75V		.											.	XPO5-271	0			c.C225G						.						87	85	86					6																	43541219		1910	4111	6021	SO:0001819	synonymous_variant	57510	exon2			TTACTTGACAACG	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"Exportins"	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.225C>G	6.37:g.43541219G>C		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	433	223	NM_020750	0	0	0	2	2	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																			.		0.433	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		C	43541219	G	C	43541219	2	2	82	1	0	0	0	0	0	0	0	1	17480	1277	45	4		4	XPO5	6	43541219	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	929268	43541219	127573848	30	7588											
CDC5L	988	broad.mit.edu;bcgsc.ca	37	chr6	44390390	44390390	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctgtctttctaggactccTtctaatggagctgaagggct	7	14	10	10	0	3	1	0	1	3	0	5	3	5	3	2	3	1	2	2	3	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:44390390T>C	ENST00000371477.3	+	10	1547	c.1248T>C	c.(1246-1248)ccT>ccC	p.P416P		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	416	Interaction with PPP1R8.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTAGGACTCCTTCTAATGGAG	0.408																																					p.P416P													.	CDC5L-229	0			c.T1248C						.						77	84	82					6																	44390390		2203	4300	6503	SO:0001819	synonymous_variant	988	exon10			GACTCCTTCTAAT	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1248T>C	6.37:g.44390390T>C		Somatic	192	0		WXS	Illumina HiSeq	Phase_I	1017	39	NM_001253	0	0	0	0	0	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																			.		0.408	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			C	44390390	T	C	44390390	2	2	82	1	0	0	0	0	0	0	0	1	3088	1596	56	3		3	CDC5L	6	44390390	Silent	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	849171	44390390	126724677	31	7589											
TNFRSF21	27242	broad.mit.edu	37	chr6	47251682	47251682	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagaaggctcaccatggccaTtgcagtagtagatccatttc	11	10	10	10	0	1	2	1	0	0	2	3	3	2	2	3	2	1	4	3	2	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:47251682T>C	ENST00000296861.2	-	3	1628	c.1235A>G	c.(1234-1236)aAt>aGt	p.N412S		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	412					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			ACCATGGCCATTGCAGTAGTA	0.512																																					p.N412S													.	TNFRSF21-227	0			c.A1235G						.						97	100	99					6																	47251682		2203	4300	6503	SO:0001583	missense	27242	exon3			TGGCCATTGCAGT	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"Tumor necrosis factor receptor superfamily", "CD molecules"	13469	protein-coding gene	gene with protein product	"death receptor 6"	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1235A>G	6.37:g.47251682T>C	ENSP00000296861:p.Asn412Ser	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	254	4	NM_014452	0	0	0	0	0	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.423588	0.83559	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	D	0.89746	-2.56	6.17	6.17	0.99709	Death (1);DEATH-like (1);	0.000000	0.85682	D	0.000000	D	0.89458	0.6721	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91741	0.5404	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	412	O75509	TNR21_HUMAN	S	412;101	ENSP00000296861:N412S	ENSP00000296861:N412S	N	-	2	0	TNFRSF21	47359641	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	5.712000	0.68407	2.371000	0.80710	0.533000	0.62120	AAT	.		0.512	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		C	47251682	T	C	47251682	3	2	82	1	0	0	0	0	1	0	0	0	16327	1493	52	3	748	3	TNFRSF21	6	47251682	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	2861292	47251682	123863385	32	7590											
LATS1	9113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	150005370	150005370	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacaggagagattcgggaGattacgtattccatgtttcc	10	11	13	7	2	0	2	0	0	0	2	3	6	2	4	2	3	1	2	2	3	2	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:150005370G>T	ENST00000543571.1	-	4	1402	c.855C>A	c.(853-855)atC>atA	p.I285I	LATS1_ENST00000392273.3_Silent_p.I285I|LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Silent_p.I285I	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		AGATTCGGGAGATTACGTATT	0.532																																					p.I285I		.											.	LATS1-992	0			c.C855A						.						153	144	147					6																	150005370		2203	4300	6503	SO:0001819	synonymous_variant	9113	exon4			TCGGGAGATTACG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.855C>A	6.37:g.150005370G>T		Somatic	179	0		WXS	Illumina HiSeq	Phase_I	172	77	NM_001270519	0	0	0	4	4		Silent	SNP	ENST00000543571.1	37	CCDS34551.1																																																																																			.		0.532	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		T	150005370	G	T	150005370	2	4	82	1	0	0	0	0	0	0	0	1	8667	932	33	4		4	LATS1	6	150005370	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	102753688	150005370	21109697	33	7591											
ESR1	2099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152201893	152201893	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtaaatgctacgaagtgggAatgatgaaaggtggtaggta	14	9	15	3	2	0	2	0	2	0	0	0	4	0	3	0	4	2	4	0	4	8	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:152201893A>G	ENST00000206249.3	+	3	1109	c.747A>G	c.(745-747)ggA>ggG	p.G249G	ESR1_ENST00000443427.1_Silent_p.G249G|ESR1_ENST00000338799.5_Silent_p.G249G|ESR1_ENST00000440973.1_Silent_p.G249G|ESR1_ENST00000427531.2_Silent_p.G76G|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000456483.2_Silent_p.G249G	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	249	Mediates interaction with DNTTIP2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	ACGAAGTGGGAATGATGAAAG	0.547																																					p.G249G		.											.	ESR1-1042	0			c.A747G						.						50	50	50					6																	152201893		2203	4300	6503	SO:0001819	synonymous_variant	2099	exon3			AGTGGGAATGATG	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"Nuclear hormone receptors"	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.747A>G	6.37:g.152201893A>G		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	41	13	NM_000125	0	0	0	0	0	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	A	9.711	1.157115	0.21454	.	.	ENSG00000091831	ENST00000427531	.	.	.	5.42	-10.8	0.00216	.	.	.	.	.	T	0.33089	0.0851	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58918	-0.7551	4	.	.	.	.	11.1314	0.48349	0.3958:0.3957:0.2085:0.0	.	.	.	.	G	154	.	.	E	+	2	0	ESR1	152243586	0.000000	0.05858	0.469000	0.27204	0.972000	0.66771	-2.223000	0.01214	-2.121000	0.00825	-1.074000	0.02243	GAA	.		0.547	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			G	152201893	A	G	152201893	2	3	82	1	0	0	0	0	0	0	0	1	5269	233	9	3		3	ESR1	6	152201893	Silent	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	2196523	152201893	18913174	34	7592											
MYCT1	80177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	153043198	153043198	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccatccctttctgcaatGtccaccacttcctgtggaaa	8	14	5	14	0	1	0	0	0	1	0	5	1	5	1	5	1	1	1	5	1	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:153043198G>T	ENST00000367245.5	+	2	526	c.518G>T	c.(517-519)tGt>tTt	p.C173F	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	173						nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		TTTCTGCAATGTCCACCACTT	0.498																																					p.C173F		.											.	MYCT1-91	0			c.G518T						.						89	87	88					6																	153043198		2203	4300	6503	SO:0001583	missense	80177	exon2			TGCAATGTCCACC	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.518G>T	6.37:g.153043198G>T	ENSP00000356214:p.Cys173Phe	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	103	46	NM_025107	0	0	4	4	0	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	37	CCDS5239.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.28|18.28	3.589712|3.589712	0.66105|0.66105	.|.	.|.	ENSG00000120279|ENSG00000120279	ENST00000367245|ENST00000532295	T|.	0.32753|.	1.44|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.364348|.	0.35838|.	N|.	0.002941|.	T|T	0.64875|0.64875	0.2638|0.2638	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	P;P|.	0.50617|.	0.937;0.853|.	P;P|.	0.49999|.	0.628;0.628|.	T|T	0.61907|0.61907	-0.6966|-0.6966	10|5	0.51188|.	T|.	0.08|.	-9.8469|-9.8469	16.985|16.985	0.86338|0.86338	0.0:0.1271:0.8729:0.0|0.0:0.1271:0.8729:0.0	.|.	125;173|.	D6Q1S4;Q8N699|.	.;MYCT1_HUMAN|.	F|F	173|154	ENSP00000356214:C173F|.	ENSP00000356214:C173F|.	C|V	+|+	2|1	0|0	MYCT1|MYCT1	153084891|153084891	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.964000|0.964000	0.63967|0.63967	5.162000|5.162000	0.64942|0.64942	2.727000|2.727000	0.93392|0.93392	0.579000|0.579000	0.79373|0.79373	TGT|GTC	.		0.498	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107		T	153043198	G	T	153043198	3	4	82	1	0	0	0	0	1	0	0	0	10047	1377	48	4	524	4	MYCT1	6	153043198	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	841305	153043198	18071869	35	7593											
IPCEF1	26034	broad.mit.edu	37	chr6	154521109	154521109	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtcttcactgtattttcCagggaagagaaagaatacga	13	11	11	6	1	2	2	1	0	1	2	3	5	3	3	1	2	1	1	1	2	5	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:154521109C>G	ENST00000265198.4	-	10	755	c.600G>C	c.(598-600)ctG>ctC	p.L200L	IPCEF1_ENST00000367220.4_Silent_p.L201L|OPRM1_ENST00000337049.4_Intron|IPCEF1_ENST00000519091.1_5'UTR|IPCEF1_ENST00000422970.2_Silent_p.L201L|IPCEF1_ENST00000519344.1_Silent_p.L172L	NM_001130700.1|NM_015553.2	NP_001124172.1|NP_056368.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	200	Ser-rich.				oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						CTGTATTTTCCAGGGAAGAGA	0.418																																					p.L201L													.	IPCEF1-90	0			c.G603C						.						101	100	100					6																	154521109		2203	4300	6503	SO:0001819	synonymous_variant	26034	exon11			ATTTTCCAGGGAA	AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706		"Pleckstrin homology (PH) domain containing"	21204	protein-coding gene	gene with protein product	"phosphoinositide binding protein PIP3-E"					11804589, 19756519	Standard	NM_001130699		Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000265198.4:c.600G>C	6.37:g.154521109C>G		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	110	3	NM_001130699	0	0	0	0	0	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	Silent	SNP	ENST00000265198.4	37	CCDS5245.1																																																																																			.		0.418	IPCEF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042789.2	NM_001130699		G	154521109	C	G	154521109	2	3	82	1	0	0	0	0	0	0	0	1	7812	581	21	4		4	IPCEF1	6	154521109	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	1477911	154521109	16593958	36	7594											
TTLL2	83887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	167755036	167755036	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaccgtggcaaagctccaGatccccaagcaggcaacttt	12	6	9	14	1	0	2	0	0	0	2	2	2	2	2	4	2	3	4	4	2	3	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:167755036G>T	ENST00000239587.5	+	3	1736	c.1648G>T	c.(1648-1650)Gat>Tat	p.D550Y		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	550					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CAAAGCTCCAGATCCCCAAGC	0.502																																					p.D550Y		.											.	TTLL2-92	0			c.G1648T						.						113	104	107					6																	167755036		2203	4300	6503	SO:0001583	missense	83887	exon3			GCTCCAGATCCCC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"Tubulin tyrosine ligase-like family"	21211	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 104"	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1648G>T	6.37:g.167755036G>T	ENSP00000239587:p.Asp550Tyr	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	135	51	NM_031949	0	0	0	0	0	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	.	.	.	.	.	.	.	.	.	.	G	4.684	0.127134	0.08981	.	.	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02395	4.31	4.04	-7.0	0.01599	.	2.486670	0.01433	N	0.014832	T	0.00552	0.0018	N	0.14661	0.345	0.09310	N	1	B	0.23185	0.081	B	0.16722	0.016	T	0.45659	-0.9246	10	0.56958	D	0.05	.	3.3015	0.06984	0.368:0.3942:0.1298:0.108	.	550	Q9BWV7	TTLL2_HUMAN	Y	550;477	ENSP00000239587:D550Y	ENSP00000239587:D550Y	D	+	1	0	TTLL2	167675026	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.123000	0.15708	-1.248000	0.02503	0.491000	0.48974	GAT	.		0.502	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		T	167755036	G	T	167755036	3	4	82	1	0	0	0	0	1	0	0	0	16760	942	33	4	1658	4	TTLL2	6	167755036	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	13233927	167755036	3360031	37	7595											
AUTS2	26053	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	70255838	70255838	+	Frame_Shift_Del	DEL	T	T	-																															ggactcctcaacaagaccccTccgacagcagcgctgagcgc																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr7:70255838delT	ENST00000342771.4	+	19	3957	c.3636delT	c.(3634-3636)cctfs	p.P1213fs	AUTS2_ENST00000406775.2_Frame_Shift_Del_p.P1189fs	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1213										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		ACAAGACCCCTCCGACAGCAG	0.677																																					p.P1212fs		.											.	AUTS2-92	0			c.3636delT						.						43	48	46					7																	70255838		2203	4299	6502	SO:0001589	frameshift_variant	26053	exon19			.	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3636delT	7.37:g.70255838delT	ENSP00000344087:p.Pro1213fs	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	45	13	NM_015570	0	0	0	0	0	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Frame_Shift_Del	DEL	ENST00000342771.4	37	CCDS5539.1																																																																																			.		0.677	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			-	70255838	T	-	70255838	7	5	82	1	0	1	0	1	0	0	0	0	1226	1538	54	0	3855	0	AUTS2	7	70255838	Frame_Shift_Del	DEL	T	TCGA-BQ-7048-01A-11D-1961-08		70255838	88882825	38	7596											
TBL2	26608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	72988278	72988278	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cttgtcccacctgcagtcagGgctgaagcgcaccagggtgg	7	7	14	13	1	1	1	1	1	0	0	2	1	2	1	3	3	2	3	3	3	1	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr7:72988278G>A	ENST00000305632.5	-	3	677	c.436C>T	c.(436-438)Cct>Tct	p.P146S	TBL2_ENST00000452475.1_Missense_Mutation_p.P146S|TBL2_ENST00000432538.1_Missense_Mutation_p.P110S|TBL2_ENST00000459913.1_5'UTR	NM_012453.2	NP_036585.1	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	146							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	19		Lung NSC(55;0.0659)|all_lung(88;0.152)				CTGCAGTCAGGGCTGAAGCGC	0.612																																					p.P146S		.											.	TBL2-90	0			c.C436T						.						95	75	82					7																	72988278		2203	4300	6503	SO:0001583	missense	26608	exon3			AGTCAGGGCTGAA	AF056183	CCDS5551.1	7q11.23	2013-01-10			ENSG00000106638	ENSG00000106638		"WD repeat domain containing"	11586	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 13"	605842				9860302, 10575226	Standard	XM_006715923		Approved	WS-betaTRP, WBSCR13, DKFZP43N024	uc003tyh.3	Q9Y4P3	OTTHUMG00000023427	ENST00000305632.5:c.436C>T	7.37:g.72988278G>A	ENSP00000307260:p.Pro146Ser	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	89	27	NM_012453	0	0	0	0	0	Q9UQE2	Missense_Mutation	SNP	ENST00000305632.5	37	CCDS5551.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.841121	0.91197	.	.	ENSG00000106638	ENST00000305632;ENST00000541783;ENST00000432538;ENST00000452475	T;T;T	0.38077	1.16;1.16;1.16	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66701	-0.5857	10	0.49607	T	0.09	-9.9847	16.4333	0.83861	0.0:0.0:1.0:0.0	.	110;146	E9PF19;Q9Y4P3	.;TBL2_HUMAN	S	146;146;110;146	ENSP00000307260:P146S;ENSP00000413979:P110S;ENSP00000407371:P146S	ENSP00000307260:P146S	P	-	1	0	TBL2	72626214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.735000	0.98825	2.491000	0.84063	0.561000	0.74099	CCT	.		0.612	TBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252233.3	NM_012453		A	72988278	G	A	72988278	3	1	82	1	0	0	0	0	1	0	0	0	15674	1232	43	2	927	2	TBL2	7	72988278	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	2732440	72988278	86150385	39	7597											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8750559	8750559	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaggttgccactgtccaTcccagccatggcggggcccc	5	8	11	17	1	1	0	1	0	0	0	3	0	3	0	6	4	2	1	6	4	0	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr8:8750559T>C	ENST00000276282.6	-	1	596	c.10A>G	c.(10-12)Atg>Gtg	p.M4V	RNU6-682P_ENST00000363843.1_RNA	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	4										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CCACTGTCCATCCCAGCCATG	0.756																																					p.M4V	Melanoma(103;1201 2045 17515 28966)	.											.	MFHAS1-90	0			c.A10G						.						3	3	3					8																	8750559		1577	3199	4776	SO:0001583	missense	9258	exon1			TGTCCATCCCAGC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.10A>G	8.37:g.8750559T>C	ENSP00000276282:p.Met4Val	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	15	5	NM_004225	0	0	0	0	0	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878455	0.33162	.	.	ENSG00000147324	ENST00000276282	T	0.33216	1.42	3.87	2.66	0.31614	.	1.223050	0.06260	N	0.693747	T	0.17152	0.0412	N	0.08118	0	0.21105	N	0.99978	B	0.02656	0.0	B	0.01281	0.0	T	0.28744	-1.0034	10	0.23891	T	0.37	.	8.696	0.34296	0.0:0.0:0.1918:0.8082	.	4	Q9Y4C4	MFHA1_HUMAN	V	4	ENSP00000276282:M4V	ENSP00000276282:M4V	M	-	1	0	MFHAS1	8787969	0.980000	0.34600	0.977000	0.42913	0.611000	0.37282	2.561000	0.45905	0.513000	0.28278	0.369000	0.22263	ATG	.		0.756	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8750559	T	C	8750559	3	2	82	1	0	0	0	0	1	0	0	0	9546	1435	50	3	3160	3	MFHAS1	8	8750559	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		8750559	137613463	40	7598											
MTUS1	57509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	17581310	17581310	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaggcaaattcacccatgAcgactgtgcagttttcaagg	11	11	9	10	1	3	1	2	1	1	0	3	2	3	1	1	2	1	3	1	2	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr8:17581310A>G	ENST00000262102.6	-	4	2544	c.2320T>C	c.(2320-2322)Tca>Cca	p.S774P	MTUS1_ENST00000519263.1_Intron|MTUS1_ENST00000544260.1_5'Flank|MTUS1_ENST00000381861.3_5'Flank|MTUS1_ENST00000381869.3_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	774					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCACCCATGACGACTGTGCA	0.463																																					p.S774P		.											.	MTUS1-92	0			c.T2320C						.						152	141	144					8																	17581310		1865	4099	5964	SO:0001583	missense	57509	exon4			CCCATGACGACTG	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2320T>C	8.37:g.17581310A>G	ENSP00000262102:p.Ser774Pro	Somatic	235	1		WXS	Illumina HiSeq	Phase_I	137	59	NM_001001924	0	0	1	3	2	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.980872	0.53827	.	.	ENSG00000129422	ENST00000262102	T	0.42900	0.96	3.8	3.8	0.43715	.	2.627820	0.01895	N	0.038843	T	0.55081	0.1898	L	0.32530	0.975	0.53688	D	0.999979	D	0.69078	0.997	D	0.64410	0.925	T	0.44528	-0.9322	10	0.29301	T	0.29	-2.2162	12.137	0.53977	1.0:0.0:0.0:0.0	.	774	Q9ULD2	MTUS1_HUMAN	P	774	ENSP00000262102:S774P	ENSP00000262102:S774P	S	-	1	0	MTUS1	17625590	0.099000	0.21834	0.064000	0.19789	0.885000	0.51271	2.939000	0.48995	1.933000	0.56026	0.533000	0.62120	TCA	.		0.463	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17581310	A	G	17581310	3	3	82	1	0	0	0	0	1	0	0	0	9990	275	10	3	1859	3	MTUS1	8	17581310	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	8830751	17581310	128782712	41	7599											
CLTA	1211	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	36211662	36211662	+	Frame_Shift_Del	DEL	G	G	-																															cccaggcactgagtgggaacGggtggcccggctgtgtgact																								rs192679731		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:36211662delG	ENST00000242285.6	+	7	758	c.638delG	c.(637-639)cggfs	p.R213fs	CLTA_ENST00000396603.2_Frame_Shift_Del_p.R201fs|CLTA_ENST00000433436.2_Frame_Shift_Del_p.R213fs|CLTA_ENST00000470744.1_Frame_Shift_Del_p.R195fs|CLTA_ENST00000466396.1_Frame_Shift_Del_p.R161fs|CLTA_ENST00000540080.1_Frame_Shift_Del_p.R131fs|CLTA_ENST00000538225.1_Frame_Shift_Del_p.R195fs|CLTA_ENST00000345519.5_Frame_Shift_Del_p.R183fs			P09496	CLCA_HUMAN	clathrin, light chain A	213					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			GAGTGGGAACGGGTGGCCCGG	0.542																																					p.R213fs		.											.	CLTA-90	0			c.638delG						.						99	94	96					9																	36211662		2203	4300	6503	SO:0001589	frameshift_variant	1211	exon7			.		CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"clathrin, light polypeptide (Lca)"			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.638delG	9.37:g.36211662delG	ENSP00000242285:p.Arg213fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	111	41	NM_007096	0	0	0	0	0	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Frame_Shift_Del	DEL	ENST00000242285.6	37	CCDS6601.1																																																																																			.		0.542	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		-	36211662	G	-	36211662	7	5	82	1	0	1	0	1	0	0	0	0	3570	1116	39	0	664	0	CLTA	9	36211662	Frame_Shift_Del	DEL	G	TCGA-BQ-7048-01A-11D-1961-08		36211662	105001769	42	7600											
TGFBR1	7046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	101894937	101894937	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagtgccaaatgaagaggacCcttcattagatcgccctttt	11	11	9	10	1	1	3	1	1	0	2	2	5	1	4	3	1	1	0	3	1	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:101894937C>G	ENST00000374994.4	+	3	607	c.490C>G	c.(490-492)Cct>Gct	p.P164A	TGFBR1_ENST00000552516.1_Missense_Mutation_p.P168A|TGFBR1_ENST00000550253.1_Missense_Mutation_p.P95A|TGFBR1_ENST00000374990.2_Intron	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	164					activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TGAAGAGGACCCTTCATTAGA	0.438																																					p.P164A		.											.	TGFBR1-954	0			c.C490G						.						160	135	144					9																	101894937		2203	4300	6503	SO:0001583	missense	7046	exon3			GAGGACCCTTCAT		CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"activin A receptor type II-like kinase, 53kDa"	190181	"transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)", "multiple self-healing squamous epithelioma"	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.490C>G	9.37:g.101894937C>G	ENSP00000364133:p.Pro164Ala	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	137	43	NM_004612	0	0	7	9	2	Q6IR47|Q706C0|Q706C1	Missense_Mutation	SNP	ENST00000374994.4	37	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.864541	0.51482	.	.	ENSG00000106799	ENST00000547314;ENST00000552573;ENST00000374994;ENST00000540092;ENST00000552516;ENST00000548365;ENST00000550253;ENST00000546584	T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.68495	0.3007	L	0.58583	1.82	0.80722	D	1	B	0.28850	0.225	B	0.31290	0.127	T	0.63310	-0.6666	10	0.11182	T	0.66	.	19.3122	0.94192	0.0:1.0:0.0:0.0	.	164	P36897	TGFR1_HUMAN	A	95;99;164;164;168;99;95;161	ENSP00000449934:P95A;ENSP00000447182:P99A;ENSP00000364133:P164A;ENSP00000447297:P168A;ENSP00000448518:P99A;ENSP00000450052:P95A;ENSP00000447707:P161A	ENSP00000364133:P164A	P	+	1	0	TGFBR1	100934758	1.000000	0.71417	0.993000	0.49108	0.981000	0.71138	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	CCT	.		0.438	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			G	101894937	C	G	101894937	3	3	82	1	0	0	0	0	1	0	0	0	15853	623	22	4	500	4	TGFBR1	9	101894937	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	65683275	101894937	39318494	43	7601											
DAB2IP	153090	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	124522288	124522288	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctctatgcccgcaccacggGcaagctcaagacggacaatg	11	5	11	14	3	2	1	1	0	1	1	2	2	2	2	2	2	2	4	2	2	4	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:124522288G>T	ENST00000408936.3	+	6	922	c.740G>T	c.(739-741)gGc>gTc	p.G247V	DAB2IP_ENST00000259371.2_Missense_Mutation_p.G219V|DAB2IP_ENST00000309989.1_Missense_Mutation_p.G123V			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	247	C2.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CGCACCACGGGCAAGCTCAAG	0.597																																					p.G219V													.	DAB2IP-91	0			c.G656T						.						124	113	117					9																	124522288		2203	4300	6503	SO:0001583	missense	153090	exon6			CCACGGGCAAGCT	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.740G>T	9.37:g.124522288G>T	ENSP00000386183:p.Gly247Val	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	72	18	NM_032552	0	0	9	14	5	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	37		.	.	.	.	.	.	.	.	.	.	G	16.06	3.014511	0.54468	.	.	ENSG00000136848	ENST00000394340;ENST00000436835;ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	4.97	4.97	0.65823	.	0.087217	0.85682	D	0.000000	T	0.35480	0.0933	N	0.01761	-0.735	0.80722	D	1	B	0.21071	0.051	B	0.22152	0.038	T	0.36187	-0.9758	10	0.66056	D	0.02	.	17.5948	0.88009	0.0:0.0:1.0:0.0	.	219	G3XA90	.	V	219;123;219;247;156;123	ENSP00000377872:G219V;ENSP00000409327:G123V;ENSP00000259371:G219V;ENSP00000386183:G247V;ENSP00000362887:G156V;ENSP00000310827:G123V	ENSP00000259371:G219V	G	+	2	0	DAB2IP	123562109	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	9.869000	0.99810	2.454000	0.82982	0.561000	0.74099	GGC	.		0.597	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		T	124522288	G	T	124522288	3	4	82	1	0	0	0	0	1	0	0	0	4225	1203	42	4	678	4	DAB2IP	9	124522288	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	22627351	124522288	16691143	44	7602											
COQ4	51117	bcgsc.ca	37	chr9	131095814	131095814	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcagaacgggcgcagagccCcatgtgtcctcaacctgtac	9	8	10	14	2	2	2	2	0	0	2	3	2	3	2	4	1	4	2	4	1	3	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:131095814C>A	ENST00000300452.3	+	7	1011	c.688C>A	c.(688-690)Cca>Aca	p.P230T	COQ4_ENST00000461102.1_3'UTR	NM_016035.3	NP_057119			coenzyme Q4											endometrium(4)|large_intestine(1)|lung(4)	9						GCGCAGAGCCCCATGTGTCCT	0.607																																					p.P230T													.	COQ4-90	0			c.C688A						.						65	63	64					9																	131095814		2203	4300	6503	SO:0001583	missense	51117	exon7			AGAGCCCCATGTG	AF151850	CCDS6898.1	9q34.2	2013-10-18	2013-10-18		ENSG00000167113	ENSG00000167113			19693	protein-coding gene	gene with protein product		612898	"coenzyme Q4 homolog (yeast)", "coenzyme Q4 homolog (S. cerevisiae)"			11469793, 18474229	Standard	NM_016035		Approved	CGI-92	uc004bur.4	Q9Y3A0	OTTHUMG00000020743	ENST00000300452.3:c.688C>A	9.37:g.131095814C>A	ENSP00000300452:p.Pro230Thr	Somatic	122	3		WXS	Illumina HiSeq	Phase_1	105	40	NM_016035	0	0	50	86	36		Missense_Mutation	SNP	ENST00000300452.3	37	CCDS6898.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015381	0.35511	.	.	ENSG00000167113	ENST00000300452	T	0.40225	1.04	5.52	5.52	0.82312	.	0.104785	0.64402	D	0.000008	T	0.29524	0.0736	N	0.25060	0.705	0.80722	D	1	P	0.39352	0.669	B	0.38106	0.265	T	0.05321	-1.0892	10	0.30078	T	0.28	-32.9145	12.1376	0.53981	0.2708:0.7292:0.0:0.0	.	230	Q9Y3A0	COQ4_HUMAN	T	230	ENSP00000300452:P230T	ENSP00000300452:P230T	P	+	1	0	COQ4	130135635	1.000000	0.71417	0.836000	0.33094	0.348000	0.29142	3.429000	0.52800	2.597000	0.87782	0.655000	0.94253	CCA	.		0.607	COQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054427.1	NM_016035		A	131095814	C	A	131095814	3	1	82	1	0	0	0	0	1	0	0	0	3753	623	22	4	714	4	COQ4	9	131095814	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	6573526	131095814	10117617	45	7603											
NUP214	8021	bcgsc.ca	37	chr9	134004848	134004848	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcaactcttccttccacGgtagcagtaacctctggtga	8	12	9	12	1	2	1	0	1	2	0	4	1	4	1	3	2	4	4	3	2	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:134004848G>T	ENST00000359428.5	+	4	720	c.576G>T	c.(574-576)acG>acT	p.T192T	NUP214_ENST00000411637.2_Silent_p.T192T|NUP214_ENST00000451030.1_Silent_p.T192T|RNU6-881P_ENST00000516813.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	192	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.T192T(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCCTTCCACGGTAGCAGTAA	0.448			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.T192T	Pancreas(4;24 48 25510 30394 32571)			Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214-1131	1	Substitution - coding silent(1)	endometrium(1)	c.G576T						.						193	161	172					9																	134004848		2203	4300	6503	SO:0001819	synonymous_variant	8021	exon4			TTCCACGGTAGCA	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.576G>T	9.37:g.134004848G>T		Somatic	181	2		WXS	Illumina HiSeq	Phase_1	193	14	NM_005085	0	0	5	6	1	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	CCDS6940.1																																																																																			.		0.448	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134004848	G	T	134004848	2	4	82	1	0	0	0	0	0	0	0	1	10788	1103	39	4		4	NUP214	9	134004848	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	2909034	134004848	7208583	46	7604											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61829643	61829643	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctagattggtttctacagTggtgtcccctgactgtggct	5	15	11	10	0	2	2	0	1	2	1	3	2	3	2	2	3	1	2	2	3	2	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:61829643T>C	ENST00000280772.2	-	37	11187	c.10996A>G	c.(10996-10998)Act>Gct	p.T3666A	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3666					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GTTTCTACAGTGGTGTCCCCT	0.532																																					p.T3666A		.											.	ANK3-107	0			c.A10996G						.						105	110	108					10																	61829643		2203	4300	6503	SO:0001583	missense	288	exon37			CTACAGTGGTGTC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.10996A>G	10.37:g.61829643T>C	ENSP00000280772:p.Thr3666Ala	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	69	32	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	7.641	0.680808	0.14907	.	.	ENSG00000151150	ENST00000280772	T	0.18016	2.24	5.67	1.95	0.26073	.	0.170468	0.27831	N	0.017678	T	0.09730	0.0239	L	0.27053	0.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16748	-1.0392	10	0.41790	T	0.15	.	4.0495	0.09788	0.2679:0.1431:0.0:0.589	.	3666	Q12955	ANK3_HUMAN	A	3666	ENSP00000280772:T3666A	ENSP00000280772:T3666A	T	-	1	0	ANK3	61499649	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.468000	0.35332	0.366000	0.24427	0.533000	0.62120	ACT	.		0.532	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61829643	T	C	61829643	3	2	82	1	0	0	0	0	1	0	0	0	622	1696	59	3	2478	3	ANK3	10	61829643	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		61829643	73705104	47	7605											
SFTPD	6441	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	81702148	81702148	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaccagccacctacctttGggcccagcttctccttttgg	6	11	8	16	0	1	1	0	0	1	1	2	1	1	1	6	2	3	1	6	2	1	5	rs2077117		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:81702148G>C	ENST00000372292.3	-	4	469	c.429C>G	c.(427-429)ccC>ccG	p.P143P		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	143	Collagen-like.				defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			ACCTACCTTTGGGCCCAGCTT	0.607																																					p.P143P		.											.	SFTPD-91	0			c.C429G						.						82	75	77					10																	81702148		2203	4300	6503	SO:0001819	synonymous_variant	6441	exon4			ACCTTTGGGCCCA	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"Collectins"	10803	protein-coding gene	gene with protein product		178635	"surfactant, pulmonary-associated protein D"	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.429C>G	10.37:g.81702148G>C		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	59	22	NM_003019	0	0	0	0	0	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Silent	SNP	ENST00000372292.3	37	CCDS7362.1																																																																																			.		0.607	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1			C	81702148	G	C	81702148	2	2	82	1	0	0	0	0	0	0	0	1	14225	1335	47	4		4	SFTPD	10	81702148	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	19872505	81702148	53832599	48	7606											
ADD3	120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	111878343	111878343	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtccttctgattttttccAggtgaaagtcaatataatag	12	16	7	6	0	2	2	1	2	1	0	4	2	4	2	2	1	0	0	2	1	5	7			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:111878343A>G	ENST00000356080.4	+	6	934		c.e6-1		ADD3_ENST00000277900.8_Splice_Site|ADD3_ENST00000497125.1_Splice_Site|ADD3_ENST00000360162.3_Splice_Site	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)							cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GATTTTTTCCAGGTGAAAGTC	0.378																																					.		.											.	ADD3-157	0			c.568-2A>G						.						102	104	103					10																	111878343		2203	4300	6503	SO:0001630	splice_region_variant	120	exon6			TTTTCCAGGTGAA	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.568-1A>G	10.37:g.111878343A>G		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	82	35	NM_019903	0	0	0	0	0	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Splice_Site	SNP	ENST00000356080.4	37	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.241968	0.58995	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	.	.	.	5.28	4.11	0.48088	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8604	0.52463	0.8691:0.0:0.0:0.1309	.	.	.	.	.	-1	.	.	.	+	.	.	ADD3	111868333	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.423000	0.80229	0.905000	0.36596	0.460000	0.39030	.	.		0.378	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903	Intron	G	111878343	A	G	111878343	5	3	82	1	0	0	0	0	0	0	1	0	306	202	7	3	584	3	ADD3	10	111878343	Splice_Site	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	30176195	111878343	23656404	49	7607											
MICALCL	84953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	12316190	12316190	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccctcagactcaaagaCaaatcttttgagagtttcct	11	13	5	12	0	3	3	2	1	1	3	6	4	6	3	3	0	0	1	3	0	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:12316190C>T	ENST00000256186.2	+	3	1503	c.1212C>T	c.(1210-1212)gaC>gaT	p.D404D		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	404					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		GACTCAAAGACAAATCTTTTG	0.468																																					p.D404D		.											.	MICALCL-91	0			c.C1212T						.						121	123	122					11																	12316190		1848	4097	5945	SO:0001819	synonymous_variant	84953	exon3			CAAAGACAAATCT	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1212C>T	11.37:g.12316190C>T		Somatic	238	0		WXS	Illumina HiSeq	Phase_I	181	65	NM_032867	0	0	0	0	0	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	37	CCDS41620.1																																																																																			.		0.468	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		T	12316190	C	T	12316190	2	4	82	1	0	0	0	0	0	0	0	1	9597	477	17	2		2	MICALCL	11	12316190	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		12316190	122690326	50	7608											
TTC17	55761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	43418965	43418965	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcacacttctctgctgatgCtgctgtcgtggtccatgcag	6	12	11	12	1	1	1	0	1	1	0	4	1	2	1	1	1	5	5	1	1	0	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:43418965C>A	ENST00000039989.4	+	7	856	c.842C>A	c.(841-843)gCt>gAt	p.A281D	TTC17_ENST00000299240.6_Missense_Mutation_p.A281D|TTC17_ENST00000526774.1_3'UTR|RP11-484D2.4_ENST00000394183.2_RNA	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	281					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						TCTGCTGATGCTGCTGTCGTG	0.443																																					p.A281D		.											.	TTC17-95	0			c.C842A						.						238	201	213					11																	43418965		2203	4300	6503	SO:0001583	missense	55761	exon7			CTGATGCTGCTGT	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"Tetratricopeptide (TTC) repeat domain containing"	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.842C>A	11.37:g.43418965C>A	ENSP00000039989:p.Ala281Asp	Somatic	276	2		WXS	Illumina HiSeq	Phase_I	270	122	NM_018259	0	0	12	22	10	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	C	35	5.554829	0.96514	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.72725	-0.68;-0.68	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.86892	0.6042	M	0.85462	2.755	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.998;0.999	D	0.87691	0.2554	10	0.87932	D	0	-12.9642	20.3206	0.98668	0.0:1.0:0.0:0.0	.	281;281;281	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	D	281	ENSP00000299240:A281D;ENSP00000039989:A281D	ENSP00000039989:A281D	A	+	2	0	TTC17	43375541	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.809000	0.96659	0.655000	0.94253	GCT	.		0.443	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		A	43418965	C	A	43418965	3	1	82	1	0	0	0	0	1	0	0	0	16717	797	28	4	868	4	TTC17	11	43418965	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	31102775	43418965	91587551	51	7609											
OR5T3	390154	broad.mit.edu;bcgsc.ca	37	chr11	56019938	56019938	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggattcctggctccacaaccCcatgtattattttcttagtg	8	15	7	11	0	1	0	0	0	1	0	3	1	3	1	4	2	1	2	4	2	4	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:56019938C>T	ENST00000303059.3	+	1	263	c.263C>T	c.(262-264)cCc>cTc	p.P88L		NM_001004747.1	NP_001004747.1	Q8NGG3	OR5T3_HUMAN	olfactory receptor, family 5, subfamily T, member 3	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(23)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	39	Esophageal squamous(21;0.00448)					CTCCACAACCCCATGTATTAT	0.363																																					p.P88L													.	OR5T3-68	0			c.C263T						.						97	96	96					11																	56019938		2201	4296	6497	SO:0001583	missense	390154	exon1			ACAACCCCATGTA	AB065837	CCDS31524.1	11q11	2012-08-09			ENSG00000172489	ENSG00000172489		"GPCR / Class A : Olfactory receptors"	15297	protein-coding gene	gene with protein product							Standard	NM_001004747		Approved	OR5T3Q	uc010rjd.2	Q8NGG3	OTTHUMG00000166852	ENST00000303059.3:c.263C>T	11.37:g.56019938C>T	ENSP00000305403:p.Pro88Leu	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	99	28	NM_001004747	0	0	0	0	0	Q6IFC7	Missense_Mutation	SNP	ENST00000303059.3	37	CCDS31524.1	.	.	.	.	.	.	.	.	.	.	c	16.19	3.053057	0.55218	.	.	ENSG00000172489	ENST00000303059	T	0.02032	4.49	4.55	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39759	U	0.001271	T	0.11067	0.0270	H	0.94542	3.55	0.58432	D	0.999999	P	0.41450	0.75	B	0.43360	0.417	T	0.04090	-1.0978	10	0.87932	D	0	.	17.8308	0.88682	0.0:1.0:0.0:0.0	.	88	Q8NGG3	OR5T3_HUMAN	L	88	ENSP00000305403:P88L	ENSP00000305403:P88L	P	+	2	0	OR5T3	55776514	1.000000	0.71417	0.958000	0.39756	0.083000	0.17756	7.047000	0.76599	2.512000	0.84698	0.643000	0.83706	CCC	.		0.363	OR5T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391599.1	NM_001004747		T	56019938	C	T	56019938	3	4	82	1	0	0	0	0	1	0	0	0	11209	623	22	2	265	2	OR5T3	11	56019938	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	12600973	56019938	78986578	52	7610											
OR8U8	219417	broad.mit.edu;bcgsc.ca	37	chr11	56143937	56143937	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctctgtcttctacacaGtgatcattcccatgttgaat	8	15	7	11	0	4	2	1	2	3	0	5	2	5	2	2	1	1	1	2	1	2	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:56143937G>C	ENST00000302270.1	+	1	838	c.838G>C	c.(838-840)Gtg>Ctg	p.V280L		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					CTTCTACACAGTGATCATTCC	0.413																																					p.V280L													.	OR8U1-72	0			c.G838C						.						143	148	146					11																	56143937		2044	4227	6271	SO:0001583	missense	219417	exon1			TACACAGTGATCA	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"GPCR / Class A : Olfactory receptors"	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.838G>C	11.37:g.56143937G>C	ENSP00000304188:p.Val280Leu	Somatic	317	0		WXS	Illumina HiSeq	Phase_I	280	10	NM_001005204	0	0	0	0	0		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.254672	0.01457	.	.	ENSG00000172199	ENST00000302270	T	0.00279	8.33	5.69	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	0.174841	0.27411	N	0.019484	T	0.00178	0.0005	N	0.21448	0.665	0.09310	N	1	B	0.28933	0.228	B	0.41666	0.363	T	0.23940	-1.0174	10	0.11794	T	0.64	.	7.9511	0.30014	0.1954:0.1192:0.6855:0.0	.	280	Q8NH10	OR8U1_HUMAN	L	280	ENSP00000304188:V280L	ENSP00000304188:V280L	V	+	1	0	OR8U1	55900513	0.061000	0.20836	0.998000	0.56505	0.181000	0.23173	0.606000	0.24194	1.425000	0.47237	-0.245000	0.11935	GTG	.		0.413	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204		C	56143937	G	C	56143937	3	2	82	1	0	0	0	0	1	0	0	0	11273	1029	36	4	32	4	OR8U8	11	56143937	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	123999	56143937	78862579	53	7611											
C1QTNF5	114902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119210071	119210071	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actggggagctgtgccagtcGgagtacaccagaaatccgga	11	6	14	10	2	0	1	0	0	0	1	2	4	1	4	3	4	3	2	3	4	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:119210071G>C	ENST00000528368.1	-	3	933	c.702C>G	c.(700-702)tcC>tcG	p.S234S	C1QTNF5_ENST00000525657.1_5'UTR|MFRP_ENST00000555262.1_3'UTR|RP11-334E6.10_ENST00000501918.2_RNA|MFRP_ENST00000530681.1_3'UTR|C1QTNF5_ENST00000445041.2_Silent_p.S234S	NM_001278431.1	NP_001265360.1	Q9BXJ0	C1QT5_HUMAN	C1q and tumor necrosis factor related protein 5	234	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(2)	3		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		TGTGCCAGTCGGAGTACACCA	0.552																																					p.S234S		.											.	C1QTNF5-90	0			c.C702G						.						100	93	96					11																	119210071		2199	4295	6494	SO:0001819	synonymous_variant	114902	exon15			CCAGTCGGAGTAC	AF329841	CCDS8420.1	11q23.3	2013-05-10				ENSG00000223953			14344	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 5", "complement C1q tumor necrosis factor-related protein 5 precursor variant 3"	608752				12944416	Standard	NM_015645		Approved	CTRP5, DKFZp586B0621, LORD		Q9BXJ0	OTTHUMG00000166198	ENST00000528368.1:c.702C>G	11.37:g.119210071G>C		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_015645	0	0	66	98	32	A6NDD3|B0YJ35|Q335M2|Q8N6P2|Q9UFX4	Silent	SNP	ENST00000528368.1	37	CCDS8420.1																																																																																			.		0.552	C1QTNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388354.1	NM_015645		C	119210071	G	C	119210071	2	2	82	1	0	0	0	0	0	0	0	1	1972	1103	39	4		4	C1QTNF5	11	119210071	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	63066134	119210071	15796445	54	7612											
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12302076	12302076	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggaactgagctcacaacCacagtaaagccctagggaaa	15	5	9	12	1	1	1	1	1	0	0	2	3	1	3	2	2	4	2	2	2	6	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:12302076C>T	ENST00000261349.4	-	14	3082	c.3006G>A	c.(3004-3006)gtG>gtA	p.V1002V	LRP6_ENST00000543091.1_Silent_p.V1002V	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1002	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AGCTCACAACCACAGTAAAGC	0.453																																					p.V1002V		.											.	LRP6-661	0			c.G3006A						.						135	137	136					12																	12302076		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon14			CACAACCACAGTA	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.3006G>A	12.37:g.12302076C>T		Somatic	282	0		WXS	Illumina HiSeq	Phase_I	262	115	NM_002336	0	0	0	1	1	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			.		0.453	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12302076	C	T	12302076	2	4	82	1	0	0	0	0	0	0	0	1	8987	581	21	2		2	LRP6	12	12302076	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		12302076	121549819	55	7613											
C12orf54	121273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48888593	48888593	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacagaagcataaggccTccagattccttgatgacccc	11	8	9	13	0	0	4	0	2	0	2	2	4	2	4	5	2	1	2	5	2	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:48888593T>C	ENST00000548364.1	+	7	312	c.255T>C	c.(253-255)ccT>ccC	p.P85P	RP11-722P11.4_ENST00000551847.1_RNA|C12orf54_ENST00000314014.2_Silent_p.P85P			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	85										endometrium(1)|large_intestine(4)	5						GCATAAGGCCTCCAGATTCCT	0.488																																					p.P85P		.											.	C12orf54-90	0			c.T255C						.						114	116	116					12																	48888593		2203	4300	6503	SO:0001819	synonymous_variant	121273	exon8			AAGGCCTCCAGAT	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.255T>C	12.37:g.48888593T>C		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	183	75	NM_152319	0	0	0	0	0	Q6X4S9|Q8N5S2	Silent	SNP	ENST00000548364.1	37	CCDS8764.1																																																																																			.		0.488	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319		C	48888593	T	C	48888593	2	2	82	1	0	0	0	0	0	0	0	1	1703	1538	54	3		3	C12orf54	12	48888593	Silent	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	36586517	48888593	84963302	56	7614											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49437679	49437679	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagggaacatgtcctccAgtttgctcttcttgcgccct	7	12	9	13	1	2	0	0	0	2	0	4	1	4	1	3	1	4	3	3	1	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:49437679A>G	ENST00000301067.7	-	22	5290	c.5291T>C	c.(5290-5292)cTg>cCg	p.L1764P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1764					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CATGTCCTCCAGTTTGCTCTT	0.567											OREG0021780	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1764P		.											.	MLL2-612	0			c.T5291C						.						166	177	174					12																	49437679		2147	4242	6389	SO:0001583	missense	8085	exon22			TCCTCCAGTTTGC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.5291T>C	12.37:g.49437679A>G	ENSP00000301067:p.Leu1764Pro	Somatic	147	0	962	WXS	Illumina HiSeq	Phase_I	119	38	NM_003482	0	0	0	0	0	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.462524	0.43736	.	.	ENSG00000167548	ENST00000301067	D	0.92199	-2.99	4.93	4.93	0.64822	.	.	.	.	.	D	0.94925	0.8359	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95361	0.8455	9	0.87932	D	0	.	13.5598	0.61782	1.0:0.0:0.0:0.0	.	1764	O14686	MLL2_HUMAN	P	1764	ENSP00000301067:L1764P	ENSP00000301067:L1764P	L	-	2	0	MLL2	47723946	1.000000	0.71417	0.941000	0.38009	0.935000	0.57460	9.259000	0.95561	1.846000	0.53633	0.260000	0.18958	CTG	.		0.567	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49437679	A	G	49437679	3	3	82	1	0	0	0	0	1	0	0	0	9646	188	7	3	11454	3	MLL2	12	49437679	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	549086	49437679	84414216	57	7615											
CNOT2	4848	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	70704758	70704758	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgacgaaaacatgtactaCagccagtcttctatgtttcc	12	12	6	11	1	2	1	0	1	2	0	3	2	3	1	2	0	4	2	2	0	5	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:70704758C>T	ENST00000418359.3	+	4	583	c.132C>T	c.(130-132)taC>taT	p.Y44Y	CNOT2_ENST00000229195.3_Silent_p.Y44Y	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	44					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			ACATGTACTACAGCCAGTCTT	0.378																																					p.Y44Y													.	CNOT2-226	0			c.C132T						.						112	104	107					12																	70704758		2203	4300	6503	SO:0001819	synonymous_variant	4848	exon4			GTACTACAGCCAG	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.132C>T	12.37:g.70704758C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	80	20	NM_001199302	0	0	9	19	10	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Silent	SNP	ENST00000418359.3	37	CCDS31857.1																																																																																			.		0.378	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			T	70704758	C	T	70704758	2	4	82	1	0	0	0	0	0	0	0	1	3625	489	17	2		2	CNOT2	12	70704758	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	21267079	70704758	63147137	58	7616											
EPSTI1	94240	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr13	43462629	43462629	+	Intron	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagataggagtcaatattttCtcatataccctggaagaaaa	16	11	7	7	0	2	2	2	0	1	2	3	4	2	4	1	2	1	0	1	2	8	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr13:43462629C>A	ENST00000398762.3	-	12	957				EPSTI1_ENST00000313640.7_Missense_Mutation_p.E330D|EPSTI1_ENST00000313624.7_3'UTR			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)											endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		TCAATATTTTCTCATATACCC	0.358																																					p.E330D		.											.	EPSTI1-91	0			c.G990T						.						56	61	59					13																	43462629		2203	4300	6503	SO:0001627	intron_variant	94240	exon13			TATTTTCTCATAT	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"epithelial stromal interaction protein 1"	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.954+1G>T	13.37:g.43462629C>A		Somatic	156	2		WXS	Illumina HiSeq	Phase_I	149	57	NM_001002264	0	0	1	1	0	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	37	CCDS9387.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.280732	0.40294	.	.	ENSG00000133106	ENST00000313640	.	.	.	5.63	4.79	0.61399	.	0.094876	0.39210	N	0.001421	T	0.63474	0.2514	.	.	.	0.80722	D	1	D	0.55385	0.971	P	0.58077	0.832	T	0.59799	-0.7386	8	0.21540	T	0.41	-6.4173	10.8984	0.47036	0.0:0.9136:0.0:0.0864	.	330	Q96J88-3	.	D	330	.	ENSP00000318982:E330D	E	-	3	2	EPSTI1	42360629	1.000000	0.71417	0.995000	0.50966	0.550000	0.35303	2.068000	0.41471	1.538000	0.49270	0.655000	0.94253	GAG	.		0.358	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		A	43462629	C	A	43462629	1	1	82	0	1	0	0	0	0	0	0	0	5211	912	32	4		4	EPSTI1	13	43462629	Intron	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		43462629	71707249	59	7617											
KCTD4	386618	broad.mit.edu	37	chr13	45768267	45768269	+	In_Frame_Del	DEL	TTA	TTA	-																															tgaacgatcgtggttatctgTtatttccaagaaagtagtct																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	TTA	TTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr13:45768267_45768269delTTA	ENST00000379108.1	-	1	583_585	c.434_436delTAA	c.(433-438)ataaca>aca	p.I145del	KCTD4_ENST00000405872.1_In_Frame_Del_p.I145del|GTF2F2_ENST00000340473.6_Intron			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	145					protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		TGGTTATCTGTTATTTCCAAGAA	0.414																																					p.145_146del													.	KCTD4-90	0			c.434_436del						.																																			SO:0001651	inframe_deletion	386618	exon2			TATCTGTTATTTC	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.434_436delTAA	13.37:g.45768267_45768269delTTA	ENSP00000368402:p.Ile145del	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	154	15	NM_198404	0	0	0	0	0	Q5W0P9	In_Frame_Del	DEL	ENST00000379108.1	37	CCDS9396.1																																																																																			.		0.414	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			-	45768269	TTA	-	45768267	7	5	82	1	0	1	0	1	0	0	0	0	8132	1725	60	0	347	0	KCTD4	13	45768267	In_Frame_Del	DEL	TTA	TCGA-BQ-7048-01A-11D-1961-08	2305638	45768267	69401611	60	7618											
POTEG	404785	broad.mit.edu;bcgsc.ca	37	chr14	19553567	19553567	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcacttctggagaccacgacGattctgctatgaagacactc	11	9	9	12	2	2	3	0	1	2	2	3	6	2	3	1	1	1	2	1	1	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr14:19553567G>A	ENST00000409832.3	+	1	203	c.151G>A	c.(151-153)Gat>Aat	p.D51N		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	51										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						AGACCACGACGATTCTGCTAT	0.602																																					p.D51N													.	POTEG-1	0			c.G151A						.						101	139	126					14																	19553567		2198	4286	6484	SO:0001583	missense	404785	exon1			CACGACGATTCTG		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33896	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 4"	608916	"ANKRD26-like family C, member 2"	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.151G>A	14.37:g.19553567G>A	ENSP00000386971:p.Asp51Asn	Somatic	1420	1		WXS	Illumina HiSeq	Phase_I	1334	50	NM_001005356	0	0	0	0	0	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	11.02	1.515679	0.27123	.	.	ENSG00000222036	ENST00000409832	T	0.39997	1.05	.	.	.	.	.	.	.	.	T	0.48572	0.1507	L	0.43152	1.355	0.09310	N	1	D	0.89917	1.0	D	0.68353	0.957	T	0.34304	-0.9834	7	0.36615	T	0.2	.	.	.	.	.	51	Q6S5H5	POTEG_HUMAN	N	51	ENSP00000386971:D51N	ENSP00000386971:D51N	D	+	1	0	POTEG	18623567	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	0.488000	0.22371	0.162000	0.19483	0.165000	0.16767	GAT	.		0.602	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356		A	19553567	G	A	19553567	3	1	82	1	0	0	0	0	1	0	0	0	12292	1058	37	1	153	1	POTEG	14	19553567	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		19553567	87795973	61	7619											
NFKBIA	4792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	35872504	35872504	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagctcaggatcacagccAgctcccagaagtgcctcagc	10	5	11	15	1	3	1	3	0	0	1	4	3	4	3	3	2	5	2	3	2	1	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr14:35872504A>G	ENST00000216797.5	-	3	500	c.399T>C	c.(397-399)gcT>gcC	p.A133A	NFKBIA_ENST00000557389.1_Silent_p.A43A|NFKBIA_ENST00000557140.1_Silent_p.A133A|NFKBIA_ENST00000557100.1_5'UTR	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	133					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	GATCACAGCCAGCTCCCAGAA	0.562																																					p.A133A		.											.	NFKBIA-721	0			c.T399C						.						91	96	95					14																	35872504		2203	4300	6503	SO:0001819	synonymous_variant	4792	exon3			ACAGCCAGCTCCC		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"Ankyrin repeat domain containing"	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.399T>C	14.37:g.35872504A>G		Somatic	151	1		WXS	Illumina HiSeq	Phase_I	139	7	NM_020529	0	0	121	137	16	B2R8L6	Silent	SNP	ENST00000216797.5	37	CCDS9656.1																																																																																			.		0.562	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		G	35872504	A	G	35872504	2	3	82	1	0	0	0	0	0	0	0	1	10403	175	7	3		3	NFKBIA	14	35872504	Silent	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	16318937	35872504	71477036	62	7620											
KLHDC1	122773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	50196254	50196254	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaaacctagacacctggaCttggtctggaaggtaagttt	11	12	10	8	0	2	1	0	0	2	1	2	3	2	3	2	4	1	2	2	4	5	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr14:50196254C>G	ENST00000359332.2	+	8	788	c.698C>G	c.(697-699)aCt>aGt	p.T233S	KLHDC1_ENST00000554512.1_3'UTR	NM_172193.2	NP_751943.1	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	233						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	12	all_epithelial(31;0.00244)|Breast(41;0.00964)					GACACCTGGACTTGGTCTGGA	0.348																																					p.T233S		.											.	KLHDC1-91	0			c.C698G						.						115	104	108					14																	50196254		2203	4299	6502	SO:0001583	missense	122773	exon8			CCTGGACTTGGTC	AF111806	CCDS9692.1	14q21.3	2007-08-01			ENSG00000197776	ENSG00000197776			19836	protein-coding gene	gene with protein product		611281					Standard	NM_172193		Approved	MST025	uc001www.3	Q8N7A1	OTTHUMG00000140295	ENST00000359332.2:c.698C>G	14.37:g.50196254C>G	ENSP00000352282:p.Thr233Ser	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	61	24	NM_172193	0	0	0	0	0	B3KXD9|Q8WYI1	Missense_Mutation	SNP	ENST00000359332.2	37	CCDS9692.1	.	.	.	.	.	.	.	.	.	.	C	9.838	1.190260	0.21954	.	.	ENSG00000197776	ENST00000359332;ENST00000557128	T;T	0.67523	-0.27;-0.27	5.78	1.34	0.21922	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.164679	0.53938	D	0.000057	T	0.48241	0.1489	N	0.25485	0.75	0.23636	N	0.997233	B;B	0.30361	0.277;0.085	B;B	0.31547	0.132;0.038	T	0.30297	-0.9983	10	0.21014	T	0.42	-0.3182	9.4425	0.38677	0.0:0.5979:0.0:0.4021	.	104;233	G3V3T1;Q8N7A1	.;KLDC1_HUMAN	S	233;104	ENSP00000352282:T233S;ENSP00000451407:T104S	ENSP00000352282:T233S	T	+	2	0	KLHDC1	49266004	0.933000	0.31639	0.991000	0.47740	0.956000	0.61745	0.163000	0.16520	-0.028000	0.13850	-0.237000	0.12165	ACT	.		0.348	KLHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276882.2	NM_172193		G	50196254	C	G	50196254	3	3	82	1	0	0	0	0	1	0	0	0	8375	565	20	4	728	4	KLHDC1	14	50196254	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	14323750	50196254	57153286	63	7621											
ENTPD5	957	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	74443764	74443765	+	Splice_Site	INS	-	-	A																															taacccaagctaatatgcctINSaaaaagaaagaaagacaagg																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr14:74443764_74443765insA	ENST00000334696.6	-	8	837		c.e8-2		ENTPD5_ENST00000557325.1_Splice_Site	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5						'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CTAATATGCCTAAAAAGAAAGA	0.366																																					.		.											.	ENTPD5-91	0			c.518-2->T						.																																			SO:0001630	splice_region_variant	957	exon9			.	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"proto-oncogene CPH"	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.518-2->T	14.37:g.74443769_74443769dupA		Somatic	144	0		WXS	Illumina HiSeq	Phase_I	100	38	NM_001249	0	0	0	0	0	A1L4C5|Q96RX0	Splice_Site	INS	ENST00000334696.6	37	CCDS9825.1																																																																																			.		0.366	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	Intron	A	74443765	-	A	74443764	8	5	82	1	0	1	1	0	0	0	1	0	5155	1536	53	0	806	0	ENTPD5	14	74443764	Splice_Site	INS	-	TCGA-BQ-7048-01A-11D-1961-08	24247510	74443764	32905776	64	7622											
ATP10A	57194	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	25959142	25959142	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagctccgaggcccagttgtCcgcctggctgctgtagccgt	5	9	13	14	3	0	0	0	0	0	0	2	1	2	0	5	2	3	5	5	2	2	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr15:25959142C>A	ENST00000356865.6	-	10	2134	c.2023G>T	c.(2023-2025)Gac>Tac	p.D675Y		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	675					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCCCAGTTGTCCGCCTGGCTG	0.692																																					p.D675Y													.	ATP10A-139	0			c.G2023T						.						24	26	25					15																	25959142		2199	4296	6495	SO:0001583	missense	57194	exon10			AGTTGTCCGCCTG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"ATPases / P-type"	13542	protein-coding gene	gene with protein product		605855	"ATPase, Class V, type 10C", "ATPase, Class V, type 10A"	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2023G>T	15.37:g.25959142C>A	ENSP00000349325:p.Asp675Tyr	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	50	14	NM_024490	0	0	0	0	0	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	8.047	0.765185	0.15914	.	.	ENSG00000206190	ENST00000356865	T	0.10860	2.83	3.77	2.83	0.33086	HAD-like domain (1);	1.723910	0.02350	N	0.075817	T	0.15305	0.0369	L	0.29908	0.895	0.09310	N	1	P	0.38395	0.629	P	0.45474	0.482	T	0.32613	-0.9900	10	0.59425	D	0.04	-3.2906	8.5411	0.33393	0.1612:0.525:0.3138:0.0	.	675	O60312	AT10A_HUMAN	Y	675	ENSP00000349325:D675Y	ENSP00000349325:D675Y	D	-	1	0	ATP10A	23510235	0.002000	0.14202	0.003000	0.11579	0.038000	0.13279	1.500000	0.35682	0.911000	0.36747	0.561000	0.74099	GAC	.		0.692	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25959142	C	A	25959142	3	1	82	1	0	0	0	0	1	0	0	0	1117	855	30	4	2524	4	ATP10A	15	25959142	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		25959142	76572250	65	7623											
GABRG3	2567	broad.mit.edu	37	chr15	27777965	27777965	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggactcgtactcccgggtcTttttccccacgtccttcctg	3	14	8	16	3	1	0	0	0	1	0	6	1	5	1	5	2	1	1	5	2	1	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr15:27777965T>C	ENST00000333743.6	+	10	1596	c.1342T>C	c.(1342-1344)Ttt>Ctt	p.F448L	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	448					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)	CTCCCGGGTCTTTTTCCCCAC	0.473																																					p.F448L	NSCLC(114;800 1656 7410 37729 45293)												.	.	0			c.T1342C						.						72	73	73					15																	27777965		1952	4142	6094	SO:0001583	missense	2567	exon10			CGGGTCTTTTTCC		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.1342T>C	15.37:g.27777965T>C	ENSP00000331912:p.Phe448Leu	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_033223	0	0	0	0	0	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.954120	0.53293	.	.	ENSG00000182256	ENST00000333743	T	0.80824	-1.42	5.75	3.4	0.38934	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.175067	0.50627	D	0.000109	T	0.65080	0.2657	N	0.20401	0.57	0.80722	D	1	B	0.25206	0.12	B	0.33196	0.159	T	0.49504	-0.8933	10	0.08837	T	0.75	.	7.9945	0.30261	0.0:0.0709:0.1369:0.7922	.	448	Q99928	GBRG3_HUMAN	L	448	ENSP00000331912:F448L	ENSP00000331912:F448L	F	+	1	0	GABRG3	25451560	1.000000	0.71417	0.319000	0.25293	0.894000	0.52154	4.846000	0.62860	0.422000	0.26005	0.528000	0.53228	TTT	.		0.473	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			C	27777965	T	C	27777965	3	2	82	1	0	0	0	0	1	0	0	0	6192	1609	56	3	1380	3	GABRG3	15	27777965	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	1818823	27777965	74753427	66	7624											
PLA2G4F	255189	broad.mit.edu	37	chr15	42444915	42444915	+	Frame_Shift_Del	DEL	C	C	-																															cccgtggggctgtcccatctCcccggagcgtgccctggatt																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr15:42444915delC	ENST00000382396.4	-	7	658	c.572delG	c.(571-573)ggafs	p.G191fs	PLA2G4F_ENST00000397272.3_Frame_Shift_Del_p.G191fs			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	191					arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		TGTCCCATCTCCCCGGAGCGT	0.622																																					p.G191fs													.	PLA2G4F-94	0			c.572delG						.						48	40	42					15																	42444915		2187	4269	6456	SO:0001589	frameshift_variant	255189	exon7			CCATCTCCCCGGA		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.572delG	15.37:g.42444915delC	ENSP00000371833:p.Gly191fs	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_213600	0	0	0	0	0	Q6ZMC8	Frame_Shift_Del	DEL	ENST00000382396.4	37	CCDS32204.1																																																																																			.		0.622	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		-	42444915	C	-	42444915	7	5	82	1	0	1	0	1	0	0	0	0	12032	855	30	0	2033	0	PLA2G4F	15	42444915	Frame_Shift_Del	DEL	C	TCGA-BQ-7048-01A-11D-1961-08	14666950	42444915	60086477	67	7625											
MESDC2	23184	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	81282037	81282037	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgggcgagccttcggccgcGcaggacccaggcggtggtag	5	4	18	14	6	0	0	0	0	0	0	1	2	0	1	4	6	1	2	4	6	1	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr15:81282037G>A	ENST00000261758.4	-	1	182	c.96C>T	c.(94-96)tgC>tgT	p.C32C	RP11-775C24.3_ENST00000563737.1_lincRNA	NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	32	Chaperone domain. {ECO:0000250}.				mesoderm development (GO:0007498)|protein folding (GO:0006457)|protein localization to cell surface (GO:0034394)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(5)|ovary(1)|urinary_tract(1)	8						CTTCGGCCGCGCAGGACCCAG	0.637																																					p.C32C		.											.	MESDC2-90	0			c.C96T						.						35	35	35					15																	81282037		2203	4298	6501	SO:0001819	synonymous_variant	23184	exon1			GGCCGCGCAGGAC	D42039	CCDS32308.1	15q13	2008-07-18							13520	protein-coding gene	gene with protein product		607783				7788527, 11247670	Standard	NM_015154		Approved	KIAA0081, BOCA, MESD	uc002bfy.1	Q14696		ENST00000261758.4:c.96C>T	15.37:g.81282037G>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	68	33	NM_015154	0	0	10	22	12	B4DW84|D3DW96|Q969U1	Silent	SNP	ENST00000261758.4	37	CCDS32308.1																																																																																			.		0.637	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		A	81282037	G	A	81282037	2	1	82	1	0	0	0	0	0	0	0	1	9506	1079	38	1		1	MESDC2	15	81282037	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	38837122	81282037	21249355	68	7626											
C16orf53	79447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	29830999	29830999	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggacctcttcagcctggactCggaggaccccagccccgcca	7	5	11	18	2	2	0	1	0	1	0	3	4	2	4	7	4	2	0	7	4	0	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr16:29830999C>G	ENST00000320330.6	+	3	1251	c.689C>G	c.(688-690)tCg>tGg	p.S230W	PAGR1_ENST00000609618.1_Missense_Mutation_p.S230W|MVP_ENST00000357402.5_5'Flank|AC009133.12_ENST00000569809.1_RNA|AC009133.20_ENST00000569039.1_RNA|AC009133.12_ENST00000564980.1_RNA|MVP_ENST00000395353.1_5'Flank|MVP_ENST00000452209.2_5'Flank			Q9BTK6	PAGR1_HUMAN	PAXIP1 associated glutamate-rich protein 1	230						histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)											AGCCTGGACTCGGAGGACCCC	0.637																																					p.S230W		.											.	.	0			c.C689G						.						67	72	70					16																	29830999		2197	4300	6497	SO:0001583	missense	79447	exon3			TGGACTCGGAGGA	BC003640	CCDS10655.1	16p11.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000185928	ENSG00000185928			28707	protein-coding gene	gene with protein product	"glutamate-rich coactivator interacting with SRC1/NCOA1", "PTIP-associated 1 protein", "glutamate-rich coactivator associated with SRC1"	612033	"chromosome 16 open reading frame 53"	C16orf53		17500065, 19039327	Standard	NM_024516		Approved	MGC4606, GAS, PA1	uc002dug.4	Q9BTK6	OTTHUMG00000132117	ENST00000320330.6:c.689C>G	16.37:g.29830999C>G	ENSP00000326519:p.Ser230Trp	Somatic	147	1		WXS	Illumina HiSeq	Phase_I	113	23	NM_024516	0	0	31	41	10	A2ICR6	Missense_Mutation	SNP	ENST00000320330.6	37	CCDS10655.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524695	0.85600	.	.	ENSG00000185928	ENST00000320330	.	.	.	5.82	5.82	0.92795	.	0.357942	0.29424	N	0.012191	T	0.65471	0.2694	L	0.36672	1.1	0.45161	D	0.998178	D	0.59357	0.985	P	0.58577	0.841	T	0.67098	-0.5756	9	0.87932	D	0	-3.3155	17.5892	0.87991	0.0:1.0:0.0:0.0	.	230	Q9BTK6	PA1_HUMAN	W	230	.	ENSP00000326519:S230W	S	+	2	0	C16orf53	29738500	0.977000	0.34250	1.000000	0.80357	0.863000	0.49368	1.880000	0.39628	2.767000	0.95098	0.655000	0.94253	TCG	.		0.637	PAGR1-002	PUTATIVE	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000473165.1	NM_024516		G	29830999	C	G	29830999	3	3	82	1	0	0	0	0	1	0	0	0	1822	893	31	4	699	4	C16orf53	16	29830999	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		29830999	60523754	69	7627											
ABCC12	94160	broad.mit.edu	37	chr16	48180262	48180262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtcttcaggctggggtcaTatctttctgcaaaggatctc	7	14	11	9	0	6	0	2	0	4	0	7	1	6	1	0	5	1	2	0	5	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr16:48180262T>C	ENST00000311303.3	-	1	419	c.74A>G	c.(73-75)tAt>tGt	p.Y25C	ABCC12_ENST00000416054.1_Missense_Mutation_p.Y25C|ABCC12_ENST00000448542.1_Missense_Mutation_p.Y25C	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	25						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				GCTGGGGTCATATCTTTCTGC	0.587																																					p.Y25C													.	ABCC12-93	0			c.A74G						.						173	148	156					16																	48180262		2201	4300	6501	SO:0001583	missense	94160	exon1			GGGTCATATCTTT	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"ATP binding cassette transporters / subfamily C"	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.74A>G	16.37:g.48180262T>C	ENSP00000311030:p.Tyr25Cys	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	148	5	NM_033226	0	0	0	0	0	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.403980	0.62288	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054;ENST00000527640	D;D;D;D	0.95412	-3.11;-3.37;-3.52;-3.7	5.45	4.35	0.52113	.	0.146288	0.47093	D	0.000255	D	0.97306	0.9119	M	0.86651	2.83	0.44635	D	0.997611	P;D	0.63046	0.871;0.992	P;D	0.64776	0.779;0.929	D	0.96898	0.9658	10	0.87932	D	0	.	9.5569	0.39343	0.0:0.0:0.177:0.823	.	25;25	Q96J65-2;Q96J65	.;MRP9_HUMAN	C	25	ENSP00000311030:Y25C;ENSP00000401855:Y25C;ENSP00000413046:Y25C;ENSP00000436647:Y25C	ENSP00000311030:Y25C	Y	-	2	0	ABCC12	46737763	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.858000	0.55979	0.875000	0.35847	0.496000	0.49642	TAT	.		0.587	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		C	48180262	T	C	48180262	3	2	82	1	0	0	0	0	1	0	0	0	52	1406	49	3	4121	3	ABCC12	16	48180262	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	18349263	48180262	42174491	70	7628											
ZNF423	23090	broad.mit.edu;ucsc.edu	37	chr16	49670868	49670868	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgcacctggatggacaccTtggagtcgaagacctcctga	9	8	13	11	1	0	2	0	1	0	1	2	6	1	5	4	4	1	1	4	4	1	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr16:49670868T>A	ENST00000561648.1	-	4	2248	c.2195A>T	c.(2194-2196)aAg>aTg	p.K732M	ZNF423_ENST00000567169.1_Missense_Mutation_p.K615M|ZNF423_ENST00000262383.2_Missense_Mutation_p.K732M|ZNF423_ENST00000563137.2_Missense_Mutation_p.K672M|ZNF423_ENST00000562520.1_Missense_Mutation_p.K672M|ZNF423_ENST00000562871.1_Missense_Mutation_p.K672M|ZNF423_ENST00000535559.1_Missense_Mutation_p.K615M	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	732					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GATGGACACCTTGGAGTCGAA	0.562																																					p.K732M													.	ZNF423-228	0			c.A2195T						.						100	92	95					16																	49670868		2198	4300	6498	SO:0001583	missense	23090	exon4			GACACCTTGGAGT	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"Zinc fingers, C2H2-type"	16762	protein-coding gene	gene with protein product	"OLF-1/EBF associated zinc finger gene", " Smad- and Olf-interacting zinc finger protein", "early B-cell factor associated zinc finger protein"	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.2195A>T	16.37:g.49670868T>A	ENSP00000455426:p.Lys732Met	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	49	6	NM_015069	0	0	3	3	0	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.101470	0.56183	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.31247	1.5;1.5	5.05	5.05	0.67936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.51143	0.1657	L	0.58669	1.825	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	T	0.48658	-0.9016	9	.	.	.	.	14.8066	0.69962	0.0:0.0:0.0:1.0	.	732	Q2M1K9	ZN423_HUMAN	M	732;615	ENSP00000262383:K732M;ENSP00000442321:K615M	.	K	-	2	0	ZNF423	48228369	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	1.907000	0.55213	0.459000	0.35465	AAG	.		0.562	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49670868	T	A	49670868	3	1	82	1	0	0	0	0	1	0	0	0	17930	1609	56	5	1679	5	ZNF423	16	49670868	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	1490606	49670868	40683885	71	7629											
MAF	4094	hgsc.bcm.edu	37	chr16	79633040	79633040	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtcgtcgaagtgcaggcCgccggcggcgtggtgcgggt	3	6	21	11	8	0	0	0	0	0	0	2	1	0	0	2	6	2	1	2	6	1	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr16:79633040C>G	ENST00000393350.1	-	1	1571	c.760G>C	c.(760-762)Ggc>Cgc	p.G254R	MAF_ENST00000326043.4_Missense_Mutation_p.G254R|MAF_ENST00000569649.1_Missense_Mutation_p.G254R	NM_001031804.2	NP_001026974.1	O75444	MAF_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog	254	Gly-rich.|Represses ARE-mediated transcription.				cell development (GO:0048468)|cytokine production (GO:0001816)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of chondrocyte differentiation (GO:0032330)|transcription from RNA polymerase II promoter (GO:0006366)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)	10		all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211)		UCEC - Uterine corpus endometrioid carcinoma (2;0.0178)		AAGTGCAGGCCGCCGGCGGCG	0.791			T	IGH@	MM																																p.G254R		.		Dom	yes		16	16q22-q23	4094	v-maf musculoaponeurotic fibrosarcoma oncogene homolog		L	.	MAF-1270	0			c.G760C						.						6	7	6					16																	79633040		2125	4201	6326	SO:0001583	missense	4094	exon1			GCAGGCCGCCGGC		CCDS10928.1, CCDS42198.1	16q22-q23	2013-07-09	2013-07-09		ENSG00000178573	ENSG00000178573			6776	protein-coding gene	gene with protein product		177075				14998484	Standard	NM_005360		Approved	c-MAF	uc002ffm.3	O75444	OTTHUMG00000137621	ENST00000393350.1:c.760G>C	16.37:g.79633040C>G	ENSP00000377019:p.Gly254Arg	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_001031804	0	0	45	81	36	Q66I47|Q9UP93	Missense_Mutation	SNP	ENST00000393350.1	37	CCDS42198.1	.	.	.	.	.	.	.	.	.	.	C	4.402	0.074251	0.08485	.	.	ENSG00000178573	ENST00000326043;ENST00000393350	T;T	0.80123	-1.34;-1.34	3.26	2.26	0.28386	.	0.620036	0.12924	U	0.427943	T	0.64148	0.2572	N	0.19112	0.55	0.25604	N	0.986568	B;P	0.39391	0.399;0.671	B;B	0.41946	0.048;0.371	T	0.53865	-0.8378	10	0.10636	T	0.68	-14.237	5.2354	0.15443	0.0:0.6509:0.2161:0.133	.	254;254	O75444;O75444-1	MAF_HUMAN;.	R	254	ENSP00000327048:G254R;ENSP00000377019:G254R	ENSP00000327048:G254R	G	-	1	0	MAF	78190541	.	.	0.980000	0.43619	0.978000	0.69477	.	.	1.540000	0.49301	0.442000	0.29010	GGC	.		0.791	MAF-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317037.1			G	79633040	C	G	79633040	3	3	82	1	0	0	0	0	1	0	0	0	9180	652	23	4	463	4	MAF	16	79633040	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	29962172	79633040	10721713	72	7630											
GFAP	2670	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	42987523	42987523	+	Intron	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctaaccgcgagccggcggcGttccatttacaatctggtga	8	9	12	12	5	1	1	0	1	1	0	2	2	2	1	3	3	3	2	3	3	3	4	rs9908084|rs386797323	byFrequency	TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:42987523G>C	ENST00000253408.5	-	7	1237				GFAP_ENST00000588735.1_Intron|GFAP_ENST00000435360.2_Missense_Mutation_p.T426R	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein						astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				AGCCGGCGGCGTTCCATTTAC	0.537																																					p.T426R		.											.	GFAP-516	0			c.C1277G						.						215	191	198					17																	42987523		1568	3582	5150	SO:0001627	intron_variant	2670	exon8			GGCGGCGTTCCAT	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"Intermediate filaments type III"	4235	protein-coding gene	gene with protein product	"intermediate filament protein"	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1171+459C>G	17.37:g.42987523G>C		Somatic	158	1		WXS	Illumina HiSeq	Phase_I	149	48	NM_001131019	0	0	0	0	0	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.251401	0.39797	.	.	ENSG00000131095	ENST00000435360	D	0.84516	-1.86	4.79	3.8	0.43715	.	.	.	.	.	T	0.70193	0.3196	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.67791	-0.5579	9	0.66056	D	0.02	.	9.5131	0.39089	0.0951:0.0:0.9049:0.0	.	426	E9PAX3	.	R	426	ENSP00000403962:T426R	ENSP00000403962:T426R	T	-	2	0	GFAP	40343049	1.000000	0.71417	0.910000	0.35882	0.158000	0.22134	1.941000	0.40233	1.599000	0.50093	0.655000	0.94253	ACG	G|0.911;A|0.089		0.537	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		C	42987523	G	C	42987523	1	2	82	0	1	0	0	0	0	0	0	0	6357	1145	40	4		4	GFAP	17	42987523	Intron	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		42987523	38207687	73	7631											
HSF5	124535	broad.mit.edu;bcgsc.ca	37	chr17	56565509	56565509	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcggcctcgaagagcggctGatcgataagcagcccctcgc	8	6	12	15	5	0	2	0	1	0	1	4	4	0	2	3	2	3	2	3	2	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:56565509G>A	ENST00000323777.3	-	1	236	c.127C>T	c.(127-129)Cag>Tag	p.Q43*		NM_001080439.1	NP_001073908.1	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	43					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	16	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAGAGCGGCTGATCGATAAGC	0.726																																					p.Q43X													.	HSF5-71	0			c.C127T						.						8	10	10					17																	56565509		1895	3831	5726	SO:0001587	stop_gained	124535	exon1			GCGGCTGATCGAT	BC033020	CCDS32690.1	17q23.2	2006-04-25				ENSG00000176160			26862	protein-coding gene	gene with protein product							Standard	NM_001080439		Approved	FLJ40311	uc002iwi.1	Q4G112		ENST00000323777.3:c.127C>T	17.37:g.56565509G>A	ENSP00000313243:p.Gln43*	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	35	18	NM_001080439	0	0	0	0	0	Q08EH7|Q8N7V2	Nonsense_Mutation	SNP	ENST00000323777.3	37	CCDS32690.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.96|18.96	3.733181|3.733181	0.69189|0.69189	.|.	.|.	ENSG00000176160|ENSG00000176160	ENST00000323777|ENST00000412540	.|.	.|.	.|.	4.09|4.09	4.09|4.09	0.47781|0.47781	.|.	0.000000|.	0.45361|.	D|.	0.000367|.	.|T	.|0.60818	.|0.2298	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73164	.|-0.4069	.|4	0.40728|0.87932	T|D	0.16|0	.|.	10.7446|10.7446	0.46172|0.46172	0.0:0.0:0.8095:0.1905|0.0:0.0:0.8095:0.1905	.|.	.|.	.|.	.|.	X|L	43|64	.|.	ENSP00000313243:Q43X|ENSP00000396453:S64L	Q|S	-|-	1|2	0|0	HSF5|HSF5	53920508|53920508	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.244000|0.244000	0.25665|0.25665	4.373000|4.373000	0.59537|0.59537	2.269000|2.269000	0.75478|0.75478	0.462000|0.462000	0.41574|0.41574	CAG|TCA	.		0.726	HSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444719.1	XM_064190		A	56565509	G	A	56565509	4	1	82	1	0	0	0	0	0	1	0	0	7420	1299	45	2	1687	2	HSF5	17	56565509	Nonsense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	13577986	56565509	24629701	74	7632											
GPR142	350383	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72368139	72368139	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tacactgccctgtgccacccCctgcaccatcgggccgcctc	5	7	8	21	2	0	0	0	0	0	0	2	0	0	0	7	1	4	1	7	1	1	1	rs143074832		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:72368139C>A	ENST00000335666.4	+	4	837	c.789C>A	c.(787-789)ccC>ccA	p.P263P		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	263						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						TGTGCCACCCCCTGCACCATC	0.667																																					p.P263P													.	GPR142-93	0			c.C789A						.						61	48	52					17																	72368139		2202	4300	6502	SO:0001819	synonymous_variant	350383	exon4			CCACCCCCTGCAC	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"GPCR / Class A : Orphans"	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.789C>A	17.37:g.72368139C>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	51	9	NM_181790	0	0	0	0	0	A4CYJ8|Q86SL3	Silent	SNP	ENST00000335666.4	37	CCDS11698.1																																																																																			C|0.999;T|0.001		0.667	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		A	72368139	C	A	72368139	2	1	82	1	0	0	0	0	0	0	0	1	6670	610	22	4		4	GPR142	17	72368139	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	15802630	72368139	8827071	75	7633											
RNF157	114804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74158077	74158077	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttatcactcacttcgtcttCagccacctggccaaggagaa	10	10	8	13	1	4	1	3	0	1	1	5	2	4	1	3	2	1	1	3	2	3	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:74158077C>A	ENST00000269391.6	-	10	931	c.799G>T	c.(799-801)Gaa>Taa	p.E267*	RNF157_ENST00000319945.6_Nonsense_Mutation_p.E267*	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	267							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			ACTTCGTCTTCAGCCACCTGG	0.527																																					p.E267X	GBM(186;507 2120 27388 27773 52994)	.											.	RNF157-228	0			c.G799T						.						96	68	78					17																	74158077		2203	4300	6503	SO:0001587	stop_gained	114804	exon10			CGTCTTCAGCCAC	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"RING-type (C3HC4) zinc fingers"	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.799G>T	17.37:g.74158077C>A	ENSP00000269391:p.Glu267*	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	67	31	NM_052916	0	0	0	0	0	Q8NB72|Q96N56	Nonsense_Mutation	SNP	ENST00000269391.6	37	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	38	6.984953	0.97983	.	.	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	.	.	.	5.73	5.73	0.89815	.	0.044080	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-18.6068	19.893	0.96937	0.0:1.0:0.0:0.0	.	.	.	.	X	267;267;229	.	ENSP00000269391:E267X	E	-	1	0	RNF157	71669672	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.782000	0.85680	2.693000	0.91896	0.655000	0.94253	GAA	.		0.527	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		A	74158077	C	A	74158077	4	1	82	1	0	0	0	0	0	1	0	0	13486	835	29	4	1280	4	RNF157	17	74158077	Nonsense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	1789938	74158077	7037133	76	7634											
TMC6	11322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	76115385	76115385	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agaggaccctcaccaggtcaGagtctgcccataaatcagct	12	7	9	13	0	4	2	3	0	1	2	4	3	4	3	3	2	2	1	3	2	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:76115385G>C	ENST00000590602.1	-	14	1963	c.1804C>G	c.(1804-1806)Ctg>Gtg	p.L602V	TMC6_ENST00000591436.1_Missense_Mutation_p.L181V|TMC6_ENST00000322914.3_Missense_Mutation_p.L602V|TMC6_ENST00000392467.3_Missense_Mutation_p.L602V|TMC6_ENST00000322933.4_Missense_Mutation_p.L181V|TMC6_ENST00000592076.1_Intron|TMC6_ENST00000306591.7_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	602					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CACCAGGTCAGAGTCTGCCCA	0.622																																					p.L602V		.											.	TMC6-90	0			c.C1804G						.						133	117	123					17																	76115385		2203	4300	6503	SO:0001583	missense	11322	exon14			AGGTCAGAGTCTG	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"epidermodysplasia verruciformis 1"	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.1804C>G	17.37:g.76115385G>C	ENSP00000465261:p.Leu602Val	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	100	31	NM_001127198	0	0	0	0	0	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.992746	0.74703	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933;ENST00000392466	T;T;T	0.67698	-0.28;-0.28;-0.28	4.72	4.72	0.59763	.	0.000000	0.64402	D	0.000002	T	0.79707	0.4492	L	0.60904	1.88	0.47994	D	0.999565	D;D	0.89917	0.998;1.0	D;D	0.83275	0.98;0.996	T	0.82232	-0.0559	10	0.72032	D	0.01	-16.0397	17.6365	0.88123	0.0:0.0:1.0:0.0	.	602;181	Q7Z403;Q7Z403-3	TMC6_HUMAN;.	V	602;602;181;68	ENSP00000313408:L602V;ENSP00000376260:L602V;ENSP00000313479:L181V	ENSP00000313408:L602V	L	-	1	2	TMC6	73626980	1.000000	0.71417	0.980000	0.43619	0.951000	0.60555	3.385000	0.52485	2.164000	0.68074	0.555000	0.69702	CTG	.		0.622	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			C	76115385	G	C	76115385	3	2	82	1	0	0	0	0	1	0	0	0	16021	933	33	4	641	4	TMC6	17	76115385	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	1957308	76115385	5079825	77	7635											
SERPINB11	89778	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	61379816	61379816	+	RNA	DEL	A	A	-																															cagtgcagccaagctggaagAattcattccgagtttggtgt																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr18:61379816delA	ENST00000382749.5	+	0	491				SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000536691.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				AAGCTGGAAGAATTCATTCCG	0.423																																					.	Ovarian(27;496 784 5942 8975 23930)	.											.	SERPINB11-67	0			.						.						96	96	96					18																	61379816		1888	4113	6001			89778	.			.			18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"Serine (or cysteine) peptidase inhibitors"	14221	protein-coding gene	gene with protein product		615682	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11", "serpin peptidase inhibitor, clade B (ovalbumin), member 11"			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61379816delA		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	127	50	.	0	0	0	0	0	A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	Targeted_Region	DEL	ENST00000382749.5	37																																																																																				.		0.423	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475		-	61379816	A	-	61379816	6	5	82	0	1	1	0	1	0	0	0	0	14130	243	9	0		0	SERPINB11	18	61379816	RNA	DEL	A	TCGA-BQ-7048-01A-11D-1961-08		61379816	16697432	78	7636											
LGI4	163175	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	35617832	35617832	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caggcagcggccggcgaaggGctgtgccagcacaatgtgag	9	4	17	11	3	0	1	0	1	0	0	0	2	0	1	2	4	3	3	2	4	2	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr19:35617832G>T	ENST00000310123.3	-	7	1237	c.718C>A	c.(718-720)Ccc>Acc	p.P240T	LGI4_ENST00000392225.3_Missense_Mutation_p.P240T|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	240					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCGGCGAAGGGCTGTGCCAGC	0.662																																					p.P240T		.											.	LGI4-91	0			c.C718A						.						40	46	44					19																	35617832		2203	4300	6503	SO:0001583	missense	163175	exon7			CGAAGGGCTGTGC	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.718C>A	19.37:g.35617832G>T	ENSP00000312273:p.Pro240Thr	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	334	26	NM_139284	0	0	4	4	0	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	37	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.222746	0.58668	.	.	ENSG00000153902	ENST00000310123;ENST00000392225;ENST00000437421	D;D	0.81579	-1.51;-1.51	3.94	3.94	0.45596	.	0.000000	0.64402	D	0.000013	D	0.87245	0.6129	M	0.64170	1.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88525	0.3099	10	0.72032	D	0.01	.	13.5039	0.61474	0.0:0.0:1.0:0.0	.	151;240	Q658V8;Q8N135	.;LGI4_HUMAN	T	240	ENSP00000312273:P240T;ENSP00000376059:P240T	ENSP00000312273:P240T	P	-	1	0	LGI4	40309672	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	7.564000	0.82326	2.025000	0.59659	0.313000	0.20887	CCC	.		0.662	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			T	35617832	G	T	35617832	3	4	82	1	0	0	0	0	1	0	0	0	8776	1203	42	4	907	4	LGI4	19	35617832	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		35617832	23511151	79	7637											
ZNF335	63925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44579218	44579218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggggccgtaggcttgagTgctgtgccatgtgcgcctgc	3	10	18	10	2	0	1	0	1	0	0	0	1	0	1	3	4	4	3	3	4	1	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr20:44579218T>C	ENST00000322927.2	-	21	3306	c.3206A>G	c.(3205-3207)cAc>cGc	p.H1069R	ZNF335_ENST00000426788.1_Missense_Mutation_p.H914R	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1069					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TAGGCTTGAGTGCTGTGCCAT	0.592																																					p.H1069R		.											.	ZNF335-94	0			c.A3206G						.						126	137	133					20																	44579218		2203	4300	6503	SO:0001583	missense	63925	exon21			CTTGAGTGCTGTG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3206A>G	20.37:g.44579218T>C	ENSP00000325326:p.His1069Arg	Somatic	256	0		WXS	Illumina HiSeq	Phase_I	229	25	NM_022095	0	0	5	5	0	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	37	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.613272	0.66672	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	D;D	0.88975	-2.45;-2.45	4.82	4.82	0.62117	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97235	0.9096	H	0.99783	4.775	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.98479	1.0604	10	0.87932	D	0	-30.0634	14.0159	0.64523	0.0:0.0:0.0:1.0	.	914;1069	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	R	1069;846;914	ENSP00000325326:H1069R;ENSP00000397098:H914R	ENSP00000243961:H846R	H	-	2	0	ZNF335	44012625	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.442000	0.80503	2.166000	0.68216	0.460000	0.39030	CAC	.		0.592	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		C	44579218	T	C	44579218	3	2	82	1	0	0	0	0	1	0	0	0	17884	1696	59	3	854	3	ZNF335	20	44579218	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		44579218	18446302	80	7638											
ZFP64	55734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	50701575	50701575	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggtcggcctggtgcagccGgctgtgctccaggaggtcag	4	8	18	11	2	1	0	1	0	0	0	3	1	2	1	3	6	3	3	3	6	0	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr20:50701575G>A	ENST00000361387.2	-	9	1519	c.1459C>T	c.(1459-1461)Cgg>Tgg	p.R487W	ZFP64_ENST00000371523.4_Missense_Mutation_p.R268W|ZFP64_ENST00000371518.2_Intron	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	335					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(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TGGTGCAGCCGGCTGTGCTCC	0.632																																					p.R487W		.											.	ZFP64-155	0			c.C1459T						.						55	59	58					20																	50701575		2203	4300	6503	SO:0001583	missense	55734	exon9			GCAGCCGGCTGTG	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.1459C>T	20.37:g.50701575G>A	ENSP00000355179:p.Arg487Trp	Somatic	134	1		WXS	Illumina HiSeq	Phase_I	145	37	NM_199427	0	0	1	4	3	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000361387.2	37	CCDS13439.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.187374	0.78789	.	.	ENSG00000020256	ENST00000371523;ENST00000361387	T;T	0.09073	3.02;3.03	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.34483	0.0899	M	0.89214	3.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.988;0.999	T	0.27706	-1.0066	9	0.87932	D	0	.	14.6115	0.68519	0.0:0.0:0.8542:0.1458	.	487;268	Q9NTW7;Q9NTW7-2	ZF64B_HUMAN;.	W	268;487	ENSP00000360578:R268W;ENSP00000355179:R487W	ENSP00000355179:R487W	R	-	1	2	ZFP64	50134982	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.318000	0.33643	2.569000	0.86673	0.655000	0.94253	CGG	.		0.632	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197		A	50701575	G	A	50701575	3	1	82	1	0	0	0	0	1	0	0	0	17684	1115	39	1	482	1	ZFP64	20	50701575	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	6122357	50701575	12323945	81	7639											
ZBTB46	140685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62421455	62421455	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gaggcccgtagcccacgtctCcaggccatagaggctgtgaa	9	6	13	13	2	1	2	0	1	1	1	2	3	1	2	4	3	1	2	4	3	3	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr20:62421455C>G	ENST00000245663.4	-	2	806	c.656G>C	c.(655-657)gGa>gCa	p.G219A	ZBTB46_ENST00000395104.1_Missense_Mutation_p.G219A|ZBTB46_ENST00000480766.1_5'Flank|ZBTB46_ENST00000302995.2_Missense_Mutation_p.G219A	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	219					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCCCACGTCTCCAGGCCATAG	0.602																																					p.G219A		.											.	ZBTB46-154	0			c.G656C						.						65	61	62					20																	62421455		2203	4300	6503	SO:0001583	missense	140685	exon2			ACGTCTCCAGGCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.656G>C	20.37:g.62421455C>G	ENSP00000245663:p.Gly219Ala	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	59	23	NM_025224	0	0	3	4	1	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	37	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	C	7.452	0.642959	0.14451	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.08807	3.05;3.05;3.05	5.53	5.53	0.82687	.	0.168310	0.53938	D	0.000060	T	0.08846	0.0219	L	0.40543	1.245	0.26386	N	0.976659	B	0.12630	0.006	B	0.10450	0.005	T	0.34428	-0.9829	10	0.08837	T	0.75	.	18.4243	0.90604	0.0:1.0:0.0:0.0	.	219	Q86UZ6	ZBT46_HUMAN	A	219	ENSP00000245663:G219A;ENSP00000303102:G219A;ENSP00000378536:G219A	ENSP00000245663:G219A	G	-	2	0	ZBTB46	61891899	0.511000	0.26179	0.923000	0.36655	0.092000	0.18411	3.313000	0.51935	2.609000	0.88269	0.650000	0.86243	GGA	.		0.602	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		G	62421455	C	G	62421455	3	3	82	1	0	0	0	0	1	0	0	0	17579	855	30	4	1129	4	ZBTB46	20	62421455	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	11719880	62421455	604065	82	7640											
KRTAP27-1	643812	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	31709825	31709825	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcagctggtggtttcattGcaggtttcttgaaagttgtc	6	16	13	6	0	2	1	1	1	1	0	3	1	2	1	0	4	2	6	0	4	1	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr21:31709825G>A	ENST00000382835.2	-	1	187	c.162C>T	c.(160-162)tgC>tgT	p.C54C		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	54						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						TGGTTTCATTGCAGGTTTCTT	0.448																																					p.C54C		.											.	KRTAP27-1-24	0			c.C162T						.						159	150	153					21																	31709825		2203	4300	6503	SO:0001819	synonymous_variant	643812	exon1			TTCATTGCAGGTT	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"Keratin associated proteins"	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.162C>T	21.37:g.31709825G>A		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	145	50	NM_001077711	0	0	0	0	0		Silent	SNP	ENST00000382835.2	37	CCDS33532.1																																																																																			.		0.448	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		A	31709825	G	A	31709825	2	1	82	1	0	0	0	0	0	0	0	1	8565	1311	46	2		2	KRTAP27-1	21	31709825	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		31709825	16420070	83	7641											
TIAM1	7074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	32638551	32638551	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatttgctccccggccccccGtttgctgtcactccagagtt	5	12	8	16	2	1	1	1	0	0	1	3	1	3	1	6	1	2	4	6	1	1	3	rs202182190	byFrequency	TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr21:32638551G>A	ENST00000286827.3	-	5	1209	c.738C>T	c.(736-738)aaC>aaT	p.N246N	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Silent_p.N246N	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	246					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CCGGCCCCCCGTTTGCTGTCA	0.537													G|||	2	0.000399361	0	0	5008	,	,		16227	0.001		0	False		,,,				2504	0.001				p.N246N		.											.	TIAM1-724	0			c.C738T						.						68	72	71					21																	32638551		2203	4300	6503	SO:0001819	synonymous_variant	7074	exon5			CCCCCCGTTTGCT		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.738C>T	21.37:g.32638551G>A		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	147	48	NM_003253	0	0	0	0	0	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																			G|0.999;A|0.000		0.537	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32638551	G	A	32638551	2	1	82	1	0	0	0	0	0	0	0	1	15922	1136	40	1		1	TIAM1	21	32638551	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	928726	32638551	15491344	84	7642											
XKR3	150165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	17280836	17280836	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatcgtgtttctctttgtGatgctaacttgagtctcttc	6	18	8	9	1	2	2	0	2	2	0	6	2	2	2	0	0	3	3	0	0	1	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:17280836G>T	ENST00000331428.5	-	3	516	c.414C>A	c.(412-414)atC>atA	p.I138I		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TTCTCTTTGTGATGCTAACTT	0.398																																					p.I138I		.											.	XKR3-92	0			c.C414A						.						209	186	193					22																	17280836		1885	4131	6016	SO:0001819	synonymous_variant	150165	exon3			CTTTGTGATGCTA	AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"X Kell blood group precursor-related family, member 3"			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.414C>A	22.37:g.17280836G>T		Somatic	152	2		WXS	Illumina HiSeq	Phase_I	123	54	NM_175878	0	0	0	0	0	B2RPN1|Q52PG8|Q8N7E1	Silent	SNP	ENST00000331428.5	37	CCDS42975.1																																																																																			.		0.398	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		T	17280836	G	T	17280836	2	4	82	1	0	0	0	0	0	0	0	1	17465	1280	45	4		4	XKR3	22	17280836	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		17280836	34023730	85	7643											
SMARCB1	6598	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	24145544	24145544	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcagcccgaggtgctggtccCcatccggctggacatggaga	7	7	14	13	2	1	1	1	0	0	1	3	4	3	2	4	5	2	2	4	5	0	0	rs137986695		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:24145544C>T	ENST00000263121.7	+	5	759	c.563C>T	c.(562-564)cCc>cTc	p.P188L	SMARCB1_ENST00000344921.6_Missense_Mutation_p.P197L|SMARCB1_ENST00000407422.3_Missense_Mutation_p.P179L|SMARCB1_ENST00000407082.3_Missense_Mutation_p.P142L	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	188	2 X approximate tandem repeats.|HIV-1 integrase-binding.|MYC-binding.				ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(6)|p.P188L(1)|p.V185_M193del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GTGCTGGTCCCCATCCGGCTG	0.592			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.P188L		.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1-2699	8	Unknown(3)|Deletion - Frameshift(3)|Substitution - Missense(1)|Deletion - In frame(1)	soft_tissue(5)|central_nervous_system(2)|skin(1)	c.C563T						.						114	103	107					22																	24145544		2203	4300	6503	SO:0001583	missense	6598	exon5			TGGTCCCCATCCG	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.563C>T	22.37:g.24145544C>T	ENSP00000263121:p.Pro188Leu	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	114	10	NM_003073	0	0	142	147	5	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	37	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	C	34	5.321447	0.95682	.	.	ENSG00000099956	ENST00000417137;ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71;-3.71	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.98251	0.9421	M	0.92784	3.345	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.993;0.999	D;D;D;D	0.97110	0.982;1.0;0.983;0.997	D	0.99323	1.0907	10	0.72032	D	0.01	-25.3436	17.5295	0.87810	0.0:1.0:0.0:0.0	.	197;179;188;206	G5E975;Q17S11;Q12824;C9JTA6	.;.;SNF5_HUMAN;.	L	206;197;188;179;142	ENSP00000388489:P206L;ENSP00000340883:P197L;ENSP00000263121:P188L;ENSP00000383984:P179L;ENSP00000385226:P142L	ENSP00000263121:P188L	P	+	2	0	SMARCB1	22475544	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.810000	0.86072	2.472000	0.83506	0.644000	0.83932	CCC	.		0.592	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		T	24145544	C	T	24145544	3	4	82	1	0	0	0	0	1	0	0	0	14806	623	22	2	581	2	SMARCB1	22	24145544	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	6864708	24145544	27159022	86	7644											
DRG1	4733	hgsc.bcm.edu;broad.mit.edu	37	chr22	31799189	31799189	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacaaaggtgccaagatccAggtgagtcaagcctgcagac	14	6	11	10	0	1	3	1	1	0	2	2	3	2	3	3	2	4	1	3	2	4	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:31799189A>G	ENST00000331457.4	+	3	502	c.341A>G	c.(340-342)cAg>cGg	p.Q114R	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	114	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						GCCAAGATCCAGGTGAGTCAA	0.458																																					p.Q114R		.											.	DRG1-90	0			c.A341G						.						63	55	57					22																	31799189		2203	4300	6503	SO:0001630	splice_region_variant	4733	exon3			AGATCCAGGTGAG	AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"developmentally regulated GTP-binding protein 1"	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.342+1A>G	22.37:g.31799189A>G		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	52	3	NM_004147	0	0	0	0	0	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Missense_Mutation	SNP	ENST00000331457.4	37	CCDS13897.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.565846	0.86439	.	.	ENSG00000185721	ENST00000331457	T	0.31247	1.5	5.25	5.25	0.73442	Small GTP-binding protein domain (1);GTP-binding domain, HSR1-related (1);	0.103621	0.64402	D	0.000002	T	0.57975	0.2090	M	0.90922	3.16	0.80722	D	1	P	0.50943	0.94	P	0.55011	0.766	T	0.69026	-0.5254	10	0.87932	D	0	-19.5383	15.0384	0.71767	1.0:0.0:0.0:0.0	.	114	Q9Y295	DRG1_HUMAN	R	114	ENSP00000329715:Q114R	ENSP00000329715:Q114R	Q	+	2	0	DRG1	30129189	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.378000	0.90144	2.288000	0.76882	0.533000	0.62120	CAG	.		0.458	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147	Missense_Mutation	G	31799189	A	G	31799189	5	3	82	1	0	0	0	0	0	0	1	0	4772	202	7	3	351	3	DRG1	22	31799189	Splice_Site	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	7653645	31799189	19505377	87	7645											
C1QTNF6	114904	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37578392	37578392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctctgcatgatgctgcgctCgctgggctgcgcgtacagga	5	9	15	12	4	1	1	0	1	1	0	2	2	1	2	0	2	5	7	0	2	1	1	rs369130130		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:37578392C>T	ENST00000337843.2	-	3	748	c.673G>A	c.(673-675)Gag>Aag	p.E225K	C1QTNF6_ENST00000470655.1_5'UTR|C1QTNF6_ENST00000255836.6_Missense_Mutation_p.E101K|C1QTNF6_ENST00000397110.2_Missense_Mutation_p.E225K|RP1-151B14.6_ENST00000419128.1_RNA	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	206	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						ATGCTGCGCTCGCTGGGCTGC	0.577																																					p.E225K													.	C1QTNF6-90	0			c.G673A						.	C	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	85	65	72		673,673	4.9	1	22		72	0,8600		0,0,4300	no	missense,missense	C1QTNF6	NM_031910.3,NM_182486.1	56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	225/279,225/279	37578392	1,13005	2203	4300	6503	SO:0001583	missense	114904	exon3			TGCGCTCGCTGGG	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.673G>A	22.37:g.37578392C>T	ENSP00000338812:p.Glu225Lys	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	42	10	NM_182486	0	0	7	11	4	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.200483	0.79015	2.27E-4	0.0	ENSG00000133466	ENST00000397110;ENST00000337843;ENST00000255836	T;T;T	0.21191	2.02;2.02;2.02	4.94	4.94	0.65067	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.226034	0.45361	D	0.000377	T	0.30135	0.0755	L	0.38838	1.175	0.58432	D	0.999999	D;D	0.58970	0.984;0.973	P;P	0.53450	0.726;0.608	T	0.01661	-1.1301	10	0.40728	T	0.16	.	18.1776	0.89766	0.0:1.0:0.0:0.0	.	225;206	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	K	225;225;101	ENSP00000380299:E225K;ENSP00000338812:E225K;ENSP00000255836:E101K	ENSP00000255836:E101K	E	-	1	0	C1QTNF6	35908338	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.818000	0.86416	2.286000	0.76751	0.561000	0.74099	GAG	.		0.577	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486		T	37578392	C	T	37578392	3	4	82	1	0	0	0	0	1	0	0	0	1973	893	31	1	167	1	C1QTNF6	22	37578392	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	5779203	37578392	13726174	88	7646											
MKL1	57591	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	40816560	40816562	+	In_Frame_Del	DEL	CCC	CCC	-																															ctgggggggtcccgctgcttCccagggcctcgcctgctgac																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:40816560_40816562delCCC	ENST00000355630.3	-	11	1490_1492	c.900_902delGGG	c.(898-903)ctggga>cta	p.G301del	MKL1_ENST00000396617.3_In_Frame_Del_p.G301del|MKL1_ENST00000402042.1_In_Frame_Del_p.G251del|MKL1_ENST00000407029.1_In_Frame_Del_p.G301del	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	301					negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						CCCGCTGCTTCCCAGGGCCTCGC	0.665			T	RBM15	acute megakaryocytic leukemia																																p.300_301del		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	0			c.900_902del						.																																			SO:0001651	inframe_deletion	57591	exon11			.	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.900_902delGGG	22.37:g.40816560_40816562delCCC	ENSP00000347847:p.Gly301del	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	97	39	NM_020831	0	0	0	0	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	In_Frame_Del	DEL	ENST00000355630.3	37	CCDS14003.1																																																																																			.		0.665	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		-	40816562	CCC	-	40816560	7	5	82	1	0	1	0	1	0	0	0	0	9626	855	30	0	1913	0	MKL1	22	40816560	In_Frame_Del	DEL	CCC	TCGA-BQ-7048-01A-11D-1961-08	3238168	40816560	10488006	89	7647											
ATAD3A	55210	hgsc.bcm.edu	37	chr1	1458174	1458174	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctactcagccaagaatgcCacgcttgtcgccggccgctt	7	9	10	15	4	2	1	1	0	1	1	3	1	2	1	4	1	3	2	4	1	3	3			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:1458174C>G	ENST00000378755.5	+	8	1039	c.945C>G	c.(943-945)gcC>gcG	p.A315A	ATAD3A_ENST00000536055.1_Silent_p.A188A|ATAD3A_ENST00000378756.3_Silent_p.A267A	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	315					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	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;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CCAAGAATGCCACGCTTGTCG	0.687																																					p.A315A		.											.	ATAD3A-91	0			c.C945G						.						41	52	49					1																	1458174		2195	4300	6495	SO:0001819	synonymous_variant	55210	exon8			GAATGCCACGCTT	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"ATPases / AAA-type"	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.945C>G	1.37:g.1458174C>G		Somatic	28	2		WXS	Illumina HiSeq	Phase_I	40	2	NM_018188	0	0	8	8	0	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	.	.	.	.	.	.	.	.	.	.	c	1.378	-0.584146	0.03827	.	.	ENSG00000197785	ENST00000339113	.	.	.	5.11	-5.52	0.02560	.	.	.	.	.	T	0.38665	0.1049	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37596	-0.9699	4	.	.	.	.	3.4	0.07320	0.0896:0.4395:0.1791:0.2918	.	.	.	.	D	253	.	.	H	+	1	0	ATAD3A	1448037	0.811000	0.29063	0.062000	0.19696	0.001000	0.01503	-0.076000	0.11412	-1.066000	0.03164	-1.938000	0.00498	CAC	.		0.687	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188		G	1458174	C	G	1458174	2	3	83	1	0	0	0	0	0	0	0	1	1074	581	21	4		4	ATAD3A	1	1458174	Silent	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		1458174	247792447	1	7648											
ASH1L	55870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155317614	155317614	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctcatcaatctgggctgAtgcctcatgccgggcattgt	8	12	10	11	1	4	1	3	1	2	0	5	1	4	1	2	2	2	2	2	2	2	1			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:155317614A>G	ENST00000368346.3	-	20	8290	c.7651T>C	c.(7651-7653)Tca>Cca	p.S2551P	ASH1L_ENST00000392403.3_Missense_Mutation_p.S2546P|MIR555_ENST00000384987.1_RNA			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2551					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			ATCTGGGCTGATGCCTCATGC	0.488																																					p.S2546P		.											.	ASH1L-234	0			c.T7636C						.						197	160	173					1																	155317614		2203	4300	6503	SO:0001583	missense	55870	exon20			GGGCTGATGCCTC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.7651T>C	1.37:g.155317614A>G	ENSP00000357330:p.Ser2551Pro	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	137	59	NM_018489	0	0	5	13	8	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	A	17.35	3.367145	0.61513	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	T;T	0.16743	2.32;2.32	5.4	5.4	0.78164	Bromodomain (3);	0.058282	0.64402	D	0.000002	T	0.07007	0.0178	N	0.08118	0	0.80722	D	1	P;P	0.50272	0.89;0.933	B;P	0.49752	0.417;0.621	T	0.21177	-1.0253	10	0.45353	T	0.12	.	10.9753	0.47463	0.7253:0.2747:0.0:0.0	.	2551;2546	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	P	2551;2546	ENSP00000357330:S2551P;ENSP00000376204:S2546P	ENSP00000357330:S2551P	S	-	1	0	ASH1L	153584238	0.923000	0.31300	1.000000	0.80357	0.998000	0.95712	2.017000	0.40981	2.266000	0.75297	0.533000	0.62120	TCA	.		0.488	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		G	155317614	A	G	155317614	3	3	83	1	0	0	0	0	1	0	0	0	1042	333	12	3	1294	3	ASH1L	1	155317614	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08	153859440	155317614	93933007	2	7649											
ATP1B1	481	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169076130	169076130	+	Frame_Shift_Del	DEL	G	G	-																															ttcatctggaactcagagaaGaaggagtttctgggcaggac																										TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:169076130delG	ENST00000367816.1	+	2	592	c.63delG	c.(61-63)aagfs	p.K22fs	ATP1B1_ENST00000499679.3_5'Flank|ATP1B1_ENST00000367815.4_Frame_Shift_Del_p.K22fs|RP5-1018K9.1_ENST00000415637.1_RNA			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	22					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					ACTCAGAGAAGAAGGAGTTTC	0.657																																					p.K21fs		.											.	ATP1B1-540	0			c.63delG						.						51	57	55					1																	169076130		2203	4300	6503	SO:0001589	frameshift_variant	481	exon1			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.63delG	1.37:g.169076130delG	ENSP00000356790:p.Lys22fs	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	42	10	NM_001677	0	0	0	0	0	Q5TGZ3	Frame_Shift_Del	DEL	ENST00000367816.1	37	CCDS1276.1																																																																																			.		0.657	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			-	169076130	G	-	169076130	7	5	83	1	0	1	0	1	0	0	0	0	1133	933	33	0	65	0	ATP1B1	1	169076130	Frame_Shift_Del	DEL	G	TCGA-BQ-7050-01A-11D-1961-08	13758516	169076130	80174491	3	7650											
NEK7	140609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	198231718	198231718	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttagatatttgatttaaTggatgccaaagcacgtgctg	11	16	9	5	1	0	2	0	1	0	1	0	3	0	3	1	1	3	2	1	1	4	7			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:198231718T>G	ENST00000367385.4	+	4	554	c.212T>G	c.(211-213)aTg>aGg	p.M71R	NEK7_ENST00000538004.1_Missense_Mutation_p.M71R	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	71	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						TTTGATTTAATGGATGCCAAA	0.289																																					p.M71R		.											.	NEK7-358	0			c.T212G						.						125	134	131					1																	198231718		2203	4292	6495	SO:0001583	missense	140609	exon4			ATTTAATGGATGC	AB062450	CCDS1394.1	1q31.3	2012-11-15	2012-11-15		ENSG00000151414	ENSG00000151414			13386	protein-coding gene	gene with protein product		606848	"NIMA (never in mitosis gene a)-related kinase 7"			11701951	Standard	NM_133494		Approved		uc001gun.4	Q8TDX7	OTTHUMG00000035658	ENST00000367385.4:c.212T>G	1.37:g.198231718T>G	ENSP00000356355:p.Met71Arg	Somatic	208	0		WXS	Illumina HiSeq	Phase_I	173	28	NM_133494	0	0	9	11	2	A6NGT8	Missense_Mutation	SNP	ENST00000367385.4	37	CCDS1394.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394506	0.83011	.	.	ENSG00000151414	ENST00000367385;ENST00000538004;ENST00000391974	T;T;T	0.63913	-0.07;-0.07;3.21	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67924	0.2945	L	0.28192	0.835	0.80722	D	1	D	0.57257	0.979	D	0.65573	0.936	T	0.71751	-0.4498	10	0.66056	D	0.02	.	15.4982	0.75673	0.0:0.0:0.0:1.0	.	71	Q8TDX7	NEK7_HUMAN	R	71	ENSP00000356355:M71R;ENSP00000444621:M71R;ENSP00000375835:M71R	ENSP00000356355:M71R	M	+	2	0	NEK7	196498341	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.506000	0.81665	2.198000	0.70561	0.528000	0.53228	ATG	.		0.289	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		G	198231718	T	G	198231718	3	3	83	1	0	0	0	0	1	0	0	0	10355	1464	51	5	222	5	NEK7	1	198231718	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	29155588	198231718	51018903	4	7651											
IL1F9	56300	bcgsc.ca	37	chr2	113736864	113736864	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggacccttcagggtcagaAccttgtggcagttccacgaa	9	9	12	11	1	2	1	2	0	0	1	3	3	3	2	3	3	1	2	3	3	2	3	rs575481711		TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr2:113736864A>G	ENST00000259205.4	+	3	191	c.122A>G	c.(121-123)aAc>aGc	p.N41S	IL36G_ENST00000376489.2_Intron	NM_019618.2	NP_062564.1	Q9NZH8	IL36G_HUMAN	interleukin 36, gamma	41					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						CAGGGTCAGAACCTTGTGGCA	0.473																																					p.N41S													.	IL36G-91	0			c.A122G						.						71	68	69					2																	113736864		2203	4300	6503	SO:0001583	missense	56300	exon3			GTCAGAACCTTGT	AF200492	CCDS2108.1, CCDS62992.1	2q12-q21	2011-07-14	2011-06-06	2011-06-06	ENSG00000136688	ENSG00000136688		"Interleukins and interleukin receptors"	15741	protein-coding gene	gene with protein product	"interleukin-1 homolog 1", "interleukin 1-related protein 2", "interleukin-1 epsilon"	605542	"interleukin 1 family, member 9"	IL1F9		10860666, 10744718, 11991722, 11991723	Standard	NM_019618		Approved	IL-1H1, IL-1RP2, IL-1F9, IL1H1, IL1E	uc002tio.1	Q9NZH8	OTTHUMG00000131336	ENST00000259205.4:c.122A>G	2.37:g.113736864A>G	ENSP00000259205:p.Asn41Ser	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	74	4	NM_019618	0	0	0	0	0	Q56B91|Q6UVX7|Q7RTZ9	Missense_Mutation	SNP	ENST00000259205.4	37	CCDS2108.1	.	.	.	.	.	.	.	.	.	.	A	11.82	1.753551	0.31046	.	.	ENSG00000136688	ENST00000259205	T	0.59083	0.29	5.09	-7.34	0.01427	.	0.781468	0.11761	N	0.532067	T	0.19886	0.0478	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19844	-1.0293	9	.	.	.	-2.993	0.7823	0.01043	0.3063:0.183:0.3003:0.2104	.	41	Q9NZH8	IL36G_HUMAN	S	41	ENSP00000259205:N41S	.	N	+	2	0	IL36G	113453335	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.905000	0.01591	-1.386000	0.02098	-0.869000	0.02991	AAC	.		0.473	IL36G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330713.2	NM_019618		G	113736864	A	G	113736864	3	3	83	1	0	0	0	0	1	0	0	0	7678	43	2	3	128	3	IL1F9	2	113736864	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08		113736864	129462509	5	7652											
DNAJC13	23317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132184844	132184844	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgcttttttcagacagcTaagtagacatttagtgggac	10	14	10	7	0	2	2	1	0	1	2	2	3	2	3	0	1	2	3	0	1	3	7			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr3:132184844T>C	ENST00000260818.6	+	18	2146	c.1898T>C	c.(1897-1899)cTa>cCa	p.L633P	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	633					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TTCAGACAGCTAAGTAGACAT	0.338																																					p.L633P		.											.	DNAJC13-272	0			c.T1898C						.						72	70	70					3																	132184844		2203	4300	6503	SO:0001583	missense	23317	exon18			GACAGCTAAGTAG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.1898T>C	3.37:g.132184844T>C	ENSP00000260818:p.Leu633Pro	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	42	12	NM_015268	0	0	0	0	0	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419736	0.83559	.	.	ENSG00000138246	ENST00000260818	T	0.34859	1.34	5.53	5.53	0.82687	Armadillo-type fold (1);	0.000000	0.64402	D	0.000007	T	0.64159	0.2573	M	0.82193	2.58	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.70226	-0.4930	10	0.87932	D	0	.	15.6649	0.77221	0.0:0.0:0.0:1.0	.	633;633	A7E2Y5;O75165	.;DJC13_HUMAN	P	633	ENSP00000260818:L633P	ENSP00000260818:L633P	L	+	2	0	DNAJC13	133667534	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.813000	0.86123	2.103000	0.63969	0.528000	0.53228	CTA	.		0.338	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132184844	T	C	132184844	3	2	83	1	0	0	0	0	1	0	0	0	4643	1522	53	3	1964	3	DNAJC13	3	132184844	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08		132184844	65837586	6	7653											
XRN1	54464	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	142141468	142141468	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catatgttccataaagaagaGgcagtgcatcatgattaata	16	11	8	6	0	1	3	1	1	0	2	2	3	2	3	1	1	1	3	1	1	6	5			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr3:142141468G>C	ENST00000264951.4	-	8	1040	c.923C>G	c.(922-924)cCt>cGt	p.P308R	XRN1_ENST00000544157.1_Missense_Mutation_p.P98R|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000392981.2_Missense_Mutation_p.P308R|XRN1_ENST00000463916.1_Missense_Mutation_p.P308R	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	308					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						ATAAAGAAGAGGCAGTGCATC	0.358																																					p.P308R		.											.	XRN1-93	0			c.C923G						.						84	86	85					3																	142141468		2203	4298	6501	SO:0001583	missense	54464	exon8			AGAAGAGGCAGTG	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.923C>G	3.37:g.142141468G>C	ENSP00000264951:p.Pro308Arg	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	118	10	NM_001042604	0	0	0	0	0	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716498	0.89205	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000544157	T;T	0.30448	1.53;1.53	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.87682	2.9	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.997;0.997;0.994	D;D;P;D;D	0.87578	0.998;0.998;0.887;0.984;0.963	T	0.68659	-0.5350	10	0.59425	D	0.04	-9.0623	19.3082	0.94173	0.0:0.0:1.0:0.0	.	98;308;169;308;308	B4E2K3;Q8IZH2-3;B3KW17;Q8IZH2-2;Q8IZH2	.;.;.;.;XRN1_HUMAN	R	308;308;308;98	ENSP00000264951:P308R;ENSP00000376707:P308R	ENSP00000264951:P308R	P	-	2	0	XRN1	143624158	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.363000	0.97131	2.572000	0.86782	0.650000	0.86243	CCT	.		0.358	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		C	142141468	G	C	142141468	3	2	83	1	0	0	0	0	1	0	0	0	17492	1000	35	4	4337	4	XRN1	3	142141468	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08	9956624	142141468	55880962	7	7654											
PDE5A	8654	broad.mit.edu	37	chr4	120463679	120463679	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacatctgcgtgttctggaTccccaagccacaaaagatga	13	9	8	11	1	2	2	0	1	2	1	3	3	3	3	3	1	3	1	3	1	4	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr4:120463679T>C	ENST00000354960.3	-	10	1826	c.1507A>G	c.(1507-1509)Atc>Gtc	p.I503V	PDE5A_ENST00000512739.1_5'UTR|PDE5A_ENST00000394439.1_Missense_Mutation_p.I451V|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000264805.5_Missense_Mutation_p.I461V	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	503	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	GTGTTCTGGATCCCCAAGCCA	0.463																																					p.I503V													.	PDE5A-90	0			c.A1507G						.						119	109	112					4																	120463679		2203	4300	6503	SO:0001583	missense	8654	exon10			TCTGGATCCCCAA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1507A>G	4.37:g.120463679T>C	ENSP00000347046:p.Ile503Val	Somatic	98	6		WXS	Illumina HiSeq	Phase_I	85	10	NM_001083	0	0	7	8	1	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567004	0.86439	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	T;T;T	0.71103	-0.54;-0.54;-0.54	5.11	5.11	0.69529	GAF (2);	0.050190	0.85682	D	0.000000	D	0.85199	0.5642	M	0.87381	2.88	0.80722	D	1	D;B	0.65815	0.995;0.335	D;B	0.75484	0.986;0.19	D	0.85789	0.1366	10	0.36615	T	0.2	.	15.1994	0.73122	0.0:0.0:0.0:1.0	.	503;461	O76074;O76074-2	PDE5A_HUMAN;.	V	503;451;461	ENSP00000347046:I503V;ENSP00000377957:I451V;ENSP00000264805:I461V	ENSP00000264805:I461V	I	-	1	0	PDE5A	120683127	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.242000	0.72376	2.062000	0.61559	0.528000	0.53228	ATC	.		0.463	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		C	120463679	T	C	120463679	3	2	83	1	0	0	0	0	1	0	0	0	11670	1435	50	3	1168	3	PDE5A	4	120463679	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08		120463679	70690597	8	7655											
TCERG1	10915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	145836845	145836845	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgactgctcctggtactccaGcactacctcctacggaggag	8	9	10	14	1	0	1	0	1	0	0	3	3	3	3	4	3	5	3	4	3	3	3			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr5:145836845G>A	ENST00000296702.5	+	3	423	c.385G>A	c.(385-387)Gca>Aca	p.A129T	TCERG1_ENST00000394421.2_Missense_Mutation_p.A129T	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	129	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTACTCCAGCACTACCTCC	0.458																																					p.A129T		.											.	TCERG1-92	0			c.G385A						.						101	95	97					5																	145836845		2203	4300	6503	SO:0001583	missense	10915	exon3			ACTCCAGCACTAC	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"transcription factor CA150", "co-activator of 150 kDa", "TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD", "TATA box-binding protein-associated factor 2S"	605409	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.385G>A	5.37:g.145836845G>A	ENSP00000296702:p.Ala129Thr	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	120	41	NM_006706	0	0	4	6	2	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.742261	0.49151	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.25912	1.77;1.77	5.28	4.29	0.51040	.	0.308756	0.35124	N	0.003438	T	0.15392	0.0371	N	0.21282	0.65	0.33542	D	0.595008	B;B;B	0.17038	0.02;0.003;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.11324	-1.0592	10	0.27082	T	0.32	-18.8301	9.1164	0.36760	0.1984:0.0:0.8016:0.0	.	129;129;129	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	T	129	ENSP00000296702:A129T;ENSP00000377943:A129T	ENSP00000296702:A129T	A	+	1	0	TCERG1	145817038	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.771000	0.38542	2.463000	0.83235	0.491000	0.48974	GCA	.		0.458	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		A	145836845	G	A	145836845	3	1	83	1	0	0	0	0	1	0	0	0	15717	971	34	2	395	2	TCERG1	5	145836845	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		145836845	35078415	9	7656											
RSPH3	83861	hgsc.bcm.edu;broad.mit.edu	37	chr6	159414935	159414935	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttctgtcatacattatgtttCcataatgcataggttcttca	10	18	5	8	0	4	0	2	0	2	0	5	0	5	0	1	1	2	3	1	1	4	8			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr6:159414935C>T	ENST00000252655.1	-	2	755	c.566G>A	c.(565-567)gGa>gAa	p.G189E	RSPH3_ENST00000367069.2_Missense_Mutation_p.G47E|RP1-111C20.4_ENST00000607391.1_RNA|RSPH3_ENST00000449822.1_Missense_Mutation_p.G47E|RSPH3_ENST00000297262.3_Missense_Mutation_p.G189E	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	189										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		CATTATGTTTCCATAATGCAT	0.358																																					p.G189E		.											.	RSPH3-92	0			c.G566A						.						177	137	151					6																	159414935		2203	4300	6503	SO:0001583	missense	83861	exon2			ATGTTTCCATAAT	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.566G>A	6.37:g.159414935C>T	ENSP00000252655:p.Gly189Glu	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	58	8	NM_031924	0	0	8	9	1	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613112	0.87258	.	.	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.18657	2.26;2.27;2.26;2.2	5.67	5.67	0.87782	.	0.057536	0.64402	D	0.000002	T	0.41650	0.1168	M	0.85373	2.75	0.28855	N	0.895835	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	T	0.38178	-0.9673	10	0.39692	T	0.17	-36.5398	17.2674	0.87090	0.0:1.0:0.0:0.0	.	189;189	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	E	47;47;189;189	ENSP00000356036:G47E;ENSP00000393195:G47E;ENSP00000252655:G189E;ENSP00000297262:G189E	ENSP00000252655:G189E	G	-	2	0	RSPH3	159334923	1.000000	0.71417	0.887000	0.34795	0.897000	0.52465	2.936000	0.48971	2.668000	0.90789	0.655000	0.94253	GGA	.		0.358	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		T	159414935	C	T	159414935	3	4	83	1	0	0	0	0	1	0	0	0	13737	855	30	2	1144	2	RSPH3	6	159414935	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		159414935	11700132	10	7657											
CAV1	857	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116166677	116166677	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgagaagcaagtgtacgaCgcgcacaccaaggagatcga	15	3	13	10	5	0	2	0	0	0	2	1	6	0	2	1	1	3	3	1	1	4	1	rs201261029	byFrequency	TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr7:116166677C>T	ENST00000341049.2	+	2	407	c.129C>T	c.(127-129)gaC>gaT	p.D43D	CAV1_ENST00000393467.1_Silent_p.D12D|CAV1_ENST00000405348.1_Silent_p.D12D|CAV1_ENST00000393470.1_Silent_p.D32D|CAV1_ENST00000393468.1_Silent_p.D12D	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	43					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			AAGTGTACGACGCGCACACCA	0.572											OREG0018273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0	0	5008	,	,		16976	0		0	False		,,,				2504	0.0031				p.D43D													.	CAV1-946	0			c.C129T						.	C	,,,	0,4406		0,0,2203	239	163	189		36,36,36,129	4.5	1	7		189	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAV1	NM_001172895.1,NM_001172896.1,NM_001172897.1,NM_001753.4	,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,	12/148,12/148,12/148,43/179	116166677	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	857	exon2			GTACGACGCGCAC	AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"caveolin 1, caveolae protein, 22kD"	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.129C>T	7.37:g.116166677C>T		Somatic	69	0	1471	WXS	Illumina HiSeq	Phase_I	76	9	NM_001753	0	0	6	7	1	Q9UGP1|Q9UNG1|Q9UQH6	Silent	SNP	ENST00000341049.2	37	CCDS5767.1																																																																																			C|0.999;T|0.001		0.572	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753		T	116166677	C	T	116166677	2	4	83	1	0	0	0	0	0	0	0	1	2699	535	19	1		1	CAV1	7	116166677	Silent	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		116166677	42971986	11	7658											
EPHB6	2051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142568111	142568111	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggctgcatttgacaagAtgatccgcaagccagatacc	11	9	11	10	1	0	4	0	2	0	2	1	4	1	4	3	2	3	3	3	2	3	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr7:142568111A>G	ENST00000392957.2	+	18	3539	c.2752A>G	c.(2752-2754)Atg>Gtg	p.M918V	EPHB6_ENST00000442129.1_Missense_Mutation_p.M918V|EPHB6_ENST00000476059.1_3'UTR|EPHB6_ENST00000411471.2_Missense_Mutation_p.M641V	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	918	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					ATTTGACAAGATGATCCGCAA	0.577																																					p.M918V		.											.	EPHB6-1489	0			c.A2752G						.						65	75	72					7																	142568111		2203	4300	6503	SO:0001583	missense	2051	exon18			GACAAGATGATCC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.2752A>G	7.37:g.142568111A>G	ENSP00000376684:p.Met918Val	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	190	19	NM_004445	0	0	14	14	0	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180826	0.57800	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.61392	0.11;0.11;0.11	5.58	5.58	0.84498	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000016	T	0.60625	0.2283	L	0.49126	1.545	0.42496	D	0.992913	P;P	0.52463	0.953;0.946	P;P	0.51101	0.458;0.659	T	0.65561	-0.6138	10	0.87932	D	0	.	11.0016	0.47609	0.8441:0.1559:0.0:0.0	.	918;641	O15197;O15197-2	EPHB6_HUMAN;.	V	918;918;641	ENSP00000376684:M918V;ENSP00000410789:M918V;ENSP00000409061:M641V	ENSP00000376684:M918V	M	+	1	0	EPHB6	142278233	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.307000	0.33516	2.107000	0.64212	0.533000	0.62120	ATG	.		0.577	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			G	142568111	A	G	142568111	3	3	83	1	0	0	0	0	1	0	0	0	5191	333	12	3	2806	3	EPHB6	7	142568111	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08	26401434	142568111	16570552	12	7659											
ATP6V0E2	155066	hgsc.bcm.edu	37	chr7	149571035	149571035	+	5'Flank	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcggcccggcccggctgAtcgcttcgggtgctcgactc	2	8	15	16	7	0	1	0	1	0	0	4	2	0	1	2	4	2	3	2	4	0	1	rs145697964	byFrequency	TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr7:149571035A>C	ENST00000425642.2	+	0	0				ATP6V0E2-AS1_ENST00000461019.1_RNA|ATP6V0E2_ENST00000606024.1_5'Flank|ATP6V0E2-AS1_ENST00000464939.1_RNA|ATP6V0E2_ENST00000421974.2_Missense_Mutation_p.I10L|ATP6V0E2-AS1_ENST00000488315.1_RNA|ATP6V0E2_ENST00000464662.1_5'Flank|ATP6V0E2_ENST00000479613.1_5'Flank|ATP6V0E2_ENST00000456496.2_Missense_Mutation_p.I10L			Q8NHE4	VA0E2_HUMAN	ATPase, H+ transporting V0 subunit e2						ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|hydrogen ion transmembrane transporter activity (GO:0015078)			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00256)			GGCCCGGCTGATCGCTTCGGG	0.721													A|||	78	0.0155751	0.0575	0.0029	5008	,	,		12043	0		0	False		,,,				2504	0				p.I10L		.											.	.	0			c.A28C						.	A	LEU/ILE,LEU/ILE	108,3620		0,108,1756	3	5	4		28,28	-4.7	0	7	dbSNP_134	4	2,7856		0,2,3927	yes	missense,missense	ATP6V0E2	NM_145230.2,NM_001100592.1	5,5	0,110,5683	CC,CA,AA		0.0255,2.897,0.9494	benign,benign	10/131,10/214	149571035	110,11476	1864	3929	5793	SO:0001631	upstream_gene_variant	155066	exon1			CGGCTGATCGCTT	AK057700	CCDS47742.1, CCDS55181.1	7q36.1	2010-04-21	2006-10-12	2006-10-12	ENSG00000171130	ENSG00000171130		"ATPases / V-type"	21723	protein-coding gene	gene with protein product		611019	"chromosome 7 open reading frame 32", "ATPase, H+ transporting V0 subunit E isoform 2-like (rat)"	C7orf32, ATP6V0E2L			Standard	XM_005249958		Approved		uc003wgs.3	Q8NHE4	OTTHUMG00000158094		7.37:g.149571035A>C	Exception_encountered	Somatic	5	2		WXS	Illumina HiSeq	Phase_I	9	4	NM_001100592	0	0	0	0	0	A2T863|A2T8L7|B5MDP5|J3KQW7|Q6MZW1|Q75L47|Q7Z4R7|Q8N7I8	Missense_Mutation	SNP	ENST00000425642.2	37		30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	A	14.71	2.615378	0.46631	0.02897	2.55E-4	ENSG00000171130	ENST00000421974;ENST00000456496	.	.	.	3.25	-4.66	0.03329	.	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.20638	N	0.999877	B	0.02656	0.0	B	0.01281	0.0	T	0.18116	-1.0347	8	0.87932	D	0	.	0.853	0.01176	0.2739:0.3374:0.2233:0.1654	.	10	E9PAS2	.	L	10	.	ENSP00000411672:I10L	I	+	1	0	ATP6V0E2	149201968	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.210000	0.02999	-0.957000	0.03627	-0.376000	0.06991	ATC	A|0.986;C|0.014		0.721	ATP6V0E2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470874.1	NM_145230		C	149571035	A	C	149571035	1	2	83	0	1	0	0	0	0	0	0	0	1177	333	12	5		5	ATP6V0E2	7	149571035	5'Flank	SNP	A	TCGA-BQ-7050-01A-11D-1961-08	7002924	149571035	9567628	13	7660											
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	144940482	144940482	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagatctgctgcccggtgtAggggtcggtgtagccggtga	5	9	19	8	3	1	2	0	1	1	1	2	3	1	2	2	6	3	3	2	6	2	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr8:144940482A>G	ENST00000525985.1	-	2	7011	c.6940T>C	c.(6940-6942)Tac>Cac	p.Y2314H				P58107	EPIPL_HUMAN	epiplakin 1	2314						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGCCCGGTGTAGGGGTCGGTG	0.711																																					p.Y2314H		.											.	EPPK1-25	0			c.T6940C						.						190	184	186					8																	144940482		2184	4264	6448	SO:0001583	missense	83481	exon1			CGGTGTAGGGGTC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"epidermal autoantigen 450K"	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6940T>C	8.37:g.144940482A>G	ENSP00000436337:p.Tyr2314His	Somatic	352	0		WXS	Illumina HiSeq	Phase_I	336	27	NM_031308	0	0	4	4	0	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	A	19.61	3.860098	0.71834	.	.	ENSG00000227184	ENST00000525985	T	0.69040	-0.37	4.63	4.63	0.57726	.	.	.	.	.	T	0.78666	0.4319	M	0.74881	2.28	0.27571	N	0.949888	D	0.60575	0.988	D	0.74674	0.984	T	0.69289	-0.5184	9	0.20046	T	0.44	.	12.1078	0.53821	1.0:0.0:0.0:0.0	.	2314	E9PPU0	.	H	2314	ENSP00000436337:Y2314H	ENSP00000436337:Y2314H	Y	-	1	0	EPPK1	145012470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.597000	0.54031	1.957000	0.56846	0.477000	0.44152	TAC	.		0.711	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144940482	A	G	144940482	3	3	83	1	0	0	0	0	1	0	0	0	5203	420	15	3	326	3	EPPK1	8	144940482	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08		144940482	1423540	14	7661											
NTRK2	4915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	87342656	87342656	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaaggcaaccccaaaccagCgcttcagtggttctataacg	13	7	9	12	2	2	0	1	0	1	0	2	1	2	0	3	2	4	3	3	2	5	4			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr9:87342656C>G	ENST00000323115.4	+	8	1294	c.941C>G	c.(940-942)gCg>gGg	p.A314G	NTRK2_ENST00000395882.1_Missense_Mutation_p.A314G|NTRK2_ENST00000376213.1_Missense_Mutation_p.A314G|NTRK2_ENST00000277120.3_Missense_Mutation_p.A314G|NTRK2_ENST00000376214.1_Missense_Mutation_p.A314G|NTRK2_ENST00000395866.2_Missense_Mutation_p.A158G|NTRK2_ENST00000359847.3_Missense_Mutation_p.A314G|NTRK2_ENST00000376208.1_Missense_Mutation_p.A314G|NTRK2_ENST00000304053.6_Missense_Mutation_p.A314G			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	314	Ig-like C2-type 2.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	CCCAAACCAGCGCTTCAGTGG	0.443										TSP Lung(25;0.17)																											p.A314G		.											.	NTRK2-1404	0			c.C941G						.						94	96	95					9																	87342656		2203	4300	6503	SO:0001583	missense	4915	exon9			AACCAGCGCTTCA	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.941C>G	9.37:g.87342656C>G	ENSP00000314586:p.Ala314Gly	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	87	33	NM_001018065	0	0	25	35	10	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	37	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321558	0.60634	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.385251	0.29900	N	0.010905	T	0.58090	0.2098	N	0.14661	0.345	0.30052	N	0.811719	B;B;B;B;B;B;B;B	0.27316	0.045;0.009;0.009;0.011;0.11;0.011;0.175;0.009	B;B;B;B;B;B;B;B	0.36766	0.064;0.022;0.022;0.039;0.232;0.043;0.148;0.023	T	0.52351	-0.8587	10	0.23891	T	0.37	.	20.2873	0.98536	0.0:1.0:0.0:0.0	.	158;314;314;314;314;314;360;314	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	G	314;314;314;314;314;314;314;314;158	ENSP00000365387:A314G;ENSP00000365386:A314G;ENSP00000379221:A314G;ENSP00000365381:A314G;ENSP00000306167:A314G;ENSP00000277120:A314G;ENSP00000314586:A314G;ENSP00000352906:A314G;ENSP00000379207:A158G	ENSP00000277120:A314G	A	+	2	0	NTRK2	86532476	0.561000	0.26578	1.000000	0.80357	0.998000	0.95712	2.910000	0.48766	2.799000	0.96334	0.585000	0.79938	GCG	.		0.443	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			G	87342656	C	G	87342656	3	3	83	1	0	0	0	0	1	0	0	0	10733	768	27	4	971	4	NTRK2	9	87342656	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		87342656	53870775	15	7662											
CYLC2	1539	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr9	105767702	105767702	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaaggatgccaagaaagaTgcaaaggagattaaaaaagg	20	5	12	4	1	0	3	0	0	0	3	1	6	0	4	1	3	2	1	1	3	7	1	rs2298052	byFrequency	TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr9:105767702T>A	ENST00000374798.3	+	5	859	c.789T>A	c.(787-789)gaT>gaA	p.D263E	CYLC2_ENST00000487798.1_Missense_Mutation_p.D263E	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	263	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.D263D(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				CCAAGAAAGATGCAAAGGAGA	0.388																																					p.D263E		.											.	CYLC2-91	1	Substitution - coding silent(1)	stomach(1)	c.T789A						.						117	112	114					9																	105767702		2203	4300	6503	SO:0001583	missense	1539	exon5			GAAAGATGCAAAG	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.789T>A	9.37:g.105767702T>A	ENSP00000420256:p.Asp263Glu	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	70	14	NM_001340	0	0	0	0	0	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	37	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	T	2.261	-0.369199	0.05069	.	.	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.14022	2.54;2.54	4.21	-5.98	0.02220	.	1.421110	0.04878	N	0.447237	T	0.06050	0.0157	L	0.29908	0.895	0.80722	P	0.0	B	0.23891	0.093	B	0.23574	0.047	T	0.37244	-0.9714	9	0.02654	T	1	-0.742	0.3139	0.00292	0.3842:0.1819:0.2128:0.221	.	263	Q14093	CYLC2_HUMAN	E	263	ENSP00000420256:D263E;ENSP00000417674:D263E	ENSP00000420256:D263E	D	+	3	2	CYLC2	104807523	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-0.647000	0.05397	-0.974000	0.03550	0.477000	0.44152	GAT	T|0.972;C|0.028		0.388	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		A	105767702	T	A	105767702	3	1	83	1	0	0	0	0	1	0	0	0	4148	1461	51	5	807	5	CYLC2	9	105767702	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	18425046	105767702	35445729	16	7663											
FBXW5	54461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139837319	139837319	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccttgttgaactgggagAactgggtgtagctccagttg	7	12	14	8	1	0	2	0	1	0	1	2	3	2	2	2	2	3	4	2	2	3	4			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr9:139837319A>C	ENST00000325285.3	-	4	507	c.428T>G	c.(427-429)tTc>tGc	p.F143C	FBXW5_ENST00000483559.1_5'UTR|C8G_ENST00000224181.3_5'Flank	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	143					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GAACTGGGAGAACTGGGTGTA	0.612																																					p.F143C		.											.	FBXW5-226	0			c.T428G						.						116	112	113					9																	139837319		2203	4300	6503	SO:0001583	missense	54461	exon4			TGGGAGAACTGGG	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"F-boxes / WD-40 domains", "WD repeat domain containing"	13613	protein-coding gene	gene with protein product		609072	"F-box and WD-40 domain protein 5"				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.428T>G	9.37:g.139837319A>C	ENSP00000313034:p.Phe143Cys	Somatic	197	1		WXS	Illumina HiSeq	Phase_I	186	22	NM_018998	0	0	67	96	29	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.303923	0.81136	.	.	ENSG00000159069	ENST00000325285;ENST00000428398	T;T	0.62498	0.02;1.73	4.16	4.16	0.48862	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.78735	0.4330	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81640	-0.0841	10	0.59425	D	0.04	0.5774	13.3962	0.60853	1.0:0.0:0.0:0.0	.	143	Q969U6	FBXW5_HUMAN	C	143;153	ENSP00000313034:F143C;ENSP00000404829:F153C	ENSP00000313034:F143C	F	-	2	0	FBXW5	138957140	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.563000	0.90723	1.751000	0.51876	0.454000	0.30748	TTC	.		0.612	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		C	139837319	A	C	139837319	3	2	83	1	0	0	0	0	1	0	0	0	5787	246	9	5	1296	5	FBXW5	9	139837319	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08	34069617	139837319	1376112	17	7664											
EXD3	54932	hgsc.bcm.edu	37	chr9	140247165	140247165	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggcacactgggcggccGtgactgggtcactgtgggag	6	7	17	11	2	1	1	1	1	0	0	1	2	1	2	2	5	0	1	2	5	0	0	rs370293169		TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr9:140247165G>C	ENST00000340951.4	-	11	1139	c.944C>G	c.(943-945)aCg>aGg	p.T315R	EXD3_ENST00000342129.4_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CTGGGCGGCCGTGACTGGGTC	0.687																																					p.T315R		.											.	EXD3-90	0			c.C944G						.	G	ARG/THR	3,4051		0,3,2024	10	13	12		944	-2.2	0	9		12	0,8302		0,0,4151	no	missense	EXD3	NM_017820.3	71	0,3,6175	CC,CG,GG		0.0,0.074,0.0243	possibly-damaging	315/877	140247165	3,12353	2027	4151	6178	SO:0001583	missense	54932	exon11			GCGGCCGTGACTG		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.944C>G	9.37:g.140247165G>C	ENSP00000340474:p.Thr315Arg	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	15	7	NM_017820	0	0	1	4	3	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.488891	0.26686	7.4E-4	0.0	ENSG00000187609	ENST00000340951	T	0.51325	0.71	3.61	-2.19	0.07015	.	0.331027	0.30859	N	0.008729	T	0.36413	0.0966	L	0.43152	1.355	0.09310	N	0.999998	P	0.50710	0.938	P	0.46320	0.512	T	0.44967	-0.9293	10	0.21540	T	0.41	.	8.8151	0.34991	0.414:0.0:0.586:0.0	.	315	Q8N9H8	MUT7_HUMAN	R	315	ENSP00000340474:T315R	ENSP00000340474:T315R	T	-	2	0	EXD3	139366986	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.751000	0.04803	-0.882000	0.03987	-0.678000	0.03780	ACG	.		0.687	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820		C	140247165	G	C	140247165	3	2	83	1	0	0	0	0	1	0	0	0	5312	1145	40	4	1734	4	EXD3	9	140247165	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08	409846	140247165	966266	18	7665											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82875304	82875304	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccctagcatctccactcCtccaattgttcctgatatac	8	14	3	16	0	1	1	0	1	1	0	6	1	5	1	6	0	2	2	6	0	4	6			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr11:82875304C>T	ENST00000298281.4	+	4	1015	c.563C>T	c.(562-564)cCt>cTt	p.P188L		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	188					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						ATCTCCACTCCTCCAATTGTT	0.393																																					p.P188L		.											.	PCF11-23	0			c.C563T						.						64	59	60					11																	82875304		1868	4092	5960	SO:0001583	missense	51585	exon4			CCACTCCTCCAAT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.563C>T	11.37:g.82875304C>T	ENSP00000298281:p.Pro188Leu	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	53	14	NM_015885	0	0	5	6	1	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.462969	0.63513	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.49432	1.74;0.78;0.79	5.73	5.73	0.89815	.	0.118143	0.39687	N	0.001292	T	0.36580	0.0972	L	0.36672	1.1	0.80722	D	1	P;B	0.35328	0.495;0.421	B;B	0.28849	0.095;0.058	T	0.13176	-1.0519	9	.	.	.	.	15.3998	0.74830	0.0:0.8614:0.1386:0.0	.	188;188	E9PQ01;O94913	.;PCF11_HUMAN	L	188	ENSP00000298281:P188L;ENSP00000434540:P188L;ENSP00000431567:P188L	.	P	+	2	0	PCF11	82552952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.304000	0.65744	2.710000	0.92621	0.650000	0.86243	CCT	.		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82875304	C	T	82875304	3	4	83	1	0	0	0	0	1	0	0	0	11599	681	24	2	577	2	PCF11	11	82875304	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		82875304	52131212	19	7666											
RDX	5962	hgsc.bcm.edu;broad.mit.edu	37	chr11	110134893	110134893	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taattcctcagaaacatcttCaggaaagaatttagctctaa	16	12	5	8	0	4	2	2	0	2	2	5	3	5	3	1	1	2	1	1	1	6	6			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr11:110134893C>T	ENST00000343115.4	-	5	578	c.259G>A	c.(259-261)Gaa>Aaa	p.E87K	RDX_ENST00000405097.1_Missense_Mutation_p.E87K|RDX_ENST00000528900.1_Intron|RDX_ENST00000530301.1_Missense_Mutation_p.E55K|RDX_ENST00000528498.1_Missense_Mutation_p.E87K|RDX_ENST00000544551.1_Intron	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	87	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GAAACATCTTCAGGAAAGAAT	0.328																																					p.E87K	Esophageal Squamous(55;25 1062 11040 28755 44273)	.											.	RDX-90	0			c.G259A						.						39	40	40					11																	110134893		2201	4297	6498	SO:0001583	missense	5962	exon5			CATCTTCAGGAAA	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"deafness, autosomal recessive 24"	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.259G>A	11.37:g.110134893C>T	ENSP00000342830:p.Glu87Lys	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	55	11	NM_001260493	0	0	11	12	1	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Missense_Mutation	SNP	ENST00000343115.4	37	CCDS8343.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.729873	0.89390	.	.	ENSG00000137710	ENST00000528498;ENST00000429481;ENST00000405097;ENST00000530301;ENST00000343115;ENST00000532118;ENST00000533991	T;T;T;T;D;D	0.89681	-1.21;-1.21;-1.21;-1.21;-2.55;-2.55	4.99	4.99	0.66335	Band 4.1 domain (1);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96374	0.8817	H	0.95437	3.67	0.80722	D	1	P;D;P	0.89917	0.516;1.0;0.938	P;D;P	0.85130	0.533;0.997;0.537	D	0.97615	1.0132	10	0.87932	D	0	.	18.6342	0.91371	0.0:1.0:0.0:0.0	.	55;87;87	A7YIK0;A7YIJ8;P35241	.;.;RADI_HUMAN	K	87;87;87;55;87;76;76	ENSP00000432112:E87K;ENSP00000384136:E87K;ENSP00000436277:E55K;ENSP00000342830:E87K;ENSP00000437140:E76K;ENSP00000432572:E76K	ENSP00000342830:E87K	E	-	1	0	RDX	109640103	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.454000	0.82982	0.650000	0.86243	GAA	.		0.328	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		T	110134893	C	T	110134893	3	4	83	1	0	0	0	0	1	0	0	0	13230	835	29	2	1532	2	RDX	11	110134893	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08	27259589	110134893	24871623	20	7667											
PAN2	9924	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56720460	56720460	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagtgtgtcagtggtgagTgggacagggatgagggaaag	12	7	20	2	0	1	3	1	2	0	1	1	6	1	6	0	4	0	0	0	4	2	0			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr12:56720460T>C	ENST00000425394.2	-	7	1579	c.1203A>G	c.(1201-1203)ccA>ccG	p.P401P	PAN2_ENST00000440411.3_Silent_p.P401P|PAN2_ENST00000548043.1_Silent_p.P401P|PAN2_ENST00000257931.5_Silent_p.P401P	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CAGTGGTGAGTGGGACAGGGA	0.597																																					p.P401P		.											.	PAN2-702	0			c.A1203G						.						70	61	64					12																	56720460		2203	4300	6503	SO:0001819	synonymous_variant	9924	exon7			GGTGAGTGGGACA	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1203A>G	12.37:g.56720460T>C		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	47	22	NM_014871	0	0	5	13	8		Silent	SNP	ENST00000425394.2	37	CCDS44922.1																																																																																			.		0.597	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		C	56720460	T	C	56720460	2	2	83	1	0	0	0	0	0	0	0	1	11440	1683	59	3		3	PAN2	12	56720460	Silent	SNP	T	TCGA-BQ-7050-01A-11D-1961-08		56720460	77131435	21	7668											
ZFC3H1	196441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	72017888	72017888	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtaccaagtgcttacctgtAaaattgccagtgcactttgg	10	13	9	9	0	0	0	0	0	0	0	0	0	0	0	3	1	5	4	3	1	5	5			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr12:72017888A>T	ENST00000378743.3	-	23	4860	c.4502T>A	c.(4501-4503)tTa>tAa	p.L1501*		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1501					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GCTTACCTGTAAAATTGCCAG	0.358																																					p.L1501X		.											.	ZFC3H1-138	0			c.T4502A						.						153	145	147					12																	72017888		1838	4095	5933	SO:0001587	stop_gained	196441	exon23			ACCTGTAAAATTG	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"Zinc finger, C3H1-type containing"	28328	protein-coding gene	gene with protein product			"proline/serine-rich coiled-coil 2", "coiled-coil domain containing 131"	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4502T>A	12.37:g.72017888A>T	ENSP00000368017:p.Leu1501*	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	218	40	NM_144982	0	0	0	0	0	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Nonsense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	A	45	11.914642	0.99617	.	.	ENSG00000133858	ENST00000378743	.	.	.	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4122	0.74937	1.0:0.0:0.0:0.0	.	.	.	.	X	1501	.	ENSP00000368017:L1501X	L	-	2	0	ZFC3H1	70304155	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	8.262000	0.89862	2.038000	0.60285	0.533000	0.62120	TTA	.		0.358	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72017888	A	T	72017888	4	4	83	1	0	0	0	0	0	1	0	0	17665	372	13	5	1519	5	ZFC3H1	12	72017888	Nonsense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08	15297428	72017888	61834007	22	7669											
PCCA	5095	ucsc.edu	37	chr13	100925449	100925449	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacatttttttgtatatgtaGcatttttttggatgcggaga	10	19	9	3	1	0	1	0	0	0	1	0	3	0	2	0	2	3	3	0	2	4	9	rs367615795		TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr13:100925449G>A	ENST00000376285.1	+	12	952		c.e12-1		PCCA_ENST00000376279.3_Splice_Site|PCCA_ENST00000376286.4_Splice_Site	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide						biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	TGTATATGTAGCATTTTTTTG	0.373																																					.													.	PCCA-227	0			c.915-1G>A						.	G	,,	1,4405		0,1,2202	62	64	64		,,	5.6	1	13		64	0,8600		0,0,4300	no	splice-3,splice-3,splice-3	PCCA	NM_000282.3,NM_001127692.2,NM_001178004.1	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	,,	100925449	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	5095	exon12			TATGTAGCATTTT	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"propionyl Coenzyme A carboxylase, alpha polypeptide"			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.915-1G>A	13.37:g.100925449G>A		Somatic	41	0		WXS	Illumina HiSeq		42	3	NM_001178004	0	0	0	21	21	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Splice_Site	SNP	ENST00000376285.1	37	CCDS9496.2	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637486	0.67130	2.27E-4	0.0	ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8818	0.96901	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCCA	99723450	1.000000	0.71417	0.983000	0.44433	0.497000	0.33675	9.710000	0.98732	2.773000	0.95371	0.655000	0.94253	.	.		0.373	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2		Intron	A	100925449	G	A	100925449	5	1	83	1	0	0	0	0	0	0	1	0	11530	985	34	2	960	2	PCCA	13	100925449	Splice_Site	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		100925449	14244429	23	7670											
TTC8	123016	bcgsc.ca	37	chr14	89338026	89338026	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggctgaaaatgaagaaGaggcagctgatgtctggtac	12	10	13	6	0	1	5	0	3	1	2	1	5	1	5	0	3	2	4	0	3	5	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr14:89338026G>T	ENST00000345383.5	+	11	1237	c.1153G>T	c.(1153-1155)Gag>Tag	p.E385*	TTC8_ENST00000536576.1_Nonsense_Mutation_p.E156*|TTC8_ENST00000358622.5_Nonsense_Mutation_p.E197*|TTC8_ENST00000346301.4_Nonsense_Mutation_p.E355*|TTC8_ENST00000354441.6_Nonsense_Mutation_p.E130*|TTC8_ENST00000338104.6_Nonsense_Mutation_p.E411*|TTC8_ENST00000380656.2_Nonsense_Mutation_p.E395*	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	421					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						AAATGAAGAAGAGGCAGCTGA	0.423																																					p.E395X													.	TTC8-90	0			c.G1183T						.						144	132	136					14																	89338026		2203	4300	6503	SO:0001587	stop_gained	123016	exon12			GAAGAAGAGGCAG	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"Tetratricopeptide (TTC) repeat domain containing"	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1153G>T	14.37:g.89338026G>T	ENSP00000339486:p.Glu385*	Somatic	132	0		WXS	Illumina HiSeq	Phase_1	133	9	NM_144596	0	0	22	22	0	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Nonsense_Mutation	SNP	ENST00000345383.5	37	CCDS9885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	32|32|32	5.179614|5.179614|5.179614	0.94846|0.94846|0.94846	.|.|.	.|.|.	ENSG00000165533|ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686|ENST00000557580	.|.|.	.|.|.	.|.|.	5.73|5.73|5.73	5.73|5.73|5.73	0.89815|0.89815|0.89815	.|.|.	0.047433|.|.	0.85682|.|.	D|.|.	0.000000|.|.	.|T|T	.|0.79834|0.79834	.|0.4514|0.4514	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.77699|0.77699	.|-0.2490|-0.2490	.|3|3	0.10636|.|.	T|.|.	0.68|.|.	-20.9321|-20.9321|-20.9321	19.8984|19.8984|19.8984	0.96975|0.96975|0.96975	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	385;156;355;411;130;395;197|344|183	.|.|.	ENSP00000337653:E411X|.|.	E|K|R	+|+|+	1|3|2	0|2|0	TTC8|TTC8|TTC8	88407779|88407779|88407779	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	9.474000|9.474000|9.474000	0.97718|0.97718|0.97718	2.712000|2.712000|2.712000	0.92718|0.92718|0.92718	0.555000|0.555000|0.555000	0.69702|0.69702|0.69702	GAG|AAG|AGA	.		0.423	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		T	89338026	G	T	89338026	4	4	83	1	0	0	0	0	0	1	0	0	16747	943	33	4	1229	4	TTC8	14	89338026	Nonsense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		89338026	18011514	24	7671											
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	39882095	39882095	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggccactatagcgacccCatgtaccgctgcgagtgcaa	9	7	11	14	3	0	0	0	0	0	0	0	2	0	0	4	1	4	3	4	1	4	3			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr15:39882095C>G	ENST00000260356.5	+	13	2181	c.2016C>G	c.(2014-2016)ccC>ccG	p.P672P		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	672	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ATAGCGACCCCATGTACCGCT	0.607																																					p.P672P		.											.	THBS1-653	0			c.C2016G						.						111	92	99					15																	39882095		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon13			CGACCCCATGTAC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2016C>G	15.37:g.39882095C>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	48	9	NM_003246	0	0	145	176	31	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			.		0.607	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		G	39882095	C	G	39882095	2	3	83	1	0	0	0	0	0	0	0	1	15885	581	21	4		4	THBS1	15	39882095	Silent	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		39882095	62649297	25	7672											
MYO9A	4649	broad.mit.edu	37	chr15	72146822	72146822	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcaatgtagtttatgagcTtttccactactaaaggaaca	13	15	6	7	0	1	1	1	1	0	0	2	2	2	2	1	1	3	3	1	1	7	8			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr15:72146822T>C	ENST00000356056.5	-	35	6714	c.6242A>G	c.(6241-6243)aAg>aGg	p.K2081R	MYO9A_ENST00000444904.1_Missense_Mutation_p.K2062R|MYO9A_ENST00000564571.1_Missense_Mutation_p.K2081R|MYO9A_ENST00000424560.1_Missense_Mutation_p.K2152R	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2081	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.|Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GTTTATGAGCTTTTCCACTAC	0.408																																					p.K2081R													.	MYO9A-93	0			c.A6242G						.						148	134	138					15																	72146822		2199	4297	6496	SO:0001583	missense	4649	exon35			ATGAGCTTTTCCA	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"Myosins / Myosin superfamily : Class IX"	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.6242A>G	15.37:g.72146822T>C	ENSP00000348349:p.Lys2081Arg	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	122	3	NM_006901	0	0	19	19	0	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.787450	0.90367	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.21031	2.03;2.03;2.03	5.99	5.99	0.97316	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	.	.	.	.	T	0.30039	0.0752	N	0.17278	0.47	0.58432	D	0.999996	D	0.76494	0.999	D	0.85130	0.997	T	0.11108	-1.0601	9	0.19147	T	0.46	.	16.4719	0.84113	0.0:0.0:0.0:1.0	.	2081	B2RTY4	MYO9A_HUMAN	R	2081;2152;2062	ENSP00000348349:K2081R;ENSP00000399162:K2152R;ENSP00000398250:K2062R	ENSP00000348349:K2081R	K	-	2	0	MYO9A	69933876	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.013000	0.88655	2.292000	0.77174	0.482000	0.46254	AAG	.		0.408	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72146822	T	C	72146822	3	2	83	1	0	0	0	0	1	0	0	0	10109	1609	56	3	1436	3	MYO9A	15	72146822	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	32264727	72146822	30384570	26	7673											
ZNF532	55205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	56586514	56586514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaccatccctgaagcaacCggatagtcccagaagcatct	15	6	7	13	1	1	2	0	1	1	1	3	3	3	3	4	1	4	2	4	1	6	1			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr18:56586514C>T	ENST00000336078.4	+	4	1771	c.995C>T	c.(994-996)cCg>cTg	p.P332L	ZNF532_ENST00000591083.1_Missense_Mutation_p.P332L|ZNF532_ENST00000591230.1_Missense_Mutation_p.P332L|ZNF532_ENST00000591808.1_Missense_Mutation_p.P332L|ZNF532_ENST00000589288.1_Missense_Mutation_p.P332L	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	332					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(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						CTGAAGCAACCGGATAGTCCC	0.522																																					p.P332L		.											.	ZNF532-154	0			c.C995T						.						97	100	99					18																	56586514		2203	4300	6503	SO:0001583	missense	55205	exon4			AGCAACCGGATAG	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.995C>T	18.37:g.56586514C>T	ENSP00000338217:p.Pro332Leu	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	152	61	NM_018181	0	0	2	6	4	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	c	14.64	2.595026	0.46318	.	.	ENSG00000074657	ENST00000336078	T	0.02158	4.42	4.97	4.97	0.65823	.	0.114354	0.64402	N	0.000009	T	0.05456	0.0144	M	0.76574	2.34	0.80722	D	1	D	0.58620	0.983	B	0.41135	0.348	T	0.24657	-1.0154	10	0.87932	D	0	-11.3748	17.8864	0.88856	0.0:1.0:0.0:0.0	.	332	Q9HCE3	ZN532_HUMAN	L	332	ENSP00000338217:P332L	ENSP00000338217:P332L	P	+	2	0	ZNF532	54737494	1.000000	0.71417	0.494000	0.27515	0.027000	0.11550	7.737000	0.84957	2.320000	0.78422	0.550000	0.68814	CCG	.		0.522	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56586514	C	T	56586514	3	4	83	1	0	0	0	0	1	0	0	0	18004	652	23	1	997	1	ZNF532	18	56586514	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		56586514	21490734	27	7674											
ZNF440	126070	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	11943483	11943485	+	In_Frame_Del	DEL	GTT	GTT	-																															gttcagtagttccttcagtaGttccagttccttttgatatc																										TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr19:11943483_11943485delGTT	ENST00000304060.5	+	4	1656_1658	c.1492_1494delGTT	c.(1492-1494)gttdel	p.V498del		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	498					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(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TCCTTCAGTAGTTCCAGTTCCTT	0.404																																					p.498_498del		.											.	ZNF440-68	0			c.1492_1494del						.																																			SO:0001651	inframe_deletion	126070	exon4			.	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"Zinc fingers, C2H2-type", "-"	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.1492_1494delGTT	19.37:g.11943483_11943485delGTT	ENSP00000305373:p.Val498del	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	45	18	NM_152357	0	0	0	0	0	Q8N1R9	In_Frame_Del	DEL	ENST00000304060.5	37	CCDS42503.1																																																																																			.		0.404	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357		-	11943485	GTT	-	11943483	7	5	83	1	0	1	0	1	0	0	0	0	17945	1029	36	0	1506	0	ZNF440	19	11943483	In_Frame_Del	DEL	GTT	TCGA-BQ-7050-01A-11D-1961-08		11943483	47185500	28	7675											
ZFP36	7538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39898403	39898403	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctcctgtcgctgagcccTgacgtgcccgtgccatccga	5	8	11	17	4	0	2	0	2	0	0	3	3	2	2	6	0	4	1	6	0	0	0			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr19:39898403T>C	ENST00000248673.3	+	2	103	c.45T>C	c.(43-45)ccT>ccC	p.P15P	ZFP36_ENST00000594045.1_3'UTR|MIR4530_ENST00000581459.1_RNA|ZFP36_ENST00000597629.1_Silent_p.P21P	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	15					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CGCTGAGCCCTGACGTGCCCG	0.667																																					p.P21P	NSCLC(67;1164 1324 12056 21056 30097)	.											.	ZFP36-227	0			c.T63C						.						102	114	110					19																	39898403		2202	4298	6500	SO:0001819	synonymous_variant	7538	exon2			GAGCCCTGACGTG	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"RING-type (C3HC4) zinc fingers"	12862	protein-coding gene	gene with protein product		190700	"zinc finger protein 36, C3H type, homolog (mouse)"			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.45T>C	19.37:g.39898403T>C		Somatic	331	0		WXS	Illumina HiSeq	Phase_I	295	105	NM_003407	0	0	24	49	25	B2RA54	Silent	SNP	ENST00000248673.3	37																																																																																				.		0.667	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				C	39898403	T	C	39898403	2	2	83	1	0	0	0	0	0	0	0	1	17677	1567	55	3		3	ZFP36	19	39898403	Silent	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	27954920	39898403	19230580	29	7676											
ZNF615	284370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52497088	52497088	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgttgatgtaccatgagaCagtgcttcattgaaaagcct	11	13	9	8	1	1	3	1	3	0	1	2	4	1	3	2	0	3	3	2	0	3	5			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr19:52497088C>A	ENST00000602063.1	-	6	1590	c.1241G>T	c.(1240-1242)tGt>tTt	p.C414F	ZNF615_ENST00000598071.1_Missense_Mutation_p.C425F|ZNF615_ENST00000594083.1_Missense_Mutation_p.C425F|ZNF615_ENST00000376716.5_Missense_Mutation_p.C414F|ZNF615_ENST00000391795.3_Missense_Mutation_p.C419F			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	414					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)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TACCATGAGACAGTGCTTCAT	0.403																																					p.C425F		.											.	ZNF615-95	0			c.G1274T						.						93	84	87					19																	52497088		2203	4300	6503	SO:0001583	missense	284370	exon7			ATGAGACAGTGCT	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1241G>T	19.37:g.52497088C>A	ENSP00000473089:p.Cys414Phe	Somatic	64	1		WXS	Illumina HiSeq	Phase_I	78	29	NM_001199324	0	0	2	5	3	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	C	3.261	-0.151138	0.06585	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.06933	3.24;3.24	2.99	0.551	0.17225	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04861	0.0131	N	0.21142	0.635	0.09310	N	1	B;B;B;B	0.31318	0.213;0.319;0.319;0.213	B;B;B;B	0.28638	0.029;0.092;0.092;0.029	T	0.38672	-0.9650	9	0.52906	T	0.07	.	2.961	0.05893	0.0:0.3825:0.2294:0.3881	.	419;421;425;414	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	F	414;424;419;424	ENSP00000365906:C414F;ENSP00000375672:C419F	ENSP00000347019:C424F	C	-	2	0	ZNF615	57188900	0.000000	0.05858	0.024000	0.17045	0.986000	0.74619	-3.101000	0.00604	0.570000	0.29347	0.585000	0.79938	TGT	.		0.403	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		A	52497088	C	A	52497088	3	1	83	1	0	0	0	0	1	0	0	0	18072	478	17	4	958	4	ZNF615	19	52497088	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08	12598685	52497088	6631895	30	7677											
PLCH2	9651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	2436173	2436173	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgccaagtccaagagcctgGgcgacctcactgctgatgac	9	7	11	14	1	1	3	1	2	0	1	2	4	2	3	4	1	3	1	4	1	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:2436173G>A	ENST00000419816.2	+	22	4046	c.3772G>A	c.(3772-3774)Ggc>Agc	p.G1258S	PLCH2_ENST00000378488.3_Missense_Mutation_p.G1222S|PLCH2_ENST00000378486.3_Missense_Mutation_p.G1258S|PLCH2_ENST00000449969.1_3'UTR			O75038	PLCH2_HUMAN	phospholipase C, eta 2	1258					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		CAAGAGCCTGGGCGACCTCAC	0.701																																					p.G1258S		.											.	PLCH2-229	0			c.G3772A						.						28	34	32					1																	2436173		2066	4170	6236	SO:0001583	missense	9651	exon22			AGCCTGGGCGACC	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.3772G>A	1.37:g.2436173G>A	ENSP00000389803:p.Gly1258Ser	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_014638	0	0	27	41	14	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.88|18.88	3.718362|3.718362	0.68844|0.68844	.|.	.|.	ENSG00000149527|ENSG00000149527	ENST00000378486;ENST00000378488;ENST00000278878|ENST00000419816	T;T|.	0.76578|.	-0.69;-1.03|.	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	1.629000|.	0.03724|.	N|.	0.252361|.	T|.	0.74504|.	0.3725|.	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.998;0.998|.	T|.	0.76214|.	-0.3041|.	10|.	0.87932|.	D|.	0|.	.|.	15.9517|15.9517	0.79843|0.79843	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1010;1258|.	B9DI82;O75038|.	.;PLCH2_HUMAN|.	S|X	1258;1222;1010|552	ENSP00000367747:G1258S;ENSP00000367749:G1222S|.	ENSP00000278878:G1010S|.	G|W	+|+	1|3	0|0	PLCH2|PLCH2	2426033|2426033	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.712000|0.712000	0.41017|0.41017	5.901000|5.901000	0.69861|0.69861	1.999000|1.999000	0.58509|0.58509	0.491000|0.491000	0.48974|0.48974	GGC|TGG	.		0.701	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2436173	G	A	2436173	3	1	84	1	0	0	0	0	1	0	0	0	12064	1232	43	2	3858	2	PLCH2	1	2436173	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		2436173	246814448	1	7678											
MFN2	9927	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	12061548	12061549	+	Frame_Shift_Del	DEL	TT	TT	-																															aggccggggaccgcatcttcTttgtgtctgctaaggaggtg																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:12061548_12061549delTT	ENST00000235329.5	+	9	1229_1230	c.907_908delTT	c.(907-909)tttfs	p.F303fs	MFN2_ENST00000444836.1_Frame_Shift_Del_p.F303fs	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	303	Dynamin-type G.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		CCGCATCTTCTTTGTGTCTGCT	0.574																																					p.303_303del		.											.	MFN2-91	0			c.907_908del						.																																			SO:0001589	frameshift_variant	9927	exon9			.	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.907_908delTT	1.37:g.12061548_12061549delTT	ENSP00000235329:p.Phe303fs	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	47	26	NM_014874	0	0	0	0	0	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Frame_Shift_Del	DEL	ENST00000235329.5	37	CCDS30587.1																																																																																			.		0.574	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		-	12061549	TT	-	12061548	7	5	84	1	0	1	0	1	0	0	0	0	9549	1609	56	0	933	0	MFN2	1	12061548	Frame_Shift_Del	DEL	TT	TCGA-BQ-7051-01A-12D-1961-08	9625375	12061548	237189073	2	7679											
HSPG2	3339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22214014	22214014	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcatgcggcctcctggggcCcacagggcaggggcctgacg	5	4	18	14	2	0	1	0	1	0	0	1	1	1	1	4	7	1	2	4	7	0	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:22214014C>A	ENST00000374695.3	-	8	936	c.857G>T	c.(856-858)gGg>gTg	p.G286V		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	286	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CTCCTGGGGCCCACAGGGCAG	0.657																																					p.G286V		.											.	HSPG2-141	0			c.G857T						.						67	82	77					1																	22214014		2203	4299	6502	SO:0001583	missense	3339	exon8			TGGGGCCCACAGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"Proteoglycans / Extracellular Matrix : Other", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5273	protein-coding gene	gene with protein product	"perlecan proteoglycan"	142461	"Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.857G>T	1.37:g.22214014C>A	ENSP00000363827:p.Gly286Val	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	80	37	NM_005529	0	0	18	23	5	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.61|18.61	3.661500|3.661500	0.67700|0.67700	.|.	.|.	ENSG00000142798|ENSG00000142798	ENST00000412328;ENST00000374673|ENST00000374695	T;D|D	0.95918|0.95853	0.35;-3.85|-3.83	5.09|5.09	3.22|3.22	0.36961|0.36961	.|.	0.178923|0.178923	0.27027|0.27027	N|N	0.021295|0.021295	D|D	0.94771|0.94771	0.8312|0.8312	M|M	0.80183|0.80183	2.485|2.485	0.52501|0.52501	D|D	0.999955|0.999955	D|P	0.89917|0.36683	1.0|0.565	D|B	0.69479|0.41374	0.964|0.355	D|D	0.91702|0.91702	0.5374|0.5374	10|10	0.59425|0.38643	D|T	0.04|0.18	.|.	9.1776|9.1776	0.37120|0.37120	0.0:0.8213:0.0:0.1787|0.0:0.8213:0.0:0.1787	.|.	209|286	Q5SZI5|P98160	.|PGBM_HUMAN	C|V	209;113|286	ENSP00000405412:G209C;ENSP00000363805:G113C|ENSP00000363827:G286V	ENSP00000363805:G113C|ENSP00000363827:G286V	G|G	-|-	1|2	0|0	HSPG2|HSPG2	22086601|22086601	0.001000|0.001000	0.12720|0.12720	0.995000|0.995000	0.50966|0.50966	0.549000|0.549000	0.35272|0.35272	0.204000|0.204000	0.17335|0.17335	0.566000|0.566000	0.29273|0.29273	0.462000|0.462000	0.41574|0.41574	GGC|GGG	.		0.657	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22214014	C	A	22214014	3	1	84	1	0	0	0	0	1	0	0	0	7451	623	22	4	12678	4	HSPG2	1	22214014	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	10152466	22214014	227036607	3	7680											
HIVEP3	59269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	42048585	42048585	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccttcttggtctttttggtAagctcgctttccttgggttc	2	19	9	11	1	2	0	0	0	2	0	5	0	3	0	2	3	1	4	2	3	1	8			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:42048585A>T	ENST00000372583.1	-	4	2769	c.1884T>A	c.(1882-1884)ctT>ctA	p.L628L	HIVEP3_ENST00000372584.1_Silent_p.L628L|HIVEP3_ENST00000247584.5_Silent_p.L628L|HIVEP3_ENST00000429157.2_Silent_p.L628L	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	628	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TCTTTTTGGTAAGCTCGCTTT	0.493																																					p.L628L		.											.	HIVEP3-157	0			c.T1884A						.						123	120	121					1																	42048585		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			TTTGGTAAGCTCG	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.1884T>A	1.37:g.42048585A>T		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	152	61	NM_024503	0	0	5	5	0	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	37	CCDS463.1																																																																																			.		0.493	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42048585	A	T	42048585	2	4	84	1	0	0	0	0	0	0	0	1	7209	349	13	5		5	HIVEP3	1	42048585	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	19834571	42048585	207202036	4	7681											
CYP4A11	1579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	47402352	47402352	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcaccagcatcactcgtacaGagtctgccatgagccccaca	11	7	7	16	1	3	2	2	1	1	1	4	2	3	2	4	0	4	2	4	0	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:47402352G>C	ENST00000310638.4	-	4	525	c.494C>G	c.(493-495)tCt>tGt	p.S165C	CYP4A11_ENST00000496519.1_5'Flank|CYP4A11_ENST00000462347.1_Missense_Mutation_p.S165C|CYP4A11_ENST00000371904.4_Missense_Mutation_p.S165C|CYP4A11_ENST00000371905.1_Missense_Mutation_p.S165C|CYP4A11_ENST00000457840.2_Missense_Mutation_p.S61C	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	165					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CACTCGTACAGAGTCTGCCAT	0.562																																					p.S165C		.											.	CYP4A11-94	0			c.C494G						.						88	70	76					1																	47402352		2203	4300	6503	SO:0001583	missense	1579	exon4			CGTACAGAGTCTG	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.494C>G	1.37:g.47402352G>C	ENSP00000311095:p.Ser165Cys	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	62	23	NM_000778	0	0	5	7	2	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	37	CCDS543.1	.	.	.	.	.	.	.	.	.	.	N	18.30	3.593520	0.66219	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905;ENST00000457840	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	L	0.48642	1.525	0.41496	D	0.988252	P	0.45768	0.866	P	0.53988	0.739	T	0.71517	-0.4569	10	0.45353	T	0.12	.	15.1292	0.72507	0.0:0.1409:0.859:0.0	.	165	Q02928	CP4AB_HUMAN	C	165;165;165;61	ENSP00000311095:S165C;ENSP00000360971:S165C;ENSP00000360972:S165C;ENSP00000406272:S61C	ENSP00000311095:S165C	S	-	2	0	CYP4A11	47174939	1.000000	0.71417	0.448000	0.26945	0.053000	0.15095	4.950000	0.63603	2.640000	0.89533	0.644000	0.83932	TCT	.		0.562	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		C	47402352	G	C	47402352	3	2	84	1	0	0	0	0	1	0	0	0	4189	942	33	4	1101	4	CYP4A11	1	47402352	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5353767	47402352	201848269	5	7682											
ZCCHC11	23318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52902541	52902541	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgggtctctaaagtctcGagtatcgtggaggtctcggg	6	12	14	9	4	4	0	0	0	4	0	9	2	4	1	0	4	0	1	0	4	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:52902541G>T	ENST00000371544.3	-	26	4307	c.4045C>A	c.(4045-4047)Cga>Aga	p.R1349R	ZCCHC11_ENST00000257177.4_Silent_p.R1350R	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1349					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						CTAAAGTCTCGAGTATCGTGG	0.483																																					p.R1350R		.											.	ZCCHC11-93	0			c.C4048A						.						185	188	187					1																	52902541		2203	4300	6503	SO:0001819	synonymous_variant	23318	exon26			AGTCTCGAGTATC	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4045C>A	1.37:g.52902541G>T		Somatic	178	0		WXS	Illumina HiSeq	Phase_I	160	72	NM_001009881	0	0	33	57	24	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Silent	SNP	ENST00000371544.3	37	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	G	8.051	0.765950	0.15983	.	.	ENSG00000134744	ENST00000474453	.	.	.	3.77	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7235	0.34456	0.0:0.0:0.7739:0.2261	.	.	.	.	X	194	.	.	S	-	2	0	ZCCHC11	52675129	1.000000	0.71417	0.958000	0.39756	0.893000	0.52053	1.976000	0.40579	1.155000	0.42497	0.655000	0.94253	TCG	.		0.483	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		T	52902541	G	T	52902541	2	4	84	1	0	0	0	0	0	0	0	1	17612	1066	37	4		4	ZCCHC11	1	52902541	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5500189	52902541	196348080	6	7683											
ZNF326	284695	broad.mit.edu;bcgsc.ca	37	chr1	90475714	90475714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatcaaaacaaatccaccaAtgtgacagttgctgctgcaa	15	9	6	11	0	1	1	1	1	0	0	2	1	2	1	2	0	4	4	2	0	6	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:90475714A>G	ENST00000340281.4	+	6	826	c.683A>G	c.(682-684)aAt>aGt	p.N228S	ZNF326_ENST00000455342.2_Missense_Mutation_p.N22S|ZNF326_ENST00000370447.3_Missense_Mutation_p.N139S	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	228					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		AAATCCACCAATGTGACAGTT	0.363																																					p.N228S													.	ZNF326-91	0			c.A683G						.						103	108	106					1																	90475714		2203	4300	6503	SO:0001583	missense	284695	exon6			CCACCAATGTGAC	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"Zinc fingers, C2H2-type"	14104	protein-coding gene	gene with protein product	"ZNF-protein interacting with nuclear mRNPs and DBC1"	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.683A>G	1.37:g.90475714A>G	ENSP00000340796:p.Asn228Ser	Somatic	142	1		WXS	Illumina HiSeq	Phase_I	140	7	NM_182976	0	0	44	44	0	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	9.648	1.140917	0.21205	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.15952	2.38;2.38;2.38	5.65	3.31	0.37934	.	0.463950	0.22905	N	0.054220	T	0.01523	0.0049	N	0.03608	-0.345	0.23776	N	0.996876	B;B	0.13594	0.006;0.008	B;B	0.08055	0.003;0.003	T	0.47142	-0.9140	10	0.09843	T	0.71	-12.6231	5.7857	0.18333	0.6555:0.1833:0.1612:0.0	.	228;228	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	S	228;228;139;22	ENSP00000340796:N228S;ENSP00000359476:N139S;ENSP00000403470:N22S	ENSP00000340796:N228S	N	+	2	0	ZNF326	90248302	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.135000	0.31454	0.970000	0.38263	0.472000	0.43445	AAT	.		0.363	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		G	90475714	A	G	90475714	3	3	84	1	0	0	0	0	1	0	0	0	17878	101	4	3	709	3	ZNF326	1	90475714	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	37573173	90475714	158774907	7	7684											
MSTO1	55154	hgsc.bcm.edu	37	chr1	155581021	155581021	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcaggcaggggaagctcaCcacacacaaagaggaactct	14	6	10	11	0	3	1	2	0	1	1	3	3	3	3	1	4	2	2	1	4	3	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:155581021C>G	ENST00000245564.2	+	4	329	c.305C>G	c.(304-306)aCc>aGc	p.T102S	MSTO1_ENST00000452804.2_Missense_Mutation_p.T102S|MSTO1_ENST00000483734.1_3'UTR|RP11-29H23.4_ENST00000456382.2_RNA|MSTO1_ENST00000368341.4_Missense_Mutation_p.T102S|MSTO1_ENST00000538143.1_Intron	NM_001256532.1|NM_001256533.1|NM_018116.3	NP_001243461.1|NP_001243462.1|NP_060586.2	Q9BUK6	MSTO1_HUMAN	misato 1, mitochondrial distribution and morphology regulator	102					mitochondrion distribution (GO:0048311)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)				breast(2)|endometrium(1)|lung(3)|skin(1)	7	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)					GGGAAGCTCACCACACACAAA	0.493																																					p.T102S		.											.	MSTO1-90	0			c.C305G						.																																			SO:0001583	missense	55154	exon4			AGCTCACCACACA	BX537684	CCDS1114.1	1q22	2013-08-21	2013-08-21		ENSG00000125459	ENSG00000125459			29678	protein-coding gene	gene with protein product			"misato homolog 1 (Drosophila)"			16545939, 17349998	Standard	NM_018116		Approved	FLJ10504, LST005, MST, misato	uc001fky.4	Q9BUK6	OTTHUMG00000014014	ENST00000245564.2:c.305C>G	1.37:g.155581021C>G	ENSP00000245564:p.Thr102Ser	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	132	23	NM_018116	0	0	18	36	18	Q53GR8|Q5CZ69|Q5T717|Q68CT6|Q7LBZ8|Q7Z3M7|Q7Z558|Q8TE05|Q9NQX2|Q9NVU4	Missense_Mutation	SNP	ENST00000245564.2	37	CCDS1114.1	.	.	.	.	.	.	.	.	.	.	.	11.67	1.708166	0.30322	.	.	ENSG00000125459	ENST00000452804;ENST00000245564;ENST00000368341	T;T	0.42900	0.96;0.96	3.07	2.12	0.27331	Tubulin/FtsZ, GTPase domain (1);Misato Segment II, myosin-like (1);	0.338788	0.30219	N	0.010139	T	0.09905	0.0243	N	0.21545	0.675	0.80722	D	1	B;B;B	0.24618	0.036;0.107;0.061	B;B;B	0.22386	0.018;0.039;0.015	T	0.13495	-1.0507	10	0.07175	T	0.84	.	11.2789	0.49181	0.0:0.8131:0.1868:0.0	.	102;102;102	Q9BUK6;Q9BUK6-2;Q9BUK6-3	MSTO1_HUMAN;.;.	S	102	ENSP00000245564:T102S;ENSP00000357325:T102S	ENSP00000245564:T102S	T	+	2	0	MSTO1	153847645	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	1.168000	0.31859	0.569000	0.29329	0.313000	0.20887	ACC	.		0.493	MSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039408.1	NM_018116		G	155581021	C	G	155581021	3	3	84	1	0	0	0	0	1	0	0	0	9919	507	18	4	319	4	MSTO1	1	155581021	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	65105307	155581021	93669600	8	7685											
CEP350	9857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	180000535	180000535	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctcccatcaaggaaagAaatctgggaccagcagcaaa	15	5	11	10	0	2	1	1	0	1	1	3	3	3	3	2	3	2	3	2	3	4	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:180000535A>C	ENST00000367607.3	+	15	4049	c.3631A>C	c.(3631-3633)Aaa>Caa	p.K1211Q		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1211	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCAAGGAAAGAAATCTGGGAC	0.398																																					p.K1211Q		.											.	CEP350-26	0			c.A3631C						.						50	52	51					1																	180000535		2203	4300	6503	SO:0001583	missense	9857	exon15			GGAAAGAAATCTG	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.3631A>C	1.37:g.180000535A>C	ENSP00000356579:p.Lys1211Gln	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	38	16	NM_014810	0	0	5	10	5	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816051	0.90790	.	.	ENSG00000135837	ENST00000367607	T	0.59906	0.23	6.02	6.02	0.97574	.	0.000000	0.49916	D	0.000133	T	0.66616	0.2807	L	0.32530	0.975	0.42214	D	0.991828	D;D	0.76494	0.999;0.998	D;P	0.78314	0.991;0.796	T	0.64884	-0.6302	9	.	.	.	.	16.2108	0.82158	1.0:0.0:0.0:0.0	.	1211;1211	E7EU22;Q5VT06	.;CE350_HUMAN	Q	1211	ENSP00000356579:K1211Q	.	K	+	1	0	CEP350	178267158	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.354000	0.73036	2.299000	0.77371	0.528000	0.53228	AAA	.		0.398	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	180000535	A	C	180000535	3	2	84	1	0	0	0	0	1	0	0	0	3260	247	9	5	3685	5	CEP350	1	180000535	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	24419514	180000535	69250086	9	7686											
PTPN14	5784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214556993	214556993	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccagggccgcctgcagctgGgcactgtactccatcttctc	5	9	11	16	1	2	0	0	0	2	0	4	0	3	0	4	2	3	4	4	2	1	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:214556993G>A	ENST00000366956.5	-	13	2399	c.2205C>T	c.(2203-2205)gcC>gcT	p.A735A	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	735					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CCTGCAGCTGGGCACTGTACT	0.632																																					p.A735A	Colon(92;557 1424 24372 34121 40073)	.											.	PTPN14-290	0			c.C2205T						.						35	41	39					1																	214556993		2201	4295	6496	SO:0001819	synonymous_variant	5784	exon13			CAGCTGGGCACTG	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2205C>T	1.37:g.214556993G>A		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	67	30	NM_005401	0	0	7	23	16	Q5VSI0	Silent	SNP	ENST00000366956.5	37	CCDS1514.1																																																																																			.		0.632	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214556993	G	A	214556993	2	1	84	1	0	0	0	0	0	0	0	1	12813	1219	43	2		2	PTPN14	1	214556993	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	34556458	214556993	34693628	10	7687											
ZNF514	84874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95815880	95815880	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaactggccatcacaaccgCaggctgctttcaacttcgag	10	9	8	14	2	2	0	2	0	0	0	3	1	2	0	2	2	4	3	2	2	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:95815880C>T	ENST00000295208.2	-	5	812	c.350G>A	c.(349-351)tGc>tAc	p.C117Y	ZNF514_ENST00000411425.1_Missense_Mutation_p.C117Y|MRPS5_ENST00000475040.1_5'Flank	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	117					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)			large_intestine(4)|lung(6)|urinary_tract(1)	11						ATCACAACCGCAGGCTGCTTT	0.438																																					p.C117Y		.											.	ZNF514-90	0			c.G350A						.						121	120	120					2																	95815880		2203	4300	6503	SO:0001583	missense	84874	exon5			CAACCGCAGGCTG	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.350G>A	2.37:g.95815880C>T	ENSP00000295208:p.Cys117Tyr	Somatic	154	1		WXS	Illumina HiSeq	Phase_I	152	63	NM_032788	0	0	14	21	7	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	37	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	C	0.252	-1.006088	0.02112	.	.	ENSG00000144026	ENST00000295208;ENST00000411425	T;T	0.05025	3.51;3.51	3.18	0.178	0.15058	.	.	.	.	.	T	0.04497	0.0123	L	0.43152	1.355	0.09310	N	1	P	0.42785	0.79	B	0.32289	0.143	T	0.41413	-0.9510	9	0.29301	T	0.29	.	6.8351	0.23931	0.0:0.3742:0.5135:0.1122	.	117	Q96K75	ZN514_HUMAN	Y	117	ENSP00000295208:C117Y;ENSP00000405509:C117Y	ENSP00000295208:C117Y	C	-	2	0	ZNF514	95179607	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.114000	0.15520	0.020000	0.15106	0.655000	0.94253	TGC	.		0.438	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		T	95815880	C	T	95815880	3	4	84	1	0	0	0	0	1	0	0	0	17991	710	25	2	856	2	ZNF514	2	95815880	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08		95815880	147383493	11	7688											
SULT1C4	27233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109002781	109002781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatggcaaactattcatcgaTtcctgctgaaatcatggacc	13	11	7	10	1	2	1	2	1	0	0	4	3	3	2	2	2	2	2	2	2	4	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:109002781T>C	ENST00000272452.2	+	6	1075	c.749T>C	c.(748-750)aTt>aCt	p.I250T	SULT1C4_ENST00000409309.3_Missense_Mutation_p.I175T	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	250					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						TATTCATCGATTCCTGCTGAA	0.299																																					p.I250T		.											.	SULT1C4-22	0			c.T749C						.						92	89	90					2																	109002781		2203	4300	6503	SO:0001583	missense	27233	exon6			CATCGATTCCTGC	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.749T>C	2.37:g.109002781T>C	ENSP00000272452:p.Ile250Thr	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	119	59	NM_006588	0	0	193	394	201	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	37	CCDS2077.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502652	0.26949	.	.	ENSG00000198075	ENST00000272452;ENST00000409309	D;D	0.82344	-1.6;-1.6	4.69	3.51	0.40186	Sulfotransferase domain (1);	0.823783	0.10424	N	0.676268	T	0.81034	0.4739	L	0.39147	1.195	0.09310	N	1	P;B	0.39480	0.675;0.05	P;B	0.47603	0.551;0.131	T	0.69650	-0.5088	10	0.54805	T	0.06	.	6.7246	0.23348	0.1598:0.0:0.1461:0.6941	.	175;250	Q08AS5;O75897	.;ST1C4_HUMAN	T	250;175	ENSP00000272452:I250T;ENSP00000387225:I175T	ENSP00000272452:I250T	I	+	2	0	SULT1C4	108369213	0.086000	0.21541	0.001000	0.08648	0.087000	0.18053	3.039000	0.49791	0.904000	0.36572	0.496000	0.49642	ATT	.		0.299	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		C	109002781	T	C	109002781	3	2	84	1	0	0	0	0	1	0	0	0	15411	1493	52	3	771	3	SULT1C4	2	109002781	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	13186901	109002781	134196592	12	7689											
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu	37	chr2	109370389	109370389	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggactacctaataaagattAtagatgacagtgattcaaat	17	11	8	5	0	1	4	1	2	0	2	1	5	1	5	1	1	1	0	1	1	7	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:109370389A>T	ENST00000283195.6	+	15	2290	c.2164A>T	c.(2164-2166)Ata>Tta	p.I722L		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	722					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AATAAAGATTATAGATGACAG	0.378																																					p.I722L		.											.	RANBP2-675	0			c.A2164T						.						67	80	76					2																	109370389		2181	4289	6470	SO:0001583	missense	5903	exon15			AAGATTATAGATG	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2164A>T	2.37:g.109370389A>T	ENSP00000283195:p.Ile722Leu	Somatic	442	0		WXS	Illumina HiSeq	Phase_I	353	114	NM_006267	0	0	9	17	8	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	2.546	-0.305085	0.05495	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.20069	2.1	5.09	-2.11	0.07187	.	.	.	.	.	T	0.06554	0.0168	N	0.04508	-0.205	0.09310	N	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.39461	-0.9613	9	0.05833	T	0.94	4.0E-4	5.8231	0.18538	0.5189:0.1341:0.0:0.3471	.	722	P49792	RBP2_HUMAN	L	722	ENSP00000283195:I722L	ENSP00000283195:I722L	I	+	1	0	RANBP2	108736821	0.325000	0.24660	0.968000	0.41197	0.973000	0.67179	-0.324000	0.07986	-0.548000	0.06199	-1.802000	0.00618	ATA	.		0.378	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		T	109370389	A	T	109370389	3	4	84	1	0	0	0	0	1	0	0	0	13060	449	16	5	2222	5	RANBP2	2	109370389	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	367608	109370389	133828984	13	7690											
RPRM	56475	broad.mit.edu;bcgsc.ca	37	chr2	154334999	154334999	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgcctgggtgcagcagcgCacggctcgctccagcgcctc	5	5	14	17	5	0	0	0	0	0	0	3	1	1	0	3	2	4	5	3	2	0	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:154334999C>T	ENST00000325926.3	-	1	323	c.81G>A	c.(79-81)gtG>gtA	p.V27V	AC012501.2_ENST00000424322.1_RNA	NM_019845.2	NP_062819.1	Q9NS64	RPRM_HUMAN	reprimo, TP53 dependent G2 arrest mediator candidate	27					cell cycle arrest (GO:0007050)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)|prostate(1)	4						TGCAGCAGCGCACGGCTCGCT	0.701																																					p.V27V													.	RPRM-204	0			c.G81A						.						44	32	36					2																	154334999		2202	4299	6501	SO:0001819	synonymous_variant	56475	exon1			GCAGCGCACGGCT	AK074808	CCDS2198.1	2q24.1	2011-01-26	2005-12-01		ENSG00000177519	ENSG00000177519			24201	protein-coding gene	gene with protein product	"candidate mediator of the p53 dependent G2 arrest", "REPRIMO"	612171	"reprimo, TP53 dependant G2 arrest mediator candidate"			10930422	Standard	NM_019845		Approved	FLJ90327, REPRIMO	uc002tyq.1	Q9NS64	OTTHUMG00000131905	ENST00000325926.3:c.81G>A	2.37:g.154334999C>T		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_019845	0	0	0	0	0	B2R4V1	Silent	SNP	ENST00000325926.3	37	CCDS2198.1																																																																																			.		0.701	RPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254856.1	NM_019845		T	154334999	C	T	154334999	2	4	84	1	0	0	0	0	0	0	0	1	13650	697	25	2		2	RPRM	2	154334999	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	44964610	154334999	88864374	14	7691											
BAZ2B	29994	ucsc.edu	37	chr2	160295143	160295143	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tggctggtgtattcttttttCctgggctttttcagttgctt	2	22	10	7	0	2	0	1	0	1	0	3	0	3	0	1	3	1	5	1	3	1	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:160295143C>T	ENST00000392783.2	-	8	1459	c.964G>A	c.(964-966)Gaa>Aaa	p.E322K	BAZ2B_ENST00000343439.5_Missense_Mutation_p.E320K|BAZ2B_ENST00000392782.1_Missense_Mutation_p.E320K|BAZ2B_ENST00000355831.2_Missense_Mutation_p.E322K	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						ATTCTTTTTTCCTGGGCTTTT	0.428																																					p.E322K													.	BAZ2B-94	0			c.G964A						.						173	174	173					2																	160295143		1836	4105	5941	SO:0001583	missense	29994	exon8			TTTTTTCCTGGGC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"Zinc fingers, PHD-type"	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.964G>A	2.37:g.160295143C>T	ENSP00000376534:p.Glu322Lys	Somatic	239	6		WXS	Illumina HiSeq		243	3	NM_013450	0	0	14	15	1	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	20.1	3.938406	0.73557	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	T;T;T;T	0.08807	3.05;3.05;3.05;3.05	5.05	5.05	0.67936	.	0.000000	0.38058	U	0.001839	T	0.27169	0.0666	L	0.57536	1.79	0.52099	D	0.999944	D;D;P;P;P	0.61697	0.99;0.99;0.827;0.827;0.734	D;D;B;B;B	0.72982	0.979;0.979;0.345;0.442;0.257	T	0.00587	-1.1657	10	0.62326	D	0.03	-19.7068	18.7769	0.91915	0.0:1.0:0.0:0.0	.	320;322;320;320;322	Q6MZK7;Q9UIF8-3;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;BAZ2B_HUMAN	K	320;322;322;320;259	ENSP00000376533:E320K;ENSP00000376534:E322K;ENSP00000348087:E322K;ENSP00000339670:E320K	ENSP00000339670:E320K	E	-	1	0	BAZ2B	160003389	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.934000	0.70138	2.485000	0.83878	0.650000	0.86243	GAA	.		0.428	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160295143	C	T	160295143	3	4	84	1	0	0	0	0	1	0	0	0	1333	864	30	2	5662	2	BAZ2B	2	160295143	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	5960144	160295143	82904230	15	7692											
MYO3B	140469	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	171375969	171375969	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctcaggggctctgtacatcGtaggagccattcacaagcag	10	9	11	11	1	3	0	2	0	2	0	5	1	3	1	1	3	3	4	1	3	3	3	rs372050798		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:171375969G>A	ENST00000408978.4	+	30	3637	c.3494G>A	c.(3493-3495)cGt>cAt	p.R1165H	MYO3B_ENST00000409044.3_Missense_Mutation_p.R1138H|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Missense_Mutation_p.R1174H	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	1165			R -> C (in dbSNP:rs56052422). {ECO:0000269|PubMed:17344846}.		peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TCTGTACATCGTAGGAGCCAT	0.468													g|||	1	0.000199681	8e-04	0	5008	,	,		17494	0		0	False		,,,				2504	0				p.R1165H													.	MYO3B-530	0			c.G3494A						.	G	HIS/ARG,HIS/ARG,HIS/ARG	2,3826		0,2,1912	78	79	78		3413,3494,3494	-6.1	0	2		78	0,8252		0,0,4126	no	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	29,29,29	0,2,6038	AA,AG,GG		0.0,0.0522,0.0166	benign,benign,benign	1138/1315,1165/1276,1165/1342	171375969	2,12078	1914	4126	6040	SO:0001583	missense	140469	exon30			TACATCGTAGGAG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"Myosins / Myosin superfamily : Class III"	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.3494G>A	2.37:g.171375969G>A	ENSP00000386213:p.Arg1165His	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	68	24	NM_138995	0	0	0	0	0	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	g	7.696	0.692180	0.15039	5.22E-4	0.0	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000334231	T;T;T	0.77877	-1.13;-1.12;-1.12	3.82	-6.05	0.02172	.	1.065760	0.07515	N	0.909616	T	0.42944	0.1225	N	0.01874	-0.695	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.21177	-1.0253	10	0.33940	T	0.23	.	1.306	0.02088	0.2439:0.3051:0.3014:0.1496	.	1165;1138;1165	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	H	1138;1165;1164;1174	ENSP00000386497:R1138H;ENSP00000386213:R1165H;ENSP00000335100:R1174H	ENSP00000314213:R1164H	R	+	2	0	MYO3B	171084215	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.898000	0.04105	-0.977000	0.03537	-0.537000	0.04273	CGT	.		0.468	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171375969	G	A	171375969	3	1	84	1	0	0	0	0	1	0	0	0	10102	1145	40	1	3612	1	MYO3B	2	171375969	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	11080826	171375969	71823404	16	7693											
NFE2L2	4780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	178098803	178098803	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgaattgggagaaattcaCctgtctcttcatctagttgt	9	15	9	8	0	4	2	2	1	2	1	5	3	4	2	1	1	0	2	1	1	3	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:178098803C>A	ENST00000397062.3	-	2	796	c.242G>T	c.(241-243)gGt>gTt	p.G81V	NFE2L2_ENST00000423513.1_Missense_Mutation_p.G65V|NFE2L2_ENST00000446151.2_Missense_Mutation_p.G65V|NFE2L2_ENST00000464747.1_Missense_Mutation_p.G65V|NFE2L2_ENST00000397063.4_Missense_Mutation_p.G65V	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	81					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81D(5)|p.G81V(4)|p.G81_F83delGEF(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			GAGAAATTCACCTGTCTCTTC	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.G81V		.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2-90	10	Substitution - Missense(9)|Deletion - In frame(1)	lung(4)|oesophagus(2)|liver(2)|endometrium(1)|kidney(1)	c.G242T						.						143	142	142					2																	178098803		1901	4105	6006	SO:0001583	missense	4780	exon2			AATTCACCTGTCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.242G>T	2.37:g.178098803C>A	ENSP00000380252:p.Gly81Val	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	98	51	NM_006164	0	0	98	175	77	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.0|28.0	4.883817|4.883817	0.91814|0.91814	.|.	.|.	ENSG00000116044|ENSG00000116044	ENST00000449627|ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	.|T;T;T;T;T;T	.|0.52983	.|1.19;1.19;1.19;0.64;0.64;1.19	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.75110	.|0.3805	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;0.999;1.0;0.999	.|T	.|0.78563	.|-0.2156	.|10	.|0.87932	.|D	.|0	.|.	19.9976|19.9976	0.97389|0.97389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|65;65;65;81	.|E9PGJ7;B4DNB0;C9JFL6;Q16236	.|.;.;.;NF2L2_HUMAN	.|V	-1|65;81;65;65;65;65	.|ENSP00000380253:G65V;ENSP00000380252:G81V;ENSP00000411575:G65V;ENSP00000400073:G65V;ENSP00000412191:G65V;ENSP00000410015:G65V	.|ENSP00000380252:G81V	.|G	-|-	.|2	.|0	NFE2L2|NFE2L2	177807049|177807049	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.993000|0.993000	0.82548|0.82548	7.298000|7.298000	0.78815|0.78815	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	.|GGT	.		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098803	C	A	178098803	3	1	84	1	0	0	0	0	1	0	0	0	10394	507	18	4	1591	4	NFE2L2	2	178098803	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	6722834	178098803	65100570	17	7694											
COPS7B	64708	hgsc.bcm.edu;broad.mit.edu	37	chr2	232663673	232663673	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcagcaggtagaagcagAggtaaggaaggaaaggaaca	18	3	15	5	0	1	2	1	0	0	2	1	5	1	5	0	5	4	5	0	5	6	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:232663673A>G	ENST00000350033.3	+	6	776	c.635A>G	c.(634-636)gAg>gGg	p.E212G	COPS7B_ENST00000409091.1_Splice_Site_p.E105G|COPS7B_ENST00000410017.1_Splice_Site_p.E212G|COPS7B_ENST00000410024.1_Splice_Site_p.E212G|COPS7B_ENST00000409295.1_Splice_Site_p.E178G|COPS7B_ENST00000373608.3_Splice_Site_p.E212G	NM_001282949.1|NM_022730.1	NP_001269878.1|NP_073567.1	Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	212					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTAGAAGCAGAGGTAAGGAAG	0.448																																					p.E212G		.											.	COPS7B-228	0			c.A635G						.						114	86	96					2																	232663673		2203	4300	6503	SO:0001630	splice_region_variant	64708	exon6			AAGCAGAGGTAAG	AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524			16760	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B", "COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)"			9707402	Standard	NM_001282950		Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000350033.3:c.636+1A>G	2.37:g.232663673A>G		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	21	9	NM_022730	0	0	0	0	0	Q53S22|Q5BJG3|Q9H7V6	Missense_Mutation	SNP	ENST00000350033.3	37	CCDS2488.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141236	0.77775	.	.	ENSG00000144524	ENST00000410024;ENST00000409295;ENST00000409091;ENST00000350033;ENST00000410017;ENST00000373608;ENST00000537799;ENST00000449174	T;T;T;T;T;T;T	0.52295	1.17;1.17;1.17;1.17;0.7;0.67;1.17	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.66479	0.2793	M	0.69185	2.1	0.80722	D	1	D;D;D	0.89917	1.0;0.992;0.998	D;D;D	0.83275	0.996;0.921;0.968	T	0.70124	-0.4958	10	0.66056	D	0.02	-1.6914	14.6136	0.68531	1.0:0.0:0.0:0.0	.	212;212;212	Q53GQ2;Q9H9Q2-3;Q9H9Q2	.;.;CSN7B_HUMAN	G	212;178;105;212;212;212;105;76	ENSP00000386567:E212G;ENSP00000386438:E178G;ENSP00000386527:E105G;ENSP00000272995:E212G;ENSP00000386880:E212G;ENSP00000362710:E212G;ENSP00000403300:E76G	ENSP00000272995:E212G	E	+	2	0	COPS7B	232371917	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.777000	0.91781	2.044000	0.60594	0.533000	0.62120	GAG	.		0.448	COPS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256964.2	NM_022730	Missense_Mutation	G	232663673	A	G	232663673	5	3	84	1	0	0	0	0	0	0	1	0	3745	318	11	3	653	3	COPS7B	2	232663673	Splice_Site	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	54564870	232663673	10535700	18	7695											
SLC22A13	9390	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38317429	38317429	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagtgggggacttcggccTggacgtctatctgacgcagc	7	8	14	12	3	2	1	0	1	2	0	3	3	2	3	2	4	1	1	2	4	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:38317429T>C	ENST00000311856.4	+	7	1128	c.1079T>C	c.(1078-1080)cTg>cCg	p.L360P	SLC22A13_ENST00000450935.2_3'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	360					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		GACTTCGGCCTGGACGTCTAT	0.572																																					p.L360P		.											.	SLC22A13-91	0			c.T1079C						.						80	77	78					3																	38317429		2203	4300	6503	SO:0001583	missense	9390	exon7			TCGGCCTGGACGT	AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.1079T>C	3.37:g.38317429T>C	ENSP00000310241:p.Leu360Pro	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	77	29	NM_004256	0	0	0	0	0	B2RCV9|Q8IYG1	Missense_Mutation	SNP	ENST00000311856.4	37	CCDS2676.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652783	0.67472	.	.	ENSG00000172940	ENST00000311856	T	0.62639	0.01	5.04	5.04	0.67666	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	T	0.81408	0.4816	M	0.91196	3.185	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.70227	0.945;0.968	T	0.82623	-0.0366	10	0.28530	T	0.3	.	14.2827	0.66224	0.0:0.0:0.0:1.0	.	360;360	Q9Y226-2;Q9Y226	.;S22AD_HUMAN	P	360	ENSP00000310241:L360P	ENSP00000310241:L360P	L	+	2	0	SLC22A13	38292433	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	5.806000	0.69150	2.040000	0.60383	0.533000	0.62120	CTG	.		0.572	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38317429	T	C	38317429	3	2	84	1	0	0	0	0	1	0	0	0	14476	1580	55	3	1105	3	SLC22A13	3	38317429	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08		38317429	159705001	19	7696											
SACM1L	22908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	45773632	45773632	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatcaggtagcagaaatgcaAgatgaattaaggtaagctat	17	9	11	4	0	1	3	1	1	0	2	1	4	1	3	0	2	3	5	0	2	7	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:45773632A>T	ENST00000389061.5	+	13	1293	c.1089A>T	c.(1087-1089)caA>caT	p.Q363H	SACM1L_ENST00000418611.1_Missense_Mutation_p.Q260H|SACM1L_ENST00000541314.1_Missense_Mutation_p.Q302H	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	363	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		CAGAAATGCAAGATGAATTAA	0.338																																					p.Q363H		.											.	SACM1L-91	0			c.A1089T						.						105	115	112					3																	45773632		2203	4299	6502	SO:0001583	missense	22908	exon13			AATGCAAGATGAA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1089A>T	3.37:g.45773632A>T	ENSP00000373713:p.Gln363His	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	146	69	NM_014016	0	0	0	0	0	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.391717	0.42410	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314;ENST00000433336	T;T;T;T	0.43294	0.95;0.95;0.95;1.53	5.99	-5.27	0.02763	Synaptojanin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.88031	2.925	0.52501	D	0.999958	D;D	0.76494	0.999;0.998	D;D	0.65987	0.94;0.912	T	0.68716	-0.5335	10	0.36615	T	0.2	-3.4019	15.7038	0.77563	0.4825:0.0:0.5175:0.0	.	302;363	B4DK71;Q9NTJ5	.;SAC1_HUMAN	H	260;363;302;40	ENSP00000396387:Q260H;ENSP00000373713:Q363H;ENSP00000443373:Q302H;ENSP00000412883:Q40H	ENSP00000373713:Q363H	Q	+	3	2	SACM1L	45748636	0.993000	0.37304	0.874000	0.34290	0.998000	0.95712	0.423000	0.21313	-1.249000	0.02500	0.533000	0.62120	CAA	.		0.338	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		T	45773632	A	T	45773632	3	4	84	1	0	0	0	0	1	0	0	0	13835	69	3	5	1139	5	SACM1L	3	45773632	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	7456203	45773632	152248798	20	7697											
SLC38A3	10991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50252997	50252997	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccgtgcctatgagcagcTgggctaccgtgcctttggga	6	10	13	12	2	0	1	0	1	0	0	1	2	1	2	4	2	5	3	4	2	2	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:50252997T>C	ENST00000420502.1	+	0	548									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		TATGAGCAGCTGGGCTACCGT	0.622																																					p.L132P		.											.	SLC38A3-67	0			c.T395C						.						47	51	50					3																	50252997		2095	4216	6311			10991	exon6			AGCAGCTGGGCTA	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		3.37:g.50252997T>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	65	29	NM_006841	0	0	0	0	0		Missense_Mutation	SNP	ENST00000420502.1	37																																																																																				.		0.622	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		C	50252997	T	C	50252997	1	2	84	0	1	0	0	0	0	0	0	0	14637	1580	55	3		3	SLC38A3	3	50252997	RNA	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	4479365	50252997	147769433	21	7698											
PPM1M	132160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52282683	52282683	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtgtggagaaatcggatctCaagtacccactgatccatgg	11	9	11	10	2	1	2	1	1	1	1	4	4	2	3	2	3	1	1	2	3	3	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:52282683C>T	ENST00000296487.4	+	7	866	c.462C>T	c.(460-462)ctC>ctT	p.L154L	PPM1M_ENST00000457351.2_Silent_p.L315L|PPM1M_ENST00000323588.4_Silent_p.L154L|PPM1M_ENST00000409502.3_Silent_p.L103L			Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1M	154	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			prostate(1)|urinary_tract(1)	2				BRCA - Breast invasive adenocarcinoma(193;2.4e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)		AATCGGATCTCAAGTACCCAC	0.572																																					p.L315L	NSCLC(151;810 2688 34365 49863)	.											.	.	0			c.C945T						.						156	139	145					3																	52282683		2203	4300	6503	SO:0001819	synonymous_variant	132160	exon7			GGATCTCAAGTAC	AK096681	CCDS46840.1	3p21.31	2012-04-17	2010-03-05		ENSG00000164088	ENSG00000164088		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	26506	protein-coding gene	gene with protein product	"protein phosphatase 2C eta"	608979	"protein phosphatase 1M (PP2C domain containing)"			12477932	Standard	NM_001122870		Approved	PP2Ceta, FLJ32332	uc011bed.2	Q96MI6	OTTHUMG00000153046	ENST00000296487.4:c.462C>T	3.37:g.52282683C>T		Somatic	140	0		WXS	Illumina HiSeq	Phase_I	150	70	NM_144641	0	0	17	29	12	Q8N8J9|Q96DB8	Silent	SNP	ENST00000296487.4	37		.	.	.	.	.	.	.	.	.	.	C	9.454	1.091407	0.20471	.	.	ENSG00000164088	ENST00000457454	.	.	.	4.78	3.9	0.45041	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54957	-0.8215	4	.	.	.	.	8.0844	0.30762	0.0:0.7542:0.1611:0.0848	.	.	.	.	L	210	.	.	S	+	2	0	PPM1M	52257723	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.991000	0.29654	1.205000	0.43262	0.561000	0.74099	TCA	.		0.572	PPM1M-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000329230.2	NM_144641		T	52282683	C	T	52282683	2	4	84	1	0	0	0	0	0	0	0	1	12374	813	29	2		2	PPM1M	3	52282683	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	2029686	52282683	145739747	22	7699											
SLMAP	7871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	57827089	57827089	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggtatggaagcccggcTccgctcagagtgagtataat	11	9	13	8	2	1	3	1	1	0	2	2	4	2	4	2	3	1	4	2	3	4	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:57827089T>C	ENST00000428312.1	+	3	504	c.410T>C	c.(409-411)cTc>cCc	p.L137P	SLMAP_ENST00000295952.3_Missense_Mutation_p.L137P|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000383718.3_Missense_Mutation_p.L137P|SLMAP_ENST00000295951.3_Missense_Mutation_p.L137P|SLMAP_ENST00000449503.2_Missense_Mutation_p.L137P			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	137	Necessary for targeting to centrosomes. {ECO:0000250}.				muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GAAGCCCGGCTCCGCTCAGAG	0.338																																					p.L137P		.											.	SLMAP-90	0			c.T410C						.						67	70	69					3																	57827089		2203	4300	6503	SO:0001583	missense	7871	exon3			CCCGGCTCCGCTC	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"Sarcolemmal-associated protein"	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.410T>C	3.37:g.57827089T>C	ENSP00000398661:p.Leu137Pro	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	81	39	NM_007159	0	0	0	0	0	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Missense_Mutation	SNP	ENST00000428312.1	37		.	.	.	.	.	.	.	.	.	.	T	11.27	1.589587	0.28357	.	.	ENSG00000163681	ENST00000295951;ENST00000295952;ENST00000383718;ENST00000428312;ENST00000449503	T;T;T;T;T	0.47177	1.45;1.45;0.85;1.44;1.49	4.85	4.85	0.62838	.	0.259220	0.31438	N	0.007646	T	0.24586	0.0596	N	0.01874	-0.695	0.80722	D	1	P;P;P;B	0.50369	0.816;0.934;0.898;0.002	P;B;B;B	0.45712	0.491;0.418;0.434;0.005	T	0.11299	-1.0593	10	0.26408	T	0.33	-2.0339	10.587	0.45288	0.0:0.0:0.1615:0.8385	.	137;137;137;137	Q14BN4-2;Q14BN4;Q14BN4-3;Q14BN4-6	.;SLMAP_HUMAN;.;.	P	137	ENSP00000295951:L137P;ENSP00000295952:L137P;ENSP00000373224:L137P;ENSP00000398661:L137P;ENSP00000412945:L137P	ENSP00000295951:L137P	L	+	2	0	SLMAP	57802129	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.864000	0.69575	1.799000	0.52666	0.533000	0.62120	CTC	.		0.338	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		C	57827089	T	C	57827089	3	2	84	1	0	0	0	0	1	0	0	0	14781	1551	54	3	420	3	SLMAP	3	57827089	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	5544406	57827089	140195341	23	7700											
ADAMTS9	56999	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	64536694	64536703	+	Frame_Shift_Del	DEL	CACCACCTTG	CACCACCTTG	-																															tttttgttgtcatccacacaCaccaccttgcggtacctgga																								rs17071010|rs146412036|rs138988394	byFrequency	TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CACCACCTTG	CACCACCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:64536694_64536703delCACCACCTTG	ENST00000498707.1	-	31	5076_5085	c.4734_4743delCAAGGTGGTG	c.(4732-4743)cgcaaggtggtgfs	p.RKVV1578fs	ADAMTS9_ENST00000295903.4_Frame_Shift_Del_p.RKVV1550fs	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1578	TSP type-1 13. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V1581M(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CATCCACACACACCACCTTGCGGTACCTGG	0.5																																					p.1578_1581del		.											.	ADAMTS9-230	1	Substitution - Missense(1)	large_intestine(1)	c.4734_4743del						.																																			SO:0001589	frameshift_variant	56999	exon31			.	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"ADAM metallopeptidases with thrombospondin type 1 motif"	13202	protein-coding gene	gene with protein product		605421	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4734_4743delCAAGGTGGTG	3.37:g.64536694_64536703delCACCACCTTG	ENSP00000418735:p.Arg1578fs	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	135	26	NM_182920	0	0	0	0	0	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Frame_Shift_Del	DEL	ENST00000498707.1	37	CCDS2903.1																																																																																			.		0.5	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			-	64536703	CACCACCTTG	-	64536694	7	5	84	1	0	1	0	1	0	0	0	0	273	465	17	0	1100	0	ADAMTS9	3	64536694	Frame_Shift_Del	DEL	CACCACCTTG	TCGA-BQ-7051-01A-12D-1961-08	6709605	64536694	133485736	24	7701											
KIAA1524	57650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	108282018	108282018	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagcctccaataatattCtcagtccagactgtacttgt	11	12	7	11	0	1	1	1	0	1	1	4	2	3	1	3	0	3	2	3	0	4	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:108282018C>A	ENST00000295746.8	-	13	1665	c.1589G>T	c.(1588-1590)aGa>aTa	p.R530I	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_Missense_Mutation_p.R371I	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	530					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R530T(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAATAATATTCTCAGTCCAGA	0.393																																					p.R530I		.											.	KIAA1524-92	1	Substitution - Missense(1)	ovary(1)	c.G1589T						.						154	159	158					3																	108282018		2203	4300	6503	SO:0001583	missense	57650	exon13			AATATTCTCAGTC	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.1589G>T	3.37:g.108282018C>A	ENSP00000295746:p.Arg530Ile	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	204	74	NM_020890	0	0	3	6	3	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	37	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770678	0.69992	.	.	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.35048	1.33;1.33	5.3	4.43	0.53597	.	0.494865	0.23127	N	0.051633	T	0.40067	0.1102	L	0.53249	1.67	0.53005	D	0.999964	P	0.46706	0.883	P	0.46172	0.506	T	0.31024	-0.9958	10	0.62326	D	0.03	-4.6479	11.7182	0.51666	0.0:0.8541:0.0:0.1459	.	530	Q8TCG1	CIP2A_HUMAN	I	371;530	ENSP00000419487:R371I;ENSP00000295746:R530I	ENSP00000295746:R530I	R	-	2	0	KIAA1524	109764708	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.617000	0.46385	1.237000	0.43756	0.563000	0.77884	AGA	.		0.393	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		A	108282018	C	A	108282018	3	1	84	1	0	0	0	0	1	0	0	0	8260	913	32	4	1164	4	KIAA1524	3	108282018	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	43745324	108282018	89740412	25	7702											
PLXND1	23129	hgsc.bcm.edu;broad.mit.edu	37	chr3	129290142	129290142	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtggagttgagaaccttgCagagctggtgcaggagagcc	9	7	18	7	0	0	3	0	1	0	3	0	6	0	4	2	4	5	4	2	4	1	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:129290142C>G	ENST00000324093.4	-	18	3519	c.3341G>C	c.(3340-3342)tGc>tCc	p.C1114S	PLXND1_ENST00000393239.1_Missense_Mutation_p.C1114S	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1114	IPT/TIG 3.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GAGAACCTTGCAGAGCTGGTG	0.637																																					p.C1114S	Ovarian(97;366 1484 3738 22084 39045)	.											.	PLXND1-90	0			c.G3341C						.						15	17	16					3																	129290142		2179	4277	6456	SO:0001583	missense	23129	exon18			ACCTTGCAGAGCT	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3341G>C	3.37:g.129290142C>G	ENSP00000317128:p.Cys1114Ser	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	21	8	NM_015103	0	0	2	2	0	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.143494	0.57044	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.60171	0.21;0.21	4.91	4.91	0.64330	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.134947	0.50627	D	0.000119	T	0.61800	0.2376	M	0.83603	2.65	0.80722	D	1	P	0.34934	0.476	B	0.32393	0.145	T	0.69540	-0.5118	10	0.66056	D	0.02	.	16.2882	0.82736	0.0:1.0:0.0:0.0	.	1114	Q9Y4D7	PLXD1_HUMAN	S	1114	ENSP00000317128:C1114S;ENSP00000376931:C1114S	ENSP00000317128:C1114S	C	-	2	0	PLXND1	130772832	1.000000	0.71417	1.000000	0.80357	0.374000	0.29953	6.510000	0.73729	2.279000	0.76181	0.313000	0.20887	TGC	.		0.637	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		G	129290142	C	G	129290142	3	3	84	1	0	0	0	0	1	0	0	0	12153	710	25	4	2512	4	PLXND1	3	129290142	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	21008124	129290142	68732288	26	7703											
ZNF721	170960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	436019	436019	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagtttatctccagtatgaAttttcttatattcgttcagg	10	18	7	6	1	3	2	1	1	2	1	5	2	3	2	1	1	0	3	1	1	5	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:436019A>C	ENST00000338977.5	-	2	2249	c.2201T>G	c.(2200-2202)aTt>aGt	p.I734S	ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000511833.2_Missense_Mutation_p.I746S|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	734					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						TCCAGTATGAATTTTCTTATA	0.378																																					p.T746R		.											.	ZNF721-47	0			c.C2237G						.						31	33	32					4																	436019		1990	4173	6163	SO:0001583	missense	170960	exon3			GTATGAATTTTCT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"Zinc fingers, C2H2-type", "-"	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.2201T>G	4.37:g.436019A>C	ENSP00000340524:p.Ile734Ser	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_133474	0	0	5	13	8	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	A	10.61	1.397775	0.25205	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.00949	5.51;5.51	1.28	-0.782	0.10961	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	L	0.52266	1.64	0.09310	N	1	P;P;P	0.41569	0.65;0.755;0.711	P;B;B	0.47102	0.537;0.239;0.154	T	0.44651	-0.9314	9	0.56958	D	0.05	.	4.9522	0.14021	0.6885:0.3115:0.0:0.0	.	734;746;746	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	S	734;746	ENSP00000340524:I734S;ENSP00000428878:I746S	ENSP00000340524:I734S	I	-	2	0	ZNF721	426019	0.000000	0.05858	0.003000	0.11579	0.055000	0.15305	0.796000	0.26986	-0.422000	0.07405	0.155000	0.16302	ATT	.		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		C	436019	A	C	436019	3	2	84	1	0	0	0	0	1	0	0	0	18154	101	4	5	538	5	ZNF721	4	436019	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		436019	190718257	27	7704											
NSUN7	79730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	40778094	40778094	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaagtcttgctgtccattCtgtaaaggctttattaaata	11	16	7	7	1	2	0	0	0	2	0	4	1	3	0	1	1	1	3	1	1	7	7			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:40778094C>A	ENST00000381782.2	+	7	1349	c.854C>A	c.(853-855)tCt>tAt	p.S285Y	NSUN7_ENST00000463952.1_3'UTR|NSUN7_ENST00000316607.5_Missense_Mutation_p.S285Y	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	285							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GCTGTCCATTCTGTAAAGGCT	0.333																																					p.S285Y		.											.	NSUN7-90	0			c.C854A						.						92	92	92					4																	40778094		2202	4298	6500	SO:0001583	missense	79730	exon7			TCCATTCTGTAAA	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.854C>A	4.37:g.40778094C>A	ENSP00000371201:p.Ser285Tyr	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	41	19	NM_024677	0	0	4	7	3	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	37	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	C	22.7	4.318911	0.81469	.	.	ENSG00000179299	ENST00000381782;ENST00000316607	T;T	0.09163	3.01;3.01	5.61	5.61	0.85477	.	0.180007	0.49305	D	0.000151	T	0.31918	0.0812	L	0.59436	1.845	0.51767	D	0.999938	D;D	0.71674	0.997;0.998	D;D	0.72075	0.931;0.976	T	0.00666	-1.1619	10	0.66056	D	0.02	-20.3807	19.2661	0.93985	0.0:1.0:0.0:0.0	.	285;285	Q8NE18;Q8NE18-2	NSUN7_HUMAN;.	Y	285	ENSP00000371201:S285Y;ENSP00000319127:S285Y	ENSP00000319127:S285Y	S	+	2	0	NSUN7	40472851	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.610000	0.67668	2.643000	0.89663	0.557000	0.71058	TCT	.		0.333	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		A	40778094	C	A	40778094	3	1	84	1	0	0	0	0	1	0	0	0	10709	913	32	4	876	4	NSUN7	4	40778094	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	40342075	40778094	150376182	28	7705											
POLR2B	5431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57861558	57861558	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtactatatgggttagcatgCtggcaagaggaggacaggta	12	9	15	5	0	0	1	0	0	0	1	0	3	0	3	0	5	3	6	0	5	6	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:57861558C>A	ENST00000381227.1	+	7	1131	c.718C>A	c.(718-720)Ctg>Atg	p.L240M	snoU13_ENST00000459266.1_RNA|POLR2B_ENST00000441246.2_Missense_Mutation_p.L233M|POLR2B_ENST00000314595.5_Missense_Mutation_p.L240M|POLR2B_ENST00000431623.2_Missense_Mutation_p.L165M			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	240					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GGTTAGCATGCTGGCAAGAGG	0.408																																					p.L240M		.											.	POLR2B-92	0			c.C718A						.						121	125	123					4																	57861558		2203	4300	6503	SO:0001583	missense	5431	exon6			AGCATGCTGGCAA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.718C>A	4.37:g.57861558C>A	ENSP00000370625:p.Leu240Met	Somatic	147	1		WXS	Illumina HiSeq	Phase_I	122	55	NM_000938	0	0	55	109	54	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	37	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	C	8.067	0.769398	0.15983	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	4.84	3.1	0.35709	RNA polymerase, beta subunit, protrusion (1);RNA polymerase Rpb2, domain 2 (1);	0.055810	0.64402	D	0.000001	T	0.46795	0.1411	L	0.28115	0.83	0.58432	D	0.999992	B;B	0.17268	0.021;0.012	B;B	0.27262	0.078;0.078	T	0.19516	-1.0303	10	0.16420	T	0.52	.	10.8237	0.46620	0.0:0.8452:0.0:0.1548	.	165;240	C9J4M6;P30876	.;RPB2_HUMAN	M	240;165;233;240	ENSP00000370625:L240M;ENSP00000391096:L165M;ENSP00000391452:L233M;ENSP00000312735:L240M	ENSP00000312735:L240M	L	+	1	2	POLR2B	57556315	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.904000	0.56325	0.565000	0.29255	0.563000	0.77884	CTG	.		0.408	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		A	57861558	C	A	57861558	3	1	84	1	0	0	0	0	1	0	0	0	12241	796	28	4	740	4	POLR2B	4	57861558	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	17083464	57861558	133292718	29	7706											
POLR2B	5431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57891054	57891054	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacttttttttttaaaaggtAtcggctaacaagggtgaaat	13	16	8	4	1	0	1	0	1	0	0	1	1	0	1	0	3	2	2	0	3	7	8			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:57891054A>G	ENST00000381227.1	+	23	3380	c.2967A>G	c.(2965-2967)gtA>gtG	p.V989V	POLR2B_ENST00000441246.2_Silent_p.V982V|POLR2B_ENST00000314595.5_Silent_p.V989V|POLR2B_ENST00000431623.2_Silent_p.V914V			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	989					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TTTAAAAGGTATCGGCTAACA	0.313																																					p.V989V		.											.	POLR2B-92	0			c.A2967G						.						118	119	119					4																	57891054		2203	4300	6503	SO:0001819	synonymous_variant	5431	exon22			AAAGGTATCGGCT		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2967A>G	4.37:g.57891054A>G		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	86	38	NM_000938	0	0	0	0	0	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			.		0.313	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		G	57891054	A	G	57891054	2	3	84	1	0	0	0	0	0	0	0	1	12241	436	16	3		3	POLR2B	4	57891054	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	29496	57891054	133263222	30	7707											
DHX29	54505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	54591351	54591351	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaatccttcaggaagtgcAtcttaaaataaaagaaacta	18	10	6	7	0	2	2	1	1	1	1	3	3	3	3	1	1	2	1	1	1	8	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:54591351A>G	ENST00000251636.5	-	5	655	c.507T>C	c.(505-507)gaT>gaC	p.D169D	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	169						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CAGGAAGTGCATCTTAAAATA	0.348																																					p.D169D		.											.	DHX29-229	0			c.T507C						.						73	74	74					5																	54591351		2203	4300	6503	SO:0001630	splice_region_variant	54505	exon5			AAGTGCATCTTAA	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.506-1T>C	5.37:g.54591351A>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	58	24	NM_019030	0	0	0	0	0	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Silent	SNP	ENST00000251636.5	37	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.781171	0.31502	.	.	ENSG00000067248	ENST00000508346	.	.	.	5.95	3.44	0.39384	.	.	.	.	.	T	0.57873	0.2083	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53746	-0.8395	4	.	.	.	.	8.1903	0.31363	0.7953:0.1348:0.07:0.0	.	.	.	.	R	134	.	.	C	-	1	0	DHX29	54627108	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.848000	0.39309	1.075000	0.40932	0.528000	0.53228	TGC	.		0.348	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030	Silent	G	54591351	A	G	54591351	5	3	84	1	0	0	0	0	0	0	1	0	4514	231	8	3	3694	3	DHX29	5	54591351	Splice_Site	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		54591351	126323909	31	7708											
MAST4	375449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	66448594	66448594	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccagtccacatcagccgaTtgtgatccacagttcgggga	9	9	11	12	2	1	1	1	1	0	0	4	3	3	2	4	2	2	1	4	2	0	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:66448594T>C	ENST00000403625.2	+	25	3720	c.3425T>C	c.(3424-3426)aTt>aCt	p.I1142T	MAST4_ENST00000261569.7_Missense_Mutation_p.I948T|MAST4_ENST00000405643.1_Missense_Mutation_p.I963T|MAST4_ENST00000404260.3_Missense_Mutation_p.I1145T|MAST4_ENST00000403666.1_Missense_Mutation_p.I953T	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1145						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CATCAGCCGATTGTGATCCAC	0.542																																					p.I1142T		.											.	MAST4-647	0			c.T3425C						.						97	97	97					5																	66448594		1969	4170	6139	SO:0001583	missense	375449	exon25			AGCCGATTGTGAT	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.3425T>C	5.37:g.66448594T>C	ENSP00000385727:p.Ile1142Thr	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	150	78	NM_001164664	1	0	26	38	11	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688980	0.88735	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	6.17	6.17	0.99709	PDZ/DHR/GLGF (2);	0.305290	0.35708	N	0.003034	T	0.56140	0.1965	L	0.47190	1.495	0.53688	D	0.999975	D;P	0.53619	0.961;0.921	P;P	0.59825	0.864;0.662	T	0.56798	-0.7919	10	0.72032	D	0.01	-6.8421	16.8222	0.85835	0.0:0.0:0.0:1.0	.	1145;953	O15021;O15021-3	MAST4_HUMAN;.	T	1145;1142;953;963;963;948;881	ENSP00000385048:I1145T;ENSP00000385727:I1142T;ENSP00000384313:I953T;ENSP00000384099:I963T;ENSP00000261569:I948T	ENSP00000261569:I948T	I	+	2	0	MAST4	66484350	0.998000	0.40836	0.949000	0.38748	0.731000	0.41821	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	ATT	.		0.542	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			C	66448594	T	C	66448594	3	2	84	1	0	0	0	0	1	0	0	0	9352	1493	52	3	3653	3	MAST4	5	66448594	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	11857243	66448594	114466666	32	7709											
BDP1	55814	ucsc.edu	37	chr5	70858261	70858261	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atccattcaatgaaagccagGaaaaaaatcgagagtcctct	17	8	7	9	1	2	2	1	1	1	1	5	4	4	3	3	1	1	0	3	1	5	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:70858261G>A	ENST00000358731.4	+	38	7920	c.7657G>A	c.(7657-7659)Gaa>Aaa	p.E2553K	BDP1_ENST00000380675.2_3'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2553					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGAAAGCCAGGAAAAAAATCG	0.368																																					p.E2553K													.	BDP1-92	0			c.G7657A						.						80	74	76					5																	70858261		1821	4085	5906	SO:0001583	missense	55814	exon38			AGCCAGGAAAAAA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.7657G>A	5.37:g.70858261G>A	ENSP00000351575:p.Glu2553Lys	Somatic	89	0		WXS	Illumina HiSeq		74	1	NM_018429	0	0	8	9	1	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	G	4.258	0.046834	0.08243	.	.	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.02345	4.33	5.87	-2.58	0.06228	.	0.923345	0.09237	N	0.829799	T	0.00608	0.0020	N	0.00128	-2.045	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50415	-0.8831	10	0.02654	T	1	.	6.4772	0.22043	0.4318:0.145:0.4233:0.0	.	2553	A6H8Y1	BDP1_HUMAN	K	2553;2101	ENSP00000351575:E2553K	ENSP00000351575:E2553K	E	+	1	0	BDP1	70894017	0.059000	0.20769	0.602000	0.28890	0.782000	0.44232	-0.052000	0.11865	-0.680000	0.05211	-0.247000	0.11927	GAA	.		0.368	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		A	70858261	G	A	70858261	3	1	84	1	0	0	0	0	1	0	0	0	1396	1175	41	2	7807	2	BDP1	5	70858261	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	4409667	70858261	110056999	33	7710											
CTNNA1	1495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	138268291	138268291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccgactcggcttgcaagcagGacctgctggcctacctgcaa	8	7	11	15	2	0	0	0	0	0	0	1	2	0	1	4	3	5	5	4	3	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:138268291G>A	ENST00000302763.7	+	17	2413	c.2323G>A	c.(2323-2325)Gac>Aac	p.D775N	CTNNA1_ENST00000540387.1_Missense_Mutation_p.D405N|CTNNA1_ENST00000355078.5_Missense_Mutation_p.D672N|CTNNA1_ENST00000518825.1_Missense_Mutation_p.D775N	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	775					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTGCAAGCAGGACCTGCTGGC	0.607																																					p.D775N		.											.	CTNNA1-671	0			c.G2323A						.						53	46	49					5																	138268291		2203	4300	6503	SO:0001583	missense	1495	exon17			AAGCAGGACCTGC	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2323G>A	5.37:g.138268291G>A	ENSP00000304669:p.Asp775Asn	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	34	19	NM_001903	0	0	586	1185	599	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	35	5.472975	0.96274	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.57695	0.2071	M	0.65677	2.01	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.977	D;D;P	0.87578	0.996;0.998;0.893	T	0.45614	-0.9249	10	0.13108	T	0.6	-22.7863	19.2223	0.93803	0.0:0.0:1.0:0.0	.	775;652;775	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	N	672;775;775;760;775;405	ENSP00000347190:D672N;ENSP00000304669:D775N;ENSP00000427821:D775N;ENSP00000438476:D405N	ENSP00000304669:D775N	D	+	1	0	CTNNA1	138296190	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.635000	0.98437	2.873000	0.98535	0.563000	0.77884	GAC	.		0.607	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		A	138268291	G	A	138268291	3	1	84	1	0	0	0	0	1	0	0	0	4018	1174	41	2	2385	2	CTNNA1	5	138268291	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	67410030	138268291	42646969	34	7711											
ANKHD1	54882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	139864824	139864824	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggggctgaccctactcaTcgactcaaggtagtctactt	9	11	9	12	1	3	1	2	1	1	0	4	2	3	1	1	3	2	2	1	3	4	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:139864824T>C	ENST00000360839.2	+	12	2143	c.1989T>C	c.(1987-1989)caT>caC	p.H663H	ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.H663H|ANKHD1_ENST00000297183.6_Silent_p.H663H	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	663						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCCTACTCATCGACTCAAGG	0.498																																					p.H663H		.											.	ANKHD1-185	0			c.T1989C						.						85	75	78					5																	139864824		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon12			TACTCATCGACTC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1989T>C	5.37:g.139864824T>C		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	46	18	NM_017747	0	0	0	0	0	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	T	9.851	1.193672	0.22037	.	.	ENSG00000131503	ENST00000246149	.	.	.	5.29	2.6	0.31112	.	.	.	.	.	T	0.58864	0.2152	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54807	-0.8238	4	.	.	.	.	9.6999	0.40180	0.0:0.2399:0.0:0.7601	.	.	.	.	T	158	.	.	I	+	2	0	ANKHD1	139845008	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.439000	0.44846	0.939000	0.37446	0.459000	0.35465	ATC	.		0.498	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139864824	T	C	139864824	2	2	84	1	0	0	0	0	0	0	0	1	628	1432	50	3		3	ANKHD1	5	139864824	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	1596533	139864824	41050436	35	7712											
TMCO6	55374	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140021512	140021512	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accagcaaccaggccctgctGcagcttgaggcggctcggtg	7	6	14	14	2	0	1	0	1	0	0	1	1	0	1	3	4	5	5	3	4	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:140021512G>A	ENST00000394671.3	+	4	473	c.372G>A	c.(370-372)ctG>ctA	p.L124L	TMCO6_ENST00000537378.1_Intron|TMCO6_ENST00000252100.6_Silent_p.L124L|TMCO6_ENST00000511410.1_3'UTR|NDUFA2_ENST00000510680.1_Intron	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	124					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCCCTGCTGCAGCTTGAGG	0.622																																					p.L124L		.											.	TMCO6-90	0			c.G372A						.						40	45	44					5																	140021512		2033	4188	6221	SO:0001819	synonymous_variant	55374	exon4			CCTGCTGCAGCTT	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.372G>A	5.37:g.140021512G>A		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	89	37	NM_018502	0	0	12	28	16	Q9BUU0|Q9P198	Silent	SNP	ENST00000394671.3	37	CCDS4233.2																																																																																			.		0.622	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502		A	140021512	G	A	140021512	2	1	84	1	0	0	0	0	0	0	0	1	16032	1306	46	2		2	TMCO6	5	140021512	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	156688	140021512	40893748	36	7713											
C6orf47	57827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31627425	31627425	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtctcccagactcttgAgtgctagagataggctggtc	8	11	11	11	0	2	3	0	1	2	2	5	4	3	3	2	2	1	2	2	2	2	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:31627425A>G	ENST00000375911.1	-	1	1124	c.300T>C	c.(298-300)acT>acC	p.T100T	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	100						cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						CAGACTCTTGAGTGCTAGAGA	0.577																																					p.T100T		.											.	C6orf47-91	0			c.T300C						.						61	65	64					6																	31627425		1510	2708	4218	SO:0001819	synonymous_variant	57827	exon1			CTCTTGAGTGCTA	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.300T>C	6.37:g.31627425A>G		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	86	35	NM_021184	0	0	44	86	42	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Silent	SNP	ENST00000375911.1	37	CCDS34399.1																																																																																			.		0.577	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		G	31627425	A	G	31627425	2	3	84	1	0	0	0	0	0	0	0	1	2370	291	11	3		3	C6orf47	6	31627425	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		31627425	139487642	37	7714											
PHF1	5252	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33380325	33380325	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtctggtccagtttgaggAtgattcgcagtttctggttc	5	16	13	7	1	2	2	0	2	2	0	5	3	3	3	1	3	0	4	1	3	0	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:33380325A>T	ENST00000374516.3	+	3	471	c.200A>T	c.(199-201)gAt>gTt	p.D67V	PHF1_ENST00000459809.1_3'UTR|PHF1_ENST00000374512.3_Missense_Mutation_p.D67V	NM_024165.2	NP_077084.1	O43189	PHF1_HUMAN	PHD finger protein 1	67	Tudor.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of histone H3-K27 methylation (GO:0061087)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19		Ovarian(999;0.0443)				CAGTTTGAGGATGATTCGCAG	0.478																																					p.D67V		.											.	PHF1-226	0			c.A200T						.						166	162	163					6																	33380325		2203	4300	6503	SO:0001583	missense	5252	exon3			TTGAGGATGATTC	AF029678	CCDS4777.1, CCDS4778.1	6p21.3	2013-01-28			ENSG00000112511	ENSG00000112511		"Tudor domain containing", "Zinc fingers, PHD-type"	8919	protein-coding gene	gene with protein product	"tudor domain containing 19C"	602881				9545646, 18385154	Standard	NM_024165		Approved	MTF2L2, TDRD19C	uc003oeh.3	O43189	OTTHUMG00000031105	ENST00000374516.3:c.200A>T	6.37:g.33380325A>T	ENSP00000363640:p.Asp67Val	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	114	45	NM_024165	0	0	32	63	31	B1AZX2|B1AZX3|O60929|Q5SU07|Q5SU08|Q96KM7	Missense_Mutation	SNP	ENST00000374516.3	37	CCDS4777.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.967657	0.74131	.	.	ENSG00000112511	ENST00000427004;ENST00000428274;ENST00000374512;ENST00000374516	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	4.58	4.58	0.56647	Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.73651	0.3614	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.99	T	0.77910	-0.2411	10	0.87932	D	0	-21.3302	11.944	0.52918	1.0:0.0:0.0:0.0	.	67;67	O43189-2;O43189	.;PHF1_HUMAN	V	67	ENSP00000410494:D67V;ENSP00000392697:D67V;ENSP00000363636:D67V;ENSP00000363640:D67V	ENSP00000363636:D67V	D	+	2	0	PHF1	33488303	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	8.976000	0.93442	1.928000	0.55862	0.460000	0.39030	GAT	.		0.478	PHF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076175.3			T	33380325	A	T	33380325	3	4	84	1	0	0	0	0	1	0	0	0	11846	333	12	5	206	5	PHF1	6	33380325	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	1752900	33380325	137734742	38	7715											
NCR2	9436	broad.mit.edu	37	chr6	41303624	41303624	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaggaccacatggcctggCgagccctacacccactgcta	12	5	9	15	1	0	0	0	0	0	0	0	2	0	1	4	3	3	1	4	3	4	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:41303624C>T	ENST00000373089.5	+	1	98	c.10C>T	c.(10-12)Cga>Tga	p.R4*	NCR2_ENST00000373086.3_Nonsense_Mutation_p.R4*|NCR2_ENST00000373083.4_Nonsense_Mutation_p.R4*	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	4					cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					CATGGCCTGGCGAGCCCTACA	0.627																																					p.R4X													.	NCR2-91	0			c.C10T						.						54	46	49					6																	41303624		2199	4291	6490	SO:0001587	stop_gained	9436	exon1			GCCTGGCGAGCCC	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	6732	protein-coding gene	gene with protein product		604531	"lymphocyte antigen 95 (activating NK-receptor; NK-p44)"	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.10C>T	6.37:g.41303624C>T	ENSP00000362181:p.Arg4*	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	5	3	NM_004828	0	0	0	0	0	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Nonsense_Mutation	SNP	ENST00000373089.5	37	CCDS4855.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.913031	0.72983	.	.	ENSG00000096264	ENST00000373083;ENST00000373089;ENST00000373086	.	.	.	3.72	-1.29	0.09288	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.5174	0.11943	0.6015:0.1817:0.2169:0.0	.	.	.	.	X	4	.	ENSP00000362175:R4X	R	+	1	2	NCR2	41411602	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.551000	0.06027	-0.099000	0.12263	-1.081000	0.02215	CGA	.		0.627	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3			T	41303624	C	T	41303624	4	4	84	1	0	0	0	0	0	1	0	0	10264	760	27	1	12	1	NCR2	6	41303624	Nonsense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	7923299	41303624	129811443	39	7716											
GUCA1B	2979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42152609	42152609	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccagctgctgggattcatgtCcatctgcagcatcttcatca	8	12	8	13	0	5	0	3	0	2	0	6	1	6	1	2	1	4	4	2	1	0	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:42152609C>A	ENST00000230361.3	-	4	642	c.547G>T	c.(547-549)Gac>Tac	p.D183Y		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	183					body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			GGATTCATGTCCATCTGCAGC	0.587																																					p.D183Y		.											.	GUCA1B-92	0			c.G547T						.						131	112	118					6																	42152609		2203	4300	6503	SO:0001583	missense	2979	exon4			TCATGTCCATCTG	AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"EF-hand domain containing"	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.547G>T	6.37:g.42152609C>A	ENSP00000230361:p.Asp183Tyr	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	89	46	NM_002098	0	0	0	0	0	Q9NU15	Missense_Mutation	SNP	ENST00000230361.3	37	CCDS4865.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274245	0.80580	.	.	ENSG00000112599	ENST00000230361	T	0.53640	0.61	4.36	4.36	0.52297	EF-hand-like domain (1);	0.102162	0.64402	D	0.000004	T	0.38719	0.1051	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.52711	-0.8539	10	0.54805	T	0.06	.	15.1849	0.72993	0.0:1.0:0.0:0.0	.	183	Q9UMX6	GUC1B_HUMAN	Y	183	ENSP00000230361:D183Y	ENSP00000230361:D183Y	D	-	1	0	GUCA1B	42260587	1.000000	0.71417	0.992000	0.48379	0.874000	0.50279	5.791000	0.69045	2.361000	0.80049	0.655000	0.94253	GAC	.		0.587	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098		A	42152609	C	A	42152609	3	1	84	1	0	0	0	0	1	0	0	0	6910	855	30	4	59	4	GUCA1B	6	42152609	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	848985	42152609	128962458	40	7717											
SYNJ2	8871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	158450005	158450005	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tctcgctttgacctgactgtCcgcacgcagaagcaggggga	8	8	13	12	3	1	3	0	2	1	1	3	4	2	4	2	2	1	4	2	2	1	1	rs372960799		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:158450005C>T	ENST00000355585.4	+	3	507	c.432C>T	c.(430-432)gtC>gtT	p.V144V	SYNJ2_ENST00000449859.2_Silent_p.V93V|SYNJ2_ENST00000367122.2_Silent_p.V144V|SYNJ2_ENST00000367121.3_Silent_p.V144V	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	144	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		ACCTGACTGTCCGCACGCAGA	0.582													C|||	1	0.000199681	8e-04	0	5008	,	,		16943	0		0	False		,,,				2504	0				p.V144V		.											.	SYNJ2-227	0			c.C432T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	65	67	66		,432	-0.5	0.7	6		66	0,8600		0,0,4300	no	utr-5,coding-synonymous	SYNJ2	NM_001178088.1,NM_003898.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	,144/1497	158450005	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8871	exon3			GACTGTCCGCACG	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.432C>T	6.37:g.158450005C>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	89	34	NM_003898	0	0	10	15	5	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	0.979	-0.697726	0.03279	2.27E-4	0.0	ENSG00000078269	ENST00000367113	.	.	.	4.62	-0.532	0.11890	.	.	.	.	.	T	0.45875	0.1364	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51857	-0.8652	4	.	.	.	.	11.4359	0.50068	0.0:0.2478:0.6114:0.1408	.	.	.	.	F	119	.	.	S	+	2	0	SYNJ2	158369993	0.753000	0.28349	0.672000	0.29872	0.084000	0.17831	0.009000	0.13219	1.108000	0.41662	0.655000	0.94253	TCC	.		0.582	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158450005	C	T	158450005	2	4	84	1	0	0	0	0	0	0	0	1	15485	842	30	2		2	SYNJ2	6	158450005	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	116297396	158450005	12665062	41	7718											
DNAH11	8701	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	21678590	21678590	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaaaaagctctcgctgaataCctggaaaccaagcgcatagc	15	6	9	11	2	1	1	0	1	1	0	2	3	1	2	2	1	5	3	2	1	7	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:21678590C>A	ENST00000409508.3	+	28	4882	c.4851C>A	c.(4849-4851)taC>taA	p.Y1617*	DNAH11_ENST00000328843.6_Nonsense_Mutation_p.Y1622*	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1622	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TCGCTGAATACCTGGAAACCA	0.388									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						167	165	166					7																	21678590		1865	4096	5961	SO:0001587	stop_gained	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TGAATACCTGGAA	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4851C>A	7.37:g.21678590C>A	ENSP00000475939:p.Tyr1617*	Somatic	145	1		WXS	Illumina HiSeq	Phase_I	174	45	.	0	0	0	0	0	Q9UJ82	Nonsense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	C	44	11.195013	0.99529	.	.	ENSG00000105877	ENST00000328843	.	.	.	5.78	3.99	0.46301	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.878	0.35356	0.0:0.7691:0.0:0.2309	.	.	.	.	X	1622	.	ENSP00000330671:Y1622X	Y	+	3	2	DNAH11	21645115	0.893000	0.30496	1.000000	0.80357	0.601000	0.36947	0.076000	0.14712	0.800000	0.34041	0.650000	0.86243	TAC	.		0.388	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21678590	C	A	21678590	4	1	84	1	0	0	0	0	0	1	0	0	4610	518	18	4	4976	4	DNAH11	7	21678590	Nonsense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08		21678590	137460073	42	7719											
OR2AE1	81392	broad.mit.edu	37	chr7	99474253	99474253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccaccttcttgttcatgAgcacagcatagcgcagtgga	9	10	10	12	1	2	1	1	1	1	0	3	2	3	2	2	1	3	4	2	1	1	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:99474253A>G	ENST00000316368.2	-	1	427	c.404T>C	c.(403-405)cTc>cCc	p.L135P		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					CTTGTTCATGAGCACAGCATA	0.483																																					p.L135P													.	OR2AE1-90	0			c.T404C						.						132	122	125					7																	99474253		2203	4300	6503	SO:0001583	missense	81392	exon1			TTCATGAGCACAG	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"GPCR / Class A : Olfactory receptors"	15087	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily AE, member 2"	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.404T>C	7.37:g.99474253A>G	ENSP00000313936:p.Leu135Pro	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	109	3	NM_001005276	0	0	2	2	0	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.746641	0.30955	.	.	ENSG00000244623	ENST00000316368	T	0.33654	1.4	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.220932	0.23137	N	0.051518	T	0.66436	0.2789	M	0.93328	3.405	0.45439	D	0.998412	D	0.76494	0.999	D	0.85130	0.997	T	0.74150	-0.3758	10	0.87932	D	0	.	10.6046	0.45386	1.0:0.0:0.0:0.0	.	135	Q8NHA4	O2AE1_HUMAN	P	135	ENSP00000313936:L135P	ENSP00000313936:L135P	L	-	2	0	OR2AE1	99312189	0.009000	0.17119	0.955000	0.39395	0.142000	0.21351	2.152000	0.42272	1.826000	0.53198	0.321000	0.21382	CTC	.		0.483	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1			G	99474253	A	G	99474253	3	3	84	1	0	0	0	0	1	0	0	0	11009	304	11	3	571	3	OR2AE1	7	99474253	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	77795663	99474253	59664410	43	7720											
ARMC10	83787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	102724230	102724230	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggatcctgtaattattgaaAgagctttgattactttgggt	11	16	10	4	0	0	3	0	2	0	1	1	4	1	4	1	2	2	2	1	2	4	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:102724230A>G	ENST00000323716.3	+	3	738	c.346A>G	c.(346-348)Aga>Gga	p.R116G	ARMC10_ENST00000441711.2_Missense_Mutation_p.R81G|ARMC10_ENST00000425331.1_Missense_Mutation_p.R81G|ARMC10_ENST00000454559.1_Missense_Mutation_p.R81G|ARMC10_ENST00000541300.1_Missense_Mutation_p.R81G|ARMC10_ENST00000428183.2_Missense_Mutation_p.R116G	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	116					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						AATTATTGAAAGAGCTTTGAT	0.398																																					p.R116G		.											.	ARMC10-91	0			c.A346G						.						94	96	95					7																	102724230		2203	4300	6503	SO:0001583	missense	83787	exon3			ATTGAAAGAGCTT	AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"Armadillo repeat containing"	21706	protein-coding gene	gene with protein product	"specific Splicing Variant involved in Hepatocarcinogenesis"	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.346A>G	7.37:g.102724230A>G	ENSP00000319412:p.Arg116Gly	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	98	32	NM_031905	0	0	62	89	27	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	37	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017384	0.54576	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153	T;T;T;T;T;T;T	0.47869	1.5;1.6;1.5;1.6;1.5;1.6;0.83	5.28	4.11	0.48088	Armadillo-like helical (1);Armadillo-type fold (1);	0.413848	0.28209	N	0.016195	T	0.54464	0.1860	L	0.59436	1.845	0.23809	N	0.996789	P;B;B;D;P;P	0.58268	0.741;0.039;0.096;0.982;0.852;0.863	P;B;B;P;B;P	0.54889	0.497;0.05;0.073;0.763;0.436;0.627	T	0.47799	-0.9089	10	0.49607	T	0.09	-8.0575	9.962	0.41701	0.6711:0.3289:0.0:0.0	.	81;81;81;116;81;116	B4DWJ8;F5GX65;Q8N2F6-4;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;ARM10_HUMAN	G	116;116;81;81;81;81;116	ENSP00000319412:R116G;ENSP00000396654:R116G;ENSP00000413619:R81G;ENSP00000405612:R81G;ENSP00000397969:R81G;ENSP00000440463:R81G;ENSP00000398201:R116G	ENSP00000319412:R116G	R	+	1	2	ARMC10	102511466	0.988000	0.35896	0.991000	0.47740	0.941000	0.58515	1.811000	0.38942	0.948000	0.37687	0.456000	0.33151	AGA	.		0.398	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905		G	102724230	A	G	102724230	3	3	84	1	0	0	0	0	1	0	0	0	951	64	3	3	356	3	ARMC10	7	102724230	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	3249977	102724230	56414433	44	7721											
ZNF862	643641	broad.mit.edu	37	chr7	149559260	149559260	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccattgcccagcacctccCgttctccatgctctgcaaaa	10	9	5	17	1	2	0	0	0	2	0	4	0	3	0	5	0	5	4	5	0	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:149559260C>A	ENST00000223210.4	+	7	3256	c.3011C>A	c.(3010-3012)cCg>cAg	p.P1004Q	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	1004					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CAGCACCTCCCGTTCTCCATG	0.597																																					p.P1004Q													.	ZNF862-69	0			c.C3011A						.						46	53	50					7																	149559260		2080	4203	6283	SO:0001583	missense	643641	exon7			ACCTCCCGTTCTC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.3011C>A	7.37:g.149559260C>A	ENSP00000223210:p.Pro1004Gln	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	107	5	NM_001099220	0	0	0	0	0	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	37	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.130134	0.37630	.	.	ENSG00000106479	ENST00000223210	T	0.01043	5.41	5.39	4.5	0.54988	HAT dimerisation (1);	0.000000	0.53938	D	0.000055	T	0.03959	0.0111	L	0.51422	1.61	0.20873	N	0.999839	D	0.76494	0.999	D	0.76071	0.987	T	0.38134	-0.9675	10	0.34782	T	0.22	.	10.511	0.44862	0.0:0.9097:0.0:0.0903	.	1004	O60290	ZN862_HUMAN	Q	1004	ENSP00000223210:P1004Q	ENSP00000223210:P1004Q	P	+	2	0	ZNF862	149190193	0.301000	0.24444	0.549000	0.28204	0.816000	0.46133	1.681000	0.37618	1.253000	0.44018	0.655000	0.94253	CCG	.		0.597	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		A	149559260	C	A	149559260	3	1	84	1	0	0	0	0	1	0	0	0	18227	652	23	4	3037	4	ZNF862	7	149559260	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	46835030	149559260	9579403	45	7722											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	151880116	151880116	+	Frame_Shift_Del	DEL	A	A	-																															ctttgctttaaaggatctttAaaaagctccgaatcaatacg																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:151880116delA	ENST00000262189.6	-	35	5426	c.5208delT	c.(5206-5208)tttfs	p.F1736fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.F1736fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1736	Gln-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AAGGATCTTTAAAAAGCTCCG	0.343																																					p.F1736fs		.											.	MLL3-1398	0			c.5208delT						.						216	218	217					7																	151880116		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon35			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5208delT	7.37:g.151880116delA	ENSP00000262189:p.Phe1736fs	Somatic	340	0		WXS	Illumina HiSeq	Phase_I	463	289	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.343	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151880116	A	-	151880116	7	5	84	1	0	1	0	1	0	0	0	0	9647	359	13	0	9627	0	MLL3	7	151880116	Frame_Shift_Del	DEL	A	TCGA-BQ-7051-01A-12D-1961-08	2320856	151880116	7258547	46	7723											
RP1	6101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	55534829	55534829	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtaccccaagggaaatgcAaagtcagaaagcagaaagag	18	4	12	7	0	1	3	1	0	0	3	1	4	1	4	2	1	3	3	2	1	6	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:55534829A>G	ENST00000220676.1	+	3	916	c.768A>G	c.(766-768)gcA>gcG	p.A256A		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	256					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AGGGAAATGCAAAGTCAGAAA	0.403																																					p.A256A	Colon(91;1014 1389 7634 14542 40420)	.											.	RP1-102	0			c.A768G						.						78	80	80					8																	55534829		2203	4300	6503	SO:0001819	synonymous_variant	6101	exon3			AAATGCAAAGTCA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.768A>G	8.37:g.55534829A>G		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_006269	0	0	0	0	0		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			.		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55534829	A	G	55534829	2	3	84	1	0	0	0	0	0	0	0	1	13564	117	5	3		3	RP1	8	55534829	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		55534829	90829193	47	7724											
MATN2	4147	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	98943606	98943609	+	Frame_Shift_Del	DEL	CTAA	CTAA	-																															aggcacgggacacgggcatcCtaatctttgccattggtgtg																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CTAA	CTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:98943606_98943609delCTAA	ENST00000520016.1	+	2	692_695	c.568_571delCTAA	c.(568-573)ctaatcfs	p.LI190fs	MATN2_ENST00000522025.2_Intron|MATN2_ENST00000521689.1_Frame_Shift_Del_p.LI190fs|MATN2_ENST00000524308.1_Frame_Shift_Del_p.LI190fs|MATN2_ENST00000254898.5_Frame_Shift_Del_p.LI190fs			O00339	MATN2_HUMAN	matrilin 2	190	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			CACGGGCATCCTAATCTTTGCCAT	0.559																																					p.190_191del		.											.	MATN2-24	0			c.568_571del						.																																			SO:0001589	frameshift_variant	4147	exon3			.	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.568_571delCTAA	8.37:g.98943606_98943609delCTAA	ENSP00000430487:p.Leu190fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	44	19	NM_002380	0	0	0	0	0	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Frame_Shift_Del	DEL	ENST00000520016.1	37	CCDS55264.1																																																																																			.		0.559	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			-	98943609	CTAA	-	98943606	7	5	84	1	0	1	0	1	0	0	0	0	9359	680	24	0	574	0	MATN2	8	98943606	Frame_Shift_Del	DEL	CTAA	TCGA-BQ-7051-01A-12D-1961-08	43408777	98943606	47420416	48	7725											
POP1	10940	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	99152324	99152324	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggtgggagaggacacagagGagacacctcaccgctggtgg	11	4	17	9	1	1	3	1	0	0	3	1	6	1	4	2	6	0	1	2	6	0	0	rs184169115		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:99152324G>T	ENST00000401707.2	+	10	1462	c.1381G>T	c.(1381-1383)Gag>Tag	p.E461*	POP1_ENST00000349693.3_Nonsense_Mutation_p.E461*	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	461					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GGACACAGAGGAGACACCTCA	0.448																																					p.E461X		.											.	POP1-154	0			c.G1381T						.						90	92	92					8																	99152324		2203	4300	6503	SO:0001587	stop_gained	10940	exon10			ACAGAGGAGACAC	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.1381G>T	8.37:g.99152324G>T	ENSP00000385787:p.Glu461*	Somatic	54	1		WXS	Illumina HiSeq	Phase_I	59	25	NM_001145860	0	0	4	4	0	A8K5W9|Q15037	Nonsense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926907	0.92319	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	.	.	.	4.95	0.063	0.14346	.	1.014390	0.07865	N	0.966905	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-11.2415	5.3727	0.16148	0.3376:0.0:0.5049:0.1575	.	.	.	.	X	461	.	ENSP00000339529:E461X	E	+	1	0	POP1	99221500	0.969000	0.33509	0.995000	0.50966	0.424000	0.31475	1.393000	0.34497	0.052000	0.16007	-0.484000	0.04775	GAG	G|0.999;A|0.000		0.448	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		T	99152324	G	T	99152324	4	4	84	1	0	0	0	0	0	1	0	0	12277	1175	41	4	1415	4	POP1	8	99152324	Nonsense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	208718	99152324	47211698	49	7726											
SLC45A4	57210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	142238284	142238284	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgagcattctaacctttctGaagactccattgatttgacc	10	15	6	10	0	2	5	0	4	2	1	3	5	3	5	3	0	2	1	3	0	2	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:142238284G>A	ENST00000024061.3	-	1	389	c.82C>T	c.(82-84)Cag>Tag	p.Q28*	SLC45A4_ENST00000519067.1_Nonsense_Mutation_p.Q28*|SLC45A4_ENST00000433583.2_Intron|SLC45A4_ENST00000517878.1_Intron	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			TAACCTTTCTGAAGACTCCAT	0.537																																					p.Q28X		.											.	SLC45A4-70	0			c.C82T						.						191	177	181					8																	142238284		2203	4300	6503	SO:0001587	stop_gained	57210	exon1			CTTTCTGAAGACT	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"Solute carriers"	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.82C>T	8.37:g.142238284G>A	ENSP00000024061:p.Gln28*	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	187	83	NM_001080431	0	0	0	0	0	Q6ZRI2|Q9ULU3	Nonsense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.134082	0.77662	.	.	ENSG00000022567	ENST00000519067;ENST00000024061	.	.	.	1.79	-1.83	0.07833	.	0.589005	0.15260	U	0.271852	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	4.245	0.10667	0.1675:0.4643:0.3682:0.0	.	.	.	.	X	28	.	ENSP00000024061:Q28X	Q	-	1	0	SLC45A4	142307466	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.632000	0.02024	-0.542000	0.06249	0.556000	0.70494	CAG	.		0.537	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		A	142238284	G	A	142238284	4	1	84	1	0	0	0	0	0	1	0	0	14675	1299	45	2	2346	2	SLC45A4	8	142238284	Nonsense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	43085960	142238284	4125738	50	7727											
PITRM1	10531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	3206029	3206029	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cactgagtacgtgtggtcagGaagaagtctgttctgaaggt	10	11	14	6	1	3	3	1	2	2	1	3	4	3	4	0	3	1	2	0	3	4	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:3206029G>A	ENST00000224949.4	-	7	713	c.679C>T	c.(679-681)Cct>Tct	p.P227S	PITRM1_ENST00000380989.2_Missense_Mutation_p.P227S|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.P195S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	227					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						GTGTGGTCAGGAAGAAGTCTG	0.448																																					p.P227S		.											.	PITRM1-91	0			c.C679T						.						124	122	123					10																	3206029		1934	4132	6066	SO:0001583	missense	10531	exon7			GGTCAGGAAGAAG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.679C>T	10.37:g.3206029G>A	ENSP00000224949:p.Pro227Ser	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	63	28	NM_014889	0	0	0	90	90	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	g	19.62	3.860856	0.71834	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.31247	1.5;1.5;1.5	5.7	5.7	0.88788	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	M	0.88241	2.94	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.995;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.927;0.947;1.0;0.998;0.998;0.998	T	0.70960	-0.4730	10	0.87932	D	0	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	220;195;227;227;227;220	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	S	227;220;227;195	ENSP00000224949:P227S;ENSP00000370377:P227S;ENSP00000401201:P195S	ENSP00000224949:P227S	P	-	1	0	PITRM1	3196029	1.000000	0.71417	0.997000	0.53966	0.075000	0.17131	9.162000	0.94745	2.698000	0.92095	0.655000	0.94253	CCT	.		0.448	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			A	3206029	G	A	3206029	3	1	84	1	0	0	0	0	1	0	0	0	11979	1174	41	2	2518	2	PITRM1	10	3206029	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		3206029	132328718	51	7728											
MCM10	55388	hgsc.bcm.edu	37	chr10	13251301	13251301	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	catgctaaatttctgaacagCcttaaataacccgaacttca	15	11	4	11	1	2	1	1	1	1	0	2	2	2	1	2	0	5	1	2	0	7	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:13251301C>G	ENST00000484800.2	+	20	2722	c.2619C>G	c.(2617-2619)agC>agG	p.S873R	MCM10_ENST00000378694.1_3'UTR|MCM10_ENST00000378714.3_Missense_Mutation_p.S872R			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	873					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						TTCTGAACAGCCTTAAATAAC	0.398																																					p.S873R		.											.	MCM10-653	0			c.C2619G						.						95	90	92					10																	13251301		2203	4300	6503	SO:0001583	missense	55388	exon20			GAACAGCCTTAAA	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.2619C>G	10.37:g.13251301C>G	ENSP00000418268:p.Ser873Arg	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	46	3	NM_182751	0	0	2	2	0	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909860	0.72983	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800	T;T	0.49432	0.78;0.78	5.38	5.38	0.77491	Replication factor Mcm10 (1);	0.000000	0.85682	D	0.000000	T	0.72851	0.3512	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77175	-0.2684	10	0.87932	D	0	.	18.7533	0.91823	0.0:1.0:0.0:0.0	.	872;873	Q7L590-2;Q7L590	.;MCM10_HUMAN	R	872;873;873	ENSP00000367986:S872R;ENSP00000418268:S873R	ENSP00000354945:S873R	S	+	3	2	MCM10	13291307	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	1.345000	0.33953	2.512000	0.84698	0.561000	0.74099	AGC	.		0.398	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		G	13251301	C	G	13251301	3	3	84	1	0	0	0	0	1	0	0	0	9410	738	26	4	2693	4	MCM10	10	13251301	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	10045272	13251301	122283446	52	7729											
NCOA4	8031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	51586276	51586276	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcttttattgcaggaagtAttacttaattcacctctaca	11	18	4	8	0	3	0	1	0	2	0	3	1	3	1	1	1	3	2	1	1	6	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:51586276A>T	ENST00000443446.1	+	9	1933	c.1704A>T	c.(1702-1704)gtA>gtT	p.V568V	NCOA4_ENST00000438493.1_Silent_p.V584V|NCOA4_ENST00000430396.2_Silent_p.V468V|NCOA4_ENST00000452682.1_Silent_p.V584V|NCOA4_ENST00000374087.4_Silent_p.V568V|NCOA4_ENST00000344348.6_Silent_p.V568V|NCOA4_ENST00000414907.2_Silent_p.V402V|NCOA4_ENST00000374082.1_Missense_Mutation_p.Y523F	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	568					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						TGCAGGAAGTATTACTTAATT	0.398			T	RET	papillary thyroid																																p.V584V		.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4-1042	0			c.A1752T						.						114	111	112					10																	51586276		2203	4300	6503	SO:0001819	synonymous_variant	8031	exon10			GGAAGTATTACTT	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1704A>T	10.37:g.51586276A>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	127	48	NM_001145261	0	0	0	0	0	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Silent	SNP	ENST00000443446.1	37	CCDS7237.1	.	.	.	.	.	.	.	.	.	.	A	3.664	-0.068949	0.07228	.	.	ENSG00000138293	ENST00000374082	T	0.26223	1.75	5.41	1.78	0.24846	.	.	.	.	.	T	0.08670	0.0215	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29181	-1.0020	6	0.02654	T	1	-2.9612	2.9009	0.05705	0.482:0.309:0.077:0.132	.	.	.	.	F	523	ENSP00000363195:Y523F	ENSP00000363195:Y523F	Y	+	2	0	NCOA4	51256282	0.994000	0.37717	0.999000	0.59377	0.958000	0.62258	0.292000	0.19011	0.141000	0.18875	0.533000	0.62120	TAT	.		0.398	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		T	51586276	A	T	51586276	2	4	84	1	0	0	0	0	0	0	0	1	10257	436	16	5		5	NCOA4	10	51586276	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	38334975	51586276	83948471	53	7730											
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	89717669	89717669	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcctccaattcaggacccAcacgacgggaagacaagttc	13	7	8	13	2	1	1	1	0	0	1	4	4	3	3	3	2	0	1	3	2	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:89717669A>G	ENST00000371953.3	+	7	2051	c.694A>G	c.(694-696)Aca>Gca	p.T232A	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	232	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTCAGGACCCACACGACGGGA	0.423		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.T232A		.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN-17735	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.A694G						.						155	133	140					10																	89717669		2203	4300	6503	SO:0001583	missense	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	GGACCCACACGAC	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.694A>G	10.37:g.89717669A>G	ENSP00000361021:p.Thr232Ala	Somatic	116	1		WXS	Illumina HiSeq	Phase_I	91	30	NM_000314	0	0	57	102	45	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.030305	0.35797	.	.	ENSG00000171862	ENST00000371953	D	0.85773	-2.03	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.158008	0.56097	D	0.000030	T	0.74711	0.3752	N	0.25647	0.755	0.51482	D	0.999926	B	0.16802	0.019	B	0.16289	0.015	T	0.68519	-0.5387	9	.	.	.	-10.0511	10.8662	0.46856	0.8504:0.0:0.0:0.1496	.	232	P60484	PTEN_HUMAN	A	232	ENSP00000361021:T232A	.	T	+	1	0	PTEN	89707649	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.612000	0.67681	1.928000	0.55862	0.477000	0.44152	ACA	.		0.423	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717669	A	G	89717669	3	3	84	1	0	0	0	0	1	0	0	0	12767	159	6	3	720	3	PTEN	10	89717669	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	38131393	89717669	45817078	54	7731											
DRD4	1815	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	639919	639919	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcggcctgcagcgctgggagGtggcacgtcgcgccaagctg	5	5	18	13	5	0	0	0	0	0	0	1	1	0	1	2	4	3	4	2	4	1	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:639919G>A	ENST00000176183.5	+	3	682	c.670G>A	c.(670-672)Gtg>Atg	p.V224M		NM_000797.3	NP_000788.2	P21917	DRD4_HUMAN	dopamine receptor D4	224					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult locomotory behavior (GO:0008344)|arachidonic acid secretion (GO:0050482)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|cellular calcium ion homeostasis (GO:0006874)|circadian rhythm (GO:0007623)|dopamine metabolic process (GO:0042417)|dopamine receptor signaling pathway (GO:0007212)|fear response (GO:0042596)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein secretion (GO:0050709)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|olfactory learning (GO:0008355)|photoperiodism (GO:0009648)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of kinase activity (GO:0033674)|positive regulation of penile erection (GO:0060406)|positive regulation of sodium:proton antiporter activity (GO:0032417)|regulation of calcium-mediated signaling (GO:0050848)|regulation of circadian rhythm (GO:0042752)|regulation of dopamine metabolic process (GO:0042053)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of neurotransmitter secretion (GO:0046928)|response to amphetamine (GO:0001975)|response to histamine (GO:0034776)|response to steroid hormone (GO:0048545)|retina development in camera-type eye (GO:0060041)|short-term memory (GO:0007614)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)	cell cortex (GO:0005938)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|vesicle membrane (GO:0012506)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)|SH3 domain binding (GO:0017124)			NS(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Ziprasidone(DB00246)	GCGCTGGGAGGTGGCACGTCG	0.741																																					p.V224M		.											.	DRD4-90	0			c.G670A						.						30	23	25					11																	639919		2194	4290	6484	SO:0001583	missense	1815	exon3			TGGGAGGTGGCAC	L12398	CCDS7710.1	11p15.5	2012-08-08			ENSG00000069696	ENSG00000069696		"GPCR / Class A : Dopamine receptors"	3025	protein-coding gene	gene with protein product		126452					Standard	NM_000797		Approved		uc001lqp.2	P21917	OTTHUMG00000133312	ENST00000176183.5:c.670G>A	11.37:g.639919G>A	ENSP00000176183:p.Val224Met	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	33	15	NM_000797	0	0	1	2	1	B0M0J7|Q7Z7Q5|Q8NGM5	Missense_Mutation	SNP	ENST00000176183.5	37	CCDS7710.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.506330	0.44558	.	.	ENSG00000069696	ENST00000176183	T	0.37915	1.17	2.79	1.81	0.25067	GPCR, rhodopsin-like superfamily (1);	0.391968	0.24476	N	0.038200	T	0.30916	0.0780	.	.	.	0.24791	N	0.992753	P	0.47604	0.898	B	0.42138	0.377	T	0.14811	-1.0459	9	0.56958	D	0.05	.	10.3373	0.43858	0.0:0.2038:0.7962:0.0	.	224	P21917	DRD4_HUMAN	M	224	ENSP00000176183:V224M	ENSP00000176183:V224M	V	+	1	0	DRD4	629919	1.000000	0.71417	0.365000	0.25901	0.758000	0.43043	4.570000	0.60872	0.461000	0.27071	0.313000	0.20887	GTG	.		0.741	DRD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257109.1	NM_000797		A	639919	G	A	639919	3	1	84	1	0	0	0	0	1	0	0	0	4770	1261	44	2	680	2	DRD4	11	639919	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		639919	134366597	55	7732											
OR4A16	81327	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	55110978	55110978	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcatgggtcagctcttcaTagaacacttacttggtggtg	8	14	11	8	0	3	1	2	0	1	1	3	1	3	1	0	3	4	2	0	3	3	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:55110978T>C	ENST00000314721.2	+	1	352	c.302T>C	c.(301-303)aTa>aCa	p.I101T		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						CAGCTCTTCATAGAACACTTA	0.443																																					p.I101T		.											.	OR4A16-69	0			c.T302C						.						203	189	193					11																	55110978		2201	4296	6497	SO:0001583	missense	81327	exon1			TCTTCATAGAACA	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.302T>C	11.37:g.55110978T>C	ENSP00000325128:p.Ile101Thr	Somatic	317	0		WXS	Illumina HiSeq	Phase_I	268	22	NM_001005274	0	0	0	0	0	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	t	0.119	-1.128496	0.01756	.	.	ENSG00000181961	ENST00000314721	T	0.00864	5.6	2.57	1.45	0.22620	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00906	0.0030	L	0.39085	1.19	0.09310	N	1	B	0.16802	0.019	B	0.15484	0.013	T	0.46317	-0.9200	9	0.20519	T	0.43	.	5.5053	0.16850	0.0:0.1562:0.0:0.8438	.	101	Q8NH70	O4A16_HUMAN	T	101	ENSP00000325128:I101T	ENSP00000325128:I101T	I	+	2	0	OR4A16	54867554	0.000000	0.05858	0.009000	0.14445	0.018000	0.09664	0.028000	0.13644	1.186000	0.42985	0.346000	0.21813	ATA	.		0.443	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		C	55110978	T	C	55110978	3	2	84	1	0	0	0	0	1	0	0	0	11067	1406	49	3	304	3	OR4A16	11	55110978	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	54471059	55110978	79895538	56	7733											
BAD	572	hgsc.bcm.edu	37	chr11	64039200	64039200	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgaaaggggctgggctccTcccccatcccttcgtcgtcc	4	8	10	19	3	0	0	0	0	0	0	6	1	4	0	6	3	0	2	6	3	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:64039200T>C	ENST00000394532.3	-	2	533	c.263A>G	c.(262-264)gAg>gGg	p.E88G	BAD_ENST00000544785.1_Intron|BAD_ENST00000394531.3_Missense_Mutation_p.R135G|BAD_ENST00000309032.3_Missense_Mutation_p.E88G	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death	88					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						GCTGGGCTCCTCCCCCATCCC	0.706																																					p.E88G		.											.	BAD-1271	0			c.A263G						.						17	17	17					11																	64039200		2191	4282	6473	SO:0001583	missense	572	exon3			GGCTCCTCCCCCA	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.263A>G	11.37:g.64039200T>C	ENSP00000378040:p.Glu88Gly	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_032989	0	0	28	78	50	O14803|Q6FH21	Missense_Mutation	SNP	ENST00000394532.3	37	CCDS8065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.96|13.96	2.394026|2.394026	0.42410|0.42410	.|.	.|.	ENSG00000002330|ENSG00000002330	ENST00000394532;ENST00000540152;ENST00000309032;ENST00000493798;ENST00000492141|ENST00000394531	T;T;T;T|.	0.53640|.	0.61;0.61;0.61;0.61|.	5.72|5.72	4.6|4.6	0.57074|0.57074	.|.	0.349556|.	0.31358|.	N|.	0.007795|.	T|T	0.52948|0.52948	0.1766|0.1766	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	B|.	0.13594|.	0.008|.	B|.	0.17722|.	0.019|.	T|T	0.47142|0.47142	-0.9140|-0.9140	10|5	0.49607|.	T|.	0.09|.	-16.5166|-16.5166	8.4964|8.4964	0.33130|0.33130	0.0:0.088:0.0:0.912|0.0:0.088:0.0:0.912	.|.	88|.	Q92934|.	BAD_HUMAN|.	G|G	88;88;88;3;3|135	ENSP00000378040:E88G;ENSP00000309103:E88G;ENSP00000438975:E3G;ENSP00000439202:E3G|.	ENSP00000309103:E88G|.	E|R	-|-	2|1	0|2	BAD|BAD	63795776|63795776	0.948000|0.948000	0.32251|0.32251	0.979000|0.979000	0.43373|0.43373	0.926000|0.926000	0.56050|0.56050	1.553000|1.553000	0.36255|0.36255	1.003000|1.003000	0.39130|0.39130	0.459000|0.459000	0.35465|0.35465	GAG|AGG	.		0.706	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989		C	64039200	T	C	64039200	3	2	84	1	0	0	0	0	1	0	0	0	1286	1551	54	3	251	3	BAD	11	64039200	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	8928222	64039200	70967316	57	7734											
SF3B2	10992	hgsc.bcm.edu	37	chr11	65819834	65819859	+	Start_Codon_Del	DEL	CGCGCGCCTTCCTGCGGCTAAGATGG	CGCGCGCCTTCCTGCGGCTAAGATGG	-																															gccccagcttccgggttggtCgcgcgccttcctgcggctaa																								rs553967166|rs370381998		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CGCGCGCCTTCCTGCGGCTAAGATGG	CGCGCGCCTTCCTGCGGCTAAGATGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:65819834_65819859delCGCGCGCCTTCCTGCGGCTAAGATGG	ENST00000322535.6	+	0	28_53				SF3B2_ENST00000534307.1_3'UTR|snoU13_ENST00000459530.1_RNA|SF3B2_ENST00000528302.1_Start_Codon_Del	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa						gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						CCGGGTTGGTCGCGCGCCTTCCTGCGGCTAAGATGGCGACGGAGCA	0.681																																							.											.	SF3B2-92	0									.																																			SO:0001582	initiator_codon_variant	10992	wholegene			.	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751		11.37:g.65819834_65819859delCGCGCGCCTTCCTGCGGCTAAGATGG		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	47	10	NM_006842	0	0	0	0	0	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Frame_Shift_Del	DEL	ENST00000322535.6	37	CCDS31612.1																																																																																			.		0.681	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			-	65819859	CGCGCGCCTTCCTGCGGCTAAGATGG	-	65819834	7	5	84	1	0	1	0	1	0	0	0	0	14183	899	31	0		0	SF3B2	11	65819834	Start_Codon_Del	DEL	CGCGCGCCTTCCTGCGGCTAAGATGG	TCGA-BQ-7051-01A-12D-1961-08	1780634	65819834	69186682	58	7735											
PAK1	5058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	77047284	77047284	+	Frame_Shift_Del	DEL	T	T	-																															gttcctaccatggtgctccgTttgctctgctctggggttat																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:77047284delT	ENST00000356341.3	-	13	1791	c.1260delA	c.(1258-1260)aaafs	p.K420fs	PAK1_ENST00000530617.1_Frame_Shift_Del_p.K420fs|PAK1_ENST00000528203.1_Frame_Shift_Del_p.K322fs|PAK1_ENST00000525542.1_5'UTR|PAK1_ENST00000278568.4_Frame_Shift_Del_p.K420fs	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	420	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					TGGTGCTCCGTTTGCTCTGCT	0.473																																					p.K420fs		.											.	PAK1-957	0			c.1260delA						.						148	145	146					11																	77047284		2200	4292	6492	SO:0001589	frameshift_variant	5058	exon13			.	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.1260delA	11.37:g.77047284delT	ENSP00000348696:p.Lys420fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	104	43	NM_001128620	0	0	0	0	0	O75561|Q13567|Q32M53|Q32M54|Q86W79	Frame_Shift_Del	DEL	ENST00000356341.3	37	CCDS8250.1																																																																																			.		0.473	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		-	77047284	T	-	77047284	7	5	84	1	0	1	0	1	0	0	0	0	11425	1722	60	0	442	0	PAK1	11	77047284	Frame_Shift_Del	DEL	T	TCGA-BQ-7051-01A-12D-1961-08	11227450	77047284	57959232	59	7736											
UBE4A	9354	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118250228	118250228	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggttgcctggcgggatgctCagcaaagttctagccctgct	7	10	13	11	1	2	0	1	0	1	0	2	1	2	1	2	3	5	5	2	3	2	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:118250228C>T	ENST00000431736.2	+	11	1732	c.1660C>T	c.(1660-1662)Cag>Tag	p.Q554*	UBE4A_ENST00000252108.3_Nonsense_Mutation_p.Q547*|UBE4A_ENST00000545354.1_Nonsense_Mutation_p.Q19*					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		GCGGGATGCTCAGCAAAGTTC	0.493																																					p.Q554X		.											.	UBE4A-229	0			c.C1660T						.						107	101	103					11																	118250228		2200	4296	6496	SO:0001587	stop_gained	9354	exon11			GATGCTCAGCAAA	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"U-box domain containing"	12499	protein-coding gene	gene with protein product		603753	"ubiquitination factor E4A (homologous to yeast UFD2)", "ubiquitination factor E4A (UFD2 homolog, yeast)"			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1660C>T	11.37:g.118250228C>T	ENSP00000387362:p.Gln554*	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	97	51	NM_004788	0	0	24	29	5		Nonsense_Mutation	SNP	ENST00000431736.2	37	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	C	40	8.417745	0.98803	.	.	ENSG00000110344	ENST00000252108;ENST00000431736;ENST00000545354	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2921	19.4627	0.94924	0.0:1.0:0.0:0.0	.	.	.	.	X	547;554;19	.	ENSP00000252108:Q547X	Q	+	1	0	UBE4A	117755438	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.487000	0.81328	2.588000	0.87417	0.655000	0.94253	CAG	.		0.493	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		T	118250228	C	T	118250228	4	4	84	1	0	0	0	0	0	1	0	0	16915	827	29	2	1698	2	UBE4A	11	118250228	Nonsense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	41202944	118250228	16756288	60	7737											
NLRX1	79671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119044337	119044337	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgatgagctacttcgcccaCccgcggagctggccctggag	6	7	13	15	3	0	2	0	2	0	0	1	4	0	4	3	3	3	2	3	3	1	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:119044337C>T	ENST00000409109.1	+	5	966	c.379C>T	c.(379-381)Ccc>Tcc	p.P127S	NLRX1_ENST00000409991.1_Missense_Mutation_p.P127S|NLRX1_ENST00000474751.2_3'UTR|NLRX1_ENST00000292199.2_Missense_Mutation_p.P127S|NLRX1_ENST00000409265.4_Missense_Mutation_p.P127S|NLRX1_ENST00000525863.1_Missense_Mutation_p.P127S	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	127	Required for interaction with MAVS.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		ACTTCGCCCACCCGCGGAGCT	0.667																																					p.P127S		.											.	NLRX1-92	0			c.C379T						.						43	44	44					11																	119044337		2200	4295	6495	SO:0001583	missense	79671	exon5			CGCCCACCCGCGG	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"Nucleotide-binding domain and leucine rich repeat containing"	29890	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat containing X1", "NOD-like receptor X1", "NLR family, X1"	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.379C>T	11.37:g.119044337C>T	ENSP00000387334:p.Pro127Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	46	18	NM_024618	0	0	16	40	24	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.139675	0.00335	.	.	ENSG00000160703	ENST00000454811;ENST00000449394;ENST00000422249;ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T;T;T;T	0.69561	1.73;1.73;1.17;-0.31;-0.31;-0.41;-0.31;-0.41	5.6	-7.76	0.01232	.	1.215480	0.05625	N	0.580711	T	0.32406	0.0828	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.13953	-1.0490	10	0.18710	T	0.47	.	3.4574	0.07521	0.0971:0.1552:0.1941:0.5535	.	127;127	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	S	127	ENSP00000400268:P127S;ENSP00000402801:P127S;ENSP00000402381:P127S;ENSP00000386851:P127S;ENSP00000292199:P127S;ENSP00000386858:P127S;ENSP00000387334:P127S;ENSP00000433442:P127S	ENSP00000292199:P127S	P	+	1	0	NLRX1	118549547	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.553000	0.06012	-1.611000	0.01581	-0.459000	0.05422	CCC	.		0.667	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		T	119044337	C	T	119044337	3	4	84	1	0	0	0	0	1	0	0	0	10511	507	18	2	393	2	NLRX1	11	119044337	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	794109	119044337	15962179	61	7738											
TRIM29	23650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119988941	119988941	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaagctcacctttcagggaGaaggaggagctgccttggac	10	7	14	10	0	2	1	2	0	0	1	2	5	2	4	2	4	3	3	2	4	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:119988941G>A	ENST00000341846.5	-	7	2038	c.1617C>T	c.(1615-1617)ttC>ttT	p.F539F	TRIM29_ENST00000525887.1_5'UTR|TRIM29_ENST00000541857.1_Silent_p.F272F|TRIM29_ENST00000524816.3_Silent_p.F105F|TRIM29_ENST00000528870.1_Silent_p.F72F|TRIM29_ENST00000529044.1_Silent_p.F278F	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	539					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		CTTTCAGGGAGAAGGAGGAGC	0.592																																					p.F539F		.											.	TRIM29-291	0			c.C1617T						.						100	85	90					11																	119988941		2199	4295	6494	SO:0001819	synonymous_variant	23650	exon7			CAGGGAGAAGGAG	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"Tripartite motif containing / Tripartite motif containing"	17274	protein-coding gene	gene with protein product	"tripartite motif protein TRIM29", "ataxia-telangiectasia group D-associated protein"	610658	"tripartite motif-containing 29"			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1617C>T	11.37:g.119988941G>A		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_012101	0	0	0	0	0	Q96AA9|Q9BZY7	Silent	SNP	ENST00000341846.5	37	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	G	9.447	1.089611	0.20390	.	.	ENSG00000137699	ENST00000525327;ENST00000524956	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	T	0.69187	0.3083	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68135	-0.5489	4	.	.	.	.	13.87	0.63612	0.0:0.0:1.0:0.0	.	.	.	.	F	132;77	.	.	L	-	1	0	TRIM29	119494151	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.287000	0.51732	2.343000	0.79666	0.407000	0.27541	CTC	.		0.592	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		A	119988941	G	A	119988941	2	1	84	1	0	0	0	0	0	0	0	1	16536	933	33	2		2	TRIM29	11	119988941	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	944604	119988941	15017575	62	7739											
FKBP4	2288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2909052	2909052	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgggaaggaaaagttccaAatcccaccaaatgctgagct	14	8	10	9	0	0	1	0	1	0	0	2	3	2	3	3	2	2	4	3	2	5	2	rs201311104		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:2909052A>G	ENST00000001008.4	+	6	895	c.708A>G	c.(706-708)caA>caG	p.Q236Q	RP4-816N1.6_ENST00000547834.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	236	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			AAAAGTTCCAAATCCCACCAA	0.438																																					p.Q236Q		.											.	FKBP4-226	0			c.A708G						.						86	89	88					12																	2909052		2203	4300	6503	SO:0001819	synonymous_variant	2288	exon6			GTTCCAAATCCCA	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.708A>G	12.37:g.2909052A>G		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	33	19	NM_002014	0	0	106	186	80	D3DUQ1|Q9UCP1|Q9UCV7	Silent	SNP	ENST00000001008.4	37	CCDS8512.1																																																																																			A|0.999;G|0.001		0.438	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			G	2909052	A	G	2909052	2	3	84	1	0	0	0	0	0	0	0	1	5929	11	1	3		3	FKBP4	12	2909052	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		2909052	130942843	63	7740											
DPPA3	359787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7867786	7867786	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctctttcaggggcctcTcaaatctcctccgagacgtt	6	13	7	15	2	4	1	2	0	3	1	8	2	5	1	4	2	0	1	4	2	1	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:7867786T>A	ENST00000345088.2	+	2	207	c.90T>A	c.(88-90)tcT>tcA	p.S30S		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	30					chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CAGGGGCCTCTCAAATCTCCT	0.468																																					p.S30S		.											.	DPPA3-226	0			c.T90A						.						122	136	131					12																	7867786		2203	4300	6503	SO:0001819	synonymous_variant	359787	exon2			GGCCTCTCAAATC	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.90T>A	12.37:g.7867786T>A		Somatic	235	0		WXS	Illumina HiSeq	Phase_I	223	102	NM_199286	0	0	0	0	0	Q0P5U3|Q6JZS6	Silent	SNP	ENST00000345088.2	37	CCDS8582.1																																																																																			.		0.468	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286		A	7867786	T	A	7867786	2	1	84	1	0	0	0	0	0	0	0	1	4746	1538	54	5		5	DPPA3	12	7867786	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	4958734	7867786	125984109	64	7741											
CNTN1	1272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	41323760	41323760	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccagtccttctattacaaAgagcgtgttcagcaaattca	12	13	6	10	1	3	1	2	0	1	1	5	1	5	1	2	0	3	2	2	0	4	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:41323760A>G	ENST00000551295.2	+	7	776	c.659A>G	c.(658-660)aAg>aGg	p.K220R	CNTN1_ENST00000360099.3_Missense_Mutation_p.K220R|CNTN1_ENST00000348761.2_Missense_Mutation_p.K209R|CNTN1_ENST00000547702.1_Missense_Mutation_p.K220R|CNTN1_ENST00000347616.1_Missense_Mutation_p.K220R|CNTN1_ENST00000547849.1_Missense_Mutation_p.K220R	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	220	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TCTATTACAAAGAGCGTGTTC	0.383																																					p.K220R		.											.	CNTN1-1149	0			c.A659G						.						174	169	171					12																	41323760		2203	4300	6503	SO:0001583	missense	1272	exon7			TTACAAAGAGCGT	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing", "Endogenous ligands"	2171	protein-coding gene	gene with protein product	"glycoprotein gP135"	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.659A>G	12.37:g.41323760A>G	ENSP00000447006:p.Lys220Arg	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	210	85	NM_001256063	0	0	0	0	0	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.375898	0.61735	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.39	5.39	0.77823	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.78534	0.4298	L	0.53671	1.685	0.58432	D	0.99999	P;P;D	0.53151	0.61;0.948;0.958	B;P;P	0.53593	0.298;0.611;0.73	T	0.77059	-0.2728	10	0.33141	T	0.24	.	15.7149	0.77661	1.0:0.0:0.0:0.0	.	220;209;220	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	R	220;220;220;220;220;209	ENSP00000448004:K220R;ENSP00000447006:K220R;ENSP00000448653:K220R;ENSP00000325660:K220R;ENSP00000353213:K220R;ENSP00000261160:K209R	ENSP00000325660:K220R	K	+	2	0	CNTN1	39610027	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	2.180000	0.69256	0.533000	0.62120	AAG	.		0.383	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41323760	A	G	41323760	3	3	84	1	0	0	0	0	1	0	0	0	3646	72	3	3	681	3	CNTN1	12	41323760	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	33455974	41323760	92528135	65	7742											
ADAMTS20	80070	hgsc.bcm.edu;broad.mit.edu	37	chr12	43823478	43823478	+	Frame_Shift_Del	DEL	A	A	-																															ttatgagaacagttggtaatAaagcggtctcaagtttagaa																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:43823478delA	ENST00000389420.3	-	24	3430	c.3431delT	c.(3430-3432)ttafs	p.L1145fs	ADAMTS20_ENST00000395541.2_Intron|ADAMTS20_ENST00000553158.1_Frame_Shift_Del_p.L1145fs	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1145					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AGTTGGTAATAAAGCGGTCTC	0.343																																					p.L1144fs		.											.	ADAMTS20-795	0			c.3431delT						.						60	56	57					12																	43823478		2203	4298	6501	SO:0001589	frameshift_variant	80070	exon24			.	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"ADAM metallopeptidases with thrombospondin type 1 motif"	17178	protein-coding gene	gene with protein product		611681	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3431delT	12.37:g.43823478delA	ENSP00000374071:p.Leu1145fs	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	27	12	NM_025003	0	0	0	0	0	A6NNC9|J3QT00	Frame_Shift_Del	DEL	ENST00000389420.3	37	CCDS31778.2																																																																																			.		0.343	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		-	43823478	A	-	43823478	7	5	84	1	0	1	0	1	0	0	0	0	266	372	13	0	2364	0	ADAMTS20	12	43823478	Frame_Shift_Del	DEL	A	TCGA-BQ-7051-01A-12D-1961-08	2499718	43823478	90028417	66	7743											
CCNT1	904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49087909	49087909	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttgaaccatcctgtggtaagGaatgatcaactcctgtaagt	12	12	9	8	0	1	2	1	2	0	0	3	3	3	3	3	2	2	2	3	2	5	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:49087909G>T	ENST00000261900.3	-	9	1310	c.1088C>A	c.(1087-1089)tCc>tAc	p.S363Y		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	363					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						CTGTGGTAAGGAATGATCAAC	0.458																																					p.S363Y		.											.	CCNT1-418	0			c.C1088A						.						177	170	172					12																	49087909		2203	4300	6503	SO:0001583	missense	904	exon9			GGTAAGGAATGAT	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1088C>A	12.37:g.49087909G>T	ENSP00000261900:p.Ser363Tyr	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	176	78	NM_001240	0	0	12	21	9	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	37	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.543525	0.45280	.	.	ENSG00000129315	ENST00000261900	T	0.52057	0.68	5.49	4.54	0.55810	.	0.669254	0.16281	N	0.221349	T	0.44623	0.1302	N	0.22421	0.69	0.37399	D	0.912769	D	0.63880	0.993	P	0.50440	0.641	T	0.52815	-0.8525	10	0.56958	D	0.05	-7.9232	14.673	0.68958	0.0:0.1463:0.8536:0.0	.	363	O60563	CCNT1_HUMAN	Y	363	ENSP00000261900:S363Y	ENSP00000261900:S363Y	S	-	2	0	CCNT1	47374176	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.968000	0.56809	2.587000	0.87381	0.491000	0.48974	TCC	.		0.458	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		T	49087909	G	T	49087909	3	4	84	1	0	0	0	0	1	0	0	0	2940	1174	41	4	1096	4	CCNT1	12	49087909	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5264431	49087909	84763986	67	7744											
KRT80	144501	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52579248	52579248	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctggctcactttgcgcagttCctcctgcagccggccctgat	4	11	10	16	2	1	1	1	1	0	0	3	1	3	1	4	2	3	4	4	2	0	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:52579248C>G	ENST00000394815.2	-	2	521	c.424G>C	c.(424-426)Gaa>Caa	p.E142Q	KRT80_ENST00000313234.5_Missense_Mutation_p.E142Q	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	142	Coil 1B.|Rod.					cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(2)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.108)		TTGCGCAGTTCCTCCTGCAGC	0.612																																					p.E142Q	GBM(178;2309 2916 15678 35873)	.											.	KRT80-226	0			c.G424C						.						68	68	68					12																	52579248		2203	4300	6503	SO:0001583	missense	144501	exon2			GCAGTTCCTCCTG	BX537567	CCDS8821.2, CCDS41784.1	12q13.13	2013-01-16			ENSG00000167767	ENSG00000167767		"-", "Intermediate filaments type II, keratins (basic)"	27056	protein-coding gene	gene with protein product		611161				16831889	Standard	NM_001081492		Approved	KB20	uc001rzx.3	Q6KB66	OTTHUMG00000150193	ENST00000394815.2:c.424G>C	12.37:g.52579248C>G	ENSP00000378292:p.Glu142Gln	Somatic	117	1		WXS	Illumina HiSeq	Phase_I	89	42	NM_182507	0	0	16	37	21	Q6P1A5|Q7Z3Q0	Missense_Mutation	SNP	ENST00000394815.2	37	CCDS8821.2	.	.	.	.	.	.	.	.	.	.	C	3.574	-0.087018	0.07097	.	.	ENSG00000167767	ENST00000313234;ENST00000394815	T;T	0.76448	-1.02;-1.02	5.08	3.25	0.37280	Filament (1);	0.183620	0.26503	N	0.024016	T	0.31104	0.0786	N	0.00049	-2.415	0.29420	N	0.860606	B;B;B	0.23377	0.005;0.016;0.084	B;B;B	0.21917	0.007;0.011;0.037	T	0.50013	-0.8877	10	0.02654	T	1	.	9.7671	0.40567	0.0:0.7822:0.1405:0.0773	.	142;142;79	Q6KB66-2;Q6KB66;Q6KB66-3	.;K2C80_HUMAN;.	Q	142	ENSP00000369361:E142Q;ENSP00000378292:E142Q	ENSP00000369361:E142Q	E	-	1	0	KRT80	50865515	0.955000	0.32602	0.352000	0.25734	0.959000	0.62525	1.307000	0.33516	0.721000	0.32231	0.655000	0.94253	GAA	.		0.612	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507		G	52579248	C	G	52579248	3	3	84	1	0	0	0	0	1	0	0	0	8515	864	30	4	1001	4	KRT80	12	52579248	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	3491339	52579248	81272647	68	7745											
CAND1	55832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	67699344	67699344	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaactacagtaaaggcattGacactgattgctgggtcacc	12	11	9	9	0	1	2	1	2	0	0	1	2	1	2	1	2	3	3	1	2	4	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:67699344G>A	ENST00000545606.1	+	10	2333	c.1896G>A	c.(1894-1896)ttG>ttA	p.L632L		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	632					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TAAAGGCATTGACACTGATTG	0.408																																					p.L632L		.											.	CAND1-516	0			c.G1896A						.						110	112	112					12																	67699344		2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			GGCATTGACACTG		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"TBP interacting protein"	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.1896G>A	12.37:g.67699344G>A		Somatic	150	1		WXS	Illumina HiSeq	Phase_I	152	78	NM_018448	0	0	27	50	23	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	37	CCDS8977.1																																																																																			.		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67699344	G	A	67699344	2	1	84	1	0	0	0	0	0	0	0	1	2621	1281	45	2		2	CAND1	12	67699344	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	15120096	67699344	66152551	69	7746											
DCLK1	9201	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	36700222	36700222	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctcggctgtatctctgcGccttatcccgctcgtcgaag	5	11	9	16	5	1	0	0	0	1	0	6	1	2	0	3	1	1	3	3	1	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr13:36700222G>A	ENST00000360631.3	-	2	264	c.53C>T	c.(52-54)gCg>gTg	p.A18V	DCLK1_ENST00000379892.4_Missense_Mutation_p.A18V|DCLK1_ENST00000255448.4_Missense_Mutation_p.A18V			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	18					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GTATCTCTGCGCCTTATCCCG	0.622																																					p.A18V													.	DCLK1-826	0			c.C53T						.						61	62	62					13																	36700222		2203	4300	6503	SO:0001583	missense	9201	exon2			CTCTGCGCCTTAT	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.53C>T	13.37:g.36700222G>A	ENSP00000353846:p.Ala18Val	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	87	17	NM_004734	0	0	0	0	0	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	15.01	2.706275	0.48412	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	T;T;T	0.67523	-0.27;-0.27;1.88	5.67	5.67	0.87782	.	0.110579	0.64402	D	0.000012	T	0.56848	0.2013	N	0.22421	0.69	0.50632	D	0.999889	B	0.22346	0.068	B	0.18263	0.021	T	0.51379	-0.8713	10	0.44086	T	0.13	.	19.7802	0.96413	0.0:0.0:1.0:0.0	.	18	O15075-2	.	V	18	ENSP00000255448:A18V;ENSP00000353846:A18V;ENSP00000369222:A18V	ENSP00000255448:A18V	A	-	2	0	DCLK1	35598222	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.096000	0.64535	2.675000	0.91044	0.655000	0.94253	GCG	.		0.622	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		A	36700222	G	A	36700222	3	1	84	1	0	0	0	0	1	0	0	0	4297	1087	38	1	2204	1	DCLK1	13	36700222	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		36700222	78469656	70	7747											
FREM2	341640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	39450406	39450406	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacgtgactactcagggaccTatactgtgaagctggtgcca	10	10	11	10	1	1	2	1	2	0	0	1	3	1	3	2	2	5	1	2	2	5	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr13:39450406T>G	ENST00000280481.7	+	20	8647	c.8431T>G	c.(8431-8433)Tat>Gat	p.Y2811D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2811					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)		CTCAGGGACCTATACTGTGAA	0.448																																					p.Y2811D		.											.	FREM2-100	0			c.T8431G						.						124	112	116					13																	39450406		2203	4300	6503	SO:0001583	missense	341640	exon20			GGGACCTATACTG	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.8431T>G	13.37:g.39450406T>G	ENSP00000280481:p.Tyr2811Asp	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	82	42	NM_207361	0	0	18	37	19	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.712772	0.68730	.	.	ENSG00000150893	ENST00000280481	T	0.47528	0.84	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.73853	0.3640	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.79769	-0.1664	10	0.87932	D	0	.	15.9477	0.79806	0.0:0.0:0.0:1.0	.	2811	Q5SZK8	FREM2_HUMAN	D	2811	ENSP00000280481:Y2811D	ENSP00000280481:Y2811D	Y	+	1	0	FREM2	38348406	1.000000	0.71417	0.984000	0.44739	0.366000	0.29705	7.967000	0.87967	2.179000	0.69175	0.460000	0.39030	TAT	.		0.448	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39450406	T	G	39450406	3	3	84	1	0	0	0	0	1	0	0	0	6064	1522	53	5	8509	5	FREM2	13	39450406	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	2750184	39450406	75719472	71	7748											
KBTBD6	89890	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	41705610	41705612	+	In_Frame_Del	DEL	CAC	CAC	-																															ctggggtgtccaaagaagatCaccatctccttggcacacat																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr13:41705610_41705612delCAC	ENST00000379485.1	-	1	1270_1272	c.1036_1038delGTG	c.(1036-1038)gtgdel	p.V346del	KBTBD6_ENST00000499385.2_In_Frame_Del_p.V280del	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	346										NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CAAAGAAGATCACCATCTCCTTG	0.527																																					p.346_346del		.											.	KBTBD6-92	0			c.1036_1038del						.																																			SO:0001651	inframe_deletion	89890	exon1			.	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.1036_1038delGTG	13.37:g.41705610_41705612delCAC	ENSP00000368799:p.Val346del	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	94	29	NM_152903	0	0	0	0	0	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	In_Frame_Del	DEL	ENST00000379485.1	37	CCDS9376.1																																																																																			.		0.527	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		-	41705612	CAC	-	41705610	7	5	84	1	0	1	0	1	0	0	0	0	8018	813	29	0	990	0	KBTBD6	13	41705610	In_Frame_Del	DEL	CAC	TCGA-BQ-7051-01A-12D-1961-08	2255204	41705610	73464268	72	7749											
TEP1	7011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20845481	20845481	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggaagtggccagtcctaGcacaggcttctggaatctgg	8	9	14	10	0	2	0	0	0	2	0	3	2	3	2	2	5	1	2	2	5	3	2	rs375172392		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:20845481G>A	ENST00000262715.5	-	41	6086	c.6046C>T	c.(6046-6048)Cta>Tta	p.L2016L	TEP1_ENST00000545983.1_Silent_p.L354L|TEP1_ENST00000556935.1_Silent_p.L1908L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2016					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GCCAGTCCTAGCACAGGCTTC	0.507																																					p.L2016L		.											.	TEP1-95	0			c.C6046T						.						36	36	36					14																	20845481		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon41			GTCCTAGCACAGG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6046C>T	14.37:g.20845481G>A		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	49	22	NM_007110	0	0	17	30	13	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			.		0.507	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20845481	G	A	20845481	2	1	84	1	0	0	0	0	0	0	0	1	15791	962	34	2		2	TEP1	14	20845481	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		20845481	86504059	73	7750											
PNP	4860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20944608	20944608	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgagtctttggcttctcaCtcatcactaacaaggtcatc	9	14	6	12	1	5	0	4	0	2	0	8	1	5	0	0	2	1	1	0	2	2	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:20944608C>T	ENST00000361505.5	+	6	864	c.718C>T	c.(718-720)Ctc>Ttc	p.L240F	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						TGGCTTCTCACTCATCACTAA	0.458																																					p.L240F		.											.	PNP-229	0			c.C718T						.						150	128	135					14																	20944608		2203	4300	6503	SO:0001583	missense	4860	exon6			TTCTCACTCATCA		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"nucleoside phosphorylase"	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.718C>T	14.37:g.20944608C>T	ENSP00000354532:p.Leu240Phe	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	93	43	NM_000270	0	0	131	213	82		Missense_Mutation	SNP	ENST00000361505.5	37	CCDS9552.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542982	0.86022	.	.	ENSG00000198805	ENST00000361505	D	0.88046	-2.33	4.88	4.88	0.63580	Nucleoside phosphorylase domain (1);	0.064044	0.64402	D	0.000003	D	0.93762	0.8006	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94473	0.7686	10	0.72032	D	0.01	-21.5214	16.9641	0.86281	0.0:1.0:0.0:0.0	.	240	P00491	PNPH_HUMAN	F	240	ENSP00000354532:L240F	ENSP00000354532:L240F	L	+	1	0	PNP	20014448	0.999000	0.42202	0.994000	0.49952	0.951000	0.60555	4.327000	0.59247	2.528000	0.85240	0.655000	0.94253	CTC	.		0.458	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2		T	20944608	C	T	20944608	3	4	84	1	0	0	0	0	1	0	0	0	12189	565	20	2	740	2	PNP	14	20944608	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	99127	20944608	86404932	74	7751											
RNF31	55072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24626550	24626550	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggacttccagaactggaaaCgcatgaacgacccagaatac	16	5	9	11	2	0	3	0	1	0	2	1	6	1	5	2	2	4	1	2	2	5	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:24626550C>T	ENST00000324103.6	+	15	2865	c.2545C>T	c.(2545-2547)Cgc>Tgc	p.R849C	RNA5SP383_ENST00000362934.1_RNA|RNF31_ENST00000559275.1_Missense_Mutation_p.R698C|RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.R324C|RNF31_ENST00000382687.3_Missense_Mutation_p.R698C	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	849					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GAACTGGAAACGCATGAACGA	0.567																																					p.R849C		.											.	RNF31-90	0			c.C2545T						.						75	81	79					14																	24626550		1988	4157	6145	SO:0001583	missense	55072	exon15			TGGAAACGCATGA	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"RING-type (C3HC4) zinc fingers"	16031	protein-coding gene	gene with protein product	"HOIL-1-interacting protein"	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.2545C>T	14.37:g.24626550C>T	ENSP00000315112:p.Arg849Cys	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	28	16	NM_017999	0	0	29	49	20	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997602	0.54147	.	.	ENSG00000092098	ENST00000382682;ENST00000324103;ENST00000382687	T;T	0.77877	-1.13;-1.13	5.34	4.44	0.53790	.	0.000000	0.85682	D	0.000000	D	0.85296	0.5664	L	0.61218	1.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.951;0.996;0.998	D	0.86555	0.1837	10	0.87932	D	0	-19.6302	12.2841	0.54783	0.308:0.692:0.0:0.0	.	849;608;849;698	A0A962;B3KV71;Q96EP0;Q96EP0-3	.;.;RNF31_HUMAN;.	C	282;849;698	ENSP00000315112:R849C;ENSP00000372134:R698C	ENSP00000315112:R849C	R	+	1	0	RNF31	23696390	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	0.675000	0.25232	1.467000	0.48044	-0.203000	0.12734	CGC	.		0.567	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		T	24626550	C	T	24626550	3	4	84	1	0	0	0	0	1	0	0	0	13519	536	19	1	2603	1	RNF31	14	24626550	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	3681942	24626550	82722990	75	7752											
KIAA0391	9692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	35592664	35592664	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagatatctcaggaaagaTgagggcagtaataagcaagt	16	7	12	6	0	1	3	1	1	1	2	2	4	1	4	1	2	1	3	1	2	5	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:35592664T>G	ENST00000557565.1	+	2	594	c.213T>G	c.(211-213)gaT>gaG	p.D71E	KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000603544.1_Missense_Mutation_p.D71E|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000534898.4_Missense_Mutation_p.D71E|KIAA0391_ENST00000250377.7_De_novo_Start_OutOfFrame|PPP2R3C_ENST00000555644.1_5'Flank|PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000321130.10_Missense_Mutation_p.D71E	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	71					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		TCAGGAAAGATGAGGGCAGTA	0.408																																					p.D71E		.											.	KIAA0391-226	0			c.T213G						.						65	62	63					14																	35592664		2203	4300	6503	SO:0001583	missense	9692	exon2			GAAAGATGAGGGC	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.213T>G	14.37:g.35592664T>G	ENSP00000454657:p.Asp71Glu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	52	25	NM_014672	0	0	21	39	18	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	37	CCDS32063.1	.	.	.	.	.	.	.	.	.	.	T	2.705	-0.270055	0.05716	.	.	ENSG00000100890	ENST00000321130;ENST00000534898;ENST00000556121	T;T	0.40756	1.03;1.02	5.25	-5.42	0.02640	.	0.854894	0.10131	N	0.712121	T	0.21509	0.0518	N	0.22421	0.69	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18116	-1.0347	10	0.25751	T	0.34	-0.2169	6.1442	0.20276	0.2948:0.0:0.2418:0.4635	.	71;71	O15091-2;O15091	.;MRRP3_HUMAN	E	71	ENSP00000324697:D71E;ENSP00000440915:D71E	ENSP00000324697:D71E	D	+	3	2	KIAA0391	34662415	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.292000	0.08332	-1.164000	0.02790	-1.783000	0.00646	GAT	.		0.408	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		G	35592664	T	G	35592664	3	3	84	1	0	0	0	0	1	0	0	0	8193	1461	51	5	215	5	KIAA0391	14	35592664	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	10966114	35592664	71756876	76	7753											
VTI1B	10490	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	68118141	68118141	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtagtaaaccaggcctccCaggatggcgagctccagtaa	11	8	11	11	1	0	0	0	0	0	0	2	2	2	1	4	3	2	4	4	3	4	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:68118141C>T	ENST00000554659.1	-	6	1001	c.660G>A	c.(658-660)ctG>ctA	p.L220L	ARG2_ENST00000261783.3_3'UTR	NM_006370.2	NP_006361.1	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with t-SNAREs 1B	220					cell proliferation (GO:0008283)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			endometrium(1)|large_intestine(2)|stomach(1)|upper_aerodigestive_tract(1)	5				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)		CCAGGCCTCCCAGGATGGCGA	0.453																																					p.L220L		.											.	VTI1B-90	0			c.G660A						.						69	71	70					14																	68118141		2203	4300	6503	SO:0001819	synonymous_variant	10490	exon6			GCCTCCCAGGATG	AF060902	CCDS9786.1	14q23.3	2012-12-10	2012-12-10		ENSG00000100568	ENSG00000100568			17793	protein-coding gene	gene with protein product		603207	"vesicle transport through interaction with t-SNAREs homolog 1B (yeast)"			9636656, 9446565	Standard	NM_006370		Approved	VTI2	uc001xjt.3	Q9UEU0	OTTHUMG00000171251	ENST00000554659.1:c.660G>A	14.37:g.68118141C>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	89	48	NM_006370	0	0	135	257	122	O43547|Q96J28	Silent	SNP	ENST00000554659.1	37	CCDS9786.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801303	0.70567	.	.	ENSG00000100568	ENST00000554636	.	.	.	6.17	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6819	0.28518	0.1315:0.7266:0.0:0.1419	.	.	.	.	X	98	.	.	W	-	2	0	VTI1B	67187894	0.123000	0.22298	1.000000	0.80357	0.996000	0.88848	-0.529000	0.06186	1.560000	0.49568	0.655000	0.94253	TGG	.		0.453	VTI1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412558.2			T	68118141	C	T	68118141	2	4	84	1	0	0	0	0	0	0	0	1	17269	581	21	2		2	VTI1B	14	68118141	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	32525477	68118141	39231399	77	7754											
HHIPL1	84439	hgsc.bcm.edu	37	chr14	100119115	100119115	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcaggctctacgtctactaCtcagtgggtatccgcagcag	8	9	11	13	3	3	0	1	0	2	0	4	0	4	0	1	2	4	5	1	2	4	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:100119115C>G	ENST00000330710.5	+	2	908	c.810C>G	c.(808-810)taC>taG	p.Y270*	HHIPL1_ENST00000357223.2_Nonsense_Mutation_p.Y270*	NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1	270					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				ACGTCTACTACTCAGTGGGTA	0.617																																					p.Y270X		.											.	HHIPL1-70	0			c.C810G						.						46	37	40					14																	100119115		2203	4300	6503	SO:0001587	stop_gained	84439	exon2			CTACTACTCAGTG	AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"KIAA1822"	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.810C>G	14.37:g.100119115C>G	ENSP00000330601:p.Tyr270*	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_032425	0	0	0	0	0	A2RUF8|B2RN09|Q6UXX2	Nonsense_Mutation	SNP	ENST00000330710.5	37	CCDS45162.1	.	.	.	.	.	.	.	.	.	.	c	36	5.713025	0.96830	.	.	ENSG00000182218	ENST00000330710;ENST00000357223	.	.	.	4.59	3.68	0.42216	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.5806	0.17248	0.0:0.614:0.0:0.386	.	.	.	.	X	270	.	ENSP00000330601:Y270X	Y	+	3	2	HHIPL1	99188868	1.000000	0.71417	0.996000	0.52242	0.657000	0.38888	0.890000	0.28295	0.885000	0.36088	0.655000	0.94253	TAC	.		0.617	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566		G	100119115	C	G	100119115	4	3	84	1	0	0	0	0	0	1	0	0	7114	576	20	4	816	4	HHIPL1	14	100119115	Nonsense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	32000974	100119115	7230425	78	7755											
COX5A	9377	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	75221461	75221461	+	Frame_Shift_Del	DEL	A	A	-																															tttatgttccaattacctttAcgcaattcccaggcatctat																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr15:75221461delA	ENST00000322347.6	-	2	366	c.213delT	c.(211-213)cgtfs	p.R71fs	COX5A_ENST00000568517.1_5'UTR|COX5A_ENST00000562233.1_Frame_Shift_Del_p.R71fs|COX5A_ENST00000564811.1_Frame_Shift_Del_p.R71fs|COX5A_ENST00000567270.1_Intron|COX5A_ENST00000568783.1_Frame_Shift_Del_p.R71fs	NM_004255.3	NP_004246.2	P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	71					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						AATTACCTTTACGCAATTCCC	0.413																																					p.R71fs		.											.	COX5A-90	0			c.213delT						.						140	129	133					15																	75221461		2197	4295	6492	SO:0001589	frameshift_variant	9377	exon2			.	M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2267	protein-coding gene	gene with protein product		603773				10072584, 2853101	Standard	NM_004255		Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000322347.6:c.213delT	15.37:g.75221461delA	ENSP00000317780:p.Arg71fs	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	108	34	NM_004255	0	0	0	0	0	P30045|Q8TB65	Frame_Shift_Del	DEL	ENST00000322347.6	37	CCDS10273.1																																																																																			.		0.413	COX5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286417.1	NM_004255		-	75221461	A	-	75221461	7	5	84	1	0	1	0	1	0	0	0	0	3778	378	14	0	251	0	COX5A	15	75221461	Frame_Shift_Del	DEL	A	TCGA-BQ-7051-01A-12D-1961-08		75221461	27309931	79	7756											
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75664533	75664533	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatctctgatgtagacgcttGcttacacgctcatgggactg	9	12	10	10	2	2	2	1	1	1	1	3	3	2	3	0	1	2	4	0	1	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr15:75664533G>A	ENST00000394947.3	-	21	3923	c.3609C>T	c.(3607-3609)agC>agT	p.S1203S	SIN3A_ENST00000394949.4_Silent_p.S1203S|SIN3A_ENST00000360439.4_Silent_p.S1203S|RP11-817O13.8_ENST00000563278.1_lincRNA	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GTAGACGCTTGCTTACACGCT	0.433																																					p.S1203S		.											.	SIN3A-230	0			c.C3609T						.						109	105	106					15																	75664533		2197	4294	6491	SO:0001819	synonymous_variant	25942	exon21			ACGCTTGCTTACA	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3609C>T	15.37:g.75664533G>A		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	135	47	NM_001145358	0	0	33	66	33		Silent	SNP	ENST00000394947.3	37	CCDS10279.1																																																																																			.		0.433	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75664533	G	A	75664533	2	1	84	1	0	0	0	0	0	0	0	1	14357	1310	46	2		2	SIN3A	15	75664533	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	443072	75664533	26866859	80	7757											
C15orf42	90381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90138745	90138745	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccagatggcagtccggaTgtggctggggagaaaggaat	11	7	16	7	1	0	2	0	0	0	2	2	5	2	4	2	6	0	2	2	6	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr15:90138745T>C	ENST00000268138.7	+	7	1908	c.1803T>C	c.(1801-1803)gaT>gaC	p.D601D	TICRR_ENST00000560985.1_Silent_p.D600D			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	601					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										GCAGTCCGGATGTGGCTGGGG	0.443																																					p.D601D		.											.	.	0			c.T1803C						.						112	107	108					15																	90138745		1888	4113	6001	SO:0001819	synonymous_variant	90381	exon7			TCCGGATGTGGCT	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.1803T>C	15.37:g.90138745T>C		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	88	40	NM_152259	0	0	0	0	0	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			.		0.443	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		C	90138745	T	C	90138745	2	2	84	1	0	0	0	0	0	0	0	1	1800	1461	51	3		3	C15orf42	15	90138745	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	14474212	90138745	12392647	81	7758											
GUCY2D	3000	ucsc.edu	37	chr17	7919110	7919110	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accatgccgcggtactgcctGtttggggacacggtcaacac	8	8	12	13	3	1	0	1	0	0	0	1	1	1	1	3	4	4	2	3	4	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:7919110G>A	ENST00000254854.4	+	16	3144	c.2994G>A	c.(2992-2994)ctG>ctA	p.L998L		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	998	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				GGTACTGCCTGTTTGGGGACA	0.706																																					p.L998L													.	GUCY2D-319	0			c.G2994A						.						26	24	25					17																	7919110		2203	4299	6502	SO:0001819	synonymous_variant	3000	exon16			CTGCCTGTTTGGG	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"cone rod dystrophy 6"	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.2994G>A	17.37:g.7919110G>A		Somatic	27	0		WXS	Illumina HiSeq		35	4	NM_000180	0	0	0	0	0	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			.		0.706	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			A	7919110	G	A	7919110	2	1	84	1	0	0	0	0	0	0	0	1	6918	1364	48	2		2	GUCY2D	17	7919110	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		7919110	73276100	82	7759											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	345	51		WXS	Illumina HiSeq		524	80	NM_145301	0	0	20	123	103	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		T	15457087	C	T	15457087	3	4	84	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	7537977	15457087	65738123	83	7760											
SLC46A1	113235	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	26731859	26731859	+	Frame_Shift_Del	DEL	C	C	-																															ttcataaagggttaagatgtCctgggccccaaagtgcacag																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:26731859delC	ENST00000440501.1	-	2	951	c.856delG	c.(856-858)gacfs	p.D286fs	CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000321666.5_Frame_Shift_Del_p.D286fs|CTD-2350C19.2_ENST00000580714.1_RNA|SLC46A1_ENST00000584729.1_5'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	286					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	GTTAAGATGTCCTGGGCCCCA	0.542																																					p.D286fs		.											.	SLC46A1-22	0			c.856delG						.						109	118	115					17																	26731859		2022	4180	6202	SO:0001589	frameshift_variant	113235	exon2			.	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.856delG	17.37:g.26731859delC	ENSP00000395653:p.Asp286fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	112	70	NM_001242366	0	0	0	0	0	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Frame_Shift_Del	DEL	ENST00000440501.1	37																																																																																				.		0.542	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		-	26731859	C	-	26731859	7	5	84	1	0	1	0	1	0	0	0	0	14676	855	30	0	540	0	SLC46A1	17	26731859	Frame_Shift_Del	DEL	C	TCGA-BQ-7051-01A-12D-1961-08	11274772	26731859	54463351	84	7761											
SPAG5	10615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26911390	26911390	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctctgggtaagctggcagAgtaactcatccttcatagcc	9	11	10	11	0	3	1	2	0	1	1	4	1	4	1	2	2	4	5	2	2	3	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:26911390A>G	ENST00000321765.5	-	12	2602	c.2270T>C	c.(2269-2271)cTc>cCc	p.L757P		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	757	Gln-rich.|Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					AAGCTGGCAGAGTAACTCATC	0.522																																					p.L757P		.											.	SPAG5-90	0			c.T2270C						.						218	200	206					17																	26911390		2203	4300	6503	SO:0001583	missense	10615	exon12			TGGCAGAGTAACT	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2270T>C	17.37:g.26911390A>G	ENSP00000323300:p.Leu757Pro	Somatic	291	0		WXS	Illumina HiSeq	Phase_I	368	253	NM_006461	0	0	4	9	5	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.998487	0.54147	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	6.02	6.02	0.97574	.	0.363685	0.23744	N	0.044981	T	0.64394	0.2594	L	0.34521	1.04	0.48901	D	0.999721	D	0.76494	0.999	D	0.66497	0.944	T	0.65030	-0.6267	9	0.49607	T	0.09	-0.4993	12.9338	0.58303	1.0:0.0:0.0:0.0	.	757	Q96R06	SPAG5_HUMAN	P	757;254	.	ENSP00000323300:L757P	L	-	2	0	SPAG5	23935517	0.987000	0.35691	1.000000	0.80357	0.573000	0.36030	4.247000	0.58750	2.304000	0.77564	0.528000	0.53228	CTC	.		0.522	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		G	26911390	A	G	26911390	3	3	84	1	0	0	0	0	1	0	0	0	15013	304	11	3	1363	3	SPAG5	17	26911390	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	179531	26911390	54283820	85	7762											
KRT27	342574	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	38938378	38938378	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacggcaagaaccaggtccaAatttctcataccaccccttg	12	8	6	15	1	1	1	1	0	1	1	3	1	2	1	5	2	2	1	5	2	4	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:38938378A>G	ENST00000301656.3	-	1	408	c.368T>C	c.(367-369)tTt>tCt	p.F123S		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				ACCAGGTCCAAATTTCTCATA	0.498																																					p.F123S		.											.	KRT27-90	0			c.T368C						.						154	135	141					17																	38938378		2203	4300	6503	SO:0001583	missense	342574	exon1			GGTCCAAATTTCT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.368T>C	17.37:g.38938378A>G	ENSP00000301656:p.Phe123Ser	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	190	10	NM_181537	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	A	6.807	0.517981	0.13005	.	.	ENSG00000171446	ENST00000301656	D	0.87729	-2.29	5.66	1.89	0.25635	Filament (1);	0.279078	0.31290	N	0.007902	T	0.74030	0.3663	N	0.12182	0.205	0.30019	N	0.814529	B	0.13145	0.007	B	0.15870	0.014	T	0.67496	-0.5656	10	0.49607	T	0.09	.	10.0469	0.42192	0.5272:0.0:0.0:0.4728	.	123	Q7Z3Y8	K1C27_HUMAN	S	123	ENSP00000301656:F123S	ENSP00000301656:F123S	F	-	2	0	KRT27	36191904	0.001000	0.12720	0.987000	0.45799	0.444000	0.32077	0.662000	0.25038	0.449000	0.26747	-0.344000	0.07964	TTT	.		0.498	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		G	38938378	A	G	38938378	3	3	84	1	0	0	0	0	1	0	0	0	8485	14	1	3	1043	3	KRT27	17	38938378	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	12026988	38938378	42256832	86	7763											
COL1A1	1277	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	48275830	48275830	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaaattcctccggttgatttCtcatcatagccataagacag	12	12	7	10	1	2	2	2	1	1	1	5	3	4	2	3	1	1	1	3	1	3	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:48275830C>G	ENST00000225964.5	-	6	625	c.507G>C	c.(505-507)gaG>gaC	p.E169D		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	169	Nonhelical region (N-terminal).				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	CGGTTGATTTCTCATCATAGC	0.512			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta				OREG0024560	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E169D		.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1-986	0			c.G507C						.						52	49	50					17																	48275830		2203	4300	6503	SO:0001583	missense	1277	exon6			TGATTTCTCATCA	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.507G>C	17.37:g.48275830C>G	ENSP00000225964:p.Glu169Asp	Somatic	50	1	953	WXS	Illumina HiSeq	Phase_I	69	21	NM_000088	0	0	13	15	2	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	SNP	ENST00000225964.5	37	CCDS11561.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.206410	0.39003	.	.	ENSG00000108821	ENST00000225964	D	0.89810	-2.57	5.36	3.34	0.38264	.	0.066795	0.64402	D	0.000020	T	0.79197	0.4405	N	0.25957	0.775	0.42720	D	0.993676	B	0.09022	0.002	B	0.10450	0.005	T	0.67189	-0.5733	10	0.13470	T	0.59	.	9.4551	0.38750	0.0:0.7658:0.0:0.2342	.	169	P02452	CO1A1_HUMAN	D	169	ENSP00000225964:E169D	ENSP00000225964:E169D	E	-	3	2	COL1A1	45630829	0.992000	0.36948	1.000000	0.80357	0.977000	0.68977	0.324000	0.19610	0.625000	0.30304	0.650000	0.86243	GAG	.		0.512	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			G	48275830	C	G	48275830	3	3	84	1	0	0	0	0	1	0	0	0	3683	912	32	4	4071	4	COL1A1	17	48275830	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	9337452	48275830	32919380	87	7764											
DYNLL2	140735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	56164457	56164457	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtagtgtcacaccatgtcTgaccggaaggcagtgatcaa	11	9	11	10	1	3	2	2	2	1	0	3	3	3	3	2	2	0	2	2	2	3	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:56164457T>A	ENST00000579991.2	+	2	284	c.6T>A	c.(4-6)tcT>tcA	p.S2S		NM_080677.2	NP_542408.1	Q96FJ2	DYL2_HUMAN	dynein, light chain, LC8-type 2	2					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|microtubule-based process (GO:0007017)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|synaptic target recognition (GO:0008039)|transport (GO:0006810)	centrosome (GO:0005813)|cytosol (GO:0005829)|dynein complex (GO:0030286)|membrane (GO:0016020)|microtubule (GO:0005874)|myosin complex (GO:0016459)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	motor activity (GO:0003774)			lung(3)	3						ACACCATGTCTGACCGGAAGG	0.532																																					p.S2S		.											.	DYNLL2-90	0			c.T6A						.						90	77	81					17																	56164457		2203	4300	6503	SO:0001819	synonymous_variant	140735	exon2			CATGTCTGACCGG	AF112997	CCDS11601.1	17q23.2	2009-11-18				ENSG00000264364		"Cytoplasmic dyneins"	24596	protein-coding gene	gene with protein product	"radial spoke 22 homolog (Chlamydomonas)"	608942				16260502	Standard	NM_080677		Approved	MGC17810, Dlc2, DNCL1B, RSPH22	uc010wnn.1	Q96FJ2		ENST00000579991.2:c.6T>A	17.37:g.56164457T>A		Somatic	75	1		WXS	Illumina HiSeq	Phase_I	90	62	NM_080677	0	0	101	311	210	B2R5B4	Silent	SNP	ENST00000579991.2	37	CCDS11601.1																																																																																			.		0.532	DYNLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443338.2	NM_080677		A	56164457	T	A	56164457	2	1	84	1	0	0	0	0	0	0	0	1	4860	1567	55	5		5	DYNLL2	17	56164457	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	7888627	56164457	25030753	88	7765											
HEXDC	284004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80382347	80382347	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttccctacgagggcccTctgaggctgctgagggccaa	7	9	13	12	1	1	2	0	2	1	0	2	3	2	2	3	3	2	3	3	3	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:80382347T>C	ENST00000327949.9	+	2	173	c.162T>C	c.(160-162)ccT>ccC	p.P54P	HEXDC_ENST00000577944.1_Silent_p.P54P|HEXDC_ENST00000337014.6_Silent_p.P54P			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	54					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACGAGGGCCCTCTGAGGCTGC	0.612																																					p.P54P		.											.	HEXDC-92	0			c.T162C						.						97	92	94					17																	80382347		1940	4131	6071	SO:0001819	synonymous_variant	284004	exon3			GGGCCCTCTGAGG	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.162T>C	17.37:g.80382347T>C		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	139	38	NM_173620	0	0	22	42	20	B7UUP6|Q8IYN4|Q8TE81	Silent	SNP	ENST00000327949.9	37																																																																																				.		0.612	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620		C	80382347	T	C	80382347	2	2	84	1	0	0	0	0	0	0	0	1	7096	1538	54	3		3	HEXDC	17	80382347	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	24217890	80382347	812863	89	7766											
ZNF521	25925	broad.mit.edu	37	chr18	22902006	22902006	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgattaatcttgtgttctgtGatatcgctcagcgattcaaa	10	16	8	7	2	4	2	2	2	2	0	5	3	4	2	0	0	1	2	0	0	3	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr18:22902006G>C	ENST00000361524.3	-	3	334	c.186C>G	c.(184-186)atC>atG	p.I62M	ZNF521_ENST00000584787.1_De_novo_Start_InFrame|ZNF521_ENST00000579111.1_5'UTR|ZNF521_ENST00000538137.2_Missense_Mutation_p.I62M	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	62					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TGTGTTCTGTGATATCGCTCA	0.418			T	PAX5	ALL																																p.I62M				Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521-275	0			c.C186G						.						141	125	131					18																	22902006		2203	4300	6503	SO:0001583	missense	25925	exon3			TTCTGTGATATCG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.186C>G	18.37:g.22902006G>C	ENSP00000354794:p.Ile62Met	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	102	3	NM_015461	0	0	0	0	0	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.889596	0.33348	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.28895	1.59;1.59	6.06	5.19	0.71726	Zinc finger, C2H2-like (1);	0.073305	0.56097	D	0.000033	T	0.23926	0.0579	N	0.14661	0.345	0.30187	N	0.799882	P	0.47034	0.889	P	0.44860	0.462	T	0.11470	-1.0586	10	0.87932	D	0	-31.4656	13.5532	0.61745	0.0716:0.0:0.9284:0.0	.	62	Q96K83	ZN521_HUMAN	M	62;96;62	ENSP00000354794:I62M;ENSP00000382352:I62M	ENSP00000354794:I62M	I	-	3	3	ZNF521	21156004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.711000	0.54868	1.555000	0.49500	0.655000	0.94253	ATC	.		0.418	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		C	22902006	G	C	22902006	3	2	84	1	0	0	0	0	1	0	0	0	17997	1280	45	4	3773	4	ZNF521	18	22902006	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		22902006	55175242	90	7767											
C18orf55	29090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	71816322	71816322	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagtcagagagggggaacCgccgtcccaacatcacaaaa	15	3	12	11	2	2	1	2	0	0	1	3	4	3	3	3	3	2	0	3	3	4	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr18:71816322C>G	ENST00000169551.6	+	1	577	c.279C>G	c.(277-279)acC>acG	p.T93T	TIMM21_ENST00000580087.1_Silent_p.T93T|FBXO15_ENST00000419743.2_5'Flank|FBXO15_ENST00000269500.5_5'Flank	NM_014177.2	NP_054896.2	Q9BVV7	TIM21_HUMAN	translocase of inner mitochondrial membrane 21 homolog (yeast)	93					cellular protein metabolic process (GO:0044267)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane presequence translocase complex (GO:0005744)											GAGGGGGAACCGCCGTCCCAA	0.498																																					p.T93T		.											.	.	0			c.C279G						.						57	58	58					18																	71816322		2203	4300	6503	SO:0001819	synonymous_variant	29090	exon1			GGGAACCGCCGTC	BC000892	CCDS12003.1	18q22.3	2011-11-25	2011-11-25	2011-11-25	ENSG00000075336	ENSG00000075336			25010	protein-coding gene	gene with protein product		615180	"chromosome 18 open reading frame 55"	C18orf55		11042152	Standard	NM_014177		Approved	HSPC154, TIM21	uc010dqr.1	Q9BVV7	OTTHUMG00000132844	ENST00000169551.6:c.279C>G	18.37:g.71816322C>G		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	67	32	NM_014177	0	0	25	42	17	Q9P010	Silent	SNP	ENST00000169551.6	37	CCDS12003.1																																																																																			.		0.498	TIMM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256318.1	NM_014177		G	71816322	C	G	71816322	2	3	84	1	0	0	0	0	0	0	0	1	1911	639	23	4		4	C18orf55	18	71816322	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	48914316	71816322	6260926	91	7768											
STXBP2	6813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7712265	7712265	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcggtcactggcacaagAacaaggctggcatagaagcc	12	6	12	11	1	1	2	1	0	0	2	2	2	1	2	1	4	2	4	1	4	5	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:7712265A>T	ENST00000221283.5	+	18	1595	c.1564A>T	c.(1564-1566)Aac>Tac	p.N522Y	STXBP2_ENST00000441779.2_Missense_Mutation_p.N533Y|STXBP2_ENST00000414284.2_Missense_Mutation_p.N519Y|STXBP2_ENST00000602355.1_Missense_Mutation_p.N57Y	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	522					leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						CTGGCACAAGAACAAGGCTGG	0.662																																					p.N533Y		.											.	STXBP2-91	0			c.A1597T						.						24	33	30					19																	7712265		2192	4284	6476	SO:0001583	missense	6813	exon18			CACAAGAACAAGG	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.1564A>T	19.37:g.7712265A>T	ENSP00000221283:p.Asn522Tyr	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	52	21	NM_001272034	0	1	3	154	150	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	37	CCDS12181.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.846916	0.71603	.	.	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902	T;T;T	0.80480	-1.38;-1.38;-1.38	5.26	4.18	0.49190	.	0.112112	0.64402	D	0.000017	D	0.82761	0.5107	L	0.55481	1.735	0.44611	D	0.997588	P;P;P;P	0.48407	0.91;0.91;0.889;0.91	P;P;P;P	0.55161	0.689;0.77;0.562;0.689	D	0.84034	0.0361	10	0.72032	D	0.01	-1.3267	10.063	0.42286	0.8312:0.1688:0.0:0.0	.	533;488;519;522	E7EQD5;B4DY46;Q15833-2;Q15833	.;.;.;STXB2_HUMAN	Y	522;519;533;522	ENSP00000221283:N522Y;ENSP00000409471:N519Y;ENSP00000413606:N533Y	ENSP00000221283:N522Y	N	+	1	0	STXBP2	7618265	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	5.775000	0.68915	2.003000	0.58678	0.454000	0.30748	AAC	.		0.662	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949		T	7712265	A	T	7712265	3	4	84	1	0	0	0	0	1	0	0	0	15385	246	9	5	1634	5	STXBP2	19	7712265	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		7712265	51416718	92	7769											
DOCK6	57572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	11312640	11312640	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgagcagcgtcttacgCttgtgttgctcgggcagctc	4	12	14	11	3	1	1	0	1	1	0	3	1	1	1	0	1	6	7	0	1	1	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:11312640C>A	ENST00000294618.7	-	44	5624	c.5613G>T	c.(5611-5613)aaG>aaT	p.K1871N	DOCK6_ENST00000586702.1_5'UTR|CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Missense_Mutation_p.K1210N	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1871	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCGTCTTACGCTTGTGTTGCT	0.637																																					p.K1871N		.											.	DOCK6-93	0			c.G5613T						.						75	82	80					19																	11312640		2150	4243	6393	SO:0001583	missense	57572	exon44			CTTACGCTTGTGT		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.5613G>T	19.37:g.11312640C>A	ENSP00000294618:p.Lys1871Asn	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	20	11	NM_020812	0	0	30	45	15	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205580	0.79127	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.20200	2.09;2.09	4.98	2.85	0.33270	.	0.000000	0.85682	D	0.000000	T	0.48750	0.1517	M	0.90082	3.085	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.988;0.99;0.997	T	0.49153	-0.8969	10	0.87932	D	0	-31.2742	7.885	0.29644	0.0:0.7188:0.0:0.2812	.	1210;1871;1210	C9IZV6;Q96HP0;B4DIL4	.;DOCK6_HUMAN;.	N	1871;1210	ENSP00000294618:K1871N;ENSP00000321556:K1210N	ENSP00000294618:K1871N	K	-	3	2	DOCK6	11173640	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.212000	0.32394	0.478000	0.27488	0.491000	0.48974	AAG	.		0.637	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11312640	C	A	11312640	3	1	84	1	0	0	0	0	1	0	0	0	4702	796	28	4	550	4	DOCK6	19	11312640	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	3600375	11312640	47816343	93	7770											
DOCK6	57572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11312680	11312680	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccgtgtgcgcgcccatccGgcgtgaacggcgtgcagaac	6	5	14	16	7	0	2	0	1	0	1	1	2	1	2	4	2	4	1	4	2	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:11312680G>C	ENST00000294618.7	-	44	5584	c.5573C>G	c.(5572-5574)cCg>cGg	p.P1858R	DOCK6_ENST00000586702.1_5'UTR|CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Missense_Mutation_p.P1197R	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1858	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCGCCCATCCGGCGTGAACGG	0.597																																					p.P1858R		.											.	DOCK6-93	0			c.C5573G						.						85	91	89					19																	11312680		2135	4244	6379	SO:0001583	missense	57572	exon44			CCATCCGGCGTGA		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.5573C>G	19.37:g.11312680G>C	ENSP00000294618:p.Pro1858Arg	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	35	10	NM_020812	0	0	14	24	10	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	4.448	0.083033	0.08533	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.16457	2.34;2.34	4.84	3.8	0.43715	.	0.164262	0.43747	D	0.000521	T	0.09686	0.0238	N	0.20986	0.625	0.34097	D	0.661381	B;B;B	0.23058	0.026;0.079;0.055	B;B;B	0.32149	0.017;0.141;0.064	T	0.19063	-1.0317	10	0.07325	T	0.83	-15.5866	5.6208	0.17455	0.2773:0.0:0.7227:0.0	.	1197;1858;1197	C9IZV6;Q96HP0;B4DIL4	.;DOCK6_HUMAN;.	R	1858;1197	ENSP00000294618:P1858R;ENSP00000321556:P1197R	ENSP00000294618:P1858R	P	-	2	0	DOCK6	11173680	1.000000	0.71417	0.710000	0.30468	0.153000	0.21895	5.138000	0.64795	2.213000	0.71641	0.491000	0.48974	CCG	.		0.597	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		C	11312680	G	C	11312680	3	2	84	1	0	0	0	0	1	0	0	0	4702	1116	39	4	590	4	DOCK6	19	11312680	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	40	11312680	47816303	94	7771											
OR7A17	26333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	14991895	14991895	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgcagcctgcataggtgatGactctgctctgtgtctggat	7	13	12	9	0	3	2	0	2	3	0	3	3	3	3	1	2	4	3	1	2	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:14991895G>A	ENST00000327462.2	-	1	369	c.273C>T	c.(271-273)gtC>gtT	p.V91V		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					CATAGGTGATGACTCTGCTCT	0.468																																					p.V91V		.											.	OR7A17-68	0			c.C273T						.						151	131	138					19																	14991895		2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			GGTGATGACTCTG	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"GPCR / Class A : Olfactory receptors"	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.273C>T	19.37:g.14991895G>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	126	59	NM_030901	0	0	0	0	0	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			.		0.468	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		A	14991895	G	A	14991895	2	1	84	1	0	0	0	0	0	0	0	1	11241	1277	45	2		2	OR7A17	19	14991895	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	3679215	14991895	44137088	95	7772											
USHBP1	83878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17362478	17362478	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccacctgttccagctccctgCgcagagactgcagctgctcc	6	8	9	18	1	0	1	0	0	0	1	3	2	3	1	5	0	5	6	5	0	0	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:17362478C>G	ENST00000252597.3	-	12	2008	c.1835G>C	c.(1834-1836)cGc>cCc	p.R612P	USHBP1_ENST00000431146.2_Missense_Mutation_p.R548P|AC010646.3_ENST00000594059.1_5'UTR	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						CAGCTCCCTGCGCAGAGACTG	0.602																																					p.R612P		.											.	USHBP1-91	0			c.G1835C						.						75	74	74					19																	17362478		2203	4300	6503	SO:0001583	missense	83878	exon12			TCCCTGCGCAGAG	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1835G>C	19.37:g.17362478C>G	ENSP00000252597:p.Arg612Pro	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	104	48	NM_031941	0	0	3	4	1		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	.	.	.	.	.	.	.	.	.	.	C	5.320	0.244414	0.10077	.	.	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.19250	2.17;2.16	4.28	1.98	0.26296	.	0.610995	0.13794	N	0.362329	T	0.19927	0.0479	L	0.57536	1.79	0.09310	N	1	P;P	0.45240	0.854;0.854	B;B	0.43301	0.415;0.415	T	0.13845	-1.0494	10	0.49607	T	0.09	-11.2307	4.0967	0.09995	0.234:0.6445:0.0:0.1215	.	548;612	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	P	612;548	ENSP00000252597:R612P;ENSP00000407902:R548P	ENSP00000252597:R612P	R	-	2	0	USHBP1	17223478	0.000000	0.05858	0.005000	0.12908	0.023000	0.10783	0.206000	0.17375	2.108000	0.64289	0.561000	0.74099	CGC	.		0.602	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		G	17362478	C	G	17362478	3	3	84	1	0	0	0	0	1	0	0	0	17070	768	27	4	284	4	USHBP1	19	17362478	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	2370583	17362478	41766505	96	7773											
CRTC1	23373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18876245	18876245	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctggctcctctccacagcaCcgcccagctggcgtcagccc	5	6	9	21	2	2	0	1	0	1	0	4	0	3	0	6	2	3	3	6	2	0	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:18876245C>G	ENST00000321949.8	+	9	944	c.918C>G	c.(916-918)caC>caG	p.H306Q	CRTC1_ENST00000338797.6_Missense_Mutation_p.H322Q|CRTC1_ENST00000594658.1_Missense_Mutation_p.H265Q|CRTC1_ENST00000601916.1_Missense_Mutation_p.H231Q	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1										CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						CTCCACAGCACCGCCCAGCTG	0.622																																					p.H322Q		.											.	CRTC1-1361	0			c.C966G						.						131	128	129					19																	18876245		2203	4300	6503	SO:0001583	missense	23373	exon10			ACAGCACCGCCCA	AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"transducer of regulated cAMP response element-binding protein"	607536	"mucoepidermoid carcinoma translocated 1"	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.918C>G	19.37:g.18876245C>G	ENSP00000323332:p.His306Gln	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	180	66	NM_001098482	0	0	19	25	6		Missense_Mutation	SNP	ENST00000321949.8	37	CCDS32963.1	.	.	.	.	.	.	.	.	.	.	C	4.850	0.158062	0.09236	.	.	ENSG00000105662	ENST00000262813;ENST00000338797;ENST00000321949	T;T	0.11495	2.77;2.77	4.23	3.18	0.36537	.	0.533386	0.19393	N	0.115375	T	0.07548	0.0190	L	0.46157	1.445	0.41761	D	0.989719	P;B;B	0.35348	0.496;0.284;0.112	B;B;B	0.27608	0.081;0.071;0.037	T	0.22208	-1.0223	10	0.17832	T	0.49	-19.0333	7.3343	0.26601	0.0:0.7971:0.0:0.2029	.	306;322;306	Q6UUV9-3;Q6UUV9-2;Q6UUV9	.;.;CRTC1_HUMAN	Q	306;322;306	ENSP00000345001:H322Q;ENSP00000323332:H306Q	ENSP00000262813:H306Q	H	+	3	2	CRTC1	18737245	0.713000	0.27926	0.992000	0.48379	0.498000	0.33706	0.107000	0.15375	2.077000	0.62373	0.561000	0.74099	CAC	.		0.622	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021		G	18876245	C	G	18876245	3	3	84	1	0	0	0	0	1	0	0	0	3905	506	18	4	1004	4	CRTC1	19	18876245	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	1513767	18876245	40252738	97	7774											
ZNF253	56242	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	20003291	20003291	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tacctggccctcaatcctctCcaaacataaaagaactcata	15	9	3	14	0	3	1	2	0	1	1	5	1	4	1	4	1	3	0	4	1	7	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:20003291C>T	ENST00000589717.1	+	4	1327	c.1235C>T	c.(1234-1236)tCc>tTc	p.S412F	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Missense_Mutation_p.S336F|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	412				Missing (in Ref. 1; AAC26844). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCAATCCTCTCCAAACATAAA	0.388																																					p.S412F		.											.	ZNF253-90	0			c.C1235T						.						39	43	42					19																	20003291		2087	4250	6337	SO:0001583	missense	56242	exon4			TCCTCTCCAAACA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1235C>T	19.37:g.20003291C>T	ENSP00000468720:p.Ser412Phe	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	38	19	NM_021047	0	0	13	25	12	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	37	CCDS42532.1	.	.	.	.	.	.	.	.	.	.	c	3.372	-0.128115	0.06753	.	.	ENSG00000256771	ENST00000355650	.	.	.	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25938	0.0632	L	0.35542	1.07	0.09310	N	1	P	0.34562	0.457	B	0.39299	0.296	T	0.21415	-1.0246	7	.	.	.	.	3.9875	0.09522	0.409:0.591:0.0:0.0	.	412	O75346	ZN253_HUMAN	F	412	.	.	S	+	2	0	ZNF253	19864291	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	0.021000	0.13489	0.293000	0.22520	0.298000	0.19748	TCC	.		0.388	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		T	20003291	C	T	20003291	3	4	84	1	0	0	0	0	1	0	0	0	17829	855	30	2	1249	2	ZNF253	19	20003291	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	1127046	20003291	39125692	98	7775											
KIR3DL2	3812	bcgsc.ca	37	chr19	55362679	55362679	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatctttctttccagggttCttcttgctgcagggggcctg	3	16	12	10	0	4	1	0	1	4	0	5	1	5	1	2	3	2	3	2	3	0	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:55362679C>A	ENST00000326321.3	+	2	72	c.39C>A	c.(37-39)ttC>ttA	p.F13L	KIR3DL1_ENST00000402254.2_Intron|KIR3DL2_ENST00000270442.5_Missense_Mutation_p.F13L|KIR2DS4_ENST00000339924.8_RNA	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	13					cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		TTCCAGGGTTCTTCTTGCTGC	0.557																																					p.F13L													.	KIR3DL2-92	0			c.C39A						.						53	70	65					19																	55362679		1241	3127	4368	SO:0001583	missense	3812	exon2			AGGGTTCTTCTTG	L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.39C>A	19.37:g.55362679C>A	ENSP00000325525:p.Phe13Leu	Somatic	280	3		WXS	Illumina HiSeq	Phase_1	309	18	NM_001242867	0	0	0	0	0	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	c	8.766	0.924679	0.18056	.	.	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.00448	7.4;7.38	0.847	0.847	0.18961	.	.	.	.	.	T	0.00271	0.0008	L	0.28400	0.85	0.23784	N	0.996854	B;B	0.06786	0.001;0.0	B;B	0.12156	0.007;0.002	T	0.34700	-0.9818	9	0.42905	T	0.14	.	5.0537	0.14522	0.0:1.0:0.0:0.0	.	13;13	Q95366;P43630	.;KI3L2_HUMAN	L	13	ENSP00000325525:F13L;ENSP00000270442:F13L	ENSP00000270442:F13L	F	+	3	2	KIR3DL2	60054491	0.000000	0.05858	0.401000	0.26359	0.048000	0.14542	-0.428000	0.06991	0.764000	0.33197	0.184000	0.17185	TTC	.		0.557	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1			A	55362679	C	A	55362679	3	1	84	1	0	0	0	0	1	0	0	0	8342	912	32	4	45	4	KIR3DL2	19	55362679	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	35359388	55362679	3766304	99	7776											
ZNF471	57573	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57037192	57037192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttagtgatagctcatccTgtgctcagcatcaaagactc	10	13	7	11	0	3	2	3	1	0	1	5	2	4	2	1	0	3	3	1	0	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:57037192T>C	ENST00000308031.5	+	5	1889	c.1756T>C	c.(1756-1758)Tgt>Cgt	p.C586R	ZNF471_ENST00000593197.1_3'UTR|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	586					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		TAGCTCATCCTGTGCTCAGCA	0.408																																					p.C586R	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	.											.	ZNF471-154	0			c.T1756C						.						78	74	75					19																	57037192		2203	4300	6503	SO:0001583	missense	57573	exon5			TCATCCTGTGCTC	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1756T>C	19.37:g.57037192T>C	ENSP00000309161:p.Cys586Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	76	33	NM_020813	0	0	0	0	0	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	T	4.114	0.019231	0.08006	.	.	ENSG00000196263	ENST00000308031	T	0.00949	5.51	3.68	-2.53	0.06326	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00724	0.0024	N	0.11789	0.175	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.45498	-0.9257	9	0.87932	D	0	.	9.1979	0.37240	0.0:0.4048:0.0:0.5952	.	586	Q9BX82	ZN471_HUMAN	R	586	ENSP00000309161:C586R	ENSP00000309161:C586R	C	+	1	0	ZNF471	61729004	0.000000	0.05858	0.017000	0.16124	0.514000	0.34195	-1.549000	0.02182	-0.322000	0.08615	-0.464000	0.05259	TGT	.		0.408	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57037192	T	C	57037192	3	2	84	1	0	0	0	0	1	0	0	0	17962	1580	55	3	1770	3	ZNF471	19	57037192	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	1674513	57037192	2091791	100	7777											
PTPRT	11122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	41100970	41100970	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccctcggggttagacagcaaGagtcgcagccggatggtcat	9	7	14	11	3	1	2	1	0	0	2	3	3	1	3	2	4	2	3	2	4	2	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr20:41100970G>A	ENST00000373187.1	-	8	1385	c.1386C>T	c.(1384-1386)ctC>ctT	p.L462L	PTPRT_ENST00000356100.2_Silent_p.L462L|PTPRT_ENST00000373198.4_Silent_p.L462L|PTPRT_ENST00000373190.1_Silent_p.L462L|PTPRT_ENST00000373201.1_Silent_p.L462L|PTPRT_ENST00000373193.3_Silent_p.L462L|PTPRT_ENST00000373184.1_Silent_p.L462L			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	462	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TAGACAGCAAGAGTCGCAGCC	0.612																																					p.L462L		.											.	PTPRT-664	0			c.C1386T						.						57	62	60					20																	41100970		2134	4245	6379	SO:0001819	synonymous_variant	11122	exon8			CAGCAAGAGTCGC	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1386C>T	20.37:g.41100970G>A		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	147	51	NM_007050	0	0	0	0	0	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			.		0.612	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41100970	G	A	41100970	2	1	84	1	0	0	0	0	0	0	0	1	12844	929	33	2		2	PTPRT	20	41100970	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		41100970	21924550	101	7778											
ZGPAT	84619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62366823	62366823	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagagtgccaagcgggcccTgagcctgcggctcttccaga	8	6	13	14	2	1	3	0	1	1	2	2	3	2	3	4	2	4	1	4	2	2	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr20:62366823T>C	ENST00000328969.5	+	6	1491	c.1364T>C	c.(1363-1365)cTg>cCg	p.L455P	LIME1_ENST00000309546.3_5'Flank|ZGPAT_ENST00000448100.2_Missense_Mutation_p.L435P|ZGPAT_ENST00000355969.6_Missense_Mutation_p.L435P|RP4-583P15.14_ENST00000467211.1_5'Flank|RP4-583P15.15_ENST00000490623.2_Nonstop_Mutation_p.*341R|ZGPAT_ENST00000357119.4_Missense_Mutation_p.L426P|ZGPAT_ENST00000369967.3_Missense_Mutation_p.L435P	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	455					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					AAGCGGGCCCTGAGCCTGCGG	0.667																																					p.L455P		.											.	ZGPAT-90	0			c.T1364C						.						23	27	26					20																	62366823		2200	4300	6500	SO:0001583	missense	84619	exon6			GGGCCCTGAGCCT	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.1364T>C	20.37:g.62366823T>C	ENSP00000332013:p.Leu455Pro	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	51	30	NM_032527	0	0	14	52	38	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	37	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234362	0.79800	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000369967;ENST00000328969	T;T;T;T;T	0.32988	1.45;1.45;1.47;1.45;1.43	5.69	4.57	0.56435	.	0.072010	0.56097	D	0.000022	T	0.53738	0.1815	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.54490	-0.8286	10	0.52906	T	0.07	-25.847	11.8041	0.52143	0.1318:0.0:0.0:0.8682	.	426;455;435	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	P	435;435;426;435;455	ENSP00000391176:L435P;ENSP00000348242:L435P;ENSP00000349634:L426P;ENSP00000358984:L435P;ENSP00000332013:L455P	ENSP00000332013:L455P	L	+	2	0	ZGPAT	61837267	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.891000	0.69782	0.955000	0.37878	0.460000	0.39030	CTG	.		0.667	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		C	62366823	T	C	62366823	3	2	84	1	0	0	0	0	1	0	0	0	17706	1580	55	3	1382	3	ZGPAT	20	62366823	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	21265853	62366823	658697	102	7779											
SFI1	9814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	32002357	32002357	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agaacaccatggcccgagtgGatgaagccaaaaaaaccttt	16	6	9	10	1	0	2	0	1	0	1	0	4	0	3	4	2	3	0	4	2	5	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr22:32002357G>C	ENST00000400288.2	+	21	2203	c.2098G>C	c.(2098-2100)Gat>Cat	p.D700H	SFI1_ENST00000540643.1_Missense_Mutation_p.D645H|SFI1_ENST00000414585.1_Missense_Mutation_p.D547H|SFI1_ENST00000432498.1_Missense_Mutation_p.D669H|SFI1_ENST00000443326.1_Missense_Mutation_p.D618H|SFI1_ENST00000400289.1_Missense_Mutation_p.D618H|SFI1_ENST00000443011.1_Missense_Mutation_p.D547H	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	700					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GGCCCGAGTGGATGAAGCCAA	0.517																																					p.D700H		.											.	SFI1-90	0			c.G2098C						.						88	88	88					22																	32002357		2023	4185	6208	SO:0001583	missense	9814	exon21			CGAGTGGATGAAG	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.2098G>C	22.37:g.32002357G>C	ENSP00000383145:p.Asp700His	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	63	25	NM_001007467	0	0	8	20	12	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	G	8.780	0.928003	0.18131	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288;ENST00000417682	T;T;T;T;T;T;T;T	0.14266	3.1;3.1;2.94;2.93;2.93;2.94;3.1;2.52	5.06	0.509	0.16977	.	0.751926	0.13001	N	0.421651	T	0.10035	0.0246	N	0.08118	0	0.09310	N	1	P;P;P;P;P	0.42757	0.789;0.603;0.603;0.789;0.573	P;B;B;P;B	0.49922	0.626;0.366;0.277;0.626;0.366	T	0.28364	-1.0046	10	0.40728	T	0.16	.	6.8814	0.24174	0.4019:0.0:0.5981:0.0	.	645;618;618;669;700	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3	.;.;.;.;SFI1_HUMAN	H	669;645;618;547;547;618;700;283	ENSP00000402679:D669H;ENSP00000443025:D645H;ENSP00000416469:D618H;ENSP00000397148:D547H;ENSP00000401199:D547H;ENSP00000383146:D618H;ENSP00000383145:D700H;ENSP00000398871:D283H	ENSP00000383145:D700H	D	+	1	0	SFI1	30332357	0.001000	0.12720	0.033000	0.17914	0.025000	0.11179	0.187000	0.16998	0.237000	0.21200	-0.995000	0.02519	GAT	.		0.517	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		C	32002357	G	C	32002357	3	2	84	1	0	0	0	0	1	0	0	0	14188	1174	41	4	2176	4	SFI1	22	32002357	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		32002357	19302209	103	7780											
C1QTNF6	114904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37578251	37578251	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcgtcctcggccttgatgaGgtggccgctgaaggtgatgt	5	11	16	9	3	0	4	0	4	0	0	3	4	1	4	3	4	0	1	3	4	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr22:37578251G>C	ENST00000337843.2	-	3	889	c.814C>G	c.(814-816)Ctc>Gtc	p.L272V	RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000470655.1_5'UTR|C1QTNF6_ENST00000255836.6_Missense_Mutation_p.L148V|C1QTNF6_ENST00000397110.2_Missense_Mutation_p.L272V	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	253					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						GCCTTGATGAGGTGGCCGCTG	0.657																																					p.L272V		.											.	C1QTNF6-90	0			c.C814G						.						61	57	58					22																	37578251		2203	4300	6503	SO:0001583	missense	114904	exon3			TGATGAGGTGGCC	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.814C>G	22.37:g.37578251G>C	ENSP00000338812:p.Leu272Val	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	35	18	NM_182486	0	0	6	8	2	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981527	0.74474	.	.	ENSG00000133466	ENST00000397110;ENST00000337843;ENST00000255836	T;T;T	0.51574	0.7;0.7;0.7	4.84	4.84	0.62591	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.64402	D	0.000001	T	0.78444	0.4284	H	0.97265	3.97	0.58432	D	0.999997	D;D	0.76494	0.999;0.998	D;D	0.72075	0.976;0.971	D	0.85842	0.1398	10	0.87932	D	0	.	13.3544	0.60619	0.0787:0.0:0.9213:0.0	.	272;253	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	V	272;272;148	ENSP00000380299:L272V;ENSP00000338812:L272V;ENSP00000255836:L148V	ENSP00000255836:L148V	L	-	1	0	C1QTNF6	35908197	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	5.704000	0.68347	2.238000	0.73509	0.491000	0.48974	CTC	.		0.657	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486		C	37578251	G	C	37578251	3	2	84	1	0	0	0	0	1	0	0	0	1973	1000	35	4	26	4	C1QTNF6	22	37578251	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5575894	37578251	13726315	104	7781											
ARFGAP3	26286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	43213794	43213794	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaacattttttttgccactAatgttcatcttttcgtcttt	7	22	3	9	1	4	0	2	0	2	0	5	0	4	0	1	0	2	1	1	0	2	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr22:43213794A>G	ENST00000263245.5	-	10	1101	c.882T>C	c.(880-882)atT>atC	p.I294I	ARFGAP3_ENST00000429508.2_Silent_p.I222I|ARFGAP3_ENST00000437119.2_Silent_p.I250I	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	294					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TTTTGCCACtaatgttcatct	0.348																																					p.I294I	GBM(58;544 1030 21460 27159 48838)	.											.	ARFGAP3-153	0			c.T882C						.						296	266	276					22																	43213794		2203	4300	6503	SO:0001819	synonymous_variant	26286	exon10			GCCACTAATGTTC	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"ADP-ribosylation factor GTPase activating proteins"	661	protein-coding gene	gene with protein product		612439	"ADP-ribosylation factor GTPase activating protein 1"	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.882T>C	22.37:g.43213794A>G		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	139	63	NM_014570	0	0	22	46	24	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Silent	SNP	ENST00000263245.5	37	CCDS14042.1	.	.	.	.	.	.	.	.	.	.	A	7.151	0.583739	0.13749	.	.	ENSG00000242247	ENST00000453516	.	.	.	5.35	-2.94	0.05581	.	.	.	.	.	.	.	.	.	.	.	0.32559	N	0.531383	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1118	4.5685	0.12198	0.2139:0.5126:0.1904:0.0831	.	.	.	.	Q	141	.	.	X	-	1	0	ARFGAP3	41543738	0.000000	0.05858	0.062000	0.19696	0.849000	0.48306	-0.717000	0.04986	-0.307000	0.08804	-0.291000	0.09656	TAG	.		0.348	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		G	43213794	A	G	43213794	2	3	84	1	0	0	0	0	0	0	0	1	851	358	13	3		3	ARFGAP3	22	43213794	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	5635543	43213794	8090772	105	7782											
SYN1	6853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	47432308	47432308	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacttcctcaggctgcggatGgtctcagctttcacctcgtc	5	12	10	14	2	3	0	3	0	1	0	7	2	4	1	2	3	2	2	2	3	0	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:47432308G>C	ENST00000295987.7	-	13	2197	c.2073C>G	c.(2071-2073)acC>acG	p.T691T	SYN1_ENST00000340666.4_3'UTR	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	691	E.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						GGCTGCGGATGGTCTCAGCTT	0.582																																					p.T691T		.											.	SYN1-131	0			c.C2073G						.						108	91	97					X																	47432308		2203	4300	6503	SO:0001819	synonymous_variant	6853	exon13			GCGGATGGTCTCA		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.2073C>G	X.37:g.47432308G>C		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	58	56	NM_006950	0	0	0	0	0	B1AJQ1|O75825|Q5H9A9	Silent	SNP	ENST00000295987.7	37	CCDS14280.1																																																																																			.		0.582	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		C	47432308	G	C	47432308	2	2	84	1	0	0	0	0	0	0	0	1	15472	1335	47	4		4	SYN1	23	47432308	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		47432308	107838252	106	7783											
RRAGB	10325	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	55744773	55744773	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttgcgcaatggaagaatctGactctgagaaaacgacggag	14	7	13	7	3	2	3	0	2	2	2	2	7	2	5	0	2	2	2	0	2	5	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:55744773G>A	ENST00000262850.7	+	1	456	c.13G>A	c.(13-15)Gac>Aac	p.D5N	RRAGB_ENST00000374941.4_Missense_Mutation_p.D5N	NM_016656.3	NP_057740.2			Ras-related GTP binding B											breast(1)|endometrium(3)|large_intestine(5)|lung(3)|pancreas(1)|prostate(1)	14						GGAAGAATCTGACTCTGAGAA	0.463											OREG0019812	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D5N													.	RRAGB-130	0			c.G13A						.						75	70	72					X																	55744773		2203	4300	6503	SO:0001583	missense	10325	exon1			GAATCTGACTCTG	X90530	CCDS14371.1, CCDS14372.1	Xp11.21	2008-02-05			ENSG00000083750	ENSG00000083750			19901	protein-coding gene	gene with protein product		300725				7499430, 9394008	Standard	NM_006064		Approved		uc004dup.3	Q5VZM2	OTTHUMG00000021662	ENST00000262850.7:c.13G>A	X.37:g.55744773G>A	ENSP00000262850:p.Asp5Asn	Somatic	14	0	1010	WXS	Illumina HiSeq	Phase_I	11	10	NM_016656	0	0	1	43	42		Missense_Mutation	SNP	ENST00000262850.7	37	CCDS14372.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.211068	0.58343	.	.	ENSG00000083750	ENST00000374941;ENST00000262850	T	0.67865	-0.29	4.34	3.45	0.39498	.	0.285164	0.25355	N	0.031261	T	0.47021	0.1423	N	0.19112	0.55	0.28194	N	0.927647	B;B	0.13145	0.007;0.004	B;B	0.16289	0.015;0.007	T	0.30909	-0.9962	10	0.22706	T	0.39	-3.0781	9.0206	0.36198	0.0:0.2192:0.7808:0.0	.	5;5	Q5VZM2-2;Q5VZM2	.;RRAGB_HUMAN	N	5	ENSP00000364077:D5N	ENSP00000262850:D5N	D	+	1	0	RRAGB	55761498	0.999000	0.42202	0.999000	0.59377	0.981000	0.71138	1.371000	0.34250	1.138000	0.42230	0.600000	0.82982	GAC	.		0.463	RRAGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056878.1	NM_016656		A	55744773	G	A	55744773	3	1	84	1	0	0	0	0	1	0	0	0	13705	1290	45	2	15	2	RRAGB	23	55744773	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	8312465	55744773	99525787	107	7784											
HEPH	9843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	65390505	65390505	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcgagtctactacctgggCatccgggatgtgcagtggaa	9	9	13	10	2	1	0	0	0	1	0	3	3	2	2	2	3	3	2	2	3	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:65390505C>T	ENST00000343002.2	+	1	757	c.93C>T	c.(91-93)ggC>ggT	p.G31G	HEPH_ENST00000419594.1_Silent_p.G34G|HEPH_ENST00000441993.2_Silent_p.G34G|HEPH_ENST00000519389.1_Silent_p.G85G|HEPH_ENST00000374727.3_Silent_p.G34G|HEPH_ENST00000336279.5_Intron			Q9BQS7	HEPH_HUMAN	hephaestin	31	Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						ACTACCTGGGCATCCGGGATG	0.527																																					p.G85G		.											.	HEPH-135	0			c.C255T						.						94	64	74					X																	65390505		2203	4300	6503	SO:0001819	synonymous_variant	9843	exon2			CCTGGGCATCCGG	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.93C>T	X.37:g.65390505C>T		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	23	19	NM_138737	0	0	1	1	0	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Silent	SNP	ENST00000343002.2	37																																																																																				.		0.527	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		T	65390505	C	T	65390505	2	4	84	1	0	0	0	0	0	0	0	1	7075	697	25	2		2	HEPH	23	65390505	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	9645732	65390505	89880055	108	7785											
ARHGAP36	158763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	130215818	130215818	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctctctgagctggagcGtctgaagctgcaagagactg	9	8	13	11	1	2	3	0	2	2	1	3	5	2	4	1	1	5	3	1	1	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:130215818G>A	ENST00000276211.5	+	2	524	c.179G>A	c.(178-180)cGt>cAt	p.R60H	ARHGAP36_ENST00000370921.1_5'Flank|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.R48H	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	60					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R60H(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						GAGCTGGAGCGTCTGAAGCTG	0.532																																					p.R60H		.											.	ARHGAP36-133	1	Substitution - Missense(1)	large_intestine(1)	c.G179A						.						125	107	113					X																	130215818		2203	4300	6503	SO:0001583	missense	158763	exon2			TGGAGCGTCTGAA		CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.179G>A	X.37:g.130215818G>A	ENSP00000276211:p.Arg60His	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	96	87	NM_144967	0	0	0	0	0	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	37	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358508	0.82243	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432	T;T;T	0.28666	1.6;1.61;1.68	4.16	4.16	0.48862	.	0.000000	0.47455	D	0.000238	T	0.40886	0.1135	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.994	T	0.30387	-0.9980	10	0.87932	D	0	.	10.8111	0.46547	0.0:0.0:1.0:0.0	.	29;48;60	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	H	60;48;12;29	ENSP00000276211:R60H;ENSP00000359960:R48H;ENSP00000408515:R29H	ENSP00000276211:R60H	R	+	2	0	ARHGAP36	130043499	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.627000	0.67784	2.315000	0.78130	0.544000	0.68410	CGT	.		0.532	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		A	130215818	G	A	130215818	3	1	84	1	0	0	0	0	1	0	0	0	883	1145	40	1	181	1	ARHGAP36	23	130215818	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	64825313	130215818	25054742	109	7786											
SPEN	23013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	16258648	16258648	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaacgaggccaaggaaccTgcagaaacactcaagccacc	16	2	10	13	1	1	2	1	0	0	2	1	5	1	3	4	2	5	1	4	2	5	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr1:16258648T>C	ENST00000375759.3	+	11	6117	c.5913T>C	c.(5911-5913)ccT>ccC	p.P1971P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1971					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCAAGGAACCTGCAGAAACAC	0.597																																					p.P1971P		.											.	SPEN-298	0			c.T5913C						.						32	34	33					1																	16258648		2199	4292	6491	SO:0001819	synonymous_variant	23013	exon11			GGAACCTGCAGAA		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.5913T>C	1.37:g.16258648T>C		Somatic	67	1		WXS	Illumina HiSeq	Phase_I	76	24	NM_015001	0	0	6	9	3	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																			.		0.597	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		C	16258648	T	C	16258648	2	2	85	1	0	0	0	0	0	0	0	1	15070	1567	55	3		3	SPEN	1	16258648	Silent	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		16258648	232991973	1	7787											
MYSM1	114803	broad.mit.edu	37	chr1	59125680	59125680	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaaaataatcacattaacaAttcctttgtacagttctctt	14	17	2	8	0	2	0	1	0	1	0	4	0	3	0	1	0	2	2	1	0	6	8			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr1:59125680A>G	ENST00000472487.1	-	20	2515	c.2476T>C	c.(2476-2478)Ttg>Ctg	p.L826L	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	826					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CACATTAACAATTCCTTTGTA	0.299																																					p.L826L													.	MYSM1-501	0			c.T2476C						.						77	75	76					1																	59125680		1805	4073	5878	SO:0001819	synonymous_variant	114803	exon20			TTAACAATTCCTT	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.2476T>C	1.37:g.59125680A>G		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	85	4	NM_001085487	0	0	4	4	0	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			.		0.299	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		G	59125680	A	G	59125680	2	3	85	1	0	0	0	0	0	0	0	1	10126	98	4	3		3	MYSM1	1	59125680	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	42867032	59125680	190124941	2	7788											
CD84	8832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160523192	160523192	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttctcttgaacaaacggaAcaaaaacactgaagacagaa	19	7	6	9	1	2	4	0	2	2	2	3	5	2	5	0	1	4	0	0	1	7	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr1:160523192A>G	ENST00000311224.4	-	4	802	c.736T>C	c.(736-738)Ttc>Ctc	p.F246L	CD84_ENST00000368051.3_Missense_Mutation_p.F246L|CD84_ENST00000368048.3_Missense_Mutation_p.F246L|CD84_ENST00000534968.1_Missense_Mutation_p.F132L|CD84_ENST00000368054.3_Missense_Mutation_p.F246L|CD84_ENST00000368047.3_5'Flank|RP11-528G1.2_ENST00000446952.1_RNA	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	246					blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			AACAAACGGAACAAAAACACT	0.468																																					p.F246L		.											.	CD84-93	0			c.T736C						.						92	91	92					1																	160523192		2203	4300	6503	SO:0001583	missense	8832	exon4			AACGGAACAAAAA	AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1704	protein-coding gene	gene with protein product		604513	"CD84 antigen (leukocyte antigen)", "CD84 molecule "			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.736T>C	1.37:g.160523192A>G	ENSP00000312367:p.Phe246Leu	Somatic	49	1		WXS	Illumina HiSeq	Phase_I	66	26	NM_001184881	0	0	2	2	0	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Missense_Mutation	SNP	ENST00000311224.4	37	CCDS53396.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.161810	0.38217	.	.	ENSG00000066294	ENST00000534968;ENST00000368054;ENST00000368048;ENST00000311224;ENST00000368051;ENST00000360056	T;T;T;T;T;T	0.62941	2.54;0.21;0.2;0.17;1.7;-0.01	4.93	-1.95	0.07548	.	2.237860	0.02657	N	0.107102	T	0.29588	0.0738	M	0.65498	2.005	0.09310	N	1	B;B;B;B;B;B	0.21606	0.001;0.058;0.004;0.016;0.027;0.021	B;B;B;B;B;B	0.17433	0.004;0.013;0.013;0.008;0.018;0.013	T	0.02070	-1.1219	10	0.19590	T	0.45	-0.0085	1.0227	0.01521	0.4506:0.1508:0.2528:0.1458	.	246;246;132;246;246;246	Q9UIB8-5;Q9UIB8-4;Q9UIB8-7;Q9UIB8;Q9UIB8-2;Q9UIB8-3	.;.;.;SLAF5_HUMAN;.;.	L	132;246;246;246;246;246	ENSP00000442845:F132L;ENSP00000357033:F246L;ENSP00000357027:F246L;ENSP00000312367:F246L;ENSP00000357030:F246L;ENSP00000353163:F246L	ENSP00000312367:F246L	F	-	1	0	CD84	158789816	0.000000	0.05858	0.000000	0.03702	0.169000	0.22640	0.086000	0.14935	-0.437000	0.07243	-0.323000	0.08544	TTC	.		0.468	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1	NM_003874		G	160523192	A	G	160523192	3	3	85	1	0	0	0	0	1	0	0	0	3048	43	2	3	321	3	CD84	1	160523192	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	101397512	160523192	88727429	3	7789											
KCNIP3	30818	hgsc.bcm.edu	37	chr2	96012772	96012772	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggcagcccggcttgccatggGcatccagggcatggagctgt	6	7	16	12	1	0	0	0	0	0	0	1	1	1	1	3	5	3	5	3	5	0	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:96012772G>C	ENST00000295225.5	+	3	316				KCNIP3_ENST00000468529.1_Missense_Mutation_p.G2A|KCNIP3_ENST00000377181.2_Intron|KCNIP3_ENST00000360990.3_Intron	NM_013434.4	NP_038462.1	Q9Y2W7	CSEN_HUMAN	Kv channel interacting protein 3, calsenilin						apoptotic process (GO:0006915)|behavioral response to pain (GO:0048266)|intracellular protein transport (GO:0006886)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	axon terminus (GO:0043679)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|voltage-gated ion channel activity (GO:0005244)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	16				READ - Rectum adenocarcinoma(193;0.13)		CTTGCCATGGGCATCCAGGGC	0.716																																					p.G2A		.											.	KCNIP3-154	0			c.G5C						.						62	51	55					2																	96012772		2203	4300	6503	SO:0001627	intron_variant	30818	exon1			CCATGGGCATCCA	AF199599	CCDS2013.1, CCDS33245.1	2q21.1	2013-01-10	2006-02-11	2006-02-11	ENSG00000115041	ENSG00000115041		"EF-hand domain containing"	15523	protein-coding gene	gene with protein product		604662	"calsenilin, presenilin-binding protein, EF hand transcription factor"	CSEN		9771752, 10078534	Standard	NM_013434		Approved	DREAM, KCHIP3, calsenilin	uc002sup.3	Q9Y2W7	OTTHUMG00000130392	ENST00000295225.5:c.182-27272G>C	2.37:g.96012772G>C		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	25	3	NM_001034914	0	0	42	42	0	H7BY46|Q3YAC3|Q3YAC4|Q53TJ5|Q96T40|Q9UJ84|Q9UJ85	Missense_Mutation	SNP	ENST00000295225.5	37	CCDS2013.1	.	.	.	.	.	.	.	.	.	.	g	10.76	1.440425	0.25900	.	.	ENSG00000115041	ENST00000468529	T	0.69435	-0.4	3.04	3.04	0.35103	.	.	.	.	.	T	0.57607	0.2065	.	.	.	0.80722	D	1	B	0.21452	0.056	B	0.18561	0.022	T	0.61192	-0.7112	8	0.62326	D	0.03	.	11.8579	0.52449	0.0:0.0:1.0:0.0	.	2	Q9Y2W7-3	.	A	2	ENSP00000417499:G2A	ENSP00000417499:G2A	G	+	2	0	KCNIP3	95376499	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	5.744000	0.68664	1.671000	0.50874	0.290000	0.19541	GGC	.		0.716	KCNIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252770.1	NM_013434		C	96012772	G	C	96012772	1	2	85	0	1	0	0	0	0	0	0	0	8062	1203	42	4		4	KCNIP3	2	96012772	Intron	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		96012772	147186601	4	7790											
ADRA2B	151	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	96781259	96781259	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccctgcccaggccccccCttggccctgggacctctgcg	3	7	10	21	1	2	0	1	0	1	0	2	1	2	1	7	3	2	0	7	3	0	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:96781259C>T	ENST00000409345.3	-	1	725	c.630G>A	c.(628-630)aaG>aaA	p.K210K		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	210					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CAGGCCCCCCCTTGGCCCTGG	0.622																																					p.K210K													.	ADRA2B-229	0			c.G630A						.						32	35	34					2																	96781259		2038	4173	6211	SO:0001819	synonymous_variant	151	exon1			CCCCCCCTTGGCC	M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"GPCR / Class A : Adrenoceptors : alpha"	282	protein-coding gene	gene with protein product		104260	"adrenergic, alpha-2B-, receptor"	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.630G>A	2.37:g.96781259C>T		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	36	6	NM_000682	0	0	0	0	0	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																			.		0.622	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			T	96781259	C	T	96781259	2	4	85	1	0	0	0	0	0	0	0	1	338	680	24	2		2	ADRA2B	2	96781259	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	768487	96781259	146418114	5	7791											
TTN	7273	hgsc.bcm.edu	37	chr2	179611917	179611917	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggggtgtggagtatctctcTagagtctctcctggaggtgt	5	13	16	7	0	3	1	0	0	3	1	6	3	4	3	1	5	0	1	1	5	2	2	rs578160962		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:179611917T>C	ENST00000591111.1	-	46	10585				TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.L5070L|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTATCTCTCTAGAGTCTCTC	0.522													T|||	1	0.000199681	0	0.0014	5008	,	,		15437	0		0	False		,,,				2504	0				p.L5070L		.											.	TTN-636	0			c.A15210G						.						70	74	72					2																	179611917		2203	4300	6503	SO:0001627	intron_variant	7273	exon46			TCTCTCTAGAGTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-5269A>G	2.37:g.179611917T>C		Somatic	123	1		WXS	Illumina HiSeq	Phase_I	133	8	NM_133379	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.522	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179611917	T	C	179611917	1	2	85	0	1	0	0	0	0	0	0	0	16768	1509	53	3		3	TTN	2	179611917	Intron	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	82830658	179611917	63587456	6	7792											
PGAP1	80055	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197767380	197767380	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcctgaacgaacttggtaatCccggaatcctccagctacag	11	9	8	13	2	0	1	0	1	0	0	4	3	4	2	4	2	4	2	4	2	5	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:197767380C>T	ENST00000354764.4	-	5	850	c.736G>A	c.(736-738)Gat>Aat	p.D246N	PGAP1_ENST00000409188.1_Missense_Mutation_p.D204N|PGAP1_ENST00000409475.1_Missense_Mutation_p.D246N|PGAP1_ENST00000485830.1_5'UTR	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	246					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						ACTTGGTAATCCCGGAATCCT	0.353																																					p.D246N		.											.	PGAP1-93	0			c.G736A						.						89	96	94					2																	197767380		2203	4300	6503	SO:0001583	missense	80055	exon5			GGTAATCCCGGAA		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.736G>A	2.37:g.197767380C>T	ENSP00000346809:p.Asp246Asn	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	90	32	NM_024989	0	0	0	1	1	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812990	0.90707	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.96491	-4.03;-4.03;-4.03	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.98585	0.9527	M	0.92122	3.275	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.99628	1.0985	10	0.87932	D	0	-16.6327	18.3788	0.90443	0.0:1.0:0.0:0.0	.	204;246;246	B4DYY6;Q75T13-3;Q75T13	.;.;PGAP1_HUMAN	N	246;246;204	ENSP00000346809:D246N;ENSP00000387028:D246N;ENSP00000386802:D204N	ENSP00000346809:D246N	D	-	1	0	PGAP1	197475625	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.144000	0.64832	2.568000	0.86640	0.650000	0.86243	GAT	.		0.353	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		T	197767380	C	T	197767380	3	4	85	1	0	0	0	0	1	0	0	0	11803	855	30	2	2124	2	PGAP1	2	197767380	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	18155463	197767380	45431993	7	7793											
LRRFIP1	9208	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	238636568	238636568	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atcacagtccctgaatagaaGatctggcagggttagtatag	13	10	11	7	0	2	3	1	1	1	2	3	3	3	3	1	2	0	3	1	2	6	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:238636568G>C	ENST00000392000.4	+	4	366				LRRFIP1_ENST00000308482.9_Missense_Mutation_p.R145T|LRRFIP1_ENST00000244815.5_Intron|LRRFIP1_ENST00000289175.6_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		CTGAATAGAAGATCTGGCAGG	0.318																																					p.R145T		.											.	LRRFIP1-153	0			c.G434C						.						204	199	201					2																	238636568		1568	3582	5150	SO:0001627	intron_variant	9208	exon8			ATAGAAGATCTGG	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.249+7103G>C	2.37:g.238636568G>C		Somatic	194	0		WXS	Illumina HiSeq	Phase_I	189	66	NM_001137550	0	0	0	0	0	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945238	0.53079	.	.	ENSG00000124831	ENST00000308482;ENST00000391999;ENST00000420665	T	0.48201	0.82	5.3	4.2	0.49525	.	.	.	.	.	T	0.29288	0.0729	N	0.24115	0.695	0.80722	D	1	B	0.31318	0.319	B	0.32624	0.149	T	0.08207	-1.0733	9	0.23891	T	0.37	.	5.5337	0.16999	0.2308:0.0:0.7692:0.0	.	145	E9PGZ2	.	T	145;135;100	ENSP00000310109:R145T	ENSP00000310109:R145T	R	+	2	0	LRRFIP1	238301307	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.587000	0.53957	2.652000	0.90054	0.655000	0.94253	AGA	.		0.318	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		C	238636568	G	C	238636568	1	2	85	0	1	0	0	0	0	0	0	0	9052	942	33	4		4	LRRFIP1	2	238636568	Intron	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	40869188	238636568	4562805	8	7794											
NKIRAS1	28512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	23942484	23942484	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taactgttcttttactcctcGgtctgtttctactgaagcca	7	17	6	11	1	3	1	0	1	3	0	5	1	4	1	2	1	4	2	2	1	4	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:23942484G>A	ENST00000443659.2	-	3	928	c.151C>T	c.(151-153)Cga>Tga	p.R51*	NKIRAS1_ENST00000425478.2_Nonsense_Mutation_p.R51*|NKIRAS1_ENST00000416026.2_Nonsense_Mutation_p.R51*|NKIRAS1_ENST00000412028.1_Nonsense_Mutation_p.R51*|NKIRAS1_ENST00000437230.1_Nonsense_Mutation_p.R51*|NKIRAS1_ENST00000388759.3_Nonsense_Mutation_p.R51*|NKIRAS1_ENST00000421515.2_Nonsense_Mutation_p.R51*|NKIRAS1_ENST00000415901.2_Nonsense_Mutation_p.R51*			Q9NYS0	KBRS1_HUMAN	NFKB inhibitor interacting Ras-like 1	51					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	7						TTTACTCCTCGGTCTGTTTCT	0.403																																					p.R51X		.											.	NKIRAS1-659	0			c.C151T						.						182	179	180					3																	23942484		2203	4300	6503	SO:0001587	stop_gained	28512	exon4			CTCCTCGGTCTGT	AF229839	CCDS33717.1	3p24.1	2014-05-09	2004-05-20		ENSG00000197885	ENSG00000197885			17899	protein-coding gene	gene with protein product		604496	"NFKB inhibitor interacting Ras-like protein 1"			10657303	Standard	NM_020345		Approved	KBRAS1, kappaB-Ras1	uc003ccj.3	Q9NYS0	OTTHUMG00000155605	ENST00000443659.2:c.151C>T	3.37:g.23942484G>A	ENSP00000393785:p.Arg51*	Somatic	166	1		WXS	Illumina HiSeq	Phase_I	193	56	NM_020345	0	0	9	16	7	Q96K18	Nonsense_Mutation	SNP	ENST00000443659.2	37	CCDS33717.1	.	.	.	.	.	.	.	.	.	.	G	44	10.950539	0.99494	.	.	ENSG00000197885	ENST00000388759;ENST00000443659;ENST00000421515;ENST00000425478;ENST00000437230;ENST00000412028;ENST00000415901;ENST00000416026	.	.	.	5.56	5.56	0.83823	.	0.058012	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-18.985	19.1246	0.93376	0.0:0.0:1.0:0.0	.	.	.	.	X	51	.	ENSP00000373411:R51X	R	-	1	2	NKIRAS1	23917488	1.000000	0.71417	0.894000	0.35097	0.950000	0.60333	7.894000	0.87336	2.618000	0.88619	0.491000	0.48974	CGA	.		0.403	NKIRAS1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340876.2	NM_020345		A	23942484	G	A	23942484	4	1	85	1	0	0	0	0	0	1	0	0	10470	1124	39	1	435	1	NKIRAS1	3	23942484	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		23942484	174079946	9	7795											
VPRBP	9730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	51457622	51457622	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctagcggaccctgggggggCcgtggctgaggatgagcagt	6	6	20	9	2	0	2	0	2	0	0	0	4	0	4	2	6	2	3	2	6	1	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:51457622C>G	ENST00000335891.5	-	7	1464	c.1455G>C	c.(1453-1455)cgG>cgC	p.R485R				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	934	Protein kinase-like.				B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CCTGGGGGGGCCGTGGCTGAG	0.592																																					p.R881R		.											.	VPRBP-92	0			c.G2643C						.						44	47	46					3																	51457622		1981	4163	6144	SO:0001819	synonymous_variant	9730	exon14			GGGGGGCCGTGGC	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.1455G>C	3.37:g.51457622C>G		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	60	27	NM_014703	0	0	15	28	13	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	37																																																																																				.		0.592	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		G	51457622	C	G	51457622	2	3	85	1	0	0	0	0	0	0	0	1	17218	726	26	4		4	VPRBP	3	51457622	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	27515138	51457622	146564808	10	7796											
GMPS	8833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	155654202	155654202	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgggacccacttcaaaagcAgccttcatgccagagatctg	11	8	9	13	1	3	1	2	0	1	1	4	3	3	2	3	1	3	1	3	1	2	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:155654202A>T	ENST00000496455.2	+	15	2218	c.1883A>T	c.(1882-1884)cAg>cTg	p.Q628L	GMPS_ENST00000295920.7_Missense_Mutation_p.Q529L	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	628					glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	CTTCAAAAGCAGCCTTCATGC	0.443			T	MLL	AML																																p.Q628L	Ovarian(153;896 1876 4149 15499 28134)	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS-229	0			c.A1883T						.						128	120	122					3																	155654202		1870	4103	5973	SO:0001583	missense	8833	exon15			AAAAGCAGCCTTC	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"GMP synthase"	600358	"guanine monphosphate synthetase"			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.1883A>T	3.37:g.155654202A>T	ENSP00000419851:p.Gln628Leu	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	165	49	NM_003875	0	0	28	49	21	A8K639|B4DXV7|F8W720	Missense_Mutation	SNP	ENST00000496455.2	37	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.524899	0.44969	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.53	5.53	0.82687	GMP synthase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58308	0.2113	L	0.55990	1.75	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.53954	-0.8365	9	0.30854	T	0.27	-12.4699	15.6641	0.77213	1.0:0.0:0.0:0.0	.	529;628	F8W720;P49915	.;GUAA_HUMAN	L	628;529;577;628	.	ENSP00000295920:Q529L	Q	+	2	0	GMPS	157136896	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.800000	0.91900	2.086000	0.62901	0.459000	0.35465	CAG	.		0.443	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2			T	155654202	A	T	155654202	3	4	85	1	0	0	0	0	1	0	0	0	6518	188	7	5	1941	5	GMPS	3	155654202	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	104196580	155654202	42368228	11	7797											
PRKCI	5584	hgsc.bcm.edu;broad.mit.edu	37	chr3	169940480	169940480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccgacccagagggacagcaGcaccatgtcccacacggtcg	10	3	12	16	3	0	1	0	0	0	1	2	3	1	2	4	2	2	2	4	2	0	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:169940480G>A	ENST00000295797.4	+	1	328	c.23G>A	c.(22-24)aGc>aAc	p.S8N		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	8	Regulatory domain.|Required for interaction with RAB2.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	AGGGACAGCAGCACCATGTCC	0.731																																					p.S8N		.											.	PRKCI-1378	0			c.G23A						.						20	18	19					3																	169940480		2190	4295	6485	SO:0001583	missense	5584	exon1			ACAGCAGCACCAT		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.23G>A	3.37:g.169940480G>A	ENSP00000295797:p.Ser8Asn	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_002740	0	0	2	2	0	D3DNQ4|Q8WW06	Missense_Mutation	SNP	ENST00000295797.4	37	CCDS3212.2	.	.	.	.	.	.	.	.	.	.	G	11.48	1.650664	0.29336	.	.	ENSG00000163558	ENST00000295797	T	0.68765	-0.35	3.88	2.98	0.34508	.	0.135420	0.44483	U	0.000449	T	0.38612	0.1047	N	0.03608	-0.345	0.24090	N	0.995912	B	0.02656	0.0	B	0.01281	0.0	T	0.18209	-1.0344	9	.	.	.	.	10.6095	0.45412	0.0:0.1966:0.8033:0.0	.	8	P41743	KPCI_HUMAN	N	8	ENSP00000295797:S8N	.	S	+	2	0	PRKCI	171423174	1.000000	0.71417	0.996000	0.52242	0.287000	0.27160	1.154000	0.31688	0.711000	0.32018	0.411000	0.27672	AGC	.		0.731	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		A	169940480	G	A	169940480	3	1	85	1	0	0	0	0	1	0	0	0	12543	971	34	2	25	2	PRKCI	3	169940480	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	14286278	169940480	28081950	12	7798											
MAP3K13	9175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	185146747	185146747	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcaggtcaggcagtggCagtggtgggtttcttgaagg	7	11	17	6	0	3	1	2	1	1	0	3	1	3	1	0	6	1	4	0	6	1	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:185146747C>T	ENST00000265026.3	+	2	712	c.378C>T	c.(376-378)ggC>ggT	p.G126G	MAP3K13_ENST00000424227.1_Silent_p.G126G|MAP3K13_ENST00000535426.1_Intron|MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000443863.1_Intron	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			CAGGCAGTGGCAGTGGTGGGT	0.493																																					p.G126G		.											.	MAP3K13-548	0			c.C378T						.						93	94	94					3																	185146747		2203	4300	6503	SO:0001819	synonymous_variant	9175	exon2			CAGTGGCAGTGGT	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.378C>T	3.37:g.185146747C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	94	27	NM_004721	0	0	3	6	3		Silent	SNP	ENST00000265026.3	37	CCDS3270.1																																																																																			.		0.493	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		T	185146747	C	T	185146747	2	4	85	1	0	0	0	0	0	0	0	1	9272	697	25	2		2	MAP3K13	3	185146747	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	15206267	185146747	12875683	13	7799											
DOK7	285489	broad.mit.edu	37	chr4	3478168	3478168	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgtcttggccagggacaTccccccggctgtcacggggc	4	7	13	17	3	2	0	1	0	1	0	4	1	3	1	5	5	0	1	5	5	0	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:3478168T>C	ENST00000340083.5	+	4	496	c.431T>C	c.(430-432)aTc>aCc	p.I144T	DOK7_ENST00000507039.1_Missense_Mutation_p.I144T|DOK7_ENST00000389653.2_Missense_Mutation_p.I144T	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	144	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GCCAGGGACATCCCCCCGGCT	0.632																																					p.I144T													.	DOK7-91	0			c.T431C						.						93	79	84					4																	3478168		2203	4299	6502	SO:0001583	missense	285489	exon4			GGGACATCCCCCC	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"chromosome 4 open reading frame 25"	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.431T>C	4.37:g.3478168T>C	ENSP00000344432:p.Ile144Thr	Somatic	113	1		WXS	Illumina HiSeq	Phase_I	105	3	NM_001164673	0	0	2	2	0	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	.	.	.	.	.	.	.	.	.	.	T	16.26	3.072772	0.55646	.	.	ENSG00000175920	ENST00000389653;ENST00000507039;ENST00000340083	T;T;T	0.69040	-0.37;-0.37;-0.37	4.42	4.42	0.53409	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (2);	0.536026	0.19327	N	0.117000	T	0.57403	0.2051	L	0.43152	1.355	0.28966	N	0.88953	B	0.30406	0.278	B	0.30251	0.113	T	0.52726	-0.8537	10	0.25751	T	0.34	-2.7144	12.845	0.57825	0.0:0.0:0.0:1.0	.	144	Q18PE1	DOK7_HUMAN	T	144	ENSP00000374304:I144T;ENSP00000423614:I144T;ENSP00000344432:I144T	ENSP00000344432:I144T	I	+	2	0	DOK7	3447966	0.465000	0.25815	0.801000	0.32222	0.978000	0.69477	3.432000	0.52824	1.625000	0.50366	0.402000	0.26972	ATC	.		0.632	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660		C	3478168	T	C	3478168	3	2	85	1	0	0	0	0	1	0	0	0	4713	1435	50	3	445	3	DOK7	4	3478168	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		3478168	187676108	14	7800											
WFS1	7466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	6303094	6303094	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atggcacagctgaggaatttCaagggcacctactgctacct	11	9	10	11	0	1	1	1	1	0	0	1	2	1	2	2	3	4	4	2	3	4	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:6303094C>T	ENST00000226760.1	+	8	1742	c.1572C>T	c.(1570-1572)ttC>ttT	p.F524F	WFS1_ENST00000503569.1_Silent_p.F524F	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	524					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		TGAGGAATTTCAAGGGCACCT	0.597																																					p.F524F		.											.	WFS1-91	0			c.C1572T						.						119	105	109					4																	6303094		2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			GAATTTCAAGGGC	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.1572C>T	4.37:g.6303094C>T		Somatic	223	0		WXS	Illumina HiSeq	Phase_I	196	79	NM_001145853	0	0	20	31	11	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1																																																																																			.		0.597	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			T	6303094	C	T	6303094	2	4	85	1	0	0	0	0	0	0	0	1	17393	825	29	2		2	WFS1	4	6303094	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	2824926	6303094	184851182	15	7801											
ADAMTS3	9508	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	73280662	73280662	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagggttcaatgaaatactcTtcattatcactttttatcat	13	17	4	7	0	5	1	4	1	1	0	5	1	5	1	0	1	1	1	0	1	6	7	rs374567996		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:73280662T>A	ENST00000286657.4	-	4	567	c.531A>T	c.(529-531)gaA>gaT	p.E177D		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	177					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGAAATACTCTTCATTATCAC	0.353																																					p.E177D	NSCLC(168;1941 2048 2918 13048 43078)												.	ADAMTS3-651	0			c.A531T						.						132	132	132					4																	73280662		2203	4300	6503	SO:0001583	missense	9508	exon4			ATACTCTTCATTA	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"ADAM metallopeptidases with thrombospondin type 1 motif"	219	protein-coding gene	gene with protein product		605011	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.531A>T	4.37:g.73280662T>A	ENSP00000286657:p.Glu177Asp	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	144	15	NM_014243	0	0	1	1	0	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458851	0.43634	.	.	ENSG00000156140	ENST00000286657	T	0.06933	3.24	5.15	3.96	0.45880	Peptidase M12B, propeptide (1);	0.084546	0.43416	N	0.000568	T	0.05044	0.0135	N	0.20357	0.565	0.31403	N	0.676395	B	0.02656	0.0	B	0.04013	0.001	T	0.28522	-1.0041	10	0.14252	T	0.57	.	8.6456	0.34003	0.7492:0.0:0.0:0.2508	.	177	O15072	ATS3_HUMAN	D	177	ENSP00000286657:E177D	ENSP00000286657:E177D	E	-	3	2	ADAMTS3	73499526	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.693000	0.37742	0.792000	0.33850	0.533000	0.62120	GAA	.		0.353	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			A	73280662	T	A	73280662	3	1	85	1	0	0	0	0	1	0	0	0	267	1606	56	5	3162	5	ADAMTS3	4	73280662	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	66977568	73280662	117873614	16	7802											
MAML3	55534	hgsc.bcm.edu;broad.mit.edu	37	chr4	140811108	140811108	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgctgctgctgctgttgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:140811108C>T	ENST00000509479.2	-	2	2338	c.1482G>A	c.(1480-1482)caG>caA	p.Q494Q	MAML3_ENST00000398940.1_Silent_p.Q33Q|MAML3_ENST00000327122.5_Silent_p.Q338Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.537																																					p.Q494Q		.											.	MAML3-455	0			c.G1482A						.						14	19	17					4																	140811108		2165	4272	6437	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1482G>A	4.37:g.140811108C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_018717	0	1	889	901	11		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.		0.537	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811108	C	T	140811108	2	4	85	1	0	0	0	0	0	0	0	1	9232	796	28	2		2	MAML3	4	140811108	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	67530446	140811108	50343168	17	7803											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	151935707	151935707	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcagagacaatgcaccccCttcagtaggggtttcttctc	8	13	8	12	0	4	1	2	0	2	1	5	2	4	1	2	2	1	3	2	2	2	5			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:151935707C>A	ENST00000357115.3	-	2	331	c.88G>T	c.(88-90)Ggg>Tgg	p.G30W	LRBA_ENST00000535741.1_Missense_Mutation_p.G30W|LRBA_ENST00000510413.1_Missense_Mutation_p.G30W|LRBA_ENST00000507224.1_Missense_Mutation_p.G30W	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	30						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AATGCACCCCCTTCAGTAGGG	0.537																																					p.G30W		.											.	LRBA-157	0			c.G88T						.						63	53	56					4																	151935707		2203	4300	6503	SO:0001583	missense	987	exon2			CACCCCCTTCAGT	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.88G>T	4.37:g.151935707C>A	ENSP00000349629:p.Gly30Trp	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	60	23	NM_006726	0	0	6	10	4	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529711	0.64860	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.56444	0.88;1.03;0.88;0.46	5.33	5.33	0.75918	.	1.239200	0.06405	U	0.719521	T	0.52386	0.1731	L	0.47716	1.5	0.37618	D	0.921196	P;P;P	0.49447	0.876;0.924;0.924	B;B;B	0.43360	0.219;0.417;0.391	T	0.50432	-0.8829	10	0.48119	T	0.1	.	11.3073	0.49342	0.0:0.9149:0.0:0.0851	.	30;30;30	P50851;Q6P1X2;P50851-2	LRBA_HUMAN;.;.	W	30	ENSP00000446299:G30W;ENSP00000421552:G30W;ENSP00000349629:G30W;ENSP00000422180:G30W	ENSP00000349629:G30W	G	-	1	0	LRBA	152155157	0.031000	0.19500	0.961000	0.40146	0.587000	0.36485	1.159000	0.31749	2.514000	0.84764	0.555000	0.69702	GGG	.		0.537	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151935707	C	A	151935707	3	1	85	1	0	0	0	0	1	0	0	0	8956	681	24	4	8731	4	LRBA	4	151935707	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	11124599	151935707	39218569	18	7804											
TRIM2	23321	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	154237027	154237027	+	Frame_Shift_Del	DEL	G	G	-																															caaaagtcgttttggcatacGgggacgctctccggggcagc																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:154237027delG	ENST00000437508.2	+	8	1778	c.1577delG	c.(1576-1578)cggfs	p.R526fs	TRIM2_ENST00000338700.5_Frame_Shift_Del_p.R553fs	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	526					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TTTGGCATACGGGGACGCTCT	0.463																																					p.R553fs		.											.	TRIM2-650	0			c.1658delG						.						80	90	87					4																	154237027		2203	4300	6503	SO:0001589	frameshift_variant	23321	exon8			.	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.1577delG	4.37:g.154237027delG	ENSP00000415812:p.Arg526fs	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	136	52	NM_015271	0	0	0	0	0	D3DP09|O60272|Q9BSI9|Q9UFZ1	Frame_Shift_Del	DEL	ENST00000437508.2	37	CCDS47147.1																																																																																			.		0.463	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			-	154237027	G	-	154237027	7	5	85	1	0	1	0	1	0	0	0	0	16527	1116	39	0	1688	0	TRIM2	4	154237027	Frame_Shift_Del	DEL	G	TCGA-BQ-7053-01A-11D-1961-08	2301320	154237027	36917249	19	7805											
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	163211	163211	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgggaacctgcgcaaccActgtccggcctccctggacg	6	6	12	17	3	0	0	0	0	0	0	2	2	2	2	6	3	3	1	6	3	2	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:163211A>G	ENST00000283426.6	+	11	2006	c.1956A>G	c.(1954-1956)ccA>ccG	p.P652P		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	652							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CTGCGCAACCACTGTCCGGCC	0.667																																					p.P652P		.											.	PLEKHG4B-228	0			c.A1956G						.						11	11	11					5																	163211		2170	4268	6438	SO:0001819	synonymous_variant	153478	exon11			GCAACCACTGTCC	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1956A>G	5.37:g.163211A>G		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	12	6	NM_052909	0	0	0	0	0		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			.		0.667	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		G	163211	A	G	163211	2	3	85	1	0	0	0	0	0	0	0	1	12098	146	6	3		3	PLEKHG4B	5	163211	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		163211	180752049	20	7806											
SLC6A18	348932	broad.mit.edu	37	chr5	1245991	1245991	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcgcgtcaggagaagcTctacccgggctgggcgcgcg	5	5	15	16	6	2	1	1	0	1	1	3	2	2	1	3	3	2	2	3	3	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:1245991T>G	ENST00000324642.3	+	12	1808	c.1685T>G	c.(1684-1686)cTc>cGc	p.L562R		NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	562					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CAGGAGAAGCTCTACCCGGGC	0.711																																					p.L562R													.	SLC6A18-91	0			c.T1685G						.						20	22	21					5																	1245991		2200	4296	6496	SO:0001583	missense	348932	exon12			AGAAGCTCTACCC	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"Solute carriers"	26441	protein-coding gene	gene with protein product		610300	"solute carrier family 6 (neurotransmitter transporter), member 18", "solute carrier family 6, member 18"			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1685T>G	5.37:g.1245991T>G	ENSP00000323549:p.Leu562Arg	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	24	4	NM_182632	0	0	0	0	0		Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	T	1.184	-0.637176	0.03557	.	.	ENSG00000164363	ENST00000324642	T	0.74947	-0.89	4.3	0.531	0.17108	.	1.329440	0.05175	N	0.500186	T	0.66886	0.2835	L	0.40543	1.245	0.09310	N	0.999999	P	0.36027	0.533	B	0.40038	0.317	T	0.50039	-0.8874	10	0.15499	T	0.54	.	7.945	0.29980	0.0:0.1401:0.0:0.8599	.	562	Q96N87	S6A18_HUMAN	R	562	ENSP00000323549:L562R	ENSP00000323549:L562R	L	+	2	0	SLC6A18	1298991	0.000000	0.05858	0.002000	0.10522	0.059000	0.15707	-0.024000	0.12435	-0.079000	0.12707	0.254000	0.18369	CTC	.		0.711	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632		G	1245991	T	G	1245991	3	3	85	1	0	0	0	0	1	0	0	0	14713	1551	54	5	1731	5	SLC6A18	5	1245991	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	1082780	1245991	179669269	21	7807											
XRCC4	7518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82406899	82406899	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gacatggcaatggaaaaaggGaaatatgttggtgaactgag	16	8	14	3	0	0	2	0	2	0	0	0	5	0	4	0	4	1	2	0	4	6	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:82406899G>T	ENST00000511817.1	+	3	272	c.192G>T	c.(190-192)ggG>ggT	p.G64G	XRCC4_ENST00000338635.6_Silent_p.G64G|XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Silent_p.G64G|XRCC4_ENST00000282268.3_Silent_p.G64G			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	64					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		TGGAAAAAGGGAAATATGTTG	0.338								Non-homologous end-joining																													p.G64G		.											.	XRCC4-229	0			c.G192T						.						98	95	96					5																	82406899		2203	4300	6503	SO:0001819	synonymous_variant	7518	exon3			AAAAGGGAAATAT	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"X-ray repair, complementing defective, repair in Chinese hamster", "DNA repair protein XRCC4"	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.192G>T	5.37:g.82406899G>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	53	22	NM_003401	0	0	5	5	0	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	37	CCDS4059.1																																																																																			.		0.338	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		T	82406899	G	T	82406899	2	4	85	1	0	0	0	0	0	0	0	1	17488	1161	41	4		4	XRCC4	5	82406899	Silent	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	81160908	82406899	98508361	22	7808											
ERAP1	51752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	96139212	96139212	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtacgggagcccgacaaGgaggggctcgggagccagca	9	4	18	10	3	0	0	0	0	0	0	1	4	0	3	2	5	4	3	2	5	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:96139212G>A	ENST00000443439.2	-	2	484	c.418C>T	c.(418-420)Ctt>Ttt	p.L140F	CTD-2260A17.3_ENST00000606656.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.L140F|CTD-2260A17.3_ENST00000606346.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	140					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		AGCCCGACAAGGAGGGGCTCG	0.557																																					p.L140F		.											.	ERAP1-70	0			c.C418T						.						63	70	68					5																	96139212		2203	4300	6503	SO:0001583	missense	51752	exon2			CGACAAGGAGGGG	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"aminopeptidase regulator of TNFR1 shedding", "adipocyte-derived leucine aminopeptidase", "puromycin-insensitive leucyl-specific aminopeptidase"	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.418C>T	5.37:g.96139212G>A	ENSP00000406304:p.Leu140Phe	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	101	40	NM_001198541	0	0	16	27	11	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	G	4.542	0.100606	0.08731	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02763	4.17;4.17	5.51	2.68	0.31781	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.757856	0.12763	N	0.441158	T	0.03564	0.0102	L	0.52011	1.625	0.09310	N	1	B;B	0.15719	0.014;0.004	B;B	0.23852	0.049;0.019	T	0.48456	-0.9034	10	0.11182	T	0.66	.	9.253	0.37566	0.0:0.2989:0.4675:0.2337	.	140;140	Q9NZ08;Q9NZ08-2	ERAP1_HUMAN;.	F	140	ENSP00000296754:L140F;ENSP00000406304:L140F	ENSP00000296754:L140F	L	-	1	0	ERAP1	96164968	0.156000	0.22821	0.002000	0.10522	0.010000	0.07245	0.894000	0.28350	0.243000	0.21327	0.561000	0.74099	CTT	.		0.557	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		A	96139212	G	A	96139212	3	1	85	1	0	0	0	0	1	0	0	0	5216	1000	35	2	2512	2	ERAP1	5	96139212	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	13732313	96139212	84776048	23	7809											
ADAMTS19	171019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	129030431	129030431	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaaaggaagacaacagTgtcctgcacaaaaatcatga	19	5	10	7	0	1	3	1	1	0	2	2	5	2	4	1	2	2	1	1	2	5	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:129030431T>G	ENST00000274487.4	+	19	2964	c.2819T>G	c.(2818-2820)gTg>gGg	p.V940G	ADAMTS19_ENST00000509467.1_3'UTR|CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	940	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AAGACAACAGTGTCCTGCACA	0.348																																					p.V940G		.											.	ADAMTS19-295	0			c.T2819G						.						85	79	81					5																	129030431		2203	4300	6503	SO:0001583	missense	171019	exon19			CAACAGTGTCCTG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2819T>G	5.37:g.129030431T>G	ENSP00000274487:p.Val940Gly	Somatic	53	2		WXS	Illumina HiSeq	Phase_I	69	22	NM_133638	0	0	0	0	0		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111892	0.56398	.	.	ENSG00000145808	ENST00000274487	T	0.64260	-0.09	4.07	4.07	0.47477	.	0.000000	0.64402	D	0.000008	T	0.80633	0.4660	H	0.94423	3.535	0.80722	D	1	D	0.56287	0.975	P	0.55455	0.776	D	0.86836	0.2014	9	.	.	.	.	14.0973	0.65032	0.0:0.0:0.0:1.0	.	940	Q8TE59	ATS19_HUMAN	G	940	ENSP00000274487:V940G	.	V	+	2	0	ADAMTS19	129058330	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	5.684000	0.68197	2.068000	0.61886	0.454000	0.30748	GTG	.		0.348	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	129030431	T	G	129030431	3	3	85	1	0	0	0	0	1	0	0	0	264	1696	59	5	2893	5	ADAMTS19	5	129030431	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	32891219	129030431	51884829	24	7810											
LY6G6F	259215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31677862	31677862	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggctgggacatgccttggAttctgatgctgctgctcaca	6	11	13	11	1	2	1	1	1	1	0	2	3	2	3	1	3	4	4	1	3	0	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:31677862A>T	ENST00000375832.4	+	4	728	c.706A>T	c.(706-708)Att>Ttt	p.I236F	MEGT1_ENST00000503322.1_Missense_Mutation_p.I236F|LY6G6F_ENST00000556581.1_Missense_Mutation_p.I236F|XXbac-BPG32J3.20_ENST00000461287.1_Intron	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						CATGCCTTGGATTCTGATGCT	0.617																																					p.I236F		.											.	LY6G6F-567	0			c.A706T						.						93	67	76					6																	31677862		1511	2708	4219	SO:0001583	missense	259215	exon4			CCTTGGATTCTGA		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"Immunoglobulin superfamily / V-set domain containing"	13933	protein-coding gene	gene with protein product		611404	"chromosome 6 open reading frame 21"	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.706A>T	6.37:g.31677862A>T	ENSP00000364992:p.Ile236Phe	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	54	17	NM_001003693	0	0	0	0	0	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015117	0.35511	.	.	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.26957	1.99;1.7;1.99	5.25	4.09	0.47781	.	0.098536	0.44688	D	0.000436	T	0.20981	0.0505	M	0.66939	2.045	0.32179	N	0.580661	D;P	0.54047	0.964;0.906	P;P	0.51101	0.659;0.546	T	0.12319	-1.0552	10	0.87932	D	0	-13.2059	7.687	0.28546	0.9038:0.0:0.0962:0.0	.	236;236	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	F	236	ENSP00000452432:I236F;ENSP00000364992:I236F;ENSP00000421232:I236F	ENSP00000364992:I236F	I	+	1	0	XXbac-BPG32J3.19;LY6G6F	31785841	1.000000	0.71417	1.000000	0.80357	0.262000	0.26303	1.214000	0.32419	0.844000	0.35094	0.477000	0.44152	ATT	.		0.617	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693		T	31677862	A	T	31677862	3	4	85	1	0	0	0	0	1	0	0	0	9121	333	12	5	720	5	LY6G6F	6	31677862	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		31677862	139437205	25	7811											
GSTA2	2939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	52617715	52617715	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcaaggcaagcttggcatcTtgttcctcaggttgactaaa	11	12	9	9	0	3	1	2	1	1	0	4	1	4	1	1	3	1	5	1	3	4	5	rs200252041		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:52617715T>A	ENST00000493422.1	-	5	506	c.351A>T	c.(349-351)caA>caT	p.Q117H		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	117	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	GCTTGGCATCTTGTTCCTCAG	0.393																																					p.Q117H		.											.	GSTA2-91	0			c.A351T						.						240	229	233					6																	52617715		2203	4300	6503	SO:0001583	missense	2939	exon5			GGCATCTTGTTCC	AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"Glutathione S-transferases / Soluble"	4627	protein-coding gene	gene with protein product		138360	"glutathione S-transferase A2"	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.351A>T	6.37:g.52617715T>A	ENSP00000420168:p.Gln117His	Somatic	329	0		WXS	Illumina HiSeq	Phase_I	366	132	NM_000846	0	0	0	0	0	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	37	CCDS4944.1	.	.	.	.	.	.	.	.	.	.	t	10.44	1.349542	0.24426	.	.	ENSG00000244067	ENST00000493422	T	0.02067	4.47	2.26	2.26	0.28386	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.539313	0.17882	N	0.158839	T	0.01092	0.0036	L	0.31926	0.97	0.09310	N	1	B	0.28233	0.204	B	0.38056	0.264	T	0.45775	-0.9238	10	0.87932	D	0	.	8.464	0.32944	0.0:0.0:0.0:1.0	.	117	P09210	GSTA2_HUMAN	H	117	ENSP00000420168:Q117H	ENSP00000420168:Q117H	Q	-	3	2	GSTA2	52725674	0.000000	0.05858	0.030000	0.17652	0.008000	0.06430	-0.493000	0.06459	1.310000	0.45006	0.254000	0.18369	CAA	T|1.000;C|0.000		0.393	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846		A	52617715	T	A	52617715	3	1	85	1	0	0	0	0	1	0	0	0	6852	1606	56	5	329	5	GSTA2	6	52617715	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	20939853	52617715	118497352	26	7812											
TMEM30A	55754	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	75975041	75975042	+	Frame_Shift_Del	DEL	AT	AT	-																															aattagacagtccataatacAtaaacacgttgccctagaga																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:75975041_75975042delAT	ENST00000230461.6	-	3	687_688	c.358_359delAT	c.(358-360)atgfs	p.M120fs	TMEM30A_ENST00000475111.2_Frame_Shift_Del_p.M84fs|TMEM30A_ENST00000370050.5_Start_Codon_Del	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	120					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCCATAATACATAAACACGTTG	0.327																																					p.120_120del		.											.	TMEM30A-90	0			c.358_359del						.																																			SO:0001589	frameshift_variant	55754	exon3			.	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"chromosome 6 open reading frame 67"	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.358_359delAT	6.37:g.75975041_75975042delAT	ENSP00000230461:p.Met120fs	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	35	14	NM_018247	0	0	0	0	0	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Frame_Shift_Del	DEL	ENST00000230461.6	37	CCDS4983.1																																																																																			.		0.327	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		-	75975042	AT	-	75975041	7	5	85	1	0	1	0	1	0	0	0	0	16185	217	8	0	746	0	TMEM30A	6	75975041	Frame_Shift_Del	DEL	AT	TCGA-BQ-7053-01A-11D-1961-08	23357326	75975041	95140026	27	7813											
CPVL	54504	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	29135764	29135764	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcccatgttccacaaagaGtccaaacatggatgaacctc	14	7	8	12	0	0	2	0	1	0	1	3	3	2	3	4	2	2	1	4	2	3	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr7:29135764G>T	ENST00000409850.1	-	8	1004	c.358C>A	c.(358-360)Ctc>Atc	p.L120I	CPVL_ENST00000265394.5_Missense_Mutation_p.L120I|CPVL_ENST00000396276.3_Missense_Mutation_p.L120I|CPVL_ENST00000488891.2_5'UTR			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	120						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						TCCACAAAGAGTCCAAACATG	0.468																																					p.L120I		.											.	CPVL-92	0			c.C358A						.						177	165	169					7																	29135764		2203	4300	6503	SO:0001583	missense	54504	exon4			CAAAGAGTCCAAA	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"carboxypeptidase WUG", "vitellogenic carboxypeptidase-like protein", "CP-Mac carboxypeptidase"	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.358C>A	7.37:g.29135764G>T	ENSP00000387164:p.Leu120Ile	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	218	71	NM_019029	1	0	250	380	129	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	37	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911407	0.92178	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000409850;ENST00000542995;ENST00000448959;ENST00000458405;ENST00000447426	D;D;D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.93789	0.8014	M	0.85777	2.775	0.80722	D	1	D	0.69078	0.997	D	0.65573	0.936	D	0.93612	0.6940	10	0.46703	T	0.11	-0.6878	18.7662	0.91874	0.0:0.0:1.0:0.0	.	120	Q9H3G5	CPVL_HUMAN	I	120;120;120;4;50;4;50	ENSP00000265394:L120I;ENSP00000379572:L120I;ENSP00000387164:L120I;ENSP00000409036:L50I;ENSP00000417015:L4I;ENSP00000395690:L50I	ENSP00000265394:L120I	L	-	1	0	CPVL	29102289	1.000000	0.71417	0.998000	0.56505	0.918000	0.54935	6.732000	0.74790	2.519000	0.84933	0.491000	0.48974	CTC	.		0.468	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029		T	29135764	G	T	29135764	3	4	85	1	0	0	0	0	1	0	0	0	3841	1029	36	4	1112	4	CPVL	7	29135764	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		29135764	130002899	28	7814											
POMZP3	22932	hgsc.bcm.edu	37	chr7	76255360	76255360	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtcaggaggggcgatcctcaGagtcactgggctacacacca	10	6	13	12	1	3	1	3	0	0	1	4	3	4	2	2	4	1	1	2	4	1	1	rs200164764		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr7:76255360G>C	ENST00000310842.4	-	2	706	c.22C>G	c.(22-24)Ctg>Gtg	p.L8V	UPK3B_ENST00000419923.2_Intron|POMZP3_ENST00000275569.4_Missense_Mutation_p.L8V|UPK3B_ENST00000443097.2_Intron|AC004980.7_ENST00000418663.1_RNA	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	8										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				GCGATCCTCAGAGTCACTGGG	0.512																																					p.L8V		.											.	POMZP3-90	0			c.C22G						.						169	124	139					7																	76255360		2202	4299	6501	SO:0001583	missense	22932	exon2			TCCTCAGAGTCAC	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"POM-ZP3 fusion protein", "POM121/ZP3 fusion protein"	600587	"POM (POM121 rat homolog) and ZP3 fusion", "POM (POM121 homolog, rat) and ZP3 fusion"			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.22C>G	7.37:g.76255360G>C	ENSP00000309233:p.Leu8Val	Somatic	32	2		WXS	Illumina HiSeq	Phase_I	43	5	NM_152992	0	0	9	88	79	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	37	CCDS43606.1	.	.	.	.	.	.	.	.	.	.	N	6.841	0.524357	0.13066	.	.	ENSG00000146707	ENST00000275569;ENST00000310842;ENST00000454397	T;T	0.16073	2.68;2.37	0.694	0.694	0.18062	.	1.516020	0.04115	N	0.315408	T	0.02649	0.0080	N	0.00063	-2.32	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.44406	-0.9330	10	0.02654	T	1	.	4.5941	0.12322	0.0:0.5861:0.4139:0.0	rs1056120;rs3196740;rs17422445	8	Q6PJE2	POZP3_HUMAN	V	8	ENSP00000309233:L8V;ENSP00000405319:L8V	ENSP00000275569:L8V	L	-	1	2	POMZP3	76093296	0.946000	0.32159	0.111000	0.21465	0.250000	0.25880	0.979000	0.29500	-0.107000	0.12088	-0.363000	0.07495	CTG	.		0.512	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230		C	76255360	G	C	76255360	3	2	85	1	0	0	0	0	1	0	0	0	12273	933	33	4	568	4	POMZP3	7	76255360	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	47119596	76255360	82883303	29	7815											
FZD1	8321	hgsc.bcm.edu	37	chr7	90894862	90894862	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagttcccggtgcacggcGccggcgagctgtgcgtgggc	5	6	18	12	6	0	1	0	0	0	1	1	2	1	1	2	4	3	3	2	4	1	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr7:90894862G>C	ENST00000287934.2	+	1	1080	c.667G>C	c.(667-669)Gcc>Ccc	p.A223P		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	223	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			GGTGCACGGCGCCGGCGAGCT	0.682																																					p.A223P		.											.	FZD1-658	0			c.G667C						.						26	29	28					7																	90894862		2200	4299	6499	SO:0001583	missense	8321	exon1			CACGGCGCCGGCG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.667G>C	7.37:g.90894862G>C	ENSP00000287934:p.Ala223Pro	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_003505	0	0	44	44	0	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	37	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.725537	0.30593	.	.	ENSG00000157240	ENST00000287934	T	0.79247	-1.25	4.79	4.79	0.61399	Frizzled domain (5);	0.000000	0.64402	D	0.000005	T	0.58836	0.2150	N	0.03016	-0.435	0.47659	D	0.999484	B	0.17465	0.022	B	0.21708	0.036	T	0.55464	-0.8137	10	0.30078	T	0.28	.	18.0269	0.89272	0.0:0.0:1.0:0.0	.	223	Q9UP38	FZD1_HUMAN	P	223	ENSP00000287934:A223P	ENSP00000287934:A223P	A	+	1	0	FZD1	90732798	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	5.130000	0.64745	2.488000	0.83962	0.561000	0.74099	GCC	.		0.682	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		C	90894862	G	C	90894862	3	2	85	1	0	0	0	0	1	0	0	0	6147	1087	38	4	669	4	FZD1	7	90894862	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	14639502	90894862	68243801	30	7816											
ASH2L	9070	broad.mit.edu;bcgsc.ca	37	chr8	37963231	37963231	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgctgctccgacagttgagCccagttccggggaggctgaa	7	8	14	12	2	0	2	0	2	0	0	2	4	2	3	3	3	3	5	3	3	1	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr8:37963231C>T	ENST00000343823.6	+	1	472	c.163C>T	c.(163-165)Ccc>Tcc	p.P55S	ASH2L_ENST00000428278.2_5'Flank|ASH2L_ENST00000250635.7_5'UTR|ASH2L_ENST00000545394.1_5'UTR|ASH2L_ENST00000521652.1_5'Flank	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	55					cellular response to DNA damage stimulus (GO:0006974)|hemopoiesis (GO:0030097)|histone H3-K4 methylation (GO:0051568)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)	19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				GACAGTTGAGCCCAGTTCCGG	0.692																																					p.P55S													.	ASH2L-131	0			c.C163T						.						22	24	24					8																	37963231		2198	4294	6492	SO:0001583	missense	9070	exon1			GTTGAGCCCAGTT	AF056717	CCDS6101.1, CCDS47840.1, CCDS59100.1, CCDS64872.1	8p11.2	2013-01-28	2001-11-28		ENSG00000129691	ENSG00000129691		"Zinc fingers, PHD-type"	744	protein-coding gene	gene with protein product		604782	"ash2 (absent, small, or homeotic, Drosophila, homolog)-like"	ASH2L1		10393421	Standard	NM_004674		Approved	ASH2L2, ASH2, Bre2	uc003xkt.5	Q9UBL3	OTTHUMG00000164016	ENST00000343823.6:c.163C>T	8.37:g.37963231C>T	ENSP00000340896:p.Pro55Ser	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	48	11	NM_004674	0	0	14	27	13	A8K7C3|D3DSW9|O60659|O60660|Q96B62	Missense_Mutation	SNP	ENST00000343823.6	37	CCDS6101.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.578337	0.86645	.	.	ENSG00000129691	ENST00000343823;ENST00000517719	T	0.65364	-0.15	5.78	3.95	0.45737	.	0.520604	0.19855	N	0.104556	T	0.38480	0.1042	N	0.08118	0	0.80722	D	1	B	0.20052	0.041	B	0.17098	0.017	T	0.12192	-1.0557	10	0.31617	T	0.26	.	8.2137	0.31499	0.0:0.7587:0.1574:0.0839	.	55	Q9UBL3	ASH2L_HUMAN	S	55	ENSP00000340896:P55S	ENSP00000340896:P55S	P	+	1	0	ASH2L	38082388	0.583000	0.26757	0.925000	0.36789	0.745000	0.42441	0.492000	0.22435	0.874000	0.35823	0.655000	0.94253	CCC	.		0.692	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	NM_004674		T	37963231	C	T	37963231	3	4	85	1	0	0	0	0	1	0	0	0	1043	739	26	2	165	2	ASH2L	8	37963231	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		37963231	108400791	31	7817											
EIF3E	3646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	109215296	109215296	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaggcttttggtcttttcAatcacttgctgatagggtga	9	15	11	6	0	3	2	2	2	1	0	3	3	3	2	0	3	1	2	0	3	3	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr8:109215296A>T	ENST00000220849.5	-	12	1277	c.1215T>A	c.(1213-1215)atT>atA	p.I405I	EIF3E_ENST00000519517.1_5'Flank|EIF3E_ENST00000519030.1_Silent_p.I312I	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TGGTCTTTTCAATCACTTGCT	0.393																																					p.I405I	GBM(15;360 410 8460 34179 52246)	.											.	EIF3E-188	0			c.T1215A						.						157	141	147					8																	109215296		2203	4297	6500	SO:0001819	synonymous_variant	3646	exon12			CTTTTCAATCACT	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"eukaryotic translation initiation factor 3, subunit 6 48kDa"	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1215T>A	8.37:g.109215296A>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	112	41	NM_001568	0	0	257	444	187		Silent	SNP	ENST00000220849.5	37	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.431022	0.25726	.	.	ENSG00000104408	ENST00000522352	.	.	.	5.7	3.26	0.37387	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.5683	7.9818	0.30188	0.8114:0.0:0.0671:0.1214	.	.	.	.	R	116	.	.	X	-	1	0	EIF3E	109284472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.959000	0.40412	0.964000	0.38108	0.477000	0.44152	TGA	.		0.393	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		T	109215296	A	T	109215296	2	4	85	1	0	0	0	0	0	0	0	1	5028	126	5	5		5	EIF3E	8	109215296	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	71252065	109215296	37148726	32	7818											
ZHX2	22882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	123965471	123965471	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgagcaggagagagatcgActcctggttctcggagaggc	9	7	16	9	2	1	4	0	1	1	3	4	8	2	4	1	4	1	3	1	4	0	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr8:123965471A>G	ENST00000314393.4	+	3	2556	c.1721A>G	c.(1720-1722)gAc>gGc	p.D574G		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	574					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AGAGAGATCGACTCCTGGTTC	0.512																																					p.D574G	Esophageal Squamous(94;1056 1388 11767 13799 49639)	.											.	ZHX2-227	0			c.A1721G						.						65	67	66					8																	123965471		2203	4300	6503	SO:0001583	missense	22882	exon3			AGATCGACTCCTG	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	18513	protein-coding gene	gene with protein product		609185	"zinc-fingers and homeoboxes 2"			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1721A>G	8.37:g.123965471A>G	ENSP00000314709:p.Asp574Gly	Somatic	78	1		WXS	Illumina HiSeq	Phase_I	94	35	NM_014943	0	0	67	128	61		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.540777	0.45280	.	.	ENSG00000178764	ENST00000314393	D	0.96104	-3.91	5.94	3.48	0.39840	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.047074	0.85682	D	0.000000	D	0.93517	0.7931	M	0.76838	2.35	0.80722	D	1	B	0.19331	0.035	B	0.09377	0.004	D	0.90501	0.4474	10	0.46703	T	0.11	-23.565	8.1252	0.30995	0.8139:0.0:0.0656:0.1204	.	574	Q9Y6X8	ZHX2_HUMAN	G	574	ENSP00000314709:D574G	ENSP00000314709:D574G	D	+	2	0	ZHX2	124034652	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.139000	0.77314	1.079000	0.41038	0.459000	0.35465	GAC	.		0.512	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		G	123965471	A	G	123965471	3	3	85	1	0	0	0	0	1	0	0	0	17708	275	10	3	1723	3	ZHX2	8	123965471	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	14750175	123965471	22398551	33	7819											
FAM83H	286077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144811207	144811207	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgacgtggcccttgaaggActtcccagtgcggcagtagt	7	10	13	11	2	0	2	0	2	0	0	1	3	1	3	2	3	1	2	2	3	2	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr8:144811207A>G	ENST00000388913.3	-	4	792	c.667T>C	c.(667-669)Tcc>Ccc	p.S223P		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	223					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CCCTTGAAGGACTTCCCAGTG	0.652																																					p.S223P		.											.	FAM83H-92	0			c.T667C						.						70	81	77					8																	144811207		2096	4203	6299	SO:0001583	missense	286077	exon4			TGAAGGACTTCCC	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.667T>C	8.37:g.144811207A>G	ENSP00000373565:p.Ser223Pro	Somatic	154	2		WXS	Illumina HiSeq	Phase_I	139	43	NM_198488	0	0	16	35	19	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	a	21.3	4.127238	0.77549	.	.	ENSG00000180921	ENST00000388913	T	0.11930	2.73	5.01	5.01	0.66863	.	0.193102	0.46145	N	0.000314	T	0.30324	0.0761	L	0.57536	1.79	0.39172	D	0.962616	D	0.89917	1.0	D	0.80764	0.994	T	0.05354	-1.0890	10	0.56958	D	0.05	.	9.5807	0.39486	0.8435:0.0:0.0:0.1565	.	223	Q6ZRV2	FA83H_HUMAN	P	223	ENSP00000373565:S223P	ENSP00000373565:S223P	S	-	1	0	FAM83H	144883195	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.965000	0.56788	2.003000	0.58678	0.459000	0.35465	TCC	.		0.652	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		G	144811207	A	G	144811207	3	3	85	1	0	0	0	0	1	0	0	0	5659	275	10	3	2880	3	FAM83H	8	144811207	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	20845736	144811207	1552815	34	7820											
CNTNAP3	79937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	39140600	39140600	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcccagacgggttccctcGgtgcttgtgggcttcacaag	7	9	13	12	2	1	1	1	0	0	1	3	1	2	1	2	3	2	3	2	3	2	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr9:39140600G>A	ENST00000297668.6	-	12	1865	c.1792C>T	c.(1792-1794)Cga>Tga	p.R598*	CNTNAP3_ENST00000358144.2_Nonsense_Mutation_p.R510*|CNTNAP3_ENST00000323947.7_Nonsense_Mutation_p.R505*|CNTNAP3_ENST00000377659.1_Nonsense_Mutation_p.R598*|CNTNAP3_ENST00000377656.2_Nonsense_Mutation_p.R598*	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	598	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GGGTTCCCTCGGTGCTTGTGG	0.468																																					p.R598X		.											.	CNTNAP3-91	0			c.C1792T						.						38	44	42					9																	39140600		2203	4300	6503	SO:0001587	stop_gained	79937	exon12			TCCCTCGGTGCTT	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.1792C>T	9.37:g.39140600G>A	ENSP00000297668:p.Arg598*	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	98	32	NM_033655	0	0	1	1	0	B1AMA0|Q9C0E9	Nonsense_Mutation	SNP	ENST00000297668.6	37	CCDS6616.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.384365	0.82792	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144;ENST00000323947;ENST00000377659	.	.	.	2.85	1.69	0.24217	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	7.9696	0.30119	0.0:0.0:0.2419:0.7581	.	.	.	.	X	598;598;510;505;598	.	ENSP00000297668:R598X	R	-	1	2	CNTNAP3	39130600	0.593000	0.26840	0.377000	0.26055	0.034000	0.12701	0.720000	0.25896	0.328000	0.23435	0.440000	0.28878	CGA	.		0.468	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		A	39140600	G	A	39140600	4	1	85	1	0	0	0	0	0	1	0	0	3654	1124	39	1	2126	1	CNTNAP3	9	39140600	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		39140600	102072831	35	7821											
FLJ46321	389763	broad.mit.edu;bcgsc.ca	37	chr9	84608476	84608476	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccttagaagaggtactacaGattttcaaagcgaaaaatta	17	10	7	7	1	1	3	1	0	0	3	1	4	1	3	1	1	3	1	1	1	8	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr9:84608476G>C	ENST00000344803.2	+	4	3138	c.3091G>C	c.(3091-3093)Gat>Cat	p.D1031H		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1031					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGGTACTACAGATTTTCAAAG	0.458																																					p.D1031H													.	.	0			c.G3091C						.						156	160	159					9																	84608476		1852	4095	5947	SO:0001583	missense	389763	exon4			ACTACAGATTTTC		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3091G>C	9.37:g.84608476G>C	ENSP00000341988:p.Asp1031His	Somatic	301	1		WXS	Illumina HiSeq	Phase_I	362	9	NM_001001670	0	0	0	0	0		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	8.738	0.918353	0.17982	.	.	ENSG00000214929	ENST00000344803	T	0.05855	3.38	0.496	0.496	0.16896	.	.	.	.	.	T	0.04634	0.0126	N	0.14661	0.345	0.09310	N	1	P	0.50272	0.933	P	0.46685	0.524	T	0.45352	-0.9267	8	0.22109	T	0.4	1.4307	.	.	.	.	1031	Q6ZQQ2	F75D1_HUMAN	H	1031	ENSP00000341988:D1031H	ENSP00000341988:D1031H	D	+	1	0	FAM75D1	83798296	0.002000	0.14202	0.003000	0.11579	0.004000	0.04260	1.217000	0.32455	0.533000	0.28675	0.537000	0.68136	GAT	.		0.458	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		C	84608476	G	C	84608476	3	2	85	1	0	0	0	0	1	0	0	0	5951	942	33	4	3105	4	FLJ46321	9	84608476	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	45467876	84608476	56604955	36	7822											
INVS	27130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	103059359	103059359	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccactgcagtaagcaaggccCccaagagtccatccaagggc	12	4	10	15	0	0	1	0	0	0	1	2	1	2	1	5	2	2	3	5	2	4	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr9:103059359C>A	ENST00000262457.2	+	15	3132	c.2947C>A	c.(2947-2949)Ccc>Acc	p.P983T	INVS_ENST00000541287.1_Missense_Mutation_p.P887T|INVS_ENST00000262456.2_Missense_Mutation_p.P813T	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	983					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				AAGCAAGGCCCCCAAGAGTCC	0.498																																					p.P983T		.											.	INVS-92	0			c.C2947A						.						89	83	85					9																	103059359		2203	4300	6503	SO:0001583	missense	27130	exon15			AAGGCCCCCAAGA	AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"Ankyrin repeat domain containing"	17870	protein-coding gene	gene with protein product	"nephrocystin 2"	243305	"nephronophthisis 2 (infantile)"	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.2947C>A	9.37:g.103059359C>A	ENSP00000262457:p.Pro983Thr	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	53	31	NM_014425	0	0	2	36	34	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Missense_Mutation	SNP	ENST00000262457.2	37	CCDS6746.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.983872	0.00443	.	.	ENSG00000119509	ENST00000262457;ENST00000541287;ENST00000262456	T;T;T	0.38722	1.15;1.15;1.12	5.25	-0.716	0.11212	.	0.687064	0.14809	N	0.297151	T	0.16854	0.0405	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.11329	0.006;0.001;0.0	T	0.13899	-1.0492	10	0.56958	D	0.05	.	3.4624	0.07537	0.1837:0.4859:0.231:0.0995	.	887;983;813	F5GZH2;Q9Y283;Q9Y283-2	.;INVS_HUMAN;.	T	983;887;813	ENSP00000262457:P983T;ENSP00000444454:P887T;ENSP00000262456:P813T	ENSP00000262456:P813T	P	+	1	0	INVS	102099180	0.023000	0.18921	0.222000	0.23844	0.317000	0.28152	0.424000	0.21330	0.160000	0.19432	0.650000	0.86243	CCC	.		0.498	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425		A	103059359	C	A	103059359	3	1	85	1	0	0	0	0	1	0	0	0	7808	623	22	4	3001	4	INVS	9	103059359	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	18450883	103059359	38154072	37	7823											
PRKG1	5592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	53227571	53227571	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaattggctattctttacaaCtgtacccggacagcgaccgt	10	11	9	11	3	1	0	0	0	1	0	1	3	1	1	2	2	4	2	2	2	5	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr10:53227571C>G	ENST00000401604.2	+	3	716	c.522C>G	c.(520-522)aaC>aaG	p.N174K	PRKG1_ENST00000373980.4_Missense_Mutation_p.N189K|PRKG1_ENST00000373985.1_Missense_Mutation_p.N162K			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	174	cGMP-binding, high affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTCTTTACAACTGTACCCGGA	0.383																																					p.N189K		.											.	PRKG1-523	0			c.C567G						.						154	141	145					10																	53227571		2203	4300	6503	SO:0001583	missense	5592	exon3			TTACAACTGTACC		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.522C>G	10.37:g.53227571C>G	ENSP00000384200:p.Asn174Lys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	119	40	NM_006258	0	0	2	2	0	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475767	0.84640	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.96940	-4.18;-4.18;-1.92;-1.92	5.79	4.89	0.63831	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.115539	0.56097	D	0.000027	D	0.97983	0.9336	M	0.85462	2.755	0.80722	D	1	D;D;D	0.89917	0.983;1.0;0.998	P;D;D	0.75484	0.82;0.985;0.986	D	0.98576	1.0648	10	0.87932	D	0	-19.8616	12.5809	0.56390	0.0:0.9197:0.0:0.0803	.	174;189;174	B4DT93;Q13976-2;Q13976	.;.;KGP1_HUMAN	K	174;162;189;47	ENSP00000384200:N174K;ENSP00000363097:N162K;ENSP00000363092:N189K;ENSP00000363087:N47K	ENSP00000363087:N47K	N	+	3	2	PRKG1	52897577	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.118000	0.31246	1.450000	0.47717	0.563000	0.77884	AAC	.		0.383	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	53227571	C	G	53227571	3	3	85	1	0	0	0	0	1	0	0	0	12551	564	20	4	847	4	PRKG1	10	53227571	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		53227571	82307176	38	7824											
CDH23	64072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	73406335	73406335	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtacaacatcagcctgtaCgagaacgtcaccgtggggac	11	7	11	12	3	2	1	2	0	0	1	2	3	2	2	2	2	5	2	2	2	4	2	rs549569431	byFrequency	TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr10:73406335C>T	ENST00000224721.6	+	13	1430	c.1425C>T	c.(1423-1425)taC>taT	p.Y475Y	CDH23_ENST00000398809.4_Silent_p.Y470Y|CDH23_ENST00000461841.3_Silent_p.Y515Y|CDH23_ENST00000398842.3_Silent_p.Y470Y|CDH23_ENST00000299366.7_Silent_p.Y515Y	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	470	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TCAGCCTGTACGAGAACGTCA	0.577													C|||	2	0.000399361	0	0	5008	,	,		19433	0		0	False		,,,				2504	0.002				p.Y470Y		.											.	CDH23-563	0			c.C1410T						.						160	169	166					10																	73406335		2132	4248	6380	SO:0001819	synonymous_variant	64072	exon13			CCTGTACGAGAAC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"Cadherins / Cadherin-related"	13733	protein-coding gene	gene with protein product	"cadherin-related family member 23"	605516	"cadherin related 23", "cadherin-like 23"	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1425C>T	10.37:g.73406335C>T		Somatic	235	0		WXS	Illumina HiSeq	Phase_I	219	64	NM_052836	0	0	0	0	0	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				.		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73406335	C	T	73406335	2	4	85	1	0	0	0	0	0	0	0	1	3114	547	19	1		1	CDH23	10	73406335	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	20178764	73406335	62128412	39	7825											
DGKZ	8525	ucsc.edu;bcgsc.ca	37	chr11	46401423	46401423	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagaaggctcaggacaccGagctggccgcctacctggag	9	5	14	13	2	1	1	1	1	0	1	1	5	1	3	4	4	2	2	4	4	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:46401423G>T	ENST00000454345.1	+	32	3405	c.3280G>T	c.(3280-3282)Gag>Tag	p.E1094*	DGKZ_ENST00000343674.6_Nonsense_Mutation_p.E922*|MDK_ENST00000405308.2_5'Flank|DGKZ_ENST00000528615.1_Nonsense_Mutation_p.E684*|DGKZ_ENST00000318201.8_Nonsense_Mutation_p.E883*|DGKZ_ENST00000543978.1_Nonsense_Mutation_p.E258*|DGKZ_ENST00000532868.2_Nonsense_Mutation_p.E910*|DGKZ_ENST00000421244.2_Nonsense_Mutation_p.E906*|MDK_ENST00000395569.4_5'Flank|DGKZ_ENST00000456247.2_Nonsense_Mutation_p.E905*|DGKZ_ENST00000527911.1_Nonsense_Mutation_p.E911*|MDK_ENST00000359803.3_5'Flank|DGKZ_ENST00000395574.3_Nonsense_Mutation_p.E872*|MDK_ENST00000407067.1_5'Flank|MDK_ENST00000395566.4_5'Flank|MDK_ENST00000395565.1_5'Flank	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	1094					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		TCAGGACACCGAGCTGGCCGC	0.697																																					p.E1094X													.	DGKZ-676	0			c.G3280T						.						17	19	18					11																	46401423		2181	4284	6465	SO:0001587	stop_gained	8525	exon32			GACACCGAGCTGG	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"diacylglycerol kinase, zeta 104kDa"			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.3280G>T	11.37:g.46401423G>T	ENSP00000412178:p.Glu1094*	Somatic	28	0		WXS	Illumina HiSeq		13	4	NM_001105540	0	0	51	71	20	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Nonsense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	.	.	.	.	.	.	.	.	.	.	G	38	7.279372	0.98182	.	.	ENSG00000149091	ENST00000343674;ENST00000528615;ENST00000395574;ENST00000532868;ENST00000543978;ENST00000527911;ENST00000456247;ENST00000421244;ENST00000318201;ENST00000454345	.	.	.	3.89	3.89	0.44902	.	0.244651	0.39759	N	0.001278	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	12.9371	0.58320	0.0:0.1641:0.8359:0.0	.	.	.	.	X	922;684;872;871;258;911;905;906;883;1094	.	ENSP00000320340:E883X	E	+	1	0	DGKZ	46357999	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.243000	0.65395	2.164000	0.68074	0.549000	0.68633	GAG	.		0.697	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		T	46401423	G	T	46401423	4	4	85	1	0	0	0	0	0	1	0	0	4485	1059	37	4	3849	4	DGKZ	11	46401423	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		46401423	88605093	40	7826											
SSSCA1	10534	ucsc.edu	37	chr11	65338205	65338205	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggttaccgcatgctgggCgagacgtgtgcggactgcgg	5	7	18	11	7	0	1	0	0	0	1	0	3	0	2	1	4	4	3	1	4	1	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:65338205C>T	ENST00000309328.3	+	2	212	c.150C>T	c.(148-150)ggC>ggT	p.G50G	SSSCA1_ENST00000526877.1_Silent_p.G50G|SSSCA1-AS1_ENST00000567594.1_RNA|FAM89B_ENST00000530349.1_5'Flank|FAM89B_ENST00000449319.2_5'Flank|FAM89B_ENST00000316409.2_5'Flank|SSSCA1_ENST00000527920.1_Silent_p.G13G|SSSCA1_ENST00000531405.1_Silent_p.G13G	NM_006396.1	NP_006387.1	O60232	SSA27_HUMAN	Sjogren syndrome/scleroderma autoantigen 1	50					mitotic nuclear division (GO:0007067)					kidney(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8						GCATGCTGGGCGAGACGTGTG	0.706																																					p.G50G													.	SSSCA1-92	0			c.C150T						.						28	34	32					11																	65338205		2200	4295	6495	SO:0001819	synonymous_variant	10534	exon2			GCTGGGCGAGACG	AB001740	CCDS8104.1	11q13.1	2007-10-04	2007-10-04			ENSG00000173465			11328	protein-coding gene	gene with protein product		606044	"Sjogren's syndrome/scleroderma autoantigen 1"			9486406	Standard	NM_006396		Approved	p27	uc001oek.3	O60232		ENST00000309328.3:c.150C>T	11.37:g.65338205C>T		Somatic	43	0		WXS	Illumina HiSeq		36	4	NM_006396	0	0	98	98	0		Silent	SNP	ENST00000309328.3	37	CCDS8104.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872118	0.33069	.	.	ENSG00000173465	ENST00000526433	.	.	.	5.64	1.43	0.22495	.	.	.	.	.	T	0.57446	0.2054	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50659	-0.8802	4	.	.	.	-12.8182	9.068	0.36475	0.2444:0.2941:0.4615:0.0	.	.	.	.	V	18	.	.	A	+	2	0	SSSCA1	65094781	0.953000	0.32496	1.000000	0.80357	0.994000	0.84299	-0.026000	0.12392	0.311000	0.23014	0.555000	0.69702	GCG	.		0.706	SSSCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389511.1	NM_006396		T	65338205	C	T	65338205	2	4	85	1	0	0	0	0	0	0	0	1	15227	755	27	1		1	SSSCA1	11	65338205	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	18936782	65338205	69668311	41	7827											
PC	5091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66636376	66636376	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgggagttgacctcgatgaaGtagtgcttgccgtgcctgtc	6	11	14	10	3	0	2	0	2	0	0	2	4	0	3	3	1	3	3	3	1	2	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:66636376G>T	ENST00000393958.2	-	9	1056	c.963C>A	c.(961-963)taC>taA	p.Y321*	PC_ENST00000524491.1_Nonsense_Mutation_p.Y281*|PC_ENST00000393955.2_Nonsense_Mutation_p.Y321*|PC_ENST00000355677.3_Nonsense_Mutation_p.Y321*|PC_ENST00000393960.1_Nonsense_Mutation_p.Y321*	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	321	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CCTCGATGAAGTAGTGCTTGC	0.677																																					p.Y321X		.											.	PC-228	0			c.C963A						.						90	79	83					11																	66636376		2200	4295	6495	SO:0001587	stop_gained	5091	exon9			GATGAAGTAGTGC	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.963C>A	11.37:g.66636376G>T	ENSP00000377530:p.Tyr321*	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	123	38	NM_000920	0	0	7	8	1	B4DN00|Q16705	Nonsense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	G	36	5.754004	0.96890	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	.	.	.	4.65	2.37	0.29283	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.0017	6.9367	0.24470	0.3253:0.0:0.6747:0.0	.	.	.	.	X	321;321;321;281;321	.	ENSP00000347900:Y321X	Y	-	3	2	PC	66392952	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.978000	0.49305	0.954000	0.37851	0.561000	0.74099	TAC	.		0.677	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66636376	G	T	66636376	4	4	85	1	0	0	0	0	0	1	0	0	11523	1024	36	4	2629	4	PC	11	66636376	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	1298171	66636376	68370140	42	7828											
ALDH3B2	222	ucsc.edu	37	chr11	67432821	67432821	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcagcccagcaatgccCgcagccgctggaactgtttc	7	7	12	15	2	0	0	0	0	0	0	1	1	0	1	3	2	6	6	3	2	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:67432821C>T	ENST00000349015.3	-	7	1079	c.641G>A	c.(640-642)cGg>cAg	p.R214Q	ALDH3B2_ENST00000530069.1_Missense_Mutation_p.R214Q|ALDH3B2_ENST00000531881.1_5'Flank	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	214					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						CAGCAATGCCCGCAGCCGCTG	0.652																																					p.R214Q													.	ALDH3B2-226	0			c.G641A						.						50	56	54					11																	67432821		2200	4294	6494	SO:0001583	missense	222	exon7			AATGCCCGCAGCC	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"Aldehyde dehydrogenases"	411	protein-coding gene	gene with protein product	"aldehyde dehydrogenase 8", "acetaldehyde dehydrogenase 8"	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.641G>A	11.37:g.67432821C>T	ENSP00000255084:p.Arg214Gln	Somatic	144	0		WXS	Illumina HiSeq		110	1	NM_001031615	0	0	46	97	51	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	37	CCDS31622.1	.	.	.	.	.	.	.	.	.	.	C	8.019	0.759224	0.15846	.	.	ENSG00000132746	ENST00000530069;ENST00000349015	T;T	0.75260	-0.92;-0.92	4.16	-6.56	0.01848	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.742635	0.13033	N	0.419127	T	0.37100	0.0991	N	0.02985	-0.445	0.09310	N	0.999999	B;B	0.21688	0.059;0.025	B;B	0.21917	0.025;0.037	T	0.43376	-0.9395	10	0.11794	T	0.64	.	3.9776	0.09481	0.114:0.5449:0.1154:0.2256	.	99;214	B4DSX1;P48448	.;AL3B2_HUMAN	Q	214	ENSP00000431595:R214Q;ENSP00000255084:R214Q	ENSP00000255084:R214Q	R	-	2	0	ALDH3B2	67189397	0.002000	0.14202	0.081000	0.20488	0.909000	0.53808	-0.391000	0.07323	-1.259000	0.02468	0.462000	0.41574	CGG	.		0.652	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695		T	67432821	C	T	67432821	3	4	85	1	0	0	0	0	1	0	0	0	500	652	23	1	532	1	ALDH3B2	11	67432821	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	796445	67432821	67573695	43	7829											
GNPTAB	79158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	102147162	102147162	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatttaccattcctgcagcTcatgcatatgaaggaaacgg	13	10	9	9	1	1	1	1	1	0	0	2	3	2	2	2	2	5	3	2	2	5	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:102147162T>C	ENST00000299314.7	-	19	3852	c.3590A>G	c.(3589-3591)gAg>gGg	p.E1197G		NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	1197					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TTCCTGCAGCTCATGCATATG	0.383																																					p.E1197G		.											.	GNPTAB-92	0			c.A3590G						.						126	114	118					12																	102147162		2203	4300	6503	SO:0001583	missense	79158	exon19			TGCAGCTCATGCA	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.3590A>G	12.37:g.102147162T>C	ENSP00000299314:p.Glu1197Gly	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	77	28	NM_024312	0	0	0	0	0	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	37	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490528	0.64074	.	.	ENSG00000111670	ENST00000299314	D	0.83163	-1.69	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.89196	0.6646	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88424	0.3030	10	0.39692	T	0.17	-26.24	15.9351	0.79698	0.0:0.0:0.0:1.0	.	1197	Q3T906	GNPTA_HUMAN	G	1197	ENSP00000299314:E1197G	ENSP00000299314:E1197G	E	-	2	0	GNPTAB	100671293	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.694000	0.84235	2.167000	0.68274	0.482000	0.46254	GAG	.		0.383	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			C	102147162	T	C	102147162	3	2	85	1	0	0	0	0	1	0	0	0	6565	1551	54	3	192	3	GNPTAB	12	102147162	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		102147162	31704733	44	7830											
RASAL1	8437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113565934	113565934	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccagaggcaggtgcaccgTgtactcctccccccagaagg	9	6	11	15	1	0	2	0	0	0	2	3	2	3	2	6	3	2	3	6	3	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:113565934T>A	ENST00000261729.5	-	4	487	c.172A>T	c.(172-174)Acg>Tcg	p.T58S	RASAL1_ENST00000446861.3_Missense_Mutation_p.T58S|RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000548055.1_Missense_Mutation_p.T58S|RASAL1_ENST00000546530.1_Missense_Mutation_p.T58S			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	58	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		T -> M (in dbSNP:rs34598602). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						AGGTGCACCGTGTACTCCTCC	0.617																																					p.T58S		.											.	RASAL1-229	0			c.A172T						.						197	195	196					12																	113565934		2203	4300	6503	SO:0001583	missense	8437	exon4			GCACCGTGTACTC	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.172A>T	12.37:g.113565934T>A	ENSP00000261729:p.Thr58Ser	Somatic	327	0		WXS	Illumina HiSeq	Phase_I	349	118	NM_004658	0	0	21	36	15	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.130000	0.77549	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.12	5.12	0.69794	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.74846	0.3770	L	0.45137	1.4	0.41650	D	0.98912	D;D;D;P;D;D	0.89917	1.0;1.0;1.0;0.698;0.994;1.0	D;D;D;P;D;D	0.91635	0.999;0.999;0.999;0.503;0.932;0.999	T	0.74191	-0.3745	10	0.36615	T	0.2	.	13.8909	0.63738	0.0:0.0:0.0:1.0	.	58;58;70;58;58;58	B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;RASL1_HUMAN;.	S	58	ENSP00000450244:T58S;ENSP00000261729:T58S;ENSP00000395920:T58S;ENSP00000448510:T58S	ENSP00000261729:T58S	T	-	1	0	RASAL1	112050317	1.000000	0.71417	0.993000	0.49108	0.930000	0.56654	7.259000	0.78381	1.939000	0.56221	0.402000	0.26972	ACG	.		0.617	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		A	113565934	T	A	113565934	3	1	85	1	0	0	0	0	1	0	0	0	13095	1696	59	5	2318	5	RASAL1	12	113565934	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	11418772	113565934	20285961	45	7831											
PLBD2	196463	hgsc.bcm.edu	37	chr12	113826272	113826272	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctgtccccaggtgaccagCatgtcactggccaggatcct	7	8	10	16	0	1	1	1	1	0	0	3	2	3	2	6	3	1	1	6	3	0	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:113826272C>G	ENST00000280800.3	+	12	1642	c.1611C>G	c.(1609-1611)agC>agG	p.S537R	PLBD2_ENST00000545182.2_Missense_Mutation_p.S505R	NM_173542.3	NP_775813.2	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2	537					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						AGGTGACCAGCATGTCACTGG	0.701																																					p.S537R		.											.	PLBD2-68	0			c.C1611G						.						17	17	17					12																	113826272		2200	4294	6494	SO:0001583	missense	196463	exon12			GACCAGCATGTCA	BC030618	CCDS9168.1, CCDS53834.1	12q24.13	2013-10-11				ENSG00000151176			27283	protein-coding gene	gene with protein product	"PLB homolog 2 (Dictyostelium)", "mannose-6-phosphate protein associated protein p76"					17105447, 15193148, 19019078	Standard	NM_001159727		Approved	p76	uc001tve.2	Q8NHP8	OTTHUMG00000169567	ENST00000280800.3:c.1611C>G	12.37:g.113826272C>G	ENSP00000280800:p.Ser537Arg	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	16	2	NM_173542	0	0	0	0	0	F5H5E2	Missense_Mutation	SNP	ENST00000280800.3	37	CCDS9168.1	.	.	.	.	.	.	.	.	.	.	c	14.26	2.481503	0.44147	.	.	ENSG00000151176	ENST00000545182;ENST00000280800	T;T	0.17054	2.3;2.3	4.64	0.45	0.16624	.	0.242419	0.42053	D	0.000770	T	0.37865	0.1019	M	0.84585	2.705	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.91635	0.954;0.999	T	0.17531	-1.0366	10	0.72032	D	0.01	-37.7263	5.6463	0.17592	0.0:0.5989:0.1458:0.2553	.	505;537	F5H5E2;Q8NHP8	.;PLBL2_HUMAN	R	505;537	ENSP00000443463:S505R;ENSP00000280800:S537R	ENSP00000280800:S537R	S	+	3	2	PLBD2	112310655	0.083000	0.21467	0.236000	0.24074	0.573000	0.36030	0.935000	0.28924	0.507000	0.28148	0.550000	0.68814	AGC	.		0.701	PLBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404835.1	NM_173542		G	113826272	C	G	113826272	3	3	85	1	0	0	0	0	1	0	0	0	12052	709	25	4	1657	4	PLBD2	12	113826272	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	260338	113826272	20025623	46	7832											
TBX3	6926	broad.mit.edu	37	chr12	115112487	115112488	+	Frame_Shift_Del	DEL	GC	GC	-																															tgtcccggggccgctcagcaGcgaaaaggtgagccttgacc																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:115112487_115112488delGC	ENST00000257566.3	-	7	1641_1642	c.1252_1253delGC	c.(1252-1254)gctfs	p.A419fs	TBX3_ENST00000349155.2_Frame_Shift_Del_p.A399fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	419					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CCGCTCAGCAGCGAAAAGGTGA	0.718																																					p.418_418del													.	TBX3-93	0			c.1252_1253del						.																																			SO:0001589	frameshift_variant	6926	exon7			TCAGCAGCGAAAA	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"T-boxes"	11602	protein-coding gene	gene with protein product		601621	"ulnar mammary syndrome"	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1252_1253delGC	12.37:g.115112487_115112488delGC	ENSP00000257566:p.Ala419fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	21	8	NM_016569	0	0	0	0	0	Q8TB20|Q9UKF8	Frame_Shift_Del	DEL	ENST00000257566.3	37	CCDS9176.1																																																																																			.		0.718	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		-	115112488	GC	-	115112487	7	5	85	1	0	1	0	1	0	0	0	0	15691	971	34	0	986	0	TBX3	12	115112487	Frame_Shift_Del	DEL	GC	TCGA-BQ-7053-01A-11D-1961-08	1286215	115112487	18739408	47	7833											
EP400	57634	broad.mit.edu	37	chr12	132445250	132445251	+	Frame_Shift_Ins	INS	-	-	G																															agcgagggtgaggagcagccINSggcccaccccaacccacccc																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:132445250_132445251insG	ENST00000333577.4	+	2	195_196	c.86_87insG	c.(85-90)ccggccfs	p.A30fs	EP400_ENST00000389561.2_Frame_Shift_Ins_p.A30fs|EP400_ENST00000330386.6_Frame_Shift_Ins_p.A30fs|EP400_ENST00000332482.4_Frame_Shift_Ins_p.A30fs|EP400_ENST00000389562.2_Frame_Shift_Ins_p.A30fs			Q96L91	EP400_HUMAN	E1A binding protein p400	30					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		GAGGAGCAGCCGGCCCACCCCA	0.653																																					p.P29fs													.	EP400-520	0			c.86_87insG						.																																			SO:0001589	frameshift_variant	57634	exon2			AGCAGCCGGCCCA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.88dupG	12.37:g.132445252_132445252dupG	ENSP00000333602:p.Ala30fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_015409	0	0	0	0	0	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Frame_Shift_Ins	INS	ENST00000333577.4	37																																																																																				.		0.653	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		G	132445251	-	G	132445250	7	5	85	1	0	1	1	0	0	0	0	0	5162	652	23	0	88	0	EP400	12	132445250	Frame_Shift_Ins	INS	-	TCGA-BQ-7053-01A-11D-1961-08	17332763	132445250	1406645	48	7834											
SACS	26278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	23906994	23906994	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttataagaggaagtgttccaTttacctcttgatattgagga	12	15	9	5	0	1	3	0	2	1	1	2	5	2	5	2	2	1	1	2	2	5	8			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr13:23906994T>C	ENST00000382292.3	-	9	11294	c.11021A>G	c.(11020-11022)aAt>aGt	p.N3674S	SACS_ENST00000382298.3_Missense_Mutation_p.N3674S|SACS_ENST00000402364.1_Missense_Mutation_p.N2924S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3674					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AAGTGTTCCATTTACCTCTTG	0.393																																					p.N3674S		.											.	SACS-298	0			c.A11021G						.						85	85	85					13																	23906994		2203	4300	6503	SO:0001583	missense	26278	exon10			GTTCCATTTACCT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.11021A>G	13.37:g.23906994T>C	ENSP00000371729:p.Asn3674Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	102	43	NM_014363	0	0	2	2	0	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	11.44	1.639656	0.29157	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87571	-2.12;-2.27;-2.12	5.8	5.8	0.92144	.	0.045544	0.85682	D	0.000000	T	0.79118	0.4392	N	0.17082	0.46	0.33015	D	0.528049	B	0.17465	0.022	B	0.14023	0.01	T	0.78450	-0.2199	10	0.33940	T	0.23	.	16.1429	0.81539	0.0:0.0:0.0:1.0	.	3674	Q9NZJ4	SACS_HUMAN	S	3674;2924;3674	ENSP00000371729:N3674S;ENSP00000385844:N2924S;ENSP00000371735:N3674S	ENSP00000371729:N3674S	N	-	2	0	SACS	22804994	1.000000	0.71417	0.981000	0.43875	0.722000	0.41435	4.970000	0.63742	2.209000	0.71365	0.460000	0.39030	AAT	.		0.393	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23906994	T	C	23906994	3	2	85	1	0	0	0	0	1	0	0	0	13836	1493	52	3	2722	3	SACS	13	23906994	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		23906994	91262884	49	7835											
KBTBD6	89890	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	41706340	41706340	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctgctggctctcgtacatgCcacctgtgaacatgctcttg	6	12	9	14	1	2	1	0	1	2	0	3	1	2	1	3	1	5	4	3	1	2	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr13:41706340C>T	ENST00000379485.1	-	1	542	c.308G>A	c.(307-309)gGc>gAc	p.G103D	KBTBD6_ENST00000499385.2_Intron	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	103	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CTCGTACATGCCACCTGTGAA	0.627																																					p.G103D		.											.	KBTBD6-92	0			c.G308A						.						64	50	55					13																	41706340		2203	4300	6503	SO:0001583	missense	89890	exon1			TACATGCCACCTG	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.308G>A	13.37:g.41706340C>T	ENSP00000368799:p.Gly103Asp	Somatic	54	1		WXS	Illumina HiSeq	Phase_I	50	18	NM_152903	0	0	11	16	5	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	c	16.25	3.070386	0.55539	.	.	ENSG00000165572	ENST00000379485	T	0.70399	-0.48	3.59	2.71	0.32032	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.73434	0.3586	L	0.39692	1.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67197	-0.5731	10	0.16420	T	0.52	.	10.7007	0.45926	0.0:0.8037:0.1963:0.0	.	103	Q86V97	KBTB6_HUMAN	D	103	ENSP00000368799:G103D	ENSP00000368799:G103D	G	-	2	0	KBTBD6	40604340	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	2.242000	0.43106	0.819000	0.34492	0.313000	0.20887	GGC	.		0.627	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		T	41706340	C	T	41706340	3	4	85	1	0	0	0	0	1	0	0	0	8018	739	26	2	1720	2	KBTBD6	13	41706340	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	17799346	41706340	73463538	50	7836											
FSCB	84075	hgsc.bcm.edu	37	chr14	44974805	44974805	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttctgcagtggtctctttAggtaatggagactgaaattc	9	15	10	7	0	3	2	0	1	3	1	5	3	3	2	0	3	1	2	0	3	3	5			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr14:44974805A>G	ENST00000340446.4	-	1	1677	c.1386T>C	c.(1384-1386)ccT>ccC	p.P462P	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	462						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TGGTCTCTTTAGGTAATGGAG	0.512																																					p.P462P		.											.	FSCB-587	0			c.T1386C						.						26	26	26					14																	44974805		2202	4300	6502	SO:0001819	synonymous_variant	84075	exon1			CTCTTTAGGTAAT	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1386T>C	14.37:g.44974805A>G		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_032135	0	0	0	0	0	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																			.		0.512	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		G	44974805	A	G	44974805	2	3	85	1	0	0	0	0	0	0	0	1	6085	407	15	3		3	FSCB	14	44974805	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		44974805	62374735	51	7837											
CHRFAM7A	89832	hgsc.bcm.edu;broad.mit.edu	37	chr15	30665308	30665308	+	Frame_Shift_Del	DEL	A	A	-																															cagtgctgcacatcaaagggAaaccagcgtacatcgatgta																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr15:30665308delA	ENST00000299847.2	-	6	654	c.201delT	c.(199-201)tttfs	p.F67fs	CHRFAM7A_ENST00000397827.3_5'UTR|CHRFAM7A_ENST00000567722.1_5'Flank|CHRFAM7A_ENST00000401522.3_5'UTR	NM_139320.1	NP_647536.1	Q494W8	CRFM7_HUMAN	CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion	67						integral component of membrane (GO:0016021)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(1)|skin(2)	6		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CATCAAAGGGAAACCAGCGTA	0.483																																					p.F67fs		.											.	CHRFAM7A-45	0			c.201delT						.						61	60	61					15																	30665308		2176	4256	6432	SO:0001589	frameshift_variant	89832	exon6			.	AF029838	CCDS32184.1, CCDS42008.1	15q13.2	2013-04-24	2006-02-01		ENSG00000166664	ENSG00000166664			15781	protein-coding gene	gene with protein product		609756				11829490	Standard	NM_139320		Approved	D-10, CHRNA7-DR1	uc001zdt.1	Q494W8	OTTHUMG00000175645	ENST00000299847.2:c.201delT	15.37:g.30665308delA	ENSP00000299847:p.Phe67fs	Somatic	779	0		WXS	Illumina HiSeq	Phase_I	732	118	NM_139320	0	0	0	0	0	A8KAB9	Frame_Shift_Del	DEL	ENST00000299847.2	37	CCDS32184.1																																																																																			.		0.483	CHRFAM7A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430700.1	NM_148911		-	30665308	A	-	30665308	7	5	85	1	0	1	0	1	0	0	0	0	3381	243	9	0	1057	0	CHRFAM7A	15	30665308	Frame_Shift_Del	DEL	A	TCGA-BQ-7053-01A-11D-1961-08		30665308	71866084	52	7838											
ACTC1	70	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	35083348	35083348	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctaggagccagagcagtGatttccttctgcatacgatc	9	11	11	10	1	1	2	0	1	1	1	3	4	2	3	2	1	5	3	2	1	2	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr15:35083348G>T	ENST00000290378.4	-	6	1612	c.957C>A	c.(955-957)atC>atA	p.I319I	RP11-814P5.1_ENST00000503496.1_RNA|ACTC1_ENST00000557860.1_5'Flank|RP11-814P5.1_ENST00000558707.1_RNA	NM_005159.4	NP_005150.1	P68032	ACTC_HUMAN	actin, alpha, cardiac muscle 1	319					actin filament-based movement (GO:0030048)|actin-myosin filament sliding (GO:0033275)|actomyosin structure organization (GO:0031032)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle filament sliding (GO:0030049)|negative regulation of apoptotic process (GO:0043066)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|skeletal muscle thin filament assembly (GO:0030240)	actin filament (GO:0005884)|actomyosin, actin portion (GO:0042643)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|I band (GO:0031674)|membrane (GO:0016020)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|myosin binding (GO:0017022)			central_nervous_system(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	31		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		CCAGAGCAGTGATTTCCTTCT	0.453																																					p.I319I													.	ACTC1-92	0			c.C957A						.						312	283	293					15																	35083348		2201	4298	6499	SO:0001819	synonymous_variant	70	exon6			AGCAGTGATTTCC	BC009978	CCDS10041.1	15q14	2014-09-17	2006-08-24	2006-08-24	ENSG00000159251	ENSG00000159251			143	protein-coding gene	gene with protein product		102540	"actin, alpha, cardiac muscle"	ACTC		1639426	Standard	NM_005159		Approved	CMD1R	uc001ziu.1	P68032	OTTHUMG00000129675	ENST00000290378.4:c.957C>A	15.37:g.35083348G>T		Somatic	311	1		WXS	Illumina HiSeq	Phase_I	319	113	NM_005159	0	0	1	1	0	P04270	Silent	SNP	ENST00000290378.4	37	CCDS10041.1																																																																																			.		0.453	ACTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251876.3	NM_005159		T	35083348	G	T	35083348	2	4	85	1	0	0	0	0	0	0	0	1	195	1280	45	4		4	ACTC1	15	35083348	Silent	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	4418040	35083348	67448044	53	7839											
IQGAP1	8826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	91009552	91009552	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtagaaagtggtgatgttgGcaaaacactgagtgcccttc	12	10	12	7	0	0	3	0	2	0	1	1	3	0	3	1	2	2	3	1	2	4	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr15:91009552G>T	ENST00000268182.5	+	17	2043	c.1919G>T	c.(1918-1920)gGc>gTc	p.G640V	IQGAP1_ENST00000560738.1_Missense_Mutation_p.G68V	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	640					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGTGATGTTGGCAAAACACTG	0.443																																					p.G640V		.											.	IQGAP1-950	0			c.G1919T						.						148	124	132					15																	91009552		2198	4298	6496	SO:0001583	missense	8826	exon17			ATGTTGGCAAAAC	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"RasGAP-like with IQ motifs"	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.1919G>T	15.37:g.91009552G>T	ENSP00000268182:p.Gly640Val	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	123	33	NM_003870	0	0	22	44	22	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.470092	0.26423	.	.	ENSG00000140575	ENST00000268182	D	0.95171	-3.63	5.29	3.3	0.37823	.	0.339619	0.31268	N	0.007960	D	0.88444	0.6438	N	0.16478	0.41	0.33977	D	0.647533	B	0.02656	0.0	B	0.04013	0.001	D	0.87361	0.2344	10	0.35671	T	0.21	-7.5112	14.694	0.69107	0.0:0.4098:0.5901:0.0	.	640	P46940	IQGA1_HUMAN	V	640	ENSP00000268182:G640V	ENSP00000268182:G640V	G	+	2	0	IQGAP1	88810556	0.653000	0.27358	0.946000	0.38457	0.974000	0.67602	2.180000	0.42537	1.438000	0.47492	0.655000	0.94253	GGC	.		0.443	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	91009552	G	T	91009552	3	4	85	1	0	0	0	0	1	0	0	0	7835	1203	42	4	1985	4	IQGAP1	15	91009552	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	55926204	91009552	11521840	54	7840											
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500668	91500668	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcgggcacgccagctggaGctgggcgccgagcacgcgtt	5	5	17	14	6	0	0	0	0	0	0	0	2	0	1	2	3	4	5	2	3	0	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr15:91500668G>A	ENST00000394258.2	+	3	694	c.492G>A	c.(490-492)gaG>gaA	p.E164E	AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000555155.1_Silent_p.E164E|RCCD1_ENST00000556774.1_Intron|RCCD1_ENST00000556618.1_Silent_p.E164E	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	164				RLPLLPCARAYVSPRAPFYRPLAPELRARQLELGAEHALLL DAAGQVFSWGGGR -> GGAAGGLVRLRFLRLRAGAGLRTR APGAQPQSAAGGRRHLPRERELELHRFRDP (in Ref. 3; AAI13827). {ECO:0000305}.		cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			GCCAGCTGGAGCTGGGCGCCG	0.741																																					p.E164E		.											.	RCCD1-90	0			c.G492A						.						3	4	3					15																	91500668		1896	3773	5669	SO:0001819	synonymous_variant	91433	exon3			GCTGGAGCTGGGC		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.492G>A	15.37:g.91500668G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_001017919	0	0	5	15	10	B2RTP9|Q29RX6	Silent	SNP	ENST00000394258.2	37	CCDS32333.1																																																																																			.		0.741	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		A	91500668	G	A	91500668	2	1	85	1	0	0	0	0	0	0	0	1	13207	962	34	2		2	RCCD1	15	91500668	Silent	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	491116	91500668	11030724	55	7841											
PKD1	5310	ucsc.edu	37	chr16	2165459	2165459	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggggccccgggtagccctgGccctgacgtgcagccattgg	4	6	17	14	2	0	1	0	1	0	0	0	1	0	1	5	5	3	2	5	5	1	2	rs372961544		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr16:2165459G>C	ENST00000262304.4	-	10	2225	c.2017C>G	c.(2017-2019)Cca>Gca	p.P673A	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.P673A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	673					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GGTAGCCCTGGCCCTGACGTG	0.701																																					p.P673A													.	PKD1-91	0			c.C2017G						.	G	ALA/PRO,ALA/PRO	13,4315		0,13,2151	15	17	16		2017,2017	1.9	0	16		16	0,8514		0,0,4257	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	27,27	0,13,6408	CC,CG,GG		0.0,0.3004,0.1012	benign,benign	673/4303,673/4304	2165459	13,12829	2164	4257	6421	SO:0001583	missense	5310	exon10			GCCCTGGCCCTGA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.2017C>G	16.37:g.2165459G>C	ENSP00000262304:p.Pro673Ala	Somatic	31	5		WXS	Illumina HiSeq		31	3	NM_000296	0	0	14	14	0	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.375442	0.24857	0.003004	0.0	ENSG00000008710	ENST00000262304;ENST00000423118	T;T	0.35605	1.3;1.3	5.17	1.91	0.25777	Polycystin cation channel (1);	1.262000	0.05316	N	0.525692	T	0.32010	0.0815	L	0.56769	1.78	0.09310	N	1	P;P	0.35745	0.459;0.518	B;B	0.33254	0.16;0.114	T	0.22138	-1.0225	10	0.22706	T	0.39	.	5.259	0.15563	0.0773:0.2616:0.5267:0.1344	.	673;673	P98161-3;P98161	.;PKD1_HUMAN	A	673	ENSP00000262304:P673A;ENSP00000399501:P673A	ENSP00000262304:P673A	P	-	1	0	PKD1	2105460	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	0.072000	0.14617	0.524000	0.28502	0.557000	0.71058	CCA	.		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2165459	G	C	2165459	3	2	85	1	0	0	0	0	1	0	0	0	11989	1203	42	4	11042	4	PKD1	16	2165459	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		2165459	88189294	56	7842											
NLRC5	84166	hgsc.bcm.edu	37	chr16	57099179	57099179	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccctgttagaagtctgcGcccaggcctcaggcagtgtc	6	10	11	14	1	3	1	1	0	2	1	5	1	3	1	3	2	1	2	3	2	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr16:57099179G>C	ENST00000262510.6	+	33	4435	c.4210G>C	c.(4210-4212)Gcc>Ccc	p.A1404P	NLRC5_ENST00000436936.1_Missense_Mutation_p.A1404P|NLRC5_ENST00000308149.7_Missense_Mutation_p.A1375P|NLRC5_ENST00000539144.1_Missense_Mutation_p.A1375P	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1404					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGAAGTCTGCGCCCAGGCCTC	0.557																																					p.A1404P		.											.	NLRC5-159	0			c.G4210C						.						34	35	35					16																	57099179		2198	4300	6498	SO:0001583	missense	84166	exon32			GTCTGCGCCCAGG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"Nucleotide-binding domain and leucine rich repeat containing"	29933	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5", "NOD-like receptor C5"	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4210G>C	16.37:g.57099179G>C	ENSP00000262510:p.Ala1404Pro	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_032206	0	0	9	9	0	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.359043	0.41801	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.72505	0.6;-0.66;0.6;-0.66	3.71	-0.625	0.11548	.	.	.	.	.	T	0.69815	0.3153	M	0.65975	2.015	0.20403	N	0.999902	D	0.55385	0.971	P	0.49561	0.615	T	0.60434	-0.7264	9	0.54805	T	0.06	.	6.3118	0.21169	0.4974:0.0:0.5026:0.0	.	1404	Q86WI3	NLRC5_HUMAN	P	1404;1375;1404;1375	ENSP00000262510:A1404P;ENSP00000308886:A1375P;ENSP00000389739:A1404P;ENSP00000441727:A1375P	ENSP00000262510:A1404P	A	+	1	0	NLRC5	55656680	0.885000	0.30320	0.594000	0.28785	0.558000	0.35554	0.021000	0.13489	-0.085000	0.12573	-0.170000	0.13304	GCC	.		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		C	57099179	G	C	57099179	3	2	85	1	0	0	0	0	1	0	0	0	10496	1087	38	4	4332	4	NLRC5	16	57099179	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	54933720	57099179	33255574	57	7843											
CNOT1	23019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	58620607	58620607	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactgacgtctgcgtcaatgTaagaacgcagaagatctgga	13	8	11	9	3	3	4	1	1	2	3	3	5	3	5	0	1	2	2	0	1	4	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr16:58620607T>C	ENST00000317147.5	-	7	811	c.479A>G	c.(478-480)tAc>tGc	p.Y160C	CNOT1_ENST00000441024.2_Missense_Mutation_p.Y160C|CNOT1_ENST00000569240.1_Missense_Mutation_p.Y160C	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	160					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TGCGTCAATGTAAGAACGCAG	0.458																																					p.Y160C		.											.	CNOT1-95	0			c.A479G						.						218	225	223					16																	58620607		2198	4300	6498	SO:0001583	missense	23019	exon7			TCAATGTAAGAAC	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.479A>G	16.37:g.58620607T>C	ENSP00000320949:p.Tyr160Cys	Somatic	397	0		WXS	Illumina HiSeq	Phase_I	385	106	NM_206999	0	0	19	20	1	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651332	0.88056	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.24350	1.86;1.86	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.49813	0.1579	M	0.71206	2.165	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.999	D;P;P	0.81914	0.995;0.808;0.871	T	0.49380	-0.8946	9	.	.	.	-13.1581	15.1793	0.72941	0.0:0.0:0.0:1.0	.	160;160;160	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	C	160	ENSP00000320949:Y160C;ENSP00000413113:Y160C	.	Y	-	2	0	CNOT1	57178108	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.041000	0.60428	0.454000	0.30748	TAC	.		0.458	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58620607	T	C	58620607	3	2	85	1	0	0	0	0	1	0	0	0	3623	1638	57	3	7045	3	CNOT1	16	58620607	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	1521428	58620607	31734146	58	7844											
BCMO1	53630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81298288	81298288	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaaatctggcaacgtcacAtccccattatgatgaggctg	11	10	10	10	1	2	2	1	2	1	0	3	2	3	2	2	3	1	3	2	3	4	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr16:81298288A>G	ENST00000258168.2	+	5	976	c.515A>G	c.(514-516)cAt>cGt	p.H172R	BCMO1_ENST00000425577.2_Missense_Mutation_p.H103R	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						GCAACGTCACATCCCCATTAT	0.403																																					p.H172R		.											.	BCMO1-90	0			c.A515G						.						160	135	143					16																	81298288		2202	4300	6502	SO:0001583	missense	53630	exon5			CGTCACATCCCCA																												ENST00000258168.2:c.515A>G	16.37:g.81298288A>G	ENSP00000258168:p.His172Arg	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	102	31	NM_017429	0	0	5	7	2		Missense_Mutation	SNP	ENST00000258168.2	37	CCDS10934.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125684	0.77436	.	.	ENSG00000135697	ENST00000258168;ENST00000425577	D;D	0.99545	-6.13;-6.13	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.99715	0.9890	H	0.94658	3.565	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.76575	0.988;0.971	D	0.97280	0.9917	10	0.87932	D	0	-25.987	14.8045	0.69942	1.0:0.0:0.0:0.0	.	103;172	E7EM88;Q9HAY6	.;BCDO1_HUMAN	R	172;103	ENSP00000258168:H172R;ENSP00000400586:H103R	ENSP00000258168:H172R	H	+	2	0	BCMO1	79855789	1.000000	0.71417	0.989000	0.46669	0.843000	0.47879	8.759000	0.91667	1.896000	0.54893	0.449000	0.29647	CAT	.		0.403	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1			G	81298288	A	G	81298288	3	3	85	1	0	0	0	0	1	0	0	0	1385	217	8	3	533	3	BCMO1	16	81298288	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	22677681	81298288	9056465	59	7845											
MED13	9969	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	60040331	60040331	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactttatcccgatccatcgTgctaaaatttaaggtagaaa	14	12	6	9	2	0	1	0	0	0	1	3	2	2	1	2	1	1	2	2	1	6	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr17:60040331T>G	ENST00000397786.2	-	21	4922	c.4846A>C	c.(4846-4848)Acg>Ccg	p.T1616P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1616					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CGATCCATCGTGCTAAAATTT	0.398																																					p.T1616P		.											.	MED13-136	0			c.A4846C						.						62	60	60					17																	60040331		1850	4094	5944	SO:0001630	splice_region_variant	9969	exon21			CCATCGTGCTAAA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.4845-1A>C	17.37:g.60040331T>G		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	131	34	NM_005121	0	0	0	0	0	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.199056	0.79015	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.76060	-0.99	5.44	4.34	0.51931	.	0.045205	0.85682	D	0.000000	T	0.76786	0.4036	M	0.64997	1.995	0.80722	D	1	D	0.57899	0.981	P	0.52109	0.69	T	0.73544	-0.3949	10	0.29301	T	0.29	-33.0615	11.6656	0.51372	0.1329:0.0:0.0:0.8671	.	1616	Q9UHV7	MED13_HUMAN	P	1616;1615	ENSP00000380888:T1616P	ENSP00000262436:T1615P	T	-	1	0	MED13	57395113	1.000000	0.71417	0.989000	0.46669	0.957000	0.61999	5.940000	0.70187	0.864000	0.35578	0.533000	0.62120	ACG	.		0.398	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	Missense_Mutation	G	60040331	T	G	60040331	5	3	85	1	0	0	0	0	0	0	1	0	9455	1710	59	5	1718	5	MED13	17	60040331	Splice_Site	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		60040331	21154879	60	7846											
ITGB4	3691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73746316	73746316	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggaagatccatttcaactgGctgcccccttctggcaagcc	9	9	9	14	0	2	1	1	0	1	1	3	2	3	2	4	3	3	2	4	3	3	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr17:73746316G>A	ENST00000200181.3	+	28	3628	c.3441G>A	c.(3439-3441)tgG>tgA	p.W1147*	ITGB4_ENST00000339591.3_Nonsense_Mutation_p.W1147*|ITGB4_ENST00000579662.1_Nonsense_Mutation_p.W1147*|ITGB4_ENST00000450894.3_Nonsense_Mutation_p.W1147*|ITGB4_ENST00000449880.2_Nonsense_Mutation_p.W1147*	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1147	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATTTCAACTGGCTGCCCCCTT	0.632											OREG0024739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W1147X		.											.	ITGB4-227	0			c.G3441A						.						33	34	33					17																	73746316		2203	4300	6503	SO:0001587	stop_gained	3691	exon28			CAACTGGCTGCCC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3441G>A	17.37:g.73746316G>A	ENSP00000200181:p.Trp1147*	Somatic	58	0	1147	WXS	Illumina HiSeq	Phase_I	90	46	NM_001005731	0	0	22	24	2	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Nonsense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	45	11.812557	0.99605	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.7383	0.96217	0.0:0.0:1.0:0.0	.	.	.	.	X	1147	.	ENSP00000200181:W1147X	W	+	3	0	ITGB4	71257911	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.280000	0.89903	2.675000	0.91044	0.655000	0.94253	TGG	.		0.632	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73746316	G	A	73746316	4	1	85	1	0	0	0	0	0	1	0	0	7918	1212	42	2	3547	2	ITGB4	17	73746316	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	13705985	73746316	7448894	61	7847											
NPC1	4864	hgsc.bcm.edu	37	chr18	21119433	21119433	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggggcgaagcctattcgggTactagagaggacagacaggg	11	5	18	7	2	0	2	0	0	0	2	1	5	0	3	1	5	2	1	1	5	4	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr18:21119433T>C	ENST00000269228.5	-	19	3351	c.2797A>G	c.(2797-2799)Acc>Gcc	p.T933A	NPC1_ENST00000540608.1_5'Flank|NPC1_ENST00000412552.2_Splice_Site_p.T615A	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	933					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCTATTCGGGTACTAGAGAGG	0.468																																					p.T933A		.											.	NPC1-92	0			c.A2797G						.						53	44	47					18																	21119433		2203	4300	6503	SO:0001630	splice_region_variant	4864	exon19			TTCGGGTACTAGA	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2796-1A>G	18.37:g.21119433T>C		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_000271	0	0	1	1	0	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.296914	0.81025	.	.	ENSG00000141458	ENST00000269228;ENST00000412552	D;D	0.93189	-3.18;-3.18	5.47	5.47	0.80525	.	0.046376	0.85682	D	0.000000	D	0.95351	0.8491	M	0.86651	2.83	0.80722	D	1	P;P	0.40875	0.604;0.731	B;P	0.46208	0.354;0.507	D	0.95927	0.8935	10	0.72032	D	0.01	-36.1746	15.8487	0.78910	0.0:0.0:0.0:1.0	.	944;933	Q59GR1;O15118	.;NPC1_HUMAN	A	933;615	ENSP00000269228:T933A;ENSP00000408606:T615A	ENSP00000269228:T933A	T	-	1	0	NPC1	19373431	1.000000	0.71417	0.993000	0.49108	0.489000	0.33432	5.949000	0.70257	2.197000	0.70478	0.533000	0.62120	ACC	.		0.468	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	Missense_Mutation	C	21119433	T	C	21119433	5	2	85	1	0	0	0	0	0	0	1	0	10596	1652	57	3	1067	3	NPC1	18	21119433	Splice_Site	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		21119433	56957815	62	7848											
DCC	1630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	50683788	50683788	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtccctgtcttggtttccAgccgatttgtccgtctcagc	3	15	10	13	2	2	0	1	0	2	0	6	1	5	0	4	2	2	1	4	2	0	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr18:50683788A>T	ENST00000442544.2	+	8	1940	c.1324A>T	c.(1324-1326)Agc>Tgc	p.S442C	DCC_ENST00000412726.1_Missense_Mutation_p.S290C|DCC_ENST00000581580.1_Missense_Mutation_p.S97C	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	442	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTTGGTTTCCAGCCGATTTGT	0.532																																					p.S442C		.											.	DCC-225	0			c.A1324T						.						169	154	159					18																	50683788		2203	4300	6503	SO:0001583	missense	1630	exon8			GTTTCCAGCCGAT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2701	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 1"	120470	"deleted in colorectal carcinoma"			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1324A>T	18.37:g.50683788A>T	ENSP00000389140:p.Ser442Cys	Somatic	215	1		WXS	Illumina HiSeq	Phase_I	239	77	NM_005215	0	0	0	0	0		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.764133	0.49574	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T;T	0.60672	0.17;0.23;0.17	5.44	5.44	0.79542	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.76659	0.4018	M	0.81942	2.565	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.78314	0.99;0.99;0.991	T	0.80266	-0.1454	10	0.72032	D	0.01	.	14.4926	0.67663	1.0:0.0:0.0:0.0	.	290;290;442	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	C	442;375;290	ENSP00000389140:S442C;ENSP00000304146:S375C;ENSP00000397322:S290C	ENSP00000304146:S375C	S	+	1	0	DCC	48937786	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	8.400000	0.90200	2.076000	0.62316	0.459000	0.35465	AGC	.		0.532	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50683788	A	T	50683788	3	4	85	1	0	0	0	0	1	0	0	0	4288	188	7	5	1354	5	DCC	18	50683788	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	29564355	50683788	27393460	63	7849											
ABCA7	10347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1061844	1061844	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cgtttcgcatggtgacggggGacacattggccagcaggggc	7	7	17	10	3	0	1	0	1	0	0	1	2	0	2	1	6	1	3	1	6	0	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:1061844G>A	ENST00000263094.6	+	41	5758	c.5527G>A	c.(5527-5529)Gac>Aac	p.D1843N	ABCA7_ENST00000433129.1_Missense_Mutation_p.D1843N|ABCA7_ENST00000435683.2_Missense_Mutation_p.D1705N	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1843	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGACGGGGGACACATTGGC	0.642																																					p.D1843N		.											.	ABCA7-98	0			c.G5527A						.						98	83	88					19																	1061844		2203	4299	6502	SO:0001583	missense	10347	exon41			ACGGGGGACACAT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"ATP binding cassette transporters / subfamily A"	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5527G>A	19.37:g.1061844G>A	ENSP00000263094:p.Asp1843Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	60	16	NM_019112	0	0	13	23	10	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.975956	0.53720	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.96200	-3.94;-3.94	3.57	2.52	0.30459	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.94837	0.8332	L	0.27053	0.805	0.43133	D	0.994875	D;D	0.76494	0.999;0.978	D;P	0.79784	0.993;0.906	D	0.93757	0.7063	9	0.87932	D	0	.	9.6422	0.39846	0.1075:0.0:0.8925:0.0	.	968;1843	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	N	1843	ENSP00000263094:D1843N;ENSP00000414062:D1843N	ENSP00000263094:D1843N	D	+	1	0	ABCA7	1012844	1.000000	0.71417	0.969000	0.41365	0.089000	0.18198	7.374000	0.79633	0.692000	0.31613	-0.258000	0.10820	GAC	.		0.642	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1061844	G	A	1061844	3	1	85	1	0	0	0	0	1	0	0	0	37	1174	41	2	5685	2	ABCA7	19	1061844	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		1061844	58067139	64	7850											
SHD	56961	broad.mit.edu	37	chr19	4284873	4284873	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cccagcctgcggagcgtgtgGacccagccctgcccctggag	5	5	14	17	2	0	0	0	0	0	0	0	3	0	3	6	3	5	0	6	3	0	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:4284873G>C	ENST00000543264.2	+	4	2151	c.688G>C	c.(688-690)Gac>Cac	p.D230H	SHD_ENST00000599689.1_Missense_Mutation_p.D230H|SHD_ENST00000600475.1_3'UTR	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	230										breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGCGTGTGGACCCAGCCCT	0.607																																					p.D230H													.	SHD-90	0			c.G688C						.						38	45	42					19																	4284873		2203	4300	6503	SO:0001583	missense	56961	exon4			CGTGTGGACCCAG	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"SH2 domain containing"	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.688G>C	19.37:g.4284873G>C	ENSP00000446058:p.Asp230His	Somatic	85	1		WXS	Illumina HiSeq	Phase_I	59	3	NM_020209	0	0	0	0	0	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	37	CCDS12125.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671070	0.88348	.	.	ENSG00000105251	ENST00000543264;ENST00000221852	T	0.40756	1.02	4.44	4.44	0.53790	SH2 motif (1);	0.053023	0.64402	D	0.000001	T	0.61825	0.2378	M	0.66297	2.02	0.54753	D	0.999981	D;D	0.89917	1.0;1.0	D;D	0.81914	0.993;0.995	T	0.65948	-0.6044	10	0.72032	D	0.01	-20.3921	14.5886	0.68347	0.0:0.0:1.0:0.0	.	137;230	Q9NPN8;Q96IW2	.;SHD_HUMAN	H	230;145	ENSP00000446058:D230H	ENSP00000221852:D145H	D	+	1	0	SHD	4235873	1.000000	0.71417	0.957000	0.39632	0.780000	0.44128	8.569000	0.90744	2.306000	0.77630	0.491000	0.48974	GAC	.		0.607	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209		C	4284873	G	C	4284873	3	2	85	1	0	0	0	0	1	0	0	0	14307	1174	41	4	702	4	SHD	19	4284873	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	3223029	4284873	54844110	65	7851											
SH2D3A	10045	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6760836	6760836	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgctcatcctccagttgaaAgagggctgtgggtcggcctg	6	11	14	10	1	1	2	1	1	0	1	4	2	3	2	3	3	1	3	3	3	1	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:6760836A>G	ENST00000245908.6	-	3	501	c.232T>C	c.(232-234)Ttt>Ctt	p.F78L	SH2D3A_ENST00000437152.3_Intron|SH2D3A_ENST00000599563.1_5'UTR	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	78	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						TCCAGTTGAAAGAGGGCTGTG	0.642																																					p.F78L		.											.	SH2D3A-290	0			c.T232C						.						64	63	64					19																	6760836		2203	4300	6503	SO:0001583	missense	10045	exon3			GTTGAAAGAGGGC	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.232T>C	19.37:g.6760836A>G	ENSP00000245908:p.Phe78Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	99	32	NM_005490	0	0	4	8	4	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	37	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.431070	0.62844	.	.	ENSG00000125731	ENST00000245908	T	0.65178	-0.14	4.88	4.88	0.63580	SH2 motif (4);	0.000000	0.43747	D	0.000537	T	0.66366	0.2782	M	0.74546	2.27	0.80722	D	1	B	0.33883	0.43	B	0.39876	0.312	T	0.71310	-0.4631	10	0.87932	D	0	-15.1205	12.5273	0.56093	1.0:0.0:0.0:0.0	.	78	Q9BRG2	SH23A_HUMAN	L	78	ENSP00000245908:F78L	ENSP00000245908:F78L	F	-	1	0	SH2D3A	6711836	1.000000	0.71417	1.000000	0.80357	0.318000	0.28184	7.241000	0.78201	2.062000	0.61559	0.454000	0.30748	TTT	.		0.642	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		G	6760836	A	G	6760836	3	3	85	1	0	0	0	0	1	0	0	0	14265	72	3	3	1530	3	SH2D3A	19	6760836	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	2475963	6760836	52368147	66	7852											
MAP2K7	5609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7976338	7976338	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtggagctggcaacaggAcagtttccctacaagaactg	12	7	12	10	0	0	1	0	0	0	1	1	3	1	3	1	4	4	3	1	4	4	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:7976338A>G	ENST00000397979.3	+	9	1008	c.954A>G	c.(952-954)ggA>ggG	p.G318G	MAP2K7_ENST00000545011.1_Silent_p.G360G|MAP2K7_ENST00000397983.3_Silent_p.G334G|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000397981.3_Silent_p.G325G	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						TGGCAACAGGACAGTTTCCCT	0.607																																					p.G318G		.											.	MAP2K7-1450	0			c.A954G						.						44	49	47					19																	7976338		1939	4121	6060	SO:0001819	synonymous_variant	5609	exon9			AACAGGACAGTTT	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.954A>G	19.37:g.7976338A>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	40	12	NM_145185	0	0	22	38	16	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Silent	SNP	ENST00000397979.3	37	CCDS42491.1																																																																																			.		0.607	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			G	7976338	A	G	7976338	2	3	85	1	0	0	0	0	0	0	0	1	9267	262	10	3		3	MAP2K7	19	7976338	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	1215502	7976338	51152645	67	7853											
ZNF799	90576	ucsc.edu	37	chr19	12502924	12502924	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggacctactccaggaagAgtgttcttggtcacaatact	11	12	9	9	0	2	1	1	0	1	1	3	3	3	3	2	3	2	1	2	3	5	5			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:12502924A>T	ENST00000430385.3	-	4	488	c.288T>A	c.(286-288)acT>acA	p.T96T	CTD-3105H18.16_ENST00000595562.1_Silent_p.T96T|ZNF799_ENST00000419318.1_Silent_p.T64T|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	96					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(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CTCCAGGAAGAGTGTTCTTGG	0.413																																					p.T96T													.	ZNF799-74	0			c.T288A						.						111	104	107					19																	12502924		2203	4300	6503	SO:0001819	synonymous_variant	90576	exon4			AGGAAGAGTGTTC	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.288T>A	19.37:g.12502924A>T		Somatic	90	1		WXS	Illumina HiSeq		104	4	NM_001080821	0	0	9	13	4		Silent	SNP	ENST00000430385.3	37	CCDS45989.1																																																																																			.		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		T	12502924	A	T	12502924	2	4	85	1	0	0	0	0	0	0	0	1	18198	291	11	5		5	ZNF799	19	12502924	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	4526586	12502924	46626059	68	7854											
SLC27A1	376497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17615314	17615314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgagagggctttgacccaCgccagacctcagaccggctc	9	5	12	15	3	1	4	1	1	0	3	2	5	1	4	4	2	1	2	4	2	0	1	rs149575978	byFrequency	TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:17615314C>T	ENST00000252595.7	+	12	1931	c.1834C>T	c.(1834-1836)Cgc>Tgc	p.R612C	SLC27A1_ENST00000598424.1_Missense_Mutation_p.R433C|SLC27A1_ENST00000598848.1_3'UTR|SLC27A1_ENST00000442725.1_Missense_Mutation_p.R612C|CTD-3131K8.2_ENST00000596643.1_lincRNA	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	612					adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CTTTGACCCACGCCAGACCTC	0.602													C|||	7	0.00139776	0.0038	0	5008	,	,		19768	0		0	False		,,,				2504	0.002				p.R612C		.											.	SLC27A1-226	0			c.C1834T						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	93	77	83		1834	3	0.6	19	dbSNP_134	83	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLC27A1	NM_198580.1	180	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	possibly-damaging	612/647	17615314	3,13003	2203	4300	6503	SO:0001583	missense	376497	exon12			GACCCACGCCAGA	BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"Acyl-CoA synthetase family", "Solute carriers"	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.1834C>T	19.37:g.17615314C>T	ENSP00000252595:p.Arg612Cys	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	116	32	NM_198580	0	0	38	72	34	A6NIH2|B7Z662	Missense_Mutation	SNP	ENST00000252595.7	37	CCDS32953.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	7.143	0.582248	0.13749	2.27E-4	2.33E-4	ENSG00000130304	ENST00000442725;ENST00000252595	T;T	0.50001	0.76;0.76	4.13	3.0	0.34707	.	0.130544	0.52532	D	0.000072	T	0.43344	0.1243	M	0.61703	1.905	0.29136	N	0.879322	B;B	0.16396	0.002;0.017	B;B	0.09377	0.002;0.004	T	0.50118	-0.8865	10	0.62326	D	0.03	-6.0443	10.9108	0.47108	0.0:0.8075:0.1925:0.0	.	433;612	B7Z662;Q6PCB7	.;S27A1_HUMAN	C	612	ENSP00000413424:R612C;ENSP00000252595:R612C	ENSP00000252595:R612C	R	+	1	0	SLC27A1	17476314	0.000000	0.05858	0.593000	0.28771	0.007000	0.05969	0.553000	0.23391	1.831000	0.53308	0.561000	0.74099	CGC	C|1.000;T|0.000		0.602	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580		T	17615314	C	T	17615314	3	4	85	1	0	0	0	0	1	0	0	0	14557	536	19	1	1880	1	SLC27A1	19	17615314	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	5112390	17615314	41513669	69	7855											
DMWD	1762	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46294234	46294234	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacttgacccgctgagaagcCcaccagcagcgagatggtct	10	6	11	14	2	1	3	0	2	1	2	1	5	1	3	3	1	3	2	3	1	1	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:46294234C>A	ENST00000270223.6	-	2	598	c.553G>T	c.(553-555)Ggc>Tgc	p.G185C	DMWD_ENST00000601370.1_5'UTR|DMWD_ENST00000377735.3_Missense_Mutation_p.G185C	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	185										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GCTGAGAAGCCCACCAGCAGC	0.557																																					p.G185C		.											.	DMWD-90	0			c.G553T						.						162	154	157					19																	46294234		2203	4300	6503	SO:0001583	missense	1762	exon2			AGAAGCCCACCAG	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"WD repeat domain containing"	2936	protein-coding gene	gene with protein product		609857	"dystrophia myotonica-containing WD repeat motif"			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.553G>T	19.37:g.46294234C>A	ENSP00000270223:p.Gly185Cys	Somatic	149	1		WXS	Illumina HiSeq	Phase_I	128	41	NM_004943	0	0	39	71	32		Missense_Mutation	SNP	ENST00000270223.6	37	CCDS33054.1	.	.	.	.	.	.	.	.	.	.	c	20.9	4.060250	0.76074	.	.	ENSG00000185800	ENST00000377735;ENST00000270223	T;T	0.41758	0.99;0.99	4.44	3.4	0.38934	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.156128	0.41396	D	0.000891	T	0.53481	0.1799	L	0.50333	1.59	0.80722	D	1	D;D	0.69078	0.997;0.995	D;P	0.65874	0.939;0.871	T	0.56074	-0.8039	10	0.87932	D	0	-24.3543	10.5669	0.45177	0.0:0.9038:0.0:0.0962	.	185;185	G5E9A7;Q09019	.;DMWD_HUMAN	C	185	ENSP00000366964:G185C;ENSP00000270223:G185C	ENSP00000270223:G185C	G	-	1	0	DMWD	50986074	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.467000	0.66737	1.225000	0.43566	0.561000	0.74099	GGC	.		0.557	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943		A	46294234	C	A	46294234	3	1	85	1	0	0	0	0	1	0	0	0	4604	623	22	4	1487	4	DMWD	19	46294234	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	28678920	46294234	12834749	70	7856											
ZNF613	79898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52448014	52448014	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatatatatgcagtgattGtggaaaaggcttcatcaaga	14	12	10	5	0	3	2	3	1	0	1	3	3	3	3	0	2	1	2	0	2	6	5			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:52448014G>T	ENST00000293471.6	+	6	1557	c.878G>T	c.(877-879)tGt>tTt	p.C293F	ZNF613_ENST00000391794.4_Missense_Mutation_p.C257F	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	293					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(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		TGCAGTGATTGTGGAAAAGGC	0.438																																					p.C293F		.											.	ZNF613-91	0			c.G878T						.						67	73	71					19																	52448014		2203	4300	6503	SO:0001583	missense	79898	exon6			GTGATTGTGGAAA	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.878G>T	19.37:g.52448014G>T	ENSP00000293471:p.Cys293Phe	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	107	30	NM_001031721	0	0	2	5	3	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	37	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176698	0.57692	.	.	ENSG00000176024	ENST00000293471;ENST00000391794	D;D	0.85861	-2.04;-2.04	3.1	3.1	0.35709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36034	N	0.002824	D	0.94673	0.8282	H	0.97415	4	0.43662	D	0.99608	D	0.89917	1.0	D	0.91635	0.999	D	0.96089	0.9060	10	0.87932	D	0	.	13.4498	0.61163	0.0:0.0:1.0:0.0	.	293	Q6PF04	ZN613_HUMAN	F	293;257	ENSP00000293471:C293F;ENSP00000375671:C257F	ENSP00000293471:C293F	C	+	2	0	ZNF613	57139826	1.000000	0.71417	0.876000	0.34364	0.804000	0.45430	8.406000	0.90216	1.730000	0.51580	0.655000	0.94253	TGT	.		0.438	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		T	52448014	G	T	52448014	3	4	85	1	0	0	0	0	1	0	0	0	18070	1377	48	4	892	4	ZNF613	19	52448014	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	6153780	52448014	6680969	71	7857											
ZNF845	91664	broad.mit.edu	37	chr19	53855052	53855052	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaccttgaaagacataggaAaattcatactggagagaaac	20	7	8	6	0	1	3	1	1	0	2	1	6	1	5	1	2	3	0	1	2	7	4	rs62115343		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:53855052A>G	ENST00000595091.1	+	5	1343	c.1124A>G	c.(1123-1125)aAa>aGa	p.K375R	ZNF845_ENST00000458035.1_Missense_Mutation_p.K375R			Q96IR2	ZN845_HUMAN	zinc finger protein 845	375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AGACATAGGAAAATTCATACT	0.403																																					p.K375R													.	.	0			c.A1124G						.						31	31	31					19																	53855052		692	1591	2283	SO:0001583	missense	91664	exon4			ATAGGAAAATTCA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"Zinc fingers, C2H2-type", "-"	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1124A>G	19.37:g.53855052A>G	ENSP00000470005:p.Lys375Arg	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_138374	0	4	13	42	25		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	2.473	-0.321469	0.05386	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.17213	2.29	2.05	-4.11	0.03928	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02888	0.0086	N	0.00879	-1.12	0.09310	N	1	B	0.11235	0.004	B	0.18871	0.023	T	0.26430	-1.0103	9	0.02654	T	1	.	0.7406	0.00973	0.2094:0.1443:0.3556:0.2906	rs62115343	375	Q96IR2	ZN845_HUMAN	R	375	ENSP00000388311:K375R	ENSP00000412086:K375R	K	+	2	0	ZNF845	58546864	0.000000	0.05858	0.000000	0.03702	0.786000	0.44442	-0.260000	0.08708	-1.557000	0.01692	0.172000	0.16884	AAA	.		0.403	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		G	53855052	A	G	53855052	3	3	85	1	0	0	0	0	1	0	0	0	18223	14	1	3	1134	3	ZNF845	19	53855052	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	1407038	53855052	5273931	72	7858											
LAMA5	3911	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	60927089	60927089	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cacgtagcagcggcgagtagGagaaattcatggcgcccgga	11	5	15	10	5	1	1	1	0	0	1	1	4	1	2	1	4	2	3	1	4	3	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr20:60927089G>T	ENST00000252999.3	-	5	800	c.734C>A	c.(733-735)tCc>tAc	p.S245Y	RP11-157P1.5_ENST00000477848.1_RNA|LAMA5_ENST00000370677.3_Missense_Mutation_p.S245Y|RP11-157P1.5_ENST00000487421.1_RNA|RP11-157P1.5_ENST00000456721.2_RNA|LAMA5_ENST00000370692.3_Missense_Mutation_p.S245Y|RP11-157P1.5_ENST00000478167.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	245	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CGGCGAGTAGGAGAAATTCAT	0.637																																					p.S245Y													.	LAMA5-93	0			c.C734A						.						85	62	70					20																	60927089		2202	4298	6500	SO:0001583	missense	3911	exon5			GAGTAGGAGAAAT	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.734C>A	20.37:g.60927089G>T	ENSP00000252999:p.Ser245Tyr	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	23	9	NM_005560	0	0	9	10	1	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	g	20.9	4.066561	0.76187	.	.	ENSG00000130702	ENST00000252999;ENST00000370692;ENST00000370677	T;T;T	0.75704	-0.96;-0.96;-0.96	4.34	4.34	0.51931	Laminin, N-terminal (3);	0.000000	0.85682	U	0.000000	T	0.80281	0.4594	L	0.33339	1.005	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.83490	0.0069	10	0.87932	D	0	.	16.8522	0.85996	0.0:0.0:1.0:0.0	.	245	O15230	LAMA5_HUMAN	Y	245	ENSP00000252999:S245Y;ENSP00000359726:S245Y;ENSP00000359711:S245Y	ENSP00000252999:S245Y	S	-	2	0	LAMA5	60360484	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	9.661000	0.98601	1.973000	0.57446	0.486000	0.48141	TCC	.		0.637	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60927089	G	T	60927089	3	4	85	1	0	0	0	0	1	0	0	0	8630	1174	41	4	10657	4	LAMA5	20	60927089	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		60927089	2098431	73	7859											
CBR1	873	broad.mit.edu;bcgsc.ca	37	chr21	37442617	37442626	+	Frame_Shift_Del	DEL	GAGCATCCGC	GAGCATCCGC	-																															ctggacatcgacgatctgcaGagcatccgcgccctgcgcga																								rs543800905	byFrequency	TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	GAGCATCCGC	GAGCATCCGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr21:37442617_37442626delGAGCATCCGC	ENST00000290349.6	+	1	379_388	c.204_213delGAGCATCCGC	c.(202-213)cagagcatccgcfs	p.QSIR68fs	CBR1_ENST00000466328.2_3'UTR|CBR1_ENST00000530908.1_Frame_Shift_Del_p.QSIR68fs|SETD4_ENST00000399201.1_Intron|CBR1_ENST00000439427.2_Frame_Shift_Del_p.QSIR68fs|CBR1_ENST00000399191.3_Frame_Shift_Del_p.QSIR68fs|AP000688.14_ENST00000535199.1_RNA	NM_001757.2	NP_001748.1	P16152	CBR1_HUMAN	carbonyl reductase 1	68					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|drug metabolic process (GO:0017144)|epithelial cell differentiation (GO:0030855)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin K metabolic process (GO:0042373)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	15-hydroxyprostaglandin dehydrogenase (NADP+) activity (GO:0047021)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|prostaglandin-E2 9-reductase activity (GO:0050221)			endometrium(2)|kidney(3)	5					Doxorubicin(DB00997)|Haloperidol(DB00502)|Lubiprostone(DB01046)|Tetrabenazine(DB04844)	ACGATCTGCAGAGCATCCGCGCCCTGCGCG	0.7																																					p.68_71del													.	CBR1-90	0			c.204_213del						.																																			SO:0001589	frameshift_variant	873	exon1			TCTGCAGAGCATC		CCDS13641.1, CCDS68202.1	21q22.1	2011-09-14			ENSG00000159228	ENSG00000159228	1.1.1.184	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	1548	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 21C, member 1"	114830		CBR		8432528, 19027726	Standard	NM_001757		Approved	SDR21C1	uc002yvb.1	P16152	OTTHUMG00000086618	ENST00000290349.6:c.204_213delGAGCATCCGC	21.37:g.37442617_37442626delGAGCATCCGC	ENSP00000290349:p.Gln68fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	47	9	NM_001757	0	0	0	0	0	B2RBZ7|B4DFK7|Q3LHW8	Frame_Shift_Del	DEL	ENST00000290349.6	37	CCDS13641.1																																																																																			.		0.7	CBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194633.2			-	37442626	GAGCATCCGC	-	37442617	7	5	85	1	0	1	0	1	0	0	0	0	2714	933	33	0	206	0	CBR1	21	37442617	Frame_Shift_Del	DEL	GAGCATCCGC	TCGA-BQ-7053-01A-11D-1961-08		37442617	10687278	74	7860											
KCNJ15	3772	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	39672237	39672239	+	In_Frame_Del	DEL	GAG	GAG	-																															attctgagaaacagcaactcGaggagaagtacaggcaggag																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr21:39672237_39672239delGAG	ENST00000328656.4	+	4	1357_1359	c.1054_1056delGAG	c.(1054-1056)gagdel	p.E353del	KCNJ15_ENST00000398938.2_In_Frame_Del_p.E353del|KCNJ15_ENST00000398932.1_In_Frame_Del_p.E353del|KCNJ15_ENST00000398930.1_In_Frame_Del_p.E353del|KCNJ15_ENST00000398934.1_In_Frame_Del_p.E353del	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	353					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	ACAGCAACTCGAGGAGAAGTACA	0.443																																					p.352_352del		.											.	KCNJ15-157	0			c.1054_1056del						.																																			SO:0001651	inframe_deletion	3772	exon4			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.1054_1056delGAG	21.37:g.39672240_39672242delGAG	ENSP00000331698:p.Glu353del	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	66	18	NM_002243	0	0	0	0	0	D3DSH5|O00564|Q96L28|Q99446	In_Frame_Del	DEL	ENST00000328656.4	37	CCDS13656.1																																																																																			.		0.443	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		-	39672239	GAG	-	39672237	7	5	85	1	0	1	0	1	0	0	0	0	8070	1059	37	0	1056	0	KCNJ15	21	39672237	In_Frame_Del	DEL	GAG	TCGA-BQ-7053-01A-11D-1961-08	2229620	39672237	8457658	75	7861											
SGSM3	57591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40803806	40803806	+	IGR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgcagatcgtgtctcagaAggacgagcactgctgggtgg	8	9	16	8	2	1	2	1	0	1	2	3	4	1	3	0	3	3	3	0	3	1	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr22:40803806A>C	ENST00000355630.3	-	0	4496				SGSM3_ENST00000248929.9_Missense_Mutation_p.K513T|SGSM3_ENST00000454798.2_Missense_Mutation_p.K446T	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1						negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GTGTCTCAGAAGGACGAGCAC	0.622			T	RBM15	acute megakaryocytic leukemia																																p.K513T		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	SGSM3-494	0			c.A1538C						.						60	61	60					22																	40803806		2203	4300	6503	SO:0001628	intergenic_variant	27352	exon14			CTCAGAAGGACGA	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146		22.37:g.40803806A>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	108	31	NM_015705	0	0	3	4	1	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958990	0.92726	.	.	ENSG00000100359	ENST00000248929;ENST00000454798	T;T	0.49720	0.77;0.77	5.23	5.23	0.72850	Src homology-3 domain (4);	0.045898	0.85682	D	0.000000	T	0.47911	0.1471	N	0.04820	-0.15	0.80722	D	1	D;D;D;D	0.65815	0.985;0.958;0.981;0.995	P;P;P;D	0.69479	0.876;0.904;0.905;0.964	T	0.61222	-0.7106	10	0.87932	D	0	.	15.4205	0.75006	1.0:0.0:0.0:0.0	.	450;446;541;513	B4DVE3;B4DMS2;Q96HU1-2;Q96HU1	.;.;.;SGSM3_HUMAN	T	513;446	ENSP00000248929:K513T;ENSP00000390998:K446T	ENSP00000248929:K513T	K	+	2	0	SGSM3	39133752	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.528000	0.90598	2.109000	0.64355	0.459000	0.35465	AAG	.		0.622	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		C	40803806	A	C	40803806	1	2	85	0	1	0	0	0	0	0	0	0	14256	72	3	5		5	SGSM3	22	40803806	IGR	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		40803806	10500760	76	7862											
TFE3	7030	ucsc.edu	37	chrX	48895570	48895570	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagtcctgtggtgcctccggGcagatagctgagcatttcat	7	11	12	11	1	1	2	1	1	0	1	3	2	3	2	3	2	3	3	3	2	1	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chrX:48895570G>C	ENST00000315869.7	-	5	1109	c.850C>G	c.(850-852)Ccc>Gcc	p.P284A	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	284					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GTGCCTCCGGGCAGATAGCTG	0.473			T	"SFPQ, ASPSCR1, PRCC, NONO, CLTC"	"papillary renal, alveolar soft part sarcoma, renal"																																p.P284A				Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3-658	0			c.C850G						.						63	43	49					X																	48895570		2202	4300	6502	SO:0001583	missense	7030	exon5			CTCCGGGCAGATA	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"Basic helix-loop-helix proteins"	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.850C>G	X.37:g.48895570G>C	ENSP00000314129:p.Pro284Ala	Somatic	23	0		WXS	Illumina HiSeq		20	1	NM_006521	0	0	51	71	20	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	37	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	g	18.56	3.650908	0.67472	.	.	ENSG00000068323	ENST00000315869	T	0.13657	2.57	5.89	5.89	0.94794	.	0.000000	0.56097	D	0.000028	T	0.11836	0.0288	L	0.36672	1.1	0.30279	N	0.791477	P	0.51057	0.941	B	0.43728	0.429	T	0.04153	-1.0973	10	0.05833	T	0.94	-14.1778	14.4424	0.67327	0.0:0.0:1.0:0.0	.	284	P19532	TFE3_HUMAN	A	284	ENSP00000314129:P284A	ENSP00000314129:P284A	P	-	1	0	TFE3	48782514	0.027000	0.19231	0.997000	0.53966	0.951000	0.60555	1.112000	0.31172	2.488000	0.83962	0.509000	0.49947	CCC	.		0.473	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		C	48895570	G	C	48895570	3	2	85	1	0	0	0	0	1	0	0	0	15832	1203	42	4	901	4	TFE3	23	48895570	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		48895570	106374990	77	7863											
TEX11	56159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	69898664	69898664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attctcaaacctcaaaactaCtggcagcttgtctccacaga	13	10	5	13	0	3	1	2	0	2	1	5	1	3	1	2	1	4	2	2	1	4	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chrX:69898664C>T	ENST00000395889.2	-	16	1432	c.1277G>A	c.(1276-1278)aGt>aAt	p.S426N	TEX11_ENST00000374320.2_Missense_Mutation_p.S101N|TEX11_ENST00000344304.3_Missense_Mutation_p.S426N|TEX11_ENST00000374333.2_Missense_Mutation_p.S411N	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	426					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					CTCAAAACTACTGGCAGCTTG	0.338																																					p.S426N		.											.	TEX11-178	0			c.G1277A						.						111	97	102					X																	69898664		2203	4300	6503	SO:0001583	missense	56159	exon16			AAACTACTGGCAG	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1277G>A	X.37:g.69898664C>T	ENSP00000379226:p.Ser426Asn	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	48	17	NM_001003811	0	0	0	0	0	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	C	4.605	0.112373	0.08831	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	4.58	-1.09	0.09904	Tetratricopeptide-like helical (1);	0.437979	0.23803	N	0.044403	T	0.45875	0.1364	N	0.08118	0	0.09310	N	1	B;B	0.26195	0.119;0.144	B;B	0.30251	0.069;0.113	T	0.30416	-0.9979	9	.	.	.	0.0168	3.6866	0.08331	0.1899:0.282:0.0:0.5281	.	411;426	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	N	411;426;101;426	ENSP00000363453:S411N;ENSP00000379226:S426N;ENSP00000363440:S101N;ENSP00000340995:S426N	.	S	-	2	0	TEX11	69815389	0.996000	0.38824	0.062000	0.19696	0.495000	0.33615	0.274000	0.18680	-0.223000	0.09943	-0.371000	0.07208	AGT	.		0.338	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	69898664	C	T	69898664	3	4	85	1	0	0	0	0	1	0	0	0	15806	565	20	2	1609	2	TEX11	23	69898664	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	21003094	69898664	85371896	78	7864											
NXF5	55998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	101096014	101096014	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatttctttcagtgatctTcagggtggcagccatgcagt	9	13	11	8	0	4	1	2	1	2	0	4	2	4	1	1	2	2	2	1	2	1	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chrX:101096014T>A	ENST00000361708.2	-	8	813	c.454A>T	c.(454-456)Aag>Tag	p.K152*	NXF5_ENST00000537026.1_Nonsense_Mutation_p.K152*|NXF5_ENST00000473265.2_Nonsense_Mutation_p.K152*			Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	152					mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|skin(1)	30						TCAGTGATCTTCAGGGTGGCA	0.483																																					p.K152X		.											.	NXF5-204	0			c.A454T						.						150	137	141					X																	101096014		2201	4298	6499	SO:0001587	stop_gained	55998	exon8			TGATCTTCAGGGT	AJ277654	CCDS14491.1, CCDS14491.2	Xq22	2008-07-28			ENSG00000126952	ENSG00000126952			8075	protein-coding gene	gene with protein product		300319				11566096	Standard	NM_032946		Approved		uc011mrk.1	Q9H1B4	OTTHUMG00000022042	ENST00000361708.2:c.454A>T	X.37:g.101096014T>A	ENSP00000355286:p.Lys152*	Somatic	477	0		WXS	Illumina HiSeq	Phase_I	428	115	NM_032946	0	0	0	0	0	A2RRM0|B1AV82|B1AV83|B1AV84|B1AV85|Q9H1B0|Q9H1B1|Q9H1B2|Q9H1B3	Nonsense_Mutation	SNP	ENST00000361708.2	37		.	.	.	.	.	.	.	.	.	.	.	33	5.216054	0.95104	.	.	ENSG00000126952	ENST00000537026;ENST00000473265;ENST00000361708	.	.	.	2.05	-1.72	0.08107	.	0.398739	0.24511	U	0.037890	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	4.5662	0.12187	0.0:0.1905:0.5335:0.2761	.	.	.	.	X	152	.	ENSP00000263032:K152X	K	-	1	0	NXF5	100982670	1.000000	0.71417	0.095000	0.20976	0.203000	0.24098	0.944000	0.29043	-0.554000	0.06150	0.220000	0.17776	AAG	.		0.483	NXF5-201	KNOWN	basic	protein_coding	protein_coding				A	101096014	T	A	101096014	4	1	85	1	0	0	0	0	0	1	0	0	10812	1792	62	5	679	5	NXF5	23	101096014	Nonsense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	31197350	101096014	54174546	79	7865											
ZMYM1	79830	broad.mit.edu	37	chr1	35579564	35579564	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagttgatatggataaaatAcatggccaggcctatgatag	14	10	12	5	0	0	2	0	2	0	0	0	4	0	4	2	4	1	1	2	4	6	6			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr1:35579564A>G	ENST00000373330.1	+	11	2307	c.2133A>G	c.(2131-2133)atA>atG	p.I711M	ZMYM1_ENST00000359858.4_Missense_Mutation_p.I711M|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	711						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGGATAAAATACATGGCCAGG	0.353																																					p.I711M													.	ZMYM1-90	0			c.A2133G						.						69	66	67					1																	35579564		1840	4090	5930	SO:0001583	missense	79830	exon10			TAAAATACATGGC	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.2133A>G	1.37:g.35579564A>G	ENSP00000362427:p.Ile711Met	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	27	3	NM_024772	0	0	2	2	0	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	37	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	A	5.170	0.216892	0.09810	.	.	ENSG00000197056	ENST00000359858;ENST00000373329;ENST00000373330	T;T;T	0.26518	1.73;1.73;1.73	4.24	1.87	0.25490	Ribonuclease H-like (1);	0.336982	0.25836	N	0.027985	T	0.39989	0.1099	L	0.61387	1.9	0.09310	N	1	D;D	0.76494	0.999;0.997	D;D	0.87578	0.998;0.996	T	0.10359	-1.0633	9	.	.	.	-8.2445	4.7047	0.12844	0.7354:0.0:0.096:0.1686	.	692;711	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	M	711;636;711	ENSP00000352920:I711M;ENSP00000362426:I636M;ENSP00000362427:I711M	.	I	+	3	3	ZMYM1	35352151	0.031000	0.19500	0.031000	0.17742	0.009000	0.06853	0.443000	0.21644	0.395000	0.25257	0.455000	0.32223	ATA	.		0.353	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		G	35579564	A	G	35579564	3	3	86	1	0	0	0	0	1	0	0	0	17731	381	14	3	2167	3	ZMYM1	1	35579564	Missense_Mutation	SNP	A	TCGA-BQ-7055-01A-11D-1961-08		35579564	213671057	1	7866											
TGFBRAP1	9392	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	105886051	105886051	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acaggcagtagtcctcggccGctgcaaagtcctgcagctcg	8	7	12	14	3	0	0	0	0	0	0	4	0	2	0	3	2	3	6	3	2	2	1			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr2:105886051G>A	ENST00000393359.2	-	11	2510	c.2084C>T	c.(2083-2085)gCg>gTg	p.A695V	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.A695V			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	695					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						GTCCTCGGCCGCTGCAAAGTC	0.657																																					p.A695V	Esophageal Squamous(183;794 2019 9730 21801 48859)	.											.	TGFBRAP1-91	0			c.C2084T						.						26	27	27					2																	105886051		2203	4300	6503	SO:0001583	missense	9392	exon11			TCGGCCGCTGCAA	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2084C>T	2.37:g.105886051G>A	ENSP00000377027:p.Ala695Val	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	35	6	NM_004257	0	0	5	6	1	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625045	0.66901	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.19806	2.12;2.12	5.54	4.64	0.57946	.	0.053015	0.85682	D	0.000000	T	0.49406	0.1555	M	0.86178	2.8	0.54753	D	0.999985	D;D	0.89917	1.0;0.992	D;D	0.68039	0.955;0.909	T	0.56098	-0.8035	10	0.46703	T	0.11	-29.6428	15.5761	0.76387	0.0:0.0:0.8611:0.1389	.	150;695	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	V	695;695;150	ENSP00000377027:A695V;ENSP00000258449:A695V	ENSP00000258449:A695V	A	-	2	0	TGFBRAP1	105252483	1.000000	0.71417	0.404000	0.26397	0.158000	0.22134	9.470000	0.97683	1.293000	0.44690	0.462000	0.41574	GCG	.		0.657	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105886051	G	A	105886051	3	1	86	1	0	0	0	0	1	0	0	0	15856	1087	38	1	506	1	TGFBRAP1	2	105886051	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08		105886051	137313322	2	7867											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179659659	179659659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgacagtacctctttagcaCcagtggcaacagcctctgct	9	10	8	14	0	2	1	0	1	2	0	2	1	2	1	3	1	5	4	3	1	3	3			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr2:179659659C>T	ENST00000591111.1	-	7	1459	c.1235G>A	c.(1234-1236)gGt>gAt	p.G412D	TTN_ENST00000360870.5_Missense_Mutation_p.G412D|TTN_ENST00000589042.1_Missense_Mutation_p.G412D|TTN_ENST00000359218.5_Missense_Mutation_p.G412D|TTN_ENST00000460472.2_Missense_Mutation_p.G412D|TTN_ENST00000342175.6_Missense_Mutation_p.G412D|TTN_ENST00000342992.6_Missense_Mutation_p.G412D			Q8WZ42	TITIN_HUMAN	titin	0	Ala-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCTTTAGCACCAGTGGCAAC	0.493																																					p.G412D		.											.	TTN-636	0			c.G1235A						.						88	89	89					2																	179659659		2203	4300	6503	SO:0001583	missense	7273	exon7			TTAGCACCAGTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.1235G>A	2.37:g.179659659C>T	ENSP00000465570:p.Gly412Asp	Somatic	114	1		WXS	Illumina HiSeq	Phase_I	114	43	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.70	1.717780	0.30413	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000436599	T;T;T;T;T;T	0.63580	-0.05;0.15;0.14;0.13;0.28;0.56	5.87	4.99	0.66335	.	.	.	.	.	T	0.60689	0.2288	M	0.66939	2.045	0.24546	N	0.994045	B;B;B;B;P	0.35628	0.049;0.049;0.049;0.049;0.513	B;B;B;B;B	0.29598	0.018;0.018;0.018;0.018;0.104	T	0.58912	-0.7552	9	0.87932	D	0	.	15.3811	0.74658	0.0:0.8613:0.1387:0.0	.	412;412;412;412;412	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	D	412;412;412;412;412;412;8	ENSP00000343764:G412D;ENSP00000434586:G412D;ENSP00000340554:G412D;ENSP00000352154:G412D;ENSP00000354117:G412D;ENSP00000405517:G8D	ENSP00000340554:G412D	G	-	2	0	TTN	179367904	0.004000	0.15560	0.087000	0.20705	0.026000	0.11368	-0.064000	0.11636	1.456000	0.47831	0.655000	0.94253	GGT	.		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179659659	C	T	179659659	3	4	86	1	0	0	0	0	1	0	0	0	16768	507	18	2	110177	2	TTN	2	179659659	Missense_Mutation	SNP	C	TCGA-BQ-7055-01A-11D-1961-08	73773608	179659659	63539714	3	7868											
CCDC71	64925	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	49200861	49200862	+	Frame_Shift_Del	DEL	CT	CT	-																															gacactgggggacccagtggCtctgttggttttgctctggt																										TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr3:49200861_49200862delCT	ENST00000321895.6	-	2	886_887	c.780_781delAG	c.(778-783)agagccfs	p.RA260fs		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	260										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GACCCAGTGGCTCTGTTGGTTT	0.624																																					p.260_261del		.											.	CCDC71-91	0			c.780_781del						.																																			SO:0001589	frameshift_variant	64925	exon2			.	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.780_781delAG	3.37:g.49200863_49200864delCT	ENSP00000319006:p.Arg260fs	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	152	43	NM_022903	0	0	0	0	0	Q6IPE2|Q9H8H4|Q9H9F1	Frame_Shift_Del	DEL	ENST00000321895.6	37	CCDS2790.1																																																																																			.		0.624	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		-	49200862	CT	-	49200861	7	5	86	1	0	1	0	1	0	0	0	0	2850	797	28	0	626	0	CCDC71	3	49200861	Frame_Shift_Del	DEL	CT	TCGA-BQ-7055-01A-11D-1961-08		49200861	148821569	4	7869											
MUC13	56667	broad.mit.edu	37	chr3	124632011	124632011	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcacgcacgcacactcAggggccccaccactcttctt	7	6	9	19	3	3	0	1	0	2	0	3	0	3	0	4	3	0	3	4	3	0	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr3:124632011A>G	ENST00000311075.3	-	8	1196	c.1158T>C	c.(1156-1158)ccT>ccC	p.P386P		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	387	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						ACGCACACTCAGGGGCCCCAC	0.488																																					p.P386P													.	MUC13-90	0			c.T1158C						.						69	70	70					3																	124632011		2203	4300	6503	SO:0001819	synonymous_variant	56667	exon8			ACACTCAGGGGCC	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"Mucins"	7511	protein-coding gene	gene with protein product		612181	"down-regulated in colon cancer 1", "mucin 13, epithelial transmembrane"	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.1158T>C	3.37:g.124632011A>G		Somatic	84	1		WXS	Illumina HiSeq	Phase_I	81	4	NM_033049	0	0	0	0	0	Q6UWD9|Q9NXT5	Silent	SNP	ENST00000311075.3	37																																																																																				.		0.488	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		G	124632011	A	G	124632011	2	3	86	1	0	0	0	0	0	0	0	1	9996	175	7	3		3	MUC13	3	124632011	Silent	SNP	A	TCGA-BQ-7055-01A-11D-1961-08	75431150	124632011	73390419	5	7870											
DEFB114	245928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	49931770	49931770	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacatctatcttacctggtaGaatgaaggtcacataacaca	15	10	7	9	0	3	2	1	1	2	1	3	3	3	2	1	2	2	1	1	2	6	4			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr6:49931770G>A	ENST00000322066.3	-	1	48	c.49C>T	c.(49-51)Cta>Tta	p.L17L		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	17					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TTACCTGGTAGAATGAAGGTC	0.284																																					p.L17L		.											.	DEFB114-91	0			c.C49T						.						69	68	68					6																	49931770		2202	4293	6495	SO:0001819	synonymous_variant	245928	exon1			CTGGTAGAATGAA	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"Defensins, beta"	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.49C>T	6.37:g.49931770G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	60	11	NM_001037499	0	0	0	0	0	Q8NES9	Silent	SNP	ENST00000322066.3	37	CCDS34474.1																																																																																			.		0.284	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499		A	49931770	G	A	49931770	2	1	86	1	0	0	0	0	0	0	0	1	4413	933	33	2		2	DEFB114	6	49931770	Silent	SNP	G	TCGA-BQ-7055-01A-11D-1961-08		49931770	121183297	6	7871											
MPDZ	8777	hgsc.bcm.edu	37	chr9	13183483	13183483	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaagaactgccatgaagAgataaaatagaggcttgagt	17	7	10	7	0	0	5	0	2	0	3	0	6	0	5	2	1	2	1	2	1	6	3			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr9:13183483A>G	ENST00000319217.7	-	19	2830	c.2583T>C	c.(2581-2583)tcT>tcC	p.S861S	MPDZ_ENST00000447879.1_Silent_p.S861S|MPDZ_ENST00000546205.1_Silent_p.S861S|MPDZ_ENST00000381022.2_Silent_p.S861S|MPDZ_ENST00000541718.1_Silent_p.S861S|MPDZ_ENST00000536827.1_Silent_p.S861S|MPDZ_ENST00000381015.4_Silent_p.S861S	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	861					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TGCCATGAAGAGATAAAATAG	0.408																																					p.S861S		.											.	MPDZ-231	0			c.T2583C						.						95	92	93					9																	13183483		1893	4126	6019	SO:0001819	synonymous_variant	8777	exon19			ATGAAGAGATAAA	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2583T>C	9.37:g.13183483A>G		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	48	3	NM_003829	0	0	15	15	0	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				.		0.408	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		G	13183483	A	G	13183483	2	3	86	1	0	0	0	0	0	0	0	1	9747	291	11	3		3	MPDZ	9	13183483	Silent	SNP	A	TCGA-BQ-7055-01A-11D-1961-08		13183483	128029948	7	7872											
CPSF7	79869	broad.mit.edu	37	chr11	61183647	61183647	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggccccactgtagcgtttgGtggggggaagaaggctggat	8	8	18	7	1	0	1	0	0	0	1	0	3	0	3	2	7	1	3	2	7	3	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr11:61183647G>T	ENST00000394888.4	-	6	1067	c.895C>A	c.(895-897)Cca>Aca	p.P299T	CPSF7_ENST00000439958.3_Missense_Mutation_p.P290T|CPSF7_ENST00000340437.4_Missense_Mutation_p.P342T|CPSF7_ENST00000448745.1_Missense_Mutation_p.P290T	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	299	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						GTAGCGTTTGGTGGGGGGAAG	0.557																																					p.P342T													.	CPSF7-90	0			c.C1024A						.						59	65	63					11																	61183647		2202	4298	6500	SO:0001583	missense	79869	exon6			CGTTTGGTGGGGG		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.895C>A	11.37:g.61183647G>T	ENSP00000378352:p.Pro299Thr	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	168	6	NM_024811	0	0	27	28	1	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	37	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551345	0.86127	.	.	ENSG00000149532	ENST00000340437;ENST00000394888;ENST00000439958;ENST00000448745;ENST00000544147	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.71	5.71	0.89125	.	0.287486	0.32819	N	0.005601	D	0.86810	0.6022	N	0.25890	0.77	0.80722	D	1	B;B;P;P	0.36438	0.418;0.418;0.553;0.553	B;B;P;P	0.48334	0.301;0.301;0.574;0.496	D	0.84301	0.0505	10	0.32370	T	0.25	-2.2755	19.4877	0.95037	0.0:0.0:1.0:0.0	.	290;299;342;290	B4DGF8;Q8N684;Q8N684-3;Q8N684-2	.;CPSF7_HUMAN;.;.	T	342;299;290;290;65	ENSP00000345412:P342T;ENSP00000378352:P299T;ENSP00000397203:P290T;ENSP00000407394:P290T	ENSP00000345412:P342T	P	-	1	0	CPSF7	60940223	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.408000	0.90221	2.686000	0.91538	0.650000	0.86243	CCA	.		0.557	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		T	61183647	G	T	61183647	3	4	86	1	0	0	0	0	1	0	0	0	3836	1261	44	4	536	4	CPSF7	11	61183647	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08		61183647	73822869	8	7873											
PYGM	5837	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	64522811	64522811	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggtccaacacagcctggatGtagccaccgacattgactga	11	7	10	13	2	0	2	0	2	0	0	1	4	1	3	4	2	3	1	4	2	2	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr11:64522811G>A	ENST00000164139.3	-	7	1187	c.789C>T	c.(787-789)taC>taT	p.Y263Y	PYGM_ENST00000377432.3_Silent_p.Y175Y	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	263					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAGCCTGGATGTAGCCACCGA	0.617																																					p.Y263Y		.											.	PYGM-92	0			c.C789T						.						119	118	118					11																	64522811		2201	4297	6498	SO:0001819	synonymous_variant	5837	exon7			CTGGATGTAGCCA		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.789C>T	11.37:g.64522811G>A		Somatic	216	1		WXS	Illumina HiSeq	Phase_I	211	11	NM_005609	0	0	2	2	0	A0AVK1|A6NDY6	Silent	SNP	ENST00000164139.3	37	CCDS8079.1																																																																																			.		0.617	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		A	64522811	G	A	64522811	2	1	86	1	0	0	0	0	0	0	0	1	12894	1372	48	2		2	PYGM	11	64522811	Silent	SNP	G	TCGA-BQ-7055-01A-11D-1961-08	3339164	64522811	70483705	9	7874											
CRY1	1407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	107399011	107399011	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcatactcaattgaaagttTagtaatgttccattcctaaa	15	15	4	7	0	2	1	2	1	0	0	4	1	4	1	2	0	1	3	2	0	7	8			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr12:107399011T>C	ENST00000008527.5	-	3	1150	c.283A>G	c.(283-285)Aaa>Gaa	p.K95E		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	95	Photolyase/cryptochrome alpha/beta.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						ATTGAAAGTTTAGTAATGTTC	0.343																																					p.K95E		.											.	CRY1-93	0			c.A283G						.						137	132	134					12																	107399011		2203	4300	6503	SO:0001583	missense	1407	exon3			AAAGTTTAGTAAT	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.283A>G	12.37:g.107399011T>C	ENSP00000008527:p.Lys95Glu	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	167	64	NM_004075	0	0	2	4	2		Missense_Mutation	SNP	ENST00000008527.5	37	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.847284	0.51164	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.61	5.61	0.85477	Rossmann-like alpha/beta/alpha sandwich fold (1);DNA photolyase, N-terminal (2);	0.160218	0.53938	D	0.000048	T	0.54319	0.1851	L	0.49640	1.575	0.41632	D	0.989029	B	0.19073	0.033	B	0.19666	0.026	T	0.52472	-0.8571	9	0.06757	T	0.87	-12.0027	15.8086	0.78538	0.0:0.0:0.0:1.0	.	95	Q16526	CRY1_HUMAN	E	95	.	ENSP00000008527:K95E	K	-	1	0	CRY1	105923141	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	5.296000	0.65698	2.147000	0.66899	0.477000	0.44152	AAA	.		0.343	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		C	107399011	T	C	107399011	3	2	86	1	0	0	0	0	1	0	0	0	3909	1763	61	3	1517	3	CRY1	12	107399011	Missense_Mutation	SNP	T	TCGA-BQ-7055-01A-11D-1961-08		107399011	26452884	10	7875											
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39190845	39190846	+	Missense_Mutation	DNP	GG	GG	CA																															agttccgcaggagctggtctGgcagcagcttggctggcagc																										TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr17:39190845_39190846GG>CA	ENST00000344363.5	-	1	261_262	c.228_229CC>TG	c.(226-231)tgCCag>tgTGag	p.Q77E		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	87			Missing (in allele KAP1.9). {ECO:0000269|PubMed:12228244}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GAGCTGGTCTGGCAGCAGCTTG	0.614																																					p.Q77E		.											.	.	0			c.C228T						.																																			SO:0001583	missense	81850	exon1			GGTCTGGCAGCAG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.228_229delinsCA	17.37:g.39190845_39190846delinsCA	ENSP00000344420:p.Gln77Glu	Somatic	101	2		WXS	Illumina HiSeq	Phase_I	128	8		0	0	0	0	0	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	DNP	ENST00000344363.5	37	CCDS42323.1																																																																																			.		0.614	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			CA	39190846	GG	CA	39190845	3	2	86	1	0	0	0	0	1	0	0	0	8524	1357	47	4	278	4	KRTAP1-3	17	39190845	Missense_Mutation	DNP	GG	TCGA-BQ-7055-01A-11D-1961-08		39190845	42004365	11	7876											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	159	2		WXS	Illumina HiSeq		145	2	NM_031203	0	0	1	1	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	86	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-BQ-7055-01A-11D-1961-08		8527467	50601516	12	7877											
ZNF181	339318	hgsc.bcm.edu	37	chr19	35232372	35232372	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggccttcattcataggtcAtctctcattcaccatcagaa	12	12	5	12	0	7	1	6	0	1	1	8	1	7	1	2	2	0	0	2	2	3	4	rs2607244		TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:35232372A>G	ENST00000492450.1	+	4	1175	c.1086A>G	c.(1084-1086)tcA>tcG	p.S362S	ZNF181_ENST00000392232.3_Silent_p.S406S|ZNF181_ENST00000459757.2_Silent_p.S361S			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTCATAGGTCATCTCTCATTC	0.398																																					p.S362S		.											.	ZNF181-91	0			c.A1086G						.						58	57	57					19																	35232372		2203	4300	6503	SO:0001819	synonymous_variant	339318	exon4			TAGGTCATCTCTC	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"Zinc fingers, C2H2-type", "-"	12971	protein-coding gene	gene with protein product		606741	"zinc finger protein 181 (HHZ181)"				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.1086A>G	19.37:g.35232372A>G		Somatic	56	2		WXS	Illumina HiSeq	Phase_I	49	5	NM_001029997	0	0	11	11	0	B7ZKX3|Q49A75	Silent	SNP	ENST00000492450.1	37	CCDS32990.2																																																																																			A|1.000;|0.000		0.398	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		G	35232372	A	G	35232372	2	3	86	1	0	0	0	0	0	0	0	1	17781	204	8	3		3	ZNF181	19	35232372	Silent	SNP	A	TCGA-BQ-7055-01A-11D-1961-08	26704905	35232372	23896611	13	7878											
SYT3	84258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	51135675	51135675	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcaggggatgtttggctcGgtttgaccccagcggccact	5	10	14	12	2	1	1	1	1	0	0	2	2	1	2	3	5	1	4	3	5	0	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:51135675G>A	ENST00000338916.4	-	2	1175	c.542C>T	c.(541-543)cCg>cTg	p.P181L	SYT3_ENST00000600079.1_Missense_Mutation_p.P181L|SYT3_ENST00000593901.1_Missense_Mutation_p.P181L|SYT3_ENST00000544769.1_Missense_Mutation_p.P181L	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	181					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		TGTTTGGCTCGGTTTGACCCC	0.657																																					p.P181L		.											.	SYT3-155	0			c.C542T						.						33	34	34					19																	51135675		2203	4300	6503	SO:0001583	missense	84258	exon2			TGGCTCGGTTTGA	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.542C>T	19.37:g.51135675G>A	ENSP00000340914:p.Pro181Leu	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	74	23	NM_032298	0	0	0	0	0	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	37	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.907284	0.33628	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.54479	0.57;0.57	5.24	5.24	0.73138	.	0.715640	0.12228	U	0.487701	T	0.29355	0.0731	N	0.03608	-0.345	0.09310	N	0.999994	B	0.09022	0.002	B	0.04013	0.001	T	0.06110	-1.0845	10	0.49607	T	0.09	.	8.4467	0.32847	0.169:0.0:0.831:0.0	.	181	Q9BQG1	SYT3_HUMAN	L	181	ENSP00000340914:P181L;ENSP00000438883:P181L	ENSP00000340914:P181L	P	-	2	0	SYT3	55827487	0.978000	0.34361	0.974000	0.42286	0.996000	0.88848	3.207000	0.51106	2.605000	0.88082	0.655000	0.94253	CCG	.		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		A	51135675	G	A	51135675	3	1	86	1	0	0	0	0	1	0	0	0	15507	1116	39	1	1258	1	SYT3	19	51135675	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08	15903303	51135675	7993308	14	7879											
ZNF304	57343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57869057	57869057	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcctcattctgcaccagaGggttcacactggagaaaagc	11	8	11	11	0	3	2	2	0	1	2	3	3	3	2	2	3	2	2	2	3	2	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:57869057G>A	ENST00000282286.5	+	3	1993	c.1820G>A	c.(1819-1821)aGg>aAg	p.R607K	ZNF304_ENST00000598744.1_Missense_Mutation_p.R565K|ZNF304_ENST00000391705.3_Missense_Mutation_p.R607K|ZNF304_ENST00000443917.2_Missense_Mutation_p.R654K			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	607					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(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CTGCACCAGAGGGTTCACACT	0.478																																					p.R607K		.											.	ZNF304-91	0			c.G1820A						.						84	81	82					19																	57869057		2203	4300	6503	SO:0001583	missense	57343	exon3			ACCAGAGGGTTCA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"Zinc fingers, C2H2-type", "-"	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.1820G>A	19.37:g.57869057G>A	ENSP00000282286:p.Arg607Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	106	23	NM_020657	0	0	4	5	1		Missense_Mutation	SNP	ENST00000282286.5	37	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814001	0.70912	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.18338	2.22;2.22;2.22	3.89	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29126	0.0724	L	0.42744	1.35	0.23056	N	0.998366	P;D	0.58970	0.898;0.984	P;D	0.69142	0.483;0.962	T	0.07462	-1.0771	9	0.45353	T	0.12	.	9.2462	0.37527	0.1894:0.0:0.8106:0.0	.	607;654	Q9HCX3;E7EQD3	ZN304_HUMAN;.	K	607;607;654	ENSP00000282286:R607K;ENSP00000375586:R607K;ENSP00000401642:R654K	ENSP00000282286:R607K	R	+	2	0	ZNF304	62560869	0.892000	0.30473	0.763000	0.31416	0.981000	0.71138	5.266000	0.65525	0.600000	0.29862	0.650000	0.86243	AGG	.		0.478	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1			A	57869057	G	A	57869057	3	1	86	1	0	0	0	0	1	0	0	0	17865	1000	35	2	1830	2	ZNF304	19	57869057	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08	6733382	57869057	1259926	15	7880											
XPNPEP2	7512	bcgsc.ca	37	chrX	128895980	128895980	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtttatgtcttcctttctAgggccagtgggattccagtc	6	16	10	9	0	2	0	0	0	2	0	5	1	4	1	3	2	0	1	3	2	2	6			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chrX:128895980A>G	ENST00000371106.3	+	18	1795		c.e18-1			NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound							anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						CTTCCTTTCTAGGGCCAGTGG	0.522																																					.													.	XPNPEP2-130	0			c.1604-2A>G						.						274	199	225					X																	128895980		2203	4300	6503	SO:0001630	splice_region_variant	7512	exon18			CTTTCTAGGGCCA	U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.1604-1A>G	X.37:g.128895980A>G		Somatic	73	0		WXS	Illumina HiSeq	Phase_1	63	4	NM_003399	0	0	0	0	0	A0AV16|O75994	Splice_Site	SNP	ENST00000371106.3	37	CCDS14613.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.129036	0.37533	.	.	ENSG00000122121	ENST00000371106	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2853	0.60239	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	XPNPEP2	128723661	1.000000	0.71417	0.963000	0.40424	0.321000	0.28281	6.894000	0.75655	1.779000	0.52309	0.350000	0.21858	.	.		0.522	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399	Intron	G	128895980	A	G	128895980	5	3	86	1	0	0	0	0	0	0	1	0	17476	434	15	3	1672	3	XPNPEP2	23	128895980	Splice_Site	SNP	A	TCGA-BQ-7055-01A-11D-1961-08		128895980	26374580	16	7881											
MAGEA6	4105	broad.mit.edu	37	chrX	151870045	151870045	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcggggatcccaagaagctGctcacccaatatttcgtgca	10	10	9	12	2	1	1	1	0	0	1	4	2	2	2	2	2	3	3	2	2	4	3			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chrX:151870045G>A	ENST00000329342.5	+	3	960	c.735G>A	c.(733-735)ctG>ctA	p.L245L		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	245	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					CCAAGAAGCTGCTCACCCAAT	0.562																																					p.L245L													.	MAGEA6-90	0			c.G735A						.						152	147	149					X																	151870045		2203	4299	6502	SO:0001819	synonymous_variant	4105	exon3			GAAGCTGCTCACC		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"MAGE-6 antigen", "melanoma-associated antigen 6", "melanoma antigen family A 6", "cancer/testis antigen family 1, member 6"	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.735G>A	X.37:g.151870045G>A		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	214	7	NM_005363	0	0	0	0	0	A8IF93|Q6NW44	Silent	SNP	ENST00000329342.5	37	CCDS14708.1																																																																																			.		0.562	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363		A	151870045	G	A	151870045	2	1	86	1	0	0	0	0	0	0	0	1	9195	1306	46	2		2	MAGEA6	23	151870045	Silent	SNP	G	TCGA-BQ-7055-01A-11D-1961-08	22974065	151870045	3400515	17	7882											
TRIT1	54802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40307511	40307511	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaacactctgactttctaTggtgttgacagcatctgagt	10	13	10	8	0	3	3	0	3	3	0	3	4	3	4	0	2	2	2	0	2	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:40307511T>C	ENST00000316891.5	-	11	1323	c.1309A>G	c.(1309-1311)Ata>Gta	p.I437V	TRIT1_ENST00000537440.1_Missense_Mutation_p.I133V|TRIT1_ENST00000537223.1_Missense_Mutation_p.I133V|TRIT1_ENST00000441669.2_Missense_Mutation_p.I355V|TRIT1_ENST00000372818.1_Missense_Mutation_p.I411V|TRIT1_ENST00000545233.1_Missense_Mutation_p.I191V|TRIT1_ENST00000491865.1_5'UTR|TRIT1_ENST00000541099.1_Missense_Mutation_p.I55V	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	437					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGACTTTCTATGGTGTTGACA	0.418																																					p.I437V		.											.	TRIT1-91	0			c.A1309G						.						266	252	257					1																	40307511		2203	4300	6503	SO:0001583	missense	54802	exon11			TTTCTATGGTGTT	AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.1309A>G	1.37:g.40307511T>C	ENSP00000321810:p.Ile437Val	Somatic	259	0		WXS	Illumina HiSeq	Phase_I	249	99	NM_017646	0	0	14	18	4	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Missense_Mutation	SNP	ENST00000316891.5	37	CCDS30681.1	.	.	.	.	.	.	.	.	.	.	T	0.782	-0.761836	0.02996	.	.	ENSG00000043514	ENST00000046894;ENST00000372825;ENST00000441669;ENST00000316891;ENST00000372818;ENST00000534869;ENST00000545233;ENST00000537440;ENST00000537223;ENST00000541099	T;T	0.41065	1.02;1.01	5.67	-5.07	0.02938	.	2.410530	0.01192	N	0.007346	T	0.21761	0.0524	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.06463	-1.0825	10	0.20519	T	0.43	0.246	1.1747	0.01832	0.3107:0.2806:0.0931:0.3157	.	437;411;355;133	Q9H3H1;Q9H3H1-4;Q9H3H1-5;Q3T7B5	MOD5_HUMAN;.;.;.	V	411;355;349;437;411;330;191;133;133;55	ENSP00000321810:I437V;ENSP00000361905:I411V	ENSP00000046894:I411V	I	-	1	0	TRIT1	40080098	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-0.878000	0.04192	-0.471000	0.06891	-0.242000	0.12053	ATA	.		0.418	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646		C	40307511	T	C	40307511	3	2	87	1	0	0	0	0	1	0	0	0	16593	1464	51	3	98	3	TRIT1	1	40307511	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		40307511	208943110	1	7883											
MIER1	57708	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	67423741	67423741	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttttattttgatttatttaGgaaggcgacatgccaattca	11	17	7	6	1	1	1	1	1	0	0	1	3	1	2	1	2	1	0	1	2	5	9			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:67423741G>C	ENST00000355356.3	+	4	329		c.e4-1		MIER1_ENST00000357692.2_Splice_Site|MIER1_ENST00000479067.1_Splice_Site|MIER1_ENST00000401042.3_Splice_Site|MIER1_ENST00000371014.1_Splice_Site|MIER1_ENST00000371016.1_Splice_Site|MIER1_ENST00000371018.3_Splice_Site|MIER1_ENST00000355977.6_Splice_Site|MIER1_ENST00000401041.1_Splice_Site	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator						positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						GATTTATTTAGGAAGGCGACA	0.373																																					.		.											.	MIER1-91	0			c.232-1G>C						.						87	80	82					1																	67423741		1874	4116	5990	SO:0001630	splice_region_variant	57708	exon6			TATTTAGGAAGGC		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.181-1G>C	1.37:g.67423741G>C		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	53	15	NM_001146111	0	0	0	0	0	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Splice_Site	SNP	ENST00000355356.3	37	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468581	0.63625	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8992	0.96978	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MIER1	67196329	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	8.843000	0.92142	2.789000	0.95967	0.591000	0.81541	.	.		0.373	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	Intron	C	67423741	G	C	67423741	5	2	87	1	0	0	0	0	0	0	1	0	9605	1014	35	4	434	4	MIER1	1	67423741	Splice_Site	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	27116230	67423741	181826880	2	7884											
USP33	23032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	78163088	78163088	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaccggaggtcgcaggataaCttcaggccctccaccataaa	13	6	9	13	2	1	0	1	0	0	0	3	2	2	2	4	4	2	1	4	4	4	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:78163088C>A	ENST00000370793.1	-	25	3089	c.2743G>T	c.(2743-2745)Gtt>Ttt	p.V915F	USP33_ENST00000370794.3_Missense_Mutation_p.V884F|USP33_ENST00000357428.1_Missense_Mutation_p.V915F	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	915	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						CGCAGGATAACTTCAGGCCCT	0.373																																					p.V915F	Melanoma(152;72 1870 11110 26780 42647)	.											.	USP33-659	0			c.G2743T						.						107	112	110					1																	78163088		2203	4300	6503	SO:0001583	missense	23032	exon25			GGATAACTTCAGG	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.2743G>T	1.37:g.78163088C>A	ENSP00000359829:p.Val915Phe	Somatic	139	1		WXS	Illumina HiSeq	Phase_I	131	47	NM_015017	0	0	7	18	11	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417992	0.62622	.	.	ENSG00000077254	ENST00000370794;ENST00000370793;ENST00000357428	T;T;T	0.12672	2.67;2.66;2.66	5.25	5.25	0.73442	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (3);	0.123739	0.53938	D	0.000042	T	0.12092	0.0294	L	0.41415	1.275	0.51012	D	0.999908	P	0.49447	0.924	P	0.55455	0.776	T	0.00978	-1.1493	10	0.87932	D	0	.	7.1563	0.25639	0.0:0.7905:0.0:0.2095	.	915	Q8TEY7	UBP33_HUMAN	F	884;915;915	ENSP00000359830:V884F;ENSP00000359829:V915F;ENSP00000350009:V915F	ENSP00000350009:V915F	V	-	1	0	USP33	77935676	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	1.037000	0.30241	2.602000	0.87976	0.650000	0.86243	GTT	.		0.373	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		A	78163088	C	A	78163088	3	1	87	1	0	0	0	0	1	0	0	0	17097	565	20	4	89	4	USP33	1	78163088	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	10739347	78163088	171087533	3	7885											
ZNHIT6	54680	broad.mit.edu	37	chr1	86123544	86123544	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttaccttggtgaagaactTtcatgtcattattggatcct	10	16	7	8	0	2	2	2	1	0	1	3	3	3	3	2	2	2	0	2	2	4	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:86123544T>G	ENST00000370574.3	-	9	1491	c.1358A>C	c.(1357-1359)aAa>aCa	p.K453T	ZNHIT6_ENST00000431532.2_Missense_Mutation_p.K414T			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	453					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						GTGAAGAACTTTCATGTCATT	0.328																																					p.K453T													.	ZNHIT6-153	0			c.A1358C						.						123	125	124					1																	86123544		2202	4289	6491	SO:0001583	missense	54680	exon9			AGAACTTTCATGT	AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.1358A>C	1.37:g.86123544T>G	ENSP00000359606:p.Lys453Thr	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	155	5	NM_017953	0	0	0	0	0	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Missense_Mutation	SNP	ENST00000370574.3	37	CCDS707.1	.	.	.	.	.	.	.	.	.	.	T	7.146	0.582748	0.13749	.	.	ENSG00000117174	ENST00000431532;ENST00000370574	T;T	0.45668	0.9;0.89	5.67	1.28	0.21552	.	0.875078	0.10215	N	0.701695	T	0.12390	0.0301	L	0.38175	1.15	0.09310	N	1	B;B	0.24092	0.097;0.097	B;B	0.16722	0.016;0.016	T	0.25950	-1.0117	10	0.39692	T	0.17	-1.7217	5.4691	0.16660	0.4588:0.0:0.128:0.4132	.	414;453	B4DP13;Q9NWK9	.;BCD1_HUMAN	T	414;453	ENSP00000414344:K414T;ENSP00000359606:K453T	ENSP00000359606:K453T	K	-	2	0	ZNHIT6	85896132	0.022000	0.18835	0.121000	0.21740	0.985000	0.73830	0.713000	0.25794	0.447000	0.26695	0.533000	0.62120	AAA	.		0.328	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		G	86123544	T	G	86123544	3	3	87	1	0	0	0	0	1	0	0	0	18241	1841	64	5	62	5	ZNHIT6	1	86123544	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	7960456	86123544	163127077	4	7886											
ARHGAP29	9411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94668261	94668261	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgcatgcataataattttgCctttttgagagcattctctg	9	18	7	7	0	1	1	0	1	1	1	2	2	1	1	1	0	4	3	1	0	2	8			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:94668261C>A	ENST00000260526.6	-	11	1164	c.982G>T	c.(982-984)Gca>Tca	p.A328S	ARHGAP29_ENST00000370217.3_Missense_Mutation_p.A328S	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	328					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		AATAATTTTGCCTTTTTGAGA	0.388																																					p.A328S		.											.	ARHGAP29-296	0			c.G982T						.						145	130	135					1																	94668261		2203	4300	6503	SO:0001583	missense	9411	exon11			ATTTTGCCTTTTT		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.982G>T	1.37:g.94668261C>A	ENSP00000260526:p.Ala328Ser	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	77	26	NM_004815	0	0	0	3	3	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.652915	0.88056	.	.	ENSG00000137962	ENST00000260526;ENST00000370217	T;T	0.47869	0.83;0.83	6.06	5.16	0.70880	.	0.000000	0.38381	N	0.001718	T	0.58278	0.2111	M	0.69358	2.11	0.58432	D	0.999999	P;D	0.89917	0.944;1.0	P;D	0.83275	0.646;0.996	T	0.60622	-0.7227	10	0.41790	T	0.15	-25.713	15.6619	0.77193	0.0:0.9344:0.0:0.0656	.	328;328	Q52LW3-2;Q52LW3	.;RHG29_HUMAN	S	328	ENSP00000260526:A328S;ENSP00000359237:A328S	ENSP00000260526:A328S	A	-	1	0	ARHGAP29	94440849	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.054000	0.76649	1.578000	0.49821	0.650000	0.86243	GCA	.		0.388	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		A	94668261	C	A	94668261	3	1	87	1	0	0	0	0	1	0	0	0	878	739	26	4	2855	4	ARHGAP29	1	94668261	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	8544717	94668261	154582360	5	7887											
KCNC4	3749	ucsc.edu	37	chr1	110774883	110774883	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccccttcagcattcaccTgaggctgcatgccctccaac	7	10	6	18	0	2	1	2	1	0	0	4	1	4	1	5	1	4	3	5	1	1	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:110774883T>C	ENST00000369787.3	+	4	1887	c.1860T>C	c.(1858-1860)ccT>ccC	p.P620P	KCNC4_ENST00000413138.3_Intron|KCNC4_ENST00000438661.2_Intron|KCNC4_ENST00000412512.2_Intron	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	620					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		AGCATTCACCTGAGGCTGCAT	0.547																																					p.P620P													.	KCNC4-154	0			c.T1860C						.						99	73	82					1																	110774883		2203	4300	6503	SO:0001819	synonymous_variant	3749	exon4			TTCACCTGAGGCT	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.1860T>C	1.37:g.110774883T>C		Somatic	41	0		WXS	Illumina HiSeq		33	4	NM_004978	0	0	0	0	0	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	37	CCDS821.1																																																																																			.		0.547	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		C	110774883	T	C	110774883	2	2	87	1	0	0	0	0	0	0	0	1	8038	1567	55	3		3	KCNC4	1	110774883	Silent	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	16106622	110774883	138475738	6	7888											
BCL9	607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	147086309	147086309	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaaatgctacagcccccAggtcttctaccccctcccat	9	9	4	19	0	3	0	1	0	2	0	4	0	4	0	5	1	4	1	5	1	3	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:147086309A>C	ENST00000234739.3	+	6	1194	c.454A>C	c.(454-456)Agg>Cgg	p.R152R	BCL9_ENST00000473292.1_3'UTR	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	152					canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					TACAGCCCCCAGGTCTTCTAC	0.498			T	"IGH@, IGL@"	B-ALL																																p.R152R		.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9-707	0			c.A454C						.						118	119	119					1																	147086309		2203	4300	6503	SO:0001819	synonymous_variant	607	exon6			GCCCCCAGGTCTT	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.454A>C	1.37:g.147086309A>C		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	76	30	NM_004326	0	0	2	2	0	Q5T489	Silent	SNP	ENST00000234739.3	37	CCDS30833.1																																																																																			.		0.498	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		C	147086309	A	C	147086309	2	2	87	1	0	0	0	0	0	0	0	1	1382	179	7	5		5	BCL9	1	147086309	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	36311426	147086309	102164312	7	7889											
BCL9	607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	147086367	147086367	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagcccacacctgctcagaAgactccagccaaagtggtgt	12	6	10	13	0	1	3	1	0	0	3	2	3	2	3	4	1	3	1	4	1	2	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:147086367A>G	ENST00000234739.3	+	6	1252	c.512A>G	c.(511-513)aAg>aGg	p.K171R	BCL9_ENST00000473292.1_3'UTR	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	171					canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					CCTGCTCAGAAGACTCCAGCC	0.537			T	"IGH@, IGL@"	B-ALL																																p.K171R		.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9-707	0			c.A512G						.						106	100	102					1																	147086367		2203	4300	6503	SO:0001583	missense	607	exon6			CTCAGAAGACTCC	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.512A>G	1.37:g.147086367A>G	ENSP00000234739:p.Lys171Arg	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	63	34	NM_004326	0	0	0	1	1	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492914	0.84962	.	.	ENSG00000116128	ENST00000234739	T	0.63580	-0.05	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.64382	0.2593	L	0.41824	1.3	0.58432	D	0.999993	D;D	0.63880	0.993;0.993	D;D	0.72625	0.978;0.978	T	0.63598	-0.6601	10	0.36615	T	0.2	-20.3683	15.8615	0.79026	1.0:0.0:0.0:0.0	.	171;171	Q1JQ81;O00512	.;BCL9_HUMAN	R	171	ENSP00000234739:K171R	ENSP00000234739:K171R	K	+	2	0	BCL9	145552991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.962000	0.76048	2.333000	0.79357	0.533000	0.62120	AAG	.		0.537	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		G	147086367	A	G	147086367	3	3	87	1	0	0	0	0	1	0	0	0	1382	72	3	3	522	3	BCL9	1	147086367	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	58	147086367	102164254	8	7890											
KPRP	448834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152733695	152733695	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggggcaagagagtggtgctgGctgtgggcctggtgatgtgt	5	10	21	5	0	0	2	0	1	0	1	0	3	0	2	1	6	1	3	1	6	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:152733695G>A	ENST00000606109.1	+	1	1659	c.1631G>A	c.(1630-1632)gGc>gAc	p.G544D	KPRP_ENST00000368773.1_Missense_Mutation_p.G544D			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	544						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTGGTGCTGGCTGTGGGCCT	0.577																																					p.G544D		.											.	KPRP-95	0			c.G1631A						.						78	72	74					1																	152733695		2203	4300	6503	SO:0001583	missense	448834	exon2			GTGCTGGCTGTGG	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"chromosome 1 open reading frame 45"	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1631G>A	1.37:g.152733695G>A	ENSP00000475216:p.Gly544Asp	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	117	52	NM_001025231	0	0	0	0	0		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.224172	0.58668	.	.	ENSG00000203786	ENST00000368773	T	0.12672	2.66	3.95	3.03	0.35002	.	0.773292	0.11405	N	0.567368	T	0.05181	0.0138	L	0.40543	1.245	0.09310	N	1	P	0.44044	0.825	B	0.41691	0.364	T	0.28170	-1.0052	10	0.51188	T	0.08	-1.4837	7.7874	0.29099	0.114:0.0:0.886:0.0	.	544	Q5T749	KPRP_HUMAN	D	544	ENSP00000357762:G544D	ENSP00000357762:G544D	G	+	2	0	KPRP	151000319	0.168000	0.22989	0.022000	0.16811	0.516000	0.34256	0.680000	0.25306	1.243000	0.43853	0.313000	0.20887	GGC	.		0.577	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152733695	G	A	152733695	3	1	87	1	0	0	0	0	1	0	0	0	8457	1203	42	2	1633	2	KPRP	1	152733695	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	5647328	152733695	96516926	9	7891											
NID1	4811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	236195870	236195870	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacgtaagagtggaggtcAgtgttctcaaagacaatggg	13	9	13	6	1	2	2	2	0	1	2	3	3	2	3	0	3	1	2	0	3	4	3	rs564280440		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:236195870A>G	ENST00000264187.6	-	6	1450	c.1368T>C	c.(1366-1368)acT>acC	p.T456T	NID1_ENST00000366595.3_Silent_p.T456T	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	456	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	AGTGGAGGTCAGTGTTCTCAA	0.537													A|||	1	0.000199681	0	0.0014	5008	,	,		18327	0		0	False		,,,				2504	0				p.T456T		.											.	NID1-154	0			c.T1368C						.						89	80	83					1																	236195870		2203	4300	6503	SO:0001819	synonymous_variant	4811	exon6			GAGGTCAGTGTTC	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"nidogen (enactin)"	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.1368T>C	1.37:g.236195870A>G		Somatic	45	1		WXS	Illumina HiSeq	Phase_I	59	23	NM_002508	0	0	6	8	2	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																			.		0.537	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		G	236195870	A	G	236195870	2	3	87	1	0	0	0	0	0	0	0	1	10440	175	7	3		3	NID1	1	236195870	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	83462175	236195870	13054751	10	7892											
NLRP3	114548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247597496	247597496	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggagctggacctgagtGacaacgccctcggtgacttc	7	9	14	11	2	0	3	0	3	0	0	2	5	0	5	2	4	2	1	2	4	1	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:247597496G>T	ENST00000336119.3	+	5	3165	c.2419G>T	c.(2419-2421)Gac>Tac	p.D807Y	NLRP3_ENST00000348069.2_Missense_Mutation_p.D750Y|NLRP3_ENST00000391827.2_Missense_Mutation_p.D750Y|NLRP3_ENST00000366497.2_Missense_Mutation_p.D807Y|NLRP3_ENST00000391828.3_Missense_Mutation_p.D807Y|NLRP3_ENST00000366496.2_Missense_Mutation_p.D807Y	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	807					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GGACCTGAGTGACAACGCCCT	0.577																																					p.D807Y		.											.	NLRP3-674	0			c.G2419T						.						136	123	127					1																	247597496		2203	4300	6503	SO:0001583	missense	114548	exon5			CTGAGTGACAACG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2419G>T	1.37:g.247597496G>T	ENSP00000337383:p.Asp807Tyr	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	121	38	NM_004895	0	0	0	0	0	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	g	1.230	-0.624429	0.03636	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;D;T;D	0.87729	0.56;0.63;0.56;-2.29;0.63;-2.29	3.44	1.55	0.23275	.	0.684628	0.12798	N	0.438274	T	0.69369	0.3103	N	0.13198	0.31	0.09310	N	0.999996	B;B;B;B;B	0.33826	0.427;0.004;0.279;0.013;0.015	B;B;B;B;B	0.34301	0.179;0.01;0.086;0.043;0.012	T	0.61153	-0.7120	10	0.02654	T	1	.	4.9238	0.13883	0.1408:0.2854:0.5737:0.0	.	787;750;750;807;807	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	Y	807;807;807;750;807;750	ENSP00000375704:D807Y;ENSP00000355453:D807Y;ENSP00000337383:D807Y;ENSP00000294752:D750Y;ENSP00000355452:D807Y;ENSP00000375703:D750Y	ENSP00000337383:D807Y	D	+	1	0	NLRP3	245664119	0.000000	0.05858	0.947000	0.38551	0.104000	0.19210	-1.135000	0.03225	0.475000	0.27415	0.472000	0.43445	GAC	.		0.577	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247597496	G	T	247597496	3	4	87	1	0	0	0	0	1	0	0	0	10504	1290	45	4	2437	4	NLRP3	1	247597496	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	11401626	247597496	1653125	11	7893											
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32726845	32726845	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttggatgccatatcagttGgggatggattatttaccata	10	14	12	5	0	1	0	1	0	0	0	1	3	1	3	2	5	2	2	2	5	4	7			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:32726845G>A	ENST00000421745.2	+	47	9231	c.9097G>A	c.(9097-9099)Ggg>Agg	p.G3033R		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3033					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CATATCAGTTGGGGATGGATT	0.363																																					p.G3033R	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.G9097A						.						126	121	123					2																	32726845		2203	4300	6503	SO:0001583	missense	57448	exon47			TCAGTTGGGGATG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.9097G>A	2.37:g.32726845G>A	ENSP00000393596:p.Gly3033Arg	Somatic	138	1		WXS	Illumina HiSeq	Phase_I	116	23	NM_016252	0	0	0	0	0	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	33	5.269920	0.95429	.	.	ENSG00000115760	ENST00000421745	T	0.75154	-0.91	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.83774	0.5327	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84031	0.0359	10	0.66056	D	0.02	.	20.0137	0.97470	0.0:0.0:1.0:0.0	.	3033	Q9NR09	BIRC6_HUMAN	R	3033	ENSP00000393596:G3033R	ENSP00000393596:G3033R	G	+	1	0	BIRC6	32580349	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.734000	0.93682	0.563000	0.77884	GGG	.		0.363	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32726845	G	A	32726845	3	1	87	1	0	0	0	0	1	0	0	0	1439	1348	47	2	9283	2	BIRC6	2	32726845	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		32726845	210472528	12	7894											
HEATR5B	54497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37280725	37280725	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagcttgtttaacacattCagcaaagtgatccaacattt	13	15	5	8	0	1	1	1	1	0	0	2	1	2	1	1	0	4	3	1	0	4	7			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:37280725C>A	ENST00000233099.5	-	17	2520	c.2425G>T	c.(2425-2427)Gaa>Taa	p.E809*	HEATR5B_ENST00000354531.2_Nonsense_Mutation_p.E809*	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	809						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TTAACACATTCAGCAAAGTGA	0.328																																					p.E809X		.											.	HEATR5B-142	0			c.G2425T						.						51	52	52					2																	37280725		2203	4300	6503	SO:0001587	stop_gained	54497	exon17			CACATTCAGCAAA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2425G>T	2.37:g.37280725C>A	ENSP00000233099:p.Glu809*	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	28	8	NM_019024	0	0	0	0	0	B5MDU8|Q7Z3B2|Q9NVL7	Nonsense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	42	9.667231	0.99233	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-27.7923	20.1736	0.98170	0.0:1.0:0.0:0.0	.	.	.	.	X	809	.	ENSP00000233099:E809X	E	-	1	0	HEATR5B	37134229	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.771000	0.85420	2.767000	0.95098	0.557000	0.71058	GAA	.		0.328	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37280725	C	A	37280725	4	1	87	1	0	0	0	0	0	1	0	0	7053	835	29	4	3870	4	HEATR5B	2	37280725	Nonsense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	4553880	37280725	205918648	13	7895											
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	109379713	109379713	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcccagtctatggcatgaaTaggcttccaccccaacagca	11	7	9	14	0	1	1	0	1	1	0	2	1	2	1	4	3	2	3	4	3	4	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:109379713T>C	ENST00000283195.6	+	20	2844	c.2718T>C	c.(2716-2718)aaT>aaC	p.N906N		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	906					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATGGCATGAATAGGCTTCCAC	0.413																																					p.N906N		.											.	RANBP2-675	0			c.T2718C						.						76	72	73					2																	109379713		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon20			CATGAATAGGCTT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2718T>C	2.37:g.109379713T>C		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	93	29	NM_006267	0	0	0	0	0	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			.		0.413	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109379713	T	C	109379713	2	2	87	1	0	0	0	0	0	0	0	1	13060	1403	49	3		3	RANBP2	2	109379713	Silent	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	72098988	109379713	133819660	14	7896											
UBXN4	23190	hgsc.bcm.edu	37	chr2	136505919	136505919	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcaaacagttttgttgcTattaaaatcgataccaaaag	15	14	5	7	1	2	0	1	0	1	0	3	1	2	0	1	0	3	3	1	0	7	7			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:136505919T>C	ENST00000272638.9	+	2	476	c.165T>C	c.(163-165)gcT>gcC	p.A55A		NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	55					response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						GTTTTGTTGCTATTAAAATCG	0.284																																					p.A55A		.											.	UBXN4-92	0			c.T165C						.						85	76	79					2																	136505919		1813	4081	5894	SO:0001819	synonymous_variant	23190	exon2			TGTTGCTATTAAA	D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"UBX domain containing"	14860	protein-coding gene	gene with protein product	"erasin"	611216	"UBX domain-containing 2", "UBX domain containing 2"	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.165T>C	2.37:g.136505919T>C		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_014607	0	0	19	19	0	A8K9W4|Q4ZG56|Q8IYM5	Silent	SNP	ENST00000272638.9	37	CCDS42761.1																																																																																			.		0.284	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607		C	136505919	T	C	136505919	2	2	87	1	0	0	0	0	0	0	0	1	16949	1509	53	3		3	UBXN4	2	136505919	Silent	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	27126206	136505919	106693454	15	7897											
ZNF804A	91752	ucsc.edu;bcgsc.ca	37	chr2	185802049	185802049	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaccaatttcagaaaagcaGtatttagctgcagagcaatt	16	10	8	7	0	1	2	1	0	0	2	1	3	1	2	1	0	5	5	1	0	7	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:185802049G>T	ENST00000302277.6	+	4	2520	c.1926G>T	c.(1924-1926)caG>caT	p.Q642H		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	642							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						CAGAAAAGCAGTATTTAGCTG	0.348																																					p.Q642H													.	ZNF804A-163	0			c.G1926T						.						94	104	101					2																	185802049		2203	4297	6500	SO:0001583	missense	91752	exon4			AAAGCAGTATTTA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1926G>T	2.37:g.185802049G>T	ENSP00000303252:p.Gln642His	Somatic	195	4		WXS	Illumina HiSeq		136	53	NM_194250	0	0	0	0	0	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	9.524	1.109178	0.20714	.	.	ENSG00000170396	ENST00000302277	T	0.06218	3.33	5.65	-3.11	0.05299	.	1.188910	0.06060	N	0.658227	T	0.04182	0.0116	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.45381	-0.9265	10	0.40728	T	0.16	0.2582	0.8399	0.01148	0.3584:0.1165:0.2907:0.2344	.	642	Q7Z570	Z804A_HUMAN	H	642	ENSP00000303252:Q642H	ENSP00000303252:Q642H	Q	+	3	2	ZNF804A	185510294	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.555000	0.05999	-0.453000	0.07076	0.655000	0.94253	CAG	.		0.348	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185802049	G	T	185802049	3	4	87	1	0	0	0	0	1	0	0	0	18202	1020	36	4	1940	4	ZNF804A	2	185802049	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	49296130	185802049	57397324	16	7898											
SLC40A1	30061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190428768	190428768	+	Missense_Mutation	SNP	G	G	A																															ggacagtcatataaaggaaaGcaagacccatgccagccaga																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:190428768G>A	ENST00000261024.2	-	7	1370	c.944C>T	c.(943-945)gCt>gTt	p.A315V		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	315					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			ATAAAGGAAAGCAAGACCCAT	0.532																																					p.A315V		.											.	SLC40A1-91	0			c.C944T						.						106	86	92					2																	190428768		2203	4300	6503	SO:0001583	missense	30061	exon7			AGGAAAGCAAGAC	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.944C>T	2.37:g.190428768G>A	ENSP00000261024:p.Ala315Val	Somatic	50	1		WXS	Illumina HiSeq	Phase_I	60	25	NM_014585	0	0	19	19	0	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	37	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	G	36	5.785758	0.96937	.	.	ENSG00000138449	ENST00000261024;ENST00000544056	D	0.94723	-3.5	6.16	6.16	0.99307	Major facilitator superfamily domain, general substrate transporter (1);	0.089656	0.85682	D	0.000000	D	0.96818	0.8961	M	0.70903	2.155	0.80722	D	1	D	0.63046	0.992	D	0.65773	0.938	D	0.94766	0.7940	10	0.28530	T	0.3	-24.5676	20.8598	0.99761	0.0:0.0:1.0:0.0	.	315	Q9NP59	S40A1_HUMAN	V	315;50	ENSP00000261024:A315V	ENSP00000261024:A315V	A	-	2	0	SLC40A1	190137013	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.850000	0.99511	2.937000	0.99478	0.650000	0.86243	GCT	.		0.532	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			A	190428768	G	A	190428768	3	1	87	1	0	0	0	0	1	0	0	0	14660	971	34	2	779	2	SLC40A1	2	190428768	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	4626719	190428768	52770605	17	7899	85	2									
SLC40A1	30061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190428774	190428774	+	Missense_Mutation	SNP	C	C	G																															tcatataaaggaaagcaagaCccatgccagccagaaacaca																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:190428774C>G	ENST00000261024.2	-	7	1364	c.938G>C	c.(937-939)gGt>gCt	p.G313A		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	313					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			GAAAGCAAGACCCATGCCAGC	0.527																																					p.G313A		.											.	SLC40A1-91	0			c.G938C						.						109	88	95					2																	190428774		2203	4300	6503	SO:0001583	missense	30061	exon7			GCAAGACCCATGC	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.938G>C	2.37:g.190428774C>G	ENSP00000261024:p.Gly313Ala	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	68	28	NM_014585	0	0	25	25	0	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	37	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.246458	0.59103	.	.	ENSG00000138449	ENST00000261024;ENST00000544056	D	0.92752	-3.1	6.16	3.02	0.34903	Major facilitator superfamily domain, general substrate transporter (1);	0.199649	0.53938	N	0.000049	T	0.82102	0.4964	N	0.16903	0.455	0.49915	D	0.999833	P	0.34826	0.471	B	0.35470	0.203	T	0.79320	-0.1852	10	0.02654	T	1	-15.2428	12.8928	0.58082	0.1134:0.5621:0.3246:0.0	.	313	Q9NP59	S40A1_HUMAN	A	313;48	ENSP00000261024:G313A	ENSP00000261024:G313A	G	-	2	0	SLC40A1	190137019	0.713000	0.27926	1.000000	0.80357	0.999000	0.98932	1.166000	0.31834	1.561000	0.49584	0.650000	0.86243	GGT	.		0.527	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			G	190428774	C	G	190428774	3	3	87	1	0	0	0	0	1	0	0	0	14660	507	18	4	785	4	SLC40A1	2	190428774	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	6	190428774	52770599	18	7900	85	2									
SETD2	29072	hgsc.bcm.edu;bcgsc.ca	37	chr3	47164376	47164377	+	Frame_Shift_Ins	INS	-	-	T																															aaactaaaagaatgagactgINStttgatttcttcatttaatt																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:47164376_47164377insT	ENST00000409792.3	-	3	1791_1792	c.1749_1750insA	c.(1747-1752)aaacagfs	p.Q584fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	584					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GAATGAGACTGTTTGATTTCTT	0.332			"N, F, S, Mis"		clear cell renal carcinoma																																p.Q584fs		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.1750_1751insA						.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1750dupA	3.37:g.47164379_47164379dupT	ENSP00000386759:p.Gln584fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	95	44	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.332	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47164377	-	T	47164376	7	5	87	1	0	1	1	0	0	0	0	0	14163	1386	48	0	6020	0	SETD2	3	47164376	Frame_Shift_Ins	INS	-	TCGA-BQ-7058-01A-11D-1961-08		47164376	150858054	19	7901											
VPRBP	9730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	51456171	51456171	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgatggctgagttgtgacaGttatagctggcctcctcctg	6	13	13	9	0	0	3	0	3	0	0	2	3	2	3	3	2	1	4	3	2	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:51456171G>T	ENST00000335891.5	-	8	2058	c.2049C>A	c.(2047-2049)aaC>aaA	p.N683K				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	1132					B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		AGTTGTGACAGTTATAGCTGG	0.502																																					p.N1079K		.											.	VPRBP-92	0			c.C3237A						.						135	138	137					3																	51456171		2033	4194	6227	SO:0001583	missense	9730	exon15			GTGACAGTTATAG	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"DDB1 and CUL4 associated factors"	30911	protein-coding gene	gene with protein product	"DDB1 and CUL4 associated factor 1"					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.2049C>A	3.37:g.51456171G>T	ENSP00000338857:p.Asn683Lys	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	208	171	NM_014703	0	0	0	2	2	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	G	13.79	2.340869	0.41498	.	.	ENSG00000145041	ENST00000423656;ENST00000335891	T;T	0.01240	5.12;5.12	5.99	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.127622	0.64402	D	0.000001	T	0.01156	0.0038	L	0.31926	0.97	0.58432	D	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.45614	-0.9249	10	0.07175	T	0.84	-19.5801	6.0918	0.19999	0.2259:0.1364:0.6376:0.0	.	1132	Q9Y4B6	VPRBP_HUMAN	K	703;683	ENSP00000393183:N703K;ENSP00000338857:N683K	ENSP00000338857:N683K	N	-	3	2	VPRBP	51431211	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.575000	0.46025	1.377000	0.46286	0.655000	0.94253	AAC	.		0.502	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		T	51456171	G	T	51456171	3	4	87	1	0	0	0	0	1	0	0	0	17218	1020	36	4	1167	4	VPRBP	3	51456171	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	4291795	51456171	146566259	20	7902											
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52584609	52584609	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctggatgtgggccgggAtatggaggtggtgcctgctg	5	9	19	8	1	0	0	0	0	0	0	0	3	0	3	3	6	3	2	3	6	1	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:52584609A>T	ENST00000296302.7	-	29	4726	c.4725T>A	c.(4723-4725)taT>taA	p.Y1575*	RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Y1488*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Y1468*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Y1520*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Y1483*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Y1468*|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Y1538*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Y1495*			Q86U86	PB1_HUMAN	polybromo 1	1575	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTGGGCCGGGATATGGAGGTG	0.572			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.Y1468X		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.T4404A						.						81	84	83					3																	52584609		2203	4300	6503	SO:0001587	stop_gained	55193	exon29			GCCGGGATATGGA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4725T>A	3.37:g.52584609A>T	ENSP00000296302:p.Tyr1575*	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	95	68	NM_018313	0	0	1	2	1	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	A	43	9.940619	0.99300	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767	.	.	.	5.93	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.079	8.842	0.35148	0.7955:0.0:0.2045:0.0	.	.	.	.	X	1488;1468;1575;1468;1520;1495;1538;1483	.	ENSP00000296302:Y1575X	Y	-	3	2	PBRM1	52559649	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.050000	0.30404	1.087000	0.41251	-0.250000	0.11733	TAT	.		0.572	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52584609	A	T	52584609	4	4	87	1	0	0	0	0	0	1	0	0	11517	340	12	5	352	5	PBRM1	3	52584609	Nonsense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	1128438	52584609	145437821	21	7903											
COL8A1	1295	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	99513269	99513269	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggagccatgggcatgcCtggggcaaaaggagaaattg	12	5	16	8	0	0	1	0	0	0	1	0	3	0	2	3	5	2	2	3	5	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:99513269C>T	ENST00000261037.3	+	5	904	c.524C>T	c.(523-525)cCt>cTt	p.P175L	COL8A1_ENST00000273342.4_Missense_Mutation_p.P175L	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	175	Triple-helical region (COL1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						ATGGGCATGCCTGGGGCAAAA	0.552																																					p.P175L		.											.	COL8A1-90	0			c.C524T						.						44	48	46					3																	99513269		2203	4300	6503	SO:0001583	missense	1295	exon5			GCATGCCTGGGGC	AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"Collagens"	2215	protein-coding gene	gene with protein product		120251	"chromosome 3 open reading frame 7"	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.524C>T	3.37:g.99513269C>T	ENSP00000261037:p.Pro175Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	52	44	NM_001850	0	0	3	3	0	D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	ENST00000261037.3	37	CCDS2934.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294831	0.40594	.	.	ENSG00000144810	ENST00000261037;ENST00000273342	D;D	0.96685	-4.09;-4.09	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.97945	0.9324	M	0.88450	2.955	0.58432	D	0.999999	P;P	0.51449	0.945;0.945	P;P	0.57204	0.815;0.815	D	0.98294	1.0515	10	0.54805	T	0.06	.	16.849	0.85988	0.0:1.0:0.0:0.0	.	176;175	E7EPK9;P27658	.;CO8A1_HUMAN	L	175	ENSP00000261037:P175L;ENSP00000273342:P175L	ENSP00000261037:P175L	P	+	2	0	COL8A1	100995959	0.976000	0.34144	0.960000	0.40013	0.992000	0.81027	2.529000	0.45632	2.583000	0.87209	0.655000	0.94253	CCT	.		0.552	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850		T	99513269	C	T	99513269	3	4	87	1	0	0	0	0	1	0	0	0	3711	681	24	2	530	2	COL8A1	3	99513269	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	46928660	99513269	98509161	22	7904											
PDIA5	10954	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122821610	122821610	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgacagggatggtgcattTcatactgaatataaccgagc	12	12	10	7	1	1	2	1	2	0	0	1	4	1	3	1	2	4	1	1	2	4	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:122821610T>A	ENST00000316218.7	+	5	449	c.354T>A	c.(352-354)ttT>ttA	p.F118L		NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	118					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		ATGGTGCATTTCATACTGAAT	0.393																																					p.F118L		.											.	PDIA5-91	0			c.T354A						.						138	121	127					3																	122821610		2203	4300	6503	SO:0001583	missense	10954	exon5			TGCATTTCATACT	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"Protein disulfide isomerases"	24811	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 5"			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.354T>A	3.37:g.122821610T>A	ENSP00000323313:p.Phe118Leu	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	27	24	NM_006810	0	0	0	0	0	D3DN95|Q9BV43	Missense_Mutation	SNP	ENST00000316218.7	37	CCDS3020.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.148995	0.78001	.	.	ENSG00000065485	ENST00000316218;ENST00000484644	T	0.20598	2.06	4.97	4.97	0.65823	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41903	0.1179	M	0.76574	2.34	0.53688	D	0.999974	D	0.76494	0.999	D	0.75484	0.986	T	0.30621	-0.9972	10	0.14656	T	0.56	.	12.261	0.54651	0.0:0.0:0.0:1.0	.	118	Q14554	PDIA5_HUMAN	L	118;22	ENSP00000323313:F118L	ENSP00000323313:F118L	F	+	3	2	PDIA5	124304300	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.656000	0.46716	2.080000	0.62538	0.460000	0.39030	TTT	.		0.393	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810		A	122821610	T	A	122821610	3	1	87	1	0	0	0	0	1	0	0	0	11697	1780	62	5	372	5	PDIA5	3	122821610	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	23308341	122821610	75200820	23	7905											
CSN3	1448	hgsc.bcm.edu;broad.mit.edu	37	chr4	71114720	71114720	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttattttttttgcagtgccaTgagaatgatgaaagaccatt	12	16	8	5	0	0	4	0	3	0	2	0	5	0	4	2	0	2	1	2	0	3	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:71114720T>A	ENST00000304954.3	+	4	179	c.93T>A	c.(91-93)caT>caA	p.H31Q		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	171					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						tGCAGTGCCATGAGAATGATG	0.294																																					p.H31Q		.											.	CSN3-93	0			c.T93A						.						71	71	71					4																	71114720		2203	4300	6503	SO:0001583	missense	1448	exon4			GTGCCATGAGAAT	U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"casein, kappa"	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.93T>A	4.37:g.71114720T>A	ENSP00000304822:p.His31Gln	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	65	7	NM_005212	0	0	0	0	0	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000304954.3	37	CCDS3538.1	.	.	.	.	.	.	.	.	.	.	T	4.544	0.101098	0.08731	.	.	ENSG00000171209	ENST00000304954	T	0.21932	1.98	4.38	0.665	0.17896	.	2.181060	0.01313	N	0.010690	T	0.13157	0.0319	N	0.14661	0.345	0.09310	N	1	B	0.30686	0.29	B	0.31101	0.124	T	0.20240	-1.0281	10	0.20046	T	0.44	-5.3853	6.2755	0.20979	0.0:0.303:0.0:0.697	.	31	P07498	CASK_HUMAN	Q	31	ENSP00000304822:H31Q	ENSP00000304822:H31Q	H	+	3	2	CSN3	71149309	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.050000	0.14120	0.131000	0.18576	-0.379000	0.06801	CAT	.		0.294	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212		A	71114720	T	A	71114720	3	1	87	1	0	0	0	0	1	0	0	0	3955	1461	51	5	103	5	CSN3	4	71114720	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		71114720	120039556	24	7906											
AFM	173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	74364944	74364944	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgtacgctaagtgaagagtTtgcctgtgttgataatttgg	9	15	12	5	1	0	3	0	2	0	1	0	3	0	3	1	1	2	4	1	1	4	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:74364944T>C	ENST00000226355.3	+	11	1496	c.1403T>C	c.(1402-1404)tTt>tCt	p.F468S		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	468	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTGAAGAGTTTGCCTGTGTT	0.403																																					p.F468S		.											.	AFM-92	0			c.T1403C						.						184	158	167					4																	74364944		2203	4300	6503	SO:0001583	missense	173	exon11			AAGAGTTTGCCTG	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.1403T>C	4.37:g.74364944T>C	ENSP00000226355:p.Phe468Ser	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	49	18	NM_001133	0	0	0	0	0	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	37	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.595211	0.28445	.	.	ENSG00000079557	ENST00000226355	T	0.57107	0.42	5.55	4.38	0.52667	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.351548	0.26931	N	0.021779	T	0.55401	0.1918	L	0.41356	1.27	0.29327	N	0.866933	D	0.69078	0.997	D	0.65773	0.938	T	0.49000	-0.8984	10	0.21014	T	0.42	.	7.4141	0.27034	0.0:0.0943:0.0:0.9057	.	468	P43652	AFAM_HUMAN	S	468	ENSP00000226355:F468S	ENSP00000226355:F468S	F	+	2	0	AFM	74583808	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	2.017000	0.40981	2.111000	0.64477	0.533000	0.62120	TTT	.		0.403	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			C	74364944	T	C	74364944	3	2	87	1	0	0	0	0	1	0	0	0	361	1841	64	3	1445	3	AFM	4	74364944	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	3250224	74364944	116789332	25	7907											
AFF1	4299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	88029422	88029422	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagagcgagagcagttcAagtgacagcgaagaaaatga	17	5	13	6	2	2	5	2	2	0	3	2	8	2	5	0	0	3	2	0	0	4	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:88029422A>T	ENST00000307808.6	+	10	1887	c.1467A>T	c.(1465-1467)tcA>tcT	p.S489S	AFF1_ENST00000395146.4_Silent_p.S496S|AFF1_ENST00000544085.1_Silent_p.S127S	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	489	Poly-Ser.				positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		AGAGCAGTTCAAGTGACAGCG	0.542																																					p.S496S		.											.	AFF1-289	0			c.A1488T						.						101	96	98					4																	88029422		2203	4300	6503	SO:0001819	synonymous_variant	4299	exon11			CAGTTCAAGTGAC	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1467A>T	4.37:g.88029422A>T		Somatic	68	1		WXS	Illumina HiSeq	Phase_I	73	8	NM_001166693	0	0	6	7	1	B4DTU1|E9PBM3	Silent	SNP	ENST00000307808.6	37	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.868153	0.32977	.	.	ENSG00000172493	ENST00000541943	.	.	.	5.91	-4.33	0.03677	.	.	.	.	.	T	0.60340	0.2261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66618	-0.5878	5	0.66056	D	0.02	-6.0776	10.0883	0.42432	0.2811:0.5837:0.062:0.0732	.	.	.	.	L	149	.	ENSP00000446349:Q149L	Q	+	2	0	AFF1	88248446	0.000000	0.05858	0.948000	0.38648	0.997000	0.91878	-2.633000	0.00869	-0.424000	0.07382	0.533000	0.62120	CAA	.		0.542	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	88029422	A	T	88029422	2	4	87	1	0	0	0	0	0	0	0	1	356	117	5	5		5	AFF1	4	88029422	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	13664478	88029422	103124854	26	7908											
LEF1	51176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	109084775	109084775	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgacatgtatgggtcgttAttcatatttggcatcattat	9	19	8	5	1	2	1	2	1	0	0	3	1	2	1	0	2	0	3	0	2	4	7			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:109084775A>C	ENST00000265165.1	-	3	1017	c.363T>G	c.(361-363)aaT>aaG	p.N121K	LEF1_ENST00000438313.2_Missense_Mutation_p.N121K|LEF1_ENST00000512172.1_Missense_Mutation_p.N53K|LEF1_ENST00000379951.2_Missense_Mutation_p.N121K|LEF1_ENST00000510624.1_Missense_Mutation_p.N53K	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1	121	Pro-rich.				alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		ATGGGTCGTTATTCATATTTG	0.428																																					p.N121K		.											.	LEF1-721	0			c.T363G						.						196	173	181					4																	109084775		2203	4300	6503	SO:0001583	missense	51176	exon3			GTCGTTATTCATA		CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.363T>G	4.37:g.109084775A>C	ENSP00000265165:p.Asn121Lys	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	103	40	NM_001130714	0	0	1	1	0	B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Missense_Mutation	SNP	ENST00000265165.1	37	CCDS3679.1	.	.	.	.	.	.	.	.	.	.	A	9.451	1.090605	0.20471	.	.	ENSG00000138795	ENST00000265165;ENST00000379951;ENST00000438313;ENST00000510624;ENST00000515500;ENST00000512172	D;D;D;D	0.99113	-5.42;-5.42;-5.42;-5.44	5.74	-3.28	0.05033	CTNNB1 binding, N-teminal (1);	0.187580	0.53938	D	0.000050	D	0.96728	0.8932	L	0.47716	1.5	0.32383	N	0.554276	P;P;P;P;B	0.42078	0.77;0.643;0.728;0.732;0.322	B;B;B;B;B	0.40901	0.184;0.132;0.156;0.343;0.216	D	0.94059	0.7325	10	0.28530	T	0.3	-19.1486	13.7994	0.63190	0.4778:0.0:0.5222:0.0	.	53;6;121;121;121	E9PDK3;B4DZY5;Q9UJU2-6;Q9UJU2-5;Q9UJU2	.;.;.;.;LEF1_HUMAN	K	121;121;121;53;53;53	ENSP00000265165:N121K;ENSP00000369284:N121K;ENSP00000406176:N121K;ENSP00000422840:N53K	ENSP00000265165:N121K	N	-	3	2	LEF1	109304224	0.997000	0.39634	0.018000	0.16275	0.994000	0.84299	0.624000	0.24462	-0.783000	0.04534	0.460000	0.39030	AAT	.		0.428	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2			C	109084775	A	C	109084775	3	2	87	1	0	0	0	0	1	0	0	0	8735	446	16	5	956	5	LEF1	4	109084775	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	21055353	109084775	82069501	27	7909											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	151827549	151827549	+	Frame_Shift_Del	DEL	A	A	-																															attccatgataaaggccagcAaggttgaactagaatttttt																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:151827549delA	ENST00000357115.3	-	12	1745	c.1502delT	c.(1501-1503)ttgfs	p.L502fs	LRBA_ENST00000510413.1_Frame_Shift_Del_p.L502fs|LRBA_ENST00000535741.1_Frame_Shift_Del_p.L502fs|LRBA_ENST00000507224.1_Frame_Shift_Del_p.L502fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	502						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AAAGGCCAGCAAGGTTGAACT	0.333																																					p.L501fs		.											.	LRBA-157	0			c.1502delT						.						85	89	88					4																	151827549		2203	4300	6503	SO:0001589	frameshift_variant	987	exon12			.	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1502delT	4.37:g.151827549delA	ENSP00000349629:p.Leu502fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	120	36	NM_006726	0	0	0	0	0	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Del	DEL	ENST00000357115.3	37	CCDS3773.1																																																																																			.		0.333	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			-	151827549	A	-	151827549	7	5	87	1	0	1	0	1	0	0	0	0	8956	131	5	0	7277	0	LRBA	4	151827549	Frame_Shift_Del	DEL	A	TCGA-BQ-7058-01A-11D-1961-08	42742774	151827549	39326727	28	7910											
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	155226303	155226303	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aagtatggtggttgtcactaCctctccagtgtcagaattta	10	14	9	8	0	3	1	2	0	1	1	4	1	3	1	2	2	1	2	2	2	5	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:155226303C>A	ENST00000357232.4	-	16	3975	c.3976G>T	c.(3976-3978)Gta>Tta	p.V1326L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1326	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTTGTCACTACCTCTCCAGTG	0.338																																					p.V1326L		.											.	DCHS2-94	0			c.G3976T						.						43	43	43					4																	155226303		2203	4300	6503	SO:0001583	missense	54798	exon16			TCACTACCTCTCC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3976G>T	4.37:g.155226303C>A	ENSP00000349768:p.Val1326Leu	Somatic	58	2		WXS	Illumina HiSeq	Phase_I	43	17	NM_017639	0	0	0	0	0	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	8.031	0.761814	0.15914	.	.	ENSG00000197410	ENST00000357232	T	0.60171	0.21	6.03	4.32	0.51571	Cadherin (4);Cadherin-like (1);	0.306795	0.27424	N	0.019429	T	0.26195	0.0639	N	0.02985	-0.445	0.80722	D	1	B	0.29552	0.248	B	0.27380	0.079	T	0.06285	-1.0835	10	0.33940	T	0.23	.	2.2328	0.04001	0.1217:0.4475:0.226:0.2048	.	1326	Q6V1P9	PCD23_HUMAN	L	1326	ENSP00000349768:V1326L	ENSP00000349768:V1326L	V	-	1	0	DCHS2	155445753	0.023000	0.18921	0.984000	0.44739	0.510000	0.34073	0.027000	0.13621	0.879000	0.35944	0.655000	0.94253	GTA	.		0.338	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155226303	C	A	155226303	3	1	87	1	0	0	0	0	1	0	0	0	4294	507	18	4	4814	4	DCHS2	4	155226303	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	3398754	155226303	35927973	29	7911											
TRIP13	9319	broad.mit.edu	37	chr5	916037	916037	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaagagcgagggcctcagCggccgggtcctgagaaaact	11	4	16	10	3	1	2	1	1	0	2	2	5	2	3	3	4	3	0	3	4	3	0	rs147247158		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr5:916037C>T	ENST00000166345.3	+	12	1508	c.1152C>T	c.(1150-1152)agC>agT	p.S384S	TRIP13_ENST00000510412.1_3'UTR	NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	384					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			AGGGCCTCAGCGGCCGGGTCC	0.537																																					p.S384S													.	TRIP13-90	0			c.C1152T						.	C		0,4406		0,0,2203	156	171	166		1152	-10.8	0	5	dbSNP_134	166	1,8599		0,1,4299	no	coding-synonymous	TRIP13	NM_004237.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		384/433	916037	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9319	exon12			CCTCAGCGGCCGG	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.1152C>T	5.37:g.916037C>T		Somatic	305	0		WXS	Illumina HiSeq	Phase_I	281	7	NM_004237	0	0	5	5	0	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	37	CCDS3858.1																																																																																			C|1.000;T|0.000		0.537	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		T	916037	C	T	916037	2	4	87	1	0	0	0	0	0	0	0	1	16590	767	27	1		1	TRIP13	5	916037	Silent	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		916037	179999223	30	7912											
FAM105A	54491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	14609077	14609077	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctctgatcctttgagctTcatgatgaatcacctgaatt	10	15	6	10	0	3	5	2	5	1	0	5	5	5	5	3	0	1	1	3	0	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr5:14609077T>C	ENST00000274217.3	+	7	968	c.848T>C	c.(847-849)tTc>tCc	p.F283S		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	283	OTU.									large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					CCTTTGAGCTTCATGATGAAT	0.433																																					p.F283S		.											.	FAM105A-91	0			c.T848C						.						149	153	152					5																	14609077		2203	4300	6503	SO:0001583	missense	54491	exon7			TGAGCTTCATGAT		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.848T>C	5.37:g.14609077T>C	ENSP00000274217:p.Phe283Ser	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	222	83	NM_019018	0	0	5	11	6	Q53H50|Q9H037	Missense_Mutation	SNP	ENST00000274217.3	37	CCDS3884.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756651	0.69648	.	.	ENSG00000145569	ENST00000274217	T	0.16743	2.32	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	T	0.37625	0.1010	M	0.72894	2.215	0.41254	D	0.986734	D	0.76494	0.999	D	0.68943	0.961	T	0.23691	-1.0181	10	0.87932	D	0	-22.3388	10.4145	0.44314	0.1462:0.0:0.0:0.8538	.	283	Q9NUU6	F105A_HUMAN	S	283	ENSP00000274217:F283S	ENSP00000274217:F283S	F	+	2	0	FAM105A	14662077	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.702000	0.61817	1.819000	0.53055	0.477000	0.44152	TTC	.		0.433	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		C	14609077	T	C	14609077	3	2	87	1	0	0	0	0	1	0	0	0	5403	1783	62	3	874	3	FAM105A	5	14609077	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	13693040	14609077	166306183	31	7913											
NSD1	64324	bcgsc.ca	37	chr5	176637986	176637986	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgaaacatgttttatcCgagttgaaggaactctctta	11	14	10	6	1	1	2	0	2	1	0	3	4	2	3	1	2	2	2	1	2	5	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr5:176637986C>T	ENST00000439151.2	+	5	2631	c.2586C>T	c.(2584-2586)tcC>tcT	p.S862S	NSD1_ENST00000354179.4_Silent_p.S593S|NSD1_ENST00000347982.4_Silent_p.S593S|NSD1_ENST00000361032.4_Silent_p.S759S	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	862					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		ATGTTTTATCCGAGTTGAAGG	0.403			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.S862S				Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.C2586T						.						144	139	141					5																	176637986		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTATCCGAGTTG	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2586C>T	5.37:g.176637986C>T		Somatic	115	0		WXS	Illumina HiSeq	Phase_1	136	6	NM_022455	0	0	1	1	0	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			.		0.403	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176637986	C	T	176637986	2	4	87	1	0	0	0	0	0	0	0	1	10695	639	23	1		1	NSD1	5	176637986	Silent	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	162028909	176637986	4277274	32	7914											
TXNDC5	81567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	7889004	7889004	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacggtctccgtcgctccAgtctctgtgcgctgcagctg	3	11	13	14	4	2	1	0	1	2	0	6	1	3	1	2	1	3	4	2	1	0	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr6:7889004A>C	ENST00000379757.4	-	7	934	c.897T>G	c.(895-897)acT>acG	p.T299T	TXNDC5_ENST00000473453.1_Silent_p.T191T|TXNDC5_ENST00000539054.1_Silent_p.T227T|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	299					apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					CCGTCGCTCCAGTCTCTGTGC	0.642																																					p.T299T	Ovarian(119;1430 1625 3928 26125 34589)	.											.	TXNDC5-90	0			c.T897G						.						136	131	132					6																	7889004		2203	4300	6503	SO:0001819	synonymous_variant	81567	exon7			CGCTCCAGTCTCT	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"Protein disulfide isomerases"	21073	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 15"		"thioredoxin domain containing 5"				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.897T>G	6.37:g.7889004A>C		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	275	114	NM_030810	0	0	19	27	8	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Silent	SNP	ENST00000379757.4	37	CCDS4505.1																																																																																			.		0.642	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		C	7889004	A	C	7889004	2	2	87	1	0	0	0	0	0	0	0	1	16832	175	7	5		5	TXNDC5	6	7889004	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		7889004	163226063	33	7915											
HCRTR2	3062	broad.mit.edu	37	chr6	55039406	55039406	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtccggcaccaaattggaGgactcccccccttgtcgcaa	9	8	9	15	2	0	0	0	0	0	0	3	2	2	2	5	3	0	2	5	3	2	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr6:55039406G>T	ENST00000370862.3	+	1	357	c.21G>T	c.(19-21)gaG>gaT	p.E7D		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	7					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)			breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CCAAATTGGAGGACTCCCCCC	0.567																																					p.E7D													.	HCRTR2-525	0			c.G21T						.						96	92	93					6																	55039406		2203	4300	6503	SO:0001583	missense	3062	exon1			ATTGGAGGACTCC	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.21G>T	6.37:g.55039406G>T	ENSP00000359899:p.Glu7Asp	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	117	5	NM_001526	0	0	0	0	0	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	37	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883677	0.51908	.	.	ENSG00000137252	ENST00000370862	T	0.61627	0.09	4.99	4.99	0.66335	.	0.129886	0.53938	D	0.000050	T	0.25344	0.0616	N	0.16478	0.41	0.35600	D	0.80775	B	0.10296	0.003	B	0.06405	0.002	T	0.06463	-1.0825	10	0.30854	T	0.27	.	13.4409	0.61112	0.0:0.0:0.8433:0.1567	.	7	O43614	OX2R_HUMAN	D	7	ENSP00000359899:E7D	ENSP00000359899:E7D	E	+	3	2	HCRTR2	55147365	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.863000	0.48396	2.599000	0.87857	0.563000	0.77884	GAG	.		0.567	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			T	55039406	G	T	55039406	3	4	87	1	0	0	0	0	1	0	0	0	7023	991	35	4	23	4	HCRTR2	6	55039406	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	47150402	55039406	116075661	34	7916											
LIN28B	389421	broad.mit.edu	37	chr6	105405976	105405976	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtcctgttccttctcaggcGgggctagcaaaggtggtgga	6	11	15	9	1	1	0	1	0	1	0	4	1	3	1	2	6	1	3	2	6	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr6:105405976G>A	ENST00000345080.4	+	2	216	c.13G>A	c.(13-15)Ggg>Agg	p.G5R		NM_001004317.3	NP_001004317.1	Q6ZN17	LN28B_HUMAN	lin-28 homolog B (C. elegans)	5					miRNA catabolic process (GO:0010587)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA 3'-end processing (GO:0031123)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(10)|ovary(1)	12		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)				CTTCTCAGGCGGGGCTAGCAA	0.517																																					p.G5R													.	LIN28B-90	0			c.G13A						.						44	50	48					6																	105405976		2203	4300	6503	SO:0001583	missense	389421	exon2			TCAGGCGGGGCTA	AK131411	CCDS34504.1	6q21	2010-04-06			ENSG00000187772	ENSG00000187772			32207	protein-coding gene	gene with protein product		611044					Standard	NM_001004317		Approved	FLJ16517, CSDD2	uc003pqv.2	Q6ZN17	OTTHUMG00000015290	ENST00000345080.4:c.13G>A	6.37:g.105405976G>A	ENSP00000344401:p.Gly5Arg	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	116	4	NM_001004317	0	0	0	0	0	A1L165|B2RPN6|Q5TCM4	Missense_Mutation	SNP	ENST00000345080.4	37	CCDS34504.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486186	0.63962	.	.	ENSG00000187772	ENST00000345080	.	.	.	5.78	5.78	0.91487	.	0.050237	0.85682	D	0.000000	T	0.76248	0.3961	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75539	-0.3282	9	0.52906	T	0.07	-5.991	20.0044	0.97430	0.0:0.0:1.0:0.0	.	5	Q6ZN17	LN28B_HUMAN	R	5	.	ENSP00000344401:G5R	G	+	1	0	LIN28B	105512669	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.434000	0.97515	2.714000	0.92807	0.650000	0.86243	GGG	.		0.517	LIN28B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041646.2	NM_001004317		A	105405976	G	A	105405976	3	1	87	1	0	0	0	0	1	0	0	0	8829	1116	39	1	19	1	LIN28B	6	105405976	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	50366570	105405976	65709091	35	7917											
CARD11	84433	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	2963967	2963967	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggaggagtggatggaggAgggtccgaaggagtagcgtt	10	6	22	3	2	0	0	0	0	0	0	1	8	1	7	1	8	1	2	1	8	2	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr7:2963967A>T	ENST00000396946.4	-	15	2243	c.1840T>A	c.(1840-1842)Tcc>Acc	p.S614T		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	614					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		TGGATGGAGGAGGGTCCGAAG	0.612			Mis		DLBCL																																p.S614T		.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11-870	0			c.T1840A						.						90	75	80					7																	2963967		2203	4300	6503	SO:0001583	missense	84433	exon15			TGGAGGAGGGTCC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1840T>A	7.37:g.2963967A>T	ENSP00000380150:p.Ser614Thr	Somatic	86	1		WXS	Illumina HiSeq	Phase_I	81	28	NM_032415	0	0	0	0	0	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	8.933	0.963857	0.18583	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.44083	0.93;0.93	5.15	2.24	0.28232	.	0.185348	0.47852	D	0.000202	T	0.24160	0.0585	N	0.14661	0.345	0.19945	N	0.999941	B	0.15719	0.014	B	0.18263	0.021	T	0.17561	-1.0365	10	0.52906	T	0.07	-14.7989	8.2592	0.31775	0.2504:0.0:0.7496:0.0	.	614	Q9BXL7	CAR11_HUMAN	T	614;85	ENSP00000380150:S614T;ENSP00000347695:S85T	ENSP00000347695:S85T	S	-	1	0	CARD11	2930493	1.000000	0.71417	0.427000	0.26684	0.393000	0.30537	2.109000	0.41863	0.203000	0.20529	-0.345000	0.07892	TCC	.		0.612	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2963967	A	T	2963967	3	4	87	1	0	0	0	0	1	0	0	0	2651	304	11	5	1668	5	CARD11	7	2963967	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		2963967	156174696	36	7918											
HOXA5	3202	broad.mit.edu	37	chr7	27182960	27182966	+	Frame_Shift_Del	DEL	CGGCTGG	CGGCTGG	-																															ggagagtgcgtggacgtggcCggctggctgtacctgggctc																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	CGGCTGG	CGGCTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr7:27182960_27182966delCGGCTGG	ENST00000222726.3	-	1	321_327	c.261_267delCCAGCCG	c.(259-267)agccagccgfs	p.SQP87fs	HOXA-AS3_ENST00000518848.1_RNA|HOXA5_ENST00000520854.1_5'Flank|RP1-170O19.22_ENST00000467897.2_RNA|HOXA6_ENST00000521478.1_5'Flank|HOXA-AS3_ENST00000521197.1_RNA	NM_019102.3	NP_061975.2	P20719	HXA5_HUMAN	homeobox A5	87					anterior/posterior pattern specification (GO:0009952)|bronchiole development (GO:0060435)|cell migration (GO:0016477)|cell-cell signaling involved in mammary gland development (GO:0060764)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|intestinal epithelial cell maturation (GO:0060574)|lung alveolus development (GO:0048286)|lung goblet cell differentiation (GO:0060480)|lung-associated mesenchyme development (GO:0060484)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal-epithelial cell signaling (GO:0060638)|multicellular organism growth (GO:0035264)|negative regulation of angiogenesis (GO:0016525)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of apoptotic process (GO:0043065)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|respiratory system process (GO:0003016)|thyroid gland development (GO:0030878)|trachea cartilage morphogenesis (GO:0060535)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(12)|skin(1)	16						TGGACGTGGCCGGCTGGCTGTACCTGG	0.744																																					p.87_89del	Colon(119;75 2200 7557 42868)												.	HOXA5-514	0			c.261_267del						.																																			SO:0001589	frameshift_variant	3202	exon1			CGTGGCCGGCTGG		CCDS5406.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106004	ENSG00000106004		"Homeoboxes / ANTP class : HOXL subclass"	5106	protein-coding gene	gene with protein product		142952	"homeo box A5"	HOX1C, HOX1		1973146, 1358459	Standard	NM_019102		Approved		uc003syn.2	P20719	OTTHUMG00000023214	ENST00000222726.3:c.261_267delCCAGCCG	7.37:g.27182960_27182966delCGGCTGG	ENSP00000222726:p.Ser87fs	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	29	8	NM_019102	0	0	0	0	0	A4D179|O43367|Q96CY6	Frame_Shift_Del	DEL	ENST00000222726.3	37	CCDS5406.1																																																																																			.		0.744	HOXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358705.1			-	27182966	CGGCTGG	-	27182960	7	5	87	1	0	1	0	1	0	0	0	0	7316	639	23	0	553	0	HOXA5	7	27182960	Frame_Shift_Del	DEL	CGGCTGG	TCGA-BQ-7058-01A-11D-1961-08	24218993	27182960	131955703	37	7919											
PNPLA8	50640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	108112970	108112970	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacttttttcattttttgttCatttctttctatgtatttca	7	26	2	6	0	5	0	3	0	2	0	5	0	5	0	0	0	1	2	0	0	3	12			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr7:108112970C>T	ENST00000422087.1	-	12	2630	c.2224G>A	c.(2224-2226)Gaa>Aaa	p.E742K	PNPLA8_ENST00000257694.8_Missense_Mutation_p.E742K|PNPLA8_ENST00000426128.2_Missense_Mutation_p.E680K|PNPLA8_ENST00000388728.5_Missense_Mutation_p.E680K|PNPLA8_ENST00000453144.1_Missense_Mutation_p.E642K|PNPLA8_ENST00000436062.1_Missense_Mutation_p.E742K	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	742					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						ATTTTTTGTTCATTTCTTTCT	0.299																																					p.E742K		.											.	PNPLA8-135	0			c.G2224A						.						42	44	43					7																	108112970		2202	4298	6500	SO:0001583	missense	50640	exon10			TTTGTTCATTTCT	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"Patatin-like phospholipase domain containing"	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.2224G>A	7.37:g.108112970C>T	ENSP00000410804:p.Glu742Lys	Somatic	85	2		WXS	Illumina HiSeq	Phase_I	67	24	NM_001256008	0	0	7	15	8	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661045	0.88154	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062	T;T;T;T;T;T	0.76968	-1.06;-1.03;-1.03;-1.03;-1.03;-1.03	5.57	5.57	0.84162	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.263816	0.42964	D	0.000628	T	0.77698	0.4169	M	0.64997	1.995	0.37310	D	0.909096	P	0.45396	0.857	B	0.40982	0.345	T	0.81346	-0.0974	10	0.42905	T	0.14	.	19.5466	0.95300	0.0:1.0:0.0:0.0	.	742	Q9NP80	PLPL8_HUMAN	K	677;742;680;742;642;742	ENSP00000394988:E677K;ENSP00000257694:E742K;ENSP00000373380:E680K;ENSP00000410804:E742K;ENSP00000387789:E642K;ENSP00000406779:E742K	ENSP00000257694:E742K	E	-	1	0	PNPLA8	107900206	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.433000	0.80362	2.604000	0.88044	0.650000	0.86243	GAA	.		0.299	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		T	108112970	C	T	108112970	3	4	87	1	0	0	0	0	1	0	0	0	12197	835	29	2	128	2	PNPLA8	7	108112970	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	80930010	108112970	51025693	38	7920											
LOC441294	441294	hgsc.bcm.edu	37	chr7	143270001	143270001	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaatcttcagactcaacaagCatctttgcaatcagaaaaca	18	9	4	10	0	5	2	3	0	2	2	5	2	5	2	0	0	4	2	0	0	6	2	rs201104924	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr7:143270001C>T	ENST00000420911.2	+	1	1108	c.1091C>T	c.(1090-1092)gCa>gTa	p.A364V	RNU6-162P_ENST00000516228.1_RNA	NM_001008747.1	NP_001008747.1	A4D2H0	CTGEF_HUMAN	CTAGE family, member 15	364						integral component of membrane (GO:0016021)											ACTCAACAAGCATCTTTGCAA	0.299													.|||	1090	0.217652	0.171	0.3213	5008	,	,		25006	0.1002		0.3419	False		,,,				2504	0.2004				p.A364V		.											.	.	0			c.C1091T						.						2	2	2					7																	143270001		1060	2315	3375	SO:0001583	missense	441294	exon1			AACAAGCATCTTT		CCDS64788.1	7q35	2013-02-25	2013-02-25	2013-02-25	ENSG00000176227	ENSG00000271079			37295	protein-coding gene	gene with protein product			"CTAGE family, member 15, pseudogene"	CTAGE15P			Standard	NM_001008747		Approved		uc011kth.3	A4D2H0	OTTHUMG00000153233	ENST00000420911.2:c.1091C>T	7.37:g.143270001C>T	ENSP00000474204:p.Ala364Val	Somatic	46	1		WXS	Illumina HiSeq	Phase_I	58	9	NM_001008747	0	0	0	3	3	A6H8Z8	Missense_Mutation	SNP	ENST00000420911.2	37																																																																																				C|0.500;A|0.500		0.299	CTAGE15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330280.2	NM_001008747		T	143270001	C	T	143270001	3	4	87	1	0	0	0	0	1	0	0	0	8905	710	25	2	1093	2	LOC441294	7	143270001	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	35157031	143270001	15868662	39	7921											
UNC5D	137970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	35541184	35541184	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggactcaggaaattacacCtgcatggcagccaacatcgt	12	8	9	12	2	1	0	1	0	0	0	3	2	1	2	2	3	4	2	2	3	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:35541184C>T	ENST00000404895.2	+	5	1018	c.690C>T	c.(688-690)acC>acT	p.T230T	UNC5D_ENST00000287272.2_Silent_p.T230T|UNC5D_ENST00000453357.2_Silent_p.T225T|UNC5D_ENST00000420357.1_Silent_p.T230T|UNC5D_ENST00000416672.1_Silent_p.T230T	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	230	Ig-like C2-type.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.T225T(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		GAAATTACACCTGCATGGCAG	0.537																																					p.T230T		.											.	UNC5D-96	1	Substitution - coding silent(1)	lung(1)	c.C690T						.						86	72	77					8																	35541184		2203	4300	6503	SO:0001819	synonymous_variant	137970	exon5			TTACACCTGCATG	AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"Immunoglobulin superfamily / I-set domain containing"	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.690C>T	8.37:g.35541184C>T		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	58	22	NM_080872	0	0	0	0	0	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																			.		0.537	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			T	35541184	C	T	35541184	2	4	87	1	0	0	0	0	0	0	0	1	17028	668	24	2		2	UNC5D	8	35541184	Silent	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		35541184	110822838	40	7922											
CDH17	1015	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	95158391	95158391	+	Frame_Shift_Del	DEL	C	C	-																															gacacagagctcaaggaagaCccccctaaggaattgaatga																								rs537643053	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:95158391delC	ENST00000027335.3	-	15	2056	c.1932delG	c.(1930-1932)gggfs	p.G644fs	CDH17_ENST00000441892.2_Frame_Shift_Del_p.G430fs|CDH17_ENST00000450165.2_Frame_Shift_Del_p.G644fs	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	644	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCAAGGAAGACCCCCCTAAGG	0.438																																					p.G644fs		.											.	CDH17-96	0			c.1932delG						.						80	74	76					8																	95158391		2203	4300	6503	SO:0001589	frameshift_variant	1015	exon15			.	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1932delG	8.37:g.95158391delC	ENSP00000027335:p.Gly644fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	76	24	NM_004063	0	0	0	0	0	Q15336|Q2M2E0	Frame_Shift_Del	DEL	ENST00000027335.3	37	CCDS6260.1																																																																																			.		0.438	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		-	95158391	C	-	95158391	7	5	87	1	0	1	0	1	0	0	0	0	3108	494	18	0	582	0	CDH17	8	95158391	Frame_Shift_Del	DEL	C	TCGA-BQ-7058-01A-11D-1961-08	59617207	95158391	51205631	41	7923											
NOV	4856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	120429171	120429171	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtggcctctactgtgatcGcagcgcggaccccagcaacc	8	6	11	16	3	1	1	0	1	1	0	2	2	1	2	4	2	4	2	4	2	2	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:120429171G>C	ENST00000259526.3	+	2	499	c.272G>C	c.(271-273)cGc>cCc	p.R91P	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TACTGTGATCGCAGCGCGGAC	0.612											OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R91P		.											.	NOV-228	0			c.G272C						.						48	44	46					8																	120429171		2203	4300	6503	SO:0001583	missense	4856	exon2			GTGATCGCAGCGC	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.272G>C	8.37:g.120429171G>C	ENSP00000259526:p.Arg91Pro	Somatic	44	0	1503	WXS	Illumina HiSeq	Phase_I	49	23	NM_002514	0	0	1	3	2		Missense_Mutation	SNP	ENST00000259526.3	37	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.796255	0.70567	.	.	ENSG00000136999	ENST00000259526	T	0.61274	0.12	4.93	4.05	0.47172	Insulin-like growth factor-binding protein, IGFBP (2);	0.205916	0.45126	D	0.000394	T	0.50497	0.1619	N	0.11313	0.125	0.37745	D	0.925773	D	0.71674	0.998	P	0.61132	0.884	T	0.56932	-0.7897	10	0.45353	T	0.12	-42.0353	8.4948	0.33121	0.0773:0.0:0.7703:0.1525	.	91	P48745	NOV_HUMAN	P	91	ENSP00000259526:R91P	ENSP00000259526:R91P	R	+	2	0	NOV	120498352	0.151000	0.22747	1.000000	0.80357	0.990000	0.78478	0.194000	0.17135	1.436000	0.47453	0.561000	0.74099	CGC	.		0.612	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		C	120429171	G	C	120429171	3	2	87	1	0	0	0	0	1	0	0	0	10579	1087	38	4	278	4	NOV	8	120429171	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	25270780	120429171	25934851	42	7924											
FAM135B	51059	broad.mit.edu	37	chr8	139151264	139151264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttggtagaggaaacatttgCgcaaatcagcattatccctg	12	11	10	8	1	1	1	1	0	0	1	2	2	2	2	1	2	3	4	1	2	4	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:139151264C>T	ENST00000395297.1	-	18	4036	c.3866G>A	c.(3865-3867)cGc>cAc	p.R1289H		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1289										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GAAACATTTGCGCAAATCAGC	0.438										HNSCC(54;0.14)																											p.R1289H													.	FAM135B-31	0			c.G3866A						.						133	128	129					8																	139151264		1877	4117	5994	SO:0001583	missense	51059	exon18			CATTTGCGCAAAT	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3866G>A	8.37:g.139151264C>T	ENSP00000378710:p.Arg1289His	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	102	6	NM_015912	0	0	1	1	0	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	34	5.406433	0.96051	.	.	ENSG00000147724	ENST00000395297	T	0.42900	0.96	5.58	5.58	0.84498	Domain of unknown function DUF676, lipase-like (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73452	-0.3978	10	0.87932	D	0	-20.3154	18.5599	0.91096	0.0:1.0:0.0:0.0	.	1289	Q49AJ0	F135B_HUMAN	H	1289	ENSP00000378710:R1289H	ENSP00000378710:R1289H	R	-	2	0	FAM135B	139220446	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.644000	0.89710	0.655000	0.94253	CGC	.		0.438	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139151264	C	T	139151264	3	4	87	1	0	0	0	0	1	0	0	0	5465	768	27	1	366	1	FAM135B	8	139151264	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	18722093	139151264	7212758	43	7925											
RASEF	158158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	85597649	85597649	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggaattggtcccggttagAttggtaatggatctgctgtc	7	15	13	6	1	1	1	0	0	1	1	3	3	2	3	1	5	1	3	1	5	3	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:85597649A>C	ENST00000376447.3	-	17	2426	c.2166T>G	c.(2164-2166)aaT>aaG	p.N722K		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	722					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TCCCGGTTAGATTGGTAATGG	0.433																																					p.N722K		.											.	RASEF-280	0			c.T2166G						.						391	359	370					9																	85597649		2203	4300	6503	SO:0001583	missense	158158	exon17			GGTTAGATTGGTA	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"EF-hand domain containing", "RAB, member RAS oncogene"	26464	protein-coding gene	gene with protein product		611344	"RAB45, member RAS oncogene family"	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.2166T>G	9.37:g.85597649A>C	ENSP00000365630:p.Asn722Lys	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	273	87	NM_152573	0	0	7	11	4	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	A	8.015	0.758440	0.15846	.	.	ENSG00000165105	ENST00000376447	T	0.60797	0.16	5.05	-4.07	0.03975	.	0.378995	0.27640	N	0.018471	T	0.26774	0.0655	N	0.12746	0.255	0.20563	N	0.999889	B	0.09022	0.002	B	0.04013	0.001	T	0.36138	-0.9760	10	0.05721	T	0.95	.	9.4599	0.38778	0.2492:0.0:0.6328:0.118	.	722	Q8IZ41	RASEF_HUMAN	K	722	ENSP00000365630:N722K	ENSP00000365630:N722K	N	-	3	2	RASEF	84787469	0.953000	0.32496	0.062000	0.19696	0.834000	0.47266	0.266000	0.18534	-0.671000	0.05274	-0.353000	0.07706	AAT	.		0.433	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		C	85597649	A	C	85597649	3	2	87	1	0	0	0	0	1	0	0	0	13100	330	12	5	60	5	RASEF	9	85597649	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		85597649	55615782	44	7926											
PAPPA	5069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	118969850	118969850	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggcaggagtagcaacttggCcatgggacaaggaggccctg	10	6	16	9	0	0	0	0	0	0	0	0	3	0	3	2	6	2	3	2	6	3	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:118969850C>T	ENST00000328252.3	+	3	1963	c.1594C>T	c.(1594-1596)Cca>Tca	p.P532S	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	532	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						AGCAACTTGGCCATGGGACAA	0.433																																					p.P532S		.											.	PAPPA-77	0			c.C1594T						.						72	68	69					9																	118969850		2203	4300	6503	SO:0001583	missense	5069	exon3			ACTTGGCCATGGG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.1594C>T	9.37:g.118969850C>T	ENSP00000330658:p.Pro532Ser	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	74	23	NM_002581	0	0	0	0	0	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	35	5.509017	0.96386	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.05258	3.47	6.07	6.07	0.98685	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.61826	-0.6983	10	0.87932	D	0	-9.2416	20.6439	0.99570	0.0:1.0:0.0:0.0	.	74;532	E7EMD3;Q13219	.;PAPP1_HUMAN	S	532;74	ENSP00000330658:P532S	ENSP00000330658:P532S	P	+	1	0	PAPPA	118009671	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	2.884000	0.98904	0.655000	0.94253	CCA	.		0.433	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118969850	C	T	118969850	3	4	87	1	0	0	0	0	1	0	0	0	11458	739	26	2	1604	2	PAPPA	9	118969850	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	33372201	118969850	22243581	45	7927											
ASTN2	23245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	119495750	119495750	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctccaccggcagcgggaTcaccaacagcccatcggcca	9	4	9	19	3	1	0	1	0	0	0	4	1	3	1	6	3	3	1	6	3	1	0	rs150944935	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:119495750T>A	ENST00000313400.4	-	14	2549	c.2449A>T	c.(2449-2451)Atc>Ttc	p.I817F	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.I813F|ASTN2_ENST00000361209.2_Missense_Mutation_p.I766F			O75129	ASTN2_HUMAN	astrotactin 2	817					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GGCAGCGGGATCACCAACAGC	0.602																																					p.I766F		.											.	ASTN2-161	0			c.A2296T						.						73	78	76					9																	119495750		2203	4300	6503	SO:0001583	missense	23245	exon13			GCGGGATCACCAA	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.2449A>T	9.37:g.119495750T>A	ENSP00000314038:p.Ile817Phe	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	165	16	NM_014010	0	0	1	1	0	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	T	19.46	3.831645	0.71258	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.15372	2.75;2.74;2.43;2.77	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	N	0.14661	0.345	0.80722	D	1	D;D;D	0.71674	0.991;0.998;0.978	P;P;P	0.61874	0.791;0.895;0.877	T	0.08351	-1.0726	9	.	.	.	-20.5951	14.7786	0.69749	0.0:0.0:0.0:1.0	.	766;817;813	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	F	817;813;540;766	ENSP00000314038:I817F;ENSP00000363108:I813F;ENSP00000363098:I540F;ENSP00000354504:I766F	.	I	-	1	0	ASTN2	118535571	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.962000	0.87912	1.890000	0.54733	0.459000	0.35465	ATC	T|1.000;C|0.000		0.602	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119495750	T	A	119495750	3	1	87	1	0	0	0	0	1	0	0	0	1066	1435	50	5	1842	5	ASTN2	9	119495750	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	525900	119495750	21717681	46	7928											
DDX50	79009	broad.mit.edu;bcgsc.ca	37	chr10	70670998	70670998	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aattaaaaaaagccgctcacCaaaggtaatcgttatagggg	17	8	9	7	2	1	0	1	0	0	0	2	0	1	0	2	3	1	3	2	3	9	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr10:70670998C>T	ENST00000373585.3	+	4	742	c.635C>T	c.(634-636)cCa>cTa	p.P212L	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	212	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						AGCCGCTCACCAAAGGTAATC	0.388																																					p.P212L													.	DDX50-91	0			c.C635T						.						57	63	61					10																	70670998		2203	4300	6503	SO:0001583	missense	79009	exon4			GCTCACCAAAGGT	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.635C>T	10.37:g.70670998C>T	ENSP00000362687:p.Pro212Leu	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	96	7	NM_024045	0	0	0	0	0	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	37	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.690120	0.68271	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.04603	3.59	5.31	5.31	0.75309	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.093786	0.85682	D	0.000000	T	0.23410	0.0566	M	0.76433	2.335	0.80722	D	1	D;D	0.89917	1.0;0.99	D;D	0.80764	0.994;0.992	T	0.00223	-1.1903	10	0.72032	D	0.01	-10.7506	19.4076	0.94655	0.0:1.0:0.0:0.0	.	212;212	Q9BQ39;B4DED6	DDX50_HUMAN;.	L	212	ENSP00000362687:P212L	ENSP00000362687:P212L	P	+	2	0	DDX50	70341004	1.000000	0.71417	1.000000	0.80357	0.082000	0.17680	7.030000	0.76484	2.645000	0.89757	0.556000	0.70494	CCA	.		0.388	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		T	70670998	C	T	70670998	3	4	87	1	0	0	0	0	1	0	0	0	4374	594	21	2	649	2	DDX50	10	70670998	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		70670998	64863749	47	7929											
ECD	11319	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	74906091	74906091	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccatttctagcctttccCggtactgagcagaaccttct	7	13	7	14	1	2	2	0	1	2	1	3	2	3	2	4	1	5	2	4	1	3	5	rs147908494	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr10:74906091C>G	ENST00000372979.4	-	9	1276	c.1070G>C	c.(1069-1071)cGg>cCg	p.R357P	ECD_ENST00000454759.2_Missense_Mutation_p.R314P|ECD_ENST00000430082.2_Missense_Mutation_p.R357P	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	357					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TAGCCTTTCCCGGTACTGAGC	0.388																																					p.R357P		.											.	ECD-91	0			c.G1070C						.						70	60	64					10																	74906091		2203	4300	6503	SO:0001583	missense	11319	exon9			CTTTCCCGGTACT	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1070G>C	10.37:g.74906091C>G	ENSP00000362070:p.Arg357Pro	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	40	7	NM_001135752	0	0	5	7	2	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	c	16.22	3.061911	0.55432	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.18657	2.2;2.2;2.2	5.86	3.46	0.39613	.	0.479204	0.25307	N	0.031608	T	0.22704	0.0548	L	0.46157	1.445	0.25782	N	0.984718	P;P;P	0.48694	0.583;0.719;0.914	P;P;P	0.52793	0.511;0.518;0.709	T	0.11397	-1.0589	10	0.36615	T	0.2	-20.0372	1.3395	0.02151	0.2109:0.0988:0.1488:0.5415	.	314;357;357	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	P	357;357;314	ENSP00000362070:R357P;ENSP00000401566:R357P;ENSP00000395786:R314P	ENSP00000362070:R357P	R	-	2	0	ECD	74576097	0.515000	0.26210	1.000000	0.80357	0.871000	0.50021	0.390000	0.20768	1.054000	0.40438	-0.310000	0.09108	CGG	C|0.999;T|0.001		0.388	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		G	74906091	C	G	74906091	3	3	87	1	0	0	0	0	1	0	0	0	4899	652	23	4	991	4	ECD	10	74906091	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	4235093	74906091	60628656	48	7930											
ADK	132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	76468112	76468112	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggtctctgacaagcctcTgactgaatgtatccgtgctg	8	12	10	11	1	2	3	0	3	2	0	4	3	3	3	2	1	2	2	2	1	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr10:76468112T>C	ENST00000286621.2	+	11	1048	c.998T>C	c.(997-999)cTg>cCg	p.L333P	ADK_ENST00000539909.1_Missense_Mutation_p.L276P|ADK_ENST00000541550.1_Missense_Mutation_p.L298P|ADK_ENST00000372734.3_Missense_Mutation_p.L316P	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	333					adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	GACAAGCCTCTGACTGAATGT	0.453																																					p.L333P		.											.	ADK-228	0			c.T998C						.						148	145	146					10																	76468112		2203	4300	6503	SO:0001583	missense	132	exon11			AGCCTCTGACTGA	U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"adenosine 5'-phosphotransferase"	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.998T>C	10.37:g.76468112T>C	ENSP00000286621:p.Leu333Pro	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	184	67	NM_006721	0	0	40	63	23	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Missense_Mutation	SNP	ENST00000286621.2	37	CCDS7343.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992018	0.74703	.	.	ENSG00000156110	ENST00000539909;ENST00000286621;ENST00000372734;ENST00000541550	D;D;D;D	0.90620	-2.7;-1.54;-1.54;-1.54	5.48	5.48	0.80851	Carbohydrate/purine kinase (1);	0.220948	0.39210	N	0.001422	D	0.94656	0.8277	M	0.79011	2.435	0.80722	D	1	D;B;D;B	0.69078	0.997;0.226;0.997;0.042	D;B;D;B	0.66847	0.947;0.275;0.947;0.173	D	0.94816	0.7983	10	0.54805	T	0.06	-6.7191	14.538	0.67973	0.0:0.0:0.0:1.0	.	298;276;316;333	B7Z800;B7Z783;Q5JQ10;P55263	.;.;.;ADK_HUMAN	P	276;333;316;298	ENSP00000443965:L276P;ENSP00000286621:L333P;ENSP00000361819:L316P;ENSP00000438321:L298P	ENSP00000286621:L333P	L	+	2	0	ADK	76138118	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.195000	0.77798	2.078000	0.62432	0.533000	0.62120	CTG	.		0.453	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721		C	76468112	T	C	76468112	3	2	87	1	0	0	0	0	1	0	0	0	320	1580	55	3	1058	3	ADK	10	76468112	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	1562021	76468112	59066635	49	7931											
NRAP	4892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115381720	115381720	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccgctgtcttgtagcctaCgtctgtggctaaatgctgag	6	14	11	10	2	2	1	0	1	2	0	3	1	3	1	2	1	3	4	2	1	4	5	rs200031510	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr10:115381720C>T	ENST00000359988.3	-	24	2921	c.2677G>A	c.(2677-2679)Gta>Ata	p.V893I	NRAP_ENST00000369360.3_Missense_Mutation_p.V866I|NRAP_ENST00000360478.3_Missense_Mutation_p.V858I|NRAP_ENST00000369358.4_Missense_Mutation_p.V901I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TTGTAGCCTACGTCTGTGGCT	0.522													T|||	2	0.000399361	0	0.0014	5008	,	,		23471	0		0	False		,,,				2504	0.001				p.V893I		.											.	NRAP-522	0			c.G2677A						.	T	ILE/VAL,ILE/VAL	1,4405	826.1+/-416.6	0,1,2202	288	219	243		2677,2572	-0.2	0.9	10		243	0,8600		0,0,4300	no	missense,missense	NRAP	NM_198060.2,NM_006175.3	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	893/1731,858/1696	115381720	1,13005	2203	4300	6503	SO:0001583	missense	4892	exon24			AGCCTACGTCTGT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2677G>A	10.37:g.115381720C>T	ENSP00000353078:p.Val893Ile	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	147	51	NM_001261463	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	6.299	0.423219	0.11928	2.27E-4	0.0	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.99	-0.164	0.13359	.	0.321128	0.38492	N	0.001669	T	0.12433	0.0302	N	0.05078	-0.115	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31052	-0.9957	10	0.13853	T	0.58	.	10.9817	0.47499	0.0:0.3842:0.0:0.6158	.	893;858;893	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	I	901;866;893;858	ENSP00000358365:V901I;ENSP00000358367:V866I;ENSP00000353078:V893I;ENSP00000353666:V858I	ENSP00000353078:V893I	V	-	1	0	NRAP	115371710	0.260000	0.24053	0.933000	0.37362	0.951000	0.60555	0.212000	0.17497	-0.541000	0.06257	-0.254000	0.11334	GTA	C|1.000;T|0.000		0.522	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115381720	C	T	115381720	3	4	87	1	0	0	0	0	1	0	0	0	10664	536	19	1	2591	1	NRAP	10	115381720	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	38913608	115381720	20153027	50	7932											
NLRP6	171389	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	281108	281108	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcgtcctcggacgcagggcGcagtttgccgagaaggaact	8	6	16	11	5	0	1	0	0	0	1	2	4	1	3	2	4	2	3	2	4	2	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:281108G>C	ENST00000312165.5	+	4	1374	c.1374G>C	c.(1372-1374)gcG>gcC	p.A458A	NLRP6_ENST00000534750.1_Silent_p.A458A	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	458	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		GACGCAGGGCGCAGTTTGCCG	0.662																																					p.A458A		.											.	NLRP6-583	0			c.G1374C						.						58	65	63					11																	281108		2201	4300	6501	SO:0001819	synonymous_variant	171389	exon4			CAGGGCGCAGTTT	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1374G>C	11.37:g.281108G>C		Somatic	169	1		WXS	Illumina HiSeq	Phase_I	188	68	NM_138329	0	0	3	8	5	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			.		0.662	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		C	281108	G	C	281108	2	2	87	1	0	0	0	0	0	0	0	1	10507	1074	38	4		4	NLRP6	11	281108	Silent	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		281108	134725408	51	7933											
KCNQ1	3784	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	2466713	2466713	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcgtttaccacttcgccGtgtgagtatcgccaccggcg	5	11	11	14	6	0	1	0	1	0	0	3	1	0	1	4	1	1	3	4	1	2	5	rs199472683		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:2466713G>A	ENST00000155840.5	+	1	493	c.385G>A	c.(385-387)Gtc>Atc	p.V129I		NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	129					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	CCACTTCGCCGTGTGAGTATC	0.682																																					p.V129I		.											.	KCNQ1-515	0			c.G385A						.						10	11	11					11																	2466713		2130	4214	6344	SO:0001630	splice_region_variant	3784	exon1			TTCGCCGTGTGAG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6294	protein-coding gene	gene with protein product	"Jervell and Lange-Nielsen syndrome 1"	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.386+1G>A	11.37:g.2466713G>A		Somatic	30	1		WXS	Illumina HiSeq	Phase_I	30	10	NM_000218	0	0	0	0	0	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Missense_Mutation	SNP	ENST00000155840.5	37	CCDS7736.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.398120	0.83120	.	.	ENSG00000053918	ENST00000496887;ENST00000155840	D;D	0.97066	-4.23;-4.23	3.17	3.17	0.36434	.	0.185677	0.34025	N	0.004327	D	0.94735	0.8301	M	0.64080	1.96	0.80722	D	1	P	0.46512	0.879	B	0.38616	0.277	D	0.94080	0.7343	10	0.49607	T	0.09	-20.4654	11.9712	0.53065	0.0:0.0:1.0:0.0	.	129	P51787	KCNQ1_HUMAN	I	42;129	ENSP00000434560:V42I;ENSP00000155840:V129I	ENSP00000155840:V129I	V	+	1	0	KCNQ1	2423289	1.000000	0.71417	0.968000	0.41197	0.837000	0.47467	8.420000	0.90256	1.771000	0.52183	0.561000	0.74099	GTC	.		0.682	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	Missense_Mutation	A	2466713	G	A	2466713	5	1	87	1	0	0	0	0	0	0	1	0	8103	1159	40	1	387	1	KCNQ1	11	2466713	Splice_Site	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	2185605	2466713	132539803	52	7934											
OR1S1	219959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57982376	57982376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtacctggtcactgtgattGggaacgggctcatcattgtg	7	13	13	8	1	3	1	3	1	0	0	3	2	3	2	1	3	2	2	1	3	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:57982376G>A	ENST00000309433.6	+	1	160	c.160G>A	c.(160-162)Ggg>Agg	p.G54R		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	54						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				CACTGTGATTGGGAACGGGCT	0.448																																					p.G54R		.											.	OR1S1-113	0			c.G160A						.						323	297	306					11																	57982376		2201	4296	6497	SO:0001583	missense	219959	exon1			GTGATTGGGAACG	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"GPCR / Class A : Olfactory receptors"	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.160G>A	11.37:g.57982376G>A	ENSP00000311688:p.Gly54Arg	Somatic	322	0		WXS	Illumina HiSeq	Phase_I	229	90	NM_001004458	0	0	0	0	0	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.576223	0.45902	.	.	ENSG00000172774	ENST00000309433	T	0.15256	2.44	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000137	T	0.49558	0.1564	H	0.95328	3.655	0.09310	N	0.999999	D	0.89917	1.0	D	0.70935	0.971	T	0.50406	-0.8832	10	0.87932	D	0	.	10.0621	0.42282	0.1064:0.0:0.8936:0.0	.	54	Q8NH92	OR1S1_HUMAN	R	54	ENSP00000311688:G54R	ENSP00000311688:G54R	G	+	1	0	OR1S1	57738952	0.784000	0.28713	0.803000	0.32268	0.673000	0.39480	2.153000	0.42282	1.770000	0.52166	0.479000	0.44913	GGG	.		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458		A	57982376	G	A	57982376	3	1	87	1	0	0	0	0	1	0	0	0	10998	1348	47	2	162	2	OR1S1	11	57982376	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	55515663	57982376	77024140	53	7935											
TRMT112	51504	hgsc.bcm.edu;broad.mit.edu	37	chr11	64084953	64084953	+	Frame_Shift_Del	DEL	C	C	-																															ggggaagccacgggaccccaCcccccgcacatgcgagctca																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:64084953delC	ENST00000544844.1	-	1	603	c.46delG	c.(46-48)gtgfs	p.V16fs	TRMT112_ENST00000535750.1_5'UTR|PRDX5_ENST00000265462.4_5'Flank|PRDX5_ENST00000352435.4_5'Flank|TRMT112_ENST00000308774.2_Frame_Shift_Del_p.V16fs|PRDX5_ENST00000347941.4_5'Flank|TRMT112_ENST00000539854.1_Frame_Shift_Del_p.V16fs|TRMT112_ENST00000535126.1_Frame_Shift_Del_p.G4fs			Q9UI30	TR112_HUMAN	tRNA methyltransferase 11-2 homolog (S. cerevisiae)	16	TRM112.				peptidyl-glutamine methylation (GO:0018364)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protein methyltransferase activity (GO:0008276)			large_intestine(1)|upper_aerodigestive_tract(1)	2						CGGGACCCCACCCCCCGCACA	0.657																																					p.V16fs		.											.	TRMT112-90	0			c.46delG						.						22	22	22					11																	64084953		2200	4294	6494	SO:0001589	frameshift_variant	51504	exon1			.	AF110774	CCDS8068.1, CCDS66113.1, CCDS73312.1	11q13.1	2013-07-23			ENSG00000173113	ENSG00000173113			26940	protein-coding gene	gene with protein product						11042152	Standard	NM_001286082		Approved	HSPC152, HSPC170, TRM112, TRMT11-2	uc001nzt.3	Q9UI30	OTTHUMG00000167848	ENST00000544844.1:c.46delG	11.37:g.64084953delC	ENSP00000438349:p.Val16fs	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	34	11	NM_016404	0	0	0	0	0	B2R539|J3KNG5|Q3MHC7|Q8N2Z4	Frame_Shift_Del	DEL	ENST00000544844.1	37	CCDS8068.1																																																																																			.		0.657	TRMT112-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396598.2	NM_016404		-	64084953	C	-	64084953	7	5	87	1	0	1	0	1	0	0	0	0	16596	507	18	0	347	0	TRMT112	11	64084953	Frame_Shift_Del	DEL	C	TCGA-BQ-7058-01A-11D-1961-08	6102577	64084953	70921563	54	7936											
DPF2	5977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65113439	65113439	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattggccttgcccaacaacTactgtgacttctgcctgggg	7	11	11	12	0	1	1	0	1	1	0	1	2	1	1	3	3	5	0	3	3	3	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:65113439T>C	ENST00000528416.1	+	8	947	c.814T>C	c.(814-816)Tac>Cac	p.Y272H	DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Missense_Mutation_p.Y286H|DPF2_ENST00000415073.2_Intron	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	272					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						GCCCAACAACTACTGTGACTT	0.537																																					p.Y272H		.											.	DPF2-91	0			c.T814C						.						123	125	124					11																	65113439		2201	4297	6498	SO:0001583	missense	5977	exon8			AACAACTACTGTG	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.814T>C	11.37:g.65113439T>C	ENSP00000436901:p.Tyr272His	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	220	95	NM_006268	0	0	4	10	6	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	37	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.025345	0.93518	.	.	ENSG00000133884	ENST00000528416;ENST00000252268	D;D	0.91011	-2.75;-2.77	5.92	5.92	0.95590	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.34338	N	0.004057	D	0.95739	0.8614	M	0.87900	2.915	0.54753	D	0.999988	D	0.63046	0.992	D	0.87578	0.998	D	0.96274	0.9201	10	0.87932	D	0	-23.8316	14.3154	0.66446	0.0:0.0:0.0:1.0	.	272	Q92785	REQU_HUMAN	H	272;286	ENSP00000436901:Y272H;ENSP00000252268:Y286H	ENSP00000252268:Y286H	Y	+	1	0	DPF2	64870015	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.946000	0.87746	2.270000	0.75569	0.459000	0.35465	TAC	.		0.537	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		C	65113439	T	C	65113439	3	2	87	1	0	0	0	0	1	0	0	0	4728	1522	53	3	844	3	DPF2	11	65113439	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	1028486	65113439	69893077	55	7937											
SPTBN2	6712	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66488565	66488565	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacctcacctgccagagcCttaatgcgagacctctcaaa	11	8	7	15	1	2	3	2	1	1	2	3	4	2	3	5	0	3	0	5	0	2	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:66488565C>G	ENST00000533211.1	-	3	478	c.147G>C	c.(145-147)aaG>aaC	p.K49N	SPTBN2_ENST00000529997.1_Missense_Mutation_p.K49N|SPTBN2_ENST00000309996.2_Missense_Mutation_p.K49N			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	49	Actin-binding.				actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTGCCAGAGCCTTAATGCGAG	0.572																																					p.K49N		.											.	SPTBN2-155	0			c.G147C						.						76	65	68					11																	66488565		2200	4295	6495	SO:0001583	missense	6712	exon2			CAGAGCCTTAATG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"Pleckstrin homology (PH) domain containing"	11276	protein-coding gene	gene with protein product		604985	"spinocerebellar ataxia 5"	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.147G>C	11.37:g.66488565C>G	ENSP00000432568:p.Lys49Asn	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	74	37	NM_006946	0	0	0	0	0	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576172	0.65878	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997;ENST00000443262;ENST00000527010	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	4.58	3.67	0.42095	Calponin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.76133	0.3945	M	0.92169	3.28	0.52099	D	0.999946	D	0.67145	0.996	P	0.61477	0.889	T	0.79100	-0.1942	10	0.87932	D	0	.	8.4196	0.32692	0.0:0.8157:0.0:0.1843	.	49	O15020	SPTN2_HUMAN	N	49	ENSP00000432568:K49N;ENSP00000311489:K49N;ENSP00000433593:K49N;ENSP00000433631:K49N	ENSP00000311489:K49N	K	-	3	2	SPTBN2	66245141	0.999000	0.42202	1.000000	0.80357	0.959000	0.62525	0.667000	0.25112	1.062000	0.40625	0.561000	0.74099	AAG	.		0.572	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		G	66488565	C	G	66488565	3	3	87	1	0	0	0	0	1	0	0	0	15152	680	24	4	7169	4	SPTBN2	11	66488565	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	1375126	66488565	68517951	56	7938											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877707	82877707	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaatgtagaaaactggcaaAgttccaagtctgccaaaaga	18	7	9	7	0	1	3	0	0	1	3	2	3	2	3	2	1	2	3	2	1	8	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:82877707A>C	ENST00000298281.4	+	5	2220	c.1768A>C	c.(1768-1770)Agt>Cgt	p.S590R		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	590					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						AAACTGGCAAAGTTCCAAGTC	0.373																																					p.S590R		.											.	PCF11-23	0			c.A1768C						.						69	70	70					11																	82877707		1801	3982	5783	SO:0001583	missense	51585	exon5			TGGCAAAGTTCCA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1768A>C	11.37:g.82877707A>C	ENSP00000298281:p.Ser590Arg	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	151	57	NM_015885	0	0	1	2	1	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.199720	0.38905	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.46063	1.89;0.89;0.88	6.07	4.96	0.65561	.	0.165679	0.43747	D	0.000537	T	0.27063	0.0663	N	0.19112	0.55	0.28203	N	0.927278	P;B	0.50528	0.936;0.244	P;B	0.45099	0.469;0.143	T	0.13072	-1.0523	9	.	.	.	.	4.9308	0.13916	0.7534:0.0:0.2466:0.0	.	590;590	E9PQ01;O94913	.;PCF11_HUMAN	R	590	ENSP00000298281:S590R;ENSP00000434540:S590R;ENSP00000431567:S590R	.	S	+	1	0	PCF11	82555355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.144000	0.64832	2.326000	0.78906	0.533000	0.62120	AGT	.		0.373	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		C	82877707	A	C	82877707	3	2	87	1	0	0	0	0	1	0	0	0	11599	72	3	5	1786	5	PCF11	11	82877707	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	16389142	82877707	52128809	57	7939											
B4GALNT3	283358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	662534	662534	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcggaaactcctggctcagcCccgggagggcctgctggccc	5	5	15	16	2	1	0	1	0	0	0	2	2	2	2	5	5	3	2	5	5	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr12:662534C>A	ENST00000266383.5	+	14	1458	c.1445C>A	c.(1444-1446)cCc>cAc	p.P482H		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	482					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CTGGCTCAGCCCCGGGAGGGC	0.627																																					p.P482H		.											.	B4GALNT3-92	0			c.C1445A						.						55	63	60					12																	662534		2203	4300	6503	SO:0001583	missense	283358	exon14			CTCAGCCCCGGGA	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1445C>A	12.37:g.662534C>A	ENSP00000266383:p.Pro482His	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	132	40	NM_173593	0	0	0	0	0	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.387397	0.42308	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.32988	3.47;1.43	5.75	1.75	0.24633	.	0.694092	0.14730	N	0.301809	T	0.20861	0.0502	L	0.36672	1.1	0.09310	N	1	P;P	0.41265	0.744;0.61	B;B	0.39027	0.288;0.167	T	0.08249	-1.0731	10	0.39692	T	0.17	-7.1623	5.6204	0.17453	0.0:0.6186:0.1433:0.238	.	385;482	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	H	482;385	ENSP00000266383:P482H;ENSP00000322953:P385H	ENSP00000266383:P482H	P	+	2	0	B4GALNT3	532795	0.000000	0.05858	0.001000	0.08648	0.072000	0.16883	-0.111000	0.10807	0.790000	0.33803	0.650000	0.86243	CCC	.		0.627	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		A	662534	C	A	662534	3	1	87	1	0	0	0	0	1	0	0	0	1269	623	22	4	1499	4	B4GALNT3	12	662534	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		662534	133189361	58	7940											
TMTC3	160418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	88548132	88548132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctagcagcttttttgtcatAtaccagatcaaaaggaccag	13	12	7	9	0	3	1	2	0	1	1	3	2	3	2	2	1	3	2	2	1	5	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr12:88548132A>G	ENST00000266712.6	+	4	696	c.476A>G	c.(475-477)tAt>tGt	p.Y159C		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	159					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						TTTTTGTCATATACCAGATCA	0.318																																					p.Y159C		.											.	TMTC3-91	0			c.A476G						.						82	80	81					12																	88548132		2203	4296	6499	SO:0001583	missense	160418	exon4			TGTCATATACCAG		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.476A>G	12.37:g.88548132A>G	ENSP00000266712:p.Tyr159Cys	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	82	30	NM_181783	0	0	0	0	0	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	37	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.221546	0.79464	.	.	ENSG00000139324	ENST00000266712;ENST00000551088	T	0.71698	-0.59	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.86682	0.5991	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89279	0.3610	9	.	.	.	-14.1188	15.2357	0.73430	1.0:0.0:0.0:0.0	.	159	Q6ZXV5-2	.	C	159;86	ENSP00000266712:Y159C	.	Y	+	2	0	TMTC3	87072263	1.000000	0.71417	0.995000	0.50966	0.908000	0.53690	6.888000	0.75622	1.998000	0.58463	0.455000	0.32223	TAT	.		0.318	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		G	88548132	A	G	88548132	3	3	87	1	0	0	0	0	1	0	0	0	16294	449	16	3	486	3	TMTC3	12	88548132	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	87885598	88548132	45303763	59	7941											
FOXO1	2308	broad.mit.edu	37	chr13	41134463	41134467	+	Frame_Shift_Del	DEL	CAGTT	CAGTT	-																															aggtgaggactgggtcgaaaCagttaatgatgttggtgatg																								rs199719831		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	CAGTT	CAGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr13:41134463_41134467delCAGTT	ENST00000379561.5	-	2	1545_1549	c.1161_1165delAACTG	c.(1159-1167)ttaactgttfs	p.LTV387fs	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	387	Required for interaction with RUNX2. {ECO:0000250}.|Sufficient for interaction with NLK. {ECO:0000250}.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		TGGGTCGAAACAGTTAATGATGTTG	0.473																																					p.387_389del													.	FOXO1-1295	0			c.1161_1165del						.																																			SO:0001589	frameshift_variant	2308	exon2			TCGAAACAGTTAA		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"Forkhead boxes"	3819	protein-coding gene	gene with protein product		136533	"forkhead homolog in rhabdomyosarcoma"	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.1161_1165delAACTG	13.37:g.41134463_41134467delCAGTT	ENSP00000368880:p.Leu387fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	130	7	NM_002015	0	0	0	0	0	O43523|Q5VYC7|Q6NSK6	Frame_Shift_Del	DEL	ENST00000379561.5	37	CCDS9371.1																																																																																			.		0.473	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		-	41134467	CAGTT	-	41134463	7	5	87	1	0	1	0	1	0	0	0	0	6042	478	17	0	806	0	FOXO1	13	41134463	Frame_Shift_Del	DEL	CAGTT	TCGA-BQ-7058-01A-11D-1961-08		41134463	74035415	60	7942	86	2									
FOXO1	2308	bcgsc.ca	37	chr13	41134471	41134471	+	Missense_Mutation	SNP	G	G	A																															actgggtcgaaacagttaatGatgttggtgatgagagaagg																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr13:41134471G>A	ENST00000379561.5	-	2	1541	c.1157C>T	c.(1156-1158)tCa>tTa	p.S386L	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	386	Required for interaction with RUNX2. {ECO:0000250}.|Sufficient for interaction with NLK. {ECO:0000250}.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		AACAGTTAATGATGTTGGTGA	0.478																																					p.S386L													.	FOXO1-1295	0			c.C1157T						.						184	169	174					13																	41134471		2203	4300	6503	SO:0001583	missense	2308	exon2			GTTAATGATGTTG		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"Forkhead boxes"	3819	protein-coding gene	gene with protein product		136533	"forkhead homolog in rhabdomyosarcoma"	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.1157C>T	13.37:g.41134471G>A	ENSP00000368880:p.Ser386Leu	Somatic	192	0		WXS	Illumina HiSeq	Phase_1	118	7	NM_002015	0	0	1	1	0	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	37	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968769	0.53614	.	.	ENSG00000150907	ENST00000379561	D	0.94650	-3.48	5.84	5.84	0.93424	.	0.316112	0.34156	N	0.004220	D	0.94450	0.8214	M	0.64997	1.995	0.49130	D	0.999756	B;D	0.53151	0.096;0.958	B;P	0.47827	0.068;0.558	D	0.92586	0.6079	10	0.23302	T	0.38	0.0571	19.1261	0.93384	0.0:0.0:1.0:0.0	.	360;386	F8TAD1;Q12778	.;FOXO1_HUMAN	L	386	ENSP00000368880:S386L	ENSP00000368880:S386L	S	-	2	0	FOXO1	40032471	1.000000	0.71417	0.544000	0.28141	0.430000	0.31655	9.476000	0.97823	2.779000	0.95612	0.655000	0.94253	TCA	.		0.478	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		A	41134471	G	A	41134471	3	1	87	1	0	0	0	0	1	0	0	0	6042	1294	45	2	814	2	FOXO1	13	41134471	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	8	41134471	74035407	61	7943	86	2									
HECTD1	25831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31598378	31598378	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tccgttccgttttggtcgaaCccaagctgatgtcgctgcta	6	13	10	12	4	0	1	0	1	0	0	4	2	2	1	3	1	3	5	3	1	3	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr14:31598378C>A	ENST00000399332.1	-	25	4687	c.4199G>T	c.(4198-4200)gGt>gTt	p.G1400V	HECTD1_ENST00000553700.1_Missense_Mutation_p.G1400V	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1400	Ser-rich.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTTGGTCGAACCCAAGCTGAT	0.468																																					p.G1400V		.											.	HECTD1-570	0			c.G4199T						.						187	182	184					14																	31598378		2062	4202	6264	SO:0001583	missense	25831	exon25			GTCGAACCCAAGC	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.4199G>T	14.37:g.31598378C>A	ENSP00000382269:p.Gly1400Val	Somatic	306	1		WXS	Illumina HiSeq	Phase_I	267	87	NM_015382	0	0	4	4	0	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672271	0.29693	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.44482	0.92;0.92;1.43	5.52	4.63	0.57726	.	0.136560	0.49305	U	0.000153	T	0.25419	0.0618	N	0.08118	0	0.58432	D	0.999998	B;B	0.24186	0.099;0.099	B;B	0.19946	0.027;0.025	T	0.03493	-1.1031	10	0.24483	T	0.36	-8.1627	16.9601	0.86270	0.0:0.8726:0.1274:0.0	.	1400;1400	D3DS86;Q9ULT8	.;HECD1_HUMAN	V	1400;1402;1400;827	ENSP00000450697:G1400V;ENSP00000382269:G1400V;ENSP00000451860:G827V	ENSP00000261312:G1402V	G	-	2	0	HECTD1	30668129	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.549000	0.67261	1.442000	0.47568	0.557000	0.71058	GGT	.		0.468	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31598378	C	A	31598378	3	1	87	1	0	0	0	0	1	0	0	0	7060	507	18	4	3709	4	HECTD1	14	31598378	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		31598378	75751162	62	7944											
NID2	22795	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	52474565	52474565	+	Frame_Shift_Del	DEL	A	A	-																															agcagtttagagaaagggtcAaaggttaagccattgggcaa																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr14:52474565delA	ENST00000216286.5	-	19	3842	c.3843delT	c.(3841-3843)tttfs	p.F1281fs	NID2_ENST00000541773.1_Frame_Shift_Del_p.F1180fs	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1281					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					agaaagggtcaaaggttaagc	0.403																																					p.F1281fs		.											.	NID2-158	0			c.3843delT						.						126	116	120					14																	52474565		2203	4300	6503	SO:0001589	frameshift_variant	22795	exon19			.	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3843delT	14.37:g.52474565delA	ENSP00000216286:p.Phe1281fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	61	21	NM_007361	0	0	0	0	0	A8K6I7|B4DU19|O43710	Frame_Shift_Del	DEL	ENST00000216286.5	37	CCDS9706.1																																																																																			.		0.403	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			-	52474565	A	-	52474565	7	5	87	1	0	1	0	1	0	0	0	0	10441	127	5	0	300	0	NID2	14	52474565	Frame_Shift_Del	DEL	A	TCGA-BQ-7058-01A-11D-1961-08	20876187	52474565	54874975	63	7945											
PCNX	22990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	71413816	71413816	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaaggcaactgttcaaccaGgagaaaagacagcaatggac	18	4	10	9	0	1	2	1	0	0	2	1	4	1	3	1	3	3	3	1	3	6	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr14:71413816G>T	ENST00000304743.2	+	2	784	c.338G>T	c.(337-339)aGg>aTg	p.R113M	PCNX_ENST00000238570.5_Missense_Mutation_p.R113M|PCNX_ENST00000439984.3_Missense_Mutation_p.R113M	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	113						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TGTTCAACCAGGAGAAAAGAC	0.398																																					p.R113M		.											.	PCNX-91	0			c.G338T						.						108	94	99					14																	71413816		2203	4300	6503	SO:0001583	missense	22990	exon2			CAACCAGGAGAAA	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"pecanex-like 1 (Drosophila)"	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.338G>T	14.37:g.71413816G>T	ENSP00000304192:p.Arg113Met	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	24	9	NM_014982	0	0	0	0	0	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149085	0.57151	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.42513	0.97;0.97;0.97	5.87	5.87	0.94306	.	0.248009	0.40144	N	0.001174	T	0.54013	0.1832	L	0.48642	1.525	0.47737	D	0.999505	D;D;D	0.71674	0.99;0.99;0.998	P;P;P	0.61592	0.707;0.707;0.891	T	0.52124	-0.8617	10	0.56958	D	0.05	.	13.8269	0.63357	0.0783:0.0:0.9217:0.0	.	113;113;113	B2RTR6;Q96RV3;Q96RV3-2	.;PCX1_HUMAN;.	M	113	ENSP00000304192:R113M;ENSP00000238570:R113M;ENSP00000396617:R113M	ENSP00000238570:R113M	R	+	2	0	PCNX	70483569	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.762000	0.68809	2.779000	0.95612	0.655000	0.94253	AGG	.		0.398	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71413816	G	T	71413816	3	4	87	1	0	0	0	0	1	0	0	0	11617	1000	35	4	344	4	PCNX	14	71413816	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	18939251	71413816	35935724	64	7946											
HERC1	8925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64005696	64005696	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggatcacggagttgcatgcaGcagtgtacacatcctgaccc	10	8	11	12	1	1	1	1	1	0	0	2	3	2	3	2	2	4	5	2	2	1	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr15:64005696G>C	ENST00000443617.2	-	23	4406	c.4319C>G	c.(4318-4320)gCt>gGt	p.A1440G	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1440					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GTTGCATGCAGCAGTGTACAC	0.537																																					p.A1440G		.											.	HERC1-666	0			c.C4319G						.						104	101	102					15																	64005696		2101	4230	6331	SO:0001583	missense	8925	exon23			CATGCAGCAGTGT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.4319C>G	15.37:g.64005696G>C	ENSP00000390158:p.Ala1440Gly	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	96	33	NM_003922	0	0	0	0	0	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.853473	0.51270	.	.	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.34859	1.34	5.53	5.53	0.82687	.	0.069961	0.56097	D	0.000037	T	0.22513	0.0543	N	0.08118	0	0.44417	D	0.997336	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.003	T	0.04678	-1.0934	10	0.49607	T	0.09	.	14.9975	0.71443	0.0:0.1421:0.8579:0.0	.	424;1440	B4DKS2;Q15751	.;HERC1_HUMAN	G	1440;424	ENSP00000390158:A1440G	ENSP00000389613:A424G	A	-	2	0	HERC1	61792749	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.377000	0.79668	2.599000	0.87857	0.655000	0.94253	GCT	.		0.537	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	64005696	G	C	64005696	3	2	87	1	0	0	0	0	1	0	0	0	7078	971	34	4	10490	4	HERC1	15	64005696	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		64005696	38525696	65	7947											
CILP	8483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65496681	65496681	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgagtacaatgggggcaaActtgacctttgtgatcttca	10	13	11	7	0	2	3	1	3	1	0	2	3	2	3	1	2	2	2	1	2	3	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr15:65496681A>T	ENST00000261883.4	-	6	1010	c.844T>A	c.(844-846)Ttt>Att	p.F282I		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	282					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						ATGGGGGCAAACTTGACCTTT	0.527																																					p.F282I		.											.	CILP-97	0			c.T844A						.						119	105	110					15																	65496681		2201	4299	6500	SO:0001583	missense	8483	exon6			GGGCAAACTTGAC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.844T>A	15.37:g.65496681A>T	ENSP00000261883:p.Phe282Ile	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	128	53	NM_003613	0	0	0	0	0	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.541043	0.65085	.	.	ENSG00000138615	ENST00000261883	T	0.38722	1.12	5.63	5.63	0.86233	Carboxypeptidase-like, regulatory domain (1);	0.095383	0.64402	D	0.000001	T	0.45337	0.1337	M	0.69358	2.11	0.36495	D	0.868693	B	0.29341	0.242	B	0.29942	0.109	T	0.56414	-0.7983	10	0.72032	D	0.01	-4.1505	15.024	0.71653	1.0:0.0:0.0:0.0	.	282	O75339	CILP1_HUMAN	I	282	ENSP00000261883:F282I	ENSP00000261883:F282I	F	-	1	0	CILP	63283734	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.410000	0.73294	2.148000	0.66965	0.460000	0.39030	TTT	.		0.527	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		T	65496681	A	T	65496681	3	4	87	1	0	0	0	0	1	0	0	0	3435	43	2	5	2726	5	CILP	15	65496681	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	1490985	65496681	37034711	66	7948											
SRL	6345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4245669	4245669	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctaggaaattctggccAaacttctcaaggggtgagaa	12	11	10	8	0	3	1	1	1	3	1	5	3	3	2	1	4	1	0	1	4	5	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr16:4245669A>C	ENST00000399609.3	-	5	507	c.495T>G	c.(493-495)ttT>ttG	p.F165L	SRL_ENST00000537996.1_Missense_Mutation_p.F123L	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	624	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						AATTCTGGCCAAACTTCTCAA	0.527																																					p.F165L		.											.	SRL-73	0			c.T495G						.						92	93	93					16																	4245669		1908	4134	6042	SO:0001583	missense	6345	exon5			CTGGCCAAACTTC	AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.495T>G	16.37:g.4245669A>C	ENSP00000382518:p.Phe165Leu	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	217	154	NM_001098814	0	0	0	0	0		Missense_Mutation	SNP	ENST00000399609.3	37	CCDS42113.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436347	0.83885	.	.	ENSG00000185739	ENST00000399609;ENST00000330063;ENST00000537996	D;D	0.96041	-3.89;-3.89	5.1	4.01	0.46588	.	0.000000	0.85682	U	0.000000	D	0.95475	0.8530	M	0.75264	2.295	0.80722	D	1	P	0.51147	0.942	P	0.49953	0.627	D	0.94708	0.7889	10	0.87932	D	0	-10.1449	9.749	0.40464	0.8549:0.0:0.1451:0.0	.	165	Q86TD4-2	.	L	165;623;123	ENSP00000382518:F165L;ENSP00000440350:F123L	ENSP00000333285:F623L	F	-	3	2	SRL	4185670	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.492000	0.45311	1.065000	0.40693	0.533000	0.62120	TTT	.		0.527	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		C	4245669	A	C	4245669	3	2	87	1	0	0	0	0	1	0	0	0	15182	127	5	5	934	5	SRL	16	4245669	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		4245669	86109084	67	7949											
RBL2	5934	broad.mit.edu	37	chr16	53468508	53468508	+	Frame_Shift_Del	DEL	C	C	-																															agtcgccaccgcccccgcctCcccctccggcggcggcagcc																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr16:53468508delC	ENST00000262133.6	+	1	177	c.40delC	c.(40-42)cccfs	p.P16fs		NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	16	Poly-Pro.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GCCCCCGCCTCCCCCTCCGGC	0.746																																					p.P14fs													.	RBL2-841	0			c.40delC						.																																			SO:0001589	frameshift_variant	5934	exon1			CCGCCTCCCCCTC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.40delC	16.37:g.53468508delC	ENSP00000262133:p.Pro16fs	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_005611	0	0	0	0	0	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Del	DEL	ENST00000262133.6	37	CCDS10748.1																																																																																			.		0.746	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		-	53468508	C	-	53468508	7	5	87	1	0	1	0	1	0	0	0	0	13142	855	30	0	42	0	RBL2	16	53468508	Frame_Shift_Del	DEL	C	TCGA-BQ-7058-01A-11D-1961-08	49222839	53468508	36886245	68	7950											
GSG2	83903	hgsc.bcm.edu	37	chr17	3629036	3629036	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgaccagctcttcattgtgCtggaatttgagtttggaggg	8	13	13	7	1	2	1	1	1	1	0	2	4	2	3	1	3	2	3	1	3	1	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:3629036C>G	ENST00000325418.4	+	1	1826	c.1807C>G	c.(1807-1809)Ctg>Gtg	p.L603V	ITGAE_ENST00000263087.4_Intron|ITGAE_ENST00000571185.1_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										CTTCATTGTGCTGGAATTTGA	0.473																																					p.L603V		.											.	GSG2-297	0			c.C1807G						.						109	107	108					17																	3629036		2203	4300	6503	SO:0001583	missense	83903	exon1			ATTGTGCTGGAAT	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.1807C>G	17.37:g.3629036C>G	ENSP00000325290:p.Leu603Val	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_031965	0	0	0	0	0	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.448766	0.43531	.	.	ENSG00000177602	ENST00000325418	T	0.68181	-0.31	4.87	2.73	0.32206	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000076	T	0.74114	0.3674	L	0.55103	1.725	0.46167	D	0.9989	D	0.60575	0.988	D	0.69824	0.966	T	0.73748	-0.3885	10	0.87932	D	0	-7.7857	9.0105	0.36137	0.0:0.8109:0.0:0.1891	.	603	Q8TF76	HASP_HUMAN	V	603	ENSP00000325290:L603V	ENSP00000325290:L603V	L	+	1	2	GSG2	3575785	0.240000	0.23847	0.994000	0.49952	0.963000	0.63663	0.635000	0.24629	0.643000	0.30638	-0.345000	0.07892	CTG	.		0.473	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965		G	3629036	C	G	3629036	3	3	87	1	0	0	0	0	1	0	0	0	6843	796	28	4	1809	4	GSG2	17	3629036	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		3629036	77566174	69	7951											
NLK	51701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26490600	26490600	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccattcagctggcattttAcatcgagacattaagccagg	11	11	8	11	1	1	1	1	0	0	1	3	2	2	1	2	2	3	2	2	2	2	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:26490600A>G	ENST00000407008.3	+	5	1501	c.783A>G	c.(781-783)ttA>ttG	p.L261L		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for interaction with TAB2. {ECO:0000250}.|Sufficient for interaction with DAPK3.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CTGGCATTTTACATCGAGACA	0.318																																					p.L261L		.											.	NLK-1403	0			c.A783G						.						85	83	83					17																	26490600		2203	4300	6503	SO:0001819	synonymous_variant	51701	exon5			CATTTTACATCGA	AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"nemo like kinase"			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.783A>G	17.37:g.26490600A>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	46	17	NM_016231	0	0	3	9	6	B2RCX1|Q2PNI9|Q6P2A3	Silent	SNP	ENST00000407008.3	37	CCDS11224.2																																																																																			.		0.318	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231		G	26490600	A	G	26490600	2	3	87	1	0	0	0	0	0	0	0	1	10492	388	14	3		3	NLK	17	26490600	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	22861564	26490600	54704610	70	7952											
PPP1R9B	84687	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	48226606	48226607	+	Frame_Shift_Ins	INS	-	-	G																															caccccgactcgggctcgtaINSggggggctccccatcctcct																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:48226606_48226607insG	ENST00000316878.6	-	3	1268_1269	c.1266_1267insC	c.(1264-1269)ccctacfs	p.Y423fs	PPP1R9B_ENST00000501501.2_5'UTR	NM_032595.3	NP_115984.3	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	423	Interacts with protein phosphatase 1. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to morphine (GO:0071315)|dendrite development (GO:0016358)|filopodium assembly (GO:0046847)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of cell proliferation (GO:0042127)|regulation of exit from mitosis (GO:0007096)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of protein phosphorylation (GO:0001932)|RNA splicing (GO:0008380)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|protein phosphatase type 1 complex (GO:0000164)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						TCGGGCTCGTAGGGGGGCTCCC	0.678																																					.		.											.	PPP1R9B-90	0			.						.																																			SO:0001589	frameshift_variant	84687	.			.	AJ401189	CCDS74102.1	17q21.33	2013-01-31	2011-10-04	2001-07-02	ENSG00000108819	ENSG00000108819		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9298	protein-coding gene	gene with protein product	"spinophilin", "Neurabin-2"	603325	"protein phosphatase 1, regulatory subunit 9B, spinophilin", "protein phosphatase 1, regulatory (inhibitor) subunit 9B"	PPP1R6, PPP1R9		9275233	Standard	NM_032595		Approved	Spn, SPINO	uc002iqh.4	Q96SB3	OTTHUMG00000162008	ENST00000316878.6:c.1267dupC	17.37:g.48226612_48226612dupG	ENSP00000475417:p.Tyr423fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	58	16	.	0	0	0	0	0	Q8TCR9	Targeted_Region	INS	ENST00000316878.6	37																																																																																				.		0.678	PPP1R9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032595		G	48226607	-	G	48226606	7	5	87	1	0	1	1	0	0	0	0	0	12408	407	15	0	1220	0	PPP1R9B	17	48226606	Frame_Shift_Ins	INS	-	TCGA-BQ-7058-01A-11D-1961-08	21736006	48226606	32968604	71	7953											
COX11	1353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	53045784	53045784	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtgaaagggttcgagctcTtaggccgccgcggcggctgc	5	8	17	11	5	1	1	0	1	1	0	2	2	1	1	2	4	2	3	2	4	2	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:53045784T>G	ENST00000299335.3	-	1	362	c.224A>C	c.(223-225)aAg>aCg	p.K75T	STXBP4_ENST00000434978.2_5'Flank|STXBP4_ENST00000376352.2_5'Flank|STXBP4_ENST00000405898.1_5'Flank|STXBP4_ENST00000398391.2_5'Flank|STXBP4_ENST00000299341.4_5'Flank|COX11_ENST00000571584.1_Missense_Mutation_p.K75T	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)	75					hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						GTTCGAGCTCTTAGGCCGCCG	0.677																																					p.K75T		.											.	COX11-91	0			c.A224C						.						36	39	38					17																	53045784		2193	4279	6472	SO:0001583	missense	1353	exon1			GAGCTCTTAGGCC	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"Mitochondrial respiratory chain complex assembly factors"	2261	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit 11", "cytochrome c oxidase assembly protein COX11"	603648	"COX11 (yeast) homolog, cytochrome c oxidase assembly protein", "COX11 cytochrome c oxidase assembly homolog (yeast)"			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.224A>C	17.37:g.53045784T>G	ENSP00000299335:p.Lys75Thr	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	149	75	NM_001162861	0	0	8	19	11	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Missense_Mutation	SNP	ENST00000299335.3	37	CCDS11583.1	.	.	.	.	.	.	.	.	.	.	T	8.726	0.915585	0.17907	.	.	ENSG00000166260	ENST00000299335	T	0.46451	0.87	5.02	2.75	0.32379	.	0.295867	0.40728	N	0.001025	T	0.34890	0.0913	M	0.61703	1.905	0.29814	N	0.831394	B;B	0.18863	0.031;0.007	B;B	0.14023	0.01;0.003	T	0.27468	-1.0073	10	0.22706	T	0.39	-11.5209	7.4832	0.27417	0.0:0.2509:0.0:0.7491	.	75;75	B4DI26;Q9Y6N1	.;COX11_HUMAN	T	75	ENSP00000299335:K75T	ENSP00000299335:K75T	K	-	2	0	COX11	50400783	0.913000	0.31002	0.971000	0.41717	0.013000	0.08279	1.102000	0.31050	0.364000	0.24374	-0.250000	0.11733	AAG	.		0.677	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375		G	53045784	T	G	53045784	3	3	87	1	0	0	0	0	1	0	0	0	3769	1609	56	5	688	5	COX11	17	53045784	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	4819178	53045784	28149426	72	7954											
DDX5	1655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62500170	62500170	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttagagcaactggccaTccctgagcttgaatagcagt	11	9	9	12	0	0	3	0	2	0	1	1	3	1	3	3	1	4	3	3	1	4	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:62500170T>C	ENST00000225792.5	-	4	773	c.372A>G	c.(370-372)ggA>ggG	p.G124G	DDX5_ENST00000450599.2_Intron|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000580026.1_5'Flank|CEP95_ENST00000553412.1_5'Flank|CEP95_ENST00000581056.1_5'Flank|DDX5_ENST00000578804.1_Silent_p.G124G|CEP95_ENST00000556440.2_5'Flank	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	124					cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CAACTGGCCATCCCTGAGCTT	0.398			T	ETV4	prostate																																p.G124G	NSCLC(22;406 813 4871 19580 40307)	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5-228	0			c.A372G						.						143	136	138					17																	62500170		2203	4300	6503	SO:0001819	synonymous_variant	1655	exon4			TGGCCATCCCTGA	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"DEAD-boxes"	2746	protein-coding gene	gene with protein product		180630	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.372A>G	17.37:g.62500170T>C		Somatic	173	1		WXS	Illumina HiSeq	Phase_I	172	103	NM_004396	0	0	40	96	56	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	37	CCDS11659.1																																																																																			.		0.398	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		C	62500170	T	C	62500170	2	2	87	1	0	0	0	0	0	0	0	1	4373	1422	50	3		3	DDX5	17	62500170	Silent	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	9454386	62500170	18695040	73	7955											
SLC9A3R1	9368	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	72745286	72745286	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacggacgagcagctgcagAagctcggcgtccaggtccga	10	4	15	12	5	0	2	0	0	0	2	3	5	2	3	2	3	4	4	2	3	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:72745286A>T	ENST00000262613.5	+	1	496	c.301A>T	c.(301-303)Aag>Tag	p.K101*	MIR3615_ENST00000585285.1_RNA|MIR3615_ENST00000581999.1_RNA	NM_004252.4	NP_004243.1	O14745	NHRF1_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 1	101					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|bile acid secretion (GO:0032782)|cellular phosphate ion homeostasis (GO:0030643)|cellular protein localization (GO:0034613)|glutathione transport (GO:0034635)|microvillus assembly (GO:0030033)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of sodium:proton antiporter activity (GO:0032416)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein complex assembly (GO:0006461)|regulation of excretion (GO:0044062)|regulation of protein kinase activity (GO:0045859)|regulation of sodium:proton antiporter activity (GO:0032415)|renal absorption (GO:0070293)|renal phosphate ion absorption (GO:0097291)|renal sodium ion transport (GO:0003096)|Wnt signaling pathway (GO:0016055)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|membrane raft (GO:0045121)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle (GO:0031982)	beta-2 adrenergic receptor binding (GO:0031698)|beta-catenin binding (GO:0008013)|chloride channel regulator activity (GO:0017081)|growth factor receptor binding (GO:0070851)|PDZ domain binding (GO:0030165)|phosphatase binding (GO:0019902)|protein self-association (GO:0043621)|receptor binding (GO:0005102)			large_intestine(4)	4						GCAGCTGCAGAAGCTCGGCGT	0.736																																					p.K101X		.											.	SLC9A3R1-90	0			c.A301T						.						3	5	4					17																	72745286		1866	3862	5728	SO:0001587	stop_gained	9368	exon1			CTGCAGAAGCTCG	AF015926	CCDS11705.1	17q25.1	2014-09-04	2012-03-22		ENSG00000109062	ENSG00000109062			11075	protein-coding gene	gene with protein product		604990	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1", "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 1", "solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1"			9314537, 9430655	Standard	NM_004252		Approved	NHERF, EBP50	uc002jlo.4	O14745	OTTHUMG00000178863	ENST00000262613.5:c.301A>T	17.37:g.72745286A>T	ENSP00000262613:p.Lys101*	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	28	15	NM_004252	0	0	19	21	2	B3KY21|O43552|Q86WQ5	Nonsense_Mutation	SNP	ENST00000262613.5	37	CCDS11705.1	.	.	.	.	.	.	.	.	.	.	A	39	7.293378	0.98192	.	.	ENSG00000109062	ENST00000262613;ENST00000413388	.	.	.	4.34	4.34	0.51931	.	0.194752	0.44097	D	0.000484	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.2354	7.5228	0.27637	0.901:0.0:0.099:0.0	.	.	.	.	X	101;51	.	ENSP00000262613:K101X	K	+	1	0	SLC9A3R1	70256881	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.636000	0.54317	1.831000	0.53308	0.402000	0.26972	AAG	.		0.736	SLC9A3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443671.1			T	72745286	A	T	72745286	4	4	87	1	0	0	0	0	0	1	0	0	14746	247	9	5	303	5	SLC9A3R1	17	72745286	Nonsense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	10245116	72745286	8449924	74	7956											
FASN	2194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80038618	80038618	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgagccgggaggccaggCtgtggaacacggtggtggag	7	6	20	8	2	0	1	0	1	0	0	0	4	0	4	2	7	3	2	2	7	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:80038618C>T	ENST00000306749.2	-	39	6994	c.6776G>A	c.(6775-6777)aGc>aAc	p.S2259N	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2259	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGAGGCCAGGCTGTGGAACAC	0.687																																					p.S2259N	Colon(59;314 1043 11189 28578 32273)	.											.	FASN-90	0			c.G6776A						.						45	45	45					17																	80038618		2191	4290	6481	SO:0001583	missense	2194	exon39			GCCAGGCTGTGGA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6776G>A	17.37:g.80038618C>T	ENSP00000304592:p.Ser2259Asn	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	32	7	NM_004104	0	0	39	53	14	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.242946	0.22796	.	.	ENSG00000169710	ENST00000306749	T	0.26067	1.76	4.47	2.3	0.28687	Thioesterase (1);	0.302769	0.35407	N	0.003229	T	0.10252	0.0251	N	0.08118	0	0.34398	D	0.694932	B	0.06786	0.001	B	0.06405	0.002	T	0.16541	-1.0399	10	0.19147	T	0.46	-34.0126	6.0153	0.19598	0.0:0.6205:0.1749:0.2047	.	2259	P49327	FAS_HUMAN	N	2259	ENSP00000304592:S2259N	ENSP00000304592:S2259N	S	-	2	0	FASN	77631907	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	0.914000	0.28624	1.091000	0.41335	0.591000	0.81541	AGC	.		0.687	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80038618	C	T	80038618	3	4	87	1	0	0	0	0	1	0	0	0	5702	797	28	2	779	2	FASN	17	80038618	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	7293332	80038618	1156592	75	7957											
METTL4	64863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	2554953	2554953	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggcttactacccttgtcctGtttttcaaaaagtggataaa	11	14	8	8	0	1	0	1	0	0	0	2	1	2	1	2	2	2	2	2	2	6	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr18:2554953G>C	ENST00000574538.1	-	4	1319	c.544C>G	c.(544-546)Cag>Gag	p.Q182E	snoU109_ENST00000459316.1_RNA|METTL4_ENST00000319888.6_Missense_Mutation_p.Q182E	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	182					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						CCCTTGTCCTGTTTTTCAAAA	0.388																																					p.Q182E		.											.	METTL4-227	0			c.C544G						.						119	124	122					18																	2554953		2203	4300	6503	SO:0001583	missense	64863	exon4			TGTCCTGTTTTTC		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.544C>G	18.37:g.2554953G>C	ENSP00000458290:p.Gln182Glu	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	104	61	NM_022840	0	0	0	0	0	B2RNA1|Q2TAA7|Q9H5U9	Missense_Mutation	SNP	ENST00000574538.1	37	CCDS11826.1	.	.	.	.	.	.	.	.	.	.	G	7.036	0.561490	0.13498	.	.	ENSG00000101574	ENST00000319888	T	0.21031	2.03	5.85	0.516	0.17019	.	1.312720	0.04780	N	0.429705	T	0.14743	0.0356	L	0.42245	1.32	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.26744	-1.0094	10	0.02654	T	1	0.1066	4.6714	0.12691	0.2571:0.2993:0.4436:0.0	.	182	Q8N3J2	METL4_HUMAN	E	182	ENSP00000320349:Q182E	ENSP00000320349:Q182E	Q	-	1	0	METTL4	2544953	0.000000	0.05858	0.000000	0.03702	0.916000	0.54674	0.407000	0.21049	0.055000	0.16094	0.655000	0.94253	CAG	.		0.388	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840		C	2554953	G	C	2554953	3	2	87	1	0	0	0	0	1	0	0	0	9527	1386	48	4	898	4	METTL4	18	2554953	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		2554953	75522295	76	7958											
OSBPL1A	114876	broad.mit.edu;bcgsc.ca	37	chr18	21819191	21819191	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcccagagttacctgacagCgcatcatagaactcgtcctc	11	9	7	14	2	1	3	1	1	0	2	5	3	3	3	3	0	3	2	3	0	3	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr18:21819191C>A	ENST00000319481.3	-	16	1643	c.1437G>T	c.(1435-1437)gcG>gcT	p.A479A	OSBPL1A_ENST00000357041.4_Silent_p.A97A|OSBPL1A_ENST00000399443.3_5'UTR	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	479					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					TACCTGACAGCGCATCATAGA	0.522																																					p.A479A													.	OSBPL1A-94	0			c.G1437T						.						171	134	146					18																	21819191		2203	4300	6503	SO:0001819	synonymous_variant	114876	exon16			TGACAGCGCATCA	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1437G>T	18.37:g.21819191C>A		Somatic	88	1		WXS	Illumina HiSeq	Phase_I	68	5	NM_080597	0	0	0	0	0	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			.		0.522	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		A	21819191	C	A	21819191	2	1	87	1	0	0	0	0	0	0	0	1	11303	755	27	4		4	OSBPL1A	18	21819191	Silent	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	19264238	21819191	56258057	77	7959											
PALM	5064	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	746543	746543	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccggccaggagcccccggTcacaatgatcttcatgggtt	7	8	12	14	2	3	1	2	1	1	0	3	2	3	2	4	4	1	1	4	4	1	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:746543T>G	ENST00000338448.5	+	9	939	c.893T>G	c.(892-894)gTc>gGc	p.V298G	PALM_ENST00000264560.7_Missense_Mutation_p.V254G|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	298					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		GAGCCCCCGGTCACAATGATC	0.667																																					p.V298G		.											.	PALM-68	0			c.T893G						.						34	32	32					19																	746543		2203	4299	6502	SO:0001583	missense	5064	exon9			CCCCGGTCACAAT	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.893T>G	19.37:g.746543T>G	ENSP00000341911:p.Val298Gly	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	56	19	NM_002579	0	0	16	21	5	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	37	CCDS32857.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.706659	0.68615	.	.	ENSG00000099864	ENST00000338448;ENST00000264560;ENST00000538247	T;T	0.28666	1.6;1.6	4.92	3.83	0.44106	.	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.60627	-0.7226	10	0.87932	D	0	-41.4159	9.8074	0.40801	0.1538:0.0:0.0:0.8462	.	254;298	O75781-2;O75781	.;PALM_HUMAN	G	298;254;163	ENSP00000341911:V298G;ENSP00000264560:V254G	ENSP00000264560:V254G	V	+	2	0	PALM	697543	1.000000	0.71417	0.998000	0.56505	0.546000	0.35178	5.847000	0.69451	1.839000	0.53478	0.379000	0.24179	GTC	.		0.667	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579		G	746543	T	G	746543	3	3	87	1	0	0	0	0	1	0	0	0	11434	1667	58	5	927	5	PALM	19	746543	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		746543	58382440	78	7960											
CELF5	60680	broad.mit.edu	37	chr19	3293390	3293390	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacggcttccagatcggcatGaagaggctcaaagtccagct	12	7	11	11	2	1	3	1	1	0	2	4	3	3	3	2	3	2	4	2	3	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:3293390G>T	ENST00000292672.2	+	12	1441	c.1404G>T	c.(1402-1404)atG>atT	p.M468I	CELF5_ENST00000541430.2_3'UTR	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	468	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						AGATCGGCATGAAGAGGCTCA	0.642																																					p.M468I													.	CELF5-92	0			c.G1404T						.						92	82	85					19																	3293390		2203	4300	6503	SO:0001583	missense	60680	exon12			CGGCATGAAGAGG	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"RNA binding motif (RRM) containing"	14058	protein-coding gene	gene with protein product		612680	"Bruno (Drosophila) -like 5, RNA binding protein", "bruno-like 5, RNA binding protein (Drosophila)"	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.1404G>T	19.37:g.3293390G>T	ENSP00000292672:p.Met468Ile	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	94	6	NM_021938	0	0	1	1	0	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Missense_Mutation	SNP	ENST00000292672.2	37	CCDS12106.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.315867	0.81469	.	.	ENSG00000161082	ENST00000292672	T	0.05855	3.38	4.73	4.73	0.59995	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.09992	0.0245	N	0.04508	-0.205	0.80722	D	1	D	0.63046	0.992	D	0.67900	0.954	T	0.50021	-0.8876	10	0.72032	D	0.01	-29.5717	16.6332	0.85039	0.0:0.0:1.0:0.0	.	468	Q8N6W0	CELF5_HUMAN	I	468	ENSP00000292672:M468I	ENSP00000292672:M468I	M	+	3	0	CELF5	3244390	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.515000	0.73751	2.333000	0.79357	0.561000	0.74099	ATG	.		0.642	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938		T	3293390	G	T	3293390	3	4	87	1	0	0	0	0	1	0	0	0	3225	1290	45	4	1450	4	CELF5	19	3293390	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	2546847	3293390	55835593	79	7961											
PIAS4	51588	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4013072	4013072	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgttcaagaagatcaaggAgctgtacgagacccgctacg	12	7	12	10	3	2	3	2	0	0	3	2	5	2	4	1	1	3	5	1	1	5	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:4013072A>C	ENST00000262971.2	+	2	294	c.179A>C	c.(178-180)gAg>gCg	p.E60A		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	60					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGATCAAGGAGCTGTACGAG	0.632																																					p.E60A		.											.	PIAS4-659	0			c.A179C						.						58	57	57					19																	4013072		2203	4300	6503	SO:0001583	missense	51588	exon2			TCAAGGAGCTGTA	AF077952	CCDS12118.1	19p13.3	2011-10-11						"Zinc fingers, MIZ-type"	17002	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 6"	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.179A>C	19.37:g.4013072A>C	ENSP00000262971:p.Glu60Ala	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	86	38	NM_015897	0	0	2	4	2	O75926|Q96G19|Q9UN16	Missense_Mutation	SNP	ENST00000262971.2	37	CCDS12118.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.769648	0.90020	.	.	ENSG00000105229	ENST00000262971	T	0.39592	1.07	5.14	5.14	0.70334	DNA-binding SAP (1);	0.053905	0.85682	D	0.000000	T	0.60444	0.2269	L	0.61036	1.89	0.53688	D	0.999975	D	0.69078	0.997	D	0.68765	0.96	T	0.64571	-0.6376	10	0.87932	D	0	-35.6334	14.1251	0.65215	1.0:0.0:0.0:0.0	.	60	Q8N2W9	PIAS4_HUMAN	A	60	ENSP00000262971:E60A	ENSP00000262971:E60A	E	+	2	0	PIAS4	3964072	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.283000	0.95860	1.938000	0.56188	0.459000	0.35465	GAG	.		0.632	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897		C	4013072	A	C	4013072	3	2	87	1	0	0	0	0	1	0	0	0	11904	304	11	5	185	5	PIAS4	19	4013072	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	719682	4013072	55115911	80	7962											
FBXW9	84261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12807385	12807385	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aatcatcgcaccgccctaggGgaagctccattgcgaccggg	9	6	12	14	4	1	0	1	0	0	0	3	2	2	1	4	3	2	2	4	3	3	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:12807385G>T	ENST00000380339.3	-	1	47	c.11C>A	c.(10-12)cCc>cAc	p.P4H	FBXW9_ENST00000393261.3_Missense_Mutation_p.P4H|FBXW9_ENST00000587955.1_Missense_Mutation_p.P4H|FBXW9_ENST00000544494.1_5'UTR			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	4					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CCGCCCTAGGGGAAGCTCCAT	0.662																																					p.P4H		.											.	FBXW9-227	0			c.C11A						.						34	36	35					19																	12807385		1899	3937	5836	SO:0001583	missense	84261	exon1			CCTAGGGGAAGCT	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.11C>A	19.37:g.12807385G>T	ENSP00000369696:p.Pro4His	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	99	31	NM_032301	0	0	7	14	7	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		.	.	.	.	.	.	.	.	.	.	G	12.20	1.867154	0.32977	.	.	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.47869	1.86;0.83	3.77	1.64	0.23874	.	0.182213	0.26646	N	0.023231	T	0.42810	0.1219	L	0.27053	0.805	0.22142	N	0.999336	D;D	0.61697	0.99;0.99	P;P	0.55824	0.785;0.785	T	0.20605	-1.0270	10	0.87932	D	0	-7.2791	6.1222	0.20159	0.2273:0.0:0.7727:0.0	.	4;4	Q5XUX1-2;Q5XUX1-3	.;.	H	4	ENSP00000376945:P4H;ENSP00000369696:P4H	ENSP00000369696:P4H	P	-	2	0	FBXW9	12668385	0.169000	0.23002	0.087000	0.20705	0.044000	0.14063	2.195000	0.42677	0.575000	0.29434	0.462000	0.41574	CCC	.		0.662	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		T	12807385	G	T	12807385	3	4	87	1	0	0	0	0	1	0	0	0	5790	1232	43	4	1405	4	FBXW9	19	12807385	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	8794313	12807385	46321598	81	7963											
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38976604	38976604	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggagttggagtcaccacttCgctgaggcccccgcatcatt	7	9	12	13	2	2	1	2	1	0	0	3	3	2	3	3	3	0	3	3	3	0	3	rs398123472		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:38976604C>T	ENST00000359596.3	+	34	5309	c.5309C>T	c.(5308-5310)tCg>tTg	p.S1770L	RYR1_ENST00000355481.4_Missense_Mutation_p.S1770L|RYR1_ENST00000360985.3_Missense_Mutation_p.S1770L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1770	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GTCACCACTTCGCTGAGGCCC	0.682																																					p.S1770L		.											.	RYR1-100	0			c.C5309T						.						41	40	40					19																	38976604		2203	4300	6503	SO:0001583	missense	6261	exon34			CCACTTCGCTGAG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5309C>T	19.37:g.38976604C>T	ENSP00000352608:p.Ser1770Leu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	87	41	NM_001042723	0	0	0	0	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376736	0.24857	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.73469	-0.75;-0.75;-0.75	3.62	3.62	0.41486	.	0.079974	0.50627	U	0.000120	T	0.68311	0.2987	M	0.62723	1.935	0.32730	N	0.509105	P;P	0.52170	0.945;0.951	B;B	0.40134	0.273;0.32	T	0.79472	-0.1789	10	0.72032	D	0.01	.	10.3775	0.44090	0.0:0.612:0.388:0.0	.	1770;1770	P21817-2;P21817	.;RYR1_HUMAN	L	1770	ENSP00000352608:S1770L;ENSP00000347667:S1770L;ENSP00000354254:S1770L	ENSP00000347667:S1770L	S	+	2	0	RYR1	43668444	0.864000	0.29904	1.000000	0.80357	0.159000	0.22180	1.096000	0.30976	1.850000	0.53721	0.585000	0.79938	TCG	.		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38976604	C	T	38976604	3	4	87	1	0	0	0	0	1	0	0	0	13800	893	31	1	5443	1	RYR1	19	38976604	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	26169219	38976604	20152379	82	7964											
PSG3	5671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	43237192	43237192	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtataagttgctgctggaGatggagggcttgggagtctc	7	11	18	5	0	1	1	0	0	1	1	2	4	1	3	0	5	2	5	0	5	2	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:43237192G>T	ENST00000327495.5	-	3	637	c.453C>A	c.(451-453)atC>atA	p.I151I	PSG3_ENST00000595140.1_Silent_p.I151I|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	151	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				TGCTGCTGGAGATGGAGGGCT	0.522																																					p.I151I		.											.	PSG3-92	0			c.C453A						.						160	160	160					19																	43237192		2203	4300	6503	SO:0001819	synonymous_variant	5671	exon3			GCTGGAGATGGAG		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.453C>A	19.37:g.43237192G>T		Somatic	341	1		WXS	Illumina HiSeq	Phase_I	310	117	NM_021016	0	0	0	0	0	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Silent	SNP	ENST00000327495.5	37	CCDS12611.1																																																																																			.		0.522	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		T	43237192	G	T	43237192	2	4	87	1	0	0	0	0	0	0	0	1	12685	932	33	4		4	PSG3	19	43237192	Silent	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	4260588	43237192	15891791	83	7965											
PPP1R15A	23645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49377875	49377875	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgattcagaagcagccttggGagaagctgagtcagacccac	12	7	12	10	0	2	5	2	2	0	3	2	6	2	5	2	1	3	2	2	1	2	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:49377875G>A	ENST00000200453.5	+	2	1654	c.1385G>A	c.(1384-1386)gGa>gAa	p.G462E		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	462	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GCAGCCTTGGGAGAAGCTGAG	0.562																																					p.G462E		.											.	PPP1R15A-226	0			c.G1385A						.						74	74	74					19																	49377875		2203	4300	6503	SO:0001583	missense	23645	exon2			CCTTGGGAGAAGC	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1385G>A	19.37:g.49377875G>A	ENSP00000200453:p.Gly462Glu	Somatic	85	1		WXS	Illumina HiSeq	Phase_I	115	32	NM_014330	0	0	54	72	18	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	0.790	-0.759239	0.03019	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.04603	3.59	0.884	-1.77	0.07982	.	1.784130	0.03162	N	0.169529	T	0.02418	0.0074	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38200	-0.9672	10	0.02654	T	1	-0.2961	5.0156	0.14335	0.6685:0.0:0.3315:0.0	.	462	O75807	PR15A_HUMAN	E	462;302;420	ENSP00000200453:G462E	ENSP00000200453:G462E	G	+	2	0	PPP1R15A	54069687	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	-0.455000	0.06762	-1.201000	0.02659	-1.131000	0.01979	GGA	.		0.562	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		A	49377875	G	A	49377875	3	1	87	1	0	0	0	0	1	0	0	0	12392	1174	41	2	1387	2	PPP1R15A	19	49377875	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	6140683	49377875	9751108	84	7966											
PCBP3	54039	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47333926	47333926	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcctccacccctgtcatttTtgcaggtggtcaggtaagag	7	11	11	12	1	2	1	2	0	0	1	3	1	3	1	4	3	1	2	4	3	1	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr21:47333926T>G	ENST00000400314.1	+	10	1000	c.662T>G	c.(661-663)tTt>tGt	p.F221C	PCBP3_ENST00000400304.1_Missense_Mutation_p.F189C|PCBP3_ENST00000400310.1_Missense_Mutation_p.F221C|PCBP3_ENST00000449640.1_Missense_Mutation_p.F221C|PCBP3_ENST00000400308.1_Intron|PCBP3_ENST00000400309.1_Missense_Mutation_p.F221C			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	221					mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		CCTGTCATTTTTGCAGGTGGT	0.602																																					p.F221C		.											.	PCBP3-227	0			c.T662G						.						64	72	69					21																	47333926		1987	4167	6154	SO:0001583	missense	54039	exon8			TCATTTTTGCAGG	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.662T>G	21.37:g.47333926T>G	ENSP00000383168:p.Phe221Cys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	100	39	NM_020528	0	0	0	0	0	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Missense_Mutation	SNP	ENST00000400314.1	37	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250671	0.80135	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000449640;ENST00000346743;ENST00000400304	T;T;T;T;T	0.47177	1.49;1.41;1.43;1.49;0.85	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.58206	0.2106	L	0.52364	1.645	0.80722	D	1	D;B;D;B	0.67145	0.986;0.039;0.996;0.004	P;B;P;B	0.58391	0.838;0.099;0.784;0.029	T	0.59445	-0.7453	10	0.48119	T	0.1	-3.3437	14.9659	0.71193	0.0:0.0:0.0:1.0	.	189;221;221;221	E9PFP8;P57721-4;P57721;P57721-5	.;.;PCBP3_HUMAN;.	C	221;221;221;221;221;189	ENSP00000383168:F221C;ENSP00000383165:F221C;ENSP00000383164:F221C;ENSP00000401198:F221C;ENSP00000383159:F189C	ENSP00000330225:F221C	F	+	2	0	PCBP3	46158354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.577000	0.82486	1.933000	0.56026	0.460000	0.39030	TTT	.		0.602	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			G	47333926	T	G	47333926	3	3	87	1	0	0	0	0	1	0	0	0	11528	1841	64	5	692	5	PCBP3	21	47333926	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		47333926	795969	85	7967											
FAM123B	139285	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	63412033	63412033	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcttcttcctcctcgtcAtcatcatctggcaaggccat	6	14	5	16	1	6	0	3	0	3	0	10	0	9	0	4	2	0	1	4	2	1	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chrX:63412033A>G	ENST00000330258.3	-	2	1406	c.1134T>C	c.(1132-1134)gaT>gaC	p.D378D	AMER1_ENST00000374869.3_Silent_p.D378D|AMER1_ENST00000403336.1_Silent_p.D378D	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	378	Glu-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									cctcctcGTCATCATCATCTG	0.522																																					p.D378D		.											.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T1134C						.						153	142	146					X																	63412033		2203	4300	6503	SO:0001819	synonymous_variant	139285	exon2			CTCGTCATCATCA	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1134T>C	X.37:g.63412033A>G		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	85	7	NM_152424	0	0	1	1	0	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			.		0.522	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63412033	A	G	63412033	2	3	87	1	0	0	0	0	0	0	0	1	5439	214	8	3		3	FAM123B	23	63412033	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		63412033	91858527	86	7968											
GPRASP1	9737	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	101912417	101912418	+	Frame_Shift_Del	DEL	TC	TC	-																															caatttacccgagatttcatTcgagattcaggtgttgtctc																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chrX:101912417_101912418delTC	ENST00000361600.5	+	5	4377_4378	c.3576_3577delTC	c.(3574-3579)attcgafs	p.IR1192fs	GPRASP1_ENST00000444152.1_Frame_Shift_Del_p.IR1192fs|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000537097.1_Frame_Shift_Del_p.IR1192fs|GPRASP1_ENST00000415986.1_Frame_Shift_Del_p.IR1192fs	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1192	OPRD1-binding.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						GAGATTTCATTCGAGATTCAGG	0.371																																					p.1192_1193del		.											.	GPRASP1-131	0			c.3576_3577del						.																																			SO:0001589	frameshift_variant	9737	exon3			.	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3576_3577delTC	X.37:g.101912417_101912418delTC	ENSP00000355146:p.Ile1192fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	69	52	NM_001099411	0	0	0	0	0	O43168|Q96LA1	Frame_Shift_Del	DEL	ENST00000361600.5	37	CCDS35352.1																																																																																			.		0.371	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		-	101912418	TC	-	101912417	7	5	87	1	0	1	0	1	0	0	0	0	6743	1771	62	0	3578	0	GPRASP1	23	101912417	Frame_Shift_Del	DEL	TC	TCGA-BQ-7058-01A-11D-1961-08	38500384	101912417	53358143	87	7969											
PEX10	5192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	2340282	2340282	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgatgctgacgtactcctccCccagggtctggtagcctgcg	5	10	12	14	2	1	2	0	2	1	0	3	2	3	2	4	2	4	3	4	2	2	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:2340282C>G	ENST00000447513.2	-	3	277	c.209G>C	c.(208-210)gGg>gCg	p.G70A	PEX10_ENST00000288774.3_Missense_Mutation_p.G70A|PEX10_ENST00000515760.1_5'UTR|PEX10_ENST00000507596.1_Missense_Mutation_p.G70A	NM_002617.3	NP_002608.1	O60683	PEX10_HUMAN	peroxisomal biogenesis factor 10	70					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	integral component of peroxisomal membrane (GO:0005779)|intracellular (GO:0005622)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	7	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		GTACTCCTCCCCCAGGGTCTG	0.677																																					p.G70A	GBM(12;9 508 1649 13619)	.											.	PEX10-90	0			c.G209C						.						94	95	95					1																	2340282		2203	4300	6503	SO:0001583	missense	5192	exon3			TCCTCCCCCAGGG	AF060502	CCDS41.1, CCDS44045.1	1p36.32	2013-01-09	2008-08-26		ENSG00000157911	ENSG00000157911		"RING-type (C3HC4) zinc fingers"	8851	protein-coding gene	gene with protein product		602859	"peroxisome biogenesis factor 10"			9683594	Standard	NM_002617		Approved	RNF69	uc001ajg.3	O60683	OTTHUMG00000001637	ENST00000447513.2:c.209G>C	1.37:g.2340282C>G	ENSP00000407922:p.Gly70Ala	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	58	14	NM_002617	0	0	17	33	16	B3KWD8|Q5T095|Q9BW90	Missense_Mutation	SNP	ENST00000447513.2	37	CCDS44045.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.210641	0.79240	.	.	ENSG00000157911	ENST00000288774;ENST00000447513;ENST00000507596	D;D;D	0.88201	-2.35;-2.35;-2.35	4.48	4.48	0.54585	Pex, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95661	0.8589	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96912	0.9668	10	0.87932	D	0	2.6652	16.1137	0.81283	0.0:1.0:0.0:0.0	.	70;70	O60683;O60683-2	PEX10_HUMAN;.	A	70	ENSP00000288774:G70A;ENSP00000407922:G70A;ENSP00000424291:G70A	ENSP00000288774:G70A	G	-	2	0	PEX10	2330142	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	5.505000	0.66981	2.035000	0.60131	0.462000	0.41574	GGG	.		0.677	PEX10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367454.1	NM_153818		G	2340282	C	G	2340282	3	3	88	1	0	0	0	0	1	0	0	0	11762	623	22	4	847	4	PEX10	1	2340282	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		2340282	246910339	1	7970											
PER3	8863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	7887456	7887456	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcacccggaagagaatacGcagcccccggaactgcaccg	11	3	10	17	4	1	1	1	0	0	1	1	4	1	3	5	2	4	2	5	2	4	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:7887456G>A	ENST00000361923.2	+	17	2618	c.2443G>A	c.(2443-2445)Gca>Aca	p.A815T	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.A823T	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	815	Pro-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		AAGAGAATACGCAGCCCCCGG	0.622																																					p.A815T		.											.	PER3-93	0			c.G2443A						.						67	69	68					1																	7887456		2203	4300	6503	SO:0001583	missense	8863	exon17			GAATACGCAGCCC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2443G>A	1.37:g.7887456G>A	ENSP00000355031:p.Ala815Thr	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	112	28	NM_016831	0	0	10	13	3	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	7.390	0.630557	0.14322	.	.	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.10192	2.9;2.9	3.68	-2.56	0.06268	.	2.865610	0.00841	N	0.001740	T	0.04003	0.0112	N	0.11427	0.14	0.09310	N	1	B;P;B;B	0.34662	0.07;0.462;0.41;0.07	B;B;B;B	0.24541	0.011;0.054;0.053;0.011	T	0.20009	-1.0288	10	0.17369	T	0.5	.	0.9429	0.01359	0.3343:0.3073:0.2098:0.1487	.	815;823;823;815	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	T	823;815;26	ENSP00000366755:A823T;ENSP00000355031:A815T	ENSP00000355031:A815T	A	+	1	0	PER3	7810043	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.918000	0.28678	-0.394000	0.07727	0.561000	0.74099	GCA	.		0.622	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		A	7887456	G	A	7887456	3	1	88	1	0	0	0	0	1	0	0	0	11757	1087	38	1	2509	1	PER3	1	7887456	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	5547174	7887456	241363165	2	7971											
CELA2A	63036	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15793929	15793929	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgtctgacggccggtggCaggtgcacggcatcgtcagc	6	6	17	12	5	2	1	1	1	1	0	3	1	2	1	1	6	2	3	1	6	0	0	rs375207414		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:15793929C>T	ENST00000359621.4	+	7	713	c.688C>T	c.(688-690)Cag>Tag	p.Q230*	CELA2B_ENST00000494280.1_3'UTR	NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	230	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						CGGCCGGTGGCAGGTGCACGG	0.607																																					p.Q230X													.	CELA2A-92	0			c.C688T						.						67	64	65					1																	15793929		2203	4300	6503	SO:0001587	stop_gained	63036	exon7			CGGTGGCAGGTGC		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"elastase 2A"	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.688C>T	1.37:g.15793929C>T	ENSP00000352639:p.Gln230*	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	66	8	NM_033440	0	0	0	0	0	B2R5I4|Q14243	Nonsense_Mutation	SNP	ENST00000359621.4	37	CCDS157.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.440241	0.25900	.	.	ENSG00000142615	ENST00000359621	.	.	.	3.08	-4.98	0.03019	.	0.467062	0.18391	U	0.142670	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	16.3146	0.82913	0.0:0.6887:0.3113:0.0	.	.	.	.	X	230	.	ENSP00000352639:Q230X	Q	+	1	0	CELA2A	15666516	1.000000	0.71417	0.110000	0.21437	0.023000	0.10783	2.255000	0.43222	-1.584000	0.01636	-0.689000	0.03729	CAG	.		0.607	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440		T	15793929	C	T	15793929	4	4	88	1	0	0	0	0	0	1	0	0	3217	711	25	2	714	2	CELA2A	1	15793929	Nonsense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	7906473	15793929	233456692	3	7972											
CLCNKB	1188	broad.mit.edu	37	chr1	16378296	16378296	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaccaatcccatcatgccAggggggtatgctctggcagg	9	8	12	12	0	3	0	2	0	1	0	4	0	4	0	3	5	2	3	3	5	2	1	rs199755248		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:16378296A>C	ENST00000375679.4	+	14	1500	c.1389A>C	c.(1387-1389)ccA>ccC	p.P463P	CLCNKB_ENST00000375667.3_Silent_p.P294P	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	463					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CCATCATGCCAGGGGGGTATG	0.622													C|||	1	0.000199681	0	0	5008	,	,		18264	0.001		0	False		,,,				2504	0				p.P463P													.	CLCNKB-91	0			c.A1389C	GRCh37	CD004305	CLCNKB	D		.						66	66	66					1																	16378296		2203	4300	6503	SO:0001819	synonymous_variant	1188	exon14			CATGCCAGGGGGG	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"Ion channels / Chloride channels : Voltage-sensitive"	2027	protein-coding gene	gene with protein product		602023	"chloride channel Kb"				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1389A>C	1.37:g.16378296A>C		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	99	5	NM_000085	0	0	7	7	0	B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	CCDS168.1																																																																																			A|0.992;C|0.008		0.622	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085		C	16378296	A	C	16378296	2	2	88	1	0	0	0	0	0	0	0	1	3476	175	7	5		5	CLCNKB	1	16378296	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	584367	16378296	232872325	4	7973											
THRAP3	9967	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	36767245	36767245	+	Frame_Shift_Del	DEL	G	G	-																															cgattttcaaaaaagaaaccGggaagaggagtgggacccag																								rs566092059		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:36767245delG	ENST00000354618.5	+	11	2818	c.2594delG	c.(2593-2595)cggfs	p.R865fs	THRAP3_ENST00000469141.2_Frame_Shift_Del_p.R865fs	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	865	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AAAAGAAACCGGGAAGAGGAG	0.478			T	USP6	aneurysmal bone cysts																																p.R865fs	Pancreas(129;785 1795 20938 23278 32581)	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3-663	0			c.2594delG						.						66	68	67					1																	36767245		2203	4300	6503	SO:0001589	frameshift_variant	9967	exon11			.	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.2594delG	1.37:g.36767245delG	ENSP00000346634:p.Arg865fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	78	21	NM_005119	0	0	0	0	0	D3DPS5|Q5VTK6	Frame_Shift_Del	DEL	ENST00000354618.5	37	CCDS405.1																																																																																			.		0.478	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		-	36767245	G	-	36767245	7	5	88	1	0	1	0	1	0	0	0	0	15906	1116	39	0	2628	0	THRAP3	1	36767245	Frame_Shift_Del	DEL	G	TCGA-BQ-7059-01A-11D-1961-08	20388949	36767245	212483376	5	7974											
ATXN7L2	127002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110034064	110034064	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgaagcgggcagggcccCtggactgtcgtggctcccct	5	7	16	13	2	0	1	0	1	0	0	2	3	1	2	4	4	1	2	4	4	1	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:110034064C>A	ENST00000369870.3	+	10	1894	c.1879C>A	c.(1879-1881)Ctg>Atg	p.L627M	CYB561D1_ENST00000533024.1_5'Flank|CYB561D1_ENST00000496961.1_5'Flank|CYB561D1_ENST00000420578.2_5'Flank|CYB561D1_ENST00000527072.1_5'Flank|CYB561D1_ENST00000393709.3_5'Flank|CYB561D1_ENST00000528785.1_5'Flank|CYB561D1_ENST00000310611.4_5'Flank|CYB561D1_ENST00000369868.3_5'Flank|CYB561D1_ENST00000430195.2_5'Flank|ATXN7L2_ENST00000459635.1_3'UTR	NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	627										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GGCAGGGCCCCTGGACTGTCG	0.622																																					p.L627M		.											.	ATXN7L2-92	0			c.C1879A						.						35	40	38					1																	110034064		2203	4300	6503	SO:0001583	missense	127002	exon10			GGGCCCCTGGACT	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1879C>A	1.37:g.110034064C>A	ENSP00000358886:p.Leu627Met	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	52	20	NM_153340	0	0	3	5	2		Missense_Mutation	SNP	ENST00000369870.3	37	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.514316	0.44763	.	.	ENSG00000162650	ENST00000369870;ENST00000369869	T	0.38560	1.13	5.36	3.26	0.37387	.	0.440276	0.19115	N	0.122331	T	0.23451	0.0567	N	0.24115	0.695	0.25930	N	0.983008	P;D	0.64830	0.946;0.994	P;P	0.55222	0.714;0.771	T	0.04678	-1.0934	10	0.72032	D	0.01	-0.0215	7.9316	0.29905	0.0:0.7788:0.0:0.2212	.	254;627	Q5T6C4;Q5T6C5	.;AT7L2_HUMAN	M	627;254	ENSP00000358886:L627M	ENSP00000358885:L254M	L	+	1	2	ATXN7L2	109835587	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.056000	0.41355	0.647000	0.30713	-0.258000	0.10820	CTG	.		0.622	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		A	110034064	C	A	110034064	3	1	88	1	0	0	0	0	1	0	0	0	1218	680	24	4	1917	4	ATXN7L2	1	110034064	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	73266819	110034064	139216557	6	7975											
INSRR	3645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156811976	156811976	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcggtgcacaaacttgtTggcagcaaggtaggccatgc	10	9	12	10	1	1	0	0	0	1	0	2	0	1	0	1	4	4	5	1	4	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:156811976T>G	ENST00000368195.3	-	19	3721	c.3325A>C	c.(3325-3327)Aac>Cac	p.N1109H	NTRK1_ENST00000392302.2_Missense_Mutation_p.L38W	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	1109	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACAAACTTGTTGGCAGCAAGG	0.572																																					p.N1109H		.											.	INSRR-1403	0			c.A3325C						.						104	95	98					1																	156811976		2203	4300	6503	SO:0001583	missense	3645	exon19			ACTTGTTGGCAGC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.3325A>C	1.37:g.156811976T>G	ENSP00000357178:p.Asn1109His	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	41	12	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.413045|4.413045	0.83449|0.83449	.|.	.|.	ENSG00000198400|ENSG00000027644	ENST00000392302|ENST00000368195	T|D	0.76839|0.82803	-1.05|-1.65	4.83|4.83	4.83|4.83	0.62350|0.62350	.|Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.|0.260110	.|0.27223	.|N	.|0.020345	T|T	0.67664|0.67664	0.2917|0.2917	N|N	0.17594|0.17594	0.5|0.5	0.37606|0.37606	D|D	0.920732|0.920732	D|P	0.76494|0.41102	0.999|0.738	D|P	0.64042|0.44623	0.921|0.455	T|T	0.76490|0.76490	-0.2940|-0.2940	9|10	0.87932|0.72032	D|D	0|0.01	.|.	13.364|13.364	0.60674|0.60674	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	38|1109	A6NF12|P14616	.|INSRR_HUMAN	W|H	38|1109	ENSP00000376120:L38W|ENSP00000357178:N1109H	ENSP00000376120:L38W|ENSP00000357178:N1109H	L|N	+|-	2|1	0|0	NTRK1|INSRR	155078600|155078600	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	7.868000|7.868000	0.87116|0.87116	2.041000|2.041000	0.60428|0.60428	0.459000|0.459000	0.35465|0.35465	TTG|AAC	.		0.572	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		G	156811976	T	G	156811976	3	3	88	1	0	0	0	0	1	0	0	0	7795	1821	63	5	583	5	INSRR	1	156811976	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	46777912	156811976	92438645	7	7976											
C1orf21	81563	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	184476745	184476745	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agtataggatcaaaccagtgGaagaggtcaaatacatgaaa	19	7	10	5	0	2	2	2	1	0	1	2	4	2	4	1	3	2	1	1	3	7	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:184476745G>T	ENST00000235307.6	+	3	553	c.118G>T	c.(118-120)Gaa>Taa	p.E40*		NM_030806.3	NP_110433.1	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21	40										breast(1)|lung(1)	2		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		CAAACCAGTGGAAGAGGTCAA	0.348																																					p.E40X													.	C1orf21-90	0			c.G118T						.						79	82	81					1																	184476745		2203	4300	6503	SO:0001587	stop_gained	81563	exon3			CCAGTGGAAGAGG	AF312864	CCDS1362.1	1q25	2008-07-18			ENSG00000116667	ENSG00000116667			15494	protein-coding gene	gene with protein product	"proliferation-inducing protein 13"					11318611	Standard	NM_030806		Approved	PIG13	uc001gqv.1	Q9H246	OTTHUMG00000035386	ENST00000235307.6:c.118G>T	1.37:g.184476745G>T	ENSP00000235307:p.Glu40*	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	85	17	NM_030806	0	0	25	26	1	B2R551	Nonsense_Mutation	SNP	ENST00000235307.6	37	CCDS1362.1	.	.	.	.	.	.	.	.	.	.	G	41	8.721385	0.98929	.	.	ENSG00000116667	ENST00000235307	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.6012	0.95563	0.0:0.0:1.0:0.0	.	.	.	.	X	40	.	ENSP00000235307:E40X	E	+	1	0	C1orf21	182743368	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.777000	0.62361	2.876000	0.98609	0.655000	0.94253	GAA	.		0.348	C1orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085784.2	NM_030806		T	184476745	G	T	184476745	4	4	88	1	0	0	0	0	0	1	0	0	2034	1175	41	4	124	4	C1orf21	1	184476745	Nonsense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	27664769	184476745	64773876	8	7977											
PLEKHA6	22874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204198070	204198070	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctggctccactcacctcctTattgatgtccacgtcataat	8	13	5	15	1	2	1	2	1	0	0	5	1	5	1	5	1	0	1	5	1	2	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:204198070T>C	ENST00000272203.3	-	19	3062	c.2746A>G	c.(2746-2748)Aag>Gag	p.K916E	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.K936E	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	916										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			CTCACCTCCTTATTGATGTCC	0.587																																					p.K916E		.											.	PLEKHA6-654	0			c.A2746G						.						116	112	113					1																	204198070		2203	4300	6503	SO:0001583	missense	22874	exon19			CCTCCTTATTGAT	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2746A>G	1.37:g.204198070T>C	ENSP00000272203:p.Lys916Glu	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	187	49	NM_014935	0	0	0	0	0	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.148801	0.57151	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.45276	0.9;0.9	5.3	5.3	0.74995	.	0.265846	0.36628	N	0.002497	T	0.59649	0.2209	M	0.72894	2.215	0.35019	D	0.757628	D	0.58268	0.982	D	0.67548	0.952	T	0.71002	-0.4718	10	0.49607	T	0.09	-32.3486	10.459	0.44567	0.0:0.0786:0.0:0.9214	.	916	Q9Y2H5	PKHA6_HUMAN	E	916;936	ENSP00000272203:K916E;ENSP00000402046:K936E	ENSP00000272203:K916E	K	-	1	0	PLEKHA6	202464693	1.000000	0.71417	0.875000	0.34327	0.332000	0.28634	5.520000	0.67080	1.995000	0.58328	0.460000	0.39030	AAG	.		0.587	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		C	204198070	T	C	204198070	3	2	88	1	0	0	0	0	1	0	0	0	12086	1763	61	3	416	3	PLEKHA6	1	204198070	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	19721325	204198070	45052551	9	7978											
USH2A	7399	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	216019211	216019211	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctgcactgttgatgctgtGgactccattgaagacagaga	10	11	11	9	0	0	4	0	2	0	2	2	6	2	5	2	1	2	3	2	1	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:216019211G>T	ENST00000307340.3	-	45	9396	c.9010C>A	c.(9010-9012)Cac>Aac	p.H3004N	USH2A_ENST00000366943.2_Missense_Mutation_p.H3004N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3004	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTGATGCTGTGGACTCCATTG	0.433										HNSCC(13;0.011)																											p.H3004N													.	USH2A-115	0			c.C9010A						.						97	90	92					1																	216019211		2203	4300	6503	SO:0001583	missense	7399	exon45			TGCTGTGGACTCC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9010C>A	1.37:g.216019211G>T	ENSP00000305941:p.His3004Asn	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	68	13	NM_206933	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314024	0.40996	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52754	0.65;0.65	5.91	1.85	0.25348	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.292176	0.24165	N	0.040943	T	0.53238	0.1784	M	0.73598	2.24	0.39147	D	0.962158	P	0.44659	0.84	P	0.50270	0.636	T	0.50608	-0.8808	10	0.38643	T	0.18	.	7.7082	0.28663	0.1958:0.1221:0.6821:0.0	.	3004	O75445	USH2A_HUMAN	N	3004	ENSP00000305941:H3004N;ENSP00000355910:H3004N	ENSP00000305941:H3004N	H	-	1	0	USH2A	214085834	1.000000	0.71417	0.966000	0.40874	0.991000	0.79684	3.052000	0.49893	0.078000	0.16900	0.655000	0.94253	CAC	.		0.433	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216019211	G	T	216019211	3	4	88	1	0	0	0	0	1	0	0	0	17069	1348	47	4	6710	4	USH2A	1	216019211	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	11821141	216019211	33231410	10	7979											
TP53BP2	7159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223984099	223984099	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactctggtttcggtaaggAttagataagaaaggcagtaa	14	11	11	5	1	2	2	1	0	1	2	3	3	2	3	0	4	0	4	0	4	5	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:223984099A>G	ENST00000343537.7	-	13	2433	c.2142T>C	c.(2140-2142)aaT>aaC	p.N714N	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000391878.2_Silent_p.N585N	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	708					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		TTCGGTAAGGATTAGATAAGA	0.438																																					p.N714N		.											.	TP53BP2-229	0			c.T2142C						.						143	139	140					1																	223984099		2203	4300	6503	SO:0001819	synonymous_variant	7159	exon13			GTAAGGATTAGAT	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	12000	protein-coding gene	gene with protein product		602143	"tumor protein p53-binding protein, 2"			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2142T>C	1.37:g.223984099A>G		Somatic	208	0		WXS	Illumina HiSeq	Phase_I	228	52	NM_001031685	0	0	40	75	35	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																			.		0.438	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		G	223984099	A	G	223984099	2	3	88	1	0	0	0	0	0	0	0	1	16417	330	12	3		3	TP53BP2	1	223984099	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	7964888	223984099	25266522	11	7980											
SMEK2	57223	broad.mit.edu;ucsc.edu	37	chr2	55844410	55844410	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaccttcactcgccgccgCgtatccgacatggtggctgc	6	9	11	15	5	1	1	1	0	0	1	3	2	2	1	4	2	1	2	4	2	2	3	rs142775723		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr2:55844410C>T	ENST00000345102.5	-	1	313	c.12G>A	c.(10-12)acG>acA	p.T4T	SMEK2_ENST00000272313.5_Silent_p.T4T|RP11-554J4.1_ENST00000608113.1_RNA|SMEK2_ENST00000477749.1_5'UTR|SMEK2_ENST00000407823.3_Silent_p.T4T	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	4	WH1.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTCGCCGCCGCGTATCCGACA	0.622																																					p.T4T													.	SMEK2-228	0			c.G12A						.	C	,	1,4405	2.1+/-5.4	0,1,2202	55	45	48		12,12	1.5	1	2	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SMEK2	NM_001122964.1,NM_020463.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	4/850,4/765	55844410	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57223	exon1			CCGCCGCGTATCC	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.12G>A	2.37:g.55844410C>T		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	26	4	NM_001122964	0	0	28	35	7	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Silent	SNP	ENST00000345102.5	37	CCDS46289.1																																																																																			C|1.000;T|0.000		0.622	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		T	55844410	C	T	55844410	2	4	88	1	0	0	0	0	0	0	0	1	14826	755	27	1		1	SMEK2	2	55844410	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		55844410	187354963	12	7981											
DUSP11	8446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74007101	74007101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatgatgccactggctcaTgtgggtcccaagaagccgcc	8	7	14	12	1	1	2	1	1	0	1	2	3	2	3	4	3	2	1	4	3	2	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr2:74007101T>C	ENST00000272444.3	-	1	183	c.142A>G	c.(142-144)Atg>Gtg	p.M48V	DUSP11_ENST00000377706.4_Start_Codon_SNP_p.M1V|DUSP11_ENST00000443070.1_Missense_Mutation_p.M48V|DUSP11_ENST00000480948.1_5'Flank	NM_003584.2	NP_003575.2	O75319	DUS11_HUMAN	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	1					peptidyl-tyrosine dephosphorylation (GO:0035335)|polynucleotide 5' dephosphorylation (GO:0098507)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphatase activity (GO:0016791)|poly(A) RNA binding (GO:0044822)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|skin(1)	12						CACTGGCTCATGTGGGTCCCA	0.607											OREG0014714	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M48V		.											.	DUSP11-227	0			c.A142G						.						61	61	61					2																	74007101		2203	4300	6503	SO:0001583	missense	8446	exon1			GGCTCATGTGGGT	AF023917	CCDS1928.2	2p13.1	2011-06-09			ENSG00000144048	ENSG00000144048		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3066	protein-coding gene	gene with protein product		603092				9685386	Standard	NM_003584		Approved	PIR1	uc002sjp.3	O75319	OTTHUMG00000129816	ENST00000272444.3:c.142A>G	2.37:g.74007101T>C	ENSP00000272444:p.Met48Val	Somatic	108	0	1149	WXS	Illumina HiSeq	Phase_I	82	24	NM_003584	0	0	15	19	4	B2RCT8|Q6AI47|Q9BWE3	Missense_Mutation	SNP	ENST00000272444.3	37	CCDS1928.2	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742276	0.49151	.	.	ENSG00000144048	ENST00000272444;ENST00000443070;ENST00000377706	T;T	0.32988	1.43;2.01	4.6	4.6	0.57074	.	0.059637	0.56097	D	0.000024	T	0.35008	0.0917	.	.	.	0.80722	D	1	P;D	0.55172	0.882;0.97	B;P	0.48627	0.428;0.584	T	0.10291	-1.0636	9	0.51188	T	0.08	-4.2088	10.6571	0.45682	0.0:0.0:0.0:1.0	.	48;1	C9JYA6;O75319	.;DUS11_HUMAN	V	48;48;1	ENSP00000413444:M48V;ENSP00000366935:M1V	ENSP00000272444:M48V	M	-	1	0	DUSP11	73860609	1.000000	0.71417	0.998000	0.56505	0.013000	0.08279	3.027000	0.49697	2.285000	0.76669	0.533000	0.62120	ATG	.		0.607	DUSP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252047.3			C	74007101	T	C	74007101	3	2	88	1	0	0	0	0	1	0	0	0	4822	1464	51	3	1027	3	DUSP11	2	74007101	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	18162691	74007101	169192272	13	7982											
DPP10	57628	broad.mit.edu	37	chr2	116572492	116572492	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggaagtggattccagggTctgaaaattttgcaggagat	13	10	14	4	0	1	3	0	1	1	2	2	6	2	5	1	4	1	1	1	4	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr2:116572492T>C	ENST00000410059.1	+	20	2304	c.1824T>C	c.(1822-1824)ggT>ggC	p.G608G	DPP10_ENST00000393147.2_Silent_p.G612G|DPP10_ENST00000409163.1_Silent_p.G558G|DPP10_ENST00000310323.8_Silent_p.G601G	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	608						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GATTCCAGGGTCTGAAAATTT	0.393																																					p.G612G													.	DPP10-142	0			c.T1836C						.						123	126	125					2																	116572492		2203	4300	6503	SO:0001819	synonymous_variant	57628	exon20			CCAGGGTCTGAAA	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"dipeptidylpeptidase 10", "dipeptidyl-peptidase 10"			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1824T>C	2.37:g.116572492T>C		Somatic	102	1		WXS	Illumina HiSeq	Phase_I	103	3	NM_001178034	0	0	0	0	0	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	CCDS46400.1																																																																																			.		0.393	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		C	116572492	T	C	116572492	2	2	88	1	0	0	0	0	0	0	0	1	4738	1654	58	3		3	DPP10	2	116572492	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	42565391	116572492	126626881	14	7983											
ARHGEF4	50649	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	131801882	131801882	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctggcaggacctgctccGccgcgacgtgttgtactaca	7	9	11	14	4	1	0	0	0	1	0	2	2	2	1	3	2	3	4	3	2	2	3	rs376653204		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr2:131801882G>A	ENST00000326016.5	+	12	2129	c.1610G>A	c.(1609-1611)cGc>cAc	p.R537H	ARHGEF4_ENST00000525839.1_Missense_Mutation_p.R537H|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.R466H|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.R537H|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.R477H	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	537	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GACCTGCTCCGCCGCGACGTG	0.642																																					p.R537H													.	ARHGEF4-292	0			c.G1610A						.	G	HIS/ARG,HIS/ARG	0,4400		0,0,2200	43	36	39		1610,1610	4.1	1	2		39	1,8599		0,1,4299	no	missense,missense	ARHGEF4	NM_015320.2,NM_032995.1	29,29	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	,	537/691,537/671	131801882	1,12999	2200	4300	6500	SO:0001583	missense	50649	exon12			TGCTCCGCCGCGA	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1610G>A	2.37:g.131801882G>A	ENSP00000316845:p.Arg537His	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_032995	0	0	0	0	0	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	37	CCDS2165.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.491248	0.84962	0.0	1.16E-4	ENSG00000136002	ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52	4.96	4.08	0.47627	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.93743	0.8000	M	0.83953	2.67	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.71414	0.973;0.954;0.973	D	0.93816	0.7114	10	0.87932	D	0	.	11.1025	0.48184	0.0912:0.0:0.9088:0.0	.	477;537;537	E9PEM0;Q9NR80-4;Q9NR80	.;.;ARHG4_HUMAN	H	537;537;537;477;466	ENSP00000316845:R537H;ENSP00000376680:R537H;ENSP00000432267:R537H;ENSP00000387285:R477H;ENSP00000348017:R466H	ENSP00000316845:R537H	R	+	2	0	ARHGEF4	131518352	1.000000	0.71417	0.988000	0.46212	0.864000	0.49448	7.373000	0.79623	1.097000	0.41459	0.561000	0.74099	CGC	.		0.642	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			A	131801882	G	A	131801882	3	1	88	1	0	0	0	0	1	0	0	0	908	1087	38	1	1648	1	ARHGEF4	2	131801882	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	15229390	131801882	111397491	15	7984											
CNTN6	27255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	1371578	1371578	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcttttcccagggcagctatCtcttggaaaagaggaacgga	11	9	12	9	1	1	1	0	0	1	1	3	4	2	4	1	4	2	3	1	4	4	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:1371578C>G	ENST00000446702.2	+	11	1950	c.1323C>G	c.(1321-1323)atC>atG	p.I441M	CNTN6_ENST00000350110.2_Missense_Mutation_p.I441M|CNTN6_ENST00000539053.1_Missense_Mutation_p.I369M			Q9UQ52	CNTN6_HUMAN	contactin 6	441	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GGGCAGCTATCTCTTGGAAAA	0.333																																					p.I441M		.											.	CNTN6-345	0			c.C1323G						.						57	59	58					3																	1371578		2202	4299	6501	SO:0001583	missense	27255	exon11			AGCTATCTCTTGG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1323C>G	3.37:g.1371578C>G	ENSP00000407822:p.Ile441Met	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	59	14	NM_014461	0	0	27	42	15	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929637	0.52759	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.72282	-0.64;-0.64;-0.64	5.71	0.115	0.14643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.491996	0.18537	N	0.138338	T	0.81128	0.4758	M	0.92604	3.325	0.09310	N	1	P	0.48350	0.909	P	0.57371	0.819	T	0.70901	-0.4746	10	0.72032	D	0.01	.	4.4769	0.11748	0.0:0.2343:0.1888:0.5769	.	441	Q9UQ52	CNTN6_HUMAN	M	441;369;441	ENSP00000407822:I441M;ENSP00000442791:I369M;ENSP00000341882:I441M	ENSP00000341882:I441M	I	+	3	3	CNTN6	1346578	0.000000	0.05858	0.482000	0.27366	0.987000	0.75469	-0.078000	0.11375	0.093000	0.17368	0.563000	0.77884	ATC	.		0.333	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		G	1371578	C	G	1371578	3	3	88	1	0	0	0	0	1	0	0	0	3651	903	32	4	1361	4	CNTN6	3	1371578	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		1371578	196650852	16	7985											
OGG1	8536	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	9800959	9800960	+	Intron	INS	-	-	T																															gaattacagacttcttcctcINStagacttggaggtgagggac																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:9800959_9800960insT	ENST00000256460.3	-	10	1090				OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_3'UTR|OGG1_ENST00000302008.8_Frame_Shift_Ins_p.R347fs|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000383826.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I						cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		ACTTCTTCCTCTAGACTTGGAG	0.46																																					p.S346fs		.											.	OGG1-660	0			c.1037_1038insT						.																																			SO:0001627	intron_variant	4968	exon7			.	L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.912+211->A	3.37:g.9800960_9800960dupT		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	157	32	NM_016828	0	0	0	0	0	Q3KPF6	Frame_Shift_Ins	INS	ENST00000256460.3	37	CCDS2582.1																																																																																			.		0.46	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		T	9800960	-	T	9800959	6	5	88	0	1	1	1	0	0	0	0	0	10871	913	32	0		0	OGG1	3	9800959	Intron	INS	-	TCGA-BQ-7059-01A-11D-1961-08	8429381	9800959	188221471	17	7986											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48456619	48456619	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagggtccaagggaacatGccgtctccgggaccacgcga	10	4	15	12	4	1	0	0	0	1	0	3	4	2	3	4	4	2	0	4	4	2	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:48456619G>C	ENST00000358536.4	-	20	4201	c.3932C>G	c.(3931-3933)gCa>gGa	p.A1311G	PLXNB1_ENST00000296440.6_Missense_Mutation_p.A1311G|PLXNB1_ENST00000465117.1_Splice_Site|PLXNB1_ENST00000358459.4_Missense_Mutation_p.A1128G|PLXNB1_ENST00000456774.1_Missense_Mutation_p.A1128G|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1311	IPT/TIG 3.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AAGGGAACATGCCGTCTCCGG	0.642																																					p.A1311G		.											.	PLXNB1-293	0			c.C3932G						.						62	62	62					3																	48456619		2203	4300	6503	SO:0001583	missense	5364	exon20			GAACATGCCGTCT	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3932C>G	3.37:g.48456619G>C	ENSP00000351338:p.Ala1311Gly	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_001130082	0	0	85	85	0	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	G	5.873	0.345186	0.11126	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99	5.14	-2.76	0.05896	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);	1.568640	0.03917	N	0.282842	T	0.43122	0.1233	N	0.02539	-0.55	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.23154	-1.0196	10	0.23891	T	0.37	.	1.1745	0.01832	0.2302:0.1071:0.1985:0.4641	.	1311;1128	O43157;O43157-2	PLXB1_HUMAN;.	G	1311;1128;1311;1128	ENSP00000296440:A1311G;ENSP00000351242:A1128G;ENSP00000351338:A1311G;ENSP00000414199:A1128G	ENSP00000296440:A1311G	A	-	2	0	PLXNB1	48431623	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.040000	0.13905	-0.007000	0.14345	0.655000	0.94253	GCA	.		0.642	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		C	48456619	G	C	48456619	3	2	88	1	0	0	0	0	1	0	0	0	12149	1319	46	4	2551	4	PLXNB1	3	48456619	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	38655660	48456619	149565811	18	7987											
CHDH	55349	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	53857341	53857341	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaccactaccttcatggAtggtcatgtccatccagccg	9	9	10	13	1	2	1	2	0	0	1	4	3	4	2	5	3	2	0	5	3	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:53857341A>G	ENST00000315251.6	-	3	1132	c.695T>C	c.(694-696)aTc>aCc	p.I232T		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	232					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	ACCTTCATGGATGGTCATGTC	0.612																																					p.I232T		.											.	CHDH-91	0			c.T695C						.						46	48	47					3																	53857341		2203	4300	6503	SO:0001583	missense	55349	exon3			TCATGGATGGTCA	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.695T>C	3.37:g.53857341A>G	ENSP00000319851:p.Ile232Thr	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_018397	0	0	0	0	0	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	37	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.898970	0.52227	.	.	ENSG00000016391	ENST00000315251	T	0.39592	1.07	5.72	5.72	0.89469	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.161948	0.52532	D	0.000066	T	0.56046	0.1959	L	0.55103	1.725	0.53688	D	0.999973	D	0.63046	0.992	D	0.66084	0.941	T	0.57106	-0.7868	10	0.52906	T	0.07	-30.1407	11.1366	0.48378	0.8624:0.0:0.0:0.1376	.	232	Q8NE62	CHDH_HUMAN	T	232	ENSP00000319851:I232T	ENSP00000319851:I232T	I	-	2	0	CHDH	53832381	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.882000	0.92420	2.182000	0.69389	0.455000	0.32223	ATC	.		0.612	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		G	53857341	A	G	53857341	3	3	88	1	0	0	0	0	1	0	0	0	3339	333	12	3	1117	3	CHDH	3	53857341	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	5400722	53857341	144165089	19	7988											
VGLL3	389136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	87017993	87017993	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgggcatgagggtggtggtgCcgcatgtacacgtcatgcat	7	10	16	8	2	1	1	1	1	0	0	1	1	1	1	1	4	3	4	1	4	1	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:87017993C>T	ENST00000398399.2	-	3	1047	c.684G>A	c.(682-684)cgG>cgA	p.R228R	VGLL3_ENST00000383698.3_Silent_p.R228R	NM_016206.2	NP_057290.2			vestigial-like family member 3											NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		GGTGGTGGTGCCGCATGTACA	0.612																																					p.R228R		.											.	VGLL3-90	0			c.G684A						.						90	91	91					3																	87017993		2183	4286	6469	SO:0001819	synonymous_variant	389136	exon3			GTGGTGCCGCATG	AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538			24327	protein-coding gene	gene with protein product		609980	"vestigial like 3 (Drosophila)"			12376544	Standard	NM_016206		Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.684G>A	3.37:g.87017993C>T		Somatic	77	1		WXS	Illumina HiSeq	Phase_I	78	21	NM_016206	0	0	0	0	0		Silent	SNP	ENST00000398399.2	37	CCDS43110.1	.	.	.	.	.	.	.	.	.	.	C	8.637	0.895168	0.17613	.	.	ENSG00000206538	ENST00000494229	.	.	.	5.81	-2.88	0.05682	.	.	.	.	.	T	0.36608	0.0973	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33394	-0.9870	4	.	.	.	-10.5859	0.3879	0.00405	0.2096:0.2183:0.2673:0.3047	.	.	.	.	T	162	.	.	A	-	1	0	VGLL3	87100683	0.025000	0.19082	0.985000	0.45067	0.991000	0.79684	-0.558000	0.05978	-0.371000	0.08004	-0.409000	0.06214	GCA	.		0.612	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352805.1	NM_016206		T	87017993	C	T	87017993	2	4	88	1	0	0	0	0	0	0	0	1	17193	726	26	2		2	VGLL3	3	87017993	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	33160652	87017993	111004437	20	7989											
PARP14	54625	broad.mit.edu;ucsc.edu	37	chr3	122414352	122414352	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctccaagacttctggaagtGacaaacacaatcagggttga	14	9	9	9	0	3	3	1	2	2	1	4	4	3	4	1	2	1	1	1	2	4	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:122414352G>A	ENST00000474629.2	+	5	944	c.678G>A	c.(676-678)gtG>gtA	p.V226V		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	226					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TTCTGGAAGTGACAAACACAA	0.373																																					p.V226V													.	PARP14-525	0			c.G678A						.						42	41	42					3																	122414352		1840	4083	5923	SO:0001819	synonymous_variant	54625	exon5			GGAAGTGACAAAC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.678G>A	3.37:g.122414352G>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	25	5	NM_017554	0	0	10	18	8	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	1.080	-0.667224	0.03428	.	.	ENSG00000173193	ENST00000494811	.	.	.	5.65	-2.94	0.05581	.	.	.	.	.	T	0.42177	0.1191	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	T	0.29579	-1.0007	4	.	.	.	.	4.0851	0.09943	0.5094:0.1036:0.2814:0.1056	.	.	.	.	N	154	.	.	D	+	1	0	PARP14	123897042	0.001000	0.12720	0.001000	0.08648	0.388000	0.30384	-0.265000	0.08644	-0.886000	0.03966	-0.137000	0.14449	GAC	.		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		A	122414352	G	A	122414352	2	1	88	1	0	0	0	0	0	0	0	1	11484	1277	45	2		2	PARP14	3	122414352	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	35396359	122414352	75608078	21	7990											
EPHB1	2047	broad.mit.edu;bcgsc.ca	37	chr3	134873005	134873005	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctccacagccccctccaccGttcccatcatgcaccaagtc	8	8	4	21	1	2	0	1	0	1	0	6	0	4	0	7	0	2	2	7	0	1	1	rs183234182		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:134873005G>A	ENST00000398015.3	+	6	1679	c.1309G>A	c.(1309-1311)Gtt>Att	p.V437I	EPHB1_ENST00000493838.1_5'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	437	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CCCCTCCACCGTTCCCATCAT	0.532													G|||	1	0.000199681	8e-04	0	5008	,	,		20316	0		0	False		,,,				2504	0				p.V437I													.	EPHB1-1492	0			c.G1309A						.	G	ILE/VAL	0,4304		0,0,2152	199	212	207		1309	5	1	3		207	1,8563		0,1,4281	no	missense	EPHB1	NM_004441.4	29	0,1,6433	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	437/985	134873005	1,12867	2152	4282	6434	SO:0001583	missense	2047	exon6			TCCACCGTTCCCA	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3392	protein-coding gene	gene with protein product		600600	"EphB1"	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1309G>A	3.37:g.134873005G>A	ENSP00000381097:p.Val437Ile	Somatic	370	1		WXS	Illumina HiSeq	Phase_I	359	18	NM_004441	0	0	0	0	0	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	19.63	3.862742	0.71949	0.0	1.17E-4	ENSG00000154928	ENST00000398015	T	0.55588	0.51	5.0	5.0	0.66597	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.066621	0.64402	D	0.000014	T	0.50922	0.1644	M	0.64997	1.995	0.80722	D	1	P	0.42556	0.783	B	0.36885	0.235	T	0.56408	-0.7984	10	0.41790	T	0.15	.	18.0819	0.89443	0.0:0.0:1.0:0.0	.	437	P54762	EPHB1_HUMAN	I	437	ENSP00000381097:V437I	ENSP00000381097:V437I	V	+	1	0	EPHB1	136355695	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.657000	0.98554	2.610000	0.88304	0.655000	0.94253	GTT	G|0.999;A|0.000		0.532	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134873005	G	A	134873005	3	1	88	1	0	0	0	0	1	0	0	0	5187	1145	40	1	1331	1	EPHB1	3	134873005	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	12458653	134873005	63149425	22	7991											
TLR1	7096	broad.mit.edu;bcgsc.ca	37	chr4	38798114	38798114	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttctttgcttgctctgtcAgcttaatattaatggctgcc	7	18	7	9	0	3	0	1	0	2	0	3	0	3	0	1	1	4	4	1	1	3	6	rs151285692		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:38798114A>T	ENST00000502213.2	-	3	2568	c.2339T>A	c.(2338-2340)cTg>cAg	p.L780Q	TLR1_ENST00000308979.2_Missense_Mutation_p.L780Q|TLR1_ENST00000510552.1_5'Flank			Q15399	TLR1_HUMAN	toll-like receptor 1	780					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TTGCTCTGTCAGCTTAATATT	0.388																																					p.L780Q	GBM(5;216 373 40795 46382)												.	TLR1-524	0			c.T2339A						.						73	70	71					4																	38798114		2203	4300	6503	SO:0001583	missense	7096	exon4			TCTGTCAGCTTAA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.2339T>A	4.37:g.38798114A>T	ENSP00000421259:p.Leu780Gln	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	67	7	NM_003263	0	0	23	24	1	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167950	0.78339	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.02216	4.39;4.39	5.1	3.83	0.44106	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.346719	0.20408	N	0.092903	T	0.13286	0.0322	M	0.87547	2.89	0.18873	N	0.999989	D	0.89917	1.0	D	0.75020	0.985	T	0.01401	-1.1364	10	0.87932	D	0	.	11.844	0.52374	0.8539:0.1461:0.0:0.0	.	780	Q15399	TLR1_HUMAN	Q	780	ENSP00000354932:L780Q;ENSP00000421259:L780Q	ENSP00000354932:L780Q	L	-	2	0	TLR1	38474509	0.147000	0.22687	0.273000	0.24645	0.669000	0.39330	4.139000	0.58024	2.057000	0.61298	0.460000	0.39030	CTG	A|1.000;G|0.000		0.388	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			T	38798114	A	T	38798114	3	4	88	1	0	0	0	0	1	0	0	0	15981	188	7	5	25	5	TLR1	4	38798114	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		38798114	152356162	23	7992											
SLC30A9	10463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	42072612	42072612	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcatggtctcagcattccTcatctacactaacacagaag	13	9	7	12	0	3	1	2	0	2	1	5	1	4	1	1	2	3	2	1	2	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:42072612T>A	ENST00000264451.7	+	15	1502	c.1322T>A	c.(1321-1323)cTc>cAc	p.L441H		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	441					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCAGCATTCCTCATCTACACT	0.458																																					p.L441H		.											.	SLC30A9-91	0			c.T1322A						.						211	177	188					4																	42072612		2203	4300	6503	SO:0001583	missense	10463	exon15			CATTCCTCATCTA	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.1322T>A	4.37:g.42072612T>A	ENSP00000264451:p.Leu441His	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	133	43	NM_006345	0	0	34	66	32	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512256	0.85389	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.71817	-0.6	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.87188	0.6115	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90228	0.4277	10	0.87932	D	0	-6.7973	15.4439	0.75213	0.0:0.0:0.0:1.0	.	441	Q6PML9	ZNT9_HUMAN	H	441;269	ENSP00000264451:L441H	ENSP00000264451:L441H	L	+	2	0	SLC30A9	41767369	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.951000	0.87819	2.099000	0.63709	0.533000	0.62120	CTC	.		0.458	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			A	42072612	T	A	42072612	3	1	88	1	0	0	0	0	1	0	0	0	14594	1551	54	5	1380	5	SLC30A9	4	42072612	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	3274498	42072612	149081664	24	7993											
KCTD8	386617	hgsc.bcm.edu	37	chr4	44449962	44449962	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccgccgccgccaccaccGtgcgctcccgggcccgaggg	3	2	14	22	8	0	0	0	0	0	0	1	1	1	0	9	2	1	1	9	2	0	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:44449962G>C	ENST00000360029.3	-	1	862	c.579C>G	c.(577-579)caC>caG	p.H193Q	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	193					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						cgccaccaccgtgcgctcccg	0.761										HNSCC(17;0.042)																											p.H193Q		.											.	KCTD8-92	0			c.C579G						.						2	2	2					4																	44449962		1063	2306	3369	SO:0001583	missense	386617	exon1			ACCACCGTGCGCT	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 8"				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.579C>G	4.37:g.44449962G>C	ENSP00000353129:p.His193Gln	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	3	2	NM_198353	0	0	0	0	0	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	37	CCDS3467.1	.	.	.	.	.	.	.	.	.	.	G	2.286	-0.363634	0.05103	.	.	ENSG00000183783	ENST00000360029	T	0.36520	1.25	4.23	2.48	0.30137	.	1.393860	0.05249	U	0.513652	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.27625	0.183	B	0.09377	0.004	T	0.21109	-1.0255	10	0.15066	T	0.55	.	6.621	0.22802	0.3052:0.0:0.6948:0.0	.	193	Q6ZWB6	KCTD8_HUMAN	Q	193	ENSP00000353129:H193Q	ENSP00000353129:H193Q	H	-	3	2	KCTD8	44144719	0.000000	0.05858	0.021000	0.16686	0.174000	0.22865	-0.252000	0.08806	0.416000	0.25844	-0.203000	0.12734	CAC	.		0.761	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			C	44449962	G	C	44449962	3	2	88	1	0	0	0	0	1	0	0	0	8136	1136	40	4	850	4	KCTD8	4	44449962	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	2377350	44449962	146704314	25	7994											
TXK	7294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48076056	48076056	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaagaactgacatactcaTcatccaaaacgtacctaagt	18	8	4	11	1	2	2	2	1	0	1	3	2	3	2	2	0	4	1	2	0	8	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:48076056T>A	ENST00000264316.4	-	13	1338	c.1253A>T	c.(1252-1254)gAt>gTt	p.D418V	TXK_ENST00000507351.1_Missense_Mutation_p.D73V	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						GACATACTCATCATCCAAAAC	0.368																																					p.D418V		.											.	TXK-521	0			c.A1253T						.						100	97	98					4																	48076056		2203	4300	6503	SO:0001583	missense	7294	exon13			TACTCATCATCCA	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"SH2 domain containing"	12434	protein-coding gene	gene with protein product		600058	"PTK4 protein tyrosine kinase 4"	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.1253A>T	4.37:g.48076056T>A	ENSP00000264316:p.Asp418Val	Somatic	66	1		WXS	Illumina HiSeq	Phase_I	104	18	NM_003328	0	0	0	0	0	Q14220	Missense_Mutation	SNP	ENST00000264316.4	37	CCDS3480.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.382395	0.61845	.	.	ENSG00000074966	ENST00000264316;ENST00000507351	D;D	0.84146	-1.81;-1.81	5.64	5.64	0.86602	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.063498	0.64402	D	0.000008	D	0.91314	0.7261	M	0.67569	2.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.92105	0.5691	10	0.87932	D	0	.	15.1937	0.73067	0.0:0.0:0.0:1.0	.	105;418	B4DTB5;P42681	.;TXK_HUMAN	V	418;73	ENSP00000264316:D418V;ENSP00000423481:D73V	ENSP00000264316:D418V	D	-	2	0	TXK	47770813	1.000000	0.71417	1.000000	0.80357	0.262000	0.26303	7.868000	0.87116	2.367000	0.80283	0.528000	0.53228	GAT	.		0.368	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		A	48076056	T	A	48076056	3	1	88	1	0	0	0	0	1	0	0	0	16819	1435	50	5	342	5	TXK	4	48076056	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	3626094	48076056	143078220	26	7995											
WDFY3	23001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	85781624	85781624	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttccttctgagtcatgtGccggggaggatggcacaact	7	12	13	9	1	2	1	1	1	1	0	3	3	3	3	2	4	2	2	2	4	1	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:85781624G>A	ENST00000295888.4	-	4	528	c.121C>T	c.(121-123)Cac>Tac	p.H41Y	WDFY3_ENST00000322366.6_Missense_Mutation_p.H41Y	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	41					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TGAGTCATGTGCCGGGGAGGA	0.577																																					p.H41Y		.											.	WDFY3-93	0			c.C121T						.						140	129	133					4																	85781624		2203	4300	6503	SO:0001583	missense	23001	exon4			TCATGTGCCGGGG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.121C>T	4.37:g.85781624G>A	ENSP00000295888:p.His41Tyr	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	156	30	NM_014991	0	0	4	4	0	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238404	0.79800	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000509172	T;T	0.63744	-0.06;-0.06	5.72	5.72	0.89469	.	0.045076	0.85682	D	0.000000	T	0.43255	0.1239	N	0.08118	0	0.80722	D	1	D;D	0.52996	0.957;0.957	B;B	0.43575	0.402;0.424	T	0.48364	-0.9042	10	0.02654	T	1	.	19.8968	0.96969	0.0:0.0:1.0:0.0	.	41;41	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	Y	41	ENSP00000318466:H41Y;ENSP00000295888:H41Y	ENSP00000295888:H41Y	H	-	1	0	WDFY3	86000648	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.580000	0.98207	2.691000	0.91804	0.655000	0.94253	CAC	.		0.577	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85781624	G	A	85781624	3	1	88	1	0	0	0	0	1	0	0	0	17303	1319	46	2	10762	2	WDFY3	4	85781624	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	37705568	85781624	105372652	27	7996											
CENPE	1062	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	104117130	104117130	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgggtataactcccaaatGatcttctgaacccatcatgg	11	11	7	12	0	3	2	1	2	2	0	4	2	4	2	3	2	2	1	3	2	4	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:104117130G>A	ENST00000265148.3	-	4	393	c.304C>T	c.(304-306)Cat>Tat	p.H102Y	CENPE_ENST00000380026.3_Missense_Mutation_p.H102Y	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	102	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.H102Y(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ACTCCCAAATGATCTTCTGAA	0.348																																					p.H102Y													.	CENPE-277	1	Substitution - Missense(1)	skin(1)	c.C304T						.						111	105	107					4																	104117130		2203	4300	6503	SO:0001583	missense	1062	exon4			CCAAATGATCTTC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.304C>T	4.37:g.104117130G>A	ENSP00000265148:p.His102Tyr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	44	8	NM_001813	0	0	0	0	0	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	G	0.240	-1.014671	0.02095	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705;ENST00000514974	T;T;T;T	0.72725	-0.68;-0.68;-0.68;2.3	5.17	2.4	0.29515	Kinesin, motor domain (4);	.	.	.	.	T	0.48572	0.1507	N	0.25201	0.72	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32981	-0.9886	9	0.02654	T	1	.	7.6421	0.28300	0.7877:0.0:0.0778:0.1344	.	102;102	Q02224-3;Q02224	.;CENPE_HUMAN	Y	102	ENSP00000265148:H102Y;ENSP00000369365:H102Y;ENSP00000423981:H102Y;ENSP00000426023:H102Y	ENSP00000265148:H102Y	H	-	1	0	CENPE	104336579	0.071000	0.21146	0.997000	0.53966	0.978000	0.69477	1.290000	0.33319	0.817000	0.34445	-0.373000	0.07131	CAT	.		0.348	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104117130	G	A	104117130	3	1	88	1	0	0	0	0	1	0	0	0	3236	1290	45	2	7985	2	CENPE	4	104117130	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	18335506	104117130	87037146	28	7997											
NR3C2	4306	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	149357285	149357285	+	Frame_Shift_Del	DEL	T	T	-																															tgtgcgacctggagcctcgaTtttcaacattaggggagcat																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:149357285delT	ENST00000358102.3	-	2	1090	c.728delA	c.(727-729)aatfs	p.N243fs	NR3C2_ENST00000512865.1_Frame_Shift_Del_p.N243fs|NR3C2_ENST00000511528.1_Frame_Shift_Del_p.N243fs|NR3C2_ENST00000355292.3_Frame_Shift_Del_p.N243fs|NR3C2_ENST00000344721.4_Frame_Shift_Del_p.N243fs	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	243	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	GGAGCCTCGATTTTCAACATT	0.527																																					p.N243fs	Melanoma(27;428 957 40335 51025 51111)	.											.	NR3C2-154	0			c.728delA						.						74	76	75					4																	149357285		2203	4300	6503	SO:0001589	frameshift_variant	4306	exon2			.	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.728delA	4.37:g.149357285delT	ENSP00000350815:p.Asn243fs	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	149	46	NM_001166104	0	0	0	0	0	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Frame_Shift_Del	DEL	ENST00000358102.3	37	CCDS3772.1																																																																																			.		0.527	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			-	149357285	T	-	149357285	7	5	88	1	0	1	0	1	0	0	0	0	10657	1493	52	0	2258	0	NR3C2	4	149357285	Frame_Shift_Del	DEL	T	TCGA-BQ-7059-01A-11D-1961-08	45240155	149357285	41796991	29	7998											
ADAMTS19	171019	broad.mit.edu	37	chr5	128983499	128983499	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagcaggacctcagcaccTgaacatctggccggagagtg	11	5	12	13	1	2	2	1	1	1	1	2	4	2	3	4	3	3	2	4	3	1	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:128983499T>C	ENST00000274487.4	+	12	2041	c.1896T>C	c.(1894-1896)ccT>ccC	p.P632P	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	632	Disintegrin.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CCTCAGCACCTGAACATCTGG	0.502																																					p.P632P													.	ADAMTS19-295	0			c.T1896C						.						149	147	147					5																	128983499		2203	4300	6503	SO:0001819	synonymous_variant	171019	exon12			AGCACCTGAACAT	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"ADAM metallopeptidases with thrombospondin type 1 motif"	17111	protein-coding gene	gene with protein product		607513	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1896T>C	5.37:g.128983499T>C		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	213	8	NM_133638	0	0	0	0	0		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			.		0.502	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128983499	T	C	128983499	2	2	88	1	0	0	0	0	0	0	0	1	264	1567	55	3		3	ADAMTS19	5	128983499	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		128983499	51931761	30	7999											
RAD50	10111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131976367	131976367	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggggcttttttccaggtaTtagcctcactcatcattcgc	7	15	8	11	1	3	0	3	0	0	0	5	0	4	0	2	3	1	2	2	3	3	7			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:131976367T>C	ENST00000265335.6	+	24	4009	c.3622T>C	c.(3622-3624)Tta>Cta	p.L1208L	AC004041.2_ENST00000458509.1_RNA|AC004041.2_ENST00000417516.1_RNA|AC004041.2_ENST00000457489.1_RNA|AC004041.2_ENST00000435042.1_RNA|RAD50_ENST00000378823.3_Silent_p.L1069L			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1208	Ala/Asp-rich (DA-box).				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTTCCAGGTATTAGCCTCACT	0.498								Homologous recombination																													p.L1208L		.											.	RAD50-229	0			c.T3622C						.						168	156	160					5																	131976367		2203	4300	6503	SO:0001819	synonymous_variant	10111	exon24			CAGGTATTAGCCT	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"RAD50 (S. cerevisiae) homolog"			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.3622T>C	5.37:g.131976367T>C		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	177	36	NM_005732	0	0	0	0	0	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Silent	SNP	ENST00000265335.6	37	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963735	0.34659	.	.	ENSG00000113522	ENST00000455677	.	.	.	5.94	1.0	0.19881	.	.	.	.	.	T	0.55226	0.1907	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.46275	-0.9203	4	.	.	.	-7.5964	8.3809	0.32470	0.0:0.5216:0.0:0.4784	.	.	.	.	T	86	.	.	I	+	2	0	RAD50	132004266	0.068000	0.21057	0.032000	0.17829	0.920000	0.55202	0.417000	0.21214	0.177000	0.19895	0.528000	0.53228	ATT	.		0.498	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		C	131976367	T	C	131976367	2	2	88	1	0	0	0	0	0	0	0	1	13016	1490	52	3		3	RAD50	5	131976367	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	2992868	131976367	48938893	31	8000											
PCDHGA11	56105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140802438	140802438	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccctcagcagcaacgtgtcGctgagcctgttcgtgctgga	6	9	12	14	3	1	1	1	1	0	0	3	2	1	2	3	1	5	5	3	1	1	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:140802438G>C	ENST00000398587.2	+	1	1677	c.1644G>C	c.(1642-1644)tcG>tcC	p.S548S	PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Silent_p.S548S|PCDHGA1_ENST00000517417.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	548	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAACGTGTCGCTGAGCCTGT	0.607																																					p.S548S		.											.	.	0			c.G1644C						.						151	172	165					5																	140802438		2203	4300	6503	SO:0001819	synonymous_variant	56105	exon1			CGTGTCGCTGAGC	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"Cadherins / Protocadherins : Clustered"	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1644G>C	5.37:g.140802438G>C		Somatic	349	1		WXS	Illumina HiSeq	Phase_I	301	52	NM_032091	0	0	0	1	1	B7ZVY8|Q9Y5D8|Q9Y5D9	Silent	SNP	ENST00000398587.2	37	CCDS47294.1																																																																																			.		0.607	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		C	140802438	G	C	140802438	2	2	88	1	0	0	0	0	0	0	0	1	11578	1074	38	4		4	PCDHGA11	5	140802438	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	8826071	140802438	40112822	32	8001											
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	179193559	179193560	+	Frame_Shift_Ins	INS	-	-	C																															tggactacggcaatacaaaaINScccctttctcattacaaagc																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:179193559_179193560insC	ENST00000292599.3	+	2	1811_1812	c.1548_1549insC	c.(1549-1551)cccfs	p.P517fs	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAATACAAAACCCCTTTCTCA	0.559																																					p.K516fs		.											.	MAML1-848	0			c.1548_1549insC						.																																			SO:0001589	frameshift_variant	9794	exon2			.	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1552dupC	5.37:g.179193563_179193563dupC	ENSP00000292599:p.Pro517fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	80	19	NM_014757	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000292599.3	37	CCDS34315.1																																																																																			.		0.559	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		C	179193560	-	C	179193559	7	5	88	1	0	1	1	0	0	0	0	0	9230	40	2	0	1554	0	MAML1	5	179193559	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	38391121	179193559	1721701	33	8002											
TBC1D9B	23061	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	179318454	179318455	+	Frame_Shift_Ins	INS	-	-	A																															tgtagttgttggagatgaacINSatctggccagggatgtgcag																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:179318454_179318455insA	ENST00000356834.3	-	6	1005_1006	c.968_969insT	c.(967-969)atgfs	p.M323fs	TBC1D9B_ENST00000355235.3_Frame_Shift_Ins_p.M323fs	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	323	GRAM 2.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGAGATGAACATCTGGCCAGG	0.599																																					p.M323fs		.											.	TBC1D9B-154	0			c.969_970insT						.																																			SO:0001589	frameshift_variant	23061	exon6			.	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.969dupT	5.37:g.179318455_179318455dupA	ENSP00000349291:p.Met323fs	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	176	41	NM_198868	0	0	0	0	0	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Frame_Shift_Ins	INS	ENST00000356834.3	37	CCDS43408.1																																																																																			.		0.599	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		A	179318455	-	A	179318454	7	5	88	1	0	1	1	0	0	0	0	0	15660	478	17	0	2851	0	TBC1D9B	5	179318454	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	124895	179318454	1596806	34	8003											
TRIM38	10475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	25967011	25967011	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgaagccctcaaagagacGgatcaagaaatgtcatgtga	16	8	10	7	1	3	4	3	2	0	2	3	6	3	5	1	1	1	0	1	1	4	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:25967011G>C	ENST00000357085.3	+	3	737	c.261G>C	c.(259-261)acG>acC	p.T87T	TRIM38_ENST00000349458.3_Silent_p.T87T	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	87					negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.T87T(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						TCAAAGAGACGGATCAAGAAA	0.562																																					p.T87T		.											.	TRIM38-226	1	Substitution - coding silent(1)	lung(1)	c.G261C						.						61	58	59					6																	25967011		2203	4300	6503	SO:0001819	synonymous_variant	10475	exon3			AGAGACGGATCAA	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10059	protein-coding gene	gene with protein product			"ring finger protein 15", "tripartite motif-containing 38"	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.261G>C	6.37:g.25967011G>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	54	17	NM_006355	0	0	50	78	28	B2R862	Silent	SNP	ENST00000357085.3	37	CCDS4568.1																																																																																			.		0.562	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2			C	25967011	G	C	25967011	2	2	88	1	0	0	0	0	0	0	0	1	16545	1103	39	4		4	TRIM38	6	25967011	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08		25967011	145148056	35	8004											
ITPR3	3710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33644599	33644599	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	actacaaggtgatcaagtcgGagctggaccggctgcggacc	10	6	14	11	3	1	1	1	1	0	0	2	4	1	4	2	5	3	2	2	5	3	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:33644599G>A	ENST00000374316.5	+	27	4397	c.3337G>A	c.(3337-3339)Gag>Aag	p.E1113K	ITPR3_ENST00000605930.1_Missense_Mutation_p.E1113K			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1113					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GATCAAGTCGGAGCTGGACCG	0.622																																					p.E1113K		.											.	ITPR3-1085	0			c.G3337A						.						93	80	85					6																	33644599		2203	4300	6503	SO:0001583	missense	3710	exon26			AAGTCGGAGCTGG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"Ion channels / Inositol triphosphate receptors"	6182	protein-coding gene	gene with protein product		147267	"inositol 1,4,5-triphosphate receptor, type 3"			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.3337G>A	6.37:g.33644599G>A	ENSP00000363435:p.Glu1113Lys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	67	19	NM_002224	0	0	35	61	26	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.587672	0.86851	.	.	ENSG00000096433	ENST00000374316	D	0.91237	-2.81	5.22	5.22	0.72569	.	0.111019	0.64402	D	0.000010	D	0.85822	0.5786	L	0.44542	1.39	0.58432	D	0.999993	P	0.45594	0.862	B	0.41917	0.37	D	0.88575	0.3132	10	0.87932	D	0	-36.8399	18.8137	0.92070	0.0:0.0:1.0:0.0	.	1113	Q14573	ITPR3_HUMAN	K	1113	ENSP00000363435:E1113K	ENSP00000363435:E1113K	E	+	1	0	ITPR3	33752577	1.000000	0.71417	0.943000	0.38184	0.927000	0.56198	8.010000	0.88615	2.435000	0.82474	0.655000	0.94253	GAG	.		0.622	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33644599	G	A	33644599	3	1	88	1	0	0	0	0	1	0	0	0	7943	1175	41	2	3439	2	ITPR3	6	33644599	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	7677588	33644599	137470468	36	8005											
CPNE5	57699	broad.mit.edu;bcgsc.ca	37	chr6	36712081	36712081	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacgccgacgataatgaTggacatggggagcttggcag	10	6	15	10	3	0	1	0	1	0	0	0	5	0	3	2	4	1	2	2	4	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:36712081T>A	ENST00000244751.2	-	19	2077	c.1453A>T	c.(1453-1455)Atc>Ttc	p.I485F	CPNE5_ENST00000393189.2_Missense_Mutation_p.I193F|CPNE5_ENST00000459703.1_5'UTR	NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	485	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						ACGATAATGATGGACATGGGG	0.607																																					p.I485F													.	CPNE5-91	0			c.A1453T						.						66	47	53					6																	36712081		2197	4296	6493	SO:0001583	missense	57699	exon19			TAATGATGGACAT	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.1453A>T	6.37:g.36712081T>A	ENSP00000244751:p.Ile485Phe	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	10	6	NM_020939	0	0	1	1	0	Q7Z6C8	Missense_Mutation	SNP	ENST00000244751.2	37	CCDS4825.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847684	0.91277	.	.	ENSG00000124772	ENST00000244751;ENST00000393189	T;T	0.35421	1.31;1.31	5.19	5.19	0.71726	von Willebrand factor, type A (2);Copine (1);	0.104258	0.64402	D	0.000006	T	0.68613	0.3020	H	0.98612	4.28	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	T	0.81645	-0.0839	10	0.87932	D	0	.	13.0484	0.58939	0.0:0.0:0.0:1.0	.	485	Q9HCH3	CPNE5_HUMAN	F	485;193	ENSP00000244751:I485F;ENSP00000376885:I193F	ENSP00000244751:I485F	I	-	1	0	CPNE5	36820059	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.693000	0.84214	1.983000	0.57843	0.369000	0.22263	ATC	.		0.607	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		A	36712081	T	A	36712081	3	1	88	1	0	0	0	0	1	0	0	0	3821	1464	51	5	340	5	CPNE5	6	36712081	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	3067482	36712081	134402986	37	8006											
DOPEY1	23033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	83839062	83839062	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaatgggacagaaattcaCaaggagatgtaaaagagaaa	22	5	10	4	0	1	3	1	0	0	3	1	6	1	4	0	2	0	1	0	2	7	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:83839062C>A	ENST00000349129.2	+	16	2436	c.2176C>A	c.(2176-2178)Caa>Aaa	p.Q726K	DOPEY1_ENST00000237163.5_Missense_Mutation_p.Q707K|DOPEY1_ENST00000369739.3_Missense_Mutation_p.Q717K	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	726					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CAGAAATTCACAAGGAGATGT	0.398																																					p.Q726K		.											.	DOPEY1-155	0			c.C2176A						.						78	77	78					6																	83839062		2203	4300	6503	SO:0001583	missense	23033	exon16			AATTCACAAGGAG	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.2176C>A	6.37:g.83839062C>A	ENSP00000195654:p.Gln726Lys	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	85	16	NM_015018	0	0	4	5	1	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.151734	0.38021	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.21734	1.99;1.99	5.68	5.68	0.88126	.	0.594531	0.18093	N	0.151930	T	0.15392	0.0371	L	0.57536	1.79	0.80722	D	1	B;B;B	0.15473	0.004;0.013;0.004	B;B;B	0.13407	0.006;0.009;0.006	T	0.02610	-1.1134	10	0.32370	T	0.25	.	19.7974	0.96491	0.0:1.0:0.0:0.0	.	617;717;726	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	K	726;707;707	ENSP00000195654:Q726K;ENSP00000237163:Q707K	ENSP00000237163:Q707K	Q	+	1	0	DOPEY1	83895781	0.879000	0.30193	0.997000	0.53966	0.964000	0.63967	3.092000	0.50207	2.673000	0.90976	0.650000	0.86243	CAA	.		0.398	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		A	83839062	C	A	83839062	3	1	88	1	0	0	0	0	1	0	0	0	4718	479	17	4	2230	4	DOPEY1	6	83839062	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	47126981	83839062	87276005	38	8007											
FAM120B	84498	hgsc.bcm.edu;bcgsc.ca	37	chr6	170700175	170700175	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgaaggagaacagacgcatCactggccgagcccactgggg	12	4	14	11	2	1	3	1	1	0	2	1	5	1	3	2	4	2	1	2	4	2	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:170700175C>G	ENST00000476287.1	+	8	2673	c.2565C>G	c.(2563-2565)atC>atG	p.I855M	FAM120B_ENST00000540480.1_Missense_Mutation_p.I867M|FAM120B_ENST00000252510.9_Missense_Mutation_p.I187M|FAM120B_ENST00000537664.1_Missense_Mutation_p.I878M	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	855					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		ACAGACGCATCACTGGCCGAG	0.562																																					p.I855M		.											.	FAM120B-91	0			c.C2565G						.						72	62	65					6																	170700175		2203	4300	6503	SO:0001583	missense	84498	exon8			ACGCATCACTGGC	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2565C>G	6.37:g.170700175C>G	ENSP00000417970:p.Ile855Met	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	58	4	NM_032448	0	0	37	37	0	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.500782	0.26861	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287;ENST00000252510	T;T;T	0.09723	2.96;2.95;2.97	5.5	-3.03	0.05429	.	0.167917	0.40469	N	0.001099	T	0.06371	0.0164	L	0.27053	0.805	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.967;0.974	T	0.22382	-1.0218	10	0.56958	D	0.05	-19.2842	7.8011	0.29174	0.1064:0.3727:0.0:0.5209	.	855;855	Q96EK7;F2Z2E1	F120B_HUMAN;.	M	867;878;855;187	ENSP00000444125:I867M;ENSP00000440125:I878M;ENSP00000417970:I855M	ENSP00000252510:I187M	I	+	3	3	FAM120B	170542100	0.002000	0.14202	0.000000	0.03702	0.051000	0.14879	-0.226000	0.09139	-0.631000	0.05560	0.655000	0.94253	ATC	.		0.562	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		G	170700175	C	G	170700175	3	3	88	1	0	0	0	0	1	0	0	0	5433	816	29	4	2591	4	FAM120B	6	170700175	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	86861113	170700175	414892	39	8008											
KLHL7	55975	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	23163475	23163476	+	Frame_Shift_Ins	INS	-	-	T																															gttcttgctgcagccagtcaINStttttttaacttaatgttca																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr7:23163475_23163476insT	ENST00000339077.5	+	2	443_444	c.200_201insT	c.(199-204)cattttfs	p.HF67fs	KLHL7_ENST00000545771.1_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000322275.5_Frame_Shift_Ins_p.HF67fs|KLHL7_ENST00000545443.1_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000539124.1_Intron|KLHL7_ENST00000410047.1_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000322231.7_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000479288.1_Intron|KLHL7_ENST00000409689.1_Frame_Shift_Ins_p.HF19fs	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	67	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCAGCCAGTCATTTTTTTAACT	0.332																																					p.H67fs		.											.	KLHL7-90	0			c.200_201insT						.																																			SO:0001589	frameshift_variant	55975	exon2			.		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"Kelch-like", "BTB/POZ domain containing"	15646	protein-coding gene	gene with protein product	"retinitis pigmentosa 42"	611119	"kelch-like 7 (Drosophila)"			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.207dupT	7.37:g.23163482_23163482dupT	ENSP00000343273:p.His67fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	94	30	NM_001172428	0	0	0	0	0	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Frame_Shift_Ins	INS	ENST00000339077.5	37	CCDS34609.1																																																																																			.		0.332	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		T	23163476	-	T	23163475	7	5	88	1	0	1	1	0	0	0	0	0	8415	217	8	0	206	0	KLHL7	7	23163475	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08		23163475	135975188	40	8009											
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44685022	44685022	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgaggctccctggctgctGtggcccatgcacagtccctg	4	8	13	16	1	0	0	0	0	0	0	2	1	2	0	4	3	2	4	4	3	0	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr7:44685022G>T	ENST00000222673.5	+	3	361	c.319G>T	c.(319-321)Gtg>Ttg	p.V107L	OGDH_ENST00000449767.1_Missense_Mutation_p.V107L|OGDH_ENST00000447398.1_Missense_Mutation_p.V107L|OGDH_ENST00000543843.1_Missense_Mutation_p.V47L|OGDH_ENST00000444676.1_Missense_Mutation_p.V107L|OGDH_ENST00000443864.2_Missense_Mutation_p.V107L|OGDH_ENST00000439616.2_Intron	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	107					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CCTGGCTGCTGTGGCCCATGC	0.597																																					p.V107L		.											.	OGDH-228	0			c.G319T						.						85	83	83					7																	44685022		2203	4300	6503	SO:0001583	missense	4967	exon3			GCTGCTGTGGCCC	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.319G>T	7.37:g.44685022G>T	ENSP00000222673:p.Val107Leu	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	169	35	NM_001165036	0	0	95	128	33	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.775197	0.31411	.	.	ENSG00000105953	ENST00000443864;ENST00000449767;ENST00000447398;ENST00000419661;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.81	-4.96	0.03038	.	1.033080	0.07585	N	0.921017	T	0.10680	0.0261	N	0.02181	-0.65	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.27054	-1.0085	10	0.05620	T	0.96	-2.8184	1.8649	0.03196	0.4868:0.1815:0.1602:0.1715	.	107;107;107;107	E9PBM1;E9PDF2;Q02218;Q96DD3	.;.;ODO1_HUMAN;.	L	107;107;107;107;107;107;47	ENSP00000388084:V107L;ENSP00000392878:V107L;ENSP00000388183:V107L;ENSP00000411830:V107L;ENSP00000414662:V107L;ENSP00000222673:V107L;ENSP00000443821:V47L	ENSP00000222673:V107L	V	+	1	0	OGDH	44651547	0.003000	0.15002	0.000000	0.03702	0.974000	0.67602	0.473000	0.22132	-0.618000	0.05656	0.655000	0.94253	GTG	.		0.597	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			T	44685022	G	T	44685022	3	4	88	1	0	0	0	0	1	0	0	0	10865	1377	48	4	325	4	OGDH	7	44685022	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	21521547	44685022	114453641	41	8010											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116423407	116423407	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgattttggtcttgccagaGacatgtatgataaagaatac	13	13	9	6	0	1	4	0	2	1	2	1	5	1	4	1	1	2	1	1	1	5	6	rs121913671		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr7:116423407G>C	ENST00000318493.6	+	19	3923	c.3736G>C	c.(3736-3738)Gac>Cac	p.D1246H	MET_ENST00000539704.1_Missense_Mutation_p.D98H|MET_ENST00000397752.3_Missense_Mutation_p.D1228H			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D1246H(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TCTTGCCAGAGACATGTATGA	0.378			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.D1246H		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.G3736C	GRCh37	CM970946	MET	M	rs121913671	.						106	99	102					7																	116423407		1841	4093	5934	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GCCAGAGACATGT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3736G>C	7.37:g.116423407G>C	ENSP00000317272:p.Asp1246His	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	101	30	NM_001127500	0	0	132	323	191	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.285616	0.80803	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	D;D;D	0.83837	-1.77;-1.77;-1.77	5.46	5.46	0.80206	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91327	0.7265	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91745	0.5407	10	0.87932	D	0	.	19.6667	0.95895	0.0:0.0:1.0:0.0	.	1246;1228	P08581-2;P08581	.;MET_HUMAN	H	1228;1246;98	ENSP00000380860:D1228H;ENSP00000317272:D1246H;ENSP00000445020:D98H	ENSP00000317272:D1246H	D	+	1	0	MET	116210643	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.813000	0.99286	2.721000	0.93114	0.563000	0.77884	GAC	.		0.378	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423407	G	C	116423407	3	2	88	1	0	0	0	0	1	0	0	0	9510	942	33	4	3806	4	MET	7	116423407	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	71738385	116423407	42715256	42	8011											
MCPH1	79648	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	6335132	6335133	+	Frame_Shift_Ins	INS	-	-	A																															agccaacaagaacattagtcINSatgacaagcatgccatctga																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:6335132_6335133insA	ENST00000344683.5	+	10	2029_2030	c.1953_1954insA	c.(1954-1956)atgfs	p.M652fs		NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	652	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GAACATTAGTCATGACAAGCAT	0.317																																					p.V651fs	Colon(95;1448 1467 8277 34473 35819)	.											.	MCPH1-229	0			c.1953_1954insA						.																																			SO:0001589	frameshift_variant	79648	exon10			.	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1954dupA	8.37:g.6335133_6335133dupA	ENSP00000342924:p.Met652fs	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	281	77	NM_024596	0	0	0	0	0	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Frame_Shift_Ins	INS	ENST00000344683.5	37	CCDS43689.1																																																																																			.		0.317	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		A	6335133	-	A	6335132	7	5	88	1	0	1	1	0	0	0	0	0	9423	813	29	0	1999	0	MCPH1	8	6335132	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08		6335132	140028890	43	8012											
HR	55806	broad.mit.edu	37	chr8	21984840	21984840	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcttggtgtggtggctggggGgacaggccctggggccagag	4	7	22	8	0	0	1	0	0	0	1	0	2	0	2	2	9	0	2	2	9	0	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:21984840G>A	ENST00000381418.4	-	3	2595	c.1115C>T	c.(1114-1116)cCc>cTc	p.P372L	HR_ENST00000312841.8_Missense_Mutation_p.P372L	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	372					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GTGGCTGGGGGGACAGGCCCT	0.657																																					p.P372L													.	HR-154	0			c.C1115T						.						110	125	120					8																	21984840		2203	4300	6503	SO:0001583	missense	55806	exon3			CTGGGGGGACAGG	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1115C>T	8.37:g.21984840G>A	ENSP00000370826:p.Pro372Leu	Somatic	348	0		WXS	Illumina HiSeq	Phase_I	325	8	NM_018411	0	0	0	0	0	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.528779	0.27387	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.72167	-0.63;-0.63	6.04	3.02	0.34903	.	0.358324	0.24245	N	0.040228	T	0.50034	0.1592	N	0.16656	0.425	0.43729	D	0.99621	B;B	0.17038	0.02;0.012	B;B	0.16722	0.016;0.007	T	0.26155	-1.0111	10	0.31617	T	0.26	-2.4697	6.8335	0.23923	0.3373:0.0:0.6627:0.0	.	372;372	O43593-2;O43593	.;HAIR_HUMAN	L	372	ENSP00000370826:P372L;ENSP00000326765:P372L	ENSP00000326765:P372L	P	-	2	0	HR	22040785	0.079000	0.21365	0.908000	0.35775	0.600000	0.36913	0.167000	0.16602	0.304000	0.22809	0.563000	0.77884	CCC	.		0.657	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			A	21984840	G	A	21984840	3	1	88	1	0	0	0	0	1	0	0	0	7368	1232	43	2	2522	2	HR	8	21984840	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	15649708	21984840	124379182	44	8013											
NEFL	4747	ucsc.edu	37	chr8	24813289	24813289	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcgggcttggtcacgtcCatctccacggagatctgcgc	6	9	13	13	4	3	1	1	0	2	1	6	2	4	1	2	4	1	1	2	4	0	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:24813289C>T	ENST00000221169.5	-	0	1335				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		TGGTCACGTCCATCTCCACGG	0.567																																					p.M247I													.	NEFL-24	0			c.G741A						.						49	54	52					8																	24813289		2151	4251	6402			4747	exon1			CACGTCCATCTCC		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24813289C>T		Somatic	31	0		WXS	Illumina HiSeq		34	4	NM_006158	0	0	21	21	0	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	37																																																																																				.		0.567	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		T	24813289	C	T	24813289	1	4	88	0	1	0	0	0	0	0	0	0	10341	594	21	2		2	NEFL	8	24813289	RNA	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	2828449	24813289	121550733	45	8014											
ADAM32	203102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	39044454	39044454	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggagataactctggaggcAtttgcagttattgtcaccca	12	11	10	8	0	2	1	1	0	1	1	2	3	2	2	1	3	2	3	1	3	3	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:39044454A>G	ENST00000379907.4	+	11	1069	c.942A>G	c.(940-942)gcA>gcG	p.A314A	ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	314	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CTCTGGAGGCATTTGCAGTTA	0.358																																					p.A314A		.											.	ADAM32-227	0			c.A942G						.						79	76	77					8																	39044454		1814	4076	5890	SO:0001819	synonymous_variant	203102	exon11			GGAGGCATTTGCA	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"ADAM metallopeptidase domain containing"	15479	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 32"			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.942A>G	8.37:g.39044454A>G		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	139	34	NM_145004	0	0	0	0	0	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			.		0.358	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		G	39044454	A	G	39044454	2	3	88	1	0	0	0	0	0	0	0	1	249	204	8	3		3	ADAM32	8	39044454	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	14231165	39044454	107319568	46	8015											
OSGIN2	734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	90936955	90936955	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caagagaaactgggaaattaGgggttatcagcgaatagctg	15	8	13	5	1	1	1	1	0	0	1	1	4	1	2	0	3	3	2	0	3	7	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:90936955G>C	ENST00000297438.2	+	6	1068	c.713G>C	c.(712-714)aGg>aCg	p.R238T	OSGIN2_ENST00000451899.2_Missense_Mutation_p.R282T	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	238					meiotic nuclear division (GO:0007126)					breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TGGGAAATTAGGGGTTATCAG	0.418																																					p.R282T		.											.	OSGIN2-68	0			c.G845C						.						75	77	76					8																	90936955		2203	4300	6503	SO:0001583	missense	734	exon6			AAATTAGGGGTTA	AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.713G>C	8.37:g.90936955G>C	ENSP00000297438:p.Arg238Thr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	95	30	NM_001126111	0	1	10	23	12		Missense_Mutation	SNP	ENST00000297438.2	37	CCDS6248.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.436313	0.25813	.	.	ENSG00000164823	ENST00000297438;ENST00000451899	T;T	0.22539	1.95;1.95	5.25	5.25	0.73442	.	0.041552	0.85682	D	0.000000	T	0.16769	0.0403	L	0.43152	1.355	0.80722	D	1	B;B	0.31077	0.307;0.163	B;B	0.26416	0.069;0.068	T	0.05209	-1.0899	10	0.17832	T	0.49	-3.8246	12.2313	0.54490	0.0783:0.0:0.9217:0.0	.	282;238	Q9Y236-2;Q9Y236	.;OSGI2_HUMAN	T	238;282	ENSP00000297438:R238T;ENSP00000396445:R282T	ENSP00000297438:R238T	R	+	2	0	OSGIN2	91006130	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.061000	0.89467	2.461000	0.83175	0.555000	0.69702	AGG	.		0.418	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		C	90936955	G	C	90936955	3	2	88	1	0	0	0	0	1	0	0	0	11316	1000	35	4	867	4	OSGIN2	8	90936955	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	51892501	90936955	55427067	47	8016											
GSN	2934	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	124089637	124089638	+	Frame_Shift_Ins	INS	-	-	C																															cgatgcctttgttctgaaaaINSccccctcagccgcctacctg																								rs376326631		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr9:124089637_124089638insC	ENST00000373818.4	+	13	1861_1862	c.1792_1793insC	c.(1792-1794)accfs	p.T598fs	GSN_ENST00000341272.2_Frame_Shift_Ins_p.T547fs|GSN_ENST00000373806.1_Frame_Shift_Ins_p.T23fs|GSN_ENST00000545652.1_Frame_Shift_Ins_p.T555fs|GSN_ENST00000412819.1_Frame_Shift_Ins_p.T547fs|GSN_ENST00000436847.1_Frame_Shift_Ins_p.T558fs|GSN_ENST00000394353.2_Frame_Shift_Ins_p.T558fs|GSN_ENST00000373807.1_Frame_Shift_Ins_p.T329fs|GSN_ENST00000373808.2_Frame_Shift_Ins_p.T547fs|GSN_ENST00000373823.3_Frame_Shift_Ins_p.T547fs|GSN_ENST00000449733.1_Frame_Shift_Ins_p.T547fs	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	598	Actin-binding, Ca-sensitive. {ECO:0000255}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						TGTTCTGAAAACCCCCTCAGCC	0.594																																					p.T598fs		.											.	GSN-154	0			c.1792_1793insC						.																																			SO:0001589	frameshift_variant	2934	exon13			.	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"amyloidosis, Finnish type"	137350	"gelsolin (amyloidosis, Finnish type)"			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.1797dupC	9.37:g.124089642_124089642dupC	ENSP00000362924:p.Thr598fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	85	16	NM_000177	0	0	0	0	0	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Frame_Shift_Ins	INS	ENST00000373818.4	37	CCDS6828.1																																																																																			.		0.594	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177		C	124089638	-	C	124089637	7	5	88	1	0	1	1	0	0	0	0	0	6846	43	2	0	1870	0	GSN	9	124089637	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08		124089637	17123794	48	8017											
SLC2A8	29988	broad.mit.edu;bcgsc.ca	37	chr9	130160364	130160364	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctcaccggcctggccTgcggtgttgcctccctagtg	2	10	12	17	2	1	0	1	0	0	0	3	0	3	0	7	3	2	1	7	3	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr9:130160364T>A	ENST00000373371.3	+	3	489	c.400T>A	c.(400-402)Tgc>Agc	p.C134S	SLC2A8_ENST00000373360.3_Missense_Mutation_p.C134S|SLC2A8_ENST00000373352.1_Intron	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	134					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						CGGCCTGGCCTGCGGTGTTGC	0.697																																					p.C134S													.	SLC2A8-92	0			c.T400A						.						8	10	9					9																	130160364		2148	4227	6375	SO:0001583	missense	29988	exon3			CTGGCCTGCGGTG	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"Solute carriers"	13812	protein-coding gene	gene with protein product		605245	"solute carrier family 2 (facilitated glucose transporter) member 8"			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.400T>A	9.37:g.130160364T>A	ENSP00000362469:p.Cys134Ser	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	24	8	NM_014580	0	0	11	14	3	Q8WUZ9|Q9NSC4	Missense_Mutation	SNP	ENST00000373371.3	37	CCDS6870.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.544394	0.27563	.	.	ENSG00000136856	ENST00000373371;ENST00000373360	T;T	0.74526	-0.85;-0.85	5.24	2.51	0.30379	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.079753	0.85682	D	0.000000	T	0.43567	0.1253	N	0.02296	-0.605	0.34103	D	0.662034	B;B	0.22276	0.067;0.02	B;B	0.23716	0.048;0.006	T	0.48328	-0.9045	10	0.32370	T	0.25	.	4.8407	0.13489	0.401:0.0:0.1361:0.463	.	134;134	Q5VVV9;Q9NY64	.;GTR8_HUMAN	S	134	ENSP00000362469:C134S;ENSP00000362458:C134S	ENSP00000362458:C134S	C	+	1	0	SLC2A8	129200185	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.375000	0.52410	1.990000	0.58119	0.528000	0.53228	TGC	.		0.697	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580		A	130160364	T	A	130160364	3	1	88	1	0	0	0	0	1	0	0	0	14583	1580	55	5	410	5	SLC2A8	9	130160364	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	6070727	130160364	11053067	49	8018											
DNAJC1	64215	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	22171214	22171214	+	Frame_Shift_Del	DEL	T	T	-																															ttataaagcttatttacctgTtttttctgtgttcggttcct																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr10:22171214delT	ENST00000376980.3	-	8	1265	c.975delA	c.(973-975)aaafs	p.K325fs		NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	325	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				TATTTACCTGTTTTTTCTGTG	0.323																																					p.K325fs		.											.	DNAJC1-226	0			c.975delA						.						142	132	135					10																	22171214		2202	4300	6502	SO:0001589	frameshift_variant	64215	exon8			.	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.975delA	10.37:g.22171214delT	ENSP00000366179:p.Lys325fs	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	77	16	NM_022365	0	0	0	0	0	B0YIZ8|Q5VX89|Q9H6B8	Frame_Shift_Del	DEL	ENST00000376980.3	37	CCDS7136.1																																																																																			.		0.323	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		-	22171214	T	-	22171214	7	5	88	1	0	1	0	1	0	0	0	0	4639	1722	60	0	709	0	DNAJC1	10	22171214	Frame_Shift_Del	DEL	T	TCGA-BQ-7059-01A-11D-1961-08		22171214	113363533	50	8019											
PTCHD3	374308	broad.mit.edu;bcgsc.ca	37	chr10	27687672	27687673	+	In_Frame_Ins	INS	-	-	GTATAT																															tcctgcacatggaaacacccINSatatatactgcttatgatgt																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr10:27687672_27687673insGTATAT	ENST00000438700.3	-	4	1971_1972	c.1854_1855insATATAC	c.(1852-1857)tatggg>tatATATACggg	p.617_618insYI		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	617					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TGGAAACACCCATATATACTGC	0.361																																					p.G619delinsIYG													.	PTCHD3-94	0			c.1855_1856insATATAC						.																																			SO:0001652	inframe_insertion	374308	exon4			AACACCCATATAT	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1854_1855insATATAC	10.37:g.27687672_27687673insGTATAT	ENSP00000417658:p.Ile617_Tyr618insTyrIle	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	102	12	NM_001034842	0	0	0	0	0	I3L499|Q6ZU28	In_Frame_Ins	INS	ENST00000438700.3	37	CCDS31173.1																																																																																			.		0.361	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		GTATAT	27687673	-	GTATAT	27687672	7	5	88	1	0	1	1	0	0	0	0	0	12763	594	21	0	452	0	PTCHD3	10	27687672	In_Frame_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	5516458	27687672	107847075	51	8020											
PHRF1	57661	ucsc.edu	37	chr11	608874	608874	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcaggcacaagcatcagcggGaacgcagccacgagcggcca	12	1	14	14	4	1	0	1	0	0	0	1	2	1	1	2	3	5	4	2	3	2	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:608874G>A	ENST00000264555.5	+	14	3546	c.3418G>A	c.(3418-3420)Gaa>Aaa	p.E1140K	PHRF1_ENST00000533464.1_Missense_Mutation_p.E1136K|PHRF1_ENST00000413872.2_Missense_Mutation_p.E1138K|PHRF1_ENST00000416188.2_Missense_Mutation_p.E1139K	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1140	Arg-rich.				mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GCATCAGCGGGAACGCAGCCA	0.652																																					p.E1139K													.	PHRF1-22	0			c.G3415A						.						23	29	27					11																	608874		2200	4294	6494	SO:0001583	missense	57661	exon14			CAGCGGGAACGCA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	24351	protein-coding gene	gene with protein product	"CTD binding SR like protein rA9", "protein phosphatase 1, regulatory subunit 125"	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3418G>A	11.37:g.608874G>A	ENSP00000264555:p.Glu1140Lys	Somatic	55	0		WXS	Illumina HiSeq		46	4	NM_020901	0	0	41	41	0	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	37		.	.	.	.	.	.	.	.	.	.	G	13.66	2.302829	0.40795	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	4.69	3.73	0.42828	.	0.348665	0.20929	N	0.083136	T	0.25531	0.0621	L	0.32530	0.975	0.31444	N	0.671646	D;D;D;D	0.59767	0.976;0.986;0.986;0.976	P;P;P;P	0.56088	0.622;0.791;0.791;0.622	T	0.09335	-1.0679	10	0.72032	D	0.01	-26.6618	15.9627	0.79941	0.0:0.1469:0.8531:0.0	.	1136;1138;1139;1140	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	K	1140;1138;1139;1136	ENSP00000264555:E1140K;ENSP00000388589:E1138K;ENSP00000410626:E1139K;ENSP00000431870:E1136K	ENSP00000264555:E1140K	E	+	1	0	PHRF1	598874	0.995000	0.38212	0.782000	0.31804	0.013000	0.08279	1.843000	0.39259	2.441000	0.82636	0.561000	0.74099	GAA	.		0.652	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	608874	G	A	608874	3	1	88	1	0	0	0	0	1	0	0	0	11887	1175	41	2	3465	2	PHRF1	11	608874	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08		608874	134397642	52	8021											
ATG2A	23130	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64679328	64679328	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcaccagctgggtgggccTgggcagagagccggcgggag	7	4	19	11	2	1	1	1	0	0	1	1	3	1	2	3	5	2	2	3	5	0	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:64679328T>A	ENST00000377264.3	-	9	1326	c.1214A>T	c.(1213-1215)cAg>cTg	p.Q405L	ATG2A_ENST00000421419.2_Missense_Mutation_p.Q405L	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	405					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						TGGGTGGGCCTGGGCAGAGAG	0.647																																					p.Q405L													.	ATG2A-69	0			c.A1214T						.						27	31	30					11																	64679328		2201	4295	6496	SO:0001583	missense	23130	exon9			TGGGCCTGGGCAG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1214A>T	11.37:g.64679328T>A	ENSP00000366475:p.Gln405Leu	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_015104	0	0	11	20	9	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.898377	0.33535	.	.	ENSG00000110046	ENST00000421419;ENST00000377264;ENST00000227459	T;T	0.07567	3.18;3.18	4.42	3.32	0.38043	.	1.024010	0.07881	U	0.969545	T	0.06645	0.0170	N	0.19112	0.55	0.29096	N	0.881767	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	10	0.30854	T	0.27	.	9.1303	0.36841	0.0:0.0:0.2379:0.7621	.	405	Q2TAZ0	ATG2A_HUMAN	L	405	ENSP00000410522:Q405L;ENSP00000366475:Q405L	ENSP00000227459:Q405L	Q	-	2	0	ATG2A	64435904	0.992000	0.36948	0.830000	0.32933	0.974000	0.67602	1.816000	0.38992	0.912000	0.36772	0.459000	0.35465	CAG	.		0.647	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		A	64679328	T	A	64679328	3	1	88	1	0	0	0	0	1	0	0	0	1094	1580	55	5	4734	5	ATG2A	11	64679328	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	64070454	64679328	70327188	53	8022											
BBS1	582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66282135	66282135	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctggaacaagacctttggAaccaggccaaagaggtaaat	15	7	10	9	0	1	2	0	0	1	2	1	4	1	4	3	4	2	1	3	4	6	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:66282135A>G	ENST00000318312.7	+	4	469	c.418A>G	c.(418-420)Aac>Gac	p.N140D	BBS1_ENST00000529766.1_3'UTR|BBS1_ENST00000537537.1_Silent_p.G43G|BBS1_ENST00000393994.2_Missense_Mutation_p.N140D|CTD-3074O7.11_ENST00000419755.3_Missense_Mutation_p.N177D|BBS1_ENST00000455748.2_Missense_Mutation_p.N140D	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	140					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						AGACCTTTGGAACCAGGCCAA	0.502									Bardet-Biedl syndrome																												p.N140D	GBM(152;173 2612 9770 10137)	.											.	BBS1-91	0			c.A418G						.						74	72	72					11																	66282135		2200	4295	6495	SO:0001583	missense	582	exon4	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CTTTGGAACCAGG	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.418A>G	11.37:g.66282135A>G	ENSP00000317469:p.Asn140Asp	Somatic	151	1		WXS	Illumina HiSeq	Phase_I	127	25	NM_024649	0	0	47	91	44	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	37	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	A	8.126	0.781967	0.16189	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748;ENST00000393994;ENST00000524705	D;D;D;D;D	0.90004	-2.6;-2.6;-2.6;-2.6;-2.6	4.95	2.59	0.31030	.	.	.	.	.	T	0.80793	0.4691	L	0.45581	1.43	0.80722	D	1	B;B;B;B	0.11235	0.0;0.0;0.004;0.003	B;B;B;B	0.11329	0.001;0.001;0.004;0.006	T	0.65356	-0.6188	9	0.13470	T	0.59	.	4.2202	0.10554	0.6433:0.1757:0.181:0.0	.	140;140;140;177	E7EQH1;Q32MM9;Q8NFJ9;Q8NFJ9-2	.;.;BBS1_HUMAN;.	D	177;140;140;140;47	ENSP00000398526:N177D;ENSP00000317469:N140D;ENSP00000405764:N140D;ENSP00000377563:N140D;ENSP00000436927:N47D	ENSP00000317469:N140D	N	+	1	0	BBS1;CTD-3074O7.11	66038711	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	0.988000	0.29616	0.316000	0.23135	-0.472000	0.04984	AAC	.		0.502	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2			G	66282135	A	G	66282135	3	3	88	1	0	0	0	0	1	0	0	0	1336	246	9	3	432	3	BBS1	11	66282135	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	1602807	66282135	68724381	54	8023											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825431	95825431	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgttgctgctgttgctgTtgggtgtagtgtaggagaga	5	15	17	4	0	0	1	0	0	0	1	0	3	0	2	0	2	4	9	0	2	2	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:95825431T>C	ENST00000524717.1	-	2	3048	c.1764A>G	c.(1762-1764)caA>caG	p.Q588Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	588					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgTTGGGTGTAGT	0.522			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q588Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.A1764G						.																																			SO:0001819	synonymous_variant	84441	exon2			TTGCTGTTGGGTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1764A>G	11.37:g.95825431T>C		Somatic	11	2		WXS	Illumina HiSeq	Phase_I	11	3	NM_032427	0	0	21	21	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.522	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825431	T	C	95825431	2	2	88	1	0	0	0	0	0	0	0	1	9231	1722	60	3		3	MAML2	11	95825431	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	29543296	95825431	39181085	55	8024											
TMEM133	83935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	100863392	100863392	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaaatgtgccagttccacTtggtaataacgttgggaaaa	14	11	9	7	1	1	0	1	0	0	0	2	1	2	1	2	2	2	3	2	2	6	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:100863392T>A	ENST00000303130.2	+	1	582	c.353T>A	c.(352-354)cTt>cAt	p.L118H		NM_032021.2	NP_114410.1	Q9H2Q1	TM133_HUMAN	transmembrane protein 133	118						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)|lung(1)|prostate(1)	5		Acute lymphoblastic leukemia(157;0.000869)|all_hematologic(158;0.014)		BRCA - Breast invasive adenocarcinoma(274;0.0675)		CCAGTTCCACTTGGTAATAAC	0.388																																					p.L118H		.											.	TMEM133-90	0			c.T353A						.						142	137	138					11																	100863392		2203	4299	6502	SO:0001583	missense	83935	exon1			TTCCACTTGGTAA	AF247167	CCDS8309.1	11q22.1	2006-03-09				ENSG00000170647			24033	protein-coding gene	gene with protein product						12477932	Standard	NM_032021		Approved	AD031	uc001pgf.3	Q9H2Q1		ENST00000303130.2:c.353T>A	11.37:g.100863392T>A	ENSP00000303999:p.Leu118His	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	153	28	NM_032021	0	0	10	21	11		Missense_Mutation	SNP	ENST00000303130.2	37	CCDS8309.1	.	.	.	.	.	.	.	.	.	.	T	8.089	0.774082	0.16051	.	.	ENSG00000170647	ENST00000303130	.	.	.	2.67	-1.16	0.09678	.	.	.	.	.	T	0.22704	0.0548	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	P	0.56398	0.797	T	0.14448	-1.0472	8	0.87932	D	0	.	4.3705	0.11246	0.1931:0.0:0.4529:0.3539	.	118	Q9H2Q1	TM133_HUMAN	H	118	.	ENSP00000303999:L118H	L	+	2	0	TMEM133	100368602	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.318000	0.08050	-0.257000	0.09459	-0.329000	0.08387	CTT	.		0.388	TMEM133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395137.1	NM_032021		A	100863392	T	A	100863392	3	1	88	1	0	0	0	0	1	0	0	0	16081	1609	56	5	355	5	TMEM133	11	100863392	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	5037961	100863392	34143124	56	8025											
PHLDB1	23187	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	118516164	118516164	+	Frame_Shift_Del	DEL	A	A	-																															gtgccagtgggatgcccttcAcggggcagcacccttcccag																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:118516164delA	ENST00000361417.2	+	17	3623	c.3212delA	c.(3211-3213)cacfs	p.H1071fs	PHLDB1_ENST00000524713.1_Frame_Shift_Del_p.H214fs|PHLDB1_ENST00000527898.1_Frame_Shift_Del_p.H122fs|PHLDB1_ENST00000356063.5_Frame_Shift_Del_p.H1024fs|PHLDB1_ENST00000534672.1_3'UTR	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1071										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GATGCCCTTCACGGGGCAGCA	0.652																																					p.H1071fs		.											.	PHLDB1-90	0			c.3212delA						.						42	51	48					11																	118516164		2200	4295	6495	SO:0001589	frameshift_variant	23187	exon16			.		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3212delA	11.37:g.118516164delA	ENSP00000354498:p.His1071fs	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	92	27	NM_001144758	0	0	0	0	0	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Frame_Shift_Del	DEL	ENST00000361417.2	37	CCDS8401.1																																																																																			.		0.652	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		-	118516164	A	-	118516164	7	5	88	1	0	1	0	1	0	0	0	0	11877	159	6	0	3270	0	PHLDB1	11	118516164	Frame_Shift_Del	DEL	A	TCGA-BQ-7059-01A-11D-1961-08	17652772	118516164	16490352	57	8026	87	3									
PHLDB1	23187	hgsc.bcm.edu;bcgsc.ca	37	chr11	118516166	118516166	+	Missense_Mutation	SNP	G	G	C																															gccagtgggatgcccttcacGgggcagcacccttcccagcg																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:118516166G>C	ENST00000361417.2	+	17	3625	c.3214G>C	c.(3214-3216)Ggg>Cgg	p.G1072R	PHLDB1_ENST00000524713.1_Missense_Mutation_p.G215R|PHLDB1_ENST00000527898.1_Missense_Mutation_p.G123R|PHLDB1_ENST00000356063.5_Missense_Mutation_p.G1025R|PHLDB1_ENST00000534672.1_3'UTR	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1072										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		TGCCCTTCACGGGGCAGCACC	0.657																																					p.G1072R		.											.	PHLDB1-90	0			c.G3214C						.						43	52	49					11																	118516166		2200	4295	6495	SO:0001583	missense	23187	exon16			CTTCACGGGGCAG		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3214G>C	11.37:g.118516166G>C	ENSP00000354498:p.Gly1072Arg	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	90	26	NM_001144758	0	0	22	22	0	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268966	0.80469	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063;ENST00000527898;ENST00000524713	T;T;T;T	0.50277	1.41;1.48;0.75;0.76	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.65883	0.2734	L	0.59436	1.845	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;0.997;0.999;0.995;0.991	D;D;D;D;D	0.97110	1.0;0.966;0.989;0.976;0.922	T	0.57124	-0.7865	10	0.21014	T	0.42	-37.8382	19.9036	0.96999	0.0:0.0:1.0:0.0	.	215;436;831;1025;1072	B4DK17;B0YJ65;Q5W9G0;Q86UU1-2;Q86UU1	.;.;.;.;PHLB1_HUMAN	R	1072;846;436;1025;123;215	ENSP00000354498:G1072R;ENSP00000348359:G1025R;ENSP00000435388:G123R;ENSP00000434905:G215R	ENSP00000348359:G1025R	G	+	1	0	PHLDB1	118021376	1.000000	0.71417	0.821000	0.32701	0.728000	0.41692	5.896000	0.69822	2.706000	0.92434	0.655000	0.94253	GGG	.		0.657	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		C	118516166	G	C	118516166	3	2	88	1	0	0	0	0	1	0	0	0	11877	1116	39	4	3272	4	PHLDB1	11	118516166	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	2	118516166	16490350	58	8027	87	3									
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118516168	118516168	+	Frame_Shift_Del	DEL	G	G	-																															cagtgggatgcccttcacggGgcagcacccttcccagcggg																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:118516168delG	ENST00000361417.2	+	17	3627	c.3216delG	c.(3214-3216)gggfs	p.G1072fs	PHLDB1_ENST00000524713.1_Frame_Shift_Del_p.G215fs|PHLDB1_ENST00000527898.1_Frame_Shift_Del_p.G123fs|PHLDB1_ENST00000356063.5_Frame_Shift_Del_p.G1025fs|PHLDB1_ENST00000534672.1_3'UTR	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1072										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCCTTCACGGGGCAGCACCCT	0.657																																					p.G1072fs		.											.	PHLDB1-90	0			c.3216delG						.						44	53	50					11																	118516168		2200	4295	6495	SO:0001589	frameshift_variant	23187	exon16			.		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3216delG	11.37:g.118516168delG	ENSP00000354498:p.Gly1072fs	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	90	19	NM_001144758	0	0	0	0	0	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Frame_Shift_Del	DEL	ENST00000361417.2	37	CCDS8401.1																																																																																			.		0.657	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		-	118516168	G	-	118516168	7	5	88	1	0	1	0	1	0	0	0	0	11877	1219	43	0	3274	0	PHLDB1	11	118516168	Frame_Shift_Del	DEL	G	TCGA-BQ-7059-01A-11D-1961-08	2	118516168	16490348	59	8028	87	3									
GRIK4	2900	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	120745883	120745883	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttaccggccacattgaattCaacagcaaaggccagaggtc	13	7	9	12	1	1	2	1	1	0	1	2	2	1	2	3	3	3	1	3	3	4	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:120745883C>T	ENST00000527524.2	+	11	1382	c.1095C>T	c.(1093-1095)ttC>ttT	p.F365F	RP11-640N11.2_ENST00000505153.2_RNA|GRIK4_ENST00000438375.2_Silent_p.F365F	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	365					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		ACATTGAATTCAACAGCAAAG	0.502																																					p.F365F		.											.	GRIK4-92	0			c.C1095T						.						130	112	118					11																	120745883		2203	4299	6502	SO:0001819	synonymous_variant	2900	exon9			TGAATTCAACAGC	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1095C>T	11.37:g.120745883C>T		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	136	24	NM_014619	0	0	0	0	0	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																			.		0.502	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		T	120745883	C	T	120745883	2	4	88	1	0	0	0	0	0	0	0	1	6797	825	29	2		2	GRIK4	11	120745883	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	2229715	120745883	14260633	60	8029											
CDON	50937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	125880565	125880565	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcacttactggtgccgtaAttataactggcttgaatcca	10	14	8	9	1	0	1	0	1	0	0	1	1	1	1	2	2	4	3	2	2	5	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:125880565A>T	ENST00000392693.3	-	8	1350	c.1223T>A	c.(1222-1224)aTt>aAt	p.I408N	CDON_ENST00000263577.7_Missense_Mutation_p.I408N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	408	Ig-like C2-type 5.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TGGTGCCGTAATTATAACTGG	0.428																																					p.I408N		.											.	CDON-158	0			c.T1223A						.						63	61	62					11																	125880565		2201	4299	6500	SO:0001583	missense	50937	exon8			GCCGTAATTATAA	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	17104	protein-coding gene	gene with protein product	"cell adhesion molecule-related/down-regulated by oncogenes"	608707	"Cdon homolog (mouse)"			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.1223T>A	11.37:g.125880565A>T	ENSP00000376458:p.Ile408Asn	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	75	18	NM_016952	0	0	1	2	1	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.259|7.259	0.604826|0.604826	0.14002|0.14002	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000392693;ENST00000263577|ENST00000534661	T;T|.	0.29142|.	1.58;1.58|.	5.01|5.01	2.7|2.7	0.31948|0.31948	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.421653|.	0.19358|.	N|.	0.116221|.	T|T	0.38612|0.38612	0.1047|0.1047	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	0.999999|0.999999	P;P|.	0.36392|.	0.551;0.496|.	B;B|.	0.39738|.	0.308;0.205|.	T|T	0.21965|0.21965	-1.0230|-1.0230	10|5	0.66056|.	D|.	0.02|.	-2.7576|-2.7576	8.6995|8.6995	0.34316|0.34316	0.7929:0.0:0.2071:0.0|0.7929:0.0:0.2071:0.0	.|.	408;408|.	Q4KMG0;Q4KMG0-2|.	CDON_HUMAN;.|.	N|K	408|383	ENSP00000376458:I408N;ENSP00000263577:I408N|.	ENSP00000263577:I408N|.	I|N	-|-	2|3	0|2	CDON|CDON	125385775|125385775	0.210000|0.210000	0.23517|0.23517	0.307000|0.307000	0.25127|0.25127	0.339000|0.339000	0.28857|0.28857	1.941000|1.941000	0.40233|0.40233	0.272000|0.272000	0.22027|0.22027	0.482000|0.482000	0.46254|0.46254	ATT|AAT	.		0.428	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		T	125880565	A	T	125880565	3	4	88	1	0	0	0	0	1	0	0	0	3176	101	4	5	2623	5	CDON	11	125880565	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	5134682	125880565	9125951	61	8030											
CACNA1C	775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2716231	2716231	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggagaacagcaagtttgaCtttgacaatgttctggcagc	11	11	12	7	0	1	3	0	2	1	1	1	4	1	3	0	2	3	4	0	2	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:2716231C>T	ENST00000347598.4	+	27	3351	c.3351C>T	c.(3349-3351)gaC>gaT	p.D1117D	CACNA1C_ENST00000480911.1_Silent_p.D1097D|CACNA1C_ENST00000399634.1_Silent_p.D1097D|CACNA1C_ENST00000399644.1_Silent_p.D1097D|CACNA1C_ENST00000399637.1_Silent_p.D1097D|CACNA1C_ENST00000399603.1_Silent_p.D1097D|CACNA1C_ENST00000399649.1_Silent_p.D1097D|CACNA1C-AS3_ENST00000543559.1_RNA|CACNA1C_ENST00000402845.3_Silent_p.D1097D|CACNA1C_ENST00000399638.1_Silent_p.D1097D|CACNA1C_ENST00000399629.1_Silent_p.D1097D|CACNA1C_ENST00000399601.1_Silent_p.D1097D|CACNA1C_ENST00000399595.1_Silent_p.D1097D|CACNA1C_ENST00000399617.1_Silent_p.D1097D|CACNA1C_ENST00000399597.1_Silent_p.D1097D|CACNA1C_ENST00000327702.7_Silent_p.D1097D|CACNA1C_ENST00000399621.1_Silent_p.D1097D|CACNA1C_ENST00000406454.3_Silent_p.D1097D|CACNA1C_ENST00000399591.1_Silent_p.D1097D|CACNA1C_ENST00000399606.1_Silent_p.D1117D|CACNA1C_ENST00000335762.5_Silent_p.D1122D|CACNA1C_ENST00000399641.1_Silent_p.D1097D|CACNA1C_ENST00000399655.1_Silent_p.D1097D|CACNA1C_ENST00000344100.3_Silent_p.D1097D	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1117	Dihydropyridine binding. {ECO:0000250}.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCAAGTTTGACTTTGACAATG	0.567																																					p.D1117D		.											.	CACNA1C-34	0			c.C3351T						.						59	64	62					12																	2716231		2169	4287	6456	SO:0001819	synonymous_variant	775	exon27			GTTTGACTTTGAC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.3351C>T	12.37:g.2716231C>T		Somatic	50	2		WXS	Illumina HiSeq	Phase_I	45	12	NM_199460	0	0	2	2	0	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																			.		0.567	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2716231	C	T	2716231	2	4	88	1	0	0	0	0	0	0	0	1	2546	564	20	2		2	CACNA1C	12	2716231	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		2716231	131135664	62	8031											
SLC2A14	144195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7982586	7982586	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagccaacaggttgacaaTcagcattgaattgcgcctgt	11	9	11	10	1	1	2	1	2	0	0	1	2	1	2	2	2	4	3	2	2	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:7982586T>A	ENST00000543909.1	-	10	1117	c.358A>T	c.(358-360)Att>Ttt	p.I120F	SLC2A14_ENST00000539924.1_Missense_Mutation_p.I135F|SLC2A14_ENST00000396589.2_Missense_Mutation_p.I120F|SLC2A14_ENST00000431042.2_Missense_Mutation_p.I97F|SLC2A14_ENST00000340749.5_Missense_Mutation_p.I97F|SLC2A14_ENST00000542546.1_Missense_Mutation_p.I11F|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000535295.1_Missense_Mutation_p.I11F			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	120					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		AGGTTGACAATCAGCATTGAA	0.458																																					p.I120F		.											.	SLC2A14-91	0			c.A358T						.						62	61	61					12																	7982586		2203	4300	6503	SO:0001583	missense	144195	exon6			TGACAATCAGCAT	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.358A>T	12.37:g.7982586T>A	ENSP00000440480:p.Ile120Phe	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	81	16	NM_153449	0	0	31	31	0	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	t	10.42	1.346517	0.24426	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924;ENST00000546234;ENST00000542782;ENST00000535344;ENST00000537557;ENST00000535266	T;T;T;T;T;T;T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	3.11	1.89	0.25635	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.451473	0.22797	N	0.055529	T	0.63094	0.2482	L	0.49455	1.56	0.09310	N	1	B;B;B;B	0.17852	0.02;0.006;0.002;0.024	B;B;B;B	0.24394	0.049;0.049;0.013;0.053	T	0.46076	-0.9217	10	0.15499	T	0.54	.	7.3787	0.26843	0.0:0.0:0.4716:0.5284	.	135;11;97;120	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	F	97;120;97;120;11;11;135;97;97;97;120;120	ENSP00000340450:I97F;ENSP00000440480:I120F;ENSP00000407287:I97F;ENSP00000379834:I120F;ENSP00000440492:I11F;ENSP00000443903:I11F;ENSP00000445929:I135F;ENSP00000440043:I97F;ENSP00000438312:I97F;ENSP00000443217:I97F;ENSP00000440044:I120F;ENSP00000437653:I120F	ENSP00000340450:I97F	I	-	1	0	SLC2A14	7873853	0.000000	0.05858	0.522000	0.27862	0.249000	0.25844	-0.458000	0.06737	0.201000	0.20466	0.377000	0.23210	ATT	.		0.458	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		A	7982586	T	A	7982586	3	1	88	1	0	0	0	0	1	0	0	0	14575	1435	50	5	1232	5	SLC2A14	12	7982586	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	5266355	7982586	125869309	63	8032											
H2AFJ	55766	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	14927683	14927684	+	Frame_Shift_Ins	INS	-	-	T																															ccatccgcaacgacgaggagINSttaaacaagctgctgggcaa																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:14927683_14927684insT	ENST00000544848.1	+	1	414_415	c.279_280insT	c.(280-282)ttafs	p.L94fs		NM_177925.2	NP_808760.1	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	94						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E93D(1)		NS(1)|central_nervous_system(1)|kidney(1)|ovary(1)|skin(1)	5						ACGACGAGGAGTTAAACAAGCT	0.614																																					p.E93fs		.											.	H2AFJ-69	1	Substitution - Missense(1)	ovary(1)	c.279_280insT						.																																			SO:0001589	frameshift_variant	55766	exon1			.	AK001765	CCDS31752.1	12p12.3	2012-09-11			ENSG00000246705	ENSG00000246705		"Histones / Replication-independent"	14456	protein-coding gene	gene with protein product							Standard	NM_177925		Approved	FLJ10903, MGC921	uc009zia.3	Q9BTM1	OTTHUMG00000168736	ENST00000544848.1:c.281dupT	12.37:g.14927685_14927685dupT	ENSP00000438553:p.Leu94fs	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	159	58	NM_177925	0	0	0	0	0	Q9NV63	Frame_Shift_Ins	INS	ENST00000544848.1	37	CCDS31752.1																																																																																			.		0.614	H2AFJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400845.1	NM_177925		T	14927684	-	T	14927683	7	5	88	1	0	1	1	0	0	0	0	0	6947	1020	36	0	281	0	H2AFJ	12	14927683	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	6945097	14927683	118924212	64	8033											
SLC38A1	81539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46633478	46633478	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcacctatttatctgaccatTttctacttcggtgaaatcat	10	17	4	10	1	4	2	2	2	2	0	5	2	4	2	2	1	1	0	2	1	4	7			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:46633478T>A	ENST00000398637.5	-	3	800	c.106A>T	c.(106-108)Aat>Tat	p.N36Y	SLC38A1_ENST00000546893.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000552197.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000439706.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000549633.1_Intron|SLC38A1_ENST00000549049.1_Missense_Mutation_p.N36Y	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	36					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)			NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			ATCTGACCATTTTCTACTTCG	0.413																																					p.N36Y		.											.	SLC38A1-518	0			c.A106T						.						159	147	151					12																	46633478		1872	4125	5997	SO:0001583	missense	81539	exon3			GACCATTTTCTAC	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"Solute carriers"	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.106A>T	12.37:g.46633478T>A	ENSP00000381634:p.Asn36Tyr	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	171	33	NM_030674	0	0	15	20	5	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	37	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.844471	0.71488	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197;ENST00000550173	T;T;T;T;T	0.07688	3.33;3.33;3.33;3.33;3.17	4.93	4.93	0.64822	.	0.000000	0.56097	D	0.000026	T	0.13457	0.0326	N	0.08118	0	0.46437	D	0.999046	D;P	0.89917	1.0;0.871	D;B	0.87578	0.998;0.327	T	0.35076	-0.9803	10	0.66056	D	0.02	-24.0257	14.896	0.70644	0.0:0.0:0.0:1.0	.	36;36	F8VX04;Q9H2H9	.;S38A1_HUMAN	Y	36	ENSP00000449607:N36Y;ENSP00000398142:N36Y;ENSP00000381634:N36Y;ENSP00000447853:N36Y;ENSP00000449756:N36Y	ENSP00000381634:N36Y	N	-	1	0	SLC38A1	44919745	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.732000	0.62029	1.975000	0.57531	0.477000	0.44152	AAT	.		0.413	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			A	46633478	T	A	46633478	3	1	88	1	0	0	0	0	1	0	0	0	14633	1841	64	5	1417	5	SLC38A1	12	46633478	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	31705795	46633478	87218417	65	8034											
TCTN1	79600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	111070319	111070319	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagattcgtttctgagatttCcttcgtccctgacatcatct	7	16	6	12	2	3	3	1	2	2	2	7	4	5	3	2	0	0	1	2	0	0	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:111070319C>T	ENST00000551590.1	+	5	823	c.667C>T	c.(667-669)Cct>Tct	p.P223S	TCTN1_ENST00000397655.3_Missense_Mutation_p.P223S|TCTN1_ENST00000551555.2_3'UTR|TCTN1_ENST00000377654.3_Missense_Mutation_p.P45S|HVCN1_ENST00000548312.1_Intron|AC144522.1_ENST00000408319.1_RNA|TCTN1_ENST00000397659.4_Missense_Mutation_p.P223S			Q2MV58	TECT1_HUMAN	tectonic family member 1	223					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						TCTGAGATTTCCTTCGTCCCT	0.398																																					p.P223S		.											.	TCTN1-90	0			c.C667T						.						197	184	188					12																	111070319		1898	4131	6029	SO:0001583	missense	79600	exon5			AGATTTCCTTCGT	AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"Tectonic proteins"	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.667C>T	12.37:g.111070319C>T	ENSP00000448735:p.Pro223Ser	Somatic	182	1		WXS	Illumina HiSeq	Phase_I	244	52	NM_024549	0	0	78	117	39	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Missense_Mutation	SNP	ENST00000551590.1	37	CCDS41835.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656513	0.88154	.	.	ENSG00000204852	ENST00000397650;ENST00000551590;ENST00000397655;ENST00000377654;ENST00000547868;ENST00000548095;ENST00000397657;ENST00000397659;ENST00000397652	D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86	5.97	5.97	0.96955	Domain of unknown function DUF1619 (1);	0.000000	0.85682	D	0.000000	D	0.99099	0.9690	M	0.87180	2.865	0.58432	D	0.999993	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99716	1.1008	10	0.87932	D	0	-15.0486	18.9916	0.92794	0.0:1.0:0.0:0.0	.	223;223;223;163;167	Q2MV58;Q2MV58-3;Q2MV58-2;C9J1H5;C9J1H4	TECT1_HUMAN;.;.;.;.	S	163;223;223;45;45;223;45;223;167	ENSP00000448735:P223S;ENSP00000380775:P223S;ENSP00000366882:P45S;ENSP00000380779:P223S	ENSP00000366882:P45S	P	+	1	0	TCTN1	109554702	1.000000	0.71417	0.767000	0.31495	0.782000	0.44232	4.913000	0.63341	2.835000	0.97688	0.591000	0.81541	CCT	.		0.398	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549		T	111070319	C	T	111070319	3	4	88	1	0	0	0	0	1	0	0	0	15754	855	30	2	785	2	TCTN1	12	111070319	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	64436841	111070319	22781576	66	8035											
ATXN2	6311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	111908459	111908459	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggagtaagctggtggggtgGctgcaatcggtgggcccgct	5	9	19	8	2	0	0	0	0	0	0	1	1	0	1	1	7	2	5	1	7	2	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:111908459G>C	ENST00000377617.3	-	19	3247	c.3086C>G	c.(3085-3087)gCc>gGc	p.A1029G	ATXN2_ENST00000535949.1_Missense_Mutation_p.A740G|ATXN2_ENST00000608853.1_Missense_Mutation_p.A869G|ATXN2_ENST00000389153.4_Missense_Mutation_p.A766G|ATXN2_ENST00000542287.2_Missense_Mutation_p.A764G|ATXN2_ENST00000550104.1_3'UTR	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1029	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TGGTGGGGTGGCTGCAATCGG	0.532																																					p.A1029G		.											.	ATXN2-136	0			c.C3086G						.						139	128	132					12																	111908459		2203	4300	6503	SO:0001583	missense	6311	exon19			GGGGTGGCTGCAA	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.3086C>G	12.37:g.111908459G>C	ENSP00000366843:p.Ala1029Gly	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	179	63	NM_002973	0	0	17	38	21	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351916	0.95830	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949	T	0.77620	-1.11	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.85444	0.5698	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.997;0.993;0.999;0.998	D;D;D;D;D	0.85130	0.994;0.985;0.978;0.997;0.994	T	0.81564	-0.0875	10	0.27082	T	0.32	-9.4636	19.888	0.96917	0.0:0.0:1.0:0.0	.	48;1029;740;764;766	Q99700-3;Q99700;Q24JQ7;F8VQP2;F8WB06	.;ATX2_HUMAN;.;.;.	G	84;766;1029;48;764;740	ENSP00000366843:A1029G	ENSP00000366843:A1029G	A	-	2	0	ATXN2	110392842	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.476000	0.97823	2.720000	0.93068	0.591000	0.81541	GCC	.		0.532	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		C	111908459	G	C	111908459	3	2	88	1	0	0	0	0	1	0	0	0	1212	1203	42	4	883	4	ATXN2	12	111908459	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	838140	111908459	21943436	67	8036											
SBNO1	55206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123806180	123806180	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcatagtcactttcttcaTtatcagaggcatcagattca	11	15	5	10	0	7	2	6	0	2	2	8	2	7	2	0	1	0	1	0	1	2	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:123806180T>C	ENST00000602398.1	-	17	2352	c.2225A>G	c.(2224-2226)aAt>aGt	p.N742S	SBNO1_ENST00000420886.2_Missense_Mutation_p.N742S|SBNO1_ENST00000267176.4_Missense_Mutation_p.N741S|SBNO1_ENST00000602750.1_Missense_Mutation_p.N741S			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	742					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		ACTTTCTTCATTATCAGAGGC	0.403																																					p.N742S		.											.	SBNO1-292	0			c.A2225G						.						193	173	180					12																	123806180		2203	4300	6503	SO:0001583	missense	55206	exon16			TCTTCATTATCAG	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2225A>G	12.37:g.123806180T>C	ENSP00000473665:p.Asn742Ser	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	218	90	NM_001167856	0	0	5	14	9	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	3.761	-0.049616	0.07407	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	T;T	0.28666	1.6;1.6	5.33	4.15	0.48705	.	0.449012	0.24209	N	0.040557	T	0.09949	0.0244	N	0.00926	-1.1	0.35755	D	0.819721	B;B;B	0.19200	0.0;0.001;0.034	B;B;B	0.21917	0.001;0.001;0.037	T	0.20538	-1.0272	10	0.06365	T	0.9	-14.1214	12.2297	0.54480	0.0:0.0:0.1426:0.8574	.	742;741;740	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	S	742;741	ENSP00000387361:N742S;ENSP00000267176:N741S	ENSP00000267176:N741S	N	-	2	0	SBNO1	122372133	0.996000	0.38824	0.986000	0.45419	0.996000	0.88848	1.100000	0.31025	0.819000	0.34492	0.460000	0.39030	AAT	.		0.403	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		C	123806180	T	C	123806180	3	2	88	1	0	0	0	0	1	0	0	0	13894	1493	52	3	2020	3	SBNO1	12	123806180	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	11897721	123806180	10045715	68	8037											
MTHFD1	4522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64915025	64915025	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagtagtagtggccgtgAatgcattcaagtaagtgtag	11	12	12	6	1	1	1	1	1	0	0	2	1	2	1	2	1	1	5	2	1	6	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr14:64915025A>C	ENST00000545908.1	+	23	2666	c.2437A>C	c.(2437-2439)Aat>Cat	p.N813H	CTD-2555O16.2_ENST00000556640.1_RNA|MTHFD1_ENST00000216605.8_Missense_Mutation_p.N757H			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	757	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	AGTGGCCGTGAATGCATTCAA	0.383																																					p.N757H	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	.											.	MTHFD1-92	0			c.A2269C						.						79	78	78					14																	64915025		2203	4300	6503	SO:0001583	missense	4522	exon23			GCCGTGAATGCAT	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2437A>C	14.37:g.64915025A>C	ENSP00000438588:p.Asn813His	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	59	12	NM_005956	0	0	3	9	6	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		.	.	.	.	.	.	.	.	.	.	A	21.0	4.077868	0.76528	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.47177	0.85;0.85;0.85	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.82898	0.5137	H	0.99573	4.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.90598	0.4542	10	0.87932	D	0	-21.8056	16.1926	0.82004	1.0:0.0:0.0:0.0	.	813;757	F5H2F4;G3V2B8	.;.	H	813;757;813	ENSP00000438588:N813H;ENSP00000450560:N757H;ENSP00000216605:N813H	ENSP00000216605:N757H	N	+	1	0	MTHFD1	63984778	1.000000	0.71417	0.914000	0.36105	0.594000	0.36715	9.339000	0.96797	2.219000	0.72066	0.533000	0.62120	AAT	.		0.383	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			C	64915025	A	C	64915025	3	2	88	1	0	0	0	0	1	0	0	0	9952	246	9	5	2359	5	MTHFD1	14	64915025	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		64915025	42434515	69	8038											
GALNTL1	57452	bcgsc.ca	37	chr14	69787575	69787575	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accggcccatccgggacaccCgccattacaggtacggcctc	8	5	10	18	4	0	0	0	0	0	0	2	1	1	1	6	4	2	1	6	4	2	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr14:69787575C>A	ENST00000337827.4	+	2	652	c.325C>A	c.(325-327)Cgc>Agc	p.R109S	GALNT16_ENST00000448469.3_Missense_Mutation_p.R109S|GALNT16_ENST00000553669.1_Missense_Mutation_p.R109S	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	109					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CCGGGACACCCGCCATTACAG	0.532																																					p.R109S													.	.	0			c.C325A						.						58	54	56					14																	69787575		2203	4300	6503	SO:0001583	missense	57452	exon2			GACACCCGCCATT	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"Glycosyltransferase family 2 domain containing"	23233	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 16"	615132	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1", "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.325C>A	14.37:g.69787575C>A	ENSP00000336729:p.Arg109Ser	Somatic	75	0		WXS	Illumina HiSeq	Phase_1	97	6	NM_001168368	0	0	0	0	0	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366029	0.82463	.	.	ENSG00000100626	ENST00000337827;ENST00000448469;ENST00000553669	T;T;T	0.62105	0.05;0.05;0.05	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.82365	0.5021	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.85654	0.1284	10	0.87932	D	0	.	12.7073	0.57067	0.275:0.725:0.0:0.0	.	109;109	Q8N428;Q58A55	GLTL1_HUMAN;.	S	109	ENSP00000336729:R109S;ENSP00000402970:R109S;ENSP00000451200:R109S	ENSP00000336729:R109S	R	+	1	0	GALNTL1	68857328	0.997000	0.39634	1.000000	0.80357	0.843000	0.47879	3.698000	0.54771	2.660000	0.90430	0.650000	0.86243	CGC	.		0.532	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		A	69787575	C	A	69787575	3	1	88	1	0	0	0	0	1	0	0	0	6241	652	23	4	331	4	GALNTL1	14	69787575	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	4872550	69787575	37561965	70	8039											
STON2	85439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	81744521	81744521	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttttcaacagcatcagaGtgtgactgggttttgcttga	9	15	11	6	0	2	3	2	2	0	1	2	3	2	3	0	1	3	4	0	1	1	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr14:81744521G>A	ENST00000267540.2	-	4	1334	c.1134C>T	c.(1132-1134)caC>caT	p.H378H	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Silent_p.H378H	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	378					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		CAGCATCAGAGTGTGACTGGG	0.448																																					p.H378H		.											.	STON2-95	0			c.C1134T						.						95	95	95					14																	81744521		2203	4300	6503	SO:0001819	synonymous_variant	85439	exon6			ATCAGAGTGTGAC	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.1134C>T	14.37:g.81744521G>A		Somatic	131	1		WXS	Illumina HiSeq	Phase_I	129	29	NM_001256430	0	0	5	7	2	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Silent	SNP	ENST00000267540.2	37	CCDS9875.1																																																																																			.		0.448	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		A	81744521	G	A	81744521	2	1	88	1	0	0	0	0	0	0	0	1	15350	1020	36	2		2	STON2	14	81744521	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	11956946	81744521	25605019	71	8040											
ATG2B	55102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	96784101	96784101	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtattaatgagctgactggCtactgaaagcccaatgccat	13	10	9	9	0	0	3	0	3	0	0	0	3	0	3	2	1	4	3	2	1	5	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr14:96784101C>G	ENST00000359933.4	-	19	3864	c.2971G>C	c.(2971-2973)Gcc>Ccc	p.A991P		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	991					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AGCTGACTGGCTACTGAAAGC	0.343																																					p.A991P		.											.	ATG2B-93	0			c.G2971C						.						101	96	98					14																	96784101		1833	4104	5937	SO:0001583	missense	55102	exon19			GACTGGCTACTGA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 103", "ATG2 autophagy related 2 homolog B (S. cerevisiae)"	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.2971G>C	14.37:g.96784101C>G	ENSP00000353010:p.Ala991Pro	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	189	35	NM_018036	0	0	5	7	2	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998612	0.74818	.	.	ENSG00000066739	ENST00000359933	T	0.39997	1.05	5.54	5.54	0.83059	.	0.164574	0.39759	U	0.001274	T	0.63034	0.2477	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.54576	-0.8273	10	0.25751	T	0.34	.	19.8585	0.96775	0.0:1.0:0.0:0.0	.	991	Q96BY7	ATG2B_HUMAN	P	991	ENSP00000353010:A991P	ENSP00000353010:A991P	A	-	1	0	ATG2B	95853854	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.496000	0.81526	2.760000	0.94817	0.655000	0.94253	GCC	.		0.343	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96784101	C	G	96784101	3	3	88	1	0	0	0	0	1	0	0	0	1095	797	28	4	3361	4	ATG2B	14	96784101	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	15039580	96784101	10565439	72	8041											
SCAPER	49855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	77087751	77087751	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacacctgtgggagccagAcgaggagctggcactgtgcc	8	6	15	12	1	0	2	0	1	0	1	0	5	0	4	3	3	3	2	3	3	0	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr15:77087751A>T	ENST00000563290.1	-	8	737	c.642T>A	c.(640-642)cgT>cgA	p.R214R	SCAPER_ENST00000538941.2_5'UTR|SCAPER_ENST00000324767.7_Silent_p.R214R|SCAPER_ENST00000562890.1_5'UTR			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	214						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TGGGAGCCAGACGAGGAGCTG	0.418																																					p.R214R		.											.	SCAPER-137	0			c.T642A						.						65	63	63					15																	77087751		1863	4094	5957	SO:0001819	synonymous_variant	49855	exon7			AGCCAGACGAGGA	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.642T>A	15.37:g.77087751A>T		Somatic	76	1		WXS	Illumina HiSeq	Phase_I	83	20	NM_020843	0	0	3	3	0	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Silent	SNP	ENST00000563290.1	37	CCDS53962.1																																																																																			.		0.418	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	77087751	A	T	77087751	2	4	88	1	0	0	0	0	0	0	0	1	13910	262	10	5		5	SCAPER	15	77087751	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		77087751	25443641	73	8042											
TMED3	23423	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	79606106	79606106	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatggttgtcaggtcatcaCtggaggccactacgatgttg	8	13	12	8	1	3	0	3	0	0	0	3	2	3	1	1	4	1	2	1	4	2	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr15:79606106C>G	ENST00000299705.5	+	2	364	c.176C>G	c.(175-177)aCt>aGt	p.T59S	TMED3_ENST00000536821.1_Missense_Mutation_p.T59S|TMED3_ENST00000424155.2_Missense_Mutation_p.T59S	NM_007364.2	NP_031390.1	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 protein transport domain containing 3	59	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|skin(1)	9						CAGGTCATCACTGGAGGCCAC	0.478																																					p.T59S		.											.	TMED3-92	0			c.C176G						.						94	82	86					15																	79606106		2196	4293	6489	SO:0001583	missense	23423	exon2			TCATCACTGGAGG	BC022232	CCDS10310.1, CCDS73768.1	15q24-q25	2011-02-09	2005-08-26	2005-01-07	ENSG00000166557	ENSG00000166557			28889	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 22", "transmembrane emp24 domain containing 3"	C15orf22		12975309	Standard	XM_005254263		Approved	p24B	uc002beu.3	Q9Y3Q3	OTTHUMG00000144170	ENST00000299705.5:c.176C>G	15.37:g.79606106C>G	ENSP00000299705:p.Thr59Ser	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	51	8	NM_007364	0	0	0	0	0	A8K069|B4DN05|Q2T9F8	Missense_Mutation	SNP	ENST00000299705.5	37	CCDS10310.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220785	0.58560	.	.	ENSG00000166557	ENST00000299705;ENST00000424155;ENST00000536821;ENST00000543455	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	4.88	4.88	0.63580	GOLD (3);	0.258714	0.39407	N	0.001373	T	0.12220	0.0297	L	0.28694	0.88	0.47698	D	0.999498	B;B	0.29085	0.232;0.004	B;B	0.35607	0.206;0.01	T	0.06954	-1.0798	10	0.08599	T	0.76	-25.4826	15.9067	0.79436	0.0:1.0:0.0:0.0	.	59;59	B4DN05;Q9Y3Q3	.;TMED3_HUMAN	S	59	ENSP00000299705:T59S;ENSP00000414983:T59S;ENSP00000446062:T59S;ENSP00000440228:T59S	ENSP00000299705:T59S	T	+	2	0	TMED3	77393161	0.995000	0.38212	0.976000	0.42696	0.985000	0.73830	3.616000	0.54174	2.680000	0.91292	0.655000	0.94253	ACT	.		0.478	TMED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291369.1	NM_007364		G	79606106	C	G	79606106	3	3	88	1	0	0	0	0	1	0	0	0	16037	565	20	4	182	4	TMED3	15	79606106	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	2518355	79606106	22925286	74	8043											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2808492	2808492	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttgttcgggagtctagcagTtctcgctcaccaaccccaaa	9	10	8	14	2	3	0	1	0	2	0	5	1	3	1	3	1	2	4	3	1	3	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:2808492T>A	ENST00000301740.8	+	5	1086	c.537T>A	c.(535-537)agT>agA	p.S179R		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	179	Ser-rich.			SS -> NN (in Ref. 2; AAF21439). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AGTCTAGCAGTTCTCGCTCAC	0.423																																					p.S179R		.											.	SRRM2-93	0			c.T537A						.						161	166	165					16																	2808492		2198	4300	6498	SO:0001583	missense	23524	exon5			TAGCAGTTCTCGC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.537T>A	16.37:g.2808492T>A	ENSP00000301740:p.Ser179Arg	Somatic	268	0		WXS	Illumina HiSeq	Phase_I	274	50	NM_016333	0	0	31	48	17	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.195477	0.58126	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000396975;ENST00000426305	T	0.25250	1.81	5.15	2.81	0.32909	.	0.000000	0.64402	D	0.000006	T	0.29749	0.0743	N	0.19112	0.55	0.32407	N	0.551109	D	0.71674	0.998	D	0.76071	0.987	T	0.32955	-0.9887	10	0.87932	D	0	-4.3082	6.3143	0.21182	0.0:0.2621:0.0:0.7379	.	179	Q9UQ35	SRRM2_HUMAN	R	179;179;83;144	ENSP00000301740:S179R	ENSP00000301740:S179R	S	+	3	2	SRRM2	2748493	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.382000	0.20635	0.797000	0.33971	0.528000	0.53228	AGT	.		0.423	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2808492	T	A	2808492	3	1	88	1	0	0	0	0	1	0	0	0	15201	1722	60	5	551	5	SRRM2	16	2808492	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		2808492	87546261	75	8044											
SRCAP	10847	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30750805	30750805	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggccccagttggtgggagTcctgggctggcaaagcgggg	5	6	21	9	1	0	0	0	0	0	0	1	1	1	1	3	8	1	3	3	8	1	1	rs142948420	byFrequency	TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:30750805T>A	ENST00000262518.4	+	34	9829	c.9444T>A	c.(9442-9444)agT>agA	p.S3148R	SRCAP_ENST00000344771.4_Missense_Mutation_p.S2990R|RP11-2C24.4_ENST00000483578.1_lincRNA|SRCAP_ENST00000395059.2_Missense_Mutation_p.S3086R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	3148					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			TTGGTGGGAGTCCTGGGCTGG	0.647																																					p.S3148R													.	SRCAP-94	0			c.T9444A						.						21	25	24					16																	30750805		2197	4299	6496	SO:0001583	missense	10847	exon34			TGGGAGTCCTGGG	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.9444T>A	16.37:g.30750805T>A	ENSP00000262518:p.Ser3148Arg	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	40	6	NM_006662	0	1	48	81	32	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	T	6.071	0.381466	0.11524	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.92048	-2.95;-2.96;-2.96	4.97	-3.81	0.04294	.	0.629076	0.14021	N	0.346808	T	0.79287	0.4420	N	0.08118	0	0.09310	N	1	B;B	0.25105	0.118;0.021	B;B	0.30401	0.115;0.039	T	0.69022	-0.5255	10	0.87932	D	0	-0.0059	3.9292	0.09276	0.1722:0.5003:0.1321:0.1954	.	3086;3148	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	R	3148;3086;2990	ENSP00000262518:S3148R;ENSP00000378499:S3086R;ENSP00000343042:S2990R	ENSP00000262518:S3148R	S	+	3	2	SRCAP	30658306	0.586000	0.26782	0.072000	0.20136	0.980000	0.70556	-0.209000	0.09358	-0.600000	0.05790	0.379000	0.24179	AGT	T|0.997;C|0.003		0.647	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30750805	T	A	30750805	3	1	88	1	0	0	0	0	1	0	0	0	15167	1664	58	5	9570	5	SRCAP	16	30750805	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	27942313	30750805	59603948	76	8045											
HEATR3	55027	bcgsc.ca	37	chr16	50112873	50112889	+	Frame_Shift_Del	DEL	GGAATTTCTCATAAAAG	GGAATTTCTCATAAAAG	-																															ttgaagatgatgaaatggaaGgaatttctcataaaagaaga																								rs11645775		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	GGAATTTCTCATAAAAG	GGAATTTCTCATAAAAG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:50112873_50112889delGGAATTTCTCATAAAAG	ENST00000299192.7	+	7	1176_1192	c.985_1001delGGAATTTCTCATAAAAG	c.(985-1002)ggaatttctcataaaagafs	p.GISHKR329fs	HEATR3_ENST00000285767.4_Frame_Shift_Del_p.GISHKR243fs	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	329										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TGAAATGGAAGGAATTTCTCATAAAAGAAGAGTCAGA	0.369																																					p.329_334del													.	HEATR3-92	0			c.985_1001del						.																																			SO:0001589	frameshift_variant	55027	exon7			ATGGAAGGAATTT	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.985_1001delGGAATTTCTCATAAAAG	16.37:g.50112873_50112889delGGAATTTCTCATAAAAG	ENSP00000299192:p.Gly329fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_1	72	6	NM_182922	0	0	0	0	0	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Frame_Shift_Del	DEL	ENST00000299192.7	37	CCDS10739.1																																																																																			.		0.369	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		-	50112889	GGAATTTCTCATAAAAG	-	50112873	7	5	88	1	0	1	0	1	0	0	0	0	7050	1001	35	0	1011	0	HEATR3	16	50112873	Frame_Shift_Del	DEL	GGAATTTCTCATAAAAG	TCGA-BQ-7059-01A-11D-1961-08	19362068	50112873	40241880	77	8046											
ELMO3	1874	broad.mit.edu;bcgsc.ca	37	chr16	67233265	67233265	+	IGR	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgtggtgaagattgccatCaagatgcgtgacgccatccc	11	8	11	11	3	1	4	1	2	0	2	2	4	2	4	3	1	3	0	3	1	3	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:67233265C>A	ENST00000379378.3	+	0	2096				ELMO3_ENST00000477898.1_5'Flank|ELMO3_ENST00000393997.2_Silent_p.I65I|ELMO3_ENST00000360833.1_Silent_p.I65I|MIR328_ENST00000385213.1_RNA	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		AGATTGCCATCAAGATGCGTG	0.682																																					p.I65I													.	ELMO3-90	0			c.C195A						.						32	40	37					16																	67233265		2111	4222	6333	SO:0001628	intergenic_variant	79767	exon1			TGCCATCAAGATG	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67233265C>A		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	86	15	NM_024712	0	0	0	8	8	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	37	CCDS32464.1																																																																																			.		0.682	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		A	67233265	C	A	67233265	1	1	88	0	1	0	0	0	0	0	0	0	5080	816	29	4		4	ELMO3	16	67233265	IGR	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	17120392	67233265	23121488	78	8047											
WSCD1	23302	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	6012935	6012935	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttccctggcaggagttcccCttggccattctcaggggctg	4	11	13	13	0	1	0	1	0	1	0	4	1	3	1	4	5	0	4	4	5	0	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:6012935C>G	ENST00000574946.1	+	6	1248	c.858C>G	c.(856-858)ccC>ccG	p.P286P	WSCD1_ENST00000539421.1_Silent_p.P286P|WSCD1_ENST00000317744.5_Silent_p.P286P|WSCD1_ENST00000574232.1_Silent_p.P286P|WSCD1_ENST00000573634.1_Silent_p.P170P			Q658N2	WSCD1_HUMAN	WSC domain containing 1	286	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)	p.P286P(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						AGGAGTTCCCCTTGGCCATTC	0.557																																					p.P286P		.											.	WSCD1-90	1	Substitution - coding silent(1)	endometrium(1)	c.C858G						.						260	245	250					17																	6012935		2203	4300	6503	SO:0001819	synonymous_variant	23302	exon6			GTTCCCCTTGGCC		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.858C>G	17.37:g.6012935C>G		Somatic	483	1		WXS	Illumina HiSeq	Phase_I	392	87	NM_015253	0	0	0	0	0	A8K0N8|D3DTM3|O60276|Q96G45	Silent	SNP	ENST00000574946.1	37	CCDS32538.1																																																																																			.		0.557	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		G	6012935	C	G	6012935	2	3	88	1	0	0	0	0	0	0	0	1	17439	668	24	4		4	WSCD1	17	6012935	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		6012935	75182275	79	8048											
POLR2A	5430	ucsc.edu	37	chr17	7414839	7414839	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggacggcgtgagcttgatgCgggtgctgagtgagaaggac	8	7	19	7	4	0	4	0	4	0	1	0	7	0	6	0	4	3	2	0	4	1	1	rs142714917		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:7414839C>T	ENST00000322644.6	+	24	4432	c.4033C>T	c.(4033-4035)Cgg>Tgg	p.R1345W		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1345					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GAGCTTGATGCGGGTGCTGAG	0.572																																					p.R1345W													.	POLR2A-91	0			c.C4033T						.	C	TRP/ARG	0,4406		0,0,2203	138	99	112		4033	4.6	1	17	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	missense	POLR2A	NM_000937.4	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1345/1971	7414839	1,13005	2203	4300	6503	SO:0001583	missense	5430	exon24			TTGATGCGGGTGC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4033C>T	17.37:g.7414839C>T	ENSP00000314949:p.Arg1345Trp	Somatic	40	0		WXS	Illumina HiSeq		40	4	NM_000937	0	0	110	110	0	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313368	0.81358	0.0	1.16E-4	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.77620	-1.11	4.59	4.59	0.56863	RNA polymerase Rpb1, domain 5 (1);	0.000000	0.64402	D	0.000001	D	0.86230	0.5883	M	0.76170	2.325	0.80722	D	1	D	0.76494	0.999	P	0.61658	0.892	D	0.88200	0.2883	10	0.87932	D	0	-10.9548	16.7406	0.85458	0.0:1.0:0.0:0.0	.	1345	P24928	RPB1_HUMAN	W	1301;244;1345	ENSP00000314949:R1345W	ENSP00000314949:R1345W	R	+	1	2	SLC35G6	7355563	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.890000	0.39728	2.564000	0.86499	0.449000	0.29647	CGG	C|1.000;T|0.000		0.572	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		T	7414839	C	T	7414839	3	4	88	1	0	0	0	0	1	0	0	0	12240	759	27	1	4127	1	POLR2A	17	7414839	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	1401904	7414839	73780371	80	8049											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	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_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	377	53		WXS	Illumina HiSeq		397	58	NM_145301	0	0	5	40	35	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		T	15457087	C	T	15457087	3	4	88	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	8042248	15457087	65738123	81	8050											
ZNF830	91603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33289281	33289281	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgagaaagcagaaatacaTgaaaaagtggtggaaaggag	20	6	13	2	0	0	3	0	2	0	2	0	6	0	5	0	3	2	1	0	3	6	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:33289281T>C	ENST00000361952.3	+	1	733	c.696T>C	c.(694-696)caT>caC	p.H232H	CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000421975.3_5'Flank|CCT6B_ENST00000436961.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	232					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				CAGAAATACATGAAAAAGTGG	0.448																																					p.H232H		.											.	ZNF830-89	0			c.T696C						.						49	48	48					17																	33289281		2203	4300	6503	SO:0001819	synonymous_variant	91603	exon1			AATACATGAAAAA	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.696T>C	17.37:g.33289281T>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	59	16	NM_052857	0	0	18	32	14	Q96F60|Q96GZ5|Q9BU38	Silent	SNP	ENST00000361952.3	37	CCDS32618.1																																																																																			.		0.448	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		C	33289281	T	C	33289281	2	2	88	1	0	0	0	0	0	0	0	1	18216	1461	51	3		3	ZNF830	17	33289281	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	17832194	33289281	47905929	82	8051											
NR1D1	9572	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	38253601	38253601	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcactatagagggattcAgggctggtgcggcttgggga	7	11	17	6	1	2	1	2	0	0	1	2	3	2	3	0	6	1	2	0	6	2	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:38253601A>G	ENST00000246672.3	-	2	717	c.87T>C	c.(85-87)ccT>ccC	p.P29P		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	29	Modulating.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					AGAGGGATTCAGGGCTGGTGC	0.592																																					p.P29P		.											.	NR1D1-226	0			c.T87C						.						57	62	60					17																	38253601		2203	4300	6503	SO:0001819	synonymous_variant	9572	exon2			GGATTCAGGGCTG	X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"Nuclear hormone receptors"	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.87T>C	17.37:g.38253601A>G		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	30	12	NM_021724	0	0	23	51	28	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	37	CCDS11361.1																																																																																			.		0.592	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1			G	38253601	A	G	38253601	2	3	88	1	0	0	0	0	0	0	0	1	10641	175	7	3		3	NR1D1	17	38253601	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	4964320	38253601	42941609	83	8052											
NAGS	162417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42083544	42083544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgtcgctggccaaggcgcTgcggcccaccaaaatcatct	8	6	11	16	5	2	0	1	0	1	0	3	0	2	0	3	3	1	2	3	3	3	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:42083544T>C	ENST00000293404.3	+	3	972	c.854T>C	c.(853-855)cTg>cCg	p.L285P	PYY_ENST00000360085.2_5'Flank	NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	285	Amino-acid kinase domain (AAK).				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCCAAGGCGCTGCGGCCCACC	0.662																																					p.L285P		.											.	NAGS-90	0			c.T854C						.						29	29	29					17																	42083544		2200	4297	6497	SO:0001583	missense	162417	exon3			AGGCGCTGCGGCC	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.854T>C	17.37:g.42083544T>C	ENSP00000293404:p.Leu285Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	60	14	NM_153006	0	0	0	0	0	B2RAZ9|Q8IWR4	Missense_Mutation	SNP	ENST00000293404.3	37	CCDS11473.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478496	0.84747	.	.	ENSG00000161653	ENST00000541745;ENST00000293404	D	0.94576	-3.46	4.49	4.49	0.54785	Aspartate/glutamate/uridylate kinase (2);	0.000000	0.64402	D	0.000014	D	0.96815	0.8960	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	D	0.97143	0.9826	10	0.87932	D	0	-18.0769	11.7799	0.52008	0.0:0.0:0.0:1.0	.	119;285	Q2NKP2;Q8N159	.;NAGS_HUMAN	P	119;285	ENSP00000293404:L285P	ENSP00000293404:L285P	L	+	2	0	NAGS	39439070	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.544000	0.73878	1.883000	0.54544	0.374000	0.22700	CTG	.		0.662	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006		C	42083544	T	C	42083544	3	2	88	1	0	0	0	0	1	0	0	0	10170	1580	55	3	864	3	NAGS	17	42083544	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	3829943	42083544	39111666	84	8053											
DCXR	51181	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79994491	79994491	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacgatggcccctgggactCcccgggctattaagcccctg	6	8	11	16	2	1	0	1	0	0	0	2	2	2	1	6	3	1	1	6	3	2	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:79994491C>A	ENST00000306869.2	-	5	426	c.377G>T	c.(376-378)gGa>gTa	p.G126V	RP13-650J16.1_ENST00000584705.1_RNA|DCXR_ENST00000584318.1_5'UTR|RP13-650J16.1_ENST00000582558.1_RNA	NM_001195218.1|NM_016286.3	NP_001182147.1|NP_057370.1	Q7Z4W1	DCXR_HUMAN	dicarbonyl/L-xylulose reductase	126					D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997)	brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)	L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)			kidney(1)|lung(3)	4	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CCCTGGGACTCCCCGGGCTAT	0.622																																					p.G126V													.	DCXR-90	0			c.G377T						.						47	52	50					17																	79994491		2203	4300	6503	SO:0001583	missense	51181	exon5			GGGACTCCCCGGG	AB013846	CCDS11799.1	17q25.3	2011-09-14				ENSG00000169738	1.1.1.10	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18985	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 20C, member 1"	608347				11882650, 19027726	Standard	NM_016286		Approved	KIDCR, DCR, SDR20C1	uc002kdg.3	Q7Z4W1		ENST00000306869.2:c.377G>T	17.37:g.79994491C>A	ENSP00000303356:p.Gly126Val	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	85	16	NM_016286	0	0	99	143	44	Q9BTZ3|Q9UHY9	Missense_Mutation	SNP	ENST00000306869.2	37	CCDS11799.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987714	0.35036	.	.	ENSG00000169738	ENST00000306869	T	0.33216	1.42	5.12	5.12	0.69794	NAD(P)-binding domain (1);	0.136289	0.49305	D	0.000159	T	0.61912	0.2385	M	0.89163	3.01	0.80722	D	1	D	0.63046	0.992	D	0.64687	0.928	T	0.69595	-0.5103	9	.	.	.	.	18.5287	0.90983	0.0:1.0:0.0:0.0	.	126	Q7Z4W1	DCXR_HUMAN	V	126	ENSP00000303356:G126V	.	G	-	2	0	DCXR	77587780	1.000000	0.71417	0.825000	0.32803	0.457000	0.32468	5.611000	0.67674	2.355000	0.79922	0.655000	0.94253	GGA	.		0.622	DCXR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442153.2			A	79994491	C	A	79994491	3	1	88	1	0	0	0	0	1	0	0	0	4325	855	30	4	373	4	DCXR	17	79994491	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	37910947	79994491	1200719	85	8054											
SCAMP4	113178	ucsc.edu	37	chr19	1924169	1924169	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcacagacggagtggaacacGggcacttggcggaacccacc	11	3	14	13	3	0	1	0	0	0	1	0	4	0	4	2	5	2	2	2	5	2	1	rs574299368		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:1924169G>A	ENST00000316097.8	+	7	843	c.576G>A	c.(574-576)acG>acA	p.T192T	SCAMP4_ENST00000409472.1_Silent_p.T158T	NM_079834.2	NP_524558.1	Q969E2	SCAM4_HUMAN	secretory carrier membrane protein 4	192					protein transport (GO:0015031)	integral component of membrane (GO:0016021)							Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTGGAACACGGGCACTTGGC	0.617													G|||	1	0.000199681	0	0	5008	,	,		15318	0		0	False		,,,				2504	0.001				p.T192T													.	SCAMP4-68	0			c.G576A						.						42	52	49					19																	1924169		2033	4178	6211	SO:0001819	synonymous_variant	113178	exon7			GAACACGGGCACT	AK091166	CCDS45903.1	19p13.3	2013-02-21			ENSG00000227500	ENSG00000227500		"Secretory carrier membrane proteins"	30385	protein-coding gene	gene with protein product		613764					Standard	NM_079834		Approved	FLJ33847	uc002luj.4	Q969E2	OTTHUMG00000154590	ENST00000316097.8:c.576G>A	19.37:g.1924169G>A		Somatic	14	0		WXS	Illumina HiSeq		21	3	NM_079834	0	0	37	67	30	Q8N2N1|Q8NAV0	Silent	SNP	ENST00000316097.8	37	CCDS45903.1	.	.	.	.	.	.	.	.	.	.	g	0.171	-1.071883	0.01918	.	.	ENSG00000227500	ENST00000414057	.	.	.	4.97	-9.94	0.00449	.	.	.	.	.	T	0.35508	0.0934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44467	-0.9326	4	.	.	.	-22.8526	3.3328	0.07091	0.1707:0.2631:0.3836:0.1826	.	.	.	.	Q	202	.	.	R	+	2	0	SCAMP4	1875169	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-7.020000	0.00046	-2.994000	0.00278	-0.487000	0.04747	CGG	.		0.617	SCAMP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336210.3	NM_079834		A	1924169	G	A	1924169	2	1	88	1	0	0	0	0	0	0	0	1	13905	1103	39	1		1	SCAMP4	19	1924169	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08		1924169	57204814	86	8055											
TMEM146	257062	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	5744442	5744442	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtttgtttcataggcagAaatcattgggtctttaggcg	8	16	11	6	1	4	1	2	0	2	1	4	1	4	1	0	3	0	3	0	3	3	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:5744442A>G	ENST00000381624.3	+	8	639	c.578A>G	c.(577-579)gAa>gGa	p.E193G	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	193					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											TCATAGGCAGAAATCATTGGG	0.368																																					p.E193G		.											.	.	0			c.A578G						.						177	156	162					19																	5744442		1821	4093	5914	SO:0001583	missense	257062	exon8			AGGCAGAAATCAT	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.578A>G	19.37:g.5744442A>G	ENSP00000371037:p.Glu193Gly	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	125	16	NM_152784	0	0	0	0	0	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	A	11.28	1.590905	0.28357	.	.	ENSG00000174898	ENST00000394548;ENST00000381624	T	0.16597	2.33	2.61	-0.961	0.10337	.	1.018470	0.07916	U	0.975045	T	0.14227	0.0344	L	0.60455	1.87	0.09310	N	0.999999	P	0.46512	0.879	B	0.40009	0.316	T	0.20974	-1.0259	10	0.66056	D	0.02	.	0.3749	0.00385	0.3898:0.2527:0.1457:0.2118	.	193	Q86XM0	TM146_HUMAN	G	119;193	ENSP00000371037:E193G	ENSP00000371037:E193G	E	+	2	0	TMEM146	5695442	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	0.059000	0.14322	-0.283000	0.09115	0.260000	0.18958	GAA	.		0.368	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		G	5744442	A	G	5744442	3	3	88	1	0	0	0	0	1	0	0	0	16092	246	9	3	608	3	TMEM146	19	5744442	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	3820273	5744442	53384541	87	8056											
PNPLA6	10908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7619510	7619510	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caccgtatcgtactctaccaGacggacgcctcgctgacgcc	8	7	9	17	6	1	2	0	1	1	1	3	3	1	3	4	1	2	3	4	1	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:7619510G>A	ENST00000221249.6	+	24	2852	c.2421G>A	c.(2419-2421)caG>caA	p.Q807Q	PNPLA6_ENST00000450331.3_Silent_p.Q807Q|PNPLA6_ENST00000545201.2_Silent_p.Q780Q|PNPLA6_ENST00000600737.1_Silent_p.Q845Q|PNPLA6_ENST00000414982.3_Silent_p.Q855Q	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	846					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						TACTCTACCAGACGGACGCCT	0.667																																					p.Q855Q		.											.	PNPLA6-47	0			c.G2565A						.						87	74	79					19																	7619510		2203	4300	6503	SO:0001819	synonymous_variant	10908	exon23			CTACCAGACGGAC	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"Patatin-like phospholipase domain containing"	16268	protein-coding gene	gene with protein product	"neuropathy target esterase"	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.2421G>A	19.37:g.7619510G>A		Somatic	144	1		WXS	Illumina HiSeq	Phase_I	127	35	NM_001166111	0	1	79	114	34	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																			.		0.667	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		A	7619510	G	A	7619510	2	1	88	1	0	0	0	0	0	0	0	1	12195	933	33	2		2	PNPLA6	19	7619510	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	1875068	7619510	51509473	88	8057											
QTRT1	81890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10823458	10823458	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggctctgccctggtgcccActgggaacctgcagttgagg	5	10	14	12	0	1	1	0	1	1	0	1	2	1	2	3	4	4	3	3	4	1	2	rs568561273		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:10823458A>G	ENST00000250237.5	+	8	896	c.886A>G	c.(886-888)Act>Gct	p.T296A		NM_031209.2	NP_112486.1	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	296					queuosine biosynthetic process (GO:0008616)|tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|queuine tRNA-ribosyltransferase activity (GO:0008479)			large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			CCTGGTGCCCACTGGGAACCT	0.622																																					p.T296A		.											.	QTRT1-91	0			c.A886G						.						118	111	113					19																	10823458		2203	4300	6503	SO:0001583	missense	81890	exon8			GTGCCCACTGGGA	AF302783	CCDS12248.1	19p13.3	2014-06-11	2008-07-31		ENSG00000213339	ENSG00000213339	2.4.2.29		23797	protein-coding gene	gene with protein product	"tRNA-guanine transglycosylase"	609615				20354154	Standard	NM_031209		Approved	TGT	uc002mpr.3	Q9BXR0		ENST00000250237.5:c.886A>G	19.37:g.10823458A>G	ENSP00000250237:p.Thr296Ala	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	228	44	NM_031209	0	0	41	63	22	B4DFM7|Q96BQ4|Q9BXQ9	Missense_Mutation	SNP	ENST00000250237.5	37	CCDS12248.1	.	.	.	.	.	.	.	.	.	.	A	0.571	-0.841326	0.02692	.	.	ENSG00000213339	ENST00000250237	.	.	.	3.87	3.87	0.44632	.	0.163748	0.42821	U	0.000652	T	0.28067	0.0692	L	0.43923	1.385	0.26123	N	0.980526	B	0.14805	0.011	B	0.17433	0.018	T	0.21143	-1.0254	9	0.07990	T	0.79	-8.686	6.4838	0.22077	0.7837:0.0:0.0:0.2163	.	296	Q9BXR0	TGT_HUMAN	A	296	.	ENSP00000250237:T296A	T	+	1	0	QTRT1	10684458	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	5.570000	0.67398	1.631000	0.50456	0.379000	0.24179	ACT	.		0.622	QTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452086.1	NM_031209		G	10823458	A	G	10823458	3	3	88	1	0	0	0	0	1	0	0	0	12917	159	6	3	916	3	QTRT1	19	10823458	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	3203948	10823458	48305525	89	8058											
NOTCH3	4854	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	15289675	15289675	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtcagcccacccccaggacCcgggctaggacggcactggc	7	3	14	17	2	1	0	1	0	0	0	1	2	1	2	4	6	1	2	4	6	1	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:15289675C>G	ENST00000263388.2	-	23	3871	c.3796G>C	c.(3796-3798)Ggt>Cgt	p.G1266R		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1266	EGF-like 32. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CCCCCAGGACCCGGGCTAGGA	0.652																																					p.G1266R		.											.	NOTCH3-855	0			c.G3796C						.						36	32	33					19																	15289675		2198	4296	6494	SO:0001583	missense	4854	exon23			CAGGACCCGGGCT	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"Ankyrin repeat domain containing"	7883	protein-coding gene	gene with protein product		600276	"Notch (Drosophila) homolog 3", "Notch homolog 3 (Drosophila)"	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3796G>C	19.37:g.15289675C>G	ENSP00000263388:p.Gly1266Arg	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_000435	0	0	10	10	0	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333583	0.41297	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.92099	-2.97	3.54	2.41	0.29592	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.94016	0.8083	M	0.72894	2.215	0.09310	N	1	P;D	0.89917	0.566;1.0	B;D	0.87578	0.131;0.998	D	0.84646	0.0698	9	0.54805	T	0.06	.	4.1418	0.10196	0.0:0.7058:0.0:0.2942	.	1217;1266	Q59FL3;Q9UM47	.;NOTC3_HUMAN	R	1266;1216	ENSP00000263388:G1266R	ENSP00000263388:G1266R	G	-	1	0	NOTCH3	15150675	0.011000	0.17503	0.110000	0.21437	0.729000	0.41735	0.970000	0.29383	1.813000	0.52934	0.561000	0.74099	GGT	.		0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		G	15289675	C	G	15289675	3	3	88	1	0	0	0	0	1	0	0	0	10576	623	22	4	3213	4	NOTCH3	19	15289675	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	4466217	15289675	43839308	90	8059											
CEACAM5	1048	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42219580	42219580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctccagatggcccggatGcccccaccatttcccctcta	6	10	7	18	1	1	1	0	0	1	1	3	2	3	2	7	2	2	1	7	2	1	3	rs199857011		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:42219580G>A	ENST00000221992.6	+	4	829	c.715G>A	c.(715-717)Gcc>Acc	p.A239T	CEACAM5_ENST00000398599.4_Missense_Mutation_p.A239T|CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000405816.1_Missense_Mutation_p.A239T	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	239	Ig-like 3.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		TGGCCCGGATGCCCCCACCAT	0.507																																					p.A239T													.	CEACAM5-92	0			c.G715A						.						71	73	73					19																	42219580		2203	4300	6503	SO:0001583	missense	1048	exon4			CCGGATGCCCCCA	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.715G>A	19.37:g.42219580G>A	ENSP00000221992:p.Ala239Thr	Somatic	100	1		WXS	Illumina HiSeq	Phase_I	106	30	NM_004363	0	0	0	0	0	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.003|0.003	-2.415378|-2.415378	0.00191|0.00191	.|.	.|.	ENSG00000105388|ENSG00000105388	ENST00000221992;ENST00000405816|ENST00000398599	T;T|.	0.14144|.	2.53;2.53|.	3.18|3.18	-4.69|-4.69	0.03299|0.03299	.|.	.|.	.|.	.|.	.|.	T|T	0.10981|0.10981	0.0268|0.0268	N|N	0.01771|0.01771	-0.73|-0.73	0.09310|0.09310	N|N	1|1	B;B|.	0.18863|.	0.003;0.031|.	B;B|.	0.26517|.	0.023;0.07|.	T|T	0.34875|0.34875	-0.9811|-0.9811	9|5	0.05833|.	T|.	0.94|.	.|.	8.6733|8.6733	0.34163|0.34163	0.4851:0.0:0.5149:0.0|0.4851:0.0:0.5149:0.0	.|.	239;239|.	P06731;Q53G30|.	CEAM5_HUMAN;.|.	T|Y	239|235	ENSP00000221992:A239T;ENSP00000385072:A239T|.	ENSP00000221992:A239T|.	A|C	+|+	1|2	0|0	CEACAM5|CEACAM5	46911420|46911420	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.028000|0.028000	0.11728|0.11728	-0.933000|-0.933000	0.03959|0.03959	-0.755000|-0.755000	0.04709|0.04709	0.305000|0.305000	0.20034|0.20034	GCC|TGC	G|1.000;T|0.000		0.507	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		A	42219580	G	A	42219580	3	1	88	1	0	0	0	0	1	0	0	0	3201	1319	46	2	729	2	CEACAM5	19	42219580	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	26929905	42219580	16909403	91	8060											
RASIP1	54922	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49230414	49230414	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcggggaccccctcagggtGgcttgaaaaagaggaaggaa	12	5	15	9	1	1	2	1	1	0	1	2	5	1	5	2	6	0	1	2	6	4	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:49230414G>T	ENST00000222145.4	-	7	2077	c.1873C>A	c.(1873-1875)Cac>Aac	p.H625N	RASIP1_ENST00000594232.1_5'Flank	NM_017805.2	NP_060275.2	Q5U651	RAIN_HUMAN	Ras interacting protein 1	625	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|negative regulation of autophagy (GO:0010507)|regulation of Rho GTPase activity (GO:0032319)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	Golgi apparatus (GO:0005794)				central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	21		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000272)|Epithelial(262;0.0155)|GBM - Glioblastoma multiforme(486;0.0222)		CCCTCAGGGTGGCTTGAAAAA	0.552																																					p.H625N													.	RASIP1-228	0			c.C1873A						.						27	30	29					19																	49230414		2202	4300	6502	SO:0001630	splice_region_variant	54922	exon7			CAGGGTGGCTTGA	BC028614	CCDS12731.1	19q13.33	2008-02-05				ENSG00000105538			24716	protein-coding gene	gene with protein product		609623				15031288	Standard	NM_017805		Approved	FLJ20401, RAIN	uc002pki.3	Q5U651		ENST00000222145.4:c.1872-1C>A	19.37:g.49230414G>T		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	44	16	NM_017805	0	0	0	0	0	Q6U676	Missense_Mutation	SNP	ENST00000222145.4	37	CCDS12731.1	.	.	.	.	.	.	.	.	.	.	G	10.31	1.315668	0.23908	.	.	ENSG00000105538	ENST00000222145	T	0.21191	2.02	5.46	4.43	0.53597	Dilute (1);	0.203282	0.40818	N	0.001002	T	0.16981	0.0408	L	0.38838	1.175	0.33974	D	0.647144	B	0.22604	0.072	B	0.18871	0.023	T	0.14587	-1.0467	10	0.32370	T	0.25	-11.7215	12.111	0.53840	0.0837:0.0:0.9163:0.0	.	625	Q5U651	RAIN_HUMAN	N	625	ENSP00000222145:H625N	ENSP00000222145:H625N	H	-	1	0	RASIP1	53922226	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	2.411000	0.44600	1.459000	0.47892	0.591000	0.81541	CAC	.		0.552	RASIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466185.1	NM_017805	Missense_Mutation	T	49230414	G	T	49230414	5	4	88	1	0	0	0	0	0	0	1	0	13110	1362	47	4	1042	4	RASIP1	19	49230414	Splice_Site	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	7010834	49230414	9898569	92	8061											
IL4I1	259307	ucsc.edu	37	chr19	50397531	50397531	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caggcggtacccacctggttGagagccatctggtagatgtc	8	9	13	11	1	1	2	0	1	1	2	2	3	1	2	3	4	2	3	3	4	2	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:50397531G>C	ENST00000391826.2	-	5	703	c.561C>G	c.(559-561)ctC>ctG	p.L187L	IL4I1_ENST00000341114.3_Silent_p.L209L|IL4I1_ENST00000595948.1_Silent_p.L209L	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	187						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	CCACCTGGTTGAGAGCCATCT	0.622																																					p.L209L													.	IL4I1-523	0			c.C627G						.						90	87	88					19																	50397531		2203	4300	6503	SO:0001819	synonymous_variant	259307	exon7			CTGGTTGAGAGCC	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.561C>G	19.37:g.50397531G>C		Somatic	21	0		WXS	Illumina HiSeq		23	4	NM_172374	0	0	0	0	0	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			.		0.622	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			C	50397531	G	C	50397531	2	2	88	1	0	0	0	0	0	0	0	1	7718	1277	45	4		4	IL4I1	19	50397531	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	1167117	50397531	8731452	93	8062											
GPR32	2854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	51273914	51273914	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacaggcaacctggggtcctGacacgtgatcgctcttgttc	7	10	12	12	2	1	2	0	2	1	0	4	3	2	2	2	3	1	3	2	3	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:51273914G>C	ENST00000270590.4	+	1	194	c.57G>C	c.(55-57)ctG>ctC	p.L19L		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	19					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CTGGGGTCCTGACACGTGATC	0.512																																					p.L19L	Esophageal Squamous(113;152 1581 5732 15840 44398)	.											.	GPR32-91	0			c.G57C						.						80	65	70					19																	51273914		2203	4300	6503	SO:0001819	synonymous_variant	2854	exon1			GGTCCTGACACGT	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"GPCR / Class A : Resolvin receptors"	4487	protein-coding gene	gene with protein product	"resolvin D1 receptor"	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.57G>C	19.37:g.51273914G>C		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	45	8	NM_001506	0	0	0	0	0	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	37	CCDS12801.1																																																																																			.		0.512	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			C	51273914	G	C	51273914	2	2	88	1	0	0	0	0	0	0	0	1	6708	1277	45	4		4	GPR32	19	51273914	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	876383	51273914	7855069	94	8063											
ZNF416	55659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58084258	58084258	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatgttcaataaggttggaActttggctaaaagatttccc	13	13	8	7	0	1	1	1	0	0	1	2	2	2	2	1	3	1	3	1	3	6	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:58084258A>G	ENST00000196489.3	-	4	1236	c.1014T>C	c.(1012-1014)agT>agC	p.S338S		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	338					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(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		TAAGGTTGGAACTTTGGCTAA	0.428																																					p.S338S		.											.	ZNF416-90	0			c.T1014C						.						96	93	94					19																	58084258		2203	4300	6503	SO:0001819	synonymous_variant	55659	exon4			GTTGGAACTTTGG	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"Zinc fingers, C2H2-type", "-"	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.1014T>C	19.37:g.58084258A>G		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	75	15	NM_017879	0	0	4	6	2	Q9NWW8	Silent	SNP	ENST00000196489.3	37	CCDS12954.1																																																																																			.		0.428	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		G	58084258	A	G	58084258	2	3	88	1	0	0	0	0	0	0	0	1	17925	40	2	3		3	ZNF416	19	58084258	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	6810344	58084258	1044725	95	8064											
CSE1L	1434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47691344	47691344	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgatgaagaagcatttgaAgataattctgaggagtacat	15	11	11	4	0	1	6	0	4	1	2	1	7	1	7	0	1	2	3	0	1	5	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr20:47691344A>G	ENST00000262982.2	+	11	1212	c.1089A>G	c.(1087-1089)gaA>gaG	p.E363E	CSE1L_ENST00000396192.3_Silent_p.E307E|CSE1L_ENST00000542325.1_Silent_p.E146E	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	363					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AAGCATTTGAAGATAATTCTG	0.383																																					p.E363E		.											.	CSE1L-290	0			c.A1089G						.						172	158	163					20																	47691344		2203	4300	6503	SO:0001819	synonymous_variant	1434	exon11			ATTTGAAGATAAT	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.1089A>G	20.37:g.47691344A>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	58	12	NM_001316	0	0	25	50	25	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	37	CCDS13412.1																																																																																			.		0.383	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		G	47691344	A	G	47691344	2	3	88	1	0	0	0	0	0	0	0	1	3936	69	3	3		3	CSE1L	20	47691344	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		47691344	15334176	96	8065											
BRWD1	54014	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	40582820	40582820	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttccagttgctttcaacataGttcgtagctctgatgctttt	7	18	7	9	1	2	1	1	1	1	0	4	1	3	1	1	0	4	6	1	0	3	8			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr21:40582820G>T	ENST00000333229.2	-	35	4263	c.3936C>A	c.(3934-3936)aaC>aaA	p.N1312K	BRWD1_ENST00000380800.3_Missense_Mutation_p.N1312K|BRWD1_ENST00000342449.3_Missense_Mutation_p.N1312K	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1312					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TTTCAACATAGTTCGTAGCTC	0.348																																					p.N1312K	Melanoma(170;988 1986 4794 16843 39731)												.	BRWD1-94	0			c.C3936A						.						108	100	103					21																	40582820		2203	4300	6503	SO:0001583	missense	54014	exon35			AACATAGTTCGTA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.3936C>A	21.37:g.40582820G>T	ENSP00000330753:p.Asn1312Lys	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	72	14	NM_018963	0	0	2	5	3	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	G	7.370	0.626714	0.14257	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.53857	0.6;0.62;0.7	5.36	2.35	0.29111	Bromodomain (1);	1.097550	0.06850	N	0.797170	T	0.36054	0.0953	L	0.34521	1.04	0.09310	N	0.999994	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.29640	-1.0005	10	0.07644	T	0.81	-0.1417	5.4851	0.16745	0.1606:0.0:0.5729:0.2665	.	1312;1312	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	K	1312	ENSP00000330753:N1312K;ENSP00000344333:N1312K;ENSP00000370178:N1312K	ENSP00000330753:N1312K	N	-	3	2	BRWD1	39504690	0.688000	0.27680	0.321000	0.25320	0.990000	0.78478	1.019000	0.30014	1.346000	0.45694	0.585000	0.79938	AAC	.		0.348	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40582820	G	T	40582820	3	4	88	1	0	0	0	0	1	0	0	0	1528	1020	36	4	3297	4	BRWD1	21	40582820	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08		40582820	7547075	97	8066											
TXN2	25828	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	36876727	36876727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaggagatcctcgtggtgTatattgtccgggctgggttg	6	13	15	7	2	1	1	1	0	0	1	4	2	3	1	2	4	0	3	2	4	3	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr22:36876727T>C	ENST00000216185.2	-	2	624	c.158A>G	c.(157-159)tAc>tGc	p.Y53C	TXN2_ENST00000416967.1_De_novo_Start_OutOfFrame|TXN2_ENST00000403313.1_Missense_Mutation_p.Y53C|TXN2_ENST00000487725.1_5'UTR			Q99757	THIOM_HUMAN	thioredoxin 2	53					cell redox homeostasis (GO:0045454)|cellular response to nutrient levels (GO:0031669)|glycerol ether metabolic process (GO:0006662)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)	dendrite (GO:0030425)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)	protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|lung(1)|prostate(1)	3						CCTCGTGGTGTATATTGTCCG	0.542																																					p.Y53C		.											.	TXN2-90	0			c.A158G						.						162	137	145					22																	36876727		2203	4300	6503	SO:0001583	missense	25828	exon2			GTGGTGTATATTG	U78678	CCDS13928.1	22q13.1	2008-06-11			ENSG00000100348	ENSG00000100348			17772	protein-coding gene	gene with protein product		609063				9006939, 17220299	Standard	NM_012473		Approved	MT-TRX	uc003apk.1	Q99757	OTTHUMG00000150596	ENST00000216185.2:c.158A>G	22.37:g.36876727T>C	ENSP00000216185:p.Tyr53Cys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	117	24	NM_012473	0	0	113	183	70	Q5JZA0|Q6FH60|Q9UH29	Missense_Mutation	SNP	ENST00000216185.2	37	CCDS13928.1	.	.	.	.	.	.	.	.	.	.	t	4.360	0.066374	0.08388	.	.	ENSG00000100348	ENST00000216185;ENST00000403313	T;T	0.11495	2.77;2.77	5.59	-4.59	0.03400	Thioredoxin-like fold (1);	1.054490	0.07330	N	0.879042	T	0.07413	0.0187	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44559	-0.9320	10	0.38643	T	0.18	.	0.2548	0.00210	0.3331:0.1924:0.2444:0.2301	.	53	Q99757	THIOM_HUMAN	C	53	ENSP00000216185:Y53C;ENSP00000385393:Y53C	ENSP00000216185:Y53C	Y	-	2	0	TXN2	35206673	0.001000	0.12720	0.004000	0.12327	0.028000	0.11728	-0.205000	0.09411	-0.499000	0.06623	-0.459000	0.05422	TAC	.		0.542	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473		C	36876727	T	C	36876727	3	2	88	1	0	0	0	0	1	0	0	0	16824	1638	57	3	354	3	TXN2	22	36876727	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		36876727	14427839	98	8067											
VSIG4	11326	ucsc.edu	37	chrX	65244923	65244923	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatggtaaaaaccaccataCagcacaaggagatgatgagg	17	5	10	9	0	0	3	0	2	0	1	0	4	0	3	3	3	3	2	3	3	5	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chrX:65244923C>T	ENST00000374737.4	-	6	992	c.884G>A	c.(883-885)tGt>tAt	p.C295Y	VSIG4_ENST00000455586.2_Missense_Mutation_p.C295Y|VSIG4_ENST00000412866.2_Missense_Mutation_p.C201Y	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	295					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AACCACCATACAGCACAAGGA	0.423																																					p.C295Y													.	VSIG4-130	0			c.G884A						.						125	89	101					X																	65244923		2203	4300	6503	SO:0001583	missense	11326	exon6			ACCATACAGCACA	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.884G>A	X.37:g.65244923C>T	ENSP00000363869:p.Cys295Tyr	Somatic	13	0		WXS	Illumina HiSeq		16	4	NM_001257403	0	0	160	160	0	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	.	.	.	.	.	.	.	.	.	.	C	8.447	0.852121	0.17034	.	.	ENSG00000155659	ENST00000374737;ENST00000455586;ENST00000412866	T;T;T	0.33654	1.54;1.4;1.81	4.29	1.42	0.22433	.	0.346876	0.24755	N	0.035868	T	0.49150	0.1540	M	0.72894	2.215	0.09310	N	1	B;D;D;D;D	0.76494	0.031;0.994;0.995;0.999;0.996	B;P;D;D;P	0.85130	0.01;0.904;0.986;0.997;0.804	T	0.33007	-0.9885	10	0.87932	D	0	-4.7028	1.7676	0.03005	0.2098:0.4659:0.2011:0.1232	.	201;295;285;201;295	C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.;.;.;.;VSIG4_HUMAN	Y	295;295;201	ENSP00000363869:C295Y;ENSP00000411581:C295Y;ENSP00000394143:C201Y	ENSP00000363869:C295Y	C	-	2	0	VSIG4	65161648	0.353000	0.24904	0.032000	0.17829	0.007000	0.05969	0.388000	0.20735	0.827000	0.34685	-0.191000	0.12829	TGT	.		0.423	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		T	65244923	C	T	65244923	3	4	88	1	0	0	0	0	1	0	0	0	17258	478	17	2	331	2	VSIG4	23	65244923	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		65244923	90025637	99	8068											
THOC2	57187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	122770007	122770007	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatatttacgaaaaactgcAccacagaaactagccagacc	17	6	7	11	1	0	2	0	0	0	2	0	4	0	3	3	1	5	1	3	1	6	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chrX:122770007A>G	ENST00000245838.8	-	19	1972	c.1941T>C	c.(1939-1941)ggT>ggC	p.G647G	THOC2_ENST00000491737.1_Silent_p.G532G|THOC2_ENST00000355725.4_Silent_p.G647G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	647					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						GAAAAACTGCACCACAGAAAC	0.323																																					p.G647G		.											.	THOC2-133	0			c.T1941C						.						99	82	88					X																	122770007		1821	4069	5890	SO:0001819	synonymous_variant	57187	exon19			AACTGCACCACAG	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.1941T>C	X.37:g.122770007A>G		Somatic	59	1		WXS	Illumina HiSeq	Phase_I	72	36	NM_001081550	0	0	1	12	11	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																			.		0.323	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			G	122770007	A	G	122770007	2	3	88	1	0	0	0	0	0	0	0	1	15897	146	6	3		3	THOC2	23	122770007	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	57525084	122770007	32500553	100	8069											
ZNF275	10838	ucsc.edu	37	chrX	152613054	152613054	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcggcaagctcttccgaaGgagctcggagctcaccaagc	9	6	12	14	3	2	0	1	0	1	0	4	3	3	2	2	3	5	4	2	3	3	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chrX:152613054G>A	ENST00000421401.3	+	4	1088	c.911G>A	c.(910-912)aGg>aAg	p.R304K	ZNF275_ENST00000370251.3_Missense_Mutation_p.R304K|ZNF275_ENST00000440091.1_Missense_Mutation_p.R334K|ZNF275_ENST00000370249.2_Missense_Mutation_p.R251K			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	304					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTCTTCCGAAGGAGCTCGGAG	0.682																																					p.R304K													.	ZNF275-109	0			c.G911A						.						17	19	18					X																	152613054		2195	4290	6485	SO:0001583	missense	10838	exon4			TCCGAAGGAGCTC	BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"Zinc fingers, C2H2-type", "-"	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.911G>A	X.37:g.152613054G>A	ENSP00000398977:p.Arg304Lys	Somatic	14	0		WXS	Illumina HiSeq		7	2	NM_001080485	0	0	1	6	5	A6NE92	Missense_Mutation	SNP	ENST00000421401.3	37		.	.	.	.	.	.	.	.	.	.	G	14.74	2.624733	0.46840	.	.	ENSG00000063587	ENST00000370251;ENST00000421401;ENST00000440091;ENST00000370249	T;T;T;T	0.57107	0.42;3.2;3.2;3.2	4.49	4.49	0.54785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31051	N	0.008343	T	0.42017	0.1184	L	0.46614	1.455	0.09310	N	1	B;B	0.26635	0.036;0.155	B;B	0.25759	0.017;0.063	T	0.27191	-1.0081	10	0.36615	T	0.2	-33.123	7.5945	0.28039	0.1167:0.0:0.8833:0.0	.	304;304	Q9NSD4;A6NFS0	ZN275_HUMAN;.	K	304;304;334;251	ENSP00000359271:R304K;ENSP00000398977:R304K;ENSP00000411097:R334K;ENSP00000359269:R251K	ENSP00000359269:R251K	R	+	2	0	ZNF275	152266248	0.000000	0.05858	0.488000	0.27440	0.300000	0.27592	0.263000	0.18478	2.218000	0.71995	0.436000	0.28706	AGG	.		0.682	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485		A	152613054	G	A	152613054	3	1	88	1	0	0	0	0	1	0	0	0	17842	1000	35	2	921	2	ZNF275	23	152613054	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	29843047	152613054	2657506	101	8070											
MUL1	79594	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	20827614	20827614	+	Frame_Shift_Del	DEL	G	G	-																															gccttgtttgggcggctgcaGgcggacagagttgttgtcca																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:20827614delG	ENST00000264198.3	-	4	764	c.628delC	c.(628-630)ctgfs	p.L210fs		NM_024544.2	NP_078820.2	Q969V5	MUL1_HUMAN	mitochondrial E3 ubiquitin protein ligase 1	210					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|cellular response to exogenous dsRNA (GO:0071360)|mitochondrial fission (GO:0000266)|mitochondrion localization (GO:0051646)|negative regulation of cell growth (GO:0030308)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of innate immune response (GO:0045824)|negative regulation of mitochondrial fusion (GO:0010637)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein sumoylation (GO:0033235)|protein stabilization (GO:0050821)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)	cytoplasm (GO:0005737)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(5)	11		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		GGCGGCTGCAGGCGGACAGAG	0.607																																					p.L210fs		.											.	MUL1-90	0			c.628delC						.						87	84	85					1																	20827614		2203	4300	6503	SO:0001589	frameshift_variant	79594	exon4			.	BC014010	CCDS208.1	1p36.12	2013-01-11	2010-09-17	2008-03-26	ENSG00000090432	ENSG00000090432		"RING-type (C3HC4) zinc fingers"	25762	protein-coding gene	gene with protein product	"ring finger protein 218", "mitochondria-anchored protein ligase", "growth inhibition and death E3 ligase", "mitochondrial ubiquitin ligase activator of NFKB 1"	612037	"chromosome 1 open reading frame 166"	C1orf166		18591963, 12761501, 18213395, 18207745	Standard	NM_024544		Approved	FLJ12875, MULAN, RNF218, MAPL, GIDE	uc001bdi.4	Q969V5	OTTHUMG00000002838	ENST00000264198.3:c.628delC	1.37:g.20827614delG	ENSP00000264198:p.Leu210fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	142	45	NM_024544	0	0	0	0	0	B5M497|Q7Z431|Q9H9B5	Frame_Shift_Del	DEL	ENST00000264198.3	37	CCDS208.1																																																																																			.		0.607	MUL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007951.1	NM_024544		-	20827614	G	-	20827614	7	5	89	1	0	1	0	1	0	0	0	0	10009	991	35	0	434	0	MUL1	1	20827614	Frame_Shift_Del	DEL	G	TCGA-BQ-7060-01A-11D-1961-08		20827614	228423007	1	8071											
EPHA8	2046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22903099	22903099	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcaagcgcggcttctacctGgccttccaggacataggtgc	8	8	12	13	2	1	0	0	0	1	0	2	1	2	1	3	4	4	2	3	4	3	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:22903099G>T	ENST00000166244.3	+	3	621	c.549G>T	c.(547-549)ctG>ctT	p.L183L	EPHA8_ENST00000374644.4_Silent_p.L183L|EPHA8_ENST00000538803.1_Silent_p.L183L	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	183	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCTTCTACCTGGCCTTCCAGG	0.617																																					p.L183L		.											.	EPHA8-1380	0			c.G549T						.						73	66	69					1																	22903099		2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			CTACCTGGCCTTC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.549G>T	1.37:g.22903099G>T		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	69	25	NM_020526	0	0	0	0	0	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			.		0.617	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22903099	G	T	22903099	2	4	89	1	0	0	0	0	0	0	0	1	5186	1335	47	4		4	EPHA8	1	22903099	Silent	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	2075485	22903099	226347522	2	8072											
RCC1	1104	broad.mit.edu	37	chr1	28862497	28862497	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctttgccatctcccatgaggGccacgtgtacggcttcggcc	5	10	11	15	3	1	1	0	1	1	0	3	1	1	1	4	3	2	2	4	3	1	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:28862497G>A	ENST00000373833.6	+	10	1061	c.776G>A	c.(775-777)gGc>gAc	p.G259D	RCC1_ENST00000398958.2_Missense_Mutation_p.G259D|RCC1_ENST00000373831.3_Missense_Mutation_p.G290D|RCC1_ENST00000373832.1_Missense_Mutation_p.G259D			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	259					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		TCCCATGAGGGCCACGTGTAC	0.592																																					p.G290D													.	RCC1-228	0			c.G869A						.						138	116	124					1																	28862497		2203	4300	6503	SO:0001583	missense	1104	exon8			ATGAGGGCCACGT	X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"chromosome condensation 1"	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.776G>A	1.37:g.28862497G>A	ENSP00000362939:p.Gly259Asp	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	69	5	NM_001048194	0	0	21	24	3	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	37	CCDS323.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781523	0.90282	.	.	ENSG00000180198	ENST00000398958;ENST00000373833;ENST00000419074;ENST00000373832;ENST00000373831;ENST00000411533;ENST00000430407	D;D;D;D;D;D;D	0.97959	-4.63;-4.63;-2.36;-4.63;-4.63;-4.63;-4.63	5.56	5.56	0.83823	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.98795	0.9594	M	0.85945	2.785	0.80722	D	1	D;D;D	0.89917	0.972;1.0;1.0	P;D;D	0.83275	0.581;0.996;0.987	D	0.99110	1.0846	9	.	.	.	-17.227	18.2548	0.90016	0.0:0.0:1.0:0.0	.	290;276;259	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	D	259;259;259;259;290;276;259	ENSP00000381931:G259D;ENSP00000362939:G259D;ENSP00000402260:G259D;ENSP00000362938:G259D;ENSP00000362937:G290D;ENSP00000413644:G276D;ENSP00000394650:G259D	.	G	+	2	0	RCC1	28735084	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.556000	0.98127	2.890000	0.99128	0.655000	0.94253	GGC	.		0.592	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269		A	28862497	G	A	28862497	3	1	89	1	0	0	0	0	1	0	0	0	13205	1203	42	2	895	2	RCC1	1	28862497	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	5959398	28862497	220388124	3	8073											
RAB3B	5865	bcgsc.ca	37	chr1	52398990	52398990	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatgtgtcatgtacatacCaagctgctctgcaaggagct	11	11	9	10	0	2	0	1	0	1	0	2	1	2	1	1	1	7	5	1	1	5	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:52398990C>A	ENST00000371655.3	-	4	684	c.472G>T	c.(472-474)Ggg>Tgg	p.G158W		NM_002867.3	NP_002858.2	P20337	RAB3B_HUMAN	RAB3B, member RAS oncogene family	158					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle size (GO:0097494)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9						ATGTACATACCAAGCTGCTCT	0.468																																					p.G158W													.	RAB3B-228	0			c.G472T						.						188	145	160					1																	52398990		2203	4300	6503	SO:0001630	splice_region_variant	5865	exon4			ACATACCAAGCTG	BC005035	CCDS560.1	1p32-p31	2008-02-05			ENSG00000169213	ENSG00000169213		"RAB, member RAS oncogene"	9778	protein-coding gene	gene with protein product		179510					Standard	NM_002867		Approved		uc001cth.3	P20337	OTTHUMG00000008627	ENST00000371655.3:c.472+1G>T	1.37:g.52398990C>A		Somatic	138	2		WXS	Illumina HiSeq	Phase_1	124	9	NM_002867	0	0	0	0	0	Q5VUL2|Q9BSI1	Missense_Mutation	SNP	ENST00000371655.3	37	CCDS560.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699082	0.68501	.	.	ENSG00000169213	ENST00000371655;ENST00000537650	D	0.82803	-1.65	5.15	5.15	0.70609	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95027	0.8390	H	0.98295	4.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96813	0.9598	9	.	.	.	.	18.4044	0.90529	0.0:1.0:0.0:0.0	.	158	P20337	RAB3B_HUMAN	W	158	ENSP00000360718:G158W	.	G	-	1	0	RAB3B	52171578	1.000000	0.71417	1.000000	0.80357	0.224000	0.24922	7.340000	0.79292	2.692000	0.91855	0.655000	0.94253	GGG	.		0.468	RAB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023816.1	NM_002867	Missense_Mutation	A	52398990	C	A	52398990	5	1	89	1	0	0	0	0	0	0	1	0	12964	608	21	4	195	4	RAB3B	1	52398990	Splice_Site	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	23536493	52398990	196851631	4	8074											
NOTCH2	4853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	120458888	120458888	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtgaggagattctagggAatcaacaggggataaagtta	14	9	14	4	1	2	2	1	1	1	1	2	5	2	4	0	4	1	1	0	4	6	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:120458888A>T	ENST00000256646.2	-	34	6676	c.6457T>A	c.(6457-6459)Tcc>Acc	p.S2153T		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2153					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GATTCTAGGGAATCAACAGGG	0.498			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.S2153T		.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2-1441	0			c.T6457A						.						158	143	148					1																	120458888		2203	4300	6503	SO:0001583	missense	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTAGGGAATCAAC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"Ankyrin repeat domain containing"	7882	protein-coding gene	gene with protein product		600275	"Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)"			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.6457T>A	1.37:g.120458888A>T	ENSP00000256646:p.Ser2153Thr	Somatic	123	1		WXS	Illumina HiSeq	Phase_I	111	36	NM_024408	0	0	61	124	63	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.006662	0.54361	.	.	ENSG00000134250	ENST00000256646	D	0.84589	-1.87	5.71	5.71	0.89125	.	0.000000	0.36854	U	0.002366	D	0.89908	0.6851	M	0.71871	2.18	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	D	0.91129	0.4936	10	0.66056	D	0.02	.	15.1655	0.72821	1.0:0.0:0.0:0.0	.	2153	Q04721	NOTC2_HUMAN	T	2153	ENSP00000256646:S2153T	ENSP00000256646:S2153T	S	-	1	0	NOTCH2	120260411	1.000000	0.71417	0.976000	0.42696	0.192000	0.23643	9.339000	0.96797	2.179000	0.69175	0.459000	0.35465	TCC	.		0.498	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120458888	A	T	120458888	3	4	89	1	0	0	0	0	1	0	0	0	10574	246	9	5	962	5	NOTCH2	1	120458888	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	68059898	120458888	128791733	5	8075											
NBPF9	400818	broad.mit.edu	37	chr1	144823878	144823878	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggactcactgtatagatgttAttcaactccttcaggttgtc	9	15	8	9	0	3	1	3	0	0	1	5	2	4	2	1	2	1	3	1	2	4	6			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:144823878A>C	ENST00000281815.8	+	9	946	c.200A>C	c.(199-201)tAt>tCt	p.Y67S	NBPF9_ENST00000338347.4_Missense_Mutation_p.Y382S|NBPF9_ENST00000468645.1_3'UTR|NBPF9_ENST00000440491.2_Missense_Mutation_p.Y382S			Q3BBW0	NBPF9_HUMAN	neuroblastoma breakpoint family, member 9	715						cytoplasm (GO:0005737)				NS(2)|prostate(1)	3						TATAGATGTTATTCAACTCCT	0.483																																					.													.	.	0			.						.																																			SO:0001583	missense	400818	.			GATGTTATTCAAC		CCDS72895.1, CCDS72896.1	1q21.1	2013-01-17			ENSG00000168614	ENSG00000269713		"neuroblastoma breakpoint family"	31991	protein-coding gene	gene with protein product		613999				16079250	Standard	NM_001037675		Approved	AE01		Q3BBW0	OTTHUMG00000013845	ENST00000281815.8:c.200A>C	1.37:g.144823878A>C	ENSP00000281815:p.Tyr67Ser	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	117	4	.	0	0	8	8	0		Missense_Mutation	SNP	ENST00000281815.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	8.138|8.138	0.784620|0.784620	0.16189|0.16189	.|.	.|.	ENSG00000168614|ENSG00000168614	ENST00000375552|ENST00000338347;ENST00000440491;ENST00000281815	.|T;T;T	.|0.08282	.|3.11;3.11;3.11	0.431|0.431	-0.862|-0.862	0.10673|0.10673	.|.	.|.	.|.	.|.	.|.	T|T	0.06325|0.06325	0.0163|0.0163	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.91635	.|0.999	T|T	0.20638|0.20638	-1.0269|-1.0269	3|7	.|0.20046	.|T	.|0.44	.|.	.|.	.|.	.|.	.|.	.|380	.|A2BGT5	.|.	L|S	381|382;382;67	.|ENSP00000342975:Y382S;ENSP00000390934:Y382S;ENSP00000281815:Y67S	.|ENSP00000281815:Y67S	I|Y	+|+	1|2	0|0	NBPF9|NBPF9	143535235|143535235	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.041000|0.041000	0.13682|0.13682	-1.315000|-1.315000	0.02713|0.02713	-0.698000|-0.698000	0.05085|0.05085	0.163000|0.163000	0.16589|0.16589	ATT|TAT	.		0.483	NBPF9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001037675		C	144823878	A	C	144823878	3	2	89	1	0	0	0	0	1	0	0	0	10225	449	16	5	1971	5	NBPF9	1	144823878	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	24364990	144823878	104426743	6	8076											
ZNF619	285267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	40529349	40529349	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggttcagcatcagcgagttCacactggggagaaaccttat	11	10	11	9	1	3	1	3	0	0	1	3	3	3	1	1	3	3	3	1	3	2	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:40529349C>T	ENST00000314686.5	+	6	1705	c.1300C>T	c.(1300-1302)Cac>Tac	p.H434Y	ZNF619_ENST00000521353.1_Missense_Mutation_p.H490Y|ZNF619_ENST00000429348.2_Missense_Mutation_p.H450Y|ZNF619_ENST00000447116.2_Missense_Mutation_p.H490Y|ZNF619_ENST00000522736.1_Missense_Mutation_p.H441Y|ZNF619_ENST00000456778.1_Missense_Mutation_p.H406Y|ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000432264.2_Missense_Mutation_p.H450Y			Q8N2I2	ZN619_HUMAN	zinc finger protein 619	434					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)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCAGCGAGTTCACACTGGGGA	0.463																																					p.H490Y		.											.	ZNF619-91	0			c.C1468T						.						92	95	94					3																	40529349		2203	4300	6503	SO:0001583	missense	285267	exon6			CGAGTTCACACTG	AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"Zinc fingers, C2H2-type", "-"	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.1300C>T	3.37:g.40529349C>T	ENSP00000322529:p.His434Tyr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	115	64	NM_001145082	0	0	4	6	2	B4E271|C9JRN5|D4PHA2|E9PCD9	Missense_Mutation	SNP	ENST00000314686.5	37		.	.	.	.	.	.	.	.	.	.	C	16.06	3.017099	0.54576	.	.	ENSG00000177873	ENST00000314686;ENST00000447116;ENST00000429348;ENST00000456778;ENST00000442066;ENST00000522736;ENST00000521353;ENST00000432264	T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	2.44	2.44	0.29823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.82010	0.4944	M	0.87269	2.87	0.30841	N	0.735643	D;D;D;D;D;D	0.89917	0.999;0.998;0.998;1.0;0.998;0.999	D;D;D;D;D;D	0.91635	0.996;0.982;0.976;0.999;0.976;0.996	T	0.79495	-0.1780	9	0.87932	D	0	.	10.5917	0.45314	0.0:1.0:0.0:0.0	.	406;450;490;392;441;434	B4E271;C9JRN5;E9PCD9;B7Z9B3;Q17RW3;Q8N2I2	.;.;.;.;.;ZN619_HUMAN	Y	434;490;450;406;71;441;490;450	ENSP00000322529:H434Y;ENSP00000411132:H490Y;ENSP00000398024:H450Y;ENSP00000397232:H406Y;ENSP00000428004:H441Y;ENSP00000430705:H490Y;ENSP00000388710:H450Y	ENSP00000322529:H434Y	H	+	1	0	ZNF619	40504353	0.998000	0.40836	0.972000	0.41901	0.869000	0.49853	3.961000	0.56759	1.376000	0.46267	0.563000	0.77884	CAC	.		0.463	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656		T	40529349	C	T	40529349	3	4	89	1	0	0	0	0	1	0	0	0	18075	826	29	2	1508	2	ZNF619	3	40529349	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		40529349	157493081	7	8077											
RPL29	6159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52029445	52029445	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggcccaaaaaacttacactgGttgtgtgtggtgtggttctt	8	14	12	7	0	1	0	0	0	1	0	1	0	1	0	1	4	2	2	1	4	4	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:52029445G>A	ENST00000466397.1	-	2	173	c.33C>T	c.(31-33)aaC>aaT	p.N11N	RPL29_ENST00000294189.6_Silent_p.N11N|RPL29_ENST00000495383.1_Silent_p.N11N|RPL29_ENST00000479017.1_Silent_p.N11N|RPL29_ENST00000475248.1_Silent_p.N11N|RPL29_ENST00000481629.1_Silent_p.N11N			P47914	RL29_HUMAN	ribosomal protein L29	11					cellular protein metabolic process (GO:0044267)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ACTTACACTGGTTGTGTGTGG	0.567																																					p.N11N		.											.	RPL29-90	0			c.C33T						.						130	106	114					3																	52029445		2203	4300	6503	SO:0001819	synonymous_variant	6159	exon2			ACACTGGTTGTGT	U10248	CCDS2845.1	3p21.3-p21.2	2013-03-11			ENSG00000162244	ENSG00000162244		"L ribosomal proteins"	10331	protein-coding gene	gene with protein product	"60S ribosomal protein L29", "heparin/heparan sulfate-interacting protein", "HP/HS-interacting protein", "heparin/heparan sulfate-binding protein", "cell surface heparin-binding protein HIP"	601832	"ribosomal protein L29 pseudogene 10"	RPL29P10		8597591	Standard	NM_000992		Approved	HIP, HUMRPL29, L29	uc003dcs.3	P47914	OTTHUMG00000155262	ENST00000466397.1:c.33C>T	3.37:g.52029445G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	116	26	NM_000992	0	0	0	0	0	A8K0H3|B2R4M8|Q6IPY3	Silent	SNP	ENST00000466397.1	37	CCDS2845.1																																																																																			.		0.567	RPL29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349680.2	NM_000992		A	52029445	G	A	52029445	2	1	89	1	0	0	0	0	0	0	0	1	13610	1252	44	2		2	RPL29	3	52029445	Silent	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	11500096	52029445	145992985	8	8078											
HGD	3081	broad.mit.edu	37	chr3	120366724	120366724	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagtcttcagaactcacCaatcaagaagtccccatctg	13	9	6	13	0	5	3	3	1	2	2	6	3	6	3	3	0	1	0	3	0	5	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:120366724C>G	ENST00000283871.5	-	7	928	c.469G>C	c.(469-471)Gtt>Ctt	p.V157L		NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	157					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		CAGAACTCACCAATCAAGAAG	0.353																																					p.V157L													.	HGD-68	0			c.G469C						.						128	135	133					3																	120366724		2203	4296	6499	SO:0001630	splice_region_variant	3081	exon7			ACTCACCAATCAA		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"homogentisate oxidase"	607474	"homogentisate 1,2-dioxygenase (homogentisate oxidase)"	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.469+1G>C	3.37:g.120366724C>G		Somatic	211	0		WXS	Illumina HiSeq	Phase_I	261	7	NM_000187	0	0	0	0	0	A8K417|B2R8Z0	Missense_Mutation	SNP	ENST00000283871.5	37	CCDS3000.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829413	0.90955	.	.	ENSG00000113924	ENST00000283871;ENST00000476082	D;D	0.99023	-5.34;-5.34	6.02	6.02	0.97574	Cupin, RmlC-type (1);	0.119337	0.56097	D	0.000028	D	0.99086	0.9686	M	0.85542	2.76	0.80722	D	1	D	0.54601	0.967	P	0.54346	0.749	D	0.99497	1.0952	9	.	.	.	-0.0022	18.0346	0.89296	0.0:1.0:0.0:0.0	.	157	Q93099	HGD_HUMAN	L	157;116	ENSP00000283871:V157L;ENSP00000419560:V116L	.	V	-	1	0	HGD	121849414	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	6.405000	0.73272	2.865000	0.98341	0.655000	0.94253	GTT	.		0.353	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1		Missense_Mutation	G	120366724	C	G	120366724	5	3	89	1	0	0	0	0	0	0	1	0	7105	608	21	4	900	4	HGD	3	120366724	Splice_Site	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	68337279	120366724	77655706	9	8079											
POLQ	10721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121168266	121168266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccattccataaatgatcccaTagcaaatctgaaagggagtc	15	9	7	10	0	1	2	0	2	1	0	4	3	3	3	3	1	1	1	3	1	5	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:121168266T>C	ENST00000264233.5	-	26	7288	c.7160A>G	c.(7159-7161)tAt>tGt	p.Y2387C		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2387					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AATGATCCCATAGCAAATCTG	0.358								DNA polymerases (catalytic subunits)																													p.Y2387C	Pancreas(152;907 1925 26081 31236 36904)	.											.	POLQ-664	0			c.A7160G						.						166	164	164					3																	121168266		2203	4300	6503	SO:0001583	missense	10721	exon26			ATCCCATAGCAAA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7160A>G	3.37:g.121168266T>C	ENSP00000264233:p.Tyr2387Cys	Somatic	343	1		WXS	Illumina HiSeq	Phase_I	395	195	NM_199420	0	0	0	0	0	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.113078	0.77210	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.98221	-4.8	5.26	5.26	0.73747	DNA-directed DNA polymerase, family A, palm domain (2);DNA-directed DNA polymerase, family A, conserved site (1);	0.061290	0.64402	D	0.000002	D	0.99184	0.9717	M	0.93854	3.465	0.45502	D	0.99846	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99211	1.0876	10	0.87932	D	0	.	14.8334	0.70164	0.0:0.0:0.0:1.0	.	2387;1559	O75417;O75417-2	DPOLQ_HUMAN;.	C	2010;2387;2523	ENSP00000264233:Y2387C	ENSP00000264233:Y2387C	Y	-	2	0	POLQ	122650956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.345000	0.79337	1.968000	0.57251	0.533000	0.62120	TAT	.		0.358	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121168266	T	C	121168266	3	2	89	1	0	0	0	0	1	0	0	0	12234	1406	49	3	632	3	POLQ	3	121168266	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	801542	121168266	76854164	10	8080											
KPNA4	3840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	160249255	160249255	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaataatgtactcacttgtcAtctctttcaagacaatggac	14	13	5	9	0	4	1	3	0	1	1	5	2	4	2	0	1	1	1	0	1	5	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:160249255A>G	ENST00000334256.4	-	6	683	c.378T>C	c.(376-378)gaT>gaC	p.D126D		NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	126					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			CTCACTTGTCATCTCTTTCAA	0.303																																					p.D126D		.											.	KPNA4-226	0			c.T378C						.						78	85	83					3																	160249255		2202	4296	6498	SO:0001819	synonymous_variant	3840	exon6			CTTGTCATCTCTT	AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"Importins", "Armadillo repeat containing"	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.378T>C	3.37:g.160249255A>G		Somatic	182	0		WXS	Illumina HiSeq	Phase_I	235	128	NM_002268	0	0	0	0	0	A8K4S6|D3DNM2|O00190	Silent	SNP	ENST00000334256.4	37	CCDS3191.1																																																																																			.		0.303	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268		G	160249255	A	G	160249255	2	3	89	1	0	0	0	0	0	0	0	1	8453	214	8	3		3	KPNA4	3	160249255	Silent	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	39080989	160249255	37773175	11	8081											
DGKG	1608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186006591	186006591	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggggattccgagcttgaaGaccgagggacggggggttcc	7	7	18	9	3	0	2	0	1	0	1	2	6	2	4	3	6	1	2	3	6	1	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:186006591G>A	ENST00000265022.3	-	6	991	c.452C>T	c.(451-453)tCt>tTt	p.S151F	DGKG_ENST00000382164.4_Missense_Mutation_p.S151F|DGKG_ENST00000544847.1_Missense_Mutation_p.S151F|DGKG_ENST00000344484.4_Missense_Mutation_p.S151F	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	151	Poly-Ser.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CGAGCTTGAAGACCGAGGGAC	0.552																																					p.S151F		.											.	DGKG-714	0			c.C452T						.						138	151	147					3																	186006591		2203	4300	6503	SO:0001583	missense	1608	exon6			CTTGAAGACCGAG	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.452C>T	3.37:g.186006591G>A	ENSP00000265022:p.Ser151Phe	Somatic	346	0		WXS	Illumina HiSeq	Phase_I	420	97	NM_001346	0	0	0	0	0	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439692	0.43326	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.74	1.92	0.25849	.	2.306020	0.01541	N	0.019244	T	0.42765	0.1217	L	0.38175	1.15	0.09310	N	1	B;B;B;B	0.31435	0.323;0.219;0.323;0.217	B;B;B;B	0.38378	0.272;0.188;0.272;0.092	T	0.20273	-1.0280	10	0.34782	T	0.22	.	3.4838	0.07611	0.1475:0.1347:0.5782:0.1396	.	151;151;151;151	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	F	151;151;151;151;154	ENSP00000265022:S151F;ENSP00000339777:S151F;ENSP00000371599:S151F;ENSP00000440507:S151F	ENSP00000265022:S151F	S	-	2	0	DGKG	187489285	0.974000	0.33945	0.001000	0.08648	0.025000	0.11179	3.286000	0.51724	0.139000	0.18822	0.563000	0.77884	TCT	.		0.552	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			A	186006591	G	A	186006591	3	1	89	1	0	0	0	0	1	0	0	0	4480	942	33	2	2003	2	DGKG	3	186006591	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	25757336	186006591	12015839	12	8082											
KLHL8	57563	broad.mit.edu;bcgsc.ca	37	chr4	88091355	88091355	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacgctagataaagaagcCattccatcattgccacctac	13	9	5	14	1	1	2	1	0	0	2	3	2	3	2	5	0	3	1	5	0	5	5			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr4:88091355C>T	ENST00000273963.5	-	8	1754	c.1413G>A	c.(1411-1413)atG>atA	p.M471I	KLHL8_ENST00000425278.2_Missense_Mutation_p.M288I|KLHL8_ENST00000512111.1_Missense_Mutation_p.M471I|KLHL8_ENST00000545252.1_Missense_Mutation_p.M120I|KLHL8_ENST00000498875.2_Missense_Mutation_p.M395I	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	471					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		ATAAAGAAGCCATTCCATCAT	0.368																																					p.M471I													.	KLHL8-90	0			c.G1413A						.						87	83	84					4																	88091355		2203	4300	6503	SO:0001583	missense	57563	exon8			AGAAGCCATTCCA	AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332		"Kelch-like", "BTB/POZ domain containing"	18644	protein-coding gene	gene with protein product		611967	"kelch-like 8 (Drosophila)"				Standard	XM_005263153		Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000273963.5:c.1413G>A	4.37:g.88091355C>T	ENSP00000273963:p.Met471Ile	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	127	9	NM_020803	0	0	6	7	1	Q53XA3|Q6N018	Missense_Mutation	SNP	ENST00000273963.5	37	CCDS3617.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.492809	0.44352	.	.	ENSG00000145332	ENST00000273963;ENST00000498875;ENST00000425278;ENST00000545252;ENST00000512111	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.9	3.07	0.35406	Galactose oxidase, beta-propeller (1);	0.316179	0.33401	N	0.004948	T	0.49423	0.1556	N	0.04090	-0.28	0.26143	N	0.980252	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.28396	-1.0045	10	0.23891	T	0.37	.	3.0759	0.06246	0.3035:0.3389:0.0:0.3576	.	288;395;471	Q68DU9;Q6N018;Q9P2G9	.;.;KLHL8_HUMAN	I	471;395;288;120;471	ENSP00000273963:M471I;ENSP00000426451:M395I;ENSP00000408854:M288I;ENSP00000439514:M120I;ENSP00000424131:M471I	ENSP00000273963:M471I	M	-	3	0	KLHL8	88310379	0.994000	0.37717	1.000000	0.80357	0.979000	0.70002	0.363000	0.20301	0.294000	0.22547	0.563000	0.77884	ATG	.		0.368	KLHL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253040.1			T	88091355	C	T	88091355	3	4	89	1	0	0	0	0	1	0	0	0	8416	594	21	2	461	2	KLHL8	4	88091355	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		88091355	103062921	13	8083											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	151271258	151271259	+	Frame_Shift_Ins	INS	-	-	AT																															cttgctgtttatagccaaaaINSatgagatcaatccattggtg																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr4:151271258_151271259insAT	ENST00000357115.3	-	49	7523_7524	c.7280_7281insAT	c.(7279-7281)attfs	p.I2427fs	LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000507224.1_Frame_Shift_Ins_p.I2416fs|LRBA_ENST00000510413.1_Frame_Shift_Ins_p.I2416fs|LRBA_ENST00000535741.1_Frame_Shift_Ins_p.I2416fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2427	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TATAGCCAAAAATGAGATCAAT	0.391																																					p.I2427fs		.											.	LRBA-157	0			c.7281_7282insAT						.																																			SO:0001589	frameshift_variant	987	exon49			.	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.7279_7280dupAT	4.37:g.151271259_151271260dupAT	ENSP00000349629:p.Ile2427fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	70	12	NM_006726	0	0	0	0	0	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Ins	INS	ENST00000357115.3	37	CCDS3773.1																																																																																			.		0.391	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			AT	151271259	-	AT	151271258	7	5	89	1	0	1	1	0	0	0	0	0	8956	10	1	0	1350	0	LRBA	4	151271258	Frame_Shift_Ins	INS	-	TCGA-BQ-7060-01A-11D-1961-08	63179903	151271258	39883018	14	8084											
NSD1	64324	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176637880	176637880	+	Frame_Shift_Del	DEL	T	T	-																															aggctctcctttggccagcaTttctaaaagtgggaaagtgg																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr5:176637880delT	ENST00000439151.2	+	5	2525	c.2480delT	c.(2479-2481)attfs	p.I827fs	NSD1_ENST00000354179.4_Frame_Shift_Del_p.I558fs|NSD1_ENST00000361032.4_Frame_Shift_Del_p.I724fs|NSD1_ENST00000347982.4_Frame_Shift_Del_p.I558fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	827					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TTGGCCAGCATTTCTAAAAGT	0.413			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.I827fs		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.2480delT						.						69	70	69					5																	176637880		2203	4300	6503	SO:0001589	frameshift_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	.	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2480delT	5.37:g.176637880delT	ENSP00000395929:p.Ile827fs	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	49	13	NM_022455	0	0	0	0	0	Q96PD8|Q96RN7	Frame_Shift_Del	DEL	ENST00000439151.2	37	CCDS4412.1																																																																																			.		0.413	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		-	176637880	T	-	176637880	7	5	89	1	0	1	0	1	0	0	0	0	10695	1493	52	0	2494	0	NSD1	5	176637880	Frame_Shift_Del	DEL	T	TCGA-BQ-7060-01A-11D-1961-08		176637880	4277380	15	8085											
GRM4	2914	ucsc.edu	37	chr6	34100765	34100765	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcactgaccttgaagaggCgaaggatgttggccaccatg	11	7	14	9	1	0	3	0	2	0	1	0	5	0	4	3	4	0	2	3	4	2	2	rs375789000		TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr6:34100765C>T	ENST00000538487.2	-	2	952	c.509G>A	c.(508-510)cGc>cAc	p.R170H	GRM4_ENST00000374181.4_Missense_Mutation_p.R170H|GRM4_ENST00000374177.3_Intron	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	170					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.R170H(2)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						CTTGAAGAGGCGAAGGATGTT	0.642																																					p.R170H													.	GRM4-525	2	Substitution - Missense(2)	prostate(2)	c.G509A						.	C	HIS/ARG	0,4406		0,0,2203	69	60	63		509	3.9	1	6		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	GRM4	NM_000841.1	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	170/913	34100765	1,13005	2203	4300	6503	SO:0001583	missense	2914	exon2			AAGAGGCGAAGGA	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.509G>A	6.37:g.34100765C>T	ENSP00000440556:p.Arg170His	Somatic	53	0		WXS	Illumina HiSeq		31	4	NM_001256811	0	0	0	0	0	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550463	0.86127	0.0	1.16E-4	ENSG00000124493	ENST00000374181;ENST00000538487	D;D	0.83419	-1.72;-1.72	3.91	3.91	0.45181	GPCR, family 3, conserved site (1);Extracellular ligand-binding receptor (1);	0.071236	0.56097	U	0.000026	D	0.92077	0.7489	M	0.93197	3.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.985;0.997;0.947	D	0.93784	0.7086	10	0.59425	D	0.04	.	15.6761	0.77326	0.0:1.0:0.0:0.0	.	170;170;170	B7ZLU9;A1L4F9;Q14833	.;.;GRM4_HUMAN	H	170	ENSP00000363296:R170H;ENSP00000440556:R170H	ENSP00000363296:R170H	R	-	2	0	GRM4	34208743	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.612000	0.82975	2.005000	0.58758	0.467000	0.42956	CGC	.		0.642	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			T	34100765	C	T	34100765	3	4	89	1	0	0	0	0	1	0	0	0	6820	768	27	1	2269	1	GRM4	6	34100765	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		34100765	137014302	16	8086											
RUNX2	860	hgsc.bcm.edu;broad.mit.edu	37	chr6	45390466	45390466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcagcagcagcagcagcaAcagcagcagcagcagcagga	15	0	13	13	0	0	0	0	0	0	0	0	1	0	1	0	1	12	11	0	1	1	0	rs575896136	byFrequency	TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000352853.5_Silent_p.Q133Q|RUNX2_ENST00000371432.3_Silent_p.Q51Q|RUNX2_ENST00000359524.5_Silent_p.Q51Q|RUNX2_ENST00000541979.1_Silent_p.Q133Q|RUNX2_ENST00000465038.2_Silent_p.Q65Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Silent_p.Q65Q|RUNX2_ENST00000576263.1_Silent_p.Q65Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0	5008	,	,		7675	0.002		0	False		,,,				2504	0.0031				p.Q65Q		.											.	RUNX2-417	0			c.A195G						.						10	15	14					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	6.37:g.45390466A>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	48	4	NM_001024630	2	6	156	7180	7016	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	CCDS43467.2																																																																																			.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390466	A	G	45390466	2	3	89	1	0	0	0	0	0	0	0	1	13780	40	2	3		3	RUNX2	6	45390466	Silent	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	11289701	45390466	125724601	17	8087											
MYO6	4646	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	76542650	76542650	+	Frame_Shift_Del	DEL	A	A	-																															gccggcaaaacagaaaatacAaaatttgttctaaggtgagt																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr6:76542650delA	ENST00000369977.3	+	6	622	c.483delA	c.(481-483)acafs	p.T161fs	MYO6_ENST00000369975.1_Frame_Shift_Del_p.T161fs|MYO6_ENST00000369985.4_Frame_Shift_Del_p.T161fs|MYO6_ENST00000369981.3_Frame_Shift_Del_p.T161fs	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	161	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CAGAAAATACAAAATTTGTTC	0.413																																					p.T161fs		.											.	MYO6-92	0			c.483delA						.						74	80	78					6																	76542650		2203	4300	6503	SO:0001589	frameshift_variant	4646	exon6			.	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.483delA	6.37:g.76542650delA	ENSP00000358994:p.Thr161fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	140	43	NM_004999	0	0	0	0	0	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Frame_Shift_Del	DEL	ENST00000369977.3	37	CCDS34487.1																																																																																			.		0.413	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		-	76542650	A	-	76542650	7	5	89	1	0	1	0	1	0	0	0	0	10106	117	5	0	501	0	MYO6	6	76542650	Frame_Shift_Del	DEL	A	TCGA-BQ-7060-01A-11D-1961-08	31152184	76542650	94572417	18	8088											
C7orf57	136288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48081007	48081007	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtcccagatcccaggtctCagcaatttgggagactcaca	10	8	10	13	1	2	2	2	0	1	2	5	3	4	2	2	2	1	1	2	2	1	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr7:48081007C>A	ENST00000348904.3	+	3	344	c.132C>A	c.(130-132)ctC>ctA	p.L44L	C7orf57_ENST00000430738.1_Silent_p.L89L|C7orf57_ENST00000539619.1_Silent_p.L44L|C7orf57_ENST00000435376.1_5'UTR|C7orf57_ENST00000420324.1_Silent_p.L89L	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	44										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TCCCAGGTCTCAGCAATTTGG	0.542																																					p.L44L		.											.	C7orf57-1	0			c.C132A						.						51	55	54					7																	48081007		1920	4141	6061	SO:0001819	synonymous_variant	136288	exon3			AGGTCTCAGCAAT	BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.132C>A	7.37:g.48081007C>A		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	100	46	NM_001100159	0	0	0	0	0	C9JBJ8	Silent	SNP	ENST00000348904.3	37	CCDS47583.1																																																																																			.		0.542	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159		A	48081007	C	A	48081007	2	1	89	1	0	0	0	0	0	0	0	1	2410	813	29	4		4	C7orf57	7	48081007	Silent	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		48081007	111057656	19	8089											
ST7	7982	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116863027	116863027	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcaatctcaacatttccAaaactgaactcatcacccct	14	10	1	16	0	4	1	4	1	1	0	6	1	5	1	4	0	3	0	4	0	5	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr7:116863027A>G	ENST00000265437.5	+	16	1965	c.1751A>G	c.(1750-1752)cAa>cGa	p.Q584R	ST7_ENST00000422922.1_Intron|ST7_ENST00000393451.3_Intron|ST7_ENST00000393449.1_Intron|ST7_ENST00000393447.4_Intron|ST7_ENST00000432298.1_Intron|ST7_ENST00000323984.3_Intron|ST7_ENST00000393446.2_Intron|ST7_ENST00000393443.1_Intron|ST7_ENST00000393444.3_Intron	NM_021908.2	NP_068708.1	Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		caacatttccaaaactgaact	0.517																																					p.Q584R		.											.	ST7-515	0			c.A1751G						.						86	86	86					7																	116863027		2203	4300	6503	SO:0001583	missense	7982	exon16			ATTTCCAAAACTG	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000265437.5:c.1751A>G	7.37:g.116863027A>G	ENSP00000265437:p.Gln584Arg	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	84	42	NM_021908	0	0	17	67	50	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000265437.5	37	CCDS5770.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.575245	0.28092	.	.	ENSG00000004866	ENST00000265437	T	0.18174	2.23	4.5	-2.45	0.06481	.	0.926145	0.09155	N	0.840984	T	0.07548	0.0190	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16394	-1.0404	10	0.48119	T	0.1	-0.0371	5.8835	0.18868	0.2864:0.5195:0.1941:0.0	.	561;584	B7Z573;Q9NRC1	.;ST7_HUMAN	R	584	ENSP00000265437:Q584R	ENSP00000265437:Q584R	Q	+	2	0	ST7	116650263	0.048000	0.20356	0.982000	0.44146	0.470000	0.32858	-0.930000	0.03972	-0.261000	0.09405	-0.331000	0.08364	CAA	.		0.517	ST7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141622.1	NM_021908		G	116863027	A	G	116863027	3	3	89	1	0	0	0	0	1	0	0	0	15261	130	5	3	1813	3	ST7	7	116863027	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	68782020	116863027	42275636	20	8090											
POP1	10940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	99161148	99161148	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattcagcagccaggaaaaGtgactggtgaagatcgacta	14	8	12	7	1	1	4	1	3	0	1	2	6	1	5	1	2	2	1	1	2	4	2			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr8:99161148G>A	ENST00000401707.2	+	13	1897	c.1816G>A	c.(1816-1818)Gtg>Atg	p.V606M	POP1_ENST00000349693.3_Missense_Mutation_p.V606M	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	606					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GCCAGGAAAAGTGACTGGTGA	0.478																																					p.V606M		.											.	POP1-154	0			c.G1816A						.						83	72	76					8																	99161148		2203	4300	6503	SO:0001583	missense	10940	exon13			GGAAAAGTGACTG	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.1816G>A	8.37:g.99161148G>A	ENSP00000385787:p.Val606Met	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	47	16	NM_001145860	0	0	4	6	2	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.075851	0.36662	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.37411	1.2;1.2	5.46	4.58	0.56647	.	0.468009	0.23298	N	0.049711	T	0.25232	0.0613	L	0.38838	1.175	0.33165	D	0.54748	B	0.28233	0.204	B	0.21151	0.033	T	0.31420	-0.9944	10	0.41790	T	0.15	-5.9978	7.3479	0.26674	0.2299:0.0:0.7701:0.0	.	606	Q99575	POP1_HUMAN	M	606	ENSP00000385787:V606M;ENSP00000339529:V606M	ENSP00000339529:V606M	V	+	1	0	POP1	99230324	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.436000	0.52856	1.311000	0.45024	-0.150000	0.13652	GTG	.		0.478	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		A	99161148	G	A	99161148	3	1	89	1	0	0	0	0	1	0	0	0	12277	1029	36	2	1862	2	POP1	8	99161148	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08		99161148	47202874	21	8091											
ASPN	54829	hgsc.bcm.edu	37	chr9	95237030	95237030	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagagagttgtcctcatcAtcatcatcatcatcatcatc	14	12	4	11	0	8	1	8	0	0	1	10	2	9	1	1	0	0	1	1	0	2	1	rs143279922		TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr9:95237030A>C	ENST00000375544.3	-	2	393	c.150T>G	c.(148-150)gaT>gaG	p.D50E	CENPP_ENST00000375587.3_Intron|ASPN_ENST00000450139.2_Missense_Mutation_p.D22E|ASPN_ENST00000375543.1_Missense_Mutation_p.D50E|ASPN_ENST00000395538.3_Missense_Mutation_p.D50E	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	50	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						TGTCCtcatcatcatcatcat	0.398																																					p.D50E		.											.	ASPN-514	0			c.T150G						.						112	102	105					9																	95237030		2203	4300	6503	SO:0001583	missense	54829	exon2			CTCATCATCATCA	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.150T>G	9.37:g.95237030A>C	ENSP00000364694:p.Asp50Glu	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	34	5	NM_001193335	0	0	0	0	0	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	37		.	.	.	.	.	.	.	.	.	.	A	2.759	-0.258312	0.05791	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538;ENST00000450139	T;T;T	0.52983	0.64;0.69;0.69	3.41	-5.95	0.02241	.	1.551710	0.03954	N	0.288946	T	0.32645	0.0836	L	0.40543	1.245	0.09310	N	1	B;B	0.32245	0.361;0.001	B;B	0.27380	0.079;0.001	T	0.11941	-1.0567	10	0.22109	T	0.4	.	7.6964	0.28598	0.4608:0.1193:0.4198:0.0	.	50;50	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	E	50;50;50;22	ENSP00000364694:D50E;ENSP00000364693:D50E;ENSP00000378909:D50E	ENSP00000364693:D50E	D	-	3	2	ASPN	94276851	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.911000	0.01583	-2.152000	0.00794	-2.339000	0.00246	GAT	A|1.000;C|0.000		0.398	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		C	95237030	A	C	95237030	3	2	89	1	0	0	0	0	1	0	0	0	1058	214	8	5	1020	5	ASPN	9	95237030	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08		95237030	45976401	22	8092											
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	113163288	113163288	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggctcccaggttccatcaAgctaagtgacaaataacaaa	15	8	8	10	0	1	1	1	1	0	0	3	1	3	1	2	2	2	3	2	2	5	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr9:113163288A>C	ENST00000401783.2	-	40	10004	c.9668T>G	c.(9667-9669)cTt>cGt	p.L3223R	SVEP1_ENST00000297826.5_Splice_Site_p.L1149R|SVEP1_ENST00000374469.1_Splice_Site_p.L3200R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3223	Sushi 30. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GGTTCCATCAAGCTAAGTGAC	0.358																																					p.L3223R		.											.	SVEP1-75	0			c.T9668G						.						71	69	70					9																	113163288		1863	4093	5956	SO:0001630	splice_region_variant	79987	exon40			CCATCAAGCTAAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.9667-1T>G	9.37:g.113163288A>C		Somatic	110	1		WXS	Illumina HiSeq	Phase_I	102	33	NM_153366	0	0	0	0	0	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	A	11.59	1.682850	0.29872	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.64438	-0.1;-0.1;-0.1	5.77	0.841	0.18918	Complement control module (2);Sushi/SCR/CCP (3);	0.788063	0.11913	N	0.517487	T	0.50905	0.1643	L	0.43923	1.385	0.80722	D	1	P	0.38335	0.627	B	0.42827	0.399	T	0.35025	-0.9805	10	0.16420	T	0.52	.	4.5369	0.12038	0.4726:0.0:0.31:0.2173	.	3223	Q4LDE5	SVEP1_HUMAN	R	3223;3200;1149	ENSP00000384917:L3223R;ENSP00000363593:L3200R;ENSP00000297826:L1149R	ENSP00000297826:L1149R	L	-	2	0	SVEP1	112203109	0.984000	0.35163	0.995000	0.50966	0.842000	0.47809	1.505000	0.35736	-0.072000	0.12864	0.524000	0.50904	CTT	.		0.358	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation	C	113163288	A	C	113163288	5	2	89	1	0	0	0	0	0	0	1	0	15452	86	3	5	1083	5	SVEP1	9	113163288	Splice_Site	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	17926258	113163288	28050143	23	8093											
KBTBD4	55709	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	47597183	47597183	+	Frame_Shift_Del	DEL	T	T	-																															tgactctgcaaaagcctctcTttcctctttattaaagttga																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr11:47597183delT	ENST00000526005.1	-	3	811	c.658delA	c.(658-660)agafs	p.R220fs	KBTBD4_ENST00000395288.2_Frame_Shift_Del_p.R220fs|NDUFS3_ENST00000533507.1_Intron|RNU5E-10P_ENST00000363506.1_RNA|KBTBD4_ENST00000533290.1_Frame_Shift_Del_p.R245fs|KBTBD4_ENST00000450908.1_5'Flank|KBTBD4_ENST00000525720.1_Frame_Shift_Del_p.R269fs|KBTBD4_ENST00000430070.2_Frame_Shift_Del_p.R236fs			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	220	BACK.									NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						AAAGCCTCTCTTTCCTCTTTA	0.443																																					p.R236fs		.											.	KBTBD4-91	0			c.706delA						.						164	158	160					11																	47597183		2201	4298	6499	SO:0001589	frameshift_variant	55709	exon3			.	AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"BTB/POZ domain containing"	23761	protein-coding gene	gene with protein product			"BTB and kelch domain containing 4"	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.658delA	11.37:g.47597183delT	ENSP00000433340:p.Arg220fs	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	176	44	NM_018095	0	0	0	0	0	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Frame_Shift_Del	DEL	ENST00000526005.1	37	CCDS7940.1																																																																																			.		0.443	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	NM_016506		-	47597183	T	-	47597183	7	5	89	1	0	1	0	1	0	0	0	0	8016	1617	56	0	906	0	KBTBD4	11	47597183	Frame_Shift_Del	DEL	T	TCGA-BQ-7060-01A-11D-1961-08		47597183	87409333	24	8094											
TNKS1BP1	85456	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57085299	57085299	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggataactcacatcagcaGgtagctccgagctggctgcc	10	7	12	12	1	2	0	2	0	0	0	3	3	3	1	2	3	5	5	2	3	2	2			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr11:57085299G>A	ENST00000532437.1	-	3	1102	c.791C>T	c.(790-792)cCt>cTt	p.P264L	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P264L			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	264	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CACATCAGCAGGTAGCTCCGA	0.502																																					p.P264L													.	TNKS1BP1-91	0			c.C791T						.						69	65	67					11																	57085299		2201	4296	6497	SO:0001583	missense	85456	exon4			TCAGCAGGTAGCT	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.791C>T	11.37:g.57085299G>A	ENSP00000437271:p.Pro264Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	49	8	NM_033396	0	0	0	0	0	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	G	9.170	1.020971	0.19433	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.38077	1.16;1.16	3.96	3.04	0.35103	.	0.185799	0.26234	N	0.025556	T	0.24547	0.0595	L	0.32530	0.975	0.09310	N	0.999999	B	0.13594	0.008	B	0.17098	0.017	T	0.10428	-1.0630	10	0.49607	T	0.09	-2.5359	6.8012	0.23752	0.1261:0.0:0.8739:0.0	.	264	Q9C0C2	TB182_HUMAN	L	264	ENSP00000350990:P264L;ENSP00000437271:P264L	ENSP00000350990:P264L	P	-	2	0	TNKS1BP1	56841875	0.169000	0.23002	0.605000	0.28930	0.178000	0.23041	0.774000	0.26675	2.206000	0.71126	0.462000	0.41574	CCT	.		0.502	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57085299	G	A	57085299	3	1	89	1	0	0	0	0	1	0	0	0	16352	1000	35	2	4430	2	TNKS1BP1	11	57085299	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	9488116	57085299	77921217	25	8095											
NAA16	79612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41905433	41905433	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctttagaagagaggcttcaaAtttatgaagaaattagtaag	17	12	9	3	0	1	4	1	1	0	3	1	5	1	4	0	1	0	2	0	1	8	7			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr13:41905433A>T	ENST00000379406.3	+	8	1159	c.835A>T	c.(835-837)Att>Ttt	p.I279F	NAA16_ENST00000403412.3_Missense_Mutation_p.I279F|NAA16_ENST00000379367.3_Missense_Mutation_p.I279F	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	279					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						GAGGCTTCAAATTTATGAAGA	0.318																																					p.I279F		.											.	NAA16-90	0			c.A835T						.						73	81	78					13																	41905433		2203	4296	6499	SO:0001583	missense	79612	exon8			CTTCAAATTTATG	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"N(alpha)-acetyltransferase subunits", "Tetratricopeptide (TTC) repeat domain containing"	26164	protein-coding gene	gene with protein product			"NMDA receptor regulated 1-like"	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.835A>T	13.37:g.41905433A>T	ENSP00000368716:p.Ile279Phe	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	148	47	NM_001110798	0	0	6	10	4	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242909	0.39598	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.45276	0.9;0.9;0.9	5.53	1.72	0.24424	.	0.233772	0.36167	N	0.002755	T	0.35008	0.0917	L	0.47716	1.5	0.49915	D	0.999832	B;P;B	0.37423	0.031;0.594;0.002	B;P;B	0.44860	0.049;0.462;0.008	T	0.09443	-1.0674	10	0.13470	T	0.59	-3.7053	5.4616	0.16619	0.647:0.1367:0.2163:0.0	.	279;279;279	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	F	279	ENSP00000368674:I279F;ENSP00000368716:I279F;ENSP00000386103:I279F	ENSP00000368674:I279F	I	+	1	0	NAA16	40803433	1.000000	0.71417	0.989000	0.46669	0.977000	0.68977	2.768000	0.47645	0.070000	0.16634	0.459000	0.35465	ATT	.		0.318	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41905433	A	T	41905433	3	4	89	1	0	0	0	0	1	0	0	0	10144	101	4	5	865	5	NAA16	13	41905433	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08		41905433	73264445	26	8096											
TEP1	7011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20841196	20841196	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtggccacagccttagcttCctgccacaagattagttccc	8	11	8	14	0	0	1	0	0	0	1	2	1	2	1	5	1	3	2	5	1	3	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr14:20841196C>T	ENST00000262715.5	-	48	6965	c.6925G>A	c.(6925-6927)Gaa>Aaa	p.E2309K	TEP1_ENST00000556935.1_Missense_Mutation_p.E2201K|TEP1_ENST00000545983.1_Missense_Mutation_p.E647K	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2309					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GCCTTAGCTTCCTGCCACAAG	0.517																																					p.E2309K		.											.	TEP1-95	0			c.G6925A						.						77	78	78					14																	20841196		2203	4300	6503	SO:0001583	missense	7011	exon48			TAGCTTCCTGCCA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.6925G>A	14.37:g.20841196C>T	ENSP00000262715:p.Glu2309Lys	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	103	41	NM_007110	0	0	4	8	4	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.58|12.58	1.981914|1.981914	0.34942|0.34942	.|.	.|.	ENSG00000129566|ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983|ENST00000553984	T;T;T|.	0.56103|.	2.26;2.26;0.48|.	5.77|5.77	2.31|2.31	0.28768|0.28768	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.860064|.	0.10567|.	N|.	0.659553|.	T|T	0.19485|0.19485	0.0468|0.0468	N|N	0.14661|0.14661	0.345|0.345	0.20638|0.20638	N|N	0.999872|0.999872	B;B;B;B|.	0.14805|.	0.007;0.004;0.011;0.002|.	B;B;B;B|.	0.13407|.	0.006;0.007;0.009;0.003|.	T|T	0.25467|0.25467	-1.0131|-1.0131	10|5	0.06757|.	T|.	0.87|.	0.0511|0.0511	5.2313|5.2313	0.15424|0.15424	0.0:0.62:0.1541:0.2259|0.0:0.62:0.1541:0.2259	.|.	647;2201;1652;2309|.	B4E0B6;G3V5X7;G3V2A4;Q99973|.	.;.;.;TEP1_HUMAN|.	K|E	2309;2309;2201;647|15	ENSP00000262715:E2309K;ENSP00000452574:E2201K;ENSP00000438849:E647K|.	ENSP00000262715:E2309K|.	E|G	-|-	1|2	0|0	TEP1|TEP1	19911036|19911036	0.182000|0.182000	0.23173|0.23173	0.350000|0.350000	0.25708|0.25708	0.972000|0.972000	0.66771|0.66771	0.105000|0.105000	0.15333|0.15333	0.154000|0.154000	0.19237|0.19237	-0.150000|-0.150000	0.13652|0.13652	GAA|GGA	.		0.517	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20841196	C	T	20841196	3	4	89	1	0	0	0	0	1	0	0	0	15791	864	30	2	990	2	TEP1	14	20841196	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		20841196	86508344	27	8097											
AHNAK2	113146	ucsc.edu	37	chr14	105415291	105415291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgatggacttgcctggggcaGacaccccaaacgacggcatc	10	5	12	14	3	0	1	0	0	0	1	1	4	0	2	3	4	2	2	3	4	1	1	rs568117634		TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr14:105415291G>A	ENST00000333244.5	-	7	6616	c.6497C>T	c.(6496-6498)tCt>tTt	p.S2166F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2166						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCTGGGGCAGACACCCCAAA	0.592													.|||	0	0	0	0	5008	,	,		16538	0		0	False		,,,				2504	0				p.S2166F													.	AHNAK2-47	0			c.C6497T						.						208	149	170					14																	105415291		1940	3520	5460	SO:0001583	missense	113146	exon7			GGGGCAGACACCC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.6497C>T	14.37:g.105415291G>A	ENSP00000353114:p.Ser2166Phe	Somatic	539	0		WXS	Illumina HiSeq		485	2	NM_138420	0	0	96	96	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	16.92	3.256462	0.59321	.	.	ENSG00000185567	ENST00000333244	T	0.01025	5.43	4.35	4.35	0.52113	.	.	.	.	.	T	0.08403	0.0209	M	0.91406	3.205	0.09310	N	1	D	0.71674	0.998	D	0.87578	0.998	T	0.04752	-1.0929	9	0.52906	T	0.07	.	16.9291	0.86184	0.0:0.0:1.0:0.0	.	2166	Q8IVF2	AHNK2_HUMAN	F	2166	ENSP00000353114:S2166F	ENSP00000353114:S2166F	S	-	2	0	AHNAK2	104486336	0.018000	0.18449	0.006000	0.13384	0.001000	0.01503	1.888000	0.39708	1.995000	0.58328	0.306000	0.20318	TCT	.		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105415291	G	A	105415291	3	1	89	1	0	0	0	0	1	0	0	0	415	942	33	2	10894	2	AHNAK2	14	105415291	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	84574095	105415291	1934249	28	8098											
NDNL2	56160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	29561225	29561225	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtattccaggtaacgctgtcGcacaaagtcctcagtaatga	12	10	9	10	2	1	1	1	1	0	0	4	1	3	1	2	1	1	5	2	1	4	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr15:29561225G>C	ENST00000332303.4	-	1	808	c.685C>G	c.(685-687)Cga>Gga	p.R229G	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	229	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)		p.R229*(1)		breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		TAACGCTGTCGCACAAAGTCC	0.532																																					p.R229G		.											.	NDNL2-90	1	Substitution - Nonsense(1)	large_intestine(1)	c.C685G						.						68	75	73					15																	29561225		2203	4300	6503	SO:0001583	missense	56160	exon1			GCTGTCGCACAAA	AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.685C>G	15.37:g.29561225G>C	ENSP00000330694:p.Arg229Gly	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	134	50	NM_138704	0	0	17	34	17	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.392428	0.62066	.	.	ENSG00000185115	ENST00000332303	T	0.06142	3.34	4.1	3.16	0.36331	.	0.069228	0.56097	D	0.000039	T	0.24470	0.0593	M	0.86864	2.845	0.41871	D	0.990272	D	0.64830	0.994	D	0.68483	0.958	T	0.02150	-1.1205	10	0.87932	D	0	.	9.1001	0.36662	0.0:0.0:0.7819:0.2181	.	229	Q96MG7	MAGG1_HUMAN	G	229	ENSP00000330694:R229G	ENSP00000330694:R229G	R	-	1	2	NDNL2	27348517	0.989000	0.36119	0.984000	0.44739	0.885000	0.51271	1.680000	0.37607	1.262000	0.44165	0.563000	0.77884	CGA	.		0.532	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704		C	29561225	G	C	29561225	3	2	89	1	0	0	0	0	1	0	0	0	10274	1095	38	4	233	4	NDNL2	15	29561225	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08		29561225	72970167	29	8099											
ARHGAP11A	9824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	32928906	32928906	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccagaggaaaatctattTgaaactaatgatttgactat	16	12	7	6	0	1	4	0	3	1	1	1	5	1	5	1	1	2	0	1	1	6	5			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr15:32928906T>G	ENST00000361627.3	+	12	2654	c.1932T>G	c.(1930-1932)ttT>ttG	p.F644L	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.F455L|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.F455L	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	644					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AAAATCTATTTGAAACTAATG	0.358																																					p.F644L	Colon(45;757 1134 30003 36652)	.											.	ARHGAP11A-292	0			c.T1932G						.						30	32	31					15																	32928906		2197	4296	6493	SO:0001583	missense	9824	exon12			TCTATTTGAAACT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"Rho GTPase activating proteins"	15783	protein-coding gene	gene with protein product	"GAP (1-12)"	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1932T>G	15.37:g.32928906T>G	ENSP00000355090:p.Phe644Leu	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	46	25	NM_014783	0	0	0	0	0	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	3.671	-0.067535	0.07273	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.08370	3.1	4.68	0.799	0.18667	.	0.649114	0.13886	N	0.355958	T	0.05686	0.0149	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40869	-0.9540	10	0.27785	T	0.31	.	6.2376	0.20772	0.2542:0.0:0.2632:0.4826	.	644	Q6P4F7	RHGBA_HUMAN	L	644;455	ENSP00000355090:F644L	ENSP00000355090:F644L	F	+	3	2	ARHGAP11A	30716198	0.999000	0.42202	0.595000	0.28798	0.557000	0.35523	1.332000	0.33805	-0.039000	0.13602	0.455000	0.32223	TTT	.		0.358	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		G	32928906	T	G	32928906	3	3	89	1	0	0	0	0	1	0	0	0	863	1809	63	5	2001	5	ARHGAP11A	15	32928906	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	3367681	32928906	69602486	30	8100											
NR2F2	7026	broad.mit.edu	37	chr15	96877563	96877563	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccggaacatccccttcttccCcgacctgcagatcacggacc	8	7	7	19	3	2	1	1	0	1	1	4	4	4	3	7	2	2	1	7	2	1	2			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr15:96877563C>G	ENST00000394166.3	+	2	2090	c.701C>G	c.(700-702)cCc>cGc	p.P234R	NR2F2_ENST00000453270.2_Missense_Mutation_p.P81R|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000421109.2_Missense_Mutation_p.P101R|NR2F2_ENST00000394171.2_Missense_Mutation_p.P81R	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	234	Interaction with ZFPM2. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			CCCTTCTTCCCCGACCTGCAG	0.617																																					p.P234R													.	NR2F2-228	0			c.C701G						.						133	123	126					15																	96877563		2197	4298	6495	SO:0001583	missense	7026	exon2			TCTTCCCCGACCT	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.701C>G	15.37:g.96877563C>G	ENSP00000377721:p.Pro234Arg	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	159	6	NM_021005	0	0	357	357	0	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	37	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175228	0.94807	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81	5.09	5.09	0.68999	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.96131	0.8739	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.989	D	0.97151	0.9831	10	0.72032	D	0.01	.	18.4813	0.90812	0.0:1.0:0.0:0.0	.	234;101	P24468;Q3KQR7	COT2_HUMAN;.	R	101;234;81;81	ENSP00000401674:P101R;ENSP00000377721:P234R;ENSP00000377726:P81R;ENSP00000389853:P81R	ENSP00000377721:P234R	P	+	2	0	NR2F2	94678567	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.818000	0.86416	2.376000	0.81061	0.655000	0.94253	CCC	.		0.617	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			G	96877563	C	G	96877563	3	3	89	1	0	0	0	0	1	0	0	0	10654	623	22	4	754	4	NR2F2	15	96877563	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	63948657	96877563	5653829	31	8101											
MAPK8IP3	23162	hgsc.bcm.edu	37	chr16	1817800	1817807	+	Splice_Site	DEL	CCACAGGC	CCACAGGC	-																															gccaccctgaccgctctcccCcacaggcactggcaagctgg																								rs201517459|rs181043730	byFrequency	TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	CCACAGGC	CCACAGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:1817800_1817807delCCACAGGC	ENST00000250894.4	+	28	3563_3565	c.3406_3408delCCACAGGC	c.(3406-3408)ccadel	p.P1136fs	MAPK8IP3_ENST00000356010.5_Splice_Site_p.P1130fs	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	1136					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)	p.?(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						CCGCTCTCCCCCACAGGCACTGGCAAGC	0.654																																					p.1136_1136del		.											.	MAPK8IP3-1109	1	Unknown(1)	lung(1)	c.3407_3408del						.																																			SO:0001630	splice_region_variant	23162	exon28			.	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"homolog of Drosophila Sunday driver 2"	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.3407-1CCACAGGC>-	16.37:g.1817800_1817807delCCACAGGC		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	66	14	NM_015133	0	0	0	0	0	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Frame_Shift_Del	DEL	ENST00000250894.4	37	CCDS10442.2																																																																																			.		0.654	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	Frame_Shift_Del	-	1817807	CCACAGGC	-	1817800	8	5	89	1	0	1	0	1	0	0	1	0	9311	638	22	0		0	MAPK8IP3	16	1817800	Splice_Site	DEL	CCACAGGC	TCGA-BQ-7060-01A-11D-1961-08		1817800	88536953	32	8102											
TMC5	79838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19490814	19490814	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctgatggattttgtgttctCtttagtcaattccttcctgg	5	20	8	8	0	3	1	1	1	2	0	6	2	5	2	2	2	0	1	2	2	2	7			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:19490814C>G	ENST00000396229.2	+	14	2980	c.2231C>G	c.(2230-2232)tCt>tGt	p.S744C	TMC5_ENST00000219821.5_Missense_Mutation_p.S498C|TMC5_ENST00000564959.1_Missense_Mutation_p.S427C|TMC5_ENST00000541464.1_Missense_Mutation_p.S692C|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000542583.2_Missense_Mutation_p.S744C|TMC5_ENST00000381414.4_Missense_Mutation_p.S744C|TMC5_ENST00000561503.1_Missense_Mutation_p.S385C	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	744					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTTGTGTTCTCTTTAGTCAAT	0.473																																					p.S744C		.											.	TMC5-91	0			c.C2231G						.						246	253	250					16																	19490814		2197	4300	6497	SO:0001583	missense	79838	exon14			TGTTCTCTTTAGT	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2231C>G	16.37:g.19490814C>G	ENSP00000379531:p.Ser744Cys	Somatic	344	1		WXS	Illumina HiSeq	Phase_I	389	116	NM_001105249	0	0	0	0	0	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.684070	0.29872	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.15	5.15	0.70609	.	0.292700	0.35207	N	0.003365	T	0.49864	0.1582	N	0.26042	0.785	0.34863	D	0.742852	B;B;B;B;B;B	0.31548	0.068;0.12;0.008;0.01;0.328;0.281	B;B;B;B;B;B	0.30401	0.07;0.081;0.023;0.026;0.115;0.07	T	0.62973	-0.6740	10	0.48119	T	0.1	-9.1731	14.3209	0.66487	0.0:0.8051:0.1949:0.0	.	692;427;498;498;744;744	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	C	692;744;744;744;498;427	ENSP00000441227:S692C;ENSP00000370822:S744C;ENSP00000379531:S744C;ENSP00000446274:S744C;ENSP00000219821:S498C	ENSP00000219821:S498C	S	+	2	0	TMC5	19398315	0.525000	0.26290	0.987000	0.45799	0.873000	0.50193	0.913000	0.28611	2.387000	0.81309	0.555000	0.69702	TCT	.		0.473	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		G	19490814	C	G	19490814	3	3	89	1	0	0	0	0	1	0	0	0	16020	913	32	4	2591	4	TMC5	16	19490814	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	17673014	19490814	70863939	33	8103											
EEF2K	29904	ucsc.edu	37	chr16	22274500	22274500	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggatgaccctgagcccCgagaacatgtaaggaacccc	12	5	11	13	1	0	3	0	2	0	1	0	6	0	5	5	2	4	2	5	2	3	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:22274500C>T	ENST00000263026.5	+	12	1843	c.1369C>T	c.(1369-1371)Cga>Tga	p.R457*		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	457					insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CCCTGAGCCCCGAGAACATGT	0.552																																					p.R457X	NSCLC(195;1411 2157 20319 27471 51856)												.	EEF2K-856	0			c.C1369T						.						80	65	71					16																	22274500		2197	4300	6497	SO:0001587	stop_gained	29904	exon12			GAGCCCCGAGAAC	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.1369C>T	16.37:g.22274500C>T	ENSP00000263026:p.Arg457*	Somatic	26	0		WXS	Illumina HiSeq		28	4	NM_013302	0	0	0	0	0	Q8N588	Nonsense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	C	41	8.849534	0.98976	.	.	ENSG00000103319	ENST00000263026	.	.	.	5.39	3.37	0.38596	.	0.826423	0.11375	N	0.570474	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.031	8.9336	0.35686	0.3659:0.5072:0.1269:0.0	.	.	.	.	X	457	.	ENSP00000263026:R457X	R	+	1	2	EEF2K	22182001	0.894000	0.30519	1.000000	0.80357	0.951000	0.60555	0.801000	0.27055	0.722000	0.32252	0.650000	0.86243	CGA	.		0.552	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		T	22274500	C	T	22274500	4	4	89	1	0	0	0	0	0	1	0	0	4941	644	23	1	1411	1	EEF2K	16	22274500	Nonsense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	2783686	22274500	68080253	34	8104											
ITGAX	3687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31383749	31383749	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttgcgtctgaacttcacGctggtgggcaagcccctcct	6	10	10	15	2	2	1	1	1	1	0	3	1	3	1	4	2	3	2	4	2	2	2			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:31383749G>A	ENST00000268296.4	+	18	2332	c.2211G>A	c.(2209-2211)acG>acA	p.T737T	ITGAX_ENST00000562522.1_Silent_p.T737T	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	737					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TGAACTTCACGCTGGTGGGCA	0.637																																					p.T737T		.											.	ITGAX-229	0			c.G2211A						.						87	76	80					16																	31383749		2197	4300	6497	SO:0001819	synonymous_variant	3687	exon18			CTTCACGCTGGTG	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2211G>A	16.37:g.31383749G>A		Somatic	101	1		WXS	Illumina HiSeq	Phase_I	130	68	NM_000887	0	0	24	25	1	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			.		0.637	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31383749	G	A	31383749	2	1	89	1	0	0	0	0	0	0	0	1	7910	1074	38	1		1	ITGAX	16	31383749	Silent	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	9109249	31383749	58971004	35	8105											
C16orf70	80262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67168085	67168085	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcagcccaattttgcccaTggcctggcttctctccagat	6	13	8	14	0	1	1	0	0	1	1	3	1	2	1	4	2	3	2	4	2	1	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:67168085T>C	ENST00000219139.3	+	7	653	c.465T>C	c.(463-465)caT>caC	p.H155H	C16orf70_ENST00000569683.1_3'UTR|C16orf70_ENST00000569600.1_Silent_p.H155H	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	155										cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		ATTTTGCCCATGGCCTGGCTT	0.483																																					p.H155H		.											.	C16orf70-70	0			c.T465C						.						107	100	102					16																	67168085		2200	4300	6500	SO:0001819	synonymous_variant	80262	exon7			TGCCCATGGCCTG	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.465T>C	16.37:g.67168085T>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	175	52	NM_025187	0	0	8	11	3	Q9HA86	Silent	SNP	ENST00000219139.3	37	CCDS10828.1																																																																																			.		0.483	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		C	67168085	T	C	67168085	2	2	89	1	0	0	0	0	0	0	0	1	1833	1461	51	3		3	C16orf70	16	67168085	Silent	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	35784336	67168085	23186668	36	8106											
MYH13	8735	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10267725	10267725	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatacatttccttattatcCgctacaaagcaggctttctt	11	15	4	11	1	1	0	0	0	1	0	3	0	3	0	2	1	3	3	2	1	5	7	rs374269997		TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr17:10267725C>T	ENST00000418404.3	-	2	286	c.123G>A	c.(121-123)gcG>gcA	p.A41A	MYH13_ENST00000252172.4_Silent_p.A41A			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	41					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CCTTATTATCCGCTACAAAGC	0.453																																					p.A41A													.	MYH13-6	0			c.G123A						.						118	113	114					17																	10267725		1929	4139	6068	SO:0001819	synonymous_variant	8735	exon3			ATTATCCGCTACA	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.123G>A	17.37:g.10267725C>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	64	13	NM_003802	0	0	0	0	0	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			.		0.453	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10267725	C	T	10267725	2	4	89	1	0	0	0	0	0	0	0	1	10057	639	23	1		1	MYH13	17	10267725	Silent	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		10267725	70927485	37	8107											
ERAL1	26284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27182278	27182278	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctggaccacttcctcggaTtctctcagcccgacagttcg	6	10	8	17	3	2	0	1	0	1	0	6	3	3	2	4	2	1	1	4	2	0	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr17:27182278T>C	ENST00000254928.5	+	1	323	c.226T>C	c.(226-228)Ttc>Ctc	p.F76L	FAM222B_ENST00000583953.1_5'Flank|ERAL1_ENST00000578001.1_3'UTR	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	76					ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			CTTCCTCGGATTCTCTCAGCC	0.602																																					p.F76L		.											.	ERAL1-91	0			c.T226C						.						41	43	42					17																	27182278		2203	4300	6503	SO:0001583	missense	26284	exon1			CTCGGATTCTCTC	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"Era (E. coli G-protein homolog)-like 1", "Era G-protein-like 1 (E. coli)"			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.226T>C	17.37:g.27182278T>C	ENSP00000254928:p.Phe76Leu	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	95	56	NM_005702	0	0	39	110	71	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Missense_Mutation	SNP	ENST00000254928.5	37	CCDS11244.1	.	.	.	.	.	.	.	.	.	.	T	9.501	1.103237	0.20632	.	.	ENSG00000132591	ENST00000254928	.	.	.	5.25	-1.46	0.08800	.	0.850078	0.10643	N	0.650826	T	0.07188	0.0182	N	0.02011	-0.69	0.09310	N	0.999995	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.33904	-0.9850	9	0.02654	T	1	-3.854	1.1254	0.01734	0.3213:0.163:0.3615:0.1542	.	76;76	O75616;O75616-2	ERAL1_HUMAN;.	L	76	.	ENSP00000254928:F76L	F	+	1	0	ERAL1	24206404	0.113000	0.22115	0.236000	0.24074	0.049000	0.14656	-0.256000	0.08757	-0.052000	0.13311	0.459000	0.35465	TTC	.		0.602	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2			C	27182278	T	C	27182278	3	2	89	1	0	0	0	0	1	0	0	0	5215	1493	52	3	228	3	ERAL1	17	27182278	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	16914553	27182278	54012932	38	8108											
DLGAP1	9229	broad.mit.edu;bcgsc.ca	37	chr18	3499238	3499238	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgatgctctcggcgctctcgGtggccgagttctggcggacg	3	9	16	13	7	3	0	0	0	3	0	5	3	3	1	1	5	1	3	1	5	0	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr18:3499238G>T	ENST00000315677.3	-	13	3474	c.2879C>A	c.(2878-2880)aCc>aAc	p.T960N	DLGAP1_ENST00000584874.1_Missense_Mutation_p.T960N|DLGAP1_ENST00000534970.1_Missense_Mutation_p.T644N|DLGAP1_ENST00000539435.1_Missense_Mutation_p.T668N|DLGAP1_ENST00000400150.3_Missense_Mutation_p.T676N|DLGAP1_ENST00000400147.2_Missense_Mutation_p.T658N|DLGAP1_ENST00000400155.1_Missense_Mutation_p.T666N|DLGAP1_ENST00000400149.3_Missense_Mutation_p.T650N|DLGAP1_ENST00000581699.1_Missense_Mutation_p.T666N	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	960					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				GGCGCTCTCGGTGGCCGAGTT	0.731																																					p.T960N													.	DLGAP1-229	0			c.C2879A						.						9	10	10					18																	3499238		2182	4274	6456	SO:0001583	missense	9229	exon13			CTCTCGGTGGCCG	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.2879C>A	18.37:g.3499238G>T	ENSP00000316377:p.Thr960Asn	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	25	6	NM_004746	0	0	2	2	0	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	37	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.687473	0.68157	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435	T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.51483	0.1677	M	0.81497	2.545	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;1.0;0.998;1.0;1.0;1.0	T	0.57458	-0.7808	10	0.87932	D	0	-28.0728	18.7351	0.91751	0.0:0.0:1.0:0.0	.	644;656;666;668;960;658	B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;O14490;O14490-2	.;.;.;.;DLGP1_HUMAN;.	N	960;658;676;650;666;644;668	ENSP00000316377:T960N;ENSP00000383011:T658N;ENSP00000383014:T676N;ENSP00000383013:T650N;ENSP00000383019:T666N;ENSP00000437817:T644N;ENSP00000446312:T668N	ENSP00000316377:T960N	T	-	2	0	DLGAP1	3489238	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.661000	0.98601	2.426000	0.82243	0.557000	0.71058	ACC	.		0.731	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			T	3499238	G	T	3499238	3	4	89	1	0	0	0	0	1	0	0	0	4570	1261	44	4	58	4	DLGAP1	18	3499238	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08		3499238	74578010	39	8109											
ZNF559	84527	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	9453288	9453288	+	Frame_Shift_Del	DEL	A	A	-																															tatcaatgtaaggaatgtggAaaagcctttattaattcctc																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr19:9453288delA	ENST00000393883.2	+	6	1809	c.1161delA	c.(1159-1161)ggafs	p.G387fs	ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000586255.1_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000538743.1_Frame_Shift_Del_p.G307fs|ZNF177_ENST00000605471.1_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000603380.1_Frame_Shift_Del_p.G387fs|ZNF559_ENST00000587557.1_Frame_Shift_Del_p.G451fs|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						AGGAATGTGGAAAAGCCTTTA	0.393																																					p.G451fs		.											.	ZNF559-91	0			c.1353delA						.						62	57	59					19																	9453288		2203	4300	6503	SO:0001589	frameshift_variant	84527	exon6			.	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1161delA	19.37:g.9453288delA	ENSP00000377461:p.Gly387fs	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	72	20	NM_001202406	0	0	0	0	0	K7EMG6	Frame_Shift_Del	DEL	ENST00000393883.2	37	CCDS12211.1																																																																																			.		0.393	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		-	9453288	A	-	9453288	7	5	89	1	0	1	0	1	0	0	0	0	18022	233	9	0	1175	0	ZNF559	19	9453288	Frame_Shift_Del	DEL	A	TCGA-BQ-7060-01A-11D-1961-08		9453288	49675695	40	8110	88	2									
ZNF559	84527	hgsc.bcm.edu;bcgsc.ca	37	chr19	9453293	9453293	+	Missense_Mutation	SNP	C	C	G																															atgtaaggaatgtggaaaagCctttattaattcctcttcct																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr19:9453293C>G	ENST00000393883.2	+	6	1814	c.1166C>G	c.(1165-1167)gCc>gGc	p.A389G	ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000586255.1_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000538743.1_Missense_Mutation_p.A309G|ZNF177_ENST00000605471.1_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.A389G|ZNF559_ENST00000587557.1_Missense_Mutation_p.A453G|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	389					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						TGTGGAAAAGCCTTTATTAAT	0.403																																					p.A453G		.											.	ZNF559-91	0			c.C1358G						.						63	58	60					19																	9453293		2203	4300	6503	SO:0001583	missense	84527	exon6			GAAAAGCCTTTAT	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1166C>G	19.37:g.9453293C>G	ENSP00000377461:p.Ala389Gly	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	74	26	NM_001202406	0	0	6	6	0	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599554	0.46318	.	.	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	T;T	0.13901	2.55;2.55	2.22	-0.134	0.13481	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10766	0.0263	N	0.21324	0.655	0.09310	N	1	B;B;B	0.25441	0.028;0.126;0.108	B;B;B	0.38500	0.035;0.275;0.114	T	0.44682	-0.9312	9	0.72032	D	0.01	.	2.8735	0.05624	0.0:0.4172:0.241:0.3417	.	389;389;309	B3KPL8;Q9BR84;B4DP29	.;ZN559_HUMAN;.	G	389;309;389	ENSP00000442832:A309G;ENSP00000377461:A389G	ENSP00000325393:A389G	A	+	2	0	ZNF559	9314293	0.000000	0.05858	0.051000	0.19133	0.916000	0.54674	-0.790000	0.04604	0.024000	0.15214	0.313000	0.20887	GCC	.		0.403	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		G	9453293	C	G	9453293	3	3	89	1	0	0	0	0	1	0	0	0	18022	739	26	4	1180	4	ZNF559	19	9453293	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	5	9453293	49675690	41	8111	88	2									
HSPBP1	23640	ucsc.edu	37	chr19	55777303	55777303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaggggctgtgctctgtccGcaccagggccaccagctgct	6	7	14	14	1	1	0	0	0	1	0	2	1	2	0	4	3	3	5	4	3	1	0			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr19:55777303G>A	ENST00000255631.5	-	7	1154	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	HSPBP1_ENST00000376343.3_Intron|HSPBP1_ENST00000433386.2_Missense_Mutation_p.R282W|HSPBP1_ENST00000587922.1_Missense_Mutation_p.R282W	NM_001130106.1|NM_012267.4	NP_001123578.1|NP_036399.3	Q9NZL4	HPBP1_HUMAN	HSPA (heat shock 70kDa) binding protein, cytoplasmic cochaperone 1	285					negative regulation of catalytic activity (GO:0043086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)		enzyme inhibitor activity (GO:0004857)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	8			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		TGCTCTGTCCGCACCAGGGCC	0.687																																					p.R282W													.	HSPBP1-90	0			c.C844T						.						18	19	19					19																	55777303		2201	4298	6499	SO:0001583	missense	23640	exon6			CTGTCCGCACCAG		CCDS33111.1	19q13.42	2008-12-16			ENSG00000133265	ENSG00000133265			24989	protein-coding gene	gene with protein product	"hsp70 interacting protein", "Hsp70 binding protein 1"	612939				10786638, 9830037	Standard	NM_001130106		Approved	HspBP1, FES1	uc002qkd.3	Q9NZL4		ENST00000255631.5:c.844C>T	19.37:g.55777303G>A	ENSP00000255631:p.Arg282Trp	Somatic	33	0		WXS	Illumina HiSeq		34	4	NM_012267	0	0	111	111	0	B3KQP0|B4DG11|O95351|Q6ZNU5	Missense_Mutation	SNP	ENST00000255631.5	37	CCDS33111.1	.	.	.	.	.	.	.	.	.	.	g	15.51	2.854878	0.51376	.	.	ENSG00000133265	ENST00000433386;ENST00000255631	T;T	0.52983	0.64;0.64	4.19	3.03	0.35002	Armadillo-like helical (1);Armadillo-type fold (1);	0.201340	0.43110	D	0.000614	T	0.57021	0.2025	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.71656	0.974;0.622	T	0.56189	-0.8020	10	0.72032	D	0.01	-5.7405	7.7056	0.28648	0.0:0.1554:0.5988:0.2458	.	285;328	Q9NZL4;B4DG11	HPBP1_HUMAN;.	W	282	ENSP00000398244:R282W;ENSP00000255631:R282W	ENSP00000255631:R282W	R	-	1	2	HSPBP1	60469115	1.000000	0.71417	0.893000	0.35052	0.981000	0.71138	5.268000	0.65536	0.659000	0.30945	0.486000	0.48141	CGG	.		0.687	HSPBP1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452670.1	NM_012267		A	55777303	G	A	55777303	3	1	89	1	0	0	0	0	1	0	0	0	7447	1086	38	1	247	1	HSPBP1	19	55777303	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	46324010	55777303	3351680	42	8112											
ZNRF3	84133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	29445350	29445350	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcccacggcaaccccgTcaccttgctgaccatggacc	8	6	9	18	2	1	1	1	1	0	0	2	3	2	3	6	3	2	2	6	3	1	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr22:29445350T>C	ENST00000544604.2	+	8	1356	c.1181T>C	c.(1180-1182)gTc>gCc	p.V394A	ZNRF3_ENST00000402174.1_Missense_Mutation_p.V294A|ZNRF3_ENST00000332811.4_Missense_Mutation_p.V294A|ZNRF3_ENST00000406323.3_Missense_Mutation_p.V294A	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	394					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GGCAACCCCGTCACCTTGCTG	0.667																																					p.V394A		.											.	ZNRF3-69	0			c.T1181C						.						56	64	61					22																	29445350		2180	4280	6460	SO:0001583	missense	84133	exon8			ACCCCGTCACCTT	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1181T>C	22.37:g.29445350T>C	ENSP00000443824:p.Val394Ala	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	55	15	NM_001206998	0	0	12	23	11	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	37	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345420	0.24426	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.53	4.5	0.54988	.	0.316033	0.36665	N	0.002471	T	0.67702	0.2921	L	0.44542	1.39	0.34781	D	0.734712	P	0.45531	0.86	B	0.37692	0.256	T	0.70029	-0.4984	10	0.07325	T	0.83	-5.454	10.3398	0.43870	0.0:0.0764:0.0:0.9236	.	394	Q9ULT6	ZNRF3_HUMAN	A	394;294;101;294;294	ENSP00000443824:V394A;ENSP00000328614:V294A;ENSP00000384456:V294A;ENSP00000384553:V294A	ENSP00000328614:V294A	V	+	2	0	ZNRF3	27775350	1.000000	0.71417	0.291000	0.24904	0.272000	0.26649	7.390000	0.79816	0.945000	0.37605	0.533000	0.62120	GTC	.		0.667	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		C	29445350	T	C	29445350	3	2	89	1	0	0	0	0	1	0	0	0	18245	1667	58	3	907	3	ZNRF3	22	29445350	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08		29445350	21859216	43	8113											
BEND2	139105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	18195783	18195783	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggatttccttggagaacaaAatacgaaccaagtagcaggc	16	7	10	8	1	0	1	0	0	0	1	1	4	1	2	2	3	4	2	2	3	7	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chrX:18195783A>T	ENST00000380033.4	-	10	1668	c.1536T>A	c.(1534-1536)atT>atA	p.I512I	BEND2_ENST00000380030.3_Silent_p.I421I	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	512	BEN 1. {ECO:0000255|PROSITE- ProRule:PRU00784}.									NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						TGGAGAACAAAATACGAACCA	0.428																																					p.I512I		.											.	BEND2-133	0			c.T1536A						.						267	253	258					X																	18195783		2203	4300	6503	SO:0001819	synonymous_variant	139105	exon10			GAACAAAATACGA	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"BEN domain containing"	28509	protein-coding gene	gene with protein product			"chromosome X open reading frame 20"	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.1536T>A	X.37:g.18195783A>T		Somatic	265	0		WXS	Illumina HiSeq	Phase_I	291	207	NM_153346	0	0	0	0	0	E9PFY2|Q4V9S2|Q5JXE5	Silent	SNP	ENST00000380033.4	37	CCDS14184.1																																																																																			.		0.428	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346		T	18195783	A	T	18195783	2	4	89	1	0	0	0	0	0	0	0	1	1399	10	1	5		5	BEND2	23	18195783	Silent	SNP	A	TCGA-BQ-7060-01A-11D-1961-08		18195783	137074777	44	8114											
KDM6A	7403	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	44733231	44733231	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacgaaggccctactgggcAaggtaaggcagctgcgagtc	10	5	16	10	2	0	0	0	0	0	0	1	3	0	1	1	5	3	4	1	5	4	2			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chrX:44733231A>T	ENST00000377967.4	+	2	264	c.223A>T	c.(223-225)Aag>Tag	p.K75*	KDM6A_ENST00000543216.1_Nonsense_Mutation_p.K75*|KDM6A_ENST00000536777.1_Nonsense_Mutation_p.K75*|KDM6A_ENST00000382899.4_Nonsense_Mutation_p.K75*	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	75	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0(8)|p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						CCTACTGGGCAAGGTAAGGCA	0.657			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.K75X	Colon(129;1273 1667 15230 27352 52914)			Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	14	No detectable mRNA/protein(8)|Whole gene deletion(6)	haematopoietic_and_lymphoid_tissue(6)|oesophagus(4)|breast(2)|pancreas(2)	c.A223T						.						68	56	60					X																	44733231		2203	4300	6503	SO:0001587	stop_gained	7403	exon2			CTGGGCAAGGTAA	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.223A>T	X.37:g.44733231A>T	ENSP00000367203:p.Lys75*	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	12	8	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Nonsense_Mutation	SNP	ENST00000377967.4	37	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	A	38	7.137178	0.98088	.	.	ENSG00000147050	ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000542299	.	.	.	4.84	4.84	0.62591	.	0.050879	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8412	12.3196	0.54977	1.0:0.0:0.0:0.0	.	.	.	.	X	75	.	ENSP00000367203:K75X	K	+	1	0	KDM6A	44618175	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.813000	0.86123	1.584000	0.49913	0.486000	0.48141	AAG	.		0.657	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		T	44733231	A	T	44733231	4	4	89	1	0	0	0	0	0	1	0	0	8158	131	5	5	229	5	KDM6A	23	44733231	Nonsense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	26537448	44733231	110537329	45	8115											
KIF1B	23095	ucsc.edu	37	chr1	10328256	10328256	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaacaagtagccgttcccacGctgtgtttacgattgttttc	9	14	8	10	3	0	0	0	0	0	0	2	1	1	0	2	0	3	5	2	0	4	7			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:10328256G>A	ENST00000377086.1	+	7	857	c.655G>A	c.(655-657)Gct>Act	p.A219T	KIF1B_ENST00000377093.4_Missense_Mutation_p.A219T|KIF1B_ENST00000377081.1_Missense_Mutation_p.A219T|KIF1B_ENST00000377083.1_Missense_Mutation_p.A219T|KIF1B_ENST00000263934.6_Missense_Mutation_p.A219T			O60333	KIF1B_HUMAN	kinesin family member 1B	219	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.			AVF -> VVY (in Ref. 3; AAK49332, 4; AAK85155 and 5; AAN17742). {ECO:0000305}.	anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCGTTCCCACGCTGTGTTTAC	0.428																																					p.A219T													.	KIF1B-93	0			c.G655A						.						101	85	90					1																	10328256		2203	4300	6503	SO:0001583	missense	23095	exon7			TCCCACGCTGTGT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.655G>A	1.37:g.10328256G>A	ENSP00000366290:p.Ala219Thr	Somatic	56	0		WXS	Illumina HiSeq		41	5	NM_183416	0	0	22	22	0	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	G	37	6.031073	0.97221	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	D;D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5;-2.5	5.94	5.94	0.96194	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	D	0.94059	0.8096	M	0.64170	1.965	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.985;1.0;1.0	D;D;D;D;P;D;D	0.91635	0.998;0.998;0.999;0.998;0.719;0.995;0.998	D	0.93833	0.7129	10	0.87932	D	0	.	20.3736	0.98901	0.0:0.0:1.0:0.0	.	219;219;219;219;219;219;219	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	T	219	ENSP00000263934:A219T;ENSP00000366297:A219T;ENSP00000366290:A219T;ENSP00000366287:A219T;ENSP00000366284:A219T	ENSP00000263934:A219T	A	+	1	0	KIF1B	10250843	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.869000	0.99810	2.820000	0.97059	0.650000	0.86243	GCT	.		0.428	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			A	10328256	G	A	10328256	3	1	90	1	0	0	0	0	1	0	0	0	8305	1087	38	1	677	1	KIF1B	1	10328256	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		10328256	238922365	1	8116											
MTOR	2475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11307790	11307790	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcagcacccactggcacaCctgagagaggaaggataaag	14	6	11	10	0	1	2	1	1	0	1	1	5	1	4	2	3	1	2	2	3	3	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:11307790C>A	ENST00000361445.4	-	8	1193	c.1117G>T	c.(1117-1119)Gtg>Ttg	p.V373L		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	373	Interaction with NBN.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CACTGGCACACCTGAGAGAGG	0.498																																					p.V373L		.											.	MTOR-1439	0			c.G1117T						.						95	94	94					1																	11307790		2203	4300	6503	SO:0001630	splice_region_variant	2475	exon8			GGCACACCTGAGA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.1117-1G>T	1.37:g.11307790C>A		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	90	18	NM_004958	0	0	0	0	0	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.796328	0.50208	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.57273	0.41	5.74	5.74	0.90152	Armadillo-like helical (1);Armadillo-type fold (2);	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.69823	2.125	0.80722	D	1	B	0.26744	0.158	B	0.19391	0.025	T	0.53092	-0.8487	10	0.56958	D	0.05	-0.496	13.1719	0.59604	0.0:0.9275:0.0:0.0725	.	373	P42345	MTOR_HUMAN	L	373	ENSP00000354558:V373L	ENSP00000354558:V373L	V	-	1	0	MTOR	11230377	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	5.752000	0.68728	2.712000	0.92718	0.650000	0.86243	GTG	.		0.498	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	Missense_Mutation	A	11307790	C	A	11307790	5	1	90	1	0	0	0	0	0	0	1	0	9979	521	18	4	6736	4	MTOR	1	11307790	Splice_Site	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	979534	11307790	237942831	2	8117											
ZMYM6	9204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	35476600	35476600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctgagacaggggcaccGccgaagagtttgttcctttt	7	10	13	11	2	0	2	0	1	0	2	1	4	1	2	4	3	0	3	4	3	1	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:35476600G>A	ENST00000357182.4	-	9	1327	c.1100C>T	c.(1099-1101)gCg>gTg	p.A367V	ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000373340.2_Missense_Mutation_p.A367V|ZMYM6_ENST00000487874.1_Missense_Mutation_p.A367V	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	367					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A367V(1)|p.A367E(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				CAGGGGCACCGCCGAAGAGTT	0.458																																					p.A367V		.											.	ZMYM6-93	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1100T						.						53	53	53					1																	35476600		2203	4300	6503	SO:0001583	missense	9204	exon9			GGCACCGCCGAAG	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"Zinc fingers, MYM type", "Zinc fingers, BED-type"	13050	protein-coding gene	gene with protein product	"zinc finger, BED-type containing 7"	613567	"zinc finger protein 258", "zinc finger, MYM-type containing 6"	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.1100C>T	1.37:g.35476600G>A	ENSP00000349708:p.Ala367Val	Somatic	87	1		WXS	Illumina HiSeq	Phase_I	95	37	NM_007167	0	0	2	6	4	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	G	0.993	-0.693458	0.03303	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	T;T	0.21191	2.02;3.19	5.2	-0.779	0.10973	.	0.649416	0.15854	N	0.241338	T	0.05181	0.0138	N	0.00926	-1.1	0.19575	N	0.999966	B;B;B	0.16166	0.016;0.004;0.001	B;B;B	0.08055	0.002;0.001;0.003	T	0.42716	-0.9435	10	0.07644	T	0.81	-7.0E-4	10.0213	0.42044	0.749:0.0:0.251:0.0	.	270;367;367	B4DWC0;O95789;O95789-1	.;ZMYM6_HUMAN;.	V	367	ENSP00000362437:A367V;ENSP00000349708:A367V	ENSP00000349708:A367V	A	-	2	0	ZMYM6	35249187	0.006000	0.16342	0.025000	0.17156	0.615000	0.37417	0.331000	0.19733	-0.009000	0.14296	0.655000	0.94253	GCG	.		0.458	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		A	35476600	G	A	35476600	3	1	90	1	0	0	0	0	1	0	0	0	17736	1087	38	1	2909	1	ZMYM6	1	35476600	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	24168810	35476600	213774021	3	8118											
GLMN	11146	hgsc.bcm.edu;broad.mit.edu	37	chr1	92712096	92712096	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aaatggaactttcactttatCccaatattttcttcagaggt	12	16	5	8	0	3	1	2	0	1	1	4	2	4	2	1	2	1	0	1	2	5	7			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:92712096C>G	ENST00000370360.3	-	19	1857	c.1776G>C	c.(1774-1776)ggG>ggC	p.G592G	GLMN_ENST00000534881.1_Silent_p.G578G	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	592					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		TTCACTTTATCCCAATATTTT	0.259									Multiple Glomus Tumors (of the Skin), Familial																												p.G592G		.											.	GLMN-227	0			c.G1776C						.						68	67	67					1																	92712096		2203	4297	6500	SO:0001819	synonymous_variant	11146	exon19	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	CTTTATCCCAATA	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1776G>C	1.37:g.92712096C>G		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_053274	0	0	1	1	0	Q5VVC3|Q9BVE8	Silent	SNP	ENST00000370360.3	37	CCDS738.1																																																																																			.		0.259	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070		G	92712096	C	G	92712096	2	3	90	1	0	0	0	0	0	0	0	1	6468	842	30	4		4	GLMN	1	92712096	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	57235496	92712096	156538525	4	8119											
LCE2A	353139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152671691	152671691	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgccacagctctggggactGctgctgaccagacctcgaac	8	7	11	15	1	1	2	0	1	1	1	2	4	1	3	3	2	5	3	3	2	1	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:152671691G>C	ENST00000368779.1	+	2	365	c.314G>C	c.(313-315)tGc>tCc	p.C105S		NM_178428.3	NP_848515.1	Q5TA79	LCE2A_HUMAN	late cornified envelope 2A	105	Cys-rich.				keratinization (GO:0031424)					breast(1)|large_intestine(1)|liver(2)|lung(4)	8	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTGGGGACTGCTGCTGACCA	0.587																																					p.C105S		.											.	LCE2A-68	0			c.G314C						.						41	46	45					1																	152671691		2203	4300	6503	SO:0001583	missense	353139	exon2			GGGACTGCTGCTG		CCDS1021.1	1q21.3	2008-02-05			ENSG00000187173	ENSG00000187173		"Late cornified envelopes"	29469	protein-coding gene	gene with protein product		612609				11698679	Standard	NM_178428		Approved	LEP9	uc001faj.3	Q5TA79	OTTHUMG00000012392	ENST00000368779.1:c.314G>C	1.37:g.152671691G>C	ENSP00000357768:p.Cys105Ser	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	127	32	NM_178428	0	0	0	0	0	A4QMZ9	Missense_Mutation	SNP	ENST00000368779.1	37	CCDS1021.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.291835	0.23564	.	.	ENSG00000187173	ENST00000368779	T	0.03496	3.91	4.41	4.41	0.53225	.	.	.	.	.	T	0.09069	0.0224	M	0.71206	2.165	0.27116	N	0.962263	D	0.76494	0.999	D	0.78314	0.991	T	0.02691	-1.1123	9	0.87932	D	0	.	12.3335	0.55054	0.0:0.0:1.0:0.0	.	105	Q5TA79	LCE2A_HUMAN	S	105	ENSP00000357768:C105S	ENSP00000357768:C105S	C	+	2	0	LCE2A	150938315	0.999000	0.42202	1.000000	0.80357	0.737000	0.42083	1.350000	0.34010	2.253000	0.74438	0.650000	0.86243	TGC	.		0.587	LCE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034512.1	NM_178428		C	152671691	G	C	152671691	3	2	90	1	0	0	0	0	1	0	0	0	8686	1319	46	4	316	4	LCE2A	1	152671691	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	59959595	152671691	96578930	5	8120											
DHX9	1660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	182850707	182850707	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgagcacaaaagacttaatAtggctacactaagaatgact	17	9	8	7	0	0	4	0	2	0	2	0	4	0	4	0	1	2	2	0	1	7	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:182850707A>G	ENST00000367549.3	+	24	2949	c.2839A>G	c.(2839-2841)Atg>Gtg	p.M947V	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	947					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AAGACTTAATATGGCTACACT	0.363																																					p.M947V	Colon(69;210 1162 3697 13559 39565)	.											.	DHX9-92	0			c.A2839G						.						111	103	105					1																	182850707		1829	4080	5909	SO:0001583	missense	1660	exon24			CTTAATATGGCTA	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.2839A>G	1.37:g.182850707A>G	ENSP00000356520:p.Met947Val	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	105	76	NM_001357	0	0	12	154	142	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	9.958	1.221960	0.22457	.	.	ENSG00000135829	ENST00000367549	T	0.03468	3.92	5.94	5.94	0.96194	.	0.041899	0.85682	D	0.000000	T	0.05593	0.0147	L	0.52126	1.63	0.52501	D	0.999959	B;B	0.16396	0.002;0.017	B;B	0.10450	0.005;0.005	T	0.41197	-0.9522	10	0.17369	T	0.5	.	16.3945	0.83586	1.0:0.0:0.0:0.0	.	226;947	B3KU66;Q08211	.;DHX9_HUMAN	V	947	ENSP00000356520:M947V	ENSP00000356520:M947V	M	+	1	0	DHX9	181117330	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	6.735000	0.74806	2.265000	0.75225	0.482000	0.46254	ATG	.		0.363	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182850707	A	G	182850707	3	3	90	1	0	0	0	0	1	0	0	0	4527	449	16	3	2929	3	DHX9	1	182850707	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	30179016	182850707	66399914	6	8121											
ASPM	259266	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	197073973	197073974	+	Frame_Shift_Ins	INS	-	-	A																															ctataccatgattgtatgatINSaatagcagaattttcttctt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:197073973_197073974insA	ENST00000367409.4	-	18	4663_4664	c.4407_4408insT	c.(4405-4410)attatcfs	p.I1470fs	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1470					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GATTGTATGATAATAGCAGAAT	0.292																																					p.I1470fs		.											.	ASPM-615	0			c.4408_4409insT						.																																			SO:0001589	frameshift_variant	259266	exon18			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.4408dupT	1.37:g.197073975_197073975dupA	ENSP00000356379:p.Ile1470fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	58	45	NM_018136	0	0	0	0	0	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Ins	INS	ENST00000367409.4	37	CCDS1389.1																																																																																			.		0.292	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197073974	-	A	197073973	7	5	90	1	0	1	1	0	0	0	0	0	1057	1406	49	0	6069	0	ASPM	1	197073973	Frame_Shift_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08	14223266	197073973	52176648	7	8122											
KHK	3795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27317347	27317347	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttactccgccctagcagttTtgtcctggatgacctccgcc	5	12	9	15	2	0	1	0	1	0	0	3	2	3	2	6	1	2	3	6	1	2	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:27317347T>A	ENST00000260599.6	+	3	725	c.212T>A	c.(211-213)tTt>tAt	p.F71Y	KHK_ENST00000260598.5_Intron|KHK_ENST00000490823.1_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	71					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTAGCAGTTTTGTCCTGGAT	0.602																																					p.F71Y		.											.	KHK-115	0			c.T212A						.						80	80	80					2																	27317347		2203	4300	6503	SO:0001583	missense	3795	exon3			GCAGTTTTGTCCT		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.212T>A	2.37:g.27317347T>A	ENSP00000260599:p.Phe71Tyr	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	125	35	NM_000221	0	0	7	14	7	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	37	CCDS1734.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.922187	0.92319	.	.	ENSG00000138030	ENST00000260599;ENST00000429697	T;T	0.76578	-1.03;-1.03	5.63	5.63	0.86233	Carbohydrate/purine kinase (1);	0.047856	0.85682	D	0.000000	D	0.85779	0.5776	M	0.77616	2.38	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.83297	-0.0030	10	0.08837	T	0.75	-12.7927	13.7817	0.63087	0.0:0.0:0.0:1.0	.	71;71	Q6IBK2;P50053	.;KHK_HUMAN	Y	71	ENSP00000260599:F71Y;ENSP00000404741:F71Y	ENSP00000260599:F71Y	F	+	2	0	KHK	27170851	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.258000	0.72487	2.140000	0.66376	0.459000	0.35465	TTT	.		0.602	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1			A	27317347	T	A	27317347	3	1	90	1	0	0	0	0	1	0	0	0	8170	1841	64	5	222	5	KHK	2	27317347	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08		27317347	215882026	8	8123											
USP34	9736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	61450209	61450209	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	acttacatgttctgcaagtcGattattgtatcgacacaggc	11	13	8	9	2	1	0	0	0	1	0	3	2	1	0	0	1	2	3	0	1	4	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:61450209G>C	ENST00000398571.2	-	64	7811	c.7735C>G	c.(7735-7737)Cga>Gga	p.R2579G	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2579					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TCTGCAAGTCGATTATTGTAT	0.383																																					p.R2579G		.											.	USP34-579	0			c.C7735G						.						76	66	69					2																	61450209		1841	4093	5934	SO:0001583	missense	9736	exon64			CAAGTCGATTATT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.7735C>G	2.37:g.61450209G>C	ENSP00000381577:p.Arg2579Gly	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	38	10	NM_014709	0	0	1	3	2	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.54|16.54	3.151332|3.151332	0.57151|0.57151	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571|ENST00000411912	T|.	0.64803|.	-0.12|.	6.06|6.06	5.17|5.17	0.71159|0.71159	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67702|0.67702	0.2921|0.2921	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D|.	0.60160|.	0.987|.	D|.	0.67725|.	0.953|.	T|T	0.65598|0.65598	-0.6129|-0.6129	10|5	0.72032|.	D|.	0.01|.	.|.	15.4863|15.4863	0.75571|0.75571	0.0:0.0:0.6762:0.3238|0.0:0.0:0.6762:0.3238	.|.	2579|.	Q70CQ2|.	UBP34_HUMAN|.	G|W	2427;2427;2579|338	ENSP00000381577:R2579G|.	ENSP00000263989:R2427G|.	R|S	-|-	1|2	2|0	USP34|USP34	61303713|61303713	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.187000|5.187000	0.65087|0.65087	1.558000|1.558000	0.49541|0.49541	0.650000|0.650000	0.86243|0.86243	CGA|TCG	.		0.383	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61450209	G	C	61450209	3	2	90	1	0	0	0	0	1	0	0	0	17098	1066	37	4	2973	4	USP34	2	61450209	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	34132862	61450209	181749164	9	8124											
ZNF638	27332	broad.mit.edu	37	chr2	71576384	71576384	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagaaggggaagcctcaTggtagccggtgggatgatga	12	6	17	6	1	1	4	1	2	0	2	1	6	1	6	2	5	2	1	2	5	4	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:71576384T>G	ENST00000409544.1	+	2	930	c.300T>G	c.(298-300)caT>caG	p.H100Q	ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000355812.3_Missense_Mutation_p.H100Q|ZNF638_ENST00000377802.2_Missense_Mutation_p.H100Q|ZNF638_ENST00000264447.4_Missense_Mutation_p.H100Q	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	100					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GGAAGCCTCATGGTAGCCGGT	0.448																																					p.H100Q													.	ZNF638-94	0			c.T300G						.						92	93	92					2																	71576384		2203	4300	6503	SO:0001583	missense	27332	exon2			GCCTCATGGTAGC	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.300T>G	2.37:g.71576384T>G	ENSP00000386433:p.His100Gln	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	90	3	NM_014497	0	0	18	18	0	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.127020	0.37533	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544;ENST00000437658	T;T;T;T;T;T;T	0.72282	-0.05;-0.64;0.53;-0.04;1.53;1.53;0.98	5.48	-1.16	0.09678	.	0.231642	0.38548	N	0.001644	T	0.64929	0.2643	N	0.19112	0.55	0.31517	N	0.662829	D;D;D;D;D	0.76494	0.991;0.984;0.999;0.998;0.991	D;D;D;D;P	0.80764	0.946;0.974;0.994;0.986;0.889	T	0.64097	-0.6487	10	0.59425	D	0.04	-5.8407	3.6183	0.08086	0.2769:0.3207:0.0:0.4023	.	206;100;100;100;100	F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;ZN638_HUMAN;.	Q	100;206;100;100;100;100;100	ENSP00000386669:H100Q;ENSP00000438189:H206Q;ENSP00000348066:H100Q;ENSP00000367033:H100Q;ENSP00000264447:H100Q;ENSP00000386433:H100Q;ENSP00000388164:H100Q	ENSP00000264447:H100Q	H	+	3	2	ZNF638	71429892	0.728000	0.28080	0.996000	0.52242	0.823000	0.46562	0.015000	0.13355	-0.192000	0.10432	-0.376000	0.06991	CAT	.		0.448	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		G	71576384	T	G	71576384	3	3	90	1	0	0	0	0	1	0	0	0	18087	1461	51	5	302	5	ZNF638	2	71576384	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	10126175	71576384	171622989	10	8125											
C2orf3	6936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	75921529	75921529	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tactccctcaggtgtgagcgGtgagtttcctgtagtaatgt	7	14	12	8	1	1	2	1	2	0	0	3	2	3	2	2	2	2	3	2	2	3	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:75921529G>C	ENST00000321027.3	-	6	991	c.858C>G	c.(856-858)caC>caG	p.H286Q	GCFC2_ENST00000409857.3_Missense_Mutation_p.H248Q|GCFC2_ENST00000541687.1_Missense_Mutation_p.P248A	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	286					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										GGTGTGAGCGGTGAGTTTCCT	0.294																																					p.H286Q		.											.	.	0			c.C858G						.						148	150	149					2																	75921529		2203	4300	6503	SO:0001583	missense	6936	exon6			TGAGCGGTGAGTT	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.858C>G	2.37:g.75921529G>C	ENSP00000318690:p.His286Gln	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	98	40	NM_003203	0	0	3	6	3	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.83|17.83	3.486559|3.486559	0.63962|0.63962	.|.	.|.	ENSG00000005436|ENSG00000005436	ENST00000321027;ENST00000409857|ENST00000541687	T;T|T	0.19105|0.39229	2.17;2.28|1.09	5.29|5.29	0.803|0.803	0.18691|0.18691	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.41282|0.41282	0.1152|0.1152	M|M	0.80982|0.80982	2.52|2.52	0.20926|0.20926	N|N	0.999823|0.999823	D|.	0.64830|.	0.994|.	P|.	0.59288|.	0.855|.	T|T	0.43877|0.43877	-0.9364|-0.9364	10|7	0.42905|0.02654	T|T	0.14|1	-15.9173|-15.9173	7.4758|7.4758	0.27376|0.27376	0.5377:0.0:0.4623:0.0|0.5377:0.0:0.4623:0.0	.|.	286|.	P16383|.	GCF_HUMAN|.	Q|A	286;248|248	ENSP00000318690:H286Q;ENSP00000386552:H248Q|ENSP00000437767:P248A	ENSP00000318690:H286Q|ENSP00000437767:P248A	H|P	-|-	3|1	2|0	C2orf3|C2orf3	75775037|75775037	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	1.338000|1.338000	0.33873|0.33873	0.152000|0.152000	0.19188|0.19188	-0.140000|-0.140000	0.14226|0.14226	CAC|CCG	.		0.294	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		C	75921529	G	C	75921529	3	2	90	1	0	0	0	0	1	0	0	0	2168	1252	44	4	1535	4	C2orf3	2	75921529	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	4345145	75921529	167277844	11	8126											
C2orf55	343990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	99411105	99411105	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctctcttcagctgatgcaGttccttctccatcatcactg	6	14	7	14	0	5	1	3	1	2	0	8	1	6	1	2	1	2	4	2	1	0	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:99411105G>C	ENST00000397899.2	-	10	3110	c.2779C>G	c.(2779-2781)Ctg>Gtg	p.L927V		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	927																	AGCTGATGCAGTTCCTTCTCC	0.478																																					p.L927V		.											.	.	0			c.C2779G						.						109	107	108					2																	99411105		1996	4184	6180	SO:0001583	missense	343990	exon10			GATGCAGTTCCTT	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 55"	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.2779C>G	2.37:g.99411105G>C	ENSP00000380996:p.Leu927Val	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	144	60	NM_207362	0	0	5	7	2		Missense_Mutation	SNP	ENST00000397899.2	37	CCDS42720.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.057396	0.36277	.	.	ENSG00000196872	ENST00000397899	T	0.46819	0.86	5.27	0.764	0.18465	.	.	.	.	.	T	0.55449	0.1921	L	0.59436	1.845	0.24768	N	0.992884	D	0.76494	0.999	D	0.80764	0.994	T	0.49532	-0.8930	9	0.08599	T	0.76	-7.2777	8.2997	0.32006	0.3464:0.0:0.6536:0.0	.	927	Q6NV74	CB055_HUMAN	V	927	ENSP00000380996:L927V	ENSP00000380996:L927V	L	-	1	2	C2orf55	98777537	0.018000	0.18449	0.911000	0.35937	0.969000	0.65631	-0.303000	0.08210	-0.047000	0.13423	-0.255000	0.11280	CTG	.		0.478	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		C	99411105	G	C	99411105	3	2	90	1	0	0	0	0	1	0	0	0	2182	1020	36	4	113	4	C2orf55	2	99411105	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	23489576	99411105	143788268	12	8127											
ARHGAP15	55843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	143986166	143986166	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaggaaaaactggtctactTcctggattgttctttctagt	10	16	8	7	0	3	0	0	0	3	0	4	2	4	2	1	3	2	1	1	3	5	7			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:143986166T>C	ENST00000295095.6	+	5	480	c.313T>C	c.(313-315)Tcc>Ccc	p.S105P	ARHGAP15_ENST00000409869.1_Missense_Mutation_p.S105P	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	105	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		CTGGTCTACTTCCTGGATTGT	0.318																																					p.S105P		.											.	ARHGAP15-653	0			c.T313C						.						88	94	92					2																	143986166		2203	4299	6502	SO:0001583	missense	55843	exon5			TCTACTTCCTGGA	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.313T>C	2.37:g.143986166T>C	ENSP00000295095:p.Ser105Pro	Somatic	117	1		WXS	Illumina HiSeq	Phase_I	90	25	NM_018460	0	0	7	7	0	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Missense_Mutation	SNP	ENST00000295095.6	37	CCDS2184.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937046	0.73557	.	.	ENSG00000075884	ENST00000409869;ENST00000295095	T;T	0.79454	-0.94;-1.27	5.6	4.43	0.53597	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.260794	0.38164	N	0.001794	D	0.85427	0.5694	M	0.81682	2.555	0.42157	D	0.991583	P;P	0.42203	0.773;0.758	B;P	0.55667	0.399;0.781	D	0.86101	0.1556	10	0.87932	D	0	.	10.8511	0.46771	0.1403:0.0:0.0:0.8597	.	105;105	B4E0R3;Q53QZ3	.;RHG15_HUMAN	P	105	ENSP00000386560:S105P;ENSP00000295095:S105P	ENSP00000295095:S105P	S	+	1	0	ARHGAP15	143702636	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.362000	0.52314	0.931000	0.37242	0.528000	0.53228	TCC	.		0.318	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460		C	143986166	T	C	143986166	3	2	90	1	0	0	0	0	1	0	0	0	866	1783	62	3	327	3	ARHGAP15	2	143986166	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	44575061	143986166	99213207	13	8128											
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	168103542	168103542	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacttaaagaatcaagccaTcgatggaaagaatctaaaca	19	8	6	8	1	3	2	2	0	1	2	4	4	3	3	1	1	2	0	1	1	8	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:168103542T>A	ENST00000409195.1	+	9	5729	c.5640T>A	c.(5638-5640)caT>caA	p.H1880Q	XIRP2_ENST00000295237.9_Missense_Mutation_p.H1880Q|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.H1658Q|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1705					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AATCAAGCCATCGATGGAAAG	0.383																																					p.H1880Q		.											.	XIRP2-104	0			c.T5640A						.						83	75	77					2																	168103542		1885	4124	6009	SO:0001583	missense	129446	exon9			AAGCCATCGATGG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5640T>A	2.37:g.168103542T>A	ENSP00000386840:p.His1880Gln	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	72	18	NM_152381	0	0	0	0	0	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.991182	0.00439	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02280	4.36;4.36;4.36	5.46	-10.9	0.00192	.	1.270260	0.04947	N	0.459528	T	0.01254	0.0041	L	0.27053	0.805	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.45279	-0.9272	10	0.20519	T	0.43	4.4394	1.0633	0.01605	0.3314:0.095:0.2197:0.3539	.	1705;1705;1658	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	1880;1880;1658	ENSP00000386840:H1880Q;ENSP00000295237:H1880Q;ENSP00000387255:H1658Q	ENSP00000295237:H1880Q	H	+	3	2	XIRP2	167811788	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.516000	0.00222	-2.709000	0.00395	-1.577000	0.00868	CAT	.		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168103542	T	A	168103542	3	1	90	1	0	0	0	0	1	0	0	0	17463	1432	50	5	5670	5	XIRP2	2	168103542	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	24117376	168103542	75095831	14	8129											
SPEG	10290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	220309733	220309733	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggcaaccggggccgggcCacggcacctgggggtggagc	7	2	19	13	3	0	0	0	0	0	0	0	1	0	1	4	8	2	2	4	8	1	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:220309733C>G	ENST00000312358.7	+	3	797	c.665C>G	c.(664-666)cCa>cGa	p.P222R	SPEG_ENST00000396698.1_Missense_Mutation_p.P118R|SPEG_ENST00000396695.2_Intron	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	222					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GGGGCCGGGCCACGGCACCTG	0.716																																					p.P222R		.											.	SPEG-383	0			c.C665G						.						10	14	13					2																	220309733		1928	4078	6006	SO:0001583	missense	10290	exon3			CCGGGCCACGGCA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.665C>G	2.37:g.220309733C>G	ENSP00000311684:p.Pro222Arg	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	22	9	NM_005876	0	0	0	0	0	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.587755	0.46110	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698	T;T	0.69175	-0.38;-0.11	4.86	4.86	0.63082	.	0.000000	0.36932	U	0.002335	T	0.61739	0.2371	N	0.14661	0.345	0.80722	D	1	D	0.59357	0.985	P	0.58077	0.832	T	0.61058	-0.7139	10	0.31617	T	0.26	.	11.9491	0.52944	0.0:0.9075:0.0:0.0925	.	222	Q15772	SPEG_HUMAN	R	222;222;118	ENSP00000311684:P222R;ENSP00000379926:P118R	ENSP00000265327:P222R	P	+	2	0	SPEG	220017977	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.189000	0.42621	2.227000	0.72691	0.442000	0.29010	CCA	.		0.716	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		G	220309733	C	G	220309733	3	3	90	1	0	0	0	0	1	0	0	0	15068	594	21	4	675	4	SPEG	2	220309733	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	52206191	220309733	22889640	15	8130											
MRPL44	65080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	224824513	224824513	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaagacgagtacccagacAtgcccactgaaggcataaaa	16	6	9	10	1	0	4	0	2	0	2	0	5	0	4	2	1	2	2	2	1	5	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:224824513A>G	ENST00000258383.3	+	2	511	c.442A>G	c.(442-444)Atg>Gtg	p.M148V		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	148	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		GTACCCAGACATGCCCACTGA	0.428																																					p.M148V		.											.	MRPL44-90	0			c.A442G						.						76	80	79					2																	224824513		2203	4300	6503	SO:0001583	missense	65080	exon2			CCAGACATGCCCA	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"Mitochondrial ribosomal proteins / large subunits"	16650	protein-coding gene	gene with protein product	"39S ribosomal protein L44, mitochondrial"	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.442A>G	2.37:g.224824513A>G	ENSP00000258383:p.Met148Val	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	106	47	NM_022915	0	0	50	81	31	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	37	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	A	3.222	-0.159303	0.06544	.	.	ENSG00000135900	ENST00000258383	T	0.39997	1.05	5.42	-3.5	0.04710	Ribonuclease III (3);	0.216533	0.40222	N	0.001151	T	0.15046	0.0363	N	0.04880	-0.145	0.21020	N	0.9998	B	0.02656	0.0	B	0.06405	0.002	T	0.07539	-1.0767	10	0.38643	T	0.18	-2.8434	4.3393	0.11101	0.5634:0.2199:0.0:0.2166	.	148	Q9H9J2	RM44_HUMAN	V	148	ENSP00000258383:M148V	ENSP00000258383:M148V	M	+	1	0	MRPL44	224532757	0.005000	0.15991	0.981000	0.43875	0.030000	0.12068	0.015000	0.13355	-0.206000	0.10203	-2.558000	0.00175	ATG	.		0.428	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915		G	224824513	A	G	224824513	3	3	90	1	0	0	0	0	1	0	0	0	9833	217	8	3	448	3	MRPL44	2	224824513	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	4514780	224824513	18374860	16	8131											
SP110	3431	broad.mit.edu	37	chr2	231050754	231050754	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttagttcttgccttttggAccctcatcatgacctctgag	7	16	7	11	0	4	2	2	2	2	0	4	3	4	3	3	1	1	1	3	1	1	6			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:231050754A>G	ENST00000358662.4	-	11	1313	c.1235T>C	c.(1234-1236)gTc>gCc	p.V412A	SP110_ENST00000392048.3_Missense_Mutation_p.V410A|SP110_ENST00000540870.1_Missense_Mutation_p.V418A|SP110_ENST00000258381.6_Missense_Mutation_p.V412A|SP110_ENST00000338556.3_Missense_Mutation_p.V114A|SP110_ENST00000258382.5_Missense_Mutation_p.V412A	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	412					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TGCCTTTTGGACCCTCATCAT	0.478																																					p.V418A													.	SP110-155	0			c.T1253C						.						228	196	207					2																	231050754		2203	4300	6503	SO:0001583	missense	3431	exon12			TTTTGGACCCTCA	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1235T>C	2.37:g.231050754A>G	ENSP00000351488:p.Val412Ala	Somatic	174	1		WXS	Illumina HiSeq	Phase_I	162	5	NM_001185015	0	0	31	31	0	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	.	.	.	.	.	.	.	.	.	.	A	0.014	-1.589058	0.00864	.	.	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.62941	1.2;1.06;-0.01;-0.01;-0.01;2.68	2.59	-0.621	0.11564	.	1.906820	0.02978	N	0.145300	T	0.35998	0.0951	N	0.11064	0.09	0.09310	N	1	B;B;B;B;B	0.11235	0.0;0.003;0.0;0.004;0.003	B;B;B;B;B	0.09377	0.001;0.002;0.001;0.002;0.004	T	0.15263	-1.0443	10	0.08179	T	0.78	.	2.252	0.04045	0.3215:0.0:0.4368:0.2417	.	410;114;418;412;412	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	A	412;412;410;412;418;114	ENSP00000258381:V412A;ENSP00000351488:V412A;ENSP00000375902:V410A;ENSP00000258382:V412A;ENSP00000439558:V418A;ENSP00000344049:V114A	ENSP00000258381:V412A	V	-	2	0	SP110	230758998	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.215000	0.09279	-0.155000	0.11098	-0.475000	0.04921	GTC	.		0.478	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		G	231050754	A	G	231050754	3	3	90	1	0	0	0	0	1	0	0	0	14993	275	10	3	1006	3	SP110	2	231050754	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	6226241	231050754	12148619	17	8132											
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	37365472	37365472	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgtcagaagtattaaaaGcccgtcacaaactagaagag	18	7	8	8	1	2	3	2	0	0	3	2	3	2	3	1	0	3	1	1	0	8	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:37365472G>A	ENST00000361924.2	+	14	2469	c.2095G>A	c.(2095-2097)Gcc>Acc	p.A699T	GOLGA4_ENST00000356847.4_Missense_Mutation_p.A721T|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	699	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AGTATTAAAAGCCCGTCACAA	0.358																																					p.A721T		.											.	GOLGA4-93	0			c.G2161A						.						32	35	34					3																	37365472		2195	4266	6461	SO:0001583	missense	2803	exon15			TTAAAAGCCCGTC	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.2095G>A	3.37:g.37365472G>A	ENSP00000354486:p.Ala699Thr	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	39	29	NM_001172713	0	0	0	18	18	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	6.302	0.423898	0.11928	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000429018;ENST00000437131	T;T;T	0.22539	1.99;1.99;1.95	5.22	3.44	0.39384	.	0.449282	0.16613	N	0.206829	T	0.13329	0.0323	N	0.25890	0.77	0.09310	N	1	B;B;B;B	0.12013	0.005;0.001;0.001;0.002	B;B;B;B	0.09377	0.004;0.004;0.004;0.003	T	0.30563	-0.9974	10	0.15066	T	0.55	.	10.028	0.42083	0.2751:0.0:0.7249:0.0	.	699;699;721;699	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	T	699;721;260;570	ENSP00000354486:A699T;ENSP00000349305:A721T;ENSP00000405842:A570T	ENSP00000349305:A721T	A	+	1	0	GOLGA4	37340476	0.002000	0.14202	0.168000	0.22838	0.683000	0.39861	0.601000	0.24119	0.721000	0.32231	0.655000	0.94253	GCC	.		0.358	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37365472	G	A	37365472	3	1	90	1	0	0	0	0	1	0	0	0	6575	971	34	2	2219	2	GOLGA4	3	37365472	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		37365472	160656958	18	8133											
SETD2	29072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	47164114	47164114	+	Frame_Shift_Del	DEL	A	A	-																															caggagatccatttatatttAattctatgggacaaaaactt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:47164114delA	ENST00000409792.3	-	3	2054	c.2012delT	c.(2011-2013)ttafs	p.L671fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	671					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ATTTATATTTAATTCTATGGG	0.328			"N, F, S, Mis"		clear cell renal carcinoma																																p.L671X		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.2012delT						.						58	63	61					3																	47164114		2203	4299	6502	SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2012delT	3.37:g.47164114delA	ENSP00000386759:p.Leu671fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	85	70	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	DEL	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.328	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47164114	A	-	47164114	7	5	90	1	0	1	0	1	0	0	0	0	14163	372	13	0	5758	0	SETD2	3	47164114	Frame_Shift_Del	DEL	A	TCGA-BQ-7061-01A-11D-1961-08	9798642	47164114	150858316	19	8134											
ACY1	95	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52023049	52023049	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatatatacacgcctgctGcctgcccttgccagtgtgcc	7	10	9	15	1	0	0	0	0	0	0	0	1	0	0	5	0	6	1	5	0	3	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:52023049G>C	ENST00000404366.2	+	15	1331	c.1185G>C	c.(1183-1185)ctG>ctC	p.L395L	ACY1_ENST00000494103.1_Silent_p.L323L|ABHD14A-ACY1_ENST00000463937.1_Silent_p.L496L|ACY1_ENST00000476351.1_Silent_p.L360L|ACY1_ENST00000458031.2_Silent_p.L485L|ACY1_ENST00000476854.1_Silent_p.L330L	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	395					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CACGCCTGCTGCCTGCCCTTG	0.607																																					p.L395L		.											.	ACY1-154	0			c.G1185C						.						116	102	107					3																	52023049		2203	4300	6503	SO:0001819	synonymous_variant	95	exon15			CCTGCTGCCTGCC	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.1185G>C	3.37:g.52023049G>C		Somatic	167	1		WXS	Illumina HiSeq	Phase_I	125	98	NM_001198895	0	0	6	495	489	C9J6I6|C9J9D8|C9JWD4	Silent	SNP	ENST00000404366.2	37	CCDS2844.1																																																																																			.		0.607	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666		C	52023049	G	C	52023049	2	2	90	1	0	0	0	0	0	0	0	1	226	1306	46	4		4	ACY1	3	52023049	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	4858935	52023049	145999381	20	8135											
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52651555	52651555	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctttcttatgttctttttaCtgttgagggggaggtagaaa	8	17	12	4	0	2	2	0	1	2	1	2	3	2	3	0	3	1	4	0	3	4	8			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:52651555C>T	ENST00000296302.7	-	14	1543		c.e14-1		PBRM1_ENST00000356770.4_Splice_Site|PBRM1_ENST00000337303.4_Splice_Site|PBRM1_ENST00000409057.1_Splice_Site|PBRM1_ENST00000409767.1_Splice_Site|PBRM1_ENST00000410007.1_Splice_Site|PBRM1_ENST00000409114.3_Splice_Site|PBRM1_ENST00000394830.3_Splice_Site			Q86U86	PB1_HUMAN	polybromo 1						chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTTCTTTTTACTGTTGAGGGG	0.348			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																.		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1-575	0			c.1542-1G>A						.						52	52	52					3																	52651555		2202	4300	6502	SO:0001630	splice_region_variant	55193	exon16			TTTTTACTGTTGA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1542-1G>A	3.37:g.52651555C>T		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	35	23	NM_018313	0	0	0	0	0	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Splice_Site	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	21.4	4.147027	0.77888	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.139	0.98050	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PBRM1	52626595	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.810000	0.55613	2.764000	0.94973	0.655000	0.94253	.	.		0.348	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	Intron	T	52651555	C	T	52651555	5	4	90	1	0	0	0	0	0	0	1	0	11517	579	20	2	3427	2	PBRM1	3	52651555	Splice_Site	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	628506	52651555	145370875	21	8136											
KIAA2018	205717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113377559	113377559	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtggtttgcattgtatcTgatgaatcttgctcaactct	7	17	8	9	0	4	2	1	2	3	0	4	2	4	2	1	1	3	4	1	1	3	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:113377559T>C	ENST00000478658.1	-	5	2987	c.2970A>G	c.(2968-2970)tcA>tcG	p.S990S	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.S990S			Q68DE3	K2018_HUMAN	KIAA2018	990						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						GCATTGTATCTGATGAATCTT	0.393																																					p.S990S		.											.	KIAA2018-93	0			c.A2970G						.						113	106	108					3																	113377559		1870	4096	5966	SO:0001819	synonymous_variant	205717	exon7			TGTATCTGATGAA	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.2970A>G	3.37:g.113377559T>C		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	134	104	NM_001009899	0	0	0	2	2	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.393	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113377559	T	C	113377559	2	2	90	1	0	0	0	0	0	0	0	1	8289	1567	55	3		3	KIAA2018	3	113377559	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	60726004	113377559	84644871	22	8137											
CD86	942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121822644	121822644	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tatcatccatcacaaaaagcCcacaggaatgattcgcatcc	15	8	5	13	1	2	1	2	1	0	0	5	2	4	2	3	1	1	1	3	1	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:121822644C>G	ENST00000330540.2	+	3	466	c.350C>G	c.(349-351)cCc>cGc	p.P117R	CD86_ENST00000469710.1_Missense_Mutation_p.P35R|CD86_ENST00000264468.5_Intron|CD86_ENST00000393627.2_Missense_Mutation_p.P111R|CD86_ENST00000493101.1_Intron	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	117	Ig-like V-type.				aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	CACAAAAAGCCCACAGGAATG	0.453																																					p.P117R	GBM(67;1379 1389 36064 39806)	.											.	CD86-92	0			c.C350G						.						129	134	132					3																	121822644		2203	4300	6503	SO:0001583	missense	942	exon3			AAAAGCCCACAGG		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1705	protein-coding gene	gene with protein product	"B-lymphocyte antigen B7-2"	601020	"CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.350C>G	3.37:g.121822644C>G	ENSP00000332049:p.Pro117Arg	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	77	64	NM_175862	0	0	6	6	0	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Missense_Mutation	SNP	ENST00000330540.2	37	CCDS3009.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.769867	0.49680	.	.	ENSG00000114013	ENST00000469710;ENST00000330540;ENST00000482356;ENST00000393627	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.54	4.67	0.58626	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.828917	0.10874	N	0.624588	T	0.55768	0.1941	M	0.82630	2.6	0.25045	N	0.991176	D	0.64830	0.994	D	0.65987	0.94	T	0.44574	-0.9319	10	0.41790	T	0.15	-0.8312	10.1893	0.43017	0.0:0.9112:0.0:0.0888	.	117	P42081	CD86_HUMAN	R	35;117;111;111	ENSP00000418988:P35R;ENSP00000332049:P117R;ENSP00000419116:P111R;ENSP00000377248:P111R	ENSP00000332049:P117R	P	+	2	0	CD86	123305334	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.065000	0.14466	1.578000	0.49821	0.655000	0.94253	CCC	.		0.453	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889		G	121822644	C	G	121822644	3	3	90	1	0	0	0	0	1	0	0	0	3049	623	22	4	360	4	CD86	3	121822644	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	8445085	121822644	76199786	23	8138											
USP38	84640	hgsc.bcm.edu;bcgsc.ca	37	chr4	144141548	144141548	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacgacccaccaggaagctGtggaccaactggtggagggg	11	4	15	11	1	0	0	0	0	0	0	0	4	0	3	3	6	3	1	3	6	3	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:144141548G>C	ENST00000307017.4	+	10	3574	c.3068G>C	c.(3067-3069)tGt>tCt	p.C1023S		NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	1023					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CCAGGAAGCTGTGGACCAACT	0.512																																					p.C1023S		.											.	USP38-660	0			c.G3068C						.						92	94	93					4																	144141548		2203	4300	6503	SO:0001583	missense	84640	exon10			GAAGCTGTGGACC	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.3068G>C	4.37:g.144141548G>C	ENSP00000303434:p.Cys1023Ser	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	71	4	NM_032557	0	0	26	26	0	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	37	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.312440	0.81358	.	.	ENSG00000170185	ENST00000307017	T	0.10477	2.87	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.35799	0.0944	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.01452	-1.1351	10	0.62326	D	0.03	-13.0776	20.1294	0.97995	0.0:0.0:1.0:0.0	.	1023	Q8NB14	UBP38_HUMAN	S	1023	ENSP00000303434:C1023S	ENSP00000303434:C1023S	C	+	2	0	USP38	144360998	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.835000	0.99442	2.758000	0.94735	0.591000	0.81541	TGT	.		0.512	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144141548	G	C	144141548	3	2	90	1	0	0	0	0	1	0	0	0	17102	1377	48	4	3106	4	USP38	4	144141548	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		144141548	47012728	24	8139											
SMAD1	4086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	146475084	146475084	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgggtgtagtctgaaaatTtttaacaaccaagaatttgc	14	13	9	5	0	1	2	0	1	1	1	1	2	1	2	1	1	3	1	1	1	7	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:146475084T>G	ENST00000515385.1	+	6	1688	c.1146T>G	c.(1144-1146)atT>atG	p.I382M	SMAD1_ENST00000394092.2_Missense_Mutation_p.I382M|SMAD1_ENST00000302085.4_Missense_Mutation_p.I382M			Q15797	SMAD1_HUMAN	SMAD family member 1	382	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle cell proliferation (GO:0060038)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|embryonic pattern specification (GO:0009880)|gamete generation (GO:0007276)|hindbrain development (GO:0030902)|homeostatic process (GO:0042592)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|mesodermal cell fate commitment (GO:0001710)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|osteoblast fate commitment (GO:0002051)|positive regulation of cartilage development (GO:0061036)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of gene expression (GO:0010628)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|primary miRNA processing (GO:0031053)|protein phosphorylation (GO:0006468)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|signal transduction (GO:0007165)|SMAD protein complex assembly (GO:0007183)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	17	all_hematologic(180;0.151)					GTCTGAAAATTTTTAACAACC	0.398																																					p.I382M	Pancreas(182;1287 2092 10326 35158 50562)	.											.	SMAD1-415	0			c.T1146G						.						165	158	160					4																	146475084		2203	4300	6503	SO:0001583	missense	4086	exon6			GAAAATTTTTAAC	U59423	CCDS3765.1	4q31.21	2013-10-22	2006-11-06	2004-05-26	ENSG00000170365	ENSG00000170365		"SMADs"	6767	protein-coding gene	gene with protein product		601595	"MAD, mothers against decapentaplegic homolog 1 (Drosophila)", "SMAD, mothers against DPP homolog 1 (Drosophila)"	MADH1		8653785, 8673135	Standard	NM_005900		Approved	MADR1, JV4-1	uc003ikc.3	Q15797	OTTHUMG00000161592	ENST00000515385.1:c.1146T>G	4.37:g.146475084T>G	ENSP00000426568:p.Ile382Met	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	101	36	NM_005900	0	0	8	14	6	A8KAJ0|D3DNZ9|Q16636|Q9UFT8	Missense_Mutation	SNP	ENST00000515385.1	37	CCDS3765.1	.	.	.	.	.	.	.	.	.	.	T	19.20	3.782414	0.70222	.	.	ENSG00000170365	ENST00000302085;ENST00000394092;ENST00000515385	D;D;D	0.97811	-4.55;-4.55;-4.55	5.73	2.08	0.27032	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98836	0.9607	H	0.95712	3.71	0.80722	D	1	D	0.54397	0.966	D	0.73708	0.981	D	0.98389	1.0562	10	0.87932	D	0	.	9.1222	0.36795	0.0:0.1974:0.0:0.8026	.	382	Q15797	SMAD1_HUMAN	M	382	ENSP00000305769:I382M;ENSP00000377652:I382M;ENSP00000426568:I382M	ENSP00000305769:I382M	I	+	3	3	SMAD1	146694534	0.995000	0.38212	1.000000	0.80357	0.983000	0.72400	0.316000	0.19469	0.136000	0.18733	0.528000	0.53228	ATT	.		0.398	SMAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365467.1	NM_005900		G	146475084	T	G	146475084	3	3	90	1	0	0	0	0	1	0	0	0	14789	1829	64	5	1164	5	SMAD1	4	146475084	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	2333536	146475084	44679192	25	8140											
IRF2	3660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	185339324	185339324	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaatcacccaagattaccttGatgtgcttaactttgtcttc	10	15	6	10	0	2	2	1	1	1	1	3	3	2	2	2	0	3	1	2	0	4	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:185339324G>C	ENST00000393593.3	-	5	615	c.408C>G	c.(406-408)atC>atG	p.I136M	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	136					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AGATTACCTTGATGTGCTTAA	0.398																																					p.I136M		.											.	IRF2-91	0			c.C408G						.						317	261	280					4																	185339324		2203	4300	6503	SO:0001583	missense	3660	exon5			TACCTTGATGTGC		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.408C>G	4.37:g.185339324G>C	ENSP00000377218:p.Ile136Met	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	186	64	NM_002199	0	0	0	0	0	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Missense_Mutation	SNP	ENST00000393593.3	37	CCDS3835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.31|11.31	1.601714|1.601714	0.28534|0.28534	.|.	.|.	ENSG00000168310|ENSG00000168310	ENST00000393593;ENST00000507523;ENST00000510814;ENST00000506230;ENST00000505316|ENST00000505067	D;D;D;D|.	0.98090|.	-4.66;-4.65;-4.63;-4.71|.	6.17|6.17	5.17|5.17	0.71159|0.71159	.|.	0.584493|.	0.19685|.	N|.	0.108406|.	T|T	0.49047|0.49047	0.1534|0.1534	L|L	0.44542|0.44542	1.39|1.39	0.42544|0.42544	D|D	0.993085|0.993085	B|.	0.23854|.	0.092|.	B|.	0.18263|.	0.021|.	T|T	0.44205|0.44205	-0.9343|-0.9343	10|5	0.45353|.	T|.	0.12|.	-20.7082|-20.7082	5.7421|5.7421	0.18100|0.18100	0.129:0.0:0.6708:0.2002|0.129:0.0:0.6708:0.2002	.|.	136|.	P14316|.	IRF2_HUMAN|.	M|E	136|35	ENSP00000377218:I136M;ENSP00000427204:I136M;ENSP00000424552:I136M;ENSP00000422860:I136M|.	ENSP00000377218:I136M|.	I|Q	-|-	3|1	3|0	IRF2|IRF2	185576318|185576318	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	0.647000|0.647000	0.24812|0.24812	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	ATC|CAA	.		0.398	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			C	185339324	G	C	185339324	3	2	90	1	0	0	0	0	1	0	0	0	7849	1280	45	4	661	4	IRF2	4	185339324	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	38864240	185339324	5814952	26	8141											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	187525694	187525694	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcctcatctgttactaccAgctgcagcacgctgaagccc	10	9	7	15	1	2	1	1	1	1	0	3	1	3	1	3	0	6	5	3	0	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:187525694A>G	ENST00000441802.2	-	18	10594	c.10385T>C	c.(10384-10386)cTg>cCg	p.L3462P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3462	Cadherin 32. {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						TGTTACTACCAGCTGCAGCAC	0.418										HNSCC(5;0.00058)																											p.L3462P	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.T10385C						.						55	54	54					4																	187525694		1923	4142	6065	SO:0001583	missense	2195	exon18			ACTACCAGCTGCA	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.10385T>C	4.37:g.187525694A>G	ENSP00000406229:p.Leu3462Pro	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	38	13	NM_005245	0	0	94	173	79		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.031570	0.54790	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.56941	0.43	5.42	5.42	0.78866	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.93808	3.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84979	0.0887	10	0.66056	D	0.02	.	15.6278	0.76874	1.0:0.0:0.0:0.0	.	3462	Q14517	FAT1_HUMAN	P	3462;3464	ENSP00000406229:L3462P	ENSP00000260147:L3464P	L	-	2	0	FAT1	187762688	1.000000	0.71417	0.847000	0.33407	0.014000	0.08584	8.761000	0.91691	2.280000	0.76307	0.460000	0.39030	CTG	.		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187525694	A	G	187525694	3	3	90	1	0	0	0	0	1	0	0	0	5708	188	7	3	3421	3	FAT1	4	187525694	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	2186370	187525694	3628582	27	8142											
ADCY2	108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7766912	7766912	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgcgcagaatttattttTcctcccggtaagaacattgc	9	13	9	10	3	0	2	0	0	0	2	2	2	2	2	2	1	3	2	2	1	4	6			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr5:7766912T>G	ENST00000338316.4	+	17	2296	c.2207T>G	c.(2206-2208)tTc>tGc	p.F736C	ADCY2_ENST00000537121.1_Missense_Mutation_p.F556C	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	736					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						AATTTATTTTTCCTCCCGGTA	0.428																																					p.F736C		.											.	ADCY2-97	0			c.T2207G						.						185	191	189					5																	7766912		2203	4300	6503	SO:0001583	missense	108	exon17			TATTTTTCCTCCC	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2207T>G	5.37:g.7766912T>G	ENSP00000342952:p.Phe736Cys	Somatic	265	1		WXS	Illumina HiSeq	Phase_I	252	87	NM_020546	0	0	0	1	1	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	T	14.34	2.505571	0.44558	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;D	0.82433	-1.12;-1.61	5.46	5.46	0.80206	.	0.174588	0.52532	D	0.000064	T	0.77942	0.4206	L	0.47716	1.5	0.58432	D	0.999999	B;B	0.12013	0.0;0.005	B;B	0.08055	0.003;0.003	T	0.73591	-0.3934	10	0.41790	T	0.15	.	12.9176	0.58214	0.0:0.0:0.0:1.0	.	556;736	B7Z2C1;Q08462	.;ADCY2_HUMAN	C	736;569;556	ENSP00000342952:F736C;ENSP00000444803:F556C	ENSP00000342952:F736C	F	+	2	0	ADCY2	7819912	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.354000	0.44098	2.070000	0.61991	0.533000	0.62120	TTC	.		0.428	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		G	7766912	T	G	7766912	3	3	90	1	0	0	0	0	1	0	0	0	294	1783	62	5	2273	5	ADCY2	5	7766912	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08		7766912	173148348	28	8143											
UGT3A2	167127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	36039694	36039694	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accccttggggtaggtgagcAaaggcattgttcatctcctt	8	12	11	10	0	2	1	1	1	1	0	3	1	2	1	3	4	1	4	3	4	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr5:36039694A>C	ENST00000282507.3	-	5	1061	c.960T>G	c.(958-960)ttT>ttG	p.F320L	UGT3A2_ENST00000545528.1_Missense_Mutation_p.F18L|UGT3A2_ENST00000504954.1_5'Flank|UGT3A2_ENST00000513300.1_Missense_Mutation_p.F286L	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	320					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GTAGGTGAGCAAAGGCATTGT	0.493																																					p.F320L		.											.	UGT3A2-158	0			c.T960G						.						142	130	134					5																	36039694		2203	4300	6503	SO:0001583	missense	167127	exon5			GTGAGCAAAGGCA		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.960T>G	5.37:g.36039694A>C	ENSP00000282507:p.Phe320Leu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	126	46	NM_174914	0	0	0	0	0	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	A	8.718	0.913757	0.17907	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.50001	0.76;0.76;4.06	3.18	3.18	0.36537	.	0.000000	0.85682	D	0.000000	T	0.46210	0.1381	L	0.35414	1.06	0.36452	D	0.866122	D;D	0.89917	0.998;1.0	D;D	0.91635	0.986;0.999	T	0.54543	-0.8278	10	0.02654	T	1	.	6.7806	0.23643	0.8835:0.0:0.1165:0.0	.	286;320	E9PFK7;Q3SY77	.;UD3A2_HUMAN	L	320;286;18	ENSP00000282507:F320L;ENSP00000427404:F286L;ENSP00000445367:F18L	ENSP00000282507:F320L	F	-	3	2	UGT3A2	36075451	0.999000	0.42202	0.882000	0.34594	0.212000	0.24457	0.703000	0.25646	1.689000	0.51079	0.482000	0.46254	TTT	.		0.493	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		C	36039694	A	C	36039694	3	2	90	1	0	0	0	0	1	0	0	0	16997	127	5	5	623	5	UGT3A2	5	36039694	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	28272782	36039694	144875566	29	8144											
GFRA3	2676	hgsc.bcm.edu	37	chr5	137610073	137610073	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagcagcaacatcaggActacgggcggcagcggtcgc	10	3	15	13	4	1	0	1	0	0	0	2	1	1	1	0	4	6	5	0	4	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr5:137610073A>G	ENST00000274721.3	-	1	287	c.41T>C	c.(40-42)gTc>gCc	p.V14A	GFRA3_ENST00000378362.3_Missense_Mutation_p.V14A	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3	14					nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			caacatcaggactacgggcgg	0.731																																					p.V14A		.											.	GFRA3-91	0			c.T41C						.						6	10	8					5																	137610073		2055	4108	6163	SO:0001583	missense	2676	exon1			ATCAGGACTACGG	AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.41T>C	5.37:g.137610073A>G	ENSP00000274721:p.Val14Ala	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	9	6	NM_001496	0	0	0	0	0	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Missense_Mutation	SNP	ENST00000274721.3	37	CCDS4201.1	.	.	.	.	.	.	.	.	.	.	A	10.66	1.413148	0.25465	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	T;T	0.49139	1.38;0.79	3.8	2.63	0.31362	.	2.674420	0.01678	N	0.025995	T	0.31071	0.0785	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.01	B;B	0.18263	0.021;0.009	T	0.24261	-1.0165	10	0.51188	T	0.08	0.3298	5.8269	0.18558	0.879:0.0:0.121:0.0	.	14;14	O60609-2;O60609	.;GFRA3_HUMAN	A	14	ENSP00000274721:V14A;ENSP00000367613:V14A	ENSP00000274721:V14A	V	-	2	0	GFRA3	137637972	0.015000	0.18098	0.128000	0.21923	0.007000	0.05969	1.017000	0.29989	0.799000	0.34018	0.477000	0.44152	GTC	.		0.731	GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496		G	137610073	A	G	137610073	3	3	90	1	0	0	0	0	1	0	0	0	6369	275	10	3	1193	3	GFRA3	5	137610073	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	101570379	137610073	43305187	30	8145											
SNRPC	6631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	34730469	34730469	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagcaggctcagagcctgaTtgacaaaacaagtatgtttc	14	9	10	8	0	1	4	1	2	0	2	2	4	1	4	1	1	3	4	1	1	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:34730469T>C	ENST00000244520.5	+	3	287	c.149T>C	c.(148-150)aTt>aCt	p.I50T	SNRPC_ENST00000474635.1_3'UTR|SNRPC_ENST00000374018.1_Missense_Mutation_p.I9T|SNRPC_ENST00000374017.3_Missense_Mutation_p.I71T	NM_003093.2	NP_003084.1			small nuclear ribonucleoprotein polypeptide C											endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	6						CAGAGCCTGATTGACAAAACA	0.413																																					p.I50T	NSCLC(131;576 1831 5287 11175 13324)	.											.	SNRPC-90	0			c.T149C						.						81	72	75					6																	34730469		2203	4300	6503	SO:0001583	missense	6631	exon3			GCCTGATTGACAA		CCDS34436.1	6p21	2014-03-06			ENSG00000124562	ENSG00000124562			11157	protein-coding gene	gene with protein product		603522				2971157, 8532530	Standard	NR_029472		Approved	U1-C, Yhc1	uc003ojt.2	P09234	OTTHUMG00000014555	ENST00000244520.5:c.149T>C	6.37:g.34730469T>C	ENSP00000244520:p.Ile50Thr	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	22	6	NM_003093	0	0	0	0	0		Missense_Mutation	SNP	ENST00000244520.5	37	CCDS34436.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330727	0.60853	.	.	ENSG00000124562	ENST00000244520;ENST00000374018;ENST00000374017	T;T;T	0.32988	1.43;1.43;1.43	6.17	4.99	0.66335	.	0.093403	0.64402	N	0.000001	T	0.20170	0.0485	M	0.80422	2.495	0.80722	D	1	P	0.36144	0.539	B	0.28709	0.093	T	0.05273	-1.0895	10	0.52906	T	0.07	.	12.5154	0.56030	0.1252:0.0:0.0:0.8748	.	50	P09234	RU1C_HUMAN	T	50;9;71	ENSP00000244520:I50T;ENSP00000363130:I9T;ENSP00000363129:I71T	ENSP00000244520:I50T	I	+	2	0	SNRPC	34838447	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.602000	0.82796	1.111000	0.41721	0.533000	0.62120	ATT	.		0.413	SNRPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040255.1	NM_003093		C	34730469	T	C	34730469	3	2	90	1	0	0	0	0	1	0	0	0	14895	1493	52	3	159	3	SNRPC	6	34730469	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08		34730469	136384598	31	8146											
PPARD	5467	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35392132	35392132	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatccacgacatcgagacAttgtggcaggcagagaaggg	12	6	15	8	2	0	3	0	1	0	2	2	6	1	3	1	3	0	2	1	3	1	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:35392132A>C	ENST00000311565.4	+	8	1003	c.654A>C	c.(652-654)acA>acC	p.T218T	PPARD_ENST00000337400.2_Silent_p.T218T|PPARD_ENST00000418635.2_Silent_p.T120T|PPARD_ENST00000448077.2_Silent_p.T179T|PPARD_ENST00000444397.1_Silent_p.T218T|PPARD_ENST00000360694.3_Silent_p.T218T|PPARD_ENST00000540939.1_Silent_p.T115T	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	218					adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	ACATCGAGACATTGTGGCAGG	0.597																																					p.T218T		.											.	PPARD-187	0			c.A654C						.						56	54	55					6																	35392132		2203	4300	6503	SO:0001819	synonymous_variant	5467	exon8			CGAGACATTGTGG	L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033		"Nuclear hormone receptors"	9235	protein-coding gene	gene with protein product		600409	"peroxisome proliferative activated receptor, delta"			1333051	Standard	NM_177435		Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.654A>C	6.37:g.35392132A>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	62	22	NM_001171818	0	0	25	34	9	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	Silent	SNP	ENST00000311565.4	37	CCDS4803.1																																																																																			.		0.597	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1	NM_006238		C	35392132	A	C	35392132	2	2	90	1	0	0	0	0	0	0	0	1	12324	204	8	5		5	PPARD	6	35392132	Silent	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	661663	35392132	135722935	32	8147											
TCTE1	202500	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	44254102	44254102	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacatgcgtttccagctgcCgccatggtgggccacgtggc	6	8	14	13	3	0	0	0	0	0	0	1	1	1	0	4	3	4	2	4	3	1	1	rs149566851		TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:44254102C>T	ENST00000371505.4	-	3	567	c.445G>A	c.(445-447)Ggc>Agc	p.G149S	RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_5'Flank|TCTE1_ENST00000371503.3_5'UTR|TMEM151B_ENST00000438774.2_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	149										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTCCAGCTGCCGCCATGGTGG	0.612																																					p.G149S		.											.	TCTE1-94	0			c.G445A						.						69	62	64					6																	44254102		2203	4300	6503	SO:0001583	missense	202500	exon3			AGCTGCCGCCATG	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.445G>A	6.37:g.44254102C>T	ENSP00000360560:p.Gly149Ser	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	108	22	NM_182539	0	0	0	0	0	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172677	0.38413	.	.	ENSG00000146221	ENST00000371505	T	0.53857	0.6	4.95	0.751	0.18392	.	0.494509	0.24332	N	0.039444	T	0.22666	0.0547	M	0.66939	2.045	0.31913	N	0.614463	B	0.29508	0.246	B	0.15484	0.013	T	0.02698	-1.1122	10	0.42905	T	0.14	-22.0618	3.2087	0.06675	0.1282:0.533:0.1253:0.2135	.	149	Q5JU00	TCTE1_HUMAN	S	149	ENSP00000360560:G149S	ENSP00000360560:G149S	G	-	1	0	TCTE1	44362080	0.194000	0.23325	0.977000	0.42913	0.826000	0.46750	1.144000	0.31565	1.073000	0.40885	0.563000	0.77884	GGC	C|1.000;A|0.000		0.612	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539		T	44254102	C	T	44254102	3	4	90	1	0	0	0	0	1	0	0	0	15749	652	23	1	1072	1	TCTE1	6	44254102	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	8861970	44254102	126860965	33	8148											
TDRD6	221400	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	46660547	46660547	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggagaacaggtagcagacaGgagaaattgtatcccatgtc	14	8	12	7	0	0	3	0	0	0	3	2	5	1	3	1	3	2	3	1	3	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:46660547G>C	ENST00000316081.6	+	1	4682	c.4682G>C	c.(4681-4683)aGg>aCg	p.R1561T	TDRD6_ENST00000544460.1_Missense_Mutation_p.R1561T	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1561					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GTAGCAGACAGGAGAAATTGT	0.383																																					p.R1561T		.											.	TDRD6-138	0			c.G4682C						.						143	136	139					6																	46660547		2203	4300	6503	SO:0001583	missense	221400	exon1			CAGACAGGAGAAA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"Tudor domain containing"	21339	protein-coding gene	gene with protein product	"cancer/testis antigen 41.2", "spermatogenesis associated 36"	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.4682G>C	6.37:g.46660547G>C	ENSP00000346065:p.Arg1561Thr	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	70	30	NM_001168359	0	0	0	0	0	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	4.125	0.021357	0.08006	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.14640	2.49;2.49	5.77	1.57	0.23409	Maternal tudor protein (1);	2.015520	0.01660	N	0.025077	T	0.01870	0.0059	N	0.17082	0.46	0.09310	N	1	B;B	0.20550	0.037;0.046	B;B	0.16289	0.009;0.015	T	0.36040	-0.9764	10	0.14252	T	0.57	-1.2406	1.4939	0.02462	0.3025:0.1233:0.4278:0.1465	.	1561;1561	F5H5M3;O60522	.;TDRD6_HUMAN	T	1561	ENSP00000443299:R1561T;ENSP00000346065:R1561T	ENSP00000346065:R1561T	R	+	2	0	TDRD6	46768506	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.037000	0.13840	-0.027000	0.13873	-0.345000	0.07892	AGG	.		0.383	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		C	46660547	G	C	46660547	3	2	90	1	0	0	0	0	1	0	0	0	15766	1000	35	4	4684	4	TDRD6	6	46660547	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	2406445	46660547	124454520	34	8149											
FAM46A	55603	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	82461531	82461531	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcggacgccaatgcgcttctCggccaggcgccgccgcacca	6	4	13	18	7	1	0	0	0	1	0	2	1	1	1	5	3	1	2	5	3	1	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:82461531C>T	ENST00000320172.6	-	2	642	c.328G>A	c.(328-330)Gag>Aag	p.E110K	FAM46A_ENST00000369754.3_Missense_Mutation_p.E129K|FAM46A_ENST00000369756.3_Missense_Mutation_p.E191K	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	110					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		ATGCGCTTCTCGGCCAGGCGC	0.672																																					p.E110K		.											.	FAM46A-90	0			c.G328A						.						33	33	33					6																	82461531		2199	4296	6495	SO:0001583	missense	55603	exon2			GCTTCTCGGCCAG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.328G>A	6.37:g.82461531C>T	ENSP00000318298:p.Glu110Lys	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	67	31	NM_017633	0	0	0	0	0	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Missense_Mutation	SNP	ENST00000320172.6	37	CCDS34489.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133356	0.77662	.	.	ENSG00000112773	ENST00000369754;ENST00000320172;ENST00000369756	T;T;T	0.24538	1.85;1.85;1.85	5.38	5.38	0.77491	Domain of unknown function DUF1693 (1);	0.093645	0.64402	D	0.000001	T	0.12902	0.0313	L	0.39514	1.22	0.80722	D	1	P;P	0.41748	0.524;0.761	B;B	0.35413	0.202;0.128	T	0.03268	-1.1054	9	.	.	.	-16.9061	18.9095	0.92477	0.0:1.0:0.0:0.0	.	110;129	Q96IP4;Q96IP4-2	FA46A_HUMAN;.	K	129;110;191	ENSP00000358769:E129K;ENSP00000318298:E110K;ENSP00000358771:E191K	.	E	-	1	0	FAM46A	82518250	0.983000	0.35010	0.952000	0.39060	0.004000	0.04260	2.564000	0.45931	2.786000	0.95864	0.563000	0.77884	GAG	.		0.672	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			T	82461531	C	T	82461531	3	4	90	1	0	0	0	0	1	0	0	0	5584	893	31	1	1008	1	FAM46A	6	82461531	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	35800984	82461531	88653536	35	8150											
ROS1	6098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	117706858	117706858	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taactcaccacatatgtcttTccagcccagtagagaaagtg	13	10	7	11	0	2	1	1	0	1	1	3	2	3	1	3	0	2	1	3	0	4	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:117706858T>A	ENST00000368508.3	-	15	2490	c.2292A>T	c.(2290-2292)ggA>ggT	p.G764G	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.G759G	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	764					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CATATGTCTTTCCAGCCCAGT	0.423			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.G764G		.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1-1353	0			c.A2292T						.						94	87	89					6																	117706858		2203	4300	6503	SO:0001819	synonymous_variant	6098	exon15			TGTCTTTCCAGCC	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"Fibronectin type III domain containing"	10261	protein-coding gene	gene with protein product		165020	"v-ros avian UR2 sarcoma virus oncogene homolog 1", "v-ros UR2 sarcoma virus oncogene homolog 1 (avian)", "c-ros oncogene 1 , receptor tyrosine kinase"			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.2292A>T	6.37:g.117706858T>A		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	118	53	NM_002944	0	0	0	0	0	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			.		0.423	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117706858	T	A	117706858	2	1	90	1	0	0	0	0	0	0	0	1	13563	1770	62	5		5	ROS1	6	117706858	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	35245327	117706858	53408209	36	8151											
PDE7B	27115	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	136512787	136512788	+	Frame_Shift_Ins	INS	-	-	A																															cgtggagccgctcttccgggINSaatgggcccatttcacgggt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:136512787_136512788insA	ENST00000308191.6	+	13	1465_1466	c.1162_1163insA	c.(1162-1164)gaafs	p.E388fs	RP13-143G15.4_ENST00000591521.1_RNA|RP13-143G15.4_ENST00000417643.1_RNA|RP13-143G15.4_ENST00000585946.1_RNA	NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	388	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)	p.E388*(1)		breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	GCTCTTCCGGGAATGGGCCCAT	0.589																																					p.E388fs		.											.	PDE7B-91	1	Substitution - Nonsense(1)	lung(1)	c.1162_1163insA						.																																			SO:0001589	frameshift_variant	27115	exon13			.	AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"Phosphodiesterases"	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.1164dupA	6.37:g.136512789_136512789dupA	ENSP00000310661:p.Glu388fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	35	12	NM_018945	0	0	0	0	0	Q5W154	Frame_Shift_Ins	INS	ENST00000308191.6	37	CCDS5175.1																																																																																			.		0.589	PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1			A	136512788	-	A	136512787	7	5	90	1	0	1	1	0	0	0	0	0	11678	1175	41	0	1212	0	PDE7B	6	136512787	Frame_Shift_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08	18805929	136512787	34602280	37	8152											
RAET1G	353091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	150240371	150240371	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtcaaagaggaggaagaTctgtccatcgaaactgagct	14	8	12	7	1	2	4	1	2	1	2	4	7	3	6	1	2	2	1	1	2	3	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:150240371T>C	ENST00000367360.2	-	3	506	c.439A>G	c.(439-441)Atc>Gtc	p.I147V	RAET1E-AS1_ENST00000446954.2_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1G_ENST00000479265.1_Missense_Mutation_p.I147V|RAET1E-AS1_ENST00000605899.1_RNA	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		AGGAGGAAGATCTGTCCATCG	0.507																																					p.I147V		.											.	RAET1G-90	0			c.A439G						.						210	194	200					6																	150240371		2203	4300	6503	SO:0001583	missense	353091	exon3			GGAAGATCTGTCC	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"retinoic acid early transcript 1G pseudogene"			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.439A>G	6.37:g.150240371T>C	ENSP00000356329:p.Ile147Val	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	130	59	NM_001001788	0	0	1	2	1		Missense_Mutation	SNP	ENST00000367360.2	37	CCDS43514.1	.	.	.	.	.	.	.	.	.	.	T	2.316	-0.356879	0.05138	.	.	ENSG00000203722	ENST00000367360;ENST00000479265	T;T	0.00695	5.83;5.83	2.4	-0.116	0.13555	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00356	0.0011	L	0.39898	1.24	0.09310	N	1	B	0.24043	0.096	B	0.37091	0.241	T	0.33650	-0.9860	9	0.22706	T	0.39	.	6.0143	0.19594	0.0:0.1591:0.0:0.8409	.	147	Q6H3X3	RET1G_HUMAN	V	147	ENSP00000356329:I147V;ENSP00000417503:I147V	ENSP00000356329:I147V	I	-	1	0	RAET1G	150282064	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-1.019000	0.03622	-0.018000	0.14079	-1.493000	0.00968	ATC	.		0.507	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2			C	150240371	T	C	150240371	3	2	90	1	0	0	0	0	1	0	0	0	13032	1435	50	3	577	3	RAET1G	6	150240371	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	13727584	150240371	20874696	38	8153											
PSMB1	5689	broad.mit.edu	37	chr6	170844433	170844433	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagacatctttcaccagccGcatggctctgtccaaggaca	11	8	9	13	1	3	1	1	0	2	1	4	3	4	2	3	2	1	2	3	2	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:170844433G>A	ENST00000262193.6	-	6	699	c.601C>T	c.(601-603)Cgg>Tgg	p.R201W	PSMB1_ENST00000462957.1_5'UTR	NM_002793.3	NP_002784.1	P20618	PSB1_HUMAN	proteasome (prosome, macropain) subunit, beta type, 1	201					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)|Carfilzomib(DB08889)	TTCACCAGCCGCATGGCTCTG	0.517																																					p.R201W													.	PSMB1-91	0			c.C601T						.						112	92	99					6																	170844433		2203	4300	6503	SO:0001583	missense	5689	exon6			CCAGCCGCATGGC	D00761	CCDS34577.1	6q27	2008-02-05			ENSG00000008018	ENSG00000008018		"Proteasome (prosome, macropain) subunits"	9537	protein-coding gene	gene with protein product		602017				2025653	Standard	NM_002793		Approved	PMSB1, HC5	uc011ehe.2	P20618	OTTHUMG00000016087	ENST00000262193.6:c.601C>T	6.37:g.170844433G>A	ENSP00000262193:p.Arg201Trp	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	86	6	NM_002793	0	0	416	460	44	B5BU76|Q9BWA8	Missense_Mutation	SNP	ENST00000262193.6	37	CCDS34577.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.956117	0.73902	.	.	ENSG00000008018	ENST00000262193	T	0.23348	1.91	5.24	2.36	0.29203	.	0.239529	0.43260	D	0.000583	T	0.13457	0.0326	L	0.34521	1.04	0.39062	D	0.960548	D	0.61697	0.99	P	0.49561	0.615	T	0.02326	-1.1176	10	0.72032	D	0.01	-2.7203	9.9065	0.41379	0.0:0.1264:0.4619:0.4117	.	201	P20618	PSB1_HUMAN	W	201	ENSP00000262193:R201W	ENSP00000262193:R201W	R	-	1	2	PSMB1	170686358	1.000000	0.71417	0.909000	0.35828	0.997000	0.91878	2.466000	0.45084	0.175000	0.19841	0.555000	0.69702	CGG	.		0.517	PSMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043278.2	NM_002793		A	170844433	G	A	170844433	3	1	90	1	0	0	0	0	1	0	0	0	12703	1086	38	1	128	1	PSMB1	6	170844433	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	20604062	170844433	270634	39	8154											
HEATR2	54919	broad.mit.edu	37	chr7	813765	813765	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgcggggaggacagccgCggccatccgcacggctgccg	6	3	17	15	6	0	0	0	0	0	0	1	2	1	2	4	5	3	3	4	5	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:813765C>T	ENST00000297440.6	+	10	2032	c.2012C>T	c.(2011-2013)gCg>gTg	p.A671V	HEATR2_ENST00000403952.3_Missense_Mutation_p.A96V|HEATR2_ENST00000313147.5_Missense_Mutation_p.A671V	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	671						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		AGGACAGCCGCGGCCATCCGC	0.672																																					p.A671V													.	HEATR2-69	0			c.C2012T						.						53	56	55					7																	813765		2203	4299	6502	SO:0001583	missense	54919	exon10			CAGCCGCGGCCAT	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.2012C>T	7.37:g.813765C>T	ENSP00000297440:p.Ala671Val	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	141	5	NM_017802	0	0	64	69	5	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	37	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.358942	0.82353	.	.	ENSG00000164818	ENST00000297440;ENST00000313147;ENST00000537862;ENST00000403952	T;T;T	0.58506	0.73;0.73;0.33	5.44	2.33	0.28932	Armadillo-like helical (1);Armadillo-type fold (1);	0.294063	0.36338	N	0.002648	T	0.72510	0.3469	M	0.74258	2.255	0.35527	D	0.801947	D;D;D	0.89917	0.999;1.0;1.0	P;P;D	0.66497	0.821;0.87;0.944	T	0.80652	-0.1287	10	0.36615	T	0.2	-23.4652	16.4317	0.83847	0.0:0.5274:0.4725:0.0	.	671;96;417	Q86Y56;E9PGY2;F5H8D4	HEAT2_HUMAN;.;.	V	671;671;417;96	ENSP00000297440:A671V;ENSP00000321451:A671V;ENSP00000384884:A96V	ENSP00000297440:A671V	A	+	2	0	HEATR2	780291	0.880000	0.30214	0.814000	0.32528	0.990000	0.78478	1.365000	0.34182	1.279000	0.44446	0.561000	0.74099	GCG	.		0.672	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802		T	813765	C	T	813765	3	4	90	1	0	0	0	0	1	0	0	0	7049	768	27	1	2050	1	HEATR2	7	813765	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08		813765	158324898	40	8155											
HECW1	23072	broad.mit.edu	37	chr7	43581576	43581576	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagacctcactttcactgtTaatgaagaggtttttggaca	11	15	8	7	0	2	3	2	1	0	2	2	4	2	4	1	2	0	2	1	2	3	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:43581576T>A	ENST00000395891.2	+	26	4832	c.4227T>A	c.(4225-4227)gtT>gtA	p.V1409V	HECW1_ENST00000453890.1_Silent_p.V1375V	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1409	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CTTTCACTGTTAATGAAGAGG	0.373																																					p.V1409V													.	HECW1-669	0			c.T4227A						.						177	165	169					7																	43581576		1882	4123	6005	SO:0001819	synonymous_variant	23072	exon26			CACTGTTAATGAA	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4227T>A	7.37:g.43581576T>A		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	163	7	NM_015052	0	0	24	26	2	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	T	10.63	1.403208	0.25291	.	.	ENSG00000002746	ENST00000429529	.	.	.	5.95	-4.24	0.03777	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3464	0.32275	0.0:0.2576:0.4072:0.3352	.	.	.	.	X	133	.	.	L	+	2	0	HECW1	43548101	0.787000	0.28750	0.865000	0.33974	0.921000	0.55340	-0.171000	0.09883	-0.096000	0.12329	0.460000	0.39030	TTA	.		0.373	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43581576	T	A	43581576	2	1	90	1	0	0	0	0	0	0	0	1	7063	1741	61	5		5	HECW1	7	43581576	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	42767811	43581576	115557087	41	8156											
GNAI1	2770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	79842142	79842142	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggatctctttgaagaaaaAatcaaaaagagccctctcac	18	8	6	9	0	3	3	2	1	2	2	5	4	3	4	1	1	1	0	1	1	7	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:79842142A>G	ENST00000351004.3	+	7	1204	c.831A>G	c.(829-831)aaA>aaG	p.K277K	GNAI1_ENST00000457358.2_Silent_p.K225K	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	277					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						TTGAAGAAAAAATCAAAAAGA	0.323																																					p.K277K		.											.	GNAI1-653	0			c.A831G						.						67	74	71					7																	79842142		2203	4294	6497	SO:0001819	synonymous_variant	2770	exon7			AGAAAAAATCAAA	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"Gi1 protein alpha subunit"	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.831A>G	7.37:g.79842142A>G		Somatic	198	0		WXS	Illumina HiSeq	Phase_I	263	74	NM_002069	0	0	13	16	3	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			.		0.323	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		G	79842142	A	G	79842142	2	3	90	1	0	0	0	0	0	0	0	1	6524	11	1	3		3	GNAI1	7	79842142	Silent	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	36260566	79842142	79296521	42	8157											
SAMD9	54809	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92734539	92734539	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactatttggcagtaaaactTccacaaatcttggctctcga	12	13	6	10	1	2	0	0	0	2	0	4	1	3	0	1	2	2	3	1	2	5	6			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:92734539T>G	ENST00000379958.2	-	3	1141	c.872A>C	c.(871-873)gAa>gCa	p.E291A		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	291						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGTAAAACTTCCACAAATCT	0.353																																					p.E291A		.											.	SAMD9-140	0			c.A872C						.						122	121	121					7																	92734539		2203	4300	6503	SO:0001583	missense	54809	exon2			AAAACTTCCACAA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.872A>C	7.37:g.92734539T>G	ENSP00000369292:p.Glu291Ala	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	95	52	NM_001193307	0	0	3	6	3	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372223	0.61624	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.16324	2.35;2.35	4.34	4.34	0.51931	.	0.190136	0.33127	U	0.005253	T	0.20700	0.0498	M	0.73598	2.24	0.30798	N	0.740149	P	0.40970	0.734	B	0.35114	0.196	T	0.33111	-0.9881	10	0.72032	D	0.01	-8.454	12.7423	0.57259	0.0:0.0:0.0:1.0	.	291	Q5K651	SAMD9_HUMAN	A	291	ENSP00000369292:E291A;ENSP00000414529:E291A	ENSP00000369292:E291A	E	-	2	0	SAMD9	92572475	1.000000	0.71417	0.998000	0.56505	0.879000	0.50718	2.498000	0.45363	1.948000	0.56530	0.491000	0.48974	GAA	.		0.353	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		G	92734539	T	G	92734539	3	3	90	1	0	0	0	0	1	0	0	0	13858	1783	62	5	3901	5	SAMD9	7	92734539	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	12892397	92734539	66404124	43	8158											
EPHB4	2050	broad.mit.edu	37	chr7	100417814	100417814	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcccggaagtacccgacgcGgcactggcagacggctgatc	8	5	14	14	5	0	2	0	1	0	1	1	4	0	3	2	4	2	4	2	4	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:100417814G>T	ENST00000358173.3	-	5	1381	c.913C>A	c.(913-915)Cgc>Agc	p.R305S	EPHB4_ENST00000360620.3_Missense_Mutation_p.R305S|EPHB4_ENST00000477446.1_5'UTR|RN7SL750P_ENST00000582814.1_RNA	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	305	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					TACCCGACGCGGCACTGGCAG	0.642																																					p.R305S	GBM(200;2113 3072 25865 52728)												.	EPHB4-1446	0			c.C913A						.						94	106	102					7																	100417814		2203	4300	6503	SO:0001583	missense	2050	exon5			CGACGCGGCACTG	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3395	protein-coding gene	gene with protein product		600011	"EphB4"	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.913C>A	7.37:g.100417814G>T	ENSP00000350896:p.Arg305Ser	Somatic	232	1		WXS	Illumina HiSeq	Phase_I	302	8	NM_004444	0	0	67	67	0	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.757504	0.69648	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	D;D	0.97256	-4.31;-4.31	5.35	5.35	0.76521	Fibronectin, type III (1);	0.000000	0.50627	D	0.000103	D	0.96849	0.8971	M	0.77103	2.36	0.40821	D	0.983509	P;P;P;P	0.51449	0.712;0.712;0.931;0.945	B;B;P;P	0.45071	0.185;0.185;0.468;0.468	D	0.97760	1.0220	10	0.66056	D	0.02	.	16.5291	0.84353	0.0:0.0:1.0:0.0	.	305;305;305;305	B5A972;B5A970;Q96L35;P54760	.;.;.;EPHB4_HUMAN	S	305	ENSP00000353833:R305S;ENSP00000350896:R305S	ENSP00000350896:R305S	R	-	1	0	EPHB4	100255750	1.000000	0.71417	0.981000	0.43875	0.941000	0.58515	3.510000	0.53393	2.491000	0.84063	0.655000	0.94253	CGC	.		0.642	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		T	100417814	G	T	100417814	3	4	90	1	0	0	0	0	1	0	0	0	5190	1116	39	4	2102	4	EPHB4	7	100417814	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	7683275	100417814	58720849	44	8159											
SLC26A5	375611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	103029511	103029511	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacagcagtgatcaaaccAtagtccaatcccaggaacaa	17	6	6	12	0	2	1	2	1	0	0	4	2	4	2	3	1	3	1	3	1	5	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:103029511A>G	ENST00000306312.3	-	14	1719	c.1458T>C	c.(1456-1458)taT>taC	p.Y486Y	SLC26A5_ENST00000393727.1_Silent_p.Y486Y|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000393730.1_Silent_p.Y454Y|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000432958.2_Silent_p.Y454Y|SLC26A5_ENST00000339444.6_Silent_p.Y486Y|SLC26A5_ENST00000393723.1_Silent_p.Y454Y|SLC26A5_ENST00000393729.1_Silent_p.Y449Y|SLC26A5_ENST00000393735.2_Silent_p.Y486Y	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	486					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TGATCAAACCATAGTCCAATC	0.458																																					p.Y486Y		.											.	SLC26A5-91	0			c.T1458C						.						141	108	119					7																	103029511		2203	4300	6503	SO:0001819	synonymous_variant	375611	exon14			CAAACCATAGTCC	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1458T>C	7.37:g.103029511A>G		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	78	17	NM_206883	0	0	0	0	0	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1																																																																																			.		0.458	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		G	103029511	A	G	103029511	2	3	90	1	0	0	0	0	0	0	0	1	14552	224	8	3		3	SLC26A5	7	103029511	Silent	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	2611697	103029511	56109152	45	8160											
KIAA1549	57670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	138602963	138602963	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctcaaattcagagaagTctgctacgacgctactcatt	11	12	6	12	2	4	1	3	0	1	1	5	3	5	1	1	0	3	2	1	0	4	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:138602963T>C	ENST00000422774.1	-	2	1457	c.1409A>G	c.(1408-1410)gAc>gGc	p.D470G	KIAA1549_ENST00000440172.1_Missense_Mutation_p.D470G|KIAA1549_ENST00000242365.4_Missense_Mutation_p.D420G			Q9HCM3	K1549_HUMAN	KIAA1549	470						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TTCAGAGAAGTCTGCTACGAC	0.483			O	BRAF	pilocytic astrocytoma																																p.D470G	NSCLC(119;1534 1718 44213 46230 50068)	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549-369	0			c.A1409G						.						39	40	40					7																	138602963		2029	4193	6222	SO:0001583	missense	57670	exon2			GAGAAGTCTGCTA		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1409A>G	7.37:g.138602963T>C	ENSP00000416040:p.Asp470Gly	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	77	23	NM_020910	0	0	10	14	4	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.669378	0.29693	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.41065	1.01;1.03;1.03	4.75	3.59	0.41128	.	0.100076	0.43579	N	0.000548	T	0.26448	0.0646	N	0.20986	0.625	0.20703	N	0.999861	B;B	0.23540	0.053;0.087	B;B	0.23018	0.019;0.043	T	0.14476	-1.0471	10	0.33141	T	0.24	.	8.3927	0.32537	0.0:0.089:0.0:0.911	.	470;470	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	G	470;420;470	ENSP00000406661:D470G;ENSP00000242365:D420G;ENSP00000416040:D470G	ENSP00000242365:D420G	D	-	2	0	KIAA1549	138253503	0.991000	0.36638	0.195000	0.23364	0.070000	0.16714	1.352000	0.34033	0.846000	0.35142	0.533000	0.62120	GAC	.		0.483	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			C	138602963	T	C	138602963	3	2	90	1	0	0	0	0	1	0	0	0	8265	1667	58	3	4519	3	KIAA1549	7	138602963	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	35573452	138602963	20535700	46	8161											
TMEM176B	28959	broad.mit.edu;bcgsc.ca	37	chr7	150493608	150493608	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgacgtgggtgggctgggatGgcctagaggccatagcaact	8	8	17	8	1	0	2	0	1	0	1	0	3	0	3	2	5	2	2	2	5	3	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:150493608G>C	ENST00000447204.2	-	2	422	c.50C>G	c.(49-51)cCa>cGa	p.P17R	TMEM176B_ENST00000450753.2_Missense_Mutation_p.P17R|TMEM176B_ENST00000326442.5_Missense_Mutation_p.P17R|TMEM176B_ENST00000429904.2_Missense_Mutation_p.P17R|TMEM176B_ENST00000492607.1_Missense_Mutation_p.P17R|TMEM176B_ENST00000434545.1_Missense_Mutation_p.P17R	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	17				PS -> HA (in Ref. 1; AAD23440). {ECO:0000305}.	cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGGCTGGGATGGCCTAGAGGC	0.522																																					p.P17R													.	TMEM176B-91	0			c.C50G						.						91	82	85					7																	150493608		2203	4300	6503	SO:0001583	missense	28959	exon2			TGGGATGGCCTAG	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.50C>G	7.37:g.150493608G>C	ENSP00000410269:p.Pro17Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	123	6	NM_014020	0	1	1537	1645	107	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	.	.	.	.	.	.	.	.	.	.	G	4.944	0.175328	0.09391	.	.	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.07327	3.35;3.35;3.35;3.35;3.35;3.2	4.92	-6.03	0.02185	.	2.014350	0.02708	N	0.112490	T	0.03564	0.0102	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.0	T	0.37197	-0.9716	10	0.14252	T	0.57	2.0728	0.9199	0.01312	0.193:0.1221:0.2552:0.4297	.	17;17	E9PAV4;Q3YBM2	.;T176B_HUMAN	R	17	ENSP00000419258:P17R;ENSP00000318409:P17R;ENSP00000410269:P17R;ENSP00000413531:P17R;ENSP00000397810:P17R;ENSP00000404831:P17R	ENSP00000318409:P17R	P	-	2	0	TMEM176B	150124541	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.663000	0.05299	-0.721000	0.04929	0.467000	0.42956	CCA	.		0.522	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020		C	150493608	G	C	150493608	3	2	90	1	0	0	0	0	1	0	0	0	16125	1348	47	4	786	4	TMEM176B	7	150493608	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	11890645	150493608	8645055	47	8162											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67578598	67578621	+	In_Frame_Del	DEL	TTAATGTCCTCCAGAGTGTCATGC	TTAATGTCCTCCAGAGTGTCATGC	-																															cctggcttttattggcccgcTtaatgtcctccagagtgtca																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	TTAATGTCCTCCAGAGTGTCATGC	TTAATGTCCTCCAGAGTGTCATGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr8:67578598_67578621delTTAATGTCCTCCAGAGTGTCATGC	ENST00000310421.4	-	1	831_854	c.573_596delGCATGACACTCTGGAGGACATTAA	c.(571-597)ttgcatgacactctggaggacattaag>ttg	p.HDTLEDIK192del	C8orf44_ENST00000521889.1_5'Flank|C8orf44_ENST00000519561.1_5'Flank|C8orf44-SGK3_ENST00000519289.1_5'Flank	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	192					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)	p.D193N(1)		breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			ATTGGCCCGCTTAATGTCCTCCAGAGTGTCATGCAAATACAGGA	0.549																																					p.191_199del	NSCLC(179;265 2915 6144 43644)	.											.	VCPIP1-662	1	Substitution - Missense(1)	lung(1)	c.573_596del						.																																			SO:0001651	inframe_deletion	80124	exon1			.	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"OTU domain containing"	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.573_596delGCATGACACTCTGGAGGACATTAA	8.37:g.67578598_67578621delTTAATGTCCTCCAGAGTGTCATGC	ENSP00000309031:p.His192_Lys199del	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	121	21	NM_025054	0	0	0	0	0	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	In_Frame_Del	DEL	ENST00000310421.4	37	CCDS6192.1																																																																																			.		0.549	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			-	67578621	TTAATGTCCTCCAGAGTGTCATGC	-	67578598	7	5	90	1	0	1	0	1	0	0	0	0	17174	1609	56	0	3084	0	VCPIP1	8	67578598	In_Frame_Del	DEL	TTAATGTCCTCCAGAGTGTCATGC	TCGA-BQ-7061-01A-11D-1961-08		67578598	78785424	48	8163											
ZFHX4	79776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	77617295	77617296	+	Missense_Mutation	DNP	GA	GA	TT																															gtctccgccataatacagggGattggcaaagacaaagaacc																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr8:77617295_77617296GA>TT	ENST00000521891.2	+	2	1420_1421	c.972_973GA>TT	c.(970-975)ggGAtt>ggTTtt	p.I325F	ZFHX4_ENST00000050961.6_Missense_Mutation_p.I325F|ZFHX4_ENST00000455469.2_Missense_Mutation_p.I325F|ZFHX4_ENST00000518282.1_Missense_Mutation_p.I325F|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	325					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.G324G(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TAATACAGGGGATTGGCAAAGA	0.441										HNSCC(33;0.089)																											p.I325F		.											.	ZFHX4	1	Substitution - coding silent(1)	lung(1)	c.A973T						.																																			SO:0001583	missense	79776	exon2			CAGGGGATTGGCA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	Exception_encountered	8.37:g.77617295_77617296delinsTT	ENSP00000430497:p.Ile325Phe	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	161	63		0	0	0	0	0	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	DNP	ENST00000521891.2	37	CCDS47878.2																																																																																			.		0.441	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		TT	77617296	GA	TT	77617295	3	4	90	1	0	0	0	0	1	0	0	0	17667	1161	41	4	974	4	ZFHX4	8	77617295	Missense_Mutation	DNP	GA	TCGA-BQ-7061-01A-11D-1961-08	10038697	77617295	68746727	49	8164											
ANKRD26	22852	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	27349330	27349331	+	In_Frame_Ins	INS	-	-	TCA																															tttatttggaacagaatcttINStcatttcaatggtaggctga																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr10:27349330_27349331insTCA	ENST00000376087.4	-	15	1672_1673	c.1507_1508insTGA	c.(1507-1509)aaa>aTGAaa	p.502_503insM	ANKRD26_ENST00000436985.2_In_Frame_Ins_p.518_519insM	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	502					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						AACAGAATCTTTCATTTCAATG	0.277																																					p.K503delinsMK		.											.	ANKRD26-138	0			c.1508_1509insTGA						.																																			SO:0001652	inframe_insertion	22852	exon15			.	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"Ankyrin repeat domain containing"	29186	protein-coding gene	gene with protein product		610855	"thrombocytopenia 2 (autosomal dominant)"	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1505_1507dupTGA	10.37:g.27349331_27349333dupTCA	ENSP00000365255:p.Met502_Met502dup	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	143	44	NM_001256053	0	0	0	0	0	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	In_Frame_Ins	INS	ENST00000376087.4	37	CCDS41499.1																																																																																			.		0.277	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			TCA	27349331	-	TCA	27349330	7	5	90	1	0	1	1	0	0	0	0	0	654	1841	64	0	3704	0	ANKRD26	10	27349330	In_Frame_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08		27349330	108185417	50	8165											
ABCC2	1244	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101569944	101569944	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggaggggatgacttggaCacatctgccattcgacatga	10	10	13	8	1	1	2	0	2	1	0	2	6	1	5	1	4	1	0	1	4	0	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr10:101569944C>T	ENST00000370449.4	+	14	1982	c.1869C>T	c.(1867-1869)gaC>gaT	p.D623D		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	623					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	ATGACTTGGACACATCTGCCA	0.428																																					p.D623D													.	ABCC2-91	0			c.C1869T						.						113	100	104					10																	101569944		2203	4300	6503	SO:0001819	synonymous_variant	1244	exon14			CTTGGACACATCT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1869C>T	10.37:g.101569944C>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	48	18	NM_000392	0	0	32	70	38	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																			.		0.428	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		T	101569944	C	T	101569944	2	4	90	1	0	0	0	0	0	0	0	1	53	477	17	2		2	ABCC2	10	101569944	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	74220614	101569944	33964803	51	8166											
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104112265	104112265	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgtagacatggtgcagctgCtcttcacaaggtaaacctgc	10	10	10	11	1	2	1	1	0	1	1	3	1	2	1	1	2	5	5	1	2	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr10:104112265C>G	ENST00000369983.3	+	7	834	c.574C>G	c.(574-576)Ctc>Gtc	p.L192V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	192					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GGTGCAGCTGCTCTTCACAAG	0.522											OREG0020477	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L192V		.											.	GBF1-91	0			c.C574G						.						110	104	106					10																	104112265		2203	4300	6503	SO:0001583	missense	8729	exon7			CAGCTGCTCTTCA	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.574C>G	10.37:g.104112265C>G	ENSP00000359000:p.Leu192Val	Somatic	125	2	1379	WXS	Illumina HiSeq	Phase_I	91	31	NM_001199378	0	0	0	0	0	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052602	0.75960	.	.	ENSG00000107862	ENST00000369983	T	0.71341	-0.56	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.73171	0.3553	L	0.33668	1.02	0.80722	D	1	P;P;D;D	0.62365	0.853;0.76;0.962;0.991	B;B;P;P	0.61800	0.376;0.376;0.754;0.894	T	0.64799	-0.6322	10	0.05721	T	0.95	-15.5617	20.0452	0.97606	0.0:1.0:0.0:0.0	.	192;192;192;192	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	192	ENSP00000359000:L192V	ENSP00000359000:L192V	L	+	1	0	GBF1	104102255	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.027000	0.70881	2.742000	0.94016	0.655000	0.94253	CTC	.		0.522	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104112265	C	G	104112265	3	3	90	1	0	0	0	0	1	0	0	0	6291	797	28	4	596	4	GBF1	10	104112265	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	2542321	104112265	31422482	52	8167											
TRIM68	55128	hgsc.bcm.edu;broad.mit.edu	37	chr11	4621934	4621934	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcttcccaggacgatattatAgcggtaaaatctctcaggat	12	11	9	9	2	2	0	1	0	1	0	4	3	3	2	1	3	1	2	1	3	5	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:4621934A>G	ENST00000300747.5	-	7	1319	c.1030T>C	c.(1030-1032)Tat>Cat	p.Y344H		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	344	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		ACGATATTATAGCGGTAAAAT	0.532																																					p.Y344H		.											.	TRIM68-91	0			c.T1030C						.						64	65	65					11																	4621934		2201	4298	6499	SO:0001583	missense	55128	exon7			TATTATAGCGGTA	AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21161	protein-coding gene	gene with protein product		613184	"ring finger protein 137", "tripartite motif-containing 68"	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.1030T>C	11.37:g.4621934A>G	ENSP00000300747:p.Tyr344His	Somatic	47	1		WXS	Illumina HiSeq	Phase_I	57	5	NM_018073	0	0	17	17	0	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	37	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.403551	0.62288	.	.	ENSG00000167333	ENST00000300747;ENST00000544055;ENST00000526337	T;T	0.05139	3.49;3.49	5.52	5.52	0.82312	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.47093	D	0.000243	T	0.09862	0.0242	L	0.31752	0.955	0.35969	D	0.835195	P	0.47253	0.892	P	0.52758	0.708	T	0.42515	-0.9447	10	0.16420	T	0.52	.	13.8758	0.63651	1.0:0.0:0.0:0.0	.	344	Q6AZZ1	TRI68_HUMAN	H	344;65;121	ENSP00000300747:Y344H;ENSP00000434681:Y121H	ENSP00000300747:Y344H	Y	-	1	0	TRIM68	4578510	0.005000	0.15991	0.998000	0.56505	0.801000	0.45260	1.935000	0.40173	2.230000	0.72887	0.459000	0.35465	TAT	.		0.532	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073		G	4621934	A	G	4621934	3	3	90	1	0	0	0	0	1	0	0	0	16574	420	15	3	431	3	TRIM68	11	4621934	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		4621934	130384582	53	8168											
RTN3	10313	hgsc.bcm.edu	37	chr11	63487952	63487952	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctgatagcagcctttacaGaaaccagagataaaggaata	18	7	8	8	0	0	3	0	1	0	2	0	5	0	4	3	1	4	1	3	1	7	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:63487952G>C	ENST00000377819.5	+	3	2132	c.1978G>C	c.(1978-1980)Gaa>Caa	p.E660Q	RTN3_ENST00000339997.4_Missense_Mutation_p.E641Q|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000540798.1_Missense_Mutation_p.E548Q|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000354497.4_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	660					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						AGCCTTTACAGAAACCAGAGA	0.358																																					p.E660Q		.											.	RTN3-91	0			c.G1978C						.						45	48	47					11																	63487952		2201	4298	6499	SO:0001583	missense	10313	exon3			TTTACAGAAACCA	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.1978G>C	11.37:g.63487952G>C	ENSP00000367050:p.Glu660Gln	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	43	3	NM_001265589	0	0	0	0	0	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126831	0.37533	.	.	ENSG00000133318	ENST00000377819;ENST00000339997;ENST00000540798	T;T;T	0.28255	1.62;1.62;1.65	5.77	4.86	0.63082	.	0.471231	0.19821	N	0.105314	T	0.36054	0.0953	N	0.19112	0.55	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;P;D	0.64877	0.93;0.852;0.93	T	0.11348	-1.0591	10	0.42905	T	0.14	-8.9759	11.0223	0.47726	0.0859:0.0:0.9141:0.0	.	548;660;641	F5H774;O95197;O95197-2	.;RTN3_HUMAN;.	Q	660;641;548	ENSP00000367050:E660Q;ENSP00000344106:E641Q;ENSP00000442733:E548Q	ENSP00000344106:E641Q	E	+	1	0	RTN3	63244528	0.992000	0.36948	0.386000	0.26170	0.135000	0.20990	2.937000	0.48979	1.572000	0.49736	0.655000	0.94253	GAA	.		0.358	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		C	63487952	G	C	63487952	3	2	90	1	0	0	0	0	1	0	0	0	13759	943	33	4	1988	4	RTN3	11	63487952	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	58866018	63487952	71518564	54	8169											
GAL3ST3	89792	hgsc.bcm.edu	37	chr11	65810436	65810436	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgcccgcgccagcgccgcggGgatggcggccaggcgcgagc	4	1	19	17	9	0	0	0	0	0	0	0	2	0	1	4	5	2	0	4	5	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:65810436G>C	ENST00000312006.4	-	3	1119	c.838C>G	c.(838-840)Ccc>Gcc	p.P280A	GAL3ST3_ENST00000527878.1_Missense_Mutation_p.P280A	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	280					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						agcgccgcggggATGGCGGCC	0.751																																					p.P280A		.											.	GAL3ST3-91	0			c.C838G						.						4	4	4					11																	65810436		1979	3721	5700	SO:0001583	missense	89792	exon3			CCGCGGGGATGGC	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"Sulfotransferases, membrane-bound"	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.838C>G	11.37:g.65810436G>C	ENSP00000308591:p.Pro280Ala	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_033036	0	0	0	0	0	Q14D05	Missense_Mutation	SNP	ENST00000312006.4	37	CCDS8128.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.618323	0.28801	.	.	ENSG00000175229	ENST00000312006;ENST00000527878	T;T	0.13420	2.59;2.59	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	T	0.12732	0.0309	L	0.43757	1.38	0.36719	D	0.881081	B	0.29988	0.264	B	0.26517	0.07	T	0.12400	-1.0549	10	0.35671	T	0.21	-32.1229	13.2513	0.60053	0.0:0.0:1.0:0.0	.	280	Q96A11	G3ST3_HUMAN	A	280	ENSP00000308591:P280A;ENSP00000434829:P280A	ENSP00000308591:P280A	P	-	1	0	GAL3ST3	65567012	0.999000	0.42202	1.000000	0.80357	0.181000	0.23173	2.925000	0.48884	2.256000	0.74724	0.555000	0.69702	CCC	.		0.751	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036		C	65810436	G	C	65810436	3	2	90	1	0	0	0	0	1	0	0	0	6219	1232	43	4	461	4	GAL3ST3	11	65810436	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	2322484	65810436	69196080	55	8170											
GRM5	2915	broad.mit.edu	37	chr11	88242044	88242044	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcccgtgacttcgatggccgGcagaggctggatttcggcaa	7	9	14	11	4	0	2	0	1	0	1	3	4	1	3	2	5	0	3	2	5	1	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:88242044G>A	ENST00000305447.4	-	9	3504	c.3355C>T	c.(3355-3357)Ccg>Tcg	p.P1119S	GRM5-AS1_ENST00000526448.1_RNA|GRM5_ENST00000393297.1_Intron|GRM5_ENST00000305432.5_Missense_Mutation_p.P1087S|GRM5-AS1_ENST00000531994.1_RNA|GRM5_ENST00000455756.2_Missense_Mutation_p.P1087S|GRM5_ENST00000418177.2_Missense_Mutation_p.P1119S	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	1119					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	TCGATGGCCGGCAGAGGCTGG	0.736																																					p.P1119S													.	GRM5-949	0			c.C3355T						.						10	11	11					11																	88242044		2196	4291	6487	SO:0001583	missense	2915	exon9			TGGCCGGCAGAGG	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4597	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 86"	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.3355C>T	11.37:g.88242044G>A	ENSP00000306138:p.Pro1119Ser	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	21	7	NM_001143831	0	0	1	1	0	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.721048	0.48728	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447	D;D;D;D	0.91180	-2.8;-2.8;-2.8;-2.8	4.94	4.94	0.65067	.	0.123369	0.56097	D	0.000038	D	0.92126	0.7504	L	0.29908	0.895	0.42403	D	0.992578	B;D	0.69078	0.052;0.997	B;D	0.75484	0.022;0.986	D	0.91570	0.5271	9	.	.	.	.	18.1622	0.89712	0.0:0.0:1.0:0.0	.	1087;1119	P41594-2;P41594	.;GRM5_HUMAN	S	1119;1087;1087;1119	ENSP00000402912:P1119S;ENSP00000405690:P1087S;ENSP00000305905:P1087S;ENSP00000306138:P1119S	.	P	-	1	0	GRM5	87881692	1.000000	0.71417	0.515000	0.27774	0.898000	0.52572	6.876000	0.75556	2.260000	0.74910	0.563000	0.77884	CCG	.		0.736	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88242044	G	A	88242044	3	1	90	1	0	0	0	0	1	0	0	0	6821	1203	42	2	287	2	GRM5	11	88242044	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	22431608	88242044	46764472	56	8171											
MMP27	64066	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102567479	102567479	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatccagggagacataatttGggaacatcaaggctgtttga	13	10	12	6	0	1	2	1	1	0	1	2	5	2	3	1	3	1	2	1	3	3	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:102567479G>A	ENST00000260229.4	-	5	798	c.707C>T	c.(706-708)cCa>cTa	p.P236L		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	236					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GACATAATTTGGGAACATCAA	0.398																																					p.P236L													.	MMP27-229	0			c.C707T						.						93	86	88					11																	102567479		2203	4299	6502	SO:0001583	missense	64066	exon5			TAATTTGGGAACA	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.707C>T	11.37:g.102567479G>A	ENSP00000260229:p.Pro236Leu	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	41	6	NM_022122	0	0	0	0	0	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.010972	0.93346	.	.	ENSG00000137675	ENST00000260229	T	0.55930	0.49	5.74	5.74	0.90152	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000016	D	0.83640	0.5298	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88931	0.3373	10	0.87932	D	0	.	19.9306	0.97117	0.0:0.0:1.0:0.0	.	236	Q9H306	MMP27_HUMAN	L	236	ENSP00000260229:P236L	ENSP00000260229:P236L	P	-	2	0	MMP27	102072689	1.000000	0.71417	0.984000	0.44739	0.966000	0.64601	9.476000	0.97823	2.732000	0.93576	0.591000	0.81541	CCA	.		0.398	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		A	102567479	G	A	102567479	3	1	90	1	0	0	0	0	1	0	0	0	9689	1348	47	2	858	2	MMP27	11	102567479	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	14325435	102567479	32439037	57	8172											
POU2AF1	5450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	111225200	111225200	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgcagggtggaggtgggtAgtgtggaaaggggctgaggc	8	7	22	4	0	0	1	0	1	0	0	0	3	0	3	0	8	1	3	0	8	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:111225200A>G	ENST00000393067.3	-	5	1071	c.557T>C	c.(556-558)cTa>cCa	p.L186P		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	186					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		GGAGGTGGGTAGTGTGGAAAG	0.667			T	BCL6	NHL																																p.L186P		.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1-658	0			c.T557C						.						40	47	44					11																	111225200		2201	4297	6498	SO:0001583	missense	5450	exon5			GTGGGTAGTGTGG		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"POU domain class 2, associating factor 1"			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.557T>C	11.37:g.111225200A>G	ENSP00000376786:p.Leu186Pro	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	71	25	NM_006235	0	0	1	1	0	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	37	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101018	0.76983	.	.	ENSG00000110777	ENST00000393067	T	0.36340	1.26	4.87	4.87	0.63330	.	0.098087	0.42548	D	0.000687	T	0.56077	0.1961	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59952	-0.7357	10	0.87932	D	0	-34.107	14.3077	0.66395	1.0:0.0:0.0:0.0	.	186	Q16633	OBF1_HUMAN	P	186	ENSP00000376786:L186P	ENSP00000376786:L186P	L	-	2	0	POU2AF1	110730410	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	6.561000	0.73955	2.043000	0.60533	0.460000	0.39030	CTA	.		0.667	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		G	111225200	A	G	111225200	3	3	90	1	0	0	0	0	1	0	0	0	12296	420	15	3	217	3	POU2AF1	11	111225200	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	8657721	111225200	23781316	58	8173											
NCAPD3	23310	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	134038822	134038822	+	Frame_Shift_Del	DEL	G	G	-																															cttcactgacctctctgactGggggaacttgttgtacttct																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:134038822delG	ENST00000534548.2	-	25	3293	c.3229delC	c.(3229-3231)cagfs	p.Q1077fs		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1077					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		CTCTCTGACTGGGGGAACTTG	0.443																																					p.Q1077fs		.											.	NCAPD3-229	0			c.3229delC						.						115	107	110					11																	134038822		2201	4297	6498	SO:0001589	frameshift_variant	23310	exon25			.	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.3229delC	11.37:g.134038822delG	ENSP00000433681:p.Gln1077fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	91	35	NM_015261	0	0	0	0	0	A6NFS2|Q4KMQ9	Frame_Shift_Del	DEL	ENST00000534548.2	37	CCDS31723.1																																																																																			.		0.443	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		-	134038822	G	-	134038822	7	5	90	1	0	1	0	1	0	0	0	0	10232	1357	47	0	1311	0	NCAPD3	11	134038822	Frame_Shift_Del	DEL	G	TCGA-BQ-7061-01A-11D-1961-08	22813622	134038822	967694	59	8174											
SLC6A13	6540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	346409	346409	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagagccagctcccagcgcAgggcccccaggtgctggatc	8	4	13	16	1	0	1	0	0	0	1	2	2	1	2	4	3	4	3	4	3	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:346409A>T	ENST00000343164.4	-	6	663	c.611T>A	c.(610-612)cTg>cAg	p.L204Q	SLC6A13_ENST00000445055.2_Missense_Mutation_p.L112Q	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	204					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			CTCCCAGCGCAGGGCCCCCAG	0.602																																					p.L204Q		.											.	SLC6A13-90	0			c.T611A						.						66	69	68					12																	346409		2203	4300	6503	SO:0001583	missense	6540	exon6			CAGCGCAGGGCCC	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.611T>A	12.37:g.346409A>T	ENSP00000339260:p.Leu204Gln	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	164	41	NM_016615	0	0	98	135	37	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.892851	0.91889	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164;ENST00000546319	T;T;T	0.78003	-1.14;-1.14;-1.14	5.5	5.5	0.81552	.	0.070471	0.64402	D	0.000018	D	0.90428	0.7003	M	0.92317	3.295	0.80722	D	1	D;D;D	0.76494	0.976;0.999;0.996	D;D;D	0.71414	0.964;0.973;0.964	D	0.92683	0.6160	10	0.87932	D	0	.	15.8304	0.78745	1.0:0.0:0.0:0.0	.	112;183;204	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	Q	112;183;204;112	ENSP00000407104:L112Q;ENSP00000339260:L204Q;ENSP00000444606:L112Q	ENSP00000318097:L183Q	L	-	2	0	SLC6A13	216670	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.127000	0.94417	2.322000	0.78497	0.529000	0.55759	CTG	.		0.602	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		T	346409	A	T	346409	3	4	90	1	0	0	0	0	1	0	0	0	14708	188	7	5	1237	5	SLC6A13	12	346409	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		346409	133505486	60	8175											
ATN1	1822	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	7046365	7046365	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tacggaaagagagccccgtcCccgggggcctacaagacagc	11	3	13	14	3	0	2	0	0	0	2	1	4	1	3	5	3	4	0	5	3	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:7046365C>G	ENST00000356654.4	+	5	2172	c.1935C>G	c.(1933-1935)tcC>tcG	p.S645S	ATN1_ENST00000396684.2_Silent_p.S645S	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	645					cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						GAGCCCCGTCCCCGGGGGCCT	0.672																																					p.S645S		.											.	ATN1-139	0			c.C1935G						.						22	27	25					12																	7046365		2201	4291	6492	SO:0001819	synonymous_variant	1822	exon5			CCCGTCCCCGGGG	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"dentatorubral-pallidoluysian atrophy (atrophin-1)"	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1935C>G	12.37:g.7046365C>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	95	54	NM_001007026	0	0	99	235	136	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			.		0.672	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		G	7046365	C	G	7046365	2	3	90	1	0	0	0	0	0	0	0	1	1112	610	22	4		4	ATN1	12	7046365	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	6699956	7046365	126805530	61	8176											
TAS2R13	50838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	11061866	11061866	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaattctgcaattattacaAgagtgaagatactcggcagg	14	11	10	6	1	1	4	0	2	1	2	2	4	1	4	0	2	3	2	0	2	7	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:11061866A>C	ENST00000390677.2	-	1	295	c.32T>G	c.(31-33)cTt>cGt	p.L11R	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	11					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						AATTATTACAAGAGTGAAGAT	0.388																																					p.L11R		.											.	TAS2R13-154	0			c.T32G						.						39	38	39					12																	11061866		2202	4298	6500	SO:0001583	missense	50838	exon1			ATTACAAGAGTGA	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.32T>G	12.37:g.11061866A>C	ENSP00000375095:p.Leu11Arg	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	54	31	NM_023920	0	0	0	0	0	Q4G0I5|Q502V8|Q645X2	Missense_Mutation	SNP	ENST00000390677.2	37	CCDS8635.1	.	.	.	.	.	.	.	.	.	.	A	12.87	2.068962	0.36470	.	.	ENSG00000212128	ENST00000390677	T	0.00922	5.54	3.3	2.14	0.27477	.	0.745999	0.10446	U	0.673619	T	0.02888	0.0086	M	0.76328	2.33	0.09310	N	1	P	0.48834	0.916	P	0.54026	0.74	T	0.42582	-0.9443	10	0.87932	D	0	.	5.1506	0.15007	0.8598:0.0:0.1402:0.0	.	11	Q9NYV9	T2R13_HUMAN	R	11	ENSP00000375095:L11R	ENSP00000375095:L11R	L	-	2	0	TAS2R13	10953133	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.614000	0.24314	0.456000	0.26937	0.533000	0.62120	CTT	.		0.388	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1			C	11061866	A	C	11061866	3	2	90	1	0	0	0	0	1	0	0	0	15599	72	3	5	883	5	TAS2R13	12	11061866	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	4015501	11061866	122790029	62	8177											
GPR182	11318	broad.mit.edu	37	chr12	57389326	57389326	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctgcccgtgtggatgctGgaggtcacgctggactacac	6	10	13	12	2	2	0	1	0	1	0	3	3	2	3	1	4	3	2	1	4	1	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:57389326G>A	ENST00000300098.1	+	2	552	c.333G>A	c.(331-333)ctG>ctA	p.L111L	RP11-474N8.5_ENST00000556850.1_RNA|HBCBP_ENST00000600202.1_5'Flank	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	111					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						TGTGGATGCTGGAGGTCACGC	0.582																																					p.L111L													.	GPR182-500	0			c.G333A						.						135	114	121					12																	57389326		2203	4300	6503	SO:0001819	synonymous_variant	11318	exon2			GATGCTGGAGGTC	Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"GPCR / Class A : Orphans"	13708	protein-coding gene	gene with protein product		605307	"adrenomedullin receptor"	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.333G>A	12.37:g.57389326G>A		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	108	5	NM_007264	0	0	0	0	0		Silent	SNP	ENST00000300098.1	37	CCDS8927.1																																																																																			.		0.582	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264		A	57389326	G	A	57389326	2	1	90	1	0	0	0	0	0	0	0	1	6697	1335	47	2		2	GPR182	12	57389326	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	46327460	57389326	76462569	63	8178											
DPY19L2	283417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64041138	64041138	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtgcaataccaggaggctAtgattaccttaaaaaagata	17	10	8	6	0	0	2	0	1	0	1	0	3	0	3	2	2	3	2	2	2	8	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:64041138A>T	ENST00000324472.4	-	5	779	c.596T>A	c.(595-597)aTa>aAa	p.I199K	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	199					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		CCAGGAGGCTATGATTACCTT	0.299																																					p.I199K		.											.	DPY19L2-515	0			c.T596A						.						60	65	63					12																	64041138		2203	4297	6500	SO:0001583	missense	283417	exon5			GAGGCTATGATTA		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"spermatogenesis associated 34"	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.596T>A	12.37:g.64041138A>T	ENSP00000315988:p.Ile199Lys	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	189	40	NM_173812	0	0	0	0	0	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.378802	0.24944	.	.	ENSG00000177990	ENST00000324472	T	0.56275	0.47	2.35	2.35	0.29111	.	0.184092	0.34828	U	0.003648	T	0.59046	0.2165	M	0.66939	2.045	0.58432	D	0.999995	D	0.53619	0.961	P	0.57009	0.811	T	0.57808	-0.7747	9	.	.	.	.	6.5488	0.22420	1.0:0.0:0.0:0.0	.	199	Q6NUT2	D19L2_HUMAN	K	199	ENSP00000315988:I199K	.	I	-	2	0	DPY19L2	62327405	0.987000	0.35691	0.069000	0.20011	0.326000	0.28443	5.607000	0.67648	1.080000	0.41073	0.155000	0.16302	ATA	.		0.299	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		T	64041138	A	T	64041138	3	4	90	1	0	0	0	0	1	0	0	0	4752	449	16	5	1752	5	DPY19L2	12	64041138	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	6651812	64041138	69810757	64	8179											
RFX4	5992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	107154995	107154995	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacccttttaatagccccacTtcccggatggaaccttgttt	8	14	6	13	1	0	0	0	0	0	0	1	2	1	2	5	2	3	1	5	2	4	7			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:107154995T>A	ENST00000392842.1	+	18	2370	c.1956T>A	c.(1954-1956)acT>acA	p.T652T	RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Silent_p.T661T|RFX4_ENST00000229387.5_Silent_p.T558T	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	652					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						ATAGCCCCACTTCCCGGATGG	0.468																																					p.T661T		.											.	RFX4-91	0			c.T1983A						.						190	205	200					12																	107154995		2203	4300	6503	SO:0001819	synonymous_variant	5992	exon18			CCCCACTTCCCGG	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1956T>A	12.37:g.107154995T>A		Somatic	430	1		WXS	Illumina HiSeq	Phase_I	528	282	NM_001206691	0	0	0	0	0	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			.		0.468	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		A	107154995	T	A	107154995	2	1	90	1	0	0	0	0	0	0	0	1	13297	1596	56	5		5	RFX4	12	107154995	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	43113857	107154995	26696900	65	8180											
NOS1	4842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	117655909	117655909	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcagatctaaggcggtTggtcacttcgtacgttcgca	8	11	12	10	4	3	1	2	0	1	1	5	2	3	2	0	4	1	4	0	4	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:117655909T>C	ENST00000338101.4	-	28	4337	c.4333A>G	c.(4333-4335)Aac>Gac	p.N1445D	NOS1_ENST00000317775.6_Missense_Mutation_p.N1411D|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CTAAGGCGGTTGGTCACTTCG	0.498																																					p.N1445D	Esophageal Squamous(162;1748 2599 51982 52956)	.											.	NOS1-154	0			c.A4333G						.						312	309	310					12																	117655909		1986	4167	6153	SO:0001583	missense	4842	exon29			GGCGGTTGGTCAC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4333A>G	12.37:g.117655909T>C	ENSP00000337459:p.Asn1445Asp	Somatic	458	0		WXS	Illumina HiSeq	Phase_I	603	135	NM_001204218	0	0	0	0	0		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379742	0.61845	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000338101	T;T	0.01397	4.94;4.99	4.57	4.57	0.56435	.	0.093612	0.85682	D	0.000000	T	0.02342	0.0072	L	0.59436	1.845	0.80722	D	1	P	0.36412	0.552	B	0.35039	0.194	T	0.60393	-0.7272	10	0.38643	T	0.18	-42.2525	14.0843	0.64944	0.0:0.0:0.0:1.0	.	1411	P29475	NOS1_HUMAN	D	1306;1411;1445	ENSP00000320758:N1411D;ENSP00000337459:N1445D	ENSP00000320758:N1411D	N	-	1	0	NOS1	116140292	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.501000	0.81600	1.914000	0.55421	0.459000	0.35465	AAC	.		0.498	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117655909	T	C	117655909	3	2	90	1	0	0	0	0	1	0	0	0	10567	1812	63	3	81	3	NOS1	12	117655909	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	10500914	117655909	16195986	66	8181											
RIMBP2	23504	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	130919339	130919339	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgcccctcctcttgaaGtctggagagtcataggcgtc	7	9	13	12	2	3	2	1	1	2	1	5	4	4	2	3	3	0	0	3	3	2	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:130919339G>A	ENST00000261655.4	-	11	2305	c.2142C>T	c.(2140-2142)gaC>gaT	p.D714D	RIMBP2_ENST00000535703.1_Silent_p.D622D|RIMBP2_ENST00000536002.1_Silent_p.D622D	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	714					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCCTCTTGAAGTCTGGAGAGT	0.597																																					p.D714D		.											.	RIMBP2-142	0			c.C2142T						.						74	81	79					12																	130919339		2203	4300	6503	SO:0001819	synonymous_variant	23504	exon11			CTTGAAGTCTGGA	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2142C>T	12.37:g.130919339G>A		Somatic	167	0		WXS	Illumina HiSeq	Phase_I	206	30	NM_015347	0	0	0	0	0	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			.		0.597	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130919339	G	A	130919339	2	1	90	1	0	0	0	0	0	0	0	1	13395	1020	36	2		2	RIMBP2	12	130919339	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	13263430	130919339	2932556	67	8182											
TEP1	7011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20869208	20869208	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcccgctcccaggtctctGgcctagacagcttcatcctc	5	10	8	18	1	2	1	1	0	1	1	7	1	5	1	4	2	1	3	4	2	1	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr14:20869208G>A	ENST00000262715.5	-	9	1524	c.1484C>T	c.(1483-1485)cCa>cTa	p.P495L	TEP1_ENST00000556935.1_Missense_Mutation_p.P387L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	495	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CCAGGTCTCTGGCCTAGACAG	0.557																																					p.P495L		.											.	TEP1-95	0			c.C1484T						.						125	109	114					14																	20869208		2203	4300	6503	SO:0001583	missense	7011	exon9			GTCTCTGGCCTAG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1484C>T	14.37:g.20869208G>A	ENSP00000262715:p.Pro495Leu	Somatic	133	1		WXS	Illumina HiSeq	Phase_I	125	39	NM_007110	0	0	5	7	2	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089888	0.94149	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.20069	2.1;2.1	5.71	4.81	0.61882	TROVE (2);	0.000000	0.85682	D	0.000000	T	0.34600	0.0903	M	0.84948	2.725	0.80722	D	1	B;P	0.34757	0.215;0.467	B;B	0.39119	0.139;0.291	T	0.33317	-0.9873	10	0.87932	D	0	-14.7861	13.9742	0.64262	0.0753:0.0:0.9247:0.0	.	387;495	G3V5X7;Q99973	.;TEP1_HUMAN	L	495;495;387	ENSP00000262715:P495L;ENSP00000452574:P387L	ENSP00000262715:P495L	P	-	2	0	TEP1	19939048	1.000000	0.71417	0.961000	0.40146	0.876000	0.50452	5.606000	0.67641	2.701000	0.92244	0.555000	0.69702	CCA	.		0.557	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20869208	G	A	20869208	3	1	90	1	0	0	0	0	1	0	0	0	15791	1348	47	2	6587	2	TEP1	14	20869208	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		20869208	86480332	68	8183											
HERC2	8924	hgsc.bcm.edu	37	chr15	28447597	28447597	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagctgcaccacgatcggcAgagcgggaacgggcgactgc	9	4	16	12	5	0	2	0	1	0	1	1	5	0	3	1	3	5	3	1	3	1	0	rs113634395		TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:28447597A>G	ENST00000261609.7	-	46	7484	c.7376T>C	c.(7375-7377)cTg>cCg	p.L2459P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CACGATCGGCAGAGCGGGAAC	0.592																																					p.L2459P		.											.	HERC2-234	0			c.T7376C						.						19	16	17					15																	28447597		2200	4275	6475	SO:0001583	missense	8924	exon46			ATCGGCAGAGCGG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7376T>C	15.37:g.28447597A>G	ENSP00000261609:p.Leu2459Pro	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	66	11	NM_004667	0	0	15	17	2		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	A	5.759	0.324512	0.10900	.	.	ENSG00000128731	ENST00000261609	T	0.38887	1.11	3.99	2.87	0.33458	.	0.178477	0.36591	N	0.002516	T	0.24586	0.0596	N	0.19112	0.55	0.46458	D	0.999051	B	0.33379	0.41	B	0.30029	0.11	T	0.04976	-1.0914	10	0.40728	T	0.16	.	9.0823	0.36558	0.9121:0.0:0.0879:0.0	.	2459	O95714	HERC2_HUMAN	P	2459	ENSP00000261609:L2459P	ENSP00000261609:L2459P	L	-	2	0	HERC2	26121192	0.913000	0.31002	0.140000	0.22221	0.090000	0.18270	4.904000	0.63279	0.717000	0.32145	0.374000	0.22700	CTG	.		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28447597	A	G	28447597	3	3	90	1	0	0	0	0	1	0	0	0	7079	188	7	3	7320	3	HERC2	15	28447597	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		28447597	74083795	69	8184											
MGA	23269	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	42041819	42041837	+	Frame_Shift_Del	DEL	CTAATGTAATAAAACAAAA	CTAATGTAATAAAACAAAA	-																															agaggctgtagaccctgaggCtaatgtaataaaacaaaact																								rs373448335		TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	CTAATGTAATAAAACAAAA	CTAATGTAATAAAACAAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:42041819_42041837delCTAATGTAATAAAACAAAA	ENST00000570161.1	+	16	6014_6032	c.6014_6032delCTAATGTAATAAAACAAAA	c.(6013-6033)gctaatgtaataaaacaaaacfs	p.ANVIKQN2005fs	MGA_ENST00000566586.1_Frame_Shift_Del_p.ANVIKQN1796fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.ANVIKQN1966fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.ANVIKQN2005fs|MGA_ENST00000545763.1_Frame_Shift_Del_p.ANVIKQN1796fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACCCTGAGGCTAATGTAATAAAACAAAACTCAGGAGCT	0.416																																					p.2005_2011del		.											.	MGA-522	0			c.6014_6032del						.																																			SO:0001589	frameshift_variant	23269	exon17			.	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.6014_6032delCTAATGTAATAAAACAAAA	15.37:g.42041819_42041837delCTAATGTAATAAAACAAAA	ENSP00000457035:p.Ala2005fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	111	24	NM_001164273	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	37	CCDS55959.1																																																																																			.		0.416	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	42041837	CTAATGTAATAAAACAAAA	-	42041819	7	5	90	1	0	1	0	1	0	0	0	0	9565	797	28	0	6076	0	MGA	15	42041819	Frame_Shift_Del	DEL	CTAATGTAATAAAACAAAA	TCGA-BQ-7061-01A-11D-1961-08	13594222	42041819	60489573	70	8185											
TP53BP1	7158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43749140	43749140	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaattgagaactggagacaTgggttccgtatcctcaatct	12	11	10	8	1	2	3	1	1	1	3	4	5	4	3	2	2	1	2	2	2	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:43749140T>A	ENST00000263801.3	-	12	1903	c.1651A>T	c.(1651-1653)Atg>Ttg	p.M551L	TP53BP1_ENST00000382044.4_Missense_Mutation_p.M556L|TP53BP1_ENST00000605155.1_5'Flank|TP53BP1_ENST00000450115.2_Missense_Mutation_p.M556L|TP53BP1_ENST00000382039.3_Missense_Mutation_p.M556L	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	551					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		ACTGGAGACATGGGTTCCGTA	0.403								Other conserved DNA damage response genes																													p.M556L		.											.	TP53BP1-294	0			c.A1666T						.						152	135	141					15																	43749140		2201	4298	6499	SO:0001583	missense	7158	exon12			GAGACATGGGTTC	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.1651A>T	15.37:g.43749140T>A	ENSP00000263801:p.Met551Leu	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_001141980	0	0	13	31	18	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	T	4.082	0.013103	0.07912	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.04	1.11	0.20524	.	0.534882	0.20646	N	0.088301	T	0.09730	0.0239	L	0.36672	1.1	0.19775	N	0.999951	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.37361	-0.9709	10	0.10377	T	0.69	-0.7027	5.1031	0.14770	0.3274:0.0823:0.0:0.5903	.	556;551;556;556	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	L	551;556;556;556;556	ENSP00000263801:M551L;ENSP00000371475:M556L;ENSP00000371470:M556L;ENSP00000393497:M556L;ENSP00000388028:M556L	ENSP00000263801:M551L	M	-	1	0	TP53BP1	41536432	0.005000	0.15991	0.993000	0.49108	0.768000	0.43524	0.173000	0.16724	0.321000	0.23259	-0.371000	0.07208	ATG	.		0.403	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43749140	T	A	43749140	3	1	90	1	0	0	0	0	1	0	0	0	16416	1464	51	5	4335	5	TP53BP1	15	43749140	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	1707321	43749140	58782252	71	8186											
MYO1E	4643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	59501015	59501015	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgcatcgtggcgcacacGtcatccaggatgctcatgat	9	9	11	12	3	2	1	2	1	0	0	4	2	3	2	1	2	2	4	1	2	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:59501015G>A	ENST00000288235.4	-	14	1794	c.1395C>T	c.(1393-1395)gaC>gaT	p.D465D		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	465	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TGGCGCACACGTCATCCAGGA	0.542																																					p.D465D		.											.	MYO1E-514	0			c.C1395T						.						118	99	105					15																	59501015		2191	4290	6481	SO:0001819	synonymous_variant	4643	exon14			GCACACGTCATCC	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"Myosins / Myosin superfamily : Class I"	7599	protein-coding gene	gene with protein product	"myosin-IC"	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1395C>T	15.37:g.59501015G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	71	16	NM_004998	0	0	65	73	8	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			.		0.542	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59501015	G	A	59501015	2	1	90	1	0	0	0	0	0	0	0	1	10097	1136	40	1		1	MYO1E	15	59501015	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	15751875	59501015	43030377	72	8187											
TLN2	83660	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	63011987	63011987	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagtggctgatcacatccctCagctggtccagggagtgagg	8	8	14	11	0	2	2	2	2	0	0	4	3	4	3	2	4	1	2	2	4	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:63011987C>G	ENST00000561311.1	+	24	3129	c.2899C>G	c.(2899-2901)Cag>Gag	p.Q967E	TLN2_ENST00000306829.6_Missense_Mutation_p.Q967E			Q9Y4G6	TLN2_HUMAN	talin 2	967	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TCACATCCCTCAGCTGGTCCA	0.547																																					p.Q967E		.											.	TLN2-573	0			c.C2899G						.						65	51	56					15																	63011987		2203	4300	6503	SO:0001583	missense	83660	exon22			ATCCCTCAGCTGG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.2899C>G	15.37:g.63011987C>G	ENSP00000453508:p.Gln967Glu	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	36	13	NM_015059	0	0	3	9	6	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.050280	0.55218	.	.	ENSG00000171914	ENST00000306829	T	0.67865	-0.29	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	L	0.47716	1.5	0.80722	D	1	B	0.24882	0.113	B	0.25987	0.065	T	0.56745	-0.7928	10	0.22706	T	0.39	-16.8653	19.9103	0.97024	0.0:1.0:0.0:0.0	.	967	Q9Y4G6	TLN2_HUMAN	E	967	ENSP00000303476:Q967E	ENSP00000303476:Q967E	Q	+	1	0	TLN2	60799279	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.887000	0.63156	2.765000	0.95021	0.650000	0.86243	CAG	.		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			G	63011987	C	G	63011987	3	3	90	1	0	0	0	0	1	0	0	0	15980	827	29	4	2985	4	TLN2	15	63011987	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	3510972	63011987	39519405	73	8188											
RASGRF1	5923	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	79264261	79264261	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaactggcgaatctctcGgataatatgggatatctgtg	11	13	11	6	2	2	1	0	1	2	0	4	4	2	3	0	3	1	0	0	3	5	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:79264261G>A	ENST00000419573.3	-	27	3950	c.3676C>T	c.(3676-3678)Cga>Tga	p.R1226*	RASGRF1_ENST00000394745.3_Nonsense_Mutation_p.R442*|RASGRF1_ENST00000558480.2_Nonsense_Mutation_p.R1210*	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1226	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGAATCTCTCGGATAATATGG	0.473																																					p.R1226X		.											.	RASGRF1-662	0			c.C3676T						.						268	228	242					15																	79264261		2196	4293	6489	SO:0001587	stop_gained	5923	exon27			TCTCTCGGATAAT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3676C>T	15.37:g.79264261G>A	ENSP00000405963:p.Arg1226*	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	216	75	NM_002891	0	0	1	1	0	F8VPA5|H0YKF2|J3KQP9|Q16027	Nonsense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	42	9.264118	0.99118	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	.	.	.	4.23	3.23	0.37069	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9463	0.47301	0.0:0.0:0.8013:0.1987	.	.	.	.	X	1226;1210;442	.	ENSP00000378224:R1210X	R	-	1	2	RASGRF1	77051316	1.000000	0.71417	0.999000	0.59377	0.806000	0.45545	1.206000	0.32321	2.169000	0.68431	0.561000	0.74099	CGA	.		0.473	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79264261	G	A	79264261	4	1	90	1	0	0	0	0	0	1	0	0	13104	1124	39	1	153	1	RASGRF1	15	79264261	Nonsense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	16252274	79264261	23267131	74	8189											
KIAA1024	23251	broad.mit.edu	37	chr15	79748657	79748657	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcttctacacagcttgtctCgatcccaattttccagccac	8	13	4	16	1	3	0	0	0	3	0	6	1	5	0	3	0	3	1	3	0	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:79748657C>T	ENST00000305428.3	+	2	243	c.168C>T	c.(166-168)ctC>ctT	p.L56L		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	56						integral component of membrane (GO:0016021)		p.L56L(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						CAGCTTGTCTCGATCCCAATT	0.458																																					p.L56L													.	KIAA1024-183	1	Substitution - coding silent(1)	lung(1)	c.C168T						.						106	101	103					15																	79748657		2196	4293	6489	SO:0001819	synonymous_variant	23251	exon2			TTGTCTCGATCCC	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.168C>T	15.37:g.79748657C>T		Somatic	144	0		WXS	Illumina HiSeq	Phase_I	124	6	NM_015206	0	0	0	0	0	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																			.		0.458	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		T	79748657	C	T	79748657	2	4	90	1	0	0	0	0	0	0	0	1	8226	871	31	1		1	KIAA1024	15	79748657	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	484396	79748657	22782735	75	8190											
ROGDI	79641	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4849743	4849743	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggtcccggctggtaagcaGgtaaatggcttggctcacat	8	10	13	10	1	1	0	1	0	0	0	2	0	2	0	1	6	1	6	1	6	3	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:4849743G>C	ENST00000322048.7	-	6	754	c.376C>G	c.(376-378)Ctg>Gtg	p.L126V	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	126					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						CTGGTAAGCAGGTAAATGGCT	0.622																																					p.L126V													.	ROGDI-92	0			c.C376G						.						107	84	91					16																	4849743		2197	4300	6497	SO:0001583	missense	79641	exon6			TAAGCAGGTAAAT	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.376C>G	16.37:g.4849743G>C	ENSP00000322832:p.Leu126Val	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_024589	0	0	26	46	20	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.163097	0.38217	.	.	ENSG00000067836	ENST00000322048	T	0.49432	0.78	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000001	T	0.49064	0.1535	L	0.45581	1.43	0.54753	D	0.999982	P	0.52316	0.952	P	0.55161	0.77	T	0.37776	-0.9691	10	0.11485	T	0.65	-27.1765	10.2733	0.43495	0.0926:0.0:0.9074:0.0	.	126	Q9GZN7	ROGDI_HUMAN	V	126	ENSP00000322832:L126V	ENSP00000322832:L126V	L	-	1	2	ROGDI	4789744	1.000000	0.71417	0.998000	0.56505	0.727000	0.41649	6.591000	0.74090	2.180000	0.69256	0.561000	0.74099	CTG	.		0.622	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589		C	4849743	G	C	4849743	3	2	90	1	0	0	0	0	1	0	0	0	13552	991	35	4	511	4	ROGDI	16	4849743	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		4849743	85505010	76	8191											
MYH11	4629	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	15841744	15841744	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggctcaccatgagaatgcagGcctgcttcccgtccatgaag	9	8	11	13	1	1	2	1	2	0	1	3	3	3	2	4	2	2	3	4	2	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:15841744G>T	ENST00000300036.5	-	18	2346	c.2237C>A	c.(2236-2238)gCc>gAc	p.A746D	MYH11_ENST00000576790.2_Missense_Mutation_p.A746D|MYH11_ENST00000396324.3_Missense_Mutation_p.A753D|MYH11_ENST00000452625.2_Missense_Mutation_p.A753D	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	746	Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GAGAATGCAGGCCTGCTTCCC	0.587			T	CBFB	AML																																p.A753D		.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11-666	0			c.C2258A						.						89	84	86					16																	15841744		2197	4300	6497	SO:0001583	missense	4629	exon19			ATGCAGGCCTGCT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"Myosins / Myosin superfamily : Class II"	7569	protein-coding gene	gene with protein product		160745	"myosin, heavy polypeptide 11, smooth muscle"			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2237C>A	16.37:g.15841744G>T	ENSP00000300036:p.Ala746Asp	Somatic	43	1		WXS	Illumina HiSeq	Phase_I	69	23	NM_001040114	0	0	0	0	0	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983101	0.93044	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	5.35	5.35	0.76521	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.88514	0.6457	M	0.90369	3.11	0.80722	D	1	D;D;P;D;D	0.76494	0.999;0.974;0.864;0.974;0.969	D;D;D;D;D	0.67103	0.949;0.916;0.916;0.916;0.949	D	0.90804	0.4696	10	0.87932	D	0	.	18.0422	0.89322	0.0:0.0:1.0:0.0	.	753;746;753;746;753	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	D	746;746;753;753;753	ENSP00000300036:A746D;ENSP00000345136:A746D;ENSP00000379616:A753D;ENSP00000407821:A753D	ENSP00000300036:A746D	A	-	2	0	MYH11	15749245	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.848000	0.99507	2.506000	0.84524	0.561000	0.74099	GCC	.		0.587	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15841744	G	T	15841744	3	4	90	1	0	0	0	0	1	0	0	0	10056	1203	42	4	3812	4	MYH11	16	15841744	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	10992001	15841744	74513009	77	8192											
C16orf62	57020	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	19711796	19711797	+	Stop_Codon_Ins	INS	-	-	G																															ccctctgcaaacaaggacctINSgacccccgggcccatcccca																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:19711796_19711797insG	ENST00000251143.5	+	0	2902_2903				C16orf62_ENST00000417362.2_Stop_Codon_Ins|C16orf62_ENST00000543152.1_Stop_Codon_Ins|C16orf62_ENST00000448695.1_Stop_Codon_Ins|C16orf62_ENST00000542263.1_Stop_Codon_Ins|C16orf62_ENST00000438132.3_Stop_Codon_Ins			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62							integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						AACAAGGACCTGACCCCCGGGC	0.51																																					p.X1053delinsW		.											.	C16orf62-69	0			c.3157_3158insG						.																																			SO:0001567	stop_retained_variant	57020	exon31			.		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.2890dupG	16.37:g.19711797_19711797dupG	ENSP00000251143:p.*964Trpext*54	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	85	28	NM_020314	0	0	0	0	0	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Missense_Mutation	INS	ENST00000251143.5	37																																																																																				.		0.51	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		G	19711797	-	G	19711796	7	5	90	1	0	1	1	0	0	0	0	0	1829	1593	55	0	3012	0	C16orf62	16	19711796	Stop_Codon_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08	3870052	19711796	70642957	78	8193											
ZP2	7783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21215430	21215430	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caattccattgtcatgcagcTggctcacatcaatgttctgg	9	13	8	11	0	4	0	3	0	1	0	5	0	5	0	1	2	2	4	1	2	2	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:21215430T>A	ENST00000574002.1	-	10	1375	c.893A>T	c.(892-894)cAg>cTg	p.Q298L	ZP2_ENST00000574091.1_Missense_Mutation_p.Q298L|ZP2_ENST00000219593.4_Missense_Mutation_p.Q298L|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	298					binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		GTCATGCAGCTGGCTCACATC	0.428																																					p.Q298L		.											.	ZP2-91	0			c.A893T						.						161	137	145					16																	21215430		2200	4300	6500	SO:0001583	missense	7783	exon9			TGCAGCTGGCTCA	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.893A>T	16.37:g.21215430T>A	ENSP00000460971:p.Gln298Leu	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	88	33	NM_003460	0	0	0	0	0	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.233434	0.39498	.	.	ENSG00000103310	ENST00000219593	T	0.78816	-1.21	6.08	3.74	0.42951	.	0.574315	0.17910	N	0.157889	D	0.84938	0.5583	M	0.73962	2.25	0.09310	N	1	D;B;B	0.89917	1.0;0.223;0.223	D;B;B	0.91635	0.999;0.143;0.053	T	0.73563	-0.3943	10	0.28530	T	0.3	-5.929	9.6718	0.40017	0.1165:0.0:0.1209:0.7626	.	298;298;298	B4DEV1;Q4VAP1;Q05996	.;.;ZP2_HUMAN	L	298	ENSP00000219593:Q298L	ENSP00000219593:Q298L	Q	-	2	0	ZP2	21122931	0.975000	0.34042	0.255000	0.24374	0.042000	0.13812	2.912000	0.48782	2.330000	0.79161	0.533000	0.62120	CAG	.		0.428	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			A	21215430	T	A	21215430	3	1	90	1	0	0	0	0	1	0	0	0	18248	1580	55	5	1388	5	ZP2	16	21215430	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	1503634	21215430	69139323	79	8194											
FOXC2	2303	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	86601010	86601010	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctacctgagcgagcagaaTtactaccgggctgcgggcag	9	6	13	13	3	0	2	0	1	0	1	0	3	0	2	3	2	6	3	3	2	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:86601010T>G	ENST00000320354.4	+	1	154	c.69T>G	c.(67-69)aaT>aaG	p.N23K	RP11-463O9.5_ENST00000563280.1_RNA	NM_005251.2	NP_005242.1	Q99958	FOXC2_HUMAN	forkhead box C2 (MFH-1, mesenchyme forkhead 1)	23					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|embryonic viscerocranium morphogenesis (GO:0048703)|glomerular endothelium development (GO:0072011)|glomerular mesangial cell development (GO:0072144)|glomerular visceral epithelial cell differentiation (GO:0072112)|heart development (GO:0007507)|insulin receptor signaling pathway (GO:0008286)|lymphangiogenesis (GO:0001946)|mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|paraxial mesodermal cell fate commitment (GO:0048343)|patterning of blood vessels (GO:0001569)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular wound healing (GO:0035470)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|response to hormone (GO:0009725)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	15						GCGAGCAGAATTACTACCGGG	0.701									Late-onset Hereditary Lymphedema																												p.N23K		.											.	FOXC2-226	0			c.T69G						.						34	38	37					16																	86601010		2196	4296	6492	SO:0001583	missense	2303	exon1	Familial Cancer Database	Hereditary Lymphedema type II, Meige Lymphedema	GCAGAATTACTAC	Y08223	CCDS10958.1	16q24.1	2008-04-10			ENSG00000176692	ENSG00000176692		"Forkhead boxes"	3801	protein-coding gene	gene with protein product		602402		FKHL14		9169153, 8674414	Standard	NM_005251		Approved	MFH-1	uc002fjq.3	Q99958	OTTHUMG00000137652	ENST00000320354.4:c.69T>G	16.37:g.86601010T>G	ENSP00000326371:p.Asn23Lys	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	85	32	NM_005251	0	0	2	2	0	C6KMR9|Q14DA6	Missense_Mutation	SNP	ENST00000320354.4	37	CCDS10958.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618182	0.66787	.	.	ENSG00000176692	ENST00000320354	D	0.94862	-3.54	3.49	-4.32	0.03688	.	0.351583	0.22692	U	0.056809	D	0.91768	0.7396	L	0.46157	1.445	0.37017	D	0.896014	P	0.47409	0.895	P	0.47573	0.55	D	0.88376	0.2998	10	0.39692	T	0.17	.	14.3409	0.66624	0.0:0.8175:0.0:0.1825	.	23	Q99958	FOXC2_HUMAN	K	23	ENSP00000326371:N23K	ENSP00000326371:N23K	N	+	3	2	FOXC2	85158511	0.974000	0.33945	0.948000	0.38648	0.973000	0.67179	0.371000	0.20450	-1.237000	0.02539	-0.689000	0.03729	AAT	.		0.701	FOXC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269104.2	NM_005251		G	86601010	T	G	86601010	3	3	90	1	0	0	0	0	1	0	0	0	6014	1490	52	5	71	5	FOXC2	16	86601010	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	65385580	86601010	3753743	80	8195											
TSR1	55720	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	2232753	2232753	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtcacgcctcaccaccAtattcaatactgacatctgg	11	9	7	14	1	4	1	3	1	1	0	4	1	4	1	3	2	1	0	3	2	3	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:2232753A>T	ENST00000301364.5	-	11	2866	c.1787T>A	c.(1786-1788)aTg>aAg	p.M596K	SNORD91A_ENST00000390861.1_RNA|SNORD91B_ENST00000391250.1_RNA	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	596					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						CCTCACCACCATATTCAATAC	0.438																																					p.M596K		.											.	TSR1-91	0			c.T1787A						.						89	80	83					17																	2232753		2203	4300	6503	SO:0001583	missense	55720	exon11			ACCACCATATTCA	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"TSR1, 20S rRNA accumulation, homolog (yeast)"			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.1787T>A	17.37:g.2232753A>T	ENSP00000301364:p.Met596Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_018128	0	0	18	41	23	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.337499	0.60963	.	.	ENSG00000167721	ENST00000301364	T	0.18016	2.24	5.34	5.34	0.76211	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.225116	0.52532	D	0.000063	T	0.23649	0.0572	M	0.69185	2.1	0.53688	D	0.999979	B	0.25667	0.131	B	0.29440	0.102	T	0.02533	-1.1145	10	0.54805	T	0.06	-17.0729	14.4964	0.67691	1.0:0.0:0.0:0.0	.	596	Q2NL82	TSR1_HUMAN	K	596	ENSP00000301364:M596K	ENSP00000301364:M596K	M	-	2	0	TSR1	2179503	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.017000	0.93651	2.014000	0.59158	0.459000	0.35465	ATG	.		0.438	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		T	2232753	A	T	2232753	3	4	90	1	0	0	0	0	1	0	0	0	16697	217	8	5	647	5	TSR1	17	2232753	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		2232753	78962457	81	8196											
PITPNM3	83394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	6375990	6375990	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacctaccgaggaggagggaCtgcccatcgcccagtgggaa	11	4	14	12	2	0	0	0	0	0	0	1	5	0	4	4	4	3	0	4	4	3	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:6375990C>T	ENST00000262483.8	-	11	1503	c.1416G>A	c.(1414-1416)caG>caA	p.Q472Q	PITPNM3_ENST00000421306.3_Silent_p.Q436Q|PITPNM3_ENST00000576664.1_5'UTR	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	472	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGAGGAGGGACTGCCCATCGC	0.652																																					p.Q472Q		.											.	PITPNM3-228	0			c.G1416A						.						57	57	57					17																	6375990		2202	4300	6502	SO:0001819	synonymous_variant	83394	exon11			GAGGGACTGCCCA	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"GPCR / Class A : Chemokine receptors : Atypical"	21043	protein-coding gene	gene with protein product	"atypical chemokine receptor 6"	608921	"cone rod dystrophy 5"	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1416G>A	17.37:g.6375990C>T		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	28	15	NM_031220	0	0	0	0	0	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	37	CCDS11076.1																																																																																			.		0.652	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		T	6375990	C	T	6375990	2	4	90	1	0	0	0	0	0	0	0	1	11978	564	20	2		2	PITPNM3	17	6375990	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	4143237	6375990	74819220	82	8197											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y	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	265	268					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	362	48		WXS	Illumina HiSeq		358	56	NM_145301	0	0	0	64	64	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		T	15457087	C	T	15457087	3	4	90	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	9081097	15457087	65738123	83	8198											
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39190835	39190835	+	Missense_Mutation	SNP	G	G	C																															tgccacagccagttccgcagGagctggtctggcagcagctt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:39190835G>C	ENST00000344363.5	-	1	272	c.239C>G	c.(238-240)tCc>tGc	p.S80C		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	90			Missing (in allele KAP1.9). {ECO:0000269|PubMed:12228244}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGTTCCGCAGGAGCTGGTCTG	0.617																																					p.S80C		.											.	.	0			c.C239G						.						31	35	34					17																	39190835		1998	4175	6173	SO:0001583	missense	81850	exon1			CCGCAGGAGCTGG	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.239C>G	17.37:g.39190835G>C	ENSP00000344420:p.Ser80Cys	Somatic	97	1		WXS	Illumina HiSeq	Phase_I	94	5	NM_030966	0	0	0	0	0	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	G	1.645	-0.515394	0.04200	.	.	ENSG00000221880	ENST00000344363	T	0.35973	1.28	3.45	2.46	0.29980	.	.	.	.	.	T	0.14614	0.0353	.	.	.	0.24468	N	0.994406	B	0.02656	0.0	B	0.01281	0.0	T	0.25572	-1.0128	8	0.02654	T	1	.	8.8906	0.35432	0.0:0.7644:0.2356:0.0	.	90	Q8IUG1	KRA13_HUMAN	C	80	ENSP00000344420:S80C	ENSP00000344420:S80C	S	-	2	0	KRTAP1-3	36444361	0.984000	0.35163	0.379000	0.26080	0.250000	0.25880	-0.494000	0.06451	1.020000	0.39573	-0.147000	0.13772	TCC	.		0.617	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			C	39190835	G	C	39190835	3	2	90	1	0	0	0	0	1	0	0	0	8524	1174	41	4	268	4	KRTAP1-3	17	39190835	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	23733748	39190835	42004375	84	8199	89	2									
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39190845	39190845	+	Missense_Mutation	SNP	G	G	C																															agttccgcaggagctggtctGgcagcagcttggctggcagc																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:39190845G>C	ENST00000344363.5	-	1	262	c.229C>G	c.(229-231)Cag>Gag	p.Q77E		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	87			Missing (in allele KAP1.9). {ECO:0000269|PubMed:12228244}.			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(6)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GAGCTGGTCTGGCAGCAGCTT	0.612																																					p.Q77E		.											.	.	0			c.C229G						.						32	36	35					17																	39190845		2006	4177	6183	SO:0001583	missense	81850	exon1			TGGTCTGGCAGCA	AJ406927	CCDS42323.1	17q21.2	2013-06-20			ENSG00000221880	ENSG00000221880		"Keratin associated proteins"	16771	protein-coding gene	gene with protein product		608820				11279113	Standard	NM_030966		Approved	KAP1.3	uc002hvv.3	Q8IUG1	OTTHUMG00000133583	ENST00000344363.5:c.229C>G	17.37:g.39190845G>C	ENSP00000344420:p.Gln77Glu	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	102	6	NM_030966	0	0	0	0	0	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601629	0.46423	.	.	ENSG00000221880	ENST00000344363	T	0.31247	1.5	3.73	-0.96	0.10340	.	.	.	.	.	T	0.13030	0.0316	.	.	.	0.19300	N	0.99997	B	0.33000	0.393	B	0.36959	0.237	T	0.28170	-1.0052	8	0.05525	T	0.97	.	6.3215	0.21221	0.0:0.3347:0.3233:0.342	.	87	Q8IUG1	KRA13_HUMAN	E	77	ENSP00000344420:Q77E	ENSP00000344420:Q77E	Q	-	1	0	KRTAP1-3	36444371	1.000000	0.71417	0.018000	0.16275	0.954000	0.61252	0.703000	0.25646	-0.108000	0.12066	0.655000	0.94253	CAG	.		0.612	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			C	39190845	G	C	39190845	3	2	90	1	0	0	0	0	1	0	0	0	8524	1357	47	4	278	4	KRTAP1-3	17	39190845	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	10	39190845	42004365	85	8200	89	2									
ST6GALNAC2	10610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74570497	74570497	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctttgtgttggctcaggCggtcccagagcgctggggtg	3	10	19	9	2	1	1	1	0	0	1	2	1	2	1	1	6	1	4	1	6	0	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:74570497C>T	ENST00000225276.5	-	3	630	c.311G>A	c.(310-312)cGc>cAc	p.R104H	ST6GALNAC2_ENST00000586520.1_5'UTR	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	104					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						TTGGCTCAGGCGGTCCCAGAG	0.637																																					p.R104H		.											.	ST6GALNAC2-90	0			c.G311A						.						38	35	36					17																	74570497		2203	4300	6503	SO:0001583	missense	10610	exon3			CTCAGGCGGTCCC	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"Sialyltransferases"	10867	protein-coding gene	gene with protein product		610137	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)", "sialyltransferase-like 1"	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.311G>A	17.37:g.74570497C>T	ENSP00000225276:p.Arg104His	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	44	16	NM_006456	0	1	92	177	84	Q12971	Missense_Mutation	SNP	ENST00000225276.5	37	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	c	14.90	2.674158	0.47781	.	.	ENSG00000070731	ENST00000225276	T	0.32272	1.46	4.47	-0.561	0.11785	.	0.749066	0.12928	N	0.427572	T	0.24392	0.0591	L	0.55017	1.72	0.18873	N	0.999984	B	0.29301	0.241	B	0.25884	0.064	T	0.19353	-1.0308	10	0.56958	D	0.05	-1.9719	6.7032	0.23236	0.0:0.3692:0.0:0.6308	.	104	Q9UJ37	SIA7B_HUMAN	H	104	ENSP00000225276:R104H	ENSP00000225276:R104H	R	-	2	0	ST6GALNAC2	72082092	0.001000	0.12720	0.960000	0.40013	0.859000	0.49053	0.361000	0.20267	0.093000	0.17368	-0.258000	0.10820	CGC	.		0.637	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		T	74570497	C	T	74570497	3	4	90	1	0	0	0	0	1	0	0	0	15256	768	27	1	841	1	ST6GALNAC2	17	74570497	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	35379652	74570497	6624713	86	8201											
ZNF564	163050	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	12639496	12639497	+	Frame_Shift_Del	DEL	AG	AG	-																															aagttcacagccacatcctcAgaggccactgagtcctaaaa																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:12639496_12639497delAG	ENST00000339282.7	-	2	213_214	c.17_18delCT	c.(16-18)tctfs	p.S6fs	CTD-2192J16.21_ENST00000601420.1_RNA|CTD-2192J16.20_ENST00000593682.1_3'UTR|ZNF709_ENST00000428311.1_Intron	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	6	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						CCACATCCTCAGAGGCCACTGA	0.45																																					p.6_6del		.											.	ZNF564-91	0			c.17_18del						.																																			SO:0001589	frameshift_variant	163050	exon2			.	BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.17_18delCT	19.37:g.12639498_12639499delAG	ENSP00000340004:p.Ser6fs	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	146	54	NM_144976	0	0	0	0	0	B9EGT4|Q6P1K6	Frame_Shift_Del	DEL	ENST00000339282.7	37	CCDS42505.1																																																																																			.		0.45	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		-	12639497	AG	-	12639496	7	5	90	1	0	1	0	1	0	0	0	0	18027	175	7	0	1655	0	ZNF564	19	12639496	Frame_Shift_Del	DEL	AG	TCGA-BQ-7061-01A-11D-1961-08		12639496	46489487	87	8202											
TRMT1	55621	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13226494	13226494	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtctcctgaggccaggttTtcactctctttcagttcaac	6	15	8	12	0	5	1	3	1	2	0	7	1	5	1	2	3	1	2	2	3	1	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:13226494T>A	ENST00000592062.1	-	5	969	c.399A>T	c.(397-399)gaA>gaT	p.E133D	TRMT1_ENST00000592892.1_5'UTR|TRMT1_ENST00000221504.8_Missense_Mutation_p.E133D|TRMT1_ENST00000437766.1_Missense_Mutation_p.E133D|NACC1_ENST00000292431.4_5'Flank|TRMT1_ENST00000357720.4_Missense_Mutation_p.E133D			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	133	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		AGGCCAGGTTTTCACTCTCTT	0.572																																					p.E133D		.											.	TRMT1-92	0			c.A399T						.						166	168	168					19																	13226494		2203	4300	6503	SO:0001583	missense	55621	exon4			CAGGTTTTCACTC	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.399A>T	19.37:g.13226494T>A	ENSP00000466967:p.Glu133Asp	Somatic	280	0		WXS	Illumina HiSeq	Phase_I	299	114	NM_001136035	0	0	18	32	14	O76103|Q548Y5|Q8WVA6	Missense_Mutation	SNP	ENST00000592062.1	37	CCDS12293.1	.	.	.	.	.	.	.	.	.	.	T	9.755	1.168481	0.21621	.	.	ENSG00000104907	ENST00000357720;ENST00000437766;ENST00000221504	.	.	.	3.89	2.82	0.32997	.	0.227351	0.35677	N	0.003045	T	0.31979	0.0814	N	0.19112	0.55	0.36296	D	0.856722	B;B	0.09022	0.001;0.002	B;B	0.08055	0.002;0.003	T	0.18650	-1.0330	9	0.17369	T	0.5	-2.7274	8.7051	0.34349	0.0:0.0:0.1926:0.8074	.	133;133	Q9NXH9-2;Q9NXH9	.;TRM1_HUMAN	D	133	.	ENSP00000221504:E133D	E	-	3	2	TRMT1	13087494	0.311000	0.24536	0.324000	0.25361	0.593000	0.36681	1.442000	0.35046	0.797000	0.33971	0.460000	0.39030	GAA	.		0.572	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		A	13226494	T	A	13226494	3	1	90	1	0	0	0	0	1	0	0	0	16594	1838	64	5	1636	5	TRMT1	19	13226494	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	586998	13226494	45902489	88	8203											
SIN3B	23309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	16964967	16964967	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaggtccgccgggtgcTgaagagccaggaggtgtatg	7	8	17	9	2	1	2	0	1	1	1	2	3	2	3	3	4	3	3	3	4	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:16964967T>C	ENST00000248054.5	+	8	974	c.953T>C	c.(952-954)cTg>cCg	p.L318P	SIN3B_ENST00000596802.1_Missense_Mutation_p.L318P|SIN3B_ENST00000379803.1_Missense_Mutation_p.L318P					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGCCGGGTGCTGAAGAGCCAG	0.597																																					p.L318P		.											.	SIN3B-228	0			c.T953C						.						56	53	54					19																	16964967		2203	4300	6503	SO:0001583	missense	23309	exon8			GGGTGCTGAAGAG	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.953T>C	19.37:g.16964967T>C	ENSP00000248054:p.Leu318Pro	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	65	28	NM_015260	0	0	6	14	8		Missense_Mutation	SNP	ENST00000248054.5	37		.	.	.	.	.	.	.	.	.	.	T	21.4	4.138166	0.77775	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.63580	-0.05;0.13	5.19	5.19	0.71726	.	0.064314	0.64402	D	0.000004	D	0.83275	0.5219	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.987;0.988	D	0.87560	0.2471	10	0.87932	D	0	-38.9141	14.2256	0.65858	0.0:0.0:0.0:1.0	.	318;318;318	O75182-2;O75182;O75182-3	.;SIN3B_HUMAN;.	P	318	ENSP00000369131:L318P;ENSP00000248054:L318P	ENSP00000248054:L318P	L	+	2	0	SIN3B	16825967	1.000000	0.71417	0.993000	0.49108	0.870000	0.49936	7.837000	0.86796	1.958000	0.56883	0.459000	0.35465	CTG	.		0.597	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		C	16964967	T	C	16964967	3	2	90	1	0	0	0	0	1	0	0	0	14358	1580	55	3	983	3	SIN3B	19	16964967	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	3738473	16964967	42164016	89	8204											
LSR	51599	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35757260	35757260	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgttgattgtgtcctcacAgtgtatgccgccggcaaagc	7	11	11	12	2	1	1	1	1	0	0	2	1	2	1	4	1	2	3	4	1	2	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:35757260A>G	ENST00000361790.3	+	6	1081		c.e6-1		USF2_ENST00000222305.3_5'Flank|LSR_ENST00000602122.1_Splice_Site|LSR_ENST00000347609.4_Splice_Site|LSR_ENST00000354900.3_Splice_Site|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000360798.3_Splice_Site|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000427250.1_Splice_Site|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000379134.3_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor						embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTGTCCTCACAGTGTATGCCG	0.627																																					.		.											.	LSR-90	0			c.866-2A>G						.						76	78	77					19																	35757260		2203	4300	6503	SO:0001630	splice_region_variant	51599	exon5			CCTCACAGTGTAT	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.923-1A>G	19.37:g.35757260A>G		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	140	39	NM_015925	0	0	0	1	1	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Splice_Site	SNP	ENST00000361790.3	37	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.029984	0.35797	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	.	.	.	3.99	2.94	0.34122	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7508	0.28896	0.8124:0.0:0.0:0.1876	.	.	.	.	.	-1	.	.	.	+	.	.	LSR	40449100	1.000000	0.71417	0.489000	0.27452	0.523000	0.34469	7.126000	0.77201	0.540000	0.28808	0.379000	0.24179	.	.		0.627	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	Intron	G	35757260	A	G	35757260	5	3	90	1	0	0	0	0	0	0	1	0	9089	202	7	3	943	3	LSR	19	35757260	Splice_Site	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	18792293	35757260	23371723	90	8205											
C19orf55	148137	broad.mit.edu	37	chr19	36253153	36253153	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctcaactggggcttctcaGcaggagccaacaaaccagaa	14	5	9	13	0	2	1	2	0	1	1	3	2	2	2	3	3	5	2	3	3	4	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:36253153G>A	ENST00000544099.1	+	5	502		c.e5-1		C19orf55_ENST00000396908.4_Splice_Site|C19orf55_ENST00000537459.1_Splice_Site|C19orf55_ENST00000536950.1_Intron|C19orf55_ENST00000421853.2_Splice_Site			Q2NL68	PRSR3_HUMAN												cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGCTTCTCAGCAGGAGCCAA	0.552																																					.													.	C19orf55-23	0			c.440-1G>A						.						51	56	55					19																	36253153		1968	4154	6122	SO:0001630	splice_region_variant	148137	exon5			TTCTCAGCAGGAG																												ENST00000544099.1:c.440-1G>A	19.37:g.36253153G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	21	4	NM_001039887	0	0	0	0	0	Q8NDI3|Q8WWC8|Q96NL4	Splice_Site	SNP	ENST00000544099.1	37		.	.	.	.	.	.	.	.	.	.	G	12.11	1.840477	0.32513	.	.	ENSG00000167595	ENST00000396908;ENST00000537459	.	.	.	4.12	3.07	0.35406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2689	0.26246	0.1244:0.0:0.8756:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C19orf55	40944993	0.991000	0.36638	0.987000	0.45799	0.062000	0.15995	0.609000	0.24238	1.272000	0.44329	0.650000	0.86243	.	.		0.552	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		Intron	A	36253153	G	A	36253153	5	1	90	1	0	0	0	0	0	0	1	0	1943	985	34	2	457	2	C19orf55	19	36253153	Splice_Site	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	495893	36253153	22875830	91	8206											
ZSCAN4	201516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58187881	58187881	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagattcatagaagacctgaCtgatgacagcataaatccac	16	8	8	9	0	1	6	1	3	0	3	2	7	2	6	2	0	1	1	2	0	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:58187881C>G	ENST00000318203.5	+	3	1065	c.368C>G	c.(367-369)aCt>aGt	p.T123S		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	123	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GAAGACCTGACTGATGACAGC	0.418																																					p.T123S		.											.	ZSCAN4-91	0			c.C368G						.						83	81	81					19																	58187881		2203	4300	6503	SO:0001583	missense	201516	exon3			ACCTGACTGATGA	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"-", "Zinc fingers, C2H2-type"	23709	protein-coding gene	gene with protein product		613419	"zinc finger protein 494"	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.368C>G	19.37:g.58187881C>G	ENSP00000321963:p.Thr123Ser	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	73	26	NM_152677	0	0	0	0	0	Q3MIQ2	Missense_Mutation	SNP	ENST00000318203.5	37	CCDS12958.1	.	.	.	.	.	.	.	.	.	.	C	9.547	1.114797	0.20795	.	.	ENSG00000180532	ENST00000318203	T	0.04317	3.65	4.42	-8.83	0.00806	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (1);	1.418230	0.04476	N	0.376945	T	0.04363	0.0120	L	0.53671	1.685	0.09310	N	1	B	0.14805	0.011	B	0.22386	0.039	T	0.40021	-0.9585	10	0.11794	T	0.64	0.036	5.2622	0.15580	0.3993:0.1301:0.3976:0.073	.	123	Q8NAM6	ZSCA4_HUMAN	S	123	ENSP00000321963:T123S	ENSP00000321963:T123S	T	+	2	0	ZSCAN4	62879693	0.006000	0.16342	0.000000	0.03702	0.016000	0.09150	-0.007000	0.12810	-2.018000	0.00943	-0.140000	0.14226	ACT	.		0.418	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677		G	58187881	C	G	58187881	3	3	90	1	0	0	0	0	1	0	0	0	18269	565	20	4	370	4	ZSCAN4	19	58187881	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	21934728	58187881	941102	92	8207											
ENTPD6	955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	25198149	25198149	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttctccagggcaccctgcaGgcctccccacccggctacct	5	7	8	21	1	1	0	0	0	1	0	3	0	2	0	7	3	2	3	7	3	1	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr20:25198149G>C	ENST00000376652.4	+	9	973	c.810G>C	c.(808-810)caG>caC	p.Q270H	ENTPD6_ENST00000433259.2_Missense_Mutation_p.Q270H|ENTPD6_ENST00000354989.5_Missense_Mutation_p.Q253H|ENTPD6_ENST00000360031.2_Missense_Mutation_p.Q269H|Y_RNA_ENST00000365544.1_RNA			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	270					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GCACCCTGCAGGCCTCCCCAC	0.537																																					p.Q270H		.											.	ENTPD6-90	0			c.G810C						.						93	91	92					20																	25198149		2203	4300	6503	SO:0001583	missense	955	exon9			CCTGCAGGCCTCC	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.810G>C	20.37:g.25198149G>C	ENSP00000365840:p.Gln270His	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	131	32	NM_001247	0	0	0	0	0	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	7.510|7.510|7.510	0.654527|0.654527|0.654527	0.14580|0.14580|0.14580	.|.|.	.|.|.	ENSG00000197586|ENSG00000197586|ENSG00000197586	ENST00000376666|ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000439162;ENST00000417467;ENST00000433259;ENST00000425813|ENST00000433417;ENST00000427553;ENST00000447877	.|T;T;T;T;T;T;T|.	.|0.11495|.	.|2.77;2.77;2.77;2.77;2.77;2.77;2.77|.	5.71|5.71|5.71	2.69|2.69|2.69	0.31865|0.31865|0.31865	.|.|.	.|0.866486|.	.|0.10745|.	.|N|.	.|0.638962|.	T|T|T	0.51686|0.51686|0.51686	0.1689|0.1689|0.1689	L|L|L	0.58925|0.58925|0.58925	1.835|1.835|1.835	0.33639|0.33639|0.33639	D|D|D	0.607014|0.607014|0.607014	.|B;B;B;B;B;B;B;B;B|.	.|0.20459|.	.|0.004;0.045;0.045;0.027;0.045;0.004;0.006;0.022;0.012|.	.|B;B;B;B;B;B;B;B;B|.	.|0.30105|.	.|0.021;0.076;0.076;0.049;0.111;0.029;0.033;0.037;0.037|.	T|T|T	0.58047|0.58047|0.58047	-0.7705|-0.7705|-0.7705	5|10|5	.|0.46703|.	.|T|.	.|0.11|.	-8.1099|-8.1099|-8.1099	5.5882|5.5882|5.5882	0.17287|0.17287|0.17287	0.1474:0.0:0.5745:0.2781|0.1474:0.0:0.5745:0.2781|0.1474:0.0:0.5745:0.2781	.|.|.	.|52;252;270;270;270;253;269;269;270|.	.|B4DHS2;B4DDM7;B4DNK6;E7EP89;Q5QPI9;O75354-2;D3DW49;Q5QPJ2;O75354|.	.|.;.;.;.;.;.;.;.;ENTP6_HUMAN|.	R|H|T	94|253;269;190;166;270;252;204;270;222|191;128;163	.|ENSP00000347084:Q253H;ENSP00000353131:Q269H;ENSP00000365840:Q270H;ENSP00000408098:Q252H;ENSP00000395064:Q204H;ENSP00000401895:Q270H;ENSP00000390646:Q222H|.	.|ENSP00000347084:Q253H|.	G|Q|R	+|+|+	1|3|2	0|2|0	ENTPD6|ENTPD6|ENTPD6	25146149|25146149|25146149	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.038000|0.038000|0.038000	0.18304|0.18304|0.18304	0.058000|0.058000|0.058000	0.15608|0.15608|0.15608	1.836000|1.836000|1.836000	0.39191|0.39191|0.39191	0.346000|0.346000|0.346000	0.23899|0.23899|0.23899	0.462000|0.462000|0.462000	0.41574|0.41574|0.41574	GGC|CAG|AGG	.		0.537	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			C	25198149	G	C	25198149	3	2	90	1	0	0	0	0	1	0	0	0	5156	991	35	4	847	4	ENTPD6	20	25198149	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		25198149	37827371	93	8208											
ADRBK2	157	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	26086189	26086189	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttggatgaacatggacacGcaagaatatcagatcttggt	13	11	10	7	1	3	3	1	1	2	2	3	5	3	5	0	3	1	1	0	3	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr22:26086189G>A	ENST00000324198.6	+	12	1183	c.991G>A	c.(991-993)Gca>Aca	p.A331T		NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	331	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)	p.A331T(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	ACATGGACACGCAAGAATATC	0.413																																					p.A331T													.	ADRBK2-955	1	Substitution - Missense(1)	large_intestine(1)	c.G991A						.						126	115	119					22																	26086189		2203	4300	6503	SO:0001583	missense	157	exon12			GGACACGCAAGAA	X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077		"Pleckstrin homology (PH) domain containing"	290	protein-coding gene	gene with protein product		109636				7695743	Standard	NM_005160		Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.991G>A	22.37:g.26086189G>A	ENSP00000317578:p.Ala331Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	41	8	NM_005160	0	0	1	1	0	Q9UGW9	Missense_Mutation	SNP	ENST00000324198.6	37	CCDS13832.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082989	0.36758	.	.	ENSG00000100077	ENST00000324198;ENST00000545323	T	0.26223	1.75	4.49	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.066369	0.64402	D	0.000012	T	0.26774	0.0655	L	0.42529	1.33	0.33464	D	0.585318	B;B	0.21381	0.012;0.055	B;B	0.26202	0.01;0.067	T	0.36163	-0.9759	10	0.56958	D	0.05	-17.4726	16.7419	0.85461	0.0:0.0:1.0:0.0	.	331;331	A8K869;P35626	.;ARBK2_HUMAN	T	331	ENSP00000317578:A331T	ENSP00000317578:A331T	A	+	1	0	ADRBK2	24416189	1.000000	0.71417	0.169000	0.22859	0.058000	0.15608	9.003000	0.93577	2.485000	0.83878	0.655000	0.94253	GCA	.		0.413	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317296.4	NM_005160		A	26086189	G	A	26086189	3	1	90	1	0	0	0	0	1	0	0	0	344	1087	38	1	1037	1	ADRBK2	22	26086189	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		26086189	25218377	94	8209											
GSPT2	23708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	51486959	51486960	+	Missense_Mutation	DNP	GC	GC	TT																															ctgcggggcccgactcagccGcccaccctcccggccggctc																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:51486959_51486960GC>TT	ENST00000340438.4	+	1	479_480	c.237_238GC>TT	c.(235-240)ccGCcc>ccTTcc	p.P80S		NM_018094.4	NP_060564.2	Q8IYD1	ERF3B_HUMAN	G1 to S phase transition 2	80					cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Ovarian(276;0.236)					CGACTCAGCCGCCCACCCTCCC	0.658																																					p.P80S		.											.	GSPT2	0			c.C238T						.																																			SO:0001583	missense	23708	exon1			CAGCCGCCCACCC	AI285711	CCDS14336.1	Xp11.22	2008-05-14			ENSG00000189369	ENSG00000189369			4622	protein-coding gene	gene with protein product		300418				10575220	Standard	NM_018094		Approved	eRF3b, FLJ10441	uc004dpl.3	Q8IYD1	OTTHUMG00000021538	Exception_encountered	X.37:g.51486959_51486960delinsTT	ENSP00000341247:p.Pro80Ser	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	28	9		0	0	0	0	0	Q9H909|Q9NVY0|Q9NY44	Missense_Mutation	DNP	ENST00000340438.4	37	CCDS14336.1																																																																																			.		0.658	GSPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056587.1			TT	51486960	GC	TT	51486959	3	4	90	1	0	0	0	0	1	0	0	0	6848	1074	38	4	239	4	GSPT2	23	51486959	Missense_Mutation	DNP	GC	TCGA-BQ-7061-01A-11D-1961-08		51486959	103783601	95	8210											
LAS1L	81887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	64749564	64749564	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcggcctttacatctgactCcgtacttttcccatcatcct	7	15	4	15	2	2	1	1	1	1	0	6	1	5	1	4	1	2	1	4	1	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:64749564C>A	ENST00000374811.3	-	5	749	c.709G>T	c.(709-711)Gag>Tag	p.E237*	LAS1L_ENST00000374807.5_Nonsense_Mutation_p.E237*|LAS1L_ENST00000312391.8_Nonsense_Mutation_p.E237*|LAS1L_ENST00000374804.5_Nonsense_Mutation_p.E195*	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	237					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						ACATCTGACTCCGTACTTTTC	0.453																																					p.E237X		.											.	LAS1L-196	0			c.G709T						.						219	177	191					X																	64749564		2203	4300	6503	SO:0001587	stop_gained	81887	exon5			CTGACTCCGTACT	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.709G>T	X.37:g.64749564C>A	ENSP00000363944:p.Glu237*	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	218	75	NM_031206	0	0	6	7	1	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Nonsense_Mutation	SNP	ENST00000374811.3	37	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371792	0.42003	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804;ENST00000312391	.	.	.	5.18	4.29	0.51040	.	0.478134	0.21197	N	0.078537	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	10.8918	0.47000	0.0:0.8136:0.1864:0.0	.	.	.	.	X	237;237;195;237	.	ENSP00000308649:E237X	E	-	1	0	LAS1L	64666289	0.369000	0.25039	0.062000	0.19696	0.007000	0.05969	1.842000	0.39250	1.194000	0.43101	0.600000	0.82982	GAG	.		0.453	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		A	64749564	C	A	64749564	4	1	90	1	0	0	0	0	0	1	0	0	8657	864	30	4	1535	4	LAS1L	23	64749564	Nonsense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	13262605	64749564	90520996	96	8211											
KIF4A	24137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	69637856	69637856	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaccgccagcaaggcaaggTaggatcagggctgtttcctc	10	7	13	11	1	1	0	1	0	0	0	3	2	2	1	3	4	2	5	3	4	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:69637856T>C	ENST00000374403.3	+	29	3454		c.e29+2			NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A						anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						CAAGGCAAGGTAGGATCAGGG	0.537																																					.		.											.	KIF4A-134	0			c.3372+2T>C						.						139	96	111					X																	69637856		2203	4300	6503	SO:0001630	splice_region_variant	24137	exon29			GCAAGGTAGGATC	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.3372+2T>C	X.37:g.69637856T>C		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	115	44	NM_012310	0	0	0	0	0	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Splice_Site	SNP	ENST00000374403.3	37	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	t	12.71	2.020554	0.35606	.	.	ENSG00000090889	ENST00000374403;ENST00000544650	.	.	.	5.3	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.5846	0.27985	0.0:0.0:0.2369:0.7631	.	.	.	.	.	-1	.	.	.	+	.	.	KIF4A	69554581	1.000000	0.71417	0.998000	0.56505	0.414000	0.31173	2.056000	0.41355	1.974000	0.57490	0.427000	0.28365	.	.		0.537	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	Intron	C	69637856	T	C	69637856	5	2	90	1	0	0	0	0	0	0	1	0	8324	1652	57	3	3484	3	KIF4A	23	69637856	Splice_Site	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	4888292	69637856	85632704	97	8212											
SLITRK2	84631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	144904633	144904633	+	Missense_Mutation	SNP	G	G	C																															ttacttcctctcaaggcctgGctagacaccataactgtttt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:144904633G>C	ENST00000370490.1	+	1	4945	c.690G>C	c.(688-690)tgG>tgC	p.W230C	SLITRK2_ENST00000447897.2_Missense_Mutation_p.W230C|SLITRK2_ENST00000428560.2_Missense_Mutation_p.W230C|SLITRK2_ENST00000434188.2_Missense_Mutation_p.W230C|SLITRK2_ENST00000413937.2_Missense_Mutation_p.W230C			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	230	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TCAAGGCCTGGCTAGACACCA	0.488																																					p.W230C		.											.	SLITRK2-136	0			c.G690C						.						117	108	111					X																	144904633		2203	4300	6503	SO:0001583	missense	84631	exon5			GGCCTGGCTAGAC	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.690G>C	X.37:g.144904633G>C	ENSP00000359521:p.Trp230Cys	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	171	36	NM_001144005	0	0	0	0	0	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.162254	0.57368	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47	5.0	5.0	0.66597	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81917	0.4924	H	0.97732	4.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88509	0.3088	10	0.87932	D	0	-4.6604	14.7267	0.69349	0.0:0.0:1.0:0.0	.	230	Q9H156	SLIK2_HUMAN	C	230	ENSP00000334374:W230C;ENSP00000411681:W230C;ENSP00000359521:W230C;ENSP00000397015:W230C;ENSP00000407347:W230C;ENSP00000412010:W230C	ENSP00000334374:W230C	W	+	3	0	SLITRK2	144712325	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	9.869000	0.99810	2.058000	0.61347	0.600000	0.82982	TGG	.		0.488	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		C	144904633	G	C	144904633	3	2	90	1	0	0	0	0	1	0	0	0	14775	1212	42	4	692	4	SLITRK2	23	144904633	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	75266777	144904633	10365927	98	8213	90	2									
SLITRK2	84631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	144904634	144904635	+	Nonsense_Mutation	DNP	CT	CT	TA																															tacttcctctcaaggcctggCtagacaccataactgttttt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:144904634_144904635CT>TA	ENST00000370490.1	+	1	4946_4947	c.691_692CT>TA	c.(691-693)CTa>TAa	p.L231*	SLITRK2_ENST00000447897.2_Nonsense_Mutation_p.L231*|SLITRK2_ENST00000428560.2_Nonsense_Mutation_p.L231*|SLITRK2_ENST00000434188.2_Nonsense_Mutation_p.L231*|SLITRK2_ENST00000413937.2_Nonsense_Mutation_p.L231*			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	231	LRRCT 1.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CAAGGCCTGGCTAGACACCATA	0.49																																					p.L231*		.											.	SLITRK2	0			c.T692A						.																																			SO:0001587	stop_gained	84631	exon5			CCTGGCTAGACAC	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	Exception_encountered	X.37:g.144904634_144904635delinsTA	ENSP00000359521:p.Leu231*	Somatic	187	1		WXS	Illumina HiSeq	Phase_I	173	37		0	0	0	0	0	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Nonsense_Mutation	DNP	ENST00000370490.1	37	CCDS14680.1																																																																																			.		0.49	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		TA	144904635	CT	TA	144904634	4	4	90	1	0	0	0	0	0	1	0	0	14775	796	28	2	693	2	SLITRK2	23	144904634	Nonsense_Mutation	DNP	CT	TCGA-BQ-7061-01A-11D-1961-08	1	144904634	10365926	99	8214	90	2									
OPN1MW	728458	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	153496172	153496172	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaccctggctaccccttccaCcctttgatggctgccctgcc	5	10	7	19	0	0	1	0	1	0	0	1	1	1	1	7	2	4	2	7	2	2	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:153496172C>A	ENST00000369929.4	+	5	960	c.900C>A	c.(898-900)caC>caA	p.H300Q		NM_001048181.2	NP_001041646.1	P04001	OPSG_HUMAN	opsin 1 (cone pigments), medium-wave-sensitive 2	300					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)|stomach(2)|urinary_tract(1)	6	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ACCCCTTCCACCCTTTGATGG	0.557																																					p.H300Q		.											.	.	0			c.C900A						.						143	103	117					X																	153496172		2102	3797	5899	SO:0001583	missense	728458	exon5			CTTCCACCCTTTG		CCDS35447.1	Xq28	2012-08-08			ENSG00000166160	ENSG00000166160		"GPCR / Class A : Opsin receptors"	26952	protein-coding gene	gene with protein product							Standard	NM_001048181		Approved			P04001	OTTHUMG00000024231	ENST00000369929.4:c.900C>A	X.37:g.153496172C>A	ENSP00000358945:p.His300Gln	Somatic	253	1		WXS	Illumina HiSeq	Phase_I	263	134	NM_001048181	0	0	0	0	0		Missense_Mutation	SNP	ENST00000369929.4	37	CCDS35447.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.749853	0.49257	.	.	ENSG00000166160	ENST00000369929	T	0.37058	1.22	2.81	2.81	0.32909	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	.	.	.	0.54753	D	0.999988	.	.	.	.	.	.	T	0.49143	-0.8970	7	0.51188	T	0.08	.	12.0191	0.53333	0.0:1.0:0.0:0.0	.	.	.	.	Q	300	ENSP00000358945:H300Q	ENSP00000358945:H300Q	H	+	3	2	OPN1MW2	153149366	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	0.850000	0.27737	1.263000	0.44181	0.407000	0.27541	CAC	.		0.557	OPN1MW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061149.2	NM_001048181		A	153496172	C	A	153496172	3	1	90	1	0	0	0	0	1	0	0	0	10904	506	18	4	2037	4	OPN1MW	23	153496172	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	8591538	153496172	1774388	100	8215											
NADK	65220	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1686870	1686870	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagctgaatggggtcaggaAgcccagggagcccaggtgga	12	4	17	8	0	1	1	1	1	0	0	1	4	1	4	2	6	3	1	2	6	3	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:1686870A>T	ENST00000341426.5	-	7	852	c.631T>A	c.(631-633)Ttc>Atc	p.F211I	NADK_ENST00000341991.3_Missense_Mutation_p.F211I|NADK_ENST00000492768.1_5'Flank|NADK_ENST00000378625.1_Missense_Mutation_p.F356I|NADK_ENST00000344463.4_Missense_Mutation_p.F356I|NADK_ENST00000342348.5_Missense_Mutation_p.F179I	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	211					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		GGGGTCAGGAAGCCCAGGGAG	0.607																																					p.F356I		.											.	NADK-44	0			c.T1066A						.						156	158	157					1																	1686870		2203	4300	6503	SO:0001583	missense	65220	exon9			TCAGGAAGCCCAG	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.631T>A	1.37:g.1686870A>T	ENSP00000341679:p.Phe211Ile	Somatic	259	0		WXS	Illumina HiSeq	Phase_I	268	48	NM_001198994	0	0	57	90	33	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	37	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	A	33	5.256937	0.95336	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348;ENST00000400922	T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13	5.25	5.25	0.73442	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	H	0.98199	4.17	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;0.997;0.995;0.994	D	0.90129	0.4205	10	0.87932	D	0	-34.481	14.2701	0.66147	1.0:0.0:0.0:0.0	.	179;356;356;211	F5GXR5;Q9H2P2;Q5QPS4;O95544	.;.;.;NADK_HUMAN	I	211;211;356;356;179;179	ENSP00000341679:F211I;ENSP00000344340:F211I;ENSP00000367890:F356I;ENSP00000340925:F356I;ENSP00000339727:F179I;ENSP00000383713:F179I	ENSP00000341679:F211I	F	-	1	0	NADK	1676730	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.884000	0.92432	2.119000	0.64992	0.379000	0.24179	TTC	.		0.607	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		T	1686870	A	T	1686870	3	4	91	1	0	0	0	0	1	0	0	0	10162	72	3	5	733	5	NADK	1	1686870	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		1686870	247563751	1	8216											
RPL11	6135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24021204	24021204	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatactggaaactttggtTttgggatccaggaacacatc	12	11	10	8	0	0	1	0	0	0	1	2	4	1	4	1	4	3	1	1	4	3	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:24021204T>G	ENST00000374550.3	+	4	364	c.319T>G	c.(319-321)Ttt>Gtt	p.F107V	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	107					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		AAACTTTGGTTTTGGGATCCA	0.403																																					p.F107V		.											.	RPL11-226	0			c.T319G						.						146	143	144					1																	24021204		2203	4300	6503	SO:0001583	missense	6135	exon4			TTTGGTTTTGGGA	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.319T>G	1.37:g.24021204T>G	ENSP00000363676:p.Phe107Val	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	131	43	NM_000975	0	0	1566	2399	833	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	37	CCDS238.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.400589	0.83120	.	.	ENSG00000142676	ENST00000374550;ENST00000443624;ENST00000458455	D;D;D	0.82344	-1.6;-1.6;-1.6	5.85	5.85	0.93711	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.94159	0.8126	H	0.96301	3.8	0.80722	D	1	P;P	0.52061	0.938;0.95	D;D	0.80764	0.974;0.994	D	0.95729	0.8773	10	0.87932	D	0	-9.5649	16.233	0.82357	0.0:0.0:0.0:1.0	.	106;107	P62913-2;P62913	.;RL11_HUMAN	V	107;105;105	ENSP00000363676:F107V;ENSP00000390839:F105V;ENSP00000398888:F105V	ENSP00000363676:F107V	F	+	1	0	RPL11	23893791	1.000000	0.71417	0.993000	0.49108	0.476000	0.33039	7.874000	0.87199	2.239000	0.73571	0.529000	0.55759	TTT	.		0.403	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		G	24021204	T	G	24021204	3	3	91	1	0	0	0	0	1	0	0	0	13589	1841	64	5	333	5	RPL11	1	24021204	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	22334334	24021204	225229417	2	8217											
ZSCAN20	7579	bcgsc.ca	37	chr1	33956714	33956714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttataaattctgggaaaaggAgcactgcagattacagcctg	14	10	10	7	0	1	1	0	0	1	1	1	3	1	3	1	2	4	2	1	2	6	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:33956714A>G	ENST00000361328.3	+	6	1009	c.856A>G	c.(856-858)Agc>Ggc	p.S286G	ZSCAN20_ENST00000373413.2_Missense_Mutation_p.S232G	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	286					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)				TGGGAAAAGGAGCACTGCAGA	0.468																																					p.S286G													.	ZSCAN20-93	0			c.A856G						.						55	55	55					1																	33956714		1886	4113	5999	SO:0001583	missense	7579	exon6			AAAAGGAGCACTG	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.856A>G	1.37:g.33956714A>G	ENSP00000355053:p.Ser286Gly	Somatic	77	0		WXS	Illumina HiSeq	Phase_1	78	4	NM_145238	0	0	3	3	0	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	A	6.309	0.425166	0.11987	.	.	ENSG00000121903	ENST00000373411;ENST00000326544;ENST00000373413;ENST00000361328;ENST00000401072	T	0.02140	4.43	5.64	3.3	0.37823	.	1.076990	0.06981	N	0.819956	T	0.02267	0.0070	L	0.29908	0.895	0.09310	N	1	B;B;B	0.29988	0.0;0.264;0.0	B;B;B	0.28011	0.001;0.085;0.0	T	0.50583	-0.8811	10	0.26408	T	0.33	-4.0623	5.892	0.18919	0.7468:0.1676:0.0855:0.0	.	286;232;286	P17040-3;P17040-4;P17040	.;.;ZSC20_HUMAN	G	232;286;232;220;220	ENSP00000362512:S232G	ENSP00000324450:S286G	S	+	1	0	ZSCAN20	33729301	0.934000	0.31675	0.009000	0.14445	0.304000	0.27724	1.295000	0.33377	0.495000	0.27882	0.533000	0.62120	AGC	.		0.468	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		G	33956714	A	G	33956714	3	3	91	1	0	0	0	0	1	0	0	0	18264	304	11	3	874	3	ZSCAN20	1	33956714	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	9935510	33956714	215293907	3	8218											
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52822691	52822691	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctcttgttgctccagaagCattttttgcagctgggcata	8	14	9	10	0	1	1	0	0	1	1	2	1	2	1	2	1	4	6	2	1	2	6			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:52822691C>G	ENST00000371586.2	-	16	2016	c.1878G>C	c.(1876-1878)atG>atC	p.M626I	CC2D1B_ENST00000284376.3_Missense_Mutation_p.M620I|CC2D1B_ENST00000438831.1_Start_Codon_SNP_p.M1I|CC2D1B_ENST00000460261.1_5'UTR	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	626						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						GCTCCAGAAGCATTTTTTGCA	0.602																																					p.M626I		.											.	CC2D1B-92	0			c.G1878C						.						76	74	75					1																	52822691		2188	4292	6480	SO:0001583	missense	200014	exon16			CAGAAGCATTTTT	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1878G>C	1.37:g.52822691C>G	ENSP00000360642:p.Met626Ile	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	9	3	NM_032449	0	0	44	71	27	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.42|13.42	2.232069|2.232069	0.39399|0.39399	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000438021;ENST00000450942|ENST00000371586;ENST00000284376;ENST00000371573;ENST00000438831	.|T;T;T	.|0.41400	.|2.0;2.0;1.0	5.65|5.65	3.78|3.78	0.43462|0.43462	.|.	.|0.267337	.|0.46145	.|N	.|0.000310	T|T	0.20373|0.20373	0.0490|0.0490	N|N	0.08118|0.08118	0|0	0.52501|0.52501	D|D	0.999956|0.999956	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.06405	.|0.0;0.002;0.001	T|T	0.04203|0.04203	-1.0969|-1.0969	5|10	.|0.34782	.|T	.|0.22	-7.9799|-7.9799	6.5654|6.5654	0.22509|0.22509	0.0:0.6133:0.2322:0.1544|0.0:0.6133:0.2322:0.1544	.|.	.|406;620;626	.|Q5T0G1;Q5T0F9-2;Q5T0F9	.|.;.;C2D1B_HUMAN	S|I	407;540|626;620;534;1	.|ENSP00000360642:M626I;ENSP00000284376:M620I;ENSP00000406300:M1I	.|ENSP00000284376:M620I	C|M	-|-	2|3	0|0	CC2D1B|CC2D1B	52595279|52595279	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	0.398000|0.398000	0.20899|0.20899	0.925000|0.925000	0.37094|0.37094	0.655000|0.655000	0.94253|0.94253	TGC|ATG	.		0.602	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		G	52822691	C	G	52822691	3	3	91	1	0	0	0	0	1	0	0	0	2733	710	25	4	734	4	CC2D1B	1	52822691	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	18865977	52822691	196427930	4	8219											
LMO4	8543	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	87805263	87805263	+	Frame_Shift_Del	DEL	T	T	-																															cagcgcttgcggacagtcgaTtcctgcgagtgaactcgtca																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:87805263delT	ENST00000370544.5	+	3	1061	c.281delT	c.(280-282)attfs	p.I94fs	LMO4_ENST00000489303.1_3'UTR|LMO4_ENST00000370542.1_Frame_Shift_Del_p.I94fs	NM_006769.3	NP_006760.1	P61968	LMO4_HUMAN	LIM domain only 4	94	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281)	transcription factor complex (GO:0005667)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1)	9		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GGACAGTCGATTCCTGCGAGT	0.388																																					p.I94fs		.											.	LMO4-226	0			c.281delT						.						95	95	95					1																	87805263		2203	4300	6503	SO:0001589	frameshift_variant	8543	exon3			.	U24576	CCDS713.1	1p22.3	2008-02-05			ENSG00000143013	ENSG00000143013			6644	protein-coding gene	gene with protein product		603129					Standard	NM_006769		Approved		uc001dmi.3	P61968	OTTHUMG00000010248	ENST00000370544.5:c.281delT	1.37:g.87805263delT	ENSP00000359575:p.Ile94fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	58	17	NM_006769	0	0	0	0	0	D3DT23|O00158|O88894	Frame_Shift_Del	DEL	ENST00000370544.5	37	CCDS713.1																																																																																			.		0.388	LMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028264.2	NM_006769		-	87805263	T	-	87805263	7	5	91	1	0	1	0	1	0	0	0	0	8877	1493	52	0	287	0	LMO4	1	87805263	Frame_Shift_Del	DEL	T	TCGA-BQ-7062-01A-11D-1961-08	34982572	87805263	161445358	5	8220											
KCND3	3752	bcgsc.ca	37	chr1	112525250	112525250	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcctgccgcttgttcttGtcggccggggccaggggcat	3	11	14	13	3	2	0	1	0	1	0	4	0	3	0	4	5	1	3	4	5	0	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:112525250G>T	ENST00000315987.2	-	2	578	c.99C>A	c.(97-99)gaC>gaA	p.D33E	KCND3_ENST00000369697.1_Missense_Mutation_p.D33E|KCND3_ENST00000302127.4_Missense_Mutation_p.D33E	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	33					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GCTTGTTCTTGTCGGCCGGGG	0.687																																					p.D33E													.	KCND3-155	0			c.C99A						.						42	41	41					1																	112525250		2203	4300	6503	SO:0001583	missense	3752	exon2			GTTCTTGTCGGCC	AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.99C>A	1.37:g.112525250G>T	ENSP00000319591:p.Asp33Glu	Somatic	52	0		WXS	Illumina HiSeq	Phase_1	84	5	NM_004980	0	0	1	1	0	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Missense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	G	0.198	-1.047052	0.01997	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	D;D;D	0.96619	-4.06;-4.07;-4.06	5.41	3.42	0.39159	.	0.275268	0.45361	D	0.000367	D	0.84347	0.5452	L	0.34521	1.04	0.43073	D	0.994718	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.78244	-0.2279	10	0.08381	T	0.77	.	7.0367	0.24996	0.1583:0.2332:0.6085:0.0	.	33;33	Q14D71;Q9UK17	.;KCND3_HUMAN	E	33	ENSP00000358711:D33E;ENSP00000319591:D33E;ENSP00000306923:D33E	ENSP00000306923:D33E	D	-	3	2	KCND3	112326773	0.987000	0.35691	1.000000	0.80357	0.996000	0.88848	0.145000	0.16157	1.286000	0.44565	0.561000	0.74099	GAC	.		0.687	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		T	112525250	G	T	112525250	3	4	91	1	0	0	0	0	1	0	0	0	8041	1368	48	4	1896	4	KCND3	1	112525250	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08	24719987	112525250	136725371	6	8221											
S100A7L2	645922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153409541	153409541	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtagggtgggatcactggCttcccccggaacagggtgcc	6	7	17	11	1	1	0	1	0	0	0	2	2	2	2	3	6	2	2	3	6	2	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:153409541C>A	ENST00000368725.2	-	3	331	c.332G>T	c.(331-333)aGc>aTc	p.S111I		NM_001045479.1	NP_001038944.2	Q5SY68	S1A7B_HUMAN	S100 calcium binding protein A7-like 2	100							calcium ion binding (GO:0005509)			NS(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGATCACTGGCTTCCCCCGGA	0.498																																					p.S111I		.											.	S100A7L2-69	0			c.G332T						.						158	170	166					1																	153409541		2203	4300	6503	SO:0001583	missense	645922	exon3			CACTGGCTTCCCC			1q21.3	2013-01-10			ENSG00000197364	ENSG00000197364		"EF-hand domain containing"	21655	protein-coding gene	gene with protein product							Standard	NM_001045479		Approved	s100a7b	uc010pdx.2	Q5SY68	OTTHUMG00000013129	ENST00000368725.2:c.332G>T	1.37:g.153409541C>A	ENSP00000357714:p.Ser111Ile	Somatic	375	2		WXS	Illumina HiSeq	Phase_I	309	63	NM_001045479	0	0	0	0	0		Missense_Mutation	SNP	ENST00000368725.2	37		.	.	.	.	.	.	.	.	.	.	.	11.15	1.552585	0.27739	.	.	ENSG00000197364	ENST00000368725;ENST00000368724;ENST00000453814	T;T;T	0.11495	2.82;2.82;2.77	1.7	-3.39	0.04868	EF-hand-like domain (1);	.	.	.	.	T	0.01800	0.0057	L	0.27053	0.805	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.45891	-0.9230	9	0.72032	D	0.01	.	2.8096	0.05438	0.2297:0.4461:0.0:0.3242	.	100	Q5SY68	S1A7B_HUMAN	I	100;100;111	ENSP00000357714:S100I;ENSP00000357713:S100I;ENSP00000405610:S111I	ENSP00000357713:S100I	S	-	2	0	S100A7L2	151676165	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.312000	0.02720	-1.148000	0.02847	0.407000	0.27541	AGC	.		0.498	S100A7L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000036797.2	NM_001045479		A	153409541	C	A	153409541	3	1	91	1	0	0	0	0	1	0	0	0	13817	797	28	4	10	4	S100A7L2	1	153409541	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	40884291	153409541	95841080	7	8222											
ZBTB37	84614	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	173839638	173839638	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttctgttacacagggcggaTatgcctgcaactggcagata	10	11	11	9	1	1	1	0	0	1	1	1	2	1	2	1	3	4	3	1	3	4	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:173839638T>C	ENST00000367701.5	+	2	466	c.275T>C	c.(274-276)aTa>aCa	p.I92T	ZBTB37_ENST00000432989.1_Missense_Mutation_p.I92T|GAS5_ENST00000364084.1_RNA|ZBTB37_ENST00000427304.1_Missense_Mutation_p.I92T|ZBTB37_ENST00000367704.1_Missense_Mutation_p.I92T|ZBTB37_ENST00000367702.1_Missense_Mutation_p.I92T			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	92	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						ACAGGGCGGATATGCCTGCAA	0.433																																					p.I92T		.											.	ZBTB37-90	0			c.T275C						.						74	74	74					1																	173839638		2203	4300	6503	SO:0001583	missense	84614	exon3			GGCGGATATGCCT	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.275T>C	1.37:g.173839638T>C	ENSP00000356674:p.Ile92Thr	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	80	19	NM_032522	0	0	2	3	1	Q5TC80|Q96M87|Q9BQ88	Missense_Mutation	SNP	ENST00000367701.5	37	CCDS44278.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.123564	0.77436	.	.	ENSG00000185278	ENST00000367704;ENST00000427304;ENST00000432989;ENST00000367702;ENST00000367701	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.85	5.85	0.93711	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.044936	0.85682	D	0.000000	T	0.71358	0.3330	L	0.48174	1.505	0.58432	D	0.999993	D;P	0.63880	0.993;0.941	D;P	0.68039	0.955;0.736	T	0.75639	-0.3248	10	0.87932	D	0	.	16.2271	0.82306	0.0:0.0:0.0:1.0	.	92;92	Q5TC79;Q5TC79-2	ZBT37_HUMAN;.	T	92	ENSP00000356677:I92T;ENSP00000415293:I92T;ENSP00000409408:I92T;ENSP00000356675:I92T;ENSP00000356674:I92T	ENSP00000356674:I92T	I	+	2	0	ZBTB37	172106261	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.698000	0.84413	2.234000	0.73211	0.460000	0.39030	ATA	.		0.433	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522		C	173839638	T	C	173839638	3	2	91	1	0	0	0	0	1	0	0	0	17570	1406	49	3	277	3	ZBTB37	1	173839638	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	20430097	173839638	75410983	8	8223											
NFASC	23114	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	204923960	204923960	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccacttctctccagaatCtcctctgtggcccaaggaaa	9	11	7	14	0	3	1	0	0	3	1	7	2	5	2	4	2	0	0	4	2	3	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:204923960C>A	ENST00000401399.1	+	6	615	c.416C>A	c.(415-417)tCt>tAt	p.S139Y	NFASC_ENST00000360049.4_Missense_Mutation_p.S133Y|NFASC_ENST00000339876.6_Missense_Mutation_p.S139Y|NFASC_ENST00000367171.4_Missense_Mutation_p.S139Y|NFASC_ENST00000404076.1_Missense_Mutation_p.S133Y|NFASC_ENST00000367169.4_Missense_Mutation_p.S139Y|NFASC_ENST00000338515.6_Missense_Mutation_p.S139Y|NFASC_ENST00000539706.1_Missense_Mutation_p.S133Y|NFASC_ENST00000404907.1_Missense_Mutation_p.S133Y|NFASC_ENST00000338586.6_Missense_Mutation_p.S139Y|NFASC_ENST00000367170.4_Missense_Mutation_p.S139Y|NFASC_ENST00000513543.1_Missense_Mutation_p.S133Y|NFASC_ENST00000367172.4_Missense_Mutation_p.S139Y|NFASC_ENST00000403080.1_Missense_Mutation_p.S139Y			O94856	NFASC_HUMAN	neurofascin	139					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCTCCAGAATCTCCTCTGTGG	0.597																																					p.S139Y		.											.	NFASC-139	0			c.C416A						.						105	107	106					1																	204923960		2203	4300	6503	SO:0001583	missense	23114	exon7			CAGAATCTCCTCT	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.416C>A	1.37:g.204923960C>A	ENSP00000385637:p.Ser139Tyr	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	213	51	NM_001005388	0	0	0	0	0	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.3|29.3	4.998077|4.998077	0.93227|0.93227	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.72282	.|1.09;-0.64;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	.|0.000000	.|0.52532	.|D	.|0.000064	D|D	0.83069|0.83069	0.5174|0.5174	M|M	0.64260|0.64260	1.97|1.97	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.87578	.|0.998;0.977;0.992;0.977;0.99;0.976	D|D	0.84410|0.84410	0.0565|0.0565	5|10	.|0.72032	.|D	.|0.01	.|.	18.6966|18.6966	0.91603|0.91603	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|133;133;235;139;133;139	.|O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.|.;.;.;.;.;.	I|Y	109|139;139;139;139;139;139;133;133;133;139;139;139;133;139;133;133;109	.|ENSP00000356140:S139Y;ENSP00000356139:S139Y;ENSP00000356138:S139Y;ENSP00000342128:S139Y;ENSP00000344786:S139Y;ENSP00000343509:S139Y;ENSP00000438614:S133Y;ENSP00000353154:S133Y;ENSP00000356137:S139Y;ENSP00000412161:S139Y;ENSP00000384875:S139Y;ENSP00000385676:S133Y;ENSP00000385637:S139Y;ENSP00000384061:S133Y;ENSP00000425908:S133Y;ENSP00000415031:S109Y	.|ENSP00000295776:S133Y	L|S	+|+	1|2	0|0	NFASC|NFASC	203190583|203190583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.797000|7.797000	0.85911|0.85911	2.516000|2.516000	0.84829|0.84829	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.		0.597	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204923960	C	A	204923960	3	1	91	1	0	0	0	0	1	0	0	0	10385	913	32	4	434	4	NFASC	1	204923960	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	31084322	204923960	44326661	9	8224											
FMN2	56776	bcgsc.ca	37	chr1	240371517	240371517	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataccccctcctccccctctTcccggagcgggcatacctcc	5	8	6	22	2	1	0	0	0	1	0	5	1	5	1	8	2	3	1	8	2	2	3	rs369474345		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:240371517T>A	ENST00000319653.9	+	5	3635	c.3405T>A	c.(3403-3405)ctT>ctA	p.L1135L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1135	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTCCCCCTCTTCCCGGAGCGG	0.706																																					p.L1135L													.	FMN2-145	0			c.T3405A						.	T		30,4102		0,30,2036	6	8	7		3405	-6.6	0	1		7	19,8117		0,19,4049	no	coding-synonymous	FMN2	NM_020066.4		0,49,6085	AA,AT,TT		0.2335,0.726,0.3994		1135/1723	240371517	49,12219	2066	4068	6134	SO:0001819	synonymous_variant	56776	exon5			CCCTCTTCCCGGA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3405T>A	1.37:g.240371517T>A		Somatic	32	1		WXS	Illumina HiSeq	Phase_1	41	14	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240371517	T	A	240371517	2	1	91	1	0	0	0	0	0	0	0	1	5969	1770	62	5		5	FMN2	1	240371517	Silent	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	35447557	240371517	8879104	10	8225											
KIF5C	3800	ucsc.edu	37	chr2	149799207	149799207	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgcactgagcggtttgtGtcgagccctgaggaagtcat	7	10	16	8	2	1	2	1	2	0	0	2	4	1	3	1	3	3	2	1	3	1	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr2:149799207G>A	ENST00000435030.1	+	7	890	c.522G>A	c.(520-522)gtG>gtA	p.V174V	KIF5C_ENST00000414838.2_Silent_p.V79V			O60282	KIF5C_HUMAN	kinesin family member 5C	174	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		AGCGGTTTGTGTCGAGCCCTG	0.478																																					p.V174V													.	KIF5C-69	0			c.G522A						.						75	74	74					2																	149799207		1971	4149	6120	SO:0001819	synonymous_variant	3800	exon7			GTTTGTGTCGAGC	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"Kinesins"	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.522G>A	2.37:g.149799207G>A		Somatic	25	0		WXS	Illumina HiSeq		36	4	NM_004522	0	0	0	0	0	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				.		0.478	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149799207	G	A	149799207	2	1	91	1	0	0	0	0	0	0	0	1	8328	1364	48	2		2	KIF5C	2	149799207	Silent	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		149799207	93400166	11	8226											
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233199380	233199380	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagccatggtgatgggcAtcctgaagcaagccttcgac	11	7	12	11	1	0	3	0	2	0	1	2	4	1	3	3	2	3	2	3	2	3	1	rs201503361	byFrequency	TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr2:233199380A>G	ENST00000409307.1	+	18	2329	c.2329A>G	c.(2329-2331)Atc>Gtc	p.I777V	DIS3L2_ENST00000273009.6_Intron|DIS3L2_ENST00000325385.7_Missense_Mutation_p.I777V					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		GGTGATGGGCATCCTGAAGCA	0.667																																					p.I777V		.											.	DIS3L2-136	0			c.A2329G						.						54	62	59					2																	233199380		2178	4269	6447	SO:0001583	missense	129563	exon19			ATGGGCATCCTGA	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.2329A>G	2.37:g.233199380A>G	ENSP00000386799:p.Ile777Val	Somatic	8	2		WXS	Illumina HiSeq	Phase_I	26	6	NM_152383	0	0	51	51	0		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	6.460|6.460	0.453001|0.453001	0.12283|0.12283	.|.	.|.	ENSG00000144535|ENSG00000144535	ENST00000418143|ENST00000325385;ENST00000409307	.|T;T	.|0.18338	.|2.22;2.22	4.06|4.06	3.15|3.15	0.36227|0.36227	.|.	.|0.000000	.|0.64402	.|N	.|0.000007	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.00313|0.00313	-1.665|-1.665	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.37820|0.37820	-0.9689|-0.9689	5|10	.|0.02654	.|T	.|1	-12.3444|-12.3444	9.5561|9.5561	0.39339|0.39339	0.177:0.0:0.823:0.0|0.177:0.0:0.823:0.0	.|.	.|777	.|Q8IYB7	.|DI3L2_HUMAN	R|V	4|777	.|ENSP00000315569:I777V;ENSP00000386799:I777V	.|ENSP00000315569:I777V	H|I	+|+	2|1	0|0	DIS3L2|DIS3L2	232907624|232907624	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	4.545000|4.545000	0.60698|0.60698	0.856000|0.856000	0.35383|0.35383	-0.235000|-0.235000	0.12190|0.12190	CAT|ATC	.		0.667	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		G	233199380	A	G	233199380	3	3	91	1	0	0	0	0	1	0	0	0	4548	217	8	3	2399	3	DIS3L2	2	233199380	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	83400173	233199380	9999993	12	8227											
ALPI	248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233322816	233322816	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgcctgctgagcaggaaccCccgcggcttctacctctttg	5	9	11	16	3	2	1	0	1	2	0	2	2	2	2	4	2	4	3	4	2	2	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr2:233322816C>T	ENST00000295463.3	+	8	1042	c.965C>T	c.(964-966)cCc>cTc	p.P322L		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	322					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		AGCAGGAACCCCCGCGGCTTC	0.662																																					p.P322L		.											.	ALPI-90	0			c.C965T						.						58	65	63					2																	233322816		2203	4300	6503	SO:0001583	missense	248	exon8			GGAACCCCCGCGG	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.965C>T	2.37:g.233322816C>T	ENSP00000295463:p.Pro322Leu	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	108	26	NM_001631	0	0	0	1	1	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	37	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273284	0.40194	.	.	ENSG00000163295	ENST00000295463	D	0.96300	-3.97	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.106561	0.64402	D	0.000003	D	0.97238	0.9097	M	0.93328	3.405	0.58432	D	0.999999	P	0.38223	0.623	B	0.40741	0.339	D	0.98720	1.0708	10	0.62326	D	0.03	.	16.2794	0.82664	0.0:1.0:0.0:0.0	.	322	P09923	PPBI_HUMAN	L	322	ENSP00000295463:P322L	ENSP00000295463:P322L	P	+	2	0	ALPI	233031060	1.000000	0.71417	0.784000	0.31847	0.009000	0.06853	7.289000	0.78701	2.318000	0.78349	0.561000	0.74099	CCC	.		0.662	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		T	233322816	C	T	233322816	3	4	91	1	0	0	0	0	1	0	0	0	543	623	22	2	995	2	ALPI	2	233322816	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	123436	233322816	9876557	13	8228											
SCAP	22937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47455522	47455522	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaggtcccaaaaggagacaCagccctggccgccagtcacc	11	5	10	15	1	1	1	1	0	0	1	2	2	2	1	5	3	1	0	5	3	3	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:47455522C>A	ENST00000265565.5	-	23	4074	c.3662G>T	c.(3661-3663)tGt>tTt	p.C1221F	SCAP_ENST00000441517.2_Missense_Mutation_p.C965F|SCAP_ENST00000545718.1_Missense_Mutation_p.C828F	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	1221	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		AAAGGAGACACAGCCCTGGCC	0.592																																					p.C1221F	Pancreas(149;978 1908 29304 37806 46700)	.											.	SCAP-91	0			c.G3662T						.						75	80	78					3																	47455522		2203	4300	6503	SO:0001583	missense	22937	exon23			GAGACACAGCCCT	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.3662G>T	3.37:g.47455522C>A	ENSP00000265565:p.Cys1221Phe	Somatic	127	1		WXS	Illumina HiSeq	Phase_I	163	68	NM_012235	1	0	79	205	125	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	25.1	4.604754	0.87157	.	.	ENSG00000114650	ENST00000339815;ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	T;T;T	0.39229	1.63;2.27;1.09	5.2	5.2	0.72013	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.54127	0.1839	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.71656	0.974;0.929	T	0.56932	-0.7897	10	0.72032	D	0.01	-12.5147	18.531	0.90992	0.0:1.0:0.0:0.0	.	965;1221	F8W921;Q12770	.;SCAP_HUMAN	F	713;847;1221;965;828	ENSP00000265565:C1221F;ENSP00000416847:C965F;ENSP00000438956:C828F	ENSP00000265565:C1221F	C	-	2	0	SCAP	47430526	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.296000	0.78790	2.706000	0.92434	0.655000	0.94253	TGT	.		0.592	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		A	47455522	C	A	47455522	3	1	91	1	0	0	0	0	1	0	0	0	13909	478	17	4	181	4	SCAP	3	47455522	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		47455522	150566908	14	8229											
PLXNB1	5364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48459373	48459373	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagggcactccagccacCgtgaccatgcccagcacatc	10	4	9	18	1	0	1	0	1	0	0	2	1	1	1	5	1	3	3	5	1	0	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:48459373C>A	ENST00000358536.4	-	16	3590	c.3321G>T	c.(3319-3321)acG>acT	p.T1107T	PLXNB1_ENST00000296440.6_Silent_p.T1107T|PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000456774.1_Silent_p.T924T|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.T924T	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1107	IPT/TIG 1.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTCCAGCCACCGTGACCATGC	0.662																																					p.T1107T		.											.	PLXNB1-293	0			c.G3321T						.						60	58	59					3																	48459373		2203	4300	6503	SO:0001819	synonymous_variant	5364	exon16			AGCCACCGTGACC	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3321G>T	3.37:g.48459373C>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	94	20	NM_001130082	0	0	87	131	44	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	37	CCDS2765.1																																																																																			.		0.662	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48459373	C	A	48459373	2	1	91	1	0	0	0	0	0	0	0	1	12149	639	23	4		4	PLXNB1	3	48459373	Silent	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	1003851	48459373	149563057	15	8230											
NDUFAF3	25915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49059877	49059877	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaggccgctcaggcaatgtAcatcgacagctacaacagcc	12	5	10	14	3	1	0	1	0	0	0	2	2	1	0	2	2	5	4	2	2	4	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:49059877A>T	ENST00000326925.6	+	2	1310	c.176A>T	c.(175-177)tAc>tTc	p.Y59F	DALRD3_ENST00000313778.5_5'Flank|MIR191_ENST00000384873.1_RNA|DALRD3_ENST00000440857.1_5'Flank|NDUFAF3_ENST00000395458.2_Missense_Mutation_p.Y2F|NDUFAF3_ENST00000451378.2_Missense_Mutation_p.Y2F|MIR425_ENST00000362162.1_RNA|NDUFAF3_ENST00000326912.4_Missense_Mutation_p.Y2F|DALRD3_ENST00000496568.1_5'Flank	NM_199069.1	NP_951032.1	Q9BU61	NDUF3_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 3	59					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	8						CAGGCAATGTACATCGACAGC	0.652																																					p.Y59F		.											.	NDUFAF3-90	0			c.A176T						.						23	24	23					3																	49059877		2200	4299	6499	SO:0001583	missense	25915	exon2			CAATGTACATCGA		CCDS2784.1, CCDS2785.1	3p21.31	2012-10-12	2012-05-08	2009-03-18	ENSG00000178057	ENSG00000178057		"Mitochondrial respiratory chain complex assembly factors"	29918	protein-coding gene	gene with protein product		612911	"chromosome 3 open reading frame 60", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3"	C3orf60		12653254, 9349717	Standard	NM_199069		Approved	MGC10527, DKFZP564J0123, E3-3, 2P1	uc003cvq.3	Q9BU61	OTTHUMG00000156773	ENST00000326925.6:c.176A>T	3.37:g.49059877A>T	ENSP00000323076:p.Tyr59Phe	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	106	23	NM_199069	2	0	295	422	125		Missense_Mutation	SNP	ENST00000326925.6	37	CCDS2784.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.970503	0.53614	.	.	ENSG00000178057	ENST00000326912;ENST00000326925;ENST00000395458;ENST00000451378	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.29	2.73	0.32206	.	0.264355	0.36665	N	0.002471	T	0.70885	0.3275	L	0.33485	1.01	0.31716	N	0.638898	B	0.02656	0.0	B	0.06405	0.002	T	0.58493	-0.7627	10	0.11182	T	0.66	-8.5232	4.4326	0.11535	0.598:0.0:0.09:0.312	.	59	Q9BU61	NDUF3_HUMAN	F	2;59;2;2	ENSP00000323003:Y2F;ENSP00000323076:Y59F;ENSP00000378843:Y2F;ENSP00000402465:Y2F	ENSP00000323003:Y2F	Y	+	2	0	NDUFAF3	49034881	1.000000	0.71417	0.997000	0.53966	0.638000	0.38207	4.002000	0.57053	0.833000	0.34828	0.533000	0.62120	TAC	.		0.652	NDUFAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345683.2	NM_199069		T	49059877	A	T	49059877	3	4	91	1	0	0	0	0	1	0	0	0	10302	391	14	5	182	5	NDUFAF3	3	49059877	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	600504	49059877	148962553	16	8231											
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52432935	52432935	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggcactcaaggggctggtAgtgatgtcctctcagctgga	9	9	14	9	0	2	1	2	1	1	0	4	2	3	2	1	5	1	4	1	5	3	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:52432935A>G	ENST00000420323.2	+	76	12420	c.12159A>G	c.(12157-12159)gtA>gtG	p.V4053V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	4118					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGGGGCTGGTAGTGATGTCCT	0.552																																					p.V4053V		.											.	DNAH1-67	0			c.A12159G						.						48	54	52					3																	52432935		2092	4227	6319	SO:0001819	synonymous_variant	25981	exon76			GCTGGTAGTGATG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.12159A>G	3.37:g.52432935A>G		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	49	11	NM_015512	0	0	5	7	2	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			.		0.552	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52432935	A	G	52432935	2	3	91	1	0	0	0	0	0	0	0	1	4608	407	15	3		3	DNAH1	3	52432935	Silent	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	3373058	52432935	145589495	17	8232											
HRG	3273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186383957	186383957	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaaaggcgacgggatggctAccttttccaattgctgcgga	10	10	12	9	3	0	0	0	0	0	0	1	3	1	2	2	4	3	2	2	4	4	5			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:186383957A>T	ENST00000232003.4	+	1	217	c.137A>T	c.(136-138)tAc>tTc	p.Y46F	RP11-134F2.2_ENST00000428501.1_RNA|HRG_ENST00000468154.1_3'UTR|RP11-134F2.2_ENST00000455926.1_RNA	NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	46	Cystatin 1.|Interaction with ATP5A1.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		CGGGATGGCTACCTTTTCCAA	0.527																																					p.Y46F		.											.	HRG-91	0			c.A137T						.						142	135	137					3																	186383957		2203	4300	6503	SO:0001583	missense	3273	exon1			ATGGCTACCTTTT		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"histidine-proline rich glycoprotein", "thrombophilia due to elevated HRG"	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.137A>T	3.37:g.186383957A>T	ENSP00000232003:p.Tyr46Phe	Somatic	162	1		WXS	Illumina HiSeq	Phase_I	183	76	NM_000412	0	0	0	0	0	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.550256	0.65311	.	.	ENSG00000113905	ENST00000232003	T	0.13538	2.58	5.5	4.21	0.49690	Proteinase inhibitor I25, cystatin (2);	0.000000	0.46145	D	0.000320	T	0.19406	0.0466	L	0.52905	1.665	0.29505	N	0.854602	P	0.41366	0.747	P	0.49853	0.624	T	0.02471	-1.1154	10	0.34782	T	0.22	-26.998	7.643	0.28305	0.7685:0.0:0.0:0.2315	.	46	P04196	HRG_HUMAN	F	46	ENSP00000232003:Y46F	ENSP00000232003:Y46F	Y	+	2	0	HRG	187866651	0.997000	0.39634	1.000000	0.80357	0.963000	0.63663	2.079000	0.41577	2.225000	0.72522	0.533000	0.62120	TAC	.		0.527	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412		T	186383957	A	T	186383957	3	4	91	1	0	0	0	0	1	0	0	0	7375	391	14	5	139	5	HRG	3	186383957	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	133951022	186383957	11638473	18	8233											
FTMT	94033	broad.mit.edu;bcgsc.ca	37	chr5	121187826	121187826	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccgcagccgcctcctcccgGgaccctaccgggcccgccgc	3	3	12	23	6	0	0	0	0	0	0	2	1	2	1	9	2	2	1	9	2	1	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr5:121187826G>T	ENST00000321339.1	+	1	177	c.168G>T	c.(166-168)cgG>cgT	p.R56R		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	56					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CCTCCTCCCGGGACCCTACCG	0.751																																					p.R56R													.	FTMT-91	0			c.G168T						.						9	11	10					5																	121187826		2173	4253	6426	SO:0001819	synonymous_variant	94033	exon1			CTCCCGGGACCCT	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.168G>T	5.37:g.121187826G>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	21	6	NM_177478	0	0	0	0	0		Silent	SNP	ENST00000321339.1	37	CCDS4128.1																																																																																			.		0.751	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		T	121187826	G	T	121187826	2	4	91	1	0	0	0	0	0	0	0	1	6104	1219	43	4		4	FTMT	5	121187826	Silent	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		121187826	59727434	19	8234											
PDGFRB	5159	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	149515196	149515213	+	In_Frame_Del	DEL	CCGTGTCTAGCCCAGTGA	CCGTGTCTAGCCCAGTGA	-																															gtgggtgcaaaagtattctcCcgtgtctagcccagtgaggt																								rs141870925|rs188981582|rs556826386	byFrequency	TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	CCGTGTCTAGCCCAGTGA	CCGTGTCTAGCCCAGTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr5:149515196_149515213delCCGTGTCTAGCCCAGTGA	ENST00000261799.4	-	3	738_755	c.269_286delTCACTGGGCTAGACACGG	c.(268-288)ctcactgggctagacacggga>cga	p.90_96LTGLDTG>R		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	90	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAGTATTCTCCCGTGTCTAGCCCAGTGAGGTTGGTCAG	0.592			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.90_96del		.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB-1499	0			c.269_286del						.																																			SO:0001651	inframe_deletion	5159	exon3			.	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.269_286delTCACTGGGCTAGACACGG	5.37:g.149515196_149515213delCCGTGTCTAGCCCAGTGA	ENSP00000261799:p.Leu90_Gly96delinsArg	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	116	22	NM_002609	0	0	0	0	0	B5A957|Q8N5L4	In_Frame_Del	DEL	ENST00000261799.4	37	CCDS4303.1																																																																																			.		0.592	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		-	149515213	CCGTGTCTAGCCCAGTGA	-	149515196	7	5	91	1	0	1	0	1	0	0	0	0	11688	632	22	0	3118	0	PDGFRB	5	149515196	In_Frame_Del	DEL	CCGTGTCTAGCCCAGTGA	TCGA-BQ-7062-01A-11D-1961-08	28327370	149515196	31400064	20	8235											
ASCC3	10973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	101296249	101296249	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacttcttataatctaggctTatagttttctgagtttcacc	10	18	5	8	0	4	1	1	1	3	0	4	1	4	1	1	1	1	3	1	1	6	9			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr6:101296249T>A	ENST00000369162.2	-	4	920	c.576A>T	c.(574-576)atA>atT	p.I192I	ASCC3_ENST00000522650.1_Silent_p.I192I	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	192					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AATCTAGGCTTATAGTTTTCT	0.378																																					p.I192I		.											.	ASCC3-96	0			c.A576T						.						59	58	58					6																	101296249		2203	4300	6503	SO:0001819	synonymous_variant	10973	exon4			TAGGCTTATAGTT	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"RNA helicase family"	614217	"helicase, ATP binding 1"	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.576A>T	6.37:g.101296249T>A		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	70	16	NM_006828	0	0	0	0	0	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																			.		0.378	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101296249	T	A	101296249	2	1	91	1	0	0	0	0	0	0	0	1	1034	1744	61	5		5	ASCC3	6	101296249	Silent	SNP	T	TCGA-BQ-7062-01A-11D-1961-08		101296249	69818818	21	8236											
SPDYE6	0	broad.mit.edu	37	chr7	101988946	101988946	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aactggaaccgacgcttacgGagcaagggtatgcgagagcg	12	5	15	9	5	0	1	0	0	0	1	0	5	0	3	1	3	6	3	1	3	5	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr7:101988946G>A								Y_RNA (11564 upstream) : PRKRIP1 (15397 downstream)																							GACGCTTACGGAGCAAGGGTA	0.572																																					p.L309L													.	SPDYE6-1	0			c.C927T						.						50	52	52					7																	101988946		96	587	683	SO:0001628	intergenic_variant	729597	exon6			CTTACGGAGCAAG																													7.37:g.101988946G>A		Somatic	1566	1		WXS	Illumina HiSeq	Phase_I	1717	106	NM_001146210	0	0	46	47	1		Silent	SNP		37																																																																																				.	0	0.572									A	101988946	G	A	101988946	1	1	91	0	1	0	0	0	0	0	0	0	15065	1161	41	2		2	SPDYE6	7	101988946	IGR	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		101988946	57149717	22	8237											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138546145	138546145	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgggaagggaagggctggatAcctccccagttccaccgagg	9	5	15	12	2	0	0	0	0	0	0	2	4	2	3	5	5	1	2	5	5	3	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr7:138546145A>G	ENST00000422774.1	-	16	5035	c.4987T>C	c.(4987-4989)Tat>Cat	p.Y1663H	KIAA1549_ENST00000242365.4_Missense_Mutation_p.Y1613H|KIAA1549_ENST00000440172.1_Missense_Mutation_p.Y1663H			Q9HCM3	K1549_HUMAN	KIAA1549	1663						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						AGGGCTGGATACCTCCCCAGT	0.582			O	BRAF	pilocytic astrocytoma																																p.Y1663H	NSCLC(119;1534 1718 44213 46230 50068)	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549-369	0			c.T4987C						.						30	36	34					7																	138546145		2065	4195	6260	SO:0001583	missense	57670	exon16			CTGGATACCTCCC		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4987T>C	7.37:g.138546145A>G	ENSP00000416040:p.Tyr1663His	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	53	3	NM_020910	0	1	31	32	0	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.979169	0.53827	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.24538	1.85;1.86;1.86	4.49	4.49	0.54785	.	0.398524	0.28853	N	0.013924	T	0.43831	0.1265	L	0.52573	1.65	0.37822	D	0.928436	D;D;D;D	0.89917	1.0;0.99;1.0;0.99	D;P;D;P	0.77557	0.99;0.885;0.984;0.885	T	0.47686	-0.9098	10	0.54805	T	0.06	.	13.418	0.60980	1.0:0.0:0.0:0.0	.	1663;447;1663;447	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	H	1663;1613;1663	ENSP00000406661:Y1663H;ENSP00000242365:Y1613H;ENSP00000416040:Y1663H	ENSP00000242365:Y1613H	Y	-	1	0	KIAA1549	138196685	1.000000	0.71417	0.479000	0.27329	0.345000	0.29048	5.649000	0.67936	2.010000	0.58986	0.460000	0.39030	TAT	.		0.582	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			G	138546145	A	G	138546145	3	3	91	1	0	0	0	0	1	0	0	0	8265	391	14	3	885	3	KIAA1549	7	138546145	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	36557199	138546145	20592518	23	8238											
NOM1	64434	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	156752614	156752614	+	Frame_Shift_Del	DEL	A	A	-																															ataaatacggaagcgaagggAaagagtgtgacaacctgttc																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr7:156752614delA	ENST00000275820.3	+	4	1393	c.1378delA	c.(1378-1380)aaafs	p.K460fs	NOM1_ENST00000460332.1_3'UTR	NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	460	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAGCGAAGGGAAAGAGTGTGA	0.443																																					p.K460fs		.											.	NOM1-90	0			c.1378delA						.						128	109	115					7																	156752614		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon4			.	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1378delA	7.37:g.156752614delA	ENSP00000275820:p.Lys460fs	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	61	16	NM_138400	0	0	0	0	0	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	37	CCDS34787.1																																																																																			.		0.443	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		-	156752614	A	-	156752614	7	5	91	1	0	1	0	1	0	0	0	0	10556	247	9	0	1392	0	NOM1	7	156752614	Frame_Shift_Del	DEL	A	TCGA-BQ-7062-01A-11D-1961-08	18206469	156752614	2386049	24	8239											
C8orf41	80185	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	33369560	33369560	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcattttctccatgtaggAatcctgccacagaaccgcat	10	12	6	13	1	2	1	1	0	1	1	4	2	3	2	4	1	2	2	4	1	3	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:33369560A>T	ENST00000431156.2	-	2	1190	c.572T>A	c.(571-573)tTc>tAc	p.F191Y	TTI2_ENST00000519356.1_5'Flank|SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000360742.5_Missense_Mutation_p.F191Y|TTI2_ENST00000520636.1_Missense_Mutation_p.F191Y	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	191																	TCCATGTAGGAATCCTGCCAC	0.502																																					p.F191Y		.											.	.	0			c.T572A						.						191	196	194					8																	33369560		2203	4300	6503	SO:0001583	missense	80185	exon2			TGTAGGAATCCTG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"chromosome 8 open reading frame 41", "Tel2 interacting protein 2 homolog (S. pombe)"	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.572T>A	8.37:g.33369560A>T	ENSP00000411169:p.Phe191Tyr	Somatic	353	0		WXS	Illumina HiSeq	Phase_I	363	95	NM_001265581	0	0	2	5	3	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	37	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592154	0.66219	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397	T;T;T	0.76709	-1.04;-1.04;-1.04	4.66	4.66	0.58398	.	0.101991	0.43579	D	0.000544	D	0.85102	0.5620	M	0.76838	2.35	0.25824	N	0.984245	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.60012	0.867;0.867;0.867	T	0.79057	-0.1959	10	0.72032	D	0.01	-23.4405	11.5884	0.50931	1.0:0.0:0.0:0.0	.	191;191;191	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	Y	191	ENSP00000353971:F191Y;ENSP00000411169:F191Y;ENSP00000428401:F191Y	ENSP00000353971:F191Y	F	-	2	0	C8orf41	33489102	1.000000	0.71417	0.326000	0.25389	0.530000	0.34684	5.556000	0.67307	1.954000	0.56735	0.533000	0.62120	TTC	.		0.502	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		T	33369560	A	T	33369560	3	4	91	1	0	0	0	0	1	0	0	0	2433	246	9	5	982	5	C8orf41	8	33369560	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		33369560	112994462	25	8240											
TERF1	7013	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	73921183	73921183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgtgcggatggtagggatgCcgaccctactgaggagcaga	9	7	16	9	2	0	2	0	1	0	1	0	6	0	5	2	4	4	2	2	4	2	2	rs370999354		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:73921183C>T	ENST00000276603.5	+	1	85	c.62C>T	c.(61-63)gCc>gTc	p.A21V	TERF1_ENST00000276602.6_Missense_Mutation_p.A21V	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	21	Asp/Glu-rich (acidic).				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			GGTAGGGATGCCGACCCTACT	0.637													C|||	1	0.000199681	0	0	5008	,	,		15699	0		0	False		,,,				2504	0.001				p.A21V													.	TERF1-228	0			c.C62T						.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	20	22	21		62,62	3.5	0	8		21	1,8597		0,1,4298	no	missense,missense	TERF1	NM_003218.3,NM_017489.2	64,64	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	21/420,21/440	73921183	1,13003	2203	4299	6502	SO:0001583	missense	7013	exon1			GGGATGCCGACCC	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.62C>T	8.37:g.73921183C>T	ENSP00000276603:p.Ala21Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	46	9	NM_017489	0	0	4	8	4	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	37	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496693	0.64186	0.0	1.16E-4	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000518874	.	.	.	4.41	3.52	0.40303	.	0.427983	0.25391	N	0.031013	T	0.35189	0.0923	L	0.29908	0.895	0.09310	N	1	D;D	0.56521	0.961;0.976	P;P	0.51974	0.616;0.686	T	0.11591	-1.0581	9	0.87932	D	0	.	9.781	0.40649	0.3758:0.6242:0.0:0.0	.	21;21	P54274-2;P54274	.;TERF1_HUMAN	V	21	.	ENSP00000276602:A21V	A	+	2	0	TERF1	74083737	0.001000	0.12720	0.017000	0.16124	0.002000	0.02628	0.298000	0.19120	1.436000	0.47453	-0.321000	0.08615	GCC	.		0.637	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		T	73921183	C	T	73921183	3	4	91	1	0	0	0	0	1	0	0	0	15793	739	26	2	64	2	TERF1	8	73921183	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	40551623	73921183	72442839	26	8241											
PSCA	8000	hgsc.bcm.edu	37	chr8	143762846	143762846	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagcagtgctggaccgcgCgcatccgtgagtggggggac	6	5	20	10	4	0	1	0	1	0	0	1	4	1	4	2	5	2	3	2	5	0	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:143762846C>G	ENST00000301258.4	+	2	210	c.127C>G	c.(127-129)Cgc>Ggc	p.R43G	PSCA_ENST00000513264.1_Missense_Mutation_p.R43G|PSCA_ENST00000505305.1_3'UTR	NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	52	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTGGACCGCGCGCATCCGTGA	0.607																																					p.R43G		.											.	.	0			c.C127G						.						12	16	15					8																	143762846		2125	4209	6334	SO:0001583	missense	8000	exon2			ACCGCGCGCATCC	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.127C>G	8.37:g.143762846C>G	ENSP00000301258:p.Arg43Gly	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	16	6	NM_005672	0	0	0	0	0	Q6UW92	Missense_Mutation	SNP	ENST00000301258.4	37	CCDS47925.2	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686883	0.29962	.	.	ENSG00000167653	ENST00000301258;ENST00000513264	T	0.70399	-0.48	2.97	2.09	0.27110	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.295300	0.05740	N	0.601212	T	0.75079	0.3801	M	0.72894	2.215	0.09310	N	1	P	0.43169	0.8	P	0.50162	0.633	T	0.57837	-0.7742	10	0.26408	T	0.33	.	6.0755	0.19913	0.0:0.8561:0.0:0.1439	.	52	O43653	PSCA_HUMAN	G	52	ENSP00000426508:R52G	ENSP00000301258:R52G	R	+	1	0	PSCA	143759848	0.001000	0.12720	0.001000	0.08648	0.176000	0.22953	1.247000	0.32815	0.837000	0.34925	0.456000	0.33151	CGC	.		0.607	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672		G	143762846	C	G	143762846	3	3	91	1	0	0	0	0	1	0	0	0	12674	768	27	4	133	4	PSCA	8	143762846	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	69841663	143762846	2601176	27	8242											
TLN1	7094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35698169	35698169	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcactgcgttgccagcagCctgggcagagagaaagtggc	9	7	14	11	1	1	2	1	0	0	2	1	3	1	2	2	2	4	3	2	2	1	2	rs555751291		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr9:35698169C>G	ENST00000314888.9	-	56	7725	c.7372G>C	c.(7372-7374)Gct>Cct	p.A2458P	TLN1_ENST00000540444.1_Splice_Site_p.A2346P	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2458	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTGCCAGCAGCCTGGGCAGAG	0.512																																					p.A2458P		.											.	TLN1-609	0			c.G7372C						.						74	68	70					9																	35698169		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon56			CAGCAGCCTGGGC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.7372-1G>C	9.37:g.35698169C>G		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	83	14	NM_006289	0	0	0	0	0	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417660	0.83449	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.31769	1.48;1.48	4.83	4.83	0.62350	I/LWEQ (4);	0.053747	0.85682	D	0.000000	T	0.56441	0.1985	M	0.79258	2.445	0.80722	D	1	D	0.63880	0.993	D	0.65323	0.934	T	0.60747	-0.7202	10	0.56958	D	0.05	-4.1588	18.0913	0.89476	0.0:1.0:0.0:0.0	.	2458	Q9Y490	TLN1_HUMAN	P	2458;2346	ENSP00000316029:A2458P;ENSP00000442981:A2346P	ENSP00000316029:A2458P	A	-	1	0	TLN1	35688169	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.752000	0.62176	2.509000	0.84616	0.655000	0.94253	GCT	.		0.512	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation	G	35698169	C	G	35698169	5	3	91	1	0	0	0	0	0	0	1	0	15979	753	26	4	261	4	TLN1	9	35698169	Splice_Site	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		35698169	105515262	28	8243											
FAM75C1	441452	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	90536638	90536638	+	RNA	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgagtgtgcgtcgatccTggcttgctgtcaaccaggct	5	11	13	12	3	1	1	1	1	0	0	3	2	2	1	3	2	3	3	3	2	1	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr9:90536638T>A	ENST00000602681.1	+	0	1927							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCGTCGATCCTGGCTTGCTGT	0.522																																					p.W606R													.	.	0			c.T1816A						.						40	35	36					9																	90536638		692	1591	2283			441452	exon4			CGATCCTGGCTTG	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		9.37:g.90536638T>A		Somatic	248	1		WXS	Illumina HiSeq	Phase_I	284	87	NM_001145124	0	0	0	0	0		Missense_Mutation	SNP	ENST00000602681.1	37																																																																																				.		0.522	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		A	90536638	T	A	90536638	1	1	91	0	1	0	0	0	0	0	0	0	5642	1580	55	5		5	FAM75C1	9	90536638	RNA	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	54838469	90536638	50676793	29	8244											
ITGB1	3688	broad.mit.edu	37	chr10	33208866	33208866	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgacacttgggactttcAgggatgccttcgctttggca	7	13	11	10	1	2	1	2	1	0	0	3	3	2	3	1	3	1	2	1	3	0	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:33208866A>G	ENST00000396033.2	-	11	1551	c.1416T>C	c.(1414-1416)ccT>ccC	p.P472P	ITGB1_ENST00000374956.4_Silent_p.P472P|ITGB1_ENST00000302278.3_Silent_p.P472P|ITGB1_ENST00000423113.1_Silent_p.P472P	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	472	Cysteine-rich tandem repeats.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	TGGGACTTTCAGGGATGCCTT	0.463																																					p.P472P													.	ITGB1-1084	0			c.T1416C						.						136	124	128					10																	33208866		2203	4300	6503	SO:0001819	synonymous_variant	3688	exon11			ACTTTCAGGGATG	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1416T>C	10.37:g.33208866A>G		Somatic	187	0		WXS	Illumina HiSeq	Phase_I	172	4	NM_002211	0	0	224	225	1	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																			.		0.463	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		G	33208866	A	G	33208866	2	3	91	1	0	0	0	0	0	0	0	1	7911	175	7	3		3	ITGB1	10	33208866	Silent	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		33208866	102325881	30	8245											
IFIT5	24138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	91177427	91177427	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttggaggaaagtattatcaAaaggctaaagcggcttttga	14	12	11	4	1	1	1	1	1	0	0	1	3	1	3	0	4	1	3	0	4	7	6			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:91177427A>G	ENST00000371795.4	+	2	684	c.471A>G	c.(469-471)caA>caG	p.Q157Q	IFIT5_ENST00000416601.1_Silent_p.Q157Q	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	157					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						AGTATTATCAAAAGGCTAAAG	0.443																																					p.Q157Q		.											.	IFIT5-90	0			c.A471G						.						71	74	73					10																	91177427		2203	4300	6503	SO:0001819	synonymous_variant	24138	exon2			TTATCAAAAGGCT	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.471A>G	10.37:g.91177427A>G		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	102	24	NM_012420	0	0	10	13	3	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Silent	SNP	ENST00000371795.4	37	CCDS7403.1																																																																																			.		0.443	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		G	91177427	A	G	91177427	2	3	91	1	0	0	0	0	0	0	0	1	7546	11	1	3		3	IFIT5	10	91177427	Silent	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	57968561	91177427	44357320	31	8246											
DMBT1	1755	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	124352013	124352013	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattgttctggatgatgtgcGctgctcaggacacgagtcct	7	12	12	10	2	2	1	1	1	1	0	3	4	3	3	1	2	2	3	1	2	0	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:124352013G>A	ENST00000338354.3	+	20	2508	c.2402G>A	c.(2401-2403)cGc>cAc	p.R801H	DMBT1_ENST00000368909.3_Missense_Mutation_p.R801H|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000368955.3_Missense_Mutation_p.R791H|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.R791H			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	801	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GATGATGTGCGCTGCTCAGGA	0.607																																					p.R801H	Ovarian(182;93 2026 18125 22222 38972)	.											.	DMBT1-494	0			c.G2402A						.						155	114	127					10																	124352013		2023	4110	6133	SO:0001583	missense	1755	exon20			ATGTGCGCTGCTC		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2402G>A	10.37:g.124352013G>A	ENSP00000342210:p.Arg801His	Somatic	254	1		WXS	Illumina HiSeq	Phase_I	321	21	NM_007329	0	0	0	0	0	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	G	0.015	-1.564805	0.00903	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	3.9	-0.752	0.11072	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.43233	0.1238	L	0.42008	1.315	0.09310	N	1	D;B;B;B	0.76494	0.999;0.098;0.098;0.119	D;B;B;B	0.63033	0.91;0.005;0.005;0.008	T	0.26224	-1.0109	9	0.33141	T	0.24	.	1.6023	0.02676	0.3222:0.1635:0.395:0.1192	.	562;801;791;801	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	H	801;801;801;801;801;801;791;801;791	ENSP00000342210:R801H;ENSP00000343175:R791H;ENSP00000357905:R801H;ENSP00000357951:R791H	ENSP00000342210:R801H	R	+	2	0	DMBT1	124342003	0.000000	0.05858	0.023000	0.16930	0.017000	0.09413	-1.614000	0.02057	-0.442000	0.07190	-0.219000	0.12488	CGC	.		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124352013	G	A	124352013	3	1	91	1	0	0	0	0	1	0	0	0	4588	1087	38	1	2480	1	DMBT1	10	124352013	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08	33174586	124352013	11182734	32	8247											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1268402	1268402	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacacctgcagccaccagcaGcacagtgactccctcctctg	9	6	7	19	0	1	1	0	1	1	0	3	1	3	1	5	0	4	3	5	0	0	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:1268402G>A	ENST00000529681.1	+	31	10350	c.10292G>A	c.(10291-10293)aGc>aAc	p.S3431N	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3434N	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3431	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.S3410N(1)		cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		gccaccagcagcacAGTGACT	0.682																																					p.S3431N		.											.	.	1	Substitution - Missense(1)	prostate(1)	c.G10292A						.						41	76	64					11																	1268402		2093	4144	6237	SO:0001583	missense	727897	exon31			CCAGCAGCACAGT	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.10292G>A	11.37:g.1268402G>A	ENSP00000436812:p.Ser3431Asn	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	22	6	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	3.121	-0.180464	0.06380	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637	T;T	0.20598	2.06;2.24	2.38	-2.65	0.06095	.	.	.	.	.	T	0.11965	0.0291	L	0.29908	0.895	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.31888	-0.9927	9	0.87932	D	0	.	2.2793	0.04110	0.1745:0.3567:0.3457:0.1231	.	3434	E9PBJ0	.	N	3431;3434;3403	ENSP00000436812:S3431N;ENSP00000415793:S3434N	ENSP00000343037:S3403N	S	+	2	0	MUC5B	1224978	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.426000	0.02443	-0.630000	0.05567	-0.714000	0.03626	AGC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1268402	G	A	1268402	3	1	91	1	0	0	0	0	1	0	0	0	10004	971	34	2	10423	2	MUC5B	11	1268402	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		1268402	133738114	33	8248											
AGBL2	79841	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	47726183	47726183	+	Frame_Shift_Del	DEL	G	G	-																															ttggtagacaaaatggaaaaGagctcttggggttctcgaag																								rs373862581		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:47726183delG	ENST00000525123.1	-	7	783	c.498delC	c.(496-498)ctcfs	p.L166fs	AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000298861.4_Frame_Shift_Del_p.L166fs|AGBL2_ENST00000528244.1_Frame_Shift_Del_p.L128fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.L166fs	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	166						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AAATGGAAAAGAGCTCTTGGG	0.428																																					p.L166fs		.											.	AGBL2-92	0			c.498delC						.						141	132	135					11																	47726183		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon7			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.498delC	11.37:g.47726183delG	ENSP00000435582:p.Leu166fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	98	24	NM_024783	0	0	0	0	0	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	37	CCDS7944.1																																																																																			.		0.428	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		-	47726183	G	-	47726183	7	5	91	1	0	1	0	1	0	0	0	0	376	929	33	0	2262	0	AGBL2	11	47726183	Frame_Shift_Del	DEL	G	TCGA-BQ-7062-01A-11D-1961-08	46457781	47726183	87280333	34	8249											
MS4A8B	83661	hgsc.bcm.edu;bcgsc.ca	37	chr11	60482801	60482801	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgagtgtcatctatccaAacatctatgcagcaaaccca	14	9	7	11	0	3	1	1	1	2	0	4	1	4	1	2	1	4	2	2	1	4	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:60482801A>G	ENST00000300226.2	+	7	870	c.667A>G	c.(667-669)Aac>Gac	p.N223D		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	223						integral component of membrane (GO:0016021)											CATCTATCCAAACATCTATGC	0.512																																					p.N223D		.											.	.	0			c.A667G						.						139	119	126					11																	60482801		2203	4300	6503	SO:0001583	missense	83661	exon7			TATCCAAACATCT	AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"membrane-spanning 4-domains, subfamily A, member 8B"	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.667A>G	11.37:g.60482801A>G	ENSP00000300226:p.Asn223Asp	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	75	6	NM_031457	0	0	0	0	0	Q8TCA5	Missense_Mutation	SNP	ENST00000300226.2	37	CCDS7990.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.374|5.374	0.254305|0.254305	0.10185|0.10185	.|.	.|.	ENSG00000166959|ENSG00000166959	ENST00000529752|ENST00000300226	T|T	0.18016|0.08008	2.24|3.14	4.21|4.21	1.87|1.87	0.25490|0.25490	.|.	.|.	.|.	.|.	.|.	T|T	0.05318|0.05318	0.0141|0.0141	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|P	.|0.37466	.|0.596	.|B	.|0.32864	.|0.154	T|T	0.39251|0.39251	-0.9623|-0.9623	7|9	0.15499|0.30078	T|T	0.54|0.28	-8.3887|-8.3887	5.7024|5.7024	0.17889|0.17889	0.7776:0.0:0.2223:0.0|0.7776:0.0:0.2223:0.0	.|.	.|223	.|Q9BY19	.|M4A8B_HUMAN	R|D	205|223	ENSP00000436857:K205R|ENSP00000300226:N223D	ENSP00000436857:K205R|ENSP00000300226:N223D	K|N	+|+	2|1	0|0	MS4A8B|MS4A8B	60239377|60239377	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	1.017000|1.017000	0.29989|0.29989	0.279000|0.279000	0.22186|0.22186	-0.290000|-0.290000	0.09829|0.09829	AAA|AAC	.		0.512	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1			G	60482801	A	G	60482801	3	3	91	1	0	0	0	0	1	0	0	0	9892	14	1	3	689	3	MS4A8B	11	60482801	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	12756618	60482801	74523715	35	8250											
HNRNPUL2	221092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62489600	62489600	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcatacctcacattcctCtatggtcttgggagggactg	7	13	11	10	0	3	0	1	0	2	0	4	2	4	2	2	4	1	1	2	4	2	5			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:62489600C>A	ENST00000301785.5	-	7	1540	c.1348G>T	c.(1348-1350)Gag>Tag	p.E450*	HNRNPUL2-BSCL2_ENST00000403734.2_Nonsense_Mutation_p.E450*	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	450						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCACATTCCTCTATGGTCTTG	0.517																																					p.E450X		.											.	HNRNPUL2-22	0			c.G1348T						.						72	71	71					11																	62489600		2062	4209	6271	SO:0001587	stop_gained	221092	exon7			ATTCCTCTATGGT		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1348G>T	11.37:g.62489600C>A	ENSP00000301785:p.Glu450*	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	101	25	NM_001079559	0	0	0	0	0	Q8N3B3	Nonsense_Mutation	SNP	ENST00000301785.5	37	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	C	38	7.037044	0.98017	.	.	ENSG00000214753	ENST00000301785	.	.	.	5.55	5.55	0.83447	.	0.262799	0.38217	N	0.001774	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.715	17.0466	0.86505	0.0:1.0:0.0:0.0	.	.	.	.	X	450	.	ENSP00000301785:E450X	E	-	1	0	HNRNPUL2	62246176	0.998000	0.40836	0.996000	0.52242	0.992000	0.81027	1.869000	0.39519	2.894000	0.99253	0.655000	0.94253	GAG	.		0.517	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		A	62489600	C	A	62489600	4	1	91	1	0	0	0	0	0	1	0	0	7296	922	32	4	927	4	HNRNPUL2	11	62489600	Nonsense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	2006799	62489600	72516916	36	8251											
RAD51AP1	10635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	4657343	4657343	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgtagccagtgattatttAggtaagttttttatattaat	12	19	8	2	0	0	1	0	1	0	0	0	1	0	1	1	1	1	3	1	1	7	10			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:4657343A>T	ENST00000544927.1	+	5	415	c.405A>T	c.(403-405)ttA>ttT	p.L135F	RAD51AP1_ENST00000352618.4_Splice_Site_p.L135F|RAD51AP1_ENST00000228843.9_Splice_Site_p.L152F|RAD51AP1_ENST00000321524.7_Splice_Site_p.L152F|RAD51AP1_ENST00000543041.1_Splice_Site_p.L17F					RAD51 associated protein 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			GTGATTATTTAGGTAAGtttt	0.289																																					p.L152F		.											.	RAD51AP1-227	0			c.A456T						.						59	67	64					12																	4657343		2202	4298	6500	SO:0001630	splice_region_variant	10635	exon6			TTATTTAGGTAAG	AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000544927.1:c.406+1A>T	12.37:g.4657343A>T		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	108	46	NM_001130862	0	0	0	0	0		Missense_Mutation	SNP	ENST00000544927.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.48|17.48	3.400705|3.400705	0.62177|0.62177	.|.	.|.	ENSG00000111247|ENSG00000111247	ENST00000321524;ENST00000543041;ENST00000228843;ENST00000352618;ENST00000544927|ENST00000536117	T;T;T;T;T|.	0.37058|.	1.22;1.22;1.22;1.22;1.22|.	4.97|4.97	3.82|3.82	0.43975|0.43975	.|.	0.645832|.	0.14584|.	N|.	0.310677|.	T|.	0.48223|.	0.1488|.	L|L	0.41710|0.41710	1.295|1.295	0.34395|0.34395	D|D	0.694667|0.694667	D;B;P;B|.	0.89917|.	1.0;0.185;0.492;0.047|.	D;B;B;B|.	0.85130|.	0.997;0.171;0.171;0.032|.	T|.	0.57306|.	-0.7834|.	10|.	0.46703|.	T|.	0.11|.	-1.5623|-1.5623	8.1351|8.1351	0.31050|0.31050	0.7774:0.2226:0.0:0.0|0.7774:0.2226:0.0:0.0	.|.	17;152;152;135|.	B4DUS5;Q96B01;A8K313;Q96B01-2|.	.;R51A1_HUMAN;.;.|.	F|X	152;17;152;135;135|130	ENSP00000323750:L152F;ENSP00000439960:L17F;ENSP00000228843:L152F;ENSP00000309479:L135F;ENSP00000446296:L135F|.	ENSP00000228843:L152F|.	L|R	+|+	3|1	2|2	RAD51AP1|RAD51AP1	4527604|4527604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.882000|1.882000	0.39648|0.39648	2.085000|2.085000	0.62840|0.62840	0.482000|0.482000	0.46254|0.46254	TTA|AGA	.		0.289	RAD51AP1-012	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399208.1	NM_006479	Missense_Mutation	T	4657343	A	T	4657343	5	4	91	1	0	0	0	0	0	0	1	0	13018	434	15	5	478	5	RAD51AP1	12	4657343	Splice_Site	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		4657343	129194552	37	8252											
LMBR1L	55716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49500795	49500795	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtcaggaagatgtggcagaGgatgtacagtgttgcaaaca	13	8	15	5	0	1	2	1	0	0	2	1	4	1	4	0	4	3	4	0	4	3	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:49500795G>T	ENST00000267102.8	-	2	448	c.106C>A	c.(106-108)Ctc>Atc	p.L36I	LMBR1L_ENST00000395141.4_5'Flank|LMBR1L_ENST00000547382.1_Missense_Mutation_p.L36I|LMBR1L_ENST00000553204.1_5'UTR	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	36	LCN1-binding.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATGTGGCAGAGGATGTACAGT	0.512																																					p.L36I		.											.	LMBR1L-227	0			c.C106A						.						141	161	154					12																	49500795		2105	4230	6335	SO:0001583	missense	55716	exon2			GGCAGAGGATGTA	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"limb region 1 homolog (mouse)-like"			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.106C>A	12.37:g.49500795G>T	ENSP00000267102:p.Leu36Ile	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	317	136	NM_018113	0	0	11	30	19	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	37	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	G	9.092	1.001902	0.19121	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000547675;ENST00000550137;ENST00000551854;ENST00000551782	T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36	5.25	3.45	0.39498	LMBR1-like membrane protein (1);	0.130135	0.52532	D	0.000077	T	0.19685	0.0473	N	0.16368	0.405	0.80722	D	1	P;P	0.36412	0.496;0.552	B;B	0.38428	0.126;0.273	T	0.06625	-1.0816	10	0.02654	T	1	-2.6499	10.8004	0.46485	0.1557:0.0:0.8443:0.0	.	36;36	Q6UX01-3;Q6UX01	.;LMBRL_HUMAN	I	36;36;36;36;41;36	ENSP00000267102:L36I;ENSP00000447329:L36I;ENSP00000447240:L36I;ENSP00000446641:L41I;ENSP00000449633:L36I	ENSP00000267102:L36I	L	-	1	0	LMBR1L	47787062	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	1.966000	0.40481	0.813000	0.34350	0.563000	0.77884	CTC	.		0.512	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		T	49500795	G	T	49500795	3	4	91	1	0	0	0	0	1	0	0	0	8864	1000	35	4	1427	4	LMBR1L	12	49500795	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08	44843452	49500795	84351100	38	8253											
TMEM19	55266	broad.mit.edu	37	chr12	72092800	72092800	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatttagacatttctgcccCgcagtggccaattattgcat	9	14	8	10	1	1	2	0	1	1	1	1	2	1	2	3	1	2	2	3	1	3	5			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:72092800C>A	ENST00000266673.5	+	5	1352	c.758C>A	c.(757-759)cCg>cAg	p.P253Q	TMEM19_ENST00000549735.1_Missense_Mutation_p.P253Q	NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	253						integral component of membrane (GO:0016021)				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		ATTTCTGCCCCGCAGTGGCCA	0.448																																					p.P253Q													.	TMEM19-90	0			c.C758A						.						207	185	192					12																	72092800		2203	4300	6503	SO:0001583	missense	55266	exon5			CTGCCCCGCAGTG	BC008596	CCDS9002.1	12q15	2004-03-04				ENSG00000139291			25605	protein-coding gene	gene with protein product						12477932	Standard	NM_018279		Approved	FLJ10936	uc001sws.3	Q96HH6	OTTHUMG00000169558	ENST00000266673.5:c.758C>A	12.37:g.72092800C>A	ENSP00000266673:p.Pro253Gln	Somatic	178	1		WXS	Illumina HiSeq	Phase_I	184	5	NM_018279	0	0	58	58	0	B2RDL2|Q53FY3|Q9NV41	Missense_Mutation	SNP	ENST00000266673.5	37	CCDS9002.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.863670	0.91511	.	.	ENSG00000139291	ENST00000266673;ENST00000549735;ENST00000546795	.	.	.	6.06	6.06	0.98353	.	0.240215	0.43579	D	0.000553	T	0.74989	0.3789	L	0.56280	1.765	0.80722	D	1	D;D	0.65815	0.987;0.995	P;D	0.65010	0.875;0.931	T	0.71371	-0.4613	8	.	.	.	-7.3703	18.8014	0.92018	0.0:1.0:0.0:0.0	.	253;253	Q96HH6;Q96HH6-2	TMM19_HUMAN;.	Q	253;253;97	.	.	P	+	2	0	TMEM19	70379067	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.818000	0.86416	2.882000	0.98803	0.655000	0.94253	CCG	.		0.448	TMEM19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404801.1	NM_018279		A	72092800	C	A	72092800	3	1	91	1	0	0	0	0	1	0	0	0	16145	652	23	4	776	4	TMEM19	12	72092800	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	22592005	72092800	61759095	39	8254											
PAH	5053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	103234258	103234258	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtgtatgggtcgtagcgaActgagaagggccgaggtatt	9	9	18	5	3	0	1	0	1	0	1	1	4	0	1	1	4	2	3	1	4	5	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:103234258A>G	ENST00000553106.1	-	12	1707	c.1235T>C	c.(1234-1236)gTt>gCt	p.V412A	PAH_ENST00000307000.2_Missense_Mutation_p.V407A	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	412					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GTCGTAGCGAACTGAGAAGGG	0.448																																					p.V412A		.											.	PAH-72	0			c.T1235C						.						168	151	157					12																	103234258		2203	4300	6503	SO:0001583	missense	5053	exon12			TAGCGAACTGAGA	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.1235T>C	12.37:g.103234258A>G	ENSP00000448059:p.Val412Ala	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	144	64	NM_000277	0	0	0	3	3	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.379312	0.82682	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	D;D	0.99755	-6.64;-6.64	5.63	5.63	0.86233	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99405	0.9790	M	0.78637	2.42	0.80722	D	1	P	0.39748	0.686	B	0.42422	0.387	D	0.98750	1.0720	10	0.56958	D	0.05	-29.1046	14.8162	0.70036	1.0:0.0:0.0:0.0	.	412	P00439	PH4H_HUMAN	A	412;407	ENSP00000448059:V412A;ENSP00000303500:V407A	ENSP00000303500:V407A	V	-	2	0	PAH	101758388	1.000000	0.71417	0.993000	0.49108	0.729000	0.41735	8.471000	0.90403	2.152000	0.67230	0.459000	0.35465	GTT	.		0.448	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			G	103234258	A	G	103234258	3	3	91	1	0	0	0	0	1	0	0	0	11420	43	2	3	131	3	PAH	12	103234258	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	31141458	103234258	30617637	40	8255											
GPR109A	338442	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123187395	123187395	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacagaaggcaagagatgaTggctgctgtccgattggaga	12	7	14	8	1	0	4	0	1	0	3	1	7	1	4	2	3	1	3	2	3	2	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:123187395T>A	ENST00000328880.5	-	1	495	c.436A>T	c.(436-438)Atc>Ttc	p.I146F	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	146					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	CAAGAGATGATGGCTGCTGTC	0.557																																					p.I146F		.											.	HCAR2-91	0			c.A436T						.						128	113	118					12																	123187395		2203	4300	6503	SO:0001583	missense	338442	exon1			AGATGATGGCTGC	AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	24827	protein-coding gene	gene with protein product	"niacin receptor 1"	609163	"G protein-coupled receptor 109A"	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.436A>T	12.37:g.123187395T>A	ENSP00000375066:p.Ile146Phe	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	167	36	NM_177551	0	0	2	2	0	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	37	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	T	7.211	0.595394	0.13875	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.72615	-0.67	5.55	-6.58	0.01836	GPCR, rhodopsin-like superfamily (1);	0.529882	0.18506	N	0.139204	T	0.47783	0.1464	L	0.33189	0.99	0.09310	N	1	B	0.14438	0.01	B	0.19946	0.027	T	0.45454	-0.9260	10	0.10902	T	0.67	-17.8896	9.0102	0.36137	0.0:0.4452:0.345:0.2098	.	146	Q8TDS4	HCAR2_HUMAN	F	146	ENSP00000375066:I146F	ENSP00000375066:I146F	I	-	1	0	HCAR2	121753348	0.001000	0.12720	0.001000	0.08648	0.954000	0.61252	-0.487000	0.06505	-0.941000	0.03700	0.533000	0.62120	ATC	.		0.557	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		A	123187395	T	A	123187395	3	1	91	1	0	0	0	0	1	0	0	0	6645	1464	51	5	659	5	GPR109A	12	123187395	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	19953137	123187395	10664500	41	8256											
CHRNA5	1138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	78885562	78885562	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tataaatgggcaaatatattAataccagttcatattggaaa	18	13	6	4	0	1	0	1	0	0	0	1	1	1	1	1	2	1	2	1	2	10	9	rs558115871		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr15:78885562A>C	ENST00000299565.5	+	6	1574	c.1374A>C	c.(1372-1374)ttA>ttC	p.L458F	RP11-650L12.2_ENST00000567141.1_RNA|CHRNA3_ENST00000348639.3_Intron|CHRNA5_ENST00000559554.1_3'UTR	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	458					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	CAAATATATTAATACCAGTTC	0.338																																					p.L458F		.											.	CHRNA5-516	0			c.A1374C						.						104	94	97					15																	78885562		2196	4293	6489	SO:0001583	missense	1138	exon6			TATATTAATACCA		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1959	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 5 (neuronal)"	118505	"cholinergic receptor, nicotinic, alpha polypeptide 5"			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1374A>C	15.37:g.78885562A>C	ENSP00000299565:p.Leu458Phe	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	59	13	NM_000745	0	0	1	1	0	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	37	CCDS10304.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.895619	0.33442	.	.	ENSG00000169684	ENST00000299565	T	0.78481	-1.18	5.23	-1.75	0.08031	.	0.287773	0.35870	N	0.002933	T	0.50188	0.1601	N	0.08118	0	0.47065	D	0.999304	B	0.18461	0.028	B	0.14023	0.01	T	0.08994	-1.0695	10	0.54805	T	0.06	.	3.7176	0.08444	0.5096:0.0946:0.0656:0.3301	.	458	P30532	ACHA5_HUMAN	F	458	ENSP00000299565:L458F	ENSP00000299565:L458F	L	+	3	2	CHRNA5	76672617	0.756000	0.28383	0.039000	0.18376	0.834000	0.47266	0.062000	0.14389	-0.290000	0.09025	-1.450000	0.01041	TTA	.		0.338	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1			C	78885562	A	C	78885562	3	2	91	1	0	0	0	0	1	0	0	0	3392	359	13	5	1396	5	CHRNA5	15	78885562	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		78885562	23645830	42	8257											
ADCY9	115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4029168	4029168	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggagtagacggccagtgcGggaagcgacaccaggatggc	10	4	18	9	3	0	1	0	0	0	1	0	5	0	4	2	5	2	1	2	5	2	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr16:4029168G>A	ENST00000294016.3	-	8	3166	c.2628C>T	c.(2626-2628)ccC>ccT	p.P876P		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	876					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGGCCAGTGCGGGAAGCGACA	0.582																																					p.P876P		.											.	ADCY9-139	0			c.C2628T						.						128	121	124					16																	4029168		2197	4300	6497	SO:0001819	synonymous_variant	115	exon8			CAGTGCGGGAAGC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2628C>T	16.37:g.4029168G>A		Somatic	140	0		WXS	Illumina HiSeq	Phase_I	157	30	NM_001116	0	0	25	40	15	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			.		0.582	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4029168	G	A	4029168	2	1	91	1	0	0	0	0	0	0	0	1	301	1103	39	1		1	ADCY9	16	4029168	Silent	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		4029168	86325585	43	8258											
ACSM3	6296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20787239	20787239	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcgatggagttttgaggaaCtgggatctctgtccagaaaa	11	11	13	6	1	1	2	0	1	1	1	3	6	2	5	1	3	2	1	1	3	3	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr16:20787239C>T	ENST00000289416.5	+	3	773	c.298C>T	c.(298-300)Ctg>Ttg	p.L100L	ACSM3_ENST00000450120.2_Silent_p.L55L|ACSM3_ENST00000440284.2_Silent_p.L100L	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	100			L -> P (in dbSNP:rs5713).		cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						TTTTGAGGAACTGGGATCTCT	0.458																																					p.L100L		.											.	ACSM3-91	0			c.C298T						.						119	127	125					16																	20787239		2201	4300	6501	SO:0001819	synonymous_variant	6296	exon3			GAGGAACTGGGAT	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.298C>T	16.37:g.20787239C>T		Somatic	188	0		WXS	Illumina HiSeq	Phase_I	248	53	NM_005622	0	0	16	31	15	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Silent	SNP	ENST00000289416.5	37	CCDS10589.1																																																																																			.		0.458	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622		T	20787239	C	T	20787239	2	4	91	1	0	0	0	0	0	0	0	1	185	564	20	2		2	ACSM3	16	20787239	Silent	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	16758071	20787239	69567514	44	8259											
WDR81	124997	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	1631524	1631524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttccaagccgggctctatGtgactgagtctccccagccc	7	9	9	16	1	2	2	0	2	2	0	4	2	3	2	5	1	2	1	5	1	2	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:1631524G>A	ENST00000409644.1	+	1	3271	c.3271G>A	c.(3271-3273)Gtg>Atg	p.V1091M	WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Missense_Mutation_p.V40M	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1091					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGGGCTCTATGTGACTGAGTC	0.662																																					p.V1091M		.											.	WDR81-91	0			c.G3271A						.						38	45	43					17																	1631524		2202	4299	6501	SO:0001583	missense	124997	exon1			CTCTATGTGACTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3271G>A	17.37:g.1631524G>A	ENSP00000386609:p.Val1091Met	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	152	25	NM_001163809	0	0	18	18	0	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.473006	0.84640	.	.	ENSG00000167716	ENST00000309182;ENST00000409644;ENST00000354680	T;T	0.56103	2.09;0.48	5.65	5.65	0.86999	.	0.060024	0.64402	D	0.000003	T	0.65481	0.2695	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	T	0.67589	-0.5632	10	0.87932	D	0	.	19.7221	0.96147	0.0:0.0:1.0:0.0	.	218;40	Q8TEL1;Q562E7	.;WDR81_HUMAN	M	40;1091;40	ENSP00000312074:V40M;ENSP00000386609:V1091M	ENSP00000312074:V40M	V	+	1	0	WDR81	1578274	1.000000	0.71417	0.962000	0.40283	0.655000	0.38815	9.327000	0.96396	2.679000	0.91253	0.655000	0.94253	GTG	.		0.662	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		A	1631524	G	A	1631524	3	1	91	1	0	0	0	0	1	0	0	0	17363	1377	48	2	3335	2	WDR81	17	1631524	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		1631524	79563686	45	8260											
PELP1	27043	hgsc.bcm.edu	37	chr17	4575451	4575451	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcatcctcctcttcttcTtcttcctctaactcaccttc	4	18	0	19	0	7	0	2	0	5	0	12	0	11	0	5	0	1	0	5	0	1	6	rs371486511	byFrequency	TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:4575451T>C	ENST00000574876.1	-	16	2852	c.2835A>G	c.(2833-2835)gaA>gaG	p.E945E	PELP1_ENST00000301396.4_Silent_p.E1089E|PELP1_ENST00000269230.7_Silent_p.E855E|PELP1_ENST00000572293.1_Silent_p.E995E|PELP1_ENST00000436683.2_Silent_p.E798E			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	945	Glu-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						cctcttcttcttcttcctcta	0.473													T|||	6	0.00119808	0.0045	0	5008	,	,		16232	0		0	False		,,,				2504	0				p.E945E		.											.	PELP1-24	0			c.A2835G						.	T		25,4097		0,25,2036	59	61	61		2835	-1.2	1	17		61	0,8276		0,0,4138	no	coding-synonymous	PELP1	NM_014389.2		0,25,6174	CC,CT,TT		0.0,0.6065,0.2016		945/1131	4575451	25,12373	2061	4138	6199	SO:0001819	synonymous_variant	27043	exon16			TTCTTCTTCTTCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2835A>G	17.37:g.4575451T>C		Somatic	6	2		WXS	Illumina HiSeq	Phase_I	9	4	NM_014389	0	0	33	98	65	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			.		0.473	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		C	4575451	T	C	4575451	2	2	91	1	0	0	0	0	0	0	0	1	11751	1606	56	3		3	PELP1	17	4575451	Silent	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	2943927	4575451	76619759	46	8261											
RNF167	26001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4848277	4848277	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttcaacagatcccccacTgtcccctccctcttcccctg	5	10	4	22	0	2	1	1	0	1	1	6	1	6	1	8	0	1	0	8	0	1	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:4848277T>C	ENST00000262482.6	+	10	1675	c.1019T>C	c.(1018-1020)cTg>cCg	p.L340P	RNF167_ENST00000576229.1_Missense_Mutation_p.L305P|RNF167_ENST00000575111.1_Missense_Mutation_p.L340P|RNF167_ENST00000571816.1_Missense_Mutation_p.L340P|RNF167_ENST00000572430.1_Missense_Mutation_p.L340P	NM_015528.1	NP_056343.1	Q9H6Y7	RN167_HUMAN	ring finger protein 167	340					negative regulation of cell cycle (GO:0045786)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(1)	4						GATCCCCCACTGTCCCCTCCC	0.552																																					p.L340P		.											.	RNF167-226	0			c.T1019C						.						178	184	182					17																	4848277		2203	4300	6503	SO:0001583	missense	26001	exon10			CCCCACTGTCCCC	AL050060	CCDS11060.1	17p13.3	2013-02-21			ENSG00000108523	ENSG00000108523		"RING-type (C3HC4) zinc fingers"	24544	protein-coding gene	gene with protein product		610431				23129617, 23353890	Standard	NM_015528		Approved	DKFZP566H073	uc002fzs.3	Q9H6Y7	OTTHUMG00000099397	ENST00000262482.6:c.1019T>C	17.37:g.4848277T>C	ENSP00000262482:p.Leu340Pro	Somatic	309	1		WXS	Illumina HiSeq	Phase_I	450	100	NM_015528	0	0	363	470	107	D3DTK8|Q6XYE0|Q8NDC1|Q9Y3V1	Missense_Mutation	SNP	ENST00000262482.6	37	CCDS11060.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237518	0.39498	.	.	ENSG00000108523	ENST00000262482	T	0.03772	3.81	4.54	4.54	0.55810	.	0.650642	0.14127	N	0.339643	T	0.02193	0.0068	N	0.01874	-0.695	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45614	-0.9249	10	0.29301	T	0.29	-1.1064	8.9285	0.35655	0.0:0.897:0.0:0.103	.	148;340	Q9Y4L6;Q9H6Y7	.;RN167_HUMAN	P	340	ENSP00000262482:L340P	ENSP00000262482:L340P	L	+	2	0	RNF167	4789022	0.041000	0.20044	0.029000	0.17559	0.015000	0.08874	2.010000	0.40913	1.285000	0.44548	-0.226000	0.12346	CTG	.		0.552	RNF167-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216854.3	NM_015528		C	4848277	T	C	4848277	3	2	91	1	0	0	0	0	1	0	0	0	13490	1580	55	3	1053	3	RNF167	17	4848277	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	272826	4848277	76346933	47	8262											
KIF1C	10749	ucsc.edu	37	chr17	4908297	4908297	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcctctgctctggaaggTcgaggttccagggaggggca	7	8	16	10	1	3	0	1	0	2	0	5	3	4	2	2	6	2	3	2	6	1	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:4908297T>C	ENST00000320785.5	+	13	1522		c.e13+2			NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C						ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						CTCTGGAAGGTCGAGGTTCCA	0.637																																					.	Melanoma(96;1023 1447 10250 19259 33730)												.	KIF1C-92	0			c.1165+2T>C						.						82	87	85					17																	4908297		2203	4300	6503	SO:0001630	splice_region_variant	10749	exon13			GGAAGGTCGAGGT	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"Kinesins"	6317	protein-coding gene	gene with protein product		603060	"spastic ataxia 2 (autosomal recessive)"	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.1165+2T>C	17.37:g.4908297T>C		Somatic	155	1		WXS	Illumina HiSeq		210	1	NM_006612	0	0	0	0	0	D3DTL6|O75186|Q5U618	Splice_Site	SNP	ENST00000320785.5	37	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.488597	0.44249	.	.	ENSG00000129250	ENST00000320785	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6038	0.62035	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIF1C	4849021	0.998000	0.40836	0.965000	0.40720	0.282000	0.26991	2.684000	0.46951	2.158000	0.67659	0.533000	0.62120	.	.		0.637	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		Intron	C	4908297	T	C	4908297	5	2	91	1	0	0	0	0	0	0	1	0	8306	1681	58	3	1209	3	KIF1C	17	4908297	Splice_Site	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	60020	4908297	76286913	48	8263											
SLC16A11	162515	hgsc.bcm.edu	37	chr17	6946083	6946083	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccagggcccaaccaaagcCtgcgaatgaataggagggga	14	3	13	11	1	0	1	0	1	0	0	0	4	0	3	4	4	3	0	4	4	5	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:6946083C>T	ENST00000308009.1	-	3	756		c.e3-1		SLC16A11_ENST00000447225.1_Splice_Site	NM_153357.1	NP_699188.1	Q8NCK7	MOT11_HUMAN	solute carrier family 16, member 11						lipid metabolic process (GO:0006629)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(2)|ovary(1)|skin(2)	9						CAACCAAAGCCTGCGAATGAA	0.706																																					.		.											.	SLC16A11-91	0			c.419-1G>A						.						3	4	3					17																	6946083		1887	3795	5682	SO:0001630	splice_region_variant	162515	exon4			CAAAGCCTGCGAA	AK074674	CCDS11086.1	17p13.2	2013-07-18	2013-07-18		ENSG00000174326	ENSG00000174326		"Solute carriers"	23093	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 11"	615765	"solute carrier family 16 (monocarboxylic acid transporters), member 11"				Standard	NM_153357		Approved	FLJ90193, MCT11	uc002gei.1	Q8NCK7	OTTHUMG00000102087	ENST00000308009.1:c.419-1G>A	17.37:g.6946083C>T		Somatic	8	2		WXS	Illumina HiSeq	Phase_I	13	9	NM_153357	0	0	0	0	0		Splice_Site	SNP	ENST00000308009.1	37	CCDS11086.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021913	0.54576	.	.	ENSG00000174326	ENST00000308009;ENST00000447225	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6075	0.76685	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC16A11	6886807	1.000000	0.71417	1.000000	0.80357	0.628000	0.37860	7.058000	0.76676	2.539000	0.85634	0.561000	0.74099	.	.		0.706	SLC16A11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219921.1	NM_153357	Intron	T	6946083	C	T	6946083	5	4	91	1	0	0	0	0	0	0	1	0	14436	695	24	2	1005	2	SLC16A11	17	6946083	Splice_Site	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	2037786	6946083	74249127	49	8264											
MYO19	80179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34871758	34871758	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttctatcctctctgcaaTcttgtggctctcccaagatg	6	15	7	13	0	4	1	0	0	4	1	7	1	5	1	2	1	1	3	2	1	3	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:34871758T>C	ENST00000431794.3	-	7	1012	c.490A>G	c.(490-492)Att>Gtt	p.I164V	MYO19_ENST00000268852.9_Missense_Mutation_p.I164V|MYO19_ENST00000544606.1_Missense_Mutation_p.I30V|MYO19_ENST00000586007.1_Missense_Mutation_p.I164V	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	164	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CTCTCTGCAATCTTGTGGCTC	0.522																																					p.I164V		.											.	MYO19-23	0			c.A490G						.						78	81	80					17																	34871758		1998	4151	6149	SO:0001583	missense	80179	exon8			CTGCAATCTTGTG	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"Myosins / Myosin superfamily : Class XIX"	26234	protein-coding gene	gene with protein product			"myosin head domain containing 1"	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.490A>G	17.37:g.34871758T>C	ENSP00000409936:p.Ile164Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	74	13	NM_001163735	0	0	21	32	11	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	T	4.263	0.047870	0.08243	.	.	ENSG00000141140	ENST00000431794;ENST00000268852;ENST00000544606	D;D;D	0.87103	-2.21;-2.21;-2.21	5.72	1.64	0.23874	Myosin head, motor domain (2);	0.524811	0.15805	N	0.243761	T	0.68632	0.3022	N	0.02736	-0.51	0.24560	N	0.993978	B;B;B;B	0.15473	0.0;0.0;0.0;0.013	B;B;B;B	0.12837	0.003;0.002;0.0;0.008	T	0.56679	-0.7939	10	0.30078	T	0.28	.	9.161	0.37023	0.0:0.3696:0.0:0.6304	.	30;164;164;164	B4DSL5;Q96H55;Q96H55-2;Q96H55-4	.;MYO19_HUMAN;.;.	V	164;164;30	ENSP00000409936:I164V;ENSP00000268852:I164V;ENSP00000438365:I30V	ENSP00000268852:I164V	I	-	1	0	MYO19	31945871	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.767000	0.38501	0.098000	0.17522	0.383000	0.25322	ATT	.		0.522	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		C	34871758	T	C	34871758	3	2	91	1	0	0	0	0	1	0	0	0	10092	1435	50	3	2562	3	MYO19	17	34871758	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	27925675	34871758	46323452	50	8265											
DGKE	8526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	54926211	54926211	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagatggaattaaactagAtcggtaagttacgtttcccc	13	11	9	8	2	0	2	0	0	0	2	2	3	1	3	2	2	3	4	2	2	6	5			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:54926211A>G	ENST00000284061.3	+	6	1223	c.1043A>G	c.(1042-1044)gAt>gGt	p.D348G		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	348	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ATTAAACTAGATCGGTAAGTT	0.378																																					p.D348G		.											.	DGKE-289	0			c.A1043G						.						118	114	115					17																	54926211		2203	4300	6503	SO:0001583	missense	8526	exon6			AACTAGATCGGTA	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"diacylglycerol kinase, epsilon (64kD)"			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1043A>G	17.37:g.54926211A>G	ENSP00000284061:p.Asp348Gly	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	112	26	NM_003647	0	0	0	0	0	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	37	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.750777	0.89753	.	.	ENSG00000153933	ENST00000284061	T	0.60672	0.17	5.59	5.59	0.84812	Diacylglycerol kinase, catalytic domain (3);	0.090430	0.85682	D	0.000000	T	0.81692	0.4876	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86463	0.1780	10	0.87932	D	0	.	15.7661	0.78128	1.0:0.0:0.0:0.0	.	348;348	A1L4Q0;P52429	.;DGKE_HUMAN	G	348	ENSP00000284061:D348G	ENSP00000284061:D348G	D	+	2	0	DGKE	52281210	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	8.532000	0.90613	2.134000	0.65973	0.460000	0.39030	GAT	.		0.378	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		G	54926211	A	G	54926211	3	3	91	1	0	0	0	0	1	0	0	0	4479	333	12	3	1061	3	DGKE	17	54926211	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	20054453	54926211	26268999	51	8266											
SLC14A2	8170	broad.mit.edu	37	chr18	43262338	43262338	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctcagctctcaccttcctgCtcctgacgaccaataacccc	8	10	4	19	1	2	1	2	1	2	0	6	2	4	1	6	0	3	2	6	0	2	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr18:43262338C>T	ENST00000255226.6	+	20	3433	c.2617C>T	c.(2617-2619)Ctc>Ttc	p.L873F	SLC14A2_ENST00000586448.1_Missense_Mutation_p.L873F|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A2_ENST00000589658.1_Missense_Mutation_p.L350F	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	873					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CACCTTCCTGCTCCTGACGAC	0.552																																					p.L873F													.	SLC14A2-93	0			c.C2617T						.						303	291	295					18																	43262338		2203	4300	6503	SO:0001583	missense	8170	exon21			TTCCTGCTCCTGA	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"Solute carriers"	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.2617C>T	18.37:g.43262338C>T	ENSP00000255226:p.Leu873Phe	Somatic	514	0		WXS	Illumina HiSeq	Phase_I	530	7	NM_001242692	0	0	0	0	0	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691313	0.68271	.	.	ENSG00000132874	ENST00000255226	T	0.57907	0.37	5.26	2.07	0.26955	.	0.132563	0.32055	N	0.006652	T	0.70254	0.3203	M	0.85373	2.75	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.70498	-0.4855	10	0.59425	D	0.04	-26.1111	8.5057	0.33186	0.0:0.6152:0.0:0.3848	.	873	Q15849	UT2_HUMAN	F	873	ENSP00000255226:L873F	ENSP00000255226:L873F	L	+	1	0	SLC14A2	41516336	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.678000	0.25277	0.611000	0.30052	0.561000	0.74099	CTC	.		0.552	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			T	43262338	C	T	43262338	3	4	91	1	0	0	0	0	1	0	0	0	14429	797	28	2	2691	2	SLC14A2	18	43262338	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		43262338	34814910	52	8267											
ZNF407	55628	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	72344119	72344120	+	Frame_Shift_Ins	INS	-	-	TA																															tgaaaaccagagtagaaagcINStagacaccttagtaacctca																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr18:72344119_72344120insTA	ENST00000299687.5	+	1	1144_1145	c.1144_1145insTA	c.(1144-1146)ctafs	p.L382fs	ZNF407_ENST00000582337.1_Frame_Shift_Ins_p.L382fs|ZNF407_ENST00000577538.1_Frame_Shift_Ins_p.L382fs|ZNF407_ENST00000309902.6_Frame_Shift_Ins_p.L382fs	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAGTAGAAAGCTAGACACCTTA	0.431																																					p.L382fs		.											.	ZNF407-92	0			c.1144_1145insTA						.																																			SO:0001589	frameshift_variant	55628	exon1			.	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1145_1146dupTA	18.37:g.72344120_72344121dupTA	ENSP00000299687:p.Leu382fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	94	26	NM_001146190	0	0	0	0	0	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Frame_Shift_Ins	INS	ENST00000299687.5	37	CCDS45885.1																																																																																			.		0.431	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		TA	72344120	-	TA	72344119	7	5	91	1	0	1	1	0	0	0	0	0	17919	796	28	0	1146	0	ZNF407	18	72344119	Frame_Shift_Ins	INS	-	TCGA-BQ-7062-01A-11D-1961-08	29081781	72344119	5733129	53	8268											
STAP2	55620	hgsc.bcm.edu;broad.mit.edu	37	chr19	4328673	4328673	+	Splice_Site	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagacgcgcatgcgcaccCgttgtgcatctgccgcgtgg	5	8	13	15	6	1	1	0	0	1	1	2	1	2	1	3	1	3	4	3	1	0	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr19:4328673C>G	ENST00000594605.1	-	6	712	c.589G>C	c.(589-591)Ggg>Cgg	p.G197R	STAP2_ENST00000600324.1_Splice_Site_p.G197R|STAP2_ENST00000597593.1_5'Flank	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	197	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CATGCGCACCCGTTGTGCATC	0.726																																					p.G197R		.											.	STAP2-90	0			c.G589C						.						12	13	12					19																	4328673		2187	4277	6464	SO:0001630	splice_region_variant	55620	exon6			CGCACCCGTTGTG	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.590+1G>C	19.37:g.4328673C>G		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_001013841	0	0	0	0	0	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	37	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017070	0.35606	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	4.47	3.42	0.39159	SH2 motif (3);	0.167039	0.37261	N	0.002172	T	0.62196	0.2408	M	0.77103	2.36	0.43160	D	0.99494	B;B	0.28258	0.205;0.119	B;B	0.29176	0.066;0.099	T	0.64605	-0.6368	9	0.87932	D	0	-9.4374	10.5452	0.45056	0.0:0.9014:0.0:0.0986	.	197;197	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	R	197	.	ENSP00000317912:G197R	G	-	1	0	STAP2	4279673	0.703000	0.27826	0.790000	0.31976	0.373000	0.29922	1.145000	0.31577	0.866000	0.35629	0.479000	0.44913	GGG	.		0.726	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	Missense_Mutation	G	4328673	C	G	4328673	5	3	91	1	0	0	0	0	0	0	1	0	15285	666	23	4	792	4	STAP2	19	4328673	Splice_Site	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		4328673	54800310	54	8269											
ACER1	125981	broad.mit.edu	37	chr19	6312191	6312191	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaaggaggggaaatagcAgcggggcatccatatgctat	14	6	15	6	1	0	0	0	0	0	0	1	3	1	3	1	6	3	3	1	6	6	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr19:6312191A>G	ENST00000301452.4	-	3	396	c.319T>C	c.(319-321)Tgc>Cgc	p.C107R		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	107					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						GGGAAATAGCAGCGGGGCATC	0.587																																					p.C107R													.	ACER1-90	0			c.T319C						.						45	39	41					19																	6312191		2203	4300	6503	SO:0001583	missense	125981	exon3			AATAGCAGCGGGG	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.319T>C	19.37:g.6312191A>G	ENSP00000301452:p.Cys107Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	63	8	NM_133492	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301452.4	37	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	A	8.924	0.961735	0.18583	.	.	ENSG00000167769	ENST00000301452	T	0.39406	1.08	5.13	4.04	0.47022	.	0.457935	0.25555	N	0.029861	T	0.16085	0.0387	N	0.05534	-0.03	0.52099	D	0.999949	B	0.14438	0.01	B	0.15052	0.012	T	0.15578	-1.0432	10	0.05959	T	0.93	-55.431	3.9493	0.09361	0.7184:0.0:0.097:0.1846	.	107	Q8TDN7	ACER1_HUMAN	R	107	ENSP00000301452:C107R	ENSP00000301452:C107R	C	-	1	0	ACER1	6263191	0.998000	0.40836	1.000000	0.80357	0.672000	0.39443	2.111000	0.41883	1.934000	0.56057	0.402000	0.26972	TGC	.		0.587	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		G	6312191	A	G	6312191	3	3	91	1	0	0	0	0	1	0	0	0	138	188	7	3	491	3	ACER1	19	6312191	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	1983518	6312191	52816792	55	8270											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	150	0		WXS	Illumina HiSeq		132	1	NM_031203	0	0	0	0	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	91	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	2215276	8527467	50601516	56	8271											
PPP1R16B	26051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37536822	37536822	+	Nonsense_Mutation	SNP	G	G	T																															gggagaccaggacagaccaaGagaataaggaccctgtgagt																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:37536822G>T	ENST00000299824.1	+	10	1369	c.1180G>T	c.(1180-1182)Gag>Tag	p.E394*	PPP1R16B_ENST00000373331.2_Nonsense_Mutation_p.E352*	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	394					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				GACAGACCAAGAGAATAAGGA	0.607																																					p.E394X		.											.	PPP1R16B-228	0			c.G1180T						.						88	81	84					20																	37536822		2203	4300	6503	SO:0001587	stop_gained	26051	exon10			GACCAAGAGAATA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	15850	protein-coding gene	gene with protein product	"TGF-beta-inhibited membrane-associated protein", "ankyrin repeat domain protein 4"	613275	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1180G>T	20.37:g.37536822G>T	ENSP00000299824:p.Glu394*	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	84	14	NM_015568	0	0	0	0	0	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Nonsense_Mutation	SNP	ENST00000299824.1	37	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.556183|7.556183	0.98355|0.98355	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000299824;ENST00000373331|ENST00000438192	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.154659|.	0.56097|.	D|.	0.000027|.	.|T	.|0.71341	.|0.3328	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68953	.|-0.5273	.|4	0.34782|.	T|.	0.22|.	.|.	14.8843|14.8843	0.70555|0.70555	0.0:0.0:0.8566:0.1433|0.0:0.0:0.8566:0.1433	.|.	.|.	.|.	.|.	X|N	394;352|294	.|.	ENSP00000299824:E394X|.	E|K	+|+	1|3	0|2	PPP1R16B|PPP1R16B	36970236|36970236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.369000|6.369000	0.73109|0.73109	2.771000|2.771000	0.95319|0.95319	0.644000|0.644000	0.83932|0.83932	GAG|AAG	.		0.607	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568		T	37536822	G	T	37536822	4	4	91	1	0	0	0	0	0	1	0	0	12395	943	33	4	1214	4	PPP1R16B	20	37536822	Nonsense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		37536822	25488698	57	8272	91	2									
PPP1R16B	26051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37536828	37536828	+	Missense_Mutation	SNP	A	A	G																															ccaggacagaccaagagaatAaggaccctgtgagtggcctc																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:37536828A>G	ENST00000299824.1	+	10	1375	c.1186A>G	c.(1186-1188)Aag>Gag	p.K396E	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.K354E	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	396					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				CCAAGAGAATAAGGACCCTGT	0.607																																					p.K396E		.											.	PPP1R16B-228	0			c.A1186G						.						82	77	79					20																	37536828		2203	4300	6503	SO:0001583	missense	26051	exon10			GAGAATAAGGACC	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	15850	protein-coding gene	gene with protein product	"TGF-beta-inhibited membrane-associated protein", "ankyrin repeat domain protein 4"	613275	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1186A>G	20.37:g.37536828A>G	ENSP00000299824:p.Lys396Glu	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	73	12	NM_015568	0	0	0	0	0	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	37	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.38|13.38	2.219266|2.219266	0.39201|0.39201	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.70869	.|-0.31;-0.52	5.79|5.79	4.7|4.7	0.59300|0.59300	.|.	.|0.210830	.|0.50627	.|D	.|0.000114	T|T	0.54806|0.54806	0.1881|0.1881	L|L	0.36672|0.36672	1.1|1.1	0.25150|0.25150	N|N	0.990439|0.990439	.|B;B	.|0.19445	.|0.017;0.036	.|B;B	.|0.20767	.|0.007;0.031	T|T	0.36163|0.36163	-0.9759|-0.9759	5|10	.|0.07990	.|T	.|0.79	.|.	9.383|9.383	0.38325|0.38325	0.8649:0.0:0.1351:0.0|0.8649:0.0:0.1351:0.0	.|.	.|354;396	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	M|E	296|396;354	.|ENSP00000299824:K396E;ENSP00000362428:K354E	.|ENSP00000299824:K396E	I|K	+|+	3|1	3|0	PPP1R16B|PPP1R16B	36970242|36970242	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	4.056000|4.056000	0.57448|0.57448	2.236000|2.236000	0.73375|0.73375	0.524000|0.524000	0.50904|0.50904	ATA|AAG	.		0.607	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568		G	37536828	A	G	37536828	3	3	91	1	0	0	0	0	1	0	0	0	12395	363	13	3	1220	3	PPP1R16B	20	37536828	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	6	37536828	25488692	58	8273	91	2									
ADA	100	broad.mit.edu;bcgsc.ca	37	chr20	43264929	43264929	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taggtggacatgcagttccaCctgcaagggggcagggggaa	10	6	17	8	0	0	0	0	0	0	0	1	2	1	2	2	6	2	4	2	6	3	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:43264929C>T	ENST00000372874.4	-	2	168	c.34G>A	c.(34-36)Gtg>Atg	p.V12M	ADA_ENST00000537820.1_Splice_Site_p.V12M	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	12					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	TGCAGTTCCACCTGCAAGGGG	0.473									Adenosine Deaminase Deficiency																												p.V12M													.	ADA-653	0			c.G34A						.						59	48	52					20																	43264929		2203	4300	6503	SO:0001630	splice_region_variant	100	exon2	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	GTTCCACCTGCAA	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.34-1G>A	20.37:g.43264929C>T		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	24	5	NM_000022	0	0	0	0	0	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	37	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.555611	0.65425	.	.	ENSG00000196839	ENST00000372874;ENST00000537820	D;D	0.96459	-4.02;-4.02	5.93	5.93	0.95920	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.98375	0.9460	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98920	1.0783	10	0.72032	D	0.01	-34.6306	18.5243	0.90965	0.0:1.0:0.0:0.0	.	12	P00813	ADA_HUMAN	M	12	ENSP00000361965:V12M;ENSP00000441818:V12M	ENSP00000361965:V12M	V	-	1	0	ADA	42698343	1.000000	0.71417	0.996000	0.52242	0.112000	0.19704	5.987000	0.70571	2.815000	0.96918	0.561000	0.74099	GTG	.		0.473	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	Missense_Mutation	T	43264929	C	T	43264929	5	4	91	1	0	0	0	0	0	0	1	0	230	521	18	2	1101	2	ADA	20	43264929	Splice_Site	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	5728101	43264929	19760591	59	8274											
APOL6	80830	hgsc.bcm.edu	37	chr22	36055619	36055619	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgtgtgtgtgtctgtgtgtCtgtgtgtatgtacagtttac	4	19	13	5	0	2	0	0	0	2	0	2	0	2	0	0	0	2	3	0	0	3	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr22:36055619C>G	ENST00000409652.4	+	3	1284	c.1008C>G	c.(1006-1008)gtC>gtG	p.V336V		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	336					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						gtctgtgtgtctgtgtgtatg	0.483																																					p.V336V		.											.	APOL6-90	0			c.C1008G						.						94	61	72					22																	36055619		2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			GTGTGTCTGTGTG	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"Apolipoproteins"	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.1008C>G	22.37:g.36055619C>G		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	32	3	NM_030641	0	0	11	11	0	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	37	CCDS13919.1																																																																																			.		0.483	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		G	36055619	C	G	36055619	2	3	91	1	0	0	0	0	0	0	0	1	810	900	32	4		4	APOL6	22	36055619	Silent	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		36055619	15248947	60	8275											
MICALL1	85377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38313744	38313744	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccacccagaaagggccttgCaccctgttccccgccgtctg	6	7	10	18	2	1	1	0	0	1	1	2	1	2	1	7	1	1	2	7	1	1	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr22:38313744C>T	ENST00000215957.6	+	4	494	c.368C>T	c.(367-369)gCa>gTa	p.A123V		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	123					endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					AAGGGCCTTGCACCCTGTTCC	0.622																																					p.A123V		.											.	MICALL1-153	0			c.C368T						.						80	66	71					22																	38313744		2203	4300	6503	SO:0001583	missense	85377	exon4			GCCTTGCACCCTG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.368C>T	22.37:g.38313744C>T	ENSP00000215957:p.Ala123Val	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	117	28	NM_033386	0	0	13	22	9	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.105894	0.37145	.	.	ENSG00000100139	ENST00000445494;ENST00000215957	T;T	0.73363	-0.74;0.52	3.8	2.78	0.32641	.	0.408833	0.20490	N	0.091317	T	0.55986	0.1955	N	0.19112	0.55	0.19775	N	0.999952	B	0.06786	0.001	B	0.06405	0.002	T	0.48833	-0.9000	10	0.48119	T	0.1	.	7.2373	0.26077	0.0:0.8793:0.0:0.1207	.	123	Q8N3F8	MILK1_HUMAN	V	39;123	ENSP00000404543:A39V;ENSP00000215957:A123V	ENSP00000215957:A123V	A	+	2	0	MICALL1	36643690	0.000000	0.05858	0.005000	0.12908	0.609000	0.37215	0.091000	0.15046	1.176000	0.42840	0.455000	0.32223	GCA	.		0.622	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		T	38313744	C	T	38313744	3	4	91	1	0	0	0	0	1	0	0	0	9598	710	25	2	382	2	MICALL1	22	38313744	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	2258125	38313744	12990822	61	8276											
MAOA	4128	ucsc.edu	37	chrX	43515619	43515619	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caagagaaggcgagtatcgcGggccacatgttcgacgtagt	11	7	14	9	5	0	1	0	0	0	1	2	4	0	1	1	2	0	3	1	2	4	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chrX:43515619G>A	ENST00000338702.3	+	1	153	c.30G>A	c.(28-30)gcG>gcA	p.A10A	MAOA_ENST00000542639.1_5'UTR|MAOA_ENST00000497485.1_3'UTR	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	10					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	CGAGTATCGCGGGCCACATGT	0.607																																					p.A10A													.	MAOA-194	0			c.G30A						.						139	80	100					X																	43515619		2203	4300	6503	SO:0001819	synonymous_variant	4128	exon1			TATCGCGGGCCAC		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.30G>A	X.37:g.43515619G>A		Somatic	33	0		WXS	Illumina HiSeq		34	4	NM_000240	0	0	19	19	0	B4DF46|Q16426	Silent	SNP	ENST00000338702.3	37	CCDS14260.1																																																																																			.		0.607	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		A	43515619	G	A	43515619	2	1	91	1	0	0	0	0	0	0	0	1	9250	1103	39	1		1	MAOA	23	43515619	Silent	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		43515619	111754941	62	8277											
MORC4	79710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	106201626	106201626	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggtaacatggatggatcaAtcttcccaggaagctttctc	11	11	9	10	0	3	0	1	0	2	0	5	3	4	3	1	4	2	2	1	4	3	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chrX:106201626A>G	ENST00000355610.4	-	11	1599	c.1325T>C	c.(1324-1326)aTt>aCt	p.I442T	MORC4_ENST00000255495.7_Missense_Mutation_p.I442T|MORC4_ENST00000535534.1_Missense_Mutation_p.I190T	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	442						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						GGATGGATCAATCTTCCCAGG	0.423																																					p.I442T		.											.	MORC4-131	0			c.T1325C						.						132	111	118					X																	106201626		2203	4300	6503	SO:0001583	missense	79710	exon11			GGATCAATCTTCC	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 2", "zinc finger, CW type with coiled-coil domain 2"	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1325T>C	X.37:g.106201626A>G	ENSP00000347821:p.Ile442Thr	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	59	32	NM_001085354	0	0	5	10	5	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	A	11.41	1.630627	0.28978	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.30981	2.76;1.51;2.75	5.93	5.93	0.95920	Zinc finger, CW-type (2);	0.519296	0.19062	N	0.123746	T	0.27278	0.0669	L	0.37466	1.105	0.24268	N	0.995258	B;B;B	0.26975	0.165;0.042;0.042	B;B;B	0.28385	0.089;0.055;0.055	T	0.26815	-1.0092	10	0.72032	D	0.01	-5.7895	11.5626	0.50785	1.0:0.0:0.0:0.0	.	190;442;442	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	T	442;190;442	ENSP00000347821:I442T;ENSP00000440359:I190T;ENSP00000255495:I442T	ENSP00000255495:I442T	I	-	2	0	MORC4	106088282	0.305000	0.24481	0.911000	0.35937	0.454000	0.32378	1.929000	0.40114	2.004000	0.58718	0.441000	0.28932	ATT	.		0.423	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657		G	106201626	A	G	106201626	3	3	91	1	0	0	0	0	1	0	0	0	9729	101	4	3	1516	3	MORC4	23	106201626	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	62686007	106201626	49068934	63	8278											
UBE4B	10277	broad.mit.edu;bcgsc.ca	37	chr1	10177626	10177626	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcatcgagtgtttcgacCgagttggaatagaggaaaaa	14	9	11	7	3	1	1	1	0	0	1	3	6	1	3	2	2	0	2	2	2	4	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:10177626C>A	ENST00000253251.8	+	7	1758	c.919C>A	c.(919-921)Cga>Aga	p.R307R	UBE4B_ENST00000343090.6_Silent_p.R436R|UBE4B_ENST00000377157.3_Silent_p.R191R|UBE4B_ENST00000475795.1_3'UTR					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GTGTTTCGACCGAGTTGGAAT	0.393																																					p.R436R													.	UBE4B-229	0			c.C1306A						.						63	62	62					1																	10177626		2203	4300	6503	SO:0001819	synonymous_variant	10277	exon8			TTCGACCGAGTTG	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"U-box domain containing"	12500	protein-coding gene	gene with protein product		613565	"ubiquitination factor E4B (homologous to yeast UFD2)", "ubiquitination factor E4B (UFD2 homolog, yeast)"			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.919C>A	1.37:g.10177626C>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	50	5	NM_001105562	0	0	2	2	0		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			.		0.393	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		A	10177626	C	A	10177626	2	1	92	1	0	0	0	0	0	0	0	1	16916	644	23	4		4	UBE4B	1	10177626	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08		10177626	239072995	1	8279											
VPS13D	55187	bcgsc.ca	37	chr1	12387776	12387776	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtctctttccttggcctccAccagccgagatagcccaggg	7	9	10	15	1	1	1	0	0	1	1	4	2	3	1	6	2	2	0	6	2	1	3	rs201321059		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:12387776A>C	ENST00000358136.3	+	36	8192	c.8062A>C	c.(8062-8064)Acc>Ccc	p.T2688P	VPS13D_ENST00000356315.4_Missense_Mutation_p.T2688P	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CTTGGCCTCCACCAGCCGAGA	0.488																																					p.T2688P													.	VPS13D-95	0			c.A8062C						.						158	160	160					1																	12387776		2203	4300	6503	SO:0001583	missense	55187	exon36			GCCTCCACCAGCC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8062A>C	1.37:g.12387776A>C	ENSP00000350854:p.Thr2688Pro	Somatic	220	10		WXS	Illumina HiSeq	Phase_1	201	36	NM_015378	0	0	3	3	0		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	A	7.855	0.724729	0.15439	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.45276	0.9;0.9	5.51	-1.24	0.09435	.	1.281640	0.04635	N	0.404367	T	0.28167	0.0695	L	0.27053	0.805	0.09310	N	1	B;B;B	0.12013	0.0;0.005;0.003	B;B;B	0.19666	0.0;0.026;0.012	T	0.16424	-1.0403	9	.	.	.	.	5.2921	0.15733	0.3598:0.2951:0.3451:0.0	.	595;2688;2688	B1AJZ2;Q5THJ4-2;Q5THJ4	.;.;VP13D_HUMAN	P	2688	ENSP00000348666:T2688P;ENSP00000350854:T2688P	.	T	+	1	0	VPS13D	12310363	0.000000	0.05858	0.000000	0.03702	0.253000	0.25986	-0.083000	0.11286	-0.389000	0.07786	0.533000	0.62120	ACC	.		0.488	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12387776	A	C	12387776	3	2	92	1	0	0	0	0	1	0	0	0	17225	159	6	5	8200	5	VPS13D	1	12387776	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	2210150	12387776	236862845	2	8280											
FGGY	55277	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	60133071	60133091	+	Splice_Site	DEL	TACTGGTAAGTCTGGGAAAGA	TACTGGTAAGTCTGGGAAAGA	-																															gtgcaaatgcatgcggacatTactggtaagtctgggaaaga																								rs115318188	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	TACTGGTAAGTCTGGGAAAGA	TACTGGTAAGTCTGGGAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:60133071_60133091delTACTGGTAAGTCTGGGAAAGA	ENST00000303721.7	+	13	1587_1591	c.1413_1417delTACTGGTAAGTCTGGGAAAGA	c.(1411-1419)attactggt>atgt	p.471_473ITG>M	FGGY_ENST00000371210.1_Splice_Site_p.172_174ITG>M|FGGY_ENST00000371218.4_Splice_Site_p.495_497ITG>M|FGGY_ENST00000371212.1_Splice_Site_p.383_385ITG>M	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	471					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.G361C(1)|p.G473C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					ATGCGGACATTACTGGTAAGTCTGGGAAAGAGGAGAGAAGG	0.466																																					p.495_497del		.											.	FGGY-69	2	Substitution - Missense(2)	lung(2)	c.1485_1489del						.																																			SO:0001630	splice_region_variant	55277	exon14			.		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1417+1TACTGGTAAGTCTGGGAAAGA>-	1.37:g.60133071_60133091delTACTGGTAAGTCTGGGAAAGA		Somatic	240	0		WXS	Illumina HiSeq	Phase_I	123	29	NM_001113411	0	0	0	0	0	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Frame_Shift_Del	DEL	ENST00000303721.7	37	CCDS611.2																																																																																			.		0.466	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	In_Frame_Del	-	60133091	TACTGGTAAGTCTGGGAAAGA	-	60133071	8	5	92	1	0	1	0	1	0	0	1	0	5890	1742	61	0	1535	0	FGGY	1	60133071	Splice_Site	DEL	TACTGGTAAGTCTGGGAAAGA	TCGA-DW-5560-01A-01D-1589-08	47745295	60133071	189117550	3	8281											
C1orf173	127254	bcgsc.ca	37	chr1	75037375	75037375	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctccgtgtagaacttccAcagccacaacccttcctcct	9	9	4	19	1	0	1	0	0	0	1	4	1	4	1	7	0	3	1	7	0	3	3	rs139917611|rs78115948		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:75037375A>C	ENST00000326665.5	-	14	4237	c.4019T>G	c.(4018-4020)gTg>gGg	p.V1340G	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1340	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TAGAACTTCCACAGCCACAAC	0.547																																					p.V1340G													.	C1orf173-94	0			c.T4019G						.						223	211	215					1																	75037375		2203	4300	6503	SO:0001583	missense	127254	exon14			ACTTCCACAGCCA																												ENST00000326665.5:c.4019T>G	1.37:g.75037375A>C	ENSP00000322609:p.Val1340Gly	Somatic	163	3		WXS	Illumina HiSeq	Phase_1	115	18	NM_001002912	0	0	0	0	0	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	A	8.852	0.944804	0.18356	.	.	ENSG00000178965	ENST00000326665	T	0.11169	2.8	3.98	-2.34	0.06704	.	.	.	.	.	T	0.01421	0.0046	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.15484	0.013	T	0.47761	-0.9092	9	0.22109	T	0.4	1.3381	9.7524	0.40483	0.5201:0.0:0.0:0.4799	.	1340	Q5RHP9	CA173_HUMAN	G	1340	ENSP00000322609:V1340G	ENSP00000322609:V1340G	V	-	2	0	C1orf173	74809963	0.001000	0.12720	0.002000	0.10522	0.040000	0.13550	0.391000	0.20784	-0.236000	0.09753	-0.393000	0.06486	GTG	.		0.547	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			C	75037375	A	C	75037375	3	2	92	1	0	0	0	0	1	0	0	0	2020	159	6	5	577	5	C1orf173	1	75037375	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	14904304	75037375	174213246	4	8282											
FRRS1	391059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	100214268	100214268	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattgggataattagccacAtaactaatgtgcaacagaag	16	9	8	8	0	0	1	0	0	0	1	0	2	0	2	2	1	4	1	2	1	6	5			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:100214268A>G	ENST00000414213.1	-	3	658	c.57T>C	c.(55-57)taT>taC	p.Y19Y	FRRS1_ENST00000287474.5_Silent_p.Y19Y			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	19	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AATTAGCCACATAACTAATGT	0.378																																					p.Y19Y		.											.	FRRS1-91	0			c.T57C						.						154	132	139					1																	100214268		2203	4300	6503	SO:0001819	synonymous_variant	391059	exon3			AGCCACATAACTA	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"stromal cell derived factor receptor 2 homolog (mouse)"	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.57T>C	1.37:g.100214268A>G		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	107	38	NM_001013660	0	0	0	0	0	A6NLN7	Silent	SNP	ENST00000414213.1	37																																																																																				.		0.378	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		G	100214268	A	G	100214268	2	3	92	1	0	0	0	0	0	0	0	1	6079	224	8	3		3	FRRS1	1	100214268	Silent	SNP	A	TCGA-DW-5560-01A-01D-1589-08	25176893	100214268	149036353	5	8283											
ALX3	257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110604111	110604111	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtcataggcagccgtgaaGgggttccgcccctcctggat	7	9	13	12	2	1	1	1	1	0	0	3	2	3	2	5	4	1	2	5	4	2	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:110604111G>T	ENST00000369792.4	-	3	756	c.669C>A	c.(667-669)ccC>ccA	p.P223P	RP4-773N10.4_ENST00000554749.1_RNA|RP4-773N10.4_ENST00000596959.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	223					embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|pattern specification process (GO:0007389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		CAGCCGTGAAGGGGTTCCGCC	0.622																																					p.P223P		.											.	ALX3-90	0			c.C669A						.						79	78	78					1																	110604111		2203	4300	6503	SO:0001819	synonymous_variant	257	exon3			CGTGAAGGGGTTC	AF008203	CCDS819.1	1p13.3	2014-02-04	2008-11-04		ENSG00000156150	ENSG00000156150		"Homeoboxes / PRD class"	449	protein-coding gene	gene with protein product		606014	"aristaless-like homeobox 3", "frontonasal dysplasia"	FND		15226305, 11807986, 19409524	Standard	NM_006492		Approved		uc001dzb.3	O95076	OTTHUMG00000011650	ENST00000369792.4:c.669C>A	1.37:g.110604111G>T		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	101	34	NM_006492	0	0	7	7	0	O95075|Q5T8M4	Silent	SNP	ENST00000369792.4	37	CCDS819.1																																																																																			.		0.622	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492		T	110604111	G	T	110604111	2	4	92	1	0	0	0	0	0	0	0	1	557	987	35	4		4	ALX3	1	110604111	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08	10389843	110604111	138646510	6	8284											
FCRL1	115350	bcgsc.ca	37	chr1	157776893	157776893	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaaggaagtgcaactcaccGgcaggttcacagagtggagc	14	5	13	9	1	2	1	2	0	0	1	2	3	2	3	1	4	3	3	1	4	4	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:157776893G>A	ENST00000368176.3	-	2	118	c.51C>T	c.(49-51)gcC>gcT	p.A17A	FCRL1_ENST00000358292.3_Splice_Site_p.A17A|FCRL1_ENST00000489998.1_5'Flank|FCRL1_ENST00000491942.1_Splice_Site_p.A17A	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	17	Ig-like C2-type 1.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GCAACTCACCGGCAGGTTCAC	0.483																																					p.A17A	GBM(54;482 1003 11223 30131 35730)												.	FCRL1-153	0			c.C51T						.						73	70	71					1																	157776893		2203	4300	6503	SO:0001630	splice_region_variant	115350	exon2			CTCACCGGCAGGT	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.52+1C>T	1.37:g.157776893G>A		Somatic	119	0		WXS	Illumina HiSeq	Phase_1	50	4	NM_001159397	0	0	0	0	0	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			.		0.483	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	Silent	A	157776893	G	A	157776893	5	1	92	1	0	0	0	0	0	0	1	0	5813	1130	39	1	1344	1	FCRL1	1	157776893	Splice_Site	SNP	G	TCGA-DW-5560-01A-01D-1589-08	47172782	157776893	91473728	7	8285											
DSTYK	25778	hgsc.bcm.edu	37	chr1	205132867	205132867	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctacctgtttgagataattaCtggtgatgtgaactgagaca	12	13	10	6	0	0	4	0	4	0	2	0	6	0	4	1	1	3	1	1	1	4	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:205132867C>G	ENST00000367162.3	-	4	1571	c.1541G>C	c.(1540-1542)aGt>aCt	p.S514T	DSTYK_ENST00000367161.3_Missense_Mutation_p.S514T|DSTYK_ENST00000367160.4_Intron	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	514					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						GAGATAATTACTGGTGATGTG	0.433																																					p.S514T		.											.	DSTYK-333	0			c.G1541C						.						80	72	75					1																	205132867		2203	4300	6503	SO:0001583	missense	25778	exon4			TAATTACTGGTGA	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.1541G>C	1.37:g.205132867C>G	ENSP00000356130:p.Ser514Thr	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_199462	0	0	0	0	0	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	37	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245935	0.80024	.	.	ENSG00000133059	ENST00000367161;ENST00000367162	T;T	0.81163	-1.41;-1.46	5.8	5.8	0.92144	.	0.090598	0.85682	D	0.000000	D	0.84047	0.5386	L	0.35723	1.085	0.80722	D	1	D;D	0.63880	0.993;0.977	P;P	0.58454	0.839;0.751	D	0.83764	0.0216	10	0.49607	T	0.09	-13.2589	19.6644	0.95887	0.0:1.0:0.0:0.0	.	514;514	Q6XUX3-2;Q6XUX3	.;DUSTY_HUMAN	T	514	ENSP00000356129:S514T;ENSP00000356130:S514T	ENSP00000356129:S514T	S	-	2	0	DSTYK	203399490	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.108000	0.71522	2.758000	0.94735	0.563000	0.77884	AGT	.		0.433	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		G	205132867	C	G	205132867	3	3	92	1	0	0	0	0	1	0	0	0	4796	565	20	4	1288	4	DSTYK	1	205132867	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	47355974	205132867	44117754	8	8286											
ROCK2	9475	broad.mit.edu	37	chr2	11354553	11354553	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctttcgctagtaagattttgCcgttctttaaatcttcttct	7	20	5	9	2	4	1	0	0	4	1	5	1	4	1	1	0	1	3	1	0	4	10			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:11354553C>T	ENST00000315872.6	-	17	2421	c.1973G>A	c.(1972-1974)gGc>gAc	p.G658D	ROCK2_ENST00000401753.1_Missense_Mutation_p.G415D	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	658	Interaction with PPP1R12A.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TAAGATTTTGCCGTTCTTTAA	0.303																																					p.G658D													.	ROCK2-546	0			c.G1973A						.						113	103	106					2																	11354553		1798	4064	5862	SO:0001583	missense	9475	exon17			ATTTTGCCGTTCT	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.1973G>A	2.37:g.11354553C>T	ENSP00000317985:p.Gly658Asp	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	78	4	NM_004850	0	0	0	0	0	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405987	0.42715	.	.	ENSG00000134318	ENST00000315872;ENST00000401753;ENST00000399089	T;T	0.62232	0.04;1.08	4.97	4.97	0.65823	.	0.278030	0.38778	N	0.001565	T	0.53302	0.1788	L	0.36672	1.1	0.39665	D	0.970667	B	0.34103	0.437	B	0.31495	0.131	T	0.55068	-0.8198	10	0.32370	T	0.25	.	18.2526	0.90009	0.0:1.0:0.0:0.0	.	658	O75116	ROCK2_HUMAN	D	658;415;16	ENSP00000317985:G658D;ENSP00000385509:G415D	ENSP00000317985:G658D	G	-	2	0	ROCK2	11272004	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	3.406000	0.52637	2.297000	0.77311	0.650000	0.86243	GGC	.		0.303	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			T	11354553	C	T	11354553	3	4	92	1	0	0	0	0	1	0	0	0	13550	739	26	2	2261	2	ROCK2	2	11354553	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		11354553	231844820	9	8287											
ZNF514	84874	bcgsc.ca	37	chr2	95818976	95818976	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcccactggctgaattccAcagccacatcttcaaatgtc	11	10	5	15	0	2	1	1	1	1	0	5	1	4	1	3	1	1	1	3	1	2	2	rs79400981		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:95818976A>C	ENST00000295208.2	-	3	485	c.23T>G	c.(22-24)gTg>gGg	p.V8G	ZNF514_ENST00000411425.1_Missense_Mutation_p.V8G	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	8	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			large_intestine(4)|lung(6)|urinary_tract(1)	11						GCTGAATTCCACAGCCACATC	0.478																																					p.V8G													.	ZNF514-90	0			c.T23G						.						70	69	69					2																	95818976		2203	4300	6503	SO:0001583	missense	84874	exon3			AATTCCACAGCCA	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.23T>G	2.37:g.95818976A>C	ENSP00000295208:p.Val8Gly	Somatic	101	0		WXS	Illumina HiSeq	Phase_1	72	10	NM_032788	0	0	13	13	0	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	37	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.522701	0.44866	.	.	ENSG00000144026	ENST00000295208;ENST00000411425;ENST00000447814	T;T;T	0.04758	3.56;3.56;3.56	2.96	1.69	0.24217	Krueppel-associated box (4);	.	.	.	.	T	0.23766	0.0575	H	0.95402	3.665	0.40694	D	0.982426	D	0.71674	0.998	D	0.63113	0.911	T	0.02512	-1.1148	9	0.87932	D	0	.	7.1256	0.25469	0.77:0.23:0.0:0.0	.	8	Q96K75	ZN514_HUMAN	G	8;8;24	ENSP00000295208:V8G;ENSP00000405509:V8G;ENSP00000399647:V24G	ENSP00000295208:V8G	V	-	2	0	ZNF514	95182703	0.990000	0.36364	0.996000	0.52242	0.594000	0.36715	2.815000	0.48018	0.310000	0.22990	0.533000	0.62120	GTG	.		0.478	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		C	95818976	A	C	95818976	3	2	92	1	0	0	0	0	1	0	0	0	17991	159	6	5	1191	5	ZNF514	2	95818976	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	84464423	95818976	147380397	10	8288											
PROM2	150696	bcgsc.ca	37	chr2	95945594	95945594	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtcctctctgtggcaggTggatcgtgggctgcgtgctg	3	12	16	10	2	1	0	0	0	1	0	4	1	2	1	1	4	2	3	1	4	0	0	rs199504764		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:95945594T>G	ENST00000317620.9	+	11	1409	c.1276T>G	c.(1276-1278)Tgg>Ggg	p.W426G	PROM2_ENST00000317668.4_Splice_Site_p.W426G|PROM2_ENST00000403131.2_Splice_Site_p.W426G|PROM2_ENST00000542147.1_Splice_Site_p.W426G	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	426					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)	p.W426R(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						CTGTGGCAGGTGGATCGTGGG	0.627																																					p.W426G													.	PROM2-91	1	Substitution - Missense(1)	large_intestine(1)	c.T1276G						.						115	91	99					2																	95945594		2203	4300	6503	SO:0001630	splice_region_variant	150696	exon11			GGCAGGTGGATCG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1275-1T>G	2.37:g.95945594T>G		Somatic	146	7		WXS	Illumina HiSeq	Phase_1	93	24	NM_001165977	0	0	0	0	0	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356610	0.61293	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000003	T	0.66327	0.2778	M	0.78801	2.425	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.66056	-0.6018	10	0.33141	T	0.24	-13.0314	11.4157	0.49951	0.0:0.0:0.0:1.0	.	426	Q8N271	PROM2_HUMAN	G	426	ENSP00000385716:W426G;ENSP00000318520:W426G;ENSP00000318270:W426G;ENSP00000442542:W426G	ENSP00000318270:W426G	W	+	1	0	PROM2	95309321	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	5.815000	0.69215	2.019000	0.59389	0.533000	0.62120	TGG	T|0.998;G|0.002		0.627	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	Missense_Mutation	G	95945594	T	G	95945594	5	3	92	1	0	0	0	0	0	0	1	0	12585	1710	59	5	1318	5	PROM2	2	95945594	Splice_Site	SNP	T	TCGA-DW-5560-01A-01D-1589-08	126618	95945594	147253779	11	8289											
BIN1	274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	127828371	127828371	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtaggtccggagatcctTctgcagccgggtgccctccg	5	8	14	14	3	1	1	0	0	1	1	4	2	4	1	5	4	3	2	5	4	1	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:127828371T>C	ENST00000316724.5	-	3	598	c.187A>G	c.(187-189)Aag>Gag	p.K63E	BIN1_ENST00000393040.3_Missense_Mutation_p.K63E|BIN1_ENST00000351659.3_Missense_Mutation_p.K63E|BIN1_ENST00000357970.3_Missense_Mutation_p.K63E|BIN1_ENST00000393041.3_Missense_Mutation_p.K63E|BIN1_ENST00000409400.1_Missense_Mutation_p.K63E|BIN1_ENST00000346226.3_Missense_Mutation_p.K63E|BIN1_ENST00000376113.2_Missense_Mutation_p.K63E|BIN1_ENST00000348750.4_Missense_Mutation_p.K63E|BIN1_ENST00000352848.3_Missense_Mutation_p.K63E|BIN1_ENST00000259238.4_Missense_Mutation_p.K63E	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	63	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Interaction with BIN2.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CGGAGATCCTTCTGCAGCCGG	0.647																																					p.K63E		.											.	BIN1-655	0			c.A187G						.						45	44	44					2																	127828371		2203	4300	6503	SO:0001583	missense	274	exon3			GATCCTTCTGCAG	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"amphiphysin II"	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.187A>G	2.37:g.127828371T>C	ENSP00000316779:p.Lys63Glu	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	56	24	NM_139346	0	0	22	54	32	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331702	0.81690	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.49	3.3	0.37823	BAR (3);	0.101360	0.64402	D	0.000002	T	0.71558	0.3354	M	0.66939	2.045	0.54753	D	0.999988	P;D;P;P;P;P;P;P;B;P;P;B;P	0.60575	0.947;0.988;0.457;0.942;0.606;0.952;0.938;0.884;0.432;0.837;0.941;0.047;0.929	P;D;B;P;B;P;P;B;B;B;B;B;P	0.65010	0.879;0.931;0.286;0.528;0.286;0.611;0.804;0.346;0.177;0.287;0.357;0.017;0.794	T	0.73697	-0.3901	10	0.87932	D	0	-23.223	8.0196	0.30402	0.0:0.0991:0.0:0.9009	.	63;39;63;63;63;63;63;63;63;63;63;63;63	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	E	63	ENSP00000365281:K63E;ENSP00000350654:K63E;ENSP00000376760:K63E;ENSP00000259237:K63E;ENSP00000259238:K63E;ENSP00000315411:K63E;ENSP00000376761:K63E;ENSP00000315388:K63E;ENSP00000315284:K63E;ENSP00000316779:K63E;ENSP00000386797:K63E	ENSP00000259238:K63E	K	-	1	0	BIN1	127544841	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	4.533000	0.60615	1.884000	0.54569	0.459000	0.35465	AAG	.		0.647	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		C	127828371	T	C	127828371	3	2	92	1	0	0	0	0	1	0	0	0	1433	1792	62	3	1711	3	BIN1	2	127828371	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08	31882777	127828371	115371002	12	8290											
RAB6C	84084	hgsc.bcm.edu	37	chr2	130738210	130738210	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacgtgtagcagcagctttGccgggaatggaaagcacaca	12	6	13	10	3	0	0	0	0	0	0	0	3	0	2	1	2	5	5	1	2	3	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:130738210G>A	ENST00000410061.2	+	1	976	c.522G>A	c.(520-522)ttG>ttA	p.L174L	AC079776.7_ENST00000412425.1_RNA	NM_032144.2	NP_115520.2	Q9H0N0	RAB6C_HUMAN	RAB6C, member RAS oncogene family	174	Required for centrosome localization.				cell cycle process (GO:0022402)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of centrosome duplication (GO:0010824)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	5	Colorectal(110;0.1)					CAGCAGCTTTGCCGGGAATGG	0.478																																					p.L174L		.											.	RAB6C-251	0			c.G522A						.						63	57	59					2																	130738210		2201	4279	6480	SO:0001819	synonymous_variant	84084	exon1			AGCTTTGCCGGGA	AF124200	CCDS46408.1	2q21.1	2012-07-02			ENSG00000222014	ENSG00000222014		"RAB, member RAS oncogene"	16525	protein-coding gene	gene with protein product		612909				11054569, 17426708	Standard	NM_032144		Approved	WTH3	uc002tpx.1	Q9H0N0	OTTHUMG00000153487	ENST00000410061.2:c.522G>A	2.37:g.130738210G>A		Somatic	206	0		WXS	Illumina HiSeq	Phase_I	221	62	NM_032144	0	0	8	8	0	Q53RU3|Q6FIF7|Q9P128	Silent	SNP	ENST00000410061.2	37	CCDS46408.1																																																																																			.		0.478	RAB6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331384.1	NM_032144		A	130738210	G	A	130738210	2	1	92	1	0	0	0	0	0	0	0	1	12985	1310	46	2		2	RAB6C	2	130738210	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08	2909839	130738210	112461163	13	8291											
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152512859	152512859	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctcatagtttttcttgtaCtcccgatcagattgcatctt	7	19	5	10	1	4	1	2	0	3	1	6	2	5	1	1	0	2	3	1	0	2	8			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:152512859C>T	ENST00000172853.10	-	49	6450	c.6303G>A	c.(6301-6303)gaG>gaA	p.E2101E	NEB_ENST00000603639.1_Silent_p.E2101E|NEB_ENST00000397345.3_Silent_p.E2101E|NEB_ENST00000604864.1_Silent_p.E2101E|NEB_ENST00000427231.2_Silent_p.E2101E|NEB_ENST00000409198.1_Silent_p.E2101E			P20929	NEBU_HUMAN	nebulin	2101					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTTTCTTGTACTCCCGATCAG	0.483																																					p.E2101E		.											.	NEB-145	0			c.G6303A						.						239	236	237					2																	152512859		2046	4199	6245	SO:0001819	synonymous_variant	4703	exon49			CTTGTACTCCCGA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.6303G>A	2.37:g.152512859C>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	155	66	NM_004543	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152512859	C	T	152512859	2	4	92	1	0	0	0	0	0	0	0	1	10328	564	20	2		2	NEB	2	152512859	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08	21774649	152512859	90686514	14	8292											
SCN3A	6328	bcgsc.ca	37	chr2	166012356	166012356	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctaaaggtgtcaaagcttgtGtagccatagttggggtttcg	9	13	13	6	1	1	0	1	0	0	0	2	0	1	0	1	3	2	4	1	3	5	6	rs202083628		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:166012356G>T	ENST00000360093.3	-	10	1580	c.1089C>A	c.(1087-1089)taC>taA	p.Y363*	SCN3A_ENST00000283254.7_Nonsense_Mutation_p.Y363*|SCN3A_ENST00000409101.3_Nonsense_Mutation_p.Y363*	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	363					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CAAAGCTTGTGTAGCCATAGT	0.443																																					p.Y363X													.	SCN3A-141	0			c.C1089A						.						126	121	123					2																	166012356		2203	4300	6503	SO:0001587	stop_gained	6328	exon10			GCTTGTGTAGCCA	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10590	protein-coding gene	gene with protein product		182391	"sodium channel, voltage-gated, type III, alpha polypeptide"			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1089C>A	2.37:g.166012356G>T	ENSP00000353206:p.Tyr363*	Somatic	155	0		WXS	Illumina HiSeq	Phase_1	85	11	NM_001081676	0	0	1	1	0	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Nonsense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	G	42	9.547340	0.99201	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	.	.	.	5.41	1.6	0.23607	.	0.000000	0.53938	D	0.000046	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0847	0.42410	0.2746:0.0:0.7254:0.0	.	.	.	.	X	363	.	ENSP00000283254:Y363X	Y	-	3	2	SCN3A	165720602	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	2.871000	0.48459	0.020000	0.15106	-0.237000	0.12165	TAC	.		0.443	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		T	166012356	G	T	166012356	4	4	92	1	0	0	0	0	0	1	0	0	13950	1372	48	4	4989	4	SCN3A	2	166012356	Nonsense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	13499497	166012356	77187017	15	8293											
SCN9A	6335	bcgsc.ca	37	chr2	167060900	167060900	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaattggcttttgtggcttCttggaccccagctttttcat	5	17	10	9	0	2	0	1	0	1	0	2	2	2	2	2	4	1	3	2	4	1	7	rs201748099		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:167060900C>T	ENST00000409435.1	-	24	4472	c.4473G>A	c.(4471-4473)aaG>aaA	p.K1491K	SCN9A_ENST00000375387.4_Silent_p.K1492K|SCN9A_ENST00000409672.1_Silent_p.K1480K|SCN9A_ENST00000303354.6_Silent_p.K1492K|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1491					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTGTGGCTTCTTGGACCCCA	0.308																																					p.K1480K													.	SCN9A-181	0			c.G4440A						.						76	84	81					2																	167060900		2155	4289	6444	SO:0001819	synonymous_variant	6335	exon25			TGGCTTCTTGGAC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4473G>A	2.37:g.167060900C>T		Somatic	111	1		WXS	Illumina HiSeq	Phase_1	61	15	NM_002977	0	0	0	0	0	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			.		0.308	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167060900	C	T	167060900	2	4	92	1	0	0	0	0	0	0	0	1	13957	912	32	2		2	SCN9A	2	167060900	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08	1048544	167060900	76138473	16	8294											
ABCB11	8647	bcgsc.ca	37	chr2	169847341	169847341	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcttttctcaccaccaaaaGcagccactgttctcattgat	10	13	4	14	0	3	1	2	1	3	0	5	1	3	1	3	0	2	2	3	0	2	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:169847341G>C	ENST00000263817.6	-	9	1002	c.878C>G	c.(877-879)gCt>gGt	p.A293G		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	293	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	ACCACCAAAAGCAGCCACTGT	0.423																																					p.A293G													.	ABCB11-139	0			c.C878G						.						205	209	207					2																	169847341		1903	4125	6028	SO:0001583	missense	8647	exon9			CCAAAAGCAGCCA	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"ATP binding cassette transporters / subfamily B"	42	protein-coding gene	gene with protein product	"ABC member 16, MDR/TAP subfamily"	603201	"progressive familial intrahepatic cholestasis 2", "bile salt export pump"	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.878C>G	2.37:g.169847341G>C	ENSP00000263817:p.Ala293Gly	Somatic	411	1		WXS	Illumina HiSeq	Phase_1	279	26	NM_003742	0	0	0	0	0	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267379	0.80469	.	.	ENSG00000073734	ENST00000263817	D	0.92048	-2.96	5.53	5.53	0.82687	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.94584	0.8255	M	0.87758	2.905	0.80722	D	1	B	0.28350	0.208	B	0.37508	0.252	D	0.93403	0.6762	10	0.66056	D	0.02	-2.4159	19.8195	0.96586	0.0:0.0:1.0:0.0	.	293	O95342	ABCBB_HUMAN	G	293	ENSP00000263817:A293G	ENSP00000263817:A293G	A	-	2	0	ABCB11	169555587	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.779000	0.99018	2.756000	0.94617	0.655000	0.94253	GCT	.		0.423	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		C	169847341	G	C	169847341	3	2	92	1	0	0	0	0	1	0	0	0	42	971	34	4	3167	4	ABCB11	2	169847341	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	2786441	169847341	73352032	17	8295											
PRKRA	8575	hgsc.bcm.edu	37	chr2	179306335	179306336	+	Splice_Site	DNP	AC	AC	GT																															catagctgtcaacattactcActaaagaaatgtggttctct																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:179306335_179306336AC>GT	ENST00000325748.4	-	6	810		c.e6+1		AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000438687.3_Splice_Site|PRKRA_ENST00000487082.1_Splice_Site|PRKRA_ENST00000432031.2_Splice_Site	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator						cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			AACATTACTCACTAAAGAAATG	0.351																																					.	Melanoma(200;68 3001 23825 48764)	.											.	PRKRA	1	Unknown(1)	lung(1)	c.534+1G>A						.																																			SO:0001630	splice_region_variant	8575	exon7			TACTCACTAAAGA	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.610_610delinsGT	2.37:g.179306335_179306336delinsGT		Somatic	61	1		WXS	Illumina HiSeq	Phase_I	80	5		0	0	0	0	0	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Splice_Site	DNP	ENST00000325748.4	37	CCDS2279.1																																																																																			.		0.351	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	Intron	GT	179306336	AC	GT	179306335	5	3	92	1	0	0	0	0	0	0	1	0	12553	173	6	3	342	3	PRKRA	2	179306335	Splice_Site	DNP	AC	TCGA-DW-5560-01A-01D-1589-08	9458994	179306335	63893038	18	8296											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179433843	179433843	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctcagctgtgactctaaaGtaataactgcaaccttcttg	11	14	6	10	0	3	1	1	1	3	0	4	1	3	1	1	0	4	3	1	0	5	6			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:179433843G>C	ENST00000591111.1	-	276	72317	c.72093C>G	c.(72091-72093)taC>taG	p.Y24031*	TTN_ENST00000589042.1_Nonsense_Mutation_p.Y25672*|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.Y16607*|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Y23104*|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Y16732*|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Y16799*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24031	Fibronectin type-III 74. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGACTCTAAAGTAATAACTGC	0.418																																					p.Y25672X		.											.	TTN-636	0			c.C77016G						.						171	169	170					2																	179433843		1958	4136	6094	SO:0001587	stop_gained	7273	exon326			TCTAAAGTAATAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72093C>G	2.37:g.179433843G>C	ENSP00000465570:p.Tyr24031*	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	231	99	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	63	76.472557	0.99993	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.5208	0.61566	0.071:0.0:0.929:0.0	.	.	.	.	X	23104;16607;16799;16732;16605	.	ENSP00000340554:Y16799X	Y	-	3	2	TTN	179142089	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.714000	0.68422	2.803000	0.96430	0.650000	0.86243	TAC	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179433843	G	C	179433843	4	2	92	1	0	0	0	0	0	1	0	0	16768	1024	36	4	31111	4	TTN	2	179433843	Nonsense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	127508	179433843	63765530	19	8297											
COL6A3	1293	bcgsc.ca	37	chr2	238253123	238253123	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgggtgtgttgctgaagaaaAcagccactttcctcattagg	10	12	11	8	0	1	2	1	1	0	1	2	2	2	2	2	2	3	2	2	2	4	3	rs199609978	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:238253123A>C	ENST00000295550.4	-	36	7990	c.7538T>G	c.(7537-7539)gTt>gGt	p.V2513G	COL6A3_ENST00000472056.1_Missense_Mutation_p.V1906G|COL6A3_ENST00000409809.1_Missense_Mutation_p.V2307G|COL6A3_ENST00000346358.4_Missense_Mutation_p.V2313G|COL6A3_ENST00000347401.3_Missense_Mutation_p.V2312G|COL6A3_ENST00000353578.4_Missense_Mutation_p.V2307G	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2513	Nonhelical region.|VWFA 11. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCTGAAGAAAACAGCCACTTT	0.522													A|||	144	0.028754	0.0204	0.0562	5008	,	,		21429	0.0357		0.0417	False		,,,				2504	0				p.V2513G													.	COL6A3-526	0			c.T7538G						.						154	150	151					2																	238253123		2203	4300	6503	SO:0001583	missense	1293	exon36			AAGAAAACAGCCA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7538T>G	2.37:g.238253123A>C	ENSP00000295550:p.Val2513Gly	Somatic	205	0		WXS	Illumina HiSeq	Phase_1	210	29	NM_004369	0	0	4	4	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	9.634	1.137131	0.21123	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	4.87	4.87	0.63330	von Willebrand factor, type A (3);	0.614043	0.14162	N	0.337275	D	0.93138	0.7815	M	0.74647	2.275	0.58432	D	0.999998	D;D;D;D	0.89917	0.971;0.971;0.963;1.0	P;P;P;D	0.87578	0.845;0.845;0.76;0.998	D	0.93000	0.6422	10	0.87932	D	0	.	14.8002	0.69909	1.0:0.0:0.0:0.0	.	1906;1906;2307;2513	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	G	2513;2312;2307;1906;2307;2313	ENSP00000295550:V2513G;ENSP00000315609:V2312G;ENSP00000315873:V2307G;ENSP00000418285:V1906G;ENSP00000386844:V2307G;ENSP00000295546:V2313G	ENSP00000295550:V2513G	V	-	2	0	COL6A3	237917862	0.972000	0.33761	0.029000	0.17559	0.409000	0.31022	9.118000	0.94355	1.942000	0.56320	0.533000	0.62120	GTT	.		0.522	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		C	238253123	A	C	238253123	3	2	92	1	0	0	0	0	1	0	0	0	3707	43	2	5	2031	5	COL6A3	2	238253123	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	58819280	238253123	4946250	20	8298											
RBM6	10180	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50005960	50005960	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtccagttcaagaccaaGataagtcacagctttctgga	15	9	8	9	0	3	2	2	0	1	2	4	3	4	3	2	1	1	2	2	1	4	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr3:50005960G>T	ENST00000266022.4	+	3	1361	c.1102G>T	c.(1102-1104)Gat>Tat	p.D368Y	RBM6_ENST00000442092.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.D236Y|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000441115.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	368					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TCAAGACCAAGATAAGTCACA	0.463																																					p.D368Y		.											.	RBM6-280	0			c.G1102T						.						80	76	78					3																	50005960		2203	4300	6503	SO:0001583	missense	10180	exon3			GACCAAGATAAGT	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"RNA binding motif (RRM) containing", "G patch domain containing"	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.1102G>T	3.37:g.50005960G>T	ENSP00000266022:p.Asp368Tyr	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	96	43	NM_005777	0	0	15	28	13	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043431	0.36085	.	.	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.36878	1.23;1.25	5.85	3.97	0.46021	.	0.614854	0.16479	N	0.212625	T	0.29389	0.0732	N	0.24115	0.695	0.80722	D	1	D	0.59767	0.986	P	0.49752	0.621	T	0.01988	-1.1234	9	.	.	.	-4.7397	7.5857	0.27991	0.1421:0.1365:0.7214:0.0	.	368	P78332	RBM6_HUMAN	Y	368;236	ENSP00000266022:D368Y;ENSP00000396466:D236Y	.	D	+	1	0	RBM6	49980964	1.000000	0.71417	0.999000	0.59377	0.735000	0.41995	2.640000	0.46579	1.495000	0.48549	0.491000	0.48974	GAT	.		0.463	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		T	50005960	G	T	50005960	3	4	92	1	0	0	0	0	1	0	0	0	13176	942	33	4	1108	4	RBM6	3	50005960	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08		50005960	148016470	21	8299											
DGKQ	1609	hgsc.bcm.edu	37	chr4	954919	954919	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcaccggggtggccttgAggagcgtgactcggaagtag	7	7	17	10	3	0	2	0	2	0	0	1	4	0	4	3	5	2	2	3	5	2	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr4:954919A>G	ENST00000273814.3	-	22	2718	c.2645T>C	c.(2644-2646)cTc>cCc	p.L882P	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	882					blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGTGGCCTTGAGGAGCGTGAC	0.692																																					p.L882P	Esophageal Squamous(17;537 645 4447 26373)	.											.	DGKQ-537	0			c.T2645C						.						36	43	40					4																	954919		2199	4298	6497	SO:0001583	missense	1609	exon22			GCCTTGAGGAGCG	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"diacylglycerol kinase, theta (110kD)"	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.2645T>C	4.37:g.954919A>G	ENSP00000273814:p.Leu882Pro	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001347	0	0	12	12	0	Q6P3W4	Missense_Mutation	SNP	ENST00000273814.3	37	CCDS3342.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.07|10.07	1.249271|1.249271	0.22880|0.22880	.|.	.|.	ENSG00000145214|ENSG00000145214	ENST00000273814;ENST00000515182|ENST00000509465	T;T|.	0.29397|.	1.57;1.57|.	5.45|5.45	5.45|5.45	0.79879|0.79879	Diacylglycerol kinase, accessory domain (2);|.	0.222361|.	0.45867|.	D|.	0.000338|.	T|T	0.56717|0.56717	0.2004|0.2004	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.71184|.	0.959;0.972|.	T|T	0.53961|0.53961	-0.8364|-0.8364	10|5	0.36615|.	T|.	0.2|.	.|.	13.4405|13.4405	0.61109|0.61109	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	882;882|.	E9KL49;P52824|.	.;DGKQ_HUMAN|.	P|P	882;97|816	ENSP00000273814:L882P;ENSP00000421756:L97P|.	ENSP00000273814:L882P|.	L|S	-|-	2|1	0|0	DGKQ|DGKQ	944919|944919	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.194000|0.194000	0.23727|0.23727	2.949000|2.949000	0.49074|0.49074	2.069000|2.069000	0.61940|0.61940	0.454000|0.454000	0.30748|0.30748	CTC|TCA	.		0.692	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1			G	954919	A	G	954919	3	3	92	1	0	0	0	0	1	0	0	0	4484	304	11	3	191	3	DGKQ	4	954919	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08		954919	190199357	22	8300											
RBPJ	3516	hgsc.bcm.edu	37	chr4	26426305	26426305	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acagtccgagatggctacatCcattatggacaaacagtcaa	15	8	8	10	1	1	1	1	0	0	1	3	3	3	2	2	2	2	1	2	2	4	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr4:26426305C>T	ENST00000361572.6	+	7	920	c.726C>T	c.(724-726)atC>atT	p.I242I	RBPJ_ENST00000345843.3_Silent_p.I227I|RBPJ_ENST00000342320.4_Silent_p.I228I|RBPJ_ENST00000348160.4_Silent_p.I229I|RBPJ_ENST00000507561.1_Silent_p.I207I|RBPJ_ENST00000342295.1_Silent_p.I242I|RBPJ_ENST00000504907.1_Silent_p.I228I|RBPJ_ENST00000355476.3_Silent_p.I228I			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	242					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				ATGGCTACATCCATTATGGAC	0.373																																					p.I242I		.											.	RBPJ-659	0			c.C726T						.						94	89	91					4																	26426305		2203	4300	6503	SO:0001819	synonymous_variant	3516	exon8			CTACATCCATTAT	L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"suppressor of hairless homolog (Drosophila)"	147183	"recombining binding protein suppressor of hairless (Drosophila)"	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.726C>T	4.37:g.26426305C>T		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_005349	0	0	6	6	0	B4DY22|Q5XKH9|Q6P1N3	Silent	SNP	ENST00000361572.6	37	CCDS3437.1																																																																																			.		0.373	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		T	26426305	C	T	26426305	2	4	92	1	0	0	0	0	0	0	0	1	13193	845	30	2		2	RBPJ	4	26426305	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08	25471386	26426305	164727971	23	8301											
PET112L	5188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	152592364	152592364	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaggatctcctttatcaTgactggatctgctcggcttt	6	15	8	12	1	3	1	1	1	2	0	6	3	4	3	2	3	1	2	2	3	1	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr4:152592364T>C	ENST00000515812.1	-	12	1529	c.1513A>G	c.(1513-1515)Atg>Gtg	p.M505V	RP11-164P12.4_ENST00000508664.1_RNA|PET112_ENST00000507592.1_5'UTR|PET112_ENST00000263985.6_Missense_Mutation_p.M546V																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						TCCTTTATCATGACTGGATCT	0.483																																					p.M546V		.											.	PET112-90	0			c.A1636G						.						178	163	168					4																	152592364		2203	4300	6503	SO:0001583	missense	5188	exon13			TTATCATGACTGG																												ENST00000515812.1:c.1513A>G	4.37:g.152592364T>C	ENSP00000426859:p.Met505Val	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	187	88	NM_004564	0	0	46	82	36		Missense_Mutation	SNP	ENST00000515812.1	37		.	.	.	.	.	.	.	.	.	.	T	0.061	-1.224008	0.01530	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.39592	1.07;1.08	5.8	-5.06	0.02946	Asn/Gln amidotransferase (2);	0.986159	0.08279	N	0.970181	T	0.13286	0.0322	N	0.02181	-0.65	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39961	-0.9588	10	0.06365	T	0.9	0.2792	10.1442	0.42753	0.0:0.1381:0.5532:0.3086	.	546	O75879	GATB_HUMAN	V	546;505	ENSP00000263985:M546V;ENSP00000426859:M505V	ENSP00000263985:M546V	M	-	1	0	PET112	152811814	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.347000	0.07750	-0.814000	0.04352	-0.904000	0.02843	ATG	.		0.483	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			C	152592364	T	C	152592364	3	2	92	1	0	0	0	0	1	0	0	0	11760	1464	51	3	41	3	PET112L	4	152592364	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08	126166059	152592364	38561912	24	8302											
SPEF2	79925	bcgsc.ca	37	chr5	35670228	35670228	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgcaaaacccatatatgaaCaagcctctgttaagacacta	17	9	5	10	0	1	2	0	1	1	1	1	2	1	2	2	0	4	2	2	0	8	4	rs77343152		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr5:35670228C>A	ENST00000356031.3	+	10	1577	c.1423C>A	c.(1423-1425)Caa>Aaa	p.Q475K	SPEF2_ENST00000509059.1_Missense_Mutation_p.Q475K|SPEF2_ENST00000440995.2_Missense_Mutation_p.Q475K|SPEF2_ENST00000282469.6_Missense_Mutation_p.Q475K	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	475					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATATATGAACAAGCCTCTGT	0.358																																					p.Q475K													.	SPEF2-26	0			c.C1423A						.						129	136	134					5																	35670228		2203	4299	6502	SO:0001583	missense	79925	exon10			TATGAACAAGCCT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"cancer/testis antigen 122"	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.1423C>A	5.37:g.35670228C>A	ENSP00000348314:p.Gln475Lys	Somatic	194	0		WXS	Illumina HiSeq	Phase_1	200	29	NM_024867	0	0	4	4	0	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481659	0.26598	.	.	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000440995	T;T;T;T	0.15718	2.4;2.4;2.4;2.4	5.1	3.15	0.36227	.	0.549745	0.19197	N	0.120271	T	0.10680	0.0261	L	0.34521	1.04	0.80722	D	1	P;B;B	0.38922	0.651;0.068;0.041	B;B;B	0.30943	0.122;0.014;0.011	T	0.11299	-1.0593	10	0.10111	T	0.7	.	14.19	0.65633	0.4519:0.5481:0.0:0.0	.	475;475;475	D6REZ4;Q9C093;Q9C093-3	.;SPEF2_HUMAN;.	K	475	ENSP00000282469:Q475K;ENSP00000348314:Q475K;ENSP00000421593:Q475K;ENSP00000412125:Q475K	ENSP00000282469:Q475K	Q	+	1	0	SPEF2	35705985	0.985000	0.35326	0.987000	0.45799	0.783000	0.44284	1.542000	0.36137	1.221000	0.43506	0.655000	0.94253	CAA	.		0.358	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		A	35670228	C	A	35670228	3	1	92	1	0	0	0	0	1	0	0	0	15067	479	17	4	1461	4	SPEF2	5	35670228	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		35670228	145245032	25	8303											
LOX	4015	bcgsc.ca	37	chr5	121409741	121409741	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtacatgcaaatcgcctgtgGtagccatagtcacaggatgt	11	10	11	9	1	1	0	1	0	0	0	2	1	1	1	2	2	3	3	2	2	4	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr5:121409741G>T	ENST00000231004.4	-	4	1301	c.1002C>A	c.(1000-1002)taC>taA	p.Y334*	LOX_ENST00000513319.1_5'UTR|SRFBP1_ENST00000504881.1_Intron	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	334	Lysyl-oxidase like.				blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		ATCGCCTGTGGTAGCCATAGT	0.493																																					p.Y334X													.	LOX-650	0			c.C1002A						.						200	185	190					5																	121409741		2203	4300	6503	SO:0001587	stop_gained	4015	exon4			CCTGTGGTAGCCA		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.1002C>A	5.37:g.121409741G>T	ENSP00000231004:p.Tyr334*	Somatic	329	0		WXS	Illumina HiSeq	Phase_1	226	20	NM_002317	0	0	2	2	0	B2R5Q3|Q5FWF0	Nonsense_Mutation	SNP	ENST00000231004.4	37	CCDS4129.1	.	.	.	.	.	.	.	.	.	.	G	40	7.966282	0.98585	.	.	ENSG00000113083	ENST00000231004;ENST00000543620	.	.	.	5.98	5.11	0.69529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.1432	0.36917	0.2615:0.0:0.7385:0.0	.	.	.	.	X	334;294	.	ENSP00000231004:Y334X	Y	-	3	2	LOX	121437640	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.769000	0.47654	1.540000	0.49301	0.650000	0.86243	TAC	.		0.493	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			T	121409741	G	T	121409741	4	4	92	1	0	0	0	0	0	1	0	0	8923	1256	44	4	267	4	LOX	5	121409741	Nonsense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	85739513	121409741	59505519	26	8304											
F12	2161	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176831341	176831341	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggtctggcactgtgccaGgtcgcagtactcccagctca	6	9	13	13	1	2	0	1	0	1	0	4	0	3	0	2	4	3	4	2	4	1	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr5:176831341G>A	ENST00000253496.3	-	9	922	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	292	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CACTGTGCCAGGTCGCAGTAC	0.692									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L292L		.											.	F12-90	0			c.C874T						.						17	21	19					5																	176831341		2201	4296	6497	SO:0001819	synonymous_variant	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GTGCCAGGTCGCA	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.874C>T	5.37:g.176831341G>A		Somatic	50	0	1934	WXS	Illumina HiSeq	Phase_I	35	15	NM_000505	0	0	0	0	0	P78339	Silent	SNP	ENST00000253496.3	37	CCDS34302.1																																																																																			.		0.692	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176831341	G	A	176831341	2	1	92	1	0	0	0	0	0	0	0	1	5352	991	35	2		2	F12	5	176831341	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08	55421600	176831341	4083919	27	8305											
FAM65B	9750	bcgsc.ca	37	chr6	24850081	24850081	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccaaggtcattgatgtcgAcagccactacctgaggtcgg	10	9	11	11	2	1	2	1	2	0	0	3	3	1	2	3	3	3	0	3	3	3	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr6:24850081A>C	ENST00000259698.4	-	11	1071	c.896T>G	c.(895-897)gTc>gGc	p.V299G	FAM65B_ENST00000378023.4_Missense_Mutation_p.V299G|FAM65B_ENST00000540914.1_Missense_Mutation_p.V299G|FAM65B_ENST00000538035.1_Missense_Mutation_p.V328G|FAM65B_ENST00000510784.2_Missense_Mutation_p.V333G	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	299					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						ATTGATGTCGACAGCCACTAC	0.483																																					p.V299G													.	FAM65B-91	0			c.T896G						.						196	204	201					6																	24850081		2129	4274	6403	SO:0001583	missense	9750	exon11			ATGTCGACAGCCA	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.896T>G	6.37:g.24850081A>C	ENSP00000259698:p.Val299Gly	Somatic	297	1		WXS	Illumina HiSeq	Phase_1	238	44	NM_015864	0	0	2	2	0	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.749840	0.89753	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.02631	4.22;4.22;4.22;4.22;4.22	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.10981	0.0268	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.00641	-1.1631	10	0.87932	D	0	-25.9828	16.0546	0.80788	1.0:0.0:0.0:0.0	.	333;328;299;299	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	G	299;328;299;299;333	ENSP00000259698:V299G;ENSP00000441138:V328G;ENSP00000367262:V299G;ENSP00000438425:V299G;ENSP00000441305:V333G	ENSP00000259698:V299G	V	-	2	0	FAM65B	24958060	1.000000	0.71417	0.484000	0.27391	0.997000	0.91878	8.962000	0.93254	2.191000	0.70037	0.528000	0.53228	GTC	.		0.483	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			C	24850081	A	C	24850081	3	2	92	1	0	0	0	0	1	0	0	0	5619	275	10	5	2372	5	FAM65B	6	24850081	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08		24850081	146264986	28	8306											
ZKSCAN3	80317	bcgsc.ca	37	chr6	28333714	28333714	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacagaatccacactggggaGaagccgtatcagtgcagtat	13	7	11	10	1	1	2	1	0	0	2	2	3	2	2	2	2	2	3	2	2	4	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr6:28333714G>A	ENST00000377255.3	+	7	1566	c.1269G>A	c.(1267-1269)gaG>gaA	p.E423E	ZKSCAN3_ENST00000341464.5_Silent_p.E275E|ZKSCAN3_ENST00000252211.2_Silent_p.E423E	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	423					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						ACACTGGGGAGAAGCCGTATC	0.507																																					p.E423E													.	ZKSCAN3-92	0			c.G1269A						.						66	68	67					6																	28333714		2203	4300	6503	SO:0001819	synonymous_variant	80317	exon6			TGGGGAGAAGCCG	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"Zinc fingers, C2H2-type", "-", "-", "-"	13853	protein-coding gene	gene with protein product		612791	"zinc finger protein 306", "zinc finger protein 309"	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1269G>A	6.37:g.28333714G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_1	49	14	NM_024493	0	0	4	5	1	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Silent	SNP	ENST00000377255.3	37	CCDS4650.1																																																																																			.		0.507	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		A	28333714	G	A	28333714	2	1	92	1	0	0	0	0	0	0	0	1	17720	933	33	2		2	ZKSCAN3	6	28333714	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08	3483633	28333714	142781353	29	8307											
HLA-DOA	3111	broad.mit.edu;bcgsc.ca	37	chr6	32974906	32974906	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgatgaggacggtgcccaCgaggaagcccaccaggccga	11	3	15	12	3	0	2	0	2	0	0	0	7	0	4	4	4	2	0	4	4	1	0	rs200140467		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr6:32974906C>T	ENST00000229829.5	-	4	775	c.700G>A	c.(700-702)Gtg>Atg	p.V234M	HLA-DOA_ENST00000495532.1_5'Flank|HLA-DOA_ENST00000450833.2_Intron	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	234					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						ACGGTGCCCACGAGGAAGCCC	0.627													C|||	1	0.000199681	0	0	5008	,	,		16958	0		0.001	False		,,,				2504	0				p.V234M													.	HLA-DOA-514	0			c.G700A						.	C	MET/VAL	0,4406		0,0,2203	61	65	63		700	-0.5	0.3	6		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	HLA-DOA	NM_002119.3	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	234/251	32974906	1,13005	2203	4300	6503	SO:0001583	missense	3111	exon4			TGCCCACGAGGAA	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.700G>A	6.37:g.32974906C>T	ENSP00000229829:p.Val234Met	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	106	6	NM_002119	0	0	1	1	0	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Missense_Mutation	SNP	ENST00000229829.5	37	CCDS4763.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.76	3.212303	0.58452	0.0	1.16E-4	ENSG00000204252	ENST00000229829	T	0.02197	4.4	4.81	-0.477	0.12097	.	0.529869	0.19645	N	0.109353	T	0.01523	0.0049	M	0.83312	2.635	0.31226	N	0.696848	D	0.54772	0.968	P	0.44811	0.461	T	0.35992	-0.9766	10	0.66056	D	0.02	.	2.9755	0.05936	0.1321:0.4542:0.2729:0.1408	.	234	P06340	DOA_HUMAN	M	234	ENSP00000229829:V234M	ENSP00000229829:V234M	V	-	1	0	HLA-DOA	33082884	0.000000	0.05858	0.255000	0.24374	0.944000	0.59088	-0.002000	0.12924	-0.202000	0.10268	0.650000	0.86243	GTG	C|0.999;T|0.000		0.627	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119		T	32974906	C	T	32974906	3	4	92	1	0	0	0	0	1	0	0	0	7221	536	19	1	60	1	HLA-DOA	6	32974906	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	4641192	32974906	138140161	30	8308											
FKBP5	2289	bcgsc.ca	37	chr6	35610559	35610559	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcagcaacagtggctgTggggctttcttcattgttct	5	15	11	10	0	4	0	2	0	2	0	4	0	4	0	0	3	3	5	0	3	1	4	rs139048363		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr6:35610559T>G	ENST00000539068.1	-	2	245	c.43A>C	c.(43-45)Aca>Cca	p.T15P	FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Missense_Mutation_p.T15P|FKBP5_ENST00000536438.1_Missense_Mutation_p.T15P|FKBP5_ENST00000357266.4_Missense_Mutation_p.T15P	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	15					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						ACAGTGGCTGTGGGGCTTTCT	0.418																																					p.T15P													.	FKBP5-227	0			c.A43C						.						191	191	191					6																	35610559		2203	4300	6503	SO:0001583	missense	2289	exon3			TGGCTGTGGGGCT	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"Tetratricopeptide (TTC) repeat domain containing"	3721	protein-coding gene	gene with protein product		602623	"FK506-binding protein 5"			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.43A>C	6.37:g.35610559T>G	ENSP00000441205:p.Thr15Pro	Somatic	311	0		WXS	Illumina HiSeq	Phase_1	202	23	NM_001145775	0	0	0	0	0	F5H7R1|Q59EB8|Q5TGM6	Missense_Mutation	SNP	ENST00000539068.1	37	CCDS4808.1	.	.	.	.	.	.	.	.	.	.	T	10.69	1.422509	0.25639	.	.	ENSG00000096060	ENST00000536438;ENST00000357266;ENST00000539068;ENST00000337746;ENST00000542713	D;D;D;T	0.83837	-1.77;-1.77;-1.77;-1.48	5.95	4.1	0.47936	.	0.427671	0.26065	N	0.026552	T	0.54271	0.1848	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.17465	0.0;0.022	B;B	0.18263	0.0;0.021	T	0.43909	-0.9362	10	0.31617	T	0.26	-33.2844	8.6902	0.34262	0.0:0.7651:0.0:0.2349	.	15;15	F5H7R1;Q13451	.;FKBP5_HUMAN	P	15	ENSP00000444810:T15P;ENSP00000349811:T15P;ENSP00000441205:T15P;ENSP00000442340:T15P	ENSP00000338160:T15P	T	-	1	0	FKBP5	35718537	0.096000	0.21769	0.950000	0.38849	0.279000	0.26890	0.187000	0.16998	1.513000	0.48852	-0.177000	0.13119	ACA	.		0.418	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			G	35610559	T	G	35610559	3	3	92	1	0	0	0	0	1	0	0	0	5930	1696	59	5	1428	5	FKBP5	6	35610559	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08	2635653	35610559	135504508	31	8309											
FAM184A	79632	bcgsc.ca	37	chr6	119282964	119282964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttaggtggcactggctgTggaagtggtttgctgctgtt	4	15	15	7	0	0	0	0	0	0	0	0	1	0	1	1	5	2	6	1	5	2	4	rs534758163	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr6:119282964T>G	ENST00000338891.7	-	17	3746	c.3303A>C	c.(3301-3303)ccA>ccC	p.P1101P	FAM184A_ENST00000521531.1_Silent_p.P1017P|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000368475.4_Silent_p.P897P|FAM184A_ENST00000352896.5_Silent_p.P932P	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	1101						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						GCACTGGCTGTGGAAGTGGTT	0.448													T|||	6	0.00119808	0.0023	0	5008	,	,		15675	0		0.003	False		,,,				2504	0				p.P1101P													.	FAM184A-519	0			c.A3303C						.						191	198	196					6																	119282964		1937	4147	6084	SO:0001819	synonymous_variant	79632	exon17			TGGCTGTGGAAGT	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 60"	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.3303A>C	6.37:g.119282964T>G		Somatic	355	3		WXS	Illumina HiSeq	Phase_1	325	38	NM_024581	0	0	0	0	0	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Silent	SNP	ENST00000338891.7	37	CCDS43499.1																																																																																			.		0.448	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		G	119282964	T	G	119282964	2	3	92	1	0	0	0	0	0	0	0	1	5527	1683	59	5		5	FAM184A	6	119282964	Silent	SNP	T	TCGA-DW-5560-01A-01D-1589-08	83672405	119282964	51832103	32	8310											
PLG	5340	broad.mit.edu	37	chr6	161152118	161152118	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctactgcaggaatccagatgCcgataaaggcccctggtgtt	10	9	11	11	1	0	1	0	0	0	1	1	3	1	2	4	3	3	2	4	3	4	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr6:161152118C>T	ENST00000308192.9	+	11	1355	c.1292C>T	c.(1291-1293)gCc>gTc	p.A431V		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	431	Kringle 4. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	AATCCAGATGCCGATAAAGGC	0.507																																					p.A431V													.	PLG-94	0			c.C1292T						.						86	93	90					6																	161152118		2203	4300	6503	SO:0001583	missense	5340	exon11			CAGATGCCGATAA	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1292C>T	6.37:g.161152118C>T	ENSP00000308938:p.Ala431Val	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	121	4	NM_000301	0	0	0	0	0	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	C	9.802	1.180726	0.21787	.	.	ENSG00000122194	ENST00000308192	T	0.62941	-0.01	5.11	-10.2	0.00374	Kringle (5);Kringle-like fold (1);Kringle, conserved site (1);	1.961470	0.04210	U	0.331537	T	0.35480	0.0933	M	0.61703	1.905	0.09310	N	0.999995	B	0.12013	0.005	B	0.21151	0.033	T	0.48736	-0.9009	10	0.87932	D	0	.	12.5352	0.56138	0.1802:0.5971:0.2227:0.0	.	431	P00747	PLMN_HUMAN	V	431	ENSP00000308938:A431V	ENSP00000308938:A431V	A	+	2	0	PLG	161072108	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.583000	0.02115	-2.853000	0.00330	-0.302000	0.09304	GCC	.		0.507	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		T	161152118	C	T	161152118	3	4	92	1	0	0	0	0	1	0	0	0	12112	739	26	2	1338	2	PLG	6	161152118	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	41869154	161152118	9962949	33	8311											
VPS37D	155382	hgsc.bcm.edu	37	chr7	73083798	73083798	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcctggcctccaactacgCgctggccaaggagaacctgg	8	6	12	15	2	0	1	0	0	0	1	1	2	1	1	5	4	4	1	5	4	4	1	rs370705512		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr7:73083798C>G	ENST00000324941.4	+	2	322	c.188C>G	c.(187-189)gCg>gGg	p.A63G	VPS37D_ENST00000451519.1_Intron	NM_001077621.1	NP_001071089.1			vacuolar protein sorting 37 homolog D (S. cerevisiae)											central_nervous_system(1)|ovary(1)	2		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCCAACTACGCGCTGGCCAAG	0.677																																					p.A63G		.											.	VPS37D-68	0			c.C188G						.						7	9	8					7																	73083798		1885	4067	5952	SO:0001583	missense	155382	exon2			ACTACGCGCTGGC	AY081952	CCDS43596.1	7q11.23	2007-07-27	2006-04-04	2005-08-18	ENSG00000176428	ENSG00000176428			18287	protein-coding gene	gene with protein product		610039	"Williams Beuren syndrome chromosome region 24", "vacuolar protein sorting 37D (yeast)"	WBSCR24		15218037	Standard	NM_001077621		Approved	MGC35352	uc003tyr.3	Q86XT2	OTTHUMG00000157227	ENST00000324941.4:c.188C>G	7.37:g.73083798C>G	ENSP00000320416:p.Ala63Gly	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	10	4	NM_001077621	0	0	4	10	6		Missense_Mutation	SNP	ENST00000324941.4	37	CCDS43596.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336561	0.41398	.	.	ENSG00000176428	ENST00000324941	T	0.77229	-1.08	4.3	3.41	0.39046	Modifier of rudimentary, Modr (1);	0.335218	0.24041	U	0.042099	T	0.64438	0.2598	N	0.14661	0.345	0.80722	D	1	P	0.49090	0.919	P	0.46172	0.506	T	0.66002	-0.6031	10	0.66056	D	0.02	.	8.0448	0.30542	0.0:0.8859:0.0:0.1141	.	63	Q86XT2	VP37D_HUMAN	G	63	ENSP00000320416:A63G	ENSP00000320416:A63G	A	+	2	0	VPS37D	72721734	0.015000	0.18098	0.868000	0.34077	0.570000	0.35934	1.008000	0.29872	1.024000	0.39682	0.563000	0.77884	GCG	.		0.677	VPS37D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348064.1	NM_152560		G	73083798	C	G	73083798	3	3	92	1	0	0	0	0	1	0	0	0	17241	768	27	4	194	4	VPS37D	7	73083798	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		73083798	86054865	34	8312											
DPYS	1807	hgsc.bcm.edu	37	chr8	105479134	105479134	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccgcggatcaggagccgCgagggcgccgccatagcgag	7	2	16	16	7	1	0	1	0	0	0	1	4	1	2	5	3	2	0	5	3	1	1	rs182332679	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr8:105479134C>T	ENST00000351513.2	-	1	147	c.15G>A	c.(13-15)tcG>tcA	p.S5S		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	5					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TCAGGAGCCGCGAGGGCGCCG	0.761													C|||	160	0.0319489	0.0098	0.0375	5008	,	,		8520	0.0169		0.0378	False		,,,				2504	0.0675				p.S5S		.											.	DPYS-229	0			c.G15A						.	C		59,3315		0,59,1628	4	5	5		15	0.4	0	8		5	163,6381		1,161,3110	no	coding-synonymous	DPYS	NM_001385.2		1,220,4738	TT,TC,CC		2.4908,1.7487,2.2384		5/520	105479134	222,9696	1687	3272	4959	SO:0001819	synonymous_variant	1807	exon1			GAGCCGCGAGGGC	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.15G>A	8.37:g.105479134C>T		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	6	6	NM_001385	0	0	0	0	0		Silent	SNP	ENST00000351513.2	37	CCDS6302.1																																																																																			C|0.967;T|0.033		0.761	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		T	105479134	C	T	105479134	2	4	92	1	0	0	0	0	0	0	0	1	4757	755	27	1		1	DPYS	8	105479134	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08		105479134	40884888	35	8313											
EDF1	8721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139757816	139757816	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccacctccagggtcaccCtgtcatggtgcagctcctct	5	10	9	17	0	3	0	2	0	1	0	5	0	5	0	5	2	3	2	5	2	0	0			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr9:139757816C>A	ENST00000224073.1	-	3	242	c.215G>T	c.(214-216)aGg>aTg	p.R72M	EDF1_ENST00000371649.1_Missense_Mutation_p.R72M|EDF1_ENST00000371648.4_Missense_Mutation_p.R72M	NM_003792.2	NP_003783.1	O60869	EDF1_HUMAN	endothelial differentiation-related factor 1	72	Interaction with NR5A2, PPARG and NR1H3.|Interaction with TBP and NR5A1.				endothelial cell differentiation (GO:0045446)|multicellular organismal development (GO:0007275)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			lung(1)	1	all_cancers(76;0.0841)|all_epithelial(76;0.217)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CAGGGTCACCCTGTCATGGTG	0.617																																					p.R72M		.											.	EDF1-90	0			c.G215T						.						150	112	125					9																	139757816		2203	4300	6503	SO:0001583	missense	8721	exon3			GTCACCCTGTCAT	AJ005259	CCDS7011.1, CCDS7012.1, CCDS65193.1	9q34.3	2009-11-06			ENSG00000107223	ENSG00000107223			3164	protein-coding gene	gene with protein product	"multiprotein bridging factor-1"	605107				9813014, 15112053	Standard	NM_003792		Approved	EDF-1	uc004cjt.1	O60869	OTTHUMG00000020948	ENST00000224073.1:c.215G>T	9.37:g.139757816C>A	ENSP00000224073:p.Arg72Met	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_003792	0	0	722	1601	879	Q5T5T2|Q9UIM1	Missense_Mutation	SNP	ENST00000224073.1	37	CCDS7011.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.877120	0.91664	.	.	ENSG00000107223	ENST00000371649;ENST00000224073;ENST00000371648	.	.	.	5.79	4.9	0.64082	Lambda repressor-like, DNA-binding (1);Multiprotein bridging factor 1, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76877	0.4049	M	0.80847	2.515	0.80722	D	1	P;P	0.48407	0.897;0.91	P;P	0.57425	0.725;0.82	T	0.80741	-0.1247	9	0.87932	D	0	-10.8624	14.6074	0.68489	0.0:0.9301:0.0:0.0699	.	72;72	O60869-2;O60869	.;EDF1_HUMAN	M	72	.	ENSP00000224073:R72M	R	-	2	0	EDF1	138877637	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.317000	0.79018	1.463000	0.47967	0.655000	0.94253	AGG	.		0.617	EDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055143.1			A	139757816	C	A	139757816	3	1	92	1	0	0	0	0	1	0	0	0	4925	681	24	4	278	4	EDF1	9	139757816	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		139757816	1455615	36	8314											
PIP4K2A	5305	bcgsc.ca	37	chr10	22856802	22856802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttctttgtcactagcttctCtagccactgtagagccctga	7	15	7	12	0	3	2	1	1	2	1	4	2	3	2	2	0	3	2	2	0	3	6	rs201266267		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr10:22856802C>T	ENST00000376573.4	-	6	884	c.656G>A	c.(655-657)aGa>aAa	p.R219K	PIP4K2A_ENST00000422321.1_5'UTR|PIP4K2A_ENST00000545335.1_Missense_Mutation_p.R160K|PIP4K2A_ENST00000323883.7_Missense_Mutation_p.R79K	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	219	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						ACTAGCTTCTCTAGCCACTGT	0.453																																					p.R219K													.	PIP4K2A-665	0			c.G656A						.						140	123	129					10																	22856802		2203	4300	6503	SO:0001583	missense	5305	exon6			GCTTCTCTAGCCA	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.656G>A	10.37:g.22856802C>T	ENSP00000365757:p.Arg219Lys	Somatic	211	1		WXS	Illumina HiSeq	Phase_1	126	16	NM_005028	0	0	1	1	0	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	37	CCDS7141.1	.	.	.	.	.	.	.	.	.	.	C	35	5.513277	0.96402	.	.	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335;ENST00000422321;ENST00000376565	T;T;T	0.69306	-0.39;-0.39;-0.39	5.36	5.36	0.76844	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.88130	0.6354	H	0.96301	3.8	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.80764	0.994;0.971	D	0.91774	0.5430	10	0.87932	D	0	-22.5481	19.0839	0.93194	0.0:1.0:0.0:0.0	.	79;219	B4DH09;P48426	.;PI42A_HUMAN	K	219;79;160;171;178	ENSP00000365757:R219K;ENSP00000326294:R79K;ENSP00000442098:R160K	ENSP00000326294:R79K	R	-	2	0	PIP4K2A	22896808	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.252000	0.78309	2.530000	0.85305	0.650000	0.86243	AGA	.		0.453	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		T	22856802	C	T	22856802	3	4	92	1	0	0	0	0	1	0	0	0	11962	913	32	2	584	2	PIP4K2A	10	22856802	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		22856802	112677945	37	8315											
SYT15	83849	hgsc.bcm.edu	37	chr10	46969435	46969435	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccccccgatggtgcccccaAtcaccagggccagctgctct	6	6	10	19	1	2	0	1	0	1	0	2	1	2	0	7	2	3	2	7	2	1	0	rs374015418	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr10:46969435A>G	ENST00000374321.4	-	2	92	c.26T>C	c.(25-27)aTt>aCt	p.I9T	SYT15_ENST00000374325.3_Missense_Mutation_p.I9T|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000503753.1_Missense_Mutation_p.I9T|SYT15_ENST00000374323.4_Intron	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGTGCCCCCAATCACCAGGGC	0.632													A|||	3	0.000599042	0	0.0014	5008	,	,		36778	0.001		0.001	False		,,,				2504	0				p.I9T	Ovarian(57;1152 1428 19651 37745)	.											.	SYT15-22	0			c.T26C						.	A	THR/ILE,THR/ILE	2,4202		0,2,2100	15	20	18		26,26	1.7	0.1	10		18	0,8484		0,0,4242	no	missense,missense	SYT15	NM_031912.4,NM_181519.2	89,89	0,2,6342	GG,GA,AA		0.0,0.0476,0.0158	possibly-damaging,possibly-damaging	9/422,9/391	46969435	2,12686	2102	4242	6344	SO:0001583	missense	83849	exon2			CCCCCAATCACCA	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"Synaptotagmins"	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.26T>C	10.37:g.46969435A>G	ENSP00000363441:p.Ile9Thr	Somatic	28	1		WXS	Illumina HiSeq	Phase_I	17	10	NM_031912	0	0	0	0	0	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	a	11.75	1.731353	0.30684	4.76E-4	0.0	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374321	T;T;T	0.16743	2.32;2.32;2.56	4.04	1.72	0.24424	.	.	.	.	.	T	0.13157	0.0319	L	0.51422	1.61	0.09310	N	1	B;P	0.36535	0.421;0.557	B;B	0.31191	0.041;0.125	T	0.19192	-1.0313	9	0.59425	D	0.04	.	5.2408	0.15471	0.7616:0.0:0.2384:0.0	.	9;9	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	T	9	ENSP00000363445:I9T;ENSP00000427607:I9T;ENSP00000363441:I9T	ENSP00000363441:I9T	I	-	2	0	SYT15	46389441	0.000000	0.05858	0.072000	0.20136	0.932000	0.56968	0.119000	0.15626	0.709000	0.31976	0.383000	0.25322	ATT	.		0.632	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		G	46969435	A	G	46969435	3	3	92	1	0	0	0	0	1	0	0	0	15503	101	4	3	1321	3	SYT15	10	46969435	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	24112633	46969435	88565312	38	8316											
ARHGAP22	58504	bcgsc.ca	37	chr10	49667744	49667744	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacctgtcaaacagtggcttCtccccacagtcgaaggaatc	11	8	8	14	1	2	0	1	0	1	0	5	2	2	1	3	2	1	1	3	2	3	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr10:49667744C>T	ENST00000249601.4	-	5	938	c.642G>A	c.(640-642)gaG>gaA	p.E214E	ARHGAP22_ENST00000417247.2_Silent_p.E124E|ARHGAP22_ENST00000417912.2_Silent_p.E230E|ARHGAP22_ENST00000374170.1_Silent_p.E124E|ARHGAP22_ENST00000435790.2_Silent_p.E220E|ARHGAP22_ENST00000374172.1_Silent_p.E105E	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	214	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ACAGTGGCTTCTCCCCACAGT	0.622																																					p.E230E													.	ARHGAP22-228	0			c.G690A						.						197	180	186					10																	49667744		2203	4300	6503	SO:0001819	synonymous_variant	58504	exon5			TGGCTTCTCCCCA	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.642G>A	10.37:g.49667744C>T		Somatic	280	0		WXS	Illumina HiSeq	Phase_1	209	25	NM_001256024	0	0	1	1	0	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Silent	SNP	ENST00000249601.4	37	CCDS7227.1																																																																																			.		0.622	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		T	49667744	C	T	49667744	2	4	92	1	0	0	0	0	0	0	0	1	872	912	32	2		2	ARHGAP22	10	49667744	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08	2698309	49667744	85867003	39	8317											
TMEM26	219623	bcgsc.ca	37	chr10	63195951	63195951	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtctcatggtgcaattcaaGaagccataatgatggaacga	14	9	11	7	1	2	2	2	1	1	1	3	4	2	3	1	3	3	1	1	3	5	2	rs200974700		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr10:63195951G>A	ENST00000399298.3	-	2	615	c.247C>T	c.(247-249)Ctt>Ttt	p.L83F	TMEM26_ENST00000399293.1_Missense_Mutation_p.L83F	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	83						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					TGCAATTCAAGAAGCCATAAT	0.348																																					p.L83F													.	TMEM26-90	0			c.C247T						.						68	68	68					10																	63195951		1829	4079	5908	SO:0001583	missense	219623	exon2			ATTCAAGAAGCCA	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.247C>T	10.37:g.63195951G>A	ENSP00000382237:p.Leu83Phe	Somatic	72	0		WXS	Illumina HiSeq	Phase_1	42	10	NM_178505	0	0	0	0	0	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	37	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.757789	0.69648	.	.	ENSG00000196932	ENST00000399298;ENST00000399293	.	.	.	5.55	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.79070	0.4384	M	0.84511	2.7	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.81534	-0.0889	9	0.87932	D	0	-28.2733	10.5584	0.45131	0.1464:0.0:0.8536:0.0	.	83	Q6ZUK4	TMM26_HUMAN	F	83	.	ENSP00000382232:L83F	L	-	1	0	TMEM26	62865957	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	3.466000	0.53071	2.590000	0.87494	0.655000	0.94253	CTT	.		0.348	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		A	63195951	G	A	63195951	3	1	92	1	0	0	0	0	1	0	0	0	16183	942	33	2	879	2	TMEM26	10	63195951	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	13528207	63195951	72338796	40	8318											
DNA2	1763	bcgsc.ca	37	chr10	70196869	70196869	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttacaataactctgtcAcctgccattagatttgtgac	11	13	5	12	0	2	2	1	1	1	1	2	2	2	2	3	0	3	0	3	0	4	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr10:70196869A>C	ENST00000358410.3	-	10	1595	c.1545T>G	c.(1543-1545)ggT>ggG	p.G515G	DNA2_ENST00000399179.2_Silent_p.G515G|DNA2_ENST00000399180.2_Silent_p.G601G	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	515	Nuclease activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TAACTCTGTCACCTGCCATTA	0.353																																					p.G515G													.	.	0			c.T1545G						.						182	176	178					10																	70196869		1887	4114	6001	SO:0001819	synonymous_variant	1763	exon10			TCTGTCACCTGCC	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.1545T>G	10.37:g.70196869A>C		Somatic	251	13		WXS	Illumina HiSeq	Phase_1	144	32	NM_001080449	0	0	4	4	0	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.		0.353	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			C	70196869	A	C	70196869	2	2	92	1	0	0	0	0	0	0	0	1	4607	146	6	5		5	DNA2	10	70196869	Silent	SNP	A	TCGA-DW-5560-01A-01D-1589-08	7000918	70196869	65337878	41	8319											
RIC8A	60626	broad.mit.edu;bcgsc.ca	37	chr11	208890	208890	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgcagaagccgtggagacGggtgaggaggatgtgattat	10	9	18	4	2	0	4	0	2	0	2	0	7	0	6	1	4	2	2	1	4	2	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:208890G>T	ENST00000526104.1	+	1	1380	c.36G>T	c.(34-36)acG>acT	p.T12T	BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000410108.1_5'Flank|RIC8A_ENST00000325207.5_Silent_p.T12T|RIC8A_ENST00000527696.1_5'Flank|BET1L_ENST00000382762.3_5'Flank|BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000332865.6_5'Flank|BET1L_ENST00000325147.9_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	12					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CCGTGGAGACGGGTGAGGAGG	0.721																																					p.T12T													.	RIC8A-514	0			c.G36T						.						19	20	19					11																	208890		2199	4296	6495	SO:0001819	synonymous_variant	60626	exon1			GGAGACGGGTGAG	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.36G>T	11.37:g.208890G>T		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	15	4	NM_021932	0	0	2	3	1	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Silent	SNP	ENST00000526104.1	37																																																																																				.		0.721	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		T	208890	G	T	208890	2	4	92	1	0	0	0	0	0	0	0	1	13387	1103	39	4		4	RIC8A	11	208890	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08		208890	134797626	42	8320											
ANO9	338440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	428825	428825	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagctgaagtgccatttccTcctggggagagcaccgggca	8	8	14	11	1	0	3	0	2	0	1	2	4	2	3	4	3	3	3	4	3	1	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:428825T>C	ENST00000332826.6	-	12	1001	c.917A>G	c.(916-918)gAg>gGg	p.E306G		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	306					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						TGCCATTTCCTCCTGGGGAGA	0.602																																					p.E306G		.											.	ANO9-227	0			c.A917G						.						196	142	160					11																	428825		2199	4296	6495	SO:0001630	splice_region_variant	338440	exon12			ATTTCCTCCTGGG	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	20679	protein-coding gene	gene with protein product			"tumor protein p53 inducible protein 5", "transmembrane protein 16J"	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.916-1A>G	11.37:g.428825T>C		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_001012302	0	0	0	0	0	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.782107	0.49891	.	.	ENSG00000185101	ENST00000332826	T	0.68181	-0.31	3.62	3.62	0.41486	.	7.753800	0.01393	N	0.013339	D	0.87317	0.6147	M	0.90922	3.16	0.51233	D	0.99991	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.925	T	0.73173	-0.4066	10	0.72032	D	0.01	.	12.6745	0.56887	0.0:0.0:0.0:1.0	.	7;306	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	G	306	ENSP00000332788:E306G	ENSP00000332788:E306G	E	-	2	0	ANO9	418825	1.000000	0.71417	0.844000	0.33320	0.027000	0.11550	5.539000	0.67199	1.651000	0.50673	0.379000	0.24179	GAG	.		0.602	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302	Missense_Mutation	C	428825	T	C	428825	5	2	92	1	0	0	0	0	0	0	1	0	704	1565	54	3	1479	3	ANO9	11	428825	Splice_Site	SNP	T	TCGA-DW-5560-01A-01D-1589-08	219935	428825	134577691	43	8321											
OR52H1	390067	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	5566652	5566652	+	Frame_Shift_Del	DEL	C	C	-																															atacagaagggaattccaatCcacacatggaattgctccag																								rs565760908		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:5566652delC	ENST00000322653.4	-	1	127	c.102delG	c.(100-102)tggfs	p.W34fs	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAATTCCAATCCACACATGGA	0.473																																					p.W34X		.											.	OR52H1-114	0			c.102delG						.						88	80	83					11																	5566652		2201	4297	6498	SO:0001589	frameshift_variant	390067	exon1			.	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"GPCR / Class A : Olfactory receptors"	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.102delG	11.37:g.5566652delC	ENSP00000326259:p.Trp34fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	72	27	NM_001005289	0	0	0	0	0	B9EH26|Q6IF79	Nonsense_Mutation	DEL	ENST00000322653.4	37	CCDS31386.1																																																																																			.		0.473	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		-	5566652	C	-	5566652	7	5	92	1	0	1	0	1	0	0	0	0	11145	856	30	0	863	0	OR52H1	11	5566652	Frame_Shift_Del	DEL	C	TCGA-DW-5560-01A-01D-1589-08	5137827	5566652	129439864	44	8322											
OR5B3	441608	broad.mit.edu	37	chr11	58170566	58170566	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agaggtaattttccacagtgGcaaaagctacaaagatatac	17	9	8	7	0	0	2	0	0	0	2	1	2	1	2	1	2	3	3	1	2	7	6			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:58170566G>A	ENST00000309403.2	-	1	316	c.317C>T	c.(316-318)gCc>gTc	p.A106V		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	106						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TTCCACAGTGGCAAAAGCTAC	0.453																																					p.A106V													.	OR5B3-68	0			c.C317T						.						131	121	124					11																	58170566		2201	4295	6496	SO:0001583	missense	441608	exon1			ACAGTGGCAAAAG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"GPCR / Class A : Olfactory receptors"	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.317C>T	11.37:g.58170566G>A	ENSP00000308270:p.Ala106Val	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	139	4	NM_001005469	0	0	0	0	0	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	.	.	.	.	.	.	.	.	.	.	g	6.305	0.424317	0.11928	.	.	ENSG00000172769	ENST00000309403	T	0.01359	4.98	3.96	2.06	0.26882	GPCR, rhodopsin-like superfamily (1);	0.297208	0.24150	N	0.041083	T	0.01353	0.0044	L	0.37561	1.115	0.19575	N	0.999966	B	0.16802	0.019	B	0.14578	0.011	T	0.48328	-0.9045	10	0.17369	T	0.5	-4.7308	8.991	0.36024	0.1887:0.0:0.8113:0.0	.	106	Q8NH48	OR5B3_HUMAN	V	106	ENSP00000308270:A106V	ENSP00000308270:A106V	A	-	2	0	OR5B3	57927142	0.000000	0.05858	0.966000	0.40874	0.267000	0.26476	-0.182000	0.09726	0.453000	0.26858	-0.237000	0.12165	GCC	.		0.453	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469		A	58170566	G	A	58170566	3	1	92	1	0	0	0	0	1	0	0	0	11178	1203	42	2	629	2	OR5B3	11	58170566	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	52603914	58170566	76835950	45	8323											
SAPS3	55291	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	68318634	68318637	+	Frame_Shift_Del	DEL	CATC	CATC	-																															agaggcttgtggaaatagttCatccatcgcaagaagaagat																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	CATC	CATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:68318634_68318637delCATC	ENST00000393800.2	+	6	852_855	c.598_601delCATC	c.(598-603)catccafs	p.HP200fs	PPP6R3_ENST00000265636.5_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000524904.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000265637.4_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000393799.2_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000393801.3_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000529710.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000527403.2_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000524845.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000534534.1_Intron	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	200					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGAAATAGTTCATCCATCGCAAGA	0.348																																					p.200_201del		.											.	PPP6R3-91	0			c.598_601del						.																																			SO:0001589	frameshift_variant	55291	exon6			.	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.598_601delCATC	11.37:g.68318638_68318641delCATC	ENSP00000377389:p.His200fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	55	25	NM_001164162	0	0	0	0	0	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Frame_Shift_Del	DEL	ENST00000393800.2	37	CCDS53672.1																																																																																			.		0.348	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		-	68318637	CATC	-	68318634	7	5	92	1	0	1	0	1	0	0	0	0	13870	826	29	0	612	0	SAPS3	11	68318634	Frame_Shift_Del	DEL	CATC	TCGA-DW-5560-01A-01D-1589-08	10148068	68318634	66687882	46	8324											
LARP4	113251	bcgsc.ca	37	chr12	50869377	50869377	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagccatcttcagttcttgtGcagccactacgggaacttcg	8	11	10	12	2	3	0	1	0	2	0	4	2	3	1	2	1	5	2	2	1	2	5			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:50869377G>C	ENST00000398473.2	+	16	2017	c.1905G>C	c.(1903-1905)gtG>gtC	p.V635V	LARP4_ENST00000347328.5_Silent_p.V564V|LARP4_ENST00000518444.1_Silent_p.V634V|LARP4_ENST00000429001.3_Silent_p.V641V|LARP4_ENST00000293618.8_Silent_p.V564V	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	635					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						CAGTTCTTGTGCAGCCACTAC	0.453																																					p.V635V													.	LARP4-91	0			c.G1905C						.						159	159	159					12																	50869377		1838	4094	5932	SO:0001819	synonymous_variant	113251	exon16			TCTTGTGCAGCCA	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1905G>C	12.37:g.50869377G>C		Somatic	353	0		WXS	Illumina HiSeq	Phase_1	225	34	NM_052879	0	0	3	3	0	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	37	CCDS41782.1																																																																																			.		0.453	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		C	50869377	G	C	50869377	2	2	92	1	0	0	0	0	0	0	0	1	8651	1306	46	4		4	LARP4	12	50869377	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08		50869377	82982518	47	8325											
BEST3	144453	bcgsc.ca	37	chr12	70049556	70049556	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatgcttctcataatcccAcagccactcctcgtcaggaa	10	9	6	16	1	2	0	2	0	1	0	6	1	4	1	4	1	2	1	4	1	2	2	rs75364232		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:70049556A>C	ENST00000330891.5	-	10	1364	c.1138T>G	c.(1138-1140)Tgg>Ggg	p.W380G	BEST3_ENST00000488961.1_Missense_Mutation_p.W167G|BEST3_ENST00000553096.1_Missense_Mutation_p.W274G|BEST3_ENST00000331471.4_Intron	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	380					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			TCATAATCCCACAGCCACTCC	0.552																																					p.W380G													.	BEST3-248	0			c.T1138G						.						85	88	87					12																	70049556		2071	4216	6287	SO:0001583	missense	144453	exon10			AATCCCACAGCCA	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17105	protein-coding gene	gene with protein product		607337	"vitelliform macular dystrophy 2-like 3"	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.1138T>G	12.37:g.70049556A>C	ENSP00000332413:p.Trp380Gly	Somatic	160	0		WXS	Illumina HiSeq	Phase_1	117	19	NM_032735	0	0	1	1	0	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	.	.	.	.	.	.	.	.	.	.	A	11.73	1.726777	0.30593	.	.	ENSG00000127325	ENST00000488961;ENST00000330891;ENST00000553096	D;D;D	0.97941	-4.31;-4.62;-4.59	5.63	5.63	0.86233	.	0.490168	0.21288	N	0.077038	D	0.96482	0.8852	M	0.72118	2.19	0.80722	D	1	P;D	0.57257	0.629;0.979	B;P	0.46940	0.225;0.532	D	0.94362	0.7588	10	0.16896	T	0.51	-10.6053	9.3652	0.38219	0.9188:0.0:0.0812:0.0	.	380;167	Q8N1M1;B5MDI8	BEST3_HUMAN;.	G	167;380;274	ENSP00000433213:W167G;ENSP00000332413:W380G;ENSP00000449548:W274G	ENSP00000332413:W380G	W	-	1	0	BEST3	68335823	0.999000	0.42202	0.999000	0.59377	0.382000	0.30200	4.037000	0.57311	2.130000	0.65690	0.533000	0.62120	TGG	.		0.552	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		C	70049556	A	C	70049556	3	2	92	1	0	0	0	0	1	0	0	0	1407	159	6	5	872	5	BEST3	12	70049556	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	19180179	70049556	63802339	48	8326											
RPL6	6128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	112843158	112843158	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagctttctgatcaatcttgCgctgctccgtaatctcatat	8	15	6	12	2	4	1	2	1	3	0	6	1	5	1	1	0	3	4	1	0	3	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:112843158C>T	ENST00000424576.2	-	7	922	c.737G>A	c.(736-738)cGc>cAc	p.R246H	RPL6_ENST00000202773.9_Missense_Mutation_p.R246H	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	246					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|large_intestine(6)|lung(3)	10						ATCAATCTTGCGCTGCTCCGT	0.393																																					p.R246H		.											.	RPL6-153	0			c.G737A						.						23	25	24					12																	112843158		2187	4288	6475	SO:0001583	missense	6128	exon7			ATCTTGCGCTGCT	X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"L ribosomal proteins"	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.737G>A	12.37:g.112843158C>T	ENSP00000403172:p.Arg246His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	59	16	NM_001024662	0	1	995	1890	894	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	37	CCDS9162.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.498413	0.64298	.	.	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.34072	1.38;1.38	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.66297	2.02	0.80722	D	1	B	0.30439	0.279	B	0.29524	0.103	T	0.40572	-0.9556	10	0.62326	D	0.03	.	16.8348	0.85954	0.0:1.0:0.0:0.0	.	246	Q02878	RL6_HUMAN	H	246;246;186	ENSP00000202773:R246H;ENSP00000403172:R246H	ENSP00000202773:R246H	R	-	2	0	RPL6	111327541	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.919000	0.75793	2.408000	0.81797	0.591000	0.81541	CGC	.		0.393	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1			T	112843158	C	T	112843158	3	4	92	1	0	0	0	0	1	0	0	0	13630	768	27	1	133	1	RPL6	12	112843158	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	42793602	112843158	21008737	49	8327											
SBNO1	55206	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	123801801	123801802	+	Frame_Shift_Ins	INS	-	-	T																															gctctatcagcgctccaaggINStaattctaaagtcatatgaa																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:123801801_123801802insT	ENST00000602398.1	-	21	3028_3029	c.2901_2902insA	c.(2899-2904)ttacctfs	p.P968fs	SBNO1_ENST00000602750.1_Frame_Shift_Ins_p.P967fs|SBNO1_ENST00000267176.4_Frame_Shift_Ins_p.P967fs|SBNO1_ENST00000420886.2_Frame_Shift_Ins_p.P968fs			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	968					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GCGCTCCAAGGTAATTCTAAAG	0.396																																					p.P968fs		.											.	SBNO1-292	0			c.2902_2903insA						.																																			SO:0001589	frameshift_variant	55206	exon20			.	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2902dupA	12.37:g.123801802_123801802dupT	ENSP00000473665:p.Pro968fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	115	36	NM_001167856	0	0	0	0	0	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Frame_Shift_Ins	INS	ENST00000602398.1	37	CCDS53844.1																																																																																			.		0.396	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		T	123801802	-	T	123801801	7	5	92	1	0	1	1	0	0	0	0	0	13894	1261	44	0	1327	0	SBNO1	12	123801801	Frame_Shift_Ins	INS	-	TCGA-DW-5560-01A-01D-1589-08	10958643	123801801	10050094	50	8328											
TMCO3	55002	bcgsc.ca	37	chr13	114188424	114188425	+	In_Frame_Ins	INS	-	-	GGTTTTTTTTTT																															tcttttttcactagcggcggINStttttcttttatgtcttgtt																								rs141899812		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr13:114188424_114188425insGGTTTTTTTTTT	ENST00000434316.2	+	9	1767_1768	c.1408_1409insGGTTTTTTTTTT	c.(1408-1410)gtt>gGGTTTTTTTTTTtt	p.470_470V>GFFFF	TMCO3_ENST00000375391.1_Intron|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	470						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			ACTAGCGGCGGTTTTTCTTTTA	0.406																																					p.V470delinsGFFFF													.	TMCO3-90	0			c.1408_1409insGGTTTTTTTTTT						.																																			SO:0001652	inframe_insertion	55002	exon9			GCGGCGGTTTTTC	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 11"	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	Exception_encountered	13.37:g.114188424_114188425insGGTTTTTTTTTT	ENSP00000389399:p.Val470delinsGlyPhePhePhePhe	Somatic	207	0		WXS	Illumina HiSeq	Phase_1	244	5	NM_017905	0	0	0	0	0	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	In_Frame_Ins	INS	ENST00000434316.2	37	CCDS9537.1																																																																																			.		0.406	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905		GGTTTTTTTTTT	114188425	-	GGTTTTTTTTTT	114188424	7	5	92	1	0	1	1	0	0	0	0	0	16029	1261	44	0	1438	0	TMCO3	13	114188424	In_Frame_Ins	INS	-	TCGA-DW-5560-01A-01D-1589-08		114188424	981454	51	8329											
INF2	64423	hgsc.bcm.edu;bcgsc.ca	37	chr14	105174895	105174896	+	Frame_Shift_Ins	INS	-	-	C																															caaggagcccaccatggtggINSccccccgggccaggaaggag																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr14:105174895_105174896insC	ENST00000392634.4	+	9	1970_1971	c.1858_1859insC	c.(1858-1860)gccfs	p.A620fs	INF2_ENST00000330634.7_Frame_Shift_Ins_p.A620fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	620	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CACCATGGTGGCCCCCCGGGCC	0.703											OREG0022959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A620fs		.											.	INF2-492	0			c.1858_1859insC						.																																			SO:0001589	frameshift_variant	64423	exon9			.	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"inverted formin 2"	610982	"chromosome 14 open reading frame 151", "chromosome 14 open reading frame 173"	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1864dupC	14.37:g.105174901_105174901dupC	ENSP00000376410:p.Ala620fs	Somatic	44	0	1387	WXS	Illumina HiSeq	Phase_I	43	22	NM_001031714	0	0	0	0	0	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Ins	INS	ENST00000392634.4	37	CCDS9989.2																																																																																			.		0.703	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		C	105174896	-	C	105174895	7	5	92	1	0	1	1	0	0	0	0	0	7755	1203	42	0	1892	0	INF2	14	105174895	Frame_Shift_Ins	INS	-	TCGA-DW-5560-01A-01D-1589-08		105174895	2174645	52	8330											
DMXL2	23312	broad.mit.edu;bcgsc.ca	37	chr15	51783908	51783908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagttcttcttcagcctcaGaatgaaaagcccaggcaaaa	14	9	7	11	0	5	2	3	1	2	1	5	2	5	2	2	1	2	2	2	1	5	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr15:51783908G>A	ENST00000251076.5	-	20	5107	c.4820C>T	c.(4819-4821)tCt>tTt	p.S1607F	DMXL2_ENST00000543779.2_Missense_Mutation_p.S1607F|DMXL2_ENST00000449909.3_Missense_Mutation_p.S971F|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1607						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTCAGCCTCAGAATGAAAAGC	0.388																																					p.S1607F													.	DMXL2-99	0			c.C4820T						.						88	95	93					15																	51783908		2195	4293	6488	SO:0001583	missense	23312	exon20			GCCTCAGAATGAA	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.4820C>T	15.37:g.51783908G>A	ENSP00000251076:p.Ser1607Phe	Somatic	144	2		WXS	Illumina HiSeq	Phase_I	121	49	NM_001174116	0	0	0	0	0	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841196	0.71488	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.68181	-0.31;-0.31;-0.31	5.29	4.37	0.52481	.	0.000000	0.85682	D	0.000000	D	0.85965	0.5820	H	0.94385	3.53	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.91635	0.999;0.996;0.998	D	0.89690	0.3897	10	0.87932	D	0	.	13.7623	0.62973	0.074:0.0:0.926:0.0	.	1607;971;1607	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	F	1607;1607;971	ENSP00000251076:S1607F;ENSP00000441858:S1607F;ENSP00000400855:S971F	ENSP00000251076:S1607F	S	-	2	0	DMXL2	49571200	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	9.386000	0.97228	1.363000	0.46019	0.655000	0.94253	TCT	.		0.388	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51783908	G	A	51783908	3	1	92	1	0	0	0	0	1	0	0	0	4606	942	33	2	4389	2	DMXL2	15	51783908	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08		51783908	50747484	53	8331											
CHD2	1106	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	93567925	93567925	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agattataactggaatgttcGgaaaacataaaggacagctc	17	9	9	6	1	0	1	0	0	0	1	2	4	0	4	0	3	3	2	0	3	7	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr15:93567925G>A	ENST00000394196.4	+	39	6545	c.5477G>A	c.(5476-5478)cGg>cAg	p.R1826Q		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1826					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TGGAATGTTCGGAAAACATAA	0.428																																					p.R1826Q		.											.	CHD2-229	0			c.G5477A						.						50	47	48					15																	93567925		1887	4107	5994	SO:0001583	missense	1106	exon39			ATGTTCGGAAAAC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.5477G>A	15.37:g.93567925G>A	ENSP00000377747:p.Arg1826Gln	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	44	4	NM_001271	0	0	12	12	0	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	36	5.643949	0.96704	.	.	ENSG00000173575	ENST00000394196	D	0.92647	-3.08	5.56	5.56	0.83823	.	.	.	.	.	D	0.93485	0.7921	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.94151	0.7405	9	0.72032	D	0.01	-0.1389	19.8965	0.96963	0.0:0.0:1.0:0.0	.	1826	O14647	CHD2_HUMAN	Q	1826	ENSP00000377747:R1826Q	ENSP00000377747:R1826Q	R	+	2	0	CHD2	91368929	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.932000	0.75869	2.771000	0.95319	0.563000	0.77884	CGG	.		0.428	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		A	93567925	G	A	93567925	3	1	92	1	0	0	0	0	1	0	0	0	3331	1116	39	1	5631	1	CHD2	15	93567925	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	41784017	93567925	8963467	54	8332											
SMG1	23049	hgsc.bcm.edu	37	chr16	18841542	18841542	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatccaagtccacatttaccTtttcaactaataagctgaaa	16	12	3	10	0	1	1	1	1	0	0	3	1	3	1	3	0	3	1	3	0	7	6			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:18841542T>C	ENST00000446231.2	-	52	9354	c.8942A>G	c.(8941-8943)aAg>aGg	p.K2981R	SMG1_ENST00000389467.3_Splice_Site_p.K2981R			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2981					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CACATTTACCTTTTCAACTAA	0.368																																					p.K2981R		.											.	SMG1-1160	0			c.A8942G						.						59	53	55					16																	18841542		1857	4104	5961	SO:0001630	splice_region_variant	23049	exon52			TTTACCTTTTCAA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.8943+1A>G	16.37:g.18841542T>C		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_015092	0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961864	0.53400	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01092	5.35;5.35	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000001	T	0.01421	0.0046	N	0.19112	0.55	0.49582	D	0.999805	P	0.51057	0.941	P	0.46917	0.531	T	0.75983	-0.3125	10	0.09338	T	0.73	.	16.3947	0.83586	0.0:0.0:0.0:1.0	.	2981	Q96Q15	SMG1_HUMAN	R	2981	ENSP00000402515:K2981R;ENSP00000374118:K2981R	ENSP00000374118:K2981R	K	-	2	0	SMG1	18749043	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.809000	0.86057	2.272000	0.75746	0.459000	0.35465	AAG	.		0.368	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	Missense_Mutation	C	18841542	T	C	18841542	5	2	92	1	0	0	0	0	0	0	1	0	14827	1623	56	3	2091	3	SMG1	16	18841542	Splice_Site	SNP	T	TCGA-DW-5560-01A-01D-1589-08		18841542	71513211	55	8333											
NFATC2IP	84901	hgsc.bcm.edu	37	chr16	28962357	28962357	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggagcctgtggggaagcggGgccgctggtccggaggtagc	5	5	21	10	4	0	0	0	0	0	0	1	3	1	3	3	8	3	2	3	8	2	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:28962357G>A	ENST00000320805.4	+	1	100	c.25G>A	c.(25-27)Ggc>Agc	p.G9S	NFATC2IP_ENST00000562977.1_3'UTR|NFATC2IP_ENST00000564978.1_Intron	NM_032815.3	NP_116204.3	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	9					cytokine production (GO:0001816)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(2)	11						GGGGAAGCGGGGCCGCTGGTC	0.746																																					p.G9S		.											.	NFATC2IP-91	0			c.G25A						.						8	8	8					16																	28962357		2155	4247	6402	SO:0001583	missense	84901	exon1			AAGCGGGGCCGCT	AK074761	CCDS10645.1	16p11.2	2010-09-13			ENSG00000176953	ENSG00000176953			25906	protein-coding gene	gene with protein product		614525				15698469	Standard	NM_032815		Approved	FLJ14639, NIP45, RAD60, ESC2	uc002dru.3	Q8NCF5	OTTHUMG00000097763	ENST00000320805.4:c.25G>A	16.37:g.28962357G>A	ENSP00000324792:p.Gly9Ser	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	12	5	NM_032815	0	0	0	1	1	B7Z4G5|Q66K34|Q6NVK1|Q8NFR2|Q96ST9	Missense_Mutation	SNP	ENST00000320805.4	37	CCDS10645.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066553	0.55539	.	.	ENSG00000176953	ENST00000320805	T	0.20738	2.05	3.93	1.75	0.24633	.	0.242826	0.21545	N	0.072825	T	0.33673	0.0871	M	0.63428	1.95	0.18873	N	0.999987	D;D	0.76494	0.999;0.97	D;P	0.66847	0.947;0.665	T	0.03433	-1.1037	10	0.87932	D	0	-12.4241	4.3333	0.11075	0.1322:0.2392:0.6286:0.0	.	9;9	B7Z8Y9;Q8NCF5	.;NF2IP_HUMAN	S	9	ENSP00000324792:G9S	ENSP00000324792:G9S	G	+	1	0	NFATC2IP	28869858	0.073000	0.21202	0.023000	0.16930	0.020000	0.10135	0.970000	0.29383	1.906000	0.55180	0.557000	0.71058	GGC	.		0.746	NFATC2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214999.2	NM_032815		A	28962357	G	A	28962357	3	1	92	1	0	0	0	0	1	0	0	0	10389	1232	43	2	27	2	NFATC2IP	16	28962357	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	10120815	28962357	61392396	56	8334											
PLEKHG4	25894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67315014	67315014	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gcccgaagtacaggcactggGactgacagtgctagttgatg	10	8	14	9	1	0	2	0	2	0	0	0	4	0	3	1	2	2	4	1	2	3	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:67315014G>C	ENST00000360461.5	+	4	3275	c.740G>C	c.(739-741)gGa>gCa	p.G247A	PLEKHG4_ENST00000450733.1_Missense_Mutation_p.G166A|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.G247A|PLEKHG4_ENST00000379344.3_Missense_Mutation_p.G247A	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	247							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CAGGCACTGGGACTGACAGTG	0.552																																					p.G247A		.											.	PLEKHG4-92	0			c.G740C						.						138	123	128					16																	67315014		2198	4300	6498	SO:0001583	missense	25894	exon5			CACTGGGACTGAC	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.740G>C	16.37:g.67315014G>C	ENSP00000353646:p.Gly247Ala	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	118	62	NM_001129728	0	0	2	2	0	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	37	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	34	5.393426	0.96009	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.71	5.71	0.89125	.	0.000000	0.32802	N	0.005631	T	0.66366	0.2782	M	0.88570	2.965	0.35318	D	0.78447	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.78059	-0.2352	10	0.62326	D	0.03	.	15.3559	0.74425	0.0:0.0:1.0:0.0	.	166;54;247	Q58EX7-2;B4E3H4;Q58EX7	.;.;PKHG4_HUMAN	A	247;247;247;166	ENSP00000353646:G247A;ENSP00000401118:G247A;ENSP00000368649:G247A;ENSP00000398030:G166A	ENSP00000353646:G247A	G	+	2	0	PLEKHG4	65872515	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.887000	0.69751	2.688000	0.91661	0.591000	0.81541	GGA	.		0.552	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		C	67315014	G	C	67315014	3	2	92	1	0	0	0	0	1	0	0	0	12097	1174	41	4	754	4	PLEKHG4	16	67315014	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	38352657	67315014	23039739	57	8335											
AP1G1	164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	71789972	71789972	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtctgctttaaattctggCtcacacgaatccagaaaata	14	11	6	10	1	3	1	1	0	2	1	4	2	4	1	1	1	1	2	1	1	6	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:71789972C>T	ENST00000299980.4	-	12	1620	c.1179G>A	c.(1177-1179)gaG>gaA	p.E393E	AP1G1_ENST00000433195.2_Silent_p.E416E|AP1G1_ENST00000423132.2_Silent_p.E396E|AP1G1_ENST00000569748.1_Silent_p.E393E|AP1G1_ENST00000393512.3_Silent_p.E396E|SNORD71_ENST00000411292.1_RNA	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	393					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TAAATTCTGGCTCACACGAAT	0.378																																					p.E396E		.											.	AP1G1-92	0			c.G1188A						.						90	95	93					16																	71789972		2198	4300	6498	SO:0001819	synonymous_variant	164	exon13			TTCTGGCTCACAC	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.1179G>A	16.37:g.71789972C>T		Somatic	153	1		WXS	Illumina HiSeq	Phase_I	140	59	NM_001030007	0	0	1	1	0	O75709|O75842|Q9UG09|Q9Y3U4	Silent	SNP	ENST00000299980.4	37	CCDS32480.1																																																																																			.		0.378	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			T	71789972	C	T	71789972	2	4	92	1	0	0	0	0	0	0	0	1	732	796	28	2		2	AP1G1	16	71789972	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08	4474958	71789972	18564781	58	8336											
ADAMTS18	170692	broad.mit.edu	37	chr16	77325309	77325309	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggaaagttatcagctttcCctggaagcccttctcgctgc	7	12	10	12	1	2	0	1	0	1	0	4	2	3	2	2	2	3	3	2	2	3	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:77325309C>A	ENST00000282849.5	-	21	3674	c.3256G>T	c.(3256-3258)Gga>Tga	p.G1086*	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1086	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ATCAGCTTTCCCTGGAAGCCC	0.507																																					p.G1086X													.	ADAMTS18-1036	0			c.G3256T						.						225	228	227					16																	77325309		2198	4300	6498	SO:0001587	stop_gained	170692	exon21			GCTTTCCCTGGAA	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"ADAM metallopeptidases with thrombospondin type 1 motif"	17110	protein-coding gene	gene with protein product		607512	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3256G>T	16.37:g.77325309C>A	ENSP00000282849:p.Gly1086*	Somatic	353	0		WXS	Illumina HiSeq	Phase_I	349	6	NM_199355	0	0	0	0	0	Q6P4R5|Q6ZWJ9	Nonsense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	44	10.858122	0.99479	.	.	ENSG00000140873	ENST00000282849	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	19.0575	0.93072	0.0:1.0:0.0:0.0	.	.	.	.	X	1086	.	ENSP00000282849:G1086X	G	-	1	0	ADAMTS18	75882810	1.000000	0.71417	0.974000	0.42286	0.806000	0.45545	6.818000	0.75257	2.758000	0.94735	0.563000	0.77884	GGA	.		0.507	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			A	77325309	C	A	77325309	4	1	92	1	0	0	0	0	0	1	0	0	263	632	22	4	421	4	ADAMTS18	16	77325309	Nonsense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	5535337	77325309	13029444	59	8337											
CCL23	6368	broad.mit.edu	37	chr17	34340315	34340315	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acttgcttatcactggggttGgcacagaaacgtcgcccctt	8	11	10	12	2	1	1	1	0	0	1	2	1	1	1	2	3	2	3	2	3	2	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:34340315G>A	ENST00000591423.1	-	4	349	c.285C>T	c.(283-285)gcC>gcT	p.A95A	RP11-104J23.1_ENST00000588294.1_RNA|RP11-104J23.2_ENST00000590149.1_lincRNA|CCL23_ENST00000293280.2_Silent_p.A112A|RP11-104J23.1_ENST00000590192.1_RNA	NM_145898.1	NP_665905.1	P55773	CCL23_HUMAN	chemokine (C-C motif) ligand 23	95					cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|negative regulation of C-C chemokine binding (GO:2001264)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)			large_intestine(2)|liver(1)|lung(2)|prostate(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CACTGGGGTTGGCACAGAAAC	0.527																																					p.A112A													.	CCL23-90	0			c.C336T						.						84	68	74					17																	34340315		2203	4300	6503	SO:0001819	synonymous_variant	6368	exon4			GGGGTTGGCACAG	U58913	CCDS11305.1, CCDS59282.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000167236	ENSG00000274736		"Chemokine ligands", "Endogenous ligands"	10622	protein-coding gene	gene with protein product		602494	"small inducible cytokine subfamily A (Cys-Cys), member 23"	SCYA23		9104803, 10409433	Standard	XR_429910		Approved	Ckb-8, MPIF-1, MIP-3, CKb8	uc002hks.1	P55773	OTTHUMG00000188409	ENST00000591423.1:c.285C>T	17.37:g.34340315G>A		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	68	3	NM_005064	0	0	0	0	0	B7ZKQ3|O00174|O75950|Q52LD4	Silent	SNP	ENST00000591423.1	37	CCDS59282.1																																																																																			.		0.527	CCL23-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450228.1	NM_005064, NM_145898		A	34340315	G	A	34340315	2	1	92	1	0	0	0	0	0	0	0	1	2901	1335	47	2		2	CCL23	17	34340315	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08		34340315	46854895	60	8338											
CDK12	51755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37627488	37627488	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggtgaatgtaacacatcTaaacacagaggtaaaaaatt	19	9	7	6	0	1	2	0	1	1	1	1	2	1	2	0	2	2	2	0	2	7	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:37627488T>A	ENST00000447079.4	+	2	1436	c.1403T>A	c.(1402-1404)cTa>cAa	p.L468Q	CDK12_ENST00000430627.2_Missense_Mutation_p.L468Q	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	468					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						GTAACACATCTAAACACAGAG	0.383			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.L468Q		.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12-1055	0			c.T1403A						.						98	103	101					17																	37627488		2203	4300	6503	SO:0001583	missense	51755	exon2			CACATCTAAACAC	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"Cyclin-dependent kinases"	24224	protein-coding gene	gene with protein product	"CDC2 related protein kinase 7"	615514	"Cdc2-related kinase, arginine/serine-rich"	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.1403T>A	17.37:g.37627488T>A	ENSP00000398880:p.Leu468Gln	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	187	50	NM_016507	0	0	2	3	1	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.939975	0.34283	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.39787	1.06;1.06	5.76	3.58	0.41010	.	0.608641	0.12825	N	0.436065	T	0.22589	0.0545	N	0.14661	0.345	0.21220	N	0.99976	B;B;B	0.16603	0.01;0.01;0.018	B;B;B	0.25291	0.026;0.026;0.059	T	0.18967	-1.0320	10	0.25106	T	0.35	-0.9823	2.5375	0.04717	0.2138:0.3455:0.0:0.4407	.	467;468;468	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	Q	468	ENSP00000407720:L468Q;ENSP00000398880:L468Q	ENSP00000407720:L468Q	L	+	2	0	CDK12	34881014	0.002000	0.14202	1.000000	0.80357	0.998000	0.95712	0.584000	0.23864	1.076000	0.40961	0.528000	0.53228	CTA	.		0.383	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		A	37627488	T	A	37627488	3	1	92	1	0	0	0	0	1	0	0	0	3134	1522	53	5	1409	5	CDK12	17	37627488	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08	3287173	37627488	43567722	61	8339											
CLTC	1213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	57754485	57754485	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttggaaagtattgtgagaAgagagatccacatctggcct	12	11	12	6	0	1	3	0	1	1	3	2	6	2	4	2	2	0	2	2	2	3	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:57754485A>G	ENST00000269122.3	+	17	3006	c.2732A>G	c.(2731-2733)aAg>aGg	p.K911R	CLTC_ENST00000579815.1_3'UTR|CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Missense_Mutation_p.K911R	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	911	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TATTGTGAGAAGAGAGATCCA	0.423			T	"ALK, TFE3"	"ALCL, renal "																																p.K911R		.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC-835	0			c.A2732G						.						118	116	116					17																	57754485		2203	4300	6503	SO:0001583	missense	1213	exon17			GTGAGAAGAGAGA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2732A>G	17.37:g.57754485A>G	ENSP00000269122:p.Lys911Arg	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	127	82	NM_004859	0	0	0	3	3	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	34	5.330051	0.95733	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.23552	1.9;1.9	5.69	5.69	0.88448	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56156	0.1966	M	0.85945	2.785	0.80722	D	1	D;B	0.69078	0.997;0.139	D;B	0.83275	0.996;0.394	T	0.60707	-0.7210	10	0.48119	T	0.1	.	15.9483	0.79809	1.0:0.0:0.0:0.0	.	911;911	Q00610;Q00610-2	CLH1_HUMAN;.	R	911	ENSP00000269122:K911R;ENSP00000376763:K911R	ENSP00000269122:K911R	K	+	2	0	CLTC	55109267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.228000	0.95250	2.168000	0.68352	0.455000	0.32223	AAG	.		0.423	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		G	57754485	A	G	57754485	3	3	92	1	0	0	0	0	1	0	0	0	3572	72	3	3	2798	3	CLTC	17	57754485	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	20126997	57754485	23440725	62	8340											
MRC2	9902	hgsc.bcm.edu	37	chr17	60767020	60767020	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtgtgagagccgcaatGccagcctggcctacgtgccc	6	8	13	14	2	0	1	0	1	0	1	0	2	0	1	5	1	6	2	5	1	2	1	rs376905774		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:60767020G>C	ENST00000303375.5	+	24	3874	c.3472G>C	c.(3472-3474)Gcc>Ccc	p.A1158P	MRC2_ENST00000446119.2_Intron|MRC2_ENST00000580916.1_Intron	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1158	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GAGCCGCAATGCCAGCCTGGC	0.692																																					p.A1158P		.											.	MRC2-117	0			c.G3472C						.						23	20	21					17																	60767020		2200	4300	6500	SO:0001583	missense	9902	exon24			CGCAATGCCAGCC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3472G>C	17.37:g.60767020G>C	ENSP00000307513:p.Ala1158Pro	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_006039	0	0	0	0	0	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059910	0.55325	.	.	ENSG00000011028	ENST00000303375	T	0.26810	1.71	5.1	-5.13	0.02884	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.438461	0.26116	N	0.026252	T	0.30978	0.0782	M	0.76838	2.35	0.43326	D	0.995354	P	0.43633	0.813	P	0.48627	0.584	T	0.32481	-0.9905	10	0.66056	D	0.02	-8.6135	8.0509	0.30577	0.4748:0.0:0.4249:0.1003	.	1158	Q9UBG0	MRC2_HUMAN	P	1158	ENSP00000307513:A1158P	ENSP00000307513:A1158P	A	+	1	0	MRC2	58120752	0.224000	0.23674	0.025000	0.17156	0.378000	0.30076	0.529000	0.23019	-0.836000	0.04229	-0.254000	0.11334	GCC	.		0.692	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			C	60767020	G	C	60767020	3	2	92	1	0	0	0	0	1	0	0	0	9783	1319	46	4	3566	4	MRC2	17	60767020	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	3012535	60767020	20428190	63	8341											
SLC16A6	9120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	66267173	66267173	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagaattcagtagcaaaagtAaaggcaaacagagacacagt	20	5	9	7	0	1	2	1	0	0	2	1	3	1	2	0	1	2	4	0	1	7	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:66267173A>G	ENST00000327268.4	-	6	1292	c.1128T>C	c.(1126-1128)ttT>ttC	p.F376F	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Silent_p.F376F	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	376					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	TAGCAAAAGTAAAGGCAAACA	0.443																																					p.F376F		.											.	SLC16A6-90	0			c.T1128C						.						120	112	115					17																	66267173		2203	4300	6503	SO:0001819	synonymous_variant	9120	exon6			AAAAGTAAAGGCA	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"Solute carriers"	10927	protein-coding gene	gene with protein product		603880	"solute carrier family 16 (monocarboxylic acid transporters), member 6", "solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.1128T>C	17.37:g.66267173A>G		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	130	85	NM_001174166	0	0	2	2	0	Q6P1X3	Silent	SNP	ENST00000327268.4	37	CCDS11675.1																																																																																			.		0.443	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		G	66267173	A	G	66267173	2	3	92	1	0	0	0	0	0	0	0	1	14444	359	13	3		3	SLC16A6	17	66267173	Silent	SNP	A	TCGA-DW-5560-01A-01D-1589-08	5500153	66267173	14928037	64	8342											
ZNF763	284390	hgsc.bcm.edu	37	chr19	12088187	12088187	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttctgtgtctgtattttaggGaaaaagtggaaagaccagaa	14	12	11	4	0	2	2	0	0	2	2	2	4	2	4	1	2	0	1	1	2	6	4	rs374392113		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr19:12088187G>A	ENST00000358987.3	+	3	259	c.132G>A	c.(130-132)ggG>ggA	p.G44G	ZNF763_ENST00000343949.5_Splice_Site_p.G47G|ZNF763_ENST00000538752.1_Splice_Site_p.G64G|ZNF763_ENST00000592625.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000590798.1_Splice_Site_p.G64G			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	44	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						GTATTTTAGGGAAAAAGTGGA	0.353																																					p.G47G		.											.	ZNF763-90	0			c.G141A						.	G		0,4406		0,0,2203	86	88	88		141	-1.6	0	19		88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous-near-splice	ZNF763	NM_001012753.1		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		47/398	12088187	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	284390	exon3			TTTAGGGAAAAAG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"Zinc fingers, C2H2-type", "-"	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.131-1G>A	19.37:g.12088187G>A		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	83	7	NM_001012753	0	0	2	2	0	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.		0.353	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	Silent	A	12088187	G	A	12088187	5	1	92	1	0	0	0	0	0	0	1	0	18169	1188	41	2	151	2	ZNF763	19	12088187	Splice_Site	SNP	G	TCGA-DW-5560-01A-01D-1589-08		12088187	47040796	65	8343											
CDS2	8760	bcgsc.ca	37	chr20	5157344	5157344	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagataatcactattggctaCaacgtctaccactcatatga	14	11	6	10	1	3	2	2	1	1	1	3	3	3	2	1	1	3	1	1	1	6	6	rs554837402	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:5157344C>A	ENST00000460006.1	+	4	649	c.342C>A	c.(340-342)taC>taA	p.Y114*	CDS2_ENST00000535100.1_5'Flank|CDS2_ENST00000379070.3_3'UTR|CDS2_ENST00000379062.4_Intron	NM_003818.3	NP_003809.1	O95674	CDS2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	114					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	phosphatidate cytidylyltransferase activity (GO:0004605)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|stomach(1)	14						CTATTGGCTACAACGTCTACC	0.458													C|||	240	0.0479233	0.034	0.0764	5008	,	,		18742	0.0665		0.0746	False		,,,				2504	0				p.Y114X													.	CDS2-226	0			c.C342A						.						222	207	212					20																	5157344		2203	4300	6503	SO:0001587	stop_gained	8760	exon4			TGGCTACAACGTC	AF069532	CCDS13088.1	20p13	2006-03-28			ENSG00000101290	ENSG00000101290	2.7.7.41		1801	protein-coding gene	gene with protein product		603549				9806839, 9889000	Standard	NM_003818		Approved		uc002wls.3	O95674	OTTHUMG00000031801	ENST00000460006.1:c.342C>A	20.37:g.5157344C>A	ENSP00000419879:p.Tyr114*	Somatic	303	0		WXS	Illumina HiSeq	Phase_1	252	21	NM_003818	0	0	4	4	0	B2RDC6|D3DW04|Q5TDY2|Q5TDY3|Q5TDY4|Q5TDY5|Q9BYK5|Q9NTT2	Nonsense_Mutation	SNP	ENST00000460006.1	37	CCDS13088.1	.	.	.	.	.	.	.	.	.	.	C	39	7.690869	0.98434	.	.	ENSG00000101290	ENST00000460006;ENST00000450570	.	.	.	4.72	1.76	0.24704	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.0661	7.5322	0.27689	0.0:0.6576:0.0:0.3424	.	.	.	.	X	114;59	.	ENSP00000403205:Y59X	Y	+	3	2	CDS2	5105344	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.219000	0.32479	0.712000	0.32039	0.561000	0.74099	TAC	.		0.458	CDS2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077858.2			A	5157344	C	A	5157344	4	1	92	1	0	0	0	0	0	1	0	0	3184	489	17	4	356	4	CDS2	20	5157344	Nonsense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		5157344	57868176	66	8344											
ZHX3	23051	ucsc.edu	37	chr20	39832697	39832697	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccgtgggcagtggctggTggacatggtgttgggcatgc	4	10	20	7	1	0	0	0	0	0	0	0	1	0	1	1	7	1	4	1	7	0	1	rs200146666		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:39832697T>G	ENST00000309060.3	-	4	1275	c.860A>C	c.(859-861)cAc>cCc	p.H287P	ZHX3_ENST00000544979.2_Missense_Mutation_p.H287P|ZHX3_ENST00000559234.1_Missense_Mutation_p.H287P|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000540170.1_Missense_Mutation_p.H287P|ZHX3_ENST00000560361.1_Missense_Mutation_p.H287P|ZHX3_ENST00000432768.2_Missense_Mutation_p.H287P			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	287	Required for homodimerization and interaction with NFYA.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CAGTGGCTGGTGGACATGGTG	0.582																																					p.H287P													.	ZHX3-93	0			c.A860C						.						77	66	70					20																	39832697		2203	4300	6503	SO:0001583	missense	23051	exon3			GGCTGGTGGACAT	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	15935	protein-coding gene	gene with protein product		609598	"triple homeobox 1"	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.860A>C	20.37:g.39832697T>G	ENSP00000312222:p.His287Pro	Somatic	81	5		WXS	Illumina HiSeq		116	12	NM_015035	0	0	4	4	0	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.785356	0.31593	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262;ENST00000432768	T;T;T;T;T	0.29917	1.55;2.97;2.97;2.75;1.55	5.95	5.95	0.96441	.	0.675209	0.16477	N	0.212703	T	0.32526	0.0832	L	0.57536	1.79	0.43947	D	0.996617	B;B;P	0.47106	0.002;0.002;0.89	B;B;B	0.40506	0.003;0.003;0.331	T	0.07214	-1.0784	10	0.31617	T	0.26	-16.5459	14.3566	0.66742	0.0:0.0:0.0:1.0	.	287;287;287	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	P	287;287;287;287;65;287	ENSP00000312222:H287P;ENSP00000362360:H287P;ENSP00000442290:H287P;ENSP00000443783:H287P;ENSP00000415498:H287P	ENSP00000312222:H287P	H	-	2	0	ZHX3	39266111	0.999000	0.42202	1.000000	0.80357	0.465000	0.32709	0.856000	0.27818	2.277000	0.76020	0.533000	0.62120	CAC	T|0.999;G|0.001		0.582	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035		G	39832697	T	G	39832697	3	3	92	1	0	0	0	0	1	0	0	0	17709	1696	59	5	2018	5	ZHX3	20	39832697	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08	34675353	39832697	23192823	67	8345											
NCOA3	8202	hgsc.bcm.edu;broad.mit.edu	37	chr20	46252817	46252817	+	Frame_Shift_Del	DEL	A	A	-																															gtaagacagatacgtcaaatAaaagagcaaggtaataaaaa																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:46252817delA	ENST00000371998.3	+	4	437	c.246delA	c.(244-246)atafs	p.I82fs	NCOA3_ENST00000372004.3_Frame_Shift_Del_p.I82fs|NCOA3_ENST00000341724.6_Frame_Shift_Del_p.I82fs|NCOA3_ENST00000371997.3_Frame_Shift_Del_p.I82fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	82	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TACGTCAAATAAAAGAGCAAG	0.378																																					p.I82fs		.											.	NCOA3-229	0			c.246delA						.						61	58	59					20																	46252817		2203	4300	6503	SO:0001589	frameshift_variant	8202	exon4			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.246delA	20.37:g.46252817delA	ENSP00000361066:p.Ile82fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	89	17	NM_181659	0	0	0	0	0	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			.		0.378	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		-	46252817	A	-	46252817	7	5	92	1	0	1	0	1	0	0	0	0	10256	352	13	0	252	0	NCOA3	20	46252817	Frame_Shift_Del	DEL	A	TCGA-DW-5560-01A-01D-1589-08	6420120	46252817	16772703	68	8346											
LSM14B	149986	hgsc.bcm.edu	37	chr20	60697753	60697753	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctcaggcaccccgtatctgGgcagcaagatcagcctcatc	9	7	9	16	1	4	1	3	0	1	1	5	1	4	1	4	2	2	4	4	2	2	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:60697753G>C	ENST00000279068.6	+	1	191	c.31G>C	c.(31-33)Ggc>Cgc	p.G11R	LSM14B_ENST00000253001.4_Missense_Mutation_p.G11R|LSM14B_ENST00000370915.1_Missense_Mutation_p.G11R	NM_144703.2	NP_653304.2	Q9BX40	LS14B_HUMAN	LSM14B, SCD6 homolog B (S. cerevisiae)	11					multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)	ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|lung(4)	8	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CCCGTATCTGGGCAGCAAGAT	0.706																																					p.G11R		.											.	LSM14B-22	0			c.G31C						.						37	36	36					20																	60697753		2202	4300	6502	SO:0001583	missense	149986	exon1			TATCTGGGCAGCA	AF172328	CCDS46626.1	20q13.33	2010-01-27	2006-12-21	2006-01-24	ENSG00000149657	ENSG00000149657			15887	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 40", "family with sequence similarity 61, member B", "LSM14 homolog B (SCD6, S. cerevisiae)"	C20orf40, FAM61B			Standard	NM_144703		Approved	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B	uc010gjy.1	Q9BX40	OTTHUMG00000032901	ENST00000279068.6:c.31G>C	20.37:g.60697753G>C	ENSP00000279068:p.Gly11Arg	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_144703	0	0	0	0	0	Q6PFW8|Q96LH8	Missense_Mutation	SNP	ENST00000279068.6	37	CCDS46626.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765540	0.90020	.	.	ENSG00000149657	ENST00000370915;ENST00000279068;ENST00000253001;ENST00000400318;ENST00000279069	T;T;T	0.78126	-0.98;-1.15;-1.01	3.03	3.03	0.35002	Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	U	0.000000	D	0.90232	0.6946	H	0.94620	3.56	0.80722	D	1	P;D;D	0.76494	0.946;0.997;0.999	P;D;D	0.80764	0.866;0.939;0.994	D	0.92606	0.6095	10	0.87932	D	0	.	13.1281	0.59366	0.0:0.0:1.0:0.0	.	11;11;11	Q9BX40;Q5TBQ0;Q9BX40-2	LS14B_HUMAN;.;.	R	11	ENSP00000279068:G11R;ENSP00000253001:G11R;ENSP00000383172:G11R	ENSP00000253001:G11R	G	+	1	0	LSM14B	60131148	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.991000	0.88244	1.396000	0.46663	0.305000	0.20034	GGC	.		0.706	LSM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079996.4	NM_144703		C	60697753	G	C	60697753	3	2	92	1	0	0	0	0	1	0	0	0	9080	1232	43	4	33	4	LSM14B	20	60697753	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	14444936	60697753	2327767	69	8347											
ZGPAT	84619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62340218	62340218	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggtggaggcaccagcagcgGcccgtgggtccggatcagag	7	4	18	12	4	1	1	1	0	0	1	2	3	2	3	3	6	2	2	3	6	0	0			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:62340218G>A	ENST00000328969.5	+	2	413	c.286G>A	c.(286-288)Gcc>Acc	p.A96T	ZGPAT_ENST00000369967.3_Missense_Mutation_p.A96T|ZGPAT_ENST00000448100.2_Missense_Mutation_p.A96T|ARFRP1_ENST00000359715.5_5'Flank|ARFRP1_ENST00000607873.1_5'Flank|ARFRP1_ENST00000440854.1_5'Flank|ZGPAT_ENST00000355969.6_Missense_Mutation_p.A96T|RP4-583P15.15_ENST00000490623.2_Silent_p.R1R|ZGPAT_ENST00000357119.4_Missense_Mutation_p.A96T|ARFRP1_ENST00000324228.2_5'Flank|ARFRP1_ENST00000609142.1_5'Flank	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	96					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					ACCAGCAGCGGCCCGTGGGTC	0.667																																					p.A96T		.											.	ZGPAT-90	0			c.G286A						.						36	43	41					20																	62340218		2201	4298	6499	SO:0001583	missense	84619	exon2			GCAGCGGCCCGTG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.286G>A	20.37:g.62340218G>A	ENSP00000332013:p.Ala96Thr	Somatic	135	1		WXS	Illumina HiSeq	Phase_I	122	72	NM_032527	0	0	7	25	18	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	37	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.560698	0.00136	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000431125;ENST00000369967;ENST00000328969	T;T;T;T;T;T	0.45276	1.14;1.14;1.14;0.9;1.14;1.14	0.536	-1.07	0.09968	.	2.240520	0.02968	U	0.144041	T	0.26810	0.0656	L	0.31664	0.95	0.09310	N	1	B;B;B	0.20887	0.049;0.001;0.034	B;B;B	0.24394	0.031;0.006;0.053	T	0.04946	-1.0916	9	0.15952	T	0.53	-0.5515	.	.	.	.	96;96;96	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	T	96	ENSP00000391176:A96T;ENSP00000348242:A96T;ENSP00000349634:A96T;ENSP00000403966:A96T;ENSP00000358984:A96T;ENSP00000332013:A96T	ENSP00000332013:A96T	A	+	1	0	ZGPAT	61810662	0.007000	0.16637	0.000000	0.03702	0.011000	0.07611	0.930000	0.28858	-1.719000	0.01382	-1.048000	0.02349	GCC	.		0.667	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		A	62340218	G	A	62340218	3	1	92	1	0	0	0	0	1	0	0	0	17706	1203	42	2	288	2	ZGPAT	20	62340218	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	1642465	62340218	685302	70	8348											
FBXO7	25793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	32889131	32889131	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgggttggtcgtcctccCattggaactgaaactacgga	9	12	11	9	2	0	1	0	1	0	0	3	3	2	3	2	4	3	1	2	4	3	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr22:32889131C>A	ENST00000266087.7	+	7	1334	c.1007C>A	c.(1006-1008)cCa>cAa	p.P336Q	FBXO7_ENST00000382058.3_Missense_Mutation_p.P257Q|FBXO7_ENST00000397426.1_Missense_Mutation_p.P222Q	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	336	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTCGTCCTCCCATTGGAACTG	0.438																																					p.P336Q		.											.	FBXO7-228	0			c.C1007A						.						371	310	330					22																	32889131		2203	4300	6503	SO:0001583	missense	25793	exon7			TCCTCCCATTGGA	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.1007C>A	22.37:g.32889131C>A	ENSP00000266087:p.Pro336Gln	Somatic	270	1		WXS	Illumina HiSeq	Phase_I	278	111	NM_012179	0	0	30	55	25	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.192232	0.78902	.	.	ENSG00000100225	ENST00000266087;ENST00000382058;ENST00000397426	D;D;D	0.99709	-6.48;-6.48;-6.48	6.08	6.08	0.98989	F-box domain, cyclin-like (3);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;1.0	D	0.97617	1.0133	10	0.87932	D	0	-17.0815	20.6634	0.99662	0.0:1.0:0.0:0.0	.	336;257;336	A8K7F7;Q9Y3I1-2;Q9Y3I1	.;.;FBX7_HUMAN	Q	336;257;222	ENSP00000266087:P336Q;ENSP00000371490:P257Q;ENSP00000380571:P222Q	ENSP00000266087:P336Q	P	+	2	0	FBXO7	31219131	1.000000	0.71417	0.815000	0.32552	0.630000	0.37929	5.980000	0.70516	2.894000	0.99253	0.655000	0.94253	CCA	.		0.438	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			A	32889131	C	A	32889131	3	1	92	1	0	0	0	0	1	0	0	0	5779	594	21	4	1074	4	FBXO7	22	32889131	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		32889131	18415435	71	8349											
DDX3X	1654	bcgsc.ca	37	chrX	41205659	41205659	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagcccaattttagtggctaCagcagtatgtataaacatct	14	12	7	8	0	1	0	0	0	1	0	1	0	1	0	1	1	4	4	1	1	8	6	rs200427211		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chrX:41205659C>A	ENST00000399959.2	+	13	2348	c.1493C>A	c.(1492-1494)aCa>aAa	p.T498K	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000457138.2_Missense_Mutation_p.T482K	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	498	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with GSK3B.|Necessary for interaction with XPO1.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						TTAGTGGCTACAGCAGTATGT	0.403										HNSCC(61;0.18)																											p.T498K													.	DDX3X-715	0			c.C1493A						.						79	77	78					X																	41205659		2202	4300	6502	SO:0001583	missense	1654	exon13			TGGCTACAGCAGT	U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"DEAD-boxes"	2745	protein-coding gene	gene with protein product		300160	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.1493C>A	X.37:g.41205659C>A	ENSP00000382840:p.Thr498Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_1	75	12	NM_001193416	0	0	0	0	0	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.903947	0.92035	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.13089	2.62;2.62	5.1	5.1	0.69264	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.60025	0.2237	H	0.99475	4.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.80690	-0.1270	10	0.87932	D	0	-11.1871	17.7156	0.88336	0.0:1.0:0.0:0.0	.	482;510;498	B4E3E8;Q59GX6;O00571	.;.;DDX3X_HUMAN	K	498;482	ENSP00000382840:T498K;ENSP00000392494:T482K	ENSP00000382840:T498K	T	+	2	0	DDX3X	41090603	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.771000	0.85420	2.113000	0.64589	0.600000	0.82982	ACA	.		0.403	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		A	41205659	C	A	41205659	3	1	92	1	0	0	0	0	1	0	0	0	4364	478	17	4	1543	4	DDX3X	23	41205659	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		41205659	114064901	72	8350											
PHF8	23133	hgsc.bcm.edu	37	chrX	53966769	53966769	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agcgagacttcctgacagggCctcttgtttaggctcaggag	8	10	13	10	1	2	2	1	1	1	1	3	4	3	3	2	3	1	2	2	3	1	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chrX:53966769C>G	ENST00000357988.5	-	21	3296	c.2938G>C	c.(2938-2940)Gcc>Ccc	p.A980P	PHF8_ENST00000338154.6_Missense_Mutation_p.A944P|PHF8_ENST00000338946.6_Missense_Mutation_p.A843P	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	980					brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						CCTGACAGGGCCTCTTGTTTA	0.602																																					p.A980P		.											.	PHF8-133	0			c.G2938C						.						113	88	97					X																	53966769		2202	4300	6502	SO:0001583	missense	23133	exon21			ACAGGGCCTCTTG	AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	20672	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1F"	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.2938G>C	X.37:g.53966769C>G	ENSP00000350676:p.Ala980Pro	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_001184896	0	0	7	7	0	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Missense_Mutation	SNP	ENST00000357988.5	37	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.817|9.817	1.184706|1.184706	0.21870|0.21870	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000357988;ENST00000338154;ENST00000338946;ENST00000396277|ENST00000396282	T;T;T|.	0.18502|.	2.48;2.22;2.21|.	5.08|5.08	3.25|3.25	0.37280|0.37280	.|.	0.577499|.	0.17386|.	N|.	0.176132|.	T|T	0.15435|0.15435	0.0372|0.0372	N|N	0.03608|0.03608	-0.345|-0.345	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.0;0.001;0.001|.	T|T	0.23619|0.23619	-1.0183|-1.0183	10|5	0.38643|.	T|.	0.18|.	-5.047|-5.047	7.9511|7.9511	0.30014|0.30014	0.0:0.6387:0.2521:0.1092|0.0:0.6387:0.2521:0.1092	.|.	843;879;980|.	B7Z911;Q9UPP1-3;Q9UPP1|.	.;.;PHF8_HUMAN|.	P|S	980;944;843;873|847	ENSP00000350676:A980P;ENSP00000338868:A944P;ENSP00000340051:A843P|.	ENSP00000338868:A944P|.	A|R	-|-	1|3	0|2	PHF8|PHF8	53983494|53983494	0.718000|0.718000	0.27976|0.27976	0.980000|0.980000	0.43619|0.43619	0.977000|0.977000	0.68977|0.68977	0.287000|0.287000	0.18920|0.18920	0.934000|0.934000	0.37316|0.37316	0.431000|0.431000	0.28591|0.28591	GCC|AGG	.		0.602	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107		G	53966769	C	G	53966769	3	3	92	1	0	0	0	0	1	0	0	0	11866	739	26	4	335	4	PHF8	23	53966769	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	12761110	53966769	101303791	73	8351											
UBIAD1	29914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11346095	11346095	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccaggccttcaacaaactGccccagaggactgccaagct	12	5	9	15	0	1	1	1	0	0	1	1	2	1	2	5	2	6	1	5	2	3	1			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:11346095G>C	ENST00000376810.5	+	2	1250	c.924G>C	c.(922-924)ctG>ctC	p.L308L	UBIAD1_ENST00000376804.2_Intron	NM_013319.2	NP_037451.1	Q9Y5Z9	UBIA1_HUMAN	UbiA prenyltransferase domain containing 1	308					menaquinone biosynthetic process (GO:0009234)|ubiquinone biosynthetic process (GO:0006744)|vitamin K biosynthetic process (GO:0042371)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)|prenyltransferase activity (GO:0004659)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(3)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)		TCAACAAACTGCCCCAGAGGA	0.547																																					p.L308L		.											.	UBIAD1-90	0			c.G924C						.						110	107	108					1																	11346095		2203	4300	6503	SO:0001819	synonymous_variant	29914	exon2			CAAACTGCCCCAG		CCDS129.1	1p36.22	2012-05-02			ENSG00000120942	ENSG00000120942			30791	protein-coding gene	gene with protein product	"transitional epithelia response protein"	611632	"Schnyder crystalline corneal dystrophy"	SCCD		20953171, 12497587, 11314041, 17668063, 17962451, 8894705	Standard	NM_013319		Approved	TERE1	uc001asg.3	Q9Y5Z9	OTTHUMG00000002075	ENST00000376810.5:c.924G>C	1.37:g.11346095G>C		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	152	62	NM_013319	0	0	13	19	6	B3KQG3|Q53GX3|Q5THD4	Silent	SNP	ENST00000376810.5	37	CCDS129.1																																																																																			.		0.547	UBIAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005773.1	NM_013319		C	11346095	G	C	11346095	2	2	93	1	0	0	0	0	0	0	0	1	16918	1306	46	4		4	UBIAD1	1	11346095	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		11346095	237904526	1	8352											
PADI3	51702	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	17609568	17609568	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaagtggtggaacatggtGccctgagacagctcccaccc	9	8	11	13	0	1	1	1	1	0	1	2	3	2	2	3	3	3	1	3	3	2	1			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:17609568G>A	ENST00000375460.3	+	16	2029	c.1989G>A	c.(1987-1989)gtG>gtA	p.V663V		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	663					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	GGAACATGGTGCCCTGAGACA	0.572																																					p.V663V		.											.	PADI3-132	0			c.G1989A						.						90	74	79					1																	17609568		2203	4300	6503	SO:0001819	synonymous_variant	51702	exon16			CATGGTGCCCTGA	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1989G>A	1.37:g.17609568G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	62	13	NM_016233	0	0	0	0	0	Q58EY7|Q70SX5	Silent	SNP	ENST00000375460.3	37	CCDS179.1																																																																																			.		0.572	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			A	17609568	G	A	17609568	2	1	93	1	0	0	0	0	0	0	0	1	11405	1306	46	2		2	PADI3	1	17609568	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08	6263473	17609568	231641053	2	8353											
ZDHHC18	84243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27176925	27176925	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgtggtcacccacctgacGttgcgtgagttgtgggtgag	5	12	16	8	2	1	3	1	3	0	0	1	3	1	3	2	2	1	2	2	2	0	2	rs373583803		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:27176925G>A	ENST00000374142.4	+	4	875	c.780G>A	c.(778-780)acG>acA	p.T260T		NM_032283.2	NP_115659.1	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18	260					cellular protein localization (GO:0034613)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)	3		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)		CCCACCTGACGTTGCGTGAGT	0.567																																					p.T260T		.											.	ZDHHC18-90	0			c.G780A						.	G		0,4406		0,0,2203	159	139	145		780	-3.6	1	1		145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZDHHC18	NM_032283.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		260/389	27176925	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	84243	exon4			CCTGACGTTGCGT	AK056427	CCDS30650.1	1p36.11	2008-05-02			ENSG00000204160	ENSG00000204160		"Zinc fingers, DHHC-type"	20712	protein-coding gene	gene with protein product							Standard	NM_032283		Approved	DKFZp667O2416	uc001bnb.3	Q9NUE0	OTTHUMG00000004092	ENST00000374142.4:c.780G>A	1.37:g.27176925G>A		Somatic	201	0		WXS	Illumina HiSeq	Phase_I	185	76	NM_032283	0	0	0	0	0	A6NHY9|B4DQ84|Q5JYH0|Q9H020	Silent	SNP	ENST00000374142.4	37	CCDS30650.1	.	.	.	.	.	.	.	.	.	.	G	8.860	0.946706	0.18356	0.0	2.33E-4	ENSG00000204160	ENST00000488397	.	.	.	5.05	-3.58	0.04597	.	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35968	-0.9767	4	.	.	.	-4.0065	0.8159	0.01102	0.389:0.2593:0.1417:0.21	.	.	.	.	I	25	.	.	V	+	1	0	ZDHHC18	27049512	0.000000	0.05858	0.965000	0.40720	0.894000	0.52154	-1.818000	0.01717	-0.387000	0.07809	-0.215000	0.12644	GTT	.		0.567	ZDHHC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011706.3	NM_032283		A	27176925	G	A	27176925	2	1	93	1	0	0	0	0	0	0	0	1	17640	1132	40	1		1	ZDHHC18	1	27176925	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08	9567357	27176925	222073696	3	8354											
KIAA1522	57648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	33237745	33237745	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agctggagcggcccgtgtccCctgagacccaggctgacctc	6	6	13	16	2	0	2	0	2	0	1	2	4	1	3	5	3	2	2	5	3	0	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:33237745C>A	ENST00000373480.1	+	6	2891	c.2788C>A	c.(2788-2790)Cct>Act	p.P930T	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P989T|KIAA1522_ENST00000373481.3_Missense_Mutation_p.P941T	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	930	Pro-rich.									breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GCCCGTGTCCCCTGAGACCCA	0.647																																					p.P989T		.											.	KIAA1522-90	0			c.C2965A						.						20	27	25					1																	33237745		1981	4161	6142	SO:0001583	missense	57648	exon6			GTGTCCCCTGAGA	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.2788C>A	1.37:g.33237745C>A	ENSP00000362579:p.Pro930Thr	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	40	13	NM_020888	0	0	9	20	11	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793037	0.70452	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.17054	2.3;2.33;2.35	4.85	4.85	0.62838	.	0.315683	0.28011	N	0.016953	T	0.36358	0.0964	L	0.59436	1.845	0.32817	D	0.502245	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.988;0.988	T	0.33394	-0.9870	10	0.37606	T	0.19	-12.0197	14.185	0.65601	0.0:0.8504:0.1496:0.0	.	941;930;989	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	T	989;941;930	ENSP00000383851:P989T;ENSP00000362580:P941T;ENSP00000362579:P930T	ENSP00000362579:P930T	P	+	1	0	KIAA1522	33010332	0.987000	0.35691	1.000000	0.80357	0.799000	0.45148	2.754000	0.47532	2.682000	0.91365	0.650000	0.86243	CCT	.		0.647	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33237745	C	A	33237745	3	1	93	1	0	0	0	0	1	0	0	0	8259	623	22	4	2987	4	KIAA1522	1	33237745	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	6060820	33237745	216012876	4	8355											
MACF1	23499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	39835802	39835802	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaactgaagggagtattccaCctacggaaacttctatgagt	14	10	9	8	1	1	2	0	2	1	0	2	4	2	4	2	2	3	1	2	2	6	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:39835802C>G	ENST00000372915.3	+	50	13141	c.13054C>G	c.(13054-13056)Cct>Gct	p.P4352A	MACF1_ENST00000289893.4_Missense_Mutation_p.P2787A|MACF1_ENST00000361689.2_Missense_Mutation_p.P2285A|MACF1_ENST00000567887.1_Missense_Mutation_p.P4384A|MACF1_ENST00000564288.1_Missense_Mutation_p.P4347A|MACF1_ENST00000545844.1_Missense_Mutation_p.P2285A|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.P2285A|MACF1_ENST00000539005.1_Missense_Mutation_p.P2285A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4352					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAGTATTCCACCTACGGAAAC	0.448																																					p.P2285A		.											.	MACF1-165	0			c.C6853G						.						75	76	76					1																	39835802		2203	4300	6503	SO:0001583	missense	23499	exon47			ATTCCACCTACGG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13054C>G	1.37:g.39835802C>G	ENSP00000362006:p.Pro4352Ala	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	35	18	NM_012090	0	0	5	6	1	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.632|0.632	-0.816867|-0.816867	0.02776|0.02776	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.32023|.	1.47;1.47;1.47;1.47;1.47;1.47|.	5.37|5.37	-0.194|-0.194	0.13240|0.13240	.|.	0.900226|.	0.09361|.	N|.	0.812758|.	T|T	0.20292|0.20292	0.0488|0.0488	N|N	0.16368|0.16368	0.405|0.405	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.15141|.	0.012;0.003;0.002;0.001|.	B;B;B;B|.	0.25759|.	0.063;0.004;0.007;0.006|.	T|T	0.29518|0.29518	-1.0009|-1.0009	10|5	0.07175|.	T|.	0.84|.	.|.	6.3552|6.3552	0.21397|0.21397	0.0:0.4709:0.249:0.28|0.0:0.4709:0.249:0.28	.|.	4352;2285;2285;2250|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	A|S	2285;4352;2285;2285;2285;2787|1418	ENSP00000439537:P2285A;ENSP00000362006:P4352A;ENSP00000354573:P2285A;ENSP00000313438:P2285A;ENSP00000444364:P2285A;ENSP00000289893:P2787A|.	ENSP00000289893:P2787A|.	P|T	+|+	1|2	0|0	MACF1|MACF1	39608389|39608389	0.000000|0.000000	0.05858|0.05858	0.116000|0.116000	0.21606|0.21606	0.992000|0.992000	0.81027|0.81027	0.181000|0.181000	0.16880|0.16880	0.245000|0.245000	0.21373|0.21373	0.655000|0.655000	0.94253|0.94253	CCT|ACC	.		0.448	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39835802	C	G	39835802	3	3	93	1	0	0	0	0	1	0	0	0	9169	507	18	4	13186	4	MACF1	1	39835802	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	6598057	39835802	209414819	5	8356											
IER5	51278	hgsc.bcm.edu	37	chr1	181058618	181058618	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaccggccgcgacccccCgcgctgcctgctgctgcgcg	3	5	13	20	7	0	0	0	0	0	0	0	1	0	0	6	1	5	4	6	1	1	1	rs1416829	byFrequency	TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:181058618C>G	ENST00000367577.4	+	1	981	c.580C>G	c.(580-582)Cgc>Ggc	p.R194G	RP11-309G3.3_ENST00000606938.1_lincRNA	NM_016545.4	NP_057629.2	Q5VY09	IER5_HUMAN	immediate early response 5	194			R -> G (in dbSNP:rs1416829). {ECO:0000269|PubMed:15498874}.							lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	4						CGCGACCCCCCGCGCTGCCTG	0.811													C|||	2222	0.44369	0.2489	0.4452	5008	,	,		5637	0.6012		0.3777	False		,,,				2504	0.6115				p.R194G		.											.	IER5-227	0			c.C580G						.						1	1	1					1																	181058618		352	834	1186	SO:0001583	missense	51278	exon1			ACCCCCCGCGCTG	BC000128	CCDS1343.1	1q25.3	2008-02-05			ENSG00000162783	ENSG00000162783			5393	protein-coding gene	gene with protein product		607177				10049588, 11102586	Standard	NM_016545		Approved		uc001got.4	Q5VY09	OTTHUMG00000035178	ENST00000367577.4:c.580C>G	1.37:g.181058618C>G	ENSP00000356549:p.Arg194Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_016545	0	0	0	0	0	B2RBV3|Q8WY68|Q9NY49|Q9NZP9	Missense_Mutation	SNP	ENST00000367577.4	37	CCDS1343.1	948	0.4340659340659341	135	0.27439024390243905	158	0.43646408839779005	360	0.6293706293706294	295	0.3891820580474934	C	4.540	0.100211	0.08731	.	.	ENSG00000162783	ENST00000367577	T	0.11821	2.74	3.33	-0.106	0.13596	.	1.560750	0.05354	N	0.532505	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.18610	0.029	B	0.15484	0.013	T	0.38972	-0.9636	9	0.34782	T	0.22	.	8.3021	0.32021	0.0:0.4746:0.4312:0.0942	rs1416829;rs3747953	194	Q5VY09	IER5_HUMAN	G	194	ENSP00000356549:R194G	ENSP00000356549:R194G	R	+	1	0	IER5	179325241	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-0.019000	0.12546	0.004000	0.14682	-1.520000	0.00934	CGC	C|0.566;G|0.434		0.811	IER5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085142.1	NM_016545		G	181058618	C	G	181058618	3	3	93	1	0	0	0	0	1	0	0	0	7529	652	23	4	582	4	IER5	1	181058618	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	141222816	181058618	68192003	6	8357											
HMCN1	83872	bcgsc.ca	37	chr1	186094789	186094789	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacggtcaatgagaattcaCaagccattcttccatgcgta	13	10	7	11	2	3	1	2	1	1	1	4	2	4	1	2	1	2	1	2	1	4	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:186094789C>A	ENST00000271588.4	+	82	12782	c.12553C>A	c.(12553-12555)Caa>Aaa	p.Q4185K	HMCN1_ENST00000367492.2_Missense_Mutation_p.Q4185K	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4185	Ig-like C2-type 41.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGAGAATTCACAAGCCATTCT	0.403																																					p.Q4185K													.	HMCN1-113	0			c.C12553A						.						91	92	92					1																	186094789		2203	4300	6503	SO:0001583	missense	83872	exon82			AATTCACAAGCCA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.12553C>A	1.37:g.186094789C>A	ENSP00000271588:p.Gln4185Lys	Somatic	92	7		WXS	Illumina HiSeq	Phase_1	78	16	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.954305	0.53293	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66099	-0.19;-0.19	5.04	4.1	0.47936	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.230515	0.45606	D	0.000343	T	0.43919	0.1269	N	0.21097	0.63	0.51012	D	0.999902	B	0.31153	0.31	B	0.30105	0.111	T	0.37009	-0.9724	10	0.05721	T	0.95	.	14.9957	0.71431	0.1435:0.8565:0.0:0.0	.	4185	Q96RW7	HMCN1_HUMAN	K	4185	ENSP00000271588:Q4185K;ENSP00000356462:Q4185K	ENSP00000271588:Q4185K	Q	+	1	0	HMCN1	184361412	0.997000	0.39634	0.995000	0.50966	0.975000	0.68041	3.096000	0.50243	1.200000	0.43188	0.650000	0.86243	CAA	.		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186094789	C	A	186094789	3	1	93	1	0	0	0	0	1	0	0	0	7241	479	17	4	12879	4	HMCN1	1	186094789	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	5036171	186094789	63155832	7	8358											
TMEM81	388730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205052751	205052751	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgccaccaaccactccaatgGcaattcctattcccaaggct	11	8	5	17	1	0	0	0	0	0	0	3	0	3	0	6	2	1	2	6	2	5	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:205052751G>T	ENST00000367167.3	-	1	894	c.698C>A	c.(697-699)gCc>gAc	p.A233D		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	233						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			CACTCCAATGGCAATTCCTAT	0.512																																					p.A233D		.											.	TMEM81-68	0			c.C698A						.						133	120	124					1																	205052751		2203	4300	6503	SO:0001583	missense	388730	exon1			CCAATGGCAATTC	BC061592	CCDS1450.1	1q32.1	2013-01-11			ENSG00000174529	ENSG00000174529		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32349	protein-coding gene	gene with protein product							Standard	NM_203376		Approved	UNQ2788, MGC75217, HC3107, KVLA2788	uc001hbt.3	Q6P7N7	OTTHUMG00000037103	ENST00000367167.3:c.698C>A	1.37:g.205052751G>T	ENSP00000356135:p.Ala233Asp	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	113	37	NM_203376	0	0	2	3	1	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	37	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.569050	0.65765	.	.	ENSG00000174529	ENST00000367167	T	0.35605	1.3	5.79	-0.62	0.11567	.	1.790840	0.02843	N	0.128129	T	0.37183	0.0994	L	0.57536	1.79	0.09310	N	1	P	0.37276	0.589	B	0.38616	0.277	T	0.34354	-0.9832	10	0.66056	D	0.02	-30.4547	5.7266	0.18017	0.3683:0.291:0.3406:0.0	.	233	Q6P7N7	TMM81_HUMAN	D	233	ENSP00000356135:A233D	ENSP00000356135:A233D	A	-	2	0	TMEM81	203319374	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	0.115000	0.15540	-0.133000	0.11537	0.655000	0.94253	GCC	.		0.512	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		T	205052751	G	T	205052751	3	4	93	1	0	0	0	0	1	0	0	0	16237	1203	42	4	73	4	TMEM81	1	205052751	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	18957962	205052751	44197870	8	8359											
RBBP5	5929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205064022	205064022	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtcaagggctggctgagttCcgcctgcactttacccttcg	5	12	11	13	2	1	1	1	1	0	0	3	1	2	1	3	2	2	4	3	2	2	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:205064022C>T	ENST00000264515.6	-	13	1708	c.1567G>A	c.(1567-1569)Gaa>Aaa	p.E523K	RBBP5_ENST00000367164.1_Intron	NM_001193273.1|NM_005057.3	NP_001180202.1|NP_005048.2	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	523					cellular response to DNA damage stimulus (GO:0006974)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	methylated histone binding (GO:0035064)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	27	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			TGGCTGAGTTCCGCCTGCACT	0.473																																					p.E523K		.											.	RBBP5-226	0			c.G1567A						.						144	134	138					1																	205064022		2203	4300	6503	SO:0001583	missense	5929	exon13			TGAGTTCCGCCTG	BC053856	CCDS30983.1, CCDS53463.1	1q32	2013-01-10	2001-11-28		ENSG00000117222	ENSG00000117222		"WD repeat domain containing"	9888	protein-coding gene	gene with protein product	"SWD1, Set1c WD40 repeat protein, homolog (S. cerevisiae)"	600697	"retinoblastoma-binding protein 5"			7558034	Standard	NM_005057		Approved	RBQ3, SWD1	uc001hbu.2	Q15291	OTTHUMG00000037104	ENST00000264515.6:c.1567G>A	1.37:g.205064022C>T	ENSP00000264515:p.Glu523Lys	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	143	63	NM_005057	0	0	0	3	3	A8K272|Q7Z6D8|Q8NDZ7	Missense_Mutation	SNP	ENST00000264515.6	37	CCDS30983.1	.	.	.	.	.	.	.	.	.	.	C	19.91	3.915149	0.73098	.	.	ENSG00000117222	ENST00000264515	T	0.61392	0.11	5.77	4.84	0.62591	.	0.100480	0.42548	D	0.000696	T	0.57344	0.2047	N	0.08118	0	0.80722	D	1	P;B;P	0.52842	0.927;0.021;0.956	D;B;P	0.67725	0.953;0.021;0.899	T	0.63721	-0.6573	10	0.39692	T	0.17	.	16.3504	0.83202	0.0:0.8677:0.1322:0.0	.	396;558;523	B4DLF8;B4DMM7;Q15291	.;.;RBBP5_HUMAN	K	523	ENSP00000264515:E523K	ENSP00000264515:E523K	E	-	1	0	RBBP5	203330645	1.000000	0.71417	0.989000	0.46669	0.999000	0.98932	4.843000	0.62838	1.403000	0.46800	0.655000	0.94253	GAA	.		0.473	RBBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090077.1	NM_005057		T	205064022	C	T	205064022	3	4	93	1	0	0	0	0	1	0	0	0	13134	864	30	2	57	2	RBBP5	1	205064022	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	11271	205064022	44186599	9	8360											
CR2	1380	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207642031	207642031	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taactgtttgtcttcgggaaAatggagtgctgtccccccca	8	12	10	11	1	1	0	0	0	1	0	3	2	2	2	3	2	2	2	3	2	3	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:207642031A>C	ENST00000367058.3	+	3	794	c.605A>C	c.(604-606)aAa>aCa	p.K202T	CR2_ENST00000367059.3_Missense_Mutation_p.K202T|CR2_ENST00000458541.2_Missense_Mutation_p.K202T|CR2_ENST00000485707.1_3'UTR|CR2_ENST00000367057.3_Missense_Mutation_p.K202T	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	202	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						TCTTCGGGAAAATGGAGTGCT	0.413																																					p.K202T		.											.	CR2-232	0			c.A605C						.						270	250	257					1																	207642031		2203	4300	6503	SO:0001583	missense	1380	exon3			CGGGAAAATGGAG	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"CD molecules", "Complement system"	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.605A>C	1.37:g.207642031A>C	ENSP00000356025:p.Lys202Thr	Somatic	288	0		WXS	Illumina HiSeq	Phase_I	195	85	NM_001006658	0	0	0	0	0	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	1.073	-0.669450	0.03403	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.82	-5.11	0.02901	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.25121	0.0610	N	0.02158	-0.66	0.09310	N	1	B;B;B	0.13594	0.008;0.004;0.002	B;B;B	0.17979	0.02;0.015;0.007	T	0.24870	-1.0148	9	0.13470	T	0.59	.	3.9575	0.09396	0.2886:0.4405:0.0679:0.203	.	202;202;202	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	T	202	ENSP00000356025:K202T;ENSP00000356024:K202T;ENSP00000356026:K202T;ENSP00000404222:K202T	ENSP00000356024:K202T	K	+	2	0	CR2	205708654	0.000000	0.05858	0.013000	0.15412	0.042000	0.13812	-0.669000	0.05262	-0.440000	0.07211	-0.445000	0.05633	AAA	.		0.413	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		C	207642031	A	C	207642031	3	2	93	1	0	0	0	0	1	0	0	0	3848	14	1	5	615	5	CR2	1	207642031	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	2578009	207642031	41608590	10	8361											
NCOA1	8648	broad.mit.edu	37	chr2	24930397	24930397	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catagctcattgacagaacgGcataaaattctacaccggct	14	9	7	11	2	2	2	1	1	1	1	2	2	2	2	1	2	3	3	1	2	5	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr2:24930397G>A	ENST00000406961.1	+	13	2710	c.2058G>A	c.(2056-2058)cgG>cgA	p.R686R	NCOA1_ENST00000405141.1_Silent_p.R686R|NCOA1_ENST00000348332.3_Silent_p.R686R|NCOA1_ENST00000407230.1_Silent_p.R535R|NCOA1_ENST00000288599.5_Silent_p.R686R|NCOA1_ENST00000395856.3_Silent_p.R686R|NCOA1_ENST00000538539.1_Silent_p.R686R			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	686					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGACAGAACGGCATAAAATTC	0.483			T	PAX3	alveolar rhadomyosarcoma																																p.R686R				Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1-228	0			c.G2058A						.						119	120	120					2																	24930397		2203	4300	6503	SO:0001819	synonymous_variant	8648	exon11			AGAACGGCATAAA	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.2058G>A	2.37:g.24930397G>A		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	178	6	NM_147223	0	0	7	7	0	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	37	CCDS1712.1																																																																																			.		0.483	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		A	24930397	G	A	24930397	2	1	93	1	0	0	0	0	0	0	0	1	10254	1190	42	2		2	NCOA1	2	24930397	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		24930397	218268976	11	8362											
SPEG	10290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220338577	220338577	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccctcacctgcaccgccCgaaaccgtcacggcacacag	9	3	10	19	4	2	0	2	0	0	0	2	1	2	0	5	2	2	2	5	2	1	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr2:220338577C>A	ENST00000312358.7	+	18	4531	c.4399C>A	c.(4399-4401)Cga>Aga	p.R1467R	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1467	Ig-like 7.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTGCACCGCCCGAAACCGTCA	0.647																																					p.R1467R		.											.	SPEG-383	0			c.C4399A						.						56	66	63					2																	220338577		2052	4184	6236	SO:0001819	synonymous_variant	10290	exon18			ACCGCCCGAAACC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4399C>A	2.37:g.220338577C>A		Somatic	156	0		WXS	Illumina HiSeq	Phase_I	157	86	NM_005876	0	0	0	0	0	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			.		0.647	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220338577	C	A	220338577	2	1	93	1	0	0	0	0	0	0	0	1	15068	644	23	4		4	SPEG	2	220338577	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	195408180	220338577	22860796	12	8363											
INHA	3623	hgsc.bcm.edu	37	chr2	220437360	220437360	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagccatccttttcccagcCacaggtaacgagggtggggg	9	7	13	12	1	0	0	0	0	0	0	2	1	2	0	4	4	3	1	4	4	2	3	rs559692749		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr2:220437360C>G	ENST00000243786.2	+	1	444	c.264C>G	c.(262-264)gcC>gcG	p.A88A	OBSL1_ENST00000373876.1_5'Flank|OBSL1_ENST00000404537.1_5'Flank|OBSL1_ENST00000265318.4_5'Flank|OBSL1_ENST00000603926.1_5'Flank|INHA_ENST00000489456.1_Intron|OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000373873.4_5'Flank|OBSL1_ENST00000289656.3_5'Flank	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	88					cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TTTTCCCAGCCACAGGTAACG	0.602											OREG0003991	type=REGULATORY REGION|Gene=BC045558|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1	0.000199681	8e-04	0	5008	,	,		18657	0		0	False		,,,				2504	0				p.A88A		.											.	INHA-91	0			c.C264G						.						4	5	5					2																	220437360		2078	4066	6144	SO:0001819	synonymous_variant	3623	exon1			CCCAGCCACAGGT		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.264C>G	2.37:g.220437360C>G		Somatic	2	1	2266	WXS	Illumina HiSeq	Phase_I	4	4	NM_002191	0	0	0	0	0	A8K8H5	Silent	SNP	ENST00000243786.2	37	CCDS2444.1																																																																																			.		0.602	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1			G	220437360	C	G	220437360	2	3	93	1	0	0	0	0	0	0	0	1	7761	581	21	4		4	INHA	2	220437360	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	98783	220437360	22762013	13	8364											
ATG7	10533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	11356947	11356947	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaaacactacagtgatttcTtccaaggtcaaaggacgaag	15	10	8	8	1	2	1	1	1	1	0	3	3	3	2	1	2	2	0	1	2	6	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:11356947T>A	ENST00000354449.3	+	7	683	c.658T>A	c.(658-660)Ttc>Atc	p.F220I	ATG7_ENST00000354956.5_Missense_Mutation_p.F220I|ATG7_ENST00000446450.2_Missense_Mutation_p.F181I	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	220					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CAGTGATTTCTTCCAAGGTCA	0.348																																					p.F220I		.											.	ATG7-90	0			c.T658A						.						110	97	101					3																	11356947		2203	4300	6503	SO:0001583	missense	10533	exon7			GATTTCTTCCAAG	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.658T>A	3.37:g.11356947T>A	ENSP00000346437:p.Phe220Ile	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	71	30	NM_001136031	0	0	1	6	5	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	37	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.499788	0.64298	.	.	ENSG00000197548	ENST00000446450;ENST00000354956;ENST00000354449	T;T;T	0.48522	0.81;0.81;0.81	4.67	4.67	0.58626	.	0.069886	0.64402	D	0.000020	T	0.50429	0.1615	M	0.88105	2.93	0.43381	D	0.995487	P;B;B	0.36086	0.536;0.134;0.083	B;B;B	0.29598	0.104;0.028;0.02	T	0.57751	-0.7757	9	.	.	.	-13.2176	11.6384	0.51217	0.0:0.0:0.0:1.0	.	181;220;220	E9PB95;O95352-2;O95352	.;.;ATG7_HUMAN	I	181;220;220	ENSP00000412580:F181I;ENSP00000347042:F220I;ENSP00000346437:F220I	.	F	+	1	0	ATG7	11331947	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.439000	0.59968	1.726000	0.51525	0.482000	0.46254	TTC	.		0.348	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		A	11356947	T	A	11356947	3	1	93	1	0	0	0	0	1	0	0	0	1102	1609	56	5	680	5	ATG7	3	11356947	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		11356947	186665483	14	8365											
DHX30	22907	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr3	47882520	47882520	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgaatccagagagtattCgaccagggggacctgggggc	10	6	16	9	1	0	2	0	1	0	1	2	5	1	3	3	4	1	2	3	4	2	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:47882520C>A	ENST00000445061.1	+	7	927	c.520C>A	c.(520-522)Cga>Aga	p.R174R	DHX30_ENST00000446256.2_Silent_p.R135R|DHX30_ENST00000348968.4_Silent_p.R146R|DHX30_ENST00000457607.1_Silent_p.R202R	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	174						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		AGAGAGTATTCGACCAGGGGG	0.597																																					p.R174R		.											.	DHX30-228	0			c.C520A						.						34	34	34					3																	47882520		2203	4300	6503	SO:0001819	synonymous_variant	22907	exon7			AGTATTCGACCAG	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.520C>A	3.37:g.47882520C>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	46	4	NM_138615	0	0	13	13	0	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Silent	SNP	ENST00000445061.1	37	CCDS2759.1																																																																																			.		0.597	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		A	47882520	C	A	47882520	2	1	93	1	0	0	0	0	0	0	0	1	4515	876	31	4		4	DHX30	3	47882520	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	36525573	47882520	150139910	15	8366											
CELSR3	1951	broad.mit.edu	37	chr3	48696845	48696845	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgctattctctttcacccGcacctcaaactcctcagctg	9	12	4	16	1	4	0	3	0	1	0	6	0	5	0	3	0	3	3	3	0	3	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:48696845G>A	ENST00000164024.4	-	1	3503	c.3223C>T	c.(3223-3225)Cgg>Tgg	p.R1075W	CELSR3_ENST00000544264.1_Missense_Mutation_p.R1075W	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1075	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TCTTTCACCCGCACCTCAAAC	0.557																																					p.R1075W													.	CELSR3-523	0			c.C3223T						.						116	112	113					3																	48696845		2203	4300	6503	SO:0001583	missense	1951	exon1			TCACCCGCACCTC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.3223C>T	3.37:g.48696845G>A	ENSP00000164024:p.Arg1075Trp	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	185	4	NM_001407	0	0	0	0	0	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	G	9.769	1.172192	0.21704	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.54071	0.59;0.59	5.78	2.53	0.30540	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.51381	0.1671	L	0.48174	1.505	0.09310	N	1	P;D	0.63880	0.641;0.993	P;P	0.51895	0.505;0.683	T	0.34453	-0.9828	9	0.42905	T	0.14	.	6.6689	0.23058	0.1467:0.0:0.4794:0.3739	.	1075;1145	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	W	1075	ENSP00000164024:R1075W;ENSP00000445694:R1075W	ENSP00000164024:R1075W	R	-	1	2	CELSR3	48671849	0.000000	0.05858	0.748000	0.31131	0.986000	0.74619	0.585000	0.23879	0.708000	0.31955	0.561000	0.74099	CGG	.		0.557	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48696845	G	A	48696845	3	1	93	1	0	0	0	0	1	0	0	0	3229	1086	38	1	6855	1	CELSR3	3	48696845	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	814325	48696845	149325585	16	8367											
ATP13A4	84239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	193132518	193132518	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctgaaaggcaccagcttaGggtaggcaccattcagattc	11	9	11	10	0	2	2	1	1	1	1	3	2	2	2	2	3	1	4	2	3	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:193132518G>C	ENST00000342695.4	-	26	3186	c.2864C>G	c.(2863-2865)cCt>cGt	p.P955R	ATP13A4_ENST00000392443.3_Missense_Mutation_p.P936R|ATP13A4_ENST00000400270.2_5'UTR|ATP13A4_ENST00000482964.1_5'Flank	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	955						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CACCAGCTTAGGGTAGGCACC	0.408																																					p.P955R		.											.	ATP13A4-92	0			c.C2864G						.						76	69	72					3																	193132518		2203	4300	6503	SO:0001583	missense	84239	exon26			AGCTTAGGGTAGG	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"ATPases / P-type"	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.2864C>G	3.37:g.193132518G>C	ENSP00000339182:p.Pro955Arg	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	68	23	NM_032279	0	0	0	1	1	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	37	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	19.55	3.847905	0.71603	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.89485	-2.52;-2.52	6.02	6.02	0.97574	.	0.000000	0.64402	D	0.000001	D	0.94082	0.8103	M	0.78637	2.42	0.80722	D	1	D	0.69078	0.997	D	0.67103	0.949	D	0.92892	0.6332	10	0.40728	T	0.16	-24.9732	18.0311	0.89285	0.0:0.0:1.0:0.0	.	955	Q4VNC1	AT134_HUMAN	R	936;955	ENSP00000376238:P936R;ENSP00000339182:P955R	ENSP00000339182:P955R	P	-	2	0	ATP13A4	194615212	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.191000	0.65110	2.857000	0.98124	0.650000	0.86243	CCT	.		0.408	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		C	193132518	G	C	193132518	3	2	93	1	0	0	0	0	1	0	0	0	1127	1000	35	4	746	4	ATP13A4	3	193132518	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	144435673	193132518	4889912	17	8368											
ABLIM2	84448	broad.mit.edu	37	chr4	8021392	8021392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tatagatgttatcttttacgCcagtgtctggggaagaagaa	12	13	11	5	1	2	3	0	0	2	3	2	4	2	4	1	2	1	1	1	2	7	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr4:8021392C>T	ENST00000341937.5	-	13	1341	c.1277G>A	c.(1276-1278)gGc>gAc	p.G426D	ABLIM2_ENST00000296372.8_Missense_Mutation_p.G426D|RP11-338K13.1_ENST00000608962.1_RNA|ABLIM2_ENST00000428004.2_Intron|ABLIM2_ENST00000361737.5_Intron|ABLIM2_ENST00000361581.5_Missense_Mutation_p.G426D|ABLIM2_ENST00000515079.1_5'Flank|ABLIM2_ENST00000505872.1_Intron|ABLIM2_ENST00000407564.3_Intron|ABLIM2_ENST00000514025.1_Missense_Mutation_p.G160D|ABLIM2_ENST00000546334.1_Intron|ABLIM2_ENST00000545242.1_Missense_Mutation_p.G426D|ABLIM2_ENST00000318888.4_Missense_Mutation_p.G160D|ABLIM2_ENST00000447017.2_Missense_Mutation_p.G459D	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	426					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						ATCTTTTACGCCAGTGTCTGG	0.463																																					p.G459D													.	ABLIM2-47	0			c.G1376A						.						94	93	94					4																	8021392		1568	3582	5150	SO:0001583	missense	84448	exon14			TTTACGCCAGTGT	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"actin binding LIM protein 2"				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1277G>A	4.37:g.8021392C>T	ENSP00000342813:p.Gly426Asp	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_001130083	0	0	1	1	0	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Missense_Mutation	SNP	ENST00000341937.5	37	CCDS47013.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.581016	0.65992	.	.	ENSG00000163995	ENST00000400045;ENST00000296372;ENST00000545242;ENST00000318888;ENST00000514025;ENST00000447017;ENST00000341937;ENST00000361581;ENST00000510277	T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	4.36	4.36	0.52297	.	0.213580	0.40302	N	0.001122	T	0.63931	0.2553	L	0.57536	1.79	0.45899	D	0.998747	D;D;P;P;D	0.58620	0.981;0.982;0.702;0.949;0.983	P;D;P;P;P	0.64321	0.726;0.924;0.646;0.848;0.606	T	0.68857	-0.5298	10	0.72032	D	0.01	.	17.2521	0.87045	0.0:1.0:0.0:0.0	.	426;426;160;426;459	Q6H8Q1-2;Q6H8Q1;Q6H8Q1-4;Q6H8Q1-5;E9PF39	.;ABLM2_HUMAN;.;.;.	D	458;426;426;160;160;459;426;426;227	ENSP00000296372:G426D;ENSP00000441255:G426D;ENSP00000317020:G160D;ENSP00000423661:G160D;ENSP00000393511:G459D;ENSP00000342813:G426D;ENSP00000355003:G426D;ENSP00000421718:G227D	ENSP00000296372:G426D	G	-	2	0	ABLIM2	8072292	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.003000	0.49505	2.130000	0.65690	0.555000	0.69702	GGC	.		0.463	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		T	8021392	C	T	8021392	3	4	93	1	0	0	0	0	1	0	0	0	95	739	26	2	610	2	ABLIM2	4	8021392	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08		8021392	183132884	18	8369											
ANAPC4	29945	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	25396298	25396298	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttttcattgtagtgctgAacttcagactctcttgatga	8	18	8	7	0	3	4	2	3	1	1	4	4	3	4	0	0	2	3	0	0	2	6			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr4:25396298A>G	ENST00000315368.3	+	13	1089	c.947A>G	c.(946-948)gAa>gGa	p.E316G	ANAPC4_ENST00000510092.1_Missense_Mutation_p.E316G	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	316					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				TGTAGTGCTGAACTTCAGACT	0.308																																					p.E316G		.											.	ANAPC4-293	0			c.A947G						.						90	94	93					4																	25396298		2203	4296	6499	SO:0001583	missense	29945	exon13			GTGCTGAACTTCA	AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"Anaphase promoting complex subunits"	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.947A>G	4.37:g.25396298A>G	ENSP00000318775:p.Glu316Gly	Somatic	145	1		WXS	Illumina HiSeq	Phase_I	103	43	NM_013367	0	0	2	2	0	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.857075	0.51376	.	.	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.35048	1.33;1.33	5.27	5.27	0.74061	Anaphase-promoting complex subunit 4 long domain (1);	0.000000	0.85682	D	0.000000	T	0.42988	0.1227	L	0.44542	1.39	0.80722	D	1	P;D	0.53619	0.951;0.961	P;P	0.55087	0.562;0.768	T	0.13683	-1.0500	10	0.15952	T	0.53	-15.212	14.6892	0.69072	1.0:0.0:0.0:0.0	.	316;316	E9PCR4;Q9UJX5	.;APC4_HUMAN	G	316	ENSP00000318775:E316G;ENSP00000426654:E316G	ENSP00000318775:E316G	E	+	2	0	ANAPC4	25005396	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.539000	0.90637	2.139000	0.66308	0.455000	0.32223	GAA	.		0.308	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367		G	25396298	A	G	25396298	3	3	93	1	0	0	0	0	1	0	0	0	604	246	9	3	993	3	ANAPC4	4	25396298	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	17374906	25396298	165757978	19	8370											
PARM1	25849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	75937687	75937687	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctttgtctgtttctcttccGacaaacattgtaccaccgac	8	14	5	14	2	2	0	0	0	2	0	4	2	3	0	4	0	2	2	4	0	2	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr4:75937687G>C	ENST00000307428.7	+	2	308	c.96G>C	c.(94-96)ccG>ccC	p.P32P	RP11-44F21.2_ENST00000513770.1_RNA|PARM1_ENST00000513238.1_Intron	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	32					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						TTTCTCTTCCGACAAACATTG	0.488																																					p.P32P		.											.	PARM1-1	0			c.G96C						.																																			SO:0001819	synonymous_variant	25849	exon2			TCTTCCGACAAAC	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"Prostatic androgen-repressed message 1", "Castration-induced prostatic apoptosis-related protein 1", "WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.96G>C	4.37:g.75937687G>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	67	32	NM_015393	0	0	3	3	0	B3KMQ9|Q96DV8|Q9Y4S1	Silent	SNP	ENST00000307428.7	37	CCDS47077.1																																																																																			.		0.488	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393		C	75937687	G	C	75937687	2	2	93	1	0	0	0	0	0	0	0	1	11478	1045	37	4		4	PARM1	4	75937687	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08	50541389	75937687	115216589	20	8371											
ENPEP	2028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	111397845	111397845	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggacagtggaaaaactttcGactgccggacttcgtcaacc	11	8	10	12	4	1	0	1	0	0	0	3	4	1	3	2	3	3	0	2	3	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr4:111397845G>A	ENST00000265162.5	+	1	617	c.275G>A	c.(274-276)cGa>cAa	p.R92Q		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	92					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		AAAAACTTTCGACTGCCGGAC	0.612																																					p.R92Q		.											.	ENPEP-157	0			c.G275A						.						75	80	78					4																	111397845		2203	4300	6503	SO:0001583	missense	2028	exon1			ACTTTCGACTGCC	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.275G>A	4.37:g.111397845G>A	ENSP00000265162:p.Arg92Gln	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	93	36	NM_001977	0	0	7	7	0	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.865651	0.71949	.	.	ENSG00000138792	ENST00000265162	T	0.03181	4.02	5.83	5.83	0.93111	.	0.098719	0.64402	D	0.000003	T	0.23210	0.0561	M	0.89785	3.06	0.58432	D	0.999999	D	0.89917	1.0	D	0.76575	0.988	T	0.00599	-1.1651	10	0.87932	D	0	.	14.2874	0.66254	0.0708:0.0:0.9292:0.0	.	92	Q07075	AMPE_HUMAN	Q	92	ENSP00000265162:R92Q	ENSP00000265162:R92Q	R	+	2	0	ENPEP	111617294	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	7.579000	0.82511	2.758000	0.94735	0.561000	0.74099	CGA	.		0.612	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			A	111397845	G	A	111397845	3	1	93	1	0	0	0	0	1	0	0	0	5141	1058	37	1	277	1	ENPEP	4	111397845	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	35460158	111397845	79756431	21	8372											
ADCY2	108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7820695	7820695	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtattaaccatggacctGtgatagctggtgtgattgga	10	12	13	6	0	0	2	0	2	0	0	0	4	0	4	2	4	2	2	2	4	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:7820695G>A	ENST00000338316.4	+	24	3105	c.3016G>A	c.(3016-3018)Gtg>Atg	p.V1006M	ADCY2_ENST00000537121.1_Missense_Mutation_p.V826M	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	1006					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CCATGGACCTGTGATAGCTGG	0.428																																					p.V1006M		.											.	ADCY2-97	0			c.G3016A						.						107	95	99					5																	7820695		2203	4300	6503	SO:0001583	missense	108	exon24			GGACCTGTGATAG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.3016G>A	5.37:g.7820695G>A	ENSP00000342952:p.Val1006Met	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	63	33	NM_020546	0	0	3	7	4	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	G	25.4	4.632738	0.87660	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;T	0.48522	0.81;0.81	5.19	5.19	0.71726	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	T	0.81437	0.4822	H	0.98178	4.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88857	0.3323	10	0.87932	D	0	.	18.7434	0.91782	0.0:0.0:1.0:0.0	.	826;1006	B7Z2C1;Q08462	.;ADCY2_HUMAN	M	1006;839;826	ENSP00000342952:V1006M;ENSP00000444803:V826M	ENSP00000342952:V1006M	V	+	1	0	ADCY2	7873695	1.000000	0.71417	0.968000	0.41197	0.900000	0.52787	9.565000	0.98154	2.430000	0.82344	0.655000	0.94253	GTG	.		0.428	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7820695	G	A	7820695	3	1	93	1	0	0	0	0	1	0	0	0	294	1377	48	2	3110	2	ADCY2	5	7820695	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08		7820695	173094565	22	8373											
CMBL	134147	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	10288604	10288609	+	In_Frame_Del	DEL	AAGGCT	AAGGCT	-																															ccagtcgccagaggggtcccAaggctcttgccctacaaaga																										TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	AAGGCT	AAGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:10288604_10288609delAAGGCT	ENST00000296658.3	-	3	668_673	c.248_253delAGCCTT	c.(247-255)gagccttgg>ggg	p.83_85EPW>G	CMBL_ENST00000510532.1_5'UTR	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	83						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						GAGGGGTCCCAAGGCTCTTGCCCTAC	0.456																																					p.83_85del		.											.	CMBL-69	0			c.248_253del						.																																			SO:0001651	inframe_deletion	134147	exon3			.		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"carboxymethylenebutenolidase-like (Pseudomonas)"			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.248_253delAGCCTT	5.37:g.10288604_10288609delAAGGCT	ENSP00000296658:p.Glu83_Trp85delinsGly	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	101	32	NM_138809	0	0	0	0	0	D3DTC7|Q8TED6	In_Frame_Del	DEL	ENST00000296658.3	37	CCDS3878.1																																																																																			.		0.456	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809		-	10288609	AAGGCT	-	10288604	7	5	93	1	0	1	0	1	0	0	0	0	3582	130	5	0	500	0	CMBL	5	10288604	In_Frame_Del	DEL	AAGGCT	TCGA-DW-5561-01A-01D-1589-08	2467909	10288604	170626656	23	8374											
RPS14	6208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149827271	149827271	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatgacctgttcttccttcTtttccttcccctttcgaggt	3	19	6	13	1	2	2	0	2	2	0	6	3	5	2	5	1	0	1	5	1	0	7			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:149827271T>C	ENST00000401695.3	-	2	72	c.26A>G	c.(25-27)aAg>aGg	p.K9R	RPS14_ENST00000407193.1_Missense_Mutation_p.K9R|RPS14_ENST00000312037.5_Missense_Mutation_p.K9R			P62263	RS14_HUMAN	ribosomal protein S14	9					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|maturation of SSU-rRNA (GO:0030490)|mRNA metabolic process (GO:0016071)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|ribosomal small subunit assembly (GO:0000028)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			central_nervous_system(1)|lung(1)|skin(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCTTCCTTCTTTTCCTTCCC	0.443																																					p.K9R		.											.	RPS14-90	0			c.A26G						.						125	111	116					5																	149827271		2203	4300	6503	SO:0001583	missense	6208	exon2			TCCTTCTTTTCCT		CCDS4307.1	5q31-q33	2012-10-02			ENSG00000164587	ENSG00000164587		"S ribosomal proteins"	10387	protein-coding gene	gene with protein product	"emetine resistance", "40S ribosomal protein S14"	130620				3785212, 1549121	Standard	XM_006714790		Approved	EMTB, S14	uc003lsj.3	P62263	OTTHUMG00000130080	ENST00000401695.3:c.26A>G	5.37:g.149827271T>C	ENSP00000385958:p.Lys9Arg	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	148	67	NM_001025071	0	0	643	1195	552	B2R5G5|D3DQG5|P06366|Q5BJI0	Missense_Mutation	SNP	ENST00000401695.3	37	CCDS4307.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142739	0.57044	.	.	ENSG00000164587	ENST00000401695;ENST00000407193;ENST00000521466;ENST00000312037	.	.	.	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	N	0.22421	0.69	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.28332	-1.0047	9	0.23891	T	0.37	.	15.1102	0.72349	0.0:0.0:0.0:1.0	.	9	P62263	RS14_HUMAN	R	9	.	ENSP00000311028:K9R	K	-	2	0	RPS14	149807464	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.649000	0.83500	2.023000	0.59567	0.455000	0.32223	AAG	.		0.443	RPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252373.1	NM_001025071		C	149827271	T	C	149827271	3	2	93	1	0	0	0	0	1	0	0	0	13656	1609	56	3	445	3	RPS14	5	149827271	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08	139538667	149827271	31087989	24	8375											
CPEB4	80315	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	173317605	173317605	+	Frame_Shift_Del	DEL	G	G	-																															tccgtggagcagctaccagaGtccgtcaccaacaccctcct																								rs372054497		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:173317605delG	ENST00000265085.5	+	1	2323	c.869delG	c.(868-870)agtfs	p.S290fs	CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000520867.1_Frame_Shift_Del_p.S290fs|CPEB4_ENST00000519835.1_Frame_Shift_Del_p.S290fs|CPEB4_ENST00000334035.5_Frame_Shift_Del_p.S290fs	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	290					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			AGCTACCAGAGTCCGTCACCA	0.572																																					p.S290fs		.											.	CPEB4-90	0			c.869delG						.						148	161	157					5																	173317605		2203	4300	6503	SO:0001589	frameshift_variant	80315	exon1			.	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.869delG	5.37:g.173317605delG	ENSP00000265085:p.Ser290fs	Somatic	376	0		WXS	Illumina HiSeq	Phase_I	277	108	NM_030627	0	0	0	0	0	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Frame_Shift_Del	DEL	ENST00000265085.5	37	CCDS4390.1																																																																																			.		0.572	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		-	173317605	G	-	173317605	7	5	93	1	0	1	0	1	0	0	0	0	3809	1029	36	0	871	0	CPEB4	5	173317605	Frame_Shift_Del	DEL	G	TCGA-DW-5561-01A-01D-1589-08	23490334	173317605	7597655	25	8376											
PRPF4B	8899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	4047415	4047415	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	taatttcctttaaggttcatCtcagaagaagttgttggcac	11	15	8	7	0	2	2	2	0	1	2	4	2	3	2	1	2	0	4	1	2	4	7			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr6:4047415C>G	ENST00000337659.6	+	7	1968	c.1868C>G	c.(1867-1869)tCt>tGt	p.S623C	PRPF4B_ENST00000538861.1_Missense_Mutation_p.S609C	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	623					mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				TAAGGTTCATCTCAGAAGAAG	0.284																																					p.S623C		.											.	PRPF4B-1308	0			c.C1868G						.						154	146	148					6																	4047415		2202	4298	6500	SO:0001583	missense	8899	exon7			GTTCATCTCAGAA	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1868C>G	6.37:g.4047415C>G	ENSP00000337194:p.Ser623Cys	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	195	67	NM_003913	0	0	0	0	0	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572647	0.65765	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.68479	-0.33;-0.32	5.51	4.63	0.57726	.	0.380183	0.25372	N	0.031153	T	0.31167	0.0788	N	0.14661	0.345	0.34271	D	0.681056	B	0.20164	0.042	B	0.21917	0.037	T	0.19582	-1.0301	10	0.51188	T	0.08	.	9.3135	0.37919	0.1456:0.7823:0.0:0.0721	.	623	Q13523	PRP4B_HUMAN	C	623;609	ENSP00000337194:S623C;ENSP00000439331:S609C	ENSP00000337194:S623C	S	+	2	0	PRPF4B	3992414	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.825000	0.48096	1.424000	0.47217	0.650000	0.86243	TCT	.		0.284	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			G	4047415	C	G	4047415	3	3	93	1	0	0	0	0	1	0	0	0	12602	913	32	4	1894	4	PRPF4B	6	4047415	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08		4047415	167067652	26	8377											
INTS1	26173	hgsc.bcm.edu	37	chr7	1538639	1538639	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgcagccacatctccagcTtctgcaccgccagcagccgc	7	7	8	19	2	3	0	0	0	3	0	4	0	3	0	5	0	6	4	5	0	0	1	rs200286642	byFrequency	TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr7:1538639T>C	ENST00000404767.3	-	8	1194	c.1109A>G	c.(1108-1110)aAg>aGg	p.K370R	INTS1_ENST00000389470.4_Missense_Mutation_p.K498R|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	370					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CATCTCCAGCTTCTGCACCGC	0.706													T|||	27	0.00539137	0.0204	0	5008	,	,		5621	0		0	False		,,,				2504	0				p.K370R		.											.	.	0			c.A1109G						.						11	12	12					7																	1538639		1856	4025	5881	SO:0001583	missense	26173	exon8			TCCAGCTTCTGCA	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1109A>G	7.37:g.1538639T>C	ENSP00000385722:p.Lys370Arg	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_001080453	0	0	4	11	7	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	37	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	T	6.364	0.435315	0.12045	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.38887	2.67;1.11	5.26	-0.164	0.13359	.	0.215281	0.47852	N	0.000202	T	0.11707	0.0285	N	0.00879	-1.12	0.22873	N	0.998625	B;B	0.02656	0.0;0.0	B;B	0.15870	0.014;0.006	T	0.37776	-0.9691	10	0.02654	T	1	.	12.752	0.57314	0.0:0.8201:0.0:0.1799	.	498;370	A4D212;Q8N201	.;INT1_HUMAN	R	370;498	ENSP00000385722:K370R;ENSP00000374121:K498R	ENSP00000374121:K498R	K	-	2	0	INTS1	1505165	1.000000	0.71417	0.987000	0.45799	0.863000	0.49368	2.514000	0.45503	0.009000	0.14813	0.533000	0.62120	AAG	.		0.706	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			C	1538639	T	C	1538639	3	2	93	1	0	0	0	0	1	0	0	0	7796	1609	56	3	5627	3	INTS1	7	1538639	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		1538639	157600024	27	8378											
KCND2	3751	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	119915491	119915491	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgagtatcatcgacgtggtgGccatcctgccttattacatt	8	14	9	10	2	1	1	1	1	0	0	3	2	2	1	3	2	2	1	3	2	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr7:119915491G>T	ENST00000331113.4	+	1	1770	c.805G>T	c.(805-807)Gcc>Tcc	p.A269S		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	269					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CGACGTGGTGGCCATCCTGCC	0.512																																					p.A269S		.											.	KCND2-517	0			c.G805T						.						172	142	152					7																	119915491		2203	4300	6503	SO:0001583	missense	3751	exon1			GTGGTGGCCATCC	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.805G>T	7.37:g.119915491G>T	ENSP00000333496:p.Ala269Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	102	28	NM_012281	0	0	0	0	0	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348475	0.82132	.	.	ENSG00000184408	ENST00000331113	D	0.98493	-4.96	5.27	5.27	0.74061	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	N	0.16166	0.38	0.80722	D	1	P	0.46578	0.88	P	0.57620	0.824	D	0.96477	0.9353	9	.	.	.	.	19.2668	0.93990	0.0:0.0:1.0:0.0	.	269	Q9NZV8	KCND2_HUMAN	S	269	ENSP00000333496:A269S	.	A	+	1	0	KCND2	119702727	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.813000	0.99286	2.636000	0.89361	0.557000	0.71058	GCC	.		0.512	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	119915491	G	T	119915491	3	4	93	1	0	0	0	0	1	0	0	0	8040	1203	42	4	807	4	KCND2	7	119915491	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	118376852	119915491	39223172	28	8379											
KLRG2	346689	broad.mit.edu	37	chr7	139164445	139164445	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggctggcttcccaggcctgCgcttctgcagagaagtagta	7	10	13	11	1	1	1	0	0	1	1	2	2	2	1	2	3	2	6	2	3	3	4	rs201132743		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr7:139164445C>T	ENST00000340940.4	-	3	1002	c.933G>A	c.(931-933)gcG>gcA	p.A311A	KLRG2_ENST00000393039.2_Intron	NM_198508.2	NP_940910.1	A4D1S0	KLRG2_HUMAN	killer cell lectin-like receptor subfamily G, member 2	311	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|large_intestine(2)|lung(3)	6	Melanoma(164;0.233)					CCCAGGCCTGCGCTTCTGCAG	0.617													C|||	1	0.000199681	0	0.0014	5008	,	,		17111	0		0	False		,,,				2504	0				p.A311A													.	KLRG2-90	0			c.G933A						.						66	64	65					7																	139164445		2203	4300	6503	SO:0001819	synonymous_variant	346689	exon3			GGCCTGCGCTTCT	AK126174	CCDS5854.1	7q34	2011-08-30			ENSG00000188883	ENSG00000188883		"Killer cell lectin-like receptors", "C-type lectin domain containing"	24778	protein-coding gene	gene with protein product	"C-type lectin domain family 15, member B"						Standard	XM_005250311		Approved	FLJ44186, CLEC15B	uc003vvb.3	A4D1S0	OTTHUMG00000157705	ENST00000340940.4:c.933G>A	7.37:g.139164445C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	164	4	NM_198508	0	0	1	1	0	Q2NL79|Q6ZTV6	Silent	SNP	ENST00000340940.4	37	CCDS5854.1																																																																																			C|0.999;T|0.000		0.617	KLRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349433.1	NM_198508		T	139164445	C	T	139164445	2	4	93	1	0	0	0	0	0	0	0	1	8443	755	27	1		1	KLRG2	7	139164445	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	19248954	139164445	19974218	29	8380											
CDKN2B	1030	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	22006244	22006244	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgggcgctgcccatcatcatGacctgccagagagagcagag	10	5	13	13	2	2	4	2	1	0	3	2	5	2	4	3	1	3	2	3	1	0	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr9:22006244G>A	ENST00000276925.6	-	2	568	c.159C>T	c.(157-159)gtC>gtT	p.V53V	CDKN2B-AS1_ENST00000582072.1_RNA|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000581051.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B-AS1_ENST00000584351.1_RNA|CDKN2B_ENST00000380142.4_3'UTR|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA	NM_004936.3|NM_078487.2	NP_004927.2|NP_511042.1	P42772	CDN2B_HUMAN	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	53					aging (GO:0007568)|cell cycle arrest (GO:0007050)|cellular response to extracellular stimulus (GO:0031668)|cellular response to nutrient (GO:0031670)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|liver development (GO:0001889)|megakaryocyte differentiation (GO:0030219)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to cytokine (GO:0034097)|response to organic cyclic compound (GO:0014070)|spleen development (GO:0048536)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0(1)|p.0?(1)		lung(2)	2		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;1.31e-280)|Lung NSC(2;2.28e-131)|all_lung(2;2.11e-123)|Glioma(2;5.66e-57)|all_neural(2;3.05e-50)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;8.01e-33)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00369)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;3.29e-71)|Epithelial(2;9.08e-60)|LUSC - Lung squamous cell carcinoma(2;5.8e-46)|LUAD - Lung adenocarcinoma(2;1.43e-25)|BRCA - Breast invasive adenocarcinoma(2;5.37e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;6.92e-07)|KIRC - Kidney renal clear cell carcinoma(2;8.63e-07)|OV - Ovarian serous cystadenocarcinoma(39;0.014)|COAD - Colon adenocarcinoma(8;0.143)		CCATCATCATGACCTGCCAGA	0.647																																					p.V53V		.											.	CDKN2B-792	2	Whole gene deletion(2)	lung(2)	c.C159T						.						14	17	16					9																	22006244		2175	4259	6434	SO:0001819	synonymous_variant	1030	exon2			CATCATGACCTGC	AB060808	CCDS6512.1, CCDS6513.1	9p21	2008-07-21			ENSG00000147883	ENSG00000147883			1788	protein-coding gene	gene with protein product		600431				8078588	Standard	NM_004936		Approved	P15, MTS2, INK4B, TP15, CDK4I, p15INK4b	uc003zpo.3	P42772	OTTHUMG00000019691	ENST00000276925.6:c.159C>T	9.37:g.22006244G>A		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	22	8	NM_004936	0	0	0	0	0	O15125|Q6FI09	Silent	SNP	ENST00000276925.6	37	CCDS6512.1																																																																																			.		0.647	CDKN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051932.2	NM_004936		A	22006244	G	A	22006244	2	1	93	1	0	0	0	0	0	0	0	1	3170	1277	45	2		2	CDKN2B	9	22006244	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		22006244	119207187	30	8381											
NIPSNAP3B	55335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	107531256	107531256	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gataaacaagagacggaaatTacttacctgataccatggtc	16	9	8	8	1	0	2	0	1	0	1	1	5	0	3	2	2	4	0	2	2	7	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr9:107531256T>A	ENST00000374762.3	+	3	455	c.384T>A	c.(382-384)atT>atA	p.I128I	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	128										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						AGACGGAAATTACTTACCTGA	0.383																																					p.I128I		.											.	NIPSNAP3B-92	0			c.T384A						.						79	76	77					9																	107531256		2203	4300	6503	SO:0001819	synonymous_variant	55335	exon3			GGAAATTACTTAC	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.384T>A	9.37:g.107531256T>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	77	38	NM_018376	0	0	1	3	2	Q5VX30|Q9NUM2	Silent	SNP	ENST00000374762.3	37	CCDS6761.1																																																																																			.		0.383	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376		A	107531256	T	A	107531256	2	1	93	1	0	0	0	0	0	0	0	1	10457	1742	61	5		5	NIPSNAP3B	9	107531256	Silent	SNP	T	TCGA-DW-5561-01A-01D-1589-08	85525012	107531256	33682175	31	8382											
CEP110	11064	broad.mit.edu	37	chr9	123888062	123888062	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagtgggttgcaagaatacCtggggaccattaaaggccag	12	8	13	8	0	1	1	1	0	0	1	1	2	1	2	3	4	2	2	3	4	5	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr9:123888062C>A	ENST00000373855.1	+	14	2133	c.1873C>A	c.(1873-1875)Ctg>Atg	p.L625M	CNTRL_ENST00000373850.1_Missense_Mutation_p.L73M|CNTRL_ENST00000373847.1_Missense_Mutation_p.L73M|CNTRL_ENST00000238341.5_Missense_Mutation_p.L625M			Q7Z7A1	CNTRL_HUMAN	centriolin	625					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						GCAAGAATACCTGGGGACCAT	0.458																																					p.L625M													.	CNTRL-661	0			c.C1873A						.						120	123	122					9																	123888062		2203	4300	6503	SO:0001583	missense	11064	exon12			GAATACCTGGGGA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"centrosomal protein 1", "centrosomal protein 110kDa"	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.1873C>A	9.37:g.123888062C>A	ENSP00000362962:p.Leu625Met	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	114	4	NM_007018	0	0	0	0	0	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944003	0.73672	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.65549	0.25;0.25;-0.16;0.05	5.59	4.69	0.59074	.	.	.	.	.	T	0.69214	0.3086	L	0.34521	1.04	0.37252	D	0.906593	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.997	T	0.74237	-0.3730	9	0.51188	T	0.08	.	13.301	0.60326	0.0:0.9245:0.0:0.0755	.	625;625;625	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	M	625;625;625;107;73;73	ENSP00000362962:L625M;ENSP00000238341:L625M;ENSP00000362956:L73M;ENSP00000362953:L73M	ENSP00000238341:L625M	L	+	1	2	CNTRL	122927883	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.004000	0.40854	1.349000	0.45751	0.650000	0.86243	CTG	.		0.458	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		A	123888062	C	A	123888062	3	1	93	1	0	0	0	0	1	0	0	0	3251	680	24	4	1919	4	CEP110	9	123888062	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	16356806	123888062	17325369	32	8383											
C10orf95	79946	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	104211148	104211149	+	Frame_Shift_Ins	INS	-	-	C																															gactccccactcacttgtctINSccttcagccttggggagccg																								rs144830667		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr10:104211148_104211149insC	ENST00000239125.1	-	1	151_152	c.77_78insG	c.(76-78)ggafs	p.G26fs	RP11-18I14.10_ENST00000594818.1_RNA|RP11-18I14.10_ENST00000492465.2_RNA|RP11-18I14.10_ENST00000596366.1_RNA|RP11-18I14.10_ENST00000494270.2_RNA|RP11-18I14.10_ENST00000473970.2_RNA|RP11-18I14.10_ENST00000596045.1_RNA	NM_024886.1	NP_079162.1	Q9H7T3	CJ095_HUMAN	chromosome 10 open reading frame 95	26										liver(1)	1		Colorectal(252;0.207)		Epithelial(162;8.34e-09)|all cancers(201;1.95e-07)|BRCA - Breast invasive adenocarcinoma(275;0.213)		CTCACTTGTCTCCTTCAGCCTT	0.639																																					p.G26fs		.											.	C10orf95-91	0			c.78_79insG						.																																			SO:0001589	frameshift_variant	79946	exon1			.	AK024342	CCDS7534.1	10q24.32	2014-02-19	2014-02-19	2014-02-19	ENSG00000120055	ENSG00000120055			25880	protein-coding gene	gene with protein product							Standard	NM_024886		Approved	FLJ14280	uc001kvo.1	Q9H7T3	OTTHUMG00000018959	ENST00000239125.1:c.78dupG	10.37:g.104211150_104211150dupC	ENSP00000239125:p.Gly26fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	42	18	NM_024886	0	0	0	0	0	A0AVQ7	Frame_Shift_Ins	INS	ENST00000239125.1	37	CCDS7534.1																																																																																			.		0.639	C10orf95-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050065.1	NM_024886		C	104211149	-	C	104211148	7	5	93	1	0	1	1	0	0	0	0	0	1630	1538	54	0	703	0	C10orf95	10	104211148	Frame_Shift_Ins	INS	-	TCGA-DW-5561-01A-01D-1589-08		104211148	31323599	33	8384											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6662787	6662787	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcaatggtagcaggaggtGgggcctggggctcttcatgc	7	8	17	9	0	2	0	1	0	1	0	2	1	2	1	1	7	3	4	1	7	2	2	rs201684495	byFrequency	TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr11:6662787G>A	ENST00000299441.3	-	2	469	c.58C>T	c.(58-60)Cac>Tac	p.H20Y		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	20					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		agcagGAGGTGGGGCCTGGGG	0.642													G|||	12	0.00239617	0.0091	0	5008	,	,		19029	0		0	False		,,,				2504	0				p.H20Y		.											.	DCHS1-73	0			c.C58T						.	G	TYR/HIS	28,4186		0,28,2079	10	9	9		58	2.4	0	11		9	0,8212		0,0,4106	yes	missense	DCHS1	NM_003737.2	83	0,28,6185	AA,AG,GG		0.0,0.6645,0.2253	benign	20/3299	6662787	28,12398	2107	4106	6213	SO:0001583	missense	8642	exon2			GGAGGTGGGGCCT	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.58C>T	11.37:g.6662787G>A	ENSP00000299441:p.His20Tyr	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_003737	0	0	0	0	0	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	G	0.391	-0.923232	0.02377	0.006645	0.0	ENSG00000166341	ENST00000299441	T	0.54479	0.57	5.47	2.43	0.29744	.	0.775970	0.09906	N	0.740486	T	0.26304	0.0642	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18745	-1.0327	10	0.46703	T	0.11	.	7.4287	0.27115	0.1572:0.1371:0.7056:0.0	.	20	Q96JQ0	PCD16_HUMAN	Y	20	ENSP00000299441:H20Y	ENSP00000299441:H20Y	H	-	1	0	DCHS1	6619363	0.001000	0.12720	0.001000	0.08648	0.710000	0.40934	0.902000	0.28459	0.657000	0.30906	0.579000	0.79373	CAC	.		0.642	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6662787	G	A	6662787	3	1	93	1	0	0	0	0	1	0	0	0	4293	1348	47	2	9918	2	DCHS1	11	6662787	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08		6662787	128343729	34	8385											
OR4A16	81327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55110797	55110797	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgacaatggtgggaaacCtcctcatttgggtgactact	9	13	11	8	0	1	2	1	2	0	0	2	3	2	3	2	3	2	0	2	3	3	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr11:55110797C>T	ENST00000314721.2	+	1	171	c.121C>T	c.(121-123)Ctc>Ttc	p.L41F		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						GGTGGGAAACCTCCTCATTTG	0.428																																					p.L41F		.											.	OR4A16-69	0			c.C121T						.						122	115	117					11																	55110797		2201	4296	6497	SO:0001583	missense	81327	exon1			GGAAACCTCCTCA	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"GPCR / Class A : Olfactory receptors"	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.121C>T	11.37:g.55110797C>T	ENSP00000325128:p.Leu41Phe	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	180	64	NM_001005274	0	0	0	0	0	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	c	7.100	0.573809	0.13623	.	.	ENSG00000181961	ENST00000314721	T	0.00438	7.42	2.41	1.46	0.22682	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00637	0.0021	L	0.55017	1.72	0.09310	N	0.999999	D	0.57899	0.981	D	0.63597	0.916	T	0.56938	-0.7896	9	0.37606	T	0.19	.	6.7077	0.23260	0.0:0.8361:0.0:0.1639	.	41	Q8NH70	O4A16_HUMAN	F	41	ENSP00000325128:L41F	ENSP00000325128:L41F	L	+	1	0	OR4A16	54867373	0.000000	0.05858	0.772000	0.31596	0.023000	0.10783	-0.898000	0.04105	1.353000	0.45828	0.185000	0.17295	CTC	.		0.428	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		T	55110797	C	T	55110797	3	4	93	1	0	0	0	0	1	0	0	0	11067	681	24	2	123	2	OR4A16	11	55110797	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	48448010	55110797	79895719	35	8386											
ETS1	2113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	128360461	128360461	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttaatagtgggacatctgcAcattccatatctgcatgaaa	13	12	8	8	0	2	1	0	1	2	0	3	2	3	2	1	1	2	3	1	1	4	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr11:128360461A>T	ENST00000319397.6	-	2	402	c.93T>A	c.(91-93)tgT>tgA	p.C31*	ETS1_ENST00000526145.2_Nonsense_Mutation_p.C31*|ETS1_ENST00000345075.4_Nonsense_Mutation_p.C31*|ETS1_ENST00000531611.1_Nonsense_Mutation_p.C31*|ETS1_ENST00000392668.4_Nonsense_Mutation_p.C75*|ETS1_ENST00000535549.1_Intron	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	31					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		GGACATCTGCACATTCCATAT	0.363																																					p.C75X		.											.	ETS1-1270	0			c.T225A						.						110	104	106					11																	128360461		2201	4297	6498	SO:0001587	stop_gained	2113	exon4			ATCTGCACATTCC		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.93T>A	11.37:g.128360461A>T	ENSP00000324578:p.Cys31*	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	68	26	NM_001143820	0	0	0	0	0	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Nonsense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	A	38	6.929848	0.97944	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	.	.	.	5.65	2.0	0.26442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	9.4666	0.38817	0.796:0.0:0.204:0.0	.	.	.	.	X	31;75;31;31;31	.	ENSP00000324578:C31X	C	-	3	2	ETS1	127865671	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.583000	0.36579	0.084000	0.17077	-0.376000	0.06991	TGT	.		0.363	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		T	128360461	A	T	128360461	4	4	93	1	0	0	0	0	0	1	0	0	5288	157	6	5	1260	5	ETS1	11	128360461	Nonsense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	73249664	128360461	6646055	36	8387											
SLC6A13	6540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	335609	335609	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctgagacatgaagcccAggatggagaagatggcaaag	14	5	14	8	0	0	4	0	2	0	3	1	7	1	5	2	3	1	2	2	3	3	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:335609A>G	ENST00000343164.4	-	9	1059	c.1007T>C	c.(1006-1008)cTg>cCg	p.L336P	SLC6A13_ENST00000539668.1_5'Flank|SLC6A13_ENST00000445055.2_Missense_Mutation_p.L244P	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	336					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			CATGAAGCCCAGGATGGAGAA	0.622																																					p.L336P		.											.	SLC6A13-90	0			c.T1007C						.						64	58	60					12																	335609		2203	4300	6503	SO:0001583	missense	6540	exon9			AAGCCCAGGATGG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1007T>C	12.37:g.335609A>G	ENSP00000339260:p.Leu336Pro	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	77	46	NM_016615	0	0	47	172	125	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.496459	0.85069	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	D;D	0.83075	-1.68;-1.68	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.95462	0.8526	H	0.99634	4.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.996	D	0.97664	1.0162	10	0.87932	D	0	.	15.3028	0.73966	1.0:0.0:0.0:0.0	.	244;315;336	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	P	244;315;336	ENSP00000407104:L244P;ENSP00000339260:L336P	ENSP00000318097:L315P	L	-	2	0	SLC6A13	205870	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.260000	0.95568	2.010000	0.58986	0.402000	0.26972	CTG	.		0.622	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		G	335609	A	G	335609	3	3	93	1	0	0	0	0	1	0	0	0	14708	188	7	3	829	3	SLC6A13	12	335609	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08		335609	133516286	37	8388											
GAPDH	2597	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	6646478	6646485	+	Frame_Shift_Del	DEL	TGCCTCCT	TGCCTCCT	-																															tccctctttctttgcagcaaTgcctcctgcaccaccaactg																										TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	TGCCTCCT	TGCCTCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:6646478_6646485delTGCCTCCT	ENST00000229239.5	+	7	1113_1120	c.447_454delTGCCTCCT	c.(445-456)aatgcctcctgcfs	p.NASC149fs	GAPDH_ENST00000396859.1_Frame_Shift_Del_p.NASC149fs|GAPDH_ENST00000396858.1_Frame_Shift_Del_p.NASC107fs|GAPDH_ENST00000396856.1_Frame_Shift_Del_p.NASC74fs|RP5-940J5.9_ENST00000602946.1_RNA|GAPDH_ENST00000396861.1_Frame_Shift_Del_p.NASC149fs	NM_002046.4	NP_002037.2	P04406	G3P_HUMAN	glyceraldehyde-3-phosphate dehydrogenase	149					carbohydrate metabolic process (GO:0005975)|cellular response to interferon-gamma (GO:0071346)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of translation (GO:0017148)|neuron apoptotic process (GO:0051402)|peptidyl-cysteine S-trans-nitrosylation (GO:0035606)|protein stabilization (GO:0050821)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GAIT complex (GO:0097452)|lipid particle (GO:0005811)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|identical protein binding (GO:0042802)|microtubule binding (GO:0008017)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|peptidyl-cysteine S-nitrosylase activity (GO:0035605)			central_nervous_system(1)|cervix(1)|endometrium(1)|lung(4)	7						TTTGCAGCAATGCCTCCTGCACCACCAA	0.596																																					p.149_152del		.											.	GAPDH-226	0			c.447_454del						.																																			SO:0001589	frameshift_variant	2597	exon7			.	AF261085	CCDS8549.1, CCDS58201.1	12p13.31	2012-10-02		2005-05-06	ENSG00000111640	ENSG00000111640	1.2.1.12		4141	protein-coding gene	gene with protein product		138400		GAPD		3170585	Standard	NM_002046		Approved		uc001qop.2	P04406	OTTHUMG00000137379	ENST00000229239.5:c.447_454delTGCCTCCT	12.37:g.6646478_6646485delTGCCTCCT	ENSP00000229239:p.Asn149fs	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	47	13	NM_002046	0	0	0	0	0	E7EUT4|P00354|Q53X65	Frame_Shift_Del	DEL	ENST00000229239.5	37	CCDS8549.1																																																																																			.		0.596	GAPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268059.1	NM_002046		-	6646485	TGCCTCCT	-	6646478	7	5	93	1	0	1	0	1	0	0	0	0	6256	1461	51	0	469	0	GAPDH	12	6646478	Frame_Shift_Del	DEL	TGCCTCCT	TCGA-DW-5561-01A-01D-1589-08	6310869	6646478	127205417	38	8389											
TAS2R20	259295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	11150353	11150353	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatttgatcagctgaggagAtcttttgtctcttgacccag	9	15	9	8	0	3	4	1	3	2	1	4	5	3	4	1	1	1	1	1	1	1	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:11150353A>T	ENST00000538986.1	-	1	121	c.122T>A	c.(121-123)aTc>aAc	p.I41N	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	41					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						AGCTGAGGAGATCTTTTGTCT	0.378																																					p.I41N		.											.	TAS2R20-90	0			c.T122A						.						42	47	45					12																	11150353		2203	4300	6503	SO:0001583	missense	259295	exon1			GAGGAGATCTTTT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19109	protein-coding gene	gene with protein product		613962	"taste receptor, type 2, member 49"	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.122T>A	12.37:g.11150353A>T	ENSP00000441624:p.Ile41Asn	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	100	63	NM_176889	0	0	0	0	0	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.174148	0.38413	.	.	ENSG00000255837	ENST00000538986	T	0.00966	5.49	2.77	2.77	0.32553	.	2.834990	0.02303	U	0.071363	T	0.10252	0.0251	H	0.95437	3.67	0.09310	N	1	D	0.67145	0.996	D	0.75020	0.985	T	0.13469	-1.0508	10	0.87932	D	0	.	8.9683	0.35890	1.0:0.0:0.0:0.0	.	41	P59543	T2R20_HUMAN	N	41	ENSP00000441624:I41N	ENSP00000441624:I41N	I	-	2	0	TAS2R20	11041620	0.002000	0.14202	0.015000	0.15790	0.002000	0.02628	1.473000	0.35387	1.279000	0.44446	0.482000	0.46254	ATC	.		0.378	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889		T	11150353	A	T	11150353	3	4	93	1	0	0	0	0	1	0	0	0	15603	333	12	5	811	5	TAS2R20	12	11150353	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	4503875	11150353	122701542	39	8390											
TBC1D15	64786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	72288466	72288466	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttcttcctactgcatagAaaattaaaaaggacccttat	14	15	4	8	0	1	1	0	0	1	1	2	2	2	2	2	1	2	1	2	1	8	7			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:72288466A>T	ENST00000550746.1	+	8	773	c.709A>T	c.(709-711)Aaa>Taa	p.K237*	TBC1D15_ENST00000319106.8_Splice_Site_p.K228*|TBC1D15_ENST00000393309.3_5'UTR|TBC1D15_ENST00000485960.2_Splice_Site_p.K220*	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	237					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TACTGCATAGAAAATTAAAAA	0.323																																					p.K237X		.											.	TBC1D15-90	0			c.A709T						.						39	42	41					12																	72288466		2199	4297	6496	SO:0001630	splice_region_variant	64786	exon8			GCATAGAAAATTA	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.709-1A>T	12.37:g.72288466A>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	97	51	NM_022771	0	0	0	0	0	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Nonsense_Mutation	SNP	ENST00000550746.1	37	CCDS31858.1	.	.	.	.	.	.	.	.	.	.	A	37	6.212367	0.97380	.	.	ENSG00000121749	ENST00000550746;ENST00000491063;ENST00000319106;ENST00000485960	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.4381	15.2064	0.73183	1.0:0.0:0.0:0.0	.	.	.	.	X	237;121;228;220	.	.	K	+	1	0	TBC1D15	70574733	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.336000	0.96533	1.999000	0.58509	0.473000	0.43528	AAA	.		0.323	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	Nonsense_Mutation	T	72288466	A	T	72288466	5	4	93	1	0	0	0	0	0	0	1	0	15636	260	9	5	863	5	TBC1D15	12	72288466	Splice_Site	SNP	A	TCGA-DW-5561-01A-01D-1589-08	61138113	72288466	61563429	40	8391											
CEP290	80184	broad.mit.edu	37	chr12	88479916	88479916	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttgatttggaaggggcaaaCtagggtcagggattgatcct	10	11	15	5	0	1	2	1	2	0	0	2	4	2	4	1	5	1	2	1	5	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:88479916C>A	ENST00000552810.1	-	34	4680	c.4337G>T	c.(4336-4338)aGt>aTt	p.S1446I	CEP290_ENST00000309041.7_Missense_Mutation_p.S1448I|CEP290_ENST00000547691.2_Missense_Mutation_p.S506I|CEP290_ENST00000397838.3_Missense_Mutation_p.S506I	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1446					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAGGGGCAAACTAGGGTCAGG	0.353																																					p.S1446I													.	CEP290-96	0			c.G4337T						.						125	108	113					12																	88479916		1808	4068	5876	SO:0001583	missense	80184	exon34			GGCAAACTAGGGT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.4337G>T	12.37:g.88479916C>A	ENSP00000448012:p.Ser1446Ile	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	105	4	NM_025114	0	0	20	20	0	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.809451	0.50421	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.68025	0.34;-0.3;-0.3;0.34	5.78	3.84	0.44239	.	0.296892	0.45126	D	0.000399	T	0.60209	0.2251	L	0.46157	1.445	0.32428	N	0.54847	P	0.46987	0.888	P	0.44359	0.447	T	0.68100	-0.5498	10	0.35671	T	0.21	.	10.5449	0.45054	0.0:0.5584:0.3731:0.0684	.	1446	O15078	CE290_HUMAN	I	506;1446;1448;506	ENSP00000446905:S506I;ENSP00000448012:S1446I;ENSP00000308021:S1448I;ENSP00000380938:S506I	ENSP00000308021:S1448I	S	-	2	0	CEP290	87004047	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	0.854000	0.27791	1.436000	0.47453	-0.310000	0.09108	AGT	.		0.353	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88479916	C	A	88479916	3	1	93	1	0	0	0	0	1	0	0	0	3259	565	20	4	3186	4	CEP290	12	88479916	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	16191450	88479916	45371979	41	8392											
GALNT4	8693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	89918277	89918277	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatataggccactgttaaaAacgccagcagcaggcagctc	14	6	10	11	1	0	1	0	0	0	1	1	1	0	1	2	2	4	5	2	2	5	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:89918277A>C	ENST00000529983.2	-	1	306	c.50T>G	c.(49-51)tTt>tGt	p.F17C	POC1B_ENST00000393179.4_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|GALNT4_ENST00000413530.1_Intron|POC1B-GALNT4_ENST00000547474.1_Intron|POC1B-GALNT4_ENST00000548729.1_Intron|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000549504.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	17					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						CACTGTTAAAAACGCCAGCAG	0.617											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F17C		.											.	.	0			c.T50G						.						27	30	29					12																	89918277		1943	4137	6080	SO:0001583	missense	8693	exon1			GTTAAAAACGCCA	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4126	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 4"	603565	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.50T>G	12.37:g.89918277A>C	ENSP00000436604:p.Phe17Cys	Somatic	59	0	1271	WXS	Illumina HiSeq	Phase_I	56	24	NM_003774	0	0	2	4	2	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.054156	0.36277	.	.	ENSG00000257594	ENST00000529983	T	0.54071	0.59	5.68	1.85	0.25348	.	.	.	.	.	T	0.30135	0.0755	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16630	-1.0396	8	.	.	.	.	6.3543	0.21393	0.7004:0.1382:0.1614:0.0	.	17	Q8N4A0	GALT4_HUMAN	C	17	ENSP00000436604:F17C	.	F	-	2	0	GALNT4	88442408	0.499000	0.26083	0.374000	0.26016	0.715000	0.41141	3.427000	0.52785	0.991000	0.38814	0.482000	0.46254	TTT	.		0.617	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		C	89918277	A	C	89918277	3	2	93	1	0	0	0	0	1	0	0	0	6235	14	1	5	1690	5	GALNT4	12	89918277	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	1438361	89918277	43933618	42	8393											
CHPT1	56994	hgsc.bcm.edu	37	chr12	102091671	102091671	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccggggccgggtccgcgcCgcgctggctgagggcgctga	2	4	20	15	8	0	2	0	2	0	0	1	2	1	2	4	5	0	3	4	5	0	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:102091671C>A	ENST00000229266.3	+	1	267	c.32C>A	c.(31-33)cCg>cAg	p.P11Q	CHPT1_ENST00000549872.1_Missense_Mutation_p.P11Q|CHPT1_ENST00000550385.1_Intron	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	11					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						GGGTCCGCGCCGCGCTGGCTG	0.811																																					p.P11Q		.											.	CHPT1-90	0			c.C32A						.						1	1	1					12																	102091671		820	1863	2683	SO:0001583	missense	56994	exon1			CCGCGCCGCGCTG		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"phosphatidylcholine synthesizing enzyme"					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.32C>A	12.37:g.102091671C>A	ENSP00000229266:p.Pro11Gln	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_020244	0	0	0	0	0	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Missense_Mutation	SNP	ENST00000229266.3	37	CCDS9086.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.417497	0.25552	.	.	ENSG00000111666	ENST00000229266;ENST00000549872	T;T	0.44083	0.93;0.93	3.72	0.685	0.18009	.	0.565371	0.14917	N	0.290896	T	0.29458	0.0734	L	0.46157	1.445	0.09310	N	0.999999	B;B	0.17667	0.001;0.023	B;B	0.19148	0.001;0.024	T	0.18147	-1.0346	10	0.27082	T	0.32	0.1068	4.1482	0.10225	0.1608:0.567:0.0:0.2722	.	11;11	F8W1B3;Q8WUD6	.;CHPT1_HUMAN	Q	11	ENSP00000229266:P11Q;ENSP00000448766:P11Q	ENSP00000229266:P11Q	P	+	2	0	CHPT1	100615802	0.995000	0.38212	0.022000	0.16811	0.082000	0.17680	0.224000	0.17738	0.241000	0.21283	-0.532000	0.04303	CCG	.		0.811	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244		A	102091671	C	A	102091671	3	1	93	1	0	0	0	0	1	0	0	0	3376	652	23	4	34	4	CHPT1	12	102091671	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	12173394	102091671	31760224	43	8394											
SLC7A1	6541	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	30091728	30091728	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctatgaggctggttgaaaTgttcacaattagcccagaga	13	10	10	8	0	1	3	1	2	0	1	1	4	1	3	2	2	1	3	2	2	4	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr13:30091728T>C	ENST00000380752.5	-	10	1878	c.1492A>G	c.(1492-1494)Att>Gtt	p.I498V	SLC7A1_ENST00000473577.1_5'UTR	NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	498					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CTGGTTGAAATGTTCACAATT	0.498																																					p.I498V		.											.	SLC7A1-90	0			c.A1492G						.						158	156	156					13																	30091728		2203	4300	6503	SO:0001583	missense	6541	exon10			TTGAAATGTTCAC	AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"Solute carriers"	11057	protein-coding gene	gene with protein product	"ecotropic retroviral receptor", "amino acid transporter, cationic 1"	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.1492A>G	13.37:g.30091728T>C	ENSP00000370128:p.Ile498Val	Somatic	293	0		WXS	Illumina HiSeq	Phase_I	323	93	NM_003045	0	0	0	0	0	Q5JR50	Missense_Mutation	SNP	ENST00000380752.5	37	CCDS9333.1	.	.	.	.	.	.	.	.	.	.	T	2.607	-0.291568	0.05568	.	.	ENSG00000139514	ENST00000380752	D	0.85861	-2.04	5.24	-1.65	0.08291	.	0.538057	0.20369	N	0.093684	T	0.69459	0.3113	N	0.17312	0.475	0.41573	D	0.988693	B	0.02656	0.0	B	0.04013	0.001	T	0.52859	-0.8519	10	0.17369	T	0.5	.	12.2085	0.54365	0.0:0.4844:0.0:0.5156	.	498	P30825	CTR1_HUMAN	V	498	ENSP00000370128:I498V	ENSP00000370128:I498V	I	-	1	0	SLC7A1	28989728	0.018000	0.18449	0.984000	0.44739	0.561000	0.35649	-0.909000	0.04058	-0.145000	0.11294	-0.264000	0.10439	ATT	.		0.498	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		C	30091728	T	C	30091728	3	2	93	1	0	0	0	0	1	0	0	0	14724	1464	51	3	413	3	SLC7A1	13	30091728	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		30091728	85078150	44	8395											
EFNB2	1948	broad.mit.edu;bcgsc.ca	37	chr13	107148096	107148096	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagcagatggtctttacCttgtccaactttcatgagga	11	12	9	9	0	2	2	1	1	1	1	3	3	3	3	2	2	4	2	2	2	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr13:107148096C>T	ENST00000245323.4	-	3	648	c.499G>A	c.(499-501)Gat>Aat	p.D167N		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	167					anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TGGTCTTTACCTTGTCCAACT	0.512																																					p.D167N													.	EFNB2-91	0			c.G499A						.						343	298	313					13																	107148096		2203	4300	6503	SO:0001630	splice_region_variant	1948	exon3			CTTTACCTTGTCC	L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266		"Ephrins"	3227	protein-coding gene	gene with protein product	"HTK ligand", "ligand of eph-related kinase 5", "eph-related receptor tyrosine kinase ligand 5"	600527		EPLG5		7833926	Standard	NM_004093		Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.499+1G>A	13.37:g.107148096C>T		Somatic	383	0		WXS	Illumina HiSeq	Phase_I	533	11	NM_004093	0	0	0	0	0	Q5JV56	Missense_Mutation	SNP	ENST00000245323.4	37	CCDS9507.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.400770	0.42613	.	.	ENSG00000125266	ENST00000245323	D	0.90900	-2.75	5.49	5.49	0.81192	Cupredoxin (1);	0.274101	0.46758	D	0.000280	T	0.81758	0.4890	N	0.08118	0	0.53688	D	0.999974	B	0.02656	0.0	B	0.01281	0.0	T	0.75912	-0.3150	9	.	.	.	.	19.4094	0.94662	0.0:1.0:0.0:0.0	.	167	P52799	EFNB2_HUMAN	N	167	ENSP00000245323:D167N	.	D	-	1	0	EFNB2	105946097	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.646000	0.67916	2.583000	0.87209	0.561000	0.74099	GAT	.		0.512	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045733.4	NM_004093	Missense_Mutation	T	107148096	C	T	107148096	5	4	93	1	0	0	0	0	0	0	1	0	4967	695	24	2	514	2	EFNB2	13	107148096	Splice_Site	SNP	C	TCGA-DW-5561-01A-01D-1589-08	77056368	107148096	8021782	45	8396											
GJD2	57369	broad.mit.edu	37	chr15	35044907	35044907	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagacagtcttctcagttggCcgggacacataacattccac	12	9	8	12	1	2	1	1	0	2	1	4	2	3	2	2	2	1	1	2	2	2	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr15:35044907C>T	ENST00000290374.4	-	2	1214	c.738G>A	c.(736-738)cgG>cgA	p.R246R	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	246					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TCTCAGTTGGCCGGGACACAT	0.493																																					p.R246R													.	GJD2-90	0			c.G738A						.						136	107	117					15																	35044907		2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			AGTTGGCCGGGAC	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"Ion channels / Gap junction proteins (connexins)"	19154	protein-coding gene	gene with protein product	"connexin 36"	607058	"gap junction protein, alpha 9, 36kDa"	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.738G>A	15.37:g.35044907C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	54	4	NM_020660	0	0	0	0	0	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	37	CCDS10040.1																																																																																			.		0.493	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			T	35044907	C	T	35044907	2	4	93	1	0	0	0	0	0	0	0	1	6437	726	26	2		2	GJD2	15	35044907	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08		35044907	67486485	46	8397											
TRIP4	9325	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64702017	64702017	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaaaattcactagcagagTatcatagcaggtaagtgagc	17	8	10	6	0	2	3	2	1	0	2	2	3	2	3	0	1	3	4	0	1	7	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr15:64702017T>C	ENST00000261884.3	+	7	1093	c.1033T>C	c.(1033-1035)Tat>Cat	p.Y345H		NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	345					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						ACTAGCAGAGTATCATAGCAG	0.428																																					p.Y345H		.											.	TRIP4-188	0			c.T1033C						.						77	77	77					15																	64702017		2203	4300	6503	SO:0001583	missense	9325	exon7			GCAGAGTATCATA	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.1033T>C	15.37:g.64702017T>C	ENSP00000261884:p.Tyr345His	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	75	25	NM_016213	0	0	0	0	0	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	37	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.668883	0.67814	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.74805	-0.3540	9	0.17369	T	0.5	-24.5764	16.1616	0.81721	0.0:0.0:0.0:1.0	.	345	Q15650	TRIP4_HUMAN	H	345	.	ENSP00000261884:Y345H	Y	+	1	0	TRIP4	62489070	1.000000	0.71417	0.980000	0.43619	0.327000	0.28475	7.628000	0.83189	2.221000	0.72209	0.454000	0.30748	TAT	.		0.428	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		C	64702017	T	C	64702017	3	2	93	1	0	0	0	0	1	0	0	0	16591	1638	57	3	1059	3	TRIP4	15	64702017	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08	29657110	64702017	37829375	47	8398											
ADCY9	115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4165346	4165346	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaggacagctgcttggggTtgatcttgacgcgcacgctg	6	10	16	9	3	1	2	0	2	1	0	1	4	1	4	0	4	2	5	0	4	0	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr16:4165346T>G	ENST00000294016.3	-	2	636	c.98A>C	c.(97-99)aAc>aCc	p.N33T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	33					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CTGCTTGGGGTTGATCTTGAC	0.637																																					p.N33T		.											.	ADCY9-139	0			c.A98C						.						91	66	75					16																	4165346		2197	4300	6497	SO:0001583	missense	115	exon2			TTGGGGTTGATCT	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.98A>C	16.37:g.4165346T>G	ENSP00000294016:p.Asn33Thr	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_001116	0	0	1	1	0	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	T	7.635	0.679628	0.14907	.	.	ENSG00000162104	ENST00000294016	T	0.27402	1.67	4.98	3.87	0.44632	.	0.478928	0.24490	N	0.038068	T	0.23094	0.0558	L	0.34521	1.04	0.37612	D	0.920957	B	0.23442	0.085	B	0.16289	0.015	T	0.07501	-1.0769	10	0.49607	T	0.09	.	11.1518	0.48464	0.0:0.0:0.1549:0.8451	.	33	O60503	ADCY9_HUMAN	T	33	ENSP00000294016:N33T	ENSP00000294016:N33T	N	-	2	0	ADCY9	4105347	1.000000	0.71417	0.997000	0.53966	0.064000	0.16182	4.786000	0.62425	0.728000	0.32382	-0.477000	0.04895	AAC	.		0.637	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			G	4165346	T	G	4165346	3	3	93	1	0	0	0	0	1	0	0	0	301	1725	60	5	4003	5	ADCY9	16	4165346	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		4165346	86189407	48	8399											
SUPT6H	6830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27002076	27002076	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaacatgaaaaagaagctaTtgcggaagaaatcttccagg	17	7	11	6	1	1	3	0	1	1	2	2	5	2	5	1	3	3	1	1	3	7	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr17:27002076T>C	ENST00000314616.6	+	5	717	c.434T>C	c.(433-435)aTt>aCt	p.I145T	SUPT6H_ENST00000347486.4_Missense_Mutation_p.I145T|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	145	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AAAGAAGCTATTGCGGAAGAA	0.527																																					p.I145T		.											.	SUPT6H-93	0			c.T434C						.						86	80	82					17																	27002076		2203	4300	6503	SO:0001583	missense	6830	exon5			AAGCTATTGCGGA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.434T>C	17.37:g.27002076T>C	ENSP00000319104:p.Ile145Thr	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	82	25	NM_003170	0	0	14	19	5	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.186987	0.57909	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.75889	0.3911	M	0.79693	2.465	0.80722	D	1	P	0.50156	0.932	P	0.58520	0.84	T	0.73655	-0.3914	9	0.17832	T	0.49	-10.4269	15.9812	0.80111	0.0:0.0:0.0:1.0	.	145	Q7KZ85	SPT6H_HUMAN	T	145	.	ENSP00000319104:I145T	I	+	2	0	SUPT6H	24026203	1.000000	0.71417	0.995000	0.50966	0.833000	0.47200	7.328000	0.79160	2.178000	0.69098	0.533000	0.62120	ATT	.		0.527	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		C	27002076	T	C	27002076	3	2	93	1	0	0	0	0	1	0	0	0	15432	1493	52	3	448	3	SUPT6H	17	27002076	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		27002076	54193134	49	8400											
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197360	39197360	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catagccaatgccaccaccaAtgccacagccagttccgcag	12	5	7	17	1	0	0	0	0	0	0	1	0	1	0	7	0	4	2	7	0	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr17:39197360A>G	ENST00000306271.4	-	1	353	c.290T>C	c.(289-291)aTt>aCt	p.I97T		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	97			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCCACCACCAATGCCACAGCC	0.622																																					p.I97T		.											.	.	0			c.T290C						.						32	36	34					17																	39197360		1993	4165	6158	SO:0001583	missense	81851	exon1			CCACCAATGCCAC	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"Keratin associated proteins"	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.290T>C	17.37:g.39197360A>G	ENSP00000305975:p.Ile97Thr	Somatic	54	1		WXS	Illumina HiSeq	Phase_I	83	6	NM_030967	0	0	0	0	0	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	A	9.469	1.095023	0.20471	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.38077	1.16	2.38	0.11	0.14611	.	.	.	.	.	T	0.27241	0.0668	L	0.59912	1.85	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.33954	-0.9848	9	0.13108	T	0.6	.	4.4001	0.11383	0.6661:0.0:0.3339:0.0	.	97	Q07627	KRA11_HUMAN	T	97;87	ENSP00000305975:I97T	ENSP00000305975:I97T	I	-	2	0	KRTAP1-1	36450886	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-1.377000	0.02558	-0.016000	0.14127	0.378000	0.23410	ATT	.		0.622	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		G	39197360	A	G	39197360	3	3	93	1	0	0	0	0	1	0	0	0	8523	101	4	3	247	3	KRTAP1-1	17	39197360	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	12195284	39197360	41997850	50	8401											
FSCN2	25794	hgsc.bcm.edu	37	chr17	79495866	79495866	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gatgggcgctgggtgctgcgGtccgagccgcacggccgctt	3	7	18	13	6	0	0	0	0	0	0	1	2	1	0	3	4	3	4	3	4	0	1	rs34126129	byFrequency	TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr17:79495866G>A	ENST00000417245.2	+	1	445	c.309G>A	c.(307-309)cgG>cgA	p.R103R	FSCN2_ENST00000334850.7_Silent_p.R103R|RP13-766D20.2_ENST00000430912.1_RNA|RP13-766D20.2_ENST00000442532.1_RNA	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	103					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GGGTGCTGCGGTCCGAGCCGC	0.716													G|||	35	0.00698882	0.0257	0.0014	5008	,	,		14408	0		0	False		,,,				2504	0				p.R103R		.											.	.	0			c.G309A						.	G	,	88,3916		1,86,1915	4	5	4		309,309	3.3	1	17	dbSNP_126	4	0,8012		0,0,4006	no	coding-synonymous,coding-synonymous	FSCN2	NM_001077182.2,NM_012418.3	,	1,86,5921	AA,AG,GG		0.0,2.1978,0.7324	,	103/517,103/493	79495866	88,11928	2002	4006	6008	SO:0001819	synonymous_variant	25794	exon1			GCTGCGGTCCGAG	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"Fascins"	3960	protein-coding gene	gene with protein product		607643	"fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)", "fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.309G>A	17.37:g.79495866G>A		Somatic	6	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_001077182	0	0	0	0	0	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	37	CCDS45811.1																																																																																			G|0.995;A|0.005		0.716	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		A	79495866	G	A	79495866	2	1	93	1	0	0	0	0	0	0	0	1	6087	1248	44	2		2	FSCN2	17	79495866	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08	40298506	79495866	1699344	51	8402											
SF3A2	8175	hgsc.bcm.edu	37	chr19	2248401	2248401	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcccggggtccatccgtcGgctcctggggtccaccctca	3	8	11	19	3	1	0	1	0	0	0	7	0	6	0	7	5	0	1	7	5	0	0	rs375562170	byFrequency	TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:2248401G>A	ENST00000221494.5	+	9	1669	c.1251G>A	c.(1249-1251)tcG>tcA	p.S417S	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	417	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCATCCGTCGGCTCCTGGGG	0.711													G|||	6	0.00119808	0.0045	0	5008	,	,		7987	0		0	False		,,,				2504	0				p.S417S		.											.	SF3A2-90	0			c.G1251A						.	G		29,3801		0,29,1886	5	6	6		1251	-3.8	0.1	19		6	0,8044		0,0,4022	no	coding-synonymous	SF3A2	NM_007165.4		0,29,5908	AA,AG,GG		0.0,0.7572,0.2442		417/465	2248401	29,11845	1915	4022	5937	SO:0001819	synonymous_variant	8175	exon9			TCCGTCGGCTCCT	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"splicing factor 3a, subunit 2, 66kD"			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1251G>A	19.37:g.2248401G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_007165	0	0	121	255	134	B2RBU1|D6W605|O75245	Silent	SNP	ENST00000221494.5	37	CCDS12084.1																																																																																			.		0.711	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3			A	2248401	G	A	2248401	2	1	93	1	0	0	0	0	0	0	0	1	14179	1103	39	1		1	SF3A2	19	2248401	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		2248401	56880582	52	8403											
NDUFB7	4713	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	14677078	14677078	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttcatgcgcatcacatagCtgggggaaaagcacgagagg	12	6	13	10	2	2	1	2	0	0	1	2	3	2	2	1	3	3	3	1	3	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:14677078C>A	ENST00000215565.2	-	3	343		c.e3-1			NM_004146.5	NP_004137.2	P17568	NDUB7_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CATCACATAGCTGGGGGAAAA	0.667																																					.		.											.	NDUFB7-91	0			c.282-1G>T						.						38	42	40					19																	14677078		2202	4300	6502	SO:0001630	splice_region_variant	4713	exon4			ACATAGCTGGGGG		CCDS12314.1	19p13.12	2011-07-04	2002-08-29		ENSG00000099795	ENSG00000099795		"Mitochondrial respiratory chain complex / Complex I"	7702	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase B18 subunit", "complex I B18 subunit"	603842	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 (18kD, B18)"			9763677, 10830904	Standard	NM_004146		Approved	B18, CI-B18, MGC2480	uc002mzg.3	P17568		ENST00000215565.2:c.282-1G>T	19.37:g.14677078C>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	78	35	NM_004146	0	0	2	4	2	Q6ICN9|Q9UI16	Splice_Site	SNP	ENST00000215565.2	37	CCDS12314.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.190561	0.58017	.	.	ENSG00000099795	ENST00000215565	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4537	0.84003	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NDUFB7	14538078	1.000000	0.71417	0.999000	0.59377	0.454000	0.32378	7.184000	0.77705	2.493000	0.84123	0.460000	0.39030	.	.		0.667	NDUFB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466025.1	NM_004146	Intron	A	14677078	C	A	14677078	5	1	93	1	0	0	0	0	0	0	1	0	10312	811	28	4	136	4	NDUFB7	19	14677078	Splice_Site	SNP	C	TCGA-DW-5561-01A-01D-1589-08	12428677	14677078	44451905	53	8404											
KIAA0892	23383	broad.mit.edu	37	chr19	19452209	19452209	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggtcacccactatctggatgCcgggcaggtgtgtggcgcct	5	9	15	12	2	2	0	1	0	1	0	2	1	2	1	3	5	1	1	3	5	1	1			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:19452209C>T	ENST00000392313.6	+	7	907	c.728C>T	c.(727-729)gCc>gTc	p.A243V	MAU2_ENST00000262815.8_Missense_Mutation_p.A243V	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	243					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						TATCTGGATGCCGGGCAGGTG	0.622																																					p.A243V													.	MAU2-91	0			c.C728T						.						45	50	49					19																	19452209		2176	4270	6446	SO:0001583	missense	23383	exon7			TGGATGCCGGGCA	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.728C>T	19.37:g.19452209C>T	ENSP00000376127:p.Ala243Val	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_015329	0	0	0	0	0	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Missense_Mutation	SNP	ENST00000392313.6	37	CCDS32969.2	.	.	.	.	.	.	.	.	.	.	C	10.93	1.491074	0.26774	.	.	ENSG00000129933	ENST00000392313;ENST00000262815	.	.	.	4.95	4.95	0.65309	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.44891	0.1315	N	0.16903	0.455	0.80722	D	1	B	0.26935	0.164	B	0.30943	0.122	T	0.34850	-0.9812	9	0.28530	T	0.3	.	17.1001	0.86647	0.0:1.0:0.0:0.0	.	243	Q9Y6X3	SCC4_HUMAN	V	243	.	ENSP00000262815:A243V	A	+	2	0	MAU2	19313209	1.000000	0.71417	0.873000	0.34254	0.499000	0.33736	7.610000	0.82949	2.462000	0.83206	0.561000	0.74099	GCC	.		0.622	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		T	19452209	C	T	19452209	3	4	93	1	0	0	0	0	1	0	0	0	8217	739	26	2	754	2	KIAA0892	19	19452209	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	4775131	19452209	39676774	54	8405											
ZNF681	148213	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	23927477	23927484	+	Frame_Shift_Del	DEL	TTAAAGGC	TTAAAGGC	-																															tagtaagggttaaggactgaTtaaaggctttgtcacattct																										TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	TTAAAGGC	TTAAAGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:23927477_23927484delTTAAAGGC	ENST00000402377.3	-	4	1009_1016	c.868_875delGCCTTTAA	c.(868-876)gcctttaatfs	p.AFN290fs	ZNF681_ENST00000395385.3_Frame_Shift_Del_p.AFN221fs	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	290					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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TAAGGACTGATTAAAGGCTTTGTCACAT	0.375																																					p.290_292del		.											.	.	0			c.868_875del						.																																			SO:0001589	frameshift_variant	148213	exon4			.	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"Zinc fingers, C2H2-type", "-"	26457	protein-coding gene	gene with protein product	"hypothetical protein FLJ31526"						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.868_875delGCCTTTAA	19.37:g.23927477_23927484delTTAAAGGC	ENSP00000384000:p.Ala290fs	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	108	28	NM_138286	0	0	0	0	0	B3KVF7	Frame_Shift_Del	DEL	ENST00000402377.3	37	CCDS12414.2																																																																																			.		0.375	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		-	23927484	TTAAAGGC	-	23927477	7	5	93	1	0	1	0	1	0	0	0	0	18120	1493	52	0	1066	0	ZNF681	19	23927477	Frame_Shift_Del	DEL	TTAAAGGC	TCGA-DW-5561-01A-01D-1589-08	4475268	23927477	35201506	55	8406											
LGI4	163175	broad.mit.edu	37	chr19	35622732	35622732	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcctcggaacaggaatctgGggagggtctccagatggtta	9	8	16	8	1	2	1	0	0	2	1	4	4	2	4	2	7	1	1	2	7	3	1			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:35622732G>A	ENST00000310123.3	-	5	938	c.419C>T	c.(418-420)cCc>cTc	p.P140L	LGI4_ENST00000392225.3_Missense_Mutation_p.P140L|LGI4_ENST00000591633.1_Missense_Mutation_p.P140L|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	140					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CAGGAATCTGGGGAGGGTCTC	0.607																																					p.P140L													.	LGI4-91	0			c.C419T						.						47	47	47					19																	35622732		2202	4299	6501	SO:0001583	missense	163175	exon5			AATCTGGGGAGGG	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.419C>T	19.37:g.35622732G>A	ENSP00000312273:p.Pro140Leu	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_139284	0	0	1	1	0	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	37	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628997	0.67015	.	.	ENSG00000153902	ENST00000310123;ENST00000392225;ENST00000437421	T;T	0.59364	0.27;0.27	3.8	3.8	0.43715	.	0.000000	0.56097	D	0.000021	T	0.77638	0.4160	M	0.86420	2.815	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.82242	-0.0554	10	0.72032	D	0.01	.	13.2203	0.59883	0.0:0.0:1.0:0.0	.	140;140	Q8N135-2;Q8N135	.;LGI4_HUMAN	L	140	ENSP00000312273:P140L;ENSP00000376059:P140L	ENSP00000312273:P140L	P	-	2	0	LGI4	40314572	1.000000	0.71417	0.994000	0.49952	0.517000	0.34286	8.538000	0.90634	1.686000	0.51046	0.298000	0.19748	CCC	.		0.607	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			A	35622732	G	A	35622732	3	1	93	1	0	0	0	0	1	0	0	0	8776	1232	43	2	1214	2	LGI4	19	35622732	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	11695255	35622732	23506251	56	8407											
SFRS6	6431	hgsc.bcm.edu;broad.mit.edu	37	chr20	42087023	42087023	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acggcttcgtggagttcgagGactcccgcgacgccgacgac	7	6	14	14	8	0	0	0	0	0	0	3	6	1	2	2	3	0	2	2	3	0	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr20:42087023G>A	ENST00000244020.3	+	2	236	c.130G>A	c.(130-132)Gac>Aac	p.D44N		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	44	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.D44N(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						GGAGTTCGAGGACTCCCGCGA	0.716																																					p.D44N		.											.	SRSF6-289	1	Substitution - Missense(1)	lung(1)	c.G130A						.						8	7	8					20																	42087023		2096	4170	6266	SO:0001583	missense	6431	exon2			TTCGAGGACTCCC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.130G>A	20.37:g.42087023G>A	ENSP00000244020:p.Asp44Asn	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_006275	0	0	24	69	45	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	37	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	g	26.3	4.719681	0.89205	.	.	ENSG00000124193	ENST00000244020	T	0.75050	-0.9	3.59	3.59	0.41128	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.054648	0.64402	D	0.000001	T	0.79581	0.4470	L	0.43598	1.365	0.80722	D	1	D;D	0.65815	0.995;0.986	D;P	0.63597	0.916;0.838	T	0.82418	-0.0467	10	0.87932	D	0	.	14.2003	0.65699	0.0:0.0:1.0:0.0	.	44;44	Q13247;A8K588	SRSF6_HUMAN;.	N	44	ENSP00000244020:D44N	ENSP00000244020:D44N	D	+	1	0	SRSF6	41520437	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	8.758000	0.91663	1.838000	0.53458	0.552000	0.68991	GAC	.		0.716	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		A	42087023	G	A	42087023	3	1	93	1	0	0	0	0	1	0	0	0	14213	1174	41	2	136	2	SFRS6	20	42087023	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08		42087023	20938497	57	8408											
SEC14L4	284904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30891293	30891293	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagctcacagactttgatgCgcttccggatcatatcctgc	8	11	9	13	2	2	2	2	1	0	1	4	3	4	3	2	1	3	3	2	1	1	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr22:30891293C>T	ENST00000255858.7	-	5	454	c.371G>A	c.(370-372)cGc>cAc	p.R124H	SEC14L4_ENST00000381982.3_Missense_Mutation_p.R124H|SEC14L4_ENST00000392772.2_Missense_Mutation_p.R70H|SEC14L4_ENST00000540456.1_Missense_Mutation_p.R109H|RP4-539M6.14_ENST00000610156.1_RNA|RP4-539M6.14_ENST00000442126.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	124	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> G (in dbSNP:rs9606739).			integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	GACTTTGATGCGCTTCCGGAT	0.572																																					p.R124H		.											.	SEC14L4-91	0			c.G371A						.						72	62	65					22																	30891293		2203	4300	6503	SO:0001583	missense	284904	exon5			TTGATGCGCTTCC	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.371G>A	22.37:g.30891293C>T	ENSP00000255858:p.Arg124His	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	40	17	NM_001161368	0	0	0	0	0	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	.	.	.	.	.	.	.	.	.	.	c	18.44	3.623875	0.66901	.	.	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96	4.9	2.77	0.32553	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.077270	0.52532	D	0.000077	T	0.65954	0.2741	N	0.16790	0.44	0.80722	D	1	D;D;D	0.65815	0.991;0.995;0.985	P;P;P	0.61397	0.871;0.888;0.75	T	0.60796	-0.7192	10	0.14252	T	0.57	-11.5328	5.6156	0.17430	0.0:0.6061:0.0:0.3939	.	70;109;124	B3KSF0;G3V1L4;Q9UDX3	.;.;S14L4_HUMAN	H	124;109;70;124	ENSP00000255858:R124H;ENSP00000440848:R109H;ENSP00000376525:R70H;ENSP00000371412:R124H	ENSP00000255858:R124H	R	-	2	0	SEC14L4	29221293	0.996000	0.38824	0.131000	0.22000	0.495000	0.33615	2.090000	0.41682	1.169000	0.42739	0.655000	0.94253	CGC	.		0.572	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977		T	30891293	C	T	30891293	3	4	93	1	0	0	0	0	1	0	0	0	14016	768	27	1	887	1	SEC14L4	22	30891293	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08		30891293	20413273	58	8409											
YWHAH	7533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	32352660	32352660	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgatgatgccatagctgagCtggacacactaaacgaggat	13	8	11	9	2	0	2	0	2	0	0	1	6	0	4	1	2	4	2	1	2	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr22:32352660C>T	ENST00000248975.5	+	2	895	c.622C>T	c.(622-624)Ctg>Ttg	p.L208L	YWHAH_ENST00000397492.1_3'UTR|YWHAH_ENST00000471374.1_3'UTR	NM_003405.3	NP_003396.1	Q04917	1433F_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta	208					apoptotic process (GO:0006915)|glucocorticoid catabolic process (GO:0006713)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular protein transport (GO:0006886)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane depolarization during action potential (GO:0086010)|membrane organization (GO:0061024)|negative regulation of dendrite morphogenesis (GO:0050774)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of sodium ion transport (GO:0002028)|regulation of synaptic plasticity (GO:0048167)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|glucocorticoid receptor binding (GO:0035259)|insulin-like growth factor receptor binding (GO:0005159)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|large_intestine(1)|upper_aerodigestive_tract(1)	4						CATAGCTGAGCTGGACACACT	0.527																																					p.L208L	Ovarian(98;460 2060 9263 44007)	.											.	YWHAH-1082	0			c.C622T						.						72	55	61					22																	32352660		2203	4300	6503	SO:0001819	synonymous_variant	7533	exon2			GCTGAGCTGGACA	X78138	CCDS13901.1	22q12.1-q13.1	2013-12-03	2013-12-03		ENSG00000128245	ENSG00000128245			12853	protein-coding gene	gene with protein product	"14-3-3 eta"	113508	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide"	YWHA1			Standard	NM_003405		Approved		uc003alz.3	Q04917	OTTHUMG00000030833	ENST00000248975.5:c.622C>T	22.37:g.32352660C>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	34	18	NM_003405	0	0	112	198	86		Silent	SNP	ENST00000248975.5	37	CCDS13901.1																																																																																			.		0.527	YWHAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075721.2	NM_003405		T	32352660	C	T	32352660	2	4	93	1	0	0	0	0	0	0	0	1	17537	796	28	2		2	YWHAH	22	32352660	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	1461367	32352660	18951906	59	8410											
WNK3	65267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	54319393	54319393	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaactgtcggtccaaggacAtgtacaggtaaaacagtgga	15	7	11	8	1	0	0	0	0	0	0	2	2	1	2	1	4	3	2	1	4	5	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chrX:54319393A>T	ENST00000375159.2	-	9	1964	c.1965T>A	c.(1963-1965)caT>caA	p.H655Q	WNK3_ENST00000354646.2_Missense_Mutation_p.H655Q|WNK3_ENST00000375169.3_Missense_Mutation_p.H655Q			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	655					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						GTCCAAGGACATGTACAGGTA	0.418																																					p.H655Q		.											.	WNK3-441	0			c.T1965A						.						100	87	92					X																	54319393		2203	4300	6503	SO:0001583	missense	65267	exon10			AAGGACATGTACA	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"protein kinase, lysine deficient 3"	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1965T>A	X.37:g.54319393A>T	ENSP00000364301:p.His655Gln	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	28	21	NM_001002838	0	0	0	0	0	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	1.564	-0.535847	0.04082	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.42131	0.98;0.98;0.98	5.21	2.73	0.32206	.	0.631512	0.14072	N	0.343324	T	0.23054	0.0557	N	0.19112	0.55	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.10450	0.003;0.005	T	0.22312	-1.0220	10	0.22109	T	0.4	-0.9144	4.0626	0.09846	0.7167:0.0:0.1006:0.1826	.	655;655	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	Q	655	ENSP00000364312:H655Q;ENSP00000346667:H655Q;ENSP00000364301:H655Q	ENSP00000346667:H655Q	H	-	3	2	WNK3	54336118	0.769000	0.28531	0.170000	0.22879	0.756000	0.42949	1.264000	0.33015	0.220000	0.20860	0.451000	0.29950	CAT	.		0.418	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54319393	A	T	54319393	3	4	93	1	0	0	0	0	1	0	0	0	17412	214	8	5	3497	5	WNK3	23	54319393	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08		54319393	100951167	60	8411											
FUCA1	2517	hgsc.bcm.edu	37	chr1	24194770	24194770	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccgcgacctcatccccggagCccgcatcgctacccctcagc	6	5	8	22	5	2	0	2	0	0	0	4	2	3	1	7	1	3	2	7	1	1	1	rs61996282	byFrequency	TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:24194770C>G	ENST00000374479.3	-	1	14	c.7G>C	c.(7-9)Gct>Cct	p.A3P		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	3					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		ATCCCCGGAGCCCGCATCGCT	0.721													C|||	67	0.0133786	8e-04	0.0562	5008	,	,		13629	0		0.0109	False		,,,				2504	0.0164				p.A3P		.											.	FUCA1-153	0			c.G7C						.	C	PRO/ALA	4,3362		0,4,1679	2	5	4		7	-3.6	0	1	dbSNP_129	4	18,7074		0,18,3528	no	missense	FUCA1	NM_000147.4	27	0,22,5207	GG,GC,CC		0.2538,0.1188,0.2104	possibly-damaging	3/467	24194770	22,10436	1683	3546	5229	SO:0001583	missense	2517	exon1			CCGGAGCCCGCAT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.7G>C	1.37:g.24194770C>G	ENSP00000363603:p.Ala3Pro	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	11	7	NM_000147	0	0	0	0	0	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Missense_Mutation	SNP	ENST00000374479.3	37	CCDS244.2	18	0.008241758241758242	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	6	0.0079155672823219	C	19.36	3.813328	0.70912	0.001188	0.002538	ENSG00000179163	ENST00000374479	T	0.53206	0.63	4.9	-3.58	0.04597	.	4.458410	0.00604	N	0.000389	T	0.08223	0.0205	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.06058	-1.0848	10	0.33940	T	0.23	-20.1632	0.5779	0.00707	0.2648:0.318:0.1932:0.2239	rs61996282	3	P04066	FUCO_HUMAN	P	3	ENSP00000363603:A3P	ENSP00000363603:A3P	A	-	1	0	FUCA1	24067357	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.499000	0.00968	-0.267000	0.09325	0.561000	0.74099	GCT	C|0.960;G|0.040		0.721	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		G	24194770	C	G	24194770	3	3	94	1	0	0	0	0	1	0	0	0	6113	739	26	4	1425	4	FUCA1	1	24194770	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		24194770	225055851	1	8412											
MYOM3	127294	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24421403	24421403	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccgaaaacaagcatgacaGggagaagggttccttctcac	13	8	10	10	1	1	2	1	1	1	1	4	4	3	2	2	2	2	2	2	2	4	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:24421403G>T	ENST00000374434.3	-	9	1030	c.868C>A	c.(868-870)Ctg>Atg	p.L290M	MYOM3_ENST00000329601.7_Missense_Mutation_p.L290M|MYOM3_ENST00000475306.1_5'UTR|MYOM3_ENST00000330966.7_Missense_Mutation_p.L291M	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	290	Ig-like C2-type 2.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		AAGCATGACAGGGAGAAGGGT	0.562																																					p.L290M													.	MYOM3-93	0			c.C868A						.						56	58	57					1																	24421403		1947	4154	6101	SO:0001583	missense	127294	exon9			ATGACAGGGAGAA	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	26679	protein-coding gene	gene with protein product			"myomesin family, member 3"			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.868C>A	1.37:g.24421403G>T	ENSP00000363557:p.Leu290Met	Somatic	52	2		WXS	Illumina HiSeq	Phase_I	51	17	NM_152372	0	0	6	11	5	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860822	0.51482	.	.	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.74842	-0.88;-0.88;-0.88	5.18	2.92	0.33932	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.070081	0.64402	D	0.000019	T	0.82130	0.4970	L	0.59912	1.85	0.31628	N	0.649366	D;D	0.76494	0.997;0.999	D;D	0.72075	0.976;0.942	D	0.83770	0.0219	10	0.87932	D	0	.	12.8254	0.57716	0.1763:0.0:0.8237:0.0	.	290;290	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	M	290;291;290	ENSP00000363557:L290M;ENSP00000332670:L291M;ENSP00000328415:L290M	ENSP00000328415:L290M	L	-	1	2	MYOM3	24293990	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	2.902000	0.48703	0.582000	0.29556	-1.151000	0.01829	CTG	.		0.562	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		T	24421403	G	T	24421403	3	4	94	1	0	0	0	0	1	0	0	0	10118	991	35	4	3561	4	MYOM3	1	24421403	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	226633	24421403	224829218	2	8413											
ARID1A	8289	broad.mit.edu;bcgsc.ca	37	chr1	27087947	27087947	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccttccatgaaccaatcaaGcattgcccaagatcgaggtg	12	9	8	12	1	1	2	1	1	0	1	4	3	3	2	4	1	3	1	4	1	4	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:27087947G>A	ENST00000324856.7	+	6	2605	c.2234G>A	c.(2233-2235)aGc>aAc	p.S745N	ARID1A_ENST00000374152.2_Missense_Mutation_p.S362N|ARID1A_ENST00000457599.2_Missense_Mutation_p.S745N|RN7SL501P_ENST00000578818.1_RNA	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	745					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		AACCAATCAAGCATTGCCCAA	0.547			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S745N				Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.G2234A						.						98	87	90					1																	27087947		2203	4300	6503	SO:0001583	missense	8289	exon6			AATCAAGCATTGC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.2234G>A	1.37:g.27087947G>A	ENSP00000320485:p.Ser745Asn	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	108	8	NM_006015	0	0	4	4	0	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054299	0.75960	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.22134	1.97;1.97;4.19	5.85	4.89	0.63831	.	0.218756	0.51477	D	0.000090	T	0.18425	0.0442	L	0.40543	1.245	0.80722	D	1	P;P;P	0.37276	0.454;0.589;0.454	B;B;B	0.33454	0.079;0.164;0.105	T	0.02275	-1.1184	10	0.40728	T	0.16	-14.2837	15.7952	0.78404	0.0:0.2399:0.7601:0.0	.	745;745;399	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	N	745;745;362	ENSP00000320485:S745N;ENSP00000387636:S745N;ENSP00000363267:S362N	ENSP00000320485:S745N	S	+	2	0	ARID1A	26960534	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.042000	0.49815	2.768000	0.95171	0.655000	0.94253	AGC	.		0.547	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27087947	G	A	27087947	3	1	94	1	0	0	0	0	1	0	0	0	913	971	34	2	2256	2	ARID1A	1	27087947	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	2666544	27087947	222162674	3	8414											
PEF1	553115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	32100955	32100955	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcccaggattggggtgtcCatagggccctccaccagctg	7	8	12	14	0	0	0	0	0	0	0	3	1	3	1	5	4	1	1	5	4	1	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:32100955C>A	ENST00000373703.4	-	2	215	c.193G>T	c.(193-195)Gga>Tga	p.G65*	PEF1_ENST00000492061.1_5'UTR|PEF1_ENST00000440872.2_Nonsense_Mutation_p.G65*	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	65	9 X 9 AA approximate tandem repeat of [AP]-P-G-G-P-Y-G-G-P-P.				proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		TTGGGGTGTCCATAGGGCCCT	0.627																																					p.G65X		.											.	PEF1-68	0			c.G193T						.						23	25	25					1																	32100955		2203	4299	6502	SO:0001587	stop_gained	553115	exon2			GGTGTCCATAGGG		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"EF-hand domain containing"	30009	protein-coding gene	gene with protein product	"peflin"	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.193G>T	1.37:g.32100955C>A	ENSP00000362807:p.Gly65*	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_012392	0	0	12	12	0		Nonsense_Mutation	SNP	ENST00000373703.4	37	CCDS345.1	.	.	.	.	.	.	.	.	.	.	C	34	5.384325	0.95967	.	.	ENSG00000162517	ENST00000373703;ENST00000440872	.	.	.	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	17.2908	0.87156	0.0:1.0:0.0:0.0	.	.	.	.	X	65	.	ENSP00000362807:G65X	G	-	1	0	PEF1	31873542	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	6.128000	0.71650	2.541000	0.85698	0.561000	0.74099	GGA	.		0.627	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392		A	32100955	C	A	32100955	4	1	94	1	0	0	0	0	0	1	0	0	11744	603	21	4	677	4	PEF1	1	32100955	Nonsense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	5013008	32100955	217149666	4	8415											
WDR65	149465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	43649478	43649478	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aatctggagatcagcgttggGagaccagcataatggtcaag	13	8	13	7	1	3	2	2	0	1	2	3	4	3	2	1	3	2	2	1	3	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:43649478G>C	ENST00000372492.4	+	4	1015	c.691G>C	c.(691-693)Gag>Cag	p.E231Q	WDR65_ENST00000528956.1_Missense_Mutation_p.E231Q	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		231										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TCAGCGTTGGGAGACCAGCAT	0.502																																					p.E231Q		.											.	WDR65-91	0			c.G691C						.						148	138	142					1																	43649478		2203	4300	6503	SO:0001583	missense	149465	exon4			CGTTGGGAGACCA																												ENST00000372492.4:c.691G>C	1.37:g.43649478G>C	ENSP00000361570:p.Glu231Gln	Somatic	179	1		WXS	Illumina HiSeq	Phase_I	188	50	NM_152498	0	0	0	1	1	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		.	.	.	.	.	.	.	.	.	.	G	17.74	3.463543	0.63513	.	.	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.39592	1.07;3.56	6.07	6.07	0.98685	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.56601	0.1996	M	0.77820	2.39	0.47511	D	0.999446	B;P	0.46277	0.409;0.875	B;P	0.51324	0.082;0.666	T	0.49570	-0.8926	10	0.17832	T	0.49	.	17.5684	0.87927	0.0:0.1231:0.8769:0.0	.	231;231	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	Q	231	ENSP00000361570:E231Q;ENSP00000435310:E231Q	ENSP00000361570:E231Q	E	+	1	0	WDR65	43422065	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	6.039000	0.70972	2.885000	0.99019	0.655000	0.94253	GAG	.		0.502	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			C	43649478	G	C	43649478	3	2	94	1	0	0	0	0	1	0	0	0	17349	1175	41	4	701	4	WDR65	1	43649478	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	11548523	43649478	205601143	5	8416											
DEDD	9191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161092019	161092019	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgtctacatttaccagcAgcttgatggcttcatggccc	7	12	8	14	1	2	1	1	1	1	0	3	1	2	1	3	2	4	3	3	2	2	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:161092019A>C	ENST00000368006.3	-	6	1089	c.875T>G	c.(874-876)cTg>cGg	p.L292R	DEDD_ENST00000490843.2_Missense_Mutation_p.L292R|DEDD_ENST00000458050.2_Missense_Mutation_p.L292R|DEDD_ENST00000368005.1_Missense_Mutation_p.L322R|NIT1_ENST00000368008.1_Intron|DEDD_ENST00000545495.1_Missense_Mutation_p.L292R|DEDD_ENST00000392188.1_Missense_Mutation_p.L322R|DEDD_ENST00000489249.1_5'UTR	NM_032998.2	NP_127491.1	O75618	DEDD_HUMAN	death effector domain containing	292					decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)			cervix(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|skin(1)	10	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			ATTTACCAGCAGCTTGATGGC	0.498																																					p.L292R		.											.	DEDD-90	0			c.T875G						.						100	93	95					1																	161092019		2203	4300	6503	SO:0001583	missense	9191	exon5			ACCAGCAGCTTGA	AF043733	CCDS1219.1	1q23.1	2008-02-05	2002-01-14		ENSG00000158796	ENSG00000158796			2755	protein-coding gene	gene with protein product		606841	"death effector domain-containing"			9774341, 9832420	Standard	XM_005245597		Approved	DEFT, FLDED1, CASP8IP1, KE05, DEDD1	uc001fxz.3	O75618	OTTHUMG00000033104	ENST00000368006.3:c.875T>G	1.37:g.161092019A>C	ENSP00000356985:p.Leu292Arg	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	95	32	NM_001039711	0	0	36	61	25	D3DVF5|O60737	Missense_Mutation	SNP	ENST00000368006.3	37	CCDS1219.1	.	.	.	.	.	.	.	.	.	.	A	19.68	3.871963	0.72180	.	.	ENSG00000158796	ENST00000368006;ENST00000392188;ENST00000545495;ENST00000458050;ENST00000541906;ENST00000368005;ENST00000535389	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.70386	0.3218	M	0.64997	1.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.998;0.997;0.996	T	0.74948	-0.3490	9	0.87932	D	0	.	13.2065	0.59800	1.0:0.0:0.0:0.0	.	249;322;292	B4DKM1;B1AQP5;O75618	.;.;DEDD_HUMAN	R	292;322;292;292;292;322;249	.	ENSP00000356984:L322R	L	-	2	0	DEDD	159358643	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.135000	0.94478	2.209000	0.71365	0.533000	0.62120	CTG	.		0.498	DEDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080582.1	NM_004216		C	161092019	A	C	161092019	3	2	94	1	0	0	0	0	1	0	0	0	4390	188	7	5	85	5	DEDD	1	161092019	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	117442541	161092019	88158602	6	8417											
RGS1	5996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	192547354	192547354	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccctcgtttctttttagctGgtcaaaatgtctttggaagt	7	17	8	9	1	3	0	1	0	2	0	4	1	3	1	2	2	1	2	2	2	4	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:192547354G>C	ENST00000367459.3	+	4	349	c.283G>C	c.(283-285)Ggt>Cgt	p.G95R	RGS1_ENST00000469578.2_Missense_Mutation_p.G95R	NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	95	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|immune response (GO:0006955)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			kidney(8)|large_intestine(1)|lung(13)	22		Breast(1374;0.188)				CTTTTTAGCTGGTCAAAATGT	0.343																																					p.G95R		.											.	RGS1-226	0			c.G283C						.						122	130	127					1																	192547354		2203	4300	6503	SO:0001583	missense	5996	exon4			TTAGCTGGTCAAA	AF493925	CCDS1375.2	1q31	2008-02-05	2007-08-14		ENSG00000090104	ENSG00000090104		"Regulators of G-protein signaling"	9991	protein-coding gene	gene with protein product		600323	"regulator of G-protein signalling 1"	IER1		8241276, 8602223	Standard	NM_002922		Approved	1R20, IR20, BL34	uc001gsi.1	Q08116	OTTHUMG00000035598	ENST00000367459.3:c.283G>C	1.37:g.192547354G>C	ENSP00000356429:p.Gly95Arg	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	151	40	NM_002922	0	0	2	2	0	B2RDM9|B4DZY0|Q07918|Q9H1W2	Missense_Mutation	SNP	ENST00000367459.3	37	CCDS1375.2	.	.	.	.	.	.	.	.	.	.	G	13.87	2.365805	0.41902	.	.	ENSG00000090104	ENST00000367459	T	0.02944	4.1	5.91	5.91	0.95273	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.25680	0.0625	H	0.94886	3.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.12319	-1.0552	10	0.87932	D	0	.	18.8649	0.92287	0.0:0.0:1.0:0.0	.	95;95	Q08116-2;Q08116	.;RGS1_HUMAN	R	95	ENSP00000356429:G95R	ENSP00000356429:G95R	G	+	1	0	RGS1	190813977	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.640000	0.83355	2.804000	0.96469	0.650000	0.86243	GGT	.		0.343	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086391.1	NM_002922		C	192547354	G	C	192547354	3	2	94	1	0	0	0	0	1	0	0	0	13324	1348	47	4	297	4	RGS1	1	192547354	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	31455335	192547354	56703267	7	8418											
ELF3	1999	broad.mit.edu	37	chr1	201980419	201980420	+	Frame_Shift_Ins	INS	-	-	G																															aacccccagatgtcattggaINSgggtacaggtgggtctcagc																										TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:201980419_201980420insG	ENST00000359651.3	+	1	3347_3348	c.155_156insG	c.(154-159)gagggtfs	p.EG52fs	ELF3_ENST00000367283.3_Frame_Shift_Ins_p.EG52fs|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000495848.1_3'UTR|RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367284.5_Frame_Shift_Ins_p.EG52fs					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.E52G(2)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						ATGTCATTGGAGGGTACAGGTG	0.609																																					p.E52fs													.	ELF3-226	2	Substitution - Missense(2)	lung(2)	c.155_156insG						.																																			SO:0001589	frameshift_variant	1999	exon2			CATTGGAGGGTAC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.158dupG	1.37:g.201980422_201980422dupG	ENSP00000352673:p.Glu52fs	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	138	11	NM_004433	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000359651.3	37	CCDS1419.1																																																																																			.		0.609	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		G	201980420	-	G	201980419	7	5	94	1	0	1	1	0	0	0	0	0	5068	304	11	0	157	0	ELF3	1	201980419	Frame_Shift_Ins	INS	-	TCGA-DW-7834-01A-11D-2136-08	9433065	201980419	47270202	8	8419											
PLXNA2	5362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	208215581	208215581	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgaagccacgttgcccCggtcgcgcatggagaaactg	9	6	14	12	5	0	2	0	1	0	1	1	4	0	2	3	2	4	2	3	2	2	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:208215581C>T	ENST00000367033.3	-	22	4905	c.4148G>A	c.(4147-4149)cGg>cAg	p.R1383Q		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1383					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CACGTTGCCCCGGTCGCGCAT	0.582																																					p.R1383Q		.											.	PLXNA2-92	0			c.G4148A						.						94	92	92					1																	208215581		2203	4300	6503	SO:0001583	missense	5362	exon22			TTGCCCCGGTCGC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4148G>A	1.37:g.208215581C>T	ENSP00000356000:p.Arg1383Gln	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	91	30	NM_025179	0	0	1	2	1	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504221	0.96371	.	.	ENSG00000076356	ENST00000367033	T	0.15718	2.4	5.15	5.15	0.70609	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.46092	0.1375	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.49916	-0.8888	10	0.87932	D	0	.	18.6381	0.91385	0.0:1.0:0.0:0.0	.	1383	O75051	PLXA2_HUMAN	Q	1383	ENSP00000356000:R1383Q	ENSP00000356000:R1383Q	R	-	2	0	PLXNA2	206282204	1.000000	0.71417	0.980000	0.43619	0.826000	0.46750	7.480000	0.81109	2.391000	0.81399	0.455000	0.32223	CGG	.		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208215581	C	T	208215581	3	4	94	1	0	0	0	0	1	0	0	0	12146	652	23	1	1580	1	PLXNA2	1	208215581	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	6235162	208215581	41035040	9	8420											
NUP133	55746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	229631732	229631732	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctaattcccatttactGatgtttgaactcgtcaggct	9	16	6	10	1	3	2	2	2	1	0	5	2	4	2	1	1	2	2	1	1	3	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:229631732G>T	ENST00000261396.3	-	7	973	c.882C>A	c.(880-882)atC>atA	p.I294I	NUP133_ENST00000537506.1_Silent_p.I278I	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	294			I -> V (in dbSNP:rs11805194).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CCCATTTACTGATGTTTGAAC	0.363																																					p.I294I		.											.	NUP133-271	0			c.C882A						.						105	101	103					1																	229631732		2203	4299	6502	SO:0001819	synonymous_variant	55746	exon7			TTTACTGATGTTT		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"nucleoporin 133kD"			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.882C>A	1.37:g.229631732G>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	74	31	NM_018230	0	0	6	6	0	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			.		0.363	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229631732	G	T	229631732	2	4	94	1	0	0	0	0	0	0	0	1	10780	1280	45	4		4	NUP133	1	229631732	Silent	SNP	G	TCGA-DW-7834-01A-11D-2136-08	21416151	229631732	19618889	10	8421											
LPIN1	23175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	11913751	11913751	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttttttcctccagaactcTtcctaatgatatacctccat	9	18	2	12	0	1	2	0	1	1	1	5	2	5	2	5	0	2	0	5	0	4	8			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:11913751T>C	ENST00000256720.2	+	5	695	c.602T>C	c.(601-603)cTt>cCt	p.L201P	LPIN1_ENST00000449576.2_Missense_Mutation_p.L250P|LPIN1_ENST00000396099.1_Missense_Mutation_p.L207P|LPIN1_ENST00000396098.1_Missense_Mutation_p.L207P|LPIN1_ENST00000425416.2_Missense_Mutation_p.L207P	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	201					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TCCAGAACTCTTCCTAATGAT	0.358																																					p.L250P		.											.	LPIN1-156	0			c.T749C						.						81	88	86					2																	11913751		2203	4300	6503	SO:0001583	missense	23175	exon6			GAACTCTTCCTAA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.602T>C	2.37:g.11913751T>C	ENSP00000256720:p.Leu201Pro	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	113	35	NM_001261428	0	0	0	0	0	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	T	5.891	0.348519	0.11126	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720	T;D;T;T;T	0.89270	-1.47;-2.49;-1.45;-1.47;-1.47	5.6	3.27	0.37495	.	0.457402	0.18485	N	0.139836	T	0.80884	0.4709	L	0.31926	0.97	0.09310	N	0.999998	B;B;B	0.11235	0.002;0.0;0.004	B;B;B	0.11329	0.006;0.002;0.006	T	0.66929	-0.5799	10	0.31617	T	0.26	-5.5606	7.3106	0.26473	0.0:0.2849:0.0:0.7151	.	250;201;207	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	P	250;207;207;207;201	ENSP00000397908:L250P;ENSP00000379405:L207P;ENSP00000379406:L207P;ENSP00000401522:L207P;ENSP00000256720:L201P	ENSP00000256720:L201P	L	+	2	0	LPIN1	11831202	0.012000	0.17670	0.131000	0.22000	0.489000	0.33432	1.405000	0.34635	0.974000	0.38366	0.482000	0.46254	CTT	.		0.358	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		C	11913751	T	C	11913751	3	2	94	1	0	0	0	0	1	0	0	0	8943	1609	56	3	616	3	LPIN1	2	11913751	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		11913751	231285622	11	8422											
NBAS	51594	hgsc.bcm.edu	37	chr2	15691633	15691633	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaccttgacatttcccaatAatggatgtaaaatcatcttt	13	16	4	8	0	2	1	1	1	1	0	3	2	3	2	2	1	1	1	2	1	5	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:15691633A>G	ENST00000281513.5	-	6	388	c.363T>C	c.(361-363)atT>atC	p.I121I	NBAS_ENST00000441750.1_Silent_p.I121I	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	121					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						ATTTCCCAATAATGGATGTAA	0.294																																					p.I121I		.											.	NBAS-94	0			c.T363C						.						41	40	40					2																	15691633		2201	4297	6498	SO:0001819	synonymous_variant	51594	exon6			CCCAATAATGGAT	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.363T>C	2.37:g.15691633A>G		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_015909	0	0	0	0	0	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			.		0.294	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15691633	A	G	15691633	2	3	94	1	0	0	0	0	0	0	0	1	10211	358	13	3		3	NBAS	2	15691633	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08	3777882	15691633	227507740	12	8423											
ANAPC1	64682	hgsc.bcm.edu	37	chr2	112615903	112615903	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtaactggagctgggactcTactaaaaagcacaggaactt	14	8	10	9	1	1	0	0	0	1	0	1	3	1	3	0	3	5	3	0	3	6	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:112615903T>C	ENST00000341068.3	-	11	2110	c.1338A>G	c.(1336-1338)gtA>gtG	p.V446V		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	446					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						GCTGGGACTCTACTAAAAAGC	0.328																																					p.V446V		.											.	ANAPC1-228	0			c.A1338G						.						93	86	89					2																	112615903		2203	4300	6503	SO:0001819	synonymous_variant	64682	exon11			GGACTCTACTAAA	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1338A>G	2.37:g.112615903T>C		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	58	3	NM_022662	0	0	0	0	0	Q2M3H8|Q9BSE6|Q9H8D0	Silent	SNP	ENST00000341068.3	37	CCDS2093.1																																																																																			.		0.328	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		C	112615903	T	C	112615903	2	2	94	1	0	0	0	0	0	0	0	1	598	1509	53	3		3	ANAPC1	2	112615903	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08	96924270	112615903	130583470	13	8424											
THSD7B	80731	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	137928319	137928319	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctctttttaggatttagaAcgaggcagcgccatgtcctc	8	13	9	11	2	1	1	0	0	1	1	4	3	2	2	2	2	2	1	2	2	3	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:137928319A>G	ENST00000409968.1	+	7	1712	c.1534A>G	c.(1534-1536)Acg>Gcg	p.T512A	THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Missense_Mutation_p.T512A|THSD7B_ENST00000413152.2_Missense_Mutation_p.T481A|THSD7B_ENST00000485379.1_3'UTR			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	512	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AGGATTTAGAACGAGGCAGCG	0.453																																					.													.	THSD7B-75	0			.						.						84	78	80					2																	137928319		1907	4138	6045	SO:0001583	missense	80731	.			TTTAGAACGAGGC			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.1534A>G	2.37:g.137928319A>G	ENSP00000387145:p.Thr512Ala	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	89	11	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	A	7.167	0.586912	0.13749	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.61980	0.06;0.06;0.06	5.76	3.08	0.35506	.	0.578922	0.21014	N	0.081637	T	0.49762	0.1576	L	0.42581	1.335	0.80722	D	1	B;B	0.15719	0.014;0.014	B;B	0.17722	0.019;0.019	T	0.35425	-0.9789	10	0.16420	T	0.52	.	10.3016	0.43656	0.7244:0.0:0.0:0.2756	.	512;481	Q9C0I4;C9JKN6	THS7B_HUMAN;.	A	512;512;481	ENSP00000387145:T512A;ENSP00000272643:T512A;ENSP00000413841:T481A	ENSP00000272643:T512A	T	+	1	0	THSD7B	137644789	1.000000	0.71417	0.870000	0.34147	0.031000	0.12232	2.542000	0.45744	0.987000	0.38709	-0.327000	0.08410	ACG	.		0.453	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9		G	137928319	A	G	137928319	3	3	94	1	0	0	0	0	1	0	0	0	15912	43	2	3	1463	3	THSD7B	2	137928319	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	25312416	137928319	105271054	14	8425											
IFIH1	64135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	163167397	163167397	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgcacaatcctttttagtAgctctcttacacctgattca	9	16	4	12	0	3	1	1	1	2	0	5	1	4	1	2	0	3	3	2	0	4	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:163167397A>G	ENST00000263642.2	-	2	895	c.500T>C	c.(499-501)cTa>cCa	p.L167P	IFIH1_ENST00000421365.2_Missense_Mutation_p.L167P	NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	167	CARD 2.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						CCTTTTTAGTAGCTCTCTTAC	0.358																																					p.L167P		.											.	IFIH1-91	0			c.T500C						.						81	72	75					2																	163167397		2203	4299	6502	SO:0001583	missense	64135	exon2			TTTAGTAGCTCTC	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"helicard"	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.500T>C	2.37:g.163167397A>G	ENSP00000263642:p.Leu167Pro	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	54	15	NM_022168	0	0	5	6	1	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.318793	0.60524	.	.	ENSG00000115267	ENST00000263642;ENST00000543192;ENST00000421365	T;T	0.63255	-0.03;-0.03	5.81	5.81	0.92471	DEATH-like (2);Caspase Recruitment (1);	0.140170	0.48286	D	0.000192	T	0.79411	0.4441	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81874	-0.0732	10	0.87932	D	0	-10.3294	16.1677	0.81782	1.0:0.0:0.0:0.0	.	167;167	Q9BYX4-2;Q9BYX4	.;IFIH1_HUMAN	P	167	ENSP00000263642:L167P;ENSP00000408450:L167P	ENSP00000263642:L167P	L	-	2	0	IFIH1	162875643	0.991000	0.36638	0.999000	0.59377	0.237000	0.25408	6.182000	0.71995	2.218000	0.71995	0.528000	0.53228	CTA	.		0.358	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		G	163167397	A	G	163167397	3	3	94	1	0	0	0	0	1	0	0	0	7541	420	15	3	2637	3	IFIH1	2	163167397	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	25239078	163167397	80031976	15	8426											
OBFC2A	64859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	192543405	192543405	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcccggactgaaaaacttaaAtgtcgtctttattgtcctgg	10	13	9	9	2	1	1	0	1	1	0	3	2	2	2	2	2	1	0	2	2	5	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:192543405A>C	ENST00000425611.2	+	1	148	c.65A>C	c.(64-66)aAt>aCt	p.N22T	NABP1_ENST00000410026.2_Intron|NABP1_ENST00000409510.1_Intron	NM_001031716.2	NP_001026886.1	Q96AH0	SOSB2_HUMAN	nucleic acid binding protein 1	22					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SOSS complex (GO:0070876)	RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)										AAAAACTTAAATGTCGTCTTT	0.562																																					p.N22T		.											.	.	0			c.A65C						.						42	50	47					2																	192543405		2203	4300	6503	SO:0001583	missense	64859	exon1			ACTTAAATGTCGT	BC017114	CCDS33352.1, CCDS58745.1	2q32.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000173559	ENSG00000173559			26232	protein-coding gene	gene with protein product	"single-stranded DNA-binding protein 2", "sensor of single-strand DNA complex subunit B2"	612103	"oligonucleotide/oligosaccharide-binding fold containing 2A"	OBFC2A			Standard	NM_001031716		Approved	FLJ22833, DKFZp667M1322, FLJ13624, MGC111163, SSB2, hSSB2, SOSS-B2	uc002usx.3	Q96AH0	OTTHUMG00000132720	ENST00000425611.2:c.65A>C	2.37:g.192543405A>C	ENSP00000403683:p.Asn22Thr	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	100	32	NM_001031716	0	0	1	2	1	Q658Y8|Q9H5X6	Missense_Mutation	SNP	ENST00000425611.2	37	CCDS33352.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527945	0.85706	.	.	ENSG00000173559	ENST00000425611	T	0.28255	1.62	5.51	5.51	0.81932	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.107337	0.64402	D	0.000007	T	0.46927	0.1418	M	0.68728	2.09	0.54753	D	0.999989	D	0.63046	0.992	P	0.59487	0.858	T	0.47522	-0.9111	10	0.56958	D	0.05	.	9.7659	0.40561	0.9219:0.0:0.0781:0.0	.	22	Q96AH0	SOSB2_HUMAN	T	22	ENSP00000403683:N22T	ENSP00000307968:N22T	N	+	2	0	OBFC2A	192251650	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.953000	0.70290	2.080000	0.62538	0.533000	0.62120	AAT	.		0.562	NABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256060.1	NM_022837		C	192543405	A	C	192543405	3	2	94	1	0	0	0	0	1	0	0	0	10834	101	4	5	67	5	OBFC2A	2	192543405	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	29376008	192543405	50655968	16	8427											
SF3B1	23451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198274598	198274598	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtatcacctcgtccaggaGtagcagctcccgctggtgtg	6	10	13	12	2	1	0	1	0	0	0	4	1	3	1	3	2	2	5	3	2	2	2	rs1044635		TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:198274598G>T	ENST00000335508.6	-	7	891	c.800C>A	c.(799-801)aCt>aAt	p.T267N		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	267	Interaction with PPP1R8.|U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TCGTCCAGGAGTAGCAGCTCC	0.562			Mis		myelodysplastic syndrome																																p.T267N		.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.C800A						.						170	167	168					2																	198274598		2203	4300	6503	SO:0001583	missense	23451	exon7			CCAGGAGTAGCAG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.800C>A	2.37:g.198274598G>T	ENSP00000335321:p.Thr267Asn	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	222	78	NM_012433	0	0	20	38	18	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179984	0.94846	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	L	0.44542	1.39	0.80722	D	1	D	0.55800	0.973	P	0.47346	0.544	T	0.53954	-0.8365	9	0.27082	T	0.32	.	19.0839	0.93194	0.0:0.0:1.0:0.0	.	267	O75533	SF3B1_HUMAN	N	267	.	ENSP00000335321:T267N	T	-	2	0	SF3B1	197982843	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.750000	0.98875	2.502000	0.84385	0.655000	0.94253	ACT	G|1.000;A|0.000		0.562	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198274598	G	T	198274598	3	4	94	1	0	0	0	0	1	0	0	0	14181	1029	36	4	3190	4	SF3B1	2	198274598	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	5731193	198274598	44924775	17	8428											
MTMR14	64419	broad.mit.edu;bcgsc.ca	37	chr3	9691346	9691346	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaaccagccgcctcaggagCtggggcttggggagctgctg	6	6	17	12	1	1	0	1	0	0	0	1	2	1	2	3	5	5	5	3	5	1	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr3:9691346C>G	ENST00000296003.4	+	1	201	c.79C>G	c.(79-81)Ctg>Gtg	p.L27V	MTMR14_ENST00000420925.1_Missense_Mutation_p.L27V|MTMR14_ENST00000351233.5_Missense_Mutation_p.L27V|MTMR14_ENST00000353332.5_Missense_Mutation_p.L27V	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	27					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					GCCTCAGGAGCTGGGGCTTGG	0.721																																					p.L27V													.	MTMR14-91	0			c.C79G						.						7	9	8					3																	9691346		1848	4076	5924	SO:0001583	missense	64419	exon1			CAGGAGCTGGGGC	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.79C>G	3.37:g.9691346C>G	ENSP00000296003:p.Leu27Val	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	16	4	NM_022485	0	0	1	1	0	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Missense_Mutation	SNP	ENST00000296003.4	37	CCDS43043.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.468940	0.43839	.	.	ENSG00000163719	ENST00000353332;ENST00000420925;ENST00000296003;ENST00000351233;ENST00000419048	D	0.97161	-4.27	5.23	5.23	0.72850	.	0.517985	0.19981	N	0.101768	D	0.91274	0.7249	N	0.03608	-0.345	0.21527	N	0.999658	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.82573	-0.0390	10	0.42905	T	0.14	-1.7533	15.8007	0.78453	0.0:1.0:0.0:0.0	.	27;27;27;27	C9JSR1;Q8NCE2-3;Q8NCE2-2;Q8NCE2	.;.;.;MTMRE_HUMAN	V	27	ENSP00000401993:L27V	ENSP00000296003:L27V	L	+	1	2	MTMR14	9666346	1.000000	0.71417	0.942000	0.38095	0.493000	0.33554	3.397000	0.52572	2.455000	0.83008	0.650000	0.86243	CTG	.		0.721	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		G	9691346	C	G	9691346	3	3	94	1	0	0	0	0	1	0	0	0	9967	796	28	4	81	4	MTMR14	3	9691346	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		9691346	188331084	18	8429											
DPPA2	151871	broad.mit.edu	37	chr3	109023471	109023471	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggcgtacccaacccttTgtgtctgccgagagaagtct	8	10	11	12	2	2	1	0	0	2	1	2	3	2	1	3	1	4	2	3	1	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr3:109023471T>C	ENST00000478945.1	-	7	951	c.705A>G	c.(703-705)acA>acG	p.T235T		NM_138815.3	NP_620170.3	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	235					lung-associated mesenchyme development (GO:0060484)|positive regulation of stem cell proliferation (GO:2000648)|regulation of histone methylation (GO:0031060)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCCAACCCTTTGTGTCTGCCG	0.502																																					p.T235T													.	DPPA2-93	0			c.A705G						.						77	71	73					3																	109023471		2203	4300	6503	SO:0001819	synonymous_variant	151871	exon7			ACCCTTTGTGTCT	AY283672	CCDS2956.1	3q13.13	2010-05-04			ENSG00000163530	ENSG00000163530			19197	protein-coding gene	gene with protein product	"cancer/testis antigen 100"	614445				15583978	Standard	NM_138815		Approved	PESCRG1, CT100	uc003dxo.3	Q7Z7J5	OTTHUMG00000159227	ENST00000478945.1:c.705A>G	3.37:g.109023471T>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	119	4	NM_138815	0	0	2	2	0	Q8WVF0	Silent	SNP	ENST00000478945.1	37	CCDS2956.1																																																																																			.		0.502	DPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353938.1	NM_138815		C	109023471	T	C	109023471	2	2	94	1	0	0	0	0	0	0	0	1	4745	1799	63	3		3	DPPA2	3	109023471	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08	99332125	109023471	88998959	19	8430											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561258	147561258	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcaccaccaccaccaccaTcaccaccaccaccaccacca	14	1	1	25	1	1	0	1	0	0	0	1	0	1	0	11	0	0	1	11	0	0	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:147561258T>C	ENST00000281321.3	+	2	776	c.528T>C	c.(526-528)caT>caC	p.H176H	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	176	Poly-His.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					accaccaccatcaccaccacc	0.682																																					p.H176H		.											.	POU4F2-135	0			c.T528C						.						43	45	44					4																	147561258		2203	4299	6502	SO:0001819	synonymous_variant	5458	exon2			CCACCATCACCAC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"Homeoboxes / POU class"	9219	protein-coding gene	gene with protein product		113725	"POU domain, class 4, transcription factor 2", "POU domain class 4, transcription factor 2"	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.528T>C	4.37:g.147561258T>C		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_004575	1016	1	16	1137	104	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																			.		0.682	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		C	147561258	T	C	147561258	2	2	94	1	0	0	0	0	0	0	0	1	12305	1432	50	3		3	POU4F2	4	147561258	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08		147561258	43593018	20	8431											
DDX60	55601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	169172121	169172121	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctaccctaagatatccttttCtaaagaggatttcaactaat	14	14	4	9	0	2	2	1	0	1	2	3	3	3	3	2	1	2	0	2	1	7	8			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:169172121C>T	ENST00000393743.3	-	28	4133	c.3842G>A	c.(3841-3843)aGa>aAa	p.R1281K	DDX60_ENST00000505393.1_5'Flank	NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1281	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		ATATCCTTTTCTAAAGAGGAT	0.338																																					p.R1281K		.											.	DDX60-25	0			c.G3842A						.						76	79	78					4																	169172121		2201	4297	6498	SO:0001583	missense	55601	exon28			CCTTTTCTAAAGA	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.3842G>A	4.37:g.169172121C>T	ENSP00000377344:p.Arg1281Lys	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	64	16	NM_017631	0	0	6	8	2	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.096722	0.36952	.	.	ENSG00000137628	ENST00000393743	T	0.26957	1.7	5.4	5.4	0.78164	Helicase, C-terminal (3);	0.075985	0.56097	D	0.000034	T	0.27098	0.0664	L	0.39020	1.185	0.39934	D	0.974326	P	0.36768	0.569	B	0.38880	0.284	T	0.05750	-1.0866	10	0.52906	T	0.07	.	18.7821	0.91937	0.0:1.0:0.0:0.0	.	1281	Q8IY21	DDX60_HUMAN	K	1281	ENSP00000377344:R1281K	ENSP00000377344:R1281K	R	-	2	0	DDX60	169408696	1.000000	0.71417	0.408000	0.26446	0.120000	0.20174	4.958000	0.63660	2.549000	0.85964	0.467000	0.42956	AGA	.		0.338	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		T	169172121	C	T	169172121	3	4	94	1	0	0	0	0	1	0	0	0	4384	913	32	2	1340	2	DDX60	4	169172121	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	21610863	169172121	21982155	21	8432											
PALLD	23022	broad.mit.edu	37	chr4	169433375	169433375	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtcaagtcccctggggccagGcattgctaccaggacaacca	10	6	11	14	0	1	0	1	0	0	0	2	1	2	1	5	4	3	2	5	4	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:169433375G>A	ENST00000505667.1	+	2	893	c.720G>A	c.(718-720)agG>agA	p.R240R	PALLD_ENST00000333488.4_Silent_p.R117R|PALLD_ENST00000261509.6_Silent_p.R240R|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	240					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		CTGGGGCCAGGCATTGCTACC	0.597									Pancreatic Cancer, Familial Clustering of																												p.R240R	Esophageal Squamous(109;1482 1532 18347 40239 51172)												.	PALLD-94	0			c.G720A						.						89	86	87					4																	169433375		2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GGCCAGGCATTGC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"Immunoglobulin superfamily / I-set domain containing"	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.720G>A	4.37:g.169433375G>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	115	5	NM_001166108	0	0	0	0	0	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			.		0.597	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		A	169433375	G	A	169433375	2	1	94	1	0	0	0	0	0	0	0	1	11433	1194	42	2		2	PALLD	4	169433375	Silent	SNP	G	TCGA-DW-7834-01A-11D-2136-08	261254	169433375	21720901	22	8433											
WWC2	80014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	184166688	184166688	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaaaaagaaaaacaagAtctgatgcaggtacattata	21	7	9	4	0	1	4	0	1	1	3	1	5	1	4	0	2	3	2	0	2	8	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:184166688A>C	ENST00000403733.3	+	6	921	c.722A>C	c.(721-723)gAt>gCt	p.D241A	WWC2_ENST00000448232.2_Missense_Mutation_p.D241A|WWC2_ENST00000378925.3_Missense_Mutation_p.D143A|WWC2_ENST00000513834.1_Missense_Mutation_p.D241A|WWC2_ENST00000504005.1_Intron	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	241					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		GAAAAACAAGATCTGATGCAG	0.433																																					p.D241A		.											.	WWC2-93	0			c.A722C						.						50	50	50					4																	184166688		2203	4300	6503	SO:0001583	missense	80014	exon6			AACAAGATCTGAT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.722A>C	4.37:g.184166688A>C	ENSP00000384222:p.Asp241Ala	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	50	14	NM_024949	0	0	0	0	0	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	25.0	4.591096	0.86851	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232	T;T;T;T	0.15256	3.17;2.44;3.23;3.03	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000001	T	0.38904	0.1058	M	0.77820	2.39	0.58432	D	0.999999	D	0.67145	0.996	P	0.60609	0.877	T	0.15925	-1.0420	10	0.33940	T	0.23	-24.0084	15.3161	0.74078	1.0:0.0:0.0:0.0	.	241	Q6AWC2	WWC2_HUMAN	A	241;143;241;241	ENSP00000384222:D241A;ENSP00000368205:D143A;ENSP00000425054:D241A;ENSP00000398577:D241A	ENSP00000368205:D143A	D	+	2	0	WWC2	184403682	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.856000	0.92245	2.254000	0.74563	0.533000	0.62120	GAT	.		0.433	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		C	184166688	A	C	184166688	3	2	94	1	0	0	0	0	1	0	0	0	17445	333	12	5	744	5	WWC2	4	184166688	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	14733313	184166688	6987588	23	8434											
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	32074625	32074625	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggctgaggccaagcccaGtggctcacagacagtgaacc	11	4	13	13	1	1	3	1	2	0	1	1	4	1	3	3	3	2	2	3	3	2	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:32074625G>T	ENST00000438447.1	+	18	3801	c.3413G>T	c.(3412-3414)aGt>aTt	p.S1138I	PDZD2_ENST00000282493.3_Missense_Mutation_p.S1138I			O15018	PDZD2_HUMAN	PDZ domain containing 2	1138					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCAAGCCCAGTGGCTCACAG	0.587																																					p.S1138I		.											.	PDZD2-563	0			c.G3413T						.						42	42	42					5																	32074625		2203	4300	6503	SO:0001583	missense	23037	exon17			AGCCCAGTGGCTC	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"PDZ domain containing 3"	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3413G>T	5.37:g.32074625G>T	ENSP00000402033:p.Ser1138Ile	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	49	19	NM_178140	0	0	0	0	0	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.006840	0.35415	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06933	3.24;3.24	5.21	1.07	0.20283	.	1.010820	0.07935	N	0.978210	T	0.06325	0.0163	L	0.51422	1.61	0.09310	N	1	P;B	0.37864	0.61;0.01	B;B	0.28139	0.086;0.014	T	0.38436	-0.9661	10	0.20519	T	0.43	.	4.0787	0.09916	0.1583:0.1285:0.5814:0.1318	.	964;1138	B4E3P2;O15018	.;PDZD2_HUMAN	I	1138;940;1138	ENSP00000402033:S1138I;ENSP00000282493:S1138I	ENSP00000282493:S1138I	S	+	2	0	PDZD2	32110382	0.002000	0.14202	0.001000	0.08648	0.005000	0.04900	1.151000	0.31651	0.543000	0.28864	0.655000	0.94253	AGT	.		0.587	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32074625	G	T	32074625	3	4	94	1	0	0	0	0	1	0	0	0	11727	1029	36	4	3479	4	PDZD2	5	32074625	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		32074625	148840635	24	8435											
SEPP1	6414	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	42807146	42807146	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaagagattccttgatgatTaacaacaatataagaaatat	20	11	6	4	0	0	5	0	2	0	3	1	6	1	5	1	0	2	0	1	0	8	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:42807146T>A	ENST00000514985.1	-	3	524	c.268A>T	c.(268-270)Aat>Tat	p.N90Y	SEPP1_ENST00000507920.1_Intron|CTD-2325A15.5_ENST00000606056.1_RNA|SEPP1_ENST00000511224.1_Missense_Mutation_p.N90Y|SEPP1_ENST00000509276.1_Intron|SEPP1_ENST00000506577.1_Missense_Mutation_p.N90Y	NM_005410.2	NP_005401.3	P49908	SEPP1_HUMAN	selenoprotein P, plasma, 1	90					brain development (GO:0007420)|growth (GO:0040007)|locomotory behavior (GO:0007626)|post-embryonic development (GO:0009791)|response to oxidative stress (GO:0006979)|selenium compound metabolic process (GO:0001887)|sexual reproduction (GO:0019953)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	selenium binding (GO:0008430)			kidney(10)|large_intestine(1)|lung(4)	15						CCTTGATGATTAACAACAATA	0.284																																					.													.	SEPP1-68	0			.						.						84	82	83					5																	42807146		1792	4058	5850	SO:0001583	missense	6414	.			GATGATTAACAAC	BC040075	CCDS43311.1	5q31	2012-03-01				ENSG00000250722			10751	protein-coding gene	gene with protein product		601484				8421687	Standard	NM_001085486		Approved	SeP	uc011cpu.2	P49908		ENST00000514985.1:c.268A>T	5.37:g.42807146T>A	ENSP00000420939:p.Asn90Tyr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	66	13	.	0	0	89	104	15	Q6PD59|Q6PI43|Q6PI87|Q6PJF9	Missense_Mutation	SNP	ENST00000514985.1	37	CCDS43311.1	.	.	.	.	.	.	.	.	.	.	T	19.50	3.839014	0.71373	.	.	ENSG00000250722	ENST00000514985;ENST00000511224;ENST00000506577;ENST00000514218;ENST00000510965	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	5.49	5.49	0.81192	.	0.000000	0.47852	U	0.000216	T	0.67590	0.2909	M	0.80982	2.52	0.80722	D	1	.	.	.	.	.	.	T	0.72978	-0.4127	8	0.87932	D	0	.	15.589	0.76510	0.0:0.0:0.0:1.0	.	.	.	.	Y	90	ENSP00000420939:N90Y;ENSP00000427671:N90Y;ENSP00000425915:N90Y;ENSP00000421626:N90Y;ENSP00000427414:N90Y	ENSP00000425915:N90Y	N	-	1	0	SEPP1	42842903	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	6.689000	0.74562	2.088000	0.63022	0.528000	0.53228	AAT	.		0.284	SEPP1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000367483.1	NM_005410		A	42807146	T	A	42807146	3	1	94	1	0	0	0	0	1	0	0	0	14089	1754	61	5	889	5	SEPP1	5	42807146	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	10732521	42807146	138108114	25	8436											
FCHO2	115548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	72383545	72383545	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaacttgtgggcactggctAtaggctttccttaataaaga	11	12	10	8	1	0	1	0	0	0	1	1	2	1	1	1	3	1	3	1	3	6	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:72383545A>G	ENST00000430046.2	+	25	2491	c.2375A>G	c.(2374-2376)tAt>tGt	p.Y792C	FCHO2_ENST00000341845.6_Missense_Mutation_p.Y792C|FCHO2_ENST00000512348.1_Missense_Mutation_p.Y759C	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	792	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with DAB2, EPS15, EPS15R and ITSN1.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		GGCACTGGCTATAGGCTTTCC	0.398																																					p.Y792C		.											.	FCHO2-23	0			c.A2375G						.						128	126	127					5																	72383545		1836	4085	5921	SO:0001583	missense	115548	exon25			CTGGCTATAGGCT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.2375A>G	5.37:g.72383545A>G	ENSP00000393776:p.Tyr792Cys	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	229	61	NM_138782	0	0	3	6	3	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	37	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	A	15.49	2.849389	0.51270	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.54675	0.56;0.56;0.56	4.77	4.77	0.60923	Muniscin C-terminal mu homology domain (1);	0.000000	0.85682	D	0.000000	T	0.75591	0.3870	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.81024	-0.1120	10	0.87932	D	0	-11.6205	14.7503	0.69519	1.0:0.0:0.0:0.0	.	759;792	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	C	792;792;759	ENSP00000393776:Y792C;ENSP00000344034:Y792C;ENSP00000427296:Y759C	ENSP00000344034:Y792C	Y	+	2	0	FCHO2	72419301	1.000000	0.71417	0.960000	0.40013	0.262000	0.26303	8.705000	0.91357	2.124000	0.65301	0.528000	0.53228	TAT	.		0.398	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		G	72383545	A	G	72383545	3	3	94	1	0	0	0	0	1	0	0	0	5807	449	16	3	2473	3	FCHO2	5	72383545	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	29576399	72383545	108531715	26	8437											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82785943	82785943	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggaaaaagcccaccggtgAggggctccctctctggaaaa	11	6	13	11	1	1	1	0	1	1	0	3	3	2	3	3	5	1	1	3	5	4	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:82785943A>T	ENST00000265077.3	+	3	662	c.97A>T	c.(97-99)Agg>Tgg	p.R33W	VCAN_ENST00000512590.2_De_novo_Start_InFrame|VCAN_ENST00000343200.5_Missense_Mutation_p.R33W|VCAN_ENST00000342785.4_Missense_Mutation_p.R33W|VCAN_ENST00000502527.2_Missense_Mutation_p.R33W|VCAN_ENST00000513984.1_Missense_Mutation_p.R33W	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	33	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCCACCGGTGAGGGGCTCCCT	0.403																																					p.R33W		.											.	VCAN-238	0			c.A97T						.						51	51	51					5																	82785943		2202	4293	6495	SO:0001583	missense	1462	exon3			CCGGTGAGGGGCT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.97A>T	5.37:g.82785943A>T	ENSP00000265077:p.Arg33Trp	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	115	32	NM_004385	0	0	8	10	2	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.672502	0.47781	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000513960;ENST00000513984;ENST00000502527	T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	5.99	2.17	0.27698	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.395914	0.24213	N	0.040512	T	0.72220	0.3433	L	0.50333	1.59	0.21064	N	0.999792	P;P;D;D;D	0.63880	0.804;0.857;0.986;0.993;0.965	P;P;P;D;P	0.66602	0.87;0.641;0.702;0.945;0.838	T	0.62613	-0.6817	10	0.72032	D	0.01	.	8.4359	0.32786	0.6885:0.2476:0.0639:0.0	.	33;33;33;33;33	P13611-3;P13611-4;P13611-2;P13611;Q86W61	.;.;.;CSPG2_HUMAN;.	W	33	ENSP00000265077:R33W;ENSP00000340062:R33W;ENSP00000342768:R33W;ENSP00000426251:R33W;ENSP00000426715:R33W;ENSP00000421362:R33W	ENSP00000265077:R33W	R	+	1	2	VCAN	82821699	0.054000	0.20591	0.027000	0.17364	0.046000	0.14306	1.559000	0.36320	0.134000	0.18681	-0.316000	0.08728	AGG	.		0.403	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82785943	A	T	82785943	3	4	94	1	0	0	0	0	1	0	0	0	17171	295	11	5	103	5	VCAN	5	82785943	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	10402398	82785943	98129317	27	8438											
VARS2	57176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30888201	30888201	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaaccaccccatggtacTgcccatctgcaggtaacctc	10	7	7	17	0	1	1	0	0	1	1	2	1	1	1	6	2	5	3	6	2	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:30888201T>C	ENST00000321897.5	+	13	2017	c.1385T>C	c.(1384-1386)cTg>cCg	p.L462P	VARS2_ENST00000541562.1_Missense_Mutation_p.L492P|VARS2_ENST00000542001.1_Missense_Mutation_p.L322P|VARS2_ENST00000416670.2_Missense_Mutation_p.L462P|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	462					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CCCATGGTACTGCCCATCTGC	0.527																																					p.L492P		.											.	VARS2-26	0			c.T1475C						.						41	43	42					6																	30888201		2203	4300	6503	SO:0001583	missense	57176	exon14			TGGTACTGCCCAT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1385T>C	6.37:g.30888201T>C	ENSP00000316092:p.Leu462Pro	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	61	19	NM_001167734	0	0	0	0	0	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.777854	0.70107	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	4.26	4.26	0.50523	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.64402	D	0.000002	T	0.56077	0.1961	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.996	T	0.65923	-0.6050	10	0.87932	D	0	-11.1733	11.6463	0.51263	0.0:0.0:0.0:1.0	.	460;492;462	B7ZL25;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	P	462;462;322;492	ENSP00000316092:L462P;ENSP00000394802:L462P;ENSP00000438200:L322P;ENSP00000441000:L492P	ENSP00000316092:L462P	L	+	2	0	VARS2	30996180	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.008000	0.76341	1.708000	0.51301	0.374000	0.22700	CTG	.		0.527	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		C	30888201	T	C	30888201	3	2	94	1	0	0	0	0	1	0	0	0	17157	1580	55	3	1529	3	VARS2	6	30888201	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		30888201	140226866	28	8439											
ZNF76	7629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35260658	35260658	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccttggctctcctctcccagCcgcctctgcagccgaggaga	5	8	10	18	2	3	1	0	0	3	1	5	3	3	1	6	2	3	2	6	2	0	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:35260658C>T	ENST00000373953.3	+	11	1432	c.1166C>T	c.(1165-1167)gCc>gTc	p.A389V	ZNF76_ENST00000339411.5_Splice_Site_p.A389V|ZNF76_ENST00000440666.2_Splice_Site_p.A363V	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	389					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CCTCTCCCAGCCGCCTCTGCA	0.622																																					p.A389V	Esophageal Squamous(52;92 1039 20612 23956 34676)	.											.	ZNF76-90	0			c.C1166T						.						54	58	57					6																	35260658		2203	4300	6503	SO:0001630	splice_region_variant	7629	exon11			TCCCAGCCGCCTC	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"Zinc fingers, C2H2-type"	13149	protein-coding gene	gene with protein product		194549	"zinc finger protein 76 (expressed in testis)"	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.1166-1C>T	6.37:g.35260658C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	148	45	NM_003427	0	0	0	0	0	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615788	0.46631	.	.	ENSG00000065029	ENST00000373953;ENST00000440666;ENST00000339411	T;T;T	0.10668	2.88;2.88;2.85	4.83	4.83	0.62350	.	0.000000	0.36740	N	0.002424	T	0.01835	0.0058	N	0.08118	0	0.26011	N	0.981989	B;B	0.33135	0.392;0.399	B;B	0.34452	0.115;0.183	T	0.43196	-0.9406	9	.	.	.	.	8.2836	0.31915	0.176:0.6542:0.1698:0.0	.	389;389	P36508-2;P36508	.;ZNF76_HUMAN	V	389;363;389	ENSP00000363064:A389V;ENSP00000392243:A363V;ENSP00000344097:A389V	.	A	+	2	0	ZNF76	35368636	0.001000	0.12720	1.000000	0.80357	0.876000	0.50452	1.026000	0.30103	2.487000	0.83934	0.491000	0.48974	GCC	.		0.622	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	Missense_Mutation	T	35260658	C	T	35260658	5	4	94	1	0	0	0	0	0	0	1	0	18167	753	26	2	1204	2	ZNF76	6	35260658	Splice_Site	SNP	C	TCGA-DW-7834-01A-11D-2136-08	4372457	35260658	135854409	29	8440											
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	38709565	38709565	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattggaacactggaaacgcAtgtcagccaagttcaactat	15	9	8	9	1	2	0	2	0	0	0	2	2	2	2	1	2	4	2	1	2	6	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:38709565A>G	ENST00000359357.3	+	6	798	c.544A>G	c.(544-546)Atg>Gtg	p.M182V	RN7SL465P_ENST00000468411.2_RNA|DNAH8_ENST00000441566.1_Missense_Mutation_p.M182V|DNAH8_ENST00000449981.2_Missense_Mutation_p.M399V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	182					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CTGGAAACGCATGTCAGCCAA	0.398																																					p.M399V		.											.	DNAH8-615	0			c.A1195G						.						121	105	110					6																	38709565		2203	4300	6503	SO:0001583	missense	1769	exon8			AAACGCATGTCAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.544A>G	6.37:g.38709565A>G	ENSP00000352312:p.Met182Val	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	77	27	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	16.47	3.131132	0.56828	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.56611	0.45;0.45;0.45	5.91	5.91	0.95273	Dynein heavy chain, domain-1 (1);	0.047100	0.85682	D	0.000000	T	0.36276	0.0961	L	0.29908	0.895	0.40827	D	0.983553	B	0.27765	0.188	B	0.36608	0.229	T	0.42965	-0.9420	10	0.66056	D	0.02	.	16.3429	0.83101	1.0:0.0:0.0:0.0	.	182	Q96JB1	DYH8_HUMAN	V	387;387;182;182	ENSP00000333363:M387V;ENSP00000352312:M182V;ENSP00000402294:M182V	ENSP00000333363:M387V	M	+	1	0	DNAH8	38817543	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.248000	0.72418	2.256000	0.74724	0.523000	0.50628	ATG	.		0.398	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38709565	A	G	38709565	3	3	94	1	0	0	0	0	1	0	0	0	4618	217	8	3	558	3	DNAH8	6	38709565	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	3448907	38709565	132405502	30	8441											
UBR2	23304	broad.mit.edu	37	chr6	42610219	42610220	+	Splice_Site	INS	-	-	GTAAT																															aggatgtagtaatgcttcagINSgtaatgaattaaaagcattg																										TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:42610219_42610220insGTAAT	ENST00000372899.1	+	18	2355	c.2097_2097insGTAAT	c.(2098-2100)aca>acGTAATa	p.-700fs	UBR2_ENST00000372901.1_Splice_Site_p.-700fs|UBR2_ENST00000372883.3_Splice_Site_p.-204fs	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2						cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TAATGCTTCAGGTAATGAATTA	0.312																																					p.Q699fs													.	UBR2-94	0			c.2097_2098insGTAAT						.																																			SO:0001630	splice_region_variant	23304	exon18			GCTTCAGGTAATG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.2097+1->GTAAT	6.37:g.42610220_42610224dupGTAAT		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	37	7	NM_015255	0	0	0	0	0	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Frame_Shift_Ins	INS	ENST00000372899.1	37	CCDS4870.1																																																																																			.		0.312	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	Frame_Shift_Ins	GTAAT	42610220	-	GTAAT	42610219	8	5	94	1	0	1	1	0	0	0	1	0	16935	1014	35	0	2313	0	UBR2	6	42610219	Splice_Site	INS	-	TCGA-DW-7834-01A-11D-2136-08	3900654	42610219	128504848	31	8442											
RUNX2	860	hgsc.bcm.edu;broad.mit.edu	37	chr6	45390466	45390466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcagcagcagcagcagcaAcagcagcagcagcagcagga	15	0	13	13	0	0	0	0	0	0	0	0	1	0	1	0	1	12	11	0	1	1	0	rs575896136	byFrequency	TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:45390466A>G	ENST00000371438.1	+	2	553	c.195A>G	c.(193-195)caA>caG	p.Q65Q	RUNX2_ENST00000359524.5_Silent_p.Q51Q|RUNX2_ENST00000465038.2_Silent_p.Q65Q|RUNX2_ENST00000576263.1_Silent_p.Q65Q|RUNX2_ENST00000352853.5_Silent_p.Q133Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Silent_p.Q65Q|RUNX2_ENST00000541979.1_Silent_p.Q133Q|RUNX2_ENST00000371432.3_Silent_p.Q51Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	65	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	8	0.00159744	0.0023	0	5008	,	,		7675	0.002		0	False		,,,				2504	0.0031				p.Q65Q		.											.	RUNX2-417	0			c.A195G						.						10	15	14					6																	45390466		1452	3071	4523	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.195A>G	6.37:g.45390466A>G		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	32	3	NM_001024630	6	1	73	8081	8001	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	CCDS43467.2																																																																																			.		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390466	A	G	45390466	2	3	94	1	0	0	0	0	0	0	0	1	13780	40	2	3		3	RUNX2	6	45390466	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08	2780247	45390466	125724601	32	8443											
BAI3	577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	69943243	69943243	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgcttaccgatgcatccCatacgaaatgcttatgtgat	10	13	8	10	2	0	1	0	1	0	0	1	3	1	1	2	0	5	3	2	0	4	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:69943243C>T	ENST00000370598.1	+	18	3363	c.2542C>T	c.(2542-2544)Cat>Tat	p.H848Y	BAI3_ENST00000238918.8_Missense_Mutation_p.H54Y	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	848	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CGATGCATCCCATACGAAATG	0.473																																					p.H848Y		.											.	BAI3-1148	0			c.C2542T						.						203	180	188					6																	69943243		2203	4300	6503	SO:0001583	missense	577	exon18			GCATCCCATACGA	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"-", "GPCR / Class B : Orphans"	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2542C>T	6.37:g.69943243C>T	ENSP00000359630:p.His848Tyr	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	215	68	NM_001704	0	0	0	0	0	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946496	0.53186	.	.	ENSG00000135298	ENST00000370598;ENST00000238918	T;T	0.69175	-0.38;-0.38	5.37	5.37	0.77165	GPS domain (3);	0.000000	0.85682	D	0.000000	T	0.75953	0.3920	L	0.54863	1.705	0.80722	D	1	D;D	0.89917	0.982;1.0	P;D	0.87578	0.824;0.998	T	0.77230	-0.2664	10	0.62326	D	0.03	.	19.1872	0.93648	0.0:1.0:0.0:0.0	.	54;848	B7Z356;O60242	.;BAI3_HUMAN	Y	848;54	ENSP00000359630:H848Y;ENSP00000238918:H54Y	ENSP00000238918:H54Y	H	+	1	0	BAI3	69999964	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.889000	0.69766	2.539000	0.85634	0.454000	0.30748	CAT	.		0.473	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	69943243	C	T	69943243	3	4	94	1	0	0	0	0	1	0	0	0	1301	594	21	2	2604	2	BAI3	6	69943243	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	24552777	69943243	101171824	33	8444											
RFX6	222546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	117245902	117245902	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggagacccagtttaataaTgacaaagagcaggagttaca	17	8	10	6	0	0	3	0	1	0	2	0	5	0	4	1	2	2	3	1	2	4	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:117245902T>A	ENST00000332958.2	+	15	1642	c.1626T>A	c.(1624-1626)aaT>aaA	p.N542K		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	542					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AGTTTAATAATGACAAAGAGC	0.338																																					p.N542K		.											.	RFX6-93	0			c.T1626A						.						100	99	99					6																	117245902		2203	4300	6503	SO:0001583	missense	222546	exon15			TAATAATGACAAA	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1626T>A	6.37:g.117245902T>A	ENSP00000332208:p.Asn542Lys	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	92	20	NM_173560	0	0	0	0	0	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521372	0.64747	.	.	ENSG00000185002	ENST00000332958	T	0.57107	0.42	5.32	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.46229	0.1382	L	0.49640	1.575	0.53688	D	0.999972	D	0.59357	0.985	P	0.53360	0.724	T	0.50508	-0.8820	10	0.56958	D	0.05	-21.9444	10.8185	0.46591	0.0:0.0743:0.0:0.9257	.	542	Q8HWS3	RFX6_HUMAN	K	542	ENSP00000332208:N542K	ENSP00000332208:N542K	N	+	3	2	RFX6	117352595	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.890000	0.39728	2.138000	0.66242	0.533000	0.62120	AAT	.		0.338	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117245902	T	A	117245902	3	1	94	1	0	0	0	0	1	0	0	0	13299	1461	51	5	1684	5	RFX6	6	117245902	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	47302659	117245902	53869165	34	8445											
AEBP1	165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44152208	44152208	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatggagaagaaccccttcGtgctgggagcaaatctgaac	12	7	13	9	1	1	3	0	1	1	2	2	6	1	5	2	3	4	2	2	3	4	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:44152208G>C	ENST00000223357.3	+	18	2574	c.2269G>C	c.(2269-2271)Gtg>Ctg	p.V757L	AEBP1_ENST00000450684.2_Missense_Mutation_p.V332L|MIR4649_ENST00000582839.1_RNA	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	757	Interaction with PTEN. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						GAACCCCTTCGTGCTGGGAGC	0.642																																					p.V757L		.											.	AEBP1-90	0			c.G2269C						.						48	52	51					7																	44152208		2203	4299	6502	SO:0001583	missense	165	exon18			CCCTTCGTGCTGG	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.2269G>C	7.37:g.44152208G>C	ENSP00000223357:p.Val757Leu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	151	40	NM_001129	0	0	101	145	44	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	G	32	5.147205	0.94603	.	.	ENSG00000106624	ENST00000223357;ENST00000450684	T;T	0.03524	3.9;3.9	5.08	5.08	0.68730	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	M	0.83953	2.67	0.80722	D	1	D;P	0.76494	0.999;0.887	D;P	0.81914	0.995;0.796	T	0.00473	-1.1718	10	0.62326	D	0.03	-39.5208	17.5863	0.87982	0.0:0.0:1.0:0.0	.	332;757	Q8IUX7-2;Q8IUX7	.;AEBP1_HUMAN	L	757;332	ENSP00000223357:V757L;ENSP00000398878:V332L	ENSP00000223357:V757L	V	+	1	0	AEBP1	44118733	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.597000	0.74118	2.533000	0.85409	0.491000	0.48974	GTG	.		0.642	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		C	44152208	G	C	44152208	3	2	94	1	0	0	0	0	1	0	0	0	349	1145	40	4	2339	4	AEBP1	7	44152208	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		44152208	114986455	35	8446											
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44714122	44714122	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgacaagtctagtgagaatGgcgtggactacgtgatcatg	11	11	13	6	2	2	3	1	3	1	1	2	5	2	4	0	2	1	0	0	2	4	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:44714122G>A	ENST00000222673.5	+	7	943	c.901G>A	c.(901-903)Ggc>Agc	p.G301S	OGDH_ENST00000459672.1_3'UTR|OGDH_ENST00000444676.1_Missense_Mutation_p.G316S|OGDH_ENST00000443864.2_Missense_Mutation_p.G301S|OGDH_ENST00000449767.1_Missense_Mutation_p.G297S|OGDH_ENST00000439616.2_Missense_Mutation_p.G151S|OGDH_ENST00000447398.1_Missense_Mutation_p.G312S|OGDH_ENST00000543843.1_Missense_Mutation_p.G252S	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	301					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	TAGTGAGAATGGCGTGGACTA	0.572																																					p.G301S		.											.	OGDH-228	0			c.G901A						.						136	110	119					7																	44714122		2203	4300	6503	SO:0001583	missense	4967	exon7			GAGAATGGCGTGG	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.901G>A	7.37:g.44714122G>A	ENSP00000222673:p.Gly301Ser	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	126	55	NM_002541	0	0	21	29	8	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996894	0.93167	.	.	ENSG00000105953	ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	D;T;D;D;D;D;D	0.95788	-3.81;2.48;-3.81;-3.81;-3.81;-3.81;-3.81	4.97	4.97	0.65823	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.98061	0.9361	M	0.88570	2.965	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.998;0.998;0.998;0.998;0.999	D;D;D;D;D;D;D	0.87578	0.995;0.996;0.995;0.996;0.992;0.995;0.998	D	0.99091	1.0840	10	0.87932	D	0	-17.2819	18.1993	0.89833	0.0:0.0:1.0:0.0	.	96;151;297;312;203;301;301	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3	.;.;.;.;.;ODO1_HUMAN;.	S	151;301;297;312;316;301;252	ENSP00000398576:G151S;ENSP00000388084:G301S;ENSP00000392878:G297S;ENSP00000388183:G312S;ENSP00000414662:G316S;ENSP00000222673:G301S;ENSP00000443821:G252S	ENSP00000222673:G301S	G	+	1	0	OGDH	44680647	1.000000	0.71417	0.169000	0.22859	0.771000	0.43674	9.609000	0.98334	2.462000	0.83206	0.561000	0.74099	GGC	.		0.572	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			A	44714122	G	A	44714122	3	1	94	1	0	0	0	0	1	0	0	0	10865	1348	47	2	1018	2	OGDH	7	44714122	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	561914	44714122	114424541	36	8447											
VSTM2A	222008	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	54617692	54617692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaatgccaacagccatgccCgcagaatgcaggccttcgaa	12	6	9	14	2	1	1	1	0	0	1	2	2	1	1	4	1	5	2	4	1	4	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:54617692C>T	ENST00000407838.3	+	4	869	c.463C>T	c.(463-465)Cgc>Tgc	p.R155C	VSTM2A_ENST00000302287.3_Missense_Mutation_p.R155C|VSTM2A_ENST00000402026.2_Missense_Mutation_p.R154C|VSTM2A_ENST00000404951.1_Missense_Mutation_p.R155C|VSTM2A_ENST00000498834.1_3'UTR|VSTM2A_ENST00000402613.3_Missense_Mutation_p.R155C	NM_182546.2	NP_872352.2	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2A	155						extracellular region (GO:0005576)		p.R155C(1)|p.R154C(1)		endometrium(1)|large_intestine(2)|lung(12)|prostate(1)	16			STAD - Stomach adenocarcinoma(5;0.0525)			CAGCCATGCCCGCAGAATGCA	0.577																																					p.R155C		.											.	.	2	Substitution - Missense(2)	endometrium(2)	c.C463T						.						57	54	55					7																	54617692		2203	4299	6502	SO:0001583	missense	222008	exon4			CATGCCCGCAGAA	BC028404	CCDS5512.2, CCDS75604.1	7p11.2	2013-01-11	2007-08-10	2007-08-10	ENSG00000170419	ENSG00000170419		"Immunoglobulin superfamily / V-set domain containing"	28499	protein-coding gene	gene with protein product			"V-set and transmembrane domain containing 2"	VSTM2		12477932	Standard	XM_006715663		Approved	MGC33530	uc010kzf.3	Q8TAG5	OTTHUMG00000129271	ENST00000407838.3:c.463C>T	7.37:g.54617692C>T	ENSP00000384967:p.Arg155Cys	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	32	13	NM_182546	0	0	2	11	9	A4D2E9|B5MC94	Missense_Mutation	SNP	ENST00000407838.3	37	CCDS5512.2	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950503	0.73787	.	.	ENSG00000170419	ENST00000302287;ENST00000407838;ENST00000404951;ENST00000402026;ENST00000402613	T;T;T;T;T	0.50277	0.75;0.78;0.75;0.75;0.78	5.06	3.17	0.36434	.	0.000000	0.85682	D	0.000000	T	0.64080	0.2566	M	0.68952	2.095	0.52501	D	0.999954	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.993	T	0.63440	-0.6637	10	0.51188	T	0.08	-25.8697	11.9552	0.52976	0.334:0.666:0.0:0.0	.	155;155;155	Q8TAG5;Q8TAG5-2;B5MCX6	VTM2A_HUMAN;.;.	C	155;155;155;154;155	ENSP00000303108:R155C;ENSP00000384967:R155C;ENSP00000384701:R155C;ENSP00000385933:R154C;ENSP00000384103:R155C	ENSP00000303108:R155C	R	+	1	0	VSTM2A	54585186	0.357000	0.24938	0.524000	0.27887	0.981000	0.71138	0.571000	0.23669	0.566000	0.29273	0.655000	0.94253	CGC	.		0.577	VSTM2A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318694.1	NM_182546		T	54617692	C	T	54617692	3	4	94	1	0	0	0	0	1	0	0	0	17262	652	23	1	477	1	VSTM2A	7	54617692	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	9903570	54617692	104520971	37	8448											
FEZF1	389549	broad.mit.edu	37	chr7	121944146	121944146	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgagcaggtcgctgcagcTgaatgcgggagccgagggca	8	6	18	9	3	0	2	0	2	0	0	1	4	0	3	1	3	5	6	1	3	1	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:121944146T>G	ENST00000442488.2	-	1	413	c.346A>C	c.(346-348)Agc>Cgc	p.S116R	FEZF1-AS1_ENST00000428449.1_RNA|FEZF1_ENST00000427185.2_Missense_Mutation_p.S116R|FEZF1_ENST00000331178.4_Missense_Mutation_p.S116R|FEZF1-AS1_ENST00000424404.1_RNA|FEZF1-AS1_ENST00000437317.1_RNA	NM_001024613.2|NM_001160264.1	NP_001019784.2|NP_001153736.1	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1	116					axon guidance (GO:0007411)|forebrain anterior/posterior pattern specification (GO:0021797)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)			breast(1)|large_intestine(3)|lung(18)|ovary(2)|prostate(1)	25						TCGCTGCAGCTGAATGCGGGA	0.716																																					p.S116R													.	FEZF1-91	0			c.A346C						.						8	9	8					7																	121944146		2170	4215	6385	SO:0001583	missense	389549	exon1			TGCAGCTGAATGC	AY726588	CCDS34741.1, CCDS34741.2, CCDS55157.1	7q31.32	2013-01-08	2006-08-15	2006-08-15	ENSG00000128610	ENSG00000128610		"Zinc fingers, C2H2-type"	22788	protein-coding gene	gene with protein product		613301	"zinc finger protein 312B"	ZNF312B			Standard	NM_001024613		Approved		uc003vkd.3	A0PJY2	OTTHUMG00000157091	ENST00000442488.2:c.346A>C	7.37:g.121944146T>G	ENSP00000411145:p.Ser116Arg	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	13	3	NM_001160264	0	0	0	0	0	A0PJY3|A4D0W3|B4DUP9|B7ZM98	Missense_Mutation	SNP	ENST00000442488.2	37	CCDS34741.2	.	.	.	.	.	.	.	.	.	.	T	12.47	1.946839	0.34377	.	.	ENSG00000128610	ENST00000442488;ENST00000331178;ENST00000427185	T;T;T	0.07567	3.25;3.39;3.18	4.65	4.65	0.58169	.	0.048448	0.85682	D	0.000000	T	0.15478	0.0373	L	0.43152	1.355	0.35688	D	0.814606	D;D	0.64830	0.989;0.994	P;P	0.53912	0.55;0.737	T	0.09818	-1.0657	10	0.49607	T	0.09	-24.3744	14.5205	0.67847	0.0:0.0:0.0:1.0	.	116;116	A0PJY2;A0PJY2-2	FEZF1_HUMAN;.	R	116	ENSP00000411145:S116R;ENSP00000332777:S116R;ENSP00000392727:S116R	ENSP00000332777:S116R	S	-	1	0	FEZF1	121731382	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	3.295000	0.51794	2.069000	0.61940	0.454000	0.30748	AGC	.		0.716	FEZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347410.1	NM_001024613		G	121944146	T	G	121944146	3	3	94	1	0	0	0	0	1	0	0	0	5844	1580	55	5	1097	5	FEZF1	7	121944146	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	67326454	121944146	37194517	38	8449											
LUC7L2	100996928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	139107032	139107032	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtcctatgagagtgctaaTggcagatcagaagacaggag	13	7	14	7	1	1	4	1	1	0	4	2	6	2	5	1	3	1	2	1	3	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:139107032T>A	ENST00000354926.4	+	10	1479	c.1125T>A	c.(1123-1125)aaT>aaA	p.N375K	C7orf55-LUC7L2_ENST00000541170.3_Missense_Mutation_p.N372K|C7orf55-LUC7L2_ENST00000482860.1_3'UTR|LUC7L2_ENST00000541515.3_Missense_Mutation_p.N441K|C7orf55-LUC7L2_ENST00000263545.6_Missense_Mutation_p.N374K	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AGAGTGCTAATGGCAGATCAG	0.478																																					p.N441K		.											.	.	0			c.T1323A						.						133	136	135					7																	139107032		1945	4137	6082	SO:0001583	missense	100996928	exon11			TGCTAATGGCAGA		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.1125T>A	7.37:g.139107032T>A	ENSP00000347005:p.Asn375Lys	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	200	102	NM_001244584	0	0	30	65	35		Missense_Mutation	SNP	ENST00000354926.4	37	CCDS43656.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.880250	0.51801	.	.	ENSG00000146963	ENST00000541170;ENST00000541515;ENST00000545899;ENST00000354926;ENST00000263545	T;T;T;T	0.41400	1.59;1.59;1.59;1.0	6.03	3.72	0.42706	.	0.255682	0.45126	D	0.000400	T	0.33702	0.0872	L	0.58810	1.83	0.42902	D	0.994235	P;P;P;P	0.40731	0.608;0.608;0.728;0.608	B;B;B;B	0.36186	0.109;0.109;0.219;0.109	T	0.46898	-0.9158	9	0.23891	T	0.37	-21.4412	8.941	0.35729	0.0:0.2436:0.0:0.7564	.	441;372;374;375	B7Z4Q3;B7Z500;Q9Y383-2;Q9Y383	.;.;.;LC7L2_HUMAN	K	372;441;375;375;374	ENSP00000441604:N372K;ENSP00000440222:N441K;ENSP00000347005:N375K;ENSP00000263545:N374K	ENSP00000263545:N374K	N	+	3	2	LUC7L2	138757572	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.312000	0.19397	1.117000	0.41842	0.455000	0.32223	AAT	.		0.478	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			A	139107032	T	A	139107032	3	1	94	1	0	0	0	0	1	0	0	0	9108	1461	51	5	1163	5	LUC7L2	7	139107032	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	17162886	139107032	20031631	39	8450											
PRSS55	203074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	10390473	10390473	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccaatggtcatcatggactGggaggagtgttcaaagatgt	11	10	14	6	0	3	1	3	0	0	1	3	4	3	4	1	4	0	1	1	4	2	1	rs150767306		TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr8:10390473G>A	ENST00000328655.3	+	4	696	c.656G>A	c.(655-657)tGg>tAg	p.W219*	PRSS55_ENST00000522210.1_Nonsense_Mutation_p.W219*|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	219	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						ATCATGGACTGGGAGGAGTGT	0.473																																					p.W219X		.											.	PRSS55-91	0			c.G656A						.						124	112	116					8																	10390473		2203	4300	6503	SO:0001587	stop_gained	203074	exon4			TGGACTGGGAGGA	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.656G>A	8.37:g.10390473G>A	ENSP00000333003:p.Trp219*	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	95	34	NM_001197020	0	0	0	0	0	E5RJX5	Nonsense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820578	0.71028	.	.	ENSG00000184647	ENST00000328655;ENST00000522210	.	.	.	5.27	4.39	0.52855	.	0.259915	0.20629	N	0.088631	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	10.0857	0.42417	0.094:0.0:0.906:0.0	.	.	.	.	X	219	.	ENSP00000333003:W219X	W	+	2	0	PRSS55	10427883	0.948000	0.32251	0.056000	0.19401	0.063000	0.16089	1.788000	0.38714	1.344000	0.45657	0.591000	0.81541	TGG	G|1.000;T|0.000		0.473	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10390473	G	A	10390473	4	1	94	1	0	0	0	0	0	1	0	0	12663	1357	47	2	670	2	PRSS55	8	10390473	Nonsense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		10390473	135973549	40	8451											
C8orf80	389643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	27888815	27888815	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atttccagccacttcttatcCcaatttctgtcattttctcc	7	18	2	14	0	4	0	1	0	3	0	7	0	6	0	4	0	1	0	4	0	2	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr8:27888815C>G	ENST00000413272.2	-	15	1995	c.1853G>C	c.(1852-1854)gGg>gCg	p.G618A	NUGGC_ENST00000341513.6_Missense_Mutation_p.G618A	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	618					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										ACTTCTTATCCCAATTTCTGT	0.468																																					p.G618A		.											.	.	0			c.G1853C						.						139	140	140					8																	27888815		1863	4103	5966	SO:0001583	missense	389643	exon15			CTTATCCCAATTT	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"speckled-like pattern in the germinal center"		"chromosome 8 open reading frame 80"	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1853G>C	8.37:g.27888815C>G	ENSP00000408697:p.Gly618Ala	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	192	49	NM_001010906	0	0	0	0	0	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333721	0.24167	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.32753	1.44;1.44	5.23	4.26	0.50523	.	0.580298	0.17797	N	0.161690	T	0.18002	0.0432	L	0.27053	0.805	0.09310	N	1	B	0.27229	0.172	B	0.22386	0.039	T	0.14309	-1.0477	10	0.06625	T	0.88	-16.0958	11.7736	0.51972	0.1875:0.8125:0.0:0.0	.	618	Q68CJ6	SLIP_HUMAN	A	618	ENSP00000408697:G618A;ENSP00000345031:G618A	ENSP00000345031:G618A	G	-	2	0	C8orf80	27944734	0.006000	0.16342	0.846000	0.33378	0.810000	0.45777	1.525000	0.35953	2.441000	0.82636	0.655000	0.94253	GGG	.		0.468	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		G	27888815	C	G	27888815	3	3	94	1	0	0	0	0	1	0	0	0	2445	623	22	4	557	4	C8orf80	8	27888815	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	17498342	27888815	118475207	41	8452											
NR5A1	2516	hgsc.bcm.edu	37	chr9	127262609	127262609	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagggctctgggtagccgtaCggcagcccaggctgtggggg	6	6	19	10	2	1	0	0	0	1	0	1	0	1	0	2	6	3	5	2	6	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr9:127262609C>A	ENST00000373588.4	-	4	826	c.630G>T	c.(628-630)ccG>ccT	p.P210P		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	210					adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						GGTAGCCGTACGGCAGCCCAG	0.667																																					p.P210P		.											.	NR5A1-186	0			c.G630T						.						5	6	6					9																	127262609		2112	4146	6258	SO:0001819	synonymous_variant	2516	exon4			GCCGTACGGCAGC	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"Nuclear hormone receptors"	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.630G>T	9.37:g.127262609C>A		Somatic	6	2		WXS	Illumina HiSeq	Phase_I	9	5	NM_004959	0	0	0	0	0	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			.		0.667	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		A	127262609	C	A	127262609	2	1	94	1	0	0	0	0	0	0	0	1	10661	523	19	4		4	NR5A1	9	127262609	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08		127262609	13950822	42	8453											
PCDH15	65217	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	55570392	55570392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtccagctggtggtaacaatCgacggcgactcccatattga	10	9	11	11	3	0	1	0	1	0	0	3	3	2	1	2	3	2	2	2	3	3	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr10:55570392C>T	ENST00000373965.2	-	35	4821	c.4427G>A	c.(4426-4428)cGa>cAa	p.R1476Q	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.R1476Q|PCDH15_ENST00000409834.1_Missense_Mutation_p.D1104N|PCDH15_ENST00000414778.1_Missense_Mutation_p.R1473Q|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.D1493N	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	0					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TGGTAACAATCGACGGCGACT	0.393										HNSCC(58;0.16)																											.													.	PCDH15-193	0			.						.						174	160	164					10																	55570392		1568	3582	5150	SO:0001583	missense	65217	.			AACAATCGACGGC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000373965.2:c.4427G>A	10.37:g.55570392C>T	ENSP00000363076:p.Arg1476Gln	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	210	58	.	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000373965.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.144084|5.144084	0.94603|0.94603	.|.	.|.	ENSG00000150275|ENSG00000150275	ENST00000395438;ENST00000409834|ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395445	T;T|T;T;T	0.58940|0.65916	0.33;0.3|0.11;0.23;-0.18	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	.|.	.|.	.|.	.|.	T|T	0.69940|0.69940	0.3167|0.3167	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	B|D;D;D;B	0.32128|0.76494	0.357|0.999;0.999;0.992;0.308	B|P;P;P;B	0.15870|0.58970	0.014|0.849;0.849;0.644;0.051	T|T	0.63928|0.63928	-0.6526|-0.6526	9|9	0.20519|0.32370	T|T	0.43|0.25	.|.	19.6313|19.6313	0.95704|0.95704	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1493|1474;1476;1467;1473	A2A3E3|C6ZEF5;A2A3E2;C6ZEF7;C9J4F3	.|.;.;.;.	N|Q	1493;1104|1476;1473;1469;1476	ENSP00000378826:D1493N;ENSP00000386693:D1104N|ENSP00000363076:R1476Q;ENSP00000410304:R1473Q;ENSP00000378832:R1476Q	ENSP00000378826:D1493N|ENSP00000363076:R1476Q	D|R	-|-	1|2	0|0	PCDH15|PCDH15	55240398|55240398	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.984000|0.984000	0.73092|0.73092	4.761000|4.761000	0.62243|0.62243	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GAT|CGA	.		0.393	PCDH15-008	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000291336.1	NM_033056		T	55570392	C	T	55570392	3	4	94	1	0	0	0	0	1	0	0	0	11537	884	31	1	1493	1	PCDH15	10	55570392	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		55570392	79964355	43	8454											
KIF20B	9585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	91498338	91498338	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatttacttcaattaaaagAagaagaagaagaaaccaaca	23	7	5	6	0	1	5	1	0	0	5	1	5	1	5	1	0	3	0	1	0	10	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr10:91498338A>C	ENST00000371728.3	+	20	3805	c.3740A>C	c.(3739-3741)gAa>gCa	p.E1247A	KIF20B_ENST00000416354.1_Missense_Mutation_p.E1277A|KIF20B_ENST00000394289.2_Missense_Mutation_p.E1247A|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.E1207A	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1247	Poly-Glu.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						CAATTAAAAGAAGAAGAAGAA	0.279																																					p.E1207A		.											.	KIF20B-93	0			c.A3620C						.						33	35	34					10																	91498338		2006	4193	6199	SO:0001583	missense	9585	exon20			TAAAAGAAGAAGA	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"cancer/testis antigen 90"	605498	"M-phase phosphoprotein 1"	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3740A>C	10.37:g.91498338A>C	ENSP00000360793:p.Glu1247Ala	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	59	23	NM_016195	0	0	0	0	0	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	A	12.72	2.021492	0.35701	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.71341	-0.46;-0.48;-0.56;-0.48	5.82	4.62	0.57501	.	0.125962	0.36167	N	0.002752	T	0.65375	0.2685	M	0.62723	1.935	0.32524	N	0.535885	P;P	0.52316	0.919;0.952	B;B	0.43916	0.253;0.436	T	0.75419	-0.3324	10	0.56958	D	0.05	-24.2326	5.4057	0.16320	0.6693:0.0:0.073:0.2577	.	1247;1207	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	A	1207;1277;1247;1247	ENSP00000260753:E1207A;ENSP00000411545:E1277A;ENSP00000377830:E1247A;ENSP00000360793:E1247A	ENSP00000260753:E1207A	E	+	2	0	KIF20B	91488318	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	4.090000	0.57693	2.222000	0.72286	0.383000	0.25322	GAA	.		0.279	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		C	91498338	A	C	91498338	3	2	94	1	0	0	0	0	1	0	0	0	8308	246	9	5	3694	5	KIF20B	10	91498338	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	35927946	91498338	44036409	44	8455											
TRIM8	81603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104404881	104404881	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtgccagtactgctgctaCtacagcggcgcgcatcaggg	7	8	14	12	3	1	0	1	0	0	0	1	0	1	0	1	2	7	4	1	2	3	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr10:104404881C>T	ENST00000302424.7	+	1	629	c.507C>T	c.(505-507)taC>taT	p.Y169Y	RP11-47A8.5_ENST00000607967.1_lincRNA	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	169					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		ACTGCTGCTACTACAGCGGCG	0.662																																					p.Y169Y		.											.	TRIM8-227	0			c.C507T						.						14	15	15					10																	104404881		1665	3276	4941	SO:0001819	synonymous_variant	81603	exon1			CTGCTACTACAGC	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.507C>T	10.37:g.104404881C>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	46	9	NM_030912	0	0	34	53	19	A6NI31|Q9C028	Silent	SNP	ENST00000302424.7	37	CCDS31274.1																																																																																			.		0.662	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		T	104404881	C	T	104404881	2	4	94	1	0	0	0	0	0	0	0	1	16581	576	20	2		2	TRIM8	10	104404881	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	12906543	104404881	31129866	45	8456											
PTPRJ	5795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	48149503	48149503	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgagcctcgcgctgtcatccCcggactccgctccagcacct	5	8	9	19	4	1	1	1	1	0	0	5	2	4	2	6	1	2	3	6	1	0	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr11:48149503C>T	ENST00000418331.2	+	7	1617	c.1265C>T	c.(1264-1266)cCc>cTc	p.P422L	PTPRJ_ENST00000440289.2_Missense_Mutation_p.P422L	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	422	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCTGTCATCCCCGGACTCCGC	0.552																																					p.P422L		.											.	PTPRJ-541	0			c.C1265T						.						137	112	121					11																	48149503		2201	4298	6499	SO:0001583	missense	5795	exon7			TCATCCCCGGACT	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1265C>T	11.37:g.48149503C>T	ENSP00000400010:p.Pro422Leu	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	124	42	NM_001098503	0	0	3	4	1	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329627	0.24167	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.57752	0.38;0.38	6.17	-3.83	0.04269	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.18635	0.0447	N	0.01352	-0.895	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.004	T	0.18272	-1.0342	9	0.25106	T	0.35	.	6.2032	0.20587	0.0:0.2896:0.327:0.3835	.	422;422	Q12913;Q6P4H4	PTPRJ_HUMAN;.	L	422	ENSP00000400010:P422L;ENSP00000409733:P422L	ENSP00000278456:P422L	P	+	2	0	PTPRJ	48106079	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.846000	0.04336	-1.113000	0.02981	-0.751000	0.03497	CCC	.		0.552	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			T	48149503	C	T	48149503	3	4	94	1	0	0	0	0	1	0	0	0	12836	623	22	2	1291	2	PTPRJ	11	48149503	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		48149503	86857013	46	8457											
NAALADL1	10004	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr11	64822081	64822081	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctcgtagtaggagcctcgctCcactcctgaggggggcaggt	6	8	15	12	2	0	1	0	1	0	0	4	2	2	2	3	5	1	4	3	5	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr11:64822081C>T	ENST00000358658.3	-	5	760	c.733G>A	c.(733-735)Gag>Aag	p.E245K	NAALADL1_ENST00000355369.2_Missense_Mutation_p.E245K|NAALADL1_ENST00000340252.4_Missense_Mutation_p.E245K|NAALADL1_ENST00000355721.3_Missense_Mutation_p.E204K|NAALADL1_ENST00000356632.3_Missense_Mutation_p.E245K|NAALADL1_ENST00000339885.2_Missense_Mutation_p.E245K	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GAGCCTCGCTCCACTCCTGAG	0.597											OREG0032001	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																									p.E245K		.											.	NAALADL1-90	0			c.G733A						.						56	55	55					11																	64822081		2201	4297	6498	SO:0001583	missense	10004	exon5			CTCGCTCCACTCC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.733G>A	11.37:g.64822081C>T	ENSP00000351484:p.Glu245Lys	Somatic	39	0	1079	WXS	Illumina HiSeq	Phase_I	35	8	NM_005468	0	0	0	0	0	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	37	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798953	0.90538	.	.	ENSG00000168060	ENST00000358658;ENST00000355369;ENST00000339885;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	4.7	3.78	0.43462	.	0.000000	0.85682	D	0.000000	T	0.60508	0.2274	M	0.81802	2.56	0.50632	D	0.999881	P	0.51240	0.943	P	0.57720	0.826	T	0.66842	-0.5821	10	0.87932	D	0	-32.0749	12.6604	0.56811	0.0:0.8326:0.1674:0.0	.	245	Q9UQQ1	NALDL_HUMAN	K	245;245;245;245;245;204;245	ENSP00000351484:E245K;ENSP00000347530:E245K;ENSP00000340111:E245K;ENSP00000344244:E245K;ENSP00000347955:E204K;ENSP00000349045:E245K	ENSP00000340111:E245K	E	-	1	0	NAALADL1	64578657	1.000000	0.71417	0.979000	0.43373	0.757000	0.42996	6.561000	0.73955	1.196000	0.43129	0.655000	0.94253	GAG	.		0.597	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		T	64822081	C	T	64822081	3	4	94	1	0	0	0	0	1	0	0	0	10154	864	30	2	1545	2	NAALADL1	11	64822081	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	16672578	64822081	70184435	47	8458											
IL10RA	3587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117860196	117860196	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aactccatctccaactgtagCcagaccctgtcctatgacct	10	10	5	16	0	1	2	0	1	1	1	4	2	3	2	6	0	3	1	6	0	4	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr11:117860196C>A	ENST00000227752.3	+	3	348	c.228C>A	c.(226-228)agC>agA	p.S76R	IL10RA_ENST00000541785.1_Missense_Mutation_p.S56R|IL10RA_ENST00000545409.1_Intron|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	76					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CCAACTGTAGCCAGACCCTGT	0.557																																					p.S76R		.											.	IL10RA-91	0			c.C228A						.						163	133	143					11																	117860196		2200	4296	6496	SO:0001583	missense	3587	exon3			CTGTAGCCAGACC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.228C>A	11.37:g.117860196C>A	ENSP00000227752:p.Ser76Arg	Somatic	167	1		WXS	Illumina HiSeq	Phase_I	140	50	NM_001558	0	0	7	7	0	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	C	8.842	0.942524	0.18281	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000536858	T;T	0.73575	-0.76;-0.76	5.14	1.03	0.20045	Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.091120	0.06723	N	0.775192	T	0.49490	0.1560	N	0.04018	-0.295	0.09310	N	1	B;B	0.13594	0.007;0.008	B;B	0.19391	0.009;0.025	T	0.33317	-0.9873	10	0.15499	T	0.54	-5.1363	5.495	0.16797	0.1338:0.3992:0.3907:0.0762	.	56;76	F5GYV8;Q13651	.;I10R1_HUMAN	R	76;56;56	ENSP00000227752:S76R;ENSP00000441397:S56R	ENSP00000227752:S76R	S	+	3	2	IL10RA	117365406	0.000000	0.05858	0.006000	0.13384	0.031000	0.12232	-0.257000	0.08745	0.004000	0.14682	-0.257000	0.10917	AGC	.		0.557	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			A	117860196	C	A	117860196	3	1	94	1	0	0	0	0	1	0	0	0	7641	738	26	4	238	4	IL10RA	11	117860196	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	53038115	117860196	17146320	48	8459											
DDX25	29118	hgsc.bcm.edu	37	chr11	125786980	125786980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtgtggcactttgctgAgcgaatcatccctgacccta	7	12	9	13	1	2	2	1	2	1	0	3	3	3	2	2	1	2	2	2	1	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr11:125786980A>G	ENST00000263576.6	+	9	1027	c.872A>G	c.(871-873)gAg>gGg	p.E291G	DDX25_ENST00000525943.1_3'UTR|RP11-680F20.9_ENST00000533033.2_RNA	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	291	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		CACTTTGCTGAGCGAATCATC	0.488																																					p.E291G		.											.	DDX25-227	0			c.A872G						.						99	98	98					11																	125786980		2087	4218	6305	SO:0001583	missense	29118	exon9			TTGCTGAGCGAAT	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"DEAD-boxes"	18698	protein-coding gene	gene with protein product	"gonadotropin-regulated testicular RNA helicase"	607663	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.872A>G	11.37:g.125786980A>G	ENSP00000263576:p.Glu291Gly	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_013264	0	0	0	0	0	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Missense_Mutation	SNP	ENST00000263576.6	37	CCDS44766.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.961278	0.34565	.	.	ENSG00000109832	ENST00000525943;ENST00000263576;ENST00000526875	T	0.04758	3.56	5.79	4.66	0.58398	DEAD-like helicase (2);	0.220031	0.38548	N	0.001645	T	0.05686	0.0149	L	0.41710	1.295	0.41607	D	0.988887	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.24154	-1.0168	10	0.51188	T	0.08	-0.0455	11.4559	0.50181	0.929:0.0:0.071:0.0	.	291;291	B4DHI6;Q9UHL0	.;DDX25_HUMAN	G	177;291;157	ENSP00000263576:E291G	ENSP00000263576:E291G	E	+	2	0	DDX25	125292190	1.000000	0.71417	0.998000	0.56505	0.803000	0.45373	3.983000	0.56916	1.020000	0.39573	0.533000	0.62120	GAG	.		0.488	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264		G	125786980	A	G	125786980	3	3	94	1	0	0	0	0	1	0	0	0	4358	304	11	3	906	3	DDX25	11	125786980	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	7926784	125786980	9219536	49	8460											
PZP	5858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	9356427	9356427	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagtgaagaggctcctgttTtccctgccagactccaagga	9	10	10	12	0	1	3	1	1	0	2	4	4	4	4	4	2	1	2	4	2	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr12:9356427T>A	ENST00000261336.2	-	2	232	c.204A>T	c.(202-204)gaA>gaT	p.E68D	PZP_ENST00000381997.2_5'Flank	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	68					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GGCTCCTGTTTTCCCTGCCAG	0.557																																					p.E68D	Melanoma(125;1402 1695 4685 34487 38571)	.											.	PZP-157	0			c.A204T						.						114	104	107					12																	9356427		2203	4300	6503	SO:0001583	missense	5858	exon2			CCTGTTTTCCCTG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.204A>T	12.37:g.9356427T>A	ENSP00000261336:p.Glu68Asp	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	154	51	NM_002864	0	0	0	0	0	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	0.086	-1.175971	0.01646	.	.	ENSG00000126838	ENST00000261336	T	0.08282	3.11	2.08	-0.306	0.12780	.	1.942830	0.04105	U	0.313539	T	0.10121	0.0248	M	0.70275	2.135	0.09310	N	1	B	0.22683	0.073	B	0.19946	0.027	T	0.42378	-0.9455	10	0.12766	T	0.61	.	4.2572	0.10722	0.0:0.3652:0.0:0.6348	.	68	P20742	PZP_HUMAN	D	68	ENSP00000261336:E68D	ENSP00000261336:E68D	E	-	3	2	PZP	9247694	0.000000	0.05858	0.002000	0.10522	0.396000	0.30629	-1.538000	0.02204	-0.076000	0.12775	0.383000	0.25322	GAA	.		0.557	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		A	9356427	T	A	9356427	3	1	94	1	0	0	0	0	1	0	0	0	12901	1838	64	5	4384	5	PZP	12	9356427	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		9356427	124495468	50	8461											
DNAJC22	79962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49743366	49743366	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatggagtttgtcctcctTctgccttaccggatctggag	5	14	10	12	1	3	0	1	0	2	0	5	3	5	3	4	3	2	1	4	3	1	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr12:49743366T>C	ENST00000549441.2	+	3	1915	c.711T>C	c.(709-711)ctT>ctC	p.L237L	DNAJC22_ENST00000395069.3_Silent_p.L237L			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	237						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						TTGTCCTCCTTCTGCCTTACC	0.532																																					p.L237L		.											.	DNAJC22-159	0			c.T711C						.						162	163	163					12																	49743366		2203	4300	6503	SO:0001819	synonymous_variant	79962	exon2			CCTCCTTCTGCCT	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.711T>C	12.37:g.49743366T>C		Somatic	307	0		WXS	Illumina HiSeq	Phase_I	277	87	NM_024902	0	0	13	28	15	B3KP54	Silent	SNP	ENST00000549441.2	37	CCDS8785.1																																																																																			.		0.532	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		C	49743366	T	C	49743366	2	2	94	1	0	0	0	0	0	0	0	1	4652	1770	62	3		3	DNAJC22	12	49743366	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08	40386939	49743366	84108529	51	8462											
CKAP2	26586	hgsc.bcm.edu	37	chr13	53042433	53042433	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctattgaagagatgcgacaCacgattgtagatattctaac	14	11	8	8	2	1	3	0	1	1	2	1	6	1	3	1	0	2	1	1	0	5	7			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr13:53042433C>G	ENST00000378037.5	+	7	1590	c.1500C>G	c.(1498-1500)caC>caG	p.H500Q	CKAP2_ENST00000490903.1_Missense_Mutation_p.H451Q|CKAP2_ENST00000258607.5_Missense_Mutation_p.H499Q	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		AGATGCGACACACGATTGTAG	0.299																																					p.H500Q		.											.	CKAP2-92	0			c.C1500G						.						96	99	98					13																	53042433		2203	4300	6503	SO:0001583	missense	26586	exon7			GCGACACACGATT	AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1500C>G	13.37:g.53042433C>G	ENSP00000367276:p.His500Gln	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_001098525	0	0	1	1	0		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	.	.	.	.	.	.	.	.	.	.	.	11.58	1.680018	0.29783	.	.	ENSG00000136108	ENST00000258607;ENST00000378037;ENST00000490903	T;T;T	0.23147	1.92;1.92;1.92	5.53	-0.86	0.10680	.	0.409080	0.25695	N	0.028903	T	0.24005	0.0581	M	0.78049	2.395	0.09310	N	1	B;B;B	0.30281	0.176;0.176;0.275	B;B;B	0.28916	0.046;0.046;0.096	T	0.17806	-1.0357	10	0.56958	D	0.05	-2.4737	5.1939	0.15225	0.0:0.4452:0.1743:0.3804	.	451;500;499	E9PD90;Q8WWK9;B2RMQ4	.;CKAP2_HUMAN;.	Q	499;500;451	ENSP00000258607:H499Q;ENSP00000367276:H500Q;ENSP00000417830:H451Q	ENSP00000258607:H499Q	H	+	3	2	CKAP2	51940434	0.005000	0.15991	0.036000	0.18154	0.942000	0.58702	-0.403000	0.07214	0.055000	0.16094	0.655000	0.94253	CAC	.		0.299	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2			G	53042433	C	G	53042433	3	3	94	1	0	0	0	0	1	0	0	0	3448	477	17	4	1526	4	CKAP2	13	53042433	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		53042433	62127445	52	8463											
GPR18	2841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99908051	99908051	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatacagctatagaagacaaGggctgcaattttgtattcat	14	12	9	6	0	1	2	1	0	0	2	1	3	1	2	0	1	3	4	0	1	7	7			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr13:99908051G>C	ENST00000340807.3	-	3	632	c.76C>G	c.(76-78)Ctt>Gtt	p.L26V	GPR18_ENST00000397470.2_Missense_Mutation_p.L26V|UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397473.2_Missense_Mutation_p.L26V|UBAC2_ENST00000376440.2_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	26					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	TAGAAGACAAGGGCTGCAATT	0.388																																					p.L26V		.											.	GPR18-90	0			c.C76G						.						131	130	131					13																	99908051		2203	4300	6503	SO:0001583	missense	2841	exon2			AGACAAGGGCTGC	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.76C>G	13.37:g.99908051G>C	ENSP00000343428:p.Leu26Val	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	140	31	NM_001098200	0	0	0	0	0	Q6GTM3|Q96HI6|Q9H2L2	Missense_Mutation	SNP	ENST00000340807.3	37	CCDS9491.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732792	0.48939	.	.	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807;ENST00000416594	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.95	5.08	0.68730	.	0.078514	0.52532	D	0.000062	T	0.20047	0.0482	N	0.08118	0	0.58432	D	0.999996	B	0.30605	0.287	B	0.25987	0.065	T	0.05451	-1.0884	9	.	.	.	-16.1138	16.3083	0.82859	0.0:0.0:0.8666:0.1334	.	26	Q14330	GPR18_HUMAN	V	26	ENSP00000380613:L26V;ENSP00000380610:L26V;ENSP00000343428:L26V;ENSP00000401611:L26V	.	L	-	1	0	GPR18	98706052	1.000000	0.71417	0.847000	0.33407	0.750000	0.42670	5.384000	0.66225	1.475000	0.48197	0.563000	0.77884	CTT	.		0.388	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			C	99908051	G	C	99908051	3	2	94	1	0	0	0	0	1	0	0	0	6695	1000	35	4	923	4	GPR18	13	99908051	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	46865618	99908051	15261827	53	8464											
SLC7A8	23428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23607203	23607203	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agaaatgggcatgatccaggCcatgactcctaggagcttct	11	9	11	10	0	1	3	0	2	1	1	3	4	3	4	3	3	1	2	3	3	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:23607203C>T	ENST00000316902.7	-	7	1668	c.943G>A	c.(943-945)Gcc>Acc	p.A315T	SLC7A8_ENST00000422941.2_Missense_Mutation_p.A91T|SLC7A8_ENST00000453702.1_Missense_Mutation_p.A112T|SLC7A8_ENST00000529705.2_Missense_Mutation_p.A210T|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000532568.1_5'Flank	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	315					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	ATGATCCAGGCCATGACTCCT	0.567																																					p.A315T		.											.	SLC7A8-91	0			c.G943A						.						112	104	107					14																	23607203		2203	4300	6503	SO:0001583	missense	23428	exon7			TCCAGGCCATGAC	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.943G>A	14.37:g.23607203C>T	ENSP00000320378:p.Ala315Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	113	26	NM_012244	0	0	2	2	0	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	37	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222325	0.58560	.	.	ENSG00000092068	ENST00000316902;ENST00000334354;ENST00000453702;ENST00000529705;ENST00000422941;ENST00000206514	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	5.44	4.54	0.55810	Amino acid permease domain (1);	0.306262	0.35772	N	0.002981	D	0.87815	0.6272	L	0.48877	1.53	0.49213	D	0.999763	B;B;B	0.28128	0.201;0.118;0.07	B;B;B	0.28305	0.088;0.088;0.038	D	0.86389	0.1734	10	0.72032	D	0.01	.	14.7754	0.69729	0.1459:0.8541:0.0:0.0	.	210;91;315	B4DKT4;B4DTV6;Q9UHI5	.;.;LAT2_HUMAN	T	315;112;112;210;91;112	ENSP00000320378:A315T;ENSP00000391577:A112T;ENSP00000434345:A210T;ENSP00000416398:A91T	ENSP00000206514:A112T	A	-	1	0	SLC7A8	22677043	0.979000	0.34478	1.000000	0.80357	0.997000	0.91878	0.137000	0.15995	1.409000	0.46915	0.563000	0.77884	GCC	.		0.567	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			T	23607203	C	T	23607203	3	4	94	1	0	0	0	0	1	0	0	0	14736	739	26	2	684	2	SLC7A8	14	23607203	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		23607203	83742337	54	8465											
C14orf50	145376	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	65032084	65032084	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttccaaaacaggttgacagaTaaaagacttgctgcaaaaga	18	8	8	7	0	0	4	0	1	0	3	1	4	1	4	1	1	3	3	1	1	6	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:65032084T>A	ENST00000298705.1	+	5	375	c.279T>A	c.(277-279)gaT>gaA	p.D93E	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	93					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGTTGACAGATAAAAGACTTG	0.338																																					p.D93E		.											.	.	0			c.T279A						.						91	80	83					14																	65032084		2203	4300	6503	SO:0001583	missense	145376	exon5			GACAGATAAAAGA		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	20097	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 50"	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.279T>A	14.37:g.65032084T>A	ENSP00000298705:p.Asp93Glu	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	37	13	NM_172365	0	0	0	0	0	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	T	8.979	0.974851	0.18736	.	.	ENSG00000165807	ENST00000298705	T	0.31247	1.5	5.79	2.16	0.27623	.	0.198907	0.35320	N	0.003286	T	0.17109	0.0411	L	0.39898	1.24	0.25922	N	0.983102	B	0.24721	0.11	B	0.17433	0.018	T	0.30119	-0.9989	10	0.05959	T	0.93	-17.5714	5.9771	0.19387	0.0:0.0945:0.4215:0.4839	.	93	Q96LQ0	PPR36_HUMAN	E	93	ENSP00000298705:D93E	ENSP00000298705:D93E	D	+	3	2	C14orf50	64101837	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	0.518000	0.22847	0.433000	0.26313	0.533000	0.62120	GAT	.		0.338	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		A	65032084	T	A	65032084	3	1	94	1	0	0	0	0	1	0	0	0	1781	1403	49	5	297	5	C14orf50	14	65032084	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	41424881	65032084	42317456	55	8466											
EIF2S1	1965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	67848335	67848335	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtggcttgttatggttaTgaaggcattgatgctgtaaa	11	14	13	3	0	0	2	0	2	0	0	0	3	0	2	0	3	1	6	0	3	6	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:67848335T>C	ENST00000256383.4	+	6	1067	c.606T>C	c.(604-606)taT>taC	p.Y202Y	EIF2S1_ENST00000466499.2_Silent_p.Y202Y	NM_004094.4	NP_004085.1	P05198	IF2A_HUMAN	eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa	202					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|protein autophosphorylation (GO:0046777)|regulation of translational initiation in response to stress (GO:0043558)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)		GTTATGGTTATGAAGGCATTG	0.343																																					p.Y202Y		.											.	EIF2S1-91	0			c.T606C						.						89	93	91					14																	67848335		2203	4300	6503	SO:0001819	synonymous_variant	1965	exon6			TGGTTATGAAGGC	J02645	CCDS9781.1	14q21.3	2011-01-07	2002-08-29		ENSG00000134001	ENSG00000134001			3265	protein-coding gene	gene with protein product		603907	"eukaryotic translation initiation factor 2, subunit 1 (alpha, 35kD )"	EIF2		2948954	Standard	NM_004094		Approved	EIF-2alpha, EIF2A	uc001xjg.3	P05198	OTTHUMG00000029800	ENST00000256383.4:c.606T>C	14.37:g.67848335T>C		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	166	58	NM_004094	0	0	15	29	14		Silent	SNP	ENST00000256383.4	37	CCDS9781.1	.	.	.	.	.	.	.	.	.	.	T	9.345	1.063966	0.20067	.	.	ENSG00000134001	ENST00000555876	.	.	.	6.0	2.3	0.28687	.	.	.	.	.	T	0.58779	0.2146	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51052	-0.8754	4	.	.	.	-12.7575	9.7872	0.40684	0.0:0.196:0.0:0.804	.	.	.	.	T	159	.	.	M	+	2	0	EIF2S1	66918088	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	1.756000	0.38390	0.149000	0.19098	0.528000	0.53228	ATG	.		0.343	EIF2S1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074342.3	NM_004094		C	67848335	T	C	67848335	2	2	94	1	0	0	0	0	0	0	0	1	5020	1471	51	3		3	EIF2S1	14	67848335	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08	2816251	67848335	39501205	56	8467											
C14orf43	91748	hgsc.bcm.edu	37	chr14	74186156	74186156	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggcctggccaccggcagAcccaggggcgttggactcgt	6	5	16	14	4	0	1	0	0	0	1	1	3	0	2	4	6	0	2	4	6	0	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:74186156A>G	ENST00000286523.5	-	12	3768	c.2986T>C	c.(2986-2988)Tct>Cct	p.S996P	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.S996P	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	996					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CCACCGGCAGACCCAGGGGCG	0.537																																					p.S996P		.											.	.	0			c.T2986C						.						53	47	49					14																	74186156		2203	4300	6503	SO:0001583	missense	91748	exon12			CGGCAGACCCAGG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.2986T>C	14.37:g.74186156A>G	ENSP00000286523:p.Ser996Pro	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_194278	0	0	6	6	0	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	A	11.32	1.605319	0.28623	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.14640	2.49;2.49;2.49;2.49	5.78	2.01	0.26516	.	0.247348	0.29424	N	0.012181	T	0.06554	0.0168	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.27739	-1.0065	10	0.36615	T	0.2	-7.298	4.8507	0.13535	0.5626:0.2569:0.1805:0.0	.	996;996	A0PJD3;Q6PJG2	.;CN043_HUMAN	P	996	ENSP00000377634:S996P;ENSP00000286523:S996P;ENSP00000407767:S996P;ENSP00000402380:S996P	ENSP00000286523:S996P	S	-	1	0	C14orf43	73255909	0.001000	0.12720	0.324000	0.25361	0.538000	0.34931	0.213000	0.17521	0.987000	0.38709	0.459000	0.35465	TCT	.		0.537	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		G	74186156	A	G	74186156	3	3	94	1	0	0	0	0	1	0	0	0	1778	275	10	3	155	3	C14orf43	14	74186156	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	6337821	74186156	33163384	57	8468											
CHP	11261	hgsc.bcm.edu	37	chr15	41535939	41535939	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagagaatgggactctcaggTaggcagtgtttttctttatt	9	15	12	5	0	2	1	1	0	2	1	3	4	2	2	0	3	0	3	0	3	3	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr15:41535939T>C	ENST00000334660.5	+	2	380		c.e2+2		CHP1_ENST00000558351.1_Splice_Site|CHP1_ENST00000560397.1_Splice_Site	NM_007236.4	NP_009167.1	Q99653	CHP1_HUMAN	calcineurin-like EF-hand protein 1						calcium ion-dependent exocytosis (GO:0017156)|cellular response to acidic pH (GO:0071468)|cytoplasmic microtubule organization (GO:0031122)|membrane docking (GO:0022406)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|microtubule bundle formation (GO:0001578)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein glycosylation (GO:0060050)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of protein transport (GO:0051222)|positive regulation of sodium:proton antiporter activity (GO:0032417)|potassium ion transport (GO:0006813)|protein export from nucleus (GO:0006611)|protein oligomerization (GO:0051259)|protein stabilization (GO:0050821)|regulation of intracellular pH (GO:0051453)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|kinase binding (GO:0019900)|microtubule binding (GO:0008017)|potassium channel regulator activity (GO:0015459)|protein kinase inhibitor activity (GO:0004860)|transporter activity (GO:0005215)										GACTCTCAGGTAGGCAGTGTT	0.473																																					.		.											.	.	0			c.140+2T>C						.						91	82	85					15																	41535939		2203	4300	6503	SO:0001630	splice_region_variant	11261	exon2			CTCAGGTAGGCAG		CCDS10073.1	15q13.3	2013-01-11	2013-01-11		ENSG00000187446	ENSG00000187446		"EF-hand domain containing"	17433	protein-coding gene	gene with protein product	"calcineurin homologous protein"	606988				15987692, 20720019	Standard	NM_007236		Approved	Sid470p, CHP, SLC9A1BP, p22, p24	uc001znl.3	Q99653	OTTHUMG00000130233	ENST00000334660.5:c.140+2T>C	15.37:g.41535939T>C		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_007236	0	0	0	0	0	B2R6H9|Q6FHZ9	Splice_Site	SNP	ENST00000334660.5	37	CCDS10073.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956306	0.73902	.	.	ENSG00000187446	ENST00000334660;ENST00000392151	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6022	0.68447	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	AC012652.1	39323231	1.000000	0.71417	0.999000	0.59377	0.746000	0.42486	5.515000	0.67049	2.102000	0.63906	0.528000	0.53228	.	.		0.473	CHP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252554.2	NM_007236	Intron	C	41535939	T	C	41535939	5	2	94	1	0	0	0	0	0	0	1	0	3372	1652	57	3	148	3	CHP	15	41535939	Splice_Site	SNP	T	TCGA-DW-7834-01A-11D-2136-08		41535939	60995453	58	8469											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1245531	1245531	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgttacctgggtgacacgTggaacaggctggatttcttc	8	12	13	8	1	1	1	0	1	1	0	2	3	1	3	1	4	2	2	1	4	2	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:1245531T>G	ENST00000348261.5	+	4	759	c.511T>G	c.(511-513)Tgg>Ggg	p.W171G	CACNA1H_ENST00000358590.4_Missense_Mutation_p.W171G|CACNA1H_ENST00000565831.1_Missense_Mutation_p.W171G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	171					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GGGTGACACGTGGAACAGGCT	0.622																																					p.W171G		.											.	CACNA1H-67	0			c.T511G						.						106	99	101					16																	1245531		1997	4146	6143	SO:0001583	missense	8912	exon4			GACACGTGGAACA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.511T>G	16.37:g.1245531T>G	ENSP00000334198:p.Trp171Gly	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_021098	0	0	1	1	0	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876927	0.72180	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.99186	-5.53;-5.53	3.69	3.69	0.42338	Ion transport (1);	0.258503	0.38164	N	0.001783	D	0.99426	0.9797	H	0.95079	3.62	0.43947	D	0.996619	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.98492	1.0610	10	0.87932	D	0	.	11.9796	0.53113	0.0:0.0:0.0:1.0	.	171;171	O95180-2;O95180	.;CAC1H_HUMAN	G	171	ENSP00000334198:W171G;ENSP00000351401:W171G	ENSP00000334198:W171G	W	+	1	0	CACNA1H	1185532	1.000000	0.71417	0.975000	0.42487	0.835000	0.47333	5.892000	0.69790	1.673000	0.50895	0.387000	0.25754	TGG	.		0.622	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		G	1245531	T	G	1245531	3	3	94	1	0	0	0	0	1	0	0	0	2551	1696	59	5	521	5	CACNA1H	16	1245531	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		1245531	89109222	59	8470											
NUBP2	10101	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1836594	1836594	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggtcctctcaggaaaggggGgcgttgggaaaagcaccatc	10	7	15	9	1	1	0	1	0	1	0	4	2	2	2	2	6	1	2	2	6	3	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:1836594G>C	ENST00000262302.9	+	2	193	c.73G>C	c.(73-75)Ggc>Cgc	p.G25R	NUBP2_ENST00000565134.1_Missense_Mutation_p.G25R|NUBP2_ENST00000543305.1_5'UTR|NUBP2_ENST00000568706.1_5'UTR|NUBP2_ENST00000565987.1_5'UTR	NM_001284501.1|NM_012225.2	NP_001271430.1|NP_036357.1			nucleotide binding protein 2											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						AGGAAAGGGGGGCGTTGGGAA	0.657																																					p.G25R													.	NUBP2-90	0			c.G73C						.						67	64	65					16																	1836594		2198	4300	6498	SO:0001583	missense	10101	exon2			AAGGGGGGCGTTG	AF118394	CCDS10445.1, CCDS66898.1	16p13.3	2011-05-19	2011-05-19		ENSG00000095906	ENSG00000095906			8042	protein-coding gene	gene with protein product		610779	"nucleotide binding protein 2 (E.coli MinD like)", "nucleotide binding protein 2 (MinD homolog, E. coli)"			10486206	Standard	XM_005255025		Approved	CFD1	uc002cmw.4	Q9Y5Y2	OTTHUMG00000128639	ENST00000262302.9:c.73G>C	16.37:g.1836594G>C	ENSP00000262302:p.Gly25Arg	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	143	26	NM_012225	0	0	13	29	16		Missense_Mutation	SNP	ENST00000262302.9	37	CCDS10445.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.804684	0.70682	.	.	ENSG00000095906	ENST00000262302	D	0.93076	-3.16	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	D	0.97914	0.9314	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99577	1.0972	10	0.87932	D	0	-7.9425	15.5493	0.76137	0.0:0.0:1.0:0.0	.	25	Q9Y5Y2	NUBP2_HUMAN	R	25	ENSP00000262302:G25R	ENSP00000262302:G25R	G	+	1	0	NUBP2	1776595	1.000000	0.71417	0.187000	0.23214	0.293000	0.27360	5.973000	0.70456	1.999000	0.58509	0.561000	0.74099	GGC	.		0.657	NUBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250510.1	NM_012225		C	1836594	G	C	1836594	3	2	94	1	0	0	0	0	1	0	0	0	10742	1232	43	4	79	4	NUBP2	16	1836594	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	591063	1836594	88518159	60	8471											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	8	8	NM_178167	0	0	0	2	2	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	94	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	223080	2059674	88295079	61	8472											
KIAA0556	23247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27720066	27720066	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgagatcaaagatgccaTctacgtgaccatggagatcc	14	7	10	10	2	2	5	1	1	1	4	3	7	3	5	3	1	2	0	3	1	2	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:27720066T>C	ENST00000261588.4	+	13	1449	c.1430T>C	c.(1429-1431)aTc>aCc	p.I477T	CTD-2049O4.1_ENST00000568831.1_RNA|CTD-2049O4.1_ENST00000564893.1_RNA|CTD-2049O4.1_ENST00000563052.1_RNA|KIAA0556_ENST00000567894.1_3'UTR	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	477						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AAAGATGCCATCTACGTGACC	0.453																																					p.I477T		.											.	KIAA0556-141	0			c.T1430C						.						120	105	110					16																	27720066		2197	4300	6497	SO:0001583	missense	23247	exon13			ATGCCATCTACGT	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1430T>C	16.37:g.27720066T>C	ENSP00000261588:p.Ile477Thr	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	139	28	NM_015202	0	0	3	5	2	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.818111	0.50633	.	.	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.13778	2.56	5.49	4.4	0.53042	.	0.797554	0.11412	N	0.566654	T	0.19886	0.0478	M	0.75264	2.295	0.09310	N	0.999996	B	0.21071	0.051	B	0.19391	0.025	T	0.14008	-1.0488	10	0.51188	T	0.08	-4.828	10.5152	0.44885	0.0:0.0775:0.0:0.9225	.	477	O60303	K0556_HUMAN	T	477;384	ENSP00000261588:I477T	ENSP00000261588:I477T	I	+	2	0	KIAA0556	27627567	0.986000	0.35501	0.001000	0.08648	0.582000	0.36321	3.571000	0.53841	0.912000	0.36772	0.379000	0.24179	ATC	.		0.453	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		C	27720066	T	C	27720066	3	2	94	1	0	0	0	0	1	0	0	0	8204	1435	50	3	1480	3	KIAA0556	16	27720066	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	25660392	27720066	62634687	62	8473											
SNX20	124460	bcgsc.ca	37	chr16	50707452	50707452	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgtaggccaggcggaccatGgcgtccagcagaggcgcata	9	4	16	12	4	0	1	0	0	0	1	1	2	1	2	3	5	1	3	3	5	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:50707452G>T	ENST00000330943.4	-	4	987	c.816C>A	c.(814-816)gcC>gcA	p.A272A	RP11-401P9.5_ENST00000570241.2_RNA|RP11-401P9.5_ENST00000570167.1_RNA|SNX20_ENST00000423026.2_Intron|SNX20_ENST00000300590.3_Intron	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	272					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						GGCGGACCATGGCGTCCAGCA	0.721																																					p.A272A													.	SNX20-23	0			c.C816A						.						27	28	27					16																	50707452		2197	4296	6493	SO:0001819	synonymous_variant	124460	exon4			GACCATGGCGTCC	AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"Sorting nexins"	30390	protein-coding gene	gene with protein product	"selectin ligand interactor cytoplasmic 1"	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.816C>A	16.37:g.50707452G>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_1	104	6	NM_182854	0	0	0	0	0	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Silent	SNP	ENST00000330943.4	37	CCDS10745.1																																																																																			.		0.721	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337		T	50707452	G	T	50707452	2	4	94	1	0	0	0	0	0	0	0	1	14924	1335	47	4		4	SNX20	16	50707452	Silent	SNP	G	TCGA-DW-7834-01A-11D-2136-08	22987386	50707452	39647301	63	8474											
CDH15	1013	hgsc.bcm.edu	37	chr16	89261313	89261313	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagtgtgccgccttacgAcacagccctcatctatgact	8	9	7	17	2	2	1	1	1	1	0	2	2	2	1	5	0	3	0	5	0	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:89261313A>G	ENST00000289746.2	+	14	2260	c.2195A>G	c.(2194-2196)gAc>gGc	p.D732G		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	732					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		CCGCCTTACGACACAGCCCTC	0.632																																					p.D732G		.											.	CDH15-523	0			c.A2195G						.						35	32	33					16																	89261313		2182	4291	6473	SO:0001583	missense	1013	exon14			CTTACGACACAGC	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"Cadherins / Major cadherins"	1754	protein-coding gene	gene with protein product		114019	"cadherin 15, M-cadherin (myotubule)"	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.2195A>G	16.37:g.89261313A>G	ENSP00000289746:p.Asp732Gly	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	44	3	NM_004933	0	0	0	0	0		Missense_Mutation	SNP	ENST00000289746.2	37	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.746646	0.89663	.	.	ENSG00000129910	ENST00000289746	D	0.89485	-2.52	4.93	4.93	0.64822	Cadherin, cytoplasmic domain (1);	0.000000	0.56097	D	0.000039	D	0.96097	0.8728	H	0.95982	3.75	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.97199	0.9863	10	0.87932	D	0	.	13.5526	0.61740	1.0:0.0:0.0:0.0	.	732	P55291	CAD15_HUMAN	G	732	ENSP00000289746:D732G	ENSP00000289746:D732G	D	+	2	0	CDH15	87788814	1.000000	0.71417	0.967000	0.41034	0.899000	0.52679	8.618000	0.90932	1.848000	0.53677	0.459000	0.35465	GAC	.		0.632	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		G	89261313	A	G	89261313	3	3	94	1	0	0	0	0	1	0	0	0	3106	275	10	3	2249	3	CDH15	16	89261313	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	38553861	89261313	1093440	64	8475											
TOP3A	7156	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	18212208	18212208	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctacctggccatacagAtgataatcaaattcatagat	15	10	6	10	0	2	3	2	1	0	2	2	3	2	3	3	1	2	1	3	1	5	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:18212208A>G	ENST00000321105.5	-	2	442	c.228T>C	c.(226-228)caT>caC	p.H76H	TOP3A_ENST00000542570.1_Missense_Mutation_p.I6T|TOP3A_ENST00000582230.1_5'UTR	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	76	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GGCCATACAGATGATAATCAA	0.289																																					p.H76H		.											.	TOP3A-228	0			c.T228C						.						36	33	34					17																	18212208		2201	4295	6496	SO:0001819	synonymous_variant	7156	exon2			ATACAGATGATAA	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.228T>C	17.37:g.18212208A>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	46	15	NM_004618	0	0	0	0	0	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.18|13.18	2.161482|2.161482	0.38119|0.38119	.|.	.|.	ENSG00000177302|ENSG00000177302	ENST00000542570|ENST00000412083	T|.	0.08282|.	3.11|.	5.04|5.04	-5.1|-5.1	0.02911|0.02911	.|.	.|.	.|.	.|.	.|.	T|T	0.50616|0.50616	0.1626|0.1626	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.53258|0.53258	-0.8464|-0.8464	6|4	0.21014|.	T|.	0.42|.	-4.7873|-4.7873	8.3168|8.3168	0.32104|0.32104	0.5159:0.1661:0.3181:0.0|0.5159:0.1661:0.3181:0.0	.|.	.|.	.|.	.|.	T|P	6|56	ENSP00000442336:I6T|.	ENSP00000442336:I6T|.	I|S	-|-	2|1	0|0	TOP3A|TOP3A	18152933|18152933	0.817000|0.817000	0.29147|0.29147	0.469000|0.469000	0.27204|0.27204	0.893000|0.893000	0.52053|0.52053	-0.001000|-0.001000	0.12947|0.12947	-0.503000|-0.503000	0.06586|0.06586	-0.220000|-0.220000	0.12472|0.12472	ATC|TCT	.		0.289	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			G	18212208	A	G	18212208	2	3	94	1	0	0	0	0	0	0	0	1	16400	330	12	3		3	TOP3A	17	18212208	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08		18212208	62983002	65	8476											
MED1	5469	bcgsc.ca	37	chr17	37565188	37565188	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaagaatggctatggtggcTtttgctgcctgaggaagaca	10	10	15	6	0	0	3	0	1	0	2	0	5	0	5	1	5	2	3	1	5	4	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:37565188T>C	ENST00000300651.6	-	17	3509	c.3286A>G	c.(3286-3288)Agc>Ggc	p.S1096G	MED1_ENST00000394287.3_Intron|CTB-131K11.1_ENST00000582842.1_RNA	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		CTATGGTGGCTTTTGCTGCCT	0.463										HNSCC(31;0.082)																											p.S1096G	Pancreas(21;279 768 2492 4877 24026)												.	MED1-620	0			c.A3286G						.						85	81	82					17																	37565188		2203	4300	6503	SO:0001583	missense	5469	exon17			GGTGGCTTTTGCT	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.3286A>G	17.37:g.37565188T>C	ENSP00000300651:p.Ser1096Gly	Somatic	148	0		WXS	Illumina HiSeq	Phase_1	170	5	NM_004774	0	0	8	8	0	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000300651.6	37	CCDS11336.1	.	.	.	.	.	.	.	.	.	.	T	9.253	1.041274	0.19669	.	.	ENSG00000125686	ENST00000300651	T	0.35421	1.31	5.87	5.87	0.94306	.	.	.	.	.	T	0.36276	0.0961	N	0.24115	0.695	0.49299	D	0.999771	D	0.63880	0.993	P	0.52758	0.708	T	0.05733	-1.0867	9	0.16896	T	0.51	-9.8436	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1096	Q15648	MED1_HUMAN	G	1096	ENSP00000300651:S1096G	ENSP00000300651:S1096G	S	-	1	0	MED1	34818714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.195000	0.58400	2.371000	0.80710	0.533000	0.62120	AGC	.		0.463	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		C	37565188	T	C	37565188	3	2	94	1	0	0	0	0	1	0	0	0	9450	1609	56	3	1463	3	MED1	17	37565188	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	19352980	37565188	43630022	66	8477											
EFTUD2	9343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42945230	42945230	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	actccacgaaacttctctggGagctgctagttggggccttt	7	12	11	11	1	1	0	0	0	1	0	3	2	2	1	2	3	3	3	2	3	2	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:42945230G>A	ENST00000426333.2	-	13	1391	c.1094C>T	c.(1093-1095)tCc>tTc	p.S365F	EFTUD2_ENST00000591382.1_Missense_Mutation_p.S365F|EFTUD2_ENST00000592576.1_Missense_Mutation_p.S355F|EFTUD2_ENST00000402521.3_Missense_Mutation_p.S330F	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	365	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				ACTTCTCTGGGAGCTGCTAGT	0.483																																					p.S365F	Ovarian(10;65 485 10258 29980 30707)	.											.	EFTUD2-91	0			c.C1094T						.						48	47	48					17																	42945230		2203	4300	6503	SO:0001583	missense	9343	exon13			CTCTGGGAGCTGC	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1094C>T	17.37:g.42945230G>A	ENSP00000392094:p.Ser365Phe	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	29	17	NM_004247	0	0	6	14	8	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	37	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231134	0.79688	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.76839	-1.05;-1.05	6.17	6.17	0.99709	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.81964	0.4934	L	0.56769	1.78	0.80722	D	1	P;P	0.41710	0.76;0.76	P;P	0.47891	0.56;0.56	T	0.77477	-0.2573	10	0.32370	T	0.25	0.1139	20.8794	0.99867	0.0:0.0:1.0:0.0	.	355;365	B4DMC0;Q15029	.;U5S1_HUMAN	F	365;355;330	ENSP00000392094:S365F;ENSP00000385873:S330F	ENSP00000262414:S355F	S	-	2	0	EFTUD2	40300756	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.406000	0.97321	2.941000	0.99782	0.655000	0.94253	TCC	.		0.483	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		A	42945230	G	A	42945230	3	1	94	1	0	0	0	0	1	0	0	0	4972	1174	41	2	1888	2	EFTUD2	17	42945230	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	5380042	42945230	38249980	67	8478											
WNT3	7473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	44845986	44845986	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttggcccggagggtctcCacccagcctcgggactcacg	6	7	12	16	3	2	0	1	0	1	0	4	2	2	2	4	4	2	0	4	4	1	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:44845986C>T	ENST00000225512.5	-	4	930	c.768G>A	c.(766-768)gtG>gtA	p.V256V		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	256					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GGAGGGTCTCCACCCAGCCTC	0.592																																					p.G256G		.											.	WNT3-522	0			c.A768A						.						85	91	89					17																	44845986		2203	4300	6503	SO:0001819	synonymous_variant	7473	exon4			GGTCTCCACCCAG	AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"Wingless-type MMTV integration sites", "Endogenous ligands"	12782	protein-coding gene	gene with protein product	"WNT-3 proto-oncogene protein"	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.768G>A	17.37:g.44845986C>T		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	174	79	NM_030753	0	0	0	2	2	Q2M237|Q9H1J9	Silent	SNP	ENST00000225512.5	37	CCDS11505.1																																																																																			.		0.592	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753		T	44845986	C	T	44845986	2	4	94	1	0	0	0	0	0	0	0	1	17421	581	21	2		2	WNT3	17	44845986	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	1900756	44845986	36349224	68	8479											
RNF213	57674	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	78321576	78321576	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgggttcaccccaacttccgCctgattgtcattgaagagaa	10	10	9	12	2	2	3	2	2	0	1	3	4	3	3	4	1	1	1	4	1	3	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:78321576C>T	ENST00000582970.1	+	29	9584	c.9441C>T	c.(9439-9441)cgC>cgT	p.R3147R	RNF213_ENST00000336301.6_Silent_p.R1220R|RNF213_ENST00000508628.2_Silent_p.R3196R	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3147					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCAACTTCCGCCTGATTGTCA	0.552																																					p.R3147R		.											.	RNF213-577	0			c.C9441T						.						55	53	54					17																	78321576		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon29			CTTCCGCCTGATT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.9441C>T	17.37:g.78321576C>T		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	88	6	NM_001256071	0	0	14	15	1	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			.		0.552	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78321576	C	T	78321576	2	4	94	1	0	0	0	0	0	0	0	1	13509	726	26	2		2	RNF213	17	78321576	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	33475590	78321576	2873634	69	8480											
DSEL	92126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	65181492	65181492	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattgttaccataaatttcAttccacttggcagcaaaatc	14	13	5	9	0	1	1	1	0	0	1	3	1	2	1	2	1	2	3	2	1	5	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr18:65181492A>G	ENST00000310045.7	-	2	1857	c.384T>C	c.(382-384)aaT>aaC	p.N128N	CTD-2541J13.2_ENST00000581951.1_RNA|RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	118					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CATAAATTTCATTCCACTTGG	0.403																																					p.N128N		.											.	DSEL-157	0			c.T384C						.						114	101	106					18																	65181492		2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			AATTTCATTCCAC	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"chromosome 18 open reading frame 4"	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.384T>C	18.37:g.65181492A>G		Somatic	107	1		WXS	Illumina HiSeq	Phase_I	132	41	NM_032160	0	0	0	1	1	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1																																																																																			.		0.403	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65181492	A	G	65181492	2	3	94	1	0	0	0	0	0	0	0	1	4786	214	8	3		3	DSEL	18	65181492	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08		65181492	12895756	70	8481											
CFD	1675	hgsc.bcm.edu;broad.mit.edu	37	chr19	860929	860929	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccggagccctccaagcgccTgtacgacgtgctccgcgcag	6	5	13	17	6	0	0	0	0	0	0	2	2	2	1	5	1	4	3	5	1	2	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:860929T>G	ENST00000327726.6	+	3	518	c.281T>G	c.(280-282)cTg>cGg	p.L94R	CFD_ENST00000592860.1_Missense_Mutation_p.L101R	NM_001928.2	NP_001919.2	P00746	CFAD_HUMAN	complement factor D (adipsin)	94	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			Missing (in Ref. 7; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)						Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAAGCGCCTGTACGACGTG	0.721																																					p.L94R		.											.	CFD-514	0			c.T281G						.						18	17	18					19																	860929		2185	4282	6467	SO:0001583	missense	1675	exon3			AGCGCCTGTACGA	M84526	CCDS12046.1	19p13.3	2014-09-17	2006-02-10	2006-02-10		ENSG00000197766		"Complement system"	2771	protein-coding gene	gene with protein product		134350	"D component of complement (adipsin)", "properdin factor D"	DF, PFD		1374388	Standard	NM_001928		Approved	ADN	uc002lqc.3	P00746		ENST00000327726.6:c.281T>G	19.37:g.860929T>G	ENSP00000332139:p.Leu94Arg	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	27	9	NM_001928	0	0	81	82	1	B4DV76|Q5U5S1|Q86VJ5|Q8N4E0|Q8WZB4	Missense_Mutation	SNP	ENST00000327726.6	37	CCDS12046.1	.	.	.	.	.	.	.	.	.	.	T	9.346	1.064348	0.20067	.	.	ENSG00000197766	ENST00000327726	D	0.88277	-2.36	3.66	1.38	0.22167	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.331646	0.15899	U	0.239174	T	0.73071	0.3540	N	0.02674	-0.535	0.09310	N	1	B;B	0.17038	0.02;0.015	B;B	0.16722	0.016;0.006	T	0.63778	-0.6560	10	0.59425	D	0.04	.	10.1812	0.42968	0.0:0.0:0.5042:0.4958	.	101;94	A6XNE2;P00746	.;CFAD_HUMAN	R	94	ENSP00000332139:L94R	ENSP00000332139:L94R	L	+	2	0	CFD	811929	0.000000	0.05858	0.060000	0.19600	0.958000	0.62258	-0.666000	0.05280	-0.029000	0.13827	0.334000	0.21626	CTG	.		0.721	CFD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457891.2	NM_001928		G	860929	T	G	860929	3	3	94	1	0	0	0	0	1	0	0	0	3287	1580	55	5	291	5	CFD	19	860929	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		860929	58268054	71	8482											
AP3D1	8943	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	2151253	2151253	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcacctcgtcctccttgtgGttacggatgccgcggaccaa	6	10	10	15	4	1	0	1	0	0	0	4	2	3	2	5	3	2	1	5	3	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:2151253G>C	ENST00000345016.5	-	1	312	c.81C>G	c.(79-81)aaC>aaG	p.N27K	AP3D1_ENST00000350812.6_Missense_Mutation_p.N27K|AP3D1_ENST00000356926.4_Missense_Mutation_p.N27K|AP3D1_ENST00000355272.6_Missense_Mutation_p.N27K	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	27					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCCTTGTGGTTACGGATGC	0.682																																					p.N27K		.											.	AP3D1-90	0			c.C81G						.						29	32	31					19																	2151253		1958	4139	6097	SO:0001583	missense	8943	exon1			CTTGTGGTTACGG	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.81C>G	19.37:g.2151253G>C	ENSP00000344055:p.Asn27Lys	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	34	16	NM_001261826	0	0	3	3	0	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	37	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717231	0.48622	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.18657	2.2;2.65;2.62;2.21	3.89	2.85	0.33270	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.32436	0.0829	L	0.40543	1.245	0.25610	N	0.986508	B;B;D	0.67145	0.264;0.058;0.996	B;B;D	0.78314	0.033;0.067;0.991	T	0.02860	-1.1101	10	0.52906	T	0.07	-55.1245	9.2068	0.37293	0.1883:0.0:0.8117:0.0	.	27;27;27	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	K	27	ENSP00000349398:N27K;ENSP00000344055:N27K;ENSP00000347416:N27K;ENSP00000342321:N27K	ENSP00000341579:N27K	N	-	3	2	AP3D1	2102253	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.691000	0.37721	0.971000	0.38288	0.436000	0.28706	AAC	.		0.682	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			C	2151253	G	C	2151253	3	2	94	1	0	0	0	0	1	0	0	0	746	1252	44	4	3658	4	AP3D1	19	2151253	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	1290324	2151253	56977730	72	8483											
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7533786	7533786	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgagcatgctgccatccGgcgtggggccagagtacgca	7	7	16	11	3	0	2	0	1	0	1	1	2	1	2	3	3	4	4	3	3	1	1	rs180746700	byFrequency	TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:7533786G>A	ENST00000359920.6	+	17	3245	c.2992G>A	c.(2992-2994)Ggc>Agc	p.G998S	ARHGEF18_ENST00000319670.9_Missense_Mutation_p.G840S|CTD-2207O23.3_ENST00000593531.1_Silent_p.P955P	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	998					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GCTGCCATCCGGCGTGGGGCC	0.687													G|||	3	0.000599042	0	0	5008	,	,		16123	0		0.002	False		,,,				2504	0.001				p.G998S		.											.	ARHGEF18-228	0			c.G2992A						.	G	SER/GLY,SER/GLY	3,4353		0,3,2175	11	11	11		2992,2518	-2.6	0	19		11	17,8533		0,17,4258	yes	missense,missense	ARHGEF18	NM_001130955.1,NM_015318.3	56,56	0,20,6433	AA,AG,GG		0.1988,0.0689,0.155	benign,benign	998/1174,840/1016	7533786	20,12886	2178	4275	6453	SO:0001583	missense	23370	exon17			CCATCCGGCGTGG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	17090	protein-coding gene	gene with protein product	"Rho-specific guanine nucleotide exchange factor p114"		"rho/rac guanine nucleotide exchange factor (GEF) 18"			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.2992G>A	19.37:g.7533786G>A	ENSP00000352995:p.Gly998Ser	Somatic	10	2		WXS	Illumina HiSeq	Phase_I	15	10	NM_001130955	0	0	4	6	2	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	5.500	0.277247	0.10403	6.89E-4	0.001988	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.29142	1.59;1.58	4.97	-2.59	0.06209	.	0.977536	0.08305	N	0.966245	T	0.15696	0.0378	N	0.22421	0.69	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.001	T	0.37549	-0.9701	10	0.05833	T	0.94	-0.8582	9.2231	0.37388	0.5011:0.0:0.4989:0.0	.	840;998	Q6ZSZ5-2;Q6ZSZ5	.;ARHGI_HUMAN	S	840;998	ENSP00000319200:G840S;ENSP00000352995:G998S	ENSP00000319200:G840S	G	+	1	0	ARHGEF18	7439786	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.169000	0.16641	-0.320000	0.08640	-0.244000	0.11960	GGC	G|0.999;A|0.000		0.687	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		A	7533786	G	A	7533786	3	1	94	1	0	0	0	0	1	0	0	0	901	1116	39	1	3058	1	ARHGEF18	19	7533786	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	5382533	7533786	51595197	73	8484											
PTGER1	5731	broad.mit.edu	37	chr19	14584193	14584193	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccggtgcgcccctcaccaGcattgggctccagcagatgc	6	6	13	16	2	1	1	1	0	0	1	2	1	2	1	5	3	4	3	5	3	0	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:14584193G>T	ENST00000292513.3	-	2	1057	c.940C>A	c.(940-942)Ctg>Atg	p.L314M		NM_000955.2	NP_000946.2	P34995	PE2R1_HUMAN	prostaglandin E receptor 1 (subtype EP1), 42kDa	314					G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)									Alprostadil(DB00770)|Bimatoprost(DB00905)|Bupivacaine(DB00297)|Carboprost Tromethamine(DB00429)|Dinoprostone(DB00917)|Iloprost(DB01088)	CCCCTCACCAGCATTGGGCTC	0.687											OREG0025314	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L314M													.	PTGER1-658	0			c.C940A						.						18	12	14					19																	14584193		2160	4237	6397	SO:0001583	missense	5731	exon2			TCACCAGCATTGG		CCDS12309.1	19p13.1	2012-08-08	2002-08-29		ENSG00000160951	ENSG00000160951		"GPCR / Class A : Prostanoid receptors"	9593	protein-coding gene	gene with protein product		176802	"prostaglandin E receptor 1 (subtype EP1), 42kD"			8253813	Standard	NM_000955		Approved	EP1	uc002mys.3	P34995	OTTHUMG00000039610	ENST00000292513.3:c.940C>A	19.37:g.14584193G>T	ENSP00000292513:p.Leu314Met	Somatic	16	0	696	WXS	Illumina HiSeq	Phase_I	16	5	NM_000955	0	0	0	0	0	Q5U5U4|Q86UH3|Q86VB5|Q8NHB2	Missense_Mutation	SNP	ENST00000292513.3	37	CCDS12309.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903916	0.72754	.	.	ENSG00000160951	ENST00000292513	T	0.38240	1.15	3.67	3.67	0.42095	GPCR, rhodopsin-like superfamily (1);	0.224065	0.30575	N	0.009330	T	0.51466	0.1676	M	0.63428	1.95	0.40826	D	0.983548	D	0.89917	1.0	D	0.97110	1.0	T	0.54741	-0.8248	10	0.72032	D	0.01	-9.2521	6.8966	0.24259	0.126:0.0:0.874:0.0	.	314	P34995	PE2R1_HUMAN	M	314	ENSP00000292513:L314M	ENSP00000292513:L314M	L	-	1	2	PTGER1	14445193	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.364000	0.73086	1.873000	0.54277	0.561000	0.74099	CTG	.		0.687	PTGER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095509.1			T	14584193	G	T	14584193	3	4	94	1	0	0	0	0	1	0	0	0	12772	962	34	4	276	4	PTGER1	19	14584193	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	7050407	14584193	44544790	74	8485											
SLC27A1	376497	hgsc.bcm.edu	37	chr19	17597401	17597401	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctgatccgcgtgcgccTggagctgcggcggcaccagc	4	7	16	14	5	0	1	0	1	0	0	1	2	1	2	3	3	5	3	3	3	0	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:17597401T>C	ENST00000252595.7	+	2	294	c.197T>C	c.(196-198)cTg>cCg	p.L66P	SLC27A1_ENST00000598424.1_5'UTR|SLC27A1_ENST00000442725.1_Missense_Mutation_p.L66P|CTD-3131K8.2_ENST00000596643.1_lincRNA	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	66					adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CGCGTGCGCCTGGAGCTGCGG	0.721																																					p.L66P		.											.	SLC27A1-226	0			c.T197C						.						8	7	8					19																	17597401		2039	4010	6049	SO:0001583	missense	376497	exon2			TGCGCCTGGAGCT	BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"Acyl-CoA synthetase family", "Solute carriers"	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.197T>C	19.37:g.17597401T>C	ENSP00000252595:p.Leu66Pro	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_198580	0	0	1	1	0	A6NIH2|B7Z662	Missense_Mutation	SNP	ENST00000252595.7	37	CCDS32953.1	.	.	.	.	.	.	.	.	.	.	t	15.96	2.985604	0.53934	.	.	ENSG00000130304	ENST00000442725;ENST00000252595	T;T	0.52983	0.64;0.64	4.92	1.22	0.21188	.	0.618824	0.16244	N	0.223002	T	0.41696	0.1170	M	0.64404	1.975	0.58432	D	0.999995	P	0.40875	0.731	B	0.43386	0.418	T	0.35101	-0.9802	10	0.44086	T	0.13	.	1.9726	0.03409	0.155:0.1003:0.1755:0.5692	.	66	Q6PCB7	S27A1_HUMAN	P	66	ENSP00000413424:L66P;ENSP00000252595:L66P	ENSP00000252595:L66P	L	+	2	0	SLC27A1	17458401	0.585000	0.26774	0.997000	0.53966	0.905000	0.53344	0.500000	0.22562	0.706000	0.31912	0.454000	0.30748	CTG	.		0.721	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580		C	17597401	T	C	17597401	3	2	94	1	0	0	0	0	1	0	0	0	14557	1580	55	3	203	3	SLC27A1	19	17597401	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	3013208	17597401	41531582	75	8486											
PSMC4	5704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40478461	40478461	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatcgtgggctctaccacAggtgtgctaaggacacctca	9	8	11	13	1	2	0	1	0	1	0	3	1	2	1	3	3	2	2	3	3	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:40478461A>G	ENST00000157812.2	+	3	519	c.321A>G	c.(319-321)acA>acG	p.T107T	PSMC4_ENST00000455878.2_Splice_Site_p.T76T	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	107					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)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GCTCTACCACAGGTGTGCTAA	0.512																																					p.T107T	Colon(105;1478 1543 4034 6132 38638)	.											.	PSMC4-91	0			c.A321G						.						41	36	38					19																	40478461		2203	4300	6503	SO:0001630	splice_region_variant	5704	exon3			TACCACAGGTGTG	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9551	protein-coding gene	gene with protein product	"protease 26S subunit 6", "Tat-binding protein 7", "MB67 interacting protein"	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.322+1A>G	19.37:g.40478461A>G		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	46	11	NM_006503	0	0	0	0	0	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																			.		0.512	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	Silent	G	40478461	A	G	40478461	5	3	94	1	0	0	0	0	0	0	1	0	12718	202	7	3	331	3	PSMC4	19	40478461	Splice_Site	SNP	A	TCGA-DW-7834-01A-11D-2136-08	22881060	40478461	18650522	76	8487											
MEGF8	1954	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42861598	42861598	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccgttgctggtcacaccCttactgcccgccgaggcctg	5	8	11	17	3	1	0	1	0	0	0	1	1	1	0	5	2	4	2	5	2	1	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:42861598C>G	ENST00000251268.6	+	28	4873	c.4873C>G	c.(4873-4875)Ctt>Gtt	p.L1625V	MEGF8_ENST00000334370.4_Missense_Mutation_p.L1558V	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1625					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				TGGTCACACCCTTACTGCCCG	0.652																																					p.L1625V		.											.	MEGF8-23	0			c.C4873G						.						67	68	67					19																	42861598		2203	4300	6503	SO:0001583	missense	1954	exon28			CACACCCTTACTG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.4873C>G	19.37:g.42861598C>G	ENSP00000251268:p.Leu1625Val	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	163	44	NM_001271938	0	0	1	1	0	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	C	22.5	4.302490	0.81136	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.64438	-0.1;-0.1	5.21	5.21	0.72293	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.000000	0.56097	D	0.000038	T	0.74913	0.3779	L	0.50333	1.59	0.80722	D	1	D;D	0.63046	0.992;0.99	P;D	0.72982	0.792;0.979	T	0.76110	-0.3079	10	0.56958	D	0.05	-13.3833	17.5358	0.87830	0.0:1.0:0.0:0.0	.	1625;1558	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	V	1558;1625	ENSP00000334219:L1558V;ENSP00000251268:L1625V	ENSP00000251268:L1625V	L	+	1	0	MEGF8	47553438	1.000000	0.71417	0.980000	0.43619	0.985000	0.73830	4.334000	0.59291	2.453000	0.82957	0.563000	0.77884	CTT	.		0.652	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42861598	C	G	42861598	3	3	94	1	0	0	0	0	1	0	0	0	9488	681	24	4	4778	4	MEGF8	19	42861598	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	2383137	42861598	16267385	77	8488											
ZNF8	7554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58805588	58805588	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccttatcccaccacgttaggGaaagacagggagtgtcagag	12	7	12	10	1	1	2	1	0	0	2	2	4	2	4	3	2	0	1	3	2	3	2	rs35832841	byFrequency	TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:58805588G>A	ENST00000196548.5	+	4	545	c.414G>A	c.(412-414)ggG>ggA	p.G138G	AC010642.1_ENST00000591325.1_3'UTR|ZNF8_ENST00000608843.1_Silent_p.G138G			P17098	ZNF8_HUMAN	zinc finger protein 8	138					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		CCACGTTAGGGAAAGACAGGG	0.527																																					p.G138G		.											.	ZNF8-91	0			c.G414A						.						65	50	55					19																	58805588		2203	4300	6503	SO:0001819	synonymous_variant	7554	exon4			GTTAGGGAAAGAC	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"Zinc fingers, C2H2-type", "-"	13154	protein-coding gene	gene with protein product		194532	"zinc finger protein 8 (clone HF.18)"			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.414G>A	19.37:g.58805588G>A		Somatic	59	1		WXS	Illumina HiSeq	Phase_I	38	9	NM_021089	0	0	2	3	1	Q6PI99	Silent	SNP	ENST00000196548.5	37	CCDS12974.1																																																																																			G|0.995;T|0.005		0.527	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089		A	58805588	G	A	58805588	2	1	94	1	0	0	0	0	0	0	0	1	18199	1161	41	2		2	ZNF8	19	58805588	Silent	SNP	G	TCGA-DW-7834-01A-11D-2136-08	15943990	58805588	323395	78	8489											
CHD6	84181	broad.mit.edu	37	chr20	40033403	40033405	+	In_Frame_Del	DEL	TCT	TCT	-																															gttggggttgtccccctttgTcttcttcttcttcctcttct																								rs572418298|rs146425509|rs573605078	byFrequency	TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr20:40033403_40033405delTCT	ENST00000373233.3	-	37	8153_8155	c.7976_7978delAGA	c.(7975-7980)aagaca>aca	p.K2659del	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2659					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TCCCCCTTTGTCTTCTTCTTCTT	0.586														3	0.000599042	0.0023	0	5008	,	,		18233	0		0	False		,,,				2504	0				p.2659_2660del													.	CHD6-238	0			c.7976_7978del						.			5,4259		0,5,2127						5.9	1			79	2,8252		0,2,4125	no	coding	CHD6	NM_032221.3		0,7,6252	A1A1,A1R,RR		0.0242,0.1173,0.0559				7,12511				SO:0001651	inframe_deletion	84181	exon37			CCTTTGTCTTCTT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.7976_7978delAGA	20.37:g.40033412_40033414delTCT	ENSP00000362330:p.Lys2659del	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	164	10	NM_032221	0	0	0	0	0	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	In_Frame_Del	DEL	ENST00000373233.3	37	CCDS13317.1																																																																																			.		0.586	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			-	40033405	TCT	-	40033403	7	5	94	1	0	1	0	1	0	0	0	0	3335	1667	58	0	173	0	CHD6	20	40033403	In_Frame_Del	DEL	TCT	TCGA-DW-7834-01A-11D-2136-08		40033403	22992117	79	8490											
PMEPA1	56937	broad.mit.edu	37	chr20	56227616	56227616	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcgaagggcggcacggcCaggcggtcggtgggccgagg	5	3	23	10	6	0	0	0	0	0	0	1	2	0	0	2	9	0	1	2	9	1	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr20:56227616C>T	ENST00000341744.3	-	4	676	c.357G>A	c.(355-357)ctG>ctA	p.L119L	PMEPA1_ENST00000265626.4_Silent_p.L69L|PMEPA1_ENST00000395816.3_Silent_p.L69L|PMEPA1_ENST00000347215.4_Silent_p.L84L|PMEPA1_ENST00000395814.1_Silent_p.L69L	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	119					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						GCGGCACGGCCAGGCGGTCGG	0.692																																					p.L119L													.	PMEPA1-227	0			c.G357A						.						15	17	16					20																	56227616		2188	4253	6441	SO:0001819	synonymous_variant	56937	exon4			CACGGCCAGGCGG	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"solid tumor-associated 1"	606564	"transmembrane, prostate androgen induced RNA"	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.357G>A	20.37:g.56227616C>T		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_020182	0	0	8	14	6	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	37	CCDS13463.1																																																																																			.		0.692	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		T	56227616	C	T	56227616	2	4	94	1	0	0	0	0	0	0	0	1	12158	581	21	2		2	PMEPA1	20	56227616	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	16194213	56227616	6797904	80	8491											
COL9A3	1299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	61468580	61468580	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggaccccctggataccgCggtcccactggggagctggg	6	5	16	14	3	0	0	0	0	0	0	1	4	1	3	4	6	2	1	4	6	1	1	rs144216578	byFrequency	TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr20:61468580C>T	ENST00000343916.3	+	30	1752	c.1749C>T	c.(1747-1749)cgC>cgT	p.R583R	COL9A3_ENST00000462700.1_3'UTR	NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	583	Triple-helical region 2 (COL2).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					CTGGATACCGCGGTCCCACTG	0.667													C|||	2	0.000399361	8e-04	0.0014	5008	,	,		13123	0		0	False		,,,				2504	0				p.R583R		.											.	COL9A3-514	0			c.C1749T						.	C		2,4394		0,2,2196	24	33	30		1749	-9	0.9	20	dbSNP_134	30	5,8583		0,5,4289	no	coding-synonymous	COL9A3	NM_001853.3		0,7,6485	TT,TC,CC		0.0582,0.0455,0.0539		583/685	61468580	7,12977	2198	4294	6492	SO:0001819	synonymous_variant	1299	exon30			ATACCGCGGTCCC	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2219	protein-coding gene	gene with protein product	"collagen type IX proteoglycan"	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1749C>T	20.37:g.61468580C>T		Somatic	74	1		WXS	Illumina HiSeq	Phase_I	82	25	NM_001853	0	0	0	0	0	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			C|1.000;T|0.000		0.667	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61468580	C	T	61468580	2	4	94	1	0	0	0	0	0	0	0	1	3715	755	27	1		1	COL9A3	20	61468580	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	5240964	61468580	1556940	81	8492											
DIDO1	11083	ucsc.edu	37	chr20	61512320	61512320	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagggcgccgcaaggcGgtgtgggcagcagcaccctc	6	4	17	14	3	0	0	0	0	0	0	1	0	0	0	2	4	3	6	2	4	1	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr20:61512320G>T	ENST00000266070.4	-	16	5313	c.4988C>A	c.(4987-4989)cCg>cAg	p.P1663Q	DIDO1_ENST00000395343.1_Missense_Mutation_p.P1663Q	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1663					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GCCGCAAGGCGGTGTGGGCAG	0.731																																					p.P1663Q	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)												.	DIDO1-96	0			c.C4988A						.						11	13	12					20																	61512320		2175	4250	6425	SO:0001583	missense	11083	exon16			CAAGGCGGTGTGG	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"Zinc fingers, PHD-type"	2680	protein-coding gene	gene with protein product		604140	"chromosome 20 open reading frame 158", "death associated transcription factor 1"	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.4988C>A	20.37:g.61512320G>T	ENSP00000266070:p.Pro1663Gln	Somatic	29	0		WXS	Illumina HiSeq		35	4	NM_001193369	0	0	1	1	0	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.280550	0.59758	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.24151	1.87;1.87	5.31	5.31	0.75309	.	0.000000	0.42821	D	0.000644	T	0.44350	0.1289	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.40040	-0.9584	10	0.87932	D	0	-26.6638	18.9695	0.92709	0.0:0.0:1.0:0.0	.	1663	Q9BTC0	DIDO1_HUMAN	Q	1663	ENSP00000266070:P1663Q;ENSP00000378752:P1663Q	ENSP00000266070:P1663Q	P	-	2	0	DIDO1	60982765	1.000000	0.71417	0.443000	0.26883	0.145000	0.21501	6.992000	0.76238	2.456000	0.83038	0.655000	0.94253	CCG	.		0.731	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61512320	G	T	61512320	3	4	94	1	0	0	0	0	1	0	0	0	4533	1116	39	4	1738	4	DIDO1	20	61512320	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	43740	61512320	1513200	82	8493											
NRIP1	8204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	16337670	16337670	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttacttctgtgcggggacaaAtctcgcacacagttttctga	9	13	9	10	2	3	1	0	1	3	0	4	2	3	2	0	2	2	2	0	2	2	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr21:16337670A>G	ENST00000400202.1	-	3	3556	c.2844T>C	c.(2842-2844)gaT>gaC	p.D948D	NRIP1_ENST00000400199.1_Silent_p.D948D|AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Silent_p.D948D			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	948	Interaction with ZNF366.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GCGGGGACAAATCTCGCACAC	0.428																																					p.D948D		.											.	NRIP1-186	0			c.T2844C						.						82	82	82					21																	16337670		2203	4299	6502	SO:0001819	synonymous_variant	8204	exon4			GGACAAATCTCGC	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"receptor interacting protein 140", "nuclear factor RIP140"	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.2844T>C	21.37:g.16337670A>G		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	157	44	NM_003489	0	0	4	11	7	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			.		0.428	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		G	16337670	A	G	16337670	2	3	94	1	0	0	0	0	0	0	0	1	10678	98	4	3		3	NRIP1	21	16337670	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08		16337670	31792225	83	8494											
NCAM2	4685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	22658662	22658662	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcagaagtggtttgccgAgttagcagttcacctgcacc	9	10	12	10	1	1	1	1	0	0	1	1	3	1	1	3	1	4	6	3	1	2	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr21:22658662A>T	ENST00000400546.1	+	4	660	c.411A>T	c.(409-411)cgA>cgT	p.R137R	NCAM2_ENST00000535285.1_Silent_p.R162R|NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000284894.7_Intron	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	137	Ig-like C2-type 2.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TGGTTTGCCGAGTTAGCAGTT	0.398																																					p.R137R		.											.	NCAM2-94	0			c.A411T						.						119	114	116					21																	22658662		2019	4192	6211	SO:0001819	synonymous_variant	4685	exon4			TTGCCGAGTTAGC		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.411A>T	21.37:g.22658662A>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	55	15	NM_004540	0	0	0	0	0	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																			.		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22658662	A	T	22658662	2	4	94	1	0	0	0	0	0	0	0	1	10229	291	11	5		5	NCAM2	21	22658662	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08	6320992	22658662	25471233	84	8495											
SON	6651	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr21	34932382	34932382	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaggtagtccaaggtacaActatttagcttcccgatttg	11	12	10	8	1	0	0	0	0	0	0	2	2	2	1	2	3	3	3	2	3	7	7			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr21:34932382A>G	ENST00000356577.4	+	6	7132				SON_ENST00000290239.6_Intron|SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Missense_Mutation_p.N2286S	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein						cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CCAAGGTACAACTATTTAGCT	0.473																																					p.N2286S		.											.	SON-97	0			c.A6857G						.						149	142	145					21																	34932382		2203	4300	6503	SO:0001627	intron_variant	6651	exon7			GGTACAACTATTT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.6657+301A>G	21.37:g.34932382A>G		Somatic	200	0		WXS	Illumina HiSeq	Phase_I	180	55	NM_032195	0	0	12	14	2	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.907015	0.33628	.	.	ENSG00000159140	ENST00000300278	T	0.09630	2.96	5.58	5.58	0.84498	.	.	.	.	.	T	0.32071	0.0817	.	.	.	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	T	0.03922	-1.0992	8	0.87932	D	0	.	12.1393	0.53989	1.0:0.0:0.0:0.0	.	2286	P18583-3	.	S	2286	ENSP00000300278:N2286S	ENSP00000300278:N2286S	N	+	2	0	SON	33854252	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.247000	0.58750	2.124000	0.65301	0.460000	0.39030	AAC	.		0.473	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34932382	A	G	34932382	1	3	94	0	1	0	0	0	0	0	0	0	14958	43	2	3		3	SON	21	34932382	Intron	SNP	A	TCGA-DW-7834-01A-11D-2136-08	12273720	34932382	13197513	85	8496											
CECR2	27443	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18021911	18021911	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagaggagaagcaaatgtgCggggggctgacacacctttc	11	6	14	10	1	0	3	0	1	0	2	1	4	0	3	2	4	2	2	2	4	2	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr22:18021911C>T	ENST00000400585.2	+	16	2028	c.1590C>T	c.(1588-1590)tgC>tgT	p.C530C	CECR2_ENST00000400573.5_Silent_p.C671C|CECR2_ENST00000262608.8_Silent_p.C672C			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	713					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		AGCAAATGTGCGGGGGGCTGA	0.557																																					.													.	CECR2-70	0			.						.						33	35	34					22																	18021911		1996	4163	6159	SO:0001819	synonymous_variant	27443	.			AATGTGCGGGGGG	AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.1590C>T	22.37:g.18021911C>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	27	8	.	0	0	1	1	0	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Silent	SNP	ENST00000400585.2	37																																																																																				.		0.557	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413		T	18021911	C	T	18021911	2	4	94	1	0	0	0	0	0	0	0	1	3212	776	27	1		1	CECR2	22	18021911	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08		18021911	33282655	86	8497											
RHBDD3	25807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	29656765	29656765	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggagcctcaggggccagcaCcccgccaaggtcctgcacaa	10	3	12	16	1	1	0	1	0	0	0	2	1	2	1	6	4	3	2	6	4	2	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr22:29656765C>A	ENST00000216085.7	-	5	1045	c.621G>T	c.(619-621)ggG>ggT	p.G207G	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	207					liver development (GO:0001889)|MAPK cascade (GO:0000165)|negative regulation of natural killer cell activation (GO:0032815)|positive regulation of protein catabolic process (GO:0045732)|regulation of acute inflammatory response (GO:0002673)|regulation of protein secretion (GO:0050708)|response to xenobiotic stimulus (GO:0009410)	integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			lung(1)|ovary(1)	2						GGGGCCAGCACCCCGCCAAGG	0.692																																					p.G207G		.											.	RHBDD3-91	0			c.G621T						.						17	17	17					22																	29656765		2198	4291	6489	SO:0001819	synonymous_variant	25807	exon5			CCAGCACCCCGCC	AL050346	CCDS13850.1	22q12.2	2006-02-22	2006-02-22	2006-02-22	ENSG00000100263	ENSG00000100263			1308	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 3"	C22orf3		10591208, 15105437	Standard	NM_012265		Approved	PTAG	uc003aeq.1	Q9Y3P4	OTTHUMG00000151032	ENST00000216085.7:c.621G>T	22.37:g.29656765C>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	29	9	NM_012265	0	0	6	8	2	Q6I9X3|Q9UGQ7	Silent	SNP	ENST00000216085.7	37	CCDS13850.1																																																																																			.		0.692	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265		A	29656765	C	A	29656765	2	1	94	1	0	0	0	0	0	0	0	1	13350	494	18	4		4	RHBDD3	22	29656765	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	11634854	29656765	21647801	87	8498											
RPS6KA3	6197	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	20194424	20194424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agaatgtatcttcaggcctgCccgttgcaggtttaaatggc	9	12	11	9	1	2	1	1	0	1	1	2	1	2	1	2	3	2	4	2	3	4	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chrX:20194424C>T	ENST00000379565.3	-	13	1253	c.1046G>A	c.(1045-1047)gGc>gAc	p.G349D	RPS6KA3_ENST00000379548.4_Missense_Mutation_p.G320D|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.G321D|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.G321D	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	349	AGC-kinase C-terminal.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TTCAGGCCTGCCCGTTGCAGG	0.328																																					p.G349D													.	RPS6KA3-1504	0			c.G1046A						.						80	76	78					X																	20194424		2203	4300	6503	SO:0001583	missense	6197	exon13			GGCCTGCCCGTTG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1046G>A	X.37:g.20194424C>T	ENSP00000368884:p.Gly349Asp	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	47	5	NM_004586	0	0	7	7	0	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545172	0.45280	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.4	4.53	0.55603	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	L	0.35414	1.06	0.80722	D	1	B;B;P;B	0.45715	0.282;0.254;0.865;0.103	B;B;P;B	0.48524	0.066;0.091;0.58;0.067	T	0.35325	-0.9793	10	0.37606	T	0.19	.	15.3574	0.74437	0.0:0.8638:0.1362:0.0	.	321;320;321;349	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	D	349;321;320;321	ENSP00000368884:G349D;ENSP00000440220:G321D;ENSP00000368865:G320D;ENSP00000444837:G321D	ENSP00000368865:G320D	G	-	2	0	RPS6KA3	20104345	0.998000	0.40836	0.999000	0.59377	0.986000	0.74619	3.688000	0.54699	1.038000	0.40049	0.513000	0.50165	GGC	.		0.328	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		T	20194424	C	T	20194424	3	4	94	1	0	0	0	0	1	0	0	0	13684	739	26	2	1216	2	RPS6KA3	23	20194424	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		20194424	135076136	88	8499											
MAP7D3	79649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	135314169	135314169	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggacgcttccatgcttgtgTtgcagaatacttccacattc	8	13	9	11	1	0	1	0	0	0	1	3	2	2	2	2	1	3	4	2	1	2	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chrX:135314169T>C	ENST00000316077.9	-	8	1167	c.947A>G	c.(946-948)aAc>aGc	p.N316S	MAP7D3_ENST00000370661.1_Missense_Mutation_p.N281S|MAP7D3_ENST00000370663.5_Missense_Mutation_p.N298S	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	316					microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					CATGCTTGTGTTGCAGAATAC	0.567																																					p.N316S		.											.	MAP7D3-110	0			c.A947G						.						167	168	168					X																	135314169		2132	4212	6344	SO:0001583	missense	79649	exon8			CTTGTGTTGCAGA	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.947A>G	X.37:g.135314169T>C	ENSP00000318086:p.Asn316Ser	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	192	23	NM_024597	0	0	12	12	0	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	4.011	-0.000557	0.07819	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.11930	2.73;2.73;2.73;2.73	3.62	-1.54	0.08584	.	.	.	.	.	T	0.07773	0.0195	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.26258	0.09;0.126;0.09;0.145	B;B;B;B	0.26614	0.032;0.039;0.032;0.071	T	0.44467	-0.9326	9	0.13108	T	0.6	0.3015	8.6543	0.34053	0.0:0.6237:0.0:0.3763	.	298;275;316;281	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	S	281;316;298;275	ENSP00000359695:N281S;ENSP00000318086:N316S;ENSP00000359697:N298S;ENSP00000359694:N275S	ENSP00000318086:N316S	N	-	2	0	MAP7D3	135141835	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.087000	0.14958	-0.273000	0.09246	-0.463000	0.05309	AAC	.		0.567	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			C	135314169	T	C	135314169	3	2	94	1	0	0	0	0	1	0	0	0	9294	1725	60	3	1727	3	MAP7D3	23	135314169	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	115119745	135314169	19956391	89	8500											
DNAJC16	23341	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	15890499	15890500	+	Frame_Shift_Del	DEL	GA	GA	-																															aagacccttggattgggagtGagagtgacaaatttatcctc																										TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:15890499_15890500delGA	ENST00000375847.3	+	10	1578_1579	c.1414_1415delGA	c.(1414-1416)gagfs	p.E472fs	DNAJC16_ENST00000375849.1_Frame_Shift_Del_p.E472fs|DNAJC16_ENST00000483270.1_3'UTR|RP4-680D5.8_ENST00000606186.1_RNA|DNAJC16_ENST00000375838.1_Frame_Shift_Del_p.E472fs	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	472					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GATTGGGAGTGAGAGTGACAAA	0.465																																					p.472_472del		.											.	DNAJC16-226	0			c.1414_1415del						.																																			SO:0001589	frameshift_variant	23341	exon10			.	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.1414_1415delGA	1.37:g.15890501_15890502delGA	ENSP00000365007:p.Glu472fs	Somatic	308	0		WXS	Illumina HiSeq	Phase_I	306	86	NM_015291	0	0	0	0	0	Q68D57|Q86X32|Q8N5P4	Frame_Shift_Del	DEL	ENST00000375847.3	37	CCDS30606.1																																																																																			.		0.465	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		-	15890500	GA	-	15890499	7	5	95	1	0	1	0	1	0	0	0	0	4646	1291	45	0	1448	0	DNAJC16	1	15890499	Frame_Shift_Del	DEL	GA	TCGA-DW-7837-01A-11D-2136-08		15890499	233360122	1	8501											
CYP4A22	284541	ucsc.edu	37	chr1	47614339	47614339	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagggccctgaccctgctccGctttgagctgctgcctgatc	4	10	11	16	1	0	3	0	3	0	0	2	3	1	3	4	1	4	4	4	1	0	1	rs377247931		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:47614339G>A	ENST00000371891.3	+	12	1461	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H	CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.R379H|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	477						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R477H(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACCCTGCTCCGCTTTGAGCTG	0.567																																					p.R477H	Pancreas(88;1240 1470 2099 14214 37557)												.	CYP4A22-139	1	Substitution - Missense(1)	endometrium(1)	c.G1430A						.	G	HIS/ARG	0,4406		0,0,2203	123	119	120		1430	0.7	0.9	1		120	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP4A22	NM_001010969.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	477/520	47614339	1,13005	2203	4300	6503	SO:0001583	missense	284541	exon12			TGCTCCGCTTTGA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"Cytochrome P450s"	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1430G>A	1.37:g.47614339G>A	ENSP00000360958:p.Arg477His	Somatic	212	1		WXS	Illumina HiSeq		213	3	NM_001010969	0	0	32	69	37	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	.	.	.	.	.	.	.	.	.	.	g	15.03	2.713120	0.48517	0.0	1.16E-4	ENSG00000162365	ENST00000371890;ENST00000371891	T;T	0.70045	-0.45;-0.45	1.67	0.673	0.17941	.	0.280522	0.39146	N	0.001452	T	0.46288	0.1385	N	0.21324	0.655	0.39875	D	0.973561	B	0.27951	0.195	B	0.29524	0.103	T	0.18871	-1.0323	10	0.36615	T	0.2	.	6.4299	0.21790	0.2724:0.0:0.7276:0.0	.	477	Q5TCH4	CP4AM_HUMAN	H	379;477	ENSP00000360957:R379H;ENSP00000360958:R477H	ENSP00000360957:R379H	R	+	2	0	CYP4A22	47386926	0.000000	0.05858	0.930000	0.37139	0.888000	0.51559	0.420000	0.21263	0.056000	0.16144	0.405000	0.27470	CGC	.		0.567	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		A	47614339	G	A	47614339	3	1	95	1	0	0	0	0	1	0	0	0	4190	1087	38	1	1476	1	CYP4A22	1	47614339	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	31723840	47614339	201636282	2	8502											
SSBP3	23648	hgsc.bcm.edu	37	chr1	54694017	54694017	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgctaatgccacttatgtTgttaggagaattctgtggaa	11	15	10	5	0	1	1	0	0	1	1	1	3	1	2	1	2	2	3	1	2	5	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:54694017T>G	ENST00000371320.3	-	17	1458	c.1048A>C	c.(1048-1050)Aac>Cac	p.N350H	SSBP3_ENST00000417664.2_Missense_Mutation_p.N240H|SSBP3_ENST00000371319.3_Missense_Mutation_p.N323H|SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000357475.4_Missense_Mutation_p.N330H	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	350	Gly-rich.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						CCACTTATGTTGTTAGGAGAA	0.567																																					p.N350H		.											.	SSBP3-90	0			c.A1048C						.						116	113	114					1																	54694017		2203	4300	6503	SO:0001583	missense	23648	exon17			TTATGTTGTTAGG		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"single-stranded DNA-binding protein 3"			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.1048A>C	1.37:g.54694017T>G	ENSP00000360371:p.Asn350His	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	104	8	NM_145716	0	0	0	0	0	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	37	CCDS591.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.923912	0.73213	.	.	ENSG00000157216	ENST00000417664;ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	4.52	3.35	0.38373	.	0.000000	0.85682	U	0.000000	T	0.75102	0.3804	M	0.71206	2.165	0.58432	D	0.999999	D;D;D	0.89917	0.999;0.991;1.0	D;P;D	0.83275	0.996;0.891;0.996	T	0.74420	-0.3671	9	0.52906	T	0.07	-2.2147	10.5274	0.44957	0.1453:0.0:0.0:0.8547	.	323;330;350	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	H	240;350;323;330	.	ENSP00000350067:N330H	N	-	1	0	SSBP3	54466605	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.691000	0.84191	0.673000	0.31224	0.369000	0.22263	AAC	.		0.567	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		G	54694017	T	G	54694017	3	3	95	1	0	0	0	0	1	0	0	0	15213	1812	63	5	126	5	SSBP3	1	54694017	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	7079678	54694017	194556604	3	8503											
ST6GALNAC5	81849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	77528824	77528824	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acggacattcaatattcactTttttcaaccagactggaaac	14	12	5	10	1	3	1	3	0	0	1	3	3	3	3	1	2	2	0	1	2	4	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:77528824T>G	ENST00000477717.1	+	5	1179	c.944T>G	c.(943-945)tTt>tGt	p.F315C		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	315					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						AATATTCACTTTTTTCAACCA	0.438																																					p.F315C		.											.	ST6GALNAC5-92	0			c.T944G						.						116	110	112					1																	77528824		2203	4300	6503	SO:0001583	missense	81849	exon5			TTCACTTTTTTCA		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.944T>G	1.37:g.77528824T>G	ENSP00000417583:p.Phe315Cys	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	153	49	NM_030965	0	0	10	10	0	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	37	CCDS673.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.359557	0.82353	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.58358	0.34	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.73210	0.3558	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79562	-0.1752	10	0.87932	D	0	-36.7448	16.3789	0.83431	0.0:0.0:0.0:1.0	.	315	Q9BVH7	SIA7E_HUMAN	C	315;225	ENSP00000417583:F315C	ENSP00000406658:F225C	F	+	2	0	ST6GALNAC5	77301412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.649000	0.83500	2.267000	0.75376	0.533000	0.62120	TTT	.		0.438	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		G	77528824	T	G	77528824	3	3	95	1	0	0	0	0	1	0	0	0	15259	1841	64	5	962	5	ST6GALNAC5	1	77528824	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	22834807	77528824	171721797	4	8504			1	25		2	2	12	N	T_G	1.598992e-05
ST6GALNAC5	81849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	77528835	77528835	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atattcacttttttcaaccaGactggaaaccagaatcactt	14	13	4	10	0	3	2	3	0	0	2	3	3	3	3	2	1	2	0	2	1	4	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:77528835G>A	ENST00000477717.1	+	5	1190	c.955G>A	c.(955-957)Gac>Aac	p.D319N		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	319					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						TTTTCAACCAGACTGGAAACC	0.438																																					p.D319N		.											.	ST6GALNAC5-92	0			c.G955A						.						113	106	109					1																	77528835		2203	4300	6503	SO:0001583	missense	81849	exon5			CAACCAGACTGGA		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"Sialyltransferases"	19342	protein-coding gene	gene with protein product		610134	"sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.955G>A	1.37:g.77528835G>A	ENSP00000417583:p.Asp319Asn	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	153	46	NM_030965	0	0	11	11	0	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	37	CCDS673.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.733083	0.48939	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.30714	1.52	5.93	2.92	0.33932	.	0.140018	0.64402	N	0.000006	T	0.12475	0.0303	L	0.49350	1.555	0.50467	D	0.999873	B	0.18166	0.026	B	0.16289	0.015	T	0.05022	-1.0911	10	0.23302	T	0.38	-15.1218	11.5508	0.50719	0.0636:0.2339:0.7025:0.0	.	319	Q9BVH7	SIA7E_HUMAN	N	319;229	ENSP00000417583:D319N	ENSP00000406658:D229N	D	+	1	0	ST6GALNAC5	77301423	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.553000	0.60753	0.830000	0.34757	0.655000	0.94253	GAC	.		0.438	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77528835	G	A	77528835	3	1	95	1	0	0	0	0	1	0	0	0	15259	942	33	2	973	2	ST6GALNAC5	1	77528835	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	11	77528835	171721786	5	8505			1	25		2	2	12	N	T_G	1.598992e-05
CLASP1	23332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	122206659	122206659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgtggtacaagtgctctgCttctctgctgaagtgactgt	6	14	13	8	0	2	2	0	2	2	0	3	2	2	2	0	2	4	4	0	2	3	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr2:122206659C>T	ENST00000263710.4	-	17	1950	c.1561G>A	c.(1561-1563)Gca>Aca	p.A521T	CLASP1_ENST00000541377.1_Missense_Mutation_p.A521T|CLASP1_ENST00000455322.2_Missense_Mutation_p.A521T|CLASP1_ENST00000545861.1_Missense_Mutation_p.A289T|CLASP1_ENST00000397587.3_Missense_Mutation_p.A521T|CLASP1_ENST00000409078.3_Missense_Mutation_p.A521T|CLASP1_ENST00000541859.1_Missense_Mutation_p.A290T	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	521					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					AAGTGCTCTGCTTCTCTGCTG	0.493																																					p.A521T		.											.	CLASP1-91	0			c.G1561A						.						100	99	99					2																	122206659		1961	4153	6114	SO:0001583	missense	23332	exon17			GCTCTGCTTCTCT	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.1561G>A	2.37:g.122206659C>T	ENSP00000263710:p.Ala521Thr	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	39	12	NM_001207051	0	0	3	4	1	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	C	36	5.877189	0.97055	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08;-0.08;-0.08	6.04	6.04	0.98038	Armadillo-like helical (1);Armadillo-type fold (2);CLASP N-terminal domain (1);	0.000000	0.85682	D	0.000000	D	0.83889	0.5352	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.91635	0.997;0.995;0.998;0.999	D	0.85446	0.1158	10	0.87932	D	0	-19.0221	20.5948	0.99439	0.0:1.0:0.0:0.0	.	521;521;521;521	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	T	521;521;521;521;290;521;289	ENSP00000263710:A521T;ENSP00000389372:A521T;ENSP00000380717:A521T;ENSP00000441625:A521T;ENSP00000441770:A290T;ENSP00000386442:A521T;ENSP00000438620:A289T	ENSP00000263710:A521T	A	-	1	0	CLASP1	121923129	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GCA	.		0.493	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		T	122206659	C	T	122206659	3	4	95	1	0	0	0	0	1	0	0	0	3460	797	28	2	3203	2	CLASP1	2	122206659	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		122206659	120992714	6	8506											
ZNF385B	151126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	180309603	180309603	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaggtgaggtaaacttacTgctagaatactcgggctccg	11	9	12	9	2	0	2	0	1	0	1	2	2	1	2	1	3	5	4	1	3	6	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr2:180309603T>A	ENST00000410066.1	-	9	1800	c.1197A>T	c.(1195-1197)gcA>gcT	p.A399A	ZNF385B_ENST00000336917.5_Splice_Site_p.A297A|ZNF385B_ENST00000409692.1_Splice_Site_p.A297A|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Splice_Site_p.A323A	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	399	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			GTAAACTTACTGCTAGAATAC	0.502																																					p.A399A	Colon(155;204 2491 32774 51842)	.											.	ZNF385B-23	0			c.A1197T						.						199	193	195					2																	180309603		2203	4300	6503	SO:0001630	splice_region_variant	151126	exon9			ACTTACTGCTAGA	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.1197+1A>T	2.37:g.180309603T>A		Somatic	229	1		WXS	Illumina HiSeq	Phase_I	242	72	NM_152520	0	0	0	0	0	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Silent	SNP	ENST00000410066.1	37	CCDS33339.1																																																																																			.		0.502	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520	Silent	A	180309603	T	A	180309603	5	1	95	1	0	0	0	0	0	0	1	0	17909	1594	55	5	226	5	ZNF385B	2	180309603	Splice_Site	SNP	T	TCGA-DW-7837-01A-11D-2136-08	58102944	180309603	62889770	7	8507											
ALPP	250	hgsc.bcm.edu	37	chr2	233244230	233244230	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctctgtccccagacatacaAtgtagacaaacatgtgccag	13	9	7	12	0	1	2	0	0	1	2	3	2	2	2	3	0	3	1	3	0	4	2	rs1130341		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr2:233244230A>G	ENST00000392027.2	+	4	586	c.317A>G	c.(316-318)aAt>aGt	p.N106S	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	106					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CAGACATACAATGTAGACAAA	0.577																																					p.N106S		.											.	ALPP-91	0			c.A317G						.	A	SER/ASN	1,4405		0,1,2202	56	51	52		317	-0.4	1	2	dbSNP_86	52	0,8600		0,0,4300	no	missense	ALPP	NM_001632.3	46	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	106/536	233244230	1,13005	2203	4300	6503	SO:0001583	missense	250	exon4			CATACAATGTAGA	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"Regan isozyme"	171800	"alkaline phosphatase, placental (Regan isozyme)"			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.317A>G	2.37:g.233244230A>G	ENSP00000375881:p.Asn106Ser	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	28	3	NM_001632	0	0	0	0	0	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	.	2.668	-0.278125	0.05679	2.27E-4	0.0	ENSG00000163283	ENST00000392027	D	0.95103	-3.61	2.31	-0.39	0.12450	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.295720	0.40818	N	0.001001	D	0.83487	0.5265	N	0.12831	0.26	0.29049	N	0.884612	B	0.30889	0.299	B	0.25405	0.06	T	0.75230	-0.3391	10	0.30854	T	0.27	.	6.227	0.20714	0.7126:0.1707:0.1167:0.0	rs1130341;rs3189051;rs17412756	106	P05187	PPB1_HUMAN	S	106	ENSP00000375881:N106S	ENSP00000375881:N106S	N	+	2	0	ALPP	232952474	0.992000	0.36948	0.984000	0.44739	0.510000	0.34073	0.843000	0.27640	-0.220000	0.09988	-0.817000	0.03123	AAT	A|1.000;G|0.000		0.577	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		G	233244230	A	G	233244230	3	3	95	1	0	0	0	0	1	0	0	0	548	101	4	3	331	3	ALPP	2	233244230	Missense_Mutation	SNP	A	TCGA-DW-7837-01A-11D-2136-08	52934627	233244230	9955143	8	8508											
USP40	55230	hgsc.bcm.edu	37	chr2	234450984	234450984	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactctggagatctttcagaTtcacatctggtttacttttt	8	18	6	9	0	5	2	2	0	3	2	5	3	5	2	0	2	1	1	0	2	1	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr2:234450984T>G	ENST00000427112.2	-	8	1027	c.992A>C	c.(991-993)aAt>aCt	p.N331T	USP40_ENST00000251722.6_Missense_Mutation_p.N331T|USP40_ENST00000450966.1_Missense_Mutation_p.N343T			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	331	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		ATCTTTCAGATTCACATCTGG	0.358																																					p.N343T		.											.	USP40-455	0			c.A1028C						.						120	108	112					2																	234450984		1837	4089	5926	SO:0001583	missense	55230	exon8			TTCAGATTCACAT	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"Ubiquitin-specific peptidases"	20069	protein-coding gene	gene with protein product		610570	"ubiquitin specific protease 40"			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.992A>C	2.37:g.234450984T>G	ENSP00000387898:p.Asn331Thr	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_018218	0	0	2	4	2	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	T	7.815	0.716608	0.15306	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.05025	3.51;3.51;3.51	4.76	3.61	0.41365	.	6.476770	0.00166	N	0.000001	T	0.04227	0.0117	N	0.08118	0	0.21220	N	0.999757	B	0.06786	0.001	B	0.09377	0.004	T	0.38993	-0.9635	10	0.15066	T	0.55	.	6.2681	0.20939	0.0:0.0871:0.16:0.753	.	343	Q9NVE5-3	.	T	343;331;331	ENSP00000415434:N343T;ENSP00000251722:N331T;ENSP00000387898:N331T	ENSP00000251722:N331T	N	-	2	0	USP40	234115723	0.007000	0.16637	0.954000	0.39281	0.861000	0.49209	-0.110000	0.10824	0.920000	0.36970	0.460000	0.39030	AAT	.		0.358	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		G	234450984	T	G	234450984	3	3	95	1	0	0	0	0	1	0	0	0	17105	1493	52	5	2811	5	USP40	2	234450984	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	1206754	234450984	8748389	9	8509											
C3orf19	51244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	14695999	14695999	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacaagaaaaacttctaaaaGattctggagtttttggaaaa	19	11	7	4	0	2	2	0	0	2	2	2	4	2	4	0	2	2	1	0	2	8	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr3:14695999G>C	ENST00000383794.3	+	2	182	c.109G>C	c.(109-111)Gat>Cat	p.D37H	CCDC174_ENST00000303688.7_Missense_Mutation_p.D37H	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	37						cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACTTCTAAAAGATTCTGGAGT	0.299																																					p.D37H		.											.	.	0			c.G109C						.						26	26	26					3																	14695999		1779	4049	5828	SO:0001583	missense	51244	exon2			CTAAAAGATTCTG	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 19"	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.109G>C	3.37:g.14695999G>C	ENSP00000373304:p.Asp37His	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	38	17	NM_016474	0	0	9	12	3	Q96CS5	Missense_Mutation	SNP	ENST00000383794.3	37	CCDS2620.2	.	.	.	.	.	.	.	.	.	.	G	15.54	2.862642	0.51482	.	.	ENSG00000154781	ENST00000383794;ENST00000303688	T;T	0.46063	0.88;0.89	5.58	4.7	0.59300	.	0.057430	0.64402	D	0.000001	T	0.61048	0.2316	M	0.70275	2.135	0.46981	D	0.999278	D	0.89917	1.0	D	0.71184	0.972	T	0.63005	-0.6733	10	0.59425	D	0.04	-12.7651	12.8107	0.57637	0.08:0.0:0.92:0.0	.	37	Q6PII3	CC019_HUMAN	H	37	ENSP00000373304:D37H;ENSP00000302344:D37H	ENSP00000302344:D37H	D	+	1	0	C3orf19	14671003	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.367000	0.73099	2.620000	0.88729	0.491000	0.48974	GAT	.		0.299	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474		C	14695999	G	C	14695999	3	2	95	1	0	0	0	0	1	0	0	0	2218	942	33	4	115	4	C3orf19	3	14695999	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		14695999	183326431	10	8510											
DPH3	285381	hgsc.bcm.edu;bcgsc.ca	37	chr3	16302327	16302327	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggactgtttctccacacaCaaactgatcctaagacagag	13	9	8	11	0	1	3	0	1	1	2	3	4	2	4	2	1	1	1	2	1	2	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr3:16302327C>G	ENST00000488423.1	-	3	288	c.193G>C	c.(193-195)Gtg>Ctg	p.V65L	DPH3_ENST00000383775.4_Missense_Mutation_p.V40L|DPH3_ENST00000285082.4_5'UTR	NM_206831.2	NP_996662.1	Q96FX2	DPH3_HUMAN	diphthamide biosynthesis 3	65					negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			large_intestine(2)	2						TCTCCACACACAAACTGATCC	0.388																																					p.V65L		.											.	DPH3-227	0			c.G193C						.						98	87	91					3																	16302327		2203	4300	6503	SO:0001583	missense	285381	exon3			CACACACAAACTG	BC010181	CCDS2629.1, CCDS43058.1	3p25.1	2013-06-19	2013-06-19	2006-10-25	ENSG00000154813	ENSG00000154813			27717	protein-coding gene	gene with protein product	"DPH3A, KTI11 homolog A (S. cerevisiae)"	608959	"zinc finger, CSL-type containing 2", "DPH3 homolog (KTI11, S. cerevisiae)", "DPH3, KTI11 homolog (S. cerevisiae)"	ZCSL2		14527407, 14980502, 15485916, 16648478	Standard	NM_001047434		Approved	DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A	uc003cau.3	Q96FX2	OTTHUMG00000129866	ENST00000488423.1:c.193G>C	3.37:g.16302327C>G	ENSP00000419599:p.Val65Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_206831	0	0	1	1	0		Missense_Mutation	SNP	ENST00000488423.1	37	CCDS2629.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.311440	0.23821	.	.	ENSG00000154813	ENST00000488423;ENST00000383775	.	.	.	5.73	3.22	0.36961	.	0.175580	0.64402	D	0.000016	T	0.16128	0.0388	.	.	.	0.24129	N	0.995778	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30563	-0.9974	8	0.07990	T	0.79	-32.8775	7.2848	0.26333	0.0:0.2036:0.0:0.7964	.	40;65	Q96FX2-2;Q96FX2	.;DPH3_HUMAN	L	65;40	.	ENSP00000373285:V40L	V	-	1	0	DPH3	16277331	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	1.606000	0.36826	0.362000	0.24319	0.491000	0.48974	GTG	.		0.388	DPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252108.2	NM_206831		G	16302327	C	G	16302327	3	3	95	1	0	0	0	0	1	0	0	0	4732	478	17	4	59	4	DPH3	3	16302327	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	1606328	16302327	181720103	11	8511											
DDX60L	91351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	169337906	169337906	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgaataatgacaaggaggaGctcccaaaattttgctccaa	15	9	8	9	1	0	1	0	1	0	0	3	4	2	3	2	2	2	2	2	2	6	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr4:169337906G>A	ENST00000511577.1	-	20	2900	c.2653C>T	c.(2653-2655)Ctc>Ttc	p.L885F	DDX60L_ENST00000505890.1_Missense_Mutation_p.L885F|DDX60L_ENST00000260184.7_Missense_Mutation_p.L885F			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	885	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		ACAAGGAGGAGCTCCCAAAAT	0.343																																					p.L885F		.											.	DDX60L-69	0			c.C2653T						.						107	102	104					4																	169337906		1833	4116	5949	SO:0001583	missense	91351	exon20			GGAGGAGCTCCCA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.2653C>T	4.37:g.169337906G>A	ENSP00000422423:p.Leu885Phe	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	111	33	NM_001012967	0	0	3	6	3	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		.	.	.	.	.	.	.	.	.	.	G	15.04	2.714600	0.48622	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.74526	-0.85;-0.85;1.2;1.2	3.42	3.42	0.39159	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.183055	0.25361	U	0.031226	T	0.69124	0.3076	L	0.49640	1.575	0.25638	N	0.986238	P;P;P	0.45283	0.855;0.769;0.855	B;B;B	0.41510	0.359;0.288;0.359	T	0.66164	-0.5992	10	0.66056	D	0.02	.	13.027	0.58821	0.0:0.0:1.0:0.0	.	885;885;885	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	F	885;885;885;581	ENSP00000260184:L885F;ENSP00000422423:L885F;ENSP00000422202:L885F;ENSP00000421026:L581F	ENSP00000260184:L885F	L	-	1	0	DDX60L	169574481	1.000000	0.71417	0.896000	0.35187	0.943000	0.58893	5.558000	0.67319	1.619000	0.50296	0.461000	0.40582	CTC	.		0.343	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169337906	G	A	169337906	3	1	95	1	0	0	0	0	1	0	0	0	4385	971	34	2	2543	2	DDX60L	4	169337906	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		169337906	21816370	12	8512											
MAP3K1	4214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	56177037	56177037	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactgttgttggaatttccTgctgaattttatcctcatat	9	18	7	7	0	1	2	1	1	0	1	3	3	3	3	2	1	1	3	2	1	4	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr5:56177037T>A	ENST00000399503.3	+	13	2307	c.2307T>A	c.(2305-2307)ccT>ccA	p.P769P		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	769					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TGGAATTTCCTGCTGAATTTT	0.348																																					p.P769P		.											.	MAP3K1-956	0			c.T2307A						.						164	147	152					5																	56177037		1836	4079	5915	SO:0001819	synonymous_variant	4214	exon13			ATTTCCTGCTGAA	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2307T>A	5.37:g.56177037T>A		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	76	25	NM_005921	0	0	2	5	3		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			.		0.348	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		A	56177037	T	A	56177037	2	1	95	1	0	0	0	0	0	0	0	1	9268	1567	55	5		5	MAP3K1	5	56177037	Silent	SNP	T	TCGA-DW-7837-01A-11D-2136-08		56177037	124738223	13	8513											
C4A	720	hgsc.bcm.edu	37	chr6	31964785	31964785	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagatggcagaccaggctTcggcctggctcacccgtcag	8	6	13	14	2	2	2	2	0	0	2	3	3	2	2	3	4	0	3	3	4	0	1	rs201016130	byFrequency	TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr6:31964785T>G	ENST00000428956.2	+	29	3940	c.3856T>G	c.(3856-3858)Tcg>Gcg	p.S1286A	C4A_ENST00000498271.1_Missense_Mutation_p.S1286A|C4A-AS1_ENST00000458633.1_RNA	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1286			S -> A (in allotype C4A1, allotype C4A3a, allotype C4A6; dbSNP:rs201016130). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1988494, ECO:0000269|PubMed:3696167, ECO:0000269|PubMed:6832377, ECO:0000269|Ref.3}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	AGACCAGGCTTCGGCCTGGCT	0.667													G|||	3450	0.688898	0.7799	0.7075	5008	,	,		3447	0.6964		0.6064	False		,,,				2504	0.6299				p.A1286A		.											.	C4A-44	0			c.G3856G						.						9	21	18					6																	31964785		314	1148	1462	SO:0001583	missense	720	exon29			CAGGCTTCGGCCT	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"Blood group antigens", "Complement system"	1323	protein-coding gene	gene with protein product		120810	"complement component 4A"				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3856T>G	6.37:g.31964785T>G	ENSP00000396688:p.Ser1286Ala	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_007293	0	1	0	502	501	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Silent	SNP	ENST00000428956.2	37	CCDS47404.1	.	.	.	.	.	.	.	.	.	.	N	0.023	-1.400582	0.01165	.	.	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.28895	1.59;1.59	3.27	3.27	0.37495	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.01287	0.0042	N	0.00084	-2.21	0.26565	P	0.973664	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46233	-0.9206	8	0.02654	T	1	.	7.9548	0.30035	0.0:0.0:0.7546:0.2454	.	1286;1286	A6H8M8;P0C0L4	.;CO4A_HUMAN	A	1286	ENSP00000396688:S1286A;ENSP00000420212:S1286A	ENSP00000396688:S1286A	S	+	1	0	C4A	32072763	0.956000	0.32656	0.019000	0.16419	0.401000	0.30781	4.385000	0.59613	0.717000	0.32145	-0.486000	0.04755	TCG	G|1.000;|0.000		0.667	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293		G	31964785	T	G	31964785	3	3	95	1	0	0	0	0	1	0	0	0	2253	1783	62	5	3633	5	C4A	6	31964785	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08		31964785	139150282	14	8514											
DUS4L	11062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107216872	107216872	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctgaagcaacaggagttTcatggattacagtccatgga	13	9	12	7	0	1	1	1	1	0	0	2	4	2	4	1	4	3	3	1	4	3	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr7:107216872T>A	ENST00000265720.3	+	7	903	c.541T>A	c.(541-543)Tca>Aca	p.S181T	DUS4L_ENST00000402620.1_Missense_Mutation_p.S60T	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	181							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						AACAGGAGTTTCATGGATTAC	0.353																																					p.S181T		.											.	DUS4L-90	0			c.T541A						.						81	76	78					7																	107216872		2203	4300	6503	SO:0001583	missense	11062	exon7			GGAGTTTCATGGA	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.541T>A	7.37:g.107216872T>A	ENSP00000265720:p.Ser181Thr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	114	30	NM_001270419	0	0	9	11	2	B4DLX0|Q2NKK1	Missense_Mutation	SNP	ENST00000265720.3	37	CCDS5745.1	.	.	.	.	.	.	.	.	.	.	T	8.361	0.833117	0.16820	.	.	ENSG00000105865	ENST00000265720;ENST00000402620	T;T	0.22539	1.95;1.95	6.01	3.59	0.41128	Aldolase-type TIM barrel (1);	0.166724	0.56097	D	0.000035	T	0.18130	0.0435	L	0.48935	1.535	0.51233	D	0.99991	B;B	0.16396	0.017;0.017	B;B	0.25291	0.059;0.059	T	0.05468	-1.0883	10	0.26408	T	0.33	.	8.1312	0.31029	0.1207:0.0651:0.0:0.8142	.	181;181	A4D0R5;O95620	.;DUS4L_HUMAN	T	181;60	ENSP00000265720:S181T;ENSP00000385274:S60T	ENSP00000265720:S181T	S	+	1	0	DUS4L	107004108	1.000000	0.71417	0.680000	0.29994	0.052000	0.14988	5.909000	0.69923	0.489000	0.27749	-0.297000	0.09499	TCA	.		0.353	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		A	107216872	T	A	107216872	3	1	95	1	0	0	0	0	1	0	0	0	4819	1783	62	5	559	5	DUS4L	7	107216872	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08		107216872	51921791	15	8515											
TRIM24	8805	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	138145434	138145434	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggagcgcggcggcgaggcGgcccggctcaacctgttgga	5	5	18	13	7	1	0	1	0	0	0	2	3	1	2	2	7	2	2	2	7	1	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr7:138145434G>A	ENST00000343526.4	+	1	356	c.141G>A	c.(139-141)gcG>gcA	p.A47A	TRIM24_ENST00000415680.2_Silent_p.A47A			O15164	TIF1A_HUMAN	tripartite motif containing 24	47					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						GCGGCGAGGCGGCCCGGCTCA	0.746																																					p.A47A	Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)	.											.	TRIM24-1030	0			c.G141A						.						5	7	6					7																	138145434		1615	3579	5194	SO:0001819	synonymous_variant	8805	exon1			CGAGGCGGCCCGG	AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.141G>A	7.37:g.138145434G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_003852	0	0	1	1	0	A4D1R7|A4D1R8|O95854	Silent	SNP	ENST00000343526.4	37	CCDS5847.1																																																																																			.		0.746	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		A	138145434	G	A	138145434	2	1	95	1	0	0	0	0	0	0	0	1	16531	1103	39	1		1	TRIM24	7	138145434	Silent	SNP	G	TCGA-DW-7837-01A-11D-2136-08	30928562	138145434	20993229	16	8516											
CLU	1191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	27457323	27457323	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacccgcagatagtactggtCttcgccttgcgtgaggtttg	6	12	13	10	3	1	2	0	1	1	1	2	3	1	2	2	2	2	3	2	2	2	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:27457323C>G	ENST00000316403.10	-	7	1543	c.1138G>C	c.(1138-1140)Gac>Cac	p.D380H	CLU_ENST00000560366.1_Missense_Mutation_p.D432H|CLU_ENST00000523500.1_Missense_Mutation_p.D380H|CLU_ENST00000546343.1_Missense_Mutation_p.D391H|CLU_ENST00000405140.3_Missense_Mutation_p.D380H			P10909	CLUS_HUMAN	clusterin	380					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TAGTACTGGTCTTCGCCTTGC	0.602																																					p.D380H		.											.	CLU-133	0			c.G1138C						.						71	57	62					8																	27457323		2203	4300	6503	SO:0001583	missense	1191	exon7			ACTGGTCTTCGCC	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"complement lysis inhibitor", "sulfated glycoprotein 2", "testosterone-repressed prostate message 2", "apolipoprotein J"	185430	"clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.1138G>C	8.37:g.27457323C>G	ENSP00000315130:p.Asp380His	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	27	10	NM_001831	2	8	7197	11724	4516	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	37	CCDS47832.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	17.93|17.93|17.93	3.509052|3.509052|3.509052	0.64410|0.64410|0.64410	.|.|.	.|.|.	ENSG00000120885|ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000521770|ENST00000522098	T;T;T|.|.	0.23754|.|.	1.89;1.89;1.89|.|.	5.62|5.62|5.62	3.57|3.57|3.57	0.40892|0.40892|0.40892	Clusterin, C-terminal (1);|.|.	0.252635|.|.	0.44688|.|.	D|.|.	0.000435|.|.	T|T|T	0.55768|0.55768|0.55768	0.1941|0.1941|0.1941	M|M|M	0.81942|0.81942|0.81942	2.565|2.565|2.565	0.19300|0.19300|0.19300	N|N|N	0.999975|0.999975|0.999975	D;D;D;D|.|.	0.89917|.|.	1.0;1.0;1.0;0.99|.|.	D;D;D;D|.|.	0.91635|.|.	0.995;0.999;0.999;0.912|.|.	T|T|T	0.51988|0.51988|0.51988	-0.8635|-0.8635|-0.8635	10|5|5	0.87932|.|.	D|.|.	0|.|.	-20.387|-20.387|-20.387	5.2925|5.2925|5.2925	0.15735|0.15735|0.15735	0.0:0.6574:0.0:0.3426|0.0:0.6574:0.0:0.3426|0.0:0.6574:0.0:0.3426	.|.|.	245;432;391;380|.|.	E7ETA7;P10909-2;P10909-5;P10909|.|.	.;.;.;CLUS_HUMAN|.|.	H|N|T	432;391;380;380;205;245|70|242	ENSP00000446413:D391H;ENSP00000385419:D380H;ENSP00000429620:D380H|.|.	ENSP00000315130:D432H|.|.	D|K|R	-|-|-	1|3|2	0|2|0	CLU|CLU|CLU	27513240|27513240|27513240	0.048000|0.048000|0.048000	0.20356|0.20356|0.20356	0.005000|0.005000|0.005000	0.12908|0.12908|0.12908	0.275000|0.275000|0.275000	0.26752|0.26752|0.26752	1.118000|1.118000|1.118000	0.31246|0.31246|0.31246	1.363000|1.363000|1.363000	0.46019|0.46019|0.46019	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAC|AAG|AGA	.		0.602	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831		G	27457323	C	G	27457323	3	3	95	1	0	0	0	0	1	0	0	0	3574	913	32	4	223	4	CLU	8	27457323	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		27457323	118906699	17	8517											
FGFR1	2260	ucsc.edu	37	chr8	38287416	38287416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaagctgcagcaggtcacCggggtggaccaggaaggact	10	4	17	10	2	1	0	1	0	0	0	1	4	1	3	2	6	3	3	2	6	2	0	rs121909640		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:38287416C>T	ENST00000447712.2	-	3	1083	c.142G>A	c.(142-144)Ggt>Agt	p.G48S	FGFR1_ENST00000335922.5_Missense_Mutation_p.G40S|FGFR1_ENST00000397113.2_Missense_Mutation_p.G48S|FGFR1_ENST00000341462.5_Missense_Mutation_p.G48S|FGFR1_ENST00000397103.1_Intron|FGFR1_ENST00000397091.5_Missense_Mutation_p.G48S|FGFR1_ENST00000356207.5_Intron|FGFR1_ENST00000425967.3_Missense_Mutation_p.G81S|FGFR1_ENST00000326324.6_Intron|FGFR1_ENST00000397108.4_Missense_Mutation_p.G48S|FGFR1_ENST00000532791.1_Missense_Mutation_p.G48S	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	48	Ig-like C2-type 1.		G -> S (in HH2; phenotype consistent with normosmic idiopathic hypogonadotropic hypogonadism). {ECO:0000269|PubMed:16882753}.		angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGCAGGTCACCGGGGTGGACC	0.682		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														p.G81S	Melanoma(146;1153 1840 21453 21841 43625)			Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	.	FGFR1-1793	0			c.G241A	GRCh37	CM063982	FGFR1	M	rs121909640	.						26	25	25					8																	38287416		2203	4299	6502	SO:0001583	missense	2260	exon4			GGTCACCGGGGTG	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.142G>A	8.37:g.38287416C>T	ENSP00000400162:p.Gly48Ser	Somatic	54	0		WXS	Illumina HiSeq		40	4	NM_001174067	0	0	3	3	0	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	37	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	C	36	5.747835	0.96882	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000310729;ENST00000532791;ENST00000397113;ENST00000335922;ENST00000397108;ENST00000326296;ENST00000525001;ENST00000413133	T;T;T;T;T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46	5.58	5.58	0.84498	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92047	0.7480	M	0.90425	3.115	0.80722	A	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.93129	0.6531	9	0.87932	D	0	.	19.6377	0.95744	0.0:1.0:0.0:0.0	.	48;81;48;40;48	P11362-7;P11362-21;P11362;P11362-20;P11362-2	.;.;FGFR1_HUMAN;.;.	S	48;81;48;48;48;48;48;40;48;48;48;48	ENSP00000380280:G48S;ENSP00000393312:G81S;ENSP00000400162:G48S;ENSP00000340636:G48S;ENSP00000432972:G48S;ENSP00000380302:G48S;ENSP00000337247:G40S;ENSP00000380297:G48S;ENSP00000434712:G48S;ENSP00000400708:G48S	ENSP00000311337:G48S	G	-	1	0	FGFR1	38406573	1.000000	0.71417	0.996000	0.52242	0.973000	0.67179	7.487000	0.81328	2.641000	0.89580	0.456000	0.33151	GGT	.		0.682	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	38287416	C	T	38287416	3	4	95	1	0	0	0	0	1	0	0	0	5882	652	23	1	2630	1	FGFR1	8	38287416	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	10830093	38287416	108076606	18	8518											
MYST3	7994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	41791942	41791942	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctccacctcaggctcctTggtttcggtctcaggactat	5	13	8	15	1	2	0	2	0	1	0	7	1	5	1	4	4	0	2	4	4	1	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:41791942T>G	ENST00000396930.3	-	18	4339	c.3796A>C	c.(3796-3798)Aag>Cag	p.K1266Q	KAT6A_ENST00000406337.1_Missense_Mutation_p.K1266Q|KAT6A_ENST00000265713.2_Missense_Mutation_p.K1266Q	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1266					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										tcAGGCTCCTTGGTTTCGGTC	0.582																																					p.K1266Q		.											.	.	0			c.A3796C						.						70	57	61					8																	41791942		2203	4300	6503	SO:0001583	missense	7994	exon18			GCTCCTTGGTTTC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3796A>C	8.37:g.41791942T>G	ENSP00000380136:p.Lys1266Gln	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_001099412	0	0	2	3	1	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	5.700	0.313720	0.10789	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.59772	0.24;0.24;0.24	5.95	5.95	0.96441	.	0.067727	0.64402	D	0.000010	T	0.59582	0.2204	L	0.27053	0.805	0.33409	D	0.578344	D	0.71674	0.998	P	0.59115	0.852	T	0.63382	-0.6650	10	0.18710	T	0.47	-26.6212	16.4159	0.83738	0.0:0.0:0.0:1.0	.	1266	Q92794	KAT6A_HUMAN	Q	1266	ENSP00000265713:K1266Q;ENSP00000385888:K1266Q;ENSP00000380136:K1266Q	ENSP00000265713:K1266Q	K	-	1	0	KAT6A	41911099	0.647000	0.27304	0.108000	0.21378	0.021000	0.10359	1.215000	0.32431	2.279000	0.76181	0.533000	0.62120	AAG	.		0.582	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41791942	T	G	41791942	3	3	95	1	0	0	0	0	1	0	0	0	10129	1821	63	5	2222	5	MYST3	8	41791942	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	3504526	41791942	104572080	19	8519											
POP1	10940	hgsc.bcm.edu	37	chr8	99140760	99140760	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacggttacaggagattgccCagaaagaggtaggagttcca	13	7	14	7	1	0	3	0	0	0	3	1	6	1	4	2	4	2	3	2	4	3	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:99140760C>G	ENST00000401707.2	+	4	559	c.478C>G	c.(478-480)Cag>Gag	p.Q160E	POP1_ENST00000349693.3_Missense_Mutation_p.Q160E	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	160					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			GGAGATTGCCCAGAAAGAGGT	0.413																																					p.Q160E		.											.	POP1-154	0			c.C478G						.						68	57	61					8																	99140760		2203	4300	6503	SO:0001583	missense	10940	exon4			ATTGCCCAGAAAG	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"processing of precursors 1"	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.478C>G	8.37:g.99140760C>G	ENSP00000385787:p.Gln160Glu	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	79	4	NM_001145860	0	0	0	0	0	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	C	9.868	1.198081	0.22037	.	.	ENSG00000104356	ENST00000522319;ENST00000401707;ENST00000349693	T;T;T	0.40476	1.03;1.03;1.03	5.95	5.06	0.68205	Ribonuclease P/MRP, subunit POP1 (1);	0.326421	0.32987	N	0.005418	T	0.23926	0.0579	N	0.14661	0.345	0.23519	N	0.997501	B	0.13594	0.008	B	0.23150	0.044	T	0.18178	-1.0345	10	0.05959	T	0.93	-13.3484	12.4936	0.55914	0.3844:0.6156:0.0:0.0	.	160	Q99575	POP1_HUMAN	E	160	ENSP00000428945:Q160E;ENSP00000385787:Q160E;ENSP00000339529:Q160E	ENSP00000339529:Q160E	Q	+	1	0	POP1	99209936	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	3.261000	0.51530	1.462000	0.47948	0.650000	0.86243	CAG	.		0.413	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		G	99140760	C	G	99140760	3	3	95	1	0	0	0	0	1	0	0	0	12277	595	21	4	488	4	POP1	8	99140760	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	57348818	99140760	47223262	20	8520											
GPT	2875	broad.mit.edu;bcgsc.ca	37	chr8	145730807	145730807	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgagcttcaccgtgcacTgggccaggcgcgtgaccact	6	6	14	15	4	1	1	1	1	0	0	1	2	1	1	4	3	2	2	4	3	0	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:145730807T>C	ENST00000528431.1	+	6	831	c.674T>C	c.(673-675)cTg>cCg	p.L225P	GPT_ENST00000394955.2_Missense_Mutation_p.L225P			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	225					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)		L-Alanine(DB00160)|Phenelzine(DB00780)	CACCGTGCACTGGGCCAGGCG	0.711																																					p.L225P													.	GPT-91	0			c.T674C						.						26	22	23					8																	145730807		2183	4285	6468	SO:0001583	missense	2875	exon5			GTGCACTGGGCCA		CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	ENST00000528431.1:c.674T>C	8.37:g.145730807T>C	ENSP00000433586:p.Leu225Pro	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	16	4	NM_005309	0	0	10	20	10	B0YJ18|D3DWM7|P78398|Q93076	Missense_Mutation	SNP	ENST00000528431.1	37	CCDS6430.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.412967	0.42817	.	.	ENSG00000167701	ENST00000528431;ENST00000394955	D;D	0.94417	-3.42;-3.42	4.75	4.75	0.60458	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.252905	0.32819	N	0.005613	D	0.97657	0.9232	M	0.93283	3.4	0.39426	D	0.966998	D;D	0.76494	0.998;0.999	D;D	0.73380	0.979;0.98	D	0.99187	1.0869	10	0.87932	D	0	-16.1077	12.1812	0.54214	0.0:0.0:0.0:1.0	.	225;225	B4DPT5;P24298	.;ALAT1_HUMAN	P	225	ENSP00000433586:L225P;ENSP00000378408:L225P	ENSP00000378408:L225P	L	+	2	0	GPT	145701615	0.950000	0.32346	0.039000	0.18376	0.002000	0.02628	4.295000	0.59049	1.753000	0.51906	0.454000	0.30748	CTG	.		0.711	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1			C	145730807	T	C	145730807	3	2	95	1	0	0	0	0	1	0	0	0	6758	1580	55	3	692	3	GPT	8	145730807	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	46590047	145730807	633215	21	8521											
ABL1	25	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr9	133759489	133759489	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttgttcagcgccttgatCaagaagaagaagaagacagc	16	7	10	8	1	2	6	2	1	0	5	2	6	2	6	1	0	3	1	1	0	6	3	rs201725154		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr9:133759489C>A	ENST00000318560.5	+	11	2193	c.1812C>A	c.(1810-1812)atC>atA	p.I604I		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	604					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GCGCCTTGATCAAGAAGAAGA	0.607			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.I623I		.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1-3810	0			c.C1869A						.						78	89	85					9																	133759489		2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			CTTGATCAAGAAG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1812C>A	9.37:g.133759489C>A		Somatic	258	2		WXS	Illumina HiSeq	Phase_I	257	89	NM_007313	0	0	10	20	10	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.		0.607	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		A	133759489	C	A	133759489	2	1	95	1	0	0	0	0	0	0	0	1	92	816	29	4		4	ABL1	9	133759489	Silent	SNP	C	TCGA-DW-7837-01A-11D-2136-08		133759489	7453942	22	8522											
PRPF18	8559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	13658431	13658431	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcttcagatggccattggaAatgcgccttggcccatcggt	8	11	11	11	2	2	1	1	0	1	1	3	2	2	2	3	4	1	0	3	4	1	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr10:13658431A>G	ENST00000378572.3	+	9	986	c.826A>G	c.(826-828)Aat>Gat	p.N276D		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	276					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GGCCATTGGAAATGCGCCTTG	0.413																																					p.N276D		.											.	PRPF18-90	0			c.A826G						.						152	141	145					10																	13658431		2203	4300	6503	SO:0001583	missense	8559	exon9			ATTGGAAATGCGC	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"PRP18 pre-mRNA processing factor 18 homolog (yeast)", "PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.826A>G	10.37:g.13658431A>G	ENSP00000367835:p.Asn276Asp	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	159	46	NM_003675	0	0	16	25	9	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	37	CCDS7100.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790746	0.90367	.	.	ENSG00000165630	ENST00000378572;ENST00000298451	.	.	.	5.3	5.3	0.74995	Prp18 (3);	0.000000	0.85682	D	0.000000	D	0.86356	0.5913	H	0.94886	3.595	0.80722	D	1	D	0.65815	0.995	D	0.75020	0.985	D	0.90319	0.4343	9	0.87932	D	0	-32.2513	15.2507	0.73542	1.0:0.0:0.0:0.0	.	276	Q99633	PRP18_HUMAN	D	276;38	.	ENSP00000298451:N38D	N	+	1	0	PRPF18	13698437	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.320000	0.96346	2.006000	0.58801	0.528000	0.53228	AAT	.		0.413	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			G	13658431	A	G	13658431	3	3	95	1	0	0	0	0	1	0	0	0	12592	14	1	3	860	3	PRPF18	10	13658431	Missense_Mutation	SNP	A	TCGA-DW-7837-01A-11D-2136-08		13658431	121876316	23	8523											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	16957909	16957910	+	Frame_Shift_Ins	INS	-	-	A																															ttcaaaagagatggtgagatINSagtgtccagagagcccctgg																										TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr10:16957909_16957910insA	ENST00000377833.4	-	46	7185_7186	c.7120_7121insT	c.(7120-7122)tatfs	p.Y2374fs		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2374	CUB 17. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GATGGTGAGATAGTGTCCAGAG	0.436																																					p.Y2374fs		.											.	CUBN-166	0			c.7121_7122insT						.																																			SO:0001589	frameshift_variant	8029	exon46			.	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.7121dupT	10.37:g.16957910_16957910dupA	ENSP00000367064:p.Tyr2374fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	141	51	NM_001081	0	0	0	0	0	B0YIZ4|Q5VTA6|Q96RU9	Frame_Shift_Ins	INS	ENST00000377833.4	37	CCDS7113.1																																																																																			.		0.436	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16957910	-	A	16957909	7	5	95	1	0	1	1	0	0	0	0	0	4057	1406	49	0	3838	0	CUBN	10	16957909	Frame_Shift_Ins	INS	-	TCGA-DW-7837-01A-11D-2136-08	3299478	16957909	118576838	24	8524											
PTPRCAP	5790	broad.mit.edu;bcgsc.ca	37	chr11	67203274	67203287	+	Frame_Shift_Del	DEL	GCAAAGGCGTGCAG	GCAAAGGCGTGCAG	-																															catcccaggctgcgctgccaGcaaaggcgtgcaggtcactc																								rs377555679		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	GCAAAGGCGTGCAG	GCAAAGGCGTGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr11:67203274_67203287delGCAAAGGCGTGCAG	ENST00000326294.3	-	2	985_998	c.538_551delCTGCACGCCTTTGC	c.(538-552)ctgcacgcctttgctfs	p.LHAFA180fs	AP003419.16_ENST00000535922.1_RNA|CORO1B_ENST00000539724.1_5'Flank	NM_005608.2	NP_005599.1	Q14761	PTCA_HUMAN	protein tyrosine phosphatase, receptor type, C-associated protein	180					defense response (GO:0006952)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				skin(1)|upper_aerodigestive_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			TGCGCTGCCAGCAAAGGCGTGCAGGTCACTCAGC	0.682																																					p.180_184del													.	PTPRCAP-226	0			c.538_551del						.																																			SO:0001589	frameshift_variant	5790	exon2			CTGCCAGCAAAGG		CCDS8163.1	11q13.2	2011-06-09			ENSG00000213402	ENSG00000213402			9667	protein-coding gene	gene with protein product		601577					Standard	NM_005608		Approved	LPAP, CD45-AP	uc001oli.1	Q14761	OTTHUMG00000150325	ENST00000326294.3:c.538_551delCTGCACGCCTTTGC	11.37:g.67203274_67203287delGCAAAGGCGTGCAG	ENSP00000325589:p.Leu180fs	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	34	8	NM_005608	0	0	0	0	0	B2R512|O00643|Q6I9S6	Frame_Shift_Del	DEL	ENST00000326294.3	37	CCDS8163.1																																																																																			.		0.682	PTPRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317563.1	NM_005608		-	67203287	GCAAAGGCGTGCAG	-	67203274	7	5	95	1	0	1	0	1	0	0	0	0	12830	971	34	0	73	0	PTPRCAP	11	67203274	Frame_Shift_Del	DEL	GCAAAGGCGTGCAG	TCGA-DW-7837-01A-11D-2136-08		67203274	67803242	25	8525											
ARHGEF17	9828	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	73066676	73066676	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaggaggcgaggcctgcCtttctcaagttcctagaggt	8	9	13	11	1	1	1	1	0	1	1	3	3	2	2	4	4	1	1	4	4	3	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr11:73066676C>G	ENST00000263674.3	+	4	3902	c.3552C>G	c.(3550-3552)gcC>gcG	p.A1184A	AP002761.1_ENST00000582555.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1184	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CGAGGCCTGCCTTTCTCAAGT	0.557																																					p.A1184A		.											.	ARHGEF17-227	0			c.C3552G						.						92	88	90					11																	73066676		2200	4293	6493	SO:0001819	synonymous_variant	9828	exon4			GCCTGCCTTTCTC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.3552C>G	11.37:g.73066676C>G		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	77	29	NM_014786	0	0	4	10	6	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	37	CCDS8221.1																																																																																			.		0.557	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		G	73066676	C	G	73066676	2	3	95	1	0	0	0	0	0	0	0	1	900	668	24	4		4	ARHGEF17	11	73066676	Silent	SNP	C	TCGA-DW-7837-01A-11D-2136-08	5863402	73066676	61939840	26	8526											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93806328	93806328	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaagcccatcttggaattcTtggtacagtaaaaccatccc	13	10	7	11	0	2	1	0	0	2	1	3	2	3	2	3	2	3	2	3	2	5	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr11:93806328T>C	ENST00000315765.9	+	7	1378	c.1370T>C	c.(1369-1371)cTt>cCt	p.L457P		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	457	Plastocyanin-like 3.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				CTTGGAATTCTTGGTACAGTA	0.413																																					p.L457P		.											.	HEPHL1-71	0			c.T1370C						.						73	68	69					11																	93806328		1842	4090	5932	SO:0001583	missense	341208	exon7			GAATTCTTGGTAC	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.1370T>C	11.37:g.93806328T>C	ENSP00000313699:p.Leu457Pro	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_001098672	0	0	0	0	0	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.361954	0.82353	.	.	ENSG00000181333	ENST00000315765	D	0.99232	-5.6	5.62	5.62	0.85841	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.077703	0.52532	D	0.000065	D	0.98692	0.9561	L	0.28400	0.85	0.80722	D	1	D	0.59357	0.985	P	0.62560	0.904	D	0.99915	1.1222	10	0.62326	D	0.03	.	15.8229	0.78673	0.0:0.0:0.0:1.0	.	457	Q6MZM0	HPHL1_HUMAN	P	457	ENSP00000313699:L457P	ENSP00000313699:L457P	L	+	2	0	HEPHL1	93445976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.209000	0.77916	2.126000	0.65437	0.528000	0.53228	CTT	.		0.413	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		C	93806328	T	C	93806328	3	2	95	1	0	0	0	0	1	0	0	0	7076	1609	56	3	1396	3	HEPHL1	11	93806328	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	20739652	93806328	41200188	27	8527											
AMOTL1	154810	broad.mit.edu;ucsc.edu	37	chr11	94532582	94532582	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctctttgtaacttccacTccccaaacttcctgaggatc	9	13	4	15	0	1	1	0	1	1	0	6	2	5	2	5	1	2	1	5	1	2	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr11:94532582T>G	ENST00000433060.2	+	3	367	c.226T>G	c.(226-228)Tcc>Gcc	p.S76A	AMOTL1_ENST00000317829.8_Missense_Mutation_p.S26A|AMOTL1_ENST00000317837.9_Missense_Mutation_p.S76A	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	76					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				TAACTTCCACTCCCCAAACTT	0.458																																					p.S76A													.	AMOTL1-91	0			c.T226G						.						32	29	30					11																	94532582		1874	4112	5986	SO:0001583	missense	154810	exon3			TTCCACTCCCCAA	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.226T>G	11.37:g.94532582T>G	ENSP00000387739:p.Ser76Ala	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	13	8	NM_130847	0	0	2	2	0	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	T	4.114	0.019294	0.08006	.	.	ENSG00000166025	ENST00000299004;ENST00000317829;ENST00000542840;ENST00000317837;ENST00000433060	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	4.45	-4.86	0.03132	.	0.943557	0.08802	N	0.891653	T	0.24122	0.0584	L	0.47716	1.5	0.09310	N	0.999996	B;B	0.10296	0.0;0.003	B;B	0.09377	0.0;0.004	T	0.41574	-0.9501	10	0.02654	T	1	0.0906	4.364	0.11216	0.1378:0.5246:0.1397:0.1979	.	26;76	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	A	105;26;82;76;76	ENSP00000299004:S105A;ENSP00000320968:S26A;ENSP00000323474:S76A;ENSP00000387739:S76A	ENSP00000299004:S105A	S	+	1	0	AMOTL1	94172230	0.899000	0.30636	0.516000	0.27786	0.565000	0.35776	0.442000	0.21628	-1.080000	0.03109	-0.451000	0.05528	TCC	.		0.458	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		G	94532582	T	G	94532582	3	3	95	1	0	0	0	0	1	0	0	0	583	1551	54	5	236	5	AMOTL1	11	94532582	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	726254	94532582	40473934	28	8528											
MCF2L	23263	bcgsc.ca	37	chr13	113728835	113728835	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacagcctggcgcatgtggaGcacctgctgagggacctggc	8	6	15	12	1	0	1	0	1	0	0	0	3	0	3	3	4	4	3	3	4	1	0	rs146333822	byFrequency	TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr13:113728835G>A	ENST00000375608.3	+	11	1222	c.1164G>A	c.(1162-1164)gaG>gaA	p.E388E	MCF2L_ENST00000375604.2_Silent_p.E415E|MCF2L_ENST00000442652.2_Silent_p.E388E|MCF2L_ENST00000375597.4_Silent_p.E356E|MCF2L_ENST00000535094.2_Silent_p.E358E|MCF2L_ENST00000423482.2_Silent_p.E356E|MCF2L_ENST00000375601.3_Silent_p.E362E|MCF2L_ENST00000421756.1_Silent_p.E362E|MCF2L_ENST00000434480.2_Silent_p.E364E|MCF2L_ENST00000397030.1_Silent_p.E391E			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	388					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CGCATGTGGAGCACCTGCTGA	0.622																																					p.E358E													.	MCF2L-228	0			c.G1074A						.						73	72	73					13																	113728835		2203	4300	6503	SO:0001819	synonymous_variant	23263	exon10			TGTGGAGCACCTG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1164G>A	13.37:g.113728835G>A		Somatic	143	0		WXS	Illumina HiSeq	Phase_1	94	6	NM_001112732	0	0	13	14	1	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	G	1.327	-0.597928	0.03771	.	.	ENSG00000126217	ENST00000397017	.	.	.	4.77	0.243	0.15503	.	.	.	.	.	T	0.50667	0.1629	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36625	-0.9740	4	.	.	.	.	5.0347	0.14428	0.436:0.1514:0.4126:0.0	.	.	.	.	T	19	.	.	A	+	1	0	MCF2L	112776836	0.997000	0.39634	0.454000	0.27019	0.068000	0.16541	0.371000	0.20450	0.090000	0.17273	-0.136000	0.14681	GCA	G|0.999;C|0.001		0.622	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			A	113728835	G	A	113728835	2	1	95	1	0	0	0	0	0	0	0	1	9404	962	34	2		2	MCF2L	13	113728835	Silent	SNP	G	TCGA-DW-7837-01A-11D-2136-08		113728835	1441043	29	8529											
FMN1	342184	hgsc.bcm.edu	37	chr15	33066522	33066522	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttcatcttagttagtggTcacactggcttccttctgac	6	16	8	11	0	5	1	2	1	3	0	6	1	6	1	1	2	0	2	1	2	2	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr15:33066522T>C	ENST00000559047.1	-	18	4248	c.4249A>G	c.(4249-4251)Acc>Gcc	p.T1417A	FMN1_ENST00000334528.9_Missense_Mutation_p.T1194A|FMN1_ENST00000561249.1_Missense_Mutation_p.T1319A			Q68DA7	FMN1_HUMAN	formin 1	1417					actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TAGTTAGTGGTCACACTGGCT	0.408																																					p.T1194A		.											.	FMN1-23	0			c.A3580G						.						136	133	134					15																	33066522		2005	4181	6186	SO:0001583	missense	342184	exon17			TAGTGGTCACACT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"limb deformity protein"	136535	"formin (limb deformity)"	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.4249A>G	15.37:g.33066522T>C	ENSP00000454047:p.Thr1417Ala	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001103184	0	0	0	0	0	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	T	4.846	0.157183	0.09236	.	.	ENSG00000248905	ENST00000334528	T	0.38401	1.14	5.23	1.7	0.24286	.	0.480250	0.22809	N	0.055376	T	0.14960	0.0361	N	0.08118	0	.	.	.	B	0.25169	0.119	B	0.20184	0.028	T	0.26087	-1.0113	9	0.15499	T	0.54	.	7.2583	0.26189	0.0:0.2672:0.0:0.7328	.	1194	Q68DA7-5	.	A	1194	ENSP00000333950:T1194A	ENSP00000333950:T1194A	T	-	1	0	FMN1	30853814	1.000000	0.71417	0.992000	0.48379	0.412000	0.31113	0.782000	0.26788	0.122000	0.18314	-0.297000	0.09499	ACC	.		0.408	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33066522	T	C	33066522	3	2	95	1	0	0	0	0	1	0	0	0	5968	1667	58	3	14	3	FMN1	15	33066522	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08		33066522	69464870	30	8530											
RAB11A	8766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	66180113	66180113	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgtctccaagcaacaatgtgGttcctattcatgttccacca	10	13	6	12	0	2	0	1	0	1	0	5	0	4	0	4	1	2	3	4	1	4	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr15:66180113G>C	ENST00000261890.2	+	5	714	c.586G>C	c.(586-588)Gtt>Ctt	p.V196L	RAB11A_ENST00000564910.1_Missense_Mutation_p.V126L|RAB11A_ENST00000565075.1_Missense_Mutation_p.V178L|RAB11A_ENST00000569896.1_3'UTR	NM_001206836.1|NM_004663.4	NP_001193765.1|NP_004654.1	P62491	RB11A_HUMAN	RAB11A, member RAS oncogene family	196					cytokinesis (GO:0000910)|establishment of protein localization to membrane (GO:0090150)|exosomal secretion (GO:1990182)|GTP catabolic process (GO:0006184)|melanosome transport (GO:0032402)|multivesicular body assembly (GO:0036258)|neuron projection development (GO:0031175)|plasma membrane to endosome transport (GO:0048227)|positive regulation of axon extension (GO:0045773)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of multivesicular body size (GO:0010796)|regulation of protein transport (GO:0051223)|small GTPase mediated signal transduction (GO:0007264)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	axon (GO:0030424)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|syntaxin binding (GO:0019905)			kidney(1)|large_intestine(2)|lung(1)|prostate(1)	5						CAACAATGTGGTTCCTATTCA	0.428																																					p.V196L		.											.	RAB11A-227	0			c.G586C						.						137	123	128					15																	66180113		2201	4299	6500	SO:0001583	missense	8766	exon5			AATGTGGTTCCTA	X56740	CCDS10212.1, CCDS58373.1	15q22.31	2008-05-14			ENSG00000103769	ENSG00000103769		"RAB, member RAS oncogene"	9760	protein-coding gene	gene with protein product		605570				1704119, 9662449	Standard	NM_004663		Approved	YL8	uc002apk.3	P62491	OTTHUMG00000133162	ENST00000261890.2:c.586G>C	15.37:g.66180113G>C	ENSP00000261890:p.Val196Leu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	130	15	NM_004663	0	0	147	178	31	B2R4B6|B4DT13|P24410|Q5TZN9|Q9JLX1	Missense_Mutation	SNP	ENST00000261890.2	37	CCDS10212.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783421	0.49891	.	.	ENSG00000103769	ENST00000261890	T	0.63744	-0.06	5.45	5.45	0.79879	.	0.056657	0.64402	D	0.000001	T	0.45316	0.1336	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29397	-1.0013	10	0.29301	T	0.29	.	19.3	0.94140	0.0:0.0:1.0:0.0	.	196	P62491	RB11A_HUMAN	L	196	ENSP00000261890:V196L	ENSP00000261890:V196L	V	+	1	0	RAB11A	63967167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.547000	0.85894	0.655000	0.94253	GTT	.		0.428	RAB11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256864.1			C	66180113	G	C	66180113	3	2	95	1	0	0	0	0	1	0	0	0	12923	1261	44	4	604	4	RAB11A	15	66180113	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	33113591	66180113	36351279	31	8531											
GSPT1	2935	hgsc.bcm.edu	37	chr16	12009529	12009529	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgctgccgctgctgcTcccgccgccgccgccgccgc	0	6	13	22	7	0	0	0	0	0	0	1	0	1	0	7	0	5	6	7	0	0	0			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr16:12009529T>C	ENST00000420576.2	-	1	41				GSPT1_ENST00000434724.2_Missense_Mutation_p.S17G|GSPT1_ENST00000439887.2_Missense_Mutation_p.S17G|AC007216.1_ENST00000583357.1_RNA	NM_001130007.1	NP_001123479.1	P15170	ERF3A_HUMAN	G1 to S phase transition 1						G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						ccgctgctgctcccgccgccg	0.766																																					p.S17G		.											.	GSPT1-206	0			c.A49G						.						1	1	1					16																	12009529		301	1026	1327	SO:0001627	intron_variant	2935	exon1			TGCTGCTCCCGCC	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000420576.2:c.61+369A>G	16.37:g.12009529T>C		Somatic	7	2		WXS	Illumina HiSeq	Phase_I	5	2	NM_001130006	0	0	1	1	0	J3KQG6|Q96GF2	Missense_Mutation	SNP	ENST00000420576.2	37	CCDS45414.1	.	.	.	.	.	.	.	.	.	.	t	9.437	1.087068	0.20390	.	.	ENSG00000103342	ENST00000434724;ENST00000439887	T;T	0.30981	1.51;1.51	1.67	-0.454	0.12197	.	1.131400	0.07067	N	0.834778	T	0.22781	0.0550	.	.	.	0.45962	D	0.998788	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14309	-1.0477	9	0.59425	D	0.04	-0.002	5.2784	0.15663	0.0:0.6038:0.0:0.3962	.	17;14	E7EQZ3;Q96GF2	.;.	G	17	ENSP00000398131:S17G;ENSP00000408399:S17G	ENSP00000398131:S17G	S	-	1	0	GSPT1	11917030	0.084000	0.21492	0.006000	0.13384	0.324000	0.28378	0.156000	0.16382	0.016000	0.14998	0.166000	0.16787	AGC	.		0.766	GSPT1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421514.1	NM_002094		C	12009529	T	C	12009529	1	2	95	0	1	0	0	0	0	0	0	0	6847	1551	54	3		3	GSPT1	16	12009529	Intron	SNP	T	TCGA-DW-7837-01A-11D-2136-08		12009529	78345224	32	8532											
RSPRY1	89970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57265132	57265132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atatcaacaatgtgagttcaAttttggagcaaaaccattca	16	12	6	7	0	3	1	3	1	0	0	3	2	3	2	1	1	3	2	1	1	6	5	rs368309991		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr16:57265132A>G	ENST00000537866.1	+	13	2303	c.1430A>G	c.(1429-1431)aAt>aGt	p.N477S	RSPRY1_ENST00000394420.4_Missense_Mutation_p.N477S|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	477	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						TGTGAGTTCAATTTTGGAGCA	0.333																																					p.N477S		.											.	RSPRY1-91	0			c.A1430G						.	A	SER/ASN	1,4395	2.1+/-5.4	0,1,2197	108	104	105		1430	5.8	1	16		105	0,8600		0,0,4300	no	missense	RSPRY1	NM_133368.1	46	0,1,6497	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	477/577	57265132	1,12995	2198	4300	6498	SO:0001583	missense	89970	exon13			AGTTCAATTTTGG	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1430A>G	16.37:g.57265132A>G	ENSP00000443176:p.Asn477Ser	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	89	27	NM_133368	0	0	5	13	8	Q6UX21|Q8ND53	Missense_Mutation	SNP	ENST00000537866.1	37	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.863491	0.91511	2.27E-4	0.0	ENSG00000159579	ENST00000394420;ENST00000537866	T;T	0.75704	-0.96;-0.96	5.78	5.78	0.91487	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.89777	0.6813	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92360	0.5896	10	0.87932	D	0	.	16.1167	0.81309	1.0:0.0:0.0:0.0	.	477	Q96DX4	RSPRY_HUMAN	S	477	ENSP00000377942:N477S;ENSP00000443176:N477S	ENSP00000377942:N477S	N	+	2	0	RSPRY1	55822633	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.204000	0.70986	0.528000	0.53228	AAT	.		0.333	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		G	57265132	A	G	57265132	3	3	95	1	0	0	0	0	1	0	0	0	13745	101	4	3	1476	3	RSPRY1	16	57265132	Missense_Mutation	SNP	A	TCGA-DW-7837-01A-11D-2136-08	45255603	57265132	33089621	33	8533											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	381	44		WXS	Illumina HiSeq		591	72	NM_145301	0	0	0	23	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		T	15457087	C	T	15457087	3	4	95	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		15457087	65738123	34	8534											
NCOR1	9611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	15935762	15935762	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggagtactgctgagcatccGcatagtcagagggttataag	11	10	13	7	1	1	2	1	1	0	1	2	3	2	3	1	2	3	5	1	2	4	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:15935762G>C	ENST00000268712.3	-	46	7428	c.7171C>G	c.(7171-7173)Cgg>Ggg	p.R2391G	NCOR1_ENST00000395857.3_Missense_Mutation_p.R975G|NCOR1_ENST00000395851.1_Missense_Mutation_p.R2288G	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2391	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.R2391W(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CTGAGCATCCGCATAGTCAGA	0.468																																					p.R2391G		.											.	NCOR1-229	1	Substitution - Missense(1)	prostate(1)	c.C7171G						.						117	106	110					17																	15935762		2203	4300	6503	SO:0001583	missense	9611	exon46			GCATCCGCATAGT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.7171C>G	17.37:g.15935762G>C	ENSP00000268712:p.Arg2391Gly	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	214	41	NM_006311	0	0	49	66	17	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596051	0.46318	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.61040	0.14;0.75;0.25	5.96	3.9	0.45041	.	0.048575	0.85682	D	0.000000	T	0.53367	0.1792	L	0.60455	1.87	0.58432	D	0.999992	B;B;B;B;B	0.29341	0.036;0.013;0.242;0.132;0.06	B;B;B;B;B	0.31614	0.022;0.01;0.133;0.089;0.05	T	0.52990	-0.8501	10	0.56958	D	0.05	-9.7742	10.6076	0.45402	0.0:0.1166:0.4874:0.3961	.	2294;2391;2288;910;404	E7EVK1;O75376;O75376-2;Q86YY1;Q86YY2	.;NCOR1_HUMAN;.;.;.	G	2391;2288;2294;975	ENSP00000268712:R2391G;ENSP00000379192:R2288G;ENSP00000379198:R975G	ENSP00000268712:R2391G	R	-	1	2	NCOR1	15876487	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.109000	0.50345	0.780000	0.33566	-0.181000	0.13052	CGG	.		0.468	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	15935762	G	C	15935762	3	2	95	1	0	0	0	0	1	0	0	0	10261	1086	38	4	155	4	NCOR1	17	15935762	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	478675	15935762	65259448	35	8535											
RND2	8153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41180521	41180521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggtcctctgagcgcagcGtcagggatgtcttccatgtg	5	10	13	13	3	3	1	1	1	2	0	5	2	5	2	3	2	2	1	3	2	0	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:41180521G>A	ENST00000587250.2	+	5	615	c.508G>A	c.(508-510)Gtc>Atc	p.V170I	CTD-3199J23.4_ENST00000225973.5_lincRNA|RND2_ENST00000544533.1_Missense_Mutation_p.V171I			P52198	RND2_HUMAN	Rho family GTPase 2	170					GTP catabolic process (GO:0006184)|positive regulation of collateral sprouting (GO:0048672)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|skin(1)	2		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)		TGAGCGCAGCGTCAGGGATGT	0.622																																					p.V170I		.											.	RND2-227	0			c.G508A						.						67	63	65					17																	41180521		2203	4300	6503	SO:0001583	missense	8153	exon5			CGCAGCGTCAGGG	X95456	CCDS11452.1	17q21.31	2012-10-02	2005-01-24	2005-01-24	ENSG00000108830	ENSG00000108830			18315	protein-coding gene	gene with protein product		601555	"ras homolog gene family, member N"	ARHN			Standard	XM_005257706		Approved	Rho7, RhoN	uc002icn.3	P52198	OTTHUMG00000180817	ENST00000587250.2:c.508G>A	17.37:g.41180521G>A	ENSP00000466680:p.Val170Ile	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	113	30	NM_005440	0	0	1	4	3	A8K2D4|O00690|O00734|Q5U0P6|Q99535	Missense_Mutation	SNP	ENST00000587250.2	37	CCDS11452.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941209	0.92526	.	.	ENSG00000108830	ENST00000544533;ENST00000225973	T	0.80653	-1.4	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.81621	0.4861	L	0.36672	1.1	0.80722	D	1	P	0.41643	0.758	P	0.48704	0.587	T	0.82420	-0.0466	10	0.66056	D	0.02	.	19.2909	0.94098	0.0:0.0:1.0:0.0	.	170	P52198	RND2_HUMAN	I	171;170	ENSP00000439328:V171I	ENSP00000225973:V170I	V	+	1	0	RND2	38434047	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.623000	0.98386	2.894000	0.99253	0.655000	0.94253	GTC	.		0.622	RND2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453111.2	NM_005440		A	41180521	G	A	41180521	3	1	95	1	0	0	0	0	1	0	0	0	13452	1145	40	1	526	1	RND2	17	41180521	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	25244759	41180521	40014689	36	8536											
EVPL	2125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74005355	74005355	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctccttgctcaccgtctTggtctccaccttggcccgct	3	12	7	19	2	3	0	1	0	2	0	5	0	4	0	6	2	1	2	6	2	0	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:74005355T>G	ENST00000301607.3	-	22	4184	c.3931A>C	c.(3931-3933)Aag>Cag	p.K1311Q	EVPL_ENST00000586740.1_Missense_Mutation_p.K1333Q	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1311	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CTCACCGTCTTGGTCTCCACC	0.682																																					p.K1311Q		.											.	EVPL-93	0			c.A3931C						.						105	114	111					17																	74005355		2202	4300	6502	SO:0001583	missense	2125	exon22			CCGTCTTGGTCTC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3931A>C	17.37:g.74005355T>G	ENSP00000301607:p.Lys1311Gln	Somatic	451	0		WXS	Illumina HiSeq	Phase_I	432	94	NM_001988	0	0	10	16	6	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.755797	0.31046	.	.	ENSG00000167880	ENST00000301607	T	0.56611	0.45	5.41	4.32	0.51571	.	0.092795	0.64402	D	0.000001	T	0.53384	0.1793	M	0.75777	2.31	0.37299	D	0.908594	P;B	0.39759	0.687;0.142	B;B	0.37731	0.257;0.048	T	0.63479	-0.6628	10	0.72032	D	0.01	-43.3057	12.5545	0.56246	0.0:0.0:0.1392:0.8608	.	1333;1311	B7ZLH8;Q92817	.;EVPL_HUMAN	Q	1311	ENSP00000301607:K1311Q	ENSP00000301607:K1311Q	K	-	1	0	EVPL	71516950	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	2.654000	0.46699	0.875000	0.35847	0.459000	0.35465	AAG	.		0.682	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		G	74005355	T	G	74005355	3	3	95	1	0	0	0	0	1	0	0	0	5305	1821	63	5	2174	5	EVPL	17	74005355	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	32824834	74005355	7189855	37	8537											
FASN	2194	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80053200	80053200	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaatgcccgacccacctccGtccacgatggcttcataggt	8	8	9	16	4	1	0	1	0	0	0	3	3	3	0	5	2	1	1	5	2	2	2	rs568118566		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:80053200G>A	ENST00000306749.2	-	3	494	c.276C>T	c.(274-276)gaC>gaT	p.D92D		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	92	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	ACCCACCTCCGTCCACGATGG	0.597													G|||	1	0.000199681	0	0	5008	,	,		15101	0		0	False		,,,				2504	0.001				p.D92D	Colon(59;314 1043 11189 28578 32273)												.	FASN-90	0			c.C276T						.						73	60	64					17																	80053200		2202	4300	6502	SO:0001819	synonymous_variant	2194	exon3			ACCTCCGTCCACG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.276C>T	17.37:g.80053200G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	101	13	NM_004104	0	0	0	0	0	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			.		0.597	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80053200	G	A	80053200	2	1	95	1	0	0	0	0	0	0	0	1	5702	1136	40	1		1	FASN	17	80053200	Silent	SNP	G	TCGA-DW-7837-01A-11D-2136-08	6047845	80053200	1142010	38	8538											
ZNF536	9745	broad.mit.edu	37	chr19	31039693	31039693	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taagatggccctgctgccctCgttacaatcaaacaaagacc	13	8	7	13	1	1	2	1	0	0	2	2	2	1	2	3	1	4	2	3	1	5	2	rs375517415		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr19:31039693C>T	ENST00000355537.3	+	4	3314	c.3167C>T	c.(3166-3168)tCg>tTg	p.S1056L		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1056					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CTGCTGCCCTCGTTACAATCA	0.532																																					p.S1056L													.	ZNF536-144	0			c.C3167T						.						71	68	69					19																	31039693		2203	4300	6503	SO:0001583	missense	9745	exon4			TGCCCTCGTTACA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3167C>T	19.37:g.31039693C>T	ENSP00000347730:p.Ser1056Leu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	120	7	NM_014717	0	0	0	0	0	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	9.152	1.016612	0.19355	.	.	ENSG00000198597	ENST00000355537	T	0.09073	3.02	5.74	5.74	0.90152	.	0.568976	0.17248	N	0.181300	T	0.08044	0.0201	L	0.27053	0.805	0.26134	N	0.980378	B;B	0.32781	0.384;0.384	B;B	0.16289	0.015;0.015	T	0.21621	-1.0240	10	0.72032	D	0.01	-2.9081	19.9212	0.97085	0.0:1.0:0.0:0.0	.	1056;1056	A7E228;O15090	.;ZN536_HUMAN	L	1056	ENSP00000347730:S1056L	ENSP00000347730:S1056L	S	+	2	0	ZNF536	35731533	0.982000	0.34865	0.026000	0.17262	0.021000	0.10359	5.246000	0.65411	2.697000	0.92050	0.655000	0.94253	TCG	.		0.532	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31039693	C	T	31039693	3	4	95	1	0	0	0	0	1	0	0	0	18006	893	31	1	3177	1	ZNF536	19	31039693	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		31039693	28089290	39	8539											
MEGF8	1954	ucsc.edu;bcgsc.ca	37	chr19	42861619	42861619	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactgcccgccgaggcctgTctctgctcctggtgggcggt	2	11	14	14	3	1	0	0	0	1	0	3	1	2	0	4	4	3	1	4	4	1	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr19:42861619T>C	ENST00000251268.6	+	28	4894	c.4894T>C	c.(4894-4896)Tct>Cct	p.S1632P	MEGF8_ENST00000334370.4_Missense_Mutation_p.S1565P	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1632					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCGAGGCCTGTCTCTGCTCCT	0.657																																					p.S1632P													.	MEGF8-23	0			c.T4894C						.						62	63	63					19																	42861619		2203	4300	6503	SO:0001583	missense	1954	exon28			GGCCTGTCTCTGC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"HBV pre s2 binding protein 1"	604267	"EGF-like-domain, multiple 4", "chromosome 19 open reading frame 49"	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.4894T>C	19.37:g.42861619T>C	ENSP00000251268:p.Ser1632Pro	Somatic	131	2		WXS	Illumina HiSeq		100	33	NM_001271938	0	0	1	7	6	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	T	21.7	4.190737	0.78789	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.23147	1.93;1.92	5.21	4.19	0.49359	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.157535	0.41938	D	0.000790	T	0.47284	0.1437	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.85130	0.997;0.981	T	0.35400	-0.9790	10	0.31617	T	0.26	-13.4688	10.5824	0.45263	0.1446:0.0:0.0:0.8554	.	1632;1565	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	P	1565;1632	ENSP00000334219:S1565P;ENSP00000251268:S1632P	ENSP00000251268:S1632P	S	+	1	0	MEGF8	47553459	1.000000	0.71417	0.995000	0.50966	0.850000	0.48378	5.666000	0.68059	0.814000	0.34374	0.460000	0.39030	TCT	.		0.657	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		C	42861619	T	C	42861619	3	2	95	1	0	0	0	0	1	0	0	0	9488	1667	58	3	4799	3	MEGF8	19	42861619	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	11821926	42861619	16267364	40	8540											
NLRP5	126206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56539072	56539072	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacgtggtgggggagagcgtCgcccccttcaaccaaacgct	8	6	14	13	4	1	1	1	0	0	1	2	3	1	1	3	3	3	1	3	3	2	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr19:56539072C>T	ENST00000390649.3	+	7	1473	c.1473C>T	c.(1471-1473)gtC>gtT	p.V491V		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	491	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GGGAGAGCGTCGCCCCCTTCA	0.632																																					p.V491V		.											.	NLRP5-162	0			c.C1473T						.						31	34	33					19																	56539072		2140	4237	6377	SO:0001819	synonymous_variant	126206	exon7			GAGCGTCGCCCCC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1473C>T	19.37:g.56539072C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	56	25	NM_153447	0	0	0	0	0	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			.		0.632	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56539072	C	T	56539072	2	4	95	1	0	0	0	0	0	0	0	1	10506	871	31	1		1	NLRP5	19	56539072	Silent	SNP	C	TCGA-DW-7837-01A-11D-2136-08	13677453	56539072	2589911	41	8541											
TRPC4AP	26133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33591257	33591257	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtccttgtgcaggtagtgctGctgccagaagcgcagcaggt	7	9	15	10	1	0	1	0	0	0	1	1	1	1	1	2	2	6	6	2	2	2	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr20:33591257G>T	ENST00000252015.2	-	18	2301	c.2212C>A	c.(2212-2214)Cag>Aag	p.Q738K	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.Q699K|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.Q730K|TRPC4AP_ENST00000539834.1_Missense_Mutation_p.Q340K			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	738					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGGTAGTGCTGCTGCCAGAAG	0.632																																					p.Q738K		.											.	TRPC4AP-91	0			c.C2212A						.						59	59	59					20																	33591257		2203	4300	6503	SO:0001583	missense	26133	exon18			AGTGCTGCTGCCA	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.2212C>A	20.37:g.33591257G>T	ENSP00000252015:p.Gln738Lys	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	126	36	NM_015638	0	0	26	44	18	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	6.251	0.414503	0.11870	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000539834;ENST00000432634;ENST00000541994	.	.	.	4.65	4.65	0.58169	.	0.189321	0.48767	D	0.000179	T	0.51517	0.1679	L	0.36672	1.1	0.50632	D	0.999882	B;B;B	0.20164	0.042;0.042;0.042	B;B;B	0.16289	0.015;0.015;0.015	T	0.47586	-0.9106	9	0.12766	T	0.61	.	17.7234	0.88358	0.0:0.0:1.0:0.0	.	699;730;738	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	K	738;730;340;699;723	.	ENSP00000252015:Q738K	Q	-	1	0	TRPC4AP	33054918	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.652000	0.83633	2.398000	0.81561	0.462000	0.41574	CAG	.		0.632	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		T	33591257	G	T	33591257	3	4	95	1	0	0	0	0	1	0	0	0	16614	1328	46	4	189	4	TRPC4AP	20	33591257	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		33591257	29434263	42	8542											
KCNQ2	3785	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	62078166	62078166	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gtggaaaacacagacagcacGaggcaggagaaaaccaggag	18	1	14	8	1	0	2	0	0	0	2	0	6	0	4	1	4	3	2	1	4	4	0			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr20:62078166G>C	ENST00000359125.2	-	2	495	c.321C>G	c.(319-321)ctC>ctG	p.L107L	KCNQ2_ENST00000360480.3_Silent_p.L107L|KCNQ2_ENST00000354587.3_Silent_p.L107L|KCNQ2_ENST00000344425.5_Silent_p.L107L|KCNQ2_ENST00000344462.4_Silent_p.L107L|KCNQ2_ENST00000357249.2_Silent_p.L107L|RP11-358D14.2_ENST00000436263.1_RNA|KCNQ2_ENST00000359689.1_Silent_p.L107L|KCNQ2_ENST00000370224.1_Silent_p.L107L	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	107					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CAGACAGCACGAGGCAGGAGA	0.632																																					p.L107L		.											.	KCNQ2-92	0			c.C321G						.						85	80	82					20																	62078166		2203	4300	6503	SO:0001819	synonymous_variant	3785	exon2			CAGCACGAGGCAG	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.321C>G	20.37:g.62078166G>C		Somatic	202	0		WXS	Illumina HiSeq	Phase_I	172	51	NM_172106	0	0	0	0	0	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			.		0.632	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		C	62078166	G	C	62078166	2	2	95	1	0	0	0	0	0	0	0	1	8104	1045	37	4		4	KCNQ2	20	62078166	Silent	SNP	G	TCGA-DW-7837-01A-11D-2136-08	28486909	62078166	947354	43	8543											
RFPL2	10739	ucsc.edu	37	chr22	32598347	32598347	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccttatcaccatcatgtctGcaaagtcccagtggccacac	10	10	6	15	0	3	0	2	0	1	0	5	0	5	0	4	1	1	1	4	1	2	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr22:32598347G>A	ENST00000400237.1	-	2	1027	c.92C>T	c.(91-93)gCa>gTa	p.A31V	RFPL2_ENST00000400236.3_5'UTR|RFPL2_ENST00000248983.4_5'UTR|RP1-90G24.10_ENST00000434942.1_RNA			O75678	RFPL2_HUMAN	ret finger protein-like 2	31							zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	21						catcatgtctgcaaagtccca	0.517																																					p.A31V													.	RFPL2-91	0			c.C92T						.						91	82	85					22																	32598347		1568	3581	5149	SO:0001583	missense	10739	exon2			ATGTCTGCAAAGT	AJ010231	CCDS43009.1, CCDS46694.1, CCDS43009.2	22q12.3	2008-06-12				ENSG00000128253		"RING-type (C3HC4) zinc fingers"	9979	protein-coding gene	gene with protein product		605969				10508838	Standard	NM_001098527		Approved	RNF79	uc003amg.3	O75678		ENST00000400237.1:c.92C>T	22.37:g.32598347G>A	ENSP00000383096:p.Ala31Val	Somatic	13	0		WXS	Illumina HiSeq		19	4	NM_001098527	0	0	0	0	0		Missense_Mutation	SNP	ENST00000400237.1	37	CCDS43009.2	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351246	0.24512	.	.	ENSG00000128253	ENST00000400237	T	0.57107	0.42	.	.	.	.	.	.	.	.	T	0.33673	0.0871	N	0.08118	0	0.23936	N	0.996413	P	0.43392	0.805	P	0.45506	0.483	T	0.21177	-1.0253	7	0.87932	D	0	.	.	.	.	.	31	O75678	RFPL2_HUMAN	V	31	ENSP00000383096:A31V	ENSP00000383096:A31V	A	-	2	0	RFPL2	30928347	0.008000	0.16893	0.333000	0.25482	0.334000	0.28698	-0.112000	0.10791	0.088000	0.17205	0.089000	0.15464	GCA	.		0.517	RFPL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075262.2	NM_006605		A	32598347	G	A	32598347	3	1	95	1	0	0	0	0	1	0	0	0	13286	1319	46	2	1142	2	RFPL2	22	32598347	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		32598347	18706219	44	8544											
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20195138	20195138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtttgcaggatttcgctTgaaaagcattcgtaaaagac	12	13	9	7	2	1	2	0	1	1	1	3	3	1	3	0	1	2	5	0	1	4	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chrX:20195138T>C	ENST00000379565.3	-	11	1117	c.910A>G	c.(910-912)Aag>Gag	p.K304E	RPS6KA3_ENST00000544447.1_Missense_Mutation_p.K276E|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.K275E|RPS6KA3_ENST00000540702.1_Missense_Mutation_p.K276E	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	304	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	GGATTTCGCTTGAAAAGCATT	0.318																																					p.K304E		.											.	RPS6KA3-1504	0			c.A910G						.						60	62	61					X																	20195138		2203	4300	6503	SO:0001583	missense	6197	exon11			TTCGCTTGAAAAG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.910A>G	X.37:g.20195138T>C	ENSP00000368884:p.Lys304Glu	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_004586	0	0	5	5	0	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237629	0.58886	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.64	5.64	0.86602	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.39091	0.1065	N	0.01817	-0.705	0.80722	D	1	B;B;P;B	0.52842	0.17;0.165;0.956;0.198	B;B;P;B	0.59546	0.134;0.034;0.859;0.084	T	0.55418	-0.8144	10	0.37606	T	0.19	.	14.8754	0.70491	0.0:0.0:0.0:1.0	.	276;275;276;304	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	E	304;276;275;276	ENSP00000368884:K304E;ENSP00000440220:K276E;ENSP00000368865:K275E;ENSP00000444837:K276E	ENSP00000368865:K275E	K	-	1	0	RPS6KA3	20105059	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.215000	0.72206	1.894000	0.54839	0.417000	0.27973	AAG	.		0.318	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20195138	T	C	20195138	3	2	95	1	0	0	0	0	1	0	0	0	13684	1821	63	3	1360	3	RPS6KA3	23	20195138	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08		20195138	135075422	45	8545											
PEX14	5195	hgsc.bcm.edu	37	chr1	10535061	10535061	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcagagcagccgagccaggTaaggggagtgggactgcccc	9	3	18	11	1	0	1	0	0	0	1	0	4	0	3	4	5	4	3	4	5	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:10535061T>C	ENST00000356607.4	+	1	116		c.e1+2		DFFA_ENST00000377038.3_5'Flank|PEX14_ENST00000538836.1_Splice_Site|DFFA_ENST00000377036.2_5'Flank	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14						microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		CCGAGCCAGGTAAGGGGAGTG	0.692																																					.		.											.	PEX14-90	0			c.36+2T>C						.						18	20	19					1																	10535061		2193	4296	6489	SO:0001630	splice_region_variant	5195	exon1			GCCAGGTAAGGGG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.36+2T>C	1.37:g.10535061T>C		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_004565	0	0	0	0	0	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Splice_Site	SNP	ENST00000356607.4	37	CCDS30582.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.285608	0.80803	.	.	ENSG00000142655	ENST00000356607	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4758	0.67546	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PEX14	10457648	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	4.621000	0.61233	1.821000	0.53095	0.533000	0.62120	.	.		0.692	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		Intron	C	10535061	T	C	10535061	5	2	96	1	0	0	0	0	0	0	1	0	11768	1652	57	3	40	3	PEX14	1	10535061	Splice_Site	SNP	T	TCGA-DW-7838-01A-11D-2136-08		10535061	238715560	1	8546											
TRIM63	84676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	26386776	26386776	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttggtcactcgacgggaaTcctccagctgagtgatgatg	8	10	12	11	2	1	3	1	3	0	0	4	5	3	4	3	2	1	1	3	2	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:26386776T>A	ENST00000374272.3	-	4	716	c.578A>T	c.(577-579)gAt>gTt	p.D193V	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	193	Interaction with TTN.				cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TCGACGGGAATCCTCCAGCTG	0.572																																					p.D193V		.											.	TRIM63-226	0			c.A578T						.						122	113	116					1																	26386776		2203	4300	6503	SO:0001583	missense	84676	exon4			CGGGAATCCTCCA	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	16007	protein-coding gene	gene with protein product	"muscle-specific RING finger protein 1", "iris ring finger protein", "striated muscle RING zinc finger protein"	606131	"ring finger protein 28", "tripartite motif-containing 63", "tripartite motif containing 63"	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.578A>T	1.37:g.26386776T>A	ENSP00000363390:p.Asp193Val	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	125	25	NM_032588	0	0	0	0	0	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528379	0.64860	.	.	ENSG00000158022	ENST00000374272	T	0.39787	1.06	5.21	5.21	0.72293	.	0.086183	0.85682	D	0.000000	T	0.50222	0.1603	M	0.68593	2.085	0.80722	D	1	B	0.32893	0.389	B	0.40741	0.339	T	0.55792	-0.8085	10	0.87932	D	0	.	15.0417	0.71796	0.0:0.0:0.0:1.0	.	193	Q969Q1	TRI63_HUMAN	V	193	ENSP00000363390:D193V	ENSP00000363390:D193V	D	-	2	0	TRIM63	26259363	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	5.828000	0.69307	2.081000	0.62600	0.379000	0.24179	GAT	.		0.572	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588		A	26386776	T	A	26386776	3	1	96	1	0	0	0	0	1	0	0	0	16571	1435	50	5	507	5	TRIM63	1	26386776	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	15851715	26386776	222863845	2	8547											
SERINC2	347735	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	31897695	31897695	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tctgcgtgagcagcagccggGacccccgggctgccatccag	6	5	14	16	3	1	1	0	1	1	0	2	2	2	2	5	2	5	3	5	2	0	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:31897695G>A	ENST00000373709.3	+	3	517	c.367G>A	c.(367-369)Gac>Aac	p.D123N	SERINC2_ENST00000536384.1_Missense_Mutation_p.D127N|SERINC2_ENST00000536859.1_Missense_Mutation_p.D127N|SERINC2_ENST00000373710.1_Missense_Mutation_p.D132N|SERINC2_ENST00000491976.1_3'UTR	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	123					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		CAGCAGCCGGGACCCCCGGGC	0.652																																					p.D132N													.	SERINC2-90	0			c.G394A						.																																			SO:0001583	missense	347735	exon4			AGCCGGGACCCCC	AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"tumor differentially expressed 2-like"	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.367G>A	1.37:g.31897695G>A	ENSP00000362813:p.Asp123Asn	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	33	6	NM_001199038	0	0	112	202	90	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	Missense_Mutation	SNP	ENST00000373709.3	37	CCDS30662.1	.	.	.	.	.	.	.	.	.	.	G	35	5.477629	0.96291	.	.	ENSG00000168528	ENST00000373710;ENST00000536859;ENST00000373709;ENST00000536384	T;T;T;T	0.15256	2.44;2.44;2.44;2.44	4.24	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.40040	0.1101	L	0.61036	1.89	0.80722	D	1	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;0.997	T	0.35895	-0.9770	10	0.87932	D	0	-47.5929	16.3974	0.83613	0.0:0.0:1.0:0.0	.	127;132;127;123	B4DJK5;E7EUZ9;B7Z567;Q96SA4	.;.;.;SERC2_HUMAN	N	132;127;123;127	ENSP00000362814:D132N;ENSP00000444307:D127N;ENSP00000362813:D123N;ENSP00000439048:D127N	ENSP00000362813:D123N	D	+	1	0	SERINC2	31670282	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.582000	0.98214	2.204000	0.70986	0.609000	0.83330	GAC	.		0.652	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565		A	31897695	G	A	31897695	3	1	96	1	0	0	0	0	1	0	0	0	14112	1174	41	2	377	2	SERINC2	1	31897695	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	5510919	31897695	217352926	3	8548											
KIF2C	11004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45206651	45206651	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgtttcagtggaatgggCagaaggaggtgccacaaagg	11	8	16	6	0	1	1	1	0	0	1	1	3	1	3	1	5	1	2	1	5	3	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:45206651C>A	ENST00000372224.4	+	2	250	c.137C>A	c.(136-138)gCa>gAa	p.A46E	KIF2C_ENST00000493027.1_3'UTR|KIF2C_ENST00000372218.4_Missense_Mutation_p.A46E	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	46	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					GTGGAATGGGCAGAAGGAGGT	0.413																																					p.A46E		.											.	KIF2C-228	0			c.C137A						.						106	102	103					1																	45206651		2203	4300	6503	SO:0001583	missense	11004	exon2			AATGGGCAGAAGG	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.137C>A	1.37:g.45206651C>A	ENSP00000361298:p.Ala46Glu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	75	8	NM_006845	0	0	0	0	0	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	37	CCDS512.1	.	.	.	.	.	.	.	.	.	.	c	15.02	2.708022	0.48412	.	.	ENSG00000142945	ENST00000452259;ENST00000372224;ENST00000372218;ENST00000455186	T;T;T;T	0.74947	1.14;-0.89;-0.72;0.9	5.95	0.825	0.18824	.	1.230180	0.05208	N	0.506277	T	0.64864	0.2637	L	0.43152	1.355	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.17098	0.017;0.017	T	0.55554	-0.8123	10	0.52906	T	0.07	.	2.3087	0.04181	0.1215:0.4871:0.1181:0.2733	.	46;46	B7Z6Q6;Q99661	.;KIF2C_HUMAN	E	46;46;46;37	ENSP00000410346:A46E;ENSP00000361298:A46E;ENSP00000361292:A46E;ENSP00000395050:A37E	ENSP00000361292:A46E	A	+	2	0	KIF2C	44979238	0.981000	0.34729	0.990000	0.47175	0.995000	0.86356	-0.030000	0.12308	-0.083000	0.12618	0.655000	0.94253	GCA	.		0.413	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845		A	45206651	C	A	45206651	3	1	96	1	0	0	0	0	1	0	0	0	8320	710	25	4	143	4	KIF2C	1	45206651	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	13308956	45206651	204043970	4	8549											
WDR47	22911	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	109554105	109554105	+	Frame_Shift_Del	DEL	T	T	-																															ataaacgattgttactagccTtaaaaccagcttcacttagc																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:109554105delT	ENST00000369962.3	-	5	785	c.563delA	c.(562-564)aagfs	p.K188fs	WDR47_ENST00000369965.4_Frame_Shift_Del_p.K188fs|WDR47_ENST00000361054.3_Frame_Shift_Del_p.K160fs|WDR47_ENST00000400794.3_Frame_Shift_Del_p.K195fs|WDR47_ENST00000357672.3_Frame_Shift_Del_p.K160fs			O94967	WDR47_HUMAN	WD repeat domain 47	188					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		GTTACTAGCCTTAAAACCAGC	0.413																																					p.K195fs		.											.	WDR47-91	0			c.584delA						.						206	212	210					1																	109554105		2203	4296	6499	SO:0001589	frameshift_variant	22911	exon5			.	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"WD repeat domain containing"	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.563delA	1.37:g.109554105delT	ENSP00000358979:p.Lys188fs	Somatic	435	0		WXS	Illumina HiSeq	Phase_I	342	55	NM_001142550	0	0	0	0	0	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Frame_Shift_Del	DEL	ENST00000369962.3	37	CCDS44187.1																																																																																			.		0.413	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969		-	109554105	T	-	109554105	7	5	96	1	0	1	0	1	0	0	0	0	17333	1609	56	0	2243	0	WDR47	1	109554105	Frame_Shift_Del	DEL	T	TCGA-DW-7838-01A-11D-2136-08	64347454	109554105	139696516	5	8550											
ST7L	54879	bcgsc.ca	37	chr1	113119657	113119657	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctatgaattgcttccacgGcattaatttctgctgtgctt	7	17	7	10	1	2	1	0	1	2	0	3	1	3	1	1	1	3	4	1	1	3	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:113119657G>A	ENST00000358039.4	-	11	1500	c.1196C>T	c.(1195-1197)gCc>gTc	p.A399V	ST7L_ENST00000369666.1_Missense_Mutation_p.A382V|ST7L_ENST00000490067.1_Missense_Mutation_p.A382V|ST7L_ENST00000538187.1_Missense_Mutation_p.A343V|ST7L_ENST00000360743.4_Missense_Mutation_p.A399V|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000369668.2_Missense_Mutation_p.A399V|ST7L_ENST00000544629.1_Missense_Mutation_p.A334V|ST7L_ENST00000369669.1_Missense_Mutation_p.A216V|ST7L_ENST00000543570.1_Missense_Mutation_p.A382V|ST7L_ENST00000343210.7_Missense_Mutation_p.A399V	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	399					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCTTCCACGGCATTAATTTC	0.308																																					p.A399V													.	ST7L-90	0			c.C1196T						.						51	55	53					1																	113119657		2199	4296	6495	SO:0001583	missense	54879	exon11			TCCACGGCATTAA	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.1196C>T	1.37:g.113119657G>A	ENSP00000350734:p.Ala399Val	Somatic	82	0		WXS	Illumina HiSeq	Phase_1	78	5	NM_138728	0	0	10	10	0	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	G	35	5.546942	0.96488	.	.	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187;ENST00000543570;ENST00000369665	T;T;T;T;T;T;T;T;T;T	0.59083	1.69;0.29;1.69;1.69;0.29;0.29;0.29;0.29;0.29;1.69	5.51	5.51	0.81932	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.75649	0.3878	M	0.83603	2.65	0.80722	D	1	D;D;D;D;P;P;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.939;0.939;0.969;0.985;0.975	D;D;D;D;P;P;P;P;D	0.87578	0.997;0.998;0.998;0.994;0.779;0.779;0.868;0.868;0.919	T	0.78288	-0.2262	10	0.62326	D	0.03	-9.1746	19.0163	0.92896	0.0:0.0:1.0:0.0	.	382;343;334;334;399;382;382;399;399	B7Z8V6;B7Z7D4;B7Z3J2;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;.;.;.;.;ST7L_HUMAN	V	399;399;334;216;382;399;399;382;343;382;277	ENSP00000350734:A399V;ENSP00000353972:A399V;ENSP00000445499:A334V;ENSP00000358683:A216V;ENSP00000417140:A382V;ENSP00000358682:A399V;ENSP00000345312:A399V;ENSP00000358680:A382V;ENSP00000444021:A343V;ENSP00000444088:A382V	ENSP00000345312:A399V	A	-	2	0	ST7L	112921180	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.415000	0.97375	2.582000	0.87167	0.467000	0.42956	GCC	.		0.308	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			A	113119657	G	A	113119657	3	1	96	1	0	0	0	0	1	0	0	0	15262	1203	42	2	590	2	ST7L	1	113119657	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	3565552	113119657	136130964	6	8551											
ANKRD35	148741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145561665	145561665	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actaccaatggggcacagacCtttggccctgatcatgctga	10	9	10	12	0	1	3	1	2	0	1	1	3	1	3	3	3	2	2	3	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:145561665C>T	ENST00000355594.4	+	10	1440	c.1353C>T	c.(1351-1353)acC>acT	p.T451T		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	451										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGGCACAGACCTTTGGCCCTG	0.587																																					p.T451T	Melanoma(9;127 754 22988 51047)	.											.	ANKRD35-95	0			c.C1353T						.						59	67	64					1																	145561665		2203	4300	6503	SO:0001819	synonymous_variant	148741	exon10			ACAGACCTTTGGC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1353C>T	1.37:g.145561665C>T		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	97	22	NM_144698	0	0	0	0	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	37	CCDS919.1																																																																																			.		0.587	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		T	145561665	C	T	145561665	2	4	96	1	0	0	0	0	0	0	0	1	664	668	24	2		2	ANKRD35	1	145561665	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	32442008	145561665	103688956	7	8552											
HRNR	388697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152191362	152191362	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcggccactgctggaagaccGaccggagccagacccatgtc	9	5	12	15	3	0	2	0	0	0	2	2	5	0	4	5	3	2	1	5	3	1	0	rs573793519		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:152191362G>A	ENST00000368801.2	-	3	2818	c.2743C>T	c.(2743-2745)Cgg>Tgg	p.R915W	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	915					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGAAGACCGACCGGAGCCA	0.627																																					p.R915W		.											.	HRNR-93	0			c.C2743T						.						136	149	144					1																	152191362		2203	4300	6503	SO:0001583	missense	388697	exon3			AAGACCGACCGGA	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"EF-hand domain containing"	20846	protein-coding gene	gene with protein product	"filaggrin family member 3"						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2743C>T	1.37:g.152191362G>A	ENSP00000357791:p.Arg915Trp	Somatic	304	1		WXS	Illumina HiSeq	Phase_I	250	52	NM_001009931	0	0	0	0	0	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	8.431	0.848661	0.17034	.	.	ENSG00000197915	ENST00000368801	T	0.01933	4.55	3.6	2.67	0.31697	.	.	.	.	.	T	0.00695	0.0023	N	0.22421	0.69	0.09310	N	1	B	0.20780	0.048	B	0.10450	0.005	T	0.47636	-0.9102	9	0.48119	T	0.1	.	8.8921	0.35441	0.1155:0.0:0.8845:0.0	.	915	Q86YZ3	HORN_HUMAN	W	915	ENSP00000357791:R915W	ENSP00000357791:R915W	R	-	1	2	HRNR	150457986	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.046000	0.11983	0.860000	0.35481	0.498000	0.49722	CGG	.		0.627	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		A	152191362	G	A	152191362	3	1	96	1	0	0	0	0	1	0	0	0	7380	1057	37	1	5813	1	HRNR	1	152191362	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	6629697	152191362	97059259	8	8553											
FLAD1	80308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154961016	154961016	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggtgctggaggggatgaagGgactattccaaaacccagct	11	7	15	8	0	0	1	0	1	0	0	1	4	1	4	2	5	3	2	2	5	4	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:154961016G>A	ENST00000292180.3	+	2	1130	c.808G>A	c.(808-810)Gga>Aga	p.G270R	FLAD1_ENST00000368431.3_Missense_Mutation_p.G171R|FLAD1_ENST00000295530.2_Missense_Mutation_p.G3R|FLAD1_ENST00000368433.1_Missense_Mutation_p.G270R|FLAD1_ENST00000315144.10_Missense_Mutation_p.G173R|FLAD1_ENST00000405236.2_Missense_Mutation_p.G171R|FLAD1_ENST00000368428.1_5'Flank|FLAD1_ENST00000368432.1_Missense_Mutation_p.G173R	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	270					FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGGGATGAAGGGACTATTCCA	0.572																																					p.G270R		.											.	FLAD1-93	0			c.G808A						.						43	41	42					1																	154961016		2203	4300	6503	SO:0001583	missense	80308	exon2			ATGAAGGGACTAT		CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)", "FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)", "flavin adenine dinucleotide synthetase"				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.808G>A	1.37:g.154961016G>A	ENSP00000292180:p.Gly270Arg	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	69	9	NM_025207	0	0	27	36	9	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	37	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.391696	0.25118	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000368431;ENST00000292180;ENST00000405236;ENST00000295530	.	.	.	5.51	1.43	0.22495	Molybdopterin binding (2);	0.470755	0.24384	N	0.038987	T	0.05777	0.0151	N	0.25890	0.77	0.09310	N	1	P;B;P	0.45474	0.859;0.05;0.491	B;B;B	0.37304	0.246;0.124;0.076	T	0.32188	-0.9916	9	0.21014	T	0.42	-1.0E-4	6.7182	0.23314	0.2278:0.3684:0.4038:0.0	.	3;270;171	Q5T191;Q8NFF5;Q8NFF5-4	.;FAD1_HUMAN;.	R	270;173;173;171;270;171;3	.	ENSP00000292180:G270R	G	+	1	0	FLAD1	153227640	0.089000	0.21612	0.069000	0.20011	0.879000	0.50718	1.889000	0.39718	0.419000	0.25927	0.561000	0.74099	GGA	.		0.572	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207		A	154961016	G	A	154961016	3	1	96	1	0	0	0	0	1	0	0	0	5939	1233	43	2	889	2	FLAD1	1	154961016	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	2769654	154961016	94289605	9	8554											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228522554	228522554	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgccccgaatgctggagAggttcacccccaagaaagtg	10	6	12	13	2	1	2	1	0	0	2	1	4	1	2	5	2	2	2	5	2	3	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:228522554A>G	ENST00000422127.1	+	61	16170	c.16126A>G	c.(16126-16128)Agg>Ggg	p.R5376G	OBSCN_ENST00000366707.4_Missense_Mutation_p.R3010G|OBSCN_ENST00000284548.11_Missense_Mutation_p.R5376G|OBSCN_ENST00000570156.2_Missense_Mutation_p.R6333G|OBSCN_ENST00000366709.4_Missense_Mutation_p.R2495G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5376	Ig-like 51.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AATGCTGGAGAGGTTCACCCC	0.612																																					p.R6333G		.											.	OBSCN-403	0			c.A18997G						.						31	37	35					1																	228522554		2041	4158	6199	SO:0001583	missense	84033	exon72			CTGGAGAGGTTCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16126A>G	1.37:g.228522554A>G	ENSP00000409493:p.Arg5376Gly	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	10	2	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	a	33	5.261450	0.95368	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.87	4.72	0.59763	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.381287	0.28327	N	0.015748	T	0.71829	0.3386	L	0.47190	1.495	0.33354	D	0.57147	D;D	0.60575	0.988;0.985	P;P	0.58266	0.836;0.747	T	0.78081	-0.2343	10	0.39692	T	0.17	.	13.1041	0.59237	0.866:0.134:0.0:0.0	.	5376;5376	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	5376;5376;3010;2495	ENSP00000284548:R5376G;ENSP00000409493:R5376G;ENSP00000355668:R3010G;ENSP00000355670:R2495G	ENSP00000284548:R5376G	R	+	1	2	OBSCN	226589177	1.000000	0.71417	0.899000	0.35326	0.980000	0.70556	5.690000	0.68241	1.016000	0.39470	0.478000	0.44815	AGG	.		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228522554	A	G	228522554	3	3	96	1	0	0	0	0	1	0	0	0	10838	295	11	3	16364	3	OBSCN	1	228522554	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	73561538	228522554	20728067	10	8555											
C1orf124	83932	hgsc.bcm.edu	37	chr1	231474336	231474336	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccgtcgaggtgaagtggagCgtgcgaatgaccctgtgagt	8	8	17	8	4	0	3	0	3	0	0	1	6	0	4	2	2	2	0	2	2	2	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:231474336C>T	ENST00000295050.7	+	1	543	c.207C>T	c.(205-207)agC>agT	p.S69S	SPRTN_ENST00000391858.4_Silent_p.S69S|EXOC8_ENST00000360394.2_5'Flank|SPRTN_ENST00000008440.9_Silent_p.S69S|EXOC8_ENST00000366645.1_5'Flank	NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	69	SprT-like.				cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)										TGAAGTGGAGCGTGCGAATGA	0.602																																					p.S69S		.											.	.	0			c.C207T						.						85	92	90					1																	231474336		2203	4300	6503	SO:0001819	synonymous_variant	83932	exon1			GTGGAGCGTGCGA	AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"SprT-like domain at the N terminus", "DNA damage-targeting VCP (p97) adaptor"		"chromosome 1 open reading frame 124"	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.207C>T	1.37:g.231474336C>T		Somatic	187	0		WXS	Illumina HiSeq	Phase_I	159	15	NM_032018	0	0	5	10	5	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Silent	SNP	ENST00000295050.7	37	CCDS1594.1																																																																																			.		0.602	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018		T	231474336	C	T	231474336	2	4	96	1	0	0	0	0	0	0	0	1	1998	767	27	1		1	C1orf124	1	231474336	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	2951782	231474336	17776285	11	8556											
ADCY3	109	bcgsc.ca	37	chr2	25141697	25141697	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccggcacgaaagtcagccGcatgaagcgaggcaggcaca	12	3	13	13	4	1	1	1	1	0	0	2	3	2	1	2	3	2	4	2	3	2	0	rs368104984		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:25141697G>A	ENST00000260600.5	-	1	1011	c.160C>T	c.(160-162)Cgg>Tgg	p.R54W		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	54					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					AAAGTCAGCCGCATGAAGCGA	0.642																																					p.R54W													.	ADCY3-94	0			c.C160T						.						43	48	46					2																	25141697		2203	4300	6503	SO:0001583	missense	109	exon1			TCAGCCGCATGAA	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.160C>T	2.37:g.25141697G>A	ENSP00000260600:p.Arg54Trp	Somatic	67	0		WXS	Illumina HiSeq	Phase_1	80	5	NM_004036	0	0	0	0	0	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186456	0.78789	.	.	ENSG00000138031	ENST00000260600;ENST00000415879;ENST00000435135;ENST00000438445	T;T;T	0.81330	-1.48;-1.11;0.58	4.27	3.39	0.38822	.	0.131649	0.52532	D	0.000068	D	0.85570	0.5727	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68483	0.941;0.958	D	0.86290	0.1673	10	0.87932	D	0	.	12.2745	0.54726	0.0:0.0:0.8291:0.1709	.	54;54	B7ZLX9;O60266	.;ADCY3_HUMAN	W	54;29;54;54	ENSP00000260600:R54W;ENSP00000389799:R54W;ENSP00000406153:R54W	ENSP00000260600:R54W	R	-	1	2	ADCY3	24995201	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.317000	0.51968	0.996000	0.38943	0.563000	0.77884	CGG	.		0.642	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			A	25141697	G	A	25141697	3	1	96	1	0	0	0	0	1	0	0	0	295	1086	38	1	3358	1	ADCY3	2	25141697	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		25141697	218057676	12	8557											
LOXL3	84695	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74761483	74761483	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgagacagaaactagctttGtggccctcagccaccttggt	9	10	10	12	1	1	2	1	0	0	2	2	3	1	2	3	2	3	1	3	2	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:74761483G>A	ENST00000264094.3	-	11	1970	c.1899C>T	c.(1897-1899)caC>caT	p.H633H	LOXL3_ENST00000409249.1_Intron|LOXL3_ENST00000409549.1_Silent_p.H577H|LOXL3_ENST00000393937.2_Silent_p.H488H|LOXL3_ENST00000409986.1_Silent_p.H488H	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	633	Lysyl-oxidase like.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						AACTAGCTTTGTGGCCCTCAG	0.502																																					p.H633H		.											.	LOXL3-226	0			c.C1899T						.						190	183	185					2																	74761483		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon11			AGCTTTGTGGCCC	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1899C>T	2.37:g.74761483G>A		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	121	20	NM_032603	0	0	3	3	0	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	37	CCDS1953.1																																																																																			.		0.502	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		A	74761483	G	A	74761483	2	1	96	1	0	0	0	0	0	0	0	1	8926	1368	48	2		2	LOXL3	2	74761483	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	49619786	74761483	168437890	13	8558											
POLR1A	25885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	86279952	86279952	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacttacccaaggtgaagcCtctgtagagctgcaggtagg	10	8	13	10	0	1	2	0	1	1	1	1	2	1	2	2	3	4	5	2	3	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:86279952C>T	ENST00000263857.6	-	16	2758	c.2380G>A	c.(2380-2382)Ggc>Agc	p.G794S	POLR1A_ENST00000483538.1_5'Flank|POLR1A_ENST00000409681.1_Missense_Mutation_p.G794S			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	794					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						AAGGTGAAGCCTCTGTAGAGC	0.652																																					p.G794S		.											.	POLR1A-93	0			c.G2380A						.						31	35	34					2																	86279952		1926	4147	6073	SO:0001583	missense	25885	exon16			TGAAGCCTCTGTA	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"RNA polymerase subunits"	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.2380G>A	2.37:g.86279952C>T	ENSP00000263857:p.Gly794Ser	Somatic	91	1		WXS	Illumina HiSeq	Phase_I	76	9	NM_015425	0	0	0	0	0	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.675456	0.88445	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.78481	-1.18;-1.18	4.79	4.79	0.61399	RNA polymerase Rpb1, domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.90834	0.7121	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92973	0.6399	10	0.72032	D	0.01	-20.0332	17.6405	0.88135	0.0:1.0:0.0:0.0	.	794	O95602	RPA1_HUMAN	S	794	ENSP00000263857:G794S;ENSP00000386300:G794S	ENSP00000263857:G794S	G	-	1	0	POLR1A	86133463	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.614000	0.67695	2.496000	0.84212	0.655000	0.94253	GGC	.		0.652	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		T	86279952	C	T	86279952	3	4	96	1	0	0	0	0	1	0	0	0	12235	681	24	2	2858	2	POLR1A	2	86279952	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	11518469	86279952	156919421	14	8559											
TUBA3D	113457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	132236969	132236969	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcagccaataattacgccagGggccattacaccatcggcaa	13	6	9	13	2	0	0	0	0	0	0	1	0	0	0	4	3	3	2	4	3	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:132236969G>A	ENST00000321253.6	+	3	422	c.315G>A	c.(313-315)agG>agA	p.R105R	TUBA3D_ENST00000409047.2_3'UTR	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	105					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		ATTACGCCAGGGGCCATTACA	0.527																																					p.R105R	Ovarian(137;2059 2432 35543 39401)	.											.	TUBA3D-44	0			c.G315A						.						209	172	184					2																	132236969		2203	4300	6503	SO:0001819	synonymous_variant	113457	exon3			CGCCAGGGGCCAT	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"Tubulins"	24071	protein-coding gene	gene with protein product	"alpha-tubulin isotype H2-alpha"					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.315G>A	2.37:g.132236969G>A		Somatic	273	0		WXS	Illumina HiSeq	Phase_I	256	40	NM_080386	0	0	0	0	0	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000321253.6	37	CCDS33290.1																																																																																			.		0.527	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		A	132236969	G	A	132236969	2	1	96	1	0	0	0	0	0	0	0	1	16780	1223	43	2		2	TUBA3D	2	132236969	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	45957017	132236969	110962404	15	8560											
FIGN	55137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	164466515	164466515	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtgtccagttgcatcagAaattcggttctcatccgact	10	12	8	11	2	2	1	2	0	1	1	6	2	4	1	2	1	1	3	2	1	1	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:164466515A>T	ENST00000333129.3	-	3	2141	c.1827T>A	c.(1825-1827)ttT>ttA	p.F609L	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'Flank	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	609					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GTTGCATCAGAAATTCGGTTC	0.458																																					p.F609L		.											.	FIGN-156	0			c.T1827A						.						105	99	101					2																	164466515		1948	4151	6099	SO:0001583	missense	55137	exon3			CATCAGAAATTCG	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"ATPases / AAA-type"	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.1827T>A	2.37:g.164466515A>T	ENSP00000333836:p.Phe609Leu	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	105	23	NM_018086	0	0	0	0	0	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	12.72	2.023844	0.35701	.	.	ENSG00000182263	ENST00000333129	D	0.86865	-2.18	5.47	2.81	0.32909	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.055714	0.64402	D	0.000001	T	0.74504	0.3725	N	0.00771	-1.2	0.58432	D	0.999996	B	0.32324	0.364	P	0.51999	0.687	T	0.66767	-0.5840	10	0.21014	T	0.42	-19.2916	5.9791	0.19397	0.6913:0.0:0.3087:0.0	.	609	Q5HY92	FIGN_HUMAN	L	609	ENSP00000333836:F609L	ENSP00000333836:F609L	F	-	3	2	FIGN	164174761	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.691000	0.37721	1.009000	0.39289	0.383000	0.25322	TTT	.		0.458	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164466515	A	T	164466515	3	4	96	1	0	0	0	0	1	0	0	0	5910	243	9	5	456	5	FIGN	2	164466515	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	32229546	164466515	78732858	16	8561											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179650403	179650403	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaaacagtaaagtgagggcTagctgtgcgggggcgtttat	10	10	16	5	2	0	2	0	2	0	0	0	2	0	2	0	3	3	4	0	3	5	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:179650403T>A	ENST00000591111.1	-	15	2661	c.2437A>T	c.(2437-2439)Agc>Tgc	p.S813C	TTN_ENST00000359218.5_Missense_Mutation_p.S767C|TTN_ENST00000460472.2_Missense_Mutation_p.S767C|TTN_ENST00000360870.5_Missense_Mutation_p.S813C|TTN_ENST00000589042.1_Missense_Mutation_p.S813C|TTN_ENST00000342992.6_Missense_Mutation_p.S813C|TTN_ENST00000342175.6_Missense_Mutation_p.S767C			Q8WZ42	TITIN_HUMAN	titin	33644					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGTGAGGGCTAGCTGTGCGG	0.373																																					p.S813C		.											.	TTN-636	0			c.A2437T						.						172	167	169					2																	179650403		2203	4300	6503	SO:0001583	missense	7273	exon15			GAGGGCTAGCTGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2437A>T	2.37:g.179650403T>A	ENSP00000465570:p.Ser813Cys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	88	16	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.88	2.071468	0.36566	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67523	-0.27;-0.03;-0.03;-0.04;0.15	5.51	5.51	0.81932	Ribonuclease H-like (1);	.	.	.	.	T	0.70159	0.3192	L	0.27053	0.805	0.24564	N	0.993953	D;D;D;D;D	0.89917	0.993;0.993;0.993;0.993;1.0	P;P;P;P;D	0.69479	0.628;0.628;0.628;0.628;0.964	T	0.62699	-0.6799	9	0.87932	D	0	.	10.3027	0.43661	0.0:0.0737:0.0:0.9263	.	767;767;767;813;813	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	C	813;767;767;767;767;813	ENSP00000343764:S813C;ENSP00000434586:S767C;ENSP00000340554:S767C;ENSP00000352154:S767C;ENSP00000354117:S813C	ENSP00000340554:S767C	S	-	1	0	TTN	179358648	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.566000	0.45948	2.210000	0.71456	0.533000	0.62120	AGC	.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179650403	T	A	179650403	3	1	96	1	0	0	0	0	1	0	0	0	16768	1522	53	5	108943	5	TTN	2	179650403	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	15183888	179650403	63548970	17	8562											
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238303376	238303376	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattgagcggttcacttgctAtttcttttaacgctccttca	7	18	6	10	2	3	1	2	1	1	0	4	1	4	1	1	1	3	3	1	1	3	9			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:238303376A>G	ENST00000295550.4	-	3	1015	c.563T>C	c.(562-564)aTa>aCa	p.I188T	COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000347401.3_Missense_Mutation_p.I188T|COL6A3_ENST00000392004.3_Intron|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000346358.4_Missense_Mutation_p.I188T|COL6A3_ENST00000392003.2_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	188	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTCACTTGCTATTTCTTTTAA	0.433																																					p.I188T		.											.	COL6A3-526	0			c.T563C						.						127	124	125					2																	238303376		2203	4300	6503	SO:0001583	missense	1293	exon3			CTTGCTATTTCTT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.563T>C	2.37:g.238303376A>G	ENSP00000295550:p.Ile188Thr	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	85	13	NM_004369	0	0	1	1	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	6.536	0.467096	0.12402	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000346358;ENST00000433762	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	4.9	3.72	0.42706	von Willebrand factor, type A (3);	0.267710	0.25584	U	0.029678	D	0.88437	0.6436	H	0.94886	3.595	0.47778	D	0.999513	B;B	0.19445	0.009;0.036	B;B	0.20767	0.021;0.031	D	0.85506	0.1194	10	0.62326	D	0.03	.	10.6923	0.45877	0.9233:0.0:0.0766:0.0	.	188;188	E9PCV6;P12111	.;CO6A3_HUMAN	T	188	ENSP00000295550:I188T;ENSP00000315609:I188T;ENSP00000295546:I188T;ENSP00000389539:I188T	ENSP00000295550:I188T	I	-	2	0	COL6A3	237968115	1.000000	0.71417	0.997000	0.53966	0.219000	0.24729	6.121000	0.71602	0.699000	0.31761	0.374000	0.22700	ATA	.		0.433	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238303376	A	G	238303376	3	3	96	1	0	0	0	0	1	0	0	0	3707	449	16	3	9185	3	COL6A3	2	238303376	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	58652973	238303376	4895997	18	8563											
RNPEPL1	57140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	241516157	241516157	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcactcttcctggaccggctCctggatgggtccccgctgcc	3	9	12	17	2	1	0	0	0	1	0	4	2	4	2	6	4	1	3	6	4	0	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:241516157C>T	ENST00000270357.4	+	9	1616	c.1023C>T	c.(1021-1023)ctC>ctT	p.L341L	RNPEPL1_ENST00000464550.1_3'UTR	NM_018226.4	NP_060696.4	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like 1	341					leukotriene biosynthetic process (GO:0019370)		aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	13		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)		TGGACCGGCTCCTGGATGGGT	0.687																																					p.L572L		.											.	RNPEPL1-154	0			c.C1716T						.						29	33	32					2																	241516157		2196	4289	6485	SO:0001819	synonymous_variant	57140	exon9			CCGGCTCCTGGAT			2q37.3	2012-03-06			ENSG00000142327	ENSG00000142327			10079	protein-coding gene	gene with protein product		605287				19508204	Standard	NM_018226		Approved		uc002vzi.4	Q9HAU8	OTTHUMG00000133357	ENST00000270357.4:c.1023C>T	2.37:g.241516157C>T		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	83	11	NM_018226	0	0	42	62	20	Q5XKC3|Q6NX56|Q96AC9|Q9H033|Q9NVD0	Silent	SNP	ENST00000270357.4	37																																																																																				.		0.687	RNPEPL1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257190.4	NM_018226		T	241516157	C	T	241516157	2	4	96	1	0	0	0	0	0	0	0	1	13542	842	30	2		2	RNPEPL1	2	241516157	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	3212781	241516157	1683216	19	8564											
SCAP	22937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47456625	47456625	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagggcagtgtgggtctcCaaggagaagaaatcaaggga	13	6	16	6	0	2	3	1	1	1	2	3	5	2	4	1	4	0	1	1	4	4	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:47456625C>T	ENST00000265565.5	-	19	3514	c.3102G>A	c.(3100-3102)ttG>ttA	p.L1034L	SCAP_ENST00000441517.2_Silent_p.L778L|SCAP_ENST00000545718.1_Silent_p.L641L	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	1034	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		TGTGGGTCTCCAAGGAGAAGA	0.632																																					p.L1034L	Pancreas(149;978 1908 29304 37806 46700)	.											.	SCAP-91	0			c.G3102A						.						51	53	52					3																	47456625		2202	4299	6501	SO:0001819	synonymous_variant	22937	exon19			GGTCTCCAAGGAG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.3102G>A	3.37:g.47456625C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	69	17	NM_012235	0	0	32	44	12	Q8N2E0|Q8WUA1	Silent	SNP	ENST00000265565.5	37	CCDS2755.2																																																																																			.		0.632	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		T	47456625	C	T	47456625	2	4	96	1	0	0	0	0	0	0	0	1	13909	593	21	2		2	SCAP	3	47456625	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08		47456625	150565805	20	8565											
C3orf18	51161	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50602964	50602964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggtacccacgccggccGtgccaccagctgcatcaggg	7	5	13	16	3	1	0	1	0	0	0	1	0	1	0	5	3	4	4	5	3	1	1	rs559763162		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:50602964G>A	ENST00000357203.3	-	3	706	c.167C>T	c.(166-168)aCg>aTg	p.T56M	C3orf18_ENST00000449241.1_Missense_Mutation_p.T56M|C3orf18_ENST00000426034.1_Missense_Mutation_p.T56M|C3orf18_ENST00000441239.1_Missense_Mutation_p.T56M|C3orf18_ENST00000486175.1_Intron	NM_016210.4	NP_057294.2	Q9UK00	CC018_HUMAN	chromosome 3 open reading frame 18	56						integral component of membrane (GO:0016021)				lung(1)|pancreas(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CACGCCGGCCGTGCCACCAGC	0.607																																					p.T56M		.											.	C3orf18-279	0			c.C167T						.						88	76	80					3																	50602964		2202	4300	6502	SO:0001583	missense	51161	exon3			CCGGCCGTGCCAC	AF188706	CCDS2829.1, CCDS54589.1	3p21.3	2006-01-11			ENSG00000088543	ENSG00000088543			24837	protein-coding gene	gene with protein product						12477932	Standard	NM_016210		Approved	G20	uc010hlp.3	Q9UK00	OTTHUMG00000156854	ENST00000357203.3:c.167C>T	3.37:g.50602964G>A	ENSP00000349732:p.Thr56Met	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	65	13	NM_016210	0	0	0	1	1	C9JNP0	Missense_Mutation	SNP	ENST00000357203.3	37	CCDS2829.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.495028	0.26774	.	.	ENSG00000088543	ENST00000426034;ENST00000357203;ENST00000449241;ENST00000441239	T;T;T;T	0.42513	2.52;2.52;2.52;0.97	5.24	3.36	0.38483	.	0.821587	0.11279	N	0.580514	T	0.24851	0.0603	N	0.19112	0.55	0.21105	N	0.999781	P;P	0.52577	0.89;0.954	B;B	0.37780	0.258;0.251	T	0.05920	-1.0856	10	0.52906	T	0.07	-12.7022	7.5988	0.28065	0.0:0.3237:0.5385:0.1378	.	56;56	C9JNP0;Q9UK00	.;CC018_HUMAN	M	56	ENSP00000387606:T56M;ENSP00000349732:T56M;ENSP00000404913:T56M;ENSP00000414124:T56M	ENSP00000349732:T56M	T	-	2	0	C3orf18	50577968	0.019000	0.18553	0.001000	0.08648	0.388000	0.30384	2.265000	0.43311	1.193000	0.43086	0.462000	0.41574	ACG	.		0.607	C3orf18-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346260.2	NM_016210		A	50602964	G	A	50602964	3	1	96	1	0	0	0	0	1	0	0	0	2217	1145	40	1	337	1	C3orf18	3	50602964	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	3146339	50602964	147419466	21	8566											
BBX	56987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	107491690	107491690	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggaattgagaaattttgaGgcattgcaaatagatgacat	17	11	10	3	0	0	4	0	3	0	2	0	6	0	5	0	2	1	2	0	2	5	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:107491690G>C	ENST00000325805.8	+	11	1409	c.1122G>C	c.(1120-1122)gaG>gaC	p.E374D	BBX_ENST00000415149.2_Missense_Mutation_p.E374D|BBX_ENST00000406780.1_Missense_Mutation_p.E374D|BBX_ENST00000416476.2_Intron|BBX_ENST00000402543.1_Missense_Mutation_p.E374D			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	374					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			GAAATTTTGAGGCATTGCAAA	0.323																																					p.E374D		.											.	BBX-94	0			c.G1122C						.						58	68	64					3																	107491690		2203	4298	6501	SO:0001583	missense	56987	exon11			TTTTGAGGCATTG	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"x 001 protein"					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1122G>C	3.37:g.107491690G>C	ENSP00000319974:p.Glu374Asp	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	109	48	NM_001142568	0	0	2	7	5	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	G	4.952	0.176823	0.09443	.	.	ENSG00000114439	ENST00000415149;ENST00000325767;ENST00000402543;ENST00000325805;ENST00000402163;ENST00000406780	D;D;D;D;D	0.98747	-4.6;-4.6;-4.61;-5.11;-4.6	6.16	-0.709	0.11237	.	0.342008	0.33253	N	0.005119	D	0.94486	0.8225	N	0.24115	0.695	0.28521	N	0.91307	B;B;B	0.18461	0.012;0.028;0.009	B;B;B	0.14023	0.004;0.01;0.009	D	0.88666	0.3192	10	0.45353	T	0.12	-10.7263	7.4111	0.27017	0.5975:0.0:0.282:0.1205	.	374;374;374	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	D	374;225;374;374;374;374	ENSP00000408358:E374D;ENSP00000385317:E374D;ENSP00000319974:E374D;ENSP00000385518:E374D;ENSP00000385530:E374D	ENSP00000319742:E225D	E	+	3	2	BBX	108974380	0.991000	0.36638	0.873000	0.34254	0.130000	0.20726	0.223000	0.17719	-0.449000	0.07117	-1.871000	0.00553	GAG	.		0.323	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		C	107491690	G	C	107491690	3	2	96	1	0	0	0	0	1	0	0	0	1344	991	35	4	1152	4	BBX	3	107491690	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	56888726	107491690	90530740	22	8567											
ADCY5	111	broad.mit.edu	37	chr3	123166392	123166392	+	Frame_Shift_Del	DEL	A	A	-																															tgtagatggtgtagatgaagAacacggtccaccagatgccc																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:123166392delA	ENST00000462833.1	-	1	2213	c.1001delT	c.(1000-1002)ttcfs	p.F335fs		NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	335					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GTAGATGAAGAACACGGTCCA	0.692																																					p.F334fs													.	ADCY5-94	0			c.1001delT						.						31	31	31					3																	123166392		2202	4297	6499	SO:0001589	frameshift_variant	111	exon1			ATGAAGAACACGG	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1001delT	3.37:g.123166392delA	ENSP00000419361:p.Phe335fs	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	36	8	NM_183357	0	0	0	0	0	B7Z8A6|Q7RTV7|Q8NFM3	Frame_Shift_Del	DEL	ENST00000462833.1	37	CCDS3022.1																																																																																			.		0.692	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		-	123166392	A	-	123166392	7	5	96	1	0	1	0	1	0	0	0	0	297	246	9	0	2868	0	ADCY5	3	123166392	Frame_Shift_Del	DEL	A	TCGA-DW-7838-01A-11D-2136-08	15674702	123166392	74856038	23	8568											
EHHADH	1962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	184922367	184922367	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacagctcctcctccttcttGatgcccacttcatagggata	9	12	6	14	0	2	1	1	1	1	0	5	2	5	2	4	1	3	1	4	1	3	5	rs149294851		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:184922367G>A	ENST00000231887.3	-	6	822	c.747C>T	c.(745-747)atC>atT	p.I249I	EHHADH_ENST00000456310.1_Silent_p.I153I	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	249	Enoyl-CoA hydratase / isomerase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CCTCCTTCTTGATGCCCACTT	0.517																																					p.I249I		.											.	EHHADH-93	0			c.C747T						.						131	128	129					3																	184922367		2203	4300	6503	SO:0001819	synonymous_variant	1962	exon6			CTTCTTGATGCCC	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.747C>T	3.37:g.184922367G>A		Somatic	234	0		WXS	Illumina HiSeq	Phase_I	289	88	NM_001966	0	0	5	32	27	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	37	CCDS33901.1																																																																																			G|1.000;C|0.000		0.517	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184922367	G	A	184922367	2	1	96	1	0	0	0	0	0	0	0	1	4993	1280	45	2		2	EHHADH	3	184922367	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	61755975	184922367	13100063	24	8569											
MFSD10	10227	hgsc.bcm.edu	37	chr4	2934901	2934901	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccagtgagtggcgcacacaGaaactgcaggacagagaatg	14	4	13	10	1	0	3	0	1	0	2	0	5	0	4	1	2	2	2	1	2	2	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:2934901G>C	ENST00000329687.4	-	3	838	c.304C>G	c.(304-306)Ctg>Gtg	p.L102V	NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000514800.1_Missense_Mutation_p.L102V|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000507999.1_RNA|MFSD10_ENST00000508221.1_Missense_Mutation_p.L102V|NOP14-AS1_ENST00000512712.2_RNA|MFSD10_ENST00000507555.1_Missense_Mutation_p.L102V|MFSD10_ENST00000355443.4_Missense_Mutation_p.L102V	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	102					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCGCACACAGAAACTGCAGG	0.617																																					p.L102V		.											.	MFSD10-68	0			c.C304G						.						53	53	53					4																	2934901		2202	4299	6501	SO:0001583	missense	10227	exon3			CACACAGAAACTG	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"tetracycline transporter like protein"	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.304C>G	4.37:g.2934901G>C	ENSP00000332646:p.Leu102Val	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	54	9	NM_001120	0	0	26	64	38	Q07706	Missense_Mutation	SNP	ENST00000329687.4	37	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	G	5.826	0.336718	0.11013	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	4.19	-0.214	0.13161	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.370891	0.28062	N	0.016760	T	0.33585	0.0868	L	0.45422	1.42	0.20307	N	0.999916	B;B;B;B	0.23735	0.012;0.022;0.09;0.007	B;B;B;B	0.29267	0.042;0.078;0.1;0.032	T	0.09796	-1.0658	10	0.14656	T	0.56	-10.5579	0.8156	0.01102	0.2667:0.3381:0.2238:0.1713	.	102;102;102;102	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	V	102	ENSP00000426907:L102V;ENSP00000347619:L102V;ENSP00000332646:L102V;ENSP00000425757:L102V;ENSP00000423402:L102V	ENSP00000332646:L102V	L	-	1	2	MFSD10	2904699	0.985000	0.35326	0.153000	0.22517	0.211000	0.24417	0.178000	0.16820	0.045000	0.15804	0.561000	0.74099	CTG	.		0.617	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120		C	2934901	G	C	2934901	3	2	96	1	0	0	0	0	1	0	0	0	9553	933	33	4	1103	4	MFSD10	4	2934901	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		2934901	188219375	25	8570											
JAKMIP1	152789	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	6066676	6066676	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttgtaggatgtttcggaCaacgtttctgagtccacaga	9	13	12	7	2	1	2	0	1	1	1	3	4	2	4	1	2	1	4	1	2	2	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:6066676C>T	ENST00000282924.5	-	9	1847	c.1362G>A	c.(1360-1362)ttG>ttA	p.L454L	JAKMIP1_ENST00000410077.2_Silent_p.L289L|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409831.1_Silent_p.L454L|JAKMIP1_ENST00000409021.3_Silent_p.L454L|JAKMIP1_ENST00000409371.3_Silent_p.L269L	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	454	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ATGTTTCGGACAACGTTTCTG	0.488																																					p.L454L		.											.	JAKMIP1-292	0			c.G1362A						.						192	163	173					4																	6066676		2203	4300	6503	SO:0001819	synonymous_variant	152789	exon9			TTCGGACAACGTT	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1362G>A	4.37:g.6066676C>T		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	92	6	NM_001099433	0	0	0	0	0	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	37	CCDS3385.1																																																																																			.		0.488	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6066676	C	T	6066676	2	4	96	1	0	0	0	0	0	0	0	1	7961	477	17	2		2	JAKMIP1	4	6066676	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	3131775	6066676	185087600	26	8571											
BOD1L	259282	broad.mit.edu;bcgsc.ca	37	chr4	13601157	13601157	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctcttctgcatttatgAggtgtaaagtgctctctttc	6	19	7	9	0	4	1	0	1	4	0	7	1	4	1	0	1	2	3	0	1	3	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:13601157A>G	ENST00000040738.5	-	10	7502	c.7367T>C	c.(7366-7368)cTc>cCc	p.L2456P		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2456						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGCATTTATGAGGTGTAAAGT	0.468											OREG0016115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L2456P													.	.	0			c.T7367C						.						164	147	153					4																	13601157		2203	4300	6503	SO:0001583	missense	259282	exon10			TTTATGAGGTGTA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7367T>C	4.37:g.13601157A>G	ENSP00000040738:p.Leu2456Pro	Somatic	109	0	688	WXS	Illumina HiSeq	Phase_I	107	5	NM_148894	0	0	4	5	1	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	A	13.05	2.120234	0.37436	.	.	ENSG00000038219	ENST00000040738	T	0.09350	2.99	4.17	-0.642	0.11486	.	0.433636	0.16546	N	0.209707	T	0.06781	0.0173	L	0.27053	0.805	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.30937	-0.9961	10	0.40728	T	0.16	.	8.0002	0.30293	0.597:0.0:0.403:0.0	.	2456	Q8NFC6	BOD1L_HUMAN	P	2456	ENSP00000040738:L2456P	ENSP00000040738:L2456P	L	-	2	0	BOD1L	13210255	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	0.222000	0.17699	-0.013000	0.14199	0.454000	0.30748	CTC	.		0.468	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13601157	A	G	13601157	3	3	96	1	0	0	0	0	1	0	0	0	1484	304	11	3	1856	3	BOD1L	4	13601157	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	7534481	13601157	177553119	27	8572											
RELL1	768211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	37650975	37650975	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctttcttcttaagcaggTggcaaatgaggacgccaaag	12	9	11	9	1	2	1	0	1	2	0	2	2	2	2	2	3	2	2	2	3	3	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:37650975T>A	ENST00000454158.2	-	2	324	c.236A>T	c.(235-237)cAc>cTc	p.H79L	RELL1_ENST00000314117.4_Missense_Mutation_p.H79L	NM_001085400.1	NP_001078869.1	Q8IUW5	RELL1_HUMAN	RELT-like 1	79						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6						CTTAAGCAGGTGGCAAATGAG	0.443																																					p.H79L		.											.	RELL1-68	0			c.A236T						.						174	179	178					4																	37650975		1930	4130	6060	SO:0001583	missense	768211	exon2			AGCAGGTGGCAAA	AK025431	CCDS43221.1	4p14	2011-10-11				ENSG00000181826			27379	protein-coding gene	gene with protein product		611212				16389068	Standard	NM_001085399		Approved		uc003gsz.2	Q8IUW5		ENST00000454158.2:c.236A>T	4.37:g.37650975T>A	ENSP00000398778:p.His79Leu	Somatic	274	1		WXS	Illumina HiSeq	Phase_I	258	29	NM_001085399	0	0	8	16	8	Q8NBK1	Missense_Mutation	SNP	ENST00000454158.2	37	CCDS43221.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.783032	0.90282	.	.	ENSG00000181826	ENST00000314117;ENST00000454158;ENST00000512114	T;T;T	0.38560	1.19;1.19;1.13	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.64349	0.2590	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68390	-0.5421	10	0.87932	D	0	-7.8098	15.2746	0.73732	0.0:0.0:0.0:1.0	.	79	Q8IUW5	RELL1_HUMAN	L	79;79;100	ENSP00000313385:H79L;ENSP00000398778:H79L;ENSP00000424031:H100L	ENSP00000313385:H79L	H	-	2	0	RELL1	37327370	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.515000	0.73751	2.084000	0.62774	0.533000	0.62120	CAC	.		0.443	RELL1-002	KNOWN	alternative_3_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360485.1	NM_001085400		A	37650975	T	A	37650975	3	1	96	1	0	0	0	0	1	0	0	0	13250	1696	59	5	599	5	RELL1	4	37650975	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	24049818	37650975	153503301	28	8573											
DMP1	1758	broad.mit.edu	37	chr4	88583660	88583660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaaatcaaaagaatctggaGaaaacagtgagcaagcaaac	21	5	9	6	0	2	4	1	2	1	2	2	5	2	4	0	1	4	2	0	1	8	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:88583660G>A	ENST00000339673.6	+	6	829	c.730G>A	c.(730-732)Gaa>Aaa	p.E244K	RP11-742B18.1_ENST00000506480.1_RNA|DMP1_ENST00000282479.7_Missense_Mutation_p.E228K|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	244					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AGAATCTGGAGAAAACAGTGA	0.468																																					p.E244K													.	DMP1-132	0			c.G730A						.						51	49	50					4																	88583660		2203	4300	6503	SO:0001583	missense	1758	exon6			TCTGGAGAAAACA	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"dentin matrix acidic phosphoprotein"			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.730G>A	4.37:g.88583660G>A	ENSP00000340935:p.Glu244Lys	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_004407	0	0	0	0	0	A1L4L3|O43265	Missense_Mutation	SNP	ENST00000339673.6	37	CCDS3623.1	.	.	.	.	.	.	.	.	.	.	G	7.750	0.703146	0.15172	.	.	ENSG00000152592	ENST00000339673;ENST00000282479	T;T	0.43688	0.94;0.94	4.89	3.09	0.35607	.	1.553400	0.03623	N	0.236681	T	0.45538	0.1347	L	0.34521	1.04	0.09310	N	1	P;P	0.38167	0.567;0.621	P;P	0.48873	0.458;0.593	T	0.39440	-0.9614	10	0.27082	T	0.32	-2.3267	8.1076	0.30896	0.0847:0.2894:0.6259:0.0	.	228;244	Q13316-2;Q13316	.;DMP1_HUMAN	K	244;228	ENSP00000340935:E244K;ENSP00000282479:E228K	ENSP00000282479:E228K	E	+	1	0	DMP1	88802684	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.456000	0.21859	1.072000	0.40860	0.650000	0.86243	GAA	.		0.468	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1			A	88583660	G	A	88583660	3	1	96	1	0	0	0	0	1	0	0	0	4594	943	33	2	748	2	DMP1	4	88583660	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	50932685	88583660	102570616	29	8574											
CENPE	1062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	104070327	104070327	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtggtctctctctgtttcaAatgacttctgtaattccttt	6	19	7	9	0	4	1	1	1	3	0	7	1	5	1	1	2	0	2	1	2	2	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:104070327A>T	ENST00000265148.3	-	27	3724	c.3635T>A	c.(3634-3636)tTt>tAt	p.F1212Y	CENPE_ENST00000380026.3_Missense_Mutation_p.F1187Y	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1212					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CTCTGTTTCAAATGACTTCTG	0.323																																					p.F1212Y		.											.	CENPE-277	0			c.T3635A						.						82	88	86					4																	104070327		2203	4298	6501	SO:0001583	missense	1062	exon27			GTTTCAAATGACT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.3635T>A	4.37:g.104070327A>T	ENSP00000265148:p.Phe1212Tyr	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	74	17	NM_001813	0	0	1	1	0	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.613801	0.46631	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.72167	-0.63;-0.63	4.01	2.82	0.32997	.	.	.	.	.	T	0.68247	0.2980	L	0.60455	1.87	0.26955	N	0.965944	P;P	0.50528	0.886;0.936	P;B	0.46825	0.528;0.322	T	0.58053	-0.7704	9	0.41790	T	0.15	.	7.9506	0.30012	0.9036:0.0:0.0964:0.0	.	1187;1212	Q02224-3;Q02224	.;CENPE_HUMAN	Y	1212;1212;1187	ENSP00000265148:F1212Y;ENSP00000369365:F1187Y	ENSP00000265148:F1212Y	F	-	2	0	CENPE	104289776	0.093000	0.21703	0.999000	0.59377	0.848000	0.48234	2.181000	0.42547	0.699000	0.31761	0.533000	0.62120	TTT	.		0.323	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	104070327	A	T	104070327	3	4	96	1	0	0	0	0	1	0	0	0	3236	14	1	5	4562	5	CENPE	4	104070327	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	15486667	104070327	87083949	30	8575											
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	89953910	89953915	+	In_Frame_Del	DEL	AAATCA	AAATCA	-																															tcagacagggagaaactaacAaatcattcattatttctgca																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	AAATCA	AAATCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:89953910_89953915delAAATCA	ENST00000405460.2	+	21	4663_4668	c.4567_4572delAAATCA	c.(4567-4572)aaatcadel	p.KS1523del		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1523	Calx-beta 10. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGAAACTAACAAATCATTCATTATTT	0.374																																					p.1523_1524del		.											.	GPR98-103	0			c.4567_4572del						.																																			SO:0001651	inframe_deletion	84059	exon21			.	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4567_4572delAAATCA	5.37:g.89953910_89953915delAAATCA	ENSP00000384582:p.Lys1523_Ser1524del	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	126	30	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	In_Frame_Del	DEL	ENST00000405460.2	37	CCDS47246.1																																																																																			.		0.374	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		-	89953915	AAATCA	-	89953910	7	5	96	1	0	1	0	1	0	0	0	0	6742	131	5	0	4649	0	GPR98	5	89953910	In_Frame_Del	DEL	AAATCA	TCGA-DW-7838-01A-11D-2136-08		89953910	90961350	31	8576											
C5orf36	285600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	93856481	93856481	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggaattatcttcaacagAatgaagagacgtcctagaga	17	8	10	6	1	2	5	1	1	1	4	3	8	3	6	1	1	1	0	1	1	6	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:93856481A>C	ENST00000329378.7	-	5	691	c.442T>G	c.(442-444)Tct>Gct	p.S148A	KIAA0825_ENST00000513200.3_Missense_Mutation_p.S148A|KIAA0825_ENST00000312498.7_Missense_Mutation_p.S148A|KIAA0825_ENST00000427991.2_Missense_Mutation_p.S148A	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	148										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TCTTCAACAGAATGAAGAGAC	0.418																																					p.S148A		.											.	KIAA0825-91	0			c.T442G						.						68	68	68					5																	93856481		2203	4299	6502	SO:0001583	missense	285600	exon5			CAACAGAATGAAG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.442T>G	5.37:g.93856481A>C	ENSP00000331385:p.Ser148Ala	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	60	15	NM_173665	0	0	0	0	0	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000329378.7	37	CCDS4070.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.938185	0.00484	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498;ENST00000329378	T;T;T;T	0.38077	1.18;1.18;1.16;1.18	5.27	4.16	0.48862	.	1.670800	0.02660	N	0.107410	T	0.19644	0.0472	N	0.11560	0.145	0.21445	N	0.999683	B;B	0.11235	0.001;0.004	B;B	0.08055	0.002;0.003	T	0.37197	-0.9716	10	0.05436	T	0.98	.	6.5441	0.22397	0.4544:0.4284:0.0:0.1172	.	148;148	Q8IV33;Q8IV33-2	K0825_HUMAN;.	A	148	ENSP00000424618:S148A;ENSP00000400288:S148A;ENSP00000312205:S148A;ENSP00000331385:S148A	ENSP00000312205:S148A	S	-	1	0	KIAA0825	93882237	1.000000	0.71417	0.939000	0.37840	0.025000	0.11179	2.208000	0.42797	1.984000	0.57885	0.477000	0.44152	TCT	.		0.418	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665		C	93856481	A	C	93856481	3	2	96	1	0	0	0	0	1	0	0	0	2301	246	9	5	3458	5	C5orf36	5	93856481	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	3902571	93856481	87058779	32	8577											
HSD17B4	3295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	118824931	118824931	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatgtggcacctcttgtcCtttggctttgtcacgagagt	6	15	11	9	1	2	1	1	0	1	1	3	2	3	1	2	2	0	3	2	2	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:118824931C>T	ENST00000256216.6	+	9	800	c.667C>T	c.(667-669)Ctt>Ttt	p.L223F	HSD17B4_ENST00000513628.1_Missense_Mutation_p.L86F|HSD17B4_ENST00000504811.1_Missense_Mutation_p.L248F|HSD17B4_ENST00000510025.1_Missense_Mutation_p.L199F|HSD17B4_ENST00000509514.1_5'UTR|HSD17B4_ENST00000414835.2_Missense_Mutation_p.L83F|HSD17B4_ENST00000515320.1_Missense_Mutation_p.L205F	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	223	(3R)-hydroxyacyl-CoA dehydrogenase.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		ACCTCTTGTCCTTTGGCTTTG	0.378																																					p.L248F	Colon(35;490 801 34689 41394 43344)	.											.	HSD17B4-92	0			c.C742T						.						221	214	217					5																	118824931		2202	4300	6502	SO:0001583	missense	3295	exon10			CTTGTCCTTTGGC		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5213	protein-coding gene	gene with protein product	"17beta-estradiol dehydrogenase type IV", "peroxisomal multifunctional protein 2", "17-beta-HSD IV", "17-beta-hydroxysteroid dehydrogenase 4", "D-bifunctional protein, peroxisomal", "D-3-hydroxyacyl-CoA dehydratase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase", "beta-keto-reductase", "beta-hydroxyacyl dehydrogenase", "short chain dehydrogenase/reductase family 8C, member 1"	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.667C>T	5.37:g.118824931C>T	ENSP00000256216:p.Leu223Phe	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	186	61	NM_001199291	0	0	49	116	67	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490542	0.64074	.	.	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	5.97	5.97	0.96955	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95262	0.8463	M	0.87381	2.88	0.80722	D	1	D;P;P;P	0.71674	0.998;0.891;0.746;0.891	D;B;B;B	0.71414	0.973;0.266;0.266;0.194	D	0.94345	0.7574	10	0.39692	T	0.17	-19.2226	13.265	0.60128	0.0:0.9271:0.0:0.0729	.	248;205;199;223	F5HE57;E9PB82;E7EWE5;P51659	.;.;.;DHB4_HUMAN	F	223;205;199;248;83;86	ENSP00000256216:L223F;ENSP00000424613:L205F;ENSP00000424940:L199F;ENSP00000420914:L248F;ENSP00000411960:L83F;ENSP00000425993:L86F	ENSP00000256216:L223F	L	+	1	0	HSD17B4	118852830	0.999000	0.42202	1.000000	0.80357	0.393000	0.30537	3.986000	0.56937	2.834000	0.97654	0.650000	0.86243	CTT	.		0.378	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414		T	118824931	C	T	118824931	3	4	96	1	0	0	0	0	1	0	0	0	7407	681	24	2	701	2	HSD17B4	5	118824931	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	24968450	118824931	62090329	33	8578											
ZNF608	57507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	123980011	123980011	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtcgtacatctgtgggtaaGgataagcatgcaagtactgt	11	11	13	6	1	1	0	0	0	1	0	2	1	1	1	0	3	4	5	0	3	5	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:123980011G>A	ENST00000306315.5	-	5	4484	c.4049C>T	c.(4048-4050)cCt>cTt	p.P1350L	ZNF608_ENST00000504926.1_Missense_Mutation_p.P923L|ZNF608_ENST00000513985.1_5'UTR	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1350							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CTGTGGGTAAGGATAAGCATG	0.502																																					p.P1350L		.											.	ZNF608-229	0			c.C4049T						.						216	161	179					5																	123980011		2203	4300	6503	SO:0001583	missense	57507	exon5			GGGTAAGGATAAG	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"Zinc fingers, C2H2-type"	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.4049C>T	5.37:g.123980011G>A	ENSP00000307746:p.Pro1350Leu	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	105	17	NM_020747	0	0	12	16	4	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704307	0.88924	.	.	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.50813	0.78;0.73	5.55	5.55	0.83447	.	0.063529	0.64402	D	0.000002	T	0.68961	0.3058	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.70439	-0.4871	10	0.87932	D	0	-13.536	19.8645	0.96799	0.0:0.0:1.0:0.0	.	1350	Q9ULD9	ZN608_HUMAN	L	923;1350	ENSP00000427657:P923L;ENSP00000307746:P1350L	ENSP00000307746:P1350L	P	-	2	0	ZNF608	124007910	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.896000	0.87350	2.766000	0.95052	0.643000	0.83706	CCT	.		0.502	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	123980011	G	A	123980011	3	1	96	1	0	0	0	0	1	0	0	0	18066	1000	35	2	509	2	ZNF608	5	123980011	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	5155080	123980011	56935249	34	8579											
GPR116	221395	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	46867766	46867766	+	Splice_Site	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagcaagagtttacatacCggctcgtttttgcctcagtg	9	12	9	11	2	1	1	1	0	0	1	2	1	1	1	3	1	4	4	3	1	4	5	rs145334563	byFrequency	TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:46867766C>A	ENST00000283296.7	-	3	445	c.157G>T	c.(157-159)Gtt>Ttt	p.V53F	GPR116_ENST00000362015.4_Splice_Site_p.V53F|GPR116_ENST00000456426.2_Splice_Site_p.V53F|GPR116_ENST00000265417.7_Splice_Site_p.V53F	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	53					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			GTTTACATACCGGCTCGTTTT	0.383																																					p.V53F	NSCLC(59;410 1274 8751 36715 50546)	.											.	GPR116-91	0			c.G157T						.						109	98	102					6																	46867766		2203	4300	6503	SO:0001630	splice_region_variant	221395	exon3			ACATACCGGCTCG	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.157+1G>T	6.37:g.46867766C>A		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	100	22	NM_015234	0	0	0	0	0	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464871	0.43839	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.29655	1.62;2.0;1.56;1.62	4.96	4.96	0.65561	.	0.286307	0.24695	N	0.036356	T	0.36082	0.0954	M	0.64997	1.995	0.80722	D	1	P;P;P	0.52842	0.956;0.911;0.956	P;P;P	0.56474	0.632;0.799;0.632	T	0.05468	-1.0883	9	.	.	.	-3.8272	14.057	0.64776	0.0:1.0:0.0:0.0	.	53;53;53	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	F	53	ENSP00000283296:V53F;ENSP00000354563:V53F;ENSP00000412866:V53F;ENSP00000265417:V53F	.	V	-	1	0	GPR116	46975725	0.983000	0.35010	0.886000	0.34754	0.036000	0.12997	3.364000	0.52328	2.479000	0.83701	0.462000	0.41574	GTT	C|0.999;T|0.001		0.383	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	Missense_Mutation	A	46867766	C	A	46867766	5	1	96	1	0	0	0	0	0	0	1	0	6653	666	23	4	3959	4	GPR116	6	46867766	Splice_Site	SNP	C	TCGA-DW-7838-01A-11D-2136-08		46867766	124247301	35	8580											
COL9A1	1297	hgsc.bcm.edu;bcgsc.ca	37	chr6	70944522	70944522	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccctggacaccaggcaggCcggtggcaccctgttctccc	5	6	13	17	1	1	0	0	0	1	0	2	1	1	1	5	6	0	3	5	6	0	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:70944522C>A	ENST00000357250.6	-	34	2392	c.2234G>T	c.(2233-2235)gGc>gTc	p.G745V	COL9A1_ENST00000320755.7_Missense_Mutation_p.G502V|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Missense_Mutation_p.G502V|RP1-149L1.1_ENST00000522264.1_RNA	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	745	Collagen-like 8.|Triple-helical region (COL2).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						ACCAGGCAGGCCGGTGGCACC	0.647																																					p.G745V		.											.	COL9A1-94	0			c.G2234T						.						36	38	37					6																	70944522		2203	4300	6503	SO:0001583	missense	1297	exon34			GGCAGGCCGGTGG		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.2234G>T	6.37:g.70944522C>A	ENSP00000349790:p.Gly745Val	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	53	5	NM_001851	0	0	0	0	0	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911377	0.72983	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.99637	-6.29;-6.29;-6.29	5.74	5.74	0.90152	.	0.149132	0.64402	D	0.000011	D	0.99846	0.9929	H	0.97758	4.07	0.80722	D	1	D;D;P	0.76494	0.999;0.996;0.918	D;D;P	0.75484	0.986;0.941;0.806	D	0.96911	0.9667	10	0.87932	D	0	.	19.9077	0.97014	0.0:1.0:0.0:0.0	.	745;502;294	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	V	745;502;502	ENSP00000349790:G745V;ENSP00000315252:G502V;ENSP00000359530:G502V	ENSP00000315252:G502V	G	-	2	0	COL9A1	71001243	1.000000	0.71417	0.988000	0.46212	0.907000	0.53573	7.556000	0.82233	2.714000	0.92807	0.585000	0.79938	GGC	.		0.647	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	70944522	C	A	70944522	3	1	96	1	0	0	0	0	1	0	0	0	3713	739	26	4	551	4	COL9A1	6	70944522	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	24076756	70944522	100170545	36	8581											
RFX6	222546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	117249981	117249981	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcggatcaatggtgaatCagcacgtttctgtcatcagc	9	11	11	10	2	5	1	4	1	1	0	6	2	5	2	0	3	2	3	0	3	2	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:117249981C>A	ENST00000332958.2	+	18	2474	c.2458C>A	c.(2458-2460)Cag>Aag	p.Q820K		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	820					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AATGGTGAATCAGCACGTTTC	0.433																																					p.Q820K		.											.	RFX6-93	0			c.C2458A						.						160	141	148					6																	117249981		2203	4300	6503	SO:0001583	missense	222546	exon18			GTGAATCAGCACG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.2458C>A	6.37:g.117249981C>A	ENSP00000332208:p.Gln820Lys	Somatic	194	1		WXS	Illumina HiSeq	Phase_I	172	32	NM_173560	0	0	0	0	0	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756755	0.89843	.	.	ENSG00000185002	ENST00000332958	T	0.57752	0.38	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.51312	0.1667	L	0.34521	1.04	0.80722	D	1	D	0.65815	0.995	P	0.55260	0.772	T	0.54200	-0.8329	10	0.72032	D	0.01	-16.3509	20.0442	0.97604	0.0:1.0:0.0:0.0	.	820	Q8HWS3	RFX6_HUMAN	K	820	ENSP00000332208:Q820K	ENSP00000332208:Q820K	Q	+	1	0	RFX6	117356674	1.000000	0.71417	0.999000	0.59377	0.763000	0.43281	7.398000	0.79919	2.814000	0.96858	0.655000	0.94253	CAG	.		0.433	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117249981	C	A	117249981	3	1	96	1	0	0	0	0	1	0	0	0	13299	827	29	4	2528	4	RFX6	6	117249981	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	46305459	117249981	53865086	37	8582											
HEBP2	23593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	138727187	138727187	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagtgagtctaccattacCatttccctgtatattccctc	8	17	4	12	0	1	1	0	1	1	0	4	1	3	1	4	0	2	1	4	0	5	8			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:138727187C>A	ENST00000607197.1	+	3	595	c.318C>A	c.(316-318)acC>acA	p.T106T	HEBP2_ENST00000448741.1_Intron|HEBP2_ENST00000367697.3_Intron	NM_014320.2	NP_055135.1	Q9Y5Z4	HEBP2_HUMAN	heme binding protein 2	106					negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of necrotic cell death (GO:0010940)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(32;0.0933)			GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171)		CTACCATTACCATTTCCCTGT	0.423																																					p.T106T		.											.	HEBP2-90	0			c.C318A						.						169	158	162					6																	138727187		2203	4300	6503	SO:0001819	synonymous_variant	23593	exon3			CATTACCATTTCC	AF117616	CCDS5191.1	6q24	2008-08-29	2002-09-23	2002-09-27	ENSG00000051620	ENSG00000051620			15716	protein-coding gene	gene with protein product		605825	"chromosome 6 open reading frame 34"	C6orf34		10640688, 17098234	Standard	NM_014320		Approved	SOUL	uc003qhw.1	Q9Y5Z4	OTTHUMG00000015671	ENST00000607197.1:c.318C>A	6.37:g.138727187C>A		Somatic	245	1		WXS	Illumina HiSeq	Phase_I	197	36	NM_014320	0	0	56	138	82	Q96P57	Silent	SNP	ENST00000607197.1	37	CCDS5191.1																																																																																			.		0.423	HEBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042426.2			A	138727187	C	A	138727187	2	1	96	1	0	0	0	0	0	0	0	1	7058	581	21	4		4	HEBP2	6	138727187	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	21477206	138727187	32387880	38	8583											
PMS2	5395	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	6035170	6035170	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaattttaaatacctttgCtgggtcacaaggccgccggt	12	11	9	9	2	1	0	1	0	0	0	1	0	1	0	3	3	2	1	3	3	6	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:6035170C>T	ENST00000265849.7	-	8	1003	c.898G>A	c.(898-900)Gca>Aca	p.A300T	PMS2_ENST00000406569.3_Missense_Mutation_p.A300T|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000441476.2_Missense_Mutation_p.A194T	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	300					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		AATACCTTTGCTGGGTCACAA	0.383			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.A300T		.	yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2-1083	0			c.G898A						.						89	84	86					7																	6035170		2203	4300	6503	SO:0001583	missense	5395	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CCTTTGCTGGGTC		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.898G>A	7.37:g.6035170C>T	ENSP00000265849:p.Ala300Thr	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	104	31	NM_000535	0	0	0	0	0	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	c	15.72	2.917497	0.52546	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	D;D;D	0.83992	-1.79;-1.79;-1.79	5.85	4.96	0.65561	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.410133	0.26345	N	0.024920	T	0.73969	0.3655	L	0.49350	1.555	0.42490	D	0.992891	B;B;B	0.34241	0.012;0.068;0.444	B;B;B	0.27262	0.007;0.013;0.078	T	0.69367	-0.5164	10	0.14656	T	0.56	-8.6094	10.6468	0.45626	0.1337:0.7984:0.0:0.0678	.	300;300;194	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	T	300;253;194;300	ENSP00000265849:A300T;ENSP00000392843:A194T;ENSP00000384308:A300T	ENSP00000265849:A300T	A	-	1	0	PMS2	6001696	0.544000	0.26441	1.000000	0.80357	0.989000	0.77384	0.265000	0.18515	1.469000	0.48083	0.650000	0.86243	GCA	.		0.383	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		T	6035170	C	T	6035170	3	4	96	1	0	0	0	0	1	0	0	0	12169	797	28	2	1722	2	PMS2	7	6035170	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		6035170	153103493	39	8584											
POU6F2	11281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	39446255	39446255	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagcagccatgagctcCatagcaagctcacaggcctt	10	7	10	14	0	1	1	1	1	0	0	2	1	2	1	3	1	6	6	3	1	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:39446255C>T	ENST00000403058.1	+	7	1096	c.942C>T	c.(940-942)tcC>tcT	p.S314S	POU6F2_ENST00000559001.1_Intron|POU6F2_ENST00000518318.2_Silent_p.S314S|POU6F2-AS1_ENST00000433519.1_RNA	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	314	Gln-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CCATGAGCTCCATAGCAAGCT	0.532																																					p.S314S		.											.	POU6F2-90	0			c.C942T						.						57	57	57					7																	39446255		2203	4300	6503	SO:0001819	synonymous_variant	11281	exon7			GAGCTCCATAGCA	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.942C>T	7.37:g.39446255C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	99	31	NM_007252	0	0	0	0	0	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Silent	SNP	ENST00000403058.1	37	CCDS34620.2																																																																																			.		0.532	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		T	39446255	C	T	39446255	2	4	96	1	0	0	0	0	0	0	0	1	12311	581	21	2		2	POU6F2	7	39446255	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	33411085	39446255	119692408	40	8585											
ZMIZ2	83637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44805818	44805818	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttcccacccaccacgccCagcaccccaacccttgctga	8	6	4	23	1	0	1	0	1	0	0	2	1	2	1	8	0	3	2	8	0	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:44805818C>G	ENST00000309315.4	+	17	2421	c.2298C>G	c.(2296-2298)ccC>ccG	p.P766P	ZMIZ2_ENST00000463931.1_3'UTR|ZMIZ2_ENST00000441627.1_Silent_p.P766P|ZMIZ2_ENST00000413916.1_Silent_p.P708P|ZMIZ2_ENST00000433667.1_Silent_p.P734P|ZMIZ2_ENST00000265346.7_Silent_p.P740P	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	766	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCACCACGCCCAGCACCCCAA	0.632																																					p.P766P	NSCLC(20;604 852 1948 16908 50522)	.											.	ZMIZ2-137	0			c.C2298G						.						58	66	64					7																	44805818		1960	4127	6087	SO:0001819	synonymous_variant	83637	exon17			CACGCCCAGCACC	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"Zinc fingers, MIZ-type"	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2298C>G	7.37:g.44805818C>G		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	138	19	NM_031449	0	0	36	60	24	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Silent	SNP	ENST00000309315.4	37	CCDS43576.1																																																																																			.		0.632	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		G	44805818	C	G	44805818	2	3	96	1	0	0	0	0	0	0	0	1	17729	581	21	4		4	ZMIZ2	7	44805818	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	5359563	44805818	114332845	41	8586											
DMTF1	9988	hgsc.bcm.edu;broad.mit.edu	37	chr7	86808890	86808890	+	Frame_Shift_Del	DEL	C	C	-																															ataaaagatgctacagaaatCatctttgagatgtcaaaaga																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:86808890delC	ENST00000394703.5	+	10	1112	c.549delC	c.(547-549)atcfs	p.I184fs	DMTF1_ENST00000331242.7_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000411766.2_Frame_Shift_Del_p.I143fs|DMTF1_ENST00000413276.2_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000432937.2_Frame_Shift_Del_p.I96fs|DMTF1_ENST00000394702.3_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000414194.2_5'UTR	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	184	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CTACAGAAATCATCTTTGAGA	0.363																																					p.I183fs		.											.	DMTF1-91	0			c.549delC						.						63	58	60					7																	86808890		2203	4300	6503	SO:0001589	frameshift_variant	9988	exon8			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.549delC	7.37:g.86808890delC	ENSP00000378193:p.Ile184fs	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	51	10	NM_001142327	0	0	0	0	0	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	ENST00000394703.5	37	CCDS5601.1																																																																																			.		0.363	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		-	86808890	C	-	86808890	7	5	96	1	0	1	0	1	0	0	0	0	4603	816	29	0	571	0	DMTF1	7	86808890	Frame_Shift_Del	DEL	C	TCGA-DW-7838-01A-11D-2136-08	42003072	86808890	72329773	42	8587											
ABCB4	5244	hgsc.bcm.edu;bcgsc.ca	37	chr7	87051487	87051487	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcccagaaataagaaaatcaAagagaatatgttgcacttct	18	10	6	7	0	2	3	1	0	1	3	3	4	3	3	1	0	1	2	1	0	7	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:87051487A>G	ENST00000265723.4	-	18	2377	c.2266T>C	c.(2266-2268)Ttg>Ctg	p.L756L	ABCB4_ENST00000545634.1_Silent_p.L756L|ABCB4_ENST00000453593.1_Silent_p.L756L|ABCB4_ENST00000359206.3_Silent_p.L756L|ABCB4_ENST00000358400.3_Silent_p.L756L	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	756	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AAGAAAATCAAAGAGAATATG	0.338																																					p.L756L		.											.	ABCB4-96	0			c.T2266C						.						56	56	56					7																	87051487		2203	4300	6503	SO:0001819	synonymous_variant	5244	exon18			AAATCAAAGAGAA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2266T>C	7.37:g.87051487A>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	58	4	NM_018850	0	0	3	3	0	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	CCDS5606.1																																																																																			.		0.338	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		G	87051487	A	G	87051487	2	3	96	1	0	0	0	0	0	0	0	1	43	11	1	3		3	ABCB4	7	87051487	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	242597	87051487	72087176	43	8588											
CYP3A43	64816	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99454477	99454477	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcgagtagatttctttcaaCagatgatcgactcccagaat	13	12	7	9	2	2	4	1	1	1	3	5	6	3	4	1	0	1	1	1	0	3	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:99454477C>A	ENST00000354829.2	+	9	923	c.820C>A	c.(820-822)Cag>Aag	p.Q274K	CYP3A43_ENST00000222382.5_Missense_Mutation_p.Q274K|CYP3A43_ENST00000342499.4_Missense_Mutation_p.Q134K|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000415413.1_Missense_Mutation_p.Q63K|CYP3A43_ENST00000312017.5_Missense_Mutation_p.Q274K|CYP3A43_ENST00000444905.1_Missense_Mutation_p.Q21K|CYP3A43_ENST00000417625.1_Missense_Mutation_p.Q164K	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	274			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TTTCTTTCAACAGATGATCGA	0.438																																					p.Q274K		.											.	CYP3A43-92	0			c.C820A						.						92	99	97					7																	99454477		2203	4300	6503	SO:0001583	missense	64816	exon9			TTTCAACAGATGA	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.820C>A	7.37:g.99454477C>A	ENSP00000346887:p.Gln274Lys	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	188	18	NM_057096	0	0	0	0	0	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731904	0.30684	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000342499;ENST00000444905;ENST00000415413;ENST00000312017;ENST00000222382	T;T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.23;-0.28;-0.28	2.26	0.94	0.19513	.	0.176318	0.37623	U	0.002017	T	0.55625	0.1932	L	0.37697	1.125	0.20873	N	0.999837	B;P;B;B;B	0.39094	0.048;0.659;0.023;0.029;0.012	B;P;B;B;B	0.44732	0.067;0.459;0.006;0.011;0.011	T	0.50742	-0.8792	10	0.87932	D	0	.	4.1559	0.10260	0.0:0.6974:0.0:0.3026	.	164;134;274;274;274	Q495Y1;F8W6L8;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;.;CP343_HUMAN	K	274;164;134;21;63;274;274	ENSP00000346887:Q274K;ENSP00000416581:Q164K;ENSP00000345351:Q134K;ENSP00000405557:Q21K;ENSP00000401521:Q63K;ENSP00000312110:Q274K;ENSP00000222382:Q274K	ENSP00000222382:Q274K	Q	+	1	0	CYP3A43	99292413	0.985000	0.35326	0.730000	0.30809	0.247000	0.25773	0.188000	0.17018	0.257000	0.21650	0.195000	0.17529	CAG	.		0.438	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			A	99454477	C	A	99454477	3	1	96	1	0	0	0	0	1	0	0	0	4185	479	17	4	854	4	CYP3A43	7	99454477	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	12402990	99454477	59684186	44	8589											
ZAN	7455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100361742	100361742	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagcacctgctgtgcaCacacatgtccaccatgacca	10	7	8	16	0	0	1	0	1	0	0	1	1	1	1	4	0	4	5	4	0	0	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:100361742C>T	ENST00000348028.3	+	0	4355				ZAN_ENST00000443370.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000427578.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CTGCTGTGCACACACATGTCC	0.607																																					.													.	ZAN-142	0			.						.						39	39	39					7																	100361742		2160	4267	6427			7455	.			TGTGCACACACAT	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100361742C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	50	21	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	C	6.803	0.517130	0.13005	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.77098	-1.07;-1.07;-1.07	4.01	-0.285	0.12866	Uncharacterised domain, cysteine-rich (2);	2.329540	0.02057	N	0.050511	T	0.76104	0.3941	M	0.78049	2.395	0.27427	N	0.954134	B;B	0.13145	0.005;0.007	B;B	0.13407	0.005;0.009	T	0.54057	-0.8350	10	0.54805	T	0.06	.	2.8794	0.05642	0.1982:0.4601:0.0:0.3417	.	1397;1397	F5H0T8;Q9Y493	.;ZAN_HUMAN	I	1397	ENSP00000445943:T1397I;ENSP00000445091:T1397I;ENSP00000444427:T1397I	ENSP00000423579:T1397I	T	+	2	0	ZAN	100199678	0.000000	0.05858	0.007000	0.13788	0.070000	0.16714	0.105000	0.15333	0.097000	0.17492	0.561000	0.74099	ACA	.		0.607	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		T	100361742	C	T	100361742	1	4	96	0	1	0	0	0	0	0	0	0	17546	478	17	2		2	ZAN	7	100361742	RNA	SNP	C	TCGA-DW-7838-01A-11D-2136-08	907265	100361742	58776921	45	8590											
CPA4	51200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	129962495	129962495	+	Silent	SNP	T	T	C																															ctgaagaccatcatggagcaTgtgcgggacaacctctacta																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:129962495T>C	ENST00000222482.4	+	11	1273	c.1245T>C	c.(1243-1245)caT>caC	p.H415H	CPA4_ENST00000493259.1_Silent_p.H311H|CPA4_ENST00000445470.2_Silent_p.H382H	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	415					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					TCATGGAGCATGTGCGGGACA	0.537																																					p.H415H		.											.	CPA4-515	0			c.T1245C						.						198	161	173					7																	129962495		2203	4300	6503	SO:0001819	synonymous_variant	51200	exon11			GGAGCATGTGCGG	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1245T>C	7.37:g.129962495T>C		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	188	39	NM_016352	0	0	4	4	0	B7Z576|Q86UY9	Silent	SNP	ENST00000222482.4	37	CCDS5818.1																																																																																			.		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		C	129962495	T	C	129962495	2	2	96	1	0	0	0	0	0	0	0	1	3798	1461	51	3		3	CPA4	7	129962495	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	29600753	129962495	29176168	46	8591	92	2									
CPA4	51200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	129962499	129962499	+	Missense_Mutation	SNP	C	C	T																															agaccatcatggagcatgtgCgggacaacctctactaggcg																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:129962499C>T	ENST00000222482.4	+	11	1277	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	CPA4_ENST00000493259.1_Missense_Mutation_p.R313W|CPA4_ENST00000445470.2_Missense_Mutation_p.R384W	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	417					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GGAGCATGTGCGGGACAACCT	0.542																																					p.R417W		.											.	CPA4-515	0			c.C1249T						.						193	157	169					7																	129962499		2203	4300	6503	SO:0001583	missense	51200	exon11			CATGTGCGGGACA	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1249C>T	7.37:g.129962499C>T	ENSP00000222482:p.Arg417Trp	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	185	42	NM_016352	0	0	2	2	0	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.286285	0.40494	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.03468	3.92;3.92;3.92	5.75	2.87	0.33458	.	0.218110	0.40908	D	0.000989	T	0.13970	0.0338	M	0.79475	2.455	0.09310	N	1	D;D	0.89917	0.999;1.0	P;D	0.65443	0.827;0.935	T	0.01956	-1.1240	10	0.56958	D	0.05	.	9.1872	0.37178	0.2596:0.6719:0.0:0.0685	.	384;417	B7Z576;Q9UI42	.;CBPA4_HUMAN	W	384;417;222;313	ENSP00000412947:R384W;ENSP00000222482:R417W;ENSP00000419660:R313W	ENSP00000222482:R417W	R	+	1	2	CPA4	129749735	0.000000	0.05858	0.981000	0.43875	0.111000	0.19643	0.043000	0.13971	0.763000	0.33175	0.563000	0.77884	CGG	.		0.542	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		T	129962499	C	T	129962499	3	4	96	1	0	0	0	0	1	0	0	0	3798	759	27	1	1291	1	CPA4	7	129962499	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	4	129962499	29176164	47	8592	92	2									
AKR1B15	441282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	134260620	134260620	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gagaaactgatccagtactgCcactccaagggcatcaccgt	12	7	9	13	1	1	2	1	1	0	1	3	3	3	2	4	1	3	2	4	1	3	1	rs267601304		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:134260620C>T	ENST00000457545.2	+	8	944	c.684C>T	c.(682-684)tgC>tgT	p.C228C	AKR1B15_ENST00000423958.1_Silent_p.C200C	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	228							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						TCCAGTACTGCCACTCCAAGG	0.532																																					p.C228C		.											.	AKR1B15-23	0			c.C684T						.						111	88	96					7																	134260620		2203	4300	6503	SO:0001819	synonymous_variant	441282	exon8			GTACTGCCACTCC		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.684C>T	7.37:g.134260620C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	105	20	NM_001080538	0	0	307	312	5	C9J3V2	Silent	SNP	ENST00000457545.2	37	CCDS47715.2																																																																																			.		0.532	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134260620	C	T	134260620	2	4	96	1	0	0	0	0	0	0	0	1	468	747	26	2		2	AKR1B15	7	134260620	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	4298121	134260620	24878043	48	8593											
SVOPL	136306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	138281232	138281232	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcatacaacacagacagatGagaagagacacagggccccc	16	2	10	13	1	0	4	0	1	0	4	0	6	0	4	2	1	2	1	2	1	3	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:138281232G>A	ENST00000419765.3	-	14	1430	c.1397C>T	c.(1396-1398)tCa>tTa	p.S466L	SVOPL_ENST00000463557.1_5'UTR|SVOPL_ENST00000421622.1_Missense_Mutation_p.S346L|SVOPL_ENST00000436657.1_Missense_Mutation_p.S314L|SVOPL_ENST00000288513.5_Missense_Mutation_p.S314L	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	466						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						ACAGACAGATGAGAAGAGACA	0.463																																					p.S466L		.											.	SVOPL-68	0			c.C1397T						.						117	111	113					7																	138281232		2203	4300	6503	SO:0001583	missense	136306	exon14			ACAGATGAGAAGA	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"SV2 related protein homolog (rat)-like"				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1397C>T	7.37:g.138281232G>A	ENSP00000405482:p.Ser466Leu	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	107	14	NM_001139456	0	0	0	1	1		Missense_Mutation	SNP	ENST00000419765.3	37	CCDS47721.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.826903	0.32329	.	.	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.260251	0.37483	N	0.002067	T	0.40145	0.1105	N	0.22421	0.69	0.35878	D	0.828749	B;B	0.33171	0.012;0.4	B;B	0.28011	0.055;0.085	T	0.51317	-0.8721	10	0.45353	T	0.12	-3.3112	17.1313	0.86727	0.0:0.0:1.0:0.0	.	466;314	Q8N434;Q8N434-2	SVOPL_HUMAN;.	L	314;346;314;466	ENSP00000288513:S314L;ENSP00000412830:S346L;ENSP00000417018:S314L;ENSP00000405482:S466L	ENSP00000288513:S314L	S	-	2	0	SVOPL	137931772	1.000000	0.71417	0.821000	0.32701	0.024000	0.10985	5.924000	0.70054	2.563000	0.86464	0.655000	0.94253	TCA	.		0.463	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959		A	138281232	G	A	138281232	3	1	96	1	0	0	0	0	1	0	0	0	15456	1294	45	2	89	2	SVOPL	7	138281232	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	4020612	138281232	20857431	49	8594											
ZNF777	27153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	149152518	149152518	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcatggcctgggcctccAgcttcctctccactgcttgg	3	11	10	17	0	2	0	1	0	1	0	5	0	4	0	6	3	2	2	6	3	0	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:149152518A>T	ENST00000247930.4	-	2	919	c.596T>A	c.(595-597)cTg>cAg	p.L199Q		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	199					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTGGGCCTCCAGCTTCCTCTC	0.597																																					p.L199Q		.											.	ZNF777-136	0			c.T596A						.						67	76	73					7																	149152518		2188	4291	6479	SO:0001583	missense	27153	exon2			GCCTCCAGCTTCC	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.596T>A	7.37:g.149152518A>T	ENSP00000247930:p.Leu199Gln	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	209	46	NM_015694	0	0	8	15	7	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	37	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802961	0.70682	.	.	ENSG00000196453	ENST00000247930	T	0.06294	3.32	4.93	4.93	0.64822	.	0.234968	0.21936	N	0.066956	T	0.06554	0.0168	N	0.08118	0	0.33892	D	0.637431	D	0.54207	0.965	P	0.51355	0.667	T	0.32322	-0.9911	10	0.72032	D	0.01	-14.7997	11.0022	0.47614	1.0:0.0:0.0:0.0	.	199	Q9ULD5-2	.	Q	199	ENSP00000247930:L199Q	ENSP00000247930:L199Q	L	-	2	0	ZNF777	148783451	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.489000	0.66875	1.856000	0.53863	0.533000	0.62120	CTG	.		0.597	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		T	149152518	A	T	149152518	3	4	96	1	0	0	0	0	1	0	0	0	18182	188	7	5	1919	5	ZNF777	7	149152518	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	10871286	149152518	9986145	50	8595											
VIPR2	7434	broad.mit.edu;bcgsc.ca	37	chr7	158902583	158902587	+	Frame_Shift_Del	DEL	GTGAT	GTGAT	-																															cattggcaggccgccagcacGtgatgttgtcccagacgcca																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	GTGAT	GTGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:158902583_158902587delGTGAT	ENST00000262178.2	-	3	360_364	c.175_179delATCAC	c.(175-180)atcacgfs	p.IT59fs	VIPR2_ENST00000402066.1_Frame_Shift_Del_p.IT200fs	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	59					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CCGCCAGCACGTGATGTTGTCCCAG	0.527																																					p.59_60del	Pancreas(154;1876 1931 2329 17914 20079)												.	VIPR2-91	0			c.175_179del						.																																			SO:0001589	frameshift_variant	7434	exon3			CAGCACGTGATGT	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	12695	protein-coding gene	gene with protein product	"VIP and PACAP receptor 2"	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.175_179delATCAC	7.37:g.158902583_158902587delGTGAT	ENSP00000262178:p.Ile59fs	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	111	7	NM_003382	0	0	0	0	0	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Frame_Shift_Del	DEL	ENST00000262178.2	37	CCDS5950.1																																																																																			.		0.527	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		-	158902587	GTGAT	-	158902583	7	5	96	1	0	1	0	1	0	0	0	0	17203	1145	40	0	1181	0	VIPR2	7	158902583	Frame_Shift_Del	DEL	GTGAT	TCGA-DW-7838-01A-11D-2136-08	9750065	158902583	236080	51	8596											
USP17L2	377630	hgsc.bcm.edu	37	chr8	11996075	11996075	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctactcagaggaagcttcttCctgggagcaagctgtcttgc	8	11	11	11	0	3	1	1	0	2	1	4	3	4	3	1	2	5	3	1	2	3	4	rs267601745		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr8:11996075C>G	ENST00000333796.3	-	1	511	c.195G>C	c.(193-195)agG>agC	p.R65S	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	65					apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						GAAGCTTCTTCCTGGGAGCAA	0.572																																					p.R65S		.											.	USP17L2-435	0			c.G195C						.						43	58	53					8																	11996075		1248	2766	4014	SO:0001583	missense	377630	exon1			CTTCTTCCTGGGA	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"deubiquitinating enzyme 3"	610186	"ubiquitin specific peptidase 17-like 2"				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.195G>C	8.37:g.11996075C>G	ENSP00000333329:p.Arg65Ser	Somatic	6	1		WXS	Illumina HiSeq	Phase_I	9	2	NM_201402	0	0	0	0	0		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	c	1.018	-0.685613	0.03328	.	.	ENSG00000223443	ENST00000333796	T	0.11821	2.74	0.36	0.36	0.16097	.	3.094940	0.01992	U	0.045606	T	0.06462	0.0166	N	0.08118	0	0.26403	N	0.976385	B	0.06786	0.001	B	0.06405	0.002	T	0.30238	-0.9985	10	0.02654	T	1	.	6.6522	0.22969	0.0:0.9999:0.0:1.0E-4	.	65	Q6R6M4	U17L2_HUMAN	S	65	ENSP00000333329:R65S	ENSP00000333329:R65S	R	-	3	2	USP17L2	12033484	0.005000	0.15991	0.016000	0.15963	0.015000	0.08874	-0.190000	0.09615	0.469000	0.27268	0.472000	0.43445	AGG	.		0.572	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		G	11996075	C	G	11996075	3	3	96	1	0	0	0	0	1	0	0	0	17081	854	30	4	1401	4	USP17L2	8	11996075	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		11996075	134367947	52	8597											
TSNARE1	203062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	143381927	143381927	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gtccgggagcagcgcctgctCctggccctgccacatgttgt	4	9	13	15	2	0	0	0	0	0	0	2	1	2	1	5	2	4	3	5	2	0	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr8:143381927C>G	ENST00000307180.3	-	10	1327	c.1210G>C	c.(1210-1212)Gag>Cag	p.E404Q	TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000524325.1_Missense_Mutation_p.E403Q|TSNARE1_ENST00000519651.1_Missense_Mutation_p.E185Q|TSNARE1_ENST00000520166.1_Missense_Mutation_p.E404Q	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	404					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AGCGCCTGCTCCTGGCCCTGC	0.617																																					p.E404Q		.											.	TSNARE1-90	0			c.G1210C						.						73	66	69					8																	143381927		2203	4300	6503	SO:0001583	missense	203062	exon10			CCTGCTCCTGGCC			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.1210G>C	8.37:g.143381927C>G	ENSP00000303437:p.Glu404Gln	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	103	14	NM_145003	0	0	8	9	1	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	C	7.933	0.741084	0.15642	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	4.76	3.89	0.44902	t-SNARE (1);	0.233173	0.21158	U	0.079203	T	0.16214	0.0390	L	0.37630	1.12	0.23254	N	0.998034	P;B;P;P	0.47409	0.895;0.421;0.895;0.895	B;B;B;B	0.41299	0.353;0.058;0.353;0.353	T	0.08351	-1.0726	10	0.27082	T	0.32	-20.6332	10.2182	0.43182	0.0:0.9055:0.0:0.0945	.	403;185;404;405	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	Q	403;404;404;185	ENSP00000428763:E403Q;ENSP00000303437:E404Q;ENSP00000427770:E404Q;ENSP00000429679:E185Q	ENSP00000303437:E404Q	E	-	1	0	TSNARE1	143379834	0.970000	0.33590	0.175000	0.22980	0.206000	0.24218	1.184000	0.32053	1.001000	0.39076	-0.137000	0.14449	GAG	.		0.617	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		G	143381927	C	G	143381927	3	3	96	1	0	0	0	0	1	0	0	0	16663	864	30	4	347	4	TSNARE1	8	143381927	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	131385852	143381927	2982095	53	8598											
TSTD2	158427	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	100368460	100368460	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagtttctgcaatcaagaaGgatagtatcactttgttctt	12	15	8	6	0	4	1	2	0	2	1	4	3	4	2	0	1	1	4	0	1	6	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:100368460G>T	ENST00000341170.4	-	7	1301	c.919C>A	c.(919-921)Ctt>Att	p.L307I	TSTD2_ENST00000354801.2_Missense_Mutation_p.L47I	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	307	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.							p.L307I(1)		large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						CAATCAAGAAGGATAGTATCA	0.353																																					p.L307I		.											.	TSTD2-92	1	Substitution - Missense(1)	ovary(1)	c.C919A						.						117	116	117					9																	100368460		2203	4300	6503	SO:0001583	missense	158427	exon7			CAAGAAGGATAGT	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 97"	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.919C>A	9.37:g.100368460G>T	ENSP00000342499:p.Leu307Ile	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	72	9	NM_139246	0	0	4	4	0	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	37	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	G	14.49	2.552202	0.45487	.	.	ENSG00000136925	ENST00000375172;ENST00000341170;ENST00000375165;ENST00000354801	T;T;T	0.27104	1.69;1.69;1.69	5.18	3.31	0.37934	Rhodanese-like (5);	0.066943	0.64402	N	0.000014	T	0.17916	0.0430	L	0.41492	1.28	0.32895	D	0.512421	B;B	0.33477	0.013;0.413	B;B	0.35607	0.032;0.206	T	0.14172	-1.0482	10	0.20046	T	0.44	-5.0176	5.6795	0.17767	0.1448:0.0:0.666:0.1892	.	81;307	B3KVC7;Q5T7W7	.;TSTD2_HUMAN	I	81;307;47;47	ENSP00000342499:L307I;ENSP00000364308:L47I;ENSP00000346856:L47I	ENSP00000342499:L307I	L	-	1	0	TSTD2	99408281	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.989000	0.40707	1.490000	0.48466	0.655000	0.94253	CTT	.		0.353	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		T	100368460	G	T	100368460	3	4	96	1	0	0	0	0	1	0	0	0	16708	1000	35	4	647	4	TSTD2	9	100368460	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		100368460	40844971	54	8599											
FKBP15	23307	hgsc.bcm.edu	37	chr9	115973833	115973833	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattcatttccatggccagcAgctgcctgatccagtccaaa	11	10	7	13	0	1	1	1	1	0	0	4	1	4	1	5	1	3	2	5	1	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:115973833A>G	ENST00000238256.3	-	2	210	c.93T>C	c.(91-93)gcT>gcC	p.A31A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	31					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CATGGCCAGCAGCTGCCTGAT	0.423																																					p.A31A		.											.	FKBP15-25	0			c.T93C						.						80	77	78					9																	115973833		1885	4142	6027	SO:0001819	synonymous_variant	23307	exon2			GCCAGCAGCTGCC	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	23397	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 76", "WASP and FKBP-like protein"		"KIAA0674"	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.93T>C	9.37:g.115973833A>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_015258	0	0	6	6	0	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			.		0.423	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		G	115973833	A	G	115973833	2	3	96	1	0	0	0	0	0	0	0	1	5924	175	7	3		3	FKBP15	9	115973833	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	15605373	115973833	25239598	55	8600											
SLC31A1	1317	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	116018468	116018469	+	Frame_Shift_Ins	INS	-	-	C																															ggggatgagctatatggactINSccaacagtaccatgcaacct																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:116018468_116018469insC	ENST00000374212.4	+	2	192_193	c.40_41insC	c.(40-42)tccfs	p.S14fs	SLC31A1_ENST00000374210.6_Frame_Shift_Ins_p.S14fs|CDC26_ENST00000490408.1_Intron	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	14					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CTATATGGACTCCAACAGTACC	0.436																																					p.S14fs	Ovarian(135;1049 1799 4519 17564 28677)	.											.	SLC31A1-90	0			c.40_41insC						.																																			SO:0001589	frameshift_variant	1317	exon2			.	U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"Solute carriers"	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.42dupC	9.37:g.116018470_116018470dupC	ENSP00000363329:p.Ser14fs	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	118	18	NM_001859	0	0	0	0	0	A8K8Z6|Q53GR5|Q5T1M4	Frame_Shift_Ins	INS	ENST00000374212.4	37	CCDS6789.1																																																																																			.		0.436	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859		C	116018469	-	C	116018468	7	5	96	1	0	1	1	0	0	0	0	0	14595	1551	54	0	42	0	SLC31A1	9	116018468	Frame_Shift_Ins	INS	-	TCGA-DW-7838-01A-11D-2136-08	44635	116018468	25194963	56	8601											
OR1N2	138882	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	125316283	125316283	+	Frame_Shift_Del	DEL	C	C	-																															ttatgggtgtgtatttacttCctccatcaacttactctaca																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:125316283delC	ENST00000373688.2	+	1	893	c.835delC	c.(835-837)cctfs	p.P280fs		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						GTATTTACTTCCTCCATCAAC	0.463																																					p.P279fs		.											.	OR1N2-72	0			c.835delC						.						196	199	198					9																	125316283		2203	4300	6503	SO:0001589	frameshift_variant	138882	exon1			.		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.835delC	9.37:g.125316283delC	ENSP00000362792:p.Pro280fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	140	21	NM_001004457	0	0	0	0	0	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Frame_Shift_Del	DEL	ENST00000373688.2	37	CCDS35123.1																																																																																			.		0.463	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			-	125316283	C	-	125316283	7	5	96	1	0	1	0	1	0	0	0	0	10996	855	30	0	837	0	OR1N2	9	125316283	Frame_Shift_Del	DEL	C	TCGA-DW-7838-01A-11D-2136-08	9297815	125316283	15897148	57	8602											
HSPA5	3309	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr9	128001454	128001454	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggtcaaagtcttctccAcccagatgagtatctccatt	9	12	7	13	1	4	2	1	1	3	1	6	2	4	2	3	1	0	2	3	1	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:128001454A>G	ENST00000324460.6	-	5	965	c.762T>C	c.(760-762)ggT>ggC	p.G254G	RP11-65N13.8_ENST00000468244.1_RNA	NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	254					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	AGTCTTCTCCACCCAGATGAG	0.468										Prostate(1;0.17)																											p.G254G		.											.	HSPA5-230	0			c.T762C						.						58	57	57					9																	128001454		2203	4300	6503	SO:0001819	synonymous_variant	3309	exon5			TTCTCCACCCAGA		CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"Heat shock proteins / HSP70"	5238	protein-coding gene	gene with protein product		138120	"heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.762T>C	9.37:g.128001454A>G		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	52	7	NM_005347	5	0	253	488	230	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Silent	SNP	ENST00000324460.6	37	CCDS6863.1																																																																																			.		0.468	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1			G	128001454	A	G	128001454	2	3	96	1	0	0	0	0	0	0	0	1	7435	146	6	3		3	HSPA5	9	128001454	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	2685171	128001454	13211977	58	8603											
GARNL3	84253	hgsc.bcm.edu	37	chr9	130149608	130149608	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttccttcttccctgggggAaggtgaagtccaagttttac	8	14	10	9	0	1	1	0	1	1	0	4	2	4	2	3	3	1	1	3	3	4	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:130149608A>G	ENST00000373387.4	+	25	2877	c.2525A>G	c.(2524-2526)gAa>gGa	p.E842G	GARNL3_ENST00000314904.5_Intron|GARNL3_ENST00000496711.1_3'UTR|GARNL3_ENST00000435213.2_Missense_Mutation_p.E820G	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	842					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						TCCCTGGGGGAAGGTGAAGTC	0.438																																					p.E842G		.											.	GARNL3-516	0			c.A2525G						.						42	44	44					9																	130149608		2203	4300	6503	SO:0001583	missense	84253	exon25			TGGGGGAAGGTGA	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"GTPase activating RANGAP domain-like 3"			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.2525A>G	9.37:g.130149608A>G	ENSP00000362485:p.Glu842Gly	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_032293	0	0	0	0	0	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	37	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	A	18.50	3.636537	0.67130	.	.	ENSG00000136895	ENST00000435213;ENST00000373387	D;D	0.88277	-2.36;-2.36	5.66	5.66	0.87406	.	0.097775	0.64402	D	0.000001	T	0.82245	0.4995	L	0.32530	0.975	0.80722	D	1	B;P	0.37781	0.421;0.608	B;B	0.32980	0.081;0.156	T	0.81134	-0.1071	9	.	.	.	.	14.7222	0.69314	1.0:0.0:0.0:0.0	.	842;820	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	G	820;842	ENSP00000396205:E820G;ENSP00000362485:E842G	.	E	+	2	0	GARNL3	129189429	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.066000	0.89486	2.140000	0.66376	0.533000	0.62120	GAA	.		0.438	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		G	130149608	A	G	130149608	3	3	96	1	0	0	0	0	1	0	0	0	6261	246	9	3	2623	3	GARNL3	9	130149608	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	2148154	130149608	11063823	59	8604											
PKN3	29941	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131476565	131476565	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctgcccccctgcagctccCcgagcacaatcagcccccct	6	6	7	22	1	1	0	1	0	0	0	2	1	2	0	8	0	6	4	8	0	1	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:131476565C>A	ENST00000291906.4	+	11	1795	c.1402C>A	c.(1402-1404)Ccg>Acg	p.P468T		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	468	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CTGCAGCTCCCCGAGCACAAT	0.647																																					p.P468T		.											.	PKN3-521	0			c.C1402A						.						62	70	67					9																	131476565		2203	4300	6503	SO:0001583	missense	29941	exon11			AGCTCCCCGAGCA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1402C>A	9.37:g.131476565C>A	ENSP00000291906:p.Pro468Thr	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	240	42	NM_013355	0	0	2	4	2	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	C	6.729	0.503216	0.12822	.	.	ENSG00000160447	ENST00000291906	T	0.27256	1.68	5.3	4.36	0.52297	.	.	.	.	.	T	0.22742	0.0549	L	0.51422	1.61	0.26351	N	0.977203	P	0.42827	0.791	B	0.40901	0.343	T	0.05616	-1.0874	9	0.09590	T	0.72	.	11.1984	0.48726	0.3181:0.6818:0.0:0.0	.	468	Q6P5Z2	PKN3_HUMAN	T	468	ENSP00000291906:P468T	ENSP00000291906:P468T	P	+	1	0	PKN3	130516386	0.031000	0.19500	0.911000	0.35937	0.516000	0.34256	1.330000	0.33781	2.478000	0.83669	0.563000	0.77884	CCG	.		0.647	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131476565	C	A	131476565	3	1	96	1	0	0	0	0	1	0	0	0	12007	623	22	4	1444	4	PKN3	9	131476565	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	1326957	131476565	9736866	60	8605											
ZER1	10444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131512978	131512978	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacactctgctctgagcggtActcggaatttgttaggtaga	9	12	11	9	2	2	2	0	1	2	1	3	3	2	3	0	3	3	4	0	3	4	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:131512978A>G	ENST00000291900.2	-	8	1682	c.1276T>C	c.(1276-1278)Tac>Cac	p.Y426H	ZER1_ENST00000494461.1_5'Flank|snoU13_ENST00000459043.1_RNA	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	426					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TCTGAGCGGTACTCGGAATTT	0.562																																					p.Y426H		.											.	ZER1-91	0			c.T1276C						.						102	89	94					9																	131512978		2203	4300	6503	SO:0001583	missense	10444	exon8			AGCGGTACTCGGA	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1276T>C	9.37:g.131512978A>G	ENSP00000291900:p.Tyr426His	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	100	16	NM_006336	0	0	19	27	8	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	37	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082101	0.36758	.	.	ENSG00000160445	ENST00000291900	T	0.06218	3.33	4.35	4.35	0.52113	Armadillo-like helical (1);Armadillo-type fold (1);	0.146987	0.47455	D	0.000229	T	0.07234	0.0183	L	0.44542	1.39	0.58432	D	0.999999	B	0.26258	0.145	B	0.31191	0.125	T	0.29181	-1.0020	10	0.15499	T	0.54	-31.0091	12.8828	0.58026	1.0:0.0:0.0:0.0	.	426	Q7Z7L7	ZER1_HUMAN	H	426	ENSP00000291900:Y426H	ENSP00000291900:Y426H	Y	-	1	0	ZER1	130552799	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	8.478000	0.90428	1.832000	0.53329	0.383000	0.25322	TAC	.		0.562	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		G	131512978	A	G	131512978	3	3	96	1	0	0	0	0	1	0	0	0	17657	391	14	3	1060	3	ZER1	9	131512978	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	36413	131512978	9700453	61	8606											
AKR1C3	8644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	5139633	5139633	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ttaacctctgcagctttggtCcacttttcatcgaccagagt	8	14	7	12	1	2	1	1	0	1	1	4	2	3	1	3	1	3	2	3	1	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:5139633C>G	ENST00000380554.3	+	3	912	c.260C>G	c.(259-261)tCc>tGc	p.S87C	AKR1C3_ENST00000605149.1_Missense_Mutation_p.S64C|AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000439082.2_5'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	87					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	CAGCTTTGGTCCACTTTTCAT	0.393																																					p.S87C		.											.	AKR1C3-515	0			c.C260G						.						134	128	130					10																	5139633		2203	4300	6503	SO:0001583	missense	8644	exon3			TTTGGTCCACTTT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"Aldo-keto reductases"	386	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase X", "prostaglandin F synthase", "3-alpha hydroxysteroid dehydrogenase, type II"	603966	"hydroxysteroid (17-beta) dehydrogenase 5", "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.260C>G	10.37:g.5139633C>G	ENSP00000369927:p.Ser87Cys	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	134	28	NM_001253908	0	0	0	0	0	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.788233	0.00628	.	.	ENSG00000196139	ENST00000380554	T	0.26373	1.74	1.93	-3.27	0.05048	NADP-dependent oxidoreductase domain (3);	1.227770	0.05968	N	0.641929	T	0.11153	0.0272	N	0.11651	0.15	0.58432	D	0.999999	B;B	0.15473	0.011;0.013	B;B	0.23852	0.049;0.048	T	0.47045	-0.9147	10	0.05833	T	0.94	.	7.0923	0.25291	0.0:0.392:0.4898:0.1181	.	87;87	B4DKT3;P42330	.;AK1C3_HUMAN	C	87	ENSP00000369927:S87C	ENSP00000369927:S87C	S	+	2	0	AKR1C3	5129633	0.000000	0.05858	0.013000	0.15412	0.934000	0.57294	-1.103000	0.03329	-0.933000	0.03737	-0.458000	0.05436	TCC	.		0.393	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		G	5139633	C	G	5139633	3	3	96	1	0	0	0	0	1	0	0	0	471	855	30	4	270	4	AKR1C3	10	5139633	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		5139633	130395114	62	8607											
IL15RA	3601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	6008174	6008174	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgttcaacacgcactccgTcaggctggacgtgccggctt	6	10	11	14	4	2	0	2	0	0	0	3	1	3	1	2	3	2	4	2	3	1	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:6008174T>C	ENST00000379977.3	-	2	314	c.217A>G	c.(217-219)Acg>Gcg	p.T73A	IL15RA_ENST00000397255.3_Missense_Mutation_p.T73A|IL15RA_ENST00000379971.1_Intron|IL15RA_ENST00000397250.2_Intron|IL15RA_ENST00000525219.2_Missense_Mutation_p.T37A|IL15RA_ENST00000397248.2_Missense_Mutation_p.T37A|IL15RA_ENST00000528354.1_Missense_Mutation_p.T73A|IL15RA_ENST00000397251.3_Intron|IL15RA_ENST00000530685.1_Missense_Mutation_p.T73A|IL15RA_ENST00000534292.1_5'UTR			Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha	73	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron projection development (GO:0010977)|positive regulation of natural killer cell differentiation (GO:0032825)|response to nutrient levels (GO:0031667)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5						ACGCACTCCGTCAGGCTGGAC	0.557																																					p.T159A		.											.	IL15RA-90	0			c.A475G						.						91	78	82					10																	6008174		2203	4300	6503	SO:0001583	missense	3601	exon3			ACTCCGTCAGGCT	U31628	CCDS7074.1, CCDS7075.1, CCDS7075.2, CCDS58069.1, CCDS73065.1	10p15.1	2012-02-27			ENSG00000134470	ENSG00000134470		"Interleukins and interleukin receptors", "CD molecules"	5978	protein-coding gene	gene with protein product		601070				8530383	Standard	NM_002189		Approved	CD215, IL-15RA	uc021pmo.1	Q13261	OTTHUMG00000017612	ENST00000379977.3:c.217A>G	10.37:g.6008174T>C	ENSP00000369312:p.Thr73Ala	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	40	6	NM_001256765	0	0	5	6	1	B4E2C2|Q3B769|Q5JVA1|Q5JVA2|Q5JVA4|Q6B0J2|Q7LDR4|Q7Z609	Missense_Mutation	SNP	ENST00000379977.3	37	CCDS7074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.76|15.76	2.927337|2.927337	0.52759|0.52759	.|.	.|.	ENSG00000134470|ENSG00000134470	ENST00000397246;ENST00000379977;ENST00000397248;ENST00000319465;ENST00000528354;ENST00000530685;ENST00000397255;ENST00000429135;ENST00000453922|ENST00000532039	T;T;T;T;T;T;T;T|.	0.29397|.	1.92;1.57;1.57;1.92;1.92;1.57;1.92;1.57|.	4.8|4.8	4.8|4.8	0.61643|0.61643	Complement control module (2);Sushi/SCR/CCP (2);|.	0.149436|.	0.43747|.	D|.	0.000539|.	T|.	0.47414|.	0.1444|.	L|L	0.57536|0.57536	1.79|1.79	0.24971|0.24971	N|N	0.991666|0.991666	D;D|.	0.64830|.	0.994;0.994|.	P;P|.	0.61328|.	0.887;0.887|.	T|.	0.38714|.	-0.9648|.	10|.	0.51188|.	T|.	0.08|.	-16.2672|-16.2672	10.7393|10.7393	0.46143|0.46143	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	73;73|.	Q13261-3;Q13261|.	.;I15RA_HUMAN|.	A|W	37;73;37;37;73;73;73;73;37|43	ENSP00000380420:T37A;ENSP00000369312:T73A;ENSP00000380421:T37A;ENSP00000435454:T73A;ENSP00000435995:T73A;ENSP00000380426:T73A;ENSP00000395113:T73A;ENSP00000405107:T37A|.	ENSP00000322245:T37A|.	T|X	-|-	1|3	0|0	IL15RA|IL15RA	6048180|6048180	0.998000|0.998000	0.40836|0.40836	0.968000|0.968000	0.41197|0.41197	0.304000|0.304000	0.27724|0.27724	3.427000|3.427000	0.52785|0.52785	1.783000|1.783000	0.52377|0.52377	0.379000|0.379000	0.24179|0.24179	ACG|TGA	.		0.557	IL15RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046615.2	NM_172200, NM_002189		C	6008174	T	C	6008174	3	2	96	1	0	0	0	0	1	0	0	0	7653	1667	58	3	610	3	IL15RA	10	6008174	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	868541	6008174	129526573	63	8608											
BMS1	9790	ucsc.edu	37	chr10	43315737	43315737	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagccagagttcagtatgaGggttttcgacctgggatgta	10	11	14	6	1	1	2	1	1	0	1	2	5	1	3	2	2	1	4	2	2	3	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:43315737G>T	ENST00000374518.5	+	16	2697	c.2634G>T	c.(2632-2634)gaG>gaT	p.E878D		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	878					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTCAGTATGAGGGTTTTCGAC	0.433																																					p.E878D													.	BMS1-93	0			c.G2634T						.						120	118	118					10																	43315737		2203	4300	6503	SO:0001583	missense	9790	exon16			GTATGAGGGTTTT	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2634G>T	10.37:g.43315737G>T	ENSP00000363642:p.Glu878Asp	Somatic	190	4		WXS	Illumina HiSeq		181	4	NM_014753	0	0	72	109	37	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.115516	0.77323	.	.	ENSG00000165733	ENST00000374518	T	0.17854	2.25	5.05	-4.55	0.03441	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.38506	0.1043	M	0.92122	3.275	0.47778	D	0.999516	D	0.53462	0.96	P	0.58077	0.832	T	0.53995	-0.8359	10	0.39692	T	0.17	.	13.1374	0.59417	0.6341:0.0:0.3659:0.0	.	878	Q14692	BMS1_HUMAN	D	878	ENSP00000363642:E878D	ENSP00000363642:E878D	E	+	3	2	BMS1	42635743	0.998000	0.40836	0.969000	0.41365	0.964000	0.63967	0.474000	0.22148	-0.725000	0.04901	-0.396000	0.06452	GAG	.		0.433	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		T	43315737	G	T	43315737	3	4	96	1	0	0	0	0	1	0	0	0	1473	991	35	4	2692	4	BMS1	10	43315737	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	37307563	43315737	92219010	64	8609											
TYSND1	219743	hgsc.bcm.edu	37	chr10	71906010	71906010	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggtgggccgggctcgaggctCgcgcactggggcgtgcacag	4	5	20	12	5	0	0	0	0	0	0	2	1	0	0	1	6	1	4	1	6	0	0	rs11549688	byFrequency	TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:71906010C>G	ENST00000287078.6	-	1	332	c.333G>C	c.(331-333)gcG>gcC	p.A111A	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_Silent_p.A111A	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	111		Cleavage. {ECO:0000250}.			protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						GCTCGAGGCTCGCGCACTGGG	0.791													C|||	169	0.033746	0.0265	0.0072	5008	,	,		9519	0.0526		0.0368	False		,,,				2504	0.0399				p.A111A		.											.	TYSND1-135	0			c.G333C						.	C	,	40,2142		0,40,1051	1	2	2		333,333	-5.2	0	10	dbSNP_120	2	121,4671		0,121,2275	no	coding-synonymous,coding-synonymous	TYSND1	NM_001040273.1,NM_173555.2	,	0,161,3326	GG,GC,CC		2.525,1.8332,2.3086	,	111/399,111/567	71906010	161,6813	1091	2396	3487	SO:0001819	synonymous_variant	219743	exon1			GAGGCTCGCGCAC	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.333G>C	10.37:g.71906010C>G		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	4	3	NM_173555	0	0	1	1	0	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Silent	SNP	ENST00000287078.6	37	CCDS31213.1																																																																																			C|0.964;G|0.036		0.791	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		G	71906010	C	G	71906010	2	3	96	1	0	0	0	0	0	0	0	1	16850	871	31	4		4	TYSND1	10	71906010	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	28590273	71906010	63628737	65	8610											
VDAC2	7417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	76980587	76980587	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgattttgctggacctgCaatccatggttcagctgtct	6	16	9	10	0	2	1	1	1	1	0	3	2	3	2	2	2	3	4	2	2	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:76980587C>T	ENST00000332211.6	+	7	656	c.443C>T	c.(442-444)gCa>gTa	p.A148V	VDAC2_ENST00000313132.4_Missense_Mutation_p.A163V|VDAC2_ENST00000535553.1_Missense_Mutation_p.A109V|VDAC2_ENST00000472137.1_3'UTR|VDAC2_ENST00000543351.1_Missense_Mutation_p.A148V	NM_003375.3	NP_003366.2	P45880	VDAC2_HUMAN	voltage-dependent anion channel 2	148					anion transport (GO:0006820)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein polymerization (GO:0032272)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	10	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)	GCTGGACCTGCAATCCATGGT	0.418																																					p.A163V		.											.	VDAC2-93	0			c.C488T						.						97	95	95					10																	76980587		2203	4297	6500	SO:0001583	missense	7417	exon8			GACCTGCAATCCA	BC000165	CCDS7348.1, CCDS53544.1	10q22	2011-11-15			ENSG00000165637	ENSG00000165637		"Voltage-dependent anion channels"	12672	protein-coding gene	gene with protein product		193245				7517385, 10049775	Standard	NM_003375		Approved		uc021ptp.1	P45880	OTTHUMG00000018517	ENST00000332211.6:c.443C>T	10.37:g.76980587C>T	ENSP00000361686:p.Ala148Val	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	129	20	NM_001184783	0	0	164	284	120	Q5VWK1|Q5VWK3|Q6IB40|Q7L3J5|Q9BWK8|Q9Y5I6	Missense_Mutation	SNP	ENST00000332211.6	37	CCDS7348.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.501060	0.44455	.	.	ENSG00000165637	ENST00000298468;ENST00000543351;ENST00000344036;ENST00000332211;ENST00000535553;ENST00000313132;ENST00000447677	T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.48	5.48	0.80851	.	0.050056	0.85682	D	0.000000	T	0.26304	0.0642	N	0.05441	-0.05	0.58432	D	0.999999	B;B;B	0.21520	0.025;0.036;0.057	B;B;B	0.22880	0.019;0.036;0.042	T	0.10474	-1.0628	10	0.12766	T	0.61	.	19.3533	0.94401	0.0:1.0:0.0:0.0	.	109;163;148	B4DKM5;P45880-1;P45880	.;.;VDAC2_HUMAN	V	148;148;148;148;109;163;148	ENSP00000298468:A148V;ENSP00000443092:A148V;ENSP00000344876:A148V;ENSP00000361686:A148V;ENSP00000445901:A109V;ENSP00000361635:A163V;ENSP00000401492:A148V	ENSP00000298468:A148V	A	+	2	0	VDAC2	76650593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.013000	0.70776	2.588000	0.87417	0.563000	0.77884	GCA	.		0.418	VDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048792.1	NM_003375		T	76980587	C	T	76980587	3	4	96	1	0	0	0	0	1	0	0	0	17180	710	25	2	545	2	VDAC2	10	76980587	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	5074577	76980587	58554160	66	8611											
MMRN2	79812	broad.mit.edu;bcgsc.ca	37	chr10	88705024	88705026	+	Splice_Site	DEL	ATC	ATC	-																															ggctcagggattgccatggaAtctgcagaagaaagcattag																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:88705024_88705026delATC	ENST00000372027.5	-	4	722_723	c.401_402delGAT	c.(400-402)gga>g	p.G134del	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	134					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						TTGCCATGGAATCTGCAGAAGAA	0.571																																					p.134_134del													.	MMRN2-153	0			c.401_402del						.																																			SO:0001630	splice_region_variant	79812	exon4			CATGGAATCTGCA	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"EMI domain containing"	19888	protein-coding gene	gene with protein product		608925	"elastin microfibril interfacer 3"	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.401-1GAT>-	10.37:g.88705024_88705026delATC		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	61	8	NM_024756	0	0	0	0	0	Q504V7|Q6P2N2	Frame_Shift_Del	DEL	ENST00000372027.5	37	CCDS7379.1																																																																																			.		0.571	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	In_Frame_Del	-	88705026	ATC	-	88705024	8	5	96	1	0	1	0	1	0	0	1	0	9696	115	4	0	2463	0	MMRN2	10	88705024	Splice_Site	DEL	ATC	TCGA-DW-7838-01A-11D-2136-08	11724437	88705024	46829723	67	8612											
BTAF1	9044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	93773747	93773747	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcaggatcttccacctaaAattattcaagactattattg	13	15	5	8	0	2	1	1	0	1	1	3	2	3	2	2	1	1	1	2	1	6	8			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:93773747A>T	ENST00000265990.6	+	32	4853	c.4545A>T	c.(4543-4545)aaA>aaT	p.K1515N	BTAF1_ENST00000544642.1_Missense_Mutation_p.K343N	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1515					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TTCCACCTAAAATTATTCAAG	0.368																																					p.K1515N		.											.	BTAF1-92	0			c.A4545T						.						134	144	140					10																	93773747		2203	4300	6503	SO:0001583	missense	9044	exon32			ACCTAAAATTATT	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.4545A>T	10.37:g.93773747A>T	ENSP00000265990:p.Lys1515Asn	Somatic	262	0		WXS	Illumina HiSeq	Phase_I	184	23	NM_003972	0	0	7	7	0	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	37	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299734	0.81136	.	.	ENSG00000095564	ENST00000265990;ENST00000544642;ENST00000538688	D;D	0.94723	-3.5;-3.5	5.8	5.8	0.92144	SNF2-related (1);	0.050554	0.85682	D	0.000000	D	0.98726	0.9572	H	0.99719	4.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99525	1.0959	10	0.87932	D	0	-21.227	16.2031	0.82102	1.0:0.0:0.0:0.0	.	1515	O14981	BTAF1_HUMAN	N	1515;343;365	ENSP00000265990:K1515N;ENSP00000439924:K343N	ENSP00000265990:K1515N	K	+	3	2	BTAF1	93763727	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.660000	0.68018	2.231000	0.72958	0.524000	0.50904	AAA	.		0.368	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		T	93773747	A	T	93773747	3	4	96	1	0	0	0	0	1	0	0	0	1539	11	1	5	4671	5	BTAF1	10	93773747	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	5068723	93773747	41761000	68	8613											
MMS19	64210	broad.mit.edu	37	chr10	99222420	99222420	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcctccaatagtacttttctCagaactgagggctccttctc	8	14	6	13	0	2	2	1	1	2	1	7	2	5	2	3	1	2	2	3	1	4	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:99222420C>T	ENST00000438925.2	-	20	2267	c.1932G>A	c.(1930-1932)ctG>ctA	p.L644L	MMS19_ENST00000370782.2_Silent_p.L644L|MMS19_ENST00000327277.7_Silent_p.L280L|MMS19_ENST00000327238.10_Silent_p.L546L|MMS19_ENST00000355839.6_Silent_p.L601L	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	644					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		GTACTTTTCTCAGAACTGAGG	0.468								Direct reversal of damage																													p.L644L													.	.	0			c.G1932A						.						165	135	145					10																	99222420		2203	4300	6503	SO:0001819	synonymous_variant	64210	exon20			TTTTCTCAGAACT	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"MET18 homolog (S. cerevisiae)"	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.1932G>A	10.37:g.99222420C>T		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	36	4	NM_022362	0	0	18	25	7	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Silent	SNP	ENST00000438925.2	37	CCDS7464.1																																																																																			.		0.468	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2			T	99222420	C	T	99222420	2	4	96	1	0	0	0	0	0	0	0	1	9697	813	29	2		2	MMS19	10	99222420	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	5448673	99222420	36312327	69	8614											
PSD	5662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104176443	104176443	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gactcaagccccctggagcaGgtagcccattcagtggcctc	8	7	11	15	0	2	0	2	0	0	0	3	2	2	1	4	3	3	2	4	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:104176443G>C	ENST00000020673.5	-	2	879	c.353C>G	c.(352-354)cCt>cGt	p.P118R	PSD_ENST00000406432.1_Missense_Mutation_p.P118R|PSD_ENST00000492902.2_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	118	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CCCTGGAGCAGGTAGCCCATT	0.657																																					p.P118R		.											.	PSD-272	0			c.C353G						.						29	33	32					10																	104176443		2203	4296	6499	SO:0001583	missense	5662	exon3			GGAGCAGGTAGCC	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.353C>G	10.37:g.104176443G>C	ENSP00000020673:p.Pro118Arg	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	81	17	NM_001270965	0	0	0	0	0	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	37	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.592108	0.66219	.	.	ENSG00000059915	ENST00000020673;ENST00000406432	T;T	0.28666	1.6;1.6	4.36	4.36	0.52297	.	0.109296	0.37483	N	0.002079	T	0.30665	0.0772	N	0.08118	0	0.35207	D	0.774816	D	0.62365	0.991	P	0.58013	0.831	T	0.51068	-0.8752	10	0.66056	D	0.02	.	15.5617	0.76253	0.0:0.0:1.0:0.0	.	118	A5PKW4	PSD1_HUMAN	R	118	ENSP00000020673:P118R;ENSP00000384830:P118R	ENSP00000020673:P118R	P	-	2	0	PSD	104166433	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.473000	0.45145	2.375000	0.81037	0.561000	0.74099	CCT	.		0.657	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			C	104176443	G	C	104176443	3	2	96	1	0	0	0	0	1	0	0	0	12675	1000	35	4	2785	4	PSD	10	104176443	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	4954023	104176443	31358304	70	8615											
BRSK2	9024	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	1459605	1459605	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taaagctgcacgacgtttatGaaaacaaaaaatatttgtag	18	11	7	5	2	0	1	0	1	0	0	0	2	0	1	0	0	3	4	0	0	10	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:1459605G>A	ENST00000528841.1	+	3	640	c.256G>A	c.(256-258)Gaa>Aaa	p.E86K	BRSK2_ENST00000526678.1_Missense_Mutation_p.E86K|BRSK2_ENST00000382179.1_Missense_Mutation_p.E132K|BRSK2_ENST00000308219.9_Missense_Mutation_p.E86K|BRSK2_ENST00000528710.1_Missense_Mutation_p.E26K|BRSK2_ENST00000308230.5_Missense_Mutation_p.E86K|BRSK2_ENST00000531197.1_Missense_Mutation_p.E86K			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	86	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CGACGTTTATGAAAACAAAAA	0.567																																					p.E132K		.											.	BRSK2-333	0			c.G394A						.						94	104	101					11																	1459605		2156	4273	6429	SO:0001583	missense	9024	exon3			GTTTATGAAAACA	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"serine/threonine kinase 29"	609236	"chromsosome 11 open reading frame 7"	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.256G>A	11.37:g.1459605G>A	ENSP00000432000:p.Glu86Lys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	127	15	NM_001256630	0	0	0	0	0	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	37	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766637	0.90020	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528596;ENST00000524702;ENST00000528710;ENST00000382179	T;T;T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	2.57	2.57	0.30868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.063288	0.64402	U	0.000008	T	0.78457	0.4286	M	0.71581	2.175	0.80722	D	1	P;D;B;D;D	0.71674	0.64;0.998;0.411;0.966;0.958	P;D;B;D;P	0.78314	0.602;0.991;0.354;0.923;0.875	T	0.81289	-0.1000	10	0.87932	D	0	.	12.2615	0.54652	0.0:0.0:1.0:0.0	.	86;132;86;86;86	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	K	86;86;86;86;86;26;26;26;132	ENSP00000310697:E86K;ENSP00000431152:E86K;ENSP00000310805:E86K;ENSP00000432000:E86K;ENSP00000433370:E86K;ENSP00000434075:E26K;ENSP00000432672:E26K;ENSP00000433235:E26K;ENSP00000371614:E132K	ENSP00000310697:E86K	E	+	1	0	BRSK2	1416181	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.575000	0.74018	1.455000	0.47813	0.313000	0.20887	GAA	.		0.567	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		A	1459605	G	A	1459605	3	1	96	1	0	0	0	0	1	0	0	0	1527	1291	45	2	266	2	BRSK2	11	1459605	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		1459605	133546911	71	8616											
FBXO3	26273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	33770334	33770334	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttccataccaactactccaGgtccttgaacttcttccacg	9	12	5	15	1	1	1	0	1	1	0	5	1	5	1	5	1	4	1	5	1	4	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:33770334G>T	ENST00000265651.3	-	9	1055	c.1037C>A	c.(1036-1038)cCt>cAt	p.P346H	FBXO3_ENST00000530401.1_Missense_Mutation_p.P341H|FBXO3_ENST00000534136.1_Missense_Mutation_p.P346H|FBXO3_ENST00000531080.1_Missense_Mutation_p.P33H|FBXO3_ENST00000526785.1_Missense_Mutation_p.P233H|FBXO3_ENST00000532057.1_Missense_Mutation_p.P33H|FBXO3_ENST00000448981.2_Missense_Mutation_p.P346H	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	346	ApaG. {ECO:0000255|PROSITE- ProRule:PRU00412}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		AACTACTCCAGGTCCTTGAAC	0.368																																					p.P346H		.											.	FBXO3-227	0			c.C1037A						.						103	102	102					11																	33770334		2202	4298	6500	SO:0001583	missense	26273	exon9			ACTCCAGGTCCTT	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1037C>A	11.37:g.33770334G>T	ENSP00000265651:p.Pro346His	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	79	17	NM_012175	0	0	0	0	0	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	37	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768020	0.90020	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000531080;ENST00000532057;ENST00000534136;ENST00000448981	T;T;T;T;T	0.47869	0.84;0.83;0.86;0.86;0.87	5.61	5.61	0.85477	ApaG domain (4);	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	M	0.77486	2.375	0.80722	D	1	P;P;D	0.89917	0.936;0.936;1.0	P;P;D	0.77004	0.64;0.64;0.989	T	0.69636	-0.5092	10	0.41790	T	0.15	-16.4467	19.6304	0.95699	0.0:0.0:1.0:0.0	.	341;346;346	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	H	233;346;341;33;33;346;346	ENSP00000435680:P233H;ENSP00000265651:P346H;ENSP00000433781:P341H;ENSP00000431745:P346H;ENSP00000408836:P346H	ENSP00000265651:P346H	P	-	2	0	FBXO3	33726910	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.230000	0.95299	2.663000	0.90544	0.491000	0.48974	CCT	.		0.368	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		T	33770334	G	T	33770334	3	4	96	1	0	0	0	0	1	0	0	0	5758	1000	35	4	399	4	FBXO3	11	33770334	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	32310729	33770334	101236182	72	8617											
ACY3	91703	hgsc.bcm.edu;broad.mit.edu	37	chr11	67412339	67412339	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaaaggcaggaaaggccgtAcctgtgtgggaggctgggtg	9	7	18	7	1	1	0	1	0	0	0	1	2	1	2	2	6	1	3	2	6	3	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:67412339A>G	ENST00000255082.3	-	7	806	c.636T>C	c.(634-636)ggT>ggC	p.G212G	ACY3_ENST00000529256.1_Splice_Site_p.G91G	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	212	Shielding domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	GAAAGGCCGTACCTGTGTGGG	0.657																																					p.G212G	GBM(56;346 1011 27014 29495 46841)	.											.	ACY3-90	0			c.T636C						.						54	41	45					11																	67412339		2199	4289	6488	SO:0001630	splice_region_variant	91703	exon7			GGCCGTACCTGTG	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.635-1T>C	11.37:g.67412339A>G		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	24	3	NM_080658	0	0	0	0	0		Silent	SNP	ENST00000255082.3	37	CCDS8175.1																																																																																			.		0.657	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658	Silent	G	67412339	A	G	67412339	5	3	96	1	0	0	0	0	0	0	1	0	227	405	14	3	331	3	ACY3	11	67412339	Splice_Site	SNP	A	TCGA-DW-7838-01A-11D-2136-08	33642005	67412339	67594177	73	8618											
USP5	8078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6968684	6968684	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaatgccccgacggaccctaCccaggatttcagcacccagg	10	5	10	16	2	1	0	1	0	0	0	1	4	1	2	5	3	3	1	5	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr12:6968684C>T	ENST00000229268.8	+	9	1161	c.1109C>T	c.(1108-1110)aCc>aTc	p.T370I	USP5_ENST00000389231.5_Missense_Mutation_p.T370I	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	370	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						ACGGACCCTACCCAGGATTTC	0.562																																					p.T370I		.											.	USP5-659	0			c.C1109T						.						91	83	86					12																	6968684		2203	4300	6503	SO:0001583	missense	8078	exon9			ACCCTACCCAGGA	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1109C>T	12.37:g.6968684C>T	ENSP00000229268:p.Thr370Ile	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	116	27	NM_003481	0	0	27	44	17	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	37	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072808	0.93950	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.29655	1.56;1.56	5.38	5.38	0.77491	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.046637	0.85682	D	0.000000	T	0.56232	0.1971	M	0.74546	2.27	0.80722	D	1	D;P	0.57899	0.981;0.534	D;P	0.66497	0.944;0.454	T	0.51560	-0.8690	10	0.39692	T	0.17	-8.4151	19.3333	0.94303	0.0:1.0:0.0:0.0	.	370;370	P45974;P45974-2	UBP5_HUMAN;.	I	370	ENSP00000229268:T370I;ENSP00000373883:T370I	ENSP00000229268:T370I	T	+	2	0	USP5	6838945	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.609000	0.82925	2.793000	0.96121	0.655000	0.94253	ACC	.		0.562	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			T	6968684	C	T	6968684	3	4	96	1	0	0	0	0	1	0	0	0	17114	507	18	2	1143	2	USP5	12	6968684	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		6968684	126883211	74	8619											
ATF7IP	55729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	14613823	14613823	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaacgttccttctgtgccCagtcctagtattcaaaggaa	12	11	7	11	1	2	0	1	0	1	0	4	1	4	1	3	1	3	2	3	1	6	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr12:14613823C>T	ENST00000540793.1	+	8	2708	c.2553C>T	c.(2551-2553)ccC>ccT	p.P851P	ATF7IP_ENST00000261168.4_Silent_p.P851P|ATF7IP_ENST00000543189.1_Silent_p.P850P|ATF7IP_ENST00000536444.1_Silent_p.P850P|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000544627.1_Silent_p.P859P			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	851					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						CTTCTGTGCCCAGTCCTAGTA	0.488																																					p.P851P		.											.	ATF7IP-252	0			c.C2553T						.						173	147	156					12																	14613823		2203	4300	6503	SO:0001819	synonymous_variant	55729	exon9			TGTGCCCAGTCCT	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.2553C>T	12.37:g.14613823C>T		Somatic	217	1		WXS	Illumina HiSeq	Phase_I	197	27	NM_018179	0	0	8	13	5	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																			.		0.488	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		T	14613823	C	T	14613823	2	4	96	1	0	0	0	0	0	0	0	1	1088	581	21	2		2	ATF7IP	12	14613823	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	7645139	14613823	119238072	75	8620											
EIF4B	1975	hgsc.bcm.edu;broad.mit.edu	37	chr12	53431279	53431279	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	actctccaacttctaaacctCccaaacctgatcagccccta	12	9	2	18	0	3	1	1	1	2	0	5	1	4	1	6	0	4	0	6	0	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr12:53431279C>T	ENST00000262056.9	+	11	1719	c.1393C>T	c.(1393-1395)Ccc>Tcc	p.P465S	RP11-983P16.4_ENST00000546566.1_RNA|EIF4B_ENST00000420463.3_Missense_Mutation_p.P470S|RP11-983P16.4_ENST00000550601.1_RNA|EIF4B_ENST00000416762.3_Missense_Mutation_p.P426S|RP11-983P16.4_ENST00000552905.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	465					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						TTCTAAACCTCCCAAACCTGA	0.493																																					p.P465S		.											.	EIF4B-568	0			c.C1393T						.						20	20	20					12																	53431279		1805	4043	5848	SO:0001583	missense	1975	exon11			AAACCTCCCAAAC	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.1393C>T	12.37:g.53431279C>T	ENSP00000262056:p.Pro465Ser	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	58	7	NM_001417	0	0	248	396	148	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Missense_Mutation	SNP	ENST00000262056.9	37	CCDS41788.1	.	.	.	.	.	.	.	.	.	.	C	15.52	2.856483	0.51376	.	.	ENSG00000063046	ENST00000262056;ENST00000420463;ENST00000430205;ENST00000416762	T;T;T	0.36878	1.23;1.23;1.23	5.2	5.2	0.72013	.	0.418940	0.24195	N	0.040661	T	0.36771	0.0979	L	0.57536	1.79	0.54753	D	0.999988	P;P;B;P	0.47106	0.89;0.473;0.002;0.825	B;B;B;B	0.42062	0.374;0.091;0.008;0.207	T	0.10405	-1.0631	10	0.15952	T	0.53	.	17.0418	0.86491	0.0:1.0:0.0:0.0	.	426;470;441;465	B4DS13;E7EX17;E7EPC9;P23588	.;.;.;IF4B_HUMAN	S	465;470;441;426	ENSP00000262056:P465S;ENSP00000388806:P470S;ENSP00000412530:P426S	ENSP00000262056:P465S	P	+	1	0	EIF4B	51717546	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.816000	0.38992	2.810000	0.96702	0.585000	0.79938	CCC	.		0.493	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		T	53431279	C	T	53431279	3	4	96	1	0	0	0	0	1	0	0	0	5040	855	30	2	1435	2	EIF4B	12	53431279	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	38817456	53431279	80420616	76	8621											
IRS2	8660	hgsc.bcm.edu	37	chr13	110435756	110435756	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaccgcccggccgcgctggCccaagaagccctccgggcgg	5	3	14	19	6	1	1	1	0	0	1	2	1	2	1	6	4	1	1	6	4	2	0	rs201499247	byFrequency	TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr13:110435756C>G	ENST00000375856.3	-	1	3159	c.2645G>C	c.(2644-2646)gGc>gCc	p.G882A		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	882			G -> A. {ECO:0000269|Ref.5}.		brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			GCCGCGCTGGCCCAAGAAGCC	0.766													.|||	10	0.00199681	0	0.0043	5008	,	,		7396	0		0.007	False		,,,				2504	0				p.G882A	Melanoma(100;613 2409 40847)	.											.	IRS2-1334	0			c.G2645C						.	C	ALA/GLY	1,3269		0,1,1634	2	3	2		2645	-5.4	0	13		2	7,6747		0,7,3370	no	missense	IRS2	NM_003749.2	60	0,8,5004	GG,GC,CC		0.1036,0.0306,0.0798	benign	882/1339	110435756	8,10016	1635	3377	5012	SO:0001583	missense	8660	exon1			CGCTGGCCCAAGA	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2645G>C	13.37:g.110435756C>G	ENSP00000365016:p.Gly882Ala	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	10	5	NM_003749	0	0	0	0	0	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	37	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	C	0.069	-1.206226	0.01568	3.06E-4	0.001036	ENSG00000185950	ENST00000375856	T	0.42513	0.97	4.36	-5.38	0.02673	.	1.016690	0.07871	U	0.967985	T	0.18002	0.0432	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30031	-0.9992	10	0.08837	T	0.75	-1.9461	4.3158	0.10993	0.1295:0.4165:0.3472:0.1068	.	882	Q9Y4H2	IRS2_HUMAN	A	882	ENSP00000365016:G882A	ENSP00000365016:G882A	G	-	2	0	IRS2	109233757	0.005000	0.15991	0.014000	0.15608	0.112000	0.19704	0.077000	0.14738	-0.678000	0.05224	0.561000	0.74099	GGC	.		0.766	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		G	110435756	C	G	110435756	3	3	96	1	0	0	0	0	1	0	0	0	7862	739	26	4	1379	4	IRS2	13	110435756	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		110435756	4734122	77	8622											
CGRRF1	10668	ucsc.edu	37	chr14	55005042	55005042	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgtgcaggcagtttgttcagGaatcttttgcactttgcagt	7	16	11	7	0	2	0	1	0	1	0	2	1	2	1	0	2	3	6	0	2	1	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:55005042G>C	ENST00000216420.7	+	6	1072	c.940G>C	c.(940-942)Gaa>Caa	p.E314Q		NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	314					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						GTTTGTTCAGGAATCTTTTGC	0.423																																					p.E314Q													.	CGRRF1-91	0			c.G940C						.						97	89	92					14																	55005042		2203	4300	6503	SO:0001583	missense	10668	exon6			GTTCAGGAATCTT	BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532		"RING-type (C3HC4) zinc fingers"	15528	protein-coding gene	gene with protein product		606138				8968090	Standard	NM_006568		Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308	ENST00000216420.7:c.940G>C	14.37:g.55005042G>C	ENSP00000216420:p.Glu314Gln	Somatic	79	0		WXS	Illumina HiSeq		87	4	NM_006568	0	0	14	16	2	Q96BX2	Missense_Mutation	SNP	ENST00000216420.7	37	CCDS9719.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850667	0.71719	.	.	ENSG00000100532	ENST00000216420	T	0.67523	-0.27	5.23	3.42	0.39159	Zinc finger, RING/FYVE/PHD-type (1);	0.046947	0.85682	D	0.000000	T	0.60064	0.2240	N	0.25094	0.71	0.43088	D	0.994752	D	0.54601	0.967	P	0.52159	0.691	T	0.57329	-0.7830	10	0.33141	T	0.24	-14.1511	11.656	0.51318	0.143:0.0:0.857:0.0	.	314	Q99675	CGRF1_HUMAN	Q	314	ENSP00000216420:E314Q	ENSP00000216420:E314Q	E	+	1	0	CGRRF1	54074792	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.236000	0.78154	0.794000	0.33899	0.462000	0.41574	GAA	.		0.423	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568		C	55005042	G	C	55005042	3	2	96	1	0	0	0	0	1	0	0	0	3312	1175	41	4	962	4	CGRRF1	14	55005042	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		55005042	52344498	78	8623											
GPR135	64582	hgsc.bcm.edu	37	chr14	59931931	59931931	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctggtgggcggggcggcTgcggctcctccatggggccc	1	7	19	14	4	0	0	0	0	0	0	3	0	2	0	3	8	1	3	3	8	0	0	rs1752428	byFrequency	TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:59931931T>G	ENST00000395116.1	-	1	129	c.14A>C	c.(13-15)cAg>cCg	p.Q5P		NM_022571.5	NP_072093.2	Q8IZ08	GP135_HUMAN	G protein-coupled receptor 135	5			Q -> P (in dbSNP:rs1752428).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.134)		GCGGGGCGGCTGCGGCTCCTC	0.781													G|||	2695	0.538139	0.8767	0.5821	5008	,	,		8009	0.2063		0.4722	False		,,,				2504	0.4591				p.Q5P		.											.	GPR135-90	0			c.A14C						.						1	1	1					14																	59931931		555	1498	2053	SO:0001583	missense	64582	exon1			GGCGGCTGCGGCT	AY288418	CCDS9738.1	14q23.1	2012-08-21			ENSG00000181619	ENSG00000181619		"GPCR / Class A : Orphans"	19991	protein-coding gene	gene with protein product		607970				14623098	Standard	NM_022571		Approved	HUMNPIIY20, PAFR	uc010apj.3	Q8IZ08	OTTHUMG00000140325	ENST00000395116.1:c.14A>C	14.37:g.59931931T>G	ENSP00000378548:p.Gln5Pro	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_022571	0	0	0	0	0	Q7Z604|Q86SM3|Q8NH39	Missense_Mutation	SNP	ENST00000395116.1	37	CCDS9738.1	1023	0.4684065934065934	376	0.7642276422764228	199	0.5497237569060773	107	0.18706293706293706	341	0.449868073878628	G	12.20	1.867217	0.32977	.	.	ENSG00000181619	ENST00000395116	T	0.62941	-0.01	3.25	3.25	0.37280	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999999688	B	0.02656	0.0	B	0.01281	0.0	T	0.36311	-0.9753	8	0.35671	T	0.21	-4.9918	9.4599	0.38778	0.0:0.0:0.7862:0.2138	rs1752428;rs3742644	5	Q8IZ08	GP135_HUMAN	P	5	ENSP00000378548:Q5P	ENSP00000378548:Q5P	Q	-	2	0	GPR135	59001684	0.007000	0.16637	0.970000	0.41538	0.076000	0.17211	-0.908000	0.04063	0.581000	0.29539	-0.677000	0.03784	CAG	T|0.531;G|0.469		0.781	GPR135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276941.1	NM_022571		G	59931931	T	G	59931931	3	3	96	1	0	0	0	0	1	0	0	0	6664	1580	55	5	1474	5	GPR135	14	59931931	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	4926889	59931931	47417609	79	8624											
SYNE2	23224	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64633998	64633998	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcacctgatattgaacatttGaatgaagtgagcctcaagct	13	12	8	8	0	2	5	2	5	0	0	2	5	2	5	2	0	3	1	2	0	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:64633998G>A	ENST00000344113.4	+	91	16865	c.16653G>A	c.(16651-16653)ttG>ttA	p.L5551L	SYNE2_ENST00000357395.3_Silent_p.L1936L|SYNE2_ENST00000394768.2_Silent_p.L1936L|SYNE2_ENST00000554584.1_Silent_p.L5426L|SYNE2_ENST00000555002.1_Silent_p.L2185L|SYNE2_ENST00000358025.3_Silent_p.L5551L|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5551					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TTGAACATTTGAATGAAGTGA	0.438																																					p.L5551L													.	SYNE2-164	0			c.G16653A						.						65	61	63					14																	64633998		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon91			ACATTTGAATGAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16653G>A	14.37:g.64633998G>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	57	5	NM_182914	0	0	8	16	8	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			.		0.438	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64633998	G	A	64633998	2	1	96	1	0	0	0	0	0	0	0	1	15478	1281	45	2		2	SYNE2	14	64633998	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	4702067	64633998	42715542	80	8625											
TRIP11	9321	ucsc.edu;bcgsc.ca	37	chr14	92480875	92480875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaacttgaatagttttttgCatctcatagattttagagag	13	16	8	4	0	1	4	1	1	1	3	2	5	1	4	0	0	2	2	0	0	5	8			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:92480875C>T	ENST00000267622.4	-	7	1243	c.870G>A	c.(868-870)atG>atA	p.M290I		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	290					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TAGTTTTTTGCATCTCATAGA	0.284			T	PDGFRB	AML																																p.M290I	Ovarian(84;609 1888 9852 42686)			Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11-1400	0			c.G870A						.						26	27	27					14																	92480875		2148	4260	6408	SO:0001583	missense	9321	exon7			TTTTTGCATCTCA	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.870G>A	14.37:g.92480875C>T	ENSP00000267622:p.Met290Ile	Somatic	34	0		WXS	Illumina HiSeq		30	4	NM_004239	0	0	1	1	0	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.38|11.38	1.621245|1.621245	0.28889|0.28889	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000554357|ENST00000267622;ENST00000542257	.|T	.|0.60424	.|0.19	5.1|5.1	2.23|2.23	0.28157|0.28157	.|.	.|0.530450	.|0.21569	.|N	.|0.072438	T|T	0.45175|0.45175	0.1329|0.1329	L|L	0.35723|0.35723	1.085|1.085	0.25334|0.25334	N|N	0.989007|0.989007	.|B;B	.|0.06786	.|0.001;0.001	.|B;B	.|0.11329	.|0.002;0.006	T|T	0.38067|0.38067	-0.9678|-0.9678	5|10	.|0.41790	.|T	.|0.15	.|.	10.777|10.777	0.46356|0.46356	0.0:0.783:0.0:0.217|0.0:0.783:0.0:0.217	.|.	.|55;290	.|F5H1Z0;Q15643	.|.;TRIPB_HUMAN	T|I	35|290;55	.|ENSP00000267622:M290I	.|ENSP00000267622:M290I	A|M	-|-	1|3	0|0	TRIP11|TRIP11	91550628|91550628	0.998000|0.998000	0.40836|0.40836	0.526000|0.526000	0.27913|0.27913	0.849000|0.849000	0.48306|0.48306	1.269000|1.269000	0.33074|0.33074	0.651000|0.651000	0.30788|0.30788	0.555000|0.555000	0.69702|0.69702	GCA|ATG	.		0.284	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			T	92480875	C	T	92480875	3	4	96	1	0	0	0	0	1	0	0	0	16588	710	25	2	5129	2	TRIP11	14	92480875	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	27846877	92480875	14868665	81	8626											
CLMN	79789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	95670344	95670344	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgccactcttgggctccCttcaaagcaaagggacaggt	9	10	10	12	0	2	0	1	0	1	0	3	1	3	1	2	3	2	2	2	3	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:95670344C>T	ENST00000298912.4	-	9	1455	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	448					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTTGGGCTCCCTTCAAAGCAA	0.483																																					p.G448R		.											.	CLMN-90	0			c.G1342A						.						87	82	84					14																	95670344		2203	4300	6503	SO:0001583	missense	79789	exon9			GGCTCCCTTCAAA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1342G>A	14.37:g.95670344C>T	ENSP00000298912:p.Gly448Arg	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	102	22	NM_024734	0	0	11	16	5	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.673672	0.29693	.	.	ENSG00000165959	ENST00000298912	D	0.94537	-3.45	5.63	3.66	0.41972	.	0.000000	0.38837	N	0.001556	D	0.90896	0.7139	M	0.66939	2.045	0.18873	N	0.999986	P	0.37122	0.583	B	0.32342	0.144	D	0.86083	0.1545	10	0.87932	D	0	.	5.9466	0.19221	0.3449:0.5687:0.0:0.0864	.	448	Q96JQ2	CLMN_HUMAN	R	448	ENSP00000298912:G448R	ENSP00000298912:G448R	G	-	1	0	CLMN	94740097	0.137000	0.22531	0.209000	0.23619	0.021000	0.10359	0.357000	0.20199	1.337000	0.45525	0.655000	0.94253	GGG	.		0.483	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			T	95670344	C	T	95670344	3	4	96	1	0	0	0	0	1	0	0	0	3548	681	24	2	1686	2	CLMN	14	95670344	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	3189469	95670344	11679196	82	8627											
SPTBN5	51332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42149779	42149779	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcacaacctcacctcacaggCcttctggagcttggccacct	8	8	8	17	0	3	0	2	0	1	0	3	1	3	1	5	3	2	2	5	3	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr15:42149779C>G	ENST00000320955.6	-	50	8583	c.8356G>C	c.(8356-8358)Gcc>Ccc	p.A2786P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2786					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACCTCACAGGCCTTCTGGAGC	0.652																																					p.A2751P		.											.	SPTBN5-91	0			c.G8251C						.						28	34	32					15																	42149779		2004	4170	6174	SO:0001583	missense	51332	exon50			CACAGGCCTTCTG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8356G>C	15.37:g.42149779C>G	ENSP00000317790:p.Ala2786Pro	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	23	8	NM_016642	0	0	0	0	0		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	15.93	2.979532	0.53827	.	.	ENSG00000137877	ENST00000320955	T	0.39787	1.06	4.2	3.28	0.37604	.	0.000000	0.56097	D	0.000023	T	0.62720	0.2451	M	0.78049	2.395	0.19300	N	0.99998	D	0.89917	1.0	D	0.77004	0.989	T	0.56463	-0.7975	10	0.72032	D	0.01	.	12.048	0.53491	0.0:0.916:0.0:0.084	.	2786	Q9NRC6	SPTN5_HUMAN	P	2786	ENSP00000317790:A2786P	ENSP00000317790:A2786P	A	-	1	0	SPTBN5	39937071	0.983000	0.35010	0.020000	0.16555	0.009000	0.06853	2.620000	0.46410	0.977000	0.38444	0.467000	0.42956	GCC	.		0.652	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42149779	C	G	42149779	3	3	96	1	0	0	0	0	1	0	0	0	15154	739	26	4	2744	4	SPTBN5	15	42149779	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		42149779	60381613	83	8628											
SPG11	80208	hgsc.bcm.edu	37	chr15	44861660	44861660	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatgcagcaaatcaaatatgTatgtcatctcgttgtacctt	12	15	6	8	1	3	0	2	0	1	0	4	0	3	0	1	0	3	5	1	0	6	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr15:44861660T>C	ENST00000261866.7	-	35	6537	c.6521A>G	c.(6520-6522)tAc>tGc	p.Y2174C	SPG11_ENST00000427534.2_Missense_Mutation_p.Y2174C|SPG11_ENST00000535302.2_Missense_Mutation_p.Y2061C	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	2174					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		ATCAAATATGTATGTCATCTC	0.478																																					p.Y2174C		.											.	SPG11-95	0			c.A6521G						.						112	92	99					15																	44861660		2197	4298	6495	SO:0001583	missense	80208	exon35			AATATGTATGTCA		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.6521A>G	15.37:g.44861660T>C	ENSP00000261866:p.Tyr2174Cys	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	19	2	NM_025137	0	0	36	36	0	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.109125	0.77096	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	D;T;D	0.85013	-1.91;-1.44;-1.93	6.07	6.07	0.98685	.	0.115539	0.64402	D	0.000010	D	0.91945	0.7449	M	0.76002	2.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.997;0.997	D	0.92596	0.6087	10	0.72032	D	0.01	.	15.1999	0.73126	0.0:0.0:0.0:1.0	.	2174;2061;2174;2174	C4B7M2;F5H3N6;C4B7M4;Q96JI7	.;.;.;SPTCS_HUMAN	C	2174;2061;2174	ENSP00000261866:Y2174C;ENSP00000445278:Y2061C;ENSP00000396110:Y2174C	ENSP00000261866:Y2174C	Y	-	2	0	SPG11	42648952	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.589000	0.82641	2.326000	0.78906	0.533000	0.62120	TAC	.		0.478	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			C	44861660	T	C	44861660	3	2	96	1	0	0	0	0	1	0	0	0	15073	1638	57	3	834	3	SPG11	15	44861660	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	2711881	44861660	57669732	84	8629											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_178167	0	0	0	3	3	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	96	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08		2059674	88295079	85	8630											
C16orf92	146378	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	30035201	30035219	+	Splice_Site	DEL	ACTCAGGTATGAACCAGCT	ACTCAGGTATGAACCAGCT	-																															gaaacccatcgtgttcattaActcaggtatgaaccagcttg																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	ACTCAGGTATGAACCAGCT	ACTCAGGTATGAACCAGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:30035201_30035219delACTCAGGTATGAACCAGCT	ENST00000300575.2	+	2	305_310	c.284_289delACTCAGGTATGAACCAGCT	c.(283-291)aactcaggt>agt	p.NSG95fs	DOC2A_ENST00000567824.1_5'Flank	NM_001109659.1|NM_001109660.1	NP_001103129.1|NP_001103130.1	Q96LL3	CP092_HUMAN	chromosome 16 open reading frame 92	95						integral component of membrane (GO:0016021)				breast(3)|lung(3)	6						GTGTTCATTAACTCAGGTATGAACCAGCTTGAGAAGGGA	0.543																																					p.95_97del		.											.	C16orf92-68	0			c.284_289del						.																																			SO:0001630	splice_region_variant	146378	exon2			.	AK058133	CCDS42146.1	16p11.2	2012-05-30			ENSG00000167194	ENSG00000167194			26346	protein-coding gene	gene with protein product							Standard	NM_001109659		Approved	FLJ25404	uc002dvs.2	Q96LL3	OTTHUMG00000177107	ENST00000300575.2:c.289+1ACTCAGGTATGAACCAGCT>-	16.37:g.30035201_30035219delACTCAGGTATGAACCAGCT		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	73	15	NM_001109660	0	0	0	0	0	Q494R8	In_Frame_Del	DEL	ENST00000300575.2	37	CCDS42146.1																																																																																			.		0.543	C16orf92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435351.1	NM_001109659	Frame_Shift_Del	-	30035219	ACTCAGGTATGAACCAGCT	-	30035201	8	5	96	1	0	1	0	1	0	0	1	0	1849	43	2	0	304	0	C16orf92	16	30035201	Splice_Site	DEL	ACTCAGGTATGAACCAGCT	TCGA-DW-7838-01A-11D-2136-08	27975527	30035201	60319552	86	8631											
SALL1	6299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	51172851	51172851	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactgtcctgaggagaaacAtgcacgaagccgttgacctc	11	9	10	11	2	0	3	0	2	0	1	2	5	1	3	3	1	4	2	3	1	3	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:51172851A>G	ENST00000251020.4	-	2	3315	c.3282T>C	c.(3280-3282)caT>caC	p.H1094H	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.H997H|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1094					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAGGAGAAACATGCACGAAGC	0.572																																					p.H1094H	GBM(103;1352 1446 1855 4775 8890)	.											.	SALL1-98	0			c.T3282C						.						116	104	108					16																	51172851		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			AGAAACATGCACG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3282T>C	16.37:g.51172851A>G		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	123	18	NM_002968	0	0	25	45	20	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			.		0.572	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		G	51172851	A	G	51172851	2	3	96	1	0	0	0	0	0	0	0	1	13842	214	8	3		3	SALL1	16	51172851	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	21137650	51172851	39181902	87	8632											
SLC38A7	55238	hgsc.bcm.edu;broad.mit.edu	37	chr16	58713827	58713827	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gctgctgggaagttgagtaaCcctgcacccaggcacgcgtt	8	8	13	12	2	0	1	0	1	0	0	0	2	0	2	2	2	3	7	2	2	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:58713827C>T	ENST00000570101.1	-	2	1087	c.204G>A	c.(202-204)ggG>ggA	p.G68G	SLC38A7_ENST00000566953.1_Intron|SLC38A7_ENST00000219320.4_Silent_p.G68G|SLC38A7_ENST00000564391.1_Silent_p.G68G|SLC38A7_ENST00000564100.1_Silent_p.G68G|SLC38A7_ENST00000564010.1_Intron			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	68					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						AGTTGAGTAACCCTGCACCCA	0.632																																					p.G68G		.											.	SLC38A7-69	0			c.G204A						.						50	46	48					16																	58713827		2198	4300	6498	SO:0001819	synonymous_variant	55238	exon3			GAGTAACCCTGCA	BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"Solute carriers"	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.204G>A	16.37:g.58713827C>T		Somatic	50	1		WXS	Illumina HiSeq	Phase_I	57	8	NM_018231	0	0	5	6	1	Q53GJ9|Q9H9I5	Silent	SNP	ENST00000570101.1	37	CCDS10800.1																																																																																			.		0.632	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231		T	58713827	C	T	58713827	2	4	96	1	0	0	0	0	0	0	0	1	14641	494	18	2		2	SLC38A7	16	58713827	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	7540976	58713827	31640926	88	8633											
FAM65A	79567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67577079	67577079	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaggaggcactgggggcccTaatggctgccctggatgact	7	7	17	10	0	0	1	0	1	0	0	0	4	0	4	2	7	1	2	2	7	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:67577079T>A	ENST00000379312.3	+	13	2523	c.2402T>A	c.(2401-2403)cTa>cAa	p.L801Q	FAM65A_ENST00000422602.2_Missense_Mutation_p.L817Q|FAM65A_ENST00000540839.3_Missense_Mutation_p.L817Q|CTD-2012K14.3_ENST00000563083.1_RNA|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000042381.4_Missense_Mutation_p.L797Q|FAM65A_ENST00000428437.2_Missense_Mutation_p.L811Q	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	801						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)		CTGGGGGCCCTAATGGCTGCC	0.642																																					p.L817Q		.											.	FAM65A-92	0			c.T2450A						.						17	16	17					16																	67577079		2198	4298	6496	SO:0001583	missense	79567	exon13			GGGCCCTAATGGC	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.2402T>A	16.37:g.67577079T>A	ENSP00000368614:p.Leu801Gln	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	40	14	NM_001193523	0	0	17	39	22	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237952	0.79800	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.49432	0.78;0.78;0.78	5.52	5.52	0.82312	.	0.070064	0.56097	D	0.000022	T	0.67258	0.2874	M	0.72894	2.215	0.09310	N	0.999991	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.68765	0.96;0.96;0.96;0.96	T	0.63664	-0.6586	10	0.87932	D	0	-9.5432	15.6534	0.77115	0.0:0.0:0.0:1.0	.	811;817;801;817	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	Q	801;797;817;811	ENSP00000368614:L801Q;ENSP00000042381:L797Q;ENSP00000400099:L817Q	ENSP00000042381:L797Q	L	+	2	0	FAM65A	66134580	0.901000	0.30685	0.994000	0.49952	0.920000	0.55202	4.728000	0.62000	2.120000	0.65058	0.454000	0.30748	CTA	.		0.642	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		A	67577079	T	A	67577079	3	1	96	1	0	0	0	0	1	0	0	0	5618	1522	53	5	2436	5	FAM65A	16	67577079	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	8863252	67577079	22777674	89	8634											
ZZEF1	23140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3919676	3919676	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcacttgcacctccattcCtggctcctccatgaactggc	6	11	6	18	0	1	1	1	1	0	0	5	1	5	1	6	2	2	2	6	2	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:3919676C>A	ENST00000381638.2	-	49	8210	c.8086G>T	c.(8086-8088)Gga>Tga	p.G2696*		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2696							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ACCTCCATTCCTGGCTCCTCC	0.597																																					p.G2696X		.											.	ZZEF1-93	0			c.G8086T						.						154	114	127					17																	3919676		2203	4300	6503	SO:0001587	stop_gained	23140	exon49			CCATTCCTGGCTC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8086G>T	17.37:g.3919676C>A	ENSP00000371051:p.Gly2696*	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	162	39	NM_015113	0	0	14	14	0	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Nonsense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	50	17.192008	0.99881	.	.	ENSG00000074755	ENST00000381638	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-14.3127	20.0271	0.97525	0.0:1.0:0.0:0.0	.	.	.	.	X	2696	.	ENSP00000371051:G2696X	G	-	1	0	ZZEF1	3866425	1.000000	0.71417	0.961000	0.40146	0.948000	0.59901	7.487000	0.81328	2.744000	0.94065	0.650000	0.86243	GGA	.		0.597	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		A	3919676	C	A	3919676	4	1	96	1	0	0	0	0	0	1	0	0	18287	690	24	4	827	4	ZZEF1	17	3919676	Nonsense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		3919676	77275534	90	8635											
ZFP3	124961	hgsc.bcm.edu	37	chr17	4995909	4995909	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctatgtatgtaaggaatgTgggaaggccttcagggggaa	11	9	15	6	0	1	0	1	0	0	0	1	3	1	3	2	5	0	2	2	5	6	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:4995909T>C	ENST00000318833.3	+	2	1446	c.1110T>C	c.(1108-1110)tgT>tgC	p.C370C		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	370					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)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						GTAAGGAATGTGGGAAGGCCT	0.413																																					p.C370C		.											.	ZFP3-90	0			c.T1110C						.						46	48	48					17																	4995909		2203	4300	6503	SO:0001819	synonymous_variant	124961	exon2			GGAATGTGGGAAG	BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"Zinc fingers, C2H2-type"	12861	protein-coding gene	gene with protein product		194480	"zinc finger protein homologous to Zfp-3 in mouse", "zinc finger protein 3 homolog (mouse)"				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.1110T>C	17.37:g.4995909T>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	72	4	NM_153018	0	0	0	0	0	A5PLL4	Silent	SNP	ENST00000318833.3	37	CCDS11067.1																																																																																			.		0.413	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018		C	4995909	T	C	4995909	2	2	96	1	0	0	0	0	0	0	0	1	17675	1702	59	3		3	ZFP3	17	4995909	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	1076233	4995909	76199301	91	8636											
SOX15	6665	hgsc.bcm.edu	37	chr17	7492829	7492829	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcggagctccacaccatgaAcgcgttcatcggccgcttca	9	7	10	15	5	2	1	2	1	0	0	4	2	3	2	3	2	3	3	3	2	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:7492829A>G	ENST00000250055.2	-	1	659	c.166T>C	c.(166-168)Ttc>Ctc	p.F56L	SOX15_ENST00000570788.1_Missense_Mutation_p.F56L|SOX15_ENST00000538513.2_Missense_Mutation_p.F56L|MPDU1_ENST00000423172.2_Intron|FXR2_ENST00000573057.1_5'Flank	NM_006942.1	NP_008873.1	O60248	SOX15_HUMAN	SRY (sex determining region Y)-box 15	56					cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|male gonad development (GO:0008584)|myoblast development (GO:0048627)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue regeneration (GO:0043403)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)	2						CACACCATGAACGCGTTCATC	0.687											OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F56L		.											.	SOX15-135	0			c.T166C						.						24	26	25					17																	7492829		2203	4300	6503	SO:0001583	missense	6665	exon1			CCATGAACGCGTT	AJ006222	CCDS32549.1	17p13.1	2014-08-12	2002-07-22	2002-07-26	ENSG00000129194	ENSG00000129194		"SRY (sex determining region Y)-boxes"	11196	protein-coding gene	gene with protein product		601297	"SRY (sex determining region Y)-box 20"	SOX20		8978787, 9730625	Standard	NM_006942		Approved	SOX27, SOX26	uc002ghz.1	O60248	OTTHUMG00000178146	ENST00000250055.2:c.166T>C	17.37:g.7492829A>G	ENSP00000355354:p.Phe56Leu	Somatic	35	0	642	WXS	Illumina HiSeq	Phase_I	32	2	NM_006942	0	0	0	0	0	B4DWU7|D3DTQ0|P35717|Q9Y6W7	Missense_Mutation	SNP	ENST00000250055.2	37	CCDS32549.1	.	.	.	.	.	.	.	.	.	.	A	37	6.038607	0.97226	.	.	ENSG00000129194	ENST00000250055;ENST00000538513	D;D	0.99239	-5.61;-5.61	5.38	5.38	0.77491	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.56097	D	0.000029	D	0.99606	0.9857	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97827	1.0260	10	0.87932	D	0	.	13.4332	0.61068	1.0:0.0:0.0:0.0	.	56	O60248	SOX15_HUMAN	L	56	ENSP00000355354:F56L;ENSP00000439311:F56L	ENSP00000355354:F56L	F	-	1	0	SOX15	7433553	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.139000	0.94554	2.276000	0.75962	0.454000	0.30748	TTC	.		0.687	SOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440757.1	NM_006942		G	7492829	A	G	7492829	3	3	96	1	0	0	0	0	1	0	0	0	14978	43	2	3	543	3	SOX15	17	7492829	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	2496920	7492829	73702381	92	8637											
WIPF2	147179	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	38420795	38420800	+	In_Frame_Del	DEL	CCAAGG	CCAAGG	-																															ccagttctcgagctgctgccCcaaggcctccagtatctgcc																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	CCAAGG	CCAAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:38420795_38420800delCCAAGG	ENST00000323571.4	+	5	607_612	c.367_372delCCAAGG	c.(367-372)ccaaggdel	p.PR123del	WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000583130.1_In_Frame_Del_p.PR123del|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000585043.1_In_Frame_Del_p.PR123del	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	123					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)		p.R124G(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						AGCTGCTGCCCCAAGGCCTCCAGTAT	0.573										HNSCC(43;0.11)																											p.123_124del		.											.	WIPF2-93	1	Substitution - Missense(1)	kidney(1)	c.367_372del						.																																			SO:0001651	inframe_deletion	147179	exon5			.	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.367_372delCCAAGG	17.37:g.38420795_38420800delCCAAGG	ENSP00000320924:p.Pro123_Arg124del	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	141	24	NM_133264	0	0	0	0	0	A8K0L3|Q658J8|Q71RE1|Q8TE44	In_Frame_Del	DEL	ENST00000323571.4	37	CCDS11364.1																																																																																			.		0.573	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		-	38420800	CCAAGG	-	38420795	7	5	96	1	0	1	0	1	0	0	0	0	17401	623	22	0	381	0	WIPF2	17	38420795	In_Frame_Del	DEL	CCAAGG	TCGA-DW-7838-01A-11D-2136-08	30927966	38420795	42774415	93	8638			1	26		2	2	12	N	CCAAGG_A	4.370524e-05
WIPF2	147179	hgsc.bcm.edu;bcgsc.ca	37	chr17	38420806	38420806	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgccccaaggcctccAgtatctgccgccagcgggcg	5	6	13	17	3	1	0	0	0	1	0	2	0	2	0	6	2	4	3	6	2	2	1	rs139121244		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:38420806A>G	ENST00000323571.4	+	5	618	c.378A>G	c.(376-378)ccA>ccG	p.P126P	WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000583130.1_Silent_p.P126P|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000585043.1_Silent_p.P126P	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	126					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						CAAGGCCTCCAGTATCTGCCG	0.582										HNSCC(43;0.11)																											p.P126P		.											.	WIPF2-93	0			c.A378G						.			1,4405	2.1+/-5.4	0,1,2202	60	69	66		378	-5.5	0.3	17	dbSNP_134	66	0,8600		0,0,4300	no	coding-synonymous	WIPF2	NM_133264.4		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		126/441	38420806	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	147179	exon5			GCCTCCAGTATCT	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.378A>G	17.37:g.38420806A>G		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	151	35	NM_133264	0	0	7	7	0	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	37	CCDS11364.1																																																																																			A|1.000;G|0.000		0.582	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		G	38420806	A	G	38420806	2	3	96	1	0	0	0	0	0	0	0	1	17401	175	7	3		3	WIPF2	17	38420806	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	11	38420806	42774404	94	8639			1	26		2	2	12	N	CCAAGG_A	4.370524e-05
KRT37	8688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39577782	39577782	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatgaggctctgcatctgggCcagctctgtgccgtagcggt	6	10	14	11	2	3	1	0	1	3	0	3	1	3	1	2	3	4	4	2	3	2	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:39577782C>G	ENST00000225550.3	-	6	1077	c.1078G>C	c.(1078-1080)Gcc>Ccc	p.A360P	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	360	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				TGCATCTGGGCCAGCTCTGTG	0.567																																					p.A360P		.											.	KRT37-91	0			c.G1078C						.						66	63	64					17																	39577782		2203	4300	6503	SO:0001583	missense	8688	exon6			TCTGGGCCAGCTC	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"-", "Intermediate filaments type I, keratins (acidic)"	6455	protein-coding gene	gene with protein product		604541	"keratin, hair, acidic, 7"	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.1078G>C	17.37:g.39577782C>G	ENSP00000225550:p.Ala360Pro	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	101	13	NM_003770	0	0	0	0	0		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037494	0.54896	.	.	ENSG00000108417	ENST00000225550	T	0.14640	2.49	5.44	2.17	0.27698	Filament (1);	0.000000	0.49305	D	0.000155	T	0.32763	0.0840	H	0.96861	3.895	0.28206	N	0.92715	B	0.34349	0.45	B	0.37239	0.244	T	0.42582	-0.9443	10	0.66056	D	0.02	.	13.3764	0.60741	0.5453:0.4547:0.0:0.0	.	360	O76014	KRT37_HUMAN	P	360	ENSP00000225550:A360P	ENSP00000225550:A360P	A	-	1	0	KRT37	36831308	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	-0.196000	0.09532	0.197000	0.20387	0.655000	0.94253	GCC	.		0.567	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		G	39577782	C	G	39577782	3	3	96	1	0	0	0	0	1	0	0	0	8495	739	26	4	279	4	KRT37	17	39577782	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	1156976	39577782	41617428	95	8640											
SCRN2	90507	broad.mit.edu	37	chr17	45916884	45916884	+	Frame_Shift_Del	DEL	A	A	-																															cagtgcggtcagccagcaggAaggtgctatggtaggagaat																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:45916884delA	ENST00000290216.9	-	4	607	c.482delT	c.(481-483)ttcfs	p.F161fs	SCRN2_ENST00000407215.3_Frame_Shift_Del_p.F161fs|SCRN2_ENST00000584123.1_Frame_Shift_Del_p.F169fs	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	161						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						AGCCAGCAGGAAGGTGCTATG	0.617																																					p.F161fs													.	SCRN2-91	0			c.482delT						.						106	99	102					17																	45916884		2203	4300	6503	SO:0001589	frameshift_variant	90507	exon4			AGCAGGAAGGTGC	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.482delT	17.37:g.45916884delA	ENSP00000290216:p.Phe161fs	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	198	11	NM_138355	0	0	0	0	0	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Frame_Shift_Del	DEL	ENST00000290216.9	37	CCDS11519.1																																																																																			.		0.617	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		-	45916884	A	-	45916884	7	5	96	1	0	1	0	1	0	0	0	0	13971	246	9	0	833	0	SCRN2	17	45916884	Frame_Shift_Del	DEL	A	TCGA-DW-7838-01A-11D-2136-08	6339102	45916884	35278326	96	8641											
MED13	9969	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	60023946	60023946	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccaggagagtgcattgtaCtgttccaaaacaaacctgaa	15	8	9	9	0	0	2	0	1	0	1	1	3	1	2	3	1	5	3	3	1	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:60023946C>G	ENST00000397786.2	-	30	6484	c.6408G>C	c.(6406-6408)caG>caC	p.Q2136H		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2136					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GTGCATTGTACTGTTCCAAAA	0.378																																					p.Q2136H		.											.	MED13-136	0			c.G6408C						.						79	74	76					17																	60023946		1866	4104	5970	SO:0001583	missense	9969	exon30			ATTGTACTGTTCC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"thyroid hormone receptor associated protein 1"	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.6408G>C	17.37:g.60023946C>G	ENSP00000380888:p.Gln2136His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	77	24	NM_005121	0	0	7	19	12	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.576706	0.45902	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.83837	-1.77	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.90748	0.7096	M	0.75447	2.3	0.80722	D	1	D	0.67145	0.996	D	0.81914	0.995	D	0.90884	0.4756	10	0.48119	T	0.1	-4.4995	18.2754	0.90081	0.0:1.0:0.0:0.0	.	2136	Q9UHV7	MED13_HUMAN	H	2136;2135	ENSP00000380888:Q2136H	ENSP00000262436:Q2135H	Q	-	3	2	MED13	57378728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.403000	0.79983	2.315000	0.78130	0.591000	0.81541	CAG	.		0.378	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60023946	C	G	60023946	3	3	96	1	0	0	0	0	1	0	0	0	9455	564	20	4	120	4	MED13	17	60023946	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	14107062	60023946	21171264	97	8642											
RNF157	114804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74163165	74163165	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgacacactcctcgcttgtaCtgcacagtctccgactggag	8	10	9	14	2	1	1	0	1	1	0	4	3	2	2	2	1	2	3	2	1	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:74163165C>A	ENST00000269391.6	-	5	618	c.486G>T	c.(484-486)caG>caT	p.Q162H	RNF157_ENST00000319945.6_Missense_Mutation_p.Q162H	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	162							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CTCGCTTGTACTGCACAGTCT	0.567																																					p.Q162H	GBM(186;507 2120 27388 27773 52994)	.											.	RNF157-228	0			c.G486T						.						127	114	118					17																	74163165		2203	4300	6503	SO:0001583	missense	114804	exon5			CTTGTACTGCACA	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"RING-type (C3HC4) zinc fingers"	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.486G>T	17.37:g.74163165C>A	ENSP00000269391:p.Gln162His	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	219	29	NM_052916	0	0	4	7	3	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	37	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	4.577	0.107271	0.08780	.	.	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	T;T	0.27890	1.64;1.64	5.43	2.38	0.29361	.	0.131468	0.64402	N	0.000001	T	0.05593	0.0147	N	0.00152	-1.975	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40757	-0.9546	10	0.02654	T	1	-4.6639	10.0104	0.41984	0.0971:0.1243:0.7785:0.0	.	162;162	Q96PX1-2;Q96PX1	.;RN157_HUMAN	H	162;162;124	ENSP00000269391:Q162H;ENSP00000321837:Q162H	ENSP00000269391:Q162H	Q	-	3	2	RNF157	71674760	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.577000	0.23758	0.271000	0.22005	-0.128000	0.14901	CAG	.		0.567	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		A	74163165	C	A	74163165	3	1	96	1	0	0	0	0	1	0	0	0	13486	564	20	4	1613	4	RNF157	17	74163165	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	14139219	74163165	7032045	98	8643											
BIRC5	332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	76212806	76212806	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtcaagaagcagtttgaaGaattaacccttggtgaattt	13	13	9	6	0	1	4	1	2	0	2	1	4	1	4	1	1	2	2	1	1	6	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:76212806G>A	ENST00000350051.3	+	3	402	c.283G>A	c.(283-285)Gaa>Aaa	p.E95K	BIRC5_ENST00000301633.4_Missense_Mutation_p.E118K|BIRC5_ENST00000374948.2_Intron|AC087645.1_ENST00000600484.1_Missense_Mutation_p.S264F|BIRC5_ENST00000589892.1_3'UTR|BIRC5_ENST00000592734.1_Intron	NM_001168.2	NP_001159.2	O15392	BIRC5_HUMAN	baculoviral IAP repeat containing 5	95					apoptotic process (GO:0006915)|cell division (GO:0051301)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|establishment of chromosome localization (GO:0051303)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of mitotic cell cycle (GO:0045931)|protein complex localization (GO:0031503)|protein phosphorylation (GO:0006468)|spindle checkpoint (GO:0031577)|transcription, DNA-templated (GO:0006351)	centriole (GO:0005814)|chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|interphase microtubule organizing center (GO:0031021)|microtubule (GO:0005874)|midbody (GO:0030496)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	chaperone binding (GO:0051087)|cobalt ion binding (GO:0050897)|cofactor binding (GO:0048037)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Ran GTPase binding (GO:0008536)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			kidney(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.153)			GCAGTTTGAAGAATTAACCCT	0.398																																					p.E118K		.											.	BIRC5-1083	0			c.G352A						.						72	79	77					17																	76212806		2203	4300	6503	SO:0001583	missense	332	exon4			TTTGAAGAATTAA	U75285	CCDS11755.1, CCDS32751.1, CCDS32752.1	17q25.3	2013-01-17	2011-01-25		ENSG00000089685	ENSG00000089685		"Baculoviral IAP repeat containing"	593	protein-coding gene	gene with protein product	"survivin variant 3 alpha"	603352	"apoptosis inhibitor 4", "baculoviral IAP repeat-containing 5"	API4		8106347, 7947793	Standard	XR_243654		Approved	EPR-1, survivin	uc002jvf.3	O15392		ENST00000350051.3:c.283G>A	17.37:g.76212806G>A	ENSP00000324180:p.Glu95Lys	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	117	29	NM_001012271	0	0	0	0	0	A2SUH6|B2R4R1|Q2I3N8|Q4VGX0|Q53F61|Q5MGC6|Q6FHL2|Q75SP2|Q9P2W8	Missense_Mutation	SNP	ENST00000350051.3	37	CCDS11755.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456362	0.84317	.	.	ENSG00000089685	ENST00000301633;ENST00000350051;ENST00000432014	T;T	0.03920	3.76;3.76	5.62	5.62	0.85841	Baculoviral inhibition of apoptosis protein repeat (1);	0.384181	0.30762	N	0.008935	T	0.07728	0.0194	L	0.59436	1.845	0.80722	D	1	B;B;B;P	0.50617	0.18;0.118;0.415;0.937	B;B;B;B	0.39590	0.053;0.036;0.202;0.304	T	0.18335	-1.0340	10	0.40728	T	0.16	-19.2617	17.1223	0.86705	0.0:0.0:1.0:0.0	.	95;95;118;95	O15392-4;O15392;O15392-2;A3E0Z5	.;BIRC5_HUMAN;.;.	K	118;95;118	ENSP00000301633:E118K;ENSP00000324180:E95K	ENSP00000301633:E118K	E	+	1	0	BIRC5	73724401	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	4.796000	0.62496	2.648000	0.89879	0.462000	0.41574	GAA	.		0.398	BIRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437231.2	NM_001168		A	76212806	G	A	76212806	3	1	96	1	0	0	0	0	1	0	0	0	1438	943	33	2	366	2	BIRC5	17	76212806	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	2049641	76212806	4982404	99	8644											
APCDD1	147495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	10471914	10471914	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgccatgcatgaacttcaGctcatccgggtggagaagca	10	10	11	10	1	2	2	2	1	0	1	3	3	3	2	2	2	5	3	2	2	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:10471914G>A	ENST00000355285.5	+	3	984	c.630G>A	c.(628-630)caG>caA	p.Q210Q	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		ATGAACTTCAGCTCATCCGGG	0.582																																					p.Q210Q		.											.	APCDD1-90	0			c.G630A						.						145	132	136					18																	10471914		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			ACTTCAGCTCATC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.630G>A	18.37:g.10471914G>A		Somatic	271	0		WXS	Illumina HiSeq	Phase_I	219	38	NM_153000	0	0	0	1	1		Silent	SNP	ENST00000355285.5	37	CCDS11849.1																																																																																			.		0.582	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		A	10471914	G	A	10471914	2	1	96	1	0	0	0	0	0	0	0	1	765	962	34	2		2	APCDD1	18	10471914	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08		10471914	67605334	100	8645											
CEP192	55125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	13071144	13071144	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcacctggaccttgcttaGatattccatcgattttgtcc	7	16	7	11	1	1	1	1	0	0	1	4	3	3	2	4	1	1	1	4	1	2	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:13071144G>T	ENST00000325971.8	+	26	5086	c.3493G>T	c.(3493-3495)Gat>Tat	p.D1165Y	CEP192_ENST00000506447.1_Missense_Mutation_p.D1761Y|CEP192_ENST00000430049.2_Missense_Mutation_p.D1286Y			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1165					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACCTTGCTTAGATATTCCATC	0.423																																					p.D1761Y		.											.	CEP192-27	0			c.G5281T						.						110	110	110					18																	13071144		2203	4300	6503	SO:0001583	missense	55125	exon28			TGCTTAGATATTC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25515	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 62"					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3493G>T	18.37:g.13071144G>T	ENSP00000317156:p.Asp1165Tyr	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	61	14	NM_032142	0	0	2	2	0	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	G	17.34	3.365339	0.61513	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.47869	0.83;0.83;0.83	5.35	3.54	0.40534	.	0.121003	0.53938	D	0.000055	T	0.64875	0.2638	M	0.73962	2.25	0.58432	D	0.999998	B;D;B	0.89917	0.368;1.0;0.328	B;D;B	0.79108	0.091;0.992;0.104	T	0.67692	-0.5605	10	0.87932	D	0	-11.9129	9.8383	0.40982	0.0725:0.0:0.7869:0.1406	.	1286;1761;363	C9JT09;E9PF99;Q9HCK3	.;.;.	Y	1761;1165;1165;1286	ENSP00000427550:D1761Y;ENSP00000317156:D1165Y;ENSP00000389190:D1286Y	ENSP00000317156:D1165Y	D	+	1	0	CEP192	13061144	1.000000	0.71417	0.650000	0.29550	0.606000	0.37113	3.512000	0.53407	1.230000	0.43646	0.650000	0.86243	GAT	.		0.423	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13071144	G	T	13071144	3	4	96	1	0	0	0	0	1	0	0	0	3257	942	33	4	5387	4	CEP192	18	13071144	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	2599230	13071144	65006104	101	8646											
ZNF519	162655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	14105675	14105675	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacatttgtaaggtttctcTccagtatgaattttctgatg	9	19	7	6	0	2	2	0	2	2	0	4	2	3	2	1	1	1	3	1	1	4	7			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:14105675T>C	ENST00000590202.1	-	3	1016	c.864A>G	c.(862-864)ggA>ggG	p.G288G	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	288					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AAGGTTTCTCTCCAGTATGAA	0.363																																					p.G288G		.											.	ZNF519-90	0			c.A864G						.						49	53	52					18																	14105675		2203	4299	6502	SO:0001819	synonymous_variant	162655	exon3			TTTCTCTCCAGTA	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"Zinc fingers, C2H2-type", "-"	30574	protein-coding gene	gene with protein product	"similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.864A>G	18.37:g.14105675T>C		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	83	18	NM_145287	0	0	11	12	1		Silent	SNP	ENST00000590202.1	37	CCDS32797.1																																																																																			.		0.363	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		C	14105675	T	C	14105675	2	2	96	1	0	0	0	0	0	0	0	1	17996	1538	54	3		3	ZNF519	18	14105675	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	1034531	14105675	63971573	102	8647											
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	21451430	21451430	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagcagccgtgccccagtGtctagggaggagctgatgac	8	6	15	12	1	1	2	0	2	1	0	1	4	1	4	4	2	4	2	4	2	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:21451430G>T	ENST00000313654.9	+	38	5044	c.4803G>T	c.(4801-4803)gtG>gtT	p.V1601V	LAMA3_ENST00000587184.1_5'Flank|LAMA3_ENST00000399516.3_Silent_p.V1601V|LAMA3_ENST00000269217.6_5'Flank	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1601	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GTGCCCCAGTGTCTAGGGAGG	0.552																																					p.V1601V		.											.	LAMA3-100	0			c.G4803T						.						66	69	68					18																	21451430		2040	4193	6233	SO:0001819	synonymous_variant	3909	exon38			CCCAGTGTCTAGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4803G>T	18.37:g.21451430G>T		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	85	14	NM_001127717	0	0	0	0	0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			.		0.552	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21451430	G	T	21451430	2	4	96	1	0	0	0	0	0	0	0	1	8628	1364	48	4		4	LAMA3	18	21451430	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	7345755	21451430	56625818	103	8648											
ZNF521	25925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	22805629	22805629	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgcaagatgtgcacctataGactttcttttcgttactgtg	8	17	8	8	1	1	2	0	0	1	2	2	2	1	2	1	0	3	3	1	0	4	7			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:22805629G>C	ENST00000361524.3	-	4	2401	c.2253C>G	c.(2251-2253)gtC>gtG	p.V751V	ZNF521_ENST00000538137.2_Silent_p.V751V|ZNF521_ENST00000584787.1_Silent_p.V531V|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	751					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TGCACCTATAGACTTTCTTTT	0.468			T	PAX5	ALL																																p.V751V		.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521-275	0			c.C2253G						.						75	71	72					18																	22805629		2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			CCTATAGACTTTC	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"Zinc fingers, C2H2-type"	24605	protein-coding gene	gene with protein product	"early hematopoietic zinc finger"	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2253C>G	18.37:g.22805629G>C		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	83	16	NM_015461	0	0	0	0	0	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			.		0.468	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		C	22805629	G	C	22805629	2	2	96	1	0	0	0	0	0	0	0	1	17997	929	33	4		4	ZNF521	18	22805629	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	1354199	22805629	55271619	104	8649											
KIAA1328	57536	broad.mit.edu	37	chr18	34802114	34802114	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtcctctaaaatcaacccGgaagaagatggggatgcaca	15	6	10	10	1	2	2	1	0	1	2	3	4	3	4	2	3	2	1	2	3	5	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:34802114G>C	ENST00000280020.5	+	10	1680	c.1658G>C	c.(1657-1659)cGg>cCg	p.R553P	KIAA1328_ENST00000591619.1_Missense_Mutation_p.R549P|KIAA1328_ENST00000543923.1_Intron|KIAA1328_ENST00000586135.1_3'UTR	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	553										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		AAATCAACCCGGAAGAAGATG	0.463																																					p.R553P													.	KIAA1328-90	0			c.G1658C						.						32	30	31					18																	34802114		1845	4092	5937	SO:0001583	missense	57536	exon10			CAACCCGGAAGAA	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1658G>C	18.37:g.34802114G>C	ENSP00000280020:p.Arg553Pro	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	14	6	NM_020776	0	0	0	0	0	Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	37	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	G	5.413	0.261419	0.10239	.	.	ENSG00000150477	ENST00000280020;ENST00000383055	T	0.46819	0.86	5.93	5.93	0.95920	.	0.517672	0.19767	N	0.106536	T	0.38427	0.1040	N	0.08118	0	0.46954	D	0.999262	P;D	0.58268	0.721;0.982	P;P	0.51999	0.567;0.687	T	0.20505	-1.0273	10	0.34782	T	0.22	.	12.7607	0.57363	0.077:0.0:0.923:0.0	.	553;553	A8K8C3;Q86T90	.;K1328_HUMAN	P	553	ENSP00000280020:R553P	ENSP00000280020:R553P	R	+	2	0	KIAA1328	33056112	0.994000	0.37717	0.943000	0.38184	0.043000	0.13939	3.760000	0.55235	2.814000	0.96858	0.591000	0.81541	CGG	.		0.463	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		C	34802114	G	C	34802114	3	2	96	1	0	0	0	0	1	0	0	0	8246	1116	39	4	1696	4	KIAA1328	18	34802114	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	11996485	34802114	43275134	105	8650											
ZNF430	80264	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	21240780	21240780	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcaaccagtcctcaaacCttattgaacaaagtaattca	15	12	3	11	0	3	1	3	1	0	0	4	1	4	1	3	0	3	1	3	0	6	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:21240780C>G	ENST00000261560.5	+	5	1847	c.1666C>G	c.(1666-1668)Ctt>Gtt	p.L556V	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	556					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						GTCCTCAAACCTTATTGAACA	0.383																																					p.L556V		.											.	ZNF430-516	0			c.C1666G						.						36	41	40					19																	21240780		2182	4285	6467	SO:0001583	missense	80264	exon5			TCAAACCTTATTG	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.1666C>G	19.37:g.21240780C>G	ENSP00000261560:p.Leu556Val	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	39	10	NM_025189	0	0	3	3	0	Q86V70	Missense_Mutation	SNP	ENST00000261560.5	37	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	7.976	0.750166	0.15778	.	.	ENSG00000118620	ENST00000261560	T	0.68331	-0.32	1.01	1.01	0.19927	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81341	0.4802	M	0.88105	2.93	0.09310	N	1	D;P	0.57571	0.98;0.457	D;B	0.68353	0.957;0.329	T	0.68685	-0.5343	9	0.87932	D	0	.	8.8921	0.35441	0.0:1.0:0.0:0.0	.	555;556	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	V	556	ENSP00000261560:L556V	ENSP00000261560:L556V	L	+	1	0	ZNF430	21032620	0.000000	0.05858	0.014000	0.15608	0.014000	0.08584	-0.502000	0.06390	0.453000	0.26858	0.456000	0.33151	CTT	.		0.383	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		G	21240780	C	G	21240780	3	3	96	1	0	0	0	0	1	0	0	0	17936	681	24	4	1684	4	ZNF430	19	21240780	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		21240780	37888203	106	8651											
DPY19L3	147991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	32930113	32930113	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcaattacatatttccTgagaccaaacttacagcctc	14	10	5	12	0	0	1	0	1	0	1	2	2	1	1	3	0	6	2	3	0	5	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:32930113T>G	ENST00000342179.5	+	7	907	c.692T>G	c.(691-693)cTg>cGg	p.L231R	DPY19L3_ENST00000392250.2_Missense_Mutation_p.L231R|DPY19L3_ENST00000586987.1_Missense_Mutation_p.L231R	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	231						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					ACATATTTCCTGAGACCAAAC	0.363																																					p.L231R		.											.	DPY19L3-72	0			c.T692G						.						133	131	132					19																	32930113		2203	4300	6503	SO:0001583	missense	147991	exon7			ATTTCCTGAGACC		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.692T>G	19.37:g.32930113T>G	ENSP00000344937:p.Leu231Arg	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	80	15	NM_001172774	0	0	2	4	2	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	37	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.333525	0.81801	.	.	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.65549	-0.16;-0.16	5.66	5.66	0.87406	.	0.075638	0.53938	D	0.000041	T	0.81331	0.4800	M	0.84683	2.71	0.53005	D	0.99996	D	0.76494	0.999	D	0.76575	0.988	D	0.84659	0.0705	10	0.87932	D	0	-8.1242	15.8965	0.79338	0.0:0.0:0.0:1.0	.	231	Q6ZPD9	D19L3_HUMAN	R	231	ENSP00000376081:L231R;ENSP00000344937:L231R	ENSP00000315672:L231R	L	+	2	0	DPY19L3	37621953	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.816000	0.86201	2.163000	0.67991	0.460000	0.39030	CTG	.		0.363	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		G	32930113	T	G	32930113	3	3	96	1	0	0	0	0	1	0	0	0	4753	1580	55	5	714	5	DPY19L3	19	32930113	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	11689333	32930113	26198870	107	8652											
SERTAD1	29950	hgsc.bcm.edu;ucsc.edu	37	chr19	40928862	40928862	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cttgcccggcccatcctcagGgcctggtttgaggccctcag	4	9	12	16	1	2	1	2	1	0	0	3	1	3	1	5	4	1	1	5	4	0	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:40928862G>A	ENST00000357949.4	-	2	750	c.592C>T	c.(592-594)Cct>Tct	p.P198S		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	198					positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CCATCCTCAGGGCCTGGTTTG	0.582																																					p.P198S		.											.	SERTAD1-226	0			c.C592T						.						25	22	23					19																	40928862		2203	4300	6503	SO:0001583	missense	29950	exon2			CCTCAGGGCCTGG	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"CDK4-binding protein p34SEI", "transcriptional regulator interacting with the PHD-bromodomain 1"					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.592C>T	19.37:g.40928862G>A	ENSP00000350633:p.Pro198Ser	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	15	3	NM_013376	0	0	36	50	14	Q9BUE7	Missense_Mutation	SNP	ENST00000357949.4	37	CCDS12557.1	.	.	.	.	.	.	.	.	.	.	G	4.055	0.007937	0.07866	.	.	ENSG00000197019	ENST00000357949	T	0.45668	0.89	5.3	1.48	0.22813	.	0.429768	0.23577	N	0.046681	T	0.16471	0.0396	N	0.11064	0.09	0.09310	N	0.99999	B	0.10296	0.003	B	0.06405	0.002	T	0.29941	-0.9995	10	0.02654	T	1	6.2956	6.6333	0.22869	0.2439:0.1426:0.6135:0.0	.	198	Q9UHV2	SRTD1_HUMAN	S	198	ENSP00000350633:P198S	ENSP00000350633:P198S	P	-	1	0	SERTAD1	45620702	0.995000	0.38212	0.483000	0.27378	0.010000	0.07245	2.607000	0.46300	0.623000	0.30267	-0.314000	0.08810	CCT	.		0.582	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376		A	40928862	G	A	40928862	3	1	96	1	0	0	0	0	1	0	0	0	14152	1232	43	2	122	2	SERTAD1	19	40928862	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	7998749	40928862	18200121	108	8653											
CD177	57126	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	43858482	43858482	+	RNA	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacaccttcgtgtgccgccAggaggacttctgcaacaacc	9	8	9	15	2	1	0	0	0	1	0	2	2	1	2	4	2	5	1	4	2	3	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:43858482A>G	ENST00000607517.1	+	0	373				CD177_ENST00000378012.2_RNA|CD177_ENST00000378009.4_RNA			Q8N6Q3	CD177_HUMAN	CD177 molecule						blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5		Prostate(69;0.00682)				GTGTGCCGCCAGGAGGACTTC	0.682																																					.													.	CD177-22	0			.						.						63	70	68					19																	43858482		1963	4126	6089			57126	.			GCCGCCAGGAGGA	AF146747	CCDS62700.1	19q13.31	2013-10-02	2006-03-28		ENSG00000204936	ENSG00000204936		"CD molecules"	30072	protein-coding gene	gene with protein product	"polycythemia rubra vera 1"	162860	"CD177 antigen"			10753836, 5552408	Standard	NM_020406		Approved	PRV1, HNA2A, NB1	uc002owi.3	Q8N6Q3	OTTHUMG00000185320		19.37:g.43858482A>G		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	82	14	.	0	0	1	1	0	Q711Q2|Q8NCV9|Q96QH1|Q9HDA5	Missense_Mutation	SNP	ENST00000607517.1	37		.	.	.	.	.	.	.	.	.	.	a	1.488	-0.555479	0.03967	.	.	ENSG00000204936	ENST00000378009;ENST00000378012;ENST00000457794	T;T;T	0.14022	3.11;2.54;2.54	3.05	0.928	0.19443	.	.	.	.	.	T	0.07324	0.0185	N	0.22421	0.69	0.09310	N	1	B	0.28636	0.218	B	0.24006	0.05	T	0.36311	-0.9753	9	0.32370	T	0.25	.	3.442	0.07466	0.6353:0.2352:0.1295:0.0	.	106	Q8N6Q3	CD177_HUMAN	R	106	ENSP00000367248:Q106R;ENSP00000367251:Q106R;ENSP00000388794:Q106R	ENSP00000367248:Q106R	Q	+	2	0	CD177	48550322	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.400000	0.20932	0.123000	0.18342	-0.256000	0.11100	CAG	.		0.682	CD177-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000470162.1	NM_020406		G	43858482	A	G	43858482	1	3	96	0	1	0	0	0	0	0	0	0	2977	188	7	3		3	CD177	19	43858482	RNA	SNP	A	TCGA-DW-7838-01A-11D-2136-08	2929620	43858482	15270501	109	8654											
ZNF227	7770	broad.mit.edu;bcgsc.ca	37	chr19	44739499	44739499	+	Frame_Shift_Del	DEL	T	T	-																															gtcatgaatctggtgattgcTtcaataagagctcttttcat																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:44739499delT	ENST00000313040.7	+	6	1121	c.916delT	c.(916-918)ttcfs	p.F306fs	ZNF227_ENST00000391961.2_Frame_Shift_Del_p.F255fs|ZNF227_ENST00000589005.1_Frame_Shift_Del_p.F255fs	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	306					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)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				TGGTGATTGCTTCAATAAGAG	0.418																																					p.F306fs													.	ZNF227-91	0			c.916delT						.						58	58	58					19																	44739499		2203	4300	6503	SO:0001589	frameshift_variant	7770	exon6			GATTGCTTCAATA	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.916delT	19.37:g.44739499delT	ENSP00000321049:p.Phe306fs	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	82	9	NM_182490	0	0	0	0	0	B3KRU7|B7Z5P9	Frame_Shift_Del	DEL	ENST00000313040.7	37	CCDS12636.1																																																																																			.		0.418	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		-	44739499	T	-	44739499	7	5	96	1	0	1	0	1	0	0	0	0	17813	1609	56	0	930	0	ZNF227	19	44739499	Frame_Shift_Del	DEL	T	TCGA-DW-7838-01A-11D-2136-08	881017	44739499	14389484	110	8655											
FUT2	2524	hgsc.bcm.edu;broad.mit.edu	37	chr19	49206557	49206557	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcaccctgccggtgctgcAcagcgccacggccagcagga	9	4	12	16	3	1	0	1	0	0	0	1	1	1	1	4	3	5	3	4	3	1	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:49206557A>C	ENST00000425340.2	+	2	461	c.344A>C	c.(343-345)cAc>cCc	p.H115P	FUT2_ENST00000391876.4_Missense_Mutation_p.H115P	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	115					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		CCGGTGCTGCACAGCGCCACG	0.652																																					p.H115P		.											.	FUT2-90	0			c.A344C						.						24	25	25					19																	49206557		2202	4293	6495	SO:0001583	missense	2524	exon2			TGCTGCACAGCGC		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"Fucosyltransferases"	4013	protein-coding gene	gene with protein product	"alpha (1,2) fucosyltransferase", "galactoside 2-alpha-L-fucosyltransferase 2", "GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2", "alpha(1,2)FT2", "secretor factor", "secretor blood group alpha-2-fucosyltransferase"	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.344A>C	19.37:g.49206557A>C	ENSP00000387498:p.His115Pro	Somatic	106	1		WXS	Illumina HiSeq	Phase_I	84	6	NM_001097638	0	0	0	0	0	Q0VAG5|Q14338|Q5D0G2	Missense_Mutation	SNP	ENST00000425340.2	37	CCDS33069.1	.	.	.	.	.	.	.	.	.	.	A	7.979	0.750695	0.15778	.	.	ENSG00000176920	ENST00000522966;ENST00000425340;ENST00000391876	D;D;D	0.96522	-4.04;-4.04;-4.04	4.77	-2.42	0.06542	.	.	.	.	.	D	0.96346	0.8808	M	0.74881	2.28	0.09310	N	1	D	0.63046	0.992	P	0.61800	0.894	D	0.90292	0.4323	9	0.26408	T	0.33	.	6.7207	0.23328	0.3886:0.4411:0.1703:0.0	.	115	Q10981	FUT2_HUMAN	P	115	ENSP00000430227:H115P;ENSP00000387498:H115P;ENSP00000375748:H115P	ENSP00000375748:H115P	H	+	2	0	FUT2	53898369	0.000000	0.05858	0.004000	0.12327	0.053000	0.15095	-0.018000	0.12568	-0.254000	0.09500	-0.504000	0.04507	CAC	.		0.652	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511		C	49206557	A	C	49206557	3	2	96	1	0	0	0	0	1	0	0	0	6123	159	6	5	346	5	FUT2	19	49206557	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	4467058	49206557	9922426	111	8656											
ZNF473	25888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50550199	50550199	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccatctcaaccagcacctGagagttcacacccaggagac	12	5	8	16	0	2	2	2	1	1	2	3	4	2	2	4	1	2	2	4	1	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:50550199G>T	ENST00000595661.1	+	6	2994	c.2499G>T	c.(2497-2499)ctG>ctT	p.L833L	CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000601364.1_Intron|ZNF473_ENST00000445728.3_Silent_p.L821L|ZNF473_ENST00000391821.2_Silent_p.L833L|ZNF473_ENST00000270617.3_Silent_p.L833L|CTD-2126E3.3_ENST00000599914.1_RNA			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	833					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		ACCAGCACCTGAGAGTTCACA	0.517											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L833L		.											.	ZNF473-91	0			c.G2499T						.						68	71	70					19																	50550199		2203	4300	6503	SO:0001819	synonymous_variant	25888	exon5			GCACCTGAGAGTT	AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.2499G>T	19.37:g.50550199G>T		Somatic	77	0	970	WXS	Illumina HiSeq	Phase_I	79	18	NM_015428	0	0	1	1	0	A8K8T7|Q9ULS9|Q9Y4Q7	Silent	SNP	ENST00000595661.1	37	CCDS33077.1																																																																																			.		0.517	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		T	50550199	G	T	50550199	2	4	96	1	0	0	0	0	0	0	0	1	17963	1277	45	4		4	ZNF473	19	50550199	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	1343642	50550199	8578784	112	8657											
SIGLEC12	89858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52004707	52004707	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgggtccccaaggaggTggaatcggtcccgagtctcc	6	9	14	12	2	2	0	0	0	2	0	6	3	4	2	4	5	0	0	4	5	2	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:52004707T>A	ENST00000291707.3	-	1	336	c.281A>T	c.(280-282)cAc>cTc	p.H94L	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	94	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CCCAAGGAGGTGGAATCGGTC	0.552																																					p.H94L		.											.	SIGLEC12-96	0			c.A281T						.						164	144	151					19																	52004707		2203	4300	6503	SO:0001583	missense	89858	exon1			AGGAGGTGGAATC	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15482	protein-coding gene	gene with protein product		606094	"SIGLEC-like 1", "sialic acid binding Ig-like lectin 12"	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.281A>T	19.37:g.52004707T>A	ENSP00000291707:p.His94Leu	Somatic	275	1		WXS	Illumina HiSeq	Phase_I	243	30	NM_053003	0	0	22	22	0	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	.	.	.	.	.	.	.	.	.	.	.	5.108	0.205613	0.09704	.	.	ENSG00000254521	ENST00000291707	T	0.65178	-0.14	2.42	-1.97	0.07503	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.48714	0.1515	L	0.54323	1.7	0.09310	N	1	B	0.23540	0.087	B	0.17098	0.017	T	0.39272	-0.9622	9	0.56958	D	0.05	.	2.2193	0.03968	0.4626:0.1603:0.0:0.3772	.	94	Q96PQ1	SIG12_HUMAN	L	94	ENSP00000291707:H94L	ENSP00000291707:H94L	H	-	2	0	SIGLEC12	56696519	0.000000	0.05858	0.002000	0.10522	0.333000	0.28666	-1.760000	0.01806	-1.003000	0.03425	0.325000	0.21440	CAC	.		0.552	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		A	52004707	T	A	52004707	3	1	96	1	0	0	0	0	1	0	0	0	14340	1696	59	5	1611	5	SIGLEC12	19	52004707	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	1454508	52004707	7124276	113	8658											
ZNF28	7576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53303801	53303801	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtaaggcttctctccagtgtGaattatactatgttttgcca	9	16	8	8	0	1	1	0	1	1	0	3	1	2	1	2	1	2	3	2	1	5	7			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:53303801G>C	ENST00000457749.2	-	4	1416	c.1297C>G	c.(1297-1299)Cac>Gac	p.H433D	ZNF28_ENST00000414252.2_Missense_Mutation_p.H380D|ZNF28_ENST00000438150.2_Missense_Mutation_p.H380D|ZNF28_ENST00000360272.4_Missense_Mutation_p.H380D	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H380Y(2)|p.H433Y(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TCTCCAGTGTGAATTATACTA	0.373																																					p.H433D		.											.	ZNF28-91	3	Substitution - Missense(3)	breast(3)	c.C1297G						.						113	120	118					19																	53303801		2203	4300	6503	SO:0001583	missense	7576	exon4			CAGTGTGAATTAT	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"Zinc fingers, C2H2-type", "-"	13073	protein-coding gene	gene with protein product			"zinc finger protein 28 (KOX 24)"				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1297C>G	19.37:g.53303801G>C	ENSP00000397693:p.His433Asp	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	200	30	NM_006969	0	0	2	3	1	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	14.52	2.559448	0.45590	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28	1.74	0.624	0.17659	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84433	0.5471	H	0.96460	3.825	0.27520	N	0.951416	D	0.63880	0.993	D	0.79784	0.993	T	0.73257	-0.4040	9	0.87932	D	0	.	6.9561	0.24572	0.1616:0.0:0.8384:0.0	.	433	P17035	ZNF28_HUMAN	D	380;433;380;380;380	ENSP00000412143:H380D;ENSP00000397693:H433D;ENSP00000353410:H380D;ENSP00000444965:H380D;ENSP00000375661:H380D	ENSP00000353410:H380D	H	-	1	0	ZNF28	57995613	1.000000	0.71417	0.003000	0.11579	0.128000	0.20619	4.471000	0.60182	0.072000	0.16694	0.186000	0.17326	CAC	.		0.373	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		C	53303801	G	C	53303801	3	2	96	1	0	0	0	0	1	0	0	0	17845	1290	45	4	863	4	ZNF28	19	53303801	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	1299094	53303801	5825182	114	8659											
ZNF761	388561	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	53958007	53958007	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacatgaaagtcatcacaaTggagatttttgctaccagga	15	11	8	7	0	2	2	2	1	0	1	2	4	2	3	1	2	3	1	1	2	4	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:53958007T>G	ENST00000454407.1	+	0	699							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GTCATCACAATGGAGATTTTT	0.398																																					p.N82K		.											.	ZNF761-91	0			c.T246G						.						89	86	87					19																	53958007		2203	4300	6503			388561	exon7			TCACAATGGAGAT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958007T>G		Somatic	111	1		WXS	Illumina HiSeq	Phase_I	100	9	NM_001008401	0	0	0	2	2	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				.		0.398	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		G	53958007	T	G	53958007	1	3	96	0	1	0	0	0	0	0	0	0	18168	1461	51	5		5	ZNF761	19	53958007	RNA	SNP	T	TCGA-DW-7838-01A-11D-2136-08	654206	53958007	5170976	115	8660											
FCAR	2204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55401195	55401196	+	Missense_Mutation	DNP	TG	TG	GT																															acagatgtgtcagccaggatTgacctttgcacgaacaccaa																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:55401195_55401196TG>GT	ENST00000355524.3	+	5	840_841	c.830_831TG>GT	c.(829-831)tTG>tGT	p.L277C	FCAR_ENST00000391725.3_Missense_Mutation_p.L255C|FCAR_ENST00000353758.4_Missense_Mutation_p.L168C|FCAR_ENST00000391726.3_Missense_Mutation_p.L169C|FCAR_ENST00000391724.3_Missense_Mutation_p.L243C|FCAR_ENST00000359272.4_Missense_Mutation_p.L265C|FCAR_ENST00000482092.2_3'UTR|CTB-61M7.2_ENST00000594721.1_lincRNA|FCAR_ENST00000391723.3_3'UTR|FCAR_ENST00000345937.4_Missense_Mutation_p.L181C	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	277					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		CAGCCAGGATTGACCTTTGCAC	0.525																																					p.L277C		.											.	FCAR	0			c.G831T						.																																			SO:0001583	missense	2204	exon5			AGGATTGACCTTT	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	Exception_encountered	19.37:g.55401195_55401196delinsGT	ENSP00000347714:p.Leu277Cys	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	228	36		0	0	0	0	0	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	DNP	ENST00000355524.3	37	CCDS12907.1																																																																																			.		0.525	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		GT	55401196	TG	GT	55401195	3	3	96	1	0	0	0	0	1	0	0	0	5792	1821	63	5	919	5	FCAR	19	55401195	Missense_Mutation	DNP	TG	TCGA-DW-7838-01A-11D-2136-08	1443188	55401195	3727788	116	8661											
WFDC12	128488	broad.mit.edu;bcgsc.ca	37	chr20	43752864	43752864	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggggaggatcggacttgaagCagcgtacgttgtcagctggg	8	8	18	7	3	1	1	1	1	0	0	2	4	1	4	0	5	4	4	0	5	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr20:43752864C>T	ENST00000372785.3	-	2	139	c.122G>A	c.(121-123)tGc>tAc	p.C41Y		NM_080869.1	NP_543145.1	Q8WWY7	WFD12_HUMAN	WAP four-disulfide core domain 12	41	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				defense response to bacterium (GO:0042742)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(2)|lung(2)|skin(1)	6		Myeloproliferative disorder(115;0.0122)				GGACTTGAAGCAGCGTACGTT	0.547																																					p.C41Y													.	WFDC12-90	0			c.G122A						.						119	96	104					20																	43752864		2203	4300	6503	SO:0001583	missense	128488	exon2			TTGAAGCAGCGTA	Z93016	CCDS13343.1	20q13.12	2013-01-21	2003-02-21	2003-02-21	ENSG00000168703	ENSG00000168703		"WAP four-disulfide core domain containing"	16115	protein-coding gene	gene with protein product		609872	"chromosome 20 open reading frame 122"	C20orf122		11779191, 12206714	Standard	NM_080869		Approved	dJ211D12.4, WAP2	uc002xnf.1	Q8WWY7	OTTHUMG00000046412	ENST00000372785.3:c.122G>A	20.37:g.43752864C>T	ENSP00000361871:p.Cys41Tyr	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	126	7	NM_080869	0	0	10	13	3	Q5H980|Q9BR31	Missense_Mutation	SNP	ENST00000372785.3	37	CCDS13343.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065496	0.36470	.	.	ENSG00000168703	ENST00000372785	T	0.80214	-1.35	3.46	2.48	0.30137	Whey acidic protein, 4-disulphide core (5);	.	.	.	.	D	0.92335	0.7568	H	0.98111	4.15	0.09310	N	1	D	0.89917	1.0	D	0.74674	0.984	T	0.83064	-0.0146	9	0.87932	D	0	-3.5146	8.5723	0.33576	0.0:0.7615:0.2385:0.0	.	41	Q8WWY7	WFD12_HUMAN	Y	41	ENSP00000361871:C41Y	ENSP00000361871:C41Y	C	-	2	0	WFDC12	43186278	0.197000	0.23362	0.003000	0.11579	0.043000	0.13939	0.984000	0.29565	0.405000	0.25532	0.557000	0.71058	TGC	.		0.547	WFDC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000107194.1			T	43752864	C	T	43752864	3	4	96	1	0	0	0	0	1	0	0	0	17383	710	25	2	221	2	WFDC12	20	43752864	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		43752864	19272656	117	8662											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60887506	60887506	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgtcgtgttcagccgctTgaggtccacatacttgccca	6	11	10	14	2	1	1	1	1	0	0	3	1	2	1	4	1	3	2	4	1	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr20:60887506T>G	ENST00000252999.3	-	68	9376	c.9310A>C	c.(9310-9312)Aag>Cag	p.K3104Q		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3104	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TTCAGCCGCTTGAGGTCCACA	0.682																																					p.K3104Q		.											.	LAMA5-93	0			c.A9310C						.						43	39	40					20																	60887506		2190	4296	6486	SO:0001583	missense	3911	exon68			GCCGCTTGAGGTC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9310A>C	20.37:g.60887506T>G	ENSP00000252999:p.Lys3104Gln	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_005560	0	0	71	71	0	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	22.3	4.275756	0.80580	.	.	ENSG00000130702	ENST00000252999	T	0.41400	1.0	4.26	4.26	0.50523	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.052784	0.64402	D	0.000001	T	0.53318	0.1789	M	0.64997	1.995	0.80722	D	1	D	0.69078	0.997	P	0.58520	0.84	T	0.50346	-0.8839	10	0.23891	T	0.37	.	13.1986	0.59754	0.0:0.0:0.0:1.0	.	3104	O15230	LAMA5_HUMAN	Q	3104	ENSP00000252999:K3104Q	ENSP00000252999:K3104Q	K	-	1	0	LAMA5	60320901	0.989000	0.36119	0.997000	0.53966	0.953000	0.61014	1.425000	0.34859	1.794000	0.52575	0.454000	0.30748	AAG	.		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		G	60887506	T	G	60887506	3	3	96	1	0	0	0	0	1	0	0	0	8630	1821	63	5	1829	5	LAMA5	20	60887506	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	17134642	60887506	2138014	118	8663											
SLC2A4RG	56731	hgsc.bcm.edu;broad.mit.edu	37	chr20	62374341	62374341	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgccagcggttcctggacTaagtccggctcgttcaagaa	8	9	11	13	3	1	1	1	0	0	1	4	2	3	2	4	3	2	3	4	3	3	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr20:62374341T>C	ENST00000266077.2	+	8	1214	c.1162T>C	c.(1162-1164)Taa>Caa	p.*388Q	SLC2A4RG_ENST00000493772.1_3'UTR|RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GTTCCTGGACTAAGTCCGGCT	0.652																																					p.X388Q		.											.	SLC2A4RG-90	0			c.T1162C						.						25	34	31					20																	62374341		2200	4300	6500	SO:0001578	stop_lost	56731	exon8			CTGGACTAAGTCC	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"GLUT4 enhancer factor", "Huntington's disease gene regulatory region-binding protein 1"	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.1162T>C	20.37:g.62374341T>C	ENSP00000266077:p.*388Glnext*69	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	23	6	NM_020062	0	0	41	67	26	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Missense_Mutation	SNP	ENST00000266077.2	37	CCDS13537.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.238393	0.39598	.	.	ENSG00000125520	ENST00000266077	.	.	.	4.17	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0424	0.53460	0.0:0.0:0.0:1.0	.	.	.	.	Q	388	.	.	X	+	1	0	SLC2A4RG	61844785	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	4.553000	0.60753	1.525000	0.49052	0.260000	0.18958	TAA	.		0.652	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062		C	62374341	T	C	62374341	4	2	96	1	0	0	0	0	0	0	0	0	14579	1535	53	3	1192	3	SLC2A4RG	20	62374341	Nonstop_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	1486835	62374341	651179	119	8664											
POLA1	5422	hgsc.bcm.edu	37	chrX	24906193	24906193	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccccttcaattctcccgaaCtgggcctctttgcccagcct	5	12	6	18	1	3	0	1	0	2	0	5	1	4	0	6	1	3	0	6	1	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:24906193C>G	ENST00000379059.3	+	35	4115	c.4100C>G	c.(4099-4101)aCt>aGt	p.T1367S	POLA1_ENST00000379068.3_Missense_Mutation_p.T1373S	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1367	DNA-binding region. {ECO:0000255}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	TTCTCCCGAACTGGGCCTCTT	0.493																																					p.T1367S		.											.	POLA1-229	0			c.C4100G						.						130	102	112					X																	24906193		2203	4300	6503	SO:0001583	missense	5422	exon35			CCCGAACTGGGCC		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.4100C>G	X.37:g.24906193C>G	ENSP00000368349:p.Thr1367Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_016937	0	0	6	6	0	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	3.682	-0.065364	0.07273	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.16597	2.33;2.33	5.58	0.599	0.17519	Zinc finger, DNA-directed DNA polymerase, family B, alpha (1);	0.491223	0.22316	N	0.061661	T	0.04679	0.0127	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.41928	-0.9481	10	0.09338	T	0.73	-4.7704	5.5775	0.17231	0.4882:0.1503:0.3615:0.0	.	1367	P09884	DPOLA_HUMAN	S	1373;1367	ENSP00000368358:T1373S;ENSP00000368349:T1367S	ENSP00000368349:T1367S	T	+	2	0	POLA1	24816114	0.966000	0.33281	0.851000	0.33527	0.481000	0.33189	1.521000	0.35910	-0.000000	0.14550	-1.090000	0.02178	ACT	.		0.493	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		G	24906193	C	G	24906193	3	3	96	1	0	0	0	0	1	0	0	0	12213	565	20	4	4238	4	POLA1	23	24906193	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		24906193	130364367	120	8665											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41200810	41200810	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatagcagttttggatctcgTagtgattcaagagggaagtc	11	13	12	5	1	2	2	1	1	1	1	4	4	2	4	0	2	1	3	0	2	5	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:41200810T>C	ENST00000399959.2	+	4	1080	c.225T>C	c.(223-225)cgT>cgC	p.R75R	DDX3X_ENST00000457138.2_Silent_p.R59R|DDX3X_ENST00000441189.2_Silent_p.R75R|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000542215.1_Silent_p.R119R	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	75	Interaction with EIF4E.|Required for TBK1 and IKBKE-dependent IFN-beta activation.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						TTGGATCTCGTAGTGATTCAA	0.383										HNSCC(61;0.18)																											p.R75R		.											.	DDX3X-715	0			c.T225C						.						130	127	128					X																	41200810		2169	4284	6453	SO:0001819	synonymous_variant	1654	exon4			ATCTCGTAGTGAT	U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"DEAD-boxes"	2745	protein-coding gene	gene with protein product		300160	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.225T>C	X.37:g.41200810T>C		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_001193416	0	0	86	86	0	A8K538|B4E3E8|O15536	Silent	SNP	ENST00000399959.2	37	CCDS43931.1																																																																																			.		0.383	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		C	41200810	T	C	41200810	2	2	96	1	0	0	0	0	0	0	0	1	4364	1625	57	3		3	DDX3X	23	41200810	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	16294617	41200810	114069750	121	8666											
ZXDB	158586	hgsc.bcm.edu;broad.mit.edu	37	chrX	57619097	57619097	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgctcctgcccagcagcccGggtgtctgatcgccccgcaa	5	6	11	19	4	1	1	0	1	1	0	3	1	2	1	6	1	3	3	6	1	1	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:57619097G>A	ENST00000374888.1	+	1	829	c.616G>A	c.(616-618)Ggg>Agg	p.G206R		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.G206R(2)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						CCAGCAGCCCGGGTGTCTGAT	0.711																																					p.G206R		.											.	ZXDB-130	2	Substitution - Missense(2)	lung(1)|prostate(1)	c.G616A						.						12	14	13					X																	57619097		2186	4257	6443	SO:0001583	missense	158586	exon1			CAGCCCGGGTGTC	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.616G>A	X.37:g.57619097G>A	ENSP00000364023:p.Gly206Arg	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_007157	0	0	1	2	1	A8K151|Q9UBB3	Missense_Mutation	SNP	ENST00000374888.1	37	CCDS35313.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.654782	0.00108	.	.	ENSG00000198455	ENST00000374888	T	0.11063	2.81	2.65	1.78	0.24846	.	0.160870	0.29602	N	0.011697	T	0.04452	0.0122	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41787	-0.9489	10	0.15952	T	0.53	.	4.3042	0.10938	0.3435:0.0:0.6565:0.0	.	206	P98169	ZXDB_HUMAN	R	206	ENSP00000364023:G206R	ENSP00000364023:G206R	G	+	1	0	ZXDB	57635822	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-0.287000	0.08388	0.520000	0.28426	0.556000	0.70494	GGG	.		0.711	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		A	57619097	G	A	57619097	3	1	96	1	0	0	0	0	1	0	0	0	18283	1116	39	1	618	1	ZXDB	23	57619097	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	16418287	57619097	97651463	122	8667											
KIF4A	24137	broad.mit.edu	37	chrX	69595071	69595071	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taggttgagtgagcgccgccGcaaacgtctccaggagctgg	8	7	15	11	4	1	2	0	2	1	0	2	3	1	3	3	3	3	3	3	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:69595071G>A	ENST00000374403.3	+	17	1878	c.1796G>A	c.(1795-1797)cGc>cAc	p.R599H	KIF4A_ENST00000374388.3_Missense_Mutation_p.R599H	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	599					anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						GAGCGCCGCCGCAAACGTCTC	0.468																																					p.R599H													.	KIF4A-134	0			c.G1796A						.						67	58	61					X																	69595071		2203	4300	6503	SO:0001583	missense	24137	exon17			GCCGCCGCAAACG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1796G>A	X.37:g.69595071G>A	ENSP00000363524:p.Arg599His	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_012310	0	0	0	0	0	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.716466	0.68844	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.70869	2.3;-0.52	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000035	T	0.76292	0.3967	M	0.83483	2.645	0.80722	D	1	B;B	0.28713	0.143;0.22	B;B	0.33254	0.038;0.16	T	0.76394	-0.2975	10	0.52906	T	0.07	.	17.3242	0.87243	0.0:0.0:1.0:0.0	.	599;599	O95239;O95239-2	KIF4A_HUMAN;.	H	599	ENSP00000363509:R599H;ENSP00000363524:R599H	ENSP00000363509:R599H	R	+	2	0	KIF4A	69511796	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.912000	0.92726	2.562000	0.86427	0.600000	0.82982	CGC	.		0.468	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		A	69595071	G	A	69595071	3	1	96	1	0	0	0	0	1	0	0	0	8324	1087	38	1	1858	1	KIF4A	23	69595071	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	11975974	69595071	85675489	123	8668											
PAK3	5063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	110366494	110366494	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcgctctatcttcccaggaGgaggggataaaagtaaagta	13	10	11	7	1	2	0	0	0	2	0	4	3	3	3	1	4	0	3	1	4	6	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:110366494G>A	ENST00000372010.1	+	5	605	c.163G>A	c.(163-165)Gga>Aga	p.G55R	PAK3_ENST00000518291.1_Missense_Mutation_p.G55R|PAK3_ENST00000519681.1_Missense_Mutation_p.G55R|PAK3_ENST00000417227.1_Missense_Mutation_p.G55R|PAK3_ENST00000446737.1_Missense_Mutation_p.G55R|PAK3_ENST00000425146.1_Missense_Mutation_p.G55R|PAK3_ENST00000372007.5_Missense_Mutation_p.G55R|PAK3_ENST00000360648.4_Missense_Mutation_p.G55R|PAK3_ENST00000262836.4_Missense_Mutation_p.G55R			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	55					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTTCCCAGGAGGAGGGGATAA	0.448										TSP Lung(19;0.15)																											p.G55R		.											.	PAK3-1043	0			c.G163A						.						70	69	70					X																	110366494		2203	4300	6503	SO:0001583	missense	5063	exon3			CCAGGAGGAGGGG	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.163G>A	X.37:g.110366494G>A	ENSP00000361080:p.Gly55Arg	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	47	15	NM_001128166	0	0	0	1	1	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	37	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.257186	0.59321	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000429193;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.71461	-0.55;-0.55;-0.57;-0.56;-0.55;-0.54;-0.54;-0.56;-0.57	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.68284	0.2984	L	0.29908	0.895	0.80722	D	1	P;P;B;B	0.43607	0.801;0.812;0.399;0.037	P;P;B;B	0.48454	0.578;0.578;0.194;0.049	T	0.64322	-0.6435	10	0.22706	T	0.39	.	18.4314	0.90627	0.0:0.0:1.0:0.0	.	55;55;55;55	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	R	55	ENSP00000410853:G55R;ENSP00000401982:G55R;ENSP00000361080:G55R;ENSP00000429113:G55R;ENSP00000361077:G55R;ENSP00000428921:G55R;ENSP00000353864:G55R;ENSP00000389172:G55R;ENSP00000262836:G55R	ENSP00000262836:G55R	G	+	1	0	PAK3	110253150	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.143000	0.94623	2.380000	0.81148	0.600000	0.82982	GGA	.		0.448	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		A	110366494	G	A	110366494	3	1	96	1	0	0	0	0	1	0	0	0	11428	1001	35	2	165	2	PAK3	23	110366494	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	40771423	110366494	44904066	124	8669											
COL11A1	1301	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	103400626	103400626	+	Frame_Shift_Del	DEL	G	G	-																															gaatactcacagcaattccaGgggcaccaactggtccttga																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:103400626delG	ENST00000370096.3	-	45	3794	c.3482delC	c.(3481-3483)cctfs	p.P1161fs	COL11A1_ENST00000353414.4_Frame_Shift_Del_p.P1122fs|COL11A1_ENST00000512756.1_Frame_Shift_Del_p.P1045fs|COL11A1_ENST00000358392.2_Frame_Shift_Del_p.P1173fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1161	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AGCAATTCCAGGGGCACCAAC	0.448																																					p.P1173fs		.											.	COL11A1-586	0			c.3518delC						.						37	39	38					1																	103400626		2203	4300	6503	SO:0001589	frameshift_variant	1301	exon45			.	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"Collagens"	2186	protein-coding gene	gene with protein product	"collagen XI, alpha-1 polypeptide"	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3482delC	1.37:g.103400626delG	ENSP00000359114:p.Pro1161fs	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	48	18	NM_080629	0	0	0	0	0	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Del	DEL	ENST00000370096.3	37	CCDS778.1																																																																																			.		0.448	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		-	103400626	G	-	103400626	7	5	97	1	0	1	0	1	0	0	0	0	3673	1000	35	0	2030	0	COL11A1	1	103400626	Frame_Shift_Del	DEL	G	TCGA-DW-7839-01A-11D-2136-08		103400626	145849995	1	8670											
CR1L	1379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207818592	207818592	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgctcatggcgcctcccgTccgtctcgagcgtccctttc	2	10	10	19	6	2	0	1	0	1	0	7	1	5	0	5	1	1	1	5	1	0	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:207818592T>G	ENST00000508064.2	+	1	74	c.14T>G	c.(13-15)gTc>gGc	p.V5G		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	5						cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCGCCTCCCGTCCGTCTCGAG	0.657																																					p.V5G		.											.	CR1L-46	0			c.T14G						.						62	68	66					1																	207818592		2203	4300	6503	SO:0001583	missense	1379	exon1			CTCCCGTCCGTCT	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.14T>G	1.37:g.207818592T>G	ENSP00000421736:p.Val5Gly	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	117	59	NM_175710	0	0	0	0	0	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	.	.	.	.	.	.	.	.	.	.	T	10.27	1.304420	0.23736	.	.	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.32023	1.47	2.95	-5.9	0.02275	.	.	.	.	.	T	0.04952	0.0133	N	0.00436	-1.5	0.09310	N	1	P	0.41475	0.751	B	0.36989	0.238	T	0.23404	-1.0189	9	0.16420	T	0.52	.	0.9185	0.01310	0.2027:0.1365:0.2268:0.434	.	5	Q2VPA4	CR1L_HUMAN	G	5	ENSP00000421736:V5G	ENSP00000437875:V5G	V	+	2	0	CR1L	205885215	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.381000	0.01065	-1.286000	0.02384	-1.304000	0.01323	GTC	.		0.657	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		G	207818592	T	G	207818592	3	3	97	1	0	0	0	0	1	0	0	0	3847	1667	58	5	16	5	CR1L	1	207818592	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	104417966	207818592	41432029	2	8671											
ATF3	467	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	212791490	212791490	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagcccctgaagaagatgaaAggaaaaagaggcgacgagaa	19	3	13	6	2	0	6	0	2	0	4	0	9	0	7	2	2	1	0	2	2	7	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:212791490A>G	ENST00000341491.4	+	3	527	c.262A>G	c.(262-264)Agg>Ggg	p.R88G	ATF3_ENST00000336937.4_Missense_Mutation_p.R59G|ATF3_ENST00000366985.1_Missense_Mutation_p.R31G|ATF3_ENST00000366987.2_Missense_Mutation_p.R88G|RN7SL512P_ENST00000578962.1_RNA|ATF3_ENST00000492118.1_Intron|ATF3_ENST00000366983.1_Missense_Mutation_p.R88G	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	88	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|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 transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	AGAAGATGAAAGGAAAAAGAG	0.438																																					p.R88G		.											.	ATF3-658	0			c.A262G						.						119	119	119					1																	212791490		2203	4300	6503	SO:0001583	missense	467	exon3			GATGAAAGGAAAA	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"basic leucine zipper proteins"	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.262A>G	1.37:g.212791490A>G	ENSP00000344352:p.Arg88Gly	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	90	47	NM_001674	0	0	5	7	2	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Missense_Mutation	SNP	ENST00000341491.4	37	CCDS1506.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.459129	0.63401	.	.	ENSG00000162772	ENST00000366981;ENST00000366987;ENST00000341491;ENST00000366985;ENST00000366983;ENST00000336937	T;T;T;T;T;T	0.64260	0.47;0.47;0.47;0.47;-0.09;-0.09	5.51	4.37	0.52481	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.083039	0.85682	D	0.000000	T	0.78394	0.4276	.	.	.	0.58432	D	0.999996	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.998;0.998;0.995	T	0.80289	-0.1445	9	0.87932	D	0	-15.5255	11.4427	0.50107	0.7123:0.2877:0.0:0.0	.	88;88;88	Q7Z567;Q8WYM6;P18847	.;.;ATF3_HUMAN	G	88;88;88;31;88;59	ENSP00000355948:R88G;ENSP00000355954:R88G;ENSP00000344352:R88G;ENSP00000355952:R31G;ENSP00000355950:R88G;ENSP00000336908:R59G	ENSP00000336908:R59G	R	+	1	2	ATF3	210858113	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	1.306000	0.33505	1.002000	0.39104	-0.435000	0.05868	AGG	.		0.438	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674		G	212791490	A	G	212791490	3	3	97	1	0	0	0	0	1	0	0	0	1082	63	3	3	268	3	ATF3	1	212791490	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	4972898	212791490	36459131	3	8672											
C1orf35	79169	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	228290925	228290925	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcctccacgactggagccgaAcatggcgccgggaaggcagt	9	4	15	13	4	0	0	0	0	0	0	1	4	1	2	4	4	2	1	4	4	2	0			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:228290925A>C	ENST00000272139.4	-	1	238	c.4T>G	c.(4-6)Ttc>Gtc	p.F2V	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	2							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CTGGAGCCGAACATGGCGCCG	0.682																																					p.F2V		.											.	C1orf35-90	0			c.T4G						.						30	31	31					1																	228290925		2201	4299	6500	SO:0001583	missense	79169	exon1			AGCCGAACATGGC	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"multiple myeloma tumor-associated protein 2"					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.4T>G	1.37:g.228290925A>C	ENSP00000272139:p.Phe2Val	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	48	28	NM_024319	0	0	7	17	10	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Missense_Mutation	SNP	ENST00000272139.4	37	CCDS1566.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.510193	0.64522	.	.	ENSG00000143793	ENST00000272139	.	.	.	3.88	2.74	0.32292	.	0.000000	0.85682	D	0.000000	T	0.61009	0.2313	M	0.62723	1.935	0.53005	D	0.999965	D	0.58268	0.982	P	0.52554	0.702	T	0.61207	-0.7109	9	0.66056	D	0.02	-15.7163	8.1877	0.31348	0.8997:0.0:0.1003:0.0	.	2	Q9BU76	MMTA2_HUMAN	V	2	.	ENSP00000272139:F2V	F	-	1	0	C1orf35	226357548	1.000000	0.71417	0.996000	0.52242	0.219000	0.24729	6.640000	0.74319	0.548000	0.28955	0.254000	0.18369	TTC	.		0.682	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319		C	228290925	A	C	228290925	3	2	97	1	0	0	0	0	1	0	0	0	2044	43	2	5	819	5	C1orf35	1	228290925	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	15499435	228290925	20959696	4	8673											
ALMS1	7840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	73827935	73827935	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttggtcagaagaaaaacgTgaagagaaaatgctctttac	16	10	9	6	1	3	4	1	1	2	3	3	5	3	4	0	1	3	1	0	1	7	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr2:73827935T>C	ENST00000264448.6	+	18	11907	c.11796T>C	c.(11794-11796)cgT>cgC	p.R3932R	ALMS1_ENST00000409009.1_Silent_p.R3890R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3932					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AAGAAAAACGTGAAGAGAAAA	0.408																																					p.R3932R		.											.	ALMS1-142	0			c.T11796C						.						91	92	91					2																	73827935		2203	4300	6503	SO:0001819	synonymous_variant	7840	exon18			AAAACGTGAAGAG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.11796T>C	2.37:g.73827935T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	51	28	NM_015120	0	0	20	44	24	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			.		0.408	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73827935	T	C	73827935	2	2	97	1	0	0	0	0	0	0	0	1	535	1683	59	3		3	ALMS1	2	73827935	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08		73827935	169371438	5	8674											
SPAG16	79582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	214161997	214161997	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatctagataccagatgaCaattttagcatcccagaagg	14	10	9	8	0	1	5	0	2	1	3	2	5	2	5	2	1	2	1	2	1	5	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr2:214161997C>G	ENST00000331683.5	+	3	290	c.195C>G	c.(193-195)gaC>gaG	p.D65E	SPAG16_ENST00000432529.2_Missense_Mutation_p.D65E|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000413312.1_Missense_Mutation_p.D34E|SPAG16_ENST00000374309.3_Missense_Mutation_p.T11R|SPAG16_ENST00000272898.7_Missense_Mutation_p.D65E|SPAG16_ENST00000447990.1_Missense_Mutation_p.D65E	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	65					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TACCAGATGACAATTTTAGCA	0.358																																					p.D65E		.											.	SPAG16-188	0			c.C195G						.						79	82	81					2																	214161997		2203	4300	6503	SO:0001583	missense	79582	exon3			AGATGACAATTTT	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"WD repeat domain containing"	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.195C>G	2.37:g.214161997C>G	ENSP00000332592:p.Asp65Glu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	99	36	NM_024532	0	0	0	0	0	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.42|12.42	1.932017|1.932017	0.34096|0.34096	.|.	.|.	ENSG00000144451|ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000413312;ENST00000272898;ENST00000447990|ENST00000374309	T|T	0.57752|0.58210	0.38|0.35	5.7|5.7	1.2|1.2	0.21068|0.21068	.|.	0.071260|.	0.51477|.	D|.	0.000088|.	T|T	0.40322|0.40322	0.1112|0.1112	L|L	0.41632|0.41632	1.29|1.29	0.23309|0.23309	N|N	0.997933|0.997933	P;P;B;P;B|B;B	0.43287|0.12013	0.75;0.802;0.036;0.734;0.06|0.001;0.005	B;B;B;B;B|B;B	0.43478|0.17433	0.168;0.137;0.014;0.421;0.082|0.002;0.018	T|T	0.37709|0.37709	-0.9694|-0.9694	10|9	0.52906|0.87932	T|D	0.07|0	.|.	5.0287|5.0287	0.14398|0.14398	0.0:0.4882:0.1541:0.3577|0.0:0.4882:0.1541:0.3577	.|.	34;5;65;65;65|11;2	Q8N0X2-3;Q4G1A2;Q8N0X2;E7EWV3;Q8N0X2-4|B4DYB5;Q8N0X2-2	.;.;SPG16_HUMAN;.;.|.;.	E|R	65;65;34;65;65|11	ENSP00000332592:D65E|ENSP00000363428:T11R	ENSP00000272898:D65E|ENSP00000363428:T11R	D|T	+|+	3|2	2|0	SPAG16|SPAG16	213870242|213870242	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.625000|0.625000	0.37756|0.37756	0.625000|0.625000	0.24477|0.24477	0.022000|0.022000	0.15160|0.15160	-1.151000|-1.151000	0.01829|0.01829	GAC|ACA	.		0.358	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		G	214161997	C	G	214161997	3	3	97	1	0	0	0	0	1	0	0	0	15010	477	17	4	205	4	SPAG16	2	214161997	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	140334062	214161997	29037376	6	8675											
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73673578	73673578	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccactggccgcgcgtcgcaGgcgtcgcgcatgtgcgcctc	3	6	14	18	8	0	0	0	0	0	0	3	0	0	0	3	2	1	2	3	2	0	0	rs6763344	byFrequency	TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr3:73673578G>C	ENST00000263666.4	-	1	513	c.399C>G	c.(397-399)gcC>gcG	p.A133A	PDZRN3_ENST00000308537.4_Silent_p.A133A|PDZRN3-AS1_ENST00000478988.1_RNA|PDZRN3-AS1_ENST00000608304.1_RNA|PDZRN3-AS1_ENST00000608743.1_RNA	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	133					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GCGCGTCGCAGGCGTCGCGCA	0.776													C|||	4619	0.922324	0.9781	0.8977	5008	,	,		6325	0.9385		0.8757	False		,,,				2504	0.8957				p.A133A		.											.	PDZRN3-232	0			c.C399G						.						1	1	1					3																	73673578		356	609	965	SO:0001819	synonymous_variant	23024	exon1			GTCGCAGGCGTCG	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"RING-type (C3HC4) zinc fingers"	17704	protein-coding gene	gene with protein product	"likely ortholog of mouse semaF cytoplasmic domain associated protein 3"	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.399C>G	3.37:g.73673578G>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_015009	0	0	0	0	0	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			G|0.119;C|0.881		0.776	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		C	73673578	G	C	73673578	2	2	97	1	0	0	0	0	0	0	0	1	11735	987	35	4		4	PDZRN3	3	73673578	Silent	SNP	G	TCGA-DW-7839-01A-11D-2136-08		73673578	124348852	7	8676											
XRN1	54464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142141567	142141567	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcatctattatcctttcaAtatcatatttaaatgtgatc	14	18	2	7	0	4	1	3	1	1	0	6	1	5	1	1	0	0	0	1	0	8	7			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr3:142141567A>T	ENST00000264951.4	-	8	941	c.824T>A	c.(823-825)aTt>aAt	p.I275N	XRN1_ENST00000392981.2_Missense_Mutation_p.I275N|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000544157.1_Missense_Mutation_p.I65N|XRN1_ENST00000463916.1_Missense_Mutation_p.I275N	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	275					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TATCCTTTCAATATCATATTT	0.323																																					p.I275N		.											.	XRN1-93	0			c.T824A						.						70	77	75					3																	142141567		2202	4299	6501	SO:0001583	missense	54464	exon8			CTTTCAATATCAT	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.824T>A	3.37:g.142141567A>T	ENSP00000264951:p.Ile275Asn	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	66	28	NM_001042604	0	0	2	4	2	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.466391	0.84425	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000544157;ENST00000477237	T;T	0.34472	1.36;1.36	5.69	5.69	0.88448	.	0.163395	0.56097	D	0.000029	T	0.60301	0.2258	M	0.77103	2.36	0.54753	D	0.999985	D;P;D;D;P	0.56968	0.978;0.879;0.963;0.96;0.932	D;P;P;P;P	0.65323	0.934;0.754;0.615;0.782;0.492	T	0.63033	-0.6727	10	0.51188	T	0.08	-19.9739	15.9662	0.79974	1.0:0.0:0.0:0.0	.	65;275;136;275;275	B4E2K3;Q8IZH2-3;B3KW17;Q8IZH2-2;Q8IZH2	.;.;.;.;XRN1_HUMAN	N	275;275;275;65;136	ENSP00000264951:I275N;ENSP00000376707:I275N	ENSP00000264951:I275N	I	-	2	0	XRN1	143624257	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.930000	0.92872	2.171000	0.68590	0.528000	0.53228	ATT	.		0.323	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142141567	A	T	142141567	3	4	97	1	0	0	0	0	1	0	0	0	17492	101	4	5	4436	5	XRN1	3	142141567	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	68467989	142141567	55880863	8	8677											
ATP11B	23200	bcgsc.ca	37	chr3	182597406	182597429	+	In_Frame_Del	DEL	GCTGTCGTATGGCTCCACTGCAGA	GCTGTCGTATGGCTCCACTGCAGA	-																															aaattgttcagctgtattatGctgtcgtatggctccactgc																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	GCTGTCGTATGGCTCCACTGCAGA	GCTGTCGTATGGCTCCACTGCAGA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr3:182597406_182597429delGCTGTCGTATGGCTCCACTGCAGA	ENST00000323116.5	+	20	2635_2658	c.2375_2398delGCTGTCGTATGGCTCCACTGCAGA	c.(2374-2400)tgctgtcgtatggctccactgcagaaa>taa	p.792_800CCRMAPLQK>*		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	792					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.P797L(1)|p.P797R(1)|p.Q799H(1)		breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			GCTGTATTATGCTGTCGTATGGCTCCACTGCAGAAAGCAAAAGT	0.366																																					p.792_800del													.	ATP11B-93	3	Substitution - Missense(3)	lung(1)|breast(1)|skin(1)	c.2375_2398del						.																																			SO:0001651	inframe_deletion	23200	exon20			TATTATGCTGTCG	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2375_2398delGCTGTCGTATGGCTCCACTGCAGA	3.37:g.182597406_182597429delGCTGTCGTATGGCTCCACTGCAGA	ENSP00000321195:p.Cys792_Lys800delins*	Somatic	93	0		WXS	Illumina HiSeq	Phase_1	51	5	NM_014616	0	0	0	0	0	Q96FN1|Q9UKK7	In_Frame_Del	DEL	ENST00000323116.5	37	CCDS33896.1																																																																																			.		0.366	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		-	182597429	GCTGTCGTATGGCTCCACTGCAGA	-	182597406	7	5	97	1	0	1	0	1	0	0	0	0	1121	1319	46	0	2453	0	ATP11B	3	182597406	In_Frame_Del	DEL	GCTGTCGTATGGCTCCACTGCAGA	TCGA-DW-7839-01A-11D-2136-08	40455839	182597406	15425024	9	8678											
SLBP	7884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1701385	1701385	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	taggacactttcatctgtctCaaagtcagccggcacagtag	11	10	9	11	1	4	0	3	0	2	0	5	1	4	1	1	2	1	2	1	2	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr4:1701385C>G	ENST00000489418.1	-	5	751	c.385G>C	c.(385-387)Gag>Cag	p.E129Q	SLBP_ENST00000429429.2_Missense_Mutation_p.E90Q|SLBP_ENST00000488267.1_Missense_Mutation_p.E94Q|SLBP_ENST00000318386.4_Missense_Mutation_p.E136Q	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	129	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			TCATCTGTCTCAAAGTCAGCC	0.398																																					p.E129Q		.											.	SLBP-90	0			c.G385C						.						126	117	120					4																	1701385		2203	4300	6503	SO:0001583	missense	7884	exon5			CTGTCTCAAAGTC	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"histone binding protein"	602422	"stem-loop (histone) binding protein"			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.385G>C	4.37:g.1701385C>G	ENSP00000417686:p.Glu129Gln	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	114	56	NM_006527	0	0	23	56	33	B3KRJ5	Missense_Mutation	SNP	ENST00000489418.1	37	CCDS3350.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	29.7|29.7|29.7	5.030846|5.030846|5.030846	0.93575|0.93575|0.93575	.|.|.	.|.|.	ENSG00000163950|ENSG00000163950|ENSG00000163950	ENST00000429429;ENST00000489418;ENST00000460392;ENST00000318386;ENST00000488267|ENST00000483348|ENST00000480936	.|.|.	.|.|.	.|.|.	5.08|5.08|5.08	5.08|5.08|5.08	0.68730|0.68730|0.68730	.|.|.	0.103824|.|.	0.64402|.|.	D|.|.	0.000005|.|.	D|D|.	0.84781|0.84781|.	0.5548|0.5548|.	M|M|M	0.89534|0.89534|0.89534	3.04|3.04|3.04	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;P;D;D;D|.|.	0.89917|.|.	1.0;0.915;0.985;0.985;0.985|.|.	D;P;P;P;P|.|.	0.91635|.|.	0.999;0.653;0.804;0.804;0.804|.|.	D|D|.	0.87783|0.87783|.	0.2613|0.2613|.	9|5|.	0.72032|.|.	D|.|.	0.01|.|.	-9.2509|-9.2509|-9.2509	18.53|18.53|18.53	0.90987|0.90987|0.90987	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	94;136;90;109;129|.|.	E7EUV9;F8W8D3;B3KRJ5;C9IY53;Q14493|.|.	.;.;.;.;SLBP_HUMAN|.|.	Q|F|S	90;129;109;136;94|83|136	.|.|.	ENSP00000316490:E136Q|.|.	E|L|X	-|-|-	1|3|2	0|2|2	SLBP|SLBP|SLBP	1671183|1671183|1671183	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.949000|0.949000|0.949000	0.38748|0.38748|0.38748	0.969000|0.969000|0.969000	0.65631|0.65631|0.65631	7.142000|7.142000|7.142000	0.77339|0.77339|0.77339	2.382000|2.382000|2.382000	0.81193|0.81193|0.81193	0.644000|0.644000|0.644000	0.83932|0.83932|0.83932	GAG|TTG|TGA	.		0.398	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527		G	1701385	C	G	1701385	3	3	97	1	0	0	0	0	1	0	0	0	14404	835	29	4	443	4	SLBP	4	1701385	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		1701385	189452891	10	8679											
BOD1L	259282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	13604361	13604361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caatcacgcccgttaacttaCttccaagaggcatgattacc	12	10	6	13	2	1	2	1	1	0	1	2	2	2	2	3	1	3	2	3	1	5	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr4:13604361C>T	ENST00000040738.5	-	10	4298	c.4163G>A	c.(4162-4164)aGt>aAt	p.S1388N		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1388						nucleus (GO:0005634)	DNA binding (GO:0003677)										CGTTAACTTACTTCCAAGAGG	0.418																																					p.S1388N		.											.	.	0			c.G4163A						.						139	134	135					4																	13604361		2203	4300	6503	SO:0001583	missense	259282	exon10			AACTTACTTCCAA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4163G>A	4.37:g.13604361C>T	ENSP00000040738:p.Ser1388Asn	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	125	63	NM_148894	0	0	3	7	4	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	8.574	0.880637	0.17467	.	.	ENSG00000038219	ENST00000040738	T	0.06768	3.26	5.02	0.266	0.15617	.	0.228445	0.31577	N	0.007419	T	0.04952	0.0133	N	0.24115	0.695	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.34775	-0.9815	10	0.38643	T	0.18	0.0109	6.4855	0.22087	0.0:0.5089:0.1283:0.3629	.	1388	Q8NFC6	BOD1L_HUMAN	N	1388	ENSP00000040738:S1388N	ENSP00000040738:S1388N	S	-	2	0	BOD1L	13213459	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.472000	0.22116	0.111000	0.17947	-0.136000	0.14681	AGT	.		0.418	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13604361	C	T	13604361	3	4	97	1	0	0	0	0	1	0	0	0	1484	565	20	2	5060	2	BOD1L	4	13604361	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	11902976	13604361	177549915	11	8680											
GRIA1	2890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	153078528	153078528	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcagagattgccaagcaCgtgggctactcctaccgtct	8	8	12	13	3	1	1	0	0	1	1	2	2	2	1	3	2	4	3	3	2	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr5:153078528C>G	ENST00000285900.5	+	10	1690	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	GRIA1_ENST00000518142.1_Missense_Mutation_p.H369Q|GRIA1_ENST00000521843.2_Missense_Mutation_p.H380Q|GRIA1_ENST00000518783.1_Missense_Mutation_p.H459Q|GRIA1_ENST00000448073.4_Missense_Mutation_p.H459Q|GRIA1_ENST00000340592.5_Missense_Mutation_p.H449Q	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	449					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	TTGCCAAGCACGTGGGCTACT	0.537																																					p.H459Q		.											.	GRIA1-96	0			c.C1377G						.						110	98	102					5																	153078528		2203	4300	6503	SO:0001583	missense	2890	exon10			CAAGCACGTGGGC		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1347C>G	5.37:g.153078528C>G	ENSP00000285900:p.His449Gln	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	74	33	NM_001258021	0	0	0	0	0	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955998	0.53293	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.37584	1.8;1.8;1.19;1.8;1.8;1.8;1.19	5.44	-4.24	0.03777	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.44891	0.1315	L	0.55103	1.725	0.58432	D	0.999994	D;D;B;D;D;D	0.56521	0.976;0.976;0.012;0.976;0.971;0.962	P;P;B;P;P;P	0.59761	0.82;0.863;0.018;0.82;0.726;0.849	T	0.44997	-0.9291	10	0.44086	T	0.13	.	15.008	0.71527	0.0:0.6256:0.0:0.3744	.	459;459;369;459;449;449	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	Q	449;449;369;403;449;380;380;459;459	ENSP00000285900:H449Q;ENSP00000427920:H369Q;ENSP00000339343:H449Q;ENSP00000427864:H380Q;ENSP00000442108:H380Q;ENSP00000428994:H459Q;ENSP00000415569:H459Q	ENSP00000285900:H449Q	H	+	3	2	GRIA1	153058721	0.000000	0.05858	0.981000	0.43875	0.975000	0.68041	-1.954000	0.01525	-0.842000	0.04195	-0.794000	0.03295	CAC	.		0.537	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			G	153078528	C	G	153078528	3	3	97	1	0	0	0	0	1	0	0	0	6788	535	19	4	1385	4	GRIA1	5	153078528	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		153078528	27836732	12	8681											
PTK7	5754	hgsc.bcm.edu;bcgsc.ca	37	chr6	43044271	43044271	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagaccccgccggttgccTctgctcagcgtcctgctgct	3	9	11	18	3	2	1	1	0	1	1	3	1	3	1	6	1	5	4	6	1	0	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr6:43044271T>G	ENST00000230419.4	+	1	266	c.45T>G	c.(43-45)ccT>ccG	p.P15P	PTK7_ENST00000352931.2_Silent_p.P15P|PTK7_ENST00000345201.2_Silent_p.P15P|PTK7_ENST00000481273.1_5'Flank|PTK7_ENST00000471863.1_Silent_p.P15P|RP11-387M24.5_ENST00000606123.1_RNA|PTK7_ENST00000349241.2_Silent_p.P15P|PTK7_ENST00000476760.1_Silent_p.P15P	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	15					actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			GCCGGTTGCCTCTGCTCAGCG	0.716																																					p.P15P		.											.	PTK7-1493	0			c.T45G						.						7	10	9					6																	43044271		2101	4167	6268	SO:0001819	synonymous_variant	5754	exon1			GTTGCCTCTGCTC	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.45T>G	6.37:g.43044271T>G		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	25	18	NM_152882	0	0	4	7	3	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1																																																																																			.		0.716	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			G	43044271	T	G	43044271	2	3	97	1	0	0	0	0	0	0	0	1	12795	1538	54	5		5	PTK7	6	43044271	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08		43044271	128070796	13	8682											
SP8	221833	hgsc.bcm.edu	37	chr7	20824953	20824953	+	Silent	SNP	G	G	C																															gcggaggagccgccgccgccGcccccgccgccgccgccgct																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:20824953G>C	ENST00000361443.4	-	3	666	c.429C>G	c.(427-429)ggC>ggG	p.G143G	SP8_ENST00000418710.2_Silent_p.G161G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	143					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						cgccgccgccgcccccgccgc	0.736																																					p.G161G		.											.	SP8-91	0			c.C483G						.						2	2	2					7																	20824953		584	1454	2038	SO:0001819	synonymous_variant	221833	exon2			GCCGCCGCCCCCG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.429C>G	7.37:g.20824953G>C		Somatic	9	2		WXS	Illumina HiSeq	Phase_I	14	5	NM_182700	0	0	0	0	0	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.		0.736	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			C	20824953	G	C	20824953	2	2	97	1	0	0	0	0	0	0	0	1	15002	1074	38	4		4	SP8	7	20824953	Silent	SNP	G	TCGA-DW-7839-01A-11D-2136-08		20824953	138313710	14	8683	93	2									
SP8	221833	hgsc.bcm.edu	37	chr7	20824956	20824956	+	Silent	SNP	C	C	G																															gaggagccgccgccgccgccCccgccgccgccgccgctgcc																								rs201180283		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:20824956C>G	ENST00000361443.4	-	3	663	c.426G>C	c.(424-426)ggG>ggC	p.G142G	SP8_ENST00000418710.2_Silent_p.G160G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	142					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						cgccgccgcccccgccgccgc	0.741																																					p.G160G		.											.	SP8-91	0			c.G480C						.						2	2	2					7																	20824956		542	1367	1909	SO:0001819	synonymous_variant	221833	exon2			GCCGCCCCCGCCG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.426G>C	7.37:g.20824956C>G		Somatic	9	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_182700	2	0	0	10	8	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.		0.741	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			G	20824956	C	G	20824956	2	3	97	1	0	0	0	0	0	0	0	1	15002	610	22	4		4	SP8	7	20824956	Silent	SNP	C	TCGA-DW-7839-01A-11D-2136-08	3	20824956	138313707	15	8684	93	2									
HNRNPA2B1	3181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	26235509	26235509	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attatagccatccccaaatcCacgtccactgccatatccat	12	10	3	16	1	0	0	0	0	0	0	4	0	4	0	7	0	2	0	7	0	4	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:26235509C>T	ENST00000354667.4	-	8	883	c.715G>A	c.(715-717)Gga>Aga	p.G239R	HNRNPA2B1_ENST00000356674.7_Missense_Mutation_p.G227R	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	239	Gly-rich.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)		HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						TCCCCAAATCCACGTCCACTG	0.378			T	ETV1	prostate																																p.G239R		.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1-70	0			c.G715A						.						110	94	100					7																	26235509		2203	4300	6503	SO:0001583	missense	3181	exon8			CAAATCCACGTCC	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"RNA binding motif (RRM) containing"	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.715G>A	7.37:g.26235509C>T	ENSP00000346694:p.Gly239Arg	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	74	33	NM_031243	0	0	405	822	417	A8K064|P22627|Q9UC98|Q9UDJ2	Missense_Mutation	SNP	ENST00000354667.4	37	CCDS43557.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.379588	0.61845	.	.	ENSG00000122566	ENST00000354667;ENST00000356674	D;D	0.86627	-2.15;-2.15	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000002	D	0.89015	0.6595	M	0.65677	2.01	0.40149	D	0.976921	D;D	0.56968	0.978;0.963	P;B	0.48524	0.58;0.376	D	0.86218	0.1629	10	0.20046	T	0.44	.	20.327	0.98704	0.0:1.0:0.0:0.0	.	227;239	P22626-2;P22626	.;ROA2_HUMAN	R	239;227	ENSP00000346694:G239R;ENSP00000349101:G227R	ENSP00000346694:G239R	G	-	1	0	HNRNPA2B1	26202034	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.505000	0.60421	2.794000	0.96219	0.650000	0.86243	GGA	.		0.378	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		T	26235509	C	T	26235509	3	4	97	1	0	0	0	0	1	0	0	0	7280	603	21	2	362	2	HNRNPA2B1	7	26235509	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	5410553	26235509	132903154	16	8685											
SAMD9	54809	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	92734994	92734994	+	Frame_Shift_Del	DEL	T	T	-																															ttatcttctatgagctcaacTtttagtgacttagaaccttt																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:92734994delT	ENST00000379958.2	-	3	686	c.417delA	c.(415-417)aaafs	p.K139fs		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	139						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TGAGCTCAACTTTTAGTGACT	0.358																																					p.K139fs		.											.	SAMD9-140	0			c.417delA						.						124	134	130					7																	92734994		2203	4300	6503	SO:0001589	frameshift_variant	54809	exon2			.	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.417delA	7.37:g.92734994delT	ENSP00000369292:p.Lys139fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	113	50	NM_001193307	0	0	0	0	0	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Frame_Shift_Del	DEL	ENST00000379958.2	37	CCDS34680.1																																																																																			.		0.358	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		-	92734994	T	-	92734994	7	5	97	1	0	1	0	1	0	0	0	0	13858	1606	56	0	4356	0	SAMD9	7	92734994	Frame_Shift_Del	DEL	T	TCGA-DW-7839-01A-11D-2136-08	66499485	92734994	66403669	17	8686											
MGAM	8972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	141731533	141731533	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaatcccaactgtgctgtTtggtggacaaaggaatttga	12	11	10	8	0	0	1	0	1	0	0	1	3	1	3	2	3	2	2	2	3	4	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:141731533T>G	ENST00000549489.2	+	13	1619	c.1524T>G	c.(1522-1524)gtT>gtG	p.V508V	MGAM_ENST00000475668.2_Silent_p.V508V	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	508	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ACTGTGCTGTTTGGTGGACAA	0.363																																					p.V508V		.											.	MGAM-70	0			c.T1524G						.						169	157	161					7																	141731533		1835	4091	5926	SO:0001819	synonymous_variant	8972	exon13			TGCTGTTTGGTGG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1524T>G	7.37:g.141731533T>G		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	149	70	NM_004668	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			.		0.363	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141731533	T	G	141731533	2	3	97	1	0	0	0	0	0	0	0	1	9566	1828	64	5		5	MGAM	7	141731533	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08	48996539	141731533	17407130	18	8687											
TAS2R41	259287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	143175477	143175477	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctgggaacatgacctacaAgtggaatacaaggatagaaa	17	8	10	6	0	1	2	0	1	1	1	1	5	1	5	1	3	3	0	1	3	8	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:143175477A>T	ENST00000408916.1	+	1	512	c.512A>T	c.(511-513)aAg>aTg	p.K171M	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	171					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					ATGACCTACAAGTGGAATACA	0.358																																					p.K171M		.											.	TAS2R41-92	0			c.A512T						.						65	63	63					7																	143175477		1827	4093	5920	SO:0001583	missense	259287	exon1			CCTACAAGTGGAA	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.512A>T	7.37:g.143175477A>T	ENSP00000386201:p.Lys171Met	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	50	20	NM_176883	0	0	0	0	0	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	37	CCDS43663.1	.	.	.	.	.	.	.	.	.	.	A	2.606	-0.291927	0.05568	.	.	ENSG00000221855	ENST00000408916	T	0.00824	5.65	5.79	3.37	0.38596	.	2.257240	0.02520	U	0.092493	T	0.01454	0.0047	L	0.49571	1.57	0.09310	N	1	B	0.32573	0.376	B	0.26202	0.067	T	0.48115	-0.9063	10	0.41790	T	0.15	.	6.5138	0.22236	0.6261:0.2953:0.0786:0.0	.	171	P59536	T2R41_HUMAN	M	171	ENSP00000386201:K171M	ENSP00000386201:K171M	K	+	2	0	TAS2R41	142885599	0.000000	0.05858	0.119000	0.21687	0.009000	0.06853	0.535000	0.23114	1.000000	0.39049	0.533000	0.62120	AAG	.		0.358	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175477	A	T	143175477	3	4	97	1	0	0	0	0	1	0	0	0	15611	72	3	5	514	5	TAS2R41	7	143175477	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	1443944	143175477	15963186	19	8688											
LRRC14	9684	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	145746824	145746825	+	Frame_Shift_Del	DEL	AT	AT	-																															atgtgctctggaccacggacAtctacgggcgactggctgcg																								rs571447719		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr8:145746824_145746825delAT	ENST00000292524.1	+	4	1590_1591	c.1444_1445delAT	c.(1444-1446)atcfs	p.I482fs	LRRC14_ENST00000529022.1_Frame_Shift_Del_p.I482fs	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	482										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GACCACGGACATCTACGGGCGA	0.589																																					p.482_482del		.											.	LRRC14-90	0			c.1444_1445del						.																																			SO:0001589	frameshift_variant	9684	exon5			.	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.1444_1445delAT	8.37:g.145746824_145746825delAT	ENSP00000292524:p.Ile482fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	47	23	NM_001272036	0	0	0	0	0	A8K0A8|D3DWM8	Frame_Shift_Del	DEL	ENST00000292524.1	37	CCDS6432.1																																																																																			.		0.589	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		-	145746825	AT	-	145746824	7	5	97	1	0	1	0	1	0	0	0	0	8993	217	8	0	1454	0	LRRC14	8	145746824	Frame_Shift_Del	DEL	AT	TCGA-DW-7839-01A-11D-2136-08		145746824	617198	20	8689											
DENND4C	55667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	19316719	19316719	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcttgagatggaaattcaAgaggcatttttgcgctttat	11	14	10	6	1	1	2	1	1	0	2	1	4	1	3	0	2	2	3	0	2	3	6			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr9:19316719A>T	ENST00000380432.2	+	8	1014	c.981A>T	c.(979-981)caA>caT	p.Q327H	DENND4C_ENST00000602925.1_Missense_Mutation_p.Q563H|DENND4C_ENST00000434457.2_Missense_Mutation_p.Q563H			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	327	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TGGAAATTCAAGAGGCATTTT	0.403																																					p.Q563H		.											.	DENND4C-92	0			c.A1689T						.						121	135	130					9																	19316719		2203	4300	6503	SO:0001583	missense	55667	exon12			AATTCAAGAGGCA	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.981A>T	9.37:g.19316719A>T	ENSP00000369797:p.Gln327His	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	212	95	NM_017925	0	0	0	1	1	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	A	16.63	3.176330	0.57692	.	.	ENSG00000137145	ENST00000380437	.	.	.	4.98	-1.92	0.07618	dDENN (3);	0.051808	0.85682	D	0.000000	T	0.75547	0.3864	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75616	-0.3256	9	0.87932	D	0	-12.7766	11.8182	0.52224	0.5022:0.0:0.4978:0.0	.	327	Q5VZ89	DEN4C_HUMAN	H	327	.	ENSP00000369802:Q327H	Q	+	3	2	DENND4C	19306719	0.437000	0.25593	0.989000	0.46669	0.789000	0.44602	-0.194000	0.09559	-0.503000	0.06586	-0.561000	0.04177	CAA	.		0.403	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		T	19316719	A	T	19316719	3	4	97	1	0	0	0	0	1	0	0	0	4446	69	3	5	1011	5	DENND4C	9	19316719	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08		19316719	121896712	21	8690											
DENND1A	57706	hgsc.bcm.edu;bcgsc.ca	37	chr9	126214605	126214605	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctttggtctttacagtatTcagaattgctccacttcctt	7	18	6	10	0	2	1	1	0	1	1	4	1	4	1	2	1	3	3	2	1	3	8			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr9:126214605T>C	ENST00000373624.2	-	17	1450	c.1249A>G	c.(1249-1251)Aat>Gat	p.N417D	DENND1A_ENST00000394219.3_Missense_Mutation_p.N385D|DENND1A_ENST00000373618.1_Missense_Mutation_p.N385D|DENND1A_ENST00000373620.3_Missense_Mutation_p.N417D|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394215.2_Missense_Mutation_p.N387D|DENND1A_ENST00000542603.1_Missense_Mutation_p.N159D	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	417					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						TTTACAGTATTCAGAATTGCT	0.413																																					p.N417D		.											.	DENND1A-92	0			c.A1249G						.						173	152	159					9																	126214605		2203	4300	6503	SO:0001583	missense	57706	exon17			CAGTATTCAGAAT	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"DENN/MADD domain containing"	29324	protein-coding gene	gene with protein product		613633	"KIAA1608"	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1249A>G	9.37:g.126214605T>C	ENSP00000362727:p.Asn417Asp	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	79	5	NM_024820	0	0	17	17	0	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369121	0.82463	.	.	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T;T	0.25085	3.28;1.82;3.18;3.32;3.17;3.19	5.47	5.47	0.80525	.	0.093202	0.64402	D	0.000001	T	0.54775	0.1879	M	0.83012	2.62	0.54753	D	0.99998	D;D;D;D;D;D;D	0.76494	0.975;0.975;0.984;0.999;0.984;0.958;0.996	P;P;P;D;P;P;P	0.77557	0.883;0.883;0.84;0.99;0.879;0.767;0.877	T	0.60722	-0.7207	10	0.59425	D	0.04	-17.7065	15.5608	0.76244	0.0:0.0:0.0:1.0	.	385;375;385;387;417;417;237	Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3;Q9HCG4	.;.;.;.;.;DEN1A_HUMAN;.	D	417;159;385;417;387;385	ENSP00000362727:N417D;ENSP00000437457:N159D;ENSP00000377766:N385D;ENSP00000362722:N417D;ENSP00000377763:N387D;ENSP00000362720:N385D	ENSP00000362720:N385D	N	-	1	0	DENND1A	125254426	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.570000	0.67398	2.076000	0.62316	0.459000	0.35465	AAT	.		0.413	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		C	126214605	T	C	126214605	3	2	97	1	0	0	0	0	1	0	0	0	4437	1783	62	3	1911	3	DENND1A	9	126214605	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	106897886	126214605	14998826	22	8691											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16943441	16943441	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcactccactgtcacctaTctgtattccgccacaatctg	9	12	5	15	1	4	0	2	0	2	0	6	1	6	0	4	0	0	1	4	0	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr10:16943441T>C	ENST00000377833.4	-	52	8145	c.8080A>G	c.(8080-8082)Ata>Gta	p.I2694V		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2694	CUB 20. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTGTCACCTATCTGTATTCCG	0.443																																					p.I2694V		.											.	CUBN-166	0			c.A8080G						.						130	105	114					10																	16943441		2203	4300	6503	SO:0001583	missense	8029	exon52			CACCTATCTGTAT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8080A>G	10.37:g.16943441T>C	ENSP00000367064:p.Ile2694Val	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	92	53	NM_001081	0	0	1	1	0	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	6.883	0.532398	0.13127	.	.	ENSG00000107611	ENST00000377833	T	0.17528	2.27	5.63	0.664	0.17890	CUB (5);	0.936616	0.08810	N	0.890473	T	0.08313	0.0207	N	0.17594	0.5	0.32205	N	0.577314	B	0.18310	0.027	B	0.21708	0.036	T	0.42085	-0.9472	10	0.22109	T	0.4	.	0.1187	0.00063	0.2416:0.2042:0.2266:0.3276	.	2694	O60494	CUBN_HUMAN	V	2694	ENSP00000367064:I2694V	ENSP00000367064:I2694V	I	-	1	0	CUBN	16983447	0.835000	0.29415	0.056000	0.19401	0.756000	0.42949	1.368000	0.34216	-0.064000	0.13043	0.477000	0.44152	ATA	.		0.443	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16943441	T	C	16943441	3	2	97	1	0	0	0	0	1	0	0	0	4057	1435	50	3	2855	3	CUBN	10	16943441	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08		16943441	118591306	23	8692											
NRG3	10718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	83635770	83635770	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcaatgccctcctggcCtactgcggcatacgctacct	7	8	9	17	2	0	0	0	0	0	0	1	0	1	0	5	3	5	3	5	3	4	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr10:83635770C>A	ENST00000404547.1	+	1	674	c.674C>A	c.(673-675)cCt>cAt	p.P225H	NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000556918.1_5'Flank|NRG3_ENST00000372141.2_Missense_Mutation_p.P225H|NRG3_ENST00000404576.2_5'Flank			P56975	NRG3_HUMAN	neuregulin 3	225	Ser/Thr-rich.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		CCCTCCTGGCCTACTGCGGCA	0.617																																					p.P225H		.											.	NRG3-522	0			c.C674A						.						101	80	87					10																	83635770		2203	4300	6503	SO:0001583	missense	10718	exon1			CCTGGCCTACTGC	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.674C>A	10.37:g.83635770C>A	ENSP00000384796:p.Pro225His	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	58	28	NM_001165972	0	0	3	7	4	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273875	0.59649	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.33438	1.41;1.43	3.89	3.89	0.44902	.	0.000000	0.45361	D	0.000364	T	0.44074	0.1276	L	0.40543	1.245	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66847	0.947;0.947	T	0.44050	-0.9353	10	0.87932	D	0	-21.024	13.7841	0.63099	0.0:1.0:0.0:0.0	.	225;225	B9EGV5;P56975-4	.;.	H	225	ENSP00000361214:P225H;ENSP00000384796:P225H	ENSP00000361214:P225H	P	+	2	0	NRG3	83625750	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.474000	0.66781	2.186000	0.69663	0.549000	0.68633	CCT	.		0.617	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		A	83635770	C	A	83635770	3	1	97	1	0	0	0	0	1	0	0	0	10675	681	24	4	676	4	NRG3	10	83635770	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	66692329	83635770	51898977	24	8693											
LIPJ	142910	bcgsc.ca	37	chr10	90362367	90362367	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtatttttcacacaacccagCaggaacatctgttcaaaata	15	11	5	10	0	3	0	2	0	1	0	3	1	3	1	1	1	3	3	1	1	6	5			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr10:90362367C>A	ENST00000371939.3	+	9	1072	c.758C>A	c.(757-759)gCa>gAa	p.A253E		NM_001010939.2	NP_001010939.2	Q5W064	LIPJ_HUMAN	lipase, family member J	253					lipid catabolic process (GO:0016042)		hydrolase activity, acting on ester bonds (GO:0016788)			large_intestine(4)|lung(4)|ovary(1)	9		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		CACAACCCAGCAGGAACATCT	0.323																																					p.A253E													.	LIPJ-91	0			c.C758A						.						119	111	114					10																	90362367		2203	4300	6503	SO:0001583	missense	142910	exon9			ACCCAGCAGGAAC	BC031219	CCDS31240.1	10q23.31	2008-02-04	2008-02-04	2007-02-27	ENSG00000204022	ENSG00000204022			21773	protein-coding gene	gene with protein product		613921	"lipase-like, ab-hydrolase domain containing 1", "lipase, family member J"	LIPL1			Standard	NM_001010939		Approved	bA425M17.2	uc001kff.3	Q5W064	OTTHUMG00000018691	ENST00000371939.3:c.758C>A	10.37:g.90362367C>A	ENSP00000361007:p.Ala253Glu	Somatic	55	0		WXS	Illumina HiSeq	Phase_1	61	5	NM_001010939	0	0	0	0	0	A8MT98|Q0P671	Missense_Mutation	SNP	ENST00000371939.3	37	CCDS31240.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.045055	0.55110	.	.	ENSG00000204022	ENST00000371939;ENST00000531458	T;T	0.72167	0.04;-0.63	3.94	1.93	0.25924	Alpha/beta hydrolase fold-1 (1);	0.382752	0.18848	N	0.129499	D	0.84142	0.5407	M	0.91920	3.255	0.35171	D	0.77155	D	0.67145	0.996	D	0.74674	0.984	D	0.85936	0.1455	10	0.87932	D	0	-21.7415	7.6994	0.28613	0.1867:0.6328:0.1805:0.0	.	253	Q5W064	LIPJ_HUMAN	E	253;68	ENSP00000361007:A253E;ENSP00000434211:A68E	ENSP00000361007:A253E	A	+	2	0	LIPJ	90352347	0.996000	0.38824	1.000000	0.80357	0.919000	0.55068	3.523000	0.53488	0.379000	0.24794	-0.310000	0.09108	GCA	.		0.323	LIPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049248.2	XM_084377		A	90362367	C	A	90362367	3	1	97	1	0	0	0	0	1	0	0	0	8849	710	25	4	784	4	LIPJ	10	90362367	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	6726597	90362367	45172380	25	8694											
EPS8L2	64787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	723296	723296	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaagcacagccccacttCagagcccacccccccggggg	9	2	10	20	1	1	2	1	0	0	2	1	2	1	2	7	2	3	1	7	2	1	1	rs142895363		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:723296C>A	ENST00000533256.1	+	16	1772	c.1397C>A	c.(1396-1398)tCa>tAa	p.S466*	EPS8L2_ENST00000530636.1_Nonsense_Mutation_p.S466*|EPS8L2_ENST00000318562.8_Nonsense_Mutation_p.S466*|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Nonsense_Mutation_p.S482*			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	466					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCCCCACTTCAGAGCCCACC	0.602											OREG0020659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S466X		.											.	EPS8L2-91	0			c.C1397A						.						85	84	85					11																	723296		2203	4300	6503	SO:0001587	stop_gained	64787	exon15			CCACTTCAGAGCC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.1397C>A	11.37:g.723296C>A	ENSP00000435585:p.Ser466*	Somatic	184	0	590	WXS	Illumina HiSeq	Phase_I	134	59	NM_022772	0	0	50	75	25	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Nonsense_Mutation	SNP	ENST00000533256.1	37	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	c	34	5.392509	0.96009	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	.	.	.	2.79	1.87	0.25490	.	3.938280	0.01227	U	0.008254	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.7601	7.8157	0.29258	0.0:0.868:0.0:0.132	.	.	.	.	X	466;466;466;482	.	ENSP00000320828:S466X	S	+	2	0	EPS8L2	713296	0.002000	0.14202	0.005000	0.12908	0.020000	0.10135	0.499000	0.22546	0.538000	0.28769	-0.642000	0.03964	TCA	C|0.999;T|0.001		0.602	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		A	723296	C	A	723296	4	1	97	1	0	0	0	0	0	1	0	0	5209	838	29	4	1451	4	EPS8L2	11	723296	Nonsense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		723296	134283220	26	8695											
SCUBE2	57758	hgsc.bcm.edu	37	chr11	9113002	9113002	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccccgccagcagcagcAgtggcggcagcagcagcagc	8	1	15	17	3	0	0	0	0	0	0	0	0	0	0	3	3	7	7	3	3	0	0	rs60494098	byFrequency	TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:9113002A>G	ENST00000309263.3	-	1	146	c.74T>C	c.(73-75)cTg>cCg	p.L25P	MIR5691_ENST00000579525.1_RNA|SCUBE2_ENST00000450649.2_Missense_Mutation_p.L25P|SCUBE2_ENST00000520467.1_Missense_Mutation_p.L25P|SCUBE2_ENST00000534295.1_Intron|SCUBE2_ENST00000457346.2_Missense_Mutation_p.L25P			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	25						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		cagcagcagcagtggcggcag	0.786													G|||	1639	0.327276	0.2595	0.4035	5008	,	,		5931	0.4534		0.159	False		,,,				2504	0.408				p.L25P		.											.	SCUBE2-92	0			c.T74C						.						1	1	1					11																	9113002		368	855	1223	SO:0001583	missense	57758	exon1			AGCAGCAGTGGCG	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.74T>C	11.37:g.9113002A>G	ENSP00000310658:p.Leu25Pro	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	4	3	NM_001170690	0	0	0	0	0	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		658	0.30128205128205127	118	0.23983739837398374	134	0.3701657458563536	267	0.46678321678321677	139	0.18337730870712401	G	9.091	1.001643	0.19121	.	.	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;D;T	0.84516	-1.28;-1.38;-1.86;-1.45	2.52	-4.38	0.03622	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.37371	P	0.08837099999999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.21381	-1.0247	8	0.32370	T	0.25	.	3.6865	0.08329	0.4265:0.0:0.3373:0.2362	rs60494098	25;25;25	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	P	25	ENSP00000390481:L25P;ENSP00000310658:L25P;ENSP00000415187:L25P;ENSP00000429969:L25P	ENSP00000310658:L25P	L	-	2	0	SCUBE2	9069578	0.005000	0.15991	0.054000	0.19295	0.010000	0.07245	0.347000	0.20014	-1.087000	0.03081	-0.665000	0.03846	CTG	A|0.699;G|0.301		0.786	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		G	9113002	A	G	9113002	3	3	97	1	0	0	0	0	1	0	0	0	13977	188	7	3	3104	3	SCUBE2	11	9113002	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	8389706	9113002	125893514	27	8696											
SPRYD5	84767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55658774	55658774	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcacatctggcaaatattAttgggaggttcatatggggg	10	14	12	5	0	3	0	2	0	1	0	3	1	3	1	0	5	0	2	0	5	4	6			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:55658774A>G	ENST00000449290.2	+	7	1117	c.1025A>G	c.(1024-1026)tAt>tGt	p.Y342C	TRIM51_ENST00000244891.3_Missense_Mutation_p.Y199C	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	342	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)										GGCAAATATTATTGGGAGGTT	0.423																																					p.Y342C		.											.	.	0			c.A1025G						.						82	88	86					11																	55658774		2101	4042	6143	SO:0001583	missense	84767	exon7			AATATTATTGGGA	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.1025A>G	11.37:g.55658774A>G	ENSP00000395086:p.Tyr342Cys	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	125	56	NM_032681	0	0	0	0	0	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		.	.	.	.	.	.	.	.	.	.	.	14.48	2.548928	0.45383	.	.	ENSG00000124900	ENST00000449290;ENST00000244891	T;T	0.74947	-0.89;-0.89	1.36	1.36	0.22044	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	D	0.85561	0.5725	M	0.89715	3.055	0.27185	N	0.960562	D	0.89917	1.0	D	0.97110	1.0	T	0.73235	-0.4047	9	0.87932	D	0	.	5.1325	0.14917	1.0:0.0:0.0:0.0	.	342	Q9BSJ1	SPRY5_HUMAN	C	342;199	ENSP00000395086:Y342C;ENSP00000244891:Y199C	ENSP00000244891:Y199C	Y	+	2	0	SPRYD5	55415350	1.000000	0.71417	0.075000	0.20258	0.398000	0.30690	3.446000	0.52928	0.540000	0.28808	0.136000	0.15936	TAT	.		0.423	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		G	55658774	A	G	55658774	3	3	97	1	0	0	0	0	1	0	0	0	15143	449	16	3	1047	3	SPRYD5	11	55658774	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	46545772	55658774	79347742	28	8697											
B3GNT1	11041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66114291	66114291	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggttgctctgatccagcatTtcccgcaggcctctccacag	6	11	9	15	1	2	1	0	1	2	0	5	1	4	1	4	2	2	4	4	2	0	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:66114291T>A	ENST00000311181.4	-	1	872	c.726A>T	c.(724-726)gaA>gaT	p.E242D	BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank|RP11-867G23.8_ENST00000531602.1_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	242					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						GATCCAGCATTTCCCGCAGGC	0.612																																					p.E242D		.											.	B3GNT1-90	0			c.A726T						.						75	79	78					11																	66114291		2200	4295	6495	SO:0001583	missense	11041	exon1			CAGCATTTCCCGC	AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"Beta 3-glycosyltransferases"	15685	protein-coding gene	gene with protein product	"N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"	605517	"UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.726A>T	11.37:g.66114291T>A	ENSP00000309096:p.Glu242Asp	Somatic	240	0		WXS	Illumina HiSeq	Phase_I	169	82	NM_006876	0	0	33	66	33	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	37	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	T	10.34	1.322423	0.23994	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.22539	1.95	5.29	0.868	0.19090	.	0.396932	0.27876	N	0.017483	T	0.08044	0.0201	N	0.10837	0.055	0.28440	N	0.916866	B	0.13145	0.007	B	0.15052	0.012	T	0.31420	-0.9944	10	0.15066	T	0.55	-16.142	4.6684	0.12676	0.0:0.3853:0.1676:0.4471	.	242	O43505	B3GN1_HUMAN	D	242;13	ENSP00000309096:E242D	ENSP00000309096:E242D	E	-	3	2	B3GNT1	65870867	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.024000	0.13555	0.256000	0.21614	0.379000	0.24179	GAA	.		0.612	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876		A	66114291	T	A	66114291	3	1	97	1	0	0	0	0	1	0	0	0	1257	1838	64	5	529	5	B3GNT1	11	66114291	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	10455517	66114291	68892225	29	8698											
PICALM	8301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	85722090	85722090	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacctctgcaactttgaggaActctgagattcttgtcatcc	9	14	7	11	0	4	2	1	2	3	1	5	4	5	3	2	1	4	1	2	1	3	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:85722090A>G	ENST00000393346.3	-	7	896	c.748T>C	c.(748-750)Ttc>Ctc	p.F250L	PICALM_ENST00000526033.1_Missense_Mutation_p.F250L|PICALM_ENST00000356360.5_Missense_Mutation_p.F250L|PICALM_ENST00000532317.1_Missense_Mutation_p.F250L|PICALM_ENST00000528398.1_Missense_Mutation_p.F199L			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	250	Interaction with FAM64A.				axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				ACTTTGAGGAACTCTGAGATT	0.343			T	"MLLT10, MLL"	"TALL, AML, "																																p.F250L		.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM-659	0			c.T748C						.						128	112	118					11																	85722090		2202	4298	6500	SO:0001583	missense	8301	exon7			TGAGGAACTCTGA	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.748T>C	11.37:g.85722090A>G	ENSP00000377015:p.Phe250Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	30	18	NM_007166	0	0	75	149	74	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Missense_Mutation	SNP	ENST00000393346.3	37	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	A	34	5.324333	0.95708	.	.	ENSG00000073921	ENST00000532317;ENST00000526033;ENST00000447890;ENST00000393346;ENST00000528398;ENST00000356360	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.48	5.48	0.80851	ANTH (1);Clathrin adaptor, phosphoinositide-binding, GAT-like (1);	0.000000	0.85682	D	0.000000	T	0.76248	0.3961	M	0.87617	2.895	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.991;1.0	D;D;D;D	0.97110	0.994;1.0;0.981;1.0	T	0.80236	-0.1466	9	.	.	.	-19.6257	15.8605	0.79017	1.0:0.0:0.0:0.0	.	199;250;250;250	E9PN05;F8VPG7;Q13492;Q13492-3	.;.;PICAL_HUMAN;.	L	250;250;250;250;199;250	ENSP00000436958:F250L;ENSP00000433846:F250L;ENSP00000377015:F250L;ENSP00000434884:F199L;ENSP00000348718:F250L	.	F	-	1	0	PICALM	85399738	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.197000	0.70478	0.533000	0.62120	TTC	.		0.343	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		G	85722090	A	G	85722090	3	3	97	1	0	0	0	0	1	0	0	0	11906	43	2	3	1294	3	PICALM	11	85722090	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	19607799	85722090	49284426	30	8699											
FAT3	120114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	92590392	92590392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcacaggaggactgtgtcCggggtccaacgatccttgtg	7	10	14	10	2	1	0	1	0	0	0	4	3	4	2	3	4	1	0	3	4	1	1	rs368909373		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:92590392C>T	ENST00000298047.6	+	19	11395	c.11378C>T	c.(11377-11379)cCg>cTg	p.P3793L	FAT3_ENST00000409404.2_Missense_Mutation_p.P3793L|FAT3_ENST00000525166.1_Missense_Mutation_p.P3643L|FAT3_ENST00000533797.1_Missense_Mutation_p.P128L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3793					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGACTGTGTCCGGGGTCCAAC	0.527										TCGA Ovarian(4;0.039)																											p.P3793L		.											.	FAT3-73	0			c.C11378T						.	C	LEU/PRO	2,4000		0,2,1999	103	106	105		11378	5.9	0.9	11		105	0,8334		0,0,4167	no	missense	FAT3	NM_001008781.2	98	0,2,6166	TT,TC,CC		0.0,0.05,0.0162	benign	3793/4558	92590392	2,12334	2001	4167	6168	SO:0001583	missense	120114	exon19			TGTGTCCGGGGTC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11378C>T	11.37:g.92590392C>T	ENSP00000298047:p.Pro3793Leu	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	113	51	NM_001008781	0	0	0	0	0	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	20.7	4.040675	0.75732	5.0E-4	0.0	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.95	5.95	0.96441	.	.	.	.	.	T	0.34832	0.0911	L	0.53249	1.67	0.80722	D	1	D;B	0.59357	0.985;0.399	B;B	0.41271	0.352;0.04	T	0.13045	-1.0524	9	0.51188	T	0.08	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	3793;3793	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	L	3793;3793;3643;128	ENSP00000298047:P3793L;ENSP00000387040:P3793L;ENSP00000432586:P3643L;ENSP00000436399:P128L	ENSP00000298047:P3793L	P	+	2	0	FAT3	92230040	0.995000	0.38212	0.922000	0.36590	0.908000	0.53690	6.655000	0.74392	2.824000	0.97209	0.655000	0.94253	CCG	.		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92590392	C	T	92590392	3	4	97	1	0	0	0	0	1	0	0	0	5710	652	23	1	11452	1	FAT3	11	92590392	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	6868302	92590392	42416124	31	8700											
PPFIBP1	8496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	27787953	27787953	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaagacctgcgtggattgTtagagatgatggaaacagat	13	10	14	4	1	0	4	0	1	0	3	0	8	0	7	1	3	2	1	1	3	3	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:27787953T>C	ENST00000318304.8	+	4	458	c.175T>C	c.(175-177)Tta>Cta	p.L59L	PPFIBP1_ENST00000535047.1_Silent_p.L59L|PPFIBP1_ENST00000228425.6_Silent_p.L59L|PPFIBP1_ENST00000542629.1_Silent_p.L59L|PPFIBP1_ENST00000537927.1_Intron|PPFIBP1_ENST00000545334.1_Silent_p.L59L	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	59					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)					GCGTGGATTGTTAGAGATGAT	0.458																																					p.L59L		.											.	PPFIBP1-228	0			c.T175C						.						108	110	110					12																	27787953		2203	4300	6503	SO:0001819	synonymous_variant	8496	exon4			GGATTGTTAGAGA	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.175T>C	12.37:g.27787953T>C		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	103	46	NM_003622	0	0	12	19	7	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			.		0.458	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		C	27787953	T	C	27787953	2	2	97	1	0	0	0	0	0	0	0	1	12339	1722	60	3		3	PPFIBP1	12	27787953	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08		27787953	106063942	32	8701											
ARF3	377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49333834	49333834	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcgaatcttgtcctggccacCcacatcccacactgtaaagc	10	9	6	16	1	1	0	0	0	1	0	4	1	3	0	4	1	1	1	4	1	3	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:49333834C>G	ENST00000256682.4	-	3	539	c.205G>C	c.(205-207)Ggt>Cgt	p.G69R	ARF3_ENST00000541967.1_5'Flank|ARF3_ENST00000541959.1_Missense_Mutation_p.G69R|ARF3_ENST00000447318.2_Intron|AC073610.5_ENST00000537495.1_5'Flank|RP11-302B13.5_ENST00000398092.4_Missense_Mutation_p.G69R	NM_001659.2	NP_001650.1	P61204	ARF3_HUMAN	ADP-ribosylation factor 3	69					GTP catabolic process (GO:0006184)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|skin(1)	4						TCCTGGCCACCCACATCCCAC	0.502																																					p.G69R	Pancreas(189;1862 2134 4419 30933 49364)	.											.	ARF3-227	0			c.G205C						.						198	158	171					12																	49333834		2203	4300	6503	SO:0001583	missense	377	exon3			GGCCACCCACATC	M74491	CCDS8774.1	12q13.12	2013-01-22			ENSG00000134287	ENSG00000134287		"ADP-ribosylation factors"	654	protein-coding gene	gene with protein product	"small GTP binding protein"	103190				8661066	Standard	NM_001659		Approved		uc001rsr.2	P61204	OTTHUMG00000168080	ENST00000256682.4:c.205G>C	12.37:g.49333834C>G	ENSP00000256682:p.Gly69Arg	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	101	41	NM_001659	0	0	144	281	137	A8K6G8|B7ZB63|P16587	Missense_Mutation	SNP	ENST00000256682.4	37	CCDS8774.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243385	0.58995	.	.	ENSG00000134287	ENST00000398092;ENST00000256682;ENST00000541959;ENST00000541236	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	4.72	3.82	0.43975	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.96030	0.8707	H	0.99887	4.895	0.80722	D	1	D	0.67145	0.996	D	0.70716	0.97	D	0.97028	0.9748	10	0.87932	D	0	.	13.5059	0.61483	0.1577:0.8423:0.0:0.0	.	69	P61204	ARF3_HUMAN	R	69	ENSP00000438507:G69R;ENSP00000256682:G69R;ENSP00000438510:G69R;ENSP00000438063:G69R	ENSP00000256682:G69R	G	-	1	0	ARF3	47620101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.814000	0.86154	1.096000	0.41439	0.462000	0.41574	GGT	.		0.502	ARF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258242.2	NM_001659		G	49333834	C	G	49333834	3	3	97	1	0	0	0	0	1	0	0	0	845	623	22	4	352	4	ARF3	12	49333834	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	21545881	49333834	84518061	33	8702											
MBD6	114785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57920964	57920964	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcatagctttaaattctgCgctgctggctgccaccctgg	6	12	9	14	1	2	0	1	0	1	0	2	0	2	0	3	2	4	4	3	2	3	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:57920964C>T	ENST00000355673.3	+	7	2392	c.2036C>T	c.(2035-2037)gCg>gTg	p.A679V	MBD6_ENST00000431731.2_Missense_Mutation_p.A679V	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	679	Pro-rich.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						TTAAATTCTGCGCTGCTGGCT	0.597																																					p.A679V		.											.	MBD6-516	0			c.C2036T						.						11	12	12					12																	57920964		2195	4290	6485	SO:0001583	missense	114785	exon7			ATTCTGCGCTGCT	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.2036C>T	12.37:g.57920964C>T	ENSP00000347896:p.Ala679Val	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	18	13	NM_052897	0	0	13	34	21	Q8N3M0|Q8NA81|Q96Q00	Missense_Mutation	SNP	ENST00000355673.3	37	CCDS8944.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.737980	0.49045	.	.	ENSG00000166987	ENST00000355673;ENST00000431731;ENST00000300263	.	.	.	5.2	4.32	0.51571	.	0.738053	0.11966	N	0.512271	T	0.26011	0.0634	N	0.08118	0	0.41634	D	0.989031	P;P	0.45428	0.858;0.675	B;B	0.32928	0.109;0.155	T	0.14643	-1.0465	9	0.66056	D	0.02	-3.2719	12.8722	0.57970	0.0:0.9201:0.0:0.0799	.	679;679	Q6P0P0;Q96DN6	.;MBD6_HUMAN	V	679;679;143	.	ENSP00000300263:A143V	A	+	2	0	MBD6	56207231	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.754000	0.47532	1.350000	0.45770	0.561000	0.74099	GCG	.		0.597	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			T	57920964	C	T	57920964	3	4	97	1	0	0	0	0	1	0	0	0	9373	768	27	1	2054	1	MBD6	12	57920964	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	8587130	57920964	75930931	34	8703											
HCFC2	29915	bcgsc.ca	37	chr12	104473281	104473281	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctggtgttgtgggttggAgcattccagtgactaaaggg	7	12	16	6	0	1	1	0	1	1	0	2	2	2	2	1	4	1	4	1	4	2	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:104473281A>G	ENST00000229330.4	+	4	636	c.532A>G	c.(532-534)Agc>Ggc	p.S178G		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	178					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TGTGGGTTGGAGCATTCCAGT	0.348																																					p.S178G	Esophageal Squamous(184;1814 2036 4771 6974 15702)												.	HCFC2-92	0			c.A532G						.						103	109	107					12																	104473281		2203	4300	6503	SO:0001583	missense	29915	exon4			GGTTGGAGCATTC	AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.532A>G	12.37:g.104473281A>G	ENSP00000229330:p.Ser178Gly	Somatic	99	1		WXS	Illumina HiSeq	Phase_1	99	4	NM_013320	0	0	1	1	0	B2R8Q5|C0H5X3	Missense_Mutation	SNP	ENST00000229330.4	37	CCDS9097.1	.	.	.	.	.	.	.	.	.	.	A	12.91	2.078672	0.36662	.	.	ENSG00000111727	ENST00000229330	T	0.75260	-0.92	5.93	5.93	0.95920	Kelch-type beta propeller (1);	0.195982	0.64402	D	0.000006	T	0.71779	0.3380	L	0.58583	1.82	0.42169	D	0.991631	B	0.27229	0.172	B	0.22386	0.039	T	0.69800	-0.5047	10	0.46703	T	0.11	-7.4295	16.3756	0.83387	1.0:0.0:0.0:0.0	.	178	Q9Y5Z7	HCFC2_HUMAN	G	178	ENSP00000229330:S178G	ENSP00000229330:S178G	S	+	1	0	HCFC2	102997411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.494000	0.53273	2.270000	0.75569	0.460000	0.39030	AGC	.		0.348	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407780.1	NM_013320		G	104473281	A	G	104473281	3	3	97	1	0	0	0	0	1	0	0	0	7014	304	11	3	546	3	HCFC2	12	104473281	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	46552317	104473281	29378614	35	8704											
BTBD11	121551	bcgsc.ca	37	chr12	108011117	108011117	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttgctgttggagcgtggtgCcgatcccctgataggaacca	7	11	13	10	2	0	1	0	1	0	0	1	4	1	3	4	3	4	2	4	3	2	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:108011117C>T	ENST00000280758.5	+	9	2663	c.2135C>T	c.(2134-2136)gCc>gTc	p.A712V	BTBD11_ENST00000420571.2_Intron|BTBD11_ENST00000357167.4_Missense_Mutation_p.A249V|RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000490090.2_Missense_Mutation_p.A712V	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	712						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GAGCGTGGTGCCGATCCCCTG	0.483																																					p.A712V													.	BTBD11-93	0			c.C2135T						.						113	121	118					12																	108011117		2203	4300	6503	SO:0001583	missense	121551	exon9			GTGGTGCCGATCC	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2135C>T	12.37:g.108011117C>T	ENSP00000280758:p.Ala712Val	Somatic	239	0		WXS	Illumina HiSeq	Phase_1	157	6	NM_001018072	0	0	1	1	0	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.784837	0.90282	.	.	ENSG00000151136	ENST00000280758;ENST00000490090;ENST00000357167	T;T;T	0.70399	-0.48;-0.48;-0.48	5.49	5.49	0.81192	Ankyrin repeat-containing domain (4);	0.047856	0.85682	D	0.000000	T	0.81346	0.4803	L	0.58302	1.8	0.80722	D	1	P;D;D	0.89917	0.84;0.969;1.0	P;P;D	0.79108	0.634;0.843;0.992	T	0.82800	-0.0278	10	0.87932	D	0	.	14.9248	0.70868	0.0:0.8572:0.1427:0.0	.	249;712;712	E9PHS4;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	V	712;712;249	ENSP00000280758:A712V;ENSP00000447319:A712V;ENSP00000349690:A249V	ENSP00000280758:A712V	A	+	2	0	BTBD11	106535247	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.005000	0.70716	2.572000	0.86782	0.655000	0.94253	GCC	.		0.483	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		T	108011117	C	T	108011117	3	4	97	1	0	0	0	0	1	0	0	0	1542	739	26	2	2274	2	BTBD11	12	108011117	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	3537836	108011117	25840778	36	8705											
MED13L	23389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	116429670	116429670	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcctgccccactattgctgGctggggcagcgctgttcaac	5	10	11	15	1	1	0	1	0	0	0	2	0	2	0	3	3	4	5	3	3	2	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:116429670G>C	ENST00000281928.3	-	17	3295	c.3089C>G	c.(3088-3090)gCc>gGc	p.A1030G		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1030						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ACTATTGCTGGCTGGGGCAGC	0.572																																					p.A1030G		.											.	MED13L-232	0			c.C3089G						.						63	55	58					12																	116429670		2203	4300	6503	SO:0001583	missense	23389	exon17			TTGCTGGCTGGGG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3089C>G	12.37:g.116429670G>C	ENSP00000281928:p.Ala1030Gly	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	77	35	NM_015335	0	0	8	17	9	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582626	0.46006	.	.	ENSG00000123066	ENST00000281928	T	0.75260	-0.92	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.75019	0.3793	L	0.36672	1.1	0.49915	D	0.999835	D	0.58268	0.982	P	0.49999	0.628	T	0.75639	-0.3248	10	0.51188	T	0.08	.	19.6873	0.95984	0.0:0.0:1.0:0.0	.	1030	Q71F56	MD13L_HUMAN	G	1030	ENSP00000281928:A1030G	ENSP00000281928:A1030G	A	-	2	0	MED13L	114914053	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.549000	0.67261	2.890000	0.99128	0.585000	0.79938	GCC	.		0.572	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			C	116429670	G	C	116429670	3	2	97	1	0	0	0	0	1	0	0	0	9456	1203	42	4	3603	4	MED13L	12	116429670	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08	8418553	116429670	17422225	37	8706											
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20601376	20601376	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgccatttttgtaagcgaaActctttacctcaataccaag	12	14	5	10	1	2	0	1	0	1	0	2	1	2	0	3	0	5	1	3	0	6	7			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr13:20601376A>G	ENST00000382874.2	+	10	1959	c.1769A>G	c.(1768-1770)aAc>aGc	p.N590S	ZMYM2_ENST00000382883.3_Missense_Mutation_p.N72S|ZMYM2_ENST00000382871.2_Missense_Mutation_p.N590S|ZMYM2_ENST00000382869.3_Missense_Mutation_p.N590S	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	590					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TGTAAGCGAAACTCTTTACCT	0.318																																					p.N590S		.											.	ZMYM2-685	0			c.A1769G						.						83	76	78					13																	20601376		1823	4068	5891	SO:0001583	missense	7750	exon10			AGCGAAACTCTTT	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"Zinc fingers, MYM type"	12989	protein-coding gene	gene with protein product		602221	"zinc finger protein 198"	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.1769A>G	13.37:g.20601376A>G	ENSP00000372327:p.Asn590Ser	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	16	2	NM_001190964	0	0	25	25	0	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	37	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.478970	0.26511	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382883	T;T;T;T	0.42513	2.31;2.31;2.31;0.97	5.35	5.35	0.76521	TRASH (1);Zinc finger, MYM-type (1);	0.000000	0.85682	D	0.000000	T	0.30510	0.0767	N	0.15975	0.35	0.51482	D	0.999924	P	0.45827	0.867	P	0.50314	0.637	T	0.17776	-1.0358	10	0.02654	T	1	0.0	11.1375	0.48383	0.8619:0.0:0.0:0.1381	.	590	Q9UBW7	ZMYM2_HUMAN	S	590;590;590;590;72	ENSP00000372322:N590S;ENSP00000372327:N590S;ENSP00000372324:N590S;ENSP00000372336:N72S	ENSP00000372322:N590S	N	+	2	0	ZMYM2	19499376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.552000	0.60747	2.015000	0.59207	0.477000	0.44152	AAC	.		0.318	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		G	20601376	A	G	20601376	3	3	97	1	0	0	0	0	1	0	0	0	17732	43	2	3	1795	3	ZMYM2	13	20601376	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08		20601376	94568502	38	8707											
STARD13	90627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	33700266	33700266	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcagtgcttgctgaatactTtgaggcaggggctgtcccgt	6	12	13	10	1	1	2	1	2	0	0	2	2	2	2	1	3	3	4	1	3	2	3	rs143789881		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr13:33700266T>G	ENST00000336934.5	-	7	2150	c.2034A>C	c.(2032-2034)caA>caC	p.Q678H	STARD13_ENST00000255486.4_Missense_Mutation_p.Q670H|STARD13_ENST00000399365.3_Missense_Mutation_p.Q560H	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	678	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GCTGAATACTTTGAGGCAGGG	0.542																																					p.Q678H		.											.	STARD13-94	0			c.A2034C						.						174	146	156					13																	33700266		2203	4300	6503	SO:0001583	missense	90627	exon7			AATACTTTGAGGC	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	19164	protein-coding gene	gene with protein product		609866	"START domain containing 13", "long intergenic non-protein coding RNA 464"	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.2034A>C	13.37:g.33700266T>G	ENSP00000338785:p.Gln678His	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	185	91	NM_178006	0	0	2	3	1	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.399557	0.42512	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.18502	2.21;2.21;2.21	6.17	2.43	0.29744	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.120228	0.64402	D	0.000011	T	0.25827	0.0629	L	0.51914	1.62	0.80722	D	1	D;B;B	0.53745	0.962;0.048;0.129	P;B;B	0.58928	0.848;0.193;0.084	T	0.00970	-1.1496	10	0.40728	T	0.16	.	7.0057	0.24836	0.112:0.6413:0.0:0.2467	.	643;678;670	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	H	560;670;678;670	ENSP00000382300:Q560H;ENSP00000255486:Q670H;ENSP00000338785:Q678H	ENSP00000255486:Q670H	Q	-	3	2	STARD13	32598266	0.993000	0.37304	0.981000	0.43875	0.797000	0.45037	0.424000	0.21330	0.174000	0.19809	-1.082000	0.02213	CAA	T|1.000;C|0.000		0.542	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		G	33700266	T	G	33700266	3	3	97	1	0	0	0	0	1	0	0	0	15288	1838	64	5	1339	5	STARD13	13	33700266	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	13098890	33700266	81469612	39	8708											
SLC38A6	145389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	61449295	61449295	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaatttgatgaatgccatcAtgggaagtggcatccttggc	10	13	11	7	0	1	2	1	2	0	0	2	3	2	3	2	3	1	1	2	3	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr14:61449295A>C	ENST00000267488.4	+	2	291	c.175A>C	c.(175-177)Atg>Ctg	p.M59L	SLC38A6_ENST00000554304.1_3'UTR|SLC38A6_ENST00000354886.2_Missense_Mutation_p.M59L|TRMT5_ENST00000261249.6_5'Flank|SLC38A6_ENST00000456840.2_Missense_Mutation_p.M36L|RP11-193F5.1_ENST00000553946.1_RNA	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	59					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		GAATGCCATCATGGGAAGTGG	0.368																																					p.M59L		.											.	SLC38A6-92	0			c.A175C						.						209	187	195					14																	61449295		2203	4300	6503	SO:0001583	missense	145389	exon2			GCCATCATGGGAA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.175A>C	14.37:g.61449295A>C	ENSP00000267488:p.Met59Leu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	102	48	NM_153811	0	0	5	9	4	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.655540	0.67586	.	.	ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000526105	T;T;T;T;T	0.02121	4.44;4.44;4.44;4.44;4.44	5.63	5.63	0.86233	.	0.149549	0.85682	D	0.000000	T	0.02929	0.0087	L	0.35542	1.07	0.54753	D	0.999988	B;B;B	0.14012	0.009;0.004;0.006	B;B;B	0.15052	0.005;0.01;0.012	T	0.55398	-0.8147	10	0.35671	T	0.21	.	16.1307	0.81436	1.0:0.0:0.0:0.0	.	36;59;59	E7ETF2;Q8IZM9-2;Q8IZM9	.;.;S38A6_HUMAN	L	59;59;54;36;5	ENSP00000346959:M59L;ENSP00000267488:M59L;ENSP00000395851:M54L;ENSP00000413863:M36L;ENSP00000451244:M5L	ENSP00000267488:M59L	M	+	1	0	SLC38A6	60519048	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.794000	0.75135	2.263000	0.75096	0.533000	0.62120	ATG	.		0.368	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			C	61449295	A	C	61449295	3	2	97	1	0	0	0	0	1	0	0	0	14640	217	8	5	181	5	SLC38A6	14	61449295	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08		61449295	45900245	40	8709											
TJP1	7082	bcgsc.ca	37	chr15	30033565	30033565	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catcttcatgagttgaattaGgtaggacaccatcagatgga	13	11	10	7	0	3	3	2	2	1	1	3	5	3	5	1	3	0	2	1	3	3	4	rs569819076		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr15:30033565G>A	ENST00000346128.6	-	10	1700	c.1226C>T	c.(1225-1227)cCt>cTt	p.P409L	TJP1_ENST00000545208.2_Missense_Mutation_p.P409L|TJP1_ENST00000356107.6_Missense_Mutation_p.P409L|TJP1_ENST00000400011.2_Missense_Mutation_p.P413L	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	409				QPDVDLPVSPSDGVLPNSTHEDGI -> NQMWIYLSVHLMV SYLIQLMKMGF (in Ref. 1; AAA02891). {ECO:0000305}.	apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		AGTTGAATTAGGTAGGACACC	0.343													G|||	1	0.000199681	0	0	5008	,	,		16296	0		0	False		,,,				2504	0.001				p.P409L	Melanoma(77;681 1843 6309 6570)												.	TJP1-95	0			c.C1226T						.						68	68	68					15																	30033565		1827	4084	5911	SO:0001583	missense	7082	exon10			GAATTAGGTAGGA		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.1226C>T	15.37:g.30033565G>A	ENSP00000281537:p.Pro409Leu	Somatic	93	0		WXS	Illumina HiSeq	Phase_1	69	5	NM_175610	0	0	14	14	0	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167877	0.57476	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.08008	3.15;3.32;3.25;3.14	5.54	5.54	0.83059	PDZ/DHR/GLGF (1);	1.110610	0.06608	N	0.755084	T	0.25568	0.0622	L	0.59436	1.845	0.80722	D	1	B;B;P;D	0.58620	0.033;0.057;0.947;0.983	B;B;P;P	0.54544	0.058;0.07;0.735;0.755	T	0.03025	-1.1081	9	.	.	.	.	19.4859	0.95028	0.0:0.0:1.0:0.0	.	402;409;409;413	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	L	409;413;409;409;409	ENSP00000281537:P409L;ENSP00000382890:P413L;ENSP00000441202:P409L;ENSP00000348416:P409L	.	P	-	2	0	TJP1	27820857	1.000000	0.71417	0.129000	0.21949	0.290000	0.27261	9.864000	0.99589	2.608000	0.88229	0.555000	0.69702	CCT	.		0.343	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30033565	G	A	30033565	3	1	97	1	0	0	0	0	1	0	0	0	15961	1000	35	2	4096	2	TJP1	15	30033565	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08		30033565	72497827	41	8710											
HOMER2	9455	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	83518619	83518620	+	Frame_Shift_Ins	INS	-	-	T																															tctgtctttaaggaacgcacINStttgtcttccaggttttgat																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr15:83518619_83518620insT	ENST00000304231.8	-	9	1104_1105	c.912_913insA	c.(910-915)aaagtgfs	p.V305fs	HOMER2_ENST00000426485.1_Frame_Shift_Ins_p.V250fs|HOMER2_ENST00000399166.2_Frame_Shift_Ins_p.V239fs|HOMER2_ENST00000450735.2_Frame_Shift_Ins_p.V294fs	NM_199330.2	NP_955362.1	Q9NSB8	HOME2_HUMAN	homer homolog 2 (Drosophila)	305					behavioral response to cocaine (GO:0048148)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|chemical homeostasis within a tissue (GO:0048875)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				cervix(1)|endometrium(2)|lung(6)	9						AAGGAACGCACTTTGTCTTCCA	0.505											OREG0023389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V305fs		.											.	HOMER2-67	0			c.913_914insA						.																																			SO:0001589	frameshift_variant	9455	exon9			.	AF093264	CCDS45334.1, CCDS45336.1	15q24.3	2008-02-05				ENSG00000103942			17513	protein-coding gene	gene with protein product		604799				9808459, 9808458	Standard	NM_199330		Approved	CPD, Cupidin, Vesl-2, HOMER-2B, HOMER-2, HOMER-2A	uc002bjg.3	Q9NSB8		ENST00000304231.8:c.913dupA	15.37:g.83518622_83518622dupT	ENSP00000305632:p.Val305fs	Somatic	152	0	1222	WXS	Illumina HiSeq	Phase_I	112	53	NM_199330	0	0	0	0	0	O95269|O95349|Q9NSB6|Q9NSB7|Q9UNT7	Frame_Shift_Ins	INS	ENST00000304231.8	37	CCDS45334.1																																																																																			.		0.505	HOMER2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418689.1			T	83518620	-	T	83518619	7	5	97	1	0	1	1	0	0	0	0	0	7300	565	20	0	155	0	HOMER2	15	83518619	Frame_Shift_Ins	INS	-	TCGA-DW-7839-01A-11D-2136-08	53485054	83518619	19012773	42	8711											
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	24802526	24802526	+	Frame_Shift_Del	DEL	G	G	-																															ggtggtctgtttctgccagtGataactggggagaaacttca																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr16:24802526delG	ENST00000395799.3	+	6	2692	c.2563delG	c.(2563-2565)gatfs	p.D855fs	TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.D855fs	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	855	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TTCTGCCAGTGATAACTGGGG	0.478																																					p.D855fs		.											.	TNRC6A-92	0			c.2563delG						.						80	79	79					16																	24802526		2197	4300	6497	SO:0001589	frameshift_variant	27327	exon6			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2563delG	16.37:g.24802526delG	ENSP00000379144:p.Asp855fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	67	28	NM_014494	0	0	0	0	0	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Frame_Shift_Del	DEL	ENST00000395799.3	37	CCDS10624.2																																																																																			.		0.478	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		-	24802526	G	-	24802526	7	5	97	1	0	1	0	1	0	0	0	0	16372	1290	45	0	2585	0	TNRC6A	16	24802526	Frame_Shift_Del	DEL	G	TCGA-DW-7839-01A-11D-2136-08		24802526	65552227	43	8712											
WWP2	11060	bcgsc.ca	37	chr16	69971116	69971116	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccccgctggagtggctgcGctactttgacgagaaagagc	8	7	15	11	3	0	3	0	1	0	2	0	5	0	4	2	3	3	3	2	3	2	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr16:69971116G>A	ENST00000359154.2	+	20	2314	c.2213G>A	c.(2212-2214)cGc>cAc	p.R738H	WWP2_ENST00000448661.1_Missense_Mutation_p.R738H|WWP2_ENST00000356003.2_Missense_Mutation_p.R738H|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000542271.1_Missense_Mutation_p.R622H|WWP2_ENST00000568684.1_Missense_Mutation_p.R299H	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	738	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GAGTGGCTGCGCTACTTTGAC	0.607																																					p.R738H													.	WWP2-658	0			c.G2213A						.						67	64	65					16																	69971116		2198	4300	6498	SO:0001583	missense	11060	exon20			GGCTGCGCTACTT	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2213G>A	16.37:g.69971116G>A	ENSP00000352069:p.Arg738His	Somatic	104	0		WXS	Illumina HiSeq	Phase_1	97	6	NM_001270454	0	0	44	44	0	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679133	0.88542	.	.	ENSG00000198373	ENST00000359154;ENST00000545099;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.21	4.26	0.50523	HECT (4);	0.000000	0.85682	D	0.000000	T	0.38799	0.1054	N	0.17723	0.515	0.80722	D	1	P	0.41131	0.739	B	0.34779	0.189	T	0.20140	-1.0284	9	.	.	.	.	13.815	0.63285	0.0739:0.0:0.9261:0.0	.	738	O00308	WWP2_HUMAN	H	738;299;738;738;625;622	ENSP00000352069:R738H;ENSP00000396871:R738H;ENSP00000348283:R738H;ENSP00000445616:R622H	.	R	+	2	0	WWP2	68528617	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.770000	0.62309	1.312000	0.45043	0.655000	0.94253	CGC	.		0.607	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		A	69971116	G	A	69971116	3	1	97	1	0	0	0	0	1	0	0	0	17449	1087	38	1	2291	1	WWP2	16	69971116	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08	45168590	69971116	20383637	44	8713											
ADAD2	161931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	84228944	84228944	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgaaggagatctacaagcTggtggctctgggcaccggca	9	7	15	10	2	2	2	0	1	2	1	2	3	2	2	1	5	2	4	1	5	3	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr16:84228944T>A	ENST00000315906.5	+	5	828	c.776T>A	c.(775-777)cTg>cAg	p.L259Q	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.L341Q	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	259					RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						ATCTACAAGCTGGTGGCTCTG	0.677																																					p.L341Q		.											.	ADAD2-68	0			c.T1022A						.						13	15	15					16																	84228944		2167	4266	6433	SO:0001583	missense	161931	exon6			ACAAGCTGGTGGC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.776T>A	16.37:g.84228944T>A	ENSP00000325153:p.Leu259Gln	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	28	11	NM_139174	0	0	0	0	0	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937894	0.52972	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	T;T	0.19938	2.11;2.12	5.22	5.22	0.72569	.	0.300709	0.27618	N	0.018561	T	0.39462	0.1079	L	0.49126	1.545	0.38021	D	0.934833	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.40059	-0.9583	10	0.87932	D	0	-12.5673	11.7794	0.52003	0.0:0.0:0.0:1.0	.	259;341	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	Q	259;341	ENSP00000325153:L259Q;ENSP00000268624:L341Q	ENSP00000268624:L341Q	L	+	2	0	ADAD2	82786445	1.000000	0.71417	0.881000	0.34555	0.081000	0.17604	5.029000	0.64121	2.088000	0.63022	0.528000	0.53228	CTG	.		0.677	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84228944	T	A	84228944	3	1	97	1	0	0	0	0	1	0	0	0	232	1580	55	5	1044	5	ADAD2	16	84228944	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	14257828	84228944	6125809	45	8714											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	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-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|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	265	268					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	410	56		WXS	Illumina HiSeq		503	62	NM_145301	0	0	12	75	63	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		T	15457087	C	T	15457087	3	4	97	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		15457087	65738123	46	8715											
SREBF1	6720	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17721579	17721579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagccaggactcactgcttTtgtggacagcagtgcgcaga	11	8	12	10	1	1	1	1	0	0	1	1	3	1	3	1	2	4	3	1	2	1	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr17:17721579T>C	ENST00000261646.5	-	6	1362	c.1178A>G	c.(1177-1179)aAa>aGa	p.K393R	SREBF1_ENST00000355815.4_Missense_Mutation_p.K423R|SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000435530.2_Missense_Mutation_p.K393R|SREBF1_ENST00000338854.5_Missense_Mutation_p.K393R|SREBF1_ENST00000395757.1_Missense_Mutation_p.K139R	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	393	Interaction with LMNA. {ECO:0000250}.|Leucine-zipper.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						CTCACTGCTTTTGTGGACAGC	0.567																																					p.K423R		.											.	SREBF1-91	0			c.A1268G						.						126	105	112					17																	17721579		2203	4300	6503	SO:0001583	missense	6720	exon7			CTGCTTTTGTGGA	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"Basic helix-loop-helix proteins"	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.1178A>G	17.37:g.17721579T>C	ENSP00000261646:p.Lys393Arg	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	102	27	NM_001005291	0	0	0	0	0	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	37	CCDS11189.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.472206	0.84533	.	.	ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000395757;ENST00000418712;ENST00000423161;ENST00000435530	T;T;T;T;T	0.80738	0.37;0.4;0.4;0.88;-1.41	5.13	2.6	0.31112	Helix-loop-helix DNA-binding (2);	0.049203	0.85682	N	0.000000	D	0.83496	0.5267	L	0.50333	1.59	0.58432	D	0.999998	D;B;D;D	0.89917	0.998;0.402;1.0;1.0	D;B;D;D	0.91635	0.993;0.235;0.997;0.999	T	0.79674	-0.1705	10	0.51188	T	0.08	-4.0837	6.0908	0.19993	0.0:0.1068:0.1545:0.7388	.	393;369;393;423	B0I4X3;B0I4X4;P36956;P36956-4	.;.;SRBP1_HUMAN;.	R	393;423;393;139;230;319;393	ENSP00000345822:K393R;ENSP00000348069:K423R;ENSP00000261646:K393R;ENSP00000379106:K139R;ENSP00000413389:K393R	ENSP00000261646:K393R	K	-	2	0	SREBF1	17662304	0.997000	0.39634	0.970000	0.41538	0.899000	0.52679	2.228000	0.42981	0.187000	0.20147	0.459000	0.35465	AAA	.		0.567	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		C	17721579	T	C	17721579	3	2	97	1	0	0	0	0	1	0	0	0	15173	1841	64	3	2321	3	SREBF1	17	17721579	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	2264492	17721579	63473631	47	8716											
ERBB2	2064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37880219	37880220	+	Missense_Mutation	DNP	TT	TT	CC																															ttccagtggccatcaaagtgTtgagggaaaacacatccccc																								rs121913470|rs121913469		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr17:37880219_37880220TT>CC	ENST00000269571.5	+	19	2422_2423	c.2263_2264TT>CC	c.(2263-2265)TTg>CCg	p.L755P	ERBB2_ENST00000584450.1_Missense_Mutation_p.L755P|ERBB2_ENST00000406381.2_Missense_Mutation_p.L725P|ERBB2_ENST00000541774.1_Missense_Mutation_p.L740P|ERBB2_ENST00000540147.1_Missense_Mutation_p.L725P|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584601.1_Missense_Mutation_p.L725P|ERBB2_ENST00000445658.2_Missense_Mutation_p.L479P			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	755	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> P (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:15457249}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.L755S(10)|p.L755P(2)|p.L755_S760>A(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CATCAAAGTGTTGAGGGAAAAC	0.53	L755S(LN229_CENTRAL_NERVOUS_SYSTEM)	1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.L755P		.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	ERBB2,NS,carcinoma,0	ERBB2	13	Substitution - Missense(12)|Complex - insertion inframe(1)	breast(7)|lung(3)|stomach(2)|large_intestine(1)	c.T2264C						.																																			SO:0001583	missense	2064	exon19			AAGTGTTGAGGGA	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		Exception_encountered	17.37:g.37880219_37880220delinsCC	ENSP00000269571:p.Leu755Pro	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	71	45		0	0	0	0	0	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	DNP	ENST00000269571.5	37	CCDS32642.1																																																																																			.		0.53	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			CC	37880220	TT	CC	37880219	3	2	97	1	0	0	0	0	1	0	0	0	5219	1722	60	3	2337	3	ERBB2	17	37880219	Missense_Mutation	DNP	TT	TCGA-DW-7839-01A-11D-2136-08	20158640	37880219	43314991	48	8717											
CYP2A6	1548	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	41352945	41352945	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtttcatcaccgaagagaaCatctcatagagctggggttg	11	11	11	8	1	3	2	3	0	1	2	4	4	3	2	1	2	2	3	1	2	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:41352945C>T	ENST00000301141.5	-	5	686	c.666G>A	c.(664-666)atG>atA	p.M222I	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	222					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCGAAGAGAACATCTCATAGA	0.537																																					p.M222I		.											.	CYP2A6-92	0			c.G666A						.						48	40	43					19																	41352945		2203	4297	6500	SO:0001583	missense	1548	exon5			AGAGAACATCTCA	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.666G>A	19.37:g.41352945C>T	ENSP00000301141:p.Met222Ile	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	110	25	NM_000762	0	0	0	0	0	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	5.838	0.338918	0.11069	.	.	ENSG00000255974	ENST00000301141	T	0.01240	5.12	2.37	1.3	0.21679	.	0.182151	0.48767	D	0.000168	T	0.00998	0.0033	N	0.16233	0.39	0.25269	N	0.989535	B;B	0.25206	0.099;0.12	B;B	0.34346	0.18;0.18	T	0.48692	-0.9013	10	0.09338	T	0.73	.	4.7113	0.12873	0.0:0.5458:0.0:0.4542	.	222;222	Q13120;P11509	.;CP2A6_HUMAN	I	222	ENSP00000301141:M222I	ENSP00000301141:M222I	M	-	3	0	CYP2A6	46044785	0.020000	0.18652	0.953000	0.39169	0.845000	0.48019	-0.094000	0.11094	0.334000	0.23590	0.386000	0.25728	ATG	.		0.537	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		T	41352945	C	T	41352945	3	4	97	1	0	0	0	0	1	0	0	0	4168	478	17	2	838	2	CYP2A6	19	41352945	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		41352945	17776038	49	8718											
CYP2A7	1549	hgsc.bcm.edu;broad.mit.edu	37	chr19	41384830	41384830	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtttcatcaccgaagagaaCatctcatagagctggggttg	11	11	11	8	1	3	2	3	0	1	2	4	4	3	2	1	2	2	3	1	2	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:41384830C>T	ENST00000301146.4	-	5	1207	c.666G>A	c.(664-666)atG>atA	p.M222I	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.M171I	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	222						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCGAAGAGAACATCTCATAGA	0.532																																					p.M222I		.											.	CYP2A7-93	0			c.G666A						.						36	33	34					19																	41384830		2203	4296	6499	SO:0001583	missense	1549	exon5			AGAGAACATCTCA	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"Cytochrome P450s"	2611	protein-coding gene	gene with protein product		608054	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.666G>A	19.37:g.41384830C>T	ENSP00000301146:p.Met222Ile	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	65	9	NM_000764	0	0	0	0	0	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	C	8.228	0.803977	0.16467	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.66815	5.12;-0.23	2.18	1.08	0.20341	.	0.182151	0.48767	D	0.000168	T	0.43366	0.1244	N	0.12569	0.235	0.23876	N	0.996596	B;B;B	0.25206	0.099;0.058;0.12	B;B;B	0.38562	0.276;0.169;0.276	T	0.34179	-0.9839	10	0.08837	T	0.75	.	2.9623	0.05896	0.0:0.4535:0.2402:0.3063	.	222;171;222	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	I	222;171	ENSP00000301146:M222I;ENSP00000291764:M171I	ENSP00000291764:M171I	M	-	3	0	CYP2A7	46076670	0.490000	0.26012	0.683000	0.30040	0.473000	0.32948	0.500000	0.22562	0.240000	0.21263	0.184000	0.17185	ATG	.		0.532	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		T	41384830	C	T	41384830	3	4	97	1	0	0	0	0	1	0	0	0	4169	478	17	2	838	2	CYP2A7	19	41384830	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	31885	41384830	17744153	50	8719											
DMPK	1760	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46281110	46281110	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacaggtagtctggggtgcCcacagccaccagcgaccgca	9	4	14	14	2	1	0	0	0	1	0	1	2	1	1	4	4	3	2	4	4	1	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:46281110C>T	ENST00000291270.4	-	7	822	c.697G>A	c.(697-699)Ggc>Agc	p.G233S	DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000447742.2_Missense_Mutation_p.G233S|DMPK_ENST00000343373.4_Missense_Mutation_p.G243S|DMPK_ENST00000458663.2_Missense_Mutation_p.G233S|DMPK_ENST00000600757.1_Missense_Mutation_p.G243S|DMPK_ENST00000354227.5_Missense_Mutation_p.G233S	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		TCTGGGGTGCCCACAGCCACC	0.692																																					p.G243S	Esophageal Squamous(35;307 869 9153 24033 28903)	.											.	DMPK-546	0			c.G727A						.						34	38	37					19																	46281110		2200	4292	6492	SO:0001583	missense	1760	exon6			GGGTGCCCACAGC	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"dystrophia myotonica 1", "DM protein kinase", "myotonin protein kinase A", "myotonic dystrophy associated protein kinase", "thymopoietin homolog"	605377	"dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.697G>A	19.37:g.46281110C>T	ENSP00000291270:p.Gly233Ser	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	98	43	NM_001081563	0	0	9	19	10	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	c	35	5.523740	0.96431	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	4.77	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43747	D	0.000533	T	0.80929	0.4718	H	0.95982	3.75	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;1.0;1.0;1.0;1.0	D	0.87078	0.2164	10	0.87932	D	0	.	15.3285	0.74186	0.0:1.0:0.0:0.0	.	233;233;259;233;233;233;280;243	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	S	233;259;233;233;233;243;243;233	ENSP00000401753:G233S;ENSP00000291270:G233S;ENSP00000413417:G233S;ENSP00000345997:G243S;ENSP00000346168:G233S	ENSP00000291270:G233S	G	-	1	0	DMPK	50972950	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.606000	0.82863	2.455000	0.83008	0.655000	0.94253	GGC	.		0.692	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		T	46281110	C	T	46281110	3	4	97	1	0	0	0	0	1	0	0	0	4595	623	22	2	1235	2	DMPK	19	46281110	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	4896280	46281110	12847873	51	8720											
NLRP2	55655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55494859	55494859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtaagggtggacattcaaCggtgacagacctgcaggagc	11	8	14	8	1	1	2	1	1	0	1	1	4	1	4	1	4	3	2	1	4	2	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:55494859C>T	ENST00000543010.1	+	6	1936	c.1793C>T	c.(1792-1794)aCg>aTg	p.T598M	NLRP2_ENST00000391721.4_Missense_Mutation_p.T574M|NLRP2_ENST00000263437.6_Missense_Mutation_p.T595M|NLRP2_ENST00000448584.2_Missense_Mutation_p.T598M|NLRP2_ENST00000427260.2_Missense_Mutation_p.T575M|NLRP2_ENST00000538819.1_Missense_Mutation_p.T574M|NLRP2_ENST00000339757.7_Missense_Mutation_p.T576M|NLRP2_ENST00000537859.1_Missense_Mutation_p.T576M	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	598					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGACATTCAACGGTGACAGAC	0.537																																					p.T598M		.											.	NLRP2-120	0			c.C1793T						.						107	92	97					19																	55494859		2203	4300	6503	SO:0001583	missense	55655	exon6			ATTCAACGGTGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1793C>T	19.37:g.55494859C>T	ENSP00000445135:p.Thr598Met	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	84	39	NM_017852	0	0	0	0	0	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048824	0.36181	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.74842	-0.87;-0.78;-0.8;-0.87;-0.8;-0.88;-0.78;-0.87	1.94	-0.27	0.12926	.	.	.	.	.	T	0.72095	0.3418	L	0.40543	1.245	0.09310	N	1	D;D;D;D;D	0.63880	0.993;0.993;0.988;0.993;0.988	P;P;P;P;P	0.58391	0.749;0.838;0.693;0.838;0.693	T	0.59894	-0.7368	9	0.48119	T	0.1	.	4.2569	0.10721	0.0:0.6265:0.0:0.3735	.	575;576;595;574;598	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	M	598;574;576;598;576;575;574;595	ENSP00000445135:T598M;ENSP00000375601:T574M;ENSP00000344074:T576M;ENSP00000409370:T598M;ENSP00000440601:T576M;ENSP00000402474:T575M;ENSP00000441133:T574M;ENSP00000263437:T595M	ENSP00000263437:T595M	T	+	2	0	NLRP2	60186671	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.276000	0.08514	-0.000000	0.14550	0.561000	0.74099	ACG	.		0.537	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55494859	C	T	55494859	3	4	97	1	0	0	0	0	1	0	0	0	10503	536	19	1	1811	1	NLRP2	19	55494859	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	9213749	55494859	3634124	52	8721											
SNX5	27131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	17933351	17933351	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcttaaacacagcgagataCtcactgaaaagagatgtgca	16	9	8	8	1	2	3	1	1	1	2	2	5	2	3	0	0	4	1	0	0	5	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr20:17933351C>G	ENST00000377768.3	-	6	705	c.393G>C	c.(391-393)gaG>gaC	p.E131D	SNX5_ENST00000377759.4_Missense_Mutation_p.E131D|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	131	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						CAGCGAGATACTCACTGAAAA	0.453																																					p.E131D		.											.	SNX5-289	0			c.G393C						.						53	47	49					20																	17933351		2203	4300	6503	SO:0001583	missense	27131	exon5			GAGATACTCACTG	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.393G>C	20.37:g.17933351C>G	ENSP00000366998:p.Glu131Asp	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	33	15	NM_014426	0	0	0	0	0	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763778	0.49574	.	.	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277;ENST00000419004	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.66	-7.72	0.01250	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	M	0.68593	2.085	0.52099	D	0.999949	B;P	0.44006	0.435;0.824	B;P	0.48141	0.366;0.568	T	0.60311	-0.7288	10	0.38643	T	0.18	.	16.5172	0.84304	0.0:0.2582:0.0:0.7418	.	152;131	B7Z476;Q9Y5X3	.;SNX5_HUMAN	D	131;131;94;96	ENSP00000366998:E131D;ENSP00000366988:E131D;ENSP00000404448:E94D;ENSP00000406731:E96D	ENSP00000366988:E131D	E	-	3	2	SNX5	17881351	0.985000	0.35326	0.546000	0.28166	0.781000	0.44180	0.195000	0.17155	-1.620000	0.01564	-1.124000	0.02001	GAG	.		0.453	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			G	17933351	C	G	17933351	3	3	97	1	0	0	0	0	1	0	0	0	14937	564	20	4	857	4	SNX5	20	17933351	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		17933351	45092169	53	8722											
WFDC10A	140832	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	44258534	44258534	+	Frame_Shift_Del	DEL	A	A	-																															gaggataccgtgacaagaagAggatgcagagtaggtgatgg																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr20:44258534delA	ENST00000372643.3	+	1	370	c.82delA	c.(82-84)aggfs	p.R28fs	WFDC9_ENST00000326000.1_Intron	NM_080753.2	NP_542791.1	Q9H1F0	WF10A_HUMAN	WAP four-disulfide core domain 10A	28						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)	2		Myeloproliferative disorder(115;0.0122)				TGACAAGAAGAGGATGCAGAG	0.577											OREG0025983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R28fs		.											.	WFDC10A-90	0			c.82delA						.						165	130	142					20																	44258534		2203	4300	6503	SO:0001589	frameshift_variant	140832	exon1			.	AL031671	CCDS13363.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000180305	ENSG00000180305		"WAP four-disulfide core domain containing"	16139	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 146"	C20orf146		12206714	Standard	NM_080753		Approved	dJ688G8.3, WAP10	uc002xoz.3	Q9H1F0	OTTHUMG00000046331	ENST00000372643.3:c.82delA	20.37:g.44258534delA	ENSP00000361726:p.Arg28fs	Somatic	53	0	922	WXS	Illumina HiSeq	Phase_I	49	20	NM_080753	0	0	0	0	0	A2RRE9|Q5TGZ7	Frame_Shift_Del	DEL	ENST00000372643.3	37	CCDS13363.1																																																																																			.		0.577	WFDC10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106944.2			-	44258534	A	-	44258534	7	5	97	1	0	1	0	1	0	0	0	0	17380	295	11	0	84	0	WFDC10A	20	44258534	Frame_Shift_Del	DEL	A	TCGA-DW-7839-01A-11D-2136-08	26325183	44258534	18766986	54	8723											
NUDT10	170685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	51075840	51075840	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtgcaaacccaaccagaCacggacctacgaccccgagg	14	2	10	15	3	0	1	0	0	0	1	0	5	0	2	5	2	4	1	5	2	4	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chrX:51075840C>T	ENST00000376006.3	+	2	243	c.23C>T	c.(22-24)aCa>aTa	p.T8I	NUDT10_ENST00000356450.2_Missense_Mutation_p.T8I	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	0					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					CCCAACCAGACACGGACCTAC	0.677																																					p.T8I	NSCLC(90;1817 2035 37909 38249)	.											.	NUDT10-90	0			c.C23T						.						48	36	40					X																	51075840		2203	4300	6503	SO:0001583	missense	170685	exon2			ACCAGACACGGAC	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"Nudix motif containing"	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.23C>T	X.37:g.51075840C>T	ENSP00000365174:p.Thr8Ile	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	68	12	NM_153183	0	0	0	0	0	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000376006.3	37	CCDS35278.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.619529	0.46736	.	.	ENSG00000122824	ENST00000376006;ENST00000356450	T;T	0.41758	0.99;0.99	2.61	2.61	0.31194	NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	L	0.40543	1.245	0.38831	D	0.955848	B	0.06786	0.001	B	0.08055	0.003	T	0.39440	-0.9614	9	0.33141	T	0.24	-26.7854	10.5501	0.45083	0.0:1.0:0.0:0.0	.	8	Q8NFP7	NUD10_HUMAN	I	8	ENSP00000365174:T8I;ENSP00000348831:T8I	ENSP00000348831:T8I	T	+	2	0	NUDT10	51092580	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	4.938000	0.63519	1.602000	0.50124	0.429000	0.28392	ACA	.		0.677	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183		T	51075840	C	T	51075840	3	4	97	1	0	0	0	0	1	0	0	0	10752	478	17	2	25	2	NUDT10	23	51075840	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		51075840	104194720	55	8724											
NUDT11	55190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	51239274	51239274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcggggtcgtaggtccgcGtctggttgggtttgcacttc	2	13	15	11	4	1	0	0	0	1	0	5	0	2	0	2	5	1	4	2	5	1	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chrX:51239274G>A	ENST00000375992.3	-	1	174	c.23C>T	c.(22-24)aCg>aTg	p.T8M		NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 11	8					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9	Ovarian(276;0.236)					GTAGGTCCGCGTCTGGTTGGG	0.682										HNSCC(48;0.14)																											p.T8M	GBM(38;198 791 1498 11752 13599)	.											.	NUDT11-130	0			c.C23T						.						20	17	18					X																	51239274		2199	4298	6497	SO:0001583	missense	55190	exon1			GTCCGCGTCTGGT	AK001490	CCDS43952.1	Xp11.22-p11.1	2014-05-20			ENSG00000196368	ENSG00000196368		"Nudix motif containing"	18011	protein-coding gene	gene with protein product						12105228	Standard	NM_018159		Approved	DIPP3b, FLJ10628, hDIPP3beta	uc010njt.3	Q96G61	OTTHUMG00000021531	ENST00000375992.3:c.23C>T	X.37:g.51239274G>A	ENSP00000365160:p.Thr8Met	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	26	12	NM_018159	0	0	0	0	0	Q9NVN0	Missense_Mutation	SNP	ENST00000375992.3	37	CCDS43952.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134884	0.56828	.	.	ENSG00000196368	ENST00000375992	T	0.40756	1.02	3.0	2.01	0.26516	NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.36635	0.0974	M	0.70275	2.135	0.36766	D	0.883520	P	0.43750	0.816	B	0.37692	0.256	T	0.55270	-0.8167	9	0.48119	T	0.1	-26.7854	8.2508	0.31717	0.0:0.0:0.7647:0.2353	.	8	Q96G61	NUD11_HUMAN	M	8	ENSP00000365160:T8M	ENSP00000365160:T8M	T	-	2	0	NUDT11	51256014	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.357000	0.90088	1.514000	0.48869	0.544000	0.68410	ACG	.		0.682	NUDT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056579.1			A	51239274	G	A	51239274	3	1	97	1	0	0	0	0	1	0	0	0	10753	1145	40	1	479	1	NUDT11	23	51239274	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08	163434	51239274	104031286	56	8725											
RGAG4	340526	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	71351213	71351213	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgcaaggacgggcactaTgggtactggccagcggatgt	8	7	15	11	3	0	0	0	0	0	0	1	2	1	2	2	5	2	3	2	5	3	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chrX:71351213T>C	ENST00000545866.1	-	1	545	c.178A>G	c.(178-180)Ata>Gta	p.I60V	NHSL2_ENST00000535692.1_5'Flank|NHSL2_ENST00000373677.1_5'Flank|NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Missense_Mutation_p.I60V|NHSL2_ENST00000510661.1_5'Flank	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	60										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					ACGGGCACTATGGGTACTGGC	0.617													T|||	3	0.000794702	0	0.0043	3775	,	,		8298	0		0	False		,,,				2504	0				p.I60V		.											.	RGAG4-132	0			c.A178G						.						49	52	52					X																	71351213		1948	4125	6073	SO:0001583	missense	340526	exon1			GCACTATGGGTAC	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.178A>G	X.37:g.71351213T>C	ENSP00000441366:p.Ile60Val	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	118	53	NM_001024455	0	0	7	7	0	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	T	0.155	-1.087731	0.01873	.	.	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.12774	2.65;2.65	3.58	-1.73	0.08081	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43130	-0.9410	8	.	.	.	.	4.2089	0.10502	0.2097:0.5432:0.0:0.2471	.	60	Q5HYW3	RGAG4_HUMAN	V	60	ENSP00000441366:I60V;ENSP00000418667:I60V	.	I	-	1	0	RGAG4	71267938	0.096000	0.21769	0.004000	0.12327	0.666000	0.39218	-0.475000	0.06599	-0.475000	0.06852	-0.438000	0.05819	ATA	.		0.617	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		C	71351213	T	C	71351213	3	2	97	1	0	0	0	0	1	0	0	0	13307	1464	51	3	1535	3	RGAG4	23	71351213	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	20111939	71351213	83919347	57	8726											
KIAA1751	85452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1887063	1887063	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcccctgggcccctcagccCcctggaatgctgccctgagg	4	7	11	19	0	1	1	1	1	0	0	2	2	2	2	7	3	3	1	7	3	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:1887063C>T								TMEM52 (36351 upstream) : C1orf222 (32499 downstream)																							CCCCTCAGCCCCCTGGAATGC	0.597																																					p.G748E		.											.	KIAA1751-69	0			c.G2243A						.						61	67	65					1																	1887063		1913	4097	6010	SO:0001628	intergenic_variant	85452	exon18			TCAGCCCCCTGGA																													1.37:g.1887063C>T		Somatic	149	0		WXS	Illumina HiSeq	Phase_I	149	38	NM_001080484	0	0	0	0	0		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	11.65	1.701128	0.30142	.	.	ENSG00000142609	ENST00000270720	.	.	.	1.45	-0.582	0.11709	.	0.105878	0.36665	N	0.002476	T	0.14657	0.0354	N	0.08118	0	0.09310	N	1	B	0.19817	0.039	B	0.11329	0.006	T	0.11494	-1.0585	9	0.87932	D	0	.	3.7893	0.08713	0.0:0.5066:0.0:0.4934	.	748	Q9C0B2	K1751_HUMAN	E	748	.	ENSP00000270720:G748E	G	-	2	0	C1orf222	1876923	0.000000	0.05858	0.001000	0.08648	0.193000	0.23685	0.050000	0.14120	-0.199000	0.10317	0.462000	0.41574	GGG	.	0	0.597									T	1887063	C	T	1887063	1	4	98	0	1	0	0	0	0	0	0	0	8277	623	22	2		2	KIAA1751	1	1887063	IGR	SNP	C	TCGA-DW-7840-01A-11D-2136-08		1887063	247363558	1	8727											
CAMTA1	23261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	7721912	7721912	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggacccacaactgcctctGcaccggcagcctgggtgagc	7	5	13	16	2	1	1	0	1	1	0	1	2	1	2	4	3	5	2	4	3	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:7721912G>C	ENST00000303635.7	+	8	998	c.791G>C	c.(790-792)tGc>tCc	p.C264S	CAMTA1_ENST00000439411.2_Missense_Mutation_p.C264S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	264					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AACTGCCTCTGCACCGGCAGC	0.687			T	WWTR1	epitheliod hemangioendothelioma																																p.C264S		.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1-520	0			c.G791C						.						26	25	26					1																	7721912		2199	4298	6497	SO:0001583	missense	23261	exon8			GCCTCTGCACCGG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.791G>C	1.37:g.7721912G>C	ENSP00000306522:p.Cys264Ser	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	23	9	NM_015215	0	0	0	0	0	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	g	18.00	3.526318	0.64860	.	.	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.52526	0.66;0.66	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.42539	0.1207	L	0.58101	1.795	0.80722	D	1	B	0.32573	0.376	B	0.27380	0.079	T	0.38112	-0.9676	10	0.10902	T	0.67	-19.7455	18.2029	0.89844	0.0:0.0:1.0:0.0	.	264	Q9Y6Y1	CMTA1_HUMAN	S	264	ENSP00000306522:C264S;ENSP00000402561:C264S	ENSP00000306522:C264S	C	+	2	0	CAMTA1	7644499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.654000	0.98509	2.382000	0.81193	0.543000	0.68304	TGC	.		0.687	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		C	7721912	G	C	7721912	3	2	98	1	0	0	0	0	1	0	0	0	2619	1319	46	4	821	4	CAMTA1	1	7721912	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	5834849	7721912	241528709	2	8728											
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	8424145	8424145	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actccgccgtgtcctcatgcTatgcttcccactgagcccat	6	11	7	17	2	1	1	1	1	0	0	4	1	4	1	5	0	3	2	5	0	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:8424145T>A	ENST00000337907.3	-	16	2345	c.1711A>T	c.(1711-1713)Agc>Tgc	p.S571C	RERE_ENST00000377464.1_Missense_Mutation_p.S303C|RERE_ENST00000476556.1_Missense_Mutation_p.S17C|RERE_ENST00000400907.2_Intron|RERE_ENST00000460659.1_5'Flank|RERE_ENST00000400908.2_Missense_Mutation_p.S571C	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	571					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTCCTCATGCTATGCTTCCCA	0.602																																					p.S571C		.											.	RERE-515	0			c.A1711T						.						76	65	69					1																	8424145		2203	4300	6503	SO:0001583	missense	473	exon16			TCATGCTATGCTT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1711A>T	1.37:g.8424145T>A	ENSP00000338629:p.Ser571Cys	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	100	42	NM_012102	0	0	13	20	7	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.182080	0.78677	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T	0.06768	3.26;3.26;3.26	5.17	5.17	0.71159	.	.	.	.	.	T	0.26122	0.0637	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.995	T	0.00498	-1.1704	9	0.59425	D	0.04	-23.1488	14.3401	0.66619	0.0:0.0:0.0:1.0	.	303;571	B1AKN3;Q9P2R6	.;RERE_HUMAN	C	571;303;17;571	ENSP00000338629:S571C;ENSP00000366684:S303C;ENSP00000383700:S571C	ENSP00000338629:S571C	S	-	1	0	RERE	8346732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.520000	0.81821	2.171000	0.68590	0.459000	0.35465	AGC	.		0.602	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			A	8424145	T	A	8424145	3	1	98	1	0	0	0	0	1	0	0	0	13263	1522	53	5	3025	5	RERE	1	8424145	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	702233	8424145	240826476	3	8729											
ECE1	1889	hgsc.bcm.edu	37	chr1	21546592	21546592	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcggtgatgaggccttcgtgGgagctctcaggtgtgcggac	5	10	17	9	3	1	2	1	2	1	0	4	4	1	4	1	5	2	1	1	5	0	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:21546592G>C	ENST00000374893.6	-	19	2243	c.2169C>G	c.(2167-2169)tcC>tcG	p.S723S	ECE1_ENST00000264205.6_Silent_p.S720S|ECE1_ENST00000415912.2_Silent_p.S707S|ECE1_ENST00000357071.4_Silent_p.S711S|ECE1_ENST00000436918.2_Silent_p.S691S	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	723					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		GGCCTTCGTGGGAGCTCTCAG	0.637																																					p.S723S		.											.	ECE1-93	0			c.C2169G						.						68	58	62					1																	21546592		2203	4300	6503	SO:0001819	synonymous_variant	1889	exon19			TTCGTGGGAGCTC	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.2169C>G	1.37:g.21546592G>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_001397	0	0	40	40	0	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	37	CCDS215.1																																																																																			.		0.637	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		C	21546592	G	C	21546592	2	2	98	1	0	0	0	0	0	0	0	1	4900	1219	43	4		4	ECE1	1	21546592	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	13122447	21546592	227704029	4	8730											
HMGCL	3155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24147039	24147039	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcggggaccaacttccacAattttcacccgctttggtaa	9	12	7	13	2	2	0	1	0	1	0	4	1	3	1	3	3	1	2	3	3	3	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:24147039A>C	ENST00000374490.3	-	2	148	c.105T>G	c.(103-105)atT>atG	p.I35M	HMGCL_ENST00000374483.4_Missense_Mutation_p.I10M|HMGCL_ENST00000436439.2_Missense_Mutation_p.I35M|HMGCL_ENST00000509389.1_5'UTR	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	35					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		CAACTTCCACAATTTTCACCC	0.403																																					p.I35M		.											.	HMGCL-90	0			c.T105G						.						159	141	147					1																	24147039		2203	4300	6503	SO:0001583	missense	3155	exon2			TTCCACAATTTTC	BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.105T>G	1.37:g.24147039A>C	ENSP00000363614:p.Ile35Met	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	149	53	NM_000191	0	0	11	29	18	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Missense_Mutation	SNP	ENST00000374490.3	37	CCDS243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.82|14.82	2.650811|2.650811	0.47362|0.47362	.|.	.|.	ENSG00000117305|ENSG00000117305	ENST00000374490;ENST00000436439;ENST00000374483;ENST00000543166|ENST00000235958	D;D;D|.	0.98862|.	-5.19;-5.1;-5.19|.	5.27|5.27	0.302|0.302	0.15786|0.15786	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (1);|.	0.147080|.	0.64402|.	D|.	0.000011|.	T|T	0.30448|0.30448	0.0765|0.0765	N|N	0.08118|0.08118	0|0	0.41038|0.41038	D|D	0.985205|0.985205	P;B;B;B|.	0.37141|.	0.584;0.08;0.08;0.08|.	B;B;B;B|.	0.40741|.	0.338;0.339;0.232;0.339|.	T|T	0.04440|0.04440	-1.0951|-1.0951	10|5	0.66056|.	D|.	0.02|.	-0.2207|-0.2207	8.6087|8.6087	0.33789|0.33789	0.566:0.0:0.434:0.0|0.566:0.0:0.434:0.0	.|.	35;35;10;35|.	B4DUP4;Q6IBC0;B1AK13;P35914|.	.;.;.;HMGCL_HUMAN|.	M|W	35;35;10;10|31	ENSP00000363614:I35M;ENSP00000389281:I35M;ENSP00000363607:I10M|.	ENSP00000363607:I10M|.	I|L	-|-	3|2	3|0	HMGCL|HMGCL	24019626|24019626	0.519000|0.519000	0.26242|0.26242	1.000000|1.000000	0.80357|0.80357	0.931000|0.931000	0.56810|0.56810	-0.299000|-0.299000	0.08254|0.08254	0.132000|0.132000	0.18615|0.18615	-0.385000|-0.385000	0.06624|0.06624	ATT|TTG	.		0.403	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191		C	24147039	A	C	24147039	3	2	98	1	0	0	0	0	1	0	0	0	7250	126	5	5	904	5	HMGCL	1	24147039	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	2600447	24147039	225103582	5	8731											
C1orf63	57035	bcgsc.ca	37	chr1	25573160	25573160	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagtatctcctggtgaaccCgtagcgcctctctcggtaac	7	11	10	13	3	2	1	0	1	2	0	5	1	2	1	3	2	3	4	3	2	5	4	rs201238140		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:25573160C>A	ENST00000243189.7	-	2	571	c.295G>T	c.(295-297)Ggg>Tgg	p.G99W	C1orf63_ENST00000417642.2_Missense_Mutation_p.G92W|C1orf63_ENST00000431849.2_Missense_Mutation_p.G99W|RP3-465N24.6_ENST00000607698.1_lincRNA	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		99	Arg/Ser-rich.									breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CTGGTGAACCCGTAGCGCCTC	0.672																																					p.G99W													.	C1orf63-91	0			c.G295T						.						39	36	37					1																	25573160		2203	4300	6503	SO:0001583	missense	57035	exon2			TGAACCCGTAGCG																												ENST00000243189.7:c.295G>T	1.37:g.25573160C>A	ENSP00000243189:p.Gly99Trp	Somatic	53	0		WXS	Illumina HiSeq	Phase_1	67	5	NM_020317	0	0	13	13	0	A8K917|Q49AA4|Q5TH71|Q9GZP6	Missense_Mutation	SNP	ENST00000243189.7	37	CCDS260.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.575558	0.45902	.	.	ENSG00000117616	ENST00000243189;ENST00000417642;ENST00000431849	T;T;T	0.45276	1.5;1.5;0.9	3.91	2.99	0.34606	.	1.048650	0.07579	N	0.919965	T	0.48429	0.1499	L	0.36672	1.1	0.09310	N	1	D	0.67145	0.996	D	0.63381	0.914	T	0.31447	-0.9943	10	0.66056	D	0.02	-2.3987	4.1231	0.10114	0.0:0.5882:0.1964:0.2154	.	99	Q9BUV0	CA063_HUMAN	W	99;92;99	ENSP00000243189:G99W;ENSP00000411631:G92W;ENSP00000391510:G99W	ENSP00000243189:G99W	G	-	1	0	C1orf63	25445747	0.000000	0.05858	0.004000	0.12327	0.058000	0.15608	-0.259000	0.08721	0.985000	0.38656	0.561000	0.74099	GGG	C|0.999;T|0.000		0.672	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2			A	25573160	C	A	25573160	3	1	98	1	0	0	0	0	1	0	0	0	2059	652	23	4	593	4	C1orf63	1	25573160	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	1426121	25573160	223677461	6	8732											
PHACTR4	65979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	28785697	28785697	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaagagcaagttctcaggcTttggcaagatcttcaagccc	11	9	11	10	0	3	2	2	0	2	2	4	3	3	3	1	3	2	4	1	3	4	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:28785697T>C	ENST00000373839.3	+	3	379	c.118T>C	c.(118-120)Ttt>Ctt	p.F40L	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.F50L	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	40					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		GTTCTCAGGCTTTGGCAAGAT	0.448																																					p.F50L		.											.	PHACTR4-90	0			c.T148C						.						87	84	85					1																	28785697		1904	4119	6023	SO:0001583	missense	65979	exon2			TCAGGCTTTGGCA	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.118T>C	1.37:g.28785697T>C	ENSP00000362945:p.Phe40Leu	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	84	28	NM_023923	0	0	1	5	4	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706660	0.48412	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.12465	2.68;2.69	5.28	5.28	0.74379	.	0.185233	0.48767	N	0.000178	T	0.06234	0.0161	N	0.04132	-0.27	0.36529	D	0.870593	B;B;B	0.14012	0.005;0.003;0.009	B;B;B	0.16722	0.009;0.004;0.016	T	0.13469	-1.0508	10	0.02654	T	1	-1.0711	14.6855	0.69047	0.0:0.0:0.0:1.0	.	50;40;24	Q8IZ21-2;Q8IZ21;Q8IZ21-3	.;PHAR4_HUMAN;.	L	40;50;39	ENSP00000362945:F40L;ENSP00000362942:F50L	ENSP00000362942:F50L	F	+	1	0	PHACTR4	28658284	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.667000	0.37471	2.128000	0.65567	0.528000	0.53228	TTT	.		0.448	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		C	28785697	T	C	28785697	3	2	98	1	0	0	0	0	1	0	0	0	11838	1609	56	3	174	3	PHACTR4	1	28785697	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3212537	28785697	220464924	7	8733											
PUM1	9698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	31406096	31406096	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggggccacagatgggccctaAgtcaacaccgttcttcatgt	9	9	11	12	1	3	1	2	0	1	1	3	1	3	1	3	3	1	1	3	3	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:31406096A>T	ENST00000257075.5	-	22	3616	c.3523T>A	c.(3523-3525)Tta>Ata	p.L1175I	PUM1_ENST00000440538.2_Missense_Mutation_p.L1151I|PUM1_ENST00000373741.4_Missense_Mutation_p.L1213I|PUM1_ENST00000424085.2_Missense_Mutation_p.L933I|SNORD103A_ENST00000363284.1_RNA|PUM1_ENST00000373742.2_Missense_Mutation_p.L1116I|PUM1_ENST00000426105.2_Missense_Mutation_p.L1177I|PUM1_ENST00000373747.3_Missense_Mutation_p.L1178I|PUM1_ENST00000423018.2_Missense_Mutation_p.L1033I	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	1175					membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		ATGGGCCCTAAGTCAACACCG	0.552																																					p.L1177I		.											.	PUM1-92	0			c.T3529A						.						187	165	173					1																	31406096		2203	4300	6503	SO:0001583	missense	9698	exon22			GCCCTAAGTCAAC	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.3523T>A	1.37:g.31406096A>T	ENSP00000257075:p.Leu1175Ile	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	162	63	NM_001020658	0	0	28	46	18	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.95|17.95	3.512828|3.512828	0.64522|0.64522	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000525843;ENST00000498419|ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	.|T;T;T;T;T;T;T;T	.|0.20332	.|2.14;2.08;2.34;2.34;2.42;2.33;2.44;2.1	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000002|0.000002	T|T	0.34658|0.34658	0.0905|0.0905	L|L	0.56396|0.56396	1.775|1.775	0.80722|0.80722	D|D	1|1	.|D;B;B;B;B;P;B;D	.|0.67145	.|0.991;0.125;0.259;0.33;0.374;0.58;0.374;0.996	.|D;B;B;B;B;B;B;D	.|0.65773	.|0.938;0.076;0.076;0.159;0.168;0.183;0.168;0.913	T|T	0.14172|0.14172	-1.0482|-1.0482	6|10	.|0.51188	.|T	.|0.08	-3.3845|-3.3845	5.2679|5.2679	0.15609|0.15609	0.7814:0.0:0.2186:0.0|0.7814:0.0:0.2186:0.0	.|.	.|1116;1033;1213;1151;1175;1177;1178;1177	.|B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.|.;.;.;.;PUM1_HUMAN;.;.;.	H|I	1113;888|933;1175;1178;915;1177;1151;1213;1033;1116	.|ENSP00000400141:L933I;ENSP00000257075:L1175I;ENSP00000362852:L1178I;ENSP00000391723:L1177I;ENSP00000401777:L1151I;ENSP00000362846:L1213I;ENSP00000399440:L1033I;ENSP00000362847:L1116I	.|ENSP00000257075:L1175I	L|L	-|-	2|1	0|2	PUM1|PUM1	31178683|31178683	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.430000|1.430000	0.34914|0.34914	2.095000|2.095000	0.63458|0.63458	0.454000|0.454000	0.30748|0.30748	CTT|TTA	.		0.552	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			T	31406096	A	T	31406096	3	4	98	1	0	0	0	0	1	0	0	0	12857	69	3	5	41	5	PUM1	1	31406096	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	2620399	31406096	217844525	8	8734											
INADL	10207	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	62582269	62582269	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagacctggatgggagatTgattcagggagatcagatct	11	9	14	7	1	3	5	2	1	1	4	3	8	3	6	1	3	0	1	1	3	0	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:62582269T>C	ENST00000371158.2	+	36	4835	c.4721T>C	c.(4720-4722)tTg>tCg	p.L1574S	INADL_ENST00000543708.1_Missense_Mutation_p.L388S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1574	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GATGGGAGATTGATTCAGGGA	0.493																																					p.L1574S		.											.	INADL-94	0			c.T4721C						.						75	78	77					1																	62582269		1945	4135	6080	SO:0001583	missense	10207	exon36			GGAGATTGATTCA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4721T>C	1.37:g.62582269T>C	ENSP00000360200:p.Leu1574Ser	Somatic	53	1		WXS	Illumina HiSeq	Phase_I	47	20	NM_176877	0	0	1	5	4	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	T	25.3	4.623798	0.87460	.	.	ENSG00000132849	ENST00000371158;ENST00000543708	T;T	0.50548	0.74;0.74	5.56	5.56	0.83823	PDZ/DHR/GLGF (4);	0.000000	0.52532	D	0.000075	T	0.81197	0.4772	H	0.98314	4.2	0.80722	D	1	D;D;D	0.89917	1.0;0.972;1.0	D;P;D	0.91635	0.998;0.88;0.999	D	0.88783	0.3272	10	0.87932	D	0	.	15.7125	0.77641	0.0:0.0:0.0:1.0	.	388;1033;1574	B4DE90;Q8NI35-5;Q8NI35	.;.;INADL_HUMAN	S	1574;388	ENSP00000360200:L1574S;ENSP00000445790:L388S	ENSP00000360200:L1574S	L	+	2	0	INADL	62354857	1.000000	0.71417	0.992000	0.48379	0.915000	0.54546	8.008000	0.88588	2.108000	0.64289	0.533000	0.62120	TTG	.		0.493	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62582269	T	C	62582269	3	2	98	1	0	0	0	0	1	0	0	0	7752	1821	63	3	4859	3	INADL	1	62582269	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	31176173	62582269	186668352	9	8735											
FNBP1L	54874	broad.mit.edu	37	chr1	93996339	93996339	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagttgaatctgcgtacgCatatggccgatgaaaataaa	15	9	10	7	3	1	2	0	2	1	0	1	3	1	2	1	1	3	4	1	1	7	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:93996339C>T	ENST00000271234.7	+	7	689	c.538C>T	c.(538-540)Cat>Tat	p.H180Y	FNBP1L_ENST00000604705.1_Missense_Mutation_p.H180Y|FNBP1L_ENST00000370253.2_Missense_Mutation_p.H180Y|FNBP1L_ENST00000260506.8_Missense_Mutation_p.H180Y|FNBP1L_ENST00000370256.4_Missense_Mutation_p.H180Y	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	180	F-BAR domain. {ECO:0000250}.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		TCTGCGTACGCATATGGCCGA	0.318																																					p.H180Y													.	FNBP1L-227	0			c.C538T						.						38	37	38					1																	93996339		1829	4087	5916	SO:0001583	missense	54874	exon7			CGTACGCATATGG		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.538C>T	1.37:g.93996339C>T	ENSP00000271234:p.His180Tyr	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	20	7	NM_001164473	0	0	1	4	3	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Missense_Mutation	SNP	ENST00000271234.7	37	CCDS53343.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065606	0.76187	.	.	ENSG00000137942	ENST00000370256;ENST00000271234;ENST00000260506;ENST00000370253;ENST00000424449	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.32466	0.0830	M	0.62723	1.935	0.80722	D	1	D;D	0.69078	0.997;0.985	D;P	0.74348	0.983;0.714	T	0.01951	-1.1241	10	0.48119	T	0.1	-39.0929	19.0931	0.93235	0.0:1.0:0.0:0.0	.	180;180	Q5T0N5-4;Q5T0N5-3	.;.	Y	180;180;180;180;47	ENSP00000359278:H180Y;ENSP00000271234:H180Y;ENSP00000260506:H180Y;ENSP00000359275:H180Y	ENSP00000260506:H180Y	H	+	1	0	FNBP1L	93768927	1.000000	0.71417	0.973000	0.42090	0.528000	0.34623	7.487000	0.81328	2.527000	0.85204	0.655000	0.94253	CAT	.		0.318	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		T	93996339	C	T	93996339	3	4	98	1	0	0	0	0	1	0	0	0	5985	710	25	2	564	2	FNBP1L	1	93996339	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	31414070	93996339	155254282	10	8736											
RBM15	64783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110883658	110883658	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcagcctctgcccttgaCtcattatgagctggtgacag	7	12	10	12	0	3	3	1	3	2	0	3	3	3	3	2	1	4	2	2	1	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:110883658C>G	ENST00000369784.3	+	1	2531	c.1631C>G	c.(1630-1632)aCt>aGt	p.T544S	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000487146.2_Missense_Mutation_p.T544S|RBM15_ENST00000602849.1_Missense_Mutation_p.T544S	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	544					negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		CTGCCCTTGACTCATTATGAG	0.547			T	MKL1	acute megakaryocytic leukemia																																p.T544S		.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15-661	0			c.C1631G						.						74	71	72					1																	110883658		2203	4300	6503	SO:0001583	missense	64783	exon1			CCTTGACTCATTA	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.1631C>G	1.37:g.110883658C>G	ENSP00000358799:p.Thr544Ser	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	143	57	NM_022768	0	0	0	0	0	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	C	6.069	0.381059	0.11466	.	.	ENSG00000162775	ENST00000369784	T	0.15952	2.38	4.44	4.44	0.53790	.	0.000000	0.44688	D	0.000431	T	0.03915	0.0110	N	0.22421	0.69	0.27060	N	0.963566	B;B	0.24426	0.103;0.063	B;B	0.22386	0.039;0.017	T	0.31251	-0.9950	10	0.10636	T	0.68	-8.2962	13.8608	0.63559	0.0:0.8463:0.1537:0.0	.	544;544	Q96T37-3;Q96T37	.;RBM15_HUMAN	S	544	ENSP00000358799:T544S	ENSP00000358799:T544S	T	+	2	0	RBM15	110685181	0.985000	0.35326	1.000000	0.80357	0.993000	0.82548	2.270000	0.43355	2.306000	0.77630	0.655000	0.94253	ACT	.		0.547	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		G	110883658	C	G	110883658	3	3	98	1	0	0	0	0	1	0	0	0	13148	565	20	4	1633	4	RBM15	1	110883658	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	16887319	110883658	138366963	11	8737											
ADCY10	55811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167870956	167870956	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggtctcaaacaatccaTggatctccaggctacattta	11	11	7	12	0	2	0	1	0	2	0	5	1	3	1	3	3	2	1	3	3	4	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:167870956T>A	ENST00000367851.4	-	5	564	c.380A>T	c.(379-381)cAt>cTt	p.H127L	ADCY10_ENST00000545172.1_Intron|ADCY10_ENST00000367848.1_Missense_Mutation_p.H35L	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	127	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						AAACAATCCATGGATCTCCAG	0.478																																					p.H127L		.											.	ADCY10-493	0			c.A380T						.						170	167	168					1																	167870956		2203	4300	6503	SO:0001583	missense	55811	exon5			AATCCATGGATCT	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.380A>T	1.37:g.167870956T>A	ENSP00000356825:p.His127Leu	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	237	83	NM_018417	0	0	0	0	0	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.859754	0.71834	.	.	ENSG00000143199	ENST00000367851;ENST00000367848	T;T	0.78003	-1.14;1.49	5.76	5.76	0.90799	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.177315	0.39985	N	0.001214	T	0.67468	0.2896	L	0.27053	0.805	0.35716	D	0.816771	D;D	0.61697	0.988;0.99	P;P	0.62491	0.844;0.903	T	0.66666	-0.5866	9	0.11794	T	0.64	-17.7472	12.4728	0.55797	0.0:0.0:0.0:1.0	.	35;127	Q96PN6-2;Q96PN6	.;ADCYA_HUMAN	L	127;35	ENSP00000356825:H127L;ENSP00000356822:H35L	ENSP00000356822:H35L	H	-	2	0	ADCY10	166137580	1.000000	0.71417	0.922000	0.36590	0.701000	0.40568	4.710000	0.61873	2.193000	0.70182	0.450000	0.29827	CAT	.		0.478	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		A	167870956	T	A	167870956	3	1	98	1	0	0	0	0	1	0	0	0	293	1464	51	5	4568	5	ADCY10	1	167870956	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	56987298	167870956	81379665	12	8738											
IKBKE	9641	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	206651658	206651658	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccaggcagtcctgcaccAcatctatatccatgcccaca	10	8	6	17	0	1	0	0	0	1	0	4	0	4	0	5	1	2	2	5	1	2	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:206651658A>G	ENST00000367120.3	+	9	1341	c.968A>G	c.(967-969)cAc>cGc	p.H323R	IKBKE_ENST00000537984.1_Missense_Mutation_p.H238R	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	323					immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GTCCTGCACCACATCTATATC	0.572																																					p.H323R		.											.	IKBKE-1061	0			c.A968G						.						201	170	181					1																	206651658		2203	4300	6503	SO:0001583	missense	9641	exon9			TGCACCACATCTA	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.968A>G	1.37:g.206651658A>G	ENSP00000356087:p.His323Arg	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	241	66	NM_001193322	0	0	2	4	2	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	a	6.092	0.385235	0.11524	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.62105	0.05;0.2	5.31	2.99	0.34606	.	0.288882	0.40818	N	0.001016	T	0.39226	0.1070	N	0.17474	0.49	0.23351	N	0.997852	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.18871	-1.0323	10	0.11182	T	0.66	-5.285	8.6511	0.34035	0.7589:0.0:0.2411:0.0	.	238;323	Q3B754;Q14164	.;IKKE_HUMAN	R	323;238	ENSP00000356087:H323R;ENSP00000444529:H238R	ENSP00000356087:H323R	H	+	2	0	IKBKE	204718281	0.715000	0.27946	0.538000	0.28064	0.720000	0.41350	1.322000	0.33689	0.345000	0.23873	0.454000	0.30748	CAC	.		0.572	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			G	206651658	A	G	206651658	3	3	98	1	0	0	0	0	1	0	0	0	7633	159	6	3	994	3	IKBKE	1	206651658	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	38780702	206651658	42598963	13	8739											
SYT14	255928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	210267875	210267875	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaggtcatgaaatagaaagTtttcataataaaggatatga	19	11	8	3	0	2	3	2	2	0	1	2	4	2	4	0	2	0	1	0	2	7	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:210267875T>C	ENST00000472886.1	+	5	665	c.651T>C	c.(649-651)agT>agC	p.S217S	SYT14_ENST00000422431.1_Silent_p.S262S|SYT14_ENST00000367015.1_Silent_p.S179S|SYT14_ENST00000367019.1_Silent_p.S217S|SYT14_ENST00000399639.2_Silent_p.S217S|SYT14_ENST00000537238.1_Silent_p.S179S|SYT14_ENST00000534859.1_Silent_p.S217S|SYT14_ENST00000271745.7_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	217					cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		AAATAGAAAGTTTTCATAATA	0.393																																					p.S262S		.											.	SYT14-92	0			c.T786C						.						82	81	81					1																	210267875		2203	4300	6503	SO:0001819	synonymous_variant	255928	exon6			AGAAAGTTTTCAT	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"Synaptotagmins"	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.651T>C	1.37:g.210267875T>C		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	66	26	NM_001146264	0	0	0	0	0	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Silent	SNP	ENST00000472886.1	37	CCDS31014.1																																																																																			.		0.393	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		C	210267875	T	C	210267875	2	2	98	1	0	0	0	0	0	0	0	1	15502	1722	60	3		3	SYT14	1	210267875	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3616217	210267875	38982746	14	8740											
EPRS	2058	hgsc.bcm.edu	37	chr1	220180553	220180553	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagttcttacttgtgtattTttgtaatgttgaggttgccc	8	19	9	5	0	1	1	0	1	1	0	1	1	1	1	1	1	2	5	1	1	4	9			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:220180553T>G	ENST00000366923.3	-	14	2002	c.1733A>C	c.(1732-1734)aAa>aCa	p.K578T		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	578	Glutamate--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CTTGTGTATTTTTGTAATGTT	0.318																																					p.K578T		.											.	EPRS-92	0			c.A1733C						.						54	54	54					1																	220180553		2203	4300	6503	SO:0001583	missense	2058	exon14			TGTATTTTTGTAA	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.1733A>C	1.37:g.220180553T>G	ENSP00000355890:p.Lys578Thr	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_004446	0	0	0	0	0	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.258740	0.59321	.	.	ENSG00000136628	ENST00000366923;ENST00000536921;ENST00000435048	T	0.08370	3.1	5.81	3.5	0.40072	Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain (1);Ribosomal protein L25/Gln-tRNA synthetase, beta-barrel domain (1);Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain (1);	0.089451	0.85682	D	0.000000	T	0.18383	0.0441	M	0.81239	2.535	0.80722	D	1	P;B;P	0.38223	0.623;0.006;0.587	B;B;P	0.45577	0.401;0.183;0.486	T	0.00449	-1.1732	10	0.62326	D	0.03	-14.9339	10.2231	0.43209	0.0:0.1342:0.0:0.8658	.	602;585;578	E7EMN0;Q3KQZ8;P07814	.;.;SYEP_HUMAN	T	578;585;602	ENSP00000355890:K578T	ENSP00000355890:K578T	K	-	2	0	EPRS	218247176	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	3.386000	0.52492	0.477000	0.27464	0.473000	0.43528	AAA	.		0.318	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		G	220180553	T	G	220180553	3	3	98	1	0	0	0	0	1	0	0	0	5204	1841	64	5	2881	5	EPRS	1	220180553	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	9912678	220180553	29070068	15	8741											
SLC30A6	55676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32422810	32422810	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttccgggacttagcagtatcTtccttccccgaatgaatcca	9	12	7	13	2	1	1	0	1	1	0	5	3	5	2	5	1	1	2	5	1	4	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:32422810T>A	ENST00000282587.5	+	10	617	c.580T>A	c.(580-582)Ttc>Atc	p.F194I	SLC30A6_ENST00000538303.1_Missense_Mutation_p.F165I|SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000406369.1_Missense_Mutation_p.F120I|SLC30A6_ENST00000435660.1_Missense_Mutation_p.F194I|SLC30A6_ENST00000379343.2_Missense_Mutation_p.F234I	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	194					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TAGCAGTATCTTCCTTCCCCG	0.348																																					p.F234I		.											.	SLC30A6-90	0			c.T700A						.						195	185	188					2																	32422810		2203	4300	6503	SO:0001583	missense	55676	exon11			AGTATCTTCCTTC	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"Solute carriers"	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.580T>A	2.37:g.32422810T>A	ENSP00000282587:p.Phe194Ile	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	151	58	NM_001193513	0	0	0	1	1	A5YM45|B7Z901|Q8N5C9|Q96NC3	Missense_Mutation	SNP	ENST00000282587.5	37	CCDS1780.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.093791	0.76870	.	.	ENSG00000152683	ENST00000379343;ENST00000440718;ENST00000282587;ENST00000435660;ENST00000538303;ENST00000406369	T;T;T;T;T;T	0.62105	0.07;0.05;0.07;0.07;0.07;0.07	6.07	6.07	0.98685	.	0.101567	0.64402	D	0.000002	T	0.57051	0.2027	L	0.34521	1.04	0.80722	D	1	B;B;B;B	0.34399	0.367;0.452;0.202;0.31	B;B;B;B	0.40702	0.338;0.164;0.205;0.113	T	0.53457	-0.8436	10	0.23302	T	0.38	-14.6144	15.6102	0.76710	0.0:0.0:0.0:1.0	.	165;194;234;194	B7Z901;Q6NXT4-3;Q6NXT4-2;Q6NXT4	.;.;.;ZNT6_HUMAN	I	234;165;194;194;165;120	ENSP00000368648:F234I;ENSP00000393946:F165I;ENSP00000282587:F194I;ENSP00000399005:F194I;ENSP00000440678:F165I;ENSP00000384041:F120I	ENSP00000282587:F194I	F	+	1	0	SLC30A6	32276314	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.462000	0.66707	2.330000	0.79161	0.528000	0.53228	TTC	.		0.348	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2			A	32422810	T	A	32422810	3	1	98	1	0	0	0	0	1	0	0	0	14591	1609	56	5	618	5	SLC30A6	2	32422810	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08		32422810	210776563	16	8742											
MTIF2	4528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55470636	55470636	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgttcttttctttctaaaaAccgtagaattgatctcttct	9	20	4	8	1	5	2	0	1	5	1	6	2	5	2	1	0	1	2	1	0	5	9			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:55470636A>G	ENST00000263629.4	-	12	1795	c.1480T>C	c.(1480-1482)Ttt>Ctt	p.F494L	MTIF2_ENST00000394600.3_Missense_Mutation_p.F494L|MTIF2_ENST00000403721.1_Missense_Mutation_p.F494L	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	494					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						CTTTCTAAAAACCGTAGAATT	0.338																																					p.F494L		.											.	MTIF2-91	0			c.T1480C						.						146	146	146					2																	55470636		2203	4300	6503	SO:0001583	missense	4528	exon12			CTAAAAACCGTAG	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.1480T>C	2.37:g.55470636A>G	ENSP00000263629:p.Phe494Leu	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	145	48	NM_002453	0	0	9	14	5	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.584682	0.28268	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	T;T;T;T	0.56275	0.47;0.47;0.47;1.05	5.6	5.6	0.85130	Translation initiation factor IF- 2, domain 3 (1);	0.270733	0.37577	N	0.002040	T	0.41766	0.1173	L	0.38175	1.15	0.42010	D	0.990935	B	0.02656	0.0	B	0.01281	0.0	T	0.33394	-0.9870	10	0.09084	T	0.74	-2.2567	15.7861	0.78304	1.0:0.0:0.0:0.0	.	494	P46199	IF2M_HUMAN	L	494;494;494;172	ENSP00000384481:F494L;ENSP00000263629:F494L;ENSP00000378099:F494L;ENSP00000403492:F172L	ENSP00000263629:F494L	F	-	1	0	MTIF2	55324140	1.000000	0.71417	0.207000	0.23584	0.007000	0.05969	6.152000	0.71812	2.136000	0.66102	0.533000	0.62120	TTT	.		0.338	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		G	55470636	A	G	55470636	3	3	98	1	0	0	0	0	1	0	0	0	9959	43	2	3	723	3	MTIF2	2	55470636	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	23047826	55470636	187728737	17	8743											
USP34	9736	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	61493234	61493234	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgaagaatgtgatttgcaCtttggctgttgtcggtcctt	6	17	11	7	1	0	3	0	2	0	1	2	3	1	3	1	2	1	3	1	2	2	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:61493234C>T	ENST00000398571.2	-	42	5578	c.5502G>A	c.(5500-5502)aaG>aaA	p.K1834K		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1834					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GTGATTTGCACTTTGGCTGTT	0.408																																					p.K1834K		.											.	USP34-579	0			c.G5502A						.						123	111	115					2																	61493234		1848	4096	5944	SO:0001819	synonymous_variant	9736	exon42			TTTGCACTTTGGC	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"Ubiquitin-specific peptidases"	20066	protein-coding gene	gene with protein product		615295	"ubiquitin specific protease 34"			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5502G>A	2.37:g.61493234C>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	82	33	NM_014709	0	0	3	4	1	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1																																																																																			.		0.408	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61493234	C	T	61493234	2	4	98	1	0	0	0	0	0	0	0	1	17098	564	20	2		2	USP34	2	61493234	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08	6022598	61493234	181706139	18	8744											
IL1F5	26525	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	113820191	113820191	+	Frame_Shift_Del	DEL	G	G	-																															cagcctgtcagactcacccaGcttcccgagaatggtggctg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:113820191delG	ENST00000393200.2	+	5	566	c.405delG	c.(403-405)cagfs	p.Q135fs	IL36RN_ENST00000346807.3_Frame_Shift_Del_p.Q135fs	NM_012275.2	NP_036407.1	Q9UBH0	I36RA_HUMAN	interleukin 36 receptor antagonist	135					antifungal humoral response (GO:0019732)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of interferon-gamma secretion (GO:1902714)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)	extracellular space (GO:0005615)	interleukin-1 receptor antagonist activity (GO:0005152)			large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						GACTCACCCAGCTTCCCGAGA	0.632																																					p.Q135fs		.											.	IL36RN-91	0			c.405delG						.						50	48	49					2																	113820191		2203	4300	6503	SO:0001589	frameshift_variant	26525	exon5			.	AF201830	CCDS2111.1	2q14	2014-09-17	2011-06-06	2011-06-06	ENSG00000136695	ENSG00000136695		"Interleukins and interleukin receptors"	15561	protein-coding gene	gene with protein product	"family of interleukin 1-delta", "interleukin-1 receptor antagonist homolog 1", "interleukin-1 HY1", "IL-1 related protein 3"	605507	"interleukin 1 family, member 5 (delta)"	IL1F5		10625660, 10512743, 11574262	Standard	NM_012275		Approved	FIL1, FIL1(DELTA), FIL1D, IL1HY1, IL1RP3, IL1L1, IL-1F5, IL36RA, MGC29840	uc002tit.3	Q9UBH0	OTTHUMG00000131337	ENST00000393200.2:c.405delG	2.37:g.113820191delG	ENSP00000376896:p.Gln135fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	71	18	NM_012275	0	0	0	0	0	A8K2I4|Q56AT9|Q7RTZ6	Frame_Shift_Del	DEL	ENST00000393200.2	37	CCDS2111.1																																																																																			.		0.632	IL36RN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330729.1	NM_173170		-	113820191	G	-	113820191	7	5	98	1	0	1	0	1	0	0	0	0	7674	962	34	0	419	0	IL1F5	2	113820191	Frame_Shift_Del	DEL	G	TCGA-DW-7840-01A-11D-2136-08	52326957	113820191	129379182	19	8745											
RAB3GAP1	22930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	135891507	135891507	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgtgtctctgtatgatcaAtttttaccatggagggttga	8	18	10	5	0	2	2	1	2	1	0	3	3	2	3	1	2	1	2	1	2	3	6	rs578182809		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:135891507A>G	ENST00000264158.8	+	15	1446	c.1403A>G	c.(1402-1404)aAt>aGt	p.N468S	SNORA40_ENST00000385573.1_RNA|ZRANB3_ENST00000412849.1_5'Flank|RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.N424S|RAB3GAP1_ENST00000487003.1_3'UTR|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.N468S	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	468					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		TGTATGATCAATTTTTACCAT	0.383													A|||	1	0.000199681	8e-04	0	5008	,	,		16221	0		0	False		,,,				2504	0				p.N468S		.											.	RAB3GAP1-92	0			c.A1403G						.						134	133	133					2																	135891507		2203	4300	6503	SO:0001583	missense	22930	exon15			TGATCAATTTTTA	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.1403A>G	2.37:g.135891507A>G	ENSP00000264158:p.Asn468Ser	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	128	46	NM_001172435	0	0	7	11	4	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.421038	0.83559	.	.	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.48522	0.81;0.81;0.81	4.95	4.95	0.65309	.	0.043485	0.85682	D	0.000000	T	0.58337	0.2115	L	0.50333	1.59	0.58432	D	0.999995	D;D	0.76494	0.999;0.999	D;P	0.63283	0.913;0.883	T	0.53570	-0.8420	10	0.22109	T	0.4	-20.1443	14.9142	0.70781	1.0:0.0:0.0:0.0	.	468;468	C9J837;Q15042	.;RB3GP_HUMAN	S	468;424;468	ENSP00000264158:N468S;ENSP00000444306:N424S;ENSP00000411418:N468S	ENSP00000264158:N468S	N	+	2	0	RAB3GAP1	135607977	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.127000	0.94417	1.992000	0.58205	0.482000	0.46254	AAT	.		0.383	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		G	135891507	A	G	135891507	3	3	98	1	0	0	0	0	1	0	0	0	12967	101	4	3	1461	3	RAB3GAP1	2	135891507	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	22071316	135891507	107307866	20	8746											
TNS1	7145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	218713668	218713668	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtcgctgctcacagaaagCgtgtgttccacgtggttggg	7	10	15	9	3	1	1	1	0	0	1	3	2	2	1	1	2	2	4	1	2	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:218713668C>G	ENST00000171887.4	-	17	1649	c.1197G>C	c.(1195-1197)acG>acC	p.T399T	TNS1_ENST00000419504.1_Silent_p.T399T|TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Silent_p.T399T	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	399					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TCACAGAAAGCGTGTGTTCCA	0.612																																					p.T399T		.											.	TNS1-156	0			c.G1197C						.						143	137	139					2																	218713668		2203	4300	6503	SO:0001819	synonymous_variant	7145	exon17			AGAAAGCGTGTGT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1197G>C	2.37:g.218713668C>G		Somatic	195	1		WXS	Illumina HiSeq	Phase_I	226	95	NM_022648	0	0	3	3	0	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			.		0.612	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218713668	C	G	218713668	2	3	98	1	0	0	0	0	0	0	0	1	16375	755	27	4		4	TNS1	2	218713668	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08	82822161	218713668	24485705	21	8747											
C3orf22	152065	ucsc.edu;bcgsc.ca	37	chr3	126268739	126268739	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccctggacagccctgccGccttgctggtctgggggcag	3	7	16	15	1	1	0	0	0	1	0	1	1	1	1	5	5	3	2	5	5	0	1	rs373190783		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:126268739G>A	ENST00000318225.2	-	4	776	c.398C>T	c.(397-399)gCg>gTg	p.A133V		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	133										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		CAGCCCTGCCGCCTTGCTGGT	0.627																																					p.A133V													.	C3orf22-90	0			c.C398T						.	G	VAL/ALA	0,4406		0,0,2203	55	53	54		398	-0.5	0	3		54	1,8599	1.2+/-3.3	0,1,4299	no	missense	C3orf22	NM_152533.1	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	133/142	126268739	1,13005	2203	4300	6503	SO:0001583	missense	152065	exon4			CCTGCCGCCTTGC		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.398C>T	3.37:g.126268739G>A	ENSP00000316644:p.Ala133Val	Somatic	54	0		WXS	Illumina HiSeq		34	4	NM_152533	0	0	0	0	0	B3KUS9	Missense_Mutation	SNP	ENST00000318225.2	37	CCDS3040.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228530	0.39399	0.0	1.16E-4	ENSG00000180697	ENST00000318225	.	.	.	1.92	-0.536	0.11876	.	.	.	.	.	T	0.09818	0.0241	N	0.19112	0.55	0.09310	N	1	P	0.41188	0.741	B	0.25405	0.06	T	0.22730	-1.0208	8	0.02654	T	1	6.4871	4.5161	0.11935	0.4702:0.0:0.5298:0.0	.	133	Q8N5N4	CC022_HUMAN	V	133	.	ENSP00000316644:A133V	A	-	2	0	C3orf22	127751429	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.292000	0.08332	-0.154000	0.11118	0.313000	0.20887	GCG	.		0.627	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533		A	126268739	G	A	126268739	3	1	98	1	0	0	0	0	1	0	0	0	2221	1087	38	1	31	1	C3orf22	3	126268739	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08		126268739	71753691	22	8748											
ABTB1	80325	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	127396051	127396051	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgaaggtgctgaccatCgagcccccacctgcagaccc	8	7	11	15	1	0	3	0	2	0	1	1	4	0	3	5	1	3	2	5	1	1	0	rs368024563		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:127396051C>A	ENST00000232744.8	+	8	770	c.684C>A	c.(682-684)atC>atA	p.I228I	ABTB1_ENST00000393363.3_Silent_p.I86I|ABTB1_ENST00000453791.2_Silent_p.I86I|ABTB1_ENST00000468137.1_Silent_p.I86I					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						TGCTGACCATCGAGCCCCCAC	0.682																																					p.I228I		.											.	ABTB1-90	0			c.C684A						.						36	32	33					3																	127396051		2201	4297	6498	SO:0001819	synonymous_variant	80325	exon8			GACCATCGAGCCC	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.684C>A	3.37:g.127396051C>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	19	8	NM_172027	0	0	18	27	9		Silent	SNP	ENST00000232744.8	37	CCDS3045.1																																																																																			.		0.682	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027		A	127396051	C	A	127396051	2	1	98	1	0	0	0	0	0	0	0	1	102	874	31	4		4	ABTB1	3	127396051	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08	1127312	127396051	70626379	23	8749											
LSG1	55341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	194379786	194379786	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcccaggcactccgctgcTcagcagtcagcaagtctgcc	7	7	11	16	1	3	0	2	0	1	0	4	0	4	0	3	2	4	5	3	2	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:194379786T>G	ENST00000265245.5	-	7	973	c.659A>C	c.(658-660)gAg>gCg	p.E220A		NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	220	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		ACTCCGCTGCTCAGCAGTCAG	0.458																																					p.E220A		.											.	LSG1-90	0			c.A659C						.						160	168	165					3																	194379786		2203	4300	6503	SO:0001583	missense	55341	exon7			CGCTGCTCAGCAG		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"large subunit GTPase 1 homolog (S. cerevisiae)"			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.659A>C	3.37:g.194379786T>G	ENSP00000265245:p.Glu220Ala	Somatic	263	0		WXS	Illumina HiSeq	Phase_I	265	96	NM_018385	0	0	0	4	4	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	37	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.586546	0.66105	.	.	ENSG00000041802	ENST00000265245	D	0.91631	-2.88	6.17	2.65	0.31530	.	0.224693	0.45867	D	0.000326	D	0.88028	0.6327	L	0.35288	1.05	0.58432	D	0.999998	P	0.41498	0.752	P	0.46208	0.507	D	0.83890	0.0284	10	0.26408	T	0.33	.	9.937	0.41556	0.0:0.1846:0.0:0.8154	.	220	Q9H089	LSG1_HUMAN	A	220	ENSP00000265245:E220A	ENSP00000265245:E220A	E	-	2	0	LSG1	195861075	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	3.985000	0.56930	1.160000	0.42584	0.533000	0.62120	GAG	.		0.458	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		G	194379786	T	G	194379786	3	3	98	1	0	0	0	0	1	0	0	0	9074	1551	54	5	1349	5	LSG1	3	194379786	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	66983735	194379786	3642644	24	8750											
TFRC	7037	hgsc.bcm.edu;bcgsc.ca	37	chr3	195782165	195782166	+	Missense_Mutation	DNP	TC	TC	AG																															tggtacccaaataaggataaTctgtgtcctgcaagacaacg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:195782165_195782166TC>AG	ENST00000360110.4	-	17	1853_1854	c.1684_1685GA>CT	c.(1684-1686)GAt>CTt	p.D562L	TFRC_ENST00000465288.1_5'Flank|TFRC_ENST00000392396.3_Missense_Mutation_p.D562L|TFRC_ENST00000420415.1_Missense_Mutation_p.D481L|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000535031.1_Missense_Mutation_p.D280L	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	562					cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	ATAAGGATAATCTGTGTCCTGC	0.5			T	BCL6	NHL																																p.D562L		.		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	.	TFRC	0			c.G1684C						.																																			SO:0001583	missense	7037	exon17			GATAATCTGTGTC	X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"CD molecules"	11763	protein-coding gene	gene with protein product		190010	"transferrin receptor (p90, CD71)"				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.1684_1685delinsAG	3.37:g.195782165_195782166delinsAG	ENSP00000353224:p.Asp562Leu	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	67	25		0	0	0	0	0	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	DNP	ENST00000360110.4	37	CCDS3312.1																																																																																			.		0.5	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			AG	195782166	TC	AG	195782165	3	1	98	1	0	0	0	0	1	0	0	0	15844	1435	50	5	609	5	TFRC	3	195782165	Missense_Mutation	DNP	TC	TCGA-DW-7840-01A-11D-2136-08	1402379	195782165	2240265	25	8751											
CEP135	9662	hgsc.bcm.edu;bcgsc.ca	37	chr4	56874494	56874494	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttgtaatttctataggAaaaagctgttgctcaaatga	14	16	7	4	0	2	1	1	1	1	0	2	2	2	2	0	1	2	4	0	1	6	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:56874494A>G	ENST00000257287.4	+	18	2406	c.2282A>G	c.(2281-2283)gAa>gGa	p.E761G		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	761					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TTTCTATAGGAAAAAGCTGTT	0.289																																					p.E761G		.											.	CEP135-94	0			c.A2282G						.						60	64	63					4																	56874494		2201	4299	6500	SO:0001630	splice_region_variant	9662	exon18			TATAGGAAAAAGC	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2281-1A>G	4.37:g.56874494A>G		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	84	5	NM_025009	0	0	0	0	0	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463771	0.43736	.	.	ENSG00000174799	ENST00000257287	T	0.35048	1.33	5.48	5.48	0.80851	.	0.043970	0.85682	D	0.000000	T	0.50137	0.1598	M	0.78049	2.395	0.54753	D	0.999988	D	0.56287	0.975	P	0.51385	0.668	T	0.55341	-0.8156	10	0.54805	T	0.06	.	12.2418	0.54546	1.0:0.0:0.0:0.0	.	761	Q66GS9	CP135_HUMAN	G	761	ENSP00000257287:E761G	ENSP00000257287:E761G	E	+	2	0	CEP135	56569251	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	5.412000	0.66392	2.182000	0.69389	0.528000	0.53228	GAA	.		0.289	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	Missense_Mutation	G	56874494	A	G	56874494	5	3	98	1	0	0	0	0	0	0	1	0	3253	260	9	3	2348	3	CEP135	4	56874494	Splice_Site	SNP	A	TCGA-DW-7840-01A-11D-2136-08		56874494	134279782	26	8752											
RCHY1	25898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76415883	76415883	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtcatatctaaagcagAgtgcatacataatggacatc	14	10	8	9	0	2	1	1	0	1	1	3	2	2	2	1	2	3	2	1	2	5	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:76415883A>C	ENST00000324439.5	-	8	963	c.565T>G	c.(565-567)Tct>Gct	p.S189A	RCHY1_ENST00000451788.1_Missense_Mutation_p.L188R|RCHY1_ENST00000514021.1_5'Flank|RCHY1_ENST00000512706.1_Missense_Mutation_p.S167A|RCHY1_ENST00000513257.1_Missense_Mutation_p.S180A|RCHY1_ENST00000380840.2_Missense_Mutation_p.S149A	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	189					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCTAAAGCAGAGTGCATACAT	0.373																																					p.S189A		.											.	RCHY1-228	0			c.T565G						.						133	113	120					4																	76415883		2203	4300	6503	SO:0001583	missense	25898	exon8			AAGCAGAGTGCAT	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.565T>G	4.37:g.76415883A>C	ENSP00000321239:p.Ser189Ala	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	80	26	NM_015436	0	0	10	16	6	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Missense_Mutation	SNP	ENST00000324439.5	37	CCDS3567.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.67|14.67	2.604259|2.604259	0.46423|0.46423	.|.	.|.	ENSG00000163743|ENSG00000163743	ENST00000451788|ENST00000324439;ENST00000380840;ENST00000512706;ENST00000513257;ENST00000507014	.|T;T;T	.|0.35048	.|1.38;1.33;1.38	5.87|5.87	5.87|5.87	0.94306|0.94306	.|Zinc finger, RING/FYVE/PHD-type (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60235|0.60235	0.2253|0.2253	.|.	.|.	.|.	0.32406|0.32406	N|N	0.551239|0.551239	.|D;D;D;D	.|0.89917	.|0.996;0.997;0.996;1.0	.|D;D;D;D	.|0.79108	.|0.987;0.992;0.987;0.987	T|T	0.71721|0.71721	-0.4507|-0.4507	5|9	0.22706|0.66056	T|D	0.39|0.02	-9.2258|-9.2258	14.2238|14.2238	0.65845|0.65845	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|140;167;180;189	.|E7EMC8;E7ETW5;Q96PM5-2;Q96PM5	.|.;.;.;ZN363_HUMAN	R|A	188|189;149;167;180;140	.|ENSP00000321239:S189A;ENSP00000370220:S149A;ENSP00000423976:S167A	ENSP00000401041:L188R|ENSP00000321239:S189A	L|S	-|-	2|1	0|0	RCHY1|RCHY1	76634907|76634907	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	7.352000|7.352000	0.79404|0.79404	2.239000|2.239000	0.73571|0.73571	0.528000|0.528000	0.53228|0.53228	CTC|TCT	.		0.373	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		C	76415883	A	C	76415883	3	2	98	1	0	0	0	0	1	0	0	0	13209	304	11	5	228	5	RCHY1	4	76415883	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	19541389	76415883	114738393	27	8753											
BMP2K	55589	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	79786783	79786783	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaaaggccaactctgctacTactgccactcccagtgtgct	9	9	7	16	0	1	0	0	0	1	0	2	0	2	0	4	1	6	2	4	1	4	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:79786783T>C	ENST00000335016.5	+	10	1306	c.1140T>C	c.(1138-1140)acT>acC	p.T380T	BMP2K_ENST00000502871.1_Silent_p.T380T	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	380					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						ACTCTGCTACTACTGCCACTC	0.418																																					p.T380T		.											.	BMP2K-383	0			c.T1140C						.						122	110	114					4																	79786783		2203	4300	6503	SO:0001819	synonymous_variant	55589	exon10			TGCTACTACTGCC	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1140T>C	4.37:g.79786783T>C		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	104	44	NM_017593	0	0	1	1	0	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	T	7.526	0.657778	0.14645	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.26	-0.259	0.12971	.	.	.	.	.	T	0.56156	0.1966	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50800	-0.8785	4	.	.	.	-3.7779	9.9454	0.41604	0.0:0.4316:0.0:0.5684	.	.	.	.	H	73	.	.	Y	+	1	0	BMP2K	80005807	0.986000	0.35501	0.891000	0.34965	0.665000	0.39181	0.684000	0.25364	0.047000	0.15862	-0.290000	0.09829	TAC	.		0.418	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		C	79786783	T	C	79786783	2	2	98	1	0	0	0	0	0	0	0	1	1461	1509	53	3		3	BMP2K	4	79786783	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3370900	79786783	111367493	28	8754											
DSPP	1834	hgsc.bcm.edu	37	chr4	88535323	88535324	+	In_Frame_Ins	INS	-	-	GGCAGTGACTCAAAAGGAGCAGAA																															aatcaaaagataatggcaatINSggcagtgactcaaaaggagc																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:88535323_88535324insGGCAGTGACTCAAAAGGAGCAGAA	ENST00000282478.7	+	4	1542_1543	c.1509_1510insGGCAGTGACTCAAAAGGAGCAGAA	c.(1510-1512)ggc>GGCAGTGACTCAAAAGGAGCAGAAggc	p.504_504G>GSDSKGAEG	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Ins_p.504_504G>GSDSKGAEG			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	504	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		ATAATGGCAATGGCAGTGACTC	0.381																																					p.N503delinsNGSDSKGAE		.											.	DSPP-90	0			c.1509_1510insGGCAGTGACTCAAAAGGAGCAGAA						.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.1510_1533dupGGCAGTGACTCAAAAGGAGCAGAA	4.37:g.88535323_88535324insGGCAGTGACTCAAAAGGAGCAGAA	Exception_encountered	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	115	19	NM_014208	0	0	0	0	0	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.381	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		GGCAGTGACTCAAAAGGAGCAGAA	88535324	-	GGCAGTGACTCAAAAGGAGCAGAA	88535323	7	5	98	1	0	1	1	0	0	0	0	0	4793	1461	51	0	1523	0	DSPP	4	88535323	In_Frame_Ins	INS	-	TCGA-DW-7840-01A-11D-2136-08	8748540	88535323	102618953	29	8755											
CENPE	1062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	104081805	104081805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttcctcagcctttctacttCagaaggtaaagatttcaatt	11	16	5	9	0	4	2	3	0	1	2	5	2	5	2	2	1	2	1	2	1	5	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:104081805C>T	ENST00000265148.3	-	21	2352	c.2263G>A	c.(2263-2265)Gaa>Aaa	p.E755K	CENPE_ENST00000380026.3_Missense_Mutation_p.E730K	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	755					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CTTTCTACTTCAGAAGGTAAA	0.318																																					p.E755K		.											.	CENPE-277	0			c.G2263A						.						65	69	67					4																	104081805		2201	4291	6492	SO:0001583	missense	1062	exon21			CTACTTCAGAAGG	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2263G>A	4.37:g.104081805C>T	ENSP00000265148:p.Glu755Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	85	39	NM_001813	0	0	0	0	0	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761920	0.49468	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.71817	3.8;-0.6;3.8	4.58	4.58	0.56647	.	.	.	.	.	T	0.77631	0.4159	L	0.54323	1.7	0.51767	D	0.999931	D;D	0.76494	0.974;0.999	P;D	0.65987	0.726;0.94	T	0.78155	-0.2314	9	0.54805	T	0.06	.	10.406	0.44256	0.0:0.8981:0.0:0.1019	.	730;755	Q02224-3;Q02224	.;CENPE_HUMAN	K	755;755;730;755	ENSP00000265148:E755K;ENSP00000369365:E730K;ENSP00000423981:E755K	ENSP00000265148:E755K	E	-	1	0	CENPE	104301254	0.998000	0.40836	0.762000	0.31397	0.169000	0.22640	2.456000	0.44997	2.254000	0.74563	0.650000	0.86243	GAA	.		0.318	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	104081805	C	T	104081805	3	4	98	1	0	0	0	0	1	0	0	0	3236	835	29	2	5958	2	CENPE	4	104081805	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	15546482	104081805	87072471	30	8756											
LRBA	987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	151821345	151821345	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaatgaattccgtggacaGataagtatagagcatcagtt	15	10	9	7	1	1	3	1	1	0	2	2	4	2	4	2	1	1	3	2	1	5	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:151821345G>T	ENST00000357115.3	-	14	2023	c.1780C>A	c.(1780-1782)Ctg>Atg	p.L594M	LRBA_ENST00000510413.1_Missense_Mutation_p.L594M|LRBA_ENST00000507224.1_Missense_Mutation_p.L594M|LRBA_ENST00000535741.1_Missense_Mutation_p.L594M	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	594						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					TCCGTGGACAGATAAGTATAG	0.413																																					p.L594M		.											.	LRBA-157	0			c.C1780A						.						108	100	103					4																	151821345		2203	4300	6503	SO:0001583	missense	987	exon14			TGGACAGATAAGT	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.1780C>A	4.37:g.151821345G>T	ENSP00000349629:p.Leu594Met	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	68	24	NM_006726	0	0	0	0	0	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255995	0.59321	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.59	2.91	0.33838	Armadillo-type fold (1);	0.000000	0.52532	D	0.000071	T	0.22589	0.0545	L	0.58669	1.825	0.44380	D	0.997282	P;P;P	0.46277	0.802;0.776;0.875	B;B;B	0.40825	0.122;0.282;0.341	T	0.02352	-1.1172	10	0.54805	T	0.06	.	5.799	0.18403	0.3233:0.0:0.5523:0.1244	.	594;594;594	E9PEM5;P50851;P50851-2	.;LRBA_HUMAN;.	M	594	ENSP00000446299:L594M;ENSP00000421552:L594M;ENSP00000349629:L594M;ENSP00000422180:L594M	ENSP00000349629:L594M	L	-	1	2	LRBA	152040795	1.000000	0.71417	0.984000	0.44739	0.998000	0.95712	1.337000	0.33862	0.714000	0.32081	0.655000	0.94253	CTG	.		0.413	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151821345	G	T	151821345	3	4	98	1	0	0	0	0	1	0	0	0	8956	933	33	4	6991	4	LRBA	4	151821345	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	47739540	151821345	39332931	31	8757											
WWC2	80014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	184182067	184182067	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctttttgtctttcagcctcTctgccagcaccctgtccatg	4	15	7	15	0	3	0	1	0	2	0	5	0	4	0	4	0	3	2	4	0	0	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:184182067T>A	ENST00000403733.3	+	11	1490	c.1291T>A	c.(1291-1293)Tct>Act	p.S431T	WWC2_ENST00000513834.1_Missense_Mutation_p.S431T|WWC2_ENST00000504005.1_Missense_Mutation_p.S113T|WWC2_ENST00000378925.3_Missense_Mutation_p.S333T|WWC2_ENST00000448232.2_Missense_Mutation_p.S431T	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	431	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TTTCAGCCTCTCTGCCAGCAC	0.507																																					p.S431T		.											.	WWC2-93	0			c.T1291A						.						29	29	29					4																	184182067		2203	4300	6503	SO:0001583	missense	80014	exon11			AGCCTCTCTGCCA	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.1291T>A	4.37:g.184182067T>A	ENSP00000384222:p.Ser431Thr	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	36	18	NM_024949	0	0	0	0	0	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	T	24.6	4.551586	0.86127	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	4.86	4.86	0.63082	.	0.000000	0.64402	D	0.000002	T	0.65207	0.2669	M	0.80183	2.485	0.58432	D	0.999996	D	0.69078	0.997	D	0.75020	0.985	T	0.68864	-0.5296	10	0.49607	T	0.09	-16.2476	14.628	0.68635	0.0:0.0:0.0:1.0	.	431	Q6AWC2	WWC2_HUMAN	T	431;333;431;431;113	ENSP00000384222:S431T;ENSP00000368205:S333T;ENSP00000425054:S431T;ENSP00000398577:S431T;ENSP00000427569:S113T	ENSP00000368205:S333T	S	+	1	0	WWC2	184419061	1.000000	0.71417	0.993000	0.49108	0.935000	0.57460	7.833000	0.86765	2.046000	0.60703	0.528000	0.53228	TCT	.		0.507	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		A	184182067	T	A	184182067	3	1	98	1	0	0	0	0	1	0	0	0	17445	1551	54	5	1333	5	WWC2	4	184182067	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	32360722	184182067	6972209	32	8758											
KIAA0947	23379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	5461992	5461992	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaatcctgtagaattcaagAccactgcatcggtgttgcct	11	11	8	11	1	1	2	1	0	0	2	3	2	2	2	3	1	2	3	3	1	4	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:5461992A>T	ENST00000296564.7	+	13	2767	c.2545A>T	c.(2545-2547)Acc>Tcc	p.T849S		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		849					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AGAATTCAAGACCACTGCATC	0.413																																					p.T849S		.											.	KIAA0947-48	0			c.A2545T						.						92	87	89					5																	5461992		1888	4110	5998	SO:0001583	missense	23379	exon13			TTCAAGACCACTG																												ENST00000296564.7:c.2545A>T	5.37:g.5461992A>T	ENSP00000296564:p.Thr849Ser	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	96	41	NM_015325	0	0	1	2	1	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	a	5.614	0.297970	0.10622	.	.	ENSG00000164151	ENST00000296564	T	0.09445	2.98	4.94	0.61	0.17580	.	0.400941	0.21055	N	0.080924	T	0.04407	0.0121	N	0.08118	0	0.09310	N	1	B	0.20780	0.048	B	0.14023	0.01	T	0.43750	-0.9372	10	0.20046	T	0.44	-7.0261	7.5819	0.27970	0.1086:0.5191:0.3723:0.0	.	849	Q9Y2F5	K0947_HUMAN	S	849	ENSP00000296564:T849S	ENSP00000296564:T849S	T	+	1	0	KIAA0947	5514992	0.000000	0.05858	0.000000	0.03702	0.233000	0.25261	0.042000	0.13949	-0.216000	0.10048	0.378000	0.23410	ACC	.		0.413	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5461992	A	T	5461992	3	4	98	1	0	0	0	0	1	0	0	0	8223	275	10	5	2595	5	KIAA0947	5	5461992	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08		5461992	175453268	33	8759											
ITGA1	3672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	52211309	52211309	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagcgtattccatcaggtGgggatggtaagacactgaaa	13	8	12	8	1	1	2	1	1	0	1	2	3	2	3	1	4	1	2	1	4	3	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:52211309G>T	ENST00000282588.6	+	15	2331	c.1873G>T	c.(1873-1875)Ggg>Tgg	p.G625W		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	625					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TCCATCAGGTGGGGATGGTAA	0.388																																					p.G625W		.											.	ITGA1-228	0			c.G1873T						.						146	147	147					5																	52211309		2203	4300	6503	SO:0001583	missense	3672	exon15			TCAGGTGGGGATG	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1873G>T	5.37:g.52211309G>T	ENSP00000282588:p.Gly625Trp	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	157	62	NM_181501	0	0	1	1	0	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	37	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672050	0.88348	.	.	ENSG00000213949	ENST00000282588	T	0.56103	0.48	5.53	5.53	0.82687	.	0.053424	0.85682	D	0.000000	T	0.69557	0.3124	L	0.56769	1.78	0.80722	D	1	D	0.71674	0.998	D	0.68192	0.956	T	0.65693	-0.6106	10	0.38643	T	0.18	.	19.8228	0.96604	0.0:0.0:1.0:0.0	.	625	P56199	ITA1_HUMAN	W	625	ENSP00000282588:G625W	ENSP00000282588:G625W	G	+	1	0	ITGA1	52247066	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.066000	0.93949	2.759000	0.94783	0.650000	0.86243	GGG	.		0.388	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		T	52211309	G	T	52211309	3	4	98	1	0	0	0	0	1	0	0	0	7893	1348	47	4	1931	4	ITGA1	5	52211309	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	46749317	52211309	128703951	34	8760											
LHFPL2	10184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	77784725	77784725	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgtctcttccaaactaaaGgaggcagatcagatttttcc	12	13	7	9	0	2	2	1	0	1	2	5	3	4	3	2	2	1	1	2	2	3	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:77784725G>A	ENST00000515007.2	-	3	992	c.682C>T	c.(682-684)Ctt>Ttt	p.L228F	LHFPL2_ENST00000380345.2_Missense_Mutation_p.L228F			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	228						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	6		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		CCAAACTAAAGGAGGCAGATC	0.408																																					p.L228F		.											.	LHFPL2-90	0			c.C682T						.						128	127	127					5																	77784725		2203	4300	6503	SO:0001583	missense	10184	exon5			ACTAAAGGAGGCA	D86961	CCDS4042.1	5q13	2008-02-05			ENSG00000145685	ENSG00000145685			6588	protein-coding gene	gene with protein product		609718				10329012	Standard	NM_005779		Approved	KIAA0206	uc003kfo.3	Q6ZUX7	OTTHUMG00000107579	ENST00000515007.2:c.682C>T	5.37:g.77784725G>A	ENSP00000425906:p.Leu228Phe	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	124	52	NM_005779	0	0	0	0	0	B2RMQ6|Q7Z5P0|Q92605	Missense_Mutation	SNP	ENST00000515007.2	37	CCDS4042.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.026712	0.93518	.	.	ENSG00000145685	ENST00000380345;ENST00000515007	T;T	0.78924	-1.22;-1.22	5.94	5.94	0.96194	.	0.055945	0.64402	D	0.000001	D	0.84115	0.5401	M	0.72118	2.19	0.80722	D	1	P	0.50272	0.933	P	0.51193	0.662	D	0.85187	0.1007	10	0.72032	D	0.01	.	19.3618	0.94442	0.0:0.0:1.0:0.0	.	228	Q6ZUX7	LHPL2_HUMAN	F	228	ENSP00000369702:L228F;ENSP00000425906:L228F	ENSP00000369702:L228F	L	-	1	0	LHFPL2	77820481	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	9.476000	0.97823	2.820000	0.97059	0.650000	0.86243	CTT	.		0.408	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779		A	77784725	G	A	77784725	3	1	98	1	0	0	0	0	1	0	0	0	8787	1000	35	2	8	2	LHFPL2	5	77784725	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	25573416	77784725	103130535	35	8761											
SLCO6A1	133482	hgsc.bcm.edu;broad.mit.edu	37	chr5	101735268	101735268	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tatatacataccgcgtcatgGccaagacgattggtacacca	13	9	8	11	3	1	1	1	0	0	1	1	2	1	1	3	2	3	1	3	2	6	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:101735268G>A	ENST00000506729.1	-	10	1976	c.1805C>T	c.(1804-1806)gCc>gTc	p.A602V	SLCO6A1_ENST00000379810.1_Missense_Mutation_p.A349V|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.A540V|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.A349V|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.A602V			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	602						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		CCGCGTCATGGCCAAGACGAT	0.284																																					p.A602V		.											.	SLCO6A1-96	0			c.C1805T						.						66	63	64					5																	101735268		2203	4300	6503	SO:0001583	missense	133482	exon10			GTCATGGCCAAGA	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1805C>T	5.37:g.101735268G>A	ENSP00000421339:p.Ala602Val	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_173488	0	0	0	0	0	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.414291	0.25465	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	5.42	0.231	0.15377	Major facilitator superfamily domain, general substrate transporter (1);	1.303550	0.05317	N	0.525853	T	0.30135	0.0755	L	0.43152	1.355	0.09310	N	1	B;B;B	0.30361	0.135;0.277;0.1	B;B;B	0.39935	0.054;0.314;0.083	T	0.24548	-1.0157	10	0.02654	T	1	.	4.3381	0.11095	0.4699:0.195:0.3351:0.0	.	540;349;602	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	V	602;602;540;349;349	ENSP00000421339:A602V;ENSP00000369135:A602V;ENSP00000373671:A540V;ENSP00000421990:A349V;ENSP00000369138:A349V	ENSP00000369135:A602V	A	-	2	0	SLCO6A1	101763167	0.013000	0.17824	0.000000	0.03702	0.000000	0.00434	-0.072000	0.11486	-0.156000	0.11079	-0.150000	0.13652	GCC	.		0.284	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101735268	G	A	101735268	3	1	98	1	0	0	0	0	1	0	0	0	14764	1203	42	2	370	2	SLCO6A1	5	101735268	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	23950543	101735268	79179992	36	8762											
PCDHB14	56122	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140605207	140605207	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggtgctcctgttcgtggcGgtgcggctgtgcaggaggag	3	10	19	9	4	0	0	0	0	0	0	3	2	1	2	1	6	3	4	1	6	0	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:140605207G>C	ENST00000239449.4	+	1	2130	c.2130G>C	c.(2128-2130)gcG>gcC	p.A710A	PCDHB14_ENST00000515856.2_Silent_p.A557A	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	710					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCGTGGCGGTGCGGCTGT	0.701																																					p.A710A	Ovarian(141;50 1831 27899 33809 37648)	.											.	PCDHB14-91	0			c.G2130C						.						68	84	79					5																	140605207		2184	4245	6429	SO:0001819	synonymous_variant	56122	exon1			CGTGGCGGTGCGG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"Cadherins / Protocadherins : Clustered"	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2130G>C	5.37:g.140605207G>C		Somatic	391	0		WXS	Illumina HiSeq	Phase_I	333	109	NM_018934	3	0	18	21	0	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			.		0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		C	140605207	G	C	140605207	2	2	98	1	0	0	0	0	0	0	0	1	11565	1103	39	4		4	PCDHB14	5	140605207	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	38869939	140605207	40310053	37	8763											
SOX30	11063	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	157078648	157078648	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcgaggccccactgactgatCcaggctgggccccagcttct	6	8	11	16	1	1	2	0	2	1	0	3	3	2	2	5	3	1	2	5	3	0	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:157078648C>T	ENST00000265007.6	-	1	780	c.439G>A	c.(439-441)Gat>Aat	p.D147N	SOX30_ENST00000519442.1_Intron|SOX30_ENST00000311371.5_Missense_Mutation_p.D147N	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	147					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACTGACTGATCCAGGCTGGGC	0.687																																					p.D147N	Esophageal Squamous(31;525 799 19355 21125 41744)	.											.	SOX30-91	0			c.G439A						.						13	15	14					5																	157078648		2180	4260	6440	SO:0001583	missense	11063	exon1			ACTGATCCAGGCT	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.439G>A	5.37:g.157078648C>T	ENSP00000265007:p.Asp147Asn	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	48	20	NM_178424	0	0	0	0	0	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	C	8.733	0.917147	0.17982	.	.	ENSG00000039600	ENST00000311371;ENST00000265007	D;D	0.98221	-4.8;-4.41	4.62	4.62	0.57501	.	0.851364	0.09951	N	0.734643	D	0.94503	0.8230	N	0.24115	0.695	0.20196	N	0.999926	B;B	0.29037	0.231;0.039	B;B	0.27715	0.082;0.017	D	0.88993	0.3416	10	0.27785	T	0.31	.	7.1995	0.25873	0.0:0.6448:0.2614:0.0938	.	147;147	O94993-2;O94993	.;SOX30_HUMAN	N	147	ENSP00000309343:D147N;ENSP00000265007:D147N	ENSP00000265007:D147N	D	-	1	0	SOX30	157011226	0.125000	0.22332	0.395000	0.26283	0.028000	0.11728	3.076000	0.50081	2.098000	0.63641	0.305000	0.20034	GAT	.		0.687	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		T	157078648	C	T	157078648	3	4	98	1	0	0	0	0	1	0	0	0	14984	855	30	2	1842	2	SOX30	5	157078648	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	16473441	157078648	23836612	38	8764											
NKX2-5	1482	hgsc.bcm.edu	37	chr5	172659920	172659920	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcaggcggcggcggcggCgggggcagccccaccagctc	4	1	20	16	6	0	0	0	0	0	0	1	0	0	0	3	8	2	3	3	8	0	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:172659920C>G	ENST00000329198.4	-	2	900	c.627G>C	c.(625-627)ccG>ccC	p.P209P	NKX2-5_ENST00000424406.2_3'UTR|NKX2-5_ENST00000521848.1_3'UTR	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	209	Ala/Pro-rich.				adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			gcggcggcggcgggggcAGCC	0.701																																					p.P209P	Esophageal Squamous(72;810 1219 2387 13420 44943)	.											.	NKX2-5-90	0			c.G627C						.						5	6	6					5																	172659920		1935	3790	5725	SO:0001819	synonymous_variant	1482	exon2			CGGCGGCGGGGGC	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.627G>C	5.37:g.172659920C>G		Somatic	10	1		WXS	Illumina HiSeq	Phase_I	18	2	NM_004387	0	0	0	0	0	A8K3K0|B4DNB6|E9PBU6	Silent	SNP	ENST00000329198.4	37	CCDS4387.1																																																																																			.		0.701	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			G	172659920	C	G	172659920	2	3	98	1	0	0	0	0	0	0	0	1	10479	755	27	4		4	NKX2-5	5	172659920	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08	15581272	172659920	8255340	39	8765											
C6orf105	84830	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	11723657	11723657	+	Frame_Shift_Del	DEL	C	C	-																															gtagctgagagagaagaaagCtgctagacccaagaggctga																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:11723657delC	ENST00000414691.3	-	5	993	c.583delG	c.(583-585)gctfs	p.A195fs	ADTRP_ENST00000379413.2_Frame_Shift_Del_p.A195fs|ADTRP_ENST00000514824.1_5'UTR|ADTRP_ENST00000229583.5_Frame_Shift_Del_p.A213fs	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GAGAAGAAAGCTGCTAGACCC	0.483																																					p.A213fs		.											.	.	0			c.637delG						.						209	208	209					6																	11723657		2203	4300	6503	SO:0001589	frameshift_variant	84830	exon6			.	AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"androgen-induced 1-like"	614348	"chromosome 6 open reading frame 105"	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.583delG	6.37:g.11723657delC	ENSP00000404416:p.Ala195fs	Somatic	246	0		WXS	Illumina HiSeq	Phase_I	259	92	NM_001143948	0	0	0	0	0	B2R7T9|B4DV39|Q5THW1	Frame_Shift_Del	DEL	ENST00000414691.3	37	CCDS4521.1																																																																																			.		0.483	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039864.3	NM_032744		-	11723657	C	-	11723657	7	5	98	1	0	1	0	1	0	0	0	0	2324	797	28	0	117	0	C6orf105	6	11723657	Frame_Shift_Del	DEL	C	TCGA-DW-7840-01A-11D-2136-08		11723657	159391410	40	8766											
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32191691	32191691	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcagcagcagcagcagTgaagggggctgcattccaca	12	4	14	11	0	0	1	0	1	0	0	1	1	1	1	1	2	7	8	1	2	1	1	rs372487717		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:32191691T>C	ENST00000375023.3	-	1	153	c.15A>G	c.(13-15)tcA>tcG	p.S5S		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	5					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						gcagcagcagTGAAGGGGGCT	0.642																																					p.S5S		.											.	NOTCH4-1321	0			c.A15G						.						53	39	44					6																	32191691		1511	2708	4219	SO:0001819	synonymous_variant	4855	exon1			CAGCAGTGAAGGG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.15A>G	6.37:g.32191691T>C		Somatic	38	1		WXS	Illumina HiSeq	Phase_I	57	4	NM_004557	0	0	1	1	0	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			.		0.642	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			C	32191691	T	C	32191691	2	2	98	1	0	0	0	0	0	0	0	1	10577	1683	59	3		3	NOTCH4	6	32191691	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	20468034	32191691	138923376	41	8767											
BRD2	6046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32945538	32945538	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtgcctctttgtaggatgTatttgagttccgttatgcca	6	18	10	7	1	1	1	0	1	1	0	2	2	2	2	3	1	2	4	3	1	3	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:32945538T>C	ENST00000374825.4	+	9	3035	c.1334T>C	c.(1333-1335)gTa>gCa	p.V445A	BRD2_ENST00000395289.2_Missense_Mutation_p.V445A|BRD2_ENST00000443797.2_Missense_Mutation_p.V325A|BRD2_ENST00000395287.1_Missense_Mutation_p.V445A|BRD2_ENST00000374831.4_Missense_Mutation_p.V445A|BRD2_ENST00000449085.2_Missense_Mutation_p.V398A	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	445					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TTGTAGGATGTATTTGAGTTC	0.463																																					p.V445A		.											.	BRD2-398	0			c.T1334C						.						118	132	127					6																	32945538		1509	2709	4218	SO:0001583	missense	6046	exon9			AGGATGTATTTGA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1334T>C	6.37:g.32945538T>C	ENSP00000363958:p.Val445Ala	Somatic	180	1		WXS	Illumina HiSeq	Phase_I	155	82	NM_005104	0	0	0	0	0	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	37	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.5|22.5	4.302909|4.302909	0.81136|0.81136	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085|ENST00000449025	T;T;T;T;T;T|.	0.19250|.	2.16;2.16;2.16;2.16;2.16;2.16|.	5.63|5.63	5.63|5.63	0.86233|0.86233	Bromodomain (3);|.	0.000000|.	0.45606|.	D|.	0.000350|.	T|T	0.76814|0.76814	0.4040|0.4040	M|M	0.89785|0.89785	3.06|3.06	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.997|.	D;D|.	0.70716|.	0.97;0.97|.	T|T	0.81758|0.81758	-0.0786|-0.0786	10|5	0.87932|.	D|.	0|.	-14.8434|-14.8434	13.8401|13.8401	0.63432|0.63432	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	445;445|.	A2AAU0;P25440|.	.;BRD2_HUMAN|.	A|H	445;445;445;325;445;398|451	ENSP00000363958:V445A;ENSP00000363964:V445A;ENSP00000378704:V445A;ENSP00000413495:V325A;ENSP00000378702:V445A;ENSP00000409145:V398A|.	ENSP00000363958:V445A|.	V|Y	+|+	2|1	0|0	BRD2|BRD2	33053516|33053516	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.982000|0.982000	0.71751|0.71751	7.753000|7.753000	0.85153|0.85153	2.363000|2.363000	0.80096|0.80096	0.523000|0.523000	0.50628|0.50628	GTA|TAT	.		0.463	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			C	32945538	T	C	32945538	3	2	98	1	0	0	0	0	1	0	0	0	1505	1638	57	3	1364	3	BRD2	6	32945538	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	753847	32945538	138169529	42	8768											
SLC22A7	10864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43267444	43267444	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catctgcagcctccgtcagcTatgtaatgtttgccatcacc	8	12	7	14	1	3	0	2	0	1	0	4	0	4	0	4	0	4	4	4	0	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:43267444T>C	ENST00000372585.5	+	4	678	c.583T>C	c.(583-585)Tat>Cat	p.Y195H	SLC22A7_ENST00000487175.1_3'UTR|SLC22A7_ENST00000372574.3_Missense_Mutation_p.Y193H|SLC22A7_ENST00000372589.3_Missense_Mutation_p.Y193H	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	195					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	CTCCGTCAGCTATGTAATGTT	0.602																																					p.Y195H		.											.	SLC22A7-90	0			c.T583C						.						91	89	89					6																	43267444		2203	4300	6503	SO:0001583	missense	10864	exon3			GTCAGCTATGTAA	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.583T>C	6.37:g.43267444T>C	ENSP00000361666:p.Tyr195His	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	178	68	NM_153320	0	0	6	12	6	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	37	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	26.8	4.776980	0.90195	.	.	ENSG00000137204	ENST00000451757;ENST00000449231;ENST00000372589;ENST00000372585;ENST00000372574	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	5.56	5.56	0.83823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.068530	0.64402	D	0.000011	T	0.73273	0.3566	M	0.92077	3.27	0.45295	D	0.998297	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.99;0.986	T	0.80795	-0.1223	10	0.72032	D	0.01	.	13.2267	0.59919	0.0:0.0:0.0:1.0	.	195;193;193	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	H	64;254;193;195;193	ENSP00000416052:Y64H;ENSP00000411818:Y254H;ENSP00000361670:Y193H;ENSP00000361666:Y195H;ENSP00000361655:Y193H	ENSP00000361655:Y193H	Y	+	1	0	SLC22A7	43375422	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	4.783000	0.62403	2.109000	0.64355	0.379000	0.24179	TAT	.		0.602	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			C	43267444	T	C	43267444	3	2	98	1	0	0	0	0	1	0	0	0	14491	1522	53	3	593	3	SLC22A7	6	43267444	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	10321906	43267444	127847623	43	8769											
EPHA7	2045	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	93969151	93969151	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacagctctatttgggtcCtcataggtttcagggtcaat	8	14	11	8	0	4	0	3	0	1	0	5	1	5	1	1	4	1	2	1	4	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:93969151C>A	ENST00000369303.4	-	10	2029	c.1845G>T	c.(1843-1845)gaG>gaT	p.E615D		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	615					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TATTTGGGTCCTCATAGGTTT	0.428																																					p.E615D		.											.	EPHA7-1453	0			c.G1845T						.						221	199	206					6																	93969151		2203	4300	6503	SO:0001583	missense	2045	exon10			TGGGTCCTCATAG	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3390	protein-coding gene	gene with protein product		602190	"EphA7"			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1845G>T	6.37:g.93969151C>A	ENSP00000358309:p.Glu615Asp	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	168	72	NM_004440	0	0	4	9	5	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622257	0.28889	.	.	ENSG00000135333	ENST00000369303	T	0.22336	1.96	5.9	5.9	0.94986	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.37320	0.0999	M	0.91972	3.26	0.80722	D	1	B;B;B	0.33755	0.424;0.002;0.001	P;B;B	0.46419	0.516;0.002;0.001	T	0.26538	-1.0100	10	0.59425	D	0.04	.	14.4356	0.67279	0.0:0.93:0.0:0.07	.	611;610;615	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	D	615	ENSP00000358309:E615D	ENSP00000358309:E615D	E	-	3	2	EPHA7	94025872	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.753000	0.38359	2.786000	0.95864	0.563000	0.77884	GAG	.		0.428	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	93969151	C	A	93969151	3	1	98	1	0	0	0	0	1	0	0	0	5185	680	24	4	1183	4	EPHA7	6	93969151	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	50701707	93969151	77145916	44	8770											
AIM1	202	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	106967843	106967843	+	Frame_Shift_Del	DEL	T	T	-																															cctgtgtctcgtcagaacaaTgagaaaatgccacttttaga																								rs551716379		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:106967843delT	ENST00000369066.3	+	2	2023	c.1536delT	c.(1534-1536)aatfs	p.N512fs		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GTCAGAACAATGAGAAAATGC	0.453																																					p.N512fs		.											.	AIM1-139	0			c.1536delT						.						82	90	87					6																	106967843		2203	4300	6503	SO:0001589	frameshift_variant	202	exon2			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1536delT	6.37:g.106967843delT	ENSP00000358062:p.Asn512fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	150	60	NM_001624	0	0	0	0	0	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	37	CCDS34506.1																																																																																			.		0.453	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106967843	T	-	106967843	7	5	98	1	0	1	0	1	0	0	0	0	430	1461	51	0	1542	0	AIM1	6	106967843	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	12998692	106967843	64147224	45	8771											
SOBP	55084	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	107827597	107827597	+	Frame_Shift_Del	DEL	T	T	-																															agtgtgcccattattgtaccTttaattccaccacctttcat																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:107827597delT	ENST00000317357.5	+	3	1046	c.387delT	c.(385-387)cctfs	p.P129fs		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		TTATTGTACCTTTAATTCCAC	0.423																																					p.P129fs		.											.	SOBP-91	0			c.387delT						.						204	194	197					6																	107827597		1912	4142	6054	SO:0001589	frameshift_variant	55084	exon3			.	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.387delT	6.37:g.107827597delT	ENSP00000318900:p.Pro129fs	Somatic	256	0		WXS	Illumina HiSeq	Phase_I	300	100	NM_018013	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000317357.5	37	CCDS43488.1																																																																																			.		0.423	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		-	107827597	T	-	107827597	7	5	98	1	0	1	0	1	0	0	0	0	14944	1596	56	0	397	0	SOBP	6	107827597	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	859754	107827597	63287470	46	8772											
OSTM1	28962	hgsc.bcm.edu	37	chr6	108395713	108395713	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctccagcaactgctgctccGacaggaggtcgtggaagacc	9	6	12	14	2	0	1	0	0	0	1	3	4	2	3	4	3	4	3	4	3	2	0	rs201176284	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:108395713G>C	ENST00000193322.3	-	1	228	c.143C>G	c.(142-144)tCg>tGg	p.S48W		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	48					ion transmembrane transport (GO:0034220)|osteoclast differentiation (GO:0030316)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)		CTGCTGCTCCGACAGGAGGTC	0.711													G|||	5	0.000998403	0.0038	0	5008	,	,		12709	0		0	False		,,,				2504	0				p.S48W	Melanoma(162;1427 1909 3096 17430 21396)	.											.	OSTM1-68	0			c.C143G						.	G	TRP/SER	12,4304		0,12,2146	7	7	7		143	4.1	1	6		7	0,8426		0,0,4213	yes	missense	OSTM1	NM_014028.3	177	0,12,6359	CC,CG,GG		0.0,0.278,0.0942	probably-damaging	48/335	108395713	12,12730	2158	4213	6371	SO:0001583	missense	28962	exon1			TGCTCCGACAGGA	AF533891	CCDS5062.1	6q21	2014-06-17			ENSG00000081087	ENSG00000081087			21652	protein-coding gene	gene with protein product	"CLCN7 accessory beta subunit"	607649				12627228, 21527911	Standard	NM_014028		Approved	HSPC019, GL	uc003psd.3	Q86WC4	OTTHUMG00000015317	ENST00000193322.3:c.143C>G	6.37:g.108395713G>C	ENSP00000193322:p.Ser48Trp	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_014028	0	0	1	1	0	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	37	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.828523	0.71258	0.00278	0.0	ENSG00000081087	ENST00000193322	T	0.55234	0.53	4.96	4.08	0.47627	.	0.095194	0.43110	D	0.000605	T	0.37865	0.1019	M	0.70595	2.14	0.44627	D	0.9976	B	0.16166	0.016	B	0.14023	0.01	T	0.48281	-0.9049	10	0.87932	D	0	-17.7201	12.5335	0.56128	0.0:0.1806:0.8194:0.0	.	48	Q86WC4	OSTM1_HUMAN	W	48	ENSP00000193322:S48W	ENSP00000193322:S48W	S	-	2	0	OSTM1	108502406	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	5.376000	0.66178	1.199000	0.43173	0.655000	0.94253	TCG	.		0.711	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		C	108395713	G	C	108395713	3	2	98	1	0	0	0	0	1	0	0	0	11324	1059	37	4	885	4	OSTM1	6	108395713	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	568116	108395713	62719354	47	8773											
MAP3K4	4216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	161470014	161470014	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttttgctaaagcttacctCagtctcaaagaaaaaagaca	17	10	5	9	0	2	2	2	0	1	2	3	2	2	2	1	0	3	2	1	0	7	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:161470014C>A	ENST00000392142.4	+	3	858	c.710C>A	c.(709-711)tCa>tAa	p.S237*	MAP3K4_ENST00000348824.7_Nonsense_Mutation_p.S237*|MAP3K4_ENST00000366920.2_Nonsense_Mutation_p.S237*|MAP3K4_ENST00000366919.2_Nonsense_Mutation_p.S237*	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	237					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.S237L(2)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AAGCTTACCTCAGTCTCAAAG	0.433																																					p.S237X		.											.	MAP3K4-548	2	Substitution - Missense(2)	cervix(2)	c.C710A						.						41	41	41					6																	161470014		2203	4300	6503	SO:0001587	stop_gained	4216	exon3			TTACCTCAGTCTC	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.710C>A	6.37:g.161470014C>A	ENSP00000375986:p.Ser237*	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	54	23	NM_006724	0	0	0	0	0	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Nonsense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	38	6.894608	0.97916	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	.	.	.	6.14	6.14	0.99180	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.6238	20.819	0.99723	0.0:1.0:0.0:0.0	.	.	.	.	X	237	.	ENSP00000297332:S237X	S	+	2	0	MAP3K4	161390004	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.454000	0.80714	2.927000	0.99377	0.637000	0.83480	TCA	.		0.433	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161470014	C	A	161470014	4	1	98	1	0	0	0	0	0	1	0	0	9277	838	29	4	720	4	MAP3K4	6	161470014	Nonsense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	53074301	161470014	9645053	48	8774											
HEATR2	54919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	803456	803456	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccaggcacaggagacgaTggactcactggccatggtgg	9	6	14	12	1	1	1	1	0	0	1	2	4	2	2	3	6	0	1	3	6	0	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:803456T>G	ENST00000297440.6	+	8	1648	c.1628T>G	c.(1627-1629)aTg>aGg	p.M543R	HEATR2_ENST00000313147.5_Missense_Mutation_p.M543R	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	543						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		CAGGAGACGATGGACTCACTG	0.607																																					p.M543R		.											.	HEATR2-69	0			c.T1628G						.						132	110	117					7																	803456		2202	4300	6502	SO:0001583	missense	54919	exon8			AGACGATGGACTC	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.1628T>G	7.37:g.803456T>G	ENSP00000297440:p.Met543Arg	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	261	44	NM_017802	0	0	17	23	6	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	37	CCDS34580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.28|14.28	2.488084|2.488084	0.44249|0.44249	.|.	.|.	ENSG00000164818|ENSG00000164818	ENST00000440747|ENST00000297440;ENST00000313147;ENST00000537862	.|T;T	.|0.67523	.|-0.27;-0.27	5.03|5.03	5.03|5.03	0.67393|0.67393	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.303789	.|0.36893	.|N	.|0.002346	T|T	0.70055|0.70055	0.3180|0.3180	M|M	0.68317|0.68317	2.08|2.08	0.09310|0.09310	N|N	0.999993|0.999993	.|P;P	.|0.45715	.|0.788;0.865	.|B;P	.|0.45610	.|0.272;0.487	T|T	0.68070|0.68070	-0.5506|-0.5506	5|10	.|0.72032	.|D	.|0.01	-30.0578|-30.0578	15.0356|15.0356	0.71744|0.71744	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|543;289	.|Q86Y56;F5H8D4	.|HEAT2_HUMAN;.	E|R	344|543;543;289	.|ENSP00000297440:M543R;ENSP00000321451:M543R	.|ENSP00000297440:M543R	D|M	+|+	3|2	2|0	HEATR2|HEATR2	769982|769982	0.998000|0.998000	0.40836|0.40836	0.021000|0.021000	0.16686|0.16686	0.005000|0.005000	0.04900|0.04900	2.733000|2.733000	0.47360|0.47360	2.008000|2.008000	0.58898|0.58898	0.459000|0.459000	0.35465|0.35465	GAT|ATG	.		0.607	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802		G	803456	T	G	803456	3	3	98	1	0	0	0	0	1	0	0	0	7049	1464	51	5	1658	5	HEATR2	7	803456	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08		803456	158335207	49	8775											
TMEM184A	202915	hgsc.bcm.edu	37	chr7	1589783	1589783	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttacagaagcgcaggaacccGatggagtaggtcatgccccg	11	6	13	11	3	1	1	1	0	0	1	1	4	1	3	3	3	4	2	3	3	4	2	rs139449337	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:1589783G>A	ENST00000297477.5	-	5	844	c.528C>T	c.(526-528)atC>atT	p.I176I		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	176					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)		p.I176I(1)		endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GCAGGAACCCGATGGAGTAGG	0.721													g|||	14	0.00279553	0.0098	0.0014	5008	,	,		12338	0		0	False		,,,				2504	0				p.I176I		.											.	TMEM184A-90	1	Substitution - coding silent(1)	lung(1)	c.C528T						.			34,4162		0,34,2064	12	15	14		528	-4.1	0.1	7	dbSNP_134	14	2,8474		0,2,4236	no	coding-synonymous	TMEM184A	NM_001097620.1		0,36,6300	AA,AG,GG		0.0236,0.8103,0.2841		176/414	1589783	36,12636	2098	4238	6336	SO:0001819	synonymous_variant	202915	exon5			GAACCCGATGGAG		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.528C>T	7.37:g.1589783G>A		Somatic	14	2		WXS	Illumina HiSeq	Phase_I	37	26	NM_001097620	0	0	3	3	0	Q8TBQ6	Silent	SNP	ENST00000297477.5	37	CCDS43537.1																																																																																			G|0.997;A|0.003		0.721	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		A	1589783	G	A	1589783	2	1	98	1	0	0	0	0	0	0	0	1	16136	1048	37	1		1	TMEM184A	7	1589783	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	786327	1589783	157548880	50	8776											
PKD1L1	168507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	47870900	47870900	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcagagctccaccaaggctGaagggcccttgaccactggg	9	6	13	13	0	0	3	0	2	0	1	1	3	1	3	4	3	2	3	4	3	2	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:47870900G>C	ENST00000289672.2	-	42	6438	c.6388C>G	c.(6388-6390)Cag>Gag	p.Q2130E		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2130					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CACCAAGGCTGAAGGGCCCTT	0.562																																					p.Q2130E		.											.	PKD1L1-145	0			c.C6388G						.						93	83	86					7																	47870900		2203	4300	6503	SO:0001583	missense	168507	exon42			AAGGCTGAAGGGC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"polycystin-1L1"	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.6388C>G	7.37:g.47870900G>C	ENSP00000289672:p.Gln2130Glu	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	211	48	NM_138295	0	0	0	0	0	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.099	0.776205	0.16051	.	.	ENSG00000158683	ENST00000289672	T	0.18960	2.18	5.1	2.25	0.28309	.	1.969070	0.02438	N	0.084314	T	0.13157	0.0319	N	0.22421	0.69	0.09310	N	1	B	0.13145	0.007	B	0.14578	0.011	T	0.23655	-1.0182	10	0.06625	T	0.88	1.9044	4.372	0.11253	0.1915:0.0:0.629:0.1795	.	2130	Q8TDX9	PK1L1_HUMAN	E	2130	ENSP00000289672:Q2130E	ENSP00000289672:Q2130E	Q	-	1	0	PKD1L1	47837425	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.141000	0.16076	0.166000	0.19597	0.563000	0.77884	CAG	.		0.562	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47870900	G	C	47870900	3	2	98	1	0	0	0	0	1	0	0	0	11990	1299	45	4	2225	4	PKD1L1	7	47870900	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	46281117	47870900	111267763	51	8777											
COL1A2	1278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	94057039	94057039	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctacagggctgaccagcctcGctcagcaccttctctcagac	8	8	8	17	1	3	2	2	1	1	1	5	2	3	2	3	1	3	3	3	1	1	2	rs145541630		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:94057039G>T	ENST00000297268.6	+	49	3839	c.3368G>T	c.(3367-3369)cGc>cTc	p.R1123L		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1123				Missing (in Ref. 17; CAA23761). {ECO:0000305}.	blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GACCAGCCTCGCTCAGCACCT	0.547										HNSCC(75;0.22)																											p.R1123L		.											.	COL1A2-521	0			c.G3368T						.						98	97	98					7																	94057039		2203	4300	6503	SO:0001583	missense	1278	exon49			AGCCTCGCTCAGC	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3368G>T	7.37:g.94057039G>T	ENSP00000297268:p.Arg1123Leu	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	261	53	NM_000089	0	0	64	75	11	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.401592	0.62288	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89552	-2.53	5.71	5.71	0.89125	.	0.000000	0.56097	D	0.000040	D	0.88757	0.6523	N	0.14661	0.345	0.34308	D	0.68511	D	0.60160	0.987	D	0.67725	0.953	D	0.90766	0.4668	10	0.41790	T	0.15	.	15.7376	0.77859	0.0:0.0:1.0:0.0	.	1123	P08123	CO1A2_HUMAN	L	1123;1124	ENSP00000297268:R1123L	ENSP00000297268:R1123L	R	+	2	0	COL1A2	93894975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.489000	0.60309	2.873000	0.98535	0.561000	0.74099	CGC	G|1.000;A|0.000		0.547	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94057039	G	T	94057039	3	4	98	1	0	0	0	0	1	0	0	0	3684	1087	38	4	3562	4	COL1A2	7	94057039	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	46186139	94057039	65081624	52	8778											
SRRT	51593	broad.mit.edu;bcgsc.ca	37	chr7	100485469	100485473	+	Frame_Shift_Del	DEL	GCCCC	GCCCC	-																															caagccagcccagccacctgGccccgcccagagtaagatac																								rs568329863		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	GCCCC	GCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:100485469_100485473delGCCCC	ENST00000347433.4	+	17	2473_2477	c.2315_2319delGCCCC	c.(2314-2319)ggccccfs	p.GP772fs	SRRT_ENST00000388793.4_Frame_Shift_Del_p.GP771fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.GP771fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.GP772fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	772	Pro-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CAGCCACCTGGCCCCGCCCAGAGTA	0.512																																					p.772_773del													.	SRRT-92	0			c.2315_2319del						.																																			SO:0001589	frameshift_variant	51593	exon17			CACCTGGCCCCGC		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2315_2319delGCCCC	7.37:g.100485469_100485473delGCCCC	ENSP00000314491:p.Gly772fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	224	18	NM_001128853	0	0	0	0	0	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Del	DEL	ENST00000347433.4	37	CCDS34709.1																																																																																			.		0.512	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		-	100485473	GCCCC	-	100485469	7	5	98	1	0	1	0	1	0	0	0	0	15204	1203	42	0	2377	0	SRRT	7	100485469	Frame_Shift_Del	DEL	GCCCC	TCGA-DW-7840-01A-11D-2136-08	6428430	100485469	58653194	53	8779											
DOCK4	9732	hgsc.bcm.edu;broad.mit.edu	37	chr7	111629106	111629106	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccgggcagtaatgtggcgcTtcacgtccttcatccggtcg	5	10	13	13	5	2	0	2	0	0	0	5	0	4	0	3	3	0	3	3	3	1	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:111629106T>C	ENST00000437633.1	-	6	684	c.428A>G	c.(427-429)aAg>aGg	p.K143R	DOCK4_ENST00000428084.1_Missense_Mutation_p.K143R|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	143					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				AATGTGGCGCTTCACGTCCTT	0.572																																					p.K143R		.											.	DOCK4-26	0			c.A428G						.						66	68	67					7																	111629106		2077	4198	6275	SO:0001583	missense	9732	exon6			TGGCGCTTCACGT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.428A>G	7.37:g.111629106T>C	ENSP00000404179:p.Lys143Arg	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	63	12	NM_014705	0	0	0	0	0	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	33|33	5.207833|5.207833	0.95033|0.95033	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250|ENST00000445943	T;T|.	0.03358|.	3.96;3.97|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73753|0.73753	0.3627|0.3627	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.987;0.997;0.997;0.999|.	P;D;D;D|.	0.70935|.	0.834;0.952;0.952;0.971|.	T|T	0.73783|0.73783	-0.3874|-0.3874	10|5	0.72032|.	D|.	0.01|.	.|.	15.2728|15.2728	0.73717|0.73717	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	143;143;143;143|.	A4D0S8;Q149N6;Q149N5;Q8N1I0|.	.;.;.;DOCK4_HUMAN|.	R|G	131;143;143;131;142|131	ENSP00000410746:K143R;ENSP00000404179:K143R|.	ENSP00000345432:K131R|.	K|S	-|-	2|1	0|0	DOCK4|DOCK4	111416342|111416342	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.988000|7.988000	0.88194|0.88194	2.186000|2.186000	0.69663|0.69663	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.		0.572	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111629106	T	C	111629106	3	2	98	1	0	0	0	0	1	0	0	0	4700	1609	56	3	5660	3	DOCK4	7	111629106	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	11143637	111629106	47509557	54	8780											
GPR37	2861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	124404923	124404923	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctcccccagacaagtttcGtttctggacgcaggggcgac	7	9	11	14	3	2	1	0	0	2	1	4	3	2	2	2	3	0	3	2	3	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:124404923G>C	ENST00000303921.2	-	1	758	c.108C>G	c.(106-108)aaC>aaG	p.N36K		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	36					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GACAAGTTTCGTTTCTGGACG	0.652																																					p.N36K		.											.	GPR37-523	0			c.C108G						.						23	24	24					7																	124404923		2203	4300	6503	SO:0001583	missense	2861	exon1			AGTTTCGTTTCTG		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.108C>G	7.37:g.124404923G>C	ENSP00000306449:p.Asn36Lys	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	86	61	NM_005302	0	0	0	0	0	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	37	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	6.209	0.406650	0.11754	.	.	ENSG00000170775	ENST00000303921	T	0.08896	3.04	5.31	-0.565	0.11771	.	0.220305	0.48286	N	0.000186	T	0.04861	0.0131	L	0.27053	0.805	0.09310	N	0.999998	B	0.09022	0.002	B	0.06405	0.002	T	0.30001	-0.9993	10	0.49607	T	0.09	-16.1704	4.5608	0.12160	0.2984:0.3038:0.3978:0.0	.	36	O15354	GPR37_HUMAN	K	36	ENSP00000306449:N36K	ENSP00000306449:N36K	N	-	3	2	GPR37	124192159	0.000000	0.05858	0.005000	0.12908	0.024000	0.10985	0.501000	0.22578	-0.292000	0.08999	0.655000	0.94253	AAC	.		0.652	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		C	124404923	G	C	124404923	3	2	98	1	0	0	0	0	1	0	0	0	6711	1136	40	4	1741	4	GPR37	7	124404923	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	12775817	124404923	34733740	55	8781											
MLL3	58508	hgsc.bcm.edu;bcgsc.ca	37	chr7	151962168	151962168	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacattgccaacctgcaCgttttaatggagtaaccgct	11	10	9	11	2	0	0	0	0	0	0	0	2	0	2	3	2	4	4	3	2	3	4	rs138908625	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:151962168C>G	ENST00000262189.6	-	8	1357	c.1139G>C	c.(1138-1140)cGt>cCt	p.R380P	KMT2C_ENST00000355193.2_Missense_Mutation_p.R380P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	380					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R380L(4)									CCAACCTGCACGTTTTAATGG	0.443																																					p.R380P		.											.	MLL3-1398	4	Substitution - Missense(4)	skin(4)	c.G1139C						.						410	369	383					7																	151962168		2203	4300	6503	SO:0001583	missense	58508	exon8			CCTGCACGTTTTA	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1139G>C	7.37:g.151962168C>G	ENSP00000262189:p.Arg380Pro	Somatic	771	0		WXS	Illumina HiSeq	Phase_I	901	146	NM_170606	0	0	2	2	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.337586	0.41398	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98849	-5.18;-5.18	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38548	U	0.001645	D	0.98701	0.9564	L	0.52759	1.655	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.99905	1.1175	10	0.66056	D	0.02	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	380	Q8NEZ4	MLL3_HUMAN	P	380	ENSP00000262189:R380P;ENSP00000347325:R380P	ENSP00000262189:R380P	R	-	2	0	MLL3	151593101	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	6.039000	0.70972	2.271000	0.75665	0.557000	0.71058	CGT	C|0.500;A|0.500		0.443	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151962168	C	G	151962168	3	3	98	1	0	0	0	0	1	0	0	0	9647	536	19	4	13804	4	MLL3	7	151962168	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	27557245	151962168	7176495	56	8782											
PRSS3	5646	bcgsc.ca	37	chr9	33796657	33796657	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagttgctgtcccctttgaCgatgatgacaagattgttgg	8	13	11	9	1	0	4	0	3	0	1	1	5	1	4	3	1	1	3	3	1	1	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr9:33796657C>T	ENST00000361005.5	+	2	228	c.228C>T	c.(226-228)gaC>gaT	p.D76D	PRSS3_ENST00000342836.4_Silent_p.D33D|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000429677.3_Silent_p.D12D|PRSS3_ENST00000379405.3_Silent_p.D19D	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	76					cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			TCCCCTTTGACGATGATGACA	0.547																																					p.D76D													.	PRSS3-90	0			c.C228T						.						192	180	184					9																	33796657		2203	4300	6503	SO:0001819	synonymous_variant	5646	exon2			CTTTGACGATGAT		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"Serine peptidases / Serine peptidases"	9486	protein-coding gene	gene with protein product	"mesotrypsin"	613578	"protease, serine, 4 (trypsin 4, brain)", "protease, serine, 3 (mesotrypsin)"	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.228C>T	9.37:g.33796657C>T		Somatic	319	15		WXS	Illumina HiSeq	Phase_1	310	34	NM_007343	0	0	0	0	0	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	CCDS47958.1																																																																																			.		0.547	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		T	33796657	C	T	33796657	2	4	98	1	0	0	0	0	0	0	0	1	12651	535	19	1		1	PRSS3	9	33796657	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08		33796657	107416774	57	8783											
UCK1	83549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134404931	134404931	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accgttttgccctccacgatGttcttcagagtcctgtgcat	6	14	8	13	2	2	1	1	0	1	1	4	2	4	1	4	0	2	3	4	0	0	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr9:134404931G>A	ENST00000372215.4	-	3	402	c.309C>T	c.(307-309)aaC>aaT	p.N103N	UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372211.3_Silent_p.N108N|UCK1_ENST00000372210.3_Silent_p.N94N|UCK1_ENST00000372208.3_Silent_p.N103N	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	103					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		CCTCCACGATGTTCTTCAGAG	0.547																																					p.N108N	Melanoma(42;523 1129 28385 43975 48113)	.											.	UCK1-90	0			c.C324T						.						278	229	246					9																	134404931		2203	4300	6503	SO:0001819	synonymous_variant	83549	exon3			CACGATGTTCTTC	AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.309C>T	9.37:g.134404931G>A		Somatic	192	1		WXS	Illumina HiSeq	Phase_I	179	79	NM_001261451	0	0	28	55	27	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Silent	SNP	ENST00000372215.4	37	CCDS6944.1																																																																																			.		0.547	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432		A	134404931	G	A	134404931	2	1	98	1	0	0	0	0	0	0	0	1	16956	1368	48	2		2	UCK1	9	134404931	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	100608274	134404931	6808500	58	8784											
SETX	23064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	135156906	135156906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatctcctactaggatgagcTtattgcagcgatggatgagt	10	12	12	7	1	1	2	0	2	1	0	2	6	1	4	1	2	4	2	1	2	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr9:135156906T>C	ENST00000224140.5	-	20	6784	c.6602A>G	c.(6601-6603)aAg>aGg	p.K2201R	SETX_ENST00000393220.1_Missense_Mutation_p.K2201R|SETX_ENST00000372169.2_Missense_Mutation_p.K2201R	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2201					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TAGGATGAGCTTATTGCAGCG	0.418																																					p.K2201R		.											.	SETX-93	0			c.A6602G						.						127	117	121					9																	135156906		2203	4300	6503	SO:0001583	missense	23064	exon20			ATGAGCTTATTGC	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.6602A>G	9.37:g.135156906T>C	ENSP00000224140:p.Lys2201Arg	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	118	53	NM_015046	0	0	2	4	2	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.263460	0.59431	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.56	5.56	0.83823	.	0.148494	0.47455	D	0.000240	D	0.85141	0.5629	N	0.25825	0.765	0.37682	D	0.923524	B;D;D	0.69078	0.123;0.99;0.997	B;D;D	0.77557	0.42;0.956;0.99	D	0.86395	0.1738	10	0.36615	T	0.2	.	14.907	0.70727	0.0:0.0:0.0:1.0	.	2201;2201;2201	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	R	2201;443;2201;2201	ENSP00000224140:K2201R;ENSP00000409143:K443R;ENSP00000361242:K2201R;ENSP00000376913:K2201R	ENSP00000224140:K2201R	K	-	2	0	SETX	134146727	1.000000	0.71417	1.000000	0.80357	0.457000	0.32468	3.550000	0.53691	2.123000	0.65237	0.528000	0.53228	AAG	.		0.418	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		C	135156906	T	C	135156906	3	2	98	1	0	0	0	0	1	0	0	0	14173	1609	56	3	1459	3	SETX	9	135156906	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	751975	135156906	6056525	59	8785											
TSC1	7248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	135781374	135781374	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtaaaggctcagggttcaCgctggcgccctgagaactgg	8	8	15	10	2	2	1	2	1	0	1	2	2	2	1	1	4	1	4	1	4	3	2	rs377279170		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr9:135781374C>T	ENST00000298552.3	-	15	1812	c.1591G>A	c.(1591-1593)Gtg>Atg	p.V531M	TSC1_ENST00000545250.1_Missense_Mutation_p.V480M|TSC1_ENST00000440111.2_Missense_Mutation_p.V531M	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	531					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		TCAGGGTTCACGCTGGCGCCC	0.587			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.V531M		.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1-1906	1	Unknown(1)	bone(1)	c.G1591A						.	C	MET/VAL,MET/VAL,MET/VAL	0,4406		0,0,2203	70	69	69		1591,1588,1438	1	0	9		69	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	21,21,21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	531/1165,530/1164,480/1114	135781374	1,13005	2203	4300	6503	SO:0001583	missense	7248	exon15	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GGTTCACGCTGGC	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.1591G>A	9.37:g.135781374C>T	ENSP00000298552:p.Val531Met	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	89	32	NM_000368	0	0	0	0	0	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	37	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	C	5.777	0.327722	0.10956	0.0	1.16E-4	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;T	0.82167	-1.58;-1.58;-1.39	6.05	0.967	0.19674	.	0.902905	0.09848	N	0.748020	T	0.67135	0.2861	N	0.22421	0.69	0.09310	N	1	B;B	0.23937	0.045;0.094	B;B	0.20767	0.022;0.031	T	0.52555	-0.8560	10	0.33141	T	0.24	-7.0E-4	2.3538	0.04291	0.1018:0.4483:0.1801:0.2698	.	480;531	B7Z897;Q92574	.;TSC1_HUMAN	M	531;531;480	ENSP00000298552:V531M;ENSP00000394524:V531M;ENSP00000444017:V480M	ENSP00000298552:V531M	V	-	1	0	TSC1	134771195	0.000000	0.05858	0.001000	0.08648	0.266000	0.26442	0.364000	0.20325	0.137000	0.18759	-0.897000	0.02905	GTG	.		0.587	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			T	135781374	C	T	135781374	3	4	98	1	0	0	0	0	1	0	0	0	16638	536	19	1	1939	1	TSC1	9	135781374	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	624468	135781374	5432057	60	8786											
SUV39H2	79723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	14939337	14939338	+	Missense_Mutation	DNP	AC	AC	TT																															aaattaaaatcccacctggtActcccatctatgaatgcaac																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:14939337_14939338AC>TT	ENST00000354919.6	+	3	670_671	c.670_671AC>TT	c.(670-672)ACt>TTt	p.T224F	SUV39H2_ENST00000313519.5_Missense_Mutation_p.T164F|SUV39H2_ENST00000378325.3_Intron	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	224	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						CCCACCTGGTACTCCCATCTAT	0.396																																					p.T224F		.											.	SUV39H2	0			c.C671T						.																																			SO:0001583	missense	79723	exon3			CTGGTACTCCCAT	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"Chromatin-modifying enzymes / K-methyltransferases"	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	Exception_encountered	10.37:g.14939337_14939338delinsTT	ENSP00000346997:p.Thr224Phe	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	131	49		0	0	0	0	0	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	DNP	ENST00000354919.6	37	CCDS53494.1																																																																																			.		0.396	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670		TT	14939338	AC	TT	14939337	3	4	98	1	0	0	0	0	1	0	0	0	15445	391	14	5	492	5	SUV39H2	10	14939337	Missense_Mutation	DNP	AC	TCGA-DW-7840-01A-11D-2136-08		14939337	120595410	61	8787											
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	24835172	24835172	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagggcaccaggaccatccaTactcccagcctcaccagcta	12	5	7	17	0	1	0	1	0	0	0	3	1	3	1	6	2	3	2	6	2	3	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:24835172T>C	ENST00000376454.3	+	21	5781	c.5751T>C	c.(5749-5751)caT>caC	p.H1917H	KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Silent_p.H1348H|KIAA1217_ENST00000376462.1_Silent_p.H1238H|KIAA1217_ENST00000458595.1_Silent_p.H1323H	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1917					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GGACCATCCATACTCCCAGCC	0.532																																					p.H1917H		.											.	KIAA1217-98	0			c.T5751C						.						76	70	72					10																	24835172		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon21			CATCCATACTCCC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5751T>C	10.37:g.24835172T>C		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	99	51	NM_019590	0	0	26	57	31	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.		0.532	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		C	24835172	T	C	24835172	2	2	98	1	0	0	0	0	0	0	0	1	8237	1403	49	3		3	KIAA1217	10	24835172	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	9895835	24835172	110699575	62	8788											
ARMC4	55130	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	28270470	28270470	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtttttataaattgaaccTtttctctcataattaacgtc	12	18	4	7	1	2	1	1	1	1	0	4	1	2	1	1	1	2	1	1	1	6	9			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:28270470T>C	ENST00000305242.5	-	7	953	c.861A>G	c.(859-861)aaA>aaG	p.K287K	ARMC4_ENST00000537576.1_5'UTR|ARMC4_ENST00000545014.1_5'UTR|ARMC4_ENST00000239715.3_Silent_p.K144K|ARMC4_ENST00000480504.1_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	287					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						AAATTGAACCTTTTCTCTCAT	0.294																																					p.K287K		.											.	ARMC4-96	0			c.A861G						.						99	104	102					10																	28270470		2202	4296	6498	SO:0001819	synonymous_variant	55130	exon7			TGAACCTTTTCTC	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.861A>G	10.37:g.28270470T>C		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	127	8	NM_018076	0	0	0	0	0	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	37	CCDS7157.1																																																																																			.		0.294	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		C	28270470	T	C	28270470	2	2	98	1	0	0	0	0	0	0	0	1	954	1606	56	3		3	ARMC4	10	28270470	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3435298	28270470	107264277	63	8789											
CUL2	8453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	35324145	35324145	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctcgaaggccctcatcatgGatgtggttttgcagctcctg	6	12	12	11	1	2	0	2	0	0	0	4	2	3	1	2	3	2	4	2	3	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:35324145G>T	ENST00000374748.1	-	11	1270	c.957C>A	c.(955-957)atC>atA	p.I319I	CUL2_ENST00000602371.1_Silent_p.I262I|CUL2_ENST00000374751.3_Silent_p.I319I|CUL2_ENST00000537177.1_Silent_p.I338I|CUL2_ENST00000374746.1_Silent_p.I319I|CUL2_ENST00000374749.3_Silent_p.I319I|CUL2_ENST00000374742.1_Silent_p.I319I			Q13617	CUL2_HUMAN	cullin 2	319					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						CCTCATCATGGATGTGGTTTT	0.473																																					p.I338I		.											.	CUL2-229	0			c.C1014A						.						155	126	136					10																	35324145		2203	4300	6503	SO:0001819	synonymous_variant	8453	exon10			ATCATGGATGTGG	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.957C>A	10.37:g.35324145G>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	63	21	NM_001198778	0	0	1	3	2	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Silent	SNP	ENST00000374748.1	37	CCDS7179.1																																																																																			.		0.473	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		T	35324145	G	T	35324145	2	4	98	1	0	0	0	0	0	0	0	1	4061	1164	41	4		4	CUL2	10	35324145	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	7053675	35324145	100210602	64	8790											
ALOX5	240	hgsc.bcm.edu;broad.mit.edu	37	chr10	45869784	45869784	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggttcgccggcactgaCgactacatctacctcagcct	8	9	9	15	3	2	1	1	1	1	0	3	2	2	1	3	2	3	2	3	2	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:45869784C>A	ENST00000374391.2	+	1	110	c.57C>A	c.(55-57)gaC>gaA	p.D19E	ALOX5_ENST00000542434.1_Missense_Mutation_p.D19E	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	19	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	CCGGCACTGACGACTACATCT	0.701																																					p.D19E		.											.	ALOX5-228	0			c.C57A						.						28	19	22					10																	45869784		2161	4260	6421	SO:0001583	missense	240	exon1			CACTGACGACTAC	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.57C>A	10.37:g.45869784C>A	ENSP00000363512:p.Asp19Glu	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_000698	0	0	5	9	4	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	37	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	c	13.35	2.210677	0.39102	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	T;T	0.66280	-0.2;-0.2	4.82	1.81	0.25067	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.051214	0.85682	D	0.000000	T	0.75042	0.3796	M	0.88310	2.945	0.49798	D	0.999823	D;D;D	0.76494	0.998;0.999;0.985	P;D;P	0.69142	0.757;0.962;0.554	T	0.70651	-0.4813	10	0.30854	T	0.27	-37.9305	4.7968	0.13276	0.0:0.5691:0.1591:0.2717	.	19;19;19	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	E	19	ENSP00000437634:D19E;ENSP00000363512:D19E	ENSP00000363512:D19E	D	+	3	2	ALOX5	45189790	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	1.011000	0.29911	0.420000	0.25954	-0.533000	0.04299	GAC	.		0.701	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			A	45869784	C	A	45869784	3	1	98	1	0	0	0	0	1	0	0	0	540	535	19	4	59	4	ALOX5	10	45869784	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	10545639	45869784	89664963	65	8791											
GRID1	2894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	87407050	87407050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcagcaaacgtgctgtccTgctccagggggttggtgccc	5	10	14	12	1	1	0	1	0	0	0	3	0	3	0	3	3	5	5	3	3	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:87407050T>C	ENST00000327946.7	-	13	2187	c.2102A>G	c.(2101-2103)cAg>cGg	p.Q701R	GRID1_ENST00000536331.1_Missense_Mutation_p.Q272R|RN7SKP238_ENST00000516483.1_RNA|RP11-93H12.4_ENST00000474115.2_RNA	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	701					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CGTGCTGTCCTGCTCCAGGGG	0.552										Multiple Myeloma(13;0.14)																											p.Q701R		.											.	GRID1-142	0			c.A2102G						.						271	252	259					10																	87407050		2203	4300	6503	SO:0001583	missense	2894	exon13			CTGTCCTGCTCCA	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2102A>G	10.37:g.87407050T>C	ENSP00000330148:p.Gln701Arg	Somatic	418	0		WXS	Illumina HiSeq	Phase_I	427	157	NM_017551	0	0	0	0	0	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.261225	0.39995	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.27402	1.67;1.67	5.7	5.7	0.88788	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.35248	0.0925	N	0.11106	0.095	0.80722	D	1	D	0.59357	0.985	D	0.74023	0.982	T	0.28650	-1.0037	10	0.26408	T	0.33	.	15.1462	0.72653	0.0:0.0:0.0:1.0	.	701	Q9ULK0	GRID1_HUMAN	R	701;272	ENSP00000330148:Q701R;ENSP00000444455:Q272R	ENSP00000330148:Q701R	Q	-	2	0	GRID1	87397030	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.175000	0.68902	0.528000	0.53228	CAG	.		0.552	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		C	87407050	T	C	87407050	3	2	98	1	0	0	0	0	1	0	0	0	6792	1580	55	3	943	3	GRID1	10	87407050	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	41537266	87407050	48127697	66	8792											
NRAP	4892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115411657	115411657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgttcatcatgccctctctTatactccacctgatgagaag	9	12	7	13	1	3	2	2	2	1	1	5	3	4	2	3	0	2	1	3	0	3	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:115411657T>C	ENST00000359988.3	-	7	824	c.580A>G	c.(580-582)Aag>Gag	p.K194E	NRAP_ENST00000369360.3_Missense_Mutation_p.K194E|NRAP_ENST00000369358.4_Missense_Mutation_p.K194E|NRAP_ENST00000360478.3_Missense_Mutation_p.K194E	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGCCCTCTCTTATACTCCACC	0.547																																					p.K194E		.											.	NRAP-522	0			c.A580G						.						108	88	94					10																	115411657		2203	4300	6503	SO:0001583	missense	4892	exon7			CTCTCTTATACTC		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.580A>G	10.37:g.115411657T>C	ENSP00000353078:p.Lys194Glu	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	71	21	NM_001261463	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	T	18.89	3.719870	0.68844	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37	6.03	6.03	0.97812	.	0.044427	0.85682	D	0.000000	D	0.82393	0.5027	M	0.87827	2.91	0.43988	D	0.996689	D;D;D	0.59357	0.985;0.982;0.985	P;P;D	0.64506	0.868;0.879;0.926	D	0.85146	0.0983	10	0.66056	D	0.02	.	12.952	0.58407	0.0:0.0:0.0:1.0	.	194;194;194	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	E	194	ENSP00000358365:K194E;ENSP00000358367:K194E;ENSP00000353078:K194E;ENSP00000353666:K194E	ENSP00000353078:K194E	K	-	1	0	NRAP	115401647	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	6.117000	0.71577	2.313000	0.78055	0.454000	0.30748	AAG	.		0.547	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		C	115411657	T	C	115411657	3	2	98	1	0	0	0	0	1	0	0	0	10664	1763	61	3	4756	3	NRAP	10	115411657	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	28004607	115411657	20123090	67	8793											
DMBT1	1755	bcgsc.ca	37	chr10	124351971	124351971	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcggccccaggaaatgcccGgtttggccagggctcaggac	7	6	15	13	2	1	0	1	0	0	0	2	2	1	2	4	6	1	2	4	6	1	1	rs199833346		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:124351971G>A	ENST00000338354.3	+	20	2466	c.2360G>A	c.(2359-2361)cGg>cAg	p.R787Q	DMBT1_ENST00000368909.3_Missense_Mutation_p.R787Q|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.R777Q|DMBT1_ENST00000368955.3_Missense_Mutation_p.R777Q|DMBT1_ENST00000330163.4_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	787	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGAAATGCCCGGTTTGGCCAG	0.622													G|||	1	0.000199681	0	0	5008	,	,		17838	0		0.001	False		,,,				2504	0				p.R787Q	Ovarian(182;93 2026 18125 22222 38972)												.	DMBT1-494	0			c.G2360A						.	G	,GLN/ARG,GLN/ARG	0,3976		0,0,1988	175	138	150		,2360,2330	-3.3	0	10		150	2,8224		0,2,4111	no	intron,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,43,43	0,2,6099	AA,AG,GG		0.0243,0.0,0.0164	,probably-damaging,probably-damaging	,787/2414,777/2404	124351971	2,12200	1988	4113	6101	SO:0001583	missense	1755	exon20			ATGCCCGGTTTGG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2360G>A	10.37:g.124351971G>A	ENSP00000342210:p.Arg787Gln	Somatic	318	1		WXS	Illumina HiSeq	Phase_1	363	10	NM_007329	0	0	0	0	0	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	5.842	0.339525	0.11069	0.0	2.43E-4	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	3.86	-3.27	0.05048	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.16557	0.0398	N	0.12502	0.225	0.09310	N	1	P;B;B;B	0.37276	0.589;0.04;0.04;0.049	B;B;B;B	0.25987	0.065;0.006;0.006;0.01	T	0.14448	-1.0472	9	0.27082	T	0.32	.	6.8244	0.23874	0.6813:0.0:0.1778:0.1409	.	548;787;777;787	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	Q	787;787;787;787;787;787;777;787;777	ENSP00000342210:R787Q;ENSP00000343175:R777Q;ENSP00000357905:R787Q;ENSP00000357951:R777Q	ENSP00000342210:R787Q	R	+	2	0	DMBT1	124341961	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.763000	0.04740	-0.732000	0.04856	-0.259000	0.10710	CGG	G|0.999;A|0.000		0.622	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124351971	G	A	124351971	3	1	98	1	0	0	0	0	1	0	0	0	4588	1116	39	1	2438	1	DMBT1	10	124351971	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	8940314	124351971	11182776	68	8794											
IFITM1	8519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	315058	315058	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cctgttactggtattcggctCtgtgacagtctaccatatta	8	15	8	10	1	2	1	0	1	2	0	3	1	2	1	2	2	2	3	2	2	5	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:315058C>G	ENST00000408968.3	+	2	641	c.323C>G	c.(322-324)tCt>tGt	p.S108C	IFITM1_ENST00000328221.5_Missense_Mutation_p.S108C|IFITM1_ENST00000528780.1_Missense_Mutation_p.S108C	NM_003641.3	NP_003632	P13164	IFM1_HUMAN	interferon induced transmembrane protein 1	108	Interaction with CAV1.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of immune response (GO:0050776)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			large_intestine(1)|lung(3)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTATTCGGCTCTGTGACAGTC	0.507																																					p.S108C		.											.	.	0			c.C323G						.						129	129	129					11																	315058		1942	4128	6070	SO:0001583	missense	8519	exon2			TCGGCTCTGTGAC	J04164	CCDS41584.1	11p15.5	2012-03-15	2012-03-13		ENSG00000185885	ENSG00000185885		"CD molecules"	5412	protein-coding gene	gene with protein product	"interferon-induced transmembrane protein 1"	604456	"interferon induced transmembrane protein 1 (9-27)"	IFI17		7559564	Standard	NM_003641		Approved	9-27, CD225	uc001loy.4	P13164		ENST00000408968.3:c.323C>G	11.37:g.315058C>G	ENSP00000386187:p.Ser108Cys	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	122	35	NM_003641	0	0	20	22	2	Q15322|Q53XZ0	Missense_Mutation	SNP	ENST00000408968.3	37	CCDS41584.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150346	0.37923	.	.	ENSG00000185885	ENST00000528780;ENST00000328221;ENST00000408968	T;T;T	0.80304	-1.36;-1.36;-1.36	3.73	-0.746	0.11095	.	.	.	.	.	T	0.61578	0.2358	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.15870	0.014	T	0.45571	-0.9252	9	0.38643	T	0.18	.	0.8934	0.01259	0.1942:0.4108:0.1719:0.2231	.	108	P13164	IFM1_HUMAN	C	108	ENSP00000437057:S108C;ENSP00000330825:S108C;ENSP00000386187:S108C	ENSP00000330825:S108C	S	+	2	0	IFITM1	305058	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.419000	0.02460	-0.422000	0.07405	0.313000	0.20887	TCT	.		0.507	IFITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383595.1	NM_003641		G	315058	C	G	315058	3	3	98	1	0	0	0	0	1	0	0	0	7547	913	32	4	329	4	IFITM1	11	315058	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		315058	134691458	69	8795											
SIGIRR	59307	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	407548	407548	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagtcgctgtaggagacgtAggcgtcgtagagcttcccgt	7	9	15	10	5	0	2	0	0	0	2	3	3	1	2	1	2	1	6	1	2	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:407548A>G	ENST00000431843.2	-	6	808	c.502T>C	c.(502-504)Tac>Cac	p.Y168H	SIGIRR_ENST00000397632.3_Missense_Mutation_p.Y168H|SIGIRR_ENST00000332725.3_Missense_Mutation_p.Y168H|SIGIRR_ENST00000531205.1_Missense_Mutation_p.Y168H|SIGIRR_ENST00000529486.1_5'UTR|SIGIRR_ENST00000382520.2_Missense_Mutation_p.Y168H	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	168	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TAGGAGACGTAGGCGTCGTAG	0.647																																					p.Y168H		.											.	SIGIRR-90	0			c.T502C						.						26	27	27					11																	407548		2189	4291	6480	SO:0001583	missense	59307	exon6			AGACGTAGGCGTC		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30575	protein-coding gene	gene with protein product	"single immunoglobulin domain IL1R1 related"	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.502T>C	11.37:g.407548A>G	ENSP00000403104:p.Tyr168His	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	40	10	NM_001135053	0	0	18	30	12	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	37	CCDS31325.1	.	.	.	.	.	.	.	.	.	.	a	17.94	3.510696	0.64522	.	.	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520;ENST00000528209	T;T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71;2.71	2.75	2.75	0.32379	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.240626	0.36303	N	0.002663	T	0.36082	0.0954	M	0.83118	2.625	0.58432	D	0.999999	D;D	0.76494	0.999;0.987	D;D	0.72625	0.978;0.944	T	0.30001	-0.9993	10	0.87932	D	0	.	10.2759	0.43510	1.0:0.0:0.0:0.0	.	168;168	C9JFX4;Q6IA17	.;SIGIR_HUMAN	H	168;168;168;168;168;64	ENSP00000403104:Y168H;ENSP00000380756:Y168H;ENSP00000333656:Y168H;ENSP00000433022:Y168H;ENSP00000371960:Y168H;ENSP00000435135:Y64H	ENSP00000333656:Y168H	Y	-	1	0	SIGIRR	397548	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	4.453000	0.60061	1.525000	0.49052	0.240000	0.17902	TAC	.		0.647	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805		G	407548	A	G	407548	3	3	98	1	0	0	0	0	1	0	0	0	14336	420	15	3	750	3	SIGIRR	11	407548	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	92490	407548	134598968	70	8796											
TRIM3	10612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6479061	6479061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccgtctcacaggcctcaCagtaaaactccatcgtctgc	9	9	8	15	2	3	0	2	0	2	0	6	0	4	0	3	2	2	1	3	2	2	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:6479061C>T	ENST00000525074.1	-	4	774	c.380G>A	c.(379-381)tGt>tAt	p.C127Y	TRIM3_ENST00000529058.1_5'Flank|TRIM3_ENST00000345851.3_Missense_Mutation_p.C127Y|TRIM3_ENST00000536344.1_Missense_Mutation_p.C8Y|TRIM3_ENST00000537602.1_Missense_Mutation_p.C127Y|TRIM3_ENST00000359518.3_Missense_Mutation_p.C127Y	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	127					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACAGGCCTCACAGTAAAACTC	0.612																																					p.C127Y	Melanoma(6;5 510 1540 25169 29084)	.											.	TRIM3-714	0			c.G380A						.						90	80	84					11																	6479061		2201	4296	6497	SO:0001583	missense	10612	exon4			GCCTCACAGTAAA	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10064	protein-coding gene	gene with protein product	"ring finger protein 22", "brain expressed ring finger", "tripartite motif protein TRIM3"	605493	"tripartite motif-containing 3"	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.380G>A	11.37:g.6479061C>T	ENSP00000433102:p.Cys127Tyr	Somatic	123	1		WXS	Illumina HiSeq	Phase_I	118	41	NM_001248006	0	0	1	1	0	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	37	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.349821	0.61183	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344;ENST00000528227	D;D;D;D;D;D	0.99080	-5.4;-5.4;-5.4;-5.4;-5.4;-5.4	5.06	4.15	0.48705	Zinc finger, B-box (3);	0.000000	0.85682	D	0.000000	D	0.99489	0.9818	H	0.97131	3.945	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98378	1.0557	10	0.87932	D	0	-8.0526	12.1727	0.54167	0.0:0.9156:0.0:0.0844	.	8;8;127	F5H2Q8;D3DQT4;O75382	.;.;TRIM3_HUMAN	Y	127;127;127;127;127;127;127;8;127	ENSP00000433102:C127Y;ENSP00000340797:C127Y;ENSP00000441091:C127Y;ENSP00000352508:C127Y;ENSP00000445460:C8Y;ENSP00000433070:C127Y	ENSP00000337094:C127Y	C	-	2	0	TRIM3	6435637	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.440000	0.80464	1.129000	0.42072	0.462000	0.41574	TGT	.		0.612	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		T	6479061	C	T	6479061	3	4	98	1	0	0	0	0	1	0	0	0	16537	478	17	2	1890	2	TRIM3	11	6479061	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	6071513	6479061	128527455	71	8797											
ALKBH3	221120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	43905565	43905565	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctgagccacgagtgatTgagtaagtaatttgctgtct	9	13	11	8	1	1	3	0	3	1	0	2	4	2	3	2	0	2	4	2	0	2	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:43905565T>C	ENST00000302708.4	+	4	627	c.216T>C	c.(214-216)atT>atC	p.I72I	ALKBH3_ENST00000532410.1_3'UTR|ALKBH3_ENST00000378840.4_Silent_p.I72I	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	72					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	CACGAGTGATTGAGTAAGTAA	0.433								Direct reversal of damage																													p.I72I		.											.	ALKBH3-90	0			c.T216C						.						256	225	236					11																	43905565		2203	4300	6503	SO:0001819	synonymous_variant	221120	exon4			AGTGATTGAGTAA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"Alkylation repair homologs"	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.216T>C	11.37:g.43905565T>C		Somatic	233	0		WXS	Illumina HiSeq	Phase_I	214	83	NM_139178	0	0	0	0	0	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	37	CCDS7906.1																																																																																			.		0.433	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178		C	43905565	T	C	43905565	2	2	98	1	0	0	0	0	0	0	0	1	528	1800	63	3		3	ALKBH3	11	43905565	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	37426504	43905565	91100951	72	8798											
RCE1	9986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66613413	66613413	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcggccttggagcacccAcagaggcggcccctgctggc	5	5	15	16	3	0	1	0	0	0	1	0	2	0	2	4	5	3	2	4	5	0	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:66613413A>C	ENST00000309657.3	+	8	881	c.837A>C	c.(835-837)ccA>ccC	p.P279P	PC_ENST00000528224.1_5'Flank|RCE1_ENST00000525356.1_Silent_p.P156P|RCE1_ENST00000524506.1_Silent_p.P258P	NM_001032279.1|NM_005133.2	NP_001027450.1|NP_005124.1	Q9Y256	FACE2_HUMAN	Ras converting CAAX endopeptidase 1	279					CAAX-box protein processing (GO:0071586)|proteolysis (GO:0006508)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|metalloendopeptidase activity (GO:0004222)			breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10						TGGAGCACCCACAGAGGCGGC	0.622																																					p.P279P		.											.	RCE1-290	0			c.A837C						.						96	93	94					11																	66613413		2200	4295	6495	SO:0001819	synonymous_variant	9986	exon8			GCACCCACAGAGG	AF121951	CCDS8151.1	11q13	2013-10-18	2013-10-18	2001-06-29	ENSG00000173653	ENSG00000173653			13721	protein-coding gene	gene with protein product	"farnesylated protein-converting enzyme 2", "prenyl protein-specific endoprotease 2", "RCE1 homolog, prenyl protein protease", "CAAX prenyl protease 2"	605385	"RCE1 (S. Cerevisiae) homolog, prenyl protein protease", "RCE1 homolog, prenyl protein peptidase (S. cerevisiae)", "RCE1 homolog, prenyl protein protease (S. cerevisiae)"	RCE1A, RCE1B		10085068, 10373325	Standard	NM_005133		Approved	hRCE1, FACE-2, FACE2	uc001ojk.1	Q9Y256	OTTHUMG00000167098	ENST00000309657.3:c.837A>C	11.37:g.66613413A>C		Somatic	199	1		WXS	Illumina HiSeq	Phase_I	190	73	NM_005133	0	0	18	35	17	Q52LZ9	Silent	SNP	ENST00000309657.3	37	CCDS8151.1																																																																																			.		0.622	RCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393105.1	NM_005133		C	66613413	A	C	66613413	2	2	98	1	0	0	0	0	0	0	0	1	13208	146	6	5		5	RCE1	11	66613413	Silent	SNP	A	TCGA-DW-7840-01A-11D-2136-08	22707848	66613413	68393103	73	8799			1	27		4	4	12476	N	A_-	1.908483e-05
PC	5091	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	66617140	66617141	+	Frame_Shift_Ins	INS	-	-	G																															gcgagtattcaggctatccaINSgggggccaaaggtggcagtg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:66617140_66617141insG	ENST00000393958.2	-	20	3181_3182	c.3088_3089insC	c.(3088-3090)ctgfs	p.L1030fs	PC_ENST00000393955.2_Frame_Shift_Ins_p.L1030fs|PC_ENST00000528224.1_5'UTR|PC_ENST00000393960.1_Frame_Shift_Ins_p.L1030fs|PC_ENST00000529047.1_Frame_Shift_Ins_p.L150fs	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1030					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CAGGCTATCCAGGGGGCCAAAG	0.604																																					p.L1030fs		.											.	PC-228	0			c.3089_3090insC						.																																			SO:0001589	frameshift_variant	5091	exon19			.	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.3089dupC	11.37:g.66617145_66617145dupG	ENSP00000377530:p.Leu1030fs	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	77	18	NM_022172	0	0	0	0	0	B4DN00|Q16705	Frame_Shift_Ins	INS	ENST00000393958.2	37	CCDS8152.1																																																																																			.		0.604	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		G	66617141	-	G	66617140	7	5	98	1	0	1	1	0	0	0	0	0	11523	188	7	0	459	0	PC	11	66617140	Frame_Shift_Ins	INS	-	TCGA-DW-7840-01A-11D-2136-08	3727	66617140	68389376	74	8800			1	27		4	4	12476	N	A_-	1.908483e-05
PC	5091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66620716	66620716	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtctcgggccagaccgaggtAgtgcaacagcttttgggccc	7	8	14	12	2	1	1	0	0	1	1	2	2	1	1	3	3	3	3	3	3	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:66620716A>T	ENST00000393958.2	-	12	1600	c.1507T>A	c.(1507-1509)Tac>Aac	p.Y503N	PC_ENST00000393955.2_Missense_Mutation_p.Y503N|PC_ENST00000393960.1_Missense_Mutation_p.Y503N|PC_ENST00000529047.1_5'Flank	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	503					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	AGACCGAGGTAGTGCAACAGC	0.622																																					p.Y503N		.											.	PC-228	0			c.T1507A						.						122	92	102					11																	66620716		2200	4295	6495	SO:0001583	missense	5091	exon12			CGAGGTAGTGCAA	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.1507T>A	11.37:g.66620716A>T	ENSP00000377530:p.Tyr503Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	88	28	NM_000920	0	0	0	0	0	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370348	0.61624	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960	D;D;D	0.96745	-4.11;-4.11;-4.11	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	D	0.98435	0.9479	H	0.95780	3.72	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.98985	1.0806	10	0.87932	D	0	-24.4033	11.2003	0.48736	1.0:0.0:0.0:0.0	.	503	P11498	PYC_HUMAN	N	503	ENSP00000377527:Y503N;ENSP00000377530:Y503N;ENSP00000377532:Y503N	ENSP00000377527:Y503N	Y	-	1	0	PC	66377292	1.000000	0.71417	1.000000	0.80357	0.264000	0.26372	8.288000	0.89921	1.744000	0.51775	0.379000	0.24179	TAC	.		0.622	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66620716	A	T	66620716	3	4	98	1	0	0	0	0	1	0	0	0	11523	420	15	5	2073	5	PC	11	66620716	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	3576	66620716	68385800	75	8801			1	27		4	4	12476	N	A_-	1.908483e-05
LRFN4	78999	broad.mit.edu	37	chr11	66625888	66625889	+	Frame_Shift_Ins	INS	-	-	C																															tgatgcagaggcctctcccgINScccccctggtgctgagcttt																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:66625888_66625889insC	ENST00000309602.4	+	1	916_917	c.673_674insC	c.(673-675)gccfs	p.A225fs	PC_ENST00000393955.2_Intron|LRFN4_ENST00000393952.3_Frame_Shift_Ins_p.A225fs|PC_ENST00000393960.1_Intron|PC_ENST00000393958.2_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	225						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						GGCCTCTCCCGCCCCCCTGGTG	0.698																																					p.A225fs													.	LRFN4-90	0			c.673_674insC						.																																			SO:0001589	frameshift_variant	78999	exon1			TCTCCCGCCCCCC	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.679dupC	11.37:g.66625894_66625894dupC	ENSP00000312535:p.Ala225fs	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_024036	0	0	0	0	0	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Frame_Shift_Ins	INS	ENST00000309602.4	37	CCDS8153.1																																																																																			.		0.698	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		C	66625889	-	C	66625888	7	5	98	1	0	1	1	0	0	0	0	0	8965	1087	38	0	675	0	LRFN4	11	66625888	Frame_Shift_Ins	INS	-	TCGA-DW-7840-01A-11D-2136-08	5172	66625888	68380628	76	8802			1	27		4	4	12476	N	A_-	1.908483e-05
UVRAG	7405	hgsc.bcm.edu	37	chr11	75526481	75526481	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctccgcgtcggtcgggggccCcgtcccccagccacccccgg	2	4	13	22	6	0	0	0	0	0	0	4	0	2	0	8	4	1	0	8	4	0	0	rs386755092|rs7118567	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:75526481C>A	ENST00000356136.3	+	1	270	c.29C>A	c.(28-30)cCc>cAc	p.P10H	RP11-535A19.2_ENST00000533945.1_RNA|RP11-535A19.2_ENST00000531263.1_RNA|RP11-535A19.2_ENST00000527219.1_RNA|RP11-535A19.2_ENST00000533590.1_RNA|RP11-535A19.2_ENST00000529719.1_RNA	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	10			P -> H (in dbSNP:rs7118567).		DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						GTCGGGGGCCCCGTCCCCCAG	0.776													A|||	971	0.19389	0.3389	0.1153	5008	,	,		9602	0.2401		0.0815	False		,,,				2504	0.1217				p.P10H		.											.	UVRAG-229	0			c.C29A						.						1	1	1					11																	75526481		706	1693	2399	SO:0001583	missense	7405	exon1			GGGGCCCCGTCCC	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"beclin 1 binding protein"	602493	"UV radiation resistance associated gene"			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.29C>A	11.37:g.75526481C>A	ENSP00000348455:p.Pro10His	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_003369	0	0	0	0	0	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	37	CCDS8241.1	377	0.17261904761904762	147	0.29878048780487804	48	0.13259668508287292	116	0.20279720279720279	66	0.0870712401055409	A	10.69	1.420343	0.25552	.	.	ENSG00000198382	ENST00000356136	T	0.54479	0.57	5.01	2.06	0.26882	C2 calcium/lipid-binding domain, CaLB (1);	0.244913	0.34853	N	0.003637	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.99999999749761	B	0.32693	0.38	B	0.31547	0.132	T	0.29150	-1.0021	9	0.72032	D	0.01	-1.9932	7.7013	0.28625	0.2862:0.6307:0.0:0.0831	rs7118567	10	Q9P2Y5	UVRAG_HUMAN	H	10	ENSP00000348455:P10H	ENSP00000348455:P10H	P	+	2	0	UVRAG	75204129	0.480000	0.25933	0.967000	0.41034	0.005000	0.04900	0.039000	0.13884	0.382000	0.24878	-3.014000	0.00075	CCC	C|0.828;A|0.172		0.776	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		A	75526481	C	A	75526481	3	1	98	1	0	0	0	0	1	0	0	0	17141	623	22	4	31	4	UVRAG	11	75526481	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	8900593	75526481	59480035	77	8803											
PHLDB1	23187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118513026	118513026	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagtggtaccaggagctgAtggccgggctggggactggc	7	6	19	9	1	0	1	0	1	0	0	0	3	0	3	2	7	3	4	2	7	1	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:118513026A>T	ENST00000361417.2	+	14	3202	c.2791A>T	c.(2791-2793)Atg>Ttg	p.M931L	PHLDB1_ENST00000524713.1_Missense_Mutation_p.M74L|PHLDB1_ENST00000534672.1_Intron|PHLDB1_ENST00000356063.5_Intron|PHLDB1_ENST00000527898.1_Intron	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	931										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCAGGAGCTGATGGCCGGGCT	0.642																																					p.M931L		.											.	PHLDB1-90	0			c.A2791T						.						76	79	78					11																	118513026		2200	4295	6495	SO:0001583	missense	23187	exon13			GAGCTGATGGCCG		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"Pleckstrin homology (PH) domain containing"	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2791A>T	11.37:g.118513026A>T	ENSP00000354498:p.Met931Leu	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	155	53	NM_001144758	0	0	1	1	0	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.870388	0.51588	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000524713	T;T	0.50813	1.52;0.73	5.14	5.14	0.70334	.	0.543120	0.21674	N	0.070828	T	0.34832	0.0911	L	0.40543	1.245	0.26911	N	0.966889	B;B;B	0.24576	0.106;0.039;0.01	B;B;B	0.25614	0.062;0.019;0.011	T	0.27706	-1.0066	10	0.02654	T	1	-9.3743	12.3456	0.55119	1.0:0.0:0.0:0.0	.	69;74;931	B7Z2B9;B4DK17;Q86UU1	.;.;PHLB1_HUMAN	L	931;690;295;74	ENSP00000354498:M931L;ENSP00000434905:M74L	ENSP00000350921:M295L	M	+	1	0	PHLDB1	118018236	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.723000	0.54955	1.925000	0.55765	0.379000	0.24179	ATG	.		0.642	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118513026	A	T	118513026	3	4	98	1	0	0	0	0	1	0	0	0	11877	333	12	5	2837	5	PHLDB1	11	118513026	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	42986545	118513026	16493490	78	8804											
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12334248	12334248	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatgtagccttccacaggatCgtaatctatggcaatggcat	11	11	10	9	1	1	0	0	0	1	0	3	2	2	1	2	3	1	4	2	3	4	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:12334248C>T	ENST00000261349.4	-	6	1178	c.1102G>A	c.(1102-1104)Gat>Aat	p.D368N	LRP6_ENST00000543091.1_Missense_Mutation_p.D368N	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	368	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TCCACAGGATCGTAATCTATG	0.453																																					p.D368N		.											.	LRP6-661	0			c.G1102A						.						199	170	180					12																	12334248		2203	4300	6503	SO:0001583	missense	4040	exon6			CAGGATCGTAATC	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1102G>A	12.37:g.12334248C>T	ENSP00000261349:p.Asp368Asn	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	295	162	NM_002336	0	0	0	0	0	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848081	0.91277	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.92545	-3.06;-3.06	5.82	5.82	0.92795	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000006	D	0.96396	0.8824	M	0.89534	3.04	0.80722	D	1	D;D	0.67145	0.994;0.996	P;P	0.57960	0.79;0.83	D	0.96559	0.9414	10	0.72032	D	0.01	.	20.0991	0.97865	0.0:1.0:0.0:0.0	.	368;368	F5H7J9;O75581	.;LRP6_HUMAN	N	368	ENSP00000261349:D368N;ENSP00000442472:D368N	ENSP00000261349:D368N	D	-	1	0	LRP6	12225515	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	5.999000	0.70665	2.752000	0.94435	0.655000	0.94253	GAT	.		0.453	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12334248	C	T	12334248	3	4	98	1	0	0	0	0	1	0	0	0	8987	884	31	1	3811	1	LRP6	12	12334248	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		12334248	121517647	79	8805											
PPFIA2	8499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	81671123	81671123	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatgttggcttgcttcccGtcttctttctagttcttttc	2	22	6	11	1	5	0	1	0	4	0	7	0	6	0	1	1	1	4	1	1	1	10			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:81671123G>A	ENST00000549396.1	-	28	3443	c.3283C>T	c.(3283-3285)Cgg>Tgg	p.R1095W	PPFIA2_ENST00000541570.2_Missense_Mutation_p.R631W|PPFIA2_ENST00000333447.7_Missense_Mutation_p.R1083W|PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000550584.2_Missense_Mutation_p.R1095W|PPFIA2_ENST00000549325.1_Missense_Mutation_p.R1080W|PPFIA2_ENST00000443686.3_Missense_Mutation_p.R990W|PPFIA2_ENST00000552948.1_Missense_Mutation_p.R1074W|PPFIA2_ENST00000407050.4_Missense_Mutation_p.R994W|RP11-121G22.3_ENST00000549161.1_lincRNA|PPFIA2_ENST00000541017.1_Missense_Mutation_p.R281W|PPFIA2_ENST00000548586.1_Missense_Mutation_p.R1089W|PPFIA2_ENST00000550359.2_Missense_Mutation_p.R942W	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	1095					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						CTTGCTTCCCGTCTTCTTTCT	0.274																																					p.R1095W		.											.	PPFIA2-231	0			c.C3283T						.						130	117	121					12																	81671123		1797	4055	5852	SO:0001583	missense	8499	exon27			CTTCCCGTCTTCT	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"Sterile alpha motif (SAM) domain containing"	9246	protein-coding gene	gene with protein product	"Liprin-alpha2"	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.3283C>T	12.37:g.81671123G>A	ENSP00000450337:p.Arg1095Trp	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	20	12	NM_001220473	0	0	0	0	0	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686642	0.68157	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000541017;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948	T;T;T;T;T;T;T;T;T	0.38240	1.92;1.93;1.55;1.15;1.5;1.92;1.92;1.6;1.85	5.71	3.83	0.44106	Sterile alpha motif/pointed domain (1);	0.131846	0.49916	D	0.000132	T	0.69178	0.3082	H	0.94847	3.59	0.58432	D	0.999996	D	0.89917	1.0	D	0.83275	0.996	T	0.77705	-0.2488	10	0.87932	D	0	-12.2793	13.6442	0.62270	0.0:0.0:0.4348:0.5652	.	1095	O75334	LIPA2_HUMAN	W	1095;1080;631;281;994;1106;1083;1089;990;1074	ENSP00000450337:R1095W;ENSP00000450298:R1080W;ENSP00000438337:R631W;ENSP00000445532:R281W;ENSP00000385093:R994W;ENSP00000327416:R1083W;ENSP00000449338:R1089W;ENSP00000388373:R990W;ENSP00000447868:R1074W	ENSP00000327416:R1083W	R	-	1	2	PPFIA2	80195254	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.119000	0.50422	0.721000	0.32231	-0.181000	0.13052	CGG	.		0.274	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81671123	G	A	81671123	3	1	98	1	0	0	0	0	1	0	0	0	12336	1144	40	1	510	1	PPFIA2	12	81671123	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	69336875	81671123	52180772	80	8806											
RASSF9	9182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	86199543	86199543	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctttcggagcctctccacTtctctatgatgcagtaatca	8	13	6	14	1	3	1	1	1	2	0	6	2	3	2	3	1	2	2	3	1	2	4	rs367564230		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:86199543T>C	ENST00000361228.3	-	2	613	c.245A>G	c.(244-246)aAg>aGg	p.K82R		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	82	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)			endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GCCTCTCCACTTCTCTATGAT	0.473																																					p.K82R		.											.	RASSF9-23	0			c.A245G						.						95	95	95					12																	86199543		1885	4121	6006	SO:0001583	missense	9182	exon2			CTCCACTTCTCTA		CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.245A>G	12.37:g.86199543T>C	ENSP00000354884:p.Lys82Arg	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	216	53	NM_005447	0	0	0	0	0	B3KMQ4|Q8N5U8	Missense_Mutation	SNP	ENST00000361228.3	37	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.084459	0.55861	.	.	ENSG00000198774	ENST00000361228	T	0.46451	0.87	4.82	4.82	0.62117	Ras-association (2);	0.139782	0.47852	D	0.000216	T	0.30479	0.0766	L	0.33485	1.01	0.37061	D	0.898052	P	0.46784	0.884	B	0.39152	0.292	T	0.22487	-1.0215	10	0.16420	T	0.52	-5.5864	14.68	0.69009	0.0:0.0:0.0:1.0	.	82	O75901	RASF9_HUMAN	R	82	ENSP00000354884:K82R	ENSP00000354884:K82R	K	-	2	0	RASSF9	84723674	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.997000	0.40786	1.941000	0.56285	0.421000	0.28195	AAG	.		0.473	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			C	86199543	T	C	86199543	3	2	98	1	0	0	0	0	1	0	0	0	13125	1609	56	3	1066	3	RASSF9	12	86199543	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	4528420	86199543	47652352	81	8807											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	100048989	100048989	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgattgtagatgaggttctCtgaaattaaatttatatcat	13	18	7	3	0	2	4	1	3	1	1	3	4	2	4	0	1	0	2	0	1	6	8			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:100048989C>G	ENST00000547776.2	-	9	1128		c.e9-1		ANKS1B_ENST00000547010.1_Splice_Site|ANKS1B_ENST00000329257.7_Splice_Site	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ATGAGGTTCTCTGAAATTAAA	0.323																																					.		.											.	.	0			c.1129-1G>C						.						68	61	63					12																	100048989		1821	4073	5894	SO:0001630	splice_region_variant	56899	exon10			GGTTCTCTGAAAT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1129-1G>C	12.37:g.100048989C>G		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	23	2	NM_152788	0	0	0	0	0	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Splice_Site	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802946	0.70682	.	.	ENSG00000185046	ENST00000547776;ENST00000329257;ENST00000549866	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4502	0.83977	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKS1B	98573120	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.743000	0.62110	2.616000	0.88540	0.650000	0.86243	.	.		0.323	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	Intron	G	100048989	C	G	100048989	5	3	98	1	0	0	0	0	0	0	1	0	689	927	32	4	2978	4	ANKS1B	12	100048989	Splice_Site	SNP	C	TCGA-DW-7840-01A-11D-2136-08	13849446	100048989	33802906	82	8808											
TDG	6996	hgsc.bcm.edu	37	chr12	104378526	104378526	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tataaaatgttgtgattctaGctctgctatgttatgccatc	10	17	7	7	0	2	1	0	1	2	0	3	1	2	1	1	0	3	4	1	0	6	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:104378526G>T	ENST00000392872.3	+	8	1026		c.e8-1		TDG_ENST00000542036.1_Splice_Site|TDG_ENST00000544861.1_Splice_Site|TDG_ENST00000266775.9_Splice_Site|AC078819.1_ENST00000401157.1_RNA	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase						base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		TGTGATTCTAGCTCTGCTATG	0.323								Base excision repair (BER), DNA glycosylases																													.		.											.	TDG-661	0			c.793-1G>T						.						45	42	43					12																	104378526		2203	4300	6503	SO:0001630	splice_region_variant	6996	exon8			ATTCTAGCTCTGC	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.793-1G>T	12.37:g.104378526G>T		Somatic	36	1		WXS	Illumina HiSeq	Phase_I	77	4	NM_003211	0	0	0	0	0	Q8IUZ6|Q8IZM3	Splice_Site	SNP	ENST00000392872.3	37	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099218	0.76983	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TDG	102902656	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	9.869000	0.99810	2.840000	0.97914	0.655000	0.94253	.	.		0.323	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		Intron	T	104378526	G	T	104378526	5	4	98	1	0	0	0	0	0	0	1	0	15757	985	34	4	822	4	TDG	12	104378526	Splice_Site	SNP	G	TCGA-DW-7840-01A-11D-2136-08	4329537	104378526	29473369	83	8809											
ATP2A2	488	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	110765478	110765478	+	Frame_Shift_Del	DEL	C	C	-																															aggagagaacaccccttcagCaaaaactagatgaatttggg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:110765478delC	ENST00000539276.2	+	8	860	c.751delC	c.(751-753)caafs	p.Q251fs	ATP2A2_ENST00000395494.2_Frame_Shift_Del_p.Q224fs|ATP2A2_ENST00000308664.6_Frame_Shift_Del_p.Q251fs			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	251					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						ACCCCTTCAGCAAAAACTAGA	0.453																																					p.Q251fs		.											.	ATP2A2-94	0			c.751delC						.						166	166	166					12																	110765478		2203	4300	6503	SO:0001589	frameshift_variant	488	exon8			.		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"ATPases / P-type"	812	protein-coding gene	gene with protein product	"sarcoplasmic/endoplasmic reticulum calcium ATPase 2", "calcium pump 2"	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.751delC	12.37:g.110765478delC	ENSP00000440045:p.Gln251fs	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	346	90	NM_001681	0	0	0	0	0	A6NDN7|B4DF05|P16614|Q86VJ2	Frame_Shift_Del	DEL	ENST00000539276.2	37	CCDS9144.1																																																																																			.		0.453	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		-	110765478	C	-	110765478	7	5	98	1	0	1	0	1	0	0	0	0	1138	711	25	0	781	0	ATP2A2	12	110765478	Frame_Shift_Del	DEL	C	TCGA-DW-7840-01A-11D-2136-08	6386952	110765478	23086417	84	8810											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124829474	124829474	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagccagtggtggacgcgccGgtgtcgtacttgagcggggt	5	8	19	9	5	0	1	0	1	0	0	1	3	0	2	2	5	3	1	2	5	1	2	rs61241227	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:124829474G>A	ENST00000405201.1	-	32	4383	c.4383C>T	c.(4381-4383)acC>acT	p.T1461T	NCOR2_ENST00000397355.1_Silent_p.T1452T|NCOR2_ENST00000404621.1_Silent_p.T1451T|NCOR2_ENST00000429285.2_Silent_p.T1451T|NCOR2_ENST00000356219.3_Silent_p.T1468T|NCOR2_ENST00000404121.2_Silent_p.T1022T			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1469					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TGGACGCGCCGGTGTCGTACT	0.667													G|||	16	0.00319489	0.0121	0	5008	,	,		15692	0		0	False		,,,				2504	0				p.T1461T		.											.	NCOR2-229	0			c.C4383T						.	G	,,	43,4243		0,43,2100	50	61	57		4353,4353,4383	-4.7	0	12	dbSNP_129	57	2,8472		0,2,4235	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,45,6335	AA,AG,GG		0.0236,1.0033,0.3527	,,	1451/2459,1451/2505,1461/2515	124829474	45,12715	2143	4237	6380	SO:0001819	synonymous_variant	9612	exon34			CGCGCCGGTGTCG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.4383C>T	12.37:g.124829474G>A		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	11	5	NM_006312	0	0	0	14	14	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			A|0.000;C|0.003;G|0.996		0.667	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124829474	G	A	124829474	2	1	98	1	0	0	0	0	0	0	0	1	10262	1103	39	1		1	NCOR2	12	124829474	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	14063996	124829474	9022421	85	8811											
SCARB1	949	hgsc.bcm.edu	37	chr12	125348148	125348148	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctcacccaccttaaggAcctgctgcttgatgagcgac	8	9	8	16	1	1	2	1	2	0	0	2	4	2	3	4	1	3	2	4	1	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:125348148A>G	ENST00000415380.2	-	1	244	c.119T>C	c.(118-120)gTc>gCc	p.V40A	SCARB1_ENST00000546215.1_Missense_Mutation_p.V40A|SCARB1_ENST00000376788.1_Missense_Mutation_p.V40A|SCARB1_ENST00000339570.5_Missense_Mutation_p.V40A|SCARB1_ENST00000535005.1_Intron|SCARB1_ENST00000261693.6_Missense_Mutation_p.V40A			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	40					adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	CACCTTAAGGACCTGCTGCTT	0.731																																					p.V40A		.											.	SCARB1-226	0			c.T119C						.						25	22	23					12																	125348148		2201	4300	6501	SO:0001583	missense	949	exon1			TTAAGGACCTGCT	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.119T>C	12.37:g.125348148A>G	ENSP00000414979:p.Val40Ala	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_005505	0	0	0	0	0	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37		.	.	.	.	.	.	.	.	.	.	A	18.80	3.701743	0.68501	.	.	ENSG00000073060	ENST00000339570;ENST00000415380;ENST00000261693;ENST00000376788;ENST00000546215;ENST00000545493	T;T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.39;-0.81;-0.81	3.48	3.48	0.39840	.	0.070854	0.56097	U	0.000034	T	0.81432	0.4821	M	0.76002	2.32	0.80722	D	1	P;D;D;P;D	0.58268	0.951;0.982;0.982;0.775;0.977	P;P;P;B;P	0.60236	0.755;0.871;0.871;0.425;0.725	T	0.82744	-0.0306	10	0.87932	D	0	-21.358	8.9206	0.35610	1.0:0.0:0.0:0.0	.	40;40;40;40;40	B7ZKQ9;B4E3I1;Q8WTV0;F8W8N0;Q8WTV0-2	.;.;SCRB1_HUMAN;.;.	A	40	ENSP00000343795:V40A;ENSP00000414979:V40A;ENSP00000261693:V40A;ENSP00000365984:V40A;ENSP00000442862:V40A;ENSP00000443454:V40A	ENSP00000261693:V40A	V	-	2	0	SCARB1	123914101	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	4.239000	0.58694	1.528000	0.49103	0.358000	0.22013	GTC	.		0.731	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505		G	125348148	A	G	125348148	3	3	98	1	0	0	0	0	1	0	0	0	13913	275	10	3	1582	3	SCARB1	12	125348148	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	518674	125348148	8503747	86	8812											
POLE	5426	hgsc.bcm.edu	37	chr12	133235892	133235892	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctcacctctccgtgacAggggagccctcgggcttgcg	5	7	13	16	3	2	1	1	1	1	0	4	2	2	2	4	3	3	1	4	3	0	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:133235892A>G	ENST00000320574.5	-	26	3307	c.3264T>C	c.(3262-3264)ccT>ccC	p.P1088P	POLE_ENST00000535270.1_Silent_p.P1061P	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1088					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TCTCCGTGACAGGGGAGCCCT	0.657								DNA polymerases (catalytic subunits)																													p.P1088P		.											.	POLE-233	0			c.T3264C						.						40	38	39					12																	133235892		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon26			CGTGACAGGGGAG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"DNA polymerases"	9177	protein-coding gene	gene with protein product	"DNA polymerase epsilon catalytic subunit A"	174762	"polymerase (DNA directed), epsilon"			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3264T>C	12.37:g.133235892A>G		Somatic	48	2		WXS	Illumina HiSeq	Phase_I	84	7	NM_006231	0	0	0	0	0	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			.		0.657	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		G	133235892	A	G	133235892	2	3	98	1	0	0	0	0	0	0	0	1	12222	175	7	3		3	POLE	12	133235892	Silent	SNP	A	TCGA-DW-7840-01A-11D-2136-08	7887744	133235892	616003	87	8813											
TECPR2	9895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102906785	102906786	+	Missense_Mutation	DNP	GG	GG	TT																															ttccataggagcccttctctGgaagattgaacagaaatcta																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr14:102906785_102906786GG>TT	ENST00000359520.7	+	11	2817_2818	c.2591_2592GG>TT	c.(2590-2592)tGG>tTT	p.W864F	TECPR2_ENST00000558678.1_Missense_Mutation_p.W864F	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	864					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						GCCCTTCTCTGGAAGATTGAAC	0.446																																					p.W864F		.											.	TECPR2	0			c.G2592T						.																																			SO:0001583	missense	9895	exon11			TCTCTGGAAGATT	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"KIAA0329"	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		Exception_encountered	14.37:g.102906785_102906786delinsTT	ENSP00000352510:p.Trp864Phe	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	183	63		0	0	0	0	0	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	DNP	ENST00000359520.7	37	CCDS32162.1																																																																																			.		0.446	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		TT	102906786	GG	TT	102906785	3	4	98	1	0	0	0	0	1	0	0	0	15776	1357	47	4	2629	4	TECPR2	14	102906785	Missense_Mutation	DNP	GG	TCGA-DW-7840-01A-11D-2136-08		102906785	4442755	88	8814											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921074	24921074	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccggcccctgccagggccAgggcgtggcgcccccgctcc	2	3	15	21	5	0	0	0	0	0	0	1	0	1	0	8	4	1	1	8	4	0	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:24921074A>G	ENST00000329468.2	+	1	534	c.60A>G	c.(58-60)ccA>ccG	p.P20P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	20					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TGCCAGGGCCAGGGCGTGGCG	0.682																																					p.P20P		.											.	.	0			c.A60G						.						6	8	7					15																	24921074		1783	3773	5556	SO:0001819	synonymous_variant	23742	exon1			AGGGCCAGGGCGT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.60A>G	15.37:g.24921074A>G		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_018958	0	0	0	0	0		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.		0.682	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		G	24921074	A	G	24921074	2	3	98	1	0	0	0	0	0	0	0	1	1788	175	7	3		3	C15orf2	15	24921074	Silent	SNP	A	TCGA-DW-7840-01A-11D-2136-08		24921074	77610318	89	8815											
TRPM1	4308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	31362391	31362391	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggtgttgcacttggcagaGgggggatatgctggttggtg	5	12	20	4	0	0	1	0	0	0	1	0	2	0	2	0	7	2	5	0	7	1	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:31362391G>T	ENST00000256552.6	-	4	269	c.122C>A	c.(121-123)cCt>cAt	p.P41H	TRPM1_ENST00000397795.2_Missense_Mutation_p.P19H|TRPM1_ENST00000542188.1_Missense_Mutation_p.P58H|TRPM1_ENST00000559179.1_Missense_Mutation_p.P19H	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		ACTTGGCAGAGGGGGGATATG	0.507																																					p.P58H		.											.	TRPM1-94	0			c.C173A						.						243	229	234					15																	31362391		1976	4162	6138	SO:0001583	missense	4308	exon3			GGCAGAGGGGGGA	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"Voltage-gated ion channels / Transient receptor potential cation channels"	7146	protein-coding gene	gene with protein product		603576	"melastatin 1"	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.122C>A	15.37:g.31362391G>T	ENSP00000256552:p.Pro41His	Somatic	370	1		WXS	Illumina HiSeq	Phase_I	382	147	NM_001252020	0	0	0	0	0		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336399	0.24253	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.55760	0.5;0.5;0.5	6.03	5.12	0.69794	.	0.408600	0.22654	U	0.057296	T	0.60340	0.2261	L	0.36672	1.1	0.33691	D	0.613333	D;D	0.71674	0.998;0.983	D;P	0.73708	0.981;0.827	T	0.71192	-0.4665	10	0.72032	D	0.01	-15.4292	9.4507	0.38725	0.2106:0.0:0.7894:0.0	.	19;19	Q6PE48;Q7Z4N2	.;TRPM1_HUMAN	H	19;58;41;19	ENSP00000380897:P19H;ENSP00000437849:P58H;ENSP00000256552:P41H	ENSP00000256552:P41H	P	-	2	0	TRPM1	29149683	1.000000	0.71417	0.918000	0.36340	0.307000	0.27823	3.722000	0.54948	1.541000	0.49316	0.655000	0.94253	CCT	.		0.507	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31362391	G	T	31362391	3	4	98	1	0	0	0	0	1	0	0	0	16618	1000	35	4	4855	4	TRPM1	15	31362391	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	6441317	31362391	71169001	90	8816											
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48584051	48584051	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgacatcaacattaggccaAacaaagagaggtatgaaata	19	7	9	6	0	1	3	1	2	0	1	1	4	1	3	1	2	2	1	1	2	7	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:48584051A>G	ENST00000558405.1	+	23	2964	c.2950A>G	c.(2950-2952)Aac>Gac	p.N984D	SLC12A1_ENST00000396577.3_Missense_Mutation_p.N984D|SLC12A1_ENST00000380993.3_Missense_Mutation_p.N984D			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	984					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CATTAGGCCAAACAAAGAGAG	0.323																																					p.N984D		.											.	SLC12A1-24	0			c.A2950G						.						51	50	50					15																	48584051		2195	4290	6485	SO:0001583	missense	6557	exon24			AGGCCAAACAAAG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"Solute carriers"	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.2950A>G	15.37:g.48584051A>G	ENSP00000453409:p.Asn984Asp	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_001184832	0	0	0	0	0	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	A	13.79	2.341269	0.41498	.	.	ENSG00000074803	ENST00000380993;ENST00000396577	D;D	0.84516	-1.86;-1.86	5.44	5.44	0.79542	.	0.202548	0.51477	D	0.000096	T	0.76428	0.3986	L	0.27053	0.805	0.29554	N	0.851145	B;B	0.28820	0.224;0.147	B;B	0.24701	0.055;0.045	T	0.68981	-0.5266	10	0.23891	T	0.37	.	15.1563	0.72746	1.0:0.0:0.0:0.0	.	984;984	E9PDW4;Q13621	.;S12A1_HUMAN	D	984	ENSP00000370381:N984D;ENSP00000379822:N984D	ENSP00000370381:N984D	N	+	1	0	SLC12A1	46371343	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.657000	0.67996	2.057000	0.61298	0.533000	0.62120	AAC	.		0.323	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			G	48584051	A	G	48584051	3	3	98	1	0	0	0	0	1	0	0	0	14414	14	1	3	3140	3	SLC12A1	15	48584051	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	17221660	48584051	53947341	91	8817											
ANKDD1A	348094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65223120	65223120	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggaggagcagaatgcggTgagtcaccgcctggggatgg	8	6	18	9	2	1	2	1	1	0	1	1	5	1	5	3	6	2	1	3	6	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:65223120T>G	ENST00000380230.3	+	7	698		c.e7+2		ANKDD1A_ENST00000395720.1_Splice_Site|ANKDD1A_ENST00000357698.3_Splice_Site|ANKDD1A_ENST00000491145.1_Splice_Site|ANKDD1A_ENST00000496660.1_Splice_Site|ANKDD1A_ENST00000319580.8_Splice_Site|ANKDD1A_ENST00000395723.1_Splice_Site	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A						signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						CAGAATGCGGTGAGTCACCGC	0.607																																					.		.											.	ANKDD1A-69	0			c.669+2T>G						.						68	54	59					15																	65223120		2202	4299	6501	SO:0001630	splice_region_variant	348094	exon7			ATGCGGTGAGTCA		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.669+2T>G	15.37:g.65223120T>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	33	14	NM_182703	0	0	0	0	0	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Splice_Site	SNP	ENST00000380230.3	37	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360134	0.61403	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000319597;ENST00000496660;ENST00000483400;ENST00000395723	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.27	0.37666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKDD1A	63010173	1.000000	0.71417	0.940000	0.37924	0.376000	0.30014	5.235000	0.65348	1.699000	0.51192	0.459000	0.35465	.	.		0.607	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	Intron	G	65223120	T	G	65223120	5	3	98	1	0	0	0	0	0	0	1	0	624	1710	59	5	697	5	ANKDD1A	15	65223120	Splice_Site	SNP	T	TCGA-DW-7840-01A-11D-2136-08	16639069	65223120	37308272	92	8818											
IGDCC4	57722	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	65684505	65684505	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatactgcttcactttctTcttgagccggacaggcccca	7	12	7	15	1	4	1	2	1	2	0	4	2	4	2	3	2	3	1	3	2	1	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:65684505T>A	ENST00000352385.2	-	11	2298	c.2089A>T	c.(2089-2091)Aag>Tag	p.K697*		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	697	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						TTCACTTTCTTCTTGAGCCGG	0.632																																					p.K697X		.											.	IGDCC4-93	0			c.A2089T						.						32	39	37					15																	65684505		2184	4286	6470	SO:0001587	stop_gained	57722	exon11			CTTTCTTCTTGAG		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2089A>T	15.37:g.65684505T>A	ENSP00000319623:p.Lys697*	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	112	44	NM_020962	0	0	0	0	0	Q9HCE4	Nonsense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	T	41	8.769097	0.98948	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	.	.	.	5.49	4.38	0.52667	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-23.8407	10.907	0.47086	0.0:0.0731:0.0:0.9269	.	.	.	.	X	697;426	.	ENSP00000319623:K697X	K	-	1	0	IGDCC4	63471558	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.434000	0.66526	0.947000	0.37659	0.533000	0.62120	AAG	.		0.632	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65684505	T	A	65684505	4	1	98	1	0	0	0	0	0	1	0	0	7590	1792	62	5	1703	5	IGDCC4	15	65684505	Nonsense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	461385	65684505	36846887	93	8819											
MAP2K5	5607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	67985904	67985904	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttggaacaaatgcttatatgGcggtaagtaaacttatgcaa	15	12	9	5	1	0	0	0	0	0	0	0	1	0	1	0	3	4	4	0	3	9	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:67985904G>T	ENST00000178640.5	+	15	1597	c.970G>T	c.(970-972)Gcg>Tcg	p.A324S	MAP2K5_ENST00000340972.4_Missense_Mutation_p.A134S|MAP2K5_ENST00000395476.2_Missense_Mutation_p.A324S|MAP2K5_ENST00000354498.5_Missense_Mutation_p.A288S	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	324	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						TGCTTATATGGCGGTAAGTAA	0.303																																					p.A324S		.											.	MAP2K5-546	0			c.G970T						.						132	126	128					15																	67985904		2200	4297	6497	SO:0001583	missense	5607	exon15			TATATGGCGGTAA	U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.970G>T	15.37:g.67985904G>T	ENSP00000178640:p.Ala324Ser	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	95	30	NM_145160	0	0	0	0	0	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	37	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107121	0.37145	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.36358	0.0964	L	0.31752	0.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.02728	-1.1118	10	0.28530	T	0.3	-16.1519	19.5552	0.95342	0.0:0.0:1.0:0.0	.	134;324;324	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	S	324;324;324;288;134	ENSP00000378859:A324S;ENSP00000178640:A324S;ENSP00000346493:A288S;ENSP00000342101:A134S	ENSP00000178640:A324S	A	+	1	0	MAP2K5	65772958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.968000	0.93407	2.630000	0.89119	0.585000	0.79938	GCG	.		0.303	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162		T	67985904	G	T	67985904	3	4	98	1	0	0	0	0	1	0	0	0	9265	1203	42	4	1028	4	MAP2K5	15	67985904	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	2301399	67985904	34545488	94	8820											
ACSBG1	23205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	78485857	78485857	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttccccaaaccttcaggatCttttccagctgcttctgcgt	6	14	6	15	1	3	0	1	0	2	0	5	1	5	1	4	1	4	2	4	1	1	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:78485857C>G	ENST00000258873.4	-	5	859	c.654G>C	c.(652-654)aaG>aaC	p.K218N	ACSBG1_ENST00000558828.1_5'Flank|ACSBG1_ENST00000541759.1_Intron|ACSBG1_ENST00000560817.1_Intron	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	218					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						CCTTCAGGATCTTTTCCAGCT	0.577																																					p.K218N		.											.	ACSBG1-91	0			c.G654C						.						114	111	112					15																	78485857		2196	4293	6489	SO:0001583	missense	23205	exon5			CAGGATCTTTTCC	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"Acyl-CoA synthetase family"	29567	protein-coding gene	gene with protein product	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.654G>C	15.37:g.78485857C>G	ENSP00000258873:p.Lys218Asn	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	148	62	NM_015162	0	0	0	0	0	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	37	CCDS10298.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409343	0.62399	.	.	ENSG00000103740	ENST00000258873	T	0.44482	0.92	4.49	3.56	0.40772	AMP-dependent synthetase/ligase (1);	0.062950	0.64402	D	0.000012	T	0.66025	0.2748	M	0.89840	3.065	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.984	T	0.68104	-0.5497	10	0.66056	D	0.02	-37.6924	7.8278	0.29326	0.0:0.8072:0.0:0.1928	.	214;218	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	N	218	ENSP00000258873:K218N	ENSP00000258873:K218N	K	-	3	2	ACSBG1	76272912	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.007000	0.29860	0.871000	0.35750	0.655000	0.94253	AAG	.		0.577	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162		G	78485857	C	G	78485857	3	3	98	1	0	0	0	0	1	0	0	0	173	912	32	4	1560	4	ACSBG1	15	78485857	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	10499953	78485857	24045535	95	8821											
RASGRF1	5923	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	79254568	79254568	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaaagattggtccagtaaaTattgcgttacctgagaaaag	16	10	9	6	1	0	2	0	1	0	2	1	3	1	2	2	1	2	2	2	1	8	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:79254568T>C	ENST00000419573.3	-	28	4014	c.3740A>G	c.(3739-3741)tAt>tGt	p.Y1247C	RASGRF1_ENST00000558480.2_Missense_Mutation_p.Y1231C|RASGRF1_ENST00000394745.3_Missense_Mutation_p.Y463C	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1247	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTCCAGTAAATATTGCGTTAC	0.468																																					p.Y1247C		.											.	RASGRF1-662	0			c.A3740G						.						58	56	56					15																	79254568		2196	4290	6486	SO:0001583	missense	5923	exon28			AGTAAATATTGCG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3740A>G	15.37:g.79254568T>C	ENSP00000405963:p.Tyr1247Cys	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	13	5	NM_002891	0	0	0	0	0	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.169141	0.57584	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.34472	1.36;1.36	3.96	3.96	0.45880	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000003	T	0.56381	0.1981	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.998;0.999	P;D	0.68483	0.867;0.958	T	0.60826	-0.7186	10	0.87932	D	0	.	9.5252	0.39160	0.0:0.0:0.0:1.0	.	1249;1231	Q13972;F8VPA5	RGRF1_HUMAN;.	C	1247;1231;463	ENSP00000405963:Y1247C;ENSP00000378228:Y463C	ENSP00000378224:Y1231C	Y	-	2	0	RASGRF1	77041623	1.000000	0.71417	0.170000	0.22879	0.948000	0.59901	6.883000	0.75595	1.545000	0.49373	0.402000	0.26972	TAT	.		0.468	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		C	79254568	T	C	79254568	3	2	98	1	0	0	0	0	1	0	0	0	13104	1406	49	3	85	3	RASGRF1	15	79254568	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	768711	79254568	23276824	96	8822											
PKD1	5310	broad.mit.edu	37	chr16	2142548	2142548	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggactggttcccgtggacGtagggcagcagcacgtgggc	6	7	17	11	3	0	0	0	0	0	0	1	2	1	2	1	5	2	5	1	5	1	2	rs555704322		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr16:2142548G>A	ENST00000262304.4	-	39	11410	c.11202C>T	c.(11200-11202)taC>taT	p.Y3734Y	RP11-304L19.3_ENST00000565937.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_Silent_p.Y3733Y|MIR1225_ENST00000408729.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3734					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TCCCGTGGACGTAGGGCAGCA	0.672													g|||	1	0.000199681	0	0	5008	,	,		16033	0.001		0	False		,,,				2504	0				p.Y3734Y													.	PKD1-91	0			c.C11202T						.						35	37	36					16																	2142548		2195	4296	6491	SO:0001819	synonymous_variant	5310	exon39			GTGGACGTAGGGC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.11202C>T	16.37:g.2142548G>A		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	53	4	NM_001009944	0	0	10	10	0	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.672	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2142548	G	A	2142548	2	1	98	1	0	0	0	0	0	0	0	1	11989	1140	40	1		1	PKD1	16	2142548	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08		2142548	88212205	97	8823											
SENP3	26168	broad.mit.edu	37	chr17	7470323	7470323	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaaaggtggaccaaaaacGtgagttttgaattcacatcc	15	10	9	7	1	1	3	1	3	0	0	2	4	2	4	2	2	1	1	2	2	5	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr17:7470323G>A	ENST00000429205.2	+	8	1390		c.e8+1		SENP3_ENST00000321337.7_Splice_Site|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_Splice_Site			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3							cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				GACCAAAAACGTGAGTTTTGA	0.408																																					.													.	SENP3-659	0			c.1341+1G>A						.						194	207	203					17																	7470323		1015	2129	3144	SO:0001630	splice_region_variant	26168	exon8			AAAAACGTGAGTT	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"SUMO1/sentrin/SMT3 specific protease 3"			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1341+1G>A	17.37:g.7470323G>A		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	15	3	NM_015670	0	0	0	0	0	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Splice_Site	SNP	ENST00000429205.2	37		.	.	.	.	.	.	.	.	.	.	G	20.3	3.967950	0.74131	.	.	ENSG00000161956	ENST00000321337;ENST00000429205	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4768	0.84134	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SENP3	7411047	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.891000	0.87319	2.550000	0.86006	0.514000	0.50259	.	.		0.408	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Intron	A	7470323	G	A	7470323	5	1	98	1	0	0	0	0	0	0	1	0	14080	1159	40	1	1365	1	SENP3	17	7470323	Splice_Site	SNP	G	TCGA-DW-7840-01A-11D-2136-08		7470323	73724887	98	8824											
MYH8	4626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10312636	10312636	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaaaagagactggctagAgtcttcattgcagacttctg	11	11	12	7	0	3	3	1	0	2	3	3	5	3	4	0	2	1	2	0	2	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr17:10312636A>T	ENST00000403437.2	-	16	1951	c.1857T>A	c.(1855-1857)acT>acA	p.T619T	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	619	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GACTGGCTAGAGTCTTCATTG	0.423									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.T619T		.											.	MYH8-101	0			c.T1857A						.						67	69	68					17																	10312636		2203	4300	6503	SO:0001819	synonymous_variant	4626	exon16	Familial Cancer Database	Carney Complex Variant	GGCTAGAGTCTTC		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1857T>A	17.37:g.10312636A>T		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	147	77	NM_002472	0	0	0	0	0	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			.		0.423	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10312636	A	T	10312636	2	4	98	1	0	0	0	0	0	0	0	1	10066	291	11	5		5	MYH8	17	10312636	Silent	SNP	A	TCGA-DW-7840-01A-11D-2136-08	2842313	10312636	70882574	99	8825											
AATK	9625	hgsc.bcm.edu	37	chr17	79096272	79096272	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagcgtggccgggaaggcCtccgcgccgcggcccgcctc	3	4	15	19	7	1	0	1	0	0	0	3	1	2	1	6	4	1	0	6	4	1	0	rs371390882	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr17:79096272C>A	ENST00000326724.4	-	11	1488	c.1464G>T	c.(1462-1464)gaG>gaT	p.E488D	AATK_ENST00000572339.1_5'Flank|MIR657_ENST00000385003.1_RNA|AATK_ENST00000417379.1_Missense_Mutation_p.E385D	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	488					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCGGGAAGGCCTCCGCGCCGC	0.746													C|||	13	0.00259585	0.0098	0	5008	,	,		6046	0		0	False		,,,				2504	0				p.E488D		.											.	AATK-933	0			c.G1464T						.	C	ASP/GLU,ASP/GLU	17,2637		0,17,1310	2	3	3		1464,1155	-0.8	0	17		3	0,5580		0,0,2790	no	missense,missense	AATK	NM_001080395.2,NM_004920.2	45,45	0,17,4100	AA,AC,CC		0.0,0.6405,0.2065	probably-damaging,probably-damaging	488/1375,385/1272	79096272	17,8217	1327	2790	4117	SO:0001583	missense	9625	exon11			GAAGGCCTCCGCG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.1464G>T	17.37:g.79096272C>A	ENSP00000324196:p.Glu488Asp	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	6	3	NM_001080395	0	0	1	1	0	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.968|8.968	0.972137|0.972137	0.18736|0.18736	0.006405|0.006405	0.0|0.0	ENSG00000181409|ENSG00000181409	ENST00000326724|ENST00000417379	T|.	0.78595|.	-1.19|.	3.88|3.88	-0.75|-0.75	0.11080|0.11080	.|.	0.224693|.	0.37669|.	N|.	0.001994|.	T|T	0.24967|0.24967	0.0606|0.0606	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	1|1	P|.	0.36144|.	0.539|.	B|.	0.33254|.	0.16|.	T|T	0.26018|0.26018	-1.0115|-1.0115	10|5	0.62326|.	D|.	0.03|.	.|.	3.6985|3.6985	0.08374|0.08374	0.2648:0.3981:0.2583:0.0788|0.2648:0.3981:0.2583:0.0788	.|.	488|.	Q6ZMQ8|.	LMTK1_HUMAN|.	D|M	488|441	ENSP00000324196:E488D|.	ENSP00000324196:E488D|.	E|R	-|-	3|2	2|0	AATK|AATK	76710867|76710867	0.305000|0.305000	0.24481|0.24481	0.018000|0.018000	0.16275|0.16275	0.125000|0.125000	0.20455|0.20455	0.342000|0.342000	0.19926|0.19926	-0.284000|-0.284000	0.09102|0.09102	-0.304000|-0.304000	0.09214|0.09214	GAG|AGG	.		0.746	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		A	79096272	C	A	79096272	3	1	98	1	0	0	0	0	1	0	0	0	26	680	24	4	2676	4	AATK	17	79096272	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	68783636	79096272	2098938	100	8826											
C19orf21	126353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	758211	758211	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggtgaaccgcatcccacCtgatgcctaccagccgtacc	10	6	9	16	2	0	2	0	2	0	0	1	3	1	2	7	1	5	2	7	1	4	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:758211C>A	ENST00000215582.6	+	2	1368	c.1265C>A	c.(1264-1266)cCt>cAt	p.P422H		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	422					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CGCATCCCACCTGATGCCTAC	0.652																																					p.P422H		.											.	C19orf21-91	0			c.C1265A						.						25	20	22					19																	758211		2201	4298	6499	SO:0001583	missense	126353	exon2			TCCCACCTGATGC	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1265C>A	19.37:g.758211C>A	ENSP00000215582:p.Pro422His	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	47	25	NM_173481	0	0	2	5	3		Missense_Mutation	SNP	ENST00000215582.6	37	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819234	0.50633	.	.	ENSG00000099812	ENST00000215582	T	0.35421	1.31	4.11	-1.68	0.08212	.	2.124670	0.02785	N	0.121388	T	0.47173	0.1431	L	0.54323	1.7	0.09310	N	1	D	0.69078	0.997	P	0.57548	0.823	T	0.41875	-0.9484	10	0.59425	D	0.04	-0.009	5.8678	0.18786	0.0:0.4423:0.1475:0.4102	.	422	Q8IVT2	CS021_HUMAN	H	422	ENSP00000215582:P422H	ENSP00000215582:P422H	P	+	2	0	C19orf21	709211	0.000000	0.05858	0.001000	0.08648	0.398000	0.30690	-0.883000	0.04170	-0.165000	0.10908	0.491000	0.48974	CCT	.		0.652	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	758211	C	A	758211	3	1	98	1	0	0	0	0	1	0	0	0	1919	681	24	4	1267	4	C19orf21	19	758211	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		758211	58370772	101	8827											
TUBB4	10382	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6501326	6501326	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttgtccggccgaaagatCtgaccgaaggggccagaacg	12	5	14	10	4	1	3	0	1	1	2	2	5	2	3	4	3	1	1	4	3	4	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:6501326C>A	ENST00000264071.2	-	3	620	c.249G>T	c.(247-249)caG>caT	p.Q83H	TUBB4A_ENST00000601152.1_Missense_Mutation_p.R58I|TUBB4A_ENST00000598006.1_Missense_Mutation_p.R69I|TUBB4A_ENST00000596926.1_Missense_Mutation_p.Q83H|TUBB4A_ENST00000540257.1_Missense_Mutation_p.Q83H			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	83					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										GCCGAAAGATCTGACCGAAGG	0.577																																					p.Q83H		.											.	.	0			c.G249T						.						49	44	46					19																	6501326		2203	4300	6503	SO:0001583	missense	10382	exon3			AAAGATCTGACCG	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"Tubulins"	20774	protein-coding gene	gene with protein product	"class IVa beta-tubulin"	602662	"tubulin, beta 4", "tubulin, beta 4 class IVa", "dystonia 4, torsion (autosomal dominant)"	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.249G>T	19.37:g.6501326C>A	ENSP00000264071:p.Gln83His	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	53	27	NM_006087	0	0	4	9	5	B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	37	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	C	5.184	0.219490	0.09863	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	T;T	0.70164	-0.46;-0.46	3.83	1.13	0.20643	.	0.000000	0.64402	D	0.000003	T	0.65491	0.2696	M	0.82923	2.615	0.40614	D	0.981708	B	0.10296	0.003	B	0.08055	0.003	T	0.67039	-0.5771	10	0.87932	D	0	.	9.7907	0.40704	0.0:0.7717:0.0:0.2283	.	83	P04350	TBB4A_HUMAN	H	83	ENSP00000264071:Q83H;ENSP00000443590:Q83H	ENSP00000264071:Q83H	Q	-	3	2	TUBB4	6452326	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	2.026000	0.41069	0.592000	0.29728	0.313000	0.20887	CAG	.		0.577	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		A	6501326	C	A	6501326	3	1	98	1	0	0	0	0	1	0	0	0	16791	912	32	4	1093	4	TUBB4	19	6501326	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	5743115	6501326	52627657	102	8828											
ZNF557	79230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7083599	7083599	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaatcctatgagtgcagTgattgtggaaaatcctttaa	14	12	10	5	0	0	3	0	2	0	1	2	5	2	4	2	1	1	1	2	1	5	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:7083599T>C	ENST00000439035.2	+	8	1356	c.1116T>C	c.(1114-1116)agT>agC	p.S372S	ZNF557_ENST00000414706.1_Silent_p.S379S|ZNF557_ENST00000252840.6_Silent_p.S379S			Q8N988	ZN557_HUMAN	zinc finger protein 557	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		ATGAGTGCAGTGATTGTGGAA	0.368																																					p.S379S		.											.	ZNF557-92	0			c.T1137C						.						64	68	67					19																	7083599		2125	4254	6379	SO:0001819	synonymous_variant	79230	exon8			GTGCAGTGATTGT	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.1116T>C	19.37:g.7083599T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	65	16	NM_001044387	0	0	0	1	1	Q6PEJ3|Q9BTZ1	Silent	SNP	ENST00000439035.2	37	CCDS45945.1																																																																																			.		0.368	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341		C	7083599	T	C	7083599	2	2	98	1	0	0	0	0	0	0	0	1	18020	1693	59	3		3	ZNF557	19	7083599	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	582273	7083599	52045384	103	8829											
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11135092	11135092	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggcgtgctgctgactgAtggctccgagaaggacaaga	11	6	15	9	2	0	4	0	2	0	2	1	6	1	5	1	3	2	3	1	3	3	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:11135092A>G	ENST00000429416.3	+	22	3340	c.3059A>G	c.(3058-3060)gAt>gGt	p.D1020G	SMARCA4_ENST00000444061.3_Missense_Mutation_p.D1020G|SMARCA4_ENST00000589677.1_Missense_Mutation_p.D1020G|SMARCA4_ENST00000358026.2_Missense_Mutation_p.D1020G|SMARCA4_ENST00000344626.4_Missense_Mutation_p.D1020G|SMARCA4_ENST00000541122.2_Missense_Mutation_p.D1020G|SMARCA4_ENST00000413806.3_Missense_Mutation_p.D1020G|SMARCA4_ENST00000590574.1_Missense_Mutation_p.D1020G|SMARCA4_ENST00000450717.3_Missense_Mutation_p.D1020G	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1020					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CTGCTGACTGATGGCTCCGAG	0.632			"F, N, Mis"		NSCLC																																p.D1020G		.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.A3059G						.						73	58	63					19																	11135092		2203	4300	6503	SO:0001583	missense	6597	exon21			TGACTGATGGCTC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3059A>G	19.37:g.11135092A>G	ENSP00000395654:p.Asp1020Gly	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	66	21	NM_003072	0	0	18	31	13	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.166378	0.57476	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47	4.76	4.76	0.60689	SNF2-related (1);	0.000000	0.85682	D	0.000000	T	0.82130	0.4970	L	0.37897	1.145	0.58432	D	0.999994	D;B;P;B;D;B;P;P	0.56287	0.975;0.418;0.78;0.002;0.975;0.0;0.78;0.78	P;B;B;B;P;B;P;P	0.57720	0.826;0.304;0.377;0.007;0.826;0.014;0.531;0.531	D	0.84375	0.0546	10	0.87932	D	0	-36.5944	13.3812	0.60768	1.0:0.0:0.0:0.0	.	1020;1020;1020;1020;1020;240;1020;1020	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	G	1020;1020;1084;1020;1020;1020;1020;1020	ENSP00000395654:D1020G;ENSP00000350720:D1020G;ENSP00000343896:D1020G;ENSP00000445036:D1020G;ENSP00000392837:D1020G;ENSP00000397783:D1020G;ENSP00000414727:D1020G	ENSP00000343896:D1020G	D	+	2	0	SMARCA4	10996092	1.000000	0.71417	0.922000	0.36590	0.498000	0.33706	8.908000	0.92640	1.997000	0.58415	0.533000	0.62120	GAT	.		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11135092	A	G	11135092	3	3	98	1	0	0	0	0	1	0	0	0	14802	333	12	3	3137	3	SMARCA4	19	11135092	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	4051493	11135092	47993891	104	8830											
ZNF443	10224	hgsc.bcm.edu;broad.mit.edu	37	chr19	12541116	12541116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaactgagagaagcaaatgCtttcccacattccttacatt	13	11	7	10	0	0	2	0	1	0	1	2	4	2	3	2	1	4	2	2	1	4	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:12541116C>T	ENST00000301547.5	-	4	2067	c.1870G>A	c.(1870-1872)Gca>Aca	p.A624T	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	624					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						GAAGCAAATGCTTTCCCACAT	0.408																																					p.A624T		.											.	ZNF443-91	0			c.G1870A						.						62	68	66					19																	12541116		2200	4292	6492	SO:0001583	missense	10224	exon4			CAAATGCTTTCCC	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"Zinc fingers, C2H2-type", "-"	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1870G>A	19.37:g.12541116C>T	ENSP00000301547:p.Ala624Thr	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	218	64	NM_005815	0	0	3	4	1		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.473549	0.26423	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.13778	2.56	1.36	-0.965	0.10323	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09686	0.0238	L	0.28504	0.86	0.09310	N	1	B	0.30664	0.289	B	0.37888	0.26	T	0.39231	-0.9624	9	0.38643	T	0.18	.	1.9484	0.03361	0.2638:0.3516:0.0:0.3846	.	624	Q9Y2A4	ZN443_HUMAN	T	624;596	ENSP00000301547:A624T	ENSP00000301547:A624T	A	-	1	0	ZNF443	12402116	0.000000	0.05858	0.001000	0.08648	0.586000	0.36452	-1.775000	0.01783	-0.214000	0.10078	0.454000	0.30748	GCA	.		0.408	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		T	12541116	C	T	12541116	3	4	98	1	0	0	0	0	1	0	0	0	17948	797	28	2	149	2	ZNF443	19	12541116	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	1406024	12541116	46587867	105	8831											
NOSIP	51070	hgsc.bcm.edu	37	chr19	50060443	50060443	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccccgcacatggtcctGcgaggccgcccgctgaagct	7	5	13	16	4	0	1	0	1	0	0	1	3	1	1	5	2	3	3	5	2	2	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:50060443G>C	ENST00000596358.1	-	5	380	c.322C>G	c.(322-324)Cag>Gag	p.Q108E	NOSIP_ENST00000391853.3_Missense_Mutation_p.Q108E|NOSIP_ENST00000339093.3_Missense_Mutation_p.Q108E	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	108					negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		ACATGGTCCTGCGAGGCCGCC	0.682																																					p.Q108E		.											.	NOSIP-91	0			c.C322G						.						24	25	25					19																	50060443		2203	4300	6503	SO:0001583	missense	51070	exon6			GGTCCTGCGAGGC	AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.322C>G	19.37:g.50060443G>C	ENSP00000470034:p.Gln108Glu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_015953	0	0	36	36	0	Q96FD2	Missense_Mutation	SNP	ENST00000596358.1	37	CCDS12772.1	.	.	.	.	.	.	.	.	.	.	G	3.928	-0.016700	0.07681	.	.	ENSG00000142546	ENST00000339093;ENST00000391853	T;T	0.75938	-0.98;-0.98	5.15	2.91	0.33838	.	0.386687	0.27214	N	0.020382	T	0.47192	0.1432	N	0.11673	0.155	0.32994	D	0.525399	B	0.09022	0.002	B	0.08055	0.003	T	0.47262	-0.9131	10	0.02654	T	1	-32.2216	7.9334	0.29916	0.0:0.158:0.5163:0.3258	.	108	Q9Y314	NOSIP_HUMAN	E	108	ENSP00000343497:Q108E;ENSP00000375726:Q108E	ENSP00000343497:Q108E	Q	-	1	0	NOSIP	54752255	0.887000	0.30362	0.516000	0.27786	0.517000	0.34286	1.364000	0.34171	0.501000	0.28013	0.462000	0.41574	CAG	.		0.682	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1			C	50060443	G	C	50060443	3	2	98	1	0	0	0	0	1	0	0	0	10571	1328	46	4	603	4	NOSIP	19	50060443	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	37519327	50060443	9068540	106	8832											
ZSCAN5A	79149	bcgsc.ca	37	chr19	56733626	56733626	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacgcaggcagaaggtgtgTcagcatccacattttccaca	12	8	9	12	1	1	1	1	0	0	1	3	1	3	1	2	2	2	3	2	2	2	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:56733626T>C	ENST00000587340.1	-	7	1504	c.809A>G	c.(808-810)gAc>gGc	p.D270G	ZSCAN5A_ENST00000254165.3_Missense_Mutation_p.D153G|ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.D269G|ZSCAN5A_ENST00000587492.1_Missense_Mutation_p.D124G|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.D270G			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	270					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						AGAAGGTGTGTCAGCATCCAC	0.512																																					p.D270G													.	ZSCAN5A-155	0			c.A809G						.						98	99	98					19																	56733626		2203	4300	6503	SO:0001583	missense	79149	exon5			GGTGTGTCAGCAT	AK098700	CCDS12941.1	19q13.43	2013-01-08	2008-06-10	2008-06-10	ENSG00000131848	ENSG00000131848		"-", "Zinc fingers, C2H2-type"	23710	protein-coding gene	gene with protein product			"zinc finger protein 495", "zinc finger and SCAN domain containing 5"	ZNF495, ZSCAN5			Standard	NM_024303		Approved	MGC4161	uc002qmq.3	Q9BUG6		ENST00000587340.1:c.809A>G	19.37:g.56733626T>C	ENSP00000467631:p.Asp270Gly	Somatic	178	3		WXS	Illumina HiSeq	Phase_1	176	7	NM_024303	0	0	2	2	0	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.784761	0.31593	.	.	ENSG00000131848	ENST00000391713;ENST00000254165	T;T	0.06768	3.28;3.26	1.94	-2.12	0.07165	.	.	.	.	.	T	0.20495	0.0493	M	0.78916	2.43	0.09310	N	1	D;D	0.89917	1.0;0.997	D;D	0.83275	0.996;0.989	T	0.09885	-1.0654	9	0.40728	T	0.16	.	2.5813	0.04819	0.4024:0.1449:0.0:0.4527	.	153;270	B4DX98;Q9BUG6	.;ZSA5A_HUMAN	G	270;153	ENSP00000375593:D270G;ENSP00000254165:D153G	ENSP00000254165:D153G	D	-	2	0	ZSCAN5A	61425438	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.127000	0.10547	-0.687000	0.05162	-0.496000	0.04628	GAC	.		0.512	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303		C	56733626	T	C	56733626	3	2	98	1	0	0	0	0	1	0	0	0	18270	1667	58	3	685	3	ZSCAN5A	19	56733626	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	6673183	56733626	2395357	107	8833											
ZNF814	730051	broad.mit.edu	37	chr19	58386399	58386399	+	Frame_Shift_Del	DEL	T	T	-																															tcccccaggcctcacacctgTgcagtttctgcttgtgatgt																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:58386399delT	ENST00000435989.2	-	3	593	c.359delA	c.(358-360)cacfs	p.H120fs	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	120					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CTCACACCTGTGCAGTTTCTG	0.502																																					p.H120fs													.	.	0			c.359delA						.						18	14	15					19																	58386399		692	1568	2260	SO:0001589	frameshift_variant	730051	exon3			CACCTGTGCAGTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.359delA	19.37:g.58386399delT	ENSP00000410545:p.His120fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	116	16	NM_001144989	0	0	0	0	0	A6NF35	Frame_Shift_Del	DEL	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.502	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		-	58386399	T	-	58386399	7	5	98	1	0	1	0	1	0	0	0	0	18208	1696	59	0	2212	0	ZNF814	19	58386399	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	1652773	58386399	742584	108	8834											
DNMT3B	1789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31374365	31374365	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggcacaggccttccccaCgttccacccgaggccggcag	8	4	12	17	3	0	1	0	0	0	1	2	2	2	1	6	4	0	3	6	4	0	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:31374365C>G	ENST00000328111.2	+	5	685	c.364C>G	c.(364-366)Cgt>Ggt	p.R122G	DNMT3B_ENST00000353855.2_Missense_Mutation_p.R122G|DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000348286.2_Missense_Mutation_p.R122G|DNMT3B_ENST00000201963.3_Missense_Mutation_p.R134G|DNMT3B_ENST00000375623.4_Intron|DNMT3B_ENST00000344505.4_Missense_Mutation_p.R122G|DNMT3B_ENST00000443239.3_Intron	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	122	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.R134C(1)|p.R122C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCCTTCCCCACGTTCCACCCG	0.632																																					p.R134G		.											.	DNMT3B-660	2	Substitution - Missense(2)	lung(2)	c.C400G						.						68	66	66					20																	31374365		2203	4300	6503	SO:0001583	missense	1789	exon5			TCCCCACGTTCCA		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.364C>G	20.37:g.31374365C>G	ENSP00000328547:p.Arg122Gly	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	123	54	NM_175850	0	0	0	1	1	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.465264	0.26335	.	.	ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000344505;ENST00000201963	D;D;D;D;D	0.98400	-4.67;-4.89;-4.82;-4.77;-4.91	4.84	3.86	0.44501	.	0.246993	0.38326	N	0.001738	D	0.97219	0.9091	L	0.27053	0.805	0.23070	N	0.998346	D;P;P;P	0.71674	0.998;0.811;0.804;0.752	D;B;B;B	0.80764	0.994;0.309;0.28;0.191	D	0.92382	0.5914	10	0.26408	T	0.33	-6.5354	9.8664	0.41145	0.2125:0.7875:0.0:0.0	.	134;122;122;122	Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;DNM3B_HUMAN	G	122;208;122;122;122;134	ENSP00000328547:R122G;ENSP00000313397:R122G;ENSP00000337764:R122G;ENSP00000345105:R122G;ENSP00000201963:R134G	ENSP00000201963:R134G	R	+	1	0	DNMT3B	30838026	0.456000	0.25744	0.018000	0.16275	0.031000	0.12232	1.919000	0.40015	1.211000	0.43351	0.561000	0.74099	CGT	.		0.632	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		G	31374365	C	G	31374365	3	3	98	1	0	0	0	0	1	0	0	0	4688	536	19	4	418	4	DNMT3B	20	31374365	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		31374365	31651155	109	8835											
MMP24	10893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	33851627	33851627	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtggctgtgcatgagcTgggccacgcgctgggactgg	4	8	18	11	2	0	1	0	1	0	0	0	2	0	2	2	5	2	4	2	5	0	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:33851627T>C	ENST00000246186.6	+	5	936	c.851T>C	c.(850-852)cTg>cCg	p.L284P	MMP24-AS1_ENST00000438751.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	284					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	GTGCATGAGCTGGGCCACGCG	0.622																																					p.L284P		.											.	.	0			c.T851C						.						24	24	24					20																	33851627		2203	4300	6503	SO:0001583	missense	10893	exon5			ATGAGCTGGGCCA	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"membrane-type 5 matrix metalloproteinase"	604871	"matrix metalloproteinase 24 (membrane-inserted)"			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.851T>C	20.37:g.33851627T>C	ENSP00000246186:p.Leu284Pro	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_006690	0	0	7	10	3	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	37	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.546808	0.86022	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.35605	1.3	5.05	5.05	0.67936	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.72145	0.3424	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82337	-0.0507	10	0.87932	D	0	.	14.1037	0.65075	0.0:0.0:0.0:1.0	.	284	Q9Y5R2	MMP24_HUMAN	P	284;232	ENSP00000246186:L284P	ENSP00000246186:L284P	L	+	2	0	MMP24	33315043	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.819000	0.86621	2.105000	0.64084	0.533000	0.62120	CTG	.		0.622	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		C	33851627	T	C	33851627	3	2	98	1	0	0	0	0	1	0	0	0	9686	1580	55	3	619	3	MMP24	20	33851627	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	2477262	33851627	29173893	110	8836											
SGK2	10110	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	42203603	42203603	+	Frame_Shift_Del	DEL	T	T	-																															atgatcgagcagtggactggTggtgcttgggggcagtcctc																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:42203603delT	ENST00000341458.4	+	9	1051	c.832delT	c.(832-834)tggfs	p.W278fs	SGK2_ENST00000373092.3_Frame_Shift_Del_p.W218fs|SGK2_ENST00000426287.1_Frame_Shift_Del_p.W244fs|SGK2_ENST00000423407.3_Frame_Shift_Del_p.W218fs|SGK2_ENST00000373100.1_Frame_Shift_Del_p.W218fs|SGK2_ENST00000373077.1_Frame_Shift_Del_p.W217fs	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			AGTGGACTGGTGGTGCTTGGG	0.512																																					p.W278fs		.											.	SGK2-990	0			c.832delT						.						114	103	107					20																	42203603		2203	4300	6503	SO:0001589	frameshift_variant	10110	exon9			.	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.832delT	20.37:g.42203603delT	ENSP00000340608:p.Trp278fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	48	21	NM_016276	0	0	0	0	0	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Frame_Shift_Del	DEL	ENST00000341458.4	37	CCDS13320.1																																																																																			.		0.512	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			-	42203603	T	-	42203603	7	5	98	1	0	1	0	1	0	0	0	0	14241	1696	59	0	866	0	SGK2	20	42203603	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	8351976	42203603	20821917	111	8837											
KRTAP10-12	386685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46117131	46117131	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccatgtccgtctgctcCagcgacctgagctatggcag	7	9	10	15	2	1	1	0	1	1	0	4	2	4	1	5	1	3	3	5	1	1	1	rs554572469|rs372249758	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr21:46117131C>T	ENST00000400365.3	+	1	45	c.15C>T	c.(13-15)tcC>tcT	p.S5S	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	5						keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CCGTCTGCTCCAGCGACCTGA	0.632																																					p.S5S		.											.	KRTAP10-12-90	0			c.C15T						.	C	,	0,4330		0,0,2165	83	95	91		,15	2.2	1	21		91	1,8545		0,1,4272	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	0,1,6437	TT,TC,CC		0.0117,0.0,0.0078	,	,5/246	46117131	1,12875	2165	4273	6438	SO:0001819	synonymous_variant	386685	exon1			CTGCTCCAGCGAC	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"Keratin associated proteins"	20533	protein-coding gene	gene with protein product			"keratin associated protein 18-12"	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.15C>T	21.37:g.46117131C>T		Somatic	217	0		WXS	Illumina HiSeq	Phase_I	188	70	NM_198699	0	0	0	0	0	B2RPA3	Silent	SNP	ENST00000400365.3	37	CCDS42967.1																																																																																			.		0.632	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		T	46117131	C	T	46117131	2	4	98	1	0	0	0	0	0	0	0	1	8529	581	21	2		2	KRTAP10-12	21	46117131	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08		46117131	2012764	112	8838											
C21orf58	54058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47731374	47731374	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatggaacacttaccttcCttaatacttcctgaccgttg	11	14	5	11	1	0	1	0	1	0	0	2	2	2	2	4	1	3	1	4	1	6	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr21:47731374C>A	ENST00000291691.7	-	6	1853	c.717G>T	c.(715-717)aaG>aaT	p.K239N	C21orf58_ENST00000472607.1_5'UTR|C21orf58_ENST00000397680.1_Missense_Mutation_p.K133N|C21orf58_ENST00000397683.1_Missense_Mutation_p.K133N|C21orf58_ENST00000397682.3_Missense_Mutation_p.K133N|C21orf58_ENST00000397679.1_Missense_Mutation_p.K133N	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	239										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		ACTTACCTTCCTTAATACTTC	0.488																																					p.K239N		.											.	C21orf58-91	0			c.G717T						.						109	90	97					21																	47731374		2202	4299	6501	SO:0001583	missense	54058	exon6			ACCTTCCTTAATA		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.717G>T	21.37:g.47731374C>A	ENSP00000291691:p.Lys239Asn	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_058180	0	0	0	0	0	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	37	CCDS13735.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.674609	0.47781	.	.	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.68903	0.21;-0.34;0.21;-0.36;0.21;0.21	5.46	1.62	0.23740	.	0.148272	0.42548	D	0.000695	T	0.69806	0.3152	L	0.39898	1.24	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.79784	0.993;0.993;0.985	T	0.68911	-0.5284	10	0.87932	D	0	-21.1468	7.2122	0.25939	0.0:0.6518:0.0:0.3482	.	239;133;239	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	N	133;201;133;239;133;133	ENSP00000380799:K133N;ENSP00000402356:K201N;ENSP00000380798:K133N;ENSP00000291691:K239N;ENSP00000380796:K133N;ENSP00000380797:K133N	ENSP00000291691:K239N	K	-	3	2	C21orf58	46555802	0.998000	0.40836	1.000000	0.80357	0.392000	0.30506	0.249000	0.18216	0.711000	0.32018	-0.199000	0.12753	AAG	.		0.488	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180		A	47731374	C	A	47731374	3	1	98	1	0	0	0	0	1	0	0	0	2135	680	24	4	263	4	C21orf58	21	47731374	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	1614243	47731374	398521	113	8839											
ZNRF3	84133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	29445939	29445939	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccaccttccgcagctccctCagcagcgactatgacccctt	7	9	6	19	2	1	1	1	1	0	0	4	2	4	1	6	0	3	3	6	0	1	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr22:29445939C>G	ENST00000544604.2	+	8	1945	c.1770C>G	c.(1768-1770)ctC>ctG	p.L590L	ZNRF3_ENST00000406323.3_Silent_p.L490L|ZNRF3_ENST00000402174.1_Silent_p.L490L|ZNRF3_ENST00000332811.4_Silent_p.L490L	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	590					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GCAGCTCCCTCAGCAGCGACT	0.672																																					p.L590L		.											.	ZNRF3-69	0			c.C1770G						.						54	62	59					22																	29445939		2076	4222	6298	SO:0001819	synonymous_variant	84133	exon8			CTCCCTCAGCAGC	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"RING-type (C3HC4) zinc fingers"	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1770C>G	22.37:g.29445939C>G		Somatic	220	0		WXS	Illumina HiSeq	Phase_I	235	81	NM_001206998	0	0	6	6	0	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Silent	SNP	ENST00000544604.2	37	CCDS56225.1																																																																																			.		0.672	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		G	29445939	C	G	29445939	2	3	98	1	0	0	0	0	0	0	0	1	18245	813	29	4		4	ZNRF3	22	29445939	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08		29445939	21858627	114	8840											
RFPL3	10738	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	32754385	32754386	+	Frame_Shift_Del	DEL	GC	GC	-																															atcaaggaactggagcccaaGctgaagaagattctacagat																								rs9621427	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr22:32754385_32754386delGC	ENST00000249007.4	+	1	532_533	c.327_328delGC	c.(325-330)aagctgfs	p.KL109fs	RFPL3_ENST00000397468.1_Frame_Shift_Del_p.KL80fs|RFPL3_ENST00000382088.3_Frame_Shift_Del_p.KL80fs|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	109	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TGGAGCCCAAGCTGAAGAAGAT	0.5																																					p.109_110del		.											.	RFPL3-91	0			c.327_328del						.																																			SO:0001589	frameshift_variant	10738	exon1			.	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.327_328delGC	22.37:g.32754385_32754386delGC	ENSP00000249007:p.Lys109fs	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	184	72	NM_001098535	0	0	0	0	0	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Frame_Shift_Del	DEL	ENST00000249007.4	37	CCDS43011.1																																																																																			.		0.5	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		-	32754386	GC	-	32754385	7	5	98	1	0	1	0	1	0	0	0	0	13287	962	34	0	329	0	RFPL3	22	32754385	Frame_Shift_Del	DEL	GC	TCGA-DW-7840-01A-11D-2136-08	3308446	32754385	18550181	115	8841											
EP300	2033	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	41574164	41574176	+	Frame_Shift_Del	DEL	CACAGCAGCAACT	CACAGCAGCAACT	-																															tggcctgccccagcagcaacCacagcagcaactccagccac																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	CACAGCAGCAACT	CACAGCAGCAACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr22:41574164_41574176delCACAGCAGCAACT	ENST00000263253.7	+	31	7668_7680	c.6449_6461delCACAGCAGCAACT	c.(6448-6462)ccacagcagcaactcfs	p.PQQQL2150fs	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2150	Interaction with HTLV-1 Tax.|Interaction with NCOA2.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAGCAGCAACCACAGCAGCAACTCCAGCCACCC	0.582			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.2150_2154del		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300-2011	0			c.6449_6461del						.																																			SO:0001589	frameshift_variant	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6449_6461delCACAGCAGCAACT	22.37:g.41574164_41574176delCACAGCAGCAACT	ENSP00000263253:p.Pro2150fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	106	42	NM_001429	0	0	0	0	0	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	37	CCDS14010.1																																																																																			.		0.582	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41574176	CACAGCAGCAACT	-	41574164	7	5	98	1	0	1	0	1	0	0	0	0	5161	594	21	0	6571	0	EP300	22	41574164	Frame_Shift_Del	DEL	CACAGCAGCAACT	TCGA-DW-7840-01A-11D-2136-08	8819779	41574164	9730402	116	8842											
TXLNG	55787	hgsc.bcm.edu	37	chrX	16804661	16804661	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaagaggcggcggcgccgaAgaggcgactgaggccggacg	9	1	21	10	7	0	3	0	1	0	2	0	7	0	5	2	7	0	0	2	7	2	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:16804661A>G	ENST00000380122.5	+	1	112	c.51A>G	c.(49-51)gaA>gaG	p.E17E	TXLNG_ENST00000398155.4_Silent_p.E17E	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	17					cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)			breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						GCGGCGCCGAAGAGGCGACTG	0.706													A|||	23	0.00609272	0.0166	0.0014	3775	,	,		6753	0		0	False		,,,				2504	0				p.E17E		.											.	TXLNG-130	0			c.A51G						.						3	4	4					X																	16804661		1550	2886	4436	SO:0001819	synonymous_variant	55787	exon1			CGCCGAAGAGGCG	AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"lipopolysaccharide specific response-5 protein", "factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"	300677	"chromosome X open reading frame 15"	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.51A>G	X.37:g.16804661A>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_018360	0	0	0	2	2	Q2KQ75|Q5JNZ7|Q9P0X1	Silent	SNP	ENST00000380122.5	37	CCDS14178.1																																																																																			.		0.706	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055912.1	NM_018360		G	16804661	A	G	16804661	2	3	98	1	0	0	0	0	0	0	0	1	16822	69	3	3		3	TXLNG	23	16804661	Silent	SNP	A	TCGA-DW-7840-01A-11D-2136-08		16804661	138465899	117	8843											
SH3KBP1	30011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	19626146	19626146	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagctctccttcccaccaGcctacgtcgatgcagtccta	7	11	6	17	2	2	0	1	0	1	0	6	1	4	0	5	0	4	2	5	0	2	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:19626146G>T	ENST00000397821.3	-	9	1205	c.915C>A	c.(913-915)ggC>ggA	p.G305G	SH3KBP1_ENST00000477102.1_5'UTR|SH3KBP1_ENST00000379698.4_Silent_p.G268G|SH3KBP1_ENST00000541422.1_Silent_p.G44G|SH3KBP1_ENST00000379716.1_Silent_p.G67G|SH3KBP1_ENST00000379697.3_Silent_p.G349G	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	305	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						CTTCCCACCAGCCTACGTCGA	0.537																																					p.G305G		.											.	SH3KBP1-130	0			c.C915A						.						82	64	70					X																	19626146		2203	4300	6503	SO:0001819	synonymous_variant	30011	exon9			CCACCAGCCTACG	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.915C>A	X.37:g.19626146G>T		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	50	40	NM_031892	0	0	2	4	2	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Silent	SNP	ENST00000397821.3	37	CCDS14193.1																																																																																			.		0.537	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		T	19626146	G	T	19626146	2	4	98	1	0	0	0	0	0	0	0	1	14287	958	34	4		4	SH3KBP1	23	19626146	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	2821485	19626146	135644414	118	8844											
MAGEB4	4115	broad.mit.edu	37	chrX	30261230	30261230	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagttgcagccaggcgtggCactacagccatgactagtgc	10	7	13	11	1	0	2	0	1	0	1	0	2	0	2	2	2	5	3	2	2	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:30261230C>A	ENST00000378982.2	+	1	1174	c.978C>A	c.(976-978)ggC>ggA	p.G326G	MAGEB1_ENST00000378981.3_5'Flank|MAGEB1_ENST00000397550.1_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	326										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						CCAGGCGTGGCACTACAGCCA	0.512																																					p.G326G													.	MAGEB4-131	0			c.C978A						.						50	43	46					X																	30261230		2202	4300	6502	SO:0001819	synonymous_variant	4115	exon1			GCGTGGCACTACA		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.978C>A	X.37:g.30261230C>A		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	23	3	NM_002367	0	0	0	0	0	B2R9G0|Q6FHH4|Q8IZ00	Silent	SNP	ENST00000378982.2	37	CCDS14221.1																																																																																			.		0.512	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		A	30261230	C	A	30261230	2	1	98	1	0	0	0	0	0	0	0	1	9203	697	25	4		4	MAGEB4	23	30261230	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08	10635084	30261230	125009330	119	8845											
KDM5C	8242	bcgsc.ca	37	chrX	53239616	53239616	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcacaccatgggacatgaGggtgttgggattcatgaggg	9	9	17	6	0	1	2	1	2	0	0	1	4	1	4	1	5	0	2	1	5	0	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:53239616G>T	ENST00000375401.3	-	12	2258	c.1726C>A	c.(1726-1728)Ctc>Atc	p.L576I	KDM5C_ENST00000375383.3_Missense_Mutation_p.L535I|KDM5C_ENST00000452825.3_Missense_Mutation_p.L509I|KDM5C_ENST00000375379.3_Missense_Mutation_p.L576I|KDM5C_ENST00000465402.1_5'UTR|KDM5C_ENST00000404049.3_Missense_Mutation_p.L575I|KDM5C-IT1_ENST00000412242.1_RNA	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	576	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						TGGGACATGAGGGTGTTGGGA	0.512			"N, F, S"		clear cell renal carcinoma																																p.L576I				Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C-1272	0			c.C1726A						.						181	152	162					X																	53239616		2203	4300	6503	SO:0001583	missense	8242	exon12			ACATGAGGGTGTT	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.1726C>A	X.37:g.53239616G>T	ENSP00000364550:p.Leu576Ile	Somatic	52	0		WXS	Illumina HiSeq	Phase_1	46	4	NM_004187	0	0	12	12	0	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420223	0.83559	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	T;T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28;-1.28	5.62	5.62	0.85841	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.90779	0.7105	M	0.86740	2.835	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.991;0.995;0.995	D	0.92296	0.5845	10	0.87932	D	0	-13.9148	15.8643	0.79052	0.0:0.0:1.0:0.0	.	509;575;576	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	I	509;576;575;576;535	ENSP00000445176:L509I;ENSP00000364550:L576I;ENSP00000385394:L575I;ENSP00000364528:L576I;ENSP00000364532:L535I	ENSP00000364528:L576I	L	-	1	0	KDM5C	53256341	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.792000	0.69052	2.344000	0.79699	0.600000	0.82982	CTC	.		0.512	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		T	53239616	G	T	53239616	3	4	98	1	0	0	0	0	1	0	0	0	8156	1000	35	4	3114	4	KDM5C	23	53239616	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	22978386	53239616	102030944	120	8846											
PCDH11X	27328	ucsc.edu;bcgsc.ca	37	chrX	91456392	91456392	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccaatgaaggaggttgtgCgatcttgcacccccatgaaa	12	8	11	10	1	1	2	0	2	1	0	1	4	1	3	3	2	3	2	3	2	3	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:91456392C>T	ENST00000373094.1	+	3	3897	c.3052C>T	c.(3052-3054)Cga>Tga	p.R1018*	PCDH11X_ENST00000361655.2_Nonsense_Mutation_p.R1018*|PCDH11X_ENST00000406881.1_Nonsense_Mutation_p.R1018*|PCDH11X_ENST00000298274.8_Intron|PCDH11X_ENST00000373088.1_Intron|PCDH11X_ENST00000373097.1_Nonsense_Mutation_p.R1018*|PCDH11X_ENST00000504220.2_Nonsense_Mutation_p.R1018*	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1018			R -> Q (in dbSNP:rs4252205).		homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1018*(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GGAGGTTGTGCGATCTTGCAC	0.398																																					p.R1018X	NSCLC(38;925 1092 2571 38200 45895)												.	PCDH11X-193	2	Substitution - Nonsense(2)	large_intestine(2)	c.C3052T						.						84	74	77					X																	91456392		2203	4300	6503	SO:0001587	stop_gained	27328	exon3			GTTGTGCGATCTT	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3052C>T	X.37:g.91456392C>T	ENSP00000362186:p.Arg1018*	Somatic	35	0		WXS	Illumina HiSeq		36	4	NM_001168363	0	0	0	0	0	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Nonsense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	c	22.2	4.264023	0.80358	.	.	ENSG00000102290	ENST00000373094;ENST00000373097;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934	.	.	.	4.18	-6.23	0.02052	.	0.372941	0.19414	U	0.114870	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9714	0.41757	0.7199:0.1664:0.1137:0.0	.	.	.	.	X	1018	.	ENSP00000349408:R1018X	R	+	1	2	PCDH11X	91343048	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.837000	0.04377	-0.980000	0.03524	-0.341000	0.08007	CGA	.		0.398	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91456392	C	T	91456392	4	4	98	1	0	0	0	0	0	1	0	0	11534	760	27	1	3144	1	PCDH11X	23	91456392	Nonsense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	38216776	91456392	63814168	121	8847											
DCAF12L1	139170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	125685498	125685498	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagccctgaccggtgcccAcagtgatgatgtggcggtag	7	7	17	10	2	0	3	0	3	0	0	0	4	0	4	3	4	2	1	3	4	1	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:125685498A>C	ENST00000371126.1	-	1	1336	c.1094T>G	c.(1093-1095)gTg>gGg	p.V365G		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	365										breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						ACCGGTGCCCACAGTGATGAT	0.632																																					p.V365G		.											.	DCAF12L1-132	0			c.T1094G						.						35	38	37					X																	125685498		2203	4299	6502	SO:0001583	missense	139170	exon1			GTGCCCACAGTGA	BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"WD repeat domain containing"	29395	protein-coding gene	gene with protein product			"WD repeat domain 40B"	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.1094T>G	X.37:g.125685498A>C	ENSP00000360167:p.Val365Gly	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	66	55	NM_178470	0	0	0	0	0	Q8IYK3	Missense_Mutation	SNP	ENST00000371126.1	37	CCDS14610.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414963	0.42817	.	.	ENSG00000198889	ENST00000371126	T	0.66099	-0.19	3.64	3.64	0.41730	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.343553	0.17248	N	0.181261	T	0.65491	0.2696	M	0.73962	2.25	0.58432	D	0.999996	D	0.54397	0.966	P	0.47299	0.543	T	0.70691	-0.4802	10	0.87932	D	0	.	9.8475	0.41037	1.0:0.0:0.0:0.0	.	365	Q5VU92	DC121_HUMAN	G	365	ENSP00000360167:V365G	ENSP00000360167:V365G	V	-	2	0	DCAF12L1	125513179	1.000000	0.71417	0.124000	0.21820	0.171000	0.22731	5.855000	0.69510	1.683000	0.51011	0.350000	0.21858	GTG	.		0.632	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058186.1	NM_178470		C	125685498	A	C	125685498	3	2	98	1	0	0	0	0	1	0	0	0	4270	159	6	5	301	5	DCAF12L1	23	125685498	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	34229106	125685498	29585062	122	8848											
ERRFI1	54206	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	8075357	8075374	+	Splice_Site	DEL	AGAATACATACCAAGTGG	AGAATACATACCAAGTGG	-																															cttactgtgatcagattttcAgaatacataccaagtggtat																								rs147802351	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	AGAATACATACCAAGTGG	AGAATACATACCAAGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:8075357_8075374delAGAATACATACCAAGTGG	ENST00000377482.5	-	3	419_426	c.196_203delCCACTTGGTATGTATTCT	c.(196-204)ccacttggt>t	p.PLG66del	ERRFI1_ENST00000467067.1_In_Frame_Del_p.PLGMYS66del|ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000469499.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	66					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TCAGATTTTCAGAATACATACCAAGTGGTATTAGGCGC	0.404																																					p.66_68del		.											.	ERRFI1-91	0			c.196_202del						.																																			SO:0001630	splice_region_variant	54206	exon3			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.202+1CCACTTGGTATGTATTCT>-	1.37:g.8075357_8075374delAGAATACATACCAAGTGG		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	80	12	NM_018948	0	0	0	0	0	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Del	DEL	ENST00000377482.5	37	CCDS94.1																																																																																			.		0.404	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948	In_Frame_Del	-	8075374	AGAATACATACCAAGTGG	-	8075357	8	5	99	1	0	1	0	1	0	0	1	0	5257	203	7	0		0	ERRFI1	1	8075357	Splice_Site	DEL	AGAATACATACCAAGTGG	TCGA-DW-7841-01A-11D-2136-08		8075357	241175264	1	8849											
FBXO2	26232	hgsc.bcm.edu	37	chr1	11710791	11710791	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaggtacgcggcggcggcCgccgcctcctcctcctgctg	2	7	13	19	6	0	0	0	0	0	0	4	0	4	0	7	4	2	2	7	4	1	1	rs61749273		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:11710791C>G	ENST00000354287.4	-	2	464	c.123G>C	c.(121-123)gcG>gcC	p.A41A	FBXO2_ENST00000475961.1_5'Flank	NM_012168.5	NP_036300.2	Q9UK22	FBX2_HUMAN	F-box protein 2	41					cellular protein modification process (GO:0006464)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of protein ubiquitination (GO:0031396)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|SCF ubiquitin ligase complex (GO:0019005)	beta-amyloid binding (GO:0001540)|carbohydrate binding (GO:0030246)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(1)|lung(4)	6	Ovarian(185;0.249)	Lung NSC(185;9.37e-06)|all_lung(284;1.39e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|BRCA - Breast invasive adenocarcinoma(304;1.88e-06)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|Lung(427;0.0146)|LUSC - Lung squamous cell carcinoma(448;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		CGGCGGCGGccgccgcctcct	0.756																																					p.A41A		.											.	FBXO2-226	0			c.G123C						.						2	2	2					1																	11710791		1408	2892	4300	SO:0001819	synonymous_variant	26232	exon2			GGCGGCCGCCGCC	AF174594	CCDS130.1	1p36.21	2010-04-21	2004-06-15		ENSG00000116661	ENSG00000116661		"F-boxes /  "other""	13581	protein-coding gene	gene with protein product		607112	"F-box only protein 2", "organ of Corti protein 1"	OCP1		10531035, 10531037	Standard	NM_012168		Approved	FBX2, Nfb42, Fbs1, Fbg1	uc001asj.3	Q9UK22	OTTHUMG00000002072	ENST00000354287.4:c.123G>C	1.37:g.11710791C>G		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_012168	0	0	0	0	0	B2R7K7|Q5TGY0|Q6FGJ7|Q8TB29|Q9UKC6	Silent	SNP	ENST00000354287.4	37	CCDS130.1																																																																																			.		0.756	FBXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005764.1	NM_012168		G	11710791	C	G	11710791	2	3	99	1	0	0	0	0	0	0	0	1	5751	639	23	4		4	FBXO2	1	11710791	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08	3635434	11710791	237539830	2	8850											
SYDE2	84144	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	85648788	85648788	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttatctggcaatgaccaatTaattgaactgccttttttca	11	17	5	8	0	2	2	1	2	1	0	2	2	2	2	2	1	2	1	2	1	5	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:85648788T>C	ENST00000341460.5	-	3	1586	c.1537A>G	c.(1537-1539)Aat>Gat	p.N513D		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	513					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AATGACCAATTAATTGAACTG	0.383																																					p.N513D		.											.	SYDE2-70	0			c.A1537G						.						118	120	119					1																	85648788		1831	4083	5914	SO:0001583	missense	84144	exon3			ACCAATTAATTGA	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1537A>G	1.37:g.85648788T>C	ENSP00000340594:p.Asn513Asp	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	156	9	NM_032184	0	0	0	0	0	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237512	0.58886	.	.	ENSG00000097096	ENST00000341460	T	0.09073	3.02	5.41	3.06	0.35304	.	0.205916	0.48767	D	0.000174	T	0.04770	0.0129	M	0.68952	2.095	0.28339	N	0.921432	D;P	0.52996	0.957;0.787	B;B	0.44278	0.445;0.295	T	0.20207	-1.0282	10	0.56958	D	0.05	.	8.1975	0.31405	0.0:0.0701:0.1349:0.795	.	513;513	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	D	513	ENSP00000340594:N513D	ENSP00000340594:N513D	N	-	1	0	SYDE2	85421376	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	3.969000	0.56816	0.359000	0.24239	0.528000	0.53228	AAT	.		0.383	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			C	85648788	T	C	85648788	3	2	99	1	0	0	0	0	1	0	0	0	15468	1754	61	3	2067	3	SYDE2	1	85648788	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	73937997	85648788	163601833	3	8851											
LAMB3	3914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	209800244	209800244	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccacgtctccataggtcCggtctggacactggcggatg	6	9	14	12	3	2	0	0	0	2	0	4	2	3	2	3	6	0	0	3	6	1	1	rs144249951		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:209800244C>T	ENST00000356082.4	-	13	1699	c.1565G>A	c.(1564-1566)cGg>cAg	p.R522Q	LAMB3_ENST00000391911.1_Missense_Mutation_p.R522Q|LAMB3_ENST00000367030.3_Missense_Mutation_p.R522Q	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	522	Laminin EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCCATAGGTCCGGTCTGGACA	0.672													C|||	1	0.000199681	0	0	5008	,	,		20065	0		0.001	False		,,,				2504	0				p.R522Q		.											.	LAMB3-156	0			c.G1565A						.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	54	45	48		1565,1565,1565	-0.5	0.1	1	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	522/1173,522/1173,522/1173	209800244	1,13005	2203	4300	6503	SO:0001583	missense	3914	exon13			TAGGTCCGGTCTG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"Laminins"	6490	protein-coding gene	gene with protein product		150310	"laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.1565G>A	1.37:g.209800244C>T	ENSP00000348384:p.Arg522Gln	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	73	15	NM_000228	0	0	2	6	4	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.471943	0.26423	0.0	1.16E-4	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.61158	0.13;0.13;0.13	5.7	-0.461	0.12172	EGF-like, laminin (3);	0.489478	0.22676	N	0.057015	T	0.41305	0.1153	L	0.35854	1.095	0.09310	N	1	B	0.28082	0.2	B	0.27076	0.076	T	0.24548	-1.0157	10	0.21540	T	0.41	.	10.3743	0.44073	0.0:0.6147:0.0:0.3853	.	522	Q13751	LAMB3_HUMAN	Q	522	ENSP00000375778:R522Q;ENSP00000348384:R522Q;ENSP00000355997:R522Q	ENSP00000348384:R522Q	R	-	2	0	LAMB3	207866867	0.000000	0.05858	0.055000	0.19348	0.114000	0.19823	0.138000	0.16016	-0.213000	0.10094	0.650000	0.86243	CGG	C|1.000;T|0.000		0.672	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209800244	C	T	209800244	3	4	99	1	0	0	0	0	1	0	0	0	8633	652	23	1	1997	1	LAMB3	1	209800244	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	124151456	209800244	39450377	4	8852											
FBXO28	23219	hgsc.bcm.edu;broad.mit.edu	37	chr1	224302059	224302059	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtagccatcgagaacatcctCagctttatgtcctacgacga	11	10	8	12	3	1	1	1	0	0	1	4	4	3	1	3	0	4	2	3	0	4	4			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:224302059C>G	ENST00000366862.5	+	1	271	c.228C>G	c.(226-228)ctC>ctG	p.L76L	FBXO28_ENST00000424254.2_Silent_p.L76L	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	76	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		AGAACATCCTCAGCTTTATGT	0.647																																					p.L76L		.											.	FBXO28-661	0			c.C228G						.						30	31	31					1																	224302059		2202	4298	6500	SO:0001819	synonymous_variant	23219	exon1			CATCCTCAGCTTT	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"F-boxes /  "other""	29046	protein-coding gene	gene with protein product	"centromere protein 30"	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.228C>G	1.37:g.224302059C>G		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	25	3	NM_001136115	0	0	4	4	0	E9PEM8|O75070	Silent	SNP	ENST00000366862.5	37	CCDS1539.1																																																																																			.		0.647	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176		G	224302059	C	G	224302059	2	3	99	1	0	0	0	0	0	0	0	1	5757	813	29	4		4	FBXO28	1	224302059	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08	14501815	224302059	24948562	5	8853											
LRPPRC	10128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44207047	44207047	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaggcaagagagaaccacaActacgtagtagaagcaaggc	17	4	11	9	1	1	3	1	0	0	3	1	4	1	3	1	2	4	4	1	2	8	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr2:44207047A>G	ENST00000260665.7	-	3	444	c.387T>C	c.(385-387)agT>agC	p.S129S	LRPPRC_ENST00000409659.1_Silent_p.S129S|LRPPRC_ENST00000409946.1_Silent_p.S129S	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	129					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GAGAACCACAACTACGTAGTA	0.368																																					p.S129S		.											.	LRPPRC-93	0			c.T387C						.						86	79	82					2																	44207047		2203	4300	6503	SO:0001819	synonymous_variant	10128	exon3			ACCACAACTACGT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.387T>C	2.37:g.44207047A>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	75	23	NM_133259	0	0	6	8	2	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			.		0.368	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		G	44207047	A	G	44207047	2	3	99	1	0	0	0	0	0	0	0	1	8990	40	2	3		3	LRPPRC	2	44207047	Silent	SNP	A	TCGA-DW-7841-01A-11D-2136-08		44207047	198992326	6	8854											
ACVR2A	92	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	148684830	148684834	+	Frame_Shift_Del	DEL	AATCT	AATCT	-																															tgttgactttcctcccaaagAatctagtctatgatggttgc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	AATCT	AATCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr2:148684830_148684834delAATCT	ENST00000241416.7	+	11	2165_2169	c.1529_1533delAATCT	c.(1528-1533)gaatctfs	p.ES510fs	ACVR2A_ENST00000495775.1_3'UTR|ACVR2A_ENST00000535787.1_Frame_Shift_Del_p.ES402fs|ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.ES510fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	510					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CCTCCCAAAGAATCTAGTCTATGAT	0.395																																					p.510_511del		.											.	ACVR2A-831	0			c.1529_1533del						.																																			SO:0001589	frameshift_variant	92	exon11			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1529_1533delAATCT	2.37:g.148684830_148684834delAATCT	ENSP00000241416:p.Glu510fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	80	17	NM_001616	0	0	0	0	0	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	37	CCDS33301.1																																																																																			.		0.395	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148684834	AATCT	-	148684830	7	5	99	1	0	1	0	1	0	0	0	0	223	246	9	0	1571	0	ACVR2A	2	148684830	Frame_Shift_Del	DEL	AATCT	TCGA-DW-7841-01A-11D-2136-08	104477783	148684830	94514543	7	8855											
SCN7A	6332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	167284362	167284362	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaaccaattgttctctacaAtcttgcagcaggttttcctg	10	15	6	10	0	2	0	0	0	2	0	4	0	3	0	2	1	4	4	2	1	5	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr2:167284362A>T	ENST00000409855.1	-	17	2915	c.2789T>A	c.(2788-2790)aTt>aAt	p.I930N		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	930					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GTTCTCTACAATCTTGCAGCA	0.458																																					p.I930N		.											.	SCN7A-67	0			c.T2789A						.						134	128	130					2																	167284362		1885	4118	6003	SO:0001583	missense	6332	exon17			TCTACAATCTTGC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10594	protein-coding gene	gene with protein product		182392	"sodium channel, voltage-gated, type VI, alpha", "sodium channel, voltage-gated, type VII, alpha"	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.2789T>A	2.37:g.167284362A>T	ENSP00000386796:p.Ile930Asn	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	46	15	NM_002976	0	0	0	0	0		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.242192	0.79912	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.89617	-2.54	5.02	5.02	0.67125	Sodium ion transport-associated (1);	0.000000	0.64402	D	0.000008	D	0.94932	0.8361	M	0.89904	3.07	0.52501	D	0.99995	D	0.76494	0.999	D	0.72338	0.977	D	0.95644	0.8701	10	0.87932	D	0	.	12.9965	0.58650	1.0:0.0:0.0:0.0	.	930	Q01118	SCN7A_HUMAN	N	930	ENSP00000386796:I930N	ENSP00000259060:I930N	I	-	2	0	SCN7A	166992608	1.000000	0.71417	0.999000	0.59377	0.861000	0.49209	7.324000	0.79115	2.228000	0.72767	0.482000	0.46254	ATT	.		0.458	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167284362	A	T	167284362	3	4	99	1	0	0	0	0	1	0	0	0	13955	101	4	5	2295	5	SCN7A	2	167284362	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	18599532	167284362	75915011	8	8856											
SHISA5	51246	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48510782	48510782	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagggtctcgtggtaggcCggtgggcccatgggctgggc	3	7	20	11	2	1	0	0	0	1	0	2	0	1	0	3	7	0	2	3	7	1	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr3:48510782C>T	ENST00000296444.2	-	5	957	c.621G>A	c.(619-621)ccG>ccA	p.P207P	SHISA5_ENST00000442747.1_Silent_p.P176P|SHISA5_ENST00000444115.1_Silent_p.P176P|SHISA5_ENST00000426002.1_Silent_p.P104P|SHISA5_ENST00000443308.2_Silent_p.P200P|SHISA5_ENST00000465449.1_5'UTR	NM_001272065.1|NM_016479.3	NP_001258994.1|NP_057563.3	Q8N114	SHSA5_HUMAN	shisa family member 5	207	Pro-rich.				intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			large_intestine(1)|lung(1)	2						CGTGGTAGGCCGGTGGGCCCA	0.657																																					p.P207P		.											.	SHISA5-68	0			c.G621A						.						97	95	96					3																	48510782		2203	4300	6503	SO:0001819	synonymous_variant	51246	exon5			GTAGGCCGGTGGG	AF520698	CCDS2770.1, CCDS63621.1, CCDS63622.1, CCDS63623.1	3p21.31	2013-07-31	2013-07-31		ENSG00000164054	ENSG00000164054		"Shisa homologs"	30376	protein-coding gene	gene with protein product		607290	"shisa homolog 5 (Xenopus laevis)"			11042152, 12135983	Standard	NM_016479		Approved	SCOTIN, hShisa5	uc011bbk.1	Q8N114	OTTHUMG00000133529	ENST00000296444.2:c.621G>A	3.37:g.48510782C>T		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	135	30	NM_016479	0	0	102	139	37	B3KW99|F8W9N8|Q69YY9|Q7Z433|Q8NHL9|Q96MW8|Q9BV58	Silent	SNP	ENST00000296444.2	37	CCDS2770.1	.	.	.	.	.	.	.	.	.	.	C	3.542	-0.093509	0.07053	.	.	ENSG00000164054	ENST00000536074	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.47563	0.1452	.	.	.	0.42593	D	0.993257	.	.	.	.	.	.	T	0.60895	-0.7172	5	0.87932	D	0	-31.2522	1.378	0.02225	0.2716:0.1192:0.152:0.4572	.	.	.	.	Q	28	.	ENSP00000445956:R28Q	R	-	2	0	SHISA5	48485786	0.000000	0.05858	0.031000	0.17742	0.469000	0.32828	-4.182000	0.00278	-2.526000	0.00494	-0.251000	0.11542	CGG	.		0.657	SHISA5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257504.3	NM_016479		T	48510782	C	T	48510782	2	4	99	1	0	0	0	0	0	0	0	1	14315	639	23	1		1	SHISA5	3	48510782	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		48510782	149511648	9	8857											
SLC35A5	55032	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	112282282	112282290	+	In_Frame_Del	DEL	TATGCTCCT	TATGCTCCT	-																															gtgctgtagtcatcctgtaaTatgctccttgtcaacaatgt																								rs201886373|rs377335674|rs369182750		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	TATGCTCCT	TATGCTCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr3:112282282_112282290delTATGCTCCT	ENST00000492406.1	+	2	315_323	c.32_40delTATGCTCCT	c.(31-42)atatgctccttg>atg	p.11_14ICSL>M	ATG3_ENST00000402314.2_5'Flank|ATG3_ENST00000283290.5_5'Flank|ATG3_ENST00000495756.1_5'Flank	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	11					nucleotide-sugar transport (GO:0015780)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)|sugar:proton symporter activity (GO:0005351)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|skin(1)	11						CATCCTGTAATATGCTCCTTGTCAACAAT	0.378																																					p.11_14del		.											.	SLC35A5-91	0			c.32_40del						.																																			SO:0001651	inframe_deletion	55032	exon2			.	AK000737	CCDS2967.1	3q13.13	2013-05-22			ENSG00000138459	ENSG00000138459		"Solute carriers"	20792	protein-coding gene	gene with protein product							Standard	NM_017945		Approved	FLJ20730	uc003dze.4	Q9BS91	OTTHUMG00000159263	ENST00000492406.1:c.32_40delTATGCTCCT	3.37:g.112282282_112282290delTATGCTCCT	ENSP00000417654:p.Ile11_Leu14delinsMet	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	89	19	NM_017945	0	0	0	0	0	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	In_Frame_Del	DEL	ENST00000492406.1	37	CCDS2967.1																																																																																			.		0.378	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945		-	112282290	TATGCTCCT	-	112282282	7	5	99	1	0	1	0	1	0	0	0	0	14606	1406	49	0	34	0	SLC35A5	3	112282282	In_Frame_Del	DEL	TATGCTCCT	TCGA-DW-7841-01A-11D-2136-08	63771500	112282282	85740148	10	8858											
KPNA4	3840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	160249310	160249310	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagattttattaagtcaTcaattggtggatttcgatca	11	17	7	6	1	3	1	3	0	0	1	5	3	4	2	1	2	0	0	1	2	3	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr3:160249310T>C	ENST00000334256.4	-	6	628	c.323A>G	c.(322-324)gAt>gGt	p.D108G		NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	108					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			TATTAAGTCATCAATTGGTGG	0.269																																					p.D108G		.											.	KPNA4-226	0			c.A323G						.						86	97	93					3																	160249310		2203	4293	6496	SO:0001583	missense	3840	exon6			AAGTCATCAATTG	AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"Importins", "Armadillo repeat containing"	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.323A>G	3.37:g.160249310T>C	ENSP00000334373:p.Asp108Gly	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	139	31	NM_002268	0	0	18	23	5	A8K4S6|D3DNM2|O00190	Missense_Mutation	SNP	ENST00000334256.4	37	CCDS3191.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.773313	0.90108	.	.	ENSG00000186432	ENST00000334256	T	0.32272	1.46	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65688	0.2715	M	0.93328	3.405	0.80722	D	1	D	0.67145	0.996	D	0.72075	0.976	T	0.75769	-0.3201	10	0.72032	D	0.01	.	15.6624	0.77197	0.0:0.0:0.0:1.0	.	108	O00629	IMA4_HUMAN	G	108	ENSP00000334373:D108G	ENSP00000334373:D108G	D	-	2	0	KPNA4	161732004	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.797000	0.85911	2.284000	0.76573	0.528000	0.53228	GAT	.		0.269	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268		C	160249310	T	C	160249310	3	2	99	1	0	0	0	0	1	0	0	0	8453	1435	50	3	1290	3	KPNA4	3	160249310	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	47967028	160249310	37773120	11	8859											
SLC30A9	10463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	42037333	42037333	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattaagagaatacagagatTtcttgggaaataccaaggta	17	11	9	4	0	1	2	0	0	1	2	1	5	1	3	1	2	2	1	1	2	8	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr4:42037333T>G	ENST00000264451.7	+	7	832	c.652T>G	c.(652-654)Ttc>Gtc	p.F218V		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	218					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F218V(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATACAGAGATTTCTTGGGAAA	0.299																																					p.F218V		.											.	SLC30A9-91	1	Substitution - Missense(1)	kidney(1)	c.T652G						.						56	62	60					4																	42037333		2200	4282	6482	SO:0001583	missense	10463	exon7			AGAGATTTCTTGG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.652T>G	4.37:g.42037333T>G	ENSP00000264451:p.Phe218Val	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	139	33	NM_006345	0	0	4	10	6	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	37	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	T	9.461	1.093124	0.20471	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.54866	0.55	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.37732	0.1014	L	0.34521	1.04	0.58432	D	0.999996	P	0.43352	0.804	B	0.38842	0.283	T	0.13872	-1.0493	10	0.16420	T	0.52	-12.6044	11.5359	0.50636	0.0:0.0:0.0:1.0	.	218	Q6PML9	ZNT9_HUMAN	V	218;46	ENSP00000264451:F218V	ENSP00000264451:F218V	F	+	1	0	SLC30A9	41732090	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	4.876000	0.63079	2.003000	0.58678	0.397000	0.26171	TTC	.		0.299	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			G	42037333	T	G	42037333	3	3	99	1	0	0	0	0	1	0	0	0	14594	1841	64	5	678	5	SLC30A9	4	42037333	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08		42037333	149116943	12	8860											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23526915	23526915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctcattcaccagaggaTacacacaggggagaagccct	12	6	9	14	0	2	2	2	0	0	2	3	4	3	3	4	3	2	0	4	3	2	2	rs199686868		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:23526915T>C	ENST00000296682.3	+	11	1900	c.1718T>C	c.(1717-1719)aTa>aCa	p.I573T		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	573					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						CACCAGAGGATACACACAGGG	0.567										HNSCC(3;0.000094)																											p.I573T		.											.	PRDM9-139	0			c.T1718C						.						73	81	78					5																	23526915		2190	4296	6486	SO:0001583	missense	56979	exon11			AGAGGATACACAC	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.1718T>C	5.37:g.23526915T>C	ENSP00000296682:p.Ile573Thr	Somatic	133	1		WXS	Illumina HiSeq	Phase_I	153	8	NM_020227	0	0	0	0	0	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-2.000672	0.00431	.	.	ENSG00000164256	ENST00000296682	T	0.04015	3.73	2.31	1.41	0.22369	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.249761	0.20968	N	0.082442	T	0.02119	0.0066	N	0.12422	0.21	0.18873	N	0.999989	B	0.02656	0.0	B	0.06405	0.002	T	0.48043	-0.9069	10	0.06891	T	0.86	-2.9928	5.0646	0.14576	0.0:0.5362:0.0:0.4638	.	573	Q9NQV7	PRDM9_HUMAN	T	573	ENSP00000296682:I573T	ENSP00000296682:I573T	I	+	2	0	PRDM9	23562672	0.000000	0.05858	0.999000	0.59377	0.648000	0.38561	-0.775000	0.04679	0.078000	0.16900	-0.511000	0.04467	ATA	.		0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		C	23526915	T	C	23526915	3	2	99	1	0	0	0	0	1	0	0	0	12492	1406	49	3	1756	3	PRDM9	5	23526915	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08		23526915	157388345	13	8861											
ZCCHC9	84240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	80600585	80600585	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actgatgaaattatgaccagGtgggcccgagttagtaccac	12	9	11	9	1	0	3	0	3	0	0	0	4	0	3	3	2	1	2	3	2	4	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:80600585G>A	ENST00000254037.2	+	1	3164	c.9G>A	c.(7-9)agG>agA	p.R3R	ZCCHC9_ENST00000438268.2_Silent_p.R3R|ZCCHC9_ENST00000380199.5_Silent_p.R3R|ZCCHC9_ENST00000506458.1_Intron|ZCCHC9_ENST00000407610.3_Silent_p.R3R			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	3					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		TTATGACCAGGTGGGCCCGAG	0.423																																					p.R3R		.											.	ZCCHC9-91	0			c.G9A						.						81	76	77					5																	80600585		2203	4300	6503	SO:0001819	synonymous_variant	84240	exon2			GACCAGGTGGGCC	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"Zinc fingers, CCHC domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	25424	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 41"					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.9G>A	5.37:g.80600585G>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	124	34	NM_001131036	0	0	5	6	1	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	37	CCDS4054.1																																																																																			.		0.423	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		A	80600585	G	A	80600585	2	1	99	1	0	0	0	0	0	0	0	1	17627	1252	44	2		2	ZCCHC9	5	80600585	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08	57073670	80600585	100314675	14	8862											
PCDHGA6	56109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140753888	140753888	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttttctctctgaatccgCgaaacggcagcttggtcacc	8	11	9	13	3	3	1	1	1	2	0	5	2	4	1	2	2	3	3	2	2	2	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:140753888C>T	ENST00000517434.1	+	1	238	c.238C>T	c.(238-240)Cga>Tga	p.R80*	PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGAATCCGCGAAACGGCAG	0.577																																					p.R80X		.											.	PCDHGA6-67	0			c.C238T						.						51	58	55					5																	140753888		2200	4300	6500	SO:0001587	stop_gained	56109	exon1			AATCCGCGAAACG	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"Cadherins / Protocadherins : Clustered"	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.238C>T	5.37:g.140753888C>T	ENSP00000429601:p.Arg80*	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	103	36	NM_018919	0	0	1	1	0	A6H8K7|B2RN55|Q9Y5D1	Nonsense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	12.46	1.943892	0.34283	.	.	ENSG00000253731	ENST00000517434	.	.	.	5.09	-0.279	0.12890	.	0.000000	0.29253	U	0.012681	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.6064	0.02684	0.3336:0.2219:0.2969:0.1477	.	.	.	.	X	80	.	ENSP00000429601:R80X	R	+	1	2	PCDHGA6	140734072	0.000000	0.05858	0.001000	0.08648	0.189000	0.23516	-0.696000	0.05104	0.091000	0.17302	0.650000	0.86243	CGA	.		0.577	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140753888	C	T	140753888	4	4	99	1	0	0	0	0	0	1	0	0	11584	760	27	1	240	1	PCDHGA6	5	140753888	Nonsense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	60153303	140753888	40161372	15	8863											
PWWP2A	114825	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	159520919	159520919	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagctcagctcgggatgcggGacaggagaagggtcatcggg	10	5	18	8	3	2	1	2	0	0	1	4	4	2	3	0	5	3	2	0	5	2	0			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:159520919G>A	ENST00000307063.7	-	2	772	c.738C>T	c.(736-738)gtC>gtT	p.V246V	PWWP2A_ENST00000456329.3_Silent_p.V246V|PWWP2A_ENST00000523662.1_Silent_p.V246V	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	246	Pro-rich.									kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGGATGCGGGACAGGAGAAG	0.512																																					p.V246V		.											.	PWWP2A-68	0			c.C738T						.						115	114	114					5																	159520919		1983	4144	6127	SO:0001819	synonymous_variant	114825	exon2			ATGCGGGACAGGA		CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.738C>T	5.37:g.159520919G>A		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	116	33	NM_052927	0	0	3	5	2	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Silent	SNP	ENST00000307063.7	37	CCDS47332.1																																																																																			.		0.512	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1			A	159520919	G	A	159520919	2	1	99	1	0	0	0	0	0	0	0	1	12877	1161	41	2		2	PWWP2A	5	159520919	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08	18767031	159520919	21394341	16	8864											
RPL10A	4736	broad.mit.edu	37	chr6	35436591	35436591	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagcagcaaagtctctcgCgacaccctgtacgaggcggt	9	6	12	14	5	1	0	0	0	1	0	3	2	1	0	1	2	3	4	1	2	2	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr6:35436591C>T	ENST00000322203.6	+	2	48	c.21C>T	c.(19-21)cgC>cgT	p.R7R	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	7					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						AAGTCTCTCGCGACACCCTGT	0.697																																					p.R7R													.	RPL10A-91	0			c.C21T						.						11	12	12					6																	35436591		2197	4293	6490	SO:0001819	synonymous_variant	4736	exon2			CTCTCGCGACACC	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.21C>T	6.37:g.35436591C>T		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	21	4	NM_007104	2	0	991	1569	576	B2R801|P52859|P53025|Q5TZT6|Q8J013	Silent	SNP	ENST00000322203.6	37	CCDS4806.1																																																																																			.		0.697	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		T	35436591	C	T	35436591	2	4	99	1	0	0	0	0	0	0	0	1	13587	755	27	1		1	RPL10A	6	35436591	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		35436591	135678476	17	8865											
TNFAIP3	7128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	138200108	138200108	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcaacttcacgccagccacgCcccagaccacacaaggcact	12	3	7	19	2	1	1	1	0	0	1	1	1	1	1	5	1	2	2	5	1	2	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr6:138200108C>T	ENST00000237289.4	+	7	1592	c.1526C>T	c.(1525-1527)gCc>gTc	p.A509V		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	509	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.A506fs*21(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GCCAGCCACGCCCCAGACCAC	0.562			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.A509V	GBM(130;153 1739 22295 28918 47987)	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3-1498	26	Whole gene deletion(25)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(26)	c.C1526T						.						53	57	56					6																	138200108		2203	4300	6503	SO:0001583	missense	7128	exon7			GCCACGCCCCAGA	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1526C>T	6.37:g.138200108C>T	ENSP00000237289:p.Ala509Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	73	17	NM_001270507	0	0	40	44	4	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	C	8.783	0.928799	0.18131	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.23950	1.88	5.88	0.17	0.15021	.	2.360930	0.01293	N	0.010090	T	0.06005	0.0156	L	0.29908	0.895	0.09310	N	1	B	0.20671	0.047	B	0.19148	0.024	T	0.21690	-1.0238	10	0.31617	T	0.26	-3.2172	3.4733	0.07575	0.336:0.2854:0.3007:0.078	.	509	P21580	TNAP3_HUMAN	V	509	ENSP00000237289:A509V	ENSP00000237289:A509V	A	+	2	0	TNFAIP3	138241801	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	0.071000	0.14594	0.072000	0.16694	0.655000	0.94253	GCC	.		0.562	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			T	138200108	C	T	138200108	3	4	99	1	0	0	0	0	1	0	0	0	16306	739	26	2	1548	2	TNFAIP3	6	138200108	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	102763517	138200108	32914959	18	8866											
CBX3	11335	hgsc.bcm.edu	37	chr7	26251700	26251700	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttctttttcttaaaacAggaaagattcagatgaggca	14	15	7	5	0	3	3	1	1	2	2	3	4	3	4	0	2	1	1	0	2	3	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr7:26251700A>T	ENST00000337620.4	+	6	853		c.e6-1		CBX3_ENST00000409747.1_Splice_Site|CBX3_ENST00000396386.2_Splice_Site	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						TTCTTAAAACAGGAAAGATTC	0.358																																					.		.											.	CBX3-227	0			c.426-2A>T						.						49	50	50					7																	26251700		2203	4300	6503	SO:0001630	splice_region_variant	11335	exon6			TAAAACAGGAAAG	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"HP1 gamma homolog (Drosophila)"	604477	"chromobox homolog 3 (Drosophila HP1 gamma)"			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.426-1A>T	7.37:g.26251700A>T		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	68	5	NM_007276	0	0	0	0	0	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Splice_Site	SNP	ENST00000337620.4	37	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397838	0.62177	.	.	ENSG00000122565	ENST00000337620;ENST00000396386	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9596	0.79918	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBX3	26218225	1.000000	0.71417	0.985000	0.45067	0.622000	0.37654	9.240000	0.95396	2.231000	0.72958	0.533000	0.62120	.	.		0.358	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	Intron	T	26251700	A	T	26251700	5	4	99	1	0	0	0	0	0	0	1	0	2725	202	7	5	442	5	CBX3	7	26251700	Splice_Site	SNP	A	TCGA-DW-7841-01A-11D-2136-08		26251700	132886963	19	8867											
ADAM9	8754	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	38880710	38880711	+	Frame_Shift_Ins	INS	-	-	GG																															atattcgaattgtgctagttINSggactggagatttggaccaa																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr8:38880710_38880711insGG	ENST00000487273.2	+	9	858_859	c.780_781insGG	c.(781-783)ggafs	p.G261fs		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	261	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			TTGTGCTAGTTGGACTGGAGAT	0.376																																					p.V260fs		.											.	ADAM9-227	0			c.780_781insGG						.																																			SO:0001589	frameshift_variant	8754	exon9			.	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.781_782dupGG	8.37:g.38880711_38880712dupGG	ENSP00000419446:p.Gly261fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	80	26	NM_003816	0	0	0	0	0	B7ZLN7|Q10718|Q8NFM6	Frame_Shift_Ins	INS	ENST00000487273.2	37	CCDS6112.1																																																																																			.		0.376	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			GG	38880711	-	GG	38880710	7	5	99	1	0	1	1	0	0	0	0	0	253	1799	63	0	814	0	ADAM9	8	38880710	Frame_Shift_Ins	INS	-	TCGA-DW-7841-01A-11D-2136-08		38880710	107483312	20	8868											
FAM91A1	157769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	124787418	124787418	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaaagatgaacgcagataCtatgaggaactgctaaagta	19	7	10	5	1	0	5	0	2	0	3	0	6	0	6	0	1	4	3	0	1	9	4			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr8:124787418C>A	ENST00000334705.7	+	3	435	c.189C>A	c.(187-189)taC>taA	p.Y63*	FAM91A1_ENST00000521166.1_Nonsense_Mutation_p.Y63*	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	63										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			AACGCAGATACTATGAGGAAC	0.363																																					p.Y63X		.											.	FAM91A1-91	0			c.C189A						.						91	80	84					8																	124787418		1882	4109	5991	SO:0001587	stop_gained	157769	exon3			CAGATACTATGAG	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.189C>A	8.37:g.124787418C>A	ENSP00000335082:p.Tyr63*	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	74	33	NM_144963	0	0	1	1	0	B6YY23|Q658T5|Q8TE89	Nonsense_Mutation	SNP	ENST00000334705.7	37	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892276	0.91889	.	.	ENSG00000176853	ENST00000521166;ENST00000334705;ENST00000395537	.	.	.	5.33	3.52	0.40303	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0665	0.42306	0.0:0.7624:0.0:0.2376	.	.	.	.	X	63	.	ENSP00000335082:Y63X	Y	+	3	2	FAM91A1	124856599	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	1.080000	0.30779	0.619000	0.30197	0.655000	0.94253	TAC	.		0.363	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		A	124787418	C	A	124787418	4	1	99	1	0	0	0	0	0	1	0	0	5670	576	20	4	199	4	FAM91A1	8	124787418	Nonsense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	85906708	124787418	21576604	21	8869											
SUSD1	64420	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	114820886	114820886	+	Frame_Shift_Del	DEL	C	C	-																															catcagcatcagaggcgttgCtaaagaaggaggaagcgcct																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:114820886delC	ENST00000374270.3	-	14	2103	c.1931delG	c.(1930-1932)agcfs	p.S644fs	SUSD1_ENST00000374264.2_Frame_Shift_Del_p.S644fs|SUSD1_ENST00000374263.3_Frame_Shift_Del_p.S644fs	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	644						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGAGGCGTTGCTAAAGAAGGA	0.473																																					p.S644fs		.											.	SUSD1-90	0			c.1931delG						.						114	111	112					9																	114820886		2203	4300	6503	SO:0001589	frameshift_variant	64420	exon14			.	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1931delG	9.37:g.114820886delC	ENSP00000363388:p.Ser644fs	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	144	34	NM_022486	0	0	0	0	0	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Frame_Shift_Del	DEL	ENST00000374270.3	37	CCDS6783.1																																																																																			.		0.473	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		-	114820886	C	-	114820886	7	5	99	1	0	1	0	1	0	0	0	0	15439	797	28	0	328	0	SUSD1	9	114820886	Frame_Shift_Del	DEL	C	TCGA-DW-7841-01A-11D-2136-08		114820886	26392545	22	8870	94	3									
SUSD1	64420	hgsc.bcm.edu;bcgsc.ca	37	chr9	114820888	114820888	+	Missense_Mutation	SNP	A	A	T																															tcagcatcagaggcgttgctAaagaaggaggaagcgccttc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:114820888A>T	ENST00000374270.3	-	14	2101	c.1929T>A	c.(1927-1929)ttT>ttA	p.F643L	SUSD1_ENST00000374264.2_Missense_Mutation_p.F643L|SUSD1_ENST00000374263.3_Missense_Mutation_p.F643L	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	643						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGGCGTTGCTAAAGAAGGAGG	0.478																																					p.F643L		.											.	SUSD1-90	0			c.T1929A						.						113	110	111					9																	114820888		2203	4300	6503	SO:0001583	missense	64420	exon14			GTTGCTAAAGAAG	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1929T>A	9.37:g.114820888A>T	ENSP00000363388:p.Phe643Leu	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	146	36	NM_022486	0	0	3	3	0	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Missense_Mutation	SNP	ENST00000374270.3	37	CCDS6783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.65|17.65	3.441634|3.441634	0.63067|0.63067	.|.	.|.	ENSG00000106868|ENSG00000106868	ENST00000374270;ENST00000374263;ENST00000374264|ENST00000355396	T;T;T|.	0.51817|.	0.69;0.69;0.69|.	5.44|5.44	1.84|1.84	0.25277|0.25277	.|.	0.000000|.	0.49305|.	D|.	0.000147|.	T|.	0.55369|.	0.1916|.	M|M	0.64630|0.64630	1.985|1.985	0.31889|0.31889	N|N	0.617461|0.617461	D;D;D|.	0.71674|.	0.998;0.998;0.997|.	D;D;D|.	0.80764|.	0.987;0.994;0.985|.	T|.	0.58918|.	-0.7551|.	10|.	0.62326|.	D|.	0.03|.	-9.2496|-9.2496	9.0743|9.0743	0.36511|0.36511	0.7896:0.0:0.2104:0.0|0.7896:0.0:0.2104:0.0	.|.	643;643;643|.	F8WAQ1;Q6UWL2-2;Q6UWL2|.	.;.;SUSD1_HUMAN|.	L|K	643|627	ENSP00000363388:F643L;ENSP00000363381:F643L;ENSP00000363382:F643L|.	ENSP00000363381:F643L|.	F|X	-|-	3|1	2|0	SUSD1|SUSD1	113860709|113860709	1.000000|1.000000	0.71417|0.71417	0.911000|0.911000	0.35937|0.35937	0.551000|0.551000	0.35334|0.35334	1.139000|1.139000	0.31504|0.31504	0.066000|0.066000	0.16515|0.16515	-0.411000|-0.411000	0.06167|0.06167	TTT|TAG	.		0.478	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		T	114820888	A	T	114820888	3	4	99	1	0	0	0	0	1	0	0	0	15439	359	13	5	330	5	SUSD1	9	114820888	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	2	114820888	26392543	23	8871	94	3									
SUSD1	64420	hgsc.bcm.edu	37	chr9	114820890	114820890	+	Frame_Shift_Del	DEL	A	A	-																															agcatcagaggcgttgctaaAgaaggaggaagcgccttcag																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:114820890delA	ENST00000374270.3	-	14	2099	c.1927delT	c.(1927-1929)tttfs	p.F643fs	SUSD1_ENST00000374264.2_Frame_Shift_Del_p.F643fs|SUSD1_ENST00000374263.3_Frame_Shift_Del_p.F643fs	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	643						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						GCGTTGCTAAAGAAGGAGGAA	0.478																																					p.F643fs		.											.	SUSD1-90	0			c.1927delT						.						113	110	111					9																	114820890		2203	4300	6503	SO:0001589	frameshift_variant	64420	exon14			.	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1927delT	9.37:g.114820890delA	ENSP00000363388:p.Phe643fs	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	142	26	NM_022486	0	0	0	0	0	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Frame_Shift_Del	DEL	ENST00000374270.3	37	CCDS6783.1																																																																																			.		0.478	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		-	114820890	A	-	114820890	7	5	99	1	0	1	0	1	0	0	0	0	15439	72	3	0	332	0	SUSD1	9	114820890	Frame_Shift_Del	DEL	A	TCGA-DW-7841-01A-11D-2136-08	2	114820890	26392541	24	8872	94	3									
BSPRY	54836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	116132384	116132384	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggggcccctcttcccagtcTttgctgtggccgatcagacc	4	10	11	16	2	3	1	1	0	2	1	4	2	4	1	5	3	1	1	5	3	0	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:116132384T>A	ENST00000374183.4	+	6	1210	c.1171T>A	c.(1171-1173)Ttt>Att	p.F391I	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	391	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CTTCCCAGTCTTTGCTGTGGC	0.597																																					p.F391I		.											.	BSPRY-135	0			c.T1171A						.						50	55	53					9																	116132384		1936	4110	6046	SO:0001583	missense	54836	exon6			CCAGTCTTTGCTG	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.1171T>A	9.37:g.116132384T>A	ENSP00000363298:p.Phe391Ile	Somatic	156	1		WXS	Illumina HiSeq	Phase_I	118	37	NM_017688	0	0	7	10	3	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943124	0.92526	.	.	ENSG00000119411	ENST00000374183	T	0.33216	1.42	5.69	5.69	0.88448	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.094068	0.85682	D	0.000000	T	0.62768	0.2455	M	0.90309	3.105	0.54753	D	0.999988	D	0.76494	0.999	D	0.74674	0.984	T	0.70766	-0.4783	10	0.62326	D	0.03	-8.7766	15.1216	0.72447	0.0:0.0:0.0:1.0	.	391	Q5W0U4	BSPRY_HUMAN	I	391	ENSP00000363298:F391I	ENSP00000363298:F391I	F	+	1	0	BSPRY	115172205	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.686000	0.68211	2.171000	0.68590	0.459000	0.35465	TTT	.		0.597	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688		A	116132384	T	A	116132384	3	1	99	1	0	0	0	0	1	0	0	0	1535	1609	56	5	1193	5	BSPRY	9	116132384	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	1311494	116132384	25081047	25	8873											
DFNB31	25861	hgsc.bcm.edu	37	chr9	117170277	117170277	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccctggacagcctcgccagTttcctccaggtccagagtgt	6	9	11	15	1	0	1	0	0	0	1	4	2	3	2	6	2	1	1	6	2	0	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:117170277T>C	ENST00000362057.3	-	8	1816	c.1648A>G	c.(1648-1650)Act>Gct	p.T550A	DFNB31_ENST00000265134.6_Missense_Mutation_p.T167A|DFNB31_ENST00000374059.3_Missense_Mutation_p.T199A	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	550					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCCTCGCCAGTTTCCTCCAGG	0.537																																					p.T550A		.											.	DFNB31-95	0			c.A1648G						.						89	75	80					9																	117170277		2203	4300	6503	SO:0001583	missense	25861	exon8			CGCCAGTTTCCTC	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"whirlin"	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1648A>G	9.37:g.117170277T>C	ENSP00000354623:p.Thr550Ala	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_001173425	0	0	8	8	0	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	.	.	.	.	.	.	.	.	.	.	T	9.254	1.041483	0.19669	.	.	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.07908	4.04;4.01;3.15	5.53	5.53	0.82687	.	0.379172	0.27227	N	0.020331	T	0.09468	0.0233	M	0.62723	1.935	0.25402	N	0.988439	B;B;B	0.23058	0.003;0.002;0.079	B;B;B	0.22386	0.007;0.007;0.039	T	0.24512	-1.0158	10	0.24483	T	0.36	-12.0315	6.7837	0.23662	0.0:0.1301:0.0:0.8699	.	550;550;199	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	A	167;199;550	ENSP00000265134:T167A;ENSP00000363172:T199A;ENSP00000354623:T550A	ENSP00000265134:T167A	T	-	1	0	DFNB31	116210098	0.157000	0.22836	0.041000	0.18516	0.209000	0.24338	2.043000	0.41231	2.099000	0.63709	0.460000	0.39030	ACT	.		0.537	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404		C	117170277	T	C	117170277	3	2	99	1	0	0	0	0	1	0	0	0	4466	1725	60	3	1095	3	DFNB31	9	117170277	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	1037893	117170277	24043154	26	8874											
RPL7A	6130	ucsc.edu	37	chr9	136216909	136216909	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctgtccttcgagcaggTgagtaggccccaccttaggg	7	8	12	14	1	0	1	0	1	0	0	2	2	1	1	6	3	1	2	6	3	2	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:136216909T>A	ENST00000323345.6	+	4	445		c.e4+2		SURF1_ENST00000495952.1_5'Flank|MED22_ENST00000343730.5_5'Flank|RPL7A_ENST00000463740.1_Splice_Site|RPL7A_ENST00000315731.4_Splice_Site|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000371999.1_5'Flank|SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000491289.1_5'Flank|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000471524.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		TTCGAGCAGGTGAGTAGGCCC	0.532																																					.													.	RPL7A-90	0			c.415+2T>A						.						56	60	59					9																	136216909		2203	4300	6503	SO:0001630	splice_region_variant	6130	exon4			AGCAGGTGAGTAG	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.415+2T>A	9.37:g.136216909T>A		Somatic	105	1		WXS	Illumina HiSeq		116	1	NM_000972	0	0	1	1	0	P11518|Q5T8U4	Splice_Site	SNP	ENST00000323345.6	37	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.574485	0.65878	.	.	ENSG00000148303	ENST00000323345;ENST00000426651;ENST00000315731	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0455	0.64702	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPL7A	135206730	1.000000	0.71417	0.983000	0.44433	0.667000	0.39255	7.104000	0.77024	1.911000	0.55334	0.482000	0.46254	.	.		0.532	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	Intron	A	136216909	T	A	136216909	5	1	99	1	0	0	0	0	0	0	1	0	13632	1710	59	5	431	5	RPL7A	9	136216909	Splice_Site	SNP	T	TCGA-DW-7841-01A-11D-2136-08	19046632	136216909	4996522	27	8875											
C9orf172	389813	broad.mit.edu	37	chr9	139739071	139739071	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cggccatggagaccctgccgGagccaccgccgccggagtcc	6	3	14	18	5	0	1	0	0	0	1	1	4	1	3	8	4	2	0	8	4	0	0	rs375666127	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:139739071G>C	ENST00000436881.1	+	1	205	c.205G>C	c.(205-207)Gag>Cag	p.E69Q		NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	69	Pro-rich.									endometrium(2)|large_intestine(1)|lung(6)	9						GACCCTGCCGGAGCCACCGCC	0.781																																					p.E69Q													.	.	0			c.G205C						.						3	3	3					9																	139739071		1641	3660	5301	SO:0001583	missense	389813	exon1			CTGCCGGAGCCAC		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.205G>C	9.37:g.139739071G>C	ENSP00000412388:p.Glu69Gln	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_001080482	0	0	1	2	1		Missense_Mutation	SNP	ENST00000436881.1	37	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	3.908	-0.020622	0.07634	.	.	ENSG00000232434	ENST00000436881	.	.	.	3.45	2.52	0.30459	.	.	.	.	.	T	0.21718	0.0523	N	0.14661	0.345	0.18873	N	0.999982	B	0.30281	0.275	B	0.35688	0.208	T	0.29212	-1.0019	8	0.19590	T	0.45	.	7.5628	0.27862	0.0:0.1825:0.6295:0.188	.	69	C9J069	CI172_HUMAN	Q	69	.	ENSP00000412388:E69Q	E	+	1	0	C9orf172	138858892	0.069000	0.21087	0.114000	0.21550	0.093000	0.18481	2.111000	0.41883	0.718000	0.32166	-0.521000	0.04368	GAG	.		0.781	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		C	139739071	G	C	139739071	3	2	99	1	0	0	0	0	1	0	0	0	2477	1175	41	4	207	4	C9orf172	9	139739071	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	3522162	139739071	1474360	28	8876											
COL17A1	1308	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	105793785	105793785	+	Frame_Shift_Del	DEL	G	G	-																															gctcccaatagtccgccattGccagcatacatgccgccttc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr10:105793785delG	ENST00000353479.5	-	52	4364	c.4074delC	c.(4072-4074)ggcfs	p.G1358fs	COL17A1_ENST00000369733.3_Frame_Shift_Del_p.G1276fs	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1358	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GTCCGCCATTGCCAGCATACA	0.572																																					p.G1358fs		.											.	COL17A1-95	0			c.4074delC						.						98	95	96					10																	105793785		2203	4300	6503	SO:0001589	frameshift_variant	1308	exon52			.	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.4074delC	10.37:g.105793785delG	ENSP00000340937:p.Gly1358fs	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	99	17	NM_000494	0	0	0	0	0	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Frame_Shift_Del	DEL	ENST00000353479.5	37	CCDS7554.1																																																																																			.		0.572	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		-	105793785	G	-	105793785	7	5	99	1	0	1	0	1	0	0	0	0	3680	1306	46	0	439	0	COL17A1	10	105793785	Frame_Shift_Del	DEL	G	TCGA-DW-7841-01A-11D-2136-08		105793785	29740962	29	8877											
SBF2	81846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	10011061	10011061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacatttttgaatagttgctCagcaagttccctgacatgct	10	15	7	9	0	1	2	1	2	0	0	2	2	2	2	1	0	4	5	1	0	4	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr11:10011061C>T	ENST00000256190.8	-	13	1515	c.1378G>A	c.(1378-1380)Gag>Aag	p.E460K		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	460					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		AATAGTTGCTCAGCAAGTTCC	0.303																																					p.E460K		.											.	SBF2-93	0			c.G1378A						.						99	101	100					11																	10011061		2200	4292	6492	SO:0001583	missense	81846	exon13			GTTGCTCAGCAAG	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins", "DENN/MADD domain containing", "Pleckstrin homology (PH) domain containing"	2135	protein-coding gene	gene with protein product	"myotubularin related 13"	607697	"Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)", "DENN/MADD domain containing 7B"	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.1378G>A	11.37:g.10011061C>T	ENSP00000256190:p.Glu460Lys	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	61	15	NM_030962	0	0	2	2	0	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489124	0.84962	.	.	ENSG00000133812	ENST00000256190	D	0.85629	-2.01	6.04	6.04	0.98038	.	0.230274	0.43416	D	0.000562	D	0.90539	0.7035	L	0.48986	1.54	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86724	0.1944	10	0.25106	T	0.35	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	460	Q86WG5	MTMRD_HUMAN	K	460	ENSP00000256190:E460K	ENSP00000256190:E460K	E	-	1	0	SBF2	9967637	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.324000	0.65863	2.873000	0.98535	0.563000	0.77884	GAG	.		0.303	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		T	10011061	C	T	10011061	3	4	99	1	0	0	0	0	1	0	0	0	13891	835	29	2	4283	2	SBF2	11	10011061	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		10011061	124995455	30	8878											
SLCO2B1	11309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74880776	74880776	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctgggcagcctcatgctgCgcctttatgtggacattaac	7	11	12	11	1	1	0	1	0	0	0	1	1	1	1	2	3	4	3	2	3	2	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr11:74880776C>A	ENST00000289575.5	+	6	1143	c.748C>A	c.(748-750)Cgc>Agc	p.R250S	SLCO2B1_ENST00000454962.2_Intron|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.R106S|SLCO2B1_ENST00000531756.1_Intron|SLCO2B1_ENST00000532236.1_Missense_Mutation_p.R134S|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.R228S|SLCO2B1_ENST00000341411.4_Intron|SLCO2B1_ENST00000526660.1_Intron	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	250					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.R250C(1)		breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	CCTCATGCTGCGCCTTTATGT	0.542																																					p.R250S		.											.	SLCO2B1-154	1	Substitution - Missense(1)	large_intestine(1)	c.C748A						.						128	120	123					11																	74880776		2200	4293	6493	SO:0001583	missense	11309	exon6			ATGCTGCGCCTTT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.748C>A	11.37:g.74880776C>A	ENSP00000289575:p.Arg250Ser	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	155	43	NM_007256	0	0	10	11	1	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	37	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.010553	0.54361	.	.	ENSG00000137491	ENST00000289575;ENST00000532236;ENST00000525650;ENST00000428359;ENST00000526839	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	4.83	2.77	0.32553	Major facilitator superfamily domain, general substrate transporter (1);	0.060626	0.64402	N	0.000004	T	0.41558	0.1164	L	0.39566	1.225	0.80722	D	1	P;P	0.49358	0.812;0.923	B;P	0.51170	0.425;0.661	T	0.15838	-1.0423	10	0.29301	T	0.29	.	11.6849	0.51481	0.326:0.674:0.0:0.0	.	106;250	E9PPU8;O94956	.;SO2B1_HUMAN	S	250;134;106;228;126	ENSP00000289575:R250S;ENSP00000434112:R134S;ENSP00000436324:R106S;ENSP00000388912:R228S;ENSP00000434742:R126S	ENSP00000289575:R250S	R	+	1	0	SLCO2B1	74558424	0.932000	0.31603	0.996000	0.52242	0.937000	0.57800	1.528000	0.35985	1.218000	0.43458	0.650000	0.86243	CGC	.		0.542	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		A	74880776	C	A	74880776	3	1	99	1	0	0	0	0	1	0	0	0	14759	768	27	4	770	4	SLCO2B1	11	74880776	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	64869715	74880776	60125740	31	8879											
BAZ2A	11176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57005874	57005874	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctagggagactgctggggagGttgttggcgagactgctggt	6	10	19	6	1	0	2	0	0	0	2	0	5	0	3	0	6	2	4	0	6	1	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr12:57005874G>A	ENST00000551812.1	-	6	1491	c.1298C>T	c.(1297-1299)aCc>aTc	p.T433I	BAZ2A_ENST00000179765.5_Missense_Mutation_p.T401I|BAZ2A_ENST00000549884.1_Missense_Mutation_p.T431I|BAZ2A_ENST00000379441.3_Missense_Mutation_p.T403I	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	433					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						TGCTGGGGAGGTTGTTGGCGA	0.542																																					p.T433I		.											.	BAZ2A-22	0			c.C1298T						.						101	115	110					12																	57005874		2101	4218	6319	SO:0001583	missense	11176	exon6			GGGGAGGTTGTTG	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"Zinc fingers, PHD-type"	962	protein-coding gene	gene with protein product	"TTF-I interacting peptide 5"	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.1298C>T	12.37:g.57005874G>A	ENSP00000446880:p.Thr433Ile	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	73	55	NM_013449	0	0	4	14	10	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.854|6.854	0.526813|0.526813	0.13066|0.13066	.|.	.|.	ENSG00000076108|ENSG00000076108	ENST00000551996|ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	.|T;T;T;T	.|0.58210	.|0.35;0.35;0.35;0.35	5.45|5.45	-0.694|-0.694	0.11294|0.11294	.|.	.|1.012260	.|0.07909	.|N	.|0.973899	T|T	0.29355|0.29355	0.0731|0.0731	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999997|0.999997	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.23048|0.23048	-1.0199|-1.0199	5|10	.|0.72032	.|D	.|0.01	.|.	5.0786|5.0786	0.14644|0.14644	0.2123:0.0:0.5335:0.2543|0.2123:0.0:0.5335:0.2543	.|.	.|431;433	.|F8VU39;Q9UIF9	.|.;BAZ2A_HUMAN	S|I	81|403;401;433;431	.|ENSP00000368754:T403I;ENSP00000179765:T401I;ENSP00000446880:T433I;ENSP00000447941:T431I	.|ENSP00000179765:T401I	P|T	-|-	1|2	0|0	BAZ2A|BAZ2A	55292141|55292141	0.835000|0.835000	0.29415|0.29415	0.009000|0.009000	0.14445|0.14445	0.194000|0.194000	0.23727|0.23727	0.260000|0.260000	0.18424|0.18424	-0.209000|-0.209000	0.10156|0.10156	-0.182000|-0.182000	0.12963|0.12963	CCT|ACC	.		0.542	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	57005874	G	A	57005874	3	1	99	1	0	0	0	0	1	0	0	0	1332	1261	44	2	4515	2	BAZ2A	12	57005874	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08		57005874	76846021	32	8880											
ASCL1	429	hgsc.bcm.edu	37	chr12	103352211	103352211	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagcagcagcagcaggcGccgcagctgagaccggcggc	9	1	16	15	4	0	1	0	1	0	1	0	2	0	1	2	3	6	7	2	3	0	0	rs376318467	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr12:103352211G>C	ENST00000266744.3	+	1	748	c.189G>C	c.(187-189)gcG>gcC	p.A63A		NM_004316.3	NP_004307.2	P50553	ASCL1_HUMAN	achaete-scute family bHLH transcription factor 1	63					adrenal chromaffin cell differentiation (GO:0061104)|carotid body glomus cell differentiation (GO:0061103)|cell maturation (GO:0048469)|cellular response to magnetism (GO:0071259)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|lung epithelial cell differentiation (GO:0060487)|lung neuroendocrine cell differentiation (GO:0061100)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroblast fate determination (GO:0007400)|neuroblast proliferation (GO:0007405)|neurogenesis (GO:0022008)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron fate commitment (GO:0003359)|Notch signaling pathway (GO:0007219)|olfactory pit development (GO:0060166)|oligodendrocyte development (GO:0014003)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial cell differentiation (GO:0030856)|regulation of gene expression (GO:0010468)|regulation of mitotic cell cycle (GO:0007346)|regulation of timing of subpallium neuron differentiation (GO:0060165)|response to epidermal growth factor (GO:0070849)|response to folic acid (GO:0051593)|response to lithium ion (GO:0010226)|response to retinoic acid (GO:0032526)|spinal cord association neuron differentiation (GO:0021527)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|stomach neuroendocrine cell differentiation (GO:0061102)|subpallium neuron fate commitment (GO:0060163)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)|vestibular nucleus development (GO:0021750)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			NS(3)|large_intestine(1)|lung(1)	5						agcagcagGCGCCGCAGCTGA	0.721													g|||	62	0.0123802	0.0446	0.0043	5008	,	,		10181	0		0	False		,,,				2504	0				p.A63A		.											.	ASCL1-90	0			c.G189C						.			59,2685		1,57,1314	3	3	3		189	3.6	1	12		3	2,5798		0,2,2898	no	coding-synonymous	ASCL1	NM_004316.3		1,59,4212	CC,CG,GG		0.0345,2.1501,0.714		63/237	103352211	61,8483	1372	2900	4272	SO:0001819	synonymous_variant	429	exon1			GCAGGCGCCGCAG	L08424	CCDS31886.1	12q22-q23	2013-10-17	2013-10-17			ENSG00000139352		"Basic helix-loop-helix proteins"	738	protein-coding gene	gene with protein product		100790	"achaete-scute complex (Drosophila) homolog-like 1", "achaete-scute complex-like 1 (Drosophila)", "achaete-scute complex homolog 1 (Drosophila)"			8390674	Standard	NM_004316		Approved	ASH1, HASH1, bHLHa46	uc001tjr.4	P50553		ENST00000266744.3:c.189G>C	12.37:g.103352211G>C		Somatic	7	2		WXS	Illumina HiSeq	Phase_I	14	5	NM_004316	0	0	0	0	0	A8K3C4|Q9BQ30	Silent	SNP	ENST00000266744.3	37	CCDS31886.1																																																																																			.		0.721	ASCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406707.1			C	103352211	G	C	103352211	2	2	99	1	0	0	0	0	0	0	0	1	1035	1074	38	4		4	ASCL1	12	103352211	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08	46346337	103352211	30499684	33	8881											
KBTBD7	84078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41767953	41767953	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccagctgtagcatgtcggaGgccgcgtacaggcgctgcac	7	7	14	13	4	0	0	0	0	0	0	2	1	1	1	2	3	4	6	2	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr13:41767953G>A	ENST00000379483.3	-	1	749	c.441C>T	c.(439-441)gcC>gcT	p.A147A		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	147										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		GCATGTCGGAGGCCGCGTACA	0.587																																					p.A147A		.											.	KBTBD7-91	0			c.C441T						.						109	91	97					13																	41767953		2203	4300	6503	SO:0001819	synonymous_variant	84078	exon1			GTCGGAGGCCGCG	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.441C>T	13.37:g.41767953G>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	105	31	NM_032138	0	0	2	3	1	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Silent	SNP	ENST00000379483.3	37	CCDS9377.1																																																																																			.		0.587	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		A	41767953	G	A	41767953	2	1	99	1	0	0	0	0	0	0	0	1	8019	987	35	2		2	KBTBD7	13	41767953	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08		41767953	73401925	34	8882											
PCDH8	5100	broad.mit.edu	37	chr13	53421017	53421018	+	Frame_Shift_Ins	INS	-	-	AT																															tcccggtcgcgggcggccacINScgtggccaggtaggcgcctg																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr13:53421017_53421018insAT	ENST00000377942.3	-	1	1757_1758	c.1554_1555insAT	c.(1552-1557)acggtgfs	p.V519fs	PCDH8_ENST00000338862.4_Frame_Shift_Ins_p.V519fs	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	519	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CGGGCGGCCACCGTGGCCAGGT	0.723																																					p.V519fs	GBM(36;25 841 9273 49207)												.	PCDH8-153	0			c.1555_1556insAT						.																																			SO:0001589	frameshift_variant	5100	exon1			CGGCCACCGTGGC	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.1554_1555insAT	13.37:g.53421017_53421018insAT	ENSP00000367177:p.Val519fs	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	7	3	NM_032949	0	0	0	0	0	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Frame_Shift_Ins	INS	ENST00000377942.3	37	CCDS9438.1																																																																																			.		0.723	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		AT	53421018	-	AT	53421017	7	5	99	1	0	1	1	0	0	0	0	0	11543	507	18	0	1669	0	PCDH8	13	53421017	Frame_Shift_Ins	INS	-	TCGA-DW-7841-01A-11D-2136-08	11653064	53421017	61748861	35	8883											
TDRD3	81550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	61103190	61103190	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agccagcaggacctgtcacaGctgtaccctgtgatgataaa	12	8	10	11	0	1	2	1	2	0	0	1	3	1	3	3	1	4	3	3	1	3	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr13:61103190G>A	ENST00000196169.3	+	11	2340	c.1552G>A	c.(1552-1554)Gct>Act	p.A518T	TDRD3_ENST00000377894.2_Missense_Mutation_p.A518T|TDRD3_ENST00000377881.2_Missense_Mutation_p.A518T|TDRD3_ENST00000535286.1_Missense_Mutation_p.A611T	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	518					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		ACCTGTCACAGCTGTACCCTG	0.398																																					p.A611T	Colon(36;164 906 35820 50723)	.											.	TDRD3-516	0			c.G1831A						.						54	54	54					13																	61103190		2203	4300	6503	SO:0001583	missense	81550	exon11			GTCACAGCTGTAC	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.1552G>A	13.37:g.61103190G>A	ENSP00000196169:p.Ala518Thr	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	84	32	NM_001146070	0	0	12	15	3	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	0.227	-1.023813	0.02061	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.26	5.84	-1.01	0.10169	.	0.741305	0.14224	N	0.333183	D	0.85974	0.5822	L	0.47716	1.5	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.68911	-0.5284	10	0.12103	T	0.63	-1.2106	3.7879	0.08707	0.4174:0.0981:0.3852:0.0994	.	611;517;518	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	T	518;518;518;611	ENSP00000196169:A518T;ENSP00000367113:A518T;ENSP00000367126:A518T;ENSP00000440190:A611T	ENSP00000196169:A518T	A	+	1	0	TDRD3	60001191	0.000000	0.05858	0.000000	0.03702	0.389000	0.30415	0.087000	0.14958	-0.343000	0.08351	-0.813000	0.03139	GCT	.		0.398	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61103190	G	A	61103190	3	1	99	1	0	0	0	0	1	0	0	0	15764	971	34	2	1873	2	TDRD3	13	61103190	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	7682173	61103190	54066688	36	8884											
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23597353	23597353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgaccacaggctgaagAccagcaggaaggcccagaac	13	3	12	13	0	1	4	0	2	1	2	1	5	1	5	3	3	2	3	3	3	3	0			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:23597353A>G	ENST00000316902.7	-	10	2041	c.1316T>C	c.(1315-1317)gTc>gCc	p.V439A	SLC7A8_ENST00000453702.1_Missense_Mutation_p.V236A|SLC7A8_ENST00000422941.2_Missense_Mutation_p.V215A|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000529705.2_Missense_Mutation_p.V334A	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	439					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	CAGGCTGAAGACCAGCAGGAA	0.562																																					p.V439A		.											.	SLC7A8-91	0			c.T1316C						.						153	129	137					14																	23597353		2203	4300	6503	SO:0001583	missense	23428	exon10			CTGAAGACCAGCA	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.1316T>C	14.37:g.23597353A>G	ENSP00000320378:p.Val439Ala	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_012244	0	0	4	4	0	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	37	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.628933	0.46944	.	.	ENSG00000092068	ENST00000316902;ENST00000453702;ENST00000529705;ENST00000422941;ENST00000206514	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	5.53	5.53	0.82687	Amino acid permease domain (1);	0.329841	0.34460	N	0.003958	D	0.84529	0.5492	N	0.25380	0.74	0.37260	D	0.906967	B;B;B	0.20368	0.044;0.02;0.001	B;B;B	0.25614	0.062;0.034;0.013	T	0.81466	-0.0920	10	0.16896	T	0.51	.	14.6571	0.68841	1.0:0.0:0.0:0.0	.	334;215;439	B4DKT4;B4DTV6;Q9UHI5	.;.;LAT2_HUMAN	A	439;236;334;215;236	ENSP00000320378:V439A;ENSP00000391577:V236A;ENSP00000434345:V334A;ENSP00000416398:V215A	ENSP00000206514:V236A	V	-	2	0	SLC7A8	22667193	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.214000	0.77958	2.109000	0.64355	0.459000	0.35465	GTC	.		0.562	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			G	23597353	A	G	23597353	3	3	99	1	0	0	0	0	1	0	0	0	14736	275	10	3	299	3	SLC7A8	14	23597353	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08		23597353	83752187	37	8885											
FANCM	57697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	45650876	45650876	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagttgattctccacttcatGctgtcaaaaagcgcagattt	12	13	7	9	1	3	2	2	1	1	1	4	2	3	2	1	0	2	3	1	0	3	4			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:45650876G>A	ENST00000267430.5	+	16	4439	c.4354G>A	c.(4354-4356)Gct>Act	p.A1452T	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Missense_Mutation_p.A1426T	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1452					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TCCACTTCATGCTGTCAAAAA	0.318								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A1452T		.											.	FANCM-569	0			c.G4354A						.						59	60	60					14																	45650876		2203	4296	6499	SO:0001583	missense	57697	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTTCATGCTGTCA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.4354G>A	14.37:g.45650876G>A	ENSP00000267430:p.Ala1452Thr	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	50	13	NM_020937	0	0	1	2	1	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.81|19.81	3.897408|3.897408	0.72639|0.72639	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.20069|.	2.7;2.7;2.1|.	5.25|5.25	4.36|4.36	0.52297|0.52297	.|.	0.807093|.	0.11373|.	N|.	0.570657|.	T|T	0.39600|0.39600	0.1084|0.1084	L|L	0.43152|0.43152	1.355|1.355	0.29859|0.29859	N|N	0.827775|0.827775	D;P|.	0.65815|.	0.995;0.953|.	P;P|.	0.53760|.	0.734;0.631|.	T|T	0.35051|0.35051	-0.9804|-0.9804	10|5	0.14656|.	T|.	0.56|.	.|.	8.1721|8.1721	0.31260|0.31260	0.1826:0.0:0.8174:0.0|0.1826:0.0:0.8174:0.0	.|.	1426;1452|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	T|Y	1452;1426;968|384	ENSP00000267430:A1452T;ENSP00000442493:A1426T;ENSP00000452033:A968T|.	ENSP00000267430:A1452T|.	A|C	+|+	1|2	0|0	FANCM|FANCM	44720626|44720626	0.997000|0.997000	0.39634|0.39634	0.995000|0.995000	0.50966|0.50966	0.985000|0.985000	0.73830|0.73830	3.470000|3.470000	0.53100|0.53100	1.348000|1.348000	0.45733|0.45733	0.467000|0.467000	0.42956|0.42956	GCT|TGC	.		0.318	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45650876	G	A	45650876	3	1	99	1	0	0	0	0	1	0	0	0	5690	1319	46	2	4416	2	FANCM	14	45650876	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	22053523	45650876	61698664	38	8886											
TBPL2	387332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55890942	55890942	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggttttaccattctataaAtaagaccaggaaacagttca	15	12	7	7	0	2	1	1	0	1	1	2	2	2	2	2	2	2	2	2	2	6	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:55890942A>C	ENST00000247219.5	-	6	1056	c.986T>G	c.(985-987)aTt>aGt	p.I329S		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						CATTCTATAAATAAGACCAGG	0.348																																					p.I329S		.											.	TBPL2-90	0			c.T986G						.						110	102	105					14																	55890942		2203	4298	6501	SO:0001583	missense	387332	exon6			CTATAAATAAGAC	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.986T>G	14.37:g.55890942A>C	ENSP00000247219:p.Ile329Ser	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	142	40	NM_199047	0	0	0	0	0		Missense_Mutation	SNP	ENST00000247219.5	37	CCDS9724.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.464312	0.84425	.	.	ENSG00000182521	ENST00000247219	T	0.57273	0.41	5.41	5.41	0.78517	Transcription factor TFIID, C-terminal/DNA glycosylase, N-terminal (1);Beta2-adaptin/TATA-box binding, C-terminal (1);	0.054773	0.64402	D	0.000001	T	0.75889	0.3911	M	0.93939	3.475	0.80722	D	1	D	0.63880	0.993	P	0.57776	0.827	T	0.83328	-0.0014	10	0.87932	D	0	-12.6468	14.6315	0.68660	1.0:0.0:0.0:0.0	.	329	Q6SJ96	TBPL2_HUMAN	S	329	ENSP00000247219:I329S	ENSP00000247219:I329S	I	-	2	0	TBPL2	54960695	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.138000	0.94501	2.050000	0.60909	0.528000	0.53228	ATT	.		0.348	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047		C	55890942	A	C	55890942	3	2	99	1	0	0	0	0	1	0	0	0	15678	101	4	5	149	5	TBPL2	14	55890942	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	10240066	55890942	51458598	39	8887											
GPR135	64582	hgsc.bcm.edu	37	chr14	59931931	59931931	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctggtgggcggggcggcTgcggctcctccatggggccc	1	7	19	14	4	0	0	0	0	0	0	3	0	2	0	3	8	1	3	3	8	0	0	rs1752428	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:59931931T>G	ENST00000395116.1	-	1	129	c.14A>C	c.(13-15)cAg>cCg	p.Q5P		NM_022571.5	NP_072093.2	Q8IZ08	GP135_HUMAN	G protein-coupled receptor 135	5			Q -> P (in dbSNP:rs1752428).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.134)		GCGGGGCGGCTGCGGCTCCTC	0.781													G|||	2695	0.538139	0.8767	0.5821	5008	,	,		8009	0.2063		0.4722	False		,,,				2504	0.4591				p.Q5P		.											.	GPR135-90	0			c.A14C						.						1	1	1					14																	59931931		555	1498	2053	SO:0001583	missense	64582	exon1			GGCGGCTGCGGCT	AY288418	CCDS9738.1	14q23.1	2012-08-21			ENSG00000181619	ENSG00000181619		"GPCR / Class A : Orphans"	19991	protein-coding gene	gene with protein product		607970				14623098	Standard	NM_022571		Approved	HUMNPIIY20, PAFR	uc010apj.3	Q8IZ08	OTTHUMG00000140325	ENST00000395116.1:c.14A>C	14.37:g.59931931T>G	ENSP00000378548:p.Gln5Pro	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_022571	0	0	0	0	0	Q7Z604|Q86SM3|Q8NH39	Missense_Mutation	SNP	ENST00000395116.1	37	CCDS9738.1	1023	0.4684065934065934	376	0.7642276422764228	199	0.5497237569060773	107	0.18706293706293706	341	0.449868073878628	G	12.20	1.867217	0.32977	.	.	ENSG00000181619	ENST00000395116	T	0.62941	-0.01	3.25	3.25	0.37280	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999999688	B	0.02656	0.0	B	0.01281	0.0	T	0.36311	-0.9753	8	0.35671	T	0.21	-4.9918	9.4599	0.38778	0.0:0.0:0.7862:0.2138	rs1752428;rs3742644	5	Q8IZ08	GP135_HUMAN	P	5	ENSP00000378548:Q5P	ENSP00000378548:Q5P	Q	-	2	0	GPR135	59001684	0.007000	0.16637	0.970000	0.41538	0.076000	0.17211	-0.908000	0.04063	0.581000	0.29539	-0.677000	0.03784	CAG	T|0.531;G|0.469		0.781	GPR135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276941.1	NM_022571		G	59931931	T	G	59931931	3	3	99	1	0	0	0	0	1	0	0	0	6664	1580	55	5	1474	5	GPR135	14	59931931	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	4040989	59931931	47417609	40	8888											
KCNH5	27133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	63447722	63447722	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctccaccgggccccacGaaagtcgtgtgaaaatttaa	12	8	8	13	3	1	1	0	1	1	0	3	2	1	1	5	1	0	0	5	1	4	2	rs376391048		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:63447722G>T	ENST00000322893.7	-	6	1078	c.810C>A	c.(808-810)ttC>ttA	p.F270L	KCNH5_ENST00000420622.2_Missense_Mutation_p.F270L|KCNH5_ENST00000394964.2_Missense_Mutation_p.F212L|KCNH5_ENST00000394968.1_Missense_Mutation_p.F212L	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	270					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CGGGCCCCACGAAAGTCGTGT	0.433																																					p.F270L		.											.	KCNH5-98	0			c.C810A						.						61	63	62					14																	63447722		2203	4300	6503	SO:0001583	missense	27133	exon6			CCCCACGAAAGTC	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.810C>A	14.37:g.63447722G>T	ENSP00000321427:p.Phe270Leu	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	81	35	NM_172375	0	0	0	0	0	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505267	0.64410	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	5.54	1.95	0.26073	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	M	0.64404	1.975	0.80722	D	1	P;P;D;D	0.61080	0.893;0.899;0.963;0.989	P;P;P;D	0.66084	0.602;0.603;0.603;0.941	D	0.93621	0.6948	10	0.87932	D	0	.	8.8508	0.35199	0.7805:0.0:0.2195:0.0	.	212;212;270;270	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	L	270;270;212;212	ENSP00000321427:F270L;ENSP00000395439:F270L;ENSP00000378419:F212L;ENSP00000378415:F212L	ENSP00000321427:F270L	F	-	3	2	KCNH5	62517475	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	1.301000	0.33447	0.086000	0.17137	-0.482000	0.04802	TTC	.		0.433	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63447722	G	T	63447722	3	4	99	1	0	0	0	0	1	0	0	0	8056	1049	37	4	2214	4	KCNH5	14	63447722	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	3515791	63447722	43901818	41	8889											
RYR3	6263	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	33603296	33603296	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagatccagtttctgaggaCtgtgagtctccgcggcgggg	6	9	16	10	4	2	3	0	2	2	1	4	5	3	4	2	4	0	1	2	4	0	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr15:33603296C>T	ENST00000389232.4	+	1	120	c.50C>T	c.(49-51)aCt>aTt	p.T17I	RP11-489D6.2_ENST00000561458.1_RNA|RP11-489D6.2_ENST00000559457.1_RNA|RYR3_ENST00000415757.3_Splice_Site_p.T17I	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	17					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTTCTGAGGACTGTGAGTCTC	0.756																																					p.T17I		.											.	RYR3-520	0			c.C50T						.						25	32	30					15																	33603296		1919	4113	6032	SO:0001630	splice_region_variant	6263	exon1			TGAGGACTGTGAG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.51+1C>T	15.37:g.33603296C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	47	16	NM_001243996	0	0	0	0	0	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.077125	0.55753	.	.	ENSG00000198838	ENST00000389232;ENST00000415757	D;D	0.98090	-4.71;-4.71	4.63	3.7	0.42460	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	1.170300	0.06443	U	0.726384	D	0.96987	0.9016	L	0.49126	1.545	0.38096	D	0.937129	B;B	0.29253	0.144;0.239	B;B	0.38264	0.126;0.269	D	0.90850	0.4730	10	0.54805	T	0.06	.	12.9534	0.58413	0.1639:0.8361:0.0:0.0	.	17;17	Q15413-2;Q15413	.;RYR3_HUMAN	I	17	ENSP00000373884:T17I;ENSP00000399610:T17I	ENSP00000373884:T17I	T	+	2	0	RYR3	31390588	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.045000	0.64220	1.130000	0.42092	0.462000	0.41574	ACT	.		0.756	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		Missense_Mutation	T	33603296	C	T	33603296	5	4	99	1	0	0	0	0	0	0	1	0	13802	579	20	2	52	2	RYR3	15	33603296	Splice_Site	SNP	C	TCGA-DW-7841-01A-11D-2136-08		33603296	68928096	42	8890											
ADPGK	83440	hgsc.bcm.edu	37	chr15	73045222	73045222	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcccaagggaagtcacCgcgggaaagacctgctaaca	13	5	11	12	2	2	1	2	0	0	1	2	3	2	3	3	2	3	1	3	2	4	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr15:73045222C>A	ENST00000311669.8	-	7	1044	c.951G>T	c.(949-951)gcG>gcT	p.A317A	ADPGK_ENST00000567733.1_5'Flank|ADPGK_ENST00000456471.2_Silent_p.A43A	NM_031284.4	NP_112574.3	Q9BRR6	ADPGK_HUMAN	ADP-dependent glucokinase	318	ADPK. {ECO:0000255|PROSITE- ProRule:PRU00584}.				glycolytic process (GO:0006096)	extracellular region (GO:0005576)|membrane (GO:0016020)	ADP-specific glucokinase activity (GO:0043843)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	7						GGGAAGTCACCGCGGGAAAGA	0.478																																					p.A317A		.											.	ADPGK-90	0			c.G951T						.						36	36	36					15																	73045222		1925	4115	6040	SO:0001819	synonymous_variant	83440	exon7			AGTCACCGCGGGA	AL136873	CCDS42057.1	15q24.1	2012-07-02			ENSG00000159322	ENSG00000159322			25250	protein-coding gene	gene with protein product		611861				11230166	Standard	NM_031284		Approved	DKFZp434B195, ADP-GK	uc002avf.4	Q9BRR6	OTTHUMG00000172777	ENST00000311669.8:c.951G>T	15.37:g.73045222C>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	71	4	NM_031284	0	0	21	22	1	Q49AU7|Q8NBI1|Q8WZ90|Q96NF8|Q9H0A7	Silent	SNP	ENST00000311669.8	37	CCDS42057.1																																																																																			.		0.478	ADPGK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420434.1	NM_031284		A	73045222	C	A	73045222	2	1	99	1	0	0	0	0	0	0	0	1	330	639	23	4		4	ADPGK	15	73045222	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08	39441926	73045222	29486170	43	8891											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75982391	75982391	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctggtgtcaggcccaggcGgtgttcctggaggtgacgag	5	9	17	10	2	2	1	1	1	1	0	3	3	3	2	2	6	0	1	2	6	0	1	rs200187536		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr15:75982391G>A	ENST00000308508.5	-	3	1107	c.1015C>T	c.(1015-1017)Cgc>Tgc	p.R339C		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	339	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGGCCCAGGCGGTGTTCCTGG	0.642																																					p.R339C		.											.	CSPG4-229	0			c.C1015T						.						17	15	16					15																	75982391		2192	4283	6475	SO:0001583	missense	1464	exon3			CCAGGCGGTGTTC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1015C>T	15.37:g.75982391G>A	ENSP00000312506:p.Arg339Cys	Somatic	33	1		WXS	Illumina HiSeq	Phase_I	41	5	NM_001897	0	0	3	3	0	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	15.76	2.927450	0.52759	.	.	ENSG00000173546	ENST00000308508	T	0.19938	2.11	5.26	4.26	0.50523	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.181054	0.36815	N	0.002398	T	0.34803	0.0910	L	0.40543	1.245	0.43593	D	0.995946	D	0.89917	1.0	D	0.65987	0.94	T	0.02553	-1.1142	10	0.37606	T	0.19	.	15.6861	0.77411	0.0:0.0:0.8538:0.1462	.	339	Q6UVK1	CSPG4_HUMAN	C	339	ENSP00000312506:R339C	ENSP00000312506:R339C	R	-	1	0	CSPG4	73769446	0.996000	0.38824	1.000000	0.80357	0.667000	0.39255	2.026000	0.41069	2.463000	0.83235	0.555000	0.69702	CGC	G|0.999;A|0.001		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		A	75982391	G	A	75982391	3	1	99	1	0	0	0	0	1	0	0	0	3966	1116	39	1	5985	1	CSPG4	15	75982391	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	2937169	75982391	26549001	44	8892											
WDR90	197335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	716291	716291	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcacagggacaaccttcCgtgtgctgagtgaccaccag	9	7	11	14	1	0	2	0	2	0	0	1	3	1	3	5	1	3	2	5	1	1	1	rs143767432	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr16:716291C>A	ENST00000293879.4	+	37	4681	c.4681C>A	c.(4681-4683)Cgt>Agt	p.R1561S	WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000315764.4_Missense_Mutation_p.R160S|WDR90_ENST00000547944.1_Missense_Mutation_p.R160S|WDR90_ENST00000549091.1_Missense_Mutation_p.R1563S|RHOT2_ENST00000315082.4_5'Flank			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1561										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GACAACCTTCCGTGTGCTGAG	0.627																																					p.R1561S		.											.	WDR90-92	0			c.C4681A						.						46	55	52					16																	716291		2025	4175	6200	SO:0001583	missense	197335	exon37			ACCTTCCGTGTGC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4681C>A	16.37:g.716291C>A	ENSP00000293879:p.Arg1561Ser	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	98	27	NM_145294	0	0	20	35	15	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.532400	0.64972	.	.	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944;ENST00000315764	T;T;T;T	0.66099	3.39;1.54;-0.19;1.59	3.96	3.0	0.34707	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.649291	0.16302	N	0.220408	T	0.74898	0.3777	M	0.84433	2.695	0.49051	D	0.999749	D;D;D;D	0.89917	0.999;1.0;0.98;0.998	D;D;P;P	0.71184	0.972;0.968;0.671;0.892	T	0.73981	-0.3811	10	0.08837	T	0.75	.	9.2755	0.37696	0.0:0.8986:0.0:0.1014	.	160;160;160;1561	Q96KV7-10;Q96KV7-7;G3V201;Q96KV7	.;.;.;WDR90_HUMAN	S	1563;1561;160;160	ENSP00000448122:R1563S;ENSP00000293879:R1561S;ENSP00000449576:R160S;ENSP00000322808:R160S	ENSP00000293879:R1561S	R	+	1	0	WDR90	656292	0.083000	0.21467	0.303000	0.25071	0.729000	0.41735	1.907000	0.39897	0.877000	0.35895	0.561000	0.74099	CGT	C|0.996;T|0.004		0.627	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	716291	C	A	716291	3	1	99	1	0	0	0	0	1	0	0	0	17370	652	23	4	4827	4	WDR90	16	716291	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		716291	89638462	45	8893											
TMC5	79838	hgsc.bcm.edu	37	chr16	19498618	19498618	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcccatccttcaccggggTcttgtgcaccctggccatca	5	12	8	16	1	3	0	2	0	1	0	5	0	5	0	5	3	1	1	5	3	0	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr16:19498618T>C	ENST00000396229.2	+	17	3292	c.2543T>C	c.(2542-2544)gTc>gCc	p.V848A	TMC5_ENST00000542583.2_Missense_Mutation_p.V848A|TMC5_ENST00000219821.5_Missense_Mutation_p.V602A|TMC5_ENST00000561503.1_Missense_Mutation_p.V489A|TMC5_ENST00000564959.1_Missense_Mutation_p.V531A|TMC5_ENST00000381414.4_Missense_Mutation_p.V848A|TMC5_ENST00000541464.1_Missense_Mutation_p.V796A|CTA-363E6.6_ENST00000561762.1_RNA	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	848					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTCACCGGGGTCTTGTGCACC	0.522																																					p.V848A		.											.	TMC5-91	0			c.T2543C						.						67	58	61					16																	19498618		2197	4300	6497	SO:0001583	missense	79838	exon17			CCGGGGTCTTGTG	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2543T>C	16.37:g.19498618T>C	ENSP00000379531:p.Val848Ala	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_001105249	0	0	0	0	0	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.144011	0.57044	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.67523	-0.11;-0.09;-0.13;-0.13;-0.27	5.72	3.48	0.39840	.	0.235749	0.43110	N	0.000604	T	0.43010	0.1228	N	0.13299	0.325	0.37439	D	0.914337	B;B;B;B;B;B	0.26120	0.142;0.001;0.025;0.014;0.019;0.018	B;B;B;B;B;B	0.24006	0.05;0.003;0.05;0.022;0.022;0.034	T	0.28073	-1.0055	10	0.08837	T	0.75	-19.7366	9.3727	0.38264	0.0:0.148:0.0:0.852	.	796;531;602;602;848;848	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	A	796;848;848;848;602;531	ENSP00000441227:V796A;ENSP00000370822:V848A;ENSP00000379531:V848A;ENSP00000446274:V848A;ENSP00000219821:V602A	ENSP00000219821:V602A	V	+	2	0	TMC5	19406119	1.000000	0.71417	0.948000	0.38648	0.985000	0.73830	3.080000	0.50112	0.443000	0.26582	0.533000	0.62120	GTC	.		0.522	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		C	19498618	T	C	19498618	3	2	99	1	0	0	0	0	1	0	0	0	16020	1667	58	3	2915	3	TMC5	16	19498618	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	18782327	19498618	70856135	46	8894											
GTF3C1	2975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27519910	27519910	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcacagcattcttgcttctAgttttcccacattcatagcc	8	14	6	13	0	3	0	1	0	2	0	4	0	4	0	2	1	3	4	2	1	2	8			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr16:27519910A>G	ENST00000356183.4	-	8	1208	c.1193T>C	c.(1192-1194)cTa>cCa	p.L398P	GTF3C1_ENST00000561623.1_Missense_Mutation_p.L398P	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	398					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TCTTGCTTCTAGTTTTCCCAC	0.468																																					p.L398P		.											.	GTF3C1-94	0			c.T1193C						.						195	159	171					16																	27519910		2197	4300	6497	SO:0001583	missense	2975	exon8			GCTTCTAGTTTTC	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"General transcription factors"	4664	protein-coding gene	gene with protein product		603246	"general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.1193T>C	16.37:g.27519910A>G	ENSP00000348510:p.Leu398Pro	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	118	36	NM_001520	0	0	2	2	0	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.353988	0.82243	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.32272	1.46	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	T	0.45597	0.1350	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.45190	-0.9278	10	0.72032	D	0.01	-4.7197	15.1534	0.72720	1.0:0.0:0.0:0.0	.	398;398	Q12789;Q12789-3	TF3C1_HUMAN;.	P	398;396	ENSP00000348510:L398P	ENSP00000348510:L398P	L	-	2	0	GTF3C1	27427411	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.677000	0.91203	2.054000	0.61138	0.528000	0.53228	CTA	.		0.468	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		G	27519910	A	G	27519910	3	3	99	1	0	0	0	0	1	0	0	0	6893	420	15	3	5256	3	GTF3C1	16	27519910	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	8021292	27519910	62834843	47	8895											
PELP1	27043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4575082	4575082	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtcactcccatcctcagtCtcctcttccaacagggttgg	6	13	7	15	0	4	0	2	0	2	0	8	0	7	0	4	2	1	1	4	2	1	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:4575082C>T	ENST00000574876.1	-	16	3221	c.3204G>A	c.(3202-3204)gaG>gaA	p.E1068E	PELP1_ENST00000269230.7_Silent_p.E978E|PELP1_ENST00000301396.4_Silent_p.E1212E|PELP1_ENST00000572293.1_Silent_p.E1118E|PELP1_ENST00000436683.2_Silent_p.E844E			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	1068	Glu-rich.|Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CATCCTCAGTCTCCTCTTCCA	0.602																																					p.E1068E		.											.	PELP1-24	0			c.G3204A						.						27	28	27					17																	4575082		1913	4111	6024	SO:0001819	synonymous_variant	27043	exon16			CTCAGTCTCCTCT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"proline, glutamic acid and leucine rich protein 1"			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.3204G>A	17.37:g.4575082C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	67	12	NM_014389	0	0	74	109	35	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			.		0.602	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4575082	C	T	4575082	2	4	99	1	0	0	0	0	0	0	0	1	11751	912	32	2		2	PELP1	17	4575082	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		4575082	76620128	48	8896											
SOX15	6665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7492754	7492754	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactgcgcgcccaggcgctTggagatctcggagttgtgca	6	8	14	13	4	1	1	0	0	1	1	2	3	1	2	2	3	2	3	2	3	0	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:7492754T>C	ENST00000250055.2	-	1	734	c.241A>G	c.(241-243)Aag>Gag	p.K81E	MPDU1_ENST00000423172.2_Intron|SOX15_ENST00000570788.1_Missense_Mutation_p.K81E|FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000538513.2_Missense_Mutation_p.K81E	NM_006942.1	NP_008873.1	O60248	SOX15_HUMAN	SRY (sex determining region Y)-box 15	81					cell differentiation (GO:0030154)|chromatin organization (GO:0006325)|male gonad development (GO:0008584)|myoblast development (GO:0048627)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G0 to G1 transition (GO:0070318)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue regeneration (GO:0043403)	cytoplasm (GO:0005737)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)	2						CCCAGGCGCTTGGAGATCTCG	0.667											OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K81E		.											.	SOX15-135	0			c.A241G						.						31	34	33					17																	7492754		2203	4300	6503	SO:0001583	missense	6665	exon1			GGCGCTTGGAGAT	AJ006222	CCDS32549.1	17p13.1	2014-08-12	2002-07-22	2002-07-26	ENSG00000129194	ENSG00000129194		"SRY (sex determining region Y)-boxes"	11196	protein-coding gene	gene with protein product		601297	"SRY (sex determining region Y)-box 20"	SOX20		8978787, 9730625	Standard	NM_006942		Approved	SOX27, SOX26	uc002ghz.1	O60248	OTTHUMG00000178146	ENST00000250055.2:c.241A>G	17.37:g.7492754T>C	ENSP00000355354:p.Lys81Glu	Somatic	52	0	642	WXS	Illumina HiSeq	Phase_I	58	22	NM_006942	0	0	0	1	1	B4DWU7|D3DTQ0|P35717|Q9Y6W7	Missense_Mutation	SNP	ENST00000250055.2	37	CCDS32549.1	.	.	.	.	.	.	.	.	.	.	T	35	5.577422	0.96565	.	.	ENSG00000129194	ENST00000250055;ENST00000538513	D;D	0.98717	-5.09;-5.09	5.38	5.38	0.77491	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.111127	0.41097	D	0.000944	D	0.99414	0.9793	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98487	1.0608	10	0.87932	D	0	.	13.4332	0.61068	0.0:0.0:0.0:1.0	.	81	O60248	SOX15_HUMAN	E	81	ENSP00000355354:K81E;ENSP00000439311:K81E	ENSP00000355354:K81E	K	-	1	0	SOX15	7433478	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.098000	0.71458	2.276000	0.75962	0.454000	0.30748	AAG	.		0.667	SOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440757.1	NM_006942		C	7492754	T	C	7492754	3	2	99	1	0	0	0	0	1	0	0	0	14978	1821	63	3	468	3	SOX15	17	7492754	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	2917672	7492754	73702456	49	8897											
TMEM88	92162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	7758402	7758402	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcgggccatggcggatGtccccggggcacagcgagcg	6	3	18	14	5	0	0	0	0	0	0	1	2	1	1	4	6	2	1	4	6	0	0			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:7758402G>T	ENST00000301599.6	+	1	20	c.10G>T	c.(10-12)Gtc>Ttc	p.V4F	CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000570555.1_5'Flank|CYB5D1_ENST00000570446.1_5'Flank|TMEM88_ENST00000574668.1_Missense_Mutation_p.V4F	NM_203411.1	NP_981956.1	Q6PEY1	TMM88_HUMAN	transmembrane protein 88	4					multicellular organismal development (GO:0007275)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(1)	1		all_cancers(10;0.00528)|Prostate(122;0.202)				CATGGCGGATGTCCCCGGGGC	0.697																																					p.V4F		.											.	TMEM88-68	0			c.G10T						.						26	29	28					17																	7758402		2200	4296	6496	SO:0001583	missense	92162	exon1			GCGGATGTCCCCG	BC057812	CCDS11121.1	17p13.1	2005-12-13				ENSG00000167874			32371	protein-coding gene	gene with protein product							Standard	NM_203411		Approved	MGC71744, FLJ20025	uc002giy.3	Q6PEY1		ENST00000301599.6:c.10G>T	17.37:g.7758402G>T	ENSP00000301599:p.Val4Phe	Somatic	33	1		WXS	Illumina HiSeq	Phase_I	43	11	NM_203411	0	0	6	6	0		Missense_Mutation	SNP	ENST00000301599.6	37	CCDS11121.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814355	0.32053	.	.	ENSG00000167874	ENST00000301599	T	0.49720	0.77	5.8	2.79	0.32731	.	0.447252	0.22406	N	0.060477	T	0.31702	0.0805	N	0.22421	0.69	0.09310	N	0.999998	B	0.18968	0.032	B	0.16289	0.015	T	0.26292	-1.0107	10	0.87932	D	0	-2.4095	8.5767	0.33603	0.2397:0.0:0.7603:0.0	.	4	Q6PEY1	TMM88_HUMAN	F	4	ENSP00000301599:V4F	ENSP00000301599:V4F	V	+	1	0	TMEM88	7699127	0.031000	0.19500	0.984000	0.44739	0.916000	0.54674	1.620000	0.36976	0.388000	0.25054	0.561000	0.74099	GTC	.		0.697	TMEM88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440252.1	NM_203411		T	7758402	G	T	7758402	3	4	99	1	0	0	0	0	1	0	0	0	16244	1377	48	4	12	4	TMEM88	17	7758402	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	265648	7758402	73436808	50	8898											
TLCD1	116238	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27052951	27052951	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccagatccccgacacaatGgagtgagcgaaggagacgag	13	3	14	11	3	0	3	0	1	0	2	1	8	1	4	3	2	1	0	3	2	2	0			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:27052951G>T	ENST00000292090.3	-	1	275	c.165C>A	c.(163-165)tcC>tcA	p.S55S	SNORD42A_ENST00000459584.1_RNA|NEK8_ENST00000268766.6_5'Flank|AC010761.14_ENST00000587898.1_RNA|SNORD4B_ENST00000459083.1_RNA|TLCD1_ENST00000394933.3_Intron	NM_138463.3	NP_612472.1	Q96CP7	TLCD1_HUMAN	TLC domain containing 1	55	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(2)|lung(2)	7	Lung NSC(42;0.00431)					CCGACACAATGGAGTGAGCGA	0.682																																					p.S55S		.											.	TLCD1-68	0			c.C165A						.						25	24	24					17																	27052951		2203	4300	6503	SO:0001819	synonymous_variant	116238	exon1			CACAATGGAGTGA	BC014072	CCDS11242.1, CCDS54102.1	17q11.2	2007-03-23			ENSG00000160606	ENSG00000160606			25177	protein-coding gene	gene with protein product						12151215	Standard	NM_138463		Approved		uc002hco.3	Q96CP7	OTTHUMG00000132683	ENST00000292090.3:c.165C>A	17.37:g.27052951G>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	82	31	NM_138463	0	0	6	9	3	A8MYP9	Silent	SNP	ENST00000292090.3	37	CCDS11242.1																																																																																			.		0.682	TLCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255973.1	NM_138463		T	27052951	G	T	27052951	2	4	99	1	0	0	0	0	0	0	0	1	15969	1335	47	4		4	TLCD1	17	27052951	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08	19294549	27052951	54142259	51	8899											
PIPOX	51268	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	27380072	27380083	+	In_Frame_Del	DEL	GGTTGCCCAGGG	GGTTGCCCAGGG	-																															gcaacgtttcccaaatattcGgttgcccaggggagaagtgg																								rs148024165	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	GGTTGCCCAGGG	GGTTGCCCAGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:27380072_27380083delGGTTGCCCAGGG	ENST00000323372.4	+	3	724_735	c.398_409delGGTTGCCCAGGG	c.(397-411)cggttgcccagggga>cga	p.LPRG134del	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	134					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)			endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	CCAAATATTCGGTTGCCCAGGGGAGAAGTGGG	0.495																																					p.133_137del		.											.	PIPOX-90	0			c.398_409del						.																																			SO:0001651	inframe_deletion	51268	exon3			.	AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"L-pipecolic acid oxidase"					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.398_409delGGTTGCCCAGGG	17.37:g.27380072_27380083delGGTTGCCCAGGG	ENSP00000317721:p.Leu134_Gly137del	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	126	27	NM_016518	0	0	0	0	0	B3KNH0|Q96H28|Q9C070	In_Frame_Del	DEL	ENST00000323372.4	37	CCDS11248.1																																																																																			.		0.495	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518		-	27380083	GGTTGCCCAGGG	-	27380072	7	5	99	1	0	1	0	1	0	0	0	0	11969	1116	39	0	408	0	PIPOX	17	27380072	In_Frame_Del	DEL	GGTTGCCCAGGG	TCGA-DW-7841-01A-11D-2136-08	327121	27380072	53815138	52	8900											
DDX52	11056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	36003445	36003445	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgaaagagatcgtggacgTccatctttacccagaaagcg	12	7	12	10	4	1	2	0	0	1	2	3	5	2	3	2	2	2	0	2	2	3	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:36003445T>C	ENST00000349699.2	-	1	48	c.5A>G	c.(4-6)gAc>gGc	p.D2G	DDX52_ENST00000394367.3_5'UTR|RP11-697E22.2_ENST00000586950.1_RNA|RP11-697E22.2_ENST00000586163.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	2						membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				ATCGTGGACGTCCATCTTTAC	0.622																																					p.D2G		.											.	DDX52-228	0			c.A5G						.						43	43	43					17																	36003445		2203	4300	6503	SO:0001583	missense	11056	exon1			TGGACGTCCATCT	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"DEAD-boxes"	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.5A>G	17.37:g.36003445T>C	ENSP00000268854:p.Asp2Gly	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	85	17	NM_007010	0	0	0	1	1	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847823	0.91277	.	.	ENSG00000141141	ENST00000349699	T	0.18960	2.18	5.26	5.26	0.73747	.	37.662000	0.00397	N	0.000053	T	0.40196	0.1107	L	0.54323	1.7	0.80722	D	1	D	0.61697	0.99	P	0.54140	0.743	T	0.03545	-1.1026	10	0.87932	D	0	.	11.4972	0.50415	0.0:0.0:0.0:1.0	.	2	Q9Y2R4	DDX52_HUMAN	G	2	ENSP00000268854:D2G	ENSP00000268854:D2G	D	-	2	0	DDX52	33077558	0.996000	0.38824	0.931000	0.37212	0.923000	0.55619	3.812000	0.55628	2.218000	0.71995	0.533000	0.62120	GAC	.		0.622	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		C	36003445	T	C	36003445	3	2	99	1	0	0	0	0	1	0	0	0	4376	1667	58	3	1854	3	DDX52	17	36003445	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	8623373	36003445	45191765	53	8901											
KRT27	342574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38933310	38933310	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggatttctcttccacagTgtgaactctggatgagagaa	10	12	12	7	0	2	3	0	2	2	1	4	6	3	5	1	3	1	0	1	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:38933310T>C	ENST00000301656.3	-	8	1361	c.1321A>G	c.(1321-1323)Act>Gct	p.T441A	KRT27_ENST00000540723.1_5'UTR	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TCTTCCACAGTGTGAACTCTG	0.413																																					p.T441A		.											.	KRT27-90	0			c.A1321G						.						118	121	120					17																	38933310		2203	4300	6503	SO:0001583	missense	342574	exon8			CCACAGTGTGAAC	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.1321A>G	17.37:g.38933310T>C	ENSP00000301656:p.Thr441Ala	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	133	28	NM_181537	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053696	0.36277	.	.	ENSG00000171446	ENST00000301656	D	0.82081	-1.57	5.66	1.64	0.23874	.	0.290739	0.30260	N	0.010040	T	0.63534	0.2519	N	0.19112	0.55	0.19945	N	0.999941	B	0.02656	0.0	B	0.01281	0.0	T	0.47849	-0.9085	10	0.36615	T	0.2	.	0.5754	0.00702	0.2019:0.1756:0.1465:0.4761	.	441	Q7Z3Y8	K1C27_HUMAN	A	441	ENSP00000301656:T441A	ENSP00000301656:T441A	T	-	1	0	KRT27	36186836	0.000000	0.05858	0.645000	0.29479	0.941000	0.58515	-0.027000	0.12371	0.471000	0.27319	0.528000	0.53228	ACT	.		0.413	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		C	38933310	T	C	38933310	3	2	99	1	0	0	0	0	1	0	0	0	8485	1696	59	3	62	3	KRT27	17	38933310	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	2929865	38933310	42261900	54	8902											
FOXJ1	2302	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74134123	74134123	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggtcaatgcgccagaagcCccccttgcctggttcgtcct	5	9	12	15	2	1	1	1	0	0	1	3	1	2	1	6	3	3	1	6	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:74134123C>A	ENST00000322957.6	-	3	931	c.577G>T	c.(577-579)Ggc>Tgc	p.G193C	RNF157-AS1_ENST00000590137.1_RNA|RNF157-AS1_ENST00000585542.1_RNA	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	193					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			CGCCAGAAGCCCCCCTTGCCT	0.607																																					p.G193C		.											.	FOXJ1-227	0			c.G577T						.						39	43	41					17																	74134123		2203	4300	6503	SO:0001583	missense	2302	exon3			AGAAGCCCCCCTT	X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"Forkhead boxes"	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.577G>T	17.37:g.74134123C>A	ENSP00000323880:p.Gly193Cys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	58	19	NM_001454	0	0	5	14	9	O00630	Missense_Mutation	SNP	ENST00000322957.6	37	CCDS32739.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986309	0.74589	.	.	ENSG00000129654	ENST00000322957	D	0.95482	-3.72	4.68	4.68	0.58851	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96580	0.8884	L	0.42581	1.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97558	1.0096	10	0.87932	D	0	.	17.5787	0.87958	0.0:1.0:0.0:0.0	.	193	Q92949	FOXJ1_HUMAN	C	193	ENSP00000323880:G193C	ENSP00000323880:G193C	G	-	1	0	FOXJ1	71645718	1.000000	0.71417	0.999000	0.59377	0.602000	0.36980	5.893000	0.69798	2.153000	0.67306	0.561000	0.74099	GGC	.		0.607	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454		A	74134123	C	A	74134123	3	1	99	1	0	0	0	0	1	0	0	0	6030	623	22	4	692	4	FOXJ1	17	74134123	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	35200813	74134123	7061087	55	8903											
C17orf70	80233	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	79514289	79514299	+	Frame_Shift_Del	DEL	TGAGACTGTAG	TGAGACTGTAG	-																															ggccccgcccaccacctcccTgagactgtagaacagcgtgc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	TGAGACTGTAG	TGAGACTGTAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:79514289_79514299delTGAGACTGTAG	ENST00000327787.8	-	5	1855_1865	c.1809_1819delCTACAGTCTCA	c.(1807-1821)ttctacagtctcaggfs	p.FYSLR603fs	C17orf70_ENST00000537152.1_Frame_Shift_Del_p.FYSLR452fs|C17orf70_ENST00000425898.2_Frame_Shift_Del_p.FYSLR252fs			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	603					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			ACCACCTCCCTGAGACTGTAGAACAGCGTGC	0.682																																					p.603_607del		.											.	C17orf70-92	0			c.1809_1819del						.																																			SO:0001589	frameshift_variant	80233	exon5			.	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 100kDa"	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.1809_1819delCTACAGTCTCA	17.37:g.79514289_79514299delTGAGACTGTAG	ENSP00000333283:p.Phe603fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	90	31	NM_025161	0	0	0	0	0	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Frame_Shift_Del	DEL	ENST00000327787.8	37	CCDS32765.2																																																																																			.		0.682	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		-	79514299	TGAGACTGTAG	-	79514289	7	5	99	1	0	1	0	1	0	0	0	0	1882	1579	55	0	846	0	C17orf70	17	79514289	Frame_Shift_Del	DEL	TGAGACTGTAG	TCGA-DW-7841-01A-11D-2136-08	5380166	79514289	1680921	56	8904											
ARID3A	1820	hgsc.bcm.edu	37	chr19	971936	971936	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctcccaacaaaggaggCggcggcggcggcggcagcag	8	3	17	13	5	1	0	0	0	1	0	2	1	2	1	1	7	3	3	1	7	2	0	rs138086881	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr19:971936C>G	ENST00000263620.3	+	9	1980	c.1653C>G	c.(1651-1653)ggC>ggG	p.G551G		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	551	Gly-rich.|Important for cytoplasmic localization. {ECO:0000250}.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAAAGGAggcggcggcggcg	0.657																																					p.G551G	Pancreas(29;54 1022 32760 50921)	.											.	ARID3A-90	0			c.C1653G						.						25	33	30					19																	971936		2196	4289	6485	SO:0001819	synonymous_variant	1820	exon9			AGGAGGCGGCGGC	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1653C>G	19.37:g.971936C>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	89	5	NM_005224	0	0	0	0	0	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Silent	SNP	ENST00000263620.3	37	CCDS12050.1																																																																																			C|0.999;T|0.001		0.657	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		G	971936	C	G	971936	2	3	99	1	0	0	0	0	0	0	0	1	916	755	27	4		4	ARID3A	19	971936	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		971936	58157047	57	8905											
HNRNPM	4670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8551158	8551158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggccatgggtggcggtggcGgtgccagctttgaccgtgcc	3	9	18	11	3	0	1	0	1	0	0	0	1	0	1	4	6	3	1	4	6	0	1	rs199749036		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr19:8551158G>A	ENST00000325495.4	+	14	1887	c.1846G>A	c.(1846-1848)Ggt>Agt	p.G616S	HNRNPM_ENST00000348943.3_Missense_Mutation_p.G577S	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	616	Poly-Gly.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						TGGCGGTGGCGGTGCCAGCTT	0.682													G|||	1	0.000199681	0	0	5008	,	,		16026	0.001		0	False		,,,				2504	0				p.G616S		.											.	HNRNPM-68	0			c.G1846A						.						33	37	36					19																	8551158		2202	4300	6502	SO:0001583	missense	4670	exon14			GGTGGCGGTGCCA	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.1846G>A	19.37:g.8551158G>A	ENSP00000325376:p.Gly616Ser	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	74	28	NM_005968	0	0	56	91	35	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	37	CCDS12203.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.91	2.379400	0.42207	.	.	ENSG00000099783	ENST00000325495;ENST00000348943;ENST00000544159;ENST00000539473	T;T	0.18960	2.18;2.52	4.52	2.41	0.29592	.	0.100454	0.64402	N	0.000002	T	0.35856	0.0946	M	0.62723	1.935	0.52501	D	0.999953	P;P;D;P	0.89917	0.907;0.906;1.0;0.774	B;B;D;B	0.69479	0.205;0.126;0.964;0.074	T	0.05801	-1.0863	10	0.51188	T	0.08	.	6.939	0.24483	0.2022:0.0:0.7978:0.0	.	456;616;577;501	Q7KYM9;P52272;P52272-2;Q59ES8	.;HNRPM_HUMAN;.;.	S	616;577;501;173	ENSP00000325376:G616S;ENSP00000325732:G577S	ENSP00000325376:G616S	G	+	1	0	HNRNPM	8457158	1.000000	0.71417	0.953000	0.39169	1.000000	0.99986	4.448000	0.60027	0.839000	0.34971	0.655000	0.94253	GGT	G|0.999;A|0.000		0.682	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1			A	8551158	G	A	8551158	3	1	99	1	0	0	0	0	1	0	0	0	7292	1116	39	1	1900	1	HNRNPM	19	8551158	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	7579222	8551158	50577825	58	8906											
ZNF497	162968	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58867603	58867603	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcaagcgtagggcctctCgcccgtgtgcgtgcgccggt	3	7	16	15	7	1	0	0	0	1	0	2	0	1	0	4	2	3	2	4	2	2	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr19:58867603C>A	ENST00000311044.3	-	3	1587	c.1399G>T	c.(1399-1401)Gag>Tag	p.E467*	A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|CTD-2619J13.9_ENST00000599952.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|ZNF497_ENST00000425453.3_Nonsense_Mutation_p.E467*|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG_ENST00000263100.3_5'Flank|A1BG-AS1_ENST00000595302.1_RNA	NM_198458.2	NP_940860.2	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|lung(3)|skin(2)	7		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0278)		TAGGGCCTCTCGCCCGTGTGC	0.692																																					p.E467X		.											.	ZNF497-90	0			c.G1399T						.						15	17	16					19																	58867603		2194	4293	6487	SO:0001587	stop_gained	162968	exon2			GCCTCTCGCCCGT	AK126727	CCDS12977.1	19q13.43	2013-01-08			ENSG00000174586	ENSG00000174586		"Zinc fingers, C2H2-type"	23714	protein-coding gene	gene with protein product							Standard	NM_198458		Approved	FLJ44773	uc002qsi.2	Q6ZNH5		ENST00000311044.3:c.1399G>T	19.37:g.58867603C>A	ENSP00000311183:p.Glu467*	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	30	9	NM_001207009	0	0	3	8	5	Q05AG8|Q0VF48|Q6ZTD2|Q9UIA8	Nonsense_Mutation	SNP	ENST00000311044.3	37	CCDS12977.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.257589	0.80246	.	.	ENSG00000174586	ENST00000311044;ENST00000425453	.	.	.	1.24	0.059	0.14330	.	.	.	.	.	.	.	.	.	.	.	0.53005	D	0.999969	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	8.3137	0.32086	0.0:0.7513:0.2487:0.0	.	.	.	.	X	467	.	ENSP00000311183:E467X	E	-	1	0	ZNF497	63559415	0.568000	0.26635	0.001000	0.08648	0.280000	0.26924	2.887000	0.48586	0.066000	0.16515	0.195000	0.17529	GAG	.		0.692	ZNF497-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466942.2	NM_198458		A	58867603	C	A	58867603	4	1	99	1	0	0	0	0	0	1	0	0	17978	893	31	4	101	4	ZNF497	19	58867603	Nonsense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	50316445	58867603	261380	59	8907											
CTCFL	140690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	56090837	56090837	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatagctgcactggcaacaCtgaaaggggcgctccccagt	10	6	12	13	1	0	1	0	1	0	0	1	1	1	1	2	3	3	5	2	3	3	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr20:56090837C>G	ENST00000608263.1	-	5	1774	c.1113G>C	c.(1111-1113)caG>caC	p.Q371H	CTCFL_ENST00000539382.1_Missense_Mutation_p.Q166H|CTCFL_ENST00000609232.1_Missense_Mutation_p.Q371H|CTCFL_ENST00000422869.2_Missense_Mutation_p.Q371H|CTCFL_ENST00000433949.3_Missense_Mutation_p.Q166H|CTCFL_ENST00000423479.3_Missense_Mutation_p.Q371H|CTCFL_ENST00000371196.2_Missense_Mutation_p.Q371H|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000502686.2_Missense_Mutation_p.Q109H|CTCFL_ENST00000429804.3_Missense_Mutation_p.Q371H|CTCFL_ENST00000608440.1_Missense_Mutation_p.Q371H|CTCFL_ENST00000608425.1_Missense_Mutation_p.Q371H|CTCFL_ENST00000608903.1_Missense_Mutation_p.Q109H|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Missense_Mutation_p.Q371H	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	371					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ACTGGCAACACTGAAAGGGGC	0.473																																					p.Q371H		.											.	CTCFL-292	0			c.G1113C						.						173	164	167					20																	56090837		2203	4300	6503	SO:0001583	missense	140690	exon5			GCAACACTGAAAG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1113G>C	20.37:g.56090837C>G	ENSP00000476783:p.Gln371His	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	296	139	NM_001269044	0	0	0	0	0	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042881	0.36085	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15	5.24	3.07	0.35406	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.342601	0.21292	N	0.076960	T	0.15869	0.0382	L	0.37466	1.105	0.39176	D	0.962686	B;B;B;B;B	0.25390	0.025;0.077;0.03;0.077;0.125	B;B;B;B;B	0.28011	0.05;0.045;0.082;0.045;0.085	T	0.09271	-1.0682	10	0.72032	D	0.01	-35.7918	5.7172	0.17966	0.0:0.5692:0.2418:0.1889	.	371;371;371;371;371	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	H	371;371;371;371;371;109;371;371;166;371	ENSP00000415579:Q371H;ENSP00000243914:Q371H;ENSP00000360239:Q371H;ENSP00000415329:Q371H;ENSP00000392034:Q371H;ENSP00000437999:Q109H;ENSP00000413713:Q371H;ENSP00000403369:Q371H;ENSP00000439998:Q166H;ENSP00000399061:Q371H	ENSP00000243914:Q371H	Q	-	3	2	CTCFL	55524243	1.000000	0.71417	0.998000	0.56505	0.813000	0.45954	1.660000	0.37397	1.327000	0.45338	0.650000	0.86243	CAG	.		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		G	56090837	C	G	56090837	3	3	99	1	0	0	0	0	1	0	0	0	4007	564	20	4	902	4	CTCFL	20	56090837	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		56090837	6934683	60	8908											
PDE9A	5152	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	44185564	44185565	+	Frame_Shift_Ins	INS	-	-	G																															gattctttcaaagagaaaatINSggagaattttgactacagca																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr21:44185564_44185565insG	ENST00000291539.6	+	15	1376_1377	c.1316_1317insG	c.(1315-1320)atggagfs	p.E440fs	PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398234.3_Frame_Shift_Ins_p.E339fs|PDE9A_ENST00000398225.3_Frame_Shift_Ins_p.E399fs|PDE9A_ENST00000398227.3_Frame_Shift_Ins_p.E280fs|PDE9A_ENST00000539837.1_Frame_Shift_Ins_p.E312fs|PDE9A_ENST00000328862.6_Frame_Shift_Ins_p.E414fs|PDE9A_ENST00000349112.3_Frame_Shift_Ins_p.E312fs|PDE9A_ENST00000398224.3_Frame_Shift_Ins_p.E313fs|PDE9A_ENST00000335440.6_Frame_Shift_Ins_p.E338fs|PDE9A_ENST00000398236.3_Frame_Shift_Ins_p.E354fs|PDE9A_ENST00000335512.4_Frame_Shift_Ins_p.E380fs|PDE9A_ENST00000398232.3_Frame_Shift_Ins_p.E373fs|PDE9A_ENST00000380328.2_Frame_Shift_Ins_p.E387fs|PDE9A_ENST00000398229.3_Frame_Shift_Ins_p.E306fs	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	440	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	AAAGAGAAAATGGAGAATTTTG	0.48																																					p.M439fs		.											.	PDE9A-92	0			c.1316_1317insG						.																																			SO:0001589	frameshift_variant	5152	exon15			.	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1318dupG	21.37:g.44185566_44185566dupG	ENSP00000291539:p.Glu440fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	41	16	NM_002606	0	0	0	0	0	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Frame_Shift_Ins	INS	ENST00000291539.6	37	CCDS13690.1																																																																																			.		0.48	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			G	44185565	-	G	44185564	7	5	99	1	0	1	1	0	0	0	0	0	11681	1464	51	0	1454	0	PDE9A	21	44185564	Frame_Shift_Ins	INS	-	TCGA-DW-7841-01A-11D-2136-08		44185564	3944331	61	8909											
MICAL3	57553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18293564	18293564	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttggcattcagttcctcctCcgtgtaggttcttggctgga	4	15	11	11	1	2	0	1	0	1	0	5	1	5	1	3	4	0	5	3	4	1	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:18293564C>T	ENST00000441493.2	-	28	5813	c.5461G>A	c.(5461-5463)Gag>Aag	p.E1821K	MICAL3_ENST00000580469.1_5'UTR|XXbac-B461K10.4_ENST00000476405.1_RNA	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1821					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		AGTTCCTCCTCCGTGTAGGTT	0.602																																					p.E1821K		.											.	MICAL3-68	0			c.G5461A						.						78	81	80					22																	18293564		2181	4279	6460	SO:0001583	missense	57553	exon28			CCTCCTCCGTGTA	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.5461G>A	22.37:g.18293564C>T	ENSP00000416015:p.Glu1821Lys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	93	21	NM_015241	0	0	8	17	9	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305044	0.60305	.	.	ENSG00000093100	ENST00000441493	T	0.65178	-0.14	4.81	4.81	0.61882	.	0.182495	0.46442	D	0.000288	T	0.66519	0.2797	L	0.34521	1.04	0.80722	D	1	D	0.67145	0.996	P	0.60415	0.874	T	0.62407	-0.6861	10	0.21540	T	0.41	.	17.8904	0.88870	0.0:1.0:0.0:0.0	.	1821	Q7RTP6	MICA3_HUMAN	K	1821	ENSP00000416015:E1821K	ENSP00000416015:E1821K	E	-	1	0	XXbac-B461K10.4	16673564	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.818000	0.86416	2.215000	0.71742	0.462000	0.41574	GAG	.		0.602	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18293564	C	T	18293564	3	4	99	1	0	0	0	0	1	0	0	0	9596	864	30	2	567	2	MICAL3	22	18293564	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		18293564	33011002	62	8910											
AP1B1	162	hgsc.bcm.edu	37	chr22	29738275	29738275	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaggttggggcacccaccTgagtggccaaactgaggacc	9	5	16	11	0	0	2	0	2	0	0	0	4	0	4	4	6	1	2	4	6	1	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:29738275T>C	ENST00000405198.1	-	11	1566	c.1535A>G	c.(1534-1536)cAg>cGg	p.Q512R	AP1B1_ENST00000432560.2_Splice_Site_p.Q512R|AP1B1_ENST00000356015.2_Splice_Site_p.Q512R|AP1B1_ENST00000317368.7_Splice_Site_p.Q512R|AP1B1_ENST00000472057.1_5'Flank|AP1B1_ENST00000415447.1_Splice_Site_p.Q512R|AP1B1_ENST00000402502.1_Splice_Site_p.Q512R|AP1B1_ENST00000357586.2_Splice_Site_p.Q512R			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	512					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGCACCCACCTGAGTGGCCAA	0.587																																					p.Q512R		.											.	AP1B1-92	0			c.A1535G						.						55	49	51					22																	29738275		2203	4300	6503	SO:0001630	splice_region_variant	162	exon12			CCCACCTGAGTGG	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.1536+1A>G	22.37:g.29738275T>C		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	38	3	NM_001127	0	0	0	0	0	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Missense_Mutation	SNP	ENST00000405198.1	37	CCDS13855.1	.	.	.	.	.	.	.	.	.	.	T	15.83	2.949549	0.53186	.	.	ENSG00000100280	ENST00000357586;ENST00000356015;ENST00000432560;ENST00000405198;ENST00000317368;ENST00000402502;ENST00000415447;ENST00000421126	T;T;T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63	5.64	5.64	0.86602	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.30135	0.0755	L	0.55990	1.75	0.80722	D	1	P;B;B;P;P	0.47302	0.486;0.037;0.033;0.893;0.638	P;B;B;P;B	0.58331	0.837;0.145;0.035;0.801;0.387	T	0.00653	-1.1625	10	0.54805	T	0.06	-21.1529	15.5235	0.75885	0.0:0.0:0.0:1.0	.	65;512;512;512;512	B4DS79;F8WDL0;Q10567-2;Q10567;Q10567-3	.;.;.;AP1B1_HUMAN;.	R	512	ENSP00000350199:Q512R;ENSP00000348297:Q512R;ENSP00000400065:Q512R;ENSP00000384194:Q512R;ENSP00000319361:Q512R;ENSP00000386071:Q512R;ENSP00000387612:Q512R;ENSP00000400022:Q512R	ENSP00000319361:Q512R	Q	-	2	0	AP1B1	28068275	1.000000	0.71417	0.999000	0.59377	0.363000	0.29612	7.961000	0.87903	2.145000	0.66743	0.460000	0.39030	CAG	.		0.587	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127	Missense_Mutation	C	29738275	T	C	29738275	5	2	99	1	0	0	0	0	0	0	1	0	731	1594	55	3	1362	3	AP1B1	22	29738275	Splice_Site	SNP	T	TCGA-DW-7841-01A-11D-2136-08	11444711	29738275	21566291	63	8911											
SEC14L2	23541	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	30805476	30805477	+	Splice_Site	INS	-	-	T																															cgtctttttgttgttaaaggINStaagttgggaatttcttgtg																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:30805476_30805477insT	ENST00000312932.9	+	7	840		c.e7+1		SEC14L2_ENST00000402592.3_Splice_Site|SEC14L2_ENST00000405717.3_Splice_Site|RP4-539M6.19_ENST00000439838.1_Splice_Site|SEC14L2_ENST00000403484.1_Splice_Site	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)						positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	GTTGTTAAAGGTAAGTTGGGAA	0.436																																					.		.											.	SEC14L2-90	0			c.580+1->T						.																																			SO:0001630	splice_region_variant	23541	exon7			.	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"supernatant protein factor"	607558	"SEC14 (S. cerevisiae)-like 2"	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.580+1->T	22.37:g.30805477_30805477dupT		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	122	33	NM_033382	0	0	0	0	0	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Splice_Site	INS	ENST00000312932.9	37	CCDS13876.1																																																																																			.		0.436	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429	Intron	T	30805477	-	T	30805476	8	5	99	1	0	1	1	0	0	0	1	0	14014	1275	44	0	607	0	SEC14L2	22	30805476	Splice_Site	INS	-	TCGA-DW-7841-01A-11D-2136-08	1067201	30805476	20499090	64	8912											
MEI1	150365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42154472	42154472	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcgccagtacatggagggAgctgctcgccagagacagta	11	6	14	10	2	0	1	0	0	0	1	2	5	0	3	2	2	3	4	2	2	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:42154472A>C	ENST00000401548.3	+	18	2095	c.2055A>C	c.(2053-2055)ggA>ggC	p.G685G	MEI1_ENST00000540880.1_Silent_p.G3G|MEI1_ENST00000540833.1_Silent_p.G425G|MEI1_ENST00000400107.1_Silent_p.G53G|MEI1_ENST00000300398.4_5'UTR	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						ACATGGAGGGAGCTGCTCGCC	0.582																																					p.G685G		.											.	MEI1-70	0			c.A2055C						.						56	58	57					22																	42154472		2038	4190	6228	SO:0001819	synonymous_variant	150365	exon18			GGAGGGAGCTGCT	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.2055A>C	22.37:g.42154472A>C		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	36	12	NM_152513	0	0	0	0	0		Silent	SNP	ENST00000401548.3	37	CCDS46718.1																																																																																			.		0.582	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		C	42154472	A	C	42154472	2	2	99	1	0	0	0	0	0	0	0	1	9490	291	11	5		5	MEI1	22	42154472	Silent	SNP	A	TCGA-DW-7841-01A-11D-2136-08	11348996	42154472	9150094	65	8913											
POLDIP3	84271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	43010826	43010826	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctttcgccgccgccccgCgcttcctgatgagttcgtcc	2	11	10	18	6	0	2	0	2	0	0	5	2	3	2	7	0	0	2	7	0	0	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:43010826C>T	ENST00000252115.5	-	1	142	c.38G>A	c.(37-39)cGc>cAc	p.R13H	RNU12_ENST00000362512.1_lincRNA|POLDIP3_ENST00000348657.2_Missense_Mutation_p.R13H|POLDIP3_ENST00000339677.6_Missense_Mutation_p.R13H	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	13					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						CGCCGCCCCGCGCTTCCTGAT	0.667																																					p.R13H	Ovarian(52;967 1128 5875 19997 42537)	.											.	POLDIP3-90	0			c.G38A						.						45	50	48					22																	43010826		2203	4300	6503	SO:0001583	missense	84271	exon1			GCCCCGCGCTTCC		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"RNA binding motif (RRM) containing"	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.38G>A	22.37:g.43010826C>T	ENSP00000252115:p.Arg13His	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	110	26	NM_178136	0	0	5	7	2	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	.	.	.	.	.	.	.	.	.	.	C	34	5.316914	0.95682	.	.	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.76506	0.3997	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.974;0.998;0.992;0.965	T	0.79654	-0.1713	9	0.87932	D	0	-17.6392	17.5459	0.87861	0.0:1.0:0.0:0.0	.	13;13;13;13	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	H	13	.	ENSP00000252115:R13H	R	-	2	0	POLDIP3	41340770	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.800000	0.69108	2.439000	0.82584	0.557000	0.71058	CGC	.		0.667	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		T	43010826	C	T	43010826	3	4	99	1	0	0	0	0	1	0	0	0	12221	768	27	1	1263	1	POLDIP3	22	43010826	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	856354	43010826	8293740	66	8914											
MCAT	27349	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	43533107	43533107	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcttggtgtcctgaaatcaCcctgcaatctggaaagaggt	10	11	10	10	0	3	2	1	1	2	1	4	3	4	3	2	3	1	1	2	3	3	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:43533107C>T	ENST00000290429.6	-	3	754	c.709G>A	c.(709-711)Gtg>Atg	p.V237M	MCAT_ENST00000327555.5_Intron	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	237					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				CCTGAAATCACCCTGCAATCT	0.532											OREG0026613	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V237M		.											.	MCAT-91	0			c.G709A						.						194	185	188					22																	43533107		2203	4300	6503	SO:0001583	missense	27349	exon3			AAATCACCCTGCA	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.709G>A	22.37:g.43533107C>T	ENSP00000290429:p.Val237Met	Somatic	211	0	917	WXS	Illumina HiSeq	Phase_I	245	62	NM_173467	0	0	30	54	24	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	37	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667793	0.88348	.	.	ENSG00000100294	ENST00000290429	T	0.52295	0.67	5.13	5.13	0.70059	Acyl transferase/acyl hydrolase/lysophospholipase (1);Malonyl-CoA ACP transacylase, ACP-binding (1);Acyl transferase (1);	0.000000	0.85682	D	0.000000	T	0.80859	0.4704	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88241	0.2910	10	0.87932	D	0	-25.5062	18.5829	0.91178	0.0:1.0:0.0:0.0	.	237	Q8IVS2	FABD_HUMAN	M	237	ENSP00000290429:V237M	ENSP00000290429:V237M	V	-	1	0	MCAT	41863051	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.277000	0.78572	2.387000	0.81309	0.591000	0.81541	GTG	.		0.532	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467		T	43533107	C	T	43533107	3	4	99	1	0	0	0	0	1	0	0	0	9397	507	18	2	471	2	MCAT	22	43533107	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	522281	43533107	7771459	67	8915											
KIAA1522	57648	ucsc.edu;bcgsc.ca	37	chr1	33236309	33236309	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacccactccctccatcagcGgggcttagcagtgcctgatg	7	8	11	15	1	1	1	1	1	0	0	3	2	3	1	4	2	3	2	4	2	1	1	rs370409288		TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:33236309G>A	ENST00000373480.1	+	6	1455	c.1352G>A	c.(1351-1353)cGg>cAg	p.R451Q	KIAA1522_ENST00000401073.2_Missense_Mutation_p.R510Q|KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000373481.3_Missense_Mutation_p.R462Q	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	451	Pro-rich.									breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CTCCATCAGCGGGGCTTAGCA	0.657													G|||	1	0.000199681	0	0	5008	,	,		15500	0.001		0	False		,,,				2504	0				p.R510Q													.	KIAA1522-90	0			c.G1529A						.	G	GLN/ARG,GLN/ARG,	0,4066		0,0,2033	16	19	18		1352,1529,	3.6	1	1		18	1,8363		0,1,4181	no	missense,missense,intron	KIAA1522	NM_001198972.1,NM_020888.2,NM_001198973.1	43,43,	0,1,6214	AA,AG,GG		0.012,0.0,0.0080	possibly-damaging,possibly-damaging,	451/1036,510/1095,	33236309	1,12429	2033	4182	6215	SO:0001583	missense	57648	exon6			ATCAGCGGGGCTT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.1352G>A	1.37:g.33236309G>A	ENSP00000362579:p.Arg451Gln	Somatic	33	0		WXS	Illumina HiSeq		37	4	NM_020888	0	0	44	44	0	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.302446	0.40694	0.0	1.2E-4	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.12879	2.64;2.65;2.66	4.55	3.56	0.40772	.	0.231822	0.29529	N	0.011887	T	0.07324	0.0185	L	0.41236	1.265	0.25554	N	0.987056	P;P;P	0.37997	0.614;0.614;0.614	B;B;B	0.26770	0.073;0.073;0.073	T	0.24190	-1.0167	10	0.33141	T	0.24	-12.1615	2.7924	0.05392	0.2252:0.0:0.5308:0.244	.	462;451;510	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	Q	510;462;451	ENSP00000383851:R510Q;ENSP00000362580:R462Q;ENSP00000362579:R451Q	ENSP00000362579:R451Q	R	+	2	0	KIAA1522	33008896	0.998000	0.40836	1.000000	0.80357	0.923000	0.55619	1.042000	0.30303	2.225000	0.72522	0.462000	0.41574	CGG	.		0.657	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33236309	G	A	33236309	3	1	100	1	0	0	0	0	1	0	0	0	8259	1116	39	1	1551	1	KIAA1522	1	33236309	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08		33236309	216014312	1	8916											
FOXE3	2301	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	47882415	47882415	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggcaacccgggcaagggcaActactggacgctggaccccg	9	3	15	14	3	0	0	0	0	0	0	0	2	0	2	3	5	3	4	3	5	4	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:47882415A>C	ENST00000335071.2	+	1	672	c.428A>C	c.(427-429)aAc>aCc	p.N143T		NM_012186.2	NP_036318.1	Q13461	FOXE3_HUMAN	forkhead box E3	143					camera-type eye development (GO:0043010)|cell development (GO:0048468)|positive regulation of epithelial cell proliferation (GO:0050679)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|upper_aerodigestive_tract(1)	5				READ - Rectum adenocarcinoma(2;0.0908)		GGCAAGGGCAACTACTGGACG	0.687																																					p.N143T		.											.	FOXE3-130	0			c.A428C						.						41	43	43					1																	47882415		2203	4299	6502	SO:0001583	missense	2301	exon1			AGGGCAACTACTG	AF275722	CCDS550.1	1p32	2008-02-05			ENSG00000186790	ENSG00000186790		"Forkhead boxes"	3808	protein-coding gene	gene with protein product		601094		FKHL12		8825632	Standard	NM_012186		Approved	FREAC8	uc001crk.3	Q13461	OTTHUMG00000007954	ENST00000335071.2:c.428A>C	1.37:g.47882415A>C	ENSP00000334472:p.Asn143Thr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	103	30	NM_012186	1	0	1	2	0	Q5SVY9|Q9NQV9	Missense_Mutation	SNP	ENST00000335071.2	37	CCDS550.1	.	.	.	.	.	.	.	.	.	.	a	20.1	3.934136	0.73442	.	.	ENSG00000186790	ENST00000335071	D	0.95518	-3.73	3.45	3.45	0.39498	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.41097	U	0.000952	D	0.97467	0.9171	M	0.87328	2.875	0.54753	D	0.999982	D	0.71674	0.998	D	0.70487	0.969	D	0.97641	1.0148	10	0.62326	D	0.03	.	12.082	0.53675	1.0:0.0:0.0:0.0	.	143	Q13461	FOXE3_HUMAN	T	143	ENSP00000334472:N143T	ENSP00000334472:N143T	N	+	2	0	FOXE3	47655002	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	3.748000	0.55142	1.427000	0.47276	0.373000	0.22412	AAC	.		0.687	FOXE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021836.1	NM_012186		C	47882415	A	C	47882415	3	2	100	1	0	0	0	0	1	0	0	0	6023	43	2	5	430	5	FOXE3	1	47882415	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08	14646106	47882415	201368206	2	8917											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94054978	94054978	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacaaggttttcagacaccTttgggacaaaaaggtgagtg	13	9	12	7	0	1	2	1	1	0	1	1	3	1	3	1	3	0	2	1	3	3	3			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:94054978T>C	ENST00000370244.1	-	7	775		c.e7-2		RP5-1033H22.2_ENST00000417401.1_RNA|RP5-1033H22.2_ENST00000431770.1_RNA|RP5-1033H22.2_ENST00000427243.1_RNA|BCAR3_ENST00000370247.3_Splice_Site|BCAR3_ENST00000370243.1_Splice_Site|BCAR3_ENST00000260502.6_Splice_Site	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3						lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		TTCAGACACCTTTGGGACAAA	0.483																																					.		.											.	BCAR3-228	0			c.487-2A>G						.						41	41	41					1																	94054978		2203	4300	6503	SO:0001630	splice_region_variant	8412	exon6			GACACCTTTGGGA	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"SH2 domain containing"	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.487-2A>G	1.37:g.94054978T>C		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_003567	0	0	2	2	0	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Splice_Site	SNP	ENST00000370244.1	37	CCDS745.1	.	.	.	.	.	.	.	.	.	.	T	10.82	1.458136	0.26161	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7375	0.62827	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	BCAR3	93827566	1.000000	0.71417	0.996000	0.52242	0.119000	0.20118	7.280000	0.78610	2.052000	0.61016	0.533000	0.62120	.	.		0.483	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		Intron	C	94054978	T	C	94054978	5	2	100	1	0	0	0	0	0	0	1	0	1350	1623	56	3	2024	3	BCAR3	1	94054978	Splice_Site	SNP	T	TCGA-DW-7842-01A-11D-2136-08	46172563	94054978	155195643	3	8918											
SYPL2	284612	ucsc.edu	37	chr1	110022091	110022091	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacagggccagggccaggAccaggaccaggaccaggacc	11	1	16	13	0	0	0	0	0	0	0	0	5	0	5	6	7	0	0	6	7	0	0	rs201865079	byFrequency	TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:110022091A>G	ENST00000369872.3	+	6	956	c.740A>G	c.(739-741)gAc>gGc	p.D247G	SYPL2_ENST00000401021.3_Missense_Mutation_p.D183G	NM_001040709.1	NP_001035799.1	Q5VXT5	SYPL2_HUMAN	synaptophysin-like 2	247					cellular calcium ion homeostasis (GO:0006874)|substantia nigra development (GO:0021762)	integral component of synaptic vesicle membrane (GO:0030285)	transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)		cagggccaggaccaggaccag	0.602													A|||	11	0.00219649	0	0.0014	5008	,	,		16187	0		0	False		,,,				2504	0.0102				p.D247G													.	SYPL2-91	0			c.A740G						.	A	GLY/ASP	3,4047		0,3,2022	77	90	86		740	0.7	0.8	1		86	49,8357		0,49,4154	yes	missense	SYPL2	NM_001040709.1	94	0,52,6176	GG,GA,AA		0.5829,0.0741,0.4175	benign	247/273	110022091	52,12404	2025	4203	6228	SO:0001583	missense	284612	exon6			GCCAGGACCAGGA	AK131459	CCDS41365.1	1p13.3	2008-02-05			ENSG00000143028	ENSG00000143028			27638	protein-coding gene	gene with protein product	"mitsugumin-29"					12975309	Standard	NM_001040709		Approved	Mg29	uc001dxp.3	Q5VXT5	OTTHUMG00000010969	ENST00000369872.3:c.740A>G	1.37:g.110022091A>G	ENSP00000358888:p.Asp247Gly	Somatic	90	1		WXS	Illumina HiSeq		83	1	NM_001040709	0	0	18	24	6	A8K0E8|A8KAL7|I0IT67|Q6ZMX1	Missense_Mutation	SNP	ENST00000369872.3	37	CCDS41365.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	A	6.239	0.412302	0.11812	7.41E-4	0.005829	ENSG00000143028	ENST00000401021;ENST00000369872	T	0.30714	1.52	0.736	0.736	0.18307	.	1.039220	0.07570	N	0.918460	T	0.06371	0.0164	N	0.08118	0	0.22552	N	0.998991	P;P	0.43392	0.805;0.805	P;P	0.47134	0.539;0.539	T	0.14811	-1.0459	10	0.17832	T	0.49	.	3.6722	0.08279	1.0:0.0:0.0:0.0	.	183;247	B4DYR7;Q5VXT5	.;SYPL2_HUMAN	G	183;247	ENSP00000358888:D247G	ENSP00000358888:D247G	D	+	2	0	SYPL2	109823614	0.999000	0.42202	0.830000	0.32933	0.496000	0.33645	0.643000	0.24750	0.115000	0.18071	0.113000	0.15668	GAC	A|0.994;G|0.006		0.602	SYPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030191.1	NM_001006603		G	110022091	A	G	110022091	3	3	100	1	0	0	0	0	1	0	0	0	15495	275	10	3	762	3	SYPL2	1	110022091	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08	15967113	110022091	139228530	4	8919											
PEA15	8682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160181403	160181403	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgaagatctagaacagctCaagtcggcctgcaaggaaga	14	7	11	9	1	2	4	1	1	1	3	3	5	2	5	1	2	3	2	1	2	6	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:160181403C>A	ENST00000360472.4	+	2	257	c.69C>A	c.(67-69)ctC>ctA	p.L23L	PEA15_ENST00000368077.1_Silent_p.L23L|RP11-536C5.7_ENST00000418602.1_RNA|PEA15_ENST00000368076.1_Silent_p.L44L|PEA15_ENST00000488858.1_3'UTR	NM_003768.3	NP_003759.1	Q15121	PEA15_HUMAN	phosphoprotein enriched in astrocytes 15	23	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|DNA damage checkpoint (GO:0000077)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of glucose import (GO:0046325)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|response to morphine (GO:0043278)|transport (GO:0006810)	cytoplasm (GO:0005737)|microtubule associated complex (GO:0005875)				large_intestine(1)|lung(4)	5	all_cancers(52;3.11e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TAGAACAGCTCAAGTCGGCCT	0.542																																					p.L23L		.											.	PEA15-658	0			c.C69A						.						135	112	120					1																	160181403		2203	4300	6503	SO:0001819	synonymous_variant	8682	exon2			ACAGCTCAAGTCG	Y13736	CCDS1199.1, CCDS72954.1	1q21.1	2008-07-18			ENSG00000162734	ENSG00000162734			8822	protein-coding gene	gene with protein product	"Phosphoprotein enriched in astrocytes, 15kD", "homolog of mouse MAT-1 oncogene"	603434				9205133	Standard	XM_005245564		Approved	HMAT1, MAT1, PED, PEA-15, MAT1H, HUMMAT1H	uc001fvk.3	Q15121	OTTHUMG00000031605	ENST00000360472.4:c.69C>A	1.37:g.160181403C>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	100	16	NM_003768	0	0	87	106	19	B1AKZ3|O00511	Silent	SNP	ENST00000360472.4	37	CCDS1199.1																																																																																			.		0.542	PEA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077407.1	NM_003768		A	160181403	C	A	160181403	2	1	100	1	0	0	0	0	0	0	0	1	11737	813	29	4		4	PEA15	1	160181403	Silent	SNP	C	TCGA-DW-7842-01A-11D-2136-08	50159312	160181403	89069218	5	8920											
DENND1B	163486	hgsc.bcm.edu	37	chr1	197684159	197684159	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaaaaattatgtggtaccaAcctggtctccaaagtcctct	13	12	6	10	0	2	0	0	0	2	0	4	0	3	0	4	2	2	1	4	2	7	3			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:197684159A>G	ENST00000367396.3	-	3	296		c.e3+1		DENND1B_ENST00000235453.4_Splice_Site|DENND1B_ENST00000400967.2_Splice_Site	NM_144977.4	NP_659414.2	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B						positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|kidney(2)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	22						tGTGGTACCAACCTGGTCTCC	0.328																																					.		.											.	DENND1B-44	0			c.126+2T>C						.						56	54	55					1																	197684159		1808	4072	5880	SO:0001630	splice_region_variant	163486	exon4			GTACCAACCTGGT	BC016588	CCDS41452.2, CCDS72996.1, CCDS72997.1	1q31.3	2012-10-03	2005-08-17	2005-08-17	ENSG00000213047	ENSG00000213047		"DENN/MADD domain containing"	28404	protein-coding gene	gene with protein product		613292	"family with sequence similarity 31, member B", "chromosome 1 open reading frame 218"	FAM31B, C1orf218		12477932	Standard	NM_144977		Approved	MGC27044, FLJ20054	uc021pgu.1	Q6P3S1	OTTHUMG00000035653	ENST00000367396.3:c.126+1T>C	1.37:g.197684159A>G		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_001195215	0	0	0	0	0	B5MD89|D3PFD5|Q5T3B8|Q5T3B9|Q5T3C1|Q5TAI8|Q6B0I8|Q8NDT1|Q8TBE6|Q9H774|Q9NXU2	Splice_Site	SNP	ENST00000367396.3	37	CCDS41452.2	.	.	.	.	.	.	.	.	.	.	A	19.22	3.785719	0.70337	.	.	ENSG00000213047	ENST00000542760;ENST00000450419;ENST00000235453;ENST00000367396;ENST00000400967	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3422	0.66636	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DENND1B	195950782	1.000000	0.71417	0.999000	0.59377	0.838000	0.47535	7.530000	0.81962	2.185000	0.69588	0.455000	0.32223	.	.		0.328	DENND1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086539.1	NM_144977	Intron	G	197684159	A	G	197684159	5	3	100	1	0	0	0	0	0	0	1	0	4438	57	2	3	2324	3	DENND1B	1	197684159	Splice_Site	SNP	A	TCGA-DW-7842-01A-11D-2136-08	37502756	197684159	51566462	6	8921											
APOB	338	bcgsc.ca	37	chr2	21232458	21232458	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggtggtaatcaaatgactTtaatttctttatcaacatgt	12	17	6	6	0	3	1	2	1	1	0	3	1	3	1	0	2	1	1	0	2	5	6			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr2:21232458T>G	ENST00000233242.1	-	26	7409	c.7282A>C	c.(7282-7284)Aag>Cag	p.K2428Q		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2428					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAAATGACTTTAATTTCTTT	0.338																																					p.K2428Q													.	APOB-175	0			c.A7282C						.						76	74	75					2																	21232458		2203	4300	6503	SO:0001583	missense	338	exon26			ATGACTTTAATTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7282A>C	2.37:g.21232458T>G	ENSP00000233242:p.Lys2428Gln	Somatic	108	0		WXS	Illumina HiSeq	Phase_1	107	4	NM_000384	0	0	0	0	0	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.746669	0.30955	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00976	5.48	5.49	1.64	0.23874	.	0.368885	0.23635	N	0.046088	T	0.01061	0.0035	L	0.43152	1.355	0.09310	N	0.999995	B	0.17038	0.02	B	0.13407	0.009	T	0.44590	-0.9318	10	0.44086	T	0.13	.	8.4238	0.32716	0.0:0.0716:0.2644:0.664	.	2428	P04114	APOB_HUMAN	Q	2428	ENSP00000233242:K2428Q	ENSP00000233242:K2428Q	K	-	1	0	APOB	21085963	0.794000	0.28838	0.972000	0.41901	0.981000	0.71138	2.774000	0.47694	0.870000	0.35726	0.459000	0.35465	AAG	.		0.338	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21232458	T	G	21232458	3	3	100	1	0	0	0	0	1	0	0	0	785	1850	64	5	6425	5	APOB	2	21232458	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08		21232458	221966915	7	8922											
PROM2	150696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95941238	95941238	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggccctactgaatgagctgGcctccgtgaaggtgaatgag	10	8	14	9	1	0	5	0	5	0	0	1	5	1	5	3	3	2	1	3	3	4	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr2:95941238G>A	ENST00000317620.9	+	2	407	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	PROM2_ENST00000542147.1_Missense_Mutation_p.A92T|PROM2_ENST00000403131.2_Missense_Mutation_p.A92T|PROM2_ENST00000317668.4_Missense_Mutation_p.A92T|PROM2_ENST00000463580.1_3'UTR	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	92					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						GAATGAGCTGGCCTCCGTGAA	0.602																																					p.A92T		.											.	PROM2-91	0			c.G274A						.						99	87	91					2																	95941238		2203	4300	6503	SO:0001583	missense	150696	exon2			GAGCTGGCCTCCG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.274G>A	2.37:g.95941238G>A	ENSP00000318270:p.Ala92Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	82	27	NM_001165977	0	0	0	0	0	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.194115	0.38707	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.57	-4.2	0.03823	.	1.178410	0.06360	N	0.711489	T	0.34077	0.0885	L	0.44542	1.39	0.09310	N	1	P	0.43578	0.811	B	0.40602	0.334	T	0.37079	-0.9721	10	0.14252	T	0.57	-1.8729	15.0393	0.71777	0.0:0.0:0.1886:0.8114	.	92	Q8N271	PROM2_HUMAN	T	92	ENSP00000385716:A92T;ENSP00000318520:A92T;ENSP00000318270:A92T;ENSP00000442542:A92T	ENSP00000318270:A92T	A	+	1	0	PROM2	95304965	0.000000	0.05858	0.001000	0.08648	0.580000	0.36256	-2.235000	0.01202	-0.468000	0.06922	0.462000	0.41574	GCC	.		0.602	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		A	95941238	G	A	95941238	3	1	100	1	0	0	0	0	1	0	0	0	12585	1203	42	2	280	2	PROM2	2	95941238	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	74708780	95941238	147258135	8	8923											
ATG16L1	55054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234173559	234173559	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgcagaatgtttgcagacTatctctgacctggagacgga	11	11	11	8	1	1	4	0	1	1	3	2	6	1	5	1	2	2	3	1	2	2	3			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr2:234173559T>C	ENST00000392017.4	+	5	668	c.411T>C	c.(409-411)acT>acC	p.T137T	ATG16L1_ENST00000347464.5_Intron|ATG16L1_ENST00000392018.1_Silent_p.T137T|ATG16L1_ENST00000392020.4_Silent_p.T137T|ATG16L1_ENST00000373525.5_Intron	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	137					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		GTTTGCAGACTATCTCTGACC	0.527																																					p.T137T		.											.	ATG16L1-90	0			c.T411C						.						109	97	101					2																	234173559		2203	4300	6503	SO:0001819	synonymous_variant	55054	exon5			GCAGACTATCTCT	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.411T>C	2.37:g.234173559T>C		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	114	38	NM_017974	0	0	17	25	8	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Silent	SNP	ENST00000392017.4	37	CCDS2503.2																																																																																			.		0.527	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		C	234173559	T	C	234173559	2	2	100	1	0	0	0	0	0	0	0	1	1092	1509	53	3		3	ATG16L1	2	234173559	Silent	SNP	T	TCGA-DW-7842-01A-11D-2136-08	138232321	234173559	9025814	9	8924											
SCRN1	9805	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr7	29994945	29994945	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatcattatggcataggtcCttggaacttggtcgattgaa	10	15	10	6	1	1	1	1	1	0	0	3	3	2	2	1	4	1	1	1	4	5	6	rs75604334	byFrequency	TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr7:29994945C>T	ENST00000426154.1	-	3	367	c.191G>A	c.(190-192)aGg>aAg	p.R64K	SCRN1_ENST00000494620.1_5'UTR|SCRN1_ENST00000409497.1_Missense_Mutation_p.R64K|SCRN1_ENST00000409570.1_Missense_Mutation_p.R64K|SCRN1_ENST00000416113.2_5'Flank|SCRN1_ENST00000425819.2_5'UTR|SCRN1_ENST00000434476.2_Missense_Mutation_p.R84K|SCRN1_ENST00000242059.5_Missense_Mutation_p.R64K	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	64					exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						GGCATAGGTCCTTGGAACTTG	0.488																																					p.R84K		.											.	SCRN1-92	0			c.G251A						.						109	105	107					7																	29994945		2203	4300	6503	SO:0001583	missense	9805	exon3			TAGGTCCTTGGAA	D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.191G>A	7.37:g.29994945C>T	ENSP00000409068:p.Arg64Lys	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	164	53	NM_001145514	0	0	97	152	55	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	37	CCDS5422.1	.	.	.	.	.	.	.	.	.	.	C	5.644	0.303441	0.10678	.	.	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000409497;ENST00000434476;ENST00000421434;ENST00000438497;ENST00000409570	T;T;T;T;T;T;T	0.28666	3.37;3.37;3.37;3.35;2.36;1.63;1.6	5.7	3.89	0.44902	.	0.133460	0.52532	N	0.000069	T	0.14184	0.0343	N	0.11789	0.175	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.09487	-1.0672	9	.	.	.	-20.2169	6.2825	0.21015	0.0:0.6834:0.0:0.3166	.	84;64	C9JPG0;Q12765	.;SCRN1_HUMAN	K	64;64;64;84;64;64;64	ENSP00000242059:R64K;ENSP00000409068:R64K;ENSP00000386872:R64K;ENSP00000388942:R84K;ENSP00000413184:R64K;ENSP00000406289:R64K;ENSP00000387052:R64K	.	R	-	2	0	SCRN1	29961470	1.000000	0.71417	0.996000	0.52242	0.879000	0.50718	1.824000	0.39072	1.426000	0.47256	0.557000	0.71058	AGG	C|0.982;G|0.018		0.488	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2	NM_014766		T	29994945	C	T	29994945	3	4	100	1	0	0	0	0	1	0	0	0	13970	681	24	2	1077	2	SCRN1	7	29994945	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		29994945	129143718	10	8925											
DOCK4	9732	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	111368503	111368503	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tagcgggacggggcgccgcaGagtccgctcgtagacgctgt	6	6	17	12	7	0	2	0	0	0	2	2	3	1	3	2	3	1	4	2	3	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr7:111368503G>C	ENST00000437633.1	-	52	5984	c.5728C>G	c.(5728-5730)Ctg>Gtg	p.L1910V	DOCK4_ENST00000428084.1_Missense_Mutation_p.L1919V|DOCK4_ENST00000494651.2_Missense_Mutation_p.L793V	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1910	Pro-rich.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GGGCGCCGCAGAGTCCGCTCG	0.726																																					p.L1910V		.											.	DOCK4-26	0			c.C5728G						.						22	29	27					7																	111368503		2060	4183	6243	SO:0001583	missense	9732	exon52			GCCGCAGAGTCCG		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.5728C>G	7.37:g.111368503G>C	ENSP00000404179:p.Leu1910Val	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	113	6	NM_014705	0	0	21	21	0	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.033027	0.35893	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	T;T;T	0.32023	1.47;1.47;1.47	5.59	3.43	0.39272	.	0.139401	0.49305	N	0.000144	T	0.15392	0.0371	N	0.19112	0.55	0.29489	N	0.855803	B;B;B;B;B;P	0.39181	0.0;0.045;0.046;0.001;0.036;0.663	B;B;B;B;B;B	0.33196	0.002;0.045;0.019;0.002;0.009;0.159	T	0.07635	-1.0762	10	0.34782	T	0.22	.	7.1126	0.25399	0.1735:0.1686:0.6579:0.0	.	779;793;1955;1910;1881;223	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2;Q8N1I0-4	.;.;.;DOCK4_HUMAN;.;.	V	1898;1919;793;1910;1869	ENSP00000410746:L1919V;ENSP00000440944:L793V;ENSP00000404179:L1910V	ENSP00000345432:L1869V	L	-	1	2	DOCK4	111155739	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.165000	0.31822	1.340000	0.45581	0.655000	0.94253	CTG	.		0.726	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111368503	G	C	111368503	3	2	100	1	0	0	0	0	1	0	0	0	4700	933	33	4	176	4	DOCK4	7	111368503	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	81373558	111368503	47770160	11	8926											
GALNT11	63917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151805279	151805279	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacagctcgtcccctgtcgTccgcggagggttcaactggg	5	9	13	14	4	1	0	1	0	0	0	5	1	3	1	3	3	3	2	3	3	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr7:151805279T>C	ENST00000434507.1	+	8	1306	c.869T>C	c.(868-870)gTc>gCc	p.V290A	GALNT11_ENST00000452146.2_Missense_Mutation_p.V209A|GALNT11_ENST00000430044.2_Missense_Mutation_p.V290A|GALNT11_ENST00000422997.2_3'UTR|GALNT11_ENST00000320311.2_Missense_Mutation_p.V290A			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	290					cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		TCCCCTGTCGTCCGCGGAGGG	0.602																																					p.V290A		.											.	GALNT11-90	0			c.T869C						.						70	69	69					7																	151805279		2203	4300	6503	SO:0001583	missense	63917	exon6			CTGTCGTCCGCGG	AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19875	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 11"	615130	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"			11925450	Standard	NM_022087		Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000434507.1:c.869T>C	7.37:g.151805279T>C	ENSP00000416787:p.Val290Ala	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	143	106	NM_022087	0	0	155	418	263	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Missense_Mutation	SNP	ENST00000434507.1	37	CCDS5930.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.690916	0.88735	.	.	ENSG00000178234	ENST00000430044;ENST00000452146;ENST00000443352;ENST00000434507;ENST00000320311	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	N	0.13235	0.315	0.80722	D	1	D;D;D	0.89917	0.988;1.0;0.998	D;D;D	0.91635	0.934;0.999;0.971	T	0.58301	-0.7660	10	0.22109	T	0.4	.	15.2076	0.73192	0.0:0.0:0.0:1.0	.	209;290;290	B7Z5G5;B3KWF4;Q8NCW6	.;.;GLT11_HUMAN	A	290;209;290;290;290	ENSP00000395122:V290A;ENSP00000393399:V209A;ENSP00000416787:V290A;ENSP00000315835:V290A	ENSP00000315835:V290A	V	+	2	0	GALNT11	151436212	1.000000	0.71417	0.696000	0.30242	0.671000	0.39405	6.290000	0.72712	1.980000	0.57719	0.528000	0.53228	GTC	.		0.602	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087		C	151805279	T	C	151805279	3	2	100	1	0	0	0	0	1	0	0	0	6229	1667	58	3	887	3	GALNT11	7	151805279	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08	40436776	151805279	7333384	12	8927											
MYOM2	9172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	2063780	2063780	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aattaaatgtgacaaagctaCtggcattattgagatggtga	15	12	10	4	0	0	3	0	3	0	1	0	4	0	3	0	2	2	2	0	2	6	4			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr8:2063780C>T	ENST00000262113.4	+	26	3350	c.3209C>T	c.(3208-3210)aCt>aTt	p.T1070I	MYOM2_ENST00000523438.1_Missense_Mutation_p.T495I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1070					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GACAAAGCTACTGGCATTATT	0.383																																					p.T1070I		.											.	MYOM2-95	0			c.C3209T						.						180	173	175					8																	2063780		2203	4300	6503	SO:0001583	missense	9172	exon26			AAGCTACTGGCAT		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7614	protein-coding gene	gene with protein product		603509	"myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa"				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.3209C>T	8.37:g.2063780C>T	ENSP00000262113:p.Thr1070Ile	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	79	36	NM_003970	0	0	0	1	1	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106096	0.37145	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.43688	0.94;0.94	5.32	5.32	0.75619	.	0.155634	0.56097	D	0.000032	T	0.50292	0.1607	M	0.72118	2.19	0.09310	N	1	P	0.43542	0.81	P	0.47118	0.538	T	0.53627	-0.8412	10	0.72032	D	0.01	.	11.9689	0.53051	0.1347:0.7352:0.13:0.0	.	1070	P54296	MYOM2_HUMAN	I	1070;495	ENSP00000262113:T1070I;ENSP00000428396:T495I	ENSP00000262113:T1070I	T	+	2	0	MYOM2	2051187	0.950000	0.32346	0.017000	0.16124	0.264000	0.26372	3.170000	0.50816	2.495000	0.84180	0.655000	0.94253	ACT	.		0.383	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2063780	C	T	2063780	3	4	100	1	0	0	0	0	1	0	0	0	10117	565	20	2	3307	2	MYOM2	8	2063780	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		2063780	144300242	13	8928											
OPLAH	26873	hgsc.bcm.edu	37	chr8	145110805	145110805	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagatgtcccctgtcttggTcacctctgcctggcaacctg	5	11	10	15	0	3	1	1	0	2	1	4	1	4	1	5	2	2	2	5	2	1	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr8:145110805T>C	ENST00000426825.1	-	16	2215	c.2134A>G	c.(2134-2136)Acc>Gcc	p.T712A	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	712					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)			CCTGTCTTGGTCACCTCTGCC	0.652																																					p.T712A		.											.	OPLAH-68	0			c.A2134G						.						36	37	37					8																	145110805		2033	4178	6211	SO:0001583	missense	26873	exon16			TCTTGGTCACCTC	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.2134A>G	8.37:g.145110805T>C	ENSP00000475943:p.Thr712Ala	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	14	2	NM_017570	0	0	21	21	0	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	T	10.89	1.477922	0.26511	.	.	ENSG00000178814	ENST00000426825	.	.	.	5.54	5.54	0.83059	.	0.144870	0.64402	D	0.000009	T	0.54191	0.1843	.	.	.	0.44547	D	0.997501	B	0.23806	0.091	B	0.33254	0.16	T	0.62789	-0.6780	7	0.45353	T	0.12	.	13.6163	0.62110	0.0:0.0:0.0:1.0	.	712	O14841	OPLA_HUMAN	A	712	.	ENSP00000412071:T712A	T	-	1	0	OPLAH	145182793	1.000000	0.71417	0.860000	0.33809	0.281000	0.26958	5.722000	0.68485	2.108000	0.64289	0.533000	0.62120	ACC	.		0.652	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		C	145110805	T	C	145110805	3	2	100	1	0	0	0	0	1	0	0	0	10902	1667	58	3	1782	3	OPLAH	8	145110805	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08	143047025	145110805	1253217	14	8929											
KIAA1529	100499483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	100117239	100117239	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgtggaccttattttcatAgagaaaatccagcggttgct	10	14	9	8	1	2	1	1	0	1	1	3	3	3	2	2	2	2	2	2	2	4	5			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr9:100117239A>G	ENST00000357054.1	+	35	4193	c.3258A>G	c.(3256-3258)atA>atG	p.I1086M	CCDC180_ENST00000529487.1_Missense_Mutation_p.I1115M|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.I1115M|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1086						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TTATTTTCATAGAGAAAATCC	0.418																																					p.I1115M		.											.	.	0			c.A3345G						.						74	75	75					9																	100117239		2203	4300	6503	SO:0001583	missense	0	exon24			TTTCATAGAGAAA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3258A>G	9.37:g.100117239A>G	ENSP00000349562:p.Ile1086Met	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	108	48	NM_020893	0	0	0	1	1	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	A	14.21	2.467293	0.43839	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.10099	3.17;2.91;2.91	5.16	-0.113	0.13568	.	0.642133	0.16850	N	0.196982	T	0.04952	0.0133	N	0.16478	0.41	0.80722	D	1	B;P	0.37370	0.083;0.592	B;B	0.35240	0.044;0.198	T	0.49707	-0.8911	10	0.27785	T	0.31	-2.8056	4.2902	0.10874	0.6091:0.0:0.2494:0.1415	.	1254;1086	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	M	1086;1115;1115	ENSP00000349562:I1086M;ENSP00000364348:I1115M;ENSP00000434727:I1115M	ENSP00000349562:I1086M	I	+	3	3	C9orf174	99157060	0.990000	0.36364	0.986000	0.45419	0.999000	0.98932	0.166000	0.16583	0.022000	0.15160	0.533000	0.62120	ATA	.		0.418	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		G	100117239	A	G	100117239	3	3	100	1	0	0	0	0	1	0	0	0	8261	410	15	3	3352	3	KIAA1529	9	100117239	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		100117239	41096192	15	8930											
DNAJC25-GNG10	2790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	114429094	114429094	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgctgtccctttgtttcaGgtctctcaggcagctgcaga	5	14	11	11	0	3	1	2	0	1	1	5	1	4	1	1	2	3	6	1	2	0	3			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr9:114429094G>A	ENST00000374293.4	+	2	381		c.e2-1		DNAJC25_ENST00000556107.1_Splice_Site|DNAJC25-GNG10_ENST00000374294.3_Splice_Site	NM_001017998.3|NM_001198664.1	NP_001017998.1|NP_001185593.1	P50151	GBG10_HUMAN	guanine nucleotide binding protein (G protein), gamma 10						cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			kidney(1)	1						CTTTGTTTCAGGTCTCTCAGG	0.522																																					.		.											.	DNAJC25-GNG10-159	0			c.337-1G>A						.						80	67	71					9																	114429094		2203	4300	6503	SO:0001630	splice_region_variant	552891	exon2			GTTTCAGGTCTCT		CCDS35107.1	9q31.3	2010-08-17			ENSG00000242616	ENSG00000242616			4402	protein-coding gene	gene with protein product		604389				7665596	Standard	NM_001017998		Approved			P50151	OTTHUMG00000157193	ENST00000374293.4:c.82-1G>A	9.37:g.114429094G>A		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	43	14	NM_004125	0	0	0	1	1	Q3B7K2|Q4VC27	Splice_Site	SNP	ENST00000374293.4	37	CCDS35107.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486423	0.84854	.	.	ENSG00000059769;ENSG00000244115;ENSG00000242616	ENST00000556107;ENST00000374294;ENST00000374293	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1488	0.93479	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAJC25-GNG10;GNG10;DNAJC25	113468915	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	9.460000	0.97641	2.688000	0.91661	0.655000	0.94253	.	.		0.522	GNG10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053644.2		Intron	A	114429094	G	A	114429094	5	1	100	1	0	0	0	0	0	0	1	0	4655	1014	35	2	342	2	DNAJC25-GNG10	9	114429094	Splice_Site	SNP	G	TCGA-DW-7842-01A-11D-2136-08	14311855	114429094	26784337	16	8931											
ZER1	10444	hgsc.bcm.edu	37	chr9	131513498	131513498	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcaggccggtgctccgtgTaggcctcgatggcattcagc	5	10	13	13	3	2	0	2	0	1	0	5	1	3	0	3	4	2	3	3	4	1	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr9:131513498T>C	ENST00000291900.2	-	7	1494	c.1088A>G	c.(1087-1089)tAc>tGc	p.Y363C	snoU13_ENST00000459043.1_RNA|ZER1_ENST00000494461.1_5'Flank	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	363					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						GTGCTCCGTGTAGGCCTCGAT	0.602																																					p.Y363C		.											.	ZER1-91	0			c.A1088G						.						93	76	82					9																	131513498		2203	4300	6503	SO:0001583	missense	10444	exon7			TCCGTGTAGGCCT	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1088A>G	9.37:g.131513498T>C	ENSP00000291900:p.Tyr363Cys	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	34	3	NM_006336	0	0	61	61	0	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	37	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.785754	0.70337	.	.	ENSG00000160445	ENST00000291900	T	0.07688	3.17	5.24	5.24	0.73138	Armadillo-type fold (1);	0.060055	0.64402	D	0.000002	T	0.22781	0.0550	L	0.51914	1.62	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.00425	-1.1747	10	0.44086	T	0.13	-35.0868	14.3759	0.66874	0.0:0.0:0.0:1.0	.	363	Q7Z7L7	ZER1_HUMAN	C	363	ENSP00000291900:Y363C	ENSP00000291900:Y363C	Y	-	2	0	ZER1	130553319	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	7.499000	0.81566	2.011000	0.59026	0.254000	0.18369	TAC	.		0.602	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		C	131513498	T	C	131513498	3	2	100	1	0	0	0	0	1	0	0	0	17657	1638	57	3	1252	3	ZER1	9	131513498	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08	17084404	131513498	9699933	17	8932											
VIM	7431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	17276732	17276732	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccaaccggaacaatgacgCcctgcgccaggcaaagcagg	12	3	12	14	3	0	1	0	1	0	0	0	2	0	2	4	3	5	2	4	3	4	0			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr10:17276732C>G	ENST00000224237.5	+	5	1068	c.923C>G	c.(922-924)gCc>gGc	p.A308G	RP11-124N14.3_ENST00000456355.1_RNA|VIM_ENST00000544301.1_Missense_Mutation_p.A308G			P08670	VIME_HUMAN	vimentin	308	Coil 2.|Rod.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AACAATGACGCCCTGCGCCAG	0.512																																					p.A308G		.											.	VIM-291	0			c.C923G						.						94	89	91					10																	17276732		2203	4300	6503	SO:0001583	missense	7431	exon6			ATGACGCCCTGCG	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.923C>G	10.37:g.17276732C>G	ENSP00000224237:p.Ala308Gly	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	116	17	NM_003380	3	3	2221	2592	365	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	37	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.627666	0.87560	.	.	ENSG00000026025	ENST00000544301;ENST00000224237;ENST00000545533;ENST00000421459	D;D;D	0.89681	-2.55;-2.55;-2.55	6.05	6.05	0.98169	Filament (1);	0.000000	0.46442	D	0.000298	D	0.95439	0.8519	M	0.91090	3.175	0.80722	D	1	D;D;D;D	0.69078	0.989;0.985;0.995;0.997	P;P;D;D	0.69479	0.897;0.902;0.941;0.964	D	0.92981	0.6406	10	0.18710	T	0.47	.	20.6031	0.99464	0.0:1.0:0.0:0.0	.	295;295;308;308	F5H288;B3KRK8;B0YJC4;P08670	.;.;.;VIME_HUMAN	G	308;308;295;134	ENSP00000446007:A308G;ENSP00000224237:A308G;ENSP00000391842:A134G	ENSP00000224237:A308G	A	+	2	0	VIM	17316738	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	7.811000	0.86092	2.881000	0.98747	0.637000	0.83480	GCC	.		0.512	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		G	17276732	C	G	17276732	3	3	100	1	0	0	0	0	1	0	0	0	17199	739	26	4	941	4	VIM	10	17276732	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		17276732	118258015	18	8933											
ARHGAP21	57584	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	24885703	24885704	+	Frame_Shift_Ins	INS	-	-	G																															tggtgggcagtcatctagtcINSggacgccgaaagttcctgta																										TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr10:24885703_24885704insG	ENST00000396432.2	-	17	3928_3929	c.3442_3443insC	c.(3442-3444)cgafs	p.R1148fs	ARHGAP21_ENST00000320481.6_Frame_Shift_Ins_p.R935fs|ARHGAP21_ENST00000493154.1_5'Flank	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1147	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						GTCATCTAGTCGGACGCCGAAA	0.455																																					p.R1148fs		.											.	ARHGAP21-235	0			c.3443_3444insC						.																																			SO:0001589	frameshift_variant	57584	exon17			.	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.3443dupC	10.37:g.24885705_24885705dupG	ENSP00000379709:p.Arg1148fs	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	99	42	NM_020824	0	0	0	0	0	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Ins	INS	ENST00000396432.2	37	CCDS7144.2																																																																																			.		0.455	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		G	24885704	-	G	24885703	7	5	100	1	0	1	1	0	0	0	0	0	871	884	31	0	2473	0	ARHGAP21	10	24885703	Frame_Shift_Ins	INS	-	TCGA-DW-7842-01A-11D-2136-08	7608971	24885703	110649044	19	8934											
C11orf49	79096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47074069	47074069	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaactgtgggcaaaaatggcGgtaagtcttcccaaattctt	12	11	10	8	1	2	0	0	0	2	0	3	1	3	0	1	3	1	2	1	3	5	4			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:47074069G>T	ENST00000278460.7	+	3	339	c.280G>T	c.(280-282)Gat>Tat	p.D94Y	C11orf49_ENST00000378618.2_Splice_Site_p.D94Y|C11orf49_ENST00000543718.1_Intron|C11orf49_ENST00000395460.2_Splice_Site_p.D94Y|C11orf49_ENST00000527268.1_3'UTR|C11orf49_ENST00000536126.1_5'UTR|C11orf49_ENST00000378615.3_Splice_Site_p.D94Y	NM_001003677.1|NM_024113.3	NP_001003677.1|NP_077018.1	Q9H6J7	CK049_HUMAN	chromosome 11 open reading frame 49	94						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(1)	11						CAAAAATGGCGGTAAGTCTTC	0.463																																					p.D94Y		.											.	C11orf49-90	0			c.G280T						.						101	102	102					11																	47074069		2201	4299	6500	SO:0001630	splice_region_variant	79096	exon3			AATGGCGGTAAGT	AL136575	CCDS7925.1, CCDS31479.1, CCDS31480.1, CCDS41641.1	11p11.2	2006-02-02			ENSG00000149179	ENSG00000149179			28720	protein-coding gene	gene with protein product							Standard	NM_001003677		Approved	FLJ22210, MGC4707	uc001ndr.4	Q9H6J7	OTTHUMG00000166725	ENST00000278460.7:c.280+1G>T	11.37:g.47074069G>T		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	102	47	NM_001003677	0	0	0	0	0	D3DQQ8|E9PAX7|Q7L077|Q96CS8|Q9BQH4|Q9BUW5	Missense_Mutation	SNP	ENST00000278460.7	37	CCDS7925.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.879678	0.91740	.	.	ENSG00000149179	ENST00000278460;ENST00000378618;ENST00000395460;ENST00000378615;ENST00000526827	T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9	6.03	6.03	0.97812	.	0.097269	0.64402	D	0.000002	T	0.55289	0.1911	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.79784	0.993;0.977;0.977	T	0.54351	-0.8307	10	0.87932	D	0	-17.2898	20.5568	0.99304	0.0:0.0:1.0:0.0	.	94;94;94	E9PAX7;Q9H6J7-2;Q9H6J7	.;.;CK049_HUMAN	Y	94;94;94;94;20	ENSP00000278460:D94Y;ENSP00000367881:D94Y;ENSP00000378844:D94Y;ENSP00000367878:D94Y;ENSP00000433707:D20Y	ENSP00000278460:D94Y	D	+	1	0	C11orf49	47030645	1.000000	0.71417	0.986000	0.45419	0.971000	0.66376	8.948000	0.93006	2.861000	0.98227	0.655000	0.94253	GAT	.		0.463	C11orf49-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391218.1	NM_024113	Missense_Mutation	T	47074069	G	T	47074069	5	4	100	1	0	0	0	0	0	0	1	0	1649	1130	39	4	290	4	C11orf49	11	47074069	Splice_Site	SNP	G	TCGA-DW-7842-01A-11D-2136-08		47074069	87932447	20	8935											
ANKRD13D	338692	hgsc.bcm.edu;bcgsc.ca	37	chr11	67059495	67059495	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgatggaagtggaccatgAccggcaggtggtgcatgtgg	8	8	19	6	1	0	2	0	2	0	0	0	4	0	4	2	7	1	2	2	7	1	0			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:67059495A>G	ENST00000447274.2	+	6	1489	c.314A>G	c.(313-315)gAc>gGc	p.D105G	ANKRD13D_ENST00000511455.2_Missense_Mutation_p.D192G|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.D105G|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.D105G			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	105						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GTGGACCATGACCGGCAGGTG	0.672																																					p.D192G		.											.	ANKRD13D-91	0			c.A575G						.						36	38	37					11																	67059495		2200	4294	6494	SO:0001583	missense	338692	exon6			ACCATGACCGGCA	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.314A>G	11.37:g.67059495A>G	ENSP00000402616:p.Asp105Gly	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	57	4	NM_207354	1	0	28	30	1	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	37		.	.	.	.	.	.	.	.	.	.	A	24.6	4.554741	0.86231	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	3.9	3.9	0.45041	.	0.074445	0.52532	D	0.000070	T	0.63462	0.2513	M	0.80183	2.485	0.58432	D	0.999999	D;P	0.89917	1.0;0.624	D;P	0.75484	0.986;0.525	T	0.66736	-0.5848	10	0.48119	T	0.1	-35.5096	12.1809	0.54211	1.0:0.0:0.0:0.0	.	192;105	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	G	105;192;105;105	ENSP00000402616:D105G;ENSP00000427130:D192G;ENSP00000310874:D105G;ENSP00000444404:D105G	ENSP00000310874:D105G	D	+	2	0	ANKRD13D	66816071	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.912000	0.92726	1.785000	0.52413	0.459000	0.35465	GAC	.		0.672	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		G	67059495	A	G	67059495	3	3	100	1	0	0	0	0	1	0	0	0	644	275	10	3	597	3	ANKRD13D	11	67059495	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08	19985426	67059495	67947021	21	8936											
ARHGEF17	9828	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	73020470	73020470	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggcccgccgcagctgcctGgagcccagagtccggcctac	6	4	14	17	3	0	1	0	0	0	1	1	2	1	2	6	3	4	2	6	3	1	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:73020470G>A	ENST00000263674.3	+	1	1137	c.787G>A	c.(787-789)Gga>Aga	p.G263R	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	263					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						GCAGCTGCCTGGAGCCCAGAG	0.721																																					p.G263R		.											.	ARHGEF17-227	0			c.G787A						.						10	14	13					11																	73020470		2079	4096	6175	SO:0001583	missense	9828	exon1			CTGCCTGGAGCCC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.787G>A	11.37:g.73020470G>A	ENSP00000263674:p.Gly263Arg	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	44	23	NM_014786	0	0	9	19	10	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.654144	0.29425	.	.	ENSG00000110237	ENST00000263674	T	0.64260	-0.09	4.85	0.091	0.14466	.	0.445825	0.16707	N	0.202865	T	0.43656	0.1257	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39251	-0.9623	10	0.87932	D	0	-19.5376	8.2312	0.31599	0.1586:0.385:0.4564:0.0	.	263	Q96PE2	ARHGH_HUMAN	R	263	ENSP00000263674:G263R	ENSP00000263674:G263R	G	+	1	0	ARHGEF17	72698118	0.001000	0.12720	0.001000	0.08648	0.237000	0.25408	0.062000	0.14389	0.096000	0.17463	-0.502000	0.04539	GGA	.		0.721	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73020470	G	A	73020470	3	1	100	1	0	0	0	0	1	0	0	0	900	1349	47	2	789	2	ARHGEF17	11	73020470	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	5960975	73020470	61986046	22	8937											
MYO7A	4647	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	76890090	76890090	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgccactactgctgtttcaGgtctaactttctgaagctga	8	13	9	11	1	3	2	1	2	2	0	3	2	3	2	1	1	4	3	1	1	3	4	rs397516295		TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:76890090G>T	ENST00000409709.3	+	20	2554		c.e20-1		MYO7A_ENST00000409893.1_Splice_Site|MYO7A_ENST00000409619.2_Splice_Site|MYO7A_ENST00000458637.2_Splice_Site	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA						actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TGCTGTTTCAGGTCTAACTTT	0.587																																					.		.											.	MYO7A-138	0			c.2283-1G>T	GRCh37	CS064428	MYO7A	S		.						34	38	37					11																	76890090		2134	4237	6371	SO:0001630	splice_region_variant	4647	exon20			GTTTCAGGTCTAA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.2283-1G>T	11.37:g.76890090G>T		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	18	9	NM_001127179	0	0	0	0	0	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Splice_Site	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569249	0.28003	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5355	0.84372	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MYO7A	76567738	1.000000	0.71417	0.998000	0.56505	0.147000	0.21601	7.778000	0.85637	2.319000	0.78375	0.289000	0.19496	.	.		0.587	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	Intron	T	76890090	G	T	76890090	5	4	100	1	0	0	0	0	0	0	1	0	10107	1014	35	4	2356	4	MYO7A	11	76890090	Splice_Site	SNP	G	TCGA-DW-7842-01A-11D-2136-08	3869620	76890090	58116426	23	8938											
MED17	9440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	93542943	93542943	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggttatgggctggcaagtaCtgagcttcagtaatcatgtg	10	12	13	6	0	2	1	2	1	0	0	2	1	2	1	0	3	2	6	0	3	4	4			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:93542943C>A	ENST00000251871.3	+	11	1932	c.1645C>A	c.(1645-1647)Ctg>Atg	p.L549M	MED17_ENST00000533367.1_3'UTR	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	549					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTGGCAAGTACTGAGCTTCAG	0.493																																					p.L549M		.											.	MED17-187	0			c.C1645A						.						233	193	206					11																	93542943		2201	4298	6499	SO:0001583	missense	9440	exon11			CAAGTACTGAGCT	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)", "cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.1645C>A	11.37:g.93542943C>A	ENSP00000251871:p.Leu549Met	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	163	71	NM_004268	0	0	24	47	23	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	37	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067027	0.93898	.	.	ENSG00000042429	ENST00000251871;ENST00000427225	T	0.64991	-0.13	5.65	5.65	0.86999	.	0.063209	0.64402	D	0.000003	T	0.79040	0.4379	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.79424	-0.1809	10	0.72032	D	0.01	-15.3186	20.0822	0.97779	0.0:1.0:0.0:0.0	.	549	Q9NVC6	MED17_HUMAN	M	549;519	ENSP00000251871:L549M	ENSP00000251871:L549M	L	+	1	2	MED17	93182591	1.000000	0.71417	0.719000	0.30619	0.979000	0.70002	4.846000	0.62860	2.826000	0.97356	0.563000	0.77884	CTG	.		0.493	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		A	93542943	C	A	93542943	3	1	100	1	0	0	0	0	1	0	0	0	9460	564	20	4	1687	4	MED17	11	93542943	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08	16652853	93542943	41463573	24	8939											
VPS26B	112936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	134115448	134115448	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccctgggtgaggtgcggacCcccagccagctgtctgacaa	7	7	13	14	1	1	2	0	2	1	0	2	3	2	3	4	3	3	1	4	3	1	0			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:134115448C>T	ENST00000281187.5	+	6	1453	c.975C>T	c.(973-975)acC>acT	p.T325T	VPS26B_ENST00000525095.2_Silent_p.T325T	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	325					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		AGGTGCGGACCCCCAGCCAGC	0.652																																					p.T325T	Colon(171;1263 1952 15904 45703 47982)	.											.	VPS26B-90	0			c.C975T						.						44	37	39					11																	134115448		2201	4297	6498	SO:0001819	synonymous_variant	112936	exon6			GCGGACCCCCAGC		CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"vacuolar protein sorting 26 homolog B (yeast)"			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.975C>T	11.37:g.134115448C>T		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	32	18	NM_052875	0	0	11	21	10	Q96A55	Silent	SNP	ENST00000281187.5	37	CCDS8495.1																																																																																			.		0.652	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393591.1	NM_052875		T	134115448	C	T	134115448	2	4	100	1	0	0	0	0	0	0	0	1	17231	610	22	2		2	VPS26B	11	134115448	Silent	SNP	C	TCGA-DW-7842-01A-11D-2136-08	40572505	134115448	891068	25	8940											
RPAP3	79657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	48080648	48080648	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatccctcgagtatagcattCaattgctctttcatatttcc	9	17	4	11	1	3	0	2	0	1	0	6	1	5	0	2	0	2	3	2	0	5	8			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr12:48080648C>T	ENST00000005386.3	-	9	1022	c.907G>A	c.(907-909)Gaa>Aaa	p.E303K	RPAP3_ENST00000380650.4_Missense_Mutation_p.E303K|RPAP3_ENST00000432584.3_Missense_Mutation_p.E144K	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	303										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					GTATAGCATTCAATTGCTCTT	0.353																																					p.E303K		.											.	RPAP3-69	0			c.G907A						.						154	140	145					12																	48080648		2203	4300	6503	SO:0001583	missense	79657	exon9			AGCATTCAATTGC	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"Tetratricopeptide (TTC) repeat domain containing"	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.907G>A	12.37:g.48080648C>T	ENSP00000005386:p.Glu303Lys	Somatic	86	1		WXS	Illumina HiSeq	Phase_I	79	45	NM_024604	0	0	9	19	10	B4DRW9|Q6PHR5	Missense_Mutation	SNP	ENST00000005386.3	37	CCDS8753.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.998449	0.93227	.	.	ENSG00000005175	ENST00000005386;ENST00000432584;ENST00000380650	T;T;T	0.61274	0.12;0.12;0.12	4.71	4.71	0.59529	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.254766	0.44688	D	0.000421	T	0.60663	0.2286	L	0.35341	1.055	0.58432	D	0.999998	D;D	0.61697	0.99;0.98	P;P	0.60173	0.794;0.87	T	0.52320	-0.8591	10	0.10636	T	0.68	.	17.52	0.87784	0.0:1.0:0.0:0.0	.	303;303	Q9H6T3-2;Q9H6T3	.;RPAP3_HUMAN	K	303;144;303	ENSP00000005386:E303K;ENSP00000401823:E144K;ENSP00000370024:E303K	ENSP00000005386:E303K	E	-	1	0	RPAP3	46366915	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.309000	0.78937	2.554000	0.86153	0.555000	0.69702	GAA	.		0.353	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604		T	48080648	C	T	48080648	3	4	100	1	0	0	0	0	1	0	0	0	13575	835	29	2	1126	2	RPAP3	12	48080648	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		48080648	85771247	26	8941											
PTGDR	5729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	52734893	52734894	+	Missense_Mutation	DNP	CT	CT	AG																															tctttgggctctcctcgacaCtgcaactcctggccatggca																										TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr14:52734893_52734894CT>AG	ENST00000306051.2	+	1	463_464	c.361_362CT>AG	c.(361-363)CTg>AGg	p.L121R	PTGDR_ENST00000553372.1_Missense_Mutation_p.L121R	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	121					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	CTCCTCGACACTGCAACTCCTG	0.629																																					p.L121R		.											.	PTGDR	0			c.T362G						.																																			SO:0001583	missense	5729	exon1			CGACACTGCAACT	U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"GPCR / Class A : Prostanoid receptors"	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	Exception_encountered	14.37:g.52734893_52734894delinsAG	ENSP00000303424:p.Leu121Arg	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	231	81		0	0	0	0	0	G3V5L3|Q13250|Q13251|Q1ZZ52	Missense_Mutation	DNP	ENST00000306051.2	37	CCDS9707.1																																																																																			.		0.629	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953		AG	52734894	CT	AG	52734893	3	1	100	1	0	0	0	0	1	0	0	0	12770	564	20	4	363	4	PTGDR	14	52734893	Missense_Mutation	DNP	CT	TCGA-DW-7842-01A-11D-2136-08		52734893	54614647	27	8942											
PLA2G4F	255189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42442584	42442584	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttacctcccccagggccAcagaacactgttcctcctgg	7	8	8	18	0	0	1	0	0	0	1	3	1	3	1	7	2	2	1	7	2	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr15:42442584A>G	ENST00000382396.4	-	9	958	c.872T>C	c.(871-873)gTg>gCg	p.V291A	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.V291A			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	291					arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		CCCCAGGGCCACAGAACACTG	0.652																																					p.V291A		.											.	PLA2G4F-94	0			c.T872C						.						22	23	22					15																	42442584		2203	4299	6502	SO:0001583	missense	255189	exon9			AGGGCCACAGAAC		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.872T>C	15.37:g.42442584A>G	ENSP00000371833:p.Val291Ala	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	29	15	NM_213600	0	0	0	0	0	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.632244	0.29068	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000357924;ENST00000443825	T;T	0.01560	4.77;4.82	4.88	4.88	0.63580	Lysophospholipase, catalytic domain (1);	0.320592	0.21644	N	0.071298	T	0.02848	0.0085	M	0.64404	1.975	0.31744	N	0.635362	P;P	0.46395	0.877;0.877	B;B	0.38106	0.265;0.197	T	0.12142	-1.0559	10	0.72032	D	0.01	-9.9511	11.1909	0.48685	1.0:0.0:0.0:0.0	.	78;291	A2RRC4;Q68DD2	.;PA24F_HUMAN	A	287;291;291;291;291	ENSP00000380442:V291A;ENSP00000371833:V291A	ENSP00000290497:V287A	V	-	2	0	PLA2G4F	40229876	0.055000	0.20627	0.840000	0.33206	0.044000	0.14063	4.335000	0.59298	1.982000	0.57802	0.533000	0.62120	GTG	.		0.652	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		G	42442584	A	G	42442584	3	3	100	1	0	0	0	0	1	0	0	0	12032	159	6	3	1725	3	PLA2G4F	15	42442584	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		42442584	60088808	28	8943											
C15orf42	90381	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	90129030	90129030	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatgatcctcactgtgtgccGcaccaaggaggctgaatttc	9	11	10	11	1	1	2	1	2	0	0	3	3	2	3	3	2	1	2	3	2	3	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr15:90129030G>A	ENST00000268138.7	+	4	1373	c.1268G>A	c.(1267-1269)cGc>cAc	p.R423H	RP11-429B14.1_ENST00000559041.1_RNA|TICRR_ENST00000560985.1_Missense_Mutation_p.R422H			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	423					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										ACTGTGTGCCGCACCAAGGAG	0.542																																					p.R423H		.											.	.	0			c.G1268A						.						86	88	87					15																	90129030		1978	4151	6129	SO:0001583	missense	90381	exon4			TGTGCCGCACCAA	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.1268G>A	15.37:g.90129030G>A	ENSP00000268138:p.Arg423His	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	68	6	NM_152259	0	0	0	0	0	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	g	3.132	-0.178303	0.06380	.	.	ENSG00000140534	ENST00000268138	T	0.13901	2.55	5.24	-2.38	0.06622	.	0.846013	0.11198	N	0.589141	T	0.08447	0.0210	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.28964	-1.0027	10	0.46703	T	0.11	0.7395	7.3452	0.26660	0.4494:0.1087:0.4419:0.0	.	423	Q7Z2Z1	TICRR_HUMAN	H	423	ENSP00000268138:R423H	ENSP00000268138:R423H	R	+	2	0	C15orf42	87930034	0.000000	0.05858	0.005000	0.12908	0.010000	0.07245	-0.060000	0.11712	-0.695000	0.05105	-0.150000	0.13652	CGC	.		0.542	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90129030	G	A	90129030	3	1	100	1	0	0	0	0	1	0	0	0	1800	1087	38	1	1282	1	C15orf42	15	90129030	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	47686446	90129030	12402362	29	8944											
PKD1	5310	ucsc.edu	37	chr16	2168072	2168072	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acctcggcggagccgtctccGaagtcccagcgtgtggcagt	6	7	14	14	5	1	0	0	0	1	0	4	2	2	1	4	3	2	1	4	3	1	0	rs554071267		TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr16:2168072G>A	ENST00000262304.4	-	5	1129	c.921C>T	c.(919-921)ttC>ttT	p.F307F	PKD1_ENST00000423118.1_Silent_p.F307F|RP11-304L19.2_ENST00000562027.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	307	PKD 1. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGCCGTCTCCGAAGTCCCAGC	0.716													g|||	1	0.000199681	0	0	5008	,	,		14557	0		0	False		,,,				2504	0.001				p.F307F													.	PKD1-91	0			c.C921T						.						5	7	7					16																	2168072		2005	4072	6077	SO:0001819	synonymous_variant	5310	exon5			GTCTCCGAAGTCC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.921C>T	16.37:g.2168072G>A		Somatic	37	0		WXS	Illumina HiSeq		26	2	NM_000296	0	0	4	4	0	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.716	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2168072	G	A	2168072	2	1	100	1	0	0	0	0	0	0	0	1	11989	1049	37	1		1	PKD1	16	2168072	Silent	SNP	G	TCGA-DW-7842-01A-11D-2136-08		2168072	88186681	30	8945											
KPNB1	3837	broad.mit.edu	37	chr17	45727756	45727756	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actttcctccccctagatcgGctggagctggaagcggcgca	7	8	12	14	3	0	1	0	0	0	1	3	3	2	3	3	4	2	3	3	4	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr17:45727756G>A	ENST00000290158.4	+	2	452	c.45G>A	c.(43-45)cgG>cgA	p.R15R	RP11-580I16.2_ENST00000582389.1_RNA|KPNB1_ENST00000540627.1_5'Flank|RP11-580I16.2_ENST00000584391.1_RNA|KPNB1_ENST00000577918.1_3'UTR|KPNB1_ENST00000535458.2_Intron|RP11-580I16.2_ENST00000580045.1_RNA	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	15					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						CCCTAGATCGGCTGGAGCTGG	0.716																																					p.G15G													.	KPNB1-229	0			c.A45A						.						16	18	17					17																	45727756		2203	4299	6502	SO:0001819	synonymous_variant	3837	exon2			AGATCGGCTGGAG	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"Importins", "Armadillo repeat containing"	6400	protein-coding gene	gene with protein product	"importin 1"	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.45G>A	17.37:g.45727756G>A		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_002265	0	0	1	1	0	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Silent	SNP	ENST00000290158.4	37	CCDS11513.1																																																																																			.		0.716	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265		A	45727756	G	A	45727756	2	1	100	1	0	0	0	0	0	0	0	1	8456	1190	42	2		2	KPNB1	17	45727756	Silent	SNP	G	TCGA-DW-7842-01A-11D-2136-08		45727756	35467454	31	8946											
APCDD1	147495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	10487950	10487950	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggaagcagcctgtatggccGggcccctgggaggcacacct	7	6	15	13	1	0	0	0	0	0	0	0	2	0	2	5	5	2	3	5	5	2	1	rs112875590		TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr18:10487950G>A	ENST00000355285.5	+	5	1814	c.1460G>A	c.(1459-1461)cGg>cAg	p.R487Q		NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CTGTATGGCCGGGCCCCTGGG	0.592													G|||	1	0.000199681	0	0.0014	5008	,	,		15602	0		0	False		,,,				2504	0				p.R487Q		.											.	APCDD1-90	0			c.G1460A						.	G	GLN/ARG	3,4399	6.2+/-15.9	0,3,2198	50	57	55		1460	0.4	0	18	dbSNP_132	55	0,8600		0,0,4300	yes	missense	APCDD1	NM_153000.4	43	0,3,6498	AA,AG,GG		0.0,0.0682,0.0231	benign	487/515	10487950	3,12999	2201	4300	6501	SO:0001583	missense	147495	exon5			ATGGCCGGGCCCC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1460G>A	18.37:g.10487950G>A	ENSP00000347433:p.Arg487Gln	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	149	44	NM_153000	1	0	6	7	0		Missense_Mutation	SNP	ENST00000355285.5	37	CCDS11849.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.83	1.755053	0.31046	6.82E-4	0.0	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.36699	1.24	5.32	0.44	0.16572	.	1.125910	0.06382	N	0.715392	T	0.30823	0.0777	L	0.50333	1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26815	-1.0092	10	0.37606	T	0.19	-4.4675	5.3468	0.16014	0.2761:0.2485:0.4753:0.0	.	487	Q8J025	APCD1_HUMAN	Q	487;538	ENSP00000347433:R487Q	ENSP00000347433:R487Q	R	+	2	0	APCDD1	10477950	0.001000	0.12720	0.003000	0.11579	0.069000	0.16628	0.165000	0.16564	-0.217000	0.10033	0.563000	0.77884	CGG	G|0.999;A|0.001		0.592	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		A	10487950	G	A	10487950	3	1	100	1	0	0	0	0	1	0	0	0	765	1116	39	1	1478	1	APCDD1	18	10487950	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08		10487950	67589298	32	8947											
DSG4	147409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	28980927	28980927	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attttctagagaatttgataAgaagtcaaaatatattatca	18	15	5	3	0	3	3	2	1	1	2	3	4	3	3	0	0	0	0	0	0	9	8			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr18:28980927A>T	ENST00000308128.4	+	10	1496	c.1361A>T	c.(1360-1362)aAg>aTg	p.K454M	DSG4_ENST00000359747.4_Missense_Mutation_p.K454M|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	454	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GAATTTGATAAGAAGTCAAAA	0.289																																					p.K454M		.											.	DSG4-177	0			c.A1361T						.						43	48	47					18																	28980927		2199	4283	6482	SO:0001583	missense	147409	exon10			TTGATAAGAAGTC	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.1361A>T	18.37:g.28980927A>T	ENSP00000311859:p.Lys454Met	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	78	37	NM_001134453	0	0	0	0	0	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.710083	0.30322	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.52754	0.65;0.65	5.24	-7.62	0.01294	Cadherin (4);Cadherin-like (1);	1.092760	0.07279	N	0.870439	T	0.14657	0.0354	N	0.01188	-0.97	0.21740	N	0.999565	B;B	0.18013	0.025;0.003	B;B	0.19666	0.025;0.026	T	0.23226	-1.0194	10	0.62326	D	0.03	.	2.8038	0.05422	0.1395:0.4432:0.1978:0.2195	.	454;454	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	M	454	ENSP00000311859:K454M;ENSP00000352785:K454M	ENSP00000311859:K454M	K	+	2	0	DSG4	27234925	0.528000	0.26314	0.657000	0.29651	0.818000	0.46254	0.238000	0.18004	-1.023000	0.03342	-2.955000	0.00083	AAG	.		0.289	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28980927	A	T	28980927	3	4	100	1	0	0	0	0	1	0	0	0	4790	72	3	5	1399	5	DSG4	18	28980927	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08	18492977	28980927	49096321	33	8948											
WDR18	57418	hgsc.bcm.edu;broad.mit.edu	37	chr19	992048	992048	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccccacttcaacaagcAcctgctgggcgccgagcacg	8	5	11	17	3	1	0	1	0	0	0	1	1	1	0	4	1	5	4	4	1	2	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:992048A>G	ENST00000251289.5	+	8	1048	c.1025A>G	c.(1024-1026)cAc>cGc	p.H342R	WDR18_ENST00000587001.2_Missense_Mutation_p.H342R	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	342					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTCAACAAGCACCTGCTGGGC	0.716																																					p.H342R		.											.	WDR18-91	0			c.A1025G						.						9	10	9					19																	992048		2129	4155	6284	SO:0001583	missense	57418	exon8			ACAAGCACCTGCT		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.1025A>G	19.37:g.992048A>G	ENSP00000251289:p.His342Arg	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	27	16	NM_024100	1	0	37	65	27	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	37	CCDS12051.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.692269	0.30052	.	.	ENSG00000065268	ENST00000251289	T	0.69435	-0.4	4.28	4.28	0.50868	.	0.056115	0.64402	D	0.000001	T	0.60843	0.2300	M	0.63843	1.955	0.44798	D	0.997803	P	0.50272	0.933	B	0.44108	0.441	T	0.62020	-0.6942	10	0.06757	T	0.87	.	12.3826	0.55315	1.0:0.0:0.0:0.0	.	342	Q9BV38	WDR18_HUMAN	R	342	ENSP00000251289:H342R	ENSP00000251289:H342R	H	+	2	0	WDR18	943048	1.000000	0.71417	1.000000	0.80357	0.541000	0.35023	5.202000	0.65169	1.806000	0.52798	0.402000	0.26972	CAC	.		0.716	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			G	992048	A	G	992048	3	3	100	1	0	0	0	0	1	0	0	0	17311	159	6	3	1055	3	WDR18	19	992048	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		992048	58136935	34	8949											
NDUFA11	126328	ucsc.edu	37	chr19	5897010	5897010	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggcagcggcggtcaggccTgcgagacagaggagggaggc	9	3	20	9	3	1	2	1	0	0	2	1	5	1	4	1	7	2	1	1	7	1	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:5897010T>A	ENST00000308961.4	-	2	145		c.e2-2		AC104532.3_ENST00000589277.1_RNA|NDUFA11_ENST00000592634.1_Splice_Site|NDUFA11_ENST00000418389.2_Splice_Site|AC024592.12_ENST00000586349.1_Splice_Site|FUT5_ENST00000252675.5_Splice_Site|AC104532.3_ENST00000590441.1_RNA	NM_175614.4	NP_783313.1	Q86Y39	NDUAB_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 11, 14.7kDa						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)				central_nervous_system(1)|lung(1)	2						CGGTCAGGCCTGCGAGACAGA	0.612																																					.													.	NDUFA11-90	0			c.98-2A>T						.						118	102	108					19																	5897010		2203	4300	6503	SO:0001630	splice_region_variant	126328	exon3			CAGGCCTGCGAGA	AJ539081	CCDS12155.1, CCDS54203.1	19p13.3	2011-07-04				ENSG00000174886		"Mitochondrial respiratory chain complex / Complex I"	20371	protein-coding gene	gene with protein product	"complex I B14.7 subunit"	612638				12381726	Standard	NM_001193375		Approved	B14.7	uc002mdp.2	Q86Y39		ENST00000308961.4:c.98-2A>T	19.37:g.5897010T>A		Somatic	129	0		WXS	Illumina HiSeq		102	1	NM_001193375	0	0	0	0	0	C9JT23|Q6ZS66	Splice_Site	SNP	ENST00000308961.4	37	CCDS12155.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.620763	0.46736	.	.	ENSG00000174886	ENST00000418389;ENST00000308961	.	.	.	3.96	3.96	0.45880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5079	0.39058	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NDUFA11	5848010	0.976000	0.34144	0.906000	0.35671	0.227000	0.25037	2.368000	0.44222	1.583000	0.49898	0.334000	0.21626	.	.		0.612	NDUFA11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452218.1	NM_175614	Intron	A	5897010	T	A	5897010	5	1	100	1	0	0	0	0	0	0	1	0	10287	1594	55	5	341	5	NDUFA11	19	5897010	Splice_Site	SNP	T	TCGA-DW-7842-01A-11D-2136-08	4904962	5897010	53231973	35	8950											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31770237	31770237	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacagctgctgctgctgctActgctgctgctgctgctgcc	3	11	11	16	0	0	0	0	0	0	0	0	0	0	0	2	0	12	10	2	0	1	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:31770237A>G	ENST00000240587.4	-	2	789	c.462T>C	c.(460-462)agT>agC	p.S154S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	154	Ser-rich.				in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					tgctgctgctactgctgctgc	0.607																																					p.S154S		.											.	TSHZ3-232	0			c.T462C						.						39	44	42					19																	31770237		2184	4294	6478	SO:0001819	synonymous_variant	57616	exon2			GCTGCTACTGCTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.462T>C	19.37:g.31770237A>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	29	2	NM_020856	4	2	33	6569	6530	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			.		0.607	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		G	31770237	A	G	31770237	2	3	100	1	0	0	0	0	0	0	0	1	16658	388	14	3		3	TSHZ3	19	31770237	Silent	SNP	A	TCGA-DW-7842-01A-11D-2136-08	25873227	31770237	27358746	36	8951											
AKT2	208	hgsc.bcm.edu	37	chr19	40743950	40743950	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatctctgcaccataaaaccGggcccgctcctctgtgaaga	11	8	8	14	2	2	2	0	1	2	1	4	2	3	2	4	1	2	2	4	1	4	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:40743950G>A	ENST00000392038.2	-	9	1055	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	AKT2_ENST00000579047.1_Missense_Mutation_p.R191W|AKT2_ENST00000424901.1_Missense_Mutation_p.R253W|AKT2_ENST00000311278.6_Missense_Mutation_p.R253W	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			CCATAAAACCGGGCCCGCTCC	0.622			A		"ovarian, pancreatic "																																p.R253W		.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2-978	0			c.C757T						.						105	80	88					19																	40743950		2203	4300	6503	SO:0001583	missense	208	exon9			AAAACCGGGCCCG	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.757C>T	19.37:g.40743950G>A	ENSP00000375892:p.Arg253Trp	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_001626	0	0	228	242	14	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	37	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818854	0.90873	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.27104	1.69;1.69;1.69	4.7	3.66	0.41972	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51075	0.1653	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.997;0.999	T	0.57596	-0.7784	10	0.87932	D	0	.	12.1535	0.54064	0.0852:0.0:0.9148:0.0	.	191;253;253	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	W	253;154;253;253;73	ENSP00000375892:R253W;ENSP00000399532:R253W;ENSP00000309428:R253W	ENSP00000309428:R253W	R	-	1	2	AKT2	45435790	1.000000	0.71417	0.925000	0.36789	0.991000	0.79684	7.677000	0.84024	1.342000	0.45619	0.655000	0.94253	CGG	.		0.622	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		A	40743950	G	A	40743950	3	1	100	1	0	0	0	0	1	0	0	0	480	1115	39	1	712	1	AKT2	19	40743950	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	8973713	40743950	18385033	37	8952											
PVRL2	5819	broad.mit.edu	37	chr19	45349842	45349844	+	In_Frame_Del	DEL	GCT	GCT	-																															ccgacgccgctgctgtggccGctgctgctgctgctgctcct																										TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:45349842_45349844delGCT	ENST00000252483.5	+	1	60_62	c.60_62delGCT	c.(58-63)ccgctg>ccg	p.L27del	PVRL2_ENST00000252485.4_In_Frame_Del_p.L27del	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	27					acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		tgctgtggccgctgctgctgctg	0.759																																					p.20_21del													.	PVRL2-90	0			c.60_62del						.		,	17,1559		4,9,775					,	-4.8	0			1	20,3132		3,14,1559	no	coding,coding	PVRL2	NM_002856.2,NM_001042724.1	,	7,23,2334	A1A1,A1R,RR		0.6345,1.0787,0.7826	,	,		37,4691				SO:0001651	inframe_deletion	5819	exon1			GTGGCCGCTGCTG	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.60_62delGCT	19.37:g.45349851_45349853delGCT	ENSP00000252483:p.Leu27del	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_002856	0	0	0	0	0	A8K5L5|O75455|Q6IBI6|Q96J29	In_Frame_Del	DEL	ENST00000252483.5	37	CCDS42576.1																																																																																			.		0.759	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		-	45349844	GCT	-	45349842	7	5	100	1	0	1	0	1	0	0	0	0	12872	1074	38	0	62	0	PVRL2	19	45349842	In_Frame_Del	DEL	GCT	TCGA-DW-7842-01A-11D-2136-08	4605892	45349842	13779141	38	8953											
KLK7	5650	hgsc.bcm.edu	37	chr19	51485616	51485616	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtttccaaggctaaggataGcagtaagatctgcaggggca	13	8	13	7	0	1	1	0	0	1	1	2	2	2	2	1	4	2	6	1	4	4	4	rs372381913		TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:51485616G>C	ENST00000391807.1	-	2	141	c.40C>G	c.(40-42)Cta>Gta	p.L14V	KLK7_ENST00000595638.1_5'UTR|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_5'UTR|KLK7_ENST00000595820.1_Missense_Mutation_p.L14V|KLK7_ENST00000597707.1_Intron	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	14					epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		GCTAAGGATAGCAGTAAGATC	0.607																																					p.A56G		.											.	KLK7-650	0			c.C167G						.						62	47	52					19																	51485616		2203	4298	6501	SO:0001583	missense	5650	exon2			AGGATAGCAGTAA	L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"Kallikreins", "Serine peptidases / Serine peptidases"	6368	protein-coding gene	gene with protein product		604438	"kallikrein 7 (chymotryptic, stratum corneum)"	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.40C>G	19.37:g.51485616G>C	ENSP00000375683:p.Leu14Val	Somatic	16	2		WXS	Illumina HiSeq	Phase_I	9	3	NM_001243126	0	0	0	0	0	A8K0U5|Q8N5N9|Q8NFV7	Missense_Mutation	SNP	ENST00000391807.1	37	CCDS12812.1	.	.	.	.	.	.	.	.	.	.	g	6.488	0.458260	0.12342	.	.	ENSG00000169035	ENST00000304045;ENST00000391807	D	0.92965	-3.14	2.77	1.72	0.24424	.	.	.	.	.	D	0.89880	0.6843	N	0.20483	0.58	0.21933	N	0.999467	D	0.63880	0.993	D	0.73708	0.981	T	0.79741	-0.1676	9	0.22109	T	0.4	.	5.6632	0.17680	0.1529:0.0:0.8471:0.0	.	14	P49862	KLK7_HUMAN	V	14	ENSP00000375683:L14V	ENSP00000304791:L14V	L	-	1	2	KLK7	56177428	0.779000	0.28652	0.175000	0.22980	0.024000	0.10985	1.316000	0.33620	0.749000	0.32854	0.645000	0.84053	CTA	.		0.607	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046		C	51485616	G	C	51485616	3	2	100	1	0	0	0	0	1	0	0	0	8430	962	34	4	741	4	KLK7	19	51485616	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	6135774	51485616	7643367	39	8954											
NLRP5	126206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56511120	56511120	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcaggaggacttgaacttgGagctgctgctctgctctcag	7	11	13	10	0	2	1	1	1	2	0	3	4	2	4	0	3	6	5	0	3	1	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:56511120G>A	ENST00000390649.3	+	1	29	c.29G>A	c.(28-30)gGa>gAa	p.G10E		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	10					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		cttgaacttggagctgcTGCT	0.517																																					p.G10E		.											.	NLRP5-162	0			c.G29A						.						208	212	210					19																	56511120		2101	4218	6319	SO:0001583	missense	126206	exon1			AACTTGGAGCTGC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"Nucleotide-binding domain and leucine rich repeat containing"	21269	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"	609658	"NACHT, leucine rich repeat and PYD containing 5"	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.29G>A	19.37:g.56511120G>A	ENSP00000375063:p.Gly10Glu	Somatic	241	0		WXS	Illumina HiSeq	Phase_I	234	35	NM_153447	0	0	0	0	0	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	7.564	0.665223	0.14710	.	.	ENSG00000171487	ENST00000390649	T	0.74106	-0.81	0.492	0.492	0.16872	.	.	.	.	.	T	0.68860	0.3047	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.59215	-0.7496	8	0.87932	D	0	.	.	.	.	.	10	P59047	NALP5_HUMAN	E	10	ENSP00000375063:G10E	ENSP00000375063:G10E	G	+	2	0	NLRP5	61202932	0.005000	0.15991	0.037000	0.18230	0.032000	0.12392	-0.354000	0.07681	0.528000	0.28580	0.298000	0.19748	GGA	.		0.517	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		A	56511120	G	A	56511120	3	1	100	1	0	0	0	0	1	0	0	0	10506	1174	41	2	31	2	NLRP5	19	56511120	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	5025504	56511120	2617863	40	8955											
C20orf12	55184	hgsc.bcm.edu	37	chr20	18435935	18435935	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	attttcaacattgtcttcagGagagactatatttggtggtt	10	17	9	5	0	3	1	2	0	1	1	3	3	3	2	0	3	1	1	0	3	3	8			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr20:18435935G>C	ENST00000358866.6	-	3	356	c.334C>G	c.(334-336)Cct>Gct	p.P112A	DZANK1_ENST00000357236.4_5'UTR|DZANK1_ENST00000329494.5_Missense_Mutation_p.P112A|DZANK1_ENST00000487128.1_5'Flank|DZANK1_ENST00000262547.5_Missense_Mutation_p.P112A			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	112							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						TTGTCTTCAGGAGAGACTATA	0.353																																					p.P112A		.											.	.	0			c.C334G						.						118	107	110					20																	18435935		1877	4108	5985	SO:0001583	missense	55184	exon4			CTTCAGGAGAGAC	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.334C>G	20.37:g.18435935G>C	ENSP00000351734:p.Pro112Ala	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_001099407	0	0	6	6	0	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	37	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.212554	0.00289	.	.	ENSG00000089091	ENST00000262547;ENST00000329494	T;T	0.62498	0.02;0.71	5.82	2.33	0.28932	.	0.424852	0.22007	U	0.065935	T	0.37265	0.0997	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.15473	0.013;0.013	B;B	0.13407	0.009;0.009	T	0.14811	-1.0459	10	0.22109	T	0.4	-0.7175	4.7495	0.13054	0.7013:0.0:0.1593:0.1394	.	112;112	B7Z631;Q9NVP4	.;DZAN1_HUMAN	A	112	ENSP00000262547:P112A;ENSP00000328866:P112A	ENSP00000262547:P112A	P	-	1	0	C20orf12	18383935	0.321000	0.24625	0.014000	0.15608	0.019000	0.09904	0.431000	0.21444	0.127000	0.18452	-1.284000	0.01376	CCT	.		0.353	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		C	18435935	G	C	18435935	3	2	100	1	0	0	0	0	1	0	0	0	2091	1174	41	4	1996	4	C20orf12	20	18435935	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08		18435935	44589585	41	8956											
SLC19A1	6573	hgsc.bcm.edu	37	chr21	46935688	46935688	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgcagcctcagggcctgAggcttgggcggagcacagag	8	6	16	11	1	2	2	1	1	1	1	2	3	2	3	2	4	3	3	2	4	0	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr21:46935688A>G	ENST00000311124.4	-	6	1812	c.1660T>C	c.(1660-1662)Tca>Cca	p.S554P	SLC19A1_ENST00000380010.4_Intron|SLC19A1_ENST00000485649.2_Missense_Mutation_p.S514P|SLC19A1_ENST00000468508.1_5'Flank|SLC19A1_ENST00000567670.1_Intron	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	554					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	TCAGGGCCTGAGGCTTGGGCG	0.637																																					p.S554P		.											.	SLC19A1-90	0			c.T1660C						.						44	44	44					21																	46935688		2203	4300	6503	SO:0001583	missense	6573	exon6			GGCCTGAGGCTTG	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"Solute carriers"	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.1660T>C	21.37:g.46935688A>G	ENSP00000308895:p.Ser554Pro	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	57	4	NM_194255	0	0	14	14	0	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.430071	0.43122	.	.	ENSG00000173638	ENST00000311124;ENST00000485649	D;D	0.84944	-1.91;-1.92	2.86	-2.08	0.07254	.	.	.	.	.	T	0.64713	0.2623	N	0.19112	0.55	0.09310	N	1	P;P	0.42078	0.77;0.77	B;B	0.32090	0.14;0.14	T	0.59700	-0.7405	9	0.87932	D	0	.	0.6492	0.00823	0.4614:0.2055:0.1326:0.2004	.	514;554	B7Z8C3;P41440	.;S19A1_HUMAN	P	554;514	ENSP00000308895:S554P;ENSP00000441772:S514P	ENSP00000308895:S554P	S	-	1	0	SLC19A1	45760116	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	-0.670000	0.05256	-0.524000	0.06400	-0.456000	0.05471	TCA	.		0.637	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1			G	46935688	A	G	46935688	3	3	100	1	0	0	0	0	1	0	0	0	14460	304	11	3	119	3	SLC19A1	21	46935688	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		46935688	1194207	42	8957											
CXorf59	286464	hgsc.bcm.edu	37	chrX	36156552	36156552	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgattattgtaaatactcttTatgaaattgactttgacgtg	12	18	7	4	1	1	4	0	4	1	0	1	4	1	4	0	0	1	1	0	0	6	8			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chrX:36156552T>C	ENST00000313548.4	+	10	1417	c.1231T>C	c.(1231-1233)Tat>Cat	p.Y411H		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	411	CH.					integral component of membrane (GO:0016021)											AAATACTCTTTATGAAATTGA	0.289																																					p.Y411H		.											.	.	0			c.T1231C						.						76	71	72					X																	36156552		2201	4293	6494	SO:0001583	missense	286464	exon10			ACTCTTTATGAAA	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.1231T>C	X.37:g.36156552T>C	ENSP00000324767:p.Tyr411His	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_173695	0	0	1	1	0		Missense_Mutation	SNP	ENST00000313548.4	37	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.826393	0.00589	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	5.16	1.19	0.21007	Calponin homology domain (1);	1.689990	0.03708	N	0.249711	T	0.10252	0.0251	N	0.00707	-1.245	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21655	-1.0239	9	0.19147	T	0.46	-5.0E-4	6.2666	0.20930	0.1325:0.6632:0.0:0.2043	.	411	Q8N9S7	CX059_HUMAN	H	411	.	ENSP00000324767:Y411H	Y	+	1	0	CXorf59	36066473	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	0.719000	0.25881	-0.165000	0.10908	-1.043000	0.02367	TAT	.		0.289	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		C	36156552	T	C	36156552	3	2	100	1	0	0	0	0	1	0	0	0	4121	1754	61	3	1265	3	CXorf59	23	36156552	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08		36156552	119114008	43	8958											
ZBTB33	10009	broad.mit.edu	37	chrX	119387346	119387346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaactccttgaatgagcaaCgtggccatggactcttctgt	9	12	10	10	1	2	3	0	3	2	0	3	4	3	4	2	2	3	1	2	2	3	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chrX:119387346C>T	ENST00000326624.2	+	2	304	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C	ZBTB33_ENST00000557385.1_Missense_Mutation_p.R26C	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	26	Interaction with NCOR1.|Self-association. {ECO:0000250}.				intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						GAATGAGCAACGTGGCCATGG	0.448																																					p.R26C													.	ZBTB33-132	0			c.C76T						.						161	153	156					X																	119387346		2203	4300	6503	SO:0001583	missense	10009	exon2			GAGCAACGTGGCC	BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.76C>T	X.37:g.119387346C>T	ENSP00000314153:p.Arg26Cys	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	148	6	NM_006777	0	0	14	15	1	B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	Missense_Mutation	SNP	ENST00000326624.2	37	CCDS14596.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.190149	0.58017	.	.	ENSG00000177485;ENSG00000177485;ENSG00000258974	ENST00000326624;ENST00000540105;ENST00000557385	T;T	0.26067	1.76;1.76	5.96	5.96	0.96718	BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.64011	0.2560	M	0.93808	3.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73805	-0.3867	10	0.87932	D	0	-10.6374	18.2055	0.89853	0.0:1.0:0.0:0.0	.	26	Q86T24	KAISO_HUMAN	C	26	ENSP00000314153:R26C;ENSP00000450969:R26C	ENSP00000314153:R26C	R	+	1	0	ZBTB33;AC002086.1	119271374	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	4.500000	0.60387	2.523000	0.85059	0.594000	0.82650	CGT	.		0.448	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2	NM_006777		T	119387346	C	T	119387346	3	4	100	1	0	0	0	0	1	0	0	0	17568	536	19	1	78	1	ZBTB33	23	119387346	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08	83230794	119387346	35883214	44	8959											
KIAA2013	90231	hgsc.bcm.edu	37	chr1	11986231	11986231	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggccaagcaggcagaggaGgcggcgggcccagctgctcg	8	2	19	12	3	0	1	0	0	0	1	1	3	0	2	2	6	3	4	2	6	1	0	rs552116013	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:11986231G>A	ENST00000376572.3	-	1	249	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	KIAA2013_ENST00000376576.3_Missense_Mutation_p.L22F	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	22						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGGCAGAGGAGGCGGCGGGCC	0.771													G|||	26	0.00519169	0.0166	0.0043	5008	,	,		4617	0		0.001	False		,,,				2504	0				p.L22F		.											.	KIAA2013-91	0			c.C64T						.						1	1	1					1																	11986231		852	2025	2877	SO:0001583	missense	90231	exon1			AGAGGAGGCGGCG	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.64C>T	1.37:g.11986231G>A	ENSP00000365756:p.Leu22Phe	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_138346	0	0	0	0	0	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Missense_Mutation	SNP	ENST00000376572.3	37	CCDS141.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.691701	0.68271	.	.	ENSG00000116685	ENST00000376572;ENST00000376576	.	.	.	2.55	1.47	0.22746	.	0.221922	0.29040	U	0.013323	T	0.31638	0.0803	N	0.14661	0.345	0.29766	N	0.835158	D;P	0.61080	0.989;0.954	P;P	0.59487	0.858;0.812	T	0.08659	-1.0711	9	0.46703	T	0.11	-19.9466	7.5843	0.27982	0.0:0.4455:0.5544:0.0	.	22;22	Q8IYS2-2;Q8IYS2	.;K2013_HUMAN	F	22	.	ENSP00000365756:L22F	L	-	1	0	KIAA2013	11908818	0.998000	0.40836	0.999000	0.59377	0.991000	0.79684	0.719000	0.25881	1.409000	0.46915	0.563000	0.77884	CTC	.		0.771	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346		A	11986231	G	A	11986231	3	1	101	1	0	0	0	0	1	0	0	0	8288	1000	35	2	1852	2	KIAA2013	1	11986231	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		11986231	237264390	1	8960											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608848	26608853	+	In_Frame_Del	DEL	CTGGGG	CTGGGG	-																															ggccgggaccgggaccgggaCtggggccgggaccgggaccg																								rs61775089|rs199707978		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	CTGGGG	CTGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:26608848_26608853delCTGGGG	ENST00000374222.1	-	16	1964_1969	c.1500_1505delCCCCAG	c.(1498-1506)ggccccagt>ggt	p.PS501del	UBXN11_ENST00000374217.2_In_Frame_Del_p.PS468del|UBXN11_ENST00000314675.7_In_Frame_Del_p.PS381del|UBXN11_ENST00000374221.3_In_Frame_Del_p.PS501del|UBXN11_ENST00000374223.1_In_Frame_Del_p.PS258del|UBXN11_ENST00000357089.4_In_Frame_Del_p.PS468del			Q5T124	UBX11_HUMAN	UBX domain protein 11	501	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|P -> S (in dbSNP:rs17838088).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggaccgggactggggccgggaccgg	0.728																																					p.500_502del		.											.	UBXN11-91	1	Deletion - In frame(1)	ovary(1)	c.1500_1505del						.																																			SO:0001651	inframe_deletion	91544	exon16			.	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1500_1505delCCCCAG	1.37:g.26608848_26608853delCTGGGG	ENSP00000363339:p.Pro501_Ser502del	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	25	13	NM_183008	0	0	0	0	0	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	In_Frame_Del	DEL	ENST00000374222.1	37	CCDS41288.1																																																																																			.		0.728	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		-	26608853	CTGGGG	-	26608848	7	5	101	1	0	1	0	1	0	0	0	0	16946	565	20	0	61	0	UBXN11	1	26608848	In_Frame_Del	DEL	CTGGGG	TCGA-DW-7963-01B-11D-A28G-10	14622617	26608848	222641773	2	8961			1	28		3	2	18	N	CTGGGG_C_A	3.130125e-05
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608861	26608861	+	Missense_Mutation	SNP	C	C	T																															accgggactggggccgggacCgggaccgggactggggccgg																								rs200313935		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:26608861C>T	ENST00000374222.1	-	16	1956	c.1492G>A	c.(1492-1494)Ggt>Agt	p.G498S	UBXN11_ENST00000374217.2_Missense_Mutation_p.G465S|UBXN11_ENST00000314675.7_Missense_Mutation_p.G378S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G498S|UBXN11_ENST00000374223.1_Missense_Mutation_p.G255S|UBXN11_ENST00000357089.4_Missense_Mutation_p.G465S			Q5T124	UBX11_HUMAN	UBX domain protein 11	498	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggccgggaccgggaccggga	0.726																																					p.G498S		.											.	UBXN11-91	1	Deletion - In frame(1)	ovary(1)	c.G1492A						.						23	26	25					1																	26608861		1731	3974	5705	SO:0001583	missense	91544	exon16			CGGGACCGGGACC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1492G>A	1.37:g.26608861C>T	ENSP00000363339:p.Gly498Ser	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	32	18	NM_183008	0	0	0	0	0	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	C	10.29	1.310153	0.23821	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.17370	2.28;2.29;2.59;2.56;2.56;2.59	.	.	.	.	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.20074	N	0.999939	D;D;D;D	0.65815	0.995;0.995;0.995;0.991	B;B;B;B	0.40901	0.343;0.343;0.343;0.185	T	0.29274	-1.0017	8	0.56958	D	0.05	.	5.9752	0.19375	0.0:1.0:0.0:0.0	.	465;460;378;498	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	378;255;465;498;498;465	ENSP00000324721:G378S;ENSP00000363340:G255S;ENSP00000349601:G465S;ENSP00000363338:G498S;ENSP00000363339:G498S;ENSP00000363334:G465S	ENSP00000324721:G378S	G	-	1	0	UBXN11	26481448	0.000000	0.05858	0.143000	0.22291	0.150000	0.21749	-1.043000	0.03535	-0.000000	0.14550	0.000000	0.15137	GGT	C|0.988;T|0.012		0.726	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		T	26608861	C	T	26608861	3	4	101	1	0	0	0	0	1	0	0	0	16946	652	23	1	74	1	UBXN11	1	26608861	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	13	26608861	222641760	3	8962	95	2	1	28		3	2	18	N	CTGGGG_C_A	3.130125e-05
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608865	26608865	+	Silent	SNP	A	A	G																															ggactggggccgggaccgggAccgggactggggccgggacc																										TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:26608865A>G	ENST00000374222.1	-	16	1952	c.1488T>C	c.(1486-1488)ggT>ggC	p.G496G	UBXN11_ENST00000374217.2_Silent_p.G463G|UBXN11_ENST00000314675.7_Silent_p.G376G|UBXN11_ENST00000374221.3_Silent_p.G496G|UBXN11_ENST00000374223.1_Silent_p.G253G|UBXN11_ENST00000357089.4_Silent_p.G463G			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						cgggaccgggaccgggactgg	0.721																																					p.G496G		.											.	UBXN11-91	1	Deletion - In frame(1)	ovary(1)	c.T1488C						.						25	29	28					1																	26608865		1768	4016	5784	SO:0001819	synonymous_variant	91544	exon16			ACCGGGACCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"UBX domain containing"	30600	protein-coding gene	gene with protein product	"socius"	609151	"UBX domain containing 5"	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1488T>C	1.37:g.26608865A>G		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	32	18	NM_183008	0	0	0	0	0	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			.		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		G	26608865	A	G	26608865	2	3	101	1	0	0	0	0	0	0	0	1	16946	262	10	3		3	UBXN11	1	26608865	Silent	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	4	26608865	222641756	4	8963	95	2	1	28		3	2	18	N	CTGGGG_C_A	3.130125e-05
LAPTM5	7805	broad.mit.edu	37	chr1	31208088	31208088	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgatcaatctgtagcaccGccacacgcacttgaacatgt	11	10	7	13	2	2	2	1	2	1	0	2	2	2	2	2	0	2	3	2	0	3	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:31208088G>A	ENST00000294507.3	-	7	705	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W		NM_006762.2	NP_006753.1	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5	211					transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)				large_intestine(2)|lung(7)|skin(1)	10		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTAGCACCGCCACACGCAC	0.557																																					p.R211W													.	LAPTM5-226	0			c.C631T						.						253	221	232					1																	31208088		2203	4300	6503	SO:0001583	missense	7805	exon7			AGCACCGCCACAC	U51240	CCDS337.1	1p34	2009-07-20	2009-07-20		ENSG00000162511	ENSG00000162511			29612	protein-coding gene	gene with protein product		601476	"lysosomal multispanning membrane protein 5"			8661146, 12527926	Standard	NM_006762		Approved		uc001bsc.2	Q13571	OTTHUMG00000003707	ENST00000294507.3:c.631C>T	1.37:g.31208088G>A	ENSP00000294507:p.Arg211Trp	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	99	5	NM_006762	0	0	31	31	0	Q13240|Q14698|Q3KP54	Missense_Mutation	SNP	ENST00000294507.3	37	CCDS337.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368200	0.61513	.	.	ENSG00000162511	ENST00000294507;ENST00000424259	T	0.47528	0.84	5.81	0.658	0.17855	.	0.132879	0.51477	D	0.000082	T	0.62429	0.2427	M	0.67953	2.075	0.28772	N	0.900296	D	0.89917	1.0	D	0.68192	0.956	T	0.62506	-0.6840	10	0.72032	D	0.01	-10.4451	13.2343	0.59961	0.0:0.0:0.5902:0.4098	.	211	Q13571	LAPM5_HUMAN	W	211	ENSP00000294507:R211W	ENSP00000294507:R211W	R	-	1	2	LAPTM5	30980675	0.992000	0.36948	0.993000	0.49108	0.621000	0.37620	0.431000	0.21444	-0.131000	0.11578	-0.262000	0.10625	CGG	.		0.557	LAPTM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010463.1	NM_006762		A	31208088	G	A	31208088	3	1	101	1	0	0	0	0	1	0	0	0	8647	1086	38	1	165	1	LAPTM5	1	31208088	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	4599223	31208088	218042533	5	8964											
ECHDC2	55268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53362195	53362195	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaggttaaaatgggggtcaTttgccaacaaatttgggagt	13	11	13	4	0	1	0	1	0	0	0	1	2	1	1	1	4	2	1	1	4	5	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:53362195T>C	ENST00000371522.4	-	10	969	c.876A>G	c.(874-876)aaA>aaG	p.K292K	ECHDC2_ENST00000536120.1_Silent_p.K246K|ECHDC2_ENST00000358358.5_Silent_p.K261K	NM_001198961.1	NP_001185890.1	Q86YB7	ECHD2_HUMAN	enoyl CoA hydratase domain containing 2	292					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	lyase activity (GO:0016829)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	12						ATGGGGGTCATTTGCCAACAA	0.488																																					p.K292K		.											.	ECHDC2-90	0			c.A876G						.						71	73	72					1																	53362195		2203	4300	6503	SO:0001819	synonymous_variant	55268	exon10			GGGTCATTTGCCA	AF258590	CCDS571.1, CCDS55600.1, CCDS72794.1	1p32.3	2010-04-30	2010-04-30		ENSG00000121310	ENSG00000121310			23408	protein-coding gene	gene with protein product			"enoyl Coenzyme A hydratase domain containing 2"				Standard	NM_018281		Approved	FLJ10948	uc001cup.4	Q86YB7	OTTHUMG00000008927	ENST00000371522.4:c.876A>G	1.37:g.53362195T>C		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	49	13	NM_001198961	0	0	17	32	15	D3DQ36|Q9NV38	Silent	SNP	ENST00000371522.4	37	CCDS55600.1																																																																																			.		0.488	ECHDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024712.3	NM_018281		C	53362195	T	C	53362195	2	2	101	1	0	0	0	0	0	0	0	1	4905	1490	52	3		3	ECHDC2	1	53362195	Silent	SNP	T	TCGA-DW-7963-01B-11D-A28G-10	22154107	53362195	195888426	6	8965											
RNF2	6045	broad.mit.edu	37	chr1	185060812	185060812	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgttgaagaacaccatgacTacaaaggagtgtttacatcg	15	10	9	7	1	0	3	0	2	0	1	1	4	0	4	1	1	3	2	1	1	5	4			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:185060812T>C	ENST00000367510.3	+	3	477	c.189T>C	c.(187-189)acT>acC	p.T63T	RNF2_ENST00000367509.4_Silent_p.T63T	NM_007212.3	NP_009143.1	Q99496	RING2_HUMAN	ring finger protein 2	63	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|large_intestine(4)|lung(3)|skin(2)	14		Breast(1374;0.000496)		Colorectal(1306;6.9e-08)|KIRC - Kidney renal clear cell carcinoma(1967;8.12e-06)		ACACCATGACTACAAAGGAGT	0.383																																					p.T63T													.	RNF2-658	0			c.T189C						.						203	182	189					1																	185060812		2203	4300	6503	SO:0001819	synonymous_variant	6045	exon3			CATGACTACAAAG	BC012583, Y10571	CCDS1365.1	1q25.3	2013-01-09			ENSG00000121481	ENSG00000121481		"RING-type (C3HC4) zinc fingers"	10061	protein-coding gene	gene with protein product		608985				11513855	Standard	XM_005245413		Approved	BAP-1, BAP1, DING, HIPI3, RING1B, RING2	uc001grc.1	Q99496	OTTHUMG00000035391	ENST00000367510.3:c.189T>C	1.37:g.185060812T>C		Somatic	163	0		WXS	Illumina HiSeq	Phase_I	151	3	NM_007212	0	0	1	1	0	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Silent	SNP	ENST00000367510.3	37	CCDS1365.1																																																																																			.		0.383	RNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085793.1	NM_007212		C	185060812	T	C	185060812	2	2	101	1	0	0	0	0	0	0	0	1	13504	1509	53	3		3	RNF2	1	185060812	Silent	SNP	T	TCGA-DW-7963-01B-11D-A28G-10	131698617	185060812	64189809	7	8966											
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	216262462	216262462	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgccatgatcattagttgtaGttacttccactggtgacccc	8	14	8	11	0	1	2	1	2	0	0	2	2	2	2	4	1	2	3	4	1	3	5			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:216262462G>T	ENST00000307340.3	-	23	5164	c.4778C>A	c.(4777-4779)aCt>aAt	p.T1593N	RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.T1593N|RP11-22M7.2_ENST00000445619.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1593	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATTAGTTGTAGTTACTTCCAC	0.333										HNSCC(13;0.011)																											p.T1593N		.											.	USH2A-115	0			c.C4778A						.						184	168	173					1																	216262462		2203	4300	6503	SO:0001583	missense	7399	exon23			GTTGTAGTTACTT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4778C>A	1.37:g.216262462G>T	ENSP00000305941:p.Thr1593Asn	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	52	18	NM_206933	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336688	0.60963	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.80304	-1.36;-1.36	5.8	4.88	0.63580	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.45361	D	0.000370	D	0.87006	0.6070	M	0.73962	2.25	0.38859	D	0.95643	D	0.61080	0.989	P	0.58780	0.845	D	0.87966	0.2733	10	0.41790	T	0.15	.	15.1749	0.72903	0.0:0.2669:0.7331:0.0	.	1593	O75445	USH2A_HUMAN	N	1593	ENSP00000305941:T1593N;ENSP00000355910:T1593N	ENSP00000305941:T1593N	T	-	2	0	USH2A	214329085	1.000000	0.71417	0.699000	0.30290	0.787000	0.44495	5.826000	0.69293	1.417000	0.47077	0.655000	0.94253	ACT	.		0.333	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216262462	G	T	216262462	3	4	101	1	0	0	0	0	1	0	0	0	17069	1029	36	4	11030	4	USH2A	1	216262462	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	31201650	216262462	32988159	8	8967											
OBSCN	84033	broad.mit.edu	37	chr1	228444409	228444410	+	Frame_Shift_Ins	INS	-	-	G																															agggaggtgcaggcccaggcINSgggggccagcaccacactca																										TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:228444409_228444410insG	ENST00000422127.1	+	15	4411_4412	c.4367_4368insG	c.(4366-4371)gcggggfs	p.AG1456fs	OBSCN_ENST00000570156.2_Frame_Shift_Ins_p.AG1548fs|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Frame_Shift_Ins_p.AG1456fs|OBSCN_ENST00000359599.6_Frame_Shift_Ins_p.AG20fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1456	Ig-like 15.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGGCCCAGGCGGGGGCCAGCA	0.619																																					p.A1548fs													.	OBSCN-403	0			c.4643_4644insG						.																																			SO:0001589	frameshift_variant	84033	exon16			CCCAGGCGGGGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.4372dupG	1.37:g.228444414_228444414dupG	ENSP00000409493:p.Ala1456fs	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	388	8	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Ins	INS	ENST00000422127.1	37	CCDS58065.1																																																																																			.		0.619	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228444410	-	G	228444409	7	5	101	1	0	1	1	0	0	0	0	0	10838	768	27	0	4421	0	OBSCN	1	228444409	Frame_Shift_Ins	INS	-	TCGA-DW-7963-01B-11D-A28G-10	12181947	228444409	20806212	9	8968											
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	237730023	237730023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtcgtcctggttgtcaacCggatcaggagcttggctcag	7	10	14	10	2	3	0	3	0	0	0	5	3	4	2	2	4	2	3	2	4	1	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:237730023C>G	ENST00000366574.2	+	28	3688	c.3371C>G	c.(3370-3372)cCg>cGg	p.P1124R	RYR2_ENST00000360064.6_Missense_Mutation_p.P1122R|RYR2_ENST00000542537.1_Missense_Mutation_p.P1108R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1124	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGTTGTCAACCGGATCAGGAG	0.532																																					p.P1124R		.											.	RYR2-158	0			c.C3371G						.						218	216	217					1																	237730023		2066	4209	6275	SO:0001583	missense	6262	exon28			GTCAACCGGATCA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.3371C>G	1.37:g.237730023C>G	ENSP00000355533:p.Pro1124Arg	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	185	48	NM_001035	0	0	0	0	0	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966699	0.74131	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.55588	0.51;0.51;0.51	5.29	5.29	0.74685	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000008	T	0.72558	0.3475	M	0.72894	2.215	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.75814	-0.3185	10	0.87932	D	0	.	18.9442	0.92615	0.0:1.0:0.0:0.0	.	1124	Q92736	RYR2_HUMAN	R	1124;1122;1108	ENSP00000355533:P1124R;ENSP00000353174:P1122R;ENSP00000443798:P1108R	ENSP00000353174:P1122R	P	+	2	0	RYR2	235796646	1.000000	0.71417	0.114000	0.21550	0.563000	0.35712	7.814000	0.86154	2.465000	0.83290	0.655000	0.94253	CCG	.		0.532	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237730023	C	G	237730023	3	3	101	1	0	0	0	0	1	0	0	0	13801	652	23	4	3481	4	RYR2	1	237730023	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	9285614	237730023	11520598	10	8969											
OXER1	165140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	42990999	42990999	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggccaaactgttccccacCaggcccaggacaaactccag	12	4	9	16	0	0	0	0	0	0	0	2	1	2	1	6	3	2	1	6	3	2	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr2:42990999C>A	ENST00000378661.2	-	1	402	c.321G>T	c.(319-321)ctG>ctT	p.L107L		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	107					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						TGTTCCCCACCAGGCCCAGGA	0.647																																					p.L107L		.											.	OXER1-500	0			c.G321T						.						43	47	45					2																	42990999		2203	4300	6503	SO:0001819	synonymous_variant	165140	exon1			CCCCACCAGGCCC	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"GPCR / Class A : Leukotriene receptors"	24884	protein-coding gene	gene with protein product	"5-oxo-ETE acid G-protein-coupled receptor 1"					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.321G>T	2.37:g.42990999C>A		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	100	34	NM_148962	0	0	5	5	0	Q86WP7|Q8NGW4	Silent	SNP	ENST00000378661.2	37	CCDS1810.1																																																																																			.		0.647	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962		A	42990999	C	A	42990999	2	1	101	1	0	0	0	0	0	0	0	1	11357	581	21	4		4	OXER1	2	42990999	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		42990999	200208374	11	8970											
OSBPL11	114885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	125298795	125298795	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgatattacagctcctgcaAgctgcaaagttcctctaggt	10	12	9	10	0	1	1	0	1	1	0	3	1	3	1	2	1	5	5	2	1	5	4			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr3:125298795A>T	ENST00000296220.5	-	3	612	c.323T>A	c.(322-324)cTt>cAt	p.L108H		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	108	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						AGCTCCTGCAAGCTGCAAAGT	0.403																																					p.L108H		.											.	OSBPL11-135	0			c.T323A						.						118	121	120					3																	125298795		2203	4300	6503	SO:0001583	missense	114885	exon3			CCTGCAAGCTGCA	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.323T>A	3.37:g.125298795A>T	ENSP00000296220:p.Leu108His	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	130	25	NM_022776	0	0	2	3	1	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	37	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.595561	0.86953	.	.	ENSG00000144909	ENST00000296220	D	0.84223	-1.82	5.07	5.07	0.68467	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.071226	0.56097	D	0.000021	D	0.94739	0.8302	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96314	0.9231	10	0.87932	D	0	0.5235	14.9917	0.71393	1.0:0.0:0.0:0.0	.	108	Q9BXB4	OSB11_HUMAN	H	108	ENSP00000296220:L108H	ENSP00000296220:L108H	L	-	2	0	OSBPL11	126781485	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.073000	0.93992	2.124000	0.65301	0.533000	0.62120	CTT	.		0.403	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		T	125298795	A	T	125298795	3	4	101	1	0	0	0	0	1	0	0	0	11302	72	3	5	1964	5	OSBPL11	3	125298795	Missense_Mutation	SNP	A	TCGA-DW-7963-01B-11D-A28G-10		125298795	72723635	12	8971											
NPHP3	27031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132418235	132418235	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttctacattcacagaaacAattactcttacattcactgg	13	14	4	10	0	4	1	2	0	2	1	4	1	4	1	0	1	4	1	0	1	5	6			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr3:132418235A>T	ENST00000337331.5	-	13	2033	c.1947T>A	c.(1945-1947)atT>atA	p.I649I	NPHP3_ENST00000326682.8_Silent_p.I649I	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	649					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCACAGAAACAATTACTCTTA	0.328																																					p.I649I		.											.	NPHP3-91	0			c.T1947A						.						122	107	112					3																	132418235		2203	4300	6503	SO:0001819	synonymous_variant	27031	exon13			AGAAACAATTACT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"Tetratricopeptide (TTC) repeat domain containing"	7907	protein-coding gene	gene with protein product	"nephrocystin-3", "Meckel syndrome, type 7", "cilia and flagella associated protein 31"	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.1947T>A	3.37:g.132418235A>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	61	22	NM_153240	0	0	0	0	0	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Silent	SNP	ENST00000337331.5	37	CCDS3078.1																																																																																			.		0.328	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		T	132418235	A	T	132418235	2	4	101	1	0	0	0	0	0	0	0	1	10606	126	5	5		5	NPHP3	3	132418235	Silent	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	7119440	132418235	65604195	13	8972											
SDHA	6389	hgsc.bcm.edu	37	chr5	218487	218487	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agacatgtcgggggtccgggGcctgtcgcggctgctgagcg	4	7	19	11	5	0	2	0	1	0	1	3	2	1	2	2	5	2	2	2	5	0	0	rs187964306	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr5:218487G>A	ENST00000264932.6	+	1	132	c.17G>A	c.(16-18)gGc>gAc	p.G6D	CTD-2083E4.4_ENST00000565521.1_RNA|SDHA_ENST00000510361.1_Missense_Mutation_p.G6D|CCDC127_ENST00000296824.3_5'Flank|SDHA_ENST00000504309.1_Missense_Mutation_p.G6D	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	6					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GGGGTCCGGGGCCTGTCGCGG	0.781									Familial Paragangliomas				G|||	20	0.00399361	0.0151	0	5008	,	,		8006	0		0	False		,,,				2504	0				p.G6D		.											.	SDHA-226	0			c.G17A						.	G	ASP/GLY	55,3035		0,55,1490	5	7	6		17	-1.9	0	5		6	0,7136		0,0,3568	no	missense	SDHA	NM_004168.2	94	0,55,5058	AA,AG,GG		0.0,1.7799,0.5378	possibly-damaging	6/665	218487	55,10171	1545	3568	5113	SO:0001583	missense	6389	exon1	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	TCCGGGGCCTGTC	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.17G>A	5.37:g.218487G>A	ENSP00000264932:p.Gly6Asp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	9	NM_004168	0	0	8	16	8	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	5.417	0.262064	0.10239	0.017799	0.0	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.71698	-0.59;0.26;-0.59	3.66	-1.91	0.07641	.	0.522646	0.15819	U	0.243080	T	0.25005	0.0607	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.19583	0.004;0.037;0.004;0.004;0.004	B;B;B;B;B	0.20955	0.004;0.032;0.004;0.004;0.019	T	0.12477	-1.0546	10	0.21540	T	0.41	.	4.3656	0.11223	0.0:0.2691:0.2152:0.5156	.	6;6;6;6;12	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	D	6	ENSP00000264932:G6D;ENSP00000426514:G6D;ENSP00000427703:G6D	ENSP00000264932:G6D	G	+	2	0	SDHA	271487	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.926000	0.03988	-0.485000	0.06754	0.471000	0.43371	GGC	G|0.996;A|0.004		0.781	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		A	218487	G	A	218487	3	1	101	1	0	0	0	0	1	0	0	0	13995	1203	42	2	19	2	SDHA	5	218487	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		218487	180696773	14	8973											
NSUN2	54888	hgsc.bcm.edu	37	chr5	6633071	6633071	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgctgttgctggagccgccGaccccgcgaccgccgcccca	4	5	12	20	6	0	0	0	0	0	0	0	3	0	1	8	1	3	3	8	1	0	1	rs181415619	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr5:6633071G>A	ENST00000264670.6	-	1	333	c.22C>T	c.(22-24)Cgg>Tgg	p.R8W	NSUN2_ENST00000539938.1_5'UTR|SRD5A1_ENST00000537411.1_5'Flank|NSUN2_ENST00000506139.1_Missense_Mutation_p.R8W|SRD5A1_ENST00000538824.1_5'Flank|SRD5A1_ENST00000274192.5_5'Flank	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	8					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TGGAGCCGCCGACCCCGCGAC	0.756													G|||	125	0.0249601	0.0893	0.0101	5008	,	,		10402	0		0	False		,,,				2504	0				p.R8W		.											.	NSUN2-91	0			c.C22T						.	G	TRP/ARG,TRP/ARG	120,1992		0,120,936	1	2	2		22,22	2.6	0.9	5		2	3,4631		0,3,2314	no	missense,missense	NSUN2	NM_001193455.1,NM_017755.5	101,101	0,123,3250	AA,AG,GG		0.0647,5.6818,1.8233	probably-damaging,probably-damaging	8/733,8/768	6633071	123,6623	1056	2317	3373	SO:0001583	missense	54888	exon1			GCCGCCGACCCCG	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.22C>T	5.37:g.6633071G>A	ENSP00000264670:p.Arg8Trp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	7	NM_017755	0	0	0	0	0	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	57	0.0260989010989011	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	17.62	3.434487	0.62955	0.056818	6.47E-4	ENSG00000037474	ENST00000264670;ENST00000506139	T;T	0.38722	1.12;1.12	4.5	2.59	0.31030	.	0.397846	0.23951	N	0.042944	T	0.03477	0.0100	L	0.51422	1.61	0.09310	P	0.99999999735625	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	T	0.42085	-0.9472	9	0.72032	D	0.01	-12.5115	9.6603	0.39952	0.0:0.0:0.6264:0.3736	.	8;8	B4DQW2;Q08J23	.;NSUN2_HUMAN	W	8	ENSP00000264670:R8W;ENSP00000420957:R8W	ENSP00000264670:R8W	R	-	1	2	NSUN2	6686071	0.066000	0.20996	0.881000	0.34555	0.921000	0.55340	0.367000	0.20382	0.860000	0.35481	0.557000	0.71058	CGG	G|0.974;A|0.026		0.756	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		A	6633071	G	A	6633071	3	1	101	1	0	0	0	0	1	0	0	0	10704	1057	37	1	2357	1	NSUN2	5	6633071	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	6414584	6633071	174282189	15	8974											
ISL1	3670	broad.mit.edu	37	chr5	50687165	50687165	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagtccagagagacacgacGgtggcttacaggctaaccca	12	5	11	13	2	0	2	0	0	0	2	1	4	1	2	3	3	2	2	3	3	2	2	rs371918442		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr5:50687165G>T	ENST00000230658.7	+	5	1408	c.823G>T	c.(823-825)Ggt>Tgt	p.G275C	ISL1_ENST00000505475.2_3'UTR|ISL1_ENST00000511384.1_Intron	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	275	Gln-rich.|LIM-binding domain (LID). {ECO:0000250}.				atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				GAGACACGACGGTGGCTTACA	0.517																																					p.G275C													.	ISL1-515	0			c.G823T						.						62	65	64					5																	50687165		1934	4139	6073	SO:0001583	missense	3670	exon5			CACGACGGTGGCT	BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"Homeoboxes / LIM class"	6132	protein-coding gene	gene with protein product		600366	"ISL1 transcription factor, LIM/homeodomain, (islet-1)"			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.823G>T	5.37:g.50687165G>T	ENSP00000230658:p.Gly275Cys	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	142	5	NM_002202	0	0	0	0	0	P20663|P47894	Missense_Mutation	SNP	ENST00000230658.7	37	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647492	0.87958	.	.	ENSG00000016082	ENST00000230658	D	0.85484	-1.99	5.93	5.93	0.95920	.	0.053759	0.85682	D	0.000000	D	0.88840	0.6546	L	0.38175	1.15	0.80722	D	1	D	0.71674	0.998	P	0.62184	0.899	D	0.88870	0.3332	10	0.62326	D	0.03	.	20.3311	0.98718	0.0:0.0:1.0:0.0	.	275	P61371	ISL1_HUMAN	C	275	ENSP00000230658:G275C	ENSP00000230658:G275C	G	+	1	0	ISL1	50722922	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	6.671000	0.74472	2.797000	0.96272	0.655000	0.94253	GGT	.		0.517	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202		T	50687165	G	T	50687165	3	4	101	1	0	0	0	0	1	0	0	0	7877	1116	39	4	841	4	ISL1	5	50687165	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	44054094	50687165	130228095	16	8975											
F12	2161	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176833055	176833058	+	Frame_Shift_Del	DEL	AGTG	AGTG	-																															tggcagggctccccggtgacAgtgagaactgcagggacaac																								rs149368999	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	AGTG	AGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr5:176833055_176833058delAGTG	ENST00000253496.3	-	3	168_171	c.120_123delCACT	c.(118-123)ctcactfs	p.LT40fs	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	40					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CCCCGGTGACAGTGAGAACTGCAG	0.588									Hereditary Angioedema																												p.40_41del		.											.	F12-90	0			c.120_123del						.																																			SO:0001589	frameshift_variant	2161	exon3	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	.	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.120_123delCACT	5.37:g.176833055_176833058delAGTG	ENSP00000253496:p.Leu40fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	71	23	NM_000505	0	0	0	0	0	P78339	Frame_Shift_Del	DEL	ENST00000253496.3	37	CCDS34302.1																																																																																			.		0.588	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			-	176833058	AGTG	-	176833055	7	5	101	1	0	1	0	1	0	0	0	0	5352	175	7	0	1772	0	F12	5	176833055	Frame_Shift_Del	DEL	AGTG	TCGA-DW-7963-01B-11D-A28G-10	126145890	176833055	4082205	17	8976											
PRDM13	59336	hgsc.bcm.edu	37	chr6	100061624	100061625	+	In_Frame_Ins	INS	-	-	CCG																															agtgcctgctcgctggggacINSccgccgccgccgccgccgcc																								rs370363311|rs577768379|rs112674667	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr6:100061624_100061625insCCG	ENST00000369215.4	+	4	1418_1419	c.1113_1114insCCG	c.(1114-1116)ccg>CCGccg	p.372_372P>PP		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	372	Poly-Pro.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		TCGCTGGGGACccgccgccgcc	0.757														1281	0.255791	0.3979	0.2017	5008	,	,		7609	0.1062		0.2734	False		,,,				2504	0.2382				p.D371delinsDP		.											.	PRDM13-135	0			c.1113_1114insCCG						.																																			SO:0001652	inframe_insertion	59336	exon4			.	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.1129_1131dupCCG	6.37:g.100061631_100061633dupCCG	ENSP00000358217:p.Pro378dup	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	13	11	NM_021620	0	0	0	0	0	Q5TGC1|Q5TGC2	In_Frame_Ins	INS	ENST00000369215.4	37	CCDS43487.1																																																																																			.		0.757	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			CCG	100061625	-	CCG	100061624	7	5	101	1	0	1	1	0	0	0	0	0	12483	506	18	0	1127	0	PRDM13	6	100061624	In_Frame_Ins	INS	-	TCGA-DW-7963-01B-11D-A28G-10		100061624	71053443	18	8977											
REV3L	5980	ucsc.edu;bcgsc.ca	37	chr6	111701285	111701285	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctgtggttcattttcttCatcatcactattttgtggat	8	20	6	7	0	6	0	4	0	2	0	6	1	6	1	0	2	0	1	0	2	2	7			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr6:111701285C>A	ENST00000358835.3	-	12	1808	c.1354G>T	c.(1354-1356)Gaa>Taa	p.E452*	REV3L_ENST00000368802.3_Nonsense_Mutation_p.E452*|REV3L_ENST00000435970.1_Nonsense_Mutation_p.E374*|REV3L_ENST00000368805.1_Nonsense_Mutation_p.E452*			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	452					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TCATTTTCTTCATCATCACTA	0.398								DNA polymerases (catalytic subunits)																													p.E452X													.	REV3L-294	0			c.G1354T						.						279	252	261					6																	111701285		2203	4300	6503	SO:0001587	stop_gained	5980	exon11			TTTCTTCATCATC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.1354G>T	6.37:g.111701285C>A	ENSP00000351697:p.Glu452*	Somatic	121	2		WXS	Illumina HiSeq		109	35	NM_002912	0	0	0	0	0	O43214|Q5TC33	Nonsense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	46	12.327003	0.99657	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	.	.	.	5.71	5.71	0.89125	.	0.058399	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-8.3219	19.8632	0.96793	0.0:1.0:0.0:0.0	.	.	.	.	X	452;452;452;374	.	ENSP00000351697:E452X	E	-	1	0	REV3L	111807978	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.350000	0.79385	2.699000	0.92147	0.655000	0.94253	GAA	.		0.398	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		A	111701285	C	A	111701285	4	1	101	1	0	0	0	0	0	1	0	0	13272	835	29	4	8126	4	REV3L	6	111701285	Nonsense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	11639661	111701285	59413782	19	8978											
SLC22A3	6581	hgsc.bcm.edu	37	chr6	160769796	160769796	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgcgcggacccactcgcCgccttccccaaccgctcggc	5	5	10	21	6	0	0	0	0	0	0	3	1	1	1	6	2	3	2	6	2	1	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr6:160769796C>T	ENST00000275300.2	+	1	497	c.345C>T	c.(343-345)gcC>gcT	p.A115A	SLC22A3_ENST00000392145.1_Silent_p.A115A	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	115					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	ACCCACTCGCCGCCTTCCCCA	0.756																																					p.A115A		.											.	SLC22A3-517	0			c.C345T						.						3	3	3					6																	160769796		1659	3388	5047	SO:0001819	synonymous_variant	6581	exon1			ACTCGCCGCCTTC	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"Solute carriers"	10967	protein-coding gene	gene with protein product		604842	"solute carrier family 22 (extraneuronal monoamine transporter), member 3"			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.345C>T	6.37:g.160769796C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	23	11	NM_021977	0	0	0	0	0	Q5SYN6|Q9UP02	Silent	SNP	ENST00000275300.2	37	CCDS5277.1																																																																																			.		0.756	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977		T	160769796	C	T	160769796	2	4	101	1	0	0	0	0	0	0	0	1	14487	639	23	1		1	SLC22A3	6	160769796	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	49068511	160769796	10345271	20	8979											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		.											.	TBP-91	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	6.37:g.170871004G>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	75	10	NM_003194	0	0	2	2	0	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	101	1	0	0	0	0	0	0	0	1	15676	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	10101208	170871004	244063	21	8980											
TAF6	6878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99707631	99707631	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttgctcagcacagggccGtccagcacactgcggatccg	8	7	12	14	3	1	0	1	0	0	0	3	1	3	1	3	2	4	4	3	2	0	1	rs148894017		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr7:99707631G>A	ENST00000344095.4	-	12	1749	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TAF6_ENST00000452041.1_Silent_p.D408D|AP4M1_ENST00000421755.1_Intron|TAF6_ENST00000437822.2_Silent_p.D445D|TAF6_ENST00000472509.1_Silent_p.D465D|TAF6_ENST00000453269.2_Silent_p.D408D|TAF6_ENST00000418432.2_Silent_p.D332D	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	408					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCACAGGGCCGTCCAGCACAC	0.587																																					p.D445D		.											.	TAF6-91	0			c.C1335T						.	G	,,	0,4406		0,0,2203	110	97	101		1335,1224,1224	-6.5	0.9	7	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TAF6	NM_001190415.1,NM_005641.3,NM_139315.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	445/715,408/678,408/678	99707631	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6878	exon12			AGGGCCGTCCAGC		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.1224C>T	7.37:g.99707631G>A		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	155	37	NM_001190415	1	0	23	35	11	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Silent	SNP	ENST00000344095.4	37	CCDS5686.1																																																																																			G|1.000;A|0.000		0.587	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		A	99707631	G	A	99707631	2	1	101	1	0	0	0	0	0	0	0	1	15562	1136	40	1		1	TAF6	7	99707631	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		99707631	59431032	22	8981											
SSPO	23145	hgsc.bcm.edu	37	chr7	149487608	149487608	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgagggccccgacgcctgcgTtgaggctcccgcgcccccgg	3	4	15	19	7	0	1	0	1	0	0	1	3	1	1	6	3	1	2	6	3	0	1	rs1635798	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr7:149487608T>G	ENST00000378016.2	+	0	4921							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GACGCCTGCGTTGAGGCTCCC	0.776													G|||	1320	0.263578	0.6959	0.1095	5008	,	,		8211	0.1171		0.0885	False		,,,				2504	0.1196				.		.											.	.	0			c.4921+1T>G						.						1	1	1					7																	149487608		434	1167	1601			23145	exon32			CCTGCGTTGAGGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149487608T>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_198455	0	0	0	0	0	Q76B61	Splice_Site	SNP	ENST00000378016.2	37																																																																																				T|0.784;G|0.216		0.776	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149487608	T	G	149487608	1	3	101	0	1	0	0	0	0	0	0	0	15221	1739	60	5		5	SSPO	7	149487608	RNA	SNP	T	TCGA-DW-7963-01B-11D-A28G-10	49779977	149487608	9651055	23	8982											
GIMAP8	155038	broad.mit.edu	37	chr7	150174500	150174500	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcactgaagaggacaaaacaGctgtggcgaaactggaggcc	14	5	13	9	1	1	2	1	1	0	1	1	5	1	4	1	4	3	1	1	4	4	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr7:150174500G>T	ENST00000307271.3	+	5	2204	c.1630G>T	c.(1630-1632)Gct>Tct	p.A544S		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	544	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		GGACAAAACAGCTGTGGCGAA	0.502																																					p.A544S													.	GIMAP8-95	0			c.G1630T						.						80	77	78					7																	150174500		2203	4300	6503	SO:0001583	missense	155038	exon5			AAAACAGCTGTGG	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1630G>T	7.37:g.150174500G>T	ENSP00000305107:p.Ala544Ser	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	194	8	NM_175571	0	0	1	1	0		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.633250	0.47049	.	.	ENSG00000171115	ENST00000307271	T	0.34859	1.34	4.44	1.39	0.22231	AIG1 (1);	3.096750	0.01386	N	0.013095	T	0.33673	0.0871	L	0.41236	1.265	0.09310	N	1	P	0.35793	0.521	B	0.38378	0.272	T	0.23833	-1.0177	10	0.45353	T	0.12	.	5.6382	0.17548	0.3651:0.0:0.6349:0.0	.	544	Q8ND71	GIMA8_HUMAN	S	544	ENSP00000305107:A544S	ENSP00000305107:A544S	A	+	1	0	GIMAP8	149805433	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.442000	0.21628	0.518000	0.28383	-0.150000	0.13652	GCT	.		0.502	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		T	150174500	G	T	150174500	3	4	101	1	0	0	0	0	1	0	0	0	6405	971	34	4	1644	4	GIMAP8	7	150174500	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	686892	150174500	8964163	24	8983											
HR	55806	hgsc.bcm.edu	37	chr8	21974513	21974513	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atccaggtagcagctgcctgGggcgccaggctccagggcgc	6	5	16	14	2	0	0	0	0	0	0	2	0	2	0	4	5	3	4	4	5	1	1	rs143782421	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr8:21974513G>C	ENST00000381418.4	-	17	4733	c.3253C>G	c.(3253-3255)Cca>Gca	p.P1085A	HR_ENST00000312841.8_Intron	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1085	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CAGCTGCCTGGGGCGCCAGGC	0.716													G|||	40	0.00798722	0.028	0.0043	5008	,	,		13773	0		0	False		,,,				2504	0				p.P1085A		.											.	HR-154	0			c.C3253G						.	G	ALA/PRO,	28,3236		0,28,1604	2	3	3		3253,	4.4	0	8	dbSNP_134	3	0,6902		0,0,3451	no	missense,intron	HR	NM_005144.4,NM_018411.4	27,	0,28,5055	CC,CG,GG		0.0,0.8578,0.2754	probably-damaging,	1085/1190,	21974513	28,10138	1632	3451	5083	SO:0001583	missense	55806	exon17			TGCCTGGGGCGCC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.3253C>G	8.37:g.21974513G>C	ENSP00000370826:p.Pro1085Ala	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	17	8	NM_005144	0	0	0	0	0	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	G	16.79	3.221593	0.58560	0.008578	0.0	ENSG00000168453	ENST00000381418	T	0.70282	-0.47	5.32	4.44	0.53790	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.123995	0.37715	N	0.001968	T	0.49167	0.1541	L	0.36672	1.1	0.33054	D	0.533176	P	0.43750	0.816	P	0.46362	0.514	T	0.70890	-0.4749	10	0.59425	D	0.04	-10.3405	9.9179	0.41446	0.0936:0.0:0.9064:0.0	.	1085	O43593	HAIR_HUMAN	A	1085	ENSP00000370826:P1085A	ENSP00000370826:P1085A	P	-	1	0	HR	22030458	0.909000	0.30893	0.029000	0.17559	0.847000	0.48162	3.053000	0.49901	1.367000	0.46095	0.655000	0.94253	CCA	G|0.994;C|0.006		0.716	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			C	21974513	G	C	21974513	3	2	101	1	0	0	0	0	1	0	0	0	7368	1232	43	4	328	4	HR	8	21974513	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		21974513	124389509	25	8984			2	29		2	2	38	N	G_C	6.8125e-05
HR	55806	hgsc.bcm.edu	37	chr8	21974550	21974550	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcctgccccggccgggcaCacctcaaagaagagaagggg	10	2	15	14	3	1	2	1	0	0	2	1	3	1	2	5	4	1	1	5	4	3	0	rs146855847	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr8:21974550C>T	ENST00000381418.4	-	17	4696	c.3216G>A	c.(3214-3216)gtG>gtA	p.V1072V	HR_ENST00000312841.8_Intron	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1072	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CGGCCGGGCACACCTCAAAGA	0.687													C|||	40	0.00798722	0.028	0.0043	5008	,	,		14630	0		0	False		,,,				2504	0				p.V1072V		.											.	HR-154	0			c.G3216A						.	C	,	44,3144		0,44,1550	3	3	3		3216,	3.5	1	8	dbSNP_134	3	1,6735		0,1,3367	no	coding-synonymous,intron	HR	NM_005144.4,NM_018411.4	,	0,45,4917	TT,TC,CC		0.0148,1.3802,0.4534	,	1072/1190,	21974550	45,9879	1594	3368	4962	SO:0001819	synonymous_variant	55806	exon17			CGGGCACACCTCA	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.3216G>A	8.37:g.21974550C>T		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	15	5	NM_005144	0	0	0	0	0	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			C|0.994;T|0.006		0.687	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			T	21974550	C	T	21974550	2	4	101	1	0	0	0	0	0	0	0	1	7368	465	17	2		2	HR	8	21974550	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	37	21974550	124389472	26	8985			2	29		2	2	38	N	G_C	6.8125e-05
STMN4	81551	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	27099960	27099960	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggggatcggccaggaagcaGgagcagaacaaggacaccag	15	1	16	9	1	0	1	0	0	0	1	1	5	0	5	2	6	3	2	2	6	3	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr8:27099960G>A	ENST00000265770.7	-	3	199	c.63C>T	c.(61-63)tcC>tcT	p.S21S	STMN4_ENST00000519997.1_Silent_p.S12S|STMN4_ENST00000350889.4_Silent_p.S21S|STMN4_ENST00000523048.1_Silent_p.S21S|STMN4_ENST00000519614.1_Silent_p.S21S|STMN4_ENST00000522908.1_Silent_p.S21S			Q9H169	STMN4_HUMAN	stathmin-like 4	21					regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	CCAGGAAGCAGGAGCAGAACA	0.577																																					p.S21S													.	STMN4-154	0			c.C63T						.						104	97	100					8																	27099960		2203	4300	6503	SO:0001819	synonymous_variant	81551	exon3			GAAGCAGGAGCAG		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.63C>T	8.37:g.27099960G>A		Somatic	113	1		WXS	Illumina HiSeq	Phase_I	138	43	NM_030795	0	0	0	0	0	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Silent	SNP	ENST00000265770.7	37																																																																																				.		0.577	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		A	27099960	G	A	27099960	2	1	101	1	0	0	0	0	0	0	0	1	15343	987	35	2		2	STMN4	8	27099960	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	5125410	27099960	119264062	27	8986											
C9orf156	51531	broad.mit.edu	37	chr9	100672508	100672508	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggccaatttgttcttctGccacgctggaactctgatca	8	13	9	11	1	4	1	1	1	3	0	4	2	4	2	2	2	2	2	2	2	2	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr9:100672508G>T	ENST00000375119.3	-	4	876	c.800C>A	c.(799-801)gCa>gAa	p.A267E	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	267					viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				TTGTTCTTCTGCCACGCTGGA	0.468																																					p.A267E													.	C9orf156-90	0			c.C800A						.						168	163	165					9																	100672508		2203	4300	6503	SO:0001583	missense	51531	exon4			TCTTCTGCCACGC	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"Nef (lentivirus myristoylated factor) associated protein 1"						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.800C>A	9.37:g.100672508G>T	ENSP00000364260:p.Ala267Glu	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	207	6	NM_016481	0	0	6	6	0	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	.	.	.	.	.	.	.	.	.	.	G	2.642	-0.283955	0.05642	.	.	ENSG00000136932	ENST00000375119;ENST00000375118;ENST00000325350	T;T	0.32272	1.88;1.46	5.03	3.07	0.35406	Uncharacterised domain UPF0066, YaeB-like domain (1);	1.008340	0.07952	N	0.981024	T	0.28466	0.0704	L	0.29908	0.895	0.09310	N	1	B;D;P	0.53462	0.082;0.96;0.483	B;P;B	0.47891	0.069;0.56;0.058	T	0.13282	-1.0515	10	0.48119	T	0.1	-1.4593	6.9791	0.24694	0.0908:0.0:0.6546:0.2546	.	164;121;267	Q6Y2L2;Q5T114;Q9BU70	.;.;NAP1_HUMAN	E	267;121;164	ENSP00000364260:A267E;ENSP00000364259:A121E	ENSP00000324426:A164E	A	-	2	0	C9orf156	99712329	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.188000	0.17018	1.253000	0.44018	0.563000	0.77884	GCA	.		0.468	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481		T	100672508	G	T	100672508	3	4	101	1	0	0	0	0	1	0	0	0	2471	1319	46	4	533	4	C9orf156	9	100672508	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		100672508	40540923	28	8987											
AKNA	80709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	117143567	117143567	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccgccgctgggggcccttcCccaggccaggctcagcccag	4	4	14	19	2	1	0	1	0	0	0	2	0	2	0	7	4	1	2	7	4	0	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr9:117143567C>A	ENST00000307564.4	-	2	208	c.47G>T	c.(46-48)gGg>gTg	p.G16V	AKNA_ENST00000374088.3_Missense_Mutation_p.G16V|AKNA_ENST00000312033.3_Missense_Mutation_p.G16V	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	16					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GGGGCCCTTCCCCAGGCCAGG	0.622																																					p.G16V		.											.	AKNA-94	0			c.G47T						.						35	28	31					9																	117143567		2201	4299	6500	SO:0001583	missense	80709	exon2			CCCTTCCCCAGGC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.47G>T	9.37:g.117143567C>A	ENSP00000303769:p.Gly16Val	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	83	25	NM_030767	0	0	2	2	0	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.167000	0.38217	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000312033;ENST00000394574	T;T;T	0.58940	1.58;1.58;0.3	3.83	3.83	0.44106	.	0.000000	0.43919	D	0.000520	T	0.64023	0.2561	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66614	-0.5879	10	0.87932	D	0	-30.4003	11.5452	0.50690	0.0:1.0:0.0:0.0	.	16;16	Q7Z591-6;Q7Z591	.;AKNA_HUMAN	V	16	ENSP00000303769:G16V;ENSP00000363201:G16V;ENSP00000309222:G16V	ENSP00000303769:G16V	G	-	2	0	AKNA	116183388	0.873000	0.30073	0.977000	0.42913	0.053000	0.15095	1.457000	0.35212	2.460000	0.83146	0.561000	0.74099	GGG	.		0.622	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		A	117143567	C	A	117143567	3	1	101	1	0	0	0	0	1	0	0	0	463	623	22	4	4356	4	AKNA	9	117143567	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	16471059	117143567	24069864	29	8988											
GAD2	2572	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	26506915	26506915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caactacgcgtttctccatgCaacaggtaaagactcagcgg	12	8	9	12	3	2	1	1	0	1	1	3	1	2	1	1	2	5	3	1	2	5	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr10:26506915C>T	ENST00000376261.3	+	3	784	c.281C>T	c.(280-282)gCa>gTa	p.A94V	GAD2_ENST00000376248.1_5'Flank|GAD2_ENST00000259271.3_Missense_Mutation_p.A94V	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	94					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTTCTCCATGCAACAGGTAAA	0.721																																					p.A94V		.											.	GAD2-515	0			c.C281T						.						27	36	33					10																	26506915		2200	4295	6495	SO:0001583	missense	2572	exon3			TCCATGCAACAGG	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.281C>T	10.37:g.26506915C>T	ENSP00000365437:p.Ala94Val	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	195	54	NM_000818	0	0	0	0	0	Q9UD87	Missense_Mutation	SNP	ENST00000376261.3	37	CCDS7149.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996975	0.54147	.	.	ENSG00000136750	ENST00000376261;ENST00000259271;ENST00000428517	T;T;T	0.59638	0.25;0.25;0.25	5.84	4.88	0.63580	.	0.414814	0.27068	N	0.021100	T	0.51398	0.1672	L	0.54323	1.7	0.80722	D	1	P;B	0.39480	0.675;0.048	B;B	0.32864	0.154;0.016	T	0.59289	-0.7482	10	0.56958	D	0.05	-3.897	16.0867	0.81060	0.0:0.866:0.134:0.0	.	94;94	Q4G154;Q05329	.;DCE2_HUMAN	V	94	ENSP00000365437:A94V;ENSP00000259271:A94V;ENSP00000390434:A94V	ENSP00000259271:A94V	A	+	2	0	GAD2	26546921	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.858000	0.62947	2.768000	0.95171	0.561000	0.74099	GCA	.		0.721	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26506915	C	T	26506915	3	4	101	1	0	0	0	0	1	0	0	0	6199	710	25	2	291	2	GAD2	10	26506915	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		26506915	109027832	30	8989											
KIF5B	3799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	32326205	32326205	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttcactaccagctaaatcaaCcagataaagttttccactca	15	11	3	12	0	3	1	3	0	0	1	4	1	4	1	3	0	3	2	3	0	6	6			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr10:32326205C>A	ENST00000302418.4	-	8	1145	c.688G>T	c.(688-690)Gtt>Ttt	p.V230F		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	230	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				GCTAAATCAACCAGATAAAGT	0.338			T	"RET, ALK"	NSCLC																																p.V230F		.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B-399	0			c.G688T						.						127	110	116					10																	32326205		2202	4298	6500	SO:0001583	missense	3799	exon8			AATCAACCAGATA	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.688G>T	10.37:g.32326205C>A	ENSP00000307078:p.Val230Phe	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	77	10	NM_004521	0	0	4	5	1	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891963	0.91889	.	.	ENSG00000170759	ENST00000302418	D	0.83335	-1.71	5.0	5.0	0.66597	Kinesin, motor domain (5);Kinesin, motor region, conserved site (1);	0.062994	0.64402	D	0.000007	D	0.95404	0.8508	H	0.99299	4.505	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97679	1.0171	10	0.87932	D	0	.	18.6607	0.91471	0.0:1.0:0.0:0.0	.	230	P33176	KINH_HUMAN	F	230	ENSP00000307078:V230F	ENSP00000307078:V230F	V	-	1	0	KIF5B	32366211	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.811000	0.86092	2.449000	0.82847	0.557000	0.71058	GTT	.		0.338	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		A	32326205	C	A	32326205	3	1	101	1	0	0	0	0	1	0	0	0	8327	507	18	4	2275	4	KIF5B	10	32326205	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	5819290	32326205	103208542	31	8990											
MUC2	4583	bcgsc.ca	37	chr11	1093061	1093061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccactggcacacagacccCaaccccaacagccatcacca	14	2	4	21	0	1	1	1	0	0	1	1	1	1	1	7	1	3	1	7	1	2	0	rs111210454		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:1093061C>T	ENST00000441003.2	+	30	4907	c.4880C>T	c.(4879-4881)cCa>cTa	p.P1627L	MUC2_ENST00000359061.5_Missense_Mutation_p.P1594L|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	acacagaccccaaccccaaca	0.632																																					p.P1627L													.	MUC2-90	0			c.C4880T						.						128	165	153					11																	1093061		1874	3606	5480	SO:0001583	missense	4583	exon30			AGACCCCAACCCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4880C>T	11.37:g.1093061C>T	ENSP00000415183:p.Pro1627Leu	Somatic	86	1		WXS	Illumina HiSeq	Phase_1	90	7	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	6.096	0.386050	0.11524	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13657	2.57;2.97	1.61	1.61	0.23674	.	13.230700	0.00633	U	0.000492	T	0.09774	0.0240	.	.	.	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.22906	-1.0203	9	0.27785	T	0.31	.	6.7045	0.23242	0.0:1.0:0.0:0.0	.	1627	E7EUV1	.	L	1627;1594	ENSP00000415183:P1627L;ENSP00000351956:P1594L	ENSP00000351956:P1594L	P	+	2	0	MUC2	1083061	0.000000	0.05858	0.009000	0.14445	0.048000	0.14542	0.279000	0.18771	0.910000	0.36722	0.121000	0.15741	CCA	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093061	C	T	1093061	3	4	101	1	0	0	0	0	1	0	0	0	10000	594	21	2	4998	2	MUC2	11	1093061	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		1093061	133913455	32	8991											
MUC2	4583	broad.mit.edu	37	chr11	1093204	1093204	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccggcacacagtccccaaccCcaacagccatcaccaccacc	12	2	4	23	1	1	0	1	0	0	0	2	0	2	0	9	1	3	1	9	1	2	0	rs56299570		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:1093204C>A	ENST00000441003.2	+	30	5050	c.5023C>A	c.(5023-5025)Cca>Aca	p.P1675T	MUC2_ENST00000359061.5_Missense_Mutation_p.P1642T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.P1675T(1)|p.P1642T(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gtccccaaccccaacagccat	0.627																																					p.P1675T													.	MUC2-90	2	Substitution - Missense(2)	kidney(2)	c.C5023A						.																																			SO:0001583	missense	4583	exon30			CCAACCCCAACAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5023C>A	11.37:g.1093204C>A	ENSP00000415183:p.Pro1675Thr	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	55	5	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.954	-0.705464	0.03255	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.09073	3.02;3.53	1.75	-3.49	0.04724	.	0.575351	0.10542	U	0.662513	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	9	0.16896	T	0.51	.	6.9769	0.24681	0.6778:0.3222:0.0:0.0	rs56299570	1675	E7EUV1	.	T	1675;1642	ENSP00000415183:P1675T;ENSP00000351956:P1642T	ENSP00000351956:P1642T	P	+	1	0	MUC2	1083204	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.268000	0.00533	-1.450000	0.01936	0.184000	0.17185	CCA	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093204	C	A	1093204	3	1	101	1	0	0	0	0	1	0	0	0	10000	623	22	4	5141	4	MUC2	11	1093204	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	143	1093204	133913312	33	8992											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253980	1253980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggcgtacagctcagcgActggagggacggcgtctgca	9	5	16	11	4	2	0	1	0	1	0	2	3	2	2	0	4	4	3	0	4	2	1	rs202127660		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:1253980A>G	ENST00000529681.1	+	17	2103	c.2045A>G	c.(2044-2046)gAc>gGc	p.D682G	MUC5B_ENST00000447027.1_Missense_Mutation_p.D685G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	682					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGCTCAGCGACTGGAGGGAC	0.682																																					p.D682G		.											.	.	0			c.A2045G						.						21	24	23					11																	1253980		2116	4228	6344	SO:0001583	missense	727897	exon17			TCAGCGACTGGAG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2045A>G	11.37:g.1253980A>G	ENSP00000436812:p.Asp682Gly	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	96	6	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	A	7.541	0.660740	0.14645	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76060	-0.99;-0.99	4.6	2.72	0.32119	Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.50103	0.1596	N	0.02960	-0.455	0.24874	N	0.992269	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45920	-0.9228	9	0.87932	D	0	.	8.6635	0.34108	0.2416:0.0:0.7584:0.0	.	682;1341;685	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	682;685;683;718	ENSP00000436812:D682G;ENSP00000415793:D685G	ENSP00000343037:D683G	D	+	2	0	MUC5B	1210556	0.999000	0.42202	0.632000	0.29296	0.070000	0.16714	2.607000	0.46300	0.373000	0.24621	-1.983000	0.00453	GAC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1253980	A	G	1253980	3	3	101	1	0	0	0	0	1	0	0	0	10004	275	10	3	2120	3	MUC5B	11	1253980	Missense_Mutation	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	160776	1253980	133752536	34	8993											
STIM1	6786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4104179	4104179	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggcccacagctcttcccTggatgatgtagatcataaaa	11	10	9	11	1	2	2	1	1	1	1	3	3	3	3	2	2	1	2	2	2	3	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:4104179T>G	ENST00000300737.4	+	9	1774	c.1205T>G	c.(1204-1206)cTg>cGg	p.L402R	STIM1_ENST00000533977.1_Missense_Mutation_p.L229R|STIM1_ENST00000527651.1_Missense_Mutation_p.L402R	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	402	SOAR/CAD.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		AGCTCTTCCCTGGATGATGTA	0.448																																					p.L402R		.											.	STIM1-91	0			c.T1205G						.						104	93	97					11																	4104179		2201	4298	6499	SO:0001583	missense	6786	exon9			CTTCCCTGGATGA	BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"Sterile alpha motif (SAM) domain containing"	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.1205T>G	11.37:g.4104179T>G	ENSP00000300737:p.Leu402Arg	Somatic	365	0		WXS	Illumina HiSeq	Phase_I	324	102	NM_003156	0	0	1	1	0	E9PQJ4|Q8N382	Missense_Mutation	SNP	ENST00000300737.4	37	CCDS7749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.99|19.99	3.928765|3.928765	0.73327|0.73327	.|.	.|.	ENSG00000167323|ENSG00000167323	ENST00000300737;ENST00000527651;ENST00000533977|ENST00000526596	T;T;T|.	0.81330|.	-0.52;-1.48;-0.51|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73009|0.73009	0.3532|0.3532	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.69307|.	0.946;0.963|.	T|T	0.73528|0.73528	-0.3954|-0.3954	10|5	0.87932|.	D|.	0|.	-15.7324|-15.7324	14.4442|14.4442	0.67338|0.67338	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	402;402|.	E9PQJ4;Q13586|.	.;STIM1_HUMAN|.	R|G	402;402;229|133	ENSP00000300737:L402R;ENSP00000436208:L402R;ENSP00000434767:L229R|.	ENSP00000300737:L402R|.	L|W	+|+	2|1	0|0	STIM1|STIM1	4060755|4060755	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.687000|7.687000	0.84139|0.84139	2.007000|2.007000	0.58848|0.58848	0.374000|0.374000	0.22700|0.22700	CTG|TGG	.		0.448	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156		G	4104179	T	G	4104179	3	3	101	1	0	0	0	0	1	0	0	0	15315	1580	55	5	1239	5	STIM1	11	4104179	Missense_Mutation	SNP	T	TCGA-DW-7963-01B-11D-A28G-10	2850199	4104179	130902337	35	8994											
GPR44	11251	hgsc.bcm.edu	37	chr11	60620166	60620167	+	In_Frame_Ins	INS	-	-	GCG																															gagcgggcggtggaggaggtINSgcggcggcggcggctgcttc																								rs55642873	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:60620166_60620167insGCG	ENST00000332539.4	-	2	1140_1141	c.1029_1030insCGC	c.(1027-1032)cgcacc>cgcCGCacc	p.343_344insR	RP11-804A23.4_ENST00000538705.1_RNA	NM_004778.2	NP_004769.2	Q9Y5Y4	PD2R2_HUMAN	prostaglandin D2 receptor 2	343					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|calcium-mediated signaling (GO:0019722)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|prostaglandin D receptor activity (GO:0004956)|prostaglandin F receptor activity (GO:0004958)|prostaglandin J receptor activity (GO:0001785)									Indomethacin(DB00328)|Sulindac(DB00605)	GTGGAGGAGGTGCGGCGGCGGC	0.748														93	0.0185703	0.0514	0.0086	5008	,	,		8844	0		0.0119	False		,,,				2504	0.0072				p.T344delinsRT		.											.	.	0			c.1030_1031insCGC						.																																			SO:0001652	inframe_insertion	11251	exon2			.	AF118265	CCDS7994.1	11q12-q13.3	2012-08-08	2011-11-11	2011-11-11		ENSG00000183134		"CD molecules", "GPCR / Class A : Prostanoid receptors"	4502	protein-coding gene	gene with protein product	"chemoattractant receptor homologous molecule expressed on T helper type 2 cells"	604837	"G protein-coupled receptor 44"	GPR44		10036181	Standard	NM_004778		Approved	CRTH2, CD294, DP2	uc001nqc.2	Q9Y5Y4		ENST00000332539.4:c.1027_1029dupCGC	11.37:g.60620173_60620175dupGCG	ENSP00000332812:p.Arg343_Arg343dup	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	48	12	NM_004778	0	0	0	0	0	O94765|Q4QRI6	In_Frame_Ins	INS	ENST00000332539.4	37	CCDS7994.1																																																																																			.		0.748	PTGDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396328.1	NM_004778		GCG	60620167	-	GCG	60620166	7	5	101	1	0	1	1	0	0	0	0	0	6715	1696	59	0	161	0	GPR44	11	60620166	In_Frame_Ins	INS	-	TCGA-DW-7963-01B-11D-A28G-10	56515987	60620166	74386350	36	8995											
PRPH	5630	hgsc.bcm.edu	37	chr12	49689404	49689404	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggagccggcgcgcgccGaccagctgtgccagcaggag	7	2	17	15	5	0	0	0	0	0	0	0	3	0	2	5	3	4	2	5	3	0	0	rs58599399	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr12:49689404G>T	ENST00000257860.4	+	1	1920	c.421G>T	c.(421-423)Gac>Tac	p.D141Y	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						GGCGCGCGCCGACCAGCTGTG	0.716													G|||	12	0.00239617	0	0.0029	5008	,	,		14065	0		0.0099	False		,,,				2504	0				p.D141Y		.											.	PRPH-90	0			c.G421T	GRCh37	CM044928	PRPH	M	rs58599399	.	G	TYR/ASP	2,3866		0,2,1932	3	4	3	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	421	4.7	1	12	dbSNP_129	3	42,7412		0,42,3685	yes	missense	PRPH	NM_006262.3	160	0,44,5617	TT,TG,GG		0.5635,0.0517,0.3886	possibly-damaging	141/471	49689404	44,11278	1934	3727	5661	SO:0001583	missense	5630	exon1			CGCGCCGACCAGC		CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.421G>T	12.37:g.49689404G>T	ENSP00000257860:p.Asp141Tyr	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	99	56	NM_006262	0	0	0	0	0	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000257860.4	37	CCDS8783.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	21.9	4.223071	0.79464	5.17E-4	0.005635	ENSG00000135406	ENST00000257860	D	0.88509	-2.39	4.68	4.68	0.58851	Filament (1);	0.000000	0.42053	D	0.000774	D	0.83344	0.5234	N	0.20881	0.62	0.41388	D	0.987592	P	0.43392	0.805	P	0.54210	0.745	D	0.85943	0.1459	10	0.66056	D	0.02	.	10.2156	0.43166	0.0:0.0:0.802:0.198	rs58599399	141	P41219	PERI_HUMAN	Y	141	ENSP00000257860:D141Y	ENSP00000257860:D141Y	D	+	1	0	PRPH	47975671	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	7.738000	0.84966	2.443000	0.82685	0.462000	0.41574	GAC	G|0.999;T|0.001		0.716	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		T	49689404	G	T	49689404	3	4	101	1	0	0	0	0	1	0	0	0	12605	1058	37	4	423	4	PRPH	12	49689404	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		49689404	84162491	37	8996											
GNS	2799	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	65152878	65152878	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttaccatgccgccgagcActtcgtcctggtcgtccgtg	5	10	12	14	5	0	0	0	0	0	0	4	2	2	0	5	1	3	2	5	1	1	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr12:65152878A>T	ENST00000258145.3	-	1	349	c.179T>A	c.(178-180)gTg>gAg	p.V60E	RP11-629N8.3_ENST00000434563.3_RNA|GNS_ENST00000543646.1_Missense_Mutation_p.V60E|GNS_ENST00000542058.1_Missense_Mutation_p.V60E|snoU13_ENST00000458789.1_RNA	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	60					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		GCCGCCGAGCACTTCGTCCTG	0.652																																					p.V60E													.	GNS-514	0			c.T179A						.						32	32	32					12																	65152878		2195	4284	6479	SO:0001583	missense	2799	exon1			CCGAGCACTTCGT		CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"Sanfilippo disease IIID", "N-acetylglucosamine-6-sulfatase"	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.179T>A	12.37:g.65152878A>T	ENSP00000258145:p.Val60Glu	Somatic	159	1		WXS	Illumina HiSeq	Phase_I	229	52	NM_002076	0	0	0	0	0	B4DYH8|Q53F05	Missense_Mutation	SNP	ENST00000258145.3	37	CCDS8970.1	.	.	.	.	.	.	.	.	.	.	A	5.620	0.299140	0.10622	.	.	ENSG00000135677	ENST00000258145;ENST00000543646;ENST00000542058	D;D;D	0.98419	-4.92;-3.89;-3.89	4.48	3.3	0.37823	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.545721	0.18931	N	0.127212	D	0.92773	0.7702	N	0.10945	0.07	0.28091	N	0.931782	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.14023	0.01;0.004;0.002	D	0.85646	0.1279	9	.	.	.	-13.4349	8.0519	0.30583	0.8117:0.0:0.0:0.1883	.	60;60;60	B4DYH8;F6S8M0;P15586	.;.;GNS_HUMAN	E	60	ENSP00000258145:V60E;ENSP00000438497:V60E;ENSP00000444819:V60E	.	V	-	2	0	GNS	63439145	0.993000	0.37304	1.000000	0.80357	0.933000	0.57130	0.814000	0.27239	0.823000	0.34589	0.397000	0.26171	GTG	.		0.652	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2			T	65152878	A	T	65152878	3	4	101	1	0	0	0	0	1	0	0	0	6570	159	6	5	1535	5	GNS	12	65152878	Missense_Mutation	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	15463474	65152878	68699017	38	8997											
TMTC2	160335	broad.mit.edu	37	chr12	83251082	83251082	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcttgatgtttgcttctcAccccattcacacggaggcag	7	12	10	12	1	2	1	2	1	1	0	3	2	2	2	2	3	1	4	2	3	0	4			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr12:83251082A>C	ENST00000321196.3	+	2	1084	c.377A>C	c.(376-378)cAc>cCc	p.H126P	TMTC2_ENST00000548305.1_Missense_Mutation_p.H126P|TMTC2_ENST00000549919.1_Missense_Mutation_p.H120P	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	126					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TTTGCTTCTCACCCCATTCAC	0.522																																					p.H126P													.	TMTC2-92	0			c.A377C						.						124	111	116					12																	83251082		2203	4300	6503	SO:0001583	missense	160335	exon2			CTTCTCACCCCAT	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"Tetratricopeptide (TTC) repeat domain containing"	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.377A>C	12.37:g.83251082A>C	ENSP00000322300:p.His126Pro	Somatic	119	21		WXS	Illumina HiSeq	Phase_I	181	33	NM_152588	0	0	0	0	0	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	A	18.60	3.658613	0.67586	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	T;T;T	0.78246	-0.79;-1.16;-1.06	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.91945	0.7449	H	0.96662	3.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94358	0.7585	10	0.87932	D	0	-21.9399	14.6569	0.68838	1.0:0.0:0.0:0.0	.	126;126	Q8N394;F8VSH2	TMTC2_HUMAN;.	P	126;126;120	ENSP00000322300:H126P;ENSP00000448292:H126P;ENSP00000447609:H120P	ENSP00000322300:H126P	H	+	2	0	TMTC2	81775213	1.000000	0.71417	0.957000	0.39632	0.649000	0.38597	8.904000	0.92590	2.251000	0.74343	0.528000	0.53228	CAC	.		0.522	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		C	83251082	A	C	83251082	3	2	101	1	0	0	0	0	1	0	0	0	16293	159	6	5	383	5	TMTC2	12	83251082	Missense_Mutation	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	18098204	83251082	50600813	39	8998											
CEP290	80184	broad.mit.edu;bcgsc.ca	37	chr12	88471486	88471486	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaattacctgtaatccactGgttagtcttttaatttgcct	11	17	5	8	0	1	0	0	0	1	0	2	0	2	0	3	1	2	2	3	1	6	6			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr12:88471486G>T	ENST00000552810.1	-	40	5917	c.5574C>A	c.(5572-5574)acC>acA	p.T1858T	CEP290_ENST00000547691.2_Silent_p.T918T|CEP290_ENST00000309041.7_Silent_p.T1860T|CEP290_ENST00000397838.3_Silent_p.T918T	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1858					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						GTAATCCACTGGTTAGTCTTT	0.269																																					p.T1858T													.	CEP290-96	0			c.C5574A						.						51	50	51					12																	88471486		1799	4036	5835	SO:0001819	synonymous_variant	80184	exon40			TCCACTGGTTAGT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5574C>A	12.37:g.88471486G>T		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_025114	0	0	0	0	0	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	37	CCDS55858.1																																																																																			.		0.269	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88471486	G	T	88471486	2	4	101	1	0	0	0	0	0	0	0	1	3259	1335	47	4		4	CEP290	12	88471486	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	5220404	88471486	45380409	40	8999											
RXFP2	122042	bcgsc.ca	37	chr13	32352703	32352703	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagatgtgtgcccaaatGcctcaactcaactgggtgtg	11	9	11	10	0	2	1	2	0	0	1	2	1	2	1	2	1	5	1	2	1	4	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr13:32352703G>T	ENST00000298386.2	+	9	839	c.768G>T	c.(766-768)atG>atT	p.M256I	RXFP2_ENST00000380314.1_Missense_Mutation_p.M256I	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	256					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		GTGCCCAAATGCCTCAACTCA	0.328																																					p.M256I													.	RXFP2-90	0			c.G768T						.						128	136	133					13																	32352703		2203	4298	6501	SO:0001583	missense	122042	exon9			CCAAATGCCTCAA	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.768G>T	13.37:g.32352703G>T	ENSP00000298386:p.Met256Ile	Somatic	49	0		WXS	Illumina HiSeq	Phase_1	63	4	NM_001166058	0	0	0	0	0	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556594	0.45487	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.04502	4.29;3.61	5.49	5.49	0.81192	.	0.079417	0.85682	D	0.000000	T	0.07279	0.0184	L	0.53780	1.695	0.47698	D	0.999496	B;B	0.29590	0.25;0.25	B;B	0.29942	0.109;0.109	T	0.30851	-0.9964	10	0.27082	T	0.32	.	14.881	0.70534	0.0:0.0:1.0:0.0	.	256;256	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	I	256	ENSP00000369670:M256I;ENSP00000298386:M256I	ENSP00000298386:M256I	M	+	3	0	RXFP2	31250703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.963000	0.63694	2.578000	0.87016	0.655000	0.94253	ATG	.		0.328	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		T	32352703	G	T	32352703	3	4	101	1	0	0	0	0	1	0	0	0	13792	1319	46	4	802	4	RXFP2	13	32352703	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		32352703	82817175	41	9000											
ZIC5	85416	hgsc.bcm.edu	37	chr13	100623585	100623585	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcggctgccggagcctcCgggtgtgccgggaacgcctg	3	5	19	14	6	0	0	0	0	0	0	1	2	1	2	5	5	4	1	5	5	1	0	rs370840169	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr13:100623585C>T	ENST00000267294.4	-	1	578	c.345G>A	c.(343-345)ccG>ccA	p.P115P		NM_033132.3	NP_149123.2	Q96T25	ZIC5_HUMAN	Zic family member 5	115	Pro-rich.				cell differentiation (GO:0030154)|forebrain development (GO:0030900)|neural tube closure (GO:0001843)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|lung(2)|prostate(1)|skin(2)	9	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCGGAGCCTCCGGGTGTGCCG	0.781													c|||	6	0.00119808	0.0045	0	5008	,	,		6715	0		0	False		,,,				2504	0				p.P115P		.											.	ZIC5-90	0			c.G345A						.			21,3461		0,21,1720	3	3	3		345	0	0.2	13		3	0,6836		0,0,3418	no	coding-synonymous	ZIC5	NM_033132.3		0,21,5138	TT,TC,CC		0.0,0.6031,0.2035		115/664	100623585	21,10297	1741	3418	5159	SO:0001819	synonymous_variant	85416	exon1			AGCCTCCGGGTGT	AF378304	CCDS9494.2	13q32.2	2013-01-08	2011-05-19		ENSG00000139800	ENSG00000139800		"Zinc fingers, C2H2-type"	20322	protein-coding gene	gene with protein product			"Zic family member 5 (odd-paired homolog, Drosophila)"				Standard	NM_033132		Approved		uc001vom.1	Q96T25	OTTHUMG00000017280	ENST00000267294.4:c.345G>A	13.37:g.100623585C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	9	NM_033132	0	0	0	0	0	Q5VYB0	Silent	SNP	ENST00000267294.4	37	CCDS9494.2																																																																																			.		0.781	ZIC5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000045623.3	NM_033132		T	100623585	C	T	100623585	2	4	101	1	0	0	0	0	0	0	0	1	17714	639	23	1		1	ZIC5	13	100623585	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	68270882	100623585	14546293	42	9001											
HECTD1	25831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31576342	31576342	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caagaaaattccaaggaaatGaaacagtttcgtgatccttt	16	11	7	7	1	0	3	0	2	0	1	3	4	2	4	2	1	1	1	2	1	6	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr14:31576342G>A	ENST00000399332.1	-	38	7224	c.6736C>T	c.(6736-6738)Cat>Tat	p.H2246Y	HECTD1_ENST00000553700.1_Missense_Mutation_p.H2246Y	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2246	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CCAAGGAAATGAAACAGTTTC	0.383																																					p.H2246Y		.											.	HECTD1-570	0			c.C6736T						.						113	108	110					14																	31576342		1901	4112	6013	SO:0001583	missense	25831	exon38			GGAAATGAAACAG	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6736C>T	14.37:g.31576342G>A	ENSP00000382269:p.His2246Tyr	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	161	36	NM_015382	0	0	2	4	2	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	3.742	-0.053467	0.07362	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332	T;T	0.56941	0.43;0.43	6.06	6.06	0.98353	HECT (4);	0.256570	0.26903	U	0.021909	T	0.31949	0.0813	N	0.11201	0.11	0.46298	D	0.99897	P	0.35208	0.49	B	0.32762	0.152	T	0.28138	-1.0053	10	0.02654	T	1	-11.499	18.8088	0.92050	0.0:0.0:1.0:0.0	.	2246	Q9ULT8	HECD1_HUMAN	Y	2246;2248;2246	ENSP00000450697:H2246Y;ENSP00000382269:H2246Y	ENSP00000261312:H2248Y	H	-	1	0	HECTD1	30646093	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.391000	0.73208	2.871000	0.98454	0.655000	0.94253	CAT	.		0.383	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31576342	G	A	31576342	3	1	101	1	0	0	0	0	1	0	0	0	7060	1290	45	2	1120	2	HECTD1	14	31576342	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		31576342	75773198	43	9002											
KIF7	374654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90174782	90174782	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgatctccaggcgctgctTgagcagcgagtccttctcct	5	11	11	14	3	2	1	0	1	2	0	6	3	3	1	3	1	3	3	3	1	0	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr15:90174782T>G	ENST00000394412.3	-	15	3131	c.3055A>C	c.(3055-3057)Aag>Cag	p.K1019Q	KIF7_ENST00000558928.1_5'Flank	NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	1019					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			AGGCGCTGCTTGAGCAGCGAG	0.677																																					p.K1019Q		.											.	KIF7-523	0			c.A3055C						.						29	27	27					15																	90174782		2199	4292	6491	SO:0001583	missense	374654	exon15			GCTGCTTGAGCAG	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"Kinesins"	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.3055A>C	15.37:g.90174782T>G	ENSP00000377934:p.Lys1019Gln	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	100	32	NM_198525	0	0	0	0	0	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.877591	0.91664	.	.	ENSG00000166813	ENST00000394412	T	0.48836	0.8	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.66577	0.2803	M	0.70275	2.135	0.54753	D	0.999983	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.994	T	0.67321	-0.5700	10	0.40728	T	0.16	.	14.4086	0.67101	0.0:0.0:0.0:1.0	.	505;1019	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	Q	1019	ENSP00000377934:K1019Q	ENSP00000377934:K1019Q	K	-	1	0	KIF7	87975786	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.570000	0.82390	1.802000	0.52723	0.379000	0.24179	AAG	.		0.677	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		G	90174782	T	G	90174782	3	3	101	1	0	0	0	0	1	0	0	0	8330	1821	63	5	996	5	KIF7	15	90174782	Missense_Mutation	SNP	T	TCGA-DW-7963-01B-11D-A28G-10		90174782	12356610	44	9003											
FAM100A	124402	broad.mit.edu	37	chr16	4659850	4659850	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggggaagtgtggcgggggTgacgtggctgtcgcggccat	4	8	22	7	4	0	1	0	1	0	0	1	2	0	2	1	7	0	1	1	7	1	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr16:4659850T>G	ENST00000283474.7	-	3	446	c.318A>C	c.(316-318)tcA>tcC	p.S106S	UBALD1_ENST00000587649.1_3'UTR|UBALD1_ENST00000591897.1_Silent_p.S46S|UBALD1_ENST00000590965.1_3'UTR|UBALD1_ENST00000590891.1_Silent_p.S141S|UBALD1_ENST00000587615.1_Silent_p.S81S|UBALD1_ENST00000591401.1_Silent_p.S85S	NM_145253.2	NP_660296.1	Q8TB05	UBAD1_HUMAN	UBA-like domain containing 1	106																	GTGGCGGGGGTGACGTGGCTG	0.716																																					p.S106S													.	.	0			c.A318C						.						6	7	7					16																	4659850		2008	3990	5998	SO:0001819	synonymous_variant	124402	exon3			CGGGGGTGACGTG	BC025327	CCDS10518.1	16p13.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000153443	ENSG00000153443			29576	protein-coding gene	gene with protein product			"family with sequence similarity 100, member A"	FAM100A			Standard	NM_145253		Approved		uc002cwx.2	Q8TB05	OTTHUMG00000129472	ENST00000283474.7:c.318A>C	16.37:g.4659850T>G		Somatic	18	7		WXS	Illumina HiSeq	Phase_I	61	26	NM_145253	0	0	1	4	3	Q71MF6	Silent	SNP	ENST00000283474.7	37	CCDS10518.1																																																																																			.		0.716	UBALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251635.2	NM_145253		G	4659850	T	G	4659850	2	3	101	1	0	0	0	0	0	0	0	1	5394	1683	59	5		5	FAM100A	16	4659850	Silent	SNP	T	TCGA-DW-7963-01B-11D-A28G-10		4659850	85694903	45	9004											
USP31	57478	hgsc.bcm.edu	37	chr16	23160421	23160422	+	In_Frame_Ins	INS	-	-	GAGGAGGGC																															agctgcccaccgagcgtgcaINSgaggagggcgaggagggcga																								rs555380492	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr16:23160421_23160422insGAGGAGGGC	ENST00000219689.7	-	1	169_170	c.170_171insGCCCTCCTC	c.(169-171)tct>tcGCCCTCCTCt	p.57_57S>SPSS		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCGAGCGTGCAGAGGAGGGCGA	0.762														35	0.00698882	0.025	0.0014	5008	,	,		3570	0.001		0	False		,,,				2504	0				p.S57delinsSPSS		.											.	USP31-663	0			c.171_172insGCCCTCCTC						.																																			SO:0001652	inframe_insertion	57478	exon1			.	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"Ubiquitin-specific peptidases"	20060	protein-coding gene	gene with protein product			"ubiquitin specific protease 31"			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.162_170dupGCCCTCCTC	16.37:g.23160422_23160430dupGAGGAGGGC	ENSP00000219689:p.ProSerSer57dup	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	58	12	NM_020718	0	0	0	0	0	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	In_Frame_Ins	INS	ENST00000219689.7	37	CCDS10607.1																																																																																			.		0.762	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		GAGGAGGGC	23160422	-	GAGGAGGGC	23160421	7	5	101	1	0	1	1	0	0	0	0	0	17095	175	7	0	3951	0	USP31	16	23160421	In_Frame_Ins	INS	-	TCGA-DW-7963-01B-11D-A28G-10	18500571	23160421	67194332	46	9005											
TRIM72	260434	hgsc.bcm.edu	37	chr16	31226442	31226442	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgccgaggcccacgcacGcctcaaggtgcgggatccgc	6	4	14	17	6	1	0	1	0	0	0	2	2	2	1	5	3	2	1	5	3	1	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr16:31226442G>A	ENST00000302964.3	-	0	813				TRIM72_ENST00000322122.3_Missense_Mutation_p.R128H|PYDC1_ENST00000568383.1_5'Flank	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1						innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						GCCCACGCACGCCTCAAGGTG	0.687																																					p.R128H		.											.	TRIM72-44	0			c.G383A						.						9	9	9					16																	31226442		1778	3412	5190	SO:0001628	intergenic_variant	493829	exon2			ACGCACGCCTCAA		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"pyrin domain containing 1"			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407		16.37:g.31226442G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	31	19	NM_001008274	0	0	0	0	0	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	37	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.815564	0.70912	.	.	ENSG00000177238	ENST00000322122	T	0.57436	0.4	4.93	4.93	0.64822	.	0.080103	0.48767	D	0.000171	T	0.62441	0.2428	L	0.58101	1.795	0.34316	D	0.686018	D	0.89917	1.0	D	0.67725	0.953	T	0.65340	-0.6192	10	0.16420	T	0.52	.	10.896	0.47023	0.0887:0.0:0.9113:0.0	.	128	Q6ZMU5	TRI72_HUMAN	H	128	ENSP00000312675:R128H	ENSP00000312675:R128H	R	+	2	0	TRIM72	31133943	0.998000	0.40836	0.997000	0.53966	0.042000	0.13812	3.403000	0.52615	2.454000	0.82982	0.655000	0.94253	CGC	.		0.687	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		A	31226442	G	A	31226442	1	1	101	0	1	0	0	0	0	0	0	0	16578	1087	38	1		1	TRIM72	16	31226442	IGR	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	8066021	31226442	59128311	47	9006											
ZDHHC7	55625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	85010785	85010785	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agaagaccctcaaggcacagGaagatcaacaggattacagt	17	5	10	9	0	2	3	2	0	0	3	2	5	2	5	1	3	2	1	1	3	5	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr16:85010785G>A	ENST00000313732.4	-	7	1018	c.666C>T	c.(664-666)ttC>ttT	p.F222F	ZDHHC7_ENST00000569488.1_5'UTR|ZDHHC7_ENST00000564466.1_Silent_p.F259F	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	222					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						CAAGGCACAGGAAGATCAACA	0.463																																					p.F259F		.											.	ZDHHC7-289	0			c.C777T						.						155	139	144					16																	85010785		2199	4300	6499	SO:0001819	synonymous_variant	55625	exon8			GCACAGGAAGATC	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"Zinc fingers, DHHC-type"	18459	protein-coding gene	gene with protein product	"Sertoli cell gene with zinc finger domain-&#946;"	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.666C>T	16.37:g.85010785G>A		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	209	45	NM_001145548	0	0	3	3	0	D3DUM1|Q8WV42|Q9NVD8	Silent	SNP	ENST00000313732.4	37	CCDS10950.1																																																																																			.		0.463	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		A	85010785	G	A	85010785	2	1	101	1	0	0	0	0	0	0	0	1	17652	1165	41	2		2	ZDHHC7	16	85010785	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	53784343	85010785	5343968	48	9007											
FSCN2	25794	hgsc.bcm.edu	37	chr17	79504052	79504052	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgcgcggcggcgcctcgggCctgctgcgggccgatgccga	2	5	18	16	8	0	0	0	0	0	0	1	2	0	0	4	4	4	1	4	4	0	0	rs398123553	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr17:79504052C>A	ENST00000417245.2	+	5	1561	c.1425C>A	c.(1423-1425)ggC>ggA	p.G475G	FSCN2_ENST00000334850.7_Silent_p.G499G	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	475					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GCGCCTCGGGCCTGCTGCGGG	0.726													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		8785	0		0	False		,,,				2504	0				p.G499G		.											.	.	0			c.C1497A						.						2	2	2					17																	79504052		1250	2873	4123	SO:0001819	synonymous_variant	25794	exon5			CTCGGGCCTGCTG	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"Fascins"	3960	protein-coding gene	gene with protein product		607643	"fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)", "fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.1425C>A	17.37:g.79504052C>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	8	5	NM_001077182	0	0	0	0	0	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	37	CCDS45811.1																																																																																			.		0.726	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		A	79504052	C	A	79504052	2	1	101	1	0	0	0	0	0	0	0	1	6087	726	26	4		4	FSCN2	17	79504052	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		79504052	1691158	49	9008											
ZNF567	163081	broad.mit.edu	37	chr19	37210687	37210687	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgaagtcacacctcattcGtcatcagagaactcacacgg	13	9	7	12	2	5	2	5	1	0	1	6	3	5	2	1	1	1	0	1	1	2	2	rs562512567		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr19:37210687G>A	ENST00000536254.2	+	6	1283	c.1061G>A	c.(1060-1062)cGt>cAt	p.R354H	ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Missense_Mutation_p.R323H|ZNF567_ENST00000360729.4_Missense_Mutation_p.R323H|ZNF567_ENST00000585696.1_Missense_Mutation_p.R323H|ZNF567_ENST00000392163.2_Missense_Mutation_p.R323H			Q8N184	ZN567_HUMAN	zinc finger protein 567	354					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CACCTCATTCGTCATCAGAGA	0.458																																					p.R323H													.	ZNF567-90	0			c.G968A						.						75	68	71					19																	37210687		2203	4300	6503	SO:0001583	missense	163081	exon4			TCATTCGTCATCA	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.1061G>A	19.37:g.37210687G>A	ENSP00000441838:p.Arg354His	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	111	5	NM_152603	0	0	0	0	0	B3KX49|Q6N044	Missense_Mutation	SNP	ENST00000536254.2	37		.	.	.	.	.	.	.	.	.	.	G	14.55	2.568648	0.45798	.	.	ENSG00000189042	ENST00000536254;ENST00000360729;ENST00000423498;ENST00000392163	T;T;T	0.07567	3.18;3.18;3.18	4.53	3.48	0.39840	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.190951	0.26654	N	0.023191	T	0.24890	0.0604	M	0.70842	2.15	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.73380	0.97;0.98	T	0.00998	-1.1486	10	0.45353	T	0.12	.	12.1099	0.53834	0.0:0.0:0.8276:0.1724	.	354;323	Q8N184;F8WEL6	ZN567_HUMAN;.	H	354;323;353;323	ENSP00000441838:R354H;ENSP00000353957:R323H;ENSP00000376003:R323H	ENSP00000353957:R323H	R	+	2	0	ZNF567	41902527	0.000000	0.05858	0.994000	0.49952	0.912000	0.54170	-0.782000	0.04643	1.231000	0.43661	0.462000	0.41574	CGT	.		0.458	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		A	37210687	G	A	37210687	3	1	101	1	0	0	0	0	1	0	0	0	18030	1145	40	1	978	1	ZNF567	19	37210687	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		37210687	21918296	50	9009											
DNMT3B	1789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31389169	31389169	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gatgaccggccgttcttctgGatgtttgagaatgttgtagc	7	14	13	7	2	2	2	0	2	2	1	2	5	2	3	2	2	1	4	2	2	2	5			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:31389169G>C	ENST00000328111.2	+	19	2403	c.2082G>C	c.(2080-2082)tgG>tgC	p.W694C	DNMT3B_ENST00000456297.2_Missense_Mutation_p.W598C|DNMT3B_ENST00000443239.3_Missense_Mutation_p.W632C|DNMT3B_ENST00000344505.4_Missense_Mutation_p.W674C|DNMT3B_ENST00000353855.2_Missense_Mutation_p.W674C|DNMT3B_ENST00000348286.2_Missense_Mutation_p.W674C|DNMT3B_ENST00000201963.3_Missense_Mutation_p.W686C	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	694	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGTTCTTCTGGATGTTTGAGA	0.532																																					p.W694C		.											.	DNMT3B-660	0			c.G2082C						.						105	95	98					20																	31389169		2203	4300	6503	SO:0001583	missense	1789	exon19			CTTCTGGATGTTT		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.2082G>C	20.37:g.31389169G>C	ENSP00000328547:p.Trp694Cys	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	264	77	NM_006892	0	0	0	0	0	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875757	0.91664	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	D;D;D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.91858	0.7423	M	0.80508	2.5	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.992;0.998;0.999;0.999;0.987;0.999;0.999	D	0.92078	0.5670	10	0.87932	D	0	-23.2234	19.2924	0.94105	0.0:0.0:1.0:0.0	.	598;632;393;686;674;674;694	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	C	694;674;674;632;598;674;686	ENSP00000328547:W694C;ENSP00000313397:W674C;ENSP00000337764:W674C;ENSP00000403169:W632C;ENSP00000412305:W598C;ENSP00000345105:W674C;ENSP00000201963:W686C	ENSP00000201963:W686C	W	+	3	0	DNMT3B	30852830	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.835000	0.99442	2.878000	0.98634	0.650000	0.86243	TGG	.		0.532	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		C	31389169	G	C	31389169	3	2	101	1	0	0	0	0	1	0	0	0	4688	1183	41	4	2192	4	DNMT3B	20	31389169	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		31389169	31636351	51	9010											
L3MBTL	26013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42162966	42162966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaatatgaagctggaggctGtggaccgcaggaacccagcc	11	6	13	11	1	1	1	1	1	0	0	1	4	1	4	3	4	3	3	3	4	4	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:42162966G>A	ENST00000427442.2	+	15	1735	c.1576G>A	c.(1576-1578)Gtg>Atg	p.V526M	L3MBTL1_ENST00000373134.1_Missense_Mutation_p.V458M|L3MBTL1_ENST00000444063.1_Missense_Mutation_p.V458M|L3MBTL1_ENST00000373135.3_Missense_Mutation_p.V458M|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.V526M			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	458					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						GCTGGAGGCTGTGGACCGCAG	0.632																																					p.V526M		.											.	L3MBTL1-227	0			c.G1576A						.						45	47	46					20																	42162966		2203	4300	6503	SO:0001583	missense	26013	exon15			GAGGCTGTGGACC	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1576G>A	20.37:g.42162966G>A	ENSP00000402107:p.Val526Met	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	101	25	NM_032107	0	0	0	0	0	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	37	CCDS46602.2	.	.	.	.	.	.	.	.	.	.	G	31	5.080728	0.94050	.	.	ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861;ENST00000373133	T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19	5.39	5.39	0.77823	.	0.115236	0.64402	D	0.000019	T	0.69324	0.3098	M	0.91459	3.21	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.997;1.0;0.996	T	0.76170	-0.3057	10	0.87932	D	0	.	18.0965	0.89492	0.0:0.0:1.0:0.0	.	526;110;458;458	Q9Y468-5;Q9Y468-3;Q9Y468-2;Q9Y468-1	.;.;.;.	M	526;526;458;458;458;244;110	ENSP00000402107:V526M;ENSP00000398516:V526M;ENSP00000362227:V458M;ENSP00000403316:V458M;ENSP00000362226:V458M;ENSP00000410139:V244M	ENSP00000362225:V110M	V	+	1	0	L3MBTL1	41596380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.598000	0.98277	2.804000	0.96469	0.655000	0.94253	GTG	.		0.632	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		A	42162966	G	A	42162966	3	1	101	1	0	0	0	0	1	0	0	0	8612	1377	48	2	1418	2	L3MBTL	20	42162966	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	10773797	42162966	20862554	52	9011											
SLC13A3	64849	broad.mit.edu	37	chr20	45194975	45194975	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagcacagccagggcgggggGcacattctccagggggtgca	8	4	17	12	1	1	0	0	0	1	0	2	0	1	0	2	6	3	3	2	6	0	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:45194975G>A	ENST00000279027.4	-	11	1405	c.1387C>T	c.(1387-1389)Ccc>Tcc	p.P463S	SLC13A3_ENST00000396360.1_Missense_Mutation_p.P381S|SLC13A3_ENST00000435032.1_Missense_Mutation_p.P48S|SLC13A3_ENST00000290317.5_Missense_Mutation_p.P416S|SLC13A3_ENST00000413164.2_Missense_Mutation_p.P413S|SLC13A3_ENST00000495082.1_Missense_Mutation_p.P416S|SLC13A3_ENST00000472148.1_Missense_Mutation_p.P381S	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	463					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	AGGGCGGGGGGCACATTCTCC	0.607																																					p.P463S													.	SLC13A3-91	0			c.C1387T						.						95	98	97					20																	45194975		2203	4300	6503	SO:0001583	missense	64849	exon11			CGGGGGGCACATT	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1387C>T	20.37:g.45194975G>A	ENSP00000279027:p.Pro463Ser	Somatic	227	0		WXS	Illumina HiSeq	Phase_I	236	4	NM_022829	0	0	5	5	0	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125209	0.37533	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000435032;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082	T;T;T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93;3.93;3.93	5.25	3.3	0.37823	.	0.169329	0.53938	N	0.000051	T	0.06462	0.0166	L	0.48260	1.515	0.80722	D	1	P;P;P;B;B;P	0.40476	0.581;0.718;0.622;0.28;0.327;0.471	P;P;P;B;B;B	0.46585	0.521;0.451;0.465;0.253;0.37;0.3	T	0.25152	-1.0140	10	0.62326	D	0.03	-17.9448	8.7132	0.34395	0.2304:0.0:0.7696:0.0	.	413;48;381;416;365;463	B4DIR8;B4E181;Q8WWT9-3;F6WI18;B4DF27;Q8WWT9	.;.;.;.;.;S13A3_HUMAN	S	416;381;48;463;381;413;416	ENSP00000290317:P416S;ENSP00000379648:P381S;ENSP00000403394:P48S;ENSP00000279027:P463S;ENSP00000420177:P381S;ENSP00000415852:P413S;ENSP00000419621:P416S	ENSP00000279027:P463S	P	-	1	0	SLC13A3	44628382	1.000000	0.71417	0.307000	0.25127	0.310000	0.27922	4.143000	0.58051	0.601000	0.29879	0.561000	0.74099	CCC	.		0.607	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			A	45194975	G	A	45194975	3	1	101	1	0	0	0	0	1	0	0	0	14425	1203	42	2	433	2	SLC13A3	20	45194975	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	3032009	45194975	17830545	53	9012											
PREX1	57580	broad.mit.edu	37	chr20	47258948	47258948	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggggcaaaggtcctacctgGttaaagaggtgctccaggca	10	8	14	9	0	0	1	0	0	0	1	2	1	2	1	3	6	2	4	3	6	4	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:47258948G>A	ENST00000371941.3	-	28	3703	c.3681C>T	c.(3679-3681)aaC>aaT	p.N1227N	PREX1_ENST00000396220.1_Silent_p.N1227N|PREX1_ENST00000496915.1_5'UTR	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1227					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GTCCTACCTGGTTAAAGAGGT	0.607																																					p.N1227N													.	PREX1-231	0			c.C3681T						.						67	65	66					20																	47258948		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon28			TACCTGGTTAAAG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3681C>T	20.37:g.47258948G>A		Somatic	142	1		WXS	Illumina HiSeq	Phase_I	140	4	NM_020820	0	0	0	0	0	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			.		0.607	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47258948	G	A	47258948	2	1	101	1	0	0	0	0	0	0	0	1	12505	1252	44	2		2	PREX1	20	47258948	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	2063973	47258948	15766572	54	9013											
FAM65C	140876	broad.mit.edu	37	chr20	49208955	49208955	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcacaccctcggagtgcCgtccagctggagcagcgccc	6	5	12	18	3	0	0	0	0	0	0	2	2	1	2	5	2	5	3	5	2	0	0	rs77093450	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:49208955C>G	ENST00000327979.2	-	19	2902	c.2491G>C	c.(2491-2493)Ggc>Cgc	p.G831R	FAM65C_ENST00000462842.1_5'Flank|FAM65C_ENST00000535356.1_Missense_Mutation_p.G835R|FAM65C_ENST00000045083.2_Missense_Mutation_p.G831R			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	831										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCGGAGTGCCGTCCAGCTGG	0.672																																					p.G831R													.	FAM65C-92	0			c.G2491C						.						32	36	34					20																	49208955		1970	4144	6114	SO:0001583	missense	140876	exon19			GAGTGCCGTCCAG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.2491G>C	20.37:g.49208955C>G	ENSP00000332663:p.Gly831Arg	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	127	6	NM_080829	0	0	2	2	0	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	37	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948982	0.73787	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.77750	-1.12;-1.12;-1.12	4.81	4.81	0.61882	.	0.941590	0.08689	U	0.908334	D	0.83631	0.5296	L	0.54323	1.7	0.38977	D	0.958862	P;D	0.60575	0.767;0.988	P;P	0.54460	0.457;0.753	T	0.80120	-0.1515	10	0.39692	T	0.17	-29.6403	17.893	0.88878	0.0:1.0:0.0:0.0	.	835;831	F5H0X2;Q96MK2	.;FA65C_HUMAN	R	831;831;835	ENSP00000332663:G831R;ENSP00000045083:G831R;ENSP00000439802:G835R	ENSP00000045083:G831R	G	-	1	0	FAM65C	48642362	0.928000	0.31464	0.978000	0.43139	0.640000	0.38277	3.910000	0.56371	2.216000	0.71823	0.462000	0.41574	GGC	.		0.672	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			G	49208955	C	G	49208955	3	3	101	1	0	0	0	0	1	0	0	0	5620	652	23	4	365	4	FAM65C	20	49208955	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	1950007	49208955	13816565	55	9014											
DOPEY2	9980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	37642372	37642372	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggctcttccttggagcaaaCcagctggctaagcagaaacc	11	7	10	13	1	1	1	0	0	1	1	2	2	2	2	3	3	5	5	3	3	3	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr21:37642372C>T	ENST00000399151.3	+	27	5634	c.5549C>T	c.(5548-5550)aCc>aTc	p.T1850I		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1850					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTGGAGCAAACCAGCTGGCTA	0.493																																					p.T1850I		.											.	DOPEY2-91	0			c.C5549T						.						104	109	108					21																	37642372		2203	4300	6503	SO:0001583	missense	9980	exon27			AGCAAACCAGCTG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.5549C>T	21.37:g.37642372C>T	ENSP00000382104:p.Thr1850Ile	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	82	25	NM_005128	0	0	4	6	2	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422737	0.83559	.	.	ENSG00000142197	ENST00000399151	T	0.14516	2.5	5.47	4.59	0.56863	.	0.049713	0.85682	N	0.000000	T	0.41119	0.1145	M	0.85542	2.76	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.41998	-0.9477	10	0.51188	T	0.08	-3.5123	13.7957	0.63168	0.0:0.9267:0.0:0.0733	.	1850;1850	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	I	1850	ENSP00000382104:T1850I	ENSP00000382104:T1850I	T	+	2	0	DOPEY2	36564242	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.300000	0.78841	1.311000	0.45024	0.650000	0.86243	ACC	.		0.493	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37642372	C	T	37642372	3	4	101	1	0	0	0	0	1	0	0	0	4719	507	18	2	5651	2	DOPEY2	21	37642372	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		37642372	10487523	56	9015											
KCNJ4	3761	broad.mit.edu	37	chr22	38822920	38822920	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcccgcctcctccttggaAcccgcctccaggcccaggcc	5	6	9	21	2	0	0	0	0	0	0	3	1	3	1	9	3	2	0	9	3	1	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr22:38822920A>C	ENST00000303592.3	-	2	1476	c.1218T>G	c.(1216-1218)ggT>ggG	p.G406G	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	406					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					CCTCCTTGGAACCCGCCTCCA	0.672																																					p.G406G													.	KCNJ4-90	0			c.T1218G						.						45	55	52					22																	38822920		2200	4299	6499	SO:0001819	synonymous_variant	3761	exon2			CTTGGAACCCGCC	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.1218T>G	22.37:g.38822920A>C		Somatic	66	4		WXS	Illumina HiSeq	Phase_I	191	23	NM_004981	0	0	0	0	0	Q14D44	Silent	SNP	ENST00000303592.3	37	CCDS13971.1																																																																																			.		0.672	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		C	38822920	A	C	38822920	2	2	101	1	0	0	0	0	0	0	0	1	8074	30	2	5		5	KCNJ4	22	38822920	Silent	SNP	A	TCGA-DW-7963-01B-11D-A28G-10		38822920	12481646	57	9016											
ZBED4	9889	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50279802	50279802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgtgcagtgcttcagccataCggtgaacctgatcgtcagcg	8	9	12	12	4	2	2	2	2	0	0	3	2	2	2	2	1	6	2	2	1	2	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr22:50279802C>T	ENST00000216268.5	+	2	2969	c.2492C>T	c.(2491-2493)aCg>aTg	p.T831M		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	831						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TTCAGCCATACGGTGAACCTG	0.642																																					p.T831M													.	ZBED4-92	0			c.C2492T						.						35	35	35					22																	50279802		2202	4300	6502	SO:0001583	missense	9889	exon2			GCCATACGGTGAA	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"Zinc fingers, BED-type"	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2492C>T	22.37:g.50279802C>T	ENSP00000216268:p.Thr831Met	Somatic	114	1		WXS	Illumina HiSeq	Phase_I	159	49	NM_014838	0	0	0	0	0	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.451158	0.43531	.	.	ENSG00000100426	ENST00000216268	T	0.23348	1.91	5.57	3.46	0.39613	Ribonuclease H-like (1);	0.113857	0.64402	N	0.000019	T	0.47911	0.1471	M	0.77820	2.39	0.49483	D	0.999791	D	0.89917	1.0	D	0.71656	0.974	T	0.44757	-0.9307	10	0.54805	T	0.06	-22.2447	10.3753	0.44079	0.1354:0.7951:0.0:0.0695	.	831	O75132	ZBED4_HUMAN	M	831	ENSP00000216268:T831M	ENSP00000216268:T831M	T	+	2	0	ZBED4	48665806	0.999000	0.42202	0.659000	0.29680	0.301000	0.27625	4.300000	0.59079	0.688000	0.31529	0.655000	0.94253	ACG	.		0.642	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50279802	C	T	50279802	3	4	101	1	0	0	0	0	1	0	0	0	17552	536	19	1	2494	1	ZBED4	22	50279802	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	11456882	50279802	1024764	58	9017											
ZCCHC17	51538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	31836979	31836979	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaaggcacacatcaaaagAcagcaaggcagcaaagaaga	20	1	11	9	0	1	3	1	0	0	3	1	3	1	3	0	3	2	5	0	3	6	0	rs111803813		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:31836979A>C	ENST00000373714.1	+	8	926	c.665A>C	c.(664-666)gAc>gCc	p.D222A	ZCCHC17_ENST00000422613.2_Missense_Mutation_p.D224A|FABP3_ENST00000497275.1_5'Flank|ZCCHC17_ENST00000344147.5_Missense_Mutation_p.D222A|ZCCHC17_ENST00000546109.1_Missense_Mutation_p.D214A	NM_001282568.1|NM_001282570.1	NP_001269497.1|NP_001269499.1	Q9NP64	NO40_HUMAN	zinc finger, CCHC domain containing 17	222	Lys-rich.					cytosolic large ribosomal subunit (GO:0022625)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)		ACATCAAAAGACAGCAAGGCA	0.433																																					p.D222A		.											.	ZCCHC17-91	0			c.A665C						.						82	86	85					1																	31836979		2203	4300	6503	SO:0001583	missense	51538	exon8			CAAAAGACAGCAA	AF151085	CCDS341.1, CCDS60061.1, CCDS72741.1, CCDS72742.1, CCDS72743.1, CCDS72744.1	1p35.2	2008-05-02			ENSG00000121766	ENSG00000121766		"Zinc fingers, CCHC domain containing"	30246	protein-coding gene	gene with protein product						12202495, 12893261	Standard	NM_001282572		Approved	PS1D, HSPC251, pNO40	uc001bsp.1	Q9NP64	OTTHUMG00000003791	ENST00000373714.1:c.665A>C	1.37:g.31836979A>C	ENSP00000362819:p.Asp222Ala	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	133	23	NM_016505	0	0	32	41	9	B4DY38|D3DPN4|Q6PKH4|Q9NYG4|Q9P0M8	Missense_Mutation	SNP	ENST00000373714.1	37	CCDS341.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025038	0.54683	.	.	ENSG00000121766	ENST00000344147;ENST00000373714;ENST00000546109;ENST00000422613	.	.	.	5.08	5.08	0.68730	.	0.376195	0.32055	N	0.006643	T	0.41488	0.1161	N	0.19112	0.55	0.25685	N	0.98575	D;B;B	0.69078	0.997;0.023;0.008	D;B;B	0.75484	0.986;0.007;0.001	T	0.23904	-1.0175	9	0.66056	D	0.02	.	9.0275	0.36239	0.814:0.186:0.0:0.0	.	224;214;222	E7EPF0;B4DY38;Q9NP64	.;.;NO40_HUMAN	A	222;222;214;224	.	ENSP00000343557:D222A	D	+	2	0	ZCCHC17	31609566	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.513000	0.45494	2.135000	0.66039	0.528000	0.53228	GAC	G|1.000;|0.000		0.433	ZCCHC17-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010665.1	NM_016505		C	31836979	A	C	31836979	3	2	102	1	0	0	0	0	1	0	0	0	17617	275	10	5	691	5	ZCCHC17	1	31836979	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08		31836979	217413642	1	9018											
ADAM30	11085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	120436921	120436921	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaattgacgagggaatcgccCctctgagcagtcctggaggc	10	7	13	11	2	1	2	0	2	1	0	3	5	2	4	3	3	1	1	3	3	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:120436921C>T	ENST00000369400.1	-	1	2197	c.2039G>A	c.(2038-2040)gGg>gAg	p.G680E		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	680					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		GGGAATCGCCCCTCTGAGCAG	0.473																																					p.G680E		.											.	ADAM30-228	0			c.G2039A						.						65	64	64					1																	120436921		2203	4300	6503	SO:0001583	missense	11085	exon1			ATCGCCCCTCTGA	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2039G>A	1.37:g.120436921C>T	ENSP00000358407:p.Gly680Glu	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	95	31	NM_021794	0	0	0	0	0	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.021307	0.00414	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01126	5.3	5.05	-10.1	0.00402	.	3.564080	0.01402	N	0.013659	T	0.00109	0.0003	N	0.05031	-0.125	0.09310	N	1	B	0.13145	0.007	B	0.13407	0.009	T	0.47394	-0.9121	10	0.02654	T	1	.	1.9545	0.03373	0.4755:0.1902:0.2118:0.1224	.	680	Q9UKF2	ADA30_HUMAN	E	680	ENSP00000358407:G680E	ENSP00000358407:G680E	G	-	2	0	ADAM30	120238444	.	.	0.000000	0.03702	0.002000	0.02628	.	.	-4.800000	0.00031	-1.047000	0.02352	GGG	.		0.473	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		T	120436921	C	T	120436921	3	4	102	1	0	0	0	0	1	0	0	0	248	623	22	2	337	2	ADAM30	1	120436921	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	88599942	120436921	128813700	2	9019											
AIM2	9447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	159033450	159033450	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggtcaaataatatgtttttCttcttttctgttacctataa	11	20	4	6	0	4	0	1	0	3	0	4	0	4	0	1	1	1	2	1	1	6	10			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:159033450C>G	ENST00000368130.4	-	5	1119	c.831G>C	c.(829-831)aaG>aaC	p.K277N	AIM2_ENST00000411768.1_5'Flank	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	277	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					ATATGTTTTTCTTCTTTTCTG	0.398																																					p.K277N		.											.	AIM2-93	0			c.G831C						.						117	121	120					1																	159033450		2203	4300	6503	SO:0001583	missense	9447	exon5			GTTTTTCTTCTTT	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.831G>C	1.37:g.159033450C>G	ENSP00000357112:p.Lys277Asn	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	199	60	NM_004833	0	0	2	2	0	A8K7M7|Q5T3V9|Q96FG9	Missense_Mutation	SNP	ENST00000368130.4	37	CCDS1181.1	.	.	.	.	.	.	.	.	.	.	C	2.160	-0.392489	0.04899	.	.	ENSG00000163568	ENST00000368130;ENST00000368129	T;T	0.14266	2.52;2.52	3.92	-4.82	0.03171	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	1.433050	0.05063	N	0.480252	T	0.01558	0.0050	N	0.17723	0.515	0.09310	N	1	B	0.21606	0.058	B	0.19391	0.025	T	0.42816	-0.9429	10	0.14252	T	0.57	-0.6466	1.0125	0.01500	0.1428:0.2093:0.2823:0.3657	.	277	O14862	AIM2_HUMAN	N	277;140	ENSP00000357112:K277N;ENSP00000357111:K140N	ENSP00000357111:K140N	K	-	3	2	AIM2	157300074	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.991000	0.03728	-0.739000	0.04809	-1.099000	0.02127	AAG	.		0.398	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833		G	159033450	C	G	159033450	3	3	102	1	0	0	0	0	1	0	0	0	432	912	32	4	208	4	AIM2	1	159033450	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	38596529	159033450	90217171	3	9020											
GLUL	2752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	182356292	182356292	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccttcgattgtacttgaaaActtcacataacaccagcttg	12	12	6	11	1	1	1	1	1	0	0	2	2	1	1	2	0	4	2	2	0	4	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:182356292A>T	ENST00000331872.6	-	3	842	c.302T>A	c.(301-303)gTt>gAt	p.V101D	GLUL_ENST00000417584.2_Missense_Mutation_p.V101D|GLUL_ENST00000339526.4_Missense_Mutation_p.V101D|GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000311223.5_Missense_Mutation_p.V101D	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	101					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	GTACTTGAAAACTTCACATAA	0.493																																					p.V101D		.											.	GLUL-90	0			c.T302A						.						112	101	105					1																	182356292		2203	4300	6503	SO:0001583	missense	2752	exon3			TTGAAAACTTCAC	AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"glutamine synthetase"	138290	"glutamate-ammonia ligase (glutamine synthase)"	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.302T>A	1.37:g.182356292A>T	ENSP00000356537:p.Val101Asp	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	106	10	NM_001033056	0	0	164	194	30	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Missense_Mutation	SNP	ENST00000331872.6	37	CCDS1344.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704904	0.88924	.	.	ENSG00000135821	ENST00000331872;ENST00000311223;ENST00000417584;ENST00000339526;ENST00000435013	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	4.79	4.79	0.61399	Glutamine synthetase, beta-Grasp (3);	0.057690	0.64402	D	0.000002	T	0.78534	0.4298	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84301	0.0505	10	0.72032	D	0.01	-23.933	13.4137	0.60956	1.0:0.0:0.0:0.0	.	101	P15104	GLNA_HUMAN	D	101	ENSP00000356537:V101D;ENSP00000307900:V101D;ENSP00000398320:V101D;ENSP00000344958:V101D	ENSP00000307900:V101D	V	-	2	0	GLUL	180622915	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	8.881000	0.92415	1.897000	0.54924	0.533000	0.62120	GTT	.		0.493	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065		T	182356292	A	T	182356292	3	4	102	1	0	0	0	0	1	0	0	0	6498	43	2	5	839	5	GLUL	1	182356292	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08	23322842	182356292	66894329	4	9021											
MTIF2	4528	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55473595	55473595	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaagccatcagattatcGccctttaacaataacaaacg	16	8	5	12	2	1	1	1	0	0	1	2	1	1	1	3	0	4	0	3	0	6	4	rs540448511		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr2:55473595G>A	ENST00000263629.4	-	10	1299	c.984C>T	c.(982-984)ggC>ggT	p.G328G	MTIF2_ENST00000394600.3_Silent_p.G328G|MTIF2_ENST00000403721.1_Silent_p.G328G	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	328	tr-type G.				formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TCAGATTATCGCCCTTTAACA	0.353																																					p.G328G													.	MTIF2-91	0			c.C984T						.						113	101	105					2																	55473595		2203	4300	6503	SO:0001819	synonymous_variant	4528	exon10			ATTATCGCCCTTT	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.984C>T	2.37:g.55473595G>A		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	83	10	NM_002453	0	0	0	0	0	D6W5D0	Silent	SNP	ENST00000263629.4	37	CCDS1853.1																																																																																			.		0.353	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		A	55473595	G	A	55473595	2	1	102	1	0	0	0	0	0	0	0	1	9959	1074	38	1		1	MTIF2	2	55473595	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		55473595	187725778	5	9022											
ZDBF2	57683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	207171574	207171574	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatgctgaaggaaaagaacgGcacattgacctggaagatga	16	6	13	6	1	0	5	0	3	0	2	0	8	0	7	1	3	2	2	1	3	5	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr2:207171574G>A	ENST00000374423.3	+	5	2708	c.2322G>A	c.(2320-2322)cgG>cgA	p.R774R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	774							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GAAAAGAACGGCACATTGACC	0.428																																					p.R774R		.											.	ZDBF2-3	0			c.G2322A						.						174	175	175					2																	207171574		1927	4125	6052	SO:0001819	synonymous_variant	57683	exon5			AGAACGGCACATT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"Zinc fingers, DBF-type"	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.2322G>A	2.37:g.207171574G>A		Somatic	263	0		WXS	Illumina HiSeq	Phase_I	340	54	NM_020923	0	0	2	5	3	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			.		0.428	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207171574	G	A	207171574	2	1	102	1	0	0	0	0	0	0	0	1	17631	1190	42	2		2	ZDBF2	2	207171574	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	151697979	207171574	36027799	6	9023											
ABCA12	26154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	215865517	215865517	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtttgcaattcaatgattgCtctttcaatactatcctgta	11	17	5	8	0	3	1	2	1	1	0	4	1	4	1	1	0	3	4	1	0	6	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr2:215865517C>G	ENST00000272895.7	-	22	3310	c.3091G>C	c.(3091-3093)Gca>Cca	p.A1031P	ABCA12_ENST00000389661.4_Missense_Mutation_p.A713P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1031					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCAATGATTGCTCTTTCAATA	0.428																																					p.A1031P	Ovarian(66;664 1488 5121 34295)	.											.	ABCA12-99	0			c.G3091C						.						125	131	129					2																	215865517		2203	4300	6503	SO:0001583	missense	26154	exon22			TGATTGCTCTTTC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3091G>C	2.37:g.215865517C>G	ENSP00000272895:p.Ala1031Pro	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	226	78	NM_173076	0	0	6	13	7	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864070	0.91511	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.88046	-2.33;-2.33	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000001	D	0.94896	0.8350	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95165	0.8285	10	0.87932	D	0	.	19.9082	0.97015	0.0:1.0:0.0:0.0	.	1031;713	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	1031;713	ENSP00000272895:A1031P;ENSP00000374312:A713P	ENSP00000272895:A1031P	A	-	1	0	ABCA12	215573762	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.594000	0.82698	2.705000	0.92388	0.555000	0.69702	GCA	.		0.428	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215865517	C	G	215865517	3	3	102	1	0	0	0	0	1	0	0	0	30	797	28	4	4824	4	ABCA12	2	215865517	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	8693943	215865517	27333856	7	9024											
NGLY1	55768	ucsc.edu	37	chr3	25770623	25770623	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggttttatgcattaagttaCcatgtgccagtctgtttcaa	9	17	8	7	0	2	0	1	0	1	0	2	0	2	0	2	1	3	4	2	1	4	5			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr3:25770623C>T	ENST00000280700.5	-	10	1772		c.e10+1		NGLY1_ENST00000417874.2_Splice_Site|NGLY1_ENST00000396649.3_Splice_Site|NGLY1_ENST00000422724.2_Splice_Site|NGLY1_ENST00000467224.1_Splice_Site|NGLY1_ENST00000428257.1_Splice_Site	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1						glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						CATTAAGTTACCATGTGCCAG	0.308																																					.													.	NGLY1-135	0			c.1611+1G>A						.						110	102	105					3																	25770623		2202	4299	6501	SO:0001630	splice_region_variant	55768	exon11			AAGTTACCATGTG	AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092			17646	protein-coding gene	gene with protein product		610661					Standard	NM_018297		Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000280700.5:c.1611+1G>A	3.37:g.25770623C>T		Somatic	97	0		WXS	Illumina HiSeq		133	1	NM_001145295	0	0	0	0	0	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Splice_Site	SNP	ENST00000280700.5	37	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.469638	0.84533	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000396649;ENST00000308710;ENST00000417874	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1006	0.97874	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NGLY1	25745627	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.172000	0.77604	2.757000	0.94681	0.561000	0.74099	.	.		0.308	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2		Intron	T	25770623	C	T	25770623	5	4	102	1	0	0	0	0	0	0	1	0	10424	521	18	2	364	2	NGLY1	3	25770623	Splice_Site	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		25770623	172251807	8	9025											
TRIM71	131405	ucsc.edu	37	chr3	32932841	32932841	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattctgagggcaagatcctGgtctcagacacgaggaacca	13	7	11	10	1	2	3	1	1	2	2	4	5	3	4	2	3	1	1	2	3	3	1	rs200564131	byFrequency	TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr3:32932841G>A	ENST00000383763.5	+	4	2208	c.2145G>A	c.(2143-2145)ctG>ctA	p.L715L		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	715					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCAAGATCCTGGTCTCAGACA	0.532													G|||	14	0.00279553	0	0.0043	5008	,	,		18823	0		0	False		,,,				2504	0.0112				p.L715L													.	TRIM71-92	0			c.G2145A						.	G		0,4078		0,0,2039	44	50	48		2145	-2	1	3		48	13,8363		0,13,4175	no	coding-synonymous	TRIM71	NM_001039111.1		0,13,6214	AA,AG,GG		0.1552,0.0,0.1044		715/869	32932841	13,12441	2039	4188	6227	SO:0001819	synonymous_variant	131405	exon4			GATCCTGGTCTCA		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.2145G>A	3.37:g.32932841G>A		Somatic	52	1		WXS	Illumina HiSeq		45	4	NM_001039111	0	0	6	6	0		Silent	SNP	ENST00000383763.5	37	CCDS43060.1																																																																																			G|0.999;A|0.001		0.532	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		A	32932841	G	A	32932841	2	1	102	1	0	0	0	0	0	0	0	1	16577	1335	47	2		2	TRIM71	3	32932841	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	7162218	32932841	165089589	9	9026											
HTT	3064	hgsc.bcm.edu	37	chr4	3076696	3076696	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccgccgccgccgccgccTcctcagcttcctcagccgcc	2	5	9	25	7	2	0	2	0	0	0	4	0	4	0	11	0	2	1	11	0	0	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:3076696T>G	ENST00000355072.5	+	1	289	c.144T>G	c.(142-144)ccT>ccG	p.P48P	HTT-AS_ENST00000503893.1_RNA	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	48	Poly-Pro.				anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		cgccgccgcctcctcagcttc	0.771																																					p.P48P		.											.	HTT-281	0			c.T144G						.																																			SO:0001819	synonymous_variant	3064	exon1			GCCGCCTCCTCAG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.144T>G	4.37:g.3076696T>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	2	NM_002111	0	0	0	0	0	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			.		0.771	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		G	3076696	T	G	3076696	2	3	102	1	0	0	0	0	0	0	0	1	7478	1538	54	5		5	HTT	4	3076696	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08		3076696	188077580	10	9027											
PTPN13	5783	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	87691259	87691259	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcatggtacccccaggaagtCatatctgctctcaggggaac	10	9	10	12	0	4	0	3	0	2	0	5	2	4	2	2	4	3	2	2	4	4	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:87691259C>T	ENST00000411767.2	+	30	4773	c.4710C>T	c.(4708-4710)gtC>gtT	p.V1570V	PTPN13_ENST00000316707.6_Silent_p.V1379V|PTPN13_ENST00000436978.1_Silent_p.V1575V|PTPN13_ENST00000511467.1_Silent_p.V1575V|PTPN13_ENST00000427191.2_Silent_p.V1551V			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1570	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CCCAGGAAGTCATATCTGCTC	0.443																																					p.V1575V													.	PTPN13-230	0			c.C4725T						.						71	70	70					4																	87691259		1883	4110	5993	SO:0001819	synonymous_variant	5783	exon30			GGAAGTCATATCT		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4710C>T	4.37:g.87691259C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	36	9	NM_080685	0	0	0	0	0	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			.		0.443	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87691259	C	T	87691259	2	4	102	1	0	0	0	0	0	0	0	1	12812	813	29	2		2	PTPN13	4	87691259	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	84614563	87691259	103463017	11	9028											
DAPP1	27071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100787246	100787246	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caaagaccggagtagaagctGatgagtggatcaagatatta	16	8	12	5	1	1	5	1	2	0	3	1	7	1	7	1	2	1	2	1	2	6	3			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:100787246G>C	ENST00000512369.1	+	8	810	c.742G>C	c.(742-744)Gat>Cat	p.D248H	DAPP1_ENST00000296414.7_Missense_Mutation_p.D248H	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	248	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		AGTAGAAGCTGATGAGTGGAT	0.343																																					p.D248H		.											.	DAPP1-93	0			c.G742C						.						91	83	86					4																	100787246		1863	4100	5963	SO:0001583	missense	27071	exon8			GAAGCTGATGAGT	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.742G>C	4.37:g.100787246G>C	ENSP00000423602:p.Asp248His	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	63	13	NM_014395	0	0	3	3	0	Q8TCK5|Q9UHF2	Missense_Mutation	SNP	ENST00000512369.1	37	CCDS47112.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773356	0.90108	.	.	ENSG00000070190	ENST00000296414;ENST00000512369	T;T	0.75589	-0.95;-0.95	6.07	6.07	0.98685	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.83362	0.5238	L	0.55834	1.745	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.68943	0.956;0.961	T	0.79329	-0.1848	10	0.31617	T	0.26	-8.6315	19.4308	0.94765	0.0:0.0:1.0:0.0	.	248;248	Q9UN19-2;Q9UN19	.;DAPP1_HUMAN	H	248	ENSP00000296414:D248H;ENSP00000423602:D248H	ENSP00000296414:D248H	D	+	1	0	DAPP1	101006269	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.197000	0.89727	2.885000	0.99019	0.655000	0.94253	GAT	.		0.343	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1			C	100787246	G	C	100787246	3	2	102	1	0	0	0	0	1	0	0	0	4245	1290	45	4	772	4	DAPP1	4	100787246	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	13095987	100787246	90367030	12	9029											
LRBA	987	hgsc.bcm.edu	37	chr4	151231474	151231474	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgacaaagcactgggaatGcacttgaatactttggtcta	13	11	10	7	0	1	2	0	2	1	0	1	4	1	3	0	2	3	2	0	2	5	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:151231474G>C	ENST00000357115.3	-	53	8032	c.7789C>G	c.(7789-7791)Cat>Gat	p.H2597D	LRBA_ENST00000535741.1_Missense_Mutation_p.H2586D|LRBA_ENST00000510413.1_Missense_Mutation_p.H2586D|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2597						cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					CACTGGGAATGCACTTGAATA	0.408																																					p.H2597D		.											.	LRBA-157	0			c.C7789G						.						118	114	115					4																	151231474		2203	4300	6503	SO:0001583	missense	987	exon53			GGGAATGCACTTG	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"WD repeat domain containing"	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.7789C>G	4.37:g.151231474G>C	ENSP00000349629:p.His2597Asp	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	44	3	NM_006726	0	0	39	39	0	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	37	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.74|14.74	2.624395|2.624395	0.46840|0.46840	.|.	.|.	ENSG00000198589|ENSG00000198589	ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115	.|T;T;T	.|0.70986	.|-0.53;-0.53;-0.53	4.88|4.88	4.88|4.88	0.63580|0.63580	.|WD40 repeat-like-containing domain (1);	.|0.402141	.|0.27581	.|N	.|0.018725	T|T	0.60637|0.60637	0.2284|0.2284	N|N	0.22421|0.22421	0.69|0.69	0.49915|0.49915	D|D	0.999837|0.999837	.|P;B;B;B	.|0.43231	.|0.801;0.321;0.007;0.061	.|B;B;B;B	.|0.40782	.|0.34;0.138;0.003;0.028	T|T	0.61917|0.61917	-0.6964|-0.6964	5|10	.|0.33141	.|T	.|0.24	.|.	18.4099|18.4099	0.90548|0.90548	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2597;2586;2586;492	.|P50851;F5H1X8;P50851-2;Q68D03	.|LRBA_HUMAN;.;.;.	W|D	1238|2586;2586;2597	.|ENSP00000446299:H2586D;ENSP00000421552:H2586D;ENSP00000349629:H2597D	.|ENSP00000349629:H2597D	C|H	-|-	3|1	2|0	LRBA|LRBA	151450924|151450924	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.078000|6.078000	0.71282|0.71282	2.411000|2.411000	0.81874|0.81874	0.563000|0.563000	0.77884|0.77884	TGC|CAT	.		0.408	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151231474	G	C	151231474	3	2	102	1	0	0	0	0	1	0	0	0	8956	1319	46	4	826	4	LRBA	4	151231474	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	50444228	151231474	39922802	13	9030											
GALNT7	51809	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	174225146	174225146	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caacgtgtttttccttcataGatatggcagtgtggtggcaa	9	14	11	7	1	1	1	1	0	0	1	2	1	2	1	1	3	1	3	1	3	4	5			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:174225146G>A	ENST00000265000.4	+	8	1349		c.e8-1			NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TTCCTTCATAGATATGGCAGT	0.343																																					.		.											.	GALNT7-90	0			c.1267-1G>A						.						137	126	130					4																	174225146		2203	4300	6503	SO:0001630	splice_region_variant	51809	exon8			TTCATAGATATGG	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.1267-1G>A	4.37:g.174225146G>A		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	178	57	NM_017423	0	0	0	0	0	B3KQU3|Q7Z5W7|Q9UJ28	Splice_Site	SNP	ENST00000265000.4	37	CCDS3815.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313963	0.60414	.	.	ENSG00000109586	ENST00000265000;ENST00000505308;ENST00000458613	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9439	0.97175	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GALNT7	174461721	1.000000	0.71417	0.997000	0.53966	0.593000	0.36681	9.476000	0.97823	2.706000	0.92434	0.561000	0.74099	.	.		0.343	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423	Intron	A	174225146	G	A	174225146	5	1	102	1	0	0	0	0	0	0	1	0	6238	956	33	2	1296	2	GALNT7	4	174225146	Splice_Site	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	22993672	174225146	16929130	14	9031											
ARSK	153642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	94922371	94922371	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgcactggaagatttacaAaaaaagaaattaagaatatt	21	10	6	4	0	0	3	0	0	0	3	0	4	0	4	0	1	2	1	0	1	9	5	rs201849642		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr5:94922371A>G	ENST00000380009.4	+	5	1010	c.805A>G	c.(805-807)Aaa>Gaa	p.K269E		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	269					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		AAGATTTACAAAAAAAGAAAT	0.338																																					p.K269E		.											.	ARSK-91	0			c.A805G						.						61	65	64					5																	94922371		2201	4297	6498	SO:0001583	missense	153642	exon5			TTTACAAAAAAAG		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"Arylsulfatase family"	25239	protein-coding gene	gene with protein product		610011	"arylsulfatase K"			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.805A>G	5.37:g.94922371A>G	ENSP00000369346:p.Lys269Glu	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	86	20	NM_198150	0	0	2	2	0	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	37	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	A	3.355	-0.131627	0.06753	.	.	ENSG00000164291	ENST00000380009	D	0.99891	-7.56	5.93	-1.94	0.07571	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.568944	0.20517	N	0.090774	D	0.97851	0.9294	N	0.03016	-0.435	0.30818	N	0.738095	B	0.06786	0.001	B	0.06405	0.002	D	0.99988	1.3720	10	0.02654	T	1	-0.6336	8.1825	0.31319	0.5545:0.1084:0.3371:0.0	.	269	Q6UWY0	ARSK_HUMAN	E	269	ENSP00000369346:K269E	ENSP00000369346:K269E	K	+	1	0	ARSK	94948127	0.982000	0.34865	0.741000	0.31004	0.871000	0.50021	0.596000	0.24044	-0.248000	0.09583	-0.132000	0.14878	AAA	A|0.999;G|0.001		0.338	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		G	94922371	A	G	94922371	3	3	102	1	0	0	0	0	1	0	0	0	997	15	1	3	823	3	ARSK	5	94922371	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08		94922371	85992889	15	9032											
C1QTNF2	114898	broad.mit.edu;bcgsc.ca	37	chr5	159781881	159781881	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggccctggggctcctgggggGccgggtgggccctgggggcc	0	5	23	13	1	0	0	0	0	0	0	1	0	1	0	5	10	0	1	5	10	0	0			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr5:159781881G>A	ENST00000393975.3	-	2	276	c.273C>T	c.(271-273)ggC>ggT	p.G91G		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	46	Collagen-like.				activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCCTGGGGGGCCGGGTGGGC	0.682																																					p.G91G													.	C1QTNF2-91	0			c.C273T						.						11	13	12					5																	159781881		2195	4292	6487	SO:0001819	synonymous_variant	114898	exon2			TGGGGGGCCGGGT	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.273C>T	5.37:g.159781881G>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_031908	0	0	1	1	0		Silent	SNP	ENST00000393975.3	37	CCDS4351.2																																																																																			.		0.682	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2			A	159781881	G	A	159781881	2	1	102	1	0	0	0	0	0	0	0	1	1969	1190	42	2		2	C1QTNF2	5	159781881	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	64859510	159781881	21133379	16	9033											
DNAH11	8701	ucsc.edu	37	chr7	21856097	21856097	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaaaggtttccattccaCtaaccgaaggcctggacttg	10	13	8	10	1	0	0	0	0	0	0	2	2	2	1	4	3	1	1	4	3	4	6			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr7:21856097C>A	ENST00000409508.3	+	64	10376	c.10345C>A	c.(10345-10347)Cta>Ata	p.L3449I	DNAH11_ENST00000328843.6_Missense_Mutation_p.L3456I	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3456					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTCCATTCCACTAACCGAAGG	0.433									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						66	59	61					7																	21856097		1939	4139	6078	SO:0001583	missense	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATTCCACTAACCG	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.10345C>A	7.37:g.21856097C>A	ENSP00000475939:p.Leu3449Ile	Somatic	17	0		WXS	Illumina HiSeq		27	11	.	0	0	0	0	0	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	c	0.004	-2.378914	0.00205	.	.	ENSG00000105877	ENST00000328843	T	0.22743	1.94	5.82	2.24	0.28232	.	0.222391	0.51477	N	0.000081	T	0.07098	0.0180	.	.	.	0.20873	N	0.999838	B	0.06786	0.001	B	0.09377	0.004	T	0.41484	-0.9506	9	0.02654	T	1	.	6.6285	0.22843	0.6613:0.1306:0.2081:0.0	.	3456	Q96DT5	DYH11_HUMAN	I	3456	ENSP00000330671:L3456I	ENSP00000330671:L3456I	L	+	1	2	DNAH11	21822622	0.078000	0.21339	0.358000	0.25811	0.085000	0.17905	0.612000	0.24283	0.153000	0.19213	-1.494000	0.00967	CTA	.		0.433	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21856097	C	A	21856097	3	1	102	1	0	0	0	0	1	0	0	0	4610	564	20	4	10621	4	DNAH11	7	21856097	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		21856097	137282566	17	9034											
DOCK4	9732	broad.mit.edu;bcgsc.ca	37	chr7	111368620	111368620	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cggcaggggggccgactgttCattcacctgattttcaaagc	8	10	12	11	2	3	1	3	1	0	0	3	2	3	1	2	4	1	2	2	4	1	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr7:111368620C>T	ENST00000437633.1	-	52	5867	c.5611G>A	c.(5611-5613)Gaa>Aaa	p.E1871K	DOCK4_ENST00000494651.2_Missense_Mutation_p.E754K|DOCK4_ENST00000428084.1_Missense_Mutation_p.E1880K	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1871					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GCCGACTGTTCATTCACCTGA	0.632																																					p.E1871K													.	DOCK4-26	0			c.G5611A						.						45	52	49					7																	111368620		2078	4208	6286	SO:0001583	missense	9732	exon52			ACTGTTCATTCAC		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.5611G>A	7.37:g.111368620C>T	ENSP00000404179:p.Glu1871Lys	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	124	11	NM_014705	0	0	17	19	2	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.39|17.39	3.377179|3.377179	0.61735|0.61735	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288|ENST00000423057;ENST00000445943	T;T;T|.	0.36520|.	1.25;1.25;1.25|.	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	0.164526|.	0.53938|.	D|.	0.000047|.	T|T	0.69602|0.69602	0.3129|0.3129	L|L	0.46157|0.46157	1.445|1.445	0.53688|0.53688	D|D	0.999979|0.999979	B;B;B;B;B;P|.	0.35272|.	0.034;0.136;0.039;0.319;0.135;0.493|.	B;B;B;B;B;B|.	0.27380|.	0.016;0.033;0.018;0.034;0.037;0.079|.	T|T	0.64757|0.64757	-0.6332|-0.6332	10|5	0.27785|.	T|.	0.31|.	.|.	19.5919|19.5919	0.95518|0.95518	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	740;754;1916;1871;1842;184|.	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2;Q8N1I0-4|.	.;.;.;DOCK4_HUMAN;.;.|.	K|I	1859;1880;754;1871;1830|1293;1903	ENSP00000410746:E1880K;ENSP00000440944:E754K;ENSP00000404179:E1871K|.	ENSP00000345432:E1830K|.	E|M	-|-	1|3	0|0	DOCK4|DOCK4	111155856|111155856	1.000000|1.000000	0.71417|0.71417	0.077000|0.077000	0.20336|0.20336	0.479000|0.479000	0.33129|0.33129	6.966000|6.966000	0.76073|0.76073	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	GAA|ATG	.		0.632	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		T	111368620	C	T	111368620	3	4	102	1	0	0	0	0	1	0	0	0	4700	835	29	2	293	2	DOCK4	7	111368620	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	89512523	111368620	47770043	18	9035											
TEX15	56154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	30694449	30694449	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagaagcaggtatttgagaTtgaaaatacccattcactgg	14	12	9	6	0	1	3	1	2	0	2	1	4	1	3	1	2	2	2	1	2	6	6			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr8:30694449T>C	ENST00000256246.2	-	3	8276	c.8202A>G	c.(8200-8202)caA>caG	p.Q2734Q		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2734					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GTATTTGAGATTGAAAATACC	0.408																																					p.Q2734Q		.											.	TEX15-97	0			c.A8202G						.						97	100	99					8																	30694449		2203	4300	6503	SO:0001819	synonymous_variant	56154	exon3			TTGAGATTGAAAA	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"cancer/testis antigen 42"	605795	"testis expressed sequence 15"			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.8202A>G	8.37:g.30694449T>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	104	43	NM_031271	0	0	0	0	0		Silent	SNP	ENST00000256246.2	37	CCDS6080.1																																																																																			.		0.408	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30694449	T	C	30694449	2	2	102	1	0	0	0	0	0	0	0	1	15811	1490	52	3		3	TEX15	8	30694449	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08		30694449	115669573	19	9036											
ZFAT	57623	broad.mit.edu	37	chr8	135524765	135524765	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcgcggccaccgctgccTgtgtcccttgaacgtcttct	4	10	12	15	4	2	1	0	1	2	0	3	2	3	2	4	2	3	1	4	2	1	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr8:135524765T>C	ENST00000377838.3	-	14	3488	c.3314A>G	c.(3313-3315)cAg>cGg	p.Q1105R	ZFAT_ENST00000520727.1_Missense_Mutation_p.Q1093R|ZFAT_ENST00000429442.2_Missense_Mutation_p.Q1093R|ZFAT_ENST00000520356.1_Intron|ZFAT_ENST00000520214.1_Missense_Mutation_p.Q1093R|ZFAT_ENST00000523399.1_Missense_Mutation_p.Q1043R|ZFAT_ENST00000517307.1_5'Flank	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1105					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CACCGCTGCCTGTGTCCCTTG	0.532																																					p.Q1105R													.	ZFAT-90	0			c.A3314G						.						164	175	171					8																	135524765		2020	4178	6198	SO:0001583	missense	57623	exon14			GCTGCCTGTGTCC	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3314A>G	8.37:g.135524765T>C	ENSP00000367069:p.Gln1105Arg	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	324	6	NM_020863	0	0	26	26	0	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.397232	0.42512	.	.	ENSG00000066827	ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399	T;T;T;T;T	0.10382	2.93;2.88;2.93;2.93;2.95	4.8	4.8	0.61643	.	0.058678	0.64402	D	0.000002	T	0.09730	0.0239	N	0.24115	0.695	0.34214	D	0.674611	P;P;P	0.49090	0.919;0.842;0.842	B;B;B	0.42692	0.395;0.321;0.236	T	0.14980	-1.0453	10	0.62326	D	0.03	-31.9885	13.9728	0.64252	0.0:0.0:0.0:1.0	.	224;1043;1105	B7Z741;E9PER3;Q9P243	.;.;ZFAT_HUMAN	R	1093;1093;1105;1093;992;1043	ENSP00000427831:Q1093R;ENSP00000394501:Q1093R;ENSP00000367069:Q1105R;ENSP00000428483:Q1093R;ENSP00000429091:Q1043R	ENSP00000326997:Q992R	Q	-	2	0	ZFAT	135593947	1.000000	0.71417	0.997000	0.53966	0.181000	0.23173	5.978000	0.70501	2.140000	0.66376	0.460000	0.39030	CAG	.		0.532	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		C	135524765	T	C	135524765	3	2	102	1	0	0	0	0	1	0	0	0	17664	1580	55	3	429	3	ZFAT	8	135524765	Missense_Mutation	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	104830316	135524765	10839257	20	9037											
C9orf84	158401	hgsc.bcm.edu;broad.mit.edu	37	chr9	114454268	114454270	+	In_Frame_Del	DEL	CTC	CTC	-																															aaccttttgcttcatgtgttCtccttttctgagaatttata																										TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr9:114454268_114454270delCTC	ENST00000318737.4	-	25	3923_3925	c.3795_3797delGAG	c.(3793-3798)aggaga>aga	p.1265_1266RR>R	C9orf84_ENST00000394777.4_In_Frame_Del_p.1191_1192RR>R|C9orf84_ENST00000374287.3_In_Frame_Del_p.1265_1266RR>R|C9orf84_ENST00000394779.3_In_Frame_Del_p.1226_1227RR>R	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1265										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTCATGTGTTCTCCTTTTCTGAG	0.369																																					p.1265_1266del		.											.	C9orf84-92	0			c.3795_3797del						.																																			SO:0001651	inframe_deletion	158401	exon25			.	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.3795_3797delGAG	9.37:g.114454268_114454270delCTC	ENSP00000322108:p.Arg1266del	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	56	10	NM_173521	0	0	0	0	0	A2A2V3|Q2M1H8|Q96M73	In_Frame_Del	DEL	ENST00000318737.4	37	CCDS6781.3																																																																																			.		0.369	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		-	114454270	CTC	-	114454268	7	5	102	1	0	1	0	1	0	0	0	0	2506	913	32	0	545	0	C9orf84	9	114454268	In_Frame_Del	DEL	CTC	TCGA-DZ-6131-01A-11D-1961-08		114454268	26759163	21	9038											
WDR37	22884	bcgsc.ca	37	chr10	1170912	1170915	+	Frame_Shift_Del	DEL	TGTT	TGTT	-																															tgacaaccgacaagtgagacTgtttgatatgtcaggagtgc																										TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	TGTT	TGTT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr10:1170912_1170915delTGTT	ENST00000358220.1	+	13	1445_1448	c.1301_1304delTGTT	c.(1300-1305)ctgtttfs	p.LF434fs	WDR37_ENST00000482165.1_3'UTR|WDR37_ENST00000263150.4_Frame_Shift_Del_p.LF434fs			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	434										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		CAAGTGAGACTGTTTGATATGTCA	0.539																																					p.434_435del													.	WDR37-90	0			c.1301_1304del						.																																			SO:0001589	frameshift_variant	22884	exon13			TGAGACTGTTTGA	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.1301_1304delTGTT	10.37:g.1170912_1170915delTGTT	ENSP00000350954:p.Leu434fs	Somatic	70	0		WXS	Illumina HiSeq	Phase_1	56	6	NM_014023	0	0	0	0	0	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Frame_Shift_Del	DEL	ENST00000358220.1	37	CCDS7057.1																																																																																			.		0.539	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		-	1170915	TGTT	-	1170912	7	5	102	1	0	1	0	1	0	0	0	0	17324	1580	55	0	1347	0	WDR37	10	1170912	Frame_Shift_Del	DEL	TGTT	TCGA-DZ-6131-01A-11D-1961-08		1170912	134363835	22	9039											
MUC2	4583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1099777	1099777	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctaggctgtgtgggaccTgacaatgtgcccagagaggt	8	10	14	9	0	0	2	0	1	0	1	1	4	1	3	3	3	1	1	3	3	2	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr11:1099777T>C	ENST00000441003.2	+	40	7401	c.7374T>C	c.(7372-7374)ccT>ccC	p.P2458P		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4820					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GTGTGGGACCTGACAATGTGC	0.572																																					p.P2454P		.											.	MUC2-90	0			c.T7362C						.						140	152	148					11																	1099777		2080	4206	6286	SO:0001819	synonymous_variant	4583	exon41			GGGACCTGACAAT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.7374T>C	11.37:g.1099777T>C		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	137	54	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.572	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1099777	T	C	1099777	2	2	102	1	0	0	0	0	0	0	0	1	10000	1567	55	3		3	MUC2	11	1099777	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08		1099777	133906739	23	9040											
A2ML1	144568	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	9000291	9000291	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagagagctgagcaaccgCtctgtgagtaactgtctgct	10	9	12	10	1	2	3	0	2	2	1	2	5	2	3	1	0	5	5	1	0	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:9000291C>T	ENST00000299698.7	+	15	2010	c.1830C>T	c.(1828-1830)cgC>cgT	p.R610R	A2ML1_ENST00000539547.1_Silent_p.R119R|A2ML1_ENST00000540049.1_3'UTR	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						TGAGCAACCGCTCTGTGAGTA	0.557																																					p.R610R		.											.	A2ML1-93	0			c.C1830T						.						78	77	78					12																	9000291		1955	4145	6100	SO:0001819	synonymous_variant	144568	exon15			CAACCGCTCTGTG	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1830C>T	12.37:g.9000291C>T		Somatic	173	0		WXS	Illumina HiSeq	Phase_I	199	15	NM_144670	0	0	0	0	0		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			.		0.557	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	9000291	C	T	9000291	2	4	102	1	0	0	0	0	0	0	0	1	5	784	28	2		2	A2ML1	12	9000291	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		9000291	124851604	24	9041											
TMEM5	10329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64174892	64174892	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaaactagccttcaaatatTagataaatccacgaaaggaa	20	9	5	7	1	1	1	1	0	0	1	2	3	2	2	2	1	2	0	2	1	10	6			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:64174892T>G	ENST00000261234.6	+	2	421	c.263T>G	c.(262-264)tTa>tGa	p.L88*	TMEM5_ENST00000537373.1_5'UTR|RP11-415I12.3_ENST00000509615.2_RNA|TMEM5_ENST00000537982.1_3'UTR	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	88						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		CTTCAAATATTAGATAAATCC	0.363																																					p.L88X		.											.	TMEM5-90	0			c.T263G						.						82	89	86					12																	64174892		2203	4300	6503	SO:0001587	stop_gained	10329	exon2			AAATATTAGATAA	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.263T>G	12.37:g.64174892T>G	ENSP00000261234:p.Leu88*	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	247	85	NM_014254	0	0	14	23	9	A8K017|Q6PKD6	Nonsense_Mutation	SNP	ENST00000261234.6	37	CCDS8966.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.051948	0.75960	.	.	ENSG00000118600	ENST00000261234	.	.	.	4.34	4.34	0.51931	.	0.447903	0.20965	N	0.082490	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.428	10.4561	0.44550	0.0:0.0:0.0:1.0	.	.	.	.	X	88	.	.	L	+	2	0	TMEM5	62461159	0.996000	0.38824	0.945000	0.38365	0.457000	0.32468	4.615000	0.61190	1.897000	0.54924	0.402000	0.26972	TTA	.		0.363	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254		G	64174892	T	G	64174892	4	3	102	1	0	0	0	0	0	1	0	0	16206	1764	61	5	269	5	TMEM5	12	64174892	Nonsense_Mutation	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	55174601	64174892	69677003	25	9042											
PPP1R12A	4659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	80203769	80203769	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcttcttctttgggagaaaTttttgtagctgtggttggaa	7	18	11	5	0	3	1	0	0	3	1	3	3	3	2	0	3	1	3	0	3	3	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:80203769T>G	ENST00000450142.2	-	10	1527	c.1261A>C	c.(1261-1263)Att>Ctt	p.I421L	PPP1R12A_ENST00000437004.2_Missense_Mutation_p.I421L|PPP1R12A_ENST00000550107.1_Missense_Mutation_p.I421L|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.I334L|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.I421L	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	421					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						TTGGGAGAAATTTTTGTAGCT	0.363																																					p.I421L		.											.	PPP1R12A-273	0			c.A1261C						.						86	76	79					12																	80203769		1802	4069	5871	SO:0001583	missense	4659	exon10			GAGAAATTTTTGT	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7618	protein-coding gene	gene with protein product	"myosin phosphatase-targeting subunit 1", "myosin binding subunit"	602021	"protein phosphatase 1, regulatory (inhibitor) subunit 12A"	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.1261A>C	12.37:g.80203769T>G	ENSP00000389168:p.Ile421Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	70	21	NM_002480	0	0	22	31	9	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	2.128|2.128	-0.399892|-0.399892	0.04865|0.04865	.|.	.|.	ENSG00000058272|ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107;ENST00000547330;ENST00000547131|ENST00000553081	T;T;T;T;T;T;T|T	0.39997|0.34667	1.43;1.43;1.45;1.49;1.44;1.44;1.05|1.35	5.86|5.86	0.0418|0.0418	0.14214|0.14214	.|.	0.725412|.	0.14249|.	N|.	0.331574|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.03608|0.03608	-0.345|-0.345	0.26994|0.26994	N|N	0.965072|0.965072	B;B;B;B|.	0.24823|.	0.112;0.002;0.0;0.0|.	B;B;B;B|.	0.20384|.	0.029;0.001;0.0;0.0|.	T|T	0.26224|0.26224	-1.0109|-1.0109	10|7	0.08381|0.54805	T|T	0.77|0.06	.|.	9.6186|9.6186	0.39708|0.39708	0.0:0.558:0.0:0.442|0.0:0.558:0.0:0.442	.|.	421;421;421;421|.	F8W8Q6;O14974-2;O14974-3;O14974|.	.;.;.;MYPT1_HUMAN|.	L|N	421;421;421;421;421;421;421;334;421;421;116|24	ENSP00000261207:I421L;ENSP00000389168:I421L;ENSP00000416769:I421L;ENSP00000449514:I334L;ENSP00000446855:I421L;ENSP00000446816:I421L;ENSP00000450061:I116L|ENSP00000447144:K24N	ENSP00000261207:I421L|ENSP00000447144:K24N	I|K	-|-	1|3	0|2	PPP1R12A|PPP1R12A	78727900|78727900	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.852000|0.852000	0.48524|0.48524	0.848000|0.848000	0.27710|0.27710	0.016000|0.016000	0.14998|0.14998	0.467000|0.467000	0.42956|0.42956	ATT|AAA	.		0.363	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		G	80203769	T	G	80203769	3	3	102	1	0	0	0	0	1	0	0	0	12383	1493	52	5	1895	5	PPP1R12A	12	80203769	Missense_Mutation	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	16028877	80203769	53648126	26	9043											
P2RX7	5027	hgsc.bcm.edu	37	chr12	121622232	121622232	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgactcctagatccagggAtagccccgtctggtgccagt	7	8	13	13	2	1	1	0	0	1	1	3	3	3	2	5	3	2	0	5	3	2	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:121622232A>G	ENST00000546057.1	+	13	1558	c.1415A>G	c.(1414-1416)gAt>gGt	p.D472G	P2RX7_ENST00000328963.5_Missense_Mutation_p.D302G|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Missense_Mutation_p.D382G|P2RX7_ENST00000541446.1_Missense_Mutation_p.D183G	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	472					apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AGATCCAGGGATAGCCCCGTC	0.617																																					p.D472G		.											.	P2RX7-268	0			c.A1415G						.						67	63	64					12																	121622232		2203	4300	6503	SO:0001583	missense	5027	exon13			CCAGGGATAGCCC	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1415A>G	12.37:g.121622232A>G	ENSP00000442349:p.Asp472Gly	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	68	4	NM_002562	0	0	13	13	0	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.721694	0.48728	.	.	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05081	4.39;4.01;4.18;3.5	5.21	-0.0551	0.13811	.	1.055260	0.07477	N	0.903142	T	0.06188	0.0160	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.08055	0.003;0.002;0.003;0.002	T	0.41980	-0.9478	10	0.38643	T	0.18	.	5.215	0.15338	0.6048:0.1445:0.2507:0.0	.	302;183;382;472	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	G	472;302;382;183	ENSP00000442349:D472G;ENSP00000330696:D302G;ENSP00000442572:D382G;ENSP00000437471:D183G	ENSP00000330696:D302G	D	+	2	0	P2RX7	120106615	0.000000	0.05858	0.091000	0.20842	0.830000	0.47004	-0.143000	0.10296	0.321000	0.23259	0.482000	0.46254	GAT	.		0.617	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		G	121622232	A	G	121622232	3	3	102	1	0	0	0	0	1	0	0	0	11371	333	12	3	1465	3	P2RX7	12	121622232	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08	41418463	121622232	12229663	27	9044											
PCDH8	5100	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	53422307	53422307	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccgctcgcggtccaggcCggcgtccccgacggtcagct	4	5	14	18	7	1	0	1	0	0	0	4	1	3	0	5	4	2	2	5	4	0	0	rs570624635	byFrequency	TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr13:53422307C>T	ENST00000377942.3	-	1	468	c.265G>A	c.(265-267)Ggc>Agc	p.G89S	PCDH8_ENST00000338862.4_Missense_Mutation_p.G89S	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	89	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CGGTCCAGGCCGGCGTCCCCG	0.657																																					p.G89S	GBM(36;25 841 9273 49207)	.											.	PCDH8-153	0			c.G265A						.						35	38	37					13																	53422307		2201	4296	6497	SO:0001583	missense	5100	exon1			CCAGGCCGGCGTC	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.265G>A	13.37:g.53422307C>T	ENSP00000367177:p.Gly89Ser	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	96	35	NM_032949	0	0	0	0	0	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	37	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.724665	0.68959	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.26373	1.74;1.74	4.99	4.99	0.66335	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.41605	D	0.000846	T	0.33702	0.0872	N	0.20530	0.585	0.32118	N	0.588379	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.28650	-1.0037	10	0.32370	T	0.25	.	13.1397	0.59428	0.0:0.84:0.1599:0.0	.	89;89	O95206-2;O95206	.;PCDH8_HUMAN	S	89	ENSP00000367177:G89S;ENSP00000341350:G89S	ENSP00000341350:G89S	G	-	1	0	PCDH8	52320308	0.981000	0.34729	0.997000	0.53966	0.948000	0.59901	2.542000	0.45744	2.337000	0.79520	0.561000	0.74099	GGC	.		0.657	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53422307	C	T	53422307	3	4	102	1	0	0	0	0	1	0	0	0	11543	652	23	1	2959	1	PCDH8	13	53422307	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		53422307	61747571	28	9045											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91776235	91776235	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtcgtcctcctgcaacagCagctccctgttgaggccgac	6	9	10	16	2	0	1	0	1	0	0	4	2	3	1	4	1	4	4	4	1	1	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr14:91776235C>G	ENST00000389857.6	-	16	2918	c.2832G>C	c.(2830-2832)ctG>ctC	p.L944L		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	944					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CCTGCAACAGCAGCTCCCTGT	0.612																																					p.L944L		.											.	CCDC88C-25	0			c.G2832C						.						49	56	53					14																	91776235		2098	4211	6309	SO:0001819	synonymous_variant	440193	exon16			CAACAGCAGCTCC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"Dvl-associating protein with a high frequency of leucine residues", "spinocerebellar ataxia 40"	611204	"KIAA1509"	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.2832G>C	14.37:g.91776235C>G		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_001080414	0	0	1	1	0	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			.		0.612	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		G	91776235	C	G	91776235	2	3	102	1	0	0	0	0	0	0	0	1	2871	697	25	4		4	CCDC88C	14	91776235	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		91776235	15573305	29	9046											
MAGEL2	54551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	23890238	23890238	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcttcttccgggtggcCttgccggagcggcgtggcgg	1	11	17	12	5	2	0	0	0	2	0	3	1	3	1	3	6	3	1	3	6	0	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr15:23890238C>G	ENST00000532292.1	-	1	937	c.843G>C	c.(841-843)aaG>aaC	p.K281N		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	164					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TCCGGGTGGCCTTGCCGGAGC	0.637																																					p.K884N		.											.	.	0			c.G2652C						.						42	49	47					15																	23890238		2189	4294	6483	SO:0001583	missense	54551	exon1			GGTGGCCTTGCCG	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.843G>C	15.37:g.23890238C>G	ENSP00000433433:p.Lys281Asn	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	111	13	NM_019066	0	0	0	0	0		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	C	15.19	2.758766	0.49468	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.22	0.668	0.17912	.	.	.	.	.	T	0.23688	0.0573	N	0.24115	0.695	0.24891	N	0.99217	.	.	.	.	.	.	T	0.26916	-1.0089	5	.	.	.	.	7.2244	0.26007	0.0:0.461:0.0:0.539	.	.	.	.	T	313	.	.	R	-	2	0	MAGEL2	21441331	0.347000	0.24853	0.771000	0.31576	0.872000	0.50106	-0.733000	0.04898	0.092000	0.17331	-0.302000	0.09304	AGG	.		0.637	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		G	23890238	C	G	23890238	3	3	102	1	0	0	0	0	1	0	0	0	9214	680	24	4	1101	4	MAGEL2	15	23890238	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		23890238	78641154	30	9047											
MGRN1	23295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4700468	4700468	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catggatctgaacttcctggGcagccgcccggtccaggtgg	6	8	14	13	2	1	1	0	1	1	0	3	2	3	2	4	5	2	1	4	5	1	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr16:4700468G>T	ENST00000399577.5	+	2	284	c.191G>T	c.(190-192)gGc>gTc	p.G64V	MGRN1_ENST00000262370.7_Missense_Mutation_p.G64V|MGRN1_ENST00000588994.1_Missense_Mutation_p.G64V|MGRN1_ENST00000415496.1_Missense_Mutation_p.G64V|MGRN1_ENST00000586183.1_Missense_Mutation_p.G64V	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	64					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						AACTTCCTGGGCAGCCGCCCG	0.597																																					p.G64V		.											.	MGRN1-92	0			c.G191T						.						76	81	80					16																	4700468		1892	4125	6017	SO:0001583	missense	23295	exon2			TCCTGGGCAGCCG	AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"RING-type (C3HC4) zinc fingers"	20254	protein-coding gene	gene with protein product		607559	"mahogunin, ring finger 1"			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.191G>T	16.37:g.4700468G>T	ENSP00000382487:p.Gly64Val	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	140	46	NM_001142291	0	0	34	54	20	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	37	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.518548	0.85495	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496;ENST00000536343	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.4	5.4	0.78164	.	0.099811	0.64402	D	0.000001	T	0.62183	0.2407	M	0.86864	2.845	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.998;0.979;0.996;0.991;1.0	T	0.68907	-0.5285	10	0.87932	D	0	-46.144	16.6736	0.85273	0.0:0.0:1.0:0.0	.	64;64;64;64;64;64	O60291-4;O60291-3;B4DR12;E9PB19;O60291-2;O60291	.;.;.;.;.;MGRN1_HUMAN	V	64	ENSP00000262370:G64V;ENSP00000382487:G64V;ENSP00000393311:G64V;ENSP00000443810:G64V	ENSP00000262370:G64V	G	+	2	0	MGRN1	4640469	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	9.785000	0.99042	2.537000	0.85549	0.561000	0.74099	GGC	.		0.597	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2			T	4700468	G	T	4700468	3	4	102	1	0	0	0	0	1	0	0	0	9584	1203	42	4	197	4	MGRN1	16	4700468	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		4700468	85654285	31	9048											
CMTM1	113540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	66612903	66612903	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgccccgcagaggcccgcctGaagccagcccggcgccctag	6	2	13	20	5	0	2	0	1	0	1	0	2	0	2	7	2	2	1	7	2	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr16:66612903G>A	ENST00000457188.2	+	4	630	c.509G>A	c.(508-510)tGa>tAa	p.*170*	CMTM1_ENST00000332695.7_Silent_p.*123*|CMTM1_ENST00000529506.1_Silent_p.*71*|CMTM1_ENST00000528324.1_3'UTR|CMTM2_ENST00000379486.2_5'Flank|CMTM1_ENST00000328020.6_3'UTR|CMTM1_ENST00000531885.1_3'UTR|CMTM1_ENST00000336328.6_Silent_p.*117*|CMTM2_ENST00000268595.2_5'Flank|CMTM1_ENST00000533953.1_Silent_p.*239*|CMTM1_ENST00000533666.1_3'UTR|CKLF-CMTM1_ENST00000527729.1_Silent_p.*116*|RP11-403P17.2_ENST00000568430.1_RNA|CMTM1_ENST00000379500.2_Silent_p.*287*	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1	0					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		AGGCCCGCCTGAAGCCAGCCC	0.627																																					p.X287X		.											.	CMTM1-90	0			c.G860A						.						34	41	38					16																	66612903		2201	4299	6500	SO:0001819	synonymous_variant	113540	exon4			CCGCCTGAAGCCA	AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"chemokine-like factor super family 1", "chemokine-like factor superfamily 1"	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.509G>A	16.37:g.66612903G>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	101	38	NM_052999	0	0	0	0	0	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Silent	SNP	ENST00000457188.2	37	CCDS45503.1																																																																																			.		0.627	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999		A	66612903	G	A	66612903	2	1	102	1	0	0	0	0	0	0	0	1	3588	1285	45	2		2	CMTM1	16	66612903	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	61912435	66612903	23741850	32	9049											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	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-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|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	265	268					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	351	57		WXS	Illumina HiSeq		456	68	NM_145301	0	0	8	46	38	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		T	15457087	C	T	15457087	3	4	102	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		15457087	65738123	33	9050											
TTLL6	284076	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	46862380	46862380	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacttcgagctgctgagatTgatattcctcagatcgggta	10	12	10	9	2	1	3	1	2	0	2	4	5	2	3	1	1	3	3	1	1	3	5			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr17:46862380T>G	ENST00000393382.3	-	13	2086	c.1945A>C	c.(1945-1947)Aat>Cat	p.N649H	TTLL6_ENST00000433608.2_Missense_Mutation_p.N342H	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTGCTGAGATTGATATTCCTC	0.547																																					p.N649H		.											.	TTLL6-90	0			c.A1945C						.						143	142	142					17																	46862380		2203	4300	6503	SO:0001583	missense	284076	exon13			TGAGATTGATATT	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.1945A>C	17.37:g.46862380T>G	ENSP00000377043:p.Asn649His	Somatic	222	1		WXS	Illumina HiSeq	Phase_I	228	94	NM_001130918	0	0	15	34	19		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	.	.	.	.	.	.	.	.	.	.	T	7.206	0.594532	0.13875	.	.	ENSG00000170703	ENST00000440941;ENST00000305326;ENST00000433608;ENST00000393382	.	.	.	4.39	0.921	0.19403	.	7739.210000	0.00166	N	0.000000	T	0.40473	0.1118	L	0.29908	0.895	0.09310	N	1	B;B;D	0.54964	0.0;0.006;0.969	B;B;P	0.54100	0.001;0.001;0.742	T	0.19712	-1.0297	9	0.51188	T	0.08	.	6.212	0.20633	0.0:0.3168:0.0:0.6832	.	601;402;342	Q8N841;D3DTW0;G5E937	TTLL6_HUMAN;.;.	H	649;342;327;601	.	ENSP00000302547:N342H	N	-	1	0	TTLL6	44217379	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.518000	0.06267	0.029000	0.15352	0.379000	0.24179	AAT	.		0.547	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		G	46862380	T	G	46862380	3	3	102	1	0	0	0	0	1	0	0	0	16764	1812	63	5	742	5	TTLL6	17	46862380	Missense_Mutation	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	31405293	46862380	34332830	34	9051											
EPX	8288	broad.mit.edu;bcgsc.ca	37	chr17	56274480	56274480	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgctgcggctccgcaacCggaccaactacctggggctg	6	7	12	16	4	1	0	0	0	1	0	3	1	2	1	4	4	4	4	4	4	3	1	rs143329228	byFrequency	TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr17:56274480C>T	ENST00000225371.5	+	7	1092	c.982C>T	c.(982-984)Cgg>Tgg	p.R328W		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	328					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	GCTCCGCAACCGGACCAACTA	0.617													C|||	13	0.00259585	0	0	5008	,	,		18343	0.0099		0	False		,,,				2504	0.0031				p.R328W													.	EPX-92	0			c.C982T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	119	113	115		982	-3.8	0	17	dbSNP_134	115	0,8600		0,0,4300	no	missense	EPX	NM_000502.4	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	328/716	56274480	1,13005	2203	4300	6503	SO:0001583	missense	8288	exon7			CGCAACCGGACCA	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.982C>T	17.37:g.56274480C>T	ENSP00000225371:p.Arg328Trp	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	214	11	NM_000502	0	0	0	0	0	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	37	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	C	3.883	-0.025552	0.07589	2.27E-4	0.0	ENSG00000121053	ENST00000225371	T	0.73152	-0.72	4.86	-3.76	0.04359	.	1.473130	0.03548	N	0.225033	T	0.51787	0.1695	N	0.05031	-0.125	0.09310	N	0.999991	B	0.13594	0.008	B	0.09377	0.004	T	0.37526	-0.9702	10	0.27082	T	0.32	-2.6526	16.444	0.83910	0.7426:0.2574:0.0:0.0	.	328	P11678	PERE_HUMAN	W	328	ENSP00000225371:R328W	ENSP00000225371:R328W	R	+	1	2	EPX	53629479	0.000000	0.05858	0.002000	0.10522	0.039000	0.13416	-0.004000	0.12878	-0.381000	0.07882	-0.475000	0.04921	CGG	C|1.000;T|0.000		0.617	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502		T	56274480	C	T	56274480	3	4	102	1	0	0	0	0	1	0	0	0	5213	643	23	1	1008	1	EPX	17	56274480	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	9412100	56274480	24920730	35	9052											
C17orf62	79415	ucsc.edu	37	chr17	80405455	80405455	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtggggcggggggtgctttaCctccgctgtagtaggcagca	5	9	18	9	2	0	0	0	0	0	0	1	0	1	0	2	6	3	6	2	6	3	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr17:80405455C>T	ENST00000437807.2	-	4	445		c.e4+1		C17orf62_ENST00000577732.1_Splice_Site|C17orf62_ENST00000342572.8_Intron|C17orf62_ENST00000583359.1_Splice_Site|C17orf62_ENST00000585064.1_Splice_Site|C17orf62_ENST00000336995.7_Splice_Site|C17orf62_ENST00000578919.1_Splice_Site|C17orf62_ENST00000583617.1_Splice_Site|C17orf62_ENST00000585080.1_Splice_Site|C17orf62_ENST00000306645.5_Splice_Site|C17orf62_ENST00000434650.2_Intron|C17orf62_ENST00000577436.1_Intron|C17orf62_ENST00000578913.1_Splice_Site	NM_001193653.1|NM_001193657.1	NP_001180582.1|NP_001180586.1	Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62							integral component of membrane (GO:0016021)				breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GGGTGCTTTACCTCCGCTGTA	0.547																																					.													.	C17orf62-90	0			c.127+1G>A						.						20	18	19					17																	80405455		2199	4291	6490	SO:0001630	splice_region_variant	79415	exon5			GCTTTACCTCCGC	AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927			28672	protein-coding gene	gene with protein product							Standard	NM_001100407		Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000437807.2:c.127+1G>A	17.37:g.80405455C>T		Somatic	56	0		WXS	Illumina HiSeq		85	1	NM_001100407	0	0	3	3	0	E1B6X3|Q96NR1	Splice_Site	SNP	ENST00000437807.2	37	CCDS32776.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487722	0.64074	.	.	ENSG00000178927	ENST00000437807;ENST00000306645	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0014	0.80294	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C17orf62	77998744	1.000000	0.71417	0.996000	0.52242	0.860000	0.49131	6.284000	0.72652	2.113000	0.64589	0.561000	0.74099	.	.		0.547	C17orf62-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443260.1	NM_001033046	Intron	T	80405455	C	T	80405455	5	4	102	1	0	0	0	0	0	0	1	0	1875	521	18	2	455	2	C17orf62	17	80405455	Splice_Site	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	24130975	80405455	789755	36	9053											
SIRPG	55423	ucsc.edu	37	chr20	1629910	1629910	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gattgtagattaattcccggCctggtccaactcctctgaac	9	12	8	12	1	1	2	0	1	1	1	4	3	4	2	4	2	2	1	4	2	4	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr20:1629910C>G	ENST00000303415.3	-	2	282	c.218G>C	c.(217-219)gGc>gCc	p.G73A	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000344103.4_Missense_Mutation_p.G73A|SIRPG_ENST00000216927.4_Missense_Mutation_p.G73A|SIRPG_ENST00000381580.1_Missense_Mutation_p.G40A|SIRPG_ENST00000381583.2_Missense_Mutation_p.G73A	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	73	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						TAATTCCCGGCCTGGTCCAAC	0.517																																					p.G73A													.	SIRPG-23	0			c.G218C						.						171	156	161					20																	1629910		2203	4300	6503	SO:0001583	missense	55423	exon2			TCCCGGCCTGGTC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.218G>C	20.37:g.1629910C>G	ENSP00000305529:p.Gly73Ala	Somatic	127	0		WXS	Illumina HiSeq		135	2	NM_001039508	0	0	0	0	0	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	.	.	.	.	.	.	.	.	.	.	.	4.988	0.183566	0.09495	.	.	ENSG00000089012	ENST00000381580;ENST00000344103;ENST00000303415;ENST00000381583;ENST00000216927	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	1.93	-3.09	0.05331	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.255760	0.05163	N	0.498210	T	0.56949	0.2020	L	0.56280	1.765	0.09310	N	1	B;B;B	0.14438	0.01;0.004;0.003	B;B;B	0.10450	0.005;0.001;0.003	T	0.32824	-0.9892	10	0.26408	T	0.33	.	6.3533	0.21387	0.0:0.3641:0.0:0.6359	.	73;73;73	Q9P1W8-3;Q9P1W8-4;Q9P1W8	.;.;SIRPG_HUMAN	A	40;73;73;73;73	ENSP00000370992:G40A;ENSP00000342759:G73A;ENSP00000305529:G73A;ENSP00000370995:G73A;ENSP00000216927:G73A	ENSP00000216927:G73A	G	-	2	0	SIRPG	1577910	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.760000	0.04756	-0.812000	0.04363	0.195000	0.17529	GGC	.		0.517	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		G	1629910	C	G	1629910	3	3	102	1	0	0	0	0	1	0	0	0	14368	739	26	4	961	4	SIRPG	20	1629910	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		1629910	61395610	37	9054											
COL20A1	57642	hgsc.bcm.edu	37	chr20	61944243	61944243	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgtctggcgtgcttgtctAccagatcacgtggacgcccc	5	9	11	16	4	3	1	1	0	2	1	3	2	3	2	4	2	2	1	4	2	1	2	rs143321165	byFrequency	TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr20:61944243A>G	ENST00000358894.6	+	16	2133	c.2033A>G	c.(2032-2034)tAc>tGc	p.Y678C	COL20A1_ENST00000422202.1_Missense_Mutation_p.Y685C|COL20A1_ENST00000326996.6_Missense_Mutation_p.Y678C|COL20A1_ENST00000435874.1_Missense_Mutation_p.Y685C	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	678	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GTGCTTGTCTACCAGATCACG	0.677													A|||	26	0.00519169	0.0015	0.0187	5008	,	,		15792	0		0.0089	False		,,,				2504	0.002				p.Y678C		.											.	COL20A1-90	0			c.A2033G						.	A	CYS/TYR	2,3854		0,2,1926	19	27	24		2033	4.2	0.5	20	dbSNP_134	24	40,8128		0,40,4044	yes	missense	COL20A1	NM_020882.2	194	0,42,5970	GG,GA,AA		0.4897,0.0519,0.3493	probably-damaging	678/1285	61944243	42,11982	1928	4084	6012	SO:0001583	missense	57642	exon16			TTGTCTACCAGAT	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"Collagens", "Fibronectin type III domain containing"	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2033A>G	20.37:g.61944243A>G	ENSP00000351767:p.Tyr678Cys	Somatic	5	1		WXS	Illumina HiSeq	Phase_I	6	5	NM_020882	0	0	0	0	0	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	13	0.005952380952380952	0	0.0	9	0.024861878453038673	0	0.0	4	0.005277044854881266	A	13.73	2.322939	0.41096	5.19E-4	0.004897	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	4.25	4.25	0.50352	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.234827	0.36932	N	0.002333	T	0.79799	0.4508	M	0.84948	2.725	0.36447	D	0.865874	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.87437	0.2392	10	0.87932	D	0	.	9.82	0.40876	1.0:0.0:0.0:0.0	.	685;678	Q9P218-2;Q9P218	.;COKA1_HUMAN	C	678;678;685;685	ENSP00000351767:Y678C;ENSP00000323077:Y678C;ENSP00000408690:Y685C;ENSP00000414753:Y685C	ENSP00000323077:Y678C	Y	+	2	0	COL20A1	61414688	0.342000	0.24809	0.510000	0.27712	0.059000	0.15707	3.141000	0.50593	1.583000	0.49898	0.254000	0.18369	TAC	A|0.994;G|0.006		0.677	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		G	61944243	A	G	61944243	3	3	102	1	0	0	0	0	1	0	0	0	3685	391	14	3	2091	3	COL20A1	20	61944243	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08	60314333	61944243	1081277	38	9055											
GART	2618	broad.mit.edu	37	chr21	34877874	34877874	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatttttgcttaccattccActtttggacaaaggggccag	10	14	8	9	0	0	0	0	0	0	0	1	1	1	1	3	3	2	1	3	3	3	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr21:34877874A>C	ENST00000381831.3	-	20	2982	c.2719T>G	c.(2719-2721)Tgg>Ggg	p.W907G	GART_ENST00000381815.4_Missense_Mutation_p.W907G|GART_ENST00000381839.3_Missense_Mutation_p.W907G|GART_ENST00000543717.1_Missense_Mutation_p.W459G	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	907	GART.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	TTACCATTCCACTTTTGGACA	0.398																																					p.W907G													.	GART-91	0			c.T2719G						.						81	78	79					21																	34877874		2203	4300	6503	SO:0001583	missense	2618	exon20			CATTCCACTTTTG	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2719T>G	21.37:g.34877874A>C	ENSP00000371253:p.Trp907Gly	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_001136005	0	0	0	0	0	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	37	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.406578	0.62399	.	.	ENSG00000159131	ENST00000414353;ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	5.59	5.59	0.84812	Formyl transferase, N-terminal (3);	0.121520	0.64402	D	0.000012	D	0.91640	0.7358	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94012	0.7285	10	0.87932	D	0	-2.7596	16.1134	0.81278	1.0:0.0:0.0:0.0	.	907	P22102	PUR2_HUMAN	G	171;907;907;907;459	ENSP00000371236:W907G;ENSP00000371253:W907G;ENSP00000371261:W907G;ENSP00000443579:W459G	ENSP00000371236:W907G	W	-	1	0	GART	33799744	1.000000	0.71417	0.999000	0.59377	0.448000	0.32197	8.515000	0.90548	2.266000	0.75297	0.456000	0.33151	TGG	.		0.398	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		C	34877874	A	C	34877874	3	2	102	1	0	0	0	0	1	0	0	0	6263	159	6	5	325	5	GART	21	34877874	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08		34877874	13252021	39	9056											
ZNF295	49854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43413770	43413770	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaacaatgacacttctcttTtgagaactgttttcatcatc	12	15	4	10	0	3	2	2	2	1	1	5	3	3	2	0	0	2	1	0	0	3	5			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr21:43413770T>C	ENST00000310826.5	-	3	618	c.435A>G	c.(433-435)caA>caG	p.Q145Q	ZBTB21_ENST00000398505.3_Silent_p.Q145Q|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398511.3_Silent_p.Q145Q|ZBTB21_ENST00000398499.1_Silent_p.Q145Q	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	145					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										CACTTCTCTTTTGAGAACTGT	0.403																																					p.Q145Q		.											.	.	0			c.A435G						.						98	88	91					21																	43413770		2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			TCTCTTTTGAGAA	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13083	protein-coding gene	gene with protein product			"zinc finger protein 295"	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.435A>G	21.37:g.43413770T>C		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	130	56	NM_001098402	0	0	3	4	1	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	37	CCDS13678.1																																																																																			.		0.403	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		C	43413770	T	C	43413770	2	2	102	1	0	0	0	0	0	0	0	1	17859	1838	64	3		3	ZNF295	21	43413770	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	8535896	43413770	4716125	40	9057											
KRTAP10-10	353333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46057373	46057373	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccatctgctccagcgcctgCactgactcttggcgggtagt	5	11	11	14	2	2	1	0	1	2	0	4	1	4	1	3	2	3	3	3	2	1	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr21:46057373C>T	ENST00000380095.1	+	1	101	c.39C>T	c.(37-39)tgC>tgT	p.C13C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	13						keratin filament (GO:0045095)		p.C13C(1)		NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCAGCGCCTGCACTGACTCTT	0.652																																					p.C13C		.											.	KRTAP10-10-90	1	Substitution - coding silent(1)	endometrium(1)	c.C39T						.						104	109	108					21																	46057373		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CGCCTGCACTGAC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"Keratin associated proteins"	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.39C>T	21.37:g.46057373C>T		Somatic	219	0		WXS	Illumina HiSeq	Phase_I	201	37	NM_181688	0	0	0	0	0		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			.		0.652	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46057373	C	T	46057373	2	4	102	1	0	0	0	0	0	0	0	1	8527	718	25	2		2	KRTAP10-10	21	46057373	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	2643603	46057373	2072522	41	9058											
FAM47B	170062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	34961454	34961454	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgggctcgttgtgaggcccGggagaagacaaccgaggtac	9	7	16	9	3	0	3	0	1	0	2	1	5	0	3	2	4	2	3	2	4	3	3			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chrX:34961454G>A	ENST00000329357.5	+	1	542	c.506G>A	c.(505-507)cGg>cAg	p.R169Q		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	169										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TGTGAGGCCCGGGAGAAGACA	0.592																																					p.R169Q		.											.	FAM47B-196	0			c.G506A						.						36	35	35					X																	34961454		2202	4300	6502	SO:0001583	missense	170062	exon1			AGGCCCGGGAGAA	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.506G>A	X.37:g.34961454G>A	ENSP00000328307:p.Arg169Gln	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	36	30	NM_152631	0	0	0	0	0	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	G	1.355	-0.590410	0.03799	.	.	ENSG00000189132	ENST00000329357	T	0.14266	2.52	0.843	-0.104	0.13605	.	.	.	.	.	T	0.04952	0.0133	N	0.05259	-0.085	0.09310	N	1	B	0.19073	0.033	B	0.08055	0.003	T	0.45175	-0.9279	8	0.13108	T	0.6	.	.	.	.	.	169	Q8NA70	FA47B_HUMAN	Q	169	ENSP00000328307:R169Q	ENSP00000328307:R169Q	R	+	2	0	FAM47B	34871375	0.070000	0.21116	0.001000	0.08648	0.009000	0.06853	-2.406000	0.01044	-0.099000	0.12263	-0.780000	0.03373	CGG	.		0.592	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		A	34961454	G	A	34961454	3	1	102	1	0	0	0	0	1	0	0	0	5589	1116	39	1	508	1	FAM47B	23	34961454	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		34961454	120309106	42	9059											
IQSEC2	23096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53268433	53268433	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggggaaagactgacggaaaCtgtacgtcaccaagatcttc	13	7	12	9	2	2	3	1	1	1	2	3	5	2	5	1	3	2	1	1	3	4	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chrX:53268433C>G	ENST00000375368.5	-	10	3229	c.3029G>C	c.(3028-3030)aGt>aCt	p.S1010T	IQSEC2_ENST00000375365.2_Missense_Mutation_p.S815T|IQSEC2_ENST00000396435.3_Missense_Mutation_p.S1020T			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1010	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						CTGACGGAAACTGTACGTCAC	0.502											OREG0019800	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1020T		.											.	IQSEC2-178	0			c.G3059C						.						114	103	107					X																	53268433		2203	4300	6503	SO:0001583	missense	23096	exon11			CGGAAACTGTACG	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"mental retardation, X-linked 1 (non-dysmorphic)"	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.3029G>C	X.37:g.53268433C>G	ENSP00000364517:p.Ser1010Thr	Somatic	58	0	991	WXS	Illumina HiSeq	Phase_I	42	33	NM_001111125	0	0	0	9	9	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	37		.	.	.	.	.	.	.	.	.	.	C	14.06	2.422471	0.43020	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.54071	0.59;0.59;0.59	5.61	5.61	0.85477	.	.	.	.	.	T	0.52240	0.1722	N	0.19112	0.55	0.80722	D	1	B;P	0.39903	0.039;0.694	B;P	0.56434	0.105;0.798	T	0.40001	-0.9586	9	0.02654	T	1	.	17.3443	0.87306	0.0:1.0:0.0:0.0	.	1020;815	Q5JU85-2;Q5JU85-3	.;.	T	1020;1010;815	ENSP00000379712:S1020T;ENSP00000364517:S1010T;ENSP00000364514:S815T	ENSP00000364514:S815T	S	-	2	0	IQSEC2	53285158	0.998000	0.40836	1.000000	0.80357	0.962000	0.63368	2.668000	0.46816	2.363000	0.80096	0.511000	0.50034	AGT	.		0.502	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		G	53268433	C	G	53268433	3	3	102	1	0	0	0	0	1	0	0	0	7839	565	20	4	1427	4	IQSEC2	23	53268433	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	18306979	53268433	102002127	43	9060											
SKI	6497	hgsc.bcm.edu	37	chr1	2160390	2160390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgcggccgcggtgccggCgccggtgcccgcagccaccg	2	2	19	18	9	0	0	0	0	0	0	0	0	0	0	6	5	3	1	6	5	0	0	rs28384811	byFrequency	TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:2160390C>G	ENST00000378536.4	+	1	257	c.185C>G	c.(184-186)gCg>gGg	p.A62G		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	62					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		gcggtgccggcgccggTGCCC	0.776													C|||	229	0.0457268	0.0234	0.0576	5008	,	,		4535	0.0079		0.0706	False		,,,				2504	0.0808				p.A62G	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.C185G						.						1	1	1					1																	2160390		788	1840	2628	SO:0001583	missense	6497	exon1			TGCCGGCGCCGGT	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.185C>G	1.37:g.2160390C>G	ENSP00000367797:p.Ala62Gly	Somatic	3	2		WXS	Illumina HiSeq	Phase_I	6	3	NM_003036	0	0	0	0	0	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	37	CCDS39.1	102	0.046703296703296704	20	0.04065040650406504	28	0.07734806629834254	3	0.005244755244755245	51	0.06728232189973615	C	9.688	1.151208	0.21371	.	.	ENSG00000157933	ENST00000378536	D	0.95821	-3.82	2.3	2.3	0.28687	.	.	.	.	.	T	0.47857	0.1468	N	0.08118	0	0.45733	P	0.001363000000000003	D	0.57899	0.981	P	0.58520	0.84	T	0.76271	-0.3020	8	0.20519	T	0.43	-11.9718	7.7374	0.28823	0.0:1.0:0.0:0.0	rs28384811	62	P12755	SKI_HUMAN	G	62	ENSP00000367797:A62G	ENSP00000367797:A62G	A	+	2	0	SKI	2150250	0.994000	0.37717	0.998000	0.56505	0.971000	0.66376	0.878000	0.28126	1.104000	0.41587	0.185000	0.17295	GCG	C|0.953;G|0.047		0.776	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		G	2160390	C	G	2160390	3	3	103	1	0	0	0	0	1	0	0	0	14389	768	27	4	187	4	SKI	1	2160390	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		2160390	247090231	1	9061											
SLC2A5	6518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	9097752	9097752	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggttgatctctatgaacgTcttggccttggtctccggga	5	14	12	10	2	3	2	0	2	3	0	5	3	3	3	2	4	1	1	2	4	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:9097752T>C	ENST00000377424.4	-	12	1578	c.1399A>G	c.(1399-1401)Acg>Gcg	p.T467A	SLC2A5_ENST00000535586.1_Missense_Mutation_p.T352A|SLC2A5_ENST00000536305.1_Missense_Mutation_p.T408A	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	467					carbohydrate metabolic process (GO:0005975)|cellular response to fructose stimulus (GO:0071332)|fructose transport (GO:0015755)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fructose transmembrane transporter activity (GO:0005353)|glucose transmembrane transporter activity (GO:0005355)			endometrium(6)|kidney(15)|large_intestine(6)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	36	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		TCTATGAACGTCTTGGCCTTG	0.512																																					p.T467A		.											.	SLC2A5-517	0			c.A1399G						.						127	131	130					1																	9097752		2203	4300	6503	SO:0001583	missense	6518	exon12			TGAACGTCTTGGC	BC001820	CCDS99.1, CCDS44054.1	1p36.2	2013-05-22			ENSG00000142583	ENSG00000142583		"Solute carriers"	11010	protein-coding gene	gene with protein product		138230		GLUT5		9691177	Standard	NM_003039		Approved		uc001apo.3	P22732	OTTHUMG00000001771	ENST00000377424.4:c.1399A>G	1.37:g.9097752T>C	ENSP00000366641:p.Thr467Ala	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	181	30	NM_003039	0	0	97	97	0	Q14770|Q5T977|Q8IVB3	Missense_Mutation	SNP	ENST00000377424.4	37	CCDS99.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661340	0.67700	.	.	ENSG00000142583	ENST00000377424;ENST00000456780;ENST00000536305;ENST00000535586	T;T;T	0.76448	-1.02;-1.02;-1.02	5.53	5.53	0.82687	Major facilitator superfamily domain, general substrate transporter (1);	0.047424	0.85682	D	0.000000	D	0.89842	0.6832	M	0.93197	3.39	0.53005	D	0.999969	D;D;D	0.61080	0.971;0.971;0.989	P;P;D	0.64042	0.872;0.872;0.921	D	0.92195	0.5763	10	0.87932	D	0	.	13.3288	0.60475	0.0:0.0:0.0:1.0	.	423;408;467	B4DG19;B4DU31;P22732	.;.;GTR5_HUMAN	A	467;450;408;352	ENSP00000366641:T467A;ENSP00000440688:T408A;ENSP00000442744:T352A	ENSP00000366641:T467A	T	-	1	0	SLC2A5	9020339	1.000000	0.71417	0.853000	0.33588	0.611000	0.37282	3.992000	0.56980	2.220000	0.72140	0.533000	0.62120	ACG	.		0.512	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		C	9097752	T	C	9097752	3	2	103	1	0	0	0	0	1	0	0	0	14580	1667	58	3	110	3	SLC2A5	1	9097752	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	6937362	9097752	240152869	2	9062											
ALPL	249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	21902288	21902288	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aggccctgcatgaggcggtgGagatggaccgggccatcggg	7	5	19	10	3	0	2	0	1	0	1	1	4	0	3	3	7	1	1	3	7	0	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:21902288G>A	ENST00000374840.3	+	10	1310	c.1060G>A	c.(1060-1062)Gag>Aag	p.E354K	ALPL_ENST00000425315.2_Missense_Mutation_p.E354K|ALPL_ENST00000539907.1_Missense_Mutation_p.E277K|ALPL_ENST00000540617.1_Missense_Mutation_p.E299K|ALPL_ENST00000374830.1_5'UTR|ALPL_ENST00000374832.1_Missense_Mutation_p.E354K|ALPL_ENST00000374829.1_5'UTR	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	354			E -> D (in HOPS).		cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	TGAGGCGGTGGAGATGGACCG	0.612																																					p.E354K		.											.	ALPL-94	0			c.G1060A						.						142	136	138					1																	21902288		2203	4300	6503	SO:0001583	missense	249	exon10			GCGGTGGAGATGG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.1060G>A	1.37:g.21902288G>A	ENSP00000363973:p.Glu354Lys	Somatic	278	0		WXS	Illumina HiSeq	Phase_I	186	25	NM_000478	0	0	3	3	0	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Missense_Mutation	SNP	ENST00000374840.3	37	CCDS217.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371272	0.42003	.	.	ENSG00000162551	ENST00000539907;ENST00000540617;ENST00000374840;ENST00000374832;ENST00000425315	D;D;D;D;D	0.96716	-4.1;-4.1;-4.1;-4.1;-4.1	4.91	3.99	0.46301	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.056236	0.64402	D	0.000001	D	0.96796	0.8954	M	0.83852	2.665	0.51233	D	0.999917	B;P	0.52692	0.407;0.955	P;P	0.54544	0.507;0.755	D	0.95649	0.8705	10	0.52906	T	0.07	-8.6255	7.1413	0.25558	0.0934:0.1721:0.7345:0.0	.	277;354	B7Z387;P05186	.;PPBT_HUMAN	K	277;299;354;354;354	ENSP00000437674:E277K;ENSP00000442672:E299K;ENSP00000363973:E354K;ENSP00000363965:E354K;ENSP00000394765:E354K	ENSP00000363965:E354K	E	+	1	0	ALPL	21774875	1.000000	0.71417	0.892000	0.35008	0.007000	0.05969	5.646000	0.67916	1.071000	0.40834	-0.291000	0.09656	GAG	.		0.612	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		A	21902288	G	A	21902288	3	1	103	1	0	0	0	0	1	0	0	0	547	1175	41	2	1094	2	ALPL	1	21902288	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	12804536	21902288	227348333	3	9063											
WASF2	10163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27739179	27739179	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcatccacgttttcaacAcagccaatgctgccattctg	9	12	6	14	1	2	0	1	0	1	0	3	0	3	0	3	0	5	3	3	0	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:27739179A>G	ENST00000430629.2	-	7	926	c.711T>C	c.(709-711)tgT>tgC	p.C237C	WASF2_ENST00000536657.1_Silent_p.C237C	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	237					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		CGTTTTCAACACAGCCAATGC	0.488																																					p.C237C		.											.	WASF2-228	0			c.T711C						.						153	137	142					1																	27739179		2203	4300	6503	SO:0001819	synonymous_variant	10163	exon7			TTCAACACAGCCA	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.711T>C	1.37:g.27739179A>G		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	128	22	NM_006990	0	0	55	85	30	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	37	CCDS304.1																																																																																			.		0.488	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		G	27739179	A	G	27739179	2	3	103	1	0	0	0	0	0	0	0	1	17286	157	6	3		3	WASF2	1	27739179	Silent	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	5836891	27739179	221511442	4	9064											
MACF1	23499	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	39888512	39888512	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gataccgaggagctcatagcCaatcagaaacctccatctgc	13	7	8	13	1	3	1	2	0	1	1	4	4	4	2	4	1	5	1	4	1	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:39888512C>T	ENST00000372915.3	+	59	16191	c.16104C>T	c.(16102-16104)gcC>gcT	p.A5368A	MACF1_ENST00000567887.1_Silent_p.A5400A|MACF1_ENST00000289893.4_Silent_p.A3803A|MACF1_ENST00000564288.1_Silent_p.A5363A|MACF1_ENST00000539005.1_Silent_p.A3280A|MACF1_ENST00000317713.7_Silent_p.A3301A|MACF1_ENST00000545844.1_Silent_p.A3301A|MACF1_ENST00000361689.2_Silent_p.A3301A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5368					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGCTCATAGCCAATCAGAAAC	0.468																																					p.A3301A													.	MACF1-165	0			c.C9903T						.						100	95	97					1																	39888512		2203	4300	6503	SO:0001819	synonymous_variant	23499	exon56			CATAGCCAATCAG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.16104C>T	1.37:g.39888512C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	115	11	NM_012090	0	0	36	43	7	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	9.928	1.213943	0.22289	.	.	ENSG00000127603	ENST00000372925	.	.	.	5.96	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8185	0.40867	0.1407:0.7902:0.0:0.0691	.	.	.	.	X	2414	.	.	Q	+	1	0	MACF1	39661099	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.321000	0.51999	1.481000	0.48307	0.650000	0.86243	CAA	.		0.468	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39888512	C	T	39888512	2	4	103	1	0	0	0	0	0	0	0	1	9169	581	21	2		2	MACF1	1	39888512	Silent	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	12149333	39888512	209362109	5	9065											
TESK2	10420	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45813333	45813333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caggtgccatccagaatgggGaacccaccacggccagcttc	10	5	11	15	1	0	1	0	0	0	1	2	2	1	2	5	4	3	1	5	4	2	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:45813333G>A	ENST00000372086.3	-	7	1056	c.656C>T	c.(655-657)tCc>tTc	p.S219F	TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.S219F|TESK2_ENST00000538496.1_Missense_Mutation_p.S136F|TESK2_ENST00000341771.6_Missense_Mutation_p.S219F	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	219	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CCAGAATGGGGAACCCACCAC	0.473																																					p.S219F		.											.	TESK2-624	0			c.C656T						.						112	113	113					1																	45813333		1904	4153	6057	SO:0001583	missense	10420	exon7			AATGGGGAACCCA	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.656C>T	1.37:g.45813333G>A	ENSP00000361158:p.Ser219Phe	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	175	38	NM_007170	0	0	3	3	0	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	37	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.874832	0.91664	.	.	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	T;T;T;T	0.69926	-0.44;-0.12;-0.44;-0.12	5.98	5.98	0.97165	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.104533	0.43110	N	0.000604	D	0.84933	0.5582	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86499	0.1802	10	0.87932	D	0	-17.2903	18.6171	0.91306	0.0:0.0:1.0:0.0	.	219;219	Q96S53-3;Q96S53	.;TESK2_HUMAN	F	219;219;203;219;136	ENSP00000361156:S219F;ENSP00000361158:S219F;ENSP00000343940:S219F;ENSP00000441746:S136F	ENSP00000343940:S219F	S	-	2	0	TESK2	45585920	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	7.907000	0.87430	2.843000	0.97960	0.585000	0.79938	TCC	.		0.473	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		A	45813333	G	A	45813333	3	1	103	1	0	0	0	0	1	0	0	0	15800	1174	41	2	1079	2	TESK2	1	45813333	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	5924821	45813333	203437288	6	9066											
TMEM69	51249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	46159260	46159260	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctatctttcttgggtgggAtcagatggggttttgctcta	5	17	12	7	0	4	1	1	0	3	1	5	2	5	2	1	4	1	2	1	4	2	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:46159260A>G	ENST00000372025.4	+	3	1584	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	RP11-767N6.7_ENST00000430643.1_RNA|TMEM69_ENST00000496366.1_3'UTR	NM_016486.3	NP_057570.2	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	143						integral component of membrane (GO:0016021)				kidney(3)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)					CTTGGGTGGGATCAGATGGGG	0.438																																					p.I143V		.											.	TMEM69-91	0			c.A427G						.						89	87	88					1																	46159260		1859	4090	5949	SO:0001583	missense	51249	exon3			GGTGGGATCAGAT	BC040289, BC013608	CCDS41325.1	1p34.1	2008-02-05	2005-08-17	2005-08-17	ENSG00000159596	ENSG00000159596			28035	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 154"	C1orf154			Standard	NM_016486		Approved	FLJ21029	uc001cor.1	Q5SWH9	OTTHUMG00000040993	ENST00000372025.4:c.427A>G	1.37:g.46159260A>G	ENSP00000361095:p.Ile143Val	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	176	31	NM_016486	0	0	32	48	16	Q3SWW5|Q7Z2G0|Q9P0P9	Missense_Mutation	SNP	ENST00000372025.4	37	CCDS41325.1	.	.	.	.	.	.	.	.	.	.	A	4.400	0.073919	0.08485	.	.	ENSG00000159596	ENST00000372025	.	.	.	5.83	-1.16	0.09678	.	0.588234	0.19061	N	0.123779	T	0.23330	0.0564	N	0.20357	0.565	0.19575	N	0.999966	B	0.10296	0.003	B	0.10450	0.005	T	0.25745	-1.0123	9	0.11794	T	0.64	-0.7606	12.6228	0.56614	0.7619:0.0:0.2381:0.0	.	143	Q5SWH9	TMM69_HUMAN	V	143	.	ENSP00000361095:I143V	I	+	1	0	TMEM69	45931847	0.218000	0.23608	0.138000	0.22173	0.907000	0.53573	0.632000	0.24583	-0.248000	0.09583	-0.415000	0.06103	ATC	.		0.438	TMEM69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098390.1	NM_016486		G	46159260	A	G	46159260	3	3	103	1	0	0	0	0	1	0	0	0	16230	333	12	3	433	3	TMEM69	1	46159260	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	345927	46159260	203091361	7	9067											
ZFYVE9	9372	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52704507	52704507	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacacaccagcagcaaattAtctatctaatggttgtgatt	14	12	7	8	0	2	2	0	1	2	1	2	2	2	2	1	1	2	3	1	1	4	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:52704507A>G	ENST00000371591.1	+	3	1549	c.1418A>G	c.(1417-1419)tAt>tGt	p.Y473C	ZFYVE9_ENST00000287727.3_Missense_Mutation_p.Y473C|ZFYVE9_ENST00000357206.2_Missense_Mutation_p.Y473C	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	473					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						GCAGCAAATTATCTATCTAAT	0.378																																					p.Y473C		.											.	ZFYVE9-230	0			c.A1418G						.						95	101	99					1																	52704507		2203	4299	6502	SO:0001583	missense	9372	exon4			CAAATTATCTATC	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"Zinc fingers, FYVE domain containing"	6775	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 173"	603755	"MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.1418A>G	1.37:g.52704507A>G	ENSP00000360647:p.Tyr473Cys	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	176	32	NM_007324	0	0	3	4	1	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	7.890	0.732073	0.15507	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.51574	1.19;0.7;1.19;1.19	5.69	4.78	0.61160	.	0.445610	0.20824	N	0.085019	T	0.25005	0.0607	N	0.08118	0	0.20764	N	0.99985	B;B;B	0.33512	0.415;0.01;0.0	B;B;B	0.33392	0.163;0.002;0.0	T	0.09662	-1.0664	10	0.38643	T	0.18	.	6.1713	0.20418	0.1413:0.6538:0.1348:0.0701	.	473;473;473	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	C	473	ENSP00000349737:Y473C;ENSP00000355358:Y473C;ENSP00000287727:Y473C;ENSP00000360647:Y473C	ENSP00000287727:Y473C	Y	+	2	0	ZFYVE9	52477095	1.000000	0.71417	0.843000	0.33291	0.920000	0.55202	1.818000	0.39012	1.420000	0.47138	-0.132000	0.14878	TAT	.		0.378	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		G	52704507	A	G	52704507	3	3	103	1	0	0	0	0	1	0	0	0	17703	449	16	3	1424	3	ZFYVE9	1	52704507	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	6545247	52704507	196546114	8	9068											
ZYG11B	79699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	53262039	53262039	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcaaaggatggcagttgcTatcatttctatcctggctgc	9	13	10	9	0	2	0	1	0	1	0	3	1	3	1	1	3	3	5	1	3	3	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:53262039T>C	ENST00000294353.6	+	7	1555	c.1410T>C	c.(1408-1410)gcT>gcC	p.A470A	ZYG11B_ENST00000545132.1_Silent_p.A470A|ZYG11B_ENST00000443756.2_Silent_p.A470A	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	470										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TGGCAGTTGCTATCATTTCTA	0.433																																					p.A470A		.											.	ZYG11B-94	0			c.T1410C						.						82	76	78					1																	53262039		2203	4300	6503	SO:0001819	synonymous_variant	79699	exon7			AGTTGCTATCATT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1410T>C	1.37:g.53262039T>C		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	71	10	NM_024646	0	0	9	15	6	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	37	CCDS30717.1																																																																																			.		0.433	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		C	53262039	T	C	53262039	2	2	103	1	0	0	0	0	0	0	0	1	18285	1509	53	3		3	ZYG11B	1	53262039	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	557532	53262039	195988582	9	9069											
ODF2L	57489	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	86851227	86851227	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccaactccgcttccttaaGtgttgcttccaattcagtct	8	15	5	13	1	2	0	1	0	1	0	5	0	5	0	4	0	3	3	4	0	4	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:86851227G>A	ENST00000359242.3	-	3	441	c.160C>T	c.(160-162)Ctt>Ttt	p.L54F	ODF2L_ENST00000370566.3_Missense_Mutation_p.L54F|ODF2L_ENST00000394731.1_Intron|ODF2L_ENST00000317336.7_Missense_Mutation_p.L54F|ODF2L_ENST00000294678.2_Missense_Mutation_p.L54F|ODF2L_ENST00000370567.1_Missense_Mutation_p.L54F	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	54						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		GCTTCCTTAAGTGTTGCTTCC	0.323																																					p.L54F		.											.	ODF2L-69	0			c.C160T						.						87	84	85					1																	86851227		2203	4298	6501	SO:0001583	missense	57489	exon3			CCTTAAGTGTTGC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.160C>T	1.37:g.86851227G>A	ENSP00000359600:p.Leu54Phe	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	53	12	NM_001007022	0	0	1	1	0	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	G	11.71	1.718586	0.30503	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959	T;T;T;T;T	0.39056	1.1;1.1;1.15;1.15;1.12	5.4	0.554	0.17241	.	0.523188	0.20488	N	0.091342	T	0.06280	0.0162	N	0.04768	-0.165	0.44417	D	0.997339	B;B;B;B;B	0.24043	0.001;0.027;0.008;0.011;0.096	B;B;B;B;B	0.21360	0.004;0.013;0.012;0.009;0.034	T	0.15752	-1.0426	10	0.38643	T	0.18	0.4325	1.1465	0.01776	0.2214:0.1715:0.4328:0.1743	.	54;54;54;54;54	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	F	54	ENSP00000359597:L54F;ENSP00000359600:L54F;ENSP00000320165:L54F;ENSP00000359598:L54F;ENSP00000294678:L54F	ENSP00000294678:L54F	L	-	1	0	ODF2L	86623815	0.325000	0.24660	0.872000	0.34217	0.966000	0.64601	0.460000	0.21924	0.196000	0.20367	0.650000	0.86243	CTT	.		0.323	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			A	86851227	G	A	86851227	3	1	103	1	0	0	0	0	1	0	0	0	10854	1029	36	2	1990	2	ODF2L	1	86851227	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	33589188	86851227	162399394	10	9070											
ABCA4	24	broad.mit.edu	37	chr1	94522330	94522330	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcagtggagaaagccaacaAgaacaggaagaggatgaatg	18	3	15	5	0	0	4	0	1	0	3	0	7	0	6	1	4	3	1	1	4	6	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:94522330A>G	ENST00000370225.3	-	15	2295	c.2209T>C	c.(2209-2211)Ttg>Ctg	p.L737L	ABCA4_ENST00000535735.1_Intron	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	737					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AAAGCCAACAAGAACAGGAAG	0.522																																					p.L737L													.	ABCA4-162	0			c.T2209C						.						107	96	100					1																	94522330		2203	4300	6503	SO:0001819	synonymous_variant	24	exon15			CCAACAAGAACAG	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2209T>C	1.37:g.94522330A>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			.		0.522	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		G	94522330	A	G	94522330	2	3	103	1	0	0	0	0	0	0	0	1	34	69	3	3		3	ABCA4	1	94522330	Silent	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	7671103	94522330	154728291	11	9071											
ARHGAP29	9411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94639942	94639942	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcattgtagtcttggcagttAggctgttttgttcatactgt	6	19	10	6	0	3	0	2	0	1	0	3	0	3	0	0	2	1	6	0	2	3	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:94639942A>G	ENST00000260526.6	-	23	3451	c.3269T>C	c.(3268-3270)cTa>cCa	p.L1090P	ARHGAP29_ENST00000482481.1_5'Flank	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	1090					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CTTGGCAGTTAGGCTGTTTTG	0.418																																					p.L1090P		.											.	ARHGAP29-296	0			c.T3269C						.						228	214	218					1																	94639942		2203	4300	6503	SO:0001583	missense	9411	exon23			GCAGTTAGGCTGT		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"Rho GTPase activating proteins"	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.3269T>C	1.37:g.94639942A>G	ENSP00000260526:p.Leu1090Pro	Somatic	428	0		WXS	Illumina HiSeq	Phase_I	341	56	NM_004815	0	0	104	182	78	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.660169	0.47572	.	.	ENSG00000137962	ENST00000260526	T	0.24723	1.84	5.73	-1.98	0.07480	.	1.632400	0.04169	N	0.324470	T	0.04497	0.0123	L	0.29908	0.895	0.09310	N	1	P	0.50710	0.938	B	0.33799	0.17	T	0.21827	-1.0234	10	0.48119	T	0.1	3.2259	2.7638	0.05314	0.5497:0.1174:0.2307:0.1023	.	1090	Q52LW3	RHG29_HUMAN	P	1090	ENSP00000260526:L1090P	ENSP00000260526:L1090P	L	-	2	0	ARHGAP29	94412530	0.041000	0.20044	0.000000	0.03702	0.391000	0.30476	0.816000	0.27267	-0.171000	0.10797	0.482000	0.46254	CTA	.		0.418	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94639942	A	G	94639942	3	3	103	1	0	0	0	0	1	0	0	0	878	420	15	3	520	3	ARHGAP29	1	94639942	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	117612	94639942	154610679	12	9072											
GSTM1	2944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110233169	110233169	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttcccaaatctgaaggacTtcatctcccgctttgaggtg	8	12	8	13	1	3	2	1	2	2	0	5	3	4	3	3	2	0	1	3	2	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:110233169T>G	ENST00000309851.5	+	7	604	c.550T>G	c.(550-552)Ttc>Gtc	p.F184V	GSTM1_ENST00000369823.2_Missense_Mutation_p.F203V|GSTM2_ENST00000369831.2_Intron|GSTM1_ENST00000490021.2_Intron|GSTM2_ENST00000460717.3_Intron|GSTM1_ENST00000369819.2_Intron|GSTM1_ENST00000483399.2_Intron|GSTM1_ENST00000349334.3_Intron|AC000032.2_ENST00000562538.1_RNA	NM_000561.3	NP_000552.2	P09488	GSTM1_HUMAN	glutathione S-transferase mu 1	184	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(1)|ovary(1)	3		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0122)|Colorectal(144;0.0129)|Epithelial(280;0.0146)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.047)|LUSC - Lung squamous cell carcinoma(189;0.227)	Azathioprine(DB00993)|Busulfan(DB01008)|Carboplatin(DB00958)|Cisplatin(DB00515)|Glutathione(DB00143)|Oxaliplatin(DB00526)	TCTGAAGGACTTCATCTCCCG	0.488									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.F184V		.											.	GSTM1-44	0			c.T550G						.						209	116	148					1																	110233169		2158	4209	6367	SO:0001583	missense	2944	exon7	Familial Cancer Database	incl.: Familial Head and Neck Cancer; ;AIMAH, Cushing disease, Adrenal, Familial	AAGGACTTCATCT	BC036805	CCDS809.1, CCDS810.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134184	ENSG00000134184	2.5.1.18	"Glutathione S-transferases / Soluble"	4632	protein-coding gene	gene with protein product		138350	"glutathione S-transferase M1"	GST1			Standard	NM_000561		Approved	MU, H-B	uc001dyk.3	P09488	OTTHUMG00000011635	ENST00000309851.5:c.550T>G	1.37:g.110233169T>G	ENSP00000311469:p.Phe184Val	Somatic	317	0		WXS	Illumina HiSeq	Phase_I	240	72	NM_000561	0	0	77	93	16	Q5GHG0|Q6FH88|Q8TC98|Q9UC96	Missense_Mutation	SNP	ENST00000309851.5	37	CCDS809.1	.	.	.	.	.	.	.	.	.	.	T	12.77	2.037761	0.35989	.	.	ENSG00000134184	ENST00000369823;ENST00000309851	T;T	0.02345	4.33;4.33	3.53	3.53	0.40419	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.149445	0.43416	U	0.000564	T	0.14056	0.0340	H	0.96269	3.795	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	T	0.01810	-1.1269	10	0.87932	D	0	.	9.98	0.41809	0.0:0.0:0.0:1.0	.	184	P09488	GSTM1_HUMAN	V	203;184	ENSP00000358838:F203V;ENSP00000311469:F184V	ENSP00000311469:F184V	F	+	1	0	GSTM1	110034692	1.000000	0.71417	0.979000	0.43373	0.246000	0.25737	3.033000	0.49743	1.594000	0.50039	0.459000	0.35465	TTC	.		0.488	GSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032151.2	NM_000561		G	110233169	T	G	110233169	3	3	103	1	0	0	0	0	1	0	0	0	6858	1609	56	5	576	5	GSTM1	1	110233169	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	15593227	110233169	139017452	13	9073											
INSRR	3645	ucsc.edu	37	chr1	156821562	156821562	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctttagggcacagcccctcGcacttgtggcagaatatgct	8	11	10	12	1	1	1	0	0	1	1	2	1	1	1	2	2	2	4	2	2	3	4	rs531765692		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:156821562G>A	ENST00000368195.3	-	4	1356	c.960C>T	c.(958-960)tgC>tgT	p.C320C	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	320					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACAGCCCCTCGCACTTGTGGC	0.612																																					p.C320C													.	INSRR-1403	0			c.C960T						.						91	74	80					1																	156821562		2203	4300	6503	SO:0001819	synonymous_variant	3645	exon4			CCCCTCGCACTTG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.960C>T	1.37:g.156821562G>A		Somatic	48	0		WXS	Illumina HiSeq		54	6	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			.		0.612	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156821562	G	A	156821562	2	1	103	1	0	0	0	0	0	0	0	1	7795	1079	38	1		1	INSRR	1	156821562	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	46588393	156821562	92429059	14	9074											
ATP1A2	477	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	160105252	160105252	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtggccgtgacgggtgacgGggtgaacgactcccctgcat	6	8	16	11	4	0	3	0	3	0	0	1	4	1	3	3	4	2	1	3	4	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:160105252G>A	ENST00000361216.3	+	16	2233	c.2144G>A	c.(2143-2145)gGg>gAg	p.G715E	ATP1A2_ENST00000392233.3_Missense_Mutation_p.G715E	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	715			G -> R (in FHM2; de novo mutation in a sporadic case). {ECO:0000269|PubMed:21352219}.		adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ACGGGTGACGGGGTGAACGAC	0.602																																					p.G715E		.											.	ATP1A2-518	0			c.G2144A						.						170	123	139					1																	160105252		2203	4300	6503	SO:0001583	missense	477	exon16			GTGACGGGGTGAA	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"ATPases / P-type"	800	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-2", "sodium pump subunit alpha-2", "sodium-potassium ATPase catalytic subunit alpha-2"	182340	"migraine, hemiplegic 2", "ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2144G>A	1.37:g.160105252G>A	ENSP00000354490:p.Gly715Glu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	73	12	NM_000702	0	0	1	1	0	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.642964|4.642964	0.87859|0.87859	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866|ENST00000447527	D;D|D	0.99483|0.99499	-5.99;-5.99|-6.02	4.31|4.31	4.31|4.31	0.51392|0.51392	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.99806|0.99806	0.9916|0.9916	H|H	0.99182|0.99182	4.46|4.46	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.96615|0.96615	0.9455|0.9455	10|8	0.87932|0.87932	D|D	0|0	.|.	16.0832|16.0832	0.81020|0.81020	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	615;715|.	F5GXJ7;P50993|.	.;AT1A2_HUMAN|.	E|R	715;715;418|426	ENSP00000354490:G715E;ENSP00000376066:G715E|ENSP00000411705:G426R	ENSP00000354490:G715E|ENSP00000411705:G426R	G|G	+|+	2|1	0|0	ATP1A2|ATP1A2	158371876|158371876	1.000000|1.000000	0.71417|0.71417	0.897000|0.897000	0.35233|0.35233	0.889000|0.889000	0.51656|0.51656	9.593000|9.593000	0.98250|0.98250	2.383000|2.383000	0.81215|0.81215	0.561000|0.561000	0.74099|0.74099	GGG|GGG	.		0.602	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160105252	G	A	160105252	3	1	103	1	0	0	0	0	1	0	0	0	1130	1232	43	2	2206	2	ATP1A2	1	160105252	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	3283690	160105252	89145369	15	9075											
USP21	27005	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161134645	161134645	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgaatcgattttctgccTcccgaggctccatcaaaaaa	12	11	6	12	2	3	1	1	1	2	0	6	3	5	1	3	1	1	1	3	1	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:161134645T>A	ENST00000289865.8	+	11	1626	c.1405T>A	c.(1405-1407)Tcc>Acc	p.S469T	PPOX_ENST00000432542.2_5'Flank|PPOX_ENST00000352210.5_5'Flank|PPOX_ENST00000535223.1_5'Flank|PPOX_ENST00000544598.1_5'Flank|PPOX_ENST00000367999.4_5'Flank|USP21_ENST00000368002.3_Missense_Mutation_p.S469T|USP21_ENST00000493054.1_3'UTR|USP21_ENST00000368001.1_Missense_Mutation_p.S469T	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	469	USP.				histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			ATTTTCTGCCTCCCGAGGCTC	0.527																																					p.S469T													.	USP21-660	0			c.T1405A						.						73	74	74					1																	161134645		2203	4300	6503	SO:0001583	missense	27005	exon11			TCTGCCTCCCGAG	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"Ubiquitin-specific peptidases"	12620	protein-coding gene	gene with protein product		604729	"ubiquitin specific protease 21"	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.1405T>A	1.37:g.161134645T>A	ENSP00000289865:p.Ser469Thr	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	96	21	NM_012475	0	0	13	21	8	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	37	CCDS30920.1	.	.	.	.	.	.	.	.	.	.	T	7.634	0.679545	0.14907	.	.	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.31769	1.48;1.48;1.48	5.23	5.23	0.72850	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.060634	0.64402	D	0.000002	T	0.07728	0.0194	N	0.17345	0.48	0.40024	D	0.975449	B	0.13594	0.008	B	0.14023	0.01	T	0.16424	-1.0403	10	0.23891	T	0.37	.	8.278	0.31883	0.2751:0.0:0.0:0.7249	.	469	Q9UK80	UBP21_HUMAN	T	469	ENSP00000356981:S469T;ENSP00000289865:S469T;ENSP00000356980:S469T	ENSP00000289865:S469T	S	+	1	0	USP21	159401269	0.032000	0.19561	1.000000	0.80357	0.985000	0.73830	1.537000	0.36083	2.197000	0.70478	0.454000	0.30748	TCC	.		0.527	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1			A	161134645	T	A	161134645	3	1	103	1	0	0	0	0	1	0	0	0	17086	1551	54	5	1443	5	USP21	1	161134645	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	1029393	161134645	88115976	16	9076											
NME7	29922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169102046	169102046	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attatccaagatcttgaagaAgtattgaacctgaaacggag	16	10	9	6	1	1	5	0	3	1	2	2	6	2	6	2	1	2	1	2	1	7	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:169102046A>G	ENST00000367811.3	-	12	1364	c.1108T>C	c.(1108-1110)Ttc>Ctc	p.F370L	NME7_ENST00000472647.1_Missense_Mutation_p.F334L	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	370					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					ATCTTGAAGAAGTATTGAACC	0.388																																					p.F370L		.											.	NME7-514	0			c.T1108C						.						122	110	114					1																	169102046		2203	4300	6503	SO:0001583	missense	29922	exon12			TGAAGAAGTATTG	AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"cilia and flagella associated protein 67"	613465	"non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.1108T>C	1.37:g.169102046A>G	ENSP00000356785:p.Phe370Leu	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	66	7	NM_013330	0	0	1	1	0	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Missense_Mutation	SNP	ENST00000367811.3	37	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943147	0.53079	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	T;T	0.55234	0.53;0.53	6.17	6.17	0.99709	.	0.557913	0.21023	N	0.081462	T	0.50837	0.1639	M	0.84683	2.71	0.45995	D	0.998806	B	0.20988	0.05	B	0.31686	0.134	T	0.54132	-0.8339	9	0.34782	T	0.22	-13.3948	16.8222	0.85835	1.0:0.0:0.0:0.0	.	370	Q9Y5B8	NDK7_HUMAN	L	334;370	ENSP00000433341:F334L;ENSP00000356785:F370L	ENSP00000356785:F370L	F	-	1	0	NME7	167368670	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.416000	0.90244	2.371000	0.80710	0.533000	0.62120	TTC	.		0.388	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330		G	169102046	A	G	169102046	3	3	103	1	0	0	0	0	1	0	0	0	10522	72	3	3	26	3	NME7	1	169102046	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	7967401	169102046	80148575	17	9077											
PPFIA4	8497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	203036824	203036824	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggggctgtgtgcctgcagaAccagtcttcagtatggcatc	7	10	14	10	0	2	1	1	0	1	1	3	1	2	1	2	3	3	4	2	3	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:203036824A>G	ENST00000447715.2	+	31	3427	c.2986A>G	c.(2986-2988)Acc>Gcc	p.T996A	PPFIA4_ENST00000272198.6_Splice_Site_p.T512A|PPFIA4_ENST00000599966.1_Splice_Site_p.T503A|PPFIA4_ENST00000295706.4_Splice_Site_p.T503A|PPFIA4_ENST00000367240.2_Splice_Site_p.T997A|PPFIA4_ENST00000414050.2_Splice_Site_p.T725A			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	996	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						TGCCTGCAGAACCAGTCTTCA	0.552																																					p.T512A		.											.	PPFIA4-230	0			c.A1534G						.						78	84	82					1																	203036824		2156	4266	6422	SO:0001630	splice_region_variant	8497	exon13			TGCAGAACCAGTC	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"Sterile alpha motif (SAM) domain containing"	9248	protein-coding gene	gene with protein product	"Liprin-alpha4"	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2985-1A>G	1.37:g.203036824A>G		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	67	8	NM_015053	0	0	0	0	0	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		.	.	.	.	.	.	.	.	.	.	A	10.88	1.474689	0.26511	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	3.89	2.72	0.32119	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.349867	0.20011	U	0.101127	T	0.27933	0.0688	N	0.11892	0.195	0.80722	D	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.0;0.0;0.001	T	0.04930	-1.0917	10	0.44086	T	0.13	-16.0337	9.5608	0.39369	0.9138:0.0:0.0862:0.0	.	725;996;198;503;512	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	A	997;996;503;725;512	ENSP00000356209:T997A;ENSP00000402576:T996A;ENSP00000295706:T503A;ENSP00000400379:T725A;ENSP00000272198:T512A	ENSP00000272198:T512A	T	+	1	0	PPFIA4	201303447	0.971000	0.33674	1.000000	0.80357	0.968000	0.65278	2.234000	0.43035	0.618000	0.30179	0.397000	0.26171	ACC	.		0.552	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	Missense_Mutation	G	203036824	A	G	203036824	5	3	103	1	0	0	0	0	0	0	1	0	12338	57	2	3	1584	3	PPFIA4	1	203036824	Splice_Site	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	33934778	203036824	46213797	18	9078											
PIGR	5284	ucsc.edu	37	chr1	207106513	207106513	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctgacatcgcgggacccTgcagcagggaagagtgggcc	9	4	17	11	2	0	2	0	1	0	1	1	4	0	4	2	4	2	3	2	4	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:207106513T>C	ENST00000356495.4	-	7	1889		c.e7-2		PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor						detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CGCGGGACCCTGCAGCAGGGA	0.537																																					.													.	PIGR-92	0			c.1706-2A>G						.						42	44	43					1																	207106513		2203	4300	6503	SO:0001630	splice_region_variant	5284	exon8			GGACCCTGCAGCA		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1706-2A>G	1.37:g.207106513T>C		Somatic	66	0		WXS	Illumina HiSeq		39	1	NM_002644	0	0	3	3	0	Q68D81|Q8IZY7	Splice_Site	SNP	ENST00000356495.4	37	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	T	11.33	1.605504	0.28623	.	.	ENSG00000162896	ENST00000356495	.	.	.	4.11	4.11	0.48088	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8393	0.40989	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PIGR	205173136	0.714000	0.27936	0.033000	0.17914	0.057000	0.15508	1.743000	0.38258	2.096000	0.63516	0.454000	0.30748	.	.		0.537	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	Intron	C	207106513	T	C	207106513	5	2	103	1	0	0	0	0	0	0	1	0	11923	1594	55	3	610	3	PIGR	1	207106513	Splice_Site	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	4069689	207106513	42144108	19	9079											
ANAPC1	64682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	112608404	112608404	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctttggagtactaacgccAtctagtggagtactgggccg	8	10	14	9	2	1	0	0	0	1	0	1	2	1	2	2	4	3	3	2	4	4	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:112608404A>G	ENST00000341068.3	-	14	2371	c.1599T>C	c.(1597-1599)gaT>gaC	p.D533D		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	533					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						TACTAACGCCATCTAGTGGAG	0.433																																					p.D533D		.											.	ANAPC1-228	0			c.T1599C						.						99	96	97					2																	112608404		2203	4300	6503	SO:0001819	synonymous_variant	64682	exon14			AACGCCATCTAGT	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1599T>C	2.37:g.112608404A>G		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	131	28	NM_022662	0	0	11	16	5	Q2M3H8|Q9BSE6|Q9H8D0	Silent	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	A	0.541	-0.853802	0.02630	.	.	ENSG00000153107	ENST00000427997	.	.	.	4.57	0.462	0.16695	.	.	.	.	.	T	0.50633	0.1627	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33085	-0.9882	4	.	.	.	-11.202	5.0048	0.14282	0.5191:0.0:0.3355:0.1455	.	.	.	.	R	68	.	.	W	-	1	0	ANAPC1	112324875	0.014000	0.17966	0.005000	0.12908	0.123000	0.20343	-0.736000	0.04882	-0.234000	0.09782	-1.528000	0.00924	TGG	.		0.433	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		G	112608404	A	G	112608404	2	3	103	1	0	0	0	0	0	0	0	1	598	214	8	3		3	ANAPC1	2	112608404	Silent	SNP	A	TCGA-DZ-6132-01A-11D-1961-08		112608404	130590969	20	9080											
LRP1B	53353	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141762906	141762906	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttgaaaagaacttacatGtgcaagttgtcccattttca	14	13	6	8	0	1	2	1	1	0	1	2	2	2	2	1	0	4	2	1	0	6	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:141762906G>T	ENST00000389484.3	-	15	3472	c.2501C>A	c.(2500-2502)aCa>aAa	p.T834K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	834	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAACTTACATGTGCAAGTTGT	0.413										TSP Lung(27;0.18)																											p.T834K	Colon(99;50 2074 2507 20106)												.	LRP1B-311	0			c.C2501A						.						63	61	62					2																	141762906		2203	4299	6502	SO:0001583	missense	53353	exon15			TTACATGTGCAAG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2501C>A	2.37:g.141762906G>T	ENSP00000374135:p.Thr834Lys	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	66	14	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	4.180	0.032042	0.08101	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	T	0.29397	1.57	5.79	0.917	0.19380	.	0.435292	0.23614	U	0.046306	T	0.12902	0.0313	N	0.11341	0.13	0.27373	N	0.955635	B	0.02656	0.0	B	0.04013	0.001	T	0.33420	-0.9869	10	0.06099	T	0.92	.	11.3061	0.49336	0.5028:0.0:0.4972:0.0	.	834	Q9NZR2	LRP1B_HUMAN	K	834;772	ENSP00000374135:T834K	ENSP00000374135:T834K	T	-	2	0	LRP1B	141479376	0.992000	0.36948	0.985000	0.45067	0.853000	0.48598	0.917000	0.28665	0.100000	0.17581	-0.140000	0.14226	ACA	.		0.413	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141762906	G	T	141762906	3	4	103	1	0	0	0	0	1	0	0	0	8980	1377	48	4	11606	4	LRP1B	2	141762906	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	29154502	141762906	101436467	21	9081											
FAP	2191	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	163074641	163074641	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagagcatattttgtagcaAgcatttcctctgaaaaataa	16	12	7	6	0	1	2	0	1	1	1	2	3	2	2	1	0	3	4	1	0	6	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:163074641A>T	ENST00000188790.4	-	9	824	c.617T>A	c.(616-618)cTt>cAt	p.L206H	FAP_ENST00000443424.1_Missense_Mutation_p.L181H	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TTTTGTAGCAAGCATTTCCTC	0.294																																					p.L206H													.	FAP-93	0			c.T617A						.						75	77	76					2																	163074641		2203	4299	6502	SO:0001583	missense	2191	exon9			GTAGCAAGCATTT	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.617T>A	2.37:g.163074641A>T	ENSP00000188790:p.Leu206His	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	97	14	NM_004460	0	0	0	0	0		Missense_Mutation	SNP	ENST00000188790.4	37	CCDS33311.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208352	0.79240	.	.	ENSG00000078098	ENST00000188790;ENST00000443424	T;T	0.44881	0.91;0.91	5.74	5.74	0.90152	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.059030	0.64402	D	0.000001	T	0.67353	0.2884	M	0.82323	2.585	0.52501	D	0.999954	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.979;0.986	T	0.72301	-0.4334	10	0.72032	D	0.01	-15.9727	14.9132	0.70773	1.0:0.0:0.0:0.0	.	181;206;206	B4DLR2;B2RD89;Q12884	.;.;SEPR_HUMAN	H	206;181	ENSP00000188790:L206H;ENSP00000411391:L181H	ENSP00000188790:L206H	L	-	2	0	FAP	162782887	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.571000	0.90752	2.317000	0.78254	0.460000	0.39030	CTT	.		0.294	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			T	163074641	A	T	163074641	3	4	103	1	0	0	0	0	1	0	0	0	5692	72	3	5	1737	5	FAP	2	163074641	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	21311735	163074641	80124732	22	9082											
TNS1	7145	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	218678433	218678433	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttattctgctgcatgatggtTggaggtggcgaagacacctt	8	13	13	7	1	1	2	0	1	1	1	1	4	1	3	1	4	2	3	1	4	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:218678433T>A	ENST00000171887.4	-	26	4976	c.4524A>T	c.(4522-4524)ccA>ccT	p.P1508P	TNS1_ENST00000419504.1_Silent_p.P1495P|TNS1_ENST00000430930.1_Silent_p.P1487P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1508	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GCATGATGGTTGGAGGTGGCG	0.582																																					p.P1508P													.	TNS1-156	0			c.A4524T						.						135	133	134					2																	218678433		2203	4300	6503	SO:0001819	synonymous_variant	7145	exon26			GATGGTTGGAGGT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4524A>T	2.37:g.218678433T>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	92	10	NM_022648	0	0	83	112	29	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			.		0.582	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218678433	T	A	218678433	2	1	103	1	0	0	0	0	0	0	0	1	16375	1799	63	5		5	TNS1	2	218678433	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	55603792	218678433	24520940	23	9083											
FAM134A	79137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220047044	220047044	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagacagtgagtggtggccTcactgctctgcccggcaccc	6	7	13	15	2	2	2	1	1	1	1	2	3	2	2	3	3	2	2	3	3	0	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:220047044T>C	ENST00000430297.2	+	9	1461	c.1325T>C	c.(1324-1326)cTc>cCc	p.L442P		NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	442						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	19		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGTGGTGGCCTCACTGCTCTG	0.622																																					p.L442P		.											.	FAM134A-91	0			c.T1325C						.						99	104	102					2																	220047044		2203	4300	6503	SO:0001583	missense	79137	exon9			GTGGCCTCACTGC	AK074983	CCDS2434.1	2q36.1	2008-02-05	2007-05-01	2007-05-01	ENSG00000144567	ENSG00000144567			28450	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 17"	C2orf17			Standard	NM_024293		Approved	MGC3035	uc002vjw.4	Q8NC44	OTTHUMG00000154577	ENST00000430297.2:c.1325T>C	2.37:g.220047044T>C	ENSP00000395249:p.Leu442Pro	Somatic	251	1		WXS	Illumina HiSeq	Phase_I	183	40	NM_024293	0	0	138	199	61	Q6P1P5|Q9H0K7	Missense_Mutation	SNP	ENST00000430297.2	37	CCDS2434.1	.	.	.	.	.	.	.	.	.	.	T	8.099	0.776228	0.16051	.	.	ENSG00000144567	ENST00000430297	T	0.36520	1.25	5.26	4.06	0.47325	.	0.184716	0.38058	N	0.001826	T	0.30978	0.0782	L	0.57536	1.79	0.58432	D	0.999997	B	0.11235	0.004	B	0.06405	0.002	T	0.08617	-1.0713	9	.	.	.	-2.2718	7.7924	0.29127	0.0:0.1733:0.0:0.8267	.	442	Q8NC44	F134A_HUMAN	P	442	ENSP00000395249:L442P	.	L	+	2	0	FAM134A	219755288	1.000000	0.71417	0.720000	0.30636	0.138000	0.21146	4.189000	0.58358	0.960000	0.38005	0.533000	0.62120	CTC	.		0.622	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336147.2	NM_024293		C	220047044	T	C	220047044	3	2	103	1	0	0	0	0	1	0	0	0	5461	1551	54	3	1359	3	FAM134A	2	220047044	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	1368611	220047044	23152329	24	9084											
GMPPA	29926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220370077	220370077	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatctggagtcagatcaagTccgcagggtatggaaggctg	10	9	15	7	1	3	1	2	0	1	1	4	3	4	3	1	4	0	4	1	4	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:220370077T>C	ENST00000358215.3	+	8	1117	c.748T>C	c.(748-750)Tcc>Ccc	p.S250P	GMPPA_ENST00000341142.3_Missense_Mutation_p.S250P|GMPPA_ENST00000313597.5_Missense_Mutation_p.S250P|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Missense_Mutation_p.S250P|GMPPA_ENST00000373917.3_Missense_Mutation_p.S250P	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	250					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		TCAGATCAAGTCCGCAGGGTA	0.607																																					p.S250P		.											.	GMPPA-90	0			c.T748C						.						64	65	65					2																	220370077		2203	4300	6503	SO:0001583	missense	29926	exon8			ATCAAGTCCGCAG	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.748T>C	2.37:g.220370077T>C	ENSP00000350949:p.Ser250Pro	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	120	22	NM_205847	0	0	1	1	0	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	37	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	t	25.4	4.632235	0.87660	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000435316;ENST00000341142	D;D;D;D;T;D	0.94650	-3.48;-3.48;-3.48;-3.48;1.84;-3.48	4.9	4.9	0.64082	.	0.271361	0.37530	N	0.002048	D	0.96592	0.8888	M	0.73962	2.25	0.80722	D	1	D;D	0.71674	0.998;0.97	D;P	0.66847	0.947;0.737	D	0.96980	0.9714	10	0.66056	D	0.02	-23.7265	14.211	0.65764	0.0:0.0:0.0:1.0	.	250;250	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	P	250;250;250;250;215;250	ENSP00000315925:S250P;ENSP00000363027:S250P;ENSP00000350949:S250P;ENSP00000363016:S250P;ENSP00000411060:S215P;ENSP00000340760:S250P	ENSP00000315925:S250P	S	+	1	0	GMPPA	220078321	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.745000	0.85046	1.828000	0.53243	0.529000	0.55759	TCC	.		0.607	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		C	220370077	T	C	220370077	3	2	103	1	0	0	0	0	1	0	0	0	6514	1667	58	3	774	3	GMPPA	2	220370077	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	323033	220370077	22829296	25	9085											
CAMK1	8536	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9801228	9801228	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcactcaccgactggtggaTattcttatctagagctgtat	9	14	8	10	1	4	1	2	0	2	1	4	3	4	2	1	2	1	2	1	2	4	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:9801228T>C	ENST00000256460.3	-	10	1033	c.856A>G	c.(856-858)Atc>Gtc	p.I286V	OGG1_ENST00000449570.2_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302008.8_Intron|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000302036.7_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	286	Autoinhibitory domain.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		GACTGGTGGATATTCTTATCT	0.537																																					p.I286V		.											.	CAMK1-335	0			c.A856G						.						179	171	174					3																	9801228		2203	4300	6503	SO:0001583	missense	8536	exon10			GGTGGATATTCTT	L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.856A>G	3.37:g.9801228T>C	ENSP00000256460:p.Ile286Val	Somatic	250	0		WXS	Illumina HiSeq	Phase_I	204	42	NM_003656	0	0	57	78	21	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	37	CCDS2582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.415377|4.415377	0.83449|0.83449	.|.	.|.	ENSG00000134072|ENSG00000134072	ENST00000256460|ENST00000421120	T|.	0.39056|.	1.1|.	5.95|5.95	5.95|5.95	0.96441|0.96441	Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80407|0.80407	0.4617|0.4617	M|M	0.87038|0.87038	2.855|2.855	0.80722|0.80722	D|D	1|1	P;P|.	0.48162|.	0.906;0.906|.	P;P|.	0.45099|.	0.469;0.469|.	T|T	0.83025|0.83025	-0.0165|-0.0165	10|5	0.59425|.	D|.	0.04|.	-11.1309|-11.1309	16.0971|16.0971	0.81132|0.81132	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	286;286|.	Q14012;B0YIY3|.	KCC1A_HUMAN;.|.	V|C	286|132	ENSP00000256460:I286V|.	ENSP00000256460:I286V|.	I|Y	-|-	1|2	0|0	CAMK1|CAMK1	9776228|9776228	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.589000|7.589000	0.82641|0.82641	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	ATC|TAT	.		0.537	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		C	9801228	T	C	9801228	3	2	103	1	0	0	0	0	1	0	0	0	2602	1406	49	3	268	3	CAMK1	3	9801228	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		9801228	188221202	26	9086											
GPD1L	23171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	32169609	32169609	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattggtaataatgtcaagaAacttcagaaatttgcctcca	16	12	6	7	0	2	2	2	0	0	2	3	2	3	2	2	1	2	1	2	1	6	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:32169609A>C	ENST00000282541.5	+	2	290	c.89A>C	c.(88-90)aAa>aCa	p.K30T		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	30					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						AATGTCAAGAAACTTCAGAAA	0.368																																					p.K30T		.											.	GPD1L-90	0			c.A89C						.						59	59	59					3																	32169609		2203	4300	6503	SO:0001583	missense	23171	exon2			TCAAGAAACTTCA	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.89A>C	3.37:g.32169609A>C	ENSP00000282541:p.Lys30Thr	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	49	9	NM_015141	0	0	3	7	4	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	37	CCDS33729.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.807729	0.31961	.	.	ENSG00000152642	ENST00000282541;ENST00000425459	T;T	0.58652	0.32;1.2	4.8	3.62	0.41486	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.435694	0.28257	N	0.016007	T	0.52917	0.1764	M	0.70595	2.14	0.29089	N	0.882201	B	0.06786	0.001	B	0.20184	0.028	T	0.52697	-0.8541	10	0.46703	T	0.11	-9.553	6.5277	0.22310	0.6226:0.3005:0.0769:0.0	.	30	Q8N335	GPD1L_HUMAN	T	30	ENSP00000282541:K30T;ENSP00000408770:K30T	ENSP00000282541:K30T	K	+	2	0	GPD1L	32144613	0.036000	0.19791	0.834000	0.33040	0.984000	0.73092	2.830000	0.48136	0.938000	0.37419	0.459000	0.35465	AAA	.		0.368	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141		C	32169609	A	C	32169609	3	2	103	1	0	0	0	0	1	0	0	0	6625	14	1	5	95	5	GPD1L	3	32169609	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	22368381	32169609	165852821	27	9087											
PLCD1	5333	broad.mit.edu;bcgsc.ca	37	chr3	38051199	38051201	+	In_Frame_Del	DEL	TCG	TCG	-																															catcctccatctcagcagccTcgtcttcgtctgacaccaca																								rs375010877		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	TCG	TCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:38051199_38051201delTCG	ENST00000334661.4	-	9	1611_1613	c.1389_1391delCGA	c.(1387-1392)gacgag>gag	p.D463del	PLCD1_ENST00000479619.1_5'Flank|PLCD1_ENST00000463876.1_In_Frame_Del_p.D484del	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	463					angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)	p.D484D(1)|p.D463D(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CTCAGCAGCCTCGTCTTCGTCTG	0.65																																					p.484_485del													.	PLCD1-226	2	Substitution - coding silent(2)	endometrium(2)	c.1452_1454del						.																																			SO:0001651	inframe_deletion	5333	exon9			GCAGCCTCGTCTT		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.1389_1391delCGA	3.37:g.38051199_38051201delTCG	ENSP00000335600:p.Asp463del	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	42	9	NM_001130964	0	0	0	0	0	B3KR14|Q86VN8	In_Frame_Del	DEL	ENST00000334661.4	37	CCDS2671.1																																																																																			.		0.65	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			-	38051201	TCG	-	38051199	7	5	103	1	0	1	0	1	0	0	0	0	12057	1551	54	0	907	0	PLCD1	3	38051199	In_Frame_Del	DEL	TCG	TCGA-DZ-6132-01A-11D-1961-08	5881590	38051199	159971231	28	9088											
RPL24	6152	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	101401697	101401698	+	Frame_Shift_Ins	INS	-	-	A																															tcagcaagagatgcaccagtINSaatggccctctggaatttga																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:101401697_101401698insA	ENST00000394077.3	-	4	351_352	c.246_247insT	c.(244-249)attactfs	p.T83fs	RPL24_ENST00000495401.1_Frame_Shift_Ins_p.T83fs|RPL24_ENST00000469605.1_Frame_Shift_Ins_p.T83fs	NM_000986.3	NP_000977.1	P83731	RL24_HUMAN	ribosomal protein L24	83					cellular protein metabolic process (GO:0044267)|exit from mitosis (GO:0010458)|gene expression (GO:0010467)|mitotic cell cycle checkpoint (GO:0007093)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|optic nerve development (GO:0021554)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|ribosomal large subunit assembly (GO:0000027)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(2)|urinary_tract(1)	4						GATGCACCAGTAATGGCCCTCT	0.436																																					p.T83fs		.											.	RPL24-90	0			c.247_248insT						.																																			SO:0001589	frameshift_variant	6152	exon4			.	AB007177	CCDS33809.1	3q12	2011-04-06			ENSG00000114391	ENSG00000114391		"L ribosomal proteins"	10325	protein-coding gene	gene with protein product		604180				9582194	Standard	NM_000986		Approved	L24	uc003dvh.1	P83731	OTTHUMG00000159146	ENST00000394077.3:c.247dupT	3.37:g.101401699_101401699dupA	ENSP00000377640:p.Thr83fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	98	23	NM_000986	0	0	0	0	0	B2R4Y3|P38663|Q6IBS3	Frame_Shift_Ins	INS	ENST00000394077.3	37	CCDS33809.1																																																																																			.		0.436	RPL24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353487.1	NM_000986		A	101401698	-	A	101401697	7	5	103	1	0	1	1	0	0	0	0	0	13604	1638	57	0	238	0	RPL24	3	101401697	Frame_Shift_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	63350498	101401697	96620733	29	9089											
FAM55C	91775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101540473	101540473	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctcacttcagcaccttccCtttggaagtgtacatccggc	7	12	8	14	1	2	0	2	0	1	0	5	1	4	1	3	2	2	2	3	2	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:101540473C>G	ENST00000491511.2	+	8	2311	c.1355C>G	c.(1354-1356)cCt>cGt	p.P452R	NXPE3_ENST00000477909.1_Missense_Mutation_p.P452R|RP11-49I4.3_ENST00000490324.2_RNA|NXPE3_ENST00000422132.1_Missense_Mutation_p.P452R|NXPE3_ENST00000273347.5_Missense_Mutation_p.P452R	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	452						extracellular region (GO:0005576)											AGCACCTTCCCTTTGGAAGTG	0.552																																					p.P452R		.											.	.	0			c.C1355G						.						113	99	104					3																	101540473		2203	4300	6503	SO:0001583	missense	91775	exon8			CCTTCCCTTTGGA	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"family with sequence similarity 55, member C"	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.1355C>G	3.37:g.101540473C>G	ENSP00000417485:p.Pro452Arg	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	64	11	NM_145037	0	0	20	28	8	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	37	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070163	0.93950	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	6.03	6.03	0.97812	.	0.044822	0.85682	D	0.000000	T	0.67325	0.2881	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73017	-0.4115	10	0.87932	D	0	-17.0676	20.5568	0.99304	0.0:1.0:0.0:0.0	.	452	Q969Y0	FA55C_HUMAN	R	452	ENSP00000273347:P452R;ENSP00000417485:P452R;ENSP00000418369:P452R;ENSP00000396421:P452R	ENSP00000273347:P452R	P	+	2	0	FAM55C	103023163	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.747000	0.85070	2.861000	0.98227	0.655000	0.94253	CCT	.		0.552	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		G	101540473	C	G	101540473	3	3	103	1	0	0	0	0	1	0	0	0	5605	681	24	4	1373	4	FAM55C	3	101540473	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	138776	101540473	96481957	30	9090											
MYH15	22989	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	108107907	108107918	+	In_Frame_Del	DEL	TTCCAGTTCACG	TTCCAGTTCACG	-																															atttcaccctccagttcaccTtccagttcacgaacctgcaa																								rs143417195	byFrequency	TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	TTCCAGTTCACG	TTCCAGTTCACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:108107907_108107918delTTCCAGTTCACG	ENST00000273353.3	-	39	5550_5561	c.5494_5505delCGTGAACTGGAA	c.(5494-5505)cgtgaactggaadel	p.RELE1832del		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1832						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R1832S(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCAGTTCACCTTCCAGTTCACGAACCTGCAAC	0.524																																					p.1832_1835del		.											.	MYH15-73	1	Substitution - Missense(1)	lung(1)	c.5494_5505del						.																																			SO:0001651	inframe_deletion	22989	exon39			.	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5494_5505delCGTGAACTGGAA	3.37:g.108107907_108107918delTTCCAGTTCACG	ENSP00000273353:p.Arg1832_Glu1835del	Somatic	242	0		WXS	Illumina HiSeq	Phase_I	136	21	NM_014981	0	0	0	0	0		In_Frame_Del	DEL	ENST00000273353.3	37	CCDS43127.1																																																																																			.		0.524	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		-	108107918	TTCCAGTTCACG	-	108107907	7	5	103	1	0	1	0	1	0	0	0	0	10059	1606	56	0	351	0	MYH15	3	108107907	In_Frame_Del	DEL	TTCCAGTTCACG	TCGA-DZ-6132-01A-11D-1961-08	6567434	108107907	89914523	31	9091											
POLQ	10721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121260288	121260288	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaaacccgcttcaaaataaGtaattctgccacaagagtct	16	9	5	11	1	3	1	1	0	2	1	3	1	3	1	2	0	2	2	2	0	7	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:121260288G>A	ENST00000264233.5	-	3	510	c.382C>T	c.(382-384)Ctt>Ttt	p.L128F		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	128	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		TTCAAAATAAGTAATTCTGCC	0.348								DNA polymerases (catalytic subunits)																													p.L128F	Pancreas(152;907 1925 26081 31236 36904)	.											.	POLQ-664	0			c.C382T						.						145	164	157					3																	121260288		2203	4300	6503	SO:0001583	missense	10721	exon3			AAATAAGTAATTC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.382C>T	3.37:g.121260288G>A	ENSP00000264233:p.Leu128Phe	Somatic	380	0		WXS	Illumina HiSeq	Phase_I	448	78	NM_199420	0	0	0	0	0	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569858	0.86542	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.60672	0.17	5.74	5.74	0.90152	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.275715	0.37261	N	0.002169	T	0.79787	0.4506	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81741	-0.0794	10	0.87932	D	0	.	19.9346	0.97133	0.0:0.0:1.0:0.0	.	128	O75417	DPOLQ_HUMAN	F	128;263	ENSP00000264233:L128F	ENSP00000264233:L128F	L	-	1	0	POLQ	122742978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.652000	0.54439	2.712000	0.92718	0.563000	0.77884	CTT	.		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121260288	G	A	121260288	3	1	103	1	0	0	0	0	1	0	0	0	12234	1029	36	2	7502	2	POLQ	3	121260288	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	13152381	121260288	76762142	32	9092											
SEC22A	26984	broad.mit.edu	37	chr3	122978380	122978380	+	Frame_Shift_Del	DEL	G	G	-																															tgcttttgcagagtgatggtGatgattttaattacatcatt																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:122978380delG	ENST00000309934.4	+	5	1563	c.667delG	c.(667-669)gatfs	p.D224fs	SEC22A_ENST00000481965.2_Frame_Shift_Del_p.V64fs|SEC22A_ENST00000492595.1_Frame_Shift_Del_p.D224fs	NM_012430.4	NP_036562.2	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A (S. cerevisiae)	224					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	10				GBM - Glioblastoma multiforme(114;0.0548)		GAGTGATGGTGATGATTTTAA	0.343																																					p.D223fs													.	SEC22A-91	0			c.667delG						.						102	98	99					3																	122978380		2203	4298	6501	SO:0001589	frameshift_variant	26984	exon6			GATGGTGATGATT	AF100749	CCDS3021.1	3q21.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000121542	ENSG00000121542			20260	protein-coding gene	gene with protein product		612442	"SEC22 vesicle trafficking protein-like 2 (S. cerevisiae)"	SEC22L2		9094723, 9501016	Standard	NM_012430		Approved		uc003ege.3	Q96IW7	OTTHUMG00000159495	ENST00000309934.4:c.667delG	3.37:g.122978380delG	ENSP00000310521:p.Asp224fs	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	50	8	NM_012430	0	0	0	0	0	B2RE26|Q9Y682	Frame_Shift_Del	DEL	ENST00000309934.4	37	CCDS3021.1																																																																																			.		0.343	SEC22A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355770.2	NM_012430		-	122978380	G	-	122978380	7	5	103	1	0	1	0	1	0	0	0	0	14020	1290	45	0	685	0	SEC22A	3	122978380	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	1718092	122978380	75044050	33	9093											
DNAJC13	23317	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132207161	132207161	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctactgctgacctttgaccCtatccttgttgagaaggttg	7	14	10	10	0	0	3	0	3	0	1	1	4	1	3	3	1	2	4	3	1	3	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:132207161C>A	ENST00000260818.6	+	30	3535	c.3287C>A	c.(3286-3288)cCt>cAt	p.P1096H		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1096					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						ACCTTTGACCCTATCCTTGTT	0.348																																					p.P1096H													.	DNAJC13-272	0			c.C3287A						.						89	82	84					3																	132207161		2203	4300	6503	SO:0001583	missense	23317	exon30			TTGACCCTATCCT	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.3287C>A	3.37:g.132207161C>A	ENSP00000260818:p.Pro1096His	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	69	14	NM_015268	0	0	14	23	9	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.910247	0.92107	.	.	ENSG00000138246	ENST00000260818	T	0.53206	0.63	5.75	5.75	0.90469	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76528	0.4000	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80723	-0.1255	10	0.87932	D	0	.	19.9542	0.97213	0.0:1.0:0.0:0.0	.	1096	O75165	DJC13_HUMAN	H	1096	ENSP00000260818:P1096H	ENSP00000260818:P1096H	P	+	2	0	DNAJC13	133689851	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.435000	0.80391	2.728000	0.93425	0.650000	0.86243	CCT	.		0.348	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		A	132207161	C	A	132207161	3	1	103	1	0	0	0	0	1	0	0	0	4643	681	24	4	3401	4	DNAJC13	3	132207161	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	9228781	132207161	65815269	34	9094											
ATR	545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142284995	142284995	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggcctcatggcttccaCtcacatttacaaacataagt	11	13	5	12	0	2	0	2	0	0	0	3	0	3	0	2	2	2	1	2	2	3	5	rs200407265		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:142284995C>T	ENST00000350721.4	-	3	381	c.260G>A	c.(259-261)aGt>aAt	p.S87N	ATR_ENST00000383101.3_Missense_Mutation_p.S87N	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	87					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ATGGCTTCCACTCACATTTAC	0.413								Other conserved DNA damage response genes																													p.S87N		.											.	ATR-1139	0			c.G260A						.						107	101	103					3																	142284995		2203	4300	6503	SO:0001583	missense	545	exon3			CTTCCACTCACAT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.260G>A	3.37:g.142284995C>T	ENSP00000343741:p.Ser87Asn	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	111	23	NM_001184	0	0	4	10	6	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	2.407	-0.336336	0.05278	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.30448	1.53;1.53	5.53	0.0727	0.14388	.	1.113090	0.06757	N	0.781079	T	0.07548	0.0190	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36553	-0.9743	10	0.02654	T	1	-9.1875	2.5644	0.04779	0.1129:0.2236:0.1159:0.5476	.	87	Q13535	ATR_HUMAN	N	87	ENSP00000343741:S87N;ENSP00000372581:S87N	ENSP00000343741:S87N	S	-	2	0	ATR	143767685	0.931000	0.31567	1.000000	0.80357	0.976000	0.68499	0.080000	0.14802	0.369000	0.24510	-0.414000	0.06135	AGT	C|0.999;A|0.000		0.413	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142284995	C	T	142284995	3	4	103	1	0	0	0	0	1	0	0	0	1205	565	20	2	7854	2	ATR	3	142284995	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	10077834	142284995	55737435	35	9095											
SLC7A14	57709	broad.mit.edu;bcgsc.ca	37	chr3	170201153	170201154	+	Frame_Shift_Ins	INS	-	-	A																															aaatgaccctcggcatcgggINSaagagggaccccagcaagct																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:170201153_170201154insA	ENST00000231706.5	-	6	1379_1380	c.1064_1065insT	c.(1063-1065)ttcfs	p.F355fs	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	355					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			TCGGCATCGGGAAGAGGGACCC	0.54											OREG0015917	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F355fs													.	SLC7A14-94	0			c.1065_1066insT						.																																			SO:0001589	frameshift_variant	57709	exon6			CATCGGGAAGAGG	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"Solute carriers"	29326	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 142"	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1065dupT	3.37:g.170201155_170201155dupA	ENSP00000231706:p.Phe355fs	Somatic	152	0	1883	WXS	Illumina HiSeq	Phase_I	105	12	NM_020949	0	0	0	0	0	B3KV33|Q9HCF9	Frame_Shift_Ins	INS	ENST00000231706.5	37	CCDS33892.1																																																																																			.		0.54	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170201154	-	A	170201153	7	5	103	1	0	1	1	0	0	0	0	0	14728	1165	41	0	1262	0	SLC7A14	3	170201153	Frame_Shift_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	27916158	170201153	27821277	36	9096											
WDR1	9948	ucsc.edu	37	chr4	10090323	10090323	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtggcaaatctgttccCatcaggagagaatcgcacac	11	8	11	11	1	2	1	1	0	1	1	4	3	3	2	1	3	0	4	1	3	2	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:10090323C>A	ENST00000499869.2	-	6	794	c.601G>T	c.(601-603)Ggg>Tgg	p.G201W	WDR1_ENST00000382451.2_Missense_Mutation_p.G61W|WDR1_ENST00000502702.1_Missense_Mutation_p.G61W|WDR1_ENST00000382452.2_Missense_Mutation_p.G201W|WDR1_ENST00000515743.1_5'UTR			O75083	WDR1_HUMAN	WD repeat domain 1	201					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		AATCTGTTCCCATCAGGAGAG	0.562																																					p.G201W													.	WDR1-48	0			c.G601T						.						41	45	44					4																	10090323		2016	4178	6194	SO:0001583	missense	9948	exon6			TGTTCCCATCAGG	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.601G>T	4.37:g.10090323C>A	ENSP00000427687:p.Gly201Trp	Somatic	21	0		WXS	Illumina HiSeq		23	2	NM_017491	0	0	207	273	66	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	37	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600557	0.87055	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000382451;ENST00000443592;ENST00000502702;ENST00000439733;ENST00000508079	T;T;T;T;T	0.63913	1.05;1.05;0.33;0.33;-0.07	5.44	5.44	0.79542	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.87505	0.6194	H	0.98199	4.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.92074	0.5667	10	0.87932	D	0	-27.7323	18.2591	0.90028	0.0:1.0:0.0:0.0	.	36;61;201	B4DY05;O75083-3;O75083	.;.;WDR1_HUMAN	W	201;201;61;60;61;36;205	ENSP00000427687:G201W;ENSP00000371890:G201W;ENSP00000371889:G61W;ENSP00000426725:G61W;ENSP00000425481:G205W	ENSP00000371889:G61W	G	-	1	0	WDR1	9699421	1.000000	0.71417	0.964000	0.40570	0.717000	0.41224	7.186000	0.77722	2.554000	0.86153	0.467000	0.42956	GGG	.		0.562	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			A	10090323	C	A	10090323	3	1	103	1	0	0	0	0	1	0	0	0	17305	594	21	4	1259	4	WDR1	4	10090323	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		10090323	181063953	37	9097											
BOD1L	259282	broad.mit.edu	37	chr4	13603393	13603393	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattctcatcatatttccctGggagccatccacctcttcac	8	13	4	16	0	4	0	3	0	2	0	7	1	6	1	4	1	1	0	4	1	1	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:13603393G>T	ENST00000040738.5	-	10	5266	c.5131C>A	c.(5131-5133)Cag>Aag	p.Q1711K		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1711						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Q1711K(1)									ATATTTCCCTGGGAGCCATCC	0.428																																					p.Q1711K													.	.	1	Substitution - Missense(1)	lung(1)	c.C5131A						.						172	177	175					4																	13603393		2203	4300	6503	SO:0001583	missense	259282	exon10			TTCCCTGGGAGCC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5131C>A	4.37:g.13603393G>T	ENSP00000040738:p.Gln1711Lys	Somatic	277	0		WXS	Illumina HiSeq	Phase_I	309	10	NM_148894	0	0	14	14	0	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	11.11	1.541422	0.27563	.	.	ENSG00000038219	ENST00000040738	T	0.09073	3.02	4.59	4.59	0.56863	.	0.124466	0.36555	N	0.002526	T	0.07728	0.0194	L	0.34521	1.04	0.09310	N	1	B	0.19583	0.037	B	0.19391	0.025	T	0.21861	-1.0233	10	0.36615	T	0.2	-3.04	12.0992	0.53774	0.0:0.0:0.8166:0.1834	.	1711	Q8NFC6	BOD1L_HUMAN	K	1711	ENSP00000040738:Q1711K	ENSP00000040738:Q1711K	Q	-	1	0	BOD1L	13212491	1.000000	0.71417	0.144000	0.22314	0.658000	0.38924	4.107000	0.57811	2.247000	0.74100	0.555000	0.69702	CAG	.		0.428	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13603393	G	T	13603393	3	4	103	1	0	0	0	0	1	0	0	0	1484	1357	47	4	4092	4	BOD1L	4	13603393	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	3513070	13603393	177550883	38	9098											
N4BP2	55728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	40122682	40122682	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttttaccaatagtgcacCaactgtttctggagtagtag	11	14	8	8	0	1	0	0	0	1	0	1	1	1	1	2	1	4	4	2	1	7	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:40122682C>G	ENST00000261435.6	+	9	3367	c.2951C>G	c.(2950-2952)cCa>cGa	p.P984R		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	984					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AATAGTGCACCAACTGTTTCT	0.443																																					p.P984R		.											.	N4BP2-602	0			c.C2951G						.						84	80	82					4																	40122682		2203	4300	6503	SO:0001583	missense	55728	exon9			GTGCACCAACTGT	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2951C>G	4.37:g.40122682C>G	ENSP00000261435:p.Pro984Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	58	9	NM_018177	0	0	0	0	0	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	C	3.483	-0.105433	0.06967	.	.	ENSG00000078177	ENST00000261435;ENST00000381804	T	0.21543	2.0	5.1	4.25	0.50352	.	0.600314	0.17354	N	0.177287	T	0.22898	0.0553	L	0.54323	1.7	0.09310	N	1	D;P	0.53151	0.958;0.93	P;B	0.45506	0.483;0.289	T	0.11421	-1.0588	10	0.48119	T	0.1	0.0045	8.0754	0.30714	0.0:0.8201:0.0:0.1799	.	984;984	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	R	984;904	ENSP00000261435:P984R	ENSP00000261435:P984R	P	+	2	0	N4BP2	39799077	0.020000	0.18652	0.005000	0.12908	0.002000	0.02628	2.644000	0.46613	1.513000	0.48852	0.655000	0.94253	CCA	.		0.443	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40122682	C	G	40122682	3	3	103	1	0	0	0	0	1	0	0	0	10135	594	21	4	2977	4	N4BP2	4	40122682	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	26519289	40122682	151031594	39	9099											
SCD5	79966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	83557889	83557889	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaatagaggccaagaagtaGgaattccacagactctctcc	15	7	9	10	0	1	4	0	0	1	4	4	5	3	5	3	2	0	1	3	2	6	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:83557889G>C	ENST00000319540.4	-	4	976	c.657C>G	c.(655-657)tcC>tcG	p.S219S		NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	219					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CCAAGAAGTAGGAATTCCACA	0.537																																					p.S219S		.											.	SCD5-91	0			c.C657G						.						108	95	100					4																	83557889		2203	4300	6503	SO:0001819	synonymous_variant	79966	exon4			GAAGTAGGAATTC	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.657C>G	4.37:g.83557889G>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	45	9	NM_001037582	0	0	7	13	6	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Silent	SNP	ENST00000319540.4	37	CCDS34024.1																																																																																			.		0.537	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		C	83557889	G	C	83557889	2	2	103	1	0	0	0	0	0	0	0	1	13919	987	35	4		4	SCD5	4	83557889	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	43435207	83557889	107596387	40	9100											
DMP1	1758	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	88584223	88584223	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaacagctccagccaggaGggcctccagtctcacagcag	11	4	12	14	0	1	1	1	0	1	1	4	3	3	2	4	2	4	2	4	2	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:88584223G>A	ENST00000339673.6	+	6	1392	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|RP11-742B18.1_ENST00000506814.1_RNA|DMP1_ENST00000282479.7_Silent_p.E415E	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	431					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		CCAGCCAGGAGGGCCTCCAGT	0.552																																					p.E431E													.	DMP1-132	0			c.G1293A						.						54	55	55					4																	88584223		2203	4300	6503	SO:0001819	synonymous_variant	1758	exon6			CCAGGAGGGCCTC	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"dentin matrix acidic phosphoprotein"			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.1293G>A	4.37:g.88584223G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	50	11	NM_004407	0	0	0	0	0	A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																			.		0.552	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1			A	88584223	G	A	88584223	2	1	103	1	0	0	0	0	0	0	0	1	4594	991	35	2		2	DMP1	4	88584223	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	5026334	88584223	102570053	41	9101											
ABCG2	9429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	89034494	89034494	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggattacccagcaagtttttGaatgaacgcttggaaaccca	13	10	9	9	1	0	2	0	2	0	0	0	4	0	4	2	2	4	3	2	2	5	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:89034494G>C	ENST00000237612.3	-	9	1700	c.1155C>G	c.(1153-1155)ttC>ttG	p.F385L	ABCG2_ENST00000515655.1_Missense_Mutation_p.F385L	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	385					cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	GCAAGTTTTTGAATGAACGCT	0.448																																					p.F385L		.											.	ABCG2-90	0			c.C1155G						.						128	129	128					4																	89034494		2203	4300	6503	SO:0001583	missense	9429	exon9			GTTTTTGAATGAA	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.1155C>G	4.37:g.89034494G>C	ENSP00000237612:p.Phe385Leu	Somatic	211	1		WXS	Illumina HiSeq	Phase_I	187	33	NM_004827	0	0	3	3	0	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854425	0.32791	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.71817	-0.6;-0.6	5.67	3.91	0.45181	ABC-2 type transporter (1);	0.044132	0.85682	D	0.000000	T	0.63604	0.2525	L	0.47716	1.5	0.41151	D	0.986026	B;B;B	0.24721	0.02;0.11;0.055	B;B;B	0.34873	0.03;0.191;0.05	T	0.59177	-0.7503	10	0.31617	T	0.26	-34.9217	7.6017	0.28079	0.3144:0.0:0.6856:0.0	.	385;385;385	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	L	385	ENSP00000426917:F385L;ENSP00000237612:F385L	ENSP00000237612:F385L	F	-	3	2	ABCG2	89253518	0.998000	0.40836	1.000000	0.80357	0.730000	0.41778	0.469000	0.22067	1.361000	0.45981	0.557000	0.71058	TTC	.		0.448	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		C	89034494	G	C	89034494	3	2	103	1	0	0	0	0	1	0	0	0	69	1281	45	4	844	4	ABCG2	4	89034494	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	450271	89034494	102119782	42	9102											
ANK2	287	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	114195785	114195785	+	Frame_Shift_Del	DEL	G	G	-																															tcctattggaagcaggagcaGcccactccttagctaccaag																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:114195785delG	ENST00000357077.4	+	15	1716	c.1663delG	c.(1663-1665)gccfs	p.A555fs	ANK2_ENST00000264366.6_Frame_Shift_Del_p.A555fs|ANK2_ENST00000394537.3_Frame_Shift_Del_p.A555fs|ANK2_ENST00000506722.1_Frame_Shift_Del_p.A534fs	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	555					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		AGCAGGAGCAGCCCACTCCTT	0.517																																					p.A555fs		.											.	ANK2-583	0			c.1663delG						.						80	78	79					4																	114195785		2203	4300	6503	SO:0001589	frameshift_variant	287	exon15			.	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.1663delG	4.37:g.114195785delG	ENSP00000349588:p.Ala555fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	69	12	NM_001148	0	0	0	0	0	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	37	CCDS3702.1																																																																																			.		0.517	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		-	114195785	G	-	114195785	7	5	103	1	0	1	0	1	0	0	0	0	621	971	34	0	1746	0	ANK2	4	114195785	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	25161291	114195785	76958491	43	9103											
KIAA0922	23240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	154557454	154557454	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcctcatttatacttcagcCctacctcacaagcacccgaa	11	11	3	16	1	3	0	3	0	0	0	4	1	4	0	4	0	4	1	4	0	5	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:154557454C>T	ENST00000409663.3	+	35	4608	c.4556C>T	c.(4555-4557)cCc>cTc	p.P1519L	KIAA0922_ENST00000409959.3_Splice_Site_p.P1520L|KIAA0922_ENST00000440693.1_Splice_Site_p.P1436L	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1519						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				ATACTTCAGCCCTACCTCACA	0.413																																					p.P1520L		.											.	KIAA0922-92	0			c.C4559T						.						76	85	82					4																	154557454		2203	4300	6503	SO:0001630	splice_region_variant	23240	exon35			TTCAGCCCTACCT	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.4555-1C>T	4.37:g.154557454C>T		Somatic	230	0		WXS	Illumina HiSeq	Phase_I	208	24	NM_001131007	0	0	0	0	0	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	22.5	4.298160	0.81025	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.31510	1.76;1.49;1.75;1.51	5.93	5.07	0.68467	.	0.056199	0.64402	D	0.000001	T	0.50034	0.1592	L	0.52573	1.65	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.995	D;D;P	0.68621	0.959;0.934;0.86	T	0.53129	-0.8482	10	0.87932	D	0	-12.4672	16.3753	0.83383	0.133:0.867:0.0:0.0	.	1436;1520;1519	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	L	1519;1436;1520;1297	ENSP00000386574:P1519L;ENSP00000409663:P1436L;ENSP00000386787:P1520L;ENSP00000240487:P1297L	ENSP00000240487:P1297L	P	+	2	0	KIAA0922	154776904	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.205000	0.77881	1.466000	0.48025	0.655000	0.94253	CCC	.		0.413	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation	T	154557454	C	T	154557454	5	4	103	1	0	0	0	0	0	0	1	0	8222	637	22	2	4697	2	KIAA0922	4	154557454	Splice_Site	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	40361669	154557454	36596822	44	9104											
FNIP2	57600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	159756556	159756556	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttcttgttcctttatcttaGcacacagcacaccagttgat	9	16	5	11	0	2	1	0	1	2	0	3	1	3	1	2	0	2	4	2	0	2	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:159756556G>A	ENST00000264433.6	+	7	730		c.e7-1		FNIP2_ENST00000379346.3_Splice_Site	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		CTTTATCTTAGCACACAGCAC	0.383																																					.		.											.	FNIP2-68	0			c.656-1G>A						.						258	258	258					4																	159756556		1966	4155	6121	SO:0001630	splice_region_variant	57600	exon7			ATCTTAGCACACA	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.656-1G>A	4.37:g.159756556G>A		Somatic	305	0		WXS	Illumina HiSeq	Phase_I	298	56	NM_020840	0	0	0	0	0	Q05DC3|Q96I31|Q9H994	Splice_Site	SNP	ENST00000264433.6	37	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225241	0.79576	.	.	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346;ENST00000504715	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2857	0.98533	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FNIP2	159976006	1.000000	0.71417	0.995000	0.50966	0.794000	0.44872	9.224000	0.95209	2.803000	0.96430	0.650000	0.86243	.	.		0.383	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	Intron	A	159756556	G	A	159756556	5	1	103	1	0	0	0	0	0	0	1	0	5995	985	34	2	681	2	FNIP2	4	159756556	Splice_Site	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	5199102	159756556	31397720	45	9105											
LIFR	3977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	38489203	38489203	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attctaaaaccctcatcttaGatgtgtctctttctcctttt	8	19	3	11	0	5	1	1	0	4	1	7	1	5	1	2	0	1	0	2	0	3	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:38489203G>A	ENST00000263409.4	-	16	2474	c.2312C>T	c.(2311-2313)tCt>tTt	p.S771F	LIFR_ENST00000503088.1_5'Flank|LIFR_ENST00000453190.2_Missense_Mutation_p.S771F	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	771	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					CCTCATCTTAGATGTGTCTCT	0.343			T	PLAG1	salivary adenoma																																p.S771F	Melanoma(13;4 730 6426 9861 34751)	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR-1173	0			c.C2312T						.						80	84	83					5																	38489203		2203	4300	6503	SO:0001583	missense	3977	exon16			ATCTTAGATGTGT	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"CD molecules", "Fibronectin type III domain containing"	6597	protein-coding gene	gene with protein product		151443	"leukemia inhibitory factor receptor"			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2312C>T	5.37:g.38489203G>A	ENSP00000263409:p.Ser771Phe	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	109	26	NM_002310	0	0	1	4	3	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037720	0.35989	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.53423	0.62;0.62	5.78	4.92	0.64577	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.715180	0.14869	N	0.293661	T	0.46367	0.1389	M	0.76838	2.35	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.46624	-0.9178	10	0.09084	T	0.74	-6.9518	11.4001	0.49864	0.1549:0.0:0.8451:0.0	.	771	P42702	LIFR_HUMAN	F	771	ENSP00000263409:S771F;ENSP00000398368:S771F	ENSP00000263409:S771F	S	-	2	0	LIFR	38524960	0.985000	0.35326	0.823000	0.32752	0.952000	0.60782	2.593000	0.46180	1.456000	0.47831	0.650000	0.86243	TCT	.		0.343	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38489203	G	A	38489203	3	1	103	1	0	0	0	0	1	0	0	0	8802	942	33	2	1001	2	LIFR	5	38489203	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		38489203	142426057	46	9106											
BDP1	55814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	70837317	70837317	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcatgttcattcaaaggAtaaaagccatattccttcta	13	14	4	10	0	4	0	3	0	1	0	6	1	6	1	3	1	1	1	3	1	5	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:70837317A>T	ENST00000358731.4	+	29	6322	c.6059A>T	c.(6058-6060)gAt>gTt	p.D2020V	BDP1_ENST00000380675.2_Missense_Mutation_p.D156V	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2020					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CATTCAAAGGATAAAAGCCAT	0.303																																					p.D2020V		.											.	BDP1-92	0			c.A6059T						.						112	103	106					5																	70837317		1822	4082	5904	SO:0001583	missense	55814	exon29			CAAAGGATAAAAG	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.6059A>T	5.37:g.70837317A>T	ENSP00000351575:p.Asp2020Val	Somatic	179	1		WXS	Illumina HiSeq	Phase_I	184	33	NM_018429	0	0	4	7	3	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664806	0.47572	.	.	ENSG00000145734	ENST00000358731;ENST00000451951;ENST00000380675;ENST00000545546	T;T	0.18960	2.18;2.18	5.3	1.47	0.22746	.	0.842883	0.10728	N	0.640927	T	0.38585	0.1046	M	0.62723	1.935	0.18873	N	0.999982	D;D	0.71674	0.964;0.998	P;D	0.69142	0.7;0.962	T	0.12889	-1.0530	10	0.87932	D	0	.	7.508	0.27555	0.7287:0.0:0.2713:0.0	.	2020;2020	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	V	2020;1568;156;156	ENSP00000351575:D2020V;ENSP00000370050:D156V	ENSP00000351575:D2020V	D	+	2	0	BDP1	70873073	0.736000	0.28164	0.333000	0.25482	0.856000	0.48823	2.703000	0.47110	0.394000	0.25230	0.377000	0.23210	GAT	.		0.303	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70837317	A	T	70837317	3	4	103	1	0	0	0	0	1	0	0	0	1396	333	12	5	6173	5	BDP1	5	70837317	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	32348114	70837317	110077943	47	9107											
PCDHB6	56130	ucsc.edu	37	chr5	140531445	140531445	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gggcgccacagaccgcggctCcccggcgttgagcagcgagg	6	3	17	15	6	0	2	0	1	0	1	1	3	1	2	4	4	2	3	4	4	0	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:140531445C>T	ENST00000231136.1	+	1	1607	c.1607C>T	c.(1606-1608)tCc>tTc	p.S536F	PCDHB6_ENST00000543635.1_Missense_Mutation_p.S400F	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	536	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACCGCGGCTCCCCGGCGTTG	0.672																																					p.S536F													.	PCDHB6-91	0			c.C1607T						.						54	61	59					5																	140531445		2203	4300	6503	SO:0001583	missense	56130	exon1			GCGGCTCCCCGGC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"Cadherins / Protocadherins : Clustered"	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1607C>T	5.37:g.140531445C>T	ENSP00000231136:p.Ser536Phe	Somatic	167	6		WXS	Illumina HiSeq		113	3	NM_018939	0	0	14	23	9	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.419887	0.25552	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01838	4.61;4.61	4.07	3.18	0.36537	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.04679	0.0127	L	0.59912	1.85	0.09310	N	1	B	0.30664	0.289	B	0.40477	0.33	T	0.25641	-1.0126	9	0.59425	D	0.04	.	7.5727	0.27918	0.1652:0.7455:0.0:0.0893	.	536	Q9Y5E3	PCDB6_HUMAN	F	400;536;321	ENSP00000438466:S400F;ENSP00000231136:S536F	ENSP00000231136:S536F	S	+	2	0	PCDHB6	140511629	0.000000	0.05858	0.082000	0.20525	0.800000	0.45204	0.373000	0.20484	1.986000	0.57962	0.556000	0.70494	TCC	.		0.672	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		T	140531445	C	T	140531445	3	4	103	1	0	0	0	0	1	0	0	0	11572	855	30	2	1609	2	PCDHB6	5	140531445	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	69694128	140531445	40383815	48	9108											
PCDHGC4	56098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140864817	140864817	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcttttaccacctgggttAcgtttgtgggcagatccgct	5	14	10	12	2	1	1	0	0	1	1	2	1	2	1	4	2	2	4	4	2	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:140864817A>G	ENST00000306593.1	+	1	77	c.77A>G	c.(76-78)tAc>tGc	p.Y26C	PCDHGA12_ENST00000252085.3_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	26					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACCTGGGTTACGTTTGTGGG	0.542																																					p.Y26C		.											.	PCDHGC4-72	0			c.A77G						.						61	64	63					5																	140864817		2203	4300	6503	SO:0001583	missense	56098	exon1			TGGGTTACGTTTG	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.77A>G	5.37:g.140864817A>G	ENSP00000306918:p.Tyr26Cys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	86	15	NM_018928	0	0	0	0	0	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	A	8.646	0.897050	0.17686	.	.	ENSG00000242419	ENST00000306593	T	0.46819	0.86	4.81	4.81	0.61882	.	.	.	.	.	T	0.26557	0.0649	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.001	B;B	0.16722	0.016;0.004	T	0.07888	-1.0749	9	0.38643	T	0.18	.	6.6967	0.23203	0.6868:0.231:0.0822:0.0	.	26;26	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	C	26	ENSP00000306918:Y26C	ENSP00000306918:Y26C	Y	+	2	0	PCDHGC4	140845001	0.831000	0.29352	0.975000	0.42487	0.979000	0.70002	2.204000	0.42761	2.012000	0.59069	0.459000	0.35465	TAC	.		0.542	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		G	140864817	A	G	140864817	3	3	103	1	0	0	0	0	1	0	0	0	11596	391	14	3	79	3	PCDHGC4	5	140864817	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	333372	140864817	40050443	49	9109											
SYNPO	11346	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	150027927	150027927	+	Frame_Shift_Del	DEL	A	A	-																															gtaccactggtggtttatctAaaggagaatgcagcactgct																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:150027927delA	ENST00000394243.1	+	3	1196	c.822delA	c.(820-822)ctafs	p.L274fs	SYNPO_ENST00000522122.1_Frame_Shift_Del_p.L274fs|SYNPO_ENST00000518872.1_Intron|SYNPO_ENST00000519664.1_Frame_Shift_Del_p.L30fs|SYNPO_ENST00000307662.4_Frame_Shift_Del_p.L30fs	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	274					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTTTATCTAAAGGAGAATG	0.602																																					p.L274fs		.											.	SYNPO-153	0			c.822delA						.						82	91	88					5																	150027927		2203	4300	6503	SO:0001589	frameshift_variant	11346	exon3			.	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.822delA	5.37:g.150027927delA	ENSP00000377789:p.Leu274fs	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	92	24	NM_001166209	0	0	0	0	0	A5PKZ8|D3DQG8|O15271|Q9UPX1	Frame_Shift_Del	DEL	ENST00000394243.1	37	CCDS54937.1																																																																																			.		0.602	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		-	150027927	A	-	150027927	7	5	103	1	0	1	0	1	0	0	0	0	15488	349	13	0	828	0	SYNPO	5	150027927	Frame_Shift_Del	DEL	A	TCGA-DZ-6132-01A-11D-1961-08	9163110	150027927	30887333	50	9110											
OR2J3	442186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	29079815	29079815	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaaacctgttcatcatcAtcctgtcatacctggactcc	10	12	6	13	0	4	0	4	0	0	0	6	2	6	2	4	2	2	1	4	2	3	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:29079815A>G	ENST00000377169.1	+	1	148	c.148A>G	c.(148-150)Atc>Gtc	p.I50V		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						GTTCATCATCATCCTGTCATA	0.423																																					p.I50V		.											.	OR2J3-90	0			c.A148G						.						291	305	300					6																	29079815		1349	2628	3977	SO:0001583	missense	442186	exon1			ATCATCATCCTGT		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"GPCR / Class A : Olfactory receptors"	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.148A>G	6.37:g.29079815A>G	ENSP00000366374:p.Ile50Val	Somatic	337	0		WXS	Illumina HiSeq	Phase_I	269	53	NM_001005216	0	0	0	0	0	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	A	2.071	-0.413113	0.04799	.	.	ENSG00000204701	ENST00000377169	T	0.03889	3.77	2.78	1.58	0.23477	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	N	0.05414	-0.055	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48080	-0.9066	9	0.48119	T	0.1	.	4.2981	0.10911	0.682:0.2023:0.1157:0.0	.	50	O76001	OR2J3_HUMAN	V	50	ENSP00000366374:I50V	ENSP00000366374:I50V	I	+	1	0	OR2J3	29187794	0.000000	0.05858	0.992000	0.48379	0.314000	0.28054	-0.814000	0.04486	0.295000	0.22570	0.358000	0.22013	ATC	.		0.423	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			G	29079815	A	G	29079815	3	3	103	1	0	0	0	0	1	0	0	0	11030	217	8	3	150	3	OR2J3	6	29079815	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08		29079815	142035252	51	9111											
ZBTB22	9278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33284668	33284668	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggggaagtgctgccccaCtgggagacagaggagatggc	10	4	18	9	0	0	3	0	0	0	3	0	6	0	4	2	5	2	2	2	5	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:33284668C>T	ENST00000431845.2	-	2	177	c.26G>A	c.(25-27)aGt>aAt	p.S9N	TAPBP_ENST00000489157.1_5'Flank|DAXX_ENST00000477162.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.S9N|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000456592.2_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	9					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)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						TGCTGCCCCACTGGGAGACAG	0.657																																					p.S9N		.											.	ZBTB22-69	0			c.G26A						.						18	22	21					6																	33284668		2202	4295	6497	SO:0001583	missense	9278	exon2			GCCCCACTGGGAG	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13085	protein-coding gene	gene with protein product		611439	"zinc finger protein 297"	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110	ENST00000431845.2:c.26G>A	6.37:g.33284668C>T	ENSP00000407545:p.Ser9Asn	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	47	10	NM_001145338	0	0	9	15	6	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.996665	0.35226	.	.	ENSG00000236104	ENST00000418724;ENST00000431845;ENST00000441117	T;T;T	0.64803	3.38;3.38;-0.12	4.68	2.67	0.31697	.	.	.	.	.	T	0.17831	0.0428	N	0.08118	0	0.26387	N	0.976649	B	0.16166	0.016	B	0.14578	0.011	T	0.11567	-1.0582	9	0.38643	T	0.18	.	4.8891	0.13717	0.0:0.6566:0.2229:0.1205	.	9	O15209	ZBT22_HUMAN	N	9	ENSP00000404403:S9N;ENSP00000407545:S9N;ENSP00000413172:S9N	ENSP00000404403:S9N	S	-	2	0	ZBTB22	33392646	0.013000	0.17824	1.000000	0.80357	0.995000	0.86356	1.367000	0.34204	1.172000	0.42781	0.638000	0.83543	AGT	.		0.657	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			T	33284668	C	T	33284668	3	4	103	1	0	0	0	0	1	0	0	0	17562	565	20	2	1882	2	ZBTB22	6	33284668	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	4204853	33284668	137830399	52	9112											
UBR2	23304	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42559909	42559909	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agactgtgcagttgatccaaCttgtgttttgtgcatggagt	8	15	12	6	0	0	2	0	1	0	1	1	3	1	3	1	1	3	4	1	1	1	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:42559909C>G	ENST00000372899.1	+	3	617	c.359C>G	c.(358-360)aCt>aGt	p.T120S	UBR2_ENST00000372903.2_Missense_Mutation_p.T120S|UBR2_ENST00000372901.1_Missense_Mutation_p.T120S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	120					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GTTGATCCAACTTGTGTTTTG	0.323																																					p.T120S		.											.	UBR2-94	0			c.C359G						.						112	101	105					6																	42559909		2203	4300	6503	SO:0001583	missense	23304	exon3			ATCCAACTTGTGT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"Ubiquitin protein ligase E3 component n-recognins"	21289	protein-coding gene	gene with protein product		609134	"chromosome 6 open reading frame 133"	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.359C>G	6.37:g.42559909C>G	ENSP00000361990:p.Thr120Ser	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	78	11	NM_001184801	0	0	12	18	6	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.730359	0.89390	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	D;D;D	0.82255	-1.59;-1.59;-1.59	5.24	5.24	0.73138	Zinc finger, N-recognin, metazoa (1);Zinc finger, N-recognin (2);	0.000000	0.85682	D	0.000000	D	0.88887	0.6559	M	0.73319	2.225	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.81914	0.995;0.894	D	0.87768	0.2603	10	0.41790	T	0.15	-11.9828	18.4238	0.90602	0.0:1.0:0.0:0.0	.	120;120	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	S	120	ENSP00000361994:T120S;ENSP00000361990:T120S;ENSP00000361992:T120S	ENSP00000361990:T120S	T	+	2	0	UBR2	42667887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.756000	0.74919	2.459000	0.83118	0.655000	0.94253	ACT	.		0.323	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42559909	C	G	42559909	3	3	103	1	0	0	0	0	1	0	0	0	16935	565	20	4	369	4	UBR2	6	42559909	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	9275241	42559909	128555158	53	9113											
SLC35B2	347734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	44222677	44222677	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aactgcccaatggtgtaaaaGatgaagagctggccacatgc	14	7	11	9	0	0	3	0	1	0	2	0	3	0	3	2	2	4	2	2	2	5	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:44222677G>C	ENST00000393812.3	-	4	1208	c.1065C>G	c.(1063-1065)atC>atG	p.I355M	SLC35B2_ENST00000495706.1_5'UTR|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000538577.1_Missense_Mutation_p.I262M|SLC35B2_ENST00000393810.1_3'UTR|SLC35B2_ENST00000537814.1_Missense_Mutation_p.I222M	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	355					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGGTGTAAAAGATGAAGAGCT	0.577																																					p.I355M		.											.	SLC35B2-91	0			c.C1065G						.						59	52	54					6																	44222677		2203	4300	6503	SO:0001583	missense	347734	exon4			GTAAAAGATGAAG	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"Solute carriers"	16872	protein-coding gene	gene with protein product		610788	"solute carrier family 35, member B2"				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.1065C>G	6.37:g.44222677G>C	ENSP00000377401:p.Ile355Met	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	29	6	NM_178148	0	0	48	78	30	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Missense_Mutation	SNP	ENST00000393812.3	37	CCDS34462.1	.	.	.	.	.	.	.	.	.	.	g	16.92	3.256373	0.59321	.	.	ENSG00000157593	ENST00000393812;ENST00000537814;ENST00000538577;ENST00000341553	T;T;T	0.40476	1.03;1.03;1.03	5.0	2.85	0.33270	.	0.000000	0.85682	D	0.000000	T	0.67031	0.2850	H	0.96460	3.825	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.77838	-0.2439	10	0.87932	D	0	-30.6983	12.2066	0.54355	0.1659:0.0:0.8341:0.0	.	262;355	F5H7Y9;Q8TB61	.;S35B2_HUMAN	M	355;222;262;315	ENSP00000377401:I355M;ENSP00000440340:I222M;ENSP00000443845:I262M	ENSP00000342455:I315M	I	-	3	3	SLC35B2	44330655	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.845000	0.48254	1.121000	0.41925	0.540000	0.68198	ATC	.		0.577	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			C	44222677	G	C	44222677	3	2	103	1	0	0	0	0	1	0	0	0	14608	932	33	4	237	4	SLC35B2	6	44222677	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1662768	44222677	126892390	54	9114											
UBE2CBP	90025	ucsc.edu;bcgsc.ca	37	chr6	83728805	83728805	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggaattttttgatatatttGgaatttctcaaagattcaat	13	18	7	3	0	2	2	2	1	1	1	3	4	2	4	0	2	0	0	0	2	6	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:83728805G>T	ENST00000369747.3	-	8	1019	c.897C>A	c.(895-897)tcC>tcA	p.S299S		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	299					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TGATATATTTGGAATTTCTCA	0.373																																					p.S299S													.	.	0			c.C897A						.						64	68	67					6																	83728805		2203	4300	6503	SO:0001819	synonymous_variant	90025	exon8			ATATTTGGAATTT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.897C>A	6.37:g.83728805G>T		Somatic	53	0		WXS	Illumina HiSeq		69	10	NM_198920	0	0	1	1	0	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Silent	SNP	ENST00000369747.3	37	CCDS34491.1																																																																																			.		0.373	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		T	83728805	G	T	83728805	2	4	103	1	0	0	0	0	0	0	0	1	16880	1335	47	4		4	UBE2CBP	6	83728805	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	39506128	83728805	87386262	55	9115											
TTYH3	80727	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	2691878	2691878	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccaaccccttccagcaggTgagagcctgggaggccggga	8	4	15	14	2	0	1	0	1	0	1	1	4	1	3	6	4	3	1	6	4	1	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:2691878T>C	ENST00000258796.7	+	8	1132		c.e8+2		TTYH3_ENST00000403167.1_Splice_Site|TTYH3_ENST00000407643.1_Splice_Site	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		TTCCAGCAGGTGAGAGCCTGG	0.657																																					.													.	TTYH3-90	0			c.927+2T>C						.						32	28	29					7																	2691878		2203	4300	6503	SO:0001630	splice_region_variant	80727	exon8			AGCAGGTGAGAGC		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.927+2T>C	7.37:g.2691878T>C		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	40	6	NM_025250	0	0	1	1	0	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Splice_Site	SNP	ENST00000258796.7	37	CCDS34588.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.450033	0.26074	.	.	ENSG00000136295	ENST00000258796;ENST00000407643;ENST00000403167	.	.	.	4.1	4.1	0.47936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4007	0.60881	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTYH3	2658404	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.226000	0.78060	1.635000	0.50512	0.455000	0.32223	.	.		0.657	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523	Intron	C	2691878	T	C	2691878	5	2	103	1	0	0	0	0	0	0	1	0	16774	1710	59	3	959	3	TTYH3	7	2691878	Splice_Site	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		2691878	156446785	56	9116											
GPNMB	10457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	23313792	23313792	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccgtgttcttcccgggaaaCcaggaaaaggatccgctact	10	8	11	12	3	1	0	0	0	1	0	3	3	3	3	4	3	2	2	4	3	4	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:23313792C>G	ENST00000381990.2	+	11	1829	c.1668C>G	c.(1666-1668)aaC>aaG	p.N556K	GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000258733.4_Missense_Mutation_p.N544K|GPNMB_ENST00000453162.2_Missense_Mutation_p.N498K|GPNMB_ENST00000539136.1_Missense_Mutation_p.N445K	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	556					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			TCCCGGGAAACCAGGAAAAGG	0.428																																					p.N556K		.											.	GPNMB-580	0			c.C1668G						.						86	89	88					7																	23313792		2203	4300	6503	SO:0001583	missense	10457	exon11			GGGAAACCAGGAA	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1668C>G	7.37:g.23313792C>G	ENSP00000371420:p.Asn556Lys	Somatic	104	1		WXS	Illumina HiSeq	Phase_I	109	17	NM_001005340	0	3	2994	3046	49	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936771	0.52972	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.14640	2.49;2.5;2.49;2.51	5.93	5.93	0.95920	.	0.509964	0.20778	N	0.085853	T	0.15132	0.0365	L	0.53249	1.67	0.42155	D	0.991579	P;B;P;P	0.41848	0.617;0.001;0.544;0.763	B;B;B;B	0.33960	0.173;0.004;0.122;0.173	T	0.10359	-1.0633	10	0.19147	T	0.46	-3.5709	19.9388	0.97151	0.0:1.0:0.0:0.0	.	445;498;556;544	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	K	544;591;556;439;445;498	ENSP00000258733:N544K;ENSP00000371420:N556K;ENSP00000445266:N445K;ENSP00000405586:N498K	ENSP00000258733:N544K	N	+	3	2	GPNMB	23280317	0.716000	0.27956	0.982000	0.44146	0.521000	0.34408	2.571000	0.45990	2.815000	0.96918	0.561000	0.74099	AAC	.		0.428	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		G	23313792	C	G	23313792	3	3	103	1	0	0	0	0	1	0	0	0	6640	506	18	4	1710	4	GPNMB	7	23313792	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	20621914	23313792	135824871	57	9117											
TPST1	8460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	65705725	65705725	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagaggaaaccagggtcattCcccgaatcctggccctgaag	11	6	12	12	1	1	2	1	1	0	1	3	5	3	3	5	3	1	0	5	3	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:65705725C>A	ENST00000304842.5	+	2	738	c.313C>A	c.(313-315)Ccc>Acc	p.P105T	TPST1_ENST00000480281.1_Intron	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	105					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						CAGGGTCATTCCCCGAATCCT	0.527																																					p.P105T		.											.	TPST1-90	0			c.C313A						.						96	93	94					7																	65705725		2203	4300	6503	SO:0001583	missense	8460	exon2			GTCATTCCCCGAA	AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"Sulfotransferases, membrane-bound"	12020	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog A (Drosophila)"	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.313C>A	7.37:g.65705725C>A	ENSP00000302413:p.Pro105Thr	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	96	39	NM_003596	0	0	11	31	20	A4D2M0|Q6FGM7	Missense_Mutation	SNP	ENST00000304842.5	37	CCDS5533.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574392	0.86542	.	.	ENSG00000169902	ENST00000304842;ENST00000544114;ENST00000451388	T;T	0.41065	1.01;1.01	5.78	5.78	0.91487	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.89658	3.05	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.80764	0.986;0.994	T	0.76498	-0.2937	10	0.56958	D	0.05	-14.1045	19.0054	0.92848	0.0:1.0:0.0:0.0	.	105;105	F5H7U7;O60507	.;TPST1_HUMAN	T	105	ENSP00000302413:P105T;ENSP00000391338:P105T	ENSP00000302413:P105T	P	+	1	0	TPST1	65343160	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.950000	0.75977	2.723000	0.93209	0.585000	0.79938	CCC	.		0.527	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2	NM_003596		A	65705725	C	A	65705725	3	1	103	1	0	0	0	0	1	0	0	0	16460	855	30	4	315	4	TPST1	7	65705725	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	42391933	65705725	93432938	58	9118											
ELN	2006	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	73474279	73474279	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggtgtcggtgtggctcCtggagttggcttggctcctg	1	14	16	10	1	0	0	0	0	0	0	4	1	3	1	3	6	0	4	3	6	0	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:73474279C>T	ENST00000252034.7	+	23	1877	c.1478C>T	c.(1477-1479)cCt>cTt	p.P493L	ELN_ENST00000445912.1_Missense_Mutation_p.P493L|ELN_ENST00000458204.1_Missense_Mutation_p.P483L|ELN_ENST00000357036.5_Missense_Mutation_p.P498L|ELN_ENST00000380553.4_Missense_Mutation_p.P357L|ELN_ENST00000380576.5_Missense_Mutation_p.P474L|ELN_ENST00000380584.4_Missense_Mutation_p.P460L|ELN_ENST00000380575.4_Missense_Mutation_p.P464L|ELN_ENST00000380562.4_Missense_Mutation_p.P499L|ELN_ENST00000429192.1_Missense_Mutation_p.P479L|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000320399.6_Missense_Mutation_p.P493L|ELN_ENST00000414324.1_Missense_Mutation_p.P469L|ELN_ENST00000320492.7_Missense_Mutation_p.P412L|ELN_ENST00000358929.4_Missense_Mutation_p.P528L	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GGTGTGGCTCCTGGAGTTGGC	0.612			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.P498L		.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN-95	0			c.C1493T						.						205	192	196					7																	73474279		2203	4300	6503	SO:0001583	missense	2006	exon23			TGGCTCCTGGAGT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1478C>T	7.37:g.73474279C>T	ENSP00000252034:p.Pro493Leu	Somatic	408	1		WXS	Illumina HiSeq	Phase_I	376	128	NM_001081754	0	0	12	16	4	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	.	.	.	.	.	.	.	.	.	.	C	14.98	2.695839	0.48202	.	.	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000320492;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44482	1.42;1.35;1.26;1.39;0.95;1.27;0.92;1.18;1.41;1.4;0.95;1.07;1.0;1.38	2.86	2.86	0.33363	.	.	.	.	.	T	0.41119	0.1145	.	.	.	0.80722	D	1	P;P;P;P;P;P;P;P;P;P;P;P;P	0.51351	0.573;0.573;0.573;0.573;0.573;0.573;0.573;0.573;0.573;0.944;0.573;0.573;0.573	B;B;B;B;B;B;B;B;B;P;B;B;B	0.44811	0.199;0.199;0.199;0.199;0.199;0.199;0.199;0.199;0.199;0.461;0.199;0.199;0.199	T	0.47302	-0.9128	8	0.62326	D	0.03	.	11.5518	0.50725	0.0:1.0:0.0:0.0	.	493;412;469;483;499;464;479;498;474;357;404;460;493	E7ENM0;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;B3KRT8;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.;.	L	493;493;528;412;469;499;464;460;483;498;479;357;474;493	ENSP00000389857:P493L;ENSP00000252034:P493L;ENSP00000351807:P528L;ENSP00000315607:P412L;ENSP00000392575:P469L;ENSP00000369936:P499L;ENSP00000369949:P464L;ENSP00000369958:P460L;ENSP00000403162:P483L;ENSP00000349540:P498L;ENSP00000391129:P479L;ENSP00000369926:P357L;ENSP00000369950:P474L;ENSP00000313565:P493L	ENSP00000252034:P493L	P	+	2	0	ELN	73112215	0.159000	0.22864	0.014000	0.15608	0.005000	0.04900	3.649000	0.54417	1.625000	0.50366	0.555000	0.69702	CCT	.		0.612	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		T	73474279	C	T	73474279	3	4	103	1	0	0	0	0	1	0	0	0	5084	681	24	2	1583	2	ELN	7	73474279	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	7768554	73474279	85664384	59	9119											
MCM7	4176	ucsc.edu;bcgsc.ca	37	chr7	99690937	99690937	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtctgccccttgtctcCtagaagagagtcctttgaca	8	12	9	12	0	2	3	0	1	2	2	4	4	3	3	4	0	2	1	4	0	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:99690937C>A	ENST00000303887.5	-	14	2581	c.1936G>T	c.(1936-1938)Gga>Tga	p.G646*	MIR93_ENST00000385024.1_RNA|MCM7_ENST00000343023.6_Intron|MCM7_ENST00000354230.3_Nonsense_Mutation_p.G470*|MIR106B_ENST00000385301.1_RNA|MIR25_ENST00000384816.1_RNA	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	646	Interaction with ATRIP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCCTTGTCTCCTAGAAGAGAG	0.483																																					p.G646X													.	MCM7-651	0			c.G1936T						.																																			SO:0001587	stop_gained	4176	exon14			TGTCTCCTAGAAG		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 104"	600592	"minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1936G>T	7.37:g.99690937C>A	ENSP00000307288:p.Gly646*	Somatic	265	3		WXS	Illumina HiSeq		301	31	NM_005916	0	0	75	96	21	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Nonsense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	C	42	9.787820	0.99264	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	.	.	.	5.35	2.48	0.30137	.	0.126219	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-26.219	6.5489	0.22423	0.1452:0.6947:0.0:0.1601	.	.	.	.	X	646;583;539;470	.	ENSP00000307288:G646X	G	-	1	0	MCM7	99528873	0.912000	0.30974	0.205000	0.23548	0.402000	0.30811	2.813000	0.48002	0.842000	0.35045	-0.229000	0.12294	GGA	.		0.483	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			A	99690937	C	A	99690937	4	1	103	1	0	0	0	0	0	1	0	0	9417	690	24	4	231	4	MCM7	7	99690937	Nonsense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	26216658	99690937	59447726	60	9120											
TRIM56	81844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100732355	100732355	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcagggccctgagcctcTcccaggccagccacgcggtg	5	4	15	17	3	1	1	0	1	1	0	2	1	1	1	5	4	2	1	5	4	0	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:100732355T>C	ENST00000306085.6	+	3	2059	c.1762T>C	c.(1762-1764)Tcc>Ccc	p.S588P		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	588					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTGAGCCTCTCCCAGGCCAG	0.697																																					p.S588P	Ovarian(89;1092 1379 22756 38989 39611)	.											.	TRIM56-226	0			c.T1762C						.						44	51	48					7																	100732355		2048	4159	6207	SO:0001583	missense	81844	exon3			AGCCTCTCCCAGG	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19028	protein-coding gene	gene with protein product			"tripartite motif-containing 56"				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1762T>C	7.37:g.100732355T>C	ENSP00000305161:p.Ser588Pro	Somatic	217	2		WXS	Illumina HiSeq	Phase_I	166	43	NM_030961	0	0	10	20	10	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Missense_Mutation	SNP	ENST00000306085.6	37	CCDS43625.1	.	.	.	.	.	.	.	.	.	.	T	7.472	0.646792	0.14516	.	.	ENSG00000169871	ENST00000306085	T	0.27557	1.66	3.87	-0.121	0.13535	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	T	0.14485	0.0350	N	0.14661	0.345	0.09310	N	1	B	0.26975	0.165	B	0.20384	0.029	T	0.19582	-1.0301	9	0.45353	T	0.12	.	4.0445	0.09766	0.2464:0.0:0.3462:0.4074	.	588	Q9BRZ2	TRI56_HUMAN	P	588	ENSP00000305161:S588P	ENSP00000305161:S588P	S	+	1	0	TRIM56	100519075	0.037000	0.19845	0.007000	0.13788	0.735000	0.41995	0.307000	0.19296	-0.011000	0.14247	0.477000	0.44152	TCC	.		0.697	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		C	100732355	T	C	100732355	3	2	103	1	0	0	0	0	1	0	0	0	16563	1551	54	3	1764	3	TRIM56	7	100732355	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	1041418	100732355	58406308	61	9121											
DLD	1738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107542828	107542828	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcttgaatgttggttgtaTtccttctaaggtgagcatgt	8	17	11	5	0	1	2	0	2	1	0	2	2	2	2	1	2	2	5	1	2	3	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:107542828T>C	ENST00000205402.5	+	4	538	c.257T>C	c.(256-258)aTt>aCt	p.I86T	DLD_ENST00000437604.2_Missense_Mutation_p.I86T|DLD_ENST00000494441.1_3'UTR|DLD_ENST00000537148.1_Intron|DLD_ENST00000440410.1_Intron	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	86					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	GTTGGTTGTATTCCTTCTAAG	0.368																																					p.I86T		.											.	DLD-226	0			c.T257C						.						295	259	271					7																	107542828		2203	4300	6503	SO:0001583	missense	1738	exon4			GTTGTATTCCTTC	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.257T>C	7.37:g.107542828T>C	ENSP00000205402:p.Ile86Thr	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	97	31	NM_000108	0	0	0	0	0	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	37	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430417	0.83776	.	.	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000437604;ENST00000539590	T;T;T	0.56103	0.48;0.48;0.48	6.17	6.17	0.99709	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.82365	0.5021	H	0.96691	3.865	0.80722	D	1	P;D	0.54397	0.945;0.966	D;D	0.83275	0.955;0.996	D	0.87980	0.2742	10	0.87932	D	0	-11.8281	16.0034	0.80327	0.0:0.0:0.0:1.0	.	86;86	B4DT69;P09622	.;DLDH_HUMAN	T	86;86;86;36	ENSP00000205402:I86T;ENSP00000390667:I86T;ENSP00000387542:I86T	ENSP00000205402:I86T	I	+	2	0	DLD	107330064	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.900000	0.75687	2.371000	0.80710	0.533000	0.62120	ATT	.		0.368	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		C	107542828	T	C	107542828	3	2	103	1	0	0	0	0	1	0	0	0	4562	1493	52	3	271	3	DLD	7	107542828	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	6810473	107542828	51595835	62	9122											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116417457	116417457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacagggcattttggttgtGtatatcatgggactttgttg	7	16	13	5	0	1	0	1	0	0	0	1	1	1	1	0	3	0	5	0	3	2	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:116417457G>A	ENST00000318493.6	+	16	3515	c.3328G>A	c.(3328-3330)Gta>Ata	p.V1110I	MET_ENST00000397752.3_Missense_Mutation_p.V1092I|MET_ENST00000539704.1_5'UTR			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTTTGGTTGTGTATATCATGG	0.338			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1110I		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.G3328A	GRCh37	CM990852	MET	M		.						191	176	180					7																	116417457		1827	4084	5911	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTTGTGTATATC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3328G>A	7.37:g.116417457G>A	ENSP00000317272:p.Val1110Ile	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	223	26	NM_001127500	0	0	212	305	93	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834124	0.91036	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.64991	-0.13;-0.13	5.16	5.16	0.70880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81178	0.4768	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.85130	0.997;0.99	D	0.83726	0.0195	10	0.87932	D	0	.	19.0107	0.92871	0.0:0.0:1.0:0.0	.	1110;1092	P08581-2;P08581	.;MET_HUMAN	I	1092;1110	ENSP00000380860:V1092I;ENSP00000317272:V1110I	ENSP00000317272:V1110I	V	+	1	0	MET	116204693	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.813000	0.99286	2.560000	0.86352	0.563000	0.77884	GTA	.		0.338	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116417457	G	A	116417457	3	1	103	1	0	0	0	0	1	0	0	0	9510	1377	48	2	3386	2	MET	7	116417457	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	8874629	116417457	42721206	63	9123											
DLGAP2	9228	broad.mit.edu	37	chr8	1497740	1497740	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcagctcctggtctacgcTgacggtcagccaggccaagg	7	6	14	14	3	2	1	1	1	1	0	3	1	3	1	3	4	3	3	3	4	2	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:1497740T>A	ENST00000421627.2	+	2	1015	c.881T>A	c.(880-882)cTg>cAg	p.L294Q		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	373					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		TGGTCTACGCTGACGGTCAGC	0.652																																					p.L294Q													.	DLGAP2-22	0			c.T881A						.						16	18	17					8																	1497740		2174	4272	6446	SO:0001583	missense	9228	exon2			CTACGCTGACGGT	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.881T>A	8.37:g.1497740T>A	ENSP00000400258:p.Leu294Gln	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	20	5	NM_004745	0	0	0	0	0	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.417592|4.417592	0.83449|0.83449	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000356067;ENST00000421627|ENST00000520901	T|.	0.37235|.	1.21|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.80481|.	0.4631|.	M|M	0.88704|0.88704	2.975|2.975	0.49915|0.49915	D|D	0.999833|0.999833	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.991|.	D|.	0.84080|.	0.0384|.	10|.	0.87932|.	D|.	0|.	-13.9858|-13.9858	15.2356|15.2356	0.73427|0.73427	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	373;373|.	Q9P1A6-2;Q9P1A6|.	.;DLGP2_HUMAN|.	Q|R	339;294|311	ENSP00000400258:L294Q|.	ENSP00000348366:L339Q|.	L|X	+|+	2|1	0|0	DLGAP2|DLGAP2	1485147|1485147	1.000000|1.000000	0.71417|0.71417	0.959000|0.959000	0.39883|0.39883	0.823000|0.823000	0.46562|0.46562	7.257000|7.257000	0.78362|0.78362	1.992000|1.992000	0.58205|0.58205	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.		0.652	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1497740	T	A	1497740	3	1	103	1	0	0	0	0	1	0	0	0	4571	1580	55	5	883	5	DLGAP2	8	1497740	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		1497740	144866282	64	9124											
MCPH1	79648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	6302563	6302563	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgccatcaagccctgcTcagttgagctgcagaagtct	9	9	10	13	0	3	2	2	1	1	1	3	2	3	2	2	0	6	5	2	0	2	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:6302563T>C	ENST00000344683.5	+	8	1396	c.1320T>C	c.(1318-1320)gcT>gcC	p.A440A	MCPH1_ENST00000522905.1_Silent_p.A392A|MCPH1_ENST00000519480.1_Silent_p.A440A	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	440					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CAAGCCCTGCTCAGTTGAGCT	0.403																																					p.A440A	Colon(95;1448 1467 8277 34473 35819)	.											.	MCPH1-229	0			c.T1320C						.						90	88	89					8																	6302563		1903	4122	6025	SO:0001819	synonymous_variant	79648	exon8			CCCTGCTCAGTTG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1320T>C	8.37:g.6302563T>C		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	120	18	NM_001172574	0	0	7	8	1	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			.		0.403	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		C	6302563	T	C	6302563	2	2	103	1	0	0	0	0	0	0	0	1	9423	1538	54	3		3	MCPH1	8	6302563	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	4804823	6302563	140061459	65	9125											
TM2D2	83877	ucsc.edu	37	chr8	38853742	38853742	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagcttacaggtaagagcAgaggatgaccggagagtggg	12	6	18	5	1	0	4	0	1	0	3	0	6	0	5	1	5	3	4	1	5	3	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:38853742A>T	ENST00000456397.2	-	1	310	c.217T>A	c.(217-219)Tgc>Agc	p.C73S	TM2D2_ENST00000522434.1_Intron|TM2D2_ENST00000456845.2_Intron|TM2D2_ENST00000397070.2_5'UTR|ADAM9_ENST00000481513.1_5'Flank|ADAM9_ENST00000466936.1_5'Flank|ADAM9_ENST00000487273.2_5'Flank|TM2D2_ENST00000412303.1_Intron	NM_078473.2	NP_510882.1	Q9BX73	TM2D2_HUMAN	TM2 domain containing 2	73						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		all_lung(54;0.00338)|Lung NSC(58;0.0133)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			AGGTAAGAGCAGAGGATGACC	0.657																																					p.C73S													.	TM2D2-90	0			c.T217A						.						29	32	31					8																	38853742		2203	4300	6503	SO:0001583	missense	83877	exon1			AAGAGCAGAGGAT	AF353991	CCDS6111.1, CCDS43733.1	8p11.23	2005-08-09				ENSG00000169490			24127	protein-coding gene	gene with protein product		610081				11278849	Standard	XM_005273657		Approved	BLP1	uc003xmk.3	Q9BX73		ENST00000456397.2:c.217T>A	8.37:g.38853742A>T	ENSP00000416050:p.Cys73Ser	Somatic	45	0		WXS	Illumina HiSeq		47	3	NM_078473	0	0	0	0	0	B2RBK4|D3DSX8|Q8N0X9	Missense_Mutation	SNP	ENST00000456397.2	37	CCDS6111.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.029304	0.93518	.	.	ENSG00000169490	ENST00000456397	T	0.39787	1.06	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	M	0.77406	2.37	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.70680	-0.4805	10	0.87932	D	0	-19.8572	15.7636	0.78106	1.0:0.0:0.0:0.0	.	73	Q9BX73	TM2D2_HUMAN	S	73	ENSP00000416050:C73S	ENSP00000416050:C73S	C	-	1	0	TM2D2	38972899	1.000000	0.71417	0.979000	0.43373	0.721000	0.41392	7.461000	0.80834	2.210000	0.71456	0.533000	0.62120	TGC	.		0.657	TM2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377280.1	NM_031940		T	38853742	A	T	38853742	3	4	103	1	0	0	0	0	1	0	0	0	15996	188	7	5	541	5	TM2D2	8	38853742	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	32551179	38853742	107510280	66	9126											
HGSNAT	138050	hgsc.bcm.edu;broad.mit.edu	37	chr8	43002092	43002092	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcctaatttctaccagaCttagacaaaaaaagacatgc	16	12	4	9	0	1	3	0	0	1	3	2	3	2	3	2	0	2	0	2	0	6	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:43002092C>G	ENST00000458501.2	+	2	204	c.204C>G	c.(202-204)gaC>gaG	p.D68E	HGSNAT_ENST00000379644.4_Splice_Site_p.D40E			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	68					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			TTCTACCAGACTTAGACAAAA	0.388																																					p.D40E		.											.	HGSNAT-68	0			c.C120G						.						79	71	73					8																	43002092		1832	4081	5913	SO:0001630	splice_region_variant	138050	exon2			ACCAGACTTAGAC		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"transmembrane protein 76"	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.203-1C>G	8.37:g.43002092C>G		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	28	5	NM_152419	0	0	0	0	0	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	37		.	.	.	.	.	.	.	.	.	.	C	13.07	2.126375	0.37533	.	.	ENSG00000165102	ENST00000458501;ENST00000332689;ENST00000379644	D;D	0.92495	-3.05;-3.05	5.42	-5.43	0.02632	.	0.299191	0.23658	N	0.045843	D	0.84229	0.5426	L	0.48642	1.525	0.18873	N	0.999986	B	0.33694	0.421	B	0.22386	0.039	T	0.70472	-0.4862	10	0.39692	T	0.17	.	13.0426	0.58908	0.0:0.1384:0.0:0.8616	.	68	Q68CP4	HGNAT_HUMAN	E	68;40;40	ENSP00000389524:D68E;ENSP00000368965:D40E	ENSP00000327833:D40E	D	+	3	2	HGSNAT	43121249	0.309000	0.24518	0.090000	0.20809	0.088000	0.18126	-1.048000	0.03517	-1.182000	0.02727	-0.390000	0.06520	GAC	.		0.388	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038	Missense_Mutation	G	43002092	C	G	43002092	5	3	103	1	0	0	0	0	0	0	1	0	7109	579	20	4	126	4	HGSNAT	8	43002092	Splice_Site	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	4148350	43002092	103361930	67	9127											
COL14A1	7373	broad.mit.edu	37	chr8	121170484	121170484	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgtgactccaacttcAggtaaaaacaattgactttg	12	14	6	9	0	2	2	1	2	1	0	3	2	3	2	1	1	2	1	1	1	5	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:121170484A>G	ENST00000297848.3	+	3	474	c.204A>G	c.(202-204)tcA>tcG	p.S68S	COL14A1_ENST00000309791.4_Splice_Site_p.S68S|COL14A1_ENST00000247781.3_Splice_Site_p.S68S|COL14A1_ENST00000537875.1_Splice_Site_p.S68S|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CTCCAACTTCAGGTAAAAACA	0.353																																					p.S68S													.	COL14A1-543	0			c.A204G						.						59	60	59					8																	121170484		2203	4300	6503	SO:0001630	splice_region_variant	7373	exon3			AACTTCAGGTAAA		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.205+1A>G	8.37:g.121170484A>G		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	79	3	NM_021110	0	0	0	0	0		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																			.		0.353	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	Silent	G	121170484	A	G	121170484	5	3	103	1	0	0	0	0	0	0	1	0	3677	202	7	3	210	3	COL14A1	8	121170484	Splice_Site	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	78168392	121170484	25193538	68	9128											
ADCY8	114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	131921969	131921969	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttacccagggattcctccaGattcgagtttgtttgcaata	9	14	8	10	1	0	1	0	0	0	1	3	3	2	2	3	1	2	3	3	1	3	6	rs368729916		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:131921969G>C	ENST00000286355.5	-	6	3717	c.1625C>G	c.(1624-1626)tCt>tGt	p.S542C	ADCY8_ENST00000377928.3_Missense_Mutation_p.S542C	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	542					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GATTCCTCCAGATTCGAGTTT	0.463										HNSCC(32;0.087)																											p.S542C		.											.	ADCY8-157	0			c.C1625G						.	G	CYS/SER	1,4405	2.1+/-5.4	0,1,2202	242	216	225		1625	5.9	1	8		225	0,8600		0,0,4300	no	missense	ADCY8	NM_001115.2	112	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	probably-damaging	542/1252	131921969	1,13005	2203	4300	6503	SO:0001583	missense	114	exon6			CCTCCAGATTCGA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1625C>G	8.37:g.131921969G>C	ENSP00000286355:p.Ser542Cys	Somatic	372	0		WXS	Illumina HiSeq	Phase_I	337	67	NM_001115	0	0	0	0	0		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	31	5.072076	0.93950	2.27E-4	0.0	ENSG00000155897	ENST00000286355;ENST00000377928;ENST00000522949	D;D;D	0.87029	-2.2;-2.2;-2.2	5.93	5.93	0.95920	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.052374	0.85682	D	0.000000	D	0.96423	0.8833	H	0.98276	4.19	0.49483	D	0.999792	D;D	0.69078	0.995;0.997	D;D	0.68353	0.957;0.953	D	0.97510	1.0066	10	0.87932	D	0	.	19.3421	0.94347	0.0:0.0:1.0:0.0	.	542;542	E7EVL1;P40145	.;ADCY8_HUMAN	C	542;542;157	ENSP00000286355:S542C;ENSP00000367161:S542C;ENSP00000428010:S157C	ENSP00000286355:S542C	S	-	2	0	ADCY8	131991151	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.826000	0.97356	0.655000	0.94253	TCT	.		0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			C	131921969	G	C	131921969	3	2	103	1	0	0	0	0	1	0	0	0	300	942	33	4	2182	4	ADCY8	8	131921969	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	10751485	131921969	14442053	69	9129											
NAPRT1	1936	broad.mit.edu	37	chr8	144659504	144659504	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagcccgcctcaggcccAtctctagcagccgcttctct	5	9	8	19	2	3	1	1	1	2	0	5	1	3	1	5	1	3	2	5	1	1	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:144659504A>G	ENST00000529272.1	-	0	1311				NAPRT1_ENST00000460623.1_5'Flank|RP11-661A12.7_ENST00000529247.1_RNA|NAPRT1_ENST00000449291.2_Missense_Mutation_p.M168T|NAPRT1_ENST00000426292.3_Missense_Mutation_p.M168T|RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000276844.7_Missense_Mutation_p.M168T|NAPRT1_ENST00000435154.3_Missense_Mutation_p.M168T			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CCTCAGGCCCATCTCTAGCAG	0.697																																					p.M168T													.	NAPRT1-91	0			c.T503C						.						9	11	11					8																	144659504		2175	4277	6452	SO:0001628	intergenic_variant	93100	exon4			AGGCCCATCTCTA	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191		8.37:g.144659504A>G		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	20	3	NM_145201	0	0	23	37	14	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.637134	0.67130	.	.	ENSG00000147813	ENST00000435154;ENST00000449291;ENST00000340490;ENST00000426292;ENST00000276844	T;T;T;T;T	0.46451	0.89;0.89;0.87;0.9;0.88	4.84	4.84	0.62591	Quinolinate phosphoribosyl transferase, C-terminal (1);	0.225191	0.51477	D	0.000096	T	0.49525	0.1562	M	0.83603	2.65	0.44976	D	0.997993	B;P;B;P	0.35944	0.351;0.529;0.435;0.491	B;B;B;B	0.37015	0.239;0.236;0.154;0.239	T	0.59311	-0.7478	10	0.87932	D	0	-9.6205	13.7315	0.62789	1.0:0.0:0.0:0.0	.	168;168;168;168	C9J8U2;G5E977;Q6XQN6-3;Q6XQN6	.;.;.;PNCB_HUMAN	T	168	ENSP00000405670:M168T;ENSP00000401508:M168T;ENSP00000341136:M168T;ENSP00000390949:M168T;ENSP00000276844:M168T	ENSP00000276844:M168T	M	-	2	0	NAPRT1	144730647	1.000000	0.71417	0.991000	0.47740	0.942000	0.58702	5.649000	0.67936	2.022000	0.59522	0.533000	0.62120	ATG	.		0.697	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		G	144659504	A	G	144659504	1	3	103	0	1	0	0	0	0	0	0	0	10190	217	8	3		3	NAPRT1	8	144659504	IGR	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	12737535	144659504	1704518	70	9130											
DENND4C	55667	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	19369966	19369966	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tactttcacagcaaatgaagCcaggcatgaaaagacaaagg	18	6	9	8	0	1	3	1	2	0	1	1	3	1	3	1	2	3	2	1	2	6	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:19369966C>T	ENST00000380432.2	+	26	4834	c.4801C>T	c.(4801-4803)Cca>Tca	p.P1601S	RP11-513M16.7_ENST00000609609.1_RNA|DENND4C_ENST00000434457.2_Missense_Mutation_p.P1886S|DENND4C_ENST00000602925.1_Missense_Mutation_p.P1837S			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1601					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GCAAATGAAGCCAGGCATGAA	0.338																																					p.P1837S													.	DENND4C-92	0			c.C5509T						.						86	79	81					9																	19369966		2203	4300	6503	SO:0001583	missense	55667	exon30			ATGAAGCCAGGCA	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"DENN/MADD domain containing"	26079	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 55B", "chromosome 9 open reading frame 55"	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.4801C>T	9.37:g.19369966C>T	ENSP00000369797:p.Pro1601Ser	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	63	11	NM_017925	0	0	29	45	16	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	C	13.01	2.108364	0.37242	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.24908	1.83;1.83	5.07	3.23	0.37069	.	0.284189	0.32430	N	0.006116	T	0.25717	0.0626	L	0.52905	1.665	0.37625	D	0.921457	B;B;B	0.27853	0.009;0.191;0.0	B;B;B	0.34452	0.008;0.183;0.001	T	0.10019	-1.0648	9	.	.	.	-0.5743	10.1821	0.42975	0.0:0.7786:0.1463:0.0752	.	931;783;1601	B7Z660;Q5VZ89-3;Q5VZ89	.;.;DEN4C_HUMAN	S	1601;1074;783;931;1074;783;598	ENSP00000305795:P1074S;ENSP00000443804:P931S	.	P	+	1	0	DENND4C	19359966	1.000000	0.71417	0.836000	0.33094	0.707000	0.40811	2.238000	0.43070	0.735000	0.32537	0.650000	0.86243	CCA	.		0.338	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		T	19369966	C	T	19369966	3	4	103	1	0	0	0	0	1	0	0	0	4446	739	26	2	4903	2	DENND4C	9	19369966	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		19369966	121843465	71	9131											
TEK	7010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	27197591	27197591	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atctcactgcttggacccttAgtgacagtaagtaattcatg	11	13	8	9	0	2	1	2	1	1	0	3	2	2	2	1	1	1	3	1	1	3	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:27197591A>G	ENST00000380036.4	+	12	2345	c.1903A>G	c.(1903-1905)Agt>Ggt	p.S635G	RNA5SP280_ENST00000411230.1_RNA|TEK_ENST00000406359.4_Missense_Mutation_p.S592G|TEK_ENST00000519097.1_Missense_Mutation_p.S488G	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	635	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TTGGACCCTTAGTGACAGTAA	0.493																																					p.S635G		.											.	TEK-1584	0			c.A1903G						.						39	40	40					9																	27197591		2203	4300	6503	SO:0001583	missense	7010	exon12			ACCCTTAGTGACA	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	11724	protein-coding gene	gene with protein product		600221	"venous malformations, multiple cutaneous and mucosal"	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.1903A>G	9.37:g.27197591A>G	ENSP00000369375:p.Ser635Gly	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	38	8	NM_000459	0	0	0	0	0	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	A	9.271	1.045584	0.19748	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359;ENST00000519080	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.54	5.54	0.83059	Fibronectin, type III (1);	0.000000	0.64402	D	0.000010	T	0.62816	0.2459	L	0.56769	1.78	0.51233	D	0.999913	B;P;D;B	0.63880	0.281;0.462;0.993;0.361	B;B;D;B	0.68192	0.056;0.141;0.956;0.081	T	0.58457	-0.7633	10	0.23302	T	0.38	.	15.6853	0.77405	1.0:0.0:0.0:0.0	.	488;668;592;635	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	G	488;635;592;445	ENSP00000430686:S488G;ENSP00000369375:S635G;ENSP00000383977:S592G;ENSP00000428337:S445G	ENSP00000369375:S635G	S	+	1	0	TEK	27187591	0.999000	0.42202	0.744000	0.31058	0.104000	0.19210	4.662000	0.61525	2.117000	0.64856	0.533000	0.62120	AGT	.		0.493	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			G	27197591	A	G	27197591	3	3	103	1	0	0	0	0	1	0	0	0	15783	420	15	3	1949	3	TEK	9	27197591	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	7827625	27197591	114015840	72	9132											
ZCCHC6	79670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	88943326	88943326	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtgtcccctgcagcactgtCagtatgttcccagatcacaa	9	11	8	13	0	2	1	2	0	0	1	4	1	4	1	3	0	2	4	3	0	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:88943326C>G	ENST00000375963.3	-	11	1709	c.1537G>C	c.(1537-1539)Gac>Cac	p.D513H	ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375961.2_Missense_Mutation_p.D513H|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.D390H	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	513					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						GCAGCACTGTCAGTATGTTCC	0.408																																					p.D513H		.											.	ZCCHC6-92	0			c.G1537C						.						246	214	225					9																	88943326		2203	4300	6503	SO:0001583	missense	79670	exon11			CACTGTCAGTATG	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"Zinc fingers, CCHC domain containing"	25817	protein-coding gene	gene with protein product	"TUTase7"					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.1537G>C	9.37:g.88943326C>G	ENSP00000365130:p.Asp513His	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	232	48	NM_024617	0	0	9	10	1	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662242	0.47572	.	.	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.46819	0.86;1.06;1.06	4.35	4.35	0.52113	.	0.478121	0.23602	N	0.046437	T	0.55162	0.1903	L	0.36672	1.1	0.19945	N	0.999947	D;D	0.69078	0.997;0.991	P;P	0.61132	0.884;0.769	T	0.49551	-0.8928	10	0.66056	D	0.02	-18.5595	15.1952	0.73081	0.0:1.0:0.0:0.0	.	390;513	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	H	390;513;513	ENSP00000365127:D390H;ENSP00000365128:D513H;ENSP00000365130:D513H	ENSP00000365127:D390H	D	-	1	0	ZCCHC6	88133146	0.448000	0.25681	0.092000	0.20876	0.015000	0.08874	1.298000	0.33412	2.699000	0.92147	0.462000	0.41574	GAC	.		0.408	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		G	88943326	C	G	88943326	3	3	103	1	0	0	0	0	1	0	0	0	17624	826	29	4	3018	4	ZCCHC6	9	88943326	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	61745735	88943326	52270105	73	9133											
ZFP37	7539	broad.mit.edu;bcgsc.ca	37	chr9	115806495	115806495	+	Frame_Shift_Del	DEL	G	G	-																															gactgcaacttccctgaggaGtttgttttgagatttctgga																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:115806495delG	ENST00000374227.3	-	4	430	c.403delC	c.(403-405)ctcfs	p.L136fs	ZFP37_ENST00000553380.1_Frame_Shift_Del_p.L151fs|ZFP37_ENST00000555206.1_Frame_Shift_Del_p.L137fs	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						TCCCTGAGGAGTTTGTTTTGA	0.353																																					p.L135fs													.	ZFP37-92	0			c.403delC						.						85	91	89					9																	115806495		2171	4194	6365	SO:0001589	frameshift_variant	7539	exon4			TGAGGAGTTTGTT	AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"Zinc fingers, C2H2-type", "-"	12863	protein-coding gene	gene with protein product		602951	"zinc finger protein homologous to Zfp37 in mouse", "zinc finger protein 37 homolog (mouse)"				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.403delC	9.37:g.115806495delG	ENSP00000363344:p.Leu136fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	190	27	NM_003408	0	0	0	0	0	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Frame_Shift_Del	DEL	ENST00000374227.3	37	CCDS6787.1																																																																																			.		0.353	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		-	115806495	G	-	115806495	7	5	103	1	0	1	0	1	0	0	0	0	17680	1029	36	0	1493	0	ZFP37	9	115806495	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	26863169	115806495	25406936	74	9134											
OR1N1	138883	bcgsc.ca	37	chr9	125288660	125288670	+	Frame_Shift_Del	DEL	GACTGAAGAGC	GACTGAAGAGC	-																															agaggaaacaatactcctgtGactgaagagcctctttaggg																								rs202175357		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	GACTGAAGAGC	GACTGAAGAGC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:125288660_125288670delGACTGAAGAGC	ENST00000304880.2	-	1	902_912	c.903_913delGCTCTTCAGTC	c.(901-915)aggctcttcagtcacfs	p.LFSH302fs		NM_012363.1	NP_036495.1	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N, member 1	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|large_intestine(2)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						ATACTCCTGTGACTGAAGAGCCTCTTTAGGG	0.46																																					p.301_305del													.	OR1N1-133	0			c.903_913del						.																																			SO:0001589	frameshift_variant	138883	exon1			TCCTGTGACTGAA	U86216	CCDS6844.1	9q34.11	2012-08-09			ENSG00000171505	ENSG00000171505		"GPCR / Class A : Olfactory receptors"	8221	protein-coding gene	gene with protein product				OR1N3		9500546	Standard	NM_012363		Approved	OR1-26	uc004bmn.1	Q8NGS0	OTTHUMG00000020608	ENST00000304880.2:c.903_913delGCTCTTCAGTC	9.37:g.125288660_125288670delGACTGAAGAGC	ENSP00000306974:p.Leu302fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_1	78	4	NM_012363	0	0	0	0	0	A3KFM1|O43870|Q6IF16|Q96R93	Frame_Shift_Del	DEL	ENST00000304880.2	37	CCDS6844.1																																																																																			.		0.46	OR1N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053938.1			-	125288670	GACTGAAGAGC	-	125288660	7	5	103	1	0	1	0	1	0	0	0	0	10995	1290	45	0	26	0	OR1N1	9	125288660	Frame_Shift_Del	DEL	GACTGAAGAGC	TCGA-DZ-6132-01A-11D-1961-08	9482165	125288660	15924771	75	9135											
CRAT	1384	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131864688	131864688	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccacccacctggtagttGtgtaccacggtgatgtgcgt	6	10	14	11	2	0	1	0	1	0	0	0	1	0	1	4	3	2	3	4	3	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:131864688G>T	ENST00000318080.2	-	5	915	c.621C>A	c.(619-621)caC>caA	p.H207Q	RP11-247A12.1_ENST00000434250.1_RNA|CRAT_ENST00000464290.1_5'UTR	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	207					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CCTGGTAGTTGTGTACCACGG	0.642																																					p.H207Q		.											.	CRAT-90	0			c.C621A						.						147	128	135					9																	131864688		2203	4300	6503	SO:0001583	missense	1384	exon5			GTAGTTGTGTACC	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"carnitine acetyltransferase"			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.621C>A	9.37:g.131864688G>T	ENSP00000315013:p.His207Gln	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	162	42	NM_000755	0	0	0	0	0	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	37	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.223146	0.79464	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	D	0.89343	-2.5	5.37	4.23	0.50019	.	0.000000	0.85682	D	0.000000	D	0.92528	0.7627	M	0.76170	2.325	0.80722	D	1	D	0.62365	0.991	D	0.68039	0.955	D	0.90458	0.4444	10	0.31617	T	0.26	-47.0361	10.6033	0.45379	0.12:0.0:0.88:0.0	.	207	P43155	CACP_HUMAN	Q	207	ENSP00000315013:H207Q	ENSP00000315013:H207Q	H	-	3	2	CRAT	130904509	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.076000	0.57591	0.913000	0.36797	0.561000	0.74099	CAC	.		0.642	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			T	131864688	G	T	131864688	3	4	103	1	0	0	0	0	1	0	0	0	3853	1368	48	4	1299	4	CRAT	9	131864688	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	6576028	131864688	9348743	76	9136											
ARHGAP21	57584	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	24908604	24908604	+	Frame_Shift_Del	DEL	T	T	-																															gtctggcgtccagatggaggTttttcccttaggatgacagc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:24908604delT	ENST00000396432.2	-	9	2706	c.2220delA	c.(2218-2220)aaafs	p.K740fs	ARHGAP21_ENST00000320481.6_Frame_Shift_Del_p.K527fs	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	739					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CAGATGGAGGTTTTTCCCTTA	0.453																																					p.K740fs		.											.	ARHGAP21-235	0			c.2220delA						.						102	96	98					10																	24908604		2203	4300	6503	SO:0001589	frameshift_variant	57584	exon9			.	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.2220delA	10.37:g.24908604delT	ENSP00000379709:p.Lys740fs	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	156	25	NM_020824	0	0	0	0	0	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Del	DEL	ENST00000396432.2	37	CCDS7144.2																																																																																			.		0.453	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		-	24908604	T	-	24908604	7	5	103	1	0	1	0	1	0	0	0	0	871	1722	60	0	3728	0	ARHGAP21	10	24908604	Frame_Shift_Del	DEL	T	TCGA-DZ-6132-01A-11D-1961-08		24908604	110626143	77	9137											
STOX1	219736	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	70645179	70645179	+	Frame_Shift_Del	DEL	T	T	-																															ccttggattcctcaagaatcTttgatggtaaagccaaagag																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:70645179delT	ENST00000298596.6	+	3	1710	c.1627delT	c.(1627-1629)tttfs	p.F543fs	STOX1_ENST00000399162.2_Intron|STOX1_ENST00000421961.2_Frame_Shift_Del_p.F433fs|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000399169.4_Frame_Shift_Del_p.F543fs	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	543						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						CTCAAGAATCTTTGATGGTAA	0.418																																					p.F543fs		.											.	STOX1-92	0			c.1627delT						.						66	60	62					10																	70645179		1853	4096	5949	SO:0001589	frameshift_variant	219736	exon3			.	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"chromosome 10 open reading frame 24"	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1627delT	10.37:g.70645179delT	ENSP00000298596:p.Phe543fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	53	12	NM_152709	0	0	0	0	0	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Frame_Shift_Del	DEL	ENST00000298596.6	37	CCDS41535.1																																																																																			.		0.418	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		-	70645179	T	-	70645179	7	5	103	1	0	1	0	1	0	0	0	0	15351	1609	56	0	1637	0	STOX1	10	70645179	Frame_Shift_Del	DEL	T	TCGA-DZ-6132-01A-11D-1961-08	45736575	70645179	64889568	78	9138											
LRIT1	26103	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	85997318	85997318	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacagctgctccaggcggcCcaggggcctgaaggcctcgc	6	4	14	17	2	0	1	0	1	0	0	2	1	1	1	5	5	2	2	5	5	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:85997318C>T	ENST00000372105.3	-	2	268	c.247G>A	c.(247-249)Ggc>Agc	p.G83S		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	83						integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						TCCAGGCGGCCCAGGGGCCTG	0.726																																					p.G83S													.	LRIT1-90	0			c.G247A						.						16	20	18					10																	85997318		2140	4199	6339	SO:0001583	missense	26103	exon2			GGCGGCCCAGGGG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	23404	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 9"		"leucine rich repeat containing 21"	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.247G>A	10.37:g.85997318C>T	ENSP00000361177:p.Gly83Ser	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	48	10	NM_015613	0	0	0	0	0	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	9.281	1.048267	0.19827	.	.	ENSG00000148602	ENST00000372105	T	0.47869	0.83	5.42	-0.434	0.12283	.	1.087950	0.06798	N	0.788142	T	0.20659	0.0497	N	0.05554	-0.025	0.23685	N	0.997112	B	0.06786	0.001	B	0.06405	0.002	T	0.21415	-1.0246	10	0.08837	T	0.75	.	2.4799	0.04585	0.145:0.2466:0.4241:0.1842	.	83	Q9P2V4	LRIT1_HUMAN	S	83	ENSP00000361177:G83S	ENSP00000361177:G83S	G	-	1	0	LRIT1	85987298	0.002000	0.14202	0.742000	0.31022	0.964000	0.63967	-0.057000	0.11768	0.247000	0.21414	-0.126000	0.14955	GGC	.		0.726	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		T	85997318	C	T	85997318	3	4	103	1	0	0	0	0	1	0	0	0	8972	623	22	2	1636	2	LRIT1	10	85997318	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	15352139	85997318	49537429	79	9139											
ZNF143	7702	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	9519250	9519250	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaaaagtcacgtcagaacTcatacaggagaaaagccata	19	7	7	8	1	3	2	3	0	0	2	3	3	3	2	1	1	3	0	1	1	8	3	rs373920789		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:9519250T>G	ENST00000396602.2	+	10	989	c.870T>G	c.(868-870)acT>acG	p.T290T	ZNF143_ENST00000299606.2_Silent_p.T262T|ZNF143_ENST00000396597.3_Silent_p.T259T|ZNF143_ENST00000396604.1_Silent_p.T289T|ZNF143_ENST00000530463.1_Silent_p.T289T	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	290					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		ACGTCAGAACTCATACAGGAG	0.328																																					p.T290T		.											.	ZNF143-90	0			c.T870G						.	T		3,4399	6.2+/-15.9	0,3,2198	65	66	66		870	2.7	1	11		66	0,8588		0,0,4294	no	coding-synonymous	ZNF143	NM_003442.5		0,3,6492	GG,GT,TT		0.0,0.0682,0.0231		290/639	9519250	3,12987	2201	4294	6495	SO:0001819	synonymous_variant	7702	exon10			CAGAACTCATACA	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.870T>G	11.37:g.9519250T>G		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	56	8	NM_003442	0	0	10	17	7	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	37	CCDS7799.2																																																																																			.		0.328	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		G	9519250	T	G	9519250	2	3	103	1	0	0	0	0	0	0	0	1	17764	1538	54	5		5	ZNF143	11	9519250	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		9519250	125487266	80	9140											
RAPSN	5913	ucsc.edu;bcgsc.ca	37	chr11	47469615	47469615	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaactcgcacagcttctCgttgctgcgtgccaggttca	7	11	11	12	3	2	1	1	1	1	0	4	1	2	1	1	1	5	5	1	1	1	3	rs200550567		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:47469615C>A	ENST00000298854.2	-	2	493	c.280G>T	c.(280-282)Gag>Tag	p.E94*	RAPSN_ENST00000529341.1_Nonsense_Mutation_p.E94*|RAPSN_ENST00000524487.1_Nonsense_Mutation_p.E94*|RAPSN_ENST00000352508.3_Nonsense_Mutation_p.E94*	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	94					positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						CACAGCTTCTCGTTGCTGCGT	0.622																																					p.E94X													.	RAPSN-91	0			c.G280T						.						96	74	82					11																	47469615		2201	4298	6499	SO:0001587	stop_gained	5913	exon2			GCTTCTCGTTGCT		CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917		"RING-type (C3HC4) zinc fingers"	9863	protein-coding gene	gene with protein product	"rapsyn"	601592	"receptor-associated protein of the synapse, 43kD"			8812503	Standard	NM_005055		Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000298854.2:c.280G>T	11.37:g.47469615C>A	ENSP00000298854:p.Glu94*	Somatic	70	0		WXS	Illumina HiSeq		56	12	NM_032645	0	0	0	0	0	Q8TDF3|Q9BTD9	Nonsense_Mutation	SNP	ENST00000298854.2	37	CCDS7936.1	.	.	.	.	.	.	.	.	.	.	C	38	6.680264	0.97755	.	.	ENSG00000165917	ENST00000298854;ENST00000352508;ENST00000524487;ENST00000529341	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-42.0177	18.9738	0.92725	0.0:1.0:0.0:0.0	.	.	.	.	X	94	.	ENSP00000298854:E94X	E	-	1	0	RAPSN	47426191	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.302000	0.78861	2.565000	0.86533	0.557000	0.71058	GAG	C|0.999;T|0.001		0.622	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1			A	47469615	C	A	47469615	4	1	103	1	0	0	0	0	0	1	0	0	13083	893	31	4	986	4	RAPSN	11	47469615	Nonsense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	37950365	47469615	87536901	81	9141											
GIF	2694	hgsc.bcm.edu;bcgsc.ca	37	chr11	59610049	59610049	+	Missense_Mutation	SNP	G	G	C																															tagaaggctgatgcttcagcGttggggcctccgaaggggat																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:59610049G>C	ENST00000257248.2	-	4	425	c.378C>G	c.(376-378)aaC>aaG	p.N126K	GIF_ENST00000541311.1_Missense_Mutation_p.N101K	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	126					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	ATGCTTCAGCGTTGGGGCCTC	0.522																																					p.N126K	NSCLC(53;1139 1245 16872 38474 42853)	.											.	GIF-92	0			c.C378G						.						68	61	63					11																	59610049		2201	4295	6496	SO:0001583	missense	2694	exon4			TTCAGCGTTGGGG	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.378C>G	11.37:g.59610049G>C	ENSP00000257248:p.Asn126Lys	Somatic	81	1		WXS	Illumina HiSeq	Phase_I	58	9	NM_005142	0	0	0	0	0	B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	37	CCDS7977.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.417564	0.25552	.	.	ENSG00000134812	ENST00000257248;ENST00000541311	T;T	0.35973	1.28;1.28	5.63	-11.3	0.00108	.	1.313500	0.04767	N	0.427342	T	0.21590	0.0520	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22208	-1.0223	10	0.48119	T	0.1	1.5143	8.9085	0.35539	0.1072:0.0807:0.5605:0.2515	.	126	P27352	IF_HUMAN	K	126;101	ENSP00000257248:N126K;ENSP00000440427:N101K	ENSP00000257248:N126K	N	-	3	2	GIF	59366625	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-3.689000	0.00392	-2.813000	0.00347	-2.048000	0.00412	AAC	.		0.522	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142		C	59610049	G	C	59610049	3	2	103	1	0	0	0	0	1	0	0	0	6396	1136	40	4	899	4	GIF	11	59610049	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	12140434	59610049	75396467	82	9142	96	2									
GIF	2694	broad.mit.edu;bcgsc.ca	37	chr11	59610051	59610052	+	Frame_Shift_Ins	INS	-	-	G																															aaggctgatgcttcagcgttINSggggcctccgaaggggatag																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:59610051_59610052insG	ENST00000257248.2	-	4	422_423	c.375_376insC	c.(373-378)cccaacfs	p.N126fs	GIF_ENST00000541311.1_Frame_Shift_Ins_p.N101fs	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	126					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	GCTTCAGCGTTGGGGCCTCCGA	0.525																																					p.N126fs	NSCLC(53;1139 1245 16872 38474 42853)												.	GIF-92	0			c.376_377insC						.																																			SO:0001589	frameshift_variant	2694	exon4			CAGCGTTGGGGCC	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.376dupC	11.37:g.59610055_59610055dupG	ENSP00000257248:p.Asn126fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	55	9	NM_005142	0	0	0	0	0	B2RAN8|B4DVZ1	Frame_Shift_Ins	INS	ENST00000257248.2	37	CCDS7977.1																																																																																			.		0.525	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142		G	59610052	-	G	59610051	7	5	103	1	0	1	1	0	0	0	0	0	6396	1812	63	0	901	0	GIF	11	59610051	Frame_Shift_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	2	59610051	75396465	83	9143	96	2									
FADS1	3992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	61578255	61578255	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatcttccccaaggcaaagaAgaagggatgcatgttgatgt	13	9	12	7	0	1	3	0	1	1	2	2	5	2	4	2	2	1	3	2	2	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:61578255A>C	ENST00000350997.7	-	5	1115	c.883T>G	c.(883-885)Ttc>Gtc	p.F295V	FADS1_ENST00000542506.1_Missense_Mutation_p.F154V|FADS1_ENST00000433932.1_Missense_Mutation_p.F154V|FADS2_ENST00000574708.1_Intron	NM_013402.4	NP_037534.3	O60427	FADS1_HUMAN	fatty acid desaturase 1	238					alpha-linolenic acid metabolic process (GO:0036109)|cell-cell signaling (GO:0007267)|cellular lipid metabolic process (GO:0044255)|cellular response to starvation (GO:0009267)|icosanoid biosynthetic process (GO:0046456)|linoleic acid metabolic process (GO:0043651)|phospholipid biosynthetic process (GO:0008654)|regulation of cell differentiation (GO:0045595)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	C-5 sterol desaturase activity (GO:0000248)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	AAGGCAAAGAAGAAGGGATGC	0.567																																					p.F295V		.											.	FADS1-90	0			c.T883G						.						137	150	145					11																	61578255		2112	4243	6355	SO:0001583	missense	3992	exon5			CAAAGAAGAAGGG		CCDS8011.2	11q12-q13.1	2013-01-25			ENSG00000149485	ENSG00000149485	1.14.19.3	"Fatty acid desaturases"	3574	protein-coding gene	gene with protein product	"delta-5 desaturase"	606148		LLCDL1			Standard	NM_013402		Approved	D5D, FADSD5, TU12, FADS6	uc010rlm.2	O60427	OTTHUMG00000157155	ENST00000350997.7:c.883T>G	11.37:g.61578255A>C	ENSP00000322229:p.Phe295Val	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	146	26	NM_013402	0	0	8	14	6	A8K0I7|B2RAI0|Q53GM5|Q8N3A6|Q8NCC7|Q8NCG0|Q96I39|Q96SV3|Q96T10|Q9NRP8|Q9NYX1	Missense_Mutation	SNP	ENST00000350997.7	37	CCDS8011.2	.	.	.	.	.	.	.	.	.	.	A	10.51	1.369315	0.24771	.	.	ENSG00000149485	ENST00000543488;ENST00000350997;ENST00000412725;ENST00000433932;ENST00000542506;ENST00000539999;ENST00000540767;ENST00000545245	T;T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39	5.06	2.75	0.32379	Fatty acid desaturase, type 1 (1);	0.000000	0.50627	U	0.000109	T	0.35248	0.0925	N	0.02973	-0.45	0.42328	D	0.992286	B	0.27192	0.171	B	0.27500	0.08	T	0.06770	-1.0808	10	0.25106	T	0.35	-29.7375	4.9109	0.13821	0.7052:0.0:0.1563:0.1385	.	238	O60427	FADS1_HUMAN	V	171;295;154;154;154;24;154;154	ENSP00000322229:F295V;ENSP00000405087:F154V;ENSP00000441403:F154V;ENSP00000443587:F24V;ENSP00000441871:F154V;ENSP00000442170:F154V	ENSP00000322229:F295V	F	-	1	0	FADS1	61334831	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	3.525000	0.53502	0.893000	0.36288	-0.250000	0.11733	TTC	.		0.567	FADS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347648.2	NM_013402		C	61578255	A	C	61578255	3	2	103	1	0	0	0	0	1	0	0	0	5381	72	3	5	654	5	FADS1	11	61578255	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	1968204	61578255	73428261	84	9144											
SIDT2	51092	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117052793	117052793	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggactggggagcagttcaGcttcaataccacagcagcac	12	6	11	12	0	2	0	2	0	0	0	2	2	2	2	1	3	5	5	1	3	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:117052793G>A	ENST00000324225.4	+	4	1019	c.488G>A	c.(487-489)aGc>aAc	p.S163N	SIDT2_ENST00000530948.1_Intron|SIDT2_ENST00000431081.2_Missense_Mutation_p.S163N	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	163					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		GAGCAGTTCAGCTTCAATACC	0.602																																					p.S163N													.	SIDT2-90	0			c.G488A						.						43	45	44					11																	117052793		2201	4296	6497	SO:0001583	missense	51092	exon4			AGTTCAGCTTCAA	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.488G>A	11.37:g.117052793G>A	ENSP00000314023:p.Ser163Asn	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	28	8	NM_001040455	0	0	22	27	5	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	.	.	.	.	.	.	.	.	.	.	G	9.954	1.220862	0.22457	.	.	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081;ENST00000524842;ENST00000531353	T;T;T	0.16743	2.32;2.32;2.33	5.14	4.21	0.49690	.	0.142496	0.64402	D	0.000009	T	0.09468	0.0233	N	0.17082	0.46	0.35238	D	0.77751	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.06405	0.001;0.001;0.002;0.001	T	0.12656	-1.0539	10	0.02654	T	1	-29.1739	13.9161	0.63899	0.0:0.2987:0.7013:0.0	.	163;163;163;163	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	N	163;163;163;13;62	ENSP00000314023:S163N;ENSP00000278951:S163N;ENSP00000399635:S163N	ENSP00000278951:S163N	S	+	2	0	SIDT2	116558003	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.319000	0.59197	1.358000	0.45922	0.561000	0.74099	AGC	.		0.602	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		A	117052793	G	A	117052793	3	1	103	1	0	0	0	0	1	0	0	0	14335	971	34	2	502	2	SIDT2	11	117052793	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	55474538	117052793	17953723	85	9145											
ARHGEF12	23365	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	120302543	120302543	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taacagtcagtgaggcagaaAcagatcctggagatgtactg	14	8	12	7	0	1	4	1	1	0	3	2	5	2	4	1	2	3	2	1	2	3	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:120302543A>T	ENST00000397843.2	+	11	1013	c.847A>T	c.(847-849)Aca>Tca	p.T283S	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.T180S|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.T264S	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	283					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TGAGGCAGAAACAGATCCTGG	0.473			T	MLL	AML																																p.T283S				Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12-661	0			c.A847T						.						118	116	117					11																	120302543		1938	4128	6066	SO:0001583	missense	23365	exon11			GCAGAAACAGATC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"Rho guanine nucleotide exchange factors"	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.847A>T	11.37:g.120302543A>T	ENSP00000380942:p.Thr283Ser	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	63	7	NM_015313	0	0	27	52	25	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.029964	0.35797	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.63913	0.03;-0.07;0.03	5.54	0.332	0.15938	.	1.053350	0.07512	N	0.908973	T	0.49457	0.1558	L	0.36672	1.1	0.20926	N	0.999825	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.31081	-0.9956	10	0.19147	T	0.46	0.5688	9.8555	0.41084	0.3444:0.0:0.6556:0.0	.	180;264;283	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	S	283;264;180	ENSP00000380942:T283S;ENSP00000349056:T264S;ENSP00000432984:T180S	ENSP00000349056:T264S	T	+	1	0	ARHGEF12	119807753	0.955000	0.32602	0.204000	0.23530	0.953000	0.61014	0.177000	0.16801	0.083000	0.17047	-0.462000	0.05337	ACA	.		0.473	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120302543	A	T	120302543	3	4	103	1	0	0	0	0	1	0	0	0	897	43	2	5	889	5	ARHGEF12	11	120302543	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	3249750	120302543	14703973	86	9146											
FKBP4	2288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2910312	2910312	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggacagcaacaacgagaaGggcctcttccgccggggaga	11	4	14	12	3	1	2	0	0	1	2	2	5	2	3	3	4	3	1	3	4	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:2910312G>T	ENST00000001008.4	+	9	1249	c.1062G>T	c.(1060-1062)aaG>aaT	p.K354N	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	354	Interaction with tubulin. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			ACAACGAGAAGGGCCTCTTCC	0.562																																					p.K354N		.											.	FKBP4-226	0			c.G1062T						.						63	67	65					12																	2910312		2203	4300	6503	SO:0001583	missense	2288	exon9			CGAGAAGGGCCTC	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.1062G>T	12.37:g.2910312G>T	ENSP00000001008:p.Lys354Asn	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	108	30	NM_002014	0	0	61	115	54	D3DUQ1|Q9UCP1|Q9UCV7	Missense_Mutation	SNP	ENST00000001008.4	37	CCDS8512.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.450364	0.43531	.	.	ENSG00000004478	ENST00000001008	T	0.76709	-1.04	5.57	-2.51	0.06365	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.88366	0.6417	M	0.93106	3.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88372	0.2995	10	0.87932	D	0	-31.4957	12.5158	0.56032	0.5845:0.0:0.4155:0.0	.	354	Q02790	FKBP4_HUMAN	N	354	ENSP00000001008:K354N	ENSP00000001008:K354N	K	+	3	2	FKBP4	2780573	1.000000	0.71417	0.977000	0.42913	0.029000	0.11900	0.864000	0.27926	-0.395000	0.07715	0.561000	0.74099	AAG	.		0.562	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			T	2910312	G	T	2910312	3	4	103	1	0	0	0	0	1	0	0	0	5929	991	35	4	1096	4	FKBP4	12	2910312	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		2910312	130941583	87	9147											
STYK1	55359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	10780290	10780290	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atatacttgtttttctgtgaGatcatagagaagaccatcca	13	14	7	7	0	2	3	1	1	1	3	3	5	3	3	2	0	1	1	2	0	4	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:10780290G>C	ENST00000075503.3	-	7	1187	c.667C>G	c.(667-669)Ctc>Gtc	p.L223V		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	223	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						TTTTCTGTGAGATCATAGAGA	0.398										HNSCC(73;0.22)																											p.L223V		.											.	STYK1-1379	0			c.C667G						.						209	145	167					12																	10780290		2203	4300	6503	SO:0001583	missense	55359	exon7			CTGTGAGATCATA	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.667C>G	12.37:g.10780290G>C	ENSP00000075503:p.Leu223Val	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	77	24	NM_018423	0	0	0	0	0	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	37	CCDS8629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.34|13.34	2.207320|2.207320	0.39003|0.39003	.|.	.|.	ENSG00000060140|ENSG00000060140	ENST00000542924|ENST00000075503	.|T	.|0.74106	.|-0.81	5.11|5.11	3.25|3.25	0.37280|0.37280	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.092391	.|0.47093	.|D	.|0.000250	T|T	0.73305|0.73305	0.3570|0.3570	L|L	0.56340|0.56340	1.77|1.77	0.40939|0.40939	D|D	0.984457|0.984457	.|B	.|0.22080	.|0.064	.|B	.|0.35727	.|0.209	T|T	0.72640|0.72640	-0.4232|-0.4232	5|10	.|0.87932	.|D	.|0	-6.5489|-6.5489	12.1571|12.1571	0.54083|0.54083	0.0:0.0:0.6901:0.3098|0.0:0.0:0.6901:0.3098	.|.	.|223	.|Q6J9G0	.|STYK1_HUMAN	M|V	66|223	.|ENSP00000075503:L223V	.|ENSP00000075503:L223V	I|L	-|-	3|1	3|0	STYK1|STYK1	10671557|10671557	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.014000|2.014000	0.40951|0.40951	0.706000|0.706000	0.31912|0.31912	-0.181000|-0.181000	0.13052|0.13052	ATC|CTC	.		0.398	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423		C	10780290	G	C	10780290	3	2	103	1	0	0	0	0	1	0	0	0	15391	942	33	4	621	4	STYK1	12	10780290	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	7869978	10780290	123071605	88	9148											
BCL2L14	79370	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12232370	12232370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagcacccctgctctcttctCaccaaagctgctgagaacaa	11	8	7	15	0	2	1	1	1	2	1	4	3	2	1	3	0	5	4	3	0	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:12232370C>T	ENST00000308721.5	+	2	337	c.131C>T	c.(130-132)tCa>tTa	p.S44L	BCL2L14_ENST00000589718.1_Missense_Mutation_p.S44L|BCL2L14_ENST00000266434.4_Missense_Mutation_p.S44L|BCL2L14_ENST00000396367.1_Missense_Mutation_p.S44L|BCL2L14_ENST00000396369.1_Missense_Mutation_p.S44L|BCL2L14_ENST00000586576.1_Missense_Mutation_p.S77L	NM_138723.1	NP_620049.1	Q9BZR8	B2L14_HUMAN	BCL2-like 14 (apoptosis facilitator)	44					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular organelle (GO:0043229)|membrane (GO:0016020)	protein kinase binding (GO:0019901)			large_intestine(1)|lung(2)|skin(3)	6		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		GCTCTCTTCTCACCAAAGCTG	0.478																																					p.S44L													.	BCL2L14-227	0			c.C131T						.						76	72	73					12																	12232370		2203	4300	6503	SO:0001583	missense	79370	exon2			TCTTCTCACCAAA	AF281254	CCDS8645.1, CCDS8646.1	12p13-p12	2014-03-07			ENSG00000121380	ENSG00000121380			16657	protein-coding gene	gene with protein product		606126				11054413	Standard	NM_030766		Approved	BCLG, BCL-G	uc001rac.3	Q9BZR8	OTTHUMG00000159528	ENST00000308721.5:c.131C>T	12.37:g.12232370C>T	ENSP00000309132:p.Ser44Leu	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	72	9	NM_138723	0	0	0	0	0	A8KAD0|Q96QR5|Q9BZR7	Missense_Mutation	SNP	ENST00000308721.5	37	CCDS8645.1	.	.	.	.	.	.	.	.	.	.	C	19.87	3.907145	0.72868	.	.	ENSG00000121380	ENST00000464885;ENST00000461264;ENST00000308721;ENST00000266434;ENST00000396369;ENST00000396367	.	.	.	4.11	4.11	0.48088	.	0.287741	0.28317	N	0.015794	T	0.69958	0.3169	M	0.73962	2.25	0.30374	N	0.782577	D;D	0.89917	0.999;1.0	D;D	0.85130	0.982;0.997	T	0.69731	-0.5066	9	0.87932	D	0	-5.2904	12.1533	0.54062	0.0:1.0:0.0:0.0	.	44;44	Q9BZR8-2;Q9BZR8	.;B2L14_HUMAN	L	44;47;44;44;44;44	.	ENSP00000266434:S44L	S	+	2	0	BCL2L14	12123637	0.920000	0.31207	0.739000	0.30968	0.062000	0.15995	2.922000	0.48860	2.590000	0.87494	0.563000	0.77884	TCA	.		0.478	BCL2L14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355994.3	NM_030766		T	12232370	C	T	12232370	3	4	103	1	0	0	0	0	1	0	0	0	1373	838	29	2	133	2	BCL2L14	12	12232370	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	1452080	12232370	121619525	89	9149											
PLEKHA5	54477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	19506893	19506893	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcttcgacaatagcttcctAtgtaaccttgaggaaaacta	14	12	6	9	1	1	1	0	1	1	0	3	3	2	2	2	1	3	2	2	1	7	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:19506893A>G	ENST00000299275.6	+	20	2603	c.2597A>G	c.(2596-2598)tAt>tGt	p.Y866C	PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Y810C|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Y924C|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Y624C|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Y855C|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Y924C|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Y929C|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Y848C|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Y1032C	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	866					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ATAGCTTCCTATGTAACCTTG	0.368																																					p.Y1032C	Pancreas(196;329 2193 11246 14234 19524)	.											.	PLEKHA5-227	0			c.A3095G						.						125	119	121					12																	19506893		2203	4300	6503	SO:0001583	missense	54477	exon26			CTTCCTATGTAAC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2597A>G	12.37:g.19506893A>G	ENSP00000299275:p.Tyr866Cys	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	112	25	NM_001256470	0	0	8	20	12	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845797	0.71603	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	T;T;T;T;T;T;T;T;T;T;T	0.31247	2.93;2.93;1.5;2.93;2.93;2.93;2.93;2.93;2.93;2.93;1.5	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.80746	2.51	0.50813	D	0.999898	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.992;0.998;0.996;0.997;0.999;0.994;0.959;0.982	T	0.60105	-0.7328	10	0.41790	T	0.15	-12.8632	14.8567	0.70344	1.0:0.0:0.0:0.0	.	929;848;855;1027;810;1032;866;924	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;.;PKHA5_HUMAN;.	C	929;924;810;1028;1032;866;624;924;855;848;821;147	ENSP00000325155:Y929C;ENSP00000347560:Y924C;ENSP00000352104:Y810C;ENSP00000404296:Y1032C;ENSP00000299275:Y866C;ENSP00000440611:Y624C;ENSP00000439673:Y924C;ENSP00000400411:Y855C;ENSP00000439837:Y848C;ENSP00000440371:Y821C;ENSP00000443553:Y147C	ENSP00000299275:Y866C	Y	+	2	0	PLEKHA5	19398160	1.000000	0.71417	0.690000	0.30148	0.968000	0.65278	6.016000	0.70798	1.890000	0.54733	0.372000	0.22366	TAT	.		0.368	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19506893	A	G	19506893	3	3	103	1	0	0	0	0	1	0	0	0	12085	449	16	3	2993	3	PLEKHA5	12	19506893	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	7274523	19506893	114345002	90	9150											
SLC38A4	55089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	47178364	47178364	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatggaaacaaaagctccaaTttttcccggccatccaaatg	15	9	6	11	1	0	0	0	0	0	0	3	1	3	1	4	2	2	1	4	2	6	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:47178364T>A	ENST00000447411.1	-	6	660	c.454A>T	c.(454-456)Att>Ttt	p.I152F	SLC38A4_ENST00000266579.4_Missense_Mutation_p.I152F	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	152					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					AAAGCTCCAATTTTTCCCGGC	0.333																																					p.I152F		.											.	SLC38A4-93	0			c.A454T						.						109	107	107					12																	47178364		2203	4300	6503	SO:0001583	missense	55089	exon6			CTCCAATTTTTCC	AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"Solute carriers"	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.454A>T	12.37:g.47178364T>A	ENSP00000389843:p.Ile152Phe	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	175	26	NM_001143824	0	0	0	0	0	A8K553	Missense_Mutation	SNP	ENST00000447411.1	37	CCDS8750.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.242201	0.39598	.	.	ENSG00000139209	ENST00000395426;ENST00000447411;ENST00000266579;ENST00000547477;ENST00000546940	T;T;T;T	0.02421	4.3;4.3;4.3;4.3	6.07	4.9	0.64082	.	0.311957	0.37906	N	0.001896	T	0.03053	0.0090	L	0.33624	1.015	0.50813	D	0.999895	B	0.09022	0.002	B	0.15870	0.014	T	0.50898	-0.8773	10	0.27785	T	0.31	-8.8755	11.1795	0.48620	0.2577:0.0:0.0:0.7423	.	152	Q969I6	S38A4_HUMAN	F	152	ENSP00000389843:I152F;ENSP00000266579:I152F;ENSP00000450071:I152F;ENSP00000448543:I152F	ENSP00000266579:I152F	I	-	1	0	SLC38A4	45464631	1.000000	0.71417	0.996000	0.52242	0.736000	0.42039	3.555000	0.53727	1.067000	0.40740	0.533000	0.62120	ATT	.		0.333	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1			A	47178364	T	A	47178364	3	1	103	1	0	0	0	0	1	0	0	0	14638	1493	52	5	1233	5	SLC38A4	12	47178364	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	27671471	47178364	86673531	91	9151											
EIF4B	1975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53416313	53416313	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttggccgtgatagaaatcGggattctgacaaaacagata	14	11	10	6	2	1	4	0	2	1	2	2	5	1	5	1	2	1	0	1	2	5	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:53416313G>C	ENST00000262056.9	+	6	895	c.569G>C	c.(568-570)cGg>cCg	p.R190P	EIF4B_ENST00000416762.3_Missense_Mutation_p.R151P|RP11-983P16.4_ENST00000552905.1_RNA|EIF4B_ENST00000420463.3_Missense_Mutation_p.R190P	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	190	Arg-rich.|Asp-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						GATAGAAATCGGGATTCTGAC	0.418																																					p.R190P		.											.	EIF4B-568	0			c.G569C						.						133	112	119					12																	53416313		1863	4102	5965	SO:0001583	missense	1975	exon6			GAAATCGGGATTC	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.569G>C	12.37:g.53416313G>C	ENSP00000262056:p.Arg190Pro	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	114	16	NM_001417	2	0	445	555	108	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Missense_Mutation	SNP	ENST00000262056.9	37	CCDS41788.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124924	0.56613	.	.	ENSG00000063046	ENST00000262056;ENST00000551002;ENST00000420463;ENST00000430205;ENST00000416762;ENST00000552490	T;D;D;D;D	0.94232	0.54;-3.36;-3.36;-3.38;-3.36	3.59	2.7	0.31948	.	0.065726	0.53938	D	0.000044	D	0.87993	0.6318	L	0.27053	0.805	0.58432	D	0.999999	B;B;B	0.33807	0.426;0.301;0.301	B;B;B	0.36504	0.226;0.113;0.113	D	0.86321	0.1692	10	0.56958	D	0.05	.	10.7402	0.46149	0.0982:0.0:0.9018:0.0	.	151;190;190	B4DS13;E7EX17;P23588	.;.;IF4B_HUMAN	P	190;144;190;190;151;190	ENSP00000262056:R190P;ENSP00000447192:R144P;ENSP00000388806:R190P;ENSP00000412530:R151P;ENSP00000450324:R190P	ENSP00000262056:R190P	R	+	2	0	EIF4B	51702580	1.000000	0.71417	0.979000	0.43373	0.935000	0.57460	6.380000	0.73158	1.077000	0.40990	0.650000	0.86243	CGG	.		0.418	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		C	53416313	G	C	53416313	3	2	103	1	0	0	0	0	1	0	0	0	5040	1116	39	4	591	4	EIF4B	12	53416313	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	6237949	53416313	80435582	92	9152											
RAB5B	5869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56385887	56385887	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctttttatctctagctaagaAgttgccaaagagtgaacccc	12	12	7	10	0	1	3	0	1	1	2	2	3	1	3	3	0	3	2	3	0	6	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:56385887A>T	ENST00000360299.5	+	6	760	c.539A>T	c.(538-540)aAg>aTg	p.K180M	RAB5B_ENST00000553116.1_Missense_Mutation_p.K180M|RAB5B_ENST00000448789.2_Missense_Mutation_p.K139M	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	180					antigen processing and presentation (GO:0019882)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1)	9			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			CTAGCTAAGAAGTTGCCAAAG	0.507																																					p.K180M		.											.	RAB5B-227	0			c.A539T						.						59	60	60					12																	56385887		2203	4300	6503	SO:0001583	missense	5869	exon6			CTAAGAAGTTGCC		CCDS8900.1, CCDS58244.1	12q13	2008-07-30						"RAB, member RAS oncogene"	9784	protein-coding gene	gene with protein product		179514				1541686, 10403367	Standard	NM_001252037		Approved		uc001siw.3	P61020		ENST00000360299.5:c.539A>T	12.37:g.56385887A>T	ENSP00000353444:p.Lys180Met	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	105	35	NM_002868	0	0	1	1	0	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Missense_Mutation	SNP	ENST00000360299.5	37	CCDS8900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.65|16.65	3.183016|3.183016	0.57800|0.57800	.|.	.|.	ENSG00000111540|ENSG00000111540	ENST00000549218|ENST00000553116;ENST00000360299;ENST00000448789	.|T;T;T	.|0.80033	.|-1.17;-1.17;-1.33	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	.|0.080850	.|0.49916	.|D	.|0.000138	D|D	0.84710|0.84710	0.5532|0.5532	L|L	0.54863|0.54863	1.705|1.705	0.58432|0.58432	D|D	0.999999|0.999999	.|D;P;P	.|0.53619	.|0.961;0.55;0.911	.|P;P;P	.|0.57548	.|0.823;0.575;0.69	D|D	0.86486|0.86486	0.1794|0.1794	5|10	.|0.87932	.|D	.|0	-7.6032|-7.6032	14.1258|14.1258	0.65219|0.65219	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|139;180;180	.|B4DKD7;Q6FI54;P61020	.|.;.;RAB5B_HUMAN	D|M	99|180;180;139	.|ENSP00000450168:K180M;ENSP00000353444:K180M;ENSP00000391319:K139M	.|ENSP00000353444:K180M	E|K	+|+	3|2	2|0	RAB5B|RAB5B	54672154|54672154	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.605000|5.605000	0.67634|0.67634	2.236000|2.236000	0.73375|0.73375	0.529000|0.529000	0.55759|0.55759	GAA|AAG	.		0.507	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1			T	56385887	A	T	56385887	3	4	103	1	0	0	0	0	1	0	0	0	12981	72	3	5	557	5	RAB5B	12	56385887	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	2969574	56385887	77466008	93	9153											
GRIP1	23426	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	66765625	66765625	+	Frame_Shift_Del	DEL	A	A	-																															gcgagctgctgcgctcctggAagctggcctgtcgccccagc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:66765625delA	ENST00000398016.3	-	22	2773	c.2705delT	c.(2704-2706)ttcfs	p.F902fs	GRIP1_ENST00000359742.4_Frame_Shift_Del_p.F954fs|GRIP1_ENST00000286445.7_Frame_Shift_Del_p.F939fs	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GCGCTCCTGGAAGCTGGCCTG	0.552																																					p.F902fs		.											.	GRIP1-494	0			c.2705delT						.						86	94	91					12																	66765625		2074	4214	6288	SO:0001589	frameshift_variant	23426	exon22			.	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2705delT	12.37:g.66765625delA	ENSP00000381098:p.Phe902fs	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	202	34	NM_021150	0	0	0	0	0	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Frame_Shift_Del	DEL	ENST00000398016.3	37	CCDS41807.1																																																																																			.		0.552	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			-	66765625	A	-	66765625	7	5	103	1	0	1	0	1	0	0	0	0	6808	246	9	0	537	0	GRIP1	12	66765625	Frame_Shift_Del	DEL	A	TCGA-DZ-6132-01A-11D-1961-08	10379738	66765625	67086270	94	9154											
FGD6	55785	broad.mit.edu	37	chr12	95603626	95603626	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagattccttttgcatttgAggggcagaaactcccaggtt	10	12	10	9	0	0	3	0	1	0	2	2	3	2	3	2	3	2	3	2	3	1	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:95603626A>G	ENST00000343958.4	-	2	1657	c.1434T>C	c.(1432-1434)ccT>ccC	p.P478P	FGD6_ENST00000546711.1_Silent_p.P478P|FGD6_ENST00000549499.1_Silent_p.P478P|FGD6_ENST00000550368.1_5'Flank	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	478					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						TTTGCATTTGAGGGGCAGAAA	0.393																																					p.P478P													.	FGD6-137	0			c.T1434C						.						64	68	66					12																	95603626		2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			CATTTGAGGGGCA	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1434T>C	12.37:g.95603626A>G		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	119	3	NM_018351	0	0	5	5	0	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																			.		0.393	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		G	95603626	A	G	95603626	2	3	103	1	0	0	0	0	0	0	0	1	5856	291	11	3		3	FGD6	12	95603626	Silent	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	28838001	95603626	38248269	95	9155											
CCDC38	120935	hgsc.bcm.edu;broad.mit.edu	37	chr12	96273432	96273432	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgacttacgttttatcctGtataactttttctcttttgt	8	22	4	7	1	1	1	0	1	1	0	3	1	2	1	1	0	2	2	1	0	5	9			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:96273432G>A	ENST00000344280.3	-	12	1689	c.1132C>T	c.(1132-1134)Cag>Tag	p.Q378*	SNRPF_ENST00000553192.1_Intron|SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	378										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTTTTATCCTGTATAACTTTT	0.368																																					p.Q378X		.											.	CCDC38-91	0			c.C1132T						.						156	150	152					12																	96273432		2203	4300	6503	SO:0001587	stop_gained	120935	exon12			TATCCTGTATAAC	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.1132C>T	12.37:g.96273432G>A	ENSP00000345470:p.Gln378*	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	100	19	NM_182496	0	0	0	0	0	Q8N835	Nonsense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889426	0.91889	.	.	ENSG00000165972	ENST00000344280	.	.	.	5.99	2.85	0.33270	.	0.690505	0.14783	N	0.298696	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-11.1569	11.1809	0.48627	0.0:0.1217:0.6268:0.2514	.	.	.	.	X	378	.	ENSP00000345470:Q378X	Q	-	1	0	CCDC38	94797563	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.645000	0.37238	1.549000	0.49425	-0.330000	0.08379	CAG	.		0.368	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496		A	96273432	G	A	96273432	4	1	103	1	0	0	0	0	0	1	0	0	2816	1386	48	2	579	2	CCDC38	12	96273432	Nonsense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	669806	96273432	37578463	96	9156											
TRPC4	7223	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	38237841	38237841	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatgccacatgtcccatGattctcgtggattaagggca	9	11	12	9	1	1	1	0	1	1	0	3	3	2	3	2	3	1	1	2	3	1	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:38237841G>T	ENST00000379705.3	-	6	2257	c.1400C>A	c.(1399-1401)tCa>tAa	p.S467*	TRPC4_ENST00000494529.1_5'UTR|TRPC4_ENST00000379679.1_Nonsense_Mutation_p.S294*|TRPC4_ENST00000379673.2_Nonsense_Mutation_p.S467*|TRPC4_ENST00000355779.2_Nonsense_Mutation_p.S467*|TRPC4_ENST00000379681.3_Nonsense_Mutation_p.S467*|TRPC4_ENST00000358477.2_Nonsense_Mutation_p.S467*|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000447043.1_Nonsense_Mutation_p.S467*|TRPC4_ENST00000338947.5_Nonsense_Mutation_p.S294*			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	467					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.S467L(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CATGTCCCATGATTCTCGTGG	0.423																																					p.S467X													.	TRPC4-159	2	Substitution - Missense(2)	lung(2)	c.C1400A						.						43	43	43					13																	38237841		2203	4300	6503	SO:0001587	stop_gained	7223	exon6			TCCCATGATTCTC	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.1400C>A	13.37:g.38237841G>T	ENSP00000369027:p.Ser467*	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	34	7	NM_003306	0	0	1	1	0	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Nonsense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	G	37	6.446819	0.97572	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	.	.	.	5.45	4.55	0.56014	.	0.671651	0.16287	N	0.221062	.	.	.	.	.	.	0.19300	N	0.99997	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	-11.8501	8.9999	0.36074	0.0:0.2072:0.6524:0.1405	.	.	.	.	X	467;467;294;294;467;467;467;467	.	ENSP00000342580:S294X	S	-	2	0	TRPC4	37135841	0.000000	0.05858	0.954000	0.39281	0.956000	0.61745	0.946000	0.29069	2.706000	0.92434	0.655000	0.94253	TCA	.		0.423	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		T	38237841	G	T	38237841	4	4	103	1	0	0	0	0	0	1	0	0	16613	1294	45	4	1572	4	TRPC4	13	38237841	Nonsense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		38237841	76932037	97	9157											
RCBTB1	55213	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	50115836	50115836	+	Frame_Shift_Del	DEL	C	C	-																															agcatcttctggcggcaggtCgactgtgtctgtgtagaggt																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:50115836delC	ENST00000378302.2	-	11	1560	c.1300delG	c.(1300-1302)gacfs	p.D434fs	RCBTB1_ENST00000258646.3_Frame_Shift_Del_p.D434fs|RCBTB1_ENST00000471984.1_5'Flank	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	434	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GGCGGCAGGTCGACTGTGTCT	0.458																																					p.D434fs		.											.	RCBTB1-91	0			c.1300delG						.						156	116	130					13																	50115836		2203	4300	6503	SO:0001589	frameshift_variant	55213	exon11			.	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"BTB/POZ domain containing"	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.1300delG	13.37:g.50115836delC	ENSP00000367552:p.Asp434fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	86	15	NM_018191	0	0	0	0	0	Q8IY29|Q969U9	Frame_Shift_Del	DEL	ENST00000378302.2	37	CCDS9418.1																																																																																			.		0.458	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191		-	50115836	C	-	50115836	7	5	103	1	0	1	0	1	0	0	0	0	13203	884	31	0	307	0	RCBTB1	13	50115836	Frame_Shift_Del	DEL	C	TCGA-DZ-6132-01A-11D-1961-08	11877995	50115836	65054042	98	9158	97	2									
RCBTB1	55213	bcgsc.ca	37	chr13	50115837	50115837	+	Silent	SNP	G	G	A																															gcatcttctggcggcaggtcGactgtgtctgtgtagaggta																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:50115837G>A	ENST00000378302.2	-	11	1559	c.1299C>T	c.(1297-1299)gtC>gtT	p.V433V	RCBTB1_ENST00000258646.3_Silent_p.V433V|RCBTB1_ENST00000471984.1_5'Flank	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	433	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GCGGCAGGTCGACTGTGTCTG	0.458																																					p.V433V													.	RCBTB1-91	0			c.C1299T						.						156	117	130					13																	50115837		2203	4300	6503	SO:0001819	synonymous_variant	55213	exon11			CAGGTCGACTGTG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"BTB/POZ domain containing"	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.1299C>T	13.37:g.50115837G>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_1	84	17	NM_018191	0	0	11	11	0	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			.		0.458	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191		A	50115837	G	A	50115837	2	1	103	1	0	0	0	0	0	0	0	1	13203	1045	37	1		1	RCBTB1	13	50115837	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1	50115837	65054041	99	9159	97	2									
GPR180	160897	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	95271585	95271585	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aattacattcatttctccagGtaactcaaaaccactaaaac	17	11	2	11	0	3	0	2	0	1	0	4	0	3	0	2	1	4	1	2	1	7	5	rs138676753		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:95271585G>A	ENST00000376958.4	+	4	711		c.e4+1			NM_180989.5	NP_851320.1	Q86V85	GP180_HUMAN	G protein-coupled receptor 180						G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	10	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					ATTTCTCCAGGTAACTCAAAA	0.338																																					.													.	GPR180-153	0			c.686+1G>A						.						125	122	123					13																	95271585		2203	4300	6503	SO:0001630	splice_region_variant	160897	exon4			CTCCAGGTAACTC	AF339823	CCDS9472.1	13q32.1	2006-04-05			ENSG00000152749	ENSG00000152749			28899	protein-coding gene	gene with protein product	"intimal thickness related receptor"	607787				12538434	Standard	NM_180989		Approved	ITR	uc001vly.3	Q86V85	OTTHUMG00000017207	ENST00000376958.4:c.686+1G>A	13.37:g.95271585G>A		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	83	9	NM_180989	0	0	0	0	0	A8K1D5	Splice_Site	SNP	ENST00000376958.4	37	CCDS9472.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575779	0.86645	.	.	ENSG00000152749	ENST00000376958	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0784	0.97758	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR180	94069586	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.048000	0.93830	2.736000	0.93811	0.655000	0.94253	.	G|1.000;C|0.000		0.338	GPR180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045465.3	NM_180989	Intron	A	95271585	G	A	95271585	5	1	103	1	0	0	0	0	0	0	1	0	6696	1275	44	2	701	2	GPR180	13	95271585	Splice_Site	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	45155748	95271585	19898293	100	9160											
BIVM	54841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	103492131	103492131	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgctagtttccatcaggaCtcggcatggaaaaagatgtc	12	10	11	8	1	1	1	1	0	0	1	4	3	2	3	1	3	1	3	1	3	3	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:103492131C>G	ENST00000257336.1	+	11	2107	c.1428C>G	c.(1426-1428)gaC>gaG	p.D476E	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.L448V|BIVM_ENST00000419638.1_3'UTR|BIVM_ENST00000448849.2_Missense_Mutation_p.D254E	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	476						cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|skin(2)|urinary_tract(1)	25	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TCCATCAGGACTCGGCATGGA	0.468																																					p.D476E		.											.	.	0			c.C1428G						.						154	144	147					13																	103492131		2203	4300	6503	SO:0001583	missense	0	exon9			TCAGGACTCGGCA	AF411385	CCDS9505.1, CCDS53879.1	13q33.1	2008-05-14			ENSG00000134897	ENSG00000134897			16034	protein-coding gene	gene with protein product						12036287	Standard	NM_017693		Approved	FLJ20159		Q86UB2	OTTHUMG00000017309	ENST00000257336.1:c.1428C>G	13.37:g.103492131C>G	ENSP00000257336:p.Asp476Glu	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	164	30	NM_001204425	0	0	50	87	37	Q2M1J2|Q9NXM4	Missense_Mutation	SNP	ENST00000257336.1	37	CCDS9505.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.437445	0.01098	.	.	ENSG00000134897;ENSG00000134897;ENSG00000134899	ENST00000257336;ENST00000448849;ENST00000418659	.	.	.	5.4	-0.762	0.11034	.	0.188352	0.45606	D	0.000360	T	0.03651	0.0104	N	0.00347	-1.61	0.19300	N	0.999976	B;B;B	0.21606	0.0;0.058;0.005	B;B;B	0.17098	0.001;0.017;0.004	T	0.35624	-0.9781	9	0.02654	T	1	-13.3799	2.8027	0.05419	0.0935:0.3232:0.301:0.2823	.	254;447;476	Q86UB2-2;Q59FZ7;Q86UB2	.;.;BIVM_HUMAN	E	476;254;447	.	ENSP00000257336:D476E	D	+	3	2	ERCC5;BIVM	102290132	0.097000	0.21791	0.768000	0.31515	0.791000	0.44710	-0.250000	0.08830	-0.183000	0.10585	-1.255000	0.01485	GAC	.		0.468	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2			G	103492131	C	G	103492131	3	3	103	1	0	0	0	0	1	0	0	0	1442	564	20	4	1483	4	BIVM	13	103492131	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	8220546	103492131	11677747	101	9161											
KTN1	3895	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	56079010	56079010	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgactctgagagtgtacctCgagactttaaattatcagat	12	12	8	9	2	2	3	1	1	1	3	3	6	2	3	2	0	1	1	2	0	4	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr14:56079010C>A	ENST00000395314.3	+	2	312	c.244C>A	c.(244-246)Cga>Aga	p.R82R	KTN1_ENST00000438792.2_Silent_p.R82R|KTN1_ENST00000395309.3_Silent_p.R82R|KTN1_ENST00000395308.1_Silent_p.R82R|KTN1_ENST00000413890.2_Silent_p.R82R|KTN1_ENST00000416613.1_Silent_p.R82R|KTN1_ENST00000395311.1_Silent_p.R82R	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	82					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						GAGTGTACCTCGAGACTTTAA	0.363			T	RET	papillary thryoid																																p.R82R				Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1-1147	0			c.C244A						.						74	78	77					14																	56079010		2203	4300	6503	SO:0001819	synonymous_variant	3895	exon2			GTACCTCGAGACT		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.244C>A	14.37:g.56079010C>A		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	92	19	NM_004986	0	0	20	54	34	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			.		0.363	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			A	56079010	C	A	56079010	2	1	103	1	0	0	0	0	0	0	0	1	8606	876	31	4		4	KTN1	14	56079010	Silent	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		56079010	51270530	102	9162											
ANPEP	290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90349567	90349567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcgtcacccggtaggaaTcgggtttcagcgtgttgggg	6	10	16	9	4	3	0	3	0	0	0	4	1	3	1	1	5	2	3	1	5	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr15:90349567T>C	ENST00000300060.6	-	2	561	c.248A>G	c.(247-249)gAt>gGt	p.D83G		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	83	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CCGGTAGGAATCGGGTTTCAG	0.617																																					p.D83G	NSCLC(30;827 977 2459 19669 26125)	.											.	ANPEP-94	0			c.A248G						.						126	102	110					15																	90349567		2200	4299	6499	SO:0001583	missense	290	exon2			TAGGAATCGGGTT	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.248A>G	15.37:g.90349567T>C	ENSP00000300060:p.Asp83Gly	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	85	18	NM_001150	0	0	94	95	1	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	T	6.216	0.408075	0.11754	.	.	ENSG00000166825	ENST00000300060	T	0.02631	4.22	4.74	0.264	0.15607	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	2.111890	0.01982	N	0.044922	T	0.06096	0.0158	M	0.73962	2.25	0.09310	N	1	B	0.26672	0.156	B	0.33121	0.158	T	0.46359	-0.9197	10	0.23891	T	0.37	.	4.6468	0.12575	0.3933:0.0958:0.0:0.5109	.	83	P15144	AMPN_HUMAN	G	83	ENSP00000300060:D83G	ENSP00000300060:D83G	D	-	2	0	ANPEP	88150571	0.000000	0.05858	0.011000	0.14972	0.152000	0.21847	0.560000	0.23500	0.163000	0.19507	0.383000	0.25322	GAT	.		0.617	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90349567	T	C	90349567	3	2	103	1	0	0	0	0	1	0	0	0	710	1435	50	3	2735	3	ANPEP	15	90349567	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		90349567	12181825	103	9163											
SV2B	9899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	91769497	91769497	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agtcgcagaaccaaggaatgGatgactacaagtatcaggac	16	6	11	8	1	1	2	1	1	0	1	2	5	1	5	1	3	2	2	1	3	6	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr15:91769497G>C	ENST00000394232.1	+	2	474	c.4G>C	c.(4-6)Gat>Cat	p.D2H	SV2B_ENST00000330276.4_Missense_Mutation_p.D2H|SV2B_ENST00000545111.2_Intron|SV2B_ENST00000557291.1_Intron	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	2					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CCAAGGAATGGATGACTACAA	0.478																																					p.D2H		.											.	SV2B-97	0			c.G4C						.						72	58	63					15																	91769497		2198	4298	6496	SO:0001583	missense	9899	exon3			GGAATGGATGACT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.4G>C	15.37:g.91769497G>C	ENSP00000377779:p.Asp2His	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	44	12	NM_014848	0	0	1	1	0	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469419	0.63625	.	.	ENSG00000185518	ENST00000394232;ENST00000330276	T;T	0.64803	-0.12;-0.12	5.71	4.79	0.61399	.	0.237482	0.42821	D	0.000651	T	0.65249	0.2673	M	0.68317	2.08	0.48830	D	0.999714	P	0.37015	0.578	B	0.41988	0.372	T	0.69007	-0.5259	10	0.72032	D	0.01	-15.0004	13.3113	0.60382	0.077:0.0:0.923:0.0	.	2	Q7L1I2	SV2B_HUMAN	H	2	ENSP00000377779:D2H;ENSP00000332818:D2H	ENSP00000332818:D2H	D	+	1	0	SV2B	89570501	1.000000	0.71417	0.999000	0.59377	0.874000	0.50279	7.523000	0.81856	1.411000	0.46957	0.563000	0.77884	GAT	.		0.478	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		C	91769497	G	C	91769497	3	2	103	1	0	0	0	0	1	0	0	0	15450	1174	41	4	6	4	SV2B	15	91769497	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1419930	91769497	10761895	104	9164											
LMF1	64788	hgsc.bcm.edu	37	chr16	1004476	1004476	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccagtccgagaagagccagCaagtccaggttggagttcat	11	7	12	11	1	1	2	1	0	0	2	3	4	3	3	4	2	2	3	4	2	2	2	rs115313199	byFrequency	TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr16:1004476C>G	ENST00000262301.11	-	2	402	c.384G>C	c.(382-384)ttG>ttC	p.L128F	LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000399843.2_Missense_Mutation_p.L128F|LMF1_ENST00000539379.1_Missense_Mutation_p.L121F|LMF1_ENST00000543238.1_Intron	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	128					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				GAAGAGCCAGCAAGTCCAGGT	0.572													C|||	17	0.00339457	0.0129	0	5008	,	,		20549	0		0	False		,,,				2504	0				p.L128F		.											.	LMF1-90	0			c.G384C						.	C	PHE/LEU	39,4147		0,39,2054	53	56	55		384	-6.8	0	16	dbSNP_132	55	0,8430		0,0,4215	yes	missense	LMF1	NM_022773.2	22	0,39,6269	GG,GC,CC		0.0,0.9317,0.3091	benign	128/568	1004476	39,12577	2093	4215	6308	SO:0001583	missense	64788	exon2			AGCCAGCAAGTCC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"chromosome 16 open reading frame 26", "transmembrane protein 112"	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.384G>C	16.37:g.1004476C>G	ENSP00000262301:p.Leu128Phe	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	24	6	NM_022773	0	0	20	31	11	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	37	CCDS45373.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	0.528	-0.859205	0.02610	0.009317	0.0	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000539151;ENST00000539379	T;T;T	0.51817	2.3;2.29;0.69	5.56	-6.78	0.01721	.	1.259970	0.05289	N	0.520773	T	0.14098	0.0341	L	0.43701	1.375	0.09310	N	1	P	0.36392	0.551	B	0.30179	0.112	T	0.16188	-1.0411	10	0.10111	T	0.7	-23.3338	4.3889	0.11330	0.1188:0.3332:0.3649:0.183	.	128	Q96S06	LMF1_HUMAN	F	128;128;128;121	ENSP00000262301:L128F;ENSP00000382737:L128F;ENSP00000446322:L121F	ENSP00000262301:L128F	L	-	3	2	LMF1	944477	0.031000	0.19500	0.000000	0.03702	0.001000	0.01503	0.367000	0.20382	-0.830000	0.04262	-0.165000	0.13383	TTG	C|0.996;G|0.004		0.572	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773		G	1004476	C	G	1004476	3	3	103	1	0	0	0	0	1	0	0	0	8868	709	25	4	1359	4	LMF1	16	1004476	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		1004476	89350277	105	9165											
RBBP6	5930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	24582943	24582943	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaataaaccaagggaagagaGagatttgcctaaaaaaggaa	22	5	10	4	0	0	2	0	0	0	2	0	6	0	4	2	2	2	0	2	2	9	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr16:24582943G>C	ENST00000319715.4	+	18	4988	c.4556G>C	c.(4555-4557)aGa>aCa	p.R1519T	RBBP6_ENST00000381039.3_Missense_Mutation_p.R679T|RBBP6_ENST00000348022.2_Missense_Mutation_p.R1485T	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1519	Interaction with p53. {ECO:0000250}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		AGGGAAGAGAGAGATTTGCCT	0.358																																					p.R1519T		.											.	RBBP6-230	0			c.G4556C						.						40	39	39					16																	24582943		2197	4298	6495	SO:0001583	missense	5930	exon18			AAGAGAGAGATTT		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.4556G>C	16.37:g.24582943G>C	ENSP00000317872:p.Arg1519Thr	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	45	8	NM_006910	0	0	18	24	6	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805084	0.50315	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.19105	2.17;2.4;2.41	6.03	1.9	0.25705	.	0.190657	0.41396	D	0.000897	T	0.12475	0.0303	L	0.27053	0.805	0.27887	N	0.939455	P;B;B	0.39480	0.675;0.241;0.155	B;B;B	0.35550	0.205;0.148;0.071	T	0.12502	-1.0545	10	0.30078	T	0.28	-17.338	10.6299	0.45530	0.2533:0.0:0.7467:0.0	.	679;1485;1519	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	T	679;1519;1485	ENSP00000370427:R679T;ENSP00000317872:R1519T;ENSP00000316291:R1485T	ENSP00000317872:R1519T	R	+	2	0	RBBP6	24490444	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	3.017000	0.49615	0.428000	0.26173	0.557000	0.71058	AGA	.		0.358	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		C	24582943	G	C	24582943	3	2	103	1	0	0	0	0	1	0	0	0	13135	942	33	4	4680	4	RBBP6	16	24582943	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	23578467	24582943	65771810	106	9166											
RPGRIP1L	23322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	53691402	53691402	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtgttgcataattagcAtgtttcttgtcttttccagc	6	21	7	7	0	2	0	0	0	2	0	3	0	3	0	1	0	3	4	1	0	2	9			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr16:53691402A>G	ENST00000379925.3	-	13	1594	c.1544T>C	c.(1543-1545)aTg>aCg	p.M515T	RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.M515T|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.M515T|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.M515T	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	515					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CATAATTAGCATGTTTCTTGT	0.313																																					p.M515T		.											.	RPGRIP1L-91	0			c.T1544C						.						88	81	83					16																	53691402		2196	4300	6496	SO:0001583	missense	23322	exon13			ATTAGCATGTTTC		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.1544T>C	16.37:g.53691402A>G	ENSP00000369257:p.Met515Thr	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	89	17	NM_001127897	0	0	3	5	2	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138906	0.77775	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;D	0.81579	-0.02;-1.51	6.04	6.04	0.98038	.	0.099515	0.64402	D	0.000001	D	0.87834	0.6277	M	0.72118	2.19	0.80722	D	1	D;D;D;D	0.76494	0.972;0.972;0.972;0.999	P;P;P;D	0.68765	0.632;0.706;0.706;0.96	D	0.86184	0.1608	10	0.30078	T	0.28	-18.3503	14.8183	0.70052	1.0:0.0:0.0:0.0	.	515;515;515;515	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	T	515	ENSP00000369257:M515T;ENSP00000262135:M515T	ENSP00000262135:M515T	M	-	2	0	RPGRIP1L	52248903	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.353000	0.90077	2.317000	0.78254	0.460000	0.39030	ATG	.		0.313	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		G	53691402	A	G	53691402	3	3	103	1	0	0	0	0	1	0	0	0	13582	217	8	3	2463	3	RPGRIP1L	16	53691402	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	29108459	53691402	36663351	107	9167											
ADAP2	55803	hgsc.bcm.edu;broad.mit.edu	37	chr17	29261211	29261211	+	Frame_Shift_Del	DEL	G	G	-																															ttgctgcttaaggtaaccgaGaaggattcctgtggaagcga																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:29261211delG	ENST00000330889.3	+	5	741	c.406delG	c.(406-408)gaafs	p.E136fs	ADAP2_ENST00000580525.1_Frame_Shift_Del_p.E142fs	NM_018404.2	NP_060874.1	Q9NPF8	ADAP2_HUMAN	ArfGAP with dual PH domains 2	136	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				heart development (GO:0007507)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|mitochondrial envelope (GO:0005740)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						AGGTAACCGAGAAGGATTCCT	0.478																																					p.E136fs		.											.	ADAP2-91	1	Unknown(1)	central_nervous_system(1)	c.406delG						.						96	80	85					17																	29261211		2203	4300	6503	SO:0001589	frameshift_variant	55803	exon5			.	AJ238994	CCDS11261.1	17q11.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000184060	ENSG00000184060		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16487	protein-coding gene	gene with protein product		608635	"centaurin, alpha 2"	CENTA2			Standard	XM_005258008		Approved		uc002hfx.3	Q9NPF8	OTTHUMG00000132868	ENST00000330889.3:c.406delG	17.37:g.29261211delG	ENSP00000329468:p.Glu136fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	59	10	NM_018404	0	0	0	0	0	Q8N4Q6|Q96SD5	Frame_Shift_Del	DEL	ENST00000330889.3	37	CCDS11261.1																																																																																			.		0.478	ADAP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256346.1	NM_018404		-	29261211	G	-	29261211	7	5	103	1	0	1	0	1	0	0	0	0	280	943	33	0	424	0	ADAP2	17	29261211	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08		29261211	51933999	108	9168											
AP2B1	163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	33966737	33966737	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgacaatgcagatgagttActagaaagcttcctggaggg	13	10	12	6	0	0	4	0	2	0	2	1	5	1	5	1	2	3	3	1	2	4	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:33966737A>C	ENST00000262325.7	+	11	1948	c.1395A>C	c.(1393-1395)ttA>ttC	p.L465F	AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000589344.1_Missense_Mutation_p.L465F|AP2B1_ENST00000592545.1_Missense_Mutation_p.L427F|AP2B1_ENST00000538556.1_Missense_Mutation_p.L408F|AP2B1_ENST00000537622.2_Missense_Mutation_p.L465F|AP2B1_ENST00000312678.8_Missense_Mutation_p.L465F	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	465					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CAGATGAGTTACTAGAAAGCT	0.433																																					p.L465F		.											.	AP2B1-91	0			c.A1395C						.						113	110	111					17																	33966737		2203	4300	6503	SO:0001583	missense	163	exon11			TGAGTTACTAGAA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1395A>C	17.37:g.33966737A>C	ENSP00000262325:p.Leu465Phe	Somatic	97	1		WXS	Illumina HiSeq	Phase_I	117	28	NM_001282	0	0	69	131	62	A6NJP3|P21851|Q7Z451|Q96J19	Missense_Mutation	SNP	ENST00000262325.7	37	CCDS32622.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.930330	0.73327	.	.	ENSG00000006125	ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622;ENST00000545922	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.46	1.82	0.25136	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.47060	0.1425	M	0.81942	2.565	0.80722	D	1	D;P;P;P	0.89917	1.0;0.576;0.905;0.613	D;P;B;B	0.81914	0.995;0.457;0.397;0.153	T	0.45687	-0.9244	10	0.51188	T	0.08	-0.0246	1.588	0.02648	0.5463:0.168:0.1231:0.1627	.	202;427;465;465	F5GYG9;B4DWG4;P63010;P63010-2	.;.;AP2B1_HUMAN;.	F	465;465;408;465;202	ENSP00000262325:L465F;ENSP00000314414:L465F;ENSP00000440563:L408F;ENSP00000437413:L465F	ENSP00000262325:L465F	L	+	3	2	AP2B1	30990850	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.991000	0.40727	0.954000	0.37851	0.533000	0.62120	TTA	.		0.433	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			C	33966737	A	C	33966737	3	2	103	1	0	0	0	0	1	0	0	0	741	388	14	5	1433	5	AP2B1	17	33966737	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	4705526	33966737	47228473	109	9169											
CBX1	10951	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	46152378	46152378	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgactcaccatttcatcaGgaacatgagctctccactgg	10	9	8	14	1	4	1	3	1	1	0	5	3	4	2	3	2	2	1	3	2	1	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:46152378G>A	ENST00000393408.3	-	4	883	c.403C>T	c.(403-405)Ctg>Ttg	p.L135L	CBX1_ENST00000225603.4_Silent_p.L135L|CBX1_ENST00000495350.1_Silent_p.L135L	NM_006807.4	NP_006798.1	P83916	CBX1_HUMAN	chromobox homolog 1	135	Chromo 2; shadow subtype. {ECO:0000255|PROSITE-ProRule:PRU00053}.				negative regulation of transcription, DNA-templated (GO:0045892)	chromatin (GO:0000785)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|pericentric heterochromatin (GO:0005721)|spindle (GO:0005819)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)			breast(1)|central_nervous_system(1)|kidney(1)|prostate(1)	4						CATTTCATCAGGAACATGAGC	0.483																																					p.L135L	NSCLC(136;694 2497 38792 39034)	.											.	CBX1-226	0			c.C403T						.						137	138	138					17																	46152378		2203	4300	6503	SO:0001819	synonymous_variant	10951	exon4			TCATCAGGAACAT	U35451	CCDS11525.1	17q21.32	2010-07-06	2010-06-24		ENSG00000108468	ENSG00000108468			1551	protein-coding gene	gene with protein product	"HP1 beta homolog (Drosophila )"	604511	"chromobox homolog 1 (Drosophila HP1 beta)"			9169582	Standard	NM_001127228		Approved	HP1Hs-beta, M31, MOD1, CBX, HP1-BETA	uc002ind.4	P83916	OTTHUMG00000150417	ENST00000393408.3:c.403C>T	17.37:g.46152378G>A		Somatic	273	0		WXS	Illumina HiSeq	Phase_I	268	62	NM_006807	0	0	0	0	0	P23197	Silent	SNP	ENST00000393408.3	37	CCDS11525.1																																																																																			.		0.483	CBX1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318016.1	NM_006807		A	46152378	G	A	46152378	2	1	103	1	0	0	0	0	0	0	0	1	2723	991	35	2		2	CBX1	17	46152378	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	12185641	46152378	35042832	110	9170											
MTMR4	9110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	56572475	56572475	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaggggagtccatcatcatCcaaatacagaggaggcactg	15	6	11	9	0	2	1	2	0	0	1	4	3	4	3	2	4	1	1	2	4	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:56572475C>T	ENST00000323456.5	-	16	3152	c.3028G>A	c.(3028-3030)Gat>Aat	p.D1010N	MTMR4_ENST00000579925.1_Missense_Mutation_p.D953N	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	1010					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCATCATCATCCAAATACAGA	0.512																																					p.D1010N		.											.	MTMR4-91	0			c.G3028A						.						204	179	187					17																	56572475		2203	4300	6503	SO:0001583	missense	9110	exon16			CATCATCCAAATA	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.3028G>A	17.37:g.56572475C>T	ENSP00000325285:p.Asp1010Asn	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	214	58	NM_004687	0	0	8	12	4	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	37	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689025	0.88735	.	.	ENSG00000108389	ENST00000323456	D	0.96885	-4.16	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.97626	0.9222	L	0.58101	1.795	0.48452	D	0.999659	D	0.89917	1.0	D	0.85130	0.997	D	0.98181	1.0457	10	0.66056	D	0.02	.	18.5538	0.91075	0.0:1.0:0.0:0.0	.	1010	Q9NYA4	MTMR4_HUMAN	N	1010	ENSP00000325285:D1010N	ENSP00000325285:D1010N	D	-	1	0	MTMR4	53927474	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.104000	0.77024	2.627000	0.88993	0.555000	0.69702	GAT	.		0.512	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		T	56572475	C	T	56572475	3	4	103	1	0	0	0	0	1	0	0	0	9971	855	30	2	575	2	MTMR4	17	56572475	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	10420097	56572475	24622735	111	9171											
CLTC	1213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	57771125	57771125	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgacagcaggacccagtgTtgccgtccctccccaggcac	7	6	11	17	1	0	1	0	1	0	0	2	2	2	2	5	2	2	4	5	2	0	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:57771125T>C	ENST00000269122.3	+	32	5214	c.4940T>C	c.(4939-4941)gTt>gCt	p.V1647A	CLTC_ENST00000579456.1_Missense_Mutation_p.V584A	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1647	Heavy chain arm.|Proximal segment.|Trimerization. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GGACCCAGTGTTGCCGTCCCT	0.557			T	"ALK, TFE3"	"ALCL, renal "																																p.V1647A		.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC-835	0			c.T4940C						.						144	116	125					17																	57771125		2203	4300	6503	SO:0001583	missense	1213	exon32			CCAGTGTTGCCGT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.4940T>C	17.37:g.57771125T>C	ENSP00000269122:p.Val1647Ala	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	144	55	NM_004859	0	0	180	293	113	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.923961	0.34002	.	.	ENSG00000141367	ENST00000269122	T	0.10668	2.85	6.08	6.08	0.98989	.	0.052581	0.85682	D	0.000000	T	0.07728	0.0194	N	0.14661	0.345	0.80722	D	1	B	0.13145	0.007	B	0.12156	0.007	T	0.36212	-0.9757	10	0.14252	T	0.57	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	1647	Q00610	CLH1_HUMAN	A	1647	ENSP00000269122:V1647A	ENSP00000269122:V1647A	V	+	2	0	CLTC	55125907	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.162000	0.71874	2.333000	0.79357	0.533000	0.62120	GTT	.		0.557	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		C	57771125	T	C	57771125	3	2	103	1	0	0	0	0	1	0	0	0	3572	1725	60	3	5066	3	CLTC	17	57771125	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	1198650	57771125	23424085	112	9172											
INTS2	57508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	59945081	59945082	+	In_Frame_Ins	INS	-	-	GAA																															tggtttctcctttatttgttINSgaagacctacaacataaggg																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:59945081_59945082insGAA	ENST00000444766.3	-	25	3526_3527	c.3451_3452insTTC	c.(3451-3453)caa>cTTCaa	p.1150_1151insL	INTS2_ENST00000251334.6_In_Frame_Ins_p.1142_1143insL	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1150					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						CTTTATTTGTTGAAGACCTACA	0.351																																					p.Q1151delinsLQ		.											.	INTS2-206	0			c.3452_3453insTTC						.																																			SO:0001652	inframe_insertion	57508	exon25			.	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.3449_3451dupTTC	17.37:g.59945082_59945084dupGAA	ENSP00000414237:p.Leu1150_Leu1150dup	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	132	27	NM_020748	0	0	0	0	0	Q9ULD3	In_Frame_Ins	INS	ENST00000444766.3	37	CCDS45750.1																																																																																			.		0.351	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		GAA	59945082	-	GAA	59945081	7	5	103	1	0	1	1	0	0	0	0	0	7799	1812	63	0	166	0	INTS2	17	59945081	In_Frame_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	2173956	59945081	21250129	113	9173											
ACE	1636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61570904	61570904	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agacttacctgtggccttgaGggagggtgccaaccccggct	7	8	14	12	1	0	2	0	1	0	1	0	3	0	3	5	4	3	1	5	4	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:61570904G>T	ENST00000290866.4	+	20	3044	c.3020G>T	c.(3019-3021)aGg>aTg	p.R1007M	ACE_ENST00000490216.2_Missense_Mutation_p.R433M|ACE_ENST00000577647.1_Missense_Mutation_p.R433M|ACE_ENST00000428043.1_Missense_Mutation_p.R1007M|ACE_ENST00000290863.6_Missense_Mutation_p.R433M|ACE_ENST00000421982.2_Missense_Mutation_p.R253M|ACE_ENST00000413513.3_Missense_Mutation_p.R433M	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1007	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GTGGCCTTGAGGGAGGGTGCC	0.582																																					p.R1007M		.											.	ACE-94	0			c.G3020T						.						80	74	76					17																	61570904		2203	4300	6503	SO:0001583	missense	1636	exon20			CCTTGAGGGAGGG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"CD molecules"	2707	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	106180	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.3020G>T	17.37:g.61570904G>T	ENSP00000290866:p.Arg1007Met	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	87	18	NM_000789	0	0	23	24	1	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.618950	0.46736	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.80628	0.4659	H	0.97340	3.985	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.999;1.0	D;D;D;D	0.97110	0.992;0.976;0.986;1.0	D	0.88380	0.3001	10	0.87932	D	0	-34.8796	18.0898	0.89471	0.0:0.0:1.0:0.0	.	253;433;433;1007	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	M	1007;1007;433;433;253	ENSP00000290866:R1007M;ENSP00000397593:R1007M;ENSP00000290863:R433M;ENSP00000392247:R433M;ENSP00000387760:R253M	ENSP00000290863:R433M	R	+	2	0	ACE	58924636	1.000000	0.71417	0.966000	0.40874	0.792000	0.44763	7.975000	0.88055	2.262000	0.75019	0.561000	0.74099	AGG	.		0.582	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			T	61570904	G	T	61570904	3	4	103	1	0	0	0	0	1	0	0	0	136	1000	35	4	3301	4	ACE	17	61570904	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1625823	61570904	19624306	114	9174											
TMC8	147138	broad.mit.edu;bcgsc.ca	37	chr17	76133812	76133812	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagtgctgggagaactcCgtgggggaggagctgtacaa	9	6	16	10	1	0	1	0	0	0	1	1	4	1	3	3	4	4	3	3	4	3	1	rs375990572		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:76133812C>T	ENST00000318430.5	+	11	1640	c.1266C>T	c.(1264-1266)tcC>tcT	p.S422S	TMC8_ENST00000589691.1_Silent_p.S199S	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	422					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			GGGAGAACTCCGTGGGGGAGG	0.642																																					p.S422S													.	TMC8-90	0			c.C1266T						.	C		2,4404	4.2+/-10.8	0,2,2201	114	100	104		1266	-8.6	0.9	17		104	0,8600		0,0,4300	no	coding-synonymous	TMC8	NM_152468.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		422/727	76133812	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	147138	exon11			GAACTCCGTGGGG	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"epidermodysplasia verruciformis 2"	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.1266C>T	17.37:g.76133812C>T		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	102	14	NM_152468	0	0	18	18	0	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																			.		0.642	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			T	76133812	C	T	76133812	2	4	103	1	0	0	0	0	0	0	0	1	16023	639	23	1		1	TMC8	17	76133812	Silent	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	14562908	76133812	5061398	115	9175											
BAIAP2	10458	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	79082274	79082274	+	Splice_Site	DEL	G	G	-																															tgtttctgcctctgcccccaGggcctggatgactatggagc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:79082274delG	ENST00000321300.6	+	13	1593		c.e13-1		BAIAP2_ENST00000321280.7_Splice_Site|BAIAP2_ENST00000435091.3_Splice_Site|BAIAP2_ENST00000416299.2_Splice_Site|BAIAP2_ENST00000392411.3_Splice_Site|BAIAP2_ENST00000575245.1_Splice_Site|BAIAP2_ENST00000428708.2_Splice_Site|BAIAP2_ENST00000575712.1_Splice_Site	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2						actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TCTGCCCCCAGGGCCTGGATG	0.637																																					.		.											.	BAIAP2-90	0			c.1501-1G>-						.						72	70	71					17																	79082274		2203	4300	6503	SO:0001630	splice_region_variant	10458	exon13			.	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1501-1G>-	17.37:g.79082274delG		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	55	12	NM_001144888	0	0	0	0	0	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Splice_Site	DEL	ENST00000321300.6	37	CCDS11775.1																																																																																			.		0.637	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		Intron	-	79082274	G	-	79082274	8	5	103	1	0	1	0	1	0	0	1	0	1302	1014	35	0	1550	0	BAIAP2	17	79082274	Splice_Site	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	2948462	79082274	2112936	116	9176											
DYM	54808	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	46956680	46956680	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgattccagaacgggtcatTctcagagatagattccgtgc	10	11	10	10	2	2	4	2	1	1	3	5	5	4	4	2	1	2	0	2	1	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr18:46956680T>G	ENST00000269445.6	-	2	542	c.85A>C	c.(85-87)Aat>Cat	p.N29H	DYM_ENST00000442713.2_Missense_Mutation_p.N29H|DYM_ENST00000584977.1_5'UTR|RP11-110H1.9_ENST00000583579.1_RNA	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	29					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						AACGGGTCATTCTCAGAGATA	0.423																																					p.N29H		.											.	DYM-226	0			c.A85C						.						147	146	146					18																	46956680		2203	4300	6503	SO:0001583	missense	54808	exon2			GGTCATTCTCAGA	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.85A>C	18.37:g.46956680T>G	ENSP00000269445:p.Asn29His	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	171	29	NM_017653	0	0	12	18	6	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	37	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571437	0.45798	.	.	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.82893	-1.66;-1.66	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.90841	0.7123	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.78314	0.991;0.983	D	0.91823	0.5469	10	0.87932	D	0	-23.1803	15.1469	0.72662	0.0:0.0:0.0:1.0	.	29;29	Q7RTS9-2;Q7RTS9	.;DYM_HUMAN	H	29	ENSP00000395942:N29H;ENSP00000269445:N29H	ENSP00000269445:N29H	N	-	1	0	DYM	45210678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.007000	0.76335	2.371000	0.80710	0.533000	0.62120	AAT	.		0.423	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		G	46956680	T	G	46956680	3	3	103	1	0	0	0	0	1	0	0	0	4851	1783	62	5	1988	5	DYM	18	46956680	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		46956680	31120568	117	9177											
SERPINB2	5055	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	61562567	61562567	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagagaactttaccagctgtGggttcatgcagcagatccag	11	9	11	10	0	1	2	1	0	0	2	2	3	2	2	2	1	5	4	2	1	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr18:61562567G>T	ENST00000299502.4	+	3	318	c.238G>T	c.(238-240)Ggg>Tgg	p.G80W	SERPINB2_ENST00000457692.1_Missense_Mutation_p.G80W|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	80					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G80W(1)		NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	TACCAGCTGTGGGTTCATGCA	0.428																																					p.G80W		.											.	SERPINB2-226	1	Substitution - Missense(1)	lung(1)	c.G238T						.						182	179	180					18																	61562567		2203	4300	6503	SO:0001583	missense	5055	exon3			AGCTGTGGGTTCA	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"Serine (or cysteine) peptidase inhibitors"	8584	protein-coding gene	gene with protein product		173390	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.238G>T	18.37:g.61562567G>T	ENSP00000299502:p.Gly80Trp	Somatic	231	1		WXS	Illumina HiSeq	Phase_I	205	35	NM_002575	0	0	0	0	0	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.706601	0.30232	.	.	ENSG00000197632	ENST00000404622;ENST00000299502;ENST00000457692;ENST00000413956;ENST00000443281	D;D;D;D;T	0.84370	-1.69;-1.84;-1.84;-1.66;-1.22	5.93	3.15	0.36227	Serpin domain (3);	423.867000	0.00589	U	0.000342	D	0.82889	0.5135	N	0.22421	0.69	0.09310	N	0.999995	P	0.48407	0.91	P	0.49887	0.625	T	0.68830	-0.5305	10	0.66056	D	0.02	.	6.0059	0.19547	0.1669:0.1564:0.6767:0.0	.	80	P05120	PAI2_HUMAN	W	80	ENSP00000385397:G80W;ENSP00000299502:G80W;ENSP00000401645:G80W;ENSP00000402386:G80W;ENSP00000397096:G80W	ENSP00000299502:G80W	G	+	1	0	SERPINB2	59713547	0.006000	0.16342	0.053000	0.19242	0.146000	0.21551	-0.154000	0.10130	0.391000	0.25143	0.655000	0.94253	GGG	.		0.428	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		T	61562567	G	T	61562567	3	4	103	1	0	0	0	0	1	0	0	0	14133	1348	47	4	244	4	SERPINB2	18	61562567	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	14605887	61562567	16514681	118	9178											
SOCS6	9306	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	67992496	67992496	+	Frame_Shift_Del	DEL	A	A	-																															tgaagagctcggcttctcatAatggagacctgcatcttcac																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr18:67992496delA	ENST00000397942.3	+	2	908	c.592delA	c.(592-594)aatfs	p.N198fs	SOCS6_ENST00000582322.1_Frame_Shift_Del_p.N198fs	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	198					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				GGCTTCTCATAATGGAGACCT	0.512																																					p.N198fs	Melanoma(84;1024 1361 24382 36583 42651)	.											.	SOCS6-721	0			c.592delA						.						108	94	99					18																	67992496		2203	4300	6503	SO:0001589	frameshift_variant	9306	exon2			.	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.592delA	18.37:g.67992496delA	ENSP00000381034:p.Asn198fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	129	28	NM_004232	0	0	0	0	0	Q8WUM3	Frame_Shift_Del	DEL	ENST00000397942.3	37	CCDS11998.1																																																																																			.		0.512	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			-	67992496	A	-	67992496	7	5	103	1	0	1	0	1	0	0	0	0	14950	362	13	0	594	0	SOCS6	18	67992496	Frame_Shift_Del	DEL	A	TCGA-DZ-6132-01A-11D-1961-08	6429929	67992496	10084752	119	9179											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	111	3		WXS	Illumina HiSeq		156	2	NM_031203	0	0	0	0	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	103	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		8527467	50601516	120	9180											
ZNF699	374879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9406673	9406673	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatactgtatctttccagtGtgatctctcacatgtgctct	7	17	6	11	0	5	1	2	1	3	0	7	1	6	1	1	0	2	2	1	0	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:9406673G>C	ENST00000591998.1	-	6	1635	c.1407C>G	c.(1405-1407)caC>caG	p.H469Q	ZNF699_ENST00000308650.3_Missense_Mutation_p.H469Q|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	469					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)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCTTTCCAGTGTGATCTCTCA	0.458																																					p.H469Q		.											.	ZNF699-68	0			c.C1407G						.						60	64	63					19																	9406673		2200	4296	6496	SO:0001583	missense	374879	exon5			TCCAGTGTGATCT	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"Zinc fingers, C2H2-type", "-"	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.1407C>G	19.37:g.9406673G>C	ENSP00000467723:p.His469Gln	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	55	8	NM_198535	0	0	4	5	1	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	37	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	g	13.65	2.301105	0.40694	.	.	ENSG00000196110	ENST00000308650	T	0.66995	-0.24	3.28	-0.0525	0.13822	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39407	N	0.001377	T	0.80008	0.4545	M	0.90425	3.115	0.24473	N	0.994389	D	0.71674	0.998	D	0.75484	0.986	T	0.68796	-0.5314	10	0.87932	D	0	.	5.9659	0.19325	0.4949:0.0:0.5051:0.0	.	469	Q32M78	ZN699_HUMAN	Q	469	ENSP00000311596:H469Q	ENSP00000311596:H469Q	H	-	3	2	ZNF699	9267673	0.909000	0.30893	0.019000	0.16419	0.771000	0.43674	0.275000	0.18698	0.085000	0.17107	0.550000	0.68814	CAC	.		0.458	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535		C	9406673	G	C	9406673	3	2	103	1	0	0	0	0	1	0	0	0	18133	1368	48	4	525	4	ZNF699	19	9406673	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	879206	9406673	49722310	121	9181											
ICAM5	7087	ucsc.edu	37	chr19	10402464	10402464	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtttgaaaacagctcggccCccagagagctccgaaccttc	10	8	9	14	2	0	2	0	1	0	1	3	4	1	2	4	1	4	3	4	1	3	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:10402464C>A	ENST00000221980.4	+	3	715	c.652C>A	c.(652-654)Ccc>Acc	p.P218T	CTD-2369P2.8_ENST00000589379.1_RNA	NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	218	Ig-like C2-type 2.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CAGCTCGGCCCCCAGAGAGCT	0.602																																					p.P218T													.	ICAM5-153	0			c.C652A						.						19	24	22					19																	10402464		2096	4145	6241	SO:0001583	missense	7087	exon3			TCGGCCCCCAGAG	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5348	protein-coding gene	gene with protein product	"telencephalin"	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.652C>A	19.37:g.10402464C>A	ENSP00000221980:p.Pro218Thr	Somatic	89	1		WXS	Illumina HiSeq		42	6	NM_003259	0	0	0	0	0	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	c	14.53	2.561648	0.45590	.	.	ENSG00000105376	ENST00000221980	T	0.07908	3.15	5.29	3.17	0.36434	Intercellular adhesion molecule (1);Immunoglobulin-like fold (1);	0.068731	0.56097	D	0.000021	T	0.09423	0.0232	M	0.72479	2.2	0.34597	D	0.716099	B	0.10296	0.003	B	0.17098	0.017	T	0.10753	-1.0616	10	0.13853	T	0.58	-12.7672	7.3688	0.26790	0.0:0.8052:0.0:0.1948	.	218	Q9UMF0	ICAM5_HUMAN	T	218	ENSP00000221980:P218T	ENSP00000221980:P218T	P	+	1	0	ICAM5	10263464	0.005000	0.15991	1.000000	0.80357	0.996000	0.88848	0.423000	0.21313	1.252000	0.44001	0.466000	0.42574	CCC	.		0.602	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		A	10402464	C	A	10402464	3	1	103	1	0	0	0	0	1	0	0	0	7504	623	22	4	662	4	ICAM5	19	10402464	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	995791	10402464	48726519	122	9182											
PIK3R2	5296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18274091	18274091	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aggaccagattgtcaaggagGacagcgtggaggcagtgggc	11	5	18	7	1	1	1	1	0	0	1	1	5	1	5	1	6	1	1	1	6	1	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:18274091G>A	ENST00000593731.1	+	11	1869	c.1309G>A	c.(1309-1311)Gac>Aac	p.D437N	PIK3R2_ENST00000222254.8_Missense_Mutation_p.D437N			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	437					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	TGTCAAGGAGGACAGCGTGGA	0.577																																					p.D437N		.											.	PIK3R2-1311	0			c.G1309A						.						125	107	113					19																	18274091		2203	4300	6503	SO:0001583	missense	5296	exon11			AAGGAGGACAGCG		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1309G>A	19.37:g.18274091G>A	ENSP00000471914:p.Asp437Asn	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	75	13	NM_005027	0	0	65	111	46	Q5EAT5|Q9UPH9	Missense_Mutation	SNP	ENST00000593731.1	37	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.719551	0.48728	.	.	ENSG00000105647	ENST00000222254	T	0.47869	0.83	4.08	4.08	0.47627	.	0.102115	0.64402	D	0.000002	T	0.40171	0.1106	L	0.43152	1.355	0.42153	D	0.991565	B	0.19583	0.037	B	0.15052	0.012	T	0.38950	-0.9637	10	0.52906	T	0.07	-47.255	12.9549	0.58421	0.0:0.0:0.8377:0.1623	.	437	O00459	P85B_HUMAN	N	437	ENSP00000222254:D437N	ENSP00000222254:D437N	D	+	1	0	PIK3R2	18135091	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.262000	0.65501	2.216000	0.71823	0.561000	0.74099	GAC	.		0.577	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		A	18274091	G	A	18274091	3	1	103	1	0	0	0	0	1	0	0	0	11945	1174	41	2	1347	2	PIK3R2	19	18274091	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	7871627	18274091	40854892	123	9183											
ZNF85	7639	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	21132080	21132080	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacataagaaaattcatactGgagagaaaccctacaaatgt	20	8	6	7	0	1	2	1	0	0	2	1	4	1	3	1	1	4	0	1	1	8	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:21132080G>A	ENST00000328178.8	+	4	873	c.760G>A	c.(760-762)Gga>Aga	p.G254R	ZNF85_ENST00000345030.6_Missense_Mutation_p.G221R|ZNF85_ENST00000601023.1_Missense_Mutation_p.G195R	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	254					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						AATTCATACTGGAGAGAAACC	0.353																																					p.G284R													.	ZNF85-514	0			c.G850A						.						26	29	28					19																	21132080		2163	4272	6435	SO:0001583	missense	7639	exon5			CATACTGGAGAGA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.760G>A	19.37:g.21132080G>A	ENSP00000329793:p.Gly254Arg	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	33	8	NM_001256171	0	0	91	100	9	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.63	1.695005	0.30052	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.01629	4.72;4.72	1.35	1.35	0.21983	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05135	0.0137	L	0.41632	1.29	0.80722	D	1	P;D;D	0.89917	0.523;1.0;0.993	B;D;D	0.97110	0.134;1.0;0.953	T	0.47560	-0.9108	9	0.54805	T	0.06	.	9.5712	0.39429	0.0:0.0:1.0:0.0	.	221;195;254	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	R	254;221;129	ENSP00000329793:G254R;ENSP00000342340:G221R	ENSP00000329793:G254R	G	+	1	0	ZNF85	20923920	0.998000	0.40836	0.108000	0.21378	0.096000	0.18686	2.982000	0.49337	0.681000	0.31386	0.462000	0.41574	GGA	.		0.353	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		A	21132080	G	A	21132080	3	1	103	1	0	0	0	0	1	0	0	0	18225	1349	47	2	774	2	ZNF85	19	21132080	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	2857989	21132080	37996903	124	9184											
ZNF85	7639	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	21132138	21132138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttaaccgattctcaactcTtactacccataagataattc	13	15	2	11	1	2	1	1	0	2	1	4	2	2	1	2	0	4	0	2	0	6	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:21132138T>C	ENST00000328178.8	+	4	931	c.818T>C	c.(817-819)cTt>cCt	p.L273P	ZNF85_ENST00000345030.6_Missense_Mutation_p.L240P|ZNF85_ENST00000601023.1_Missense_Mutation_p.L214P	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	273					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						TTCTCAACTCTTACTACCCAT	0.348																																					p.L303P		.											.	ZNF85-514	0			c.T908C						.						26	29	28					19																	21132138		2193	4286	6479	SO:0001583	missense	7639	exon5			CAACTCTTACTAC	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"Zinc fingers, C2H2-type", "-"	13160	protein-coding gene	gene with protein product		603899	"zinc finger protein 85 (HPF4, HTF1)"			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.818T>C	19.37:g.21132138T>C	ENSP00000329793:p.Leu273Pro	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	32	4	NM_001256171	0	0	1	1	0	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.50	1.657272	0.29425	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.53857	0.6;0.6	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.76263	0.3963	H	0.94620	3.56	0.25920	N	0.983126	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.63350	-0.6657	9	0.87932	D	0	.	7.5498	0.27790	0.0:0.0:0.0:1.0	.	240;214;273	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	P	273;240;148	ENSP00000329793:L273P;ENSP00000342340:L240P	ENSP00000329793:L273P	L	+	2	0	ZNF85	20923978	0.117000	0.22190	0.004000	0.12327	0.013000	0.08279	2.803000	0.47924	0.569000	0.29329	0.379000	0.24179	CTT	.		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		C	21132138	T	C	21132138	3	2	103	1	0	0	0	0	1	0	0	0	18225	1609	56	3	832	3	ZNF85	19	21132138	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	58	21132138	37996845	125	9185											
LGI4	163175	broad.mit.edu;ucsc.edu	37	chr19	35617765	35617765	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggggctcaccgggcagcTcttcctcgggccggaagcgc	5	5	17	14	4	2	0	1	0	1	0	4	2	3	1	3	5	2	3	3	5	1	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:35617765T>A	ENST00000310123.3	-	7	1304	c.785A>T	c.(784-786)gAg>gTg	p.E262V	LGI4_ENST00000493050.1_5'UTR|LGI4_ENST00000392225.3_Missense_Mutation_p.E262V	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	262					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			ACCGGGCAGCTCTTCCTCGGG	0.687																																					p.E262V													.	LGI4-91	0			c.A785T						.						19	23	22					19																	35617765		2202	4298	6500	SO:0001583	missense	163175	exon7			GGCAGCTCTTCCT	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.785A>T	19.37:g.35617765T>A	ENSP00000312273:p.Glu262Val	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	31	5	NM_139284	0	0	0	0	0	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	37	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.631916	0.67015	.	.	ENSG00000153902	ENST00000310123;ENST00000392225;ENST00000437421	T;T	0.64803	-0.12;-0.03	4.1	4.1	0.47936	.	0.551988	0.17037	N	0.189479	T	0.64811	0.2632	L	0.40543	1.245	0.80722	D	1	D;D	0.65815	0.995;0.995	P;P	0.57911	0.829;0.795	T	0.60944	-0.7162	10	0.33141	T	0.24	.	11.0719	0.48008	0.0:0.0:0.0:1.0	.	173;262	Q658V8;Q8N135	.;LGI4_HUMAN	V	262	ENSP00000312273:E262V;ENSP00000376059:E262V	ENSP00000312273:E262V	E	-	2	0	LGI4	40309605	0.998000	0.40836	0.993000	0.49108	0.583000	0.36354	2.147000	0.42226	1.709000	0.51313	0.260000	0.18958	GAG	.		0.687	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			A	35617765	T	A	35617765	3	1	103	1	0	0	0	0	1	0	0	0	8776	1551	54	5	840	5	LGI4	19	35617765	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	14485627	35617765	23511218	126	9186											
SUPT5H	6829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39964723	39964723	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccctcgtccccacaggtcaaCccacaatacaacccgcagac	12	4	5	20	2	1	1	1	0	0	1	3	1	2	1	5	1	3	1	5	1	4	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:39964723C>A	ENST00000599117.1	+	27	2980	c.2613C>A	c.(2611-2613)aaC>aaA	p.N871K	SUPT5H_ENST00000402194.2_Missense_Mutation_p.N867K|SUPT5H_ENST00000598725.1_Missense_Mutation_p.N871K|SUPT5H_ENST00000359191.6_Missense_Mutation_p.N867K|SUPT5H_ENST00000432763.2_Missense_Mutation_p.N871K			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	871	10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2.|Pro-rich.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CACAGGTCAACCCACAATACA	0.647											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N871K		.											.	SUPT5H-94	0			c.C2613A						.						84	89	87					19																	39964723		2203	4300	6503	SO:0001583	missense	6829	exon25			GGTCAACCCACAA	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"suppressor of Ty (S.cerevisiae) 5 homolog"			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2613C>A	19.37:g.39964723C>A	ENSP00000470252:p.Asn871Lys	Somatic	121	0	889	WXS	Illumina HiSeq	Phase_I	66	11	NM_003169	0	0	103	144	41	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910409	0.52439	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.36	3.19	0.36642	.	0.043680	0.85682	D	0.000000	T	0.51652	0.1687	L	0.53249	1.67	0.58432	D	0.999995	B;B;B	0.34200	0.367;0.387;0.441	B;B;B	0.37550	0.253;0.131;0.206	T	0.48736	-0.9009	8	.	.	.	-34.0435	10.5839	0.45271	0.0:0.8333:0.0:0.1667	.	663;867;871	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	K	871;867;849;871	.	.	N	+	3	2	SUPT5H	44656563	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	2.352000	0.44080	1.235000	0.43724	0.462000	0.41574	AAC	.		0.647	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		A	39964723	C	A	39964723	3	1	103	1	0	0	0	0	1	0	0	0	15431	506	18	4	2711	4	SUPT5H	19	39964723	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	4346958	39964723	19164260	127	9187											
LGALS13	29124	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40095901	40095901	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccgtttccgagtgcactttgGcaatcatgtggtcatgaaca	9	12	10	10	2	2	1	2	1	0	0	3	2	3	1	2	2	2	3	2	2	2	2	rs138148689		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:40095901G>T	ENST00000221797.4	+	3	221	c.176G>T	c.(175-177)gGc>gTc	p.G59V		NM_013268.2	NP_037400.1	Q9UHV8	PP13_HUMAN	lectin, galactoside-binding, soluble, 13	59	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			lung(5)|ovary(1)|urinary_tract(1)	7	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			GTGCACTTTGGCAATCATGTG	0.498																																					p.G59V													.	LGALS13-91	0			c.G176T						.	G	VAL/GLY	0,4406		0,0,2203	251	185	207		176	0.7	0	19	dbSNP_134	207	2,8598		0,2,4298	yes	missense	LGALS13	NM_013268.2	109	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	probably-damaging	59/140	40095901	2,13004	2203	4300	6503	SO:0001583	missense	29124	exon3			ACTTTGGCAATCA	AF117383	CCDS33024.1	19q13.2	2014-03-19	2008-07-25		ENSG00000105198	ENSG00000105198		"Lectins, galactoside-binding"	15449	protein-coding gene	gene with protein product	"galectin 13"	608717				6856484, 10527825	Standard	NM_013268		Approved	PP13, PLAC8	uc002omb.3	Q9UHV8	OTTHUMG00000183073	ENST00000221797.4:c.176G>T	19.37:g.40095901G>T	ENSP00000221797:p.Gly59Val	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	77	14	NM_013268	0	0	0	0	0	C5HZ15	Missense_Mutation	SNP	ENST00000221797.4	37	CCDS33024.1	.	.	.	.	.	.	.	.	.	.	.	10.64	1.407134	0.25378	0.0	2.33E-4	ENSG00000105198	ENST00000221797	T	0.19532	2.14	0.744	0.744	0.18353	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.51092	0.1654	M	0.92077	3.27	0.19300	N	0.999973	D	0.89917	1.0	D	0.87578	0.998	T	0.31364	-0.9946	8	0.87932	D	0	.	.	.	.	.	59	Q9UHV8	PP13_HUMAN	V	59	ENSP00000221797:G59V	ENSP00000221797:G59V	G	+	2	0	LGALS13	44787741	0.562000	0.26586	0.027000	0.17364	0.039000	0.13416	1.393000	0.34497	0.658000	0.30925	0.305000	0.20034	GGC	G|1.000;T|0.000		0.498	LGALS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464968.1	NM_013268		T	40095901	G	T	40095901	3	4	103	1	0	0	0	0	1	0	0	0	8761	1203	42	4	186	4	LGALS13	19	40095901	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	131178	40095901	19033082	128	9188											
LIPE	3991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42907053	42907053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctgacagcgacatctcgggGgtgtccgacgacgtctcgga	7	7	15	12	6	2	1	0	1	2	0	5	5	3	2	1	3	1	1	1	3	0	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:42907053G>A	ENST00000244289.4	-	9	2949	c.2673C>T	c.(2671-2673)acC>acT	p.T891T	LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000599276.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	891					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				ACATCTCGGGGGTGTCCGACG	0.612																																					p.T891T		.											.	LIPE-154	0			c.C2673T						.						92	73	79					19																	42907053		2203	4300	6503	SO:0001819	synonymous_variant	3991	exon9			CTCGGGGGTGTCC	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2673C>T	19.37:g.42907053G>A		Somatic	121	1		WXS	Illumina HiSeq	Phase_I	88	21	NM_005357	0	0	2	2	0	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																			.		0.612	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		A	42907053	G	A	42907053	2	1	103	1	0	0	0	0	0	0	0	1	8844	1219	43	2		2	LIPE	19	42907053	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	2811152	42907053	16221930	129	9189											
ZNF223	7766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44570872	44570872	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gagatatgtagtgtgagcttCcgtcttaggtcaagtcttaa	10	14	11	6	1	3	2	1	1	2	1	4	3	4	2	1	1	1	2	1	1	5	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:44570872C>T	ENST00000434772.3	+	5	1146	c.891C>T	c.(889-891)ttC>ttT	p.F297F	ZNF223_ENST00000591793.1_Silent_p.F407F	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GTGTGAGCTTCCGTCTTAGGT	0.448																																					p.F297F		.											.	ZNF223-91	0			c.C891T						.						131	126	128					19																	44570872		2203	4300	6503	SO:0001819	synonymous_variant	7766	exon5			GAGCTTCCGTCTT	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"Zinc fingers, C2H2-type", "-"	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.891C>T	19.37:g.44570872C>T		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	107	15	NM_013361	0	0	1	5	4	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	37	CCDS12635.1																																																																																			.		0.448	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			T	44570872	C	T	44570872	2	4	103	1	0	0	0	0	0	0	0	1	17809	854	30	2		2	ZNF223	19	44570872	Silent	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	1663819	44570872	14558111	130	9190											
PIH1D1	55011	broad.mit.edu	37	chr19	49950353	49950353	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttcaggtgaggcttttcAggcctgaggaggaacaaggt	10	9	16	6	0	2	2	2	2	0	0	2	4	2	4	1	7	1	2	1	7	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:49950353A>G	ENST00000262265.5	-	7	850	c.615T>C	c.(613-615)ccT>ccC	p.P205P	PIH1D1_ENST00000602226.1_5'Flank|PIH1D1_ENST00000596049.1_Silent_p.P205P	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	205					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GAGGCTTTTCAGGCCTGAGGA	0.607																																					p.P205P													.	PIH1D1-90	0			c.T615C						.						84	86	85					19																	49950353		2203	4300	6503	SO:0001819	synonymous_variant	55011	exon7			CTTTTCAGGCCTG	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.615T>C	19.37:g.49950353A>G		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	93	4	NM_017916	0	0	0	0	0	B4DGN7|B4E2X7|Q9BVL0	Silent	SNP	ENST00000262265.5	37	CCDS12765.1																																																																																			.		0.607	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916		G	49950353	A	G	49950353	2	3	103	1	0	0	0	0	0	0	0	1	11932	175	7	3		3	PIH1D1	19	49950353	Silent	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	5379481	49950353	9178630	131	9191											
FCGRT	2217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50017313	50017313	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaaaccaggtgtcctggtAttgggagaaagagaccacag	14	6	14	7	0	0	2	0	0	0	2	1	5	1	3	3	4	1	1	3	4	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:50017313A>G	ENST00000221466.5	+	3	734	c.248A>G	c.(247-249)tAt>tGt	p.Y83C	FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000426395.3_Missense_Mutation_p.Y83C|FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000596975.1_Missense_Mutation_p.Y83C	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	83	Alpha-1.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		GTGTCCTGGTATTGGGAGAAA	0.582																																					p.Y83C		.											.	FCGRT-91	0			c.A248G						.						41	47	45					19																	50017313		2203	4300	6503	SO:0001583	missense	2217	exon3			CCTGGTATTGGGA	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"Immunoglobulin superfamily / C1-set domain containing"	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.248A>G	19.37:g.50017313A>G	ENSP00000221466:p.Tyr83Cys	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	49	19	NM_001136019	1	0	331	388	56	Q5HYM5|Q9HBV7|Q9NZ19	Missense_Mutation	SNP	ENST00000221466.5	37	CCDS12770.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.150611	0.57151	.	.	ENSG00000104870	ENST00000221466;ENST00000426395;ENST00000415900;ENST00000452439	T;T	0.01185	5.21;5.21	4.83	2.61	0.31194	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.374848	0.19651	N	0.109214	T	0.07369	0.0186	M	0.93197	3.39	0.41878	D	0.990305	D	0.89917	1.0	D	0.83275	0.996	T	0.00662	-1.1621	10	0.87932	D	0	.	3.4456	0.07480	0.6789:0.0:0.1082:0.2129	.	83	P55899	FCGRN_HUMAN	C	83	ENSP00000221466:Y83C;ENSP00000410798:Y83C	ENSP00000221466:Y83C	Y	+	2	0	FCGRT	54709125	0.976000	0.34144	0.999000	0.59377	0.876000	0.50452	2.603000	0.46266	0.868000	0.35678	0.459000	0.35465	TAT	.		0.582	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			G	50017313	A	G	50017313	3	3	103	1	0	0	0	0	1	0	0	0	5805	449	16	3	254	3	FCGRT	19	50017313	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	66960	50017313	9111670	132	9192											
ZNF473	25888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50549983	50549983	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaaagccttatgtttgtcaGgaatgcgggaaagccttcac	12	10	11	8	1	2	0	2	0	0	0	2	3	2	2	2	2	3	1	2	2	5	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:50549983G>C	ENST00000595661.1	+	6	2778	c.2283G>C	c.(2281-2283)caG>caC	p.Q761H	CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000391821.2_Missense_Mutation_p.Q761H|ZNF473_ENST00000270617.3_Missense_Mutation_p.Q761H|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000601364.1_Intron|ZNF473_ENST00000445728.3_Missense_Mutation_p.Q749H			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	761					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		ATGTTTGTCAGGAATGCGGGA	0.522											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q761H		.											.	ZNF473-91	0			c.G2283C						.						80	80	80					19																	50549983		2203	4300	6503	SO:0001583	missense	25888	exon5			TTGTCAGGAATGC	AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.2283G>C	19.37:g.50549983G>C	ENSP00000472808:p.Gln761His	Somatic	136	0	970	WXS	Illumina HiSeq	Phase_I	111	26	NM_015428	0	0	4	6	2	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	37	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.247320	0.39697	.	.	ENSG00000142528	ENST00000270617;ENST00000391821;ENST00000445728	T;T;T	0.07800	3.16;3.16;3.16	3.84	1.72	0.24424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.611213	0.13601	N	0.375867	T	0.07007	0.0178	N	0.02916	-0.46	0.25928	N	0.983026	D	0.61080	0.989	P	0.60173	0.87	T	0.30446	-0.9978	10	0.44086	T	0.13	-0.3948	5.7557	0.18172	0.3335:0.0:0.6665:0.0	.	761	Q8WTR7	ZN473_HUMAN	H	761;761;749	ENSP00000270617:Q761H;ENSP00000375697:Q761H;ENSP00000388961:Q749H	ENSP00000270617:Q761H	Q	+	3	2	ZNF473	55241795	0.000000	0.05858	0.978000	0.43139	0.764000	0.43329	-1.663000	0.01968	0.603000	0.29913	0.650000	0.86243	CAG	.		0.522	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		C	50549983	G	C	50549983	3	2	103	1	0	0	0	0	1	0	0	0	17963	991	35	4	2297	4	ZNF473	19	50549983	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	532670	50549983	8579000	133	9193											
TTYH1	57348	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54937848	54937848	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctaccctctcccctcccAggtggctggcctacgtcctc	3	9	8	21	1	1	0	0	0	1	0	5	0	3	0	7	3	2	1	7	3	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:54937848A>G	ENST00000376530.3	+	5	741		c.e5-1		TTYH1_ENST00000391739.3_Splice_Site|TTYH1_ENST00000489425.1_Splice_Site|TTYH1_ENST00000376531.3_Splice_Site|TTYH1_ENST00000301194.4_Splice_Site	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1						cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)	p.?(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CTCCCCTCCCAGGTGGCTGGC	0.652																																					.		.											.	TTYH1-90	1	Unknown(1)	upper_aerodigestive_tract(1)	c.639-2A>G						.						96	79	85					19																	54937848		2203	4300	6503	SO:0001630	splice_region_variant	57348	exon5			CCTCCCAGGTGGC	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.639-1A>G	19.37:g.54937848A>G		Somatic	162	1		WXS	Illumina HiSeq	Phase_I	116	21	NM_001005367	0	0	0	0	0	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Splice_Site	SNP	ENST00000376530.3	37	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.478123	0.63849	.	.	ENSG00000167614	ENST00000301194;ENST00000376530;ENST00000445095;ENST00000391739;ENST00000376531	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2014	0.54328	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTYH1	59629660	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.433000	0.59929	1.836000	0.53414	0.459000	0.35465	.	.		0.652	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1		Intron	G	54937848	A	G	54937848	5	3	103	1	0	0	0	0	0	0	1	0	16772	202	7	3	655	3	TTYH1	19	54937848	Splice_Site	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	4387865	54937848	4191135	134	9194											
KIR2DL4	3811	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	55324637	55324637	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agtggccatcatcctctttaCcatccttcccttctttctcc	5	16	3	17	0	4	0	1	0	3	0	8	0	7	0	6	1	1	0	6	1	1	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:55324637C>T	ENST00000538269.1	+	2	61				KIR2DL4_ENST00000345540.5_Intron|KIR2DL4_ENST00000359085.4_Missense_Mutation_p.T255I|KIR2DL4_ENST00000463062.1_3'UTR|KIR2DL4_ENST00000357494.4_Intron|KIR2DL4_ENST00000396293.1_Intron|KIR2DL4_ENST00000346587.4_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Missense_Mutation_p.T253I			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ATCCTCTTTACCATCCTTCCC	0.502																																					p.T255I		.											.	KIR2DL4-70	0			c.C764T						.						120	185	164					19																	55324637		2009	4160	6169	SO:0001627	intron_variant	3805	exon6			TCTTTACCATCCT	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-4352C>T	19.37:g.55324637C>T		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	63	25	NM_001080772	0	0	0	0	0	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	37		.	.	.	.	.	.	.	.	.	.	c	0	-2.781565	0.00079	.	.	ENSG00000189013	ENST00000396284;ENST00000359085;ENST00000396289	T;T;T	0.00454	7.39;7.32;7.4	0.569	-1.14	0.09741	.	6.239890	0.01410	N	0.013962	T	0.00271	0.0008	N	0.25060	0.705	0.09310	N	1	B;B;B	0.16802	0.019;0.0;0.001	B;B;B	0.23852	0.049;0.002;0.016	T	0.46596	-0.9180	9	0.28530	T	0.3	.	.	.	.	.	255;253;238	Q99706;E7EST5;Q99706-2	KI2L4_HUMAN;.;.	I	253;255;253	ENSP00000379580:T253I;ENSP00000351988:T255I;ENSP00000379584:T253I	ENSP00000351988:T255I	T	+	2	0	KIR2DL4	60016449	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.795000	0.00764	-1.106000	0.03008	-1.140000	0.01884	ACC	.		0.502	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		T	55324637	C	T	55324637	1	4	103	0	1	0	0	0	0	0	0	0	8339	507	18	2		2	KIR2DL4	19	55324637	Intron	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	386789	55324637	3804346	135	9195											
STAU1	6780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47741019	47741019	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacagctatggcggcattttTctttgaaatcttcttgcttt	8	18	7	8	1	3	1	0	1	3	0	3	1	3	1	0	2	3	3	0	2	3	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr20:47741019T>A	ENST00000371856.2	-	7	1125	c.715A>T	c.(715-717)Aaa>Taa	p.K239*	STAU1_ENST00000371802.1_Nonsense_Mutation_p.K164*|STAU1_ENST00000371792.1_Nonsense_Mutation_p.K158*|STAU1_ENST00000371828.3_Nonsense_Mutation_p.K164*|STAU1_ENST00000347458.5_Nonsense_Mutation_p.K158*|STAU1_ENST00000360426.4_Nonsense_Mutation_p.K158*|STAU1_ENST00000340954.7_Nonsense_Mutation_p.K158*	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	239	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			GCGGCATTTTTCTTTGAAATC	0.483																																					p.K239X		.											.	STAU1-230	0			c.A715T						.						150	167	161					20																	47741019		2203	4300	6503	SO:0001587	stop_gained	6780	exon7			CATTTTTCTTTGA		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.715A>T	20.37:g.47741019T>A	ENSP00000360922:p.Lys239*	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	268	78	NM_017453	0	0	67	71	4	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Nonsense_Mutation	SNP	ENST00000371856.2	37	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	T	39	7.406203	0.98265	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792;ENST00000437404	.	.	.	5.33	5.33	0.75918	.	0.087311	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.3231	15.3236	0.74141	0.0:0.0:0.0:1.0	.	.	.	.	X	164;158;239;158;158;158;164;158;164	.	ENSP00000345425:K158X	K	-	1	0	STAU1	47174426	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	8.036000	0.88901	2.017000	0.59298	0.528000	0.53228	AAA	.		0.483	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		A	47741019	T	A	47741019	4	1	103	1	0	0	0	0	0	1	0	0	15304	1792	62	5	1050	5	STAU1	20	47741019	Nonsense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		47741019	15284501	136	9196											
DSCAM	1826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	41496201	41496202	+	Missense_Mutation	DNP	AA	AA	TG																															gagggggaagccaggacacaAagaccatggaggctgaggcc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr21:41496201_41496202AA>TG	ENST00000400454.1	-	20	4093_4094	c.3616_3617TT>CA	c.(3616-3618)TTt>CAt	p.F1206H		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1206	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CCAGGACACAAAGACCATGGAG	0.564																																					p.F1206H	Melanoma(134;970 1778 1785 21664 32388)	.											.	DSCAM	0			c.T3616C						.																																			SO:0001583	missense	1826	exon20			ACACAAAGACCAT	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.3616_3617delinsTG	21.37:g.41496201_41496202delinsTG	ENSP00000383303:p.Phe1206His	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	163	26		0	0	0	0	0	O60468	Missense_Mutation	DNP	ENST00000400454.1	37	CCDS42929.1																																																																																			.		0.564	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		TG	41496202	AA	TG	41496201	3	4	103	1	0	0	0	0	1	0	0	0	4779	14	1	5	2477	5	DSCAM	21	41496201	Missense_Mutation	DNP	AA	TCGA-DZ-6132-01A-11D-1961-08		41496201	6633694	137	9197											
BCR	613	broad.mit.edu;bcgsc.ca	37	chr22	23523615	23523616	+	Frame_Shift_Ins	INS	-	-	A																															gcgtggcggcgctcaggtccINSaacttcgagcggatccgcaa																								rs369883604		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr22:23523615_23523616insA	ENST00000305877.8	+	1	1219_1220	c.468_469insA	c.(469-471)aacfs	p.N157fs	BCR_ENST00000359540.3_Frame_Shift_Ins_p.N157fs|BCR_ENST00000398512.5_Frame_Shift_Ins_p.N157fs	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	157	Kinase.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	CGCTCAGGTCCAACTTCGAGCG	0.738			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.S156fs				Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR-1349	0			c.468_469insA						.																																			SO:0001589	frameshift_variant	613	exon1			CAGGTCCAACTTC		CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.470dupA	22.37:g.23523617_23523617dupA	ENSP00000303507:p.Asn157fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	83	18	NM_021574	0	0	0	0	0	P78501|Q12842|Q4LE80|Q6NZI3	Frame_Shift_Ins	INS	ENST00000305877.8	37	CCDS13806.1																																																																																			.		0.738	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		A	23523616	-	A	23523615	7	5	103	1	0	1	1	0	0	0	0	0	1389	581	21	0	470	0	BCR	22	23523615	Frame_Shift_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08		23523615	27780951	138	9198											
C22orf32	91689	ucsc.edu	37	chr22	42475836	42475836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtccggggctctccggagcGggcctagcttgaggaaagat	7	7	17	10	3	1	2	0	1	1	1	3	4	2	4	3	6	2	2	3	6	2	2	rs369810620		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr22:42475836G>A	ENST00000331479.3	+	1	138	c.64G>A	c.(64-66)Ggg>Agg	p.G22R		NM_033318.4	NP_201575.3	Q9H4I9	EMRE_HUMAN	single-pass membrane protein with aspartate-rich tail 1	22					calcium ion transmembrane import into mitochondrion (GO:0036444)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	integral component of mitochondrial inner membrane (GO:0031305)|uniplex complex (GO:1990246)											TCTCCGGAGCGGGCCTAGCTT	0.706																																					p.G22R													.	.	0			c.G64A						.	G	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	44	47	46		64	0.4	0	22		46	0,8600		0,0,4300	no	missense	C22orf32	NM_033318.4	125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	22/108	42475836	1,13005	2203	4300	6503	SO:0001583	missense	0	exon1			CGGAGCGGGCCTA	BC024237	CCDS14031.1	22q13.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000183172	ENSG00000183172			25055	protein-coding gene	gene with protein product		615588	"chromosome 22 open reading frame 32"	C22orf32		12477932	Standard	NM_033318		Approved	dJ186O1.1, DDDD	uc003bca.3	Q9H4I9	OTTHUMG00000151286	ENST00000331479.3:c.64G>A	22.37:g.42475836G>A	ENSP00000327467:p.Gly22Arg	Somatic	102	0		WXS	Illumina HiSeq		74	4	NM_033318	0	0	91	103	12	B2R5D1|Q8TAB9	Missense_Mutation	SNP	ENST00000331479.3	37	CCDS14031.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.904611	0.52333	2.27E-4	0.0	ENSG00000183172	ENST00000331479	T	0.53423	0.62	6.17	0.409	0.16382	.	0.716188	0.14806	N	0.297349	T	0.35770	0.0943	M	0.64997	1.995	0.09310	N	1	B	0.16802	0.019	B	0.09377	0.004	T	0.24012	-1.0172	10	0.26408	T	0.33	-0.8714	2.2371	0.04011	0.146:0.132:0.4489:0.273	.	22	Q9H4I9	CV032_HUMAN	R	22	ENSP00000327467:G22R	ENSP00000327467:G22R	G	+	1	0	C22orf32	40805782	0.032000	0.19561	0.001000	0.08648	0.049000	0.14656	1.145000	0.31577	-0.039000	0.13602	0.655000	0.94253	GGG	.		0.706	SMDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322086.1	NM_033318		A	42475836	G	A	42475836	3	1	103	1	0	0	0	0	1	0	0	0	2150	1116	39	1	66	1	C22orf32	22	42475836	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	18952221	42475836	8828730	139	9199											
HDHD1A	8226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	7023838	7023838	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtatttcttgtcatagcgatTacatatttcttgaaacacca	12	16	5	8	1	3	1	1	1	2	0	3	2	3	1	1	0	3	1	1	0	5	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chrX:7023838T>G	ENST00000381077.5	-	2	179	c.103A>C	c.(103-105)Aat>Cat	p.N35H	HDHD1_ENST00000424830.2_Missense_Mutation_p.N58H|HDHD1_ENST00000540122.1_Missense_Mutation_p.N35H|HDHD1_ENST00000412827.2_Missense_Mutation_p.N35H|HDHD1_ENST00000498474.2_5'UTR	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	35					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						TCATAGCGATTACATATTTCT	0.393																																					p.N58H		.											.	HDHD1-130	0			c.A172C						.						55	46	49					X																	7023838		1847	4082	5929	SO:0001583	missense	8226	exon3			AGCGATTACATAT	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"family with sequence similarity 16, member A, X-linked", "haloacid dehalogenase-like hydrolase domain containing 1A"	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.103A>C	X.37:g.7023838T>G	ENSP00000370467:p.Asn35His	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	33	12	NM_001135565	0	0	1	6	5	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Missense_Mutation	SNP	ENST00000381077.5	37	CCDS48075.1	.	.	.	.	.	.	.	.	.	.	c	7.623	0.677318	0.14841	.	.	ENSG00000130021	ENST00000381077;ENST00000544385;ENST00000412827;ENST00000424830;ENST00000540122;ENST00000486446	T;T;T;T;T	0.30714	3.42;1.52;3.42;3.42;3.42	4.01	4.01	0.46588	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.660693	0.15594	N	0.254263	T	0.23766	0.0575	N	0.21282	0.65	0.09310	N	1	D;B;P;B;B	0.53745	0.962;0.346;0.711;0.045;0.136	B;B;P;B;B	0.46419	0.4;0.382;0.516;0.057;0.201	T	0.05500	-1.0881	10	0.45353	T	0.12	-18.7046	7.1959	0.25853	0.0:0.7837:0.0:0.2163	.	35;35;58;35;35	Q08623-3;Q08623-2;E9PAV8;E7EVH9;Q08623	.;.;.;.;HDHD1_HUMAN	H	35;51;35;58;35;35	ENSP00000370467:N35H;ENSP00000406260:N35H;ENSP00000396452:N58H;ENSP00000441208:N35H;ENSP00000430995:N35H	ENSP00000370467:N35H	N	-	1	0	HDHD1	7033838	0.177000	0.23109	0.002000	0.10522	0.370000	0.29829	0.823000	0.27366	0.559000	0.29153	-0.177000	0.13119	AAT	.		0.393	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080		G	7023838	T	G	7023838	3	3	103	1	0	0	0	0	1	0	0	0	7043	1754	61	5	716	5	HDHD1A	23	7023838	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		7023838	148246722	140	9200											
GPRASP1	9737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	101910063	101910063	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagccctcattgggaccTggttctgggctacagacgag	9	8	14	10	1	2	1	1	0	1	1	2	4	2	3	2	4	2	2	2	4	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chrX:101910063T>A	ENST00000361600.5	+	5	2023	c.1222T>A	c.(1222-1224)Tgg>Agg	p.W408R	GPRASP1_ENST00000415986.1_Missense_Mutation_p.W408R|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000444152.1_Missense_Mutation_p.W408R|GPRASP1_ENST00000537097.1_Missense_Mutation_p.W408R	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	408					endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						CATTGGGACCTGGTTCTGGGC	0.562																																					p.W408R		.											.	GPRASP1-131	0			c.T1222A						.						58	61	60					X																	101910063		2203	4300	6503	SO:0001583	missense	9737	exon3			GGGACCTGGTTCT	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"Armadillo repeat containing"	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.1222T>A	X.37:g.101910063T>A	ENSP00000355146:p.Trp408Arg	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	49	22	NM_001099411	0	0	0	1	1	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	37	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.398444	0.42512	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	2.32	2.32	0.28847	.	.	.	.	.	T	0.50786	0.1636	M	0.71036	2.16	0.25851	N	0.983946	D	0.64830	0.994	D	0.79784	0.993	T	0.40961	-0.9535	9	0.12430	T	0.62	-2.7103	7.7932	0.29133	0.0:0.0:0.0:1.0	.	408	Q5JY77	GASP1_HUMAN	R	408	ENSP00000393691:W408R;ENSP00000409420:W408R;ENSP00000355146:W408R;ENSP00000445683:W408R	ENSP00000355146:W408R	W	+	1	0	GPRASP1	101796719	0.613000	0.27009	0.876000	0.34364	0.595000	0.36748	0.390000	0.20768	1.168000	0.42723	0.372000	0.22366	TGG	.		0.562	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		A	101910063	T	A	101910063	3	1	103	1	0	0	0	0	1	0	0	0	6743	1580	55	5	1224	5	GPRASP1	23	101910063	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	94886225	101910063	53360497	141	9201											
TAS1R3	83756	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1269265	1269265	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggcggccgagatcttcgtGgagtcagaactgcctctgag	8	8	14	11	3	3	3	1	1	2	2	4	5	3	4	2	3	2	0	2	3	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:1269265G>A	ENST00000339381.5	+	6	2012	c.1980G>A	c.(1978-1980)gtG>gtA	p.V660V		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	660					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		AGATCTTCGTGGAGTCAGAAC	0.697																																					p.V660V													.	TAS1R3-22	0			c.G1980A						.						27	30	29					1																	1269265		2198	4296	6494	SO:0001819	synonymous_variant	83756	exon6			CTTCGTGGAGTCA	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1980G>A	1.37:g.1269265G>A		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_152228	0	0	0	0	0	Q5TA49|Q8NGW9	Silent	SNP	ENST00000339381.5	37	CCDS30556.1																																																																																			.		0.697	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			A	1269265	G	A	1269265	2	1	104	1	0	0	0	0	0	0	0	1	15596	1335	47	2		2	TAS1R3	1	1269265	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		1269265	247981356	1	9202											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	19448476	19448477	+	Frame_Shift_Ins	INS	-	-	A																															ttgatggttcgctgggcggcINSaatctctgcacaggctttca																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:19448476_19448477insA	ENST00000375254.3	-	67	9873_9874	c.9846_9847insT	c.(9844-9849)attgccfs	p.A3283fs	UBR4_ENST00000375217.2_Frame_Shift_Ins_p.A3276fs|UBR4_ENST00000375226.2_Frame_Shift_Ins_p.A3259fs|UBR4_ENST00000375267.2_Frame_Shift_Ins_p.A3283fs	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3283					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CGCTGGGCGGCAATCTCTGCAC	0.485																																					p.A3283fs		.											.	UBR4-612	0			c.9847_9848insT						.																																			SO:0001589	frameshift_variant	23352	exon67			.	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.9847dupT	1.37:g.19448478_19448478dupA	ENSP00000364403:p.Ala3283fs	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	75	30	NM_020765	0	0	0	0	0	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Frame_Shift_Ins	INS	ENST00000375254.3	37	CCDS189.1																																																																																			.		0.485	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19448477	-	A	19448476	7	5	104	1	0	1	1	0	0	0	0	0	16937	710	25	0	5864	0	UBR4	1	19448476	Frame_Shift_Ins	INS	-	TCGA-DZ-6133-01A-11D-1961-08	18179211	19448476	229802145	2	9203											
EPHA8	2046	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22902942	22902942	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctactacctggagtcggaccGcgacctgggggccagcacac	8	5	13	15	3	0	0	0	0	0	0	1	3	0	2	4	4	3	1	4	4	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:22902942G>A	ENST00000166244.3	+	3	464	c.392G>A	c.(391-393)cGc>cAc	p.R131H	EPHA8_ENST00000538803.1_Missense_Mutation_p.R131H|EPHA8_ENST00000374644.4_Missense_Mutation_p.R131H	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	131	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GAGTCGGACCGCGACCTGGGG	0.587																																					p.R131H													.	EPHA8-1380	0			c.G392A						.						66	61	63					1																	22902942		2203	4300	6503	SO:0001583	missense	2046	exon3			CGGACCGCGACCT	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3391	protein-coding gene	gene with protein product		176945	"EphA8"	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.392G>A	1.37:g.22902942G>A	ENSP00000166244:p.Arg131His	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	49	22	NM_020526	0	0	0	0	0	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331358	0.41297	.	.	ENSG00000070886	ENST00000166244;ENST00000374644;ENST00000538803	T;T;T	0.03580	3.88;3.88;3.88	4.29	4.29	0.51040	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000001	T	0.07052	0.0179	N	0.24115	0.695	0.48341	D	0.999635	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.966	T	0.52830	-0.8523	10	0.15952	T	0.53	.	9.2953	0.37811	0.1004:0.0:0.8996:0.0	.	131;131	P29322;P29322-2	EPHA8_HUMAN;.	H	131	ENSP00000166244:R131H;ENSP00000363775:R131H;ENSP00000440274:R131H	ENSP00000166244:R131H	R	+	2	0	EPHA8	22775529	0.994000	0.37717	0.994000	0.49952	0.981000	0.71138	2.605000	0.46283	2.212000	0.71576	0.442000	0.29010	CGC	.		0.587	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22902942	G	A	22902942	3	1	104	1	0	0	0	0	1	0	0	0	5186	1087	38	1	402	1	EPHA8	1	22902942	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	3454466	22902942	226347679	3	9204											
KDM4A	9682	broad.mit.edu	37	chr1	44169937	44169937	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcttcaatgagattttcAcagagaaagaggttaagcaa	15	10	10	6	1	2	3	2	1	0	3	2	5	2	3	0	1	2	3	0	1	4	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:44169937A>G	ENST00000372396.3	+	22	3225	c.3091A>G	c.(3091-3093)Aca>Gca	p.T1031A	KDM4A-AS1_ENST00000453015.1_RNA|KDM4A-AS1_ENST00000418149.1_RNA|KDM4A-AS1_ENST00000434346.1_RNA|KDM4A-AS1_ENST00000439057.1_RNA|KDM4A-AS1_ENST00000398804.3_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	1031					cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						TGAGATTTTCACAGAGAAAGA	0.438																																					p.T1031A													.	KDM4A-227	0			c.A3091G						.						135	142	139					1																	44169937		2203	4300	6503	SO:0001583	missense	9682	exon22			ATTTTCACAGAGA	AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	22978	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 3A", "tudor domain containing 14A"	609764	"jumonji domain containing 2", "jumonji domain containing 2A"	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.3091A>G	1.37:g.44169937A>G	ENSP00000361473:p.Thr1031Ala	Somatic	241	0		WXS	Illumina HiSeq	Phase_I	182	4	NM_014663	0	0	103	103	0	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	37	CCDS491.1	.	.	.	.	.	.	.	.	.	.	A	9.454	1.091429	0.20471	.	.	ENSG00000066135	ENST00000372396	T	0.70749	-0.51	5.86	5.86	0.93980	.	0.200756	0.53938	D	0.000060	T	0.56232	0.1971	L	0.29908	0.895	0.35890	D	0.82957	B	0.09022	0.002	B	0.08055	0.003	T	0.58482	-0.7629	10	0.18710	T	0.47	-14.4805	10.8641	0.46844	0.9212:0.0:0.0788:0.0	.	1031	O75164	KDM4A_HUMAN	A	1031	ENSP00000361473:T1031A	ENSP00000361473:T1031A	T	+	1	0	KDM4A	43942524	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.878000	0.56130	2.232000	0.73038	0.533000	0.62120	ACA	.		0.438	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		G	44169937	A	G	44169937	3	3	104	1	0	0	0	0	1	0	0	0	8149	159	6	3	3173	3	KDM4A	1	44169937	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	21266995	44169937	205080684	4	9205											
SLC6A9	6536	broad.mit.edu	37	chr1	44467233	44467233	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggccatgaagccgaggatGgagaagatgacgaagccagc	13	5	15	8	2	0	4	0	2	0	2	0	8	0	5	3	3	3	0	3	3	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:44467233G>C	ENST00000360584.2	-	9	1439	c.1248C>G	c.(1246-1248)tcC>tcG	p.S416S	SLC6A9_ENST00000475075.2_Silent_p.S232S|SLC6A9_ENST00000357730.2_Silent_p.S362S|SLC6A9_ENST00000537678.1_Silent_p.S278S|SLC6A9_ENST00000372310.3_Silent_p.S343S|SLC6A9_ENST00000372306.3_Silent_p.S343S|SLC6A9_ENST00000372307.3_Silent_p.S278S	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	416					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	AGCCGAGGATGGAGAAGATGA	0.597																																					p.S416S													.	SLC6A9-90	0			c.C1248G						.						169	160	163					1																	44467233		2203	4300	6503	SO:0001819	synonymous_variant	6536	exon9			GAGGATGGAGAAG	S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"Solute carriers"	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.1248C>G	1.37:g.44467233G>C		Somatic	218	0		WXS	Illumina HiSeq	Phase_I	115	4	NM_201649	0	0	7	7	0	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Silent	SNP	ENST00000360584.2	37	CCDS41317.1																																																																																			.		0.597	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649		C	44467233	G	C	44467233	2	2	104	1	0	0	0	0	0	0	0	1	14723	1335	47	4		4	SLC6A9	1	44467233	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	297296	44467233	204783388	5	9206											
FGGY	55277	broad.mit.edu	37	chr1	59812021	59812021	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtcctccagtacgtcggggGggtgatgtctgtggaaatgc	6	11	16	8	2	1	1	0	1	1	0	4	2	3	2	2	4	2	1	2	4	2	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:59812021G>C	ENST00000303721.7	+	4	590	c.416G>C	c.(415-417)gGg>gCg	p.G139A	FGGY_ENST00000474476.1_3'UTR|FGGY_ENST00000371218.4_Missense_Mutation_p.G139A|FGGY_ENST00000371212.1_Intron	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	139					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					TACGTCGGGGGGGTGATGTCT	0.502																																					p.G139A													.	FGGY-69	0			c.G416C						.						138	106	116					1																	59812021		2203	4300	6503	SO:0001583	missense	55277	exon4			TCGGGGGGGTGAT		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.416G>C	1.37:g.59812021G>C	ENSP00000305922:p.Gly139Ala	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	50	4	NM_001113411	0	0	53	53	0	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	37	CCDS611.2	.	.	.	.	.	.	.	.	.	.	G	17.72	3.458181	0.63401	.	.	ENSG00000172456	ENST00000413489;ENST00000371218;ENST00000303721	T;T;T	0.58797	0.31;0.31;0.31	5.49	5.49	0.81192	Carbohydrate kinase, FGGY, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83519	0.5272	H	0.94658	3.565	0.80722	D	1	D;D;D	0.89917	1.0;0.993;0.997	D;D;D	0.97110	1.0;0.932;0.986	D	0.87429	0.2387	9	.	.	.	-16.3207	19.1799	0.93619	0.0:0.0:1.0:0.0	.	139;139;139	Q96C11-3;F2Z2V1;Q96C11	.;.;FGGY_HUMAN	A	139	ENSP00000406607:G139A;ENSP00000360262:G139A;ENSP00000305922:G139A	.	G	+	2	0	FGGY	59584609	1.000000	0.71417	0.591000	0.28745	0.122000	0.20287	8.580000	0.90784	2.857000	0.98124	0.650000	0.86243	GGG	.		0.502	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		C	59812021	G	C	59812021	3	2	104	1	0	0	0	0	1	0	0	0	5890	1232	43	4	426	4	FGGY	1	59812021	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	15344788	59812021	189438600	6	9207											
VANGL1	81839	ucsc.edu	37	chr1	116226588	116226588	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtaacaatgccactggcCagtcccgggccatgattgct	9	8	10	14	1	0	1	0	1	0	0	1	1	1	1	5	2	3	2	5	2	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:116226588C>T	ENST00000355485.2	+	6	1241	c.970C>T	c.(970-972)Cag>Tag	p.Q324*	VANGL1_ENST00000369509.1_Nonsense_Mutation_p.Q324*|VANGL1_ENST00000310260.3_Nonsense_Mutation_p.Q324*|VANGL1_ENST00000369510.4_Nonsense_Mutation_p.Q322*|VANGL1_ENST00000474344.1_3'UTR	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	324					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TGCCACTGGCCAGTCCCGGGC	0.522																																					p.Q324X													.	VANGL1-226	0			c.C970T						.						59	60	60					1																	116226588		2203	4300	6503	SO:0001587	stop_gained	81839	exon6			ACTGGCCAGTCCC	AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218			15512	protein-coding gene	gene with protein product		610132	"vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila)", "vang-like 1 (van gogh, Drosophila)"			11956595, 12011995	Standard	NM_001172411		Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.970C>T	1.37:g.116226588C>T	ENSP00000347672:p.Gln324*	Somatic	129	0		WXS	Illumina HiSeq		53	5	NM_001172412	1	0	23	24	0	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Nonsense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	38	6.881575	0.97908	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	.	.	.	4.76	4.76	0.60689	.	0.122019	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-2.7749	17.9983	0.89191	0.0:1.0:0.0:0.0	.	.	.	.	X	324;322;324;324	.	ENSP00000310800:Q324X	Q	+	1	0	VANGL1	116028111	1.000000	0.71417	0.998000	0.56505	0.839000	0.47603	7.313000	0.78978	2.474000	0.83562	0.551000	0.68910	CAG	.		0.522	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			T	116226588	C	T	116226588	4	4	104	1	0	0	0	0	0	1	0	0	17152	595	21	2	988	2	VANGL1	1	116226588	Nonsense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	56414567	116226588	133024033	7	9208											
PSMB4	5692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151372078	151372078	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actaagatggaagcgtttttGgggtcgcggtccggactttg	7	12	15	7	4	0	1	0	0	0	1	2	3	1	3	1	5	1	1	1	5	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:151372078G>A	ENST00000290541.6	+	1	69	c.15G>A	c.(13-15)ttG>ttA	p.L5L		NM_002796.2	NP_002787.2	P28070	PSB4_HUMAN	proteasome (prosome, macropain) subunit, beta type, 4	5					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	lipopolysaccharide binding (GO:0001530)|threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|lung(9)|ovary(2)|prostate(1)|skin(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AAGCGTTTTTGGGGTCGCGGT	0.542																																					p.L5L		.											.	PSMB4-92	0			c.G15A						.						56	61	59					1																	151372078		2202	4297	6499	SO:0001819	synonymous_variant	5692	exon1			GTTTTTGGGGTCG	D26600	CCDS996.1	1q21	2008-02-05			ENSG00000159377	ENSG00000159377		"Proteasome (prosome, macropain) subunits"	9541	protein-coding gene	gene with protein product		602177				7918633	Standard	NM_002796		Approved	HN3, PROS26	uc001eyc.1	P28070	OTTHUMG00000012494	ENST00000290541.6:c.15G>A	1.37:g.151372078G>A		Somatic	274	1		WXS	Illumina HiSeq	Phase_I	135	55	NM_002796	0	0	45	87	42	B2R9L3|P31148|Q5SZS5|Q6IBI4|Q969L6	Silent	SNP	ENST00000290541.6	37	CCDS996.1																																																																																			.		0.542	PSMB4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034885.1	NM_002796		A	151372078	G	A	151372078	2	1	104	1	0	0	0	0	0	0	0	1	12708	1339	47	2		2	PSMB4	1	151372078	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	35145490	151372078	97878543	8	9209											
C1orf66	51093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156705540	156705540	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtgcagcgggggctacagcGagtggggctagatccccagc	7	6	17	11	2	0	1	0	0	0	1	1	2	1	1	2	4	5	3	2	4	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:156705540G>A	ENST00000368216.4	+	7	1775	c.1145G>A	c.(1144-1146)cGa>cAa	p.R382Q	MRPL24_ENST00000478899.1_5'Flank|RRNAD1_ENST00000368218.4_Silent_p.A220A|RRNAD1_ENST00000476229.1_Silent_p.A97A	NM_015997.3	NP_057081.3	Q96FB5	RRNAD_HUMAN	ribosomal RNA adenine dimethylase domain containing 1	382						integral component of membrane (GO:0016021)	rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)	9						GGGCTACAGCGAGTGGGGCTA	0.547																																					p.R382Q		.											.	RRNAD1-90	0			c.G1145A						.						78	71	74					1																	156705540		2203	4300	6503	SO:0001583	missense	51093	exon7			TACAGCGAGTGGG	BC011382	CCDS1154.1, CCDS44246.1	1q23.1	2011-01-28	2011-01-28	2011-01-28	ENSG00000143303	ENSG00000143303			24273	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 66"	C1orf66		10810093, 310876	Standard	NM_015997		Approved	CGI-41	uc001fpu.3	Q96FB5	OTTHUMG00000041302	ENST00000368216.4:c.1145G>A	1.37:g.156705540G>A	ENSP00000357199:p.Arg382Gln	Somatic	145	2		WXS	Illumina HiSeq	Phase_I	76	37	NM_015997	0	0	19	25	6	D3DVC7|Q4VX71|Q5SZ03|Q9Y358	Missense_Mutation	SNP	ENST00000368216.4	37	CCDS1154.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.21|15.21	2.764513|2.764513	0.49574|0.49574	.|.	.|.	ENSG00000143303|ENSG00000143303	ENST00000522237|ENST00000368216	.|T	.|0.47177	.|0.85	4.93|4.93	4.93|4.93	0.64822|0.64822	.|.	.|0.069785	.|0.64402	.|D	.|0.000017	T|T	0.51381|0.51381	0.1671|0.1671	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|P	.|0.56865	.|0.808	T|T	0.55366|0.55366	-0.8152|-0.8152	4|9	.|0.59425	.|D	.|0.04	-14.6586|-14.6586	12.7396|12.7396	0.57243|0.57243	0.0:0.0:0.8351:0.1649|0.0:0.0:0.8351:0.1649	.|.	.|382	.|Q96FB5	.|RRNAD_HUMAN	K|Q	122|382	.|ENSP00000357199:R382Q	.|ENSP00000357199:R382Q	E|R	+|+	1|2	0|0	RRNAD1|RRNAD1	154972164|154972164	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.925000|0.925000	0.55904|0.55904	5.776000|5.776000	0.68924|0.68924	2.555000|2.555000	0.86185|0.86185	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.		0.547	RRNAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098973.1	NM_015997		A	156705540	G	A	156705540	3	1	104	1	0	0	0	0	1	0	0	0	2062	1058	37	1	1171	1	C1orf66	1	156705540	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	5333462	156705540	92545081	9	9210											
INSRR	3645	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156823725	156823725	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcagtccccagtcaatGgtggagaggtggcagagctc	9	7	15	10	0	1	2	1	0	0	2	3	3	2	2	2	4	3	4	2	4	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:156823725G>A	ENST00000368195.3	-	2	852	c.456C>T	c.(454-456)acC>acT	p.T152T	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	152					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCAGTCAATGGTGGAGAGGT	0.642																																					p.T152T													.	INSRR-1403	0			c.C456T						.						62	55	57					1																	156823725		2203	4300	6503	SO:0001819	synonymous_variant	3645	exon2			GTCAATGGTGGAG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.456C>T	1.37:g.156823725G>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			.		0.642	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156823725	G	A	156823725	2	1	104	1	0	0	0	0	0	0	0	1	7795	1335	47	2		2	INSRR	1	156823725	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	118185	156823725	92426896	10	9211											
PLEKHA6	22874	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204226699	204226699	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctagaggcggcatccagctCatcataatagactggctgcc	10	8	11	12	1	2	2	2	0	0	2	3	2	3	2	2	3	2	4	2	3	3	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:204226699C>T	ENST00000272203.3	-	9	1622	c.1306G>A	c.(1306-1308)Gag>Aag	p.E436K	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.E456K	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	436										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GCATCCAGCTCATCATAATAG	0.687																																					p.E436K													.	PLEKHA6-654	0			c.G1306A						.						13	15	14					1																	204226699		2193	4292	6485	SO:0001583	missense	22874	exon9			CCAGCTCATCATA	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"Pleckstrin homology (PH) domain containing"	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.1306G>A	1.37:g.204226699C>T	ENSP00000272203:p.Glu436Lys	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	20	12	NM_014935	0	0	15	26	11	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142058	0.77775	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.10288	2.89;3.35	5.67	5.67	0.87782	.	0.095403	0.45606	D	0.000345	T	0.29850	0.0746	L	0.54323	1.7	0.80722	D	1	D;D	0.71674	0.998;0.982	D;D	0.76071	0.987;0.952	T	0.00156	-1.1978	10	0.27785	T	0.31	-32.9148	19.7263	0.96165	0.0:1.0:0.0:0.0	.	456;436	Q5VTI5;Q9Y2H5	.;PKHA6_HUMAN	K	436;456	ENSP00000272203:E436K;ENSP00000402046:E456K	ENSP00000272203:E436K	E	-	1	0	PLEKHA6	202493322	0.998000	0.40836	0.987000	0.45799	0.762000	0.43233	3.804000	0.55568	2.837000	0.97791	0.655000	0.94253	GAG	.		0.687	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		T	204226699	C	T	204226699	3	4	104	1	0	0	0	0	1	0	0	0	12086	835	29	2	1896	2	PLEKHA6	1	204226699	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	47402974	204226699	45023922	11	9212											
KCNH1	3756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	211192165	211192165	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggtggtggaatctgatcaGcaaaaccaatcttccctgga	11	10	11	9	0	3	1	1	1	2	0	4	3	4	3	2	4	2	1	2	4	4	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:211192165G>A	ENST00000271751.4	-	6	1019	c.992C>T	c.(991-993)gCt>gTt	p.A331V	KCNH1_ENST00000367007.4_Intron			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	331					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		AATCTGATCAGCAAAACCAAT	0.448																																					p.A331V		.											.	KCNH1-94	0			c.C992T						.						184	165	171					1																	211192165		2203	4300	6503	SO:0001583	missense	3756	exon6			TGATCAGCAAAAC	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.992C>T	1.37:g.211192165G>A	ENSP00000271751:p.Ala331Val	Somatic	229	1		WXS	Illumina HiSeq	Phase_I	171	59	NM_172362	0	0	0	0	0	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	g	9.957	1.221740	0.22457	.	.	ENSG00000143473	ENST00000271751	D	0.98835	-5.17	4.23	4.23	0.50019	Ion transport (1);	0.648179	0.14275	N	0.329938	D	0.93367	0.7885	N	0.03115	-0.41	0.80722	D	1	B	0.11235	0.004	B	0.14578	0.011	D	0.89761	0.3947	10	0.29301	T	0.29	.	8.1471	0.31119	0.1091:0.0:0.8908:0.0	.	331	O95259	KCNH1_HUMAN	V	331	ENSP00000271751:A331V	ENSP00000271751:A331V	A	-	2	0	KCNH1	209258788	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.765000	0.38481	2.349000	0.79799	0.558000	0.71614	GCT	.		0.448	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	211192165	G	A	211192165	3	1	104	1	0	0	0	0	1	0	0	0	8052	971	34	2	2001	2	KCNH1	1	211192165	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	6965466	211192165	38058456	12	9213											
SPATA17	128153	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	217975148	217975148	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtcctatttcttacaaaGaacaattccgaagtgaaaat	16	12	6	7	1	1	2	0	1	1	1	3	3	3	2	2	1	2	0	2	1	8	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:217975148G>T	ENST00000366933.4	+	9	1016	c.961G>T	c.(961-963)Gaa>Taa	p.E321*	SPATA17_ENST00000471021.1_3'UTR	NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	321						cytoplasm (GO:0005737)		p.E321Q(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		TTCTTACAAAGAACAATTCCG	0.294																																					p.E321X		.											.	SPATA17-69	1	Substitution - Missense(1)	urinary_tract(1)	c.G961T						.						50	51	51					1																	217975148		2200	4289	6489	SO:0001587	stop_gained	128153	exon9			TACAAAGAACAAT	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"IQ motif containing H"	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.961G>T	1.37:g.217975148G>T	ENSP00000355900:p.Glu321*	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	62	28	NM_138796	0	0	2	5	3	A5D6N2	Nonsense_Mutation	SNP	ENST00000366933.4	37	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596073	0.46318	.	.	ENSG00000162814	ENST00000366933	.	.	.	4.9	-9.8	0.00490	.	0.673920	0.13287	N	0.399280	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	5.0379	3.3861	0.07272	0.4661:0.3189:0.0955:0.1195	.	.	.	.	X	321	.	ENSP00000355900:E321X	E	+	1	0	SPATA17	216041771	0.011000	0.17503	0.000000	0.03702	0.106000	0.19336	0.664000	0.25068	-2.528000	0.00493	-0.253000	0.11424	GAA	.		0.294	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		T	217975148	G	T	217975148	4	4	104	1	0	0	0	0	0	1	0	0	15034	943	33	4	995	4	SPATA17	1	217975148	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	6782983	217975148	31275473	13	9214											
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228494234	228494234	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccgggagccacggcttcagGgctgcaccgcggagctggtg	5	5	18	13	4	1	0	1	0	0	0	1	2	1	2	3	5	3	4	3	5	0	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:228494234G>A	ENST00000422127.1	+	44	11865	c.11821G>A	c.(11821-11823)Ggc>Agc	p.G3941S	OBSCN_ENST00000284548.11_Missense_Mutation_p.G3941S|OBSCN_ENST00000366707.4_Missense_Mutation_p.G1575S|OBSCN_ENST00000570156.2_Missense_Mutation_p.G4898S|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1060S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3941	Ig-like 40.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACGGCTTCAGGGCTGCACCGC	0.632																																					p.G4898S		.											.	OBSCN-403	0			c.G14692A						.						31	35	34					1																	228494234		1988	4166	6154	SO:0001583	missense	84033	exon55			CTTCAGGGCTGCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11821G>A	1.37:g.228494234G>A	ENSP00000409493:p.Gly3941Ser	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	61	30	NM_001271223	0	0	0	5	5	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626354	0.66901	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.071555	0.53938	D	0.000043	D	0.85452	0.5700	M	0.89968	3.075	0.32886	D	0.511166	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	D	0.89300	0.3625	10	0.48119	T	0.1	.	18.9154	0.92503	0.0:0.0:1.0:0.0	.	3941;3941	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	3941;3941;1575;1060	ENSP00000284548:G3941S;ENSP00000409493:G3941S;ENSP00000355668:G1575S;ENSP00000355670:G1060S	ENSP00000284548:G3941S	G	+	1	0	OBSCN	226560857	1.000000	0.71417	0.595000	0.28798	0.119000	0.20118	7.341000	0.79300	2.488000	0.83962	0.462000	0.41574	GGC	.		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228494234	G	A	228494234	3	1	104	1	0	0	0	0	1	0	0	0	10838	1232	43	2	11991	2	OBSCN	1	228494234	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	10519086	228494234	20756387	14	9215											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112762	248112763	+	Frame_Shift_Del	DEL	TG	TG	-																															gagggcacagtgtttttgagTgccaccatctttctcgtgtt																								rs34851853|rs4925790|rs4925789	byFrequency	TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:248112762_248112763delTG	ENST00000357191.3	+	1	603_604	c.603_604delTG	c.(601-606)agtgccfs	p.A202fs	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	202			A -> T (in dbSNP:rs4925790).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TGTTTTTGAGTGCCACCATCTT	0.49																																					p.201_202del		.											.	OR2L8-70	0			c.603_604del						.																																			SO:0001589	frameshift_variant	391190	exon1			.	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.603_604delTG	1.37:g.248112762_248112763delTG	ENSP00000349719:p.Ala202fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	64	10	NM_001001963	0	0	0	0	0	Q6IF03	Frame_Shift_Del	DEL	ENST00000357191.3	37	CCDS31101.1																																																																																			.		0.49	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			-	248112763	TG	-	248112762	7	5	104	1	0	1	0	1	0	0	0	0	11035	1693	59	0	605	0	OR2L8	1	248112762	Frame_Shift_Del	DEL	TG	TCGA-DZ-6133-01A-11D-1961-08	19618528	248112762	1137859	15	9216											
PAPOLG	64895	broad.mit.edu	37	chr2	61009021	61009021	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgcttctaatttcacaggTaaatccatcagataggtatc	12	14	6	9	0	4	1	2	0	2	1	6	1	5	1	1	2	1	3	1	2	5	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:61009021T>C	ENST00000238714.3	+	11	1157	c.908T>C	c.(907-909)gTa>gCa	p.V303A	PAPOLG_ENST00000483370.1_3'UTR	NM_022894.3	NP_075045.2	Q9BWT3	PAPOG_HUMAN	poly(A) polymerase gamma	303					mRNA polyadenylation (GO:0006378)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	35	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)			ATTTCACAGGTAAATCCATCA	0.358																																					p.V303A	GBM(183;1497 2932 21839 46797)												.	PAPOLG-69	0			c.T908C						.						155	147	150					2																	61009021		2203	4300	6503	SO:0001630	splice_region_variant	64895	exon11			CACAGGTAAATCC	AC012498	CCDS1863.1	2p16.1	2008-02-08			ENSG00000115421	ENSG00000115421	2.7.7.19		14982	protein-coding gene	gene with protein product							Standard	NM_022894		Approved	FLJ12972	uc002sai.3	Q9BWT3	OTTHUMG00000129419	ENST00000238714.3:c.907-1T>C	2.37:g.61009021T>C		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	136	4	NM_022894	0	0	0	0	0	B2RBH4|Q59G05|Q969N1|Q9H8L2|Q9HAD0	Missense_Mutation	SNP	ENST00000238714.3	37	CCDS1863.1	.	.	.	.	.	.	.	.	.	.	T	17.04	3.287040	0.59867	.	.	ENSG00000115421	ENST00000238714	.	.	.	6.07	6.07	0.98685	Poly(A) polymerase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.78266	0.4256	M	0.73430	2.235	0.80722	D	1	P	0.42203	0.773	P	0.58928	0.848	T	0.79364	-0.1834	9	0.66056	D	0.02	-17.6449	16.3021	0.82825	0.0:0.0:0.0:1.0	.	303	Q9BWT3	PAPOG_HUMAN	A	303	.	ENSP00000238714:V303A	V	+	2	0	PAPOLG	60862525	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.781000	0.85668	2.326000	0.78906	0.533000	0.62120	GTA	.		0.358	PAPOLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251577.3	NM_022894	Missense_Mutation	C	61009021	T	C	61009021	5	2	104	1	0	0	0	0	0	0	1	0	11457	1652	57	3	950	3	PAPOLG	2	61009021	Splice_Site	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		61009021	182190352	16	9217											
TGFA	7039	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	70742029	70742029	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttctccaaggcctggcacGcagccaacacaatacctgtt	10	9	8	14	1	1	0	0	0	1	0	2	0	1	0	4	2	3	4	4	2	4	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:70742029G>A	ENST00000295400.6	-	2	303	c.56C>T	c.(55-57)gCg>gTg	p.A19V	TGFA_ENST00000418333.2_Missense_Mutation_p.A19V|TGFA_ENST00000450929.1_Missense_Mutation_p.A25V|TGFA_ENST00000445399.1_Missense_Mutation_p.A19V|TGFA_ENST00000460808.1_5'UTR|TGFA_ENST00000444975.1_Missense_Mutation_p.A25V	NM_001099691.2|NM_003236.3	NP_001093161.1|NP_003227.1	P01135	TGFA_HUMAN	transforming growth factor, alpha	19					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|mammary gland alveolus development (GO:0060749)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell division (GO:0051781)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mitosis (GO:0045840)|response to drug (GO:0042493)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)	p.A19V(1)		haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						GGCCTGGCACGCAGCCAACAC	0.597																																					p.A19V													.	TGFA-683	1	Substitution - Missense(1)	lung(1)	c.C56T						.						74	65	68					2																	70742029		2203	4300	6503	SO:0001583	missense	7039	exon2			TGGCACGCAGCCA		CCDS1905.1, CCDS46316.1	2p13	2012-10-02			ENSG00000163235	ENSG00000163235			11765	protein-coding gene	gene with protein product		190170				3459638, 10552925	Standard	NM_003236		Approved		uc002sgs.4	P01135	OTTHUMG00000129669	ENST00000295400.6:c.56C>T	2.37:g.70742029G>A	ENSP00000295400:p.Ala19Val	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	49	24	NM_001099691	0	0	10	17	7	A8K286|Q15577|Q53SK7|Q9BS56|Q9UEI3|Q9UKM1|Q9UKM2|Q9UKM3	Missense_Mutation	SNP	ENST00000295400.6	37	CCDS1905.1	.	.	.	.	.	.	.	.	.	.	G	5.866	0.344039	0.11126	.	.	ENSG00000163235	ENST00000295400;ENST00000445399;ENST00000418333;ENST00000450929;ENST00000444975;ENST00000394241	T;T;T;T;T;T	0.17213	2.55;2.31;2.31;2.3;2.29;2.3	5.14	2.6	0.31112	.	0.377651	0.24940	N	0.034385	T	0.07098	0.0180	N	0.08118	0	0.24501	N	0.994259	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.36553	-0.9743	10	0.20519	T	0.43	.	6.2326	0.20744	0.7672:0.0:0.2328:0.0	.	25;25;19;19;19;19;19	E7EPT6;F8VNR3;P01135-5;Q9UKM3;P01135-3;P01135-2;P01135	.;.;.;.;.;.;TGFA_HUMAN	V	19;19;19;25;25;19	ENSP00000295400:A19V;ENSP00000387493:A19V;ENSP00000404099:A19V;ENSP00000414127:A25V;ENSP00000404131:A25V;ENSP00000377787:A19V	ENSP00000295400:A19V	A	-	2	0	TGFA	70595537	1.000000	0.71417	0.917000	0.36280	0.231000	0.25187	2.007000	0.40883	0.435000	0.26365	-0.345000	0.07892	GCG	.		0.597	TGFA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251870.2			A	70742029	G	A	70742029	3	1	104	1	0	0	0	0	1	0	0	0	15847	1087	38	1	446	1	TGFA	2	70742029	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	9733008	70742029	172457344	17	9218											
DCTN1	1639	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74597431	74597431	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccatgagcttctggagcTtcacatgctcctgcttctct	5	16	7	13	0	3	1	1	1	2	0	6	2	5	2	2	1	4	4	2	1	0	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:74597431T>A	ENST00000361874.3	-	12	1486	c.1169A>T	c.(1168-1170)aAg>aTg	p.K390M	DCTN1_ENST00000409567.3_Missense_Mutation_p.K370M|DCTN1_ENST00000407639.2_Missense_Mutation_p.K256M|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.K383M|DCTN1_ENST00000409868.1_Missense_Mutation_p.K373M|DCTN1_ENST00000409240.1_Missense_Mutation_p.K353M|DCTN1_ENST00000409438.1_Missense_Mutation_p.K256M	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	390					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CTTCTGGAGCTTCACATGCTC	0.547																																					p.K390M													.	DCTN1-95	0			c.A1169T						.						67	62	64					2																	74597431		2203	4300	6503	SO:0001583	missense	1639	exon12			TGGAGCTTCACAT		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"p150 glued homolog (Drosophila)"	601143	"dynactin 1 (p150, Glued (Drosophila) homolog)"			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1169A>T	2.37:g.74597431T>A	ENSP00000354791:p.Lys390Met	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	69	22	NM_004082	0	0	92	138	46	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.229932	0.79688	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04;-0.99;-1.04	4.86	4.86	0.63082	.	0.000000	0.45606	D	0.000354	D	0.88738	0.6518	M	0.86953	2.85	0.80722	D	1	D;D;D;D;D;D	0.76494	0.997;0.994;0.999;0.997;0.994;0.997	D;D;D;D;D;D	0.77557	0.922;0.946;0.99;0.94;0.973;0.975	D	0.90590	0.4536	10	0.72032	D	0.01	-14.2356	13.5624	0.61797	0.0:0.0:0.0:1.0	.	370;353;390;383;256;256	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	M	390;383;373;256;256;353;373;370	ENSP00000354791:K390M;ENSP00000377571:K383M;ENSP00000384844:K256M;ENSP00000387270:K256M;ENSP00000386406:K353M;ENSP00000387327:K373M;ENSP00000386843:K370M	ENSP00000354791:K390M	K	-	2	0	DCTN1	74450939	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.845000	0.86875	2.029000	0.59856	0.528000	0.53228	AAG	.		0.547	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		A	74597431	T	A	74597431	3	1	104	1	0	0	0	0	1	0	0	0	4312	1609	56	5	2751	5	DCTN1	2	74597431	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	3855402	74597431	168601942	18	9219											
MAP4K4	9448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	102493544	102493544	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaaggtctatcctcttatCaaccgaagacgatttcaaca	13	10	8	10	2	4	1	2	0	2	1	5	4	5	2	2	2	2	0	2	2	6	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:102493544C>A	ENST00000347699.4	+	24	2886	c.2886C>A	c.(2884-2886)atC>atA	p.I962I	MAP4K4_ENST00000302217.5_Silent_p.I765I|MAP4K4_ENST00000324219.4_Silent_p.I1043I|MAP4K4_ENST00000350198.4_Silent_p.I881I|MAP4K4_ENST00000425019.1_Silent_p.I995I|MAP4K4_ENST00000413150.2_Silent_p.I877I|MAP4K4_ENST00000350878.4_Silent_p.I1002I|MAP4K4_ENST00000456652.1_Silent_p.I761I	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	962	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.|Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ATCCTCTTATCAACCGAAGAC	0.453																																					p.I996I		.											.	MAP4K4-547	0			c.C2988A						.						180	175	177					2																	102493544		2019	4184	6203	SO:0001819	synonymous_variant	9448	exon25			TCTTATCAACCGA	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2886C>A	2.37:g.102493544C>A		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	94	54	NM_145686	0	0	44	99	55	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.230967	0.22542	.	.	ENSG00000071054	ENST00000421882	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	T	0.60314	0.2259	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57974	-0.7718	4	.	.	.	.	8.8578	0.35238	0.15:0.7754:0.0:0.0745	.	.	.	.	K	779	.	.	Q	+	1	0	MAP4K4	101859976	0.991000	0.36638	1.000000	0.80357	0.976000	0.68499	0.386000	0.20702	2.717000	0.92951	0.655000	0.94253	CAA	.		0.453	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		A	102493544	C	A	102493544	2	1	104	1	0	0	0	0	0	0	0	1	9287	816	29	4		4	MAP4K4	2	102493544	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	27896113	102493544	140705829	19	9220											
UPP2	151531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	158971732	158971732	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtgctgggacagacagAtactgtatgtacaaaaccgg	13	9	11	8	1	1	2	0	0	1	2	1	3	1	3	1	2	4	3	1	2	5	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:158971732A>G	ENST00000005756.4	+	3	494	c.300A>G	c.(298-300)agA>agG	p.R100R	UPP2_ENST00000605860.1_Silent_p.R157R|UPP2_ENST00000409859.4_Silent_p.R157R|UPP2_ENST00000460456.1_Intron	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	100					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	GGACAGACAGATACTGTATGT	0.458																																					p.R157R		.											.	UPP2-90	0			c.A471G						.						105	104	104					2																	158971732		2203	4300	6503	SO:0001819	synonymous_variant	151531	exon5			AGACAGATACTGT	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.300A>G	2.37:g.158971732A>G		Somatic	140	0		WXS	Illumina HiSeq	Phase_I	131	39	NM_001135098	0	0	0	0	0	B3KV87	Silent	SNP	ENST00000005756.4	37	CCDS2207.1																																																																																			.		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		G	158971732	A	G	158971732	2	3	104	1	0	0	0	0	0	0	0	1	17046	330	12	3		3	UPP2	2	158971732	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	56478188	158971732	84227641	20	9221											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	179468605	179468605	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacggaagcatacttacatAtgggatctcctgcaacctct	13	10	7	11	1	2	0	0	0	2	0	3	2	2	2	2	2	6	2	2	2	6	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:179468605A>G	ENST00000591111.1	-	232	50110	c.49886T>C	c.(49885-49887)aTa>aCa	p.I16629T	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I9397T|TTN_ENST00000342992.6_Missense_Mutation_p.I15702T|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I9330T|TTN_ENST00000460472.2_Missense_Mutation_p.I9205T|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I18270T			Q8WZ42	TITIN_HUMAN	titin	16629			I -> M. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATACTTACATATGGGATCTCC	0.398																																					p.I18270T		.											.	TTN-636	0			c.T54809C						.						65	62	63					2																	179468605		1886	4096	5982	SO:0001583	missense	7273	exon282			TTACATATGGGAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.49886T>C	2.37:g.179468605A>G	ENSP00000465570:p.Ile16629Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	78	28	NM_001267550	0	0	3	4	1	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	10.22	1.289353	0.23478	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	6.06	4.85	0.62838	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36276	0.0961	L	0.52759	1.655	0.33898	D	0.638219	B;B;B;B	0.32245	0.361;0.361;0.361;0.361	B;B;B;B	0.24155	0.051;0.051;0.051;0.051	T	0.55490	-0.8133	9	0.87932	D	0	.	12.2928	0.54827	0.8732:0.0:0.0:0.1268	.	9205;9330;9397;16629	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	15702;9205;9397;9330;9205	ENSP00000343764:I15702T;ENSP00000434586:I9205T;ENSP00000340554:I9397T;ENSP00000352154:I9330T	ENSP00000340554:I9397T	I	-	2	0	TTN	179176850	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	1.934000	0.40163	2.323000	0.78572	0.528000	0.53228	ATA	.		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179468605	A	G	179468605	3	3	104	1	0	0	0	0	1	0	0	0	16768	449	16	3	53208	3	TTN	2	179468605	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	20496873	179468605	63730768	21	9222											
RPL37A	6168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	217364692	217364692	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaagatgaagagacgagcTgtggggatctggcactgtgg	11	7	16	7	1	1	3	0	1	1	2	1	6	1	4	1	4	1	2	1	4	2	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:217364692T>A	ENST00000491306.1	+	3	839	c.153T>A	c.(151-153)gcT>gcA	p.A51A	AC098820.3_ENST00000438978.1_RNA|RPL37A_ENST00000441179.2_Silent_p.A27A|RPL37A_ENST00000598925.1_Silent_p.A27A|AC098820.3_ENST00000453157.1_RNA|RPL37A_ENST00000446558.1_Silent_p.A51A|RPL37A_ENST00000456586.1_Silent_p.A27A|RPL37A_ENST00000600880.1_Silent_p.A51A|RPL37A_ENST00000427280.2_Silent_p.A27A	NM_000998.4	NP_000989.1	P61513	RL37A_HUMAN	ribosomal protein L37a	51					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|ovary(1)	2		Renal(323;0.0458)		Epithelial(149;3.51e-06)|all cancers(144;0.000249)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGACGAGCTGTGGGGATCT	0.443																																					p.A51A		.											.	RPL37A-91	0			c.T153A						.						129	125	126					2																	217364692		2203	4300	6503	SO:0001819	synonymous_variant	6168	exon3			ACGAGCTGTGGGG		CCDS2404.1	2q35	2011-04-06			ENSG00000197756	ENSG00000197756		"L ribosomal proteins"	10348	protein-coding gene	gene with protein product		613314				1437567	Standard	NM_000998		Approved	L37A	uc002vgf.3	P61513	OTTHUMG00000133052	ENST00000491306.1:c.153T>A	2.37:g.217364692T>A		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	177	92	NM_000998	0	0	1049	3198	2149	P12751|Q6FGF5	Silent	SNP	ENST00000491306.1	37	CCDS2404.1																																																																																			.		0.443	RPL37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256665.2	NM_000998		A	217364692	T	A	217364692	2	1	104	1	0	0	0	0	0	0	0	1	13622	1567	55	5		5	RPL37A	2	217364692	Silent	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	37896087	217364692	25834681	22	9223											
SP110	3431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	231077477	231077477	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgggatctgtttctcaccTgaagtgcttcttccttcctg	5	16	9	11	0	3	1	1	1	3	0	6	3	5	2	3	1	1	2	3	1	1	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:231077477T>G	ENST00000358662.4	-	4	660	c.582A>C	c.(580-582)tcA>tcC	p.S194S	SP110_ENST00000258382.5_Splice_Site_p.S194S|SP110_ENST00000392048.3_Splice_Site_p.S194S|SP110_ENST00000486146.2_5'UTR|SP110_ENST00000338556.3_5'UTR|SP110_ENST00000540870.1_Splice_Site_p.S200S|SP110_ENST00000258381.6_Splice_Site_p.S194S	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	194					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		GTTTCTCACCTGAAGTGCTTC	0.532																																					p.S200S		.											.	SP110-155	0			c.A600C						.						222	217	219					2																	231077477		2203	4300	6503	SO:0001630	splice_region_variant	3431	exon5			CTCACCTGAAGTG	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"interferon-induced protein 41, 30kD"	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.583+1A>C	2.37:g.231077477T>G		Somatic	352	2		WXS	Illumina HiSeq	Phase_I	274	147	NM_001185015	0	0	0	0	0	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	37	CCDS2474.1																																																																																			.		0.532	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	Silent	G	231077477	T	G	231077477	5	3	104	1	0	0	0	0	0	0	1	0	14993	1594	55	5	1687	5	SP110	2	231077477	Splice_Site	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	13712785	231077477	12121896	23	9224											
NBEAL2	23218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47049869	47049869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctggacctattttccacctgGcattggggtccgaaggccag	7	10	12	12	1	0	0	0	0	0	0	2	2	2	1	5	5	0	1	5	5	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:47049869G>A	ENST00000450053.3	+	51	7995	c.7816G>A	c.(7816-7818)Gca>Aca	p.A2606T	NBEAL2_ENST00000383740.2_Missense_Mutation_p.A855T|NBEAL2_ENST00000292309.5_Missense_Mutation_p.A2422T	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2606					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TTTCCACCTGGCATTGGGGTC	0.597																																					p.A2606T		.											.	NBEAL2-69	0			c.G7816A						.						49	48	48					3																	47049869		2037	4171	6208	SO:0001583	missense	23218	exon51			CACCTGGCATTGG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"WD repeat domain containing"	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.7816G>A	3.37:g.47049869G>A	ENSP00000415034:p.Ala2606Thr	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	43	25	NM_015175	0	0	17	51	34	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.62|16.62|16.62	3.173416|3.173416|3.173416	0.57584|0.57584|0.57584	.|.|.	.|.|.	ENSG00000160796|ENSG00000160796|ENSG00000160796	ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550|ENST00000443829|ENST00000416683	T;T;T|.|.	0.20069|.|.	2.1;2.1;2.1|.|.	5.15|5.15|5.15	5.15|5.15|5.15	0.70609|0.70609|0.70609	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.|.	0.716976|.|.	0.13800|.|.	N|.|.	0.361890|.|.	T|T|.	0.71558|0.71558|.	0.3354|0.3354|.	M|M|M	0.61703|0.61703|0.61703	1.905|1.905|1.905	0.38807|0.38807|0.38807	D|D|D	0.955327|0.955327|0.955327	B;B|.|.	0.26845|.|.	0.161;0.007|.|.	B;B|.|.	0.23852|.|.	0.049;0.01|.|.	T|T|.	0.71686|0.71686|.	-0.4518|-0.4518|.	10|5|.	0.33141|.|.	T|.|.	0.24|.|.	.|.|.	16.1634|16.1634|16.1634	0.81734|0.81734|0.81734	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	2422;2606|.|.	Q6ZNJ1-2;Q6ZNJ1|.|.	.;NBEL2_HUMAN|.|.	T|D|X	2422;855;2606;549|944|1893	ENSP00000292309:A2422T;ENSP00000373246:A855T;ENSP00000415034:A2606T|.|.	ENSP00000292309:A2422T|.|.	A|G|W	+|+|+	1|2|3	0|0|0	NBEAL2|NBEAL2|NBEAL2	47024873|47024873|47024873	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.988000|0.988000|0.988000	0.46212|0.46212|0.46212	0.695000|0.695000|0.695000	0.40330|0.40330|0.40330	4.551000|4.551000|4.551000	0.60740|0.60740|0.60740	2.669000|2.669000|2.669000	0.90835|0.90835|0.90835	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GCA|GGC|TGG	.		0.597	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		A	47049869	G	A	47049869	3	1	104	1	0	0	0	0	1	0	0	0	10214	1203	42	2	8018	2	NBEAL2	3	47049869	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		47049869	150972561	24	9225											
NICN1	84276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49463424	49463424	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatattctagccatgtcacaCagcatctgacacacacacac	14	8	5	14	0	3	1	1	1	2	0	3	2	3	1	1	0	2	1	1	0	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:49463424C>G	ENST00000273598.3	-	3	401	c.315G>C	c.(313-315)ctG>ctC	p.L105L	NICN1_ENST00000422593.1_5'UTR|NICN1_ENST00000436744.2_Intron|NICN1-AS1_ENST00000424915.1_RNA	NM_032316.3	NP_115692.1	Q9BSH3	NICN1_HUMAN	nicolin 1	105						microtubule (GO:0005874)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;4.52e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCATGTCACACAGCATCTGAC	0.567																																					p.L105L		.											.	NICN1-90	0			c.G315C						.						87	65	72					3																	49463424		2203	4300	6503	SO:0001819	synonymous_variant	84276	exon3			GTCACACAGCATC	AJ299740	CCDS2798.1	3p21.31	2008-07-18			ENSG00000145029	ENSG00000145029			18317	protein-coding gene	gene with protein product		611516				12392556	Standard	NM_032316		Approved	MGC12936	uc003cwz.1	Q9BSH3	OTTHUMG00000156848	ENST00000273598.3:c.315G>C	3.37:g.49463424C>G		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	41	13	NM_032316	0	0	2	3	1	Q8IZQ2	Silent	SNP	ENST00000273598.3	37	CCDS2798.1																																																																																			.		0.567	NICN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346224.3	NM_032316		G	49463424	C	G	49463424	2	3	104	1	0	0	0	0	0	0	0	1	10439	465	17	4		4	NICN1	3	49463424	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	2413555	49463424	148559006	25	9226											
SFMBT1	51460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52988412	52988412	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttaattctacctcttccAtaccagagccggcatctaga	11	11	6	13	1	3	2	0	0	3	2	4	2	4	2	4	1	4	2	4	1	4	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:52988412A>G	ENST00000394752.3	-	3	426	c.44T>C	c.(43-45)aTg>aCg	p.M15T	SFMBT1_ENST00000470575.1_5'UTR|SFMBT1_ENST00000296295.6_Missense_Mutation_p.M15T|SFMBT1_ENST00000394750.1_Missense_Mutation_p.M15T|SFMBT1_ENST00000358080.2_Missense_Mutation_p.M15T	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	15					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		TACCTCTTCCATACCAGAGCC	0.333																																					p.M15T		.											.	SFMBT1-91	0			c.T44C						.						111	116	114					3																	52988412		2203	4300	6503	SO:0001583	missense	51460	exon3			TCTTCCATACCAG	AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.44T>C	3.37:g.52988412A>G	ENSP00000378235:p.Met15Thr	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	226	135	NM_016329	0	0	8	28	20	Q402F7|Q96C73|Q9Y4Q9	Missense_Mutation	SNP	ENST00000394752.3	37	CCDS2867.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.536575	0.27475	.	.	ENSG00000163935	ENST00000394752;ENST00000358080;ENST00000296295;ENST00000394750;ENST00000482396;ENST00000483069;ENST00000497586	T;T;T;T;T;T	0.40756	2.62;2.62;2.62;2.62;2.03;1.02	5.7	5.7	0.88788	.	0.544403	0.20072	N	0.099858	T	0.31827	0.0809	N	0.24115	0.695	0.28463	N	0.915804	B	0.02656	0.0	B	0.17722	0.019	T	0.13335	-1.0513	10	0.24483	T	0.36	.	15.6127	0.76740	1.0:0.0:0.0:0.0	.	15	Q9UHJ3	SMBT1_HUMAN	T	15	ENSP00000378235:M15T;ENSP00000350789:M15T;ENSP00000296295:M15T;ENSP00000378233:M15T;ENSP00000418860:M15T;ENSP00000418950:M15T	ENSP00000296295:M15T	M	-	2	0	SFMBT1	52963452	1.000000	0.71417	0.990000	0.47175	0.489000	0.33432	5.542000	0.67218	2.164000	0.68074	0.477000	0.44152	ATG	.		0.333	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		G	52988412	A	G	52988412	3	3	104	1	0	0	0	0	1	0	0	0	14189	217	8	3	2632	3	SFMBT1	3	52988412	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	3524988	52988412	145034018	26	9227											
LRIG1	26018	broad.mit.edu	37	chr3	66460690	66460690	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaccaggctgttgtactcCaggtgcctgcaatgacagcc	8	10	10	13	0	1	1	0	1	1	0	2	1	2	1	4	2	5	4	4	2	3	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:66460690C>A	ENST00000273261.3	-	7	1322	c.798G>T	c.(796-798)ctG>ctT	p.L266L	LRIG1_ENST00000383703.3_Silent_p.L266L	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	266					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TGTTGTACTCCAGGTGCCTGC	0.567																																					p.L266L													.	LRIG1-230	0			c.G798T						.						146	136	139					3																	66460690		2203	4300	6503	SO:0001819	synonymous_variant	26018	exon7			GTACTCCAGGTGC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.798G>T	3.37:g.66460690C>A		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	275	8	NM_015541	0	0	0	0	0	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			.		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		A	66460690	C	A	66460690	2	1	104	1	0	0	0	0	0	0	0	1	8969	581	21	4		4	LRIG1	3	66460690	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	13472278	66460690	131561740	27	9228											
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101390027	101390027	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctcctttctcaataaaaAgatctcgaaaatactcgcta	15	11	4	11	2	2	1	1	0	2	1	6	2	3	1	1	0	2	2	1	0	8	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:101390027A>G	ENST00000312938.4	-	3	1305	c.725T>C	c.(724-726)cTt>cCt	p.L242P	ZBTB11_ENST00000461821.1_3'UTR	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	242	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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						CTCAATAAAAAGATCTCGAAA	0.363																																					p.L242P		.											.	ZBTB11-91	0			c.T725C						.						73	73	73					3																	101390027		2203	4300	6503	SO:0001583	missense	27107	exon3			ATAAAAAGATCTC	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.725T>C	3.37:g.101390027A>G	ENSP00000326200:p.Leu242Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	101	29	NM_014415	0	0	13	19	6	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495399	0.85069	.	.	ENSG00000066422	ENST00000312938	T	0.73681	-0.77	5.48	5.48	0.80851	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.88948	0.6576	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91470	0.5196	10	0.87932	D	0	-12.2938	15.5729	0.76354	1.0:0.0:0.0:0.0	.	242	O95625	ZBT11_HUMAN	P	242	ENSP00000326200:L242P	ENSP00000326200:L242P	L	-	2	0	ZBTB11	102872717	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.092000	0.63282	0.533000	0.62120	CTT	.		0.363	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		G	101390027	A	G	101390027	3	3	104	1	0	0	0	0	1	0	0	0	17556	72	3	3	2472	3	ZBTB11	3	101390027	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	34929337	101390027	96632403	28	9229											
SLCO2A1	6578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	133692538	133692538	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggtgtactggtagggctcGgagaggaagtgtgggagggt	9	8	21	3	1	0	1	0	0	0	1	1	4	0	3	0	7	1	3	0	7	4	2	rs150677069		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:133692538G>C	ENST00000310926.4	-	3	639	c.366C>G	c.(364-366)tcC>tcG	p.S122S	SLCO2A1_ENST00000493729.1_Silent_p.S122S|SLCO2A1_ENST00000478651.1_5'UTR	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	122					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	GGTAGGGCTCGGAGAGGAAGT	0.582																																					p.S122S		.											.	SLCO2A1-90	0			c.C366G						.						87	73	78					3																	133692538		2203	4300	6503	SO:0001819	synonymous_variant	6578	exon3			GGGCTCGGAGAGG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"Solute carriers"	10955	protein-coding gene	gene with protein product		601460	"solute carrier family 21 (prostaglandin transporter), member 2", "matrin F/G 1"	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.366C>G	3.37:g.133692538G>C		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	34	9	NM_005630	0	0	141	195	54	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			G|1.000;A|0.000		0.582	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		C	133692538	G	C	133692538	2	2	104	1	0	0	0	0	0	0	0	1	14758	1103	39	4		4	SLCO2A1	3	133692538	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	32302511	133692538	64329892	29	9230											
ATP13A3	79572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	194146121	194146121	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttttgaaaaggcaattGccactatgaggtactgaaaa	14	12	8	7	0	0	3	0	3	0	0	1	3	1	3	2	2	2	2	2	2	7	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:194146121G>A	ENST00000439040.1	-	30	4054	c.3263C>T	c.(3262-3264)gCa>gTa	p.A1088V	ATP13A3_ENST00000256031.4_Missense_Mutation_p.A1088V			Q9H7F0	AT133_HUMAN	ATPase type 13A3	1088						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		AAAGGCAATTGCCACTATGAG	0.353																																					p.A1088V		.											.	ATP13A3-69	0			c.C3263T						.						97	90	93					3																	194146121		1821	4076	5897	SO:0001583	missense	79572	exon29			GCAATTGCCACTA	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"ATPases / P-type"	24113	protein-coding gene	gene with protein product	"ATPase family homolog up regulated in senescence cells"	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.3263C>T	3.37:g.194146121G>A	ENSP00000416508:p.Ala1088Val	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	101	54	NM_024524	0	0	26	109	83	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	37	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207024	0.95033	.	.	ENSG00000133657	ENST00000439040;ENST00000256031	T;T	0.74947	-0.89;-0.89	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.87204	0.6119	M	0.82630	2.6	0.80722	D	1	D	0.65815	0.995	D	0.66847	0.947	D	0.87360	0.2343	10	0.49607	T	0.09	-22.6896	19.4395	0.94813	0.0:0.0:1.0:0.0	.	1088	Q9H7F0	AT133_HUMAN	V	1088	ENSP00000416508:A1088V;ENSP00000256031:A1088V	ENSP00000256031:A1088V	A	-	2	0	ATP13A3	195627410	1.000000	0.71417	0.989000	0.46669	0.980000	0.70556	9.476000	0.97823	2.591000	0.87537	0.591000	0.81541	GCA	.		0.353	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		A	194146121	G	A	194146121	3	1	104	1	0	0	0	0	1	0	0	0	1126	1319	46	2	433	2	ATP13A3	3	194146121	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	60453583	194146121	3876309	30	9231											
ZBTB49	166793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	4322599	4322599	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagagctcagactctttctcCcaagacacgtctgtgacgct	9	10	8	14	2	4	4	1	1	3	3	5	4	4	4	1	0	1	2	1	0	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:4322599C>A	ENST00000337872.4	+	8	1975	c.1854C>A	c.(1852-1854)tcC>tcA	p.S618S	ZBTB49_ENST00000538529.1_Silent_p.S101S|ZBTB49_ENST00000355834.3_Silent_p.S496S|RP11-265O12.1_ENST00000509015.1_lincRNA	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	618					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(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						ACTCTTTCTCCCAAGACACGT	0.547																																					p.S618S		.											.	ZBTB49-92	0			c.C1854A						.						54	51	52					4																	4322599		2203	4300	6503	SO:0001819	synonymous_variant	166793	exon8			TTTCTCCCAAGAC	AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	19883	protein-coding gene	gene with protein product			"zinc finger protein 509"	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.1854C>A	4.37:g.4322599C>A		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	39	21	NM_145291	0	0	0	2	2	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	37	CCDS3375.1																																																																																			.		0.547	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291		A	4322599	C	A	4322599	2	1	104	1	0	0	0	0	0	0	0	1	17582	610	22	4		4	ZBTB49	4	4322599	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		4322599	186831677	31	9232											
CCKAR	886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	26483517	26483517	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggttcctgagaggcggcgctCtgcggaggcggtgtcgtagg	4	8	20	9	5	1	1	0	1	1	1	3	3	2	2	1	7	1	3	1	7	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:26483517C>T	ENST00000295589.3	-	5	1224	c.1030G>A	c.(1030-1032)Gag>Aag	p.E344K		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	344					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	AGGCGGCGCTCTGCGGAGGCG	0.592																																					p.E344K		.											.	CCKAR-523	0			c.G1030A						.						103	95	98					4																	26483517		2203	4300	6503	SO:0001583	missense	886	exon5			GGCGCTCTGCGGA	L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1030G>A	4.37:g.26483517C>T	ENSP00000295589:p.Glu344Lys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	77	34	NM_000730	0	0	1	1	0	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	37	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	C	6.038	0.375400	0.11409	.	.	ENSG00000163394	ENST00000295589	T	0.72051	-0.62	5.29	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.163417	0.52532	D	0.000076	T	0.49029	0.1533	N	0.11698	0.16	0.28765	N	0.900671	B	0.14012	0.009	B	0.17098	0.017	T	0.37731	-0.9693	10	0.23302	T	0.38	.	9.6172	0.39698	0.0:0.6564:0.2699:0.0737	.	344	P32238	CCKAR_HUMAN	K	344	ENSP00000295589:E344K	ENSP00000295589:E344K	E	-	1	0	CCKAR	26092615	0.886000	0.30341	0.983000	0.44433	0.058000	0.15608	1.765000	0.38481	1.205000	0.43262	0.563000	0.77884	GAG	.		0.592	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			T	26483517	C	T	26483517	3	4	104	1	0	0	0	0	1	0	0	0	2886	922	32	2	260	2	CCKAR	4	26483517	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	22160918	26483517	164670759	32	9233											
ANXA3	306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	79516549	79516549	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttagggcagaagagatgaAagtctgaaagtggatgagca	15	8	15	3	0	1	5	0	3	1	2	1	7	1	6	0	2	1	3	0	2	4	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:79516549A>G	ENST00000264908.6	+	8	877	c.498A>G	c.(496-498)gaA>gaG	p.E166E	ANXA3_ENST00000512884.1_Silent_p.E127E|ANXA3_ENST00000503570.2_Silent_p.E127E	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	166					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						GAAGAGATGAAAGTCTGAAAG	0.443																																					p.E166E	GBM(2;126 157 27790 28920 42492)	.											.	ANXA3-90	0			c.A498G						.						184	186	186					4																	79516549		2203	4300	6503	SO:0001819	synonymous_variant	306	exon8			AGATGAAAGTCTG	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.498A>G	4.37:g.79516549A>G		Somatic	265	0		WXS	Illumina HiSeq	Phase_I	259	95	NM_005139	0	0	0	0	0	B2R9W6|Q6LET2	Silent	SNP	ENST00000264908.6	37	CCDS3584.1																																																																																			.		0.443	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		G	79516549	A	G	79516549	2	3	104	1	0	0	0	0	0	0	0	1	719	11	1	3		3	ANXA3	4	79516549	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	53033032	79516549	111637727	33	9234											
PLRG1	5356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	155470082	155470082	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtgtacagaatgtttctgTacctcctaaaaaaaaagaat	16	12	7	6	0	1	2	0	0	1	2	2	2	2	2	2	0	2	3	2	0	9	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:155470082T>C	ENST00000499023.2	-	2	141	c.15A>G	c.(13-15)gtA>gtG	p.V5V	PLRG1_ENST00000302078.5_Silent_p.V5V|PLRG1_ENST00000393905.2_Silent_p.V5V	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	5					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				AATGTTTCTGTACCTCCTAAA	0.353																																					p.V5V		.											.	PLRG1-90	0			c.A15G						.						76	71	73					4																	155470082		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon2			TTTCTGTACCTCC	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.15A>G	4.37:g.155470082T>C		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	29	11	NM_002669	0	0	0	0	0	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			.		0.353	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		C	155470082	T	C	155470082	2	2	104	1	0	0	0	0	0	0	0	1	12132	1625	57	3		3	PLRG1	4	155470082	Silent	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	75953533	155470082	35684194	34	9235											
SLC6A18	348932	broad.mit.edu	37	chr5	1225707	1225707	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgggtttgccgtgggactgGggaacatttggcggttccca	5	11	16	9	2	0	0	0	0	0	0	1	2	1	2	2	6	2	2	2	6	1	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:1225707G>C	ENST00000324642.3	+	1	238	c.115G>C	c.(115-117)Ggg>Cgg	p.G39R	SLC6A18_ENST00000296821.4_Missense_Mutation_p.G39R	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	39					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CGTGGGACTGGGGAACATTTG	0.642																																					p.G39R													.	SLC6A18-91	0			c.G115C						.						115	103	107					5																	1225707		2203	4300	6503	SO:0001583	missense	348932	exon1			GGACTGGGGAACA	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"Solute carriers"	26441	protein-coding gene	gene with protein product		610300	"solute carrier family 6 (neurotransmitter transporter), member 18", "solute carrier family 6, member 18"			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.115G>C	5.37:g.1225707G>C	ENSP00000323549:p.Gly39Arg	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	52	25	NM_182632	0	0	0	0	0		Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.367247	0.61513	.	.	ENSG00000164363	ENST00000324642;ENST00000296821	D;D	0.82433	-1.61;-1.61	4.12	4.12	0.48240	.	0.000000	0.64402	D	0.000001	D	0.93452	0.7911	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95588	0.8652	10	0.87932	D	0	.	16.7383	0.85453	0.0:0.0:1.0:0.0	.	39	Q96N87	S6A18_HUMAN	R	39	ENSP00000323549:G39R;ENSP00000296821:G39R	ENSP00000296821:G39R	G	+	1	0	SLC6A18	1278707	1.000000	0.71417	1.000000	0.80357	0.162000	0.22319	9.544000	0.98092	2.008000	0.58898	0.313000	0.20887	GGG	.		0.642	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632		C	1225707	G	C	1225707	3	2	104	1	0	0	0	0	1	0	0	0	14713	1232	43	4	117	4	SLC6A18	5	1225707	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		1225707	179689553	35	9236											
TMEM167A	153339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82357708	82357708	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacttaccaattctggcacActtccaaaatatacccaaca	16	9	2	14	0	1	0	0	0	1	0	2	0	2	0	3	1	3	1	3	1	7	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:82357708A>G	ENST00000502346.1	-	3	308	c.136T>C	c.(136-138)Tgt>Cgt	p.C46R	TMEM167A_ENST00000511450.1_5'UTR|SCARNA18_ENST00000459004.1_RNA	NM_174909.4	NP_777569.1	Q8TBQ9	KISHA_HUMAN	transmembrane protein 167A	46						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(1)	2						ATTCTGGCACACTTCCAAAAT	0.313																																					p.C46R		.											.	TMEM167A-90	0			c.T136C						.						58	57	58					5																	82357708		2203	4299	6502	SO:0001583	missense	153339	exon3			TGGCACACTTCCA	BC107575, AK055070	CCDS34198.1	5q14.2	2008-06-06	2008-06-06	2008-06-06	ENSG00000174695	ENSG00000174695			28330	protein-coding gene	gene with protein product			"transmembrane protein 167"	TMEM167		1316117	Standard	NM_174909		Approved	FLJ30508, MGC23909	uc003khx.4	Q8TBQ9	OTTHUMG00000162570	ENST00000502346.1:c.136T>C	5.37:g.82357708A>G	ENSP00000424707:p.Cys46Arg	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	61	31	NM_174909	0	0	0	0	0	Q0P692	Missense_Mutation	SNP	ENST00000502346.1	37	CCDS34198.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.492910	0.44352	.	.	ENSG00000174695	ENST00000502346	.	.	.	6.06	6.06	0.98353	.	0.094778	0.64402	D	0.000001	T	0.52451	0.1735	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44997	-0.9291	8	0.25106	T	0.35	.	16.2741	0.82634	1.0:0.0:0.0:0.0	.	46	Q8TBQ9	KISHA_HUMAN	R	46	.	ENSP00000424707:C46R	C	-	1	0	TMEM167A	82393464	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.722000	0.84778	2.322000	0.78497	0.528000	0.53228	TGT	.		0.313	TMEM167A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369631.2	NM_174909		G	82357708	A	G	82357708	3	3	104	1	0	0	0	0	1	0	0	0	16113	159	6	3	90	3	TMEM167A	5	82357708	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	81132001	82357708	98557552	36	9237											
PCSK1	5122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	95728748	95728748	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagagcttgaagcagcCggtcgtctctgtgcttgtaa	8	10	11	12	2	1	2	0	1	1	1	3	2	1	2	3	1	4	4	3	1	2	3	rs140941383		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:95728748C>T	ENST00000311106.3	-	14	2456	c.2219G>A	c.(2218-2220)cGg>cAg	p.R740Q	PCSK1_ENST00000508626.1_Missense_Mutation_p.R693Q|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000513085.1_5'UTR	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	740					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	TTGAAGCAGCCGGTCGTCTCT	0.398																																					p.R740Q		.											.	PCSK1-92	0			c.G2219A						.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	163	170	168		2219,2078,1289	5.1	1	5	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	740/754,693/707,430/444	95728748	1,13005	2203	4300	6503	SO:0001583	missense	5122	exon14			AGCAGCCGGTCGT		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"prohormone convertase 3", "prohormone convertase 1", "neuroendocrine convertase 1", "proprotein convertase 1"	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.2219G>A	5.37:g.95728748C>T	ENSP00000308024:p.Arg740Gln	Somatic	306	1		WXS	Illumina HiSeq	Phase_I	255	109	NM_000439	0	0	0	0	0	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	34	5.313465	0.95655	0.0	1.16E-4	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.71341	-0.41;-0.56	6.03	5.11	0.69529	Prohormone convertase enzyme (1);	0.058685	0.64402	D	0.000001	T	0.74222	0.3688	L	0.34521	1.04	0.49130	D	0.999758	D;D	0.71674	0.997;0.998	P;P	0.59825	0.864;0.834	T	0.76364	-0.2986	10	0.72032	D	0.01	-22.6652	15.7754	0.78209	0.1369:0.8631:0.0:0.0	.	693;740	E9PHA1;P29120	.;NEC1_HUMAN	Q	740;693	ENSP00000308024:R740Q;ENSP00000421600:R693Q	ENSP00000308024:R740Q	R	-	2	0	PCSK1	95754504	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.354000	0.59417	2.861000	0.98227	0.655000	0.94253	CGG	C|1.000;T|0.000		0.398	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		T	95728748	C	T	95728748	3	4	104	1	0	0	0	0	1	0	0	0	11626	652	23	1	46	1	PCSK1	5	95728748	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	13371040	95728748	85186512	37	9238											
CHD1	1105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	98236974	98236974	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgcttttctctctctctTcttcagattctgaatctgaa	8	18	4	11	0	7	3	1	2	6	1	9	3	7	3	0	0	2	1	0	0	3	5	rs370850474		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:98236974T>C	ENST00000284049.3	-	5	652	c.503A>G	c.(502-504)gAa>gGa	p.E168G		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	168					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	CTCTCTCTCTTCTTCAGATTC	0.358																																					p.E168G		.											.	CHD1-274	0			c.A503G						.	T	GLY/GLU	0,4406		0,0,2203	137	133	134		503	5.6	1	5		134	4,8596	3.7+/-12.6	0,4,4296	no	missense	CHD1	NM_001270.2	98	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	benign	168/1711	98236974	4,13002	2203	4300	6503	SO:0001583	missense	1105	exon5			CTCTCTTCTTCAG	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.503A>G	5.37:g.98236974T>C	ENSP00000284049:p.Glu168Gly	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	144	63	NM_001270	0	0	8	12	4	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.388330	0.42308	0.0	4.65E-4	ENSG00000153922	ENST00000284049;ENST00000540681	D	0.90385	-2.66	5.62	5.62	0.85841	.	0.000000	0.34507	U	0.003918	D	0.82986	0.5156	N	0.14661	0.345	0.51012	D	0.999905	B	0.16603	0.018	B	0.16722	0.016	T	0.78352	-0.2237	10	0.34782	T	0.22	.	14.6925	0.69096	0.0:0.0:0.0:1.0	.	168	O14646	CHD1_HUMAN	G	168	ENSP00000284049:E168G	ENSP00000284049:E168G	E	-	2	0	CHD1	98264874	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.936000	0.48971	2.254000	0.74563	0.528000	0.53228	GAA	.		0.358	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		C	98236974	T	C	98236974	3	2	104	1	0	0	0	0	1	0	0	0	3329	1783	62	3	4753	3	CHD1	5	98236974	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	2508226	98236974	82678286	38	9239											
SLC25A46	91137	hgsc.bcm.edu	37	chr5	110075085	110075085	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtggcggcggcggcagtGtgcaggggcagagcagtggt	6	5	21	9	3	0	1	0	0	0	1	0	1	0	1	1	7	2	4	1	7	0	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:110075085G>C	ENST00000355943.3	+	1	391	c.265G>C	c.(265-267)Gtg>Ctg	p.V89L	SLC25A46_ENST00000513807.1_Intron|SLC25A46_ENST00000509442.2_Intron|SLC25A46_ENST00000447245.2_Missense_Mutation_p.V89L|SLC25A46_ENST00000504098.1_5'Flank	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	89					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		CGGCGGCAGTGTGCAGGGGCA	0.701																																					p.V89L		.											.	SLC25A46-68	0			c.G265C						.						8	10	9					5																	110075085		2151	4219	6370	SO:0001583	missense	91137	exon1			GGCAGTGTGCAGG	BC017169	CCDS4100.1	5q22.1	2013-05-22			ENSG00000164209	ENSG00000164209		"Solute carriers"	25198	protein-coding gene	gene with protein product		610826				1651562, 1651563, 16949250	Standard	NM_138773		Approved		uc003koz.3	Q96AG3	OTTHUMG00000128794	ENST00000355943.3:c.265G>C	5.37:g.110075085G>C	ENSP00000348211:p.Val89Leu	Somatic	6	1		WXS	Illumina HiSeq	Phase_I	6	3	NM_138773	1	0	28	61	32	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Missense_Mutation	SNP	ENST00000355943.3	37	CCDS4100.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.953454	0.34471	.	.	ENSG00000164209	ENST00000355943;ENST00000447245	D;D	0.82711	-1.64;-1.64	4.89	1.97	0.26223	.	1.857370	0.02892	N	0.134256	T	0.66577	0.2803	N	0.08118	0	0.21416	N	0.999695	B	0.06786	0.001	B	0.04013	0.001	T	0.54193	-0.8330	10	0.15952	T	0.53	4.363	5.3308	0.15932	0.0812:0.147:0.6292:0.1426	.	89	Q96AG3	S2546_HUMAN	L	89	ENSP00000348211:V89L;ENSP00000399717:V89L	ENSP00000348211:V89L	V	+	1	0	SLC25A46	110102984	0.890000	0.30428	0.002000	0.10522	0.597000	0.36814	3.981000	0.56902	0.199000	0.20427	0.655000	0.94253	GTG	.		0.701	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773		C	110075085	G	C	110075085	3	2	104	1	0	0	0	0	1	0	0	0	14543	1377	48	4	267	4	SLC25A46	5	110075085	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	11838111	110075085	70840175	39	9240											
KIF20A	10112	ucsc.edu	37	chr5	137519414	137519415	+	Missense_Mutation	DNP	GG	GG	TT																															tcaggatcctacaccttcagGgggaaggagatatagtcccc																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:137519414_137519415GG>TT	ENST00000394894.3	+	10	1403_1404	c.1177_1178GG>TT	c.(1177-1179)GGg>TTg	p.G393L	KIF20A_ENST00000508792.1_Missense_Mutation_p.G375L	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	393	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ACACCTTCAGGGGGAAGGAGAT	0.426																																					p.G393L													.	KIF20A-90	0			c.G1178T						.																																			SO:0001583	missense	10112	exon10			TTCAGGGGGAAGG	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"Kinesins"	9787	protein-coding gene	gene with protein product		605664	"RAB6 interacting, kinesin-like (rabkinesin6)"	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	Exception_encountered	5.37:g.137519414_137519415delinsTT	ENSP00000378356:p.Gly393Leu	Somatic	58	0		WXS	Illumina HiSeq		33	4	NM_005733	0	0	0	0	0	B4DL79|D3DQB6	Missense_Mutation	DNP	ENST00000394894.3	37	CCDS4199.1																																																																																			.		0.426	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		TT	137519415	GG	TT	137519414	3	4	104	1	0	0	0	0	1	0	0	0	8307	1232	43	4	1211	4	KIF20A	5	137519414	Missense_Mutation	DNP	GG	TCGA-DZ-6133-01A-11D-1961-08	27444329	137519414	43395846	40	9241											
HDAC3	8841	ucsc.edu	37	chr5	141007714	141007714	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgtgggttggtagaagtcCactacctggttgataaccgg	9	10	13	9	2	0	2	0	1	0	1	1	2	1	2	3	4	2	3	3	4	4	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:141007714C>A	ENST00000305264.3	-	9	811	c.732G>T	c.(730-732)gtG>gtT	p.V244V	HDAC3_ENST00000469207.1_5'Flank|AC008781.7_ENST00000422040.2_RNA	NM_003883.3	NP_003874.2	O15379	HDAC3_HUMAN	histone deacetylase 3	244	Histone deacetylase.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|protein deacetylation (GO:0006476)|regulation of mitotic cell cycle (GO:0007346)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|cyclin binding (GO:0030332)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	GGTAGAAGTCCACTACCTGGT	0.557																																					p.V244V													.	HDAC3-227	0			c.G732T						.						94	79	84					5																	141007714		2203	4300	6503	SO:0001819	synonymous_variant	8841	exon9			GAAGTCCACTACC	AF059650	CCDS4264.1	5q31.1-q31.2	2008-07-18			ENSG00000171720	ENSG00000171720	3.5.1.98		4854	protein-coding gene	gene with protein product		605166				9501169, 9464271	Standard	NM_003883		Approved	RPD3, HD3, RPD3-2	uc003llf.2	O15379	OTTHUMG00000129629	ENST00000305264.3:c.732G>T	5.37:g.141007714C>A		Somatic	60	0		WXS	Illumina HiSeq		43	5	NM_003883	0	0	42	42	0	D3DQE1|O43268|Q9UEI5|Q9UEV0	Silent	SNP	ENST00000305264.3	37	CCDS4264.1																																																																																			.		0.557	HDAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251824.2	NM_003883		A	141007714	C	A	141007714	2	1	104	1	0	0	0	0	0	0	0	1	7029	581	21	4		4	HDAC3	5	141007714	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	3488300	141007714	39907546	41	9242											
GTF2H4	2968	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30877829	30877829	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgccagaacctccgcattgcCcttctgggtgggtatgtcac	6	10	11	14	2	2	1	1	0	1	1	3	1	3	1	4	2	2	2	4	2	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:30877829C>T	ENST00000259895.4	+	4	586	c.363C>T	c.(361-363)gcC>gcT	p.A121A	GTF2H4_ENST00000376316.2_Silent_p.A121A|RN7SL175P_ENST00000580375.1_RNA|GTF2H4_ENST00000539324.1_Silent_p.A65A	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	121					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						TCCGCATTGCCCTTCTGGGTG	0.582								Nucleotide excision repair (NER)																													p.A121A		.											.	GTF2H4-661	0			c.C363T						.						114	130	124					6																	30877829		1510	2708	4218	SO:0001819	synonymous_variant	2968	exon4			CATTGCCCTTCTG	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"General transcription factors", "General transcription factor IIH complex subunits"	4658	protein-coding gene	gene with protein product		601760	"general transcription factor IIH, polypeptide 4 (52kD subunit)"			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.363C>T	6.37:g.30877829C>T		Somatic	243	1		WXS	Illumina HiSeq	Phase_I	133	57	NM_001517	0	0	0	0	0	B4DTJ5|Q76KU4	Silent	SNP	ENST00000259895.4	37	CCDS34386.1																																																																																			.		0.582	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		T	30877829	C	T	30877829	2	4	104	1	0	0	0	0	0	0	0	1	6886	610	22	2		2	GTF2H4	6	30877829	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		30877829	140237238	42	9243											
VARS2	57176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30883015	30883015	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaaacccggtgaaaagaaagGtaagtagaataagtaagaag	21	5	12	3	1	0	4	0	1	0	3	0	5	0	4	1	2	1	3	1	2	10	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:30883015G>A	ENST00000321897.5	+	2	915		c.e2+1		VARS2_ENST00000542001.1_Splice_Site|VARS2_ENST00000416670.2_Splice_Site|VARS2_ENST00000541562.1_Splice_Site			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial						gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						GAAAAGAAAGGTAAGTAGAAT	0.453																																					.		.											.	VARS2-26	0			c.283+1G>A						.						85	88	87					6																	30883015		2203	4300	6503	SO:0001630	splice_region_variant	57176	exon3			AGAAAGGTAAGTA	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.283+1G>A	6.37:g.30883015G>A		Somatic	164	1		WXS	Illumina HiSeq	Phase_I	97	50	NM_020442	0	0	0	0	0	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Splice_Site	SNP	ENST00000321897.5	37	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.467888	0.63625	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000428017;ENST00000413959;ENST00000541562;ENST00000421263	.	.	.	3.98	3.98	0.46160	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.759	0.51892	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VARS2	30990994	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.795000	0.75140	2.200000	0.70718	0.557000	0.71058	.	.		0.453	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	Intron	A	30883015	G	A	30883015	5	1	104	1	0	0	0	0	0	0	1	0	17157	1275	44	2	384	2	VARS2	6	30883015	Splice_Site	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	5186	30883015	140232052	43	9244											
VARS	7407	ucsc.edu	37	chr6	31745374	31745374	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagctgggtggtggatcaCagcatcttctggaatagggc	9	10	15	7	0	3	1	1	1	2	0	3	3	3	3	0	5	2	2	0	5	3	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:31745374C>T	ENST00000375663.3	-	30	4232	c.3792G>A	c.(3790-3792)ctG>ctA	p.L1264L	VWA7_ENST00000467576.1_5'Flank|VWA7_ENST00000375686.3_5'Flank|Y_RNA_ENST00000364685.1_RNA|VARS_ENST00000482996.1_5'Flank|VWA7_ENST00000375688.4_5'Flank|VWA7_ENST00000447450.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1264					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	TGGTGGATCACAGCATCTTCT	0.567																																					p.L1264L													.	VARS-93	0			c.G3792A						.						142	110	121					6																	31745374		2203	4300	6503	SO:0001819	synonymous_variant	7407	exon30			GGATCACAGCATC	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.3792G>A	6.37:g.31745374C>T		Somatic	42	0		WXS	Illumina HiSeq		37	4	NM_006295	0	0	61	61	0	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Silent	SNP	ENST00000375663.3	37	CCDS34412.1																																																																																			.		0.567	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		T	31745374	C	T	31745374	2	4	104	1	0	0	0	0	0	0	0	1	17156	465	17	2		2	VARS	6	31745374	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	862359	31745374	139369693	44	9245											
HLA-DQA2	3118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32714066	32714066	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcacagagactttggtctgCgccctggggttgtctgtggg	4	12	15	10	1	3	1	1	0	2	1	3	2	3	1	1	4	1	1	1	4	0	2	rs572758897		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:32714066C>T	ENST00000374940.3	+	4	765	c.663C>T	c.(661-663)tgC>tgT	p.C221C		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	221					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	CTTTGGTCTGCGCCCTGGGGT	0.552													.|||	1	0.000199681	0	0	5008	,	,		21667	0		0	False		,,,				2504	0.001				p.C221C		.											.	HLA-DQA2-90	0			c.C663T						.						163	160	161					6																	32714066		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon4			GGTCTGCGCCCTG		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.663C>T	6.37:g.32714066C>T		Somatic	217	1		WXS	Illumina HiSeq	Phase_I	154	73	NM_020056	0	0	2	2	0	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			C|1.000;T|0.000		0.552	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		T	32714066	C	T	32714066	2	4	104	1	0	0	0	0	0	0	0	1	7226	776	27	1		1	HLA-DQA2	6	32714066	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	968692	32714066	138401001	45	9246											
SCUBE3	222663	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35199528	35199528	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgagtgtgccgagggcaacGgcggctgtcagcagagctgt	8	6	17	10	4	1	1	1	0	0	1	1	3	1	1	1	3	4	4	1	3	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:35199528G>T	ENST00000274938.7	+	4	361	c.361G>T	c.(361-363)Ggc>Tgc	p.G121C	SCUBE3_ENST00000394681.1_Missense_Mutation_p.G121C	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CGAGGGCAACGGCGGCTGTCA	0.582																																					p.G121C													.	SCUBE3-91	0			c.G361T						.						87	69	75					6																	35199528		2203	4300	6503	SO:0001583	missense	222663	exon4			GGCAACGGCGGCT	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.361G>T	6.37:g.35199528G>T	ENSP00000274938:p.Gly121Cys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	39	18	NM_152753	0	0	1	1	0		Missense_Mutation	SNP	ENST00000274938.7	37	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.514824	0.85389	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	D;D	0.98437	-4.93;-4.93	4.37	4.37	0.52481	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98798	0.9595	M	0.79011	2.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99853	1.1074	10	0.87932	D	0	.	17.4734	0.87653	0.0:0.0:1.0:0.0	.	121;121	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	C	121	ENSP00000378174:G121C;ENSP00000274938:G121C	ENSP00000274938:G121C	G	+	1	0	SCUBE3	35307506	1.000000	0.71417	0.161000	0.22692	0.928000	0.56348	9.601000	0.98297	2.432000	0.82394	0.655000	0.94253	GGC	.		0.582	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		T	35199528	G	T	35199528	3	4	104	1	0	0	0	0	1	0	0	0	13978	1116	39	4	375	4	SCUBE3	6	35199528	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	2485462	35199528	135915539	46	9247											
CDC5L	988	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	44390515	44390515	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgaggatggaatggcagActatagtgatccctcttacg	10	10	11	10	2	1	2	0	1	1	1	3	5	3	4	2	3	1	1	2	3	4	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:44390515A>T	ENST00000371477.3	+	10	1672	c.1373A>T	c.(1372-1374)gAc>gTc	p.D458V		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	458	Interaction with PPP1R8.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGAATGGCAGACTATAGTGAT	0.383																																					p.D458V		.											.	CDC5L-229	0			c.A1373T						.						134	135	135					6																	44390515		2203	4300	6503	SO:0001583	missense	988	exon10			TGGCAGACTATAG	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"CDC5 (cell division cycle 5, S. pombe, homolog)-like", "CDC5 cell division cycle 5-like (S. pombe)"			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1373A>T	6.37:g.44390515A>T	ENSP00000360532:p.Asp458Val	Somatic	205	2		WXS	Illumina HiSeq	Phase_I	162	64	NM_001253	0	0	12	27	15	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	37	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340499	0.41498	.	.	ENSG00000096401	ENST00000371477	T	0.36157	1.27	5.85	4.67	0.58626	.	0.102528	0.64402	D	0.000004	T	0.09642	0.0237	N	0.12182	0.205	0.80722	D	1	B	0.32573	0.376	B	0.30029	0.11	T	0.10917	-1.0609	10	0.24483	T	0.36	-19.9685	12.1682	0.54141	0.9321:0.0:0.0679:0.0	.	458	Q99459	CDC5L_HUMAN	V	458	ENSP00000360532:D458V	ENSP00000360532:D458V	D	+	2	0	CDC5L	44498493	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.966000	0.63715	2.234000	0.73211	0.460000	0.39030	GAC	.		0.383	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			T	44390515	A	T	44390515	3	4	104	1	0	0	0	0	1	0	0	0	3088	275	10	5	1411	5	CDC5L	6	44390515	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	9190987	44390515	126724552	47	9248											
RCAN2	10231	hgsc.bcm.edu	37	chr6	46216582	46216582	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acgtctgaaactcttaaataGctggaacgtcacacagtcat	14	10	7	10	2	4	1	2	1	2	0	4	2	4	2	0	1	3	1	0	1	5	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:46216582G>C	ENST00000330430.6	-	2	327	c.139C>G	c.(139-141)Cta>Gta	p.L47V	RCAN2_ENST00000371374.1_Missense_Mutation_p.L93V|RCAN2_ENST00000306764.7_Missense_Mutation_p.L93V|RCAN2_ENST00000405162.1_Missense_Mutation_p.L93V	NM_005822.3	NP_005813.2	Q14206	RCAN2_HUMAN	regulator of calcineurin 2	47					calcineurin-NFAT signaling cascade (GO:0033173)|locomotion involved in locomotory behavior (GO:0031987)|response to oxidative stress (GO:0006979)|short-term memory (GO:0007614)		nucleotide binding (GO:0000166)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						CTCTTAAATAGCTGGAACGTC	0.418																																					p.L93V		.											.	RCAN2-90	0			c.C277G						.						116	102	106					6																	46216582		1849	4110	5959	SO:0001583	missense	10231	exon3			TAAATAGCTGGAA	D83407	CCDS43469.1, CCDS59023.1	6p12.3	2008-10-31	2007-06-26	2007-06-26	ENSG00000172348	ENSG00000172348			3041	protein-coding gene	gene with protein product		604876	"Down syndrome critical region gene 1-like 1"	DSCR1L1		8662924	Standard	NM_001251973		Approved	ZAKI-4	uc003oyc.2	Q14206	OTTHUMG00000014782	ENST00000330430.6:c.139C>G	6.37:g.46216582G>C	ENSP00000329454:p.Leu47Val	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_001251973	0	0	19	19	0	A6ND07|B3KR46|Q5VWF7|Q5VWF8|Q8N116	Missense_Mutation	SNP	ENST00000330430.6	37	CCDS43469.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.207295	0.58343	.	.	ENSG00000172348	ENST00000330430;ENST00000371374;ENST00000306764;ENST00000405162	.	.	.	6.03	6.03	0.97812	Nucleotide-binding, alpha-beta plait (1);	0.085482	0.49916	D	0.000134	T	0.54334	0.1852	L	0.52364	1.645	0.47511	D	0.999447	P;P	0.50819	0.746;0.939	B;P	0.47626	0.384;0.552	T	0.59053	-0.7526	9	0.87932	D	0	-0.7537	19.545	0.95291	0.0:0.0:1.0:0.0	.	93;47	Q14206-2;Q14206	.;RCAN2_HUMAN	V	47;93;93;93	.	ENSP00000305223:L93V	L	-	1	2	RCAN2	46324541	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	1.764000	0.38471	2.861000	0.98227	0.655000	0.94253	CTA	.		0.418	RCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040782.1			C	46216582	G	C	46216582	3	2	104	1	0	0	0	0	1	0	0	0	13201	962	34	4	466	4	RCAN2	6	46216582	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	1826067	46216582	124898485	48	9249											
PLEKHG1	57480	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	151151821	151151821	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgatcagcgtgcttcgagCgggtggagctctcagaaaca	10	8	13	10	3	2	2	2	1	1	1	4	4	2	3	0	2	5	2	0	2	1	1	rs138970683		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:151151821C>T	ENST00000358517.2	+	15	1785	c.1574C>T	c.(1573-1575)gCg>gTg	p.A525V	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.A525V			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	525							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)		GTGCTTCGAGCGGGTGGAGCT	0.547													C|||	1	0.000199681	0	0	5008	,	,		19977	0		0.001	False		,,,				2504	0				p.A525V													.	PLEKHG1-92	0			c.C1574T						.	C	VAL/ALA	0,4406		0,0,2203	92	83	86		1574	3.6	0	6	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLEKHG1	NM_001029884.1	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	525/1386	151151821	1,13005	2203	4300	6503	SO:0001583	missense	57480	exon16			TTCGAGCGGGTGG	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.1574C>T	6.37:g.151151821C>T	ENSP00000351318:p.Ala525Val	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	35	11	NM_001029884	0	0	3	4	1	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.688	0.690379	0.15039	0.0	1.16E-4	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.59502	0.26;0.26	5.4	3.57	0.40892	.	0.325353	0.36665	N	0.002464	T	0.17152	0.0412	N	0.22421	0.69	0.09310	N	1	P;P;P	0.41188	0.542;0.741;0.741	B;B;B	0.23275	0.045;0.044;0.044	T	0.03077	-1.1075	10	0.66056	D	0.02	.	10.0015	0.41931	0.0721:0.274:0.6539:0.0	.	332;525;525	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	V	525	ENSP00000356297:A525V;ENSP00000351318:A525V	ENSP00000351318:A525V	A	+	2	0	PLEKHG1	151193514	1.000000	0.71417	0.010000	0.14722	0.002000	0.02628	4.677000	0.61634	0.616000	0.30141	-0.321000	0.08615	GCG	C|0.999;T|0.000		0.547	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			T	151151821	C	T	151151821	3	4	104	1	0	0	0	0	1	0	0	0	12094	768	27	1	1628	1	PLEKHG1	6	151151821	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	104935239	151151821	19963246	49	9250											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152671451	152671451	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggtctttgactttcgccTccagactgaagacatgctcc	8	12	8	13	1	1	4	0	2	1	2	4	4	3	4	3	1	1	1	3	1	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:152671451T>C	ENST00000367255.5	-	72	12354	c.11753A>G	c.(11752-11754)gAg>gGg	p.E3918G	SYNE1_ENST00000423061.1_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.E3918G|SYNE1_ENST00000341594.5_Missense_Mutation_p.E3842G|SYNE1_ENST00000448038.1_Intron	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3918					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GACTTTCGCCTCCAGACTGAA	0.473										HNSCC(10;0.0054)																											p.E3918G		.											.	SYNE1-607	0			c.A11753G						.						102	93	96					6																	152671451		2203	4300	6503	SO:0001583	missense	23345	exon72			TTCGCCTCCAGAC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.11753A>G	6.37:g.152671451T>C	ENSP00000356224:p.Glu3918Gly	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	85	23	NM_182961	0	0	8	12	4	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	14.89	2.671137	0.47781	.	.	ENSG00000131018	ENST00000367255;ENST00000265368;ENST00000341594	T;T;T	0.41400	1.0;1.0;1.0	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000009	T	0.51041	0.1651	L	0.55481	1.735	0.80722	D	1	D;D;D	0.63046	0.992;0.992;0.992	D;D;D	0.64687	0.928;0.928;0.928	T	0.54879	-0.8227	10	0.72032	D	0.01	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	3918;3918;3918	B7ZBC3;Q8NF91;E7EQI5	.;SYNE1_HUMAN;.	G	3918;3918;3842	ENSP00000356224:E3918G;ENSP00000265368:E3918G;ENSP00000341887:E3842G	ENSP00000265368:E3918G	E	-	2	0	SYNE1	152713144	0.857000	0.29778	0.800000	0.32199	0.939000	0.58152	2.153000	0.42282	2.281000	0.76405	0.533000	0.62120	GAG	.		0.473	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152671451	T	C	152671451	3	2	104	1	0	0	0	0	1	0	0	0	15477	1551	54	3	15013	3	SYNE1	6	152671451	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	1519630	152671451	18443616	50	9251											
ARID1B	57492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	157527600	157527600	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacgccgctgcagacccaaaGgagaagcccaagcaagccag	14	1	12	14	2	0	2	0	0	0	2	0	4	0	2	4	1	4	3	4	1	4	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:157527600G>A	ENST00000350026.5	+	19	5287	c.5286G>A	c.(5284-5286)aaG>aaA	p.K1762K	ARID1B_ENST00000346085.5_Silent_p.K1775K|ARID1B_ENST00000275248.4_Silent_p.K1757K|ARID1B_ENST00000367148.1_Silent_p.K1815K	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1762					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CAGACCCAAAGGAGAAGCCCA	0.517																																					p.K1775K		.											.	ARID1B-154	0			c.G5325A						.						60	61	61					6																	157527600		2203	4296	6499	SO:0001819	synonymous_variant	57492	exon20			CCCAAAGGAGAAG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"-"	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.5286G>A	6.37:g.157527600G>A		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	114	43	NM_020732	0	0	44	72	28	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	37	CCDS5251.2																																																																																			.		0.517	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157527600	G	A	157527600	2	1	104	1	0	0	0	0	0	0	0	1	914	991	35	2		2	ARID1B	6	157527600	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	4856149	157527600	13587467	51	9252											
IGF2R	3482	ucsc.edu	37	chr6	160483635	160483636	+	Missense_Mutation	DNP	CG	CG	AA																															agaactgtggaagcctgtccCgttgtcagagtggaaggtag																								rs375087362|rs368061810		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:160483635_160483636CG>AA	ENST00000356956.1	+	26	3802_3803	c.3654_3655CG>AA	c.(3652-3657)ccCGtt>ccAAtt	p.V1219I		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1219					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.P1218P(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AAGCCTGTCCCGTTGTCAGAGT	0.46																																					p.V1219I													.	IGF2R-118	1	Substitution - coding silent(1)	urinary_tract(1)	c.G3655A						.																																			SO:0001583	missense	3482	exon26			TGTCCCGTTGTCA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	Exception_encountered	6.37:g.160483635_160483636delinsAA	ENSP00000349437:p.Val1219Ile	Somatic	82	0		WXS	Illumina HiSeq		52	5	NM_000876	0	0	0	0	0	Q7Z7G9|Q96PT5	Missense_Mutation	DNP	ENST00000356956.1	37	CCDS5273.1																																																																																			.		0.46	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		AA	160483636	CG	AA	160483635	3	1	104	1	0	0	0	0	1	0	0	0	7597	639	23	4	3756	4	IGF2R	6	160483635	Missense_Mutation	DNP	CG	TCGA-DZ-6133-01A-11D-1961-08	2956035	160483635	10631432	52	9253											
CDK13	8621	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	40117701	40117701	+	Frame_Shift_Del	DEL	T	T	-																															agaagcaatatcgtcgaaagTtaagagaagaatttgttttg																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:40117701delT	ENST00000181839.4	+	10	3483	c.2878delT	c.(2878-2880)ttafs	p.L960fs	CDK13_ENST00000340829.5_Frame_Shift_Del_p.L960fs	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	960	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TCGTCGAAAGTTAAGAGAAGA	0.348																																					p.L960X		.											.	CDK13-548	0			c.2878delT						.						152	143	146					7																	40117701		2203	4300	6503	SO:0001589	frameshift_variant	8621	exon10			.	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2878delT	7.37:g.40117701delT	ENSP00000181839:p.Leu960fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	139	64	NM_003718	0	0	0	0	0	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Nonsense_Mutation	DEL	ENST00000181839.4	37	CCDS5461.1																																																																																			.		0.348	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		-	40117701	T	-	40117701	7	5	104	1	0	1	0	1	0	0	0	0	3135	1722	60	0	2916	0	CDK13	7	40117701	Frame_Shift_Del	DEL	T	TCGA-DZ-6133-01A-11D-1961-08		40117701	119020962	53	9254											
ERV3	2086	bcgsc.ca	37	chr7	64452749	64452749	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctgactcgtgcccctagcGgtgcttttaaacctgttgtc	5	13	10	13	3	0	1	0	1	0	0	2	1	0	1	3	1	4	3	3	1	3	4	rs367626165		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:64452749G>T	ENST00000394323.2	-	2	1156	c.656C>A	c.(655-657)cCg>cAg	p.P219Q	ZNF117_ENST00000282869.6_5'Flank	NM_001007253.3	NP_001007254.2	Q14264	ENR1_HUMAN	endogenous retrovirus group 3, member 1	219						extracellular vesicular exosome (GO:0070062)|viral envelope (GO:0019031)		p.P219Q(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)	16						tgcccctagcggtgcttttaa	0.443																																					p.P219Q													.	.	1	Substitution - Missense(1)	lung(1)	c.C656A						.						153	155	154					7																	64452749		2023	4218	6241	SO:0001583	missense	2086	exon2			CCTAGCGGTGCTT	AK295189	CCDS47595.1	7p12-q11	2014-05-02	2011-05-05	2011-05-05	ENSG00000213462	ENSG00000213462			3454	other	endogenous retrovirus		131170	"endogenous retroviral sequence 3 (includes zinc finger protein H-plk/HPF9)", "endogenous retroviral sequence 3"	ERV3		2115127, 6495650, 21542922	Standard	NM_001007253		Approved	H-PLK, HERV-R, ERV-R, envR	uc011kdr.2	Q14264	OTTHUMG00000165023	ENST00000394323.2:c.656C>A	7.37:g.64452749G>T	ENSP00000391594:p.Pro219Gln	Somatic	373	1		WXS	Illumina HiSeq	Phase_1	592	19	NM_001007253	0	0	25	25	0		Missense_Mutation	SNP	ENST00000394323.2	37	CCDS47595.1	.	.	.	.	.	.	.	.	.	.	.	5.118	0.207418	0.09704	.	.	ENSG00000213462	ENST00000394323	T	0.12147	2.71	0.109	0.109	0.14578	.	.	.	.	.	T	0.06188	0.0160	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.04013	0.001	T	0.35822	-0.9773	8	0.45353	T	0.12	.	.	.	.	.	219	Q14264	ENR1_HUMAN	Q	219	ENSP00000391594:P219Q	ENSP00000391594:P219Q	P	-	2	0	ERV3-1	64090184	0.467000	0.25831	0.270000	0.24601	0.274000	0.26718	0.230000	0.17852	0.181000	0.19994	0.184000	0.17185	CCG	.		0.443	ERV3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381468.1	NM_001007253		T	64452749	G	T	64452749	3	4	104	1	0	0	0	0	1	0	0	0	5258	1116	39	4	1162	4	ERV3	7	64452749	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	24335048	64452749	94685914	54	9255											
TMEM120A	5447	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	75617587	75617587	+	IGR	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgggagccgttgttgatGaggatgctctcccggatggt	6	10	15	10	3	1	2	0	2	1	0	2	5	1	5	3	4	2	3	3	4	0	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:75617587G>T	ENST00000461988.1	+	0	2522				TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase						carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	CGTTGTTGATGAGGATGCTCT	0.657																																					.													.	.	0			.						.						49	52	51					7																	75617587		1983	4150	6133	SO:0001628	intergenic_variant	83862	.			GTTGATGAGGATG	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413		7.37:g.75617587G>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	99	40	.	0	0	208	375	167	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1																																																																																			.		0.657	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		T	75617587	G	T	75617587	1	4	104	0	1	0	0	0	0	0	0	0	16065	1277	45	4		4	TMEM120A	7	75617587	IGR	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	11164838	75617587	83521076	55	9256											
ZAN	7455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100349824	100349824	+	RNA	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacggaaaaacccaccatctCcatggaagagactatcatct	15	7	6	13	1	3	1	1	0	2	1	4	4	3	3	3	2	1	0	3	2	4	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:100349824C>A	ENST00000348028.3	+	0	2261				ZAN_ENST00000349350.6_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000542585.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CCCACCATCTCCATGGAAGAG	0.512																																					.													.	ZAN-142	0			.						.						190	208	202					7																	100349824		1861	4094	5955			7455	.			CCATCTCCATGGA	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100349824C>A		Somatic	140	1		WXS	Illumina HiSeq	Phase_I	106	47	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	c	9.555	1.116910	0.20795	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.63744	-0.06;-0.06;-0.06	3.59	1.69	0.24217	.	.	.	.	.	T	0.37625	0.1010	N	0.08118	0	0.18873	N	0.999981	P;B	0.35628	0.513;0.379	B;B	0.33890	0.172;0.083	T	0.21965	-1.0230	9	0.59425	D	0.04	.	6.1291	0.20195	0.1862:0.7055:0.0:0.1082	.	699;699	F5H0T8;Q9Y493	.;ZAN_HUMAN	Y	699	ENSP00000445943:S699Y;ENSP00000445091:S699Y;ENSP00000444427:S699Y	ENSP00000423579:S699Y	S	+	2	0	ZAN	100187760	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.482000	0.06544	0.265000	0.21872	-0.516000	0.04426	TCC	.		0.512	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		A	100349824	C	A	100349824	1	1	104	0	1	0	0	0	0	0	0	0	17546	855	30	4		4	ZAN	7	100349824	RNA	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	24732237	100349824	58788839	56	9257											
EPHB6	2051	broad.mit.edu	37	chr7	142566068	142566068	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccatccgagaacttgcccGggaagtcgatcctgcttata	9	9	11	12	3	0	1	0	0	0	1	3	4	2	2	4	2	3	1	4	2	4	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:142566068G>C	ENST00000392957.2	+	14	2775	c.1988G>C	c.(1987-1989)cGg>cCg	p.R663P	EPHB6_ENST00000442129.1_Missense_Mutation_p.R663P|EPHB6_ENST00000411471.2_Missense_Mutation_p.R386P	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	663						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.R648L(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GAACTTGCCCGGGAAGTCGAT	0.577																																					p.R663P													.	EPHB6-1489	1	Substitution - Missense(1)	lung(1)	c.G1988C						.						103	97	99					7																	142566068		2203	4300	6503	SO:0001583	missense	2051	exon14			TTGCCCGGGAAGT	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1988G>C	7.37:g.142566068G>C	ENSP00000376684:p.Arg663Pro	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	108	3	NM_004445	0	0	16	16	0	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	14.31	2.496909	0.44352	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.14640	2.49;2.49;2.49	4.21	4.21	0.49690	Protein kinase-like domain (1);	0.000000	0.39020	N	0.001483	T	0.12347	0.0300	L	0.52206	1.635	0.53005	D	0.999968	B;B	0.21071	0.051;0.032	B;B	0.16722	0.012;0.016	T	0.08411	-1.0723	10	0.87932	D	0	.	5.7674	0.18233	0.2173:0.0:0.7827:0.0	.	663;386	O15197;O15197-2	EPHB6_HUMAN;.	P	663;663;386	ENSP00000376684:R663P;ENSP00000410789:R663P;ENSP00000409061:R386P	ENSP00000376684:R663P	R	+	2	0	EPHB6	142276190	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	6.245000	0.72398	2.204000	0.70986	0.561000	0.74099	CGG	.		0.577	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			C	142566068	G	C	142566068	3	2	104	1	0	0	0	0	1	0	0	0	5191	1116	39	4	2026	4	EPHB6	7	142566068	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	42216244	142566068	16572595	57	9258											
ANGPT2	285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	6360731	6360731	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatttgtgttctgcctctgtGgatagtacattccgttcaag	7	17	9	8	1	3	0	1	0	2	0	4	1	4	1	2	1	2	3	2	1	4	7			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:6360731G>T	ENST00000325203.5	-	9	1856	c.1382C>A	c.(1381-1383)cCa>cAa	p.P461Q	ANGPT2_ENST00000415216.1_Missense_Mutation_p.P460Q|ANGPT2_ENST00000338312.6_Missense_Mutation_p.P409Q|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	461	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		CTGCCTCTGTGGATAGTACAT	0.463																																					p.P461Q		.											.	ANGPT2-91	0			c.C1382A						.						235	190	205					8																	6360731		2203	4300	6503	SO:0001583	missense	285	exon9			CTCTGTGGATAGT	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"Fibrinogen C domain containing"	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.1382C>A	8.37:g.6360731G>T	ENSP00000314897:p.Pro461Gln	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	66	24	NM_001147	0	0	1	1	0	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Missense_Mutation	SNP	ENST00000325203.5	37	CCDS5958.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.422644	0.43020	.	.	ENSG00000091879	ENST00000325203;ENST00000415216;ENST00000338312	T;T;T	0.75050	-0.9;-0.9;-0.9	6.17	6.17	0.99709	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.112483	0.64402	D	0.000006	T	0.57621	0.2066	N	0.10685	0.025	0.42845	D	0.994062	B;B;B	0.27229	0.069;0.069;0.172	B;B;B	0.25506	0.015;0.015;0.061	T	0.54761	-0.8245	10	0.22109	T	0.4	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	409;460;461	O15123-2;O15123-3;O15123	.;.;ANGP2_HUMAN	Q	461;460;409	ENSP00000314897:P461Q;ENSP00000400782:P460Q;ENSP00000343517:P409Q	ENSP00000314897:P461Q	P	-	2	0	ANGPT2	6348139	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.047000	0.57383	2.941000	0.99782	0.655000	0.94253	CCA	.		0.463	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147		T	6360731	G	T	6360731	3	4	104	1	0	0	0	0	1	0	0	0	611	1348	47	4	112	4	ANGPT2	8	6360731	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		6360731	140003291	58	9259											
BIN3	55909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	22488017	22488017	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagggccgtcaccatgttcaGaaggtcctggtcttgctcac	7	10	11	13	1	4	1	3	0	1	1	5	1	5	1	3	3	1	2	3	3	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:22488017G>A	ENST00000276416.6	-	5	303	c.235C>T	c.(235-237)Ctg>Ttg	p.L79L	BIN3_ENST00000519513.1_Silent_p.L25L|BIN3_ENST00000520292.1_Silent_p.L79L|BIN3_ENST00000399977.4_Silent_p.L31L|BIN3_ENST00000519335.1_5'UTR	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	79	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		ACCATGTTCAGAAGGTCCTGG	0.532																																					p.L79L		.											.	.	0			c.C235T						.						176	176	176					8																	22488017		2001	4169	6170	SO:0001819	synonymous_variant	55909	exon5			TGTTCAGAAGGTC		CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.235C>T	8.37:g.22488017G>A		Somatic	289	0		WXS	Illumina HiSeq	Phase_I	165	65	NM_018688	0	0	37	59	22	Q9BVG2|Q9NVY9	Silent	SNP	ENST00000276416.6	37	CCDS47825.1																																																																																			.		0.532	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1			A	22488017	G	A	22488017	2	1	104	1	0	0	0	0	0	0	0	1	1435	933	33	2		2	BIN3	8	22488017	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	16127286	22488017	123876005	59	9260											
FABP12	646486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	82441686	82441686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcctcacctttgttttgtggCcacctggcgtgatttcctca	4	15	9	13	1	2	1	2	1	0	0	3	1	3	1	5	2	0	1	5	2	0	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:82441686C>T	ENST00000360464.4	-	2	295	c.233G>A	c.(232-234)gGc>gAc	p.G78D	RP11-257P3.3_ENST00000518637.1_RNA|RP11-257P3.3_ENST00000523380.1_RNA	NM_001105281.1	NP_001098751.1	A6NFH5	FBP12_HUMAN	fatty acid binding protein 12	78							lipid binding (GO:0008289)|transporter activity (GO:0005215)			large_intestine(1)|lung(3)	4						TGTTTTGTGGCCACCTGGCGT	0.388																																					p.G78D		.											.	FABP12-46	0			c.G233A						.						160	154	156					8																	82441686		1870	4108	5978	SO:0001583	missense	646486	exon2			TTGTGGCCACCTG		CCDS47882.1	8q21.13	2013-03-01			ENSG00000197416	ENSG00000197416		"Fatty acid binding protein family"	34524	protein-coding gene	gene with protein product						18786628	Standard	NM_001105281		Approved		uc011lfp.2	A6NFH5	OTTHUMG00000164679	ENST00000360464.4:c.233G>A	8.37:g.82441686C>T	ENSP00000353650:p.Gly78Asp	Somatic	243	1		WXS	Illumina HiSeq	Phase_I	247	96	NM_001105281	0	0	0	0	0	B7SUN0	Missense_Mutation	SNP	ENST00000360464.4	37	CCDS47882.1	.	.	.	.	.	.	.	.	.	.	C	1.026	-0.683340	0.03353	.	.	ENSG00000197416	ENST00000360464	T	0.51071	0.72	4.84	0.778	0.18543	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.259107	0.39407	N	0.001371	T	0.31295	0.0792	N	0.16233	0.39	0.35132	D	0.768077	B	0.27823	0.19	B	0.42851	0.4	T	0.35226	-0.9797	10	0.02654	T	1	.	7.4582	0.27278	0.0:0.4913:0.0:0.5087	.	78	A6NFH5	FBP12_HUMAN	D	78	ENSP00000353650:G78D	ENSP00000353650:G78D	G	-	2	0	FABP12	82604241	0.916000	0.31088	0.038000	0.18304	0.032000	0.12392	1.342000	0.33919	0.261000	0.21753	-0.136000	0.14681	GGC	.		0.388	FABP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379720.1	NM_001105281		T	82441686	C	T	82441686	3	4	104	1	0	0	0	0	1	0	0	0	5372	739	26	2	199	2	FABP12	8	82441686	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	59953669	82441686	63922336	60	9261											
RIPK2	8767	broad.mit.edu	37	chr8	90798839	90798839	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggaatcatgtggatcctctCagctccatgaaaatagtggt	12	11	10	8	0	2	1	2	1	1	0	5	3	4	3	2	3	1	1	2	3	4	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:90798839C>G	ENST00000220751.4	+	9	1362	c.1048C>G	c.(1048-1050)Cag>Gag	p.Q350E	RIPK2_ENST00000540020.1_Missense_Mutation_p.Q213E	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	350					activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGGATCCTCTCAGCTCCATGA	0.323																																					p.Q350E													.	RIPK2-523	0			c.C1048G						.						102	105	104					8																	90798839		2203	4300	6503	SO:0001583	missense	8767	exon9			TCCTCTCAGCTCC	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.1048C>G	8.37:g.90798839C>G	ENSP00000220751:p.Gln350Glu	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	127	3	NM_003821	0	0	6	6	0	B7Z748|Q6UWF0	Missense_Mutation	SNP	ENST00000220751.4	37	CCDS6247.1	.	.	.	.	.	.	.	.	.	.	C	2.500	-0.315423	0.05422	.	.	ENSG00000104312	ENST00000220751;ENST00000540020	T;T	0.80480	-1.16;-1.38	5.51	3.64	0.41730	.	0.485483	0.14945	N	0.289268	T	0.61800	0.2376	N	0.19112	0.55	0.21020	N	0.999801	B	0.18166	0.026	B	0.15870	0.014	T	0.44937	-0.9295	10	0.02654	T	1	-1.3973	8.7026	0.34334	0.172:0.6623:0.1656:0.0	.	350	O43353	RIPK2_HUMAN	E	350;213	ENSP00000220751:Q350E;ENSP00000441623:Q213E	ENSP00000220751:Q350E	Q	+	1	0	RIPK2	90867980	0.808000	0.29022	0.817000	0.32601	0.824000	0.46624	1.183000	0.32041	0.815000	0.34398	0.557000	0.71058	CAG	.		0.323	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1			G	90798839	C	G	90798839	3	3	104	1	0	0	0	0	1	0	0	0	13413	827	29	4	1082	4	RIPK2	8	90798839	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	8357153	90798839	55565183	61	9262											
RHPN1	114822	broad.mit.edu	37	chr8	144462787	144462787	+	Frame_Shift_Del	DEL	G	G	-																															cacctgaagcgtgccatcctGgggcaggaggaggcgctgcg																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:144462787delG	ENST00000289013.6	+	11	1346	c.1245delG	c.(1243-1245)ctgfs	p.L415fs		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	440	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			GTGCCATCCTGGGGCAGGAGG	0.697																																					p.L415fs													.	RHPN1-67	0			c.1245delG						.						11	14	13					8																	144462787		2086	4173	6259	SO:0001589	frameshift_variant	114822	exon11			CATCCTGGGGCAG	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.1245delG	8.37:g.144462787delG	ENSP00000289013:p.Leu415fs	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_052924	0	0	0	0	0	Q8TAV1|Q96PV9	Frame_Shift_Del	DEL	ENST00000289013.6	37	CCDS47927.1																																																																																			.		0.697	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1			-	144462787	G	-	144462787	7	5	104	1	0	1	0	1	0	0	0	0	13382	1335	47	0	1287	0	RHPN1	8	144462787	Frame_Shift_Del	DEL	G	TCGA-DZ-6133-01A-11D-1961-08	53663948	144462787	1901235	62	9263											
PTPRD	5789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	8471073	8471073	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttcaaaggcacaattatTatgtagtaacctctgcacaa	14	13	5	9	0	3	0	1	0	2	0	3	0	3	0	1	1	2	4	1	1	7	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:8471073T>C	ENST00000381196.4	-	28	3969	c.3426A>G	c.(3424-3426)atA>atG	p.I1142M	PTPRD_ENST00000397617.3_Missense_Mutation_p.I721M|PTPRD_ENST00000540109.1_Missense_Mutation_p.I1142M|PTPRD_ENST00000397606.3_Missense_Mutation_p.I721M|PTPRD_ENST00000356435.5_Missense_Mutation_p.I1142M|PTPRD_ENST00000397611.3_Missense_Mutation_p.I728M|PTPRD_ENST00000537002.1_Missense_Mutation_p.I728M|PTPRD_ENST00000360074.4_Missense_Mutation_p.I1129M|PTPRD_ENST00000358503.5_Missense_Mutation_p.I1120M|PTPRD_ENST00000355233.5_Missense_Mutation_p.I731M|PTPRD_ENST00000486161.1_Missense_Mutation_p.I731M	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1142					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GCACAATTATTATGTAGTAAC	0.393										TSP Lung(15;0.13)																											p.I1142M		.											.	PTPRD-912	0			c.A3426G						.						115	113	114					9																	8471073		2203	4300	6503	SO:0001583	missense	5789	exon31			AATTATTATGTAG	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3426A>G	9.37:g.8471073T>C	ENSP00000370593:p.Ile1142Met	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	122	56	NM_002839	0	0	0	0	0	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717523	0.68844	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17	5.72	4.56	0.56223	.	0.093861	0.64402	D	0.000001	T	0.70919	0.3279	M	0.69358	2.11	0.48762	D	0.999701	P;P;B;P;D;D;B;P;B	0.59357	0.835;0.868;0.435;0.855;0.985;0.973;0.035;0.736;0.097	P;P;B;B;D;P;B;B;B	0.77557	0.707;0.501;0.221;0.359;0.99;0.807;0.026;0.372;0.016	T	0.69924	-0.5013	9	.	.	.	.	9.7155	0.40272	0.286:0.0:0.0:0.714	.	721;726;731;731;728;728;1129;1142;1142	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	M	1142;1142;1129;1120;731;721;728;728;613;1142;731;721	ENSP00000370593:I1142M;ENSP00000348812:I1142M;ENSP00000353187:I1129M;ENSP00000351293:I1120M;ENSP00000347373:I731M;ENSP00000380741:I721M;ENSP00000380735:I728M;ENSP00000440515:I728M;ENSP00000438164:I1142M;ENSP00000417093:I731M;ENSP00000380731:I721M	.	I	-	3	3	PTPRD	8461073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.376000	0.44292	0.960000	0.38005	0.533000	0.62120	ATA	.		0.393	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8471073	T	C	8471073	3	2	104	1	0	0	0	0	1	0	0	0	12831	1744	61	3	2441	3	PTPRD	9	8471073	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		8471073	132742358	63	9264											
TOPORS	10210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	32541815	32541815	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtaattacaactggggaaCgtgaagcattatctccatgg	12	11	11	7	1	1	1	0	1	1	0	2	2	1	2	1	4	4	2	1	4	6	3	rs371709773		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:32541815C>G	ENST00000360538.2	-	3	2824	c.2708G>C	c.(2707-2709)cGt>cCt	p.R903P	TOPORS_ENST00000379858.1_Missense_Mutation_p.R838P	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	903	Interaction with UBE2I.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		AACTGGGGAACGTGAAGCATT	0.368																																					p.R903P		.											.	TOPORS-230	0			c.G2708C						.						195	186	189					9																	32541815		2203	4300	6503	SO:0001583	missense	10210	exon3			GGGGAACGTGAAG	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2708G>C	9.37:g.32541815C>G	ENSP00000353735:p.Arg903Pro	Somatic	240	0		WXS	Illumina HiSeq	Phase_I	184	71	NM_005802	0	0	13	25	12	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457297	0.26161	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.15017	2.46;2.47	5.81	0.86	0.19042	.	0.565792	0.16222	N	0.224014	T	0.07999	0.0200	N	0.14661	0.345	0.18873	N	0.999987	B	0.31730	0.337	B	0.26614	0.071	T	0.24621	-1.0155	10	0.52906	T	0.07	-1.0409	5.7492	0.18138	0.0:0.4435:0.1994:0.3571	.	903	Q9NS56	TOPRS_HUMAN	P	903;838	ENSP00000353735:R903P;ENSP00000369187:R838P	ENSP00000353735:R903P	R	-	2	0	TOPORS	32531815	0.000000	0.05858	0.985000	0.45067	0.702000	0.40608	-0.615000	0.05597	0.113000	0.18004	-0.133000	0.14855	CGT	.		0.368	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		G	32541815	C	G	32541815	3	3	104	1	0	0	0	0	1	0	0	0	16403	536	19	4	433	4	TOPORS	9	32541815	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	24070742	32541815	108671616	64	9265											
VCP	7415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35061057	35061057	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagagttcatgacctcggcAtcaatggtctcatcctctag	10	11	9	11	1	4	2	3	1	2	1	7	3	5	2	2	2	0	2	2	2	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:35061057A>G	ENST00000358901.6	-	11	2209	c.1314T>C	c.(1312-1314)gaT>gaC	p.D438D		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	438					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TGACCTCGGCATCAATGGTCT	0.537																																					p.D438D		.											.	VCP-228	0			c.T1314C						.						229	212	218					9																	35061057		2203	4300	6503	SO:0001819	synonymous_variant	7415	exon11			CTCGGCATCAATG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.1314T>C	9.37:g.35061057A>G		Somatic	409	1		WXS	Illumina HiSeq	Phase_I	252	122	NM_007126	0	0	128	251	123	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Silent	SNP	ENST00000358901.6	37	CCDS6573.1																																																																																			.		0.537	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		G	35061057	A	G	35061057	2	3	104	1	0	0	0	0	0	0	0	1	17173	214	8	3		3	VCP	9	35061057	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	2519242	35061057	106152374	65	9266											
TMEM2	23670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	74313090	74313090	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	taactgtggccatgcctgtgGcttttggctttgagatacaa	8	14	11	8	0	0	1	0	1	0	1	0	2	0	1	2	3	3	2	2	3	3	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:74313090G>T	ENST00000377044.4	-	20	3947	c.3408C>A	c.(3406-3408)agC>agA	p.S1136R	TMEM2_ENST00000377066.5_Missense_Mutation_p.S1073R|TMEM2_ENST00000396272.3_Missense_Mutation_p.S129R	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1136					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		CATGCCTGTGGCTTTTGGCTT	0.413																																					p.S1136R		.											.	TMEM2-92	0			c.C3408A						.						155	125	135					9																	74313090		2203	4300	6503	SO:0001583	missense	23670	exon20			CCTGTGGCTTTTG		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.3408C>A	9.37:g.74313090G>T	ENSP00000366243:p.Ser1136Arg	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	146	54	NM_013390	0	0	13	30	17	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118919	0.37436	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272	T;T;T	0.42900	0.96;0.96;0.96	5.8	3.79	0.43588	.	0.343603	0.37053	N	0.002263	T	0.24160	0.0585	N	0.14661	0.345	0.27366	N	0.95581	B;B	0.12630	0.004;0.006	B;B	0.16722	0.007;0.016	T	0.17077	-1.0381	10	0.16420	T	0.52	.	10.9787	0.47482	0.2588:0.0:0.7412:0.0	.	1136;1073	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	R	1136;1073;129	ENSP00000366243:S1136R;ENSP00000366266:S1073R;ENSP00000379569:S129R	ENSP00000366243:S1136R	S	-	3	2	TMEM2	73502910	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	0.723000	0.25939	0.658000	0.30925	0.563000	0.77884	AGC	.		0.413	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		T	74313090	G	T	74313090	3	4	104	1	0	0	0	0	1	0	0	0	16153	1194	42	4	763	4	TMEM2	9	74313090	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	39252033	74313090	66900341	66	9267											
FLJ46321	389763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	84609482	84609482	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggtttaataaacccagcaTatcatatgaagaacaagaaa	19	9	7	6	0	1	3	1	1	0	2	1	3	1	3	1	1	3	2	1	1	9	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:84609482T>C	ENST00000344803.2	+	4	4144	c.4097T>C	c.(4096-4098)aTa>aCa	p.I1366T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1366					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAACCCAGCATATCATATGAA	0.433																																					p.I1366T		.											.	.	0			c.T4097C						.						28	25	26					9																	84609482		1844	4078	5922	SO:0001583	missense	389763	exon4			CCAGCATATCATA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.4097T>C	9.37:g.84609482T>C	ENSP00000341988:p.Ile1366Thr	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	25	12	NM_001001670	0	0	0	0	0		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	1.389	-0.581436	0.03854	.	.	ENSG00000214929	ENST00000344803	T	0.04706	3.57	3.23	-6.46	0.01908	.	.	.	.	.	T	0.01765	0.0056	N	0.12182	0.205	0.09310	N	1	B	0.20988	0.05	B	0.17722	0.019	T	0.45145	-0.9281	9	0.09084	T	0.74	5.4727	0.8658	0.01203	0.3696:0.2351:0.248:0.1473	.	1366	Q6ZQQ2	F75D1_HUMAN	T	1366	ENSP00000341988:I1366T	ENSP00000341988:I1366T	I	+	2	0	FAM75D1	83799302	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.596000	0.02091	-2.589000	0.00457	-0.313000	0.08912	ATA	.		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		C	84609482	T	C	84609482	3	2	104	1	0	0	0	0	1	0	0	0	5951	1406	49	3	4111	3	FLJ46321	9	84609482	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	10296392	84609482	56603949	67	9268											
PAPPA	5069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	118949550	118949550	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctccttgaagacagaccGagcccggcaagtgaccacca	11	7	9	14	2	1	4	0	2	1	2	2	5	1	4	5	1	1	1	5	1	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:118949550G>T	ENST00000328252.3	+	2	902	c.533G>T	c.(532-534)cGa>cTa	p.R178L	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	178					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						AAGACAGACCGAGCCCGGCAA	0.532																																					p.R178L		.											.	PAPPA-77	0			c.G533T						.						84	79	81					9																	118949550		2203	4300	6503	SO:0001583	missense	5069	exon2			CAGACCGAGCCCG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"insulin-like growth factor-dependent IGF binding protein-4 protease", "aspecific BCL2 ARE-binding protein 2", "differentially placenta 1 expressed protein"	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.533G>T	9.37:g.118949550G>T	ENSP00000330658:p.Arg178Leu	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	76	29	NM_002581	0	0	16	28	12	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.948966	0.92660	.	.	ENSG00000182752	ENST00000328252	T	0.73681	-0.77	6.07	6.07	0.98685	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.88709	0.6510	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88974	0.3403	10	0.87932	D	0	-25.065	20.6439	0.99570	0.0:0.0:1.0:0.0	.	178	Q13219	PAPP1_HUMAN	L	178	ENSP00000330658:R178L	ENSP00000330658:R178L	R	+	2	0	PAPPA	117989371	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.827000	0.99397	2.884000	0.98904	0.655000	0.94253	CGA	.		0.532	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118949550	G	T	118949550	3	4	104	1	0	0	0	0	1	0	0	0	11458	1058	37	4	539	4	PAPPA	9	118949550	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	34340068	118949550	22263881	68	9269											
ADAMTS14	140766	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	72503320	72503320	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagacgcccagaagtgtgaGctgatctgccagtcggcgga	10	6	14	11	3	1	4	0	2	1	2	2	5	1	5	2	2	2	1	2	2	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr10:72503320G>T	ENST00000373207.1	+	13	1941	c.1941G>T	c.(1939-1941)gaG>gaT	p.E647D	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.E650D	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	647	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						AGAAGTGTGAGCTGATCTGCC	0.597																																					p.E650D													.	ADAMTS14-232	0			c.G1950T						.						81	70	74					10																	72503320		2203	4300	6503	SO:0001583	missense	140766	exon13			GTGTGAGCTGATC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"ADAM metallopeptidases with thrombospondin type 1 motif"	14899	protein-coding gene	gene with protein product		607506	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1941G>T	10.37:g.72503320G>T	ENSP00000362303:p.Glu647Asp	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	47	15	NM_139155	0	0	0	2	2	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.318605	0.60524	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.69685	-0.42;-0.42	5.2	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.65481	0.2695	L	0.52905	1.665	0.35321	D	0.784791	P;P;P	0.51449	0.936;0.885;0.945	P;P;P	0.49752	0.511;0.621;0.546	T	0.72478	-0.4281	10	0.39692	T	0.17	.	9.2922	0.37793	0.2257:0.0:0.7743:0.0	.	580;647;650	Q8WXS8-2;Q8WXS8;Q5T4G1	.;ATS14_HUMAN;.	D	650;647	ENSP00000362304:E650D;ENSP00000362303:E647D	ENSP00000362303:E647D	E	+	3	2	ADAMTS14	72173326	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.838000	0.55828	1.421000	0.47157	0.655000	0.94253	GAG	.		0.597	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72503320	G	T	72503320	3	4	104	1	0	0	0	0	1	0	0	0	259	962	34	4	2000	4	ADAMTS14	10	72503320	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		72503320	63031427	69	9270											
CPEB3	22849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	93812079	93812079	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcgcccagcagtattcacAgtaatactgcagacaggtga	12	8	10	11	1	1	2	1	1	0	1	2	2	1	2	1	1	3	5	1	1	3	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr10:93812079A>G	ENST00000265997.4	-	10	2159	c.1987T>C	c.(1987-1989)Tgt>Cgt	p.C663R	CPEB3_ENST00000412050.4_Missense_Mutation_p.C649R	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	663					3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				CAGTATTCACAGTAATACTGC	0.592																																					p.C663R		.											.	CPEB3-90	0			c.T1987C						.						101	86	91					10																	93812079		2203	4300	6503	SO:0001583	missense	22849	exon10			ATTCACAGTAATA	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1987T>C	10.37:g.93812079A>G	ENSP00000265997:p.Cys663Arg	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	45	19	NM_014912	0	0	10	20	10	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	37	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.195744	0.58126	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.25414	1.8;1.8	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	M	0.89214	3.015	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.997	D;D;D	0.91635	0.999;0.986;0.994	T	0.67469	-0.5663	10	0.87932	D	0	-10.7449	15.5925	0.76543	1.0:0.0:0.0:0.0	.	663;649;649	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	R	649;649;663	ENSP00000398310:C649R;ENSP00000265997:C663R	ENSP00000265997:C663R	C	-	1	0	CPEB3	93802059	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	TGT	.		0.592	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		G	93812079	A	G	93812079	3	3	104	1	0	0	0	0	1	0	0	0	3808	188	7	3	113	3	CPEB3	10	93812079	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	21308759	93812079	41722668	70	9271											
RRP12	23223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	99120314	99120314	+	Frame_Shift_Del	DEL	G	G	-																															aagcctcaccttggtactgaGggggtatctccagctcctcc																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr10:99120314delG	ENST00000370992.4	-	31	3740	c.3629delC	c.(3628-3630)cctfs	p.P1210fs	RRP12_ENST00000536831.1_Frame_Shift_Del_p.P928fs|RRP12_ENST00000414986.1_Frame_Shift_Del_p.P1149fs|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000315563.6_Frame_Shift_Del_p.P1110fs	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1210						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TTGGTACTGAGGGGGTATCTC	0.557																																					p.P1210fs		.											.	RRP12-92	0			c.3629delC						.						170	143	152					10																	99120314		2203	4300	6503	SO:0001589	frameshift_variant	23223	exon31			.		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3629delC	10.37:g.99120314delG	ENSP00000360031:p.Pro1210fs	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	81	39	NM_015179	0	0	0	0	0	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Frame_Shift_Del	DEL	ENST00000370992.4	37	CCDS7457.1																																																																																			.		0.557	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		-	99120314	G	-	99120314	7	5	104	1	0	1	0	1	0	0	0	0	13718	1000	35	0	280	0	RRP12	10	99120314	Frame_Shift_Del	DEL	G	TCGA-DZ-6133-01A-11D-1961-08	5308235	99120314	36414433	71	9272											
KNDC1	85442	broad.mit.edu	37	chr10	135012252	135012252	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agcagccccagagcctcttgGggcgtcagtgcagcgtgact	7	7	14	13	2	2	2	1	1	1	1	2	2	2	2	3	2	5	2	3	2	0	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr10:135012252G>C	ENST00000304613.3	+	14	2261	c.2240G>C	c.(2239-2241)gGg>gCg	p.G747A	KNDC1_ENST00000368572.2_Missense_Mutation_p.G747A|KNDC1_ENST00000368571.2_Missense_Mutation_p.G682A			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	747	Pro-rich.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GAGCCTCTTGGGGCGTCAGTG	0.726																																					p.G747A													.	KNDC1-229	0			c.G2240C						.						6	9	8					10																	135012252		2105	4171	6276	SO:0001583	missense	85442	exon14			CTCTTGGGGCGTC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2240G>C	10.37:g.135012252G>C	ENSP00000304437:p.Gly747Ala	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	5	3	NM_152643	0	0	2	8	6	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	8.015	0.758350	0.15846	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.18174	2.75;2.75;2.23	3.6	0.496	0.16896	.	2.237860	0.02114	U	0.055037	T	0.15305	0.0369	L	0.46157	1.445	0.09310	N	1	P;B;B	0.41450	0.75;0.206;0.131	B;B;B	0.39562	0.303;0.086;0.026	T	0.18209	-1.0344	10	0.15952	T	0.53	-0.5875	4.1268	0.10131	0.2365:0.1947:0.5687:0.0	.	747;682;747	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	A	747;747;682	ENSP00000304437:G747A;ENSP00000357561:G747A;ENSP00000357560:G682A	ENSP00000304437:G747A	G	+	2	0	KNDC1	134862242	0.002000	0.14202	0.000000	0.03702	0.016000	0.09150	0.679000	0.25291	-0.015000	0.14150	0.306000	0.20318	GGG	.		0.726	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		C	135012252	G	C	135012252	3	2	104	1	0	0	0	0	1	0	0	0	8447	1232	43	4	2294	4	KNDC1	10	135012252	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	35891938	135012252	522495	72	9273											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411953	6411953	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctggcgctggcgctggCgctggcgctggcgctggctc	0	8	20	13	5	0	0	0	0	0	0	1	0	0	0	0	7	1	7	0	7	0	0	rs550067660|rs200577287	byFrequency	TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:6411953C>G	ENST00000342245.4	+	1	293	c.125C>G	c.(124-126)gCg>gGg	p.A42G	SMPD1_ENST00000356761.2_Missense_Mutation_p.A42G|SMPD1_ENST00000527275.1_Missense_Mutation_p.A42G|SMPD1_ENST00000299397.3_Missense_Mutation_p.A42G|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	42					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggcgctggcgctggcgctg	0.701																																					p.A42G		.											.	SMPD1-90	0			c.C125G						.						15	20	18					11																	6411953		2196	4291	6487	SO:0001583	missense	6609	exon1			CGCTGGCGCTGGC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.125C>G	11.37:g.6411953C>G	ENSP00000340409:p.Ala42Gly	Somatic	31	2		WXS	Illumina HiSeq	Phase_I	27	2	NM_000543	0	0	0	0	0	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	37	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	c	5.495	0.276322	0.10403	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.10668	2.85;2.85;2.86;2.86	4.83	1.04	0.20106	.	.	.	.	.	T	0.04452	0.0122	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.46721	-0.9171	9	0.11182	T	0.66	-29.9727	6.4547	0.21924	0.0:0.6933:0.1662:0.1405	.	42;42;40	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	G	42	ENSP00000299397:A42G;ENSP00000349203:A42G;ENSP00000340409:A42G;ENSP00000435350:A42G	ENSP00000299397:A42G	A	+	2	0	SMPD1	6368529	0.017000	0.18338	0.014000	0.15608	0.042000	0.13812	-0.478000	0.06575	0.322000	0.23283	0.563000	0.77884	GCG	.		0.701	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		G	6411953	C	G	6411953	3	3	104	1	0	0	0	0	1	0	0	0	14836	768	27	4	127	4	SMPD1	11	6411953	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		6411953	128594563	73	9274											
HARBI1	283254	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46637368	46637368	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acccccatcacccctggcatCcctgccaacccatagaattc	10	7	4	20	0	1	1	1	0	0	1	3	1	2	1	7	1	2	1	7	1	3	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:46637368C>A	ENST00000326737.3	-	2	667	c.420G>T	c.(418-420)ggG>ggT	p.G140G	ATG13_ENST00000312040.4_5'Flank|ATG13_ENST00000451945.1_5'Flank|ATG13_ENST00000529655.1_5'Flank|ATG13_ENST00000530500.1_5'Flank|ATG13_ENST00000359513.4_5'Flank|ATG13_ENST00000526508.1_5'Flank|ATG13_ENST00000434074.1_5'Flank|ATG13_ENST00000524625.1_5'Flank|ATG13_ENST00000528494.1_5'Flank	NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	140						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclease activity (GO:0004518)			large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)	3						CCCCTGGCATCCCTGCCAACC	0.512																																					p.G140G		.											.	HARBI1-90	0			c.G420T						.						201	196	198					11																	46637368		2201	4299	6500	SO:0001819	synonymous_variant	283254	exon2			TGGCATCCCTGCC	AK057237	CCDS7920.1	11p11.2	2008-07-10	2008-07-01	2008-07-01	ENSG00000180423	ENSG00000180423			26522	protein-coding gene	gene with protein product		615086	"chromosome 11 open reading frame 77"	C11orf77		15169610, 18339812	Standard	NM_173811		Approved	FLJ32675	uc001ncy.3	Q96MB7	OTTHUMG00000166537	ENST00000326737.3:c.420G>T	11.37:g.46637368C>A		Somatic	417	0		WXS	Illumina HiSeq	Phase_I	226	84	NM_173811	0	0	0	2	2	D3DQP9	Silent	SNP	ENST00000326737.3	37	CCDS7920.1																																																																																			.		0.512	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390291.1	NM_173811		A	46637368	C	A	46637368	2	1	104	1	0	0	0	0	0	0	0	1	6979	842	30	4		4	HARBI1	11	46637368	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	40225415	46637368	88369148	74	9275											
SAPS3	55291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	68377390	68377390	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgaggaagggaaactgtcTacctctcaagatgctgcttg	11	10	12	8	0	2	2	1	1	2	1	3	4	2	4	1	2	4	2	1	2	4	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:68377390T>A	ENST00000393800.2	+	23	2723	c.2469T>A	c.(2467-2469)tcT>tcA	p.S823S	PPP6R3_ENST00000265637.4_Silent_p.S777S|PPP6R3_ENST00000265636.5_Silent_p.S743S|PPP6R3_ENST00000393799.2_Silent_p.S829S|PPP6R3_ENST00000524845.1_Silent_p.S794S|PPP6R3_ENST00000393801.3_Silent_p.S829S|PPP6R3_ENST00000529710.1_Silent_p.S743S|PPP6R3_ENST00000527403.2_Silent_p.S788S|PPP6R3_ENST00000534534.1_Silent_p.S591S|PPP6R3_ENST00000524904.1_Silent_p.S817S	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	823					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGAAACTGTCTACCTCTCAAG	0.577																																					p.S829S		.											.	PPP6R3-91	0			c.T2487A						.						174	149	157					11																	68377390		2200	4294	6494	SO:0001819	synonymous_variant	55291	exon24			ACTGTCTACCTCT	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2469T>A	11.37:g.68377390T>A		Somatic	205	0		WXS	Illumina HiSeq	Phase_I	124	54	NM_001164160	0	0	43	81	38	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	37	CCDS53672.1																																																																																			.		0.577	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		A	68377390	T	A	68377390	2	1	104	1	0	0	0	0	0	0	0	1	13870	1509	53	5		5	SAPS3	11	68377390	Silent	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	21740022	68377390	66629126	75	9276											
MMP3	4314	ucsc.edu;bcgsc.ca	37	chr11	102713447	102713447	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacttcgggatgccaggaaaGgttctgaagtgaccaacatc	12	8	11	10	1	1	2	0	2	1	0	3	4	1	4	2	3	2	1	2	3	3	2	rs41380244	byFrequency	TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:102713447G>T	ENST00000299855.5	-	2	562	c.306C>A	c.(304-306)acC>acA	p.T102T		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	102					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TGCCAGGAAAGGTTCTGAAGT	0.478																																					p.T102T													.	MMP3-226	0			c.C306A						.						72	66	68					11																	102713447		2203	4299	6502	SO:0001819	synonymous_variant	4314	exon2			AGGAAAGGTTCTG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"matrix metalloproteinase 3 (stromelysin 1, progelatinase)"	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.306C>A	11.37:g.102713447G>T		Somatic	75	0		WXS	Illumina HiSeq		35	19	NM_002422	0	0	0	0	0	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1																																																																																			G|0.673;C|0.327		0.478	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422		T	102713447	G	T	102713447	2	4	104	1	0	0	0	0	0	0	0	1	9691	987	35	4		4	MMP3	11	102713447	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	34336057	102713447	32293069	76	9277											
ANKK1	255239	hgsc.bcm.edu;broad.mit.edu	37	chr11	113270078	113270078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggaacgtgaagggtggAcccctcttcacctggctgca	8	7	12	14	1	2	1	1	1	1	0	2	3	2	3	4	4	2	2	4	4	2	1	rs370088482		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:113270078A>G	ENST00000303941.3	+	8	1481	c.1387A>G	c.(1387-1389)Acc>Gcc	p.T463A		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	463							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TGAAGGGTGGACCCCTCTTCA	0.622																																					p.T463A		.											.	ANKK1-628	0			c.A1387G						.						18	22	21					11																	113270078		2092	4222	6314	SO:0001583	missense	255239	exon8			GGGTGGACCCCTC	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.1387A>G	11.37:g.113270078A>G	ENSP00000306678:p.Thr463Ala	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	9	3	NM_178510	0	0	0	0	0		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.906789	0.33628	.	.	ENSG00000170209	ENST00000303941	T	0.74737	-0.87	4.83	1.03	0.20045	Ankyrin repeat-containing domain (4);	0.096889	0.43579	D	0.000551	D	0.84419	0.5468	M	0.90252	3.1	0.39435	D	0.967155	D	0.76494	0.999	D	0.74348	0.983	T	0.81106	-0.1083	10	0.62326	D	0.03	-34.3557	4.9666	0.14094	0.637:0.0:0.079:0.284	.	463	Q8NFD2	ANKK1_HUMAN	A	463	ENSP00000306678:T463A	ENSP00000306678:T463A	T	+	1	0	ANKK1	112775288	1.000000	0.71417	0.917000	0.36280	0.059000	0.15707	2.408000	0.44574	0.005000	0.14708	0.455000	0.32223	ACC	.		0.622	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		G	113270078	A	G	113270078	3	3	104	1	0	0	0	0	1	0	0	0	631	275	10	3	1417	3	ANKK1	11	113270078	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	10556631	113270078	21736438	77	9278											
PEX5	5830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	7343122	7343122	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccccggcctctgaggcagTgagtgttcttgaggtggaaa	8	9	15	9	1	2	3	0	3	2	0	2	4	2	4	3	4	1	2	3	4	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:7343122T>C	ENST00000455147.2	+	3	727		c.e3+2		RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000412720.2_Splice_Site|PEX5_ENST00000545220.1_Intron|PEX5_ENST00000434354.2_Missense_Mutation_p.V50A|PEX5_ENST00000420616.2_Splice_Site|PEX5_ENST00000266563.5_Splice_Site|RP11-273B20.3_ENST00000543061.1_RNA|PEX5_ENST00000266564.3_Splice_Site	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5						cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						TCTGAGGCAGTGAGTGTTCTT	0.632																																					p.V50A		.											.	PEX5-91	0			c.T149C						.						24	27	26					12																	7343122		2200	4294	6494	SO:0001630	splice_region_variant	5830	exon2			AGGCAGTGAGTGT	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"Tetratricopeptide (TTC) repeat domain containing"	9719	protein-coding gene	gene with protein product		600414	"peroxisome receptor 1"	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.147+2T>C	12.37:g.7343122T>C		Somatic	22	0		WXS	Illumina HiSeq	Phase_I	21	11	NM_001131023	0	0	2	79	77	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Missense_Mutation	SNP	ENST00000455147.2	37	CCDS44823.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.99|17.99	3.522704|3.522704	0.64747|0.64747	.|.	.|.	ENSG00000139197|ENSG00000139197	ENST00000542539;ENST00000455147;ENST00000540398;ENST00000266563;ENST00000544456;ENST00000545574;ENST00000420616;ENST00000412720;ENST00000536841;ENST00000537873;ENST00000266564|ENST00000434354;ENST00000396637	.|D;D	.|0.88046	.|-2.33;-2.09	3.59|3.59	3.59|3.59	0.41128|0.41128	.|.	.|.	.|.	.|.	.|.	.|D	.|0.90950	.|0.7155	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|P	.|0.43392	.|0.805	.|P	.|0.59424	.|0.857	.|D	.|0.89996	.|0.4111	.|7	.|.	.|.	.|.	.|.	10.9229|10.9229	0.47176|0.47176	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|50	.|B4DZ45	.|.	.|A	-1|50	.|ENSP00000407401:V50A;ENSP00000379877:V50A	.|.	.|V	+|+	.|2	.|0	PEX5|PEX5	7234389|7234389	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.526000|0.526000	0.34562|0.34562	2.840000|2.840000	0.48215|0.48215	1.654000|1.654000	0.50703|0.50703	0.342000|0.342000	0.21767|0.21767	.|GTG	.		0.632	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	Intron	C	7343122	T	C	7343122	5	2	104	1	0	0	0	0	0	0	1	0	11774	1710	59	3	151	3	PEX5	12	7343122	Splice_Site	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		7343122	126508773	78	9279											
GSG1	83445	broad.mit.edu;bcgsc.ca	37	chr12	13243503	13243503	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagctccggaaggagaaccGgtcatccccagtctcccagt	10	6	11	14	2	2	1	1	0	1	1	5	4	4	2	5	3	2	1	5	3	3	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:13243503G>A	ENST00000432710.2	-	2	430	c.298C>T	c.(298-300)Cgg>Tgg	p.R100W	GSG1_ENST00000537302.1_Missense_Mutation_p.R87W|GSG1_ENST00000351606.6_Missense_Mutation_p.R100W|GSG1_ENST00000396310.2_Missense_Mutation_p.R84W|GSG1_ENST00000337630.6_Missense_Mutation_p.R87W|GSG1_ENST00000457134.2_Missense_Mutation_p.R87W|GSG1_ENST00000324458.8_Missense_Mutation_p.R100W|GSG1_ENST00000396302.3_Missense_Mutation_p.R87W	NM_001206842.1	NP_001193771.1	Q2KHT4	GSG1_HUMAN	germ cell associated 1	87						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		AAGGAGAACCGGTCATCCCCA	0.542																																					p.R100W													.	GSG1-90	0			c.C298T						.						108	98	101					12																	13243503		2203	4300	6503	SO:0001583	missense	83445	exon2			AGAACCGGTCATC	BC001796	CCDS8659.2, CCDS44835.1, CCDS44836.1, CCDS55806.1, CCDS55807.1, CCDS55808.1	12p13.31	2007-12-03			ENSG00000111305	ENSG00000111305			19716	protein-coding gene	gene with protein product							Standard	NM_031289		Approved	MGC3146	uc001rbn.3	Q2KHT4	OTTHUMG00000150148	ENST00000432710.2:c.298C>T	12.37:g.13243503G>A	ENSP00000405032:p.Arg100Trp	Somatic	208	0		WXS	Illumina HiSeq	Phase_I	147	9	NM_001080554	0	0	0	0	0	Q8N4M3|Q8NBR4|Q8NBS0|Q8NBT1|Q96LP9|Q96SI6|Q9BUY4	Missense_Mutation	SNP	ENST00000432710.2	37	CCDS55808.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.700492	0.68501	.	.	ENSG00000111305	ENST00000337630;ENST00000324458;ENST00000396310;ENST00000396302;ENST00000457134;ENST00000432710;ENST00000537302;ENST00000351606;ENST00000405543;ENST00000545401;ENST00000542415;ENST00000545699	T;T;T;T;T;T;T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14;1.14	5.55	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.59985	0.2234	M	0.83603	2.65	0.39184	D	0.96283	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;0.999;1.0;1.0;1.0	T	0.66524	-0.5902	10	0.87932	D	0	.	9.1927	0.37209	0.0731:0.0:0.7819:0.145	.	100;100;100;87;87;87;87;87	Q2KHT4-7;Q2KHT4-6;G3XAB9;Q2KHT4;Q2KHT4-5;Q2KHT4-2;F1T0A0;F1T0A1	.;.;.;GSG1_HUMAN;.;.;.;.	W	87;100;84;87;87;100;87;100;84;100;100;87	ENSP00000336816:R87W;ENSP00000320838:R100W;ENSP00000379604:R84W;ENSP00000379596:R87W;ENSP00000398384:R87W;ENSP00000405032:R100W;ENSP00000441718:R87W;ENSP00000336857:R100W;ENSP00000445884:R100W;ENSP00000439676:R100W;ENSP00000440684:R87W	ENSP00000320838:R100W	R	-	1	2	GSG1	13134770	1.000000	0.71417	0.995000	0.50966	0.895000	0.52256	2.105000	0.41825	1.342000	0.45619	0.561000	0.74099	CGG	.		0.542	GSG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316546.1	NM_031289		A	13243503	G	A	13243503	3	1	104	1	0	0	0	0	1	0	0	0	6841	1115	39	1	938	1	GSG1	12	13243503	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	5900381	13243503	120608392	79	9280											
IPO8	10526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	30790088	30790088	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcaattccaaaaggatactCagtcctattatacacatctt	14	13	4	10	0	2	0	1	0	1	0	4	1	4	1	2	1	3	1	2	1	7	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:30790088C>G	ENST00000256079.4	-	22	2861	c.2523G>C	c.(2521-2523)ctG>ctC	p.L841L	IPO8_ENST00000544829.1_Silent_p.L636L	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	841					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					AAAGGATACTCAGTCCTATTA	0.393																																					p.L841L		.											.	IPO8-227	0			c.G2523C						.						133	120	124					12																	30790088		2203	4300	6503	SO:0001819	synonymous_variant	10526	exon22			GATACTCAGTCCT	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.2523G>C	12.37:g.30790088C>G		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	126	78	NM_006390	1	0	44	114	69	B7Z7M3	Silent	SNP	ENST00000256079.4	37	CCDS8719.1																																																																																			.		0.393	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		G	30790088	C	G	30790088	2	3	104	1	0	0	0	0	0	0	0	1	7819	813	29	4		4	IPO8	12	30790088	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	17546585	30790088	103061807	80	9281											
FAM60A	58516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	31435663	31435663	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcaccactcctgagtggAgatgggcagaggctctggcc	8	7	14	12	0	2	3	1	1	1	2	3	4	3	3	3	4	0	2	3	4	0	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:31435663A>C	ENST00000337682.4	-	6	1017	c.649T>G	c.(649-651)Tcc>Gcc	p.S217A	FAM60A_ENST00000539409.1_Missense_Mutation_p.S69A|FAM60A_ENST00000542983.1_Missense_Mutation_p.S69A|FAM60A_ENST00000454658.2_Missense_Mutation_p.S217A|FAM60A_ENST00000395766.1_Missense_Mutation_p.S69A	NM_001135812.1	NP_001129284.1	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A	217					negative regulation of cell migration (GO:0030336)	Sin3 complex (GO:0016580)				large_intestine(1)|lung(2)	3	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					TCCTGAGTGGAGATGGGCAGA	0.453																																					p.S217A		.											.	FAM60A-90	0			c.T649G						.						38	40	39					12																	31435663		2203	4297	6500	SO:0001583	missense	58516	exon7			GAGTGGAGATGGG	AF212220	CCDS8723.1	12p11.21	2012-11-30	2005-04-07	2005-04-07	ENSG00000139146	ENSG00000139146			30702	protein-coding gene	gene with protein product		615027	"chromosome 12 open reading frame 14"	C12orf14		11042152, 22984288, 22865885	Standard	NM_021238		Approved	TERA	uc001rke.3	Q9NP50	OTTHUMG00000168586	ENST00000337682.4:c.649T>G	12.37:g.31435663A>C	ENSP00000337477:p.Ser217Ala	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	94	51	NM_021238	0	0	43	140	97	D3DUV8|Q9BSZ8	Missense_Mutation	SNP	ENST00000337682.4	37	CCDS8723.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.262656	0.23051	.	.	ENSG00000139146	ENST00000539409;ENST00000337682;ENST00000454658;ENST00000398170;ENST00000395766;ENST00000542983	T;T	0.41758	0.99;0.99	4.26	0.167	0.15006	.	0.592620	0.16969	N	0.192195	T	0.17704	0.0425	N	0.08118	0	0.29822	N	0.830762	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18272	-1.0342	10	0.20519	T	0.43	-15.4818	5.7799	0.18299	0.5453:0.3628:0.0919:0.0	.	217;258	Q9NP50;B7Z287	FA60A_HUMAN;.	A	69;217;217;258;69;69	ENSP00000337477:S217A;ENSP00000393279:S217A	ENSP00000337477:S217A	S	-	1	0	FAM60A	31326930	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	0.828000	0.27435	0.078000	0.16900	0.482000	0.46254	TCC	.		0.453	FAM60A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400347.1	NM_021238		C	31435663	A	C	31435663	3	2	104	1	0	0	0	0	1	0	0	0	5614	304	11	5	20	5	FAM60A	12	31435663	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	645575	31435663	102416232	81	9282											
FMNL3	91010	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	50041978	50041978	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgcaccccgtgcttgcctCagccgtcttggcgtcccgct	2	10	10	19	4	2	0	1	0	1	0	3	0	3	0	6	1	4	3	6	1	0	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:50041978C>T	ENST00000293590.5	-	22	2907	c.2674G>A	c.(2674-2676)Gag>Aag	p.E892K	FMNL3_ENST00000335154.5_Missense_Mutation_p.E892K|FMNL3_ENST00000550488.1_Missense_Mutation_p.E892K|FMNL3_ENST00000352151.5_Missense_Mutation_p.E841K			Q8IVF7	FMNL3_HUMAN	formin-like 3	892	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GTGCTTGCCTCAGCCGTCTTG	0.552																																					p.E892K													.	FMNL3-228	0			c.G2674A						.						80	83	82					12																	50041978		2073	4196	6269	SO:0001583	missense	91010	exon22			TTGCCTCAGCCGT	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.2674G>A	12.37:g.50041978C>T	ENSP00000293590:p.Glu892Lys	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	97	18	NM_175736	0	0	0	0	0	B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	ENST00000293590.5	37		.	.	.	.	.	.	.	.	.	.	C	20.4	3.989748	0.74589	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590	T;T;T;T	0.17213	2.39;2.29;2.39;2.39	4.78	3.86	0.44501	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.09905	0.0243	N	0.11364	0.135	0.53005	D	0.999965	B;B;B	0.26445	0.094;0.143;0.149	B;B;B	0.30943	0.122;0.081;0.099	T	0.15206	-1.0445	10	0.12103	T	0.63	.	14.1676	0.65488	0.0:0.8485:0.1515:0.0	.	841;892;892	Q8IVF7-2;Q8IVF7-3;Q8IVF7	.;.;FMNL3_HUMAN	K	892;892;841;892	ENSP00000335655:E892K;ENSP00000447479:E892K;ENSP00000344311:E841K;ENSP00000293590:E892K	ENSP00000293590:E892K	E	-	1	0	FMNL3	48328245	0.637000	0.27216	0.843000	0.33291	0.197000	0.23852	1.072000	0.30678	1.330000	0.45394	0.650000	0.86243	GAG	.		0.552	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		T	50041978	C	T	50041978	3	4	104	1	0	0	0	0	1	0	0	0	5972	835	29	2	429	2	FMNL3	12	50041978	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	18606315	50041978	83809917	82	9283											
SCN8A	6334	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	52145329	52145329	+	Frame_Shift_Del	DEL	C	C	-																															ctgtttatggcaatggagcaCcatcctatgacaccacaatt																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:52145329delC	ENST00000354534.6	+	14	2500	c.2322delC	c.(2320-2322)cacfs	p.H775fs	SCN8A_ENST00000545061.1_Frame_Shift_Del_p.H775fs|SCN8A_ENST00000550891.1_Frame_Shift_Del_p.H775fs	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	775					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CAATGGAGCACCATCCTATGA	0.418																																					p.H774fs		.											.	SCN8A-29	0			c.2322delC						.						147	140	142					12																	52145329		2052	4218	6270	SO:0001589	frameshift_variant	6334	exon14			.	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.2322delC	12.37:g.52145329delC	ENSP00000346534:p.His775fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	109	36	NM_014191	0	0	0	0	0	B9VWG8|O95788|Q9NYX2|Q9UPB2	Frame_Shift_Del	DEL	ENST00000354534.6	37	CCDS44891.1																																																																																			.		0.418	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		-	52145329	C	-	52145329	7	5	104	1	0	1	0	1	0	0	0	0	13956	506	18	0	2372	0	SCN8A	12	52145329	Frame_Shift_Del	DEL	C	TCGA-DZ-6133-01A-11D-1961-08	2103351	52145329	81706566	83	9284											
KRT83	3889	broad.mit.edu;ucsc.edu	37	chr12	52708468	52708468	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggtggtgttcagctggcCacagggcttgcacaaaccag	10	7	13	11	0	1	0	1	0	0	0	1	0	1	0	2	4	3	4	2	4	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:52708468C>T	ENST00000293670.3	-	9	1491	c.1429G>A	c.(1429-1431)Ggc>Agc	p.G477S	AC121757.1_ENST00000594763.1_5'Flank	NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	477	Tail.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TTCAGCTGGCCACAGGGCTTG	0.667																																					p.G477S	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)												.	KRT83-91	0			c.G1429A						.						27	22	24					12																	52708468		2199	4296	6495	SO:0001583	missense	3889	exon9			GCTGGCCACAGGG	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.1429G>A	12.37:g.52708468C>T	ENSP00000293670:p.Gly477Ser	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	14	5	NM_002282	0	0	0	0	0	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.623230	0.28889	.	.	ENSG00000170523	ENST00000293670	D	0.86497	-2.13	2.96	2.02	0.26589	.	0.231155	0.21686	U	0.070656	T	0.75975	0.3923	N	0.22421	0.69	0.27127	N	0.96199	B	0.10296	0.003	B	0.10450	0.005	T	0.64550	-0.6381	10	0.45353	T	0.12	.	7.2268	0.26020	0.2659:0.7341:0.0:0.0	.	477	P78385	KRT83_HUMAN	S	477	ENSP00000293670:G477S	ENSP00000293670:G477S	G	-	1	0	KRT83	50994735	0.328000	0.24687	0.973000	0.42090	0.064000	0.16182	-0.181000	0.09740	0.319000	0.23209	0.313000	0.20887	GGC	.		0.667	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		T	52708468	C	T	52708468	3	4	104	1	0	0	0	0	1	0	0	0	8518	594	21	2	56	2	KRT83	12	52708468	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	563139	52708468	81143427	84	9285											
TMPO	7112	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	98941479	98941479	+	Frame_Shift_Del	DEL	A	A	-																															cttggcagatgtcaagtcagAaaagacaaaaaagggacgct																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:98941479delA	ENST00000556029.1	+	9	1564	c.1208delA	c.(1207-1209)gaafs	p.E403fs	TMPO_ENST00000393053.2_Frame_Shift_Del_p.E294fs|TMPO_ENST00000548223.1_3'UTR|TMPO_ENST00000343315.5_Frame_Shift_Del_p.E363fs	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	403	Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GTCAAGTCAGAAAAGACAAAA	0.408																																					p.E403fs		.											.	TMPO-93	0			c.1208delA						.						107	107	107					12																	98941479		2203	4300	6503	SO:0001589	frameshift_variant	7112	exon9			.		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.1208delA	12.37:g.98941479delA	ENSP00000450627:p.Glu403fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	109	47	NM_001032283	0	0	0	0	0	A2T926|Q14861	Frame_Shift_Del	DEL	ENST00000556029.1	37	CCDS31879.1																																																																																			.		0.408	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		-	98941479	A	-	98941479	7	5	104	1	0	1	0	1	0	0	0	0	16269	246	9	0	2766	0	TMPO	12	98941479	Frame_Shift_Del	DEL	A	TCGA-DZ-6133-01A-11D-1961-08	46233011	98941479	34910416	85	9286											
HSP90B1	7184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	104336447	104336447	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccactcgaatcgaacacgtcTtgctaaacttcttaggttcc	10	12	6	13	3	2	0	0	0	2	0	5	2	3	0	2	1	3	2	2	1	5	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:104336447T>C	ENST00000299767.5	+	12	1699	c.1517T>C	c.(1516-1518)cTt>cCt	p.L506P		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	506					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CGAACACGTCTTGCTAAACTT	0.373																																					p.L506P		.											.	HSP90B1-93	0			c.T1517C						.						116	113	114					12																	104336447		2203	4300	6503	SO:0001583	missense	7184	exon12			CACGTCTTGCTAA	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.1517T>C	12.37:g.104336447T>C	ENSP00000299767:p.Leu506Pro	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	159	94	NM_003299	0	0	1355	4615	3260	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.696033	0.88830	.	.	ENSG00000166598	ENST00000299767;ENST00000421266	T	0.18016	2.24	6.16	6.16	0.99307	Ribosomal protein S5 domain 2-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79080	-0.1950	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	506	P14625	ENPL_HUMAN	P	506;256	ENSP00000299767:L506P	ENSP00000299767:L506P	L	+	2	0	HSP90B1	102860577	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.367000	0.80283	0.528000	0.53228	CTT	.		0.373	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		C	104336447	T	C	104336447	3	2	104	1	0	0	0	0	1	0	0	0	7424	1609	56	3	1563	3	HSP90B1	12	104336447	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	5394968	104336447	29515448	86	9287											
MYO1H	283446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	109834250	109834250	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aactaaataaccatttcatcCtcatttctggagagagtggg	13	12	8	8	0	3	1	2	0	1	1	4	3	4	2	2	2	2	0	2	2	4	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:109834250C>T	ENST00000431443.2	+	3	304	c.304C>T	c.(304-306)Ctc>Ttc	p.L102F	MYO1H_ENST00000310903.5_Missense_Mutation_p.L102F	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	102	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						CCATTTCATCCTCATTTCTGG	0.458																																					p.L102F		.											.	.	0			c.C304T						.						68	68	68					12																	109834250		1957	4152	6109	SO:0001583	missense	283446	exon3			TTCATCCTCATTT		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"Myosins / Myosin superfamily : Class I"	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.304C>T	12.37:g.109834250C>T	ENSP00000444076:p.Leu102Phe	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	88	46	NM_001101421	0	0	0	0	0	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	37		.	.	.	.	.	.	.	.	.	.	C	23.2	4.392377	0.83011	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.89875	-2.58;-2.58	4.8	4.8	0.61643	.	.	.	.	.	D	0.96914	0.8992	H	0.98370	4.215	0.46981	D	0.999273	D	0.89917	1.0	D	0.91635	0.999	D	0.98431	1.0582	9	0.87932	D	0	.	17.7816	0.88526	0.0:1.0:0.0:0.0	.	102	F5H3C6	.	F	102	ENSP00000439182:L102F;ENSP00000444076:L102F	ENSP00000439182:L102F	L	+	1	0	MYO1H	108318633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.258000	0.51507	2.615000	0.88500	0.644000	0.83932	CTC	.		0.458	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109834250	C	T	109834250	3	4	104	1	0	0	0	0	1	0	0	0	10100	681	24	2	314	2	MYO1H	12	109834250	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	5497803	109834250	24017645	87	9288											
SRRM4	84530	broad.mit.edu;bcgsc.ca	37	chr12	119568567	119568567	+	Frame_Shift_Del	DEL	C	C	-																															aagaccctctgcaaggacagCcctgaggcccagtccagtcg																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:119568567delC	ENST00000267260.4	+	8	1087	c.699delC	c.(697-699)agcfs	p.S233fs	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	233	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						GCAAGGACAGCCCTGAGGCCC	0.657																																					p.S233fs													.	SRRM4-2	0			c.699delC						.						25	30	29					12																	119568567		1929	4127	6056	SO:0001589	frameshift_variant	84530	exon8			GGACAGCCCTGAG	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.699delC	12.37:g.119568567delC	ENSP00000267260:p.Ser233fs	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	41	9	NM_194286	0	0	0	0	0	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Frame_Shift_Del	DEL	ENST00000267260.4	37	CCDS44994.1																																																																																			.		0.657	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		-	119568567	C	-	119568567	7	5	104	1	0	1	0	1	0	0	0	0	15203	738	26	0	729	0	SRRM4	12	119568567	Frame_Shift_Del	DEL	C	TCGA-DZ-6133-01A-11D-1961-08	9734317	119568567	14283328	88	9289											
NCOR2	9612	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	124848291	124848291	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggcttctggggtgaggcAttggcccgggggtcgccagt	4	9	19	9	2	1	1	0	1	1	0	2	1	1	1	2	7	0	2	2	7	0	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:124848291A>G	ENST00000405201.1	-	21	2862	c.2862T>C	c.(2860-2862)aaT>aaC	p.N954N	NCOR2_ENST00000404621.1_Silent_p.N936N|NCOR2_ENST00000397355.1_Silent_p.N937N|NCOR2_ENST00000429285.2_Silent_p.N936N|NCOR2_ENST00000356219.3_Silent_p.N954N|NCOR2_ENST00000404121.2_Silent_p.N507N			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	954					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GGGGTGAGGCATTGGCCCGGG	0.697																																					p.N954N		.											.	NCOR2-229	0			c.T2862C						.						39	56	51					12																	124848291		2023	4151	6174	SO:0001819	synonymous_variant	9612	exon23			TGAGGCATTGGCC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"nuclear receptor co-repressor 2"			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.2862T>C	12.37:g.124848291A>G		Somatic	190	0		WXS	Illumina HiSeq	Phase_I	145	77	NM_006312	0	1	31	81	49	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			.		0.697	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		G	124848291	A	G	124848291	2	3	104	1	0	0	0	0	0	0	0	1	10262	214	8	3		3	NCOR2	12	124848291	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	5279724	124848291	9003604	89	9290											
EP400	57634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132522561	132522562	+	Missense_Mutation	DNP	GC	GC	AT																															atgctggcttcccggtcaaaGctgaggagtttgtggtgctt																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:132522561_132522562GC>AT	ENST00000333577.4	+	33	6344_6345	c.6235_6236GC>AT	c.(6235-6237)GCt>ATt	p.A2079I	EP400_ENST00000332482.4_Missense_Mutation_p.A2006I|EP400_ENST00000389562.2_Missense_Mutation_p.A2042I|EP400_ENST00000330386.6_Missense_Mutation_p.A1962I|EP400_ENST00000389561.2_Missense_Mutation_p.A2043I			Q96L91	EP400_HUMAN	E1A binding protein p400	2079					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCCGGTCAAAGCTGAGGAGTTT	0.465																																					p.A2079I		.											.	EP400	0			c.C6128T						.																																			SO:0001583	missense	57634	exon32			TCAAAGCTGAGGA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		Exception_encountered	12.37:g.132522561_132522562delinsAT	ENSP00000333602:p.Ala2079Ile	Somatic	231	0		WXS	Illumina HiSeq	Phase_I	229	60		0	0	0	0	0	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	DNP	ENST00000333577.4	37																																																																																				.		0.465	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		AT	132522562	GC	AT	132522561	3	1	104	1	0	0	0	0	1	0	0	0	5162	971	34	2	6246	2	EP400	12	132522561	Missense_Mutation	DNP	GC	TCGA-DZ-6133-01A-11D-1961-08	7674270	132522561	1329334	90	9291											
KBTBD6	89890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41704906	41704906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attcatacacagtcacccggTtctttttccactgtggggtg	7	14	9	11	1	3	0	2	0	1	0	4	0	4	0	2	3	1	1	2	3	1	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr13:41704906T>C	ENST00000379485.1	-	1	1976	c.1742A>G	c.(1741-1743)aAc>aGc	p.N581S	KBTBD6_ENST00000499385.2_Missense_Mutation_p.N515S	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	581										NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		AGTCACCCGGTTCTTTTTCCA	0.408																																					p.N581S		.											.	KBTBD6-92	0			c.A1742G						.						179	179	179					13																	41704906		2203	4300	6503	SO:0001583	missense	89890	exon1			ACCCGGTTCTTTT	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"BTB/POZ domain containing"	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.1742A>G	13.37:g.41704906T>C	ENSP00000368799:p.Asn581Ser	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	257	154	NM_152903	0	0	5	14	9	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	t	14.19	2.460466	0.43736	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.66995	-0.24;-0.24	3.8	2.62	0.31277	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.67804	0.2932	L	0.32530	0.975	0.31105	N	0.710602	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.65092	-0.6252	10	0.36615	T	0.2	.	6.7322	0.23388	0.0:0.1222:0.0:0.8778	.	515;581	F5GZN7;Q86V97	.;KBTB6_HUMAN	S	581;515	ENSP00000368799:N581S;ENSP00000444326:N515S	ENSP00000368799:N581S	N	-	2	0	KBTBD6	40602906	1.000000	0.71417	0.500000	0.27589	0.968000	0.65278	3.578000	0.53892	0.649000	0.30751	0.379000	0.24179	AAC	.		0.408	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		C	41704906	T	C	41704906	3	2	104	1	0	0	0	0	1	0	0	0	8018	1725	60	3	286	3	KBTBD6	13	41704906	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		41704906	73464972	91	9292											
NALCN	259232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	101944368	101944368	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggctgttgaggtagtgctGcttctcgatccccacatttg	5	14	12	10	1	1	1	0	1	1	0	3	2	2	1	2	2	2	5	2	2	1	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr13:101944368G>T	ENST00000251127.6	-	9	1101	c.1020C>A	c.(1018-1020)agC>agA	p.S340R	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Missense_Mutation_p.S340R	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	340					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AGGTAGTGCTGCTTCTCGATC	0.438																																					p.S340R		.											.	NALCN-167	0			c.C1020A						.						317	247	271					13																	101944368		2203	4300	6503	SO:0001583	missense	259232	exon9			AGTGCTGCTTCTC	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1020C>A	13.37:g.101944368G>T	ENSP00000251127:p.Ser340Arg	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	52	33	NM_052867	0	0	0	0	0	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.936423	0.34189	.	.	ENSG00000102452	ENST00000251127;ENST00000376196	D;D	0.98362	-4.55;-4.89	6.16	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.92808	0.7713	N	0.08118	0	0.80722	D	1	B;B;B	0.22851	0.008;0.076;0.008	B;B;B	0.15870	0.006;0.014;0.006	D	0.89936	0.4069	10	0.23891	T	0.37	.	10.2255	0.43222	0.2563:0.0:0.7437:0.0	.	340;340;340	F2Z323;B3KSZ6;Q8IZF0	.;.;NALCN_HUMAN	R	340	ENSP00000251127:S340R;ENSP00000365367:S340R	ENSP00000251127:S340R	S	-	3	2	NALCN	100742369	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.963000	0.56773	1.616000	0.50265	0.650000	0.86243	AGC	.		0.438	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101944368	G	T	101944368	3	4	104	1	0	0	0	0	1	0	0	0	10173	1310	46	4	4340	4	NALCN	13	101944368	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	60239462	101944368	13225510	92	9293											
SIPA1L1	26037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	72055716	72055716	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccttggtctctggacctcTgtctcattcagccagtttta	6	16	7	12	0	4	0	2	0	3	0	7	1	5	1	3	2	1	1	3	2	1	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr14:72055716T>C	ENST00000555818.1	+	2	1475	c.1127T>C	c.(1126-1128)cTg>cCg	p.L376P	SIPA1L1_ENST00000381232.3_Missense_Mutation_p.L376P|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.L376P	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	376					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		TCTGGACCTCTGTCTCATTCA	0.498																																					p.L376P		.											.	SIPA1L1-156	0			c.T1127C						.						59	61	60					14																	72055716		2203	4300	6503	SO:0001583	missense	26037	exon2			GACCTCTGTCTCA	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1127T>C	14.37:g.72055716T>C	ENSP00000450832:p.Leu376Pro	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	68	25	NM_015556	0	0	44	74	30	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	T	7.254	0.603889	0.14002	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	T;T;T	0.78003	-1.14;-1.13;-1.14	6.07	4.94	0.65067	.	0.129948	0.56097	D	0.000037	T	0.55033	0.1895	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.53287	-0.8460	10	0.30078	T	0.28	-17.1009	11.6847	0.51479	0.0:0.0683:0.0:0.9317	.	376;376;376	A6H8W6;O43166-2;O43166	.;.;SI1L1_HUMAN	P	376	ENSP00000370630:L376P;ENSP00000450832:L376P;ENSP00000351352:L376P	ENSP00000351352:L376P	L	+	2	0	SIPA1L1	71125469	1.000000	0.71417	0.996000	0.52242	0.343000	0.28985	4.668000	0.61568	2.326000	0.78906	0.533000	0.62120	CTG	.		0.498	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72055716	T	C	72055716	3	2	104	1	0	0	0	0	1	0	0	0	14361	1580	55	3	1129	3	SIPA1L1	14	72055716	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		72055716	35293824	93	9294			1	30		2	2	19	T		7.26795e-05
SIPA1L1	26037	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	72055734	72055734	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgtctcattcagccagttTtagctccccaatgggcagca	8	12	8	13	0	3	0	2	0	2	0	5	0	4	0	3	1	3	4	3	1	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr14:72055734T>A	ENST00000555818.1	+	2	1493	c.1145T>A	c.(1144-1146)tTt>tAt	p.F382Y	SIPA1L1_ENST00000381232.3_Missense_Mutation_p.F382Y|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.F382Y	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	382					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		TCAGCCAGTTTTAGCTCCCCA	0.507																																					p.F382Y													.	SIPA1L1-156	0			c.T1145A						.						58	60	60					14																	72055734		2203	4300	6503	SO:0001583	missense	26037	exon2			CCAGTTTTAGCTC	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1145T>A	14.37:g.72055734T>A	ENSP00000450832:p.Phe382Tyr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	52	18	NM_015556	0	0	39	76	37	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	T	2.443	-0.328205	0.05314	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	T;T;T	0.76578	-1.03;-1.03;-1.03	6.07	6.07	0.98685	.	0.045544	0.85682	D	0.000000	T	0.62380	0.2423	N	0.13043	0.29	0.80722	D	1	P;B;B	0.51537	0.946;0.082;0.023	B;B;B	0.43386	0.418;0.091;0.016	T	0.65578	-0.6134	10	0.02654	T	1	-24.1026	16.6407	0.85098	0.0:0.0:0.0:1.0	.	382;382;382	A6H8W6;O43166-2;O43166	.;.;SI1L1_HUMAN	Y	382	ENSP00000370630:F382Y;ENSP00000450832:F382Y;ENSP00000351352:F382Y	ENSP00000351352:F382Y	F	+	2	0	SIPA1L1	71125487	1.000000	0.71417	0.791000	0.31998	0.902000	0.53008	3.502000	0.53332	2.326000	0.78906	0.533000	0.62120	TTT	.		0.507	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72055734	T	A	72055734	3	1	104	1	0	0	0	0	1	0	0	0	14361	1841	64	5	1147	5	SIPA1L1	14	72055734	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	18	72055734	35293806	94	9295			1	30		2	2	19	T		7.26795e-05
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	39885267	39885267	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgccagacatcgatgacaTctgtcctgagaatgttgaca	11	11	10	9	1	1	4	0	3	1	2	3	6	2	4	2	0	1	1	2	0	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:39885267T>C	ENST00000260356.5	+	18	2999	c.2834T>C	c.(2833-2835)aTc>aCc	p.I945T	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	945					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ATCGATGACATCTGTCCTGAG	0.478																																					p.I945T		.											.	THBS1-653	0			c.T2834C						.						78	68	71					15																	39885267		2200	4297	6497	SO:0001583	missense	7057	exon18			ATGACATCTGTCC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2834T>C	15.37:g.39885267T>C	ENSP00000260356:p.Ile945Thr	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	73	33	NM_003246	0	0	36	95	59	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852666	0.71719	.	.	ENSG00000137801	ENST00000260356	D	0.98164	-4.76	5.68	5.68	0.88126	.	0.000000	0.36778	N	0.002417	D	0.94598	0.8259	N	0.04880	-0.145	0.49798	D	0.999827	P;P	0.47762	0.725;0.9	B;B	0.43990	0.438;0.387	D	0.95190	0.8307	10	0.39692	T	0.17	-26.1702	15.8963	0.79336	0.0:0.0:0.0:1.0	.	860;945	B4E3J7;P07996	.;TSP1_HUMAN	T	945	ENSP00000260356:I945T	ENSP00000260356:I945T	I	+	2	0	THBS1	37672559	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.036000	0.88901	2.153000	0.67306	0.533000	0.62120	ATC	.		0.478	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		C	39885267	T	C	39885267	3	2	104	1	0	0	0	0	1	0	0	0	15885	1435	50	3	2900	3	THBS1	15	39885267	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		39885267	62646125	95	9296											
EPB42	2038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43508525	43508525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgcacggactggagcgCggaagtacaggatgatggtg	12	6	17	6	3	0	1	0	1	0	0	0	6	0	5	0	5	3	2	0	5	3	1	rs202154600		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:43508525C>T	ENST00000441366.2	-	2	362	c.137G>A	c.(136-138)cGc>cAc	p.R46H	EPB42_ENST00000300215.3_Missense_Mutation_p.R76H|EPB42_ENST00000540029.1_Missense_Mutation_p.R46H	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	46					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		GACTGGAGCGCGGAAGTACAG	0.597																																					p.R76H		.											.	EPB42-92	0			c.G227A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	102	90	94		227,137	-5	0	15		94	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	EPB42	NM_000119.2,NM_001114134.1	29,29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	76/722,46/692	43508525	1,13003	2203	4299	6502	SO:0001583	missense	2038	exon2			GGAGCGCGGAAGT	M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"Transglutaminases"	3381	protein-coding gene	gene with protein product	"Erythrocyte surface protein band 4.2"	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.137G>A	15.37:g.43508525C>T	ENSP00000396616:p.Arg46His	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	72	33	NM_000119	0	0	0	0	0	Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	37	CCDS45249.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.569261	0.28003	0.0	1.16E-4	ENSG00000166947	ENST00000300215;ENST00000540029;ENST00000441366;ENST00000397027	D;D;D	0.84873	-1.91;-1.91;-1.91	5.02	-5.0	0.03001	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	1.112950	0.06532	N	0.741688	T	0.73860	0.3641	N	0.13235	0.315	0.09310	N	1	P;B;B	0.35774	0.519;0.009;0.003	B;B;B	0.40940	0.344;0.002;0.002	T	0.66040	-0.6022	10	0.46703	T	0.11	-0.001	8.754	0.34635	0.0:0.2841:0.1106:0.6053	.	46;76;46	F5H563;P16452-2;P16452	.;.;EPB42_HUMAN	H	76;46;46;46	ENSP00000300215:R76H;ENSP00000444699:R46H;ENSP00000396616:R46H	ENSP00000300215:R76H	R	-	2	0	EPB42	41295817	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-0.989000	0.03736	-0.915000	0.03823	-0.140000	0.14226	CGC	C|0.999;T|0.001		0.597	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119		T	43508525	C	T	43508525	3	4	104	1	0	0	0	0	1	0	0	0	5171	768	27	1	1986	1	EPB42	15	43508525	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	3623258	43508525	59022867	96	9297											
TLN2	83660	ucsc.edu	37	chr15	63047869	63047869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagtcgccaacagcactGccaacctggtgaagaccatc	13	5	10	13	1	0	2	0	1	0	1	2	3	0	3	4	2	4	1	4	2	4	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:63047869G>A	ENST00000561311.1	+	36	4845	c.4615G>A	c.(4615-4617)Gcc>Acc	p.A1539T	TLN2_ENST00000306829.6_Missense_Mutation_p.A1539T|TLN2_ENST00000472902.1_5'Flank			Q9Y4G6	TLN2_HUMAN	talin 2	1539					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CAACAGCACTGCCAACCTGGT	0.557																																					p.A1539T													.	TLN2-573	0			c.G4615A						.						99	80	86					15																	63047869		2203	4300	6503	SO:0001583	missense	83660	exon34			AGCACTGCCAACC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.4615G>A	15.37:g.63047869G>A	ENSP00000453508:p.Ala1539Thr	Somatic	66	0		WXS	Illumina HiSeq		37	4	NM_015059	0	0	33	33	0	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	37	6.228070	0.97394	.	.	ENSG00000171914	ENST00000306829	T	0.32023	1.47	6.1	6.1	0.99115	.	0.000000	0.85682	D	0.000000	T	0.58177	0.2104	M	0.75447	2.3	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.46162	-0.9211	10	0.29301	T	0.29	-19.2713	20.7146	0.99709	0.0:0.0:1.0:0.0	.	1539	Q9Y4G6	TLN2_HUMAN	T	1539	ENSP00000303476:A1539T	ENSP00000303476:A1539T	A	+	1	0	TLN2	60835161	1.000000	0.71417	0.979000	0.43373	0.989000	0.77384	9.646000	0.98474	2.902000	0.99343	0.650000	0.86243	GCC	.		0.557	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63047869	G	A	63047869	3	1	104	1	0	0	0	0	1	0	0	0	15980	1319	46	2	4749	2	TLN2	15	63047869	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	19539344	63047869	39483523	97	9298											
HMG20A	10363	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	77756662	77756662	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgtggaggatctctctcAaggtcagttgcttcagagtg	8	14	12	7	0	4	1	3	0	2	1	6	3	4	3	0	3	1	2	0	3	1	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:77756662A>G	ENST00000381714.3	+	4	598	c.170A>G	c.(169-171)cAa>cGa	p.Q57R	HMG20A_ENST00000336216.4_Missense_Mutation_p.Q57R	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	57					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						GATCTCTCTCAAGGTCAGTTG	0.448																																					p.Q57R		.											.	HMG20A-228	0			c.A170G						.						130	110	117					15																	77756662		2196	4294	6490	SO:0001583	missense	10363	exon4			TCTCTCAAGGTCA	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.170A>G	15.37:g.77756662A>G	ENSP00000371133:p.Gln57Arg	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	93	38	NM_018200	0	0	19	32	13	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	37	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.099511	0.56183	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.69926	-0.44;-0.44	5.71	4.59	0.56863	.	0.387563	0.28431	N	0.015378	T	0.67211	0.2869	L	0.27053	0.805	0.36537	D	0.871089	P;B	0.39094	0.659;0.003	P;B	0.55391	0.775;0.007	T	0.72184	-0.4367	10	0.52906	T	0.07	-14.0293	9.4942	0.38978	0.9188:0.0:0.0812:0.0	.	57;57	Q9NP66;Q9NP66-2	HM20A_HUMAN;.	R	57	ENSP00000336856:Q57R;ENSP00000371133:Q57R	ENSP00000336856:Q57R	Q	+	2	0	HMG20A	75543717	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.285000	0.51716	0.993000	0.38866	0.533000	0.62120	CAA	.		0.448	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		G	77756662	A	G	77756662	3	3	104	1	0	0	0	0	1	0	0	0	7242	130	5	3	176	3	HMG20A	15	77756662	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	14708793	77756662	24774730	98	9299											
TSC2	7249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2130345	2130345	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgtgcccctgctgacccagGgctgggcggagatcctggtc	5	8	15	13	1	0	2	0	1	0	1	2	3	1	2	4	4	2	2	4	4	0	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr16:2130345G>A	ENST00000219476.3	+	30	4207	c.3577G>A	c.(3577-3579)Ggc>Agc	p.G1193S	TSC2_ENST00000401874.2_Missense_Mutation_p.G1149S|TSC2_ENST00000439673.2_Missense_Mutation_p.G1113S|TSC2_ENST00000568454.1_Missense_Mutation_p.G1160S|TSC2_ENST00000350773.4_Missense_Mutation_p.G1193S|TSC2_ENST00000382538.6_Missense_Mutation_p.G1101S|TSC2_ENST00000353929.4_Missense_Mutation_p.G1150S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1193					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GCTGACCCAGGGCTGGGCGGA	0.662			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.G1193S		.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2-1908	0			c.G3577A						.						41	46	45					16																	2130345		2198	4296	6494	SO:0001583	missense	7249	exon30	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACCCAGGGCTGGG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.3577G>A	16.37:g.2130345G>A	ENSP00000219476:p.Gly1193Ser	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	98	25	NM_001114382	0	0	55	82	27	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	34	5.377719	0.95945	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.94046	-3.28;-3.29;-3.34;-3.34;-3.24	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.96005	0.8699	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.997;0.968;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.99;0.91;1.0;0.999;0.994	D	0.95223	0.8335	10	0.34782	T	0.22	-36.9837	17.7425	0.88411	0.0:0.0:1.0:0.0	.	1101;1113;1193;1149;1149;1193	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	S	1193;1150;1150;1113;1101;1193	ENSP00000219476:G1193S;ENSP00000248099:G1150S;ENSP00000399232:G1113S;ENSP00000371978:G1101S;ENSP00000344383:G1193S	ENSP00000219476:G1193S	G	+	1	0	TSC2	2070346	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.929000	0.92859	2.196000	0.70406	0.561000	0.74099	GGC	.		0.662	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2130345	G	A	2130345	3	1	104	1	0	0	0	0	1	0	0	0	16639	1232	43	2	3691	2	TSC2	16	2130345	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		2130345	88224408	99	9300											
NLRC3	197358	ucsc.edu	37	chr16	3613310	3613310	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctcagccacctgggtcCggtaggcctggtgctcgcct	4	8	15	14	2	1	0	1	0	0	0	3	1	2	1	5	5	3	3	5	5	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr16:3613310C>T	ENST00000301749.7	-	0	2033				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CACCTGGGTCCGGTAGGCCTG	0.677																																					p.R543Q													.	NLRC3-96	0			c.G1628A						.						8	10	10					16																	3613310		2069	4167	6236			197358	exon5			TGGGTCCGGTAGG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613310C>T		Somatic	25	0		WXS	Illumina HiSeq		24	4	NM_178844	0	0	0	0	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	12.31	1.900126	0.33535	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	5.2	2.21	0.28008	.	0.271357	0.35096	N	0.003452	T	0.67571	0.2907	.	.	.	0.20074	N	0.999931	B	0.28584	0.216	B	0.16722	0.016	T	0.51671	-0.8676	9	0.23891	T	0.37	.	8.8536	0.35214	0.0:0.763:0.0:0.237	.	590	C9JLH9	.	Q	543;543;543;590;525	ENSP00000301749:R543Q;ENSP00000352039:R543Q;ENSP00000414415:R590Q;ENSP00000323897:R525Q	ENSP00000301749:R543Q	R	-	2	0	NLRC3	3553311	0.997000	0.39634	0.404000	0.26397	0.633000	0.38033	3.553000	0.53713	0.220000	0.20860	0.655000	0.94253	CGG	.		0.677	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3613310	C	T	3613310	1	4	104	0	1	0	0	0	0	0	0	0	10494	652	23	1		1	NLRC3	16	3613310	RNA	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	1482965	3613310	86741443	100	9301											
LOC81691	81691	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20851091	20851091	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacaggttcttgagcaggcCagagtggaaatccccctgtt	9	10	11	11	0	1	2	0	1	1	1	2	3	2	3	3	3	2	3	3	3	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr16:20851091C>T	ENST00000261377.6	+	14	1607	c.1398C>T	c.(1396-1398)gcC>gcT	p.A466A	ERI2_ENST00000564349.1_Intron|AC004381.6_ENST00000348433.6_Silent_p.A466A|AC004381.6_ENST00000564274.1_Silent_p.A466A	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2																					TTGAGCAGGCCAGAGTGGAAA	0.448																																					p.A466A													.	LOC81691-92	0			c.C1398T						.						288	274	279					16																	20851091		2201	4300	6501	SO:0001819	synonymous_variant	0	exon14			GCAGGCCAGAGTG																												ENST00000261377.6:c.1398C>T	16.37:g.20851091C>T		Somatic	479	1		WXS	Illumina HiSeq	Phase_I	470	297	NM_030941	0	0	0	1	1		Silent	SNP	ENST00000261377.6	37	CCDS10591.1																																																																																			.		0.448	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			T	20851091	C	T	20851091	2	4	104	1	0	0	0	0	0	0	0	1	8915	581	21	2		2	LOC81691	16	20851091	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	17237781	20851091	69503662	101	9302											
DULLARD	23399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7149598	7149598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtaatatctcctcttaagaAtgcttctgctattgtccagt	9	17	6	9	0	3	1	0	0	3	1	5	1	4	1	2	0	2	3	2	0	5	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:7149598A>G	ENST00000573600.1	-	6	873	c.452T>C	c.(451-453)aTt>aCt	p.I151T	CTDNEP1_ENST00000318988.6_Missense_Mutation_p.I151T|CTDNEP1_ENST00000572043.1_Missense_Mutation_p.I18T|CTDNEP1_ENST00000574322.1_Missense_Mutation_p.I151T|CTD-2545G14.7_ENST00000570760.2_5'Flank			O95476	CNEP1_HUMAN	CTD nuclear envelope phosphatase 1	151	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				gamete generation (GO:0007276)|mesoderm development (GO:0007498)|nuclear envelope organization (GO:0006998)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein dephosphorylation (GO:0006470)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(9)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	15						CCTCTTAAGAATGCTTCTGCT	0.498																																					p.I151T		.											.	CTDNEP1-91	0			c.T452C						.						117	108	111					17																	7149598		2203	4300	6503	SO:0001583	missense	23399	exon5			TTAAGAATGCTTC	AJ011916	CCDS11093.1	17p13	2012-11-27	2010-10-27	2010-10-27	ENSG00000175826	ENSG00000175826		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	19085	protein-coding gene	gene with protein product	"C-terminal domain nuclear envelope phosphatase 1"	610684	"dullard homolog (Xenopus laevis)"	DULLARD		12083771, 17141153	Standard	NM_015343		Approved	HSA011916, NET56	uc002gfd.2	O95476	OTTHUMG00000102180	ENST00000573600.1:c.452T>C	17.37:g.7149598A>G	ENSP00000461749:p.Ile151Thr	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	154	42	NM_001143775	0	0	188	274	86	D3DTN7|Q96GQ9	Missense_Mutation	SNP	ENST00000573600.1	37	CCDS11093.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.663502	0.47572	.	.	ENSG00000175826	ENST00000318988	T	0.17691	2.26	4.92	4.92	0.64577	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.057069	0.64402	D	0.000001	T	0.27900	0.0687	M	0.78223	2.4	0.58432	D	0.999998	B	0.21309	0.054	B	0.34038	0.174	T	0.09079	-1.0691	10	0.59425	D	0.04	-8.3255	12.5573	0.56261	1.0:0.0:0.0:0.0	.	151	O95476	CNEP1_HUMAN	T	151	ENSP00000321732:I151T	ENSP00000321732:I151T	I	-	2	0	CTDNEP1	7090322	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.729000	0.84864	2.062000	0.61559	0.482000	0.46254	ATT	.		0.498	CTDNEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440215.1	NM_015343		G	7149598	A	G	7149598	3	3	104	1	0	0	0	0	1	0	0	0	4810	101	4	3	298	3	DULLARD	17	7149598	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08		7149598	74045612	102	9303											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	376	26		WXS	Illumina HiSeq		436	39	NM_145301	0	0	9	54	45	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		T	15457087	C	T	15457087	3	4	104	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	8307489	15457087	65738123	103	9304											
NCOR1	9611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	16089949	16089949	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctgttgctgcaaaagctgtGatgcctgactcacttcaaga	10	11	10	10	0	2	3	2	2	0	1	2	3	2	3	1	0	4	5	1	0	3	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:16089949G>C	ENST00000268712.3	-	3	418	c.161C>G	c.(160-162)tCa>tGa	p.S54*	NCOR1_ENST00000395848.1_Intron|NCOR1_ENST00000395851.1_Nonsense_Mutation_p.S54*	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	54	Interaction with ZBTB33 and HEXIM1.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CAAAAGCTGTGATGCCTGACT	0.403																																					p.S54X		.											.	NCOR1-229	0			c.C161G						.						91	81	84					17																	16089949		2203	4300	6503	SO:0001587	stop_gained	9611	exon2			AGCTGTGATGCCT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.161C>G	17.37:g.16089949G>C	ENSP00000268712:p.Ser54*	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	98	29	NM_001190440	0	0	54	104	50	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Nonsense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	38	6.755855	0.97813	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000458113;ENST00000411510;ENST00000436828;ENST00000430577	.	.	.	5.78	5.78	0.91487	.	0.177313	0.39407	N	0.001372	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-9.9916	19.0021	0.92838	0.0:0.0:1.0:0.0	.	.	.	.	X	54	.	ENSP00000268712:S54X	S	-	2	0	NCOR1	16030674	1.000000	0.71417	0.991000	0.47740	0.976000	0.68499	6.537000	0.73847	2.724000	0.93272	0.563000	0.77884	TCA	.		0.403	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	16089949	G	C	16089949	4	2	104	1	0	0	0	0	0	1	0	0	10261	1294	45	4	7337	4	NCOR1	17	16089949	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	632862	16089949	65105261	104	9305											
SRCIN1	80725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	36708962	36708962	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcaggccccagacccaccCttgagctctgtcagcgtctc	6	8	9	18	2	3	2	1	1	2	1	5	2	3	2	4	1	2	2	4	1	0	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:36708962C>G	ENST00000264659.7	-	12	2555	c.2331G>C	c.(2329-2331)aaG>aaC	p.K777N	SRCIN1_ENST00000578925.1_Splice_Site_p.K811N|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	649					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						CAGACCCACCCTTGAGCTCTG	0.632																																					p.K777N		.											.	.	0			c.G2331C						.						54	63	60					17																	36708962		2142	4265	6407	SO:0001630	splice_region_variant	80725	exon12			CCCACCCTTGAGC		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.2332+1G>C	17.37:g.36708962C>G		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	99	32	NM_025248	0	0	0	0	0	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	37	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.563310	0.65538	.	.	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.54071	0.59	4.73	3.75	0.43078	.	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	M	0.75085	2.285	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.999;0.999	T	0.68047	-0.5512	10	0.62326	D	0.03	-8.7012	6.4948	0.22136	0.0:0.7228:0.0:0.2772	.	83;649;649;777	Q9C0H9-4;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	N	777;558;631	ENSP00000264659:K777N	ENSP00000264659:K777N	K	-	3	2	SRCIN1	33962488	0.960000	0.32886	1.000000	0.80357	0.960000	0.62799	0.115000	0.15540	1.341000	0.45600	0.555000	0.69702	AAG	.		0.632	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	Missense_Mutation	G	36708962	C	G	36708962	5	3	104	1	0	0	0	0	0	0	1	0	15168	695	24	4	1252	4	SRCIN1	17	36708962	Splice_Site	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	20619013	36708962	44486248	105	9306											
CASC3	22794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38319005	38319005	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gggcgtcagcgaaagctatgGaaggatgagggtcgctggga	10	6	19	6	3	1	1	1	1	0	0	2	5	1	4	0	5	2	2	0	5	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:38319005G>A	ENST00000264645.7	+	6	862	c.636G>A	c.(634-636)tgG>tgA	p.W212*		NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3	212	Necessary for RNA-binding, interaction with MAGOH and localization in nucleus speckles.|Sufficient to form the EJC.				gene expression (GO:0010467)|intracellular mRNA localization (GO:0008298)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	16						GAAAGCTATGGAAGGATGAGG	0.493																																					p.W212X		.											.	CASC3-91	0			c.G636A						.						72	66	68					17																	38319005		2203	4300	6503	SO:0001587	stop_gained	22794	exon6			GCTATGGAAGGAT	X80199	CCDS11362.1	17q21.1	2012-09-20			ENSG00000108349	ENSG00000108349			17040	protein-coding gene	gene with protein product		606504				7490069, 18332872	Standard	NM_007359		Approved	MLN51, BTZ	uc002hue.3	O15234	OTTHUMG00000133323	ENST00000264645.7:c.636G>A	17.37:g.38319005G>A	ENSP00000264645:p.Trp212*	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	59	15	NM_007359	0	0	63	66	3	A8K8R0	Nonsense_Mutation	SNP	ENST00000264645.7	37	CCDS11362.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388249	0.82902	.	.	ENSG00000108349	ENST00000264645;ENST00000418132;ENST00000394114	.	.	.	4.63	4.63	0.57726	.	0.114993	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2823	17.6407	0.88135	0.0:0.0:1.0:0.0	.	.	.	.	X	212	.	ENSP00000264645:W212X	W	+	3	0	CASC3	35572531	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.390000	0.97246	2.565000	0.86533	0.561000	0.74099	TGG	.		0.493	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	NM_007359		A	38319005	G	A	38319005	4	1	104	1	0	0	0	0	0	1	0	0	2667	1183	41	2	658	2	CASC3	17	38319005	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	1610043	38319005	42876205	106	9307											
MPO	4353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	56348163	56348163	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagatgatccggggcaatgAgatctgggccagggcctgtc	8	7	16	10	1	1	3	0	2	1	2	3	4	2	3	3	4	0	2	3	4	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:56348163A>T	ENST00000225275.3	-	12	2268	c.2092T>A	c.(2092-2094)Tca>Aca	p.S698T	MPO_ENST00000340482.3_Missense_Mutation_p.S730T	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	698					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)	CGGGGCAATGAGATCTGGGCC	0.547																																					p.S698T		.											.	MPO-156	0			c.T2092A						.						233	180	198					17																	56348163		2203	4300	6503	SO:0001583	missense	4353	exon12			GCAATGAGATCTG		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.2092T>A	17.37:g.56348163A>T	ENSP00000225275:p.Ser698Thr	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	93	57	NM_000250	0	0	0	0	0	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.973327	0.53614	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.68624	-0.34;-0.34	5.76	3.3	0.37823	.	0.161988	0.56097	N	0.000025	T	0.56601	0.1996	L	0.33792	1.035	0.80722	D	1	B	0.19817	0.039	B	0.29524	0.103	T	0.55237	-0.8172	10	0.51188	T	0.08	-34.2797	11.513	0.50504	0.7489:0.0:0.0:0.2511	.	698	P05164	PERM_HUMAN	T	730;698	ENSP00000344419:S730T;ENSP00000225275:S698T	ENSP00000225275:S698T	S	-	1	0	MPO	53703162	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	2.270000	0.43355	0.973000	0.38340	0.533000	0.62120	TCA	.		0.547	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56348163	A	T	56348163	3	4	104	1	0	0	0	0	1	0	0	0	9757	304	11	5	149	5	MPO	17	56348163	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	18029158	56348163	24847047	107	9308											
INTS2	57508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	59981846	59981846	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagtgtagaaaaggccagtaGcatacaaaaggaaagtgaaa	21	5	11	4	0	0	2	0	1	0	1	0	3	0	3	1	2	2	3	1	2	10	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:59981846G>T	ENST00000444766.3	-	9	1381	c.1306C>A	c.(1306-1308)Cta>Ata	p.L436I	INTS2_ENST00000251334.6_Missense_Mutation_p.L428I	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	436					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AAGGCCAGTAGCATACAAAAG	0.403																																					p.L436I		.											.	INTS2-206	0			c.C1306A						.						74	75	75					17																	59981846		1918	4106	6024	SO:0001583	missense	57508	exon9			CCAGTAGCATACA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1306C>A	17.37:g.59981846G>T	ENSP00000414237:p.Leu436Ile	Somatic	37	1		WXS	Illumina HiSeq	Phase_I	28	19	NM_020748	0	0	6	9	3	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	37	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.932135	0.73442	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.57436	0.4	5.33	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.66396	0.2785	L	0.55213	1.73	0.58432	D	0.999999	D	0.67145	0.996	D	0.80764	0.994	T	0.65721	-0.6099	9	.	.	.	-7.6987	14.0683	0.64844	0.0728:0.0:0.9272:0.0	.	436	Q9H0H0	INT2_HUMAN	I	436;435	ENSP00000414237:L436I	.	L	-	1	2	INTS2	57336628	1.000000	0.71417	0.987000	0.45799	0.970000	0.65996	5.045000	0.64220	1.252000	0.44001	0.467000	0.42956	CTA	.		0.403	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		T	59981846	G	T	59981846	3	4	104	1	0	0	0	0	1	0	0	0	7799	962	34	4	2376	4	INTS2	17	59981846	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	3633683	59981846	21213364	108	9309											
PALM	5064	ucsc.edu;bcgsc.ca	37	chr19	731193	731193	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagtccgggccccagcccCgagtccagccaaggaggagc	8	2	13	18	2	0	0	0	0	0	0	2	3	2	2	8	3	3	0	8	3	1	0	rs568795902		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:731193C>G	ENST00000338448.5	+	5	414	c.368C>G	c.(367-369)cCg>cGg	p.P123R	PALM_ENST00000264560.7_Missense_Mutation_p.P123R|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	123					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		GCCCCAGCCCCGAGTCCAGCC	0.662																																					p.P123R													.	PALM-68	0			c.C368G						.						28	26	27					19																	731193		2190	4298	6488	SO:0001583	missense	5064	exon5			CAGCCCCGAGTCC	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.368C>G	19.37:g.731193C>G	ENSP00000341911:p.Pro123Arg	Somatic	44	0		WXS	Illumina HiSeq		18	5	NM_002579	0	0	39	57	18	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	37	CCDS32857.1	.	.	.	.	.	.	.	.	.	.	C	5.686	0.311082	0.10789	.	.	ENSG00000099864	ENST00000338448;ENST00000264560	T;T	0.30448	2.01;1.53	3.69	1.44	0.22558	.	0.868385	0.09712	U	0.765632	T	0.37892	0.1020	L	0.56769	1.78	0.09310	N	1	P;B;P	0.44946	0.782;0.451;0.846	P;B;P	0.49561	0.53;0.242;0.615	T	0.23048	-1.0199	10	0.66056	D	0.02	-1.9056	7.2275	0.26024	0.0:0.7786:0.0:0.2214	.	123;123;123	B7Z649;O75781-2;O75781	.;.;PALM_HUMAN	R	123	ENSP00000341911:P123R;ENSP00000264560:P123R	ENSP00000264560:P123R	P	+	2	0	PALM	682193	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.318000	0.08050	0.064000	0.16427	0.511000	0.50034	CCG	.		0.662	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579		G	731193	C	G	731193	3	3	104	1	0	0	0	0	1	0	0	0	11434	652	23	4	386	4	PALM	19	731193	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		731193	58397790	109	9310											
PIP5K1C	23396	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	3648675	3648675	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagcagcagccgctcccCgcggccgttcacagcgggga	6	4	15	16	5	1	0	1	0	0	0	2	1	2	1	4	3	5	5	4	3	0	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:3648675C>T	ENST00000335312.3	-	9	1247	c.1159G>A	c.(1159-1161)Ggg>Agg	p.G387R	PIP5K1C_ENST00000587482.1_5'Flank|PIP5K1C_ENST00000589578.1_Missense_Mutation_p.G387R|PIP5K1C_ENST00000539785.1_Missense_Mutation_p.G387R|PIP5K1C_ENST00000537021.1_Missense_Mutation_p.G387R	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	387	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		AGCCGCTCCCCGCGGCCGTTC	0.692																																					p.G387R	Esophageal Squamous(135;99 1744 12852 27186 39851)												.	PIP5K1C-267	0			c.G1159A						.						34	36	35					19																	3648675		2199	4291	6490	SO:0001583	missense	23396	exon9			GCTCCCCGCGGCC	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1159G>A	19.37:g.3648675C>T	ENSP00000335333:p.Gly387Arg	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	46	24	NM_001195733	0	0	22	41	19	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731850	0.69189	.	.	ENSG00000186111	ENST00000335312;ENST00000539785;ENST00000537021	T;T;T	0.30714	1.52;1.52;1.52	4.04	4.04	0.47022	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	M	0.85859	2.78	0.80722	D	1	D;D	0.76494	0.994;0.999	P;P	0.62491	0.674;0.903	T	0.67245	-0.5719	10	0.87932	D	0	-31.0387	15.1514	0.72703	0.0:1.0:0.0:0.0	.	387;387	O60331-3;O60331	.;PI51C_HUMAN	R	387	ENSP00000335333:G387R;ENSP00000445992:G387R;ENSP00000444779:G387R	ENSP00000335333:G387R	G	-	1	0	PIP5K1C	3599675	1.000000	0.71417	0.918000	0.36340	0.204000	0.24138	7.735000	0.84939	1.795000	0.52594	0.297000	0.19635	GGG	.		0.692	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398		T	3648675	C	T	3648675	3	4	104	1	0	0	0	0	1	0	0	0	11967	652	23	1	887	1	PIP5K1C	19	3648675	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	2917482	3648675	55480308	110	9311											
APBA3	9546	bcgsc.ca	37	chr19	3760228	3760228	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaagtccatggctggaggcCccgaaggggatcgggaaatt	10	6	15	10	2	0	0	0	0	0	0	2	4	1	3	4	6	0	1	4	6	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:3760228C>T	ENST00000316757.3	-	2	235	c.35G>A	c.(34-36)gGg>gAg	p.G12E	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	12					in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCTGGAGGCCCCGAAGGGGA	0.622																																					p.G12E													.	APBA3-90	0			c.G35A						.						20	24	23					19																	3760228		2178	4268	6446	SO:0001583	missense	9546	exon2			GGAGGCCCCGAAG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"X11-like 2"	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.35G>A	19.37:g.3760228C>T	ENSP00000315136:p.Gly12Glu	Somatic	68	0		WXS	Illumina HiSeq	Phase_1	22	8	NM_004886	0	0	12	23	11	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	.	.	.	.	.	.	.	.	.	.	C	7.609	0.674440	0.14841	.	.	ENSG00000011132	ENST00000316757	T	0.47528	0.84	4.73	1.04	0.20106	.	0.940149	0.08769	N	0.896650	T	0.29491	0.0735	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.21930	-1.0231	10	0.28530	T	0.3	.	3.0292	0.06101	0.0:0.4692:0.2333:0.2976	.	12	O96018	APBA3_HUMAN	E	12	ENSP00000315136:G12E	ENSP00000315136:G12E	G	-	2	0	APBA3	3711228	0.000000	0.05858	0.071000	0.20095	0.047000	0.14425	-0.370000	0.07523	0.414000	0.25790	0.561000	0.74099	GGG	.		0.622	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			T	3760228	C	T	3760228	3	4	104	1	0	0	0	0	1	0	0	0	758	623	22	2	1732	2	APBA3	19	3760228	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	111553	3760228	55368755	111	9312											
PSMD8	5714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38874011	38874011	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcatcgagtatgcccggcAgctggagatgatcgtctgag	8	9	15	9	3	2	3	1	2	1	1	4	5	2	3	1	3	2	3	1	3	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:38874011A>G	ENST00000215071.4	+	7	1100	c.1034A>G	c.(1033-1035)cAg>cGg	p.Q345R	GGN_ENST00000591809.1_5'Flank|PSMD8_ENST00000602911.1_Missense_Mutation_p.Q282R|AC005789.9_ENST00000585411.1_RNA	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	345					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TATGCCCGGCAGCTGGAGATG	0.557																																					p.Q345R		.											.	PSMD8-68	0			c.A1034G						.						49	41	43					19																	38874011		2203	4300	6503	SO:0001583	missense	5714	exon7			CCCGGCAGCTGGA	D38047	CCDS12515.2	19q13.2	2009-05-07			ENSG00000099341	ENSG00000099341		"Proteasome (prosome, macropain) subunits"	9566	protein-coding gene	gene with protein product						7621825	Standard	NM_002812		Approved	S14, Nin1p, p31, HIP6, HYPF, Rpn12	uc002oii.4	P48556	OTTHUMG00000150691	ENST00000215071.4:c.1034A>G	19.37:g.38874011A>G	ENSP00000215071:p.Gln345Arg	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	28	9	NM_002812	0	0	73	127	54	B4DX18|Q6P1L7	Missense_Mutation	SNP	ENST00000215071.4	37	CCDS12515.2	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459422	0.84317	.	.	ENSG00000099341	ENST00000215071	.	.	.	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.48660	0.1512	L	0.47190	1.495	0.80722	D	1	D	0.54207	0.965	P	0.45071	0.468	T	0.54234	-0.8324	9	0.62326	D	0.03	-19.6009	11.6721	0.51408	1.0:0.0:0.0:0.0	.	345	P48556	PSMD8_HUMAN	R	345	.	ENSP00000215071:Q345R	Q	+	2	0	PSMD8	43565851	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.193000	0.89719	1.919000	0.55581	0.448000	0.29417	CAG	.		0.557	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	NM_002812		G	38874011	A	G	38874011	3	3	104	1	0	0	0	0	1	0	0	0	12733	188	7	3	1060	3	PSMD8	19	38874011	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	35113783	38874011	20254972	112	9313											
ZNF180	7733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44981073	44981073	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acggtttctctccagtgtgaGttctttgatgtgcaacaagc	8	14	10	9	1	2	2	0	2	2	0	4	2	3	2	1	1	3	3	1	1	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:44981073G>C	ENST00000221327.4	-	5	1906	c.1625C>G	c.(1624-1626)aCt>aGt	p.T542S	ZNF180_ENST00000391956.4_Missense_Mutation_p.T517S|ZNF180_ENST00000592529.1_Missense_Mutation_p.T515S|ZNF180_ENST00000585514.1_5'Flank|AC069278.4_ENST00000591684.1_lincRNA	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	542					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TCCAGTGTGAGTTCTTTGATG	0.423																																					p.T542S	Esophageal Squamous(180;1353 2003 32862 46574 49854)	.											.	ZNF180-92	0			c.C1625G						.						77	77	77					19																	44981073		2203	4300	6503	SO:0001583	missense	7733	exon5			GTGTGAGTTCTTT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"Zinc fingers, C2H2-type", "-"	12970	protein-coding gene	gene with protein product		606740	"zinc finger protein 180 (HHZ168)"				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1625C>G	19.37:g.44981073G>C	ENSP00000221327:p.Thr542Ser	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	89	33	NM_013256	0	0	2	4	2	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808114	0.50421	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.00662	5.93;5.93	5.23	2.85	0.33270	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43416	D	0.000561	T	0.01029	0.0034	L	0.38692	1.165	0.80722	D	1	P;P;P	0.45428	0.828;0.858;0.858	B;P;P	0.47981	0.335;0.563;0.563	T	0.68884	-0.5291	10	0.62326	D	0.03	-11.2816	5.453	0.16574	0.1458:0.0:0.6595:0.1947	.	517;541;542	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	S	542;517	ENSP00000221327:T542S;ENSP00000375818:T517S	ENSP00000221327:T542S	T	-	2	0	ZNF180	49672913	0.000000	0.05858	1.000000	0.80357	0.982000	0.71751	0.203000	0.17315	2.437000	0.82529	0.467000	0.42956	ACT	.		0.423	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44981073	G	C	44981073	3	2	104	1	0	0	0	0	1	0	0	0	17780	1029	36	4	457	4	ZNF180	19	44981073	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	6107062	44981073	14147910	113	9314											
RSPH6A	81492	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46317979	46317979	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagagaactggtctgtctgGtagaggttgaactggcccaa	10	10	13	8	0	3	3	1	1	2	2	3	4	3	3	1	4	2	2	1	4	4	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:46317979G>A	ENST00000221538.3	-	1	598	c.456C>T	c.(454-456)taC>taT	p.Y152Y	RSPH6A_ENST00000597055.1_Silent_p.Y152Y|SYMPK_ENST00000598155.1_5'Flank	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	152						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GGTCTGTCTGGTAGAGGTTGA	0.602																																					p.Y152Y													.	RSPH6A-91	0			c.C456T						.						52	55	54					19																	46317979		2203	4300	6503	SO:0001819	synonymous_variant	81492	exon1			TGTCTGGTAGAGG	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.456C>T	19.37:g.46317979G>A		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	50	12	NM_030785	0	0	0	0	0	Q53FE2|Q6PEZ9	Silent	SNP	ENST00000221538.3	37	CCDS12675.1																																																																																			.		0.602	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			A	46317979	G	A	46317979	2	1	104	1	0	0	0	0	0	0	0	1	13739	1256	44	2		2	RSPH6A	19	46317979	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	1336906	46317979	12811004	114	9315											
LILRA3	11026	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54803120	54803120	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acctgcgacttgggctcacgGggcccacggagaagatggcc	8	5	15	13	3	1	2	1	0	0	2	1	4	1	2	3	5	1	1	3	5	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:54803120G>T	ENST00000251390.3	-	4	648	c.557C>A	c.(556-558)cCc>cAc	p.P186H	LILRA3_ENST00000391745.1_Missense_Mutation_p.P203H|LILRA3_ENST00000391744.3_Intron	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	186	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGGCTCACGGGGCCCACGGA	0.587																																					p.P186H		.											.	LILRA3-91	0			c.C557A						.						134	113	120					19																	54803120		2195	4162	6357	SO:0001583	missense	11026	exon4			CTCACGGGGCCCA	U91926		19q13.4	2013-01-11						"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.557C>A	19.37:g.54803120G>T	ENSP00000251390:p.Pro186His	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	98	44	NM_006865	0	0	0	0	0	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.877305	0.33162	.	.	ENSG00000170866	ENST00000251390;ENST00000391745	T;T	0.03124	4.04;4.04	2.21	1.09	0.20402	Immunoglobulin-like fold (1);	0.593476	0.14797	N	0.297850	T	0.16214	0.0390	M	0.87269	2.87	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.03534	-1.1027	10	0.87932	D	0	.	5.2465	0.15500	0.1757:0.0:0.8243:0.0	.	186	Q8N6C8	LIRA3_HUMAN	H	186;203	ENSP00000251390:P186H;ENSP00000375625:P203H	ENSP00000251390:P186H	P	-	2	0	LILRA3	59494932	0.002000	0.14202	0.008000	0.14137	0.032000	0.12392	0.663000	0.25053	0.493000	0.27837	0.586000	0.80456	CCC	.		0.587	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			T	54803120	G	T	54803120	3	4	104	1	0	0	0	0	1	0	0	0	8808	1232	43	4	778	4	LILRA3	19	54803120	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	8485141	54803120	4325863	115	9316											
LENG8	114823	broad.mit.edu;bcgsc.ca	37	chr19	54963430	54963444	+	Splice_Site	DEL	GTGGCCAGTGCACAG	GTGGCCAGTGCACAG	-																															agtccagcagcaatgggcctGtggccagtgcacaggtgaga																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	GTGGCCAGTGCACAG	GTGGCCAGTGCACAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:54963430_54963444delGTGGCCAGTGCACAG	ENST00000326764.5	+	3	678_692	c.199_213delGTGGCCAGTGCACAG	c.(199-213)gtggccagtgcacagdel	p.VASAQ67del	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	0										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CAATGGGCCTGTGGCCAGTGCACAGGTGAGAAGGC	0.642																																					p.67_71del													.	LENG8-91	0			c.199_213del						.																																			SO:0001630	splice_region_variant	114823	exon3			GGGCCTGTGGCCA	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.213+1GTGGCCAGTGCACAG>-	19.37:g.54963430_54963444delGTGGCCAGTGCACAG		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	27	8	NM_052925	0	0	0	0	0	B0VJY9|Q8IZ27|Q8NCX6	In_Frame_Del	DEL	ENST00000326764.5	37	CCDS12894.1																																																																																			.		0.642	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	In_Frame_Del	-	54963444	GTGGCCAGTGCACAG	-	54963430	8	5	104	1	0	1	0	1	0	0	1	0	8745	1377	48	0	205	0	LENG8	19	54963430	Splice_Site	DEL	GTGGCCAGTGCACAG	TCGA-DZ-6133-01A-11D-1961-08	160310	54963430	4165553	116	9317											
SAPS1	22870	ucsc.edu	37	chr19	55752390	55752390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagctcagcatggtgctcaCgcatccctctacttgggcat	8	10	9	14	1	3	0	2	0	1	0	4	0	4	0	1	2	4	5	1	2	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:55752390C>G	ENST00000412770.2	-	10	1785	c.1219G>C	c.(1219-1221)Gtg>Ctg	p.V407L	PPP6R1_ENST00000587283.1_Missense_Mutation_p.V407L	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	407					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						ATGGTGCTCACGCATCCCTCT	0.567																																					p.V407L													.	PPP6R1-67	0			c.G1219C						.						53	57	55					19																	55752390		2067	4220	6287	SO:0001583	missense	22870	exon10			TGCTCACGCATCC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1219G>C	19.37:g.55752390C>G	ENSP00000414202:p.Val407Leu	Somatic	13	0		WXS	Illumina HiSeq		4	1	NM_014931	0	0	38	86	48	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	C	9.148	1.015480	0.19355	.	.	ENSG00000105063	ENST00000412770	T	0.55588	0.51	4.98	1.46	0.22682	.	0.132441	0.33753	N	0.004597	T	0.41190	0.1148	L	0.59436	1.845	0.24137	N	0.995745	B	0.06786	0.001	B	0.14578	0.011	T	0.21348	-1.0248	10	0.30854	T	0.27	-24.2599	4.5722	0.12216	0.0:0.4726:0.2548:0.2726	.	407	Q9UPN7	PP6R1_HUMAN	L	407	ENSP00000414202:V407L	ENSP00000414202:V407L	V	-	1	0	PPP6R1	60444202	0.003000	0.15002	0.812000	0.32479	0.168000	0.22595	0.237000	0.17985	0.631000	0.30412	0.462000	0.41574	GTG	.		0.567	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		G	55752390	C	G	55752390	3	3	104	1	0	0	0	0	1	0	0	0	13868	536	19	4	1486	4	SAPS1	19	55752390	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	788960	55752390	3376593	117	9318											
ZNF324B	388569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58966903	58966903	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcctgagcggcagaagccaTgtgcacaggaggtccctggg	8	5	16	12	2	0	2	0	1	0	1	1	3	1	3	3	4	3	2	3	4	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:58966903T>A	ENST00000336614.4	+	4	699	c.592T>A	c.(592-594)Tgt>Agt	p.C198S	ZNF324B_ENST00000545523.1_Missense_Mutation_p.C198S|ZNF324B_ENST00000391696.1_Missense_Mutation_p.C188S	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	198					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GCAGAAGCCATGTGCACAGGA	0.672																																					p.C198S		.											.	ZNF324B-91	0			c.T592A						.						36	40	39					19																	58966903		2203	4300	6503	SO:0001583	missense	388569	exon4			AAGCCATGTGCAC	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.592T>A	19.37:g.58966903T>A	ENSP00000337473:p.Cys198Ser	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	44	17	NM_207395	0	0	3	3	0	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	37	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.756192	0.31137	.	.	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.06294	3.49;3.49;3.32	2.7	-1.7	0.08159	.	3.208830	0.01016	N	0.003905	T	0.05364	0.0142	L	0.27053	0.805	0.09310	N	1	B;B	0.23185	0.081;0.003	B;B	0.16289	0.015;0.002	T	0.39078	-0.9631	10	0.62326	D	0.03	.	4.2594	0.10733	0.0:0.2411:0.2439:0.5151	.	198;188	Q6AW86;C9JTQ8	Z324B_HUMAN;.	S	198;198;188	ENSP00000337473:C198S;ENSP00000438930:C198S;ENSP00000375578:C188S	ENSP00000337473:C198S	C	+	1	0	ZNF324B	63658715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.422000	0.02453	-0.415000	0.07484	0.402000	0.26972	TGT	.		0.672	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		A	58966903	T	A	58966903	3	1	104	1	0	0	0	0	1	0	0	0	17877	1464	51	5	602	5	ZNF324B	19	58966903	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	3214513	58966903	162080	118	9319											
MMP24	10893	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33851638	33851638	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgagctgggccacgcgCtgggactggagcactccagc	7	6	15	13	2	0	1	0	1	0	0	1	3	1	3	2	3	4	4	2	3	0	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr20:33851638C>A	ENST00000246186.6	+	5	947	c.862C>A	c.(862-864)Ctg>Atg	p.L288M	EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000453892.1_RNA|MMP24-AS1_ENST00000433764.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	288					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	GGGCCACGCGCTGGGACTGGA	0.627																																					p.L288M													.	.	0			c.C862A						.						27	28	27					20																	33851638		2203	4300	6503	SO:0001583	missense	10893	exon5			CACGCGCTGGGAC	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"membrane-type 5 matrix metalloproteinase"	604871	"matrix metalloproteinase 24 (membrane-inserted)"			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.862C>A	20.37:g.33851638C>A	ENSP00000246186:p.Leu288Met	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	12	7	NM_006690	0	0	25	84	59	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	37	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.583351	0.65992	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.55588	0.51	5.05	4.03	0.46877	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.79305	0.4423	H	0.97365	3.99	0.51482	D	0.999929	D	0.76494	0.999	D	0.76071	0.987	D	0.83575	0.0114	10	0.87932	D	0	.	9.0992	0.36658	0.0:0.8266:0.0:0.1734	.	288	Q9Y5R2	MMP24_HUMAN	M	288;236	ENSP00000246186:L288M	ENSP00000246186:L288M	L	+	1	2	MMP24	33315054	0.934000	0.31675	0.984000	0.44739	0.932000	0.56968	1.902000	0.39848	2.606000	0.88127	0.655000	0.94253	CTG	.		0.627	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		A	33851638	C	A	33851638	3	1	104	1	0	0	0	0	1	0	0	0	9686	796	28	4	630	4	MMP24	20	33851638	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		33851638	29173882	119	9320											
EPB41L1	2036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34800245	34800245	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctggccattagaaagaagAttgagccggaggccgtactg	11	8	14	8	2	1	4	0	1	1	3	1	5	1	5	3	3	2	1	3	3	4	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr20:34800245A>G	ENST00000338074.2	+	16	2292	c.2131A>G	c.(2131-2133)Att>Gtt	p.I711V	EPB41L1_ENST00000202028.5_Missense_Mutation_p.I637V|EPB41L1_ENST00000373946.3_Missense_Mutation_p.I531V|EPB41L1_ENST00000373950.2_Missense_Mutation_p.I602V|EPB41L1_ENST00000373941.1_Missense_Mutation_p.I711V|EPB41L1_ENST00000479336.1_3'UTR|EPB41L1_ENST00000441639.1_Missense_Mutation_p.I637V	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	711					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					TAGAAAGAAGATTGAGCCGGA	0.493																																					p.I711V		.											.	EPB41L1-93	0			c.A2131G						.						88	79	82					20																	34800245		2203	4300	6503	SO:0001583	missense	2036	exon17			AAGAAGATTGAGC	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.2131A>G	20.37:g.34800245A>G	ENSP00000337168:p.Ile711Val	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	95	33	NM_001258329	0	0	182	286	104	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	37	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.050564	0.55218	.	.	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000338074;ENST00000373941;ENST00000454226	D;D;D;D;D;D	0.83755	-1.76;-1.59;-1.76;-1.66;-1.66;-1.62	5.78	4.61	0.57282	.	.	.	.	.	T	0.71099	0.3300	N	0.24115	0.695	0.23391	N	0.997771	B;B;B;B;B;B	0.22983	0.078;0.01;0.047;0.004;0.007;0.0	B;B;B;B;B;B	0.21917	0.018;0.004;0.037;0.004;0.002;0.001	T	0.56786	-0.7921	9	0.24483	T	0.36	.	9.5214	0.39138	0.8228:0.1772:0.0:0.0	.	711;711;531;602;602;637	B7Z653;Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;E41L1_HUMAN;.;.;.;.	V	637;602;711;602;637;531;711;711;72	ENSP00000202028:I637V;ENSP00000363061:I602V;ENSP00000399214:I637V;ENSP00000363057:I531V;ENSP00000337168:I711V;ENSP00000363052:I711V	ENSP00000202028:I637V	I	+	1	0	EPB41L1	34263659	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.624000	0.37018	2.333000	0.79357	0.533000	0.62120	ATT	.		0.493	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		G	34800245	A	G	34800245	3	3	104	1	0	0	0	0	1	0	0	0	5165	333	12	3	2189	3	EPB41L1	20	34800245	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	948607	34800245	28225275	120	9321											
NPEPL1	79716	hgsc.bcm.edu;broad.mit.edu	37	chr20	57276200	57276200	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctatgacactggaggcctcAgcatcaaagggaaggtgagg	12	7	14	8	0	3	2	2	2	1	0	3	4	3	4	1	5	1	1	1	5	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr20:57276200A>G	ENST00000356091.6	+	6	1096	c.808A>G	c.(808-810)Agc>Ggc	p.S270G	NPEPL1_ENST00000525817.1_Missense_Mutation_p.S222G|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.S242G	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	270						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TGGAGGCCTCAGCATCAAAGG	0.687																																					p.S270G		.											.	.	0			c.A808G						.						24	24	24					20																	57276200		2040	4191	6231	SO:0001583	missense	79716	exon6			GGCCTCAGCATCA	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.808A>G	20.37:g.57276200A>G	ENSP00000348395:p.Ser270Gly	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_024663	0	0	0	0	0	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241327	0.79912	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.52295	0.67;0.67;0.67	5.01	5.01	0.66863	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78413	0.4279	H	0.97265	3.97	0.58432	D	0.999999	D;D;D;D	0.76494	0.986;0.982;0.999;0.992	D;D;D;D	0.77557	0.951;0.918;0.99;0.966	D	0.85396	0.1128	10	0.72032	D	0.01	-41.2309	12.4648	0.55751	1.0:0.0:0.0:0.0	.	270;222;242;270	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	G	242;222;270	ENSP00000434810:S242G;ENSP00000437112:S222G;ENSP00000348395:S270G	ENSP00000348395:S270G	S	+	1	0	NPEPL1	56709607	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.869000	0.92326	1.875000	0.54330	0.477000	0.44152	AGC	.		0.687	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		G	57276200	A	G	57276200	3	3	104	1	0	0	0	0	1	0	0	0	10600	188	7	3	676	3	NPEPL1	20	57276200	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	22475955	57276200	5749320	121	9322											
SETD4	54093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	37410517	37410517	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgggctatgtccaaacttgtCttctcattcgtatctgaaat	9	16	7	9	1	3	1	1	1	3	0	6	1	4	1	1	1	1	2	1	1	4	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr21:37410517C>G	ENST00000399215.1	-	9	2491	c.1119G>C	c.(1117-1119)aaG>aaC	p.K373N	AP000688.1_ENST00000600312.1_Intron|SETD4_ENST00000332131.4_Missense_Mutation_p.K373N|SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000399212.1_Missense_Mutation_p.K349N			Q9NVD3	SETD4_HUMAN	SET domain containing 4	373				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						CCAAACTTGTCTTCTCATTCG	0.353																																					p.K373N		.											.	SETD4-154	0			c.G1119C						.						179	173	175					21																	37410517		2202	4300	6502	SO:0001583	missense	54093	exon10			ACTTGTCTTCTCA	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.1119G>C	21.37:g.37410517C>G	ENSP00000382163:p.Lys373Asn	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	133	62	NM_017438	0	0	7	9	2	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278952	0.59758	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131	T;T;T	0.18174	2.23;2.23;2.23	5.79	3.99	0.46301	Rubisco LS methyltransferase, substrate-binding domain (1);	0.633406	0.17880	N	0.158893	T	0.19046	0.0457	L	0.57536	1.79	0.80722	D	1	P;P	0.39920	0.646;0.695	B;B	0.40134	0.214;0.32	T	0.02307	-1.1179	10	0.18276	T	0.48	-14.3562	12.2959	0.54847	0.0:0.8635:0.0:0.1365	.	349;373	Q9NVD3-3;Q9NVD3	.;SETD4_HUMAN	N	373;349;373	ENSP00000382163:K373N;ENSP00000382161:K349N;ENSP00000329189:K373N	ENSP00000329189:K373N	K	-	3	2	SETD4	36332387	0.996000	0.38824	0.885000	0.34714	0.989000	0.77384	2.608000	0.46308	0.799000	0.34018	0.561000	0.74099	AAG	.		0.353	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		G	37410517	C	G	37410517	3	3	104	1	0	0	0	0	1	0	0	0	14165	912	32	4	211	4	SETD4	21	37410517	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		37410517	10719378	122	9323											
CERK	64781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	47108141	47108141	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatatccgcttgccttgtccTtttcctccaaacgggttgat	6	16	7	12	2	0	1	0	1	0	0	4	1	4	1	5	1	2	2	5	1	3	7			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr22:47108141T>G	ENST00000216264.8	-	4	541	c.429A>C	c.(427-429)aaA>aaC	p.K143N	CERK_ENST00000541677.1_5'UTR	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase	143	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lipid phosphorylation (GO:0046834)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)			cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TGCCTTGTCCTTTTCCTCCAA	0.388																																					p.K143N		.											.	CERK-251	0			c.A429C						.						241	179	200					22																	47108141		2203	4300	6503	SO:0001583	missense	64781	exon4			TTGTCCTTTTCCT	AB079066	CCDS14077.1	22q13.31	2008-06-10			ENSG00000100422	ENSG00000100422			19256	protein-coding gene	gene with protein product		610307				11956206, 11258795	Standard	NM_022766		Approved	hCERK, FLJ23239, dA59H18.3, DKFZp434E0211, FLJ21430, KIAA1646, LK4, dA59H18.2	uc003bia.3	Q8TCT0	OTTHUMG00000150395	ENST00000216264.8:c.429A>C	22.37:g.47108141T>G	ENSP00000216264:p.Lys143Asn	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	66	26	NM_022766	0	0	15	30	15	A0JNT4|A8K611|Q6NX59|Q9BYB3|Q9UGE5	Missense_Mutation	SNP	ENST00000216264.8	37	CCDS14077.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.686429	0.47991	.	.	ENSG00000100422	ENST00000216264	T	0.15487	2.42	5.2	-1.83	0.07833	Diacylglycerol kinase, catalytic domain (3);	0.109682	0.64402	D	0.000007	T	0.43366	0.1244	M	0.89785	3.06	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.49409	-0.8943	10	0.72032	D	0.01	-14.0309	12.0935	0.53742	0.0:0.6281:0.0:0.3719	.	143	Q8TCT0	CERK1_HUMAN	N	143	ENSP00000216264:K143N	ENSP00000216264:K143N	K	-	3	2	CERK	45486805	0.957000	0.32711	0.303000	0.25071	0.328000	0.28507	1.095000	0.30964	-0.493000	0.06678	0.460000	0.39030	AAA	.		0.388	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	NM_022766		G	47108141	T	G	47108141	3	3	104	1	0	0	0	0	1	0	0	0	3273	1606	56	5	1224	5	CERK	22	47108141	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		47108141	4196425	123	9324											
BMP15	9210	broad.mit.edu	37	chrX	50654047	50654047	+	Frame_Shift_Del	DEL	C	C	-																															gggcaccctagagagaaccgCaccattggggccaccatggt																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chrX:50654047delC	ENST00000252677.3	+	1	264	c.264delC	c.(262-264)cgcfs	p.R88fs		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	88					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					GAGAGAACCGCACCATTGGGG	0.592																																					p.R88fs													.	BMP15-132	0			c.264delC						.						23	14	17					X																	50654047		2199	4292	6491	SO:0001589	frameshift_variant	9210	exon1			GAACCGCACCATT	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"Bone morphogenetic proteins"	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.264delC	X.37:g.50654047delC	ENSP00000252677:p.Arg88fs	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_005448	0	0	0	0	0	Q17RM6|Q5JST1|Q9UMS1	Frame_Shift_Del	DEL	ENST00000252677.3	37	CCDS14334.1																																																																																			.		0.592	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		-	50654047	C	-	50654047	7	5	104	1	0	1	0	1	0	0	0	0	1459	697	25	0	266	0	BMP15	23	50654047	Frame_Shift_Del	DEL	C	TCGA-DZ-6133-01A-11D-1961-08		50654047	104616513	124	9325											
FAM123B	139285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	63411696	63411696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggggtagacaatccctgcGgacaagccccagggcctcac	9	5	12	15	2	1	1	1	0	0	1	3	2	2	2	4	4	2	1	4	4	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chrX:63411696G>A	ENST00000330258.3	-	2	1743	c.1471C>T	c.(1471-1473)Cgc>Tgc	p.R491C	AMER1_ENST00000403336.1_Missense_Mutation_p.R491C|AMER1_ENST00000374869.3_Missense_Mutation_p.R491C	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	491					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CAATCCCTGCGGACAAGCCCC	0.522																																					p.R491C		.											.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.C1471T						.						61	50	54					X																	63411696		2203	4300	6503	SO:0001583	missense	139285	exon2			CCCTGCGGACAAG	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"-"	26837	protein-coding gene	gene with protein product	"Wilms Tumor on the X", "adenomatous polyposis coli membrane recruitment 1"	300647	"family with sequence similarity 123B"	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1471C>T	X.37:g.63411696G>A	ENSP00000329117:p.Arg491Cys	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	25	21	NM_152424	0	0	0	5	5	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	7.831	0.719945	0.15372	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.19532	2.14;2.14;2.14	5.21	3.3	0.37823	.	1.072280	0.07227	N	0.861857	T	0.17704	0.0425	N	0.24115	0.695	0.09310	N	1	P	0.45531	0.86	B	0.40329	0.326	T	0.25984	-1.0116	10	0.72032	D	0.01	0.0109	11.6933	0.51529	0.0:0.0:0.6193:0.3806	.	491	Q5JTC6	F123B_HUMAN	C	491	ENSP00000364003:R491C;ENSP00000329117:R491C;ENSP00000384722:R491C	ENSP00000329117:R491C	R	-	1	0	FAM123B	63328421	0.008000	0.16893	0.004000	0.12327	0.604000	0.37047	1.430000	0.34914	1.289000	0.44618	0.600000	0.82982	CGC	.		0.522	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411696	G	A	63411696	3	1	104	1	0	0	0	0	1	0	0	0	5439	1116	39	1	1940	1	FAM123B	23	63411696	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	12757649	63411696	91858864	125	9326											
SKI	6497	hgsc.bcm.edu	37	chr1	2160390	2160390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgcggccgcggtgccggCgccggtgcccgcagccaccg	2	2	19	18	9	0	0	0	0	0	0	0	0	0	0	6	5	3	1	6	5	0	0	rs28384811	byFrequency	TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:2160390C>G	ENST00000378536.4	+	1	257	c.185C>G	c.(184-186)gCg>gGg	p.A62G		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	62					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		gcggtgccggcgccggTGCCC	0.776													C|||	229	0.0457268	0.0234	0.0576	5008	,	,		4535	0.0079		0.0706	False		,,,				2504	0.0808				p.A62G	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.C185G						.						1	1	1					1																	2160390		788	1840	2628	SO:0001583	missense	6497	exon1			TGCCGGCGCCGGT	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.185C>G	1.37:g.2160390C>G	ENSP00000367797:p.Ala62Gly	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	7	3	NM_003036	0	0	0	0	0	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	37	CCDS39.1	102	0.046703296703296704	20	0.04065040650406504	28	0.07734806629834254	3	0.005244755244755245	51	0.06728232189973615	C	9.688	1.151208	0.21371	.	.	ENSG00000157933	ENST00000378536	D	0.95821	-3.82	2.3	2.3	0.28687	.	.	.	.	.	T	0.47857	0.1468	N	0.08118	0	0.45733	P	0.001363000000000003	D	0.57899	0.981	P	0.58520	0.84	T	0.76271	-0.3020	8	0.20519	T	0.43	-11.9718	7.7374	0.28823	0.0:1.0:0.0:0.0	rs28384811	62	P12755	SKI_HUMAN	G	62	ENSP00000367797:A62G	ENSP00000367797:A62G	A	+	2	0	SKI	2150250	0.994000	0.37717	0.998000	0.56505	0.971000	0.66376	0.878000	0.28126	1.104000	0.41587	0.185000	0.17295	GCG	C|0.953;G|0.047		0.776	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		G	2160390	C	G	2160390	3	3	105	1	0	0	0	0	1	0	0	0	14389	768	27	4	187	4	SKI	1	2160390	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08		2160390	247090231	1	9327											
CLSTN1	22883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	9795602	9795602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcaggtacgagatgtgctgCatggccttatccaattcccc	8	12	9	12	1	1	1	1	0	0	1	3	2	3	1	4	2	3	3	4	2	3	4	rs190578331	byFrequency	TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:9795602C>T	ENST00000377298.4	-	13	2598	c.1806G>A	c.(1804-1806)atG>atA	p.M602I	CLSTN1_ENST00000477264.1_5'Flank|CLSTN1_ENST00000377288.3_Missense_Mutation_p.M583I|CLSTN1_ENST00000361311.4_Missense_Mutation_p.M592I	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	602					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		AGATGTGCTGCATGGCCTTAT	0.527													C|||	2	0.000399361	0	0	5008	,	,		17391	0.002		0	False		,,,				2504	0				p.M602I		.											.	CLSTN1-523	0			c.G1806A						.						169	159	163					1																	9795602		2203	4300	6503	SO:0001583	missense	22883	exon13			GTGCTGCATGGCC	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1806G>A	1.37:g.9795602C>T	ENSP00000366513:p.Met602Ile	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	188	34	NM_001009566	0	0	296	456	160	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	37	CCDS30580.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	12.87	2.066247	0.36470	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	5.91	5.0	0.66597	.	0.155624	0.64402	N	0.000001	T	0.30603	0.0770	L	0.56396	1.775	0.80722	D	1	B;B;B	0.32188	0.245;0.359;0.245	B;B;B	0.26202	0.03;0.067;0.03	T	0.06110	-1.0845	10	0.40728	T	0.16	-19.7085	15.1111	0.72359	0.0:0.9325:0.0:0.0675	.	583;592;602	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	I	602;592;403;583;583	ENSP00000366513:M602I;ENSP00000354997:M592I;ENSP00000401934:M403I;ENSP00000366502:M583I	ENSP00000354997:M592I	M	-	3	0	CLSTN1	9718189	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	4.824000	0.62701	1.505000	0.48720	-0.140000	0.14226	ATG	C|0.999;T|0.001		0.527	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			T	9795602	C	T	9795602	3	4	105	1	0	0	0	0	1	0	0	0	3567	710	25	2	1167	2	CLSTN1	1	9795602	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	7635212	9795602	239455019	2	9328											
SRRM1	10250	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24993373	24993373	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggtctccttctcccgcccctCctcctcgacggcgcaggact	3	9	9	20	4	2	0	0	0	2	0	7	2	4	1	6	3	0	1	6	3	0	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:24993373C>T	ENST00000323848.9	+	13	2011	c.1696C>T	c.(1696-1698)Cct>Tct	p.P566S	SRRM1_ENST00000374389.4_Missense_Mutation_p.P575S|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000447431.2_Missense_Mutation_p.P578S|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000537199.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	566	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		TCCCGCCCCTCCTCCTCGACG	0.537																																					p.P566S	Ovarian(68;897 1494 3282 17478)												.	SRRM1-93	0			c.C1696T						.						53	45	48					1																	24993373		2203	4300	6503	SO:0001583	missense	10250	exon13			GCCCCTCCTCCTC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"Ser/Arg-related nuclear matrix protein", "plenty of prolines 101-like"	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1696C>T	1.37:g.24993373C>T	ENSP00000326261:p.Pro566Ser	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	58	8	NM_005839	0	0	80	126	46	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.712855	0.48517	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.55760	0.5;0.7;0.83	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	T	0.63920	0.2552	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.54275	-0.8318	10	0.11794	T	0.64	-3.0627	19.3453	0.94361	0.0:1.0:0.0:0.0	.	578;566	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	S	566;578;575	ENSP00000326261:P566S;ENSP00000391430:P578S;ENSP00000363510:P575S	ENSP00000326261:P566S	P	+	1	0	SRRM1	24865960	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	3.310000	0.51911	2.654000	0.90174	0.650000	0.86243	CCT	.		0.537	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24993373	C	T	24993373	3	4	105	1	0	0	0	0	1	0	0	0	15200	855	30	2	1746	2	SRRM1	1	24993373	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	15197771	24993373	224257248	3	9329											
BSDC1	55108	broad.mit.edu	37	chr1	32842099	32842099	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatgcctctagcagctttTgggacaggtccttgggtagc	7	11	14	9	0	1	0	0	0	1	0	2	2	2	2	2	4	4	3	2	4	2	5			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:32842099T>G	ENST00000455895.2	-	9	953	c.920A>C	c.(919-921)cAa>cCa	p.Q307P	BSDC1_ENST00000446293.2_Missense_Mutation_p.Q324P|BSDC1_ENST00000463967.1_5'Flank|BSDC1_ENST00000419121.2_Missense_Mutation_p.Q251P|BSDC1_ENST00000341071.7_Missense_Mutation_p.Q324P|BSDC1_ENST00000413080.1_Missense_Mutation_p.Q246P|BSDC1_ENST00000449308.1_Missense_Mutation_p.Q307P|BSDC1_ENST00000526031.1_Missense_Mutation_p.Q212P	NM_001143888.1|NM_018045.6	NP_001137360.1|NP_060515.3	Q9NW68	BSDC1_HUMAN	BSD domain containing 1	307										breast(1)|central_nervous_system(2)|kidney(1)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TAGCAGCTTTTGGGACAGGTC	0.597																																					p.Q324P													.	BSDC1-92	0			c.A971C						.						106	98	100					1																	32842099		2203	4300	6503	SO:0001583	missense	55108	exon9			AGCTTTTGGGACA	BX641056	CCDS363.2, CCDS44101.1, CCDS44102.1, CCDS44103.1, CCDS72752.1	1p35.1	2008-02-05			ENSG00000160058	ENSG00000160058			25501	protein-coding gene	gene with protein product						12477932	Standard	XM_005270985		Approved	FLJ10276, RP4-811H24.7	uc010ohg.2	Q9NW68	OTTHUMG00000007588	ENST00000455895.2:c.920A>C	1.37:g.32842099T>G	ENSP00000412173:p.Gln307Pro	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	184	3	NM_001143888	0	0	94	94	0	B4DMS7|B4DTI7|B4DTP7|B4E2X8|Q49AT8|Q68DY6|Q6IAA3|Q6MZK1|Q6UXS1|Q9HAL9	Missense_Mutation	SNP	ENST00000455895.2	37	CCDS363.2	.	.	.	.	.	.	.	.	.	.	T	13.73	2.325416	0.41197	.	.	ENSG00000160058	ENST00000455895;ENST00000413080;ENST00000341071;ENST00000526031;ENST00000419121;ENST00000446293;ENST00000449308	T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77	4.87	3.76	0.43208	.	0.225151	0.46442	D	0.000283	T	0.36386	0.0965	L	0.43152	1.355	0.44447	D	0.997376	B;B;B;B;B	0.13594	0.008;0.002;0.002;0.002;0.002	B;B;B;B;B	0.16289	0.015;0.009;0.009;0.002;0.004	T	0.15752	-1.0426	10	0.24483	T	0.36	-9.315	9.7393	0.40409	0.0:0.0834:0.0:0.9166	.	212;251;324;324;307	Q9NW68-9;Q9NW68-8;Q9NW68-7;Q9NW68-3;Q9NW68	.;.;.;.;BSDC1_HUMAN	P	307;246;324;212;251;324;307	ENSP00000412173:Q307P;ENSP00000409114:Q246P;ENSP00000344816:Q324P;ENSP00000432382:Q212P;ENSP00000405752:Q251P;ENSP00000397759:Q324P;ENSP00000391762:Q307P	ENSP00000344816:Q324P	Q	-	2	0	BSDC1	32614686	0.999000	0.42202	0.997000	0.53966	0.967000	0.64934	3.056000	0.49923	2.131000	0.65755	0.379000	0.24179	CAA	.		0.597	BSDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020056.3	NM_018045		G	32842099	T	G	32842099	3	3	105	1	0	0	0	0	1	0	0	0	1531	1812	63	5	384	5	BSDC1	1	32842099	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	7848726	32842099	216408522	4	9330											
POGZ	23126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151378756	151378756	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgcgggtgagtgggggttgGtggtggggttgcagttgagg	3	11	24	3	1	0	2	0	2	0	0	0	2	0	2	0	8	2	4	0	8	0	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:151378756G>A	ENST00000271715.2	-	19	3069	c.2755C>T	c.(2755-2757)Cca>Tca	p.P919S	POGZ_ENST00000531094.1_Missense_Mutation_p.P857S|POGZ_ENST00000392723.1_Missense_Mutation_p.P866S|POGZ_ENST00000368863.2_Missense_Mutation_p.P824S|POGZ_ENST00000409503.1_Missense_Mutation_p.P910S|POGZ_ENST00000361398.3_Missense_Mutation_p.P866S|POGZ_ENST00000491586.1_Missense_Mutation_p.P875S|POGZ_ENST00000540984.1_Missense_Mutation_p.P281S	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	919	Pro-rich.				kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GTGGGGGTTGGTGGTGGGGTT	0.592																																					p.P919S		.											.	POGZ-93	0			c.C2755T						.						73	73	73					1																	151378756		2203	4300	6503	SO:0001583	missense	23126	exon19			GGGTTGGTGGTGG	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.2755C>T	1.37:g.151378756G>A	ENSP00000271715:p.Pro919Ser	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	140	32	NM_015100	0	0	18	31	13	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.653454	0.29425	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586	T;T;T;T;T;T;T;T	0.23552	5.88;5.91;5.88;5.84;5.89;5.88;1.9;5.37	5.87	3.95	0.45737	.	0.748779	0.12616	N	0.453449	T	0.04861	0.0131	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0	T	0.34527	-0.9825	10	0.45353	T	0.12	-1.4299	8.593	0.33699	0.0805:0.2988:0.6207:0.0	.	857;910;824;875;866;919	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	S	866;919;866;824;910;857;281;875	ENSP00000376484:P866S;ENSP00000271715:P919S;ENSP00000354467:P866S;ENSP00000357856:P824S;ENSP00000386836:P910S;ENSP00000431259:P857S;ENSP00000443547:P281S;ENSP00000418408:P875S	ENSP00000271715:P919S	P	-	1	0	POGZ	149645380	0.165000	0.22948	0.788000	0.31933	0.966000	0.64601	0.747000	0.26290	1.446000	0.47643	0.655000	0.94253	CCA	.		0.592	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151378756	G	A	151378756	3	1	105	1	0	0	0	0	1	0	0	0	12212	1261	44	2	1481	2	POGZ	1	151378756	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	118536657	151378756	97871865	5	9331											
BTG2	7832	broad.mit.edu	37	chr1	203276560	203276560	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aactacgtgatggcagtctcCagctaggcccttccgccccc	7	8	9	17	2	1	1	0	1	1	0	3	1	2	1	5	2	3	2	5	2	3	3	rs377245155		TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:203276560C>T	ENST00000290551.4	+	2	542	c.471C>T	c.(469-471)tcC>tcT	p.S157S	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	157					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			TGGCAGTCTCCAGCTAGGCCC	0.632																																					p.S157S													.	BTG2-651	0			c.C471T						.	C		0,4392		0,0,2196	24	25	25		471	4.8	1	1		25	1,8565		0,1,4282	no	coding-synonymous	BTG2	NM_006763.2		0,1,6478	TT,TC,CC		0.0117,0.0,0.0077		157/159	203276560	1,12957	2196	4283	6479	SO:0001819	synonymous_variant	7832	exon2			AGTCTCCAGCTAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.471C>T	1.37:g.203276560C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	60	4	NM_006763	0	0	70	84	14	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.		0.632	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		T	203276560	C	T	203276560	2	4	105	1	0	0	0	0	0	0	0	1	1557	581	21	2		2	BTG2	1	203276560	Silent	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	51897804	203276560	45974061	6	9332											
MOSC1	64757	broad.mit.edu	37	chr1	220964857	220964857	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcttgtgatcaaccaggaGggaaacatggttactgctcg	10	10	13	8	1	1	1	1	1	0	0	2	3	1	3	1	4	4	3	1	4	3	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:220964857G>A	ENST00000366910.5	+	2	486	c.300G>A	c.(298-300)gaG>gaA	p.E100E		NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	100					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										TCAACCAGGAGGGAAACATGG	0.522																																					p.E100E													.	.	0			c.G300A						.						104	87	93					1																	220964857		2203	4300	6503	SO:0001819	synonymous_variant	64757	exon2			CCAGGAGGGAAAC	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.300G>A	1.37:g.220964857G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	70	4	NM_022746	0	0	1	1	0	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Silent	SNP	ENST00000366910.5	37	CCDS1526.1	.	.	.	.	.	.	.	.	.	.	G	8.167	0.790793	0.16258	.	.	ENSG00000186205	ENST00000407981	.	.	.	5.07	-5.6	0.02497	.	.	.	.	.	T	0.34745	0.0908	.	.	.	0.46416	D	0.999037	.	.	.	.	.	.	T	0.44298	-0.9337	4	.	.	.	-18.3348	0.5286	0.00624	0.2115:0.2571:0.2398:0.2915	.	.	.	.	R	9	.	.	G	+	1	0	MOSC1	219031480	0.003000	0.15002	0.021000	0.16686	0.909000	0.53808	-1.803000	0.01740	-0.429000	0.07329	0.650000	0.86243	GGG	.		0.522	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		A	220964857	G	A	220964857	2	1	105	1	0	0	0	0	0	0	0	1	9738	991	35	2		2	MOSC1	1	220964857	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	17688297	220964857	28285764	7	9333											
ACTA1	58	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	229568083	229568083	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtagtcggtgagatcgcggcCcgccaggtccaggcgcatga	7	6	16	12	5	0	2	0	2	0	1	3	3	1	2	3	4	0	2	3	4	1	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:229568083C>T	ENST00000366684.3	-	4	652	c.550G>A	c.(550-552)Ggc>Agc	p.G184S	ACTA1_ENST00000366683.2_Intron	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	184			G -> D (in NEM3; mild). {ECO:0000269|PubMed:10508519, ECO:0000269|PubMed:15236405}.		cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				AGATCGCGGCCCGCCAGGTCC	0.677																																					p.G184S		.											.	ACTA1-90	0			c.G550A						.						38	37	38					1																	229568083		2203	4299	6502	SO:0001583	missense	58	exon4			CGCGGCCCGCCAG	J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"nemaline myopathy type 3"	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.550G>A	1.37:g.229568083C>T	ENSP00000355645:p.Gly184Ser	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	76	13	NM_001100	0	0	1	1	0	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	37	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399571	0.62177	.	.	ENSG00000143632	ENST00000366684;ENST00000366682	D	0.99586	-6.23	4.58	3.67	0.42095	.	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	H	0.99609	4.655	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.96775	0.9571	10	0.87932	D	0	.	12.6981	0.57016	0.0:0.9198:0.0:0.0802	.	184	P68133	ACTS_HUMAN	S	184;149	ENSP00000355645:G184S	ENSP00000355643:G149S	G	-	1	0	ACTA1	227634706	1.000000	0.71417	0.846000	0.33378	0.920000	0.55202	7.545000	0.82128	1.143000	0.42306	0.650000	0.86243	GGC	.		0.677	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100		T	229568083	C	T	229568083	3	4	105	1	0	0	0	0	1	0	0	0	191	623	22	2	599	2	ACTA1	1	229568083	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	8603226	229568083	19682538	8	9334											
PDIA6	10130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	10927529	10927529	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaatccccaacgcggtctcAagttcagactgggctccagc	9	7	9	16	2	2	1	2	0	1	1	5	1	4	1	4	2	2	2	4	2	3	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr2:10927529A>T	ENST00000272227.3	-	11	1182	c.1035T>A	c.(1033-1035)ctT>ctA	p.L345L	PDIA6_ENST00000381611.4_Silent_p.L350L|PDIA6_ENST00000404824.2_Silent_p.L393L|PDIA6_ENST00000540494.1_Silent_p.L342L|PDIA6_ENST00000404371.2_Silent_p.L397L	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	345					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		ACGCGGTCTCAAGTTCAGACT	0.488																																					p.L345L	GBM(73;509 1219 34219 41343 41551)	.											.	PDIA6-90	0			c.T1035A						.						81	83	82					2																	10927529		2203	4300	6503	SO:0001819	synonymous_variant	10130	exon11			GGTCTCAAGTTCA	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"Protein disulfide isomerases"	30168	protein-coding gene	gene with protein product	"protein disulfide isomerase-related protein"	611099	"thioredoxin domain containing 7 (protein disulfide isomerase)", "protein disulfide isomerase-associated 6"	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.1035T>A	2.37:g.10927529A>T		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	80	10	NM_005742	0	0	675	771	96	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			.		0.488	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742		T	10927529	A	T	10927529	2	4	105	1	0	0	0	0	0	0	0	1	11698	117	5	5		5	PDIA6	2	10927529	Silent	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		10927529	232271844	9	9335											
STAT1	6772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	191859893	191859893	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctgttccaattcctccaActttttaagctgctgccgaa	8	16	5	12	1	1	0	0	0	1	0	4	1	4	0	4	0	4	3	4	0	4	6			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr2:191859893A>T	ENST00000361099.3	-	10	1225	c.838T>A	c.(838-840)Ttg>Atg	p.L280M	STAT1_ENST00000392322.3_Missense_Mutation_p.L280M|STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000409465.1_Missense_Mutation_p.L280M|STAT1_ENST00000392323.2_Missense_Mutation_p.L282M	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	280					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			AATTCCTCCAACTTTTTAAGC	0.448																																					p.L280M		.											.	STAT1-1335	0			c.T838A						.						158	136	143					2																	191859893		2203	4300	6503	SO:0001583	missense	6772	exon10			CCTCCAACTTTTT		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"SH2 domain containing"	11362	protein-coding gene	gene with protein product	"transcription factor ISGF-3 components p91/p84"	600555	"signal transducer and activator of transcription 1, 91kD"			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.838T>A	2.37:g.191859893A>T	ENSP00000354394:p.Leu280Met	Somatic	96	1		WXS	Illumina HiSeq	Phase_I	109	35	NM_007315	0	0	103	164	61	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.464088	0.63513	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.66	3.89	0.44902	STAT transcription factor, all-alpha (2);STAT transcription factor, coiled coil (1);	0.000000	0.85682	D	0.000000	T	0.79246	0.4413	M	0.86651	2.83	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79108	0.98;0.992	T	0.80185	-0.1487	10	0.72032	D	0.01	-20.1979	9.7711	0.40589	0.21:0.0:0.79:0.0	.	280;280	P42224-2;P42224	.;STAT1_HUMAN	M	280;280;280;282	ENSP00000354394:L280M;ENSP00000386244:L280M;ENSP00000376136:L280M;ENSP00000376137:L282M	ENSP00000354394:L280M	L	-	1	2	STAT1	191568138	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	5.579000	0.67457	0.757000	0.33036	-1.059000	0.02297	TTG	.		0.448	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		T	191859893	A	T	191859893	3	4	105	1	0	0	0	0	1	0	0	0	15296	40	2	5	1482	5	STAT1	2	191859893	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08	180932364	191859893	51339480	10	9336											
WNT10A	80326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219754883	219754883	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actggatgcactgcagcgtgGtaagggcctgagccatgggg	8	7	17	9	1	0	1	0	1	0	0	0	2	0	2	2	5	4	3	2	5	1	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr2:219754883G>A	ENST00000258411.3	+	3	1187	c.554G>A	c.(553-555)gGt>gAt	p.G185D		NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	185					cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|epidermis morphogenesis (GO:0048730)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|neural crest cell differentiation (GO:0014033)|neuron differentiation (GO:0030182)|odontogenesis (GO:0042476)|positive regulation of gene expression (GO:0010628)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sebaceous gland development (GO:0048733)|skin development (GO:0043588)|tongue development (GO:0043586)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|cervix(1)|endometrium(2)|lung(6)|skin(2)	12		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGCAGCGTGGTAAGGGCCTG	0.672																																					p.G185D		.											.	WNT10A-523	0			c.G554A						.						48	43	45					2																	219754883		2203	4300	6503	SO:0001583	missense	80326	exon3			AGCGTGGTAAGGG	AB059569	CCDS2426.1	2q35	2008-05-23			ENSG00000135925	ENSG00000135925		"Wingless-type MMTV integration sites"	13829	protein-coding gene	gene with protein product		606268				11350055, 17847007	Standard	NM_025216		Approved		uc002vjd.1	Q9GZT5	OTTHUMG00000133085	ENST00000258411.3:c.554G>A	2.37:g.219754883G>A	ENSP00000258411:p.Gly185Asp	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	67	13	NM_025216	0	0	4	4	0	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	37	CCDS2426.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.760111	0.89932	.	.	ENSG00000135925	ENST00000258411	T	0.75821	-0.97	4.46	4.46	0.54185	.	0.408178	0.26328	N	0.025007	D	0.84165	0.5412	M	0.71581	2.175	0.80722	D	1	D	0.63880	0.993	D	0.64144	0.922	D	0.86269	0.1660	10	0.72032	D	0.01	.	16.6424	0.85129	0.0:0.0:1.0:0.0	.	185	Q9GZT5	WN10A_HUMAN	D	185	ENSP00000258411:G185D	ENSP00000258411:G185D	G	+	2	0	WNT10A	219463127	1.000000	0.71417	0.795000	0.32087	0.929000	0.56500	9.117000	0.94347	2.478000	0.83669	0.655000	0.94253	GGT	.		0.672	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216		A	219754883	G	A	219754883	3	1	105	1	0	0	0	0	1	0	0	0	17415	1261	44	2	564	2	WNT10A	2	219754883	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	27894990	219754883	23444490	11	9337											
GPR55	9290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	231775289	231775289	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgggggaccggaggtggCtcaccagtagcgggtaacgg	7	6	18	10	3	1	0	1	0	0	0	2	2	2	2	3	7	2	3	3	7	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr2:231775289C>T	ENST00000392040.1	-	2	581	c.389G>A	c.(388-390)aGc>aAc	p.S130N	GPR55_ENST00000392039.2_Missense_Mutation_p.S130N|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	130					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		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;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		CCGGAGGTGGCTCACCAGTAG	0.557																																					p.S130N		.											.	GPR55-91	0			c.G389A						.						51	46	48					2																	231775289		2203	4300	6503	SO:0001583	missense	9290	exon2			AGGTGGCTCACCA	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"GPCR / Class A : Orphans"	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.389G>A	2.37:g.231775289C>T	ENSP00000375894:p.Ser130Asn	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	78	8	NM_005683	0	0	0	0	0	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	.	.	.	.	.	.	.	.	.	.	C	10.66	1.412948	0.25465	.	.	ENSG00000135898	ENST00000392040;ENST00000392039;ENST00000438398	T;T;T	0.71698	-0.59;-0.59;-0.59	5.65	-1.33	0.09172	GPCR, rhodopsin-like superfamily (1);	0.431206	0.27464	N	0.019252	T	0.54806	0.1881	L	0.39397	1.21	0.21553	N	0.999648	B	0.02656	0.0	B	0.06405	0.002	T	0.41538	-0.9503	10	0.28530	T	0.3	-29.6367	9.6559	0.39925	0.0:0.4621:0.0:0.5379	.	130	Q9Y2T6	GPR55_HUMAN	N	130	ENSP00000375894:S130N;ENSP00000375893:S130N;ENSP00000412768:S130N	ENSP00000375893:S130N	S	-	2	0	GPR55	231483533	0.000000	0.05858	0.993000	0.49108	0.496000	0.33645	-0.132000	0.10467	-0.141000	0.11374	-0.940000	0.02684	AGC	.		0.557	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683		T	231775289	C	T	231775289	3	4	105	1	0	0	0	0	1	0	0	0	6719	797	28	2	574	2	GPR55	2	231775289	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	12020406	231775289	11424084	12	9338											
GRM2	2912	broad.mit.edu	37	chr3	51749233	51749233	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaaggcttgactctggacAccagcctcatcccatgggcc	9	7	10	15	0	2	2	1	1	1	1	3	3	3	3	4	3	1	1	4	3	1	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr3:51749233A>C	ENST00000395052.3	+	4	1678	c.1444A>C	c.(1444-1446)Acc>Ccc	p.T482P	GRM2_ENST00000475478.1_3'UTR|GRM2_ENST00000442933.2_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	482					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GACTCTGGACACCAGCCTCAT	0.627																																					p.T482P													.	GRM2-522	0			c.A1444C						.						61	51	54					3																	51749233		2203	4300	6503	SO:0001583	missense	2912	exon4			CTGGACACCAGCC	L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.1444A>C	3.37:g.51749233A>C	ENSP00000378492:p.Thr482Pro	Somatic	43	6		WXS	Illumina HiSeq	Phase_I	39	7	NM_000839	0	0	0	0	0	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	A	12.49	1.954193	0.34471	.	.	ENSG00000164082	ENST00000395052	D	0.88201	-2.35	4.95	0.946	0.19549	.	0.053035	0.85682	D	0.000000	T	0.76378	0.3979	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.62714	-0.6796	10	0.31617	T	0.26	.	6.0978	0.20031	0.716:0.1364:0.1476:0.0	.	482	Q14416	GRM2_HUMAN	P	482	ENSP00000378492:T482P	ENSP00000378492:T482P	T	+	1	0	GRM2	51724273	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	3.038000	0.49783	0.337000	0.23665	0.379000	0.24179	ACC	.		0.627	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			C	51749233	A	C	51749233	3	2	105	1	0	0	0	0	1	0	0	0	6818	159	6	5	1454	5	GRM2	3	51749233	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		51749233	146273197	13	9339											
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctacacgagatcctctctctGaaatcactgagcaggagaaa	14	8	8	11	1	3	4	1	2	2	2	5	6	4	4	1	1	2	1	1	1	3	1	rs121913273		TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA-27752	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						.						56	56	56					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	87	24	NM_006218	0	0	5	14	9	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936082	G	A	178936082	3	1	105	1	0	0	0	0	1	0	0	0	11939	1291	45	2	1658	2	PIK3CA	3	178936082	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	127186849	178936082	19086348	14	9340											
HTT	3064	broad.mit.edu	37	chr4	3076604	3076609	+	In_Frame_Del	DEL	CAGCAG	CAGCAG	-																															tcgagtccctcaagtccttcCagcagcagcagcagcagcag																								rs71180116|rs374076986	byFrequency	TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	CAGCAG	CAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr4:3076604_3076609delCAGCAG	ENST00000355072.5	+	1	197_202	c.52_57delCAGCAG	c.(52-57)cagcagdel	p.QQ36del	HTT-AS_ENST00000503893.1_RNA	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	36	Poly-Gln.				anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CAAGTCCTTCcagcagcagcagcagc	0.704														1892	0.377796	0.0741	0.3343	5008	,	,		6929	0.7421		0.327	False		,,,				2504	0.4959				p.18_19del													.	HTT-281	0			c.52_57del						.			33,28,149		16,0,1,14,0,74						2.6	1		dbSNP_119	4	239,82,669		114,3,8,38,3,329	no	codingComplex	HTT	NM_002111.6		130,3,9,52,3,403	A1A1,A1A2,A1R,A2A2,A2R,RR		32.4242,29.0476,31.8333				272,110,818				SO:0001651	inframe_deletion	3064	exon1			TCCTTCCAGCAGC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.52_57delCAGCAG	4.37:g.3076610_3076615delCAGCAG	ENSP00000347184:p.Gln36_Gln37del	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_002111	0	0	0	0	0	Q9UQB7	In_Frame_Del	DEL	ENST00000355072.5	37	CCDS43206.1																																																																																			.		0.704	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		-	3076609	CAGCAG	-	3076604	7	5	105	1	0	1	0	1	0	0	0	0	7478	595	21	0	54	0	HTT	4	3076604	In_Frame_Del	DEL	CAGCAG	TCGA-DZ-6134-01A-11D-1961-08		3076604	188077672	15	9341											
PCDHB10	56126	broad.mit.edu	37	chr5	140573732	140573732	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcgtgggcgccacagaccGcggctcccccgcgctgagca	5	3	14	19	7	0	2	0	1	0	1	1	2	1	2	5	2	1	3	5	2	0	0	rs17844579		TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr5:140573732G>A	ENST00000239446.4	+	1	1791	c.1607G>A	c.(1606-1608)cGc>cAc	p.R536H		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	536	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCCACAGACCGCGGCTCCCCC	0.682																																					p.R536H													.	PCDHB10-92	0			c.G1607A						.						52	70	64					5																	140573732		2203	4298	6501	SO:0001583	missense	56126	exon1			CAGACCGCGGCTC	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1607G>A	5.37:g.140573732G>A	ENSP00000239446:p.Arg536His	Somatic	286	0		WXS	Illumina HiSeq	Phase_I	217	5	NM_018930	0	0	3	3	0	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	g	9.720	1.159514	0.21454	.	.	ENSG00000120324	ENST00000239446	T	0.01745	4.66	3.53	2.55	0.30701	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01189	0.0039	N	0.11789	0.175	0.09310	N	1	B	0.29481	0.245	B	0.27715	0.082	T	0.49173	-0.8967	9	0.44086	T	0.13	.	3.8548	0.08971	0.2488:0.2797:0.4715:0.0	rs17844579	536	Q9UN67	PCDBA_HUMAN	H	536	ENSP00000239446:R536H	ENSP00000239446:R536H	R	+	2	0	PCDHB10	140553916	0.000000	0.05858	0.964000	0.40570	0.903000	0.53119	-0.301000	0.08232	0.821000	0.34540	0.549000	0.68633	CGC	G|1.000;T|0.000		0.682	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		A	140573732	G	A	140573732	3	1	105	1	0	0	0	0	1	0	0	0	11561	1087	38	1	1609	1	PCDHB10	5	140573732	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		140573732	40341528	16	9342											
GFPT2	9945	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179751868	179751868	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gagagcttgtatttgctccgGactccgatgagcagggggct	7	10	15	9	2	0	2	0	1	0	1	2	5	2	3	2	3	3	5	2	3	1	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr5:179751868G>A	ENST00000253778.8	-	8	793	c.624C>T	c.(622-624)gtC>gtT	p.V208V	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	208	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	ATTTGCTCCGGACTCCGATGA	0.542																																					p.V208V		.											.	GFPT2-92	0			c.C624T						.						96	104	101					5																	179751868		1961	4154	6115	SO:0001819	synonymous_variant	9945	exon8			GCTCCGGACTCCG	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.624C>T	5.37:g.179751868G>A		Somatic	181	1		WXS	Illumina HiSeq	Phase_I	168	32	NM_005110	0	0	6	7	1	Q53XM2|Q9BWS4	Silent	SNP	ENST00000253778.8	37	CCDS43411.1																																																																																			.		0.542	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		A	179751868	G	A	179751868	2	1	105	1	0	0	0	0	0	0	0	1	6366	1161	41	2		2	GFPT2	5	179751868	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	39178136	179751868	1163392	17	9343											
GRM4	2914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	34059742	34059742	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gccactgtggacacatagttCcacttgagggcacggacgat	10	8	12	11	2	0	1	0	1	0	0	1	4	1	3	2	3	0	2	2	3	1	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr6:34059742C>T	ENST00000538487.2	-	3	1097	c.654G>A	c.(652-654)tgG>tgA	p.W218*	GRM4_ENST00000544773.2_Nonsense_Mutation_p.W49*|GRM4_ENST00000374181.4_Nonsense_Mutation_p.W218*|GRM4_ENST00000455714.2_Nonsense_Mutation_p.W78*|GRM4_ENST00000609222.1_Nonsense_Mutation_p.W85*|GRM4_ENST00000535756.1_Nonsense_Mutation_p.W85*|GRM4_ENST00000374177.3_Nonsense_Mutation_p.W149*	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	218					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						ACACATAGTTCCACTTGAGGG	0.617																																					p.W218X		.											.	GRM4-525	0			c.G654A						.						101	71	81					6																	34059742		2203	4300	6503	SO:0001587	stop_gained	2914	exon3			ATAGTTCCACTTG	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"GPCR / Class C : Glutamate receptors, metabotropic", "Glutamate receptors"	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.654G>A	6.37:g.34059742C>T	ENSP00000440556:p.Trp218*	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	68	16	NM_001256811	0	0	0	0	0	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Nonsense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	37	6.085596	0.97271	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	.	.	.	4.07	4.07	0.47477	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4078	0.83697	0.0:1.0:0.0:0.0	.	.	.	.	X	218;149;85;49;218;78	.	ENSP00000363292:W149X	W	-	3	0	GRM4	34167720	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.647000	0.83462	2.080000	0.62538	0.561000	0.74099	TGG	.		0.617	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			T	34059742	C	T	34059742	4	4	105	1	0	0	0	0	0	1	0	0	6820	856	30	2	2120	2	GRM4	6	34059742	Nonsense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08		34059742	137055325	18	9344											
CRIP3	401262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43275462	43275462	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggattgtacaagtaggagccTacaccaccaatgttcacccc	12	8	8	13	0	1	0	1	0	0	0	1	2	1	2	5	2	3	3	5	2	5	5			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr6:43275462T>C	ENST00000274990.4	-	4	220	c.216A>G	c.(214-216)gtA>gtG	p.V72V	ZNF318_ENST00000607252.1_5'UTR|CRIP3_ENST00000372569.3_Silent_p.V72V			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	72					T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			AGTAGGAGCCTACACCACCAA	0.627																																					p.V72V		.											.	CRIP3-91	0			c.A216G						.						45	48	47					6																	43275462		2203	4300	6503	SO:0001819	synonymous_variant	401262	exon4			GGAGCCTACACCA	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.216A>G	6.37:g.43275462T>C		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	97	18	NM_206922	0	0	1	1	0	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Silent	SNP	ENST00000274990.4	37		.	.	.	.	.	.	.	.	.	.	T	7.040	0.562412	0.13498	.	.	ENSG00000146215	ENST00000416431	.	.	.	5.52	3.63	0.41609	.	.	.	.	.	T	0.33323	0.0859	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30592	-0.9973	4	.	.	.	-35.039	4.1803	0.10372	0.1604:0.5979:0.1554:0.0862	.	.	.	.	G	20	.	.	R	-	1	2	CRIP3	43383440	0.290000	0.24343	1.000000	0.80357	0.744000	0.42396	-0.819000	0.04462	1.470000	0.48102	-0.132000	0.14878	AGG	.		0.627	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			C	43275462	T	C	43275462	2	2	105	1	0	0	0	0	0	0	0	1	3882	1509	53	3		3	CRIP3	6	43275462	Silent	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	9215720	43275462	127839605	19	9345											
ZNF679	168417	broad.mit.edu	37	chr7	63720697	63720697	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatatagagatgtgatgttAgagaactacagaaacctggt	15	12	10	4	0	0	4	0	1	0	3	0	6	0	4	1	1	3	1	1	1	7	5			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:63720697A>G	ENST00000421025.1	+	3	407	c.138A>G	c.(136-138)ttA>ttG	p.L46L	ZNF679_ENST00000255746.4_Silent_p.L46L	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	46	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						ATGTGATGTTAGAGAACTACA	0.378																																					p.L46L													.	ZNF679-1	0			c.A138G						.						47	42	44					7																	63720697		692	1591	2283	SO:0001819	synonymous_variant	168417	exon3			GATGTTAGAGAAC	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.138A>G	7.37:g.63720697A>G		Somatic	214	0		WXS	Illumina HiSeq	Phase_I	184	4	NM_153363	0	0	6	36	30		Silent	SNP	ENST00000421025.1	37	CCDS47592.1																																																																																			.		0.378	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		G	63720697	A	G	63720697	2	3	105	1	0	0	0	0	0	0	0	1	18118	417	15	3		3	ZNF679	7	63720697	Silent	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		63720697	95417966	20	9346											
FZD1	8321	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	90894779	90894779	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctgtgcgagcgcgcgcGccagggctgcgaggcgctca	4	5	16	16	7	1	0	1	0	0	0	2	2	2	0	2	2	3	2	2	2	0	0			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:90894779G>A	ENST00000287934.2	+	1	997	c.584G>A	c.(583-585)cGc>cAc	p.R195H		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	195	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			GAGCGCGCGCGCCAGGGCTGC	0.672																																					p.R195H		.											.	FZD1-658	0			c.G584A						.						52	58	56					7																	90894779		2199	4299	6498	SO:0001583	missense	8321	exon1			GCGCGCGCCAGGG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.584G>A	7.37:g.90894779G>A	ENSP00000287934:p.Arg195His	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	169	33	NM_003505	0	0	56	76	20	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	37	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.936514	0.92458	.	.	ENSG00000157240	ENST00000287934	T	0.76839	-1.05	4.69	4.69	0.59074	Frizzled domain (5);	0.000000	0.64402	D	0.000003	D	0.90407	0.6997	H	0.94542	3.55	0.80722	D	1	D	0.65815	0.995	P	0.61132	0.884	D	0.93351	0.6718	10	0.87932	D	0	.	17.7914	0.88553	0.0:0.0:1.0:0.0	.	195	Q9UP38	FZD1_HUMAN	H	195	ENSP00000287934:R195H	ENSP00000287934:R195H	R	+	2	0	FZD1	90732715	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.543000	0.73874	2.430000	0.82344	0.561000	0.74099	CGC	.		0.672	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		A	90894779	G	A	90894779	3	1	105	1	0	0	0	0	1	0	0	0	6147	1087	38	1	586	1	FZD1	7	90894779	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	27174082	90894779	68243884	21	9347											
PTCD1	26024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99022814	99022814	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaccactgtagggggaacGgccccgggggtcaggaggtt	8	5	19	9	2	1	1	1	0	0	1	1	4	1	3	3	7	1	2	3	7	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:99022814G>A	ENST00000292478.4	-	6	1591	c.1341C>T	c.(1339-1341)gcC>gcT	p.A447A	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.A496A|PTCD1_ENST00000555673.1_Silent_p.A496A	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	447					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TAGGGGGAACGGCCCCGGGGG	0.647																																					p.A496A		.											.	.	0			c.C1488T						.						58	61	60					7																	99022814		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon7			GGGAACGGCCCCG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1341C>T	7.37:g.99022814G>A		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	149	50	NM_001198879	0	0	7	20	13	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	37	CCDS34691.1																																																																																			.		0.647	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99022814	G	A	99022814	2	1	105	1	0	0	0	0	0	0	0	1	12756	1103	39	1		1	PTCD1	7	99022814	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	8128035	99022814	60115849	22	9348											
ZCWPW1	55063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100016757	100016757	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactcctgaagggacttcTgcagaacaatctggacaatc	13	8	9	11	0	2	2	0	1	2	1	4	4	3	4	1	2	3	2	1	2	4	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:100016757T>C	ENST00000398027.2	-	5	585	c.338A>G	c.(337-339)cAg>cGg	p.Q113R	ZCWPW1_ENST00000360951.4_Missense_Mutation_p.Q113R|ZCWPW1_ENST00000490721.1_5'UTR|ZCWPW1_ENST00000324725.6_5'UTR	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	113							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AAGGGACTTCTGCAGAACAAT	0.438																																					p.Q113R		.											.	ZCWPW1-90	0			c.A338G						.						167	155	159					7																	100016757		1886	4103	5989	SO:0001583	missense	55063	exon5			GACTTCTGCAGAA	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"zinc finger, CW-type with PWWP domain 1"			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.338A>G	7.37:g.100016757T>C	ENSP00000381109:p.Gln113Arg	Somatic	235	2		WXS	Illumina HiSeq	Phase_I	246	96	NM_001258008	0	0	1	1	0	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Missense_Mutation	SNP	ENST00000398027.2	37	CCDS43623.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.841227	0.32513	.	.	ENSG00000078487	ENST00000398027;ENST00000360951;ENST00000379559	T;T	0.48522	0.82;0.81	5.59	-7.95	0.01148	.	0.871285	0.09674	N	0.770768	T	0.26195	0.0639	N	0.17474	0.49	0.80722	D	1	B;B;B;B	0.12630	0.006;0.002;0.001;0.005	B;B;B;B	0.16722	0.016;0.002;0.001;0.003	T	0.13575	-1.0504	9	.	.	.	0.2273	13.8447	0.63459	0.0:0.5835:0.0:0.4165	.	113;113;113;113	B4E3W9;B4DUQ2;C9J435;Q9H0M4	.;.;.;ZCPW1_HUMAN	R	113	ENSP00000381109:Q113R;ENSP00000354210:Q113R	.	Q	-	2	0	ZCWPW1	99854693	0.208000	0.23494	0.873000	0.34254	0.986000	0.74619	-1.340000	0.02650	-1.437000	0.01967	-0.376000	0.06991	CAG	.		0.438	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		C	100016757	T	C	100016757	3	2	105	1	0	0	0	0	1	0	0	0	17629	1580	55	3	1664	3	ZCWPW1	7	100016757	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	993943	100016757	59121906	23	9349											
SERPINE1	5054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100780346	100780346	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacagacccttcctctttgtGgtccggcacaaccccacagg	8	8	9	16	1	1	1	0	0	1	1	3	2	3	1	5	3	1	1	5	3	1	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:100780346G>C	ENST00000223095.4	+	8	1309	c.1152G>C	c.(1150-1152)gtG>gtC	p.V384V	SERPINE1_ENST00000445463.2_Silent_p.V369V	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	384					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	TCCTCTTTGTGGTCCGGCACA	0.552																																					p.V384V		.											.	SERPINE1-652	0			c.G1152C						.						139	117	125					7																	100780346		2203	4300	6503	SO:0001819	synonymous_variant	5054	exon8			CTTTGTGGTCCGG	M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"Serine (or cysteine) peptidase inhibitors"	8583	protein-coding gene	gene with protein product	"plasminogen activator inhibitor, type I"	173360	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.1152G>C	7.37:g.100780346G>C		Somatic	202	0		WXS	Illumina HiSeq	Phase_I	203	27	NM_000602	0	0	33	34	1	B7Z4S0|F8WD53	Silent	SNP	ENST00000223095.4	37	CCDS5711.1																																																																																			.		0.552	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602		C	100780346	G	C	100780346	2	2	105	1	0	0	0	0	0	0	0	1	14143	1335	47	4		4	SERPINE1	7	100780346	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	763589	100780346	58358317	24	9350											
SLC26A5	375611	broad.mit.edu;bcgsc.ca	37	chr7	103017286	103017286	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaagtatacatatataccGacgtctccatattcttttac	12	15	4	10	2	2	0	0	0	2	0	3	1	2	0	2	0	3	2	2	0	8	10	rs372287716		TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:103017286G>T	ENST00000306312.3	-	19	2271	c.2010C>A	c.(2008-2010)gtC>gtA	p.V670V	SLC26A5_ENST00000432958.2_Silent_p.V638V|SLC26A5_ENST00000339444.6_Silent_p.V670V|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393727.1_Silent_p.V672V|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000354356.4_Silent_p.V103V|SLC26A5_ENST00000393723.1_Silent_p.V640V|SLC26A5_ENST00000393730.1_Silent_p.V638V|SLC26A5_ENST00000393729.1_Silent_p.V633V	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	670	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						CATATATACCGACGTCTCCAT	0.308																																					p.V670V													.	SLC26A5-91	0			c.C2010A						.						110	113	112					7																	103017286		2203	4295	6498	SO:0001819	synonymous_variant	375611	exon19			TATACCGACGTCT	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.2010C>A	7.37:g.103017286G>T		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	171	8	NM_206883	0	0	0	0	0	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	CCDS5733.1																																																																																			.		0.308	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		T	103017286	G	T	103017286	2	4	105	1	0	0	0	0	0	0	0	1	14552	1045	37	4		4	SLC26A5	7	103017286	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	2236940	103017286	56121377	25	9351											
HSDL2	84263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	115181173	115181173	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagtatggtatgtctatgtAtgtgcttggaatggcagaag	11	14	13	3	0	1	1	0	0	1	1	1	2	1	2	0	3	1	5	0	3	7	6			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr9:115181173A>G	ENST00000398805.3	+	6	760	c.533A>G	c.(532-534)tAt>tGt	p.Y178C	HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000539114.1_Intron|HSDL2_ENST00000262542.7_Missense_Mutation_p.Y58C|HSDL2_ENST00000398803.1_Missense_Mutation_p.Y105C	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	178						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						ATGTCTATGTATGTGCTTGGA	0.274																																					p.Y178C		.											.	HSDL2-90	0			c.A533G						.						146	133	137					9																	115181173		1844	4082	5926	SO:0001583	missense	84263	exon6			CTATGTATGTGCT	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	18572	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 13C, member 1"		"chromosome 9 open reading frame 99"	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.533A>G	9.37:g.115181173A>G	ENSP00000381785:p.Tyr178Cys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	83	6	NM_032303	0	0	83	101	18	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	A	4.417	0.077003	0.08485	.	.	ENSG00000119471	ENST00000398805;ENST00000398803;ENST00000262542	D;D;T	0.89810	-2.23;-2.57;2.17	5.54	4.61	0.57282	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.043003	0.85682	N	0.000000	T	0.66237	0.2769	N	0.00611	-1.325	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.67364	-0.5689	10	0.02654	T	1	.	14.288	0.66258	0.0732:0.0:0.9268:0.0	.	105;178	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	C	178;105;58	ENSP00000381785:Y178C;ENSP00000381783:Y105C;ENSP00000262542:Y58C	ENSP00000262542:Y58C	Y	+	2	0	HSDL2	114220994	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.348000	0.79366	1.462000	0.47948	-0.321000	0.08615	TAT	.		0.274	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		G	115181173	A	G	115181173	3	3	105	1	0	0	0	0	1	0	0	0	7415	449	16	3	555	3	HSDL2	9	115181173	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		115181173	26032258	26	9352											
ALAD	210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	116151742	116151742	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctttacctcccgcacgatGtccaggtagggcattcccgg	6	10	10	15	3	0	0	0	0	0	0	4	1	4	0	5	3	1	3	5	3	2	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr9:116151742G>A	ENST00000409155.3	-	10	973	c.777C>T	c.(775-777)gaC>gaT	p.D259D	ALAD_ENST00000277315.5_Silent_p.D242D|ALAD_ENST00000482001.1_5'Flank	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	259					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	CCCGCACGATGTCCAGGTAGG	0.567																																					p.D259D		.											.	ALAD-90	0			c.C777T						.						116	110	112					9																	116151742		2203	4300	6503	SO:0001819	synonymous_variant	210	exon10			CACGATGTCCAGG	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"porphobilinogen synthase"	125270	"aminolevulinate, delta-, dehydratase"			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.777C>T	9.37:g.116151742G>A		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	112	26	NM_000031	0	0	36	63	27	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Silent	SNP	ENST00000409155.3	37	CCDS6794.2																																																																																			.		0.567	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		A	116151742	G	A	116151742	2	1	105	1	0	0	0	0	0	0	0	1	483	1368	48	2		2	ALAD	9	116151742	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	970569	116151742	25061689	27	9353											
DIP2C	22982	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	390986	390986	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacgtccacagccgccgccGcctccctggaccgcagcaac	7	4	10	20	5	0	1	0	1	0	0	2	2	2	2	7	1	3	2	7	1	1	0			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr10:390986G>A	ENST00000280886.6	-	27	3383	c.3296C>T	c.(3295-3297)gCg>gTg	p.A1099V		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1099						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		AGCCGCCGCCGCCTCCCTGGA	0.602																																					p.A1099V													.	DIP2C-156	0			c.C3296T						.						57	49	52					10																	390986		2203	4300	6503	SO:0001583	missense	22982	exon27			GCCGCCGCCTCCC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3296C>T	10.37:g.390986G>A	ENSP00000280886:p.Ala1099Val	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	36	7	NM_014974	0	0	21	38	17	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	G	34	5.405888	0.96051	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.10288	2.89	5.59	5.59	0.84812	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.34424	0.0897	M	0.73372	2.23	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00857	-1.1538	10	0.34782	T	0.22	-28.982	19.59	0.95506	0.0:0.0:1.0:0.0	.	1099	Q9Y2E4	DIP2C_HUMAN	V	1099;24	ENSP00000280886:A1099V	ENSP00000280886:A1099V	A	-	2	0	DIP2C	380986	1.000000	0.71417	0.994000	0.49952	0.641000	0.38312	9.813000	0.99286	2.639000	0.89480	0.655000	0.94253	GCG	.		0.602	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	390986	G	A	390986	3	1	105	1	0	0	0	0	1	0	0	0	4540	1087	38	1	1418	1	DIP2C	10	390986	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		390986	135143761	28	9354											
CAMK1D	57118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	12595265	12595265	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttagctgaagagaaggcaaCtggcaagctctttgctgtga	11	11	12	7	0	1	3	0	2	1	1	1	4	1	3	0	2	4	5	0	2	5	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr10:12595265C>T	ENST00000378847.3	+	2	471	c.134C>T	c.(133-135)aCt>aTt	p.T45I	CAMK1D_ENST00000378845.1_Missense_Mutation_p.T45I|CAMK1D_ENST00000487696.1_Intron	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	45	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		GAGAAGGCAACTGGCAAGCTC	0.468																																					p.T45I		.											.	CAMK1D-334	0			c.C134T						.						162	150	154					10																	12595265		2203	4300	6503	SO:0001583	missense	57118	exon2			AGGCAACTGGCAA	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.134C>T	10.37:g.12595265C>T	ENSP00000368124:p.Thr45Ile	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	189	35	NM_153498	0	0	8	9	1	B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	37	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507699	0.44558	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.49139	0.79;0.79	5.14	4.23	0.50019	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055122	0.64402	D	0.000001	T	0.57888	0.2084	M	0.89785	3.06	0.45648	D	0.99857	B;B	0.19073	0.033;0.011	B;B	0.23716	0.048;0.047	T	0.62586	-0.6823	10	0.87932	D	0	-12.4567	13.7457	0.62874	0.0:0.6876:0.3124:0.0	.	45;45	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	I	45	ENSP00000368124:T45I;ENSP00000368122:T45I	ENSP00000368122:T45I	T	+	2	0	CAMK1D	12635271	1.000000	0.71417	0.981000	0.43875	0.946000	0.59487	3.132000	0.50523	1.127000	0.42034	0.561000	0.74099	ACT	.		0.468	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		T	12595265	C	T	12595265	3	4	105	1	0	0	0	0	1	0	0	0	2603	565	20	2	140	2	CAMK1D	10	12595265	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	12204279	12595265	122939482	29	9355											
ATRNL1	26033	hgsc.bcm.edu;broad.mit.edu	37	chr10	116889093	116889093	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattatattttacagaatcAattcttgtcctaacaattgc	14	16	4	7	0	2	1	1	0	1	1	3	2	3	1	1	0	3	0	1	0	8	8			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr10:116889093A>C	ENST00000355044.3	+	5	751	c.625A>C	c.(625-627)Aat>Cat	p.N209H	ATRNL1_ENST00000527407.1_Missense_Mutation_p.N209H|ATRNL1_ENST00000529665.1_3'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	209	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.|EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TTACAGAATCAATTCTTGTCC	0.303																																					p.N209H		.											.	ATRNL1-96	0			c.A625C						.						86	84	84					10																	116889093		2203	4300	6503	SO:0001583	missense	26033	exon5			AGAATCAATTCTT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.625A>C	10.37:g.116889093A>C	ENSP00000347152:p.Asn209His	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	48	10	NM_207303	0	0	0	0	0	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.275216	0.80580	.	.	ENSG00000107518	ENST00000526946;ENST00000355044	T;T	0.51071	0.72;0.72	5.47	5.47	0.80525	CUB (3);Epidermal growth factor-like, type 3 (1);	0.040008	0.85682	D	0.000000	T	0.68815	0.3042	M	0.76002	2.32	0.80722	D	1	D;D;D	0.71674	0.977;0.998;0.986	P;D;P	0.78314	0.754;0.991;0.875	T	0.73222	-0.4051	10	0.87932	D	0	-20.838	15.5419	0.76057	1.0:0.0:0.0:0.0	.	142;209;209	E9PL90;Q5VV63;Q5VV63-2	.;ATRN1_HUMAN;.	H	142;209	ENSP00000431423:N142H;ENSP00000347152:N209H	ENSP00000347152:N209H	N	+	1	0	ATRNL1	116879083	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.307000	0.96226	2.085000	0.62840	0.383000	0.25322	AAT	.		0.303	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	116889093	A	C	116889093	3	2	105	1	0	0	0	0	1	0	0	0	1208	130	5	5	643	5	ATRNL1	10	116889093	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08	104293828	116889093	18645654	30	9356											
SLC43A1	8501	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57261478	57261478	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acactcactctcaggaaggtTttctgaggtgccccgaacat	10	10	9	12	1	3	1	2	1	2	0	4	3	3	2	2	3	2	1	2	3	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:57261478T>A	ENST00000278426.3	-	8	1214	c.859A>T	c.(859-861)Aac>Tac	p.N287Y	SLC43A1_ENST00000528450.1_Missense_Mutation_p.N287Y|SLC43A1_ENST00000533515.1_5'UTR	NM_003627.5	NP_003618.1			solute carrier family 43 (amino acid system L transporter), member 1											breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						TCAGGAAGGTTTTCTGAGGTG	0.567											OREG0020651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N287Y		.											.	SLC43A1-90	0			c.A859T						.						74	65	68					11																	57261478		2201	4296	6497	SO:0001583	missense	8501	exon8			GAAGGTTTTCTGA	AF045584	CCDS7958.1	11q12.1	2013-07-17	2013-07-17	2003-09-12	ENSG00000149150	ENSG00000149150		"Solute carriers"	9225	protein-coding gene	gene with protein product		603733	"prostate cancer overexpressed gene 1"	POV1		9255310, 9722952	Standard	NM_003627		Approved	R00504, PB39	uc001nkk.3	O75387	OTTHUMG00000167030	ENST00000278426.3:c.859A>T	11.37:g.57261478T>A	ENSP00000278426:p.Asn287Tyr	Somatic	74	0	1021	WXS	Illumina HiSeq	Phase_I	62	13	NM_001198810	0	0	0	0	0		Missense_Mutation	SNP	ENST00000278426.3	37	CCDS7958.1	.	.	.	.	.	.	.	.	.	.	t	15.67	2.901506	0.52227	.	.	ENSG00000149150	ENST00000278426;ENST00000528450;ENST00000533066	T;T;T	0.58060	0.36;0.36;1.47	5.57	-2.09	0.07232	Major facilitator superfamily domain, general substrate transporter (1);	1.826000	0.01877	N	0.037616	T	0.36524	0.0970	N	0.14661	0.345	0.09310	N	1	P	0.48911	0.917	P	0.46419	0.516	T	0.21965	-1.0230	10	0.35671	T	0.21	0.3003	1.7106	0.02891	0.1305:0.2328:0.1338:0.5029	.	287	O75387	LAT3_HUMAN	Y	287;287;256	ENSP00000278426:N287Y;ENSP00000435673:N287Y;ENSP00000435647:N256Y	ENSP00000278426:N287Y	N	-	1	0	SLC43A1	57018054	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.234000	0.17930	-0.008000	0.14320	0.459000	0.35465	AAC	.		0.567	SLC43A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392541.1	NM_003627		A	57261478	T	A	57261478	3	1	105	1	0	0	0	0	1	0	0	0	14664	1841	64	5	852	5	SLC43A1	11	57261478	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08		57261478	77745038	31	9357											
CAPN5	726	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	76825445	76825445	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgagcgcatgttaaaggtgCacagccggggcggcctcatc	8	8	14	11	3	1	1	1	1	0	0	2	1	1	1	2	4	3	3	2	4	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:76825445C>T	ENST00000278559.3	+	5	853	c.664C>T	c.(664-666)Cac>Tac	p.H222Y	CAPN5_ENST00000456580.2_Missense_Mutation_p.H262Y|CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Missense_Mutation_p.H222Y	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	222	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GTTAAAGGTGCACAGCCGGGG	0.592											OREG0021255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H222Y		.											.	CAPN5-90	0			c.C664T						.						200	190	194					11																	76825445		2200	4292	6492	SO:0001583	missense	726	exon5			AAGGTGCACAGCC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"vitreoretinopathy, neovascular inflammatory"	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.664C>T	11.37:g.76825445C>T	ENSP00000278559:p.His222Tyr	Somatic	438	1	1171	WXS	Illumina HiSeq	Phase_I	330	21	NM_004055	0	0	58	68	10	O00263	Missense_Mutation	SNP	ENST00000278559.3	37	CCDS8248.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992258	0.54041	.	.	ENSG00000149260	ENST00000278559;ENST00000360841;ENST00000529629;ENST00000456580;ENST00000544318	D;D;D	0.87179	-2.22;-2.22;-2.22	4.72	4.72	0.59763	Peptidase C2, calpain, catalytic domain (3);	0.049774	0.85682	D	0.000000	T	0.79569	0.4468	L	0.31926	0.97	0.80722	D	1	B;B;B;B	0.18461	0.028;0.022;0.01;0.028	B;B;B;B	0.22753	0.041;0.035;0.021;0.041	T	0.72821	-0.4177	10	0.02654	T	1	.	16.8563	0.86007	0.0:1.0:0.0:0.0	.	260;262;262;222	Q59GM2;E7EV01;Q6ZRM8;O15484	.;.;.;CAN5_HUMAN	Y	222;262;222;262;262	ENSP00000278559:H222Y;ENSP00000432332:H222Y;ENSP00000409996:H262Y	ENSP00000278559:H222Y	H	+	1	0	CAPN5	76503093	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.902000	0.56310	2.438000	0.82558	0.655000	0.94253	CAC	.		0.592	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		T	76825445	C	T	76825445	3	4	105	1	0	0	0	0	1	0	0	0	2635	710	25	2	678	2	CAPN5	11	76825445	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	19563967	76825445	58181071	32	9358											
USP35	57558	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	77921303	77921303	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggagctgagccaagggcCgtgctacctcatcctcacac	8	7	12	14	1	2	1	2	1	0	0	3	2	3	2	4	3	4	2	4	3	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:77921303C>T	ENST00000529308.1	+	10	2663	c.2402C>T	c.(2401-2403)cCg>cTg	p.P801L	USP35_ENST00000441408.2_Missense_Mutation_p.P387L|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000530267.1_Missense_Mutation_p.P369L|USP35_ENST00000526425.1_Missense_Mutation_p.P532L	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	801	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			AGCCAAGGGCCGTGCTACCTC	0.622																																					p.P801L		.											.	USP35-637	0			c.C2402T						.						86	98	94					11																	77921303		2167	4250	6417	SO:0001583	missense	57558	exon10			AAGGGCCGTGCTA	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"Ubiquitin-specific peptidases"	20061	protein-coding gene	gene with protein product			"ubiquitin specific protease 35"			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.2402C>T	11.37:g.77921303C>T	ENSP00000431876:p.Pro801Leu	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	112	8	NM_020798	0	0	7	8	1		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572013	0.86542	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	4.35	4.35	0.52113	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000019	D	0.96457	0.8844	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98113	1.0421	10	0.87932	D	0	-41.8622	17.0748	0.86583	0.0:1.0:0.0:0.0	.	801;387	Q9P2H5;E7EWV7	UBP35_HUMAN;.	L	369;801;387;532	ENSP00000435468:P369L;ENSP00000431876:P801L;ENSP00000400825:P387L;ENSP00000434942:P532L	ENSP00000400825:P387L	P	+	2	0	USP35	77598951	1.000000	0.71417	0.993000	0.49108	0.817000	0.46193	7.600000	0.82769	2.257000	0.74773	0.436000	0.28706	CCG	.		0.622	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		T	77921303	C	T	77921303	3	4	105	1	0	0	0	0	1	0	0	0	17099	652	23	1	2436	1	USP35	11	77921303	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	1095858	77921303	57085213	33	9359											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877713	82877713	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaaaactggcaaagttccAagtctgccaaaagatggaaa	18	7	9	7	0	1	2	0	0	1	2	2	3	2	3	2	2	2	2	2	2	8	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:82877713A>G	ENST00000298281.4	+	5	2226	c.1774A>G	c.(1774-1776)Aag>Gag	p.K592E		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	592					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GCAAAGTTCCAAGTCTGCCAA	0.368																																					p.K592E		.											.	PCF11-23	0			c.A1774G						.						71	71	71					11																	82877713		1781	3947	5728	SO:0001583	missense	51585	exon5			AGTTCCAAGTCTG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1774A>G	11.37:g.82877713A>G	ENSP00000298281:p.Lys592Glu	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	156	29	NM_015885	0	0	8	11	3	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.926781	0.52759	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.49720	1.75;0.79;0.77	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000007	T	0.58293	0.2112	L	0.32530	0.975	0.49687	D	0.999816	D;D	0.69078	0.997;0.993	D;D	0.75020	0.985;0.971	T	0.54801	-0.8239	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	592;592	E9PQ01;O94913	.;PCF11_HUMAN	E	592	ENSP00000298281:K592E;ENSP00000434540:K592E;ENSP00000431567:K592E	.	K	+	1	0	PCF11	82555361	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.414000	0.73318	2.326000	0.78906	0.533000	0.62120	AAG	.		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877713	A	G	82877713	3	3	105	1	0	0	0	0	1	0	0	0	11599	131	5	3	1792	3	PCF11	11	82877713	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08	4956410	82877713	52128803	34	9360											
ATF7	11016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53910964	53910964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtggggtcatgattacatgcGattgtatcggcatgctcagt	8	13	13	7	2	2	1	2	1	0	0	3	2	2	1	0	3	3	3	0	3	2	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr12:53910964G>A	ENST00000548446.2	-	12	1554	c.1442C>T	c.(1441-1443)tCg>tTg	p.S481L	RP11-793H13.3_ENST00000548347.1_RNA|ATF7_ENST00000328463.7_Missense_Mutation_p.S481L|ATF7_ENST00000456903.4_Missense_Mutation_p.S470L|ATF7_ENST00000420353.2_Missense_Mutation_p.S470L|RP11-793H13.10_ENST00000591834.1_Intron|ATF7_ENST00000415113.1_Missense_Mutation_p.S449L|ATF7_ENST00000546661.1_5'UTR			P17544	ATF7_HUMAN	activating transcription factor 7	481	Essential for binding adenovirus 2 E1A.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	GATTACATGCGATTGTATCGG	0.587																																					p.S470L		.											.	ATF7-455	0			c.C1409T						.						112	109	110					12																	53910964		2075	4216	6291	SO:0001583	missense	11016	exon12			ACATGCGATTGTA	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"basic leucine zipper proteins"	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.1442C>T	12.37:g.53910964G>A	ENSP00000449938:p.Ser481Leu	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	184	36	NM_006856	0	0	33	50	17	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Missense_Mutation	SNP	ENST00000548446.2	37		.	.	.	.	.	.	.	.	.	.	G	24.4	4.522447	0.85600	.	.	ENSG00000170653	ENST00000548446;ENST00000328463;ENST00000306727;ENST00000415113;ENST00000420353;ENST00000456903	T;T;T;T;T	0.56776	0.47;0.47;0.44;0.49;0.49	4.47	4.47	0.54385	.	0.132552	0.52532	D	0.000064	T	0.43233	0.1238	L	0.53249	1.67	0.54753	D	0.999981	P;P;B	0.46327	0.876;0.804;0.0	B;B;B	0.28553	0.091;0.042;0.001	T	0.58797	-0.7573	10	0.87932	D	0	-16.9898	16.5074	0.84276	0.0:0.0:1.0:0.0	.	449;470;481	P17544-2;B2RMP1;P17544	.;.;ATF7_HUMAN	L	481;481;294;449;470;470	ENSP00000449938:S481L;ENSP00000329212:S481L;ENSP00000404880:S449L;ENSP00000399465:S470L;ENSP00000387406:S470L	ENSP00000304187:S294L	S	-	2	0	ATF7	52197231	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.990000	0.76225	2.513000	0.84729	0.456000	0.33151	TCG	.		0.587	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		A	53910964	G	A	53910964	3	1	105	1	0	0	0	0	1	0	0	0	1087	1059	37	1	46	1	ATF7	12	53910964	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		53910964	79940931	35	9361											
SMARCC2	6601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56558339	56558339	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcggggaggttaatactgaTggagtcagctagactaccaa	13	8	13	7	1	1	2	1	1	0	1	1	4	1	4	1	4	4	2	1	4	5	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr12:56558339T>C	ENST00000267064.4	-	27	3402	c.3316A>G	c.(3316-3318)Atc>Gtc	p.I1106V	SMARCC2_ENST00000347471.4_Intron|SMARCC2_ENST00000550164.1_Missense_Mutation_p.I1137V|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000394023.3_Intron	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1106	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TTAATACTGATGGAGTCAGCT	0.587																																					p.I1106V		.											.	SMARCC2-229	0			c.A3316G						.						103	89	94					12																	56558339		2203	4300	6503	SO:0001583	missense	6601	exon27			TACTGATGGAGTC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.3316A>G	12.37:g.56558339T>C	ENSP00000267064:p.Ile1106Val	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	120	42	NM_003075	0	0	29	76	47	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.300338	0.23650	.	.	ENSG00000139613	ENST00000550164;ENST00000267064	T;T	0.44881	0.91;0.94	5.28	3.99	0.46301	.	0.593150	0.16689	N	0.203617	T	0.20577	0.0495	N	0.08118	0	0.25483	N	0.987717	B	0.02656	0.0	B	0.01281	0.0	T	0.19811	-1.0294	9	.	.	.	-5.712	7.8812	0.29623	0.0:0.1805:0.0:0.8195	.	1106	Q8TAQ2	SMRC2_HUMAN	V	1137;1106	ENSP00000449396:I1137V;ENSP00000267064:I1106V	.	I	-	1	0	SMARCC2	54844606	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.211000	0.32382	0.832000	0.34804	0.460000	0.39030	ATC	.		0.587	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			C	56558339	T	C	56558339	3	2	105	1	0	0	0	0	1	0	0	0	14808	1464	51	3	336	3	SMARCC2	12	56558339	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	2647375	56558339	77293556	36	9362											
VSIG10	54621	hgsc.bcm.edu	37	chr12	118506354	118506354	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcctcctcctcctcctcTtcctcttctgaatccaccaa	5	14	1	21	0	3	1	0	1	3	0	11	1	11	1	9	0	0	0	9	0	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr12:118506354T>C	ENST00000359236.5	-	8	1671	c.1395A>G	c.(1393-1395)gaA>gaG	p.E465E		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	465	Glu-rich.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						cctcctcctcttcctcttcTG	0.458																																					p.E465E		.											.	.	0			c.A1395G						.						97	90	93					12																	118506354		2037	4183	6220	SO:0001819	synonymous_variant	54621	exon8			CTCCTCTTCCTCT		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1395A>G	12.37:g.118506354T>C		Somatic	35	1		WXS	Illumina HiSeq	Phase_I	26	2	NM_019086	0	0	18	18	0	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			.		0.458	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		C	118506354	T	C	118506354	2	2	105	1	0	0	0	0	0	0	0	1	17256	1606	56	3		3	VSIG10	12	118506354	Silent	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	61948015	118506354	15345541	37	9363											
GCH1	2643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55310765	55310765	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgagagtcaggaactcttcCcgagtctttggatcctcccg	8	11	10	12	2	3	1	1	1	2	1	6	5	6	3	3	2	1	0	3	2	1	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr14:55310765C>T	ENST00000491895.2	-	6	911	c.723G>A	c.(721-723)cgG>cgA	p.R241R	GCH1_ENST00000254299.4_5'UTR|GCH1_ENST00000395514.1_Silent_p.R241R|GCH1_ENST00000543643.2_Intron|GCH1_ENST00000536224.2_Intron	NM_000161.2	NP_000152.1	P30793	GCH1_HUMAN	GTP cyclohydrolase 1	241			R -> W (in DYT5). {ECO:0000269|PubMed:9778264}.		7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|dopamine biosynthetic process (GO:0042416)|GTP catabolic process (GO:0006184)|metabolic process (GO:0008152)|negative regulation of blood pressure (GO:0045776)|neuromuscular process controlling posture (GO:0050884)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric-oxide synthase activity (GO:0051000)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|pteridine-containing compound biosynthetic process (GO:0042559)|regulation of blood pressure (GO:0008217)|regulation of lung blood pressure (GO:0014916)|regulation of nitric-oxide synthase activity (GO:0050999)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to pain (GO:0048265)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)|tetrahydrofolate biosynthetic process (GO:0046654)|vasodilation (GO:0042311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|coenzyme binding (GO:0050662)|GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(2)|lung(7)|skin(2)	11						GGAACTCTTCCCGAGTCTTTG	0.493																																					p.R241R	Pancreas(198;1245 2204 4807 21567 38372)	.											.	GCH1-91	0			c.G723A						.						185	145	158					14																	55310765		2203	4300	6503	SO:0001819	synonymous_variant	2643	exon6			CTCTTCCCGAGTC	U19523	CCDS9720.1, CCDS41954.1, CCDS45110.1	14q22.1-q22.2	2014-04-01	2008-08-01		ENSG00000131979	ENSG00000131979	3.5.4.16		4193	protein-coding gene	gene with protein product	"dopa-responsive dystonia"	600225	"dystonia 14"	GCH, DYT5, DYT14		7874165, 8695054	Standard	XM_005267530		Approved	GTPCH1, DYT5a	uc001xbi.1	P30793	OTTHUMG00000029754	ENST00000491895.2:c.723G>A	14.37:g.55310765C>T		Somatic	164	1		WXS	Illumina HiSeq	Phase_I	155	24	NM_000161	0	0	11	11	0	Q6FHY7|Q9Y4I8	Silent	SNP	ENST00000491895.2	37	CCDS9720.1																																																																																			.		0.493	GCH1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276895.3			T	55310765	C	T	55310765	2	4	105	1	0	0	0	0	0	0	0	1	6311	610	22	2		2	GCH1	14	55310765	Silent	SNP	C	TCGA-DZ-6134-01A-11D-1961-08		55310765	52038775	38	9364											
BTBD6	90135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	105716270	105716270	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatcattgtcactcgggaggCcctcaacaccaaagaggcgg	11	6	12	12	2	3	1	3	0	0	1	4	3	3	2	2	4	1	0	2	4	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr14:105716270C>T	ENST00000392554.3	+	4	1016	c.719C>T	c.(718-720)gCc>gTc	p.A240V	BRF1_ENST00000546474.1_Intron|BRF1_ENST00000551787.1_5'Flank|BRF1_ENST00000440513.3_Intron|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000536364.1_Missense_Mutation_p.A240V|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000463376.2_Missense_Mutation_p.A165V|BTBD6_ENST00000327471.3_Missense_Mutation_p.A165V|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000379932.4_5'Flank			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	240						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		ACTCGGGAGGCCCTCAACACC	0.617																																					p.A240V		.											.	BTBD6-90	0			c.C719T						.						30	27	28					14																	105716270		2201	4298	6499	SO:0001583	missense	90135	exon5			GGGAGGCCCTCAA	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"BTB/POZ domain containing"	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.719C>T	14.37:g.105716270C>T	ENSP00000376337:p.Ala240Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	44	7	NM_033271	0	0	47	71	24	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	37	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920172	0.52653	.	.	ENSG00000184887	ENST00000536364;ENST00000537513;ENST00000392554;ENST00000463376;ENST00000327471	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.07	5.07	0.68467	BTB/Kelch-associated (2);	0.118294	0.64402	D	0.000020	T	0.66218	0.2767	L	0.39898	1.24	0.48511	D	0.999668	B	0.29341	0.242	B	0.39935	0.314	T	0.69011	-0.5258	10	0.87932	D	0	-31.8506	15.9457	0.79792	0.0:1.0:0.0:0.0	.	240	Q96KE9	BTBD6_HUMAN	V	240;240;240;165;165	ENSP00000443091:A240V;ENSP00000446223:A240V;ENSP00000376337:A240V;ENSP00000418150:A165V;ENSP00000329361:A165V	ENSP00000329361:A165V	A	+	2	0	BTBD6	104787315	1.000000	0.71417	1.000000	0.80357	0.093000	0.18481	7.655000	0.83696	2.331000	0.79229	0.563000	0.77884	GCC	.		0.617	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4			T	105716270	C	T	105716270	3	4	105	1	0	0	0	0	1	0	0	0	1548	739	26	2	733	2	BTBD6	14	105716270	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	50405505	105716270	1633270	39	9365											
MYO5C	55930	broad.mit.edu	37	chr15	52504078	52504078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccacgccacggggcttcAagtctgaagcagagagagcc	11	4	12	14	2	2	3	1	1	1	2	2	4	2	3	4	2	2	2	4	2	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr15:52504078A>G	ENST00000261839.7	-	35	4306	c.4145T>C	c.(4144-4146)tTg>tCg	p.L1382S		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1382						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ACGGGGCTTCAAGTCTGAAGC	0.537																																					p.L1382S													.	MYO5C-145	0			c.T4145C						.						55	57	57					15																	52504078		2055	4216	6271	SO:0001583	missense	55930	exon35			GGCTTCAAGTCTG	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.4145T>C	15.37:g.52504078A>G	ENSP00000261839:p.Leu1382Ser	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	87	3	NM_018728	0	0	0	0	0	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.588593	0.86851	.	.	ENSG00000128833	ENST00000261839	T	0.25749	1.78	5.26	5.26	0.73747	.	0.000000	0.64402	D	0.000009	T	0.48095	0.1481	M	0.81802	2.56	0.80722	D	1	P	0.51449	0.945	P	0.55615	0.78	T	0.54616	-0.8267	10	0.87932	D	0	.	15.3487	0.74363	1.0:0.0:0.0:0.0	.	1382	Q9NQX4	MYO5C_HUMAN	S	1382	ENSP00000261839:L1382S	ENSP00000261839:L1382S	L	-	2	0	MYO5C	50291370	1.000000	0.71417	0.927000	0.36925	0.965000	0.64279	9.139000	0.94554	2.208000	0.71279	0.460000	0.39030	TTG	.		0.537	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52504078	A	G	52504078	3	3	105	1	0	0	0	0	1	0	0	0	10105	131	5	3	1111	3	MYO5C	15	52504078	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		52504078	50027314	40	9366											
ACAN	176	hgsc.bcm.edu	37	chr15	89389052	89389052	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgggccctgccacggcattCaccagtgaggacctcgtcgt	6	8	12	15	3	1	1	1	1	0	0	3	2	1	2	4	3	1	1	4	3	0	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr15:89389052C>G	ENST00000561243.1	+	6	1368	c.1368C>G	c.(1366-1368)ttC>ttG	p.F456L	ACAN_ENST00000559004.1_Missense_Mutation_p.F456L|ACAN_ENST00000439576.2_Missense_Mutation_p.F456L|ACAN_ENST00000352105.7_Missense_Mutation_p.F456L|ACAN_ENST00000558207.1_Missense_Mutation_p.F456L			P16112	PGCA_HUMAN	aggrecan	456					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CCACGGCATTCACCAGTGAGG	0.647																																					p.F456L		.											.	ACAN-25	0			c.C1368G						.						15	17	17					15																	89389052		2006	4159	6165	SO:0001583	missense	176	exon7			GGCATTCACCAGT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.1368C>G	15.37:g.89389052C>G	ENSP00000453342:p.Phe456Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_001135	0	0	2	2	0	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.531494	0.45073	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02158	4.65;4.42	5.37	4.46	0.54185	.	0.247838	0.21313	N	0.076607	T	0.03305	0.0096	M	0.66939	2.045	0.35117	D	0.766671	P;P;P	0.42908	0.793;0.793;0.731	B;B;B	0.38842	0.283;0.283;0.184	T	0.49560	-0.8927	10	0.14656	T	0.56	-15.7967	10.4531	0.44535	0.0:0.9094:0.0:0.0906	.	456;456;456	E7ENV9;E7EX88;Q6PID9	.;.;.	L	456	ENSP00000387356:F456L;ENSP00000341615:F456L	ENSP00000268134:F456L	F	+	3	2	ACAN	87190056	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	2.606000	0.46291	1.412000	0.46977	0.655000	0.94253	TTC	.		0.647	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		G	89389052	C	G	89389052	3	3	105	1	0	0	0	0	1	0	0	0	117	825	29	4	1390	4	ACAN	15	89389052	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	36884974	89389052	13142340	41	9367											
FAM86A	196483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	5140457	5140457	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtgaagactgccgggttcTcgatggcccattctgcaagg	8	10	13	10	2	2	2	0	1	2	1	3	3	2	2	2	3	2	2	2	3	3	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr16:5140457T>A	ENST00000427587.4	-	5	520	c.452A>T	c.(451-453)gAg>gTg	p.E151V	FAM86A_ENST00000458008.4_Missense_Mutation_p.E117V|FAM86A_ENST00000587133.1_Missense_Mutation_p.E90V	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	151						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						TGCCGGGTTCTCGATGGCCCA	0.642																																					p.E151V		.											.	FAM86A-90	0			c.A452T						.						86	84	85					16																	5140457		2197	4300	6497	SO:0001583	missense	196483	exon5			GGGTTCTCGATGG	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.452A>T	16.37:g.5140457T>A	ENSP00000398502:p.Glu151Val	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	159	16	NM_201400	0	0	18	21	3	D3DUF0|Q96S85	Missense_Mutation	SNP	ENST00000427587.4	37	CCDS10529.1	.	.	.	.	.	.	.	.	.	.	t	17.73	3.461895	0.63513	.	.	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.20200	2.09;2.09	5.02	5.02	0.67125	.	0.188239	0.45867	D	0.000338	T	0.21761	0.0524	N	0.26042	0.785	0.44337	D	0.997227	P;P	0.40731	0.682;0.728	P;P	0.46850	0.522;0.529	T	0.02042	-1.1224	10	0.51188	T	0.08	.	12.2508	0.54597	0.0:0.0:0.0:1.0	.	117;151	Q96G04-2;Q96G04	.;FA86A_HUMAN	V	117;151	ENSP00000389710:E117V;ENSP00000398502:E151V	ENSP00000398502:E151V	E	-	2	0	FAM86A	5080458	0.999000	0.42202	0.910000	0.35882	0.241000	0.25554	6.872000	0.75536	2.117000	0.64856	0.370000	0.22315	GAG	.		0.642	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400		A	5140457	T	A	5140457	3	1	105	1	0	0	0	0	1	0	0	0	5662	1551	54	5	556	5	FAM86A	16	5140457	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08		5140457	85214296	42	9368											
TPPP3	51673	broad.mit.edu;bcgsc.ca	37	chr16	67424233	67424233	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtgtatctgctggtgtccgtCagccggtctacagcaccccc	5	10	11	15	2	3	0	1	0	2	0	4	0	4	0	4	2	4	3	4	2	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr16:67424233C>G	ENST00000564104.1	-	3	1216	c.375G>C	c.(373-375)ctG>ctC	p.L125L	TPPP3_ENST00000393957.2_Silent_p.L125L|RNU1-123P_ENST00000458950.1_RNA|TPPP3_ENST00000290942.5_Silent_p.L125L|TPPP3_ENST00000562206.1_Silent_p.L125L			Q9BW30	TPPP3_HUMAN	tubulin polymerization-promoting protein family member 3	125					microtubule bundle formation (GO:0001578)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	tubulin binding (GO:0015631)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0336)|Epithelial(162;0.0781)		TGGTGTCCGTCAGCCGGTCTA	0.617																																					p.L125L													.	TPPP3-90	0			c.G375C						.						129	119	122					16																	67424233		2198	4300	6498	SO:0001819	synonymous_variant	51673	exon5			GTCCGTCAGCCGG	BC000691	CCDS10835.1	16q22.1	2008-02-05			ENSG00000159713	ENSG00000159713			24162	protein-coding gene	gene with protein product						15590652, 17105200	Standard	XM_005255979		Approved	CGI-38, p25gamma, p20	uc002etb.3	Q9BW30	OTTHUMG00000137516	ENST00000564104.1:c.375G>C	16.37:g.67424233C>G		Somatic	261	0		WXS	Illumina HiSeq	Phase_I	255	7	NM_016140	0	0	49	50	1	Q49AH9|Q9Y326|Q9Y6H0	Silent	SNP	ENST00000564104.1	37	CCDS10835.1																																																																																			.		0.617	TPPP3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421787.2	NM_015964		G	67424233	C	G	67424233	2	3	105	1	0	0	0	0	0	0	0	1	16448	813	29	4		4	TPPP3	16	67424233	Silent	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	62283776	67424233	22930520	43	9369											
MYH2	4620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10426831	10426831	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	accctggcctccagtttctgGatctgcttcttcccaccctt	4	14	6	17	0	3	0	0	0	3	0	5	1	5	1	5	2	1	2	5	2	0	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:10426831G>A	ENST00000245503.5	-	37	5838	c.5454C>T	c.(5452-5454)atC>atT	p.I1818I	MYH2_ENST00000397183.2_Silent_p.I1818I|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1818					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CCAGTTTCTGGATCTGCTTCT	0.507																																					p.I1818I		.											.	MYH2-194	0			c.C5454T						.						97	103	101					17																	10426831		2203	4300	6503	SO:0001819	synonymous_variant	4620	exon37			TTTCTGGATCTGC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"Myosins / Myosin superfamily : Class II"	7572	protein-coding gene	gene with protein product		160740	"myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant"	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.5454C>T	17.37:g.10426831G>A		Somatic	190	0		WXS	Illumina HiSeq	Phase_I	230	82	NM_017534	0	0	50	50	0	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			.		0.507	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10426831	G	A	10426831	2	1	105	1	0	0	0	0	0	0	0	1	10060	1164	41	2		2	MYH2	17	10426831	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		10426831	70768379	44	9370											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000519970.1_Intron|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR	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	265	268					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	395	46		WXS	Illumina HiSeq		462	56	NM_145301	0	0	10	77	67	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		T	15457087	C	T	15457087	3	4	105	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	5030256	15457087	65738123	45	9371											
RHBDL3	162494	bcgsc.ca	37	chr17	30632400	30632400	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgacatgaccgctccagtCgtgggctcttctggaggggt	5	10	15	11	2	2	2	0	2	2	0	4	3	3	3	2	4	0	3	2	4	0	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:30632400C>T	ENST00000269051.4	+	7	836	c.822C>T	c.(820-822)gtC>gtT	p.V274V	RHBDL3_ENST00000538145.1_Silent_p.V266V|RHBDL3_ENST00000536287.1_Silent_p.V176V	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	274						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				CCGCTCCAGTCGTGGGCTCTT	0.572																																					p.V274V													.	RHBDL3-91	0			c.C822T						.						174	140	151					17																	30632400		2203	4300	6503	SO:0001819	synonymous_variant	162494	exon7			TCCAGTCGTGGGC	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"EF-hand domain containing"	16502	protein-coding gene	gene with protein product			"rhomboid, veinlet-like 4 (Drosophila)"	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.822C>T	17.37:g.30632400C>T		Somatic	149	0		WXS	Illumina HiSeq	Phase_1	167	20	NM_138328	0	0	0	0	0	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Silent	SNP	ENST00000269051.4	37	CCDS32613.1																																																																																			.		0.572	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		T	30632400	C	T	30632400	2	4	105	1	0	0	0	0	0	0	0	1	13355	871	31	1		1	RHBDL3	17	30632400	Silent	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	15175313	30632400	50562810	46	9372											
RDM1	201299	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	34257138	34257138	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgccttttgggctctgtggGcagcccttgcagaataaaac	9	11	11	10	0	1	1	0	0	1	1	1	1	1	1	2	2	4	3	2	2	3	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:34257138G>A	ENST00000293273.6	-	2	263	c.218C>T	c.(217-219)gCc>gTc	p.A73V	RDM1_ENST00000394527.1_Missense_Mutation_p.A50V|RDM1_ENST00000394528.3_Missense_Mutation_p.A73V|RDM1_ENST00000431884.2_Missense_Mutation_p.A73V|RDM1_ENST00000591402.1_Missense_Mutation_p.A50V|RDM1_ENST00000430160.2_Missense_Mutation_p.A50V|RDM1_ENST00000425909.3_Missense_Mutation_p.A73V|RDM1_ENST00000419453.2_Missense_Mutation_p.A50V|RDM1_ENST00000394529.3_Missense_Mutation_p.A50V	NM_145654.3	NP_663629.1	Q8NG50	RDM1_HUMAN	RAD52 motif containing 1	73	Necessary for nuclear localization and for nucleolar accumulation in response to heat shock.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|kidney(3)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)	9		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GGCTCTGTGGGCAGCCCTTGC	0.493								Other identified genes with known or suspected DNA repair function																													p.A73V		.											.	RDM1-228	0			c.C218T						.						115	125	122					17																	34257138		2203	4300	6503	SO:0001583	missense	201299	exon2			CTGTGGGCAGCCC	AB080728	CCDS11301.1, CCDS42299.1, CCDS54111.1, CCDS54108.1, CCDS54109.1, CCDS54110.1, CCDS59280.1, CCDS59281.1	17q11.2	2014-04-10	2014-04-10	2005-10-20	ENSG00000187456	ENSG00000278023		"RNA binding motif (RRM) containing"	19950	protein-coding gene	gene with protein product		612896	"RAD52 homolog B (S. cerevisiae)", "RAD52 motif 1"	RAD52B		15611051	Standard	NM_001163120		Approved	MGC33977	uc002hkh.3	Q8NG50	OTTHUMG00000188399	ENST00000293273.6:c.218C>T	17.37:g.34257138G>A	ENSP00000293273:p.Ala73Val	Somatic	271	0		WXS	Illumina HiSeq	Phase_I	361	23	NM_001034836	0	0	0	0	0	A0JP55|A8MV46|A8MY68|A8MZ92|A8RCS5|A8RCT0|A8RCT5|A8RCT8|A8RCU3|A8RCU8|A8RCW0|A8RCW5	Missense_Mutation	SNP	ENST00000293273.6	37	CCDS11301.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.807688	0.50421	.	.	ENSG00000187456	ENST00000293273;ENST00000394529;ENST00000431884;ENST00000425909;ENST00000436836;ENST00000430160;ENST00000394528;ENST00000394527	T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	3.78	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.134512	0.49916	D	0.000140	T	0.52108	0.1714	M	0.79475	2.455	0.35240	D	0.777732	D;D;P;P;P;D;D;D;P	0.54397	0.957;0.957;0.946;0.859;0.946;0.957;0.957;0.966;0.946	P;P;B;B;P;P;P;P;P	0.61874	0.751;0.491;0.41;0.41;0.636;0.491;0.545;0.895;0.636	T	0.67090	-0.5758	10	0.54805	T	0.06	-6.8607	13.5182	0.61553	0.0:0.0:1.0:0.0	.	50;50;73;73;50;50;73;73;50	B4DZ74;Q8NG50-4;Q8NG50-5;Q8NG50-10;Q8NG50-2;Q8NG50-11;A8MY68;Q8NG50;Q8NG50-6	.;.;.;.;.;.;.;RDM1_HUMAN;.	V	73;50;73;73;73;50;73;50	ENSP00000293273:A73V;ENSP00000378037:A50V;ENSP00000391290:A73V;ENSP00000393620:A73V;ENSP00000397431:A73V;ENSP00000413421:A50V;ENSP00000378036:A73V;ENSP00000378035:A50V	ENSP00000293273:A73V	A	-	2	0	RDM1	31281251	1.000000	0.71417	0.014000	0.15608	0.101000	0.19017	4.843000	0.62838	2.141000	0.66446	0.655000	0.94253	GCC	.		0.493	RDM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256588.2	NM_145654		A	34257138	G	A	34257138	3	1	105	1	0	0	0	0	1	0	0	0	13229	1203	42	2	704	2	RDM1	17	34257138	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	3624738	34257138	46938072	47	9373											
MLX	6945	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40720856	40720856	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccatctctgagcgtagaTgatgaggacagtgattacca	11	9	10	11	1	1	5	0	4	1	1	2	6	1	6	3	1	2	1	3	1	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:40720856T>C	ENST00000246912.4	+	4	386	c.333T>C	c.(331-333)gaT>gaC	p.D111D	MLX_ENST00000435881.2_Splice_Site_p.D57D|MLX_ENST00000346833.4_Splice_Site_p.D27D	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	111					energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		TGAGCGTAGATGATGAGGACA	0.607																																					p.D111D	GBM(121;657 1601 4665 24731 34640)	.											.	MLX-90	0			c.T333C						.						30	26	27					17																	40720856		2203	4300	6503	SO:0001630	splice_region_variant	6945	exon4			CGTAGATGATGAG	AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	11645	protein-coding gene	gene with protein product		602976	"transcription factor-like 4", "MAX-like protein X"	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.332-1T>C	17.37:g.40720856T>C		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	23	6	NM_170607	0	0	0	0	0	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Silent	SNP	ENST00000246912.4	37	CCDS11430.1																																																																																			.		0.607	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607	Silent	C	40720856	T	C	40720856	5	2	105	1	0	0	0	0	0	0	1	0	9660	1478	51	3	347	3	MLX	17	40720856	Splice_Site	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	6463718	40720856	40474354	48	9374											
KCNN1	3780	broad.mit.edu	37	chr19	18109140	18109140	+	Frame_Shift_Del	DEL	C	C	-																															cccctgcctcccaggcccggCcccggcccccaagaccaggc																										TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:18109140delC	ENST00000222249.9	+	11	1876	c.1557delC	c.(1555-1557)ggcfs	p.G519fs	ARRDC2_ENST00000379656.3_5'Flank	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	519				PLPPRPGPGPQDQAARSSPCRWTPVAPSDC -> RLPRQRA GLDH (in Ref. 3; BAD86831). {ECO:0000305}.	potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	CCAGGCCCGGCCCCGGCCCCC	0.751																																					p.G519fs													.	KCNN1-22	0			c.1557delC						.						2	3	3					19																	18109140		1429	3432	4861	SO:0001589	frameshift_variant	3780	exon11			GCCCGGCCCCGGC	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1557delC	19.37:g.18109140delC	ENSP00000476519:p.Gly519fs	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_002248	0	0	0	0	0	Q5KR10|Q6DJU4	Frame_Shift_Del	DEL	ENST00000222249.9	37																																																																																				.		0.751	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		-	18109140	C	-	18109140	7	5	105	1	0	1	0	1	0	0	0	0	8099	726	26	0	1591	0	KCNN1	19	18109140	Frame_Shift_Del	DEL	C	TCGA-DZ-6134-01A-11D-1961-08		18109140	41019843	49	9375											
NR2C2AP	126382	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	19313644	19313645	+	Frame_Shift_Ins	INS	-	-	T																															tcatcctggtcgaaaagatgINStttttttccaaactgccgag																										TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:19313644_19313645insT	ENST00000331552.7	-	2	447_448	c.84_85insA	c.(82-87)aaacatfs	p.H29fs	NR2C2AP_ENST00000544883.1_Frame_Shift_Ins_p.H29fs|NR2C2AP_ENST00000420605.3_Frame_Shift_Ins_p.H29fs|NR2C2AP_ENST00000538165.2_Frame_Shift_Ins_p.H29fs	NM_176880.4	NP_795361.1	Q86WQ0	NR2CA_HUMAN	nuclear receptor 2C2-associated protein	29					cell adhesion (GO:0007155)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|kidney(2)|ovary(1)	5			Epithelial(12;0.00235)			TCGAAAAGATGTTTTTTTCCAA	0.54																																					p.H29fs		.											.	NR2C2AP-23	0			c.85_86insA						.																																			SO:0001589	frameshift_variant	126382	exon2			.	AY101377	CCDS32967.1, CCDS74316.1	19p13.11	2008-01-10				ENSG00000184162			30763	protein-coding gene	gene with protein product	"TR4 orphan receptor associated protein TRA16"	608719				12486131	Standard	XM_005259740		Approved	TRA16	uc002nlx.3	Q86WQ0		ENST00000331552.7:c.85dupA	19.37:g.19313651_19313651dupT	ENSP00000332823:p.His29fs	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	116	20	NM_176880	0	0	0	0	0	A6NGP7|B4DW92	Frame_Shift_Ins	INS	ENST00000331552.7	37	CCDS32967.1																																																																																			.		0.54	NR2C2AP-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402936.4	NM_176880		T	19313645	-	T	19313644	7	5	105	1	0	1	1	0	0	0	0	0	10650	1377	48	0	350	0	NR2C2AP	19	19313644	Frame_Shift_Ins	INS	-	TCGA-DZ-6134-01A-11D-1961-08	1204504	19313644	39815339	50	9376											
MLL4	9757	ucsc.edu	37	chr19	36228069	36228069	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccccggagcccagcgttgCcagcactataagttccgtta	8	9	9	15	3	0	0	0	0	0	0	2	1	2	1	5	1	4	4	5	1	3	5			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:36228069C>G	ENST00000222270.7	+	33	7455	c.7455C>G	c.(7453-7455)tgC>tgG	p.C2485W	IGFLR1_ENST00000587101.1_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.C2485W	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2485	FYR C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00876}.				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCCAGCGTTGCCAGCACTATA	0.627																																					p.C2485W													.	MLL4-697	0			c.C7455G						.						19	22	21					19																	36228069		2107	4231	6338	SO:0001583	missense	8085	exon33			GCGTTGCCAGCAC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7455C>G	19.37:g.36228069C>G	ENSP00000222270:p.Cys2485Trp	Somatic	28	0		WXS	Illumina HiSeq		12	2	NM_014727	0	0	18	26	8	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	9.266	1.044498	0.19748	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	T;T	0.58210	0.35;0.35	4.8	1.51	0.23008	FY-rich, C-terminal (1);FY-rich, C-terminal subgroup (1);	0.000000	0.47093	D	0.000255	T	0.69205	0.3085	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69113	-0.5231	10	0.87932	D	0	.	9.2199	0.37370	0.0:0.7553:0.0:0.2447	.	2485	Q9UMN6	MLL4_HUMAN	W	2485	ENSP00000222270:C2485W;ENSP00000398837:C2485W	ENSP00000222270:C2485W	C	+	3	2	AD000671.1	40919909	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	1.334000	0.33827	0.243000	0.21327	-0.253000	0.11424	TGC	.		0.627	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		G	36228069	C	G	36228069	3	3	105	1	0	0	0	0	1	0	0	0	9648	747	26	4	7585	4	MLL4	19	36228069	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	16914425	36228069	22900914	51	9377											
ZNF568	374900	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	37441598	37441598	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaagcctttagtcagaaaTcaaacctcactgaacatgag	17	8	7	9	0	3	3	3	2	0	1	3	4	3	3	2	0	3	0	2	0	6	2	rs201711551		TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:37441598T>C	ENST00000333987.7	+	7	2049	c.1543T>C	c.(1543-1545)Tca>Cca	p.S515P	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.S451P	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	515					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)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAGTCAGAAATCAAACCTCAC	0.383													T|||	1	0.000199681	0	0	5008	,	,		19315	0		0.001	False		,,,				2504	0				p.S515P		.											.	ZNF568-136	0			c.T1543C						.	T	PRO/SER,PRO/SER,PRO/SER,,,PRO/SER	0,4270		0,0,2135	61	67	65		1540,1351,1351,,,1543	1.6	1	19		65	4,8558		0,4,4277	yes	missense,missense,missense,intron,intron,missense	ZNF568	NM_001204835.1,NM_001204836.1,NM_001204837.1,NM_001204838.1,NM_001204839.1,NM_198539.3	74,74,74,,,74	0,4,6412	CC,CT,TT		0.0467,0.0,0.0312	probably-damaging,probably-damaging,probably-damaging,,,probably-damaging	514/644,451/581,451/581,,,515/645	37441598	4,12828	2135	4281	6416	SO:0001583	missense	374900	exon7			CAGAAATCAAACC	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"Zinc fingers, C2H2-type", "-"	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1543T>C	19.37:g.37441598T>C	ENSP00000334685:p.Ser515Pro	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	101	15	NM_198539	0	0	2	2	0	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	14.80	2.645026	0.47258	0.0	4.67E-4	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.07908	3.15;3.15	3.96	1.61	0.23674	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.28847	N	0.013944	T	0.27765	0.0683	M	0.84433	2.695	0.23865	N	0.996623	D	0.89917	1.0	D	0.91635	0.999	T	0.02333	-1.1175	10	0.87932	D	0	.	9.0886	0.36596	0.0:0.0:0.346:0.654	.	515	Q3ZCX4	ZN568_HUMAN	P	515;451	ENSP00000334685:S515P;ENSP00000394514:S451P	ENSP00000334685:S515P	S	+	1	0	ZNF568	42133438	0.000000	0.05858	0.961000	0.40146	0.992000	0.81027	-0.500000	0.06405	0.660000	0.30964	0.383000	0.25322	TCA	T|1.000;C|0.000		0.383	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		C	37441598	T	C	37441598	3	2	105	1	0	0	0	0	1	0	0	0	18031	1435	50	3	1561	3	ZNF568	19	37441598	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	1213529	37441598	21687385	52	9378											
DHDH	27294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49447704	49447704	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtcccaaaggactgcaatTttgacaacggggcaggcatg	12	7	12	10	1	0	1	0	1	0	0	1	2	1	2	1	4	2	3	1	4	3	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:49447704T>G	ENST00000221403.2	+	6	875	c.835T>G	c.(835-837)Ttt>Gtt	p.F279V	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Missense_Mutation_p.F140V	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	279					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GGACTGCAATTTTGACAACGG	0.622																																					p.F279V		.											.	DHDH-90	0			c.T835G						.						65	63	63					19																	49447704		2203	4300	6503	SO:0001583	missense	27294	exon6			TGCAATTTTGACA	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.835T>G	19.37:g.49447704T>G	ENSP00000221403:p.Phe279Val	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	110	24	NM_014475	0	0	13	32	19		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.453658	0.63290	.	.	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.21361	2.01;2.01	4.89	3.87	0.44632	.	0.210406	0.49916	D	0.000136	T	0.23330	0.0564	M	0.77616	2.38	0.80722	D	1	B	0.27117	0.168	B	0.28638	0.092	T	0.05903	-1.0857	10	0.33940	T	0.23	-6.6788	6.733	0.23393	0.0:0.1029:0.0:0.8971	.	279	Q9UQ10	DHDH_HUMAN	V	279;140	ENSP00000221403:F279V;ENSP00000428935:F140V	ENSP00000221403:F279V	F	+	1	0	DHDH	54139516	1.000000	0.71417	0.040000	0.18447	0.014000	0.08584	4.583000	0.60964	2.183000	0.69458	0.402000	0.26972	TTT	.		0.622	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		G	49447704	T	G	49447704	3	3	105	1	0	0	0	0	1	0	0	0	4490	1841	64	5	857	5	DHDH	19	49447704	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	12006106	49447704	9681279	53	9379			1	31		2	2	25	T		4.57402e-05
DHDH	27294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49447728	49447728	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaacggggcaggcatgagtTatgaggccaagcacgtctgg	11	6	15	9	2	1	2	0	2	1	0	1	2	1	2	1	5	2	4	1	5	3	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:49447728T>A	ENST00000221403.2	+	6	899	c.859T>A	c.(859-861)Tat>Aat	p.Y287N	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Missense_Mutation_p.Y148N	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	287					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AGGCATGAGTTATGAGGCCAA	0.627																																					p.Y287N		.											.	DHDH-90	0			c.T859A						.						70	67	68					19																	49447728		2203	4300	6503	SO:0001583	missense	27294	exon6			ATGAGTTATGAGG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.859T>A	19.37:g.49447728T>A	ENSP00000221403:p.Tyr287Asn	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	116	20	NM_014475	0	0	16	25	9		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	T	34	5.369860	0.95900	.	.	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.24151	1.87;1.87	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.55784	0.1942	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.63301	-0.6668	10	0.59425	D	0.04	-13.1857	11.3361	0.49505	0.0:0.0:0.0:1.0	.	287	Q9UQ10	DHDH_HUMAN	N	287;148	ENSP00000221403:Y287N;ENSP00000428935:Y148N	ENSP00000221403:Y287N	Y	+	1	0	DHDH	54139540	0.999000	0.42202	0.059000	0.19551	0.914000	0.54420	6.248000	0.72418	2.252000	0.74401	0.402000	0.26972	TAT	.		0.627	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		A	49447728	T	A	49447728	3	1	105	1	0	0	0	0	1	0	0	0	4490	1754	61	5	881	5	DHDH	19	49447728	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	24	49447728	9681255	54	9380			1	31		2	2	25	T		4.57402e-05
ZSCAN18	65982	broad.mit.edu	37	chr19	58596700	58596700	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcacccccgcgggggcGgcctcctcgcaggcgcaccc	4	2	15	20	5	0	0	0	0	0	0	2	0	1	0	5	5	1	4	5	5	0	0	rs200010643	byFrequency	TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:58596700G>A	ENST00000240727.6	-	7	1284	c.885C>T	c.(883-885)gcC>gcT	p.A295A	ZSCAN18_ENST00000600404.1_Silent_p.A351A|ZSCAN18_ENST00000421612.2_Silent_p.A159A|ZSCAN18_ENST00000601144.1_Silent_p.A295A	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	295					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CCGCGGGGGCGGCCTCCTCGC	0.741													G|||	6	0.00119808	0.0038	0.0014	5008	,	,		12777	0		0	False		,,,				2504	0				p.A351A													.	ZSCAN18-90	0			c.C1053T						.						6	8	8					19																	58596700		1513	3173	4686	SO:0001819	synonymous_variant	65982	exon7			GGGGGCGGCCTCC	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"-", "Zinc fingers, C2H2-type"	21037	protein-coding gene	gene with protein product			"zinc finger protein 447"	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.885C>T	19.37:g.58596700G>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	26	4	NM_001145542	0	0	42	62	20	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Silent	SNP	ENST00000240727.6	37	CCDS12971.1																																																																																			G|0.998;A|0.002		0.741	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926		A	58596700	G	A	58596700	2	1	105	1	0	0	0	0	0	0	0	1	18262	1103	39	1		1	ZSCAN18	19	58596700	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	9148972	58596700	532283	55	9381											
C20orf141	128653	ucsc.edu;bcgsc.ca	37	chr20	2796280	2796281	+	Nonsense_Mutation	DNP	GC	GC	TT																															cagcaggaggctctactcctGcaaatgggtacagtctcagg																										TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr20:2796280_2796281GC>TT	ENST00000380589.4	+	2	531_532	c.357_358GC>TT	c.(355-360)ctGCaa>ctTTaa	p.Q120*	TMEM239_ENST00000380593.4_Intron|C20orf141_ENST00000603872.1_Nonsense_Mutation_p.Q120*|TMEM239_ENST00000554164.1_Intron|TMEM239_ENST00000380585.1_5'Flank|TMEM239_ENST00000361033.1_5'Flank	NM_080739.2	NP_542777.1	Q9NUB4	CT141_HUMAN	chromosome 20 open reading frame 141	120	Leu-rich.					integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	10						CTCTACTCCTGCAAATGGGTAC	0.629																																					p.Q120*													.	C20orf141-90	0			c.C358T						.																																			SO:0001587	stop_gained	128653	exon2			CTCCTGCAAATGG		CCDS13034.1	20p13	2012-10-30			ENSG00000258713	ENSG00000258713			16134	protein-coding gene	gene with protein product							Standard	NM_001256538		Approved	dJ860F19.4	uc002wgw.3	Q9NUB4	OTTHUMG00000031707	Exception_encountered	20.37:g.2796280_2796281delinsTT	ENSP00000369963:p.Gln120*	Somatic	95	0		WXS	Illumina HiSeq		83	10	NM_080739	0	0	0	0	0		Nonsense_Mutation	DNP	ENST00000380589.4	37	CCDS13034.1																																																																																			.		0.629	C20orf141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077644.2	NM_080739		TT	2796281	GC	TT	2796280	4	4	105	1	0	0	0	0	0	1	0	0	2095	1306	46	4	363	4	C20orf141	20	2796280	Nonsense_Mutation	DNP	GC	TCGA-DZ-6134-01A-11D-1961-08		2796280	60229240	56	9382											
NINL	22981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	25469911	25469912	+	Nonsense_Mutation	DNP	GC	GC	TA																															gctcgtattccttcaggactGctgcgaaccgctcctcctgg																										TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr20:25469911_25469912GC>TA	ENST00000278886.6	-	13	1718_1719	c.1645_1646GC>TA	c.(1645-1647)GCa>TAa	p.A549*	NINL_ENST00000422516.1_Nonsense_Mutation_p.A549*	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	549					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CTTCAGGACTGCTGCGAACCGC	0.614																																					p.A549*		.											.	NINL	0			c.G1645T						.																																			SO:0001587	stop_gained	22981	exon13			GGACTGCTGCGAA		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"EF-hand domain containing"	29163	protein-coding gene	gene with protein product	"ninein-like protein"	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.1645_1646delinsTA	20.37:g.25469911_25469912delinsTA	ENSP00000278886:p.Ala549*	Somatic	204	1		WXS	Illumina HiSeq	Phase_I	165	24		0	0	0	0	0	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Nonsense_Mutation	DNP	ENST00000278886.6	37	CCDS33452.1																																																																																			.		0.614	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		TA	25469912	GC	TA	25469911	4	4	105	1	0	0	0	0	0	1	0	0	10446	1319	46	4	2550	4	NINL	20	25469911	Nonsense_Mutation	DNP	GC	TCGA-DZ-6134-01A-11D-1961-08	22673631	25469911	37555609	57	9383											
TP53TG5	27296	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	44005872	44005872	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccagaggagatgcggagaatCtttggaacactgagcagtga	13	7	14	7	1	1	5	0	2	1	3	1	8	1	6	1	3	3	1	1	3	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr20:44005872C>G	ENST00000372726.3	-	3	390	c.234G>C	c.(232-234)aaG>aaC	p.K78N	TP53TG5_ENST00000537995.1_Missense_Mutation_p.K62N|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1-DBNDD2_ENST00000452133.1_Intron|TP53TG5_ENST00000494455.1_5'UTR	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	78					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						TGCGGAGAATCTTTGGAACAC	0.512																																					p.K78N		.											.	TP53TG5-90	0			c.G234C						.						168	155	160					20																	44005872		2203	4300	6503	SO:0001583	missense	27296	exon3			GAGAATCTTTGGA	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 10"	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.234G>C	20.37:g.44005872C>G	ENSP00000361811:p.Lys78Asn	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	185	11	NM_014477	0	0	0	0	0		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.593647	0.46214	.	.	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.18338	2.22;2.22	5.43	5.43	0.79202	.	1.020720	0.07785	N	0.953949	T	0.25195	0.0612	L	0.39898	1.24	0.09310	N	1	P	0.49090	0.919	P	0.48704	0.587	T	0.20438	-1.0275	10	0.66056	D	0.02	-0.733	12.8311	0.57746	0.0:0.8361:0.1639:0.0	.	78	Q9Y2B4	T53G5_HUMAN	N	78;62	ENSP00000361811:K78N;ENSP00000438374:K62N	ENSP00000361811:K78N	K	-	3	2	TP53TG5	43439286	0.039000	0.19947	0.020000	0.16555	0.437000	0.31866	2.319000	0.43788	2.720000	0.93068	0.591000	0.81541	AAG	.		0.512	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477		G	44005872	C	G	44005872	3	3	105	1	0	0	0	0	1	0	0	0	16424	912	32	4	650	4	TP53TG5	20	44005872	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	18535961	44005872	19019648	58	9384											
CHST7	56548	hgsc.bcm.edu	37	chrX	46434588	46434588	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgatgccttcgcgctcaacAtgactcgcggcgcggcctac	6	8	11	16	7	1	1	1	1	0	0	4	2	1	1	2	2	3	1	2	2	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chrX:46434588A>C	ENST00000276055.3	+	1	1370	c.1222A>C	c.(1222-1224)Atg>Ctg	p.M408L		NM_019886.2	NP_063939.2	Q9NS84	CHST7_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7	408					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|N-acetylglucosamine metabolic process (GO:0006044)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			breast(3)|endometrium(2)|kidney(1)|lung(2)	8						CGCGCTCAACATGACTCGCGG	0.746																																					p.M408L		.											.	CHST7-133	0			c.A1222C						.						1	1	1					X																	46434588		1003	1936	2939	SO:0001583	missense	56548	exon1			CTCAACATGACTC	AB040711	CCDS14268.1	Xp11.3	2008-02-05			ENSG00000147119	ENSG00000147119		"Sulfotransferases, membrane-bound"	13817	protein-coding gene	gene with protein product		300375				10781596	Standard	NM_019886		Approved	C6ST-2, C6ST2	uc004dgt.3	Q9NS84	OTTHUMG00000021423	ENST00000276055.3:c.1222A>C	X.37:g.46434588A>C	ENSP00000276055:p.Met408Leu	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_019886	0	0	0	0	0	O75667	Missense_Mutation	SNP	ENST00000276055.3	37	CCDS14268.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.226851	0.79576	.	.	ENSG00000147119	ENST00000276055	D	0.81908	-1.55	4.63	3.44	0.39384	Sulfotransferase domain (1);	0.103863	0.64402	D	0.000007	D	0.84857	0.5565	L	0.49455	1.56	0.39368	D	0.966037	D	0.60575	0.988	D	0.77557	0.99	T	0.80362	-0.1414	10	0.10636	T	0.68	-25.0942	8.8051	0.34932	0.8291:0.0:0.0:0.1709	.	408	Q9NS84	CHST7_HUMAN	L	408	ENSP00000276055:M408L	ENSP00000276055:M408L	M	+	1	0	CHST7	46319532	1.000000	0.71417	0.998000	0.56505	0.939000	0.58152	7.010000	0.76353	0.602000	0.29896	0.350000	0.21858	ATG	.		0.746	CHST7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056362.1	NM_019886		C	46434588	A	C	46434588	3	2	105	1	0	0	0	0	1	0	0	0	3415	217	8	5	1224	5	CHST7	23	46434588	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		46434588	108835972	59	9385											
SKI	6497	hgsc.bcm.edu	37	chr1	2160390	2160390	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgcggccgcggtgccggCgccggtgcccgcagccaccg	2	2	19	18	9	0	0	0	0	0	0	0	0	0	0	6	5	3	1	6	5	0	0	rs28384811	byFrequency	TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:2160390C>G	ENST00000378536.4	+	1	257	c.185C>G	c.(184-186)gCg>gGg	p.A62G		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	62					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		gcggtgccggcgccggTGCCC	0.776													C|||	229	0.0457268	0.0234	0.0576	5008	,	,		4535	0.0079		0.0706	False		,,,				2504	0.0808				p.A62G	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.C185G						.						1	1	1					1																	2160390		788	1840	2628	SO:0001583	missense	6497	exon1			TGCCGGCGCCGGT	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.185C>G	1.37:g.2160390C>G	ENSP00000367797:p.Ala62Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_003036	0	0	0	0	0	Q5SYT7	Missense_Mutation	SNP	ENST00000378536.4	37	CCDS39.1	102	0.046703296703296704	20	0.04065040650406504	28	0.07734806629834254	3	0.005244755244755245	51	0.06728232189973615	C	9.688	1.151208	0.21371	.	.	ENSG00000157933	ENST00000378536	D	0.95821	-3.82	2.3	2.3	0.28687	.	.	.	.	.	T	0.47857	0.1468	N	0.08118	0	0.45733	P	0.001363000000000003	D	0.57899	0.981	P	0.58520	0.84	T	0.76271	-0.3020	8	0.20519	T	0.43	-11.9718	7.7374	0.28823	0.0:1.0:0.0:0.0	rs28384811	62	P12755	SKI_HUMAN	G	62	ENSP00000367797:A62G	ENSP00000367797:A62G	A	+	2	0	SKI	2150250	0.994000	0.37717	0.998000	0.56505	0.971000	0.66376	0.878000	0.28126	1.104000	0.41587	0.185000	0.17295	GCG	C|0.953;G|0.047		0.776	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		G	2160390	C	G	2160390	3	3	106	1	0	0	0	0	1	0	0	0	14389	768	27	4	187	4	SKI	1	2160390	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		2160390	247090231	1	9386											
MCOLN3	55283	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	85491894	85491894	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctaatcacagatctaatgcaGaggattaatgaaaccaagca	18	8	7	8	0	2	3	1	1	1	2	2	4	2	4	1	1	3	2	1	1	5	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:85491894G>C	ENST00000370589.2	-	8	958	c.906C>G	c.(904-906)ctC>ctG	p.L302L	WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000370587.1_Silent_p.L302L|MCOLN3_ENST00000474447.1_5'Flank|MCOLN3_ENST00000341115.4_Silent_p.L246L	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	302					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ATCTAATGCAGAGGATTAATG	0.398																																					p.L302L		.											.	MCOLN3-91	0			c.C906G						.						133	121	125					1																	85491894		2203	4300	6503	SO:0001819	synonymous_variant	55283	exon8			AATGCAGAGGATT	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.906C>G	1.37:g.85491894G>C		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	116	44	NM_018298	0	0	2	2	0	Q5T4H5|Q5T4H6|Q9NV09	Silent	SNP	ENST00000370589.2	37	CCDS701.1																																																																																			.		0.398	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		C	85491894	G	C	85491894	2	2	106	1	0	0	0	0	0	0	0	1	9422	929	33	4		4	MCOLN3	1	85491894	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	83331504	85491894	163758727	2	9387											
LCE3D	84648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152552161	152552161	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcctccagagccatggccGcagccagagcccccgccttg	7	4	11	19	2	0	2	0	0	0	2	1	2	1	2	8	1	4	1	8	1	0	1	rs374860616		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:152552161G>A	ENST00000368787.3	-	2	308	c.252C>T	c.(250-252)tgC>tgT	p.C84C		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	84					keratinization (GO:0031424)					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGCCATGGCCGCAGCCAGAGC	0.622																																					p.C84C		.											.	LCE3D-68	0			c.C252T						.						63	76	72					1																	152552161		2202	4299	6501	SO:0001819	synonymous_variant	84648	exon2			ATGGCCGCAGCCA	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"Late cornified envelopes"	16615	protein-coding gene	gene with protein product		612616	"small proline rich-like (epidermal differentiation complex) 6B"	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.252C>T	1.37:g.152552161G>A		Somatic	280	2		WXS	Illumina HiSeq	Phase_I	251	86	NM_032563	0	0	0	0	0	Q3MIL1	Silent	SNP	ENST00000368787.3	37	CCDS1014.1																																																																																			.		0.622	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563		A	152552161	G	A	152552161	2	1	106	1	0	0	0	0	0	0	0	1	8693	1079	38	1		1	LCE3D	1	152552161	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	67060267	152552161	96698460	3	9388											
BCAN	63827	broad.mit.edu	37	chr1	156615922	156615922	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagctttagcagatgttctgGaaggagacagctcaggtaag	12	9	13	7	0	2	2	1	0	1	2	2	4	2	3	0	3	3	5	0	3	3	4			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:156615922G>C	ENST00000329117.5	+	2	412	c.76G>C	c.(76-78)Gaa>Caa	p.E26Q	RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.E26Q	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	26					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGATGTTCTGGAAGGAGACAG	0.602																																					p.E26Q													.	BCAN-516	0			c.G76C						.						42	42	42					1																	156615922		2203	4300	6503	SO:0001583	missense	63827	exon2			GTTCTGGAAGGAG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	23059	protein-coding gene	gene with protein product	"chondroitin sulfate proteoglycan 7", "brevican proteoglycan"	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.76G>C	1.37:g.156615922G>C	ENSP00000331210:p.Glu26Gln	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	62	3	NM_198427	0	0	33	33	0	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607180	0.46527	.	.	ENSG00000132692	ENST00000441358;ENST00000255029;ENST00000329117;ENST00000457777;ENST00000424639;ENST00000361588	T;T;T;T;T	0.23147	1.92;2.49;2.73;2.19;3.21	4.32	2.4	0.29515	.	0.251422	0.22825	N	0.055179	T	0.12603	0.0306	L	0.34521	1.04	0.22446	N	0.999092	P;D	0.56968	0.458;0.978	B;P	0.56788	0.188;0.806	T	0.06917	-1.0800	10	0.23302	T	0.38	-0.3806	5.4974	0.16809	0.2526:0.0:0.7474:0.0	.	26;26	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	Q	26	ENSP00000392731:E26Q;ENSP00000331210:E26Q;ENSP00000389898:E26Q;ENSP00000401709:E26Q;ENSP00000354925:E26Q	ENSP00000255029:E26Q	E	+	1	0	BCAN	154882546	1.000000	0.71417	0.965000	0.40720	0.563000	0.35712	2.206000	0.42779	1.143000	0.42306	0.462000	0.41574	GAA	.		0.602	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		C	156615922	G	C	156615922	3	2	106	1	0	0	0	0	1	0	0	0	1346	1175	41	4	78	4	BCAN	1	156615922	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	4063761	156615922	92634699	4	9389											
TTC15	51112	hgsc.bcm.edu	37	chr2	3391827	3391827	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcccaggcagcgaagccGcgcgcccggagcaggagcct	8	2	16	15	5	0	0	0	0	0	0	1	3	1	2	4	4	4	2	4	4	1	0	rs145175293		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:3391827G>C	ENST00000324266.5	+	2	628	c.433G>C	c.(433-435)Gcg>Ccg	p.A145P	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.A145P	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	145					vesicle-mediated transport (GO:0016192)												CAGCGAAGCCGCGCGCCCGGA	0.776																																					p.A145P		.											.	.	0			c.G433C						.						2	2	2					2																	3391827		1349	3030	4379	SO:0001583	missense	51112	exon2			GAAGCCGCGCGCC	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.433G>C	2.37:g.3391827G>C	ENSP00000324318:p.Ala145Pro	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_016030	0	0	0	5	5	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	G	7.378	0.628213	0.14257	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	T;T	0.58060	0.36;0.36	4.53	-5.23	0.02798	.	5.681270	0.00166	N	0.000004	T	0.48223	0.1488	N	0.14661	0.345	0.09310	N	1	P;B;D	0.61080	0.625;0.001;0.989	B;B;P	0.54026	0.221;0.001;0.74	T	0.53781	-0.8390	10	0.45353	T	0.12	.	12.8907	0.58069	0.8464:0.0:0.1536:0.0	.	128;145;145	E7ENL7;Q8WVT3;Q53S18	.;TPC12_HUMAN;.	P	145;128;145	ENSP00000371544:A145P;ENSP00000324318:A145P	ENSP00000303612:A128P	A	+	1	0	TTC15	3370834	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.236000	0.09003	-1.229000	0.02564	-0.142000	0.14014	GCG	G|0.999;A|0.001		0.776	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		C	3391827	G	C	3391827	3	2	106	1	0	0	0	0	1	0	0	0	16715	1087	38	4	435	4	TTC15	2	3391827	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		3391827	239807546	5	9390											
SPRED2	200734	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	65561771	65561771	+	Frame_Shift_Del	DEL	C	C	-																															cttcgattgctttccttactCccctgtcaaaggctcgggca																										TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:65561771delC	ENST00000356388.4	-	3	530	c.341delG	c.(340-342)ggafs	p.G114fs	SPRED2_ENST00000474228.1_5'UTR|SPRED2_ENST00000443619.2_Frame_Shift_Del_p.G111fs	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	114	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TTTCCTTACTCCCCTGTCAAA	0.413																																					p.G114fs		.											.	SPRED2-659	0			c.341delG						.						157	146	150					2																	65561771		2203	4300	6503	SO:0001589	frameshift_variant	200734	exon3			.	AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.341delG	2.37:g.65561771delC	ENSP00000348753:p.Gly114fs	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	192	68	NM_181784	0	0	0	0	0	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Frame_Shift_Del	DEL	ENST00000356388.4	37	CCDS33211.1																																																																																			.		0.413	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1			-	65561771	C	-	65561771	7	5	106	1	0	1	0	1	0	0	0	0	15125	855	30	0	931	0	SPRED2	2	65561771	Frame_Shift_Del	DEL	C	TCGA-DZ-6135-01A-11D-1961-08	62169944	65561771	177637602	6	9391											
ACTG2	72	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74128513	74128513	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcaggcttcgcaggagaTgatgccccccgggctgtctt	7	8	14	12	2	1	2	0	1	1	1	2	3	1	2	3	4	1	4	3	4	1	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:74128513T>C	ENST00000409624.1	+	3	718	c.75T>C	c.(73-75)gaT>gaC	p.D25D	ACTG2_ENST00000409731.3_Silent_p.D25D|ACTG2_ENST00000409918.1_Silent_p.D25D|ACTG2_ENST00000345517.3_Silent_p.D25D			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	25					muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			large_intestine(3)|lung(14)|skin(1)	18						TCGCAGGAGATGATGCCCCCC	0.622																																					p.D25D		.											.	ACTG2-90	0			c.T75C						.						71	65	67					2																	74128513		2203	4300	6503	SO:0001819	synonymous_variant	72	exon2			AGGAGATGATGCC		CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3		1710027, 1673027	Standard	NM_001199893		Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409624.1:c.75T>C	2.37:g.74128513T>C		Somatic	69	1		WXS	Illumina HiSeq	Phase_I	95	32	NM_001199893	0	0	0	0	0	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Silent	SNP	ENST00000409624.1	37	CCDS1930.1																																																																																			.		0.622	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615		C	74128513	T	C	74128513	2	2	106	1	0	0	0	0	0	0	0	1	197	1461	51	3		3	ACTG2	2	74128513	Silent	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	8566742	74128513	169070860	7	9392											
SULT1C4	27233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	108994906	108994906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgacatctgggataagaTctggaacttccaagccaagc	12	9	10	10	0	2	2	0	1	2	1	3	4	3	4	2	2	3	0	2	2	4	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:108994906T>C	ENST00000272452.2	+	1	439	c.113T>C	c.(112-114)aTc>aCc	p.I38T	SULT1C4_ENST00000409309.3_Missense_Mutation_p.I38T	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	38					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						TGGGATAAGATCTGGAACTTC	0.473																																					p.I38T		.											.	SULT1C4-22	0			c.T113C						.						171	176	174					2																	108994906		2203	4300	6503	SO:0001583	missense	27233	exon1			ATAAGATCTGGAA	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.113T>C	2.37:g.108994906T>C	ENSP00000272452:p.Ile38Thr	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	315	134	NM_006588	0	0	135	293	158	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	37	CCDS2077.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.318519	0.81469	.	.	ENSG00000198075	ENST00000272452;ENST00000409309	T;T	0.01918	4.56;4.56	5.06	5.06	0.68205	.	0.127728	0.35555	N	0.003129	T	0.04452	0.0122	N	0.08118	0	0.31369	N	0.680401	P;D;D	0.63880	0.954;0.993;0.991	P;D;D	0.68765	0.476;0.96;0.918	T	0.35773	-0.9775	10	0.66056	D	0.02	.	14.1553	0.65413	0.0:0.0:0.0:1.0	.	38;38;38	Q08AS5;O75897;Q6PD90	.;ST1C4_HUMAN;.	T	38	ENSP00000272452:I38T;ENSP00000387225:I38T	ENSP00000272452:I38T	I	+	2	0	SULT1C4	108361338	0.999000	0.42202	1.000000	0.80357	0.870000	0.49936	4.416000	0.59815	2.125000	0.65367	0.496000	0.49642	ATC	.		0.473	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		C	108994906	T	C	108994906	3	2	106	1	0	0	0	0	1	0	0	0	15411	1435	50	3	115	3	SULT1C4	2	108994906	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	34866393	108994906	134204467	8	9393											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	170145584	170145584	+	Frame_Shift_Del	DEL	A	A	-																															gatgatataacctgggggacAaaaacacgctcctccatacg																										TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:170145584delA	ENST00000263816.3	-	9	1279	c.994delT	c.(994-996)tgtfs	p.C332fs	LRP2_ENST00000443831.1_Frame_Shift_Del_p.C332fs	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	332	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CCTGGGGGACAAAAACACGCT	0.483																																					p.C332fs		.											.	LRP2-175	0			c.994delT						.						107	105	106					2																	170145584		2203	4300	6503	SO:0001589	frameshift_variant	4036	exon9			.		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.994delT	2.37:g.170145584delA	ENSP00000263816:p.Cys332fs	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	142	41	NM_004525	0	0	0	0	0	O00711|Q16215	Frame_Shift_Del	DEL	ENST00000263816.3	37	CCDS2232.1																																																																																			.		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170145584	A	-	170145584	7	5	106	1	0	1	0	1	0	0	0	0	8981	130	5	0	13257	0	LRP2	2	170145584	Frame_Shift_Del	DEL	A	TCGA-DZ-6135-01A-11D-1961-08	61150678	170145584	73053789	9	9394											
ROBO1	6091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	78683096	78683096	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttacttaccagatgtactaCtgccccggtctgagctgttg	7	13	9	12	1	1	2	0	1	1	1	1	2	1	2	3	1	6	3	3	1	4	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:78683096C>A	ENST00000464233.1	-	24	3583	c.3470G>T	c.(3469-3471)aGt>aTt	p.S1157I	ROBO1_ENST00000467549.1_Missense_Mutation_p.S1057I|ROBO1_ENST00000495273.1_Missense_Mutation_p.S1112I|ROBO1_ENST00000436010.2_Missense_Mutation_p.S1118I	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1157					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AGATGTACTACTGCCCCGGTC	0.423																																					p.S1157I		.											.	ROBO1-67	0			c.G3470T						.						224	211	215					3																	78683096		1928	4130	6058	SO:0001583	missense	6091	exon24			GTACTACTGCCCC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3470G>T	3.37:g.78683096C>A	ENSP00000420321:p.Ser1157Ile	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	155	38	NM_002941	0	0	0	0	0	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.301088|4.301088	0.81136|0.81136	.|.	.|.	ENSG00000169855|ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414|ENST00000472273	D;D;D;D|.	0.91464|.	-2.85;-2.85;-2.85;-2.85|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74756|0.74756	0.3758|0.3758	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	D;B;D;P;P|.	0.76494|.	0.997;0.27;0.999;0.754;0.866|.	D;B;D;B;B|.	0.83275|.	0.994;0.082;0.996;0.293;0.376|.	T|T	0.70912|0.70912	-0.4743|-0.4743	9|5	.|.	.|.	.|.	.|.	20.1001|20.1001	0.97870|0.97870	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1121;1157;1112;1057;1118|.	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4|.	.;ROBO1_HUMAN;.;.;.|.	I|L	1118;1112;1157;1112;1057;1161|84	ENSP00000406043:S1118I;ENSP00000420321:S1157I;ENSP00000420637:S1112I;ENSP00000417992:S1057I|.	.|.	S|V	-|-	2|1	0|0	ROBO1|ROBO1	78765786|78765786	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.595000|0.595000	0.36748|0.36748	7.466000|7.466000	0.80914|0.80914	2.760000|2.760000	0.94817|0.94817	0.655000|0.655000	0.94253|0.94253	AGT|GTA	.		0.423	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78683096	C	A	78683096	3	1	106	1	0	0	0	0	1	0	0	0	13545	565	20	4	1517	4	ROBO1	3	78683096	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		78683096	119339334	10	9395											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376148	113376148	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgctgctgctgctgctgctTtatgtagagatggttactat	6	16	11	8	0	0	1	0	0	0	1	0	2	0	1	0	1	7	8	0	1	4	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:113376148T>G	ENST00000478658.1	-	5	4398	c.4381A>C	c.(4381-4383)Aag>Cag	p.K1461Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.K1461Q			Q68DE3	K2018_HUMAN	KIAA2018	1461	Gln-rich.					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						tgctgctgctTTATGTAGAGA	0.498																																					p.K1461Q		.											.	KIAA2018-93	0			c.A4381C						.						66	71	69					3																	113376148		2179	4278	6457	SO:0001583	missense	205717	exon7			GCTGCTTTATGTA	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.4381A>C	3.37:g.113376148T>G	ENSP00000420721:p.Lys1461Gln	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	105	7	NM_001009899	0	0	6	6	0	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.802014	0.50315	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.31247	1.5;1.5	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.45296	0.1335	L	0.32530	0.975	0.49213	D	0.999766	D	0.71674	0.998	D	0.78314	0.991	T	0.41822	-0.9487	10	0.62326	D	0.03	-15.6625	15.5299	0.75952	0.0:0.0:0.0:1.0	.	1461	Q68DE3	K2018_HUMAN	Q	1461	ENSP00000320794:K1461Q;ENSP00000420721:K1461Q	ENSP00000320794:K1461Q	K	-	1	0	KIAA2018	114858838	1.000000	0.71417	0.987000	0.45799	0.600000	0.36913	7.182000	0.77689	2.254000	0.74563	0.459000	0.35465	AAG	.		0.498	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		G	113376148	T	G	113376148	3	3	106	1	0	0	0	0	1	0	0	0	8289	1850	64	5	2360	5	KIAA2018	3	113376148	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	34693052	113376148	84646282	11	9396											
SSR3	6747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	156266708	156266708	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaacctttcatctttctcCttccgagacatctttctatt	8	18	2	13	1	6	1	2	0	4	1	8	2	7	1	3	0	1	0	3	0	2	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:156266708C>A	ENST00000265044.2	-	3	439	c.345G>T	c.(343-345)aaG>aaT	p.K115N	SSR3_ENST00000496050.1_Missense_Mutation_p.K63N|SSR3_ENST00000467789.1_Missense_Mutation_p.K115N|SSR3_ENST00000463503.1_Missense_Mutation_p.K63N|SSR3_ENST00000476217.1_Missense_Mutation_p.K115N|SSR3_ENST00000478842.1_5'UTR	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	115					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CATCTTTCTCCTTCCGAGACA	0.363																																					p.K115N		.											.	SSR3-90	0			c.G345T						.						88	85	86					3																	156266708		2203	4300	6503	SO:0001583	missense	6747	exon3			TTTCTCCTTCCGA	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.345G>T	3.37:g.156266708C>A	ENSP00000265044:p.Lys115Asn	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	116	26	NM_007107	0	0	3	4	1	B2R7D0|B4E2P2|D3DNK5|Q549M4	Missense_Mutation	SNP	ENST00000265044.2	37	CCDS3176.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955265	0.73902	.	.	ENSG00000114850	ENST00000265044;ENST00000467789;ENST00000476217;ENST00000463503;ENST00000496050	.	.	.	5.41	2.62	0.31277	.	0.094589	0.64402	D	0.000001	T	0.79015	0.4375	M	0.87827	2.91	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.971	T	0.81282	-0.1003	9	0.87932	D	0	-1.3739	11.1574	0.48495	0.0:0.7892:0.0:0.2108	.	115;115	B4E2P2;Q9UNL2	.;SSRG_HUMAN	N	115;115;115;63;63	.	ENSP00000265044:K115N	K	-	3	2	SSR3	157749402	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.461000	0.35255	0.767000	0.33267	0.650000	0.86243	AAG	.		0.363	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107		A	156266708	C	A	156266708	3	1	106	1	0	0	0	0	1	0	0	0	15224	680	24	4	224	4	SSR3	3	156266708	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	42890560	156266708	41755722	12	9397											
HELQ	113510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	84342848	84342848	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagcaaggtataaagaacAaaagacagatatagcctgtt	18	9	9	5	0	0	4	0	1	0	3	0	4	0	4	1	1	3	3	1	1	9	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr4:84342848A>G	ENST00000295488.3	-	15	2979	c.2817T>C	c.(2815-2817)ttT>ttC	p.F939F	HELQ_ENST00000510985.1_Silent_p.F872F	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	939					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TATAAAGAACAAAAGACAGAT	0.343								Other identified genes with known or suspected DNA repair function																													p.F939F		.											.	HELQ-155	0			c.T2817C						.						84	83	84					4																	84342848		2203	4300	6503	SO:0001819	synonymous_variant	113510	exon15			AAGAACAAAAGAC	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2817T>C	4.37:g.84342848A>G		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	61	26	NM_133636	0	0	4	9	5	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			.		0.343	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		G	84342848	A	G	84342848	2	3	106	1	0	0	0	0	0	0	0	1	7068	127	5	3		3	HELQ	4	84342848	Silent	SNP	A	TCGA-DZ-6135-01A-11D-1961-08		84342848	106811428	13	9398											
BHMT	635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	78415091	78415091	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactctcccagttcgccagcTtcatcgagagttcctcagag	8	10	8	15	2	3	2	2	0	1	2	7	3	4	2	3	0	1	3	3	0	0	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:78415091T>C	ENST00000274353.5	+	3	283	c.176T>C	c.(175-177)cTt>cCt	p.L59P	DMGDH_ENST00000520388.1_Intron|BHMT_ENST00000524080.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	59	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				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)	GTTCGCCAGCTTCATCGAGAG	0.438																																					p.L59P		.											.	BHMT-91	0			c.T176C						.						99	94	95					5																	78415091		2203	4300	6503	SO:0001583	missense	635	exon3			GCCAGCTTCATCG	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.176T>C	5.37:g.78415091T>C	ENSP00000274353:p.Leu59Pro	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	112	42	NM_001713	0	0	0	0	0	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.611557	0.87258	.	.	ENSG00000145692	ENST00000274353	T	0.13089	2.62	5.6	5.6	0.85130	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.48390	0.1497	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.61237	-0.7103	10	0.87932	D	0	-13.4798	16.0786	0.80985	0.0:0.0:0.0:1.0	.	59	Q93088	BHMT1_HUMAN	P	59	ENSP00000274353:L59P	ENSP00000274353:L59P	L	+	2	0	BHMT	78450847	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.669000	0.83911	2.254000	0.74563	0.460000	0.39030	CTT	.		0.438	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		C	78415091	T	C	78415091	3	2	106	1	0	0	0	0	1	0	0	0	1426	1609	56	3	186	3	BHMT	5	78415091	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		78415091	102500169	14	9399											
PGGT1B	5229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	114573574	114573574	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcccatcttccagctgaaGggctctcaagcccgctaagc	8	8	8	17	1	2	1	1	1	2	0	5	1	4	1	4	1	3	3	4	1	3	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:114573574G>A	ENST00000419445.1	-	4	480	c.460C>T	c.(460-462)Ctt>Ttt	p.L154F	PGGT1B_ENST00000379615.3_Missense_Mutation_p.L154F	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	154					negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|protein geranylgeranylation (GO:0018344)|response to cytokine (GO:0034097)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)	CAAX-protein geranylgeranyltransferase activity (GO:0004662)|protein geranylgeranyltransferase activity (GO:0004661)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)		TCCAGCTGAAGGGCTCTCAAG	0.383																																					p.L154F		.											.	PGGT1B-90	0			c.C460T						.						72	78	76					5																	114573574		2201	4300	6501	SO:0001583	missense	5229	exon4			GCTGAAGGGCTCT		CCDS4116.1	5q23.1	2008-02-05			ENSG00000164219	ENSG00000164219			8895	protein-coding gene	gene with protein product		602031				8106351	Standard	NM_005023		Approved	GGTI, BGGI	uc003kqw.4	P53609	OTTHUMG00000128893	ENST00000419445.1:c.460C>T	5.37:g.114573574G>A	ENSP00000404676:p.Leu154Phe	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	188	79	NM_005023	0	0	16	28	12	Q5MJP9	Missense_Mutation	SNP	ENST00000419445.1	37	CCDS4116.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.254124	0.59212	.	.	ENSG00000164219	ENST00000419445;ENST00000379615	T;T	0.32515	1.45;1.45	5.47	4.6	0.57074	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.113305	0.64402	D	0.000008	T	0.64692	0.2621	M	0.91818	3.245	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	T	0.75164	-0.3414	10	0.66056	D	0.02	-11.4224	16.6769	0.85281	0.0:0.1298:0.8702:0.0	.	154;154	P53609-2;P53609	.;PGTB1_HUMAN	F	154	ENSP00000404676:L154F;ENSP00000368935:L154F	ENSP00000368935:L154F	L	-	1	0	PGGT1B	114601473	1.000000	0.71417	0.947000	0.38551	0.329000	0.28539	9.740000	0.98839	1.422000	0.47177	0.655000	0.94253	CTT	.		0.383	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023		A	114573574	G	A	114573574	3	1	106	1	0	0	0	0	1	0	0	0	11815	1000	35	2	697	2	PGGT1B	5	114573574	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	36158483	114573574	66341686	15	9400											
WDR55	54853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140049032	140049032	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctggccagtagtggccaTgaccagcgcctcaagttttg	7	11	11	12	1	1	1	1	1	0	0	2	1	2	1	5	2	1	2	5	2	2	4			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:140049032T>C	ENST00000358337.5	+	7	1182	c.945T>C	c.(943-945)caT>caC	p.H315H	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	315					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTAGTGGCCATGACCAGCGCC	0.632																																					p.H315H		.											.	WDR55-91	0			c.T945C						.						27	30	29					5																	140049032		2203	4300	6503	SO:0001819	synonymous_variant	54853	exon7			TGGCCATGACCAG	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"WD repeat domain containing"	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.945T>C	5.37:g.140049032T>C		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	45	18	NM_017706	0	0	24	37	13	Q9NXK4	Silent	SNP	ENST00000358337.5	37	CCDS4235.1																																																																																			.		0.632	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		C	140049032	T	C	140049032	2	2	106	1	0	0	0	0	0	0	0	1	17340	1461	51	3		3	WDR55	5	140049032	Silent	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	25475458	140049032	40866228	16	9401											
FGFR4	2264	broad.mit.edu;ucsc.edu	37	chr5	176522539	176522539	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactccctctgcagggcccCtgtacgtgatcgtggagtgc	5	9	12	15	2	1	1	0	1	1	0	3	2	2	2	4	2	3	2	4	2	1	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:176522539C>T	ENST00000292408.4	+	13	1881	c.1636C>T	c.(1636-1638)Ctg>Ttg	p.L546L	FGFR4_ENST00000393637.1_Silent_p.L506L|FGFR4_ENST00000502906.1_Silent_p.L546L|FGFR4_ENST00000292410.3_Silent_p.L506L|FGFR4_ENST00000393648.2_Silent_p.L478L	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	546	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	TGCAGGGCCCCTGTACGTGAT	0.716										TSP Lung(9;0.080)																											p.L546L													.	FGFR4-1460	0			c.C1636T						.						21	23	23					5																	176522539		2202	4299	6501	SO:0001819	synonymous_variant	2264	exon13			GGGCCCCTGTACG	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1636C>T	5.37:g.176522539C>T		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	13	3	NM_002011	0	0	0	0	0	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Silent	SNP	ENST00000292408.4	37	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	C	5.620	0.299077	0.10622	.	.	ENSG00000160867	ENST00000511076	D	0.84146	-1.81	5.29	2.13	0.27403	.	.	.	.	.	D	0.84147	0.5408	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.78969	-0.1994	5	.	.	.	.	8.5441	0.33410	0.0:0.6202:0.0:0.3798	.	.	.	.	L	177	ENSP00000424670:P177L	.	P	+	2	0	FGFR4	176455145	0.963000	0.33076	0.999000	0.59377	0.469000	0.32828	2.175000	0.42491	0.631000	0.30412	0.561000	0.74099	CCT	.		0.716	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			T	176522539	C	T	176522539	2	4	106	1	0	0	0	0	0	0	0	1	5887	680	24	2		2	FGFR4	5	176522539	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	36473507	176522539	4392721	17	9402											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390482	45390482	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaacagcagcagcagcagCaggaggcggcggcggcggct	10	1	18	12	4	0	0	0	0	0	0	0	1	0	1	0	6	7	7	0	6	1	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr6:45390482C>G	ENST00000371438.1	+	2	569	c.211C>G	c.(211-213)Cag>Gag	p.Q71E	RUNX2_ENST00000541979.1_Missense_Mutation_p.Q139E|RUNX2_ENST00000352853.5_Missense_Mutation_p.Q139E|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q57E|RUNX2_ENST00000371436.6_Missense_Mutation_p.Q71E|RUNX2_ENST00000371432.3_Missense_Mutation_p.Q57E|RUNX2_ENST00000465038.2_Missense_Mutation_p.Q71E|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q71E|RP1-244F24.1_ENST00000606796.1_RNA	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						gcagcagcagcaggaggcggc	0.716																																					p.Q71E		.											.	RUNX2-417	0			c.C211G						.						6	10	9					6																	45390482		1279	2789	4068	SO:0001583	missense	860	exon3			CAGCAGCAGGAGG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.211C>G	6.37:g.45390482C>G	ENSP00000360493:p.Gln71Glu	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_001024630	0	0	1	1	0	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985548	0.35036	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	3.45	3.45	0.39498	.	1.972660	0.03402	N	0.203449	T	0.19248	0.0462	N	0.14661	0.345	0.27094	N	0.962779	B;B;B	0.23806	0.033;0.055;0.091	B;B;B	0.20384	0.029;0.013;0.029	T	0.13818	-1.0495	10	0.02654	T	1	.	14.8379	0.70197	0.0:1.0:0.0:0.0	.	139;71;57	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	E	71;139;139;71;71;57;57	ENSP00000420707:Q71E;ENSP00000319087:Q139E;ENSP00000446290:Q139E;ENSP00000360493:Q71E;ENSP00000360491:Q71E;ENSP00000352514:Q57E;ENSP00000360486:Q57E	ENSP00000319087:Q139E	Q	+	1	0	RUNX2	45498460	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.268000	0.33062	1.622000	0.50330	0.407000	0.27541	CAG	.		0.716	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390482	C	G	45390482	3	3	106	1	0	0	0	0	1	0	0	0	13780	711	25	4	233	4	RUNX2	6	45390482	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		45390482	125724585	18	9403											
REV3L	5980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	111632330	111632330	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataagaaaaacttcctctgtAttccttggcaaagataaagt	16	12	6	7	0	1	2	0	0	1	2	3	2	3	2	2	1	1	2	2	1	7	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr6:111632330A>T	ENST00000358835.3	-	30	9191	c.8737T>A	c.(8737-8739)Tac>Aac	p.Y2913N	REV3L_ENST00000435970.1_Missense_Mutation_p.Y2835N|RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000368805.1_Missense_Mutation_p.Y2913N|REV3L_ENST00000368802.3_Missense_Mutation_p.Y2913N			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2913					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTTCCTCTGTATTCCTTGGCA	0.408								DNA polymerases (catalytic subunits)																													p.Y2913N		.											.	REV3L-294	0			c.T8737A						.						179	179	179					6																	111632330		2203	4300	6503	SO:0001583	missense	5980	exon29			CTCTGTATTCCTT	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8737T>A	6.37:g.111632330A>T	ENSP00000351697:p.Tyr2913Asn	Somatic	258	0		WXS	Illumina HiSeq	Phase_I	267	91	NM_002912	0	0	20	32	12	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	27.2	4.809421	0.90707	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.48	5.48	0.80851	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.069117	0.64402	D	0.000012	T	0.41026	0.1141	M	0.88310	2.945	0.58432	D	0.999999	D	0.69078	0.997	D	0.81914	0.995	T	0.52601	-0.8554	10	0.87932	D	0	-3.7627	15.5643	0.76277	1.0:0.0:0.0:0.0	.	2913	O60673	DPOLZ_HUMAN	N	2913;2913;2913;2835	ENSP00000357792:Y2913N;ENSP00000357795:Y2913N;ENSP00000351697:Y2913N;ENSP00000402003:Y2835N	ENSP00000351697:Y2913N	Y	-	1	0	REV3L	111739023	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.266000	0.95659	2.085000	0.62840	0.455000	0.32223	TAC	.		0.408	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111632330	A	T	111632330	3	4	106	1	0	0	0	0	1	0	0	0	13272	449	16	5	671	5	REV3L	6	111632330	Missense_Mutation	SNP	A	TCGA-DZ-6135-01A-11D-1961-08	66241848	111632330	59482737	19	9404											
ACTB	60	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5567465	5567465	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctggaaggtggacagcgAggccaggatggagccgccga	9	4	18	10	3	0	0	0	0	0	0	0	6	0	4	3	6	3	1	3	6	1	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:5567465A>G	ENST00000331789.5	-	6	1233	c.1042T>C	c.(1042-1044)Tcg>Ccg	p.S348P	ACTB_ENST00000464611.1_5'UTR|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	348					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GTGGACAGCGAGGCCAGGATG	0.592																																					p.S348P													.	ACTB-226	0			c.T1042C						.						70	74	72					7																	5567465		2203	4300	6503	SO:0001583	missense	60	exon6			ACAGCGAGGCCAG	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.1042T>C	7.37:g.5567465A>G	ENSP00000349960:p.Ser348Pro	Somatic	156	1		WXS	Illumina HiSeq	Phase_I	136	59	NM_001101	2	0	3918	7075	3155	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.178644	0.57692	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713	D	0.95518	-3.73	5.55	4.35	0.52113	.	0.000000	0.53938	D	0.000041	D	0.98798	0.9595	H	0.99855	4.85	0.43965	D	0.996645	D	0.76494	0.999	D	0.97110	1.0	D	0.98206	1.0470	10	0.87932	D	0	.	11.3082	0.49347	0.8643:0.0:0.0:0.1357	.	348	P60709	ACTB_HUMAN	P	348;324;320;267	ENSP00000349960:S348P	ENSP00000440549:S267P	S	-	1	0	ACTB	5533991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.985000	0.70556	2.114000	0.64651	0.529000	0.55759	TCG	.		0.592	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		G	5567465	A	G	5567465	3	3	106	1	0	0	0	0	1	0	0	0	193	304	11	3	89	3	ACTB	7	5567465	Missense_Mutation	SNP	A	TCGA-DZ-6135-01A-11D-1961-08		5567465	153571198	20	9405											
NFE2L3	9603	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	26223344	26223347	+	Frame_Shift_Del	DEL	TTCT	TTCT	-																															catctgaatgggacagatacTtctttctctctggaagactt																								rs370809004|rs534912151	byFrequency	TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:26223344_26223347delTTCT	ENST00000056233.3	+	3	1033_1036	c.774_777delTTCT	c.(772-777)acttctfs	p.TS258fs		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	258					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GGACAGATACTTCTTTCTCTCTGG	0.402																																					p.258_259del		.											.	NFE2L3-94	0			c.774_777del						.																																			SO:0001589	frameshift_variant	9603	exon3			.	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.774_777delTTCT	7.37:g.26223348_26223351delTTCT	ENSP00000056233:p.Thr258fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	129	39	NM_004289	0	0	0	0	0	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Frame_Shift_Del	DEL	ENST00000056233.3	37	CCDS5396.1																																																																																			.		0.402	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			-	26223347	TTCT	-	26223344	7	5	106	1	0	1	0	1	0	0	0	0	10395	1596	56	0	784	0	NFE2L3	7	26223344	Frame_Shift_Del	DEL	TTCT	TCGA-DZ-6135-01A-11D-1961-08	20655879	26223344	132915319	21	9406											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgccagtgaagtggaTggctttggaaagtctgcaaa	13	9	13	6	0	1	1	0	1	1	0	1	3	1	3	1	3	3	3	1	3	4	1	rs121913245		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000539704.1_Missense_Mutation_p.M120T|MET_ENST00000397752.3_Missense_Mutation_p.M1250T			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.M1268T(4)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	.						93	92	92					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3803T>C	7.37:g.116423474T>C	ENSP00000317272:p.Met1268Thr	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	61	25	NM_001127500	0	0	254	495	241	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	5.68	5.68	0.88126	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423474	T	C	116423474	3	2	106	1	0	0	0	0	1	0	0	0	9510	1464	51	3	3873	3	MET	7	116423474	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	90200130	116423474	42715189	22	9407											
ARHGEF5	7984	hgsc.bcm.edu	37	chr7	144060273	144060273	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gacaggcagaagaagaagagGaaacctcttcagataactct	17	6	10	8	0	3	5	1	0	2	5	3	7	3	6	1	2	2	1	1	2	5	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:144060273G>C	ENST00000056217.5	+	2	685	c.511G>C	c.(511-513)Gaa>Caa	p.E171Q	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	171					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					AGAAGAAGAGGAAACCTCTTC	0.478																																					p.E171Q		.											.	ARHGEF5-229	0			c.G511C						.						14	17	16					7																	144060273		1978	4028	6006	SO:0001583	missense	7984	exon2			GAAGAGGAAACCT	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"Rho guanine nucleotide exchange factors"	13209	protein-coding gene	gene with protein product	"transforming immortalized mammary oncogene", "guanine nucleotide regulatory protein TIM"	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.511G>C	7.37:g.144060273G>C	ENSP00000056217:p.Glu171Gln	Somatic	620	1		WXS	Illumina HiSeq	Phase_I	603	101	NM_005435	0	0	40	43	3	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.460416	0.26248	.	.	ENSG00000050327	ENST00000056217	T	0.75938	-0.98	4.33	3.43	0.39272	.	0.701833	0.11649	N	0.542925	T	0.67859	0.2938	L	0.52573	1.65	0.31376	N	0.679585	B	0.20550	0.046	B	0.17098	0.017	T	0.63950	-0.6521	9	.	.	.	.	11.5373	0.50645	0.0:0.2034:0.7966:0.0	.	171	Q12774	ARHG5_HUMAN	Q	171	ENSP00000056217:E171Q	.	E	+	1	0	ARHGEF5	143691206	0.974000	0.33945	0.055000	0.19348	0.059000	0.15707	1.548000	0.36201	1.009000	0.39289	0.650000	0.86243	GAA	.		0.478	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435		C	144060273	G	C	144060273	3	2	106	1	0	0	0	0	1	0	0	0	909	1175	41	4	513	4	ARHGEF5	7	144060273	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	27636799	144060273	15078390	23	9408											
TOPORS	10210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	32543270	32543270	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatggtcctggagtttcaTcatcccatggtgcctgacta	9	12	10	10	0	2	2	2	1	0	1	4	3	4	3	3	3	1	1	3	3	2	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:32543270T>C	ENST00000360538.2	-	3	1369	c.1253A>G	c.(1252-1254)gAt>gGt	p.D418G	TOPORS_ENST00000379858.1_Missense_Mutation_p.D353G	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	418					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TGGAGTTTCATCATCCCATGG	0.423																																					p.D418G		.											.	TOPORS-230	0			c.A1253G						.						126	126	126					9																	32543270		2203	4299	6502	SO:0001583	missense	10210	exon3			GTTTCATCATCCC	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1253A>G	9.37:g.32543270T>C	ENSP00000353735:p.Asp418Gly	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	140	59	NM_005802	0	0	22	38	16	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	9.322	1.058402	0.19987	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.18657	2.2;2.21	5.63	5.63	0.86233	.	0.140255	0.33199	N	0.005175	T	0.20292	0.0488	L	0.34521	1.04	0.52099	D	0.999947	P	0.47191	0.891	B	0.42522	0.39	T	0.01252	-1.1405	10	0.59425	D	0.04	-15.9255	14.84	0.70217	0.0:0.0:0.0:1.0	.	418	Q9NS56	TOPRS_HUMAN	G	418;353	ENSP00000353735:D418G;ENSP00000369187:D353G	ENSP00000353735:D418G	D	-	2	0	TOPORS	32533270	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	7.698000	0.84413	2.145000	0.66743	0.528000	0.53228	GAT	.		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32543270	T	C	32543270	3	2	106	1	0	0	0	0	1	0	0	0	16403	1435	50	3	1888	3	TOPORS	9	32543270	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		32543270	108670161	24	9409											
TNC	3371	hgsc.bcm.edu	37	chr9	117808884	117808922	+	In_Frame_Del	DEL	CATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	CATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	-																															aaaattgtcgaagaccccttCatcagctgtccaggacagac																										TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	CATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	CATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:117808884_117808922delCATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	ENST00000350763.4	-	17	5303_5341	c.4892_4930delCCACCCCAGACGGTTTCCGTCTGTCCTGGACAGCTGATG	c.(4891-4932)gccaccccagacggtttccgtctgtcctggacagctgatgaa>gaa	p.ATPDGFRLSWTAD1631del	TNC_ENST00000423613.2_Intron|TNC_ENST00000341037.4_In_Frame_Del_p.ATPDGFRLSWTAD1449del|TNC_ENST00000340094.3_In_Frame_Del_p.ATPDGFRLSWTAD1267del|TNC_ENST00000537320.1_Intron|TNC_ENST00000345230.3_Intron|TNC_ENST00000346706.3_In_Frame_Del_p.ATPDGFRLSWTAD1085del|TNC_ENST00000481475.1_5'Flank|TNC_ENST00000542877.1_In_Frame_Del_p.ATPDGFRLSWTAD1268del|TNC_ENST00000535648.1_In_Frame_Del_p.ATPDGFRLSWTAD1176del	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1631	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.T1641K(1)|p.D1634E(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AAGACCCCTTCATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGGCATCTGAAAC	0.494																																					p.1631_1644del		.											.	TNC-517	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.4892_4930del						.																																			SO:0001651	inframe_deletion	3371	exon17			.		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	5318	protein-coding gene	gene with protein product	"hexabrachion (tenascin)"	187380	"hexabrachion (tenascin C, cytotactin)", "deafness, autosomal dominant 56"	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.4892_4930delCCACCCCAGACGGTTTCCGTCTGTCCTGGACAGCTGATG	9.37:g.117808884_117808922delCATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	ENSP00000265131:p.Ala1631_Asp1643del	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	89	22	NM_002160	0	0	0	0	0	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	In_Frame_Del	DEL	ENST00000350763.4	37	CCDS6811.1																																																																																			.		0.494	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		-	117808922	CATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	-	117808884	7	5	106	1	0	1	0	1	0	0	0	0	16302	835	29	0	1723	0	TNC	9	117808884	In_Frame_Del	DEL	CATCAGCTGTCCAGGACAGACGGAAACCGTCTGGGGTGG	TCGA-DZ-6135-01A-11D-1961-08	85265614	117808884	23404547	25	9410											
SPTAN1	6709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131361264	131361264	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtgtatggcatgatgcccaGggtaagtttcgggtgctgtg	7	12	16	6	1	0	1	0	1	0	0	1	1	0	1	1	3	2	5	1	3	2	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:131361264G>T	ENST00000372731.4	+	26	3652	c.3542G>T	c.(3541-3543)aGg>aTg	p.R1181M	SPTAN1_ENST00000358161.5_Splice_Site_p.R1181M|SPTAN1_ENST00000372739.3_Splice_Site_p.R1181M|SPTAN1_ENST00000475367.1_3'UTR	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1181					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						ATGATGCCCAGGGTAAGTTTC	0.398																																					p.R1181M	NSCLC(120;833 1744 2558 35612 37579)	.											.	SPTAN1-158	0			c.G3542T						.						195	177	183					9																	131361264		2203	4300	6503	SO:0001630	splice_region_variant	6709	exon26			TGCCCAGGGTAAG	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3543+1G>T	9.37:g.131361264G>T		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	129	57	NM_003127	0	0	1	1	0	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758441	0.49468	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.51325	0.71;0.73;0.71	5.93	2.99	0.34606	.	0.237058	0.49916	D	0.000123	T	0.27419	0.0673	N	0.08118	0	0.41841	D	0.990122	B;B;P;P;P	0.37276	0.187;0.22;0.589;0.589;0.454	B;B;B;B;B	0.37047	0.121;0.188;0.24;0.24;0.121	T	0.13045	-1.0524	10	0.72032	D	0.01	.	10.0762	0.42362	0.2288:0.0:0.7712:0.0	.	1181;1161;1161;1181;1181	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	M	1181;1181;1181;1161	ENSP00000350882:R1181M;ENSP00000361816:R1181M;ENSP00000361824:R1181M	ENSP00000350882:R1181M	R	+	2	0	SPTAN1	130401085	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	1.468000	0.35332	0.342000	0.23796	0.555000	0.69702	AGG	.		0.398	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	Missense_Mutation	T	131361264	G	T	131361264	5	4	106	1	0	0	0	0	0	0	1	0	15149	1014	35	4	3640	4	SPTAN1	9	131361264	Splice_Site	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	13552380	131361264	9852167	26	9411											
AGPAT2	10555	bcgsc.ca	37	chr9	139581687	139581687	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagacgagcgaggccacggcGgacaccgtgaagcacagcgc	11	1	15	14	6	0	2	0	1	0	1	0	5	0	3	2	3	3	1	2	3	1	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:139581687G>A	ENST00000371696.2	-	1	188	c.123C>T	c.(121-123)tcC>tcT	p.S41S	AGPAT2_ENST00000371694.3_Silent_p.S41S|AGPAT2_ENST00000538402.1_Silent_p.S41S	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	41					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		AGGCCACGGCGGACACCGTGA	0.741																																					p.S41S													.	AGPAT2-90	0			c.C123T						.						16	20	18					9																	139581687		1969	3947	5916	SO:0001819	synonymous_variant	10555	exon1			CACGGCGGACACC	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	325	protein-coding gene	gene with protein product	"LPAAT-beta", "lysophosphatidic acid acyltransferase, beta"	603100	"Berardinelli-Seip congenital lipodystrophy", "1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.123C>T	9.37:g.139581687G>A		Somatic	70	0		WXS	Illumina HiSeq	Phase_1	68	6	NM_001012727	1	0	60	61	0	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	CCDS7003.1																																																																																			.		0.741	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		A	139581687	G	A	139581687	2	1	106	1	0	0	0	0	0	0	0	1	387	1103	39	1		1	AGPAT2	9	139581687	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	8220423	139581687	1631744	27	9412											
CHD4	1108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6711561	6711561	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcctttttttggcgcttgCtcttagggattttagggtcc	3	18	10	10	1	1	0	0	0	1	0	3	1	3	1	3	3	1	2	3	3	2	7			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr12:6711561C>G	ENST00000357008.2	-	3	366	c.203G>C	c.(202-204)aGc>aCc	p.S68T	CHD4_ENST00000544484.1_Missense_Mutation_p.S65T|CHD4_ENST00000309577.6_Missense_Mutation_p.S68T|CHD4_ENST00000544040.1_Missense_Mutation_p.S68T	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	68					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						TTGGCGCTTGCTCTTAGGGAT	0.478																																					p.S68T	Colon(32;586 792 4568 16848 45314)	.											.	CHD4-228	0			c.G203C						.						238	240	239					12																	6711561		2203	4300	6503	SO:0001583	missense	1108	exon3			CGCTTGCTCTTAG	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"Zinc fingers, PHD-type"	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.203G>C	12.37:g.6711561C>G	ENSP00000349508:p.Ser68Thr	Somatic	520	0		WXS	Illumina HiSeq	Phase_I	417	127	NM_001273	0	0	57	82	25	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660131	0.29515	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942;ENST00000545584	D;D;D;D;T	0.90197	-2.63;-2.6;-2.62;-2.63;0.88	5.26	5.26	0.73747	.	0.301114	0.34879	N	0.003602	D	0.84106	0.5399	L	0.36672	1.1	0.38243	D	0.941392	B;B;B	0.31817	0.341;0.231;0.341	B;B;B	0.28011	0.085;0.027;0.059	T	0.81773	-0.0779	10	0.12766	T	0.61	-0.8518	14.1344	0.65276	0.1501:0.8499:0.0:0.0	.	68;68;68	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	T	65;68;68;68;49;68;68	ENSP00000440392:S65T;ENSP00000440542:S68T;ENSP00000312419:S68T;ENSP00000349508:S68T;ENSP00000437506:S68T	ENSP00000312419:S68T	S	-	2	0	CHD4	6581822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.832000	0.55783	2.633000	0.89246	0.555000	0.69702	AGC	.		0.478	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		G	6711561	C	G	6711561	3	3	106	1	0	0	0	0	1	0	0	0	3333	797	28	4	5687	4	CHD4	12	6711561	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		6711561	127140334	28	9413											
LNX2	222484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	28143269	28143269	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgctccacaggcactgcGcctgtccccaaacagtctgc	7	7	9	18	2	1	0	0	0	1	0	3	0	3	0	5	1	4	2	5	1	1	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:28143269G>A	ENST00000316334.3	-	3	681	c.552C>T	c.(550-552)ggC>ggT	p.G184G		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	184					protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CAGGCACTGCGCCTGTCCCCA	0.532																																					p.G184G		.											.	LNX2-228	0			c.C552T						.						241	235	237					13																	28143269		2203	4300	6503	SO:0001819	synonymous_variant	222484	exon3			CACTGCGCCTGTC	AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"RING-type (C3HC4) zinc fingers"	20421	protein-coding gene	gene with protein product		609733	"PDZ domain containing ring finger 1"	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.552C>T	13.37:g.28143269G>A		Somatic	339	1		WXS	Illumina HiSeq	Phase_I	346	119	NM_153371	0	0	9	20	11	Q5W0P0|Q6ZMH2|Q96SH4	Silent	SNP	ENST00000316334.3	37	CCDS9323.1																																																																																			.		0.532	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			A	28143269	G	A	28143269	2	1	106	1	0	0	0	0	0	0	0	1	8889	1074	38	1		1	LNX2	13	28143269	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		28143269	87026609	29	9414											
KLHL1	57626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	70549759	70549759	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagactactgtacctatgtgCaggtatctttcggttcccaa	9	13	8	11	1	1	1	0	0	1	1	3	1	2	1	2	2	3	4	2	2	5	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:70549759C>G	ENST00000377844.4	-	2	1432	c.673G>C	c.(673-675)Gca>Cca	p.A225P	KLHL1_ENST00000545028.1_Intron	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	225	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TACCTATGTGCAGGTATCTTT	0.403																																					p.A225P		.											.	KLHL1-90	0			c.G673C						.						148	136	140					13																	70549759		2203	4300	6503	SO:0001583	missense	57626	exon2			TATGTGCAGGTAT	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"Kelch-like", "BTB/POZ domain containing"	6352	protein-coding gene	gene with protein product	"Kelch-like protein 1", "Mayven-related protein 2"	605332	"kelch (Drosophila)-like 1", "kelch-like 1 (Drosophila)"			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.673G>C	13.37:g.70549759C>G	ENSP00000367075:p.Ala225Pro	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	157	50	NM_020866	0	0	0	0	0	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	37	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	C	19.70	3.876217	0.72180	.	.	ENSG00000150361	ENST00000377844	T	0.78003	-1.14	5.82	5.82	0.92795	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.172430	0.41097	D	0.000941	D	0.92795	0.7709	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94480	0.7692	10	0.87932	D	0	.	20.0951	0.97834	0.0:1.0:0.0:0.0	.	225	Q9NR64	KLHL1_HUMAN	P	225	ENSP00000367075:A225P	ENSP00000367075:A225P	A	-	1	0	KLHL1	69447760	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.197000	0.77814	2.753000	0.94483	0.467000	0.42956	GCA	.		0.403	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70549759	C	G	70549759	3	3	106	1	0	0	0	0	1	0	0	0	8386	710	25	4	1613	4	KLHL1	13	70549759	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	42406490	70549759	44620119	30	9415											
AHNAK2	113146	ucsc.edu	37	chr14	105418145	105418145	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctccaggtcagcggaaggggGctgaatgctgaggtcagtgg	8	7	18	8	1	2	2	2	2	0	0	3	3	3	3	1	6	2	2	1	6	2	0	rs375277628	byFrequency	TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr14:105418145G>A	ENST00000333244.5	-	7	3762	c.3643C>T	c.(3643-3645)Ccc>Tcc	p.P1215S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1215						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCGGAAGGGGGCTGAATGCTG	0.647													.|||	6	0.00119808	0	0	5008	,	,		15037	0		0.001	False		,,,				2504	0.0051				p.P1215S													.	AHNAK2-47	0			c.C3643T						.	G	SER/PRO	2,3852		0,2,1925	96	70	79		3643	1.6	0	14		79	3,7607		0,3,3802	no	missense	AHNAK2	NM_138420.2	74	0,5,5727	AA,AG,GG		0.0394,0.0519,0.0436	benign	1215/5796	105418145	5,11459	1927	3805	5732	SO:0001583	missense	113146	exon7			AAGGGGGCTGAAT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3643C>T	14.37:g.105418145G>A	ENSP00000353114:p.Pro1215Ser	Somatic	90	0		WXS	Illumina HiSeq		45	1	NM_138420	0	0	97	137	40	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	9.389	1.074896	0.20227	5.19E-4	3.94E-4	ENSG00000185567	ENST00000333244	T	0.00840	5.63	4.55	1.58	0.23477	.	.	.	.	.	T	0.00695	0.0023	N	0.25201	0.72	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46512	-0.9186	9	0.08837	T	0.75	.	5.6981	0.17867	0.0766:0.3467:0.4538:0.1229	.	1215	Q8IVF2	AHNK2_HUMAN	S	1215	ENSP00000353114:P1215S	ENSP00000353114:P1215S	P	-	1	0	AHNAK2	104489190	.	.	0.009000	0.14445	0.004000	0.04260	.	.	0.383000	0.24910	-1.447000	0.01057	CCC	.		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105418145	G	A	105418145	3	1	106	1	0	0	0	0	1	0	0	0	415	1203	42	2	13748	2	AHNAK2	14	105418145	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		105418145	1931395	31	9416											
UBE3A	7337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	25616649	25616649	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagacacatcatcagggccTaatttttgcaaattgttgtc	12	13	7	9	0	2	1	2	0	0	1	3	1	2	1	1	1	1	2	1	1	2	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr15:25616649T>A	ENST00000397954.2	-	4	680	c.681A>T	c.(679-681)ttA>ttT	p.L227F	UBE3A_ENST00000428984.2_Missense_Mutation_p.L204F|UBE3A_ENST00000232165.3_Missense_Mutation_p.L224F|UBE3A_ENST00000566215.1_Missense_Mutation_p.L204F|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000438097.1_Missense_Mutation_p.L204F			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	227					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		CATCAGGGCCTAATTTTTGCA	0.418																																					p.L227F		.											.	UBE3A-660	0			c.A681T						.						179	174	176					15																	25616649		2203	4300	6503	SO:0001583	missense	7337	exon7			AGGGCCTAATTTT	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.681A>T	15.37:g.25616649T>A	ENSP00000381045:p.Leu227Phe	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	231	80	NM_000462	0	0	41	75	34	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	T	5.048	0.194522	0.09599	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	5.84	2.23	0.28157	.	0.385567	0.26421	N	0.024461	T	0.09992	0.0245	N	0.14661	0.345	0.47123	D	0.999328	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17684	-1.0361	10	0.09590	T	0.72	.	9.4825	0.38908	0.0:0.293:0.0:0.707	.	224;227	Q05086-3;Q05086	.;UBE3A_HUMAN	F	224;224;227;204;204	ENSP00000232165:L224F;ENSP00000381045:L227F;ENSP00000411258:L204F;ENSP00000401265:L204F	ENSP00000232165:L224F	L	-	3	2	UBE3A	23167742	0.789000	0.28775	0.833000	0.33012	0.928000	0.56348	-0.010000	0.12743	0.448000	0.26722	0.482000	0.46254	TTA	.		0.418	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		A	25616649	T	A	25616649	3	1	106	1	0	0	0	0	1	0	0	0	16912	1519	53	5	1978	5	UBE3A	15	25616649	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		25616649	76914743	32	9417											
CCDC78	124093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	775528	775528	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggactgcacagccctggctgGtgccatctcctcgcagctcc	5	8	11	17	1	1	0	0	0	1	0	4	1	2	1	4	3	4	4	4	3	0	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:775528G>T	ENST00000293889.6	-	4	425	c.320C>A	c.(319-321)aCc>aAc	p.T107N	HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000564545.1_5'Flank|HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000549114.1_5'Flank|HAGHL_ENST00000389703.3_5'Flank|HAGHL_ENST00000564537.1_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78	107					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				GCCCTGGCTGGTGCCATCTCC	0.652																																					p.T107N		.											.	CCDC78-91	0			c.C320A						.						55	53	53					16																	775528		2194	4297	6491	SO:0001583	missense	124093	exon4			TGGCTGGTGCCAT	BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.320C>A	16.37:g.775528G>T	ENSP00000293889:p.Thr107Asn	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	58	20	NM_001031737	0	0	0	0	0	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Missense_Mutation	SNP	ENST00000293889.6	37	CCDS32353.1	.	.	.	.	.	.	.	.	.	.	G	3.380	-0.126581	0.06795	.	.	ENSG00000162004	ENST00000293889	T	0.42900	0.96	3.03	0.647	0.17796	.	0.915341	0.09100	N	0.848716	T	0.18299	0.0439	N	0.08118	0	0.09310	N	1	P;P;P;B	0.39157	0.662;0.662;0.662;0.016	B;B;B;B	0.32624	0.149;0.106;0.149;0.015	T	0.12426	-1.0548	10	0.59425	D	0.04	-0.2556	3.877	0.09061	0.156:0.2512:0.5928:0.0	.	107;107;181;107	A2IDD5-4;A2IDD5-6;A2IDD5-5;A2IDD5	.;.;.;CCD78_HUMAN	N	107	ENSP00000293889:T107N	ENSP00000293889:T107N	T	-	2	0	CCDC78	715529	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.489000	0.06490	0.376000	0.24707	0.436000	0.28706	ACC	.		0.652	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476		T	775528	G	T	775528	3	4	106	1	0	0	0	0	1	0	0	0	2858	1261	44	4	1040	4	CCDC78	16	775528	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		775528	89579225	33	9418											
SNX29	92017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	12618621	12618621	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacctgcgcagcgtcatgaaCaaagtcatccagatggtccc	11	8	9	13	2	2	2	2	1	0	1	4	2	4	2	3	1	4	1	3	1	3	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:12618621C>T	ENST00000566228.1	+	20	2310	c.2241C>T	c.(2239-2241)aaC>aaT	p.N747N	SNX29_ENST00000306030.3_Silent_p.N362N|SNX29_ENST00000323433.4_Silent_p.N362N	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	747	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GCGTCATGAACAAAGTCATCC	0.522																																					p.N747N		.											.	SNX29-23	0			c.C2241T						.						94	101	99					16																	12618621		2049	4201	6250	SO:0001819	synonymous_variant	92017	exon20			CATGAACAAAGTC	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"Sorting nexins"	30542	protein-coding gene	gene with protein product			"RUN domain containing 2A"	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.2241C>T	16.37:g.12618621C>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	110	40	NM_032167	0	0	41	80	39	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			.		0.522	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			T	12618621	C	T	12618621	2	4	106	1	0	0	0	0	0	0	0	1	14930	477	17	2		2	SNX29	16	12618621	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	11843093	12618621	77736132	34	9419											
ABCC11	85320	ucsc.edu	37	chr16	48210875	48210875	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcccaccacttcgtggccGcggatggtcaggttgatgcc	6	9	13	13	3	1	1	1	1	0	0	2	2	1	2	4	4	2	1	4	4	0	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:48210875G>A	ENST00000394747.1	-	24	3847	c.3498C>T	c.(3496-3498)cgC>cgT	p.R1166R	ABCC11_ENST00000394748.1_Silent_p.R1166R|ABCC11_ENST00000353782.5_Silent_p.R1166R|ABCC11_ENST00000565329.1_5'UTR|ABCC11_ENST00000356608.2_Silent_p.R1166R	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	1166	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CTTCGTGGCCGCGGATGGTCA	0.577																																					p.R1166R													.	ABCC11-95	0			c.C3498T						.						134	105	115					16																	48210875		2201	4300	6501	SO:0001819	synonymous_variant	85320	exon24			GTGGCCGCGGATG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"ATP binding cassette transporters / subfamily C"	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.3498C>T	16.37:g.48210875G>A		Somatic	48	0		WXS	Illumina HiSeq		42	4	NM_033151	0	0	0	0	0	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			.		0.577	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		A	48210875	G	A	48210875	2	1	106	1	0	0	0	0	0	0	0	1	51	1074	38	1		1	ABCC11	16	48210875	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	35592254	48210875	42143878	35	9420											
ODF4	146852	broad.mit.edu	37	chr17	8243446	8243446	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcagagacctggaaaggAaaggaagagtggggaggcag	16	3	17	5	0	1	2	1	0	0	2	1	7	1	6	1	6	0	1	1	6	3	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:8243446A>G	ENST00000328248.2	+	1	265	c.77A>G	c.(76-78)gAa>gGa	p.E26G	ODF4_ENST00000584943.1_Missense_Mutation_p.E26G|RP11-849F2.4_ENST00000585275.1_lincRNA	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	26					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						CCTGGAAAGGAAAGGAAGAGT	0.552																																					p.E26G													.	ODF4-69	0			c.A77G						.						74	71	72					17																	8243446		2203	4300	6503	SO:0001583	missense	146852	exon1			GAAAGGAAAGGAA	AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"cancer/testis antigen 136"	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.77A>G	17.37:g.8243446A>G	ENSP00000331086:p.Glu26Gly	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_153007	0	0	0	0	0	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	.	.	.	.	.	.	.	.	.	.	A	7.376	0.627768	0.14257	.	.	ENSG00000184650	ENST00000328248	T	0.27890	1.64	4.24	-2.76	0.05896	.	1.415640	0.04533	N	0.386762	T	0.23727	0.0574	L	0.40543	1.245	0.09310	N	1	B	0.17667	0.023	B	0.12156	0.007	T	0.33624	-0.9861	10	0.66056	D	0.02	0.2811	4.8281	0.13427	0.35:0.3516:0.2984:0.0	.	26	Q2M2E3	ODFP4_HUMAN	G	26	ENSP00000331086:E26G	ENSP00000331086:E26G	E	+	2	0	ODF4	8184171	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.058000	0.11750	-0.667000	0.05303	-0.256000	0.11100	GAA	.		0.552	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1			G	8243446	A	G	8243446	3	3	106	1	0	0	0	0	1	0	0	0	10859	246	9	3	79	3	ODF4	17	8243446	Missense_Mutation	SNP	A	TCGA-DZ-6135-01A-11D-1961-08		8243446	72951764	36	9421											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y	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	265	268					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	365	46		WXS	Illumina HiSeq		443	62	NM_145301	0	0	6	66	60	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		T	15457087	C	T	15457087	3	4	106	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	7213641	15457087	65738123	37	9422											
FAM83G	644815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18881233	18881233	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttacgtagtcgtcatcatcTtcttcttccaccccatccag	7	14	5	15	2	5	0	2	0	3	0	8	0	7	0	4	0	1	2	4	0	2	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:18881233T>A	ENST00000388995.6	-	5	1969	c.1746A>T	c.(1744-1746)gaA>gaT	p.E582D	SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.E582D|FAM83G_ENST00000585154.2_Missense_Mutation_p.E582D|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000417251.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	582					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CGTCATCATCTTCTTCTTCCA	0.657																																					p.E582D		.											.	FAM83G-69	0			c.A1746T						.						46	53	51					17																	18881233		2011	4159	6170	SO:0001583	missense	644815	exon5			ATCATCTTCTTCT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1746A>T	17.37:g.18881233T>A	ENSP00000373647:p.Glu582Asp	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	131	44	NM_001039999	0	0	5	15	10	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.701515	0.68501	.	.	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.14640	2.49;2.49	5.72	-5.84	0.02318	.	0.665977	0.14951	N	0.288895	T	0.08313	0.0207	L	0.53249	1.67	0.21802	N	0.999537	B	0.21606	0.058	B	0.17098	0.017	T	0.35425	-0.9789	10	0.19590	T	0.45	-18.4782	3.4372	0.07450	0.0963:0.4161:0.1946:0.2931	.	582	A6ND36	FA83G_HUMAN	D	582	ENSP00000373647:E582D;ENSP00000343279:E582D	ENSP00000343279:E582D	E	-	3	2	FAM83G	18821958	0.010000	0.17322	0.616000	0.29078	0.890000	0.51754	-1.760000	0.01806	-0.435000	0.07264	0.533000	0.62120	GAA	.		0.657	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18881233	T	A	18881233	3	1	106	1	0	0	0	0	1	0	0	0	5658	1606	56	5	733	5	FAM83G	17	18881233	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	3424146	18881233	62313977	38	9423											
CDK5R1	8851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	30815101	30815101	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgagctgcttcgctgcCtgggtgagtttctctgccgc	3	12	13	13	2	1	2	0	2	1	0	3	2	1	2	3	1	4	4	3	1	0	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:30815101C>T	ENST00000313401.3	+	2	1152	c.463C>T	c.(463-465)Ctg>Ttg	p.L155L		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	155					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|ephrin receptor signaling pathway (GO:0048013)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|hippocampus development (GO:0021766)|ionotropic glutamate receptor signaling pathway (GO:0035235)|layer formation in cerebral cortex (GO:0021819)|negative regulation of axon extension (GO:0030517)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of neuron differentiation (GO:0045664)|rhythmic process (GO:0048511)|serine phosphorylation of STAT3 protein (GO:0033136)|superior olivary nucleus maturation (GO:0021722)	axon (GO:0030424)|contractile fiber (GO:0043292)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|cyclin-dependent protein kinase 5 activator activity (GO:0016534)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)			cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			GCTTCGCTGCCTGGGTGAGTT	0.667																																					p.L155L		.											.	CDK5R1-651	0			c.C463T						.						44	45	45					17																	30815101		2203	4300	6503	SO:0001819	synonymous_variant	8851	exon2			CGCTGCCTGGGTG	X80343	CCDS11273.1	17q12	2006-03-28			ENSG00000176749	ENSG00000176749			1775	protein-coding gene	gene with protein product		603460				8090221	Standard	NM_003885		Approved	p35nck5a, Nck5a	uc002hhn.3	Q15078	OTTHUMG00000132814	ENST00000313401.3:c.463C>T	17.37:g.30815101C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	68	26	NM_003885	0	0	2	3	1	E1P664|Q5U0G3	Silent	SNP	ENST00000313401.3	37	CCDS11273.1																																																																																			.		0.667	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885		T	30815101	C	T	30815101	2	4	106	1	0	0	0	0	0	0	0	1	3149	680	24	2		2	CDK5R1	17	30815101	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	11933868	30815101	50380109	39	9424											
ZNF700	90592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12060395	12060395	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgtgagaaaggcttttattCtgccaagtcatttcaaacac	13	13	7	8	0	3	1	2	1	1	1	3	2	3	1	1	1	2	1	1	1	4	4			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:12060395C>G	ENST00000254321.5	+	4	1699	c.1556C>G	c.(1555-1557)tCt>tGt	p.S519C	ZNF763_ENST00000591944.1_Intron|ZNF700_ENST00000482090.1_Missense_Mutation_p.S501C|ZNF763_ENST00000590798.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	519					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						GGCTTTTATTCTGCCAAGTCA	0.383																																					p.S522C		.											.	ZNF700-90	0			c.C1565G						.						59	63	62					19																	12060395		2203	4300	6503	SO:0001583	missense	90592	exon4			TTTATTCTGCCAA	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.1556C>G	19.37:g.12060395C>G	ENSP00000254321:p.Ser519Cys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	66	33	NM_001271848	0	0	9	20	11	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	c	3.218	-0.160082	0.06502	.	.	ENSG00000196757	ENST00000254321	T	0.07688	3.17	0.672	-1.34	0.09143	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05181	0.0138	N	0.25647	0.755	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39333	-0.9619	9	0.36615	T	0.2	.	4.3948	0.11358	0.0:0.3788:0.4495:0.1717	.	519	Q9H0M5	ZN700_HUMAN	C	519	ENSP00000254321:S519C	ENSP00000254321:S519C	S	+	2	0	ZNF700	11921395	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.814000	0.04486	-1.070000	0.03149	-0.705000	0.03659	TCT	.		0.383	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		G	12060395	C	G	12060395	3	3	106	1	0	0	0	0	1	0	0	0	18136	913	32	4	1570	4	ZNF700	19	12060395	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		12060395	47068588	40	9425											
IL4I1	259307	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	50393785	50393785	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccaccacgggcgcgttcaaCagcacaagcccggacagcga	11	2	12	16	5	1	0	1	0	0	0	1	2	1	1	3	2	4	2	3	2	2	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:50393785C>T	ENST00000391826.2	-	8	988	c.846G>A	c.(844-846)ctG>ctA	p.L282L	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000595948.1_Silent_p.L304L|IL4I1_ENST00000341114.3_Silent_p.L304L	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	282						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	GCGCGTTCAACAGCACAAGCC	0.711											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L304L		.											.	IL4I1-523	0			c.G912A						.						18	18	18					19																	50393785		2202	4299	6501	SO:0001819	synonymous_variant	259307	exon10			GTTCAACAGCACA	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.846G>A	19.37:g.50393785C>T		Somatic	42	0	969	WXS	Illumina HiSeq	Phase_I	50	21	NM_172374	0	0	11	17	6	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			.		0.711	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			T	50393785	C	T	50393785	2	4	106	1	0	0	0	0	0	0	0	1	7718	465	17	2		2	IL4I1	19	50393785	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	38333390	50393785	8735198	41	9426											
ZNF615	284370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52496292	52496292	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgcagtcactgcatttgtaCggtttctctcctgtgtgaat	6	15	9	11	2	2	1	1	1	1	0	4	1	3	1	2	1	2	4	2	1	2	3	rs146634089		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:52496292C>A	ENST00000602063.1	-	6	2386	c.2037G>T	c.(2035-2037)ccG>ccT	p.P679P	ZNF615_ENST00000594083.1_Silent_p.P690P|ZNF615_ENST00000598071.1_Silent_p.P690P|ZNF615_ENST00000376716.5_Silent_p.P679P|ZNF615_ENST00000391795.3_Silent_p.P684P			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	679					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P679P(1)|p.P690P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TGCATTTGTACGGTTTCTCTC	0.408																																					p.P690P		.											.	ZNF615-95	2	Substitution - coding silent(2)	large_intestine(2)	c.G2070T						.						160	155	157					19																	52496292		2203	4300	6503	SO:0001819	synonymous_variant	284370	exon7			TTTGTACGGTTTC	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.2037G>T	19.37:g.52496292C>A		Somatic	205	2		WXS	Illumina HiSeq	Phase_I	201	83	NM_001199324	0	0	5	8	3	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Silent	SNP	ENST00000602063.1	37	CCDS12846.1																																																																																			C|1.000;T|0.000		0.408	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		A	52496292	C	A	52496292	2	1	106	1	0	0	0	0	0	0	0	1	18072	523	19	4		4	ZNF615	19	52496292	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	2102507	52496292	6632691	42	9427											
TRIM28	10155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	59057198	59057198	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtgctcggagcctctgtGtgagacctgtgtagaggcgc	6	9	17	9	2	1	2	0	1	1	2	2	5	1	4	2	3	2	2	2	3	1	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:59057198G>A	ENST00000253024.5	+	3	810	c.521G>A	c.(520-522)tGt>tAt	p.C174Y	TRIM28_ENST00000341753.6_Intron|RN7SL525P_ENST00000579267.1_RNA	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	174	RBCC domain.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGCCTCTGTGTGAGACCTGT	0.577																																					p.C174Y		.											.	TRIM28-870	0			c.G521A						.						80	75	77					19																	59057198		2203	4300	6503	SO:0001583	missense	10155	exon3			CTCTGTGTGAGAC		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.521G>A	19.37:g.59057198G>A	ENSP00000253024:p.Cys174Tyr	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	94	37	NM_005762	0	0	81	153	72	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	37	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934831	0.73442	.	.	ENSG00000130726	ENST00000253024	D	0.99080	-5.4	4.89	4.89	0.63831	Zinc finger, B-box (3);	0.000000	0.64402	D	0.000017	D	0.99453	0.9806	M	0.93638	3.44	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.98378	1.0557	10	0.87932	D	0	-16.8595	15.9183	0.79539	0.0:0.0:1.0:0.0	.	174	Q13263	TIF1B_HUMAN	Y	174	ENSP00000253024:C174Y	ENSP00000253024:C174Y	C	+	2	0	TRIM28	63749010	1.000000	0.71417	0.998000	0.56505	0.414000	0.31173	9.337000	0.96545	2.432000	0.82394	0.558000	0.71614	TGT	.		0.577	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		A	59057198	G	A	59057198	3	1	106	1	0	0	0	0	1	0	0	0	16535	1377	48	2	531	2	TRIM28	19	59057198	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	6560906	59057198	71785	43	9428											
KRTAP26-1	388818	hgsc.bcm.edu;broad.mit.edu	37	chr21	31692296	31692296	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtgagaggaatatggcGggaggttctgagagatcctg	10	8	19	4	1	1	3	0	2	1	2	2	8	2	6	1	6	0	1	1	6	2	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr21:31692296G>A	ENST00000360542.3	-	1	311	c.58C>T	c.(58-60)Cgc>Tgc	p.R20C		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	20						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GGAATATGGCGGGAGGTTCTG	0.532																																					p.R20C		.											.	KRTAP26-1-69	0			c.C58T						.																																			SO:0001583	missense	388818	exon1			TATGGCGGGAGGT	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"Keratin associated proteins"	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.58C>T	21.37:g.31692296G>A	ENSP00000353742:p.Arg20Cys	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	63	5	NM_203405	0	0	0	0	0	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	g	0.015	-1.544573	0.00934	.	.	ENSG00000197683	ENST00000360542	T	0.02837	4.14	4.95	3.8	0.43715	.	0.425318	0.22440	N	0.060032	T	0.00815	0.0027	N	0.00413	-1.525	0.28406	N	0.918409	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	10	0.02654	T	1	-2.2098	8.113	0.30926	0.9049:0.0:0.0951:0.0	.	20	Q6PEX3	KR261_HUMAN	C	20	ENSP00000353742:R20C	ENSP00000353742:R20C	R	-	1	0	KRTAP26-1	30614167	0.900000	0.30661	0.326000	0.25389	0.313000	0.28021	0.998000	0.29744	0.963000	0.38082	-0.285000	0.09966	CGC	.		0.532	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		A	31692296	G	A	31692296	3	1	106	1	0	0	0	0	1	0	0	0	8564	1116	39	1	578	1	KRTAP26-1	21	31692296	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		31692296	16437599	44	9429											
PKDREJ	10343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46654232	46654232	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcttctggatgcatacgcAttccatccaacctgatctca	9	14	5	13	1	3	1	1	1	3	0	6	2	5	2	3	1	3	2	3	1	2	4			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr22:46654232A>T	ENST00000253255.5	-	1	4987	c.4988T>A	c.(4987-4989)aTg>aAg	p.M1663K		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1663					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ATGCATACGCATTCCATCCAA	0.418																																					p.M1663K		.											.	PKDREJ-156	0			c.T4988A						.						153	131	138					22																	46654232		2203	4300	6503	SO:0001583	missense	10343	exon1			ATACGCATTCCAT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.4988T>A	22.37:g.46654232A>T	ENSP00000253255:p.Met1663Lys	Somatic	94	1		WXS	Illumina HiSeq	Phase_I	110	43	NM_006071	0	0	0	0	0	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	a	3.730	-0.055823	0.07362	.	.	ENSG00000130943	ENST00000253255	T	0.32988	1.43	4.95	0.169	0.15017	.	2.130620	0.02503	N	0.090693	T	0.21468	0.0517	L	0.40543	1.245	0.09310	N	1	B	0.13594	0.008	B	0.14023	0.01	T	0.07139	-1.0788	10	0.13108	T	0.6	-0.4046	0.9383	0.01350	0.4034:0.2768:0.1678:0.152	.	1663	Q9NTG1	PKDRE_HUMAN	K	1663	ENSP00000253255:M1663K	ENSP00000253255:M1663K	M	-	2	0	PKDREJ	45032896	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-0.426000	0.07008	-0.235000	0.09767	0.248000	0.18094	ATG	.		0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46654232	A	T	46654232	3	4	106	1	0	0	0	0	1	0	0	0	11996	217	8	5	1777	5	PKDREJ	22	46654232	Missense_Mutation	SNP	A	TCGA-DZ-6135-01A-11D-1961-08		46654232	4650334	45	9430											
C1orf94	84970	ucsc.edu	37	chr1	34677972	34677972	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccctcccctaatggcaggAgatggaccgcagtacctctt	9	8	10	14	1	1	1	0	0	1	1	2	4	2	2	5	3	1	3	5	3	2	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:34677972A>G	ENST00000488417.1	+	6	1806	c.1686A>G	c.(1684-1686)ggA>ggG	p.G562G	C1orf94_ENST00000373374.3_Silent_p.G372G	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	562										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				TAATGGCAGGAGATGGACCGC	0.567																																					p.G562G													.	C1orf94-90	0			c.A1686G						.						83	73	77					1																	34677972		2203	4300	6503	SO:0001819	synonymous_variant	84970	exon6			GGCAGGAGATGGA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1686A>G	1.37:g.34677972A>G		Somatic	65	1		WXS	Illumina HiSeq		45	5	NM_001134734	0	0	0	0	0	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																			.		0.567	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		G	34677972	A	G	34677972	2	3	107	1	0	0	0	0	0	0	0	1	2077	291	11	3		3	C1orf94	1	34677972	Silent	SNP	A	TCGA-EV-5901-01A-11D-1589-08		34677972	214572649	1	9431											
RNF115	27246	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145688091	145688091	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatttttctgtttcagcaTgacacatgtcctgtatgtag	10	17	7	7	0	2	1	1	1	1	0	3	1	3	1	1	0	1	4	1	0	4	6			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:145688091T>A	ENST00000369291.5	+	9	990	c.786T>A	c.(784-786)caT>caA	p.H262Q		NM_014455.2	NP_055270.1			ring finger protein 115											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13						TGTTTCAGCATGACACATGTC	0.418																																					p.H262Q		.											.	RNF115-91	0			c.T786A						.						117	112	114					1																	145688091		2203	4300	6503	SO:0001583	missense	27246	exon9			TCAGCATGACACA	AF419857	CCDS72863.1	1q12	2013-01-09	2008-06-16	2008-06-16	ENSG00000121848	ENSG00000265491		"RING-type (C3HC4) zinc fingers"	18154	protein-coding gene	gene with protein product			"zinc finger protein 364"	ZNF364			Standard	NM_014455		Approved	CL469780	uc001eoj.3	Q9Y4L5	OTTHUMG00000013758	ENST00000369291.5:c.786T>A	1.37:g.145688091T>A	ENSP00000358297:p.His262Gln	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	139	48	NM_014455	0	0	0	0	0		Missense_Mutation	SNP	ENST00000369291.5	37	CCDS922.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.651541	0.67472	.	.	ENSG00000121848	ENST00000369291	T	0.41758	0.99	5.65	0.199	0.15175	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.35624	0.0938	L	0.38733	1.17	0.54753	D	0.999989	D	0.71674	0.998	D	0.69824	0.966	T	0.27971	-1.0058	10	0.72032	D	0.01	-5.7379	9.6735	0.40026	0.0:0.5176:0.0:0.4824	.	262	Q9Y4L5	RN115_HUMAN	Q	262	ENSP00000358297:H262Q	ENSP00000358297:H262Q	H	+	3	2	RNF115	144399448	0.949000	0.32298	0.997000	0.53966	0.972000	0.66771	-0.007000	0.12810	-0.112000	0.11979	0.533000	0.62120	CAT	.		0.418	RNF115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038554.2	NM_014455		A	145688091	T	A	145688091	3	1	107	1	0	0	0	0	1	0	0	0	13462	1461	51	5	820	5	RNF115	1	145688091	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	111010119	145688091	103562530	2	9432											
ANP32E	81611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150201557	150201557	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaggtcaagacttttcaaaTttttaagattttgctggaaa	14	15	7	5	0	2	2	2	0	0	2	2	3	2	3	0	2	1	1	0	2	4	7			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:150201557T>G	ENST00000314136.8	-	4	710	c.341A>C	c.(340-342)aAt>aCt	p.N114T	ANP32E_ENST00000369116.4_Intron|ANP32E_ENST00000369115.2_Intron|ANP32E_ENST00000533654.1_Intron|ANP32E_ENST00000436748.2_Missense_Mutation_p.N73T|ANP32E_ENST00000369114.5_Intron|ANP32E_ENST00000369119.3_Missense_Mutation_p.N66T	NM_001136478.2|NM_001280559.1|NM_030920.3	NP_001129950.1|NP_001267488.1|NP_112182.1	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	114					histone exchange (GO:0043486)|negative regulation of catalytic activity (GO:0043086)	cytoplasmic membrane-bounded vesicle (GO:0016023)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	histone binding (GO:0042393)|phosphatase inhibitor activity (GO:0019212)			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACTTTTCAAATTTTTAAGATT	0.264																																					p.N114T		.											.	ANP32E-90	0			c.A341C						.						34	35	34					1																	150201557		2202	4300	6502	SO:0001583	missense	81611	exon4			TTCAAATTTTTAA	AK092672	CCDS946.1, CCDS44214.1, CCDS44215.1, CCDS60245.1	1q22	2008-02-05			ENSG00000143401	ENSG00000143401		"ANP32 acidic nuclear phosphoproteins"	16673	protein-coding gene	gene with protein product		609611				12438741	Standard	NM_030920		Approved	LANPL, MGC5350, LANP-L	uc001etw.3	Q9BTT0	OTTHUMG00000012547	ENST00000314136.8:c.341A>C	1.37:g.150201557T>G	ENSP00000324074:p.Asn114Thr	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	56	23	NM_030920	0	0	0	0	0	B4E0I6|E9PEA6|Q5TB18|Q5TB20|Q8N1S4|Q8WWW9	Missense_Mutation	SNP	ENST00000314136.8	37	CCDS946.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.030304	0.54790	.	.	ENSG00000143401	ENST00000314136;ENST00000369119;ENST00000436748;ENST00000532744	T;T;T;T	0.13307	2.6;2.6;7.97;2.6	5.97	3.58	0.41010	.	0.126247	0.64402	D	0.000001	T	0.13713	0.0332	L	0.60012	1.86	0.80722	D	1	D;B;D	0.61080	0.989;0.15;0.978	P;B;P	0.59221	0.854;0.295;0.776	T	0.01909	-1.1249	10	0.52906	T	0.07	.	6.1046	0.20067	0.1475:0.1013:0.0:0.7512	.	73;114;66	E9PEA6;Q9BTT0;Q5TB20	.;AN32E_HUMAN;.	T	114;66;73;64	ENSP00000324074:N114T;ENSP00000358115:N66T;ENSP00000393718:N73T;ENSP00000432684:N64T	ENSP00000324074:N114T	N	-	2	0	ANP32E	148468181	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.568000	0.36418	1.023000	0.39654	0.533000	0.62120	AAT	.		0.264	ANP32E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035056.1	NM_030920		G	150201557	T	G	150201557	3	3	107	1	0	0	0	0	1	0	0	0	709	1493	52	5	481	5	ANP32E	1	150201557	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	4513466	150201557	99049064	3	9433											
NHLH1	4807	broad.mit.edu;bcgsc.ca	37	chr1	160340735	160340735	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgccggcgccggcgccgcGccacagccaagtaccgcacg	7	1	14	19	9	0	0	0	0	0	0	0	0	0	0	6	2	3	2	6	2	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:160340735G>A	ENST00000302101.5	+	2	660	c.214G>A	c.(214-216)Gcc>Acc	p.A72T		NM_005598.3	NP_005589.1	Q02575	HEN1_HUMAN	nescient helix loop helix 1	72					cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7	all_cancers(52;7.11e-19)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ccggcgccgcgccACAGCCAA	0.731																																					p.A72T													.	NHLH1-69	0			c.G214A						.						15	18	17					1																	160340735		2197	4289	6486	SO:0001583	missense	4807	exon2			CGCCGCGCCACAG	BC013789	CCDS1204.1	1q22	2013-05-21			ENSG00000171786	ENSG00000171786		"Basic helix-loop-helix proteins"	7817	protein-coding gene	gene with protein product		162360		HEN1			Standard	NM_005598		Approved	NSCL, NSCL1, bHLHa35	uc001fwa.2	Q02575	OTTHUMG00000033121	ENST00000302101.5:c.214G>A	1.37:g.160340735G>A	ENSP00000302189:p.Ala72Thr	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	15	4	NM_005598	0	0	0	0	0		Missense_Mutation	SNP	ENST00000302101.5	37	CCDS1204.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300368	0.81136	.	.	ENSG00000171786	ENST00000302101	D	0.95756	-3.8	4.05	4.05	0.47172	Helix-loop-helix DNA-binding (2);	0.000000	0.52532	D	0.000061	T	0.82056	0.4954	N	0.12182	0.205	0.58432	D	0.999999	P	0.36199	0.543	B	0.17098	0.017	D	0.84431	0.0577	10	0.30078	T	0.28	-19.7981	15.3083	0.74011	0.0:0.0:1.0:0.0	.	72	Q02575	HEN1_HUMAN	T	72	ENSP00000302189:A72T	ENSP00000302189:A72T	A	+	1	0	NHLH1	158607359	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	6.506000	0.73712	2.238000	0.73509	0.655000	0.94253	GCC	.		0.731	NHLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080676.1	NM_005598		A	160340735	G	A	160340735	3	1	107	1	0	0	0	0	1	0	0	0	10429	1087	38	1	216	1	NHLH1	1	160340735	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	10139178	160340735	88909886	4	9434											
ARHGAP30	257106	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161021130	161021130	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccagggccaaggccagggCcagggccagggccagaggca	9	0	19	13	0	0	1	0	0	0	1	0	1	0	1	6	7	0	1	6	7	1	0			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:161021130C>A	ENST00000368013.3	-	10	1714	c.1394G>T	c.(1393-1395)gGc>gTc	p.G465V	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.G465V|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.G288V	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	465					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			aaggccagggccagggccagg	0.612																																					p.G465V		.											.	ARHGAP30-25	0			c.G1394T						.						29	31	30					1																	161021130		2203	4298	6501	SO:0001583	missense	257106	exon10			CCAGGGCCAGGGC	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"Rho GTPase activating proteins"	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1394G>T	1.37:g.161021130C>A	ENSP00000356992:p.Gly465Val	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	57	20	NM_001025598	0	0	41	41	0	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633427	0.47049	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.48201	2.6;2.35;0.82	3.83	3.83	0.44106	.	0.323164	0.22031	N	0.065593	T	0.37461	0.1004	L	0.27053	0.805	0.49389	D	0.999786	B;D	0.61697	0.354;0.99	B;P	0.57152	0.074;0.814	T	0.37407	-0.9707	10	0.72032	D	0.01	.	11.4473	0.50131	0.0:1.0:0.0:0.0	.	465;465	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	V	465;465;317;288	ENSP00000356995:G465V;ENSP00000356992:G465V;ENSP00000356994:G288V	ENSP00000356992:G465V	G	-	2	0	ARHGAP30	159287754	0.992000	0.36948	0.997000	0.53966	0.998000	0.95712	3.749000	0.55150	2.131000	0.65755	0.555000	0.69702	GGC	.		0.612	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		A	161021130	C	A	161021130	3	1	107	1	0	0	0	0	1	0	0	0	879	739	26	4	1923	4	ARHGAP30	1	161021130	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	680395	161021130	88229491	5	9435											
VPS54	51542	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	64199372	64199372	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcatctctcatgaatctTctctctctaataaaaagaca	13	14	3	11	0	5	2	1	1	4	1	8	2	5	2	0	0	1	1	0	0	5	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:64199372T>A	ENST00000272322.4	-	4	539	c.385A>T	c.(385-387)Aag>Tag	p.K129*	VPS54_ENST00000354504.3_Nonsense_Mutation_p.K12*|VPS54_ENST00000409558.4_Nonsense_Mutation_p.K117*			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	129					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						TCATGAATCTTCTCTCTCTAA	0.303																																					p.K129X		.											.	VPS54-90	0			c.A385T						.						69	67	68					2																	64199372		2202	4292	6494	SO:0001587	stop_gained	51542	exon4			GAATCTTCTCTCT	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 164"	614633	"vacuolar protein sorting 54 (yeast)"			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.385A>T	2.37:g.64199372T>A	ENSP00000272322:p.Lys129*	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	63	22	NM_016516	0	0	0	0	0	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Nonsense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	T	42	9.754681	0.99256	.	.	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	.	.	.	5.66	5.66	0.87406	.	0.089994	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8882	0.79269	0.0:0.0:0.0:1.0	.	.	.	.	X	12;129;117;117;129	.	ENSP00000272322:K129X	K	-	1	0	VPS54	64052876	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.116000	0.64661	2.166000	0.68216	0.454000	0.30748	AAG	.		0.303	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		A	64199372	T	A	64199372	4	1	107	1	0	0	0	0	0	1	0	0	17249	1792	62	5	2628	5	VPS54	2	64199372	Nonsense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		64199372	179000001	6	9436											
ARID5A	10865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97216937	97216937	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagcagggcctggcctctggGtcttctgtgtcctttgtggg	2	13	15	11	0	3	0	0	0	3	0	4	0	4	0	3	4	1	1	3	4	0	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:97216937G>A	ENST00000357485.3	+	7	750	c.672G>A	c.(670-672)ggG>ggA	p.G224G	ARID5A_ENST00000454558.2_Silent_p.G156G	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	224					chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						TGGCCTCTGGGTCTTCTGTGT	0.602																																					p.G224G		.											.	ARID5A-226	0			c.G672A						.						56	61	60					2																	97216937		2203	4300	6503	SO:0001819	synonymous_variant	10865	exon7			CTCTGGGTCTTCT	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"-"	17361	protein-coding gene	gene with protein product	"modulator recognition factor 1"	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.672G>A	2.37:g.97216937G>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	108	27	NM_212481	0	0	22	24	2	Q6NX37	Silent	SNP	ENST00000357485.3	37	CCDS33251.1																																																																																			.		0.602	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481		A	97216937	G	A	97216937	2	1	107	1	0	0	0	0	0	0	0	1	921	1248	44	2		2	ARID5A	2	97216937	Silent	SNP	G	TCGA-EV-5901-01A-11D-1589-08	33017565	97216937	145982436	7	9437											
CNNM4	26504	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97427340	97427340	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcgggcatattttctggcCtcaacctcgggcttatggcc	5	13	11	12	2	2	0	1	0	1	0	4	0	2	0	3	4	1	2	3	4	3	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:97427340C>A	ENST00000377075.2	+	1	702	c.604C>A	c.(604-606)Ctc>Atc	p.L202I		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	202	DUF21.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						ATTTTCTGGCCTCAACCTCGG	0.587																																					p.L202I		.											.	CNNM4-154	0			c.C604A						.						85	92	89					2																	97427340		2203	4300	6503	SO:0001583	missense	26504	exon1			TCTGGCCTCAACC	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.604C>A	2.37:g.97427340C>A	ENSP00000366275:p.Leu202Ile	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	125	47	NM_020184	0	0	26	41	15	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	c	20.6	4.021298	0.75275	.	.	ENSG00000158158	ENST00000377075	D	0.89485	-2.52	4.85	4.85	0.62838	Domain of unknown function DUF21 (1);	0.077015	0.50627	D	0.000112	D	0.94925	0.8359	M	0.92122	3.275	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.95382	0.8474	10	0.87932	D	0	-12.6701	10.4274	0.44387	0.0:0.908:0.0:0.092	.	202	Q6P4Q7	CNNM4_HUMAN	I	202	ENSP00000366275:L202I	ENSP00000366275:L202I	L	+	1	0	CNNM4	96791067	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	3.112000	0.50368	2.234000	0.73211	0.556000	0.70494	CTC	.		0.587	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		A	97427340	C	A	97427340	3	1	107	1	0	0	0	0	1	0	0	0	3621	681	24	4	606	4	CNNM4	2	97427340	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	210403	97427340	145772033	8	9438											
PRPF40A	55660	hgsc.bcm.edu	37	chr2	153532998	153532998	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgatcctgaatagcaggggTactagtaagttgtgcttgtt	9	15	12	5	0	0	2	0	2	0	0	1	2	1	2	1	2	3	6	1	2	5	8	rs372660010		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:153532998T>C	ENST00000410080.1	-	10	1493	c.952A>G	c.(952-954)Acc>Gcc	p.T318A		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	345					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						ATAGCAGGGGTACTAGTAAGT	0.378																																					p.T318A		.											.	PRPF40A-68	0			c.A952G						.	T	ALA/THR	0,3770		0,0,1885	81	77	78		952	3.6	1	2		78	1,8221		0,1,4110	no	missense	PRPF40A	NM_017892.3	58	0,1,5995	CC,CT,TT		0.0122,0.0,0.0083	possibly-damaging	318/931	153532998	1,11991	1885	4111	5996	SO:0001583	missense	55660	exon10			CAGGGGTACTAGT	AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"formin-binding protein 3", "formin binding protein 3", "PRP40 pre-mRNA processing factor 40 homolog A (yeast)"	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.952A>G	2.37:g.153532998T>C	ENSP00000386458:p.Thr318Ala	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_017892	0	0	64	64	0	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Missense_Mutation	SNP	ENST00000410080.1	37	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	T	4.743	0.138086	0.09083	0.0	1.22E-4	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961;ENST00000545856;ENST00000493468	T	0.30182	1.54	4.77	3.61	0.41365	.	0.488453	0.23416	N	0.048404	T	0.12732	0.0309	N	0.14661	0.345	0.34226	D	0.676017	B;B;B	0.30193	0.272;0.049;0.028	B;B;B	0.17722	0.019;0.015;0.016	T	0.20472	-1.0274	10	0.07813	T	0.8	-1.5293	7.4308	0.27126	0.0:0.1016:0.0:0.8984	.	345;327;318	O75400;O75400-3;E9PFS0	PR40A_HUMAN;.;.	A	318;327;214;265;345;320	ENSP00000386458:T318A	ENSP00000348770:T327A	T	-	1	0	PRPF40A	153241244	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	0.937000	0.28951	0.934000	0.37316	0.455000	0.32223	ACC	.		0.378	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		C	153532998	T	C	153532998	3	2	107	1	0	0	0	0	1	0	0	0	12600	1638	57	3	1908	3	PRPF40A	2	153532998	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	56105658	153532998	89666375	9	9439											
BSN	8927	hgsc.bcm.edu	37	chr3	49698758	49698759	+	Frame_Shift_Del	DEL	CT	CT	-																															gagcagaaggtgcccaccaaCtatgaggtgatcgccagccc																										TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:49698758_49698759delCT	ENST00000296452.4	+	6	9594_9595	c.9480_9481delCT	c.(9478-9483)aactatfs	p.NY3160fs		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3160					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TGCCCACCAACTATGAGGTGAT	0.604																																					p.3160_3161del		.											.	BSN-97	0			c.9480_9481del						.																																			SO:0001589	frameshift_variant	8927	exon6			.	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"zinc finger protein 231", "neuronal double zinc finger protein"	604020	"bassoon (presynaptic cytomatrix protein)"	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.9480_9481delCT	3.37:g.49698758_49698759delCT	ENSP00000296452:p.Asn3160fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	36	10	NM_003458	0	0	0	0	0	O43161|Q7LGH3	Frame_Shift_Del	DEL	ENST00000296452.4	37	CCDS2800.1																																																																																			.		0.604	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		-	49698759	CT	-	49698758	7	5	107	1	0	1	0	1	0	0	0	0	1533	564	20	0	9502	0	BSN	3	49698758	Frame_Shift_Del	DEL	CT	TCGA-EV-5901-01A-11D-1589-08		49698758	148323672	10	9440											
PSMD6	9861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	64004274	64004274	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaatatcaaccctatccttaCctaatgattggaagaaaaca	18	10	4	9	0	1	2	1	1	0	1	2	3	2	3	3	1	3	0	3	1	9	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:64004274C>A	ENST00000295901.4	-	5	967		c.e5+1		RP11-245J9.6_ENST00000605919.1_RNA|PSMD6_ENST00000394431.2_Splice_Site|PSMD6_ENST00000482510.1_Splice_Site|RP11-245J9.4_ENST00000462717.1_RNA|PSMD6_ENST00000492933.1_Splice_Site	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6						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)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		CCTATCCTTACCTAATGATTG	0.388																																					.		.											.	PSMD6-91	0			c.985+1G>T						.						78	71	73					3																	64004274		2203	4300	6503	SO:0001630	splice_region_variant	9861	exon7			TCCTTACCTAATG	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.826+1G>T	3.37:g.64004274C>A		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	34	12	NM_001271779	0	0	0	2	2	A8K2E0|E9PHI9|Q6UV22	Splice_Site	SNP	ENST00000295901.4	37	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577357	0.65878	.	.	ENSG00000163636	ENST00000295901;ENST00000480205;ENST00000492933;ENST00000394431;ENST00000482510	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3633	0.98874	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PSMD6	63979314	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	6.088000	0.71371	2.826000	0.97356	0.561000	0.74099	.	.		0.388	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814	Intron	A	64004274	C	A	64004274	5	1	107	1	0	0	0	0	0	0	1	0	12731	521	18	4	358	4	PSMD6	3	64004274	Splice_Site	SNP	C	TCGA-EV-5901-01A-11D-1589-08	14305516	64004274	134018156	11	9441											
EPHA6	285220	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	97202865	97202865	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaatttgcaaaggagattgAtccctcaagaattcgtattg	13	13	9	6	1	1	4	1	2	0	2	3	5	2	4	1	1	1	2	1	1	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:97202865A>C	ENST00000514100.1	+	7	580	c.338A>C	c.(337-339)gAt>gCt	p.D113A	EPHA6_ENST00000442602.2_Missense_Mutation_p.D87A|EPHA6_ENST00000389672.5_Missense_Mutation_p.D721A|EPHA6_ENST00000502694.1_Missense_Mutation_p.D113A	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	627	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						AAGGAGATTGATCCCTCAAGA	0.383																																					p.D721A		.											.	EPHA6-1561	0			c.A2162C						.						99	101	100					3																	97202865		1865	4106	5971	SO:0001583	missense	285220	exon10			AGATTGATCCCTC	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000514100.1:c.338A>C	3.37:g.97202865A>C	ENSP00000421711:p.Asp113Ala	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	46	26	NM_001080448	0	0	0	0	0	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	37		.	.	.	.	.	.	.	.	.	.	A	22.3	4.273321	0.80580	.	.	ENSG00000080224	ENST00000389672;ENST00000514100;ENST00000502694;ENST00000442602	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.32	5.32	0.75619	Protein kinase-like domain (1);	.	.	.	.	T	0.54615	0.1869	M	0.89785	3.06	0.80722	D	1	D;D;D;D	0.89917	0.999;0.962;1.0;1.0	P;P;D;D	0.85130	0.907;0.598;0.997;0.962	T	0.65438	-0.6168	9	0.87932	D	0	.	15.3417	0.74303	1.0:0.0:0.0:0.0	.	87;626;113;113	B4DXQ6;Q9UF33;Q9UF33-2;D6RAL5	.;EPHA6_HUMAN;.;.	A	721;113;113;87	ENSP00000374323:D721A;ENSP00000421711:D113A;ENSP00000423950:D113A;ENSP00000403100:D87A	ENSP00000374323:D721A	D	+	2	0	EPHA6	98685555	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.958000	0.93099	2.026000	0.59711	0.454000	0.30748	GAT	.		0.383	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		C	97202865	A	C	97202865	3	2	107	1	0	0	0	0	1	0	0	0	5184	333	12	5	2268	5	EPHA6	3	97202865	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	33198591	97202865	100819565	12	9442											
CD86	942	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	121825262	121825263	+	Frame_Shift_Del	DEL	AT	AT	-																															tccatcagcttgtctgtttcAttccctgatgttacgagcaa																								rs375108955		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:121825262_121825263delAT	ENST00000330540.2	+	4	734_735	c.618_619delAT	c.(616-621)tcattcfs	p.F207fs	CD86_ENST00000393627.2_Frame_Shift_Del_p.F201fs|CD86_ENST00000264468.5_Intron|CD86_ENST00000469710.1_Frame_Shift_Del_p.F125fs|CD86_ENST00000493101.1_Frame_Shift_Del_p.F95fs	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	207	Ig-like C2-type.				aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	TGTCTGTTTCATTCCCTGATGT	0.391																																					p.206_207del	GBM(67;1379 1389 36064 39806)	.											.	CD86-92	0			c.618_619del						.																																			SO:0001589	frameshift_variant	942	exon4			.		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1705	protein-coding gene	gene with protein product	"B-lymphocyte antigen B7-2"	601020	"CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.618_619delAT	3.37:g.121825262_121825263delAT	ENSP00000332049:p.Phe207fs	Somatic	263	0		WXS	Illumina HiSeq	Phase_I	362	177	NM_175862	0	0	0	0	0	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Frame_Shift_Del	DEL	ENST00000330540.2	37	CCDS3009.1																																																																																			.		0.391	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889		-	121825263	AT	-	121825262	7	5	107	1	0	1	0	1	0	0	0	0	3049	204	8	0	632	0	CD86	3	121825262	Frame_Shift_Del	DEL	AT	TCGA-EV-5901-01A-11D-1589-08	24622397	121825262	76197168	13	9443											
CEP63	80254	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	134250746	134250746	+	Frame_Shift_Del	DEL	G	G	-																															atcaagcaagagatgaccatGgaatataagcaggagttgaa																								rs544307188		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:134250746delG	ENST00000337090.3	+	4	455	c.282delG	c.(280-282)atgfs	p.M94fs	CEP63_ENST00000383229.3_Frame_Shift_Del_p.M94fs|CEP63_ENST00000513612.2_Frame_Shift_Del_p.M94fs|CEP63_ENST00000606977.1_Frame_Shift_Del_p.M94fs|CEP63_ENST00000354446.3_Frame_Shift_Del_p.M94fs|CEP63_ENST00000332047.5_Frame_Shift_Del_p.M94fs|CEP63_ENST00000504013.1_3'UTR			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	94					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AGATGACCATGGAATATAAGC	0.353																																					p.M94fs		.											.	CEP63-493	0			c.282delG						.						171	168	169					3																	134250746		2203	4300	6503	SO:0001589	frameshift_variant	80254	exon4			.	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.282delG	3.37:g.134250746delG	ENSP00000336524:p.Met94fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	80	41	NM_001042383	0	0	0	0	0	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Frame_Shift_Del	DEL	ENST00000337090.3	37	CCDS3086.1																																																																																			.		0.353	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		-	134250746	G	-	134250746	7	5	107	1	0	1	0	1	0	0	0	0	3263	1348	47	0	292	0	CEP63	3	134250746	Frame_Shift_Del	DEL	G	TCGA-EV-5901-01A-11D-1589-08	12425484	134250746	63771684	14	9444											
PHC3	80012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	169847187	169847187	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacagtgctgggatgggggtGggtcttgagttgaattctga	7	13	17	4	0	2	3	0	3	2	0	2	4	2	4	0	4	2	2	0	4	2	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:169847187G>A	ENST00000494943.1	-	8	1105	c.1037C>T	c.(1036-1038)cCa>cTa	p.P346L	PHC3_ENST00000467570.1_Missense_Mutation_p.P305L|PHC3_ENST00000495893.2_Missense_Mutation_p.P358L			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	346	Gln-rich.|Pro-rich.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			GGATGGGGGTGGGTCTTGAGT	0.488																																					p.P358L		.											.	PHC3-227	0			c.C1073T						.						205	205	205					3																	169847187		2024	4175	6199	SO:0001583	missense	80012	exon8			GGGGGTGGGTCTT		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"Sterile alpha motif (SAM) domain containing"	15682	protein-coding gene	gene with protein product	"early development regulator 3", "polyhomeotic like 3"		"polyhomeotic like 3 (Drosophila)"			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.1037C>T	3.37:g.169847187G>A	ENSP00000420271:p.Pro346Leu	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	156	45	NM_024947	0	0	20	27	7	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	37		.	.	.	.	.	.	.	.	.	.	G	12.23	1.875524	0.33162	.	.	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570;ENST00000484931	T;T	0.32515	1.45;1.47	5.35	5.35	0.76521	.	0.000000	0.64402	D	0.000001	T	0.37046	0.0989	L	0.55481	1.735	0.80722	D	1	B;P;B;B	0.47302	0.008;0.893;0.0;0.0	B;P;B;B	0.44811	0.006;0.461;0.0;0.002	T	0.08046	-1.0741	10	0.35671	T	0.21	-10.2153	18.6641	0.91483	0.0:0.0:1.0:0.0	.	305;305;346;358	B4E2T1;E7EX82;Q8NDX5;Q8NDX5-7	.;.;PHC3_HUMAN;.	L	346;358;305;184	ENSP00000420271:P346L;ENSP00000420294:P358L	ENSP00000419089:P305L	P	-	2	0	PHC3	171329881	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.385000	0.66231	2.514000	0.84764	0.561000	0.74099	CCA	.		0.488	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		A	169847187	G	A	169847187	3	1	107	1	0	0	0	0	1	0	0	0	11844	1348	47	2	1946	2	PHC3	3	169847187	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	35596441	169847187	28175243	15	9445											
PDGFRA	5156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	55139834	55139834	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtggaggagaccatcgccGtgcgatgcctggctaagaat	11	7	14	9	3	0	2	0	0	0	2	1	5	0	3	3	3	2	1	3	3	3	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr4:55139834G>A	ENST00000257290.5	+	10	1826	c.1495G>A	c.(1495-1497)Gtg>Atg	p.V499M	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	499	Ig-like C2-type 5.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.V499M(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GACCATCGCCGTGCGATGCCT	0.557			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.V499M	Pancreas(151;208 1913 7310 23853 37092)	.		Dom	yes		4	4q11-q13	5156	"platelet-derived growth factor, alpha-receptor"		"L, M, O"	.	PDGFRA-9497	1	Substitution - Missense(1)	breast(1)	c.G1495A						.						85	83	83					4																	55139834		2203	4300	6503	SO:0001583	missense	5156	exon10	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	ATCGCCGTGCGAT	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1495G>A	4.37:g.55139834G>A	ENSP00000257290:p.Val499Met	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	79	25	NM_006206	0	0	22	22	0	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863494	0.51482	.	.	ENSG00000134853	ENST00000257290	T	0.77750	-1.12	5.9	5.9	0.94986	Immunoglobulin-like fold (1);	0.000000	0.29529	U	0.011898	D	0.86401	0.5924	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.75020	0.985;0.882	D	0.86433	0.1762	10	0.56958	D	0.05	.	13.4661	0.61254	0.0709:0.0:0.9291:0.0	.	499;499	P16234-3;P16234	.;PGFRA_HUMAN	M	499	ENSP00000257290:V499M	ENSP00000257290:V499M	V	+	1	0	PDGFRA	54834591	1.000000	0.71417	0.136000	0.22124	0.003000	0.03518	6.915000	0.75770	2.788000	0.95919	0.650000	0.86243	GTG	.		0.557	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55139834	G	A	55139834	3	1	107	1	0	0	0	0	1	0	0	0	11687	1145	40	1	1529	1	PDGFRA	4	55139834	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		55139834	136014442	16	9446											
TERT	7015	broad.mit.edu	37	chr5	1268651	1268651	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacccgtcccgccgaatccCcgcaaacagcttgttctcca	8	8	6	19	4	2	0	1	0	1	0	5	1	4	0	6	0	2	3	6	0	2	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:1268651C>A	ENST00000310581.5	-	9	2623	c.2566G>T	c.(2566-2568)Ggg>Tgg	p.G856W	TERT_ENST00000508104.2_Missense_Mutation_p.G795V|TERT_ENST00000334602.6_Missense_Mutation_p.G856W|TERT_ENST00000296820.5_Missense_Mutation_p.G795V	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	856	Reverse transcriptase. {ECO:0000255|PROSITE-ProRule:PRU00405}.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CGCCGAATCCCCGCAAACAGC	0.602									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.G856W													.	TERT-1272	0			c.G2566T						.						54	52	53					5																	1268651		2203	4300	6503	SO:0001583	missense	7015	exon9	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GAATCCCCGCAAA	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.2566G>T	5.37:g.1268651C>A	ENSP00000309572:p.Gly856Trp	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	35	3	NM_001193376	0	0	0	0	0	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	37	CCDS3861.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.71|12.71	2.019452|2.019452	0.35606|0.35606	.|.	.|.	ENSG00000164362|ENSG00000164362	ENST00000296820;ENST00000508104|ENST00000310581;ENST00000334602	D;D|D;D	0.97016|0.98419	-4.21;-4.21|-4.92;-4.92	4.26|4.26	4.26|4.26	0.50523|0.50523	.|Reverse transcriptase (2);	0.130499|0.130499	0.52532|0.52532	D|D	0.000072|0.000072	D|D	0.98698|0.98698	0.9563|0.9563	M|M	0.81942|0.81942	2.565|2.565	0.34527|0.34527	D|D	0.708733|0.708733	.|D;D	.|0.89917	.|0.998;1.0	.|D;D	.|0.91635	.|0.964;0.999	D|D	0.99969|0.99969	1.1929|1.1929	8|10	0.26408|0.37606	T|T	0.33|0.19	-12.8165|-12.8165	13.6164|13.6164	0.62110|0.62110	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|856;856	.|O14746-3;O14746	.|.;TERT_HUMAN	V|W	795|856	ENSP00000296820:G795V;ENSP00000426042:G795V|ENSP00000309572:G856W;ENSP00000334346:G856W	ENSP00000296820:G795V|ENSP00000309572:G856W	G|G	-|-	2|1	0|0	TERT|TERT	1321651|1321651	0.009000|0.009000	0.17119|0.17119	0.006000|0.006000	0.13384|0.13384	0.006000|0.006000	0.05464|0.05464	1.381000|1.381000	0.34362|0.34362	1.932000|1.932000	0.55993|0.55993	0.561000|0.561000	0.74099|0.74099	GGG|GGG	.		0.602	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			A	1268651	C	A	1268651	3	1	107	1	0	0	0	0	1	0	0	0	15796	623	22	4	864	4	TERT	5	1268651	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		1268651	179646609	17	9447											
LPCAT1	79888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1488543	1488543	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcaggtcctgtttgtacaAgttccttctggaaaaatcat	11	13	9	8	0	2	0	1	0	1	0	4	1	4	1	2	3	1	4	2	3	4	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:1488543A>T	ENST00000283415.3	-	5	762	c.630T>A	c.(628-630)acT>acA	p.T210T		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	210					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		TGTTTGTACAAGTTCCTTCTG	0.323																																					p.T210T		.											.	LPCAT1-92	0			c.T630A						.						87	90	89					5																	1488543		2203	4300	6503	SO:0001819	synonymous_variant	79888	exon5			TGTACAAGTTCCT	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.630T>A	5.37:g.1488543A>T		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	107	47	NM_024830	0	0	17	27	10	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																			.		0.323	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830		T	1488543	A	T	1488543	2	4	107	1	0	0	0	0	0	0	0	1	8935	59	3	5		5	LPCAT1	5	1488543	Silent	SNP	A	TCGA-EV-5901-01A-11D-1589-08	219892	1488543	179426717	18	9448											
NSUN2	54888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	6620280	6620280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctttcctgccgtccacatCtatctggagcctgggtatgc	5	13	9	14	1	3	0	0	0	3	0	5	1	5	1	4	2	3	1	4	2	2	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:6620280C>T	ENST00000264670.6	-	7	1065	c.754G>A	c.(754-756)Gat>Aat	p.D252N	NSUN2_ENST00000539938.1_Missense_Mutation_p.D16N|NSUN2_ENST00000505264.1_5'UTR|NSUN2_ENST00000506139.1_Missense_Mutation_p.D217N	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	252					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CCGTCCACATCTATCTGGAGC	0.493																																					p.D252N		.											.	NSUN2-91	0			c.G754A						.						108	105	106					5																	6620280		2203	4300	6503	SO:0001583	missense	54888	exon7			CCACATCTATCTG	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.754G>A	5.37:g.6620280C>T	ENSP00000264670:p.Asp252Asn	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	122	40	NM_017755	0	0	22	42	20	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.273421	0.23221	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.38560	1.16;2.97;1.13	6.02	6.02	0.97574	.	0.084604	0.85682	D	0.000000	T	0.20740	0.0499	N	0.02985	-0.445	0.51767	D	0.999935	B;B	0.15930	0.015;0.005	B;B	0.20384	0.022;0.029	T	0.18808	-1.0325	10	0.12766	T	0.61	-53.9111	14.6603	0.68865	0.0:0.9312:0.0:0.0688	.	217;252	B4DQW2;Q08J23	.;NSUN2_HUMAN	N	252;16;217	ENSP00000264670:D252N;ENSP00000444338:D16N;ENSP00000420957:D217N	ENSP00000264670:D252N	D	-	1	0	NSUN2	6673280	0.863000	0.29885	0.538000	0.28064	0.018000	0.09664	2.600000	0.46240	2.865000	0.98341	0.655000	0.94253	GAT	.		0.493	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6620280	C	T	6620280	3	4	107	1	0	0	0	0	1	0	0	0	10704	913	32	2	1601	2	NSUN2	5	6620280	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	5131737	6620280	174294980	19	9449											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82836813	82836813	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatagaagccaactagAtcacatgggctttcacttca	14	10	8	9	0	3	4	3	1	0	3	3	4	3	4	1	1	2	1	1	1	5	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:82836813A>G	ENST00000265077.3	+	8	8556	c.7991A>G	c.(7990-7992)gAt>gGt	p.D2664G	VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.D1677G|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2664	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AGCCAACTAGATCACATGGGC	0.453																																					p.D2664G		.											.	VCAN-238	0			c.A7991G						.						126	122	123					5																	82836813		2203	4300	6503	SO:0001583	missense	1462	exon8			AACTAGATCACAT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7991A>G	5.37:g.82836813A>G	ENSP00000265077:p.Asp2664Gly	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	153	45	NM_004385	0	0	613	918	305	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	2.766	-0.256719	0.05829	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.35605	1.3;1.3	6.04	2.03	0.26663	.	0.465278	0.21973	N	0.066435	T	0.30324	0.0761	L	0.53249	1.67	0.09310	N	1	B;B	0.17268	0.021;0.012	B;B	0.15484	0.013;0.006	T	0.19582	-1.0301	10	0.35671	T	0.21	.	9.0589	0.36423	0.7098:0.0:0.2902:0.0	.	1677;2664	P13611-2;P13611	.;CSPG2_HUMAN	G	2664;1677	ENSP00000265077:D2664G;ENSP00000340062:D1677G	ENSP00000265077:D2664G	D	+	2	0	VCAN	82872569	0.001000	0.12720	0.002000	0.10522	0.019000	0.09904	0.608000	0.24223	0.540000	0.28808	-0.375000	0.07067	GAT	.		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82836813	A	G	82836813	3	3	107	1	0	0	0	0	1	0	0	0	17171	333	12	3	8017	3	VCAN	5	82836813	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	76216533	82836813	98078447	20	9450											
SLC22A5	6584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131729504	131729504	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagatgctaagagtcaaaggGtaagaagacctcctctgtca	14	8	10	9	0	3	4	2	0	1	4	4	4	4	4	2	1	1	2	2	1	4	2	rs386134226		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:131729504G>A	ENST00000245407.3	+	9	1807		c.e9+1		SLC22A5_ENST00000435065.2_Splice_Site	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5						carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	GAGTCAAAGGGTAAGAAGACC	0.542																																					.		.											.	SLC22A5-90	0			c.1586+1G>A						.						200	186	191					5																	131729504		2203	4300	6503	SO:0001630	splice_region_variant	6584	exon9			CAAAGGGTAAGAA	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"Solute carriers"	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.1586+1G>A	5.37:g.131729504G>A		Somatic	211	0		WXS	Illumina HiSeq	Phase_I	154	61	NM_003060	0	0	0	1	1	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Splice_Site	SNP	ENST00000245407.3	37	CCDS4154.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.828787	0.90955	.	.	ENSG00000197375	ENST00000245407;ENST00000435065	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC22A5	131757403	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.442000	0.97566	2.941000	0.99782	0.655000	0.94253	.	.		0.542	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	Intron	A	131729504	G	A	131729504	5	1	107	1	0	0	0	0	0	0	1	0	14489	1275	44	2	1621	2	SLC22A5	5	131729504	Splice_Site	SNP	G	TCGA-EV-5901-01A-11D-1589-08	48892691	131729504	49185756	21	9451											
PPP1R10	5514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30577691	30577691	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgtccaggcccttgagaaGttctttggggtctatgggac	6	12	14	9	0	2	1	0	1	2	1	3	3	3	2	2	4	0	2	2	4	2	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr6:30577691G>T	ENST00000376511.2	-	3	583	c.31C>A	c.(31-33)Ctt>Att	p.L11I	PPP1R10_ENST00000484449.1_5'Flank	NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	11	Interaction with TOX4. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						CCCTTGAGAAGTTCTTTGGGG	0.468																																					p.L11I		.											.	PPP1R10-660	0			c.C31A						.						112	107	109					6																	30577691		2203	4300	6503	SO:0001583	missense	5514	exon3			TGAGAAGTTCTTT	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9284	protein-coding gene	gene with protein product	"phosphatase 1 nuclear targeting subunit", "HLA-C associated transcript 53"	603771	"protein phosphatase 1, regulatory (inhibitor) subunit 10"			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.31C>A	6.37:g.30577691G>T	ENSP00000365694:p.Leu11Ile	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	97	33	NM_002714	0	0	20	38	18	O00405	Missense_Mutation	SNP	ENST00000376511.2	37	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.785297	0.70337	.	.	ENSG00000204569	ENST00000376511;ENST00000537132	T	0.54675	0.56	5.65	5.65	0.86999	.	0.119294	0.64402	D	0.000018	T	0.33876	0.0878	L	0.37850	1.14	0.43399	D	0.995525	B	0.30236	0.274	B	0.26416	0.069	T	0.21008	-1.0258	10	0.52906	T	0.07	-18.5396	18.8591	0.92265	0.0:0.0:1.0:0.0	.	11	Q96QC0	PP1RA_HUMAN	I	11	ENSP00000365694:L11I	ENSP00000365694:L11I	L	-	1	0	PPP1R10	30685670	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.210000	0.65214	2.825000	0.97269	0.655000	0.94253	CTT	.		0.468	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		T	30577691	G	T	30577691	3	4	107	1	0	0	0	0	1	0	0	0	12381	1029	36	4	2863	4	PPP1R10	6	30577691	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		30577691	140537376	22	9452											
CCDC129	223075	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	31683522	31683527	+	In_Frame_Del	DEL	GACTTT	GACTTT	-																															caggaagcccagttcatgacGactttgaaagcccttcagga																										TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	GACTTT	GACTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:31683522_31683527delGACTTT	ENST00000407970.3	+	11	2576_2581	c.2538_2543delGACTTT	c.(2536-2544)acgactttg>acg	p.TL847del	CCDC129_ENST00000451887.2_In_Frame_Del_p.TL873del|CCDC129_ENST00000319386.3_In_Frame_Del_p.TL699del|CCDC129_ENST00000409210.1_In_Frame_Del_p.TL755del	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	847										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AGTTCATGACGACTTTGAAAGCCCTT	0.549																																					p.872_874del		.											.	.	0			c.2616_2621del						.																																			SO:0001651	inframe_deletion	223075	exon11			.	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2538_2543delGACTTT	7.37:g.31683522_31683527delGACTTT	ENSP00000384416:p.Thr847_Leu848del	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	121	26	NM_001257968	0	0	0	0	0	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	In_Frame_Del	DEL	ENST00000407970.3	37	CCDS5435.2																																																																																			.		0.549	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		-	31683527	GACTTT	-	31683522	7	5	107	1	0	1	0	1	0	0	0	0	2770	1045	37	0	2576	0	CCDC129	7	31683522	In_Frame_Del	DEL	GACTTT	TCGA-EV-5901-01A-11D-1589-08		31683522	127455141	23	9453											
URGCP	55665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	43918184	43918184	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttgaggtcccgatgccagAagcagtcccactgcctgtgg	8	8	13	12	1	0	2	0	1	0	1	2	3	2	2	4	2	3	2	4	2	1	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:43918184A>C	ENST00000453200.1	-	6	1371	c.878T>G	c.(877-879)tTc>tGc	p.F293C	URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Missense_Mutation_p.F250C|URGCP_ENST00000336086.6_Missense_Mutation_p.F250C|URGCP_ENST00000443736.1_Missense_Mutation_p.F250C|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000223341.7_Missense_Mutation_p.F250C|URGCP_ENST00000402306.3_Missense_Mutation_p.F284C			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	293					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCGATGCCAGAAGCAGTCCCA	0.602																																					p.F293C		.											.	URGCP-94	0			c.T878G						.						43	47	45					7																	43918184		1981	4149	6130	SO:0001583	missense	55665	exon6			TGCCAGAAGCAGT		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.878T>G	7.37:g.43918184A>C	ENSP00000396918:p.Phe293Cys	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	75	21	NM_001077663	0	0	34	50	16	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914953	0.72983	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.43688	1.02;1.02;0.95;1.02;0.94;1.02	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.67720	0.2923	M	0.85945	2.785	0.49483	D	0.999796	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73665	-0.3911	10	0.87932	D	0	-32.908	13.5869	0.61937	1.0:0.0:0.0:0.0	.	284;293	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	C	250;250;284;250;293;250	ENSP00000223341:F250C;ENSP00000336872:F250C;ENSP00000384955:F284C;ENSP00000392136:F250C;ENSP00000396918:F293C;ENSP00000402803:F250C	ENSP00000223341:F250C	F	-	2	0	URGCP	43884709	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.761000	0.91691	2.104000	0.64026	0.402000	0.26972	TTC	.		0.602	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		C	43918184	A	C	43918184	3	2	107	1	0	0	0	0	1	0	0	0	17059	246	9	5	1921	5	URGCP	7	43918184	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	12234662	43918184	115220479	24	9454											
BAZ1B	9031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	72907199	72907199	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggagcccatttcctttcTcctttttttaatgaagtagg	8	16	9	8	0	1	1	0	1	1	0	3	3	2	3	3	3	1	1	3	3	3	7			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:72907199T>C	ENST00000339594.4	-	5	962	c.624A>G	c.(622-624)ggA>ggG	p.G208G	BAZ1B_ENST00000404251.1_Silent_p.G208G	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	208	Mediates the tyrosine-protein kinase activity.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				ATTTCCTTTCTCCTTTTTTTA	0.328																																					p.G208G	Esophageal Squamous(112;1167 1561 21085 43672 48228)	.											.	BAZ1B-159	0			c.A624G						.						129	125	127					7																	72907199		2203	4299	6502	SO:0001819	synonymous_variant	9031	exon5			CCTTTCTCCTTTT	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.624A>G	7.37:g.72907199T>C		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	112	26	NM_032408	0	0	48	77	29	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																			.		0.328	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72907199	T	C	72907199	2	2	107	1	0	0	0	0	0	0	0	1	1331	1538	54	3		3	BAZ1B	7	72907199	Silent	SNP	T	TCGA-EV-5901-01A-11D-1589-08	28989015	72907199	86231464	25	9455											
DNAJC2	27000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	102963052	102963053	+	Nonsense_Mutation	DNP	AT	AT	TA																															cttcttccttgaacttttttAtccttggatcacagctgtat																										TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:102963052_102963053AT>TA	ENST00000379263.3	-	9	1088_1089	c.838_839AT>TA	c.(838-840)ATa>TAa	p.I280*	PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Nonsense_Mutation_p.I280*	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	280					'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GAACTTTTTTATCCTTGGATCA	0.337																																					p.I280*		.											.	DNAJC2	0			c.A838T						.																																			SO:0001587	stop_gained	27000	exon9			TTTTTATCCTTGG	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.838_839delinsTA	7.37:g.102963052_102963053delinsTA	ENSP00000368565:p.Ile280*	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	60	33		0	0	0	0	0	A4VCI0|Q9BVX1	Nonsense_Mutation	DNP	ENST00000379263.3	37	CCDS43628.1																																																																																			.		0.337	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			TA	102963053	AT	TA	102963052	4	4	107	1	0	0	0	0	0	1	0	0	4650	449	16	5	1062	5	DNAJC2	7	102963052	Nonsense_Mutation	DNP	AT	TCGA-EV-5901-01A-11D-1589-08	30055853	102963052	56175611	26	9456											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77618779	77618779	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgccccggcggaagcagAgctttatcagtactacctag	9	8	10	14	3	1	1	1	0	0	1	2	2	1	2	4	2	4	3	4	2	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr8:77618779A>G	ENST00000521891.2	+	2	2904	c.2456A>G	c.(2455-2457)gAg>gGg	p.E819G	ZFHX4_ENST00000518282.1_Missense_Mutation_p.E819G|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.E819G|ZFHX4_ENST00000050961.6_Missense_Mutation_p.E819G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	819					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GCGGAAGCAGAGCTTTATCAG	0.507										HNSCC(33;0.089)																											p.E819G		.											.	ZFHX4-98	0			c.A2456G						.						20	20	20					8																	77618779		2018	4177	6195	SO:0001583	missense	79776	exon2			AAGCAGAGCTTTA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.2456A>G	8.37:g.77618779A>G	ENSP00000430497:p.Glu819Gly	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	15	2	NM_024721	0	0	1	1	0	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	12.39	1.922655	0.33908	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.56776	0.48;0.46;0.44;0.44	4.91	4.91	0.64330	.	0.000000	0.43579	U	0.000548	T	0.70150	0.3191	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.999;0.984	D;D;D;P	0.78314	0.979;0.991;0.991;0.885	T	0.74131	-0.3764	10	0.87932	D	0	.	14.9861	0.71348	1.0:0.0:0.0:0.0	.	819;819;819;819	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	G	819	ENSP00000430497:E819G;ENSP00000399605:E819G;ENSP00000050961:E819G;ENSP00000430848:E819G	ENSP00000050961:E819G	E	+	2	0	ZFHX4	77781334	1.000000	0.71417	0.996000	0.52242	0.913000	0.54294	9.048000	0.93830	2.179000	0.69175	0.477000	0.44152	GAG	.		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77618779	A	G	77618779	3	3	107	1	0	0	0	0	1	0	0	0	17667	304	11	3	2458	3	ZFHX4	8	77618779	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08		77618779	68745243	27	9457											
PLEC	5339	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	144997708	144997708	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctgcagccgcctgtgccTgagcccgggcctgtgcctgc	2	9	13	17	2	1	1	0	1	1	0	2	1	1	1	6	1	6	1	6	1	0	0			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr8:144997708T>A	ENST00000322810.4	-	31	6969	c.6800A>T	c.(6799-6801)cAg>cTg	p.Q2267L	PLEC_ENST00000357649.2_Missense_Mutation_p.Q2134L|PLEC_ENST00000354958.2_Missense_Mutation_p.Q2108L|PLEC_ENST00000398774.2_Missense_Mutation_p.Q2098L|PLEC_ENST00000345136.3_Missense_Mutation_p.Q2130L|PLEC_ENST00000354589.3_Missense_Mutation_p.Q2130L|PLEC_ENST00000436759.2_Missense_Mutation_p.Q2157L|PLEC_ENST00000356346.3_Missense_Mutation_p.Q2116L|PLEC_ENST00000527096.1_Missense_Mutation_p.Q2153L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2267	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CGCCTGTGCCTGAGCCCGGGC	0.741																																					p.Q2267L		.											.	PLEC-141	0			c.A6800T						.						8	10	10					8																	144997708		1949	4030	5979	SO:0001583	missense	5339	exon31			TGTGCCTGAGCCC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.6800A>T	8.37:g.144997708T>A	ENSP00000323856:p.Gln2267Leu	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	24	5	NM_201380	0	0	41	57	16	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	T	4.904	0.167918	0.09339	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.78816	-1.17;-1.17;-1.2;-1.21;-1.14;-1.17;-1.17;-1.14;-1.17	4.98	3.77	0.43336	.	0.288111	0.26875	U	0.022050	T	0.62684	0.2448	N	0.16790	0.44	0.32967	D	0.521856	B;B;B;B;B;B;B;B	0.13594	0.008;0.008;0.008;0.005;0.008;0.008;0.008;0.008	B;B;B;B;B;B;B;B	0.12156	0.007;0.007;0.007;0.003;0.007;0.007;0.007;0.007	T	0.64935	-0.6290	10	0.66056	D	0.02	.	10.4644	0.44598	0.1462:0.0:0.0:0.8538	.	2157;2116;2108;2267;2098;2130;2134;2130	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	L	2130;2134;2130;2098;2267;2108;2116;2157;2153	ENSP00000344848:Q2130L;ENSP00000350277:Q2134L;ENSP00000346602:Q2130L;ENSP00000381756:Q2098L;ENSP00000323856:Q2267L;ENSP00000347044:Q2108L;ENSP00000348702:Q2116L;ENSP00000388180:Q2157L;ENSP00000434583:Q2153L	ENSP00000323856:Q2267L	Q	-	2	0	PLEC	145069696	0.350000	0.24878	0.725000	0.30721	0.062000	0.15995	1.232000	0.32636	0.690000	0.31570	0.368000	0.22195	CAG	.		0.741	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144997708	T	A	144997708	3	1	107	1	0	0	0	0	1	0	0	0	12078	1580	55	5	7262	5	PLEC	8	144997708	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	67378929	144997708	1366314	28	9458											
ABCA2	20	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139908396	139908396	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgggcgcagtggaagcgtttGaccagcagcccgtggaactg	8	6	16	11	4	0	1	0	1	0	0	0	3	0	3	2	3	4	3	2	3	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr9:139908396G>C	ENST00000371605.3	-	27	4479	c.4332C>G	c.(4330-4332)gtC>gtG	p.V1444V	ABCA2_ENST00000341511.6_Silent_p.V1445V|ABCA2_ENST00000265662.5_Silent_p.V1445V			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1444					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GGAAGCGTTTGACCAGCAGCC	0.672																																					p.V1475V		.											.	ABCA2-90	0			c.C4425G						.						44	56	52					9																	139908396		2147	4225	6372	SO:0001819	synonymous_variant	20	exon28			GCGTTTGACCAGC	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.4332C>G	9.37:g.139908396G>C		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	33	11	NM_212533	0	0	37	70	33	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				.		0.672	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		C	139908396	G	C	139908396	2	2	107	1	0	0	0	0	0	0	0	1	32	1277	45	4		4	ABCA2	9	139908396	Silent	SNP	G	TCGA-EV-5901-01A-11D-1589-08		139908396	1305035	29	9459											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61836183	61836183	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaagtggtggggagggatcTtgttgctcctgtactccgtt	5	14	15	7	1	1	0	0	0	1	0	3	2	3	2	2	4	2	5	2	4	2	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr10:61836183T>C	ENST00000280772.2	-	37	4647	c.4456A>G	c.(4456-4458)Aga>Gga	p.R1486G	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1486					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GGGAGGGATCTTGTTGCTCCT	0.418																																					p.R1486G		.											.	ANK3-107	0			c.A4456G						.						86	86	86					10																	61836183		2203	4300	6503	SO:0001583	missense	288	exon37			GGGATCTTGTTGC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.4456A>G	10.37:g.61836183T>C	ENSP00000280772:p.Arg1486Gly	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	58	27	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	17.52	3.410662	0.62399	.	.	ENSG00000151150	ENST00000280772	T	0.70045	-0.45	5.69	5.69	0.88448	.	0.000000	0.46145	D	0.000309	T	0.71484	0.3345	L	0.57536	1.79	0.80722	D	1	D	0.56521	0.976	P	0.50109	0.631	T	0.74763	-0.3555	10	0.59425	D	0.04	.	15.9352	0.79698	0.0:0.0:0.0:1.0	.	1486	Q12955	ANK3_HUMAN	G	1486	ENSP00000280772:R1486G	ENSP00000280772:R1486G	R	-	1	2	ANK3	61506189	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.167000	0.68274	0.477000	0.44152	AGA	.		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61836183	T	C	61836183	3	2	107	1	0	0	0	0	1	0	0	0	622	1617	56	3	9018	3	ANK3	10	61836183	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		61836183	73698564	30	9460											
ZMYND17	118490	hgsc.bcm.edu;broad.mit.edu	37	chr10	75185676	75185676	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggcactaagctgaattgtgCcaggttccaggggtgaagtt	9	10	15	7	0	0	2	0	2	0	0	1	2	1	2	2	4	2	4	2	4	3	4	rs143815503	byFrequency	TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr10:75185676C>T	ENST00000372912.1	-	4	964	c.962G>A	c.(961-963)gGc>gAc	p.G321D	AL353731.1_ENST00000584907.1_RNA|MSS51_ENST00000299432.2_Missense_Mutation_p.G321D			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	321					social behavior (GO:0035176)		metal ion binding (GO:0046872)										CTGAATTGTGCCAGGTTCCAG	0.547																																					p.G321D		.											.	.	0			c.G962A						.						76	70	72					10																	75185676		2203	4300	6503	SO:0001583	missense	118490	exon5			ATTGTGCCAGGTT	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.962G>A	10.37:g.75185676C>T	ENSP00000362003:p.Gly321Asp	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_001024593	0	0	1	1	0	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	37	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004490	0.74932	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.47869	0.83;0.83	5.64	3.73	0.42828	.	0.228496	0.46758	D	0.000274	T	0.41858	0.1177	L	0.59436	1.845	0.41812	D	0.989971	B;B	0.27140	0.169;0.027	B;B	0.28553	0.091;0.018	T	0.34601	-0.9822	10	0.32370	T	0.25	-6.4632	9.5419	0.39257	0.0:0.7782:0.143:0.0788	.	100;321	Q4VC12-2;Q4VC12	.;ZMY17_HUMAN	D	321	ENSP00000299432:G321D;ENSP00000362003:G321D	ENSP00000299432:G321D	G	-	2	0	ZMYND17	74855682	1.000000	0.71417	0.995000	0.50966	0.964000	0.63967	2.882000	0.48546	1.627000	0.50400	0.650000	0.86243	GGC	C|1.000;A|0.000		0.547	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		T	75185676	C	T	75185676	3	4	107	1	0	0	0	0	1	0	0	0	17741	739	26	2	432	2	ZMYND17	10	75185676	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	13349493	75185676	60349071	31	9461											
LDB3	11155	hgsc.bcm.edu	37	chr10	88476182	88476182	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccccctcccctgcccctGcctacaccccctcacctgtc	5	7	3	26	0	1	0	1	0	0	0	3	0	2	0	10	0	3	0	10	0	1	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr10:88476182G>C	ENST00000361373.4	+	9	1351	c.1330G>C	c.(1330-1332)Gcc>Ccc	p.A444P	LDB3_ENST00000429277.2_Missense_Mutation_p.A449P|LDB3_ENST00000352360.5_Missense_Mutation_p.A187P|LDB3_ENST00000263066.6_Missense_Mutation_p.A334P|LDB3_ENST00000458213.2_Missense_Mutation_p.A334P	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						ccctgcccctgcctacacccc	0.652																																					p.A449P		.											.	LDB3-92	0			c.G1345C						.						25	24	24					10																	88476182		2192	4264	6456	SO:0001583	missense	11155	exon10			GCCCCTGCCTACA	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"cypher", "oracle", "Z-band alternatively spliced PDZ motif protein"	605906	"cardiomyopathy, dilated 1C (autosomal dominant)"	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1330G>C	10.37:g.88476182G>C	ENSP00000355296:p.Ala444Pro	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	15	3	NM_001171610	0	0	0	0	0		Missense_Mutation	SNP	ENST00000361373.4	37	CCDS7377.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.208962	0.39003	.	.	ENSG00000122367	ENST00000429277;ENST00000458213;ENST00000352360;ENST00000263066;ENST00000361373	T;T;T;T;T	0.54071	0.78;0.63;0.6;0.63;0.59	4.32	2.05	0.26809	.	0.805872	0.10145	N	0.710390	T	0.29389	0.0732	N	0.03608	-0.345	0.80722	D	1	B;B;B;D;B	0.53885	0.001;0.437;0.0;0.963;0.0	B;B;B;P;B	0.46796	0.001;0.143;0.002;0.527;0.001	T	0.04400	-1.0954	10	0.21540	T	0.41	.	4.7296	0.12957	0.1602:0.2243:0.6155:0.0	.	449;381;187;444;334	B4E3K3;F5H0C2;O75112-3;O75112;O75112-2	.;.;.;LDB3_HUMAN;.	P	449;334;187;334;444	ENSP00000401437:A449P;ENSP00000409148:A334P;ENSP00000263067:A187P;ENSP00000263066:A334P;ENSP00000355296:A444P	ENSP00000263066:A334P	A	+	1	0	LDB3	88466162	0.931000	0.31567	0.999000	0.59377	0.787000	0.44495	0.960000	0.29253	0.761000	0.33130	0.650000	0.86243	GCC	.		0.652	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			C	88476182	G	C	88476182	3	2	107	1	0	0	0	0	1	0	0	0	8718	1319	46	4	1700	4	LDB3	10	88476182	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	13290506	88476182	47058565	32	9462											
IFIT1B	439996	broad.mit.edu	37	chr10	91143275	91143275	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacacctgaaaggccagaatGaggaagccctggtcagcttg	13	6	12	10	0	1	3	1	2	0	1	1	4	1	4	3	3	3	1	3	3	4	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr10:91143275G>C	ENST00000371809.3	+	2	285	c.205G>C	c.(205-207)Gag>Cag	p.E69Q	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	69										endometrium(2)|large_intestine(3)|lung(8)	13						AGGCCAGAATGAGGAAGCCCT	0.448																																					p.E69Q													.	IFIT1B-90	0			c.G205C						.						87	87	87					10																	91143275		2203	4300	6503	SO:0001583	missense	439996	exon2			CAGAATGAGGAAG		CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"Tetratricopeptide (TTC) repeat domain containing"	23442	protein-coding gene	gene with protein product			"interferon-induced protein with tetratricopeptide repeats 1-like"	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.205G>C	10.37:g.91143275G>C	ENSP00000360874:p.Glu69Gln	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	132	3	NM_001010987	0	0	0	0	0	A7E245	Missense_Mutation	SNP	ENST00000371809.3	37	CCDS31242.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397772	0.42512	.	.	ENSG00000204010	ENST00000371809	D	0.94537	-3.45	4.61	-0.804	0.10882	Tetratricopeptide-like helical (1);	0.385721	0.27613	U	0.018591	D	0.89784	0.6815	L	0.41027	1.25	0.09310	N	1	P	0.39551	0.678	P	0.44696	0.458	T	0.81876	-0.0731	10	0.28530	T	0.3	.	4.9756	0.14138	0.3147:0.2608:0.4244:0.0	.	69	Q5T764	IFT1B_HUMAN	Q	69	ENSP00000360874:E69Q	ENSP00000360874:E69Q	E	+	1	0	IFIT1B	91133255	0.017000	0.18338	0.001000	0.08648	0.874000	0.50279	0.199000	0.17237	-0.188000	0.10499	0.557000	0.71058	GAG	.		0.448	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987		C	91143275	G	C	91143275	3	2	107	1	0	0	0	0	1	0	0	0	7543	1291	45	4	211	4	IFIT1B	10	91143275	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	2667093	91143275	44391472	33	9463											
GUCY2C	2984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	14796597	14796597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagttggtagatttcagaCgaccatggacttctgtctta	9	13	10	9	2	3	2	1	0	2	2	3	4	3	3	1	2	0	3	1	2	2	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr12:14796597C>T	ENST00000261170.3	-	17	1977	c.1841G>A	c.(1840-1842)cGt>cAt	p.R614H		NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	614	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	AGATTTCAGACGACCATGGAC	0.398																																					p.R614H		.											.	GUCY2C-338	0			c.G1841A						.						162	153	156					12																	14796597		2203	4300	6503	SO:0001583	missense	2984	exon17			TTCAGACGACCAT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.1841G>A	12.37:g.14796597C>T	ENSP00000261170:p.Arg614His	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	217	51	NM_004963	0	0	1	1	0	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	37	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110733	0.77210	.	.	ENSG00000070019	ENST00000261170	T	0.61980	0.06	5.47	5.47	0.80525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56232	0.1971	L	0.28458	0.855	0.80722	D	1	P	0.38767	0.646	B	0.39562	0.303	T	0.59862	-0.7374	10	0.54805	T	0.06	.	19.3191	0.94231	0.0:1.0:0.0:0.0	.	614	P25092	GUC2C_HUMAN	H	614	ENSP00000261170:R614H	ENSP00000261170:R614H	R	-	2	0	GUCY2C	14687864	1.000000	0.71417	0.800000	0.32199	0.988000	0.76386	4.932000	0.63476	2.549000	0.85964	0.650000	0.86243	CGT	.		0.398	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			T	14796597	C	T	14796597	3	4	107	1	0	0	0	0	1	0	0	0	6917	536	19	1	1424	1	GUCY2C	12	14796597	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		14796597	119055298	34	9464											
KDM2B	84678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	121947832	121947832	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aagccgtctatgctgggcttCctcggggcatctgtgggggc	4	10	16	11	2	2	0	0	0	2	0	4	0	3	0	2	5	2	3	2	5	2	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr12:121947832C>T	ENST00000377071.4	-	11	1257	c.1185G>A	c.(1183-1185)agG>agA	p.R395R	KDM2B_ENST00000542973.1_5'Flank|KDM2B_ENST00000377069.4_Silent_p.R364R|KDM2B_ENST00000536437.1_Silent_p.R278R|KDM2B_ENST00000538046.2_Silent_p.R305R	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	395					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TGCTGGGCTTCCTCGGGGCAT	0.577																																					p.R395R		.											.	KDM2B-638	0			c.G1185A						.						34	38	37					12																	121947832		1945	4141	6086	SO:0001819	synonymous_variant	84678	exon11			GGGCTTCCTCGGG	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.1185G>A	12.37:g.121947832C>T		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	70	24	NM_032590	0	0	0	0	0	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			.		0.577	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121947832	C	T	121947832	2	4	107	1	0	0	0	0	0	0	0	1	8146	854	30	2		2	KDM2B	12	121947832	Silent	SNP	C	TCGA-EV-5901-01A-11D-1589-08	107151235	121947832	11904063	35	9465											
SACS	26278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	23909472	23909472	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctactccaccacgtgggAaaagagtaatatcttggttc	12	10	9	10	1	1	1	0	0	1	1	3	2	2	2	2	2	2	3	2	2	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr13:23909472A>T	ENST00000382292.3	-	9	8816	c.8543T>A	c.(8542-8544)tTc>tAc	p.F2848Y	SACS_ENST00000382298.3_Missense_Mutation_p.F2848Y|SACS_ENST00000402364.1_Missense_Mutation_p.F2098Y			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2848					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ACCACGTGGGAAAAGAGTAAT	0.408																																					p.F2848Y		.											.	SACS-298	0			c.T8543A						.						85	83	84					13																	23909472		2203	4299	6502	SO:0001583	missense	26278	exon10			CGTGGGAAAAGAG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8543T>A	13.37:g.23909472A>T	ENSP00000371729:p.Phe2848Tyr	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	155	57	NM_014363	0	0	10	18	8	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889154	0.91889	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87491	-2.1;-2.26;-2.1	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.88819	0.6540	L	0.40543	1.245	0.43588	D	0.995931	D	0.59357	0.985	P	0.59221	0.854	D	0.87733	0.2580	10	0.33940	T	0.23	.	15.58	0.76425	1.0:0.0:0.0:0.0	.	2848	Q9NZJ4	SACS_HUMAN	Y	2848;2098;2848	ENSP00000371729:F2848Y;ENSP00000385844:F2098Y;ENSP00000371735:F2848Y	ENSP00000371729:F2848Y	F	-	2	0	SACS	22807472	1.000000	0.71417	0.920000	0.36463	0.995000	0.86356	8.962000	0.93254	2.084000	0.62774	0.449000	0.29647	TTC	.		0.408	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23909472	A	T	23909472	3	4	107	1	0	0	0	0	1	0	0	0	13836	246	9	5	5200	5	SACS	13	23909472	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08		23909472	91260406	36	9466											
B3GALTL	145173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	31821210	31821210	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctaaacaagaaggtgcAtggaccatacttccgttgtt	11	11	10	9	1	0	1	0	0	0	1	1	2	1	2	2	3	3	4	2	3	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr13:31821210A>G	ENST00000343307.4	+	5	470	c.321A>G	c.(319-321)gcA>gcG	p.A107A		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	107					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		AAGAAGGTGCATGGACCATAC	0.418																																					p.A107A		.											.	B3GALTL-92	0			c.A321G						.						166	132	144					13																	31821210		2203	4300	6503	SO:0001819	synonymous_variant	145173	exon5			AGGTGCATGGACC	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"Beta 3-glycosyltransferases"	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.321A>G	13.37:g.31821210A>G		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	105	30	NM_194318	0	0	8	9	1	A8K5F8|Q5W0H2|Q6NUI3	Silent	SNP	ENST00000343307.4	37	CCDS9341.1																																																																																			.		0.418	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318		G	31821210	A	G	31821210	2	3	107	1	0	0	0	0	0	0	0	1	1253	204	8	3		3	B3GALTL	13	31821210	Silent	SNP	A	TCGA-EV-5901-01A-11D-1589-08	7911738	31821210	83348668	37	9467											
AHNAK2	113146	ucsc.edu	37	chr14	105418145	105418145	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctccaggtcagcggaaggggGctgaatgctgaggtcagtgg	8	7	18	8	1	2	2	2	2	0	0	3	3	3	3	1	6	2	2	1	6	2	0	rs375277628	byFrequency	TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr14:105418145G>A	ENST00000333244.5	-	7	3762	c.3643C>T	c.(3643-3645)Ccc>Tcc	p.P1215S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1215						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCGGAAGGGGGCTGAATGCTG	0.647													.|||	6	0.00119808	0	0	5008	,	,		15037	0		0.001	False		,,,				2504	0.0051				p.P1215S													.	AHNAK2-47	0			c.C3643T						.	G	SER/PRO	2,3852		0,2,1925	96	70	79		3643	1.6	0	14		79	3,7607		0,3,3802	no	missense	AHNAK2	NM_138420.2	74	0,5,5727	AA,AG,GG		0.0394,0.0519,0.0436	benign	1215/5796	105418145	5,11459	1927	3805	5732	SO:0001583	missense	113146	exon7			AAGGGGGCTGAAT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3643C>T	14.37:g.105418145G>A	ENSP00000353114:p.Pro1215Ser	Somatic	158	1		WXS	Illumina HiSeq		136	1	NM_138420	0	1	98	122	23	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	9.389	1.074896	0.20227	5.19E-4	3.94E-4	ENSG00000185567	ENST00000333244	T	0.00840	5.63	4.55	1.58	0.23477	.	.	.	.	.	T	0.00695	0.0023	N	0.25201	0.72	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46512	-0.9186	9	0.08837	T	0.75	.	5.6981	0.17867	0.0766:0.3467:0.4538:0.1229	.	1215	Q8IVF2	AHNK2_HUMAN	S	1215	ENSP00000353114:P1215S	ENSP00000353114:P1215S	P	-	1	0	AHNAK2	104489190	.	.	0.009000	0.14445	0.004000	0.04260	.	.	0.383000	0.24910	-1.447000	0.01057	CCC	.		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105418145	G	A	105418145	3	1	107	1	0	0	0	0	1	0	0	0	415	1203	42	2	13748	2	AHNAK2	14	105418145	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		105418145	1931395	38	9468											
ZFP106	64397	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	42717056	42717056	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcaaagaatggttttgctAtggccctccagagttctgag	10	12	11	8	0	1	3	0	1	1	2	2	3	2	3	2	2	2	4	2	2	3	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr15:42717056A>C	ENST00000263805.4	-	13	5423	c.5097T>G	c.(5095-5097)caT>caG	p.H1699Q	RNU6-188P_ENST00000364207.1_RNA|ZNF106_ENST00000565660.1_5'Flank|ZNF106_ENST00000565380.1_Missense_Mutation_p.H927Q|ZNF106_ENST00000565611.1_Missense_Mutation_p.H884Q	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1699					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TGGTTTTGCTATGGCCCTCCA	0.522																																					p.H1699Q		.											.	ZFP106-515	0			c.T5097G						.						75	62	67					15																	42717056		2203	4299	6502	SO:0001583	missense	64397	exon13			TTTGCTATGGCCC	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"Zinc fingers, C2H2-type"	12886	protein-coding gene	gene with protein product	"SH3-domain binding protein 3"		"zinc finger protein 106 homolog (mouse)"	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.5097T>G	15.37:g.42717056A>C	ENSP00000263805:p.His1699Gln	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	31	14	NM_022473	0	0	22	31	9	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.779019	0.70107	.	.	ENSG00000103994	ENST00000263805;ENST00000434903	T	0.81415	-1.49	5.44	-5.28	0.02755	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.88952	0.6577	M	0.86805	2.84	0.51233	D	0.999915	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.999	D	0.89321	0.3640	10	0.87932	D	0	-15.4983	17.6295	0.88103	0.1114:0.0:0.8886:0.0	.	927;1699;927	E9PE29;Q9H2Y7;B4DZ40	.;ZF106_HUMAN;.	Q	1699;927	ENSP00000263805:H1699Q	ENSP00000263805:H1699Q	H	-	3	2	ZFP106	40504348	0.990000	0.36364	0.928000	0.36995	0.984000	0.73092	0.230000	0.17852	-0.844000	0.04184	-1.151000	0.01829	CAT	.		0.522	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		C	42717056	A	C	42717056	3	2	107	1	0	0	0	0	1	0	0	0	17669	446	16	5	582	5	ZFP106	15	42717056	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08		42717056	59814336	39	9469											
KIAA1199	57214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	81230320	81230320	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctactgggacgaggactcagGgtgagcaggcgcccacttgg	8	6	16	11	2	1	1	1	1	0	0	1	4	1	3	1	5	2	1	1	5	1	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr15:81230320G>A	ENST00000394685.3	+	25	3826	c.3407G>A	c.(3406-3408)gGg>gAg	p.G1136E	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Splice_Site_p.G1136E|KIAA1199_ENST00000220244.3_Splice_Site_p.G1136E			Q8WUJ3	CEMIP_HUMAN		1136					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GAGGACTCAGGGTGAGCAGGC	0.547																																					p.G1136E		.											.	KIAA1199-93	0			c.G3407A						.						38	33	35					15																	81230320		2203	4300	6503	SO:0001630	splice_region_variant	57214	exon24			ACTCAGGGTGAGC																												ENST00000394685.3:c.3407+1G>A	15.37:g.81230320G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	28	14	NM_018689	0	0	0	0	0	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	G	33	5.227247	0.95173	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249	T;T;T	0.50813	0.73;0.73;0.73	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.72463	0.3463	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72934	-0.4141	10	0.41790	T	0.15	-33.8466	19.3153	0.94211	0.0:0.0:1.0:0.0	.	1136	Q8WUJ3	K1199_HUMAN	E	1136	ENSP00000220244:G1136E;ENSP00000378177:G1136E;ENSP00000348583:G1136E	ENSP00000220244:G1136E	G	+	2	0	KIAA1199	79017375	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	9.063000	0.93927	2.559000	0.86315	0.655000	0.94253	GGG	.		0.547	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		Missense_Mutation	A	81230320	G	A	81230320	5	1	107	1	0	0	0	0	0	0	1	0	8234	1246	43	2	3497	2	KIAA1199	15	81230320	Splice_Site	SNP	G	TCGA-EV-5901-01A-11D-1589-08	38513264	81230320	21301072	40	9470											
AXIN1	8312	broad.mit.edu	37	chr16	354433	354433	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggacctccttcggcacccgGtacgtgcgctgcgagggaca	6	6	14	15	6	0	0	0	0	0	0	2	3	1	2	3	4	3	3	3	4	1	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr16:354433G>A	ENST00000262320.3	-	5	1496	c.1125C>T	c.(1123-1125)taC>taT	p.Y375Y	AXIN1_ENST00000354866.3_Silent_p.Y375Y|AXIN1_ENST00000481769.1_5'UTR	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	375	Interaction with GSK3B. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.?(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCGGCACCCGGTACGTGCGCT	0.617																																					p.Y375Y													.	AXIN1-684	1	Unknown(1)	liver(1)	c.C1125T						.						27	27	27					16																	354433		2199	4290	6489	SO:0001819	synonymous_variant	8312	exon5			CACCCGGTACGTG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1125C>T	16.37:g.354433G>A		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_181050	0	0	5	5	0	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			.		0.617	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	354433	G	A	354433	2	1	107	1	0	0	0	0	0	0	0	1	1237	1256	44	2		2	AXIN1	16	354433	Silent	SNP	G	TCGA-EV-5901-01A-11D-1589-08		354433	90000320	41	9471											
ROGDI	79641	hgsc.bcm.edu	37	chr16	4849745	4849745	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtcccggctggtaagcaggTaaatggcttggctcacatgg	8	9	15	9	1	1	0	1	0	0	0	2	0	2	0	1	7	1	6	1	7	3	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr16:4849745T>C	ENST00000322048.7	-	6	752	c.374A>G	c.(373-375)tAc>tGc	p.Y125C	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	125					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GGTAAGCAGGTAAATGGCTTG	0.627																																					p.Y125C		.											.	ROGDI-92	0			c.A374G						.						107	84	92					16																	4849745		2197	4300	6497	SO:0001583	missense	79641	exon6			AGCAGGTAAATGG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.374A>G	16.37:g.4849745T>C	ENSP00000322832:p.Tyr125Cys	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_024589	0	0	79	79	0	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	.	.	.	.	.	.	.	.	.	.	T	18.71	3.683056	0.68157	.	.	ENSG00000067836	ENST00000322048	T	0.42513	0.97	4.91	4.91	0.64330	.	0.134555	0.52532	D	0.000077	T	0.50309	0.1608	L	0.44542	1.39	0.49798	D	0.999821	D	0.63046	0.992	P	0.57371	0.819	T	0.50684	-0.8799	10	0.51188	T	0.08	-43.9912	13.5501	0.61728	0.0:0.0:0.0:1.0	.	125	Q9GZN7	ROGDI_HUMAN	C	125	ENSP00000322832:Y125C	ENSP00000322832:Y125C	Y	-	2	0	ROGDI	4789746	1.000000	0.71417	0.992000	0.48379	0.802000	0.45316	4.942000	0.63547	1.845000	0.53610	0.459000	0.35465	TAC	.		0.627	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589		C	4849745	T	C	4849745	3	2	107	1	0	0	0	0	1	0	0	0	13552	1638	57	3	513	3	ROGDI	16	4849745	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	4495312	4849745	85505008	42	9472											
FBRS	64319	hgsc.bcm.edu;broad.mit.edu	37	chr16	30676958	30676958	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccctccactcccctttcccaGagcacgaaccctgagctgcc	7	7	6	21	1	0	2	0	1	0	1	3	3	3	2	7	0	4	2	7	0	1	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr16:30676958G>C	ENST00000287468.5	+	5	407		c.e5-1		FBRS_ENST00000568722.1_Intron|FBRS_ENST00000395073.2_Splice_Site|FBRS_ENST00000356166.6_Splice_Site	NM_001105079.1	NP_001098549.1	Q9HAH7	FBRS_HUMAN	fibrosin											ovary(1)	1			Colorectal(24;0.103)			CCCTTTCCCAGAGCACGAACC	0.652																																					.		.											.	FBRS-23	0			c.145-1G>C						.						21	22	22					16																	30676958		1984	4156	6140	SO:0001630	splice_region_variant	64319	exon5			TTCCCAGAGCACG	AK021680		16p11.2	2008-02-05	2007-04-18	2007-04-18	ENSG00000156860	ENSG00000156860			20442	protein-coding gene	gene with protein product		608601	"fibrosin 1"	FBS1		7892239, 9809749	Standard	NM_001105079		Approved	FBS, FLJ11618	uc002dzd.4	Q9HAH7	OTTHUMG00000132390	ENST00000287468.5:c.145-1G>C	16.37:g.30676958G>C		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	12	2	NM_001105079	0	0	3	3	0	B4DP86|Q96CI9|Q9H9X4	Splice_Site	SNP	ENST00000287468.5	37		.	.	.	.	.	.	.	.	.	.	G	16.21	3.058130	0.55325	.	.	ENSG00000156860	ENST00000356166;ENST00000287468	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6054	0.76664	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FBRS	30584459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.886000	0.63149	2.419000	0.82065	0.591000	0.81541	.	.		0.652	FBRS-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_022452	Intron	C	30676958	G	C	30676958	5	2	107	1	0	0	0	0	0	0	1	0	5726	956	33	4	158	4	FBRS	16	30676958	Splice_Site	SNP	G	TCGA-EV-5901-01A-11D-1589-08	25827213	30676958	59677795	43	9473											
ALOX12	239	broad.mit.edu	37	chr17	6905026	6905026	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccgaaattcagatttcCaactgcacgagatccagtat	12	10	9	10	2	1	2	1	0	0	2	4	4	4	2	3	1	2	2	3	1	3	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr17:6905026C>A	ENST00000251535.6	+	8	1110	c.1057C>A	c.(1057-1059)Caa>Aaa	p.Q353K	AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000399540.2_3'UTR|AC027763.2_ENST00000574377.1_Intron|RP11-589P10.7_ENST00000572547.1_RNA	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	353	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						TTCAGATTTCCAACTGCACGA	0.592																																					p.Q353K													.	ALOX12-226	0			c.C1057A						.						123	111	115					17																	6905026		2203	4300	6503	SO:0001583	missense	239	exon8			GATTTCCAACTGC	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"Arachidonate lipoxygenases"	429	protein-coding gene	gene with protein product	"platelet 12-LOX"	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.1057C>A	17.37:g.6905026C>A	ENSP00000251535:p.Gln353Lys	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	224	5	NM_000697	0	0	2	2	0	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	37	CCDS11084.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.057271	0.76074	.	.	ENSG00000108839	ENST00000251535	T	0.76578	-1.03	4.9	4.9	0.64082	Lipoxygenase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.87657	0.6232	M	0.88570	2.965	0.44995	D	0.998011	P	0.49253	0.921	P	0.56648	0.803	D	0.88947	0.3384	10	0.52906	T	0.07	-10.0858	15.9493	0.79820	0.0:1.0:0.0:0.0	.	353	P18054	LOX12_HUMAN	K	353	ENSP00000251535:Q353K	ENSP00000251535:Q353K	Q	+	1	0	ALOX12	6845750	1.000000	0.71417	1.000000	0.80357	0.645000	0.38454	2.872000	0.48467	2.699000	0.92147	0.573000	0.79308	CAA	.		0.592	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2			A	6905026	C	A	6905026	3	1	107	1	0	0	0	0	1	0	0	0	536	595	21	4	1087	4	ALOX12	17	6905026	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		6905026	74290184	44	9474											
LRRC37A3	374819	ucsc.edu	37	chr17	62855652	62855652	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccgtatcccattctatctTggatgcctttacttcctgct	5	17	6	13	1	2	0	0	0	2	0	5	1	5	1	4	1	3	2	4	1	3	7			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr17:62855652T>C	ENST00000584306.1	-	11	5142	c.4612A>G	c.(4612-4614)Aag>Gag	p.K1538E	LRRC37A3_ENST00000319651.5_Missense_Mutation_p.K1538E|LRRC37A3_ENST00000339474.5_Missense_Mutation_p.K656E|LRRC37A3_ENST00000334962.5_Missense_Mutation_p.K515E|LRRC37A3_ENST00000400877.3_Missense_Mutation_p.K576E	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1538						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CATTCTATCTTGGATGCCTTT	0.522																																					p.K1538E													.	LRRC37A3-90	0			c.A4612G						.						165	172	169					17																	62855652		2202	4294	6496	SO:0001583	missense	374819	exon11			CTATCTTGGATGC	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.4612A>G	17.37:g.62855652T>C	ENSP00000464535:p.Lys1538Glu	Somatic	313	7		WXS	Illumina HiSeq		459	14	NM_199340	0	0	19	61	42	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	10.65	1.408868	0.25378	.	.	ENSG00000176809	ENST00000339474;ENST00000400877;ENST00000334962;ENST00000319651	T;T;T	0.51817	0.69;0.69;0.69	2.39	1.1	0.20463	.	.	.	.	.	T	0.56978	0.2022	M	0.65498	2.005	0.09310	N	1	P;D	0.53151	0.941;0.958	B;P	0.60682	0.323;0.878	T	0.42103	-0.9471	9	0.59425	D	0.04	.	4.8525	0.13543	0.0:0.0:0.3244:0.6756	.	656;1538	B4DG20;O60309	.;L37A3_HUMAN	E	619;576;515;1538	ENSP00000383674:K576E;ENSP00000335617:K515E;ENSP00000325713:K1538E	ENSP00000325713:K1538E	K	-	1	0	LRRC37A3	60286114	0.000000	0.05858	0.025000	0.17156	0.011000	0.07611	0.003000	0.13083	1.098000	0.41479	0.155000	0.16302	AAG	.		0.522	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		C	62855652	T	C	62855652	3	2	107	1	0	0	0	0	1	0	0	0	9018	1821	63	3	308	3	LRRC37A3	17	62855652	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	55950626	62855652	18339558	45	9475											
ABCA5	23461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	67283846	67283846	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaagattccatacaatatgtCgagaacaggggtccattcca	15	9	8	9	1	0	2	0	0	0	2	4	3	3	2	3	2	2	0	3	2	5	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr17:67283846C>T	ENST00000392676.3	-	15	2013	c.1949G>A	c.(1948-1950)cGa>cAa	p.R650Q	ABCA5_ENST00000392677.2_Missense_Mutation_p.R650Q|ABCA5_ENST00000588877.1_Missense_Mutation_p.R650Q			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	650	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TACAATATGTCGAGAACAGGG	0.408																																					p.R650Q		.											.	ABCA5-93	0			c.G1949A						.						113	109	110					17																	67283846		2203	4300	6503	SO:0001583	missense	23461	exon14			ATATGTCGAGAAC	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1949G>A	17.37:g.67283846C>T	ENSP00000376443:p.Arg650Gln	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	193	101	NM_018672	0	0	4	15	11	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	C	36	5.706333	0.96821	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	T;T	0.39997	1.05;1.05	5.63	5.63	0.86233	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.186313	0.36815	N	0.002382	T	0.70150	0.3191	M	0.85630	2.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.72707	-0.4212	9	.	.	.	.	19.2741	0.94023	0.0:1.0:0.0:0.0	.	650;650	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	Q	650	ENSP00000376444:R650Q;ENSP00000376443:R650Q	.	R	-	2	0	ABCA5	64795441	1.000000	0.71417	0.982000	0.44146	0.925000	0.55904	7.391000	0.79828	2.641000	0.89580	0.585000	0.79938	CGA	.		0.408	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		T	67283846	C	T	67283846	3	4	107	1	0	0	0	0	1	0	0	0	35	884	31	1	3079	1	ABCA5	17	67283846	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	4428194	67283846	13911364	46	9476											
POLRMT	5442	broad.mit.edu	37	chr19	621842	621842	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccgggtgcggcttcaggatgCcgatctggggtgcgacaggc	5	7	18	11	4	2	0	1	0	1	0	2	3	2	1	2	6	3	1	2	6	0	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr19:621842C>T	ENST00000588649.2	-	10	1940	c.1856G>A	c.(1855-1857)gGc>gAc	p.G619D	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	619					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCAGGATGCCGATCTGGGG	0.687																																					p.G619D													.	POLRMT-92	0			c.G1856A						.						22	25	24					19																	621842		2199	4293	6492	SO:0001583	missense	5442	exon10			AGGATGCCGATCT		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.1856G>A	19.37:g.621842C>T	ENSP00000465759:p.Gly619Asp	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	28	3	NM_005035	0	0	0	0	0	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	19.54	3.847427	0.71603	.	.	ENSG00000099821	ENST00000215591	T	0.56444	0.46	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.72890	0.3517	M	0.79926	2.475	0.80722	D	1	D	0.69078	0.997	D	0.68765	0.96	T	0.76841	-0.2810	10	0.56958	D	0.05	-44.8841	16.5929	0.84772	0.0:1.0:0.0:0.0	.	619	O00411	RPOM_HUMAN	D	619	ENSP00000215591:G619D	ENSP00000215591:G619D	G	-	2	0	POLRMT	572842	1.000000	0.71417	1.000000	0.80357	0.473000	0.32948	7.412000	0.80091	2.398000	0.81561	0.455000	0.32223	GGC	.		0.687	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		T	621842	C	T	621842	3	4	107	1	0	0	0	0	1	0	0	0	12264	739	26	2	1884	2	POLRMT	19	621842	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		621842	58507141	47	9477											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10541704	10541704	+	Intron	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccccaactttccgcagaCgccttcggcttctccgcagc	5	9	8	19	5	1	1	0	0	1	1	5	1	3	1	5	1	2	3	5	1	1	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr19:10541704C>A	ENST00000352831.6	+	1	430				PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000293683.5_Missense_Mutation_p.R62S|PDE4A_ENST00000592685.1_Intron|PDE4A_ENST00000440014.2_5'Flank	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific						cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	TTTCCGCAGACGCCTTCGGCT	0.731																																					p.R62S		.											.	PDE4A-523	0			c.C184A						.						10	10	10					19																	10541704		1557	3562	5119	SO:0001627	intron_variant	5141	exon1			CGCAGACGCCTTC		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"Phosphodiesterases"	8780	protein-coding gene	gene with protein product	"phosphodiesterase E2 dunce homolog (Drosophila)"	600126	"phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.320+9944C>A	19.37:g.10541704C>A		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	14	4	NM_001111308	0	0	7	12	5	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	.	.	.	.	.	.	.	.	.	.	c	18.49	3.635976	0.67130	.	.	ENSG00000065989	ENST00000293683	T	0.68479	-0.33	3.48	3.48	0.39840	.	.	.	.	.	T	0.48840	0.1522	N	0.20986	0.625	0.80722	D	1	P	0.44478	0.836	B	0.40444	0.329	T	0.39231	-0.9624	9	0.19147	T	0.46	.	10.7182	0.46026	0.0:1.0:0.0:0.0	.	62	P27815-2	.	S	62	ENSP00000293683:R62S	ENSP00000293683:R62S	R	+	1	0	PDE4A	10402704	0.429000	0.25530	0.993000	0.49108	0.604000	0.37047	1.697000	0.37784	1.966000	0.57179	0.537000	0.68136	CGC	.		0.731	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			A	10541704	C	A	10541704	1	1	107	0	1	0	0	0	0	0	0	0	11665	536	19	4		4	PDE4A	19	10541704	Intron	SNP	C	TCGA-EV-5901-01A-11D-1589-08	9919862	10541704	48587279	48	9478											
RAB3A	5864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18313494	18313494	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	agaatcttgaacatgtagtcGaagttctgatccgaggactc	12	11	10	8	2	2	3	0	2	2	1	5	6	3	4	1	1	1	2	1	1	4	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr19:18313494G>C	ENST00000222256.4	-	2	235	c.57C>G	c.(55-57)ttC>ttG	p.F19L	AC068499.10_ENST00000596473.1_RNA|AC068499.10_ENST00000594805.3_RNA|AC068499.10_ENST00000599416.2_RNA|RAB3A_ENST00000464076.3_Intron	NM_002866.4	NP_002857.1	P20336	RAB3A_HUMAN	RAB3A, member RAS oncogene family	19					axonogenesis (GO:0007409)|constitutive secretory pathway (GO:0045054)|glutamate secretion (GO:0014047)|GTP catabolic process (GO:0006184)|lung development (GO:0030324)|maintenance of presynaptic active zone structure (GO:0048790)|mitochondrion organization (GO:0007005)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|post-embryonic development (GO:0009791)|protein transport (GO:0015031)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|respiratory system process (GO:0003016)|response to electrical stimulus (GO:0051602)|sensory perception of touch (GO:0050975)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle recycling (GO:0036465)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	8						ACATGTAGTCGAAGTTCTGAT	0.582											OREG0025360	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F19L		.											.	RAB3A-227	0			c.C57G						.						257	217	230					19																	18313494		2203	4300	6503	SO:0001583	missense	5864	exon2			GTAGTCGAAGTTC		CCDS12372.1	19p13.2	2008-07-17			ENSG00000105649	ENSG00000105649		"RAB, member RAS oncogene"	9777	protein-coding gene	gene with protein product	"RAS-associated protein RAB3A"	179490				2687157, 7532276	Standard	NM_002866		Approved		uc002nie.2	P20336	OTTHUMG00000137378	ENST00000222256.4:c.57C>G	19.37:g.18313494G>C	ENSP00000222256:p.Phe19Leu	Somatic	246	0	724	WXS	Illumina HiSeq	Phase_I	195	56	NM_002866	0	0	4	8	4	A8K0J4|Q9NYE1	Missense_Mutation	SNP	ENST00000222256.4	37	CCDS12372.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017822	0.75161	.	.	ENSG00000105649	ENST00000222256	T	0.79141	-1.24	4.4	0.678	0.17969	.	0.000000	0.85682	D	0.000000	T	0.72890	0.3517	N	0.25890	0.77	0.80722	D	1	D	0.65815	0.995	P	0.59889	0.865	T	0.70490	-0.4857	10	0.87932	D	0	-19.6435	5.4616	0.16619	0.5735:0.0:0.4265:0.0	.	19	P20336	RAB3A_HUMAN	L	19	ENSP00000222256:F19L	ENSP00000222256:F19L	F	-	3	2	RAB3A	18174494	0.677000	0.27577	1.000000	0.80357	0.984000	0.73092	-0.040000	0.12104	0.318000	0.23185	0.313000	0.20887	TTC	.		0.582	RAB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268056.2	NM_002866		C	18313494	G	C	18313494	3	2	107	1	0	0	0	0	1	0	0	0	12963	1049	37	4	621	4	RAB3A	19	18313494	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	7771790	18313494	40815489	49	9479											
ZNF155	7711	broad.mit.edu	37	chr19	44501505	44501505	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcttgtacacaggacataccGtaaagaccagccgagagact	14	6	10	11	2	0	2	0	0	0	2	0	5	0	3	3	1	3	3	3	1	4	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr19:44501505G>A	ENST00000270014.2	+	5	1624	c.1496G>A	c.(1495-1497)cGt>cAt	p.R499H	RP11-15A1.7_ENST00000586860.1_RNA|ZNF155_ENST00000590615.1_Missense_Mutation_p.R499H|RP11-15A1.7_ENST00000589021.1_RNA|ZNF155_ENST00000407951.2_Missense_Mutation_p.R510H	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	499					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R499H(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				AGGACATACCGTAAAGACCAG	0.453																																					p.R510H	NSCLC(61;554 1277 20909 42067 42312)												.	ZNF155-154	1	Substitution - Missense(1)	kidney(1)	c.G1529A						.						89	91	91					19																	44501505		2203	4300	6503	SO:0001583	missense	7711	exon6			CATACCGTAAAGA	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"Zinc fingers, C2H2-type", "-"	12940	protein-coding gene	gene with protein product		604086	"zinc finger protein 155 (pHZ-96)"			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.1496G>A	19.37:g.44501505G>A	ENSP00000270014:p.Arg499His	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	107	4	NM_001260488	0	0	11	11	0	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Missense_Mutation	SNP	ENST00000270014.2	37	CCDS12634.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.468786	0.43839	.	.	ENSG00000204920	ENST00000407951;ENST00000270014	T;T	0.15256	2.44;2.44	2.36	1.31	0.21738	Zinc finger, C2H2 (1);	.	.	.	.	T	0.17365	0.0417	L	0.35542	1.07	0.09310	N	1	D;D	0.57899	0.981;0.981	P;P	0.49361	0.608;0.608	T	0.12656	-1.0539	9	0.72032	D	0.01	.	7.8091	0.29219	0.0:0.0:0.2272:0.7728	.	510;499	B4DM95;Q12901	.;ZN155_HUMAN	H	510;499	ENSP00000385163:R510H;ENSP00000270014:R499H	ENSP00000270014:R499H	R	+	2	0	ZNF155	49193345	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	0.433000	0.21477	0.338000	0.23692	-0.397000	0.06425	CGT	.		0.453	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445		A	44501505	G	A	44501505	3	1	107	1	0	0	0	0	1	0	0	0	17768	1145	40	1	1510	1	ZNF155	19	44501505	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	26188011	44501505	14627478	50	9480											
CSNK2A1	1457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	468205	468205	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtggacaaagcgttcccatCgctttcgagagtgtctgcag	8	11	12	10	3	1	1	0	0	1	1	4	3	2	2	1	1	2	3	1	1	1	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr20:468205C>T	ENST00000217244.3	-	12	1214	c.839G>A	c.(838-840)cGa>cAa	p.R280Q	CSNK2A1_ENST00000400217.2_Missense_Mutation_p.R144Q|CSNK2A1_ENST00000400227.3_Missense_Mutation_p.R280Q|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.R280Q	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	280	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GCGTTCCCATCGCTTTCGAGA	0.502																																					p.R280Q		.											.	CSNK2A1-791	0			c.G839A						.						85	76	80					20																	468205		2203	4300	6503	SO:0001583	missense	1457	exon11			TCCCATCGCTTTC	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.839G>A	20.37:g.468205C>T	ENSP00000217244:p.Arg280Gln	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	70	21	NM_001895	0	0	98	193	95	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	C	33	5.233597	0.95207	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.43294	3.29;3.29;3.29;0.95	5.24	5.24	0.73138	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	N	0.17594	0.5	0.80722	D	1	D	0.89917	1.0	D	0.65140	0.932	T	0.51426	-0.8707	10	0.52906	T	0.07	-6.9053	17.9724	0.89117	0.0:1.0:0.0:0.0	.	280	P68400	CSK21_HUMAN	Q	280;280;280;280;144	ENSP00000383086:R280Q;ENSP00000339247:R280Q;ENSP00000217244:R280Q;ENSP00000383076:R144Q	ENSP00000217244:R280Q	R	-	2	0	CSNK2A1	416205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.601000	0.82783	2.713000	0.92767	0.585000	0.79938	CGA	.		0.502	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		T	468205	C	T	468205	3	4	107	1	0	0	0	0	1	0	0	0	3963	884	31	1	348	1	CSNK2A1	20	468205	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		468205	62557315	51	9481											
CRYZL1	9946	broad.mit.edu	37	chr21	34974552	34974552	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacccacctatgggaggtcTgaatctttcaaggcactgct	9	12	9	11	0	3	1	1	1	2	0	3	2	3	2	2	3	2	2	2	3	4	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr21:34974552T>C	ENST00000381554.3	-	8	650	c.565A>G	c.(565-567)Aga>Gga	p.R189G	CRYZL1_ENST00000445393.1_Missense_Mutation_p.R151G|CRYZL1_ENST00000381540.3_Missense_Mutation_p.R189G|CRYZL1_ENST00000290244.5_Missense_Mutation_p.R174G|CRYZL1_ENST00000361534.2_Missense_Mutation_p.R213G|AP000304.12_ENST00000429238.1_Intron	NM_145858.2	NP_665857.2	O95825	QORL1_HUMAN	crystallin, zeta (quinone reductase)-like 1	189					quinone metabolic process (GO:1901661)	cytosol (GO:0005829)	NADP binding (GO:0050661)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			lung(1)|prostate(1)|urinary_tract(1)	3						ATGGGAGGTCTGAATCTTTCA	0.373																																					p.R189G													.	CRYZL1-90	0			c.A565G						.						142	132	135					21																	34974552		2203	4300	6503	SO:0001583	missense	9946	exon8			GAGGTCTGAATCT	AF029689	CCDS13633.2	21q22.1	2008-07-31			ENSG00000205758	ENSG00000205758			2420	protein-coding gene	gene with protein product	"quinone reductase-like 1"	603920				10191096	Standard	NM_145858		Approved	QOH-1, 4P11	uc021wio.1	O95825	OTTHUMG00000065954	ENST00000381554.3:c.565A>G	21.37:g.34974552T>C	ENSP00000370966:p.Arg189Gly	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	91	3	NM_145858	0	0	0	0	0	B2RDX1|B3KQ77|Q96DY0|Q9NVY7	Missense_Mutation	SNP	ENST00000381554.3	37	CCDS13633.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.942777|3.942777	0.73672|0.73672	.|.	.|.	ENSG00000205758|ENSG00000205758	ENST00000440526|ENST00000381554;ENST00000290244;ENST00000381540;ENST00000445393;ENST00000361534;ENST00000452332;ENST00000414079;ENST00000426935	.|T;T;T;T;T;T;T	.|0.29917	.|5.33;5.33;5.33;1.83;5.33;5.33;1.55	4.98|4.98	-2.68|-2.68	0.06041|0.06041	.|Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	.|0.115715	.|0.64402	.|D	.|0.000007	T|T	0.13329|0.13329	0.0323|0.0323	N|N	0.00569|0.00569	-1.365|-1.365	0.30079|0.30079	N|N	0.809379|0.809379	.|B;P	.|0.45634	.|0.171;0.863	.|B;P	.|0.54856	.|0.174;0.762	T|T	0.39210|0.39210	-0.9625|-0.9625	5|10	.|0.39692	.|T	.|0.17	-6.7286|-6.7286	9.2606|9.2606	0.37610|0.37610	0.1262:0.0:0.5228:0.351|0.1262:0.0:0.5228:0.351	.|.	.|189;213	.|O95825;A6NHJ8	.|QORL1_HUMAN;.	R|G	132|189;174;189;151;213;189;49;137	.|ENSP00000370966:R189G;ENSP00000290244:R174G;ENSP00000370951:R189G;ENSP00000399730:R151G;ENSP00000355075:R213G;ENSP00000409387:R49G;ENSP00000387660:R137G	.|ENSP00000290244:R174G	Q|R	-|-	2|1	0|2	CRYZL1|CRYZL1	33896422|33896422	0.876000|0.876000	0.30132|0.30132	0.008000|0.008000	0.14137|0.14137	0.603000|0.603000	0.37013|0.37013	0.722000|0.722000	0.25925|0.25925	-0.656000|-0.656000	0.05380|0.05380	-0.313000|-0.313000	0.08912|0.08912	CAG|AGA	.		0.373	CRYZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141282.2	NM_145858		C	34974552	T	C	34974552	3	2	107	1	0	0	0	0	1	0	0	0	3929	1588	55	3	508	3	CRYZL1	21	34974552	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		34974552	13155343	52	9482											
HMOX1	3162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	35779129	35779129	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatttgtcagaggccctgaaGgaggccaccaaggaggtgca	11	6	15	9	0	1	2	1	1	0	1	1	5	1	4	3	5	1	1	3	5	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr22:35779129G>T	ENST00000216117.8	+	2	393	c.54G>T	c.(52-54)aaG>aaT	p.K18N		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	18					angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	AGGCCCTGAAGGAGGCCACCA	0.577																																					p.K18N		.											.	HMOX1-91	0			c.G54T						.						85	78	80					22																	35779129		2203	4300	6503	SO:0001583	missense	3162	exon2			CCTGAAGGAGGCC		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.54G>T	22.37:g.35779129G>T	ENSP00000216117:p.Lys18Asn	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	94	29	NM_002133	0	0	25	30	5		Missense_Mutation	SNP	ENST00000216117.8	37	CCDS13914.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982022	0.74474	.	.	ENSG00000100292	ENST00000412893;ENST00000216117	T;T	0.26957	1.7;1.7	6.06	2.67	0.31697	Haem oxygenase-like, multi-helical (2);	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	M	0.91300	3.195	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.60367	-0.7277	10	0.87932	D	0	-50.6157	9.0075	0.36120	0.338:0.0:0.662:0.0	.	18	P09601	HMOX1_HUMAN	N	18	ENSP00000413316:K18N;ENSP00000216117:K18N	ENSP00000216117:K18N	K	+	3	2	HMOX1	34109129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.625000	0.37029	0.909000	0.36697	0.655000	0.94253	AAG	.		0.577	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1			T	35779129	G	T	35779129	3	4	107	1	0	0	0	0	1	0	0	0	7264	991	35	4	60	4	HMOX1	22	35779129	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		35779129	15525437	53	9483											
SUN2	25777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	39146253	39146253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaagtggccaccatccagAgtaaggagcccgcccgtgag	10	4	14	13	3	0	2	0	1	0	1	1	4	1	3	5	2	1	1	5	2	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr22:39146253A>G	ENST00000405510.1	-	6	855	c.497T>C	c.(496-498)cTc>cCc	p.L166P	SUN2_ENST00000411587.2_Missense_Mutation_p.L155P|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000405018.1_Missense_Mutation_p.L187P|SUN2_ENST00000406622.1_Missense_Mutation_p.L166P|SUN2_ENST00000216064.4_Missense_Mutation_p.L166P	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	166					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CACCATCCAGAGTAAGGAGCC	0.602																																					p.L187P		.											.	SUN2-154	0			c.T560C						.						47	52	50					22																	39146253		2203	4300	6503	SO:0001583	missense	25777	exon5			ATCCAGAGTAAGG	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.497T>C	22.37:g.39146253A>G	ENSP00000385740:p.Leu166Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	66	22	NM_001199579	0	0	105	177	72	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Missense_Mutation	SNP	ENST00000405510.1	37	CCDS13978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.41|14.41	2.527820|2.527820	0.44969|0.44969	.|.	.|.	ENSG00000100242|ENSG00000100242	ENST00000405510;ENST00000216064;ENST00000405018;ENST00000406622;ENST00000411587;ENST00000438058;ENST00000456894;ENST00000420859|ENST00000430185	T;T;T;T;T;T;T;T|.	0.40756|.	2.3;2.3;2.31;2.3;2.16;1.03;1.23;1.02|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.691574|.	0.13508|.	N|.	0.382686|.	T|T	0.49029|0.49029	0.1533|0.1533	N|N	0.19112|0.19112	0.55|0.55	0.41384|0.41384	D|D	0.987572|0.987572	P;D;D;D;D|.	0.57257|.	0.826;0.979;0.963;0.971;0.963|.	B;P;P;P;P|.	0.50617|.	0.347;0.642;0.642;0.646;0.521|.	T|T	0.46762|0.46762	-0.9168|-0.9168	10|5	0.87932|.	D|.	0|.	-3.5021|-3.5021	13.3916|13.3916	0.60827|0.60827	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	155;201;166;187;166|.	B4DIU6;B4E2A6;Q2T9F7;B0QY62;Q9UH99|.	.;.;.;.;SUN2_HUMAN|.	P|P	166;166;187;166;155;120;166;120|23	ENSP00000385740:L166P;ENSP00000216064:L166P;ENSP00000385616:L187P;ENSP00000383992:L166P;ENSP00000395601:L155P;ENSP00000406941:L120P;ENSP00000415588:L166P;ENSP00000408834:L120P|.	ENSP00000216064:L166P|.	L|S	-|-	2|1	0|0	SUN2|SUN2	37476199|37476199	0.307000|0.307000	0.24500|0.24500	0.729000|0.729000	0.30791|0.30791	0.137000|0.137000	0.21094|0.21094	1.454000|1.454000	0.35178|0.35178	2.032000|2.032000	0.59987|0.59987	0.528000|0.528000	0.53228|0.53228	CTC|TCT	.		0.602	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		G	39146253	A	G	39146253	3	3	107	1	0	0	0	0	1	0	0	0	15424	304	11	3	1712	3	SUN2	22	39146253	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	3367124	39146253	12158313	54	9484											
DDX3X	1654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	41202004	41202004	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tttgagggaactcttttctgGaggcaacactgggattaatt	10	14	11	6	0	2	1	0	1	2	0	2	4	2	4	0	4	2	1	0	4	3	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chrX:41202004G>A	ENST00000399959.2	+	6	1313	c.458G>A	c.(457-459)gGa>gAa	p.G153E	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000542215.1_Missense_Mutation_p.G197E|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000457138.2_Missense_Mutation_p.G137E|DDX3X_ENST00000441189.2_Intron	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	153	Interaction with GSK3B.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						CTCTTTTCTGGAGGCAACACT	0.363										HNSCC(61;0.18)																											p.G153E		.											.	DDX3X-715	0			c.G458A						.						102	93	96					X																	41202004		2049	4205	6254	SO:0001583	missense	1654	exon6			TTTCTGGAGGCAA	U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"DEAD-boxes"	2745	protein-coding gene	gene with protein product		300160	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.458G>A	X.37:g.41202004G>A	ENSP00000382840:p.Gly153Glu	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	145	54	NM_001193416	0	0	0	3	3	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.209130	0.39003	.	.	ENSG00000215301	ENST00000399959;ENST00000457138;ENST00000542215	T;T;T	0.42513	2.21;2.18;0.97	5.75	5.75	0.90469	.	0.050157	0.85682	D	0.000000	T	0.38799	0.1054	L	0.45228	1.405	0.80722	D	1	B;B;B;B;B	0.11235	0.004;0.002;0.001;0.004;0.004	B;B;B;B;B	0.10450	0.005;0.005;0.003;0.005;0.005	T	0.15407	-1.0438	10	0.20046	T	0.44	-0.7141	18.9517	0.92643	0.0:0.0:1.0:0.0	.	153;137;153;165;153	B4DLU5;B4E3E8;B5BTY4;Q59GX6;O00571	.;.;.;.;DDX3X_HUMAN	E	153;137;197	ENSP00000382840:G153E;ENSP00000392494:G137E;ENSP00000439799:G197E	ENSP00000382840:G153E	G	+	2	0	DDX3X	41086948	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.723000	0.61965	2.424000	0.82194	0.600000	0.82982	GGA	.		0.363	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		A	41202004	G	A	41202004	3	1	107	1	0	0	0	0	1	0	0	0	4364	1174	41	2	480	2	DDX3X	23	41202004	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		41202004	114068556	55	9485											
AHDC1	27245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27875947	27875947	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgccactgggctggcctTggctccccggctagggaagg	5	7	15	14	1	0	0	0	0	0	0	1	1	1	1	4	6	1	3	4	6	2	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:27875947T>G	ENST00000247087.5	-	5	3276	c.2680A>C	c.(2680-2682)Aag>Cag	p.K894Q	AHDC1_ENST00000374011.2_Missense_Mutation_p.K894Q			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	894							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GGGCTGGCCTTGGCTCCCCGG	0.716																																					p.K894Q		.											.	AHDC1-90	0			c.A2680C						.						19	23	22					1																	27875947		2196	4287	6483	SO:0001583	missense	27245	exon6			TGGCCTTGGCTCC	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2680A>C	1.37:g.27875947T>G	ENSP00000247087:p.Lys894Gln	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	55	33	NM_001029882	0	0	8	23	15	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	37	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943941	0.73672	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.55052	0.54;0.54	5.77	5.77	0.91146	.	0.088674	0.42548	D	0.000697	T	0.57504	0.2058	N	0.14661	0.345	0.46774	D	0.999191	D	0.76494	0.999	D	0.83275	0.996	T	0.64740	-0.6336	10	0.72032	D	0.01	-11.4835	15.0705	0.72034	0.0:0.0:0.0:1.0	.	894	Q5TGY3	AHDC1_HUMAN	Q	894	ENSP00000247087:K894Q;ENSP00000363123:K894Q	ENSP00000247087:K894Q	K	-	1	0	AHDC1	27748534	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.070000	0.76763	2.199000	0.70637	0.533000	0.62120	AAG	.		0.716	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			G	27875947	T	G	27875947	3	3	108	1	0	0	0	0	1	0	0	0	412	1821	63	5	2135	5	AHDC1	1	27875947	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		27875947	221374674	1	9486											
RLF	6018	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	40705390	40705391	+	Frame_Shift_Ins	INS	-	-	T																															tgctctacaggggaactttgINSaaatgtaatcatagttccaa																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:40705390_40705391insT	ENST00000372771.4	+	8	5043_5044	c.5016_5017insT	c.(5017-5019)aaafs	p.K1673fs		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1673					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			GGGGAACTTTGAAATGTAATCA	0.411																																					p.L1672fs		.											.	RLF-93	0			c.5016_5017insT						.																																			SO:0001589	frameshift_variant	6018	exon8			.		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"Zinc fingers, C2H2-type"	10025	protein-coding gene	gene with protein product		180610	"rearranged L-myc fusion sequence"			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	Exception_encountered	1.37:g.40705390_40705391insT	ENSP00000361857:p.Lys1673fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	103	54	NM_012421	0	0	0	0	0	Q14CQ1|Q9NU60	Frame_Shift_Ins	INS	ENST00000372771.4	37	CCDS448.1																																																																																			.		0.411	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		T	40705391	-	T	40705390	7	5	108	1	0	1	1	0	0	0	0	0	13421	1281	45	0	5046	0	RLF	1	40705390	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	12829443	40705390	208545231	2	9487											
USP24	23358	hgsc.bcm.edu;broad.mit.edu	37	chr1	55569689	55569689	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatcggctattcgctgtacTacacctagaaacaaaagaca	16	8	6	11	2	0	2	0	0	0	2	2	2	0	2	1	1	3	3	1	1	8	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:55569689T>C	ENST00000294383.6	-	42	4884	c.4885A>G	c.(4885-4887)Agt>Ggt	p.S1629G	USP24_ENST00000407756.1_Missense_Mutation_p.S1469G	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1629					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TTCGCTGTACTACACCTAGAA	0.328																																					p.S1629G		.											.	USP24-521	0			c.A4885G						.						43	40	41					1																	55569689		1867	4093	5960	SO:0001583	missense	23358	exon42			CTGTACTACACCT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"Ubiquitin-specific peptidases"	12623	protein-coding gene	gene with protein product		610569	"ubiquitin specific protease 24"			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.4885A>G	1.37:g.55569689T>C	ENSP00000294383:p.Ser1629Gly	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	21	6	NM_015306	0	0	0	0	0	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	T	15.27	2.782405	0.49891	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02323	4.34;4.34	6.05	6.05	0.98169	.	0.084787	0.85682	D	0.000000	T	0.03178	0.0093	N	0.25890	0.77	0.43152	D	0.994923	B	0.22003	0.063	B	0.22386	0.039	T	0.56944	-0.7895	10	0.23302	T	0.38	.	15.1642	0.72807	0.0:0.0:0.0:1.0	.	1469	B7WPF4	.	G	1629;1469	ENSP00000294383:S1629G;ENSP00000385700:S1469G	ENSP00000294383:S1629G	S	-	1	0	USP24	55342277	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.616000	0.83018	2.320000	0.78422	0.528000	0.53228	AGT	.		0.328	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			C	55569689	T	C	55569689	3	2	108	1	0	0	0	0	1	0	0	0	17088	1522	53	3	3085	3	USP24	1	55569689	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	14864299	55569689	193680932	3	9488											
C1orf54	79630	broad.mit.edu	37	chr1	150246559	150246559	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtctattattatacagTcacccccagttatggtgagt	9	14	10	8	0	2	1	1	1	1	0	2	1	2	1	2	3	1	1	2	3	5	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:150246559T>C	ENST00000369102.1	+	4	886	c.116T>C	c.(115-117)gTc>gCc	p.V39A	C1orf54_ENST00000369099.3_Missense_Mutation_p.V39A|C1orf54_ENST00000369098.3_Missense_Mutation_p.V39A			Q8WWF1	CA054_HUMAN	chromosome 1 open reading frame 54	39						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TATTATACAGTCACCCCCAGT	0.438																																					p.V39A													.	C1orf54-90	0			c.T116C						.						138	142	141					1																	150246559		2203	4300	6503	SO:0001583	missense	79630	exon2			ATACAGTCACCCC	BC017761	CCDS948.1, CCDS72905.1	1q21.2	2012-06-25			ENSG00000118292	ENSG00000118292			26258	protein-coding gene	gene with protein product						12477932	Standard	NM_024579		Approved	FLJ23221	uc001eud.3	Q8WWF1	OTTHUMG00000012546	ENST00000369102.1:c.116T>C	1.37:g.150246559T>C	ENSP00000358098:p.Val39Ala	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	169	4	NM_024579	0	0	0	0	0	Q9H5P3	Missense_Mutation	SNP	ENST00000369102.1	37	CCDS948.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.115321	0.77323	.	.	ENSG00000118292	ENST00000369102;ENST00000369099;ENST00000369098	.	.	.	4.9	4.9	0.64082	.	0.484707	0.17387	N	0.176072	T	0.37156	0.0993	L	0.54323	1.7	0.32047	N	0.597459	P;P	0.49961	0.93;0.93	P;P	0.47915	0.561;0.561	T	0.42783	-0.9431	9	0.72032	D	0.01	-7.2786	11.0953	0.48141	0.0:0.0:0.0:1.0	.	39;39	Q5TB16;Q8WWF1	.;CA054_HUMAN	A	39	.	ENSP00000358094:V39A	V	+	2	0	C1orf54	148513183	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.432000	0.52824	2.184000	0.69523	0.533000	0.62120	GTC	.		0.438	C1orf54-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035055.1	NM_024579		C	150246559	T	C	150246559	3	2	108	1	0	0	0	0	1	0	0	0	2052	1667	58	3	122	3	C1orf54	1	150246559	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	94676870	150246559	99004062	4	9489											
FLG	2312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152279672	152279672	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcctggctaaaactggatcCccagttcctgcttgtcctgg	6	12	10	13	0	0	0	0	0	0	0	4	1	4	1	5	3	2	3	5	3	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:152279672C>A	ENST00000368799.1	-	3	7725	c.7690G>T	c.(7690-7692)Gga>Tga	p.G2564*	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2564	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAACTGGATCCCCAGTTCCTG	0.582									Ichthyosis																												p.G2564X		.											.	FLG-106	0			c.G7690T						.						187	200	196					1																	152279672		2201	4300	6501	SO:0001587	stop_gained	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGATCCCCAGTT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7690G>T	1.37:g.152279672C>A	ENSP00000357789:p.Gly2564*	Somatic	424	1		WXS	Illumina HiSeq	Phase_I	433	213	NM_002016	0	0	0	0	0	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	46	12.137190	0.99639	.	.	ENSG00000143631	ENST00000368799	.	.	.	3.61	-1.65	0.08291	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	7.5003	0.27513	0.0:0.4216:0.4707:0.1077	.	.	.	.	X	2564	.	ENSP00000357789:G2564X	G	-	1	0	FLG	150546296	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.888000	0.28268	-0.164000	0.10927	0.306000	0.20318	GGA	.		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152279672	C	A	152279672	4	1	108	1	0	0	0	0	0	1	0	0	5941	632	22	4	4499	4	FLG	1	152279672	Nonsense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	2033113	152279672	96970949	5	9490											
MYOC	4653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171605341	171605341	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tttgtctcccaggtttgttcGagttccagattctctgggtt	4	18	10	9	1	2	1	0	0	2	1	6	2	3	1	2	2	0	4	2	2	0	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:171605341G>C	ENST00000037502.6	-	3	1310	c.1239C>G	c.(1237-1239)ctC>ctG	p.L413L		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	413	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					AGGTTTGTTCGAGTTCCAGAT	0.522																																					p.L413L		.											.	MYOC-226	0			c.C1239G						.						210	193	199					1																	171605341		2203	4300	6503	SO:0001819	synonymous_variant	4653	exon3			TTGTTCGAGTTCC	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.1239C>G	1.37:g.171605341G>C		Somatic	214	0		WXS	Illumina HiSeq	Phase_I	155	63	NM_000261	0	0	0	0	0	B2RD84|O00620|Q7Z6Q9	Silent	SNP	ENST00000037502.6	37	CCDS1297.1																																																																																			.		0.522	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		C	171605341	G	C	171605341	2	2	108	1	0	0	0	0	0	0	0	1	10111	1045	37	4		4	MYOC	1	171605341	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	19325669	171605341	77645280	6	9491											
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228473855	228473855	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tcggccaccttccgttgccgGatctccccggccaactacga	6	8	9	18	5	1	0	0	0	1	0	4	2	2	1	7	3	3	1	7	3	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:228473855G>C	ENST00000422127.1	+	34	9125	c.9081G>C	c.(9079-9081)cgG>cgC	p.R3027R	OBSCN_ENST00000366709.4_Silent_p.R146R|OBSCN_ENST00000284548.11_Silent_p.R3027R|OBSCN_ENST00000366707.4_Silent_p.R146R|OBSCN_ENST00000570156.2_Silent_p.R3456R|OBSCN_ENST00000359599.6_Silent_p.R1874R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3027	Ig-like 30.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCCGTTGCCGGATCTCCCCGG	0.627																																					p.R3456R		.											.	OBSCN-403	0			c.G10368C						.						33	43	40					1																	228473855		2117	4218	6335	SO:0001819	synonymous_variant	84033	exon39			TTGCCGGATCTCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9081G>C	1.37:g.228473855G>C		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	19	12	NM_001271223	0	0	6	8	2	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228473855	G	C	228473855	2	2	108	1	0	0	0	0	0	0	0	1	10838	1161	41	4		4	OBSCN	1	228473855	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	56868514	228473855	20776766	7	9492											
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32667276	32667276	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttggttagctggagttcAttcaaatggacccggaaggt	9	12	13	7	1	2	0	2	0	0	0	2	3	2	3	1	5	1	4	1	5	3	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:32667276A>C	ENST00000421745.2	+	18	4222	c.4088A>C	c.(4087-4089)cAt>cCt	p.H1363P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1363					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GCTGGAGTTCATTCAAATGGA	0.383																																					p.H1363P	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.A4088C						.						62	61	61					2																	32667276		2203	4300	6503	SO:0001583	missense	57448	exon18			GAGTTCATTCAAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4088A>C	2.37:g.32667276A>C	ENSP00000393596:p.His1363Pro	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	69	37	NM_016252	0	0	2	5	3	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	14.04	2.417748	0.42918	.	.	ENSG00000115760	ENST00000421745	T	0.74209	-0.82	5.4	5.4	0.78164	.	0.220885	0.39083	N	0.001466	T	0.66317	0.2777	L	0.29908	0.895	0.40728	D	0.982722	B	0.22604	0.072	B	0.25291	0.059	T	0.65697	-0.6105	10	0.59425	D	0.04	.	15.4322	0.75108	1.0:0.0:0.0:0.0	.	1363	Q9NR09	BIRC6_HUMAN	P	1363	ENSP00000393596:H1363P	ENSP00000393596:H1363P	H	+	2	0	BIRC6	32520780	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.513000	0.60476	2.039000	0.60335	0.519000	0.50382	CAT	.		0.383	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32667276	A	C	32667276	3	2	108	1	0	0	0	0	1	0	0	0	1439	217	8	5	4158	5	BIRC6	2	32667276	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		32667276	210532097	8	9493											
HNRPLL	92906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	38791355	38791355	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgatgtagaaaagcaaagcTtcaatgtatagggattggaa	17	10	11	3	0	1	2	1	1	0	1	1	4	1	4	0	2	2	4	0	2	8	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:38791355T>A	ENST00000449105.3	-	13	1937	c.1598A>T	c.(1597-1599)aAg>aTg	p.K533M	HNRNPLL_ENST00000409328.1_Missense_Mutation_p.K499M|HNRNPLL_ENST00000409636.1_Missense_Mutation_p.K528M|HNRNPLL_ENST00000378915.3_Missense_Mutation_p.K499M|HNRNPLL_ENST00000608859.1_Missense_Mutation_p.K533M			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	533					mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										AAAGCAAAGCTTCAATGTATA	0.289																																					p.K533M		.											.	HNRPLL-91	0			c.A1598T						.						86	94	91					2																	38791355		2203	4298	6501	SO:0001583	missense	92906	exon13			CAAAGCTTCAATG	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.1598A>T	2.37:g.38791355T>A	ENSP00000390625:p.Lys533Met	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	142	69	NM_138394	0	0	31	55	24	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	37		.	.	.	.	.	.	.	.	.	.	T	19.35	3.810102	0.70797	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328	.	.	.	5.83	5.83	0.93111	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.80592	0.4652	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.994;0.994;0.996	T	0.83330	-0.0013	9	0.87932	D	0	.	16.194	0.82011	0.0:0.0:0.0:1.0	.	528;533;533	C9J9G0;D6W592;Q8WVV9	.;.;HNRLL_HUMAN	M	533;528;499;499	.	ENSP00000368195:K499M	K	-	2	0	HNRPLL	38644859	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.360000	0.79487	2.225000	0.72522	0.460000	0.39030	AAG	.		0.289	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394		A	38791355	T	A	38791355	3	1	108	1	0	0	0	0	1	0	0	0	7298	1609	56	5	34	5	HNRPLL	2	38791355	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	6124079	38791355	204408018	9	9494											
DHX57	90957	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	39030017	39030017	+	Frame_Shift_Del	DEL	T	T	-																															atactcgactagtttttatcTtctcgtggtacaacaggtag																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:39030017delT	ENST00000295373.6	-	23	3983	c.3857delA	c.(3856-3858)aagfs	p.K1286fs		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1286							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				AGTTTTTATCTTCTCGTGGTA	0.468																																					p.K1286fs	Melanoma(191;1090 2095 4375 23729 47341)	.											.	DHX57-228	0			c.3857delA						.						165	163	164					2																	39030017		2203	4300	6503	SO:0001589	frameshift_variant	90957	exon23			.	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"DEAH-boxes"	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3857delA	2.37:g.39030017delT	ENSP00000295373:p.Lys1286fs	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	195	83	NM_198963	0	0	0	0	0	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Frame_Shift_Del	DEL	ENST00000295373.6	37	CCDS1800.1																																																																																			.		0.468	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		-	39030017	T	-	39030017	7	5	108	1	0	1	0	1	0	0	0	0	4524	1609	56	0	311	0	DHX57	2	39030017	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08	238662	39030017	204169356	10	9495											
SLC3A1	6519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44508525	44508525	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgtcttttactcattaGgtttaaaattaatcatcgat	14	17	5	5	1	3	0	2	0	1	0	4	2	3	0	0	1	1	1	0	1	6	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:44508525G>C	ENST00000260649.6	+	3	686		c.e3-1		SLC3A1_ENST00000409741.1_Splice_Site|SLC3A1_ENST00000409229.3_Splice_Site|SLC3A1_ENST00000409387.1_Splice_Site|SLC3A1_ENST00000410056.3_Splice_Site	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1						amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	TTACTCATTAGGTTTAAAATT	0.353																																					.		.											.	SLC3A1-90	0			c.611-1G>C						.						64	63	63					2																	44508525		2203	4300	6503	SO:0001630	splice_region_variant	6519	exon3			TCATTAGGTTTAA		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.611-1G>C	2.37:g.44508525G>C		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	74	32	NM_000341	0	0	1	3	2	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Splice_Site	SNP	ENST00000260649.6	37	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112058	0.37242	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000410056;ENST00000409741;ENST00000409229;ENST00000541289	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.147	0.86768	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC3A1	44362029	1.000000	0.71417	0.999000	0.59377	0.336000	0.28762	9.024000	0.93689	2.323000	0.78572	0.551000	0.68910	.	.		0.353	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	Intron	C	44508525	G	C	44508525	5	2	108	1	0	0	0	0	0	0	1	0	14658	1014	35	4	620	4	SLC3A1	2	44508525	Splice_Site	SNP	G	TCGA-EV-5902-01A-11D-1589-08	5478508	44508525	198690848	11	9496											
FSHR	2492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	49190328	49190328	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggatatagcagccacagatGaccacaaaggccaggacatt	15	6	10	10	0	0	2	0	1	0	1	0	4	0	4	3	3	2	1	3	3	3	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:49190328G>A	ENST00000406846.2	-	10	1751	c.1632C>T	c.(1630-1632)gtC>gtT	p.V544V	FSHR_ENST00000541117.1_Silent_p.V280V|FSHR_ENST00000304421.4_Silent_p.V518V|FSHR_ENST00000346173.3_Silent_p.V482V	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	544					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	AGCCACAGATGACCACAAAGG	0.532									Gonadal Dysgenesis, 46 XX																												p.V544V		.											.	FSHR-527	0			c.C1632T						.						141	111	121					2																	49190328		2203	4300	6503	SO:0001819	synonymous_variant	2492	exon10	Familial Cancer Database		ACAGATGACCACA		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1632C>T	2.37:g.49190328G>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	38	18	NM_000145	0	0	0	0	0	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Silent	SNP	ENST00000406846.2	37	CCDS1843.1																																																																																			.		0.532	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49190328	G	A	49190328	2	1	108	1	0	0	0	0	0	0	0	1	6092	1277	45	2		2	FSHR	2	49190328	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	4681803	49190328	194009045	12	9497											
MRPS5	64969	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95753148	95753148	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	accacacagagcgcttcattCcctgtgcagtcttcacatct	9	11	6	15	1	4	1	2	0	2	1	5	1	5	1	2	0	2	2	2	0	0	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:95753148C>G	ENST00000272418.2	-	12	1455	c.1247G>C	c.(1246-1248)gGa>gCa	p.G416A		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	416					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						GCGCTTCATTCCCTGTGCAGT	0.572																																					p.G416A		.											.	MRPS5-92	0			c.G1247C						.						103	96	99					2																	95753148		2203	4300	6503	SO:0001583	missense	64969	exon12			TTCATTCCCTGTG	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"Mitochondrial ribosomal proteins / small subunits"	14498	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S5"	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.1247G>C	2.37:g.95753148C>G	ENSP00000272418:p.Gly416Ala	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	84	41	NM_031902	0	0	38	74	36	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	37	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318910	0.60524	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.98	5.1	0.69264	.	0.052056	0.85682	D	0.000000	T	0.75781	0.3896	M	0.63843	1.955	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.78175	-0.2306	9	0.72032	D	0.01	-16.5572	13.0098	0.58725	0.0:0.9224:0.0:0.0776	.	416	P82675	RT05_HUMAN	A	416	.	ENSP00000272418:G416A	G	-	2	0	MRPS5	95116875	1.000000	0.71417	0.990000	0.47175	0.070000	0.16714	6.883000	0.75595	1.560000	0.49568	0.650000	0.86243	GGA	.		0.572	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902		G	95753148	C	G	95753148	3	3	108	1	0	0	0	0	1	0	0	0	9871	855	30	4	49	4	MRPS5	2	95753148	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	46562820	95753148	147446225	13	9498											
IL1RL2	8808	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	102836361	102836361	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccatgtctcttttcgggAacataatttgtacacagtaa	13	13	6	9	1	1	0	0	0	1	0	3	1	1	1	1	1	3	2	1	1	5	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:102836361A>C	ENST00000264257.2	+	8	1001	c.875A>C	c.(874-876)gAa>gCa	p.E292A	IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000539491.1_Missense_Mutation_p.E292A|IL1RL2_ENST00000441515.2_Missense_Mutation_p.E174A	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	292	Ig-like C2-type 3.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TCTTTTCGGGAACATAATTTG	0.358																																					p.E292A		.											.	IL1RL2-92	0			c.A875C						.						103	98	100					2																	102836361		2203	4300	6503	SO:0001583	missense	8808	exon8			TTCGGGAACATAA	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.875A>C	2.37:g.102836361A>C	ENSP00000264257:p.Glu292Ala	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	98	40	NM_003854	0	0	3	3	0	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	A	5.529	0.282573	0.10458	.	.	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.13901	2.55;2.55;2.55	5.09	2.7	0.31948	.	1.166780	0.05889	N	0.627921	T	0.11495	0.0280	L	0.36672	1.1	0.09310	N	1	B;B	0.25312	0.057;0.123	B;B	0.22753	0.028;0.041	T	0.41342	-0.9514	10	0.17369	T	0.5	.	6.8812	0.24174	0.8123:0.0:0.1877:0.0	.	174;292	A4FU63;Q9HB29	.;ILRL2_HUMAN	A	292;174;292	ENSP00000264257:E292A;ENSP00000413348:E174A;ENSP00000442184:E292A	ENSP00000264257:E292A	E	+	2	0	IL1RL2	102202793	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.965000	0.29319	0.357000	0.24183	-0.256000	0.11100	GAA	.		0.358	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		C	102836361	A	C	102836361	3	2	108	1	0	0	0	0	1	0	0	0	7685	246	9	5	901	5	IL1RL2	2	102836361	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	7083213	102836361	140363012	14	9499											
RND3	390	broad.mit.edu	37	chr2	151328205	151328205	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaatgtactaacatctgtcCgcagatcagacttgcagccg	11	10	8	12	2	2	2	1	0	1	2	3	2	3	2	2	0	4	3	2	0	3	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:151328205C>A	ENST00000375734.2	-	4	668	c.419G>T	c.(418-420)cGg>cTg	p.R140L	RND3_ENST00000472416.1_5'UTR|RND3_ENST00000409557.1_Missense_Mutation_p.R11L|RND3_ENST00000263895.4_Missense_Mutation_p.R140L	NM_001254738.1	NP_001241667.1	P61587	RND3_HUMAN	Rho family GTPase 3	140					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R140Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.106)		AACATCTGTCCGCAGATCAGA	0.403																																					p.R140L													.	RND3-659	1	Substitution - Missense(1)	lung(1)	c.G419T						.						102	96	98					2																	151328205		2203	4300	6503	SO:0001583	missense	390	exon4			TCTGTCCGCAGAT		CCDS2190.1	2q23.3	2008-02-05	2005-01-24	2005-01-27	ENSG00000115963	ENSG00000115963			671	protein-coding gene	gene with protein product		602924	"ras homolog gene family, member E"	ARHE		8649376	Standard	NM_001254738		Approved	RhoE, Rho8	uc002txe.3	P61587	OTTHUMG00000131859	ENST00000375734.2:c.419G>T	2.37:g.151328205C>A	ENSP00000364886:p.Arg140Leu	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	126	4	NM_001254738	0	0	46	47	1	D3DP95|P52199	Missense_Mutation	SNP	ENST00000375734.2	37	CCDS2190.1	.	.	.	.	.	.	.	.	.	.	C	36	5.654258	0.96724	.	.	ENSG00000115963	ENST00000375734;ENST00000263895;ENST00000409557	T;T;T	0.77620	-1.11;-1.11;-1.11	5.76	5.76	0.90799	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.88797	0.6534	M	0.77486	2.375	0.80722	D	1	D;D;D	0.89917	0.978;1.0;1.0	D;D;D	0.97110	0.969;1.0;1.0	D	0.89414	0.3705	10	0.87932	D	0	-17.2601	18.9641	0.92689	0.0:1.0:0.0:0.0	.	11;139;140	B4DSG7;D3DP96;P61587	.;.;RND3_HUMAN	L	140;140;11	ENSP00000364886:R140L;ENSP00000263895:R140L;ENSP00000386576:R11L	ENSP00000263895:R140L	R	-	2	0	RND3	151036451	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.796000	0.85898	2.713000	0.92767	0.655000	0.94253	CGG	.		0.403	RND3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254809.1	NM_005168		A	151328205	C	A	151328205	3	1	108	1	0	0	0	0	1	0	0	0	13453	652	23	4	323	4	RND3	2	151328205	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	48491844	151328205	91871168	15	9500											
XIRP2	129446	hgsc.bcm.edu;bcgsc.ca	37	chr2	168115244	168115247	+	Frame_Shift_Del	DEL	TTTC	TTTC	-																															agaagacatctattttagaaTttcttgatctattacccttg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	TTTC	TTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:168115244_168115247delTTTC	ENST00000409728.1	+	11	2376_2379	c.2287_2290delTTTC	c.(2287-2292)tttcttfs	p.FL763fs	XIRP2_ENST00000409043.1_Frame_Shift_Del_p.FL730fs|XIRP2_ENST00000420519.1_Frame_Shift_Del_p.FL763fs|XIRP2_ENST00000409605.1_Frame_Shift_Del_p.FL508fs|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Frame_Shift_Del_p.FL730fs|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409273.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1281					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TATTTTAGAATTTCTTGATCTATT	0.299																																					p.763_764del		.											.	XIRP2-104	0			c.2287_2290del						.																																			SO:0001589	frameshift_variant	129446	exon11			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2287_2290delTTTC	2.37:g.168115244_168115247delTTTC	ENSP00000386619:p.Phe763fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	92	51	NM_001199143	0	0	0	0	0	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409728.1	37	CCDS56143.1																																																																																			.		0.299	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		-	168115247	TTTC	-	168115244	7	5	108	1	0	1	0	1	0	0	0	0	17463	1493	52	0	11605	0	XIRP2	2	168115244	Frame_Shift_Del	DEL	TTTC	TCGA-EV-5902-01A-11D-1589-08	16787039	168115244	75084129	16	9501											
FAM171B	165215	hgsc.bcm.edu	37	chr2	187559029	187559029	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccgacctcagcctcatccaAcagcagcagcagcagcagca	12	4	8	17	1	2	0	2	0	0	0	4	1	4	0	4	0	8	6	4	0	1	0	rs549897920|rs56669143	byFrequency	TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:187559029A>G	ENST00000304698.5	+	1	332	c.129A>G	c.(127-129)caA>caG	p.Q43Q	AC017101.10_ENST00000453665.1_RNA	NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	43	Gln-rich.					integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCCTCATCcaacagcagcagc	0.642																																					p.Q43Q		.											.	FAM171B-141	0			c.A129G						.						18	20	19					2																	187559029		2201	4300	6501	SO:0001819	synonymous_variant	165215	exon1			CATCCAACAGCAG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"KIAA1946"	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.129A>G	2.37:g.187559029A>G		Somatic	34	1		WXS	Illumina HiSeq	Phase_I	22	4	NM_177454	0	0	0	0	0	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																			.		0.642	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		G	187559029	A	G	187559029	2	3	108	1	0	0	0	0	0	0	0	1	5507	40	2	3		3	FAM171B	2	187559029	Silent	SNP	A	TCGA-EV-5902-01A-11D-1589-08	19443785	187559029	55640344	17	9502											
CASP10	843	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	202073930	202073931	+	Frame_Shift_Del	DEL	TG	TG	-																															acggggactgcttcgtgttcTgtattctgacccatgggaga																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:202073930_202073931delTG	ENST00000272879.5	+	9	1244_1245	c.1060_1061delTG	c.(1060-1062)tgtfs	p.C354fs	CASP10_ENST00000346817.5_Frame_Shift_Del_p.C311fs|CASP10_ENST00000448480.1_Frame_Shift_Del_p.C311fs|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000286186.6_Frame_Shift_Del_p.C354fs|CASP10_ENST00000313728.7_Frame_Shift_Del_p.C287fs|CASP10_ENST00000492363.1_3'UTR	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	354					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						CTTCGTGTTCTGTATTCTGACC	0.515																																					p.354_354del		.											.	CASP10-1086	0			c.1060_1061del						.																																			SO:0001589	frameshift_variant	843	exon9			.	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"Caspases"	1500	protein-coding gene	gene with protein product		601762	"caspase 10, apoptosis-related cysteine protease"			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1060_1061delTG	2.37:g.202073930_202073931delTG	ENSP00000272879:p.Cys354fs	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	186	90	NM_032977	0	0	0	0	0	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Frame_Shift_Del	DEL	ENST00000272879.5	37	CCDS2338.1																																																																																			.		0.515	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977		-	202073931	TG	-	202073930	7	5	108	1	0	1	0	1	0	0	0	0	2675	1580	55	0	1090	0	CASP10	2	202073930	Frame_Shift_Del	DEL	TG	TCGA-EV-5902-01A-11D-1589-08	14514901	202073930	41125443	18	9503											
WNT10A	80326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219754716	219754716	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttaaccacaggtttccgagaGagcgcttttgcctacgccat	9	11	9	12	3	0	1	0	0	0	1	1	3	1	1	4	1	4	2	4	1	2	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:219754716G>C	ENST00000258411.3	+	3	1020	c.387G>C	c.(385-387)gaG>gaC	p.E129D	WNT10A_ENST00000483911.1_3'UTR	NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	129					cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|epidermis morphogenesis (GO:0048730)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|neural crest cell differentiation (GO:0014033)|neuron differentiation (GO:0030182)|odontogenesis (GO:0042476)|positive regulation of gene expression (GO:0010628)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sebaceous gland development (GO:0048733)|skin development (GO:0043588)|tongue development (GO:0043586)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|cervix(1)|endometrium(2)|lung(6)|skin(2)	12		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTTTCCGAGAGAGCGCTTTTG	0.582																																					p.E129D		.											.	WNT10A-523	0			c.G387C						.						96	86	90					2																	219754716		2203	4300	6503	SO:0001583	missense	80326	exon3			CCGAGAGAGCGCT	AB059569	CCDS2426.1	2q35	2008-05-23			ENSG00000135925	ENSG00000135925		"Wingless-type MMTV integration sites"	13829	protein-coding gene	gene with protein product		606268				11350055, 17847007	Standard	NM_025216		Approved		uc002vjd.1	Q9GZT5	OTTHUMG00000133085	ENST00000258411.3:c.387G>C	2.37:g.219754716G>C	ENSP00000258411:p.Glu129Asp	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	119	44	NM_025216	0	0	0	0	0	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	37	CCDS2426.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993868	0.74703	.	.	ENSG00000135925	ENST00000258411	D	0.84944	-1.92	4.7	3.82	0.43975	.	0.000000	0.85682	D	0.000000	D	0.94627	0.8268	H	0.97564	4.03	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95446	0.8530	10	0.72032	D	0.01	.	12.015	0.53309	0.085:0.0:0.915:0.0	.	129	Q9GZT5	WN10A_HUMAN	D	129	ENSP00000258411:E129D	ENSP00000258411:E129D	E	+	3	2	WNT10A	219462960	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.220000	0.42908	1.338000	0.45544	0.655000	0.94253	GAG	.		0.582	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216		C	219754716	G	C	219754716	3	2	108	1	0	0	0	0	1	0	0	0	17415	933	33	4	397	4	WNT10A	2	219754716	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	17680786	219754716	23444657	19	9504											
NR1D2	9975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	24003534	24003534	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattgaaatgcaaagtgcaaTgaagaccatgatgaacagcc	18	7	9	7	0	0	5	0	4	0	1	0	5	0	5	2	0	4	2	2	0	6	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:24003534T>G	ENST00000312521.4	+	5	903	c.584T>G	c.(583-585)aTg>aGg	p.M195R	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	195	Hinge.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						CAAAGTGCAATGAAGACCATG	0.413																																					p.M195R		.											.	NR1D2-227	0			c.T584G						.						72	63	66					3																	24003534		2203	4300	6503	SO:0001583	missense	9975	exon5			GTGCAATGAAGAC	BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"Nuclear hormone receptors"	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.584T>G	3.37:g.24003534T>G	ENSP00000310006:p.Met195Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	60	26	NM_005126	0	0	10	16	6	B2R8Q3|O00402|Q86XD4	Missense_Mutation	SNP	ENST00000312521.4	37	CCDS33718.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347423	0.82022	.	.	ENSG00000174738	ENST00000312521;ENST00000396676	D	0.92647	-3.08	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.95411	0.8510	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.95294	0.8397	10	0.52906	T	0.07	.	16.4614	0.84056	0.0:0.0:0.0:1.0	.	195	Q14995	NR1D2_HUMAN	R	195	ENSP00000310006:M195R	ENSP00000310006:M195R	M	+	2	0	NR1D2	23978538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.635000	0.83286	2.285000	0.76669	0.533000	0.62120	ATG	.		0.413	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341017.3			G	24003534	T	G	24003534	3	3	108	1	0	0	0	0	1	0	0	0	10642	1464	51	5	602	5	NR1D2	3	24003534	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		24003534	174018896	20	9505											
SCN11A	11280	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38889146	38889146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccggacaagcctcaggattCggccaatccgagccaagcgg	10	4	12	15	4	1	0	1	0	0	0	3	3	2	2	5	4	3	0	5	4	3	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:38889146C>T	ENST00000302328.3	-	26	4613	c.4415G>A	c.(4414-4416)cGa>cAa	p.R1472Q	SCN11A_ENST00000456224.3_Missense_Mutation_p.R1434Q|SCN11A_ENST00000450244.1_Missense_Mutation_p.R1472Q	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1472					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCTCAGGATTCGGCCAATCCG	0.498																																					p.R1472Q													.	SCN11A-99	0			c.G4415A						.						44	49	48					3																	38889146		2203	4300	6503	SO:0001583	missense	11280	exon26			AGGATTCGGCCAA	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.4415G>A	3.37:g.38889146C>T	ENSP00000307599:p.Arg1472Gln	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	37	4	NM_014139	0	0	0	0	0	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	36	5.839006	0.97009	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224	D;D;D	0.99607	-6.27;-6.27;-6.27	5.81	5.81	0.92471	Ion transport (1);	0.069151	0.64402	D	0.000010	D	0.99857	0.9933	H	0.99130	4.44	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.96576	0.9427	10	0.87932	D	0	.	20.0787	0.97763	0.0:1.0:0.0:0.0	.	1472	Q9UI33	SCNBA_HUMAN	Q	1472;1472;1434	ENSP00000307599:R1472Q;ENSP00000400945:R1472Q;ENSP00000416757:R1434Q	ENSP00000307599:R1472Q	R	-	2	0	SCN11A	38864150	1.000000	0.71417	0.962000	0.40283	0.998000	0.95712	7.789000	0.85783	2.750000	0.94351	0.637000	0.83480	CGA	.		0.498	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38889146	C	T	38889146	3	4	108	1	0	0	0	0	1	0	0	0	13945	884	31	1	964	1	SCN11A	3	38889146	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	14885612	38889146	159133284	21	9506											
TGM4	7047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	44935102	44935102	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgcctgatgaggacgagcGcaaagagtacatcctcaatg	13	7	11	10	2	1	3	1	2	0	1	2	5	2	4	2	1	3	2	2	1	3	1	rs147559877		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:44935102G>A	ENST00000296125.4	+	5	532	c.464G>A	c.(463-465)cGc>cAc	p.R155H		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	155					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GAGGACGAGCGCAAAGAGTAC	0.507													G|||	1	0.000199681	8e-04	0	5008	,	,		15581	0		0	False		,,,				2504	0				p.R155H		.											.	TGM4-91	0			c.G464A						.	G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	129	115	120		464	-1.3	0	3	dbSNP_134	120	0,8600		0,0,4300	no	missense	TGM4	NM_003241.3	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	155/685	44935102	2,13004	2203	4300	6503	SO:0001583	missense	7047	exon5			ACGAGCGCAAAGA	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"Transglutaminases"	11780	protein-coding gene	gene with protein product		600585	"transglutaminase 4 (prostate)"			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.464G>A	3.37:g.44935102G>A	ENSP00000296125:p.Arg155His	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	82	36	NM_003241	0	0	0	0	0	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455059	0.43634	4.54E-4	0.0	ENSG00000163810	ENST00000296125	D	0.92099	-2.97	2.32	-1.33	0.09172	.	0.000000	0.40818	U	0.001008	D	0.95056	0.8399	M	0.90870	3.155	0.09310	N	0.999991	D	0.89917	1.0	D	0.79784	0.993	D	0.88191	0.2877	10	0.66056	D	0.02	.	4.1154	0.10079	0.3177:0.0:0.5237:0.1586	.	155	P49221	TGM4_HUMAN	H	155	ENSP00000296125:R155H	ENSP00000296125:R155H	R	+	2	0	TGM4	44910106	0.694000	0.27738	0.000000	0.03702	0.008000	0.06430	1.522000	0.35921	-0.584000	0.05913	-0.518000	0.04402	CGC	G|1.000;A|0.000		0.507	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44935102	G	A	44935102	3	1	108	1	0	0	0	0	1	0	0	0	15864	1087	38	1	482	1	TGM4	3	44935102	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	6045956	44935102	153087328	22	9507											
LZTFL1	54585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	45874547	45874547	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaataataatattaccttgtTtaggagttctgctgttccac	12	16	6	7	0	1	0	0	0	1	0	2	1	2	1	2	1	2	4	2	1	6	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:45874547T>G	ENST00000296135.6	-	5	625	c.451A>C	c.(451-453)Aac>Cac	p.N151H	LZTFL1_ENST00000536047.1_Missense_Mutation_p.N134H|LZTFL1_ENST00000490463.1_5'UTR|LZTFL1_ENST00000539217.1_Missense_Mutation_p.N147H	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	151	Interaction with BSS9.				establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		ATTACCTTGTTTAGGAGTTCT	0.393																																					p.N151H		.											.	LZTFL1-90	0			c.A451C						.						100	99	99					3																	45874547		2203	4300	6503	SO:0001583	missense	54585	exon5			CCTTGTTTAGGAG	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.451A>C	3.37:g.45874547T>G	ENSP00000296135:p.Asn151His	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	98	35	NM_020347	0	0	0	0	0	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Missense_Mutation	SNP	ENST00000296135.6	37	CCDS2731.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.78|16.78	3.217504|3.217504	0.58560|0.58560	.|.	.|.	ENSG00000163818|ENSG00000163818	ENST00000440576|ENST00000296135;ENST00000536047;ENST00000539217	.|T;T;T	.|0.24151	.|1.87;1.87;1.87	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	.|0.131960	.|0.64402	.|D	.|0.000002	T|T	0.28333|0.28333	0.0700|0.0700	L|L	0.58302|0.58302	1.8|1.8	0.54753|0.54753	D|D	0.999989|0.999989	.|B	.|0.12013	.|0.005	.|B	.|0.16289	.|0.015	T|T	0.03166|0.03166	-1.1065|-1.1065	5|10	.|0.38643	.|T	.|0.18	-17.4947|-17.4947	14.7592|14.7592	0.69593|0.69593	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|151	.|Q9NQ48	.|LZTL1_HUMAN	T|H	108|151;134;147	.|ENSP00000296135:N151H;ENSP00000439522:N134H;ENSP00000441784:N147H	.|ENSP00000296135:N151H	K|N	-|-	2|1	0|0	LZTFL1|LZTFL1	45849551|45849551	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	7.333000|7.333000	0.79214|0.79214	2.074000|2.074000	0.62210|0.62210	0.528000|0.528000	0.53228|0.53228	AAA|AAC	.		0.393	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347		G	45874547	T	G	45874547	3	3	108	1	0	0	0	0	1	0	0	0	9161	1841	64	5	472	5	LZTFL1	3	45874547	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	939445	45874547	152147883	23	9508											
USP4	7375	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49362339	49362339	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctacctgaccctggtaTagcccagcatcctggacagt	8	9	8	16	0	0	1	0	1	0	0	2	2	2	2	6	2	3	2	6	2	3	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:49362339T>C	ENST00000265560.4	-	5	667	c.621A>G	c.(619-621)ctA>ctG	p.L207L	USP4_ENST00000351842.4_Silent_p.L207L|USP4_ENST00000416417.1_Silent_p.L207L|USP4_ENST00000415188.1_Silent_p.L207L	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	207	Necessary for interaction with SART3. {ECO:0000269|PubMed:20595234}.|Ubiquitin-like 1.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		GACCCTGGTATAGCCCAGCAT	0.547																																					p.L207L		.											.	USP4-660	0			c.A621G						.						154	156	155					3																	49362339		2203	4300	6503	SO:0001819	synonymous_variant	7375	exon5			CTGGTATAGCCCA	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"Ubiquitin-specific peptidases"	12627	protein-coding gene	gene with protein product		603486	"ubiquitin specific protease 4 (proto-oncogene)"	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.621A>G	3.37:g.49362339T>C		Somatic	276	0		WXS	Illumina HiSeq	Phase_I	204	99	NM_199443	0	0	2	3	1	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	37	CCDS2793.1																																																																																			.		0.547	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49362339	T	C	49362339	2	2	108	1	0	0	0	0	0	0	0	1	17104	1393	49	3		3	USP4	3	49362339	Silent	SNP	T	TCGA-EV-5902-01A-11D-1589-08	3487792	49362339	148660091	24	9509											
CNTN3	5067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	74350871	74350871	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	taggatataactgggctatgGttgtctttaccttctttcca	8	17	8	8	0	2	0	0	0	2	0	3	1	3	1	2	3	2	2	2	3	5	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:74350871G>T	ENST00000263665.6	-	14	1899	c.1872C>A	c.(1870-1872)aaC>aaA	p.N624K		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	624	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTGGGCTATGGTTGTCTTTAC	0.468																																					p.N624K		.											.	CNTN3-137	0			c.C1872A						.						309	273	285					3																	74350871		2203	4300	6503	SO:0001583	missense	5067	exon14			GCTATGGTTGTCT	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1872C>A	3.37:g.74350871G>T	ENSP00000263665:p.Asn624Lys	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	103	48	NM_020872	0	0	1	6	5	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579172	0.65878	.	.	ENSG00000113805	ENST00000263665	T	0.56611	0.45	5.98	2.16	0.27623	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.091203	0.85682	D	0.000000	T	0.71576	0.3356	M	0.89030	3	0.38345	D	0.944171	P	0.46020	0.871	P	0.61132	0.884	T	0.76044	-0.3103	10	0.87932	D	0	.	10.2822	0.43545	0.4578:0.0:0.5422:0.0	.	624	Q9P232	CNTN3_HUMAN	K	624	ENSP00000263665:N624K	ENSP00000263665:N624K	N	-	3	2	CNTN3	74433561	0.972000	0.33761	0.988000	0.46212	0.988000	0.76386	0.098000	0.15189	0.415000	0.25817	0.591000	0.81541	AAC	.		0.468	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		T	74350871	G	T	74350871	3	4	108	1	0	0	0	0	1	0	0	0	3648	1252	44	4	1250	4	CNTN3	3	74350871	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	24988532	74350871	123671559	25	9510											
PIK3CB	5291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	138456588	138456588	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatcaccaaaaacatattcTactctcccgctgacttgcaa	13	11	4	13	1	3	2	1	2	2	0	4	2	3	2	2	0	3	2	2	0	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:138456588T>C	ENST00000477593.1	-	5	835	c.762A>G	c.(760-762)gtA>gtG	p.V254V	PIK3CB_ENST00000289153.2_Silent_p.V254V			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	254	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	AAACATATTCTACTCTCCCGC	0.318																																					p.V254V		.											.	PIK3CB-1311	0			c.A762G						.						96	88	91					3																	138456588		2203	4300	6503	SO:0001819	synonymous_variant	5291	exon4			ATATTCTACTCTC		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.762A>G	3.37:g.138456588T>C		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	108	56	NM_006219	0	0	10	21	11	D3DNF0|Q24JU2	Silent	SNP	ENST00000477593.1	37	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	T	0.792	-0.758451	0.03019	.	.	ENSG00000051382	ENST00000462294	.	.	.	5.82	-3.54	0.04653	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.8436	11.0692	0.47993	0.1175:0.6147:0.0:0.2678	.	.	.	.	W	122	.	.	X	-	2	0	PIK3CB	139939278	0.887000	0.30362	0.907000	0.35723	0.002000	0.02628	-0.157000	0.10085	-0.658000	0.05366	-1.216000	0.01612	TAG	.		0.318	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			C	138456588	T	C	138456588	2	2	108	1	0	0	0	0	0	0	0	1	11940	1509	53	3		3	PIK3CB	3	138456588	Silent	SNP	T	TCGA-EV-5902-01A-11D-1589-08	64105717	138456588	59565842	26	9511											
PARL	55486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183551347	183551348	+	Missense_Mutation	DNP	CT	CT	GG																															ccatcccaggatcattcctgCtgtatccatggcgataatgg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:183551347_183551348CT>GG	ENST00000317096.4	-	9	1020_1021	c.960_961AG>CC	c.(958-963)acAGca>acCCca	p.A321P	PARL_ENST00000311101.5_Missense_Mutation_p.A271P|PARL_ENST00000435888.1_Missense_Mutation_p.A237P	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	321					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATCATTCCTGCTGTATCCATGG	0.446																																					p.A321P		.											.	PARL	0			c.A960C						.																																			SO:0001583	missense	55486	exon9			TCCTGCTGTATCC	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"rhomboid 7 homolog 1 (Drosophila)"	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.960_961delinsGG	3.37:g.183551347_183551348delinsGG	ENSP00000325421:p.Ala321Pro	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	101	43		0	0	0	0	0	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	DNP	ENST00000317096.4	37	CCDS3248.1																																																																																			.		0.446	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		GG	183551348	CT	GG	183551347	3	3	108	1	0	0	0	0	1	0	0	0	11477	797	28	4	186	4	PARL	3	183551347	Missense_Mutation	DNP	CT	TCGA-EV-5902-01A-11D-1589-08	45094759	183551347	14471083	27	9512											
RNF168	165918	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	196214405	196214405	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtatgtattcttcactGgctttgttttcttcttcctc	3	22	5	11	0	5	0	1	0	4	0	7	0	6	0	1	1	0	4	1	1	2	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:196214405G>T	ENST00000318037.3	-	3	1017	c.423C>A	c.(421-423)gcC>gcA	p.A141A		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	141	Glu-rich.				cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		ATTCTTCACTGGCTTTGTTTT	0.443																																					p.A141A		.											.	RNF168-90	0			c.C423A						.						223	208	213					3																	196214405		2203	4300	6503	SO:0001819	synonymous_variant	165918	exon3			TTCACTGGCTTTG	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.423C>A	3.37:g.196214405G>T		Somatic	231	0		WXS	Illumina HiSeq	Phase_I	215	105	NM_152617	0	0	8	16	8	Q8NA67|Q96NS4	Silent	SNP	ENST00000318037.3	37	CCDS3317.1																																																																																			.		0.443	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		T	196214405	G	T	196214405	2	4	108	1	0	0	0	0	0	0	0	1	13491	1335	47	4		4	RNF168	3	196214405	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	12663058	196214405	1808025	28	9513											
DRD5	1816	hgsc.bcm.edu	37	chr4	9784112	9784112	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctacaagcgcaagatgacTcagcgcatggccttggtcat	10	8	11	12	3	2	2	2	1	0	1	2	2	2	2	1	2	3	3	1	2	3	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:9784112T>C	ENST00000304374.2	+	1	855	c.459T>C	c.(457-459)acT>acC	p.T153T		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	153					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GCAAGATGACTCAGCGCATGG	0.602																																					p.T153T		.											.	DRD5-91	0			c.T459C						.						38	37	37					4																	9784112		2203	4300	6503	SO:0001819	synonymous_variant	1816	exon1			GATGACTCAGCGC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.459T>C	4.37:g.9784112T>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_000798	0	0	0	0	0	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			.		0.602	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			C	9784112	T	C	9784112	2	2	108	1	0	0	0	0	0	0	0	1	4771	1538	54	3		3	DRD5	4	9784112	Silent	SNP	T	TCGA-EV-5902-01A-11D-1589-08		9784112	181370164	29	9514											
TLR6	10333	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	38830116	38830116	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgttcatctcagaaaacaCggtgtacaaagctgtctgtg	13	11	9	8	1	3	1	2	0	2	1	4	1	3	1	0	1	3	3	0	1	5	2	rs3796508	byFrequency	TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:38830116C>A	ENST00000381950.1	-	1	1044	c.979G>T	c.(979-981)Gtg>Ttg	p.V327L	TLR6_ENST00000436693.2_Missense_Mutation_p.V327L			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	327			V -> M (in dbSNP:rs3796508). {ECO:0000269|PubMed:21618349, ECO:0000269|Ref.3}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCAGAAAACACGGTGTACAAA	0.343																																					p.V327L		.											.	TLR6-524	0			c.G979T						.						68	72	71					4																	38830116		2203	4300	6503	SO:0001583	missense	10333	exon2			AAAACACGGTGTA		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"CD molecules"	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.979G>T	4.37:g.38830116C>A	ENSP00000371376:p.Val327Leu	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	72	33	NM_006068	0	0	0	0	0	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.699200	0.00725	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.07216	3.21;3.21	5.08	0.624	0.17659	.	0.875863	0.09937	N	0.736454	T	0.03959	0.0111	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.46400	-0.9194	10	0.07482	T	0.82	.	0.9789	0.01432	0.1458:0.2038:0.2868:0.3636	.	327	Q9Y2C9	TLR6_HUMAN	L	327	ENSP00000389600:V327L;ENSP00000371376:V327L	ENSP00000371376:V327L	V	-	1	0	TLR6	38506511	0.000000	0.05858	0.152000	0.22495	0.301000	0.27625	-0.736000	0.04882	0.168000	0.19655	0.491000	0.48974	GTG	C|0.981;T|0.019		0.343	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			A	38830116	C	A	38830116	3	1	108	1	0	0	0	0	1	0	0	0	15987	536	19	4	1415	4	TLR6	4	38830116	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	29046004	38830116	152324160	30	9515											
YTHDC1	91746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	69203291	69203291	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaataatatttactaccTcagaaccatctggcgtagga	13	11	7	10	1	2	1	1	0	1	1	2	2	2	2	2	2	4	2	2	2	7	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:69203291T>G	ENST00000344157.4	-	3	793	c.458A>C	c.(457-459)gAg>gCg	p.E153A	YTHDC1_ENST00000579690.1_Splice_Site_p.E153A|YTHDC1_ENST00000355665.3_Splice_Site_p.E153A	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	153					mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						ATTTACTACCTCAGAACCATC	0.403																																					p.E153A		.											.	YTHDC1-92	0			c.A458C						.						48	47	47					4																	69203291		2200	4300	6500	SO:0001630	splice_region_variant	91746	exon3			ACTACCTCAGAAC	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.459+1A>C	4.37:g.69203291T>G		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	75	38	NM_001031732	0	0	1	7	6	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	37	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287484	0.40494	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.30448	1.68;1.53	5.29	5.29	0.74685	.	0.369189	0.29396	N	0.012273	T	0.24084	0.0583	L	0.27053	0.805	0.52099	D	0.999947	B;B	0.32573	0.376;0.0	B;B	0.34722	0.188;0.001	T	0.06826	-1.0805	10	0.49607	T	0.09	.	11.8336	0.52309	0.0:0.0:0.1463:0.8537	.	153;153	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	A	153	ENSP00000339245:E153A;ENSP00000347888:E153A	ENSP00000339245:E153A	E	-	2	0	YTHDC1	68885886	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.195000	0.58400	1.981000	0.57761	0.477000	0.44152	GAG	.		0.403	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370	Missense_Mutation	G	69203291	T	G	69203291	5	3	108	1	0	0	0	0	0	0	1	0	17529	1565	54	5	1785	5	YTHDC1	4	69203291	Splice_Site	SNP	T	TCGA-EV-5902-01A-11D-1589-08	30373175	69203291	121950985	31	9516											
ENAM	10117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	71510231	71510231	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cacctgatgaaggctccaatCcagaaggcatccaaagtcaa	15	6	8	12	0	1	3	1	2	0	1	4	3	4	3	4	2	0	2	4	2	5	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:71510231C>T	ENST00000396073.3	+	9	3369	c.3088C>T	c.(3088-3090)Cca>Tca	p.P1030S	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1030					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			AGGCTCCAATCCAGAAGGCAT	0.433																																					p.P1030S		.											.	ENAM-93	0			c.C3088T						.						119	104	109					4																	71510231		2203	4300	6503	SO:0001583	missense	10117	exon9			TCCAATCCAGAAG	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.3088C>T	4.37:g.71510231C>T	ENSP00000379383:p.Pro1030Ser	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	129	59	NM_031889	0	0	1	4	3	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	C	10.67	1.416036	0.25552	.	.	ENSG00000132464	ENST00000396073	T	0.37411	1.2	5.97	5.11	0.69529	.	0.116712	0.39407	N	0.001380	T	0.49660	0.1570	M	0.81802	2.56	0.30657	N	0.754852	P	0.50272	0.933	P	0.49477	0.612	T	0.60596	-0.7232	10	0.62326	D	0.03	-10.6665	12.7104	0.57086	0.1631:0.8369:0.0:0.0	.	1030	Q9NRM1	ENAM_HUMAN	S	1030	ENSP00000379383:P1030S	ENSP00000379383:P1030S	P	+	1	0	ENAM	71729095	0.747000	0.28283	0.848000	0.33437	0.024000	0.10985	1.284000	0.33249	2.836000	0.97738	0.655000	0.94253	CCA	.		0.433	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		T	71510231	C	T	71510231	3	4	108	1	0	0	0	0	1	0	0	0	5125	855	30	2	3118	2	ENAM	4	71510231	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	2306940	71510231	119644045	32	9517											
ANXA3	306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	79512751	79512751	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaaacatctggtgacttcCggaaagctctgttgactttg	9	12	10	10	2	2	2	0	2	2	0	3	4	3	3	2	2	2	2	2	2	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:79512751C>T	ENST00000264908.6	+	7	836	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W	ANXA3_ENST00000503570.2_Missense_Mutation_p.R114W|ANXA3_ENST00000512884.1_Missense_Mutation_p.R114W	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	153					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						TGGTGACTTCCGGAAAGCTCT	0.343																																					p.R153W	GBM(2;126 157 27790 28920 42492)	.											.	ANXA3-90	0			c.C457T						.						135	139	138					4																	79512751		2203	4300	6503	SO:0001583	missense	306	exon7			GACTTCCGGAAAG	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.457C>T	4.37:g.79512751C>T	ENSP00000264908:p.Arg153Trp	Somatic	271	0		WXS	Illumina HiSeq	Phase_I	287	114	NM_005139	0	0	132	223	91	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	37	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142653	0.77888	.	.	ENSG00000138772	ENST00000264908;ENST00000512884;ENST00000503570;ENST00000514171	T;T;T;T	0.03831	3.79;3.79;3.79;3.79	5.21	4.3	0.51218	Annexin repeat, conserved site (1);	0.348448	0.28901	N	0.013775	T	0.23410	0.0566	M	0.90759	3.145	0.46260	D	0.998954	D	0.89917	1.0	D	0.69142	0.962	T	0.00593	-1.1654	10	0.87932	D	0	.	10.6705	0.45755	0.3225:0.6775:0.0:0.0	.	153	P12429	ANXA3_HUMAN	W	153;114;114;153	ENSP00000264908:R153W;ENSP00000423068:R114W;ENSP00000421015:R114W;ENSP00000421512:R153W	ENSP00000264908:R153W	R	+	1	2	ANXA3	79731775	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.345000	0.33953	2.708000	0.92522	0.585000	0.79938	CGG	.		0.343	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		T	79512751	C	T	79512751	3	4	108	1	0	0	0	0	1	0	0	0	719	643	23	1	479	1	ANXA3	4	79512751	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	8002520	79512751	111641525	33	9518											
MTRR	4552	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7873543	7873543	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtttctaccacgggcaccGgagacccacccgacacagcc	9	5	10	17	3	1	1	0	0	1	1	1	3	1	1	5	3	2	2	5	3	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:7873543G>A	ENST00000264668.2	+	3	298	c.268G>A	c.(268-270)Gga>Aga	p.G90R	MTRR_ENST00000440940.2_Missense_Mutation_p.G63R|MTRR_ENST00000341013.6_Intron|MTRR_ENST00000502509.1_Intron	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	90	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	CACGGGCACCGGAGACCCACC	0.478																																					p.G90R		.											.	MTRR-91	0			c.G268A						.						158	161	160					5																	7873543		2203	4300	6503	SO:0001583	missense	4552	exon3			GGCACCGGAGACC	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.268G>A	5.37:g.7873543G>A	ENSP00000264668:p.Gly90Arg	Somatic	217	1		WXS	Illumina HiSeq	Phase_I	305	81	NM_024010	0	0	11	15	4	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701195	0.88924	.	.	ENSG00000124275	ENST00000264668;ENST00000440940;ENST00000502550;ENST00000512217	D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13	5.67	4.8	0.61643	Flavodoxin/nitric oxide synthase (2);	0.000000	0.85682	D	0.000000	D	0.97698	0.9245	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98911	1.0780	10	0.87932	D	0	-22.8766	14.7195	0.69294	0.0693:0.0:0.9307:0.0	.	90	Q9UBK8	MTRR_HUMAN	R	90;63;63;63	ENSP00000264668:G90R;ENSP00000402510:G63R;ENSP00000424599:G63R;ENSP00000421318:G63R	ENSP00000264668:G90R	G	+	1	0	MTRR	7926543	1.000000	0.71417	0.874000	0.34290	0.973000	0.67179	7.942000	0.87708	1.405000	0.46838	0.655000	0.94253	GGA	.		0.478	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			A	7873543	G	A	7873543	3	1	108	1	0	0	0	0	1	0	0	0	9986	1117	39	1	278	1	MTRR	5	7873543	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08		7873543	173041717	34	9519											
TRIO	7204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	14471560	14471560	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaagaaaggaaatccagctCtttaaagagaagacagtaag	19	6	11	5	0	1	3	0	0	1	3	2	6	2	5	1	2	1	2	1	2	7	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:14471560C>T	ENST00000344204.4	+	38	5921	c.5897C>T	c.(5896-5898)tCt>tTt	p.S1966F	TRIO_ENST00000537187.1_Missense_Mutation_p.S1966F	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1966					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					AAATCCAGCTCTTTAAAGAGA	0.438																																					p.S1966F		.											.	TRIO-562	0			c.C5897T						.						73	70	71					5																	14471560		2203	4300	6503	SO:0001583	missense	7204	exon38			CCAGCTCTTTAAA	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.5897C>T	5.37:g.14471560C>T	ENSP00000339299:p.Ser1966Phe	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	124	89	NM_007118	0	0	7	13	6	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936293	0.52972	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000541447	T;T	0.68479	-0.33;-0.33	5.39	5.39	0.77823	Dbl homology (DH) domain (2);	0.056462	0.64402	D	0.000001	T	0.48150	0.1484	N	0.03608	-0.345	0.47737	D	0.999501	B;B	0.14805	0.011;0.0	B;B	0.15052	0.012;0.001	T	0.45293	-0.9271	10	0.52906	T	0.07	.	19.2167	0.93781	0.0:1.0:0.0:0.0	.	1966;1966	O75962-5;O75962	.;TRIO_HUMAN	F	1966;1966;1653;46	ENSP00000339299:S1966F;ENSP00000446348:S1966F	ENSP00000339299:S1966F	S	+	2	0	TRIO	14524560	1.000000	0.71417	0.951000	0.38953	0.965000	0.64279	5.667000	0.68067	2.537000	0.85549	0.650000	0.86243	TCT	.		0.438	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		T	14471560	C	T	14471560	3	4	108	1	0	0	0	0	1	0	0	0	16585	913	32	2	6047	2	TRIO	5	14471560	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	6598017	14471560	166443700	35	9520											
RICTOR	253260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	38954924	38954924	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatggtgtactagttgtccAtaaaggtgtataggcaggta	11	14	12	4	0	0	0	0	0	0	0	1	0	1	0	1	4	1	5	1	4	8	8			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:38954924A>C	ENST00000357387.3	-	27	2679	c.2649T>G	c.(2647-2649)taT>taG	p.Y883*	RICTOR_ENST00000296782.5_Nonsense_Mutation_p.Y883*|RICTOR_ENST00000503698.1_5'UTR	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					CTAGTTGTCCATAAAGGTGTA	0.313																																					p.Y883X		.											.	RICTOR-849	0			c.T2649G						.						121	118	119					5																	38954924		2203	4300	6503	SO:0001587	stop_gained	253260	exon27			TTGTCCATAAAGG		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.2649T>G	5.37:g.38954924A>C	ENSP00000349959:p.Tyr883*	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	255	148	NM_152756	0	0	4	5	1		Nonsense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	A	38	7.042770	0.98021	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	.	.	.	5.79	3.38	0.38709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.3188	9.8756	0.41202	0.8005:0.0:0.1995:0.0	.	.	.	.	X	883	.	ENSP00000296782:Y883X	Y	-	3	2	RICTOR	38990681	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.863000	0.48396	0.449000	0.26747	0.477000	0.44152	TAT	.		0.313	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		C	38954924	A	C	38954924	4	2	108	1	0	0	0	0	0	1	0	0	13390	224	8	5	2525	5	RICTOR	5	38954924	Nonsense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	24483364	38954924	141960336	36	9521											
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	67588178	67588178	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgctgaatggtactggggAgatatctcgaggtaaggcta	11	10	15	5	1	1	2	0	1	1	1	2	5	1	2	0	5	2	4	0	5	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:67588178A>G	ENST00000521381.1	+	8	1624	c.1008A>G	c.(1006-1008)ggA>ggG	p.G336G	PIK3R1_ENST00000396611.1_Silent_p.G336G|PIK3R1_ENST00000274335.5_Silent_p.G336G|PIK3R1_ENST00000521657.1_Silent_p.G336G|PIK3R1_ENST00000523872.1_5'Flank|PIK3R1_ENST00000336483.5_Silent_p.G66G|PIK3R1_ENST00000320694.8_Silent_p.G36G	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	336	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	GGTACTGGGGAGATATCTCGA	0.393			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.G336G		.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1-4332	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.A1008G						.						153	143	146					5																	67588178		2203	4300	6503	SO:0001819	synonymous_variant	5295	exon8			CTGGGGAGATATC	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1008A>G	5.37:g.67588178A>G		Somatic	177	0		WXS	Illumina HiSeq	Phase_I	225	74	NM_181523	0	0	0	0	0	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	37	CCDS3993.1																																																																																			.		0.393	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67588178	A	G	67588178	2	3	108	1	0	0	0	0	0	0	0	1	11944	291	11	3		3	PIK3R1	5	67588178	Silent	SNP	A	TCGA-EV-5902-01A-11D-1589-08	28633254	67588178	113327082	37	9522											
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	67591286	67591286	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttcggcaaaagaagttgaAcgagtggttgggcaatgaaa	14	9	14	4	2	0	3	0	2	0	1	1	4	0	3	0	3	1	5	0	3	6	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:67591286A>T	ENST00000521381.1	+	14	2400	c.1784A>T	c.(1783-1785)aAc>aTc	p.N595I	PIK3R1_ENST00000396611.1_Missense_Mutation_p.N595I|PIK3R1_ENST00000274335.5_Missense_Mutation_p.N595I|PIK3R1_ENST00000521657.1_Missense_Mutation_p.N595I|PIK3R1_ENST00000523872.1_Missense_Mutation_p.N232I|PIK3R1_ENST00000336483.5_Missense_Mutation_p.N325I|PIK3R1_ENST00000320694.8_Missense_Mutation_p.N295I	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	595					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.M582_D605>I(4)|p.Y580fs*1(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAGAAGTTGAACGAGTGGTTG	0.368			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.N595I		.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1-4332	7	Complex - deletion inframe(4)|Whole gene deletion(1)|Deletion - Frameshift(1)|Unknown(1)	large_intestine(4)|lung(1)|ovary(1)|central_nervous_system(1)	c.A1784T						.						152	156	155					5																	67591286		2203	4300	6503	SO:0001583	missense	5295	exon14			AGTTGAACGAGTG	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1784A>T	5.37:g.67591286A>T	ENSP00000428056:p.Asn595Ile	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	126	39	NM_181523	0	0	111	168	57	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.587453	0.86851	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000523872	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	4.84	4.84	0.62591	.	0.042090	0.85682	D	0.000000	T	0.57257	0.2041	M	0.82923	2.615	0.80722	D	1	D;P;P;D	0.67145	0.991;0.811;0.901;0.996	P;P;P;D	0.67725	0.892;0.844;0.844;0.953	T	0.65084	-0.6254	10	0.87932	D	0	-28.7516	14.6086	0.68498	1.0:0.0:0.0:0.0	.	265;325;295;595	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	I	595;595;595;595;295;325;232	ENSP00000428056:N595I;ENSP00000429277:N595I;ENSP00000379855:N595I;ENSP00000274335:N595I;ENSP00000323512:N295I;ENSP00000338554:N325I;ENSP00000430098:N232I	ENSP00000274335:N595I	N	+	2	0	PIK3R1	67627042	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	9.087000	0.94110	2.036000	0.60181	0.377000	0.23210	AAC	.		0.368	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67591286	A	T	67591286	3	4	108	1	0	0	0	0	1	0	0	0	11944	43	2	5	1964	5	PIK3R1	5	67591286	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	3108	67591286	113323974	38	9523											
C5orf36	285600	broad.mit.edu;bcgsc.ca	37	chr5	93856355	93856362	+	Frame_Shift_Del	DEL	AAATTTTT	AAATTTTT	-																															taagcactgctttttcaataAaattttttgctgtgaattgt																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AAATTTTT	AAATTTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:93856355_93856362delAAATTTTT	ENST00000329378.7	-	5	810_817	c.561_568delAAAAATTT	c.(559-570)caaaaaattttafs	p.QKIL187fs	KIAA0825_ENST00000513200.3_Frame_Shift_Del_p.QKIL187fs|KIAA0825_ENST00000312498.7_Frame_Shift_Del_p.QKIL187fs|KIAA0825_ENST00000427991.2_Frame_Shift_Del_p.QKIL187fs	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	187										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTTTTCAATAAAATTTTTTGCTGTGAAT	0.322																																					p.187_190del													.	KIAA0825-91	0			c.561_568del						.																																			SO:0001589	frameshift_variant	285600	exon5			TCAATAAAATTTT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.561_568delAAAAATTT	5.37:g.93856355_93856362delAAATTTTT	ENSP00000331385:p.Gln187fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	170	24	NM_173665	0	0	0	0	0	O94914|Q6ZNN2	Frame_Shift_Del	DEL	ENST00000329378.7	37	CCDS4070.1																																																																																			.		0.322	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665		-	93856362	AAATTTTT	-	93856355	7	5	108	1	0	1	0	1	0	0	0	0	2301	11	1	0	3332	0	C5orf36	5	93856355	Frame_Shift_Del	DEL	AAATTTTT	TCGA-EV-5902-01A-11D-1589-08	26265069	93856355	87058905	39	9524	98	2									
C5orf36	285600	bcgsc.ca	37	chr5	93856363	93856363	+	Missense_Mutation	SNP	T	T	C																															gctttttcaataaaatttttTgctgtgaattgtttatttca																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:93856363T>C	ENST00000329378.7	-	5	809	c.560A>G	c.(559-561)cAa>cGa	p.Q187R	KIAA0825_ENST00000513200.3_Missense_Mutation_p.Q187R|KIAA0825_ENST00000312498.7_Missense_Mutation_p.Q187R|KIAA0825_ENST00000427991.2_Missense_Mutation_p.Q187R	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	187										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TAAAATTTTTTGCTGTGAATT	0.318																																					p.Q187R													.	KIAA0825-91	0			c.A560G						.						105	109	108					5																	93856363		2203	4300	6503	SO:0001583	missense	285600	exon5			ATTTTTTGCTGTG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.560A>G	5.37:g.93856363T>C	ENSP00000331385:p.Gln187Arg	Somatic	105	0		WXS	Illumina HiSeq	Phase_1	161	26	NM_173665	0	0	1	1	0	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000329378.7	37	CCDS4070.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.084971	0.36758	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498;ENST00000329378	T;T;D;D	0.85773	0.86;0.86;-2.03;-2.03	5.51	5.51	0.81932	.	1.945680	0.01632	N	0.023587	D	0.85199	0.5642	L	0.54323	1.7	0.30939	N	0.726027	P;P	0.42692	0.675;0.787	B;B	0.39258	0.295;0.295	T	0.74293	-0.3712	10	0.59425	D	0.04	.	11.5917	0.50949	0.0:0.0:0.1489:0.8511	.	187;187	Q8IV33;Q8IV33-2	K0825_HUMAN;.	R	187	ENSP00000424618:Q187R;ENSP00000400288:Q187R;ENSP00000312205:Q187R;ENSP00000331385:Q187R	ENSP00000312205:Q187R	Q	-	2	0	KIAA0825	93882119	0.998000	0.40836	1.000000	0.80357	0.921000	0.55340	2.676000	0.46883	2.091000	0.63221	0.477000	0.44152	CAA	.		0.318	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665		C	93856363	T	C	93856363	3	2	108	1	0	0	0	0	1	0	0	0	2301	1812	63	3	3340	3	C5orf36	5	93856363	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	8	93856363	87058897	40	9525	98	2									
ACSL6	23305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131324510	131324510	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcttacctgtattgatgaTgtagcggatagccccagggc	8	10	14	9	1	0	2	0	2	0	0	0	3	0	3	3	3	3	3	3	3	4	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:131324510T>A	ENST00000379240.1	-	6	718	c.565A>T	c.(565-567)Atc>Ttc	p.I189F	ACSL6_ENST00000379249.3_Missense_Mutation_p.I189F|ACSL6_ENST00000379244.1_Missense_Mutation_p.I189F|ACSL6_ENST00000379255.1_Missense_Mutation_p.I154F|ACSL6_ENST00000379264.2_Missense_Mutation_p.I214F|ACSL6_ENST00000357096.1_Missense_Mutation_p.I154F|ACSL6_ENST00000379272.2_Missense_Mutation_p.I189F|ACSL6_ENST00000379246.1_Missense_Mutation_p.I200F|ACSL6_ENST00000296869.4_Missense_Mutation_p.I214F|ACSL6_ENST00000543479.1_Missense_Mutation_p.I189F|ACSL6_ENST00000544770.1_Missense_Mutation_p.I98F|ACSL6_ENST00000431707.1_Missense_Mutation_p.I154F			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	189					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTATTGATGATGTAGCGGATA	0.572																																					p.I214F		.											.	ACSL6-229	0			c.A640T						.						114	112	113					5																	131324510		2203	4300	6503	SO:0001583	missense	23305	exon6			TGATGATGTAGCG	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.565A>T	5.37:g.131324510T>A	ENSP00000368542:p.Ile189Phe	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	304	104	NM_001009185	0	0	0	0	0	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	37		.	.	.	.	.	.	.	.	.	.	T	20.8	4.053835	0.75960	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479;ENST00000434099;ENST00000430403	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.79	5.79	0.91817	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.81399	0.4814	H	0.98446	4.235	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;1.0;1.0;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.993;0.995;0.999;0.996;0.988;0.995;0.995	D	0.88843	0.3314	10	0.87932	D	0	.	16.1224	0.81369	0.0:0.0:0.0:1.0	.	189;189;179;189;154;214;214	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	F	189;214;189;154;154;214;200;189;98;189;154;189;154;189	ENSP00000368551:I189F;ENSP00000368566:I214F;ENSP00000368574:I189F;ENSP00000349608:I154F;ENSP00000368557:I154F;ENSP00000296869:I214F;ENSP00000368548:I200F;ENSP00000368546:I189F;ENSP00000445154:I98F;ENSP00000368542:I189F;ENSP00000413329:I154F;ENSP00000442124:I189F;ENSP00000397507:I154F;ENSP00000398423:I189F	ENSP00000296869:I214F	I	-	1	0	ACSL6	131352409	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	7.953000	0.87836	2.208000	0.71279	0.533000	0.62120	ATC	.		0.572	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		A	131324510	T	A	131324510	3	1	108	1	0	0	0	0	1	0	0	0	181	1464	51	5	1674	5	ACSL6	5	131324510	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	37468147	131324510	49590750	41	9526											
MRPL22	29093	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	154330411	154330411	+	Frame_Shift_Del	DEL	T	T	-																															caatcatatatccacacaagTgcttctcttgacatttctcg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:154330411delT	ENST00000523037.1	+	3	149	c.108delT	c.(106-108)agtfs	p.S36fs	MRPL22_ENST00000439747.3_Frame_Shift_Del_p.S62fs|MRPL22_ENST00000265229.8_Intron|MRPL22_ENST00000522038.1_Frame_Shift_Del_p.S42fs	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	36					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCACACAAGTGCTTCTCTTG	0.398																																					p.S36fs		.											.	MRPL22-90	0			c.108delT						.						124	122	123					5																	154330411		2203	4300	6503	SO:0001589	frameshift_variant	29093	exon3			.	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.108delT	5.37:g.154330411delT	ENSP00000431040:p.Ser36fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	184	125	NM_014180	0	0	0	0	0	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Frame_Shift_Del	DEL	ENST00000523037.1	37	CCDS4331.1																																																																																			.		0.398	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			-	154330411	T	-	154330411	7	5	108	1	0	1	0	1	0	0	0	0	9813	1693	59	0	118	0	MRPL22	5	154330411	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08	23005901	154330411	26584849	42	9527											
ATP10B	23120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	160113261	160113262	+	Missense_Mutation	DNP	GG	GG	TC																															gttcaaaatcaccaggaacaGgaaatagaggttagcccatc																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:160113261_160113262GG>TC	ENST00000327245.5	-	6	1140_1141	c.294_295CC>GA	c.(292-297)ttCCtg>ttGAtg	p.98_99FL>LM	ATP10B_ENST00000518411.1_5'UTR|CTC-529G1.1_ENST00000524198.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	98					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCAGGAACAGGAAATAGAGGT	0.45																																					p.FL98LM		.											.	ATP10B	0			c.C294G						.																																			SO:0001583	missense	23120	exon6			GAACAGGAAATAG	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"ATPases / P-type"	13543	protein-coding gene	gene with protein product			"ATPase, Class V, type 10B"			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.294_295delinsTC	5.37:g.160113261_160113262delinsTC	ENSP00000313600:p.F98_L99delinsLM	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	57	12		0	0	0	0	0	Q9H725	Missense_Mutation	DNP	ENST00000327245.5	37	CCDS43394.1																																																																																			.		0.45	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		TC	160113262	GG	TC	160113261	3	4	108	1	0	0	0	0	1	0	0	0	1118	991	35	4	4174	4	ATP10B	5	160113261	Missense_Mutation	DNP	GG	TCGA-EV-5902-01A-11D-1589-08	5782850	160113261	20801999	43	9528											
BTNL8	79908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	180374575	180374575	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actgggaatactctgctgtgGcctattttttggcattgttg	6	17	11	7	0	1	0	0	0	1	0	1	1	1	1	1	3	2	3	1	3	3	7	rs371555886		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:180374575G>A	ENST00000340184.4	+	4	943	c.737G>A	c.(736-738)gGc>gAc	p.G246D	BTNL8_ENST00000511704.1_Missense_Mutation_p.G130D|BTNL8_ENST00000533815.2_Missense_Mutation_p.G62D|BTNL8_ENST00000231229.4_Missense_Mutation_p.G246D|BTNL8_ENST00000400707.3_Missense_Mutation_p.G121D|BTNL8_ENST00000505126.1_Missense_Mutation_p.G39D|BTNL8_ENST00000508408.1_Missense_Mutation_p.G246D	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	246					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCTGCTGTGGCCTATTTTTT	0.443																																					p.G246D		.											.	BTNL8-24	0			c.G737A						.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	0,4406		0,0,2203	231	240	237		737,389,737,362,185,737	-2.9	0	5		237	1,8591	1.2+/-3.3	0,1,4295	yes	missense,missense,missense,missense,missense,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	94,94,94,94,94,94	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	246/501,130/385,246/341,121/376,62/317,246/348	180374575	1,12997	2203	4296	6499	SO:0001583	missense	79908	exon4			GCTGTGGCCTATT	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.737G>A	5.37:g.180374575G>A	ENSP00000342197:p.Gly246Asp	Somatic	570	0		WXS	Illumina HiSeq	Phase_I	755	485	NM_001159708	0	0	0	0	0	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	.	.	.	.	.	.	.	.	.	.	G	6.384	0.438919	0.12104	0.0	1.16E-4	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T;T;T	0.61274	4.8;1.28;0.63;4.8;0.62;0.12;0.19	1.52	-2.87	0.05700	.	.	.	.	.	T	0.52224	0.1721	L	0.34521	1.04	0.09310	N	1	D;D;P;P;P	0.64830	0.982;0.994;0.808;0.808;0.838	P;P;B;B;B	0.59221	0.769;0.854;0.159;0.159;0.367	T	0.44034	-0.9354	9	0.35671	T	0.21	.	3.793	0.08728	0.0:0.2104:0.2868:0.5028	.	121;130;246;246;246	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	D	246;246;121;246;130;39;62	ENSP00000231229:G246D;ENSP00000342197:G246D;ENSP00000383543:G121D;ENSP00000424585:G246D;ENSP00000425207:G130D;ENSP00000427441:G39D;ENSP00000435098:G62D	ENSP00000231229:G246D	G	+	2	0	BTNL8	180307181	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.641000	0.05434	-0.893000	0.03930	0.436000	0.28706	GGC	.		0.443	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850		A	180374575	G	A	180374575	3	1	108	1	0	0	0	0	1	0	0	0	1570	1203	42	2	777	2	BTNL8	5	180374575	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	20261314	180374575	540685	44	9529											
MTCH1	23787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	36949411	36949411	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaccttcctccccagcacaTtggtcccaagggtggggggc	6	7	14	14	0	0	0	0	0	0	0	3	1	3	1	5	6	1	1	5	6	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr6:36949411T>A	ENST00000373627.5	-	2	483	c.359A>T	c.(358-360)aAt>aTt	p.N120I	MTCH1_ENST00000373616.5_Missense_Mutation_p.N120I|MTCH1_ENST00000538808.1_Intron	NM_001271641.1	NP_001258570.1	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier 1	120					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|neuronal ion channel clustering (GO:0045161)|positive regulation of apoptotic process (GO:0043065)|regulation of signal transduction (GO:0009966)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						CCCCAGCACATTGGTCCCAAG	0.562																																					p.N120I		.											.	MTCH1-227	0			c.A359T						.						59	52	54					6																	36949411		2203	4300	6503	SO:0001583	missense	23787	exon2			AGCACATTGGTCC	AF151822	CCDS4828.1, CCDS64411.1	6p21.2	2013-05-22	2011-05-19		ENSG00000137409	ENSG00000137409		"Solute carriers"	17586	protein-coding gene	gene with protein product	"solute carrier family 25, member 49"	610449	"mitochondrial carrier homolog 1 (C. elegans)"			12377771	Standard	NM_014341		Approved	CGI-64, PSAP, SLC25A49	uc003ond.2	Q9NZJ7	OTTHUMG00000014614	ENST00000373627.5:c.359A>T	6.37:g.36949411T>A	ENSP00000362730:p.Asn120Ile	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	21	21	NM_014341	0	0	3	232	229	A8KAX5|B2RCE3|Q6PK60|Q6UX45|Q7L465|Q9BW23|Q9NZR6|Q9UJZ5	Missense_Mutation	SNP	ENST00000373627.5	37		.	.	.	.	.	.	.	.	.	.	T	19.24	3.788911	0.70337	.	.	ENSG00000137409	ENST00000373616;ENST00000373627;ENST00000337855;ENST00000373550;ENST00000460219	T;T;T	0.48201	0.82;0.82;0.82	4.87	2.42	0.29668	Mitochondrial carrier domain (2);	0.078934	0.49305	D	0.000154	T	0.43787	0.1263	L	0.49126	1.545	0.80722	D	1	D;D;D	0.69078	0.997;0.991;0.99	D;P;P	0.63597	0.916;0.843;0.891	T	0.45527	-0.9255	10	0.72032	D	0.01	-3.3591	7.5839	0.27980	0.0:0.1805:0.0:0.8195	.	102;120;120	Q8IW90;Q9NZJ7;Q9NZJ7-2	.;MTCH1_HUMAN;.	I	120;120;56;56;104	ENSP00000362718:N120I;ENSP00000362730:N120I;ENSP00000419739:N104I	ENSP00000338712:N56I	N	-	2	0	MTCH1	37057389	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	4.282000	0.58971	0.713000	0.32060	0.402000	0.26972	AAT	.		0.562	MTCH1-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040396.1	NM_014341		A	36949411	T	A	36949411	3	1	108	1	0	0	0	0	1	0	0	0	9938	1493	52	5	803	5	MTCH1	6	36949411	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		36949411	134165656	45	9530											
SNX10	29887	hgsc.bcm.edu;bcgsc.ca	37	chr7	26412183	26412200	+	Stop_Codon_Del	DEL	GGAATCCTGAAAAATAAT	GGAATCCTGAAAAATAAT	-																															aaagtaaatacagctccgcaGgaatcctgaaaaataattct																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	GGAATCCTGAAAAATAAT	GGAATCCTGAAAAATAAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:26412183_26412200delGGAATCCTGAAAAATAAT	ENST00000338523.4	+	0	784_801				SNX10_ENST00000446848.2_Stop_Codon_Del|SNX10_ENST00000396376.1_Stop_Codon_Del|AC004540.4_ENST00000451264.1_RNA|SNX10_ENST00000409838.1_Stop_Codon_Del|SNX10_ENST00000462993.1_3'UTR|SNX10_ENST00000409367.1_Stop_Codon_Del|AC004540.4_ENST00000451368.1_RNA	NM_001199835.1|NM_013322.2	NP_001186764.1|NP_037454.2	Q9Y5X0	SNX10_HUMAN	sorting nexin 10						cilium assembly (GO:0042384)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|osteoclast differentiation (GO:0030316)|protein localization to centrosome (GO:0071539)|protein localization to cilium (GO:0061512)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extrinsic component of endosome membrane (GO:0031313)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|ATPase binding (GO:0051117)			endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	6						CAGCTCCGCAGGAATCCTGAAAAATAATTCTAATGTTA	0.367																																					p.199_202del		.											.	SNX10-226	0			c.597_868del						.																																			SO:0001567	stop_retained_variant	29887	exon7			.	AF121860	CCDS5399.1, CCDS56470.1	7p15.2	2008-05-22			ENSG00000086300	ENSG00000086300		"Sorting nexins"	14974	protein-coding gene	gene with protein product		614780				17012226	Standard	NM_013322		Approved		uc010kuu.3	Q9Y5X0	OTTHUMG00000023650	Exception_encountered	7.37:g.26412183_26412200delGGAATCCTGAAAAATAAT		Somatic	190	0		WXS	Illumina HiSeq	Phase_I	154	45	NM_001199835	0	0	0	0	0	E9PFH5|Q8IYT5	Frame_Shift_Del	DEL	ENST00000338523.4	37	CCDS5399.1																																																																																			.		0.367	SNX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214120.1			-	26412200	GGAATCCTGAAAAATAAT	-	26412183	7	5	108	1	0	1	0	1	0	0	0	0	14913	991	35	0	619	0	SNX10	7	26412183	Stop_Codon_Del	DEL	GGAATCCTGAAAAATAAT	TCGA-EV-5902-01A-11D-1589-08		26412183	132726480	46	9531											
GBAS	2631	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	56045954	56045955	+	Frame_Shift_Del	DEL	AC	AC	-																															acaagcaatctatacaaattAcagtgtgagtgacaggtttg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:56045954_56045955delAC	ENST00000322090.3	+	2	257_258	c.228_229delAC	c.(226-231)ttacagfs	p.Q77fs	GBAS_ENST00000446778.1_Frame_Shift_Del_p.Q77fs|GBAS_ENST00000487370.1_3'UTR	NM_001483.2	NP_001474.1	O75323	NIPS2_HUMAN	glioblastoma amplified sequence	77					ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TATACAAATTACAGTGTGAGTG	0.361																																					p.76_77del		.											.	GBAS-514	0			c.228_229del						.																																			SO:0001589	frameshift_variant	2631	exon2			.	AF029786	CCDS5521.1, CCDS56488.1	7p12	2014-03-11			ENSG00000146729	ENSG00000146729			4179	protein-coding gene	gene with protein product		603004				9615231, 9661659, 20888800	Standard	NM_001483		Approved	NIPSNAP2	uc003tre.2	O75323	OTTHUMG00000022932	ENST00000322090.3:c.228_229delAC	7.37:g.56045954_56045955delAC	ENSP00000313050:p.Gln77fs	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	148	80	NM_001483	0	0	0	0	0	C9IYJ3|O43801|Q53X96	Frame_Shift_Del	DEL	ENST00000322090.3	37	CCDS5521.1																																																																																			.		0.361	GBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251524.1	NM_001483		-	56045955	AC	-	56045954	7	5	108	1	0	1	0	1	0	0	0	0	6289	388	14	0	234	0	GBAS	7	56045954	Frame_Shift_Del	DEL	AC	TCGA-EV-5902-01A-11D-1589-08	29633771	56045954	103092709	47	9532											
C7orf43	55262	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99753405	99753405	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggcagacgacggagtccagGgcagcctgcatggcccggcg	7	4	17	13	4	0	1	0	0	0	1	1	3	1	2	3	5	2	3	3	5	0	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:99753405G>A	ENST00000316937.3	-	9	1469	c.1284C>T	c.(1282-1284)gcC>gcT	p.A428A	C7orf43_ENST00000498638.1_5'Flank|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000394035.2_Silent_p.A4A|C7orf43_ENST00000419841.1_Silent_p.A196A|C7orf43_ENST00000457641.1_Silent_p.A159A	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43	428										breast(1)|endometrium(3)|large_intestine(3)|lung(2)|prostate(1)	10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGGAGTCCAGGGCAGCCTGCA	0.637																																					p.A428A		.											.	C7orf43-90	0			c.C1284T						.						53	50	51					7																	99753405		2203	4300	6503	SO:0001819	synonymous_variant	55262	exon9			GTCCAGGGCAGCC		CCDS5687.1	7q22.1	2011-11-25			ENSG00000146826	ENSG00000146826			25604	protein-coding gene	gene with protein product						12477932	Standard	NM_018275		Approved	FLJ10925	uc003utr.3	Q8WVR3	OTTHUMG00000154862	ENST00000316937.3:c.1284C>T	7.37:g.99753405G>A		Somatic	102	1		WXS	Illumina HiSeq	Phase_I	101	50	NM_018275	0	0	10	19	9	A4D2A9|D6W5U4|Q9BQJ1|Q9BUB6|Q9NV47	Silent	SNP	ENST00000316937.3	37	CCDS5687.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981597	0.34942	.	.	ENSG00000146826	ENST00000456769	.	.	.	5.66	0.404	0.16355	.	.	.	.	.	T	0.50343	0.1610	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35025	-0.9805	4	.	.	.	-21.6416	4.7431	0.13024	0.2529:0.2971:0.4501:0.0	.	.	.	.	S	334	.	.	P	-	1	0	C7orf43	99591341	0.997000	0.39634	0.998000	0.56505	0.961000	0.63080	0.253000	0.18296	0.054000	0.16065	-0.258000	0.10820	CCT	.		0.637	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	NM_018275		A	99753405	G	A	99753405	2	1	108	1	0	0	0	0	0	0	0	1	2399	1219	43	2		2	C7orf43	7	99753405	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	43707451	99753405	59385258	48	9533											
LRRN3	54674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	110763780	110763780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagaaaaatagaagctactAacaaccctagattgtcttac	18	10	5	8	0	1	3	0	0	1	3	1	3	1	3	1	0	5	1	1	0	10	7			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:110763780A>G	ENST00000422987.3	+	2	1783	c.952A>G	c.(952-954)Aac>Gac	p.N318D	IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.N318D|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.N318D	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	318					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		AGAAGCTACTAACAACCCTAG	0.418																																					p.N318D		.											.	LRRN3-154	0			c.A952G						.						85	88	87					7																	110763780		2203	4300	6503	SO:0001583	missense	54674	exon2			GCTACTAACAACC	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	17200	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 5"					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.952A>G	7.37:g.110763780A>G	ENSP00000412417:p.Asn318Asp	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	107	59	NM_018334	0	0	0	0	0	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.814302	0.70912	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.59083	0.29;0.29;0.29	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000002	T	0.63663	0.2530	N	0.20845	0.615	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.64351	-0.6428	10	0.37606	T	0.19	.	16.4311	0.83844	1.0:0.0:0.0:0.0	.	318	Q9H3W5	LRRN3_HUMAN	D	318	ENSP00000312001:N318D;ENSP00000397312:N318D;ENSP00000412417:N318D	ENSP00000312001:N318D	N	+	1	0	LRRN3	110551016	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	9.339000	0.96797	2.277000	0.76020	0.528000	0.53228	AAC	.		0.418	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110763780	A	G	110763780	3	3	108	1	0	0	0	0	1	0	0	0	9061	362	13	3	954	3	LRRN3	7	110763780	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	11010375	110763780	48374883	49	9534											
TNPO3	23534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	128626935	128626935	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcagcagaagccaggggcTtttcacacaggcctttcatc	9	9	10	13	0	2	1	2	0	0	1	3	1	2	1	2	3	3	3	2	3	1	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:128626935T>A	ENST00000265388.5	-	12	1681	c.1538A>T	c.(1537-1539)aAg>aTg	p.K513M	TNPO3_ENST00000393245.1_Missense_Mutation_p.K547M|TNPO3_ENST00000482320.1_Missense_Mutation_p.K447M|TNPO3_ENST00000471234.1_Intron|TNPO3_ENST00000471166.1_Missense_Mutation_p.K547M			Q9Y5L0	TNPO3_HUMAN	transportin 3	513					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						AGCCAGGGGCTTTTCACACAG	0.453																																					p.K513M	Pancreas(147;583 2585 39696 52331)	.											.	TNPO3-228	0			c.A1538T						.						79	81	80					7																	128626935		2203	4300	6503	SO:0001583	missense	23534	exon12			AGGGGCTTTTCAC	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.1538A>T	7.37:g.128626935T>A	ENSP00000265388:p.Lys513Met	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	128	77	NM_012470	0	0	18	35	17	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	37	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118999	0.77323	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471166	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.95	5.95	0.96441	Armadillo-like helical (1);Armadillo-type fold (1);	0.154879	0.56097	D	0.000021	T	0.67924	0.2945	L	0.36672	1.1	0.48571	D	0.999679	D;P	0.63046	0.992;0.895	P;P	0.55999	0.789;0.497	T	0.70920	-0.4741	10	0.66056	D	0.02	-17.8899	10.4289	0.44395	0.0:0.0:0.1635:0.8365	.	547;513	C9J7E5;Q9Y5L0	.;TNPO3_HUMAN	M	547;513;447;547	ENSP00000376936:K547M;ENSP00000265388:K513M;ENSP00000420089:K447M;ENSP00000418267:K547M	ENSP00000265388:K513M	K	-	2	0	TNPO3	128414171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.677000	0.61634	2.279000	0.76181	0.533000	0.62120	AAG	.		0.453	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		A	128626935	T	A	128626935	3	1	108	1	0	0	0	0	1	0	0	0	16369	1609	56	5	1277	5	TNPO3	7	128626935	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	17863155	128626935	30511728	50	9535											
STMN4	81551	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	27097566	27097566	+	Frame_Shift_Del	DEL	T	T	-																															gattccatcttctgggccagTttttccttagccatcttgat																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr8:27097566delT	ENST00000265770.7	-	5	568	c.432delA	c.(430-432)aaafs	p.K144fs	STMN4_ENST00000523048.1_Frame_Shift_Del_p.K171fs|STMN4_ENST00000350889.4_Frame_Shift_Del_p.K171fs|STMN4_ENST00000519614.1_Frame_Shift_Del_p.K144fs|STMN4_ENST00000522908.1_Frame_Shift_Del_p.K171fs|STMN4_ENST00000519997.1_Frame_Shift_Del_p.K135fs			Q9H169	STMN4_HUMAN	stathmin-like 4	144	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	TCTGGGCCAGTTTTTCCTTAG	0.517																																					p.K171fs		.											.	STMN4-154	0			c.513delA						.						233	213	220					8																	27097566		2203	4300	6503	SO:0001589	frameshift_variant	81551	exon6			.		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.432delA	8.37:g.27097566delT	ENSP00000265770:p.Lys144fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	173	76	NM_030795	0	0	0	0	0	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Frame_Shift_Del	DEL	ENST00000265770.7	37																																																																																				.		0.517	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		-	27097566	T	-	27097566	7	5	108	1	0	1	0	1	0	0	0	0	15343	1722	60	0	145	0	STMN4	8	27097566	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08		27097566	119266456	51	9536											
C8orf76	84933	broad.mit.edu	37	chr8	124243792	124243792	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaactgtgctgtttctgaGatgacgcaagtgctgctgaa	10	12	12	7	1	1	4	0	4	1	1	1	5	1	4	0	0	4	5	0	0	3	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr8:124243792G>T	ENST00000276704.4	-	4	614	c.563C>A	c.(562-564)tCt>tAt	p.S188Y	C8orf76_ENST00000521310.1_5'UTR|ZHX1-C8ORF76_ENST00000357082.4_Missense_Mutation_p.S156Y	NM_032847.2	NP_116236.1	Q96K31	CH076_HUMAN	chromosome 8 open reading frame 76	188										NS(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(4)	17	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CTGTTTCTGAGATGACGCAAG	0.438																																					p.S188Y													.	C8orf76-228	0			c.C563A						.						145	153	150					8																	124243792		2203	4300	6503	SO:0001583	missense	84933	exon4			TTCTGAGATGACG	AK027731	CCDS6341.1	8q24.13	2012-06-27			ENSG00000189376	ENSG00000189376			25924	protein-coding gene	gene with protein product							Standard	NM_032847		Approved	FLJ14825	uc003yqc.2	Q96K31	OTTHUMG00000172562	ENST00000276704.4:c.563C>A	8.37:g.124243792G>T	ENSP00000276704:p.Ser188Tyr	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	196	6	NM_032847	0	0	25	29	4	Q53HC1	Missense_Mutation	SNP	ENST00000276704.4	37	CCDS6341.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758786	0.69763	.	.	ENSG00000189376	ENST00000276704;ENST00000357082	.	.	.	5.48	4.6	0.57074	.	0.599351	0.18054	N	0.153184	T	0.58991	0.2161	M	0.68952	2.095	0.28752	N	0.901361	P;D	0.58620	0.911;0.983	P;P	0.54759	0.76;0.653	T	0.58340	-0.7653	9	0.62326	D	0.03	-1.0579	12.0576	0.53544	0.0805:0.0:0.9195:0.0	.	156;188	Q96EF9;Q96K31	.;CH076_HUMAN	Y	188;156	.	ENSP00000276704:S188Y	S	-	2	0	C8orf76	124312973	1.000000	0.71417	0.753000	0.31225	0.940000	0.58332	2.322000	0.43814	1.325000	0.45301	0.655000	0.94253	TCT	.		0.438	C8orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381748.1	NM_032847		T	124243792	G	T	124243792	3	4	108	1	0	0	0	0	1	0	0	0	2443	942	33	4	591	4	C8orf76	8	124243792	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	97146226	124243792	22120230	52	9537											
PLEC	5339	broad.mit.edu	37	chr8	144995793	144995793	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaagcctgaggccgcctgCgcctccagcaggatgagggc	8	4	16	13	2	0	2	0	2	0	0	1	4	1	4	5	4	3	1	5	4	1	0	rs372807129		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr8:144995793C>T	ENST00000322810.4	-	32	8776	c.8607G>A	c.(8605-8607)gcG>gcA	p.A2869A	PLEC_ENST00000345136.3_Silent_p.A2732A|PLEC_ENST00000356346.3_Silent_p.A2718A|PLEC_ENST00000357649.2_Silent_p.A2736A|PLEC_ENST00000354958.2_Silent_p.A2710A|PLEC_ENST00000527096.1_Silent_p.A2755A|PLEC_ENST00000398774.2_Silent_p.A2700A|PLEC_ENST00000436759.2_Silent_p.A2759A|PLEC_ENST00000354589.3_Silent_p.A2732A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2869	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AGGCCGCCTGCGCCTCCAGCA	0.667																																					p.A2869A													.	PLEC-141	0			c.G8607A						.						26	32	30					8																	144995793		2070	4177	6247	SO:0001819	synonymous_variant	5339	exon32			CGCCTGCGCCTCC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8607G>A	8.37:g.144995793C>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_201380	0	0	72	72	0	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.		0.667	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144995793	C	T	144995793	2	4	108	1	0	0	0	0	0	0	0	1	12078	755	27	1		1	PLEC	8	144995793	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08	20752001	144995793	1368229	53	9538											
GBA2	57704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35739010	35739010	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacttttacctgggtccccaAtatcatgggggatgacgttc	8	12	11	10	1	1	1	1	1	0	0	3	3	2	2	3	3	1	1	3	3	3	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:35739010A>G	ENST00000378103.3	-	11	2307	c.1784T>C	c.(1783-1785)aTt>aCt	p.I595T	GBA2_ENST00000378094.4_Missense_Mutation_p.I595T|GBA2_ENST00000467252.1_5'UTR|GBA2_ENST00000545786.1_Missense_Mutation_p.I601T|GBA2_ENST00000378088.1_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	595					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGGGTCCCCAATATCATGGGG	0.572																																					p.I595T		.											.	GBA2-94	0			c.T1784C						.						78	76	77					9																	35739010		2203	4300	6503	SO:0001583	missense	57704	exon11			TCCCCAATATCAT	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.1784T>C	9.37:g.35739010A>G	ENSP00000367343:p.Ile595Thr	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	33	18	NM_020944	0	0	0	1	1	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	37	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	A	16.56	3.156258	0.57259	.	.	ENSG00000070610	ENST00000378103;ENST00000378094;ENST00000545786	.	.	.	5.69	5.69	0.88448	Six-hairpin glycosidase-like (1);Glucosylceramidase (1);	0.259629	0.44285	D	0.000468	T	0.64571	0.2610	L	0.58101	1.795	0.80722	D	1	B;P;P	0.35493	0.449;0.493;0.505	B;B;B	0.41374	0.241;0.079;0.355	T	0.67518	-0.5650	9	0.62326	D	0.03	-8.062	14.5115	0.67791	1.0:0.0:0.0:0.0	.	601;595;595	F5H7P6;Q9HCG7-2;Q9HCG7	.;.;GBA2_HUMAN	T	595;595;601	.	ENSP00000367334:I595T	I	-	2	0	GBA2	35729010	1.000000	0.71417	0.973000	0.42090	0.994000	0.84299	8.924000	0.92827	2.171000	0.68590	0.459000	0.35465	ATT	.		0.572	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		G	35739010	A	G	35739010	3	3	108	1	0	0	0	0	1	0	0	0	6287	101	4	3	1027	3	GBA2	9	35739010	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		35739010	105474421	54	9539											
ZNF169	169841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	97063238	97063238	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccctgattgtgggcgtggCtttggtcagaaggtcaccct	5	12	14	10	1	2	2	2	1	0	1	2	2	2	2	2	4	1	1	2	4	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:97063238C>T	ENST00000395395.2	+	5	1488	c.1398C>T	c.(1396-1398)ggC>ggT	p.G466G	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	466					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				GTGGGCGTGGCTTTGGTCAGA	0.577																																					p.G466G		.											.	ZNF169-92	0			c.C1398T						.						73	66	68					9																	97063238		2203	4300	6503	SO:0001819	synonymous_variant	169841	exon5			GCGTGGCTTTGGT	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"Zinc fingers, C2H2-type", "-"	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1398C>T	9.37:g.97063238C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	79	38	NM_194320	0	0	5	8	3	A2AGP5|A8K127|Q6PI28	Silent	SNP	ENST00000395395.2	37	CCDS6709.2																																																																																			.		0.577	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		T	97063238	C	T	97063238	2	4	108	1	0	0	0	0	0	0	0	1	17774	784	28	2		2	ZNF169	9	97063238	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08	61324228	97063238	44150193	55	9540											
C9orf84	158401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	114503767	114503767	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatctttacctgtaagcaaaAatgggttcaaagggcttcta	14	12	8	7	0	3	0	1	0	2	0	3	0	3	0	1	2	2	4	1	2	7	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:114503767A>T	ENST00000318737.4	-	9	1099	c.971T>A	c.(970-972)tTt>tAt	p.F324Y	C9orf84_ENST00000394777.4_Missense_Mutation_p.F285Y|C9orf84_ENST00000394779.3_Missense_Mutation_p.F285Y|C9orf84_ENST00000374283.5_Missense_Mutation_p.F388Y|C9orf84_ENST00000374287.3_Missense_Mutation_p.F324Y	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	324										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGTAAGCAAAAATGGGTTCAA	0.323																																					p.F324Y		.											.	C9orf84-92	0			c.T971A						.						66	65	65					9																	114503767		2202	4299	6501	SO:0001583	missense	158401	exon9			AGCAAAAATGGGT	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.971T>A	9.37:g.114503767A>T	ENSP00000322108:p.Phe324Tyr	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	103	53	NM_173521	0	0	0	0	0	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	A	12.21	1.869763	0.33069	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000374287;ENST00000318737;ENST00000374283	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	4.56	3.41	0.39046	.	1.021630	0.07826	N	0.960679	T	0.46483	0.1395	L	0.32530	0.975	0.09310	N	1	P;P;P;P	0.45827	0.718;0.844;0.867;0.867	P;P;B;P	0.49829	0.447;0.528;0.439;0.623	T	0.32745	-0.9895	10	0.62326	D	0.03	-0.5524	6.8232	0.23868	0.8939:0.0:0.1061:0.0	.	285;388;324;285	A6PVK7;Q5VXU9-2;Q5VXU9;A2A2V3	.;.;CI084_HUMAN;.	Y	285;285;324;324;388	ENSP00000378259:F285Y;ENSP00000378257:F285Y;ENSP00000363405:F324Y;ENSP00000322108:F324Y;ENSP00000363401:F388Y	ENSP00000322108:F324Y	F	-	2	0	C9orf84	113543588	0.140000	0.22579	0.106000	0.21319	0.691000	0.40173	0.554000	0.23407	0.876000	0.35872	0.455000	0.32223	TTT	.		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		T	114503767	A	T	114503767	3	4	108	1	0	0	0	0	1	0	0	0	2506	14	1	5	3435	5	C9orf84	9	114503767	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	17440529	114503767	26709664	56	9541											
AMBP	259	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	116837296	116837296	+	Frame_Shift_Del	DEL	G	G	-																															ttttctcataagctccagacGtctcctcacagacacctttc																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:116837296delG	ENST00000265132.3	-	3	543	c.281delC	c.(280-282)acgfs	p.T94fs		NM_001633.3	NP_001624.1	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin precursor	94					cell adhesion (GO:0007155)|female pregnancy (GO:0007565)|heme catabolic process (GO:0042167)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of JNK cascade (GO:0046329)|protein catabolic process (GO:0030163)|protein-chromophore linkage (GO:0018298)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|calcium oxalate binding (GO:0046904)|heme binding (GO:0020037)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)|small molecule binding (GO:0036094)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	11					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	AGCTCCAGACGTCTCCTCACA	0.453																																					p.T94fs		.											.	AMBP-91	0			c.281delC						.						143	125	131					9																	116837296		2203	4300	6503	SO:0001589	frameshift_variant	259	exon3			.	X04494	CCDS6800.1	9q32-q33	2014-01-22			ENSG00000106927	ENSG00000106927		"Lipocalins"	453	protein-coding gene	gene with protein product	"growth-inhibiting protein 19", "uristatin", "complex-forming glycoprotein heterogeneous in charge", "bikunin", "inter-alpha-trypsin inhibitor light chain", "protein HC", "uronic-acid-rich protein", "trypstatin"	176870		ITI, ITIL		1708673, 1385302	Standard	NM_001633		Approved	UTI, HCP, EDC1, HI30, IATIL, ITILC	uc004bie.4	P02760	OTTHUMG00000020534	ENST00000265132.3:c.281delC	9.37:g.116837296delG	ENSP00000265132:p.Thr94fs	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	99	46	NM_001633	0	0	0	0	0	P00977|P02759|P78491|Q2TU33|Q5TBD7|Q9UC58|Q9UDI8	Frame_Shift_Del	DEL	ENST00000265132.3	37	CCDS6800.1																																																																																			.		0.453	AMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053758.2	NM_001633		-	116837296	G	-	116837296	7	5	108	1	0	1	0	1	0	0	0	0	564	1145	40	0	809	0	AMBP	9	116837296	Frame_Shift_Del	DEL	G	TCGA-EV-5902-01A-11D-1589-08	2333529	116837296	24376135	57	9542											
GSN	2934	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	124074615	124074615	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctgggtctctgtcttccAgaacatccaccagtggtgtg	6	13	10	12	0	2	1	0	0	2	1	6	1	5	1	4	2	1	0	4	2	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:124074615A>T	ENST00000373818.4	+	5	735		c.e5-1		GSN_ENST00000341272.2_Splice_Site|GSN_ENST00000373807.1_5'UTR|GSN_ENST00000412819.1_Splice_Site|GSN_ENST00000436847.1_Splice_Site|GSN_ENST00000545652.1_Splice_Site|GSN_ENST00000485767.1_3'UTR|GSN_ENST00000449733.1_Splice_Site|GSN_ENST00000394353.2_Splice_Site|GSN_ENST00000373808.2_Splice_Site|GSN_ENST00000373823.3_Splice_Site	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin						actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						TCTGTCTTCCAGAACATCCAC	0.612																																					.		.											.	GSN-154	0			c.514-2A>T						.						97	100	99					9																	124074615		2203	4300	6503	SO:0001630	splice_region_variant	2934	exon6			TCTTCCAGAACAT	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"amyloidosis, Finnish type"	137350	"gelsolin (amyloidosis, Finnish type)"			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.667-1A>T	9.37:g.124074615A>T		Somatic	159	1		WXS	Illumina HiSeq	Phase_I	157	9	NM_198252	0	0	0	0	0	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Splice_Site	SNP	ENST00000373818.4	37	CCDS6828.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.988296	0.74589	.	.	ENSG00000148180	ENST00000373823;ENST00000432226;ENST00000449773;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0966	0.72238	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GSN	123114436	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	9.281000	0.95811	2.178000	0.69098	0.533000	0.62120	.	.		0.612	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	Intron	T	124074615	A	T	124074615	5	4	108	1	0	0	0	0	0	0	1	0	6846	202	7	5	711	5	GSN	9	124074615	Splice_Site	SNP	A	TCGA-EV-5902-01A-11D-1589-08	7237319	124074615	17138816	58	9543											
RABGAP1	23637	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	125772734	125772738	+	Frame_Shift_Del	DEL	TTCAG	TTCAG	-																															aggaaaactacagccagtccTtcagttcgcctgccacagtc																								rs201077208		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	TTCAG	TTCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:125772734_125772738delTTCAG	ENST00000373647.4	+	11	1610_1614	c.1476_1480delTTCAG	c.(1474-1482)ccttcagttfs	p.SV493fs		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	493					cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						CAGCCAGTCCTTCAGTTCGCCTGCC	0.4																																					p.492_494del		.											.	RABGAP1-500	0			c.1476_1480del						.																																			SO:0001589	frameshift_variant	23637	exon11			.	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.1476_1480delTTCAG	9.37:g.125772734_125772738delTTCAG	ENSP00000362751:p.Ser493fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	71	25	NM_012197	0	0	0	0	0	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Frame_Shift_Del	DEL	ENST00000373647.4	37	CCDS6848.2																																																																																			.		0.4	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		-	125772738	TTCAG	-	125772734	7	5	108	1	0	1	0	1	0	0	0	0	12996	1596	56	0	1514	0	RABGAP1	9	125772734	Frame_Shift_Del	DEL	TTCAG	TCGA-EV-5902-01A-11D-1589-08	1698119	125772734	15440697	59	9544											
ZER1	10444	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	131515779	131515779	+	Frame_Shift_Del	DEL	A	A	-																															agaaaatgtttgtacagccgAagaggctcaaggacaccagg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:131515779delA	ENST00000291900.2	-	4	816	c.410delT	c.(409-411)ttcfs	p.F137fs	ZER1_ENST00000494461.1_5'UTR	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	137					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TGTACAGCCGAAGAGGCTCAA	0.557																																					p.F137fs		.											.	ZER1-91	0			c.410delT						.						54	57	56					9																	131515779		2203	4300	6503	SO:0001589	frameshift_variant	10444	exon4			.	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.410delT	9.37:g.131515779delA	ENSP00000291900:p.Phe137fs	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	57	26	NM_006336	0	0	0	0	0	O00156|Q5T272|Q5T273	Frame_Shift_Del	DEL	ENST00000291900.2	37	CCDS6910.1																																																																																			.		0.557	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		-	131515779	A	-	131515779	7	5	108	1	0	1	0	1	0	0	0	0	17657	246	9	0	1942	0	ZER1	9	131515779	Frame_Shift_Del	DEL	A	TCGA-EV-5902-01A-11D-1589-08	5743045	131515779	9697652	60	9545											
TUBB2C	10383	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	140137389	140137389	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtggggtcaccacctgccTgcgcttcccaggccagctca	6	7	12	16	1	2	0	2	0	0	0	3	1	3	0	5	3	3	2	5	3	0	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:140137389T>C	ENST00000340384.4	+	4	867	c.719T>C	c.(718-720)cTg>cCg	p.L240P		NM_006088.5	NP_006079.1	P68371	TBB4B_HUMAN	tubulin, beta 4B class IVb	240					'de novo' posttranslational protein folding (GO:0051084)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|unfolded protein binding (GO:0051082)									Albendazole(DB00518)|Mebendazole(DB00643)	ACCACCTGCCTGCGCTTCCCA	0.592																																					p.L240P		.											.	.	0			c.T719C						.						30	31	31					9																	140137389		2200	4290	6490	SO:0001583	missense	10383	exon4			CCTGCCTGCGCTT	BC019359	CCDS7039.1	9q34.3	2011-10-10	2011-10-10	2011-10-10	ENSG00000188229	ENSG00000188229		"Tubulins"	20771	protein-coding gene	gene with protein product	"class IVb beta-tubulin"	602660	"tubulin, beta 2C"	TUBB2C		3999141	Standard	NM_006088		Approved	Beta2	uc004cmh.1	P68371	OTTHUMG00000131783	ENST00000340384.4:c.719T>C	9.37:g.140137389T>C	ENSP00000341289:p.Leu240Pro	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	52	24	NM_006088	0	0	173	314	141	A2BFA2|P05217	Missense_Mutation	SNP	ENST00000340384.4	37	CCDS7039.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029097	0.54790	.	.	ENSG00000188229	ENST00000340384	T	0.71934	-0.61	5.57	5.57	0.84162	.	0.000000	0.53938	D	0.000043	D	0.91955	0.7452	H	0.99919	4.95	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95434	0.8519	10	0.87932	D	0	.	14.5794	0.68274	0.0:0.0:0.0:1.0	.	240	P68371	TBB4B_HUMAN	P	240	ENSP00000341289:L240P	ENSP00000341289:L240P	L	+	2	0	TUBB2C	139257210	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.111000	0.71541	2.122000	0.65172	0.533000	0.62120	CTG	.		0.592	TUBB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254715.1	NM_006088		C	140137389	T	C	140137389	3	2	108	1	0	0	0	0	1	0	0	0	16789	1580	55	3	733	3	TUBB2C	9	140137389	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	8621610	140137389	1076042	61	9546											
WDR37	22884	hgsc.bcm.edu	37	chr10	1151150	1151150	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgacacgactttccgccTctgggatttcagggacccct	6	10	10	15	3	2	1	1	1	1	0	3	4	3	3	5	2	0	0	5	2	0	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr10:1151150T>C	ENST00000358220.1	+	11	1190	c.1046T>C	c.(1045-1047)cTc>cCc	p.L349P	WDR37_ENST00000263150.4_Missense_Mutation_p.L349P			Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	349										breast(2)|endometrium(2)|kidney(1)|lung(9)|prostate(2)|skin(1)	17		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)		ACTTTCCGCCTCTGGGATTTC	0.562																																					p.L349P		.											.	WDR37-90	0			c.T1046C						.						83	67	72					10																	1151150		2203	4300	6503	SO:0001583	missense	22884	exon11			TCCGCCTCTGGGA	AB023199	CCDS7057.1	10p15.3	2013-01-09			ENSG00000047056	ENSG00000047056		"WD repeat domain containing"	31406	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_014023		Approved	KIAA0982	uc001igf.1	Q9Y2I8	OTTHUMG00000017540	ENST00000358220.1:c.1046T>C	10.37:g.1151150T>C	ENSP00000350954:p.Leu349Pro	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_014023	0	0	14	14	0	A8K976|D3DRQ7|Q5SW03|Q8WVG2|Q9NTJ6	Missense_Mutation	SNP	ENST00000358220.1	37	CCDS7057.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843266	0.91197	.	.	ENSG00000047056	ENST00000358220;ENST00000263150	T;T	0.67345	-0.26;-0.26	5.6	5.6	0.85130	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85483	0.5707	M	0.91872	3.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88902	0.3353	10	0.87932	D	0	.	15.7724	0.78180	0.0:0.0:0.0:1.0	.	350;349	A8K976;Q9Y2I8	.;WDR37_HUMAN	P	349	ENSP00000350954:L349P;ENSP00000263150:L349P	ENSP00000263150:L349P	L	+	2	0	WDR37	1141150	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	7.736000	0.84948	2.133000	0.65898	0.459000	0.35465	CTC	.		0.562	WDR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046418.1	NM_014023		C	1151150	T	C	1151150	3	2	108	1	0	0	0	0	1	0	0	0	17324	1551	54	3	1084	3	WDR37	10	1151150	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		1151150	134383597	62	9547											
ABLIM1	3983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	116225561	116225561	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcgtggaccgatggatcAtccgatcccgaacatcctgg	8	8	12	13	4	1	0	1	0	0	0	5	5	4	2	4	4	1	1	4	4	1	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr10:116225561A>G	ENST00000277895.5	-	12	1434	c.1337T>C	c.(1336-1338)aTg>aCg	p.M446T	ABLIM1_ENST00000369266.3_Missense_Mutation_p.M158T|ABLIM1_ENST00000369253.2_Missense_Mutation_p.M104T|ABLIM1_ENST00000369252.4_Missense_Mutation_p.M386T|ABLIM1_ENST00000533213.2_Missense_Mutation_p.M386T|ABLIM1_ENST00000392952.3_Missense_Mutation_p.M158T	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	446					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CCGATGGATCATCCGATCCCG	0.557																																					p.M446T		.											.	ABLIM1-153	0			c.T1337C						.						215	192	200					10																	116225561		2203	4300	6503	SO:0001583	missense	3983	exon12			TGGATCATCCGAT	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1337T>C	10.37:g.116225561A>G	ENSP00000277895:p.Met446Thr	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	174	88	NM_002313	0	0	31	83	52	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.82|10.82	1.459451|1.459451	0.26248|0.26248	.|.	.|.	ENSG00000099204|ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000392952;ENST00000369257;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369266;ENST00000369256;ENST00000369260;ENST00000277895;ENST00000369253;ENST00000440467;ENST00000428430|ENST00000392955	T;T;T;T;T;T|.	0.54866|.	0.55;0.55;0.55;0.55;0.55;0.55|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.318695|.	0.42548|.	D|.	0.000696|.	T|.	0.38295|.	0.1035|.	N|N	0.08118|0.08118	0|0	0.36815|0.36815	D|D	0.88611|0.88611	B;B;B;B;B;B;B;B;B|.	0.15930|.	0.0;0.002;0.015;0.0;0.0;0.001;0.001;0.0;0.002|.	B;B;B;B;B;B;B;B;B|.	0.22386|.	0.002;0.005;0.039;0.002;0.001;0.004;0.003;0.001;0.009|.	T|.	0.45745|.	-0.9240|.	10|.	0.15499|.	T|.	0.54|.	.|.	14.3083|14.3083	0.66397|0.66397	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	370;130;386;414;446;158;414;370;104|.	B7Z4H1;B4DQA3;F8W8M4;A6NKJ2;O14639;O14639-5;B3KVH2;C9K0X4;O14639-4|.	.;.;.;.;ABLM1_HUMAN;.;.;.;.|.	T|R	446;386;158;104;414;386;474;370;158;370;370;474;158;111;130|355	ENSP00000358256:M386T;ENSP00000376679:M158T;ENSP00000433629:M386T;ENSP00000358270:M158T;ENSP00000414154:M111T;ENSP00000400934:M130T|.	ENSP00000277895:M474T|.	M|X	-|-	2|1	0|0	ABLIM1|ABLIM1	116215551|116215551	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.016000|6.016000	0.70798|0.70798	2.185000|2.185000	0.69588|0.69588	0.528000|0.528000	0.53228|0.53228	ATG|TGA	.		0.557	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			G	116225561	A	G	116225561	3	3	108	1	0	0	0	0	1	0	0	0	94	217	8	3	1043	3	ABLIM1	10	116225561	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	115074411	116225561	19309186	63	9548											
TRIM22	10346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	5717510	5717510	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaggaggtgacctgcccCatctgcctggagctcctgac	8	7	13	13	0	1	3	0	2	1	1	2	6	2	5	5	3	3	1	5	3	1	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:5717510C>T	ENST00000379965.3	+	2	325	c.48C>T	c.(46-48)ccC>ccT	p.P16P	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	16					defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		TGACCTGCCCCATCTGCCTGG	0.502																																					p.P16P	GBM(104;491 2336 5222)	.											.	TRIM22-90	0			c.C48T						.						87	92	90					11																	5717510		2201	4297	6498	SO:0001819	synonymous_variant	10346	exon2			CTGCCCCATCTGC	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16379	protein-coding gene	gene with protein product		606559	"tripartite motif-containing 22"			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.48C>T	11.37:g.5717510C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	72	40	NM_001199573	0	0	40	84	44	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			.		0.502	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		T	5717510	C	T	5717510	2	4	108	1	0	0	0	0	0	0	0	1	16529	581	21	2		2	TRIM22	11	5717510	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08		5717510	129289006	64	9549											
INCENP	3619	broad.mit.edu	37	chr11	61916013	61916015	+	In_Frame_Del	DEL	AGA	AGA	-																															gctgcagagggaactggaggAgaagaagaagaaggtgaggg																								rs79863590		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:61916013_61916015delAGA	ENST00000394818.3	+	16	2472_2474	c.2270_2272delAGA	c.(2269-2274)gagaag>gag	p.K761del	INCENP_ENST00000278849.4_In_Frame_Del_p.K757del	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	761					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GAACTGGAGGAGAAGAAGAAGAA	0.655																																					p.757_758del													.	INCENP-227	0			c.2270_2272del						.																																			SO:0001651	inframe_deletion	3619	exon16			TGGAGGAGAAGAA	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.2270_2272delAGA	11.37:g.61916022_61916024delAGA	ENSP00000378295:p.Lys761del	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	15	7	NM_001040694	0	0	0	0	0	A8MQD2|Q5Y192	In_Frame_Del	DEL	ENST00000394818.3	37	CCDS44624.1																																																																																			.		0.655	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		-	61916015	AGA	-	61916013	7	5	108	1	0	1	0	1	0	0	0	0	7754	304	11	0	2328	0	INCENP	11	61916013	In_Frame_Del	DEL	AGA	TCGA-EV-5902-01A-11D-1589-08	56198503	61916013	73090503	65	9550											
GPR137	56834	broad.mit.edu	37	chr11	64056826	64056826	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctgtcatagtgagcttgtgCcgtccccctaggatgggggg	5	10	15	11	1	1	1	1	1	0	0	2	2	2	2	4	4	2	1	4	4	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:64056826C>T	ENST00000313074.3	+	7	1348	c.1243C>T	c.(1243-1245)Ccg>Tcg	p.P415S	KCNK4_ENST00000538767.1_5'Flank|RP11-783K16.10_ENST00000539086.1_RNA|KCNK4_ENST00000394525.2_5'Flank|GPR137_ENST00000539851.1_3'UTR|GPR137_ENST00000438980.2_3'UTR|GPR137_ENST00000377702.4_3'UTR|GPR137_ENST00000411458.1_Missense_Mutation_p.P473S|KCNK4_ENST00000422670.2_5'Flank	NM_020155.3	NP_064540.3	Q96N19	G137A_HUMAN	G protein-coupled receptor 137	415						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(4)|skin(1)	10						TGAGCTTGTGCCGTCCCCCTA	0.647																																					p.P473S													.	GPR137-68	0			c.C1417T						.						61	61	61					11																	64056826		2201	4297	6498	SO:0001583	missense	56834	exon9			CTTGTGCCGTCCC	AJ250392	CCDS8066.1, CCDS53655.1, CCDS53656.1, CCDS53657.1, CCDS53658.1	11q13.1	2014-02-12	2006-01-26		ENSG00000173264	ENSG00000173264		"GPCR / Unclassified : 7TM orphan receptors"	24300	protein-coding gene	gene with protein product						10873569, 12732197	Standard	NM_001170726		Approved	C11orf4, GPR137A, TM7SF1L1	uc010rni.2	Q96N19	OTTHUMG00000167817	ENST00000313074.3:c.1243C>T	11.37:g.64056826C>T	ENSP00000321698:p.Pro415Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	130	4	NM_001170726	0	0	37	37	0	B4DTG7|B7Z7M1|Q4G0Y9|Q8N4K6	Missense_Mutation	SNP	ENST00000313074.3	37	CCDS8066.1	.	.	.	.	.	.	.	.	.	.	C	9.310	1.055330	0.19907	.	.	ENSG00000173264	ENST00000411458;ENST00000313074	T;T	0.51574	0.7;0.85	5.27	3.38	0.38709	.	1.323320	0.05536	N	0.564845	T	0.30293	0.0760	N	0.08118	0	0.58432	D	0.999993	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.001	T	0.06991	-1.0796	10	0.49607	T	0.09	-0.0272	7.3883	0.26895	0.0:0.7394:0.1696:0.091	.	473;415	B4DTG7;Q96N19	.;G137A_HUMAN	S	473;415	ENSP00000411827:P473S;ENSP00000321698:P415S	ENSP00000321698:P415S	P	+	1	0	GPR137	63813402	0.698000	0.27777	0.584000	0.28653	0.551000	0.35334	1.531000	0.36018	0.718000	0.32166	0.561000	0.74099	CCG	.		0.647	GPR137-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396412.1	NM_020155		T	64056826	C	T	64056826	3	4	108	1	0	0	0	0	1	0	0	0	6665	739	26	2	1557	2	GPR137	11	64056826	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	2140813	64056826	70949690	66	9551											
ARHGEF17	9828	ucsc.edu;bcgsc.ca	37	chr11	73073120	73073120	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaccctgaacagctgcccGgagccctcgcctgaggtatg	7	6	11	17	2	0	2	0	2	0	0	1	3	0	3	5	2	4	2	5	2	2	1	rs200742689		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:73073120G>T	ENST00000263674.3	+	13	4880	c.4530G>T	c.(4528-4530)ccG>ccT	p.P1510P		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1510					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						ACAGCTGCCCGGAGCCCTCGC	0.662																																					p.P1510P													.	ARHGEF17-227	0			c.G4530T						.						29	31	30					11																	73073120		2200	4292	6492	SO:0001819	synonymous_variant	9828	exon13			CTGCCCGGAGCCC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.4530G>T	11.37:g.73073120G>T		Somatic	47	0		WXS	Illumina HiSeq		36	5	NM_014786	0	0	17	17	0	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	37	CCDS8221.1																																																																																			G|0.999;A|0.000		0.662	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73073120	G	T	73073120	2	4	108	1	0	0	0	0	0	0	0	1	900	1103	39	4		4	ARHGEF17	11	73073120	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	9016294	73073120	61933396	67	9552											
OR2AT4	341152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74800733	74800733	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agacgggtgagccatccactGattcattacaggctgtggca	10	9	12	10	1	1	3	1	2	0	1	2	3	2	3	2	3	2	2	2	3	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:74800733G>A	ENST00000305159.3	-	1	66	c.26C>T	c.(25-27)tCa>tTa	p.S9L		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						GCCATCCACTGATTCATTACA	0.473																																					p.S9L		.											.	OR2AT4-69	0			c.C26T						.						50	52	51					11																	74800733		2200	4292	6492	SO:0001583	missense	341152	exon1			TCCACTGATTCAT	BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"GPCR / Class A : Olfactory receptors"	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.26C>T	11.37:g.74800733G>A	ENSP00000304846:p.Ser9Leu	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	89	43	NM_001005285	0	0	0	0	0	B9EGZ8	Missense_Mutation	SNP	ENST00000305159.3	37	CCDS31639.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970843	0.53614	.	.	ENSG00000171561	ENST00000305159	T	0.54675	0.56	4.58	4.58	0.56647	.	0.000000	0.28241	U	0.016072	T	0.31702	0.0805	N	0.08118	0	0.36873	D	0.88902	P	0.49783	0.928	B	0.37601	0.254	T	0.51903	-0.8646	10	0.87932	D	0	.	15.2827	0.73801	0.0:0.0:1.0:0.0	.	9	A6NND4	O2AT4_HUMAN	L	9	ENSP00000304846:S9L	ENSP00000304846:S9L	S	-	2	0	OR2AT4	74478381	0.991000	0.36638	0.999000	0.59377	0.919000	0.55068	2.954000	0.49113	2.533000	0.85409	0.462000	0.41574	TCA	.		0.473	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285		A	74800733	G	A	74800733	3	1	108	1	0	0	0	0	1	0	0	0	11013	1294	45	2	939	2	OR2AT4	11	74800733	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	1727613	74800733	60205783	68	9553											
MYO7A	4647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	76867021	76867021	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatctactcgccagagcaCatccgccagtataccaacaa	13	7	5	16	2	1	1	0	0	1	1	4	1	3	1	5	0	4	2	5	0	5	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:76867021C>T	ENST00000409709.3	+	5	626	c.354C>T	c.(352-354)caC>caT	p.H118H	MYO7A_ENST00000409893.1_Silent_p.H118H|MYO7A_ENST00000409619.2_Silent_p.H107H|MYO7A_ENST00000458637.2_Silent_p.H118H	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	118	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CGCCAGAGCACATCCGCCAGT	0.562																																					p.H118H		.											.	MYO7A-138	0			c.C354T						.						35	39	38					11																	76867021		2139	4251	6390	SO:0001819	synonymous_variant	4647	exon5			AGAGCACATCCGC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.354C>T	11.37:g.76867021C>T		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	13	9	NM_001127179	0	0	0	0	0	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.		0.562	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76867021	C	T	76867021	2	4	108	1	0	0	0	0	0	0	0	1	10107	477	17	2		2	MYO7A	11	76867021	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08	2066288	76867021	58139495	69	9554											
GAB2	9846	broad.mit.edu	37	chr11	77991912	77991912	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tctgggtcaccgctcatccgGccactccgcaggataaacca	9	7	9	16	3	3	0	2	0	1	0	5	1	5	1	5	3	1	2	5	3	2	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:77991912G>A	ENST00000361507.4	-	2	196	c.111C>T	c.(109-111)ggC>ggT	p.G37G	GAB2_ENST00000526030.1_5'UTR|GAB2_ENST00000340149.2_5'UTR	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	37	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			CGCTCATCCGGCCACTCCGCA	0.463																																					p.G37G													.	GAB2-663	0			c.C111T						.						83	84	83					11																	77991912		2200	4292	6492	SO:0001819	synonymous_variant	9846	exon2			CATCCGGCCACTC	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"Pleckstrin homology (PH) domain containing"	14458	protein-coding gene	gene with protein product	"Grb2-associated binder 2"	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.111C>T	11.37:g.77991912G>A		Somatic	158	0		WXS	Illumina HiSeq	Phase_I	154	7	NM_080491	0	0	10	10	0	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			.		0.463	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		A	77991912	G	A	77991912	2	1	108	1	0	0	0	0	0	0	0	1	6168	1190	42	2		2	GAB2	11	77991912	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	1124891	77991912	57014604	70	9555											
C12orf26	84190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	82752495	82752495	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatccgtgtgggaggagctgGtcgacttgccaccggagaca	9	7	15	10	3	0	1	0	0	0	1	2	5	1	3	3	4	2	1	3	4	1	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr12:82752495G>A	ENST00000248306.3	+	1	220	c.151G>A	c.(151-153)Gtc>Atc	p.V51I	CCDC59_ENST00000548126.1_5'UTR|CCDC59_ENST00000256151.7_5'UTR|METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	51							methyltransferase activity (GO:0008168)										GGAGGAGCTGGTCGACTTGCC	0.602											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V51I		.											.	.	0			c.G151A						.						94	79	84					12																	82752495		2203	4300	6503	SO:0001583	missense	84190	exon1			GAGCTGGTCGACT	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 26"	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.151G>A	12.37:g.82752495G>A	ENSP00000248306:p.Val51Ile	Somatic	83	0	1216	WXS	Illumina HiSeq	Phase_I	103	39	NM_032230	0	0	9	14	5	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434382	0.43224	.	.	ENSG00000127720	ENST00000248306;ENST00000548200	T	0.36340	1.26	5.49	1.42	0.22433	.	0.278728	0.40222	N	0.001147	T	0.25494	0.0620	L	0.44542	1.39	0.26395	N	0.976518	B	0.13145	0.007	B	0.15052	0.012	T	0.15378	-1.0439	10	0.29301	T	0.29	-2.0635	7.0129	0.24873	0.2126:0.1248:0.6626:0.0	.	51	Q8N6Q8	CL026_HUMAN	I	51	ENSP00000248306:V51I	ENSP00000248306:V51I	V	+	1	0	C12orf26	81276626	0.991000	0.36638	0.064000	0.19789	0.869000	0.49853	0.289000	0.18957	0.294000	0.22547	0.650000	0.86243	GTC	.		0.602	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		A	82752495	G	A	82752495	3	1	108	1	0	0	0	0	1	0	0	0	1683	1261	44	2	153	2	C12orf26	12	82752495	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08		82752495	51099400	71	9556											
SBNO1	55206	broad.mit.edu	37	chr12	123780522	123780522	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atagctgtttctgttggaccGcaagctgttgagactggtct	7	14	12	8	1	2	1	0	1	2	1	2	3	2	2	1	2	2	6	1	2	2	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr12:123780522G>A	ENST00000602398.1	-	32	4242	c.4115C>T	c.(4114-4116)gCg>gTg	p.A1372V	SBNO1_ENST00000602750.1_Missense_Mutation_p.A1371V|SBNO1_ENST00000267176.4_Missense_Mutation_p.A1371V|SBNO1_ENST00000420886.2_Missense_Mutation_p.A1372V			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1372					regulation of transcription, DNA-templated (GO:0006355)			p.A1371V(2)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CTGTTGGACCGCAAGCTGTTG	0.433																																					p.A1372V													.	SBNO1-292	2	Substitution - Missense(2)	lung(1)|prostate(1)	c.C4115T						.						340	303	316					12																	123780522		2203	4300	6503	SO:0001583	missense	55206	exon31			TGGACCGCAAGCT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.4115C>T	12.37:g.123780522G>A	ENSP00000473665:p.Ala1372Val	Somatic	319	0		WXS	Illumina HiSeq	Phase_I	302	6	NM_001167856	0	0	21	21	0	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.622923	0.87460	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	T;T	0.32515	1.45;1.45	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.45236	0.1332	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.73708	0.959;0.981	T	0.12785	-1.0534	10	0.33940	T	0.23	-19.465	20.5792	0.99380	0.0:0.0:1.0:0.0	.	1372;1371	A3KN83;A3KN83-2	SBNO1_HUMAN;.	V	1372;1371	ENSP00000387361:A1372V;ENSP00000267176:A1371V	ENSP00000267176:A1371V	A	-	2	0	SBNO1	122346475	1.000000	0.71417	0.790000	0.31976	0.976000	0.68499	9.431000	0.97494	2.873000	0.98535	0.561000	0.74099	GCG	.		0.433	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123780522	G	A	123780522	3	1	108	1	0	0	0	0	1	0	0	0	13894	1087	38	1	70	1	SBNO1	12	123780522	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	41028027	123780522	10071373	72	9557											
C13orf23	80209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	39587414	39587414	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctggagagacctgacaatgCaggattaaggcaagcagata	15	6	13	7	0	0	3	0	1	0	2	0	6	0	5	1	3	2	4	1	3	4	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:39587414C>A	ENST00000352251.3	-	11	2808	c.1975G>T	c.(1975-1977)Gca>Tca	p.A659S	PROSER1_ENST00000350125.3_Missense_Mutation_p.A637S|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	659	Ser-rich.																CCTGACAATGCAGGATTAAGG	0.478																																					p.A659S		.											.	.	0			c.G1975T						.						131	122	125					13																	39587414		2203	4300	6503	SO:0001583	missense	80209	exon11			ACAATGCAGGATT	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1975G>T	13.37:g.39587414C>A	ENSP00000332034:p.Ala659Ser	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	99	50	NM_025138	0	0	12	22	10	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	C	10.07	1.248685	0.22880	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.47528	0.84;0.84	5.27	2.55	0.30701	.	.	.	.	.	T	0.32793	0.0841	L	0.29908	0.895	0.09310	N	1	P;P	0.45531	0.86;0.775	B;B	0.38264	0.269;0.197	T	0.05971	-1.0853	8	.	.	.	-13.5541	10.4949	0.44772	0.0:0.7738:0.0:0.2262	.	637;659	A6NJ97;Q86XN7	.;PRSR1_HUMAN	S	659;637	ENSP00000332034:A659S;ENSP00000339123:A637S	.	A	-	1	0	PROSER1	38485414	0.982000	0.34865	0.377000	0.26055	0.533000	0.34776	2.976000	0.49289	0.711000	0.32018	0.561000	0.74099	GCA	.		0.478	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		A	39587414	C	A	39587414	3	1	108	1	0	0	0	0	1	0	0	0	1725	710	25	4	871	4	C13orf23	13	39587414	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		39587414	75582464	73	9558											
ZC3H13	23091	broad.mit.edu;bcgsc.ca	37	chr13	46543501	46543502	+	Frame_Shift_Ins	INS	-	-	T																															tcactgaatgctgtatcttcINSttttttctgggagtcctcta																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:46543501_46543502insT	ENST00000242848.4	-	14	3525_3526	c.3177_3178insA	c.(3175-3180)aaagaafs	p.E1060fs	ZC3H13_ENST00000378921.2_Frame_Shift_Ins_p.E16fs|ZC3H13_ENST00000282007.3_Frame_Shift_Ins_p.E1060fs			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1060							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		GCTGTATCTTCTTTTTTCTGGG	0.475																																					p.E1060fs	Esophageal Squamous(187;747 2077 11056 31291 44172)												.	ZC3H13-92	0			c.3178_3179insA						.																																			SO:0001589	frameshift_variant	23091	exon14			TATCTTCTTTTTT	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.3178dupA	13.37:g.46543507_46543507dupT	ENSP00000242848:p.Glu1060fs	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	189	21	NM_015070	0	0	0	0	0	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Frame_Shift_Ins	INS	ENST00000242848.4	37																																																																																				.		0.475	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		T	46543502	-	T	46543501	7	5	108	1	0	1	1	0	0	0	0	0	17597	922	32	0	1532	0	ZC3H13	13	46543501	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	6956087	46543501	68626377	74	9559											
DACH1	1602	hgsc.bcm.edu	37	chr13	72440673	72440673	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgctgccgccgccgccgcCgccgccgccgccgccggtag	1	3	14	23	11	0	0	0	0	0	0	1	0	1	0	11	1	1	2	11	1	1	1	rs200162861		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:72440673C>T	ENST00000359684.2	-	1	234	c.235G>A	c.(235-237)Ggc>Agc	p.G79S	DACH1_ENST00000354591.4_Missense_Mutation_p.G79S|DACH1_ENST00000313174.7_Missense_Mutation_p.G79S|DACH1_ENST00000305425.4_Missense_Mutation_p.G79S			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	79	Poly-Gly.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		ccgccgccgccgccgccgccg	0.801																																					p.G79S		.											.	DACH1-135	0			c.G235A						.						1	1	1					13																	72440673		224	1002	1226	SO:0001583	missense	1602	exon1			CGCCGCCGCCGCC	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.235G>A	13.37:g.72440673C>T	ENSP00000352712:p.Gly79Ser	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	3	2	NM_080759	1	0	3	4	0	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	37		.	.	.	.	.	.	.	.	.	.	c	9.793	1.178369	0.21787	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	T;T;T;D	0.87029	1.13;1.28;1.4;-2.2	3.05	3.05	0.35203	.	.	.	.	.	T	0.71787	0.3381	N	0.12182	0.205	0.25137	N	0.990525	B;B;B	0.18863	0.031;0.006;0.003	B;B;B	0.06405	0.002;0.001;0.001	T	0.55798	-0.8084	9	0.09843	T	0.71	-0.641	8.5869	0.33664	0.2302:0.7698:0.0:0.0	.	79;79;79	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	S	79	ENSP00000304994:G79S;ENSP00000318506:G79S;ENSP00000346604:G79S;ENSP00000352712:G79S	ENSP00000304994:G79S	G	-	1	0	DACH1	71338674	0.981000	0.34729	0.996000	0.52242	0.392000	0.30506	2.007000	0.40883	1.534000	0.49203	0.306000	0.20318	GGC	.		0.801	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		T	72440673	C	T	72440673	3	4	108	1	0	0	0	0	1	0	0	0	4226	652	23	1	1935	1	DACH1	13	72440673	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	25897172	72440673	42729205	75	9560											
MYCBP2	23077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	77799654	77799654	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagggtatgttgtgatttTgcttgcatccttttcgcctc	4	18	11	8	1	0	1	0	1	0	0	3	2	1	2	2	2	2	4	2	2	1	7			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:77799654T>C	ENST00000544440.2	-	19	2676	c.2659A>G	c.(2659-2661)Aaa>Gaa	p.K887E	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.K887E|MYCBP2_ENST00000407578.2_Missense_Mutation_p.K925E					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GTTGTGATTTTGCTTGCATCC	0.413																																					p.K925E		.											.	MYCBP2-236	0			c.A2773G						.						215	181	192					13																	77799654		2203	4300	6503	SO:0001583	missense	23077	exon19			TGATTTTGCTTGC	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"MYC binding protein 2"			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.2659A>G	13.37:g.77799654T>C	ENSP00000444596:p.Lys887Glu	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	146	65	NM_015057	0	0	6	13	7		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	T	21.8	4.197089	0.79015	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.28666	1.61;1.6;1.61	5.96	5.96	0.96718	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	L	0.34521	1.04	0.58432	D	0.999998	P	0.52842	0.956	D	0.65010	0.931	T	0.38156	-0.9674	10	0.66056	D	0.02	.	16.4381	0.83884	0.0:0.0:0.0:1.0	.	887	O75592	MYCB2_HUMAN	E	887;925;887	ENSP00000349892:K887E;ENSP00000384288:K925E;ENSP00000444596:K887E	ENSP00000349892:K887E	K	-	1	0	MYCBP2	76697655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.679000	0.84048	2.280000	0.76307	0.533000	0.62120	AAA	.		0.413	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77799654	T	C	77799654	3	2	108	1	0	0	0	0	1	0	0	0	10043	1821	63	3	11523	3	MYCBP2	13	77799654	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	5358981	77799654	37370224	76	9561											
COCH	1690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31355476	31355476	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtcacagatgggcagtccTatgatgatgtccaaggccct	9	11	11	10	0	1	3	1	2	0	1	3	3	3	3	3	2	0	1	3	2	2	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr14:31355476T>C	ENST00000396618.3	+	11	1491	c.1435T>C	c.(1435-1437)Tat>Cat	p.Y479H	RP11-829H16.3_ENST00000468444.2_RNA|RP11-829H16.3_ENST00000555421.1_RNA|RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000460581.2_Missense_Mutation_p.Y367H|COCH_ENST00000475087.1_Missense_Mutation_p.Y479H|COCH_ENST00000382493.4_Missense_Mutation_p.Y330H|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000216361.4_Missense_Mutation_p.Y479H	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	479	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		TGGGCAGTCCTATGATGATGT	0.453																																					p.Y479H		.											.	COCH-228	0			c.T1435C						.						62	61	61					14																	31355476		2203	4300	6503	SO:0001583	missense	1690	exon11			CAGTCCTATGATG		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.1435T>C	14.37:g.31355476T>C	ENSP00000379862:p.Tyr479His	Somatic	87	1		WXS	Illumina HiSeq	Phase_I	77	36	NM_004086	0	0	0	0	0	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	37	CCDS9640.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451692	0.84209	.	.	ENSG00000100473	ENST00000216361;ENST00000396618;ENST00000475087;ENST00000460581;ENST00000382493	T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04	5.89	5.89	0.94794	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.85392	0.5686	L	0.50333	1.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.977	D	0.86401	0.1742	10	0.66056	D	0.02	-15.6938	16.3156	0.82923	0.0:0.0:0.0:1.0	.	330;479;479	E7EN67;Q96IU6;O43405	.;.;COCH_HUMAN	H	479;479;479;367;330	ENSP00000216361:Y479H;ENSP00000379862:Y479H;ENSP00000451528:Y479H;ENSP00000451713:Y367H;ENSP00000371933:Y330H	ENSP00000216361:Y479H	Y	+	1	0	COCH	30425227	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.884000	0.87274	2.245000	0.73994	0.455000	0.32223	TAT	.		0.453	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		C	31355476	T	C	31355476	3	2	108	1	0	0	0	0	1	0	0	0	3662	1522	53	3	1473	3	COCH	14	31355476	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		31355476	75994064	77	9562											
MBIP	51562	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	36770005	36770006	+	Frame_Shift_Ins	INS	-	-	T																															cttacttgaggtggttgaacINSttttcttctttttccagaaa																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr14:36770005_36770006insT	ENST00000416007.4	-	8	999_1000	c.912_913insA	c.(910-915)aaagttfs	p.V305fs	MBIP_ENST00000359527.7_Frame_Shift_Ins_p.S272fs|MBIP_ENST00000318473.7_Frame_Shift_Ins_p.V305fs	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	305	Interaction with MAP3K12.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|inactivation of MAPK activity involved in osmosensory signaling pathway (GO:0000173)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein kinase inhibitor activity (GO:0004860)			breast(2)|large_intestine(1)|lung(5)	8	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)		GGTGGTTGAACTTTTCTTCTTT	0.243																																					p.V305fs		.											.	MBIP-658	0			c.913_914insA						.																																			SO:0001589	frameshift_variant	51562	exon8			.	BC016821	CCDS9658.1, CCDS45096.1	14q13.2	2005-01-10			ENSG00000151332	ENSG00000151332			20427	protein-coding gene	gene with protein product		609431				10801814	Standard	NM_016586		Approved		uc001wtm.2	Q9NS73	OTTHUMG00000140222	ENST00000416007.4:c.913dupA	14.37:g.36770009_36770009dupT	ENSP00000399718:p.Val305fs	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	21	11	NM_016586	0	0	0	0	0	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Frame_Shift_Ins	INS	ENST00000416007.4	37	CCDS9658.1																																																																																			.		0.243	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586		T	36770006	-	T	36770005	7	5	108	1	0	1	1	0	0	0	0	0	9374	565	20	0	129	0	MBIP	14	36770005	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	5414529	36770005	70579535	78	9563											
FERMT2	10979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	53360052	53360052	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctctaattcaagtgccTcatcttcagactggtcatct	8	13	6	14	0	7	1	4	0	3	1	7	1	7	1	3	1	1	0	3	1	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr14:53360052T>C	ENST00000395631.2	-	4	701	c.485A>G	c.(484-486)gAg>gGg	p.E162G	FERMT2_ENST00000399304.3_Missense_Mutation_p.E162G|FERMT2_ENST00000343279.4_Missense_Mutation_p.E162G|FERMT2_ENST00000553373.1_Missense_Mutation_p.E162G|FERMT2_ENST00000341590.3_Missense_Mutation_p.E162G			Q96AC1	FERM2_HUMAN	fermitin family member 2	162					cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TTCAAGTGCCTCATCTTCAGA	0.413																																					p.E162G		.											.	FERMT2-68	0			c.A485G						.						137	135	136					14																	53360052		2203	4300	6503	SO:0001583	missense	10979	exon4			AGTGCCTCATCTT	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.485A>G	14.37:g.53360052T>C	ENSP00000378993:p.Glu162Gly	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	177	72	NM_001135000	0	0	21	31	10	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	37	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	T	14.38	2.518696	0.44763	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000554288;ENST00000555692	T;T;T;T;T;T;T	0.48201	0.82;0.82;0.84;0.82;0.82;0.82;1.41	5.77	5.77	0.91146	FERM, N-terminal (1);Band 4.1 domain (1);	0.051253	0.85682	D	0.000000	T	0.36082	0.0954	N	0.14661	0.345	0.51482	D	0.999927	B;B;B	0.26602	0.043;0.154;0.01	B;B;B	0.34038	0.087;0.174;0.099	T	0.18618	-1.0331	10	0.24483	T	0.36	.	16.0828	0.81017	0.0:0.0:0.0:1.0	.	162;162;162	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	G	162;162;104;162;162;162;57;118	ENSP00000378993:E162G;ENSP00000340391:E162G;ENSP00000450741:E104G;ENSP00000342858:E162G;ENSP00000451084:E162G;ENSP00000382243:E162G;ENSP00000451268:E57G	ENSP00000340391:E162G	E	-	2	0	FERMT2	52429802	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.957000	0.70323	2.199000	0.70637	0.528000	0.53228	GAG	.		0.413	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		C	53360052	T	C	53360052	3	2	108	1	0	0	0	0	1	0	0	0	5837	1551	54	3	1642	3	FERMT2	14	53360052	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	16590047	53360052	53989488	79	9564											
MRPL46	26589	broad.mit.edu	37	chr15	89008985	89008985	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcgtggtctgaatacAggcttctctctatctcaatc	9	13	8	11	1	4	1	1	1	4	0	8	2	4	1	0	2	2	2	0	2	5	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr15:89008985A>G	ENST00000312475.4	-	2	289	c.248T>C	c.(247-249)cTg>cCg	p.L83P	MRPL46_ENST00000559538.1_5'Flank|MRPS11_ENST00000353598.6_5'Flank|MRPS11_ENST00000325844.4_5'Flank	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	83						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			GTCTGAATACAGGCTTCTCTC	0.388																																					p.L83P													.	MRPL46-90	0			c.T248C						.						83	88	86					15																	89008985		2201	4299	6500	SO:0001583	missense	26589	exon2			GAATACAGGCTTC	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"Mitochondrial ribosomal proteins / large subunits"	1192	protein-coding gene	gene with protein product		611851	"chromosome 15 open reading frame 4"	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.248T>C	15.37:g.89008985A>G	ENSP00000312311:p.Leu83Pro	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	129	3	NM_022163	0	0	7	7	0	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	37	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.961915	0.53400	.	.	ENSG00000173867	ENST00000312475	T	0.46451	0.87	5.08	2.58	0.30949	.	0.386469	0.25555	N	0.029867	T	0.56337	0.1978	M	0.83774	2.66	0.34905	D	0.746853	D	0.58620	0.983	P	0.57057	0.812	T	0.67814	-0.5573	10	0.51188	T	0.08	.	8.0952	0.30824	0.631:0.2483:0.0:0.1206	.	83	Q9H2W6	RM46_HUMAN	P	83	ENSP00000312311:L83P	ENSP00000312311:L83P	L	-	2	0	MRPL46	86809989	0.090000	0.21635	0.346000	0.25655	0.943000	0.58893	1.092000	0.30927	1.029000	0.39812	0.533000	0.62120	CTG	.		0.388	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163		G	89008985	A	G	89008985	3	3	108	1	0	0	0	0	1	0	0	0	9835	188	7	3	603	3	MRPL46	15	89008985	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		89008985	13522407	80	9565											
LINS1	55180	hgsc.bcm.edu;bcgsc.ca	37	chr15	101109778	101109778	+	Frame_Shift_Del	DEL	T	T	-																															gtgtaaagatgtctgtttacTgttagctaaacactgctctg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr15:101109778delT	ENST00000314742.8	-	7	2161	c.1939delA	c.(1939-1941)agtfs	p.S647fs	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	647										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						GTCTGTTTACTGTTAGCTAAA	0.473																																					p.S647fs		.											.	LINS-92	0			c.1939delA						.						103	100	101					15																	101109778		2203	4300	6503	SO:0001589	frameshift_variant	55180	exon7			.	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1939delA	15.37:g.101109778delT	ENSP00000318423:p.Ser647fs	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	113	22	NM_001040616	0	0	0	0	0	Q96FW2|Q9NVQ3	Frame_Shift_Del	DEL	ENST00000314742.8	37	CCDS10385.1																																																																																			.		0.473	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		-	101109778	T	-	101109778	7	5	108	1	0	1	0	1	0	0	0	0	8841	1580	55	0	338	0	LINS1	15	101109778	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08	12100793	101109778	1421614	81	9566											
CRAMP1L	57585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1718163	1718163	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acacacattagcgactccatCattgagatcgccatcagctc	12	9	6	14	2	2	1	2	1	0	1	5	3	3	1	2	0	2	1	2	0	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:1718163C>T	ENST00000397412.3	+	18	3402	c.3303C>T	c.(3301-3303)atC>atT	p.I1101I	CRAMP1L_ENST00000262317.4_Silent_p.I479I|CRAMP1L_ENST00000436138.3_Silent_p.I1098I|CRAMP1L_ENST00000293925.5_Silent_p.I1101I|LA16c-431H6.6_ENST00000454337.1_3'UTR			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	1101	Ser-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						GCGACTCCATCATTGAGATCG	0.607																																					p.I1101I		.											.	.	0			c.C3303T						.						64	65	65					16																	1718163		2165	4268	6433	SO:0001819	synonymous_variant	57585	exon17			CTCCATCATTGAG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"Crm (Cramped Drosophila)-like"				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.3303C>T	16.37:g.1718163C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	129	36	NM_020825	0	0	7	11	4	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			.		0.607	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			T	1718163	C	T	1718163	2	4	108	1	0	0	0	0	0	0	0	1	3852	816	29	2		2	CRAMP1L	16	1718163	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08		1718163	88636590	82	9567											
MKL2	57496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	14342808	14342808	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacaagcaggaatgcagaCtcagcctcagatagcaactg	15	5	9	12	0	2	2	2	0	0	2	2	3	2	3	2	1	5	3	2	1	4	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:14342808C>G	ENST00000341243.5	+	11	2240	c.2240C>G	c.(2239-2241)aCt>aGt	p.T747S	MKL2_ENST00000318282.5_Missense_Mutation_p.T708S|MKL2_ENST00000574045.1_Missense_Mutation_p.T708S|MKL2_ENST00000571589.1_Missense_Mutation_p.T758S			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	747	Gln-rich.				blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GGAATGCAGACTCAGCCTCAG	0.448																																					p.T708S		.											.	MKL2-95	0			c.C2123G						.						127	105	112					16																	14342808		2197	4300	6497	SO:0001583	missense	57496	exon13			TGCAGACTCAGCC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.2240C>G	16.37:g.14342808C>G	ENSP00000345841:p.Thr747Ser	Somatic	92	1		WXS	Illumina HiSeq	Phase_I	109	69	NM_014048	0	0	10	21	11	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	37		.	.	.	.	.	.	.	.	.	.	C	9.285	1.049055	0.19827	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.43	5.43	0.79202	.	0.708129	0.14605	N	0.309376	T	0.43478	0.1249	L	0.46157	1.445	0.22954	N	0.99852	B;B	0.22683	0.018;0.073	B;B	0.24394	0.025;0.053	T	0.32079	-0.9920	9	0.09084	T	0.74	-0.2632	18.5657	0.91115	0.0:1.0:0.0:0.0	.	758;708	B4DGT8;Q9ULH7-4	.;.	S	708;747	.	ENSP00000339086:T708S	T	+	2	0	MKL2	14250309	0.591000	0.26824	0.921000	0.36526	0.984000	0.73092	3.533000	0.53561	2.709000	0.92574	0.655000	0.94253	ACT	.		0.448	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		G	14342808	C	G	14342808	3	3	108	1	0	0	0	0	1	0	0	0	9627	565	20	4	2165	4	MKL2	16	14342808	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	12624645	14342808	76011945	83	9568											
RPGRIP1L	23322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	53636027	53636027	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtattgcttgtagacagaCtggagggcatggagagcttc	9	11	14	7	0	0	3	0	0	0	3	1	5	0	4	0	3	2	5	0	3	2	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:53636027C>A	ENST00000379925.3	-	27	3959	c.3909G>T	c.(3907-3909)caG>caT	p.Q1303H	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.Q1223H|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.Q1269H	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1303					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				TGTAGACAGACTGGAGGGCAT	0.468																																					p.Q1303H		.											.	RPGRIP1L-91	0			c.G3909T						.						115	94	101					16																	53636027		2198	4300	6498	SO:0001583	missense	23322	exon27			GACAGACTGGAGG		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134"	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3909G>T	16.37:g.53636027C>A	ENSP00000369257:p.Gln1303His	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	107	72	NM_015272	0	0	2	9	7	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	C	0.956	-0.704864	0.03255	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.63913	-0.07;-0.07	5.86	2.79	0.32731	.	0.807726	0.11522	N	0.555606	T	0.33527	0.0866	N	0.08118	0	0.80722	D	1	B;P;P	0.38250	0.13;0.49;0.624	B;B;B	0.31812	0.136;0.136;0.129	T	0.14671	-1.0464	10	0.46703	T	0.11	-0.5926	2.457	0.04532	0.1189:0.437:0.269:0.175	.	1257;1303;1223	B7ZKJ9;Q68CZ1;Q68CZ1-2	.;FTM_HUMAN;.	H	1303;1223	ENSP00000369257:Q1303H;ENSP00000262135:Q1223H	ENSP00000262135:Q1223H	Q	-	3	2	RPGRIP1L	52193528	0.184000	0.23200	0.813000	0.32504	0.392000	0.30506	0.388000	0.20735	0.840000	0.34995	-0.142000	0.14014	CAG	.		0.468	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		A	53636027	C	A	53636027	3	1	108	1	0	0	0	0	1	0	0	0	13582	564	20	4	42	4	RPGRIP1L	16	53636027	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	39293219	53636027	36718726	84	9569											
ELMO3	79767	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	67236330	67236330	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccaggacttctcacccaTgttcttcggccaagaccaga	10	8	8	15	1	2	2	1	0	2	2	4	3	2	3	4	2	1	1	4	2	1	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:67236330T>G	ENST00000360833.1	+	13	1457	c.1400T>G	c.(1399-1401)aTg>aGg	p.M467R	ELMO3_ENST00000393997.2_Missense_Mutation_p.M484R|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000477898.1_Missense_Mutation_p.M318R			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	431	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		TTCTCACCCATGTTCTTCGGC	0.597																																					p.M484R		.											.	ELMO3-90	0			c.T1451G						.						84	86	85					16																	67236330		2198	4300	6498	SO:0001583	missense	79767	exon14			CACCCATGTTCTT		CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"Engulfment and cell motility proteins"	17289	protein-coding gene	gene with protein product		606422	"engulfment and cell motility 3 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.1400T>G	16.37:g.67236330T>G	ENSP00000354077:p.Met467Arg	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	239	22	NM_024712	0	0	117	125	8	B4DV86|Q9H8A5	Missense_Mutation	SNP	ENST00000360833.1	37		.	.	.	.	.	.	.	.	.	.	T	17.46	3.395742	0.62177	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.29397	1.57;1.57	5.66	5.66	0.87406	Engulfment/cell motility, ELMO (2);	0.165679	0.64402	D	0.000003	T	0.42131	0.1189	M	0.67397	2.05	0.80722	D	1	P;D;D	0.55172	0.822;0.97;0.97	P;P;P	0.48552	0.577;0.581;0.581	T	0.44174	-0.9345	10	0.87932	D	0	-28.916	14.7211	0.69308	0.0:0.0:0.0:1.0	.	431;467;484	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	R	467;484	ENSP00000354077:M467R;ENSP00000377566:M484R	ENSP00000354077:M467R	M	+	2	0	ELMO3	65793831	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	8.040000	0.89188	2.160000	0.67779	0.533000	0.62120	ATG	.		0.597	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712		G	67236330	T	G	67236330	3	3	108	1	0	0	0	0	1	0	0	0	5080	1464	51	5	1505	5	ELMO3	16	67236330	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	13600303	67236330	23118423	85	9570											
CNTNAP4	85445	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	76587277	76587278	+	Frame_Shift_Ins	INS	-	-	GC																															gccacgtggcccctctgaagINSgcagctctgcaccccagcca																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:76587277_76587278insGC	ENST00000476707.1	+	21	3688_3689	c.3549_3550insGC	c.(3550-3552)gcafs	p.A1184fs	CNTNAP4_ENST00000478060.1_Frame_Shift_Ins_p.A1108fs|CNTNAP4_ENST00000377504.4_Frame_Shift_Ins_p.A1132fs|CNTNAP4_ENST00000469589.1_3'UTR|RP11-58C22.1_ENST00000563764.1_5'Flank|CNTNAP4_ENST00000307431.8_Frame_Shift_Ins_p.A1180fs			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1181	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						CCCCTCTGAAGGCAGCTCTGCA	0.604																																					p.K1107fs		.											.	CNTNAP4-70	0			c.3321_3322insGC						.																																			SO:0001589	frameshift_variant	85445	exon21			.	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.3550_3551dupGC	16.37:g.76587278_76587279dupGC	ENSP00000417628:p.Ala1184fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	43	25	NM_138994	0	0	0	0	0	E9PFZ6|Q86YZ7	Frame_Shift_Ins	INS	ENST00000476707.1	37																																																																																				.		0.604	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		GC	76587278	-	GC	76587277	7	5	108	1	0	1	1	0	0	0	0	0	3655	991	35	0	3639	0	CNTNAP4	16	76587277	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	9350947	76587277	13767476	86	9571											
CDK5RAP3	80279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	46051766	46051766	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtttttctgttcttactcagGattggcaggagattatagct	8	17	10	6	0	3	1	1	0	2	1	3	3	3	2	0	3	2	4	0	3	3	7			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr17:46051766G>A	ENST00000338399.4	+	5	392	c.286G>A	c.(286-288)Gat>Aat	p.D96N	RP11-6N17.9_ENST00000582262.1_RNA|CDK5RAP3_ENST00000536708.2_Splice_Site_p.D121N	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	96					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						TCTTACTCAGGATTGGCAGGA	0.493																																					p.D96N		.											.	CDK5RAP3-226	0			c.G286A						.						171	171	171					17																	46051766		1981	4164	6145	SO:0001630	splice_region_variant	80279	exon5			ACTCAGGATTGGC	AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"ischemic heart CDK5 activator-binding protein C53", "LXXLL/leucine-zipper-containing ARFbinding protein"	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.286-1G>A	17.37:g.46051766G>A		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	144	15	NM_176096	0	0	2	3	1	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Missense_Mutation	SNP	ENST00000338399.4	37	CCDS42356.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898300	0.91962	.	.	ENSG00000108465	ENST00000536708;ENST00000338399	T;T	0.54866	0.55;0.55	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.66386	0.2784	M	0.90977	3.165	0.80722	D	1	B	0.31241	0.315	B	0.35312	0.2	T	0.68511	-0.5389	9	.	.	.	-8.6694	18.4593	0.90732	0.0:0.0:1.0:0.0	.	96	Q96JB5	CK5P3_HUMAN	N	121;96	ENSP00000438886:D121N;ENSP00000344683:D96N	.	D	+	1	0	CDK5RAP3	43406765	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.231000	0.95317	2.670000	0.90874	0.655000	0.94253	GAT	.		0.493	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096	Missense_Mutation	A	46051766	G	A	46051766	5	1	108	1	0	0	0	0	0	0	1	0	3153	1188	41	2	304	2	CDK5RAP3	17	46051766	Splice_Site	SNP	G	TCGA-EV-5902-01A-11D-1589-08		46051766	35143444	87	9572											
APPBP2	10513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58525181	58525181	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtccactgtagccctcacCaaaaagtttcttccctgtaa	11	12	5	13	0	2	0	1	0	1	0	4	0	4	0	4	0	1	3	4	0	5	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr17:58525181C>A	ENST00000083182.3	-	13	1806	c.1519G>T	c.(1519-1521)Ggt>Tgt	p.G507C		NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	507					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			TAGCCCTCACCAAAAAGTTTC	0.308																																					p.G507C		.											.	APPBP2-226	0			c.G1519T						.						55	57	56					17																	58525181		2203	4300	6503	SO:0001583	missense	10513	exon13			CCTCACCAAAAAG	AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"protein interacting with APP tail 1"	605324	"amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.1519G>T	17.37:g.58525181C>A	ENSP00000083182:p.Gly507Cys	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	149	62	NM_006380	0	0	9	18	9	A8K862|O95095|Q8WVC9	Missense_Mutation	SNP	ENST00000083182.3	37	CCDS32699.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611670	0.66558	.	.	ENSG00000062725	ENST00000083182	D	0.90385	-2.66	5.5	5.5	0.81552	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.95175	0.8436	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95322	0.8421	10	0.87932	D	0	-12.3778	19.4753	0.94985	0.0:1.0:0.0:0.0	.	507	Q92624	APBP2_HUMAN	C	507	ENSP00000083182:G507C	ENSP00000083182:G507C	G	-	1	0	APPBP2	55879963	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.453000	0.80700	2.611000	0.88343	0.650000	0.86243	GGT	.		0.308	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		A	58525181	C	A	58525181	3	1	108	1	0	0	0	0	1	0	0	0	816	594	21	4	242	4	APPBP2	17	58525181	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	12473415	58525181	22670029	88	9573											
KIAA1012	22878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	29488737	29488737	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgatcgtttaattgcctaaTtgttttctctatatgtggca	8	19	7	7	1	1	1	0	1	1	0	3	1	1	1	1	1	1	3	1	1	4	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr18:29488737T>G	ENST00000283351.4	-	7	1437	c.1102A>C	c.(1102-1104)Att>Ctt	p.I368L	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.I314L|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.I368L	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	368					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AATTGCCTAATTGTTTTCTCT	0.284																																					p.I368L		.											.	TRAPPC8-159	0			c.A1102C						.						45	43	44					18																	29488737		2203	4297	6500	SO:0001583	missense	22878	exon7			GCCTAATTGTTTT	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"Trafficking protein particle complex"	29169	protein-coding gene	gene with protein product	"general sporulation gene 1 homolog (S. cerevisiae)"	614136	"KIAA1012"	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.1102A>C	18.37:g.29488737T>G	ENSP00000283351:p.Ile368Leu	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	73	31	NM_014939	0	0	10	19	9	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.211203	0.39102	.	.	ENSG00000153339	ENST00000283351	T	0.19806	2.12	5.7	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	L	0.39147	1.195	0.53005	D	0.99996	P;D	0.55605	0.655;0.972	P;P	0.56216	0.557;0.794	T	0.01228	-1.1412	10	0.23302	T	0.38	.	11.1138	0.48249	0.0:0.0717:0.0:0.9283	.	368;368	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	L	368	ENSP00000283351:I368L	ENSP00000283351:I368L	I	-	1	0	TRAPPC8	27742735	1.000000	0.71417	0.998000	0.56505	0.710000	0.40934	7.231000	0.78106	2.181000	0.69327	0.459000	0.35465	ATT	.		0.284	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		G	29488737	T	G	29488737	3	3	108	1	0	0	0	0	1	0	0	0	8225	1493	52	5	3297	5	KIAA1012	18	29488737	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		29488737	48588511	89	9574											
CNDP2	55748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	72179734	72179734	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtgtacgggggctcggtgCatgaggccatgactgatctc	6	9	17	9	2	1	3	0	3	1	0	3	3	1	3	1	5	2	3	1	5	1	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr18:72179734C>A	ENST00000324262.4	+	7	1025	c.709C>A	c.(709-711)Cat>Aat	p.H237N	CNDP2_ENST00000579847.1_Missense_Mutation_p.H237N|CNDP2_ENST00000324301.8_Missense_Mutation_p.H153N	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	237					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GGGCTCGGTGCATGAGGCCAT	0.562																																					p.H237N		.											.	CNDP2-93	0			c.C709A						.						255	196	216					18																	72179734		2203	4300	6503	SO:0001583	missense	55748	exon7			TCGGTGCATGAGG	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.709C>A	18.37:g.72179734C>A	ENSP00000325548:p.His237Asn	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	108	39	NM_018235	1	0	351	658	306	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.100562	0.37048	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T;T	0.56776	0.44;0.44	5.14	3.33	0.38152	Peptidase M20, dimerisation (1);	0.047588	0.85682	D	0.000000	T	0.59582	0.2204	M	0.73962	2.25	0.80722	D	1	B;B;B	0.25743	0.133;0.021;0.002	B;B;B	0.40410	0.328;0.267;0.084	T	0.59757	-0.7394	10	0.38643	T	0.18	-19.4529	11.6458	0.51261	0.0:0.8542:0.0:0.1458	.	142;153;237	B4DPF1;Q96KP4-2;Q96KP4	.;.;CNDP2_HUMAN	N	237;153	ENSP00000325548:H237N;ENSP00000325756:H153N	ENSP00000325548:H237N	H	+	1	0	CNDP2	70330714	0.989000	0.36119	0.949000	0.38748	0.779000	0.44077	1.712000	0.37940	1.169000	0.42739	0.655000	0.94253	CAT	.		0.562	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		A	72179734	C	A	72179734	3	1	108	1	0	0	0	0	1	0	0	0	3600	710	25	4	731	4	CNDP2	18	72179734	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	42690997	72179734	5897514	90	9575											
ZNF236	7776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	74561610	74561610	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacgccacatgagggatcacGagcgaaatgacaaggtatgt	15	6	12	8	3	1	2	1	2	0	0	1	5	1	3	1	2	2	1	1	2	4	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr18:74561610G>A	ENST00000253159.8	+	2	376	c.178G>A	c.(178-180)Gag>Aag	p.E60K	ZNF236_ENST00000320610.9_Missense_Mutation_p.E62K	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	60					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GAGGGATCACGAGCGAAATGA	0.358																																					p.E60K		.											.	ZNF236-94	0			c.G178A						.						65	62	63					18																	74561610		1875	4104	5979	SO:0001583	missense	7776	exon2			GATCACGAGCGAA	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.178G>A	18.37:g.74561610G>A	ENSP00000253159:p.Glu60Lys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	88	38	NM_007345	0	0	0	0	0	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244485	0.79912	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.16743	2.32;2.32	5.65	5.65	0.86999	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	N	0.20483	0.58	0.46725	D	0.999171	D;D	0.89917	1.0;0.998	D;P	0.91635	0.999;0.766	T	0.05305	-1.0893	10	0.20519	T	0.43	.	19.7319	0.96186	0.0:0.0:1.0:0.0	.	60;60	Q9NWI2;Q9UL36	.;ZN236_HUMAN	K	60	ENSP00000253159:E60K;ENSP00000444524:E60K	ENSP00000253159:E60K	E	+	1	0	ZNF236	72690598	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.692000	0.68256	2.668000	0.90789	0.655000	0.94253	GAG	.		0.358	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			A	74561610	G	A	74561610	3	1	108	1	0	0	0	0	1	0	0	0	17821	1059	37	1	184	1	ZNF236	18	74561610	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	2381876	74561610	3515638	91	9576											
FAM108A1	81926	hgsc.bcm.edu	37	chr19	1881550	1881550	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcagcagagctcactcaGcgacagcccattcatggcgg	10	5	13	13	2	3	1	3	0	0	1	3	3	3	1	1	3	4	3	1	3	0	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:1881550G>A	ENST00000292577.7	-	2	449	c.16C>T	c.(16-18)Ctg>Ttg	p.L6L	ABHD17A_ENST00000590661.1_Silent_p.L6L|ABHD17A_ENST00000250974.9_Silent_p.L6L	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	6						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										AGCTCACTCAGCGACAGCCCA	0.761																																					p.L6L		.											.	FAM108A1-90	0			c.C16T						.																																			SO:0001819	synonymous_variant	81926	exon2			CACTCAGCGACAG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"Abhydrolase domain containing"	28756	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 27", "family with sequence similarity 108, member A1"	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.16C>T	19.37:g.1881550G>A		Somatic	25	2		WXS	Illumina HiSeq	Phase_I	38	4	NM_031213	0	0	12	12	0	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Silent	SNP	ENST00000292577.7	37	CCDS45902.1																																																																																			.		0.761	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		A	1881550	G	A	1881550	2	1	108	1	0	0	0	0	0	0	0	1	5407	962	34	2		2	FAM108A1	19	1881550	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08		1881550	57247433	92	9577											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	213	4		WXS	Illumina HiSeq		223	1	NM_031203	0	0	1	1	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	108	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-EV-5902-01A-11D-1589-08	6645917	8527467	50601516	93	9578											
MYO1F	4542	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	8609279	8609279	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgcagcagtgtctggtCtgctcccccgcccgtggcgt	2	11	12	16	3	3	0	0	0	3	0	4	0	4	0	3	2	3	3	3	2	0	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:8609279C>A	ENST00000338257.8	-	14	1693	c.1426G>T	c.(1426-1428)Gac>Tac	p.D476Y	AC092316.2_ENST00000581156.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	476	Myosin motor.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						AGTGTCTGGTCTGCTCCCCCG	0.677																																					p.D476Y		.											.	MYO1F-93	0			c.G1426T						.						22	31	28					19																	8609279		2096	4212	6308	SO:0001583	missense	4542	exon14			TCTGGTCTGCTCC	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"Myosins / Myosin superfamily : Class I"	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.1426G>T	19.37:g.8609279C>A	ENSP00000344871:p.Asp476Tyr	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	49	24	NM_012335	0	0	5	5	0	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	c	20.5	4.009105	0.75046	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.92099	-2.97	3.49	3.49	0.39957	Myosin head, motor domain (2);	0.133964	0.47455	U	0.000236	D	0.97081	0.9046	H	0.96576	3.845	0.80722	D	1	D	0.58620	0.983	D	0.67725	0.953	D	0.98150	1.0441	10	0.87932	D	0	.	13.73	0.62781	0.0:1.0:0.0:0.0	.	476	O00160	MYO1F_HUMAN	Y	521;476	ENSP00000344871:D476Y	ENSP00000304899:D521Y	D	-	1	0	MYO1F	8515279	1.000000	0.71417	0.989000	0.46669	0.860000	0.49131	5.743000	0.68655	1.781000	0.52344	0.290000	0.19541	GAC	.		0.677	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			A	8609279	C	A	8609279	3	1	108	1	0	0	0	0	1	0	0	0	10098	913	32	4	1930	4	MYO1F	19	8609279	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	81812	8609279	50519704	94	9579											
CACNA1A	773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13397703	13397703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccaggggtgggtcttggCggcccaggtcctgctggatt	3	10	17	11	1	1	0	0	0	1	0	2	1	2	1	3	7	2	1	3	7	0	2	rs200850308		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:13397703C>T	ENST00000360228.5	-	20	3166	c.3167G>A	c.(3166-3168)cGc>cAc	p.R1056H	CACNA1A_ENST00000573710.2_Missense_Mutation_p.R1057H	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1057					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGGTCTTGGCGGCCCAGGTC	0.642																																					p.R1057H		.											.	CACNA1A-67	0			c.G3170A						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,3700		0,0,1850	19	22	21		3179,3170,3167,3170,3179	5.2	1	19		21	1,8013		0,1,4006	yes	missense,missense,missense,missense,missense	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	29,29,29,29,29	0,1,5856	TT,TC,CC		0.0125,0.0,0.0085	benign,benign,benign,benign,benign	1060/2267,1057/2262,1056/2507,1057/2264,1060/2513	13397703	1,11713	1850	4007	5857	SO:0001583	missense	773	exon20			TCTTGGCGGCCCA	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3167G>A	19.37:g.13397703C>T	ENSP00000353362:p.Arg1056His	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	54	8	NM_001127221	0	0	0	0	0	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754278	0.49362	0.0	1.25E-4	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.96168	-3.93	5.19	5.19	0.71726	.	0.663946	0.14837	N	0.295520	D	0.95108	0.8415	L	0.43152	1.355	0.42961	D	0.9944	B;B;D	0.65815	0.343;0.239;0.995	B;B;P	0.51016	0.021;0.034;0.656	D	0.94508	0.7716	10	0.44086	T	0.13	.	17.4837	0.87682	0.0:1.0:0.0:0.0	.	1057;1060;1056	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	H	1056;1060;1057;1057	ENSP00000353362:R1056H	ENSP00000317661:R1057H	R	-	2	0	CACNA1A	13258703	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.265000	0.51561	2.427000	0.82271	0.555000	0.69702	CGC	.		0.642	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13397703	C	T	13397703	3	4	108	1	0	0	0	0	1	0	0	0	2544	768	27	1	4567	1	CACNA1A	19	13397703	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	4788424	13397703	45731280	95	9580											
ZNF780B	163131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40541550	40541550	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatgaatactctggtgttGaataaggtttgaactacgat	13	13	10	5	1	1	3	0	3	1	0	1	4	1	3	0	2	4	3	0	2	6	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:40541550G>T	ENST00000434248.1	-	5	1281	c.1216C>A	c.(1216-1218)Caa>Aaa	p.Q406K	ZNF780B_ENST00000221355.6_Missense_Mutation_p.Q258K	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	406					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)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTCTGGTGTTGAATAAGGTTT	0.358																																					p.Q406K		.											.	ZNF780B-47	0			c.C1216A						.						100	107	105					19																	40541550		2203	4300	6503	SO:0001583	missense	163131	exon5			GGTGTTGAATAAG	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"Zinc fingers, C2H2-type", "-"	33109	protein-coding gene	gene with protein product			"zinc finger protein 779"	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1216C>A	19.37:g.40541550G>T	ENSP00000391641:p.Gln406Lys	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	176	79	NM_001005851	0	0	1	1	0	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	G	1.025	-0.683570	0.03353	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.35048	1.33;1.33	2.29	1.07	0.20283	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21307	0.0513	N	0.01081	-1.03	0.09310	N	1	D	0.57571	0.98	D	0.69824	0.966	T	0.17930	-1.0353	9	0.05833	T	0.94	.	8.391	0.32528	0.0:0.2421:0.7579:0.0	.	406	Q9Y6R6	Z780B_HUMAN	K	406;258	ENSP00000391641:Q406K;ENSP00000221355:Q258K	ENSP00000221355:Q258K	Q	-	1	0	ZNF780B	45233390	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-5.529000	0.00115	1.103000	0.41568	0.313000	0.20887	CAA	.		0.358	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		T	40541550	G	T	40541550	3	4	108	1	0	0	0	0	1	0	0	0	18185	1299	45	4	1289	4	ZNF780B	19	40541550	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	27143847	40541550	18587433	96	9581											
RPL18	6141	ucsc.edu	37	chr19	49118705	49118705	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccttggagcggacgtagggtCtgtggggagaggagggagtg	7	7	22	5	2	1	1	0	0	1	1	1	6	1	5	1	7	1	1	1	7	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:49118705C>T	ENST00000549920.1	-	7	884		c.e7-1		FAM83E_ENST00000595110.1_5'Flank|RPL18_ENST00000552588.1_Splice_Site|FAM83E_ENST00000263266.3_5'Flank|RPL18_ENST00000550645.1_Splice_Site|RPL18_ENST00000549273.1_3'UTR	NM_000979.3	NP_000970.1	Q07020	RL18_HUMAN	ribosomal protein L18						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|kidney(2)	3		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.89e-05)|all cancers(93;0.00011)|GBM - Glioblastoma multiforme(486;0.0061)|Epithelial(262;0.0154)		GACGTAGGGTCTGTGGGGAGA	0.592																																					.													.	RPL18-90	0			c.405-1G>A						.						61	72	68					19																	49118705		2203	4299	6502	SO:0001630	splice_region_variant	6141	exon7			TAGGGTCTGTGGG	L11566	CCDS12726.1, CCDS58669.1	19q13	2011-04-06				ENSG00000063177		"L ribosomal proteins"	10310	protein-coding gene	gene with protein product	"60S ribosomal protein L18"	604179				8218404	Standard	NM_000979		Approved	L18	uc002pjq.2	Q07020	OTTHUMG00000169760	ENST00000549920.1:c.492-1G>A	19.37:g.49118705C>T		Somatic	205	0		WXS	Illumina HiSeq		200	1	NM_001270490	0	0	1	1	0	F8VWC5|Q8WTZ6	Splice_Site	SNP	ENST00000549920.1	37	CCDS12726.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.714067	0.89112	.	.	ENSG00000063177	ENST00000549920;ENST00000084795;ENST00000550645;ENST00000552588;ENST00000546623;ENST00000550973	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7247	0.69336	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPL18	53810517	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.911000	0.75746	2.631000	0.89168	0.655000	0.94253	.	.		0.592	RPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405732.2	NM_000979	Intron	T	49118705	C	T	49118705	5	4	108	1	0	0	0	0	0	0	1	0	13596	927	32	2	79	2	RPL18	19	49118705	Splice_Site	SNP	C	TCGA-EV-5902-01A-11D-1589-08	8577155	49118705	10010278	97	9582											
ZNF320	162967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53384942	53384942	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctatgtcttcgcaaatgcAaatgaaatcttgattcaagc	13	13	6	9	1	3	2	1	2	2	0	5	2	4	2	1	0	2	2	1	0	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:53384942A>G	ENST00000595635.1	-	8	938	c.437T>C	c.(436-438)tTg>tCg	p.L146S	ZNF320_ENST00000391781.2_Missense_Mutation_p.L146S|ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000597909.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	146					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)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		TCGCAAATGCAAATGAAATCT	0.348																																					p.L146S		.											.	ZNF320-91	0			c.T437C						.						117	113	114					19																	53384942		2203	4300	6503	SO:0001583	missense	162967	exon4			AAATGCAAATGAA	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.437T>C	19.37:g.53384942A>G	ENSP00000473091:p.Leu146Ser	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	185	80	NM_207333	0	0	36	69	33	Q8NDR6	Missense_Mutation	SNP	ENST00000595635.1	37	CCDS33095.1	.	.	.	.	.	.	.	.	.	.	-	0.006	-2.115473	0.00349	.	.	ENSG00000182986	ENST00000391781	T	0.12361	2.69	1.39	0.0569	0.14321	.	.	.	.	.	T	0.04998	0.0134	N	0.11427	0.14	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.43245	-0.9403	9	0.02654	T	1	.	5.4228	0.16409	0.2247:0.0:0.7753:0.0	.	146	A2RRD8	ZN320_HUMAN	S	146	ENSP00000375660:L146S	ENSP00000375660:L146S	L	-	2	0	ZNF320	58076754	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-0.162000	0.10012	-0.124000	0.11724	0.163000	0.16589	TTG	.		0.348	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		G	53384942	A	G	53384942	3	3	108	1	0	0	0	0	1	0	0	0	17871	131	5	3	1096	3	ZNF320	19	53384942	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	4266237	53384942	5744041	98	9583											
ZSCAN22	342945	broad.mit.edu;bcgsc.ca	37	chr19	58849878	58849878	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacagaccagcgtggccGtgaatctggtgcctcgagga	8	6	13	14	3	1	2	0	1	1	1	2	4	1	3	5	3	2	0	5	3	1	0	rs558607664		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:58849878G>A	ENST00000329665.4	+	3	809	c.662G>A	c.(661-663)cGt>cAt	p.R221H		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	221					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)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		CAGCGTGGCCGTGAATCTGGT	0.512																																					p.R221H													.	ZSCAN22-91	0			c.G662A						.						154	159	158					19																	58849878		2203	4300	6503	SO:0001583	missense	342945	exon3			GTGGCCGTGAATC	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"-", "Zinc fingers, C2H2-type"	4929	protein-coding gene	gene with protein product	"oncogene HKR2"	165260	"zinc finger protein 50", "GLI-Kruppel family member HKR2"	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.662G>A	19.37:g.58849878G>A	ENSP00000332433:p.Arg221His	Somatic	273	1		WXS	Illumina HiSeq	Phase_I	275	8	NM_181846	0	0	3	3	0	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	37	CCDS12975.1	.	.	.	.	.	.	.	.	.	.	G	6.106	0.387827	0.11581	.	.	ENSG00000182318	ENST00000329665	T	0.08458	3.09	3.72	-4.75	0.03239	.	.	.	.	.	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47573	-0.9107	9	0.15499	T	0.54	.	6.0075	0.19554	0.5667:0.2768:0.1565:0.0	.	221	P10073	ZSC22_HUMAN	H	221	ENSP00000332433:R221H	ENSP00000332433:R221H	R	+	2	0	ZSCAN22	63541690	0.000000	0.05858	0.001000	0.08648	0.170000	0.22686	-0.814000	0.04486	-0.604000	0.05760	0.313000	0.20887	CGT	.		0.512	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		A	58849878	G	A	58849878	3	1	108	1	0	0	0	0	1	0	0	0	18266	1145	40	1	668	1	ZSCAN22	19	58849878	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	5464936	58849878	279105	99	9584											
PLK1S1	101929591	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	21142793	21142793	+	RNA	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatagatggaaaggcatcTcttcagattggtgagaaaat	16	10	10	5	0	2	3	1	1	1	3	3	5	2	4	0	3	1	1	0	3	5	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr20:21142793T>A	ENST00000591761.1	-	0	5142				RP5-872K7.7_ENST00000425746.2_RNA|PLK1S1_ENST00000457464.1_RNA																							GAAAGGCATCTCTTCAGATTG	0.433																																					.													.	.	0			.						.						86	87	87					20																	21142793		1964	4155	6119			55857	.			GGCATCTCTTCAG																													20.37:g.21142793T>A		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	175	132	.	0	0	7	20	13		Silent	SNP	ENST00000591761.1	37																																																																																				.		0.433	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			A	21142793	T	A	21142793	1	1	108	0	1	0	0	0	0	0	0	0	12121	1538	54	5		5	PLK1S1	20	21142793	RNA	SNP	T	TCGA-EV-5902-01A-11D-1589-08		21142793	41882727	100	9585											
NCAM2	4685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	22656582	22656582	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agataatttcaacacagaggGtagtagtgcaaaaggaaggt	17	8	12	4	0	1	2	1	0	0	2	1	3	1	3	0	3	2	3	0	3	7	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr21:22656582G>T	ENST00000400546.1	+	3	448	c.199G>T	c.(199-201)Gta>Tta	p.V67L	NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000535285.1_Missense_Mutation_p.V92L|NCAM2_ENST00000284894.7_Intron	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	67	Ig-like C2-type 1.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AACACAGAGGGTAGTAGTGCA	0.398																																					p.V67L		.											.	NCAM2-94	0			c.G199T						.						132	122	125					21																	22656582		1859	4101	5960	SO:0001583	missense	4685	exon3			CAGAGGGTAGTAG		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.199G>T	21.37:g.22656582G>T	ENSP00000383392:p.Val67Leu	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	70	24	NM_004540	0	0	0	1	1	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109633	0.37242	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	T;T	0.67345	-0.26;-0.26	5.58	4.7	0.59300	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.104866	0.64402	D	0.000003	T	0.57562	0.2062	L	0.37630	1.12	0.29058	N	0.884114	P;D	0.56968	0.799;0.978	B;P	0.44447	0.251;0.45	T	0.54510	-0.8283	10	0.09338	T	0.73	-17.3832	16.3191	0.82939	0.0715:0.0:0.9285:0.0	.	92;67	B7Z841;O15394	.;NCAM2_HUMAN	L	67;92	ENSP00000383392:V67L;ENSP00000441887:V92L	ENSP00000383392:V67L	V	+	1	0	NCAM2	21578453	1.000000	0.71417	0.498000	0.27564	0.836000	0.47400	3.223000	0.51231	0.735000	0.32537	-1.094000	0.02160	GTA	.		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22656582	G	T	22656582	3	4	108	1	0	0	0	0	1	0	0	0	10229	1261	44	4	209	4	NCAM2	21	22656582	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08		22656582	25473313	101	9586											
TTC3	7267	broad.mit.edu	37	chr21	38536463	38536463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtaacgaatatgttgtccGcaataagaagctatgggaca	15	9	10	7	2	0	1	0	0	0	1	1	3	1	2	1	1	2	4	1	1	7	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr21:38536463G>A	ENST00000399017.2	+	32	6028	c.3281G>A	c.(3280-3282)cGc>cAc	p.R1094H	TTC3_ENST00000354749.2_Missense_Mutation_p.R1094H|TTC3_ENST00000355666.1_Missense_Mutation_p.R1094H|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1094					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TATGTTGTCCGCAATAAGAAG	0.393																																					p.R1094H	Ovarian(38;194 1649 35661)												.	TTC3-590	0			c.G3281A						.						84	77	79					21																	38536463		2203	4300	6503	SO:0001583	missense	7267	exon32			TTGTCCGCAATAA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3281G>A	21.37:g.38536463G>A	ENSP00000381981:p.Arg1094His	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	96	4	NM_001001894	0	0	42	42	0	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.52|15.52	2.858057|2.858057	0.51376|0.51376	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T;T;T	.|0.12255	.|2.7;2.7;3.05;3.05;3.05	4.92|4.92	2.66|2.66	0.31614|0.31614	.|.	.|0.390747	.|0.20615	.|N	.|0.088890	T|T	0.26048|0.26048	0.0635|0.0635	L|L	0.57536|0.57536	1.79|1.79	0.22666|0.22666	N|N	0.998871|0.998871	.|D;D	.|0.89917	.|1.0;0.999	.|D;P	.|0.74023	.|0.982;0.869	T|T	0.02546|0.02546	-1.1143|-1.1143	5|10	.|0.52906	.|T	.|0.07	-5.9888|-5.9888	4.9199|4.9199	0.13865|0.13865	0.3454:0.0:0.6546:0.0|0.3454:0.0:0.6546:0.0	.|.	.|152;1094	.|Q5GIT6;P53804	.|.;TTC3_HUMAN	T|H	250|1094;1076;1094;1094;1094	.|ENSP00000403943:R1094H;ENSP00000391891:R1076H;ENSP00000347889:R1094H;ENSP00000381981:R1094H;ENSP00000346791:R1094H	.|ENSP00000346791:R1094H	A|R	+|+	1|2	0|0	TTC3|TTC3	37458333|37458333	0.000000|0.000000	0.05858|0.05858	0.882000|0.882000	0.34594|0.34594	0.975000|0.975000	0.68041|0.68041	0.380000|0.380000	0.20602|0.20602	1.204000|1.204000	0.43247|0.43247	0.591000|0.591000	0.81541|0.81541	GCA|CGC	.		0.393	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			A	38536463	G	A	38536463	3	1	108	1	0	0	0	0	1	0	0	0	16730	1087	38	1	3403	1	TTC3	21	38536463	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	15879881	38536463	9593432	102	9587											
BCL2L13	23786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18138590	18138590	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaagagcaacatctttcctCaccccaaggtattatctttg	11	12	6	12	0	3	1	1	0	2	1	4	1	4	1	3	1	2	3	3	1	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr22:18138590C>T	ENST00000317582.5	+	2	460	c.113C>T	c.(112-114)tCa>tTa	p.S38L	BCL2L13_ENST00000337612.5_5'UTR|BCL2L13_ENST00000418951.2_Missense_Mutation_p.S38L|BCL2L13_ENST00000493680.1_Missense_Mutation_p.S38L|BCL2L13_ENST00000538149.1_Missense_Mutation_p.H26Y|BCL2L13_ENST00000399782.1_Missense_Mutation_p.S38L|BCL2L13_ENST00000355028.3_Missense_Mutation_p.S38L|BCL2L13_ENST00000543133.1_5'UTR	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	38					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		CATCTTTCCTCACCCCAAGGT	0.358																																					p.S38L		.											.	BCL2L13-652	0			c.C113T						.						94	83	87					22																	18138590		2203	4300	6503	SO:0001583	missense	23786	exon2			TTTCCTCACCCCA	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.113C>T	22.37:g.18138590C>T	ENSP00000318883:p.Ser38Leu	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	34	33	NM_001270732	0	0	0	0	0	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Missense_Mutation	SNP	ENST00000317582.5	37	CCDS13746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.60|12.60	1.986267|1.986267	0.35036|0.35036	.|.	.|.	ENSG00000099968|ENSG00000099968	ENST00000538149|ENST00000399782;ENST00000317582;ENST00000493680;ENST00000355028;ENST00000418951	T|T;T;T;T;T	0.40756|0.05513	1.02|3.43;3.43;3.43;3.43;3.43	5.68|5.68	2.49|2.49	0.30216|0.30216	.|.	.|0.492205	.|0.20751	.|N	.|0.086347	T|T	0.04952|0.04952	0.0133|0.0133	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	B|B;B;B	0.06786|0.11235	0.001|0.004;0.001;0.001	B|B;B;B	0.12156|0.13407	0.007|0.009;0.003;0.004	T|T	0.39418|0.39418	-0.9615|-0.9615	9|10	0.87932|0.38643	D|T	0|0.18	-0.0021|-0.0021	8.7678|8.7678	0.34713|0.34713	0.0:0.7614:0.0:0.2386|0.0:0.7614:0.0:0.2386	.|.	26|38;38;38	B7Z238|E9PDD6;Q9BXK5;Q9BXK5-2	.|.;B2L13_HUMAN;.	Y|L	26|38	ENSP00000441344:H26Y|ENSP00000382682:S38L;ENSP00000318883:S38L;ENSP00000434764:S38L;ENSP00000347133:S38L;ENSP00000410019:S38L	ENSP00000441344:H26Y|ENSP00000318883:S38L	H|S	+|+	1|2	0|0	BCL2L13|BCL2L13	16518590|16518590	0.012000|0.012000	0.17670|0.17670	0.956000|0.956000	0.39512|0.39512	0.989000|0.989000	0.77384|0.77384	0.630000|0.630000	0.24553|0.24553	0.343000|0.343000	0.23821|0.23821	0.591000|0.591000	0.81541|0.81541	CAC|TCA	.		0.358	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367		T	18138590	C	T	18138590	3	4	108	1	0	0	0	0	1	0	0	0	1372	838	29	2	115	2	BCL2L13	22	18138590	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		18138590	33165976	103	9588											
PI4KA	5297	bcgsc.ca	37	chr22	21073055	21073055	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taaaagtccttcgctgggccGgacaaggagcctgtgatctc	9	9	12	11	2	1	1	0	1	1	0	4	3	2	3	3	3	1	1	3	3	3	2	rs530508978	byFrequency	TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr22:21073055G>A	ENST00000572273.1	-	44	5228	c.4998C>T	c.(4996-4998)tcC>tcT	p.S1666S	PI4KA_ENST00000414196.3_Silent_p.S476S|PI4KA_ENST00000255882.6_Silent_p.S1724S			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1666	Pleckstrin homology (PH) domain conferring phosphoinositide binding specificity. {ECO:0000250}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			TCGCTGGGCCGGACAAGGAGC	0.517																																					p.S1724S	GBM(136;1332 1831 3115 23601 50806)												.	PI4KA-454	0			c.C5172T						.						86	80	82					22																	21073055		2203	4300	6503	SO:0001819	synonymous_variant	5297	exon44			TGGGCCGGACAAG	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.4998C>T	22.37:g.21073055G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_1	50	4	NM_058004	8	0	22	30	0	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				.		0.517	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21073055	G	A	21073055	2	1	108	1	0	0	0	0	0	0	0	1	11899	1103	39	1		1	PI4KA	22	21073055	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	2934465	21073055	30231511	104	9589											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	30067890	30067905	+	Frame_Shift_Del	DEL	AGGCTGCTGCAGATGA	AGGCTGCTGCAGATGA	-																															cgagggatgagttggagaggAggctgctgcagatgaaagaa																								rs74315492|rs74315498		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AGGCTGCTGCAGATGA	AGGCTGCTGCAGATGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr22:30067890_30067905delAGGCTGCTGCAGATGA	ENST00000338641.4	+	11	1516_1531	c.1075_1090delAGGCTGCTGCAGATGA	c.(1075-1092)aggctgctgcagatgaaafs	p.RLLQMK359fs	NF2_ENST00000403435.1_Splice_Site_p.GC334fs|NF2_ENST00000353887.4_Frame_Shift_Del_p.RLLQMK276fs|NF2_ENST00000413209.2_Intron|NF2_ENST00000347330.5_Intron|NF2_ENST00000361676.4_Frame_Shift_Del_p.RLLQMK317fs|NF2_ENST00000403999.3_Frame_Shift_Del_p.RLLQMK359fs|NF2_ENST00000397789.3_Frame_Shift_Del_p.RLLQMK359fs|NF2_ENST00000361166.4_Frame_Shift_Del_p.RLLQMK359fs|NF2_ENST00000334961.7_Frame_Shift_Del_p.RLLQMK276fs|NF2_ENST00000361452.4_Frame_Shift_Del_p.RLLQMK318fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	359	Glu-rich.				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.Q362*(4)|p.?(3)|p.M363fs*12(2)|p.L361fs*6(1)|p.M334fs*4(1)|p.L361fs*3(1)|p.M334_Q362del(1)|p.K364fs*5(1)		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						GTTGGAGAGGAGGCTGCTGCAGATGAAAGAAGAAGC	0.565			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.359_364del		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	14	Deletion - Frameshift(6)|Substitution - Nonsense(4)|Unknown(3)|Deletion - In frame(1)	meninges(5)|soft_tissue(4)|large_intestine(1)|central_nervous_system(1)|endometrium(1)|skin(1)|stomach(1)	c.1075_1090del	GRCh37	CM066148|CM930517	NF2	M	rs74315492|rs74315498	.																																			SO:0001589	frameshift_variant	4771	exon11	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	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.1075_1090delAGGCTGCTGCAGATGA	22.37:g.30067890_30067905delAGGCTGCTGCAGATGA	ENSP00000344666:p.Arg359fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	35	23	NM_000268	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	37	CCDS13861.1																																																																																			.		0.565	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		-	30067905	AGGCTGCTGCAGATGA	-	30067890	7	5	108	1	0	1	0	1	0	0	0	0	10383	295	11	0	1117	0	NF2	22	30067890	Frame_Shift_Del	DEL	AGGCTGCTGCAGATGA	TCGA-EV-5902-01A-11D-1589-08	8994835	30067890	21236676	105	9590											
GAGE2A	729408	broad.mit.edu	37	chrX	49208295	49208296	+	In_Frame_Ins	INS	-	-	TAT																															gttggcgaggaagatcgaccINStatcggcctagaccaagacg																								rs372553636		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chrX:49208295_49208296insTAT	ENST00000404720.2	+	2	96_97	c.24_25insTAT	c.(25-27)tat>TATtat	p.9_9Y>YY		NM_001098407.1|NM_012196.1	NP_001091877.1|NP_036328.1	Q9UEU5	GGE2D_HUMAN	G antigen 2D	9					cellular defense response (GO:0006968)												GAAGATCGACCTATCGGCCTAG	0.465														477	0.126358	0.031	0.098	3775	,	,		26951	0.0972		0.1441	False		,,,				2504	0.1278				p.T8delinsTY													.	.	0			c.24_25insTAT						.			10,505,1500		1,1,3,4,46,330,82,490,187						-1.1	0			8	27,1244,2482		1,3,16,6,128,539,446,675,577	no	codingComplex	GAGE2D	NM_001098407.1		2,4,19,10,174,869,528,1165,764	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.8662,25.5583,30.9639				37,1749,3982				SO:0001652	inframe_insertion	729447	exon2			ATCGACCTATCGG			Xp11.23	2012-10-02			ENSG00000240257				31959	protein-coding gene	gene with protein product		300735					Standard	NM_001098407		Approved	GAGE8		Q9UEU5	OTTHUMG00000067393	ENST00000404720.2:c.25_27dupTAT	X.37:g.49208296_49208298dupTAT	ENSP00000386110:p.Tyr9dup	Somatic	644	0		WXS	Illumina HiSeq	Phase_I	596	4	NM_001127212	0	0	0	0	0	A6NG46|A6NNR8|B7ZL76|Q4V325	In_Frame_Ins	INS	ENST00000404720.2	37	CCDS43941.1																																																																																			.		0.465	GAGE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144212.1	NM_001098407		TAT	49208296	-	TAT	49208295	7	5	108	1	0	1	1	0	0	0	0	0	6209	668	24	0	236	0	GAGE2A	23	49208295	In_Frame_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08		49208295	106062265	106	9591											
ODZ1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123519705	123519705	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgccctgtccccagatgcagGgtctgtagcaatcggccatc	7	8	11	15	2	1	1	0	0	1	1	4	1	2	1	4	2	2	3	4	2	2	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chrX:123519705G>T	ENST00000371130.3	-	28	5940	c.5877C>A	c.(5875-5877)acC>acA	p.T1959T	TENM1_ENST00000422452.2_Silent_p.T1966T|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1959					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCAGATGCAGGGTCTGTAGCA	0.488																																					p.T1966T		.											.	.	0			c.C5898A						.						173	144	154					X																	123519705		2203	4300	6503	SO:0001819	synonymous_variant	10178	exon29			ATGCAGGGTCTGT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5877C>A	X.37:g.123519705G>T		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	124	21	NM_001163278	0	0	2	2	0	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			.		0.488	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123519705	G	T	123519705	2	4	108	1	0	0	0	0	0	0	0	1	10860	1219	43	4		4	ODZ1	23	123519705	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	74311410	123519705	31750855	107	9592											
ZDHHC9	51114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	128963040	128963040	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaagctggtcctcaacagtGtagccatggagaaaaggaag	14	7	13	7	0	1	2	1	1	0	1	2	4	2	3	2	3	3	2	2	3	6	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chrX:128963040G>T	ENST00000357166.6	-	4	636	c.245C>A	c.(244-246)aCa>aAa	p.T82K	ZDHHC9_ENST00000371064.3_Missense_Mutation_p.T82K	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	82					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						CCTCAACAGTGTAGCCATGGA	0.522																																					p.T82K		.											.	ZDHHC9-131	0			c.C245A						.						127	102	110					X																	128963040		2203	4300	6503	SO:0001583	missense	51114	exon3			AACAGTGTAGCCA	AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"Zinc fingers, DHHC-type"	18475	protein-coding gene	gene with protein product		300646	"zinc finger, DHHC-type containing 10", "chromosome X open reading frame 11"	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.245C>A	X.37:g.128963040G>T	ENSP00000349689:p.Thr82Lys	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	84	82	NM_001008222	0	0	0	49	49	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Missense_Mutation	SNP	ENST00000357166.6	37	CCDS35395.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.36|19.36	3.812188|3.812188	0.70797|0.70797	.|.	.|.	ENSG00000188706|ENSG00000188706	ENST00000433917|ENST00000357166;ENST00000371064;ENST00000406492	.|T;T;T	.|0.25085	.|1.82;1.82;1.82	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.088515	.|0.85682	.|D	.|0.000000	T|T	0.39572|0.39572	0.1083|0.1083	M|M	0.75777|0.75777	2.31|2.31	0.51482|0.51482	D|D	0.999924|0.999924	.|P	.|0.41041	.|0.736	.|P	.|0.44422	.|0.449	T|T	0.16305|0.16305	-1.0407|-1.0407	5|10	.|0.36615	.|T	.|0.2	-7.38|-7.38	18.76|18.76	0.91847|0.91847	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|82	.|Q9Y397	.|ZDHC9_HUMAN	N|K	42|82	.|ENSP00000349689:T82K;ENSP00000360103:T82K;ENSP00000383991:T82K	.|ENSP00000349689:T82K	H|T	-|-	1|2	0|0	ZDHHC9|ZDHHC9	128790721|128790721	1.000000|1.000000	0.71417|0.71417	0.972000|0.972000	0.41901|0.41901	0.891000|0.891000	0.51852|0.51852	4.787000|4.787000	0.62432|0.62432	2.375000|2.375000	0.81037|0.81037	0.594000|0.594000	0.82650|0.82650	CAC|ACA	.		0.522	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032		T	128963040	G	T	128963040	3	4	108	1	0	0	0	0	1	0	0	0	17654	1377	48	4	881	4	ZDHHC9	23	128963040	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	5443335	128963040	26307520	108	9593											
VPS13D	55187	bcgsc.ca	37	chr1	12304650	12304650	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagttaccgcctccgtagtTacaaggattgtggagaatat	11	12	10	8	2	1	1	1	0	0	1	2	3	2	2	3	2	2	3	3	2	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:12304650T>C	ENST00000358136.3	+	5	553	c.423T>C	c.(421-423)gtT>gtC	p.V141V	VPS13D_ENST00000356315.4_Silent_p.V141V	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CCTCCGTAGTTACAAGGATTG	0.413																																					p.V141V													.	VPS13D-95	0			c.T423C						.						143	133	137					1																	12304650		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon5			CGTAGTTACAAGG	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.423T>C	1.37:g.12304650T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_1	92	4	NM_015378	0	0	6	6	0		Silent	SNP	ENST00000358136.3	37	CCDS30588.1																																																																																			.		0.413	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12304650	T	C	12304650	2	2	109	1	0	0	0	0	0	0	0	1	17225	1741	61	3		3	VPS13D	1	12304650	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08		12304650	236945971	1	9594											
INADL	10207	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	62550317	62550317	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggaggaaaagacacaccCttggtaagtttctagaaata	15	9	11	6	0	1	2	0	0	1	2	1	4	1	4	1	3	0	2	1	3	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:62550317C>T	ENST00000371158.2	+	33	4488	c.4374C>T	c.(4372-4374)ccC>ccT	p.P1458P	INADL_ENST00000545929.1_Silent_p.P131P|INADL_ENST00000543708.1_Silent_p.P242P|INADL_ENST00000316485.6_Silent_p.P1458P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1458	PDZ 8. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.P1458P(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AAGACACACCCTTGGTAAGTT	0.448																																					p.P1458P		.											.	INADL-94	1	Substitution - coding silent(1)	lung(1)	c.C4374T						.						88	89	89					1																	62550317		2203	4300	6503	SO:0001819	synonymous_variant	10207	exon33			CACACCCTTGGTA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4374C>T	1.37:g.62550317C>T		Somatic	120	1		WXS	Illumina HiSeq	Phase_I	109	31	NM_176877	0	0	0	0	0	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			.		0.448	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62550317	C	T	62550317	2	4	109	1	0	0	0	0	0	0	0	1	7752	668	24	2		2	INADL	1	62550317	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08	50245667	62550317	186700304	2	9595											
FAM40A	85369	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	110587506	110587507	+	Frame_Shift_Ins	INS	-	-	TA																															gagtccagccgcagcaaattINStataggttacactctaggca																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:110587506_110587507insTA	ENST00000369795.3	+	11	1353_1354	c.1331_1332insTA	c.(1330-1335)tttatafs	p.FI444fs	STRIP1_ENST00000369796.1_Frame_Shift_Ins_p.FI349fs	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	444					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)											CGCAGCAAATTTATAGGTTACA	0.436																																					p.F444fs		.											.	.	0			c.1331_1332insTA						.																																			SO:0001589	frameshift_variant	85369	exon11			.	AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog A (yeast)"		"family with sequence similarity 40, member A"	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.1334_1335dupTA	1.37:g.110587509_110587510dupTA	ENSP00000358810:p.Phe444fs	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	107	30	NM_033088	0	0	0	0	0	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Frame_Shift_Ins	INS	ENST00000369795.3	37	CCDS30798.1																																																																																			.		0.436	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088		TA	110587507	-	TA	110587506	7	5	109	1	0	1	1	0	0	0	0	0	5579	1841	64	0	1373	0	FAM40A	1	110587506	Frame_Shift_Ins	INS	-	TCGA-EV-5903-01A-11D-1589-08	48037189	110587506	138663115	3	9596											
LY9	4063	broad.mit.edu	37	chr1	160783509	160783509	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcactctaatgtgctccGtgaagggggcagagaaaagt	13	8	12	8	1	2	2	1	1	1	1	3	3	3	2	1	2	1	2	1	2	4	1	rs568376272		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:160783509G>A	ENST00000263285.6	+	3	568	c.538G>A	c.(538-540)Gtg>Atg	p.V180M	LY9_ENST00000471816.1_3'UTR|LY9_ENST00000368037.5_Missense_Mutation_p.V180M|LY9_ENST00000368041.2_Missense_Mutation_p.V140M|LY9_ENST00000341032.4_Missense_Mutation_p.V180M|LY9_ENST00000392203.4_Missense_Mutation_p.V180M|LY9_ENST00000368040.1_5'UTR			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	180	Ig-like C2-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AATGTGCTCCGTGAAGGGGGC	0.537													G|||	1	0.000199681	0	0.0014	5008	,	,		20846	0		0	False		,,,				2504	0				p.V180M													.	LY9-91	0			c.G538A						.						113	109	111					1																	160783509		2203	4300	6503	SO:0001583	missense	4063	exon3			TGCTCCGTGAAGG	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.538G>A	1.37:g.160783509G>A	ENSP00000263285:p.Val180Met	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	131	5	NM_001261457	0	0	0	0	0	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	37	CCDS30916.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195454	0.38806	.	.	ENSG00000122224	ENST00000368041;ENST00000341032;ENST00000263285;ENST00000542780;ENST00000392203;ENST00000368037;ENST00000368036	T;T	0.03951	3.75;3.75	4.12	0.914	0.19360	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.153604	0.42964	N	0.000624	T	0.03390	0.0098	M	0.70275	2.135	0.22050	N	0.999398	D;D;D;D;D;D	0.59357	0.981;0.981;0.96;0.962;0.967;0.985	P;P;B;P;B;P	0.48795	0.509;0.509;0.235;0.516;0.328;0.59	T	0.30650	-0.9971	10	0.56958	D	0.05	-4.7988	6.5251	0.22297	0.3552:0.0:0.6447:0.0	.	180;140;140;180;180;180	B4E0J5;Q5VYH7;Q5VYH9;E7EME5;Q9HBG7-2;Q9HBG7	.;.;.;.;.;LY9_HUMAN	M	180;180;180;180;140;140;82	ENSP00000342921:V180M;ENSP00000263285:V180M	ENSP00000263285:V180M	V	+	1	0	LY9	159050133	0.001000	0.12720	0.004000	0.12327	0.008000	0.06430	-0.026000	0.12392	0.069000	0.16605	0.557000	0.71058	GTG	.		0.537	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		A	160783509	G	A	160783509	3	1	109	1	0	0	0	0	1	0	0	0	9126	1145	40	1	680	1	LY9	1	160783509	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	50196003	160783509	88467112	4	9597											
LRRC52	440699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	165514059	165514059	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccttataccacctcactactCtggagaccctgtttctgagt	8	13	6	14	0	3	2	1	1	2	1	3	3	3	2	4	1	2	1	4	1	3	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:165514059C>G	ENST00000294818.1	+	1	816	c.526C>G	c.(526-528)Ctg>Gtg	p.L176V	RP11-280O1.2_ENST00000416424.1_RNA|RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000421273.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	176					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					CCTCACTACTCTGGAGACCCT	0.512																																					p.L176V		.											.	LRRC52-91	0			c.C526G						.						148	152	151					1																	165514059		2203	4300	6503	SO:0001583	missense	440699	exon1			ACTACTCTGGAGA	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.526C>G	1.37:g.165514059C>G	ENSP00000294818:p.Leu176Val	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	188	52	NM_001005214	0	0	0	0	0	A2RUN7|Q5T9K5	Missense_Mutation	SNP	ENST00000294818.1	37	CCDS30930.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863665	0.32884	.	.	ENSG00000162763	ENST00000294818	T	0.06449	3.3	5.39	5.39	0.77823	.	0.089285	0.53938	D	0.000042	T	0.17195	0.0413	M	0.74881	2.28	0.34422	D	0.697524	D	0.65815	0.995	D	0.67231	0.95	T	0.00436	-1.1740	9	0.72032	D	0.01	.	16.6547	0.85225	0.0:1.0:0.0:0.0	.	176	Q8N7C0	LRC52_HUMAN	V	176	ENSP00000294818:L176V	ENSP00000294818:L176V	L	+	1	2	LRRC52	163780683	1.000000	0.71417	0.049000	0.19019	0.023000	0.10783	5.468000	0.66743	2.517000	0.84864	0.563000	0.77884	CTG	.		0.512	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214		G	165514059	C	G	165514059	3	3	109	1	0	0	0	0	1	0	0	0	9035	912	32	4	528	4	LRRC52	1	165514059	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	4730550	165514059	83736562	5	9598											
C1orf107	27042	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	210015618	210015618	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttccactcaaagcatttgatGaatcacatgaacctactacc	14	11	4	12	0	2	3	2	3	0	0	3	3	3	3	3	0	4	1	3	0	5	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:210015618G>A	ENST00000491415.2	+	9	1551	c.1494G>A	c.(1492-1494)atG>atA	p.M498I		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	498					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						AGCATTTGATGAATCACATGA	0.418																																					p.M498I		.											.	DIEXF-91	0			c.G1494A						.						82	74	76					1																	210015618		2203	4300	6503	SO:0001583	missense	27042	exon9			TTTGATGAATCAC	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.1494G>A	1.37:g.210015618G>A	ENSP00000419005:p.Met498Ile	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	67	17	NM_014388	0	0	0	0	0	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	37	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076476	0.76415	.	.	ENSG00000117597	ENST00000491415	T	0.37411	1.2	6.17	6.17	0.99709	.	0.069797	0.85682	D	0.000000	T	0.36580	0.0972	L	0.45228	1.405	0.58432	D	0.999996	P	0.45044	0.849	B	0.39971	0.315	T	0.03315	-1.1049	10	0.35671	T	0.21	-37.8963	20.8794	0.99867	0.0:0.0:1.0:0.0	.	498	Q68CQ4	DIEXF_HUMAN	I	498	ENSP00000419005:M498I	ENSP00000419005:M498I	M	+	3	0	DIEXF	208082241	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.791000	0.85805	2.941000	0.99782	0.655000	0.94253	ATG	.		0.418	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		A	210015618	G	A	210015618	3	1	109	1	0	0	0	0	1	0	0	0	1987	1290	45	2	1528	2	C1orf107	1	210015618	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	44501559	210015618	39235003	6	9599											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112762	248112763	+	Frame_Shift_Del	DEL	TG	TG	-																															gagggcacagtgtttttgagTgccaccatctttctcgtgtt																								rs34851853|rs4925790|rs4925789	byFrequency	TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:248112762_248112763delTG	ENST00000357191.3	+	1	603_604	c.603_604delTG	c.(601-606)agtgccfs	p.A202fs	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	202			A -> T (in dbSNP:rs4925790).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TGTTTTTGAGTGCCACCATCTT	0.49																																					p.201_202del		.											.	OR2L8-70	0			c.603_604del						.																																			SO:0001589	frameshift_variant	391190	exon1			.	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.603_604delTG	1.37:g.248112762_248112763delTG	ENSP00000349719:p.Ala202fs	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	69	14	NM_001001963	0	0	0	0	0	Q6IF03	Frame_Shift_Del	DEL	ENST00000357191.3	37	CCDS31101.1																																																																																			.		0.49	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			-	248112763	TG	-	248112762	7	5	109	1	0	1	0	1	0	0	0	0	11035	1693	59	0	605	0	OR2L8	1	248112762	Frame_Shift_Del	DEL	TG	TCGA-EV-5903-01A-11D-1589-08	38097144	248112762	1137859	7	9600											
KHK	3795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27322367	27322367	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattgctccactcggatgctTtcccgccaccccgcgtggtg	5	10	10	16	4	0	0	0	0	0	0	3	1	2	1	5	2	2	2	5	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:27322367T>C	ENST00000260599.6	+	7	1246	c.733T>C	c.(733-735)Ttc>Ctc	p.F245L	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Missense_Mutation_p.F245L|CGREF1_ENST00000402550.1_3'UTR|CGREF1_ENST00000452318.2_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	245					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCGGATGCTTTCCCGCCACC	0.637																																					p.F245L		.											.	KHK-115	0			c.T733C						.						80	82	82					2																	27322367		2203	4300	6503	SO:0001583	missense	3795	exon7			GATGCTTTCCCGC		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.733T>C	2.37:g.27322367T>C	ENSP00000260599:p.Phe245Leu	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	98	27	NM_006488	0	0	5	5	0	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	37	CCDS1734.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.519838	0.64634	.	.	ENSG00000138030	ENST00000260599;ENST00000260598	T;T	0.75477	-0.94;-0.94	5.29	4.11	0.48088	Carbohydrate/purine kinase (1);	0.048848	0.85682	D	0.000000	T	0.71324	0.3326	M	0.66939	2.045	0.80722	D	1	B;P;B;P	0.51791	0.021;0.948;0.08;0.948	B;B;B;B	0.43052	0.022;0.406;0.049;0.406	T	0.69621	-0.5096	10	0.38643	T	0.18	-12.9402	10.6793	0.45804	0.0:0.0:0.1603:0.8397	.	245;245;245;245	Q53G56;Q6IBK2;P50053-2;P50053	.;.;.;KHK_HUMAN	L	245	ENSP00000260599:F245L;ENSP00000260598:F245L	ENSP00000260598:F245L	F	+	1	0	KHK	27175871	1.000000	0.71417	0.979000	0.43373	0.490000	0.33462	4.841000	0.62824	0.811000	0.34303	0.454000	0.30748	TTC	.		0.637	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1			C	27322367	T	C	27322367	3	2	109	1	0	0	0	0	1	0	0	0	8170	1841	64	3	898	3	KHK	2	27322367	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08		27322367	215877006	8	9601											
DNAJC5G	285126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27503082	27503082	+	Nonstop_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatagcgaagatgatttttAagagatgaagaaggatgagg	18	9	13	1	1	0	6	0	3	0	3	0	9	0	7	0	2	1	0	0	2	6	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:27503082A>T	ENST00000296097.3	+	6	987	c.569A>T	c.(568-570)tAa>tTa	p.*190L	DNAJC5G_ENST00000406962.1_Nonsense_Mutation_p.K103*|TRIM54_ENST00000380075.2_5'Flank|TRIM54_ENST00000296098.4_5'Flank|DNAJC5G_ENST00000402462.1_Nonstop_Mutation_p.*190L|DNAJC5G_ENST00000404433.1_Nonstop_Mutation_p.*174L	NM_173650.1	NP_775921.1	Q8N7S2	DNJ5G_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 gamma	0						membrane (GO:0016020)				cervix(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGATTTTTAAGAGATGAAG	0.333											OREG0014517	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.X190L		.											.	DNAJC5G-226	0			c.A569T						.						141	153	149					2																	27503082		2203	4300	6503	SO:0001578	stop_lost	285126	exon6			ATTTTTAAGAGAT	AF368277	CCDS1744.1	2p23	2011-09-02			ENSG00000163793	ENSG00000163793		"Heat shock proteins / DNAJ (HSP40)"	24844	protein-coding gene	gene with protein product		613946					Standard	NM_173650		Approved	FLJ40417, CSP-gamma	uc002rjl.1	Q8N7S2	OTTHUMG00000097079	ENST00000296097.3:c.569A>T	2.37:g.27503082A>T	ENSP00000296097:p.*190Leuext*11	Somatic	244	0	794	WXS	Illumina HiSeq	Phase_I	215	64	NM_173650	0	0	0	0	0	B4DY29|Q53SY5|Q8IYQ4|Q96RJ8	Missense_Mutation	SNP	ENST00000296097.3	37	CCDS1744.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.13|16.13	3.037320|3.037320	0.54896|0.54896	.|.	.|.	ENSG00000163793|ENSG00000163793	ENST00000406962|ENST00000296097;ENST00000402462;ENST00000404433	.|.	.|.	.|.	3.86|3.86	0.87|0.87	0.19102|0.19102	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	2.2003|2.2003	0.03921|0.03921	0.5749:0.0:0.1962:0.2289|0.5749:0.0:0.1962:0.2289	.|.	.|.	.|.	.|.	X|L	103|190;190;174	.|.	.|.	K|X	+|+	1|2	0|2	DNAJC5G|DNAJC5G	27356586|27356586	0.017000|0.017000	0.18338|0.18338	0.000000|0.000000	0.03702|0.03702	0.353000|0.353000	0.29299|0.29299	0.770000|0.770000	0.26618|0.26618	0.154000|0.154000	0.19237|0.19237	0.379000|0.379000	0.24179|0.24179	AAG|TAA	.		0.333	DNAJC5G-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214200.1	NM_173650		T	27503082	A	T	27503082	4	4	109	1	0	0	0	0	0	0	0	0	4663	369	13	5	583	5	DNAJC5G	2	27503082	Nonstop_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	180715	27503082	215696291	9	9602											
LTBP1	4052	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	33359941	33359941	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caccaagggcagctgtcagaAcagctgtgagaaggggaaca	14	4	14	9	0	1	2	1	1	0	2	1	4	1	3	1	3	4	3	1	3	4	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:33359941A>C	ENST00000404816.2	+	5	1468	c.1115A>C	c.(1114-1116)aAc>aCc	p.N372T	LTBP1_ENST00000354476.3_Missense_Mutation_p.N372T|LTBP1_ENST00000418533.2_Missense_Mutation_p.N46T|LTBP1_ENST00000407925.1_Missense_Mutation_p.N46T|LTBP1_ENST00000404525.1_Missense_Mutation_p.N46T|LTBP1_ENST00000402934.1_Missense_Mutation_p.N46T|LTBP1_ENST00000390003.4_Missense_Mutation_p.N46T			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	372					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AGCTGTCAGAACAGCTGTGAG	0.562																																					p.N372T		.											.	LTBP1-230	0			c.A1115C						.						101	86	92					2																	33359941		2203	4300	6503	SO:0001583	missense	4052	exon5			GTCAGAACAGCTG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.1115A>C	2.37:g.33359941A>C	ENSP00000386043:p.Asn372Thr	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	74	23	NM_206943	0	0	18	19	1	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	A	22.4	4.287221	0.80803	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000432635;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.84873	-1.91;-1.91;-1.72;-1.66;-1.75;-1.73;-1.69	5.57	5.57	0.84162	.	.	.	.	.	D	0.91133	0.7208	M	0.62723	1.935	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.999;1.0;0.999;0.999;0.999	D;D;D;D;D;D	0.97110	0.995;0.998;1.0;0.998;0.998;0.998	D	0.92071	0.5664	9	0.87932	D	0	.	15.7244	0.77743	1.0:0.0:0.0:0.0	.	372;46;46;46;46;372	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	T	372;372;61;46;46;46;46;46	ENSP00000386043:N372T;ENSP00000346467:N372T;ENSP00000374653:N46T;ENSP00000393057:N46T;ENSP00000384373:N46T;ENSP00000385359:N46T;ENSP00000384091:N46T	ENSP00000346467:N372T	N	+	2	0	LTBP1	33213445	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.228000	0.95250	2.110000	0.64415	0.379000	0.24179	AAC	.		0.562	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33359941	A	C	33359941	3	2	109	1	0	0	0	0	1	0	0	0	9098	43	2	5	1188	5	LTBP1	2	33359941	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	5856859	33359941	209839432	10	9603											
IMMT	10989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	86371396	86371396	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaatcttcctaaacctcactCtggctgcacctgagtggttc	9	12	7	13	0	3	1	1	1	2	0	5	1	4	1	3	2	2	3	3	2	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:86371396C>G	ENST00000410111.3	-	15	2659	c.2272G>C	c.(2272-2274)Gag>Cag	p.E758Q	IMMT_ENST00000254636.5_Missense_Mutation_p.E659Q|IMMT_ENST00000409051.2_Missense_Mutation_p.E711Q|IMMT_ENST00000442664.2_Missense_Mutation_p.E757Q|IMMT_ENST00000449247.2_Missense_Mutation_p.E747Q	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	758				E -> D (in Ref. 3; CAG33074). {ECO:0000305}.	mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.E758Q(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAACCTCACTCTGGCTGCACC	0.473																																					p.E758Q		.											.	IMMT-91	1	Substitution - Missense(1)	lung(1)	c.G2272C						.						59	57	58					2																	86371396		1907	4127	6034	SO:0001583	missense	10989	exon15			CTCACTCTGGCTG	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.2272G>C	2.37:g.86371396C>G	ENSP00000387262:p.Glu758Gln	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	65	21	NM_006839	0	0	56	103	47	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.72|11.72	1.722342|1.722342	0.30503|0.30503	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715|ENST00000419070	T;T;T;T;T|.	0.35236|.	1.32;1.35;1.36;1.35;1.34|.	4.44|4.44	3.55|3.55	0.40652|0.40652	.|.	0.145672|.	0.32041|.	N|.	0.006672|.	T|T	0.13157|0.13157	0.0319|0.0319	N|N	0.02011|0.02011	-0.69|-0.69	0.24917|0.24917	N|N	0.992003|0.992003	D;D;D;D;D|.	0.71674|.	0.994;0.997;0.998;0.998;0.989|.	D;D;D;D;P|.	0.79784|.	0.979;0.985;0.993;0.993;0.742|.	T|T	0.18335|0.18335	-1.0340|-1.0340	10|5	0.49607|.	T|.	0.09|.	-13.9033|-13.9033	8.3828|8.3828	0.32481|0.32481	0.0:0.7575:0.1586:0.0839|0.0:0.7575:0.1586:0.0839	.|.	711;746;747;726;758|.	B9A067;B4DKR1;Q16891-2;Q16891-3;Q16891|.	.;.;.;.;IMMT_HUMAN|.	Q|T	659;747;758;757;711;747;726;372;659|612	ENSP00000254636:E659Q;ENSP00000396899:E747Q;ENSP00000387262:E758Q;ENSP00000407788:E757Q;ENSP00000387227:E711Q|.	ENSP00000254636:E659Q|.	E|R	-|-	1|2	0|0	IMMT|IMMT	86224907|86224907	0.036000|0.036000	0.19791|0.19791	0.972000|0.972000	0.41901|0.41901	0.346000|0.346000	0.29079|0.29079	1.134000|1.134000	0.31442|0.31442	1.467000|1.467000	0.48044|0.48044	0.650000|0.650000	0.86243|0.86243	GAG|AGA	.		0.473	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		G	86371396	C	G	86371396	3	3	109	1	0	0	0	0	1	0	0	0	7739	922	32	4	8	4	IMMT	2	86371396	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	53011455	86371396	156827977	11	9604											
ASTL	431705	broad.mit.edu;bcgsc.ca	37	chr2	96789883	96789883	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccccaggccctgcaggaacGggctggcctcccgcactgga	6	5	13	17	2	0	0	0	0	0	0	2	2	2	2	5	5	2	3	5	5	1	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:96789883G>C	ENST00000342380.2	-	9	1001	c.1002C>G	c.(1000-1002)ccC>ccG	p.P334P		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						CTGCAGGAACGGGCTGGCCTC	0.672																																					p.P334P													.	ASTL-90	0			c.C1002G						.						34	39	37					2																	96789883		2203	4297	6500	SO:0001819	synonymous_variant	431705	exon9			AGGAACGGGCTGG	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"sperm acrosomal SLLP1 binding"	608860	"astacin-like metalloendopeptidase (M12 family)"			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.1002C>G	2.37:g.96789883G>C		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	112	6	NM_001002036	0	0	0	0	0		Silent	SNP	ENST00000342380.2	37	CCDS33249.1																																																																																			.		0.672	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			C	96789883	G	C	96789883	2	2	109	1	0	0	0	0	0	0	0	1	1064	1103	39	4		4	ASTL	2	96789883	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	10418487	96789883	146409490	12	9605											
POTEE	445582	hgsc.bcm.edu;broad.mit.edu	37	chr2	132020929	132020929	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttctctttgtttacttagcTttctcttagttgtaagaaag	8	20	7	6	0	2	1	0	0	2	1	4	1	2	1	0	0	2	5	0	0	5	9			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:132020929T>G	ENST00000356920.5	+	15	1995	c.1901T>G	c.(1900-1902)cTt>cGt	p.L634R	PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	634					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TTTACTTAGCTTTCTCTTAGT	0.318																																					p.L634R		.											.	.	0			c.T1901G						.						17	19	18					2																	132020929		1871	4085	5956	SO:0001630	splice_region_variant	445582	exon15			CTTAGCTTTCTCT	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.1900-1T>G	2.37:g.132020929T>G		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	46	6	NM_001083538	0	0	0	0	0	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	10.54	1.377767	0.24944	.	.	ENSG00000188219	ENST00000356920	T	0.78003	-1.14	0.993	-0.489	0.12052	.	.	.	.	.	T	0.51924	0.1703	N	0.22421	0.69	0.22213	N	0.999286	P	0.42993	0.797	B	0.28305	0.088	T	0.51340	-0.8718	9	0.87932	D	0	.	1.3779	0.02224	0.3298:0.2367:0.0:0.4335	.	634	Q6S8J3	POTEE_HUMAN	R	634	ENSP00000439189:L634R	ENSP00000439189:L634R	L	+	2	0	AC131180.1	131737399	0.008000	0.16893	0.656000	0.29637	0.025000	0.11179	1.904000	0.39868	-0.140000	0.11394	0.155000	0.16302	CTT	.		0.318	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	Missense_Mutation	G	132020929	T	G	132020929	5	3	109	1	0	0	0	0	0	0	1	0	12290	1623	56	5	1959	5	POTEE	2	132020929	Splice_Site	SNP	T	TCGA-EV-5903-01A-11D-1589-08	35231046	132020929	111178444	13	9606											
NEB	4703	hgsc.bcm.edu	37	chr2	152553243	152553243	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttatctggatggactttgtAggtgtgctgtggggaagcaa	8	13	15	5	0	1	0	0	0	1	0	1	3	1	3	0	5	2	3	0	5	4	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:152553243A>G	ENST00000172853.10	-	17	1624	c.1477T>C	c.(1477-1479)Tac>Cac	p.Y493H	NEB_ENST00000427231.2_Missense_Mutation_p.Y493H|NEB_ENST00000397345.3_Missense_Mutation_p.Y493H|NEB_ENST00000409198.1_Missense_Mutation_p.Y493H|NEB_ENST00000603639.1_Missense_Mutation_p.Y493H|NEB_ENST00000604864.1_Missense_Mutation_p.Y493H			P20929	NEBU_HUMAN	nebulin	493					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGACTTTGTAGGTGTGCTGT	0.463																																					p.Y493H		.											.	NEB-145	0			c.T1477C						.						191	188	189					2																	152553243		1938	4128	6066	SO:0001583	missense	4703	exon17			CTTTGTAGGTGTG	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.1477T>C	2.37:g.152553243A>G	ENSP00000172853:p.Tyr493His	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	44	3	NM_004543	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	A	25.8	4.671821	0.88348	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000536533	T;T;T;T	0.12147	2.71;2.79;2.77;2.72	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.36054	0.0953	M	0.79475	2.455	0.80722	D	1	D;D	0.63880	0.993;0.985	P;P	0.61070	0.883;0.845	T	0.13926	-1.0491	10	0.87932	D	0	.	14.6206	0.68582	1.0:0.0:0.0:0.0	.	126;493	Q86TG3;P20929	.;NEBU_HUMAN	H	493;493;493;493;219	ENSP00000386259:Y493H;ENSP00000380505:Y493H;ENSP00000416578:Y493H;ENSP00000172853:Y493H	ENSP00000172853:Y493H	Y	-	1	0	NEB	152261489	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	3.275000	0.51639	2.268000	0.75426	0.455000	0.32223	TAC	.		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152553243	A	G	152553243	3	3	109	1	0	0	0	0	1	0	0	0	10328	420	15	3	24873	3	NEB	2	152553243	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	20532314	152553243	90646130	14	9607											
CWC22	57703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	180810243	180810243	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgatgtgtactttgttatAggatctctccaatttgaacc	9	17	7	8	0	2	2	0	2	2	0	4	3	3	3	2	1	2	2	2	1	5	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:180810243A>G	ENST00000410053.3	-	20	2639	c.2340T>C	c.(2338-2340)ccT>ccC	p.P780P	CWC22_ENST00000295749.6_Silent_p.P780P	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	780					mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						ACTTTGTTATAGGATCTCTCC	0.388																																					p.P780P		.											.	CWC22-90	0			c.T2340C						.						222	206	211					2																	180810243		1860	4108	5968	SO:0001819	synonymous_variant	57703	exon20			TGTTATAGGATCT		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"functional spliceosome-associated protein b"	615186	"CWC22 spliceosome-associated protein homolog (S. cerevisiae)"			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.2340T>C	2.37:g.180810243A>G		Somatic	289	0		WXS	Illumina HiSeq	Phase_I	272	71	NM_020943	0	0	9	15	6	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Silent	SNP	ENST00000410053.3	37	CCDS46465.1																																																																																			.		0.388	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		G	180810243	A	G	180810243	2	3	109	1	0	0	0	0	0	0	0	1	4074	407	15	3		3	CWC22	2	180810243	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	28257000	180810243	62389130	15	9608											
ERBB4	2066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	212295693	212295693	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccatcagcattgtactCtttttcatctccttccaaga	8	16	3	14	0	4	1	2	0	2	1	8	1	7	1	4	0	2	2	4	0	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:212295693C>A	ENST00000342788.4	-	21	2930	c.2620G>T	c.(2620-2622)Gag>Tag	p.E874*	ERBB4_ENST00000436443.1_Nonsense_Mutation_p.E874*|ERBB4_ENST00000402597.1_Nonsense_Mutation_p.E864*	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	874	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GCATTGTACTCTTTTTCATCT	0.373										TSP Lung(8;0.080)																											p.E874X		.											.	ERBB4-1461	0			c.G2620T						.						147	139	142					2																	212295693		2203	4300	6503	SO:0001587	stop_gained	2066	exon21			TGTACTCTTTTTC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2620G>T	2.37:g.212295693C>A	ENSP00000342235:p.Glu874*	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	185	54	NM_001042599	0	0	0	0	0	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Nonsense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264878	0.95399	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	.	.	.	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.0631	0.93100	0.0:1.0:0.0:0.0	.	.	.	.	X	874;874;864	.	ENSP00000342235:E874X	E	-	1	0	ERBB4	212003938	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	7.747000	0.85070	2.565000	0.86533	0.563000	0.77884	GAG	.		0.373	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212295693	C	A	212295693	4	1	109	1	0	0	0	0	0	1	0	0	5222	922	32	4	1338	4	ERBB4	2	212295693	Nonsense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	31485450	212295693	30903680	16	9609											
ARPC2	10109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219103554	219103554	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaacagggcagttatccatTatagggatgatgagaccatg	14	9	12	6	0	0	3	0	2	0	2	1	5	1	4	2	2	1	2	2	2	4	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:219103554T>A	ENST00000295685.10	+	5	697	c.436T>A	c.(436-438)Tat>Aat	p.Y146N	ARPC2_ENST00000477992.1_3'UTR|ARPC2_ENST00000315717.5_Missense_Mutation_p.Y146N	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	146					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		AGTTATCCATTATAGGGATGA	0.438																																					p.Y146N		.											.	ARPC2-91	0			c.T436A						.						74	70	72					2																	219103554		2203	4300	6503	SO:0001583	missense	10109	exon5			ATCCATTATAGGG	AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"Actin related protein 2/3 complex subunits"	705	protein-coding gene	gene with protein product		604224	"actin related protein 2/3 complex, subunit 2 (34 kD)"			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.436T>A	2.37:g.219103554T>A	ENSP00000295685:p.Tyr146Asn	Somatic	112	2		WXS	Illumina HiSeq	Phase_I	105	31	NM_005731	0	0	207	320	113	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	37	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.427174	0.62733	.	.	ENSG00000163466	ENST00000315717;ENST00000295685	.	.	.	5.65	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.85703	0.5758	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.88920	0.3365	9	0.87932	D	0	.	12.9852	0.58588	0.0:0.0:0.135:0.865	.	146	O15144	ARPC2_HUMAN	N	146	.	ENSP00000295685:Y146N	Y	+	1	0	ARPC2	218811799	1.000000	0.71417	1.000000	0.80357	0.418000	0.31294	7.868000	0.87116	1.130000	0.42092	0.533000	0.62120	TAT	.		0.438	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2	NM_005731		A	219103554	T	A	219103554	3	1	109	1	0	0	0	0	1	0	0	0	972	1754	61	5	454	5	ARPC2	2	219103554	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	6807861	219103554	24095819	17	9610											
HDAC4	9759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	239988463	239988463	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgcttccgaggcgtcgcaAatggcggtcaggtcgtggcc	6	8	15	12	5	1	0	1	0	0	0	4	1	2	0	2	5	1	2	2	5	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:239988463A>T	ENST00000345617.3	-	24	3734	c.2943T>A	c.(2941-2943)atT>atA	p.I981I	AC017028.6_ENST00000577291.1_RNA|AC017028.4_ENST00000577359.1_RNA|MIR4440_ENST00000583986.1_RNA|AC017028.5_ENST00000582834.1_RNA|AC017028.9_ENST00000581111.1_RNA|AC017028.2_ENST00000578555.1_RNA|AC017028.3_ENST00000584260.1_RNA|AC017028.10_ENST00000579161.1_RNA|HDAC4_ENST00000543185.1_Silent_p.I565I	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	981	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		AGGCGTCGCAAATGGCGGTCA	0.632																																					p.I981I		.											.	HDAC4-291	0			c.T2943A						.						78	75	76					2																	239988463		2203	4300	6503	SO:0001819	synonymous_variant	9759	exon24			GTCGCAAATGGCG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"brachydactyly-mental retardation syndrome"	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2943T>A	2.37:g.239988463A>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	124	31	NM_006037	0	0	1	2	1	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.768867	0.31320	.	.	ENSG00000068024	ENST00000430200	.	.	.	4.21	-5.54	0.02544	.	.	.	.	.	T	0.62829	0.2460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64305	-0.6439	4	.	.	.	.	14.9101	0.70749	0.3468:0.0:0.6532:0.0	.	.	.	.	Y	72	.	.	F	-	2	0	HDAC4	239653400	0.715000	0.27946	0.962000	0.40283	0.971000	0.66376	-0.071000	0.11505	-1.038000	0.03279	-0.376000	0.06991	TTT	.		0.632	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		T	239988463	A	T	239988463	2	4	109	1	0	0	0	0	0	0	0	1	7030	10	1	5		5	HDAC4	2	239988463	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	20884909	239988463	3210910	18	9611											
FARP2	9855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242433435	242433435	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcctccaggtggatggaggtGatccagggggccagcagctc	7	7	16	11	0	0	1	0	1	0	0	4	3	3	3	4	6	2	2	4	6	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:242433435G>C	ENST00000264042.3	+	27	3230	c.3060G>C	c.(3058-3060)gtG>gtC	p.V1020V	STK25_ENST00000316586.4_3'UTR|STK25_ENST00000478403.1_5'Flank	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	1020	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GGATGGAGGTGATCCAGGGGG	0.637																																					p.V1020V		.											.	FARP2-93	0			c.G3060C						.						51	56	55					2																	242433435		2202	4299	6501	SO:0001819	synonymous_variant	9855	exon27			GGAGGTGATCCAG	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.3060G>C	2.37:g.242433435G>C		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	96	22	NM_014808	0	0	0	0	0	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424530	0.25639	.	.	ENSG00000006607	ENST00000444371;ENST00000412332	.	.	.	4.94	4.04	0.47022	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5752	0.61870	0.0:0.1619:0.8381:0.0	.	.	.	.	S	163;22	.	.	X	+	2	2	FARP2	242082108	1.000000	0.71417	0.997000	0.53966	0.721000	0.41392	0.714000	0.25808	1.176000	0.42840	0.655000	0.94253	TGA	.		0.637	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			C	242433435	G	C	242433435	2	2	109	1	0	0	0	0	0	0	0	1	5696	1277	45	4		4	FARP2	2	242433435	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	2444972	242433435	765938	19	9612											
EOMES	8320	hgsc.bcm.edu	37	chr3	27762953	27762953	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggtggcggtggaatttgAgccacagaggccggttgcac	7	10	16	8	2	0	2	0	1	0	1	0	3	0	3	2	6	2	2	2	6	1	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:27762953A>G	ENST00000295743.4	-	1	1036	c.833T>C	c.(832-834)cTc>cCc	p.L278P	EOMES_ENST00000449599.1_Missense_Mutation_p.L278P|EOMES_ENST00000461503.1_Intron|EOMES_ENST00000537516.1_Intron			O95936	EOMES_HUMAN	eomesodermin	278					brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						GTGGAATTTGAGCCACAGAGG	0.637																																					p.L278P		.											.	EOMES-156	0			c.T833C						.						19	25	23					3																	27762953		2200	4298	6498	SO:0001583	missense	8320	exon1			AATTTGAGCCACA	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.833T>C	3.37:g.27762953A>G	ENSP00000295743:p.Leu278Pro	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_005442	0	0	1	1	0	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Missense_Mutation	SNP	ENST00000295743.4	37	CCDS2646.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.174990	0.78564	.	.	ENSG00000163508	ENST00000295743;ENST00000449599;ENST00000535713	T;T	0.80393	-1.37;-1.37	5.08	5.08	0.68730	Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.88941	0.6574	M	0.79926	2.475	0.80722	D	1	D;D;P	0.89917	1.0;0.972;0.953	D;P;P	0.91635	0.999;0.774;0.737	D	0.88000	0.2755	10	0.30854	T	0.27	.	13.8135	0.63276	1.0:0.0:0.0:0.0	.	278;278;278	F5H3K1;G3XAI5;O95936	.;.;EOMES_HUMAN	P	278;278;143	ENSP00000295743:L278P;ENSP00000388620:L278P	ENSP00000295743:L278P	L	-	2	0	EOMES	27737957	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.252000	0.78309	1.901000	0.55032	0.379000	0.24179	CTC	.		0.637	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		G	27762953	A	G	27762953	3	3	109	1	0	0	0	0	1	0	0	0	5160	304	11	3	1251	3	EOMES	3	27762953	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08		27762953	170259477	20	9613											
CLASP2	23122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	33552091	33552091	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctggcaaaagcaggtttaGggtttccttggacactctct	8	13	10	10	0	2	0	0	0	2	0	4	1	3	1	1	4	1	4	1	4	3	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:33552091G>T	ENST00000468888.2	-	37	4346	c.4300C>A	c.(4300-4302)Cta>Ata	p.L1434I	CLASP2_ENST00000307312.7_Missense_Mutation_p.L915I|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000480013.1_Missense_Mutation_p.L1213I|CLASP2_ENST00000359576.5_Missense_Mutation_p.L1425I|CLASP2_ENST00000461133.3_Missense_Mutation_p.L1193I|CLASP2_ENST00000399362.4_Missense_Mutation_p.L1433I			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1214					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						AGCAGGTTTAGGGTTTCCTTG	0.393																																					p.L1435I		.											.	CLASP2-93	0			c.C4303A						.						195	174	181					3																	33552091		1882	4117	5999	SO:0001583	missense	23122	exon37			GGTTTAGGGTTTC	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4300C>A	3.37:g.33552091G>T	ENSP00000419974:p.Leu1434Ile	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	74	13	NM_015097	0	0	15	23	8	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.	.	.	.	.	.	.	.	.	.	G	28.7	4.942933	0.92526	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.80210	0.4581	L	0.60845	1.875	0.80722	D	1	D;P	0.71674	0.998;0.725	D;P	0.77557	0.99;0.759	T	0.74633	-0.3600	10	0.31617	T	0.26	-16.2438	20.6634	0.99662	0.0:0.0:1.0:0.0	.	1425;1433	F5H604;E7ERI8	.;.	I	1434;1433;1425;915;1213;1193	ENSP00000419974:L1434I;ENSP00000382297:L1433I;ENSP00000352581:L1425I;ENSP00000304743:L915I;ENSP00000417518:L1213I;ENSP00000419305:L1193I	ENSP00000304743:L915I	L	-	1	2	CLASP2	33527095	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	7.666000	0.83877	2.894000	0.99253	0.655000	0.94253	CTA	.		0.393	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		T	33552091	G	T	33552091	3	4	109	1	0	0	0	0	1	0	0	0	3461	991	35	4	256	4	CLASP2	3	33552091	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	5789138	33552091	164470339	21	9614											
USP19	10869	broad.mit.edu;ucsc.edu	37	chr3	49155544	49155544	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcctgggcaacatatcgaGaccctgtctctaaaaaaaaa	16	7	7	11	1	1	1	0	0	1	1	3	2	1	1	2	1	2	1	2	1	7	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:49155544G>A	ENST00000398888.2	-	3	452	c.134C>T	c.(133-135)tCt>tTt	p.S45F	USP19_ENST00000434032.2_Missense_Mutation_p.S45F|USP19_ENST00000398898.2_Intron|USP19_ENST00000453664.1_Missense_Mutation_p.S45F|USP19_ENST00000398892.3_Intron|USP19_ENST00000488993.1_5'UTR|USP19_ENST00000398896.1_5'Flank|USP19_ENST00000417901.1_Missense_Mutation_p.S45F	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	45					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		aacatatcgagaccctgtctc	0.522																																					p.S45F													.	USP19-663	0			c.C134T						.						15	15	15					3																	49155544		1908	4109	6017	SO:0001583	missense	10869	exon3			TATCGAGACCCTG	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"Zinc fingers, MYND-type", "Ubiquitin-specific peptidases"	12617	protein-coding gene	gene with protein product		614471	"ubiquitin specific protease 19"			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.134C>T	3.37:g.49155544G>A	ENSP00000381863:p.Ser45Phe	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	13	3	NM_001199160	0	0	0	0	0	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	G	8.694	0.908135	0.17833	.	.	ENSG00000172046	ENST00000417901;ENST00000453664;ENST00000398888;ENST00000434032;ENST00000306026;ENST00000425298	T;T;T;T;T	0.00648	5.99;5.99;5.99;5.99;5.99	0.418	0.418	0.16429	.	6.701840	0.01692	U	0.026694	T	0.00552	0.0018	N	0.01686	-0.76	0.09310	N	0.999998	B;B;B;B;P	0.42941	0.044;0.054;0.011;0.004;0.794	B;B;B;B;P	0.46110	0.018;0.022;0.007;0.001;0.504	T	0.43589	-0.9382	9	0.59425	D	0.04	.	.	.	.	.	108;45;45;45;45	A5PKX8;E9PEG8;E7EN22;O94966;O94966-2	.;.;.;UBP19_HUMAN;.	F	45	ENSP00000395260:S45F;ENSP00000400090:S45F;ENSP00000381863:S45F;ENSP00000401197:S45F;ENSP00000303503:S45F	ENSP00000303503:S45F	S	-	2	0	USP19	49130548	0.762000	0.28451	0.353000	0.25747	0.354000	0.29330	0.334000	0.19787	0.452000	0.26830	0.460000	0.39030	TCT	.		0.522	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		A	49155544	G	A	49155544	3	1	109	1	0	0	0	0	1	0	0	0	17083	942	33	2	3918	2	USP19	3	49155544	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	15603453	49155544	148866886	22	9615											
LAMB2	3913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49159166	49159166	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cactgcctgccgtttcttctGctgtagaggctgccagacta	6	12	10	13	1	2	2	0	0	2	2	2	2	2	2	3	1	4	4	3	1	2	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:49159166G>A	ENST00000418109.1	-	31	5215	c.5051C>T	c.(5050-5052)gCa>gTa	p.A1684V	USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.A1684V|USP19_ENST00000417901.1_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1684	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CGTTTCTTCTGCTGTAGAGGC	0.607																																					p.A1684V		.											.	LAMB2-93	0			c.C5051T						.						75	78	77					3																	49159166		2202	4300	6502	SO:0001583	missense	3913	exon30			TCTTCTGCTGTAG		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5051C>T	3.37:g.49159166G>A	ENSP00000388325:p.Ala1684Val	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	152	43	NM_002292	0	0	171	246	75	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107341	0.77096	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.38240	1.15;1.15	5.79	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	L	0.49350	1.555	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.44574	-0.9319	10	0.07325	T	0.83	.	14.8494	0.70284	0.0689:0.0:0.9311:0.0	.	1684	P55268	LAMB2_HUMAN	V	1684	ENSP00000388325:A1684V;ENSP00000307156:A1684V	ENSP00000307156:A1684V	A	-	2	0	LAMB2	49134170	1.000000	0.71417	0.027000	0.17364	0.970000	0.65996	9.339000	0.96797	1.451000	0.47736	0.655000	0.94253	GCA	.		0.607	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49159166	G	A	49159166	3	1	109	1	0	0	0	0	1	0	0	0	8632	1319	46	2	357	2	LAMB2	3	49159166	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	3622	49159166	148863264	23	9616											
ABI3BP	25890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	100593699	100593699	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttacctaattgtgtcttgAgtgcatctgaaatctcaaac	11	14	7	9	0	3	2	1	2	3	0	4	2	3	2	1	0	3	2	1	0	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:100593699A>C	ENST00000284322.5	-	9	1026	c.917T>G	c.(916-918)cTc>cGc	p.L306R	ABI3BP_ENST00000471714.1_Missense_Mutation_p.L306R|ABI3BP_ENST00000495063.1_Missense_Mutation_p.L306R	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	306					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						TTGTGTCTTGAGTGCATCTGA	0.343																																					p.L306R		.											.	ABI3BP-138	0			c.T917G						.						102	95	97					3																	100593699		1842	4085	5927	SO:0001583	missense	25890	exon9			GTCTTGAGTGCAT	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"Fibronectin type III domain containing"	17265	protein-coding gene	gene with protein product	"target of Nesh-SH3"	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.917T>G	3.37:g.100593699A>C	ENSP00000284322:p.Leu306Arg	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	14	3	NM_015429	0	0	0	0	0	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274771	0.59649	.	.	ENSG00000154175	ENST00000471714;ENST00000284322;ENST00000495063	T;T	0.24723	2.14;1.84	5.38	4.23	0.50019	.	0.912926	0.09478	N	0.796729	T	0.32406	0.0828	L	0.43152	1.355	0.80722	D	1	D;D;P	0.59767	0.971;0.986;0.814	P;P;P	0.54100	0.736;0.742;0.534	T	0.01480	-1.1344	10	0.25106	T	0.35	-1.5191	8.2196	0.31532	0.909:0.0:0.091:0.0	.	299;306;306	Q9H717;Q5JPC9;Q7Z7G0	.;.;TARSH_HUMAN	R	306	ENSP00000420524:L306R;ENSP00000284322:L306R	ENSP00000284322:L306R	L	-	2	0	ABI3BP	102076389	0.995000	0.38212	0.933000	0.37362	0.982000	0.71751	3.127000	0.50484	0.988000	0.38734	0.533000	0.62120	CTC	.		0.343	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			C	100593699	A	C	100593699	3	2	109	1	0	0	0	0	1	0	0	0	91	304	11	5	2418	5	ABI3BP	3	100593699	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	51434533	100593699	97428731	24	9617											
POLQ	10721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121260262	121260262	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaacaaagctttcttccgCatttccaaaacccgcttcaa	14	11	3	13	2	2	0	1	0	1	0	4	0	4	0	3	0	3	3	3	0	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:121260262C>A	ENST00000264233.5	-	3	536	c.408G>T	c.(406-408)atG>atT	p.M136I		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	136	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTTTCTTCCGCATTTCCAAAA	0.348								DNA polymerases (catalytic subunits)																													p.M136I	Pancreas(152;907 1925 26081 31236 36904)	.											.	POLQ-664	0			c.G408T						.						145	161	155					3																	121260262		2203	4300	6503	SO:0001583	missense	10721	exon3			CTTCCGCATTTCC	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.408G>T	3.37:g.121260262C>A	ENSP00000264233:p.Met136Ile	Somatic	335	1		WXS	Illumina HiSeq	Phase_I	296	82	NM_199420	0	0	0	0	0	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.335029	0.41398	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.40225	1.04	5.74	2.71	0.32032	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.437807	0.27891	N	0.017433	T	0.26340	0.0643	N	0.17723	0.515	0.20764	N	0.999854	B	0.29432	0.244	B	0.36030	0.216	T	0.13953	-1.0490	10	0.44086	T	0.13	.	3.6248	0.08109	0.3565:0.3671:0.2011:0.0753	.	136	O75417	DPOLQ_HUMAN	I	136;271	ENSP00000264233:M136I	ENSP00000264233:M136I	M	-	3	0	POLQ	122742952	0.754000	0.28360	0.747000	0.31113	0.988000	0.76386	-0.046000	0.11983	0.703000	0.31848	0.563000	0.77884	ATG	.		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121260262	C	A	121260262	3	1	109	1	0	0	0	0	1	0	0	0	12234	710	25	4	7476	4	POLQ	3	121260262	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	20666563	121260262	76762168	25	9618											
TMEM22	80723	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	136573495	136573495	+	Frame_Shift_Del	DEL	G	G	-																															tgagtgaaatgaaaaaaaaaGggagagctttctttggaacc																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:136573495delG	ENST00000446465.2	+	2	821	c.193delG	c.(193-195)gggfs	p.G65fs	RP11-85F14.5_ENST00000474250.1_RNA|RP11-85F14.5_ENST00000461864.1_RNA|SLC35G2_ENST00000393079.3_Frame_Shift_Del_p.G65fs|RP11-85F14.5_ENST00000470236.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2									p.G65R(1)									GAAAAAAAAAGGGAGAGCTTT	0.403																																					p.G65fs		.											.	.	1	Substitution - Missense(1)	lung(1)	c.193delG						.						84	94	91					3																	136573495		2203	4300	6503	SO:0001589	frameshift_variant	80723	exon2			.	BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"Solute carriers"	28480	protein-coding gene	gene with protein product			"transmembrane protein 22"	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.193delG	3.37:g.136573495delG	ENSP00000400839:p.Gly65fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	162	36	NM_025246	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000446465.2	37	CCDS3091.1																																																																																			.		0.403	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246		-	136573495	G	-	136573495	7	5	109	1	0	1	0	1	0	0	0	0	16175	1000	35	0	195	0	TMEM22	3	136573495	Frame_Shift_Del	DEL	G	TCGA-EV-5903-01A-11D-1589-08	15313233	136573495	61448935	26	9619											
TNFSF10	8743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	172227069	172227069	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgagctgctactctctgaGgacctctttctctcactagg	6	14	9	12	0	4	2	1	2	3	0	6	3	4	3	1	2	3	2	1	2	2	3	rs369143448		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:172227069G>C	ENST00000241261.2	-	4	478	c.356C>G	c.(355-357)cCt>cGt	p.P119R	TNFSF10_ENST00000420541.2_Intron	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	119					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			TACTCTCTGAGGACCTCTTTC	0.388																																					p.P119R		.											.	TNFSF10-662	0			c.C356G						.						105	102	103					3																	172227069		2203	4300	6503	SO:0001583	missense	8743	exon4			CTCTGAGGACCTC	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.356C>G	3.37:g.172227069G>C	ENSP00000241261:p.Pro119Arg	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	109	25	NM_003810	1	0	223	552	328	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	37	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	G	4.858	0.159457	0.09236	.	.	ENSG00000121858	ENST00000241261	D	0.86769	-2.17	4.71	-4.74	0.03249	.	1.516980	0.03189	N	0.173149	T	0.80325	0.4602	L	0.54323	1.7	0.09310	N	1	B	0.28324	0.207	B	0.23574	0.047	T	0.64097	-0.6487	10	0.08837	T	0.75	5.0717	8.19	0.31363	0.659:0.1329:0.208:0.0	.	119	P50591	TNF10_HUMAN	R	119	ENSP00000241261:P119R	ENSP00000241261:P119R	P	-	2	0	TNFSF10	173709763	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.053000	0.03500	-0.976000	0.03542	-1.113000	0.02065	CCT	.		0.388	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			C	172227069	G	C	172227069	3	2	109	1	0	0	0	0	1	0	0	0	16333	1000	35	4	497	4	TNFSF10	3	172227069	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	35653574	172227069	25795361	27	9620											
YEATS2	55689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183508727	183508727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcagcgccacgtccctcgTgcctacaccaaaccccatct	8	7	6	20	4	2	0	1	0	1	0	4	0	3	0	6	0	4	0	6	0	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:183508727T>C	ENST00000305135.5	+	21	3251	c.3056T>C	c.(3055-3057)gTg>gCg	p.V1019A		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1019					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ACGTCCCTCGTGCCTACACCA	0.532																																					p.V1019A		.											.	YEATS2-138	0			c.T3056C						.						101	111	108					3																	183508727		2042	4199	6241	SO:0001583	missense	55689	exon21			CCCTCGTGCCTAC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3056T>C	3.37:g.183508727T>C	ENSP00000306983:p.Val1019Ala	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	89	26	NM_018023	0	0	7	16	9	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447745	0.43429	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.35236	1.32	5.68	5.68	0.88126	.	0.173852	0.36591	N	0.002520	T	0.24005	0.0581	N	0.19112	0.55	0.42581	D	0.993217	P;B	0.44139	0.827;0.38	B;B	0.38264	0.269;0.098	T	0.04870	-1.0921	10	0.27082	T	0.32	-14.1917	14.1631	0.65459	0.0:0.0:0.0:1.0	.	181;1019	Q8N5H6;Q9ULM3	.;YETS2_HUMAN	A	1019	ENSP00000306983:V1019A	ENSP00000306983:V1019A	V	+	2	0	YEATS2	184991421	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	3.246000	0.51414	2.164000	0.68074	0.477000	0.44152	GTG	.		0.532	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		C	183508727	T	C	183508727	3	2	109	1	0	0	0	0	1	0	0	0	17505	1696	59	3	3134	3	YEATS2	3	183508727	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	11281658	183508727	14513703	28	9621											
FGF12	2257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	192078247	192078247	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttcgtccttggtcccatCaatggtaccatctgggtgca	6	14	10	11	1	2	0	1	0	1	0	5	0	4	0	3	3	2	3	3	3	2	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:192078247C>A	ENST00000454309.2	-	2	1105	c.280G>T	c.(280-282)Gat>Tat	p.D94Y	FGF12_ENST00000430714.1_Intron|FGF12_ENST00000445105.2_Missense_Mutation_p.D32Y|FGF12_ENST00000450716.1_Missense_Mutation_p.D32Y|FGF12_ENST00000264730.3_Missense_Mutation_p.D32Y	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	94					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		TTGGTCCCATCAATGGTACCA	0.408																																					p.D94Y		.											.	FGF12-949	0			c.G280T						.						178	150	159					3																	192078247		2203	4300	6503	SO:0001583	missense	2257	exon2			TCCCATCAATGGT	U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"fibroblast growth factor 12B", "fibroblast growth factor homologous factor 1", "myocyte-activating factor", "fibroblast growth factor FGF-12b"	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.280G>T	3.37:g.192078247C>A	ENSP00000413496:p.Asp94Tyr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	79	20	NM_021032	0	0	9	9	0	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882126	0.72294	.	.	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	T;T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39	5.53	5.53	0.82687	.	0.192095	0.56097	D	0.000035	D	0.82857	0.5128	M	0.85630	2.765	0.80722	D	1	D;D	0.62365	0.981;0.991	P;P	0.62298	0.838;0.9	D	0.85384	0.1121	10	0.72032	D	0.01	.	18.4573	0.90725	0.0:1.0:0.0:0.0	.	32;94	P61328-2;P61328	.;FGF12_HUMAN	Y	32;32;32;94;32;8;32	ENSP00000264730:D32Y;ENSP00000393686:D32Y;ENSP00000413496:D94Y;ENSP00000397635:D32Y;ENSP00000412904:D8Y;ENSP00000395517:D32Y	ENSP00000264730:D32Y	D	-	1	0	FGF12	193560941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.390000	0.59646	2.613000	0.88420	0.591000	0.81541	GAT	.		0.408	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032		A	192078247	C	A	192078247	3	1	109	1	0	0	0	0	1	0	0	0	5860	826	29	4	467	4	FGF12	3	192078247	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	8569520	192078247	5944183	29	9622											
SPON2	10417	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	1165206	1165206	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcctcgccgcgctccgcaaAgtcgcgcagcccgttactga	6	6	12	17	7	0	1	0	1	0	0	3	1	1	1	4	1	2	4	4	1	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:1165206A>T	ENST00000290902.5	-	3	621	c.289T>A	c.(289-291)Ttt>Att	p.F97I	SPON2_ENST00000431380.1_Missense_Mutation_p.F97I	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	97	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CGCTCCGCAAAGTCGCGCAGC	0.701																																					p.F97I		.											.	SPON2-90	0			c.T289A						.						26	28	27					4																	1165206		2193	4283	6476	SO:0001583	missense	10417	exon3			CCGCAAAGTCGCG	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.289T>A	4.37:g.1165206A>T	ENSP00000290902:p.Phe97Ile	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	52	8	NM_012445	0	0	136	275	139	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	37	CCDS3347.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.757899	0.69648	.	.	ENSG00000159674	ENST00000290902;ENST00000431380;ENST00000503765	T;T;T	0.44881	0.91;0.91;0.91	4.5	4.5	0.54988	Spondin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.61236	0.2331	M	0.71296	2.17	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.76071	0.987;0.955;0.967	T	0.61187	-0.7113	10	0.35671	T	0.21	.	13.4453	0.61138	1.0:0.0:0.0:0.0	.	97;97;97	D6RB12;D3DVN9;Q9BUD6	.;.;SPON2_HUMAN	I	97	ENSP00000290902:F97I;ENSP00000394832:F97I;ENSP00000424542:F97I	ENSP00000290902:F97I	F	-	1	0	SPON2	1155206	1.000000	0.71417	0.979000	0.43373	0.095000	0.18619	5.240000	0.65378	1.667000	0.50832	0.418000	0.28097	TTT	.		0.701	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			T	1165206	A	T	1165206	3	4	109	1	0	0	0	0	1	0	0	0	15115	72	3	5	722	5	SPON2	4	1165206	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08		1165206	189989070	30	9623											
KIAA1530	57654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1347115	1347115	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaggtgacccctcagatgAggacgaggacagcgacctcg	11	4	13	13	3	1	3	1	2	0	1	2	7	1	5	3	3	1	0	3	3	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:1347115A>C	ENST00000389851.4	+	5	1295	c.848A>C	c.(847-849)gAg>gCg	p.E283A	UVSSA_ENST00000511216.1_Missense_Mutation_p.E283A|UVSSA_ENST00000507531.1_Missense_Mutation_p.E283A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	283					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										CCCTCAGATGAGGACGAGGAC	0.657																																					p.E283A		.											.	.	0			c.A848C						.						17	18	18					4																	1347115		2193	4283	6476	SO:0001583	missense	57654	exon5			CAGATGAGGACGA	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"KIAA1530"	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.848A>C	4.37:g.1347115A>C	ENSP00000374501:p.Glu283Ala	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	23	6	NM_020894	0	0	1	2	1	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Missense_Mutation	SNP	ENST00000389851.4	37	CCDS33938.1	.	.	.	.	.	.	.	.	.	.	A	6.849	0.525889	0.13066	.	.	ENSG00000163945	ENST00000511216;ENST00000389851;ENST00000507531	T;T;T	0.32988	1.43;1.43;1.43	4.13	2.89	0.33648	.	0.479895	0.23176	N	0.051071	T	0.20007	0.0481	L	0.55481	1.735	0.23204	N	0.998124	B	0.30406	0.278	B	0.24974	0.057	T	0.29058	-1.0024	10	0.05721	T	0.95	.	5.9647	0.19318	0.7766:0.0:0.2234:0.0	.	283	Q2YD98	K1530_HUMAN	A	283	ENSP00000425130:E283A;ENSP00000374501:E283A;ENSP00000421741:E283A	ENSP00000374501:E283A	E	+	2	0	KIAA1530	1337115	0.933000	0.31639	0.289000	0.24876	0.208000	0.24298	3.004000	0.49513	0.438000	0.26450	0.260000	0.18958	GAG	.		0.657	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		C	1347115	A	C	1347115	3	2	109	1	0	0	0	0	1	0	0	0	8262	304	11	5	862	5	KIAA1530	4	1347115	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	181909	1347115	189807161	31	9624											
TBC1D9	23158	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	141560501	141560501	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taccacgttgcgtttcgtagTatcctccagcgtctggatca	7	13	9	12	4	2	0	1	0	1	0	5	1	4	1	3	1	3	4	3	1	3	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:141560501T>C	ENST00000442267.2	-	14	2493	c.2419A>G	c.(2419-2421)Act>Gct	p.T807A		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	807							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CGTTTCGTAGTATCCTCCAGC	0.458																																					p.T807A		.											.	TBC1D9-23	0			c.A2419G						.						88	90	89					4																	141560501		1980	4151	6131	SO:0001583	missense	23158	exon14			TCGTAGTATCCTC	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.2419A>G	4.37:g.141560501T>C	ENSP00000411197:p.Thr807Ala	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_015130	0	0	13	21	8	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.330187	0.81690	.	.	ENSG00000109436	ENST00000442267	T	0.08984	3.03	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.16685	0.0401	M	0.66939	2.045	0.80722	D	1	P	0.46656	0.882	P	0.48952	0.596	T	0.07501	-1.0769	10	0.17369	T	0.5	-9.4557	15.4755	0.75474	0.0:0.0:0.0:1.0	.	807	Q6ZT07	TBCD9_HUMAN	A	807	ENSP00000411197:T807A	ENSP00000411197:T807A	T	-	1	0	TBC1D9	141779951	1.000000	0.71417	0.880000	0.34516	0.996000	0.88848	6.093000	0.71422	2.052000	0.61016	0.533000	0.62120	ACT	.		0.458	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		C	141560501	T	C	141560501	3	2	109	1	0	0	0	0	1	0	0	0	15659	1638	57	3	1413	3	TBC1D9	4	141560501	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	140213386	141560501	49593775	32	9625											
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	155180741	155180741	+	Frame_Shift_Del	DEL	C	C	-																															ttggctttcagacactgatgCctggtaaatgctttgttcaa																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:155180741delC	ENST00000357232.4	-	20	5379	c.5380delG	c.(5380-5382)gcafs	p.A1794fs		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1794	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GACACTGATGCCTGGTAAATG	0.413																																					p.A1794fs		.											.	DCHS2-94	0			c.5380delG						.						213	191	199					4																	155180741		2203	4300	6503	SO:0001589	frameshift_variant	54798	exon20			.	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.5380delG	4.37:g.155180741delC	ENSP00000349768:p.Ala1794fs	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	205	45	NM_017639	0	0	0	0	0	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	37	CCDS3785.1																																																																																			.		0.413	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		-	155180741	C	-	155180741	7	5	109	1	0	1	0	1	0	0	0	0	4294	739	26	0	3394	0	DCHS2	4	155180741	Frame_Shift_Del	DEL	C	TCGA-EV-5903-01A-11D-1589-08	13620240	155180741	35973535	33	9626											
RGNEF	64283	broad.mit.edu;bcgsc.ca	37	chr5	73161823	73161823	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatataacaagaacaaaccaCagaccatccttggaagtaag	20	6	6	9	0	0	2	0	0	0	2	1	3	1	3	3	1	3	1	3	1	8	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:73161823C>T	ENST00000426542.2	+	17	2157	c.2137C>T	c.(2137-2139)Cag>Tag	p.Q713*	ARHGEF28_ENST00000287898.5_Nonsense_Mutation_p.Q713*|ARHGEF28_ENST00000513042.2_Nonsense_Mutation_p.Q713*|ARHGEF28_ENST00000296794.6_Nonsense_Mutation_p.Q713*|ARHGEF28_ENST00000545377.1_Nonsense_Mutation_p.Q713*|ARHGEF28_ENST00000437974.1_Nonsense_Mutation_p.Q713*|ARHGEF28_ENST00000296799.4_Nonsense_Mutation_p.Q400*			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	713					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GAACAAACCACAGACCATCCT	0.269																																					p.Q713X													.	.	0			c.C2137T						.						53	50	51					5																	73161823		1796	4050	5846	SO:0001587	stop_gained	64283	exon18			AAACCACAGACCA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2137C>T	5.37:g.73161823C>T	ENSP00000412175:p.Gln713*	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	27	4	NM_001080479	0	0	4	6	2	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Nonsense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	C	40	8.056392	0.98632	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	17.7711	0.88493	0.0:1.0:0.0:0.0	.	.	.	.	X	713;713;713;713;713;713;400	.	ENSP00000287898:Q713X	Q	+	1	0	RP11-428C6.1	73197579	0.997000	0.39634	0.994000	0.49952	0.997000	0.91878	4.306000	0.59117	2.729000	0.93468	0.655000	0.94253	CAG	.		0.269	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73161823	C	T	73161823	4	4	109	1	0	0	0	0	0	1	0	0	13315	479	17	2	2203	2	RGNEF	5	73161823	Nonsense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		73161823	107753437	34	9627											
TMEM161B	153396	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	87521633	87521633	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtttctagatgaaggtcaAtatcctttggaatggttaat	11	17	9	4	0	2	2	1	1	1	1	3	3	3	3	1	3	0	2	1	3	6	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:87521633A>G	ENST00000296595.6	-	4	366	c.242T>C	c.(241-243)aTt>aCt	p.I81T	TMEM161B_ENST00000506536.1_5'UTR|TMEM161B_ENST00000514135.1_Missense_Mutation_p.I81T|TMEM161B_ENST00000509387.1_5'UTR|TMEM161B_ENST00000512429.1_Missense_Mutation_p.I70T	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	81						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		ATGAAGGTCAATATCCTTTGG	0.299																																					p.I81T		.											.	TMEM161B-92	0			c.T242C						.						132	129	130					5																	87521633		2202	4298	6500	SO:0001583	missense	153396	exon4			AGGTCAATATCCT	BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.242T>C	5.37:g.87521633A>G	ENSP00000296595:p.Ile81Thr	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	150	30	NM_153354	0	0	2	6	4	Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	ENST00000296595.6	37	CCDS4065.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222869	0.58668	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000512429;ENST00000443393	.	.	.	5.02	5.02	0.67125	.	0.047070	0.85682	D	0.000000	T	0.55369	0.1916	L	0.44542	1.39	0.80722	D	1	B	0.15719	0.014	B	0.18871	0.023	T	0.52056	-0.8626	9	0.35671	T	0.21	-0.078	15.0267	0.71674	1.0:0.0:0.0:0.0	.	81	Q8NDZ6	T161B_HUMAN	T	81;81;70;81	.	ENSP00000296595:I81T	I	-	2	0	TMEM161B	87557389	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.804000	0.91921	2.025000	0.59659	0.383000	0.25322	ATT	.		0.299	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354		G	87521633	A	G	87521633	3	3	109	1	0	0	0	0	1	0	0	0	16109	101	4	3	1257	3	TMEM161B	5	87521633	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	14359810	87521633	93393627	35	9628											
GALNT10	55568	broad.mit.edu	37	chr5	153755873	153755873	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgaagactacatggcccTtttccccagtgtgaggattc	8	13	9	11	0	1	3	0	2	1	1	3	4	2	4	3	2	1	0	3	2	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:153755873T>C	ENST00000297107.6	+	5	742	c.605T>C	c.(604-606)cTt>cCt	p.L202P	GALNT10_ENST00000377661.2_Intron|GALNT10_ENST00000425427.2_Missense_Mutation_p.L202P|SAP30L-AS1_ENST00000519727.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	202	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TACATGGCCCTTTTCCCCAGT	0.502																																					p.L202P													.	GALNT10-92	0			c.T605C						.						137	134	135					5																	153755873		2203	4300	6503	SO:0001583	missense	55568	exon5			TGGCCCTTTTCCC	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"Glycosyltransferase family 2 domain containing"	19873	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 10"	608043	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.605T>C	5.37:g.153755873T>C	ENSP00000297107:p.Leu202Pro	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	190	4	NM_198321	0	0	23	23	0	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	T	12.77	2.036802	0.35893	.	.	ENSG00000164574	ENST00000425427;ENST00000297107	T;T	0.59772	0.24;0.24	5.98	-6.42	0.01932	Glycosyl transferase, family 2 (1);	0.438212	0.26923	N	0.021806	T	0.38904	0.1058	L	0.33710	1.025	0.09310	N	0.999996	B;B	0.30634	0.288;0.0	B;B	0.35899	0.213;0.0	T	0.37596	-0.9699	10	0.46703	T	0.11	.	8.2076	0.31465	0.5976:0.0:0.248:0.1545	.	202;202	Q86SR1;Q86SR1-3	GLT10_HUMAN;.	P	202	ENSP00000415210:L202P;ENSP00000297107:L202P	ENSP00000297107:L202P	L	+	2	0	GALNT10	153736066	0.991000	0.36638	0.165000	0.22776	0.896000	0.52359	2.523000	0.45580	-0.512000	0.06505	0.533000	0.62120	CTT	.		0.502	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		C	153755873	T	C	153755873	3	2	109	1	0	0	0	0	1	0	0	0	6228	1609	56	3	623	3	GALNT10	5	153755873	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	66234240	153755873	27159387	36	9629											
LCP2	3937	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	169724562	169724562	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaatagtcagcaaggctGtcggggtcccagcccaggac	10	7	13	11	1	1	1	1	1	0	0	3	2	2	2	2	4	2	2	2	4	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:169724562G>C	ENST00000046794.5	-	1	669	c.54C>G	c.(52-54)gaC>gaG	p.D18E		NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	18	SAM.				blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		CAGCAAGGCTGTCGGGGTCCC	0.557																																					p.D18E		.											.	LCP2-23	0			c.C54G						.						43	45	45					5																	169724562		2003	4173	6176	SO:0001583	missense	3937	exon1			AAGGCTGTCGGGG		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.54C>G	5.37:g.169724562G>C	ENSP00000046794:p.Asp18Glu	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	15	3	NM_005565	0	0	9	9	0	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361638	0.24684	.	.	ENSG00000043462	ENST00000046794	D	0.83506	-1.73	5.44	2.13	0.27403	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.236840	0.42964	D	0.000627	T	0.66809	0.2827	L	0.29908	0.895	0.80722	D	1	B	0.10296	0.003	B	0.13407	0.009	T	0.55457	-0.8138	9	.	.	.	-17.5712	3.0362	0.06123	0.2448:0.0:0.5448:0.2105	.	18	Q13094	LCP2_HUMAN	E	18	ENSP00000046794:D18E	.	D	-	3	2	LCP2	169657140	0.998000	0.40836	0.982000	0.44146	0.798000	0.45092	1.020000	0.30027	1.198000	0.43158	-0.345000	0.07892	GAC	.		0.557	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		C	169724562	G	C	169724562	3	2	109	1	0	0	0	0	1	0	0	0	8713	1368	48	4	1631	4	LCP2	5	169724562	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	15968689	169724562	11190698	37	9630											
NSD1	64324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176639042	176639042	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccttcagcaagcatactTgaggaaccactgacagagca	14	7	8	12	0	1	3	1	2	0	1	2	4	2	4	2	1	5	3	2	1	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:176639042T>C	ENST00000439151.2	+	5	3687	c.3642T>C	c.(3640-3642)ctT>ctC	p.L1214L	NSD1_ENST00000354179.4_Silent_p.L945L|NSD1_ENST00000361032.4_Silent_p.L1111L|NSD1_ENST00000347982.4_Silent_p.L945L	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1214					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CAAGCATACTTGAGGAACCAC	0.483			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.L1214L		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.T3642C						.						84	82	83					5																	176639042		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CATACTTGAGGAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3642T>C	5.37:g.176639042T>C		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	55	18	NM_022455	0	0	7	14	7	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			.		0.483	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176639042	T	C	176639042	2	2	109	1	0	0	0	0	0	0	0	1	10695	1799	63	3		3	NSD1	5	176639042	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	6914480	176639042	4276218	38	9631											
NUP153	9972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	17688708	17688708	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcatcggcatataccagatGgtcctctttattttctggcc	7	15	7	12	1	3	1	1	0	2	1	5	1	4	1	3	3	1	1	3	3	3	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:17688708G>A	ENST00000262077.2	-	2	252	c.253C>T	c.(253-255)Cat>Tat	p.H85Y	NUP153_ENST00000537253.1_Missense_Mutation_p.H85Y	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	85					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TATACCAGATGGTCCTCTTTA	0.438																																					p.H85Y		.											.	NUP153-637	0			c.C253T						.						130	123	125					6																	17688708		2203	4300	6503	SO:0001583	missense	9972	exon2			CCAGATGGTCCTC	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"nucleoporin 153kD"			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.253C>T	6.37:g.17688708G>A	ENSP00000262077:p.His85Tyr	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	128	39	NM_005124	0	0	12	20	8	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	37	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.693922	0.48202	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.08282	3.13;3.11	5.37	5.37	0.77165	.	0.125530	0.35805	N	0.002971	T	0.06600	0.0169	L	0.29908	0.895	0.42291	D	0.99213	D;B;P	0.65815	0.995;0.021;0.94	P;B;B	0.60609	0.877;0.008;0.439	T	0.06144	-1.0843	10	0.02654	T	1	-2.2032	16.8895	0.86083	0.0:0.0:1.0:0.0	.	85;107;85	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	Y	85;107;85	ENSP00000262077:H85Y;ENSP00000444029:H85Y	ENSP00000262077:H85Y	H	-	1	0	NUP153	17796687	0.927000	0.31430	0.892000	0.35008	0.127000	0.20565	4.623000	0.61247	2.494000	0.84150	0.650000	0.86243	CAT	.		0.438	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			A	17688708	G	A	17688708	3	1	109	1	0	0	0	0	1	0	0	0	10781	1348	47	2	4258	2	NUP153	6	17688708	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		17688708	153426359	39	9632											
ZNF184	7738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	27420017	27420017	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcatagggtttctccccagTatgagttttttgatgctgag	8	16	10	7	0	2	3	1	3	1	0	3	3	2	3	2	1	1	4	2	1	2	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:27420017T>C	ENST00000211936.6	-	6	1605	c.1321A>G	c.(1321-1323)Act>Gct	p.T441A	ZNF184_ENST00000377419.1_Missense_Mutation_p.T441A	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TTCTCCCCAGTATGAGTTTTT	0.403																																					p.T441A		.											.	ZNF184-91	0			c.A1321G						.						86	86	86					6																	27420017		2203	4300	6503	SO:0001583	missense	7738	exon6			CCCCAGTATGAGT	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1321A>G	6.37:g.27420017T>C	ENSP00000211936:p.Thr441Ala	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	157	49	NM_007149	0	0	5	8	3	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937528	0.73557	.	.	ENSG00000096654	ENST00000211936;ENST00000377419	T;T	0.26518	1.73;1.73	5.27	5.27	0.74061	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.130826	0.35585	N	0.003116	T	0.11367	0.0277	L	0.33624	1.015	0.42611	D	0.993316	P	0.46706	0.883	B	0.38921	0.285	T	0.03139	-1.1068	10	0.87932	D	0	.	13.1686	0.59585	0.0:0.0:0.0:1.0	.	441	Q99676	ZN184_HUMAN	A	441	ENSP00000211936:T441A;ENSP00000366636:T441A	ENSP00000211936:T441A	T	-	1	0	ZNF184	27527996	0.995000	0.38212	0.769000	0.31535	0.998000	0.95712	2.951000	0.49089	2.214000	0.71695	0.533000	0.62120	ACT	.		0.403	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		C	27420017	T	C	27420017	3	2	109	1	0	0	0	0	1	0	0	0	17783	1638	57	3	938	3	ZNF184	6	27420017	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	9731309	27420017	143695050	40	9633											
RGL2	5863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33260849	33260849	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccatctggactcggatgaTacggcaatcagaggcccctg	9	8	11	13	2	2	2	1	1	1	1	4	4	3	4	3	4	1	1	3	4	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:33260849T>C	ENST00000497454.1	-	16	2446	c.1951A>G	c.(1951-1953)Atc>Gtc	p.I651V	RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	651	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						ACTCGGATGATACGGCAATCA	0.597																																					p.I651V		.											.	RGL2-662	0			c.A1951G						.						202	229	220					6																	33260849		2203	4300	6503	SO:0001583	missense	5863	exon16			GGATGATACGGCA		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.1951A>G	6.37:g.33260849T>C	ENSP00000420211:p.Ile651Val	Somatic	409	0		WXS	Illumina HiSeq	Phase_I	440	148	NM_004761	0	0	18	30	12	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	37	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650468	0.47362	.	.	ENSG00000237441	ENST00000497454;ENST00000421215	T	0.49139	0.79	4.6	4.6	0.57074	Ras-association (3);	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.40543	1.245	0.80722	D	1	D	0.58620	0.983	D	0.73708	0.981	T	0.45131	-0.9282	10	0.42905	T	0.14	.	10.3298	0.43816	0.0:0.0:0.0:1.0	.	651	O15211	RGL2_HUMAN	V	651;515	ENSP00000420211:I651V	ENSP00000400083:I515V	I	-	1	0	RGL2	33368827	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.349000	0.66010	1.937000	0.56155	0.523000	0.50628	ATC	.		0.597	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			C	33260849	T	C	33260849	3	2	109	1	0	0	0	0	1	0	0	0	13309	1406	49	3	394	3	RGL2	6	33260849	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	5840832	33260849	137854218	41	9634											
NUDT3	11165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	34309651	34309651	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcatacctcctcacagacTtcacgaactgctgccacact	11	9	5	16	1	2	1	2	0	0	1	3	2	3	1	3	0	5	2	3	0	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:34309651T>G	ENST00000607016.1	-	2	509	c.198A>C	c.(196-198)gaA>gaC	p.E66D	RPS10-NUDT3_ENST00000605528.1_Missense_Mutation_p.E185D	NM_006703.3	NP_006694.1	O95989	NUDT3_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 3	66	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cell-cell signaling (GO:0007267)|diadenosine polyphosphate catabolic process (GO:0015961)|diphosphoinositol polyphosphate catabolic process (GO:0071544)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|magnesium ion binding (GO:0000287)			lung(2)	2						CCTCACAGACTTCACGAACTG	0.532																																					p.E185D	GBM(96;1206 1939 18658 39482)	.											.	.	0			c.A555C						.						155	119	131					6																	34309651		2203	4300	6503	SO:0001583	missense	0	exon6			ACAGACTTCACGA	AF062530	CCDS4791.1	6p21.2	2014-07-16			ENSG00000272325	ENSG00000272325		"Nudix motif containing"	8050	protein-coding gene	gene with protein product		609228				9822604	Standard	NM_006703		Approved	DIPP		O95989	OTTHUMG00000014545	ENST00000607016.1:c.198A>C	6.37:g.34309651T>G	ENSP00000476119:p.Glu66Asp	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	56	12	NM_001202470	0	0	0	3	3	B2R8N4	Missense_Mutation	SNP	ENST00000607016.1	37	CCDS4791.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.725873	0.89298	.	.	ENSG00000112664	ENST00000358797	T	0.29917	1.55	5.66	4.5	0.54988	NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	H	0.99415	4.555	0.80722	D	1	P	0.48589	0.912	D	0.75020	0.985	T	0.76889	-0.2792	10	0.87932	D	0	-14.5823	10.5134	0.44874	0.0:0.0772:0.0:0.9228	.	66	O95989	NUDT3_HUMAN	D	66	ENSP00000351650:E66D	ENSP00000351650:E66D	E	-	3	2	NUDT3	34417629	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.537000	0.45702	0.989000	0.38761	0.477000	0.44152	GAA	.		0.532	NUDT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040224.2			G	34309651	T	G	34309651	3	3	109	1	0	0	0	0	1	0	0	0	10766	1606	56	5	336	5	NUDT3	6	34309651	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	1048802	34309651	136805416	42	9635											
ENPP4	22875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	46108114	46108114	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactacactcttatagattTgagcccagttgctgcaatac	12	13	6	10	0	1	2	0	1	1	1	1	2	1	2	1	0	6	3	1	0	6	7			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:46108114T>G	ENST00000321037.4	+	2	1024	c.794T>G	c.(793-795)tTg>tGg	p.L265W		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	265					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						CTTATAGATTTGAGCCCAGTT	0.418																																					p.L265W		.											.	ENPP4-94	0			c.T794G						.						79	78	79					6																	46108114		2203	4300	6503	SO:0001583	missense	22875	exon2			TAGATTTGAGCCC	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.794T>G	6.37:g.46108114T>G	ENSP00000318066:p.Leu265Trp	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	66	16	NM_014936	0	0	15	27	12	A8K5G1|Q7L2N1	Missense_Mutation	SNP	ENST00000321037.4	37	CCDS34468.1	.	.	.	.	.	.	.	.	.	.	T	9.575	1.121947	0.20877	.	.	ENSG00000001561	ENST00000321037;ENST00000371401	T	0.72394	-0.65	5.67	1.87	0.25490	Alkaline-phosphatase-like, core domain (1);	0.743246	0.13551	N	0.379453	T	0.33411	0.0862	L	0.41710	1.295	0.24368	N	0.994846	B	0.14438	0.01	B	0.21917	0.037	T	0.20240	-1.0281	10	0.37606	T	0.19	-1.2896	0.3197	0.00301	0.2449:0.1895:0.2931:0.2725	.	265	Q9Y6X5	ENPP4_HUMAN	W	265	ENSP00000318066:L265W	ENSP00000318066:L265W	L	+	2	0	ENPP4	46216073	0.000000	0.05858	0.992000	0.48379	0.972000	0.66771	-0.065000	0.11617	0.400000	0.25396	0.533000	0.62120	TTG	.		0.418	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2			G	46108114	T	G	46108114	3	3	109	1	0	0	0	0	1	0	0	0	5145	1821	63	5	796	5	ENPP4	6	46108114	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	11798463	46108114	125006953	43	9636											
DOPEY1	23033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	83862020	83862020	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttatagatatgttatcaccTgcaatggaaaccgcaaacat	15	12	6	8	1	1	1	1	0	0	1	1	2	1	2	2	1	3	3	2	1	7	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:83862020T>A	ENST00000349129.2	+	30	6323	c.6063T>A	c.(6061-6063)ccT>ccA	p.P2021P	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000237163.5_Intron|DOPEY1_ENST00000369739.3_Silent_p.P2012P	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2021					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TGTTATCACCTGCAATGGAAA	0.313																																					p.P2021P		.											.	DOPEY1-155	0			c.T6063A						.						59	59	59					6																	83862020		2203	4292	6495	SO:0001819	synonymous_variant	23033	exon30			ATCACCTGCAATG	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"KIAA1117"	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6063T>A	6.37:g.83862020T>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	55	17	NM_015018	0	0	4	7	3	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																			.		0.313	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		A	83862020	T	A	83862020	2	1	109	1	0	0	0	0	0	0	0	1	4718	1567	55	5		5	DOPEY1	6	83862020	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	37753906	83862020	87253047	44	9637											
CDC40	51362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	110528715	110528715	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttttgctttcaggttatgCattagacccttcattagata	9	19	6	7	0	2	2	2	0	0	2	2	2	2	2	1	1	2	3	1	1	4	9			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:110528715C>T	ENST00000368932.1	+	5	514	c.413C>T	c.(412-414)gCa>gTa	p.A138V	CDC40_ENST00000368930.1_Missense_Mutation_p.A138V|CDC40_ENST00000307731.1_Missense_Mutation_p.A138V			O60508	PRP17_HUMAN	cell division cycle 40	138					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		TCAGGTTATGCATTAGACCCT	0.249																																					p.A138V		.											.	CDC40-90	0			c.C413T						.						98	107	104					6																	110528715		2203	4295	6498	SO:0001583	missense	51362	exon4			GTTATGCATTAGA	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.413C>T	6.37:g.110528715C>T	ENSP00000357928:p.Ala138Val	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	176	50	NM_015891	0	0	0	0	0	B2RBC5|O75471|Q5SRN0|Q9UPG1	Missense_Mutation	SNP	ENST00000368932.1	37	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	C	34	5.333199	0.95758	.	.	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731;ENST00000439165;ENST00000453107	T;T;T;T	0.67171	-0.09;-0.25;-0.25;-0.09	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.79405	0.4440	M	0.86805	2.84	0.80722	D	1	D	0.67145	0.996	P	0.55965	0.788	T	0.82794	-0.0281	10	0.87932	D	0	-9.413	19.9384	0.97150	0.0:1.0:0.0:0.0	.	138	O60508	PRP17_HUMAN	V	138;138;138;138;138;35	ENSP00000357928:A138V;ENSP00000357929:A138V;ENSP00000357926:A138V;ENSP00000304370:A138V	ENSP00000304370:A138V	A	+	2	0	CDC40	110635408	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.252000	0.78309	2.717000	0.92951	0.585000	0.79938	GCA	.		0.249	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		T	110528715	C	T	110528715	3	4	109	1	0	0	0	0	1	0	0	0	3076	710	25	2	427	2	CDC40	6	110528715	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	26666695	110528715	60586352	45	9638											
SLC16A10	117247	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	111409219	111409219	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcggtgttcggcatccaGaacgcttgcggggtgctctt	4	11	16	10	4	1	1	0	0	1	1	4	1	2	1	1	5	3	4	1	5	1	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:111409219G>T	ENST00000368851.5	+	1	439	c.264G>T	c.(262-264)caG>caT	p.Q88H		NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	88					amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	TCGGCATCCAGAACGCTTGCG	0.662																																					p.Q88H		.											.	SLC16A10-514	0			c.G264T						.						51	41	44					6																	111409219		2203	4299	6502	SO:0001583	missense	117247	exon1			CATCCAGAACGCT	AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394		"Solute carriers"	17027	protein-coding gene	gene with protein product		607550	"solute carrier family 16 (monocarboxylic acid transporters), member 10"			11278508, 11827462	Standard	NM_018593		Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.264G>T	6.37:g.111409219G>T	ENSP00000357844:p.Gln88His	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	44	10	NM_018593	0	0	0	0	0	B3KWY0|Q6ZMG0|Q8WVI5	Missense_Mutation	SNP	ENST00000368851.5	37	CCDS5089.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846966	0.71603	.	.	ENSG00000112394	ENST00000535637;ENST00000368851	T	0.59364	0.27	3.79	3.79	0.43588	Major facilitator superfamily domain, general substrate transporter (1);	0.071282	0.64402	D	0.000016	T	0.33876	0.0878	N	0.13235	0.315	0.80722	D	1	P;B	0.42375	0.778;0.339	P;B	0.44647	0.456;0.134	T	0.37526	-0.9702	10	0.44086	T	0.13	.	15.8498	0.78921	0.0:0.0:1.0:0.0	.	88;88	Q8TF71;Q05BR4	MOT10_HUMAN;.	H	88	ENSP00000357844:Q88H	ENSP00000357844:Q88H	Q	+	3	2	SLC16A10	111515912	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.303000	0.89955	1.950000	0.56595	0.448000	0.29417	CAG	.		0.662	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2			T	111409219	G	T	111409219	3	4	109	1	0	0	0	0	1	0	0	0	14435	933	33	4	266	4	SLC16A10	6	111409219	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	880504	111409219	59705848	46	9639											
MAP7	9053	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	136693761	136693761	+	Frame_Shift_Del	DEL	A	A	-																															catgatgatggggctgcaagAtgctgaacgaggacaaatgg																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:136693761delA	ENST00000354570.3	-	8	1164	c.754delT	c.(754-756)tctfs	p.S252fs	MAP7_ENST00000438100.2_Frame_Shift_Del_p.S237fs|MAP7_ENST00000544465.1_Frame_Shift_Del_p.S237fs|MAP7_ENST00000432797.2_Frame_Shift_Del_p.S106fs|MAP7_ENST00000454590.1_Frame_Shift_Del_p.S274fs	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	252					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		GGGCTGCAAGATGCTGAACGA	0.488																																					p.S282fs		.											.	MAP7-90	0			c.844delT						.						175	153	161					6																	136693761		2203	4300	6503	SO:0001589	frameshift_variant	9053	exon8			.	X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.754delT	6.37:g.136693761delA	ENSP00000346581:p.Ser252fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	116	24	NM_001198609	0	0	0	0	0	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Frame_Shift_Del	DEL	ENST00000354570.3	37	CCDS5178.1																																																																																			.		0.488	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		-	136693761	A	-	136693761	7	5	109	1	0	1	0	1	0	0	0	0	9291	333	12	0	1539	0	MAP7	6	136693761	Frame_Shift_Del	DEL	A	TCGA-EV-5903-01A-11D-1589-08	25284542	136693761	34421306	47	9640											
SHPRH	257218	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	146264642	146264642	+	Frame_Shift_Del	DEL	T	T	-																															cagtcctctgtttcatgttcTtggttgaattcagagataca																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:146264642delT	ENST00000367505.2	-	9	2139	c.1875delA	c.(1873-1875)caafs	p.Q625fs	SHPRH_ENST00000367503.3_Frame_Shift_Del_p.Q625fs|SHPRH_ENST00000275233.7_Frame_Shift_Del_p.Q625fs|SHPRH_ENST00000438092.2_Frame_Shift_Del_p.Q625fs			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	625					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TTTCATGTTCTTGGTTGAATT	0.408																																					p.Q625fs		.											.	SHPRH-92	0			c.1875delA						.						196	183	187					6																	146264642		1952	4153	6105	SO:0001589	frameshift_variant	257218	exon9			.	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"RING-type (C3HC4) zinc fingers"	19336	protein-coding gene	gene with protein product		608048	"SNF2 histone linker PHD RING helicase"			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1875delA	6.37:g.146264642delT	ENSP00000356475:p.Gln625fs	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	234	64	NM_173082	0	0	0	0	0	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Frame_Shift_Del	DEL	ENST00000367505.2	37	CCDS43513.2																																																																																			.		0.408	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		-	146264642	T	-	146264642	7	5	109	1	0	1	0	1	0	0	0	0	14323	1606	56	0	3308	0	SHPRH	6	146264642	Frame_Shift_Del	DEL	T	TCGA-EV-5903-01A-11D-1589-08	9570881	146264642	24850425	48	9641											
C7orf27	221927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	2587034	2587034	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaggagaggaccccagaaCtcaggtcctggactttcagc	12	6	12	11	0	2	3	2	0	0	3	3	6	3	5	3	4	2	0	3	4	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:2587034C>G	ENST00000340611.4	-	3	462	c.206G>C	c.(205-207)aGt>aCt	p.S69T		NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	69					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						GACCCCAGAACTCAGGTCCTG	0.622																																					p.S69T		.											.	BRAT1-229	0			c.G206C						.						85	79	81					7																	2587034		2203	4300	6503	SO:0001583	missense	221927	exon3			CCAGAACTCAGGT	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"BRCA1-associated protein required for ATM activation protein 1"	614506	"chromosome 7 open reading frame 27"	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.206G>C	7.37:g.2587034C>G	ENSP00000339637:p.Ser69Thr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	108	49	NM_152743	0	0	28	59	31	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	C	9.253	1.041205	0.19669	.	.	ENSG00000106009	ENST00000340611	T	0.71103	-0.54	5.01	4.11	0.48088	Armadillo-type fold (1);	0.211492	0.47093	D	0.000255	T	0.68091	0.2963	M	0.72118	2.19	0.09310	N	1	B;P	0.46987	0.184;0.888	B;B	0.42163	0.208;0.378	T	0.66705	-0.5856	10	0.59425	D	0.04	-13.2539	9.9258	0.41492	0.0:0.8427:0.0:0.1573	.	69;69	Q6PJG6-2;Q6PJG6	.;BRAT1_HUMAN	T	69	ENSP00000339637:S69T	ENSP00000339637:S69T	S	-	2	0	BRAT1	2553560	0.000000	0.05858	0.026000	0.17262	0.004000	0.04260	0.191000	0.17076	2.331000	0.79229	0.650000	0.86243	AGT	.		0.622	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		G	2587034	C	G	2587034	3	3	109	1	0	0	0	0	1	0	0	0	2388	565	20	4	2307	4	C7orf27	7	2587034	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		2587034	156551629	49	9642											
SCIN	85477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	12679988	12679988	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagatccgagtctcccaagGcaaagagcctgttcacctac	11	8	8	14	1	3	2	2	0	1	2	5	3	4	2	4	1	2	2	4	1	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:12679988G>A	ENST00000297029.5	+	11	1528	c.1427G>A	c.(1426-1428)gGc>gAc	p.G476D	SCIN_ENST00000519209.1_Missense_Mutation_p.G229D|SCIN_ENST00000445618.2_Missense_Mutation_p.G229D	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	476	Ca(2+)-dependent actin binding.			G -> D (in Ref. 1; AAK60494). {ECO:0000305}.	actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GTCTCCCAAGGCAAAGAGCCT	0.428																																					p.G476D		.											.	SCIN-24	0			c.G1427A						.						54	52	53					7																	12679988		1843	4090	5933	SO:0001583	missense	85477	exon11			CCCAAGGCAAAGA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1427G>A	7.37:g.12679988G>A	ENSP00000297029:p.Gly476Asp	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	91	38	NM_001112706	0	0	148	362	214	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435588	0.83885	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.27256	1.68;1.68;1.68	4.56	4.56	0.56223	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69807	-0.5045	10	0.87932	D	0	-12.3981	17.3228	0.87240	0.0:0.0:1.0:0.0	.	476	Q9Y6U3	ADSV_HUMAN	D	476;229;229	ENSP00000297029:G476D;ENSP00000430997:G229D;ENSP00000390189:G229D	ENSP00000297029:G476D	G	+	2	0	SCIN	12646513	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.476000	0.97823	2.069000	0.61940	0.561000	0.74099	GGC	.		0.428	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		A	12679988	G	A	12679988	3	1	109	1	0	0	0	0	1	0	0	0	13937	1203	42	2	1469	2	SCIN	7	12679988	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	10092954	12679988	146458675	50	9643											
DNAH11	8701	ucsc.edu;bcgsc.ca	37	chr7	21784089	21784089	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttctcctgagtgtttaaaaGgtccacttgatttaatacat	11	16	6	8	0	1	2	0	2	1	0	3	2	2	2	2	1	1	1	2	1	4	7	rs28549882	byFrequency	TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:21784089G>A	ENST00000409508.3	+	50	8219	c.8188G>A	c.(8188-8190)Ggt>Agt	p.G2730S	DNAH11_ENST00000328843.6_Missense_Mutation_p.G2737S	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2737					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GTGTTTAAAAGGTCCACTTGA	0.363									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						246	238	241					7																	21784089		1834	4086	5920	SO:0001583	missense	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TTAAAAGGTCCAC	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.8188G>A	7.37:g.21784089G>A	ENSP00000475939:p.Gly2730Ser	Somatic	328	0		WXS	Illumina HiSeq		513	156	.	0	0	0	0	0	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	0.044	-1.273480	0.01421	.	.	ENSG00000105877	ENST00000328843	T	0.37235	1.21	5.91	0.806	0.18708	.	1.549630	0.03077	N	0.158047	T	0.14485	0.0350	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.17868	-1.0355	9	0.05959	T	0.93	.	1.7176	0.02905	0.142:0.2088:0.3289:0.3203	.	2737	Q96DT5	DYH11_HUMAN	S	2737	ENSP00000330671:G2737S	ENSP00000330671:G2737S	G	+	1	0	DNAH11	21750614	0.003000	0.15002	0.005000	0.12908	0.289000	0.27227	0.518000	0.22847	-0.133000	0.11537	-0.140000	0.14226	GGT	G|0.995;T|0.005		0.363	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21784089	G	A	21784089	3	1	109	1	0	0	0	0	1	0	0	0	4610	1000	35	2	8408	2	DNAH11	7	21784089	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	9104101	21784089	137354574	51	9644											
FBXO24	26261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100187679	100187679	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaaatccgatttccatccAgttgttccccccagagctgg	9	10	9	13	1	0	1	0	0	0	1	4	3	4	2	6	2	1	3	6	2	1	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:100187679A>C	ENST00000241071.6	+	2	441	c.119A>C	c.(118-120)cAg>cCg	p.Q40P	FBXO24_ENST00000427939.2_Missense_Mutation_p.Q78P|FBXO24_ENST00000468962.1_Missense_Mutation_p.Q28P|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000465843.1_Missense_Mutation_p.Q40P|PCOLCE-AS1_ENST00000442166.2_RNA|FBXO24_ENST00000360609.2_Missense_Mutation_p.Q40P|FBXO24_ENST00000498195.1_3'UTR	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	40	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					ATTTCCATCCAGTTGTTCCCC	0.557																																					p.Q78P		.											.	FBXO24-229	0			c.A233C						.						72	68	69					7																	100187679		2203	4300	6503	SO:0001583	missense	26261	exon2			CCATCCAGTTGTT	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"F-boxes /  "other""	13595	protein-coding gene	gene with protein product		609097	"F-box only protein 24"			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.119A>C	7.37:g.100187679A>C	ENSP00000241071:p.Gln40Pro	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	153	54	NM_012172	0	0	0	0	0	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.038493	0.55003	.	.	ENSG00000106336	ENST00000461079;ENST00000241071;ENST00000360609;ENST00000465843;ENST00000466053;ENST00000468962;ENST00000427939	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.67	4.67	0.58626	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.000000	0.48767	D	0.000177	T	0.45034	0.1322	N	0.03194	-0.395	0.38008	D	0.93445	D;D;D;P	0.67145	0.996;0.996;0.996;0.952	P;P;P;P	0.62089	0.898;0.898;0.898;0.536	T	0.59815	-0.7383	10	0.87932	D	0	-5.3735	10.4753	0.44661	1.0:0.0:0.0:0.0	.	28;78;40;40	B4DY42;B4DX91;O75426;O75426-2	.;.;FBX24_HUMAN;.	P	63;40;40;40;45;28;78	ENSP00000419587:Q63P;ENSP00000241071:Q40P;ENSP00000353821:Q40P;ENSP00000419602:Q40P;ENSP00000417179:Q45P;ENSP00000420239:Q28P;ENSP00000416558:Q78P	ENSP00000241071:Q40P	Q	+	2	0	FBXO24	100025615	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.861000	0.62969	1.968000	0.57251	0.449000	0.29647	CAG	.		0.557	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			C	100187679	A	C	100187679	3	2	109	1	0	0	0	0	1	0	0	0	5754	188	7	5	282	5	FBXO24	7	100187679	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	78403590	100187679	58950984	52	9645											
IMMP2L	83943	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	111127299	111127299	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgagttacttacaccaaTgatacaatgtcaccacggtg	12	12	7	10	1	2	2	1	2	1	0	2	2	2	2	2	1	3	1	2	1	5	4	rs201012120		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:111127299T>A	ENST00000405709.2	-	3	676	c.234A>T	c.(232-234)tcA>tcT	p.S78S	IMMP2L_ENST00000415362.1_Silent_p.S78S|IMMP2L_ENST00000331762.3_Silent_p.S78S|IMMP2L_ENST00000452895.1_Silent_p.S78S|IMMP2L_ENST00000437687.1_Silent_p.S78S|IMMP2L_ENST00000447215.1_Silent_p.S78S	NM_032549.3	NP_115938.1	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	78					ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|protein processing involved in protein targeting to mitochondrion (GO:0006627)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial inner membrane peptidase complex (GO:0042720)	peptidase activity (GO:0008233)|serine-type peptidase activity (GO:0008236)			endometrium(3)|large_intestine(6)|lung(5)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		CTTACACCAATGATACAATGT	0.363																																					p.S78S		.											.	IMMP2L-93	0			c.A234T						.						102	99	100					7																	111127299		2203	4300	6503	SO:0001819	synonymous_variant	83943	exon3			CACCAATGATACA	AF359563	CCDS5753.1	7q31	2014-01-06	2005-08-17		ENSG00000184903	ENSG00000184903			14598	protein-coding gene	gene with protein product		605977	"IMP2 inner mitochondrial membrane protease-like (S. cerevisiae)", "IMMP2L intronic transcript 1 (non-protein coding)"	IMMP2L-IT1		11254443	Standard	NM_032549		Approved	IMP2	uc010ljr.2	Q96T52	OTTHUMG00000155023	ENST00000405709.2:c.234A>T	7.37:g.111127299T>A		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	208	67	NM_032549	0	0	0	0	0	Q75MF1|Q75MN9|Q75MP0|Q75MS5|Q75MS8|Q96HJ2	Silent	SNP	ENST00000405709.2	37	CCDS5753.1																																																																																			T|1.000;C|0.000		0.363	IMMP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338109.4	NM_032549		A	111127299	T	A	111127299	2	1	109	1	0	0	0	0	0	0	0	1	7738	1451	51	5		5	IMMP2L	7	111127299	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	10939620	111127299	48011364	53	9646											
SSPO	23145	hgsc.bcm.edu;broad.mit.edu	37	chr7	149509420	149509420	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagctgtgggggaggcctgcGgagccggacccgggcctgtg	4	5	21	11	3	0	0	0	0	0	0	0	4	0	3	4	6	3	1	4	6	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:149509420G>A	ENST00000378016.2	+	0	9818							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGAGGCCTGCGGAGCCGGACC	0.726																																					p.R3273Q		.											.	.	0			c.G9818A						.						6	7	7					7																	149509420		1692	3840	5532			23145	exon69			GCCTGCGGAGCCG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149509420G>A		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	21	5	NM_198455	0	0	0	0	0	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.		0.726	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149509420	G	A	149509420	1	1	109	0	1	0	0	0	0	0	0	0	15221	1116	39	1		1	SSPO	7	149509420	RNA	SNP	G	TCGA-EV-5903-01A-11D-1589-08	38382121	149509420	9629243	54	9647											
ATP6V1B2	526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	20068802	20068802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcagaaaattcctatcttctCtgctgctgggctaccacaca	10	11	7	13	0	2	1	0	0	2	1	4	1	3	1	2	1	3	4	2	1	4	4	rs374210970		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:20068802C>T	ENST00000276390.2	+	6	618	c.578C>T	c.(577-579)tCt>tTt	p.S193F		NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2	193					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|ruffle (GO:0001726)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)	Gallium nitrate(DB05260)	CCTATCTTCTCTGCTGCTGGG	0.453																																					p.S193F	Pancreas(119;1230 1726 3901 4036 31644)	.											.	ATP6V1B2-90	0			c.C578T						.						110	98	102					8																	20068802		2203	4300	6503	SO:0001583	missense	526	exon6			TCTTCTCTGCTGC	L35249	CCDS6014.1	8p21.3	2010-04-21	2006-01-13	2002-05-10	ENSG00000147416	ENSG00000147416	3.6.3.14	"ATPases / V-type"	854	protein-coding gene	gene with protein product		606939	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58kD, isoform 2", "ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2"	VPP3, ATP6B2		2145275, 14580332	Standard	NM_001693		Approved	VATB, Vma2, HO57	uc003wzp.3	P21281	OTTHUMG00000131073	ENST00000276390.2:c.578C>T	8.37:g.20068802C>T	ENSP00000276390:p.Ser193Phe	Somatic	64	1		WXS	Illumina HiSeq	Phase_I	87	30	NM_001693	0	0	83	118	35	B2R5Z3|D3DSQ5|Q14544|Q15859|Q96IR0	Missense_Mutation	SNP	ENST00000276390.2	37	CCDS6014.1	.	.	.	.	.	.	.	.	.	.	C	33	5.203929	0.95033	.	.	ENSG00000147416	ENST00000276390;ENST00000542368	D	0.83250	-1.7	5.65	5.65	0.86999	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.097834	0.64402	D	0.000001	D	0.92519	0.7624	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93134	0.6535	10	0.87932	D	0	-15.587	18.6584	0.91463	0.0:1.0:0.0:0.0	.	193	P21281	VATB2_HUMAN	F	193;67	ENSP00000276390:S193F	ENSP00000276390:S193F	S	+	2	0	ATP6V1B2	20113082	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.040000	0.70980	2.822000	0.97130	0.650000	0.86243	TCT	.		0.453	ATP6V1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253732.1	NM_001693		T	20068802	C	T	20068802	3	4	109	1	0	0	0	0	1	0	0	0	1180	913	32	2	600	2	ATP6V1B2	8	20068802	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		20068802	126295220	55	9648											
SFTPC	649	bcgsc.ca	37	chr8	22020986	22020986	+	5'Flank	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccagcccctggcacctgctGctacatcatgaagatagctc	9	8	9	15	0	1	2	1	1	0	1	2	2	1	2	4	1	5	4	4	1	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:22020986G>T	ENST00000306385.5	+	0	0				SFTPC_ENST00000521315.1_Missense_Mutation_p.C121F|BMP1_ENST00000397816.3_5'Flank|SFTPC_ENST00000318561.3_Missense_Mutation_p.C121F|BMP1_ENST00000306349.8_5'Flank|SFTPC_ENST00000524255.1_Missense_Mutation_p.C68F|BMP1_ENST00000354870.5_5'Flank|SFTPC_ENST00000520605.1_Missense_Mutation_p.C68F|SFTPC_ENST00000437090.2_Missense_Mutation_p.C121F|SFTPC_ENST00000522109.1_Missense_Mutation_p.C121F|BMP1_ENST00000397814.3_5'Flank	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GGCACCTGCTGCTACATCATG	0.562																																					p.C121F													.	SFTPC-90	0			c.G362T						.						71	74	73					8																	22020986		1951	4169	6120	SO:0001631	upstream_gene_variant	6440	exon4			CCTGCTGCTACAT		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761		8.37:g.22020986G>T	Exception_encountered	Somatic	40	0		WXS	Illumina HiSeq	Phase_1	44	4	NM_003018	0	0	0	0	0	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.197672	0.79015	.	.	ENSG00000168484	ENST00000318561;ENST00000521315;ENST00000437090;ENST00000520605;ENST00000522109;ENST00000524255;ENST00000523296	D;D;D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98	5.49	5.49	0.81192	BRICHOS (2);	0.000000	0.56097	D	0.000026	D	0.98682	0.9558	M	0.74881	2.28	0.49130	D	0.99975	D;D;D;D	0.76494	0.999;0.996;0.999;0.984	D;P;D;P	0.70716	0.97;0.908;0.97;0.876	D	0.99490	1.0950	10	0.87932	D	0	-27.3137	14.864	0.70401	0.0:0.0:1.0:0.0	.	121;121;121;121	E9PGX3;C9JYF6;P11686;E5RI92	.;.;PSPC_HUMAN;.	F	121;121;121;68;121;68;68	ENSP00000316152:C121F;ENSP00000430410:C121F;ENSP00000407931:C121F;ENSP00000430266:C68F;ENSP00000429496:C121F;ENSP00000429552:C68F;ENSP00000429619:C68F	ENSP00000316152:C121F	C	+	2	0	SFTPC	22076931	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.426000	0.66476	2.570000	0.86706	0.655000	0.94253	TGC	.		0.562	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		T	22020986	G	T	22020986	1	4	109	0	1	0	0	0	0	0	0	0	14224	1319	46	4		4	SFTPC	8	22020986	5'Flank	SNP	G	TCGA-EV-5903-01A-11D-1589-08	1952184	22020986	124343036	56	9649											
PROSC	11212	broad.mit.edu	37	chr8	37630321	37630321	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggattctgtgaagttggCagacaaagtgaacagttcct	12	11	12	6	0	1	3	0	2	1	1	2	4	2	4	1	2	1	3	1	2	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:37630321C>T	ENST00000328195.3	+	5	435	c.368C>T	c.(367-369)gCa>gTa	p.A123V		NM_007198.3	NP_009129.1	O94903	PROSC_HUMAN	proline synthetase co-transcribed homolog (bacterial)	123					alpha-amino acid metabolic process (GO:1901605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)	pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		L-Proline(DB00172)	GTGAAGTTGGCAGACAAAGTG	0.438																																					p.A123V													.	PROSC-90	0			c.C368T						.						128	121	123					8																	37630321		2203	4300	6503	SO:0001583	missense	11212	exon5			AGTTGGCAGACAA	AB018566	CCDS6096.1	8p11.2	2008-01-07	2001-12-04		ENSG00000147471	ENSG00000147471			9457	protein-coding gene	gene with protein product		604436	"proline synthetase co-transcribed (bacterial homolog)"				Standard	NM_007198		Approved		uc003xkh.3	O94903	OTTHUMG00000164024	ENST00000328195.3:c.368C>T	8.37:g.37630321C>T	ENSP00000333551:p.Ala123Val	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	137	4	NM_007198	0	0	79	79	0	Q6FI94	Missense_Mutation	SNP	ENST00000328195.3	37	CCDS6096.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.544535|5.544535	0.96488|0.96488	.|.	.|.	ENSG00000147471|ENSG00000147471	ENST00000328195;ENST00000523358;ENST00000523187;ENST00000523521|ENST00000521494	T;T;T;T|.	0.52526|.	0.66;0.66;0.66;0.66|.	5.96|5.96	5.96|5.96	0.96718|0.96718	Alanine racemase, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.83482|.	0.5264|.	M|M	0.84433|0.84433	2.695|2.695	0.80722|0.80722	D|D	1|1	D|.	0.60575|.	0.988|.	D|.	0.75484|.	0.986|.	D|.	0.83718|.	0.0191|.	10|.	0.87932|.	D|.	0|.	-23.3919|-23.3919	20.017|20.017	0.97481|0.97481	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	123|.	O94903|.	PROSC_HUMAN|.	V|X	123;123;71;42|92	ENSP00000333551:A123V;ENSP00000427778:A123V;ENSP00000427886:A71V;ENSP00000429425:A42V|.	ENSP00000333551:A123V|.	A|Q	+|+	2|1	0|0	PROSC|PROSC	37749479|37749479	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.905000|0.905000	0.53344|0.53344	7.743000|7.743000	0.85020|0.85020	2.832000|2.832000	0.97577|0.97577	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.		0.438	PROSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376796.1	NM_007198		T	37630321	C	T	37630321	3	4	109	1	0	0	0	0	1	0	0	0	12588	710	25	2	386	2	PROSC	8	37630321	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	15609335	37630321	108733701	57	9650											
RRS1	23212	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	67342373	67342373	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccagggagggaagaggaaagGgggcttgggaggcaagatga	13	3	21	4	0	0	3	0	1	0	2	0	7	0	7	1	7	0	2	1	7	3	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:67342373G>A	ENST00000320270.2	+	1	1111	c.1007G>A	c.(1006-1008)gGg>gAg	p.G336E	RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000396623.3_5'Flank|ADHFE1_ENST00000379385.4_5'Flank|ADHFE1_ENST00000415254.1_5'Flank	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	336	Arg/Gly/Lys-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			AAGAGGAAAGGGGGCTTGGGA	0.602																																					p.G336E		.											.	RRS1-90	0			c.G1007A						.						34	44	41					8																	67342373		2192	4287	6479	SO:0001583	missense	23212	exon1			GGAAAGGGGGCTT	BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.1007G>A	8.37:g.67342373G>A	ENSP00000322396:p.Gly336Glu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	103	27	NM_015169	0	0	3	8	5	Q9BUX8	Missense_Mutation	SNP	ENST00000320270.2	37	CCDS6189.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.170934	0.38315	.	.	ENSG00000179041	ENST00000320270	D	0.89552	-2.53	5.26	4.38	0.52667	.	0.233360	0.44688	D	0.000435	D	0.87621	0.6223	M	0.77486	2.375	0.52501	D	0.999957	B	0.24043	0.096	B	0.18263	0.021	D	0.85609	0.1257	10	0.62326	D	0.03	-32.1208	10.2291	0.43245	0.1636:0.0:0.8364:0.0	.	336	Q15050	RRS1_HUMAN	E	336	ENSP00000322396:G336E	ENSP00000322396:G336E	G	+	2	0	RRS1	67504927	0.999000	0.42202	0.810000	0.32431	0.561000	0.35649	2.865000	0.48412	1.369000	0.46134	0.537000	0.68136	GGG	.		0.602	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169		A	67342373	G	A	67342373	3	1	109	1	0	0	0	0	1	0	0	0	13724	1232	43	2	1009	2	RRS1	8	67342373	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	29712052	67342373	79021649	58	9651											
TTC35	9694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	109462688	109462688	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgaacaggtgatgattgcAgcactagactatggtcggga	12	10	13	6	1	0	4	0	3	0	1	1	5	0	5	0	3	3	2	0	3	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:109462688A>T	ENST00000220853.3	+	3	221	c.186A>T	c.(184-186)gcA>gcT	p.A62A		NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	62						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											TGATGATTGCAGCACTAGACT	0.308																																					p.A62A		.											.	.	0			c.A186T						.						206	200	202					8																	109462688		2203	4300	6503	SO:0001819	synonymous_variant	9694	exon3			GATTGCAGCACTA	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.186A>T	8.37:g.109462688A>T		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	157	35	NM_014673	0	0	45	73	28	Q8WUE1	Silent	SNP	ENST00000220853.3	37	CCDS6309.1	.	.	.	.	.	.	.	.	.	.	A	8.680	0.904927	0.17760	.	.	ENSG00000104412	ENST00000519642	.	.	.	5.86	-9.77	0.00500	.	.	.	.	.	T	0.43743	0.1261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52328	-0.8590	4	.	.	.	-10.7326	6.6457	0.22934	0.3445:0.0:0.3347:0.3207	.	.	.	.	L	10	.	.	Q	+	2	0	TTC35	109531864	0.354000	0.24912	0.564000	0.28396	0.612000	0.37316	-0.270000	0.08584	-1.322000	0.02278	-1.132000	0.01976	CAG	.		0.308	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		T	109462688	A	T	109462688	2	4	109	1	0	0	0	0	0	0	0	1	16736	175	7	5		5	TTC35	8	109462688	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	42120315	109462688	36901334	59	9652											
COLEC10	10584	broad.mit.edu	37	chr8	120114630	120114630	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggaatacctggagaaaaAggcaaagcaggtacgatatg	16	7	12	6	1	0	1	0	0	0	1	0	4	0	2	1	4	3	3	1	4	7	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:120114630A>G	ENST00000332843.2	+	4	377	c.336A>G	c.(334-336)aaA>aaG	p.K112K	COLEC10_ENST00000521788.1_3'UTR	NM_006438.3	NP_006429.2	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 (C-type lectin)	112	Collagen-like.					collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	mannose binding (GO:0005537)	p.K112K(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			CTGGAGAAAAAGGCAAAGCAG	0.294																																					p.K112K													.	COLEC10-229	1	Substitution - coding silent(1)	kidney(1)	c.A336G						.						109	114	112					8																	120114630		2203	4300	6503	SO:0001819	synonymous_variant	10584	exon4			AGAAAAAGGCAAA	AB002631	CCDS6327.1	8q23-q24.1	2007-12-19				ENSG00000184374		"Collectins"	2220	protein-coding gene	gene with protein product		607620				10224141	Standard	NM_006438		Approved	CL-L1	uc003yoo.3	Q9Y6Z7		ENST00000332843.2:c.336A>G	8.37:g.120114630A>G		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	69	4	NM_006438	0	0	0	0	0	Q3SYH6|Q6UW19	Silent	SNP	ENST00000332843.2	37	CCDS6327.1																																																																																			.		0.294	COLEC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381225.1			G	120114630	A	G	120114630	2	3	109	1	0	0	0	0	0	0	0	1	3716	69	3	3		3	COLEC10	8	120114630	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	10651942	120114630	26249392	60	9653											
C9orf72	203228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	27548367	27548367	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcgccctctgctgttaaaTcaaggtctatcttcaggttc	8	14	8	11	1	5	0	2	0	3	0	7	1	5	0	1	2	1	3	1	2	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:27548367T>A	ENST00000380003.3	-	11	1376	c.1313A>T	c.(1312-1314)gAt>gTt	p.D438V	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	438					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		TGCTGTTAAATCAAGGTCTAT	0.348																																					p.D438V		.											.	C9orf72-517	0			c.A1313T						.						99	100	100					9																	27548367		2203	4300	6503	SO:0001583	missense	203228	exon11			GTTAAATCAAGGT	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.1313A>T	9.37:g.27548367T>A	ENSP00000369339:p.Asp438Val	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	143	27	NM_018325	0	0	4	4	0	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	37	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.338256	0.81911	.	.	ENSG00000147894	ENST00000380003	T	0.52057	0.68	5.75	5.75	0.90469	.	0.042474	0.85682	D	0.000000	T	0.52789	0.1756	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.51513	-0.8696	9	.	.	.	.	16.0488	0.80740	0.0:0.0:0.0:1.0	.	438	Q96LT7	CI072_HUMAN	V	438	ENSP00000369339:D438V	.	D	-	2	0	C9orf72	27538367	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.199000	0.70637	0.374000	0.22700	GAT	.		0.348	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		A	27548367	T	A	27548367	3	1	109	1	0	0	0	0	1	0	0	0	2501	1435	50	5	136	5	C9orf72	9	27548367	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08		27548367	113665064	61	9654											
NFX1	4799	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	33319104	33319106	+	In_Frame_Del	DEL	CCT	CCT	-																															gtggaaaagtgtgcggcaagCctctgccttgtggttcctta																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:33319104_33319106delCCT	ENST00000379540.3	+	9	1947_1949	c.1885_1887delCCT	c.(1885-1887)cctdel	p.P629del	NFX1_ENST00000318524.6_In_Frame_Del_p.P629del|NFX1_ENST00000379521.4_In_Frame_Del_p.P629del	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	629					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GTGCGGCAAGCCTCTGCCTTGTG	0.438																																					p.629_629del		.											.	NFX1-91	0			c.1885_1887del						.																																			SO:0001651	inframe_deletion	4799	exon9			.	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1885_1887delCCT	9.37:g.33319104_33319106delCCT	ENSP00000368856:p.Pro629del	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	61	22	NM_147134	0	0	0	0	0	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	In_Frame_Del	DEL	ENST00000379540.3	37	CCDS6538.1																																																																																			.		0.438	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			-	33319106	CCT	-	33319104	7	5	109	1	0	1	0	1	0	0	0	0	10413	739	26	0	1919	0	NFX1	9	33319104	In_Frame_Del	DEL	CCT	TCGA-EV-5903-01A-11D-1589-08	5770737	33319104	107894327	62	9655											
CCIN	881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	36170075	36170075	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatgaaaaccttcacgtgctCaatgaagaccaggcgctcag	13	7	10	11	2	3	3	3	2	0	1	3	4	3	3	2	1	2	2	2	1	4	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:36170075C>T	ENST00000335119.2	+	1	687	c.576C>T	c.(574-576)ctC>ctT	p.L192L		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	192	BACK.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			TTCACGTGCTCAATGAAGACC	0.507																																					p.L192L		.											.	CCIN-92	0			c.C576T						.						58	57	58					9																	36170075		2203	4300	6503	SO:0001819	synonymous_variant	881	exon1			CGTGCTCAATGAA	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.576C>T	9.37:g.36170075C>T		Somatic	87	2		WXS	Illumina HiSeq	Phase_I	83	32	NM_005893	0	0	0	0	0	Q9BXG7	Silent	SNP	ENST00000335119.2	37	CCDS6599.1																																																																																			.		0.507	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36170075	C	T	36170075	2	4	109	1	0	0	0	0	0	0	0	1	2884	813	29	2		2	CCIN	9	36170075	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08	2850971	36170075	105043356	63	9656											
FLJ46321	389763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	84605892	84605892	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcttctgcgactgagtcatcGttcactctggcttccacccc	5	12	8	16	2	4	1	2	1	2	0	6	2	5	1	3	1	1	3	3	1	0	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:84605892G>A	ENST00000344803.2	+	4	554	c.507G>A	c.(505-507)tcG>tcA	p.S169S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	169					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGAGTCATCGTTCACTCTGG	0.562																																					p.S169S		.											.	.	0			c.G507A						.						123	123	123					9																	84605892		2001	4169	6170	SO:0001819	synonymous_variant	389763	exon4			GTCATCGTTCACT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.507G>A	9.37:g.84605892G>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	73	18	NM_001001670	0	0	0	0	0		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			.		0.562	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84605892	G	A	84605892	2	1	109	1	0	0	0	0	0	0	0	1	5951	1132	40	1		1	FLJ46321	9	84605892	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	48435817	84605892	56607539	64	9657											
PHF2	5253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	96416716	96416716	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagaagaccttctatctcAtcaggccggcctcggccaac	9	7	11	14	2	3	2	2	0	2	2	5	3	3	2	4	4	1	0	4	4	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:96416716A>C	ENST00000359246.4	+	7	1178	c.811A>C	c.(811-813)Atc>Ctc	p.I271L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	271	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		CTTCTATCTCATCAGGCCGGC	0.587																																					p.I271L		.											.	PHF2-91	0			c.A811C						.						59	56	57					9																	96416716		2203	4300	6503	SO:0001583	missense	5253	exon7			TATCTCATCAGGC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	8920	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1E", "centromere protein 35"	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.811A>C	9.37:g.96416716A>C	ENSP00000352185:p.Ile271Leu	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	63	17	NM_005392	0	0	9	13	4	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	A	32	5.129480	0.94473	.	.	ENSG00000197724	ENST00000359246	T	0.74947	-0.89	4.79	4.79	0.61399	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.87026	0.6075	M	0.86028	2.79	0.80722	D	1	D	0.55385	0.971	D	0.76575	0.988	D	0.89290	0.3618	10	0.87932	D	0	-32.051	14.5008	0.67719	1.0:0.0:0.0:0.0	.	271	O75151	PHF2_HUMAN	L	271	ENSP00000352185:I271L	ENSP00000352185:I271L	I	+	1	0	PHF2	95456537	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.037000	0.93765	2.008000	0.58898	0.477000	0.44152	ATC	.		0.587	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		C	96416716	A	C	96416716	3	2	109	1	0	0	0	0	1	0	0	0	11856	217	8	5	837	5	PHF2	9	96416716	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	11810824	96416716	44796715	65	9658											
ABCA1	19	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	107599352	107599352	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccagatcatggaacacaGccagttcctggaaggtcttg	10	10	10	11	0	2	1	1	0	1	1	4	3	4	3	3	3	2	1	3	3	2	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:107599352G>T	ENST00000374736.3	-	11	1614	c.1220C>A	c.(1219-1221)gCt>gAt	p.A407D		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	407					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	ATGGAACACAGCCAGTTCCTG	0.552																																					p.A407D		.											.	ABCA1-1016	0			c.C1220A						.						86	71	76					9																	107599352		2203	4300	6503	SO:0001583	missense	19	exon11			AACACAGCCAGTT	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.1220C>A	9.37:g.107599352G>T	ENSP00000363868:p.Ala407Asp	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	53	14	NM_005502	0	0	18	21	3	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.773257	0.49786	.	.	ENSG00000165029	ENST00000374736	D	0.85861	-2.04	5.7	4.76	0.60689	.	0.209202	0.49916	D	0.000130	T	0.76807	0.4039	L	0.28192	0.835	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.70454	-0.4867	10	0.27082	T	0.32	.	15.0006	0.71469	0.0:0.2679:0.7321:0.0	.	407	O95477	ABCA1_HUMAN	D	407	ENSP00000363868:A407D	ENSP00000363868:A407D	A	-	2	0	ABCA1	106639173	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.271000	0.65553	2.687000	0.91594	0.655000	0.94253	GCT	.		0.552	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107599352	G	T	107599352	3	4	109	1	0	0	0	0	1	0	0	0	28	971	34	4	5725	4	ABCA1	9	107599352	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	11182636	107599352	33614079	66	9659											
NUP188	23511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131755475	131755475	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgttccggtctccaccaGgtggccccaatgtcagtgta	6	11	12	12	1	2	0	1	0	1	0	4	0	3	0	5	3	0	2	5	3	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:131755475G>A	ENST00000372577.2	+	26	2661		c.e26-1			NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GTCTCCACCAGGTGGCCCCAA	0.537											OREG0019527	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		.											.	NUP188-207	0			c.2641-1G>A						.						100	99	99					9																	131755475		2203	4300	6503	SO:0001630	splice_region_variant	23511	exon26			CCACCAGGTGGCC	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2641-1G>A	9.37:g.131755475G>A		Somatic	69	0	1590	WXS	Illumina HiSeq	Phase_I	88	22	NM_015354	0	0	0	1	1	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Splice_Site	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.417591	0.83449	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	.	.	.	6.0	6.0	0.97389	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4831	0.95018	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUP188	130795296	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.423000	0.80229	2.848000	0.98002	0.655000	0.94253	.	.		0.537	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		Intron	A	131755475	G	A	131755475	5	1	109	1	0	0	0	0	0	0	1	0	10784	1014	35	2	2742	2	NUP188	9	131755475	Splice_Site	SNP	G	TCGA-EV-5903-01A-11D-1589-08	24156123	131755475	9457956	67	9660											
USP20	10868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	132618631	132618631	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaccaaacctatgggccTgtctgcaggtaaaagaccct	11	7	10	13	1	1	1	0	0	1	1	1	2	1	2	5	3	2	2	5	3	4	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:132618631T>A	ENST00000315480.4	+	4	285	c.127T>A	c.(127-129)Tgt>Agt	p.C43S	USP20_ENST00000372429.3_Missense_Mutation_p.C43S|USP20_ENST00000358355.1_Missense_Mutation_p.C43S			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	43					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CCTATGGGCCTGTCTGCAGGT	0.582																																					p.C43S		.											.	USP20-658	0			c.T127A						.						136	137	137					9																	132618631		1947	4141	6088	SO:0001583	missense	10868	exon4			TGGGCCTGTCTGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.127T>A	9.37:g.132618631T>A	ENSP00000313811:p.Cys43Ser	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	215	60	NM_001008563	0	0	0	0	0	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	37	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816658	0.90790	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.72282	-0.64;-0.64;-0.64	4.99	4.99	0.66335	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.000000	0.85682	D	0.000000	D	0.89273	0.6668	H	0.97611	4.04	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.92667	0.6146	10	0.87932	D	0	.	13.5285	0.61609	0.0:0.0:0.0:1.0	.	43	Q9Y2K6	UBP20_HUMAN	S	43	ENSP00000361506:C43S;ENSP00000313811:C43S;ENSP00000351122:C43S	ENSP00000313811:C43S	C	+	1	0	USP20	131658452	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.432000	0.80349	1.880000	0.54463	0.460000	0.39030	TGT	.		0.582	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			A	132618631	T	A	132618631	3	1	109	1	0	0	0	0	1	0	0	0	17085	1580	55	5	133	5	USP20	9	132618631	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	863156	132618631	8594800	68	9661											
ABL1	25	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	133730265	133730265	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaaaaatggccaaggctggGtcccaagcaactacatcacg	14	5	9	13	1	1	0	1	0	0	0	2	0	2	0	3	3	3	2	3	3	6	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:133730265G>C	ENST00000318560.5	+	3	712	c.331G>C	c.(331-333)Gtc>Ctc	p.V111L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	111	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCAAGGCTGGGTCCCAAGCAA	0.522			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.V130L		.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1-3810	0			c.G388C						.						107	89	95					9																	133730265		2203	4300	6503	SO:0001583	missense	25	exon3			GGCTGGGTCCCAA	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.331G>C	9.37:g.133730265G>C	ENSP00000323315:p.Val111Leu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	72	15	NM_007313	0	0	34	46	12	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	G	36	5.707803	0.96821	.	.	ENSG00000097007	ENST00000372348;ENST00000438426;ENST00000318560	T;T	0.55930	0.49;0.49	5.67	5.67	0.87782	Src homology-3 domain (3);	0.000000	0.85682	D	0.000000	T	0.75057	0.3798	M	0.90977	3.165	0.80722	D	1	P;P	0.39862	0.692;0.692	P;P	0.51016	0.656;0.656	T	0.79553	-0.1756	10	0.87932	D	0	.	18.8246	0.92111	0.0:0.0:1.0:0.0	.	111;148	P00519;Q59FK4	ABL1_HUMAN;.	L	130;157;111	ENSP00000361423:V130L;ENSP00000323315:V111L	ENSP00000323315:V111L	V	+	1	0	ABL1	132720086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.812000	0.99227	2.677000	0.91161	0.638000	0.83543	GTC	.		0.522	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		C	133730265	G	C	133730265	3	2	109	1	0	0	0	0	1	0	0	0	92	1261	44	4	481	4	ABL1	9	133730265	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	1111634	133730265	7483166	69	9662											
ABL1	25	broad.mit.edu	37	chr9	133750315	133750315	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtgaaggtagctgatttTggcctgagcaggttgatgac	8	13	15	5	0	0	5	0	5	0	0	0	5	0	5	1	4	2	4	1	4	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:133750315T>G	ENST00000318560.5	+	7	1527	c.1146T>G	c.(1144-1146)ttT>ttG	p.F382L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	382	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)	p.?(1)		breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TAGCTGATTTTGGCCTGAGCA	0.537			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.F401L				Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1-3810	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1203G						.						163	142	149					9																	133750315		2203	4300	6503	SO:0001583	missense	25	exon7			TGATTTTGGCCTG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1146T>G	9.37:g.133750315T>G	ENSP00000323315:p.Phe382Leu	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	119	3	NM_007313	0	0	42	42	0	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760517	0.89932	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.81247	-1.47;-1.47	5.23	-5.23	0.02798	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86859	0.6034	M	0.89715	3.055	0.80722	D	1	P;P	0.51057	0.941;0.941	P;P	0.56042	0.79;0.79	D	0.87399	0.2368	10	0.87932	D	0	.	14.2212	0.65828	0.0:0.4481:0.0:0.5519	.	382;419	P00519;Q59FK4	ABL1_HUMAN;.	L	197;401;382	ENSP00000361423:F401L;ENSP00000323315:F382L	ENSP00000323315:F382L	F	+	3	2	ABL1	132740136	0.957000	0.32711	0.826000	0.32828	0.970000	0.65996	0.065000	0.14466	-1.415000	0.02022	-0.290000	0.09829	TTT	.		0.537	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133750315	T	G	133750315	3	3	109	1	0	0	0	0	1	0	0	0	92	1809	63	5	1312	5	ABL1	9	133750315	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	20050	133750315	7463116	70	9663											
C9orf98	158067	hgsc.bcm.edu;broad.mit.edu	37	chr9	135601117	135601117	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggattaatgatcccactctcGatgtattcgaagactgtgta	11	13	9	8	2	1	2	0	1	1	1	4	5	2	3	1	1	0	2	1	1	4	4	rs184476196	byFrequency	TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:135601117G>C	ENST00000298545.3	-	13	1919	c.1398C>G	c.(1396-1398)atC>atG	p.I466M	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	466	Adenylate kinase 2.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						TCCCACTCTCGATGTATTCGA	0.557																																					p.I466M		.											.	AK8-90	0			c.C1398G						.						71	55	61					9																	135601117		2203	4300	6503	SO:0001583	missense	158067	exon13			ACTCTCGATGTAT	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"Adenylate kinases"	26526	protein-coding gene	gene with protein product		615365	"chromosome 9 open reading frame 98"	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.1398C>G	9.37:g.135601117G>C	ENSP00000298545:p.Ile466Met	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	9	3	NM_152572	0	0	5	11	6	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	37	CCDS6954.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.456806	0.26161	.	.	ENSG00000165695	ENST00000298545	T	0.72282	-0.64	5.08	-10.2	0.00374	.	0.233363	0.35013	N	0.003515	T	0.70622	0.3245	M	0.79475	2.455	0.32487	N	0.540767	D	0.54772	0.968	P	0.57720	0.826	T	0.76002	-0.3118	10	0.87932	D	0	-3.3208	5.6233	0.17469	0.1067:0.148:0.5577:0.1876	.	466	Q96MA6	KAD8_HUMAN	M	466	ENSP00000298545:I466M	ENSP00000298545:I466M	I	-	3	3	AK8	134590938	0.221000	0.23642	0.372000	0.25991	0.016000	0.09150	-0.970000	0.03810	-2.541000	0.00485	-1.284000	0.01376	ATC	G|0.999;A|0.001		0.557	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572		C	135601117	G	C	135601117	3	2	109	1	0	0	0	0	1	0	0	0	2515	1048	37	4	45	4	C9orf98	9	135601117	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	1850802	135601117	5612314	71	9664											
LARP4B	23185	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	858887	858887	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgaggagacttggggggAgtgctctgctctcggctgag	6	9	17	9	1	2	3	0	2	2	1	3	5	2	4	0	5	2	3	0	5	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:858887A>G	ENST00000316157.3	-	17	2236	c.2196T>C	c.(2194-2196)acT>acC	p.T732T	LARP4B_ENST00000469487.1_5'Flank	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	732					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						ACTTGGGGGGAGTGCTCTGCT	0.662																																					p.T732T		.											.	LARP4B-92	0			c.T2196C						.						36	40	39					10																	858887		2202	4298	6500	SO:0001819	synonymous_variant	23185	exon18			GGGGGGAGTGCTC	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"La ribonucleoprotein domain containing"	28987	protein-coding gene	gene with protein product			"KIAA0217", "La ribonucleoprotein domain family, member 5"	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.2196T>C	10.37:g.858887A>G		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	111	34	NM_015155	0	0	7	14	7	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	37	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	A	6.457	0.452392	0.12283	.	.	ENSG00000107929	ENST00000448368	.	.	.	6.07	-5.87	0.02297	.	.	.	.	.	T	0.39036	0.1063	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41270	-0.9518	4	.	.	.	-3.3912	3.9687	0.09443	0.1675:0.3281:0.3845:0.12	.	.	.	.	P	333	.	.	S	-	1	0	LARP4B	848887	0.998000	0.40836	0.905000	0.35620	0.944000	0.59088	0.260000	0.18424	-0.881000	0.03992	-1.236000	0.01555	TCC	.		0.662	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		G	858887	A	G	858887	2	3	109	1	0	0	0	0	0	0	0	1	8652	291	11	3		3	LARP4B	10	858887	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08		858887	134675860	72	9665											
PITRM1	10531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	3191832	3191832	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggtgaggacgctgcagaAgaggggcacatagggcctca	10	6	16	9	1	1	3	1	1	0	2	1	4	1	4	1	5	1	3	1	5	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:3191832A>C	ENST00000224949.4	-	16	1886	c.1852T>G	c.(1852-1854)Ttc>Gtc	p.F618V	PITRM1_ENST00000380989.2_Missense_Mutation_p.F618V|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000464395.1_5'Flank|PITRM1_ENST00000380994.1_Missense_Mutation_p.F176V|PITRM1_ENST00000451104.2_Missense_Mutation_p.F586V|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	618					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ACGCTGCAGAAGAGGGGCACA	0.517																																					p.F618V		.											.	PITRM1-91	0			c.T1852G						.						183	187	186					10																	3191832		2033	4194	6227	SO:0001583	missense	10531	exon16			TGCAGAAGAGGGG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1852T>G	10.37:g.3191832A>C	ENSP00000224949:p.Phe618Val	Somatic	338	0		WXS	Illumina HiSeq	Phase_I	280	78	NM_014889	0	0	47	85	38	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	a	22.4	4.280763	0.80692	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.41	4.28	0.50868	Peptidase M16C associated (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	M	0.90309	3.105	0.58432	D	0.999998	D;D;D;D;D	0.89917	0.97;0.997;1.0;1.0;1.0	P;D;D;D;D	0.85130	0.824;0.994;0.997;0.997;0.997	T	0.73582	-0.3937	10	0.87932	D	0	.	11.2282	0.48897	0.9278:0.0:0.0722:0.0	.	611;586;618;618;611	E9PDX6;E7ES23;C9JSL2;Q5JRX3;B4DH07	.;.;.;PREP_HUMAN;.	V	618;611;618;176;586	ENSP00000224949:F618V;ENSP00000370377:F618V;ENSP00000370382:F176V;ENSP00000401201:F586V	ENSP00000224949:F618V	F	-	1	0	PITRM1	3181832	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.161000	0.77505	0.900000	0.36469	0.454000	0.30748	TTC	.		0.517	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			C	3191832	A	C	3191832	3	2	109	1	0	0	0	0	1	0	0	0	11979	72	3	5	1309	5	PITRM1	10	3191832	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	2332945	3191832	132342915	73	9666											
CSGALNACT2	55454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	43651227	43651227	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggtccccttggagagaaActgatatttaatgaaaatga	15	10	11	5	0	0	4	0	3	0	1	1	7	1	5	2	2	1	0	2	2	5	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:43651227A>G	ENST00000374466.3	+	2	965	c.630A>G	c.(628-630)aaA>aaG	p.K210K	CSGALNACT2_ENST00000374464.1_Silent_p.K210K	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	210					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TTGGAGAGAAACTGATATTTA	0.363																																					p.K210K		.											.	CSGALNACT2-69	0			c.A630G						.						44	46	46					10																	43651227		2203	4299	6502	SO:0001819	synonymous_variant	55454	exon2			AGAGAAACTGATA	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.630A>G	10.37:g.43651227A>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	71	17	NM_018590	0	0	6	8	2	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Silent	SNP	ENST00000374466.3	37	CCDS7201.1																																																																																			.		0.363	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		G	43651227	A	G	43651227	2	3	109	1	0	0	0	0	0	0	0	1	3945	40	2	3		3	CSGALNACT2	10	43651227	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	40459395	43651227	91883520	74	9667											
POLR3A	11128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	79741971	79741971	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	accgtgtgtggccatgactgCccgcaggttatcaccttcca	7	10	10	14	2	1	1	1	1	0	0	2	1	2	1	5	2	1	2	5	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:79741971C>G	ENST00000372371.3	-	28	3837	c.3700G>C	c.(3700-3702)Gca>Cca	p.A1234P		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1234					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			GCCATGACTGCCCGCAGGTTA	0.567																																					p.A1234P		.											.	POLR3A-90	0			c.G3700C						.						188	151	163					10																	79741971		2203	4300	6503	SO:0001583	missense	11128	exon28			TGACTGCCCGCAG	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"RNA polymerase subunits"	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.3700G>C	10.37:g.79741971C>G	ENSP00000361446:p.Ala1234Pro	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	115	34	NM_007055	0	0	5	10	5	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.192613	0.58017	.	.	ENSG00000148606	ENST00000539141;ENST00000372371;ENST00000540842	T	0.78126	-1.15	5.99	5.99	0.97316	RNA polymerase Rpb1, domain 5 (1);	0.051369	0.85682	D	0.000000	D	0.83718	0.5315	M	0.87097	2.86	0.58432	D	0.999998	P	0.35155	0.487	B	0.42112	0.376	T	0.83056	-0.0150	9	.	.	.	-11.4876	15.1985	0.73116	0.1408:0.8591:0.0:0.0	.	1234	O14802	RPC1_HUMAN	P	50;1234;1213	ENSP00000361446:A1234P	.	A	-	1	0	POLR3A	79411977	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	4.200000	0.58433	2.843000	0.97960	0.655000	0.94253	GCA	.		0.567	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		G	79741971	C	G	79741971	3	3	109	1	0	0	0	0	1	0	0	0	12254	739	26	4	488	4	POLR3A	10	79741971	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	36090744	79741971	55792776	75	9668											
KIAA1598	57698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	118689489	118689489	+	Missense_Mutation	SNP	C	C	T																															tttgtggagtgtttcattttCtagttgctcttctaattctt																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:118689489C>T	ENST00000355371.4	-	10	1380	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	KIAA1598_ENST00000260777.10_Missense_Mutation_p.E295K|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000392903.2_Missense_Mutation_p.E295K|KIAA1598_ENST00000392901.4_Missense_Mutation_p.E235K	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	295					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		GTTTCATTTTCTAGTTGCTCT	0.308																																					p.E295K		.											.	KIAA1598-90	0			c.G883A						.						163	152	155					10																	118689489		2201	4298	6499	SO:0001583	missense	57698	exon10			CATTTTCTAGTTG	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.883G>A	10.37:g.118689489C>T	ENSP00000347532:p.Glu295Lys	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	137	35	NM_001258299	0	0	11	11	0	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	37	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.982973	0.34942	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	T;T;T;T	0.75260	1.61;1.61;1.61;-0.92	5.35	4.45	0.53987	.	0.493073	0.23371	N	0.048907	T	0.65626	0.2709	L	0.52573	1.65	0.32981	D	0.52363	B;B;B	0.26845	0.069;0.008;0.161	B;B;B	0.24701	0.055;0.022;0.033	T	0.67643	-0.5618	10	0.23891	T	0.37	-14.1816	9.9478	0.41621	0.1475:0.6917:0.1608:0.0	.	295;295;265	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	K	295;295;295;235	ENSP00000376636:E295K;ENSP00000260777:E295K;ENSP00000347532:E295K;ENSP00000376635:E235K	ENSP00000260777:E295K	E	-	1	0	KIAA1598	118679479	0.984000	0.35163	0.971000	0.41717	0.986000	0.74619	2.414000	0.44627	1.404000	0.46819	0.561000	0.74099	GAA	.		0.308	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		T	118689489	C	T	118689489	3	4	109	1	0	0	0	0	1	0	0	0	8267	922	32	2	1044	2	KIAA1598	10	118689489	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	38947518	118689489	16845258	76	9669	99	2									
KIAA1598	57698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	118689491	118689491	+	Missense_Mutation	SNP	A	A	G																															tgtggagtgtttcattttctAgttgctcttctaattctttg																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:118689491A>G	ENST00000355371.4	-	10	1378	c.881T>C	c.(880-882)cTa>cCa	p.L294P	KIAA1598_ENST00000260777.10_Missense_Mutation_p.L294P|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000392903.2_Missense_Mutation_p.L294P|KIAA1598_ENST00000392901.4_Missense_Mutation_p.L234P	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	294					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		TTCATTTTCTAGTTGCTCTTC	0.303																																					p.L294P		.											.	KIAA1598-90	0			c.T881C						.						161	150	154					10																	118689491		2201	4298	6499	SO:0001583	missense	57698	exon10			TTTTCTAGTTGCT	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.881T>C	10.37:g.118689491A>G	ENSP00000347532:p.Leu294Pro	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	133	34	NM_001258299	0	0	10	10	0	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	37	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	A	18.91	3.723729	0.68959	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	T;T;T;T	0.24538	2.72;2.72;2.72;1.85	5.35	5.35	0.76521	.	0.239875	0.36268	N	0.002695	T	0.48978	0.1530	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;0.997;1.0	D;D;D	0.87578	0.998;0.994;0.996	T	0.49273	-0.8957	10	0.59425	D	0.04	-9.5016	13.8675	0.63598	1.0:0.0:0.0:0.0	.	294;294;264	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	P	294;294;294;234	ENSP00000376636:L294P;ENSP00000260777:L294P;ENSP00000347532:L294P;ENSP00000376635:L234P	ENSP00000260777:L294P	L	-	2	0	KIAA1598	118679481	0.999000	0.42202	0.840000	0.33206	0.981000	0.71138	5.819000	0.69243	2.163000	0.67991	0.459000	0.35465	CTA	.		0.303	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		G	118689491	A	G	118689491	3	3	109	1	0	0	0	0	1	0	0	0	8267	420	15	3	1046	3	KIAA1598	10	118689491	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	2	118689491	16845256	77	9670	99	2									
GLRX3	10539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	131964822	131964822	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaacataatattcagtttaGcagttttgatatcttctcag	13	16	5	7	0	3	1	2	1	2	0	4	1	3	1	0	0	2	3	0	0	5	9			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:131964822G>T	ENST00000368644.1	+	5	552	c.530G>T	c.(529-531)aGc>aTc	p.S177I	GLRX3_ENST00000331244.5_Missense_Mutation_p.S177I	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	177	Glutaredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		ATTCAGTTTAGCAGTTTTGAT	0.393																																					p.S177I		.											.	GLRX3-22	0			c.G530T						.						122	121	122					10																	131964822		2203	4300	6503	SO:0001583	missense	10539	exon5			AGTTTAGCAGTTT	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"glutaredoxin 4"	612754	"thioredoxin-like 2"	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.530G>T	10.37:g.131964822G>T	ENSP00000357633:p.Ser177Ile	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	131	31	NM_006541	0	0	15	37	22	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573832	0.86542	.	.	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.29917	1.55;1.55	5.0	5.0	0.66597	Glutaredoxin (2);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.43523	0.1251	L	0.28649	0.875	0.80722	D	1	D	0.63046	0.992	D	0.70487	0.969	T	0.23440	-1.0188	10	0.35671	T	0.21	-14.9931	17.3131	0.87215	0.0:0.0:1.0:0.0	.	177	O76003	GLRX3_HUMAN	I	177	ENSP00000330836:S177I;ENSP00000357633:S177I	ENSP00000330836:S177I	S	+	2	0	GLRX3	131854812	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.365000	0.97139	2.323000	0.78572	0.655000	0.94253	AGC	.		0.393	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541		T	131964822	G	T	131964822	3	4	109	1	0	0	0	0	1	0	0	0	6481	971	34	4	548	4	GLRX3	10	131964822	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	13275331	131964822	3569925	78	9671											
LRRC56	115399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	552211	552211	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccttggctgggctcagggCctggagggaacatggcgtgc	5	7	19	10	1	1	0	1	0	0	0	1	2	1	2	2	7	2	2	2	7	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:552211C>T	ENST00000270115.7	+	12	1660	c.1160C>T	c.(1159-1161)gCc>gTc	p.A387V		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	387										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGCTCAGGGCCTGGAGGGAA	0.657																																					p.A387V		.											.	LRRC56-91	0			c.C1160T						.						41	44	43					11																	552211		2202	4300	6502	SO:0001583	missense	115399	exon12			TCAGGGCCTGGAG		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1160C>T	11.37:g.552211C>T	ENSP00000270115:p.Ala387Val	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	78	25	NM_198075	0	0	6	11	5	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.420638	0.62622	.	.	ENSG00000161328	ENST00000270115	T	0.15952	2.38	4.38	4.38	0.52667	.	0.301734	0.24145	N	0.041134	T	0.14570	0.0352	L	0.27053	0.805	0.35067	D	0.762095	P	0.43287	0.802	B	0.42245	0.381	T	0.15549	-1.0433	10	0.59425	D	0.04	0.5026	12.6067	0.56527	0.0:1.0:0.0:0.0	.	387	Q8IYG6	LRC56_HUMAN	V	387	ENSP00000270115:A387V	ENSP00000270115:A387V	A	+	2	0	LRRC56	542211	0.208000	0.23494	0.120000	0.21714	0.036000	0.12997	2.410000	0.44592	2.441000	0.82636	0.561000	0.74099	GCC	.		0.657	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		T	552211	C	T	552211	3	4	109	1	0	0	0	0	1	0	0	0	9037	739	26	2	1194	2	LRRC56	11	552211	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		552211	134454305	79	9672											
OR51A7	119687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4929158	4929158	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcatcaggataccatgaagCtggcctgctctgacaacaag	12	9	9	11	0	3	2	2	2	1	0	3	3	3	3	2	2	4	2	2	2	4	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:4929158C>T	ENST00000359350.4	+	1	559	c.559C>T	c.(559-561)Ctg>Ttg	p.L187L	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TACCATGAAGCTGGCCTGCTC	0.398																																					p.L187L		.											.	OR51A7-70	0			c.C559T						.						199	164	176					11																	4929158		2201	4298	6499	SO:0001819	synonymous_variant	119687	exon1			ATGAAGCTGGCCT	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.559C>T	11.37:g.4929158C>T		Somatic	181	1		WXS	Illumina HiSeq	Phase_I	163	51	NM_001004749	0	0	0	0	0	Q6IFH8	Silent	SNP	ENST00000359350.4	37	CCDS31364.1																																																																																			.		0.398	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		T	4929158	C	T	4929158	2	4	109	1	0	0	0	0	0	0	0	1	11114	796	28	2		2	OR51A7	11	4929158	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08	4376947	4929158	130077358	80	9673											
TPP1	8642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6640045	6640045	+	IGR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatccgacacagcctgcaccAgctccgagagtctttccaca	10	7	8	16	2	1	1	0	0	1	1	4	4	4	1	5	0	3	2	5	0	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:6640045A>C	ENST00000299441.3	-	0	10763				TPP1_ENST00000534644.1_Intron|TPP1_ENST00000528657.1_3'UTR|TPP1_ENST00000299427.6_Missense_Mutation_p.L64R|RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000533371.1_5'UTR|RP11-732A19.9_ENST00000545572.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1						branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGCCTGCACCAGCTCCGAGAG	0.622																																					p.L64R		.											.	TPP1-90	0			c.T191G						.						77	68	71					11																	6640045		2201	4296	6497	SO:0001628	intergenic_variant	1200	exon3			TGCACCAGCTCCG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398		11.37:g.6640045A>C		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	88	24	NM_000391	0	0	91	150	59	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196515	0.79015	.	.	ENSG00000166340	ENST00000299427;ENST00000453338;ENST00000436873	T;T	0.70516	-0.49;-0.49	5.64	4.45	0.53987	Proteinase inhibitor, propeptide (1);Peptidase S53, propeptide (2);	0.231767	0.37530	N	0.002054	T	0.72407	0.3456	L	0.48260	1.515	0.80722	D	1	D;D	0.61697	0.99;0.972	P;P	0.59288	0.855;0.639	T	0.68633	-0.5357	10	0.25751	T	0.34	-18.2713	9.3741	0.38272	0.8409:0.0:0.0:0.1591	.	64;64	B4DEQ3;O14773	.;TPP1_HUMAN	R	64	ENSP00000299427:L64R;ENSP00000398136:L64R	ENSP00000299427:L64R	L	-	2	0	TPP1	6596621	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	3.517000	0.53443	2.146000	0.66826	0.379000	0.24179	CTG	.		0.622	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		C	6640045	A	C	6640045	1	2	109	0	1	0	0	0	0	0	0	0	16444	188	7	5		5	TPP1	11	6640045	IGR	SNP	A	TCGA-EV-5903-01A-11D-1589-08	1710887	6640045	128366471	81	9674											
F2	2147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46740795	46740795	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgacacactatggcgcacGtccgaggcttgcagctgcct	7	8	12	14	3	0	1	0	1	0	0	1	2	1	1	2	2	3	5	2	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:46740795G>A	ENST00000311907.5	+	1	66	c.10G>A	c.(10-12)Gtc>Atc	p.V4I	F2_ENST00000530231.1_Missense_Mutation_p.V4I	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	4					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	TATGGCGCACGTCCGAGGCTT	0.577																																					p.V4I	Esophageal Squamous(147;1147 1808 2148 38609 51144)	.											.	F2-93	0			c.G10A						.						47	40	42					11																	46740795		2201	4299	6500	SO:0001583	missense	2147	exon1			GCGCACGTCCGAG	M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"Endogenous ligands"	3535	protein-coding gene	gene with protein product	"prepro-coagulation factor II"	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.10G>A	11.37:g.46740795G>A	ENSP00000308541:p.Val4Ile	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	45	14	NM_000506	0	0	0	0	0	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	37	CCDS31476.1	.	.	.	.	.	.	.	.	.	.	G	4.679	0.126175	0.08931	.	.	ENSG00000180210	ENST00000311907;ENST00000530231	D;D	0.91295	-2.61;-2.82	5.76	1.65	0.23941	.	1.055420	0.07341	N	0.880761	D	0.84293	0.5440	L	0.34521	1.04	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.71258	-0.4646	10	0.87932	D	0	.	4.8209	0.13390	0.3861:0.1476:0.4664:0.0	.	4	P00734	THRB_HUMAN	I	4	ENSP00000308541:V4I;ENSP00000433907:V4I	ENSP00000308541:V4I	V	+	1	0	F2	46697371	0.575000	0.26692	0.994000	0.49952	0.981000	0.71138	0.307000	0.19296	0.047000	0.15862	-0.140000	0.14226	GTC	.		0.577	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			A	46740795	G	A	46740795	3	1	109	1	0	0	0	0	1	0	0	0	5355	1145	40	1	12	1	F2	11	46740795	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	40100750	46740795	88265721	82	9675											
LRFN4	78999	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	66627368	66627368	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggtcttcactgtggcctTgctggttcggggccgggggg	2	11	18	10	2	2	0	1	0	1	0	3	0	2	0	2	8	1	2	2	8	0	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:66627368T>A	ENST00000309602.4	+	2	1853	c.1610T>A	c.(1609-1611)tTg>tAg	p.L537*	PC_ENST00000393958.2_Intron|LRFN4_ENST00000393952.3_Intron|PC_ENST00000393955.2_Intron|PC_ENST00000393960.1_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	537						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						ACTGTGGCCTTGCTGGTTCGG	0.711																																					p.L537X		.											.	LRFN4-90	0			c.T1610A						.						34	28	30					11																	66627368		2188	4284	6472	SO:0001587	stop_gained	78999	exon2			TGGCCTTGCTGGT	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1610T>A	11.37:g.66627368T>A	ENSP00000312535:p.Leu537*	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	31	13	NM_024036	0	0	1	1	0	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Nonsense_Mutation	SNP	ENST00000309602.4	37	CCDS8153.1	.	.	.	.	.	.	.	.	.	.	T	39	7.854370	0.98525	.	.	ENSG00000173621	ENST00000309602	.	.	.	4.79	4.79	0.61399	.	0.484734	0.15470	N	0.260642	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2823	0.54771	0.0:0.0:0.0:1.0	.	.	.	.	X	537	.	ENSP00000312535:L537X	L	+	2	0	LRFN4	66383944	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.178000	0.58284	1.799000	0.52666	0.379000	0.24179	TTG	.		0.711	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		A	66627368	T	A	66627368	4	1	109	1	0	0	0	0	0	1	0	0	8965	1821	63	5	1616	5	LRFN4	11	66627368	Nonsense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	19886573	66627368	68379148	83	9676											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877690	82877690	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcactgaaccaaaggagaAtgtagaaaactggcaaagtt	18	6	11	6	0	0	3	0	1	0	2	0	4	0	3	1	3	2	4	1	3	7	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:82877690A>T	ENST00000298281.4	+	5	2203	c.1751A>T	c.(1750-1752)aAt>aTt	p.N584I		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	584					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CCAAAGGAGAATGTAGAAAAC	0.393																																					p.N584I		.											.	PCF11-23	0			c.A1751T						.						66	66	66					11																	82877690		1824	4044	5868	SO:0001583	missense	51585	exon5			AGGAGAATGTAGA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1751A>T	11.37:g.82877690A>T	ENSP00000298281:p.Asn584Ile	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	83	14	NM_015885	0	0	9	10	1	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.019444	0.54576	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.53206	1.58;0.64;0.63	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.54775	0.1879	L	0.29908	0.895	0.33890	D	0.637211	D;P	0.71674	0.998;0.915	P;B	0.61940	0.896;0.294	T	0.62798	-0.6778	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	584;584	E9PQ01;O94913	.;PCF11_HUMAN	I	584	ENSP00000298281:N584I;ENSP00000434540:N584I;ENSP00000431567:N584I	.	N	+	2	0	PCF11	82555338	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	3.827000	0.55745	2.326000	0.78906	0.533000	0.62120	AAT	.		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82877690	A	T	82877690	3	4	109	1	0	0	0	0	1	0	0	0	11599	101	4	5	1769	5	PCF11	11	82877690	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	16250322	82877690	52128826	84	9677											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82878314	82878314	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatcttcagattcctaaagaGttaactcttgcaagcaaaag	16	11	6	8	0	3	2	1	0	2	2	4	2	4	2	1	0	3	3	1	0	7	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:82878314G>C	ENST00000298281.4	+	6	2417	c.1965G>C	c.(1963-1965)gaG>gaC	p.E655D		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	655					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TTCCTAAAGAGTTAACTCTTG	0.368																																					p.E655D		.											.	PCF11-23	0			c.G1965C						.						62	61	61					11																	82878314		1875	4100	5975	SO:0001583	missense	51585	exon6			TAAAGAGTTAACT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1965G>C	11.37:g.82878314G>C	ENSP00000298281:p.Glu655Asp	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	80	20	NM_015885	0	0	3	3	0	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165064	0.57476	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.48836	1.78;0.82;0.8	5.98	1.48	0.22813	.	0.000000	0.64402	D	0.000015	T	0.42381	0.1200	L	0.29908	0.895	0.26221	N	0.979152	D;D	0.67145	0.996;0.985	P;P	0.54499	0.754;0.541	T	0.25398	-1.0133	9	.	.	.	.	8.1397	0.31076	0.5069:0.0:0.4931:0.0	.	655;655	E9PQ01;O94913	.;PCF11_HUMAN	D	655	ENSP00000298281:E655D;ENSP00000434540:E655D;ENSP00000431567:E655D	.	E	+	3	2	PCF11	82555962	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.998000	0.29744	0.412000	0.25729	0.591000	0.81541	GAG	.		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		C	82878314	G	C	82878314	3	2	109	1	0	0	0	0	1	0	0	0	11599	1020	36	4	1987	4	PCF11	11	82878314	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	624	82878314	52128202	85	9678											
TRIM49	57093	hgsc.bcm.edu	37	chr11	89537575	89537575	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggtgaccgggtctatgaaGtagttcatgcacagggggca	10	9	15	7	1	2	2	1	2	1	0	2	2	2	2	1	4	1	4	1	4	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:89537575G>C	ENST00000329758.1	-	3	391	c.63C>G	c.(61-63)taC>taG	p.Y21*	TRIM49_ENST00000532501.2_Nonsense_Mutation_p.Y21*	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	21						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GGTCTATGAAGTAGTTCATGC	0.473																																					p.Y21X		.											.	TRIM49-84	0			c.C63G						.						21	21	21					11																	89537575		2185	4268	6453	SO:0001587	stop_gained	57093	exon3			TATGAAGTAGTTC	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13431	protein-coding gene	gene with protein product		606124	"ring finger protein 18", "tripartite motif-containing 49"	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.63C>G	11.37:g.89537575G>C	ENSP00000327604:p.Tyr21*	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	111	28	NM_020358	0	0	0	0	0	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Nonsense_Mutation	SNP	ENST00000329758.1	37	CCDS8287.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.713868	0.30413	.	.	ENSG00000168930	ENST00000329758;ENST00000532501	.	.	.	0.821	-0.817	0.10836	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.9772	0.05941	0.6362:0.0:0.3638:0.0	.	.	.	.	X	21	.	.	Y	-	3	2	TRIM49	89177223	0.000000	0.05858	0.011000	0.14972	0.050000	0.14768	-0.246000	0.08878	-0.218000	0.10018	0.194000	0.17425	TAC	.		0.473	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358		C	89537575	G	C	89537575	4	2	109	1	0	0	0	0	0	1	0	0	16557	1024	36	4	1319	4	TRIM49	11	89537575	Nonsense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	6659261	89537575	45468941	86	9679											
RPUSD4	84881	broad.mit.edu	37	chr11	126079570	126079570	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtggccatgaagcatctttgCcaggataggtagtacatcag	11	10	12	8	0	2	1	1	1	1	0	2	2	2	2	2	3	3	3	2	3	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:126079570C>T	ENST00000298317.4	-	3	456	c.403G>A	c.(403-405)Gca>Aca	p.A135T	RP11-50B3.4_ENST00000532866.1_RNA|FAM118B_ENST00000360194.4_5'Flank|RPUSD4_ENST00000533628.1_Missense_Mutation_p.A135T|RPUSD4_ENST00000534393.1_5'UTR|FAM118B_ENST00000529731.1_5'Flank|FAM118B_ENST00000533050.1_5'Flank	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	135					pseudouridine synthesis (GO:0001522)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0761)		AGCATCTTTGCCAGGATAGGT	0.532																																					p.A135T													.	RPUSD4-153	0			c.G403A						.						212	196	202					11																	126079570		2201	4299	6500	SO:0001583	missense	84881	exon3			TCTTTGCCAGGAT	BC014131	CCDS8469.1, CCDS53721.1	11q24.2	2013-02-11			ENSG00000165526	ENSG00000165526		"RNA pseudouridylate synthase domain containing"	25898	protein-coding gene	gene with protein product							Standard	NM_032795		Approved	FLJ14494	uc001qde.3	Q96CM3	OTTHUMG00000165815	ENST00000298317.4:c.403G>A	11.37:g.126079570C>T	ENSP00000298317:p.Ala135Thr	Somatic	279	1		WXS	Illumina HiSeq	Phase_I	285	6	NM_001144827	0	0	16	16	0	E9PML2|Q96K56	Missense_Mutation	SNP	ENST00000298317.4	37	CCDS8469.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656196	0.88056	.	.	ENSG00000165526	ENST00000298317;ENST00000533628;ENST00000532674	T;T;T	0.21543	2.0;2.0;2.0	5.33	5.33	0.75918	Pseudouridine synthase, RsuA and RluB/C/D/E/F (1);Pseudouridine synthase, catalytic domain (1);	0.054402	0.64402	D	0.000001	T	0.36880	0.0983	L	0.53561	1.675	0.45172	D	0.998189	P;P	0.47191	0.872;0.891	P;P	0.57720	0.688;0.826	T	0.02471	-1.1154	10	0.15066	T	0.55	-6.8966	18.0365	0.89305	0.0:1.0:0.0:0.0	.	135;135	E9PML2;Q96CM3	.;RUSD4_HUMAN	T	135	ENSP00000298317:A135T;ENSP00000433065:A135T;ENSP00000433709:A135T	ENSP00000298317:A135T	A	-	1	0	RPUSD4	125584780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.771000	0.55318	2.495000	0.84180	0.655000	0.94253	GCA	.		0.532	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795		T	126079570	C	T	126079570	3	4	109	1	0	0	0	0	1	0	0	0	13701	739	26	2	750	2	RPUSD4	11	126079570	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	36541995	126079570	8926946	87	9680											
SLC6A13	6540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	346349	346349	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtggacttcacccccttcCagatgcagaagtagcagatg	10	9	10	12	0	1	3	1	0	0	3	2	4	2	4	3	1	2	3	3	1	2	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:346349C>G	ENST00000343164.4	-	6	723	c.671G>C	c.(670-672)tGg>tCg	p.W224S	SLC6A13_ENST00000445055.2_Missense_Mutation_p.W132S	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	224					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			CACCCCCTTCCAGATGCAGAA	0.632																																					p.W224S		.											.	SLC6A13-90	0			c.G671C						.						87	83	84					12																	346349		2203	4300	6503	SO:0001583	missense	6540	exon6			CCCTTCCAGATGC	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.671G>C	12.37:g.346349C>G	ENSP00000339260:p.Trp224Ser	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	123	30	NM_016615	0	0	21	37	16	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782040	0.90282	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164;ENST00000546319	T;T;T	0.74842	-0.88;-0.88;-0.88	5.5	5.5	0.81552	.	0.054680	0.85682	D	0.000000	D	0.85013	0.5600	M	0.76170	2.325	0.80722	D	1	D;D;D	0.57257	0.979;0.971;0.971	P;P;P	0.59546	0.859;0.827;0.827	D	0.85988	0.1487	10	0.87932	D	0	.	19.6592	0.95857	0.0:1.0:0.0:0.0	.	132;203;224	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	S	132;203;224;132	ENSP00000407104:W132S;ENSP00000339260:W224S;ENSP00000444606:W132S	ENSP00000318097:W203S	W	-	2	0	SLC6A13	216610	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.905000	0.69893	2.880000	0.98712	0.650000	0.86243	TGG	.		0.632	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		G	346349	C	G	346349	3	3	109	1	0	0	0	0	1	0	0	0	14708	595	21	4	1177	4	SLC6A13	12	346349	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		346349	133505546	88	9681											
DCP1B	196513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2064679	2064679	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgagatttggattgtcataGatggcagaggaactggttat	12	13	13	3	0	1	3	1	1	0	3	1	6	1	5	0	4	1	2	0	4	3	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:2064679G>C	ENST00000280665.6	-	6	649	c.570C>G	c.(568-570)atC>atG	p.I190M	DCP1B_ENST00000541700.1_Intron|DCP1B_ENST00000540622.1_Missense_Mutation_p.I64M|DCP1B_ENST00000397173.4_Missense_Mutation_p.I88M	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	190					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			GATTGTCATAGATGGCAGAGG	0.413																																					p.I190M		.											.	DCP1B-91	0			c.C570G						.						239	227	231					12																	2064679		2203	4300	6503	SO:0001583	missense	196513	exon6			GTCATAGATGGCA	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"DCP1 decapping enzyme homolog B (S. cerevisiae)"			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.570C>G	12.37:g.2064679G>C	ENSP00000280665:p.Ile190Met	Somatic	256	0		WXS	Illumina HiSeq	Phase_I	207	69	NM_152640	0	0	5	7	2	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Missense_Mutation	SNP	ENST00000280665.6	37	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732160	0.69189	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	T;T;T	0.23950	2.1;2.1;1.88	5.73	4.84	0.62591	.	0.054750	0.64402	D	0.000001	T	0.49029	0.1533	M	0.67953	2.075	0.45791	D	0.998674	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.971	T	0.51849	-0.8653	10	0.72032	D	0.01	-25.192	13.8354	0.63406	0.0731:0.0:0.9269:0.0	.	88;190	B4DRD1;Q8IZD4	.;DCP1B_HUMAN	M	190;88;64	ENSP00000280665:I190M;ENSP00000380358:I88M;ENSP00000444374:I64M	ENSP00000280665:I190M	I	-	3	3	DCP1B	1934940	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.749000	0.38319	1.426000	0.47256	0.655000	0.94253	ATC	.		0.413	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		C	2064679	G	C	2064679	3	2	109	1	0	0	0	0	1	0	0	0	4305	932	33	4	1299	4	DCP1B	12	2064679	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	1718330	2064679	131787216	89	9682											
DDX47	51202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12980185	12980185	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttccttcctcaggtatgAtgtggaactcttccagcgca	7	14	9	11	1	2	1	1	1	1	0	5	2	5	2	3	2	2	3	3	2	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:12980185A>C	ENST00000358007.3	+	11	1134	c.1112A>C	c.(1111-1113)gAt>gCt	p.D371A	DDX47_ENST00000352940.4_Missense_Mutation_p.D322A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	371	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CTCAGGTATGATGTGGAACTC	0.448																																					p.D371A		.											.	DDX47-226	0			c.A1112C						.						110	109	110					12																	12980185		2203	4300	6503	SO:0001583	missense	51202	exon11			GGTATGATGTGGA	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"DEAD-boxes"	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.1112A>C	12.37:g.12980185A>C	ENSP00000350698:p.Asp371Ala	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	126	42	NM_016355	0	0	0	0	0	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.939470	0.73557	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.52983	0.64;3.36	5.64	5.64	0.86602	Helicase, C-terminal (1);	0.050495	0.85682	D	0.000000	T	0.73560	0.3602	M	0.89287	3.02	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.74023	0.982;0.971	T	0.79650	-0.1715	10	0.87932	D	0	-16.8971	15.8578	0.78994	1.0:0.0:0.0:0.0	.	322;371	G5E955;Q9H0S4	.;DDX47_HUMAN	A	322;371	ENSP00000319578:D322A;ENSP00000350698:D371A	ENSP00000319578:D322A	D	+	2	0	DDX47	12871452	1.000000	0.71417	0.944000	0.38274	0.435000	0.31806	8.932000	0.92897	2.147000	0.66899	0.533000	0.62120	GAT	.		0.448	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		C	12980185	A	C	12980185	3	2	109	1	0	0	0	0	1	0	0	0	4371	333	12	5	1154	5	DDX47	12	12980185	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	10915506	12980185	120871710	90	9683											
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	26810769	26810769	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccaaacttcttcatcatcaAtgtcatctgaaaggatggag	13	11	8	9	0	6	1	4	1	2	0	6	3	6	3	1	2	1	0	1	2	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:26810769A>T	ENST00000381340.3	-	18	2479	c.2063T>A	c.(2062-2064)aTt>aAt	p.I688N		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	688					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTCATCATCAATGTCATCTGA	0.423																																					p.I688N		.											.	ITPR2-542	0			c.T2063A						.						117	109	112					12																	26810769		1908	4126	6034	SO:0001583	missense	3709	exon18			TCATCAATGTCAT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.2063T>A	12.37:g.26810769A>T	ENSP00000370744:p.Ile688Asn	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	108	33	NM_002223	0	0	0	0	0	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	8.672	0.902956	0.17760	.	.	ENSG00000123104	ENST00000381340	D	0.91894	-2.93	4.4	4.4	0.53042	.	0.556787	0.20935	N	0.083032	D	0.83815	0.5336	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.78633	-0.2128	10	0.23891	T	0.37	.	12.6771	0.56901	1.0:0.0:0.0:0.0	.	688	Q14571	ITPR2_HUMAN	N	688	ENSP00000370744:I688N	ENSP00000370744:I688N	I	-	2	0	ITPR2	26702036	0.839000	0.29477	0.973000	0.42090	0.226000	0.24999	3.396000	0.52565	1.983000	0.57843	0.533000	0.62120	ATT	.		0.423	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26810769	A	T	26810769	3	4	109	1	0	0	0	0	1	0	0	0	7942	101	4	5	6202	5	ITPR2	12	26810769	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	13830584	26810769	107041126	91	9684											
SLC2A13	114134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	40265609	40265609	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagccacctacctgctaaacTaccaaaggtaagctttctgc	12	9	6	14	0	1	0	0	0	1	0	1	0	1	0	4	1	7	3	4	1	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:40265609T>C	ENST00000280871.4	-	5	1239	c.1189A>G	c.(1189-1191)Agt>Ggt	p.S397G		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	397					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CCTGCTAAACTACCAAAGGTA	0.378										HNSCC(50;0.14)																											p.S397G		.											.	SLC2A13-515	0			c.A1189G						.						55	54	54					12																	40265609		2203	4300	6503	SO:0001583	missense	114134	exon5			CTAAACTACCAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.1189A>G	12.37:g.40265609T>C	ENSP00000280871:p.Ser397Gly	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	90	33	NM_052885	0	0	0	0	0	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	37	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	T	25.2	4.609414	0.87258	.	.	ENSG00000151229	ENST00000280871	T	0.58797	0.31	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	N	0.19112	0.55	0.80722	D	1	D	0.65815	0.995	D	0.67382	0.951	T	0.54556	-0.8276	10	0.14252	T	0.57	-16.2802	15.8683	0.79084	0.0:0.0:0.0:1.0	.	397	Q96QE2	MYCT_HUMAN	G	397	ENSP00000280871:S397G	ENSP00000280871:S397G	S	-	1	0	SLC2A13	38551876	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	7.745000	0.85046	2.214000	0.71695	0.528000	0.53228	AGT	.		0.378	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			C	40265609	T	C	40265609	3	2	109	1	0	0	0	0	1	0	0	0	14574	1522	53	3	781	3	SLC2A13	12	40265609	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	13454840	40265609	93586286	92	9685											
CCNT1	904	broad.mit.edu	37	chr12	49088009	49088009	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggacagccaacgcttgcccgGcaacatctccacactggtta	10	7	9	15	2	1	0	0	0	1	0	2	1	1	1	3	3	4	3	3	3	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:49088009G>A	ENST00000261900.3	-	9	1210	c.988C>T	c.(988-990)Ccg>Tcg	p.P330S		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	330					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						CGCTTGCCCGGCAACATCTCC	0.488																																					p.P330S													.	CCNT1-418	0			c.C988T						.						123	111	115					12																	49088009		2203	4300	6503	SO:0001583	missense	904	exon9			TGCCCGGCAACAT	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.988C>T	12.37:g.49088009G>A	ENSP00000261900:p.Pro330Ser	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	113	4	NM_001240	0	0	11	11	0	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	37	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.037628	0.00402	.	.	ENSG00000129315	ENST00000261900	T	0.40476	1.03	5.49	4.6	0.57074	.	0.466481	0.20096	N	0.099336	T	0.17195	0.0413	N	0.08118	0	0.19575	N	0.999967	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	10	0.02654	T	1	-0.5634	6.0824	0.19948	0.166:0.1564:0.6776:0.0	.	330	O60563	CCNT1_HUMAN	S	330	ENSP00000261900:P330S	ENSP00000261900:P330S	P	-	1	0	CCNT1	47374276	0.206000	0.23470	0.888000	0.34837	0.341000	0.28922	2.581000	0.46077	1.327000	0.45338	0.491000	0.48974	CCG	.		0.488	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		A	49088009	G	A	49088009	3	1	109	1	0	0	0	0	1	0	0	0	2940	1203	42	2	1196	2	CCNT1	12	49088009	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	8822400	49088009	84763886	93	9686											
MARS	4141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57891971	57891971	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagaaaggaatgtgctcAtcaccagtgccctcccttac	10	9	9	13	0	2	1	2	0	0	1	3	3	3	2	3	2	3	1	3	2	3	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:57891971A>C	ENST00000262027.5	+	8	936	c.802A>C	c.(802-804)Atc>Ctc	p.I268L	MARS_ENST00000447721.2_3'UTR|MARS_ENST00000315473.5_Missense_Mutation_p.I34L	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	268					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GAATGTGCTCATCACCAGTGC	0.537																																					p.I268L		.											.	MARS-654	0			c.A802C						.						182	131	148					12																	57891971		2203	4300	6503	SO:0001583	missense	4141	exon8			GTGCTCATCACCA	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.802A>C	12.37:g.57891971A>C	ENSP00000262027:p.Ile268Leu	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	89	28	NM_004990	0	0	23	39	16	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	37	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.760542	0.89932	.	.	ENSG00000166986	ENST00000262027;ENST00000315473	T;T	0.54675	1.05;0.56	4.7	4.7	0.59300	Aminoacyl-tRNA synthetase, class I (M) (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.070998	0.64402	D	0.000014	T	0.69223	0.3087	M	0.85630	2.765	0.54753	D	0.999982	B;P;P	0.45902	0.338;0.606;0.868	B;P;P	0.55087	0.167;0.46;0.768	T	0.74760	-0.3556	10	0.72032	D	0.01	-16.6576	11.9918	0.53180	1.0:0.0:0.0:0.0	.	34;141;268	A6NC17;B4E0E9;P56192	.;.;SYMC_HUMAN	L	268;34	ENSP00000262027:I268L;ENSP00000314653:I34L	ENSP00000262027:I268L	I	+	1	0	MARS	56178238	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.315000	0.51951	1.884000	0.54569	0.459000	0.35465	ATC	.		0.537	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		C	57891971	A	C	57891971	3	2	109	1	0	0	0	0	1	0	0	0	9341	217	8	5	832	5	MARS	12	57891971	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	8803962	57891971	75959924	94	9687											
NAV3	89795	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	78513435	78513436	+	Frame_Shift_Ins	INS	-	-	G																															gtggcattcctggccgaggaINSggccacagatccagtaccag																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:78513435_78513436insG	ENST00000397909.2	+	15	3632_3633	c.3459_3460insG	c.(3460-3462)ggcfs	p.G1154fs	NAV3_ENST00000536525.2_Frame_Shift_Ins_p.G1154fs|NAV3_ENST00000266692.7_Frame_Shift_Ins_p.G1154fs|NAV3_ENST00000228327.6_Frame_Shift_Ins_p.G1154fs			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1154	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTGGCCGAGGAGGCCACAGATC	0.525										HNSCC(70;0.22)																											p.G1153fs		.											.	NAV3-279	0			c.3459_3460insG						.																																			SO:0001589	frameshift_variant	89795	exon15			.	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3461dupG	12.37:g.78513437_78513437dupG	ENSP00000381007:p.Gly1154fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	73	20	NM_014903	0	0	0	0	0	Q8NFW7|Q9Y2E7	Frame_Shift_Ins	INS	ENST00000397909.2	37																																																																																				.		0.525	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78513436	-	G	78513435	7	5	109	1	0	1	1	0	0	0	0	0	10210	291	11	0	3517	0	NAV3	12	78513435	Frame_Shift_Ins	INS	-	TCGA-EV-5903-01A-11D-1589-08	20621464	78513435	55338460	95	9688											
PEBP1	5037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	118577332	118577332	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagtcctctccgattatgtgGgctcggggcctcccaagggc	5	9	13	14	2	1	0	0	0	1	0	5	1	3	0	4	4	0	1	4	4	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:118577332G>T	ENST00000261313.2	+	3	674	c.322G>T	c.(322-324)Ggc>Tgc	p.G108C	PEBP1_ENST00000542939.1_3'UTR	NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	108	Interaction with RAF1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGATTATGTGGGCTCGGGGCC	0.527																																					p.G108C	NSCLC(44;94 1357 12187 49467)	.											.	PEBP1-779	0			c.G322T						.						125	112	116					12																	118577332		2203	4300	6503	SO:0001583	missense	5037	exon3			TATGTGGGCTCGG	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.322G>T	12.37:g.118577332G>T	ENSP00000261313:p.Gly108Cys	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	89	16	NM_002567	0	0	430	702	272	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	37	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595001	0.86953	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.57595	0.39	5.43	4.54	0.55810	.	0.047800	0.85682	D	0.000000	D	0.82614	0.5075	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88953	0.3388	10	0.87932	D	0	.	13.8987	0.63790	0.0734:0.0:0.9265:0.0	.	108;108	B4DRT4;P30086	.;PEBP1_HUMAN	C	108	ENSP00000261313:G108C	ENSP00000261313:G108C	G	+	1	0	PEBP1	117061715	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.447000	0.97595	1.280000	0.44463	0.563000	0.77884	GGC	.		0.527	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		T	118577332	G	T	118577332	3	4	109	1	0	0	0	0	1	0	0	0	11739	1232	43	4	332	4	PEBP1	12	118577332	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	40063897	118577332	15274563	96	9689											
PSPC1	55269	hgsc.bcm.edu;bcgsc.ca	37	chr13	20356720	20356720	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtcgatagtgaaccccatctCctcgtccgggtggtcctctg	5	11	11	14	3	2	1	0	1	2	0	7	2	4	1	5	2	1	0	5	2	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr13:20356720C>T	ENST00000338910.4	-	1	337	c.178G>A	c.(178-180)Gag>Aag	p.E60K		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	60					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AACCCCATCTCCTCGTCCGGG	0.692																																					p.E60K		.											.	PSPC1-135	0			c.G178A						.						35	37	36					13																	20356720		1929	4130	6059	SO:0001583	missense	55269	exon2			CCATCTCCTCGTC	AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.178G>A	13.37:g.20356720C>T	ENSP00000343966:p.Glu60Lys	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	76	24	NM_001042414	0	0	7	9	2	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.301856	0.40694	.	.	ENSG00000121390	ENST00000338910;ENST00000427943	T;T	0.14640	2.49;2.52	4.8	4.8	0.61643	.	0.347470	0.29396	N	0.012262	T	0.12561	0.0305	L	0.36672	1.1	0.45648	D	0.998577	B	0.21688	0.059	B	0.15870	0.014	T	0.11108	-1.0601	10	0.15499	T	0.54	-5.6938	18.0489	0.89341	0.0:1.0:0.0:0.0	.	60	Q8WXF1	PSPC1_HUMAN	K	60	ENSP00000343966:E60K;ENSP00000393069:E60K	ENSP00000343966:E60K	E	-	1	0	PSPC1	19254720	0.983000	0.35010	0.801000	0.32222	0.460000	0.32559	3.317000	0.51968	2.511000	0.84671	0.313000	0.20887	GAG	.		0.692	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			T	20356720	C	T	20356720	3	4	109	1	0	0	0	0	1	0	0	0	12745	864	30	2	1429	2	PSPC1	13	20356720	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		20356720	94813158	97	9690											
SUPT16H	11198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21821861	21821861	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	actttgctctgtaagactaaCctgactcttctgcttctgat	8	16	6	11	0	4	3	0	2	4	1	4	3	4	3	1	0	3	3	1	0	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:21821861C>T	ENST00000216297.2	-	24	3259		c.e24+1			NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)						DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		GTAAGACTAACCTGACTCTTC	0.378																																					.		.											.	SUPT16H-90	0			c.2920+1G>A						.						178	155	163					14																	21821861		2203	4300	6503	SO:0001630	splice_region_variant	11198	exon25			GACTAACCTGACT	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 140 kDa subunit"	605012	"suppressor of Ty (S.cerevisiae) 16 homolog"			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.2920+1G>A	14.37:g.21821861C>T		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	147	36	NM_007192	0	0	0	3	3	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Splice_Site	SNP	ENST00000216297.2	37	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.254717	0.80135	.	.	ENSG00000092201	ENST00000216297	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9497	0.89048	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SUPT16H	20891701	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	6.568000	0.73987	2.602000	0.87976	0.558000	0.71614	.	.		0.378	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		Intron	T	21821861	C	T	21821861	5	4	109	1	0	0	0	0	0	0	1	0	15428	521	18	2	234	2	SUPT16H	14	21821861	Splice_Site	SNP	C	TCGA-EV-5903-01A-11D-1589-08		21821861	85527679	98	9691											
OR4E2	26686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	22133796	22133796	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgactattcgtctacCttactgtggccccaacatta	8	15	5	13	1	2	1	0	1	2	0	3	1	2	1	3	1	3	0	3	1	5	7			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:22133796C>G	ENST00000408935.1	+	1	500	c.500C>G	c.(499-501)cCt>cGt	p.P167R		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	167						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		ATTCGTCTACCTTACTGTGGC	0.458																																					p.P167R		.											.	OR4E2-94	0			c.C500G						.						166	157	160					14																	22133796		1998	4205	6203	SO:0001583	missense	26686	exon1			GTCTACCTTACTG		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"GPCR / Class A : Olfactory receptors"	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.500C>G	14.37:g.22133796C>G	ENSP00000386195:p.Pro167Arg	Somatic	195	1		WXS	Illumina HiSeq	Phase_I	183	58	NM_001001912	0	0	0	0	0	Q6IET6|Q96R62	Missense_Mutation	SNP	ENST00000408935.1	37	CCDS41916.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937879	0.52972	.	.	ENSG00000221977	ENST00000408935	T	0.00193	8.58	5.88	5.88	0.94601	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	U	0.001868	T	0.00637	0.0021	M	0.85041	2.73	0.39412	D	0.96676	D	0.89917	1.0	D	0.91635	0.999	T	0.70360	-0.4893	10	0.87932	D	0	.	12.6329	0.56667	0.1653:0.8346:0.0:0.0	.	167	Q8NGC2	OR4E2_HUMAN	R	167	ENSP00000386195:P167R	ENSP00000386195:P167R	P	+	2	0	OR4E2	21203636	0.013000	0.17824	0.998000	0.56505	0.982000	0.71751	2.541000	0.45735	2.777000	0.95525	0.585000	0.79938	CCT	.		0.458	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1			G	22133796	C	G	22133796	3	3	109	1	0	0	0	0	1	0	0	0	11086	681	24	4	502	4	OR4E2	14	22133796	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	311935	22133796	85215744	99	9692											
AP1G2	8906	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	24036472	24036472	+	Frame_Shift_Del	DEL	C	C	-																															ctcctgggcctgagtcttggCcccgcgaatctcttcgatga																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:24036472delC	ENST00000308724.5	-	1	807	c.52delG	c.(52-54)gccfs	p.A18fs	AP1G2_ENST00000556277.1_5'UTR|AP1G2_ENST00000397120.3_Frame_Shift_Del_p.A18fs|RP11-66N24.3_ENST00000555968.1_RNA	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	18					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TGAGTCTTGGCCCCGCGAATC	0.637											OREG0022606	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A18fs		.											.	AP1G2-45	0			c.52delG						.						53	43	46					14																	24036472		2203	4300	6503	SO:0001589	frameshift_variant	8906	exon2			.	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.52delG	14.37:g.24036472delC	ENSP00000312442:p.Ala18fs	Somatic	63	0	768	WXS	Illumina HiSeq	Phase_I	70	15	NM_003917	0	0	0	0	0	D3DS51|O75504	Frame_Shift_Del	DEL	ENST00000308724.5	37	CCDS9602.1																																																																																			.		0.637	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		-	24036472	C	-	24036472	7	5	109	1	0	1	0	1	0	0	0	0	733	739	26	0	2389	0	AP1G2	14	24036472	Frame_Shift_Del	DEL	C	TCGA-EV-5903-01A-11D-1589-08	1902676	24036472	83313068	100	9693											
NIN	51199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	51219341	51219341	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttctggcatagcatttcTgttagacgttgattaagttc	8	17	8	8	1	2	2	0	1	2	1	4	2	3	2	1	1	1	5	1	1	3	7			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:51219341T>A	ENST00000382041.3	-	21	5035	c.4845A>T	c.(4843-4845)acA>acT	p.T1615T	NIN_ENST00000389868.3_Silent_p.T902T|NIN_ENST00000245441.5_Silent_p.T1615T|NIN_ENST00000530997.2_Silent_p.T1615T|NIN_ENST00000324330.9_Silent_p.T1615T|NIN_ENST00000382043.4_Silent_p.T902T|NIN_ENST00000453196.1_Silent_p.T1615T	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1615					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					ATAGCATTTCTGTTAGACGTT	0.368			T	PDGFRB	MPD																																p.T1615T		.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN-229	0			c.A4845T						.						306	295	299					14																	51219341		2203	4300	6503	SO:0001819	synonymous_variant	51199	exon21			CATTTCTGTTAGA	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.4845A>T	14.37:g.51219341T>A		Somatic	579	0		WXS	Illumina HiSeq	Phase_I	540	165	NM_020921	0	0	25	46	21	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	T	9.123	1.009401	0.19277	.	.	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.74	-2.9	0.05648	.	.	.	.	.	.	.	.	.	.	.	0.38083	D	0.936736	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.4293	2.5367	0.04716	0.1233:0.351:0.1277:0.398	.	.	.	.	X	1106	.	.	R	-	1	2	NIN	50289091	0.799000	0.28903	0.876000	0.34364	0.839000	0.47603	-0.187000	0.09656	-0.385000	0.07833	0.533000	0.62120	AGA	.		0.368	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51219341	T	A	51219341	2	1	109	1	0	0	0	0	0	0	0	1	10443	1567	55	5		5	NIN	14	51219341	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	27182869	51219341	56130199	101	9694											
MNAT1	4331	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	61434986	61434986	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcctcaccacaggacctTgctggaggctatacttcttc	7	11	9	14	0	2	0	1	0	1	0	3	2	2	2	3	3	3	3	3	3	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:61434986T>C	ENST00000261245.4	+	8	950	c.849T>C	c.(847-849)ctT>ctC	p.L283L	MNAT1_ENST00000539616.2_Silent_p.L241L|RP11-193F5.1_ENST00000553946.1_RNA	NM_002431.3	NP_002422.1	P51948	MAT1_HUMAN	MNAT CDK-activating kinase assembly factor 1	283					7-methylguanosine mRNA capping (GO:0006370)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to calcium ion (GO:0051592)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|ventricular system development (GO:0021591)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		CACAGGACCTTGCTGGAGGCT	0.398								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.L283L		.											.	MNAT1-523	0			c.T849C						.						133	119	124					14																	61434986		2203	4300	6503	SO:0001819	synonymous_variant	4331	exon8			GGACCTTGCTGGA	X87843	CCDS9750.1, CCDS53899.1	14q23	2013-07-31	2013-07-31		ENSG00000020426	ENSG00000020426		"RING-type (C3HC4) zinc fingers", "General transcription factor IIH complex subunits"	7181	protein-coding gene	gene with protein product	"CDK-activating kinase assembly factor"	602659	"menage a trois 1 (CAK assembly factor)", "menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)"			9465303	Standard	NM_002431		Approved	MAT1, RNF66	uc001xfd.3	P51948	OTTHUMG00000152340	ENST00000261245.4:c.849T>C	14.37:g.61434986T>C		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	145	51	NM_002431	0	0	7	14	7	G3V1U8|Q15817|Q6ICQ7	Silent	SNP	ENST00000261245.4	37	CCDS9750.1																																																																																			.		0.398	MNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276956.1	NM_002431		C	61434986	T	C	61434986	2	2	109	1	0	0	0	0	0	0	0	1	9699	1799	63	3		3	MNAT1	14	61434986	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	10215645	61434986	45914554	102	9695											
PAPLN	89932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	73733497	73733497	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgatacggccaggctatTgtgtgtggtagcaggagaaa	10	9	17	5	1	0	2	0	1	0	1	0	3	0	2	1	5	2	3	1	5	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:73733497T>C	ENST00000554301.1	+	24	3621	c.3458T>C	c.(3457-3459)tTg>tCg	p.L1153S	PAPLN_ENST00000427855.1_Missense_Mutation_p.L1153S|PAPLN_ENST00000555445.1_Missense_Mutation_p.L1137S|PAPLN_ENST00000340738.5_Missense_Mutation_p.L1126S|PAPLN_ENST00000381166.3_Intron			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	1153	Ig-like C2-type 3.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GCCAGGCTATTGTGTGTGGTA	0.542																																					p.L1126S		.											.	PAPLN-70	0			c.T3377C						.						211	153	173					14																	73733497		2203	4300	6503	SO:0001583	missense	89932	exon24			GGCTATTGTGTGT	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.3458T>C	14.37:g.73733497T>C	ENSP00000451803:p.Leu1153Ser	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	29	8	NM_173462	0	0	36	78	42	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		.	.	.	.	.	.	.	.	.	.	T	2.259	-0.369785	0.05069	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000554301;ENST00000555445	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.06	-8.09	0.01090	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.28400	0.0702	N	0.03608	-0.345	0.24632	N	0.993617	P;P;B;P	0.39920	0.646;0.695;0.2;0.622	B;B;B;B	0.43331	0.292;0.416;0.077;0.217	T	0.31392	-0.9945	9	0.08837	T	0.75	.	2.1116	0.03704	0.3364:0.3542:0.1653:0.1441	.	1137;1153;352;1126	O95428-5;O95428;O95428-2;O95428-6	.;PPN_HUMAN;.;.	S	1126;1153;1153;1137	ENSP00000345395:L1126S;ENSP00000403403:L1153S;ENSP00000451803:L1153S;ENSP00000451729:L1137S	ENSP00000345395:L1126S	L	+	2	0	PAPLN	72803250	0.000000	0.05858	0.051000	0.19133	0.088000	0.18126	0.124000	0.15728	-1.220000	0.02594	-0.389000	0.06534	TTG	.		0.542	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		C	73733497	T	C	73733497	3	2	109	1	0	0	0	0	1	0	0	0	11454	1821	63	3	3467	3	PAPLN	14	73733497	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	12298511	73733497	33616043	103	9696											
DLK1	8788	broad.mit.edu	37	chr14	101198410	101198410	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcctcggccccctgtgcCaacaacaggacctgcgtgag	7	7	11	16	2	0	1	0	1	0	0	2	2	1	2	5	2	5	1	5	2	2	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:101198410C>T	ENST00000341267.4	+	4	536	c.294C>T	c.(292-294)gcC>gcT	p.A98A	DLK1_ENST00000331224.6_Silent_p.A98A	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	98	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				CCCCCTGTGCCAACAACAGGA	0.627																																					p.A98A													.	DLK1-949	0			c.C294T						.						64	61	62					14																	101198410		2203	4300	6503	SO:0001819	synonymous_variant	8788	exon4			CTGTGCCAACAAC	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"delta-like homolog (Drosophila)"			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.294C>T	14.37:g.101198410C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	83	3	NM_003836	0	0	0	0	0	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			.		0.627	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			T	101198410	C	T	101198410	2	4	109	1	0	0	0	0	0	0	0	1	4575	581	21	2		2	DLK1	14	101198410	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08	27464913	101198410	6151130	104	9697											
ACSBG1	23205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	78474881	78474881	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agactagcacacagcactggTtgggctgctgggtgtcaatg	9	9	14	9	0	1	1	1	0	0	1	1	1	1	1	0	3	3	5	0	3	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr15:78474881T>G	ENST00000258873.4	-	7	1026	c.821A>C	c.(820-822)aAc>aCc	p.N274T	ACSBG1_ENST00000541759.1_Missense_Mutation_p.N32T|ACSBG1_ENST00000560817.1_Missense_Mutation_p.N32T	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	274					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						ACAGCACTGGTTGGGCTGCTG	0.587																																					p.N274T		.											.	ACSBG1-91	0			c.A821C						.						81	67	72					15																	78474881		2196	4293	6489	SO:0001583	missense	23205	exon7			CACTGGTTGGGCT	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"Acyl-CoA synthetase family"	29567	protein-coding gene	gene with protein product	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.821A>C	15.37:g.78474881T>G	ENSP00000258873:p.Asn274Thr	Somatic	59	2		WXS	Illumina HiSeq	Phase_I	45	8	NM_015162	0	0	0	0	0	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	37	CCDS10298.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606742	0.66558	.	.	ENSG00000103740	ENST00000258873;ENST00000541759	T;T	0.11063	2.81;2.81	5.27	5.27	0.74061	AMP-dependent synthetase/ligase (1);	0.056615	0.64402	D	0.000003	T	0.20373	0.0490	L	0.52823	1.66	0.53688	D	0.999972	P;B	0.43519	0.809;0.291	P;B	0.50162	0.633;0.363	T	0.00403	-1.1761	10	0.51188	T	0.08	-47.8285	14.4501	0.67379	0.0:0.0:0.0:1.0	.	270;274	B7Z2Y6;Q96GR2	.;ACBG1_HUMAN	T	274;32	ENSP00000258873:N274T;ENSP00000439955:N32T	ENSP00000258873:N274T	N	-	2	0	ACSBG1	76261936	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.948000	0.87774	1.991000	0.58162	0.529000	0.55759	AAC	.		0.587	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162		G	78474881	T	G	78474881	3	3	109	1	0	0	0	0	1	0	0	0	173	1725	60	5	1385	5	ACSBG1	15	78474881	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08		78474881	24056511	105	9698											
SOLH	6650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	599030	599030	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggatgacagcttccctcccgGgcccgagtctgtcggcttcc	4	9	12	16	3	1	1	0	1	1	0	5	3	4	2	4	3	1	2	4	3	0	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:599030G>A	ENST00000219611.2	+	5	1850	c.1487G>A	c.(1486-1488)gGg>gAg	p.G496E	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	496	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TTCCCTCCCGGGCCCGAGTCT	0.657																																					p.G496E		.											.	SOLH-523	0			c.G1487A						.						105	94	98					16																	599030		2198	4296	6494	SO:0001583	missense	6650	exon5			CTCCCGGGCCCGA	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1487G>A	16.37:g.599030G>A	ENSP00000219611:p.Gly496Glu	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	156	33	NM_005632	0	0	21	32	11	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	g	17.87	3.495721	0.64186	.	.	ENSG00000103326	ENST00000219611	T	0.39056	1.1	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (3);	0.097082	0.64402	D	0.000001	T	0.46776	0.1410	N	0.12920	0.275	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.40496	-0.9560	10	0.21014	T	0.42	.	16.9735	0.86306	0.0:0.0:1.0:0.0	.	496	O75808	CAN15_HUMAN	E	496	ENSP00000219611:G496E	ENSP00000219611:G496E	G	+	2	0	SOLH	539031	1.000000	0.71417	0.994000	0.49952	0.379000	0.30106	7.684000	0.84104	2.347000	0.79759	0.556000	0.70494	GGG	.		0.657	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		A	599030	G	A	599030	3	1	109	1	0	0	0	0	1	0	0	0	14957	1232	43	2	1493	2	SOLH	16	599030	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		599030	89755723	106	9699											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000563630.1_5'UTR|ZNF598_ENST00000562103.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_178167	0	0	0	9	9	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	109	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	1460644	2059674	88295079	107	9700											
CORO7	79585	ucsc.edu	37	chr16	4405363	4405363	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccccagttttgccaccatgGcattcagcagctgggagaga	9	9	11	12	0	1	1	1	0	0	1	2	3	2	2	4	2	3	4	4	2	0	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:4405363G>A	ENST00000251166.4	-	27	2841	c.2696C>T	c.(2695-2697)gCc>gTc	p.A899V	CORO7_ENST00000539968.1_Missense_Mutation_p.A679V|CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.A899V|PAM16_ENST00000576217.1_Intron|CORO7-PAM16_ENST00000572274.1_5'UTR|CORO7_ENST00000574025.1_Missense_Mutation_p.A814V|CORO7_ENST00000537233.2_Missense_Mutation_p.A881V	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	899					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						TGCCACCATGGCATTCAGCAG	0.577																																					p.A899V													.	CORO7-90	0			c.C2696T						.						31	26	28					16																	4405363		2197	4300	6497	SO:0001583	missense	79585	exon27			ACCATGGCATTCA	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"Coronins", "WD repeat domain containing"	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.2696C>T	16.37:g.4405363G>A	ENSP00000251166:p.Ala899Val	Somatic	60	0		WXS	Illumina HiSeq		41	4	NM_024535	0	0	0	0	0	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	37	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.497148	0.64186	.	.	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000539968	T;T;T	0.68331	-0.32;1.48;-0.32	4.96	4.0	0.46444	.	0.486738	0.16832	N	0.197705	T	0.80042	0.4551	M	0.70595	2.14	0.80722	D	1	D;P;P;D	0.89917	1.0;0.911;0.911;1.0	D;B;B;D	0.91635	0.999;0.432;0.432;0.997	T	0.80241	-0.1464	10	0.62326	D	0.03	-20.2483	12.9016	0.58128	0.0801:0.0:0.9199:0.0	.	814;881;899;880	P57737-2;B4DFD6;P57737;B4DKU9	.;.;CORO7_HUMAN;.	V	899;814;679	ENSP00000251166:A899V;ENSP00000440460:A814V;ENSP00000446221:A679V	ENSP00000251166:A899V	A	-	2	0	CORO7	4345364	1.000000	0.71417	0.997000	0.53966	0.200000	0.23975	7.319000	0.79040	1.091000	0.41335	-0.229000	0.12294	GCC	.		0.577	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535		A	4405363	G	A	4405363	3	1	109	1	0	0	0	0	1	0	0	0	3765	1203	42	2	89	2	CORO7	16	4405363	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	2345689	4405363	85949390	108	9701											
TMEM186	25880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	8890423	8890423	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacagcttttccccgaaaccTacgcacagctcggagaaggg	11	6	10	14	3	0	1	0	0	0	1	2	3	1	1	3	2	4	3	3	2	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:8890423T>C	ENST00000333050.6	-	2	61	c.28A>G	c.(28-30)Agg>Ggg	p.R10G	PMM2_ENST00000539622.1_5'Flank|PMM2_ENST00000268261.4_5'Flank|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000569958.1_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000566983.1_Intron	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	10						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						CCCCGAAACCTACGCACAGCT	0.547																																					p.R10G		.											.	TMEM186-91	0			c.A28G						.						67	70	69					16																	8890423		2197	4300	6497	SO:0001583	missense	25880	exon2			GAAACCTACGCAC	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 51"	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.28A>G	16.37:g.8890423T>C	ENSP00000331640:p.Arg10Gly	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	94	24	NM_015421	0	0	30	40	10	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	37	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.985216	0.35036	.	.	ENSG00000184857	ENST00000333050	.	.	.	4.53	2.24	0.28232	.	0.345193	0.20611	N	0.088971	T	0.34193	0.0889	L	0.57536	1.79	0.09310	N	1	P	0.36535	0.557	B	0.33620	0.167	T	0.15983	-1.0418	9	0.36615	T	0.2	-12.3261	8.7598	0.34667	0.0:0.0:0.3002:0.6998	.	10	Q96B77	TM186_HUMAN	G	10	.	ENSP00000331640:R10G	R	-	1	2	TMEM186	8797924	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.134000	0.15932	1.030000	0.39839	0.533000	0.62120	AGG	.		0.547	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421		C	8890423	T	C	8890423	3	2	109	1	0	0	0	0	1	0	0	0	16140	1521	53	3	617	3	TMEM186	16	8890423	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	4485060	8890423	81464330	109	9702											
SPNS1	83985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	28989282	28989282	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttggctacctgggtgacAggtacaatcggaagtatctc	9	12	12	8	1	1	1	0	1	1	0	3	2	1	2	1	4	2	4	1	4	5	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:28989282A>G	ENST00000311008.11	+	3	738	c.361A>G	c.(361-363)Agg>Ggg	p.R121G	SPNS1_ENST00000323081.8_Missense_Mutation_p.R48G|SPNS1_ENST00000334536.8_Missense_Mutation_p.R121G|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000352260.7_Missense_Mutation_p.R99G|SPNS1_ENST00000565975.1_Missense_Mutation_p.R166G|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000561868.1_Intron	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	121					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CCTGGGTGACAGGTACAATCG	0.577											OREG0023711	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R121G		.											.	SPNS1-90	0			c.A361G						.						239	183	202					16																	28989282		2197	4300	6497	SO:0001583	missense	83985	exon3			GGTGACAGGTACA	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.361A>G	16.37:g.28989282A>G	ENSP00000309945:p.Arg121Gly	Somatic	166	0	806	WXS	Illumina HiSeq	Phase_I	175	79	NM_001142451	0	0	37	101	64	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Missense_Mutation	SNP	ENST00000311008.11	37	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.497831	0.64186	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260;ENST00000323081	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	4.68	3.54	0.40534	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.81202	0.4773	M	0.92880	3.355	0.58432	D	0.999996	D;D;D;D;D	0.89917	1.0;1.0;0.996;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.998;0.999;1.0	T	0.82168	-0.0591	10	0.87932	D	0	.	8.7405	0.34554	0.6228:0.3772:0.0:0.0	.	48;99;121;121;121	Q9H2V7-4;Q9H2V7-3;Q9H2V7;Q9H2V7-2;Q9H2V7-5	.;.;SPNS1_HUMAN;.;.	G	121;121;99;48	ENSP00000309945:R121G;ENSP00000335494:R121G;ENSP00000306050:R99G;ENSP00000318228:R48G	ENSP00000309945:R121G	R	+	1	2	SPNS1	28896783	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.943000	0.56621	0.774000	0.33427	0.402000	0.26972	AGG	.		0.577	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		G	28989282	A	G	28989282	3	3	109	1	0	0	0	0	1	0	0	0	15106	179	7	3	371	3	SPNS1	16	28989282	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	20098859	28989282	61365471	110	9703											
MT1B	4490	ucsc.edu	37	chr16	56686910	56686910	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgctcttgctgccccgtggGctgtgccaagtgtgcccagg	3	10	14	14	1	1	0	0	0	1	0	1	0	1	0	4	2	5	3	4	2	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:56686910G>A	ENST00000334346.2	+	3	174	c.119G>A	c.(118-120)gGc>gAc	p.G40D	MT1B_ENST00000562399.1_Silent_p.G39G|RP11-249C24.11_ENST00000568608.1_RNA	NM_005947.2	NP_005938.1	P07438	MT1B_HUMAN	metallothionein 1B	40	Alpha.				cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TGCCCCGTGGGCTGTGCCAAG	0.592																																					p.G40D													.	MT1B-90	0			c.G119A						.						123	121	122					16																	56686910		2198	4300	6498	SO:0001583	missense	4490	exon3			CCGTGGGCTGTGC	AY168638	CCDS10765.1	16q13	2008-02-05	2007-03-02		ENSG00000169688	ENSG00000169688		"Metallothioneins"	7394	protein-coding gene	gene with protein product		156349	"metallothionein 1Q"	MT1, MT1Q		6089206, 3785191	Standard	NM_005947		Approved		uc002ejs.3	P07438	OTTHUMG00000133277	ENST00000334346.2:c.119G>A	16.37:g.56686910G>A	ENSP00000334998:p.Gly40Asp	Somatic	204	1		WXS	Illumina HiSeq		251	1	NM_005947	0	0	0	0	0	Q86YX0	Missense_Mutation	SNP	ENST00000334346.2	37	CCDS10765.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.241689	0.22711	.	.	ENSG00000169688	ENST00000334346	T	0.10288	2.89	2.84	1.84	0.25277	Metallothionein domain, vertebrate (1);Metallothionein domain (1);	0.089620	0.44483	N	0.000445	T	0.09512	0.0234	.	.	.	0.37807	D	0.927896	B	0.06786	0.001	B	0.06405	0.002	T	0.11891	-1.0569	9	0.66056	D	0.02	.	9.9659	0.41723	0.1226:0.0:0.8774:0.0	.	40	P07438	MT1B_HUMAN	D	40	ENSP00000334998:G40D	ENSP00000334998:G40D	G	+	2	0	MT1B	55244411	0.672000	0.27530	0.943000	0.38184	0.706000	0.40770	2.562000	0.45914	0.086000	0.17137	-1.303000	0.01326	GGC	.		0.592	MT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257057.2	NM_005947		A	56686910	G	A	56686910	3	1	109	1	0	0	0	0	1	0	0	0	9923	1203	42	2	129	2	MT1B	16	56686910	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	27697628	56686910	33667843	111	9704											
PMFBP1	83449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	72198700	72198700	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctccatgcagagctgaTtgtcctgcaaggtcttcctc	6	12	8	15	0	1	2	0	1	1	1	6	2	5	2	5	1	3	3	5	1	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:72198700T>C	ENST00000237353.10	-	3	389	c.128A>G	c.(127-129)aAt>aGt	p.N43S	PMFBP1_ENST00000537465.1_Missense_Mutation_p.N43S|PMFBP1_ENST00000355636.6_5'UTR|PMFBP1_ENST00000543746.1_5'UTR	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	43						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				GCAGAGCTGATTGTCCTGCAA	0.542																																					p.N43S		.											.	PMFBP1-92	0			c.A128G						.						133	111	119					16																	72198700		2198	4300	6498	SO:0001583	missense	83449	exon3			AGCTGATTGTCCT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.128A>G	16.37:g.72198700T>C	ENSP00000237353:p.Asn43Ser	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	185	81	NM_031293	0	0	0	0	0	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	T	9.847	1.192729	0.21954	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000535461;ENST00000539172;ENST00000536211;ENST00000540440	T;T	0.12774	2.65;2.65	5.85	2.17	0.27698	.	0.117279	0.38959	N	0.001506	T	0.05868	0.0153	N	0.19112	0.55	0.80722	D	1	B;B	0.16396	0.017;0.017	B;B	0.12156	0.007;0.007	T	0.30504	-0.9976	10	0.09590	T	0.72	-14.5061	2.3595	0.04304	0.1534:0.0827:0.1601:0.6038	.	43;43	Q8TBY8-2;G3V1Q7	.;.	S	43	ENSP00000443817:N43S;ENSP00000237353:N43S	ENSP00000237353:N43S	N	-	2	0	PMFBP1	70756201	0.858000	0.29795	0.998000	0.56505	0.204000	0.24138	0.499000	0.22546	0.464000	0.27142	-0.290000	0.09829	AAT	.		0.542	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		C	72198700	T	C	72198700	3	2	109	1	0	0	0	0	1	0	0	0	12160	1493	52	3	3031	3	PMFBP1	16	72198700	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	15511790	72198700	18156053	112	9705											
C16orf7	9605	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	89776218	89776219	+	Frame_Shift_Del	DEL	GA	GA	-																															gcagcagaggccacagcgggGagaaaaagggttcctcaatg																								rs565573769		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:89776218_89776219delGA	ENST00000389386.3	-	11	1478_1479	c.1354_1355delTC	c.(1354-1356)tccfs	p.S452fs	VPS9D1_ENST00000561976.1_Frame_Shift_Del_p.S382fs|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000565452.1_5'Flank	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	452					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCACAGCGGGGAGAAAAAGGGT	0.619																																					p.452_452del		.											.	.	0			c.1354_1355del						.																																			SO:0001589	frameshift_variant	9605	exon11			.	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1354_1355delTC	16.37:g.89776220_89776221delGA	ENSP00000374037:p.Ser452fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	183	31	NM_004913	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000389386.3	37	CCDS42220.1																																																																																			.		0.619	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		-	89776219	GA	-	89776218	7	5	109	1	0	1	0	1	0	0	0	0	1832	1174	41	0	560	0	C16orf7	16	89776218	Frame_Shift_Del	DEL	GA	TCGA-EV-5903-01A-11D-1589-08	17577518	89776218	578535	113	9706											
AIPL1	23746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	6328845	6328845	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggctctgcagggggccctgCggacagctctgcagatggtg	5	8	17	11	1	2	1	0	0	2	1	2	2	2	2	1	5	4	4	1	5	0	0	rs201875142		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:6328845C>T	ENST00000381129.3	-	6	1170	c.1090G>A	c.(1090-1092)Gca>Aca	p.A364T	AIPL1_ENST00000576776.1_Missense_Mutation_p.A340T|AIPL1_ENST00000570466.1_Missense_Mutation_p.A342T|AIPL1_ENST00000575265.1_3'UTR|AIPL1_ENST00000250087.5_Missense_Mutation_p.A301T|AIPL1_ENST00000576307.1_Missense_Mutation_p.A304T|AIPL1_ENST00000574506.1_Missense_Mutation_p.A352T	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	364					negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		gggggccctgcggacagctct	0.701																																					p.A364T		.											.	AIPL1-90	0			c.G1090A						.						47	47	47					17																	6328845		2202	4297	6499	SO:0001583	missense	23746	exon6			GCCCTGCGGACAG	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"aryl hydrocarbon receptor-interacting protein-like 1"	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.1090G>A	17.37:g.6328845C>T	ENSP00000370521:p.Ala364Thr	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	150	65	NM_014336	0	0	0	0	0	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	37	CCDS11075.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.800010	0.00611	.	.	ENSG00000129221	ENST00000381129;ENST00000381128;ENST00000250087	D;D	0.88354	-2.37;-2.28	2.43	-4.86	0.03132	.	14.175600	0.00357	N	0.000030	T	0.68357	0.2992	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.62282	-0.6887	10	0.15066	T	0.55	.	0.3578	0.00359	0.2708:0.2404:0.1332:0.3556	.	340;342;301;304;364	Q659W3;Q659W4;Q9NZN9-3;Q9NZN9-2;Q9NZN9	.;.;.;.;AIPL1_HUMAN	T	364;304;301	ENSP00000370521:A364T;ENSP00000250087:A301T	ENSP00000250087:A301T	A	-	1	0	AIPL1	6269569	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.245000	0.01192	-4.315000	0.00057	-3.419000	0.00038	GCA	.		0.701	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		T	6328845	C	T	6328845	3	4	109	1	0	0	0	0	1	0	0	0	436	768	27	1	68	1	AIPL1	17	6328845	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		6328845	74866365	114	9707											
AIPL1	23746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	6328868	6328868	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagctctgcagatggtgctGtgggtggctctgcaggtggc	5	10	17	9	0	2	1	0	0	2	1	2	1	2	1	0	5	4	5	0	5	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:6328868G>A	ENST00000381129.3	-	6	1147	c.1067C>T	c.(1066-1068)aCa>aTa	p.T356I	AIPL1_ENST00000576776.1_Missense_Mutation_p.T332I|AIPL1_ENST00000570466.1_Missense_Mutation_p.T334I|AIPL1_ENST00000575265.1_3'UTR|AIPL1_ENST00000250087.5_Missense_Mutation_p.T293I|AIPL1_ENST00000576307.1_Missense_Mutation_p.T296I|AIPL1_ENST00000574506.1_Missense_Mutation_p.T344I	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	356					negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		agatggtgctgtgggtggctc	0.692																																					p.T356I		.											.	AIPL1-90	0			c.C1067T						.						72	65	68					17																	6328868		2203	4298	6501	SO:0001583	missense	23746	exon6			GGTGCTGTGGGTG	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"aryl hydrocarbon receptor-interacting protein-like 1"	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.1067C>T	17.37:g.6328868G>A	ENSP00000370521:p.Thr356Ile	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	171	79	NM_014336	0	0	0	0	0	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	37	CCDS11075.1	.	.	.	.	.	.	.	.	.	.	G	9.219	1.032866	0.19590	.	.	ENSG00000129221	ENST00000381129;ENST00000381128;ENST00000250087	D;D	0.88818	-2.43;-2.33	2.56	2.56	0.30785	.	13.968300	0.01841	U	0.035287	T	0.81744	0.4887	N	0.19112	0.55	0.09310	N	0.999999	B;B;B;B;B	0.26775	0.099;0.099;0.159;0.159;0.099	B;B;B;B;B	0.15870	0.005;0.005;0.014;0.011;0.005	T	0.69624	-0.5095	10	0.37606	T	0.19	.	8.5789	0.33617	0.0:0.0:1.0:0.0	.	332;334;293;296;356	Q659W3;Q659W4;Q9NZN9-3;Q9NZN9-2;Q9NZN9	.;.;.;.;AIPL1_HUMAN	I	356;296;293	ENSP00000370521:T356I;ENSP00000250087:T293I	ENSP00000250087:T293I	T	-	2	0	AIPL1	6269592	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.481000	0.02323	1.405000	0.46838	0.407000	0.27541	ACA	.		0.692	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		A	6328868	G	A	6328868	3	1	109	1	0	0	0	0	1	0	0	0	436	1377	48	2	91	2	AIPL1	17	6328868	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	23	6328868	74866342	115	9708											
AMAC1L3	643664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7386125	7386125	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acatgtgtgagctatgcggtCaccaaggcccaccctgccct	8	8	10	15	1	1	1	1	1	0	0	1	1	1	1	4	2	3	1	4	2	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:7386125C>T	ENST00000412468.2	+	2	937	c.822C>T	c.(820-822)gtC>gtT	p.V274V	ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank|POLR2A_ENST00000322644.6_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	274	EamA 2.					integral component of membrane (GO:0016021)											GCTATGCGGTCACCAAGGCCC	0.592																																					p.V274V		.											.	.	0			c.C822T						.						146	125	132					17																	7386125		2203	4300	6503	SO:0001819	synonymous_variant	643664	exon2			TGCGGTCACCAAG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.822C>T	17.37:g.7386125C>T		Somatic	213	1		WXS	Illumina HiSeq	Phase_I	211	30	NM_001102614	0	0	0	0	0		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			.		0.592	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		T	7386125	C	T	7386125	2	4	109	1	0	0	0	0	0	0	0	1	561	813	29	2		2	AMAC1L3	17	7386125	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08	1057257	7386125	73809085	116	9709											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	545	73		WXS	Illumina HiSeq		626	86	NM_145301	0	0	18	79	61	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		T	15457087	C	T	15457087	3	4	109	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	8070962	15457087	65738123	117	9710											
FLCN	201163	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17119717	17119717	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagagcacgtggggggggAtctgcacgtgcgggctgagc	7	5	21	8	3	1	2	0	1	1	1	1	4	1	3	0	6	4	3	0	6	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:17119717A>G	ENST00000285071.4	-	11	1731	c.1277T>C	c.(1276-1278)aTc>aCc	p.I426T	RP11-45M22.4_ENST00000427497.3_3'UTR	NM_144997.5	NP_659434.2	Q8NFG4	FLCN_HUMAN	folliculin	426					cell-cell junction assembly (GO:0007043)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in kidney development (GO:1901723)|negative regulation of energy homeostasis (GO:2000506)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of gene expression (GO:0010629)|negative regulation of mitochondrion organization (GO:0010823)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of gene expression (GO:0010628)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cytokinesis (GO:0032465)|regulation of histone acetylation (GO:0035065)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|regulation of TOR signaling (GO:0032006)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|stomach(1)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GTGGGGGGGGATCTGCACGTG	0.667									Familial Non-VHL Clear Cell Renal Cancer;Birt-Hogg-Dub syndrome																												p.I426T													.	FLCN-1292	0			c.T1277C						.						81	67	72					17																	17119717		2203	4300	6503	SO:0001583	missense	201163	exon11	Familial Cancer Database	Familial Clear Cell Renal Cell Cancer, FcRCC, Familial Non-VHL Non-Papillary Clear Cell Renal Cancer;BHD, Fibrofolliculomas with Trichodiscomas and Acrochordons, incl.: Hornstein-Knickenberg syndrome, Perifollicular Fibromatosis	GGGGGGATCTGCA	AF517523	CCDS32579.1, CCDS32580.1	17p11.2	2014-09-17			ENSG00000154803	ENSG00000154803			27310	protein-coding gene	gene with protein product		607273					Standard	NM_144997		Approved	BHD, MGC17998, MGC23445	uc002gra.4	Q8NFG4	OTTHUMG00000059275	ENST00000285071.4:c.1277T>C	17.37:g.17119717A>G	ENSP00000285071:p.Ile426Thr	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	41	6	NM_144997	0	0	8	10	2	A6NJJ8|Q6ZRX1|Q96BD2|Q96BE4	Missense_Mutation	SNP	ENST00000285071.4	37	CCDS32579.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.111106	0.77210	.	.	ENSG00000154803	ENST00000285071	D	0.94576	-3.46	5.9	5.9	0.94986	.	0.140262	0.64402	D	0.000005	D	0.93400	0.7895	M	0.68593	2.085	0.80722	D	1	P	0.34462	0.454	B	0.32864	0.154	D	0.93165	0.6561	10	0.72032	D	0.01	-32.1067	16.3313	0.83015	1.0:0.0:0.0:0.0	.	426	Q8NFG4	FLCN_HUMAN	T	426	ENSP00000285071:I426T	ENSP00000285071:I426T	I	-	2	0	FLCN	17060442	1.000000	0.71417	0.996000	0.52242	0.959000	0.62525	8.547000	0.90665	2.266000	0.75297	0.529000	0.55759	ATC	.		0.667	FLCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131577.1	NM_144606		G	17119717	A	G	17119717	3	3	109	1	0	0	0	0	1	0	0	0	5940	333	12	3	478	3	FLCN	17	17119717	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	1662630	17119717	64075493	118	9711											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18063318	18063318	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaagcagatcacagacaatAccagctccaagcagtgagtg	15	6	10	10	0	1	4	1	2	0	2	2	4	2	4	2	0	4	3	2	0	4	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:18063318A>G	ENST00000205890.5	+	56	9711	c.9373A>G	c.(9373-9375)Acc>Gcc	p.T3125A	MYO15A_ENST00000451725.2_Missense_Mutation_p.T17A|MYO15A_ENST00000418233.3_Missense_Mutation_p.T389A	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3125	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CACAGACAATACCAGCTCCAA	0.562																																					p.T3125A		.											.	MYO15A-97	0			c.A9373G						.						108	110	110					17																	18063318		2118	4230	6348	SO:0001583	missense	51168	exon55			GACAATACCAGCT	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.9373A>G	17.37:g.18063318A>G	ENSP00000205890:p.Thr3125Ala	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_016239	0	0	0	0	0	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.844770	0.32606	.	.	ENSG00000091536	ENST00000205890;ENST00000418233;ENST00000556535;ENST00000557190;ENST00000451725	D;D;D	0.91521	-2.86;-2.86;-2.86	5.6	4.52	0.55395	MyTH4 domain (3);	.	.	.	.	D	0.87842	0.6279	L	0.56396	1.775	0.48135	D	0.999593	B;B;B;B;P	0.44776	0.106;0.039;0.006;0.058;0.843	B;B;B;B;B	0.40659	0.147;0.052;0.02;0.076;0.336	D	0.85057	0.0932	9	0.35671	T	0.21	.	11.4255	0.50007	0.9294:0.0:0.0706:0.0	.	17;114;389;3125;132	B4DQJ3;B4DLV9;B4DFC7;Q9UKN7;Q8TCK0	.;.;.;MYO15_HUMAN;.	A	3125;114;79;17;17	ENSP00000205890:T3125A;ENSP00000451782:T79A;ENSP00000409098:T17A	ENSP00000205890:T3125A	T	+	1	0	MYO15A	18004043	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.660000	0.54496	0.967000	0.38186	0.459000	0.35465	ACC	.		0.562	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18063318	A	G	18063318	3	3	109	1	0	0	0	0	1	0	0	0	10088	391	14	3	9587	3	MYO15A	17	18063318	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	943601	18063318	63131892	119	9712											
ZNF207	7756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	30687743	30687743	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tattcctccaatggcacagcCaggactgccaccagtaccag	11	7	8	15	0	0	0	0	0	0	0	2	1	2	1	6	2	3	2	6	2	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:30687743C>A	ENST00000321233.6	+	4	588	c.434C>A	c.(433-435)cCa>cAa	p.P145Q	ZNF207_ENST00000577908.1_Missense_Mutation_p.P145Q|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000341711.6_Intron|ZNF207_ENST00000342555.6_Missense_Mutation_p.P148Q|ZNF207_ENST00000394673.2_Missense_Mutation_p.P145Q|ZNF207_ENST00000394670.4_Missense_Mutation_p.P145Q	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	145					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)			ATGGCACAGCCAGGACTGCCA	0.443																																					p.P145Q		.											.	ZNF207-90	0			c.C434A						.						60	51	54					17																	30687743		2203	4300	6503	SO:0001583	missense	7756	exon4			CACAGCCAGGACT	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.434C>A	17.37:g.30687743C>A	ENSP00000322777:p.Pro145Gln	Somatic	48	1		WXS	Illumina HiSeq	Phase_I	69	13	NM_003457	0	0	97	134	37	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	37	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.415696	0.25552	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000342555	T;T;T	0.50813	0.74;0.73;0.74	5.27	5.27	0.74061	.	0.165688	0.53938	D	0.000051	T	0.51873	0.1700	M	0.62723	1.935	0.80722	D	1	P;P;P;P;P	0.49090	0.919;0.919;0.919;0.799;0.799	P;P;P;B;B	0.46110	0.504;0.504;0.504;0.367;0.367	T	0.47873	-0.9083	10	0.18710	T	0.47	.	18.8845	0.92370	0.0:1.0:0.0:0.0	.	145;148;145;145;145	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	Q	145;145;148;145;145	ENSP00000378165:P145Q;ENSP00000378168:P145Q;ENSP00000322777:P145Q	ENSP00000322777:P145Q	P	+	2	0	ZNF207	27711856	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.611000	0.61162	2.463000	0.83235	0.655000	0.94253	CCA	.		0.443	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			A	30687743	C	A	30687743	3	1	109	1	0	0	0	0	1	0	0	0	17797	594	21	4	448	4	ZNF207	17	30687743	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	12624425	30687743	50507467	120	9713											
SKAP1	8631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	46266785	46266785	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgggtctgaccaatacCtttgcttttcttctccaagt	6	17	7	11	0	4	1	0	1	4	0	5	1	4	1	3	1	2	1	3	1	3	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:46266785C>T	ENST00000336915.6	-	5	427	c.358G>A	c.(358-360)Gat>Aat	p.D120N	SKAP1_ENST00000584924.1_Splice_Site_p.D120N|RP11-456D7.1_ENST00000582246.1_RNA	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	120	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						TGACCAATACCTTTGCTTTTC	0.433																																					p.D120N		.											.	SKAP1-90	0			c.G358A						.						183	146	158					17																	46266785		2203	4300	6503	SO:0001630	splice_region_variant	8631	exon5			CAATACCTTTGCT	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.358+1G>A	17.37:g.46266785C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	118	24	NM_003726	0	0	0	0	0	D3DTV1|O15268	Missense_Mutation	SNP	ENST00000336915.6	37	CCDS32674.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998944	0.54147	.	.	ENSG00000141293	ENST00000336915	T	0.11821	2.74	5.61	5.61	0.85477	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.35770	0.0943	L	0.60904	1.88	0.58432	D	0.999998	P;D	0.76494	0.536;0.999	P;D	0.79784	0.614;0.993	T	0.00783	-1.1568	9	.	.	.	-29.0873	19.225	0.93815	0.0:1.0:0.0:0.0	.	120;120	Q86WV1-2;Q86WV1	.;SKAP1_HUMAN	N	120	ENSP00000338171:D120N	.	D	-	1	0	SKAP1	43621784	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.108000	0.71522	2.640000	0.89533	0.563000	0.77884	GAT	.		0.433	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726	Missense_Mutation	T	46266785	C	T	46266785	5	4	109	1	0	0	0	0	0	0	1	0	14387	695	24	2	753	2	SKAP1	17	46266785	Splice_Site	SNP	C	TCGA-EV-5903-01A-11D-1589-08	15579042	46266785	34928425	121	9714											
FN3KRP	79672	broad.mit.edu	37	chr17	80674717	80674717	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggtgcatcagccagggccGgagctacgacacggatcaag	10	4	15	12	4	2	0	2	0	0	0	2	3	2	2	2	4	4	2	2	4	2	1	rs138953335		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:80674717G>A	ENST00000269373.6	+	1	159	c.86G>A	c.(85-87)cGg>cAg	p.R29Q	RP11-388C12.1_ENST00000574471.1_lincRNA|FN3KRP_ENST00000535965.1_5'UTR	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	29							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			AGCCAGGGCCGGAGCTACGAC	0.701													G|||	1	0.000199681	0	0	5008	,	,		8572	0		0.001	False		,,,				2504	0				p.R29Q													.	FN3KRP-115	0			c.G86A						.	G	GLN/ARG	0,4400		0,0,2200	29	31	30		86	0.5	1	17	dbSNP_134	30	2,8588		0,2,4293	yes	missense	FN3KRP	NM_024619.3	43	0,2,6493	AA,AG,GG		0.0233,0.0,0.0154	benign	29/310	80674717	2,12988	2200	4295	6495	SO:0001583	missense	79672	exon1			AGGGCCGGAGCTA	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.86G>A	17.37:g.80674717G>A	ENSP00000269373:p.Arg29Gln	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_024619	0	0	19	19	0	Q969F4|Q9H0U7	Missense_Mutation	SNP	ENST00000269373.6	37	CCDS11817.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433978	0.25813	0.0	2.33E-4	ENSG00000141560	ENST00000269373	T	0.51071	0.72	5.29	0.486	0.16836	Protein kinase-like domain (1);	0.111667	0.64402	N	0.000005	T	0.20495	0.0493	N	0.03154	-0.405	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.04178	-1.0971	10	0.25106	T	0.35	-18.0073	9.3104	0.37900	0.7114:0.0:0.2886:0.0	.	29	Q9HA64	KT3K_HUMAN	Q	29	ENSP00000269373:R29Q	ENSP00000269373:R29Q	R	+	2	0	FN3KRP	78268006	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	2.337000	0.43947	0.065000	0.16485	-0.312000	0.09012	CGG	G|1.000;A|0.000		0.701	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619		A	80674717	G	A	80674717	3	1	109	1	0	0	0	0	1	0	0	0	5983	1116	39	1	88	1	FN3KRP	17	80674717	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	34407932	80674717	520493	122	9715											
PTPRM	5797	broad.mit.edu	37	chr18	8376563	8376563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaactgcgtcagggagctgCggtcacggagggtgaacatg	10	6	16	9	3	2	1	2	1	0	0	2	3	2	3	0	4	5	1	0	4	2	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr18:8376563C>T	ENST00000332175.8	+	24	4428	c.3391C>T	c.(3391-3393)Cgg>Tgg	p.R1131W	PTPRM_ENST00000580170.1_Missense_Mutation_p.R1144W|PTPRM_ENST00000400053.4_Missense_Mutation_p.R1069W|PTPRM_ENST00000444013.1_Missense_Mutation_p.R918W|PTPRM_ENST00000400060.4_Missense_Mutation_p.R1145W	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1131	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CAGGGAGCTGCGGTCACGGAG	0.572																																					p.R1144W													.	PTPRM-228	0			c.C3430T						.						134	107	116					18																	8376563		2203	4300	6503	SO:0001583	missense	5797	exon26			GAGCTGCGGTCAC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3391C>T	18.37:g.8376563C>T	ENSP00000331418:p.Arg1131Trp	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_001105244	0	0	39	39	0	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.010361	0.93346	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88	5.88	5.88	0.94601	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.97845	0.9292	H	0.97540	4.025	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.98415	1.0574	10	0.72032	D	0.01	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	918;1144;1131	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	W	1131;1145;1069;918	ENSP00000331418:R1131W;ENSP00000382933:R1145W;ENSP00000382927:R1069W;ENSP00000387608:R918W	ENSP00000331418:R1131W	R	+	1	2	PTPRM	8366563	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.781000	0.62389	2.789000	0.95967	0.591000	0.81541	CGG	.		0.572	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8376563	C	T	8376563	3	4	109	1	0	0	0	0	1	0	0	0	12838	759	27	1	3532	1	PTPRM	18	8376563	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		8376563	69700685	123	9716											
TMX3	54495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	66378637	66378637	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatcatttcgattttctttAaacctaaaaaacaagaaaac	18	13	2	8	1	3	1	2	0	1	1	4	2	3	1	1	0	3	0	1	0	8	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr18:66378637A>C	ENST00000299608.2	-	3	421	c.105T>G	c.(103-105)ttT>ttG	p.F35L	TMX3_ENST00000562706.1_Missense_Mutation_p.F35L|TMX3_ENST00000443099.2_Missense_Mutation_p.F35L	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	35	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						GATTTTCTTTAAACCTAAAAA	0.279																																					p.F35L		.											.	TMX3-91	0			c.T105G						.						84	90	88					18																	66378637		2202	4289	6491	SO:0001583	missense	54495	exon3			TTCTTTAAACCTA	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.105T>G	18.37:g.66378637A>C	ENSP00000299608:p.Phe35Leu	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	92	37	NM_019022	0	0	0	0	0	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	37	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615363	0.87359	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T;T	0.06608	3.28;3.28;3.28	5.36	5.36	0.76844	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.26955	0.0660	M	0.83384	2.64	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.998;0.986;0.999	T	0.01596	-1.1316	10	0.52906	T	0.07	.	13.3017	0.60328	1.0:0.0:0.0:0.0	.	35;35;35	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	L	35	ENSP00000299608:F35L;ENSP00000444954:F35L;ENSP00000402605:F35L	ENSP00000299608:F35L	F	-	3	2	TMX3	64529617	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.620000	0.61226	2.042000	0.60477	0.528000	0.53228	TTT	.		0.279	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		C	66378637	A	C	66378637	3	2	109	1	0	0	0	0	1	0	0	0	16300	359	13	5	1315	5	TMX3	18	66378637	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	58002074	66378637	11698611	124	9717											
ATP8B3	148229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1785678	1785678	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaccacgtacagctccggCttctccaggctctgctctgc	5	9	8	19	2	3	0	0	0	3	0	5	0	4	0	4	2	4	5	4	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:1785678C>A	ENST00000310127.6	-	26	3421	c.3183G>T	c.(3181-3183)aaG>aaT	p.K1061N	ATP8B3_ENST00000539485.1_Missense_Mutation_p.K1071N|ATP8B3_ENST00000525591.1_Missense_Mutation_p.K1024N	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1061					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAGCTCCGGCTTCTCCAGGC	0.602																																					p.K1061N		.											.	.	0			c.G3183T						.						26	29	28					19																	1785678		2120	4237	6357	SO:0001583	missense	148229	exon26			CTCCGGCTTCTCC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3183G>T	19.37:g.1785678C>A	ENSP00000311336:p.Lys1061Asn	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	28	7	NM_138813	0	0	1	1	0	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	C	8.917	0.960236	0.18507	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.70516	-0.49;-0.49;-0.49	4.48	3.39	0.38822	.	0.558416	0.19418	N	0.114773	T	0.40815	0.1132	N	0.02697	-0.525	0.23855	N	0.996656	B;B	0.30664	0.289;0.086	B;B	0.23275	0.045;0.045	T	0.33420	-0.9869	10	0.66056	D	0.02	.	6.6084	0.22737	0.149:0.5306:0.3204:0.0	.	1061;1024	O60423;Q7Z485	AT8B3_HUMAN;.	N	1061;1071;1024	ENSP00000311336:K1061N;ENSP00000443574:K1071N;ENSP00000437115:K1024N	ENSP00000311336:K1061N	K	-	3	2	ATP8B3	1736678	0.965000	0.33210	0.457000	0.27056	0.051000	0.14879	1.815000	0.38981	2.027000	0.59764	0.655000	0.94253	AAG	.		0.602	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		A	1785678	C	A	1785678	3	1	109	1	0	0	0	0	1	0	0	0	1197	796	28	4	735	4	ATP8B3	19	1785678	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		1785678	57343305	125	9718											
SFRS14	10147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19115397	19115397	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaacaaattgatggacataGttcaaacactttctttcgat	15	13	6	7	1	2	1	1	1	1	0	3	4	2	2	0	1	2	1	0	1	4	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:19115397G>T	ENST00000601879.1	-	7	2806	c.2509C>A	c.(2509-2511)Cta>Ata	p.L837I	SUGP2_ENST00000600377.1_Missense_Mutation_p.L851I|SUGP2_ENST00000337018.6_Missense_Mutation_p.L837I|SUGP2_ENST00000452918.2_Missense_Mutation_p.L837I|SUGP2_ENST00000456085.2_Missense_Mutation_p.L606I			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	837					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GATGGACATAGTTCAAACACT	0.463																																					p.L837I		.											.	SUGP2-91	0			c.C2509A						.						74	73	73					19																	19115397		2203	4300	6503	SO:0001583	missense	10147	exon7			GACATAGTTCAAA	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.2509C>A	19.37:g.19115397G>T	ENSP00000472286:p.Leu837Ile	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	153	41	NM_014884	0	0	6	11	5	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	37	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.590575	0.66219	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918;ENST00000456085	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.26	5.26	0.73747	SWAP/Surp (1);	0.000000	0.42294	D	0.000725	T	0.46151	0.1378	N	0.16307	0.4	0.39998	D	0.975121	D;D;D	0.76494	0.999;0.976;0.999	D;D;D	0.87578	0.998;0.914;0.997	T	0.45366	-0.9266	10	0.41790	T	0.15	-13.6122	11.5508	0.50719	0.086:0.0:0.914:0.0	.	606;837;837	E7ETX7;A8K5G0;Q8IX01	.;.;SUGP2_HUMAN	I	837;837;837;606	ENSP00000337926:L837I;ENSP00000332373:L837I;ENSP00000389380:L837I;ENSP00000409603:L606I	ENSP00000332373:L837I	L	-	1	2	SUGP2	18976397	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	1.688000	0.37690	2.459000	0.83118	0.563000	0.77884	CTA	.		0.463	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		T	19115397	G	T	19115397	3	4	109	1	0	0	0	0	1	0	0	0	14202	1020	36	4	755	4	SFRS14	19	19115397	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	17329719	19115397	40013586	126	9719											
RINL	126432	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	39359912	39359925	+	Frame_Shift_Del	DEL	TGCAGCGTCCGCCT	TGCAGCGTCCGCCT	-																															ctctgggatgatcctttctgTgcagcgtccgcctgcggtgc																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	TGCAGCGTCCGCCT	TGCAGCGTCCGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:39359912_39359925delTGCAGCGTCCGCCT	ENST00000591812.1	-	11	1686_1699	c.1600_1613delAGGCGGACGCTGCA	c.(1600-1614)aggcggacgctgcacfs	p.RRTLH534fs	RINL_ENST00000340740.3_Frame_Shift_Del_p.RRTLH420fs|CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000602238.1_5'Flank|RINL_ENST00000598904.1_Frame_Shift_Del_p.RRTLH420fs			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	534					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						ATCCTTTCTGTGCAGCGTCCGCCTGCGGTGCCAC	0.673																																					p.534_538del		.											.	RINL-91	0			c.1600_1613del						.																																			SO:0001589	frameshift_variant	126432	exon11			.	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1600_1613delAGGCGGACGCTGCA	19.37:g.39359912_39359925delTGCAGCGTCCGCCT	ENSP00000467107:p.Arg534fs	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	101	19	NM_001195833	0	0	0	0	0	B4DPG5	Frame_Shift_Del	DEL	ENST00000591812.1	37	CCDS59386.1																																																																																			.		0.673	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445		-	39359925	TGCAGCGTCCGCCT	-	39359912	7	5	109	1	0	1	0	1	0	0	0	0	13407	1696	59	0	95	0	RINL	19	39359912	Frame_Shift_Del	DEL	TGCAGCGTCCGCCT	TCGA-EV-5903-01A-11D-1589-08	20244515	39359912	19769071	127	9720											
ALDH16A1	126133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49969107	49969107	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tccatggctacgtggctgagGgtggagccaaggacatccga	9	7	15	10	2	0	1	0	1	0	0	2	4	2	3	3	5	2	2	3	5	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:49969107G>A	ENST00000293350.4	+	13	1844	c.1681G>A	c.(1681-1683)Ggt>Agt	p.G561S	ALDH16A1_ENST00000433981.2_Missense_Mutation_p.G396S|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.G398S|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.G510S	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	561						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGTGGCTGAGGGTGGAGCCAA	0.642																																					p.G561S		.											.	ALDH16A1-91	0			c.G1681A						.						39	40	40					19																	49969107		2203	4300	6503	SO:0001583	missense	126133	exon13			GCTGAGGGTGGAG	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"Aldehyde dehydrogenases"	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1681G>A	19.37:g.49969107G>A	ENSP00000293350:p.Gly561Ser	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	55	13	NM_153329	0	1	21	44	22	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007403	0.75046	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	4.77	4.77	0.60923	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.220696	0.37623	N	0.002003	D	0.83751	0.5322	M	0.64567	1.98	0.44254	D	0.997108	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.84182	0.0440	10	0.46703	T	0.11	-20.3157	15.3078	0.74008	0.0:0.0:1.0:0.0	.	398;510;561	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	S	561;510;398;396	ENSP00000293350:G561S;ENSP00000410142:G510S;ENSP00000445088:G398S;ENSP00000398675:G396S	ENSP00000293350:G561S	G	+	1	0	ALDH16A1	54660919	0.985000	0.35326	0.999000	0.59377	0.666000	0.39218	1.078000	0.30754	2.206000	0.71126	0.561000	0.74099	GGT	.		0.642	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		A	49969107	G	A	49969107	3	1	109	1	0	0	0	0	1	0	0	0	488	1232	43	2	1731	2	ALDH16A1	19	49969107	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	10609195	49969107	9159876	128	9721											
ZNF836	162962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52659397	52659397	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaattatcttatgtcgagtGagtaatgagccctgtttaaa	12	15	9	5	1	1	3	0	3	1	0	2	4	1	3	1	0	1	2	1	0	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:52659397G>A	ENST00000322146.8	-	5	2060	c.1539C>T	c.(1537-1539)ctC>ctT	p.L513L	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Silent_p.L513L	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	513					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)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TATGTCGAGTGAGTAATGAGC	0.388																																					p.L513L		.											.	ZNF836-46	0			c.C1539T						.						75	84	81					19																	52659397		2186	4294	6480	SO:0001819	synonymous_variant	162962	exon5			TCGAGTGAGTAAT	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.1539C>T	19.37:g.52659397G>A		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	109	29	NM_001102657	0	0	3	3	0		Silent	SNP	ENST00000322146.8	37	CCDS46162.1																																																																																			.		0.388	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52659397	G	A	52659397	2	1	109	1	0	0	0	0	0	0	0	1	18219	1277	45	2		2	ZNF836	19	52659397	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	2690290	52659397	6469586	129	9722											
NLRP11	204801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56329449	56329449	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaatcaagaatcttgcgtGccagatacttcttaaaactc	14	12	6	9	1	3	3	1	1	2	2	4	3	3	3	1	0	4	0	1	0	6	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:56329449G>T	ENST00000589093.1	-	2	185	c.92C>A	c.(91-93)gCa>gAa	p.A31E	NLRP11_ENST00000443188.1_Missense_Mutation_p.A31E|NLRP11_ENST00000589824.2_Missense_Mutation_p.A31E|NLRP11_ENST00000592953.1_Intron|NLRP11_ENST00000360133.3_Missense_Mutation_p.A31E			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	31	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AATCTTGCGTGCCAGATACTT	0.413																																					p.A31E		.											.	NLRP11-169	0			c.C92A						.						135	126	129					19																	56329449		2203	4300	6503	SO:0001583	missense	204801	exon4			TTGCGTGCCAGAT	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"Nucleotide-binding domain and leucine rich repeat containing"	22945	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"	609664	"NACHT, leucine rich repeat and PYD containing 11"	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.92C>A	19.37:g.56329449G>T	ENSP00000466285:p.Ala31Glu	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	113	28	NM_145007	0	0	0	0	0	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	G	0.719	-0.784370	0.02907	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.48522	0.81;0.81	2.56	-5.13	0.02884	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.23846	0.0577	N	0.22421	0.69	0.09310	N	1	B	0.18461	0.028	B	0.26094	0.066	T	0.26360	-1.0105	9	0.18710	T	0.47	.	0.3757	0.00387	0.2979:0.2202:0.2836:0.1983	.	31	P59045	NAL11_HUMAN	E	31	ENSP00000409898:A31E;ENSP00000353251:A31E	ENSP00000353251:A31E	A	-	2	0	NLRP11	61021261	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.568000	0.02144	-1.980000	0.00990	-2.070000	0.00385	GCA	.		0.413	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		T	56329449	G	T	56329449	3	4	109	1	0	0	0	0	1	0	0	0	10499	1319	46	4	3045	4	NLRP11	19	56329449	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	3670052	56329449	2799534	130	9723											
BPIL1	80341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31601760	31601760	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacgagtttgatggcagtaaCaggtgggtgcctggtgaggg	9	9	18	5	1	0	2	0	2	0	0	0	3	0	2	1	5	3	3	1	5	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr20:31601760C>G	ENST00000170150.3	+	5	648	c.453C>G	c.(451-453)aaC>aaG	p.N151K		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	151						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										ATGGCAGTAACAGGTGGGTGC	0.582																																					p.N151K		.											.	.	0			c.C453G						.						47	41	43					20																	31601760		2203	4300	6503	SO:0001583	missense	80341	exon5			CAGTAACAGGTGG	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"BPI fold containing"	16177	protein-coding gene	gene with protein product		614108	"bactericidal/permeability-increasing protein-like 1"	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.453C>G	20.37:g.31601760C>G	ENSP00000170150:p.Asn151Lys	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	46	16	NM_025227	0	0	0	0	0	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	C	0.777	-0.763664	0.02996	.	.	ENSG00000078898	ENST00000170150	T	0.05025	3.51	3.37	1.32	0.21799	.	1.051320	0.07484	N	0.904509	T	0.04363	0.0120	L	0.27053	0.805	0.21802	N	0.999535	B	0.09022	0.002	B	0.08055	0.003	T	0.43829	-0.9367	10	0.05833	T	0.94	0.1991	7.9791	0.30172	0.4451:0.5549:0.0:0.0	.	151	Q8N4F0	BPIB2_HUMAN	K	151	ENSP00000170150:N151K	ENSP00000170150:N151K	N	+	3	2	BPIFB2	31065421	0.257000	0.24022	0.587000	0.28692	0.145000	0.21501	0.314000	0.19432	0.396000	0.25283	0.491000	0.48974	AAC	.		0.582	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		G	31601760	C	G	31601760	3	3	109	1	0	0	0	0	1	0	0	0	1494	477	17	4	467	4	BPIL1	20	31601760	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		31601760	31423760	131	9724											
ZNF341	84905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	32376706	32376706	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctcagtgtgcgagtctgcGttcaaccgcaaggacaaact	10	9	11	11	3	3	0	2	0	1	0	3	2	3	1	1	1	5	3	1	1	3	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr20:32376706G>T	ENST00000375200.1	+	13	2255	c.1890G>T	c.(1888-1890)gcG>gcT	p.A630A	RP4-553F4.6_ENST00000423074.1_RNA|RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|ZNF341_ENST00000342427.2_Silent_p.A623A	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	630					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A623A(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						GCGAGTCTGCGTTCAACCGCA	0.547																																					p.A623A		.											.	ZNF341-92	1	Substitution - coding silent(1)	endometrium(1)	c.G1869T						.						122	99	107					20																	32376706		2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GTCTGCGTTCAAC	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"Zinc fingers, C2H2-type"	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1890G>T	20.37:g.32376706G>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	57	19	NM_032819	0	0	1	2	1	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				.		0.547	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				T	32376706	G	T	32376706	2	4	109	1	0	0	0	0	0	0	0	1	17889	1132	40	4		4	ZNF341	20	32376706	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	774946	32376706	30648814	132	9725											
PTPRT	11122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	40730779	40730779	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttacatccatcagtgctgcGttgatgtaattgctggattc	8	15	9	9	1	1	1	1	1	0	0	3	2	2	2	1	1	4	4	1	1	2	5	rs146474971	byFrequency	TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr20:40730779G>A	ENST00000373187.1	-	26	3698	c.3699C>T	c.(3697-3699)aaC>aaT	p.N1233N	PTPRT_ENST00000373198.4_Silent_p.N1252N|PTPRT_ENST00000356100.2_Silent_p.N1242N|PTPRT_ENST00000373201.1_Silent_p.N1223N|PTPRT_ENST00000373184.1_Silent_p.N1243N|PTPRT_ENST00000373193.3_Silent_p.N1236N|PTPRT_ENST00000373190.1_Silent_p.N1232N			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1233	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TCAGTGCTGCGTTGATGTAAT	0.552													G|||	5	0.000998403	0	0	5008	,	,		19597	0.005		0	False		,,,				2504	0				p.N1252N		.											.	PTPRT-664	0			c.C3756T						.	G	,	1,4227		0,1,2113	76	76	76		3699,3756	-4.6	0.5	20	dbSNP_134	76	0,8508		0,0,4254	no	coding-synonymous,coding-synonymous	PTPRT	NM_007050.5,NM_133170.3	,	0,1,6367	AA,AG,GG		0.0,0.0237,0.0079	,	1233/1442,1252/1461	40730779	1,12735	2114	4254	6368	SO:0001819	synonymous_variant	11122	exon27			TGCTGCGTTGATG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3699C>T	20.37:g.40730779G>A		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	102	19	NM_133170	0	0	0	0	0	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			G|0.998;A|0.002		0.552	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40730779	G	A	40730779	2	1	109	1	0	0	0	0	0	0	0	1	12844	1136	40	1		1	PTPRT	20	40730779	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	8354073	40730779	22294741	133	9726											
C21orf45	54069	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	33651272	33651272	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttgcccttgtcgccgcaCtcacagccgccagcgcatcc	6	8	8	19	4	1	0	1	0	0	0	3	0	2	0	5	0	3	2	5	0	0	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr21:33651272C>T	ENST00000290130.3	-	1	108	c.54G>A	c.(52-54)gaG>gaA	p.E18E	MIS18A-AS1_ENST00000453549.1_RNA	NM_018944.2	NP_061817.1	Q9NYP9	MS18A_HUMAN	MIS18 kinetochore protein A	18					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of DNA methylation (GO:0044030)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	7						TGTCGCCGCACTCACAGCCGC	0.607																																					p.E18E		.											.	MIS18A-90	0			c.G54A						.						36	39	38					21																	33651272		2202	4296	6498	SO:0001819	synonymous_variant	54069	exon1			GCCGCACTCACAG	AF231921	CCDS13611.1	21q22.11	2013-10-21	2013-10-21	2011-02-23	ENSG00000159055	ENSG00000159055			1286	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 46", "chromosome 21 open reading frame 45", "MIS18 kinetochore protein homolog A (S. pombe)"	C21orf46, C21orf45		17199038	Standard	NM_018944		Approved	B28, FASP1, hMis18alpha	uc002ypi.3	Q9NYP9	OTTHUMG00000085308	ENST00000290130.3:c.54G>A	21.37:g.33651272C>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	69	16	NM_018944	0	0	2	3	1	B2R562|Q542Z0	Silent	SNP	ENST00000290130.3	37	CCDS13611.1																																																																																			.		0.607	MIS18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193090.1	NM_018944		T	33651272	C	T	33651272	2	4	109	1	0	0	0	0	0	0	0	1	2132	564	20	2		2	C21orf45	21	33651272	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08		33651272	14478623	134	9727											
SON	6651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34922663	34922663	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttggagctgcaggagtcgTcggtggcctcagcgatggag	6	8	18	9	4	1	0	1	0	0	0	3	4	1	3	1	5	3	3	1	5	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr21:34922663T>C	ENST00000356577.4	+	3	1601	c.1126T>C	c.(1126-1128)Tcg>Ccg	p.S376P	SON_ENST00000381679.4_Missense_Mutation_p.S376P|SON_ENST00000381692.2_Intron|SON_ENST00000290239.6_Missense_Mutation_p.S376P|SON_ENST00000300278.4_Missense_Mutation_p.S376P	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	376					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GCAGGAGTCGTCGGTGGCCTC	0.627																																					p.S376P		.											.	SON-97	0			c.T1126C						.						78	85	82					21																	34922663		2203	4300	6503	SO:0001583	missense	6651	exon3			GAGTCGTCGGTGG	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"G patch domain containing"	11183	protein-coding gene	gene with protein product	"NRE-binding protein", "negative regulatory element-binding protein", "Bax antagonist selected in Saccharomyces 1"	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.1126T>C	21.37:g.34922663T>C	ENSP00000348984:p.Ser376Pro	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	93	26	NM_032195	0	0	19	30	11	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.913625	0.33815	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.14022	2.71;2.72;2.72;2.54	5.43	1.29	0.21616	.	0.277107	0.26272	N	0.025322	T	0.05593	0.0147	N	0.14661	0.345	0.21802	N	0.999532	B;B;B	0.22080	0.038;0.064;0.015	B;B;B	0.22880	0.019;0.042;0.023	T	0.36335	-0.9752	10	0.15499	T	0.54	.	2.7433	0.05259	0.1873:0.2368:0.0:0.5759	.	376;376;376	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	P	376	ENSP00000348984:S376P;ENSP00000290239:S376P;ENSP00000300278:S376P;ENSP00000371095:S376P	ENSP00000290239:S376P	S	+	1	0	SON	33844533	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	0.194000	0.17135	0.413000	0.25759	0.459000	0.35465	TCG	.		0.627	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34922663	T	C	34922663	3	2	109	1	0	0	0	0	1	0	0	0	14958	1667	58	3	1136	3	SON	21	34922663	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	1271391	34922663	13207232	135	9728											
PICK1	9463	broad.mit.edu	37	chr22	38461040	38461040	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caccccagcagccttggacgGcacagtggcagctggcgatg	8	5	14	14	2	0	0	0	0	0	0	0	2	0	1	3	4	3	4	3	4	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr22:38461040G>A	ENST00000404072.3	+	4	532	c.185G>A	c.(184-186)gGc>gAc	p.G62D	PICK1_ENST00000468288.1_3'UTR|PICK1_ENST00000356976.3_Missense_Mutation_p.G62D|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	62	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					GCCTTGGACGGCACAGTGGCA	0.542																																					p.G62D													.	PICK1-226	0			c.G185A						.						127	106	113					22																	38461040		2203	4300	6503	SO:0001583	missense	9463	exon4			TGGACGGCACAGT	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.185G>A	22.37:g.38461040G>A	ENSP00000385205:p.Gly62Asp	Somatic	140	1		WXS	Illumina HiSeq	Phase_I	138	4	NM_012407	0	0	32	32	0	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	37	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052351	0.75960	.	.	ENSG00000100151	ENST00000404072;ENST00000424694;ENST00000437453;ENST00000356976;ENST00000435166	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2	5.12	5.12	0.69794	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.70150	0.3191	M	0.92317	3.295	0.80722	D	1	B	0.14438	0.01	B	0.19391	0.025	T	0.72679	-0.4220	10	0.59425	D	0.04	-35.1501	18.9552	0.92655	0.0:0.0:1.0:0.0	.	62	Q9NRD5	PICK1_HUMAN	D	62	ENSP00000385205:G62D;ENSP00000398141:G62D;ENSP00000410793:G62D;ENSP00000349465:G62D;ENSP00000397588:G62D	ENSP00000349465:G62D	G	+	2	0	PICK1	36790986	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.534000	0.98061	2.562000	0.86427	0.563000	0.77884	GGC	.		0.542	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		A	38461040	G	A	38461040	3	1	109	1	0	0	0	0	1	0	0	0	11907	1203	42	2	195	2	PICK1	22	38461040	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		38461040	12843526	136	9729											
FAM116B	414918	hgsc.bcm.edu	37	chr22	50752671	50752671	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtcttcaaccttgaaggcTttttcagcttgacttgctta	7	16	9	9	0	3	2	2	2	1	0	3	2	3	2	1	2	3	3	1	2	3	7			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr22:50752671T>C	ENST00000413817.3	-	13	1174	c.1103A>G	c.(1102-1104)aAg>aGg	p.K368R	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	368					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										CCTTGAAGGCTTTTTCAGCTT	0.642																																					p.K368R		.											.	.	0			c.A1103G						.						40	47	45					22																	50752671		1956	4125	6081	SO:0001583	missense	414918	exon13			GAAGGCTTTTTCA	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"DENN/MADD domain containing"	32690	protein-coding gene	gene with protein product			"family with sequence similarity 116, member B"	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1103A>G	22.37:g.50752671T>C	ENSP00000391524:p.Lys368Arg	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_001001794	0	0	28	28	0	A6X8I5	Missense_Mutation	SNP	ENST00000413817.3	37	CCDS46732.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.692743	0.88735	.	.	ENSG00000205593	ENST00000413817	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.74419	0.3714	M	0.62723	1.935	0.58432	D	0.999992	D;D	0.69078	0.997;0.997	D;D	0.75020	0.985;0.985	T	0.74172	-0.3751	9	0.39692	T	0.17	-29.4347	12.8207	0.57692	0.0:0.0:0.0:1.0	.	368;368	Q8NEG7;C9JIV6	F116B_HUMAN;.	R	368	.	ENSP00000391524:K368R	K	-	2	0	FAM116B	49095243	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.326000	0.59241	1.916000	0.55485	0.379000	0.24179	AAG	.		0.642	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794		C	50752671	T	C	50752671	3	2	109	1	0	0	0	0	1	0	0	0	5424	1609	56	3	686	3	FAM116B	22	50752671	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	12291631	50752671	551895	137	9730											
HDAC6	10013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	48682180	48682180	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgctgatgcagggatctagGggcctcactgatcaggtgag	9	9	15	8	0	3	3	2	3	1	0	3	4	3	4	1	4	2	2	1	4	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chrX:48682180G>A	ENST00000334136.5	+	26	3466	c.3288G>A	c.(3286-3288)agG>agA	p.R1096R	HDAC6_ENST00000444343.2_Silent_p.R1110R|HDAC6_ENST00000376619.2_Silent_p.R1096R			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	1096					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGGGATCTAGGGGCCTCACTG	0.547																																					p.R1096R	Pancreas(112;205 1675 2305 8976 15959)	.											.	HDAC6-230	0			c.G3288A						.						83	66	72					X																	48682180		2203	4300	6503	SO:0001819	synonymous_variant	10013	exon26			ATCTAGGGGCCTC	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.3288G>A	X.37:g.48682180G>A		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	17	12	NM_006044	0	0	3	39	36	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	37	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	G	3.939	-0.014623	0.07681	.	.	ENSG00000094631	ENST00000430858	.	.	.	5.56	0.474	0.16768	.	.	.	.	.	T	0.23410	0.0566	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24333	-1.0163	4	.	.	.	0.2517	3.6925	0.08351	0.2664:0.0:0.4392:0.2944	.	.	.	.	E	57	.	.	G	+	2	0	HDAC6	48567124	0.016000	0.18221	0.000000	0.03702	0.048000	0.14542	0.329000	0.19698	-0.044000	0.13491	0.600000	0.82982	GGG	.		0.547	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		A	48682180	G	A	48682180	2	1	109	1	0	0	0	0	0	0	0	1	7032	1223	43	2		2	HDAC6	23	48682180	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08		48682180	106588380	138	9731											
RGAG1	57529	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	109695935	109695935	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggatgtccatgccactaaTgagagctcaagacccaggag	13	6	12	10	0	1	2	1	1	0	2	2	5	2	4	3	2	2	1	3	2	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chrX:109695935T>G	ENST00000465301.2	+	3	2336	c.2090T>G	c.(2089-2091)aTg>aGg	p.M697R	RGAG1_ENST00000540313.1_Missense_Mutation_p.M697R	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	697								p.M697T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						ATGCCACTAATGAGAGCTCAA	0.517																																					p.M697R		.											.	RGAG1-132	1	Substitution - Missense(1)	endometrium(1)	c.T2090G						.						118	99	105					X																	109695935		2203	4300	6503	SO:0001583	missense	57529	exon3			CACTAATGAGAGC	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.2090T>G	X.37:g.109695935T>G	ENSP00000419786:p.Met697Arg	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	33	20	NM_020769	0	0	0	0	0	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	1.022	-0.684599	0.03353	.	.	ENSG00000243978	ENST00000465301;ENST00000540313	T;T	0.48201	0.82;0.82	3.63	2.48	0.30137	.	0.141438	0.32935	N	0.005468	T	0.30792	0.0776	L	0.39898	1.24	0.09310	N	1	P	0.35982	0.531	B	0.35413	0.202	T	0.10989	-1.0606	9	.	.	.	-0.0102	2.2783	0.04108	0.2497:0.1407:0.0:0.6096	.	697	Q8NET4	RGAG1_HUMAN	R	697	ENSP00000419786:M697R;ENSP00000441452:M697R	.	M	+	2	0	RGAG1	109582591	0.001000	0.12720	0.002000	0.10522	0.031000	0.12232	-0.744000	0.04839	0.596000	0.29794	0.486000	0.48141	ATG	.		0.517	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		G	109695935	T	G	109695935	3	3	109	1	0	0	0	0	1	0	0	0	13306	1464	51	5	2092	5	RGAG1	23	109695935	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	61013755	109695935	45574625	139	9732											
CGN	57530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151502428	151502428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaacagtgctggggcagcGgcgggccgcagtggagacga	8	3	20	10	4	0	1	0	0	0	1	0	3	0	1	1	6	3	4	1	6	1	0			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:151502428G>A	ENST00000271636.7	+	12	2283	c.2150G>A	c.(2149-2151)cGg>cAg	p.R717Q	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	711	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CTGGGGCAGCGGCGGGCCGCA	0.652																																					p.R717Q		.											.	CGN-93	0			c.G2150A						.						30	37	34					1																	151502428		2203	4300	6503	SO:0001583	missense	57530	exon12			GGCAGCGGCGGGC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2150G>A	1.37:g.151502428G>A	ENSP00000271636:p.Arg717Gln	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	208	105	NM_020770	0	0	0	1	1	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267974	0.40095	.	.	ENSG00000143375	ENST00000271636	T	0.64438	-0.1	5.27	5.27	0.74061	.	0.472495	0.21879	N	0.067773	T	0.62332	0.2419	L	0.50919	1.6	0.29222	N	0.87387	D	0.76494	0.999	P	0.60068	0.868	T	0.58685	-0.7593	10	0.39692	T	0.17	-10.0013	16.3784	0.83418	0.0:0.0:1.0:0.0	.	711	Q9P2M7	CING_HUMAN	Q	717	ENSP00000271636:R717Q	ENSP00000271636:R717Q	R	+	2	0	CGN	149769052	0.901000	0.30685	0.933000	0.37362	0.335000	0.28730	2.924000	0.48876	2.439000	0.82584	0.563000	0.77884	CGG	.		0.652	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		A	151502428	G	A	151502428	3	1	110	1	0	0	0	0	1	0	0	0	3309	1116	39	1	2192	1	CGN	1	151502428	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		151502428	97748193	1	9733											
SHE	126669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154471704	154471704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggtcagcatagtcttctAaaatgatgacctgaaaaaga	17	9	9	6	0	3	4	1	3	2	1	3	4	3	4	1	1	1	1	1	1	6	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:154471704A>G	ENST00000304760.2	-	2	688	c.602T>C	c.(601-603)tTa>tCa	p.L201S	TDRD10_ENST00000368482.4_5'Flank	NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	201										breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			ATAGTCTTCTAAAATGATGAC	0.448																																					p.L201S		.											.	SHE-95	0			c.T602C						.						129	108	115					1																	154471704		2203	4300	6503	SO:0001583	missense	126669	exon2			TCTTCTAAAATGA	AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"SH2 domain containing"	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.602T>C	1.37:g.154471704A>G	ENSP00000307369:p.Leu201Ser	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	133	39	NM_001010846	0	0	0	0	0	Q8TEQ5	Missense_Mutation	SNP	ENST00000304760.2	37	CCDS30877.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.353420	0.82243	.	.	ENSG00000169291	ENST00000304760	T	0.31510	1.49	5.02	5.02	0.67125	.	0.102997	0.42821	D	0.000657	T	0.41050	0.1142	M	0.72894	2.215	0.42961	D	0.9944	D	0.89917	1.0	D	0.69307	0.963	T	0.22836	-1.0205	10	0.27082	T	0.32	-29.5539	13.7207	0.62725	1.0:0.0:0.0:0.0	.	201	Q5VZ18	SHE_HUMAN	S	201	ENSP00000307369:L201S	ENSP00000307369:L201S	L	-	2	0	SHE	152738328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.237000	0.89807	2.099000	0.63709	0.533000	0.62120	TTA	.		0.448	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846		G	154471704	A	G	154471704	3	3	110	1	0	0	0	0	1	0	0	0	14308	372	13	3	905	3	SHE	1	154471704	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10	2969276	154471704	94778917	2	9734											
OR10J5	127385	broad.mit.edu	37	chr1	159505502	159505502	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taacaaaaaagaacatttgtGtagcacagcctgccaaggag	17	7	9	8	0	0	1	0	0	0	1	0	2	0	2	2	1	5	2	2	1	7	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:159505502G>A	ENST00000334857.2	-	1	340	c.296C>T	c.(295-297)aCa>aTa	p.T99I		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					GAACATTTGTGTAGCACAGCC	0.463																																					p.T99I													.	OR10J5-71	0			c.C296T						.						128	111	117					1																	159505502		2203	4300	6503	SO:0001583	missense	127385	exon1			ATTTGTGTAGCAC		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"GPCR / Class A : Olfactory receptors"	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.296C>T	1.37:g.159505502G>A	ENSP00000334441:p.Thr99Ile	Somatic	220	1		WXS	Illumina HiSeq	Phase_I	232	7	NM_001004469	0	0	0	0	0	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	37	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	G	0.914	-0.718207	0.03182	.	.	ENSG00000184155	ENST00000334857	T	0.02837	4.14	4.32	2.43	0.29744	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00936	0.0031	L	0.35542	1.07	0.09310	N	1	B	0.24043	0.096	B	0.24974	0.057	T	0.46830	-0.9163	9	0.38643	T	0.18	.	8.3927	0.32537	0.196:0.0:0.804:0.0	.	99	Q8NHC4	O10J5_HUMAN	I	99	ENSP00000334441:T99I	ENSP00000334441:T99I	T	-	2	0	OR10J5	157772126	0.005000	0.15991	0.004000	0.12327	0.225000	0.24961	1.462000	0.35266	0.561000	0.29186	0.467000	0.42956	ACA	.		0.463	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469		A	159505502	G	A	159505502	3	1	110	1	0	0	0	0	1	0	0	0	10938	1377	48	2	635	2	OR10J5	1	159505502	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	5033798	159505502	89745119	3	9735											
ATP1B1	481	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169094224	169094232	+	In_Frame_Del	DEL	AAAAGTACA	AAAAGTACA	-																															gaacatagttaggttcctggAaaagtacaaagattcagccc																										TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	AAAAGTACA	AAAAGTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:169094224_169094232delAAAAGTACA	ENST00000367816.1	+	4	858_866	c.329_337delAAAAGTACA	c.(328-339)gaaaagtacaaa>gaa	p.KYK111del	ATP1B1_ENST00000499679.3_In_Frame_Del_p.KYK55del|ATP1B1_ENST00000367815.4_In_Frame_Del_p.KYK111del|ATP1B1_ENST00000367813.3_In_Frame_Del_p.KYK103del			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	111					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					AGGTTCCTGGAAAAGTACAAAGATTCAGC	0.392																																					p.110_113del		.											.	ATP1B1-540	0			c.329_337del						.																																			SO:0001651	inframe_deletion	481	exon3			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.329_337delAAAAGTACA	1.37:g.169094224_169094232delAAAAGTACA	ENSP00000356790:p.Lys111_Lys113del	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	133	29	NM_001677	0	0	0	0	0	Q5TGZ3	In_Frame_Del	DEL	ENST00000367816.1	37	CCDS1276.1																																																																																			.		0.392	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			-	169094232	AAAAGTACA	-	169094224	7	5	110	1	0	1	0	1	0	0	0	0	1133	246	9	0	339	0	ATP1B1	1	169094224	In_Frame_Del	DEL	AAAAGTACA	TCGA-F9-A4JJ-01A-11D-A25F-10	9588722	169094224	80156397	4	9736											
IGFN1	91156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201166405	201166405	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcacagcagtaaatgcgtaCggagaggccgcttgctcagt	10	8	13	10	3	1	1	1	0	0	1	1	2	1	1	1	2	5	6	1	2	3	3	rs370452044		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:201166405C>T	ENST00000335211.4	+	5	457	c.327C>T	c.(325-327)taC>taT	p.Y109Y	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Silent_p.Y109Y	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	109	Ig-like 1.					nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TAAATGCGTACGGAGAGGCCG	0.557																																					p.Y109Y		.											.	IGFN1-71	0			c.C327T						.	C		1,1383		0,1,691	172	157	162		327	-2.2	0.1	1		162	0,3182		0,0,1591	no	coding-synonymous	IGFN1	NM_001164586.1		0,1,2282	TT,TC,CC		0.0,0.0723,0.0219		109/3709	201166405	1,4565	692	1591	2283	SO:0001819	synonymous_variant	91156	exon5			TGCGTACGGAGAG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.327C>T	1.37:g.201166405C>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	130	41	NM_001164586	0	0	10	35	25	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1																																																																																			.		0.557	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201166405	C	T	201166405	2	4	110	1	0	0	0	0	0	0	0	1	7611	547	19	1		1	IGFN1	1	201166405	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	32072181	201166405	48084216	5	9737											
CR1	1378	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	207669654	207669654	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccggagcctgtcgggccGccggcgcccggtctcccctt	2	6	14	19	6	1	0	0	0	1	0	3	1	1	1	7	4	2	0	7	4	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:207669654G>C	ENST00000367049.4	+	1	42	c.42G>C	c.(40-42)ccG>ccC	p.P14P	CR1_ENST00000367050.4_3'UTR|CR1_ENST00000367053.1_Silent_p.P14P|CR1_ENST00000367052.1_Silent_p.P14P|CR1_ENST00000400960.2_Silent_p.P14P|CR1_ENST00000367051.1_Silent_p.P14P	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	14					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CTGTCGGGCCGCCGGCGCCCG	0.632																																					p.P14P		.											.	CR1-93	0			c.G42C						.						21	27	25					1																	207669654		1819	4077	5896	SO:0001819	synonymous_variant	1378	exon1			CGGGCCGCCGGCG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"CD molecules", "Blood group antigens", "Complement system"	2334	protein-coding gene	gene with protein product		120620	"complement component (3b/4b) receptor 1, including Knops blood group system"			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.42G>C	1.37:g.207669654G>C		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	48	6	NM_000573	0	0	0	0	0	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1																																																																																			.		0.632	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		C	207669654	G	C	207669654	2	2	110	1	0	0	0	0	0	0	0	1	3846	1074	38	4		4	CR1	1	207669654	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	6503249	207669654	41580967	6	9738											
PROX1	5629	broad.mit.edu;bcgsc.ca	37	chr1	214170147	214170147	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgatgccttttccaggagCaaccataatttcccagctgt	10	12	7	12	0	0	1	0	1	0	0	2	2	2	2	4	1	4	2	4	1	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:214170147C>A	ENST00000366958.4	+	2	877	c.269C>A	c.(268-270)gCa>gAa	p.A90E	PROX1_ENST00000435016.1_Missense_Mutation_p.A90E|PROX1_ENST00000498508.2_Missense_Mutation_p.A90E|PROX1_ENST00000261454.4_Missense_Mutation_p.A90E	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	90					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		TTTCCAGGAGCAACCATAATT	0.488																																					p.A90E													.	PROX1-654	0			c.C269A						.						85	83	84					1																	214170147		2203	4300	6503	SO:0001583	missense	5629	exon2			CAGGAGCAACCAT	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"Homeoboxes / PROS class"	9459	protein-coding gene	gene with protein product		601546	"prospero-related homeobox 1"			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.269C>A	1.37:g.214170147C>A	ENSP00000355925:p.Ala90Glu	Somatic	156	1		WXS	Illumina HiSeq	Phase_I	162	8	NM_001270616	0	0	0	0	0	A6NK29|A8K2B1|Q5SW76|Q8TB91	Missense_Mutation	SNP	ENST00000366958.4	37	CCDS31021.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.981386	0.74474	.	.	ENSG00000117707	ENST00000471129;ENST00000498508;ENST00000366958;ENST00000435016;ENST00000261454	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.77	5.77	0.91146	.	0.048799	0.85682	D	0.000000	T	0.38719	0.1051	L	0.44542	1.39	0.80722	D	1	D	0.58268	0.982	P	0.59825	0.864	T	0.02950	-1.1090	10	0.72032	D	0.01	-2.6486	20.3627	0.98863	0.0:1.0:0.0:0.0	.	90	Q92786	PROX1_HUMAN	E	90	ENSP00000419517:A90E;ENSP00000420283:A90E;ENSP00000355925:A90E;ENSP00000400694:A90E;ENSP00000261454:A90E	ENSP00000261454:A90E	A	+	2	0	PROX1	212236770	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.677000	0.68142	2.885000	0.99019	0.655000	0.94253	GCA	.		0.488	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		A	214170147	C	A	214170147	3	1	110	1	0	0	0	0	1	0	0	0	12589	710	25	4	271	4	PROX1	1	214170147	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	6500493	214170147	35080474	7	9739											
FMN2	56776	hgsc.bcm.edu	37	chr1	240255571	240255571	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggcaaggggggagggggCggcggcggcggcggggagtc	5	1	26	9	6	0	0	0	0	0	0	1	2	0	2	0	12	0	1	0	12	1	0	rs71929261|rs140531536	byFrequency	TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:240255571C>G	ENST00000319653.9	+	1	392	c.162C>G	c.(160-162)ggC>ggG	p.G54G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	54					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G197delG(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGGGAgggggcggcggcggcg	0.662																																					p.G54G		.											.	FMN2-145	1	Deletion - In frame(1)	prostate(1)	c.C162G						.						2	3	3					1																	240255571		1816	3578	5394	SO:0001819	synonymous_variant	56776	exon1			AGGGGGCGGCGGC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.162C>G	1.37:g.240255571C>G		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.		0.662	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		G	240255571	C	G	240255571	2	3	110	1	0	0	0	0	0	0	0	1	5969	755	27	4		4	FMN2	1	240255571	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	26085424	240255571	8995050	8	9740											
FH	2271	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	241661272	241661272	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgctgccttgtcatacccTgaagaaaaaataaaaagacg	16	10	7	8	1	1	3	1	1	0	2	1	3	1	3	2	0	3	1	2	0	8	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:241661272T>G	ENST00000366560.3	-	10	1429		c.e10-2			NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase						cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TGTCATACCCTGAAGAAAAAA	0.378			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												.	Melanoma(148;1573 2486 7381 46575)	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH-416	0			c.1391-2A>C						.						101	99	100					1																	241661272		2203	4300	6503	SO:0001630	splice_region_variant	2271	exon11	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	ATACCCTGAAGAA	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1391-2A>C	1.37:g.241661272T>G		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	121	32	NM_000143	0	0	2	9	7	B1ANK7	Splice_Site	SNP	ENST00000366560.3	37	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987598	0.74589	.	.	ENSG00000091483	ENST00000366560	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0202	0.64550	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FH	239727895	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	6.531000	0.73820	2.188000	0.69820	0.528000	0.53228	.	.		0.378	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	Intron	G	241661272	T	G	241661272	5	3	110	1	0	0	0	0	0	0	1	0	5894	1594	55	5	147	5	FH	1	241661272	Splice_Site	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	1405701	241661272	7589349	9	9741											
LRRTM4	80059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	77746638	77746638	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgtgcagataagtaattttGttggagcttagaattaattc	12	17	9	3	0	0	2	0	0	0	2	1	3	0	3	0	1	2	4	0	1	5	9			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr2:77746638G>T	ENST00000409093.1	-	3	693	c.357C>A	c.(355-357)aaC>aaA	p.N119K	LRRTM4_ENST00000409884.1_Missense_Mutation_p.N119K|LRRTM4_ENST00000409088.3_Missense_Mutation_p.N119K|LRRTM4_ENST00000409282.1_Missense_Mutation_p.N120K|LRRTM4_ENST00000409911.1_Missense_Mutation_p.N120K			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	119					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		AAGTAATTTTGTTGGAGCTTA	0.373																																					p.N119K		.											.	LRRTM4-94	0			c.C357A						.						158	140	145					2																	77746638		1842	4084	5926	SO:0001583	missense	80059	exon3			AATTTTGTTGGAG	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.357C>A	2.37:g.77746638G>T	ENSP00000386357:p.Asn119Lys	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	100	27	NM_024993	0	0	0	0	0	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.526251	0.44969	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	5.96	4.91	0.64330	.	0.044427	0.85682	D	0.000000	D	0.87873	0.6287	H	0.96489	3.83	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.89990	0.4107	10	0.87932	D	0	.	11.0841	0.48076	0.1556:0.0:0.8444:0.0	.	120;119;119	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	K	120;119;119;119;120	ENSP00000387228:N120K;ENSP00000387297:N119K;ENSP00000386357:N119K;ENSP00000386236:N119K;ENSP00000386286:N120K	ENSP00000386236:N119K	N	-	3	2	LRRTM4	77600146	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.981000	0.49329	2.826000	0.97356	0.655000	0.94253	AAC	.		0.373	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		T	77746638	G	T	77746638	3	4	110	1	0	0	0	0	1	0	0	0	9067	1368	48	4	1429	4	LRRTM4	2	77746638	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		77746638	165452735	10	9742											
YSK4	80122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	135738691	135738691	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggccaaacgcctggcaCagccaaagtcaatcagcttt	12	6	8	15	1	2	0	2	0	0	0	2	0	2	0	4	2	3	2	4	2	3	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr2:135738691C>G	ENST00000375845.3	-	9	3650	c.3620G>C	c.(3619-3621)tGt>tCt	p.C1207S	MAP3K19_ENST00000392917.3_Missense_Mutation_p.C339S|MAP3K19_ENST00000358371.4_Missense_Mutation_p.C1094S|MAP3K19_ENST00000392918.3_Missense_Mutation_p.C341S|MAP3K19_ENST00000375844.3_Missense_Mutation_p.C389S|MAP3K19_ENST00000392915.1_3'UTR|MAP3K19_ENST00000315513.3_Missense_Mutation_p.C68S	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1207	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										ACGCCTGGCACAGCCAAAGTC	0.458																																					p.C1207S		.											.	.	0			c.G3620C						.						113	112	112					2																	135738691		2203	4300	6503	SO:0001583	missense	80122	exon9			CTGGCACAGCCAA	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3620G>C	2.37:g.135738691C>G	ENSP00000365005:p.Cys1207Ser	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	80	24	NM_025052	0	0	0	0	0	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167028	0.78339	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000437365;ENST00000315513	T;T;T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95;1.95;1.95	5.88	5.88	0.94601	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000113	T	0.27384	0.0672	N	0.05031	-0.125	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;0.999;1.0	T	0.31613	-0.9937	10	0.25106	T	0.35	.	19.2304	0.93836	0.0:1.0:0.0:0.0	.	339;1094;341;389;1207	B7ZMH9;Q56UN5-3;Q56UN5-4;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	S	1207;1094;389;341;339;597;68	ENSP00000365005:C1207S;ENSP00000351140:C1094S;ENSP00000365004:C389S;ENSP00000376650:C341S;ENSP00000376649:C339S;ENSP00000392827:C597S;ENSP00000321160:C68S	ENSP00000321160:C68S	C	-	2	0	YSK4	135455161	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.616000	0.83018	2.782000	0.95742	0.655000	0.94253	TGT	.		0.458	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		G	135738691	C	G	135738691	3	3	110	1	0	0	0	0	1	0	0	0	17528	478	17	4	374	4	YSK4	2	135738691	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	57992053	135738691	107460682	11	9743											
ATXN7	6314	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	63981359	63981359	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atagcaaatcggtaccagctCatggaaccacactaaatgca	16	7	7	11	1	1	0	1	0	0	0	2	1	1	1	2	2	5	4	2	2	6	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr3:63981359C>T	ENST00000295900.6	+	12	2411	c.1861C>T	c.(1861-1863)Cat>Tat	p.H621Y	ATXN7_ENST00000398590.3_Missense_Mutation_p.H621Y|ATXN7_ENST00000484332.1_Missense_Mutation_p.H476Y|ATXN7_ENST00000487717.1_Missense_Mutation_p.H621Y|ATXN7_ENST00000538065.1_Missense_Mutation_p.H621Y	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	621					cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		GGTACCAGCTCATGGAACCAC	0.527																																					p.H621Y													.	ATXN7-90	0			c.C1861T						.						171	176	175					3																	63981359		2194	4281	6475	SO:0001583	missense	6314	exon12			CCAGCTCATGGAA	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.1861C>T	3.37:g.63981359C>T	ENSP00000295900:p.His621Tyr	Somatic	343	1		WXS	Illumina HiSeq	Phase_I	373	107	NM_000333	0	0	5	7	2	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.309327	0.60414	.	.	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.57	5.16	4.27	0.50696	.	0.168276	0.52532	D	0.000062	T	0.25606	0.0623	L	0.35723	1.085	0.41667	D	0.98921	D;B;B	0.69078	0.997;0.018;0.01	D;B;B	0.75484	0.986;0.011;0.005	T	0.02184	-1.1199	10	0.21540	T	0.41	-8.2112	14.9298	0.70906	0.1444:0.8556:0.0:0.0	.	476;621;621	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	Y	621;621;621;621;476	ENSP00000381590:H621Y;ENSP00000295900:H621Y;ENSP00000420234:H621Y;ENSP00000439585:H621Y;ENSP00000428277:H476Y	ENSP00000295900:H621Y	H	+	1	0	ATXN7	63956399	1.000000	0.71417	0.982000	0.44146	0.990000	0.78478	5.146000	0.64845	1.155000	0.42497	0.650000	0.86243	CAT	.		0.527	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		T	63981359	C	T	63981359	3	4	110	1	0	0	0	0	1	0	0	0	1216	826	29	2	1967	2	ATXN7	3	63981359	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		63981359	134041071	12	9744											
TRIO	7204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	14497115	14497115	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggaaggactcagcaacaagGtatctgtgaaggtgtgttcg	11	9	15	6	1	2	1	1	1	1	0	3	3	2	3	0	4	2	3	0	4	5	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr5:14497115G>C	ENST00000344204.4	+	50	8032	c.8008G>C	c.(8008-8010)Gta>Cta	p.V2670L	TRIO_ENST00000344135.5_Missense_Mutation_p.V169L|TRIO_ENST00000537187.1_Missense_Mutation_p.V2494L	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2670					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CAGCAACAAGGTATCTGTGAA	0.498																																					p.V2670L		.											.	TRIO-562	0			c.G8008C						.						122	103	109					5																	14497115		2203	4300	6503	SO:0001583	missense	7204	exon50			AACAAGGTATCTG	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.8008G>C	5.37:g.14497115G>C	ENSP00000339299:p.Val2670Leu	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	154	43	NM_007118	0	0	0	0	0	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094039	0.94149	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000344135	T;T;T	0.68025	-0.3;-0.21;-0.26	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.77253	0.4103	L	0.52759	1.655	0.32172	N	0.581488	D	0.67145	0.996	D	0.67900	0.954	T	0.81075	-0.1097	10	0.59425	D	0.04	.	17.1098	0.86672	0.0:0.0:1.0:0.0	.	2670	O75962	TRIO_HUMAN	L	2670;2494;2357;169	ENSP00000339299:V2670L;ENSP00000446348:V2494L;ENSP00000339291:V169L	ENSP00000339291:V169L	V	+	1	0	TRIO	14550115	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.441000	0.97557	2.461000	0.83175	0.655000	0.94253	GTA	.		0.498	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		C	14497115	G	C	14497115	3	2	110	1	0	0	0	0	1	0	0	0	16585	1261	44	4	8206	4	TRIO	5	14497115	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		14497115	166418145	13	9745											
RICTOR	253260	broad.mit.edu	37	chr5	38947463	38947463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccatggaccgcactgaggaaGatcgttgcagggtattttga	10	10	13	8	2	0	3	0	2	0	1	1	5	0	5	2	3	1	4	2	3	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr5:38947463G>A	ENST00000357387.3	-	32	4247	c.4217C>T	c.(4216-4218)tCt>tTt	p.S1406F	RICTOR_ENST00000296782.5_Missense_Mutation_p.S1430F	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					CACTGAGGAAGATCGTTGCAG	0.388																																					p.S1406F													.	RICTOR-849	0			c.C4217T						.						132	120	124					5																	38947463		2203	4300	6503	SO:0001583	missense	253260	exon32			GAGGAAGATCGTT		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"rapamycin-insensitive companion of mTOR", "pianissimo"	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.4217C>T	5.37:g.38947463G>A	ENSP00000349959:p.Ser1406Phe	Somatic	247	0		WXS	Illumina HiSeq	Phase_I	257	6	NM_152756	0	0	4	4	0		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.751872	0.89753	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.56275	0.76;0.47	5.69	5.69	0.88448	.	0.095984	0.64402	D	0.000001	T	0.62060	0.2397	L	0.43152	1.355	0.58432	D	0.999994	D;D	0.54207	0.965;0.965	P;P	0.54312	0.748;0.748	T	0.63866	-0.6540	10	0.87932	D	0	-7.8353	19.8165	0.96571	0.0:0.0:1.0:0.0	.	1406;1430	Q6R327;Q6R327-3	RICTR_HUMAN;.	F	1406;1430	ENSP00000349959:S1406F;ENSP00000296782:S1430F	ENSP00000296782:S1430F	S	-	2	0	RICTOR	38983220	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.139000	0.77314	2.683000	0.91414	0.655000	0.94253	TCT	.		0.388	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38947463	G	A	38947463	3	1	110	1	0	0	0	0	1	0	0	0	13390	942	33	2	937	2	RICTOR	5	38947463	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	24450348	38947463	141967797	14	9746											
TNXB	7148	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	32037362	32037362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccgagatggggcccacaCgcttgccgtggtgcagcccg	5	5	16	15	5	0	1	0	0	0	1	0	2	0	1	4	4	3	2	4	4	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr6:32037362C>T	ENST00000375244.3	-	15	5756	c.5555G>A	c.(5554-5556)cGt>cAt	p.R1852H	TNXB_ENST00000375247.2_Missense_Mutation_p.R1852H			P22105	TENX_HUMAN	tenascin XB	1934					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGGGCCCACACGCTTGCCGTG	0.672																																					p.R1852H		.											.	TNXB-90	0			c.G5555A						.						27	34	32					6																	32037362		2155	4268	6423	SO:0001583	missense	7148	exon15			CCCACACGCTTGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5555G>A	6.37:g.32037362C>T	ENSP00000364393:p.Arg1852His	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	127	8	NM_019105	0	0	3	3	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	19.43	3.825390	0.71143	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.05025	3.51;3.51	5.5	4.44	0.53790	.	0.000000	0.46758	D	0.000265	T	0.22205	0.0535	M	0.93594	3.435	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.09530	-1.0670	10	0.66056	D	0.02	.	12.1698	0.54152	0.0:0.9037:0.0:0.0963	.	1852	P22105-3	.	H	1852	ENSP00000364393:R1852H;ENSP00000364396:R1852H	ENSP00000364393:R1852H	R	-	2	0	TNXB	32145340	0.757000	0.28394	0.251000	0.24312	0.105000	0.19272	2.166000	0.42406	2.598000	0.87819	0.591000	0.81541	CGT	.		0.672	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32037362	C	T	32037362	3	4	110	1	0	0	0	0	1	0	0	0	16378	536	19	1	9278	1	TNXB	6	32037362	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		32037362	139077705	15	9747											
EYA4	2070	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	133849920	133849920	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctcctggctctccaccaaGcactggaattagagtatttg	10	11	8	12	0	1	1	0	0	1	1	3	2	2	2	4	2	1	3	4	2	4	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr6:133849920G>T	ENST00000367895.5	+	20	2361	c.1897G>T	c.(1897-1899)Gca>Tca	p.A633S	EYA4_ENST00000525849.1_Missense_Mutation_p.A610S|EYA4_ENST00000431403.2_Missense_Mutation_p.A633S|EYA4_ENST00000430974.2_Intron|EYA4_ENST00000452339.2_Missense_Mutation_p.A579S|EYA4_ENST00000355167.3_Missense_Mutation_p.A633S|EYA4_ENST00000355286.6_Missense_Mutation_p.A610S|RP3-323P13.2_ENST00000607033.1_RNA|EYA4_ENST00000531901.1_Missense_Mutation_p.A639S	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	633					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		TCTCCACCAAGCACTGGAATT	0.453																																					p.A633S	Melanoma(57;398 1237 3528 4702 7415)	.											.	EYA4-578	0			c.G1897T						.						260	238	245					6																	133849920		2203	4300	6503	SO:0001583	missense	2070	exon20			CACCAAGCACTGG	Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"Protein tyrosine phosphatases / Asp-based PTPs"	3522	protein-coding gene	gene with protein product		603550	"eyes absent (Drosophila) homolog 4", "eyes absent homolog 4 (Drosophila)"	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.1897G>T	6.37:g.133849920G>T	ENSP00000356870:p.Ala633Ser	Somatic	277	0		WXS	Illumina HiSeq	Phase_I	291	15	NM_172105	0	0	3	3	0	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	37	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.636157	0.87760	.	.	ENSG00000112319	ENST00000452339;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	D;D;D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19;-3.19;-3.19	6.07	6.07	0.98685	EYA (1);	0.000000	0.85682	D	0.000000	D	0.97021	0.9027	M	0.83483	2.645	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.996;0.996;0.999;0.998	D	0.96683	0.9505	10	0.87932	D	0	-22.8527	20.6593	0.99626	0.0:0.0:1.0:0.0	.	639;579;610;633;633	F2Z2Y1;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;EYA4_HUMAN	S	579;633;633;610;639;610;633	ENSP00000395916:A579S;ENSP00000356870:A633S;ENSP00000347294:A633S;ENSP00000347434:A610S;ENSP00000432770:A639S;ENSP00000433219:A610S;ENSP00000404558:A633S	ENSP00000347294:A633S	A	+	1	0	EYA4	133891613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.837000	0.99465	2.885000	0.99019	0.655000	0.94253	GCA	.		0.453	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		T	133849920	G	T	133849920	3	4	110	1	0	0	0	0	1	0	0	0	5344	971	34	4	2076	4	EYA4	6	133849920	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	101812558	133849920	37265147	16	9748											
CCDC132	55610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92932815	92932815	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcttagagaatgagactTgggaactttgtcctgttaag	10	15	11	5	0	1	2	0	1	1	2	2	5	2	3	1	1	1	2	1	1	4	5			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr7:92932815T>G	ENST00000305866.5	+	17	1533	c.1405T>G	c.(1405-1407)Tgg>Ggg	p.W469G	CCDC132_ENST00000535481.1_Missense_Mutation_p.W189G|CCDC132_ENST00000544910.1_Missense_Mutation_p.W439G|CCDC132_ENST00000541136.1_Missense_Mutation_p.W280G|CCDC132_ENST00000317751.6_Missense_Mutation_p.W200G	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	469						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GAATGAGACTTGGGAACTTTG	0.348																																					p.W469G		.											.	CCDC132-90	0			c.T1405G						.						141	135	137					7																	92932815		1823	4079	5902	SO:0001583	missense	55610	exon17			GAGACTTGGGAAC	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1405T>G	7.37:g.92932815T>G	ENSP00000307666:p.Trp469Gly	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	42	16	NM_017667	0	0	6	8	2	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084073	0.76642	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.73681	-0.77	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.86033	0.5836	M	0.80982	2.52	0.80722	D	1	D;D;D	0.57899	0.967;0.981;0.967	D;D;D	0.70487	0.932;0.969;0.932	D	0.88196	0.2880	10	0.87932	D	0	-0.9767	15.0541	0.71897	0.0:0.0:0.0:1.0	.	189;439;469	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	G	469;439;280;189;200	ENSP00000325582:W200G	ENSP00000307666:W469G	W	+	1	0	CCDC132	92770751	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.794000	0.85869	2.200000	0.70718	0.460000	0.39030	TGG	.		0.348	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92932815	T	G	92932815	3	3	110	1	0	0	0	0	1	0	0	0	2773	1812	63	5	1513	5	CCDC132	7	92932815	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10		92932815	66205848	17	9749											
FLNC	2318	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	128482660	128482660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgagggcagccaccccgagcGggtaaaggtgtacggccccg	8	3	16	14	5	0	0	0	0	0	0	0	2	0	0	5	4	3	3	5	4	3	2	rs369935650		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr7:128482660G>A	ENST00000325888.8	+	15	2558	c.2297G>A	c.(2296-2298)cGg>cAg	p.R766Q	FLNC_ENST00000346177.6_Missense_Mutation_p.R766Q	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	766					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CACCCCGAGCGGGTAAAGGTG	0.692											OREG0018297	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R766Q													.	FLNC-141	0			c.G2297A						.	G	GLN/ARG,GLN/ARG	0,3844		0,0,1922	20	26	24		2297,2297	3.4	1	7		24	1,7821		0,1,3910	no	missense,missense	FLNC	NM_001127487.1,NM_001458.4	43,43	0,1,5832	AA,AG,GG		0.0128,0.0,0.0086	possibly-damaging,possibly-damaging	766/2693,766/2726	128482660	1,11665	1922	3911	5833	SO:0001583	missense	2318	exon15			CCGAGCGGGTAAA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.2297G>A	7.37:g.128482660G>A	ENSP00000327145:p.Arg766Gln	Somatic	112	1	1565	WXS	Illumina HiSeq	Phase_I	144	16	NM_001127487	0	0	0	0	0	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	g	19.02	3.744937	0.69418	0.0	1.28E-4	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85484	-1.99;-1.99	5.52	3.39	0.38822	Immunoglobulin E-set (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.385179	0.24571	N	0.037392	T	0.76990	0.4065	L	0.38175	1.15	0.33779	D	0.624033	B;P	0.35107	0.434;0.484	B;B	0.36666	0.135;0.23	T	0.81247	-0.1019	10	0.72032	D	0.01	.	6.4307	0.21794	0.3702:0.0:0.6298:0.0	.	766;766	Q14315-2;Q14315	.;FLNC_HUMAN	Q	766	ENSP00000327145:R766Q;ENSP00000344002:R766Q	ENSP00000327145:R766Q	R	+	2	0	FLNC	128269896	0.027000	0.19231	0.996000	0.52242	0.479000	0.33129	2.236000	0.43052	1.349000	0.45751	0.645000	0.84053	CGG	.		0.692	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128482660	G	A	128482660	3	1	110	1	0	0	0	0	1	0	0	0	5954	1116	39	1	2355	1	FLNC	7	128482660	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	35549845	128482660	30656003	18	9750											
CSMD1	64478	broad.mit.edu	37	chr8	2808726	2808727	+	Frame_Shift_Ins	INS	-	-	G																															cagtcaacagttagagtggcINSgggttgtcttttccctaaat																								rs374654290		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:2808726_2808727insG	ENST00000520002.1	-	67	10668_10669	c.10113_10114insC	c.(10111-10116)cccgccfs	p.A3372fs	CSMD1_ENST00000400186.3_Frame_Shift_Ins_p.A3195fs|CSMD1_ENST00000542608.1_Frame_Shift_Ins_p.A3194fs|CSMD1_ENST00000537824.1_Frame_Shift_Ins_p.A3371fs|CSMD1_ENST00000602557.1_Frame_Shift_Ins_p.A3372fs|CSMD1_ENST00000602723.1_Frame_Shift_Ins_p.A3195fs			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3372						integral component of membrane (GO:0016021)		p.P3370P(1)|p.P3099P(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GTTAGAGTGGCGGGTTGTCTTT	0.485																																					p.A3371fs													.	CSMD1-86	2	Substitution - coding silent(2)	prostate(2)	c.10111_10112insC						.																																			SO:0001589	frameshift_variant	64478	exon66			GAGTGGCGGGTTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.10114dupC	8.37:g.2808729_2808729dupG	ENSP00000430733:p.Ala3372fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	151	9	NM_033225	0	0	0	0	0	Q0H0J5|Q96QU9|Q96RM4	Frame_Shift_Ins	INS	ENST00000520002.1	37																																																																																				.		0.485	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2808727	-	G	2808726	7	5	110	1	0	1	1	0	0	0	0	0	3950	768	27	0	603	0	CSMD1	8	2808726	Frame_Shift_Ins	INS	-	TCGA-F9-A4JJ-01A-11D-A25F-10		2808726	143555296	19	9751											
KIF13B	23303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	29037680	29037680	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgaaaactgcatgggatcGgctactctcctcgttcatgt	8	14	9	10	2	2	1	1	1	1	0	5	2	2	2	1	2	3	3	1	2	3	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:29037680G>A	ENST00000524189.1	-	8	699	c.661C>T	c.(661-663)Cga>Tga	p.R221*	KIF13B_ENST00000521515.1_Nonsense_Mutation_p.R221*	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	221	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		GCATGGGATCGGCTACTCTCC	0.438																																					p.R221X		.											.	KIF13B-22	0			c.C661T						.						192	192	192					8																	29037680		1932	4134	6066	SO:0001587	stop_gained	23303	exon8			GGGATCGGCTACT	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.661C>T	8.37:g.29037680G>A	ENSP00000427900:p.Arg221*	Somatic	319	0		WXS	Illumina HiSeq	Phase_I	380	150	NM_015254	0	0	3	3	0	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Nonsense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	G	35	5.587513	0.96590	.	.	ENSG00000197892	ENST00000524189;ENST00000521515	.	.	.	4.77	2.84	0.33178	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.45	0.61165	0.0:0.0:0.7156:0.2844	.	.	.	.	X	221	.	ENSP00000429201:R221X	R	-	1	2	KIF13B	29093599	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.457000	0.35212	1.203000	0.43233	0.563000	0.77884	CGA	.		0.438	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			A	29037680	G	A	29037680	4	1	110	1	0	0	0	0	0	1	0	0	8296	1124	39	1	4951	1	KIF13B	8	29037680	Nonsense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	26228954	29037680	117326342	20	9752											
WWP1	11059	broad.mit.edu;bcgsc.ca	37	chr8	87443954	87443954	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacaacattcaaagatcctcGcaatgggaagtcatctgtgt	14	10	8	9	1	3	1	2	0	1	1	5	2	4	2	1	1	2	1	1	1	5	1	rs554041348		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:87443954G>A	ENST00000517970.1	+	14	1890	c.1583G>A	c.(1582-1584)cGc>cAc	p.R528H	WWP1_ENST00000349423.2_Missense_Mutation_p.R310H|WWP1_ENST00000341922.2_Missense_Mutation_p.R398H|WWP1_ENST00000265428.4_Missense_Mutation_p.R528H	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	528	WW 4. {ECO:0000255|PROSITE- ProRule:PRU00224}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						AAAGATCCTCGCAATGGGAAG	0.388													G|||	1	0.000199681	0	0	5008	,	,		18477	0		0	False		,,,				2504	0.001				p.R528H													.	WWP1-659	0			c.G1583A						.						91	90	90					8																	87443954		2203	4300	6503	SO:0001583	missense	11059	exon14			ATCCTCGCAATGG	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1583G>A	8.37:g.87443954G>A	ENSP00000427793:p.Arg528His	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	149	6	NM_007013	0	0	26	28	2	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986456	0.93044	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	T;T;T;T	0.61980	0.06;0.06;0.14;0.19	5.35	5.35	0.76521	WW/Rsp5/WWP (4);	0.302657	0.33272	N	0.005098	D	0.85592	0.5732	H	0.97732	4.065	0.80722	D	1	D;D	0.69078	0.997;0.995	P;P	0.60236	0.871;0.747	D	0.90859	0.4737	10	0.72032	D	0.01	.	19.0481	0.93030	0.0:0.0:1.0:0.0	.	310;528	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	H	528;528;398;310	ENSP00000427793:R528H;ENSP00000265428:R528H;ENSP00000340564:R398H;ENSP00000342665:R310H	ENSP00000265428:R528H	R	+	2	0	WWP1	87513070	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.744000	0.98853	2.498000	0.84270	0.563000	0.77884	CGC	.		0.388	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		A	87443954	G	A	87443954	3	1	110	1	0	0	0	0	1	0	0	0	17448	1087	38	1	1629	1	WWP1	8	87443954	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	58406274	87443954	58920068	21	9753											
PHF20L1	51105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133829702	133829702	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcttaccgtaatgaatgTcccagggcagaaaaagagga	14	8	10	9	1	1	3	0	1	1	2	3	4	3	4	3	2	1	2	3	2	5	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:133829702T>G	ENST00000395386.2	+	12	1790	c.1491T>G	c.(1489-1491)tgT>tgG	p.C497W	PHF20L1_ENST00000395390.2_Missense_Mutation_p.C472W|PHF20L1_ENST00000220847.7_5'UTR	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	497							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			GTAATGAATGTCCCAGGGCAG	0.478																																					p.C497W		.											.	PHF20L1-92	0			c.T1491G						.						74	67	70					8																	133829702		2203	4300	6503	SO:0001583	missense	51105	exon12			TGAATGTCCCAGG	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.1491T>G	8.37:g.133829702T>G	ENSP00000378784:p.Cys497Trp	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	74	9	NM_016018	0	0	8	9	1	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964653	0.53507	.	.	ENSG00000129292	ENST00000395383;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000395382;ENST00000395390	T;T;T;T;T	0.52057	0.73;0.68;1.42;0.7;1.43	5.27	3.01	0.34805	.	.	.	.	.	T	0.36524	0.0970	L	0.29908	0.895	0.80722	D	1	B;P;P	0.41569	0.32;0.602;0.755	B;B;B	0.43950	0.134;0.283;0.437	T	0.05451	-1.0884	9	0.38643	T	0.18	-0.054	6.933	0.24451	0.0:0.4761:0.0:0.5239	.	472;497;497	F8W9L8;A8MW92;A8MW92-4	.;P20L1_HUMAN;.	W	501;472;497;497;367;472	ENSP00000378781:C501W;ENSP00000355301:C472W;ENSP00000378784:C497W;ENSP00000324519:C497W;ENSP00000378788:C472W	ENSP00000324519:C497W	C	+	3	2	PHF20L1	133898884	0.394000	0.25246	0.875000	0.34327	0.928000	0.56348	1.393000	0.34497	0.385000	0.24970	0.477000	0.44152	TGT	.		0.478	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		G	133829702	T	G	133829702	3	3	110	1	0	0	0	0	1	0	0	0	11858	1673	58	5	1539	5	PHF20L1	8	133829702	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	46385748	133829702	12534320	22	9754											
FLJ46321	389763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	84608041	84608041	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtgagtgaggaccactgcGttgatacttcccaggaaatt	10	11	12	8	1	0	3	0	3	0	0	1	5	1	5	2	3	2	1	2	3	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr9:84608041G>A	ENST00000344803.2	+	4	2703	c.2656G>A	c.(2656-2658)Gtt>Att	p.V886I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	886					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGACCACTGCGTTGATACTTC	0.438																																					p.V886I		.											.	.	0			c.G2656A						.						100	85	90					9																	84608041		1867	4118	5985	SO:0001583	missense	389763	exon4			CACTGCGTTGATA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"family with sequence similarity 75, member D1"	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2656G>A	9.37:g.84608041G>A	ENSP00000341988:p.Val886Ile	Somatic	290	0		WXS	Illumina HiSeq	Phase_I	201	96	NM_001001670	0	0	0	0	0		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	6.075	0.382087	0.11524	.	.	ENSG00000214929	ENST00000344803	T	0.49432	0.78	2.92	-1.61	0.08399	.	1.757670	0.03395	N	0.202455	T	0.37237	0.0996	L	0.50333	1.59	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.06144	-1.0843	10	0.23302	T	0.38	0.4107	2.1957	0.03910	0.1774:0.3151:0.3841:0.1234	.	886	Q6ZQQ2	F75D1_HUMAN	I	886	ENSP00000341988:V886I	ENSP00000341988:V886I	V	+	1	0	FAM75D1	83797861	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.475000	0.00987	-0.318000	0.08665	-0.171000	0.13296	GTT	.		0.438	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84608041	G	A	84608041	3	1	110	1	0	0	0	0	1	0	0	0	5951	1145	40	1	2670	1	FLJ46321	9	84608041	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		84608041	56605390	23	9755											
DIRAS2	54769	ucsc.edu;bcgsc.ca	37	chr9	93375537	93375537	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcacgcacttgcctttgagCttctctttccttttctgctg	4	18	6	13	1	3	1	1	1	2	0	5	1	4	1	2	0	3	3	2	0	0	6	rs201919906		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr9:93375537C>T	ENST00000375765.3	-	2	961	c.573G>A	c.(571-573)aaG>aaA	p.K191K		NM_017594.3	NP_060064.2	Q96HU8	DIRA2_HUMAN	DIRAS family, GTP-binding RAS-like 2	191					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			kidney(1)|large_intestine(6)|lung(3)|skin(2)	12						TGCCTTTGAGCTTCTCTTTCC	0.567													C|||	1	0.000199681	0	0	5008	,	,		22124	0.001		0	False		,,,				2504	0				p.K191K													.	DIRAS2-659	0			c.G573A						.						192	171	178					9																	93375537		2203	4300	6503	SO:0001819	synonymous_variant	54769	exon2			TTTGAGCTTCTCT	AB076889	CCDS6687.1	9q22.32	2014-05-09			ENSG00000165023	ENSG00000165023			19323	protein-coding gene	gene with protein product		607863				12194967	Standard	NM_017594		Approved	Di-Ras2, DKFZp761C07121	uc004aqx.1	Q96HU8	OTTHUMG00000020196	ENST00000375765.3:c.573G>A	9.37:g.93375537C>T		Somatic	405	3		WXS	Illumina HiSeq		295	115	NM_017594	0	0	0	0	0	B3KVM2	Silent	SNP	ENST00000375765.3	37	CCDS6687.1																																																																																			C|0.999;T|0.000		0.567	DIRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053012.1			T	93375537	C	T	93375537	2	4	110	1	0	0	0	0	0	0	0	1	4542	796	28	2		2	DIRAS2	9	93375537	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	8767496	93375537	47837894	24	9756											
ITGA8	8516	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	15688856	15688856	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaattaccattgtatccaTcttggttcaggtctcctaag	10	16	6	9	0	3	0	1	0	2	0	5	0	4	0	3	2	1	2	3	2	5	7			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr10:15688856T>C	ENST00000378076.3	-	12	1549	c.1196A>G	c.(1195-1197)gAt>gGt	p.D399G		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	399					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						ATTGTATCCATCTTGGTTCAG	0.468																																					p.D399G		.											.	ITGA8-230	0			c.A1196G						.						96	89	92					10																	15688856		2203	4300	6503	SO:0001583	missense	8516	exon12			TATCCATCTTGGT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1196A>G	10.37:g.15688856T>C	ENSP00000367316:p.Asp399Gly	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	101	7	NM_003638	0	0	0	0	0	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.698910	0.88830	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.75589	-0.95	5.09	5.09	0.68999	.	0.093018	0.64402	D	0.000001	D	0.89322	0.6682	H	0.94264	3.515	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.69142	0.962;0.943	D	0.92371	0.5905	10	0.87932	D	0	.	14.8578	0.70355	0.0:0.0:0.0:1.0	.	384;399	F5H818;P53708	.;ITA8_HUMAN	G	399;384	ENSP00000367316:D399G	ENSP00000367316:D399G	D	-	2	0	ITGA8	15728862	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.040000	0.89188	1.897000	0.54924	0.460000	0.39030	GAT	.		0.468	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		C	15688856	T	C	15688856	3	2	110	1	0	0	0	0	1	0	0	0	7903	1435	50	3	2071	3	ITGA8	10	15688856	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10		15688856	119845891	25	9757											
TRPM5	29850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	2432685	2432685	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgtcatgggggtgcagcagCgcctgggtggtgacaccgta	6	7	17	11	3	1	1	1	1	0	0	1	1	1	1	3	4	3	3	3	4	1	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:2432685C>T	ENST00000155858.6	-	18	2687	c.2679G>A	c.(2677-2679)gcG>gcA	p.A893A	TRPM5_ENST00000533060.1_Silent_p.A893A|TRPM5_ENST00000452833.1_Silent_p.A895A|TRPM5_ENST00000528453.1_Silent_p.A893A	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GGTGCAGCAGCGCCTGGGTGG	0.632																																					p.A893A	NSCLC(1;49 61 17205 18850 43201)	.											.	TRPM5-137	0			c.G2679A						.						33	37	36					11																	2432685		2202	4295	6497	SO:0001819	synonymous_variant	29850	exon18			CAGCAGCGCCTGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"Voltage-gated ion channels / Transient receptor potential cation channels"	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.2679G>A	11.37:g.2432685C>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	88	27	NM_014555	0	0	0	0	0		Silent	SNP	ENST00000155858.6	37	CCDS31340.1																																																																																			.		0.632	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2432685	C	T	2432685	2	4	110	1	0	0	0	0	0	0	0	1	16622	755	27	1		1	TRPM5	11	2432685	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		2432685	132573831	26	9758											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825362	95825362	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttgctgttgctgttgctgCtgctgctgctgttgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:95825362C>T	ENST00000524717.1	-	2	3117	c.1833G>A	c.(1831-1833)caG>caA	p.Q611Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	611					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q611Q(2)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgctgctgctgct	0.542			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q611Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.G1833A						.						39	44	42					11																	95825362		2057	4042	6099	SO:0001819	synonymous_variant	84441	exon2			TTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1833G>A	11.37:g.95825362C>T		Somatic	232	0		WXS	Illumina HiSeq	Phase_I	238	12	NM_032427	0	0	56	56	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.542	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825362	C	T	95825362	2	4	110	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825362	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	93392677	95825362	39181154	27	9759			1	32		2	2	46	C		7.849354e-05
MAML2	84441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	95825407	95825407	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgctgctgttgctgctgttg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs61901862		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q596Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.532			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q596Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	1	Substitution - coding silent(1)	kidney(1)	c.G1788A						.						28	35	33					11																	95825407		2119	4148	6267	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1788G>A	11.37:g.95825407C>T		Somatic	246	0		WXS	Illumina HiSeq	Phase_I	274	55	NM_032427	0	0	413	427	14	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			C|0.250;T|0.750		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825407	C	T	95825407	2	4	110	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825407	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	45	95825407	39181109	28	9760			1	32		2	2	46	C		7.849354e-05
TRPC6	7225	ucsc.edu	37	chr11	101340201	101340201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttgaaaggtcttcatgacttCctaaaattccaagtttcttt	11	17	5	8	0	3	2	1	2	2	0	5	2	5	2	2	1	0	1	2	1	4	7	rs138519687		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:101340201C>T	ENST00000344327.3	-	10	2865	c.2441G>A	c.(2440-2442)gGa>gAa	p.G814E	TRPC6_ENST00000360497.4_Missense_Mutation_p.G759E|TRPC6_ENST00000532133.1_Missense_Mutation_p.G736E|TRPC6_ENST00000348423.4_Missense_Mutation_p.G698E	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	814					aging (GO:0007568)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|ion transmembrane transport (GO:0034220)|platelet activation (GO:0030168)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ion transmembrane transporter activity (GO:0032414)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.G814E(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(14)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		ttcatgacttcctaaaattcc	0.284																																					p.G814E	Colon(166;1315 1927 11094 12848 34731)												.	TRPC6-93	1	Substitution - Missense(1)	skin(1)	c.G2441A						.						74	72	73					11																	101340201		2198	4295	6493	SO:0001583	missense	7225	exon10			TGACTTCCTAAAA	AJ006276	CCDS8311.1	11q22.1	2014-02-04				ENSG00000137672		"Voltage-gated ion channels / Transient receptor potential cation channels"	12338	protein-coding gene	gene with protein product		603652	"focal segmental glomerulosclerosis 2"	FSGS2		9925922, 16382100, 15879175	Standard	NM_004621		Approved	TRP6	uc001pgk.4	Q9Y210		ENST00000344327.3:c.2441G>A	11.37:g.101340201C>T	ENSP00000340913:p.Gly814Glu	Somatic	50	0		WXS	Illumina HiSeq		42	4	NM_004621	0	0	0	0	0	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	C	9.959	1.222338	0.22457	.	.	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.77750	-0.95;-1.02;-0.86;-1.12	4.43	2.45	0.29901	.	2.229520	0.01753	N	0.030032	T	0.63827	0.2544	N	0.14661	0.345	0.28120	N	0.930653	B;B;B	0.30406	0.032;0.278;0.008	B;B;B	0.30316	0.055;0.114;0.011	T	0.57985	-0.7716	10	0.40728	T	0.16	-2.2809	5.3878	0.16227	0.0:0.66:0.2253:0.1147	.	759;698;814	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	E	814;736;698;759	ENSP00000340913:G814E;ENSP00000435574:G736E;ENSP00000343672:G698E;ENSP00000353687:G759E	ENSP00000340913:G814E	G	-	2	0	TRPC6	100845411	1.000000	0.71417	0.999000	0.59377	0.912000	0.54170	1.258000	0.32944	1.082000	0.41137	-0.145000	0.13849	GGA	.		0.284	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		T	101340201	C	T	101340201	3	4	110	1	0	0	0	0	1	0	0	0	16616	855	30	2	370	2	TRPC6	11	101340201	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	5514794	101340201	33666315	29	9761											
OR8G1	219865	bcgsc.ca	37	chr11	124135723	124135723	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggaataaagatgtccacgTtgccctgaagaaaacgctag	15	7	11	8	2	0	3	0	1	0	2	1	5	1	4	2	1	2	2	2	1	7	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:124135723T>C	ENST00000524943.2	+	1	1001	c.1001T>C	c.(1000-1002)gTt>gCt	p.V334A	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	334						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		GATGTCCACGTTGCCCTGAAG	0.408																																					p.V334A	Ovarian(169;523 1969 8640 31295 51256)												.	.	0			c.T1001C						.						56	55	55					11																	124135723		2026	4204	6230	SO:0001583	missense	219865	exon1			TCCACGTTGCCCT	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"GPCR / Class A : Olfactory receptors"	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.1001T>C	11.37:g.124135723T>C	ENSP00000477014:p.Val334Ala	Somatic	247	2		WXS	Illumina HiSeq	Phase_1	254	16	NM_001005198	0	0	0	0	0	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				.		0.408	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		C	124135723	T	C	124135723	3	2	110	1	0	0	0	0	1	0	0	0	11260	1725	60	3	902	3	OR8G1	11	124135723	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	22795522	124135723	10870793	30	9762											
ACAD8	27034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	134131026	134131026	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aattgggagcgaggggcaggGcttcctcattgccgtgagag	8	8	17	8	2	1	1	1	1	0	1	2	4	2	2	2	4	2	2	2	4	1	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:134131026G>A	ENST00000281182.4	+	7	900	c.794G>A	c.(793-795)gGc>gAc	p.G265D	ACAD8_ENST00000374752.4_Missense_Mutation_p.G138D|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000537423.1_Missense_Mutation_p.G188D|ACAD8_ENST00000543332.1_Missense_Mutation_p.G167D	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	265					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	GAGGGGCAGGGCTTCCTCATT	0.587																																					p.G265D	GBM(65;238 1125 33403 41853 48889)	.											.	ACAD8-90	0			c.G794A						.						70	66	67					11																	134131026		2201	4297	6498	SO:0001583	missense	27034	exon7			GGCAGGGCTTCCT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"acyl-Coenzyme A dehydrogenase family, member 8"			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.794G>A	11.37:g.134131026G>A	ENSP00000281182:p.Gly265Asp	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	170	74	NM_014384	0	0	11	21	10	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	G	34	5.343370	0.95783	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99961	-9.25;-9.25;-9.25;-9.25	5.44	5.44	0.79542	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.99971	0.9990	H	0.97874	4.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.996	D	0.96958	0.9699	10	0.87932	D	0	.	19.2501	0.93921	0.0:0.0:1.0:0.0	.	188;138;265	B7Z5W4;Q6ZWP6;Q9UKU7	.;.;ACAD8_HUMAN	D	265;188;167;138;227	ENSP00000281182:G265D;ENSP00000443763:G188D;ENSP00000438302:G167D;ENSP00000363884:G138D	ENSP00000281182:G265D	G	+	2	0	ACAD8	133636236	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.793000	0.99091	2.561000	0.86390	0.561000	0.74099	GGC	.		0.587	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		A	134131026	G	A	134131026	3	1	110	1	0	0	0	0	1	0	0	0	110	1203	42	2	820	2	ACAD8	11	134131026	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	9995303	134131026	875490	31	9763											
MYO1A	4640	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	57440666	57440666	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagtttgtgatgacaccaccGaggggggatcccttgaagtc	9	9	13	10	1	0	3	0	3	0	0	2	5	1	4	3	3	0	1	3	3	1	2	rs561295735	byFrequency	TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr12:57440666G>A	ENST00000442789.2	-	8	809	c.522C>T	c.(520-522)ctC>ctT	p.L174L	MYO1A_ENST00000544473.1_Silent_p.L12L|MYO1A_ENST00000300119.3_Silent_p.L174L	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	174	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						TGACACCACCGAGGGGGGATC	0.498													G|||	6	0.00119808	0	0	5008	,	,		20056	0		0	False		,,,				2504	0.0061				p.L174L		.											.	MYO1A-231	0			c.C522T						.						98	93	94					12																	57440666		2203	4300	6503	SO:0001819	synonymous_variant	4640	exon7			ACCACCGAGGGGG	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.522C>T	12.37:g.57440666G>A		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	188	15	NM_005379	0	0	0	0	0	Q9UQD7	Silent	SNP	ENST00000442789.2	37	CCDS8929.1																																																																																			.		0.498	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57440666	G	A	57440666	2	1	110	1	0	0	0	0	0	0	0	1	10093	1045	37	1		1	MYO1A	12	57440666	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		57440666	76411229	32	9764											
FREM2	341640	broad.mit.edu;bcgsc.ca	37	chr13	39438496	39438496	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacaagagttggaaaccacaAgtgctccaacctcctggatt	13	8	8	12	0	0	1	0	0	0	1	2	3	2	3	4	2	3	2	4	2	4	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr13:39438496A>G	ENST00000280481.7	+	16	7952	c.7736A>G	c.(7735-7737)aAg>aGg	p.K2579R		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2579					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)		GGAAACCACAAGTGCTCCAAC	0.438																																					p.K2579R													.	FREM2-100	0			c.A7736G						.						105	94	98					13																	39438496		2203	4300	6503	SO:0001583	missense	341640	exon16			ACCACAAGTGCTC	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.7736A>G	13.37:g.39438496A>G	ENSP00000280481:p.Lys2579Arg	Somatic	199	1		WXS	Illumina HiSeq	Phase_I	129	11	NM_207361	0	0	0	0	0	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	6.849	0.525823	0.13066	.	.	ENSG00000150893	ENST00000280481	T	0.18174	2.23	5.81	-0.748	0.11087	.	0.352897	0.31233	N	0.008018	T	0.05318	0.0141	N	0.05012	-0.13	0.34872	D	0.743695	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.42766	-0.9432	10	0.07175	T	0.84	.	6.1782	0.20455	0.6157:0.122:0.2623:0.0	.	2579;2579	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	R	2579	ENSP00000280481:K2579R	ENSP00000280481:K2579R	K	+	2	0	FREM2	38336496	1.000000	0.71417	0.985000	0.45067	0.980000	0.70556	2.923000	0.48868	-0.095000	0.12351	-0.280000	0.10049	AAG	.		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39438496	A	G	39438496	3	3	110	1	0	0	0	0	1	0	0	0	6064	72	3	3	7798	3	FREM2	13	39438496	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10		39438496	75731382	33	9765											
CFL2	1073	hgsc.bcm.edu	37	chr14	35182529	35182529	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggcatcgtacaaagcatatCggcaatcattcagaggtagc	13	9	10	9	2	2	1	2	0	0	1	4	1	2	1	0	3	3	5	0	3	5	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr14:35182529C>T	ENST00000341223.3	-	2	393	c.242G>A	c.(241-243)cGa>cAa	p.R81Q	CFL2_ENST00000555765.1_Missense_Mutation_p.R64Q|CFL2_ENST00000556161.1_Missense_Mutation_p.R64Q|CFL2_ENST00000298159.6_Missense_Mutation_p.R81Q	NM_001243645.1|NM_021914.7	NP_001230574.1|NP_068733.1	Q9Y281	COF2_HUMAN	cofilin 2 (muscle)	81	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament depolymerization (GO:0030042)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of actin filament depolymerization (GO:0030836)|regulation of dendritic spine morphogenesis (GO:0061001)|sarcomere organization (GO:0045214)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|nucleus (GO:0005634)				breast(3)|endometrium(2)|lung(3)	8	Breast(36;0.0361)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;6.07e-06)|Lung(238;2.23e-05)|Epithelial(34;0.0387)|all cancers(34;0.0814)	GBM - Glioblastoma multiforme(112;0.0424)		CAAAGCATATCGGCAATCATT	0.378																																					p.R81Q		.											.	CFL2-289	0			c.G242A						.						113	108	109					14																	35182529		2203	4300	6503	SO:0001583	missense	1073	exon2			GCATATCGGCAAT	AF087867	CCDS9649.1, CCDS9650.1, CCDS58311.1	14q13.2	2014-09-17			ENSG00000165410	ENSG00000165410			1875	protein-coding gene	gene with protein product	"nemaline myopathy type 7"	601443				8800436	Standard	NM_138638		Approved	NEM7	uc001wsh.3	Q9Y281	OTTHUMG00000029536	ENST00000341223.3:c.242G>A	14.37:g.35182529C>T	ENSP00000340635:p.Arg81Gln	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	94	5	NM_021914	0	0	7	7	0	G3V5P4	Missense_Mutation	SNP	ENST00000341223.3	37	CCDS9650.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521545	0.85600	.	.	ENSG00000165410	ENST00000341223;ENST00000298159;ENST00000555765;ENST00000556161	D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92	6.02	6.02	0.97574	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	D	0.95351	0.8491	H	0.96805	3.885	0.80722	D	1	D	0.71674	0.998	D	0.66847	0.947	D	0.95938	0.8944	10	0.72032	D	0.01	-0.5517	20.5407	0.99260	0.0:1.0:0.0:0.0	.	81	Q9Y281	COF2_HUMAN	Q	81;81;64;64	ENSP00000340635:R81Q;ENSP00000298159:R81Q;ENSP00000452451:R64Q;ENSP00000452188:R64Q	ENSP00000298159:R81Q	R	-	2	0	CFL2	34252280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.747000	0.85070	2.865000	0.98341	0.655000	0.94253	CGA	.		0.378	CFL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276639.1	NM_138638		T	35182529	C	T	35182529	3	4	110	1	0	0	0	0	1	0	0	0	3297	884	31	1	270	1	CFL2	14	35182529	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		35182529	72167011	34	9766											
PRC1	9055	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	91517424	91517424	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgcttgctaggtgttcgaGgagcgctgccatacagcatc	7	9	13	12	3	0	0	0	0	0	0	2	2	0	1	2	2	5	5	2	2	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr15:91517424G>T	ENST00000361188.5	-	11	2614	c.1403C>A	c.(1402-1404)cCt>cAt	p.P468H	PRC1_ENST00000361919.3_Missense_Mutation_p.P468H|PRC1-AS1_ENST00000556200.1_RNA|PRC1_ENST00000394249.3_Missense_Mutation_p.P468H|PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000442656.2_Missense_Mutation_p.P427H					protein regulator of cytokinesis 1									p.P468R(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					AGGTGTTCGAGGAGCGCTGCC	0.498																																					p.P468H		.											.	PRC1-92	1	Substitution - Missense(1)	ovary(1)	c.C1403A						.						201	170	180					15																	91517424		2198	4298	6496	SO:0001583	missense	9055	exon11			GTTCGAGGAGCGC	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"anaphase spindle elongation 1 homolog (S. cerevisiae)"	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.1403C>A	15.37:g.91517424G>T	ENSP00000354679:p.Pro468His	Somatic	274	0		WXS	Illumina HiSeq	Phase_I	249	21	NM_199413	0	0	22	29	7		Missense_Mutation	SNP	ENST00000361188.5	37	CCDS45352.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723028	0.68959	.	.	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000555455;ENST00000442656	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.37	5.37	0.77165	.	0.293466	0.39146	N	0.001451	T	0.61413	0.2345	M	0.71581	2.175	0.38985	D	0.959022	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.75484	0.976;0.976;0.976;0.986	T	0.63989	-0.6512	10	0.59425	D	0.04	-9.2179	18.9064	0.92464	0.0:0.0:1.0:0.0	.	427;468;438;468	O43663-3;F8W9B5;O43663-2;O43663	.;.;.;PRC1_HUMAN	H	468;468;468;71;427	ENSP00000377793:P468H;ENSP00000354618:P468H;ENSP00000354679:P468H;ENSP00000409549:P427H	ENSP00000354679:P468H	P	-	2	0	PRC1	89318428	1.000000	0.71417	0.781000	0.31783	0.590000	0.36582	6.445000	0.73456	2.788000	0.95919	0.650000	0.86243	CCT	.		0.498	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		T	91517424	G	T	91517424	3	4	110	1	0	0	0	0	1	0	0	0	12475	1000	35	4	479	4	PRC1	15	91517424	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		91517424	11013968	35	9767											
DCUN1D3	123879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20871250	20871250	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagccctcaggccctgagctGagtgcacctctcccttcccc	6	8	8	19	0	2	2	1	2	1	0	4	2	3	2	6	1	3	2	6	1	1	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr16:20871250G>A	ENST00000324344.4	-	3	1158	c.873C>T	c.(871-873)ctC>ctT	p.L291L	DCUN1D3_ENST00000563934.1_Silent_p.L291L|ERI2_ENST00000564349.1_Intron	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	291					negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		GCCCTGAGCTGAGTGCACCTC	0.577																																					p.L291L		.											.	DCUN1D3-92	0			c.C873T						.						73	63	66					16																	20871250		2201	4300	6501	SO:0001819	synonymous_variant	123879	exon3			TGAGCTGAGTGCA	BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.873C>T	16.37:g.20871250G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	212	91	NM_173475	0	0	4	6	2	B3KVY4	Silent	SNP	ENST00000324344.4	37	CCDS10592.1																																																																																			.		0.577	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475		A	20871250	G	A	20871250	2	1	110	1	0	0	0	0	0	0	0	1	4321	1277	45	2		2	DCUN1D3	16	20871250	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		20871250	69483503	36	9768											
CDH8	1006	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	61687954	61687954	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtcttcatcatctttgataAttaatggttcatttttatgc	9	20	5	7	1	5	1	3	1	2	0	5	1	5	1	0	1	1	1	0	1	3	8			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr16:61687954A>C	ENST00000577390.1	-	12	2912	c.1958T>G	c.(1957-1959)aTt>aGt	p.I653S	CDH8_ENST00000299345.6_Missense_Mutation_p.I653S|CDH8_ENST00000577730.1_Missense_Mutation_p.I653S	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	653					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATCTTTGATAATTAATGGTTC	0.388																																					p.I653S		.											.	CDH8-161	0			c.T1958G						.						81	78	79					16																	61687954		2203	4300	6503	SO:0001583	missense	1006	exon12			TTGATAATTAATG	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1958T>G	16.37:g.61687954A>C	ENSP00000462701:p.Ile653Ser	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	177	54	NM_001796	0	0	0	0	0	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.367372	0.82463	.	.	ENSG00000150394	ENST00000299345	T	0.78246	-1.16	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.72558	0.3475	L	0.39566	1.225	0.80722	D	1	B	0.23249	0.082	B	0.29663	0.105	T	0.68573	-0.5373	10	0.38643	T	0.18	.	15.1545	0.72730	1.0:0.0:0.0:0.0	.	653	P55286	CADH8_HUMAN	S	653	ENSP00000299345:I653S	ENSP00000299345:I653S	I	-	2	0	CDH8	60245455	1.000000	0.71417	0.984000	0.44739	0.916000	0.54674	9.251000	0.95483	2.164000	0.68074	0.533000	0.62120	ATT	.		0.388	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61687954	A	C	61687954	3	2	110	1	0	0	0	0	1	0	0	0	3122	101	4	5	445	5	CDH8	16	61687954	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10	40816704	61687954	28666799	37	9769											
RPL13	6137	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	89627425	89627425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttccacaaggactggcagCggcgcgtggccacgtggttc	7	7	14	13	4	0	0	0	0	0	0	2	1	1	1	2	5	1	2	2	5	1	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr16:89627425C>T	ENST00000393099.3	+	1	307	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	RPL13_ENST00000452368.3_Missense_Mutation_p.R20W|SNORD68_ENST00000363214.1_RNA|RPL13_ENST00000567815.1_Missense_Mutation_p.R20W|RPL13_ENST00000311528.5_Missense_Mutation_p.R20W	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	20					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|cytosolic ribosome (GO:0022626)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(3)|skin(1)|upper_aerodigestive_tract(2)	6		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		GGACTGGCAGCGGCGCGTGGC	0.711																																					p.R20W		.											.	RPL13-90	0			c.C58T						.						14	15	15					16																	89627425		2144	4198	6342	SO:0001583	missense	6137	exon2			TGGCAGCGGCGCG	AB007172	CCDS10979.1, CCDS58492.1	16q24.3	2011-04-06			ENSG00000167526	ENSG00000167526		"L ribosomal proteins"	10303	protein-coding gene	gene with protein product		113703				9582194	Standard	NM_000977		Approved	D16S444E, BBC1, L13	uc002fnm.2	P26373	OTTHUMG00000133770	ENST00000393099.3:c.58C>T	16.37:g.89627425C>T	ENSP00000376811:p.Arg20Trp	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	86	41	NM_001243131	1	2	298	617	316	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Missense_Mutation	SNP	ENST00000393099.3	37	CCDS10979.1	.	.	.	.	.	.	.	.	.	.	c	31	5.083913	0.94050	.	.	ENSG00000167526	ENST00000311528;ENST00000452368;ENST00000393099	T;T;T	0.32753	1.44;1.44;1.44	4.7	2.4	0.29515	.	0.117520	0.53938	U	0.000041	T	0.54679	0.1873	M	0.90705	3.14	0.48511	D	0.999666	D;D;D	0.61697	0.987;0.99;0.99	D;P;P	0.63793	0.918;0.851;0.851	T	0.60105	-0.7328	10	0.87932	D	0	-9.0218	7.8657	0.29535	0.2806:0.6293:0.0:0.0901	.	20;20;20	F5H1S2;A8K4C8;P26373	.;.;RL13_HUMAN	W	20	ENSP00000307889:R20W;ENSP00000438959:R20W;ENSP00000376811:R20W	ENSP00000307889:R20W	R	+	1	2	RPL13	88154926	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.902000	0.63266	1.107000	0.41642	0.563000	0.77884	CGG	.		0.711	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977		T	89627425	C	T	89627425	3	4	110	1	0	0	0	0	1	0	0	0	13591	759	27	1	60	1	RPL13	16	89627425	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	27939471	89627425	727328	38	9770											
SPAG7	9552	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4871031	4871031	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctcgggccttgcgccgAgtctcctggtcaccgaggct	4	9	12	16	4	3	0	2	0	1	0	5	2	3	0	5	3	1	1	5	3	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr17:4871031A>C	ENST00000206020.3	-	1	136	c.69T>G	c.(67-69)acT>acG	p.T23T	SPAG7_ENST00000575142.1_Silent_p.T12T|RP5-1050D4.3_ENST00000576752.1_RNA|SPAG7_ENST00000573366.1_5'Flank|SPAG7_ENST00000571023.1_5'UTR	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	23						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						CCTTGCGCCGAGTCTCCTGGT	0.627																																					p.T23T													.	SPAG7-91	0			c.T69G						.						94	105	101					17																	4871031		1986	4146	6132	SO:0001819	synonymous_variant	9552	exon1			GCGCCGAGTCTCC	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.69T>G	17.37:g.4871031A>C		Somatic	63	1		WXS	Illumina HiSeq	Phase_I	76	20	NM_004890	0	0	24	47	23	Q96EU5	Silent	SNP	ENST00000206020.3	37	CCDS42240.1																																																																																			.		0.627	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		C	4871031	A	C	4871031	2	2	110	1	0	0	0	0	0	0	0	1	15015	291	11	5		5	SPAG7	17	4871031	Silent	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10		4871031	76324179	39	9771											
GPR172B	55065	hgsc.bcm.edu;bcgsc.ca	37	chr17	4937586	4937586	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggggccagctgcctccacagGgtcaccaccagcagacccag	9	3	12	17	0	1	1	1	0	0	1	2	1	2	1	6	3	3	2	6	3	0	0			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr17:4937586G>T	ENST00000424747.1	-	3	910	c.198C>A	c.(196-198)acC>acA	p.T66T	SLC52A1_ENST00000254853.5_Silent_p.T66T|SLC52A1_ENST00000512825.2_Silent_p.T66T	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	66					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										GCCTCCACAGGGTCACCACCA	0.642																																					p.T66T		.											.	.	0			c.C198A						.						49	50	50					17																	4937586		2203	4300	6503	SO:0001819	synonymous_variant	55065	exon3			CCACAGGGTCACC	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.198C>A	17.37:g.4937586G>T		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_017986	0	0	0	0	0	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	37	CCDS11066.1																																																																																			.		0.642	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		T	4937586	G	T	4937586	2	4	110	1	0	0	0	0	0	0	0	1	6690	1219	43	4		4	GPR172B	17	4937586	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	66555	4937586	76257624	40	9772											
ITGA3	3675	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48148253	48148253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagtgggacttatctgagtAtagttacaaggacccagagg	12	9	14	6	0	1	2	0	1	1	1	1	5	1	5	1	4	1	2	1	4	5	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr17:48148253A>G	ENST00000320031.8	+	5	1040	c.710A>G	c.(709-711)tAt>tGt	p.Y237C	ITGA3_ENST00000544892.1_Missense_Mutation_p.Y12C|ITGA3_ENST00000007722.7_Missense_Mutation_p.Y237C	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	237					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						TTATCTGAGTATAGTTACAAG	0.502																																					p.Y237C		.											.	ITGA3-229	0			c.A710G						.						206	211	209					17																	48148253		2203	4300	6503	SO:0001583	missense	3675	exon5			CTGAGTATAGTTA	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"CD molecules", "Integrins"	6139	protein-coding gene	gene with protein product		605025	"antigen identified by monoclonal antibody J143"	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.710A>G	17.37:g.48148253A>G	ENSP00000315190:p.Tyr237Cys	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	237	94	NM_005501	0	0	198	403	205	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	37	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.986557	0.53934	.	.	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	T;T;T	0.57107	0.42;0.42;0.42	5.69	3.33	0.38152	.	0.874333	0.10328	N	0.687966	T	0.52108	0.1714	L	0.54323	1.7	0.27793	N	0.942745	D;P	0.56968	0.978;0.898	P;B	0.48901	0.594;0.379	T	0.43442	-0.9391	10	0.46703	T	0.11	.	5.9462	0.19219	0.6614:0.173:0.0:0.1656	.	237;237	P26006-1;P26006	.;ITA3_HUMAN	C	12;237;223;237	ENSP00000446133:Y12C;ENSP00000007722:Y237C;ENSP00000315190:Y237C	ENSP00000007722:Y237C	Y	+	2	0	ITGA3	45503252	0.979000	0.34478	0.526000	0.27913	0.985000	0.73830	1.665000	0.37449	0.961000	0.38030	0.533000	0.62120	TAT	.		0.502	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		G	48148253	A	G	48148253	3	3	110	1	0	0	0	0	1	0	0	0	7898	449	16	3	728	3	ITGA3	17	48148253	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10	43210667	48148253	33046957	41	9773											
ABCA6	23460	broad.mit.edu;bcgsc.ca	37	chr17	67081770	67081770	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	accatttcctcactacctctCcagcagttggctttgtgatc	7	14	6	14	0	2	1	1	1	1	0	5	1	3	1	4	1	2	3	4	1	1	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr17:67081770C>T	ENST00000284425.2	-	31	4199	c.4025G>A	c.(4024-4026)gGa>gAa	p.G1342E	ABCA6_ENST00000446604.2_5'UTR	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	1342	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					CACTACCTCTCCAGCAGTTGG	0.343																																					p.G1342E													.	ABCA6-159	0			c.G4025A						.						92	81	85					17																	67081770		2203	4300	6503	SO:0001583	missense	23460	exon31			ACCTCTCCAGCAG	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"ATP binding cassette transporters / subfamily A"	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.4025G>A	17.37:g.67081770C>T	ENSP00000284425:p.Gly1342Glu	Somatic	262	1		WXS	Illumina HiSeq	Phase_I	335	15	NM_080284	0	0	0	0	0	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	37	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.126830	0.56721	.	.	ENSG00000154262	ENST00000284425;ENST00000446604	D	0.97888	-4.59	4.66	4.66	0.58398	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.49305	D	0.000142	D	0.99378	0.9781	H	0.99404	4.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98055	1.0390	10	0.87932	D	0	.	17.0615	0.86548	0.0:1.0:0.0:0.0	.	1342	Q8N139	ABCA6_HUMAN	E	1342;202	ENSP00000284425:G1342E	ENSP00000284425:G1342E	G	-	2	0	ABCA6	64593365	1.000000	0.71417	0.999000	0.59377	0.085000	0.17905	6.669000	0.74462	2.576000	0.86940	0.650000	0.86243	GGA	.		0.343	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		T	67081770	C	T	67081770	3	4	110	1	0	0	0	0	1	0	0	0	36	855	30	2	864	2	ABCA6	17	67081770	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	18933517	67081770	14113440	42	9774											
ASXL3	80816	broad.mit.edu;ucsc.edu	37	chr18	31224902	31224902	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatgcaatgcttcacactaAcactcgaataggggatggaa	15	8	10	8	1	1	0	1	0	0	0	2	4	1	2	0	3	3	2	0	3	6	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr18:31224902A>G	ENST00000269197.5	+	3	182	c.182A>G	c.(181-183)aAc>aGc	p.N61S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	61					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(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						CTTCACACTAACACTCGAATA	0.393																																					p.N61S													.	ASXL3-49	0			c.A182G						.						101	89	93					18																	31224902		1862	4111	5973	SO:0001583	missense	80816	exon3			ACACTAACACTCG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.182A>G	18.37:g.31224902A>G	ENSP00000269197:p.Asn61Ser	Somatic	81	1		WXS	Illumina HiSeq	Phase_I	47	5	NM_030632	0	0	0	0	0	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.689578	0.68271	.	.	ENSG00000141431	ENST00000269197	T	0.20738	2.05	5.57	4.41	0.53225	.	.	.	.	.	T	0.21550	0.0519	M	0.62723	1.935	0.34860	D	0.742502	B	0.32653	0.379	B	0.23716	0.048	T	0.28004	-1.0057	9	0.87932	D	0	.	11.4354	0.50064	0.9295:0.0:0.0705:0.0	.	61	Q9C0F0	ASXL3_HUMAN	S	61	ENSP00000269197:N61S	ENSP00000269197:N61S	N	+	2	0	ASXL3	29478900	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.017000	0.64047	1.063000	0.40649	0.533000	0.62120	AAC	.		0.393	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			G	31224902	A	G	31224902	3	3	110	1	0	0	0	0	1	0	0	0	1069	43	2	3	192	3	ASXL3	18	31224902	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10		31224902	46852346	43	9775											
TCEB3B	51224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	44560193	44560193	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcctgggaggtcatggaGtcagaatccgaaagcggatc	10	9	14	8	2	2	1	2	0	0	1	4	5	3	4	2	4	2	0	2	4	2	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr18:44560193G>A	ENST00000332567.4	-	1	1795	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	481					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						AGGTCATGGAGTCAGAATCCG	0.582																																					p.D481D		.											.	TCEB3B-156	0			c.C1443T						.						60	66	64					18																	44560193		2203	4300	6503	SO:0001819	synonymous_variant	51224	exon1			CATGGAGTCAGAA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"transcription elongation factor (SIII) elongin A2", "elongin A2"	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1443C>T	18.37:g.44560193G>A		Somatic	197	0		WXS	Illumina HiSeq	Phase_I	153	63	NM_016427	0	0	0	0	0	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			.		0.582	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		A	44560193	G	A	44560193	2	1	110	1	0	0	0	0	0	0	0	1	15714	1020	36	2		2	TCEB3B	18	44560193	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	13335291	44560193	33517055	44	9776											
ZNF799	90576	ucsc.edu	37	chr19	12501560	12501560	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctctcatgtgaattcttTcatgtcgtagaaagcaagtg	10	15	8	8	1	4	2	2	1	3	1	7	2	4	2	0	0	1	2	0	0	4	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr19:12501560T>C	ENST00000430385.3	-	4	1852	c.1652A>G	c.(1651-1653)gAa>gGa	p.E551G	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.E519G	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	551					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(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						GTGAATTCTTTCATGTCGTAG	0.393																																					p.E551G													.	ZNF799-74	0			c.A1652G						.						93	96	95					19																	12501560		2202	4300	6502	SO:0001583	missense	90576	exon4			ATTCTTTCATGTC	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1652A>G	19.37:g.12501560T>C	ENSP00000411084:p.Glu551Gly	Somatic	171	3		WXS	Illumina HiSeq		201	1	NM_001080821	0	0	6	10	4		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.811876	0.32053	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.18657	2.2;2.2	1.53	-0.919	0.10478	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20414	0.0491	M	0.62209	1.925	0.09310	N	1	B	0.17852	0.024	B	0.29353	0.101	T	0.40720	-0.9548	9	0.62326	D	0.03	.	3.0258	0.06090	0.2117:0.1463:0.0:0.642	.	551	Q96GE5	ZN799_HUMAN	G	519;551	ENSP00000415278:E519G;ENSP00000411084:E551G	ENSP00000415278:E519G	E	-	2	0	ZNF799	12362560	0.000000	0.05858	0.005000	0.12908	0.094000	0.18550	-1.204000	0.03017	-0.358000	0.08162	0.352000	0.21897	GAA	.		0.393	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		C	12501560	T	C	12501560	3	2	110	1	0	0	0	0	1	0	0	0	18198	1783	62	3	283	3	ZNF799	19	12501560	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10		12501560	46627423	45	9777											
ZNF709	163051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12574997	12574997	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcactccagtgtgagtcCtttcatgcattcgaacagaa	10	13	8	10	1	2	2	2	1	0	1	5	3	4	2	2	0	2	2	2	0	2	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr19:12574997C>T	ENST00000397732.3	-	4	1910	c.1739G>A	c.(1738-1740)aGg>aAg	p.R580K	ZNF709_ENST00000428311.1_Missense_Mutation_p.R580K|CTD-3105H18.18_ENST00000598753.1_Intron	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	580					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						AGTGTGAGTCCTTTCATGCAT	0.423																																					p.R580K	GBM(33;565 669 12371 29134 51667)	.											.	ZNF709-90	0			c.G1739A						.						139	147	144					19																	12574997		2202	4300	6502	SO:0001583	missense	163051	exon4			TGAGTCCTTTCAT	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"Zinc fingers, C2H2-type", "-"	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.1739G>A	19.37:g.12574997C>T	ENSP00000380840:p.Arg580Lys	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	199	57	NM_152601	0	0	0	0	0	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	37	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.656147	0.67586	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.18338	2.22;2.22	2.89	1.85	0.25348	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17577	0.0422	L	0.45581	1.43	0.22127	N	0.99935	B	0.27498	0.18	B	0.33121	0.158	T	0.24190	-1.0167	9	0.48119	T	0.1	.	9.5077	0.39058	0.0:0.8844:0.0:0.1156	.	580	Q8N972	ZN709_HUMAN	K	580	ENSP00000380840:R580K;ENSP00000404127:R580K	ENSP00000404127:R580K	R	-	2	0	ZNF709;CTD-2192J16.17	12435997	0.000000	0.05858	0.050000	0.19076	0.605000	0.37080	-0.136000	0.10405	0.797000	0.33971	0.655000	0.94253	AGG	.		0.423	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		T	12574997	C	T	12574997	3	4	110	1	0	0	0	0	1	0	0	0	18145	681	24	2	190	2	ZNF709	19	12574997	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	73437	12574997	46553986	46	9778											
CILP2	148113	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19654855	19654855	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgggccaggagcccatcGgcttcaccgcctaccagggc	6	6	13	16	2	1	0	1	0	0	0	2	1	1	1	5	4	3	2	5	4	1	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr19:19654855G>A	ENST00000291495.5	+	8	1586	c.1501G>A	c.(1501-1503)Ggc>Agc	p.G501S	CILP2_ENST00000586018.1_Missense_Mutation_p.G507S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	501						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						GGAGCCCATCGGCTTCACCGC	0.672																																					p.G501S													.	CILP2-91	0			c.G1501A						.						27	30	29					19																	19654855		2203	4300	6503	SO:0001583	missense	148113	exon8			CCCATCGGCTTCA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1501G>A	19.37:g.19654855G>A	ENSP00000291495:p.Gly501Ser	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	86	32	NM_153221	0	0	0	0	0	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.549039	0.27652	.	.	ENSG00000160161	ENST00000291495	T	0.45276	0.9	3.76	3.76	0.43208	Carbohydrate-binding-like fold (1);	0.000000	0.85682	D	0.000000	T	0.31009	0.0783	L	0.35793	1.09	0.58432	D	0.999992	P;P	0.52692	0.955;0.955	B;B	0.41619	0.361;0.252	T	0.05886	-1.0858	10	0.15952	T	0.53	-24.9444	13.1257	0.59354	0.0:0.0:1.0:0.0	.	501;501	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	S	501	ENSP00000291495:G501S	ENSP00000291495:G501S	G	+	1	0	CILP2	19515855	1.000000	0.71417	0.926000	0.36857	0.540000	0.34992	4.647000	0.61418	1.657000	0.50732	0.423000	0.28283	GGC	.		0.672	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		A	19654855	G	A	19654855	3	1	110	1	0	0	0	0	1	0	0	0	3436	1116	39	1	1531	1	CILP2	19	19654855	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	7079858	19654855	39474128	47	9779											
FPR3	2359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52327625	52327625	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatcctccacttcattatTggcttcagcgtgcctatgtc	6	15	7	13	1	2	1	2	1	0	0	5	1	4	1	3	1	2	1	3	1	2	5			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr19:52327625T>A	ENST00000339223.4	+	2	803	c.624T>A	c.(622-624)atT>atA	p.I208I	FPR3_ENST00000595991.1_Silent_p.I208I	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	208					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)			NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						ACTTCATTATTGGCTTCAGCG	0.458																																					p.I208I		.											.	FPR3-501	0			c.T624A						.						146	118	128					19																	52327625		2203	4300	6503	SO:0001819	synonymous_variant	2359	exon2			CATTATTGGCTTC		CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"GPCR / Class A : Formyl peptide receptors"	3828	protein-coding gene	gene with protein product		136539	"formyl peptide receptor-like 2"	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.624T>A	19.37:g.52327625T>A		Somatic	242	0		WXS	Illumina HiSeq	Phase_I	155	67	NM_002030	0	0	0	0	0		Silent	SNP	ENST00000339223.4	37	CCDS12841.1																																																																																			.		0.458	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030		A	52327625	T	A	52327625	2	1	110	1	0	0	0	0	0	0	0	1	6059	1800	63	5		5	FPR3	19	52327625	Silent	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	32672770	52327625	6801358	48	9780											
KIAA1755	85449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	36870194	36870194	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgcagacagactgctcCtcctggggctccacttggag	8	9	12	12	0	0	3	0	1	0	2	3	4	3	4	3	3	2	3	3	3	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr20:36870194C>T	ENST00000279024.4	-	3	610	c.339G>A	c.(337-339)gaG>gaA	p.E113E		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	113										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CAGACTGCTCCTCCTGGGGCT	0.557																																					p.E113E		.											.	KIAA1755-95	0			c.G339A						.						92	90	90					20																	36870194		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CTGCTCCTCCTGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.339G>A	20.37:g.36870194C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	184	36	NM_001029864	0	0	1	1	0	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			.		0.557	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36870194	C	T	36870194	2	4	110	1	0	0	0	0	0	0	0	1	8278	680	24	2		2	KIAA1755	20	36870194	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		36870194	26155326	49	9781											
RBM11	54033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	15599303	15599303	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcactgaatcatgttccaGatcttgaggctggacccagc	9	10	9	13	0	3	3	2	2	1	1	4	4	4	4	3	2	1	2	3	2	1	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr21:15599303G>T	ENST00000400577.3	+	5	544	c.535G>T	c.(535-537)Gat>Tat	p.D179Y	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	179					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		TCATGTTCCAGATCTTGAGGC	0.458																																					p.D179Y		.											.	.	0			c.G535T						.						199	186	190					21																	15599303		1928	4131	6059	SO:0001583	missense	54033	exon5			GTTCCAGATCTTG	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"RNA binding motif (RRM) containing"	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.535G>T	21.37:g.15599303G>T	ENSP00000383421:p.Asp179Tyr	Somatic	371	1		WXS	Illumina HiSeq	Phase_I	364	149	NM_144770	0	0	9	11	2	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	.	.	.	.	.	.	.	.	.	.	G	8.231	0.804684	0.16467	.	.	ENSG00000185272	ENST00000400577	T	0.08546	3.08	2.74	1.85	0.25348	.	0.523863	0.19918	N	0.103153	T	0.08758	0.0217	L	0.51422	1.61	0.09310	N	1	P	0.40144	0.704	B	0.41571	0.36	T	0.16689	-1.0394	10	0.62326	D	0.03	-7.9775	4.814	0.13358	0.2974:0.0:0.7026:0.0	.	179	P57052	RBM11_HUMAN	Y	179	ENSP00000383421:D179Y	ENSP00000383421:D179Y	D	+	1	0	RBM11	14521174	0.201000	0.23410	0.002000	0.10522	0.803000	0.45373	0.649000	0.24843	0.712000	0.32039	0.430000	0.28490	GAT	.		0.458	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770		T	15599303	G	T	15599303	3	4	110	1	0	0	0	0	1	0	0	0	13144	942	33	4	553	4	RBM11	21	15599303	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		15599303	32530592	50	9782											
SEPT5	5413	ucsc.edu	37	chr22	19710008	19710008	+	3'UTR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagatgcaggaccagtgaCgctcgccgcggacacaccgt	10	4	13	14	5	0	2	0	1	0	1	1	4	0	4	3	2	2	3	3	2	0	0			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr22:19710008C>T	ENST00000455784.2	+	0	1236				GP1BB_ENST00000366425.3_5'Flank|SEPT5_ENST00000406395.1_3'UTR|SEPT5_ENST00000383045.3_3'UTR|SEPT5_ENST00000438754.2_3'UTR	NM_002688.5	NP_002679.2	Q99719	SEPT5_HUMAN	septin 5						cytokinesis (GO:0000910)|GTP catabolic process (GO:0006184)|regulation of exocytosis (GO:0017157)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic vesicle targeting (GO:0016080)	plasma membrane (GO:0005886)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			lung(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					GGACCAGTGACGCTCGCCGCG	0.706																																					.													.	.	0			.						.						29	29	29					22																	19710008		2181	4281	6462	SO:0001624	3_prime_UTR_variant	0	.			CAGTGACGCTCGC	Y11593	CCDS13764.1, CCDS56224.1	22q11.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000184702	ENSG00000184702		"Septins"	9164	protein-coding gene	gene with protein product		602724	"peanut-like 1 (Drosophila)"	PNUTL1		9385360, 9611266	Standard	NM_002688		Approved	HCDCREL-1, H5		Q99719	OTTHUMG00000150399	ENST00000455784.2:c.*1C>T	22.37:g.19710008C>T		Somatic	45	0		WXS	Illumina HiSeq		48	4	.	0	0	4	4	0	O15251|Q96MY5	RNA	SNP	ENST00000455784.2	37	CCDS13764.1																																																																																			.		0.706	SEPT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317937.1	NM_002688		T	19710008	C	T	19710008	1	4	110	0	1	0	0	0	0	0	0	0	14099	551	19	1		1	SEPT5	22	19710008	3'UTR	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		19710008	31594558	51	9783											
GRIPAP1	56850	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	48840222	48840222	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	taattcctgggtcaactgctCcttctcctgccctatttctt	5	17	5	14	0	3	0	1	0	2	0	6	0	5	0	4	1	3	1	4	1	3	6			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chrX:48840222C>T	ENST00000376441.1	-	15	1271	c.1237G>A	c.(1237-1239)Gag>Aag	p.E413K	GRIPAP1_ENST00000376444.3_Missense_Mutation_p.E368K|GRIPAP1_ENST00000473581.1_5'UTR|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.E360K|GRIPAP1_ENST00000376425.3_Missense_Mutation_p.E382K	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	413						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						GTCAACTGCTCCTTCTCCTGC	0.507																																					p.E413K		.											.	GRIPAP1-227	0			c.G1237A						.						268	196	221					X																	48840222		2203	4300	6503	SO:0001583	missense	56850	exon15			ACTGCTCCTTCTC	AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.1237G>A	X.37:g.48840222C>T	ENSP00000365624:p.Glu413Lys	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	245	17	NM_020137	0	0	27	27	0	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	-	17.86	3.491722	0.64074	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	4.34	4.34	0.51931	.	0.072191	0.53938	D	0.000057	T	0.40670	0.1126	L	0.50333	1.59	0.40778	D	0.983142	D;D;P	0.65815	0.995;0.982;0.873	P;P;B	0.59487	0.858;0.831;0.385	T	0.30909	-0.9962	10	0.46703	T	0.11	-19.9581	15.2526	0.73559	0.0:1.0:0.0:0.0	.	360;303;413	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	K	382;368;413;382;360	ENSP00000365608:E382K;ENSP00000365627:E368K;ENSP00000365624:E413K;ENSP00000365606:E360K	ENSP00000365606:E360K	E	-	1	0	GRIPAP1	48725166	1.000000	0.71417	0.996000	0.52242	0.011000	0.07611	5.495000	0.66912	1.925000	0.55765	0.522000	0.50473	GAG	.		0.507	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		T	48840222	C	T	48840222	3	4	110	1	0	0	0	0	1	0	0	0	6810	864	30	2	1390	2	GRIPAP1	23	48840222	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		48840222	106430338	52	9784											
PCDH11X	27328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	91133625	91133625	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcactgaagcaccagtgaccCcaaatactgagatagctgat	14	7	9	11	0	0	4	0	4	0	1	0	5	0	4	3	0	3	3	3	0	4	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chrX:91133625C>A	ENST00000373094.1	+	2	3231	c.2386C>A	c.(2386-2388)Cca>Aca	p.P796T	PCDH11X_ENST00000406881.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000504220.2_Missense_Mutation_p.P796T|PCDH11X_ENST00000373088.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000361655.2_Missense_Mutation_p.P796T|PCDH11X_ENST00000298274.8_Missense_Mutation_p.P796T|PCDH11X_ENST00000373097.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000361724.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000395337.2_Missense_Mutation_p.P796T	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	796					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						ACCAGTGACCCCAAATACTGA	0.438																																					p.P796T	NSCLC(38;925 1092 2571 38200 45895)	.											.	PCDH11X-193	0			c.C2386A						.						145	118	127					X																	91133625		2203	4300	6503	SO:0001583	missense	27328	exon2			GTGACCCCAAATA	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2386C>A	X.37:g.91133625C>A	ENSP00000362186:p.Pro796Thr	Somatic	691	1		WXS	Illumina HiSeq	Phase_I	497	213	NM_001168363	0	0	0	0	0	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.399277	0.00198	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64	5.15	2.3	0.28687	Protocadherin (1);	0.414782	0.27245	N	0.020252	T	0.25382	0.0617	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B;B;B	0.22909	0.077;0.017;0.035;0.035;0.035;0.044;0.077;0.032	B;B;B;B;B;B;B;B	0.25987	0.062;0.026;0.039;0.039;0.039;0.065;0.062;0.062	T	0.14559	-1.0468	10	0.22109	T	0.4	.	15.2794	0.73770	0.0:0.4515:0.5485:0.0	.	796;796;796;796;796;796;796;796	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	T	796	ENSP00000378746:P796T;ENSP00000362186:P796T;ENSP00000362189:P796T;ENSP00000355040:P796T;ENSP00000362180:P796T;ENSP00000423762:P796T;ENSP00000355105:P796T;ENSP00000384758:P796T;ENSP00000298274:P796T	ENSP00000298274:P796T	P	+	1	0	PCDH11X	91020281	0.999000	0.42202	0.001000	0.08648	0.003000	0.03518	1.394000	0.34509	0.053000	0.16036	-0.226000	0.12346	CCA	.		0.438	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91133625	C	A	91133625	3	1	110	1	0	0	0	0	1	0	0	0	11534	623	22	4	2392	4	PCDH11X	23	91133625	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	42293403	91133625	64136935	53	9785											
LAMP2	3920	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	119581842	119581842	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cacagtggtgtgtatggtggGtgccactgttgaagttttgt	6	15	15	5	0	0	1	0	1	0	0	0	1	0	1	1	3	1	3	1	3	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chrX:119581842G>A	ENST00000200639.4	-	5	731	c.595C>T	c.(595-597)Ccc>Tcc	p.P199S	LAMP2_ENST00000434600.2_Missense_Mutation_p.P199S|LAMP2_ENST00000538785.1_Missense_Mutation_p.P88S|LAMP2_ENST00000371335.4_Missense_Mutation_p.P199S|LAMP2_ENST00000540603.1_Missense_Mutation_p.P152S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	199	Hinge.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TGTATGGTGGGTGCCACTGTT	0.408																																					p.P199S		.											.	LAMP2-131	0			c.C595T						.						229	204	212					X																	119581842		2203	4300	6503	SO:0001583	missense	3920	exon5			TGGTGGGTGCCAC	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"CD molecules"	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.595C>T	X.37:g.119581842G>A	ENSP00000200639:p.Pro199Ser	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	125	9	NM_013995	0	0	100	100	0	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Missense_Mutation	SNP	ENST00000200639.4	37	CCDS14599.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.623881	0.46840	.	.	ENSG00000005893	ENST00000434600;ENST00000538785;ENST00000200639;ENST00000371335;ENST00000540603	T;T;T;T;T	0.66995	-0.15;0.23;-0.24;-0.13;-0.13	5.98	3.11	0.35812	.	0.053375	0.85682	D	0.000000	T	0.81823	0.4904	M	0.88704	2.975	0.19775	N	0.99996	D;D;D;D;D	0.76494	0.997;0.995;0.996;0.999;0.995	D;D;D;D;D	0.73708	0.965;0.965;0.941;0.981;0.965	T	0.72802	-0.4183	10	0.72032	D	0.01	-7.1395	10.4302	0.44403	0.0:0.1116:0.5665:0.3219	.	152;88;199;199;199	B4E2S7;B7Z2R9;P13473-2;P13473;Q6Q3G8	.;.;.;LAMP2_HUMAN;.	S	199;88;199;199;152	ENSP00000408411:P199S;ENSP00000440506:P88S;ENSP00000200639:P199S;ENSP00000360386:P199S;ENSP00000440479:P152S	ENSP00000200639:P199S	P	-	1	0	LAMP2	119465870	0.975000	0.34042	0.079000	0.20413	0.014000	0.08584	1.620000	0.36976	1.244000	0.43870	0.600000	0.82982	CCC	.		0.408	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1			A	119581842	G	A	119581842	3	1	110	1	0	0	0	0	1	0	0	0	8639	1261	44	2	948	2	LAMP2	23	119581842	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	28448217	119581842	35688718	54	9786											
CROCC	9696	broad.mit.edu	37	chr1	17294710	17294710	+	Frame_Shift_Del	DEL	A	A	-																															acctgcaggagaagatcagcAagatgaaggccaatgagaca																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:17294710delA	ENST00000375541.5	+	31	4942	c.4873delA	c.(4873-4875)aagfs	p.K1625fs		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GAAGATCAGCAAGATGAAGGC	0.652																																					p.K1625fs													.	CROCC-137	0			c.4873delA						.						20	18	19					1																	17294710		2180	4276	6456	SO:0001589	frameshift_variant	9696	exon31			ATCAGCAAGATGA	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.4873delA	1.37:g.17294710delA	ENSP00000364691:p.Lys1625fs	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_014675	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000375541.5	37	CCDS30616.1																																																																																			.		0.652	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		-	17294710	A	-	17294710	7	5	111	1	0	1	0	1	0	0	0	0	3899	131	5	0	4995	0	CROCC	1	17294710	Frame_Shift_Del	DEL	A	TCGA-G7-6789-01A-11D-1961-08		17294710	231955911	1	9787											
SNIP1	79753	ucsc.edu	37	chr1	38019775	38019775	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgccggcagcaccacgtccCcgtcccggtgtcttcgccgg	3	6	12	20	7	1	0	0	0	1	0	4	0	3	0	7	3	1	2	7	3	0	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:38019775C>A	ENST00000296215.6	-	1	128	c.56G>T	c.(55-57)gGg>gTg	p.G19V	SNIP1_ENST00000468040.1_Intron|DNALI1_ENST00000541606.1_5'Flank|DNALI1_ENST00000296218.7_5'Flank	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	19					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				CACCACGTCCCCGTCCCGGTG	0.652																																					p.G19V													.	SNIP1-227	0			c.G56T						.						38	35	36					1																	38019775		2202	4295	6497	SO:0001583	missense	79753	exon1			ACGTCCCCGTCCC		CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.56G>T	1.37:g.38019775C>A	ENSP00000296215:p.Gly19Val	Somatic	84	0		WXS	Illumina HiSeq		55	5	NM_024700	0	0	0	0	0	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	37	CCDS419.1	.	.	.	.	.	.	.	.	.	.	C	9.945	1.218512	0.22373	.	.	ENSG00000163877	ENST00000296215	T	0.14640	2.49	5.68	-2.41	0.06562	.	0.458709	0.21366	N	0.075702	T	0.07234	0.0183	N	0.19112	0.55	0.46678	D	0.999157	P	0.36065	0.535	B	0.37346	0.247	T	0.27191	-1.0081	10	0.46703	T	0.11	-0.0057	6.0189	0.19618	0.1232:0.4174:0.0:0.4595	.	19	Q8TAD8	SNIP1_HUMAN	V	19	ENSP00000296215:G19V	ENSP00000296215:G19V	G	-	2	0	SNIP1	37792362	0.013000	0.17824	0.325000	0.25375	0.001000	0.01503	-0.950000	0.03889	-0.332000	0.08489	-1.093000	0.02169	GGG	.		0.652	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700		A	38019775	C	A	38019775	3	1	111	1	0	0	0	0	1	0	0	0	14880	623	22	4	1150	4	SNIP1	1	38019775	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08	20725065	38019775	211230846	2	9788											
ZNF684	127396	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	41012446	41012446	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagacttacttaaatataatAgaagttatactgtagaaaac	19	13	5	4	0	0	3	0	0	0	3	0	3	0	3	0	0	3	2	0	0	13	9			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:41012446A>G	ENST00000372699.3	+	5	702	c.451A>G	c.(451-453)Aga>Gga	p.R151G	ZNF684_ENST00000493756.1_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	151					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(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			TAAATATAATAGAAGTTATAC	0.299																																					p.R151G		.											.	ZNF684-90	0			c.A451G						.						35	39	38					1																	41012446		2197	4296	6493	SO:0001583	missense	127396	exon5			TATAATAGAAGTT		CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"Zinc fingers, C2H2-type", "-"	28418	protein-coding gene	gene with protein product	"hypothetical protein MGC27466"					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.451A>G	1.37:g.41012446A>G	ENSP00000361784:p.Arg151Gly	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	50	35	NM_152373	0	0	0	0	0	Q2NKY4	Missense_Mutation	SNP	ENST00000372699.3	37	CCDS454.1	.	.	.	.	.	.	.	.	.	.	A	1.875	-0.459201	0.04508	.	.	ENSG00000117010	ENST00000372699	T	0.05717	3.4	3.87	0.211	0.15236	.	0.866547	0.09619	N	0.777770	T	0.06234	0.0161	L	0.41492	1.28	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37337	-0.9710	10	0.66056	D	0.02	.	7.0072	0.24844	0.6969:0.0:0.3031:0.0	.	151	Q5T5D7	ZN684_HUMAN	G	151	ENSP00000361784:R151G	ENSP00000361784:R151G	R	+	1	2	ZNF684	40785033	0.004000	0.15560	0.000000	0.03702	0.007000	0.05969	0.763000	0.26517	-0.060000	0.13132	-0.326000	0.08463	AGA	.		0.299	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373		G	41012446	A	G	41012446	3	3	111	1	0	0	0	0	1	0	0	0	18123	412	15	3	465	3	ZNF684	1	41012446	Missense_Mutation	SNP	A	TCGA-G7-6789-01A-11D-1961-08	2992671	41012446	208238175	3	9789											
TNNI3K	100526835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	74905226	74905226	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgcactcggtacaccaTcaaagcagatgtcttcagct	11	9	9	12	1	3	1	2	0	1	1	4	1	3	1	1	1	4	5	1	1	2	2			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:74905226T>G	ENST00000370899.3	+	22	2271	c.2234T>G	c.(2233-2235)aTc>aGc	p.I745S	TNNI3K_ENST00000326637.3_Missense_Mutation_p.I644S|TNNI3K_ENST00000370891.2_Missense_Mutation_p.I745S|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.I758S	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		CGGTACACCATCAAAGCAGAT	0.478																																					p.I745S		.											.	.	0			c.T2234G						.						164	136	145					1																	74905226		2203	4300	6503	SO:0001583	missense	100526835	exon22			ACACCATCAAAGC			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2234T>G	1.37:g.74905226T>G	ENSP00000359936:p.Ile745Ser	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	70	26	NM_001199327	0	0	2	2	0		Missense_Mutation	SNP	ENST00000370899.3	37		.	.	.	.	.	.	.	.	.	.	T	10.84	1.464750	0.26335	.	.	ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000557284;ENST00000370891;ENST00000326637	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.74	5.74	0.90152	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.056318	0.64402	D	0.000001	T	0.41328	0.1154	N	0.03983	-0.305	0.42989	D	0.994482	B;P;B	0.37276	0.183;0.589;0.372	B;B;B	0.32677	0.131;0.15;0.114	T	0.58451	-0.7634	10	0.08837	T	0.75	.	16.0467	0.80725	0.0:0.0:0.0:1.0	.	644;745;745	Q59H18;Q59H18-1;Q59H18-4	TNI3K_HUMAN;.;.	S	745;745;745;644	ENSP00000359936:I745S;ENSP00000450895:I745S;ENSP00000359928:I745S;ENSP00000322251:I644S	ENSP00000322251:I644S	I	+	2	0	RP11-653A5.2;AC093158.1	74677814	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	5.774000	0.68906	2.197000	0.70478	0.454000	0.30748	ATC	.		0.478	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			G	74905226	T	G	74905226	3	3	111	1	0	0	0	0	1	0	0	0	16361	1435	50	5	2364	5	TNNI3K	1	74905226	Missense_Mutation	SNP	T	TCGA-G7-6789-01A-11D-1961-08	33892780	74905226	174345395	4	9790											
GBP7	388646	hgsc.bcm.edu	37	chr1	89598981	89598981	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctttctcagttctctcataTagttttccctttccctctcc	4	20	2	15	0	5	0	2	0	4	0	10	0	7	0	3	0	0	2	3	0	2	7	rs369457817		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:89598981T>A	ENST00000294671.2	-	10	1760	c.1622A>T	c.(1621-1623)tAt>tTt	p.Y541F		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	541						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TTCTCTCATATAGTTTTCCCT	0.438																																					p.Y541F		.											.	GBP7-92	0			c.A1622T						.						311	277	289					1																	89598981		2202	4300	6502	SO:0001583	missense	388646	exon10			CTCATATAGTTTT	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1622A>T	1.37:g.89598981T>A	ENSP00000294671:p.Tyr541Phe	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	117	7	NM_207398	0	0	0	0	0		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	T	5.441	0.266483	0.10294	.	.	ENSG00000213512	ENST00000294671	T	0.52526	0.66	3.49	0.919	0.19392	Guanylate-binding protein, C-terminal (3);	2.126890	0.02428	N	0.083298	T	0.06826	0.0174	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.13045	-1.0524	10	0.45353	T	0.12	.	3.8536	0.08965	0.5682:0.2068:0.0:0.225	.	541	Q8N8V2	GBP7_HUMAN	F	541	ENSP00000294671:Y541F	ENSP00000294671:Y541F	Y	-	2	0	GBP7	89371569	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.009000	0.12765	0.053000	0.16036	-1.223000	0.01593	TAT	.		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		A	89598981	T	A	89598981	3	1	111	1	0	0	0	0	1	0	0	0	6299	1406	49	5	302	5	GBP7	1	89598981	Missense_Mutation	SNP	T	TCGA-G7-6789-01A-11D-1961-08	14693755	89598981	159651640	5	9791											
AMPD1	270	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	115218255	115218255	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctggggcttgggactcttGgaggagaacatgtggccact	7	10	15	9	0	1	1	0	0	1	1	2	4	2	3	2	6	1	1	2	6	1	2			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:115218255G>C	ENST00000520113.2	-	12	1689	c.1674C>G	c.(1672-1674)tcC>tcG	p.S558S	AMPD1_ENST00000353928.6_Silent_p.S525S|AMPD1_ENST00000369538.3_Silent_p.S554S			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	558					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	TGGGACTCTTGGAGGAGAACA	0.468																																					p.S558S													.	AMPD1-293	0			c.C1674G						.						189	179	183					1																	115218255		2203	4300	6503	SO:0001819	synonymous_variant	270	exon12			ACTCTTGGAGGAG	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"AMPD isoform M", "skeletal muscle AMPD"	102770	"adenosine monophosphate deaminase 1 (isoform M)"			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1674C>G	1.37:g.115218255G>C		Somatic	173	0		WXS	Illumina HiSeq	Phase_I	150	44	NM_000036	0	0	0	0	0	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Silent	SNP	ENST00000520113.2	37	CCDS876.2																																																																																			.		0.468	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			C	115218255	G	C	115218255	2	2	111	1	0	0	0	0	0	0	0	1	585	1335	47	4		4	AMPD1	1	115218255	Silent	SNP	G	TCGA-G7-6789-01A-11D-1961-08	25619274	115218255	134032366	6	9792											
TDRD5	163589	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	179609042	179609042	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttttattcagccgggacAtctctgttgtgtaaggattt	8	17	10	6	1	2	0	1	0	1	0	3	2	2	2	1	2	1	3	1	2	2	6			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:179609042A>C	ENST00000367614.1	+	10	1948	c.1589A>C	c.(1588-1590)cAt>cCt	p.H530P	TDRD5_ENST00000294848.8_Missense_Mutation_p.H530P|TDRD5_ENST00000444136.1_Missense_Mutation_p.H530P	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	530	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CAGCCGGGACATCTCTGTTGT	0.418																																					p.H530P		.											.	TDRD5-94	0			c.A1589C						.						206	197	200					1																	179609042		2203	4300	6503	SO:0001583	missense	163589	exon10			CGGGACATCTCTG	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1589A>C	1.37:g.179609042A>C	ENSP00000356586:p.His530Pro	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	325	51	NM_173533	0	0	0	0	0	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562855	0.65538	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.08984	3.03;3.03;3.03	5.33	4.19	0.49359	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.062123	0.64402	D	0.000003	T	0.16727	0.0402	L	0.32530	0.975	0.35819	D	0.824489	D;D	0.76494	0.999;0.999	D;D	0.73380	0.977;0.98	T	0.09122	-1.0689	10	0.54805	T	0.06	-11.2483	10.2602	0.43423	0.9209:0.0:0.0791:0.0	.	530;530	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	P	530	ENSP00000356586:H530P;ENSP00000294848:H530P;ENSP00000406052:H530P	ENSP00000294848:H530P	H	+	2	0	TDRD5	177875665	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.266000	0.51569	0.854000	0.35336	0.533000	0.62120	CAT	.		0.418	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179609042	A	C	179609042	3	2	111	1	0	0	0	0	1	0	0	0	15765	217	8	5	1623	5	TDRD5	1	179609042	Missense_Mutation	SNP	A	TCGA-G7-6789-01A-11D-1961-08	64390787	179609042	69641579	7	9793											
PTPRC	5788	broad.mit.edu;bcgsc.ca	37	chr1	198678927	198678927	+	Frame_Shift_Del	DEL	G	G	-																															ccacaagtttactaacgcaaGtaaaattattaaaacagatt																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:198678927delG	ENST00000367376.2	+	11	1310	c.1139delG	c.(1138-1140)agtfs	p.S380fs	PTPRC_ENST00000442510.2_Frame_Shift_Del_p.S382fs|PTPRC_ENST00000352140.3_Frame_Shift_Del_p.S332fs|PTPRC_ENST00000348564.6_Frame_Shift_Del_p.S221fs|PTPRC_ENST00000594404.1_Frame_Shift_Del_p.S219fs	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	380					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						ACTAACGCAAGTAAAATTATT	0.274																																					p.S382fs													.	PTPRC-295	0			c.1145delG						.						75	91	85					1																	198678927		2198	4265	6463	SO:0001589	frameshift_variant	5788	exon11			ACGCAAGTAAAAT	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1139delG	1.37:g.198678927delG	ENSP00000356346:p.Ser380fs	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	214	23	NM_002838	0	0	0	0	0	A8K7W6|Q16614|Q9H0Y6	Frame_Shift_Del	DEL	ENST00000367376.2	37																																																																																				.		0.274	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				-	198678927	G	-	198678927	7	5	111	1	0	1	0	1	0	0	0	0	12829	1029	36	0	1188	0	PTPRC	1	198678927	Frame_Shift_Del	DEL	G	TCGA-G7-6789-01A-11D-1961-08	19069885	198678927	50571694	8	9794											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33172879	33172879	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcaccagaagcagcagcTgcaggggtaagcccacaccc	11	4	12	14	0	1	1	1	0	0	1	1	1	1	1	3	3	5	6	3	3	2	2	rs62135680	byFrequency	TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr2:33172879T>C	ENST00000404816.2	+	1	841	c.488T>C	c.(487-489)cTg>cCg	p.L163P	Y_RNA_ENST00000384224.1_RNA|LTBP1_ENST00000354476.3_Missense_Mutation_p.L163P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	163					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAGCAGCAGCTGCAGGGGTAA	0.716													T|||	22	0.00439297	0	0	5008	,	,		8051	0		0.0189	False		,,,				2504	0.0031				p.L163P		.											.	LTBP1-230	0			c.T488C						.	T	PRO/LEU	5,3041		0,5,1518	6	6	6		488	3.5	1	2	dbSNP_129	6	61,5721		0,61,2830	yes	missense	LTBP1	NM_206943.2	98	0,66,4348	CC,CT,TT		1.055,0.1641,0.7476	possibly-damaging	163/1722	33172879	66,8762	1523	2891	4414	SO:0001583	missense	4052	exon1			AGCAGCTGCAGGG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.488T>C	2.37:g.33172879T>C	ENSP00000386043:p.Leu163Pro	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	18	9	NM_206943	0	0	0	0	0	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	17	0.007783882783882784	0	0.0	0	0.0	0	0.0	17	0.022427440633245383	T	20.4	3.981933	0.74474	0.001641	0.01055	ENSG00000049323	ENST00000404816;ENST00000354476	D;D	0.83992	-1.79;-1.78	4.67	3.52	0.40303	.	.	.	.	.	T	0.56124	0.1964	N	0.24115	0.695	0.80722	D	1	B	0.15930	0.015	B	0.14578	0.011	T	0.60905	-0.7170	9	0.87932	D	0	.	7.8282	0.29328	0.0:0.0979:0.0:0.9021	rs62135680	163	Q14766-4	.	P	163	ENSP00000386043:L163P;ENSP00000346467:L163P	ENSP00000346467:L163P	L	+	2	0	LTBP1	33026383	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.717000	0.54911	0.649000	0.30751	0.459000	0.35465	CTG	T|0.992;C|0.008		0.716	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33172879	T	C	33172879	3	2	111	1	0	0	0	0	1	0	0	0	9098	1580	55	3	490	3	LTBP1	2	33172879	Missense_Mutation	SNP	T	TCGA-G7-6789-01A-11D-1961-08		33172879	210026494	9	9795											
CCDC142	84865	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74702509	74702509	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaccactaaaccagcatactCactaggagcactgggaggtt	13	7	10	11	0	1	0	1	0	0	0	1	3	1	2	2	3	4	3	2	3	4	4			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr2:74702509C>T	ENST00000393965.3	-	7	2035	c.1639G>A	c.(1639-1641)Gag>Aag	p.E547K	MRPL53_ENST00000409710.1_5'Flank|MRPL53_ENST00000258105.7_5'Flank|CCDC142_ENST00000290418.4_Missense_Mutation_p.E540K	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	547										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						CCAGCATACTCACTAGGAGCA	0.532																																					p.E540K													.	CCDC142-68	0			c.G1618A						.						61	63	62					2																	74702509		2203	4300	6503	SO:0001583	missense	84865	exon7			CATACTCACTAGG	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1639G>A	2.37:g.74702509C>T	ENSP00000377537:p.Glu547Lys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	65	13	NM_032779	0	0	8	9	1	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Missense_Mutation	SNP	ENST00000393965.3	37		.	.	.	.	.	.	.	.	.	.	C	12.40	1.925984	0.34002	.	.	ENSG00000135637	ENST00000393965;ENST00000290418	T;T	0.44881	0.91;0.91	4.9	3.08	0.35506	.	0.243987	0.32161	N	0.006491	T	0.50309	0.1608	M	0.68317	2.08	0.32597	N	0.526396	D;D;D	0.58268	0.982;0.982;0.982	P;P;P	0.58013	0.831;0.831;0.831	T	0.57923	-0.7727	10	0.32370	T	0.25	-6.6459	6.4852	0.22085	0.0:0.7188:0.1836:0.0976	.	547;540;547	Q17RM4;Q17RM4-2;Q17RM4-3	CC142_HUMAN;.;.	K	547;540	ENSP00000377537:E547K;ENSP00000290418:E540K	ENSP00000290418:E540K	E	-	1	0	CCDC142	74556017	1.000000	0.71417	0.998000	0.56505	0.039000	0.13416	3.184000	0.50926	0.661000	0.30985	-0.218000	0.12543	GAG	.		0.532	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779		T	74702509	C	T	74702509	3	4	111	1	0	0	0	0	1	0	0	0	2782	835	29	2	625	2	CCDC142	2	74702509	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08	41529630	74702509	168496864	10	9796											
POLR1B	84172	broad.mit.edu;bcgsc.ca	37	chr2	113308552	113308559	+	Frame_Shift_Del	DEL	CTTTCTTC	CTTTCTTC	-																															atttaccgaaaagaactgttCtttcttcctttgggatttgc																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	CTTTCTTC	CTTTCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr2:113308552_113308559delCTTTCTTC	ENST00000263331.5	+	5	1315_1322	c.735_742delCTTTCTTC	c.(733-744)ttctttcttcctfs	p.FLP246fs	POLR1B_ENST00000537335.1_Frame_Shift_Del_p.FLP35fs|POLR1B_ENST00000417433.2_Frame_Shift_Del_p.FLP190fs|POLR1B_ENST00000541869.1_Frame_Shift_Del_p.FLP284fs|POLR1B_ENST00000409894.3_Frame_Shift_Del_p.FLP246fs	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	246					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						AAGAACTGTTCTTTCTTCCTTTGGGATT	0.394																																					p.245_248del	Ovarian(16;256 576 9537 23969 41147)												.	POLR1B-91	0			c.735_742del						.																																			SO:0001589	frameshift_variant	84172	exon5			ACTGTTCTTTCTT	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.735_742delCTTTCTTC	2.37:g.113308552_113308559delCTTTCTTC	ENSP00000263331:p.Phe246fs	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	165	25	NM_019014	0	0	0	0	0	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Frame_Shift_Del	DEL	ENST00000263331.5	37	CCDS2097.1																																																																																			.		0.394	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		-	113308559	CTTTCTTC	-	113308552	7	5	111	1	0	1	0	1	0	0	0	0	12236	912	32	0	753	0	POLR1B	2	113308552	Frame_Shift_Del	DEL	CTTTCTTC	TCGA-G7-6789-01A-11D-1961-08	38606043	113308552	129890821	11	9797											
ALPPL2	251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233272617	233272617	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgccagccggcgcctacGcccacacggtgaaccgcaac	8	3	10	20	6	0	1	0	1	0	0	1	1	0	1	6	2	4	1	6	2	3	1	rs145892470		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr2:233272617G>A	ENST00000295453.3	+	5	590	c.538G>A	c.(538-540)Gcc>Acc	p.A180T		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	180					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	CGGCGCCTACGCCCACACGGT	0.627																																					p.A180T		.											.	ALPPL2-91	0			c.G538A						.	G	THR/ALA	0,4406		0,0,2203	67	69	68		538	2.7	0.1	2	dbSNP_134	68	1,8597	1.2+/-3.3	0,1,4298	no	missense	ALPPL2	NM_031313.2	58	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	180/533	233272617	1,13003	2203	4299	6502	SO:0001583	missense	251	exon5			GCCTACGCCCACA	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.538G>A	2.37:g.233272617G>A	ENSP00000295453:p.Ala180Thr	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	170	26	NM_031313	0	0	0	0	0	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	g	14.70	2.615024	0.46631	0.0	1.16E-4	ENSG00000163286	ENST00000295453	D	0.98400	-4.91	2.71	2.71	0.32032	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.057529	0.64402	D	0.000002	D	0.99118	0.9696	H	0.94306	3.52	0.45005	D	0.998024	D	0.89917	1.0	D	0.77004	0.989	D	0.99047	1.0826	10	0.87932	D	0	.	13.8099	0.63256	0.0:0.0:1.0:0.0	.	180	P10696	PPBN_HUMAN	T	180	ENSP00000295453:A180T	ENSP00000295453:A180T	A	+	1	0	ALPPL2	232980861	1.000000	0.71417	0.066000	0.19879	0.144000	0.21451	5.834000	0.69361	1.499000	0.48617	0.205000	0.17691	GCC	G|1.000;A|0.000		0.627	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		A	233272617	G	A	233272617	3	1	111	1	0	0	0	0	1	0	0	0	549	1087	38	1	556	1	ALPPL2	2	233272617	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08	119964065	233272617	9926756	12	9798											
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52422876	52422876	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggagacggtggagaacCtgcagtacatgctcaacaac	13	5	13	10	1	1	2	1	0	0	2	1	4	1	2	1	4	6	4	1	4	4	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr3:52422876C>T	ENST00000420323.2	+	59	9679	c.9418C>T	c.(9418-9420)Ctg>Ttg	p.L3140L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3205					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGTGGAGAACCTGCAGTACAT	0.637																																					p.L3140L		.											.	DNAH1-67	0			c.C9418T						.						59	71	67					3																	52422876		2151	4243	6394	SO:0001819	synonymous_variant	25981	exon59			GAGAACCTGCAGT	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.9418C>T	3.37:g.52422876C>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	60	39	NM_015512	0	0	0	0	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			.		0.637	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52422876	C	T	52422876	2	4	111	1	0	0	0	0	0	0	0	1	4608	680	24	2		2	DNAH1	3	52422876	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		52422876	145599554	13	9799											
BEND4	389206	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	42146005	42146005	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caaaggcatccaagatcattCgactctctgaaacaaatgaa	17	8	6	10	1	2	3	1	2	1	1	5	4	3	3	1	1	1	1	1	1	5	1	rs200387125		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr4:42146005C>T	ENST00000502486.1	-	3	1073	c.494G>A	c.(493-495)cGa>cAa	p.R165Q	BEND4_ENST00000504360.1_Missense_Mutation_p.R161Q	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	165										NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						CAAGATCATTCGACTCTCTGA	0.413																																					p.R165Q													.	BEND4-90	0			c.G494A						.	C	GLN/ARG,GLN/ARG	0,3866		0,0,1933	30	28	28		494,494	5.9	0.9	4		28	1,8269		0,1,4134	yes	missense,missense	BEND4	NM_001159547.1,NM_207406.3	43,43	0,1,6067	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging,probably-damaging	165/442,165/535	42146005	1,12135	1933	4135	6068	SO:0001583	missense	389206	exon3			ATCATTCGACTCT	AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848		"BEN domain containing"	23815	protein-coding gene	gene with protein product			"coiled-coil domain containing 4"	CCDC4			Standard	NM_207406		Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.494G>A	4.37:g.42146005C>T	ENSP00000421169:p.Arg165Gln	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	26	13	NM_001159547	0	0	0	0	0	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	Missense_Mutation	SNP	ENST00000502486.1	37	CCDS47048.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.033242	0.93575	0.0	1.21E-4	ENSG00000188848	ENST00000411720;ENST00000502486;ENST00000504360	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.73369	0.3578	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.992;0.996	T	0.74589	-0.3615	9	0.87932	D	0	-14.1289	20.3539	0.98825	0.0:1.0:0.0:0.0	.	87;165;165	Q6ZU67-3;Q6ZU67;Q6ZU67-2	.;BEND4_HUMAN;.	Q	36;165;161	.	ENSP00000412495:R36Q	R	-	2	0	BEND4	41840762	1.000000	0.71417	0.920000	0.36463	0.697000	0.40408	7.487000	0.81328	2.826000	0.97356	0.655000	0.94253	CGA	.		0.413	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360975.2	NM_207406		T	42146005	C	T	42146005	3	4	111	1	0	0	0	0	1	0	0	0	1401	884	31	1	1126	1	BEND4	4	42146005	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		42146005	149008271	14	9800											
TMEM161B	153396	broad.mit.edu	37	chr5	87498782	87498782	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaatgcccatacttacaaaGggatactttctttgcccagt	12	12	6	11	0	1	0	0	0	1	0	1	1	1	1	2	1	5	0	2	1	5	5			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr5:87498782G>C	ENST00000296595.6	-	9	1035	c.911C>G	c.(910-912)cCt>cGt	p.P304R	TMEM161B_ENST00000511218.1_Missense_Mutation_p.P122R|TMEM161B_ENST00000509387.1_Missense_Mutation_p.P177R|TMEM161B_ENST00000512429.1_Missense_Mutation_p.P293R|TMEM161B_ENST00000514135.1_Missense_Mutation_p.P304R|TMEM161B_ENST00000506536.1_Missense_Mutation_p.P122R	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	304						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		TACTTACAAAGGGATACTTTC	0.368																																					p.P304R													.	TMEM161B-92	0			c.C911G						.						175	166	169					5																	87498782		2203	4300	6503	SO:0001583	missense	153396	exon9			TACAAAGGGATAC	BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.911C>G	5.37:g.87498782G>C	ENSP00000296595:p.Pro304Arg	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	165	3	NM_153354	0	0	1	1	0	Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	ENST00000296595.6	37	CCDS4065.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363061	0.82353	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000506536;ENST00000511218;ENST00000512429;ENST00000509387	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.79690	0.4489	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.78516	-0.2174	9	0.48119	T	0.1	.	19.8949	0.96954	0.0:0.0:1.0:0.0	.	122;304	B7Z6A5;Q8NDZ6	.;T161B_HUMAN	R	304;304;122;122;293;177	.	ENSP00000296595:P304R	P	-	2	0	TMEM161B	87534538	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.832000	0.86757	2.704000	0.92352	0.650000	0.86243	CCT	.		0.368	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354		C	87498782	G	C	87498782	3	2	111	1	0	0	0	0	1	0	0	0	16109	1000	35	4	568	4	TMEM161B	5	87498782	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		87498782	93416478	15	9801											
ANKS1A	23294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35051232	35051232	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagaagatccccaccatcatCctgtccatcacatacaaagg	15	7	5	14	0	2	2	2	0	0	2	5	2	5	2	5	1	1	0	5	1	4	1	rs371531749		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr6:35051232C>A	ENST00000360359.3	+	20	3084	c.2946C>A	c.(2944-2946)atC>atA	p.I982I	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	982	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CCACCATCATCCTGTCCATCA	0.547																																					p.I982I		.											.	ANKS1A-94	0			c.C2946A						.						232	185	201					6																	35051232		2203	4300	6503	SO:0001819	synonymous_variant	23294	exon20			CATCATCCTGTCC	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20961	protein-coding gene	gene with protein product		608994	"ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1"	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2946C>A	6.37:g.35051232C>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	108	72	NM_015245	0	0	2	12	10	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Silent	SNP	ENST00000360359.3	37	CCDS4798.1																																																																																			.		0.547	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	35051232	C	A	35051232	2	1	111	1	0	0	0	0	0	0	0	1	688	845	30	4		4	ANKS1A	6	35051232	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		35051232	136063835	16	9802											
AHI1	54806	hgsc.bcm.edu	37	chr6	135759585	135759585	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaaagatcataaatgataTtgaggtggccacacaattct	16	10	9	6	0	2	3	1	2	1	1	2	4	2	4	1	3	0	0	1	3	5	4			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr6:135759585T>C	ENST00000367800.4	-	13	2180	c.1964A>G	c.(1963-1965)aAt>aGt	p.N655S	AHI1_ENST00000327035.6_Missense_Mutation_p.N655S|AHI1_ENST00000457866.2_Missense_Mutation_p.N655S|AHI1_ENST00000417892.2_Missense_Mutation_p.N9S	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	655					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		ATAAATGATATTGAGGTGGCC	0.363																																					p.N655S		.											.	AHI1-227	0			c.A1964G						.						46	41	43					6																	135759585		1861	4090	5951	SO:0001583	missense	54806	exon14			ATGATATTGAGGT	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.1964A>G	6.37:g.135759585T>C	ENSP00000356774:p.Asn655Ser	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	5	3	NM_001134832	0	0	0	2	2	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.42|17.42	3.384268|3.384268	0.61845|0.61845	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367799|ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602;ENST00000327035;ENST00000367801	.|T;T;T;T;T	.|0.57595	.|0.39;0.39;0.39;0.39;0.39	5.79|5.79	5.79|5.79	0.91817|0.91817	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.050290	.|0.85682	.|D	.|0.000000	T|T	0.47783|0.47783	0.1464|0.1464	N|N	0.21545|0.21545	0.675|0.675	0.80722|0.80722	D|D	1|1	.|D;D;B	.|0.71674	.|0.997;0.998;0.145	.|D;D;B	.|0.70227	.|0.921;0.968;0.219	T|T	0.46373|0.46373	-0.9196|-0.9196	5|10	.|0.25751	.|T	.|0.34	-31.7502|-31.7502	16.1222|16.1222	0.81365|0.81365	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|655;655;655	.|Q8N157-2;Q8N157;Q4FD35	.|.;AHI1_HUMAN;.	V|S	155|655;655;9;655;655;655	.|ENSP00000356774:N655S;ENSP00000388650:N655S;ENSP00000416867:N9S;ENSP00000265602:N655S;ENSP00000322478:N655S	.|ENSP00000265602:N655S	I|N	-|-	1|2	0|0	AHI1|AHI1	135801278|135801278	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	4.305000|4.305000	0.59110|0.59110	2.215000|2.215000	0.71742|0.71742	0.528000|0.528000	0.53228|0.53228	ATA|AAT	.		0.363	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135759585	T	C	135759585	3	2	111	1	0	0	0	0	1	0	0	0	413	1493	52	3	1743	3	AHI1	6	135759585	Missense_Mutation	SNP	T	TCGA-G7-6789-01A-11D-1961-08	100708353	135759585	35355482	17	9803											
FZD1	8321	broad.mit.edu	37	chr7	90894984	90894984	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcaccgtggcggcttcccGgggggcgccggcgcgtcgga	2	4	21	14	8	0	0	0	0	0	0	2	1	1	1	3	8	0	2	3	8	0	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr7:90894984G>T	ENST00000287934.2	+	1	1202	c.789G>T	c.(787-789)ccG>ccT	p.P263P		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	263					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			GCGGCTTCCCGGGGGGCGCCG	0.697																																					p.P263P													.	FZD1-658	0			c.G789T						.						5	6	5					7																	90894984		2094	4109	6203	SO:0001819	synonymous_variant	8321	exon1			CTTCCCGGGGGGC	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"GPCR / Class F : Frizzled receptors"	4038	protein-coding gene	gene with protein product	"Wnt receptor", "frizzled, Drosophila, homolog of, 1"	603408	"frizzled (Drosophila) homolog 1", "frizzled homolog 1 (Drosophila)", "frizzled 1, seven transmembrane spanning receptor", "frizzled family receptor 1"			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.789G>T	7.37:g.90894984G>T		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	24	11	NM_003505	0	0	8	17	9	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	37	CCDS5620.1																																																																																			.		0.697	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		T	90894984	G	T	90894984	2	4	111	1	0	0	0	0	0	0	0	1	6147	1103	39	4		4	FZD1	7	90894984	Silent	SNP	G	TCGA-G7-6789-01A-11D-1961-08		90894984	68243679	18	9804											
SLC26A3	1811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107415276	107415276	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcggattttcctcaaagcTttgttgcgcttgcgtagaat	7	17	9	8	3	1	1	1	0	0	1	3	2	2	2	1	1	3	4	1	1	3	7			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr7:107415276T>G	ENST00000340010.5	-	16	1903	c.1719A>C	c.(1717-1719)aaA>aaC	p.K573N	SLC26A3_ENST00000422236.2_Missense_Mutation_p.K538N	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	573	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						TCCTCAAAGCTTTGTTGCGCT	0.393																																					p.K573N		.											.	SLC26A3-94	0			c.A1719C						.						166	145	152					7																	107415276		2203	4300	6503	SO:0001583	missense	1811	exon16			CAAAGCTTTGTTG	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"Solute carriers"	3018	protein-coding gene	gene with protein product		126650	"congenital chloride diarrhea", "solute carrier family 26, member 3"	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1719A>C	7.37:g.107415276T>G	ENSP00000345873:p.Lys573Asn	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	165	73	NM_000111	0	0	0	0	0		Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.232480	0.79688	.	.	ENSG00000091138	ENST00000422236;ENST00000340010	D;D	0.94793	-2.3;-3.52	6.11	3.74	0.42951	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.040256	0.85682	D	0.000000	D	0.96654	0.8908	M	0.82923	2.615	0.51233	D	0.999917	D;D	0.89917	0.997;1.0	D;D	0.80764	0.951;0.994	D	0.95529	0.8601	10	0.66056	D	0.02	.	8.8658	0.35284	0.0:0.2007:0.0:0.7993	.	538;573	G5E9U3;P40879	.;S26A3_HUMAN	N	538;573	ENSP00000415817:K538N;ENSP00000345873:K573N	ENSP00000345873:K573N	K	-	3	2	SLC26A3	107202512	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.954000	0.29175	0.544000	0.28883	0.533000	0.62120	AAA	.		0.393	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		G	107415276	T	G	107415276	3	3	111	1	0	0	0	0	1	0	0	0	14550	1606	56	5	599	5	SLC26A3	7	107415276	Missense_Mutation	SNP	T	TCGA-G7-6789-01A-11D-1961-08	16520292	107415276	51723387	19	9805											
GSTK1	373156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142965268	142965268	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accggatggagctgctggcgCacctgctgggtaagtaagtt	8	9	15	9	2	0	0	0	0	0	0	0	2	0	2	2	4	3	7	2	4	2	3			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr7:142965268C>T	ENST00000358406.5	+	7	693	c.622C>T	c.(622-624)Cac>Tac	p.H208Y	GSTK1_ENST00000479303.1_Missense_Mutation_p.H264Y|GSTK1_ENST00000409500.3_Missense_Mutation_p.H196Y|AC073342.12_ENST00000427392.1_RNA|GSTK1_ENST00000443571.2_Missense_Mutation_p.H165Y	NM_015917.2	NP_057001.1	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1	208					epithelial cell differentiation (GO:0030855)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|peroxisome (GO:0005777)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|protein disulfide oxidoreductase activity (GO:0015035)|receptor binding (GO:0005102)			lung(4)	4	Melanoma(164;0.059)				Glutathione(DB00143)	GCTGCTGGCGCACCTGCTGGG	0.567																																					p.H264Y		.											.	GSTK1-90	0			c.C790T						.						181	182	182					7																	142965268		2203	4300	6503	SO:0001583	missense	373156	exon6			CTGGCGCACCTGC		CCDS5877.1, CCDS47730.1, CCDS47731.1, CCDS47732.1	7q34	2012-06-21			ENSG00000197448	ENSG00000197448	2.5.1.18	"Glutathione S-transferases / Mitochondrial (kappa)"	16906	protein-coding gene	gene with protein product		602321				12720545, 14742434	Standard	NM_015917		Approved	GST13	uc003wcj.3	Q9Y2Q3	OTTHUMG00000152637	ENST00000358406.5:c.622C>T	7.37:g.142965268C>T	ENSP00000351181:p.His208Tyr	Somatic	415	0		WXS	Illumina HiSeq	Phase_I	495	101	NM_001143679	0	0	0	0	0	B4DIH1|B4DSY2|Q6P4H0|Q7Z520|Q9P1S4	Missense_Mutation	SNP	ENST00000358406.5	37	CCDS5877.1	.	.	.	.	.	.	.	.	.	.	C	4.988	0.183556	0.09495	.	.	ENSG00000197448	ENST00000409500;ENST00000443571;ENST00000358406;ENST00000479303	.	.	.	5.78	-3.58	0.04597	DSBA-like thioredoxin domain (1);Thioredoxin-like fold (1);	1.302130	0.04873	N	0.446319	T	0.28167	0.0695	N	0.25380	0.74	0.09310	N	1	B;B;B;B	0.11235	0.0;0.0;0.004;0.002	B;B;B;B	0.14578	0.003;0.005;0.011;0.004	T	0.34825	-0.9813	9	0.08837	T	0.75	-3.554	12.5207	0.56058	0.0:0.6216:0.0:0.3784	.	196;165;264;208	Q9Y2Q3-3;Q9Y2Q3-4;Q9Y2Q3-2;Q9Y2Q3	.;.;.;GSTK1_HUMAN	Y	196;165;208;264	.	ENSP00000351181:H208Y	H	+	1	0	GSTK1	142675390	0.000000	0.05858	0.003000	0.11579	0.606000	0.37113	-1.201000	0.03026	-1.038000	0.03279	-0.259000	0.10710	CAC	.		0.567	GSTK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327091.1	NM_015917		T	142965268	C	T	142965268	3	4	111	1	0	0	0	0	1	0	0	0	6857	710	25	2	812	2	GSTK1	7	142965268	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08	35549992	142965268	16173395	20	9806											
CDKN2A	1029	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	21971120	21971120	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcgtcgtgcacgggtcGggtgagagtggcggggtcgg	4	6	23	8	6	0	1	0	1	0	1	3	2	0	1	0	7	2	2	0	7	0	0	rs121913388		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr9:21971120G>A	ENST00000304494.5	-	2	508	c.238C>T	c.(238-240)Cga>Tga	p.R80*	CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	80			R -> L (in a head and neck tumor).|R -> P (in CMM2; loss of CDK4 binding). {ECO:0000269|PubMed:19260062}.		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TGCACGGGTCGGGTGAGAGTG	0.726	R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.R80X		.											.	CDKN2A-23992	1474	Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(298)|skin(206)|central_nervous_system(168)|lung(150)|urinary_tract(91)|bone(76)|oesophagus(72)|upper_aerodigestive_tract(63)|soft_tissue(60)|pleura(51)|pancreas(37)|ovary(36)|kidney(32)|breast(32)|biliary_tract(16)|thyroid(15)|NS(14)|stomach(14)|large_intestine(7)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(3)|endometrium(3)|prostate(2)	c.C238T	GRCh37	CM014695	CDKN2A	M	rs121913388	.						11	14	13					9																	21971120		2172	4246	6418	SO:0001587	stop_gained	1029	exon2			CGGGTCGGGTGAG	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.238C>T	9.37:g.21971120G>A	ENSP00000307101:p.Arg80*	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	38	26	NM_000077	0	0	0	11	11	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Nonsense_Mutation	SNP	ENST00000304494.5	37	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.328457|7.328457	0.98214|0.98214	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	D;D|.	0.86497|.	-2.13;-2.02|.	5.93|5.93	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.37136|.	N|.	0.002233|.	T|.	0.44561|.	0.1299|.	L|L	0.36672|0.36672	1.1|1.1	0.47511|0.47511	D|D	0.999443|0.999443	D|.	0.59357|.	0.985|.	B|.	0.40602|.	0.334|.	T|.	0.34825|.	-0.9813|.	10|.	0.13108|0.02654	T|T	0.6|1	-2.989|-2.989	8.7197|8.7197	0.34434|0.34434	0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526	.|.	135|.	Q8N726|.	CD2A2_HUMAN|.	L|X	135;94|80	ENSP00000355153:P135L;ENSP00000432664:P94L|.	ENSP00000355153:P135L|ENSP00000307101:R80X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961120|21961120	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	2.363000|2.363000	0.44178|0.44178	1.464000|1.464000	0.47987|0.47987	0.650000|0.650000	0.86243|0.86243	CCG|CGA	.		0.726	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		A	21971120	G	A	21971120	4	1	111	1	0	0	0	0	0	1	0	0	3167	1125	39	1	240	1	CDKN2A	9	21971120	Nonsense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		21971120	119242311	21	9807											
BAT2L1	84726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134350415	134350415	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaagattaagcaggagctaGgggaggagagtacccggctg	13	5	17	6	1	0	3	0	0	0	3	0	6	0	5	1	5	3	4	1	5	4	3			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr9:134350415G>C	ENST00000357304.4	+	15	2954	c.2899G>C	c.(2899-2901)Ggg>Cgg	p.G967R	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	967							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCAGGAGCTAGGGGAGGAGAG	0.582																																					p.G967R		.											.	PRRC2B-24	0			c.G2899C						.						37	42	40					9																	134350415		2050	4189	6239	SO:0001583	missense	84726	exon15			GAGCTAGGGGAGG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.2899G>C	9.37:g.134350415G>C	ENSP00000349856:p.Gly967Arg	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_013318	0	1	4	23	18	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.531552	0.27387	.	.	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.01918	4.56	5.87	4.98	0.66077	.	.	.	.	.	T	0.01627	0.0052	N	0.12182	0.205	0.80722	D	1	B;B	0.18166	0.026;0.004	B;B	0.18561	0.022;0.005	T	0.57985	-0.7716	8	.	.	.	.	9.9519	0.41645	0.152:0.0:0.848:0.0	.	263;967	Q5H9R5;Q5JSZ5	.;PRC2B_HUMAN	R	967;263	ENSP00000349856:G967R	.	G	+	1	0	PRRC2B	133340236	1.000000	0.71417	0.147000	0.22382	0.913000	0.54294	6.182000	0.71995	1.487000	0.48415	0.655000	0.94253	GGG	.		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	134350415	G	C	134350415	3	2	111	1	0	0	0	0	1	0	0	0	1321	1000	35	4	2957	4	BAT2L1	9	134350415	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08	112379295	134350415	6863016	22	9808											
C11orf70	85016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	101937281	101937281	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agctttcaatgtcattttttCatcggttatatgatgaagat	11	18	7	5	1	3	3	3	2	0	1	4	3	3	3	0	1	1	2	0	1	4	6			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr11:101937281C>G	ENST00000434758.2	+	4	362	c.334C>G	c.(334-336)Cat>Gat	p.H112D	C11orf70_ENST00000534360.1_Intron|C11orf70_ENST00000526781.1_Missense_Mutation_p.H112D	NM_032930.2	NP_116319.2	Q9BRQ4	CK070_HUMAN	chromosome 11 open reading frame 70	112										breast(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|skin(2)	12	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)		GTCATTTTTTCATCGGTTATA	0.303																																					p.H112D		.											.	C11orf70-91	0			c.C334G						.						107	101	103					11																	101937281		2200	4294	6494	SO:0001583	missense	85016	exon4			TTTTTTCATCGGT	AK094851	CCDS8313.1, CCDS8313.2, CCDS53698.1	11q22.1	2012-05-31			ENSG00000137691	ENSG00000137691			28188	protein-coding gene	gene with protein product							Standard	NM_032930		Approved	MGC13040	uc001pgp.3	Q9BRQ4	OTTHUMG00000167320	ENST00000434758.2:c.334C>G	11.37:g.101937281C>G	ENSP00000414390:p.His112Asp	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	66	37	NM_032930	0	0	2	13	11	E9PJU1	Missense_Mutation	SNP	ENST00000434758.2	37	CCDS8313.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.099|0.099	-1.155573|-1.155573	0.01686|0.01686	.|.	.|.	ENSG00000137691|ENSG00000137691	ENST00000529204|ENST00000434758;ENST00000526781;ENST00000423732	.|.	.|.	.|.	5.53|5.53	-5.51|-5.51	0.02568|0.02568	.|.	.|0.382417	.|0.32769	.|N	.|0.005664	T|T	0.04998|0.04998	0.0134|0.0134	N|N	0.00032|0.00032	-2.585|-2.585	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.46261|0.46261	-0.9204|-0.9204	6|9	0.87932|0.02654	D|T	0|1	-3.2945|-3.2945	9.2395|9.2395	0.37486|0.37486	0.1423:0.5247:0.3329:0.0|0.1423:0.5247:0.3329:0.0	.|.	.|112	.|Q9BRQ4	.|CK070_HUMAN	L|D	3|112;112;74	.|.	ENSP00000432322:F3L|ENSP00000392150:H74D	F|H	+|+	3|1	2|0	C11orf70|C11orf70	101442491|101442491	1.000000|1.000000	0.71417|0.71417	0.222000|0.222000	0.23844|0.23844	0.555000|0.555000	0.35460|0.35460	0.684000|0.684000	0.25364|0.25364	-0.778000|-0.778000	0.04566|0.04566	-0.474000|-0.474000	0.04947|0.04947	TTC|CAT	.		0.303	C11orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394144.1	NM_032930		G	101937281	C	G	101937281	3	3	111	1	0	0	0	0	1	0	0	0	1663	826	29	4	230	4	C11orf70	11	101937281	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		101937281	33069235	23	9809											
GYS2	2998	broad.mit.edu	37	chr12	21728873	21728873	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctcggtcatgataaggaatgCcgacactgcatgcttcccag	10	9	10	12	2	1	1	1	1	0	0	3	3	2	2	2	2	3	2	2	2	2	2			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr12:21728873C>T	ENST00000261195.2	-	3	676	c.422G>A	c.(421-423)gGc>gAc	p.G141D		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	141					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						ATAAGGAATGCCGACACTGCA	0.418																																					p.G141D	Colon(149;9 1820 3690 10544 50424)												.	GYS2-523	0			c.G422A						.						145	132	136					12																	21728873		2203	4300	6503	SO:0001583	missense	2998	exon3			GGAATGCCGACAC		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.422G>A	12.37:g.21728873C>T	ENSP00000261195:p.Gly141Asp	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	152	5	NM_021957	0	0	0	0	0	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.589443	0.86851	.	.	ENSG00000111713	ENST00000261195	T	0.68479	-0.33	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	L	0.37507	1.11	0.80722	D	1	P	0.51933	0.949	P	0.55545	0.778	T	0.64558	-0.6379	10	0.25106	T	0.35	-20.376	18.9212	0.92526	0.0:1.0:0.0:0.0	.	141	P54840	GYS2_HUMAN	D	141	ENSP00000261195:G141D	ENSP00000261195:G141D	G	-	2	0	GYS2	21620140	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	7.194000	0.77789	2.781000	0.95711	0.650000	0.86243	GGC	.		0.418	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		T	21728873	C	T	21728873	3	4	111	1	0	0	0	0	1	0	0	0	6934	739	26	2	1745	2	GYS2	12	21728873	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		21728873	112123022	24	9810											
FAR2	55711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	29485566	29485566	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgtgcgccagttgaactggTtggaatacattgaaaattat	13	12	10	6	2	0	2	0	2	0	0	0	3	0	3	1	2	3	2	1	2	6	5			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr12:29485566T>C	ENST00000536681.3	+	11	1537	c.1291T>C	c.(1291-1293)Ttg>Ctg	p.L431L	FAR2_ENST00000182377.4_Silent_p.L431L|FAR2_ENST00000547116.1_Silent_p.L334L	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	431					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						GTTGAACTGGTTGGAATACAT	0.398																																					p.L431L		.											.	FAR2-90	0			c.T1291C						.						92	89	90					12																	29485566		2203	4300	6503	SO:0001819	synonymous_variant	55711	exon11			AACTGGTTGGAAT	AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	25531	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 2"		"male sterility domain containing 1"	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.1291T>C	12.37:g.29485566T>C		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	102	45	NM_018099	0	0	8	9	1	F8VV73|Q9H0D5|Q9NVW8	Silent	SNP	ENST00000536681.3	37	CCDS8717.1																																																																																			.		0.398	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099		C	29485566	T	C	29485566	2	2	111	1	0	0	0	0	0	0	0	1	5694	1722	60	3		3	FAR2	12	29485566	Silent	SNP	T	TCGA-G7-6789-01A-11D-1961-08	7756693	29485566	104366329	25	9811											
TRHDE	29953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	72680574	72680574	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcaagcatcaagcaacctAtttatctttatctaatatgc	14	14	3	10	0	4	0	2	0	2	0	4	0	4	0	1	0	4	2	1	0	8	7			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr12:72680574A>G	ENST00000261180.4	+	2	989	c.893A>G	c.(892-894)tAt>tGt	p.Y298C		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	298					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						CAAGCAACCTATTTATCTTTA	0.408																																					p.Y298C		.											.	TRHDE-93	0			c.A893G						.						170	160	164					12																	72680574		2203	4300	6503	SO:0001583	missense	29953	exon2			CAACCTATTTATC	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"pyroglutamyl-peptidase II", "pyroglutamyl aminopeptidase II", "TRH-specific aminopeptidase"	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.893A>G	12.37:g.72680574A>G	ENSP00000261180:p.Tyr298Cys	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	274	103	NM_013381	0	0	13	20	7	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830477	0.71258	.	.	ENSG00000072657	ENST00000261180	T	0.05025	3.51	5.93	5.93	0.95920	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.32224	0.0822	M	0.88450	2.955	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.17048	-1.0382	10	0.72032	D	0.01	.	16.3943	0.83563	1.0:0.0:0.0:0.0	.	298	Q9UKU6	TRHDE_HUMAN	C	298	ENSP00000261180:Y298C	ENSP00000261180:Y298C	Y	+	2	0	TRHDE	70966841	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.327000	0.79147	2.281000	0.76405	0.533000	0.62120	TAT	.		0.408	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		G	72680574	A	G	72680574	3	3	111	1	0	0	0	0	1	0	0	0	16512	449	16	3	899	3	TRHDE	12	72680574	Missense_Mutation	SNP	A	TCGA-G7-6789-01A-11D-1961-08	43195008	72680574	61171321	26	9812											
LRRIQ1	84125	bcgsc.ca	37	chr12	85441091	85441091	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagacagtcttttgaggcttGgcaagagaaacagaaggaat	15	9	12	5	0	1	4	0	1	1	3	1	6	1	5	0	3	1	2	0	3	5	4			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr12:85441091G>T	ENST00000393217.2	+	6	582	c.521G>T	c.(520-522)tGg>tTg	p.W174L		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	174	Glu-rich.									breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		TTTGAGGCTTGGCAAGAGAAA	0.343																																					p.W174L													.	LRRIQ1-95	0			c.G521T						.						76	84	81					12																	85441091		2203	4300	6503	SO:0001583	missense	84125	exon6			AGGCTTGGCAAGA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.521G>T	12.37:g.85441091G>T	ENSP00000376910:p.Trp174Leu	Somatic	120	1		WXS	Illumina HiSeq	Phase_1	204	13	NM_001079910	0	0	0	0	0	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.162023|4.162023	0.78226|0.78226	.|.	.|.	ENSG00000133640|ENSG00000133640	ENST00000533414|ENST00000256007;ENST00000378580;ENST00000393217	.|D	.|0.84589	.|-1.87	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.234668	.|0.36200	.|N	.|0.002733	D|D	0.91085|0.91085	0.7194|0.7194	M|M	0.62723|0.62723	1.935|1.935	0.37344|0.37344	D|D	0.910531|0.910531	.|D;D;D	.|0.89917	.|1.0;0.998;1.0	.|D;D;D	.|0.91635	.|0.999;0.991;0.998	D|D	0.93375|0.93375	0.6738|0.6738	5|10	.|0.87932	.|D	.|0	.|.	16.2441|16.2441	0.82431|0.82431	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|174;174;174	.|Q96JM4-2;Q96JM4;C9JI57	.|.;LRIQ1_HUMAN;.	C|L	72|174	.|ENSP00000376910:W174L	.|ENSP00000256007:W174L	G|W	+|+	1|2	0|0	LRRIQ1|LRRIQ1	83965222|83965222	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	3.805000|3.805000	0.55575|0.55575	2.359000|2.359000	0.80004|0.80004	0.585000|0.585000	0.79938|0.79938	GGC|TGG	.		0.343	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85441091	G	T	85441091	3	4	111	1	0	0	0	0	1	0	0	0	9054	1357	47	4	539	4	LRRIQ1	12	85441091	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08	12760517	85441091	48410804	27	9813											
OR11G2	390439	broad.mit.edu	37	chr14	20666485	20666485	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accctgtgatatatagtcttAggaacaaagatatgagaaaa	18	10	8	5	0	1	3	0	2	1	2	1	5	1	4	1	1	1	0	1	1	9	5			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr14:20666485A>G	ENST00000357366.3	+	1	991	c.991A>G	c.(991-993)Agg>Ggg	p.R331G		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	331						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		atatagtCTTAGGAACAAAGA	0.373																																					p.R331G													.	OR11G2-70	0			c.A991G						.						93	99	97					14																	20666485		2203	4300	6503	SO:0001583	missense	390439	exon1			AGTCTTAGGAACA		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.991A>G	14.37:g.20666485A>G	ENSP00000349930:p.Arg331Gly	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	157	5	NM_001005503	0	0	0	0	0	Q6IF09|Q96R33	Missense_Mutation	SNP	ENST00000357366.3	37	CCDS32032.1	.	.	.	.	.	.	.	.	.	.	a	16.59	3.166574	0.57476	.	.	ENSG00000196832	ENST00000357366	T	0.40476	1.03	4.94	4.94	0.65067	.	0.000000	0.51477	D	0.000085	T	0.76800	0.4038	H	0.99042	4.41	0.25750	N	0.985068	D	0.69078	0.997	D	0.65773	0.938	T	0.77099	-0.2713	10	0.87932	D	0	.	13.7206	0.62725	1.0:0.0:0.0:0.0	.	331	Q8NGC1	O11G2_HUMAN	G	331	ENSP00000349930:R331G	ENSP00000349930:R331G	R	+	1	2	OR11G2	19736325	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	5.215000	0.65241	2.077000	0.62373	0.533000	0.62120	AGG	.		0.373	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			G	20666485	A	G	20666485	3	3	111	1	0	0	0	0	1	0	0	0	10951	411	15	3	993	3	OR11G2	14	20666485	Missense_Mutation	SNP	A	TCGA-G7-6789-01A-11D-1961-08		20666485	86683055	28	9814											
SAV1	60485	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	51132011	51132012	+	Frame_Shift_Ins	INS	-	-	A																															ggccgctttctctgaccatcINSaaaaaaattgtctgaataat																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr14:51132011_51132012insA	ENST00000324679.4	-	2	783_784	c.420_421insT	c.(418-423)tttgatfs	p.D141fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	141					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					CTCTGACCATCAAAAAAATTGT	0.396																																					p.D141_G142delinsX		.											.	SAV1-658	0			c.421_422insT						.																																			SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.421dupT	14.37:g.51132018_51132018dupA	ENSP00000324729:p.Asp141fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	63	35	NM_021818	0	0	0	0	0	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Nonsense_Mutation	INS	ENST00000324679.4	37	CCDS9701.1																																																																																			.		0.396	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			A	51132012	-	A	51132011	7	5	111	1	0	1	1	0	0	0	0	0	13888	826	29	0	746	0	SAV1	14	51132011	Frame_Shift_Ins	INS	-	TCGA-G7-6789-01A-11D-1961-08	30465526	51132011	56217529	29	9815											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR	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	265	268					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	324	52		WXS	Illumina HiSeq		535	83	NM_145301	0	0	2	97	95	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		T	15457087	C	T	15457087	3	4	111	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		15457087	65738123	30	9816											
RNF213	57674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	78355391	78355391	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgagggatccaaaaggCtttctgcagcagcacatcct	11	8	10	12	0	1	1	0	1	1	0	3	2	3	2	3	2	3	4	3	2	2	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr17:78355391C>G	ENST00000582970.1	+	57	13985	c.13842C>G	c.(13840-13842)ggC>ggG	p.G4614G	RNF213_ENST00000336301.6_Silent_p.G2687G|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Silent_p.G4663G|CTD-2047H16.4_ENST00000573394.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4614					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ATCCAAAAGGCTTTCTGCAGC	0.562																																					p.G4614G		.											.	RNF213-577	0			c.C13842G						.						109	94	99					17																	78355391		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon57			AAAAGGCTTTCTG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13842C>G	17.37:g.78355391C>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	182	99	NM_001256071	0	0	20	41	21	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			.		0.562	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78355391	C	G	78355391	2	3	111	1	0	0	0	0	0	0	0	1	13509	784	28	4		4	RNF213	17	78355391	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08	62898304	78355391	2839819	31	9817											
RPRD1A	55197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	33606995	33606995	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatctgccagcaacatacaCgcatcctctaccattttgga	12	11	5	13	1	2	0	0	0	2	0	3	1	3	1	3	1	5	2	3	1	4	5	rs202026701		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr18:33606995C>T	ENST00000399022.4	-	6	828	c.657G>A	c.(655-657)gcG>gcA	p.A219A	RPRD1A_ENST00000588737.1_Silent_p.A183A|RPRD1A_ENST00000590898.1_Silent_p.A183A|RPRD1A_ENST00000357384.4_Silent_p.A219A|RPRD1A_ENST00000337059.5_Silent_p.A183A|RPRD1A_ENST00000319040.6_Silent_p.A219A	NM_018170.3	NP_060640.2	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing 1A	219					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.A219A(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(2)	12						GCAACATACACGCATCCTCTA	0.373																																					p.A219A		.											.	RPRD1A-154	1	Substitution - coding silent(1)	lung(1)	c.G657A						.	C		0,4406		0,0,2203	90	85	87		657	-5.7	1	18		87	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	RPRD1A	NM_018170.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		219/313	33606995	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	55197	exon6			CATACACGCATCC	AF419845	CCDS11917.1	18q12.2	2012-02-09	2008-08-15		ENSG00000141425	ENSG00000141425			25560	protein-coding gene	gene with protein product	"cyclin-dependent kinase 2B-inhibitor-related protein", "Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)"	610347				12470661, 22231121	Standard	NM_018170		Approved	P15RS, FLJ10656, HsT3101	uc002kzg.3	Q96P16	OTTHUMG00000132591	ENST00000399022.4:c.657G>A	18.37:g.33606995C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	73	45	NM_018170	0	0	3	11	8	A8KA42|B2RBA3|Q7Z5G8|Q96FY9|Q9NVL4	Silent	SNP	ENST00000399022.4	37	CCDS11917.1																																																																																			C|0.999;T|0.001		0.373	RPRD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255802.1	NM_018170		T	33606995	C	T	33606995	2	4	111	1	0	0	0	0	0	0	0	1	13647	523	19	1		1	RPRD1A	18	33606995	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		33606995	44470253	32	9818											
MED16	10025	hgsc.bcm.edu	37	chr19	879943	879943	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcagctcaccttcccGtggctgtcaatccccaccag	7	7	7	20	1	2	0	2	0	0	0	4	0	4	0	7	1	2	3	7	1	1	1	rs201392672|rs76403059	byFrequency	TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000269814.4_Missense_Mutation_p.H449Q|MED16_ENST00000325464.1_Missense_Mutation_p.H449Q|MED16_ENST00000395808.3_Missense_Mutation_p.H449Q|MED16_ENST00000312090.6_Missense_Mutation_p.H449Q|MED16_ENST00000606828.1_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	449					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACCTTCCCGTGGCTGTCAA	0.672																																					p.H449Q		.											.	MED16-186	0			c.C1347G						.						13	11	12					19																	879943		2152	4247	6399	SO:0001583	missense	10025	exon8			CTTCCCGTGGCTG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1347C>G	19.37:g.879943G>C	ENSP00000464810:p.His449Gln	Somatic	34	1		WXS	Illumina HiSeq	Phase_I	18	3	NM_005481	0	0	0	0	0	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	3.376	-0.127462	0.06753	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000424039	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.21	-7.89	0.01174	WD40 repeat-like-containing domain (1);	0.323237	0.32357	N	0.006220	T	0.21307	0.0513	L	0.37850	1.14	0.37741	D	0.925623	B;B;B;B;B	0.13145	0.006;0.007;0.002;0.001;0.001	B;B;B;B;B	0.14023	0.006;0.006;0.003;0.006;0.01	T	0.20009	-1.0288	10	0.15066	T	0.55	-14.2411	8.1092	0.30905	0.4704:0.1904:0.3392:0.0	.	449;449;449;449;449	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	Q	449;449;449;449;449;305;210;208;449	ENSP00000325612:H449Q;ENSP00000308528:H449Q;ENSP00000379153:H449Q;ENSP00000269814:H449Q	ENSP00000269814:H449Q	H	-	3	2	MED16	830943	0.000000	0.05858	0.886000	0.34754	0.057000	0.15508	-3.404000	0.00482	-1.779000	0.01280	-2.326000	0.00250	CAC	.		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		C	879943	G	C	879943	3	2	111	1	0	0	0	0	1	0	0	0	9459	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		879943	58249040	33	9819											
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40408648	40408648	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcttctggaagtcatccttGgggtcgccgttgtagttccc	4	13	13	11	2	2	0	1	0	1	0	5	1	4	1	3	4	0	4	3	4	2	5			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr19:40408648G>C	ENST00000221347.6	-	8	4198	c.4191C>G	c.(4189-4191)ccC>ccG	p.P1397P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1397	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGTCATCCTTGGGGTCGCCGT	0.607																																					p.P1397P		.											.	FCGBP-98	0			c.C4191G						.						121	108	112					19																	40408648		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon8			ATCCTTGGGGTCG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4191C>G	19.37:g.40408648G>C		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	116	34	NM_003890	0	1	26	27	0	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			.		0.607	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		C	40408648	G	C	40408648	2	2	111	1	0	0	0	0	0	0	0	1	5797	1335	47	4		4	FCGBP	19	40408648	Silent	SNP	G	TCGA-G7-6789-01A-11D-1961-08	39528705	40408648	18720335	34	9820											
FAM65C	140876	bcgsc.ca	37	chr20	49219029	49219029	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctccgtgtctcgggggtcCtcagagctgaaggagtccat	6	10	14	11	2	3	2	1	1	2	1	7	3	5	3	3	3	1	1	3	3	1	0			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr20:49219029C>A	ENST00000327979.2	-	13	1638	c.1227G>T	c.(1225-1227)gaG>gaT	p.E409D	FAM65C_ENST00000045083.2_Missense_Mutation_p.E409D|FAM65C_ENST00000535356.1_Missense_Mutation_p.E413D			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	409										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCGGGGGTCCTCAGAGCTGA	0.627																																					p.E409D													.	FAM65C-92	0			c.G1227T						.						41	39	40					20																	49219029		2091	4148	6239	SO:0001583	missense	140876	exon13			GGGGTCCTCAGAG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1227G>T	20.37:g.49219029C>A	ENSP00000332663:p.Glu409Asp	Somatic	87	0		WXS	Illumina HiSeq	Phase_1	132	8	NM_080829	0	0	1	1	0	Q5QPB6|Q9NQQ2	Missense_Mutation	SNP	ENST00000327979.2	37	CCDS13431.2	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848134	0.32699	.	.	ENSG00000042062	ENST00000327979;ENST00000045083;ENST00000535356	T;T;T	0.15139	2.46;2.46;2.45	4.77	2.53	0.30540	.	0.497453	0.23202	N	0.050769	T	0.15003	0.0362	L	0.50333	1.59	0.36489	D	0.868329	B;B	0.21606	0.058;0.058	B;B	0.20184	0.028;0.028	T	0.09862	-1.0655	10	0.26408	T	0.33	-28.4224	10.6816	0.45817	0.128:0.6762:0.1958:0.0	.	413;409	F5H0X2;Q96MK2	.;FA65C_HUMAN	D	409;409;413	ENSP00000332663:E409D;ENSP00000045083:E409D;ENSP00000439802:E413D	ENSP00000045083:E409D	E	-	3	2	FAM65C	48652436	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	1.193000	0.32162	2.206000	0.71126	0.561000	0.74099	GAG	.		0.627	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			A	49219029	C	A	49219029	3	1	111	1	0	0	0	0	1	0	0	0	5620	680	24	4	1653	4	FAM65C	20	49219029	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		49219029	13806491	35	9821											
SLC6A14	11254	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	115573956	115573956	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtttgcttcttttcaaagtGaactaccatggaaaaattgt	12	16	7	6	0	2	1	1	1	1	0	2	2	2	2	1	1	3	2	1	1	5	6			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chrX:115573956G>A	ENST00000371900.4	+	4	536	c.448G>A	c.(448-450)Gaa>Aaa	p.E150K		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	150					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TTTTCAAAGTGAACTACCATG	0.323																																					p.E150K		.											.	SLC6A14-133	0			c.G448A						.						126	118	121					X																	115573956		2203	4297	6500	SO:0001583	missense	11254	exon4			CAAAGTGAACTAC	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.448G>A	X.37:g.115573956G>A	ENSP00000360967:p.Glu150Lys	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	140	83	NM_007231	0	0	0	0	0	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	37	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	5.346	0.249106	0.10130	.	.	ENSG00000087916	ENST00000371900	T	0.74526	-0.85	5.61	2.77	0.32553	.	0.454788	0.25045	N	0.033578	T	0.56171	0.1967	L	0.33339	1.005	0.22435	N	0.999103	B	0.02656	0.0	B	0.09377	0.004	T	0.35773	-0.9775	10	0.06625	T	0.88	.	8.3675	0.32395	0.0857:0.4534:0.4609:0.0	.	150	Q9UN76	S6A14_HUMAN	K	150	ENSP00000360967:E150K	ENSP00000360967:E150K	E	+	1	0	SLC6A14	115487984	0.371000	0.25056	0.448000	0.26945	0.981000	0.71138	1.623000	0.37008	0.143000	0.18926	-0.218000	0.12543	GAA	.		0.323	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			A	115573956	G	A	115573956	3	1	111	1	0	0	0	0	1	0	0	0	14709	1291	45	2	462	2	SLC6A14	23	115573956	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		115573956	39696604	36	9822											
LOC440563	0	broad.mit.edu;bcgsc.ca	37	chr1	13183399	13183399	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactcttagaattgaagccActtttgccccttcgtgaggt	8	13	8	12	1	1	3	0	2	1	1	2	3	1	3	4	1	2	0	4	1	3	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:13183399A>G								RP13-221M14.3 (18931 upstream) : PRAMEF26 (32956 downstream)																							AATTGAAGCCACTTTTGCCCC	0.512																																					p.S158S													.	.	0			c.T474C						.						56	45	48					1																	13183399		692	1591	2283	SO:0001628	intergenic_variant	0	exon2			GAAGCCACTTTTG																													1.37:g.13183399A>G		Somatic	1035	1		WXS	Illumina HiSeq	Phase_I	873	80	NM_001136561	0	0	1169	1171	2		Silent	SNP		37																																																																																				.	0	0.512									G	13183399	A	G	13183399	1	3	112	0	1	0	0	0	0	0	0	0	8904	156	6	3		3	LOC440563	1	13183399	IGR	SNP	A	TCGA-G7-6790-01A-11D-1961-08		13183399	236067222	1	9823											
C1orf64	149563	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	16332451	16332451	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catcagaagaccgtccccacGgctcacctgacttttgttat	9	11	7	14	2	2	3	2	1	0	2	3	3	3	3	4	1	0	2	4	1	2	3	rs531928100		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:16332451G>C	ENST00000329454.2	+	2	188	c.120G>C	c.(118-120)acG>acC	p.T40T	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	40										breast(2)|endometrium(1)|lung(3)	6		Colorectal(325;0.000435)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		CCGTCCCCACGGCTCACCTGA	0.562																																					p.T40T		.											.	C1orf64-153	0			c.G120C						.						220	231	228					1																	16332451		2203	4300	6503	SO:0001819	synonymous_variant	149563	exon2			CCCCACGGCTCAC	AK127425	CCDS166.1	1p36.13	2013-10-11			ENSG00000183888	ENSG00000183888			28339	protein-coding gene	gene with protein product	"ER-related factor"					22341523	Standard	NM_178840		Approved	MGC24047, ERRF	uc001axn.3	Q8NEQ6	OTTHUMG00000009523	ENST00000329454.2:c.120G>C	1.37:g.16332451G>C		Somatic	555	2		WXS	Illumina HiSeq	Phase_I	454	126	NM_178840	0	0	0	0	0	B3KXI9	Silent	SNP	ENST00000329454.2	37	CCDS166.1																																																																																			.		0.562	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840		C	16332451	G	C	16332451	2	2	112	1	0	0	0	0	0	0	0	1	2060	1103	39	4		4	C1orf64	1	16332451	Silent	SNP	G	TCGA-G7-6790-01A-11D-1961-08	3149052	16332451	232918170	2	9824											
JAK1	3716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	65330541	65330541	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatgtgagtgatttcagggaAgtaagaaaaattgttccact	15	12	10	4	0	1	3	1	2	0	1	2	4	2	4	1	1	0	2	1	1	5	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:65330541A>T	ENST00000342505.4	-	8	1353	c.1105T>A	c.(1105-1107)Ttc>Atc	p.F369I		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	369	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATTTCAGGGAAGTAAGAAAAA	0.368			Mis		ALL																																p.F369I		.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1-3900	0			c.T1105A						.						156	150	152					1																	65330541		1885	4123	6008	SO:0001583	missense	3716	exon8			CAGGGAAGTAAGA	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1105T>A	1.37:g.65330541A>T	ENSP00000343204:p.Phe369Ile	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	68	22	NM_002227	0	0	53	90	37	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.861730	0.91433	.	.	ENSG00000162434	ENST00000342505	T	0.21191	2.02	5.55	5.55	0.83447	FERM domain (1);	.	.	.	.	T	0.25382	0.0617	M	0.85462	2.755	0.52099	D	0.999945	D	0.53619	0.961	P	0.47206	0.541	T	0.10042	-1.0647	9	0.28530	T	0.3	-5.6269	16.0013	0.80294	1.0:0.0:0.0:0.0	.	369	P23458	JAK1_HUMAN	I	369	ENSP00000343204:F369I	ENSP00000343204:F369I	F	-	1	0	JAK1	65103129	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.607000	0.90891	2.247000	0.74100	0.528000	0.53228	TTC	.		0.368	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65330541	A	T	65330541	3	4	112	1	0	0	0	0	1	0	0	0	7958	72	3	5	2431	5	JAK1	1	65330541	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	48998090	65330541	183920080	3	9825											
SLC6A17	388662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110738291	110738291	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtcaccatgttcgatgacTactcggccaccctgccactc	7	11	7	16	2	1	1	1	1	0	0	4	2	1	1	4	1	2	1	4	1	1	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:110738291T>A	ENST00000331565.4	+	10	2061	c.1576T>A	c.(1576-1578)Tac>Aac	p.Y526N		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	526					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GTTCGATGACTACTCGGCCAC	0.537																																					p.Y526N		.											.	SLC6A17-92	0			c.T1576A						.						107	88	94					1																	110738291		2203	4300	6503	SO:0001583	missense	388662	exon10			GATGACTACTCGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1576T>A	1.37:g.110738291T>A	ENSP00000330199:p.Tyr526Asn	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	75	32	NM_001010898	0	0	0	0	0	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	T	32	5.131369	0.94473	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	D	0.81996	-1.56	5.65	5.65	0.86999	.	0.056027	0.64402	D	0.000001	D	0.92492	0.7616	M	0.93507	3.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94407	0.7628	10	0.87932	D	0	.	15.8499	0.78921	0.0:0.0:0.0:1.0	.	526	Q9H1V8	S6A17_HUMAN	N	526	ENSP00000330199:Y526N	ENSP00000330199:Y526N	Y	+	1	0	SLC6A17	110539814	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.934000	0.87649	2.146000	0.66826	0.533000	0.62120	TAC	.		0.537	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110738291	T	A	110738291	3	1	112	1	0	0	0	0	1	0	0	0	14712	1522	53	5	1610	5	SLC6A17	1	110738291	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	45407750	110738291	138512330	4	9826											
SIKE1	80143	hgsc.bcm.edu;bcgsc.ca	37	chr1	115323170	115323170	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggccgcatcgtgctccCgtagcctctccagcagcgtc	4	7	12	18	6	1	0	0	0	1	0	5	0	2	0	4	2	4	4	4	2	1	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:115323170C>A	ENST00000060969.5	-	1	128	c.59G>T	c.(58-60)cGg>cTg	p.R20L	SIKE1_ENST00000369528.5_Missense_Mutation_p.R20L|SIKE1_ENST00000506320.1_5'UTR			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1	20					innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						ATCGTGCTCCCGTAGCCTCTC	0.687																																					p.R20L		.											.	SIKE1-227	0			c.G59T						.						22	24	23					1																	115323170		2200	4298	6498	SO:0001583	missense	80143	exon1			TGCTCCCGTAGCC	AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"suppressor of IKK epsilon"	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.59G>T	1.37:g.115323170C>A	ENSP00000060969:p.Arg20Leu	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	57	5	NM_001102396	0	0	8	8	0	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Missense_Mutation	SNP	ENST00000060969.5	37	CCDS878.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.946346	0.92593	.	.	ENSG00000052723	ENST00000369528;ENST00000060969	.	.	.	5.39	5.39	0.77823	.	0.052522	0.64402	D	0.000001	T	0.24586	0.0596	L	0.39898	1.24	0.38578	D	0.950123	P;P	0.47191	0.891;0.8	B;B	0.41764	0.331;0.366	T	0.16247	-1.0409	9	0.48119	T	0.1	-15.9215	6.8936	0.24243	0.0:0.7981:0.0:0.2019	.	20;20	Q9BRV8-2;Q9BRV8	.;SIKE1_HUMAN	L	20	.	ENSP00000060969:R20L	R	-	2	0	SIKE1	115124693	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.668000	0.46816	2.791000	0.96007	0.655000	0.94253	CGG	.		0.687	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073		A	115323170	C	A	115323170	3	1	112	1	0	0	0	0	1	0	0	0	14352	652	23	4	596	4	SIKE1	1	115323170	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	4584879	115323170	133927451	5	9827											
FCGR1A	2209	hgsc.bcm.edu	37	chr1	149755582	149755582	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacaaaggcagtgatcactTtgcagcctccatgggtcagc	10	8	10	13	0	2	1	2	1	0	0	3	1	3	1	3	2	3	2	3	2	1	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:149755582T>G	ENST00000369168.4	+	3	130	c.76T>G	c.(76-78)Ttg>Gtg	p.L26V	RP11-196G18.3_ENST00000428289.1_RNA|RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000545683.1_Intron	NM_000566.3	NP_000557.1	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor (CD64)	26	Ig-like C2-type 1.				antibody-dependent cellular cytotoxicity (GO:0001788)|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)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intracellular signal transduction (GO:0035556)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of phagocytosis (GO:0050766)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG receptor activity (GO:0019770)|receptor signaling protein activity (GO:0005057)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)	10	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AGTGATCACTTTGCAGCCTCC	0.498																																					p.L26V		.											.	FCGR1A-23	0			c.T76G						.						1	1	1					1																	149755582		647	1295	1942	SO:0001583	missense	2209	exon3			ATCACTTTGCAGC	BC032634	CCDS933.1	1q21.2-q21.3	2014-09-17	2005-02-02		ENSG00000150337	ENSG00000150337		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3613	protein-coding gene	gene with protein product		146760	"Fc fragment of IgG, high affinity Ia, receptor for (CD64)"			8697799, 9763663	Standard	NM_000566		Approved	CD64, CD64A	uc001esp.4	P12314	OTTHUMG00000012089	ENST00000369168.4:c.76T>G	1.37:g.149755582T>G	ENSP00000358165:p.Leu26Val	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	249	40	NM_000566	0	0	6	6	0	P12315|Q5QNW7|Q92495|Q92663	Missense_Mutation	SNP	ENST00000369168.4	37	CCDS933.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.255432	0.22965	.	.	ENSG00000150337	ENST00000369168	T	0.12465	2.68	3.13	-0.514	0.11958	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40469	N	0.001099	T	0.12263	0.0298	M	0.68728	2.09	0.80722	D	1	P	0.41978	0.767	P	0.54431	0.752	T	0.06092	-1.0846	10	0.51188	T	0.08	.	5.5384	0.17023	0.0:0.4493:0.0:0.5506	.	26	P12314	FCGR1_HUMAN	V	26	ENSP00000358165:L26V	ENSP00000358165:L26V	L	+	1	2	FCGR1A	148022206	0.999000	0.42202	0.990000	0.47175	0.526000	0.34562	0.495000	0.22483	0.003000	0.14656	0.338000	0.21704	TTG	.		0.498	FCGR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033446.1	NM_000566		G	149755582	T	G	149755582	3	3	112	1	0	0	0	0	1	0	0	0	5798	1838	64	5	86	5	FCGR1A	1	149755582	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	34432412	149755582	99495039	6	9828											
TRIM46	80128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155148034	155148034	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccccagctccgagcccacctCtcctgcctccaccccttcca	5	7	4	25	1	1	0	0	0	1	0	5	1	4	0	11	0	3	1	11	0	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:155148034C>G	ENST00000334634.4	+	2	236	c.236C>G	c.(235-237)tCt>tGt	p.S79C	TRIM46_ENST00000368383.3_Missense_Mutation_p.S79C|TRIM46_ENST00000368382.1_Missense_Mutation_p.S56C|TRIM46_ENST00000545012.1_Intron|KRTCAP2_ENST00000295682.4_5'Flank|KRTCAP2_ENST00000490672.1_5'Flank|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000368385.4_Missense_Mutation_p.S79C|TRIM46_ENST00000543729.1_Missense_Mutation_p.S86C|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000392451.2_Missense_Mutation_p.S79C	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	79						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GAGCCCACCTCTCCTGCCTCC	0.677																																					p.S79C		.											.	TRIM46-228	0			c.C236G						.						56	55	55					1																	155148034		2203	4300	6503	SO:0001583	missense	80128	exon2			CCACCTCTCCTGC		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.236C>G	1.37:g.155148034C>G	ENSP00000334657:p.Ser79Cys	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	97	19	NM_025058	0	0	0	0	0	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	37	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448430	0.84101	.	.	ENSG00000163462	ENST00000543729;ENST00000430513;ENST00000368385;ENST00000392451;ENST00000368383;ENST00000368382;ENST00000334634	T;T;T;T;T;T	0.60672	0.75;0.5;0.69;0.42;0.17;0.23	4.53	4.53	0.55603	Zinc finger, RING-type (1);	0.348037	0.29205	N	0.012829	T	0.60856	0.2301	L	0.51422	1.61	0.47547	D	0.999457	D;B;D;D;B;D	0.89917	0.998;0.014;1.0;0.999;0.014;0.999	P;B;D;P;B;D	0.68765	0.889;0.033;0.96;0.867;0.033;0.924	T	0.58567	-0.7614	10	0.33141	T	0.24	.	15.1434	0.72630	0.0:1.0:0.0:0.0	.	66;79;66;56;79;79	F5H5Z2;Q5VT61;B7Z3S2;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.;.;.;.;TRI46_HUMAN;.	C	86;66;79;79;79;56;79	ENSP00000442719:S86C;ENSP00000357369:S79C;ENSP00000376245:S79C;ENSP00000357367:S79C;ENSP00000357366:S56C;ENSP00000334657:S79C	ENSP00000334657:S79C	S	+	2	0	TRIM46	153414658	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.676000	0.74498	2.222000	0.72286	0.650000	0.86243	TCT	.		0.677	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		G	155148034	C	G	155148034	3	3	112	1	0	0	0	0	1	0	0	0	16554	913	32	4	242	4	TRIM46	1	155148034	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	5392452	155148034	94102587	7	9829											
F5	2153	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169510915	169510916	+	Frame_Shift_Ins	INS	-	-	TT																															ggggtctgaagtagagtgcaINStttgatcagggtcttgaatg																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:169510915_169510916insTT	ENST00000367797.3	-	13	3613_3614	c.3412_3413insAA	c.(3412-3414)atgfs	p.M1138fs	F5_ENST00000367796.3_Frame_Shift_Ins_p.M1143fs	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1138	B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AGTAGAGTGCATTTGATCAGGG	0.48																																					p.M1138fs		.											.	F5-157	0			c.3413_3414insAA						.																																			SO:0001589	frameshift_variant	2153	exon13			.	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.3411_3412dupAA	1.37:g.169510916_169510917dupTT	ENSP00000356771:p.Met1138fs	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	276	80	NM_000130	0	0	0	0	0	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Frame_Shift_Ins	INS	ENST00000367797.3	37	CCDS1281.1																																																																																			.		0.48	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		TT	169510916	-	TT	169510915	7	5	112	1	0	1	1	0	0	0	0	0	5361	217	8	0	3313	0	F5	1	169510915	Frame_Shift_Ins	INS	-	TCGA-G7-6790-01A-11D-1961-08	14362881	169510915	79739706	8	9830											
RC3H1	149041	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	173916659	173916660	+	Frame_Shift_Del	DEL	GT	GT	-																															ggatgaggtcatcatcactgGtttctgctgctcttctctga																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:173916659_173916660delGT	ENST00000367696.2	-	15	2935_2936	c.2584_2585delAC	c.(2584-2586)accfs	p.T862fs	RC3H1_ENST00000367694.2_Frame_Shift_Del_p.T862fs|RC3H1_ENST00000258349.4_Frame_Shift_Del_p.T862fs			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	862					B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						ATCATCACTGGTTTCTGCTGCT	0.45																																					p.862_862del		.											.	RC3H1-92	0			c.2584_2585del						.																																			SO:0001589	frameshift_variant	149041	exon14			.	AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870		"RING-type (C3HC4) zinc fingers", "Zinc fingers, CCCH-type domain containing"	29434	protein-coding gene	gene with protein product	"KIAA2025 protein"	609424	"ring finger and CCCH-type zinc finger domains 1"			15917799	Standard	XM_005244918		Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.2584_2585delAC	1.37:g.173916659_173916660delGT	ENSP00000356669:p.Thr862fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	130	29	NM_172071	0	0	0	0	0	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Frame_Shift_Del	DEL	ENST00000367696.2	37	CCDS30940.1																																																																																			.		0.45	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071		-	173916660	GT	-	173916659	7	5	112	1	0	1	0	1	0	0	0	0	13198	1261	44	0	840	0	RC3H1	1	173916659	Frame_Shift_Del	DEL	GT	TCGA-G7-6790-01A-11D-1961-08	4405744	173916659	75333962	9	9831											
GRHL1	29841	broad.mit.edu;bcgsc.ca	37	chr2	10130855	10130855	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaaatcagggatgaagaacGaaagcaaagcaaaagaaaag	24	2	11	4	1	1	3	1	1	0	2	1	6	1	4	0	1	3	2	0	1	10	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:10130855G>A	ENST00000324907.9	+	10	1437	c.1301G>A	c.(1300-1302)cGa>cAa	p.R434Q	GRHL1_ENST00000324883.5_Missense_Mutation_p.R245Q|GRHL1_ENST00000405379.2_Missense_Mutation_p.R434Q	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	434					cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		GATGAAGAACGAAAGCAAAGC	0.418																																					p.R434Q													.	GRHL1-92	0			c.G1301A						.						114	99	104					2																	10130855		2203	4300	6503	SO:0001583	missense	29841	exon10			AAGAACGAAAGCA	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"transcription factor CP2-like 2"	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.1301G>A	2.37:g.10130855G>A	ENSP00000324693:p.Arg434Gln	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	29	9	NM_198182	0	0	7	8	1	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	37	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	G	27.3	4.817681	0.90790	.	.	ENSG00000134317	ENST00000405379;ENST00000324883;ENST00000324907	T;T;T	0.18016	2.24;2.24;2.24	5.76	5.76	0.90799	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.45617	0.1351	M	0.73598	2.24	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.74674	0.961;0.984	T	0.35822	-0.9773	10	0.72032	D	0.01	-7.5436	19.9574	0.97228	0.0:0.0:1.0:0.0	.	245;434	Q9NZI5-2;Q9NZI5	.;GRHL1_HUMAN	Q	434;245;434	ENSP00000384209:R434Q;ENSP00000324494:R245Q;ENSP00000324693:R434Q	ENSP00000324494:R245Q	R	+	2	0	GRHL1	10048306	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	7.066000	0.76734	2.715000	0.92844	0.561000	0.74099	CGA	.		0.418	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		A	10130855	G	A	10130855	3	1	112	1	0	0	0	0	1	0	0	0	6784	1058	37	1	1339	1	GRHL1	2	10130855	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08		10130855	233068518	10	9832											
GREB1	9687	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	11706688	11706688	+	Frame_Shift_Del	DEL	G	G	-																															cctgcgggctttctcctcgtGggggtcaagtcccccagcct																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:11706688delG	ENST00000381486.2	+	4	660	c.360delG	c.(358-360)gtgfs	p.V120fs	GREB1_ENST00000381483.2_Frame_Shift_Del_p.V120fs|GREB1_ENST00000389825.3_Frame_Shift_Del_p.V10fs|GREB1_ENST00000234142.5_Frame_Shift_Del_p.V120fs|GREB1_ENST00000263834.5_Frame_Shift_Del_p.V120fs	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	120						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TTCTCCTCGTGGGGGTCAAGT	0.597																																					p.V120fs	Ovarian(39;850 945 2785 23371 33093)	.											.	GREB1-91	0			c.360delG						.						98	91	93					2																	11706688		2203	4300	6503	SO:0001589	frameshift_variant	9687	exon4			.		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.360delG	2.37:g.11706688delG	ENSP00000370896:p.Val120fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	135	41	NM_148903	0	0	0	0	0	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Frame_Shift_Del	DEL	ENST00000381486.2	37	CCDS42655.1																																																																																			.		0.597	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		-	11706688	G	-	11706688	7	5	112	1	0	1	0	1	0	0	0	0	6781	1335	47	0	370	0	GREB1	2	11706688	Frame_Shift_Del	DEL	G	TCGA-G7-6790-01A-11D-1961-08	1575833	11706688	231492685	11	9833											
GREB1	9687	hgsc.bcm.edu;broad.mit.edu	37	chr2	11758729	11758729	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccggcacgtgggtcctgcAggcctcccagtgctccttga	4	9	13	15	2	0	1	0	1	0	0	3	1	3	1	5	3	3	3	5	3	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:11758729A>G	ENST00000381486.2	+	22	4028	c.3728A>G	c.(3727-3729)cAg>cGg	p.Q1243R	GREB1_ENST00000234142.5_Missense_Mutation_p.Q1243R|GREB1_ENST00000396123.1_Missense_Mutation_p.Q241R	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1243						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TGGGTCCTGCAGGCCTCCCAG	0.652																																					p.Q1243R	Ovarian(39;850 945 2785 23371 33093)	.											.	GREB1-91	0			c.A3728G						.						24	27	26					2																	11758729		2170	4247	6417	SO:0001583	missense	9687	exon22			TCCTGCAGGCCTC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.3728A>G	2.37:g.11758729A>G	ENSP00000370896:p.Gln1243Arg	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_014668	0	0	11	11	0	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.322801	0.41096	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.25579	3.12;3.12;1.79	4.79	4.79	0.61399	.	0.429519	0.25958	N	0.027219	T	0.27454	0.0674	L	0.56769	1.78	0.36790	D	0.884798	B	0.30709	0.291	B	0.27715	0.082	T	0.30534	-0.9975	10	0.56958	D	0.05	-42.3953	14.313	0.66429	1.0:0.0:0.0:0.0	.	1243	Q4ZG55	GREB1_HUMAN	R	1243;1243;241	ENSP00000370896:Q1243R;ENSP00000234142:Q1243R;ENSP00000379429:Q241R	ENSP00000234142:Q1243R	Q	+	2	0	GREB1	11676180	1.000000	0.71417	0.906000	0.35671	0.930000	0.56654	3.610000	0.54125	1.802000	0.52723	0.445000	0.29226	CAG	.		0.652	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11758729	A	G	11758729	3	3	112	1	0	0	0	0	1	0	0	0	6781	188	7	3	3918	3	GREB1	2	11758729	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	52041	11758729	231440644	12	9834											
NBAS	51594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	15691634	15691634	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taccttgacatttcccaataAtggatgtaaaatcatctttt	13	16	4	8	0	2	1	1	1	1	0	3	2	3	2	2	1	1	1	2	1	5	7			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:15691634A>G	ENST00000281513.5	-	6	387	c.362T>C	c.(361-363)aTt>aCt	p.I121T	NBAS_ENST00000441750.1_Missense_Mutation_p.I121T	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	121					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TTTCCCAATAATGGATGTAAA	0.299																																					p.I121T		.											.	NBAS-94	0			c.T362C						.						41	40	41					2																	15691634		2201	4297	6498	SO:0001583	missense	51594	exon6			CCAATAATGGATG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.362T>C	2.37:g.15691634A>G	ENSP00000281513:p.Ile121Thr	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	20	6	NM_015909	0	0	9	9	0	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	A	9.005	0.980968	0.18812	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.52526	0.66;0.66	5.66	5.66	0.87406	Quinoprotein amine dehydrogenase, beta chain-like (1);	0.283763	0.33854	N	0.004482	T	0.36026	0.0952	N	0.21448	0.665	0.23657	N	0.997182	B	0.06786	0.001	B	0.06405	0.002	T	0.36065	-0.9763	10	0.87932	D	0	.	13.4276	0.61035	1.0:0.0:0.0:0.0	.	121	A2RRP1	NBAS_HUMAN	T	121	ENSP00000413201:I121T;ENSP00000281513:I121T	ENSP00000281513:I121T	I	-	2	0	NBAS	15609085	1.000000	0.71417	0.995000	0.50966	0.472000	0.32918	4.934000	0.63491	2.144000	0.66660	0.477000	0.44152	ATT	.		0.299	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15691634	A	G	15691634	3	3	112	1	0	0	0	0	1	0	0	0	10211	101	4	3	6941	3	NBAS	2	15691634	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	3932905	15691634	227507739	13	9835											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33172879	33172879	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcaccagaagcagcagcTgcaggggtaagcccacaccc	11	4	12	14	0	1	1	1	0	0	1	1	1	1	1	3	3	5	6	3	3	2	2	rs62135680	byFrequency	TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:33172879T>C	ENST00000404816.2	+	1	841	c.488T>C	c.(487-489)cTg>cCg	p.L163P	Y_RNA_ENST00000384224.1_RNA|LTBP1_ENST00000354476.3_Missense_Mutation_p.L163P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	163					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAGCAGCAGCTGCAGGGGTAA	0.716													T|||	22	0.00439297	0	0	5008	,	,		8051	0		0.0189	False		,,,				2504	0.0031				p.L163P		.											.	LTBP1-230	0			c.T488C						.	T	PRO/LEU	5,3041		0,5,1518	6	6	6		488	3.5	1	2	dbSNP_129	6	61,5721		0,61,2830	yes	missense	LTBP1	NM_206943.2	98	0,66,4348	CC,CT,TT		1.055,0.1641,0.7476	possibly-damaging	163/1722	33172879	66,8762	1523	2891	4414	SO:0001583	missense	4052	exon1			AGCAGCTGCAGGG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"Latent transforming growth factor, beta binding proteins"	6714	protein-coding gene	gene with protein product	"TGF-beta1-BP-1"	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.488T>C	2.37:g.33172879T>C	ENSP00000386043:p.Leu163Pro	Somatic	11	1		WXS	Illumina HiSeq	Phase_I	21	10	NM_206943	0	0	0	0	0	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	17	0.007783882783882784	0	0.0	0	0.0	0	0.0	17	0.022427440633245383	T	20.4	3.981933	0.74474	0.001641	0.01055	ENSG00000049323	ENST00000404816;ENST00000354476	D;D	0.83992	-1.79;-1.78	4.67	3.52	0.40303	.	.	.	.	.	T	0.56124	0.1964	N	0.24115	0.695	0.80722	D	1	B	0.15930	0.015	B	0.14578	0.011	T	0.60905	-0.7170	9	0.87932	D	0	.	7.8282	0.29328	0.0:0.0979:0.0:0.9021	rs62135680	163	Q14766-4	.	P	163	ENSP00000386043:L163P;ENSP00000346467:L163P	ENSP00000346467:L163P	L	+	2	0	LTBP1	33026383	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.717000	0.54911	0.649000	0.30751	0.459000	0.35465	CTG	T|0.992;C|0.008		0.716	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33172879	T	C	33172879	3	2	112	1	0	0	0	0	1	0	0	0	9098	1580	55	3	490	3	LTBP1	2	33172879	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	17481245	33172879	210026494	14	9836											
SMEK2	57223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55812212	55812212	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactctgctgagcttcttgcAttacaaactctcggaccata	10	12	6	13	1	3	1	0	1	3	0	4	2	3	2	1	1	5	3	1	1	3	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:55812212A>G	ENST00000345102.5	-	7	1509	c.1208T>C	c.(1207-1209)aTg>aCg	p.M403T	SMEK2_ENST00000407823.3_Missense_Mutation_p.M403T|SMEK2_ENST00000272313.5_Missense_Mutation_p.M403T	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	403					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGCTTCTTGCATTACAAACTC	0.368																																					p.M403T		.											.	SMEK2-228	0			c.T1208C						.						114	111	112					2																	55812212		2203	4300	6503	SO:0001583	missense	57223	exon7			TCTTGCATTACAA	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.1208T>C	2.37:g.55812212A>G	ENSP00000339769:p.Met403Thr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	134	29	NM_001122964	0	0	33	59	26	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	37	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.325891	0.60743	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.40225	1.04;1.04;1.04	5.8	5.8	0.92144	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46852	0.1414	M	0.66939	2.045	0.80722	D	1	B;B;B;B	0.25850	0.018;0.136;0.002;0.136	B;B;B;B	0.30782	0.071;0.082;0.005;0.12	T	0.40979	-0.9534	10	0.44086	T	0.13	-11.8434	16.134	0.81465	1.0:0.0:0.0:0.0	.	403;403;403;403	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3;B4DKA9	.;P4R3B_HUMAN;.;.	T	403	ENSP00000272313:M403T;ENSP00000385912:M403T;ENSP00000339769:M403T	ENSP00000272313:M403T	M	-	2	0	SMEK2	55665716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.216000	0.71823	0.528000	0.53228	ATG	.		0.368	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		G	55812212	A	G	55812212	3	3	112	1	0	0	0	0	1	0	0	0	14826	217	8	3	1385	3	SMEK2	2	55812212	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	22639333	55812212	187387161	15	9837											
GAD1	2571	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	171687570	171687570	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgatcgctccaccaaggtgCtggactttcatcacccacac	9	10	7	15	1	2	1	2	1	0	0	4	2	3	2	3	2	1	2	3	2	1	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:171687570C>T	ENST00000358196.3	+	5	965	c.415C>T	c.(415-417)Ctg>Ttg	p.L139L	GAD1_ENST00000344257.5_Silent_p.L139L|GAD1_ENST00000375272.1_Silent_p.L139L|GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	139					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CACCAAGGTGCTGGACTTTCA	0.547																																					p.L139L		.											.	GAD1-91	0			c.C415T						.						114	99	104					2																	171687570		2203	4300	6503	SO:0001819	synonymous_variant	2571	exon5			AAGGTGCTGGACT		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.415C>T	2.37:g.171687570C>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	128	63	NM_000817	0	0	0	0	0	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	37	CCDS2239.1																																																																																			.		0.547	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171687570	C	T	171687570	2	4	112	1	0	0	0	0	0	0	0	1	6198	796	28	2		2	GAD1	2	171687570	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	115875358	171687570	71511803	16	9838											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179419674	179419674	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagcatccactattaaggcgAtcggcatctttgatgagtat	11	13	9	8	2	1	2	0	2	1	0	3	3	2	2	1	2	1	3	1	2	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:179419674A>G	ENST00000591111.1	-	281	83813	c.83589T>C	c.(83587-83589)gaT>gaC	p.D27863D	TTN_ENST00000460472.2_Silent_p.D20439D|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Silent_p.D20564D|TTN_ENST00000342992.6_Silent_p.D26936D|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.D20631D|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.D29504D|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27863	Ig-like 130.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATTAAGGCGATCGGCATCTT	0.423																																					p.D29504D		.											.	TTN-636	0			c.T88512C						.						90	86	87					2																	179419674		1936	4131	6067	SO:0001819	synonymous_variant	7273	exon331			AAGGCGATCGGCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83589T>C	2.37:g.179419674A>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	64	37	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179419674	A	G	179419674	2	3	112	1	0	0	0	0	0	0	0	1	16768	330	12	3		3	TTN	2	179419674	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	7732104	179419674	63779699	17	9839											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179650834	179650834	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtctactgcagcaacaactGttgctacagcttcagccttt	9	12	8	12	0	2	0	1	0	1	0	2	0	2	0	1	1	9	5	1	1	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:179650834G>C	ENST00000591111.1	-	14	2335	c.2111C>G	c.(2110-2112)aCa>aGa	p.T704R	TTN_ENST00000460472.2_Missense_Mutation_p.T658R|TTN_ENST00000360870.5_Missense_Mutation_p.T704R|TTN_ENST00000359218.5_Missense_Mutation_p.T658R|TTN_ENST00000342992.6_Missense_Mutation_p.T704R|TTN_ENST00000342175.6_Missense_Mutation_p.T658R|TTN_ENST00000589042.1_Missense_Mutation_p.T704R			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGCAACAACTGTTGCTACAGC	0.493																																					p.T704R		.											.	TTN-636	0			c.C2111G						.						53	55	54					2																	179650834		2203	4300	6503	SO:0001583	missense	7273	exon14			ACAACTGTTGCTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2111C>G	2.37:g.179650834G>C	ENSP00000465570:p.Thr704Arg	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	110	56	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	16.74	3.207756	0.58343	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000436599	T;T;T;T;T;T	0.70399	-0.48;-0.26;-0.26;-0.27;0.29;0.24	5.99	5.99	0.97316	Ribonuclease H-like (1);	.	.	.	.	T	0.80303	0.4598	L	0.36672	1.1	0.43574	D	0.995901	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.91635	0.996;0.996;0.996;0.996;0.999	T	0.80732	-0.1251	9	0.87932	D	0	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	658;658;658;704;704	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	R	704;658;658;658;658;704;208	ENSP00000343764:T704R;ENSP00000434586:T658R;ENSP00000340554:T658R;ENSP00000352154:T658R;ENSP00000354117:T704R;ENSP00000405517:T208R	ENSP00000340554:T658R	T	-	2	0	TTN	179359079	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.402000	0.79972	2.840000	0.97914	0.655000	0.94253	ACA	.		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179650834	G	C	179650834	3	2	112	1	0	0	0	0	1	0	0	0	16768	1377	48	4	109273	4	TTN	2	179650834	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	231160	179650834	63548539	18	9840											
ZNF804A	91752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	185801068	185801068	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccttcattttgcaagtttcaActtcagttatcttctgatgc	8	18	5	10	0	5	1	3	1	2	0	5	1	5	1	1	0	3	3	1	0	3	7			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:185801068A>G	ENST00000302277.6	+	4	1539	c.945A>G	c.(943-945)caA>caG	p.Q315Q		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	315							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						GCAAGTTTCAACTTCAGTTAT	0.333																																					p.Q315Q		.											.	ZNF804A-163	0			c.A945G						.						33	32	33					2																	185801068		2203	4296	6499	SO:0001819	synonymous_variant	91752	exon4			GTTTCAACTTCAG	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.945A>G	2.37:g.185801068A>G		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	67	41	NM_194250	0	0	0	0	0	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			.		0.333	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		G	185801068	A	G	185801068	2	3	112	1	0	0	0	0	0	0	0	1	18202	40	2	3		3	ZNF804A	2	185801068	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	6150234	185801068	57398305	19	9841											
RUFY4	285180	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	218938568	218938568	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagttccacccaaacccAgggaaggagacccagaaaaa	16	3	8	14	0	0	2	0	0	0	2	2	4	2	3	5	2	1	1	5	2	4	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:218938568A>T	ENST00000344321.7	+	8	1078	c.560A>T	c.(559-561)cAg>cTg	p.Q187L	RUFY4_ENST00000441828.2_Silent_p.P151P|RUFY4_ENST00000463872.1_Intron|RUFY4_ENST00000374155.3_Missense_Mutation_p.Q187L	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	187							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		ACCCAAACCCAGGGAAGGAGA	0.562											OREG0015195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q187L													.	RUFY4-46	0			c.A560T						.						77	86	83					2																	218938568		1983	4166	6149	SO:0001583	missense	285180	exon8			AAACCCAGGGAAG	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"Zinc fingers, FYVE domain containing"	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.560A>T	2.37:g.218938568A>T	ENSP00000345900:p.Gln187Leu	Somatic	58	0	2255	WXS	Illumina HiSeq	Phase_I	66	11	NM_198483	0	0	0	0	0	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		.	.	.	.	.	.	.	.	.	.	A	8.780	0.927938	0.18056	.	.	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.48836	1.44;0.8	3.8	-1.56	0.08532	.	1.202910	0.06250	N	0.691990	T	0.25382	0.0617	L	0.27053	0.805	0.09310	N	0.999999	B	0.33694	0.421	B	0.29267	0.1	T	0.10543	-1.0625	10	0.07644	T	0.81	-1.2143	3.9675	0.09437	0.4544:0.1956:0.35:0.0	.	187	Q6ZNE9	RUFY4_HUMAN	L	187	ENSP00000345900:Q187L;ENSP00000363270:Q187L	ENSP00000345900:Q187L	Q	+	2	0	RUFY4	218646813	0.084000	0.21492	0.030000	0.17652	0.036000	0.12997	0.189000	0.17037	-0.380000	0.07894	0.482000	0.46254	CAG	.		0.562	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		T	218938568	A	T	218938568	3	4	112	1	0	0	0	0	1	0	0	0	13773	188	7	5	582	5	RUFY4	2	218938568	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	33137500	218938568	24260805	20	9842											
COL6A3	1293	broad.mit.edu	37	chr2	238277277	238277277	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagggtccaaacgagttcAtgattctttcttctatgttg	8	15	10	8	2	4	1	1	1	3	0	5	3	5	2	1	2	1	2	1	2	2	6			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:238277277A>G	ENST00000295550.4	-	10	5281	c.4829T>C	c.(4828-4830)aTg>aCg	p.M1610T	COL6A3_ENST00000346358.4_Missense_Mutation_p.M1410T|COL6A3_ENST00000409809.1_Missense_Mutation_p.M1404T|COL6A3_ENST00000472056.1_Missense_Mutation_p.M1003T|COL6A3_ENST00000353578.4_Missense_Mutation_p.M1404T|COL6A3_ENST00000347401.3_Missense_Mutation_p.M1409T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1610	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AAACGAGTTCATGATTCTTTC	0.547																																					p.M1610T													.	COL6A3-526	0			c.T4829C						.						118	112	114					2																	238277277		2203	4300	6503	SO:0001583	missense	1293	exon10			GAGTTCATGATTC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"Collagens"	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4829T>C	2.37:g.238277277A>G	ENSP00000295550:p.Met1610Thr	Somatic	161	1		WXS	Illumina HiSeq	Phase_I	190	6	NM_004369	0	0	5	5	0	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	6.501	0.460572	0.12342	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.69	4.52	0.55395	.	0.789008	0.11541	N	0.553748	T	0.63212	0.2492	N	0.16368	0.405	0.09310	N	1	P;B;B	0.34757	0.467;0.409;0.005	B;B;B	0.37422	0.17;0.249;0.006	T	0.51663	-0.8677	10	0.26408	T	0.33	.	7.117	0.25423	0.6357:0.1219:0.0:0.2424	.	1003;1404;1610	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	T	1610;1409;1404;1003;1404;1410	ENSP00000295550:M1610T;ENSP00000315609:M1409T;ENSP00000315873:M1404T;ENSP00000418285:M1003T;ENSP00000386844:M1404T;ENSP00000295546:M1410T	ENSP00000295550:M1610T	M	-	2	0	COL6A3	237942016	0.528000	0.26314	0.001000	0.08648	0.004000	0.04260	4.745000	0.62125	0.963000	0.38082	0.533000	0.62120	ATG	.		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238277277	A	G	238277277	3	3	112	1	0	0	0	0	1	0	0	0	3707	217	8	3	4844	3	COL6A3	2	238277277	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	19338709	238277277	4922096	21	9843											
PODXL2	50512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	127379599	127379599	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagcatggggcccagctTgctgctgccttcagtcaccc	6	8	12	15	0	2	0	2	0	0	0	2	1	2	0	3	2	6	5	3	2	0	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr3:127379599T>A	ENST00000342480.6	+	3	767	c.728T>A	c.(727-729)tTg>tAg	p.L243*		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	243					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						GGGCCCAGCTTGCTGCTGCCT	0.647																																					p.L243X		.											.	PODXL2-91	0			c.T728A						.						51	57	55					3																	127379599		2203	4300	6503	SO:0001587	stop_gained	50512	exon3			CCAGCTTGCTGCT	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"endoglycan"					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.728T>A	3.37:g.127379599T>A	ENSP00000345359:p.Leu243*	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	88	18	NM_015720	0	0	1	1	0	Q6UVY4|Q8WUV6	Nonsense_Mutation	SNP	ENST00000342480.6	37	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.198338	0.38806	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	.	.	.	4.67	-0.49	0.12049	.	0.719396	0.11780	N	0.530317	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0789	7.8382	0.29382	0.0:0.3596:0.0:0.6404	.	.	.	.	X	243	.	ENSP00000304498:L243X	L	+	2	0	PODXL2	128862289	0.001000	0.12720	0.001000	0.08648	0.181000	0.23173	0.600000	0.24104	-0.256000	0.09473	0.402000	0.26972	TTG	.		0.647	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		A	127379599	T	A	127379599	4	1	112	1	0	0	0	0	0	1	0	0	12207	1821	63	5	738	5	PODXL2	3	127379599	Nonsense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08		127379599	70642831	22	9844											
XRN1	54464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142123863	142123863	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactatgttggtttcttttcCtctcttcctttttgagggag	4	20	8	9	0	2	1	0	1	2	0	5	2	4	2	2	2	0	2	2	2	1	8			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr3:142123863C>G	ENST00000264951.4	-	16	1886	c.1769G>C	c.(1768-1770)aGg>aCg	p.R590T	XRN1_ENST00000392981.2_Missense_Mutation_p.R590T|RNU6-1294P_ENST00000515995.1_RNA	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	590					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						GTTTCTTTTCCTCTCTTCCTT	0.408																																					p.R590T		.											.	XRN1-93	0			c.G1769C						.						162	148	152					3																	142123863		2203	4300	6503	SO:0001583	missense	54464	exon16			CTTTTCCTCTCTT	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.1769G>C	3.37:g.142123863C>G	ENSP00000264951:p.Arg590Thr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	82	35	NM_001042604	0	0	3	9	6	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.363718	0.41902	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.26373	1.74;1.74	5.53	2.35	0.29111	.	0.408805	0.27109	N	0.020895	T	0.15825	0.0381	L	0.31664	0.95	0.80722	D	1	B;P;B	0.34800	0.067;0.469;0.417	B;B;B	0.33121	0.024;0.158;0.142	T	0.05599	-1.0875	10	0.40728	T	0.16	-9.364	7.0395	0.25013	0.0:0.5382:0.0:0.4618	.	451;590;590	B3KW17;Q8IZH2-2;Q8IZH2	.;.;XRN1_HUMAN	T	590	ENSP00000264951:R590T;ENSP00000376707:R590T	ENSP00000264951:R590T	R	-	2	0	XRN1	143606553	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	1.245000	0.32790	0.691000	0.31592	-0.145000	0.13849	AGG	.		0.408	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		G	142123863	C	G	142123863	3	3	112	1	0	0	0	0	1	0	0	0	17492	681	24	4	3459	4	XRN1	3	142123863	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	14744264	142123863	55898567	23	9845											
CHRD	8646	hgsc.bcm.edu	37	chr3	184098193	184098193	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcccgcggcgccggcccAgagccccccgtgctgcccat	3	3	13	22	6	0	1	0	0	0	1	0	1	0	1	8	3	3	1	8	3	0	0	rs1920128		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr3:184098193A>C	ENST00000204604.1	+	1	333	c.87A>C	c.(85-87)ccA>ccC	p.P29P	THPO_ENST00000204615.7_5'Flank|THPO_ENST00000445696.2_5'Flank|CHRD_ENST00000545352.1_5'Flank|CHRD_ENST00000348986.3_Silent_p.P29P|CHRD_ENST00000450923.1_Silent_p.P29P|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000310236.3_Silent_p.P29P	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	29					BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			gcgccggcccAGAGCCCCCCG	0.796																																					p.P29P		.											.	CHRD-93	0			c.A87C						.						1	1	1					3																	184098193		283	643	926	SO:0001819	synonymous_variant	8646	exon1			CGGCCCAGAGCCC	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.87A>C	3.37:g.184098193A>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_003741	0	0	0	6	6	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			T|0.680;G|0.319		0.796	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		C	184098193	A	C	184098193	2	2	112	1	0	0	0	0	0	0	0	1	3378	175	7	5		5	CHRD	3	184098193	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	41974330	184098193	13924237	24	9846											
FRYL	285527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48578146	48578147	+	Missense_Mutation	DNP	TG	TG	CT																															gtggaagatgacgatgttgcTgcactgcagcaaaggatcag																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:48578146_48578147TG>CT	ENST00000503238.1	-	21	2620_2621	c.2621_2622CA>AG	c.(2620-2622)gCA>gAG	p.A874E	FRYL_ENST00000507711.1_Missense_Mutation_p.A874E|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.A874E|RNU5E-3P_ENST00000515913.1_RNA|FRYL_ENST00000358350.4_Missense_Mutation_p.A874E			O94915	FRYL_HUMAN	FRY-like	874					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						ACGATGTTGCTGCACTGCAGCA	0.47																																					p.A874E		.											.	FRYL	0			c.C2621A						.																																			SO:0001583	missense	285527	exon24			GTTGCTGCACTGC	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.2621_2622delinsCT	4.37:g.48578146_48578147delinsCT	ENSP00000426064:p.Ala874Glu	Somatic	149	1		WXS	Illumina HiSeq	Phase_I	99	29		0	0	0	0	0	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	DNP	ENST00000503238.1	37	CCDS43227.1																																																																																			.		0.47	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			CT	48578147	TG	CT	48578146	3	2	112	1	0	0	0	0	1	0	0	0	6083	1567	55	3	6583	3	FRYL	4	48578146	Missense_Mutation	DNP	TG	TCGA-G7-6790-01A-11D-1961-08		48578146	142576130	25	9847	100	2									
FRYL	285527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48578148	48578148	+	Missense_Mutation	SNP	C	C	T																															ggaagatgacgatgttgctgCactgcagcaaaggatcagat																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:48578148C>T	ENST00000503238.1	-	21	2619	c.2620G>A	c.(2620-2622)Gca>Aca	p.A874T	FRYL_ENST00000507711.1_Missense_Mutation_p.A874T|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.A874T|RNU5E-3P_ENST00000515913.1_RNA|FRYL_ENST00000358350.4_Missense_Mutation_p.A874T			O94915	FRYL_HUMAN	FRY-like	874					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GATGTTGCTGCACTGCAGCAA	0.468																																					p.A874T		.											.	FRYL-69	0			c.G2620A						.						122	124	124					4																	48578148		1943	4148	6091	SO:0001583	missense	285527	exon24			TTGCTGCACTGCA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.2620G>A	4.37:g.48578148C>T	ENSP00000426064:p.Ala874Thr	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	97	27	NM_015030	0	0	9	9	0	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.875024	0.51695	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711	T;T;T;T	0.34859	2.35;2.35;2.35;1.34	5.14	5.14	0.70334	.	0.163703	0.41001	U	0.000974	T	0.19685	0.0473	N	0.08118	0	0.80722	D	1	B;B	0.25441	0.043;0.126	B;B	0.24701	0.011;0.055	T	0.09707	-1.0662	10	0.02654	T	1	.	18.6027	0.91255	0.0:1.0:0.0:0.0	.	874;874	F2Z2S2;O94915	.;FRYL_HUMAN	T	874	ENSP00000426064:A874T;ENSP00000351113:A874T;ENSP00000441114:A874T;ENSP00000421584:A874T	ENSP00000351113:A874T	A	-	1	0	FRYL	48272905	1.000000	0.71417	0.894000	0.35097	0.417000	0.31264	4.730000	0.62015	2.370000	0.80446	0.467000	0.42956	GCA	.		0.468	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48578148	C	T	48578148	3	4	112	1	0	0	0	0	1	0	0	0	6083	710	25	2	6585	2	FRYL	4	48578148	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	2	48578148	142576128	26	9848	100	2									
SHROOM3	57619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	77675996	77675996	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcccctgattttgcaaacCtgaagcactatcaaaaacag	15	8	6	12	0	1	2	1	2	0	0	1	2	1	2	3	0	5	2	3	0	5	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:77675996C>A	ENST00000296043.6	+	7	5313	c.4360C>A	c.(4360-4362)Ctg>Atg	p.L1454M	RP11-359D14.2_ENST00000452412.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1454					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TTTTGCAAACCTGAAGCACTA	0.567																																					p.L1454M		.											.	SHROOM3-93	0			c.C4360A						.						52	54	54					4																	77675996		2203	4300	6503	SO:0001583	missense	57619	exon7			GCAAACCTGAAGC	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.4360C>A	4.37:g.77675996C>A	ENSP00000296043:p.Leu1454Met	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	57	21	NM_020859	0	0	13	29	16	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358823	0.24598	.	.	ENSG00000138771	ENST00000296043	T	0.22743	1.94	5.23	5.23	0.72850	.	1.171820	0.06113	N	0.667490	T	0.22820	0.0551	N	0.24115	0.695	0.09310	N	1	D	0.56521	0.976	P	0.47744	0.556	T	0.17837	-1.0356	10	0.33141	T	0.24	-1.3606	12.5341	0.56133	0.0:0.9214:0.0:0.0786	.	1454	Q8TF72	SHRM3_HUMAN	M	1454	ENSP00000296043:L1454M	ENSP00000296043:L1454M	L	+	1	2	SHROOM3	77895020	0.251000	0.23961	0.544000	0.28141	0.006000	0.05464	2.227000	0.42972	2.716000	0.92895	0.655000	0.94253	CTG	.		0.567	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		A	77675996	C	A	77675996	3	1	112	1	0	0	0	0	1	0	0	0	14327	680	24	4	4386	4	SHROOM3	4	77675996	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	29097848	77675996	113478280	27	9849											
SLC39A8	64116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	103225511	103225511	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacattatcaaaatggataTgtccattagcttctgtgaca	13	14	7	7	0	2	2	1	2	1	0	3	3	3	3	1	1	1	1	1	1	5	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:103225511T>C	ENST00000394833.2	-	5	1279	c.803A>G	c.(802-804)cAt>cGt	p.H268R	SLC39A8_ENST00000356736.4_Missense_Mutation_p.H268R|SLC39A8_ENST00000510255.1_5'Flank|SLC39A8_ENST00000424970.2_Missense_Mutation_p.H268R	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	268					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AAAATGGATATGTCCATTAGC	0.363																																					p.H268R		.											.	SLC39A8-90	0			c.A803G						.						158	138	145					4																	103225511		2203	4300	6503	SO:0001583	missense	64116	exon5			TGGATATGTCCAT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.803A>G	4.37:g.103225511T>C	ENSP00000378310:p.His268Arg	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	68	23	NM_022154	0	0	71	149	78	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Missense_Mutation	SNP	ENST00000394833.2	37	CCDS3656.1	.	.	.	.	.	.	.	.	.	.	T	9.588	1.125353	0.20959	.	.	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	T;T;T	0.44881	0.91;0.91;0.91	4.81	4.81	0.61882	.	0.460729	0.18153	U	0.150001	T	0.25938	0.0632	L	0.27053	0.805	0.33924	D	0.641179	B;B;B	0.32350	0.366;0.002;0.016	B;B;B	0.28385	0.089;0.003;0.048	T	0.32640	-0.9899	10	0.16896	T	0.51	-3.0995	9.2864	0.37760	0.1605:0.0:0.0:0.8395	.	268;268;201	B4E2H3;Q9C0K1;Q9C0K1-2	.;S39A8_HUMAN;.	R	268	ENSP00000394548:H268R;ENSP00000349174:H268R;ENSP00000378310:H268R	ENSP00000349174:H268R	H	-	2	0	SLC39A8	103444534	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.339000	0.43965	1.930000	0.55929	0.528000	0.53228	CAT	.		0.363	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		C	103225511	T	C	103225511	3	2	112	1	0	0	0	0	1	0	0	0	14656	1464	51	3	672	3	SLC39A8	4	103225511	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	25549515	103225511	87928765	28	9850											
ACSL1	2180	broad.mit.edu	37	chr4	185686012	185686012	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcctacagccatacctgcgGtccagtctccaggcatggtc	7	9	9	16	1	1	0	0	0	1	0	5	0	3	0	5	3	4	1	5	3	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:185686012G>A	ENST00000515030.1	-	15	1752	c.1427C>T	c.(1426-1428)aCc>aTc	p.T476I	ACSL1_ENST00000513317.1_Missense_Mutation_p.T476I|ACSL1_ENST00000437665.3_Missense_Mutation_p.T305I|ACSL1_ENST00000507295.1_Missense_Mutation_p.T442I|ACSL1_ENST00000454703.2_Missense_Mutation_p.T305I|ACSL1_ENST00000281455.2_Missense_Mutation_p.T476I|ACSL1_ENST00000504342.1_Missense_Mutation_p.T476I			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	476					adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CATACCTGCGGTCCAGTCTCC	0.468																																					p.T476I													.	ACSL1-92	0			c.C1427T						.						60	56	57					4																	185686012		2203	4300	6503	SO:0001583	missense	2180	exon15			CCTGCGGTCCAGT	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"Acyl-CoA synthetase family"	3569	protein-coding gene	gene with protein product	"lignoceroyl-CoA synthase", "long-chain fatty-acid-coenzyme A ligase 1"	152425	"fatty-acid-Coenzyme A ligase, long-chain 2"	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.1427C>T	4.37:g.185686012G>A	ENSP00000422607:p.Thr476Ile	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	33	9	NM_001995	0	0	0	0	0	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Missense_Mutation	SNP	ENST00000515030.1	37	CCDS3839.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252413	0.59212	.	.	ENSG00000151726	ENST00000454703;ENST00000515030;ENST00000503407;ENST00000281455;ENST00000507295;ENST00000437665;ENST00000504342;ENST00000513317	T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.58	5.58	0.84498	AMP-dependent synthetase/ligase (1);	0.130276	0.64402	D	0.000001	T	0.56396	0.1982	M	0.84082	2.675	0.54753	D	0.999987	B;B;B;B	0.21905	0.062;0.023;0.023;0.019	B;B;B;B	0.33042	0.157;0.082;0.05;0.03	T	0.57230	-0.7847	10	0.56958	D	0.05	-15.4726	19.9889	0.97359	0.0:0.0:1.0:0.0	.	442;476;476;476	E7EPM6;B7Z452;P33121;P33121-2	.;.;ACSL1_HUMAN;.	I	305;476;82;476;442;305;476;476	ENSP00000407165:T305I;ENSP00000422607:T476I;ENSP00000425098:T82I;ENSP00000281455:T476I;ENSP00000426244:T442I;ENSP00000405687:T305I;ENSP00000425006:T476I;ENSP00000426150:T476I	ENSP00000281455:T476I	T	-	2	0	ACSL1	185923006	1.000000	0.71417	0.992000	0.48379	0.901000	0.52897	6.556000	0.73932	2.804000	0.96469	0.650000	0.86243	ACC	.		0.468	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995		A	185686012	G	A	185686012	3	1	112	1	0	0	0	0	1	0	0	0	177	1261	44	2	697	2	ACSL1	4	185686012	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	82460501	185686012	5468264	29	9851											
IPO11	51194	ucsc.edu	37	chr5	61897615	61897615	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgttgatgtctcatcttgaGgaaccaaaagtaacagaaga	16	10	9	6	0	2	4	1	2	2	2	3	5	2	5	1	1	2	2	1	1	5	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr5:61897615G>T	ENST00000325324.6	+	29	2872	c.2703G>T	c.(2701-2703)gaG>gaT	p.E901D	IPO11_ENST00000409296.3_Missense_Mutation_p.E941D|IPO11_ENST00000409534.1_Missense_Mutation_p.E20D|IPO11_ENST00000512177.1_3'UTR	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	901					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		CTCATCTTGAGGAACCAAAAG	0.269																																					p.E941D													.	IPO11-227	0			c.G2823T						.						62	60	61					5																	61897615		2203	4298	6501	SO:0001583	missense	51194	exon29			TCTTGAGGAACCA	AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"Importins"	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.2703G>T	5.37:g.61897615G>T	ENSP00000316651:p.Glu901Asp	Somatic	49	0		WXS	Illumina HiSeq		32	5	NM_001134779	0	0	12	12	0	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Missense_Mutation	SNP	ENST00000325324.6	37	CCDS34167.1	.	.	.	.	.	.	.	.	.	.	G	9.497	1.102268	0.20632	.	.	ENSG00000086200	ENST00000325324;ENST00000409296;ENST00000540553;ENST00000409534	T;T;T	0.73469	-0.75;-0.75;0.18	4.92	0.572	0.17357	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	L	0.36672	1.1	0.48901	D	0.999726	P;P	0.48089	0.905;0.846	P;B	0.45276	0.475;0.283	T	0.55289	-0.8164	10	0.13853	T	0.58	.	9.1233	0.36799	0.807:0.0:0.193:0.0	.	941;901	Q9UI26-2;Q9UI26	.;IPO11_HUMAN	D	901;941;471;20	ENSP00000316651:E901D;ENSP00000386992:E941D;ENSP00000387039:E20D	ENSP00000316651:E901D	E	+	3	2	IPO11	61933371	0.986000	0.35501	1.000000	0.80357	0.992000	0.81027	0.142000	0.16096	0.217000	0.20800	-0.136000	0.14681	GAG	.		0.269	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		T	61897615	G	T	61897615	3	4	112	1	0	0	0	0	1	0	0	0	7814	991	35	4	2937	4	IPO11	5	61897615	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08		61897615	119017645	30	9852											
CTNNA1	1495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	138266342	138266342	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagatgacagactttaccCggtgagcagcaccccggccc	9	6	12	14	2	0	4	0	2	0	2	0	5	0	4	4	3	3	2	4	3	1	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr5:138266342C>T	ENST00000302763.7	+	15	2281	c.2191C>T	c.(2191-2193)Cga>Tga	p.R731*	CTNNA1_ENST00000355078.5_Splice_Site_p.R628*|CTNNA1_ENST00000518825.1_Splice_Site_p.R731*|CTNNA1_ENST00000540387.1_Splice_Site_p.R361*	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	731					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)	p.R731R(1)		NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGACTTTACCCGGTGAGCAGC	0.582																																					p.R731X		.											.	CTNNA1-671	1	Substitution - coding silent(1)	lung(1)	c.C2191T						.						134	129	130					5																	138266342		2203	4300	6503	SO:0001630	splice_region_variant	1495	exon15			TTTACCCGGTGAG	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2192+1C>T	5.37:g.138266342C>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	195	75	NM_001903	0	0	0	0	0	Q12795|Q8N1C0	Nonsense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	C	36	5.632988	0.96682	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387;ENST00000520520	.	.	.	5.77	3.89	0.44902	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7916	13.7731	0.63038	0.4172:0.5828:0.0:0.0	.	.	.	.	X	628;731;731;716;731;361;6	.	ENSP00000304669:R731X	R	+	1	2	CTNNA1	138294241	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	4.424000	0.59868	1.565000	0.49641	0.655000	0.94253	CGA	.		0.582	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	Nonsense_Mutation	T	138266342	C	T	138266342	5	4	112	1	0	0	0	0	0	0	1	0	4018	666	23	1	2245	1	CTNNA1	5	138266342	Splice_Site	SNP	C	TCGA-G7-6790-01A-11D-1961-08	76368727	138266342	42648918	31	9853											
FAM71B	153745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156590094	156590094	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagatgaggggtcccacTgctggtccttcagttctttc	5	13	13	10	0	2	2	1	1	1	1	5	3	4	2	2	4	1	2	2	4	0	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr5:156590094T>A	ENST00000302938.4	-	2	1277	c.1182A>T	c.(1180-1182)gcA>gcT	p.A394A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	394						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGGGTCCCACTGCTGGTCCTT	0.552																																					p.A394A		.											.	FAM71B-96	0			c.A1182T						.						62	65	64					5																	156590094		2203	4300	6503	SO:0001819	synonymous_variant	153745	exon2			TCCCACTGCTGGT		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1182A>T	5.37:g.156590094T>A		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	92	36	NM_130899	0	0	0	0	0	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	37	CCDS4335.1																																																																																			.		0.552	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156590094	T	A	156590094	2	1	112	1	0	0	0	0	0	0	0	1	5627	1567	55	5		5	FAM71B	5	156590094	Silent	SNP	T	TCGA-G7-6790-01A-11D-1961-08	18323752	156590094	24325166	32	9854											
BPHL	670	broad.mit.edu;bcgsc.ca	37	chr6	3123907	3123927	+	In_Frame_Del	DEL	GCCAAAGTGGCTGTGAATGGC	GCCAAAGTGGCTGTGAATGGC	-																															ctagcacctcggtaacctctGccaaagtggctgtgaatggc																								rs148622332|rs375917764	byFrequency	TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	GCCAAAGTGGCTGTGAATGGC	GCCAAAGTGGCTGTGAATGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:3123907_3123927delGCCAAAGTGGCTGTGAATGGC	ENST00000380379.5	+	2	173_193	c.124_144delGCCAAAGTGGCTGTGAATGGC	c.(124-144)gccaaagtggctgtgaatggcdel	p.AKVAVNG42del	BPHL_ENST00000380368.2_In_Frame_Del_p.AKVAVNG25del|BPHL_ENST00000380375.3_In_Frame_Del_p.AKVAVNG25del|BPHL_ENST00000434640.1_In_Frame_Del_p.AKVAVNG25del	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	42					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GGTAACCTCTGCCAAAGTGGCTGTGAATGGCGTTCAGCTGC	0.475																																					p.42_48del													.	BPHL-90	0			c.124_144del						.																																			SO:0001651	inframe_deletion	670	exon2			ACCTCTGCCAAAG	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"breast epithelial mucin-associated antigen"	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.124_144delGCCAAAGTGGCTGTGAATGGC	6.37:g.3123907_3123927delGCCAAAGTGGCTGTGAATGGC	ENSP00000369739:p.Ala42_Gly48del	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	112	8	NM_004332	0	0	0	0	0	Q00306|Q13855|Q3KP51	In_Frame_Del	DEL	ENST00000380379.5	37	CCDS4483.2																																																																																			.		0.475	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5			-	3123927	GCCAAAGTGGCTGTGAATGGC	-	3123907	7	5	112	1	0	1	0	1	0	0	0	0	1492	1319	46	0	130	0	BPHL	6	3123907	In_Frame_Del	DEL	GCCAAAGTGGCTGTGAATGGC	TCGA-G7-6790-01A-11D-1961-08		3123907	167991160	33	9855											
HIST1H3A	8350	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	26021008	26021008	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggctctgcaggaggcgtgCgaggcctacttggtagggct	6	9	17	9	2	1	0	0	0	1	0	1	2	1	1	1	6	3	4	1	6	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:26021008C>T	ENST00000357647.3	+	1	291	c.291C>T	c.(289-291)tgC>tgT	p.C97C	HIST1H4A_ENST00000359907.3_5'Flank|HIST1H1A_ENST00000244573.3_5'Flank	NM_003529.2	NP_003520.1	P68431	H31_HUMAN	histone cluster 1, H3a	97					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						AGGAGGCGTGCGAGGCCTACT	0.587																																					p.C97C													.	HIST1H3A-92	0			c.C291T						.						46	47	47					6																	26021008		2203	4300	6503	SO:0001819	synonymous_variant	8350	exon1			GGCGTGCGAGGCC	Z46261	CCDS4570.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000198366	ENSG00000275714		"Histones / Replication-dependent"	4766	protein-coding gene	gene with protein product		602810	"H3 histone family, member A", "histone 1, H3a"	H3FA		9119399, 12408966	Standard	NM_003529		Approved	H3/A	uc003nfp.1	P68431	OTTHUMG00000014418	ENST00000357647.3:c.291C>T	6.37:g.26021008C>T		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	57	14	NM_003529	0	0	0	0	0	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000357647.3	37	CCDS4570.1																																																																																			.		0.587	HIST1H3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040080.1	NM_003529		T	26021008	C	T	26021008	2	4	112	1	0	0	0	0	0	0	0	1	7176	776	27	1		1	HIST1H3A	6	26021008	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	22897101	26021008	145094059	34	9856											
RPL10A	4736	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	35437266	35437267	+	Frame_Shift_Ins	INS	-	-	A																															acatggacatcgaggcgctgINSaaaaaactcaacaagaataa																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:35437266_35437267insA	ENST00000322203.6	+	4	297_298	c.270_271insA	c.(271-273)aaafs	p.K91fs	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	91					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						TCGAGGCGCTGAAAAAACTCAA	0.55																																					p.L90fs		.											.	RPL10A-91	0			c.270_271insA						.																																			SO:0001589	frameshift_variant	4736	exon4			.	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.276dupA	6.37:g.35437272_35437272dupA	ENSP00000363018:p.Lys91fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	44	12	NM_007104	0	0	0	0	0	B2R801|P52859|P53025|Q5TZT6|Q8J013	Frame_Shift_Ins	INS	ENST00000322203.6	37	CCDS4806.1																																																																																			.		0.55	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		A	35437267	-	A	35437266	7	5	112	1	0	1	1	0	0	0	0	0	13587	1277	45	0	284	0	RPL10A	6	35437266	Frame_Shift_Ins	INS	-	TCGA-G7-6790-01A-11D-1961-08	9416258	35437266	135677801	35	9857											
FTSJD2	23070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	37442389	37442389	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgccccgggacactctgctAtctgtggaaattgtgcatga	8	11	11	11	1	2	1	0	1	2	0	2	3	2	3	2	2	3	2	2	2	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:37442389A>G	ENST00000373451.4	+	18	2075	c.1911A>G	c.(1909-1911)ctA>ctG	p.L637L		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	637					7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										ACACTCTGCTATCTGTGGAAA	0.572																																					p.L637L		.											.	FTSJD2-94	0			c.A1911G						.						105	100	102					6																	37442389		2203	4300	6503	SO:0001819	synonymous_variant	23070	exon18			TCTGCTATCTGTG	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"G patch domain containing"	21077	protein-coding gene	gene with protein product			"KIAA0082", "FtsJ methyltransferase domain containing 2"	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.1911A>G	6.37:g.37442389A>G		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	101	31	NM_015050	0	0	18	37	19	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	37	CCDS4835.1																																																																																			.		0.572	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		G	37442389	A	G	37442389	2	3	112	1	0	0	0	0	0	0	0	1	6110	436	16	3		3	FTSJD2	6	37442389	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	2005123	37442389	133672678	36	9858											
ADCY1	107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	45747951	45747951	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatctgtttacacctaggcTaagaagtccatctcctccca	10	11	5	15	0	2	1	0	0	2	1	5	1	4	1	5	1	1	2	5	1	4	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr7:45747951T>C	ENST00000297323.7	+	18	2842	c.2820T>C	c.(2818-2820)gcT>gcC	p.A940A		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	940			A -> T (in dbSNP:rs45444695).		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ACACCTAGGCTAAGAAGTCCA	0.522																																					p.A940A		.											.	ADCY1-95	0			c.T2820C						.						179	135	150					7																	45747951		2203	4300	6503	SO:0001819	synonymous_variant	107	exon18			CTAGGCTAAGAAG	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"Adenylate cyclases"	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2820T>C	7.37:g.45747951T>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	104	56	NM_021116	0	0	0	0	0	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																			.		0.522	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		C	45747951	T	C	45747951	2	2	112	1	0	0	0	0	0	0	0	1	292	1509	53	3		3	ADCY1	7	45747951	Silent	SNP	T	TCGA-G7-6790-01A-11D-1961-08		45747951	113390712	37	9859											
MLL5	55904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	104717426	104717426	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagggttcagctccagagaTtgatccttcatctgatggtt	8	15	10	8	0	3	3	2	2	1	1	5	4	5	3	2	2	1	3	2	2	1	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr7:104717426T>G	ENST00000311117.3	+	10	1330	c.785T>G	c.(784-786)aTt>aGt	p.I262S	KMT2E_ENST00000257745.4_Missense_Mutation_p.I262S|KMT2E_ENST00000476671.1_Missense_Mutation_p.I262S|KMT2E_ENST00000334914.7_De_novo_Start_InFrame|KMT2E_ENST00000334877.4_Missense_Mutation_p.I262S	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	262					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										GCTCCAGAGATTGATCCTTCA	0.418																																					p.I262S		.											.	MLL5-93	0			c.T785G						.						89	88	88					7																	104717426		2203	4300	6503	SO:0001583	missense	55904	exon9			CAGAGATTGATCC	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.785T>G	7.37:g.104717426T>G	ENSP00000312379:p.Ile262Ser	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	59	25	NM_018682	0	0	5	13	8	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.456010	0.26161	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95482	-2.85;-2.47;-2.85;-3.72;-3.22	6.07	4.92	0.64577	.	0.471220	0.25735	N	0.028644	D	0.92639	0.7661	L	0.44542	1.39	0.80722	D	1	D;B	0.54207	0.965;0.372	P;B	0.46758	0.526;0.083	D	0.89734	0.3928	10	0.08837	T	0.75	.	12.0897	0.53719	0.0:0.0668:0.0:0.9332	.	262;262	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	S	262;262;262;262;262;120;262;196	ENSP00000312379:I262S;ENSP00000335599:I262S;ENSP00000257745:I262S;ENSP00000419883:I120S;ENSP00000417888:I262S	ENSP00000257745:I262S	I	+	2	0	MLL5	104504662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.809000	0.38922	1.114000	0.41781	0.533000	0.62120	ATT	.		0.418	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104717426	T	G	104717426	3	3	112	1	0	0	0	0	1	0	0	0	9649	1493	52	5	815	5	MLL5	7	104717426	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	58969475	104717426	54421237	38	9860											
COL14A1	7373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	121237425	121237425	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctatgatgaaggacagtcAgagcctctgactggagtttt	11	12	11	7	0	3	4	1	3	2	1	3	6	3	6	1	2	1	1	1	2	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr8:121237425A>T	ENST00000297848.3	+	15	2106	c.1836A>T	c.(1834-1836)tcA>tcT	p.S612S	COL14A1_ENST00000247781.3_Silent_p.S517S|COL14A1_ENST00000537875.1_3'UTR|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.S612S	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			AAGGACAGTCAGAGCCTCTGA	0.418																																					p.S612S		.											.	COL14A1-543	0			c.A1836T						.						76	75	76					8																	121237425		2203	4300	6503	SO:0001819	synonymous_variant	7373	exon15			ACAGTCAGAGCCT		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1836A>T	8.37:g.121237425A>T		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	78	20	NM_021110	0	0	0	0	0		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																			.		0.418	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121237425	A	T	121237425	2	4	112	1	0	0	0	0	0	0	0	1	3677	175	7	5		5	COL14A1	8	121237425	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08		121237425	25126597	39	9861											
WDYHV1	55093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	124448833	124448833	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgatgacattcacccacaGtttaggaggtgaggacattc	12	10	11	8	0	1	3	1	3	0	0	2	6	1	5	1	3	0	1	1	3	1	4	rs201436036		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr8:124448833G>T	ENST00000287387.2	+	4	500	c.375G>T	c.(373-375)caG>caT	p.Q125H	WDYHV1_ENST00000523984.1_Missense_Mutation_p.Q65H|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000518125.1_Intron|WDYHV1_ENST00000523356.1_Missense_Mutation_p.Q125H	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	125					cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						TTCACCCACAGTTTAGGAGGT	0.358																																					p.Q125H		.											.	WDYHV1-92	0			c.G375T						.						179	152	161					8																	124448833		2203	4300	6503	SO:0001583	missense	55093	exon4			CCCACAGTTTAGG	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 32"	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.375G>T	8.37:g.124448833G>T	ENSP00000287387:p.Gln125His	Somatic	93	1		WXS	Illumina HiSeq	Phase_I	78	24	NM_018024	0	0	0	0	0	B4DE68|Q9NW95	Missense_Mutation	SNP	ENST00000287387.2	37	CCDS6344.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242859	0.58995	.	.	ENSG00000156795	ENST00000287387;ENST00000523984;ENST00000523356	T;T;T	0.17854	2.25;2.25;2.25	5.78	4.72	0.59763	Protein N-terminal glutamine amidohydrolase, alpha beta roll (1);Protein N-terminal glutamine amidohydrolase (1);	0.467670	0.22279	N	0.062144	T	0.17323	0.0416	L	0.39245	1.2	0.80722	D	1	P	0.46952	0.887	P	0.47118	0.538	T	0.00484	-1.1712	10	0.62326	D	0.03	-11.18	6.1363	0.20235	0.1332:0.0:0.6856:0.1812	.	125	Q96HA8	NTAQ1_HUMAN	H	125;65;125	ENSP00000287387:Q125H;ENSP00000430427:Q65H;ENSP00000428615:Q125H	ENSP00000287387:Q125H	Q	+	3	2	WDYHV1	124518014	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	1.216000	0.32443	2.724000	0.93272	0.655000	0.94253	CAG	G|0.999;A|0.000		0.358	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024		T	124448833	G	T	124448833	3	4	112	1	0	0	0	0	1	0	0	0	17376	1020	36	4	389	4	WDYHV1	8	124448833	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	3211408	124448833	21915189	40	9862											
WASH1	0	hgsc.bcm.edu	37	chr9	17011	17011	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtggaaggtgggcagttcTggaatggtgccaggggcaga	8	8	20	5	0	1	1	0	0	1	1	1	3	1	3	1	7	1	3	1	7	2	1	rs201297177	byFrequency	TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:17011T>C								None (None upstream) : MIR1302-2 (10645 downstream)																							TGGGCAGTTCTGGAATGGTGC	0.642																																					p.P279P		.											.	.	0			c.A837G						.						5	8	7					9																	17011		767	1848	2615	SO:0001628	intergenic_variant	100287171	exon7			CAGTTCTGGAATG																													9.37:g.17011T>C		Somatic	33	2		WXS	Illumina HiSeq	Phase_I	24	5	NM_182905	0	0	41	98	57		Silent	SNP		37																																																																																				.	0	0.642									C	17011	T	C	17011	1	2	112	0	1	0	0	0	0	0	0	0	17288	1567	55	3		3	WASH1	9	17011	IGR	SNP	T	TCGA-G7-6790-01A-11D-1961-08		17011	141196420	41	9863											
CNTLN	54875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	17332674	17332674	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gactcagaagagctacagaaGctgagaaaagctgaaagaaa	20	4	11	6	0	1	6	1	2	0	5	1	8	1	6	0	0	4	3	0	0	7	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:17332674G>A	ENST00000380647.3	+	10	1674	c.1590G>A	c.(1588-1590)aaG>aaA	p.K530K	CNTLN_ENST00000262360.5_Silent_p.K530K|CNTLN_ENST00000425824.1_Silent_p.K530K			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	530					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		AGCTACAGAAGCTGAGAAAAG	0.378																																					p.K530K		.											.	CNTLN-91	0			c.G1590A						.						74	70	71					9																	17332674		1836	4082	5918	SO:0001819	synonymous_variant	54875	exon10			ACAGAAGCTGAGA	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"chromosome 9 open reading frame 101", "chromosome 9 open reading frame 39"	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.1590G>A	9.37:g.17332674G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	71	17	NM_017738	0	0	3	3	0	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	37	CCDS43789.1																																																																																			.		0.378	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17332674	G	A	17332674	2	1	112	1	0	0	0	0	0	0	0	1	3645	962	34	2		2	CNTLN	9	17332674	Silent	SNP	G	TCGA-G7-6790-01A-11D-1961-08	17315663	17332674	123880757	42	9864											
ACO1	48	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	32448942	32448942	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgagcgcattcaccgcagtAacctggttgggatgggtgtg	8	9	15	9	3	1	0	1	0	0	0	1	2	1	1	2	3	2	4	2	3	1	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:32448942A>T	ENST00000309951.6	+	20	2557	c.2419A>T	c.(2419-2421)Aac>Tac	p.N807Y	ACO1_ENST00000379923.1_Missense_Mutation_p.N807Y|ACO1_ENST00000541043.1_Missense_Mutation_p.N708Y	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	807					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TCACCGCAGTAACCTGGTTGG	0.478																																					p.N807Y		.											.	ACO1-226	0			c.A2419T						.						131	111	117					9																	32448942		2203	4300	6503	SO:0001583	missense	48	exon20			CGCAGTAACCTGG	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"aconitate hydratase, cytoplasmic"	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.2419A>T	9.37:g.32448942A>T	ENSP00000309477:p.Asn807Tyr	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	74	29	NM_002197	0	0	52	89	37	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	37	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.351925	0.82132	.	.	ENSG00000122729	ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.61392	0.11;0.11;1.13	5.83	5.83	0.93111	Aconitase/3-isopropylmalate dehydratase, swivel (2);Aconitase A/isopropylmalate dehydratase small subunit, swivel (1);	0.000000	0.85682	D	0.000000	D	0.86711	0.5998	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92343	0.5883	10	0.87932	D	0	-31.6045	15.1831	0.72975	1.0:0.0:0.0:0.0	.	807	P21399	ACOC_HUMAN	Y	807;807;708	ENSP00000309477:N807Y;ENSP00000369255:N807Y;ENSP00000438733:N708Y	ENSP00000309477:N807Y	N	+	1	0	ACO1	32438942	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.996000	0.63914	2.227000	0.72691	0.528000	0.53228	AAC	.		0.478	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		T	32448942	A	T	32448942	3	4	112	1	0	0	0	0	1	0	0	0	146	362	13	5	2493	5	ACO1	9	32448942	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	15116268	32448942	108764489	43	9865											
HNRNPK	3190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	86585225	86585225	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaatccgctgaccaccttTgccaataatagatccagcca	12	11	5	13	1	0	2	0	1	0	1	2	2	2	2	6	0	2	1	6	0	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:86585225T>A	ENST00000376264.2	-	16	1471	c.1213A>T	c.(1213-1215)Aaa>Taa	p.K405*	HNRNPK_ENST00000351839.3_Nonsense_Mutation_p.K405*|MIR7-1_ENST00000384871.1_RNA|HNRNPK_ENST00000360384.5_Nonsense_Mutation_p.K405*|HNRNPK_ENST00000376281.4_Nonsense_Mutation_p.K405*|HNRNPK_ENST00000376263.3_Nonsense_Mutation_p.K405*|RP11-575L7.8_ENST00000448389.1_RNA	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	405	2 X 22 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|single-stranded DNA binding (GO:0003697)			endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						TGACCACCTTTGCCAATAATA	0.368																																					p.K405X		.											.	HNRNPK-227	0			c.A1213T						.						60	58	59					9																	86585225		2203	4300	6503	SO:0001587	stop_gained	3190	exon16			CACCTTTGCCAAT		CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"transformation upregulated nuclear protein"	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.1213A>T	9.37:g.86585225T>A	ENSP00000365440:p.Lys405*	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	71	24	NM_031262	0	0	423	431	8	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Nonsense_Mutation	SNP	ENST00000376264.2	37	CCDS6667.1	.	.	.	.	.	.	.	.	.	.	T	38	7.091735	0.98059	.	.	ENSG00000165119	ENST00000376281;ENST00000376264;ENST00000376263;ENST00000376268;ENST00000351839;ENST00000435158;ENST00000360384;ENST00000376258	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1915	15.5864	0.76485	0.0:0.0:0.0:1.0	.	.	.	.	X	405;405;405;405;405;370;405;400	.	ENSP00000317788:K405X	K	-	1	0	HNRNPK	85775045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.510000	0.81708	2.142000	0.66516	0.482000	0.46254	AAA	.		0.368	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2			A	86585225	T	A	86585225	4	1	112	1	0	0	0	0	0	1	0	0	7290	1821	63	5	224	5	HNRNPK	9	86585225	Nonsense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	54136283	86585225	54628206	44	9866											
SPTLC1	10558	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	94877626	94877626	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgtaccatctccaccagAacccactgctccgtggcggt	7	8	9	17	2	1	1	0	0	1	1	3	1	2	1	6	2	3	2	6	2	2	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:94877626A>T	ENST00000262554.2	-	1	32	c.27T>A	c.(25-27)gtT>gtA	p.V9V	SPTLC1_ENST00000482632.1_5'UTR|SPTLC1_ENST00000337841.4_Silent_p.V9V	NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	9					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	TCTCCACCAGAACCCACTGCT	0.652																																					p.V9V													.	SPTLC1-154	0			c.T27A						.						33	36	35					9																	94877626		2197	4292	6489	SO:0001819	synonymous_variant	10558	exon1			CACCAGAACCCAC	Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	"hereditary sensory neuropathy, type 1"	HSN1		9363775	Standard	NM_006415		Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.27T>A	9.37:g.94877626A>T		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	78	13	NM_006415	0	0	24	49	25	A8K681|Q5VWB4|Q96IX6	Silent	SNP	ENST00000262554.2	37	CCDS6692.1																																																																																			.		0.652	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	NM_006415		T	94877626	A	T	94877626	2	4	112	1	0	0	0	0	0	0	0	1	15155	233	9	5		5	SPTLC1	9	94877626	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	8292401	94877626	46335805	45	9867											
ADAMTS13	11093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	136305491	136305491	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcggagggcgctatgtcGtggctgggaagatgagcatc	8	8	18	7	3	0	2	0	1	0	1	3	5	0	5	0	5	1	3	0	5	2	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:136305491G>C	ENST00000371929.3	+	16	2257	c.1813G>C	c.(1813-1815)Gtg>Ctg	p.V605L	ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.V574L|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.V605L|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.V277L|ADAMTS13_ENST00000485925.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	605	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GCGCTATGTCGTGGCTGGGAA	0.627																																					p.V605L		.											.	ADAMTS13-229	0			c.G1813C						.						139	98	112					9																	136305491		2203	4300	6503	SO:0001583	missense	11093	exon16			TATGTCGTGGCTG	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"ADAM metallopeptidases with thrombospondin type 1 motif"	1366	protein-coding gene	gene with protein product		604134	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1813G>C	9.37:g.136305491G>C	ENSP00000360997:p.Val605Leu	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	77	27	NM_139027	0	0	3	5	2	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663418	0.47572	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.62788	0.04;0.0;0.06;0.49	5.21	4.31	0.51392	.	.	.	.	.	T	0.61912	0.2385	N	0.25825	0.765	0.41780	D	0.989816	D;D;D;D	0.89917	1.0;1.0;1.0;0.992	D;D;D;P	0.91635	0.997;0.999;0.99;0.742	T	0.59241	-0.7491	9	0.02654	T	1	.	12.261	0.54651	0.0833:0.0:0.9167:0.0	.	605;574;605;277	Q76LX8;Q76LX8-3;Q76LX8-2;Q9UGQ1	ATS13_HUMAN;.;.;.	L	605;605;574;277	ENSP00000360997:V605L;ENSP00000347927:V605L;ENSP00000348997:V574L;ENSP00000444504:V277L	ENSP00000347927:V605L	V	+	1	0	ADAMTS13	135295312	1.000000	0.71417	0.300000	0.25030	0.035000	0.12851	5.003000	0.63959	1.191000	0.43056	0.561000	0.74099	GTG	.		0.627	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		C	136305491	G	C	136305491	3	2	112	1	0	0	0	0	1	0	0	0	258	1145	40	4	1875	4	ADAMTS13	9	136305491	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	41427865	136305491	4907940	46	9868											
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	64968980	64968980	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggtgggctgatgtagccAaggactgggagaattctatt	10	10	16	5	0	1	2	0	1	1	1	1	4	1	3	1	5	1	2	1	5	4	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr10:64968980A>T	ENST00000399262.2	-	9	2928	c.2710T>A	c.(2710-2712)Tgg>Agg	p.W904R	JMJD1C_ENST00000399251.1_Missense_Mutation_p.W685R|JMJD1C_ENST00000402544.1_Missense_Mutation_p.W685R|JMJD1C_ENST00000542921.1_Missense_Mutation_p.W722R	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	904					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TGATGTAGCCAAGGACTGGGA	0.433																																					p.W904R		.											.	JMJD1C-275	0			c.T2710A						.						65	59	61					10																	64968980		1882	4108	5990	SO:0001583	missense	221037	exon9			GTAGCCAAGGACT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.2710T>A	10.37:g.64968980A>T	ENSP00000382204:p.Trp904Arg	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	46	19	NM_032776	0	0	5	10	5	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480118	0.84747	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.77624	0.4158	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79105	-0.1940	10	0.66056	D	0.02	-4.4645	16.5655	0.84588	1.0:0.0:0.0:0.0	.	904;722	Q15652;A0T124	JHD2C_HUMAN;.	R	904;685;685;722	ENSP00000382204:W904R;ENSP00000384990:W685R;ENSP00000382195:W685R;ENSP00000444682:W722R	ENSP00000382195:W685R	W	-	1	0	JMJD1C	64638986	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.372000	0.90127	2.302000	0.77476	0.533000	0.62120	TGG	.		0.433	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		T	64968980	A	T	64968980	3	4	112	1	0	0	0	0	1	0	0	0	7971	130	5	5	4984	5	JMJD1C	10	64968980	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		64968980	70565767	47	9869											
DBX1	120237	bcgsc.ca	37	chr11	20177947	20177947	+	Frame_Shift_Del	DEL	G	G	-																															ggcggtggctggggctgcccGggccctcctcctcctcttcg																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr11:20177947delG	ENST00000524983.2	-	4	1133	c.845delC	c.(844-846)ccgfs	p.P282fs	DBX1_ENST00000227256.3_Frame_Shift_Del_p.P321fs			A6NMT0	DBX1_HUMAN	developing brain homeobox 1	282					regulation of transcription from RNA polymerase II promoter (GO:0006357)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)	21						GGGGCTGCCCGGGCCCTCCTC	0.751																																					p.P282fs													.	DBX1-91	0			c.845delC						.						8	11	10					11																	20177947		2164	4209	6373	SO:0001589	frameshift_variant	120237	exon4			CTGCCCGGGCCCT			11p15.1	2011-06-20				ENSG00000109851		"Homeoboxes / ANTP class : NKL subclass"	33185	protein-coding gene	gene with protein product						11239429	Standard	NM_001029865		Approved		uc021qey.1	A6NMT0		ENST00000524983.2:c.845delC	11.37:g.20177947delG	ENSP00000436881:p.Pro282fs	Somatic	31	0		WXS	Illumina HiSeq	Phase_1	16	6	NM_001029865	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000524983.2	37																																																																																				.		0.751	DBX1-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387585.2	NM_001029865		-	20177947	G	-	20177947	7	5	112	1	0	1	0	1	0	0	0	0	4265	1116	39	0	190	0	DBX1	11	20177947	Frame_Shift_Del	DEL	G	TCGA-G7-6790-01A-11D-1961-08		20177947	114828569	48	9870											
LRRC4C	57689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	40136275	40136275	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgattttggtagtcttcAtgacctcatcaattcctggg	8	16	9	8	0	4	3	3	3	1	0	5	3	5	3	2	2	0	1	2	2	2	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr11:40136275A>C	ENST00000278198.2	-	2	3531	c.1568T>G	c.(1567-1569)aTg>aGg	p.M523R	LRRC4C_ENST00000528697.1_Missense_Mutation_p.M523R|LRRC4C_ENST00000530763.1_Missense_Mutation_p.M523R|LRRC4C_ENST00000527150.1_Missense_Mutation_p.M523R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	523					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				GGTAGTCTTCATGACCTCATC	0.478																																					p.M523R		.											.	LRRC4C-521	0			c.T1568G						.						174	145	155					11																	40136275		2203	4300	6503	SO:0001583	missense	57689	exon7			GTCTTCATGACCT	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"Immunoglobulin superfamily / I-set domain containing"	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1568T>G	11.37:g.40136275A>C	ENSP00000278198:p.Met523Arg	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	109	29	NM_001258419	0	0	0	0	0	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813848	0.50527	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.38887	1.11;1.11;1.11;1.11	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.63319	0.2501	M	0.69358	2.11	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.65940	-0.6046	10	0.72032	D	0.01	.	15.6754	0.77316	1.0:0.0:0.0:0.0	.	523	Q9HCJ2	LRC4C_HUMAN	R	523	ENSP00000278198:M523R;ENSP00000436976:M523R;ENSP00000437132:M523R;ENSP00000434761:M523R	ENSP00000278198:M523R	M	-	2	0	LRRC4C	40092851	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	ATG	.		0.478	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		C	40136275	A	C	40136275	3	2	112	1	0	0	0	0	1	0	0	0	9033	217	8	5	358	5	LRRC4C	11	40136275	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	19958328	40136275	94870241	49	9871											
ACCS	84680	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	44105011	44105011	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgaggaggaaatgctgcTctggcgccgctttttggaca	7	12	13	9	2	1	1	0	1	1	0	1	4	1	4	1	4	2	3	1	4	1	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr11:44105011T>C	ENST00000263776.8	+	14	1726	c.1292T>C	c.(1291-1293)cTc>cCc	p.L431P		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	431					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						GAAATGCTGCTCTGGCGCCGC	0.567																																					p.L431P	Esophageal Squamous(158;148 1889 8077 23160 41213)	.											.	ACCS-155	0			c.T1292C						.						71	65	67					11																	44105011		2203	4300	6503	SO:0001583	missense	84680	exon14			TGCTGCTCTGGCG	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.1292T>C	11.37:g.44105011T>C	ENSP00000263776:p.Leu431Pro	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	68	13	NM_032592	0	0	17	33	16	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.025435	0.54683	.	.	ENSG00000110455	ENST00000263776	D	0.93488	-3.23	5.91	5.91	0.95273	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.073130	0.56097	D	0.000026	D	0.97942	0.9323	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99297	1.0900	10	0.87932	D	0	-19.4821	16.0098	0.80391	0.0:0.0:0.0:1.0	.	431	Q96QU6	1A1L1_HUMAN	P	431	ENSP00000263776:L431P	ENSP00000263776:L431P	L	+	2	0	ACCS	44061587	0.997000	0.39634	0.041000	0.18516	0.142000	0.21351	7.315000	0.78998	2.254000	0.74563	0.533000	0.62120	CTC	.		0.567	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		C	44105011	T	C	44105011	3	2	112	1	0	0	0	0	1	0	0	0	133	1551	54	3	1342	3	ACCS	11	44105011	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	3968736	44105011	90901505	50	9872											
AHNAK	79026	broad.mit.edu	37	chr11	62288080	62288080	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgcccttcacctttggaccTttcagattcaggtcaacttc	7	14	6	14	1	4	1	4	0	0	1	6	2	4	2	3	2	1	0	3	2	1	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr11:62288080T>G	ENST00000378024.4	-	5	14083	c.13809A>C	c.(13807-13809)aaA>aaC	p.K4603N	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4603					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CCTTTGGACCTTTCAGATTCA	0.507																																					p.K4603N													.	AHNAK-109	0			c.A13809C						.						103	102	103					11																	62288080		2202	4299	6501	SO:0001583	missense	79026	exon5			TGGACCTTTCAGA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.13809A>C	11.37:g.62288080T>G	ENSP00000367263:p.Lys4603Asn	Somatic	183	1		WXS	Illumina HiSeq	Phase_I	185	5	NM_001620	0	0	172	172	0	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	12.46	1.945631	0.34377	.	.	ENSG00000124942	ENST00000378024	T	0.01665	4.7	5.43	-4.89	0.03103	.	0.190348	0.43579	D	0.000541	T	0.11281	0.0275	H	0.95187	3.635	0.30066	N	0.8105	D	0.69078	0.997	D	0.79784	0.993	T	0.03728	-1.1009	10	0.20046	T	0.44	.	15.082	0.72122	0.0:0.3027:0.0:0.6973	.	4603	Q09666	AHNK_HUMAN	N	4603	ENSP00000367263:K4603N	ENSP00000367263:K4603N	K	-	3	2	AHNAK	62044656	0.003000	0.15002	0.838000	0.33150	0.111000	0.19643	-1.791000	0.01758	-0.699000	0.05077	-0.276000	0.10085	AAA	.		0.507	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		G	62288080	T	G	62288080	3	3	112	1	0	0	0	0	1	0	0	0	414	1606	56	5	3983	5	AHNAK	11	62288080	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	18183069	62288080	72718436	51	9873											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49434235	49434235	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggactggaagcgaggggtaaCgggtgatgggcaaaaagctt	12	6	18	5	2	0	1	0	1	0	0	0	4	0	3	0	6	3	3	0	6	4	2	rs375114492		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr12:49434235C>T	ENST00000301067.7	-	31	7317	c.7318G>A	c.(7318-7320)Gtt>Att	p.V2440I		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2440	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CGAGGGGTAACGGGTGATGGG	0.622																																					p.V2440I		.											.	MLL2-612	0			c.G7318A						.	C	ILE/VAL	1,4177		0,1,2088	40	46	44		7318	5.2	0.8	12		44	0,8456		0,0,4228	no	missense	MLL2	NM_003482.3	29	0,1,6316	TT,TC,CC		0.0,0.0239,0.0079	probably-damaging	2440/5538	49434235	1,12633	2089	4228	6317	SO:0001583	missense	8085	exon31			GGGTAACGGGTGA	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.7318G>A	12.37:g.49434235C>T	ENSP00000301067:p.Val2440Ile	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	101	35	NM_003482	0	0	3	3	0	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.924285	0.34002	2.39E-4	0.0	ENSG00000167548	ENST00000301067	T	0.80033	-1.33	5.21	5.21	0.72293	.	0.000000	0.34002	N	0.004349	T	0.77136	0.4086	L	0.36672	1.1	0.26063	N	0.981323	D	0.57899	0.981	P	0.44772	0.46	T	0.74553	-0.3627	10	0.87932	D	0	.	17.9117	0.88936	0.0:1.0:0.0:0.0	.	2440	O14686	MLL2_HUMAN	I	2440	ENSP00000301067:V2440I	ENSP00000301067:V2440I	V	-	1	0	MLL2	47720502	0.544000	0.26441	0.785000	0.31869	0.974000	0.67602	3.934000	0.56553	2.596000	0.87737	0.591000	0.81541	GTT	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49434235	C	T	49434235	3	4	112	1	0	0	0	0	1	0	0	0	9646	536	19	1	9391	1	MLL2	12	49434235	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08		49434235	84417660	52	9874											
RDH5	5959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56115126	56115126	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctggaccagagaggctTccgagtcctggccagctgcc	7	6	14	14	1	0	1	0	0	0	1	2	4	2	2	5	3	3	4	5	3	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr12:56115126T>C	ENST00000257895.5	+	2	310	c.158T>C	c.(157-159)tTc>tCc	p.F53S	RDH5_ENST00000547072.1_5'UTR|RP11-644F5.10_ENST00000550412.1_Intron|RP11-644F5.10_ENST00000549424.1_Intron|RDH5_ENST00000553160.1_Intron|RDH5_ENST00000548082.1_Missense_Mutation_p.F53S	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	53					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	CAGAGAGGCTTCCGAGTCCTG	0.662											OREG0021907	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F53S		.											.	RDH5-91	0			c.T158C						.						37	40	39					12																	56115126		2202	4299	6501	SO:0001583	missense	5959	exon2			GAGGCTTCCGAGT	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	9940	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 5"	601617	"retinol dehydrogenase 5 (11-cis and 9-cis)"	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.158T>C	12.37:g.56115126T>C	ENSP00000257895:p.Phe53Ser	Somatic	120	1	1013	WXS	Illumina HiSeq	Phase_I	102	29	NM_001199771	0	0	25	45	20	O00179|Q8TAI2	Missense_Mutation	SNP	ENST00000257895.5	37	CCDS31829.1	.	.	.	.	.	.	.	.	.	.	T	16.32	3.091465	0.55968	.	.	ENSG00000135437	ENST00000257895;ENST00000548082	D;D	0.93019	-3.15;-3.15	5.11	3.88	0.44766	NAD(P)-binding domain (1);	0.095258	0.64402	D	0.000001	D	0.95636	0.8581	M	0.74881	2.28	0.58432	D	0.999993	D	0.76494	0.999	D	0.76575	0.988	D	0.95464	0.8545	10	0.87932	D	0	.	10.0549	0.42239	0.0:0.0:0.1688:0.8312	.	53	Q92781	RDH1_HUMAN	S	53	ENSP00000257895:F53S;ENSP00000447128:F53S	ENSP00000257895:F53S	F	+	2	0	RDH5	54401393	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	4.981000	0.63819	2.062000	0.61559	0.533000	0.62120	TTC	.		0.662	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905		C	56115126	T	C	56115126	3	2	112	1	0	0	0	0	1	0	0	0	13227	1783	62	3	160	3	RDH5	12	56115126	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	6680891	56115126	77736769	53	9875											
AGAP2	100130776	broad.mit.edu;bcgsc.ca	37	chr12	58120789	58120789	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcgtgatgacgacgtgggCgagctcggccgccaggtgga	6	7	18	10	6	0	2	0	2	0	0	1	5	0	3	2	4	2	1	2	4	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr12:58120789C>T	ENST00000542466.2	+	2	150	c.14C>T	c.(13-15)gCg>gTg	p.A5V	AGAP2_ENST00000547588.1_Missense_Mutation_p.A1102T|RP11-571M6.8_ENST00000548410.2_RNA|AGAP2_ENST00000257897.3_Missense_Mutation_p.A746T					AGAP2 antisense RNA 1																		ACGACGTGGGCGAGCTCGGCC	0.647											OREG0021951	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A1102T													.	AGAP2-716	0			c.G3304A						.						18	20	19					12																	58120789		2202	4300	6502	SO:0001583	missense	116986	exon18			CGTGGGCGAGCTC	BC039697, BC069024		12q14.1	2013-05-30			ENSG00000255737	ENSG00000255737		"Long non-coding RNAs"	48633	non-coding RNA	RNA, long non-coding							Standard	NR_027032		Approved				OTTHUMG00000170286	ENST00000542466.2:c.14C>T	12.37:g.58120789C>T	ENSP00000437523:p.Ala5Val	Somatic	25	0	1028	WXS	Illumina HiSeq	Phase_I	21	6	NM_001122772	0	0	1	4	3		Missense_Mutation	SNP	ENST00000542466.2	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	17.61|17.61|17.61	3.432070|3.432070|3.432070	0.62844|0.62844|0.62844	.|.|.	.|.|.	ENSG00000135439|ENSG00000255737|ENSG00000135439	ENST00000257897;ENST00000547588|ENST00000542466|ENST00000328568	T;T|.|.	0.64260|.|.	-0.09;-0.09|.|.	4.62|4.62|4.62	3.72|3.72|3.72	0.42706|0.42706|0.42706	Ankyrin repeat-containing domain (3);|.|.	0.192175|0.192175|.	0.43110|0.43110|.	D|D|.	0.000610|0.000610|.	T|T|T	0.42675|0.42675|0.42675	0.1213|0.1213|0.1213	L|L|L	0.33668|0.33668|0.33668	1.02|1.02|1.02	0.31617|0.31617|0.31617	N|N|N	0.650763|0.650763|0.650763	D;D;D|D|.	0.63880|0.65815|.	0.989;0.98;0.993|0.995|.	P;P;P|P|.	0.51055|0.49637|.	0.651;0.525;0.657|0.617|.	T|T|T	0.48352|0.48352|0.48352	-0.9043|-0.9043|-0.9043	10|9|5	0.87932|0.87932|.	D|D|.	0|0|.	.|.|.	11.8047|11.8047|11.8047	0.52147|0.52147|0.52147	0.317:0.683:0.0:0.0|0.317:0.683:0.0:0.0|0.317:0.683:0.0:0.0	.|.|.	746;1102;1102|5|.	Q99490-2;F8VVT9;Q99490|B7Z718|.	.;.;AGAP2_HUMAN|.|.	T|V|H	746;1102|5|945	ENSP00000257897:A746T;ENSP00000449241:A1102T|.|.	ENSP00000257897:A746T|ENSP00000437523:A5V|.	A|A|R	-|+|-	1|2|2	0|0|0	AGAP2|RP11-571M6.6|AGAP2	56407056|56407056|56407056	0.926000|0.926000|0.926000	0.31397|0.31397|0.31397	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.948000|0.948000|0.948000	0.59901|0.59901|0.59901	1.941000|1.941000|1.941000	0.40233|0.40233|0.40233	1.047000|1.047000|1.047000	0.40274|0.40274|0.40274	0.455000|0.455000|0.455000	0.32223|0.32223|0.32223	GCC|GCG|CGC	.		0.647	AGAP2-AS1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000408368.1			T	58120789	C	T	58120789	3	4	112	1	0	0	0	0	1	0	0	0	368	768	27	1	282	1	AGAP2	12	58120789	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	2005663	58120789	75731106	54	9876											
HNF1A	6927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	121437343	121437343	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcttcacacgccggcatctCaggccaccaccctccacgtc	7	6	8	20	3	2	0	2	0	1	0	5	0	3	0	5	3	0	2	5	3	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr12:121437343C>T	ENST00000257555.6	+	9	1907	c.1681C>T	c.(1681-1683)Cag>Tag	p.Q561*	HNF1A_ENST00000544413.1_Nonsense_Mutation_p.Q568*|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000541395.1_Nonsense_Mutation_p.Q592*			P20823	HNF1A_HUMAN	HNF1 homeobox A	561					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GCCGGCATCTCAGGCCACCAC	0.701									Hepatic Adenoma, Familial Clustering of																												p.Q561X		.											.	HNF1A-1745	0			c.C1681T	GRCh37	CM056410	HNF1A	M		.						28	28	28					12																	121437343		2201	4300	6501	SO:0001587	stop_gained	6927	exon9	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GCATCTCAGGCCA	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1681C>T	12.37:g.121437343C>T	ENSP00000257555:p.Gln561*	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_000545	0	0	46	57	11	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Nonsense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	C	37	6.366855	0.97511	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000544413	.	.	.	5.8	5.8	0.92144	.	0.246461	0.28754	N	0.014249	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-4.9172	17.2189	0.86952	0.0:1.0:0.0:0.0	.	.	.	.	X	561;453;561;382;592;568	.	ENSP00000257555:Q561X	Q	+	1	0	HNF1A	119921726	0.929000	0.31497	0.953000	0.39169	0.944000	0.59088	3.336000	0.52113	2.741000	0.93983	0.650000	0.86243	CAG	.		0.701	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121437343	C	T	121437343	4	4	112	1	0	0	0	0	0	1	0	0	7272	827	29	2	1715	2	HNF1A	12	121437343	Nonsense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	63316554	121437343	12414552	55	9877											
HMGB1	3146	broad.mit.edu	37	chr13	31035512	31035512	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttattcatcatcatcatcTtcttcttcatcttcatcttc	8	20	0	13	0	11	0	6	0	5	0	12	0	11	0	0	0	0	0	0	0	1	7	rs200836895	byFrequency	TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:31035512T>A	ENST00000405805.1	-	5	1570	c.630A>T	c.(628-630)gaA>gaT	p.E210D	HMGB1_ENST00000399494.1_Missense_Mutation_p.E210D|HMGB1_ENST00000341423.5_Missense_Mutation_p.E210D|HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000399489.1_3'UTR|HMGB1_ENST00000339872.4_Missense_Mutation_p.E210D			P09429	HMGB1_HUMAN	high mobility group box 1	210	Asp/Glu-rich (acidic).				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CATCAtcatcttcttcttcat	0.378													T|||	6	0.00119808	0.003	0	5008	,	,		18295	0		0	False		,,,				2504	0.002				p.E210D													.	HMGB1-227	0			c.A630T						.						20	25	23					13																	31035512		1894	4135	6029	SO:0001583	missense	3146	exon5			ATCATCTTCTTCT	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.630A>T	13.37:g.31035512T>A	ENSP00000384678:p.Glu210Asp	Somatic	58	1		WXS	Illumina HiSeq	Phase_I	63	4	NM_002128	1	0	549	550	0	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Missense_Mutation	SNP	ENST00000405805.1	37	CCDS9335.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.336740	0.41398	.	.	ENSG00000189403	ENST00000405805;ENST00000339872;ENST00000341423;ENST00000399494	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.68	-1.58	0.08479	Armadillo-like helical (1);	0.305542	0.22770	N	0.055856	T	0.33440	0.0863	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.02901	-1.1096	10	0.87932	D	0	.	4.5078	0.11896	0.474:0.2443:0.0:0.2817	.	171;210	B3KQ05;P09429	.;HMGB1_HUMAN	D	210	ENSP00000384678:E210D;ENSP00000343040:E210D;ENSP00000345347:E210D;ENSP00000382417:E210D	ENSP00000343040:E210D	E	-	3	2	HMGB1	29933512	0.999000	0.42202	0.997000	0.53966	0.995000	0.86356	0.152000	0.16302	-0.149000	0.11215	-0.276000	0.10085	GAA	T|0.500;A|0.500		0.378	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		A	31035512	T	A	31035512	3	1	112	1	0	0	0	0	1	0	0	0	7246	1606	56	5	21	5	HMGB1	13	31035512	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08		31035512	84134366	56	9878											
EPSTI1	94240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	43463356	43463357	+	Intron	DNP	CT	CT	TA																															aagtgacccaccttaggtgcCtcgaaaaaactaatagagaa																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:43463356_43463357CT>TA	ENST00000398762.3	-	12	948				EPSTI1_ENST00000313624.7_Intron|EPSTI1_ENST00000313640.7_Nonsense_Mutation_p.R324*			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)											endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		CCTTAGGTGCCTCGAAAAAACT	0.292																																					p.R324*		.											.	EPSTI1	0			c.A970T						.																																			SO:0001627	intron_variant	94240	exon12			GGTGCCTCGAAAA	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"epithelial stromal interaction protein 1"	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814	ENST00000398762.3:c.949_949delinsTA	13.37:g.43463356_43463357delinsTA		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	27	16		0	0	0	0	0	Q8IVC7|Q8NDQ7	Nonsense_Mutation	DNP	ENST00000398762.3	37	CCDS9387.1																																																																																			.		0.292	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		TA	43463357	CT	TA	43463356	1	4	112	0	1	0	0	0	0	0	0	0	5211	681	24	2		2	EPSTI1	13	43463356	Intron	DNP	CT	TCGA-G7-6790-01A-11D-1961-08	12427844	43463356	71706522	57	9879											
CCDC70	83446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	52439743	52439743	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactttccgaggcaagatcCatgctttccggggccagatc	8	9	12	12	2	0	2	0	0	0	2	4	4	3	3	4	4	1	2	4	4	1	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:52439743C>T	ENST00000242819.4	+	2	525	c.229C>T	c.(229-231)Cat>Tat	p.H77Y		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	77						extracellular region (GO:0005576)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		AGGCAAGATCCATGCTTTCCG	0.463																																					p.H77Y		.											.	CCDC70-90	0			c.C229T						.						58	65	62					13																	52439743		2203	4300	6503	SO:0001583	missense	83446	exon2			AAGATCCATGCTT		CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.229C>T	13.37:g.52439743C>T	ENSP00000242819:p.His77Tyr	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	127	59	NM_031290	0	0	0	0	0	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	37	CCDS9431.1	.	.	.	.	.	.	.	.	.	.	C	4.558	0.103562	0.08731	.	.	ENSG00000123171	ENST00000242819	T	0.20463	2.07	5.19	-0.626	0.11544	.	0.950993	0.08647	N	0.914676	T	0.13670	0.0331	N	0.22421	0.69	0.09310	N	1	B	0.18013	0.025	B	0.21708	0.036	T	0.35674	-0.9779	10	0.62326	D	0.03	-14.9052	6.1269	0.20184	0.4441:0.3965:0.0:0.1594	.	77	Q6NSX1	CCD70_HUMAN	Y	77	ENSP00000242819:H77Y	ENSP00000242819:H77Y	H	+	1	0	CCDC70	51337744	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.815000	0.04481	-0.051000	0.13334	-0.311000	0.09066	CAT	.		0.463	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290		T	52439743	C	T	52439743	3	4	112	1	0	0	0	0	1	0	0	0	2849	594	21	2	231	2	CCDC70	13	52439743	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	8976387	52439743	62730135	58	9880											
PCDH8	5100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	53418949	53418949	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtgacgtgctcttacagaAggttgacatctgggctggtg	8	11	14	8	1	2	3	0	2	2	1	2	3	2	3	0	3	2	3	0	3	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:53418949A>T	ENST00000377942.3	-	3	3162	c.2959T>A	c.(2959-2961)Ttc>Atc	p.F987I	PCDH8_ENST00000338862.4_Missense_Mutation_p.F890I	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	987					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CTCTTACAGAAGGTTGACATC	0.602																																					p.F987I	GBM(36;25 841 9273 49207)	.											.	PCDH8-153	0			c.T2959A						.						163	95	118					13																	53418949		2203	4300	6503	SO:0001583	missense	5100	exon3			TACAGAAGGTTGA	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.2959T>A	13.37:g.53418949A>T	ENSP00000367177:p.Phe987Ile	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	112	48	NM_002590	0	0	0	0	0	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	37	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.419256	0.62622	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.56444	0.46;0.47	5.95	5.95	0.96441	.	0.000000	0.46442	D	0.000291	T	0.62816	0.2459	L	0.34521	1.04	0.52501	D	0.999954	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	T	0.59731	-0.7399	10	0.31617	T	0.26	.	16.4069	0.83677	1.0:0.0:0.0:0.0	.	890;987	O95206-2;O95206	.;PCDH8_HUMAN	I	987;890;513;830	ENSP00000367177:F987I;ENSP00000341350:F890I	ENSP00000341350:F890I	F	-	1	0	PCDH8	52316950	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.730000	0.91510	2.272000	0.75746	0.460000	0.39030	TTC	.		0.602	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53418949	A	T	53418949	3	4	112	1	0	0	0	0	1	0	0	0	11543	72	3	5	257	5	PCDH8	13	53418949	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	979206	53418949	61750929	59	9881											
KTN1	3895	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	56107681	56107681	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacatgaattggagaagatgCaacaaaggtgactaaagtat	18	8	10	5	0	0	4	0	2	0	2	0	5	0	4	0	2	2	2	0	2	7	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr14:56107681C>T	ENST00000395314.3	+	16	2082	c.2014C>T	c.(2014-2016)Caa>Taa	p.Q672*	KTN1_ENST00000416613.1_Nonsense_Mutation_p.Q672*|KTN1_ENST00000395308.1_Nonsense_Mutation_p.Q672*|KTN1_ENST00000438792.2_Nonsense_Mutation_p.Q672*|KTN1_ENST00000395309.3_Nonsense_Mutation_p.Q672*|KTN1_ENST00000395311.1_Nonsense_Mutation_p.Q672*|KTN1_ENST00000413890.2_Nonsense_Mutation_p.Q672*	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	672					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						GGAGAAGATGCAACAAAGGTG	0.338			T	RET	papillary thryoid																																p.Q672X				Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1-1147	0			c.C2014T						.						72	65	68					14																	56107681		2203	4298	6501	SO:0001587	stop_gained	3895	exon16			AAGATGCAACAAA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.2014C>T	14.37:g.56107681C>T	ENSP00000378725:p.Gln672*	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	55	17	NM_004986	0	0	0	0	0	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Nonsense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	C	39	7.766813	0.98477	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	.	.	.	4.87	4.87	0.63330	.	0.125962	0.35495	N	0.003163	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.3869	12.113	0.53850	0.0:0.9168:0.0:0.0832	.	.	.	.	X	672	.	ENSP00000378719:Q672X	Q	+	1	0	KTN1	55177434	1.000000	0.71417	0.932000	0.37286	0.677000	0.39632	2.235000	0.43044	2.400000	0.81607	0.591000	0.81541	CAA	.		0.338	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			T	56107681	C	T	56107681	4	4	112	1	0	0	0	0	0	1	0	0	8606	711	25	2	2072	2	KTN1	14	56107681	Nonsense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08		56107681	51241859	60	9882											
ITGA11	22801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	68631978	68631978	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgacggctcccagcagaaccCcatcctggcattggggaggg	8	5	14	14	2	0	1	0	0	0	1	2	3	2	2	4	5	2	3	4	5	1	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr15:68631978C>G	ENST00000315757.7	-	11	1222	c.1136G>C	c.(1135-1137)gGg>gCg	p.G379A	ITGA11_ENST00000423218.2_Missense_Mutation_p.G379A	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	379					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)	p.G379V(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CAGCAGAACCCCATCCTGGCA	0.597																																					p.G379A		.											.	ITGA11-538	1	Substitution - Missense(1)	kidney(1)	c.G1136C						.						61	65	63					15																	68631978		2028	4187	6215	SO:0001583	missense	22801	exon11			AGAACCCCATCCT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"Integrins"	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1136G>C	15.37:g.68631978C>G	ENSP00000327290:p.Gly379Ala	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	84	19	NM_001004439	0	0	0	0	0	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049868	0.75846	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491;ENST00000537153	T;T	0.77750	-1.12;-1.12	5.09	5.09	0.68999	.	0.141219	0.64402	D	0.000005	D	0.86690	0.5993	M	0.84511	2.7	0.54753	D	0.999988	D;D	0.59357	0.985;0.984	P;P	0.55871	0.786;0.736	D	0.87055	0.2149	10	0.38643	T	0.18	.	17.5593	0.87901	0.0:1.0:0.0:0.0	.	379;379	A8K8T0;Q9UKX5	.;ITA11_HUMAN	A	379;379;14;379	ENSP00000327290:G379A;ENSP00000403392:G379A	ENSP00000327290:G379A	G	-	2	0	ITGA11	66419032	1.000000	0.71417	0.983000	0.44433	0.842000	0.47809	7.818000	0.86416	2.391000	0.81399	0.555000	0.69702	GGG	.		0.597	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		G	68631978	C	G	68631978	3	3	112	1	0	0	0	0	1	0	0	0	7895	623	22	4	2510	4	ITGA11	15	68631978	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08		68631978	33899414	61	9883											
SCAPER	49855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	76673781	76673781	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtaaactctgaatggccaCttggatggtattttgagtgt	10	14	11	6	1	1	2	0	2	1	0	1	3	1	3	1	3	1	2	1	3	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr15:76673781C>T	ENST00000563290.1	-	28	3738	c.3643G>A	c.(3643-3645)Gtg>Atg	p.V1215M	SCAPER_ENST00000324767.7_Missense_Mutation_p.V1215M|SCAPER_ENST00000538941.2_Missense_Mutation_p.V969M			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1215						endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						TGAATGGCCACTTGGATGGTA	0.443																																					p.V1215M		.											.	SCAPER-137	0			c.G3643A						.						92	88	89					15																	76673781		1939	4133	6072	SO:0001583	missense	49855	exon27			TGGCCACTTGGAT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"Zinc fingers, C2H2-type"	13081	protein-coding gene	gene with protein product		611611	"zinc finger protein 291"	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.3643G>A	15.37:g.76673781C>T	ENSP00000454973:p.Val1215Met	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	50	11	NM_020843	0	0	10	15	5	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.481299	0.63849	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.32023	1.5;1.47	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	M	0.67953	2.075	0.51767	D	0.999932	D;D	0.65815	0.975;0.995	P;D	0.67231	0.793;0.95	T	0.53599	-0.8416	10	0.87932	D	0	.	15.5231	0.75881	0.0:0.8625:0.1375:0.0	.	1214;969	Q9BY12;F5H7X8	SCAPE_HUMAN;.	M	1215;969;1237	ENSP00000326924:V1215M;ENSP00000442190:V969M	ENSP00000303560:V1237M	V	-	1	0	SCAPER	74460836	1.000000	0.71417	0.920000	0.36463	0.589000	0.36550	5.651000	0.67951	2.740000	0.93945	0.650000	0.86243	GTG	.		0.443	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	76673781	C	T	76673781	3	4	112	1	0	0	0	0	1	0	0	0	13910	565	20	2	579	2	SCAPER	15	76673781	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	8041803	76673781	25857611	62	9884											
XYLT1	64131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	17252766	17252766	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gccaccaactggtcatttgtCctgtggaaacaaaccaaggg	12	8	10	11	0	1	0	1	0	0	0	2	1	2	1	4	3	3	0	4	3	4	1	rs369970325		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr16:17252766C>G	ENST00000261381.6	-	6	1374	c.1290G>C	c.(1288-1290)agG>agC	p.R430S		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	430					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGTCATTTGTCCTGTGGAAAC	0.498																																					p.R430S		.											.	XYLT1-94	0			c.G1290C						.						82	76	78					16																	17252766		2197	4300	6497	SO:0001630	splice_region_variant	64131	exon6			ATTTGTCCTGTGG	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	15516	protein-coding gene	gene with protein product	"protein xylosyltransferase 1"	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.1290-1G>C	16.37:g.17252766C>G		Somatic	85	1		WXS	Illumina HiSeq	Phase_I	121	65	NM_022166	0	0	0	0	0	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.902489	0.72754	.	.	ENSG00000103489	ENST00000261381	T	0.11495	2.77	4.9	3.93	0.45458	.	0.000000	0.85682	D	0.000000	T	0.32793	0.0841	M	0.82056	2.57	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.07404	-1.0774	10	0.72032	D	0.01	.	11.9464	0.52930	0.0:0.8562:0.0:0.1438	.	430	Q86Y38	XYLT1_HUMAN	S	430	ENSP00000261381:R430S	ENSP00000261381:R430S	R	-	3	2	XYLT1	17160267	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.638000	0.46562	2.398000	0.81561	0.563000	0.77884	AGG	.		0.498	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	Missense_Mutation	G	17252766	C	G	17252766	5	3	112	1	0	0	0	0	0	0	1	0	17496	869	30	4	1617	4	XYLT1	16	17252766	Splice_Site	SNP	C	TCGA-G7-6790-01A-11D-1961-08		17252766	73101987	63	9885											
DCUN1D3	123879	broad.mit.edu	37	chr16	20871518	20871518	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagggcaatggctatttccCgatgcagtgaccgctgccct	8	9	11	13	2	0	1	0	1	0	0	1	2	1	1	3	2	2	4	3	2	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr16:20871518C>A	ENST00000324344.4	-	3	890	c.605G>T	c.(604-606)cGg>cTg	p.R202L	DCUN1D3_ENST00000563934.1_Missense_Mutation_p.R202L|ERI2_ENST00000564349.1_Intron	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	202	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.				negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		GGCTATTTCCCGATGCAGTGA	0.478																																					p.R202L													.	DCUN1D3-92	0			c.G605T						.						166	169	168					16																	20871518		2201	4300	6501	SO:0001583	missense	123879	exon3			ATTTCCCGATGCA	BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.605G>T	16.37:g.20871518C>A	ENSP00000319482:p.Arg202Leu	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	371	7	NM_173475	0	0	11	11	0	B3KVY4	Missense_Mutation	SNP	ENST00000324344.4	37	CCDS10592.1	.	.	.	.	.	.	.	.	.	.	C	10.29	1.310323	0.23821	.	.	ENSG00000188215	ENST00000324344	.	.	.	6.08	6.08	0.98989	Domain of unknown function DUF298 (2);	0.000000	0.85682	D	0.000000	T	0.20333	0.0489	N	0.00329	-1.635	0.80722	D	1	B	0.27791	0.189	B	0.26969	0.075	T	0.48647	-0.9017	9	0.02654	T	1	-21.6441	20.6634	0.99662	0.0:1.0:0.0:0.0	.	202	Q8IWE4	DCNL3_HUMAN	L	202	.	ENSP00000319482:R202L	R	-	2	0	DCUN1D3	20779019	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.760000	0.85248	2.894000	0.99253	0.655000	0.94253	CGG	.		0.478	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475		A	20871518	C	A	20871518	3	1	112	1	0	0	0	0	1	0	0	0	4321	652	23	4	313	4	DCUN1D3	16	20871518	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	3618752	20871518	69483235	64	9886											
MYH13	8735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10227379	10227379	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccttttcaactttcgtcAaggtcagctccaggtcatca	8	14	6	13	1	6	0	5	0	1	0	9	0	7	0	2	2	2	1	2	2	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:10227379A>T	ENST00000418404.3	-	22	3057	c.2894T>A	c.(2893-2895)tTg>tAg	p.L965*	MYH13_ENST00000252172.4_Nonsense_Mutation_p.L965*|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	965					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						AACTTTCGTCAAGGTCAGCTC	0.463																																					p.L965X		.											.	MYH13-6	0			c.T2894A						.						106	105	106					17																	10227379		2195	4300	6495	SO:0001587	stop_gained	8735	exon23			TTCGTCAAGGTCA	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"Myosins / Myosin superfamily : Class II"	7571	protein-coding gene	gene with protein product	"extraocular muscle myosin heavy chain", "extraocular myosin heavy chain"	603487	"myosin, heavy polypeptide 13, skeletal muscle"			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2894T>A	17.37:g.10227379A>T	ENSP00000404570:p.Leu965*	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	105	68	NM_003802	0	0	0	0	0	O95252|Q9P0U8	Nonsense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	A	42	9.641822	0.99227	.	.	ENSG00000006788	ENST00000252172;ENST00000418404	.	.	.	4.37	4.37	0.52481	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0394	0.64665	1.0:0.0:0.0:0.0	.	.	.	.	X	965;591	.	ENSP00000252172:L965X	L	-	2	0	MYH13	10168104	1.000000	0.71417	0.965000	0.40720	0.705000	0.40729	8.981000	0.93465	1.950000	0.56595	0.533000	0.62120	TTG	.		0.463	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		T	10227379	A	T	10227379	4	4	112	1	0	0	0	0	0	1	0	0	10057	131	5	5	2998	5	MYH13	17	10227379	Nonsense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		10227379	70967831	65	9887											
MYH8	4626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10309460	10309460	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttcatctctcatttctTccagaagacccagaagtcca	11	14	4	12	0	4	3	2	0	2	3	7	3	6	3	3	0	0	0	3	0	2	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:10309460T>C	ENST00000403437.2	-	21	2424	c.2330A>G	c.(2329-2331)gAa>gGa	p.E777G	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	777	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TCTCATTTCTTCCAGAAGACC	0.413									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.E777G		.											.	MYH8-101	0			c.A2330G						.						113	108	110					17																	10309460		2203	4300	6503	SO:0001583	missense	4626	exon21	Familial Cancer Database	Carney Complex Variant	ATTTCTTCCAGAA		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.2330A>G	17.37:g.10309460T>C	ENSP00000384330:p.Glu777Gly	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	101	54	NM_002472	0	0	0	0	0	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512766	0.85389	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.75260	-0.92	5.22	5.22	0.72569	Myosin head, motor domain (1);	0.000000	0.42420	U	0.000719	D	0.92182	0.7521	H	0.99415	4.555	0.58432	D	0.999999	D	0.71674	0.998	D	0.74674	0.984	D	0.95289	0.8393	10	0.66056	D	0.02	.	15.2675	0.73672	0.0:0.0:0.0:1.0	.	777	P13535	MYH8_HUMAN	G	777	ENSP00000384330:E777G	ENSP00000252173:E777G	E	-	2	0	MYH8	10250185	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.825000	0.86693	2.205000	0.71048	0.528000	0.53228	GAA	.		0.413	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		C	10309460	T	C	10309460	3	2	112	1	0	0	0	0	1	0	0	0	10066	1783	62	3	3563	3	MYH8	17	10309460	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	82081	10309460	70885750	66	9888											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y	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	265	268					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	346	54		WXS	Illumina HiSeq		573	78	NM_145301	0	0	15	109	94	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		T	15457087	C	T	15457087	3	4	112	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	5147627	15457087	65738123	67	9889											
NLK	51701	broad.mit.edu;bcgsc.ca	37	chr17	26459690	26459690	+	Frame_Shift_Del	DEL	T	T	-																															caacctccacacattgactaTtttgaagaaatgtatcctaa																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:26459690delT	ENST00000407008.3	+	3	1351	c.633delT	c.(631-633)tatfs	p.Y211fs		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for interaction with TAB2. {ECO:0000250}.|Sufficient for interaction with DAPK3.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		ACATTGACTATTTTGAAGAAA	0.353																																					p.Y211fs													.	NLK-1403	0			c.633delT						.						54	49	51					17																	26459690		2203	4300	6503	SO:0001589	frameshift_variant	51701	exon3			TGACTATTTTGAA	AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"nemo like kinase"			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.633delT	17.37:g.26459690delT	ENSP00000384625:p.Tyr211fs	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	37	9	NM_016231	0	0	0	0	0	B2RCX1|Q2PNI9|Q6P2A3	Frame_Shift_Del	DEL	ENST00000407008.3	37	CCDS11224.2																																																																																			.		0.353	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231		-	26459690	T	-	26459690	7	5	112	1	0	1	0	1	0	0	0	0	10492	1500	52	0	643	0	NLK	17	26459690	Frame_Shift_Del	DEL	T	TCGA-G7-6790-01A-11D-1961-08	11002603	26459690	54735520	68	9890											
STAC2	342667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37368584	37368584	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgactggcaccaggccccgCttcttgccactgctgacgcg	5	8	11	17	4	1	1	0	1	1	0	2	2	1	1	4	2	2	3	4	2	0	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:37368584C>T	ENST00000333461.5	-	11	1566	c.1197G>A	c.(1195-1197)aaG>aaA	p.K399K		NM_198993.3	NP_945344.1	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	399					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			NS(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(2)	17						CCAGGCCCCGCTTCTTGCCAC	0.622																																					p.K399K		.											.	STAC2-91	0			c.G1197A						.						58	52	54					17																	37368584		2203	4300	6503	SO:0001819	synonymous_variant	342667	exon11			GCCCCGCTTCTTG	AJ608762	CCDS11335.1	17q21.2	2012-11-19			ENSG00000141750	ENSG00000141750			23990	protein-coding gene	gene with protein product							Standard	NM_198993		Approved	24b2	uc002hrs.3	Q6ZMT1	OTTHUMG00000179039	ENST00000333461.5:c.1197G>A	17.37:g.37368584C>T		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	60	14	NM_198993	0	0	1	1	0	Q32MA3	Silent	SNP	ENST00000333461.5	37	CCDS11335.1																																																																																			.		0.622	STAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444533.2	NM_198993		T	37368584	C	T	37368584	2	4	112	1	0	0	0	0	0	0	0	1	15272	796	28	2		2	STAC2	17	37368584	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	10908894	37368584	43826626	69	9891											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73750000	73750000	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcccccggacgacggcggCgcgggcgggaagggcggcag	5	0	23	13	8	0	0	0	0	0	0	0	3	0	2	2	8	0	1	2	8	1	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:73750000C>G	ENST00000200181.3	+	33	4450	c.4263C>G	c.(4261-4263)ggC>ggG	p.G1421G	GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Intron|ITGB4_ENST00000579662.1_Intron|ITGB4_ENST00000449880.2_Intron|ITGB4_ENST00000339591.3_Intron	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1421				HGPPDDGGAGGKGGSL -> TAPRTTAARAGRAAAV (in Ref. 3; CAA37656). {ECO:0000305}.	amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACGACGGCGGCGCGGGCGGGA	0.811																																					p.G1421G		.											.	ITGB4-227	0			c.C4263G						.						1	1	1					17																	73750000		306	673	979	SO:0001819	synonymous_variant	3691	exon33			CGGCGGCGCGGGC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"CD molecules", "Integrins", "Fibronectin type III domain containing"	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4263C>G	17.37:g.73750000C>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_000213	0	0	0	0	0	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																			.		0.811	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			G	73750000	C	G	73750000	2	3	112	1	0	0	0	0	0	0	0	1	7918	755	27	4		4	ITGB4	17	73750000	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	36381416	73750000	7445210	70	9892											
C19orf21	126353	broad.mit.edu	37	chr19	757398	757398	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgtcatccagggccaggCagtcaggaagagcagcaccg	10	3	15	13	2	2	1	2	0	0	1	3	2	3	2	4	4	2	3	4	4	1	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:757398C>A	ENST00000215582.6	+	2	555	c.452C>A	c.(451-453)gCa>gAa	p.A151E		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	151					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CAGGGCCAGGCAGTCAGGAAG	0.687																																					p.A151E													.	C19orf21-91	0			c.C452A						.						33	33	33					19																	757398		2195	4295	6490	SO:0001583	missense	126353	exon2			GCCAGGCAGTCAG	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"mitotic interactor and substrate of Plk1"	615289	"chromosome 19 open reading frame 21"	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.452C>A	19.37:g.757398C>A	ENSP00000215582:p.Ala151Glu	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	18	7	NM_173481	0	0	28	42	14		Missense_Mutation	SNP	ENST00000215582.6	37	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914658	0.52546	.	.	ENSG00000099812	ENST00000215582	T	0.72167	-0.63	4.5	-0.245	0.13027	.	0.782626	0.11427	N	0.565152	T	0.75027	0.3794	M	0.62723	1.935	0.09310	N	0.999994	D	0.69078	0.997	D	0.63793	0.918	T	0.61564	-0.7037	10	0.62326	D	0.03	-21.0524	3.6537	0.08213	0.0:0.4294:0.1998:0.3708	.	151	Q8IVT2	CS021_HUMAN	E	151	ENSP00000215582:A151E	ENSP00000215582:A151E	A	+	2	0	C19orf21	708398	0.000000	0.05858	0.315000	0.25238	0.640000	0.38277	-0.256000	0.08757	0.308000	0.22923	0.313000	0.20887	GCA	.		0.687	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	757398	C	A	757398	3	1	112	1	0	0	0	0	1	0	0	0	1919	710	25	4	454	4	C19orf21	19	757398	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08		757398	58371585	71	9893											
CAPS	8498	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	5914495	5914495	+	IGR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctcgggcatccagggcctGgccaggtgagctgtcccctc	4	7	14	16	1	0	1	0	1	0	0	4	1	2	1	6	4	1	2	6	4	0	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:5914495G>T	ENST00000340578.6	-	0	3233				AC104532.2_ENST00000588891.1_3'UTR|CAPS_ENST00000452990.2_Silent_p.L26L|AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000222125.5_Silent_p.L26L|CAPS_ENST00000588776.1_Silent_p.L112L	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						TCCAGGGCCTGGCCAGGTGAG	0.667																																					p.L26L		.											.	CAPS-90	0			c.G78T						.						38	42	41					19																	5914495		2203	4300	6503	SO:0001628	intergenic_variant	828	exon2			GGGCCTGGCCAGG	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5914495G>T		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	57	22	NM_080590	0	0	0	0	0	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Silent	SNP	ENST00000340578.6	37	CCDS42478.1																																																																																			.		0.667	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		T	5914495	G	T	5914495	1	4	112	0	1	0	0	0	0	0	0	0	2643	1335	47	4		4	CAPS	19	5914495	IGR	SNP	G	TCGA-G7-6790-01A-11D-1961-08	5157097	5914495	53214488	72	9894											
C3	718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6709834	6709834	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggctgccggtcttctgacTggccgctttttaccaccagc	5	11	10	15	2	2	1	0	1	2	0	2	1	2	1	4	3	3	2	4	3	1	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:6709834T>G	ENST00000245907.6	-	14	1798	c.1706A>C	c.(1705-1707)cAg>cCg	p.Q569P		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	569					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GTCTTCTGACTGGCCGCTTTT	0.637																																					p.Q569P		.											.	C3-95	0			c.A1706C						.						51	52	52					19																	6709834		2203	4300	6503	SO:0001583	missense	718	exon14			TCTGACTGGCCGC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"Complement system", "Endogenous ligands"	1318	protein-coding gene	gene with protein product	"C3a anaphylatoxin", "complement component C3a", "complement component C3b", "prepro-C3"	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1706A>C	19.37:g.6709834T>G	ENSP00000245907:p.Gln569Pro	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	72	18	NM_000064	0	0	6	176	170	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	T	7.093	0.572475	0.13623	.	.	ENSG00000125730	ENST00000245907	T	0.60548	0.18	5.15	-4.43	0.03568	Alpha-2-macroglobulin, N-terminal 2 (1);	1.754940	0.02473	N	0.087708	T	0.26991	0.0661	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09143	-1.0688	10	0.15066	T	0.55	.	2.5674	0.04786	0.1135:0.1705:0.2356:0.4803	.	569	P01024	CO3_HUMAN	P	569	ENSP00000245907:Q569P	ENSP00000245907:Q569P	Q	-	2	0	C3	6660834	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.671000	0.01954	-0.737000	0.04824	-0.382000	0.06688	CAG	.		0.637	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		G	6709834	T	G	6709834	3	3	112	1	0	0	0	0	1	0	0	0	2210	1580	55	5	3397	5	C3	19	6709834	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	795339	6709834	52419149	73	9895											
FCER2	2208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7755293	7755293	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagagccccagcccaccTgctcctccgggctgtggatg	5	7	12	17	1	0	1	0	0	0	1	2	2	2	2	6	2	4	3	6	2	0	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:7755293T>A	ENST00000346664.5	-	9	832	c.620A>T	c.(619-621)cAg>cTg	p.Q207L	FCER2_ENST00000597921.1_Splice_Site_p.Q207L|FCER2_ENST00000360067.4_Splice_Site_p.Q206L	NM_001220500.1|NM_002002.4	NP_001207429.1|NP_001993.2	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor for (CD23)	207	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				Notch signaling pathway (GO:0007219)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10						CCAGCCCACCTGCTCCTCCGG	0.667																																					p.Q207L		.											.	FCER2-130	0			c.A620T						.						43	46	45					19																	7755293		2203	4300	6503	SO:0001630	splice_region_variant	2208	exon9			CCCACCTGCTCCT	M15059	CCDS12184.1	19p13.3	2011-08-30	2006-03-09			ENSG00000104921		"C-type lectin domain containing", "CD molecules"	3612	protein-coding gene	gene with protein product		151445	"Fc fragment of IgE, low affinity II, receptor for (CD23A)"	CD23A, FCE2			Standard	NM_002002		Approved	CLEC4J, CD23	uc002mhm.2	P06734		ENST00000346664.5:c.621+1A>T	19.37:g.7755293T>A		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	92	27	NM_002002	0	0	0	0	0		Missense_Mutation	SNP	ENST00000346664.5	37	CCDS12184.1	.	.	.	.	.	.	.	.	.	.	t	14.83	2.652954	0.47362	.	.	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.16457	2.34;2.34	4.61	4.61	0.57282	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.33477	U	0.004865	T	0.37652	0.1011	M	0.66378	2.025	0.36695	D	0.879773	D	0.76494	0.999	D	0.87578	0.998	T	0.46843	-0.9162	10	0.87932	D	0	.	10.4446	0.44486	0.0:0.0:0.0:1.0	.	207	P06734	FCER2_HUMAN	L	207;206	ENSP00000264072:Q207L;ENSP00000353178:Q206L	ENSP00000264072:Q207L	Q	-	2	0	FCER2	7661293	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	3.912000	0.56386	1.733000	0.51620	0.382000	0.24955	CAG	.		0.667	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	Missense_Mutation	A	7755293	T	A	7755293	5	1	112	1	0	0	0	0	0	0	1	0	5795	1594	55	5	357	5	FCER2	19	7755293	Splice_Site	SNP	T	TCGA-G7-6790-01A-11D-1961-08	1045459	7755293	51373690	74	9896											
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11113781	11113781	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gagtgggaagatcctcacagGcacagatgcccccaaagccg	12	4	12	13	1	1	2	1	0	0	2	2	4	2	3	4	2	2	1	4	2	2	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:11113781G>C	ENST00000429416.3	+	13	2170	c.1889G>C	c.(1888-1890)gGc>gCc	p.G630A	SMARCA4_ENST00000444061.3_Missense_Mutation_p.G630A|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G630A|SMARCA4_ENST00000450717.3_Missense_Mutation_p.G630A|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G630A|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G630A|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G630A|SMARCA4_ENST00000589677.1_Missense_Mutation_p.G630A|SMARCA4_ENST00000541122.2_Missense_Mutation_p.G630A	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	630					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				ATCCTCACAGGCACAGATGCC	0.597			"F, N, Mis"		NSCLC																																p.G630A		.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.G1889C						.						77	79	78					19																	11113781		2203	4300	6503	SO:0001583	missense	6597	exon12			TCACAGGCACAGA	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.1889G>C	19.37:g.11113781G>C	ENSP00000395654:p.Gly630Ala	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	111	28	NM_003072	0	0	19	45	26	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862182	0.91511	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83	4.57	4.57	0.56435	BRK domain (2);	0.000000	0.85682	D	0.000000	T	0.79805	0.4509	L	0.58510	1.815	0.80722	D	1	P;P;P;P;D;P;P	0.54772	0.857;0.932;0.932;0.853;0.968;0.868;0.868	P;P;P;P;P;P;P	0.53760	0.597;0.708;0.708;0.734;0.699;0.708;0.708	T	0.82386	-0.0483	10	0.66056	D	0.02	-36.4878	16.6596	0.85238	0.0:0.0:1.0:0.0	.	630;630;630;630;630;630;630	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	A	630;630;694;630;630;630;630;630	ENSP00000395654:G630A;ENSP00000350720:G630A;ENSP00000343896:G630A;ENSP00000445036:G630A;ENSP00000392837:G630A;ENSP00000397783:G630A;ENSP00000414727:G630A	ENSP00000343896:G630A	G	+	2	0	SMARCA4	10974781	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.601000	0.98297	2.526000	0.85167	0.563000	0.77884	GGC	.		0.597	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11113781	G	C	11113781	3	2	112	1	0	0	0	0	1	0	0	0	14802	1203	42	4	1931	4	SMARCA4	19	11113781	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	3358488	11113781	48015202	75	9897											
KIAA0892	23383	broad.mit.edu;bcgsc.ca	37	chr19	19431865	19431865	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccgcagcgcatcgaggcccGtacacacctgcagctgggct	7	5	13	16	4	0	0	0	0	0	0	1	1	0	0	3	2	4	6	3	2	1	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:19431865G>T	ENST00000392313.6	+	1	376	c.197G>T	c.(196-198)cGt>cTt	p.R66L	SUGP1_ENST00000247001.5_5'Flank|MAU2_ENST00000262815.8_Missense_Mutation_p.R66L|SUGP1_ENST00000585763.1_5'Flank|SUGP1_ENST00000334782.5_5'Flank	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	66	Sufficient for interaction with NIPBL.				maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						ATCGAGGCCCGTACACACCTG	0.682																																					p.R66L													.	MAU2-91	0			c.G197T						.						26	30	29					19																	19431865		2080	4228	6308	SO:0001583	missense	23383	exon1			AGGCCCGTACACA	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.197G>T	19.37:g.19431865G>T	ENSP00000376127:p.Arg66Leu	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	33	10	NM_015329	0	0	5	13	8	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Missense_Mutation	SNP	ENST00000392313.6	37	CCDS32969.2	.	.	.	.	.	.	.	.	.	.	G	33	5.199804	0.94997	.	.	ENSG00000129933	ENST00000392313;ENST00000262815	T;T	0.76060	-0.99;-0.99	5.31	5.31	0.75309	.	0.000000	0.85682	U	0.000000	T	0.73575	0.3604	L	0.47716	1.5	0.80722	D	1	P	0.42908	0.793	P	0.46275	0.51	T	0.69453	-0.5141	10	0.20519	T	0.43	.	17.548	0.87867	0.0:0.0:1.0:0.0	.	66	Q9Y6X3	SCC4_HUMAN	L	66	ENSP00000376127:R66L;ENSP00000262815:R66L	ENSP00000262815:R66L	R	+	2	0	MAU2	19292865	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	8.702000	0.91338	2.511000	0.84671	0.561000	0.74099	CGT	.		0.682	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		T	19431865	G	T	19431865	3	4	112	1	0	0	0	0	1	0	0	0	8217	1145	40	4	199	4	KIAA0892	19	19431865	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	8318084	19431865	39697118	76	9898											
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	38990577	38990577	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaaccgcctgaagaaaaccGggtgcacctgggacacgcca	12	3	13	13	3	0	2	0	1	0	1	0	4	0	4	5	3	3	1	5	3	4	0	rs201584482		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:38990577G>A	ENST00000359596.3	+	45	7244	c.7244G>A	c.(7243-7245)cGg>cAg	p.R2415Q	RYR1_ENST00000355481.4_Missense_Mutation_p.R2415Q|RYR1_ENST00000360985.3_Missense_Mutation_p.R2415Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2415	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GAAGAAAACCGGGTGCACCTG	0.632																																					p.R2415Q		.											.	RYR1-100	0			c.G7244A						.						120	97	104					19																	38990577		2203	4300	6503	SO:0001583	missense	6261	exon45			AAAACCGGGTGCA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7244G>A	19.37:g.38990577G>A	ENSP00000352608:p.Arg2415Gln	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	105	35	NM_001042723	0	0	0	0	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.704736	0.48412	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97529	-4.42;-4.42;-4.42	3.99	3.99	0.46301	.	0.000000	0.64402	U	0.000007	D	0.95726	0.8610	L	0.48362	1.52	0.38108	D	0.937463	D;D	0.63046	0.992;0.985	P;B	0.48901	0.594;0.44	D	0.95492	0.8570	10	0.33141	T	0.24	.	15.0045	0.71501	0.0:0.0:1.0:0.0	.	2415;2415	P21817-2;P21817	.;RYR1_HUMAN	Q	2415	ENSP00000352608:R2415Q;ENSP00000347667:R2415Q;ENSP00000354254:R2415Q	ENSP00000347667:R2415Q	R	+	2	0	RYR1	43682417	0.992000	0.36948	1.000000	0.80357	0.705000	0.40729	2.287000	0.43505	2.045000	0.60652	0.297000	0.19635	CGG	.		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38990577	G	A	38990577	3	1	112	1	0	0	0	0	1	0	0	0	13800	1116	39	1	7422	1	RYR1	19	38990577	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	19558712	38990577	20138406	77	9899											
MYH14	79784	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	50764757	50764757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgctggaactggaccccaAcctctaccgcgtgggacaga	9	5	13	14	3	1	1	0	0	1	1	1	4	1	4	4	4	3	1	4	4	3	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:50764757A>G	ENST00000596571.1	+	18	2327	c.2327A>G	c.(2326-2328)aAc>aGc	p.N776S	MYH14_ENST00000262269.8_Missense_Mutation_p.N817S|MYH14_ENST00000425460.1_Missense_Mutation_p.N784S|MYH14_ENST00000376970.2_Missense_Mutation_p.N809S|MYH14_ENST00000601313.1_Missense_Mutation_p.N817S|MYH14_ENST00000440075.2_Missense_Mutation_p.N817S|MYH14_ENST00000598205.1_Missense_Mutation_p.N784S			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	776	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CTGGACCCCAACCTCTACCGC	0.632																																					p.N817S		.											.	MYH14-23	0			c.A2450G						.						40	44	42					19																	50764757		2011	4174	6185	SO:0001583	missense	79784	exon21			ACCCCAACCTCTA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"Myosins / Myosin superfamily : Class II"	23212	protein-coding gene	gene with protein product		608568	"myosin, heavy polypeptide 14", "myosin, heavy chain 14"	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2327A>G	19.37:g.50764757A>G	ENSP00000472819:p.Asn776Ser	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	74	20	NM_001145809	0	0	22	53	31	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.111012	0.56398	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	4.48	4.48	0.54585	Myosin head, motor domain (2);	.	.	.	.	D	0.82770	0.5109	L	0.47016	1.485	0.80722	D	1	B;B;B	0.29909	0.144;0.261;0.22	B;B;B	0.29176	0.03;0.099;0.06	T	0.82348	-0.0502	9	0.54805	T	0.06	.	12.0425	0.53460	1.0:0.0:0.0:0.0	.	817;776;784	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	S	776;817;809;784;776;817	ENSP00000406273:N817S;ENSP00000366169:N809S;ENSP00000407879:N784S;ENSP00000262269:N817S	ENSP00000262269:N817S	N	+	2	0	MYH14	55456569	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.830000	0.92063	2.028000	0.59812	0.454000	0.30748	AAC	.		0.632	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		G	50764757	A	G	50764757	3	3	112	1	0	0	0	0	1	0	0	0	10058	43	2	3	2528	3	MYH14	19	50764757	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	11774180	50764757	8364226	78	9900											
NLRP8	126205	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56459545	56459545	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atctcttgatagagcgtttcCctggacgacgcgcttgggat	7	12	12	10	4	1	2	0	1	1	1	3	5	2	4	1	2	1	2	1	2	1	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:56459545C>A	ENST00000291971.3	+	1	348	c.277C>A	c.(277-279)Cct>Act	p.P93T	NLRP8_ENST00000590542.1_Missense_Mutation_p.P93T	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	93	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AGAGCGTTTCCCTGGACGACG	0.507																																					p.P93T													.	NLRP8-361	0			c.C277A						.						115	106	109					19																	56459545		2203	4300	6503	SO:0001583	missense	126205	exon1			CGTTTCCCTGGAC	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.277C>A	19.37:g.56459545C>A	ENSP00000291971:p.Pro93Thr	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	37	9	NM_176811	0	0	0	0	0	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024871	0.35701	.	.	ENSG00000179709	ENST00000291971	T	0.51574	0.7	2.05	2.05	0.26809	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.63177	0.2489	M	0.76170	2.325	0.09310	N	1	D;D	0.76494	0.993;0.999	D;D	0.79784	0.916;0.993	T	0.46555	-0.9183	9	0.44086	T	0.13	.	7.6404	0.28290	0.0:1.0:0.0:0.0	.	93;93	Q86W28-2;Q86W28	.;NALP8_HUMAN	T	93	ENSP00000291971:P93T	ENSP00000291971:P93T	P	+	1	0	NLRP8	61151357	0.001000	0.12720	0.262000	0.24481	0.056000	0.15407	0.287000	0.18920	1.462000	0.47948	0.514000	0.50259	CCT	.		0.507	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56459545	C	A	56459545	3	1	112	1	0	0	0	0	1	0	0	0	10509	623	22	4	279	4	NLRP8	19	56459545	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	5694788	56459545	2669438	79	9901											
ZBTB45	84878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	59027831	59027831	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttgcgacagtggctgcactCatacgtaggtggctcagcac	8	9	12	12	2	2	0	2	0	0	0	2	1	2	0	0	3	4	5	0	3	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:59027831C>G	ENST00000594051.1	-	2	1690	c.1210G>C	c.(1210-1212)Gag>Cag	p.E404Q	ZBTB45_ENST00000354590.3_Missense_Mutation_p.E404Q|ZBTB45_ENST00000600990.1_Missense_Mutation_p.E404Q			Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	404					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(2)|endometrium(3)|lung(5)|urinary_tract(1)	11		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		TGGCTGCACTCATACGTAGGT	0.642																																					p.E404Q	NSCLC(164;1383 2017 5233 27540 46677)	.											.	ZBTB45-90	0			c.G1210C						.						63	61	62					19																	59027831		2203	4300	6503	SO:0001583	missense	84878	exon2			TGCACTCATACGT	AK027392	CCDS12984.1	19q13.43	2013-10-10	2006-09-19	2006-09-19	ENSG00000119574	ENSG00000119574		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	23715	protein-coding gene	gene with protein product			"zinc finger protein 499"	ZNF499			Standard	NM_032792		Approved	FLJ14486	uc002qtd.3	Q96K62	OTTHUMG00000183545	ENST00000594051.1:c.1210G>C	19.37:g.59027831C>G	ENSP00000469089:p.Glu404Gln	Somatic	43	1		WXS	Illumina HiSeq	Phase_I	52	14	NM_032792	0	0	15	19	4		Missense_Mutation	SNP	ENST00000594051.1	37	CCDS12984.1	.	.	.	.	.	.	.	.	.	.	c	13.94	2.388310	0.42308	.	.	ENSG00000119574	ENST00000354590	T	0.35236	1.32	3.41	3.41	0.39046	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.411951	0.20599	N	0.089190	T	0.41328	0.1154	N	0.20328	0.56	0.28981	N	0.888614	D	0.71674	0.998	D	0.65874	0.939	T	0.27020	-1.0086	10	0.56958	D	0.05	.	13.1018	0.59224	0.0:1.0:0.0:0.0	.	404	Q96K62	ZBT45_HUMAN	Q	404	ENSP00000346603:E404Q	ENSP00000346603:E404Q	E	-	1	0	ZBTB45	63719643	0.226000	0.23696	0.996000	0.52242	0.534000	0.34807	1.041000	0.30291	2.221000	0.72209	0.467000	0.42956	GAG	.		0.642	ZBTB45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467067.1	NM_032792		G	59027831	C	G	59027831	3	3	112	1	0	0	0	0	1	0	0	0	17578	835	29	4	333	4	ZBTB45	19	59027831	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	2568286	59027831	101152	80	9902											
CEP250	11190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34092361	34092361	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagagctgagacatcagcAggaacgggagcagctgctgg	12	5	16	8	1	1	3	1	2	0	2	1	6	1	5	0	3	6	5	0	3	2	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr20:34092361A>G	ENST00000397527.1	+	30	6884	c.6164A>G	c.(6163-6165)cAg>cGg	p.Q2055R	CEP250_ENST00000342580.4_Missense_Mutation_p.Q1999R	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2055	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGACATCAGCAGGAACGGGAG	0.557																																					p.Q2055R		.											.	CEP250-27	0			c.A6164G						.						29	31	30					20																	34092361		2203	4300	6503	SO:0001583	missense	11190	exon30			ATCAGCAGGAACG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"centrosomal protein 2"	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.6164A>G	20.37:g.34092361A>G	ENSP00000380661:p.Gln2055Arg	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	52	17	NM_007186	0	0	6	7	1	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	7.149	0.583366	0.13749	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.43688	2.96;2.95;0.94	4.83	1.33	0.21861	.	0.879228	0.09850	N	0.747749	T	0.14743	0.0356	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.29792	-1.0000	10	0.19147	T	0.46	.	8.6927	0.34275	0.6701:0.0:0.3299:0.0	.	2055	Q9BV73	CP250_HUMAN	R	2055;1999;543	ENSP00000380661:Q2055R;ENSP00000341541:Q1999R;ENSP00000395992:Q543R	ENSP00000341541:Q1999R	Q	+	2	0	CEP250	33555775	0.990000	0.36364	0.012000	0.15200	0.910000	0.53928	0.903000	0.28475	0.045000	0.15804	0.533000	0.62120	CAG	.		0.557	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34092361	A	G	34092361	3	3	112	1	0	0	0	0	1	0	0	0	3258	188	7	3	6270	3	CEP250	20	34092361	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		34092361	28933159	81	9903											
EPB41L1	2036	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34778270	34778270	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaagagactgtggaaggtCtgcatcgagcatcatacatt	12	9	11	9	1	2	1	1	0	1	1	3	4	2	2	1	2	3	2	1	2	3	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr20:34778270C>A	ENST00000338074.2	+	10	1259	c.1098C>A	c.(1096-1098)gtC>gtA	p.V366V	EPB41L1_ENST00000373941.1_Silent_p.V366V|EPB41L1_ENST00000373950.2_Silent_p.V269V|EPB41L1_ENST00000202028.5_Silent_p.V304V|EPB41L1_ENST00000441639.1_Silent_p.V304V|EPB41L1_ENST00000373946.3_Silent_p.V335V	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	366	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.V366V(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					TGTGGAAGGTCTGCATCGAGC	0.537																																					p.V366V													.	EPB41L1-93	1	Substitution - coding silent(1)	kidney(1)	c.C1098A						.						84	71	75					20																	34778270		2203	4300	6503	SO:0001819	synonymous_variant	2036	exon11			GAAGGTCTGCATC	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1098C>A	20.37:g.34778270C>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	47	10	NM_001258329	0	0	22	37	15	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1																																																																																			.		0.537	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		A	34778270	C	A	34778270	2	1	112	1	0	0	0	0	0	0	0	1	5165	900	32	4		4	EPB41L1	20	34778270	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	685909	34778270	28247250	82	9904											
TMEM189-UBE2V1	7335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	48713266	48713266	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgtcatgtcttcgtcatcTtctagaccccagctaactgt	8	14	7	12	1	5	1	2	0	3	1	6	1	5	1	2	0	2	1	2	0	2	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr20:48713266T>C	ENST00000371674.3	-	2	158	c.114A>G	c.(112-114)gaA>gaG	p.E38E	UBE2V1_ENST00000371677.3_Silent_p.E61E|UBE2V1_ENST00000396059.3_Intron|TMEM189-UBE2V1_ENST00000341698.2_Silent_p.E261E|UBE2V1_ENST00000415862.2_Intron|UBE2V1_ENST00000420027.2_Intron|UBE2V1_ENST00000340309.3_Silent_p.E61E|TMEM189_ENST00000557021.1_Silent_p.E261E|UBE2V1_ENST00000371657.5_Silent_p.E38E	NM_001032288.2|NM_001257395.1	NP_001027459.1|NP_001244324.1	Q13404	UB2V1_HUMAN	ubiquitin-conjugating enzyme E2 variant 1	38					cell differentiation (GO:0030154)|error-free postreplication DNA repair (GO:0042275)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of DNA repair (GO:0006282)|regulation of transcription, DNA-templated (GO:0006355)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-UEV1A complex (GO:0035370)|ubiquitin conjugating enzyme complex (GO:0031371)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(4)	9			BRCA - Breast invasive adenocarcinoma(9;4.74e-06)			CTTCGTCATCTTCTAGACCCC	0.443																																					p.E261E		.											.	TMEM189-UBE2V1-454	0			c.A783G						.						140	132	134					20																	48713266		2203	4298	6501	SO:0001819	synonymous_variant	387522	exon6			GTCATCTTCTAGA	U39360	CCDS13426.1, CCDS13427.1, CCDS33483.1, CCDS58775.1, CCDS74740.1	20q13.2	2007-07-18			ENSG00000244687	ENSG00000244687		"Ubiquitin-conjugating enzymes E2"	12494	protein-coding gene	gene with protein product		602995		UBE2V		9418904, 9305758	Standard	NM_001032288		Approved	UEV-1, CROC-1, UEV1A, CROC1		Q13404	OTTHUMG00000152626	ENST00000371674.3:c.114A>G	20.37:g.48713266T>C		Somatic	210	2		WXS	Illumina HiSeq	Phase_I	196	58	NM_199203	0	0	39	60	21	E1P629|Q13403|Q13532|Q5TGE0|Q5TGE3|Q96H34|Q9GZT0|Q9GZW1|Q9H4J3|Q9H4J4|Q9UKL1|Q9UM48|Q9UM49|Q9UM50	Silent	SNP	ENST00000371674.3	37	CCDS33483.1																																																																																			.		0.443	UBE2V1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080530.1	NM_021988		C	48713266	T	C	48713266	2	2	112	1	0	0	0	0	0	0	0	1	16144	1606	56	3		3	TMEM189-UBE2V1	20	48713266	Silent	SNP	T	TCGA-G7-6790-01A-11D-1961-08	13934996	48713266	14312254	83	9905											
ADNP	23394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49510230	49510230	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattgactgaccaacactgtAaccctggcctacagatttga	12	10	7	12	0	0	4	0	3	0	1	0	4	0	4	3	1	3	1	3	1	3	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr20:49510230A>T	ENST00000396029.3	-	5	1588	c.1021T>A	c.(1021-1023)Tac>Aac	p.Y341N	ADNP_ENST00000349014.3_Missense_Mutation_p.Y341N|ADNP_ENST00000371602.4_Missense_Mutation_p.Y341N|ADNP_ENST00000396032.3_Missense_Mutation_p.Y341N	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	341					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						CCAACACTGTAACCCTGGCCT	0.443																																					p.Y341N		.											.	ADNP-92	0			c.T1021A						.						137	123	128					20																	49510230		2203	4300	6503	SO:0001583	missense	23394	exon5			CACTGTAACCCTG	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1021T>A	20.37:g.49510230A>T	ENSP00000379346:p.Tyr341Asn	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	98	31	NM_015339	0	0	13	22	9	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	37	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072885	0.36566	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	5.91	5.91	0.95273	.	0.295208	0.38663	N	0.001605	T	0.74665	0.3746	L	0.55990	1.75	0.42457	D	0.992773	D	0.76494	0.999	D	0.81914	0.995	T	0.72121	-0.4386	9	0.30078	T	0.28	-7.2492	16.3436	0.83110	1.0:0.0:0.0:0.0	.	341	Q9H2P0	ADNP_HUMAN	N	341	.	ENSP00000342905:Y341N	Y	-	1	0	ADNP	48943637	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.948000	0.93006	2.269000	0.75478	0.533000	0.62120	TAC	.		0.443	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		T	49510230	A	T	49510230	3	4	112	1	0	0	0	0	1	0	0	0	323	362	13	5	2291	5	ADNP	20	49510230	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	796964	49510230	13515290	84	9906											
ADARB1	104	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46596347	46596347	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgatcttgaacgaactgcGcccaggactcaagtatgact	12	9	10	10	2	2	3	1	3	1	0	2	6	2	4	1	1	3	1	1	1	4	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr21:46596347G>A	ENST00000360697.3	+	2	746	c.731G>A	c.(730-732)cGc>cAc	p.R244H	ADARB1_ENST00000348831.4_Missense_Mutation_p.R244H|ADARB1_ENST00000389863.4_Missense_Mutation_p.R244H|ADARB1_ENST00000437626.1_Intron|ADARB1_ENST00000539173.1_Missense_Mutation_p.R244H			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	244	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|positive regulation of viral genome replication (GO:0045070)|regulation of cell cycle (GO:0051726)|RNA processing (GO:0006396)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA adenosine deaminase activity (GO:0003726)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		AACGAACTGCGCCCAGGACTC	0.587																																					p.R244H		.											.	ADARB1-91	0			c.G731A						.						108	97	101					21																	46596347		2203	4300	6503	SO:0001583	missense	104	exon4			AACTGCGCCCAGG	U76420	CCDS33589.1, CCDS33590.1, CCDS42970.1	21q22.3	2012-03-22	2010-06-24		ENSG00000197381	ENSG00000197381	3.5.-.-		226	protein-coding gene	gene with protein product	"RED1 homolog (rat)"	601218	"adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)"			9143496, 14759252	Standard	NR_027672		Approved	ADAR2, DRADA2, ADAR2g, DRABA2, RED1, hRED1, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2a, ADAR2b, ADAR2c, ADAR2d	uc002zgy.2	P78563	OTTHUMG00000090295	ENST00000360697.3:c.731G>A	21.37:g.46596347G>A	ENSP00000353920:p.Arg244His	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	122	44	NM_001160230	0	0	5	5	0	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Missense_Mutation	SNP	ENST00000360697.3	37	CCDS33589.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564135	0.86335	.	.	ENSG00000197381	ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.28	5.28	0.74379	Double-stranded RNA-binding (2);Double-stranded RNA-binding-like (1);	0.000000	0.85682	U	0.000000	D	0.86818	0.6024	M	0.75447	2.3	0.80722	D	1	P;D;D;B;P	0.61697	0.928;0.99;0.97;0.046;0.861	P;D;P;B;P	0.66716	0.521;0.946;0.877;0.04;0.521	D	0.85797	0.1371	10	0.38643	T	0.18	-42.4461	16.7859	0.85574	0.0:0.0:1.0:0.0	.	271;244;244;272;244	P78563-4;P78563;Q4AE77;G5E9B4;P78563-3	.;RED1_HUMAN;.;.;.	H	244	ENSP00000441897:R244H;ENSP00000374513:R244H;ENSP00000015877:R244H;ENSP00000353920:R244H	ENSP00000015877:R244H	R	+	2	0	ADARB1	45420775	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	9.347000	0.97059	2.633000	0.89246	0.655000	0.94253	CGC	.		0.587	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833		A	46596347	G	A	46596347	3	1	112	1	0	0	0	0	1	0	0	0	282	1087	38	1	737	1	ADARB1	21	46596347	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08		46596347	1533548	85	9907											
CRKL	1399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	21272259	21272259	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgactcctcggaccgctccGcctggtatatggggccggtg	4	9	14	14	5	0	0	0	0	0	0	4	2	2	1	5	5	0	2	5	5	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr22:21272259G>C	ENST00000354336.3	+	1	546	c.37G>C	c.(37-39)Gcc>Ccc	p.A13P		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	13					activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			GGACCGCTCCGCCTGGTATAT	0.697																																					p.A13P	Pancreas(85;3 1441 23889 42519 42763)	.											.	CRKL-439	0			c.G37C						.						29	30	29					22																	21272259		2202	4299	6501	SO:0001583	missense	1399	exon1			CGCTCCGCCTGGT		CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"SH2 domain containing"	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.37G>C	22.37:g.21272259G>C	ENSP00000346300:p.Ala13Pro	Somatic	60	1		WXS	Illumina HiSeq	Phase_I	60	13	NM_005207	0	0	8	19	11	A8KA44|D3DX35	Missense_Mutation	SNP	ENST00000354336.3	37	CCDS13785.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.683747	0.68157	.	.	ENSG00000099942	ENST00000354336	T	0.21932	1.98	5.27	0.287	0.15714	SH2 motif (2);	0.368313	0.30611	N	0.009241	T	0.07098	0.0180	N	0.02412	-0.56	0.42745	D	0.993759	B	0.33000	0.393	B	0.29353	0.101	T	0.31888	-0.9927	10	0.14252	T	0.57	.	13.4072	0.60919	0.0:0.0:0.4263:0.5737	.	13	P46109	CRKL_HUMAN	P	13	ENSP00000346300:A13P	ENSP00000346300:A13P	A	+	1	0	CRKL	19602259	0.824000	0.29247	0.757000	0.31301	0.988000	0.76386	1.158000	0.31737	-0.041000	0.13558	0.650000	0.86243	GCC	.		0.697	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207		C	21272259	G	C	21272259	3	2	112	1	0	0	0	0	1	0	0	0	3891	1087	38	4	39	4	CRKL	22	21272259	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08		21272259	30032307	86	9908											
APOL4	80832	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	36595420	36595420	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctggatggttttgctgcAcccttgaggaagagaaaaca	12	9	12	8	0	0	2	0	1	0	1	0	5	0	4	2	3	4	3	2	3	3	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr22:36595420A>G	ENST00000405511.1	-	4	460	c.38T>C	c.(37-39)gTg>gCg	p.V13A	APOL4_ENST00000328429.4_Splice_Site_p.C31R|APOL4_ENST00000479929.1_5'UTR|APOL4_ENST00000332987.1_Missense_Mutation_p.V13A|APOL4_ENST00000352371.1_Missense_Mutation_p.V16A|APOL4_ENST00000429038.2_Missense_Mutation_p.V13A|APOL4_ENST00000397275.2_Missense_Mutation_p.C31R|APOL4_ENST00000404685.3_Missense_Mutation_p.V16A	NM_030643.3	NP_085146.2	Q9BPW4	APOL4_HUMAN	apolipoprotein L, 4	16					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	extracellular space (GO:0005615)	lipid binding (GO:0008289)			lung(1)	1						GTTTTGCTGCACCCTTGAGGA	0.557																																					.													.	APOL4-90	0			.						.						122	129	127					22																	36595420		2186	4294	6480	SO:0001583	missense	80832	.			TGCTGCACCCTTG	AF305226	CCDS74851.1, CCDS74852.1	22q11.2-q13.2	2013-01-24			ENSG00000100336	ENSG00000100336		"Apolipoproteins"	14867	protein-coding gene	gene with protein product		607254				11374903	Standard	NM_030643		Approved	APOLIV	uc003aox.3	Q9BPW4	OTTHUMG00000150630	ENST00000405511.1:c.38T>C	22.37:g.36595420A>G	ENSP00000384011:p.Val13Ala	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	152	44	.	0	0	0	0	0	Q9BQ37|Q9BXQ8	Missense_Mutation	SNP	ENST00000405511.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	5.282|5.282	0.237449|0.237449	0.10023|0.10023	.|.	.|.	ENSG00000100336|ENSG00000100336	ENST00000397275;ENST00000328429|ENST00000404685;ENST00000405511;ENST00000429038;ENST00000352371;ENST00000332987;ENST00000457630;ENST00000419360;ENST00000449084;ENST00000436763	.|T;T;T;T;T;T;T;T;T	.|0.61742	.|1.51;1.37;1.37;3.81;3.92;0.81;0.77;0.39;0.08	1.44|1.44	0.359|0.359	0.16088|0.16088	.|.	.|9.394490	.|0.00944	.|U	.|0.002875	T|T	0.40448|0.40448	0.1117|0.1117	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.17465	.|0.013;0.022	.|B;B	.|0.11329	.|0.003;0.006	T|T	0.11251|0.11251	-1.0595|-1.0595	5|9	0.87932|0.26408	D|T	0|0.33	.|.	3.4282|3.4282	0.07418|0.07418	0.767:0.0:0.233:0.0|0.767:0.0:0.233:0.0	.|.	.|16;13	.|Q9BPW4;Q9BPW4-3	.|APOL4_HUMAN;.	R|A	31|16;13;13;16;13;13;13;13;13	.|ENSP00000385119:V16A;ENSP00000384011:V13A;ENSP00000404366:V13A;ENSP00000338260:V16A;ENSP00000333229:V13A;ENSP00000409085:V13A;ENSP00000395548:V13A;ENSP00000388936:V13A;ENSP00000393096:V13A	ENSP00000331089:C31R|ENSP00000333229:V13A	C|V	-|-	1|2	0|0	APOL4|APOL4	34925366|34925366	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.001000|0.001000	0.01503|0.01503	0.524000|0.524000	0.22940|0.22940	0.051000|0.051000	0.15978|0.15978	-0.946000|-0.946000	0.02672|0.02672	TGC|GTG	.		0.557	APOL4-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000319256.2	NM_145660		G	36595420	A	G	36595420	3	3	112	1	0	0	0	0	1	0	0	0	808	159	6	3	1018	3	APOL4	22	36595420	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	15323161	36595420	14709146	87	9909											
OFD1	8481	broad.mit.edu	37	chrX	13754640	13754640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatgagttgatgcaccctgTattgagtggagaactgcagc	10	11	12	8	0	1	4	1	3	0	1	1	5	1	4	1	1	4	4	1	1	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chrX:13754640T>C	ENST00000340096.6	+	3	482	c.155T>C	c.(154-156)gTa>gCa	p.V52A	TRAPPC2_ENST00000519885.1_5'Flank|TRAPPC2_ENST00000380579.1_5'Flank|OFD1_ENST00000380550.3_Missense_Mutation_p.V52A|TRAPPC2_ENST00000453655.2_5'Flank|TRAPPC2_ENST00000358231.5_5'Flank|OFD1_ENST00000490265.1_3'UTR|TRAPPC2_ENST00000458511.2_5'Flank|TRAPPC2_ENST00000359680.5_5'Flank|OFD1_ENST00000398395.3_Missense_Mutation_p.V52A|OFD1_ENST00000380567.1_5'UTR	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	52					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						ATGCACCCTGTATTGAGTGGA	0.398																																					p.V52A													.	OFD1-108	0			c.T155C						.						152	148	149					X																	13754640		2203	4300	6503	SO:0001583	missense	8481	exon3			ACCCTGTATTGAG	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.155T>C	X.37:g.13754640T>C	ENSP00000344314:p.Val52Ala	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	156	4	NM_003611	0	0	11	11	0	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	37	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.550708	0.45383	.	.	ENSG00000046651	ENST00000380550;ENST00000398395;ENST00000340096	D;D;D	0.95412	-3.68;-3.44;-3.7	5.55	4.38	0.52667	.	0.499719	0.22428	N	0.060189	D	0.93880	0.8042	M	0.76002	2.32	0.09310	N	1	P;P;P	0.47106	0.89;0.82;0.89	B;B;B	0.42738	0.396;0.285;0.396	D	0.87609	0.2502	10	0.42905	T	0.14	-9.6943	7.333	0.26594	0.0:0.2422:0.0:0.7578	.	52;52;52	A8K2T9;O75665-3;O75665	.;.;OFD1_HUMAN	A	52	ENSP00000369923:V52A;ENSP00000381432:V52A;ENSP00000344314:V52A	ENSP00000344314:V52A	V	+	2	0	OFD1	13664561	0.946000	0.32159	0.608000	0.28969	0.837000	0.47467	1.572000	0.36461	0.740000	0.32651	-0.314000	0.08810	GTA	.		0.398	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		C	13754640	T	C	13754640	3	2	112	1	0	0	0	0	1	0	0	0	10864	1638	57	3	165	3	OFD1	23	13754640	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08		13754640	141515920	88	9910											
PNCK	139728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	152937464	152937464	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcggtcaaacagctcgccAcccgtcaccctgggggtgcc	7	6	12	16	3	2	0	2	0	0	0	3	0	2	0	4	3	4	1	4	3	1	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chrX:152937464A>T	ENST00000370150.1	-	5	463	c.285T>A	c.(283-285)ggT>ggA	p.G95G	PNCK_ENST00000370142.1_Silent_p.G95G|PNCK_ENST00000447676.2_Silent_p.G178G|PNCK_ENST00000340888.3_Silent_p.G95G|PNCK_ENST00000475172.1_5'UTR|PNCK_ENST00000370145.4_Silent_p.G112G|PNCK_ENST00000393831.2_Silent_p.G95G			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	95	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACAGCTCGCCACCCGTCACCC	0.657																																					p.G178G		.											.	PNCK-207	0			c.T534A						.						39	35	36					X																	152937464		2203	4299	6502	SO:0001819	synonymous_variant	139728	exon5			CTCGCCACCCGTC	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.285T>A	X.37:g.152937464A>T		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	21	10	NM_001039582	0	0	0	0	0	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Silent	SNP	ENST00000370150.1	37																																																																																				.		0.657	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		T	152937464	A	T	152937464	2	4	112	1	0	0	0	0	0	0	0	1	12171	146	6	5		5	PNCK	23	152937464	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	139182824	152937464	2333096	89	9911											
ESPN	83715	hgsc.bcm.edu	37	chr1	6500833	6500833	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgacctgtggggcgggaccCcgctgcacgacgccgccgag	5	4	16	16	6	0	1	0	1	0	0	0	4	0	2	5	3	1	2	5	3	0	0	rs3817921		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:6500833C>G	ENST00000377828.1	+	4	991	c.823C>G	c.(823-825)Ccg>Gcg	p.P275A	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	275					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GGGCGGGACCCCGCTGCACGA	0.746																																					p.P275A		.											.	ESPN-514	0			c.C823G						.																																			SO:0001583	missense	83715	exon4			GGGACCCCGCTGC	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"Ankyrin repeat domain containing"	13281	protein-coding gene	gene with protein product		606351	"deafness, autosomal recessive 36"	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.823C>G	1.37:g.6500833C>G	ENSP00000367059:p.Pro275Ala	Somatic	12	2		WXS	Illumina HiSeq	Phase_I	10	2	NM_031475	0	0	0	0	0	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.472642	0.63737	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.67523	-0.27;0.91	3.84	3.84	0.44239	Ankyrin repeat-containing domain (4);	0.437340	0.22224	N	0.062901	T	0.45577	0.1349	N	0.05414	-0.055	0.80722	D	1	B	0.14438	0.01	B	0.18263	0.021	T	0.39057	-0.9632	10	0.32370	T	0.25	-11.7359	12.6418	0.56714	0.0:1.0:0.0:0.0	rs3817921	275	B1AK53	ESPN_HUMAN	A	275;60	ENSP00000367059:P275A;ENSP00000401793:P60A	ENSP00000367059:P275A	P	+	1	0	ESPN	6423420	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.267000	0.78462	1.989000	0.58080	0.430000	0.28490	CCG	.		0.746	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		G	6500833	C	G	6500833	3	3	113	1	0	0	0	0	1	0	0	0	5267	623	22	4	837	4	ESPN	1	6500833	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		6500833	242749788	1	9912											
C1orf187	374946	broad.mit.edu	37	chr1	11771907	11771907	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccttctccacggtctccaGcaggcacagcccaggtctga	7	7	9	18	1	3	1	0	1	3	0	5	1	3	1	5	3	2	2	5	3	0	1	rs147444302		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:11771907G>A	ENST00000294485.5	+	4	777		c.e4-1			NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		ACGGTCTCCAGCAGGCACAGC	0.552																																					.													.	.	0			c.643-1G>A						.						54	42	46					1																	11771907		2203	4300	6503	SO:0001630	splice_region_variant	374946	exon4			TCTCCAGCAGGCA	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"dorsal repulsive axon guidance protein", "neural tissue-specific cysteine-rich protein"	612682	"chromosome 1 open reading frame 187"	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.643-1G>A	1.37:g.11771907G>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	27	6	NM_198545	0	0	0	0	0		Splice_Site	SNP	ENST00000294485.5	37	CCDS135.1	.	.	.	.	.	.	.	.	.	.	G	3.498	-0.102520	0.06967	.	.	ENSG00000162490	ENST00000294485	.	.	.	5.52	2.29	0.28610	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5109	0.44862	0.0667:0.1084:0.7246:0.1002	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf187	11694494	1.000000	0.71417	0.453000	0.27007	0.065000	0.16274	3.334000	0.52097	0.276000	0.22118	-0.797000	0.03246	.	G|1.000;C|0.000		0.552	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	Intron	A	11771907	G	A	11771907	5	1	113	1	0	0	0	0	0	0	1	0	2027	985	34	2	652	2	C1orf187	1	11771907	Splice_Site	SNP	G	TCGA-G7-6792-01A-21D-1961-08	5271074	11771907	237478714	2	9913											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109792762	109792762	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgccgccgctgctgctgctgTtgctgctgctgctgccgccg	0	10	14	17	5	0	0	0	0	0	0	0	0	0	0	4	0	8	9	4	0	0	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:109792762T>C	ENST00000271332.3	+	1	122	c.61T>C	c.(61-63)Ttg>Ctg	p.L21L		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	21					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		gctgctgctgttgctgctgct	0.746																																					p.L21L	NSCLC(158;1285 2011 34800 34852 42084)	.											.	CELSR2-526	0			c.T61C						.						9	11	11					1																	109792762		1973	3925	5898	SO:0001819	synonymous_variant	1952	exon1			CTGCTGTTGCTGC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.61T>C	1.37:g.109792762T>C		Somatic	57	1		WXS	Illumina HiSeq	Phase_I	65	4	NM_001408	0	0	5	61	56	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			.		0.746	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		C	109792762	T	C	109792762	2	2	113	1	0	0	0	0	0	0	0	1	3228	1722	60	3		3	CELSR2	1	109792762	Silent	SNP	T	TCGA-G7-6792-01A-21D-1961-08	98020855	109792762	139457859	3	9914											
DDX20	11218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	112303729	112303729	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttaatcaagctttagtctTttctaatttgcacagcaggt	11	17	6	7	0	3	0	1	0	2	0	3	0	3	0	0	1	3	3	0	1	4	8			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:112303729T>G	ENST00000369702.4	+	6	1564	c.944T>G	c.(943-945)tTt>tGt	p.F315C	DDX20_ENST00000536167.1_3'UTR|DDX20_ENST00000475700.1_5'UTR	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	315	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTTAGTCTTTTCTAATTTG	0.353																																					p.F315C		.											.	DDX20-227	0			c.T944G						.						111	114	113					1																	112303729		2203	4300	6503	SO:0001583	missense	11218	exon6			TAGTCTTTTCTAA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.944T>G	1.37:g.112303729T>G	ENSP00000358716:p.Phe315Cys	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	96	39	NM_007204	0	0	6	9	3	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962407	0.74016	.	.	ENSG00000064703	ENST00000369702	T	0.11063	2.81	5.62	5.62	0.85841	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.43344	0.1243	H	0.98178	4.165	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66106	-0.6006	10	0.87932	D	0	-23.1854	15.4768	0.75489	0.0:0.0:0.0:1.0	.	315	Q9UHI6	DDX20_HUMAN	C	315	ENSP00000358716:F315C	ENSP00000358716:F315C	F	+	2	0	DDX20	112105252	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.586000	0.82596	2.152000	0.67230	0.459000	0.35465	TTT	.		0.353	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		G	112303729	T	G	112303729	3	3	113	1	0	0	0	0	1	0	0	0	4354	1841	64	5	966	5	DDX20	1	112303729	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08	2510967	112303729	136946892	4	9915											
RXFP4	339403	broad.mit.edu;bcgsc.ca	37	chr1	155912175	155912175	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcatcaccaccagctacctGctgctgctggccttcctgca	6	10	8	17	0	2	0	2	0	0	0	3	0	3	0	5	1	6	5	5	1	1	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:155912175G>A	ENST00000368318.3	+	1	696	c.675G>A	c.(673-675)ctG>ctA	p.L225L		NM_181885.2	NP_871001.1	Q8TDU9	RL3R2_HUMAN	relaxin/insulin-like family peptide receptor 4	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)			endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	13	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCAGCTACCTGCTGCTGCTGG	0.662																																					p.L225L													.	RXFP4-90	0			c.G675A						.						45	49	48					1																	155912175		2203	4300	6503	SO:0001819	synonymous_variant	339403	exon1			CTACCTGCTGCTG	AB065617	CCDS1124.1	1q22	2012-08-08	2006-05-09	2006-03-15	ENSG00000173080	ENSG00000173080		"GPCR / Class A : Relaxin family peptide receptors"	14666	protein-coding gene	gene with protein product		609043	"G protein-coupled receptor 100", "relaxin 3 receptor 2", "relaxin family peptide receptor 4"	GPR100, RLN3R2		15956688, 16507880	Standard	NM_181885		Approved	GPCR142, RXFPR4	uc010pgs.2	Q8TDU9	OTTHUMG00000017463	ENST00000368318.3:c.675G>A	1.37:g.155912175G>A		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	97	10	NM_181885	0	0	0	0	0	B0M0L4|Q3MJB1|Q8NGZ8	Silent	SNP	ENST00000368318.3	37	CCDS1124.1																																																																																			.		0.662	RXFP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046203.1	NM_181885		A	155912175	G	A	155912175	2	1	113	1	0	0	0	0	0	0	0	1	13794	1306	46	2		2	RXFP4	1	155912175	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08	43608446	155912175	93338446	5	9916											
DSTYK	25778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205132071	205132071	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtttgatttgctcccataGcatccttgtaactgacgacc	8	14	7	12	1	0	2	0	2	0	0	2	3	2	2	3	0	3	4	3	0	2	5			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:205132071G>A	ENST00000367162.3	-	5	1651	c.1621C>T	c.(1621-1623)Cta>Tta	p.L541L	DSTYK_ENST00000367161.3_Silent_p.L541L|DSTYK_ENST00000367160.4_Intron	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	541					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						TGCTCCCATAGCATCCTTGTA	0.418																																					p.L541L		.											.	DSTYK-333	0			c.C1621T						.						205	191	196					1																	205132071		2203	4300	6503	SO:0001819	synonymous_variant	25778	exon5			CCCATAGCATCCT	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.1621C>T	1.37:g.205132071G>A		Somatic	147	0		WXS	Illumina HiSeq	Phase_I	154	67	NM_199462	0	0	8	10	2	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Silent	SNP	ENST00000367162.3	37	CCDS1451.1																																																																																			.		0.418	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		A	205132071	G	A	205132071	2	1	113	1	0	0	0	0	0	0	0	1	4796	962	34	2		2	DSTYK	1	205132071	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08	49219896	205132071	44118550	6	9917											
LEFTY1	10637	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	226075314	226075314	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacgtcgaaggccttccaGccgctctcgtggacggacac	7	7	12	15	5	2	0	1	0	1	0	5	3	3	2	3	3	1	1	3	3	1	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:226075314G>A	ENST00000272134.5	-	3	601	c.522C>T	c.(520-522)ggC>ggT	p.G174G	LEFTY1_ENST00000492457.1_5'Flank|RP4-559A3.7_ENST00000432920.2_Silent_p.L283L	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	174					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					AGGCCTTCCAGCCGCTCTCGT	0.701																																					p.G174G		.											.	LEFTY1-90	0			c.C522T						.						14	18	17					1																	226075314		2133	4177	6310	SO:0001819	synonymous_variant	10637	exon3			CTTCCAGCCGCTC	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"left-right determination, factor B"	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.522C>T	1.37:g.226075314G>A		Somatic	111	1		WXS	Illumina HiSeq	Phase_I	76	28	NM_020997	0	0	0	0	0	B2R7U0|Q53H67|Q5TE94	Silent	SNP	ENST00000272134.5	37	CCDS1548.1																																																																																			.		0.701	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997		A	226075314	G	A	226075314	2	1	113	1	0	0	0	0	0	0	0	1	8736	958	34	2		2	LEFTY1	1	226075314	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08	20943243	226075314	23175307	7	9918											
AGT	183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	230841791	230841791	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcagcaggcaggcgctctCagtgaagggcacttgagtca	10	6	14	11	1	2	2	2	2	1	0	3	2	2	2	0	3	2	5	0	3	1	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:230841791C>T	ENST00000366667.4	-	3	1226	c.1012G>A	c.(1012-1014)Gag>Aag	p.E338K		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	338					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CAGGCGCTCTCAGTGAAGGGC	0.557																																					p.E338K		.											.	AGT-226	0			c.G1012A						.						109	103	105					1																	230841791		2203	4300	6503	SO:0001583	missense	183	exon3			CGCTCTCAGTGAA	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.1012G>A	1.37:g.230841791C>T	ENSP00000355627:p.Glu338Lys	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	171	61	NM_000029	0	0	17	49	32	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	C	0.022	-1.416535	0.01136	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.87571	-2.27	5.17	1.03	0.20045	Serpin domain (3);	0.577268	0.19344	N	0.116572	T	0.70657	0.3249	N	0.11560	0.145	0.09310	N	1	B;B;B	0.16396	0.006;0.017;0.006	B;B;B	0.12156	0.003;0.007;0.003	T	0.54234	-0.8324	10	0.15499	T	0.54	.	9.4035	0.38447	0.0:0.543:0.0:0.457	.	338;338;338	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	K	338;256	ENSP00000355627:E338K	ENSP00000355627:E338K	E	-	1	0	AGT	228908414	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.077000	0.14738	0.168000	0.19655	0.655000	0.94253	GAG	.		0.557	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		T	230841791	C	T	230841791	3	4	113	1	0	0	0	0	1	0	0	0	399	835	29	2	457	2	AGT	1	230841791	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	4766477	230841791	18408830	8	9919											
FOSL2	2355	ucsc.edu	37	chr2	28631654	28631654	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaagaggaggagaagcgtcGcatccggcgggagaggaaca	13	3	18	7	4	0	4	0	1	0	3	2	8	1	6	1	5	2	1	1	5	3	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr2:28631654G>A	ENST00000264716.4	+	3	1246	c.383G>A	c.(382-384)cGc>cAc	p.R128H	FOSL2_ENST00000545753.1_Missense_Mutation_p.R89H|FOSL2_ENST00000460736.1_3'UTR|FOSL2_ENST00000379619.1_Missense_Mutation_p.R103H	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	128	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					GAGAAGCGTCGCATCCGGCGG	0.537																																					p.R128H													.	FOSL2-712	0			c.G383A						.						35	35	35					2																	28631654		2203	4300	6503	SO:0001583	missense	2355	exon3			AGCGTCGCATCCG		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"basic leucine zipper proteins"	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.383G>A	2.37:g.28631654G>A	ENSP00000264716:p.Arg128His	Somatic	47	0		WXS	Illumina HiSeq		42	4	NM_005253	0	0	251	251	0	B2RD58|B3KP27|B4DYV4|Q6FG46	Missense_Mutation	SNP	ENST00000264716.4	37	CCDS1766.1	.	.	.	.	.	.	.	.	.	.	G	36	5.689889	0.96784	.	.	ENSG00000075426	ENST00000379619;ENST00000264716;ENST00000436647;ENST00000545753	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	5.45	5.45	0.79879	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	D	0.87334	0.6151	M	0.88570	2.965	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89396	0.3692	10	0.87932	D	0	-12.7055	19.2653	0.93983	0.0:0.0:1.0:0.0	.	128	P15408	FOSL2_HUMAN	H	103;128;89;89	ENSP00000368939:R103H;ENSP00000264716:R128H;ENSP00000396497:R89H;ENSP00000439303:R89H	ENSP00000264716:R128H	R	+	2	0	FOSL2	28485158	1.000000	0.71417	0.994000	0.49952	0.968000	0.65278	9.790000	0.99075	2.554000	0.86153	0.655000	0.94253	CGC	.		0.537	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253		A	28631654	G	A	28631654	3	1	113	1	0	0	0	0	1	0	0	0	6007	1087	38	1	393	1	FOSL2	2	28631654	Missense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08		28631654	214567719	9	9920											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50574025	50574025	+	Intron	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgccgccgccgccgccGccgccgccgccgcccccggg	0	1	14	26	11	0	0	0	0	0	0	0	0	0	0	12	1	1	0	12	1	0	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr2:50574025G>C	ENST00000406316.2	-	18	4841				NRXN1_ENST00000401669.2_Intron|NRXN1_ENST00000406859.3_Intron|NRXN1_ENST00000331040.5_Intron|NRXN1_ENST00000404971.1_Intron|NRXN1_ENST00000402717.3_Intron|NRXN1_ENST00000405472.3_Intron|NRXN1_ENST00000342183.5_Silent_p.G21G|NRXN1_ENST00000401710.1_Intron	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			cgccgccgccgccgccgccgc	0.791																																					p.G21G		.											.	NRXN1-92	0			c.C63G						.						1	2	2					2																	50574025		764	1771	2535	SO:0001627	intron_variant	9378	exon1			GCCGCCGCCGCCG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3365-109917C>G	2.37:g.50574025G>C		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	4	3	NM_138735	0	0	1	1	0	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.		0.791	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			C	50574025	G	C	50574025	1	2	113	0	1	0	0	0	0	0	0	0	10691	1074	38	4		4	NRXN1	2	50574025	Intron	SNP	G	TCGA-G7-6792-01A-21D-1961-08	21942371	50574025	192625348	10	9921											
CXCR1	3577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219029397	219029397	+	Missense_Mutation	SNP	G	G	C																															aactggactggaattgtttgGatggtaagcctggcggaaaa																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr2:219029397G>C	ENST00000295683.2	-	2	658	c.538C>G	c.(538-540)Cca>Gca	p.P180A		NM_000634.2	NP_000625.1	P25024	CXCR1_HUMAN	chemokine (C-X-C motif) receptor 1	180					cell surface receptor signaling pathway (GO:0007166)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|receptor internalization (GO:0031623)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)			endometrium(1)|large_intestine(2)|lung(7)|prostate(3)	13					Ketoprofen(DB01009)	GAATTGTTTGGATGGTAAGCC	0.512																																					p.P180A		.											.	CXCR1-658	0			c.C538G						.						88	77	81					2																	219029397		2203	4300	6503	SO:0001583	missense	3577	exon2			TGTTTGGATGGTA	U11870	CCDS2409.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000163464	ENSG00000163464		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6026	protein-coding gene	gene with protein product		146929	"interleukin 8 receptor, alpha"	CMKAR1, IL8RA		1303245, 1427896	Standard	NM_000634		Approved	CKR-1, CDw128a, CD181	uc002vhc.3	P25024	OTTHUMG00000133108	ENST00000295683.2:c.538C>G	2.37:g.219029397G>C	ENSP00000295683:p.Pro180Ala	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	44	14	NM_000634	0	0	0	0	0	B2R6Q3|Q2YEF8|Q2YEG4|Q2YEG5|Q2YEG7|Q2YEG8|Q53R18|Q6IN95|Q8N6T6|Q9P2T8|Q9P2T9|Q9P2U0|Q9P2U1|Q9P2U2	Missense_Mutation	SNP	ENST00000295683.2	37	CCDS2409.1	.	.	.	.	.	.	.	.	.	.	G	0.035	-1.310146	0.01342	.	.	ENSG00000163464	ENST00000295683;ENST00000421691	T	0.38077	1.16	4.71	2.87	0.33458	GPCR, rhodopsin-like superfamily (1);	0.779117	0.10221	N	0.700944	T	0.26122	0.0637	L	0.39245	1.2	0.09310	N	1	B	0.06786	0.001	B	0.18263	0.021	T	0.29488	-1.0010	10	0.14656	T	0.56	.	6.0111	0.19575	0.1817:0.2623:0.556:0.0	.	180	P25024	CXCR1_HUMAN	A	180;124	ENSP00000295683:P180A	ENSP00000295683:P180A	P	-	1	0	CXCR1	218737642	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-0.300000	0.08243	1.109000	0.41680	0.655000	0.94253	CCA	.		0.512	CXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256773.2	NM_000634		C	219029397	G	C	219029397	3	2	113	1	0	0	0	0	1	0	0	0	4096	1174	41	4	518	4	CXCR1	2	219029397	Missense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08	168455372	219029397	24169976	11	9922	101	2									
CXCR1	3577	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219029403	219029403	+	Missense_Mutation	SNP	A	A	T																															actggaattgtttggatggtAagcctggcggaaaaggaaga																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr2:219029403A>T	ENST00000295683.2	-	2	652	c.532T>A	c.(532-534)Tac>Aac	p.Y178N		NM_000634.2	NP_000625.1	P25024	CXCR1_HUMAN	chemokine (C-X-C motif) receptor 1	178					cell surface receptor signaling pathway (GO:0007166)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|receptor internalization (GO:0031623)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)			endometrium(1)|large_intestine(2)|lung(7)|prostate(3)	13					Ketoprofen(DB01009)	TTTGGATGGTAAGCCTGGCGG	0.512																																					p.Y178N													.	CXCR1-658	0			c.T532A						.						89	78	82					2																	219029403		2203	4300	6503	SO:0001583	missense	3577	exon2			GATGGTAAGCCTG	U11870	CCDS2409.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000163464	ENSG00000163464		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6026	protein-coding gene	gene with protein product		146929	"interleukin 8 receptor, alpha"	CMKAR1, IL8RA		1303245, 1427896	Standard	NM_000634		Approved	CKR-1, CDw128a, CD181	uc002vhc.3	P25024	OTTHUMG00000133108	ENST00000295683.2:c.532T>A	2.37:g.219029403A>T	ENSP00000295683:p.Tyr178Asn	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	36	13	NM_000634	0	0	0	0	0	B2R6Q3|Q2YEF8|Q2YEG4|Q2YEG5|Q2YEG7|Q2YEG8|Q53R18|Q6IN95|Q8N6T6|Q9P2T8|Q9P2T9|Q9P2U0|Q9P2U1|Q9P2U2	Missense_Mutation	SNP	ENST00000295683.2	37	CCDS2409.1	.	.	.	.	.	.	.	.	.	.	A	9.226	1.034501	0.19590	.	.	ENSG00000163464	ENST00000295683;ENST00000421691	T	0.70986	-0.53	4.71	0.229	0.15368	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.55065	0.1897	L	0.33245	0.995	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.46205	-0.9208	9	0.62326	D	0.03	.	5.2232	0.15379	0.433:0.0:0.0791:0.4878	.	178	P25024	CXCR1_HUMAN	N	178;122	ENSP00000295683:Y178N	ENSP00000295683:Y178N	Y	-	1	0	CXCR1	218737648	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.010000	0.13242	-0.169000	0.10834	-0.333000	0.08304	TAC	.		0.512	CXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256773.2	NM_000634		T	219029403	A	T	219029403	3	4	113	1	0	0	0	0	1	0	0	0	4096	362	13	5	524	5	CXCR1	2	219029403	Missense_Mutation	SNP	A	TCGA-G7-6792-01A-21D-1961-08	6	219029403	24169970	12	9923	101	2									
CTDSPL	10217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38009318	38009318	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtctcttttttctctagcCtattagtaatgctgatttta	8	21	5	7	0	2	1	0	1	2	0	4	1	2	1	1	0	2	2	1	0	6	10			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr3:38009318C>G	ENST00000273179.5	+	5	397	c.371C>G	c.(370-372)cCt>cGt	p.P124R	MIR26A1_ENST00000362205.1_RNA|CTDSPL_ENST00000310189.3_3'UTR|CTDSPL_ENST00000443503.2_Splice_Site_p.P113R	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	124	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		TTTCTCTAGCCTATTAGTAAT	0.308											OREG0015472	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P124R		.											.	CTDSPL-90	0			c.C371G						.						64	61	62					3																	38009318		2199	4299	6498	SO:0001630	splice_region_variant	10217	exon5			TCTAGCCTATTAG	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	16890	protein-coding gene	gene with protein product	"small CTD phosphatase 3", "HYA22 protein", "RB protein serine phosphatase from chromosome 3"	608592	"chromosome 3 open reading frame 8"	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.370-1C>G	3.37:g.38009318C>G		Somatic	63	0	874	WXS	Illumina HiSeq	Phase_I	54	13	NM_001008392	0	0	0	0	0	Q3ZTU0|Q70KI4|Q7Z5Q2	Missense_Mutation	SNP	ENST00000273179.5	37	CCDS33734.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.625293	0.87560	.	.	ENSG00000144677	ENST00000443503;ENST00000273179;ENST00000447745	T;T;T	0.17213	2.29;2.29;2.29	5.15	5.15	0.70609	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.049311	0.85682	D	0.000000	T	0.46756	0.1409	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.992;0.995	T	0.49133	-0.8971	10	0.62326	D	0.03	-20.9054	19.0018	0.92837	0.0:1.0:0.0:0.0	.	113;124	O15194-2;O15194	.;CTDSL_HUMAN	R	113;124;13	ENSP00000398288:P113R;ENSP00000273179:P124R;ENSP00000407443:P13R	ENSP00000273179:P124R	P	+	2	0	CTDSPL	37984322	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.720000	0.84759	2.571000	0.86741	0.655000	0.94253	CCT	.		0.308	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808	Missense_Mutation	G	38009318	C	G	38009318	5	3	113	1	0	0	0	0	0	0	1	0	4011	695	24	4	389	4	CTDSPL	3	38009318	Splice_Site	SNP	C	TCGA-G7-6792-01A-21D-1961-08		38009318	160013112	13	9924											
FYCO1	79443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46008824	46008824	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acccaagtgccggatgctggCctgctcggcctccagggagg	6	6	15	14	2	0	0	0	0	0	0	2	2	1	2	5	5	3	2	5	5	1	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr3:46008824C>T	ENST00000296137.2	-	8	2207	c.2002G>A	c.(2002-2004)Gcc>Acc	p.A668T	FYCO1_ENST00000535325.1_Missense_Mutation_p.A668T	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	668					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CGGATGCTGGCCTGCTCGGCC	0.632																																					p.A668T		.											.	FYCO1-91	0			c.G2002A						.						48	53	52					3																	46008824		2203	4299	6502	SO:0001583	missense	79443	exon8			TGCTGGCCTGCTC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2002G>A	3.37:g.46008824C>T	ENSP00000296137:p.Ala668Thr	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	150	62	NM_024513	0	0	3	13	10	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.644029	0.47258	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21932	1.98;1.98	5.77	3.98	0.46160	.	0.365546	0.30492	N	0.009502	T	0.29355	0.0731	M	0.62723	1.935	0.25407	N	0.988398	D;D	0.60575	0.988;0.983	P;P	0.57204	0.815;0.766	T	0.12016	-1.0564	10	0.19147	T	0.46	-9.0348	5.1628	0.15070	0.0:0.5992:0.1506:0.2502	.	668;668	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	T	668	ENSP00000296137:A668T;ENSP00000441178:A668T	ENSP00000296137:A668T	A	-	1	0	FYCO1	45983828	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.289000	0.33307	0.786000	0.33708	0.655000	0.94253	GCC	.		0.632	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46008824	C	T	46008824	3	4	113	1	0	0	0	0	1	0	0	0	6144	739	26	2	2478	2	FYCO1	3	46008824	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	7999506	46008824	152013606	14	9925											
IDUA	3425	hgsc.bcm.edu	37	chr4	980971	980971	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccccgcacctggtgcaTgtggacgcggcccgcgcgct	4	5	16	16	6	0	0	0	0	0	0	0	2	0	1	4	4	1	3	4	4	0	0	rs10794537	byFrequency	TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr4:980971T>G	ENST00000247933.4	+	1	187	c.99T>G	c.(97-99)caT>caG	p.H33Q	IDUA_ENST00000453894.1_Missense_Mutation_p.H33Q|SLC26A1_ENST00000398520.2_Intron	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	33			H -> Q (in dbSNP:rs10794537). {ECO:0000269|PubMed:1362562, ECO:0000269|PubMed:1505961, ECO:0000269|PubMed:1946389, ECO:0000269|PubMed:21394825}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			ACCTGGTGCATGTGGACGCGG	0.801													G|||	4467	0.891973	0.9826	0.8386	5008	,	,		8604	0.8472		0.8042	False		,,,				2504	0.9438				p.H33Q		.											.	IDUA-91	0			c.T99G						.						1	1	1					4																	980971		552	1375	1927	SO:0001583	missense	3425	exon1			GGTGCATGTGGAC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.99T>G	4.37:g.980971T>G	ENSP00000247933:p.His33Gln	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_000203	0	0	0	7	7	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	1801|1801	0.8246336996336996|0.8246336996336996	464|464	0.943089430894309|0.943089430894309	294|294	0.8121546961325967|0.8121546961325967	448|448	0.7832167832167832|0.7832167832167832	595|595	0.7849604221635884|0.7849604221635884	G|G	3.726|3.726	-0.056533|-0.056533	0.07362|0.07362	.|.	.|.	ENSG00000127415|ENSG00000127415	ENST00000504568|ENST00000247933;ENST00000453894;ENST00000502910	.|D;D;D	.|0.93247	.|-3.18;-3.19;-3.03	3.62|3.62	-0.897|-0.897	0.10553|0.10553	.|.	.|0.728933	.|0.12190	.|N	.|0.491278	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.36817|0.36817	-0.9732|-0.9732	4|9	.|0.10111	.|T	.|0.7	.|.	1.2904|1.2904	0.02059|0.02059	0.1461:0.2669:0.3485:0.2385|0.1461:0.2669:0.3485:0.2385	rs10794537|rs10794537	.|33;33	.|B3KWK6;P35475	.|.;IDUA_HUMAN	G|Q	33|33	.|ENSP00000247933:H33Q;ENSP00000396458:H33Q;ENSP00000422952:H33Q	.|ENSP00000247933:H33Q	C|H	+|+	1|3	0|2	IDUA|IDUA	970971|970971	0.000000|0.000000	0.05858|0.05858	0.992000|0.992000	0.48379|0.48379	0.012000|0.012000	0.07955|0.07955	-2.547000|-2.547000	0.00931|0.00931	-0.253000|-0.253000	0.09514|0.09514	-1.482000|-1.482000	0.00985|0.00985	TGT|CAT	T|0.175;G|0.825		0.801	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203		G	980971	T	G	980971	3	3	113	1	0	0	0	0	1	0	0	0	7525	1461	51	5	101	5	IDUA	4	980971	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08		980971	190173305	15	9926											
FNIP2	57600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	159825696	159825696	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggctcaaatactcttataAgctaaagctcaggacagttc	13	11	8	9	0	3	0	2	0	1	0	4	1	3	1	0	2	3	4	0	2	6	5			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr4:159825696A>G	ENST00000264433.6	+	17	3420	c.3345A>G	c.(3343-3345)taA>taG	p.*1115*	C4orf45_ENST00000434826.2_Intron|FNIP2_ENST00000379346.3_Silent_p.*1138*|C4orf45_ENST00000508011.1_Intron	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	0					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TACTCTTATAAGCTAAAGCTC	0.388																																					p.X1115X		.											.	FNIP2-68	0			c.A3345G						.						141	133	136					4																	159825696		1847	4095	5942	SO:0001819	synonymous_variant	57600	exon17			CTTATAAGCTAAA	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.3345A>G	4.37:g.159825696A>G		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	121	46	NM_020840	0	0	9	14	5	Q05DC3|Q96I31|Q9H994	Silent	SNP	ENST00000264433.6	37	CCDS47155.1																																																																																			.		0.388	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159825696	A	G	159825696	2	3	113	1	0	0	0	0	0	0	0	1	5995	79	3	3		3	FNIP2	4	159825696	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08	158844725	159825696	31328580	16	9927											
SH3RF1	57630	hgsc.bcm.edu	37	chr4	170043337	170043337	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccattccagcagcagcagcAgcggcggtggcgcctggtgg	6	5	16	14	3	0	0	0	0	0	0	1	0	1	0	3	5	5	4	3	5	0	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr4:170043337A>G	ENST00000284637.9	-	7	1601	c.1260T>C	c.(1258-1260)gcT>gcC	p.A420A	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	420	Poly-Ala.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		CAGCAGCAGCAGCGGCGGTGG	0.582																																					p.A420A		.											.	SH3RF1-567	0			c.T1260C						.						47	43	44					4																	170043337		2203	4300	6503	SO:0001819	synonymous_variant	57630	exon7			AGCAGCAGCGGCG	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"RING-type (C3HC4) zinc fingers"	17650	protein-coding gene	gene with protein product	"plenty of SH3 domains"		"SH3 multiple domains 2"	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.1260T>C	4.37:g.170043337A>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_020870	0	0	15	15	0	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Silent	SNP	ENST00000284637.9	37	CCDS34099.1																																																																																			.		0.582	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		G	170043337	A	G	170043337	2	3	113	1	0	0	0	0	0	0	0	1	14290	175	7	3		3	SH3RF1	4	170043337	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08	10217641	170043337	21110939	17	9928											
ZCCHC10	54819	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	132334373	132334373	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatctgagtctgaatcagAggaggaggaagaggttgtgg	12	8	18	3	0	3	4	1	2	2	2	3	8	3	8	0	6	0	1	0	6	3	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:132334373A>G	ENST00000509437.1	-	5	488	c.481T>C	c.(481-483)Tct>Cct	p.S161P	ZCCHC10_ENST00000508080.1_5'UTR|ZCCHC10_ENST00000355372.2_Missense_Mutation_p.S155P|ZCCHC10_ENST00000513848.1_Missense_Mutation_p.S125P|ZCCHC10_ENST00000324170.3_Missense_Mutation_p.S139P|ZCCHC10_ENST00000509008.1_3'UTR|ZCCHC10_ENST00000513541.1_3'UTR			Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	161	Ser-rich.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTGAATCAgaggaggaggaa	0.478																																					p.S139P		.											.	ZCCHC10-90	0			c.T415C						.						84	89	87					5																	132334373		2203	4300	6503	SO:0001583	missense	54819	exon4			AATCAGAGGAGGA	BC005211	CCDS4165.1, CCDS75300.1, CCDS75301.1, CCDS75302.1	5q31.1	2008-05-02			ENSG00000155329	ENSG00000155329		"Zinc fingers, CCHC domain containing"	25954	protein-coding gene	gene with protein product						12477932	Standard	XM_005272024		Approved	FLJ20094	uc003kyg.3	Q8TBK6	OTTHUMG00000129013	ENST00000509437.1:c.481T>C	5.37:g.132334373A>G	ENSP00000423276:p.Ser161Pro	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	82	20	NM_017665	0	0	12	21	9	Q9NXR4	Missense_Mutation	SNP	ENST00000509437.1	37		.	.	.	.	.	.	.	.	.	.	A	14.70	2.613809	0.46631	.	.	ENSG00000155329	ENST00000324170;ENST00000355372;ENST00000509437;ENST00000513848	.	.	.	4.82	4.82	0.62117	.	0.135986	0.50627	D	0.000119	T	0.75027	0.3794	.	.	.	0.80722	D	1	D;D;D	0.69078	0.978;0.995;0.997	P;P;P	0.59288	0.629;0.795;0.855	T	0.79420	-0.1811	8	0.87932	D	0	.	14.339	0.66611	1.0:0.0:0.0:0.0	.	125;161;139	G3XAM1;Q8TBK6;Q8TBK6-2	.;ZCH10_HUMAN;.	P	139;155;161;125	.	ENSP00000324274:S139P	S	-	1	0	ZCCHC10	132362272	1.000000	0.71417	0.987000	0.45799	0.813000	0.45954	4.104000	0.57790	1.939000	0.56221	0.460000	0.39030	TCT	.		0.478	ZCCHC10-004	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000370163.1	NM_017665		G	132334373	A	G	132334373	3	3	113	1	0	0	0	0	1	0	0	0	17611	304	11	3	101	3	ZCCHC10	5	132334373	Missense_Mutation	SNP	A	TCGA-G7-6792-01A-21D-1961-08		132334373	48580887	18	9929											
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140751166	140751166	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaagataccaaaaacacatAcaggttggtgacagatggag	17	7	10	7	0	1	3	1	1	0	2	1	4	1	4	1	3	3	1	1	3	5	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:140751166A>G	ENST00000576222.1	+	1	1336	c.1205A>G	c.(1204-1206)tAc>tGc	p.Y402C	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	402	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAAACACATACAGGTTGGTG	0.448																																					p.Y402C		.											.	.	0			c.A1205G						.						64	66	66					5																	140751166		2002	4173	6175	SO:0001583	missense	56102	exon1			ACACATACAGGTT	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1205A>G	5.37:g.140751166A>G	ENSP00000461862:p.Tyr402Cys	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_018924	0	0	1	1	0	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			.		0.448	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		G	140751166	A	G	140751166	3	3	113	1	0	0	0	0	1	0	0	0	11590	391	14	3	1207	3	PCDHGB3	5	140751166	Missense_Mutation	SNP	A	TCGA-G7-6792-01A-21D-1961-08	8416793	140751166	40164094	19	9930											
RBM27	54439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	145610424	145610424	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactataacaatcatagctCttccaattcttttggtcgaa	12	16	4	9	1	3	0	1	0	2	0	5	1	4	0	1	1	3	1	1	1	7	8			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:145610424C>A	ENST00000265271.5	+	6	960	c.794C>A	c.(793-795)tCt>tAt	p.S265Y	RBM27_ENST00000506502.1_Missense_Mutation_p.S265Y	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	265					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATCATAGCTCTTCCAATTCT	0.428																																					p.S265Y		.											.	RBM27-70	0			c.C794A						.						124	108	113					5																	145610424		1568	3582	5150	SO:0001583	missense	54439	exon6			ATAGCTCTTCCAA	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.794C>A	5.37:g.145610424C>A	ENSP00000265271:p.Ser265Tyr	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	97	37	NM_018989	0	0	5	6	1	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.690372	0.48097	.	.	ENSG00000091009	ENST00000265271	T	0.48201	0.82	5.56	5.56	0.83823	.	0.344763	0.28332	N	0.015722	T	0.36496	0.0969	N	0.22421	0.69	0.35199	D	0.774129	P;P	0.51653	0.454;0.947	B;B	0.41374	0.064;0.355	T	0.53514	-0.8428	10	0.59425	D	0.04	-7.8615	15.2609	0.73621	0.1489:0.8511:0.0:0.0	.	265;265	Q9P2N5;B3KY61	RBM27_HUMAN;.	Y	265	ENSP00000265271:S265Y	ENSP00000265271:S265Y	S	+	2	0	RBM27	145590617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.339000	0.43965	2.614000	0.88457	0.563000	0.77884	TCT	.		0.428	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		A	145610424	C	A	145610424	3	1	113	1	0	0	0	0	1	0	0	0	13159	913	32	4	816	4	RBM27	5	145610424	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	4859258	145610424	35304836	20	9931											
ARSI	340075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149677576	149677576	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcggccagttgctgccccccGagaaagtctggccaccattg	7	7	12	15	2	1	1	0	0	1	1	1	2	1	1	6	2	2	2	6	2	1	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:149677576G>A	ENST00000328668.7	-	2	1490	c.911C>T	c.(910-912)tCg>tTg	p.S304L		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	304					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTGCCCCCCGAGAAAGTCTG	0.587																																					p.S304L		.											.	ARSI-92	0			c.C911T						.						36	32	34					5																	149677576		2199	4292	6491	SO:0001583	missense	340075	exon2			CCCCCCGAGAAAG	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.911C>T	5.37:g.149677576G>A	ENSP00000333395:p.Ser304Leu	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	71	28	NM_001012301	0	0	0	0	0	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	37	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.361900	0.61403	.	.	ENSG00000183876	ENST00000328668;ENST00000515301	D;D	0.96745	-4.11;-4.11	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.059421	0.64402	D	0.000001	D	0.92473	0.7610	N	0.25426	0.745	0.54753	D	0.999982	B	0.18166	0.026	B	0.18263	0.021	D	0.89036	0.3445	10	0.22109	T	0.4	.	17.6599	0.88189	0.0:0.0:1.0:0.0	.	304	Q5FYB1	ARSI_HUMAN	L	304;161	ENSP00000333395:S304L;ENSP00000426879:S161L	ENSP00000333395:S304L	S	-	2	0	ARSI	149657769	1.000000	0.71417	0.961000	0.40146	0.945000	0.59286	7.738000	0.84966	2.460000	0.83146	0.561000	0.74099	TCG	.		0.587	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		A	149677576	G	A	149677576	3	1	113	1	0	0	0	0	1	0	0	0	995	1059	37	1	802	1	ARSI	5	149677576	Missense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08	4067152	149677576	31237684	21	9932											
F12	2161	broad.mit.edu;bcgsc.ca	37	chr5	176830985	176830985	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcgtagcgccaccagcccGccaacgacgcgggtcatcga	8	3	12	18	8	1	0	1	0	0	0	2	2	1	0	5	1	3	1	5	1	2	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:176830985G>A	ENST00000253496.3	-	10	1173	c.1125C>T	c.(1123-1125)ggC>ggT	p.G375G	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	375	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CCACCAGCCCGCCAACGACGC	0.706									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G375G													.	F12-90	0			c.C1125T						.																																			SO:0001819	synonymous_variant	2161	exon10	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	CAGCCCGCCAACG	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.1125C>T	5.37:g.176830985G>A		Somatic	44	0	1934	WXS	Illumina HiSeq	Phase_I	28	16	NM_000505	0	0	0	0	0	P78339	Silent	SNP	ENST00000253496.3	37	CCDS34302.1																																																																																			G|1.000;C|0.000		0.706	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176830985	G	A	176830985	2	1	113	1	0	0	0	0	0	0	0	1	5352	1074	38	1		1	F12	5	176830985	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08	27153409	176830985	4084275	22	9933											
NDUFAF4	29078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	97344647	97344647	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagacacaggatctttggaAtcaacatacacatcttttag	15	11	7	8	0	3	1	1	0	2	1	3	4	3	3	0	2	2	0	0	2	5	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr6:97344647A>G	ENST00000316149.7	-	2	292	c.213T>C	c.(211-213)gaT>gaC	p.D71D	NDUFAF4_ENST00000489477.1_5'UTR	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	71					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)				large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						GATCTTTGGAATCAACATACA	0.358																																					p.D71D		.											.	NDUFAF4-91	0			c.T213C						.						148	149	149					6																	97344647		2203	4300	6503	SO:0001819	synonymous_variant	29078	exon2			TTTGGAATCAACA	AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"Mitochondrial respiratory chain complex assembly factors"	21034	protein-coding gene	gene with protein product		611776	"chromosome 6 open reading frame 66", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.213T>C	6.37:g.97344647A>G		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	114	32	NM_014165	0	0	5	12	7	B2R4J5	Silent	SNP	ENST00000316149.7	37	CCDS5037.1																																																																																			.		0.358	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165		G	97344647	A	G	97344647	2	3	113	1	0	0	0	0	0	0	0	1	10303	98	4	3		3	NDUFAF4	6	97344647	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08		97344647	73770420	23	9934											
CALU	813	broad.mit.edu	37	chr7	128407599	128407599	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagtttcgggataagaacCgtgatgggaagatggacaag	13	9	15	4	2	0	4	0	2	0	2	1	7	0	7	1	3	1	1	1	3	4	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr7:128407599C>A	ENST00000249364.4	+	6	835	c.733C>A	c.(733-735)Cgt>Agt	p.R245S	CALU_ENST00000535623.1_3'UTR|CALU_ENST00000479257.1_Missense_Mutation_p.R253S|CALU_ENST00000538546.1_Missense_Mutation_p.R94S|CALU_ENST00000535011.2_Intron|CALU_ENST00000542996.2_Missense_Mutation_p.R253S|CALU_ENST00000449187.2_Missense_Mutation_p.R245S	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin	245	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)			kidney(2)|large_intestine(3)|lung(5)	10						GGATAAGAACCGTGATGGGAA	0.488																																					p.R253S													.	CALU-90	0			c.C757A						.						192	179	183					7																	128407599		2203	4300	6503	SO:0001583	missense	813	exon7			AAGAACCGTGATG	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"EF-hand domain containing"	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.733C>A	7.37:g.128407599C>A	ENSP00000249364:p.Arg245Ser	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	134	5	NM_001199671	0	0	89	89	0	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	37	CCDS5805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.93|15.93	2.978015|2.978015	0.53720|0.53720	.|.	.|.	ENSG00000128595|ENSG00000128595	ENST00000493278|ENST00000542996;ENST00000538546;ENST00000249364;ENST00000449187;ENST00000479257	.|T;T;T;T;T	.|0.54866	.|0.55;0.55;0.55;0.55;0.55	5.44|5.44	4.56|4.56	0.56223|0.56223	.|EF-hand-like domain (1);	.|0.267158	.|0.39759	.|N	.|0.001271	T|T	0.34948|0.34948	0.0915|0.0915	N|N	0.17474|0.17474	0.49|0.49	0.38401|0.38401	D|D	0.945668|0.945668	.|B;B	.|0.25007	.|0.116;0.001	.|B;B	.|0.20184	.|0.028;0.003	T|T	0.18304|0.18304	-1.0341|-1.0341	5|10	.|0.20046	.|T	.|0.44	-2.8562|-2.8562	13.5218|13.5218	0.61572|0.61572	0.1568:0.8432:0.0:0.0|0.1568:0.8432:0.0:0.0	.|.	.|253;245	.|D6QS48;O43852	.|.;CALU_HUMAN	Q|S	76|253;94;245;245;253	.|ENSP00000438248:R253S;ENSP00000438994:R94S;ENSP00000249364:R245S;ENSP00000408838:R245S;ENSP00000420381:R253S	.|ENSP00000249364:R245S	P|R	+|+	2|1	0|0	CALU|CALU	128194835|128194835	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.613000|2.613000	0.46351|0.46351	1.287000|1.287000	0.44583|0.44583	0.563000|0.563000	0.77884|0.77884	CCG|CGT	.		0.488	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219		A	128407599	C	A	128407599	3	1	113	1	0	0	0	0	1	0	0	0	2600	652	23	4	949	4	CALU	7	128407599	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		128407599	30731064	24	9935											
CHCHD3	54927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	132709362	132709362	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgccagctcctcagctacTcttcttttcaattcttcatc	8	16	3	14	0	6	0	3	0	3	0	8	0	7	0	2	0	4	2	2	0	3	6			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr7:132709362T>A	ENST00000262570.5	-	3	339	c.195A>T	c.(193-195)agA>agT	p.R65S	CHCHD3_ENST00000476546.1_5'UTR|CHCHD3_ENST00000542753.1_Missense_Mutation_p.R65S|CHCHD3_ENST00000448878.1_Missense_Mutation_p.R65S	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	65					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						CCTCAGCTACTCTTCTTTTCA	0.383																																					p.R65S		.											.	CHCHD3-90	0			c.A195T						.						126	127	127					7																	132709362		2203	4300	6503	SO:0001583	missense	54927	exon3			AGCTACTCTTCTT	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"Coiled-coil-helix-coiled-coil-helix domain containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	21906	protein-coding gene	gene with protein product	"mitochondrial inner membrane organizing system 3", "protein phosphatase 1, regulatory subunit 22"	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.195A>T	7.37:g.132709362T>A	ENSP00000262570:p.Arg65Ser	Somatic	200	1		WXS	Illumina HiSeq	Phase_I	208	19	NM_017812	0	0	49	62	13		Missense_Mutation	SNP	ENST00000262570.5	37	CCDS5828.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.556929	0.86231	.	.	ENSG00000106554	ENST00000262570;ENST00000448878;ENST00000542753	T;T;T	0.42513	0.97;0.97;0.97	5.81	3.44	0.39384	.	0.092160	0.85682	D	0.000000	T	0.54631	0.1870	M	0.76574	2.34	0.34318	D	0.686194	P;D;P	0.64830	0.9;0.994;0.772	P;D;B	0.64595	0.65;0.927;0.428	T	0.62144	-0.6916	10	0.09843	T	0.71	-13.2962	9.4483	0.38710	0.0:0.1445:0.0:0.8555	.	65;65;65	G3V1K1;C9JRZ6;Q9NX63	.;.;CHCH3_HUMAN	S	65	ENSP00000262570:R65S;ENSP00000389297:R65S;ENSP00000440267:R65S	ENSP00000262570:R65S	R	-	3	2	CHCHD3	132359902	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.356000	0.44116	0.553000	0.29044	0.496000	0.49642	AGA	.		0.383	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		A	132709362	T	A	132709362	3	1	113	1	0	0	0	0	1	0	0	0	3323	1548	54	5	512	5	CHCHD3	7	132709362	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08	4301763	132709362	26429301	25	9936											
KRBA1	84626	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	149416749	149416749	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcgggagaactacgagaCgctggtctctgtgggtaagg	9	8	17	7	3	1	2	0	0	1	2	2	5	1	2	0	4	3	2	0	4	3	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr7:149416749C>T	ENST00000485033.2	+	1	20	c.20C>T	c.(19-21)aCg>aTg	p.T7M	KRBA1_ENST00000479560.1_3'UTR|KRBA1_ENST00000319551.8_Missense_Mutation_p.T7M|KRBA1_ENST00000255992.10_Missense_Mutation_p.T7M			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	7										breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AACTACGAGACGCTGGTCTCT	0.657																																					.													.	KRBA1-91	0			.						.						46	59	55					7																	149416749		2129	4258	6387	SO:0001583	missense	84626	.			ACGAGACGCTGGT	AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.20C>T	7.37:g.149416749C>T	ENSP00000420112:p.Thr7Met	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	46	10	.	0	0	4	4	0	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Missense_Mutation	SNP	ENST00000485033.2	37		.	.	.	.	.	.	.	.	.	.	C	10.86	1.468525	0.26335	.	.	ENSG00000133619	ENST00000486744;ENST00000255992;ENST00000319551;ENST00000497895;ENST00000485033	T;T;T	0.34072	1.39;1.38;1.38	4.86	3.03	0.35002	.	0.734681	0.12271	N	0.483815	T	0.15522	0.0374	N	0.14661	0.345	0.19775	N	0.99995	P	0.46220	0.874	B	0.31101	0.124	T	0.11397	-1.0589	10	0.87932	D	0	-3.3573	4.6081	0.12387	0.1745:0.6412:0.0:0.1843	.	7	A5PL33	KRBA1_HUMAN	M	7	ENSP00000255992:T7M;ENSP00000317165:T7M;ENSP00000420112:T7M	ENSP00000255992:T7M	T	+	2	0	KRBA1	149047682	0.005000	0.15991	0.217000	0.23759	0.579000	0.36224	0.249000	0.18216	1.285000	0.44548	0.561000	0.74099	ACG	.		0.657	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534		T	149416749	C	T	149416749	3	4	113	1	0	0	0	0	1	0	0	0	8460	536	19	1	22	1	KRBA1	7	149416749	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	16707387	149416749	9721914	26	9937											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101719226	101719226	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accgggcatattttggaatgCtgcattttaaagatgtgaat	12	14	10	5	1	0	2	0	1	0	1	0	3	0	3	1	2	2	3	1	2	5	5	rs112580522		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr8:101719226C>G	ENST00000318607.5	-	10	2465		c.e10-1		PABPC1_ENST00000519596.1_Intron|PABPC1_ENST00000519004.1_Splice_Site|PABPC1_ENST00000522387.1_Splice_Site|AP001205.1_ENST00000579868.1_RNA	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)	p.?(1)		breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TTTTGGAATGCTGCATTTTAA	0.413																																					.		.											.	PABPC1-68	1	Unknown(1)	lung(1)	c.1337-1G>C						.						39	41	40					8																	101719226		2203	4300	6503	SO:0001630	splice_region_variant	26986	exon11			GGAATGCTGCATT	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"RNA binding motif (RRM) containing"	8554	protein-coding gene	gene with protein product		604679	"poly(A)-binding protein, cytoplasmic 2"	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1337-1G>C	8.37:g.101719226C>G		Somatic	63	1		WXS	Illumina HiSeq	Phase_I	54	6	NM_002568	0	0	0	0	0	Q15097|Q93004	Splice_Site	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096182	0.76870	.	.	ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000517403	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5891	0.99427	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PABPC1	101788402	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	5.388000	0.66249	2.876000	0.98609	0.650000	0.86243	.	G|1.000;|0.000		0.413	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	Intron	G	101719226	C	G	101719226	5	3	113	1	0	0	0	0	0	0	1	0	11389	811	28	4	594	4	PABPC1	8	101719226	Splice_Site	SNP	C	TCGA-G7-6792-01A-21D-1961-08		101719226	44644796	27	9938											
TG	7038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133931710	133931710	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaggcagggagcttggccTgtgtcccatgtcctgtgggc	6	9	15	11	0	0	0	0	0	0	0	2	1	2	1	3	4	2	2	3	4	1	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr8:133931710T>G	ENST00000220616.4	+	21	4508	c.4468T>G	c.(4468-4470)Tgt>Ggt	p.C1490G	TG_ENST00000377869.1_Missense_Mutation_p.C1490G|TG_ENST00000542445.1_5'UTR	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1490					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GAGCTTGGCCTGTGTCCCATG	0.478																																					p.C1490G		.											.	TG-145	0			c.T4468G						.						141	112	122					8																	133931710		2203	4300	6503	SO:0001583	missense	7038	exon21			TTGGCCTGTGTCC	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4468T>G	8.37:g.133931710T>G	ENSP00000220616:p.Cys1490Gly	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	109	41	NM_003235	0	0	0	0	0	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.60|16.60	3.168293|3.168293	0.57584|0.57584	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616|ENST00000519178	D;D|.	0.86865|.	-2.18;-2.18|.	5.52|5.52	5.52|5.52	0.82312|0.82312	Tyrosine-protein kinase ephrin type A/B receptor-like (1);|.	0.194939|.	0.36703|.	N|.	0.002444|.	T|T	0.80374|0.80374	0.4611|0.4611	H|H	0.97516|0.97516	4.02|4.02	0.28752|0.28752	N|N	0.90136|0.90136	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.80527|0.80527	-0.1343|-0.1343	10|5	0.87932|.	D|.	0|.	.|.	12.3216|12.3216	0.54987|0.54987	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1490|.	P01266|.	THYG_HUMAN|.	G|R	1490;296;1490|9	ENSP00000367100:C1490G;ENSP00000220616:C1490G|.	ENSP00000220616:C1490G|.	C|L	+|+	1|2	0|0	TG|TG	134000892|134000892	1.000000|1.000000	0.71417|0.71417	0.890000|0.890000	0.34922|0.34922	0.588000|0.588000	0.36517|0.36517	5.096000|5.096000	0.64535|0.64535	2.225000|2.225000	0.72522|0.72522	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.		0.478	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		G	133931710	T	G	133931710	3	3	113	1	0	0	0	0	1	0	0	0	15845	1580	55	5	4550	5	TG	8	133931710	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08	32212484	133931710	12432312	28	9939											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039761	2039761	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgttgcctggcttgcagcaAcaacagcagcagcaacagca	13	5	10	13	1	0	0	0	0	0	0	0	0	0	0	1	1	10	8	1	1	3	2	rs13296982		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr9:2039761A>G	ENST00000382203.1	+	4	860	c.651A>G	c.(649-651)caA>caG	p.Q217Q	SMARCA2_ENST00000382194.1_Silent_p.Q217Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000349721.2_Silent_p.Q217Q|SMARCA2_ENST00000357248.2_Silent_p.Q217Q|RP11-264I13.2_ENST00000426860.1_RNA			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	217	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GCTTgcagcaacaacagcagc	0.607																																					p.Q217Q		.											.	SMARCA2-653	0			c.A651G						.	A	,	1,4405		0,1,2202	16	18	17		651,651	1.4	1	9	dbSNP_121	17	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	0,1,6499	GG,GA,AA		0.0,0.0227,0.0077	,	217/1591,217/1573	2039761	1,12999	2203	4297	6500	SO:0001819	synonymous_variant	6595	exon4			GCAGCAACAACAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.651A>G	9.37:g.2039761A>G		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_139045	0	0	33	33	0	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			A|1.000;|0.000		0.607	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		G	2039761	A	G	2039761	2	3	113	1	0	0	0	0	0	0	0	1	14801	40	2	3		3	SMARCA2	9	2039761	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08		2039761	139173670	29	9940											
KIAA1279	26128	ucsc.edu	37	chr10	70775350	70775350	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tctgaacttagagctttaagGaaaaaagaactagatgagga	18	9	10	4	0	1	5	0	2	1	3	1	7	1	7	0	2	3	1	0	2	8	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr10:70775350G>A	ENST00000361983.4	+	7	1146	c.1044G>A	c.(1042-1044)agG>agA	p.R348R		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	348					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						GAGCTTTAAGGAAAAAAGAAC	0.398																																					p.R348R													.	KIAA1279-91	0			c.G1044A						.						81	84	83					10																	70775350		2203	4300	6503	SO:0001819	synonymous_variant	26128	exon7			TTTAAGGAAAAAA	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1044G>A	10.37:g.70775350G>A		Somatic	112	0		WXS	Illumina HiSeq		99	2	NM_015634	0	0	19	22	3	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Silent	SNP	ENST00000361983.4	37	CCDS7284.1																																																																																			.		0.398	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		A	70775350	G	A	70775350	2	1	113	1	0	0	0	0	0	0	0	1	8242	1165	41	2		2	KIAA1279	10	70775350	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08		70775350	64759397	30	9941											
ERLIN1	10613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101911987	101911987	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttccagtcctaatatctgaAtatttcaaagcacatgagga	14	12	6	9	0	2	2	1	2	1	0	4	3	4	3	2	1	1	1	2	1	5	5			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr10:101911987A>G	ENST00000421367.2	-	11	3655	c.948T>C	c.(946-948)taT>taC	p.Y316Y	ERLIN1_ENST00000407654.3_Silent_p.Y316Y	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	314					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		TAATATCTGAATATTTCAAAG	0.443																																					p.Y316Y		.											.	.	0			c.T948C						.						119	115	116					10																	101911987		2203	4300	6503	SO:0001819	synonymous_variant	10613	exon11			ATCTGAATATTTC	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"	611604	"chromosome 10 open reading frame 69", "SPFH domain family, member 1"	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.948T>C	10.37:g.101911987A>G		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	132	50	NM_006459	0	0	17	28	11	B0QZ42|Q53HV0	Silent	SNP	ENST00000421367.2	37	CCDS7487.2																																																																																			.		0.443	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459		G	101911987	A	G	101911987	2	3	113	1	0	0	0	0	0	0	0	1	5245	108	4	3		3	ERLIN1	10	101911987	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08	31136637	101911987	33622760	31	9942											
PPFIBP2	8495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	7669667	7669667	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagagcgtgtgtgtgcaTggctggaggactttggcctg	6	10	17	8	1	0	1	0	0	0	1	0	3	0	3	1	4	2	3	1	4	0	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr11:7669667T>C	ENST00000299492.4	+	18	2084	c.1696T>C	c.(1696-1698)Tgg>Cgg	p.W566R	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.W408R|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.W423R|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.W454R	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	566	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TGTGTGTGCATGGCTGGAGGA	0.547																																					p.W566R		.											.	PPFIBP2-273	0			c.T1696C						.						165	124	138					11																	7669667		2201	4296	6497	SO:0001583	missense	8495	exon18			TGTGCATGGCTGG	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"Sterile alpha motif (SAM) domain containing"	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1696T>C	11.37:g.7669667T>C	ENSP00000299492:p.Trp566Arg	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	117	44	NM_003621	0	0	5	14	9	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451254	0.84209	.	.	ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.74	5.74	0.90152	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.64402	D	0.000001	D	0.82660	0.5085	H	0.95114	3.625	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.87696	0.2557	10	0.87932	D	0	-9.1173	13.9867	0.64339	0.0:0.0:0.0:1.0	.	454;454;489;408;423;566	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	R	566;408;489;454;423	ENSP00000299492:W566R;ENSP00000436498:W408R;ENSP00000435469:W454R;ENSP00000437321:W423R	ENSP00000299492:W566R	W	+	1	0	PPFIBP2	7626243	1.000000	0.71417	0.926000	0.36857	0.995000	0.86356	8.040000	0.89188	2.194000	0.70268	0.459000	0.35465	TGG	.		0.547	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		C	7669667	T	C	7669667	3	2	113	1	0	0	0	0	1	0	0	0	12340	1464	51	3	1762	3	PPFIBP2	11	7669667	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08		7669667	127336849	32	9943											
SLC22A20	440044	bcgsc.ca	37	chr11	64985059	64985059	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctgcagctggcagcttcggGggccgccacagcgtatttca	6	8	13	14	3	1	0	1	0	0	0	2	0	1	0	3	3	4	5	3	3	1	3	rs113875023	byFrequency	TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr11:64985059G>T	ENST00000525437.1	+	0	572							A6NK97	S22AK_HUMAN	solute carrier family 22, member 20						ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)	8						GCAGCTTCGGGGGCCGCCACA	0.602																																					p.G180V													.	SLC22A20-23	0			c.G539T						.						35	41	39					11																	64985059		1966	4142	6108			440044	exon3			CTTCGGGGGCCGC	DQ053017		11q13.1	2014-02-20			ENSG00000197847	ENSG00000197847		"Solute carriers"	29867	other	unknown		611696				15369770, 16478971	Standard	NM_001004326		Approved	Oat6, FLJ16331	uc021qlh.1	A6NK97	OTTHUMG00000165615		11.37:g.64985059G>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_1	46	10	NM_001004326	0	0	0	0	0	B9EJB2|Q6ZN88	Missense_Mutation	SNP	ENST00000525437.1	37																																																																																				G|0.992;A|0.008		0.602	SLC22A20-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000385336.1	NM_001004326		T	64985059	G	T	64985059	1	4	113	0	1	0	0	0	0	0	0	0	14483	1232	43	4		4	SLC22A20	11	64985059	RNA	SNP	G	TCGA-G7-6792-01A-21D-1961-08	57315392	64985059	70021457	33	9944											
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751585	76751585	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcggccacgagggcatccTggcccttcggcgtgcagctt	5	7	14	15	4	0	0	0	0	0	0	2	1	1	0	3	4	3	3	3	4	0	2	rs11292199		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr11:76751585T>C	ENST00000354301.5	+	4	1076	c.988T>C	c.(988-990)Tgg>Cgg	p.W330R	B3GNT6_ENST00000421061.1_Splice_Site|B3GNT6_ENST00000533140.1_Silent_p.P330P	NM_138706.3	NP_619651.3	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						GAGGGCATCCTGGCCCTTCGG	0.697																																					.		.											.	.	0			c.988+1T>C						.						6	5	6					11																	76751585		1175	2610	3785	SO:0001630	splice_region_variant	192134	exon3			GCATCCTGGCCCT	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000354301.5:c.988-1T>C	11.37:g.76751585T>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	5	3	NM_138706	0	0	0	0	0	Q4TTN0	Splice_Site	SNP	ENST00000354301.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.007|0.007	-1.936685|-1.936685	0.00484|0.00484	.|.	.|.	ENSG00000198488|ENSG00000198488	ENST00000354301;ENST00000421061|ENST00000354301	.|T	.|0.24538	.|1.85	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.11024	.|0.0269	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.26916	.|-1.0089	.|4	.|0.02654	.|T	.|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|R	-1|330	.|ENSP00000346256:W330R	.|ENSP00000346256:W330R	.|W	+|+	.|1	.|0	B3GNT6|B3GNT6	76429233|76429233	0.988000|0.988000	0.35896|0.35896	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	0.000000|0.000000	0.12993|0.12993	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	.|TGG	.		0.697	B3GNT6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138706	Missense_Mutation	C	76751585	T	C	76751585	5	2	113	1	0	0	0	0	0	0	1	0	1262	1567	55	3	992	3	B3GNT6	11	76751585	Splice_Site	SNP	T	TCGA-G7-6792-01A-21D-1961-08	11766526	76751585	58254931	34	9945											
KLRK1	22914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	10539567	10539567	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatcgtgttgaaaaatcaCtcttcttcagatccaagtta	12	13	6	10	1	4	2	2	1	2	1	6	2	5	2	2	0	0	2	2	0	4	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:10539567C>T	ENST00000240618.6	-	3	223	c.83G>A	c.(82-84)aGt>aAt	p.S28N	KLRC4-KLRK1_ENST00000539300.1_3'UTR|KLRK1_ENST00000540818.1_Missense_Mutation_p.S28N|RP11-277P12.20_ENST00000500682.1_RNA	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	28					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						TGAAAAATCACTCTTCTTCAG	0.363																																					p.S28N		.											.	.	0			c.G83A						.						171	159	163					12																	10539567		2203	4299	6502	SO:0001583	missense	0	exon8			AAATCACTCTTCT	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.83G>A	12.37:g.10539567C>T	ENSP00000240618:p.Ser28Asn	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	56	18	NM_001199805	0	0	0	0	0	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	37	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.506590	0.00992	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01430	4.9;4.9	4.09	-8.18	0.01053	.	2.508350	0.01286	N	0.009885	T	0.00998	0.0033	L	0.29908	0.895	0.09310	N	1	B;B;B	0.21520	0.0;0.0;0.057	B;B;B	0.15870	0.0;0.001;0.014	T	0.48958	-0.8988	10	0.11794	T	0.64	.	1.9441	0.03353	0.1238:0.2263:0.3731:0.2768	.	28;9;28	Q8WZ67;Q1HEA1;P26718	.;.;NKG2D_HUMAN	N	28	ENSP00000240618:S28N;ENSP00000446003:S28N	ENSP00000240618:S28N	S	-	2	0	KLRK1	10430834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.256000	0.00538	-1.778000	0.01282	-1.161000	0.01788	AGT	.		0.363	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		T	10539567	C	T	10539567	3	4	113	1	0	0	0	0	1	0	0	0	8444	565	20	2	591	2	KLRK1	12	10539567	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		10539567	123312328	35	9946											
STK38L	23012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	27468238	27468238	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttagcatttcagaacatgaaCtcaaagaggaaagcagaaac	19	7	8	7	0	2	4	2	1	0	3	2	5	2	5	0	1	5	2	0	1	6	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:27468238C>A	ENST00000389032.3	+	9	961	c.792C>A	c.(790-792)aaC>aaA	p.N264K	STK38L_ENST00000539577.1_Missense_Mutation_p.N171K	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					AGAACATGAACTCAAAGAGGA	0.348																																					p.N264K		.											.	STK38L-980	0			c.C792A						.						65	70	69					12																	27468238		2203	4300	6503	SO:0001583	missense	23012	exon9			CATGAACTCAAAG	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.792C>A	12.37:g.27468238C>A	ENSP00000373684:p.Asn264Lys	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	116	29	NM_015000	0	0	13	17	4		Missense_Mutation	SNP	ENST00000389032.3	37	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955368	0.53293	.	.	ENSG00000211455	ENST00000389032;ENST00000539577	T;T	0.58358	0.34;0.41	4.5	-0.848	0.10727	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.46502	0.1396	L	0.37800	1.135	0.58432	D	0.999996	P;P	0.37276	0.589;0.589	P;B	0.46208	0.507;0.405	T	0.35226	-0.9797	10	0.48119	T	0.1	.	9.8271	0.40919	0.0:0.5362:0.0:0.4638	.	171;264	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	K	264;171	ENSP00000373684:N264K;ENSP00000446386:N171K	ENSP00000373684:N264K	N	+	3	2	STK38L	27359505	1.000000	0.71417	0.991000	0.47740	0.990000	0.78478	1.582000	0.36568	-0.260000	0.09418	-0.229000	0.12294	AAC	.		0.348	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000		A	27468238	C	A	27468238	3	1	113	1	0	0	0	0	1	0	0	0	15336	564	20	4	822	4	STK38L	12	27468238	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	16928671	27468238	106383657	36	9947											
KRT18	3875	broad.mit.edu	37	chr12	53344644	53344644	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctggagacagagatcgAggctctcaaggaggagctgc	11	5	16	9	1	1	2	1	0	1	2	3	7	1	4	0	4	3	4	0	4	1	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:53344644A>G	ENST00000388835.3	+	3	821	c.611A>G	c.(610-612)gAg>gGg	p.E204G	AC107016.2_ENST00000581256.1_RNA|KRT18_ENST00000550600.1_Missense_Mutation_p.E204G|KRT18_ENST00000388837.2_Missense_Mutation_p.E204G|KRT8_ENST00000552551.1_5'Flank|KRT8_ENST00000546897.1_5'Flank|KRT8_ENST00000549198.1_5'Flank	NM_000224.2	NP_000215.1	P05783	K1C18_HUMAN	keratin 18	204	Coil 1B.|Necessary for interaction with PNN.|Rod.				anatomical structure morphogenesis (GO:0009653)|cell cycle (GO:0007049)|extrinsic apoptotic signaling pathway (GO:0097191)|Golgi to plasma membrane CFTR protein transport (GO:0043000)|hepatocyte apoptotic process (GO:0097284)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of apoptotic process (GO:0043066)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell periphery (GO:0071944)|centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	11						ACAGAGATCGAGGCTCTCAAG	0.577																																					p.E204G													.	KRT18-91	0			c.A611G						.						20	16	17					12																	53344644		2203	4300	6503	SO:0001583	missense	3875	exon3			AGATCGAGGCTCT		CCDS31809.1	12q13	2013-01-16			ENSG00000111057	ENSG00000111057		"-", "Intermediate filaments type I, keratins (acidic)"	6430	protein-coding gene	gene with protein product		148070				1705144, 16831889	Standard	NM_000224		Approved		uc001sbg.3	P05783	OTTHUMG00000169882	ENST00000388835.3:c.611A>G	12.37:g.53344644A>G	ENSP00000373487:p.Glu204Gly	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	18	4	NM_000224	1	2	679	1446	764	Q53G38|Q5U0N8|Q9BW26	Missense_Mutation	SNP	ENST00000388835.3	37	CCDS31809.1	.	.	.	.	.	.	.	.	.	.	a	23.8	4.456730	0.84317	.	.	ENSG00000111057	ENST00000388837;ENST00000550600;ENST00000388835	D;D;D	0.91351	-2.83;-2.83;-2.83	3.85	3.85	0.44370	Filament (1);	0.000000	0.64402	D	0.000013	D	0.95642	0.8583	M	0.92555	3.32	0.58432	D	0.999999	D;D	0.61697	0.99;0.984	D;D	0.68192	0.927;0.956	D	0.96030	0.9016	10	0.87932	D	0	.	11.2377	0.48951	1.0:0.0:0.0:0.0	.	204;204	F8VZY9;P05783	.;K1C18_HUMAN	G	204	ENSP00000373489:E204G;ENSP00000447278:E204G;ENSP00000373487:E204G	ENSP00000373487:E204G	E	+	2	0	KRT18	51630911	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.068000	0.93961	1.964000	0.57103	0.459000	0.35465	GAG	.		0.577	KRT18-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406405.1	NM_199187		G	53344644	A	G	53344644	3	3	113	1	0	0	0	0	1	0	0	0	8476	304	11	3	621	3	KRT18	12	53344644	Missense_Mutation	SNP	A	TCGA-G7-6792-01A-21D-1961-08	25876406	53344644	80507251	37	9948											
KRR1	11103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	75895546	75895546	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccttaggtggaataaaTgctttgtttctttcctcttg	6	21	7	7	0	2	0	0	0	2	0	4	1	4	1	2	2	1	2	2	2	4	8			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:75895546T>C	ENST00000229214.4	-	9	983	c.960A>G	c.(958-960)gcA>gcG	p.A320A	GLIPR1_ENST00000266659.3_3'UTR|KRR1_ENST00000438169.2_Silent_p.A263A	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	320	Lys-rich.				rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						GTGGAATAAATGCTTTGTTTC	0.279																																					p.A320A		.											.	KRR1-92	0			c.A960G						.						125	123	124					12																	75895546		2203	4299	6502	SO:0001819	synonymous_variant	11103	exon9			AATAAATGCTTTG	U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"HIV-1 rev binding protein 2", "HIV-1 Rev binding protein 2"	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.960A>G	12.37:g.75895546T>C		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	73	21	NM_007043	0	0	18	22	4	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	37	CCDS9012.1																																																																																			.		0.279	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043		C	75895546	T	C	75895546	2	2	113	1	0	0	0	0	0	0	0	1	8467	1451	51	3		3	KRR1	12	75895546	Silent	SNP	T	TCGA-G7-6792-01A-21D-1961-08	22550902	75895546	57956349	38	9949											
GNPTAB	79158	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	102159058	102159058	+	Frame_Shift_Del	DEL	A	A	-																															tctggtttgggagaaggatcActttatacaattcatgaaaa																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:102159058delA	ENST00000299314.7	-	13	1899	c.1637delT	c.(1636-1638)gtgfs	p.V546fs	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	546					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						GAGAAGGATCACTTTATACAA	0.358																																					p.V546fs		.											.	GNPTAB-92	0			c.1637delT						.						77	77	77					12																	102159058		2203	4300	6503	SO:0001589	frameshift_variant	79158	exon13			.	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"EF-hand domain containing"	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.1637delT	12.37:g.102159058delA	ENSP00000299314:p.Val546fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	100	33	NM_024312	0	0	0	0	0	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Frame_Shift_Del	DEL	ENST00000299314.7	37	CCDS9088.1																																																																																			.		0.358	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			-	102159058	A	-	102159058	7	5	113	1	0	1	0	1	0	0	0	0	6565	159	6	0	2169	0	GNPTAB	12	102159058	Frame_Shift_Del	DEL	A	TCGA-G7-6792-01A-21D-1961-08	26263512	102159058	31692837	39	9950											
ACACB	32	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	109692084	109692084	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gacagagaaattgaattcctCccatccagagctccctacga	13	8	7	13	1	0	3	0	1	0	2	4	6	4	3	4	0	2	1	4	0	3	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:109692084C>T	ENST00000338432.7	+	44	6230	c.6111C>T	c.(6109-6111)ctC>ctT	p.L2037L	ACACB_ENST00000543201.1_Silent_p.L703L|ACACB_ENST00000377854.5_Silent_p.L1967L|ACACB_ENST00000377848.3_Silent_p.L2037L			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2037	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TTGAATTCCTCCCATCCAGAG	0.488																																					p.L2037L		.											.	ACACB-98	0			c.C6111T						.						206	202	203					12																	109692084		2203	4300	6503	SO:0001819	synonymous_variant	32	exon43			ATTCCTCCCATCC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 2"	601557	"acetyl-Coenzyme A carboxylase beta"			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6111C>T	12.37:g.109692084C>T		Somatic	321	0		WXS	Illumina HiSeq	Phase_I	240	95	NM_001093	0	0	8	12	4	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			.		0.488	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109692084	C	T	109692084	2	4	113	1	0	0	0	0	0	0	0	1	107	842	30	2		2	ACACB	12	109692084	Silent	SNP	C	TCGA-G7-6792-01A-21D-1961-08	7533026	109692084	24159811	40	9951											
EXOC5	10640	ucsc.edu	37	chr14	57684753	57684753	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttcaattatttcttttttCttctgaaggcattcagataa	10	20	5	6	0	5	2	2	1	3	1	5	2	5	2	0	1	0	2	0	1	4	9			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr14:57684753C>T	ENST00000413566.2	-	15	1919	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	EXOC5_ENST00000340918.7_Silent_p.K455K	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	520					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						TTTCTTTTTTCTTCTGAAGGC	0.259																																					p.K520K													.	EXOC5-137	0			c.G1560A						.						67	69	68					14																	57684753		1785	4055	5840	SO:0001819	synonymous_variant	10640	exon15			TTTTTTCTTCTGA	U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"SEC10 (S. cerevisiae)-like 1", "SEC10-like 1 (S. cerevisiae)"	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1560G>A	14.37:g.57684753C>T		Somatic	96	0		WXS	Illumina HiSeq		71	1	NM_006544	0	0	14	16	2	B2R6C5	Silent	SNP	ENST00000413566.2	37	CCDS45111.1																																																																																			.		0.259	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544		T	57684753	C	T	57684753	2	4	113	1	0	0	0	0	0	0	0	1	5320	912	32	2		2	EXOC5	14	57684753	Silent	SNP	C	TCGA-G7-6792-01A-21D-1961-08		57684753	49664787	41	9952											
CDAN1	146059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43024004	43024004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaagacggtgcccccagcaCcaccagggctctgacacatc	10	4	9	18	1	1	2	0	1	1	1	2	2	1	2	5	2	2	2	5	2	1	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr15:43024004C>T	ENST00000356231.3	-	11	1576	c.1553G>A	c.(1552-1554)gGt>gAt	p.G518D		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	518					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GCCCCCAGCACCACCAGGGCT	0.532																																					p.G518D		.											.	CDAN1-92	0			c.G1553A						.						34	38	36					15																	43024004		2203	4299	6502	SO:0001583	missense	146059	exon11			CCAGCACCACCAG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.1553G>A	15.37:g.43024004C>T	ENSP00000348564:p.Gly518Asp	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	94	26	NM_138477	0	0	2	2	0	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	c	17.73	3.462735	0.63513	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86694	-2.16	5.85	4.9	0.64082	.	0.352932	0.32785	N	0.005652	D	0.88526	0.6460	L	0.41236	1.265	0.37581	D	0.919811	D	0.63046	0.992	P	0.57101	0.813	D	0.89548	0.3797	10	0.46703	T	0.11	-7.4334	16.3622	0.83271	0.1325:0.8675:0.0:0.0	.	518	Q8IWY9	CDAN1_HUMAN	D	518;516	ENSP00000348564:G518D	ENSP00000267892:G516D	G	-	2	0	CDAN1	40811296	0.601000	0.26907	0.996000	0.52242	0.629000	0.37895	3.677000	0.54619	2.773000	0.95371	0.651000	0.88453	GGT	.		0.532	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43024004	C	T	43024004	3	4	113	1	0	0	0	0	1	0	0	0	3060	507	18	2	2202	2	CDAN1	15	43024004	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		43024004	59507388	42	9953											
LACTB	114294	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	63414861	63414861	+	Frame_Shift_Del	DEL	G	G	-																															gtgggcgcaccgggcatagtGgttggagtttctgtagatgg																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr15:63414861delG	ENST00000261893.4	+	2	456	c.384delG	c.(382-384)gtgfs	p.V129fs	LACTB_ENST00000413507.2_Frame_Shift_Del_p.V129fs	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	129						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CGGGCATAGTGGTTGGAGTTT	0.488																																					p.V128fs	Melanoma(85;443 1381 6215 27308 35583)	.											.	LACTB-90	0			c.384delG						.						169	148	155					15																	63414861		2203	4300	6503	SO:0001589	frameshift_variant	114294	exon2			.	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"Mitochondrial ribosomal proteins / large subunits"	16468	protein-coding gene	gene with protein product		608440	"mitochondrial ribosomal protein L56"	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.384delG	15.37:g.63414861delG	ENSP00000261893:p.Val129fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	106	35	NM_171846	0	0	0	0	0	P83096	Frame_Shift_Del	DEL	ENST00000261893.4	37	CCDS10182.1																																																																																			.		0.488	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		-	63414861	G	-	63414861	7	5	113	1	0	1	0	1	0	0	0	0	8618	1335	47	0	390	0	LACTB	15	63414861	Frame_Shift_Del	DEL	G	TCGA-G7-6792-01A-21D-1961-08	20390857	63414861	39116531	43	9954											
PSTPIP1	9051	hgsc.bcm.edu	37	chr15	77328195	77328195	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaatgagggtgtctacacAgccatcgcagtgcaggagat	11	7	14	9	2	1	2	0	1	1	1	2	4	1	3	1	3	3	2	1	3	2	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr15:77328195A>G	ENST00000558012.1	+	14	1527	c.1038A>G	c.(1036-1038)acA>acG	p.T346T	PSTPIP1_ENST00000559295.1_Silent_p.T327T|PSTPIP1_ENST00000557995.1_3'UTR|PSTPIP1_ENST00000379595.3_Silent_p.T343T|PSTPIP1_ENST00000267939.5_Silent_p.T326T	NM_003978.3	NP_003969.2	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting protein 1	346					cell adhesion (GO:0007155)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|signal transduction (GO:0007165)	actomyosin contractile ring (GO:0005826)|cell projection (GO:0042995)|cleavage furrow (GO:0032154)|cytosol (GO:0005829)|membrane (GO:0016020)|stress fiber (GO:0001725)				breast(1)|endometrium(3)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						GTGTCTACACAGCCATCGCAG	0.617																																					p.T346T		.											.	PSTPIP1-23	0			c.A1038G						.						36	43	41					15																	77328195		1972	4126	6098	SO:0001819	synonymous_variant	9051	exon14			CTACACAGCCATC	U94778	CCDS45312.1	15q24.3	2014-09-17			ENSG00000140368	ENSG00000140368			9580	protein-coding gene	gene with protein product	"CD2 cytoplasmic tail-binding protein", "CD2 antigen-binding protein 1", "PEST phosphatase-interacting protein 1"	606347				9857189	Standard	NM_003978		Approved	PSTPIP, CD2BP1L, CD2BP1, CD2BP1S, H-PIP, PAPAS	uc002bcf.2	O43586	OTTHUMG00000172594	ENST00000558012.1:c.1038A>G	15.37:g.77328195A>G		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	32	3	NM_003978	0	0	10	10	0	B5BU74|B5BUK4|O43585|O95657	Silent	SNP	ENST00000558012.1	37	CCDS45312.1																																																																																			.		0.617	PSTPIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419373.2	NM_003978		G	77328195	A	G	77328195	2	3	113	1	0	0	0	0	0	0	0	1	12750	175	7	3		3	PSTPIP1	15	77328195	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08	13913334	77328195	25203197	44	9955											
TSC2	7249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2138135	2138135	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccgccagatggccctgcacGcaaatgtgagtgggggtggg	7	6	17	11	2	0	2	0	1	0	1	0	2	0	2	3	4	1	2	3	4	1	0	rs137854164|rs137854321|rs201206500		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr16:2138135G>A	ENST00000219476.3	+	40	5785	c.5155G>A	c.(5155-5157)Gca>Aca	p.A1719T	TSC2_ENST00000439673.2_Missense_Mutation_p.A1616T|MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000350773.4_Missense_Mutation_p.A1696T|TSC2_ENST00000401874.2_Missense_Mutation_p.A1652T|TSC2_ENST00000568454.1_Missense_Mutation_p.A1663T|TSC2_ENST00000353929.4_Missense_Mutation_p.A1676T|TSC2_ENST00000382538.6_Missense_Mutation_p.A1604T	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1719	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GGCCCTGCACGCAAATGTGAG	0.652			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis				G|||	1	0.000199681	0	0	5008	,	,		16634	0		0.001	False		,,,				2504	0				p.A1719T		.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2-1908	0			c.G5155A						.						81	79	80					16																	2138135		2198	4299	6497	SO:0001583	missense	7249	exon40	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTGCACGCAAATG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.5155G>A	16.37:g.2138135G>A	ENSP00000219476:p.Ala1719Thr	Somatic	160	1		WXS	Illumina HiSeq	Phase_I	121	41	NM_000548	0	0	0	0	0	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	17.57	3.423704	0.62733	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05;-4.05	4.51	4.51	0.55191	Rap/ran-GAP (2);	0.295757	0.31301	N	0.007885	D	0.97244	0.9099	M	0.90705	3.14	0.58432	D	0.999999	P;P;P;P;P;P;P	0.49635	0.697;0.878;0.797;0.926;0.648;0.648;0.882	P;P;P;P;B;B;P	0.50231	0.547;0.503;0.572;0.635;0.412;0.412;0.478	D	0.97347	0.9961	10	0.54805	T	0.06	-4.9954	12.3699	0.55250	0.0:0.0:0.8315:0.1685	.	1604;1616;1696;494;1675;1652;1719	B4DIL8;P49815-6;P49815-4;B3KSR9;P49815-3;P49815-5;P49815	.;.;.;.;.;.;TSC2_HUMAN	T	1719;1653;1676;1616;1604;1696	ENSP00000219476:A1719T;ENSP00000248099:A1676T;ENSP00000399232:A1616T;ENSP00000371978:A1604T;ENSP00000344383:A1696T	ENSP00000219476:A1719T	A	+	1	0	TSC2	2078136	1.000000	0.71417	0.990000	0.47175	0.076000	0.17211	7.766000	0.85320	2.065000	0.61736	0.313000	0.20887	GCA	G|1.000;A|0.000		0.652	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2138135	G	A	2138135	3	1	113	1	0	0	0	0	1	0	0	0	16639	1087	38	1	5309	1	TSC2	16	2138135	Missense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08		2138135	88216618	45	9956											
MGRN1	23295	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	4731570	4731570	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactctgacagcgtcccacCtggctacgagcccatctcgc	8	7	9	17	3	2	1	0	1	2	0	4	3	3	1	3	1	4	1	3	1	2	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr16:4731570C>A	ENST00000399577.5	+	13	1244	c.1151C>A	c.(1150-1152)cCt>cAt	p.P384H	MGRN1_ENST00000262370.7_Missense_Mutation_p.P384H|MGRN1_ENST00000586183.1_Missense_Mutation_p.P362H|MGRN1_ENST00000415496.1_Missense_Mutation_p.P363H|MGRN1_ENST00000588994.1_Missense_Mutation_p.P362H	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	384					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						AGCGTCCCACCTGGCTACGAG	0.637																																					p.P384H		.											.	MGRN1-92	0			c.C1151A						.						35	41	39					16																	4731570		2113	4219	6332	SO:0001583	missense	23295	exon13			TCCCACCTGGCTA	AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"RING-type (C3HC4) zinc fingers"	20254	protein-coding gene	gene with protein product		607559	"mahogunin, ring finger 1"			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.1151C>A	16.37:g.4731570C>A	ENSP00000382487:p.Pro384His	Somatic	94	1		WXS	Illumina HiSeq	Phase_I	83	24	NM_015246	0	0	53	104	51	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	37	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.211518	0.79240	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496	T;T;T	0.46451	0.87;0.94;1.18	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	L	0.52011	1.625	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.997;0.993;0.998;0.999	T	0.61836	-0.6981	10	0.87932	D	0	-15.6411	15.5901	0.76521	0.0:1.0:0.0:0.0	.	362;362;363;384;384	O60291-4;O60291-3;E9PB19;O60291-2;O60291	.;.;.;.;MGRN1_HUMAN	H	384;384;363	ENSP00000262370:P384H;ENSP00000382487:P384H;ENSP00000393311:P363H	ENSP00000262370:P384H	P	+	2	0	MGRN1	4671571	0.998000	0.40836	0.943000	0.38184	0.715000	0.41141	5.746000	0.68681	2.456000	0.83038	0.561000	0.74099	CCT	.		0.637	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2			A	4731570	C	A	4731570	3	1	113	1	0	0	0	0	1	0	0	0	9584	681	24	4	1204	4	MGRN1	16	4731570	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	2593435	4731570	85623183	46	9957											
PDXDC1	23042	ucsc.edu;bcgsc.ca	37	chr16	15130101	15130101	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacccagaagatgaccactCacaggtagaaggaccggaga	16	3	11	11	1	1	5	1	1	0	4	1	7	1	6	3	3	0	1	3	3	3	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr16:15130101C>A	ENST00000396410.4	+	23	2433	c.2336C>A	c.(2335-2337)tCa>tAa	p.S779*	PDXDC1_ENST00000563679.1_Nonsense_Mutation_p.S797*|PDXDC1_ENST00000325823.7_Nonsense_Mutation_p.S764*|PDXDC1_ENST00000569715.1_Nonsense_Mutation_p.S752*|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Nonsense_Mutation_p.S751*|PDXDC1_ENST00000447912.2_Nonsense_Mutation_p.S688*	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	779					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GATGACCACTCACAGGTAGAA	0.537																																					p.S779X													.	PDXDC1-91	0			c.C2336A						.						142	147	146					16																	15130101		2197	4300	6497	SO:0001587	stop_gained	23042	exon23			ACCACTCACAGGT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.2336C>A	16.37:g.15130101C>A	ENSP00000379691:p.Ser779*	Somatic	241	2		WXS	Illumina HiSeq		167	49	NM_015027	0	0	43	102	59	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Nonsense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.482807	0.84747	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	.	.	.	5.17	5.17	0.71159	.	0.745129	0.13527	N	0.381244	.	.	.	.	.	.	0.46701	D	0.999161	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-0.0189	17.8527	0.88752	0.0:1.0:0.0:0.0	.	.	.	.	X	764;688;779;751	.	ENSP00000322807:S764X	S	+	2	0	PDXDC1	15037602	0.001000	0.12720	0.721000	0.30653	0.095000	0.18619	1.280000	0.33202	2.683000	0.91414	0.655000	0.94253	TCA	.		0.537	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		A	15130101	C	A	15130101	4	1	113	1	0	0	0	0	0	1	0	0	11722	838	29	4	2426	4	PDXDC1	16	15130101	Nonsense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	10398531	15130101	75224652	47	9958											
STARD3	10948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37817259	37817259	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgaatgtccggcgcattGagcggcgcagggaccgatac	8	7	15	11	6	0	2	0	2	0	0	2	4	1	3	2	3	2	2	2	3	2	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr17:37817259G>T	ENST00000336308.5	+	13	1278	c.1060G>T	c.(1060-1062)Gag>Tag	p.E354*	STARD3_ENST00000544210.2_Nonsense_Mutation_p.E354*|STARD3_ENST00000580611.1_Nonsense_Mutation_p.E328*|STARD3_ENST00000394250.4_Nonsense_Mutation_p.E336*	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	354	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCGGCGCATTGAGCGGCGCAG	0.602																																					p.E354X		.											.	STARD3-90	0			c.G1060T						.						75	66	69					17																	37817259		2203	4300	6503	SO:0001587	stop_gained	10948	exon13			CGCATTGAGCGGC		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"StAR-related lipid transfer (START) domain containing"	17579	protein-coding gene	gene with protein product		607048	"START domain containing 3"				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.1060G>T	17.37:g.37817259G>T	ENSP00000337446:p.Glu354*	Somatic	124	2		WXS	Illumina HiSeq	Phase_I	102	42	NM_006804	0	0	17	18	1	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Nonsense_Mutation	SNP	ENST00000336308.5	37	CCDS11341.1	.	.	.	.	.	.	.	.	.	.	G	39	7.324673	0.98214	.	.	ENSG00000131748	ENST00000336308;ENST00000544210;ENST00000394250	.	.	.	5.02	5.02	0.67125	.	0.107907	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	18.3139	0.90210	0.0:0.0:1.0:0.0	.	.	.	.	X	354;354;336	.	ENSP00000337446:E354X	E	+	1	0	STARD3	35070785	1.000000	0.71417	0.985000	0.45067	0.996000	0.88848	9.015000	0.93640	2.343000	0.79666	0.561000	0.74099	GAG	.		0.602	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1			T	37817259	G	T	37817259	4	4	113	1	0	0	0	0	0	1	0	0	15289	1291	45	4	1119	4	STARD3	17	37817259	Nonsense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08		37817259	43377951	48	9959											
TMC8	147138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	76133427	76133427	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagtcctacggctacaacgtTtgtgactatcaggtggctgg	8	11	13	9	2	1	1	1	1	0	0	2	2	2	1	1	4	3	3	1	4	4	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr17:76133427T>G	ENST00000318430.5	+	10	1613	c.1239T>G	c.(1237-1239)gtT>gtG	p.V413V	TMC8_ENST00000589691.1_Silent_p.V190V	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	413					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			GCTACAACGTTTGTGACTATC	0.587																																					p.V413V		.											.	TMC8-90	0			c.T1239G						.						129	116	120					17																	76133427		2203	4300	6503	SO:0001819	synonymous_variant	147138	exon10			CAACGTTTGTGAC	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"epidermodysplasia verruciformis 2"	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.1239T>G	17.37:g.76133427T>G		Somatic	212	1		WXS	Illumina HiSeq	Phase_I	203	76	NM_152468	0	0	0	0	0	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																			.		0.587	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			G	76133427	T	G	76133427	2	3	113	1	0	0	0	0	0	0	0	1	16023	1828	64	5		5	TMC8	17	76133427	Silent	SNP	T	TCGA-G7-6792-01A-21D-1961-08	38316168	76133427	5061783	49	9960											
KIAA1632	57724	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	43464597	43464598	+	Frame_Shift_Ins	INS	-	-	AA																															ttaccttggttagcagcatgINSaaaatcatatcactgttgtc																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr18:43464597_43464598insAA	ENST00000282041.5	-	30	5322_5323	c.5288_5289insTT	c.(5287-5289)ttcfs	p.F1763fs	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1763					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TTAGCAGCATGAAAATCATATC	0.421																																					p.F1763fs		.											.	EPG5-580	0			c.5289_5290insTT						.																																			SO:0001589	frameshift_variant	57724	exon30			.	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5287_5288dupTT	18.37:g.43464600_43464601dupAA	ENSP00000282041:p.Phe1763fs	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	121	39	NM_020964	0	0	0	0	0	A2BDF3|Q9H8C8	Frame_Shift_Ins	INS	ENST00000282041.5	37	CCDS11926.2																																																																																			.		0.421	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		AA	43464598	-	AA	43464597	7	5	113	1	0	1	1	0	0	0	0	0	8270	1281	45	0	2510	0	KIAA1632	18	43464597	Frame_Shift_Ins	INS	-	TCGA-G7-6792-01A-21D-1961-08		43464597	34612651	50	9961											
APC2	10297	hgsc.bcm.edu	37	chr19	1469819	1469819	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccactgcggggctccacGcccgaggacgccccggccgg	4	3	15	19	6	0	0	0	0	0	0	1	2	1	1	6	5	2	1	6	5	0	0	rs556845921	byFrequency	TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr19:1469819G>C	ENST00000535453.1	+	14	8232	c.6519G>C	c.(6517-6519)acG>acC	p.T2173T	C19orf25_ENST00000588427.1_Intron|APC2_ENST00000238483.4_Silent_p.T1899T|APC2_ENST00000233607.2_Silent_p.T2173T			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGCTCCACGCCCGAGGAcg	0.761													G|||	26	0.00519169	0.0166	0.0058	5008	,	,		8412	0		0	False		,,,				2504	0				p.T2173T		.											.	APC2-290	0			c.G6519C						.																																			SO:0001819	synonymous_variant	10297	exon15			CTCCACGCCCGAG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"Armadillo repeat containing"	24036	protein-coding gene	gene with protein product	"adenomatous polyposis coli like"	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.6519G>C	19.37:g.1469819G>C		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_005883	0	0	0	0	0	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			.		0.761	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		C	1469819	G	C	1469819	2	2	113	1	0	0	0	0	0	0	0	1	764	1074	38	4		4	APC2	19	1469819	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08		1469819	57659164	51	9962											
RAB3D	9545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11447891	11447891	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtcatggcggtagacggtcTtgaccttgaaatcgatgccc	8	11	12	10	3	2	3	1	2	1	1	3	4	2	3	2	3	1	1	2	3	2	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr19:11447891T>A	ENST00000222120.3	-	2	445	c.185A>T	c.(184-186)aAg>aTg	p.K62M	RAB3D_ENST00000589655.1_Missense_Mutation_p.K62M	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	62					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						GTAGACGGTCTTGACCTTGAA	0.577																																					p.K62M		.											.	RAB3D-653	0			c.A185T						.						232	208	216					19																	11447891		2203	4300	6503	SO:0001583	missense	9545	exon2			ACGGTCTTGACCT	AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"RAB, member RAS oncogene"	9779	protein-coding gene	gene with protein product	"Rab3D upregulated with myeloid differentiation", "glioblastoma overexpressed"	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.185A>T	19.37:g.11447891T>A	ENSP00000222120:p.Lys62Met	Somatic	451	2		WXS	Illumina HiSeq	Phase_I	395	130	NM_004283	0	0	11	22	11		Missense_Mutation	SNP	ENST00000222120.3	37	CCDS12257.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.150596	0.78001	.	.	ENSG00000105514	ENST00000222120	T	0.79554	-1.28	4.46	3.43	0.39272	Small GTP-binding protein domain (1);	0.045218	0.85682	D	0.000000	D	0.91030	0.7178	H	0.94582	3.555	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.91079	0.4898	10	0.87932	D	0	.	9.368	0.38237	0.0:0.088:0.0:0.912	.	62	O95716	RAB3D_HUMAN	M	62	ENSP00000222120:K62M	ENSP00000222120:K62M	K	-	2	0	RAB3D	11308891	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.805000	0.86005	0.847000	0.35167	0.482000	0.46254	AAG	.		0.577	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283		A	11447891	T	A	11447891	3	1	113	1	0	0	0	0	1	0	0	0	12966	1609	56	5	490	5	RAB3D	19	11447891	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08	9978072	11447891	47681092	52	9963											
PTPRA	5786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	3016489	3016489	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccatggctggcctgaagtGggcatccccagtgacggaaa	9	8	13	11	1	0	2	0	2	0	0	2	3	2	3	4	4	0	2	4	4	2	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr20:3016489G>T	ENST00000216877.6	+	21	2473	c.2073G>T	c.(2071-2073)gtG>gtT	p.V691V	PTPRA_ENST00000318266.5_Silent_p.V691V|PTPRA_ENST00000356147.3_Silent_p.V691V|PTPRA_ENST00000380393.3_Silent_p.V700V|PTPRA_ENST00000425918.2_Silent_p.V711V|PTPRA_ENST00000399903.2_Silent_p.V700V|PTPRA_ENST00000358719.4_Silent_p.V556V	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	700	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GGCCTGAAGTGGGCATCCCCA	0.587																																					p.V700V		.											.	PTPRA-227	0			c.G2100T						.						78	73	74					20																	3016489		2203	4300	6503	SO:0001819	synonymous_variant	5786	exon26			TGAAGTGGGCATC		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.2073G>T	20.37:g.3016489G>T		Somatic	127	1		WXS	Illumina HiSeq	Phase_I	115	34	NM_002836	0	0	49	91	42	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																			.		0.587	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			T	3016489	G	T	3016489	2	4	113	1	0	0	0	0	0	0	0	1	12827	1335	47	4		4	PTPRA	20	3016489	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08		3016489	60009031	53	9964											
CST9L	128821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	23548869	23548869	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctccttccaggaattcaaGatgtgccccagtctgtaggc	8	11	10	12	0	2	1	1	0	1	1	4	2	4	2	4	2	2	2	4	2	3	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr20:23548869G>T	ENST00000376979.3	-	1	517	c.219C>A	c.(217-219)atC>atA	p.I73I		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	73						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					AGGAATTCAAGATGTGCCCCA	0.547																																					p.I73I		.											.	CST9L-90	0			c.C219A						.						155	122	133					20																	23548869		2203	4300	6503	SO:0001819	synonymous_variant	128821	exon1			ATTCAAGATGTGC		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.219C>A	20.37:g.23548869G>T		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	66	19	NM_080610	0	0	0	0	0	B2R5A1	Silent	SNP	ENST00000376979.3	37	CCDS13157.1																																																																																			.		0.547	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		T	23548869	G	T	23548869	2	4	113	1	0	0	0	0	0	0	0	1	3986	932	33	4		4	CST9L	20	23548869	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08	20532380	23548869	39476651	54	9965											
PFKL	5211	broad.mit.edu	37	chr21	45741733	45741733	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtatacgtggtgcacgatgGcttcgaaggcctagccaagg	10	8	14	9	3	0	0	0	0	0	0	1	2	0	0	2	4	3	3	2	4	5	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr21:45741733G>A	ENST00000349048.4	+	13	1368	c.1313G>A	c.(1312-1314)gGc>gAc	p.G438D	PFKL_ENST00000403390.1_Missense_Mutation_p.G485D	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	438	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		GTGCACGATGGCTTCGAAGGC	0.642																																					p.G438D													.	PFKL-251	0			c.G1313A						.						93	92	92					21																	45741733		2202	4300	6502	SO:0001583	missense	5211	exon13			ACGATGGCTTCGA		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.1313G>A	21.37:g.45741733G>A	ENSP00000269848:p.Gly438Asp	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	163	6	NM_002626	0	0	181	186	5	Q96A64|Q96IH4|Q9BR91	Missense_Mutation	SNP	ENST00000349048.4	37	CCDS33582.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.760200	0.69763	.	.	ENSG00000141959	ENST00000349048;ENST00000534847;ENST00000403390	D;D	0.97994	-4.65;-4.65	4.3	4.3	0.51218	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.99321	0.9762	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.98287	1.0511	10	0.87932	D	0	-31.7745	15.5438	0.76077	0.0:0.0:1.0:0.0	.	438;485	P17858;P17858-2	K6PL_HUMAN;.	D	438;231;485	ENSP00000269848:G438D;ENSP00000384038:G485D	ENSP00000269848:G438D	G	+	2	0	PFKL	44566161	1.000000	0.71417	0.993000	0.49108	0.160000	0.22226	9.380000	0.97202	1.912000	0.55364	0.462000	0.41574	GGC	.		0.642	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1			A	45741733	G	A	45741733	3	1	113	1	0	0	0	0	1	0	0	0	11790	1203	42	2	1363	2	PFKL	21	45741733	Missense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08		45741733	2388162	55	9966											
SGSM3	57591	hgsc.bcm.edu	37	chr22	40804935	40804935	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgacggtgccgttcccAggctgtgcagtctgtgaacg	6	9	14	12	3	1	2	0	2	1	0	2	2	2	2	2	2	4	4	2	2	1	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr22:40804935A>G	ENST00000355630.3	-	0	4496				SGSM3_ENST00000248929.9_Splice_Site|SGSM3_ENST00000454798.2_Splice_Site	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1						negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TGCCGTTCCCAGGCTGTGCAG	0.597			T	RBM15	acute megakaryocytic leukemia																																.		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	SGSM3-494	0			c.1903-2A>G						.						36	36	36					22																	40804935		2203	4298	6501	SO:0001628	intergenic_variant	27352	exon19			GTTCCCAGGCTGT	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146		22.37:g.40804935A>G		Somatic	42	1		WXS	Illumina HiSeq	Phase_I	30	2	NM_015705	0	0	0	0	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Splice_Site	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	A	15.44	2.834085	0.50951	.	.	ENSG00000100359	ENST00000248929;ENST00000454798;ENST00000427834;ENST00000417424	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2125	0.65773	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SGSM3	39134881	1.000000	0.71417	0.944000	0.38274	0.077000	0.17291	8.433000	0.90291	1.834000	0.53371	0.260000	0.18958	.	.		0.597	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		G	40804935	A	G	40804935	1	3	113	0	1	0	0	0	0	0	0	0	14256	202	7	3		3	SGSM3	22	40804935	IGR	SNP	A	TCGA-G7-6792-01A-21D-1961-08		40804935	10499631	56	9967											
USP11	8237	hgsc.bcm.edu	37	chrX	47102998	47102998	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taacgtcctgatgtaccggcTctcgtaagtgtcctcttccc	6	13	8	14	3	2	1	0	1	2	0	6	1	5	1	4	1	2	3	4	1	3	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chrX:47102998T>C	ENST00000218348.3	+	13	1916	c.1916T>C	c.(1915-1917)cTc>cCc	p.L639P	USP11_ENST00000377107.2_Missense_Mutation_p.L596P	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	639	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						ATGTACCGGCTCTCGTAAGTG	0.577																																					p.L639P		.											.	USP11-659	0			c.T1916C						.						45	43	44					X																	47102998		2203	4300	6503	SO:0001583	missense	8237	exon13			ACCGGCTCTCGTA	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.1916T>C	X.37:g.47102998T>C	ENSP00000218348:p.Leu639Pro	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_004651	0	0	0	0	0	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.808542	0.70797	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	T;T	0.25085	1.84;1.82	4.69	4.69	0.59074	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.096142	0.42821	D	0.000655	T	0.47857	0.1468	M	0.75884	2.315	0.80722	D	1	B;D	0.69078	0.389;0.997	B;D	0.68621	0.403;0.959	T	0.51458	-0.8703	10	0.87932	D	0	-17.6823	10.9784	0.47480	0.0:0.0:0.0:1.0	.	366;639	B3KP28;P51784	.;UBP11_HUMAN	P	596;639	ENSP00000366311:L596P;ENSP00000218348:L639P	ENSP00000218348:L639P	L	+	2	0	USP11	46987942	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	5.422000	0.66453	1.861000	0.53984	0.417000	0.27973	CTC	.		0.577	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		C	47102998	T	C	47102998	3	2	113	1	0	0	0	0	1	0	0	0	17075	1551	54	3	1966	3	USP11	23	47102998	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08		47102998	108167562	57	9968											
PIK3CD	5293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	9782066	9782066	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaactgaaggccctgaatGacttcgtcaagctgagctct	11	9	10	11	1	2	4	1	4	1	0	3	4	2	4	1	1	3	3	1	1	4	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:9782066G>T	ENST00000377346.4	+	17	2284	c.2089G>T	c.(2089-2091)Gac>Tac	p.D697Y	PIK3CD_ENST00000536656.1_Missense_Mutation_p.D721Y|PIK3CD_ENST00000543390.1_3'UTR|PIK3CD_ENST00000361110.2_Missense_Mutation_p.D721Y	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	697					adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	GGCCCTGAATGACTTCGTCAA	0.637											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D697Y		.											.	PIK3CD-1311	0			c.G2089T						.						74	84	81					1																	9782066		2203	4300	6503	SO:0001583	missense	5293	exon17			CTGAATGACTTCG		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase, catalytic, delta polypeptide", "phosphoinositide-3-kinase C"	602839	"phosphoinositide-3-kinase, catalytic, delta polypeptide"			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2089G>T	1.37:g.9782066G>T	ENSP00000366563:p.Asp697Tyr	Somatic	123	0	659	WXS	Illumina HiSeq	Phase_I	99	26	NM_005026	0	0	2	3	1	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	37	CCDS104.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908660	0.33721	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	D;D;D	0.82081	-1.57;-1.57;-1.57	5.4	4.48	0.54585	Protein kinase-like domain (1);	0.151853	0.64402	D	0.000020	D	0.86339	0.5909	L	0.55990	1.75	0.80722	D	1	P;D;P	0.65815	0.939;0.995;0.939	P;P;P	0.57620	0.615;0.824;0.707	D	0.87479	0.2419	10	0.87932	D	0	-44.469	13.397	0.60858	0.0756:0.0:0.9244:0.0	.	696;721;697	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	Y	721;697;721;721	ENSP00000446444:D721Y;ENSP00000366563:D697Y;ENSP00000354410:D721Y	ENSP00000353766:D721Y	D	+	1	0	PIK3CD	9704653	1.000000	0.71417	0.063000	0.19743	0.112000	0.19704	7.859000	0.86982	1.275000	0.44379	0.561000	0.74099	GAC	.		0.637	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		T	9782066	G	T	9782066	3	4	114	1	0	0	0	0	1	0	0	0	11941	1290	45	4	2147	4	PIK3CD	1	9782066	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08		9782066	239468555	1	9969											
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19186021	19186021	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaggtgaacaatgcccttcAtgttggcatggagggagaag	12	9	14	6	0	1	2	1	1	0	1	1	4	1	3	1	4	2	2	1	4	4	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:19186021A>T	ENST00000375371.3	-	1	155	c.134T>A	c.(133-135)aTg>aAg	p.M45K	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	45					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	AATGCCCTTCATGTTGGCATG	0.592																																					p.M45K		.											.	TAS1R2-93	0			c.T134A						.						118	109	112					1																	19186021		2203	4300	6503	SO:0001583	missense	80834	exon1			CCCTTCATGTTGG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.134T>A	1.37:g.19186021A>T	ENSP00000364520:p.Met45Lys	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	107	16	NM_152232	0	0	0	0	0	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	A	8.739	0.918447	0.17982	.	.	ENSG00000179002	ENST00000375371	D	0.88046	-2.33	4.47	2.07	0.26955	.	0.544004	0.13698	U	0.369069	T	0.74627	0.3741	N	0.22421	0.69	0.09310	N	0.999998	B	0.27068	0.167	B	0.18871	0.023	T	0.63093	-0.6714	10	0.52906	T	0.07	.	4.5956	0.12327	0.699:0.196:0.1051:0.0	.	45	Q8TE23	TS1R2_HUMAN	K	45	ENSP00000364520:M45K	ENSP00000364520:M45K	M	-	2	0	TAS1R2	19058608	0.239000	0.23836	0.384000	0.26145	0.776000	0.43924	1.724000	0.38064	0.201000	0.20466	0.260000	0.18958	ATG	.		0.592	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19186021	A	T	19186021	3	4	114	1	0	0	0	0	1	0	0	0	15595	217	8	5	2409	5	TAS1R2	1	19186021	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08	9403955	19186021	230064600	2	9970											
AHDC1	27245	ucsc.edu	37	chr1	27875553	27875553	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtggcaggcaggggcccccgGtaggcggtggggcatagccg	5	4	21	11	3	0	0	0	0	0	0	0	0	0	0	3	9	1	4	3	9	2	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:27875553G>A	ENST00000247087.5	-	5	3670	c.3074C>T	c.(3073-3075)aCc>aTc	p.T1025I	AHDC1_ENST00000374011.2_Missense_Mutation_p.T1025I			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1025							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GGGGCCCCCGGTAGGCGGTGG	0.682																																					p.T1025I													.	AHDC1-90	0			c.C3074T						.						15	18	17					1																	27875553		2199	4295	6494	SO:0001583	missense	27245	exon6			CCCCCGGTAGGCG	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.3074C>T	1.37:g.27875553G>A	ENSP00000247087:p.Thr1025Ile	Somatic	40	0		WXS	Illumina HiSeq		40	4	NM_001029882	0	0	37	37	0	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	37	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.817319	0.50633	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.49720	0.77;0.77	5.79	5.79	0.91817	.	0.215591	0.30510	N	0.009468	T	0.41534	0.1163	N	0.14661	0.345	0.38962	D	0.958562	D	0.53745	0.962	P	0.46825	0.528	T	0.49986	-0.8880	10	0.87932	D	0	-10.3301	18.7978	0.92003	0.0:0.0:1.0:0.0	.	1025	Q5TGY3	AHDC1_HUMAN	I	1025	ENSP00000247087:T1025I;ENSP00000363123:T1025I	ENSP00000247087:T1025I	T	-	2	0	AHDC1	27748140	0.932000	0.31603	0.942000	0.38095	0.996000	0.88848	2.672000	0.46850	2.735000	0.93741	0.655000	0.94253	ACC	.		0.682	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			A	27875553	G	A	27875553	3	1	114	1	0	0	0	0	1	0	0	0	412	1261	44	2	1741	2	AHDC1	1	27875553	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	8689532	27875553	221375068	3	9971											
LRRC8C	84230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90180336	90180336	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaacttaaaactctgaagaTtggaaaaaacagcctatctg	18	9	7	7	0	2	2	0	1	2	1	2	4	2	3	1	1	4	0	1	1	8	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:90180336T>C	ENST00000370454.4	+	3	2462	c.2207T>C	c.(2206-2208)aTt>aCt	p.I736T	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	736					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		ACTCTGAAGATTGGAAAAAAC	0.353																																					p.I736T		.											.	LRRC8C-97	0			c.T2207C						.						62	64	64					1																	90180336		2203	4300	6503	SO:0001583	missense	84230	exon3			TGAAGATTGGAAA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.2207T>C	1.37:g.90180336T>C	ENSP00000359483:p.Ile736Thr	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	88	7	NM_032270	0	0	12	15	3	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077889	0.36662	.	.	ENSG00000171488	ENST00000370454	T	0.27402	1.67	5.87	5.87	0.94306	.	0.047961	0.85682	D	0.000000	T	0.25791	0.0628	M	0.69358	2.11	0.53688	D	0.99997	B	0.21821	0.061	B	0.27715	0.082	T	0.08953	-1.0697	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	736	Q8TDW0	LRC8C_HUMAN	T	736	ENSP00000359483:I736T	ENSP00000359483:I736T	I	+	2	0	LRRC8C	89952924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.371000	0.80710	0.533000	0.62120	ATT	.		0.353	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90180336	T	C	90180336	3	2	114	1	0	0	0	0	1	0	0	0	9048	1493	52	3	2213	3	LRRC8C	1	90180336	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08	62304783	90180336	159070285	4	9972											
FCRL3	115352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	157667660	157667660	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcccctgacatctcagaatGacattgtctccttcaaagac	11	12	5	13	0	3	4	2	2	2	2	6	4	4	4	3	0	0	0	3	0	2	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:157667660G>A	ENST00000368184.3	-	5	639	c.348C>T	c.(346-348)gtC>gtT	p.V116V	RP11-367J7.3_ENST00000453692.1_RNA|FCRL3_ENST00000473231.1_5'UTR|FCRL3_ENST00000368186.5_Silent_p.V116V	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	116	Ig-like C2-type 2.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					ATCTCAGAATGACATTGTCTC	0.423																																					p.V116V		.											.	FCRL3-156	0			c.C348T						.						104	96	99					1																	157667660		2203	4300	6503	SO:0001819	synonymous_variant	115352	exon5			CAGAATGACATTG	AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.348C>T	1.37:g.157667660G>A		Somatic	72	1		WXS	Illumina HiSeq	Phase_I	70	27	NM_052939	0	0	0	0	0	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Silent	SNP	ENST00000368184.3	37	CCDS1167.1																																																																																			.		0.423	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		A	157667660	G	A	157667660	2	1	114	1	0	0	0	0	0	0	0	1	5815	1277	45	2		2	FCRL3	1	157667660	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	67487324	157667660	91582961	5	9973											
IER5	51278	hgsc.bcm.edu	37	chr1	181058618	181058618	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaccggccgcgacccccCgcgctgcctgctgctgcgcg	3	5	13	20	7	0	0	0	0	0	0	0	1	0	0	6	1	5	4	6	1	1	1	rs1416829	byFrequency	TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:181058618C>G	ENST00000367577.4	+	1	981	c.580C>G	c.(580-582)Cgc>Ggc	p.R194G	RP11-309G3.3_ENST00000606938.1_lincRNA	NM_016545.4	NP_057629.2	Q5VY09	IER5_HUMAN	immediate early response 5	194			R -> G (in dbSNP:rs1416829). {ECO:0000269|PubMed:15498874}.							lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	4						CGCGACCCCCCGCGCTGCCTG	0.811													C|||	2222	0.44369	0.2489	0.4452	5008	,	,		5637	0.6012		0.3777	False		,,,				2504	0.6115				p.R194G		.											.	IER5-227	0			c.C580G						.						1	1	1					1																	181058618		352	834	1186	SO:0001583	missense	51278	exon1			ACCCCCCGCGCTG	BC000128	CCDS1343.1	1q25.3	2008-02-05			ENSG00000162783	ENSG00000162783			5393	protein-coding gene	gene with protein product		607177				10049588, 11102586	Standard	NM_016545		Approved		uc001got.4	Q5VY09	OTTHUMG00000035178	ENST00000367577.4:c.580C>G	1.37:g.181058618C>G	ENSP00000356549:p.Arg194Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_016545	0	0	0	0	0	B2RBV3|Q8WY68|Q9NY49|Q9NZP9	Missense_Mutation	SNP	ENST00000367577.4	37	CCDS1343.1	948	0.4340659340659341	135	0.27439024390243905	158	0.43646408839779005	360	0.6293706293706294	295	0.3891820580474934	C	4.540	0.100211	0.08731	.	.	ENSG00000162783	ENST00000367577	T	0.11821	2.74	3.33	-0.106	0.13596	.	1.560750	0.05354	N	0.532505	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.18610	0.029	B	0.15484	0.013	T	0.38972	-0.9636	9	0.34782	T	0.22	.	8.3021	0.32021	0.0:0.4746:0.4312:0.0942	rs1416829;rs3747953	194	Q5VY09	IER5_HUMAN	G	194	ENSP00000356549:R194G	ENSP00000356549:R194G	R	+	1	0	IER5	179325241	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-0.019000	0.12546	0.004000	0.14682	-1.520000	0.00934	CGC	C|0.566;G|0.434		0.811	IER5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085142.1	NM_016545		G	181058618	C	G	181058618	3	3	114	1	0	0	0	0	1	0	0	0	7529	652	23	4	582	4	IER5	1	181058618	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	23390958	181058618	68192003	6	9974											
PRELP	5549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	203455866	203455866	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagatttgccccaacgacCtagtggcgttccatgacttc	8	10	8	15	2	0	2	0	1	0	1	2	3	1	2	5	1	2	1	5	1	2	4			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:203455866C>A	ENST00000343110.2	+	3	1133	c.1006C>A	c.(1006-1008)Cta>Ata	p.L336I		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	336					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			CCCCAACGACCTAGTGGCGTT	0.567																																					p.L336I		.											.	PRELP-516	0			c.C1006A						.						110	100	103					1																	203455866		2203	4300	6503	SO:0001583	missense	5549	exon3			AACGACCTAGTGG	BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	9357	protein-coding gene	gene with protein product	"prolargin proteoglycan"	601914	"proline arginine-rich end leucine-rich repeat protein"				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.1006C>A	1.37:g.203455866C>A	ENSP00000343924:p.Leu336Ile	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	125	36	NM_201348	0	1	208	209	0	Q6FG38	Missense_Mutation	SNP	ENST00000343110.2	37	CCDS1438.1	.	.	.	.	.	.	.	.	.	.	C	1.678	-0.507353	0.04231	.	.	ENSG00000188783	ENST00000343110	T	0.49139	0.79	5.45	1.38	0.22167	.	0.097389	0.42964	N	0.000628	T	0.26557	0.0649	N	0.24115	0.695	0.19775	N	0.999957	B	0.06786	0.001	B	0.12156	0.007	T	0.15607	-1.0431	10	0.18710	T	0.47	-7.7426	5.6324	0.17518	0.2531:0.5559:0.1222:0.0687	.	336	P51888	PRELP_HUMAN	I	336	ENSP00000343924:L336I	ENSP00000343924:L336I	L	+	1	2	PRELP	201722489	0.003000	0.15002	0.003000	0.11579	0.246000	0.25737	-0.032000	0.12266	0.005000	0.14708	-0.300000	0.09419	CTA	.		0.567	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725		A	203455866	C	A	203455866	3	1	114	1	0	0	0	0	1	0	0	0	12502	680	24	4	1012	4	PRELP	1	203455866	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	22397248	203455866	45794755	7	9975											
CKAP2L	150468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	113513875	113513875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaggtatacaaacttggCtggacttctgatcttgcttg	8	15	10	8	0	3	2	0	2	3	0	3	3	3	3	0	3	3	3	0	3	3	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:113513875C>T	ENST00000302450.6	-	4	1151	c.1073G>A	c.(1072-1074)aGc>aAc	p.S358N	CKAP2L_ENST00000541405.1_Missense_Mutation_p.S193N|CKAP2L_ENST00000481732.1_5'Flank	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	358						centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						ACAAACTTGGCTGGACTTCTG	0.428																																					p.S358N		.											.	CKAP2L-90	0			c.G1073A						.						149	144	145					2																	113513875		2203	4300	6503	SO:0001583	missense	150468	exon4			ACTTGGCTGGACT	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.1073G>A	2.37:g.113513875C>T	ENSP00000305204:p.Ser358Asn	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	175	64	NM_152515	0	0	2	2	0	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	.	.	.	.	.	.	.	.	.	.	c	9.225	1.034367	0.19590	.	.	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.11821	2.74;3.39	4.69	-4.0	0.04057	.	0.732493	0.12806	N	0.437566	T	0.04227	0.0117	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	10	0.24483	T	0.36	-1.0892	0.994	0.01462	0.2342:0.3464:0.1852:0.2342	.	358	Q8IYA6	CKP2L_HUMAN	N	193;358	ENSP00000438763:S193N;ENSP00000305204:S358N	ENSP00000305204:S358N	S	-	2	0	CKAP2L	113230346	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.718000	0.04980	-0.903000	0.03881	-0.911000	0.02809	AGC	.		0.428	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515		T	113513875	C	T	113513875	3	4	114	1	0	0	0	0	1	0	0	0	3449	797	28	2	1188	2	CKAP2L	2	113513875	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		113513875	129685498	8	9976											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179425266	179425266	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaggggctcaccaacaccAtatttattaacaccagttac	13	11	5	12	0	2	0	1	0	1	0	2	0	2	0	3	2	3	2	3	2	6	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:179425266A>G	ENST00000591111.1	-	276	80894	c.80670T>C	c.(80668-80670)taT>taC	p.Y26890Y	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Y19658Y|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.Y19591Y|TTN_ENST00000460472.2_Silent_p.Y19466Y|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.Y28531Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.Y25963Y|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26890	Fibronectin type-III 95. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACCAACACCATATTTATTAA	0.388																																					p.Y28531Y		.											.	TTN-636	0			c.T85593C						.						57	56	56					2																	179425266		1865	4100	5965	SO:0001819	synonymous_variant	7273	exon326			AACACCATATTTA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.80670T>C	2.37:g.179425266A>G		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	60	20	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179425266	A	G	179425266	2	3	114	1	0	0	0	0	0	0	0	1	16768	224	8	3		3	TTN	2	179425266	Silent	SNP	A	TCGA-G7-6793-01A-11D-1961-08	65911391	179425266	63774107	9	9977											
ITGA4	3676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	182399601	182399601	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatttcaccatagtgattaTttcaagtagcttgctacttg	10	18	6	7	0	2	1	2	1	0	0	2	1	2	1	1	0	3	3	1	0	6	9			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:182399601T>C	ENST00000397033.2	+	27	3372	c.2942T>C	c.(2941-2943)aTt>aCt	p.I981T		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	981					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	ATAGTGATTATTTCAAGTAGC	0.313																																					p.I981T		.											.	ITGA4-230	0			c.T2942C						.						148	140	143					2																	182399601		1850	4088	5938	SO:0001583	missense	3676	exon27			TGATTATTTCAAG		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"CD molecules", "Integrins"	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2942T>C	2.37:g.182399601T>C	ENSP00000380227:p.Ile981Thr	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	103	29	NM_000885	0	0	10	11	1	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.035378	0.75617	.	.	ENSG00000115232	ENST00000397033	T	0.74737	-0.87	6.17	6.17	0.99709	.	0.088153	0.85682	D	0.000000	T	0.78735	0.4330	M	0.78049	2.395	0.58432	D	0.999995	P	0.52577	0.954	P	0.45310	0.476	T	0.82464	-0.0444	10	0.87932	D	0	.	15.3933	0.74767	0.0:0.0:0.0:1.0	.	981	P13612	ITA4_HUMAN	T	981	ENSP00000380227:I981T	ENSP00000380227:I981T	I	+	2	0	ITGA4	182107846	1.000000	0.71417	0.171000	0.22900	0.989000	0.77384	5.141000	0.64814	2.371000	0.80710	0.533000	0.62120	ATT	.		0.313	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			C	182399601	T	C	182399601	3	2	114	1	0	0	0	0	1	0	0	0	7899	1493	52	3	3048	3	ITGA4	2	182399601	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08	2974335	182399601	60799772	10	9978											
NBEAL1	65065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	204058575	204058575	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagaagccaaccaaaataGacacttcaaccctaaacctg	17	6	5	13	0	1	2	1	0	0	2	1	2	1	2	4	0	5	1	4	0	8	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:204058575G>T	ENST00000449802.1	+	46	7225	c.6892G>T	c.(6892-6894)Gac>Tac	p.D2298Y		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2298										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AACCAAAATAGACACTTCAAC	0.343																																					p.D2298Y		.											.	NBEAL1-92	0			c.G6892T						.						157	157	157					2																	204058575		1870	4098	5968	SO:0001583	missense	65065	exon46			AAAATAGACACTT	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6892G>T	2.37:g.204058575G>T	ENSP00000399903:p.Asp2298Tyr	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	149	42	NM_001114132	0	0	1	2	1	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486179	0.63962	.	.	ENSG00000144426	ENST00000449802;ENST00000414576	T;T	0.56776	0.44;1.1	5.43	5.43	0.79202	.	0.063926	0.64402	U	0.000013	T	0.66684	0.2814	M	0.77103	2.36	0.58432	D	0.999999	P	0.49862	0.929	P	0.51487	0.671	T	0.67385	-0.5684	10	0.39692	T	0.17	.	18.8378	0.92169	0.0:0.0:1.0:0.0	.	2298	Q6ZS30	NBEL1_HUMAN	Y	2298;313	ENSP00000399903:D2298Y;ENSP00000388466:D313Y	ENSP00000388466:D313Y	D	+	1	0	NBEAL1	203766820	1.000000	0.71417	0.973000	0.42090	0.900000	0.52787	9.028000	0.93712	2.550000	0.86006	0.650000	0.86243	GAC	.		0.343	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204058575	G	T	204058575	3	4	114	1	0	0	0	0	1	0	0	0	10213	942	33	4	7070	4	NBEAL1	2	204058575	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	21658974	204058575	39140798	11	9979											
SETD5	55209	hgsc.bcm.edu	37	chr3	9495547	9495547	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctagtatctgcaaagacaAtgcaggtacgtatctaaaac	15	11	7	8	1	3	1	0	0	3	1	3	1	3	1	0	1	4	5	0	1	8	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:9495547A>G	ENST00000406341.1	+	16	2661	c.2471A>G	c.(2470-2472)aAt>aGt	p.N824S	SETD5_ENST00000402198.1_Missense_Mutation_p.N824S|SETD5_ENST00000488236.1_3'UTR|SETD5_ENST00000302463.6_Missense_Mutation_p.N726S|SETD5_ENST00000402466.1_Missense_Mutation_p.N726S|SETD5_ENST00000407969.1_Missense_Mutation_p.N843S			Q9C0A6	SETD5_HUMAN	SET domain containing 5	824										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		TGCAAAGACAATGCAGGTACG	0.353																																					p.N824S		.											.	SETD5-70	0			c.A2471G						.						86	80	82					3																	9495547		1861	4110	5971	SO:0001583	missense	55209	exon17			AAGACAATGCAGG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.2471A>G	3.37:g.9495547A>G	ENSP00000383939:p.Asn824Ser	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	61	14	NM_001080517	0	0	0	0	0	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	A	0.331	-0.956084	0.02267	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.90504	-2.37;-2.68;-2.37;-2.37;-2.68	5.4	-1.65	0.08291	.	0.396214	0.29015	N	0.013418	T	0.68879	0.3049	N	0.03608	-0.345	0.23581	N	0.997369	B;B;B;B	0.14438	0.01;0.008;0.0;0.002	B;B;B;B	0.15052	0.012;0.009;0.0;0.003	T	0.62416	-0.6859	10	0.02654	T	1	-4.8279	5.9999	0.19515	0.3801:0.2636:0.3563:0.0	.	493;726;824;843	B3KXG4;Q9C0A6-3;Q9C0A6;E7EWN3	.;.;SETD5_HUMAN;.	S	824;726;824;843;726	ENSP00000385852:N824S;ENSP00000384429:N726S;ENSP00000383939:N824S;ENSP00000384114:N843S;ENSP00000302028:N726S	ENSP00000302028:N726S	N	+	2	0	SETD5	9470547	0.998000	0.40836	0.970000	0.41538	0.385000	0.30292	0.664000	0.25068	-0.105000	0.12132	0.533000	0.62120	AAT	.		0.353	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9495547	A	G	9495547	3	3	114	1	0	0	0	0	1	0	0	0	14166	101	4	3	2529	3	SETD5	3	9495547	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08		9495547	188526883	12	9980											
MTMR14	64419	ucsc.edu	37	chr3	9691415	9691415	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaaggatggcagcgggaccGgcggctctaaggtgagattg	9	6	17	9	3	1	1	0	1	1	1	1	4	1	3	2	6	1	2	2	6	2	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:9691415G>A	ENST00000296003.4	+	1	270	c.148G>A	c.(148-150)Ggc>Agc	p.G50S	MTMR14_ENST00000351233.5_Missense_Mutation_p.G50S|MTMR14_ENST00000353332.5_Missense_Mutation_p.G50S|MTMR14_ENST00000420925.1_Missense_Mutation_p.G50S	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	50					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					CAGCGGGACCGGCGGCTCTAA	0.617																																					p.G50S													.	MTMR14-91	0			c.G148A						.						13	16	15					3																	9691415		1951	4134	6085	SO:0001583	missense	64419	exon1			GGGACCGGCGGCT	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	26190	protein-coding gene	gene with protein product	"egg-derived tyrosine phosphatase homolog (Drosophila)"	611089	"chromosome 3 open reading frame 29"	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.148G>A	3.37:g.9691415G>A	ENSP00000296003:p.Gly50Ser	Somatic	27	0		WXS	Illumina HiSeq		29	4	NM_022485	0	0	0	0	0	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Missense_Mutation	SNP	ENST00000296003.4	37	CCDS43043.1	.	.	.	.	.	.	.	.	.	.	G	8.957	0.969656	0.18659	.	.	ENSG00000163719	ENST00000353332;ENST00000420925;ENST00000296003;ENST00000351233;ENST00000419048	T;D;T;T	0.89939	1.62;-2.59;1.62;1.62	5.3	1.8	0.24995	.	0.376195	0.26099	N	0.026353	T	0.77294	0.4109	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.12630	0.003;0.006;0.004;0.001	B;B;B;B	0.11329	0.002;0.003;0.006;0.001	T	0.57015	-0.7883	10	0.06625	T	0.88	-10.6331	7.7854	0.29089	0.295:0.0:0.705:0.0	.	50;50;50;50	C9JSR1;Q8NCE2-3;Q8NCE2-2;Q8NCE2	.;.;.;MTMRE_HUMAN	S	50	ENSP00000323462:G50S;ENSP00000401993:G50S;ENSP00000296003:G50S;ENSP00000334070:G50S	ENSP00000296003:G50S	G	+	1	0	MTMR14	9666415	0.756000	0.28383	0.024000	0.17045	0.002000	0.02628	1.655000	0.37345	0.029000	0.15352	-0.142000	0.14014	GGC	.		0.617	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		A	9691415	G	A	9691415	3	1	114	1	0	0	0	0	1	0	0	0	9967	1116	39	1	150	1	MTMR14	3	9691415	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	195868	9691415	188331015	13	9981											
SLC9A10	285335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	111918287	111918287	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgttttcacagtgacagCaatttctgggtgatcatact	9	16	8	8	0	3	2	2	2	1	0	3	2	3	2	0	1	2	2	0	1	2	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:111918287C>T	ENST00000305815.5	-	20	2656	c.2404G>A	c.(2404-2406)Gct>Act	p.A802T	SLC9C1_ENST00000487372.1_Missense_Mutation_p.A754T	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	802					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										ACAGTGACAGCAATTTCTGGG	0.279																																					p.A802T		.											.	.	0			c.G2404A						.						73	73	73					3																	111918287		2201	4297	6498	SO:0001583	missense	285335	exon20			TGACAGCAATTTC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2404G>A	3.37:g.111918287C>T	ENSP00000306627:p.Ala802Thr	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	89	45	NM_183061	0	0	0	0	0	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990748	0.54041	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.80480	-1.35;-1.38	5.55	2.81	0.32909	.	0.221517	0.31577	N	0.007408	T	0.81264	0.4786	M	0.65498	2.005	0.27008	N	0.96476	P;D	0.59767	0.855;0.986	P;P	0.52909	0.713;0.655	T	0.71745	-0.4500	10	0.33940	T	0.23	.	7.6697	0.28451	0.0:0.7356:0.0:0.2644	.	754;802	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	T	802;754	ENSP00000306627:A802T;ENSP00000420688:A754T	ENSP00000306627:A802T	A	-	1	0	SLC9A10	113400977	0.902000	0.30710	0.686000	0.30086	0.473000	0.32948	1.823000	0.39062	0.310000	0.22990	-0.140000	0.14226	GCT	.		0.279	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		T	111918287	C	T	111918287	3	4	114	1	0	0	0	0	1	0	0	0	14742	710	25	2	1169	2	SLC9A10	3	111918287	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	102226872	111918287	86104143	14	9982											
TMCC1	23023	hgsc.bcm.edu	37	chr3	129390056	129390057	+	Missense_Mutation	DNP	AG	AG	TT																															gatgctgccatcggtactggAggccactgcactggatgttt																										TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:129390056_129390057AG>TT	ENST00000393238.3	-	4	967_968	c.627_628CT>AA	c.(625-630)gcCTcc>gcAAcc	p.S210T	TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000329333.5_Missense_Mutation_p.S31T|TMCC1_ENST00000426664.2_Missense_Mutation_p.S96T	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	210						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TCGGTACTGGAGGCCACTGCAC	0.52																																					p.S210T		.											.	TMCC1	0			c.C627A						.																																			SO:0001583	missense	23023	exon4			ACTGGAGGCCACT	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.627_628delinsTT	3.37:g.129390056_129390057delinsTT	ENSP00000376930:p.Ser210Thr	Somatic	143	2		WXS	Illumina HiSeq	Phase_I	180	10		0	0	0	0	0	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	DNP	ENST00000393238.3	37	CCDS33855.1																																																																																			.		0.52	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		TT	129390057	AG	TT	129390056	3	4	114	1	0	0	0	0	1	0	0	0	16024	304	11	5	1345	5	TMCC1	3	129390056	Missense_Mutation	DNP	AG	TCGA-G7-6793-01A-11D-1961-08	17471769	129390056	68632374	15	9983											
TSC22D2	9819	ucsc.edu	37	chr3	150128649	150128649	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctcacgccgtggtgccCggagttccaaacgtgcctgc	5	7	13	16	4	1	0	1	0	0	0	2	1	2	1	5	3	4	1	5	3	1	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:150128649C>T	ENST00000361875.3	+	1	2528	c.1512C>T	c.(1510-1512)ccC>ccT	p.P504P	TSC22D2_ENST00000361136.2_Silent_p.P504P	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	504					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CCGTGGTGCCCGGAGTTCCAA	0.667																																					p.P504P													.	TSC22D2-91	0			c.C1512T						.						46	46	46					3																	150128649		2203	4300	6503	SO:0001819	synonymous_variant	9819	exon1			GGTGCCCGGAGTT	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1512C>T	3.37:g.150128649C>T		Somatic	53	0		WXS	Illumina HiSeq		42	4	NM_014779	0	0	27	27	0	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1																																																																																			.		0.667	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779		T	150128649	C	T	150128649	2	4	114	1	0	0	0	0	0	0	0	1	16641	639	23	1		1	TSC22D2	3	150128649	Silent	SNP	C	TCGA-G7-6793-01A-11D-1961-08	20738593	150128649	47893781	16	9984											
N4BP2	55728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	40103811	40103811	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggtgcagcagaaagtaaaAtaatggaaaaacgtcctgaa	19	7	10	5	1	0	2	0	1	0	1	1	3	1	3	1	2	3	3	1	2	8	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr4:40103811A>G	ENST00000261435.6	+	4	762	c.346A>G	c.(346-348)Ata>Gta	p.I116V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	116					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						AGAAAGTAAAATAATGGAAAA	0.368																																					p.I116V		.											.	N4BP2-602	0			c.A346G						.						92	90	91					4																	40103811		2203	4300	6503	SO:0001583	missense	55728	exon4			AGTAAAATAATGG	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.346A>G	4.37:g.40103811A>G	ENSP00000261435:p.Ile116Val	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	90	28	NM_018177	0	0	1	1	0	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	A	0.424	-0.906575	0.02434	.	.	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.79247	-1.25;-1.25	6.08	1.18	0.20946	.	0.531518	0.19034	N	0.124467	T	0.52451	0.1735	N	0.12746	0.255	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.14578	0.011;0.003	T	0.37291	-0.9712	10	0.02654	T	1	-6.4549	8.9819	0.35970	0.7223:0.0:0.2777:0.0	.	116;116	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	V	116;36;36	ENSP00000261435:I116V;ENSP00000422057:I36V	ENSP00000261435:I116V	I	+	1	0	N4BP2	39780206	0.971000	0.33674	0.507000	0.27676	0.442000	0.32017	0.597000	0.24059	0.543000	0.28864	0.482000	0.46254	ATA	.		0.368	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40103811	A	G	40103811	3	3	114	1	0	0	0	0	1	0	0	0	10135	101	4	3	352	3	N4BP2	4	40103811	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08		40103811	151050465	17	9985											
CUTA	51596	hgsc.bcm.edu	37	chr6	33384696	33384696	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catccatctcaaagttctcaCcgaacaaaatctgtcaaagc	15	9	4	13	1	4	0	3	0	3	0	7	1	5	0	2	0	2	1	2	0	5	1	rs113648187		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr6:33384696C>G	ENST00000488034.1	-	5	535		c.e5+1		CUTA_ENST00000607266.1_Splice_Site|CUTA_ENST00000494751.1_Splice_Site|CUTA_ENST00000374496.3_Splice_Site|CUTA_ENST00000488478.1_Intron|CUTA_ENST00000492510.1_5'Flank|CUTA_ENST00000374500.5_Splice_Site|CUTA_ENST00000440279.3_Splice_Site	NM_001014837.1|NM_001014838.1|NM_001014840.1|NM_015921.2	NP_001014837.1|NP_001014838.1|NP_001014840.1|NP_057005.1	O60888	CUTA_HUMAN	cutA divalent cation tolerance homolog (E. coli)						protein localization (GO:0008104)|response to metal ion (GO:0010038)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)		SLC22A1/CUTA(2)	kidney(1)|lung(3)|urinary_tract(1)	5						AAAGTTCTCACCGAACAAAAT	0.468																																					.		.											.	CUTA-90	0			c.344+1G>C						.	C	,,,,	0,4406		0,0,2203	133	138	137		,,,,	4.1	1	6	dbSNP_132	137	1,8599	1.2+/-3.3	0,1,4299	no	splice-5,splice-5,splice-5,splice-5,splice-5	CUTA	NM_001014433.2,NM_001014837.1,NM_001014838.1,NM_001014840.1,NM_015921.2	,,,,	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	,,,,	,,,,	33384696	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	51596	exon6			TTCTCACCGAACA	AF106943	CCDS4779.1, CCDS34432.1, CCDS34433.1	6p21.32	2008-02-04	2006-02-15	2006-02-15	ENSG00000112514	ENSG00000112514			21101	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 82", "acetylcholinesterase-associated protein"	C6orf82, ACHAP			Standard	XM_006715108		Approved		uc003oen.1	O60888	OTTHUMG00000031254	ENST00000488034.1:c.413+1G>C	6.37:g.33384696C>G		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	51	3	NM_001014837	0	0	0	0	0	A2AB26|A2BEL4|Q3B784|Q5JXM9|Q5SU05|Q9NYQ9	Splice_Site	SNP	ENST00000488034.1	37	CCDS34433.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823920	0.71143	0.0	1.16E-4	ENSG00000112514	ENST00000374500;ENST00000440279;ENST00000488034;ENST00000494751;ENST00000374496	.	.	.	4.14	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8038	0.52143	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CUTA	33492674	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.873000	0.63057	2.150000	0.67090	0.561000	0.74099	.	G|1.000		0.468	CUTA-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076541.3	NM_015921	Intron	G	33384696	C	G	33384696	5	3	114	1	0	0	0	0	0	0	1	0	4068	521	18	4	133	4	CUTA	6	33384696	Splice_Site	SNP	C	TCGA-G7-6793-01A-11D-1961-08		33384696	137730371	18	9986											
MOXD1	26002	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	132649712	132649712	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcaccagactctcatggcCtctctgtatcactggctcaa	8	11	8	14	0	4	1	3	0	2	1	6	1	4	1	2	2	1	3	2	2	2	1	rs146988576	byFrequency	TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr6:132649712C>G	ENST00000367963.3	-	5	803	c.685G>C	c.(685-687)Ggc>Cgc	p.G229R	MOXD1_ENST00000336749.3_Missense_Mutation_p.G161R	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	229						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		CTCTCATGGCCTCTCTGTATC	0.488																																					p.G229R													.	MOXD1-515	0			c.G685C						.						131	109	117					6																	132649712		2203	4300	6503	SO:0001583	missense	26002	exon5			CATGGCCTCTCTG	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.685G>C	6.37:g.132649712C>G	ENSP00000356940:p.Gly229Arg	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	53	17	NM_015529	0	0	10	20	10	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738753	0.89573	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.29142	1.58;1.58	5.25	5.25	0.73442	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.057506	0.64402	D	0.000002	T	0.51041	0.1651	M	0.77103	2.36	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.71870	0.973;0.975	T	0.51631	-0.8681	10	0.49607	T	0.09	-9.5898	19.1947	0.93682	0.0:1.0:0.0:0.0	.	229;161	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	R	229;161	ENSP00000356940:G229R;ENSP00000336998:G161R	ENSP00000336998:G161R	G	-	1	0	MOXD1	132691405	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.470000	0.73558	2.592000	0.87571	0.655000	0.94253	GGC	C|0.999;T|0.001		0.488	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		G	132649712	C	G	132649712	3	3	114	1	0	0	0	0	1	0	0	0	9745	681	24	4	1188	4	MOXD1	6	132649712	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	99265016	132649712	38465355	19	9987											
KIAA0146	23514	broad.mit.edu;bcgsc.ca	37	chr8	48508505	48508506	+	In_Frame_Ins	INS	-	-	AGC																															acataccccttccaagaagaINSagcatctctttggcccagat																										TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr8:48508505_48508506insAGC	ENST00000297423.4	+	9	1614_1615	c.1230_1231insAGC	c.(1231-1233)agc>AGCagc	p.411_411S>SS	SPIDR_ENST00000541342.1_In_Frame_Ins_p.341_341S>SS|SPIDR_ENST00000518074.1_In_Frame_Ins_p.351_351S>SS|SPIDR_ENST00000521214.1_3'UTR	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	411	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											TTCCAAGAAGAAGCATCTCTTT	0.371																																					p.R410delinsRS													.	KIAA0146-68	0			c.1230_1231insAGC						.																																			SO:0001652	inframe_insertion	23514	exon9			AAGAAGAAGCATC	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"KIAA0146"	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1231_1233dupAGC	8.37:g.48508506_48508508dupAGC	ENSP00000297423:p.Ser411dup	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	53	7	NM_001080394	0	0	0	0	0	B4DFV2|B4E0Y6|Q96BI5	In_Frame_Ins	INS	ENST00000297423.4	37	CCDS43737.1																																																																																			.		0.371	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		AGC	48508506	-	AGC	48508505	7	5	114	1	0	1	1	0	0	0	0	0	8178	243	9	0	1264	0	KIAA0146	8	48508505	In_Frame_Ins	INS	-	TCGA-G7-6793-01A-11D-1961-08		48508505	97855517	20	9988											
RIPK2	8767	ucsc.edu	37	chr8	90770295	90770295	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcgcccgggaccatgaacGgggaggccatctgcagcgcc	8	3	16	14	4	1	1	0	1	1	0	1	4	1	3	4	4	4	1	4	4	1	0			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr8:90770295G>A	ENST00000220751.4	+	1	321	c.7G>A	c.(7-9)Ggg>Agg	p.G3R	RIPK2_ENST00000540020.1_5'UTR|RP11-37B2.1_ENST00000504145.1_lincRNA	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	3					activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			GACCATGAACGGGGAGGCCAT	0.726																																					p.G3R													.	RIPK2-523	0			c.G7A						.						20	22	21					8																	90770295		2195	4290	6485	SO:0001583	missense	8767	exon1			ATGAACGGGGAGG	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.7G>A	8.37:g.90770295G>A	ENSP00000220751:p.Gly3Arg	Somatic	21	0		WXS	Illumina HiSeq		30	4	NM_003821	0	0	15	15	0	B7Z748|Q6UWF0	Missense_Mutation	SNP	ENST00000220751.4	37	CCDS6247.1	.	.	.	.	.	.	.	.	.	.	G	6.747	0.506603	0.12883	.	.	ENSG00000104312	ENST00000220751	T	0.80123	-1.34	4.48	2.67	0.31697	.	0.739382	0.11020	N	0.608540	T	0.64249	0.2581	N	0.16478	0.41	0.80722	D	1	B	0.11235	0.004	B	0.06405	0.002	T	0.48293	-0.9048	10	0.14656	T	0.56	1.359	9.0698	0.36486	0.0847:0.3987:0.5166:0.0	.	3	O43353	RIPK2_HUMAN	R	3	ENSP00000220751:G3R	ENSP00000220751:G3R	G	+	1	0	RIPK2	90839430	1.000000	0.71417	0.284000	0.24805	0.935000	0.57460	1.916000	0.39986	0.494000	0.27859	0.462000	0.41574	GGG	.		0.726	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1			A	90770295	G	A	90770295	3	1	114	1	0	0	0	0	1	0	0	0	13413	1116	39	1	9	1	RIPK2	8	90770295	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	42261790	90770295	55593727	21	9989											
SMU1	55234	hgsc.bcm.edu	37	chr9	33068839	33068839	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctgtcccagcaatgccaTgagacgagatggaggcacca	12	6	11	12	1	0	2	0	1	0	2	1	5	1	3	4	2	3	2	4	2	2	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr9:33068839T>A	ENST00000397149.3	-	4	534	c.484A>T	c.(484-486)Atg>Ttg	p.M162L	SMU1_ENST00000536631.1_Start_Codon_SNP_p.M1L	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	162						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		AGCAATGCCATGAGACGAGAT	0.522																																					p.M162L		.											.	SMU1-91	0			c.A484T						.						163	132	142					9																	33068839		2203	4300	6503	SO:0001583	missense	55234	exon4			ATGCCATGAGACG	AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692		"WD repeat domain containing"	18247	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 57"					11438655, 11410362	Standard	NM_018225		Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.484A>T	9.37:g.33068839T>A	ENSP00000380336:p.Met162Leu	Somatic	84	2		WXS	Illumina HiSeq	Phase_I	59	4	NM_018225	0	0	45	45	0	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Missense_Mutation	SNP	ENST00000397149.3	37	CCDS6534.1	.	.	.	.	.	.	.	.	.	.	T	8.836	0.941179	0.18281	.	.	ENSG00000122692	ENST00000397149;ENST00000536631	T;T	0.40476	1.03;1.25	5.57	5.57	0.84162	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.14527	0.0351	N	0.00926	-1.1	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24693	-1.0153	10	0.02654	T	1	-36.168	13.9704	0.64237	0.0:0.0:0.0:1.0	.	162;1;162	A0MNN4;B4E3L0;Q2TAY7	.;.;SMU1_HUMAN	L	162;1	ENSP00000380336:M162L;ENSP00000443639:M1L	ENSP00000380336:M162L	M	-	1	0	SMU1	33058839	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.910000	0.87451	2.248000	0.74166	0.533000	0.62120	ATG	.		0.522	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225		A	33068839	T	A	33068839	3	1	114	1	0	0	0	0	1	0	0	0	14849	1464	51	5	1093	5	SMU1	9	33068839	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08		33068839	108144592	22	9990											
ITGA8	8516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	15688933	15688933	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgccagtgaggatctggggGtctctgaagaggagagagct	9	8	18	6	0	2	4	0	2	2	2	3	7	2	6	1	4	2	1	1	4	1	0			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:15688933G>A	ENST00000378076.3	-	12	1472	c.1119C>T	c.(1117-1119)gaC>gaT	p.D373D		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	373					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GGATCTGGGGGTCTCTGAAGA	0.483																																					p.D373D		.											.	ITGA8-230	0			c.C1119T						.						122	109	113					10																	15688933		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon12			CTGGGGGTCTCTG	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1119C>T	10.37:g.15688933G>A		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	106	21	NM_003638	0	0	6	6	0	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	37	CCDS31155.1																																																																																			.		0.483	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		A	15688933	G	A	15688933	2	1	114	1	0	0	0	0	0	0	0	1	7903	1252	44	2		2	ITGA8	10	15688933	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08		15688933	119845814	23	9991											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16916468	16916468	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaataggcaggacttgtgatGattccagaagagaaattgaa	16	9	12	4	0	0	5	0	3	0	2	1	8	1	6	1	2	0	1	1	2	5	4			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:16916468G>T	ENST00000377833.4	-	58	9206	c.9141C>A	c.(9139-9141)atC>atA	p.I3047I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3047	CUB 23. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GACTTGTGATGATTCCAGAAG	0.433																																					p.I3047I		.											.	CUBN-166	0			c.C9141A						.						168	135	146					10																	16916468		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon58			TGTGATGATTCCA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.9141C>A	10.37:g.16916468G>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	89	24	NM_001081	0	0	1	1	0	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			.		0.433	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16916468	G	T	16916468	2	4	114	1	0	0	0	0	0	0	0	1	4057	1280	45	4		4	CUBN	10	16916468	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	1227535	16916468	118618279	24	9992											
UBTD1	80019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	99327795	99327795	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgccttcgagggccgcaaGgagatctgggatgccctcaa	8	7	13	13	2	2	1	1	0	1	1	3	4	2	2	4	3	2	1	4	3	2	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:99327795G>A	ENST00000370664.3	+	2	531	c.195G>A	c.(193-195)aaG>aaA	p.K65K		NM_024954.3	NP_079230.1	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	65										central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		AGGGCCGCAAGGAGATCTGGG	0.632																																					p.K65K	Pancreas(100;169 2668 32720)	.											.	UBTD1-90	0			c.G195A						.						87	86	86					10																	99327795		2203	4300	6503	SO:0001819	synonymous_variant	80019	exon2			CCGCAAGGAGATC	BC007331	CCDS7465.1	10q24.2	2005-09-22			ENSG00000165886	ENSG00000165886			25683	protein-coding gene	gene with protein product						12477932	Standard	NM_024954		Approved	FLJ11807	uc001knv.1	Q9HAC8	OTTHUMG00000018856	ENST00000370664.3:c.195G>A	10.37:g.99327795G>A		Somatic	195	0		WXS	Illumina HiSeq	Phase_I	155	24	NM_024954	0	0	68	106	38	D3DR57|Q53HI3	Silent	SNP	ENST00000370664.3	37	CCDS7465.1																																																																																			.		0.632	UBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049701.1	NM_024954		A	99327795	G	A	99327795	2	1	114	1	0	0	0	0	0	0	0	1	16940	991	35	2		2	UBTD1	10	99327795	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	82411327	99327795	36206952	25	9993											
SFRP5	6425	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	99527530	99527530	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttgcgcttcagggggcccGgcttgagcagcttcttcttt	3	13	12	13	2	3	1	1	1	2	0	3	1	3	1	2	3	3	4	2	3	0	6	rs199605298	byFrequency	TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:99527530G>T	ENST00000266066.3	-	3	813	c.695C>A	c.(694-696)cCg>cAg	p.P232Q		NM_003015.3	NP_003006.2	Q5T4F7	SFRP5_HUMAN	secreted frizzled-related protein 5	232	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell differentiation (GO:0030154)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|establishment or maintenance of cell polarity (GO:0007163)|gonad development (GO:0008406)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis (GO:2000057)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|post-anal tail morphogenesis (GO:0036342)|signal transduction (GO:0007165)|vasculature development (GO:0001944)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			large_intestine(1)|lung(4)	5		Colorectal(252;0.234)		Epithelial(162;4.98e-10)|all cancers(201;3.58e-08)		CAGGGGGCCCGGCTTGAGCAG	0.587													G|||	8	0.00159744	0	0	5008	,	,		16353	0.0079		0	False		,,,				2504	0				p.P232Q		.											.	SFRP5-658	0			c.C695A						.						55	60	58					10																	99527530		2203	4300	6503	SO:0001583	missense	6425	exon3			GGGCCCGGCTTGA	AF017988	CCDS7472.1	10q24	2008-07-10			ENSG00000120057	ENSG00000120057		"Secreted frizzled-related proteins"	10779	protein-coding gene	gene with protein product	"secreted apoptosis related protein 3"	604158				9391078	Standard	NM_003015		Approved	SARP3	uc001kor.4	Q5T4F7	OTTHUMG00000018866	ENST00000266066.3:c.695C>A	10.37:g.99527530G>T	ENSP00000266066:p.Pro232Gln	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	97	43	NM_003015	0	0	0	0	0	O14780|Q86TH7	Missense_Mutation	SNP	ENST00000266066.3	37	CCDS7472.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	8.727	0.915701	0.17907	.	.	ENSG00000120057	ENST00000266066	T	0.19938	2.11	5.74	5.74	0.90152	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.747332	0.12885	N	0.431104	T	0.09774	0.0240	N	0.03608	-0.345	0.22292	N	0.999227	B	0.16396	0.017	B	0.18561	0.022	T	0.26985	-1.0087	10	0.13470	T	0.59	.	10.9329	0.47228	0.1134:0.0:0.8866:0.0	.	232	Q5T4F7	SFRP5_HUMAN	Q	232	ENSP00000266066:P232Q	ENSP00000266066:P232Q	P	-	2	0	SFRP5	99517520	0.958000	0.32768	0.999000	0.59377	0.995000	0.86356	2.473000	0.45145	2.712000	0.92718	0.561000	0.74099	CCG	G|0.999;T|0.001		0.587	SFRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049742.1	NM_003015		T	99527530	G	T	99527530	3	4	114	1	0	0	0	0	1	0	0	0	14196	1116	39	4	262	4	SFRP5	10	99527530	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	199735	99527530	36007217	26	9994											
ATE1	11101	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	123658376	123658376	+	Intron	DEL	C	C	-																															ctcagtcttcccacattcatCgggtggatcctggtgtatgg																								rs150970157		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:123658376delC	ENST00000224652.6	-	7	1028				ATE1_ENST00000543447.1_Intron|ATE1_ENST00000535655.1_Intron|ATE1_ENST00000540606.1_Frame_Shift_Del_p.D301fs|ATE1_ENST00000369040.3_Frame_Shift_Del_p.D212fs|ATE1_ENST00000369043.3_Frame_Shift_Del_p.D308fs|ATE1_ENST00000481784.1_Intron	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1						protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				CCACATTCATCGGGTGGATCC	0.423																																					p.D308fs		.											.	ATE1-90	0			c.922delG						.						189	157	168					10																	123658376		2203	4300	6503	SO:0001627	intron_variant	11101	exon7			.	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.942+1004G>-	10.37:g.123658376delC		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	73	11	NM_007041	0	0	0	0	0	O95261|Q5SQQ3|Q8WW04	Frame_Shift_Del	DEL	ENST00000224652.6	37	CCDS31300.1																																																																																			.		0.423	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976		-	123658376	C	-	123658376	6	5	114	0	1	1	0	1	0	0	0	0	1079	884	31	0		0	ATE1	10	123658376	Intron	DEL	C	TCGA-G7-6793-01A-11D-1961-08	24130846	123658376	11876371	27	9995											
CNIH2	254263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66049735	66049735	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgcccctcccccagatcatAgcctttgatgagctgcggac	8	8	9	16	2	1	3	1	2	0	1	2	4	2	4	5	1	3	1	5	1	1	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr11:66049735A>G	ENST00000311445.6	+	2	345	c.87A>G	c.(85-87)atA>atG	p.I29M	YIF1A_ENST00000526497.1_5'Flank|CNIH2_ENST00000530519.1_3'UTR|CNIH2_ENST00000528852.1_Missense_Mutation_p.I29M	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	29					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						CCCAGATCATAGCCTTTGATG	0.597																																					p.I29M		.											.	CNIH2-90	0			c.A87G						.						72	66	68					11																	66049735		2200	4295	6495	SO:0001583	missense	254263	exon2			GATCATAGCCTTT	BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"cornichon homolog 2 (Drosophila)"			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.87A>G	11.37:g.66049735A>G	ENSP00000310003:p.Ile29Met	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	42	10	NM_182553	0	0	0	0	0		Missense_Mutation	SNP	ENST00000311445.6	37	CCDS8131.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634157	0.47049	.	.	ENSG00000174871	ENST00000528852;ENST00000311445	T;T	0.55760	0.5;0.5	5.33	1.49	0.22878	.	0.000000	0.85682	D	0.000000	T	0.68869	0.3048	M	0.89478	3.035	0.58432	D	0.999998	D;D	0.71674	0.961;0.998	P;D	0.68483	0.791;0.958	T	0.68221	-0.5466	10	0.59425	D	0.04	-24.0482	4.9261	0.13894	0.3807:0.2295:0.0:0.3897	.	29;29	Q6PI25;E9PS15	CNIH2_HUMAN;.	M	29	ENSP00000432177:I29M;ENSP00000310003:I29M	ENSP00000310003:I29M	I	+	3	3	CNIH2	65806311	0.998000	0.40836	1.000000	0.80357	0.547000	0.35210	1.267000	0.33050	0.919000	0.36945	0.460000	0.39030	ATA	.		0.597	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553		G	66049735	A	G	66049735	3	3	114	1	0	0	0	0	1	0	0	0	3609	410	15	3	93	3	CNIH2	11	66049735	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08		66049735	68956781	28	9996											
NPAS4	266743	broad.mit.edu	37	chr11	66191471	66191471	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accgcagcactgggggctccCagaagcaccagcttccccag	9	4	11	17	1	0	1	0	0	0	1	2	1	2	1	5	2	3	5	5	2	1	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr11:66191471C>A	ENST00000311034.2	+	7	1286	c.1110C>A	c.(1108-1110)ccC>ccA	p.P370P		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	370					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						TGGGGGCTCCCAGAAGCACCA	0.552																																					p.P370P													.	NPAS4-90	0			c.C1110A						.						134	140	138					11																	66191471		2200	4295	6495	SO:0001819	synonymous_variant	266743	exon7			GGCTCCCAGAAGC	AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"Basic helix-loop-helix proteins"	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.1110C>A	11.37:g.66191471C>A		Somatic	317	0		WXS	Illumina HiSeq	Phase_I	222	8	NM_178864	0	0	0	0	0	B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	37	CCDS8138.1																																																																																			.		0.552	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		A	66191471	C	A	66191471	2	1	114	1	0	0	0	0	0	0	0	1	10591	581	21	4		4	NPAS4	11	66191471	Silent	SNP	C	TCGA-G7-6793-01A-11D-1961-08	141736	66191471	68815045	29	9997											
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	108380880	108380880	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggtgtggctcaggttccCactccagagatgaagcactc	10	8	12	11	0	1	3	1	1	0	2	4	4	3	3	2	3	1	3	2	3	1	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr11:108380880C>T	ENST00000265843.4	-	6	5464	c.5354G>A	c.(5353-5355)tGg>tAg	p.W1785*	EXPH5_ENST00000443411.1_Nonsense_Mutation_p.W1597*|EXPH5_ENST00000428840.1_Nonsense_Mutation_p.W1709*|EXPH5_ENST00000525344.1_Nonsense_Mutation_p.W1778*	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1785					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTCAGGTTCCCACTCCAGAGA	0.483																																					p.W1785X		.											.	EXPH5-95	0			c.G5354A						.						89	96	94					11																	108380880		2201	4298	6499	SO:0001587	stop_gained	23086	exon6			GGTTCCCACTCCA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5354G>A	11.37:g.108380880C>T	ENSP00000265843:p.Trp1785*	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	107	46	NM_015065	0	0	0	1	1	Q2KHM1|Q9Y4D6	Nonsense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	41	8.551547	0.98859	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312	.	.	.	6.17	4.26	0.50523	.	0.766008	0.12354	N	0.476287	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	1.7662	10.3652	0.44019	0.0:0.497:0.431:0.0721	.	.	.	.	X	1785;1709;1597;1778;615;1709	.	ENSP00000265843:W1785X	W	-	2	0	EXPH5	107886090	0.060000	0.20803	0.159000	0.22649	0.035000	0.12851	0.897000	0.28390	0.883000	0.36040	0.655000	0.94253	TGG	.		0.483	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108380880	C	T	108380880	4	4	114	1	0	0	0	0	0	1	0	0	5335	595	21	2	619	2	EXPH5	11	108380880	Nonsense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	42189409	108380880	26625636	30	9998											
KRT6A	3853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52882316	52882316	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctcagcatcagcaatggcgGcctgcaggttggcgcactgg	7	7	15	12	2	2	0	2	0	0	0	2	0	2	0	1	5	3	6	1	5	1	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr12:52882316G>A	ENST00000330722.6	-	7	1288	c.1220C>T	c.(1219-1221)gCc>gTc	p.A407V		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	407	Coil 2.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGCAATGGCGGCCTGCAGGTT	0.557																																					p.A407V		.											.	KRT6A-27	0			c.C1220T						.						71	66	67					12																	52882316		2203	4300	6503	SO:0001583	missense	3853	exon7			ATGGCGGCCTGCA	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"-", "Intermediate filaments type II, keratins (basic)"	6443	protein-coding gene	gene with protein product		148041	"keratin 6C", "keratin 6D"	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.1220C>T	12.37:g.52882316G>A	ENSP00000369317:p.Ala407Val	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	88	26	NM_005554	0	0	0	0	0	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	37	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	g	17.33	3.362592	0.61403	.	.	ENSG00000205420	ENST00000330722;ENST00000452121	T	0.75821	-0.97	5.15	4.21	0.49690	Filament (1);	0.570128	0.16803	N	0.198918	T	0.74344	0.3704	M	0.75085	2.285	0.26350	N	0.977228	P	0.42757	0.789	B	0.43194	0.411	T	0.70769	-0.4782	10	0.62326	D	0.03	.	9.2357	0.37464	0.076:0.0:0.7787:0.1453	.	407	P02538	K2C6A_HUMAN	V	407;363	ENSP00000369317:A407V	ENSP00000369317:A407V	A	-	2	0	KRT6A	51168583	0.003000	0.15002	0.944000	0.38274	0.754000	0.42855	1.333000	0.33816	2.549000	0.85964	0.655000	0.94253	GCC	.		0.557	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		A	52882316	G	A	52882316	3	1	114	1	0	0	0	0	1	0	0	0	8501	1203	42	2	486	2	KRT6A	12	52882316	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08		52882316	80969579	31	9999											
KDM2B	84678	broad.mit.edu;bcgsc.ca	37	chr12	122016841	122016841	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgtcgtatcgctggcggTcaatcgggcgctgcgaggac	5	9	15	12	7	2	0	1	0	1	0	6	2	2	1	0	4	1	3	0	4	2	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr12:122016841T>C	ENST00000377071.4	-	2	209	c.137A>G	c.(136-138)gAc>gGc	p.D46G	KDM2B_ENST00000377069.4_Missense_Mutation_p.D15G|KDM2B_ENST00000538046.2_Missense_Mutation_p.D46G|RP13-941N14.1_ENST00000541574.1_lincRNA|KDM2B_ENST00000536437.1_5'UTR	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	46					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TCGCTGGCGGTCAATCGGGCG	0.627																																					p.D46G													.	KDM2B-638	0			c.A137G						.						64	71	68					12																	122016841		2046	4187	6233	SO:0001583	missense	84678	exon2			TGGCGGTCAATCG	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases"	13610	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1B"	609078	"F-box and leucine-rich repeat protein 10"	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.137A>G	12.37:g.122016841T>C	ENSP00000366271:p.Asp46Gly	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	173	9	NM_032590	0	0	0	0	0	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	T	9.672	1.146946	0.21288	.	.	ENSG00000089094	ENST00000397480;ENST00000377069;ENST00000377071;ENST00000397478;ENST00000261824;ENST00000446152;ENST00000539371	T;T;T	0.42900	2.55;1.96;0.96	4.06	4.06	0.47325	.	1.411770	0.04385	N	0.361475	T	0.26521	0.0648	N	0.08118	0	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.12156	0.007;0.001;0.0	T	0.28235	-1.0050	10	0.46703	T	0.11	-14.2477	6.3037	0.21127	0.0:0.1551:0.0:0.8449	.	46;46;15	E7EML5;Q8NHM5;A8MRS1	.;KDM2B_HUMAN;.	G	46;15;46;46;46;9;15	ENSP00000366269:D15G;ENSP00000366271:D46G;ENSP00000398279:D9G	ENSP00000261824:D46G	D	-	2	0	KDM2B	120501224	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.418000	0.52721	1.711000	0.51337	0.374000	0.22700	GAC	.		0.627	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		C	122016841	T	C	122016841	3	2	114	1	0	0	0	0	1	0	0	0	8146	1667	58	3	4013	3	KDM2B	12	122016841	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08	69134525	122016841	11835054	32	10000											
OR4N4	283694	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	22382930	22382930	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggctctgtggcttgggggttTtgtccactccattatccagg	4	14	13	10	0	1	0	0	0	1	0	4	0	4	0	3	5	0	3	3	5	1	4			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr15:22382930T>C	ENST00000328795.4	+	1	549	c.458T>C	c.(457-459)tTt>tCt	p.F153S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTTGGGGGTTTTGTCCACTCC	0.527																																					p.F153S		.											.	OR4N4-73	0			c.T458C						.						100	87	91					15																	22382930		2187	4254	6441	SO:0001583	missense	283694	exon1			GGGGTTTTGTCCA	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.458T>C	15.37:g.22382930T>C	ENSP00000332500:p.Phe153Ser	Somatic	432	0		WXS	Illumina HiSeq	Phase_I	312	41	NM_001005241	0	0	0	0	0	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	10.03	1.238759	0.22711	.	.	ENSG00000183706	ENST00000328795	T	0.00216	8.53	3.37	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.00412	0.0013	M	0.62723	1.935	0.09310	N	1	D	0.67145	0.996	D	0.74348	0.983	T	0.47873	-0.9083	10	0.87932	D	0	-8.9888	10.041	0.42158	0.0:0.0:0.0:1.0	.	153	Q8N0Y3	OR4N4_HUMAN	S	153	ENSP00000332500:F153S	ENSP00000332500:F153S	F	+	2	0	OR4N4	19884294	0.006000	0.16342	0.918000	0.36340	0.103000	0.19146	1.078000	0.30754	1.522000	0.49001	0.332000	0.21555	TTT	.		0.527	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22382930	T	C	22382930	3	2	114	1	0	0	0	0	1	0	0	0	11104	1841	64	3	460	3	OR4N4	15	22382930	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08		22382930	80148462	33	10001											
FURIN	5045	ucsc.edu	37	chr15	91419099	91419099	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcatccctggaggcccagcGgtggccaacagtgtggcacg	7	5	15	14	3	0	0	0	0	0	0	1	1	1	1	3	5	2	2	3	5	1	0	rs141410539		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr15:91419099G>A	ENST00000268171.3	+	2	408	c.129G>A	c.(127-129)gcG>gcA	p.A43A		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	43			A -> V (in dbSNP:rs16944971).		cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GAGGCCCAGCGGTGGCCAACA	0.622																																					p.A43A													.	FURIN-1083	0			c.G129A						.	G		1,4387		0,1,2193	54	40	45		129	-9.5	0	15	dbSNP_134	45	1,8579		0,1,4289	no	coding-synonymous	FURIN	NM_002569.2		0,2,6482	AA,AG,GG		0.0117,0.0228,0.0154		43/795	91419099	2,12966	2194	4290	6484	SO:0001819	synonymous_variant	5045	exon2			CCCAGCGGTGGCC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.129G>A	15.37:g.91419099G>A		Somatic	22	0		WXS	Illumina HiSeq		22	4	NM_002569	0	1	201	202	0	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	37	CCDS10364.1																																																																																			G|1.000;A|0.000		0.622	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		A	91419099	G	A	91419099	2	1	114	1	0	0	0	0	0	0	0	1	6118	1103	39	1		1	FURIN	15	91419099	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	69036169	91419099	11112293	34	10002											
MRPS34	65993	hgsc.bcm.edu	37	chr16	1822947	1822947	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaggcggctctcgcggcgCacgtcggcccaggcccggac	6	3	16	16	7	1	1	0	0	1	1	3	2	1	2	2	6	0	2	2	6	1	0	rs1076695	byFrequency	TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr16:1822947C>G	ENST00000397375.2	-	1	209	c.174G>C	c.(172-174)gtG>gtC	p.V58V	MRPS34_ENST00000177742.3_Silent_p.V58V|NME3_ENST00000219302.3_5'Flank|EME2_ENST00000307394.7_5'Flank|NME3_ENST00000563498.1_5'Flank|EME2_ENST00000568449.1_5'Flank	NM_023936.1	NP_076425.1	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34	58						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|skin(2)	3						TCTCGCGGCGCACGTCGGCCC	0.726													C|||	251	0.0501198	0.0061	0.0965	5008	,	,		10499	0.002		0.1421	False		,,,				2504	0.0317				p.V58V		.											.	MRPS34-92	0			c.G174C						.	C		25,2311		0,25,1143	1	2	2		174	1.7	1	16	dbSNP_86	2	405,4871		9,387,2242	no	coding-synonymous	MRPS34	NM_023936.1		9,412,3385	GG,GC,CC		7.6763,1.0702,5.649		58/219	1822947	430,7182	1168	2638	3806	SO:0001819	synonymous_variant	65993	exon1			GCGGCGCACGTCG	BC001182	CCDS10444.1, CCDS73805.1	16p13.3	2012-09-13			ENSG00000074071	ENSG00000074071		"Mitochondrial ribosomal proteins / small subunits"	16618	protein-coding gene	gene with protein product		611994					Standard	NM_023936		Approved	MRP-S12, MGC2616	uc002cmo.3	P82930	OTTHUMG00000128636	ENST00000397375.2:c.174G>C	16.37:g.1822947C>G		Somatic	2	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_023936	0	0	0	1	1	Q9BVI7	Silent	SNP	ENST00000397375.2	37	CCDS10444.1																																																																																			C|0.923;G|0.077		0.726	MRPS34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250506.1	NM_023936		G	1822947	C	G	1822947	2	3	114	1	0	0	0	0	0	0	0	1	9868	697	25	4		4	MRPS34	16	1822947	Silent	SNP	C	TCGA-G7-6793-01A-11D-1961-08		1822947	88531806	35	10003											
E4F1	1877	broad.mit.edu;ucsc.edu	37	chr16	2284711	2284711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccacacaggcgagaagcCgttcaagtgctacaagtgcg	13	5	11	12	3	1	1	1	0	0	1	1	2	1	1	2	1	4	2	2	1	4	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr16:2284711C>T	ENST00000301727.4	+	11	1769	c.1721C>T	c.(1720-1722)cCg>cTg	p.P574L	DNASE1L2_ENST00000564065.1_5'Flank|E4F1_ENST00000564139.1_Missense_Mutation_p.P574L|RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000382437.4_5'Flank|DNASE1L2_ENST00000320700.5_5'Flank|E4F1_ENST00000565090.1_Missense_Mutation_p.P397L|DNASE1L2_ENST00000567494.1_5'Flank	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	574	Interaction with BMI1.|Mediates interaction with TP53.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						GGCGAGAAGCCGTTCAAGTGC	0.667																																					p.P574L													.	E4F1-187	0			c.C1721T						.						17	14	15					16																	2284711		2176	4283	6459	SO:0001583	missense	1877	exon11			AGAAGCCGTTCAA	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"Zinc fingers, C2H2-type"	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.1721C>T	16.37:g.2284711C>T	ENSP00000301727:p.Pro574Leu	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	18	7	NM_004424	0	0	19	36	17	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	37	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.838062	0.50951	.	.	ENSG00000167967	ENST00000301727	T	0.27557	1.66	5.38	5.38	0.77491	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.049374	0.85682	D	0.000000	T	0.56863	0.2014	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.59579	-0.7428	10	0.72032	D	0.01	-22.8742	17.7029	0.88300	0.0:1.0:0.0:0.0	.	574	Q66K89	E4F1_HUMAN	L	574	ENSP00000301727:P574L	ENSP00000301727:P574L	P	+	2	0	E4F1	2224712	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	7.722000	0.84778	2.528000	0.85240	0.549000	0.68633	CCG	.		0.667	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424		T	2284711	C	T	2284711	3	4	114	1	0	0	0	0	1	0	0	0	4885	652	23	1	1763	1	E4F1	16	2284711	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	461764	2284711	88070042	36	10004											
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	18856756	18856756	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggattattctgtacctcttTaaatggaatccagctgctcc	9	14	8	10	0	2	0	0	0	2	0	4	2	4	2	3	2	3	3	3	2	5	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr16:18856756T>C	ENST00000446231.2	-	39	6626	c.6214A>G	c.(6214-6216)Aaa>Gaa	p.K2072E	SMG1_ENST00000389467.3_Missense_Mutation_p.K2072E			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2072					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TGTACCTCTTTAAATGGAATC	0.408																																					p.K2072E		.											.	SMG1-1160	0			c.A6214G						.						57	52	54					16																	18856756		1866	4105	5971	SO:0001583	missense	23049	exon39			CCTCTTTAAATGG	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"phosphatidylinositol 3-kinase-related kinase"	607032	"smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6214A>G	16.37:g.18856756T>C	ENSP00000402515:p.Lys2072Glu	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	62	33	NM_015092	0	0	0	0	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237482	0.79800	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.80824	-1.42;-1.42	5.79	5.79	0.91817	Protein kinase-like domain (1);Armadillo-type fold (1);	0.080055	0.53938	D	0.000055	D	0.90249	0.6951	M	0.86178	2.8	0.80722	D	1	D;P	0.56035	0.974;0.743	D;B	0.67725	0.953;0.305	D	0.91308	0.5072	10	0.59425	D	0.04	.	16.1343	0.81471	0.0:0.0:0.0:1.0	.	1932;2072	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	E	2072	ENSP00000402515:K2072E;ENSP00000374118:K2072E	ENSP00000374118:K2072E	K	-	1	0	SMG1	18764257	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.155000	0.71833	2.209000	0.71365	0.533000	0.62120	AAA	.		0.408	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18856756	T	C	18856756	3	2	114	1	0	0	0	0	1	0	0	0	14827	1763	61	3	4871	3	SMG1	16	18856756	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08	16572045	18856756	71497997	37	10005											
PDILT	204474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20376785	20376785	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctttgtcaaagacgactacGttgaagttcttccccacgag	10	12	8	11	3	3	2	1	1	2	1	4	4	4	2	2	0	1	2	2	0	3	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr16:20376785G>A	ENST00000302451.4	-	9	1442	c.1194C>T	c.(1192-1194)aaC>aaT	p.N398N		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	398	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						AGACGACTACGTTGAAGTTCT	0.448																																					p.N398N		.											.	PDILT-153	0			c.C1194T						.						175	164	168					16																	20376785		2203	4300	6503	SO:0001819	synonymous_variant	204474	exon9			GACTACGTTGAAG		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1194C>T	16.37:g.20376785G>A		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	163	39	NM_174924	0	0	0	0	0	Q8IVQ5	Silent	SNP	ENST00000302451.4	37	CCDS10584.1																																																																																			.		0.448	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		A	20376785	G	A	20376785	2	1	114	1	0	0	0	0	0	0	0	1	11700	1136	40	1		1	PDILT	16	20376785	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	1520029	20376785	69977968	38	10006											
RNASEH2A	10535	ucsc.edu	37	chr19	12917561	12917561	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctgtgcccgcggtgtgccGcaaggagccttgcgtcctgg	3	8	16	14	4	0	0	0	0	0	0	1	1	1	1	5	3	4	1	5	3	1	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:12917561G>A	ENST00000221486.4	+	1	168	c.74G>A	c.(73-75)cGc>cAc	p.R25H		NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A	25					DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						GCGGTGTGCCGCAAGGAGCCT	0.706																																					p.R25H													.	RNASEH2A-524	0			c.G74A						.						17	14	15					19																	12917561		2190	4286	6476	SO:0001583	missense	10535	exon1			TGTGCCGCAAGGA	Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"ribonuclease H2, large subunit", "Aicardi-Goutieres syndrome 4"			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.74G>A	19.37:g.12917561G>A	ENSP00000221486:p.Arg25His	Somatic	12	0		WXS	Illumina HiSeq		13	4	NM_006397	0	0	33	33	0	B2RCY1|Q96F11	Missense_Mutation	SNP	ENST00000221486.4	37	CCDS12282.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425088	0.83667	.	.	ENSG00000104889	ENST00000221486	D	0.83250	-1.7	4.97	1.52	0.23074	.	0.337880	0.30142	N	0.010304	T	0.76449	0.3989	L	0.53249	1.67	0.43381	D	0.995487	D	0.54397	0.966	B	0.42522	0.39	T	0.72316	-0.4330	10	0.59425	D	0.04	-3.1733	7.5491	0.27786	0.0807:0.0:0.6165:0.3028	.	25	O75792	RNH2A_HUMAN	H	25	ENSP00000221486:R25H	ENSP00000221486:R25H	R	+	2	0	RNASEH2A	12778561	0.118000	0.22208	0.974000	0.42286	0.665000	0.39181	0.302000	0.19192	0.105000	0.17753	0.462000	0.41574	CGC	.		0.706	RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1	NM_006397		A	12917561	G	A	12917561	3	1	114	1	0	0	0	0	1	0	0	0	13444	1087	38	1	76	1	RNASEH2A	19	12917561	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08		12917561	46211422	39	10007											
SYT5	6861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55685920	55685920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcacctcgaagctgaaagCttcgttgtaataggggttca	10	10	13	8	2	1	1	1	1	0	0	3	2	1	1	1	3	2	6	1	3	4	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:55685920C>T	ENST00000354308.3	-	8	1294	c.925G>A	c.(925-927)Gct>Act	p.A309T	SYT5_ENST00000590851.1_Missense_Mutation_p.A305T|SYT5_ENST00000537500.1_Missense_Mutation_p.A309T|SYT5_ENST00000592935.1_5'Flank|CTD-2587H24.5_ENST00000591665.1_RNA	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	309	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		AAGCTGAAAGCTTCGTTGTAA	0.527																																					p.A309T		.											.	SYT5-90	0			c.G925A						.						190	182	185					19																	55685920		2203	4300	6503	SO:0001583	missense	6861	exon8			TGAAAGCTTCGTT	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"Synaptotagmins"	11513	protein-coding gene	gene with protein product	"synaptotagmin 5"	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.925G>A	19.37:g.55685920C>T	ENSP00000346265:p.Ala309Thr	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	248	62	NM_003180	0	0	2	5	3	B3KWJ8|B7Z300|Q86X72	Missense_Mutation	SNP	ENST00000354308.3	37	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.144796	0.57044	.	.	ENSG00000129990	ENST00000537500;ENST00000354308;ENST00000543844	T;T	0.67345	-0.26;-0.26	3.42	1.23	0.21249	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.175642	0.49305	D	0.000147	T	0.38401	0.1039	N	0.03071	-0.42	0.38441	D	0.946694	B;B;B	0.27594	0.081;0.102;0.182	B;B;B	0.32465	0.146;0.026;0.092	T	0.23048	-1.0199	10	0.66056	D	0.02	.	5.0538	0.14522	0.4913:0.4025:0.0:0.1062	.	305;308;309	B7Z300;Q4FD32;O00445	.;.;SYT5_HUMAN	T	309;309;305	ENSP00000442896:A309T;ENSP00000346265:A309T	ENSP00000346265:A309T	A	-	1	0	SYT5	60377732	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.882000	0.28186	0.442000	0.26555	0.561000	0.74099	GCT	.		0.527	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		T	55685920	C	T	55685920	3	4	114	1	0	0	0	0	1	0	0	0	15509	797	28	2	243	2	SYT5	19	55685920	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	42768359	55685920	3443063	40	10008											
ZNF549	256051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58049607	58049607	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatcaccatagaatccacaCgggagaaaggccttatgagt	14	8	10	9	1	1	4	1	2	0	2	2	5	2	4	3	2	0	0	3	2	4	2	rs531934209		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:58049607C>G	ENST00000376233.3	+	4	1416	c.1235C>G	c.(1234-1236)aCg>aGg	p.T412R	ZNF549_ENST00000240719.3_Missense_Mutation_p.T399R|ZNF549_ENST00000594943.1_Intron|ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGAATCCACACGGGAGAAAGG	0.433																																					p.T412R		.											.	ZNF549-91	0			c.C1235G						.						58	59	59					19																	58049607		2203	4300	6503	SO:0001583	missense	256051	exon4			TCCACACGGGAGA	AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.1235C>G	19.37:g.58049607C>G	ENSP00000365407:p.Thr412Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	49	8	NM_001199295	0	0	0	0	0	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	37	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153855	0.57259	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.25749	1.78;1.78	2.35	-0.274	0.12910	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37489	0.1005	L	0.46885	1.475	0.31073	N	0.712839	D;D	0.89917	1.0;1.0	D;D	0.87578	0.987;0.998	T	0.39683	-0.9602	9	0.72032	D	0.01	.	6.4994	0.22160	0.0:0.6894:0.1838:0.1268	.	412;399	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	R	399;412	ENSP00000240719:T399R;ENSP00000365407:T412R	ENSP00000240719:T399R	T	+	2	0	ZNF549	62741419	0.892000	0.30473	0.923000	0.36655	0.989000	0.77384	2.036000	0.41165	0.319000	0.23209	0.585000	0.79938	ACG	.		0.433	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		G	58049607	C	G	58049607	3	3	114	1	0	0	0	0	1	0	0	0	18013	536	19	4	1206	4	ZNF549	19	58049607	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	2363687	58049607	1079376	41	10009											
ZIK1	284307	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58101980	58101980	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	catactggagaaaggccttgGgagtgcaatgaatgtggaaa	14	8	14	5	0	0	2	0	1	0	1	0	5	0	4	1	4	2	1	1	4	5	2	rs577749417		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:58101980G>C	ENST00000597850.1	+	4	1016	c.801G>C	c.(799-801)tgG>tgC	p.W267C	ZIK1_ENST00000599456.1_Missense_Mutation_p.W212C|ZIK1_ENST00000536878.2_Missense_Mutation_p.W254C|ZIK1_ENST00000307468.4_3'UTR	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAAGGCCTTGGGAGTGCAATG	0.473																																					p.W267C		.											.	ZIK1-91	0			c.G801C						.						58	59	58					19																	58101980		2203	4300	6503	SO:0001583	missense	284307	exon4			GCCTTGGGAGTGC	AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"Zinc fingers, C2H2-type", "-"	33104	protein-coding gene	gene with protein product			"zinc finger protein interacting with K protein 1 homolog (mouse)"				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.801G>C	19.37:g.58101980G>C	ENSP00000472867:p.Trp267Cys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	63	11	NM_001010879	0	0	0	0	0	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	37	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497409	0.44455	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.17691	2.26	3.37	-2.36	0.06663	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09992	0.0245	N	0.01438	-0.865	0.09310	N	0.999996	D;D	0.69078	0.997;0.993	P;P	0.60173	0.821;0.87	T	0.15178	-1.0446	9	0.87932	D	0	.	2.8351	0.05512	0.1183:0.0948:0.3259:0.4609	.	254;267	F5H435;Q3SY52	.;ZIK1_HUMAN	C	254;248;267	ENSP00000438487:W254C	ENSP00000303820:W267C	W	+	3	0	ZIK1	62793792	0.000000	0.05858	0.000000	0.03702	0.547000	0.35210	-1.932000	0.01554	-0.690000	0.05142	-0.182000	0.12963	TGG	.		0.473	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879		C	58101980	G	C	58101980	3	2	114	1	0	0	0	0	1	0	0	0	17715	1241	43	4	815	4	ZIK1	19	58101980	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	52373	58101980	1027003	42	10010											
USP25	29761	broad.mit.edu	37	chr21	17138432	17138432	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcctggcaatgatagataCatcagtgtgggaagccaagc	12	9	11	9	0	1	2	1	1	0	1	2	3	2	3	2	2	3	1	2	2	5	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr21:17138432C>G	ENST00000285679.6	+	3	609	c.240C>G	c.(238-240)taC>taG	p.Y80*	USP25_ENST00000351097.5_Nonsense_Mutation_p.Y80*|USP25_ENST00000400183.2_Nonsense_Mutation_p.Y80*|USP25_ENST00000285681.2_Nonsense_Mutation_p.Y80*	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	80	SUMO interaction domain (SIM).				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		ATGATAGATACATCAGTGTGG	0.368																																					p.Y80X													.	USP25-663	0			c.C240G						.						108	98	101					21																	17138432		2203	4300	6503	SO:0001587	stop_gained	29761	exon3			TAGATACATCAGT	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"Ubiquitin-specific peptidases"	12624	protein-coding gene	gene with protein product		604736	"ubiquitin specific protease 25"			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.240C>G	21.37:g.17138432C>G	ENSP00000285679:p.Tyr80*	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_013396	0	0	55	56	1	C0LSZ0|Q6DHZ9|Q9H9W1	Nonsense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	c	36	5.933887	0.97122	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	.	.	.	5.42	0.564	0.17302	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7186	0.40289	0.0:0.6591:0.0:0.3409	.	.	.	.	X	80	.	ENSP00000285679:Y80X	Y	+	3	2	USP25	16060303	0.926000	0.31397	0.996000	0.52242	0.828000	0.46876	0.110000	0.15437	0.035000	0.15519	-0.993000	0.02533	TAC	.		0.368	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17138432	C	G	17138432	4	3	114	1	0	0	0	0	0	1	0	0	17089	489	17	4	250	4	USP25	21	17138432	Nonsense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		17138432	30991463	43	10011											
RBBP7	5931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	16864059	16864059	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagtgtgtcctccatgaatAaactgttacaagaacaaaaa	17	9	7	8	0	0	2	0	1	0	1	2	2	2	2	2	0	3	2	2	0	8	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:16864059A>G	ENST00000380087.2	-	11	1461	c.1101T>C	c.(1099-1101)ttT>ttC	p.F367F	RBBP7_ENST00000380084.4_Silent_p.F411F|RBBP7_ENST00000404022.1_Silent_p.F358F			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	367					cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)			biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					CTCCATGAATAAACTGTTACA	0.363																																					p.F411F		.											.	RBBP7-227	0			c.T1233C						.						59	54	56					X																	16864059		2203	4300	6503	SO:0001819	synonymous_variant	5931	exon11			ATGAATAAACTGT	U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"WD repeat domain containing"	9890	protein-coding gene	gene with protein product	"G1/S transition control protein-binding protein RbAp46", "retinoblastoma-binding protein 7", "retinoblastoma-binding protein RbAp46", "histone acetyltransferase type B subunit 2", "retinoblastoma-binding protein p46"	300825	"retinoblastoma-binding protein 7"			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.1101T>C	X.37:g.16864059A>G		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_001198719	0	0	0	0	0	Q5JP00	Silent	SNP	ENST00000380087.2	37	CCDS14179.1																																																																																			.		0.363	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		G	16864059	A	G	16864059	2	3	114	1	0	0	0	0	0	0	0	1	13136	359	13	3		3	RBBP7	23	16864059	Silent	SNP	A	TCGA-G7-6793-01A-11D-1961-08		16864059	138406501	44	10012											
ITIH5L	347365	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	54777529	54777529	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtactgggatgcctgtagcGgtgtcggaggactaggaact	8	9	17	7	2	0	0	0	0	0	0	1	4	0	4	1	6	4	2	1	6	4	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:54777529G>A	ENST00000218436.6	-	12	3666	c.3637C>T	c.(3637-3639)Cgc>Tgc	p.R1213C		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1213					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										TGCCTGTAGCGGTGTCGGAGG	0.632																																					p.R1213C													.	.	0			c.C3637T						.						40	32	35					X																	54777529		2202	4299	6501	SO:0001583	missense	347365	exon12			TGTAGCGGTGTCG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"inter-alpha (globulin) inhibitor H5-like"	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3637C>T	X.37:g.54777529G>A	ENSP00000218436:p.Arg1213Cys	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	34	12	NM_198510	0	0	0	0	0	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	G	8.570	0.879748	0.17467	.	.	ENSG00000102313	ENST00000218436	T	0.13778	2.56	3.58	0.739	0.18324	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	1.511080	0.04820	U	0.436715	T	0.14874	0.0359	L	0.48642	1.525	0.28420	N	0.917793	B	0.15141	0.012	B	0.08055	0.003	T	0.35919	-0.9769	10	0.87932	D	0	.	7.9091	0.29780	0.2917:0.0:0.7083:0.0	.	1213	Q6UXX5	ITH5L_HUMAN	C	1213	ENSP00000218436:R1213C	ENSP00000218436:R1213C	R	-	1	0	ITIH5L	54794254	0.236000	0.23804	0.001000	0.08648	0.494000	0.33585	0.980000	0.29513	-0.321000	0.08627	0.287000	0.19450	CGC	.		0.632	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		A	54777529	G	A	54777529	3	1	114	1	0	0	0	0	1	0	0	0	7929	1116	39	1	312	1	ITIH5L	23	54777529	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	37913470	54777529	100493031	45	10013											
ALAS2	212	broad.mit.edu	37	chrX	55051151	55051151	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggaacttgactccaacCtgtcttgaaagccttcacat	11	11	8	11	0	2	2	1	2	1	0	3	3	3	3	3	2	3	0	3	2	3	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:55051151C>A	ENST00000330807.5	-	3	441	c.304G>T	c.(304-306)Gat>Tat	p.D102Y	ALAS2_ENST00000396198.3_Splice_Site_p.G126*|ALAS2_ENST00000335854.4_Splice_Site_p.G102*	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	102					cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	TGACTCCAACCTGTCTTGAAA	0.493																																					p.G126X													.	ALAS2-131	0			c.G376T						.						224	136	166					X																	55051151		2203	4300	6503	SO:0001630	splice_region_variant	212	exon4			TCCAACCTGTCTT		CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"sideroblastic/hypochromic anemia"	301300	"aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.304+1G>T	X.37:g.55051151C>A		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	154	7	NM_001037968	0	0	0	0	0	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Nonsense_Mutation	SNP	ENST00000330807.5	37	CCDS14366.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	33|33|33	5.289644|5.289644|5.289644	0.95546|0.95546|0.95546	.|.|.	.|.|.	ENSG00000158578|ENSG00000158578|ENSG00000158578	ENST00000330807|ENST00000396198;ENST00000335854|ENST00000455688	D|.|.	0.96856|.|.	-4.15|.|.	4.75|4.75|4.75	4.75|4.75|4.75	0.60458|0.60458|0.60458	.|.|.	0.743369|.|.	0.12618|.|.	N|.|.	0.453284|.|.	T|.|T	0.55114|.|0.55114	0.1900|.|0.1900	L|L|L	0.29908|0.29908|0.29908	0.895|0.895|0.895	0.80722|0.80722|0.80722	A|A|A	1|1|1	P|.|.	0.39311|.|.	0.667|.|.	B|.|.	0.35859|.|.	0.212|.|.	T|.|T	0.60732|.|0.60732	-0.7205|.|-0.7205	8|.|4	.|.|.	.|.|.	.|.|.	-4.8311|-4.8311|-4.8311	15.9952|15.9952|15.9952	0.80234|0.80234|0.80234	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	102|.|.	P22557|.|.	HEM0_HUMAN|.|.	Y|X|H	102|126;102|53	ENSP00000332369:D102Y|.|.	.|.|.	D|G|Q	-|-|-	1|1|3	0|0|2	ALAS2|ALAS2|ALAS2	55067876|55067876|55067876	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.662000|0.662000|0.662000	0.39071|0.39071|0.39071	5.652000|5.652000|5.652000	0.67959|0.67959|0.67959	2.110000|2.110000|2.110000	0.64415|0.64415|0.64415	0.600000|0.600000|0.600000	0.82982|0.82982|0.82982	GAT|GGA|CAG	.		0.493	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032	Missense_Mutation	A	55051151	C	A	55051151	5	1	114	1	0	0	0	0	0	0	1	0	485	695	24	4	1495	4	ALAS2	23	55051151	Splice_Site	SNP	C	TCGA-G7-6793-01A-11D-1961-08	273622	55051151	100219409	46	10014											
MED12	9968	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70349198	70349198	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaatccgctcctcctgcGaccgccacctgctggctgcc	5	8	10	18	3	0	0	0	0	0	0	3	2	3	1	7	2	3	3	7	2	2	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:70349198G>T	ENST00000374080.3	+	26	3642	c.3610G>T	c.(3610-3612)Gac>Tac	p.D1204Y	MED12_ENST00000374102.1_Missense_Mutation_p.D1204Y|MED12_ENST00000333646.6_Missense_Mutation_p.D1204Y			Q93074	MED12_HUMAN	mediator complex subunit 12	1204					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					CTCCTCCTGCGACCGCCACCT	0.572			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome				OREG0019857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D1204Y		.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12-272	0			c.G3610T						.						51	54	53					X																	70349198		2101	4209	6310	SO:0001583	missense	9968	exon26			TCCTGCGACCGCC	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)", "mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)", "FG syndrome 1"	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.3610G>T	X.37:g.70349198G>T	ENSP00000363193:p.Asp1204Tyr	Somatic	103	1	1121	WXS	Illumina HiSeq	Phase_I	57	13	NM_005120	0	0	4	21	17	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	21.5	4.165566	0.78339	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.61085	0.2319	M	0.72353	2.195	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.65335	-0.6193	10	0.87932	D	0	-21.5589	17.7452	0.88419	0.0:0.0:1.0:0.0	.	1204;1051;1204;1204	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	Y	1204;1204;1204;1204;1172	ENSP00000333125:D1204Y;ENSP00000363215:D1204Y;ENSP00000363193:D1204Y;ENSP00000414203:D1172Y	ENSP00000333125:D1204Y	D	+	1	0	MED12	70265923	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.894000	0.92506	2.465000	0.83290	0.529000	0.55759	GAC	.		0.572	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		T	70349198	G	T	70349198	3	4	114	1	0	0	0	0	1	0	0	0	9453	1058	37	4	3712	4	MED12	23	70349198	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	15298047	70349198	84921362	47	10015											
ARHGEF6	9459	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	135825892	135825892	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatcctcattagtctgcttAaagttgaatcttgcttttac	9	18	5	9	0	4	1	2	1	2	0	5	1	5	1	1	0	3	3	1	0	5	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:135825892A>T	ENST00000250617.6	-	5	1718	c.513T>A	c.(511-513)ttT>ttA	p.F171L	ARHGEF6_ENST00000370620.1_Missense_Mutation_p.F17L|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.F17L|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.F17L	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	171	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TAGTCTGCTTAAAGTTGAATC	0.413																																					p.F171L		.											.	ARHGEF6-227	0			c.T513A						.						193	158	170					X																	135825892		2203	4300	6503	SO:0001583	missense	9459	exon5			CTGCTTAAAGTTG	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.513T>A	X.37:g.135825892A>T	ENSP00000250617:p.Phe171Leu	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	171	50	NM_004840	0	0	7	7	0	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.525856	0.85600	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.08	2.47	0.30058	Src homology-3 domain (3);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.58763	-0.7579	10	0.72032	D	0.01	.	8.7263	0.34471	0.7085:0.0:0.2915:0.0	.	17;171	B7Z3C7;Q15052	.;ARHG6_HUMAN	L	171;17;17;17;17	ENSP00000250617:F171L;ENSP00000359654:F17L;ENSP00000359656:F17L;ENSP00000439483:F17L	ENSP00000250617:F171L	F	-	3	2	ARHGEF6	135653558	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.119000	0.50422	0.071000	0.16664	0.486000	0.48141	TTT	.		0.413	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		T	135825892	A	T	135825892	3	4	114	1	0	0	0	0	1	0	0	0	910	359	13	5	1889	5	ARHGEF6	23	135825892	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08	65476694	135825892	19444668	48	10016											
CC2D1B	200014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52819228	52819228	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaaccagccagttctcaGtgaccatctgcacatcctgg	10	8	8	15	0	2	2	1	1	2	1	4	2	3	2	5	1	3	2	5	1	1	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:52819228G>C	ENST00000371586.2	-	24	2678	c.2540C>G	c.(2539-2541)aCt>aGt	p.T847S	RP11-155O18.6_ENST00000606527.1_RNA|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Missense_Mutation_p.T841S	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	847						nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CCAGTTCTCAGTGACCATCTG	0.592																																					p.T847S		.											.	CC2D1B-92	0			c.C2540G						.						48	46	47					1																	52819228		2203	4300	6503	SO:0001583	missense	200014	exon24			TTCTCAGTGACCA	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.2540C>G	1.37:g.52819228G>C	ENSP00000360642:p.Thr847Ser	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	46	22	NM_032449	0	0	29	58	29	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.43|16.43	3.121445|3.121445	0.56613|0.56613	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000450942|ENST00000371586;ENST00000284376	.|T;T	.|0.21543	.|2.0;2.0	4.97|4.97	4.06|4.06	0.47325|0.47325	.|.	.|0.215167	.|0.44483	.|D	.|0.000459	T|T	0.27524|0.27524	0.0676|0.0676	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|P;P	.|0.43477	.|0.808;0.757	.|P;B	.|0.46026	.|0.501;0.327	T|T	0.03051|0.03051	-1.1078|-1.1078	5|10	.|0.48119	.|T	.|0.1	-6.0069|-6.0069	13.5782|13.5782	0.61888|0.61888	0.0745:0.0:0.9255:0.0|0.0745:0.0:0.9255:0.0	.|.	.|841;847	.|Q5T0F9-2;Q5T0F9	.|.;C2D1B_HUMAN	V|S	761|847;841	.|ENSP00000360642:T847S;ENSP00000284376:T841S	.|ENSP00000284376:T841S	L|T	-|-	1|2	2|0	CC2D1B|CC2D1B	52591816|52591816	1.000000|1.000000	0.71417|0.71417	0.830000|0.830000	0.32933|0.32933	0.821000|0.821000	0.46438|0.46438	6.187000|6.187000	0.72039|0.72039	1.323000|1.323000	0.45263|0.45263	0.561000|0.561000	0.74099|0.74099	CTG|ACT	.		0.592	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		C	52819228	G	C	52819228	3	2	115	1	0	0	0	0	1	0	0	0	2733	1029	36	4	40	4	CC2D1B	1	52819228	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08		52819228	196431393	1	10017											
DPYD	1806	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	98058809	98058809	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttatattaacaaagccttTtctgaagacgatgaacacac	15	12	5	9	1	2	3	0	2	2	1	2	4	2	3	1	0	3	0	1	0	6	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:98058809T>A	ENST00000370192.3	-	10	1193	c.1093A>T	c.(1093-1095)Aaa>Taa	p.K365*		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	365					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	ACAAAGCCTTTTCTGAAGACG	0.448																																					p.K365X		.											.	DPYD-278	0			c.A1093T						.						119	116	117					1																	98058809		2203	4300	6503	SO:0001587	stop_gained	1806	exon10			AGCCTTTTCTGAA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1093A>T	1.37:g.98058809T>A	ENSP00000359211:p.Lys365*	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	140	53	NM_000110	0	0	0	0	0	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Nonsense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	T	39	7.840231	0.98519	.	.	ENSG00000188641	ENST00000370192	.	.	.	6.17	6.17	0.99709	.	0.048348	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3061	15.3933	0.74767	0.0:0.0:0.0:1.0	.	.	.	.	X	365	.	ENSP00000359211:K365X	K	-	1	0	DPYD	97831397	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.664000	0.68045	2.371000	0.80710	0.533000	0.62120	AAA	.		0.448	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	98058809	T	A	98058809	4	1	115	1	0	0	0	0	0	1	0	0	4756	1850	64	5	2040	5	DPYD	1	98058809	Nonsense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	45239581	98058809	151191812	2	10018											
YY1AP1	55249	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	155630357	155630357	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgtattgggtgaggaatccgGagcaccattttgctcggagg	8	11	15	7	2	0	1	0	1	0	0	2	4	1	4	2	5	2	3	2	5	2	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:155630357G>A	ENST00000295566.4	-	11	1505	c.1482C>T	c.(1480-1482)ctC>ctT	p.L494L	YY1AP1_ENST00000404643.1_Silent_p.L428L|YY1AP1_ENST00000368339.5_Silent_p.L586L|YY1AP1_ENST00000535662.1_Silent_p.L294L|YY1AP1_ENST00000407221.1_Silent_p.L417L|YY1AP1_ENST00000368330.2_Silent_p.L448L|YY1AP1_ENST00000368340.5_Silent_p.L566L|YY1AP1_ENST00000347088.5_Silent_p.L448L|YY1AP1_ENST00000361831.5_Silent_p.L437L|YY1AP1_ENST00000311573.5_Silent_p.L417L|YY1AP1_ENST00000355499.4_Silent_p.L448L|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000359205.5_Silent_p.L437L|MSTO1_ENST00000538143.1_Intron	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	494					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					GAGGAATCCGGAGCACCATTT	0.552																																					p.L586L		.											.	YY1AP1-93	0			c.C1758T						.						55	65	62					1																	155630357		2203	4300	6503	SO:0001819	synonymous_variant	55249	exon10			AATCCGGAGCACC	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1482C>T	1.37:g.155630357G>A		Somatic	135	1		WXS	Illumina HiSeq	Phase_I	148	40	NM_001198903	0	0	17	30	13	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Silent	SNP	ENST00000295566.4	37	CCDS1115.1																																																																																			.		0.552	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		A	155630357	G	A	155630357	2	1	115	1	0	0	0	0	0	0	0	1	17541	1161	41	2		2	YY1AP1	1	155630357	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	57571548	155630357	93620264	3	10019											
RHBG	57127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156347130	156347130	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatggtcttcgtgggctttGgcttcctcatggtcttcctg	2	16	11	12	1	3	0	1	0	2	0	6	0	5	0	3	4	0	2	3	4	0	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:156347130G>C	ENST00000368249.1	+	2	264	c.226G>C	c.(226-228)Ggc>Cgc	p.G76R	RHBG_ENST00000255013.3_Missense_Mutation_p.G7R|RHBG_ENST00000400992.2_Missense_Mutation_p.G7R|RHBG_ENST00000368246.2_Missense_Mutation_p.G76R|RHBG_ENST00000451864.2_Missense_Mutation_p.G7R|RHBG_ENST00000537040.1_Intron	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	76			G -> D (in dbSNP:rs2245623). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CGTGGGCTTTGGCTTCCTCAT	0.637																																					p.G76R		.											.	RHBG-92	0			c.G226C						.						142	144	143					1																	156347130		2203	4300	6503	SO:0001583	missense	57127	exon2			GGCTTTGGCTTCC	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"Solute carriers"	14572	protein-coding gene	gene with protein product		607079	"Rhesus blood group, B glycoprotein"			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.226G>C	1.37:g.156347130G>C	ENSP00000357232:p.Gly76Arg	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	147	47	NM_020407	0	0	0	0	0	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		.	.	.	.	.	.	.	.	.	.	G	29.7	5.031766	0.93575	.	.	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.86	4.86	0.63082	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	H	0.94582	3.555	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93736	0.7046	10	0.87932	D	0	-6.6399	16.7188	0.85405	0.0:0.0:1.0:0.0	.	76;7;113	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	R	76;76;7;7;7	ENSP00000357232:G76R;ENSP00000357229:G76R;ENSP00000383777:G7R;ENSP00000255013:G7R;ENSP00000389836:G7R	ENSP00000255013:G7R	G	+	1	0	RHBG	154613754	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.365000	0.73090	2.512000	0.84698	0.561000	0.74099	GGC	.		0.637	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395		C	156347130	G	C	156347130	3	2	115	1	0	0	0	0	1	0	0	0	13356	1348	47	4	232	4	RHBG	1	156347130	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	716773	156347130	92903491	4	10020											
TDRD5	163589	broad.mit.edu	37	chr1	179621298	179621298	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgaagaccgaaagataaGtccacagtcaaaagagagtg	19	6	10	6	1	1	4	1	1	0	3	2	6	2	4	2	0	0	0	2	0	6	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:179621298G>T	ENST00000367614.1	+	13	2485	c.2126G>T	c.(2125-2127)aGt>aTt	p.S709I	TDRD5_ENST00000294848.8_Missense_Mutation_p.S709I|TDRD5_ENST00000444136.1_Missense_Mutation_p.S709I	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	709					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CGAAAGATAAGTCCACAGTCA	0.368																																					p.S709I													.	TDRD5-94	0			c.G2126T						.						95	91	92					1																	179621298		2203	4300	6503	SO:0001583	missense	163589	exon13			AGATAAGTCCACA	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"Tudor domain containing"	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.2126G>T	1.37:g.179621298G>T	ENSP00000356586:p.Ser709Ile	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	76	4	NM_173533	0	0	0	0	0	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.385165	0.25031	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.32753	2.74;2.74;2.85;1.44	4.55	1.53	0.23141	.	0.629622	0.14481	N	0.316979	T	0.18087	0.0434	L	0.40543	1.245	0.23889	N	0.99655	P;B	0.39424	0.673;0.391	B;B	0.33521	0.165;0.079	T	0.10520	-1.0626	10	0.23891	T	0.37	-31.3686	4.7749	0.13175	0.1919:0.0:0.6278:0.1802	.	709;709	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	I	709;709;709;165	ENSP00000356586:S709I;ENSP00000294848:S709I;ENSP00000406052:S709I;ENSP00000410744:S165I	ENSP00000294848:S709I	S	+	2	0	TDRD5	177887921	0.487000	0.25988	0.332000	0.25469	0.942000	0.58702	0.029000	0.13666	0.569000	0.29329	0.557000	0.71058	AGT	.		0.368	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179621298	G	T	179621298	3	4	115	1	0	0	0	0	1	0	0	0	15765	1029	36	4	2172	4	TDRD5	1	179621298	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	23274168	179621298	69629323	5	10021											
ADAM17	6868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	9645412	9645412	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcgagttcccacaaactTtattgctgcgttcttgaaaa	10	13	6	12	2	1	1	0	1	1	0	3	2	2	1	2	0	3	3	2	0	4	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:9645412T>G	ENST00000310823.3	-	12	1609	c.1427A>C	c.(1426-1428)aAa>aCa	p.K476T	RP11-400L8.2_ENST00000472619.1_RNA|RP11-400L8.2_ENST00000480764.1_RNA	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	476	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CCCACAAACTTTATTGCTGCG	0.438																																					p.K476T		.											.	ADAM17-659	0			c.A1427C						.						178	155	163					2																	9645412		2203	4300	6503	SO:0001583	missense	6868	exon12			CAAACTTTATTGC	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.1427A>C	2.37:g.9645412T>G	ENSP00000309968:p.Lys476Thr	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	154	72	NM_003183	0	0	0	1	1	O60226	Missense_Mutation	SNP	ENST00000310823.3	37	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056207	0.36277	.	.	ENSG00000151694	ENST00000310823	T	0.21191	2.02	5.66	3.33	0.38152	Blood coagulation inhibitor, Disintegrin (1);	0.226724	0.51477	D	0.000087	T	0.18718	0.0449	L	0.46670	1.46	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.03325	-1.1048	10	0.48119	T	0.1	.	9.5244	0.39156	0.0:0.1409:0.0:0.8591	.	476;476	B2RNB2;P78536	.;ADA17_HUMAN	T	476	ENSP00000309968:K476T	ENSP00000309968:K476T	K	-	2	0	ADAM17	9562863	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	3.947000	0.56652	0.444000	0.26612	0.460000	0.39030	AAA	.		0.438	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			G	9645412	T	G	9645412	3	3	115	1	0	0	0	0	1	0	0	0	238	1841	64	5	1079	5	ADAM17	2	9645412	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08		9645412	233553961	6	10022											
MYCN	4613	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	16082320	16082321	+	Frame_Shift_Ins	INS	-	-	G																															ggccccgactcgacccccccINSgggggaggacatctggaaga																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:16082320_16082321insG	ENST00000281043.3	+	2	431_432	c.134_135insG	c.(133-138)ccggggfs	p.PG45fs	MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000453400.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	45					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TCGACCCCCCCGGGGGAGGACA	0.644			A		neuroblastoma																																p.P45fs		.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN-1271	0			c.134_135insG	GRCh37	CI084293	MYCN	I		.																																			SO:0001589	frameshift_variant	4613	exon2			.	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.139dupG	2.37:g.16082325_16082325dupG	ENSP00000281043:p.Pro45fs	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	49	23	NM_005378	0	0	0	0	0	Q53XS5|Q6LDT9	Frame_Shift_Ins	INS	ENST00000281043.3	37	CCDS1687.1																																																																																			.		0.644	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		G	16082321	-	G	16082320	7	5	115	1	0	1	1	0	0	0	0	0	10046	652	23	0	136	0	MYCN	2	16082320	Frame_Shift_Ins	INS	-	TCGA-G7-6795-01A-11D-1961-08	6436908	16082320	227117053	7	10023											
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	21260848	21260848	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accagaaacaacacttgcttGgcttcttctgtctctggggg	8	12	10	11	0	3	1	0	0	3	1	4	1	3	1	1	3	3	2	1	3	2	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:21260848G>A	ENST00000233242.1	-	5	646	c.519C>T	c.(517-519)gcC>gcT	p.A173A	APOB_ENST00000399256.4_Silent_p.A173A	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	173	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACACTTGCTTGGCTTCTTCTG	0.458																																					p.A173A		.											.	APOB-175	0			c.C519T						.						128	129	129					2																	21260848		2203	4300	6503	SO:0001819	synonymous_variant	338	exon5			TTGCTTGGCTTCT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.519C>T	2.37:g.21260848G>A		Somatic	140	0		WXS	Illumina HiSeq	Phase_I	173	94	NM_000384	0	0	0	0	0	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			.		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21260848	G	A	21260848	2	1	115	1	0	0	0	0	0	0	0	1	785	1335	47	2		2	APOB	2	21260848	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	5178528	21260848	221938525	8	10024											
ATAD2B	54454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	24051776	24051776	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgacaattttggattccagtCcctggtatggatctgtaaga	10	14	10	7	0	1	2	0	1	1	1	3	4	3	4	2	3	0	2	2	3	3	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:24051776C>A	ENST00000238789.5	-	15	2105	c.1762G>T	c.(1762-1764)Gac>Tac	p.D588Y	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	588						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGATTCCAGTCCCTGGTATGG	0.333																																					p.D588Y		.											.	ATAD2B-68	0			c.G1762T						.						121	114	116					2																	24051776		1842	4090	5932	SO:0001583	missense	54454	exon15			TCCAGTCCCTGGT	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1762G>T	2.37:g.24051776C>A	ENSP00000238789:p.Asp588Tyr	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	138	59	NM_001242338	0	0	0	0	0	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	37	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.944509	0.53079	.	.	ENSG00000119778	ENST00000238789;ENST00000458510	D;D	0.94931	-3.56;-1.77	4.7	4.7	0.59300	.	.	.	.	.	D	0.95023	0.8389	L	0.60957	1.885	0.49299	D	0.999776	D	0.54047	0.964	P	0.53912	0.737	D	0.95210	0.8324	9	0.72032	D	0.01	.	14.2998	0.66339	0.1494:0.8506:0.0:0.0	.	588	Q9ULI0	ATD2B_HUMAN	Y	588;26	ENSP00000238789:D588Y;ENSP00000392764:D26Y	ENSP00000238789:D588Y	D	-	1	0	ATAD2B	23905280	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.884000	0.56175	2.551000	0.86045	0.650000	0.86243	GAC	.		0.333	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24051776	C	A	24051776	3	1	115	1	0	0	0	0	1	0	0	0	1073	855	30	4	2670	4	ATAD2B	2	24051776	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	2790928	24051776	219147597	9	10025											
ITSN2	50618	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	24509153	24509155	+	In_Frame_Del	DEL	TTC	TTC	-																															ttttcaagagcatctaactgTtctttaagtctttggcataa																								rs201163358		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:24509153_24509155delTTC	ENST00000355123.4	-	16	2232_2234	c.1789_1791delGAA	c.(1789-1791)gaadel	p.E597del	ITSN2_ENST00000361999.3_In_Frame_Del_p.E597del|ITSN2_ENST00000406921.3_In_Frame_Del_p.E597del	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	597					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATCTAACTGTTCTTTAAGTCTT	0.286																																					p.597_597del		.											.	ITSN2-539	0			c.1789_1791del						.																																			SO:0001651	inframe_deletion	50618	exon16			.	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1789_1791delGAA	2.37:g.24509153_24509155delTTC	ENSP00000347244:p.Glu597del	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	120	24	NM_147152	0	0	0	0	0	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	In_Frame_Del	DEL	ENST00000355123.4	37	CCDS1710.2																																																																																			.		0.286	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		-	24509155	TTC	-	24509153	7	5	115	1	0	1	0	1	0	0	0	0	7948	1722	60	0	3453	0	ITSN2	2	24509153	In_Frame_Del	DEL	TTC	TCGA-G7-6795-01A-11D-1961-08	457377	24509153	218690220	10	10026											
AGBL5	60509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27291539	27291539	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctctggagacaaaccagAggctgtcatggtaatcggga	11	8	13	9	1	2	2	1	0	1	2	4	4	3	3	2	4	1	2	2	4	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:27291539A>G	ENST00000360131.4	+	13	2441	c.2282A>G	c.(2281-2283)gAg>gGg	p.E761G		NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	761					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACAAACCAGAGGCTGTCATG	0.512																																					p.E761G		.											.	AGBL5-154	0			c.A2282G						.						84	85	85					2																	27291539		2203	4300	6503	SO:0001583	missense	60509	exon13			AACCAGAGGCTGT	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.2282A>G	2.37:g.27291539A>G	ENSP00000353249:p.Glu761Gly	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	180	52	NM_021831	0	0	12	20	8	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	37	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459849	0.26248	.	.	ENSG00000084693	ENST00000360131	T	0.17370	2.28	5.61	4.46	0.54185	.	0.426245	0.25285	N	0.031768	T	0.10723	0.0262	N	0.19112	0.55	0.32634	N	0.521593	B	0.13145	0.007	B	0.09377	0.004	T	0.03641	-1.1017	10	0.87932	D	0	-0.026	7.4869	0.27439	0.9054:0.0:0.0946:0.0	.	761	Q8NDL9	CBPC5_HUMAN	G	761	ENSP00000353249:E761G	ENSP00000353249:E761G	E	+	2	0	AGBL5	27145043	1.000000	0.71417	1.000000	0.80357	0.237000	0.25408	2.781000	0.47750	2.123000	0.65237	0.459000	0.35465	GAG	.		0.512	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		G	27291539	A	G	27291539	3	3	115	1	0	0	0	0	1	0	0	0	378	304	11	3	2393	3	AGBL5	2	27291539	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	2782386	27291539	215907834	11	10027											
PAX8	7849	bcgsc.ca	37	chr2	113984805	113984805	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggatgtggggtgggtatccGggcagcgtgggccccaccat	5	7	19	10	2	0	0	0	0	0	0	1	1	1	1	4	6	1	2	4	6	1	1	rs189229644	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:113984805G>A	ENST00000429538.3	-	10	1310	c.1116C>T	c.(1114-1116)ccC>ccT	p.P372P	PAX8_ENST00000348715.5_Missense_Mutation_p.P346L|AC016683.6_ENST00000456685.1_RNA|PAX8_ENST00000263335.7_Missense_Mutation_p.P269L|PAX8_ENST00000263334.5_Missense_Mutation_p.P346L|PAX8_ENST00000397647.3_Intron	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	372					anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						GTGGGTATCCGGGCAGCGTGG	0.612			T	PPARG	follicular thyroid		Thyroid dysgenesis						G|||	8	0.00159744	0	0.0043	5008	,	,		18400	0.004		0	False		,,,				2504	0.001				p.P346L	Ovarian(188;7 2067 9084 29802 29892)			Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8-684	0			c.C1037T						.						26	31	29					2																	113984805		2021	4167	6188	SO:0001819	synonymous_variant	7849	exon10			GTATCCGGGCAGC	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"Paired boxes", "Homeoboxes / PRD class"	8622	protein-coding gene	gene with protein product		167415	"paired box gene 8"			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.1116C>T	2.37:g.113984805G>A		Somatic	15	0		WXS	Illumina HiSeq	Phase_1	32	9	NM_013952	0	0	69	122	53	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	37	CCDS46398.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	4.284|4.284	0.051899|0.051899	0.08291|0.08291	.|.	.|.	ENSG00000125618|ENSG00000125618	ENST00000263335;ENST00000348715;ENST00000263334|ENST00000465084;ENST00000468980	D;D;D|.	0.97976|.	-4.64;-4.55;-4.55|.	5.3|5.3	-2.97|-2.97	0.05530|0.05530	.|.	0.056682|.	0.64402|.	D|.	0.000001|.	T|T	0.25606|0.25606	0.0623|0.0623	.|.	.|.	.|.	0.31672|0.31672	N|N	0.644221|0.644221	B;B|.	0.09022|.	0.002;0.0|.	B;B|.	0.06405|.	0.002;0.0|.	T|T	0.41963|0.41963	-0.9479|-0.9479	9|4	0.25106|.	T|.	0.35|.	.|.	5.1393|5.1393	0.14950|0.14950	0.5248:0.0:0.2619:0.2132|0.5248:0.0:0.2619:0.2132	.|.	346;269|.	Q06710-3;Q06710-4|.	.;.|.	L|W	269;346;346|27;95	ENSP00000263335:P269L;ENSP00000314750:P346L;ENSP00000263334:P346L|.	ENSP00000263334:P346L|.	P|R	-|-	2|1	0|2	PAX8|PAX8	113701276|113701276	0.027000|0.027000	0.19231|0.19231	0.982000|0.982000	0.44146|0.44146	0.999000|0.999000	0.98932|0.98932	-1.187000|-1.187000	0.03067|0.03067	-0.463000|-0.463000	0.06973|0.06973	0.609000|0.609000	0.83330|0.83330	CCG|CGG	G|0.999;A|0.001		0.612	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			A	113984805	G	A	113984805	2	1	115	1	0	0	0	0	0	0	0	1	11511	1116	39	1		1	PAX8	2	113984805	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	86693266	113984805	129214568	12	10028											
PKP4	8502	bcgsc.ca	37	chr2	159490676	159490676	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacacaacagctacctacgcGgagccctacaggcctataca	14	5	7	15	2	0	0	0	0	0	0	0	1	0	1	3	2	8	1	3	2	7	5	rs200605632		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:159490676G>T	ENST00000389759.3	+	9	1549	c.1437G>T	c.(1435-1437)gcG>gcT	p.A479A	PKP4_ENST00000389757.3_Silent_p.A479A	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	479					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						CTACCTACGCGGAGCCCTACA	0.458										HNSCC(62;0.18)																											p.A479A													.	PKP4-97	0			c.G1437T						.						124	126	125					2																	159490676		2203	4300	6503	SO:0001819	synonymous_variant	8502	exon9			CTACGCGGAGCCC	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"Armadillo repeat containing"	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.1437G>T	2.37:g.159490676G>T		Somatic	223	1		WXS	Illumina HiSeq	Phase_1	280	12	NM_001005476	0	0	4	4	0	Q86W91	Silent	SNP	ENST00000389759.3	37	CCDS33305.1																																																																																			G|0.999;A|0.000		0.458	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			T	159490676	G	T	159490676	2	4	115	1	0	0	0	0	0	0	0	1	12013	1103	39	4		4	PKP4	2	159490676	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	45505871	159490676	83708697	13	10029											
UBR3	130507	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	170843280	170843281	+	Frame_Shift_Ins	INS	-	-	T																															agatcgacctactggattagINSttgtactgttacaagcatcc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:170843280_170843281insT	ENST00000272793.5	+	25	3810_3811	c.3760_3761insT	c.(3760-3762)gttfs	p.V1254fs	UBR3_ENST00000418381.1_Frame_Shift_Ins_p.V1254fs|UBR3_ENST00000392631.1_Frame_Shift_Ins_p.V75fs			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1254					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TACTGGATTAGTTGTACTGTTA	0.396																																					p.V1254fs		.											.	UBR3-68	0			c.3760_3761insT						.																																			SO:0001589	frameshift_variant	130507	exon25			.	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.3762dupT	2.37:g.170843282_170843282dupT	ENSP00000272793:p.Val1254fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	136	32	NM_172070	0	0	0	0	0	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Frame_Shift_Ins	INS	ENST00000272793.5	37																																																																																				.		0.396	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		T	170843281	-	T	170843280	7	5	115	1	0	1	1	0	0	0	0	0	16936	1029	36	0	3858	0	UBR3	2	170843280	Frame_Shift_Ins	INS	-	TCGA-G7-6795-01A-11D-1961-08	11352604	170843280	72356093	14	10030											
NDUFS1	4719	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	207006722	207006724	+	In_Frame_Del	DEL	AGA	AGA	-																															aacgtgggtttgtaccaaccAgaagaacaacatctgcctct																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:207006722_207006724delAGA	ENST00000233190.6	-	12	1469_1471	c.1203_1205delTCT	c.(1201-1206)cttctg>ctg	p.401_402LL>L	NDUFS1_ENST00000423725.1_In_Frame_Del_p.344_345LL>L|NDUFS1_ENST00000455934.2_In_Frame_Del_p.415_416LL>L|NDUFS1_ENST00000457011.1_In_Frame_Del_p.285_286LL>L|NDUFS1_ENST00000440274.1_In_Frame_Del_p.365_366LL>L|NDUFS1_ENST00000432169.1_In_Frame_Del_p.290_291LL>L|NDUFS1_ENST00000449699.1_In_Frame_Del_p.401_402LL>L	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	401					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGTACCAACCAGAAGAACAACAT	0.325																																					p.415_416del		.											.	NDUFS1-91	0			c.1245_1247del						.																																			SO:0001651	inframe_deletion	4719	exon12			.		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7707	protein-coding gene	gene with protein product	"complex I 75kDa subunit", "NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"	157655	"NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1203_1205delTCT	2.37:g.207006725_207006727delAGA	ENSP00000233190:p.Leu402del	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	138	21	NM_001199984	0	0	0	0	0	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	In_Frame_Del	DEL	ENST00000233190.6	37	CCDS2366.1																																																																																			.		0.325	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		-	207006724	AGA	-	207006722	7	5	115	1	0	1	0	1	0	0	0	0	10317	188	7	0	1010	0	NDUFS1	2	207006722	In_Frame_Del	DEL	AGA	TCGA-G7-6795-01A-11D-1961-08	36163442	207006722	36192651	15	10031											
TNS1	7145	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	218713795	218713795	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccatctagtggcccctgcGtgtgtcccaccacctctgca	5	10	8	18	1	2	0	0	0	2	0	4	0	4	0	6	1	2	1	6	1	1	1	rs200862766		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:218713795G>A	ENST00000171887.4	-	17	1522	c.1070C>T	c.(1069-1071)aCg>aTg	p.T357M	TNS1_ENST00000419504.1_Missense_Mutation_p.T357M|TNS1_ENST00000430930.1_Missense_Mutation_p.T357M|TNS1_ENST00000480665.1_5'UTR	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	357					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGGCCCCTGCGTGTGTCCCAC	0.577																																					p.T357M		.											.	TNS1-156	0			c.C1070T						.	G	MET/THR	0,4406		0,0,2203	89	89	89		1070	4.3	1	2		89	2,8598	2.2+/-6.3	0,2,4298	no	missense	TNS1	NM_022648.4	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	357/1736	218713795	2,13004	2203	4300	6503	SO:0001583	missense	7145	exon17			CCCTGCGTGTGTC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1070C>T	2.37:g.218713795G>A	ENSP00000171887:p.Thr357Met	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	198	38	NM_022648	0	0	1	1	0	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464168	0.63513	0.0	2.33E-4	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554	D;D;D;D;D	0.96334	-3.5;-3.49;-3.51;-3.83;-3.98	5.22	4.34	0.51931	.	0.767219	0.12422	N	0.470300	D	0.95255	0.8461	M	0.83603	2.65	0.80722	D	1	P;B;B;P;P	0.43519	0.809;0.423;0.345;0.704;0.704	B;B;B;B;B	0.32090	0.14;0.053;0.05;0.09;0.09	D	0.94356	0.7583	10	0.66056	D	0.02	.	14.202	0.65710	0.0727:0.0:0.9273:0.0	.	357;411;357;357;357	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	M	357;357;357;482;425	ENSP00000171887:T357M;ENSP00000408724:T357M;ENSP00000406016:T357M;ENSP00000405460:T482M;ENSP00000400383:T425M	ENSP00000171887:T357M	T	-	2	0	TNS1	218422040	1.000000	0.71417	0.991000	0.47740	0.969000	0.65631	7.726000	0.84824	1.404000	0.46819	0.655000	0.94253	ACG	G|0.999;A|0.001		0.577	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218713795	G	A	218713795	3	1	115	1	0	0	0	0	1	0	0	0	16375	1145	40	1	4205	1	TNS1	2	218713795	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	11707073	218713795	24485578	16	10032											
UGT1A5	54579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234622277	234622277	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgcaaagggtcaagaacAtgctctaccctctggccctg	9	9	9	14	0	3	1	1	0	2	1	4	1	4	1	3	2	4	2	3	2	4	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:234622277A>G	ENST00000373414.3	+	1	640	c.640A>G	c.(640-642)Atg>Gtg	p.M214V	UGT1A1_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.M214V|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000373445.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	214						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		GGTCAAGAACATGCTCTACCC	0.483																																					p.M214V		.											.	UGT1A5-3	0			c.A640G						.						209	197	201					2																	234622277		2203	4300	6503	SO:0001583	missense	54579	exon1			AAGAACATGCTCT	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.640A>G	2.37:g.234622277A>G	ENSP00000362513:p.Met214Val	Somatic	352	1		WXS	Illumina HiSeq	Phase_I	368	195	NM_019078	0	0	0	0	0	B8K294	Missense_Mutation	SNP	ENST00000373414.3	37	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	A	9.408	1.079672	0.20309	.	.	ENSG00000240224	ENST00000373414	T	0.61040	0.14	4.77	-0.524	0.11920	.	0.585446	0.20090	N	0.099480	T	0.34221	0.0890	N	0.25201	0.72	0.26978	N	0.965428	B;B	0.13594	0.008;0.008	B;B	0.23150	0.044;0.044	T	0.12604	-1.0541	10	0.45353	T	0.12	.	1.3681	0.02205	0.4274:0.2431:0.2117:0.1179	.	214;214	Q5DSZ9;P35504	.;UD15_HUMAN	V	214	ENSP00000362513:M214V	ENSP00000362513:M214V	M	+	1	0	UGT1A5	234287016	0.000000	0.05858	0.992000	0.48379	0.655000	0.38815	-0.882000	0.04174	-0.055000	0.13244	0.459000	0.35465	ATG	.		0.483	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		G	234622277	A	G	234622277	3	3	115	1	0	0	0	0	1	0	0	0	16981	217	8	3	642	3	UGT1A5	2	234622277	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	15908482	234622277	8577096	17	10033											
LRRFIP1	9208	broad.mit.edu	37	chr2	238672176	238672176	+	Frame_Shift_Del	DEL	A	A	-																															agatttaagtgaaattaaggAagaagagcaggtaaagtcta																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:238672176delA	ENST00000392000.4	+	11	1937	c.1820delA	c.(1819-1821)gaafs	p.E609fs	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Frame_Shift_Del_p.E553fs|LRRFIP1_ENST00000244815.5_Frame_Shift_Del_p.E585fs	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	609			E -> K (in dbSNP:rs3739041).		innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		GAAATTAAGGAAGAAGAGCAG	0.373																																					p.E607fs													.	LRRFIP1-153	0			c.1820delA						.						49	51	51					2																	238672176		2203	4300	6503	SO:0001589	frameshift_variant	9208	exon11			TTAAGGAAGAAGA	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.1820delA	2.37:g.238672176delA	ENSP00000375857:p.Glu609fs	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	43	7	NM_001137552	0	0	0	0	0	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Frame_Shift_Del	DEL	ENST00000392000.4	37	CCDS46552.1																																																																																			.		0.373	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		-	238672176	A	-	238672176	7	5	115	1	0	1	0	1	0	0	0	0	9052	246	9	0	2538	0	LRRFIP1	2	238672176	Frame_Shift_Del	DEL	A	TCGA-G7-6795-01A-11D-1961-08	4049899	238672176	4527197	18	10034											
SYNPR	132204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	63466530	63466530	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttgcaatctttgcatttgCaacatgcggtggctattctg	7	17	9	8	1	2	0	0	0	2	0	2	0	2	0	0	2	5	4	0	2	3	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:63466530C>T	ENST00000295894.5	+	2	416	c.47C>T	c.(46-48)gCa>gTa	p.A16V	SYNPR_ENST00000465156.1_Missense_Mutation_p.A16V|SYNPR_ENST00000478300.1_Missense_Mutation_p.A36V|SYNPR_ENST00000478744.1_3'UTR|SYNPR_ENST00000479198.1_Missense_Mutation_p.A16V|SYNPR-AS1_ENST00000488201.1_RNA|SYNPR_ENST00000460711.1_Missense_Mutation_p.A27V	NM_144642.4	NP_653243.1	Q8TBG9	SYNPR_HUMAN	synaptoporin	16	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					cell junction (GO:0030054)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)	transporter activity (GO:0005215)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		TTTGCATTTGCAACATGCGGT	0.433																																					p.A36V	NSCLC(29;1052 1116 20025 32519)	.											.	.	0			c.C107T						.						160	161	160					3																	63466530		1945	4146	6091	SO:0001583	missense	132204	exon3			CATTTGCAACATG	AF411860	CCDS46859.1, CCDS46860.1	3p14.3	2011-07-28			ENSG00000163630	ENSG00000163630			16507	protein-coding gene	gene with protein product						8034131, 12974474	Standard	NM_144642		Approved	MGC26651, SPO	uc003dlp.3	Q8TBG9	OTTHUMG00000158699	ENST00000295894.5:c.47C>T	3.37:g.63466530C>T	ENSP00000295894:p.Ala16Val	Somatic	280	1		WXS	Illumina HiSeq	Phase_I	239	94	NM_001130003	0	0	0	0	0	B2R675|G5E9W4	Missense_Mutation	SNP	ENST00000295894.5	37	CCDS46860.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408930	0.83340	.	.	ENSG00000163630	ENST00000478300;ENST00000295894;ENST00000479198;ENST00000460711;ENST00000465156	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	5.38	5.38	0.77491	Marvel (1);MARVEL-like domain (1);	0.105267	0.64402	D	0.000004	D	0.87597	0.6217	M	0.90870	3.155	0.80722	D	1	D;D;D	0.60160	0.979;0.979;0.987	P;P;P	0.58013	0.831;0.831;0.74	D	0.90454	0.4441	10	0.87932	D	0	-3.3962	18.124	0.89580	0.0:1.0:0.0:0.0	.	27;16;36	B3KVD8;Q8TBG9;G5E9W4	.;SYNPR_HUMAN;.	V	36;16;16;27;16	ENSP00000418994:A36V;ENSP00000295894:A16V;ENSP00000418929:A16V;ENSP00000418701:A27V;ENSP00000418123:A16V	ENSP00000295894:A16V	A	+	2	0	SYNPR	63441570	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.523000	0.85059	0.650000	0.86243	GCA	.		0.433	SYNPR-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351787.1			T	63466530	C	T	63466530	3	4	115	1	0	0	0	0	1	0	0	0	15491	710	25	2	145	2	SYNPR	3	63466530	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		63466530	134555900	19	10035											
ROBO2	6092	broad.mit.edu;bcgsc.ca	37	chr3	77542437	77542437	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaattaaccaggtggtacTggaggaagaagctgtagaat	14	8	13	6	0	0	2	0	0	0	2	0	4	0	4	2	4	3	3	2	4	7	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:77542437T>G	ENST00000461745.1	+	5	1610	c.710T>G	c.(709-711)cTg>cGg	p.L237R	ROBO2_ENST00000332191.8_Missense_Mutation_p.L237R|ROBO2_ENST00000487694.3_Missense_Mutation_p.L253R	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	237	Ig-like C2-type 3.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CAGGTGGTACTGGAGGAAGAA	0.403																																					p.L237R													.	ROBO2-328	0			c.T710G						.						135	122	126					3																	77542437		1872	4114	5986	SO:0001583	missense	6092	exon5			TGGTACTGGAGGA	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10250	protein-coding gene	gene with protein product		602431	"roundabout (axon guidance receptor, Drosophila) homolog 2"			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.710T>G	3.37:g.77542437T>G	ENSP00000417164:p.Leu237Arg	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	96	6	NM_002942	0	0	0	0	0	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.615646	0.87359	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191	T;T;T	0.65916	-0.18;-0.18;-0.18	5.88	5.88	0.94601	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.34411	U	0.003992	T	0.68220	0.2977	N	0.25060	0.705	0.42707	D	0.993639	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.998	T	0.70107	-0.4963	9	0.37606	T	0.19	.	16.2851	0.82714	0.0:0.0:0.0:1.0	.	253;237;237	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	R	253;253;253;237;237	ENSP00000417335:L253R;ENSP00000417164:L237R;ENSP00000327536:L237R	ENSP00000327536:L237R	L	+	2	0	ROBO2	77625127	1.000000	0.71417	0.990000	0.47175	0.960000	0.62799	7.982000	0.88131	2.252000	0.74401	0.402000	0.26972	CTG	.		0.403	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		G	77542437	T	G	77542437	3	3	115	1	0	0	0	0	1	0	0	0	13546	1580	55	5	730	5	ROBO2	3	77542437	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	14075907	77542437	120479993	20	10036											
TOPBP1	11073	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	133329894	133329895	+	Frame_Shift_Ins	INS	-	-	CT																															ctggattttttttctccatcINStcattgctgcaagtgctagt																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:133329894_133329895insCT	ENST00000260810.5	-	25	4257_4258	c.4126_4127insAG	c.(4126-4128)agafs	p.R1376fs		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1376					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TTTTCTCCATCTCATTGCTGCA	0.356								Other conserved DNA damage response genes																													p.R1376fs	Ovarian(21;193 658 4424 15423 17362)	.											.	TOPBP1-540	0			c.4127_4128insAG						.																																			SO:0001589	frameshift_variant	11073	exon25			.	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4126_4127insAG	3.37:g.133329894_133329895insCT	ENSP00000260810:p.Arg1376fs	Somatic	230	0		WXS	Illumina HiSeq	Phase_I	249	88	NM_007027	0	0	0	0	0	B7Z7W8|Q7LGC1|Q9UEB9	Frame_Shift_Ins	INS	ENST00000260810.5	37	CCDS46919.1																																																																																			.		0.356	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		CT	133329895	-	CT	133329894	7	5	115	1	0	1	1	0	0	0	0	0	16402	913	32	0	457	0	TOPBP1	3	133329894	Frame_Shift_Ins	INS	-	TCGA-G7-6795-01A-11D-1961-08	55787457	133329894	64692536	21	10037											
PLOD2	5352	broad.mit.edu	37	chr3	145806381	145806381	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaaatacttactttgttatGaataaaaagtttaagtgctt	15	17	5	4	0	1	1	1	1	0	0	1	1	1	1	0	0	3	3	0	0	9	8			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:145806381G>A	ENST00000360060.3	-	9	1174	c.997C>T	c.(997-999)Cat>Tat	p.H333Y	PLOD2_ENST00000494950.1_Missense_Mutation_p.H278Y|PLOD2_ENST00000461497.1_5'Flank|RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Missense_Mutation_p.H333Y	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	333					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	ACTTTGTTATGAATAAAAAGT	0.294																																					p.H333Y													.	PLOD2-92	0			c.C997T						.						55	55	55					3																	145806381		2201	4296	6497	SO:0001583	missense	5352	exon9			TGTTATGAATAAA	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"lysyl hydroxlase 2"	601865	"procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.997C>T	3.37:g.145806381G>A	ENSP00000353170:p.His333Tyr	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	30	8	NM_182943	0	0	0	0	0	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763173	0.69763	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950	D;D;D	0.84516	-1.86;-1.86;-1.86	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.89986	0.6874	L	0.48362	1.52	0.80722	D	1	D;D;B	0.76494	0.998;0.999;0.078	D;D;B	0.91635	0.99;0.999;0.1	D	0.87909	0.2696	10	0.30854	T	0.27	-8.4591	19.1315	0.93410	0.0:0.0:1.0:0.0	.	278;333;333	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	Y	333;333;278	ENSP00000282903:H333Y;ENSP00000353170:H333Y;ENSP00000420094:H278Y	ENSP00000282903:H333Y	H	-	1	0	PLOD2	147289071	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.441000	0.97557	2.523000	0.85059	0.650000	0.86243	CAT	.		0.294	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		A	145806381	G	A	145806381	3	1	115	1	0	0	0	0	1	0	0	0	12128	1290	45	2	1327	2	PLOD2	3	145806381	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	12476487	145806381	52216049	22	10038											
P2RY1	5028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	152553966	152553966	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcagaggttcatctttcAtgtgaacctctatggcagca	10	12	9	10	0	4	2	2	1	2	1	4	2	4	2	1	2	3	4	1	2	2	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:152553966A>G	ENST00000305097.3	+	1	1231	c.395A>G	c.(394-396)cAt>cGt	p.H132R		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	132					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TTCATCTTTCATGTGAACCTC	0.507																																					p.H132R		.											.	P2RY1-500	0			c.A395G						.						79	76	77					3																	152553966		2203	4300	6503	SO:0001583	missense	5028	exon1			TCTTTCATGTGAA	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.395A>G	3.37:g.152553966A>G	ENSP00000304767:p.His132Arg	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	100	34	NM_002563	0	0	0	0	0		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.019475	0.75275	.	.	ENSG00000169860	ENST00000305097	T	0.71698	-0.59	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.82944	0.5147	M	0.79475	2.455	0.80722	D	1	D	0.58268	0.982	D	0.62955	0.909	D	0.85045	0.0925	10	0.66056	D	0.02	.	15.2728	0.73717	1.0:0.0:0.0:0.0	.	132	P47900	P2RY1_HUMAN	R	132	ENSP00000304767:H132R	ENSP00000304767:H132R	H	+	2	0	P2RY1	154036656	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	9.210000	0.95106	2.186000	0.69663	0.533000	0.62120	CAT	.		0.507	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		G	152553966	A	G	152553966	3	3	115	1	0	0	0	0	1	0	0	0	11372	217	8	3	397	3	P2RY1	3	152553966	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	6747585	152553966	45468464	23	10039											
SH3TC1	54436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	8230107	8230107	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgcgggtggctcgggacCtgggccagcaaaggaaccag	8	4	16	13	2	0	0	0	0	0	0	1	2	0	2	4	5	3	2	4	5	2	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:8230107C>T	ENST00000245105.3	+	12	2753	c.2686C>T	c.(2686-2688)Ctg>Ttg	p.L896L	SH3TC1_ENST00000539824.1_Silent_p.L820L	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	896										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGCTCGGGACCTGGGCCAGCA	0.692																																					p.L896L	NSCLC(145;2298 2623 35616 37297)	.											.	SH3TC1-154	0			c.C2686T						.						37	43	41					4																	8230107		2203	4299	6502	SO:0001819	synonymous_variant	54436	exon12			CGGGACCTGGGCC	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"Tetratricopeptide (TTC) repeat domain containing"	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.2686C>T	4.37:g.8230107C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	116	57	NM_018986	0	0	4	11	7	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			.		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		T	8230107	C	T	8230107	2	4	115	1	0	0	0	0	0	0	0	1	14293	680	24	2		2	SH3TC1	4	8230107	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		8230107	182924169	24	10040											
LAP3	51056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	17586652	17586653	+	Missense_Mutation	DNP	AC	AC	GA																															gcttctgggcagaacttggcAcgccaattgatggagacgcc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:17586652_17586653AC>GA	ENST00000226299.4	+	6	871_872	c.597_598AC>GA	c.(595-600)gcACgc>gcGAgc	p.R200S	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.R169S	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	200					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						AGAACTTGGCACGCCAATTGAT	0.475																																					p.R200S		.											.	LAP3	0			c.C598A						.																																			SO:0001583	missense	51056	exon6			TTGGCACGCCAAT	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"peptidase S"	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	Exception_encountered	4.37:g.17586652_17586653delinsGA	ENSP00000226299:p.Arg200Ser	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	91	24		0	0	0	0	0	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	DNP	ENST00000226299.4	37	CCDS3422.1																																																																																			.		0.475	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			GA	17586653	AC	GA	17586652	3	3	115	1	0	0	0	0	1	0	0	0	8644	146	6	3	619	3	LAP3	4	17586652	Missense_Mutation	DNP	AC	TCGA-G7-6795-01A-11D-1961-08	9356545	17586652	173567624	25	10041											
DDX60L	91351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	169317122	169317122	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgacgtactgagtctttattCctggtaatttcagtgtgtag	8	17	10	6	1	2	2	1	2	1	0	3	2	3	2	1	1	1	3	1	1	4	7			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:169317122C>T	ENST00000511577.1	-	27	3892	c.3645G>A	c.(3643-3645)agG>agA	p.R1215R	DDX60L_ENST00000505890.1_Silent_p.R1216R|DDX60L_ENST00000260184.7_Silent_p.R1215R			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1215	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AGTCTTTATTCCTGGTAATTT	0.343																																					p.R1215R		.											.	DDX60L-69	0			c.G3645A						.						103	93	96					4																	169317122		1813	4069	5882	SO:0001819	synonymous_variant	91351	exon27			TTTATTCCTGGTA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3645G>A	4.37:g.169317122C>T		Somatic	93	1		WXS	Illumina HiSeq	Phase_I	139	72	NM_001012967	0	0	0	0	0	Q96ND6	Silent	SNP	ENST00000511577.1	37		.	.	.	.	.	.	.	.	.	.	C	0.998	-0.691845	0.03303	.	.	ENSG00000181381	ENST00000514580	.	.	.	1.42	0.293	0.15742	.	.	.	.	.	T	0.24967	0.0606	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.25950	-1.0117	4	.	.	.	.	5.6565	0.17644	0.0:0.4727:0.5273:0.0	.	.	.	.	K	103	.	.	E	-	1	0	DDX60L	169553697	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.305000	0.19254	0.010000	0.14839	0.313000	0.20887	GAA	.		0.343	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169317122	C	T	169317122	2	4	115	1	0	0	0	0	0	0	0	1	4385	854	30	2		2	DDX60L	4	169317122	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	151730470	169317122	21837154	26	10042											
WDR70	55100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	37381726	37381726	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaaagctcgcacatttgaCttggaagcaatgtttgaaca	16	10	8	7	1	0	2	0	2	0	0	1	3	0	3	0	1	3	4	0	1	6	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:37381726C>T	ENST00000265107.4	+	3	270	c.114C>T	c.(112-114)gaC>gaT	p.D38D	WDR70_ENST00000504564.1_Silent_p.D38D	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	38							enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCACATTTGACTTGGAAGCAA	0.378																																					p.D38D		.											.	WDR70-187	0			c.C114T						.						119	127	124					5																	37381726		2203	4300	6503	SO:0001819	synonymous_variant	55100	exon3			ATTTGACTTGGAA	BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068		"WD repeat domain containing"	25495	protein-coding gene	gene with protein product						12477932	Standard	NM_018034		Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000265107.4:c.114C>T	5.37:g.37381726C>T		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	220	71	NM_018034	0	0	1	1	0	Q9H053	Silent	SNP	ENST00000265107.4	37	CCDS34147.1																																																																																			.		0.378	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		T	37381726	C	T	37381726	2	4	115	1	0	0	0	0	0	0	0	1	17354	564	20	2		2	WDR70	5	37381726	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		37381726	143533534	27	10043											
NDFIP1	80762	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141524143	141524144	+	Missense_Mutation	DNP	CC	CC	AG																															ttttttaaattaggctttctCctgtttctcagaggatttat																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:141524143_141524144CC>AG	ENST00000253814.4	+	7	1040_1041	c.570_571CC>AG	c.(568-573)ctCCtg>ctAGtg	p.L191V		NM_030571.3	NP_085048.1	Q9BT67	NFIP1_HUMAN	Nedd4 family interacting protein 1	191					cellular iron ion homeostasis (GO:0006879)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of protein transport (GO:0051224)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transporter activity (GO:0032410)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein ubiquitination (GO:0031398)|regulation of isotype switching to IgG isotypes (GO:0048302)|regulation of lymphocyte differentiation (GO:0045619)|regulation of myeloid leukocyte differentiation (GO:0002761)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cell cortex (GO:0005938)|endosome (GO:0005768)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)			large_intestine(3)|lung(1)|ovary(1)	5		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAGGCTTTCTCCTGTTTCTCAG	0.356																																					p.L191V		.											.	NDFIP1	0			c.C571G						.																																			SO:0001583	missense	80762	exon7			TTTCTCCTGTTTC	BC004317	CCDS4273.1	5q31.3	2008-02-05			ENSG00000131507	ENSG00000131507			17592	protein-coding gene	gene with protein product		612050				11042109, 11748237	Standard	NM_030571		Approved	N4WBP5, MGC10924	uc003lmi.4	Q9BT67	OTTHUMG00000129659	Exception_encountered	5.37:g.141524143_141524144delinsAG	ENSP00000253814:p.Leu191Val	Somatic	194	1		WXS	Illumina HiSeq	Phase_I	207	51		0	0	0	0	0	B2RDB8|D3DQF0|Q658T8|Q8N2E3|Q8N2F9	Missense_Mutation	DNP	ENST00000253814.4	37	CCDS4273.1																																																																																			.		0.356	NDFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251859.2	NM_030571		AG	141524144	CC	AG	141524143	3	1	115	1	0	0	0	0	1	0	0	0	10271	842	30	4	596	4	NDFIP1	5	141524143	Missense_Mutation	DNP	CC	TCGA-G7-6795-01A-11D-1961-08	104142417	141524143	39391117	28	10044											
TUBE1	51175	hgsc.bcm.edu	37	chr6	112408628	112408628	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttaccctgtacgaccaccgActgggtcatggtggtgcgcc	6	9	12	14	3	1	0	1	0	0	0	1	2	1	0	4	3	3	1	4	3	2	2	rs199513778		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr6:112408628A>C	ENST00000368662.5	-	1	88	c.10T>G	c.(10-12)Tcg>Gcg	p.S4A	FAM229B_ENST00000368656.2_5'Flank|FAM229B_ENST00000604268.1_5'Flank|TUBE1_ENST00000604814.1_5'Flank	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	4					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Vinblastine(DB00570)	ACGACCACCGACTGGGTCATG	0.632													A|||	1	0.000199681	0	0	5008	,	,		16095	0		0.001	False		,,,				2504	0				p.S4A		.											.	TUBE1-91	0			c.T10G						.						13	13	13					6																	112408628		2036	3985	6021	SO:0001583	missense	51175	exon1			CCACCGACTGGGT	AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.10T>G	6.37:g.112408628A>C	ENSP00000357651:p.Ser4Ala	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	2	NM_016262	0	0	0	0	0	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	37	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	A	18.99	3.739608	0.69304	.	.	ENSG00000074935	ENST00000368662;ENST00000368657	T	0.66815	-0.23	4.86	4.86	0.63082	Tubulin/FtsZ, GTPase domain (2);	0.259719	0.40385	N	0.001104	T	0.73621	0.3610	M	0.73430	2.235	0.58432	D	0.999991	D	0.62365	0.991	P	0.60286	0.872	T	0.77981	-0.2383	10	0.66056	D	0.02	.	14.5546	0.68091	1.0:0.0:0.0:0.0	.	4	Q9UJT0	TBE_HUMAN	A	4	ENSP00000357651:S4A	ENSP00000357646:S4A	S	-	1	0	TUBE1	112515321	1.000000	0.71417	1.000000	0.80357	0.083000	0.17756	6.872000	0.75536	2.168000	0.68352	0.397000	0.26171	TCG	.		0.632	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		C	112408628	A	C	112408628	3	2	115	1	0	0	0	0	1	0	0	0	16796	275	10	5	1465	5	TUBE1	6	112408628	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08		112408628	58706439	29	10045											
ABCA13	154664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48506568	48506568	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcagcagtgggggcgacaaCttggacctcacccgtgtgct	8	7	14	12	2	1	0	1	0	0	0	1	2	1	1	2	3	4	3	2	3	1	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:48506568C>T	ENST00000435803.1	+	44	12855	c.12831C>T	c.(12829-12831)aaC>aaT	p.N4277N	ABCA13_ENST00000544596.1_Intron	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4277			N -> D (in dbSNP:rs4917152).		transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GGGGCGACAACTTGGACCTCA	0.498																																					p.N4277N		.											.	ABCA13-521	0			c.C12831T						.						109	118	115					7																	48506568		2069	4210	6279	SO:0001819	synonymous_variant	154664	exon44			CGACAACTTGGAC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12831C>T	7.37:g.48506568C>T		Somatic	144	2		WXS	Illumina HiSeq	Phase_I	237	82	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.		0.498	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48506568	C	T	48506568	2	4	115	1	0	0	0	0	0	0	0	1	31	564	20	2		2	ABCA13	7	48506568	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		48506568	110632095	30	10046											
ZNF680	340252	broad.mit.edu	37	chr7	63982808	63982808	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattttccatatcctctcagTatcactttttgaaaagaatc	12	16	3	10	0	2	2	2	1	1	1	6	2	4	2	2	0	0	1	2	0	5	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:63982808T>C	ENST00000309683.6	-	4	475	c.324A>G	c.(322-324)atA>atG	p.I108M	ZNF680_ENST00000476563.1_5'UTR	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	108					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(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				ATCCTCTCAGTATCACTTTTT	0.318																																					p.I108M													.	ZNF680-91	0			c.A324G						.						46	47	47					7																	63982808		2202	4288	6490	SO:0001583	missense	340252	exon4			TCTCAGTATCACT	AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"Zinc fingers, C2H2-type", "-"	26897	protein-coding gene	gene with protein product	"hypothetical protein FLJ90430"					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.324A>G	7.37:g.63982808T>C	ENSP00000309330:p.Ile108Met	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	136	5	NM_178558	0	0	1	1	0	B3KVJ4|Q6ZNF3|Q8NC79	Missense_Mutation	SNP	ENST00000309683.6	37	CCDS34644.1	.	.	.	.	.	.	.	.	.	.	t	5.664	0.307088	0.10733	.	.	ENSG00000173041	ENST00000309683	T	0.05580	3.42	0.468	0.468	0.16732	.	.	.	.	.	T	0.12008	0.0292	M	0.76574	2.34	0.09310	N	1	D	0.56968	0.978	P	0.49012	0.598	T	0.15607	-1.0431	8	0.45353	T	0.12	.	.	.	.	.	108	Q8NEM1	ZN680_HUMAN	M	108	ENSP00000309330:I108M	ENSP00000309330:I108M	I	-	3	3	ZNF680	63620243	0.001000	0.12720	0.034000	0.17996	0.031000	0.12232	-0.161000	0.10026	0.413000	0.25759	0.402000	0.26972	ATA	.		0.318	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558		C	63982808	T	C	63982808	3	2	115	1	0	0	0	0	1	0	0	0	18119	1628	57	3	1272	3	ZNF680	7	63982808	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	15476240	63982808	95155855	31	10047											
SLC13A1	6561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	122765636	122765636	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actcaaccaatttctcctgtAggtgtagttttagtcagtgt	9	16	8	8	0	3	0	2	0	1	0	4	0	3	0	2	1	1	3	2	1	5	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:122765636A>G	ENST00000194130.2	-	11	1266	c.1227T>C	c.(1225-1227)ccT>ccC	p.P409P	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	409					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	TTTCTCCTGTAGGTGTAGTTT	0.368																																					p.P409P		.											.	SLC13A1-92	0			c.T1227C						.						123	129	127					7																	122765636		2203	4300	6503	SO:0001819	synonymous_variant	6561	exon11			TCCTGTAGGTGTA		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"Solute carriers"	10916	protein-coding gene	gene with protein product		606193	"solute carrier family 13 (sodium/sulphate symporters), member 1"			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.1227T>C	7.37:g.122765636A>G		Somatic	192	0		WXS	Illumina HiSeq	Phase_I	384	147	NM_022444	0	0	0	0	0	Q9H5Z0	Silent	SNP	ENST00000194130.2	37	CCDS5786.1																																																																																			.		0.368	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		G	122765636	A	G	122765636	2	3	115	1	0	0	0	0	0	0	0	1	14423	407	15	3		3	SLC13A1	7	122765636	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	58782828	122765636	36373027	32	10048											
AKR1B15	441282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	134260255	134260255	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagatcgagaggctcttGaacaaacctggactgaaata	14	9	9	9	1	1	4	0	2	1	2	3	6	2	5	2	2	2	1	2	2	4	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:134260255G>T	ENST00000457545.2	+	7	857	c.597G>T	c.(595-597)ttG>ttT	p.L199F	AKR1B15_ENST00000423958.1_Missense_Mutation_p.L171F	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	199							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						AGAGGCTCTTGAACAAACCTG	0.463																																					p.L199F		.											.	AKR1B15-23	0			c.G597T						.						71	77	75					7																	134260255		2203	4300	6503	SO:0001583	missense	441282	exon7			GCTCTTGAACAAA		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.597G>T	7.37:g.134260255G>T	ENSP00000389289:p.Leu199Phe	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	265	97	NM_001080538	0	0	0	0	0	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484711	0.44147	.	.	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.21031	2.03;2.03	3.82	0.986	0.19784	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.42832	0.1220	M	0.80508	2.5	0.47308	D	0.999386	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.23619	-1.0183	9	0.87932	D	0	.	7.683	0.28524	0.2865:0.0:0.7135:0.0	.	171;199	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	F	199;171	ENSP00000389289:L199F;ENSP00000397009:L171F	ENSP00000397009:L171F	L	+	3	2	AKR1B15	133910795	0.998000	0.40836	0.832000	0.32986	0.573000	0.36030	0.344000	0.19962	-0.004000	0.14419	0.543000	0.68304	TTG	.		0.463	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134260255	G	T	134260255	3	4	115	1	0	0	0	0	1	0	0	0	468	1281	45	4	615	4	AKR1B15	7	134260255	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	11494619	134260255	24878408	33	10049											
MGAM	8972	broad.mit.edu	37	chr7	141794622	141794622	+	Frame_Shift_Del	DEL	T	T	-																															gctggatgcagctgggggccTtttaccccttctcaagaaac																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:141794622delT	ENST00000549489.2	+	40	4824	c.4729delT	c.(4729-4731)tttfs	p.F1577fs	MGAM_ENST00000475668.2_Frame_Shift_Del_p.F2473fs	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1577	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCTGGGGGCCTTTTACCCCTT	0.493																																					p.F1577fs													.	MGAM-70	0			c.4729delT						.						58	57	57					7																	141794622		1894	4106	6000	SO:0001589	frameshift_variant	8972	exon40			GGGGCCTTTTACC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4729delT	7.37:g.141794622delT	ENSP00000447378:p.Phe1577fs	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	134	7	NM_004668	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000549489.2	37	CCDS47727.1																																																																																			.		0.493	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			-	141794622	T	-	141794622	7	5	115	1	0	1	0	1	0	0	0	0	9566	1609	56	0	4883	0	MGAM	7	141794622	Frame_Shift_Del	DEL	T	TCGA-G7-6795-01A-11D-1961-08	7534367	141794622	17344041	34	10050											
TPD52	7163	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	80963849	80963851	+	In_Frame_Del	DEL	GAT	GAT	-																															cagcctgggataaggtttcaGatgtcttcttgtaactatat																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:80963849_80963851delGAT	ENST00000379097.3	-	4	779_781	c.417_419delATC	c.(415-420)acatct>act	p.S140del	TPD52_ENST00000379096.5_In_Frame_Del_p.S100del|TPD52_ENST00000537855.1_In_Frame_Del_p.S140del|TPD52_ENST00000520527.1_In_Frame_Del_p.S140del|TPD52_ENST00000448733.2_In_Frame_Del_p.S140del|TPD52_ENST00000523395.1_5'Flank|TPD52_ENST00000518937.1_In_Frame_Del_p.S100del|TPD52_ENST00000519303.2_5'UTR|TPD52_ENST00000517427.1_In_Frame_Del_p.S140del	NM_001025252.1	NP_001020423.1	P55327	TPD52_HUMAN	tumor protein D52	140					anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			TAAGGTTTCAGATGTCTTCTTGT	0.404																																					p.139_140del		.											.	TPD52-523	0			c.417_419del						.																																			SO:0001651	inframe_deletion	7163	exon4			.	U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554			12005	protein-coding gene	gene with protein product		604068				7796418	Standard	NM_001287144		Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000379097.3:c.417_419delATC	8.37:g.80963849_80963851delGAT	ENSP00000368391:p.Ser140del	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_001025252	0	0	0	0	0	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	In_Frame_Del	DEL	ENST00000379097.3	37	CCDS34912.1																																																																																			.		0.404	TPD52-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379539.2	NM_005079		-	80963851	GAT	-	80963849	7	5	115	1	0	1	0	1	0	0	0	0	16430	942	33	0	344	0	TPD52	8	80963849	In_Frame_Del	DEL	GAT	TCGA-G7-6795-01A-11D-1961-08		80963849	65400173	35	10051											
OXR1	55074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	107718929	107718929	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctactggtactcctggtcacTtaagatctgatactgaacat	11	13	7	10	0	2	3	1	2	1	1	3	3	3	3	1	2	4	1	1	2	5	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:107718929T>C	ENST00000442977.2	+	8	1282	c.1183T>C	c.(1183-1185)Tta>Cta	p.L395L	OXR1_ENST00000445937.1_Silent_p.L394L|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000312046.6_Silent_p.L387L|OXR1_ENST00000497705.1_Silent_p.L327L|OXR1_ENST00000531443.1_Silent_p.L394L|OXR1_ENST00000517566.2_Silent_p.L394L	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	395					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TCCTGGTCACTTAAGATCTGA	0.368																																					p.L395L		.											.	OXR1-68	0			c.T1183C						.						86	89	88					8																	107718929		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon8			GGTCACTTAAGAT	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 3"	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1183T>C	8.37:g.107718929T>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	71	19	NM_001198532	0	0	1	1	0	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	37	CCDS56548.1																																																																																			.		0.368	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		C	107718929	T	C	107718929	2	2	115	1	0	0	0	0	0	0	0	1	11360	1606	56	3		3	OXR1	8	107718929	Silent	SNP	T	TCGA-G7-6795-01A-11D-1961-08	26755080	107718929	38645093	36	10052											
COL22A1	169044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	139737673	139737673	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggcctgggacaccagggggtCctggagggccctgtagagaa	8	5	18	10	0	0	1	0	0	0	1	1	4	1	3	4	6	0	1	4	6	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:139737673C>T	ENST00000303045.6	-	24	2596	c.2150G>A	c.(2149-2151)gGa>gAa	p.G717E	COL22A1_ENST00000435777.1_Missense_Mutation_p.G717E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	717	Collagen-like 5.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ACCAGGGGGTCCTGGAGGGCC	0.582										HNSCC(7;0.00092)																											p.G717E		.											.	COL22A1-103	0			c.G2150A						.						50	57	55					8																	139737673		2203	4300	6503	SO:0001583	missense	169044	exon24			GGGGGTCCTGGAG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2150G>A	8.37:g.139737673C>T	ENSP00000303153:p.Gly717Glu	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	127	44	NM_152888	0	0	0	0	0	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043885	0.55110	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99353	-5.77;-5.14	4.8	4.8	0.61643	.	0.000000	0.49305	D	0.000157	D	0.99722	0.9892	H	0.99719	4.725	0.52099	D	0.999949	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96966	0.9705	10	0.87932	D	0	.	14.0818	0.64929	0.0:1.0:0.0:0.0	.	717;717	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	717;717;430	ENSP00000303153:G717E;ENSP00000387655:G717E	ENSP00000303153:G717E	G	-	2	0	COL22A1	139806855	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.436000	0.52856	2.567000	0.86603	0.655000	0.94253	GGA	.		0.582	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139737673	C	T	139737673	3	4	115	1	0	0	0	0	1	0	0	0	3687	855	30	2	2898	2	COL22A1	8	139737673	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	32018744	139737673	6626349	37	10053											
ZNF658	26149	broad.mit.edu	37	chr9	40772391	40772392	+	Frame_Shift_Del	DEL	CT	CT	-																															acattcataggatttctcccCtgtgtgaattctttgatgta																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr9:40772391_40772392delCT	ENST00000602553.1	-	5	3177_3178	c.2883_2884delAG	c.(2881-2886)acagggfs	p.G962fs	ZNF658_ENST00000377626.3_Frame_Shift_Del_p.G962fs|ZNF658_ENST00000441795.1_Intron			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	962					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(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GATTTCTCCCCTGTGTGAATTC	0.436																																					p.961_962del													.	ZNF658-45	0			c.2883_2884del						.			0,2758		0,0,1379						2.2	0			6	5,5899		2,1,2949	no	frameshift	ZNF658	NM_033160.5		2,1,4328	A1A1,A1R,RR		0.0847,0.0,0.0577				5,8657				SO:0001589	frameshift_variant	26149	exon5			TCTCCCCTGTGTG	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.2883_2884delAG	9.37:g.40772391_40772392delCT	ENSP00000473484:p.Gly962fs	Somatic	345	0		WXS	Illumina HiSeq	Phase_I	245	8	NM_033160	0	0	0	0	0	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Frame_Shift_Del	DEL	ENST00000602553.1	37	CCDS35023.1																																																																																			.		0.436	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		-	40772392	CT	-	40772391	7	5	115	1	0	1	0	1	0	0	0	0	18101	681	24	0	299	0	ZNF658	9	40772391	Frame_Shift_Del	DEL	CT	TCGA-G7-6795-01A-11D-1961-08		40772391	100441040	38	10054											
SEC16A	9919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139371469	139371469	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgagggagggaaggggatGctgctggggtgaccacaccg	8	5	20	8	1	0	2	0	2	0	0	0	5	0	5	2	6	2	3	2	6	1	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr9:139371469G>A	ENST00000371706.3	-	1	98	c.65C>T	c.(64-66)gCa>gTa	p.A22V	SEC16A_ENST00000431893.2_Missense_Mutation_p.A22V|SEC16A_ENST00000313050.7_Missense_Mutation_p.A200V|SEC16A_ENST00000290037.6_Missense_Mutation_p.A22V			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	22					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GGAAGGGGATGCTGCTGGGGT	0.652																																					p.A200V		.											.	.	0			c.C599T						.						47	53	51					9																	139371469		2113	4220	6333	SO:0001583	missense	9919	exon3			GGGGATGCTGCTG	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"KIAA0310"	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.65C>T	9.37:g.139371469G>A	ENSP00000360771:p.Ala22Val	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	63	30	NM_014866	0	0	0	0	0	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	G	14.35	2.509363	0.44660	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893	T;T;T;T	0.27256	1.87;1.68;1.68;1.68	5.39	5.39	0.77823	.	0.642215	0.15172	N	0.276561	T	0.33381	0.0861	L	0.54323	1.7	0.26691	N	0.97136	P;P;P	0.42296	0.666;0.775;0.775	B;B;B	0.42282	0.212;0.382;0.382	T	0.23119	-1.0197	10	0.66056	D	0.02	-7.54	18.5216	0.90954	0.0:0.0:1.0:0.0	.	200;22;22	F1T0I1;O15027-5;O15027-4	.;.;.	V	200;22;22;22	ENSP00000325827:A200V;ENSP00000360771:A22V;ENSP00000290037:A22V;ENSP00000387583:A22V	ENSP00000290037:A22V	A	-	2	0	SEC16A	138491290	0.015000	0.18098	0.007000	0.13788	0.065000	0.16274	1.962000	0.40442	2.692000	0.91855	0.655000	0.94253	GCA	.		0.652	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		A	139371469	G	A	139371469	3	1	115	1	0	0	0	0	1	0	0	0	14018	1319	46	2	6594	2	SEC16A	9	139371469	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	98599078	139371469	1841962	39	10055											
ADD3	120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	111860443	111860443	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgccagccaaggcgtgattaCcactcctcctcctcccagca	8	8	7	18	1	0	1	0	1	0	0	4	1	4	1	7	1	4	1	7	1	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr10:111860443C>G	ENST00000356080.4	+	2	399	c.32C>G	c.(31-33)aCc>aGc	p.T11S	ADD3_ENST00000360162.3_Missense_Mutation_p.T11S|ADD3_ENST00000277900.8_Missense_Mutation_p.T11S|ADD3_ENST00000497125.1_3'UTR	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	11						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GGCGTGATTACCACTCCTCCT	0.418																																					p.T11S		.											.	ADD3-157	0			c.C32G						.						84	70	74					10																	111860443		2203	4300	6503	SO:0001583	missense	120	exon2			TGATTACCACTCC	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.32C>G	10.37:g.111860443C>G	ENSP00000348381:p.Thr11Ser	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	72	28	NM_001121	0	0	0	0	0	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	37	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165457	0.78339	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.30714	1.52;1.52;1.52	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	M	0.76838	2.35	0.80722	D	1	P;B	0.51653	0.947;0.383	P;B	0.48400	0.576;0.155	T	0.32107	-0.9919	10	0.30078	T	0.28	-16.68	20.6397	0.99537	0.0:1.0:0.0:0.0	.	11;11	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	S	11	ENSP00000353286:T11S;ENSP00000348381:T11S;ENSP00000277900:T11S	ENSP00000277900:T11S	T	+	2	0	ADD3	111850433	1.000000	0.71417	0.988000	0.46212	0.954000	0.61252	7.481000	0.81124	2.880000	0.98712	0.650000	0.86243	ACC	.		0.418	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		G	111860443	C	G	111860443	3	3	115	1	0	0	0	0	1	0	0	0	306	507	18	4	34	4	ADD3	10	111860443	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		111860443	23674304	40	10056											
MRVI1	10335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	10647666	10647666	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttggcaagcactttctgcagCcgggggccaggttcttcagg	6	10	14	11	1	3	0	1	0	2	0	3	0	3	0	2	5	3	4	2	5	1	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:10647666C>G	ENST00000436272.1	-	8	1212	c.1134G>C	c.(1132-1134)cgG>cgC	p.R378R	MRVI1_ENST00000552103.1_Silent_p.R314R|MRVI1_ENST00000534266.2_Silent_p.R90R|MRVI1_ENST00000527509.2_Silent_p.R314R|MRVI1_ENST00000423302.2_Silent_p.R405R|MRVI1_ENST00000421747.1_Silent_p.R396R|MRVI1_ENST00000547195.1_Silent_p.R314R|MRVI1_ENST00000558540.1_Silent_p.R90R|MRVI1_ENST00000424001.1_Silent_p.R90R|MRVI1_ENST00000541483.1_Intron|MRVI1_ENST00000531107.1_Silent_p.R397R|MRVI1_ENST00000545852.1_Silent_p.R90R			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	378					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		CTTTCTGCAGCCGGGGGCCAG	0.647																																					p.R405R		.											.	MRVI1-25	0			c.G1215C						.						16	18	18					11																	10647666		1874	4079	5953	SO:0001819	synonymous_variant	10335	exon9			CTGCAGCCGGGGG	AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"inositol 1,4,5-triphosphate-associated cGMP kinase substrate", "IP3R-associated cGMP kinase substrate"	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.1134G>C	11.37:g.10647666C>G		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	30	11	NM_130385	0	0	0	0	0	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	37																																																																																				.		0.647	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		G	10647666	C	G	10647666	2	3	115	1	0	0	0	0	0	0	0	1	9878	726	26	4		4	MRVI1	11	10647666	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		10647666	124358850	41	10057											
HPS5	11234	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	18309441	18309441	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatatacaggacaacttaccGggtagcataaacaaccaaca	19	6	6	10	1	0	0	0	0	0	0	0	1	0	1	2	2	7	2	2	2	10	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:18309441G>A	ENST00000349215.3	-	17	2837	c.2560C>T	c.(2560-2562)Cgg>Tgg	p.R854W	HPS5_ENST00000438420.2_Splice_Site_p.R740W|HPS5_ENST00000396253.3_Splice_Site_p.R740W|HPS5_ENST00000537258.1_5'Flank|HPS5_ENST00000352460.3_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	854					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						ACAACTTACCGGGTAGCATAA	0.363									Hermansky-Pudlak syndrome																												p.R854W		.											.	HPS5-133	0			c.C2560T						.						140	122	129					11																	18309441		2199	4293	6492	SO:0001630	splice_region_variant	11234	exon17	Familial Cancer Database	HPS, HPS1-8	CTTACCGGGTAGC	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.2561+1C>T	11.37:g.18309441G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	53	24	NM_181507	0	0	0	0	0	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.415187	0.42817	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000544218	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	5.36	-0.639	0.11497	.	0.091394	0.85682	D	0.000000	D	0.90017	0.6883	M	0.66939	2.045	0.48830	D	0.999711	D	0.76494	0.999	D	0.65443	0.935	D	0.88319	0.2961	10	0.87932	D	0	.	10.3165	0.43740	0.0768:0.0:0.2154:0.7078	.	854	Q9UPZ3	HPS5_HUMAN	W	740;740;854;40	ENSP00000379552:R740W;ENSP00000399590:R740W;ENSP00000265967:R854W;ENSP00000441781:R40W	ENSP00000265967:R854W	R	-	1	2	HPS5	18266017	0.959000	0.32827	0.725000	0.30721	0.174000	0.22865	1.548000	0.36201	-0.008000	0.14320	-0.475000	0.04921	CGG	.		0.363	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	Missense_Mutation	A	18309441	G	A	18309441	5	1	115	1	0	0	0	0	0	0	1	0	7363	1130	39	1	857	1	HPS5	11	18309441	Splice_Site	SNP	G	TCGA-G7-6795-01A-11D-1961-08	7661775	18309441	116697075	42	10058											
NPAT	4863	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	108032024	108032024	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccggggcacaggtaaatcActactatcagcaagcctact	12	8	9	12	1	2	0	2	0	0	0	3	0	3	0	2	3	4	3	2	3	6	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:108032024A>G	ENST00000278612.8	-	17	3894	c.3789T>C	c.(3787-3789)agT>agC	p.S1263S		NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	1263					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		CAGGTAAATCACTACTATCAG	0.443																																					p.S1263S		.											.	NPAT-117	0			c.T3789C						.						107	105	106					11																	108032024		1852	4092	5944	SO:0001819	synonymous_variant	4863	exon17			TAAATCACTACTA	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.3789T>C	11.37:g.108032024A>G		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	132	54	NM_002519	0	0	2	4	2	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Silent	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.813585	0.00600	.	.	ENSG00000149308	ENST00000527296	.	.	.	3.92	-3.71	0.04424	.	.	.	.	.	T	0.35970	0.0950	.	.	.	0.44275	D	0.997137	.	.	.	.	.	.	T	0.37197	-0.9716	4	.	.	.	-0.1192	0.4805	0.00547	0.1833:0.2475:0.2586:0.3106	.	.	.	.	A	262	.	.	V	-	2	0	NPAT	107537234	0.001000	0.12720	0.012000	0.15200	0.023000	0.10783	-0.273000	0.08548	-0.420000	0.07427	-0.256000	0.11100	GTG	.		0.443	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		G	108032024	A	G	108032024	2	3	115	1	0	0	0	0	0	0	0	1	10592	156	6	3		3	NPAT	11	108032024	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	89722583	108032024	26974492	43	10059											
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	133790126	133790126	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cataccaccgggtgtccaggCcaaatgtgctggggccgccg	7	6	14	14	3	0	0	0	0	0	0	1	0	1	0	6	4	2	1	6	4	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:133790126C>A	ENST00000321016.8	-	18	3724	c.3494G>T	c.(3493-3495)gGc>gTc	p.G1165V	IGSF9B_ENST00000533871.2_Missense_Mutation_p.G1165V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1165	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGTGTCCAGGCCAAATGTGCT	0.692																																					p.G1165V		.											.	IGSF9B-68	0			c.G3494T						.						30	34	33					11																	133790126		1905	4106	6011	SO:0001583	missense	22997	exon18			TCCAGGCCAAATG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.3494G>T	11.37:g.133790126C>A	ENSP00000317980:p.Gly1165Val	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	99	39	NM_014987	0	0	0	0	0	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	C	15.82	2.946783	0.53186	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.65364	0.18;-0.15	5.08	5.08	0.68730	.	0.000000	0.45606	D	0.000349	T	0.50205	0.1602	N	0.19112	0.55	0.58432	D	0.999991	P	0.35774	0.519	B	0.34418	0.182	T	0.57225	-0.7848	10	0.62326	D	0.03	.	18.0591	0.89371	0.0:1.0:0.0:0.0	.	1165	Q9UPX0	TUTLB_HUMAN	V	1165;1007	ENSP00000317980:G1165V;ENSP00000436552:G1007V	ENSP00000317980:G1165V	G	-	2	0	IGSF9B	133295336	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.261000	0.65496	2.358000	0.79984	0.455000	0.32223	GGC	.		0.692	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133790126	C	A	133790126	3	1	115	1	0	0	0	0	1	0	0	0	7627	739	26	4	563	4	IGSF9B	11	133790126	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	25758102	133790126	1216390	44	10060											
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	133794760	133794760	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gctgggctcgctgatcagatCctgcatgacggccagaaccc	8	7	12	14	2	1	4	1	2	0	2	3	4	2	4	3	2	2	4	3	2	1	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:133794760C>T	ENST00000321016.8	-	15	2304	c.2074G>A	c.(2074-2076)Gat>Aat	p.D692N	IGSF9B_ENST00000533871.2_Missense_Mutation_p.D692N			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	692	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTGATCAGATCCTGCATGACG	0.587																																					p.D692N		.											.	IGSF9B-68	0			c.G2074A						.						114	123	120					11																	133794760		2090	4217	6307	SO:0001583	missense	22997	exon15			TCAGATCCTGCAT	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.2074G>A	11.37:g.133794760C>T	ENSP00000317980:p.Asp692Asn	Somatic	239	0		WXS	Illumina HiSeq	Phase_I	174	55	NM_014987	0	0	0	0	0	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	C	34	5.382681	0.95967	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.56941	0.43;0.43;0.43	5.02	5.02	0.67125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41500	D	0.000871	T	0.64505	0.2604	L	0.46157	1.445	0.53005	D	0.999967	P	0.42518	0.782	P	0.56278	0.795	T	0.62353	-0.6872	10	0.42905	T	0.14	.	18.7177	0.91682	0.0:1.0:0.0:0.0	.	692	Q9UPX0	TUTLB_HUMAN	N	692;534;692	ENSP00000317980:D692N;ENSP00000436552:D534N;ENSP00000436576:D692N	ENSP00000317980:D692N	D	-	1	0	IGSF9B	133299970	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.637000	0.83313	2.493000	0.84123	0.655000	0.94253	GAT	.		0.587	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133794760	C	T	133794760	3	4	115	1	0	0	0	0	1	0	0	0	7627	855	30	2	1995	2	IGSF9B	11	133794760	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	4634	133794760	1211756	45	10061											
TROAP	10024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49717751	49717751	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggatcagtcagcctcggAaccccttggaagagctcagg	9	7	14	11	1	3	1	3	0	0	1	4	4	3	4	3	5	3	1	3	5	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:49717751A>C	ENST00000257909.3	+	3	344	c.268A>C	c.(268-270)Aac>Cac	p.N90H	TROAP_ENST00000551245.1_Missense_Mutation_p.N90H|TROAP_ENST00000549275.1_Intron|TROAP_ENST00000550709.1_Missense_Mutation_p.N90H|RP11-161H23.9_ENST00000553259.1_RNA|TROAP_ENST00000549534.1_3'UTR|TROAP_ENST00000548311.1_Missense_Mutation_p.N90H|TROAP_ENST00000547923.1_5'Flank|TROAP_ENST00000380327.5_Missense_Mutation_p.N90H	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	90					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TCAGCCTCGGAACCCCTTGGA	0.602																																					p.N90H		.											.	TROAP-91	0			c.A268C						.						86	83	84					12																	49717751		2203	4300	6503	SO:0001583	missense	10024	exon3			CCTCGGAACCCCT	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.268A>C	12.37:g.49717751A>C	ENSP00000257909:p.Asn90His	Somatic	157	1		WXS	Illumina HiSeq	Phase_I	136	34	NM_001100620	0	0	2	3	1	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	37	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.979408	0.34942	.	.	ENSG00000135451	ENST00000551245;ENST00000380327;ENST00000548311;ENST00000550709;ENST00000257909;ENST00000547807;ENST00000551567	T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.77	4.43	0.53597	.	0.417260	0.22706	N	0.056634	T	0.36524	0.0970	L	0.46157	1.445	0.80722	D	1	D;D;D;D	0.60160	0.987;0.986;0.987;0.987	P;P;P;P	0.60473	0.875;0.864;0.821;0.723	T	0.11036	-1.0604	10	0.72032	D	0.01	-0.9898	8.2741	0.31862	0.8997:0.0:0.1003:0.0	.	90;90;90;90	F8W130;Q12815;Q6PJU7;F8VSF9	.;TROAP_HUMAN;.;.	H	90	ENSP00000447509:N90H;ENSP00000369684:N90H;ENSP00000448313:N90H;ENSP00000449984:N90H;ENSP00000257909:N90H;ENSP00000446646:N90H;ENSP00000447244:N90H	ENSP00000257909:N90H	N	+	1	0	TROAP	48004018	0.998000	0.40836	0.800000	0.32199	0.062000	0.15995	2.669000	0.46825	2.199000	0.70637	0.533000	0.62120	AAC	.		0.602	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		C	49717751	A	C	49717751	3	2	115	1	0	0	0	0	1	0	0	0	16608	246	9	5	274	5	TROAP	12	49717751	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08		49717751	84134144	46	10062											
RDH5	5959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56118170	56118170	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctaaccaaggtgagccgAtgcctggagcatgccctgac	10	6	12	13	1	0	2	0	2	0	0	0	5	0	3	5	2	5	1	5	2	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:56118170A>T	ENST00000257895.5	+	5	950	c.798A>T	c.(796-798)cgA>cgT	p.R266R	RP11-644F5.10_ENST00000550412.1_3'UTR|RDH5_ENST00000547072.1_Silent_p.R169R|RDH5_ENST00000548082.1_Silent_p.R266R	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	266					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	AGGTGAGCCGATGCCTGGAGC	0.592											OREG0021908	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R266R		.											.	RDH5-91	0			c.A798T						.						153	129	137					12																	56118170		2203	4300	6503	SO:0001819	synonymous_variant	5959	exon5			GAGCCGATGCCTG	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	9940	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 5"	601617	"retinol dehydrogenase 5 (11-cis and 9-cis)"	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.798A>T	12.37:g.56118170A>T		Somatic	162	1	1013	WXS	Illumina HiSeq	Phase_I	137	36	NM_001199771	0	0	298	431	133	O00179|Q8TAI2	Silent	SNP	ENST00000257895.5	37	CCDS31829.1																																																																																			.		0.592	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905		T	56118170	A	T	56118170	2	4	115	1	0	0	0	0	0	0	0	1	13227	320	12	5		5	RDH5	12	56118170	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	6400419	56118170	77733725	47	10063											
NACA	4666	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	57114205	57114205	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccactggaaaggcagccacaGtagcaggaactacctcattt	13	7	9	12	0	1	0	1	0	0	0	1	2	1	2	3	3	4	3	3	3	4	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:57114205G>A	ENST00000454682.1	-	3	1390	c.1109C>T	c.(1108-1110)aCt>aTt	p.T370I	NACA_ENST00000550952.1_Missense_Mutation_p.T370I|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	370	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GGCAGCCACAGTAGCAGGAAC	0.488			T	BCL6	NHL																																p.T370I		.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA-254	0			c.C1109T						.						60	55	56					12																	57114205		1568	3582	5150	SO:0001583	missense	4666	exon3			GCCACAGTAGCAG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"nascent-polypeptide-associated complex alpha polypeptide"			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1109C>T	12.37:g.57114205G>A	ENSP00000403817:p.Thr370Ile	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	46	27	NM_001113203	0	0	0	0	0		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	G	14.65	2.598833	0.46318	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.47869	0.83;0.9	3.29	3.29	0.37713	.	.	.	.	.	T	0.23171	0.0560	N	0.08118	0	0.09310	N	1	P;B	0.38978	0.652;0.358	B;B	0.30943	0.122;0.117	T	0.03750	-1.1007	9	0.26408	T	0.33	.	10.4563	0.44553	0.0:0.0:1.0:0.0	.	370;370	E9PAV3;F8VU71	.;.	I	370	ENSP00000403817:T370I;ENSP00000448035:T370I	ENSP00000403817:T370I	T	-	2	0	NACA	55400472	0.001000	0.12720	0.018000	0.16275	0.537000	0.34900	0.083000	0.14871	1.569000	0.49696	0.306000	0.20318	ACT	.		0.488	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		A	57114205	G	A	57114205	3	1	115	1	0	0	0	0	1	0	0	0	10158	1029	36	2	5155	2	NACA	12	57114205	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	996035	57114205	76737690	48	10064											
MBD6	114785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57918527	57918527	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggcacagagctgtcttcCttggagcaaacccggagcta	10	8	12	11	1	1	1	0	0	1	1	2	3	2	3	2	3	4	4	2	3	2	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:57918527C>A	ENST00000355673.3	+	4	494	c.138C>A	c.(136-138)tcC>tcA	p.S46S	MBD6_ENST00000549231.1_3'UTR|MBD6_ENST00000431731.2_Silent_p.S46S	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	46	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						AGCTGTCTTCCTTGGAGCAAA	0.572																																					p.S46S		.											.	MBD6-516	0			c.C138A						.						83	76	78					12																	57918527		2203	4300	6503	SO:0001819	synonymous_variant	114785	exon4			GTCTTCCTTGGAG	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.138C>A	12.37:g.57918527C>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	132	45	NM_052897	0	0	12	15	3	Q8N3M0|Q8NA81|Q96Q00	Silent	SNP	ENST00000355673.3	37	CCDS8944.1																																																																																			.		0.572	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			A	57918527	C	A	57918527	2	1	115	1	0	0	0	0	0	0	0	1	9373	668	24	4		4	MBD6	12	57918527	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	804322	57918527	75933368	49	10065											
WDR66	144406	broad.mit.edu	37	chr12	122398516	122398516	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagttttactgtggctgtttAcatgctggtggtcagaaatg	9	15	12	5	0	1	1	1	0	0	1	1	1	1	1	0	3	3	4	0	3	4	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:122398516A>G	ENST00000288912.4	+	14	3013	c.2159A>G	c.(2158-2160)tAc>tGc	p.Y720C	WDR66_ENST00000397454.2_Missense_Mutation_p.Y720C	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	720							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GTGGCTGTTTACATGCTGGTG	0.433																																					p.Y720C	Esophageal Squamous(85;849 1794 49757 52143)												.	WDR66-92	0			c.A2159G						.						124	123	123					12																	122398516		1926	4142	6068	SO:0001583	missense	144406	exon14			CTGTTTACATGCT	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"WD repeat domain containing"	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2159A>G	12.37:g.122398516A>G	ENSP00000288912:p.Tyr720Cys	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	194	3	NM_001178003	1	0	2	3	0	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.768449	0.49680	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.67345	0.86;-0.26	4.72	3.54	0.40534	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.136662	0.51477	D	0.000098	T	0.79009	0.4374	M	0.78916	2.43	0.35226	D	0.776497	D	0.89917	1.0	D	0.77557	0.99	D	0.83490	0.0069	10	0.87932	D	0	.	8.7806	0.34789	0.6981:0.0:0.0:0.3019	.	720	Q8TBY9	WDR66_HUMAN	C	720	ENSP00000288912:Y720C;ENSP00000380595:Y720C	ENSP00000288912:Y720C	Y	+	2	0	WDR66	120882899	1.000000	0.71417	0.021000	0.16686	0.016000	0.09150	4.265000	0.58865	0.717000	0.32145	0.533000	0.62120	TAC	.		0.433	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		G	122398516	A	G	122398516	3	3	115	1	0	0	0	0	1	0	0	0	17350	391	14	3	2209	3	WDR66	12	122398516	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	64479989	122398516	11453379	50	10066											
THBS1	7057	hgsc.bcm.edu	37	chr15	39880743	39880743	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtcaatggaggctggggTccttggtcaccatgggacat	9	9	14	9	0	2	0	2	0	0	0	3	2	3	2	2	6	0	1	2	6	1	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr15:39880743T>G	ENST00000260356.5	+	10	1653	c.1488T>G	c.(1486-1488)ggT>ggG	p.G496G		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	496	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GAGGCTGGGGTCCTTGGTCAC	0.507																																					p.G496G		.											.	THBS1-653	0			c.T1488G						.						66	66	66					15																	39880743		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon10			CTGGGGTCCTTGG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1488T>G	15.37:g.39880743T>G		Somatic	65	2		WXS	Illumina HiSeq	Phase_I	95	5	NM_003246	0	0	1	1	0	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			.		0.507	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		G	39880743	T	G	39880743	2	3	115	1	0	0	0	0	0	0	0	1	15885	1654	58	5		5	THBS1	15	39880743	Silent	SNP	T	TCGA-G7-6795-01A-11D-1961-08		39880743	62650649	51	10067											
UBR1	197131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43299382	43299382	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctattttcacctcctgttCttcttggcaaaggatgcacg	7	16	7	11	1	4	0	1	0	3	0	5	1	5	1	2	2	1	3	2	2	2	7			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr15:43299382C>T	ENST00000290650.4	-	30	3388	c.3310G>A	c.(3310-3312)Gaa>Aaa	p.E1104K	UBR1_ENST00000568782.1_5'UTR|UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1104					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACCTCCTGTTCTTCTTGGCAA	0.473																																					p.E1104K		.											.	UBR1-91	0			c.G3310A						.						128	115	119					15																	43299382		2203	4299	6502	SO:0001583	missense	197131	exon30			CCTGTTCTTCTTG		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3310G>A	15.37:g.43299382C>T	ENSP00000290650:p.Glu1104Lys	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	137	49	NM_174916	0	0	0	0	0	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	34	5.388214	0.95988	.	.	ENSG00000159459	ENST00000290650	T	0.55760	0.5	4.99	4.99	0.66335	Zinc finger, RING/FYVE/PHD-type (1);	0.050391	0.85682	D	0.000000	T	0.71829	0.3386	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.71066	-0.4700	10	0.40728	T	0.16	-8.6741	18.4574	0.90725	0.0:1.0:0.0:0.0	.	1104	Q8IWV7	UBR1_HUMAN	K	1104	ENSP00000290650:E1104K	ENSP00000290650:E1104K	E	-	1	0	UBR1	41086674	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.320000	0.79064	2.593000	0.87608	0.655000	0.94253	GAA	.		0.473	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		T	43299382	C	T	43299382	3	4	115	1	0	0	0	0	1	0	0	0	16934	922	32	2	2011	2	UBR1	15	43299382	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	3418639	43299382	59232010	52	10068											
SPG11	80208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	44951365	44951365	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcctgtgcaggcaagggAagtgtgaaacagttgagtac	12	8	14	7	0	0	2	0	2	0	0	0	3	0	3	1	2	4	4	1	2	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr15:44951365A>T	ENST00000261866.7	-	3	595	c.579T>A	c.(577-579)ctT>ctA	p.L193L	SPG11_ENST00000559193.1_Silent_p.L193L|SPG11_ENST00000427534.2_Silent_p.L193L|SPG11_ENST00000535302.2_Silent_p.L193L|SPG11_ENST00000558319.1_Silent_p.L193L	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	193					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		CAGGCAAGGGAAGTGTGAAAC	0.398																																					p.L193L		.											.	SPG11-95	0			c.T579A						.						136	135	135					15																	44951365		2198	4298	6496	SO:0001819	synonymous_variant	80208	exon3			CAAGGGAAGTGTG		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.579T>A	15.37:g.44951365A>T		Somatic	144	1		WXS	Illumina HiSeq	Phase_I	155	56	NM_025137	0	0	0	0	0	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Silent	SNP	ENST00000261866.7	37	CCDS10112.1																																																																																			.		0.398	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			T	44951365	A	T	44951365	2	4	115	1	0	0	0	0	0	0	0	1	15073	233	9	5		5	SPG11	15	44951365	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	1651983	44951365	57580027	53	10069											
PKD1	5310	hgsc.bcm.edu	37	chr16	2155892	2155892	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcacggtgaccagggccaAcgagtactcgatgacgtgct	10	6	13	12	4	0	2	0	2	0	0	1	4	0	2	2	2	4	3	2	2	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2613L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		Missing (in PKD1; unknown pathological significance). {ECO:0000269|PubMed:11571556}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.L2613L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACCAGGGCCAACGAGTACTCG	0.657																																					p.L2613L		.											.	PKD1-91	1	Substitution - coding silent(1)	lung(1)	c.T7837C						.						46	45	45					16																	2155892		1400	2465	3865	SO:0001819	synonymous_variant	5310	exon20			GGGCCAACGAGTA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"Voltage-gated ion channels / Transient receptor potential cation channels"	9008	protein-coding gene	gene with protein product	"polycystin 1", "transient receptor potential cation channel, subfamily P, member 1"	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.7837T>C	16.37:g.2155892A>G		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	36	4	NM_000296	0	0	2	3	1	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2155892	A	G	2155892	2	3	115	1	0	0	0	0	0	0	0	1	11989	40	2	3		3	PKD1	16	2155892	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08		2155892	88198861	54	10070											
B3GNT9	80262	broad.mit.edu;bcgsc.ca	37	chr16	67184131	67184131	+	IGR	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtccttggcgcgcaaataGcgggcgaagtcaaagggtcc	9	7	15	10	4	1	0	1	0	0	0	3	1	3	0	2	4	1	1	2	4	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:67184131G>C	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.R86R	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		CGCGCAAATAGCGGGCGAAGT	0.706																																					p.R86R													.	.	0			c.C258G						.						12	15	14					16																	67184131		1877	4071	5948	SO:0001628	intergenic_variant	84752	exon2			CAAATAGCGGGCG	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 6"	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		16.37:g.67184131G>C		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_033309	0	0	0	1	1	Q9HA86	Silent	SNP	ENST00000219139.3	37	CCDS10828.1																																																																																			.		0.706	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		C	67184131	G	C	67184131	1	2	115	0	1	0	0	0	0	0	0	0	1265	958	34	4		4	B3GNT9	16	67184131	IGR	SNP	G	TCGA-G7-6795-01A-11D-1961-08	65028239	67184131	23170622	55	10071											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992635	72992635	+	Silent	SNP	T	T	C																															tcctcctcctcctccgcctcTtcctcctcctcttcctcctc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992635T>C	ENST00000268489.5	-	2	2082	c.1410A>G	c.(1408-1410)gaA>gaG	p.E470E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	470	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctccgcctcttcctcctcct	0.587																																					p.E470E		.											.	ZFHX3-72	0			c.A1410G						.						38	42	40					16																	72992635		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CGCCTCTTCCTCC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1410A>G	16.37:g.72992635T>C		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	36	4	NM_006885	0	0	0	0	0	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			T|1.000;C|0.000		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72992635	T	C	72992635	2	2	115	1	0	0	0	0	0	0	0	1	17666	1606	56	3		3	ZFHX3	16	72992635	Silent	SNP	T	TCGA-G7-6795-01A-11D-1961-08	5808504	72992635	17362118	56	10072	102	3									
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	72992638	72992638	+	Silent	SNP	C	C	T																															tcctcctcctccgcctcttcCtcctcctcttcctcctccgc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992638C>T	ENST00000268489.5	-	2	2079	c.1407G>A	c.(1405-1407)gaG>gaA	p.E469E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	469	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ccgcctcttcctcctcctctt	0.587																																					p.E469E		.											.	ZFHX3-72	0			c.G1407A						.						38	41	40					16																	72992638		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCTTCCTCCTCC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1407G>A	16.37:g.72992638C>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	38	9	NM_006885	0	0	0	0	0	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72992638	C	T	72992638	2	4	115	1	0	0	0	0	0	0	0	1	17666	680	24	2		2	ZFHX3	16	72992638	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	3	72992638	17362115	57	10073	102	3									
ZFHX3	463	broad.mit.edu	37	chr16	72992645	72992647	+	In_Frame_Del	DEL	TCT	TCT	-																															cctccgcctcttcctcctccTcttcctcctccgcctcctct																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992645_72992647delTCT	ENST00000268489.5	-	2	2070_2072	c.1398_1400delAGA	c.(1396-1401)gaagag>gag	p.466_467EE>E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	466	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ttcctcctcctcttcctcctccg	0.586																																					p.466_467del													.	ZFHX3-72	0			c.1398_1400del						.																																			SO:0001651	inframe_deletion	463	exon2			TCCTCCTCTTCCT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1398_1400delAGA	16.37:g.72992645_72992647delTCT	ENSP00000268489:p.Glu471del	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	38	7	NM_006885	0	0	0	0	0	D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	CCDS10908.1																																																																																			.		0.586	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		-	72992647	TCT	-	72992645	7	5	115	1	0	1	0	1	0	0	0	0	17666	1551	54	0	9747	0	ZFHX3	16	72992645	In_Frame_Del	DEL	TCT	TCGA-G7-6795-01A-11D-1961-08	7	72992645	17362108	58	10074	102	3									
OR1E1	8387	broad.mit.edu	37	chr17	3301701	3301701	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggtttgattttgtcccaTcatgctctgtctccagtatc	5	17	8	11	0	3	1	1	1	2	0	6	1	4	1	2	1	1	4	2	1	1	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:3301701T>C	ENST00000322608.2	-	1	3	c.4A>G	c.(4-6)Atg>Gtg	p.M2V		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	2					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(2)|lung(5)	10						TTTTGTCCCATCATGCTCTGT	0.438																																					p.M2V													.	OR1E1-68	0			c.A4G						.						58	59	58					17																	3301701		2202	4300	6502	SO:0001583	missense	8387	exon1			GTCCCATCATGCT	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"GPCR / Class A : Olfactory receptors"	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.4A>G	17.37:g.3301701T>C	ENSP00000313384:p.Met2Val	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	264	3	NM_003553	0	0	0	0	0	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Missense_Mutation	SNP	ENST00000322608.2	37	CCDS11024.1	.	.	.	.	.	.	.	.	.	.	T	3.178	-0.168613	0.06461	.	.	ENSG00000180016	ENST00000322608	T	0.00573	6.48	3.26	0.843	0.18935	.	1.550200	0.03385	N	0.200962	T	0.00440	0.0014	N	0.10685	0.025	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45600	-0.9250	10	0.59425	D	0.04	.	3.8262	0.08855	0.2176:0.0:0.2254:0.557	.	2	P30953	OR1E1_HUMAN	V	2	ENSP00000313384:M2V	ENSP00000313384:M2V	M	-	1	0	OR1E1	3248451	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.362000	0.07602	0.134000	0.18681	0.456000	0.33151	ATG	.		0.438	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553		C	3301701	T	C	3301701	3	2	115	1	0	0	0	0	1	0	0	0	10980	1435	50	3	944	3	OR1E1	17	3301701	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08		3301701	77893509	59	10075											
MYH10	4628	broad.mit.edu	37	chr17	8416922	8416922	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtctgcttctccttcaccttCaacagctcttcatctttggc	5	16	5	15	0	7	0	3	0	4	0	8	0	7	0	2	1	3	2	2	1	1	5	rs375330015		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:8416922C>T	ENST00000269243.4	-	21	2724	c.2586G>A	c.(2584-2586)ttG>ttA	p.L862L	MYH10_ENST00000379980.4_Silent_p.L878L|MYH10_ENST00000360416.3_Silent_p.L893L|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000396239.1_Silent_p.L883L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	862					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CCTTCACCTTCAACAGCTCTT	0.483													C|||	1	0.000199681	0	0	5008	,	,		19613	0.001		0	False		,,,				2504	0				p.L893L													.	MYH10-92	0			c.G2679A						.	C		1,4405	4.2+/-10.8	0,1,2202	202	168	179		2586	4.2	1	17		179	0,8600		0,0,4300	no	coding-synonymous	MYH10	NM_005964.1		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		862/1977	8416922	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4628	exon23			CACCTTCAACAGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"Myosins / Myosin superfamily : Class II"	7568	protein-coding gene	gene with protein product		160776	"myosin, heavy polypeptide 10, non-muscle"			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2586G>A	17.37:g.8416922C>T		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	355	13	NM_001256012	0	0	4	4	0	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.		0.483	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8416922	C	T	8416922	2	4	115	1	0	0	0	0	0	0	0	1	10055	825	29	2		2	MYH10	17	8416922	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	5115221	8416922	72778288	60	10076											
MPRIP	23164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17030034	17030034	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agcccacgacccttcctcagGgcaccatcaacatgaaccag	12	5	7	17	1	2	1	2	1	0	0	3	2	3	1	5	1	3	1	5	1	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:17030034G>A	ENST00000341712.4	+	4	286	c.286G>A	c.(286-288)Ggc>Agc	p.G96S	MPRIP_ENST00000444976.1_Missense_Mutation_p.G96S|MPRIP_ENST00000395811.5_Missense_Mutation_p.G96S|MPRIP_ENST00000395804.3_Missense_Mutation_p.G96S			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	96	Interaction with F-actin. {ECO:0000250}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CCTTCCTCAGGGCACCATCAA	0.602																																					p.G96S		.											.	MPRIP-90	0			c.G286A						.						80	73	75					17																	17030034		2203	4300	6503	SO:0001583	missense	23164	exon4			CCTCAGGGCACCA	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.286G>A	17.37:g.17030034G>A	ENSP00000342379:p.Gly96Ser	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	127	36	NM_015134	0	0	13	21	8	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203730	0.95033	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73	5.59	5.59	0.84812	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.97826	0.9286	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.993	D	0.98164	1.0448	9	0.66056	D	0.02	.	19.5944	0.95530	0.0:0.0:1.0:0.0	.	96;96	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	S	96	ENSP00000400189:G96S;ENSP00000379156:G96S;ENSP00000379149:G96S;ENSP00000342379:G96S	ENSP00000342379:G96S	G	+	1	0	MPRIP	16970759	1.000000	0.71417	0.993000	0.49108	0.756000	0.42949	9.414000	0.97362	2.642000	0.89623	0.561000	0.74099	GGC	.		0.602	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17030034	G	A	17030034	3	1	115	1	0	0	0	0	1	0	0	0	9768	1232	43	2	300	2	MPRIP	17	17030034	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	8613112	17030034	64165176	61	10077											
PHF12	57649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27251080	27251080	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttcctcatccacgtcaaTgatgtcttcgtcgacatcat	8	14	7	12	3	4	1	3	1	1	0	8	2	6	1	2	1	0	1	2	1	1	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:27251080T>A	ENST00000332830.4	-	4	1372	c.562A>T	c.(562-564)Att>Ttt	p.I188F	PHF12_ENST00000577226.1_Missense_Mutation_p.I188F|PHF12_ENST00000268756.3_Missense_Mutation_p.I188F|RP11-20B24.5_ENST00000582631.1_RNA|PHF12_ENST00000582655.1_5'UTR|RP11-20B24.5_ENST00000580782.1_RNA	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			TCCACGTCAATGATGTCTTCG	0.602																																					p.I188F		.											.	PHF12-91	0			c.A562T						.						83	65	71					17																	27251080		2203	4300	6503	SO:0001583	missense	57649	exon4			CGTCAATGATGTC	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"Zinc fingers, PHD-type"	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.562A>T	17.37:g.27251080T>A	ENSP00000329933:p.Ile188Phe	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	89	51	NM_020889	0	0	4	7	3		Missense_Mutation	SNP	ENST00000332830.4	37	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962952	0.53507	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94793	-3.48;-3.52;-3.52	5.8	4.72	0.59763	.	0.213282	0.49305	D	0.000141	D	0.93527	0.7934	L	0.44542	1.39	0.46260	D	0.998956	D;D;B;D	0.57899	0.968;0.981;0.437;0.968	P;P;B;P	0.54026	0.474;0.74;0.068;0.474	D	0.91577	0.5276	10	0.36615	T	0.2	-19.0128	10.4673	0.44616	0.0:0.0766:0.0:0.9234	.	170;188;188;188	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	F	188	ENSP00000329933:I188F;ENSP00000368157:I188F;ENSP00000268756:I188F	ENSP00000268756:I188F	I	-	1	0	PHF12	24275206	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.241000	0.43097	1.031000	0.39867	0.533000	0.62120	ATT	.		0.602	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		A	27251080	T	A	27251080	3	1	115	1	0	0	0	0	1	0	0	0	11849	1464	51	5	2526	5	PHF12	17	27251080	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	10221046	27251080	53944130	62	10078											
KRT17	3872	broad.mit.edu	37	chr17	39777877	39777877	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaatcctcggcatccttgcGgttcttctctgccatcttct	4	15	6	16	2	4	0	0	0	4	0	8	0	6	0	4	2	2	2	4	2	1	4	rs560576342		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:39777877G>T	ENST00000311208.8	-	4	869	c.802C>A	c.(802-804)Cgc>Agc	p.R268S	JUP_ENST00000540235.1_Missense_Mutation_p.R427S	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	268	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				GCATCCTTGCGGTTCTTCTCT	0.592																																					p.R268S	Pancreas(92;1242 2086 39193 50508)												.	KRT17-92	0			c.C802A						.						113	100	105					17																	39777877		2203	4298	6501	SO:0001583	missense	3872	exon4			CCTTGCGGTTCTT	X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"-", "Intermediate filaments type I, keratins (acidic)"	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.802C>A	17.37:g.39777877G>T	ENSP00000308452:p.Arg268Ser	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	197	8	NM_000422	0	0	0	0	0	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Missense_Mutation	SNP	ENST00000311208.8	37	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376396	0.82682	.	.	ENSG00000128422;ENSG00000173801	ENST00000311208;ENST00000540235	D;D	0.89681	-2.55;-2.55	3.82	3.82	0.43975	Prefoldin (1);Filament (1);	0.000000	0.47852	D	0.000202	D	0.95890	0.8662	H	0.95114	3.625	0.38398	D	0.94557	D	0.62365	0.991	D	0.68943	0.961	D	0.98465	1.0598	10	0.87932	D	0	.	16.2789	0.82658	0.0:0.0:1.0:0.0	.	268	Q04695	K1C17_HUMAN	S	268;427	ENSP00000308452:R268S;ENSP00000441751:R427S	ENSP00000441751:R427S	R	-	1	0	JUP;KRT17	37031403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.624000	0.54231	2.135000	0.66039	0.655000	0.94253	CGC	.		0.592	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		T	39777877	G	T	39777877	3	4	115	1	0	0	0	0	1	0	0	0	8475	1116	39	4	516	4	KRT17	17	39777877	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	12526797	39777877	41417333	63	10079											
GJC1	10052	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42882624	42882624	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccctatcagaaaacccacctCaaacacggtccttgccagca	13	6	5	17	1	2	1	2	0	0	1	3	1	3	1	5	1	4	1	5	1	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:42882624C>G	ENST00000426548.1	-	3	831	c.562G>C	c.(562-564)Gag>Cag	p.E188Q	GJC1_ENST00000590758.1_Missense_Mutation_p.E188Q|GJC1_ENST00000592524.1_Missense_Mutation_p.E188Q|GJC1_ENST00000330514.4_Missense_Mutation_p.E188Q	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	188					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				AAACCCACCTCAAACACGGTC	0.493																																					p.E188Q		.											.	GJC1-248	0			c.G562C						.						188	173	178					17																	42882624		2203	4300	6503	SO:0001583	missense	10052	exon3			CCACCTCAAACAC	U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"Ion channels / Gap junction proteins (connexins)"	4280	protein-coding gene	gene with protein product	"connexin 45"	608655	"gap junction protein, alpha 7, 45kDa"	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.562G>C	17.37:g.42882624C>G	ENSP00000411528:p.Glu188Gln	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	358	131	NM_005497	0	0	0	0	0	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	37	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201522	0.79015	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.97850	-4.57;-4.57	5.52	5.52	0.82312	Gap junction protein, cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	D	0.99306	0.9757	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98674	1.0689	10	0.87932	D	0	.	18.419	0.90582	0.0:1.0:0.0:0.0	.	188	P36383	CXG1_HUMAN	Q	188	ENSP00000411528:E188Q;ENSP00000333193:E188Q	ENSP00000333193:E188Q	E	-	1	0	GJC1	40238150	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.805000	0.86005	2.581000	0.87130	0.514000	0.50259	GAG	.		0.493	GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497		G	42882624	C	G	42882624	3	3	115	1	0	0	0	0	1	0	0	0	6434	835	29	4	632	4	GJC1	17	42882624	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	3104747	42882624	38312586	64	10080											
SAMD14	201191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48190273	48190273	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccctagctcttcttggccTcctgctctcggcgccggagc	2	11	10	18	3	3	0	0	0	3	0	6	1	5	1	5	3	3	2	5	3	1	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:48190273T>G	ENST00000330175.4	-	10	1555	c.1238A>C	c.(1237-1239)gAg>gCg	p.E413A	SAMD14_ENST00000503131.1_Missense_Mutation_p.E441A	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	413										breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						CTTCTTGGCCTCCTGCTCTCG	0.697																																					p.E441A		.											.	SAMD14-68	0			c.A1322C						.						40	43	42					17																	48190273		2203	4300	6503	SO:0001583	missense	201191	exon11			TTGGCCTCCTGCT		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.1238A>C	17.37:g.48190273T>G	ENSP00000329144:p.Glu413Ala	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	133	51	NM_174920	0	0	34	78	44	A5D8V1|Q8N2X0	Missense_Mutation	SNP	ENST00000330175.4	37	CCDS58562.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.134428	0.56828	.	.	ENSG00000167100	ENST00000330175;ENST00000285206;ENST00000503131	.	.	.	5.11	4.02	0.46733	.	0.370723	0.24490	N	0.038069	T	0.47544	0.1451	L	0.27053	0.805	0.27885	N	0.939546	D;B	0.63880	0.993;0.137	D;B	0.68192	0.956;0.046	T	0.37911	-0.9685	9	0.59425	D	0.04	-11.4398	10.0803	0.42386	0.0:0.0:0.1686:0.8313	.	413;441	Q8IZD0;Q8IZD0-2	SAM14_HUMAN;.	A	413;425;441	.	ENSP00000285206:E425A	E	-	2	0	SAMD14	45545272	0.996000	0.38824	1.000000	0.80357	0.862000	0.49288	2.701000	0.47094	0.773000	0.33404	0.379000	0.24179	GAG	.		0.697	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		G	48190273	T	G	48190273	3	3	115	1	0	0	0	0	1	0	0	0	13851	1551	54	5	19	5	SAMD14	17	48190273	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	5307649	48190273	33004937	65	10081											
CACNA1G	8913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48669448	48669448	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttctggtggagggcttccagGcggaggtaacccactgctct	6	10	14	11	1	2	0	0	0	2	0	3	2	3	2	2	6	2	3	2	6	1	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:48669448G>A	ENST00000359106.5	+	13	2905	c.2905G>A	c.(2905-2907)Gcg>Acg	p.A969T	CACNA1G_ENST00000416767.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000503485.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514079.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507609.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000513689.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000429973.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000507336.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507510.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000510115.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000502264.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507896.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000505165.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000510366.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000354983.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000515411.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514717.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514181.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000512389.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000513964.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000360761.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000442258.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000515165.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000358244.5_Missense_Mutation_p.A969T|CACNA1G_ENST00000515765.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000352832.5_Missense_Mutation_p.A969T	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	969					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GGGCTTCCAGGCGGAGGTAAC	0.582																																					p.A969T		.											.	CACNA1G-67	0			c.G2905A						.						50	55	53					17																	48669448		2071	4210	6281	SO:0001583	missense	8913	exon13			TTCCAGGCGGAGG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2905G>A	17.37:g.48669448G>A	ENSP00000352011:p.Ala969Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	96	40	NM_001256360	0	0	0	0	0	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	14.26	2.482345	0.44147	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97186	-4.13;-4.12;-4.28;-4.08;-4.13;-4.12;-4.16;-4.26;-4.22;-4.24;-4.25;-4.11;-4.12;-4.2;-4.12;-4.07;-4.16;-4.12;-4.12;-4.16;-4.12;-4.12;-4.16;-4.11;-4.16;-4.17	5.08	1.63	0.23807	.	0.106565	0.64402	N	0.000006	D	0.88142	0.6357	N	0.02916	-0.46	0.33790	D	0.625335	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.22080	0.064;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.001;0.019;0.0;0.001;0.002;0.0;0.001;0.001;0.007;0.0;0.0;0.001;0.001;0.002;0.0;0.001;0.001;0.013	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.25987	0.017;0.005;0.001;0.005;0.001;0.006;0.004;0.001;0.004;0.013;0.001;0.017;0.02;0.001;0.004;0.007;0.029;0.005;0.001;0.008;0.003;0.007;0.001;0.007;0.001;0.065	T	0.82715	-0.0320	10	0.23891	T	0.37	.	5.465	0.16637	0.6206:0.0:0.3794:0.0	.	969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	T	969	ENSP00000353990:A969T;ENSP00000339302:A969T;ENSP00000392390:A969T;ENSP00000347078:A969T;ENSP00000409759:A969T;ENSP00000425522:A969T;ENSP00000426261:A969T;ENSP00000425451:A969T;ENSP00000422407:A969T;ENSP00000426814:A969T;ENSP00000427238:A969T;ENSP00000423112:A969T;ENSP00000420918:A969T;ENSP00000426172:A969T;ENSP00000423045:A969T;ENSP00000427173:A969T;ENSP00000426098:A969T;ENSP00000425698:A969T;ENSP00000426232:A969T;ENSP00000423317:A969T;ENSP00000350979:A969T;ENSP00000352011:A969T;ENSP00000414388:A969T;ENSP00000423155:A969T;ENSP00000422268:A969T;ENSP00000421518:A969T	ENSP00000339302:A969T	A	+	1	0	CACNA1G	46024447	1.000000	0.71417	0.982000	0.44146	0.980000	0.70556	2.660000	0.46749	0.553000	0.29044	0.462000	0.41574	GCG	.		0.582	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		A	48669448	G	A	48669448	3	1	115	1	0	0	0	0	1	0	0	0	2550	1203	42	2	2955	2	CACNA1G	17	48669448	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	479175	48669448	32525762	66	10082											
VEZF1	7716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	56060465	56060465	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggggaaccaccgtggtggggGttttctttggccgggacacc	5	9	17	10	2	1	0	0	0	1	0	1	2	1	2	4	7	1	1	4	7	1	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:56060465G>T	ENST00000581208.1	-	2	363	c.323C>A	c.(322-324)aCc>aAc	p.T108N	VEZF1_ENST00000584396.1_Missense_Mutation_p.T99N	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	108					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						CGTGGTGGGGGTTTTCTTTGG	0.547																																					p.T108N		.											.	VEZF1-136	0			c.C323A						.						91	91	91					17																	56060465		2203	4300	6503	SO:0001583	missense	7716	exon2			GTGGGGGTTTTCT	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"Zinc fingers, C2H2-type"	12949	protein-coding gene	gene with protein product		606747	"zinc finger protein 161"	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.323C>A	17.37:g.56060465G>T	ENSP00000462337:p.Thr108Asn	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	146	61	NM_007146	0	0	1	1	0		Missense_Mutation	SNP	ENST00000581208.1	37	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033269	0.54896	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.52092	0.1713	L	0.27053	0.805	0.80722	D	1	P	0.49185	0.92	B	0.44085	0.44	T	0.58142	-0.7688	9	0.66056	D	0.02	-9.6184	19.3617	0.94442	0.0:0.0:1.0:0.0	.	108	Q14119	VEZF1_HUMAN	N	108	.	ENSP00000258963:T108N	T	-	2	0	VEZF1	53415464	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.196000	0.94978	2.590000	0.87494	0.643000	0.83706	ACC	.		0.547	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			T	56060465	G	T	56060465	3	4	115	1	0	0	0	0	1	0	0	0	17188	1261	44	4	1262	4	VEZF1	17	56060465	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	7391017	56060465	25134745	67	10083											
DYM	54808	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	46645145	46645145	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttgcattatatcctgaaatGaaggatgagttcgaaattgt	13	15	9	4	1	0	3	0	3	0	0	2	5	1	4	1	1	1	2	1	1	5	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr18:46645145G>A	ENST00000269445.6	-	15	2172	c.1715C>T	c.(1714-1716)tCa>tTa	p.S572L	RP11-15F12.3_ENST00000585251.1_RNA|DYM_ENST00000442713.2_Missense_Mutation_p.S382L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	572					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						ATCCTGAAATGAAGGATGAGT	0.353																																					p.S572L		.											.	DYM-226	0			c.C1715T						.						136	120	126					18																	46645145		2203	4300	6503	SO:0001583	missense	54808	exon15			TGAAATGAAGGAT	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1715C>T	18.37:g.46645145G>A	ENSP00000269445:p.Ser572Leu	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	70	22	NM_017653	0	0	2	5	3	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	37	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094436	0.94149	.	.	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.81908	-1.55;-1.55	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.86981	0.6064	L	0.48362	1.52	0.80722	D	1	P;D;P	0.56287	0.879;0.975;0.481	B;P;B	0.56648	0.399;0.803;0.22	D	0.87691	0.2554	10	0.66056	D	0.02	-11.3305	19.412	0.94677	0.0:0.0:1.0:0.0	.	382;394;572	Q7RTS9-2;Q9NXS9;Q7RTS9	.;.;DYM_HUMAN	L	382;572	ENSP00000395942:S382L;ENSP00000269445:S572L	ENSP00000269445:S572L	S	-	2	0	DYM	44899143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.827000	0.99397	2.601000	0.87937	0.650000	0.86243	TCA	.		0.353	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		A	46645145	G	A	46645145	3	1	115	1	0	0	0	0	1	0	0	0	4851	1294	45	2	306	2	DYM	18	46645145	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08		46645145	31432103	68	10084											
TMPRSS9	360200	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2408353	2408353	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctggggtttgctcctgcaGgttccaagacccgacgaagt	8	9	13	11	2	0	1	0	0	0	1	2	3	2	1	3	3	3	5	3	3	2	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:2408353G>A	ENST00000332578.3	+	7	740		c.e7-1			NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9						plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTCCTGCAGGTTCCAAGAC	0.652																																					.													.	TMPRSS9-91	0			c.741-1G>A						.						45	44	44					19																	2408353		2203	4300	6503	SO:0001630	splice_region_variant	360200	exon7			CCTGCAGGTTCCA	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.741-1G>A	19.37:g.2408353G>A		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	59	7	NM_182973	0	0	0	0	0	Q6ZND6|Q7Z411	Splice_Site	SNP	ENST00000332578.3	37	CCDS12088.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.918286	0.33908	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	.	.	.	4.45	4.45	0.53987	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6211	0.76808	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMPRSS9	2359353	1.000000	0.71417	0.797000	0.32132	0.227000	0.25037	8.627000	0.90974	2.039000	0.60335	0.491000	0.48974	.	.		0.652	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	Intron	A	2408353	G	A	2408353	5	1	115	1	0	0	0	0	0	0	1	0	16285	1014	35	2	766	2	TMPRSS9	19	2408353	Splice_Site	SNP	G	TCGA-G7-6795-01A-11D-1961-08		2408353	56720630	69	10085											
USHBP1	83878	hgsc.bcm.edu;bcgsc.ca	37	chr19	17370111	17370111	+	Frame_Shift_Del	DEL	C	C	-																															cactgacctgtactgcaaggCcagatgcaatgctgtggcct																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:17370111delC	ENST00000252597.3	-	7	1206	c.1033delG	c.(1033-1035)gccfs	p.A345fs	USHBP1_ENST00000431146.2_Frame_Shift_Del_p.A281fs	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TACTGCAAGGCCAGATGCAAT	0.602																																					p.A345fs		.											.	USHBP1-91	0			c.1033delG						.						53	49	50					19																	17370111		2203	4300	6503	SO:0001589	frameshift_variant	83878	exon7			.	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1033delG	19.37:g.17370111delC	ENSP00000252597:p.Ala345fs	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	41	12	NM_031941	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000252597.3	37	CCDS12353.1																																																																																			.		0.602	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		-	17370111	C	-	17370111	7	5	115	1	0	1	0	1	0	0	0	0	17070	739	26	0	1106	0	USHBP1	19	17370111	Frame_Shift_Del	DEL	C	TCGA-G7-6795-01A-11D-1961-08	14961758	17370111	41758872	70	10086											
SSBP4	170463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	18538728	18538728	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcttctgggacctgtactGcgcggcgcctgacagaagag	7	8	14	12	4	2	3	0	1	2	2	2	4	2	4	2	2	2	1	2	2	2	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:18538728G>A	ENST00000270061.7	+	4	509	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	SSBP4_ENST00000598159.2_3'UTR|SSBP4_ENST00000348495.6_Missense_Mutation_p.C72Y	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	72						nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						GACCTGTACTGCGCGGCGCCT	0.667																																					p.C72Y		.											.	SSBP4-90	0			c.G215A						.						77	70	72					19																	18538728		2203	4300	6503	SO:0001583	missense	170463	exon4			TGTACTGCGCGGC		CCDS12378.1, CCDS32960.1	19p13.1	2008-02-05				ENSG00000130511			15676	protein-coding gene	gene with protein product		607391				12079286	Standard	NM_032627		Approved		uc002niy.3	Q9BWG4		ENST00000270061.7:c.215G>A	19.37:g.18538728G>A	ENSP00000270061:p.Cys72Tyr	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	107	40	NM_001009998	0	0	25	43	18	Q9BWW5	Missense_Mutation	SNP	ENST00000270061.7	37	CCDS12378.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.288142	0.40494	.	.	ENSG00000130511	ENST00000270061;ENST00000348495	.	.	.	3.7	3.7	0.42460	.	0.000000	0.85682	U	0.000000	T	0.58921	0.2156	L	0.57536	1.79	0.58432	D	0.999999	B;B	0.25048	0.048;0.117	B;B	0.27715	0.077;0.082	T	0.64193	-0.6465	9	0.72032	D	0.01	-16.1844	12.9926	0.58627	0.0:0.0:1.0:0.0	.	72;72	Q9BWW5;Q9BWG4	.;SSBP4_HUMAN	Y	72	.	ENSP00000270061:C72Y	C	+	2	0	SSBP4	18399728	1.000000	0.71417	0.932000	0.37286	0.036000	0.12997	8.730000	0.91510	1.883000	0.54544	0.561000	0.74099	TGC	.		0.667	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627		A	18538728	G	A	18538728	3	1	115	1	0	0	0	0	1	0	0	0	15214	1319	46	2	229	2	SSBP4	19	18538728	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	1168617	18538728	40590255	71	10087											
SLC25A42	284439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19218750	19218750	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgcatctcgagagaagaggGgctgaagactctctaccatg	11	7	12	11	2	2	4	0	1	2	3	4	6	2	4	2	2	1	2	2	2	3	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:19218750G>T	ENST00000318596.7	+	7	696	c.545G>T	c.(544-546)gGg>gTg	p.G182V	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	182					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			AGAGAAGAGGGGCTGAAGACT	0.572																																					p.G182V		.											.	SLC25A42-90	0			c.G545T						.						119	105	110					19																	19218750		2203	4300	6503	SO:0001583	missense	284439	exon7			AAGAGGGGCTGAA		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"Solute carriers"	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.545G>T	19.37:g.19218750G>T	ENSP00000326693:p.Gly182Val	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	134	51	NM_178526	0	0	1	8	7	D2T2J5|O14553|O43378	Missense_Mutation	SNP	ENST00000318596.7	37	CCDS32966.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441353	0.83993	.	.	ENSG00000181035	ENST00000318596	D	0.95238	-3.65	5.26	5.26	0.73747	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.98701	0.9564	H	0.99435	4.565	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99686	1.1000	10	0.87932	D	0	-10.1963	17.8525	0.88751	0.0:0.0:1.0:0.0	.	182	Q86VD7	S2542_HUMAN	V	182	ENSP00000326693:G182V	ENSP00000326693:G182V	G	+	2	0	SLC25A42	19079750	1.000000	0.71417	0.987000	0.45799	0.753000	0.42808	8.259000	0.89855	2.449000	0.82847	0.491000	0.48974	GGG	.		0.572	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		T	19218750	G	T	19218750	3	4	115	1	0	0	0	0	1	0	0	0	14539	1232	43	4	567	4	SLC25A42	19	19218750	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	680022	19218750	39910233	72	10088											
ZNF254	9534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	24310237	24310237	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatggtcctcaaccctaactAgacataagaggatgcacact	14	9	7	11	0	1	2	1	0	0	2	2	3	2	3	2	2	3	1	2	2	5	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:24310237A>T	ENST00000357002.4	+	4	1550	c.1435A>T	c.(1435-1437)Aga>Tga	p.R479*	ZNF254_ENST00000342944.6_Nonsense_Mutation_p.R394*	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	479					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				AACCCTAACTAGACATAAGAG	0.388																																					p.R479X		.											.	ZNF254-90	0			c.A1435T						.						62	62	62					19																	24310237		2203	4299	6502	SO:0001587	stop_gained	9534	exon4			CTAACTAGACATA	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1435A>T	19.37:g.24310237A>T	ENSP00000349494:p.Arg479*	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	74	21	NM_203282	0	0	0	3	3	A4QPC0|Q86XL7	Nonsense_Mutation	SNP	ENST00000357002.4	37	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	A	35	5.491375	0.96339	.	.	ENSG00000213096	ENST00000342944;ENST00000357002	.	.	.	1.07	-2.07	0.07276	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	3.7155	0.08437	0.6048:0.3952:0.0:0.0	.	.	.	.	X	394;479	.	ENSP00000445527:R394X	R	+	1	2	ZNF254	24102077	0.000000	0.05858	0.040000	0.18447	0.918000	0.54935	-0.462000	0.06704	-0.565000	0.06061	0.248000	0.18094	AGA	.		0.388	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		T	24310237	A	T	24310237	4	4	115	1	0	0	0	0	0	1	0	0	17830	412	15	5	1449	5	ZNF254	19	24310237	Nonsense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	5091487	24310237	34818746	73	10089											
SPINT2	10653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38774304	38774304	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aaggtggtgggcagatgccgGgcctccatgcctaggtggtg	6	8	18	9	1	0	1	0	0	0	1	1	1	1	1	4	6	2	1	4	6	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:38774304G>T	ENST00000301244.7	+	2	579	c.144G>T	c.(142-144)cgG>cgT	p.R48R	SPINT2_ENST00000587090.1_5'UTR|SPINT2_ENST00000454580.3_Intron	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2	48	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.	Reactive bond. {ECO:0000250}.			cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GCAGATGCCGGGCCTCCATGC	0.562																																					p.R48R		.											.	SPINT2-90	0			c.G144T						.						170	144	153					19																	38774304		2203	4300	6503	SO:0001819	synonymous_variant	10653	exon2			ATGCCGGGCCTCC	U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"placental bikunin"	605124	"serine protease inhibitor, Kunitz type, 2"			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.144G>T	19.37:g.38774304G>T		Somatic	211	0		WXS	Illumina HiSeq	Phase_I	208	55	NM_021102	0	0	37	73	36	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Silent	SNP	ENST00000301244.7	37	CCDS12510.1																																																																																			.		0.562	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2			T	38774304	G	T	38774304	2	4	115	1	0	0	0	0	0	0	0	1	15101	1219	43	4		4	SPINT2	19	38774304	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	14464067	38774304	20354679	74	10090											
CYP2S1	29785	broad.mit.edu	37	chr19	41712375	41712375	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcccactgaccttcactcCaccacgcagaccagatgaag	11	6	7	17	2	1	4	1	2	0	2	3	4	3	4	5	0	0	1	5	0	1	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:41712375C>T	ENST00000310054.4	+	9	1713	c.1497C>T	c.(1495-1497)tcC>tcT	p.S499S	CYP2S1_ENST00000542619.1_Silent_p.S224S	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	499					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						ACCTTCACTCCACCACGCAGA	0.607																																					p.S499S													.	CYP2S1-91	0			c.C1497T						.						99	92	95					19																	41712375		2203	4300	6503	SO:0001819	synonymous_variant	29785	exon9			TCACTCCACCACG	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"Cytochrome P450s"	15654	protein-coding gene	gene with protein product		611529	"cytochrome P450, subfamily IIS, polypeptide 1"			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.1497C>T	19.37:g.41712375C>T		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	95	8	NM_030622	0	0	0	0	0	Q9BZ66	Silent	SNP	ENST00000310054.4	37	CCDS12573.1																																																																																			.		0.607	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1			T	41712375	C	T	41712375	2	4	115	1	0	0	0	0	0	0	0	1	4180	581	21	2		2	CYP2S1	19	41712375	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	2938071	41712375	17416608	75	10091											
ZNF471	57573	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57037032	57037032	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagagatcacaccttgcccaAcatcagaaaactcatacagg	16	6	6	13	0	3	2	3	0	0	2	3	3	3	2	2	1	4	0	2	1	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:57037032A>G	ENST00000308031.5	+	5	1729	c.1596A>G	c.(1594-1596)caA>caG	p.Q532Q	ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	532					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		ACCTTGCCCAACATCAGAAAA	0.398																																					p.Q532Q	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	.											.	ZNF471-154	0			c.A1596G						.						105	111	109					19																	57037032		2203	4300	6503	SO:0001819	synonymous_variant	57573	exon5			TGCCCAACATCAG	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"Zinc fingers, C2H2-type", "-"	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1596A>G	19.37:g.57037032A>G		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	121	40	NM_020813	0	0	0	0	0	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Silent	SNP	ENST00000308031.5	37	CCDS12945.1																																																																																			.		0.398	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		G	57037032	A	G	57037032	2	3	115	1	0	0	0	0	0	0	0	1	17962	40	2	3		3	ZNF471	19	57037032	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	15324657	57037032	2091951	76	10092											
RALGAPA2	57186	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	20491913	20491913	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cataccactggcgggagtccAaatttttcagctctctcaat	10	12	7	12	1	3	0	2	0	1	0	5	1	4	1	2	2	2	1	2	2	3	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:20491913A>T	ENST00000202677.7	-	33	4920	c.4913T>A	c.(4912-4914)tTg>tAg	p.L1638*		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1638	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						GCGGGAGTCCAAATTTTTCAG	0.328																																					p.L1638X													.	RALGAPA2-24	0			c.T4913A						.						33	31	32					20																	20491913		1795	4058	5853	SO:0001587	stop_gained	57186	exon33			GAGTCCAAATTTT	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 74"	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4913T>A	20.37:g.20491913A>T	ENSP00000202677:p.Leu1638*	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	24	11	NM_020343	0	0	0	1	1	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Nonsense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	47|47	13.108967|13.108967	0.99720|0.99720	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000417022;ENST00000202677|ENST00000430436;ENST00000427175	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	.|T	.|0.71298	.|0.3323	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73978	.|-0.3812	.|3	0.02654|.	T|.	1|.	.|.	15.6215|15.6215	0.76810|0.76810	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|R	68;1638|1455;49	.|.	ENSP00000202677:L1638X|.	L|W	-|-	2|1	0|0	RALGAPA2|RALGAPA2	20439913|20439913	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.927000|0.927000	0.56198|0.56198	9.273000|9.273000	0.95719|0.95719	2.093000|2.093000	0.63338|0.63338	0.460000|0.460000	0.39030|0.39030	TTG|TGG	.		0.328	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		T	20491913	A	T	20491913	4	4	115	1	0	0	0	0	0	1	0	0	13046	131	5	5	736	5	RALGAPA2	20	20491913	Nonsense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08		20491913	42533607	77	10093											
SSTR4	6754	broad.mit.edu	37	chr20	23017198	23017198	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaggtggggcagggtgcAtgtgccccccactcccctgc	6	6	14	15	0	0	0	0	0	0	0	1	0	1	0	5	4	3	3	5	4	1	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:23017198A>T	ENST00000255008.3	+	1	1142	c.1078A>T	c.(1078-1080)Atg>Ttg	p.M360L	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	360					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GGCAGGGTGCATGTGCCCCCC	0.657																																					p.M360L	Esophageal Squamous(15;850 1104 16640)												.	SSTR4-522	0			c.A1078T						.						37	43	41					20																	23017198		2127	4243	6370	SO:0001583	missense	6754	exon1			GGGTGCATGTGCC		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"GPCR / Class A : Somatostatin receptors"	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.1078A>T	20.37:g.23017198A>T	ENSP00000255008:p.Met360Leu	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	108	6	NM_001052	0	0	0	0	0	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	A	0.199	-1.046780	0.01997	.	.	ENSG00000132671	ENST00000255008	T	0.63417	-0.04	3.65	1.32	0.21799	.	0.550833	0.15820	U	0.243030	T	0.40595	0.1123	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16630	-1.0396	10	0.27785	T	0.31	.	4.5158	0.11934	0.7291:0.0:0.0996:0.1712	.	360	P31391	SSR4_HUMAN	L	360	ENSP00000255008:M360L	ENSP00000255008:M360L	M	+	1	0	SSTR4	22965198	0.032000	0.19561	0.019000	0.16419	0.020000	0.10135	0.547000	0.23299	0.047000	0.15862	-0.250000	0.11733	ATG	.		0.657	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			T	23017198	A	T	23017198	3	4	115	1	0	0	0	0	1	0	0	0	15232	217	8	5	1080	5	SSTR4	20	23017198	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	2525285	23017198	40008322	78	10094											
C20orf70	140683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31761923	31761923	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcatcctggatgtcaaagCtgaaccgatcgatgatggca	11	9	10	11	2	2	2	2	2	0	0	4	5	3	3	3	2	2	2	3	2	2	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:31761923C>T	ENST00000253362.2	+	4	487	c.341C>T	c.(340-342)gCt>gTt	p.A114V	BPIFA2_ENST00000354932.5_Missense_Mutation_p.A114V			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	114						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										GATGTCAAAGCTGAACCGATC	0.507																																					p.A114V		.											.	.	0			c.C341T						.						192	132	152					20																	31761923		2203	4300	6503	SO:0001583	missense	140683	exon4			TCAAAGCTGAACC	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"BPI fold containing"	16203	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 70"	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.341C>T	20.37:g.31761923C>T	ENSP00000253362:p.Ala114Val	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	136	38	NM_080574	0	0	0	0	0	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	.	.	.	.	.	.	.	.	.	.	C	1.293	-0.607118	0.03717	.	.	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.04758	3.56;3.56	4.11	-1.34	0.09143	.	1.919610	0.02314	N	0.072384	T	0.03520	0.0101	N	0.20685	0.6	0.09310	N	1	P	0.39862	0.692	B	0.42692	0.395	T	0.35276	-0.9795	10	0.02654	T	1	-22.3913	3.4184	0.07384	0.1782:0.4121:0.0:0.4097	.	114	Q96DR5	BPIA2_HUMAN	V	114	ENSP00000253362:A114V;ENSP00000347012:A114V	ENSP00000253362:A114V	A	+	2	0	BPIFA2	31225584	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.978000	0.01494	-0.194000	0.10399	0.561000	0.74099	GCT	.		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		T	31761923	C	T	31761923	3	4	115	1	0	0	0	0	1	0	0	0	2122	797	28	2	351	2	C20orf70	20	31761923	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	8744725	31761923	31263597	79	10095											
BCR	613	ucsc.edu	37	chr22	23656859	23656859	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgccaaccccagccagccTatcaccatgactgacagctg	10	6	7	18	0	1	2	1	2	0	0	1	2	1	2	7	0	5	1	7	0	2	1	rs55715766	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr22:23656859T>A	ENST00000305877.8	+	22	4435	c.3684T>A	c.(3682-3684)ccT>ccA	p.P1228P	BCR_ENST00000359540.3_Silent_p.P1184P|BCR_ENST00000436990.2_3'UTR	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	1228	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	CCAGCCAGCCTATCACCATGA	0.612			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.P1228P				Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR-1349	0			c.T3684A						.						45	36	39					22																	23656859		2203	4296	6499	SO:0001819	synonymous_variant	613	exon22			CCAGCCTATCACC		CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.3684T>A	22.37:g.23656859T>A		Somatic	38	0		WXS	Illumina HiSeq		39	4	NM_004327	0	0	104	104	0	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			T|0.999;C|0.001		0.612	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		A	23656859	T	A	23656859	2	1	115	1	0	0	0	0	0	0	0	1	1389	1509	53	5		5	BCR	22	23656859	Silent	SNP	T	TCGA-G7-6795-01A-11D-1961-08		23656859	27647707	80	10096											
RPL22	6146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	6246873	6246873	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttggtgagatatttcaaAtacctgcagagaaaggacac	14	12	9	6	0	1	2	1	1	0	2	1	5	1	3	1	2	2	1	1	2	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:6246873A>T	ENST00000234875.4	-	4	284	c.246T>A	c.(244-246)taT>taA	p.Y82*	RPL22_ENST00000484532.1_Intron|RPL22_ENST00000497965.1_Nonsense_Mutation_p.Y49*	NM_000983.3	NP_000974.1	P35268	RL22_HUMAN	ribosomal protein L22	82					alpha-beta T cell differentiation (GO:0046632)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GATATTTCAAATACCTGCAGA	0.358			T	RUNX1	"AML, CML"																																p.Y82X		.		Dom	yes		1	1p36.31	6146	ribosomal protein L22 (EAP)		L	.	RPL22-650	0			c.T246A						.						46	47	46					1																	6246873		2202	4300	6502	SO:0001587	stop_gained	6146	exon4			TTTCAAATACCTG	BC058887	CCDS58.1	1p36.31	2011-04-06			ENSG00000116251	ENSG00000116251		"L ribosomal proteins"	10315	protein-coding gene	gene with protein product		180474				8395054	Standard	NM_000983		Approved	EAP, L22	uc001amd.3	P35268	OTTHUMG00000000953	ENST00000234875.4:c.246T>A	1.37:g.6246873A>T	ENSP00000346088:p.Tyr82*	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	81	17	NM_000983	0	0	3	6	3	B2R495|Q6IBD1	Nonsense_Mutation	SNP	ENST00000234875.4	37	CCDS58.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279556	0.80692	.	.	ENSG00000116251	ENST00000234875	.	.	.	5.43	4.31	0.51392	.	0.122602	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.2758	7.3535	0.26706	0.7815:0.0:0.2185:0.0	.	.	.	.	X	82	.	ENSP00000346088:Y82X	Y	-	3	2	RPL22	6169460	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.692000	0.47018	0.906000	0.36621	0.379000	0.24179	TAT	.		0.358	RPL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002830.1	NM_000983		T	6246873	A	T	6246873	4	4	116	1	0	0	0	0	0	1	0	0	13600	108	4	5	144	5	RPL22	1	6246873	Nonsense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		6246873	243003748	1	10097											
KIF1B	23095	broad.mit.edu	37	chr1	10352150	10352150	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgccattcgggaagatggAggaaccctaggggttttctc	8	11	14	8	1	1	1	0	0	1	1	3	4	1	4	2	5	2	2	2	5	3	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:10352150A>G	ENST00000377086.1	+	17	1762	c.1560A>G	c.(1558-1560)ggA>ggG	p.G520G	KIF1B_ENST00000377083.1_Silent_p.G474G|KIF1B_ENST00000377081.1_Silent_p.G520G|KIF1B_ENST00000377093.4_Silent_p.G474G|KIF1B_ENST00000263934.6_Silent_p.G474G			O60333	KIF1B_HUMAN	kinesin family member 1B	520					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GGGAAGATGGAGGAACCCTAG	0.408																																					p.G474G													.	KIF1B-93	0			c.A1422G						.						126	134	131					1																	10352150		2203	4300	6503	SO:0001819	synonymous_variant	23095	exon15			AGATGGAGGAACC	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.1560A>G	1.37:g.10352150A>G		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	197	4	NM_183416	0	0	0	0	0	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				.		0.408	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			G	10352150	A	G	10352150	2	3	116	1	0	0	0	0	0	0	0	1	8305	291	11	3		3	KIF1B	1	10352150	Silent	SNP	A	TCGA-G7-6796-01A-11D-1961-08	4105277	10352150	238898471	2	10098											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27094329	27094329	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaagatcaccaagttgtatGagctgggtggtgagcctgag	11	9	15	6	0	1	5	1	3	0	2	1	5	1	5	2	2	2	3	2	2	3	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:27094329G>A	ENST00000324856.7	+	11	3408	c.3037G>A	c.(3037-3039)Gag>Aag	p.E1013K	ARID1A_ENST00000457599.2_Missense_Mutation_p.E1013K|ARID1A_ENST00000374152.2_Missense_Mutation_p.E630K	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1013					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CAAGTTGTATGAGCTGGGTGG	0.488			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.E1013K		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.G3037A						.						146	122	130					1																	27094329		2203	4300	6503	SO:0001583	missense	8289	exon11			TTGTATGAGCTGG	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3037G>A	1.37:g.27094329G>A	ENSP00000320485:p.Glu1013Lys	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	142	32	NM_006015	0	0	0	0	0	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703514	0.96812	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.46819	0.86;0.86;0.86	5.17	5.17	0.71159	ARID/BRIGHT DNA-binding domain (2);	0.049842	0.85682	D	0.000000	T	0.64886	0.2639	L	0.59436	1.845	0.80722	D	1	D;D;D	0.67145	0.995;0.996;0.993	D;D;P	0.65323	0.909;0.934;0.861	T	0.64601	-0.6369	10	0.51188	T	0.08	-14.8758	18.8566	0.92255	0.0:0.0:1.0:0.0	.	1013;1013;667	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	K	1013;1013;630	ENSP00000320485:E1013K;ENSP00000387636:E1013K;ENSP00000363267:E630K	ENSP00000320485:E1013K	E	+	1	0	ARID1A	26966916	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.657000	0.98554	2.678000	0.91216	0.655000	0.94253	GAG	.		0.488	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27094329	G	A	27094329	3	1	116	1	0	0	0	0	1	0	0	0	913	1291	45	2	3079	2	ARID1A	1	27094329	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	16742179	27094329	222156292	3	10099											
PDE4DIP	9659	hgsc.bcm.edu;broad.mit.edu	37	chr1	144856892	144856892	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctatctttttgaccagcagcTtgccctccgcaatctgctgt	6	14	7	14	1	2	1	0	1	2	0	3	1	3	1	3	0	4	4	3	0	2	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:144856892T>C	ENST00000369354.3	-	40	6782	c.6593A>G	c.(6592-6594)aAg>aGg	p.K2198R	RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.K2198R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.K2092R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.K2334R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.K2283R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2198					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GACCAGCAGCTTGCCCTCCGC	0.517			T	PDGFRB	MPD																																p.K2198R		.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP-663	0			c.A6593G						.						38	34	35					1																	144856892		2193	4248	6441	SO:0001583	missense	9659	exon40			AGCAGCTTGCCCT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"myomegalin"	608117	"cardiomyopathy associated 2"	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6593A>G	1.37:g.144856892T>C	ENSP00000358360:p.Lys2198Arg	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	124	8	NM_014644	0	0	0	0	0	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	6.042|6.042	0.376140|0.376140	0.11466|0.11466	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530130	T;T;T;T;T|.	0.01430|.	4.9;5.03;5.06;4.99;5.01|.	4.52|4.52	-2.16|-2.16	0.07080|0.07080	.|.	.|.	.|.	.|.	.|.	T|T	0.12220|0.12220	0.0297|0.0297	L|L	0.33339|0.33339	1.005|1.005	0.09310|0.09310	N|N	1|1	B;B|.	0.13594|.	0.001;0.008|.	B;B|.	0.11329|.	0.003;0.006|.	T|T	0.33879|0.33879	-0.9851|-0.9851	8|5	.|.	.|.	.|.	.|.	5.6438|5.6438	0.17579|0.17579	0.0:0.2482:0.1388:0.613|0.0:0.2482:0.1388:0.613	.|.	2092;2198|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	R|G	2092;2198;2198;2283;2334|275	ENSP00000327209:K2092R;ENSP00000358360:K2198R;ENSP00000358363:K2198R;ENSP00000435654:K2283R;ENSP00000358366:K2334R|.	.|.	K|S	-|-	2|1	0|0	PDE4DIP|PDE4DIP	143568249|143568249	0.003000|0.003000	0.15002|0.15002	0.837000|0.837000	0.33122|0.33122	0.007000|0.007000	0.05969|0.05969	0.773000|0.773000	0.26661|0.26661	-0.611000|-0.611000	0.05709|0.05709	-0.475000|-0.475000	0.04921|0.04921	AAG|AGC	.		0.517	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144856892	T	C	144856892	3	2	116	1	0	0	0	0	1	0	0	0	11669	1609	56	3	467	3	PDE4DIP	1	144856892	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	117762563	144856892	104393729	4	10100											
SEC22B	9554	broad.mit.edu	37	chr1	145112418	145112418	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctctacattgacagttgtgCtcgaagaaacctaggctcca	11	10	9	11	1	1	2	0	1	1	1	3	3	2	2	2	1	3	4	2	1	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:145112418C>G	ENST00000453618.1	+	0	719							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)						ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											GACAGTTGTGCTCGAAGAAAC	0.418																																					.													.	.	0			.						.						155	139	144					1																	145112418		2068	4212	6280			9554	.			GTTGTGCTCGAAG	AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380				10700	protein-coding gene	gene with protein product		604029	"SEC22, vesicle trafficking protein (S. cerevisiae)-like 1", "SEC22 vesicle trafficking protein-like 1 (S. cerevisiae)", "SEC22 vesicle trafficking protein homolog B (S. cerevisiae)"	SEC22L1		9094723, 16354670	Standard	NM_004892		Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745		1.37:g.145112418C>G		Somatic	76	1		WXS	Illumina HiSeq	Phase_I	87	8	.	0	0	0	0	0	A8K1G0	Missense_Mutation	SNP	ENST00000453618.1	37																																																																																				.		0.418	SEC22B-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000038523.5	NM_004892		G	145112418	C	G	145112418	1	3	116	0	1	0	0	0	0	0	0	0	14021	797	28	4		4	SEC22B	1	145112418	RNA	SNP	C	TCGA-G7-6796-01A-11D-1961-08	255526	145112418	104138203	5	10101											
ADAR	103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154574720	154574720	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgatcttggtagatactcAgttcctggaaatgtgaggaa	11	12	11	7	0	2	3	1	2	1	1	3	5	3	5	2	3	1	2	2	3	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:154574720A>T	ENST00000368474.4	-	2	597	c.398T>A	c.(397-399)cTg>cAg	p.L133Q	ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000471068.1_5'UTR|ADAR_ENST00000292205.5_Missense_Mutation_p.L176Q	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	133					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GTAGATACTCAGTTCCTGGAA	0.517																																					p.L133Q		.											.	ADAR-157	0			c.T398A						.						65	67	66					1																	154574720		2203	4300	6503	SO:0001583	missense	103	exon2			ATACTCAGTTCCT	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"interferon-induced protein 4"	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.398T>A	1.37:g.154574720A>T	ENSP00000357459:p.Leu133Gln	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	102	25	NM_001111	0	0	3	4	1	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.736498	0.69304	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.79749	-1.3;-1.3;-1.3	4.47	4.47	0.54385	Winged helix-turn-helix transcription repressor DNA-binding (1);Double-stranded RNA-specific adenosine deaminase (DRADA) (2);	0.910334	0.09504	N	0.793175	D	0.86008	0.5830	M	0.63843	1.955	0.53688	D	0.999979	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.85130	0.972;0.992;0.997	D	0.83933	0.0307	10	0.87932	D	0	-11.1093	13.8697	0.63610	1.0:0.0:0.0:0.0	.	133;133;133	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	Q	176;133;128	ENSP00000292205:L176Q;ENSP00000357459:L133Q;ENSP00000431794:L128Q	ENSP00000292205:L176Q	L	-	2	0	ADAR	152841344	1.000000	0.71417	0.166000	0.22797	0.666000	0.39218	6.906000	0.75719	1.992000	0.58205	0.402000	0.26972	CTG	.		0.517	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		T	154574720	A	T	154574720	3	4	116	1	0	0	0	0	1	0	0	0	281	188	7	5	3338	5	ADAR	1	154574720	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	9462302	154574720	94675901	6	10102											
FCRL4	83417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	157559028	157559028	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcgcacagggttacttcgTggggagccccgggcctggca	7	6	16	12	3	0	0	0	0	0	0	1	1	0	1	3	5	3	3	3	5	2	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:157559028T>C	ENST00000271532.1	-	3	408	c.273A>G	c.(271-273)ccA>ccG	p.P91P	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	91	Ig-like C2-type 1.				immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				GGTTACTTCGTGGGGAGCCCC	0.498																																					p.P91P		.											.	FCRL4-229	0			c.A273G						.						74	79	77					1																	157559028		2203	4300	6503	SO:0001819	synonymous_variant	83417	exon3			ACTTCGTGGGGAG	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.273A>G	1.37:g.157559028T>C		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	165	32	NM_031282	0	0	0	0	0	Q96PJ3|Q96RE0	Silent	SNP	ENST00000271532.1	37	CCDS1166.1																																																																																			.		0.498	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282		C	157559028	T	C	157559028	2	2	116	1	0	0	0	0	0	0	0	1	5816	1683	59	3		3	FCRL4	1	157559028	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08	2984308	157559028	91691593	7	10103											
MPZL1	9019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	167745333	167745333	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagagtttgtcaccagttaAgcaggctcctcggaagtccc	10	9	11	11	1	1	1	1	0	0	1	4	3	3	2	3	2	1	4	3	2	2	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:167745333A>C	ENST00000359523.2	+	5	840	c.638A>C	c.(637-639)aAg>aCg	p.K213T	MPZL1_ENST00000392121.3_Intron|MPZL1_ENST00000403379.3_3'UTR|MPZL1_ENST00000474859.1_Intron	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	213					cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					TCACCAGTTAAGCAGGCTCCT	0.413																																					p.K213T		.											.	MPZL1-516	0			c.A638C						.						76	74	75					1																	167745333		2203	4300	6503	SO:0001583	missense	9019	exon5			CAGTTAAGCAGGC	AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965		"Immunoglobulin superfamily / V-set domain containing"	7226	protein-coding gene	gene with protein product		604376				9792637	Standard	NM_003953		Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000359523.2:c.638A>C	1.37:g.167745333A>C	ENSP00000352513:p.Lys213Thr	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	93	12	NM_003953	0	0	6	16	10	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Missense_Mutation	SNP	ENST00000359523.2	37	CCDS1264.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313200	0.81358	.	.	ENSG00000197965	ENST00000359523	D	0.96365	-3.99	5.28	5.28	0.74379	.	.	.	.	.	D	0.95370	0.8497	L	0.29908	0.895	0.33196	D	0.551469	D	0.71674	0.998	D	0.78314	0.991	D	0.94904	0.8059	8	0.33141	T	0.24	.	14.4968	0.67694	1.0:0.0:0.0:0.0	.	213	O95297	MPZL1_HUMAN	T	213	ENSP00000352513:K213T	ENSP00000352513:K213T	K	+	2	0	MPZL1	166011957	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.562000	0.53777	2.307000	0.77673	0.528000	0.53228	AAG	.		0.413	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083655.2	NM_024569		C	167745333	A	C	167745333	3	2	116	1	0	0	0	0	1	0	0	0	9774	72	3	5	656	5	MPZL1	1	167745333	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	10186305	167745333	81505288	8	10104											
CACYBP	27101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	174979129	174979129	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctaaagaaaatttatgaaGatggagacgatgatatgaag	18	11	10	2	1	1	6	0	3	1	3	1	8	1	6	0	1	0	0	0	1	8	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:174979129G>T	ENST00000367679.2	+	6	1049	c.601G>T	c.(601-603)Gat>Tat	p.D201Y	CACYBP_ENST00000405362.1_Missense_Mutation_p.D158Y|CACYBP_ENST00000367681.2_Missense_Mutation_p.D158Y|MRPS14_ENST00000498253.1_5'Flank	NM_014412.2	NP_055227.1	Q9HB71	CYBP_HUMAN	calcyclin binding protein	201	Interaction with S100A6. {ECO:0000250}.|Interaction with SKP1.|SGS. {ECO:0000255|PROSITE- ProRule:PRU00386}.				aging (GO:0007568)|cardiac muscle cell differentiation (GO:0055007)|cellular response to calcium ion (GO:0071277)|negative regulation of cell death (GO:0060548)|positive regulation of DNA replication (GO:0045740)|response to growth hormone (GO:0060416)	beta-catenin destruction complex (GO:0030877)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	11						AATTTATGAAGATGGAGACGA	0.383																																					p.D201Y		.											.	CACYBP-90	0			c.G601T						.						86	85	85					1																	174979129		2203	4300	6503	SO:0001583	missense	27101	exon6			TATGAAGATGGAG	BC022352	CCDS1315.1, CCDS30942.1	1q24-q25	2008-02-05			ENSG00000116161	ENSG00000116161			30423	protein-coding gene	gene with protein product		606186				11389839, 12421809	Standard	XM_005245092		Approved	SIP, S100A6BP	uc001gkj.1	Q9HB71	OTTHUMG00000034941	ENST00000367679.2:c.601G>T	1.37:g.174979129G>T	ENSP00000356652:p.Asp201Tyr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	68	17	NM_014412	0	0	36	61	25	B2ZWH2|B3KSF1|O60666|Q5R370|Q5R371	Missense_Mutation	SNP	ENST00000367679.2	37	CCDS1315.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891415	0.91889	.	.	ENSG00000116161	ENST00000367681;ENST00000450101;ENST00000367679;ENST00000405362	T;T	0.58060	0.36;0.36	5.89	5.89	0.94794	SGS (2);HSP20-like chaperone (1);	0.132069	0.64402	D	0.000002	T	0.68091	0.2963	M	0.79258	2.445	0.80722	D	1	P	0.48589	0.912	P	0.50791	0.65	T	0.71031	-0.4710	10	0.72032	D	0.01	-24.1569	20.2561	0.98419	0.0:0.0:1.0:0.0	.	201	Q9HB71	CYBP_HUMAN	Y	158;174;201;158	ENSP00000356654:D158Y;ENSP00000385771:D158Y	ENSP00000356652:D201Y	D	+	1	0	CACYBP	173245752	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.296000	0.96104	2.797000	0.96272	0.563000	0.77884	GAT	.		0.383	CACYBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084583.3	NM_014412		T	174979129	G	T	174979129	3	4	116	1	0	0	0	0	1	0	0	0	2570	942	33	4	623	4	CACYBP	1	174979129	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	7233796	174979129	74271492	9	10105											
RGS16	6004	ucsc.edu	37	chr1	182569597	182569597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaaagcatgtggctgtggCagtctgcaggttcatcctcg	8	11	12	10	1	3	0	2	0	1	0	5	0	4	0	1	3	2	5	1	3	1	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:182569597C>T	ENST00000367558.5	-	5	587	c.439G>A	c.(439-441)Gcc>Acc	p.A147T		NM_002928.3	NP_002919.3	O15492	RGS16_HUMAN	regulator of G-protein signaling 16	147	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			NS(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)	11						GTGGCTGTGGCAGTCTGCAGG	0.587																																					p.A147T													.	RGS16-227	0			c.G439A						.						143	111	121					1																	182569597		2203	4300	6503	SO:0001583	missense	6004	exon5			CTGTGGCAGTCTG	U70426	CCDS1348.1	1q25-q31	2008-02-05	2007-08-14		ENSG00000143333	ENSG00000143333		"Regulators of G-protein signaling"	9997	protein-coding gene	gene with protein product		602514	"regulator of G-protein signalling 16"			9469939	Standard	NM_002928		Approved	A28-RGS14, RGS-r	uc001gpl.4	O15492	OTTHUMG00000035212	ENST00000367558.5:c.439G>A	1.37:g.182569597C>T	ENSP00000356529:p.Ala147Thr	Somatic	130	0		WXS	Illumina HiSeq		126	1	NM_002928	0	0	4	4	0	B2R4M4|Q5VYN9|Q99701	Missense_Mutation	SNP	ENST00000367558.5	37	CCDS1348.1	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181561	0.21787	.	.	ENSG00000143333	ENST00000367558	T	0.29655	1.56	5.38	3.51	0.40186	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.156624	0.56097	N	0.000025	T	0.34716	0.0907	M	0.75615	2.305	0.19300	N	0.99998	B	0.33940	0.433	B	0.38156	0.266	T	0.17471	-1.0368	10	0.32370	T	0.25	.	9.3651	0.38219	0.0:0.6543:0.2723:0.0734	.	147	O15492	RGS16_HUMAN	T	147	ENSP00000356529:A147T	ENSP00000356529:A147T	A	-	1	0	RGS16	180836220	0.000000	0.05858	0.022000	0.16811	0.002000	0.02628	0.321000	0.19558	0.655000	0.30866	0.555000	0.69702	GCC	.		0.587	RGS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085188.1	NM_002928		T	182569597	C	T	182569597	3	4	116	1	0	0	0	0	1	0	0	0	13330	710	25	2	173	2	RGS16	1	182569597	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	7590468	182569597	66681024	10	10106											
NAV1	89796	hgsc.bcm.edu	37	chr1	201762968	201762968	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctggtgaatatgacatccCgcctgcgacacctggcagag	9	7	12	13	2	0	3	0	2	0	1	1	4	1	3	4	2	1	1	4	2	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:201762968C>G	ENST00000367296.4	+	14	3790	c.3370C>G	c.(3370-3372)Cgc>Ggc	p.R1124G	NAV1_ENST00000367295.1_Missense_Mutation_p.R733G|NAV1_ENST00000367300.3_Missense_Mutation_p.R1067G|NAV1_ENST00000367302.1_Missense_Mutation_p.R1080G|NAV1_ENST00000469130.1_3'UTR|NAV1_ENST00000367297.4_Missense_Mutation_p.R1116G|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000295624.6_Missense_Mutation_p.R1124G	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1124					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						TATGACATCCCGCCTGCGACA	0.582																																					p.R1124G		.											.	NAV1-228	0			c.C3370G						.						70	66	67					1																	201762968		2203	4300	6503	SO:0001583	missense	89796	exon14			ACATCCCGCCTGC	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"neuron navigator-1", "pore membrane and/or filament interacting like protein 3"	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3370C>G	1.37:g.201762968C>G	ENSP00000356265:p.Arg1124Gly	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	99	5	NM_020443	0	0	0	0	0	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.5|27.5	4.841219|4.841219	0.91197|0.91197	.|.	.|.	ENSG00000134369|ENSG00000134369	ENST00000430015|ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000391966;ENST00000367295	.|D;D;D;D;D;D	.|0.94497	.|-3.44;-3.44;-3.44;-3.44;-3.44;-3.44	4.95|4.95	4.95|4.95	0.65309|0.65309	.|.	.|0.058638	.|0.64402	.|D	.|0.000002	D|D	0.97037|0.97037	0.9032|0.9032	M|M	0.73598|0.73598	2.24|2.24	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D;D;D;D	.|0.89917	.|1.0;0.997;0.996;0.998;1.0	.|D;D;D;D;D	.|0.87578	.|0.998;0.932;0.948;0.991;0.998	D|D	0.97499|0.97499	1.0059|1.0059	5|10	.|0.72032	.|D	.|0.01	-24.902|-24.902	17.9873|17.9873	0.89159|0.89159	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1116;733;1124;624;1124	.|Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.|.;.;NAV1_HUMAN;.;.	R|G	673|1080;1124;1124;1116;1067;624;733	.|ENSP00000356271:R1080G;ENSP00000356265:R1124G;ENSP00000295624:R1124G;ENSP00000356266:R1116G;ENSP00000356269:R1067G;ENSP00000356264:R733G	.|ENSP00000295624:R1124G	P|R	+|+	2|1	0|0	NAV1|NAV1	200029591|200029591	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.939000|0.939000	0.58152|0.58152	5.512000|5.512000	0.67030|0.67030	2.557000|2.557000	0.86248|0.86248	0.462000|0.462000	0.41574|0.41574	CCG|CGC	.		0.582	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		G	201762968	C	G	201762968	3	3	116	1	0	0	0	0	1	0	0	0	10208	652	23	4	3481	4	NAV1	1	201762968	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	19193371	201762968	47487653	11	10107											
TRAF5	7188	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	211545951	211545952	+	Frame_Shift_Ins	INS	-	-	C																															gtccccgctttgtggctcatINStctgttttggagaatgccaa																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:211545951_211545952insC	ENST00000261464.5	+	11	1635_1636	c.1581_1582insC	c.(1582-1584)tctfs	p.S528fs	TRAF5_ENST00000367004.3_Frame_Shift_Ins_p.S528fs|TRAF5_ENST00000336184.2_Frame_Shift_Ins_p.S528fs|TRAF5_ENST00000427925.2_Frame_Shift_Ins_p.S422fs	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	528	Interaction with EIF2AK2/PKR.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TTGTGGCTCATTCTGTTTTGGA	0.465																																					p.H527fs		.											.	TRAF5-661	0			c.1581_1582insC						.																																			SO:0001589	frameshift_variant	7188	exon11			.	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	Exception_encountered	1.37:g.211545951_211545952insC	ENSP00000261464:p.Ser528fs	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	118	20	NM_145759	0	0	0	0	0	B4DIS9|B4E0A2|Q6FHY1	Frame_Shift_Ins	INS	ENST00000261464.5	37	CCDS1497.1																																																																																			.		0.465	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		C	211545952	-	C	211545951	7	5	116	1	0	1	1	0	0	0	0	0	16477	1490	52	0	1619	0	TRAF5	1	211545951	Frame_Shift_Ins	INS	-	TCGA-G7-6796-01A-11D-1961-08	9782983	211545951	37704670	12	10108											
ABCA12	26154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	215865500	215865500	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctgggagttccttccagtTtgcaattcaatgattgctct	7	16	8	10	0	2	1	1	1	1	0	5	2	5	2	3	1	2	4	3	1	2	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:215865500T>G	ENST00000272895.7	-	22	3327	c.3108A>C	c.(3106-3108)caA>caC	p.Q1036H	ABCA12_ENST00000389661.4_Missense_Mutation_p.Q718H	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1036					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCCTTCCAGTTTGCAATTCAA	0.428																																					p.Q1036H	Ovarian(66;664 1488 5121 34295)	.											.	ABCA12-99	0			c.A3108C						.						125	130	128					2																	215865500		2203	4300	6503	SO:0001583	missense	26154	exon22			TCCAGTTTGCAAT	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"ATP binding cassette transporters / subfamily A"	14637	protein-coding gene	gene with protein product		607800	"ichthyosis congenita II, lamellar ichthyosis B"	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3108A>C	2.37:g.215865500T>G	ENSP00000272895:p.Gln1036His	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	183	41	NM_173076	0	0	0	0	0	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533445	0.45073	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.95656	-3.77;-3.77	5.73	2.68	0.31781	.	0.087482	0.49916	D	0.000121	D	0.92456	0.7605	L	0.43152	1.355	0.80722	D	1	B;B	0.32467	0.136;0.372	B;B	0.38156	0.152;0.266	D	0.89343	0.3655	10	0.66056	D	0.02	.	8.1984	0.31411	0.0:0.731:0.0:0.269	.	1036;718	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	H	1036;718	ENSP00000272895:Q1036H;ENSP00000374312:Q718H	ENSP00000272895:Q1036H	Q	-	3	2	ABCA12	215573745	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.506000	0.45433	0.612000	0.30071	0.454000	0.30748	CAA	.		0.428	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215865500	T	G	215865500	3	3	116	1	0	0	0	0	1	0	0	0	30	1838	64	5	4807	5	ABCA12	2	215865500	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08		215865500	27333873	13	10109											
C2orf62	375307	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219222364	219222364	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcagagagggaaatacCaggaaaaactcggcatgctg	15	5	14	7	1	0	1	0	0	0	1	1	4	0	3	1	4	4	3	1	4	4	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:219222364C>T	ENST00000289388.3	+	3	255	c.226C>T	c.(226-228)Cag>Tag	p.Q76*	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		76					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGGAAATACCAGGAAAAACT	0.552																																					p.Q76X		.											.	C2orf62-68	0			c.C226T						.						72	63	66					2																	219222364		2203	4300	6503	SO:0001587	stop_gained	375307	exon3			AAATACCAGGAAA																												ENST00000289388.3:c.226C>T	2.37:g.219222364C>T	ENSP00000289388:p.Gln76*	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	93	16	NM_198559	0	0	8	8	0		Nonsense_Mutation	SNP	ENST00000289388.3	37	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987633	0.35036	.	.	ENSG00000158428	ENST00000289388	.	.	.	4.56	-4.72	0.03269	.	1.478090	0.03845	N	0.271323	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.2458	4.8866	0.13706	0.2205:0.5606:0.0905:0.1283	.	.	.	.	X	76	.	ENSP00000289388:Q76X	Q	+	1	0	C2orf62	218930608	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.212000	0.17497	-0.542000	0.06249	-0.457000	0.05445	CAG	.		0.552	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219222364	C	T	219222364	4	4	116	1	0	0	0	0	0	1	0	0	2187	595	21	2	236	2	C2orf62	2	219222364	Nonsense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	3356864	219222364	23977009	14	10110											
ZNF142	7701	hgsc.bcm.edu;bcgsc.ca	37	chr2	219509115	219509115	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcctcaaggggtggctcAgtcacagactccagctctac	9	8	9	15	0	4	1	3	0	1	1	6	1	6	1	3	3	2	2	3	3	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:219509115A>T	ENST00000449707.1	-	8	2545	c.2124T>A	c.(2122-2124)acT>acA	p.T708T	ZNF142_ENST00000411696.2_Silent_p.T708T	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	708					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(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGGGTGGCTCAGTCACAGACT	0.612																																					p.T708T	Colon(170;867 1942 8995 15834 18053)	.											.	ZNF142-137	0			c.T2124A						.						42	44	43					2																	219509115		1959	4152	6111	SO:0001819	synonymous_variant	7701	exon8			TGGCTCAGTCACA	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.2124T>A	2.37:g.219509115A>T		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	65	12	NM_001105537	0	0	1	1	0	Q92510	Silent	SNP	ENST00000449707.1	37	CCDS42817.1																																																																																			.		0.612	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		T	219509115	A	T	219509115	2	4	116	1	0	0	0	0	0	0	0	1	17763	175	7	5		5	ZNF142	2	219509115	Silent	SNP	A	TCGA-G7-6796-01A-11D-1961-08	286751	219509115	23690258	15	10111											
SP100	6672	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	231338157	231338157	+	Splice_Site	DEL	T	T	-																															caagcatctgacatgatgggTaaggctaccctagggtcttg																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:231338157delT	ENST00000264052.5	+	16	1901		c.e16+2		SP100_ENST00000409112.1_Splice_Site|SP100_ENST00000340126.4_Splice_Site	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen						cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ACATGATGGGTAAGGCTACCC	0.468																																					.		.											.	SP100-94	0			c.1546+2T>-						.						164	152	156					2																	231338157		2203	4300	6503	SO:0001630	splice_region_variant	6672	exon16			.	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"Zinc fingers, PHD-type"	11206	protein-coding gene	gene with protein product		604585	"nuclear antigen Sp100"			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1546+2T>-	2.37:g.231338157delT		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	135	23	NM_003113	0	0	0	0	0	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Splice_Site	DEL	ENST00000264052.5	37	CCDS2477.1																																																																																			.		0.468	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	Intron	-	231338157	T	-	231338157	8	5	116	1	0	1	0	1	0	0	1	0	14992	1652	57	0	1610	0	SP100	2	231338157	Splice_Site	DEL	T	TCGA-G7-6796-01A-11D-1961-08	11829042	231338157	11861216	16	10112											
CPNE9	151835	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	9758767	9758768	+	Frame_Shift_Ins	INS	-	-	T																															gctgaacttcacagtagccaINSttgacttcacggcttccaat																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr3:9758767_9758768insT	ENST00000383832.3	+	15	1100_1101	c.910_911insT	c.(910-912)attfs	p.I304fs	CPNE9_ENST00000383831.3_Frame_Shift_Ins_p.I304fs	NM_153635.2	NP_705899.2	Q8IYJ1	CPNE9_HUMAN	copine family member IX	304	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16	Medulloblastoma(99;0.227)					CACAGTAGCCATTGACTTCACG	0.45																																					.		.											.	CPNE9-70	0			.						.																																			SO:0001589	frameshift_variant	151835	.			.		CCDS2574.2	3p25.3	2008-10-30			ENSG00000144550	ENSG00000144550			24336	protein-coding gene	gene with protein product						9430674	Standard	XM_006712990		Approved	KIAA4217	uc003bsd.3	Q8IYJ1	OTTHUMG00000128418	ENST00000383832.3:c.912dupT	3.37:g.9758769_9758769dupT	ENSP00000373343:p.Ile304fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	102	21	.	0	0	0	0	0	A1L430|A6NDX6|A8MSP8	Targeted_Region	INS	ENST00000383832.3	37	CCDS2574.2																																																																																			.		0.45	CPNE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250205.4	NM_001033755		T	9758768	-	T	9758767	7	5	116	1	0	1	1	0	0	0	0	0	3825	217	8	0	964	0	CPNE9	3	9758767	Frame_Shift_Ins	INS	-	TCGA-G7-6796-01A-11D-1961-08		9758767	188263663	17	10113											
SLC25A38	54977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	39431018	39431018	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaaggctttcctgtgtggCtccatcagtgggacctgctc	6	12	11	12	0	2	0	2	0	0	0	5	1	4	1	3	3	1	3	3	3	1	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr3:39431018C>T	ENST00000273158.4	+	2	479	c.102C>T	c.(100-102)ggC>ggT	p.G34G		NM_017875.2	NP_060345.2			solute carrier family 25, member 38									p.G34G(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCCTGTGTGGCTCCATCAGTG	0.522																																					p.G34G		.											.	SLC25A38-90	1	Substitution - coding silent(1)	large_intestine(1)	c.C102T						.						209	174	186					3																	39431018		2203	4300	6503	SO:0001819	synonymous_variant	54977	exon2			GTGTGGCTCCATC	BC013194	CCDS2685.1	3p22.1	2013-05-22			ENSG00000144659	ENSG00000144659		"Solute carriers"	26054	protein-coding gene	gene with protein product		610819				16949250	Standard	NM_017875		Approved	FLJ20551	uc003cjo.2	Q96DW6	OTTHUMG00000131289	ENST00000273158.4:c.102C>T	3.37:g.39431018C>T		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	116	27	NM_017875	0	0	9	12	3		Silent	SNP	ENST00000273158.4	37	CCDS2685.1																																																																																			.		0.522	SLC25A38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254057.3	NM_017875		T	39431018	C	T	39431018	2	4	116	1	0	0	0	0	0	0	0	1	14534	784	28	2		2	SLC25A38	3	39431018	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08	29672251	39431018	158591412	18	10114											
TNFSF10	8743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	172232704	172232704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgccagcaggggctgttcaTactctcttcgtcattggggt	5	14	12	10	1	3	0	2	0	1	0	5	0	3	0	1	4	3	3	1	4	1	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr3:172232704T>C	ENST00000241261.2	-	2	339	c.217A>G	c.(217-219)Atg>Gtg	p.M73V	TNFSF10_ENST00000420541.2_Missense_Mutation_p.M73V	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	73					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			GGGCTGTTCATACTCTCTTCG	0.502																																					p.M73V		.											.	TNFSF10-662	0			c.A217G						.						144	137	140					3																	172232704		2203	4300	6503	SO:0001583	missense	8743	exon2			TGTTCATACTCTC	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.217A>G	3.37:g.172232704T>C	ENSP00000241261:p.Met73Val	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	176	41	NM_003810	0	0	141	225	84	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	37	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.547137	0.00140	.	.	ENSG00000121858	ENST00000241261;ENST00000420541	D;T	0.86366	-2.11;1.59	5.61	-1.89	0.07689	.	0.989409	0.08265	N	0.972345	T	0.71804	0.3383	L	0.34521	1.04	0.09310	N	1	B;B	0.12630	0.006;0.001	B;B	0.11329	0.006;0.001	T	0.57136	-0.7863	10	0.05351	T	0.99	-3.1928	0.8408	0.01149	0.3634:0.1464:0.1187:0.3715	.	73;73	A1Y9B3;P50591	.;TNF10_HUMAN	V	73	ENSP00000241261:M73V;ENSP00000389931:M73V	ENSP00000241261:M73V	M	-	1	0	TNFSF10	173715398	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.552000	0.23376	-0.567000	0.06046	-0.256000	0.11100	ATG	.		0.502	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			C	172232704	T	C	172232704	3	2	116	1	0	0	0	0	1	0	0	0	16333	1406	49	3	644	3	TNFSF10	3	172232704	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	132801686	172232704	25789726	19	10115											
ACOX3	8310	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	8372681	8372681	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtccagaacaaagtcaggaGgagcgatcacgtctaccagg	14	5	12	10	2	3	1	2	0	1	1	4	4	4	3	2	3	3	0	2	3	3	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:8372681G>A	ENST00000356406.5	-	17	2014	c.1937C>T	c.(1936-1938)cCt>cTt	p.P646L	ACOX3_ENST00000515797.1_5'UTR|ACOX3_ENST00000413009.2_Silent_p.S623S|ACOX3_ENST00000503233.1_Missense_Mutation_p.P646L	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	646					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						AAAGTCAGGAGGAGCGATCAC	0.562																																					p.P646L		.											.	ACOX3-90	0			c.C1937T						.						120	104	109					4																	8372681		2203	4300	6503	SO:0001583	missense	8310	exon17			TCAGGAGGAGCGA	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1937C>T	4.37:g.8372681G>A	ENSP00000348775:p.Pro646Leu	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	59	12	NM_003501	0	0	4	16	12	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577015	0.86645	.	.	ENSG00000087008	ENST00000356406;ENST00000503233	T;T	0.38401	1.14;1.14	4.88	4.88	0.63580	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.069225	0.64402	N	0.000015	T	0.50718	0.1632	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.38628	-0.9652	9	0.11182	T	0.66	-18.1485	15.4924	0.75619	0.0:0.0:1.0:0.0	.	646	O15254	ACOX3_HUMAN	L	646	ENSP00000348775:P646L;ENSP00000421625:P646L	ENSP00000348775:P646L	P	-	2	0	ACOX3	8423581	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	6.945000	0.75947	2.226000	0.72624	0.549000	0.68633	CCT	.		0.562	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8372681	G	A	8372681	3	1	116	1	0	0	0	0	1	0	0	0	160	1000	35	2	173	2	ACOX3	4	8372681	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08		8372681	182781595	20	10116											
BOD1L	259282	broad.mit.edu	37	chr4	13616069	13616069	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttttgctcactgctttcctGttgaacatccttatttagca	7	19	5	10	0	1	1	1	1	0	0	3	1	3	1	2	0	4	4	2	0	3	7			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:13616069G>T	ENST00000040738.5	-	4	1060	c.925C>A	c.(925-927)Cag>Aag	p.Q309K		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	309						nucleus (GO:0005634)	DNA binding (GO:0003677)										CTGCTTTCCTGTTGAACATCC	0.353																																					p.Q309K													.	.	0			c.C925A						.						72	65	68					4																	13616069		2203	4300	6503	SO:0001583	missense	259282	exon4			TTTCCTGTTGAAC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.925C>A	4.37:g.13616069G>T	ENSP00000040738:p.Gln309Lys	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	34	7	NM_148894	0	0	0	1	1	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	17.96	3.515408	0.64634	.	.	ENSG00000038219	ENST00000040738	T	0.08720	3.06	5.75	5.75	0.90469	.	0.169210	0.28515	N	0.015067	T	0.16385	0.0394	M	0.64997	1.995	0.29521	N	0.853525	D	0.56521	0.976	P	0.50109	0.631	T	0.03761	-1.1006	10	0.32370	T	0.25	-5.5179	14.3952	0.67005	0.0:0.0:0.852:0.148	.	309	Q8NFC6	BOD1L_HUMAN	K	309	ENSP00000040738:Q309K	ENSP00000040738:Q309K	Q	-	1	0	BOD1L	13225167	0.980000	0.34600	0.997000	0.53966	0.941000	0.58515	3.862000	0.56009	2.709000	0.92574	0.591000	0.81541	CAG	.		0.353	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13616069	G	T	13616069	3	4	116	1	0	0	0	0	1	0	0	0	1484	1386	48	4	8322	4	BOD1L	4	13616069	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	5243388	13616069	177538207	21	10117											
CENPC1	1060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	68385012	68385012	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcaaaagtgtaagtctctctCttttgggcactagatggaat	11	14	9	7	0	3	1	1	0	2	1	5	2	3	2	0	2	0	2	0	2	5	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:68385012C>G	ENST00000273853.6	-	6	790	c.540G>C	c.(538-540)aaG>aaC	p.K180N		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	180					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										AAGTCTCTCTCTTTTGGGCAC	0.323																																					p.K180N		.											.	CENPC1-205	0			c.G540C						.						88	83	84					4																	68385012		1809	4078	5887	SO:0001583	missense	1060	exon6			CTCTCTCTTTTGG	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.540G>C	4.37:g.68385012C>G	ENSP00000273853:p.Lys180Asn	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	138	36	NM_001812	0	0	0	0	0	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	37	CCDS47063.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463886	0.26335	.	.	ENSG00000145241	ENST00000273853	.	.	.	4.75	0.447	0.16608	.	0.626565	0.15039	N	0.283991	T	0.39226	0.1070	L	0.59436	1.845	0.28032	N	0.9341	D;D	0.65815	0.995;0.995	P;P	0.53954	0.738;0.738	T	0.30592	-0.9973	9	0.72032	D	0.01	-2.2885	2.5395	0.04722	0.3496:0.401:0.1533:0.0961	.	180;180	Q8IW27;Q03188	.;CENPC_HUMAN	N	180	.	ENSP00000273853:K180N	K	-	3	2	CENPC1	68067607	0.030000	0.19436	0.952000	0.39060	0.104000	0.19210	-0.627000	0.05521	0.173000	0.19788	-0.293000	0.09583	AAG	.		0.323	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			G	68385012	C	G	68385012	3	3	116	1	0	0	0	0	1	0	0	0	3235	912	32	4	2347	4	CENPC1	4	68385012	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	54768943	68385012	122769264	22	10118											
RNF150	57484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	141832440	141832440	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcgctggcacctgtgatctgGttggtgggtggacctcccag	4	11	15	11	1	1	1	0	1	1	0	3	2	2	2	3	5	0	3	3	5	0	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:141832440G>C	ENST00000515673.2	-	6	1089	c.1056C>G	c.(1054-1056)aaC>aaG	p.N352K	RNF150_ENST00000379512.2_Missense_Mutation_p.N211K|RNF150_ENST00000507500.1_Missense_Mutation_p.N352K|RNF150_ENST00000306799.3_Missense_Mutation_p.N310K|RNF150_ENST00000420921.2_Missense_Mutation_p.N211K			Q9ULK6	RN150_HUMAN	ring finger protein 150	352						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					CTGTGATCTGGTTGGTGGGTG	0.557																																					p.N352K		.											.	RNF150-227	0			c.C1056G						.						100	93	95					4																	141832440		2203	4300	6503	SO:0001583	missense	57484	exon6			GATCTGGTTGGTG	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.1056C>G	4.37:g.141832440G>C	ENSP00000425840:p.Asn352Lys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	111	14	NM_020724	0	0	0	0	0	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	37	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474491	0.63737	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000306799;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T;T	0.15139	2.45;2.45;2.49;3.47;3.48;2.51	5.74	0.749	0.18381	.	0.472179	0.23614	N	0.046304	T	0.16257	0.0391	L	0.29908	0.895	0.51767	D	0.999932	P;B;B	0.40970	0.734;0.294;0.415	P;B;B	0.47528	0.549;0.299;0.334	T	0.03103	-1.1072	10	0.46703	T	0.11	.	9.3149	0.37928	0.5802:0.0:0.4198:0.0	.	310;352;352	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	K	211;211;310;352;352;183	ENSP00000368827:N211K;ENSP00000394581:N211K;ENSP00000304321:N310K;ENSP00000425840:N352K;ENSP00000425568:N352K;ENSP00000425947:N183K	ENSP00000304321:N310K	N	-	3	2	RNF150	142051890	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.973000	0.29422	0.180000	0.19960	0.655000	0.94253	AAC	.		0.557	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		C	141832440	G	C	141832440	3	2	116	1	0	0	0	0	1	0	0	0	13483	1252	44	4	268	4	RNF150	4	141832440	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	73447428	141832440	49321836	23	10119											
DNAH5	1767	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	13928214	13928214	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagatacctgtttctgctTcctccacatcttgatagtaa	9	16	5	11	0	3	2	1	1	2	1	5	2	5	2	3	0	2	3	3	0	3	7			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr5:13928214T>A	ENST00000265104.4	-	3	370	c.266A>T	c.(265-267)gAa>gTa	p.E89V		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	89	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGTTTCTGCTTCCTCCACATC	0.378									Kartagener syndrome																												p.E89V													.	DNAH5-182	0			c.A266T						.						114	112	113					5																	13928214		2203	4300	6503	SO:0001583	missense	1767	exon3	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TCTGCTTCCTCCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.266A>T	5.37:g.13928214T>A	ENSP00000265104:p.Glu89Val	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	102	18	NM_001369	0	0	0	0	0	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	11.28	1.592955	0.28357	.	.	ENSG00000039139	ENST00000265104	T	0.24723	1.84	5.32	1.09	0.20402	.	0.308380	0.34652	N	0.003789	T	0.04861	0.0131	N	0.00413	-1.525	0.25592	N	0.986686	B	0.02656	0.0	B	0.01281	0.0	T	0.29274	-1.0017	10	0.28530	T	0.3	.	1.1003	0.01682	0.3742:0.3113:0.1656:0.1488	.	89	Q8TE73	DYH5_HUMAN	V	89	ENSP00000265104:E89V	ENSP00000265104:E89V	E	-	2	0	DNAH5	13981214	0.142000	0.22610	0.967000	0.41034	0.969000	0.65631	1.040000	0.30278	0.391000	0.25143	-0.302000	0.09304	GAA	.		0.378	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13928214	T	A	13928214	3	1	116	1	0	0	0	0	1	0	0	0	4615	1783	62	5	13916	5	DNAH5	5	13928214	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08		13928214	166987046	24	10120											
PCDHGA8	9708	broad.mit.edu	37	chr5	140772927	140772927	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accacttctccctggacgtgCagactggagacaatggagcc	10	7	11	13	1	1	2	0	0	1	2	2	5	1	4	3	3	2	1	3	3	1	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr5:140772927C>T	ENST00000398604.2	+	1	547	c.547C>T	c.(547-549)Cag>Tag	p.Q183*	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	183	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGACGTGCAGACTGGAGA	0.612																																					p.Q183X													.	.	0			c.C547T						.						52	58	56					5																	140772927		2147	4282	6429	SO:0001587	stop_gained	9708	exon1			GACGTGCAGACTG	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"Cadherins / Protocadherins : Clustered"	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.547C>T	5.37:g.140772927C>T	ENSP00000381605:p.Gln183*	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	74	8	NM_014004	0	0	0	0	0	A7MCZ4|O15039	Nonsense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	17.30	3.354337	0.61293	.	.	ENSG00000253767	ENST00000398604	.	.	.	5.41	5.41	0.78517	.	0.000000	0.30118	U	0.010368	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	13.7424	0.62855	0.1539:0.8461:0.0:0.0	.	.	.	.	X	183	.	ENSP00000381605:Q183X	Q	+	1	0	PCDHGA8	140753111	0.000000	0.05858	0.859000	0.33776	0.662000	0.39071	-0.042000	0.12063	2.552000	0.86080	0.655000	0.94253	CAG	.		0.612	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		T	140772927	C	T	140772927	4	4	116	1	0	0	0	0	0	1	0	0	11586	711	25	2	549	2	PCDHGA8	5	140772927	Nonsense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	126844713	140772927	40142333	25	10121											
LRRC16A	55604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	25600730	25600730	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggcagtcagaagtccacCtgtggactgtcccaggaagg	10	6	15	10	0	1	1	1	0	0	1	3	3	3	3	3	5	0	1	3	5	2	0			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:25600730C>A	ENST00000329474.6	+	33	3676	c.3308C>A	c.(3307-3309)cCt>cAt	p.P1103H		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1103					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AGAAGTCCACCTGTGGACTGT	0.488																																					p.P1103H		.											.	LRRC16A-137	0			c.C3308A						.						64	64	64					6																	25600730		1925	4128	6053	SO:0001583	missense	55604	exon33			GTCCACCTGTGGA	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"	609593	"leucine rich repeat containing 16"	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.3308C>A	6.37:g.25600730C>A	ENSP00000331983:p.Pro1103His	Somatic	113	2		WXS	Illumina HiSeq	Phase_I	85	25	NM_001173977	0	0	2	3	1	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.939309	0.34189	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.41758	0.99	5.2	4.33	0.51752	.	0.466121	0.23528	N	0.047208	T	0.26593	0.0650	L	0.29908	0.895	0.80722	D	1	P;P;P	0.50272	0.621;0.933;0.917	P;B;P	0.48166	0.471;0.315;0.569	T	0.06373	-1.0830	10	0.56958	D	0.05	-1.9805	13.6423	0.62257	0.0:0.925:0.0:0.075	.	1103;1103;1103	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	H	1103	ENSP00000331983:P1103H	ENSP00000331983:P1103H	P	+	2	0	LRRC16A	25708709	0.971000	0.33674	0.029000	0.17559	0.016000	0.09150	2.953000	0.49105	1.165000	0.42670	0.455000	0.32223	CCT	.		0.488	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		A	25600730	C	A	25600730	3	1	116	1	0	0	0	0	1	0	0	0	8996	681	24	4	3438	4	LRRC16A	6	25600730	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		25600730	145514337	26	10122											
HLA-F	3134	ucsc.edu	37	chr6	29692860	29692860	+	Silent	SNP	C	C	T																															atctctgaccatgaggccacCctgaggtgctgggccctggg																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:29692860C>T	ENST00000376861.1	+	5	1047	c.663C>T	c.(661-663)acC>acT	p.T221T	HLA-F_ENST00000434407.2_Intron|HLA-F_ENST00000334668.4_Silent_p.T221T|HLA-F_ENST00000440587.2_Silent_p.T103T|HLA-F_ENST00000259951.7_Silent_p.T221T			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	221	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)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|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)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						ATGAGGCCACCCTGAGGTGCT	0.587																																					p.T221T													.	HLA-F-22	0			c.C663T						.						55	54	54					6																	29692860		2203	4300	6503	SO:0001819	synonymous_variant	3134	exon4			GGCCACCCTGAGG	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.663C>T	6.37:g.29692860C>T		Somatic	87	0		WXS	Illumina HiSeq		70	1	NM_001098479	6	3	6913	6928	6	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	9.704	1.155158	0.21371	.	.	ENSG00000204642	ENST00000429294	.	.	.	1.92	1.92	0.25849	.	.	.	.	.	T	0.41673	0.1169	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33471	-0.9867	4	.	.	.	.	7.2321	0.26049	0.0:1.0:0.0:0.0	.	.	.	.	L	100	.	.	P	+	2	0	HLA-F	29800839	0.995000	0.38212	0.970000	0.41538	0.982000	0.71751	1.737000	0.38197	1.046000	0.40249	0.436000	0.28706	CCC	.		0.587	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		T	29692860	C	T	29692860	2	4	116	1	0	0	0	0	0	0	0	1	7232	610	22	2		2	HLA-F	6	29692860	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08	4092130	29692860	141422207	27	10123	103	2									
HLA-F	3134	ucsc.edu	37	chr6	29692866	29692866	+	Silent	SNP	G	G	A																															gaccatgaggccaccctgagGtgctgggccctgggcttcta																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:29692866G>A	ENST00000376861.1	+	5	1053	c.669G>A	c.(667-669)agG>agA	p.R223R	HLA-F_ENST00000434407.2_Intron|HLA-F_ENST00000334668.4_Silent_p.R223R|HLA-F_ENST00000440587.2_Silent_p.R105R|HLA-F_ENST00000259951.7_Silent_p.R223R			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	223	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)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|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)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						CCACCCTGAGGTGCTGGGCCC	0.597																																					p.R223R													.	HLA-F-22	0			c.G669A						.						54	53	53					6																	29692866		2203	4300	6503	SO:0001819	synonymous_variant	3134	exon4			CCTGAGGTGCTGG	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.669G>A	6.37:g.29692866G>A		Somatic	89	0		WXS	Illumina HiSeq		70	1	NM_001098479	4	4	6368	6379	3	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	10.18	1.278060	0.23307	.	.	ENSG00000204642	ENST00000429294	.	.	.	1.92	1.92	0.25849	.	.	.	.	.	T	0.41673	0.1169	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33471	-0.9867	4	.	.	.	.	7.2321	0.26049	0.0:0.0:1.0:0.0	.	.	.	.	D	102	.	.	G	+	2	0	HLA-F	29800845	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.835000	0.39181	1.046000	0.40249	0.436000	0.28706	GGT	.		0.597	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		A	29692866	G	A	29692866	2	1	116	1	0	0	0	0	0	0	0	1	7232	1252	44	2		2	HLA-F	6	29692866	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08	6	29692866	141422201	28	10124	103	2									
DNAH8	1769	broad.mit.edu;bcgsc.ca	37	chr6	38843585	38843585	+	Frame_Shift_Del	DEL	G	G	-																															tcaaatcaaaccatgtatgaGttttatgttactgattatgg																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:38843585delG	ENST00000359357.3	+	51	7442	c.7188delG	c.(7186-7188)gagfs	p.E2396fs	DNAH8_ENST00000449981.2_Frame_Shift_Del_p.E2613fs|DNAH8_ENST00000441566.1_Frame_Shift_Del_p.E2360fs			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2396					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CCATGTATGAGTTTTATGTTA	0.338																																					p.E2613fs													.	DNAH8-615	0			c.7839delG						.						82	82	82					6																	38843585		2203	4300	6503	SO:0001589	frameshift_variant	1769	exon53			GTATGAGTTTTAT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7188delG	6.37:g.38843585delG	ENSP00000352312:p.Glu2396fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	48	7	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Frame_Shift_Del	DEL	ENST00000359357.3	37																																																																																				.		0.338	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		-	38843585	G	-	38843585	7	5	116	1	0	1	0	1	0	0	0	0	4618	1020	36	0	7382	0	DNAH8	6	38843585	Frame_Shift_Del	DEL	G	TCGA-G7-6796-01A-11D-1961-08	9150719	38843585	132271482	29	10125											
KLC4	89953	broad.mit.edu;ucsc.edu	37	chr6	43042368	43042368	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtctgtttcaggtctcccgGggcctcagtgccagcaccat	5	11	11	14	1	4	0	2	0	2	0	5	0	4	0	4	3	2	2	4	3	0	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:43042368G>T	ENST00000394056.2	+	17	2313	c.1818G>T	c.(1816-1818)cgG>cgT	p.R606R	RP11-387M24.5_ENST00000606123.1_RNA|PTK7_ENST00000481273.1_5'Flank|PTK7_ENST00000345201.2_5'Flank|KLC4_ENST00000453940.2_Silent_p.R529R|PTK7_ENST00000230419.4_5'Flank|PTK7_ENST00000352931.2_5'Flank|KLC4_ENST00000347162.5_Silent_p.R606R|KLC4_ENST00000259708.3_Silent_p.R624R|KLC4_ENST00000394058.1_Silent_p.R606R|PTK7_ENST00000476760.1_5'Flank|KLC4_ENST00000479388.1_Silent_p.R606R|PTK7_ENST00000471863.1_5'Flank|PTK7_ENST00000349241.2_5'Flank			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	606						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			AGGTCTCCCGGGGCCTCAGTG	0.607																																					p.R624R													.	KLC4-94	0			c.G1872T						.						117	103	108					6																	43042368		2203	4300	6503	SO:0001819	synonymous_variant	89953	exon16			CTCCCGGGGCCTC	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"Tetratricopeptide (TTC) repeat domain containing"	21624	protein-coding gene	gene with protein product			"kinesin-like 8"	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1818G>T	6.37:g.43042368G>T		Somatic	108	2		WXS	Illumina HiSeq	Phase_I	80	10	NM_201523	0	0	0	0	0	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Silent	SNP	ENST00000394056.2	37	CCDS4883.1																																																																																			.		0.607	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		T	43042368	G	T	43042368	2	4	116	1	0	0	0	0	0	0	0	1	8357	1219	43	4		4	KLC4	6	43042368	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08	4198783	43042368	128072699	30	10126											
LMBRD1	55788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	70462182	70462182	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtatcatcatcatcctttTcttcataatagaagtagaca	14	15	4	8	0	5	2	4	0	1	2	6	2	6	2	1	0	0	2	1	0	6	8			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:70462182T>C	ENST00000370577.3	-	4	603	c.374A>G	c.(373-375)gAa>gGa	p.E125G	LMBRD1_ENST00000370570.1_Missense_Mutation_p.E52G	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	125					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						ATCATCCTTTTCTTCATAATA	0.294																																					p.E125G		.											.	LMBRD1-91	0			c.A374G						.						54	56	56					6																	70462182		2197	4278	6475	SO:0001583	missense	55788	exon4			TCCTTTTCTTCAT	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.374A>G	6.37:g.70462182T>C	ENSP00000359609:p.Glu125Gly	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	77	16	NM_018368	0	0	3	6	3	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102734	0.56183	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.26067	1.76;1.76	5.33	4.15	0.48705	LMBR1-like membrane protein (1);	0.051951	0.85682	D	0.000000	T	0.19805	0.0476	M	0.85462	2.755	0.58432	D	0.999998	B	0.18968	0.032	B	0.22880	0.042	T	0.09487	-1.0672	10	0.39692	T	0.17	-12.1431	10.4775	0.44674	0.0:0.0797:0.0:0.9203	.	125	Q9NUN5	LMBD1_HUMAN	G	125;52	ENSP00000359609:E125G;ENSP00000359602:E52G	ENSP00000359602:E52G	E	-	2	0	LMBRD1	70518903	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.495000	0.66912	2.022000	0.59522	0.455000	0.32223	GAA	.		0.294	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		C	70462182	T	C	70462182	3	2	116	1	0	0	0	0	1	0	0	0	8865	1783	62	3	1300	3	LMBRD1	6	70462182	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	27419814	70462182	100652885	31	10127											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152673335	152673335	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtgttctttccggacagTgctggtcagttccttcaact	6	15	9	11	1	3	0	2	0	1	0	5	1	5	1	2	2	2	3	2	2	1	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:152673335T>C	ENST00000367255.5	-	70	12008	c.11407A>G	c.(11407-11409)Act>Gct	p.T3803A	SYNE1_ENST00000341594.5_Missense_Mutation_p.T3774A|SYNE1_ENST00000265368.4_Missense_Mutation_p.T3803A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T3788A|SYNE1_ENST00000448038.1_Missense_Mutation_p.T3788A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3803					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCCGGACAGTGCTGGTCAGT	0.448										HNSCC(10;0.0054)																											p.T3803A		.											.	SYNE1-607	0			c.A11407G						.						251	230	237					6																	152673335		2203	4300	6503	SO:0001583	missense	23345	exon70			GGACAGTGCTGGT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.11407A>G	6.37:g.152673335T>C	ENSP00000356224:p.Thr3803Ala	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	261	44	NM_182961	0	0	0	0	0	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	9.518	1.107572	0.20714	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.34072	1.45;1.45;1.45;1.45;1.38	6.04	2.28	0.28536	.	0.339507	0.25194	N	0.032438	T	0.07638	0.0192	L	0.43152	1.355	0.09310	N	0.999998	B;B;B;B	0.09022	0.002;0.002;0.002;0.001	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.39603	-0.9606	10	0.08837	T	0.75	.	4.3779	0.11279	0.2094:0.2204:0.0:0.5702	.	3803;3803;3803;3788	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	A	3803;3788;3803;3788;3774	ENSP00000356224:T3803A;ENSP00000396024:T3788A;ENSP00000265368:T3803A;ENSP00000390975:T3788A;ENSP00000341887:T3774A	ENSP00000265368:T3803A	T	-	1	0	SYNE1	152715028	0.076000	0.21285	0.602000	0.28890	0.876000	0.50452	0.615000	0.24329	0.155000	0.19261	0.460000	0.39030	ACT	.		0.448	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152673335	T	C	152673335	3	2	116	1	0	0	0	0	1	0	0	0	15477	1696	59	3	15367	3	SYNE1	6	152673335	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	82211153	152673335	18441732	32	10128											
C7orf42	55069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	66410208	66410208	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattcccgcaacgtcacccaTctgtactcaaccatcttagg	10	11	5	15	2	4	0	2	0	2	0	5	0	5	0	3	1	3	2	3	1	5	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:66410208T>C	ENST00000341567.4	+	3	660	c.405T>C	c.(403-405)caT>caC	p.H135H		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	135						integral component of membrane (GO:0016021)											ACGTCACCCATCTGTACTCAA	0.527																																					p.H135H		.											.	.	0			c.T405C						.						107	105	106					7																	66410208		2203	4300	6503	SO:0001819	synonymous_variant	55069	exon3			CACCCATCTGTAC		CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 42"	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.405T>C	7.37:g.66410208T>C		Somatic	244	0		WXS	Illumina HiSeq	Phase_I	247	43	NM_017994	0	0	11	22	11	Q53H07|Q96FR2	Silent	SNP	ENST00000341567.4	37	CCDS5536.1																																																																																			.		0.527	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		C	66410208	T	C	66410208	2	2	116	1	0	0	0	0	0	0	0	1	2398	1432	50	3		3	C7orf42	7	66410208	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08		66410208	92728455	33	10129											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111387432	111387432	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtctgacactgactaatcAgagtcttcagctgctgattc	9	14	8	10	0	4	4	2	3	2	1	5	4	4	4	0	0	2	2	0	0	1	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:111387432A>G	ENST00000437633.1	-	42	4713	c.4457T>C	c.(4456-4458)cTg>cCg	p.L1486P	DOCK4_ENST00000428084.1_Missense_Mutation_p.L1495P|DOCK4_ENST00000494651.2_Missense_Mutation_p.L369P	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1486	DHR-2.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CTGACTAATCAGAGTCTTCAG	0.388																																					p.L1486P		.											.	DOCK4-26	0			c.T4457C						.						92	90	91					7																	111387432		1929	4134	6063	SO:0001583	missense	9732	exon42			CTAATCAGAGTCT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4457T>C	7.37:g.111387432A>G	ENSP00000404179:p.Leu1486Pro	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_014705	0	0	0	0	0	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.7|22.7	4.330553|4.330553	0.81690|0.81690	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288|ENST00000423057;ENST00000445943	T;T;T|.	0.19669|.	2.13;2.13;2.13|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.143240|.	0.48767|.	D|.	0.000170|.	T|.	0.80597|.	0.4653|.	M|M	0.89095|0.89095	3.005|3.005	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.999;0.997;1.0;1.0;0.998|.	D|.	0.84237|.	0.0470|.	10|.	0.87932|.	D|.	0|.	.|.	15.3585|15.3585	0.74448|0.74448	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	393;369;1531;1486;1495|.	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;.;DOCK4_HUMAN;.|.	P|R	1474;1495;369;1486;1483|947;1519	ENSP00000410746:L1495P;ENSP00000440944:L369P;ENSP00000404179:L1486P|.	ENSP00000345432:L1483P|.	L|X	-|-	2|1	0|0	DOCK4|DOCK4	111174668|111174668	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.990000|0.990000	0.78478|0.78478	9.139000|9.139000	0.94554|0.94554	2.218000|2.218000	0.71995|0.71995	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.		0.388	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		G	111387432	A	G	111387432	3	3	116	1	0	0	0	0	1	0	0	0	4700	188	7	3	1487	3	DOCK4	7	111387432	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	44977224	111387432	47751231	34	10130											
ING3	54556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	120595620	120595620	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttttcattcaggactactAtaaagctttggaagatgcag	12	14	9	6	0	2	1	2	0	0	1	2	3	2	3	0	2	3	3	0	2	5	7			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:120595620A>G	ENST00000315870.5	+	4	357	c.209A>G	c.(208-210)tAt>tGt	p.Y70C	ING3_ENST00000445699.1_Missense_Mutation_p.Y70C|ING3_ENST00000339121.5_Missense_Mutation_p.Y70C|ING3_ENST00000431467.1_Missense_Mutation_p.Y55C	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	70					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					CAGGACTACTATAAAGCTTTG	0.303																																					p.Y70C		.											.	ING3-515	0			c.A209G						.						78	79	78					7																	120595620		2203	4300	6503	SO:0001583	missense	54556	exon4			ACTACTATAAAGC	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"Zinc fingers, PHD-type"	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.209A>G	7.37:g.120595620A>G	ENSP00000320566:p.Tyr70Cys	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	36	5	NM_019071	0	0	0	0	0	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Missense_Mutation	SNP	ENST00000315870.5	37	CCDS5778.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990024	0.74589	.	.	ENSG00000071243	ENST00000315870;ENST00000339121;ENST00000445699;ENST00000431467	D;D	0.95518	-3.7;-3.73	5.54	5.54	0.83059	Inhibitor of growth protein, N-terminal (1);	0.059163	0.64402	D	0.000001	D	0.96765	0.8944	M	0.73598	2.24	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.975;0.988;0.999;0.999	D;P;P;D;D	0.67900	0.911;0.739;0.811;0.912;0.954	D	0.95906	0.8919	10	0.38643	T	0.18	-21.6296	10.2439	0.43330	0.852:0.0:0.0:0.148	.	70;70;70;70;70	B7ZKQ7;Q5GRH6;Q9NXR8;Q9NXR8-2;C9JUT0	.;.;ING3_HUMAN;.;.	C	70;70;70;55	ENSP00000320566:Y70C;ENSP00000388506:Y55C	ENSP00000320566:Y70C	Y	+	2	0	ING3	120382856	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.966000	0.76073	2.230000	0.72887	0.528000	0.53228	TAT	.		0.303	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071		G	120595620	A	G	120595620	3	3	116	1	0	0	0	0	1	0	0	0	7758	449	16	3	223	3	ING3	7	120595620	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	9208188	120595620	38543043	35	10131											
MCPH1	79648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	6302006	6302006	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggaagttggaaggatccAttaatgacattaaaagtgat	18	10	10	3	0	0	2	0	2	0	0	1	5	1	5	1	3	0	1	1	3	6	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:6302006A>T	ENST00000344683.5	+	8	839	c.763A>T	c.(763-765)Att>Ttt	p.I255F	MCPH1_ENST00000522905.1_Missense_Mutation_p.I207F|MCPH1_ENST00000519480.1_Missense_Mutation_p.I255F	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	255					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GGAAGGATCCATTAATGACAT	0.358																																					p.I255F	Colon(95;1448 1467 8277 34473 35819)	.											.	MCPH1-229	0			c.A763T						.						129	122	124					8																	6302006		1883	4107	5990	SO:0001583	missense	79648	exon8			GGATCCATTAATG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.763A>T	8.37:g.6302006A>T	ENSP00000342924:p.Ile255Phe	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	89	23	NM_001172574	0	0	2	2	0	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579572	0.86645	.	.	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.13778	2.56;2.56;2.56	5.26	-7.74	0.01241	.	1.774350	0.02525	N	0.092983	T	0.17492	0.0420	L	0.53249	1.67	0.09310	N	1	P;P;P	0.46784	0.884;0.867;0.884	P;P;P	0.52267	0.522;0.694;0.522	T	0.40289	-0.9571	10	0.32370	T	0.25	0.0924	3.4052	0.07338	0.3624:0.1106:0.4182:0.1088	.	207;255;255	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	F	255;255;207	ENSP00000342924:I255F;ENSP00000430962:I255F;ENSP00000430768:I207F	ENSP00000342924:I255F	I	+	1	0	MCPH1	6289414	0.000000	0.05858	0.000000	0.03702	0.857000	0.48899	-0.113000	0.10774	-1.605000	0.01593	0.533000	0.62120	ATT	.		0.358	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		T	6302006	A	T	6302006	3	4	116	1	0	0	0	0	1	0	0	0	9423	217	8	5	793	5	MCPH1	8	6302006	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		6302006	140062016	36	10132											
IKBKB	3551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	42173753	42173753	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgagcgactggagaagTggctgcaactgatgctgatg	9	9	16	7	1	0	4	0	3	0	1	0	6	0	4	0	3	4	4	0	3	2	0			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:42173753T>A	ENST00000520810.1	+	10	1012	c.826T>A	c.(826-828)Tgg>Agg	p.W276R	IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000379708.3_Missense_Mutation_p.W53R|IKBKB_ENST00000520835.1_Missense_Mutation_p.W274R|IKBKB_ENST00000416505.2_Missense_Mutation_p.W217R	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	276	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	ACTGGAGAAGTGGCTGCAACT	0.562																																					p.W276R		.											.	IKBKB-1164	0			c.T826A						.						66	58	61					8																	42173753		2203	4300	6503	SO:0001583	missense	3551	exon10			GAGAAGTGGCTGC	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.826T>A	8.37:g.42173753T>A	ENSP00000430684:p.Trp276Arg	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	48	10	NM_001556	0	0	2	2	0	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	37	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.617138	0.87359	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.64803	-0.12;-0.12;-0.12;1.78	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.057892	0.85682	D	0.000000	T	0.78780	0.4337	M	0.75264	2.295	0.80722	D	1	P;D;P;D;D;D	0.89917	0.879;0.998;0.836;0.999;0.995;1.0	P;D;B;D;D;D	0.97110	0.745;0.987;0.425;0.987;0.988;1.0	T	0.81621	-0.0850	10	0.72032	D	0.01	.	15.1947	0.73078	0.0:0.0:0.0:1.0	.	217;274;53;227;276;276	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920;Q32ND9	.;.;.;.;IKKB_HUMAN;.	R	276;217;274;53	ENSP00000430684:W276R;ENSP00000404920:W217R;ENSP00000430868:W274R;ENSP00000369030:W53R	ENSP00000369030:W53R	W	+	1	0	IKBKB	42292910	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.228000	0.72288	1.994000	0.58287	0.460000	0.39030	TGG	.		0.562	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			A	42173753	T	A	42173753	3	1	116	1	0	0	0	0	1	0	0	0	7632	1696	59	5	860	5	IKBKB	8	42173753	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	35871747	42173753	104190269	37	10133											
FBXL6	26233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145579793	145579793	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgtatggcaccacttcTgggtcaaaaaggggctgccc	9	8	13	11	0	2	0	1	0	1	0	2	0	2	0	2	4	1	4	2	4	3	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:145579793T>C	ENST00000331890.5	-	8	1371	c.1307A>G	c.(1306-1308)cAg>cGg	p.Q436R	SLC52A2_ENST00000540505.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank|SLC52A2_ENST00000530047.1_5'Flank|FBXL6_ENST00000526524.1_Intron|SLC52A2_ENST00000329994.2_5'Flank|SLC52A2_ENST00000532887.1_5'Flank|SLC52A2_ENST00000527078.1_5'Flank|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|FBXL6_ENST00000455319.2_Missense_Mutation_p.Q430R	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	436					protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			GCACCACTTCTGGGTCAAAAA	0.592																																					p.Q436R		.											.	FBXL6-658	0			c.A1307G						.						70	77	74					8																	145579793		2203	4299	6502	SO:0001583	missense	26233	exon8			CACTTCTGGGTCA	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"F-boxes / Leucine-rich repeats"	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.1307A>G	8.37:g.145579793T>C	ENSP00000330098:p.Gln436Arg	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	156	30	NM_012162	0	0	16	27	11	Q53G43|Q9H5W9|Q9UKC7	Missense_Mutation	SNP	ENST00000331890.5	37	CCDS6422.1	.	.	.	.	.	.	.	.	.	.	T	10.23	1.292836	0.23564	.	.	ENSG00000182325	ENST00000455319;ENST00000331890	T;T	0.24538	1.85;1.85	5.13	1.23	0.21249	.	0.612082	0.16879	N	0.195799	T	0.14141	0.0342	L	0.31207	0.915	0.22803	N	0.998711	B;B	0.14438	0.006;0.01	B;B	0.11329	0.003;0.006	T	0.32955	-0.9887	10	0.12766	T	0.61	-2.0714	6.0415	0.19736	0.0:0.403:0.0:0.597	.	436;430	Q8N531;Q8N531-2	FBXL6_HUMAN;.	R	430;436	ENSP00000403873:Q430R;ENSP00000330098:Q436R	ENSP00000330098:Q436R	Q	-	2	0	FBXL6	145550601	0.622000	0.27085	0.991000	0.47740	0.810000	0.45777	0.327000	0.19663	0.240000	0.21263	0.460000	0.39030	CAG	.		0.592	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555		C	145579793	T	C	145579793	3	2	116	1	0	0	0	0	1	0	0	0	5742	1580	55	3	320	3	FBXL6	8	145579793	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	103406040	145579793	784229	38	10134											
SVEP1	79987	broad.mit.edu	37	chr9	113198779	113198779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccccagaactaacgcacCaccacctaaggagagagaaa	16	4	8	13	1	0	3	0	0	0	3	0	5	0	3	5	1	3	1	5	1	4	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr9:113198779C>T	ENST00000401783.2	-	28	4981	c.4645G>A	c.(4645-4647)Ggt>Agt	p.G1549S	SVEP1_ENST00000374469.1_Missense_Mutation_p.G1526S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1549	Pentaxin.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACTAACGCACCACCACCTAAG	0.453																																					p.G1549S													.	SVEP1-75	0			c.G4645A						.						56	54	55					9																	113198779		1865	4103	5968	SO:0001583	missense	79987	exon28			ACGCACCACCACC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4645G>A	9.37:g.113198779C>T	ENSP00000384917:p.Gly1549Ser	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	24	6	NM_153366	0	0	0	0	0	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	35	5.491525	0.96339	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.06068	3.35;3.35	6.03	6.03	0.97812	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.39172	0.1068	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.44787	-0.9305	10	0.46703	T	0.11	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	1549	Q4LDE5	SVEP1_HUMAN	S	1549;1526	ENSP00000384917:G1549S;ENSP00000363593:G1526S	ENSP00000363593:G1526S	G	-	1	0	SVEP1	112238600	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.464000	0.80887	2.861000	0.98227	0.655000	0.94253	GGT	.		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113198779	C	T	113198779	3	4	116	1	0	0	0	0	1	0	0	0	15452	594	21	2	6154	2	SVEP1	9	113198779	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		113198779	28014652	39	10135											
KIN	22944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	7825098	7825098	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgaagccagcaatagttgtCtctgatgagattcggacata	12	11	10	8	1	1	3	0	3	1	1	3	5	1	4	1	1	2	2	1	1	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr10:7825098C>G	ENST00000379562.4	-	2	202	c.155G>C	c.(154-156)aGa>aCa	p.R52T	KIN_ENST00000543003.1_Intron|KIN_ENST00000535925.1_Missense_Mutation_p.R52T	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						CAATAGTTGTCTCTGATGAGA	0.328																																					p.R52T		.											.	KIN-230	0			c.G155C						.						61	60	60					10																	7825098		2203	4298	6501	SO:0001583	missense	22944	exon2			AGTTGTCTCTGAT	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.155G>C	10.37:g.7825098C>G	ENSP00000368881:p.Arg52Thr	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	61	8	NM_012311	0	0	4	6	2		Missense_Mutation	SNP	ENST00000379562.4	37	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266664	0.80358	.	.	ENSG00000151657	ENST00000535925;ENST00000379562	.	.	.	6.06	4.18	0.49190	DNA/RNA-binding protein Kin17, conserved domain (1);	0.132739	0.64402	D	0.000002	T	0.81331	0.4800	H	0.95114	3.625	0.80722	D	1	B;B	0.22146	0.065;0.065	B;B	0.35470	0.203;0.203	T	0.80384	-0.1405	9	0.87932	D	0	-35.5448	10.9911	0.47549	0.13:0.8027:0.0:0.0672	.	52;52	B4DX32;O60870	.;KIN17_HUMAN	T	52	.	ENSP00000368881:R52T	R	-	2	0	KIN	7865104	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.693000	0.84214	0.846000	0.35142	0.650000	0.86243	AGA	.		0.328	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311		G	7825098	C	G	7825098	3	3	116	1	0	0	0	0	1	0	0	0	8336	913	32	4	1074	4	KIN	10	7825098	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		7825098	127709649	40	10136											
PLCE1	51196	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr10	95849076	95849076	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcttcccgctctctgaggtAcccaattttaccttgttaaa	8	15	5	13	1	2	1	0	1	2	0	4	1	3	1	3	1	2	3	3	1	5	6			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr10:95849076A>G	ENST00000371380.3	+	2	1441				PLCE1_ENST00000371375.1_Silent_p.V75V|PLCE1_ENST00000371385.3_Silent_p.V75V|RP11-429H9.4_ENST00000438899.1_RNA|PLCE1_ENST00000260766.3_Intron			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1						activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				TCTCTGAGGTACCCAATTTTA	0.502																																					p.V75V		.											.	PLCE1-229	0			c.A225G						.						142	126	131					10																	95849076		1568	3582	5150	SO:0001627	intron_variant	51196	exon1			TGAGGTACCCAAT		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.1207-42855A>G	10.37:g.95849076A>G		Somatic	198	0		WXS	Illumina HiSeq	Phase_I	169	66	NM_001165979	0	0	0	0	0	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			.		0.502	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		G	95849076	A	G	95849076	1	3	116	0	1	0	0	0	0	0	0	0	12060	378	14	3		3	PLCE1	10	95849076	Intron	SNP	A	TCGA-G7-6796-01A-11D-1961-08	88023978	95849076	39685671	41	10137											
BEST1	7439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	61730354	61730354	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatggatccttattgggcCttggaaaacaggtctgtcct	9	12	10	10	0	1	0	0	0	1	0	3	2	3	2	3	4	1	0	3	4	3	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr11:61730354C>T	ENST00000378043.4	+	10	2371	c.1728C>T	c.(1726-1728)gcC>gcT	p.A576A	BEST1_ENST00000301774.9_Silent_p.A204A|BEST1_ENST00000378042.3_Silent_p.A489A|FTH1_ENST00000529191.1_Intron|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000449131.2_Silent_p.A516A	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	576					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						CTTATTGGGCCTTGGAAAACA	0.507																																					p.A576A		.											.	BEST1-90	0			c.C1728T						.						120	130	126					11																	61730354		2202	4299	6501	SO:0001819	synonymous_variant	7439	exon10			TTGGGCCTTGGAA	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	12703	protein-coding gene	gene with protein product	"Best disease"	607854	"vitelliform macular dystrophy 2"	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1728C>T	11.37:g.61730354C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	91	13	NM_004183	0	0	0	0	0	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			.		0.507	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		T	61730354	C	T	61730354	2	4	116	1	0	0	0	0	0	0	0	1	1405	668	24	2		2	BEST1	11	61730354	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08		61730354	73276162	42	10138											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825431	95825431	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgttgctgctgttgctgTtgggtgtagtgtaggagaga	5	15	17	4	0	0	1	0	0	0	1	0	3	0	2	0	2	4	9	0	2	2	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr11:95825431T>C	ENST00000524717.1	-	2	3048	c.1764A>G	c.(1762-1764)caA>caG	p.Q588Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	588					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgTTGGGTGTAGT	0.522			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q588Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.A1764G						.																																			SO:0001819	synonymous_variant	84441	exon2			TTGCTGTTGGGTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1764A>G	11.37:g.95825431T>C		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_032427	0	0	2	2	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.522	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825431	T	C	95825431	2	2	116	1	0	0	0	0	0	0	0	1	9231	1722	60	3		3	MAML2	11	95825431	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08	34095077	95825431	39181085	43	10139											
C12orf57	113246	broad.mit.edu;ucsc.edu	37	chr12	7055012	7055012	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcctgtcaggcaagctgaAggcgctgtttctgccgccca	7	8	12	14	2	2	1	1	1	1	0	2	1	2	1	3	2	3	4	3	2	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:7055012A>G	ENST00000229281.5	+	3	407	c.308A>G	c.(307-309)aAg>aGg	p.K103R	C12orf57_ENST00000540506.2_Missense_Mutation_p.K68R|PTPN6_ENST00000399448.1_5'Flank|PTPN6_ENST00000447931.2_5'Flank|U47924.31_ENST00000607421.1_RNA|RNU7-1_ENST00000458811.1_RNA|C12orf57_ENST00000542222.1_3'UTR|C12orf57_ENST00000537087.1_Missense_Mutation_p.K74R	NM_138425.2	NP_612434.1	Q99622	C10_HUMAN	chromosome 12 open reading frame 57	103						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)	2						GGCAAGCTGAAGGCGCTGTTT	0.627																																					p.K103R													.	C12orf57-90	0			c.A308G						.						70	55	60					12																	7055012		2203	4300	6503	SO:0001583	missense	113246	exon3			AGCTGAAGGCGCT	U47924	CCDS8571.1	12p13.31	2012-05-30			ENSG00000111678	ENSG00000111678			29521	protein-coding gene	gene with protein product		615140				9445485	Standard	NM_138425		Approved	GRCC10, C10	uc009zfj.2	Q99622	OTTHUMG00000169017	ENST00000229281.5:c.308A>G	12.37:g.7055012A>G	ENSP00000229281:p.Lys103Arg	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	36	4	NM_138425	0	0	156	218	62	B2R4Q6	Missense_Mutation	SNP	ENST00000229281.5	37	CCDS8571.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459836	0.26248	.	.	ENSG00000111678	ENST00000545581;ENST00000537087;ENST00000229281	T;T;T	0.78364	-0.89;-1.17;-0.89	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.58352	0.2116	N	0.13198	0.31	0.80722	D	1	B	0.23128	0.08	B	0.19946	0.027	T	0.56372	-0.7990	10	0.02654	T	1	-18.3011	13.8505	0.63494	1.0:0.0:0.0:0.0	.	103	Q99622	C10_HUMAN	R	103;74;103	ENSP00000440602:K103R;ENSP00000440937:K74R;ENSP00000229281:K103R	ENSP00000229281:K103R	K	+	2	0	C12orf57	6925273	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.092000	0.94157	2.075000	0.62263	0.379000	0.24179	AAG	.		0.627	C12orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401959.1	NM_138425		G	7055012	A	G	7055012	3	3	116	1	0	0	0	0	1	0	0	0	1705	72	3	3	318	3	C12orf57	12	7055012	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		7055012	126796883	44	10140											
ABCC9	10060	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	21962862	21962862	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcccagagtctgtcatctgtGcatttgcactctggatctaa	8	14	8	11	0	5	1	1	0	4	1	6	2	6	2	1	1	2	2	1	1	1	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:21962862G>A	ENST00000261201.4	-	35	4238	c.4239C>T	c.(4237-4239)tgC>tgT	p.C1413C	ABCC9_ENST00000261200.4_Silent_p.C1413C|ABCC9_ENST00000345162.2_Silent_p.C1377C	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1413	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TGTCATCTGTGCATTTGCACT	0.323																																					p.C1413C		.											.	ABCC9-96	0			c.C4239T						.						83	85	84					12																	21962862		2203	4300	6503	SO:0001819	synonymous_variant	10060	exon35			ATCTGTGCATTTG	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.4239C>T	12.37:g.21962862G>A		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	127	24	NM_005691	0	0	2	2	0	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																			.		0.323	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	21962862	G	A	21962862	2	1	116	1	0	0	0	0	0	0	0	1	59	1311	46	2		2	ABCC9	12	21962862	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08	14907850	21962862	111889033	45	10141											
KIAA0528	9847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	22666235	22666235	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgaatcttaccctctgtTccaacgctgattgagtctgt	9	14	8	10	1	3	3	0	3	3	0	4	3	4	3	2	0	2	2	2	0	4	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:22666235T>C	ENST00000333957.4	-	9	1286	c.1031A>G	c.(1030-1032)gAa>gGa	p.E344G	C2CD5_ENST00000544930.1_Missense_Mutation_p.E137G|C2CD5_ENST00000536386.1_Missense_Mutation_p.E335G|C2CD5_ENST00000446597.1_Missense_Mutation_p.E344G|C2CD5_ENST00000542676.1_Missense_Mutation_p.E344G|C2CD5_ENST00000545552.1_Missense_Mutation_p.E335G|C2CD5_ENST00000396028.2_Missense_Mutation_p.E335G	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	344					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										TACCCTCTGTTCCAACGCTGA	0.378																																					p.E344G		.											.	.	0			c.A1031G						.						149	131	137					12																	22666235		2203	4300	6503	SO:0001583	missense	9847	exon9			CTCTGTTCCAACG	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.1031A>G	12.37:g.22666235T>C	ENSP00000334229:p.Glu344Gly	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	187	31	NM_014802	0	0	0	0	0	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	37	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.824771	0.71143	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930;ENST00000544281	T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.0	3.85	0.44370	.	0.062767	0.64402	N	0.000006	T	0.65144	0.2663	L	0.57536	1.79	0.49915	D	0.999836	D;D;D;D;D;D	0.89917	0.999;0.992;1.0;0.992;1.0;0.979	D;P;D;P;D;P	0.85130	0.973;0.784;0.996;0.864;0.997;0.628	T	0.64045	-0.6499	10	0.51188	T	0.08	-22.0629	9.2812	0.37729	0.0:0.0816:0.0:0.9184	.	335;344;137;335;335;344	F5H2A1;B4DRN7;F5H3N1;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;.;K0528_HUMAN	G	344;344;335;335;344;335;137;96	ENSP00000334229:E344G;ENSP00000388756:E344G;ENSP00000439392:E335G;ENSP00000379345:E335G;ENSP00000441951:E344G;ENSP00000443204:E335G;ENSP00000445288:E137G;ENSP00000443479:E96G	ENSP00000334229:E344G	E	-	2	0	KIAA0528	22557502	1.000000	0.71417	0.988000	0.46212	0.978000	0.69477	7.272000	0.78516	0.920000	0.36970	0.528000	0.53228	GAA	.		0.378	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22666235	T	C	22666235	3	2	116	1	0	0	0	0	1	0	0	0	8203	1783	62	3	2039	3	KIAA0528	12	22666235	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	703373	22666235	111185660	46	10142											
CAPRIN2	65981	hgsc.bcm.edu;bcgsc.ca	37	chr12	30886574	30886574	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaactcacatgtcgttcctAccactgctttctcactacct	10	13	3	15	1	2	0	2	0	1	0	5	0	3	0	3	0	4	2	3	0	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:30886574A>G	ENST00000395805.2	-	5	1428	c.881T>C	c.(880-882)gTa>gCa	p.V294A	CAPRIN2_ENST00000538387.1_Intron|CAPRIN2_ENST00000308433.5_Intron|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.V294A|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.V294A|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.V294A	NM_001206856.1	NP_001193785.1			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TGTCGTTCCTACCACTGCTTT	0.398																																					p.V294A		.											.	CAPRIN2-92	0			c.T881C						.						164	143	150					12																	30886574		2203	4300	6503	SO:0001583	missense	65981	exon5			GTTCCTACCACTG	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.881T>C	12.37:g.30886574A>G	ENSP00000379150:p.Val294Ala	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	219	13	NM_023925	0	0	0	0	0		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	A	12.15	1.850529	0.32699	.	.	ENSG00000110888	ENST00000433722;ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045;ENST00000438006;ENST00000537108	T;T;T;T;T;T	0.21031	2.47;2.03;2.03;2.03;2.03;2.03	4.96	4.96	0.65561	.	0.276479	0.34460	N	0.003948	T	0.09730	0.0239	N	0.11201	0.11	0.80722	D	1	B;B;B;B;B	0.28783	0.142;0.222;0.029;0.049;0.013	B;B;B;B;B	0.28011	0.043;0.085;0.006;0.013;0.008	T	0.24977	-1.0145	10	0.15066	T	0.55	-12.678	7.5105	0.27571	0.8402:0.0:0.1598:0.0	.	294;294;294;294;294	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;CAPR2_HUMAN;.;.	A	40;294;294;294;294;20;213	ENSP00000415407:V40A;ENSP00000298892:V294A;ENSP00000379150:V294A;ENSP00000251071:V294A;ENSP00000391479:V294A;ENSP00000438010:V213A	ENSP00000251071:V294A	V	-	2	0	CAPRIN2	30777841	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.311000	0.51919	2.069000	0.61940	0.533000	0.62120	GTA	.		0.398	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		G	30886574	A	G	30886574	3	3	116	1	0	0	0	0	1	0	0	0	2642	391	14	3	2558	3	CAPRIN2	12	30886574	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	8220339	30886574	102965321	47	10143											
KRT85	3891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52761009	52761009	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctatccggggcccgcaggAgcccaggttgcagaggctgc	7	5	16	13	2	0	1	0	0	0	1	1	2	1	2	3	5	4	5	3	5	1	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:52761009A>G	ENST00000257901.3	-	1	256	c.181T>C	c.(181-183)Tcc>Ccc	p.S61P	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	61	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGCCCGCAGGAGCCCAGGTTG	0.716																																					p.S61P		.											.	KRT85-91	0			c.T181C						.						18	23	21					12																	52761009		2197	4295	6492	SO:0001583	missense	3891	exon1			CGCAGGAGCCCAG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.181T>C	12.37:g.52761009A>G	ENSP00000257901:p.Ser61Pro	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	58	11	NM_002283	0	0	0	0	0	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	A	5.873	0.345197	0.11126	.	.	ENSG00000135443	ENST00000257901	T	0.77877	-1.13	4.66	-2.96	0.05547	.	0.601870	0.15091	N	0.281064	T	0.51261	0.1664	N	0.12182	0.205	0.23563	N	0.997407	B	0.06786	0.001	B	0.10450	0.005	T	0.29488	-1.0010	10	0.40728	T	0.16	.	2.3992	0.04397	0.2911:0.4181:0.1687:0.1221	.	61	P78386	KRT85_HUMAN	P	61	ENSP00000257901:S61P	ENSP00000257901:S61P	S	-	1	0	KRT85	51047276	0.000000	0.05858	0.660000	0.29694	0.354000	0.29330	-0.238000	0.08977	-0.599000	0.05798	-0.366000	0.07423	TCC	.		0.716	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		G	52761009	A	G	52761009	3	3	116	1	0	0	0	0	1	0	0	0	8520	304	11	3	1378	3	KRT85	12	52761009	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	21874435	52761009	81090886	48	10144											
SYCP3	50511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	102127436	102127436	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagaaactgctgagaatattCttggttaagcttctgcctgt	10	14	9	8	0	2	2	0	1	2	2	2	3	2	2	1	1	4	3	1	1	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:102127436C>G	ENST00000392927.3	-	6	501	c.370G>C	c.(370-372)Gaa>Caa	p.E124Q	SYCP3_ENST00000266743.2_Missense_Mutation_p.E124Q|SYCP3_ENST00000392924.1_Missense_Mutation_p.E124Q	NM_001177948.1|NM_001177949.1|NM_153694.4	NP_001171419.1|NP_001171420.1|NP_710161.1	Q8IZU3	SYCP3_HUMAN	synaptonemal complex protein 3	124	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						TGAGAATATTCTTGGTTAAGC	0.308																																					p.E124Q		.											.	SYCP3-90	0			c.G370C						.						110	102	105					12																	102127436		2203	4300	6503	SO:0001583	missense	50511	exon6			AATATTCTTGGTT	AF492003, AI075991	CCDS9087.1	12q23.2	2007-02-05			ENSG00000139351	ENSG00000139351			18130	protein-coding gene	gene with protein product		604759				12213195, 10854409	Standard	NM_153694		Approved		uc001tis.3	Q8IZU3	OTTHUMG00000150132	ENST00000392927.3:c.370G>C	12.37:g.102127436C>G	ENSP00000376658:p.Glu124Gln	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	89	12	NM_001177949	0	0	0	0	0		Missense_Mutation	SNP	ENST00000392927.3	37	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.197243	0.38806	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	5.95	5.01	0.66863	.	0.115967	0.64402	D	0.000019	T	0.72078	0.3416	M	0.67953	2.075	0.44247	D	0.997095	D	0.54397	0.966	P	0.56343	0.796	T	0.69698	-0.5075	9	0.34782	T	0.22	1.5322	15.6276	0.76874	0.1381:0.8619:0.0:0.0	.	124	Q8IZU3	SYCP3_HUMAN	Q	124	.	ENSP00000266743:E124Q	E	-	1	0	SYCP3	100651567	1.000000	0.71417	0.797000	0.32132	0.043000	0.13939	4.291000	0.59025	2.817000	0.96982	0.563000	0.77884	GAA	.		0.308	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		G	102127436	C	G	102127436	3	3	116	1	0	0	0	0	1	0	0	0	15466	922	32	4	356	4	SYCP3	12	102127436	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	49366427	102127436	31724459	49	10145											
USPL1	10208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	31233386	31233386	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaacttggagagtccgatgAagactgatattttcgatgag	13	12	11	5	2	0	5	0	3	0	2	2	8	1	5	1	1	1	0	1	1	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr13:31233386A>C	ENST00000255304.4	+	9	3514	c.3172A>C	c.(3172-3174)Aag>Cag	p.K1058Q		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	1058					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		GAGTCCGATGAAGACTGATAT	0.373																																					p.K1058Q	Ovarian(60;318 1180 1554 28110 31601)	.											.	USPL1-524	0			c.A3172C						.						93	94	93					13																	31233386		2202	4300	6502	SO:0001583	missense	10208	exon9			CCGATGAAGACTG	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 22"	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.3172A>C	13.37:g.31233386A>C	ENSP00000255304:p.Lys1058Gln	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	110	20	NM_005800	0	0	15	25	10	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.675070	0.67928	.	.	ENSG00000132952	ENST00000255304	T	0.26518	1.73	5.62	5.62	0.85841	.	0.083251	0.51477	D	0.000089	T	0.46870	0.1415	M	0.64997	1.995	0.25803	N	0.984481	D	0.67145	0.996	D	0.66497	0.944	T	0.43589	-0.9382	10	0.72032	D	0.01	-19.9681	14.3888	0.66963	1.0:0.0:0.0:0.0	.	1058	Q5W0Q7	USPL1_HUMAN	Q	1058	ENSP00000255304:K1058Q	ENSP00000255304:K1058Q	K	+	1	0	USPL1	30131386	0.983000	0.35010	0.930000	0.37139	0.675000	0.39556	4.229000	0.58625	2.143000	0.66587	0.455000	0.32223	AAG	.		0.373	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		C	31233386	A	C	31233386	3	2	116	1	0	0	0	0	1	0	0	0	17125	247	9	5	3202	5	USPL1	13	31233386	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		31233386	83936492	50	10146											
ITM2B	9445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	48833064	48833064	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggaaacttacaaactgcaAcgcagagaaactattaaagg	20	6	8	7	1	0	1	0	0	0	1	0	3	0	2	0	2	6	2	0	2	9	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr13:48833064A>G	ENST00000378565.5	+	5	899	c.696A>G	c.(694-696)caA>caG	p.Q232Q	ITM2B_ENST00000378549.5_Silent_p.Q126Q	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	232					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		ACAAACTGCAACGCAGAGAAA	0.338																																					p.Q232Q		.											.	ITM2B-90	0			c.A696G						.						85	78	81					13																	48833064		2203	4300	6503	SO:0001819	synonymous_variant	9445	exon5			ACTGCAACGCAGA	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.696A>G	13.37:g.48833064A>G		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	83	13	NM_021999	4	3	3938	5724	1779	Q5W0A3|Q96B24|Q9NYH1	Silent	SNP	ENST00000378565.5	37	CCDS9409.1																																																																																			.		0.338	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		G	48833064	A	G	48833064	2	3	116	1	0	0	0	0	0	0	0	1	7934	40	2	3		3	ITM2B	13	48833064	Silent	SNP	A	TCGA-G7-6796-01A-11D-1961-08	17599678	48833064	66336814	51	10147											
RYR3	6263	ucsc.edu	37	chr15	34152846	34152846	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagaccagcaggaacaagtaCgagaagatatggaggtaatg	17	5	14	5	1	0	3	0	0	0	3	0	7	0	5	1	3	3	3	1	3	6	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr15:34152846C>T	ENST00000389232.4	+	101	14420	c.14350C>T	c.(14350-14352)Cga>Tga	p.R4784*	RP11-3D4.2_ENST00000560268.1_RNA|RYR3_ENST00000415757.3_Nonsense_Mutation_p.R4779*	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4784					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GGAACAAGTACGAGAAGATAT	0.358																																					p.R4784X													.	RYR3-520	0			c.C14350T						.						96	88	91					15																	34152846		1847	4094	5941	SO:0001587	stop_gained	6263	exon101			CAAGTACGAGAAG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.14350C>T	15.37:g.34152846C>T	ENSP00000373884:p.Arg4784*	Somatic	25	0		WXS	Illumina HiSeq		17	4	NM_001036	0	0	0	0	0	O15175|Q15412	Nonsense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	55	24.234413	0.99959	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	.	.	.	5.2	-0.603	0.11630	.	0.061993	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	16.9174	0.86155	0.7997:0.2003:0.0:0.0	.	.	.	.	X	4784;4780	.	ENSP00000354735:R4780X	R	+	1	2	RYR3	31940138	0.972000	0.33761	0.215000	0.23724	0.886000	0.51366	2.413000	0.44618	0.085000	0.17107	-0.182000	0.12963	CGA	.		0.358	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34152846	C	T	34152846	4	4	116	1	0	0	0	0	0	1	0	0	13802	528	19	1	14752	1	RYR3	15	34152846	Nonsense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		34152846	68378546	52	10148											
SGK269	79834	broad.mit.edu;bcgsc.ca	37	chr15	77406883	77406886	+	Frame_Shift_Del	DEL	TCCC	TCCC	-																															gcaggtctgctcgtgtgtatTccctctccttcagctctggg																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	TCCC	TCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr15:77406883_77406886delTCCC	ENST00000560626.2	-	7	5328_5331	c.4853_4856delGGGA	c.(4852-4857)agggaafs	p.RE1618fs	PEAK1_ENST00000312493.4_Frame_Shift_Del_p.RE1618fs			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1618	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TCGTGTGTATTCCCTCTCCTTCAG	0.559																																					p.1618_1619del													.	.	0			c.4853_4856del						.																																			SO:0001589	frameshift_variant	0	exon8			GTGTATTCCCTCT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4853_4856delGGGA	15.37:g.77406883_77406886delTCCC	ENSP00000452796:p.Arg1618fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	31	9	NM_024776	0	0	0	0	0	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Frame_Shift_Del	DEL	ENST00000560626.2	37	CCDS42062.1																																																																																			.		0.559	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			-	77406886	TCCC	-	77406883	7	5	116	1	0	1	0	1	0	0	0	0	14243	1783	62	0	388	0	SGK269	15	77406883	Frame_Shift_Del	DEL	TCCC	TCGA-G7-6796-01A-11D-1961-08	43254037	77406883	25124509	53	10149											
ZP2	7783	hgsc.bcm.edu	37	chr16	21213523	21213523	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggatgagtttcccacccTcagagtacccaggtcaagag	11	7	11	12	0	2	3	2	1	0	2	3	4	3	4	3	2	1	3	3	2	2	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr16:21213523T>C	ENST00000574002.1	-	12	1671	c.1189A>G	c.(1189-1191)Agg>Ggg	p.R397G	ZP2_ENST00000574091.1_Missense_Mutation_p.R397G|ZP2_ENST00000219593.4_Missense_Mutation_p.R397G|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	397	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TTTCCCACCCTCAGAGTACCC	0.542																																					p.R397G		.											.	ZP2-91	0			c.A1189G						.						85	79	81					16																	21213523		2200	4300	6500	SO:0001583	missense	7783	exon11			CCACCCTCAGAGT	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1189A>G	16.37:g.21213523T>C	ENSP00000460971:p.Arg397Gly	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_003460	0	0	0	0	0	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.133085	0.56828	.	.	ENSG00000103310	ENST00000219593	D	0.82984	-1.67	6.08	3.62	0.41486	Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	0.366291	0.29028	N	0.013373	D	0.88858	0.6551	M	0.84846	2.72	0.09310	N	1	P;P	0.49696	0.927;0.927	P;P	0.54174	0.744;0.744	T	0.82629	-0.0363	10	0.59425	D	0.04	-2.6547	13.5127	0.61522	0.0:0.0:0.2565:0.7435	.	397;397	Q4VAP1;Q05996	.;ZP2_HUMAN	G	397	ENSP00000219593:R397G	ENSP00000219593:R397G	R	-	1	2	ZP2	21121024	0.048000	0.20356	0.203000	0.23512	0.821000	0.46438	0.850000	0.27737	1.073000	0.40885	0.533000	0.62120	AGG	.		0.542	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			C	21213523	T	C	21213523	3	2	116	1	0	0	0	0	1	0	0	0	18248	1550	54	3	1084	3	ZP2	16	21213523	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08		21213523	69141230	54	10150											
EDC4	23644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67910484	67910484	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gactctagcatttcaagcaaGgcccggggaagcaacaaggt	13	6	12	10	1	2	0	1	0	1	0	2	2	2	1	1	4	4	3	1	4	6	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr16:67910484G>A	ENST00000358933.5	+	3	572	c.333G>A	c.(331-333)aaG>aaA	p.K111K	EDC4_ENST00000574770.1_3'UTR|AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	111					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		TTTCAAGCAAGGCCCGGGGAA	0.537																																					p.K111K		.											.	EDC4-92	0			c.G333A						.						76	65	69					16																	67910484		2198	4300	6498	SO:0001819	synonymous_variant	23644	exon3			AAGCAAGGCCCGG	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.333G>A	16.37:g.67910484G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	78	15	NM_014329	0	0	0	0	0	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	37	CCDS10849.1																																																																																			.		0.537	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		A	67910484	G	A	67910484	2	1	116	1	0	0	0	0	0	0	0	1	4919	991	35	2		2	EDC4	16	67910484	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08	46696961	67910484	22444269	55	10151											
TEKT1	83659	broad.mit.edu;bcgsc.ca	37	chr17	6718552	6718553	+	Frame_Shift_Ins	INS	-	-	A																															ttgttgagcgagaagcagatINSatcatctatggtcagggcca																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:6718552_6718553insA	ENST00000338694.2	-	5	687_688	c.558_559insT	c.(556-561)gatatcfs	p.I187fs	TEKT1_ENST00000535086.1_Frame_Shift_Ins_p.I41fs	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	187						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				GAGAAGCAGATATCATCTATGG	0.48																																					p.I187fs													.	TEKT1-92	0			c.559_560insT						.																																			SO:0001589	frameshift_variant	83659	exon5			AGCAGATATCATC		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.559dupT	17.37:g.6718553_6718553dupA	ENSP00000341346:p.Ile187fs	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	249	36	NM_053285	0	0	0	0	0	D3DTM7	Frame_Shift_Ins	INS	ENST00000338694.2	37	CCDS11083.1																																																																																			.		0.48	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		A	6718553	-	A	6718552	7	5	116	1	0	1	1	0	0	0	0	0	15784	1406	49	0	713	0	TEKT1	17	6718552	Frame_Shift_Ins	INS	-	TCGA-G7-6796-01A-11D-1961-08		6718552	74476658	56	10152											
ALKBH5	54890	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18111630	18111630	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagctctgagaactactggCgcaagtcatacgagtcctca	11	9	9	12	2	4	1	3	1	1	1	5	3	5	1	1	1	4	2	1	1	4	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:18111630C>T	ENST00000399138.4	+	4	1110	c.1105C>T	c.(1105-1107)Cgc>Tgc	p.R369C	ALKBH5_ENST00000541285.1_Missense_Mutation_p.R28C	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	369					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					GAACTACTGGCGCAAGTCATA	0.637																																					p.R369C	Ovarian(166;154 1953 40235 46283 46309)												.	ALKBH5-90	0			c.C1105T						.						52	59	57					17																	18111630		1995	4150	6145	SO:0001583	missense	54890	exon4			TACTGGCGCAAGT	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.1105C>T	17.37:g.18111630C>T	ENSP00000382091:p.Arg369Cys	Somatic	144	1		WXS	Illumina HiSeq	Phase_I	160	15	NM_017758	0	0	17	18	1	B4DVJ4|D3DXC6|Q9NXD6	Missense_Mutation	SNP	ENST00000399138.4	37	CCDS42272.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487415	0.84854	.	.	ENSG00000091542	ENST00000261650;ENST00000500385;ENST00000399138	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.72350	0.3449	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74103	-0.3773	9	0.87932	D	0	-9.4349	20.2963	0.98556	0.0:1.0:0.0:0.0	.	369	Q6P6C2-2	.	C	369;358;369	.	ENSP00000261650:R369C	R	+	1	0	ALKBH5	18052355	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.540000	0.60664	2.813000	0.96785	0.655000	0.94253	CGC	.		0.637	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		T	18111630	C	T	18111630	3	4	116	1	0	0	0	0	1	0	0	0	530	768	27	1	1119	1	ALKBH5	17	18111630	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	11393078	18111630	63083580	57	10153											
ADAP2	55803	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	29261209	29261209	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccttgctgcttaaggtaaccGagaaggattcctgtggaagc	10	10	12	9	1	0	1	0	0	0	1	1	4	1	3	3	3	4	3	3	3	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:29261209G>A	ENST00000330889.3	+	5	739	c.404G>A	c.(403-405)cGa>cAa	p.R135Q	ADAP2_ENST00000580525.1_Missense_Mutation_p.R141Q	NM_018404.2	NP_060874.1	Q9NPF8	ADAP2_HUMAN	ArfGAP with dual PH domains 2	135	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				heart development (GO:0007507)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|mitochondrial envelope (GO:0005740)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						TAAGGTAACCGAGAAGGATTC	0.483																																					p.R135Q													.	ADAP2-91	1	Unknown(1)	central_nervous_system(1)	c.G404A						.						96	80	85					17																	29261209		2203	4300	6503	SO:0001583	missense	55803	exon5			GTAACCGAGAAGG	AJ238994	CCDS11261.1	17q11.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000184060	ENSG00000184060		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16487	protein-coding gene	gene with protein product		608635	"centaurin, alpha 2"	CENTA2			Standard	XM_005258008		Approved		uc002hfx.3	Q9NPF8	OTTHUMG00000132868	ENST00000330889.3:c.404G>A	17.37:g.29261209G>A	ENSP00000329468:p.Arg135Gln	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	73	16	NM_018404	0	0	0	0	0	Q8N4Q6|Q96SD5	Missense_Mutation	SNP	ENST00000330889.3	37	CCDS11261.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981099	0.34942	.	.	ENSG00000184060	ENST00000330889	T	0.23754	1.89	5.72	5.72	0.89469	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.309320	0.36778	N	0.002418	T	0.55049	0.1896	M	0.86953	2.85	0.40187	D	0.977363	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.71414	0.973;0.93;0.972	T	0.57464	-0.7807	10	0.36615	T	0.2	.	15.3693	0.74551	0.0:0.0:1.0:0.0	.	141;135;135	Q2V6Q1;Q9NPF8-2;Q9NPF8	.;.;ADAP2_HUMAN	Q	135	ENSP00000329468:R135Q	ENSP00000329468:R135Q	R	+	2	0	ADAP2	26285335	0.988000	0.35896	0.995000	0.50966	0.291000	0.27294	4.038000	0.57318	2.705000	0.92388	0.655000	0.94253	CGA	.		0.483	ADAP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256346.1	NM_018404		A	29261209	G	A	29261209	3	1	116	1	0	0	0	0	1	0	0	0	280	1058	37	1	422	1	ADAP2	17	29261209	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	11149579	29261209	51934001	58	10154											
BRCA1	672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41244817	41244817	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gatattagactcattctttcCttgattttcttccttttgtt	6	23	4	8	0	3	2	1	1	2	1	5	3	5	2	2	0	0	1	2	0	2	11	rs80357712|rs397509003|rs80357605|rs80357917		TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:41244817C>T	ENST00000357654.3	-	10	2849	c.2731G>A	c.(2731-2733)Gga>Aga	p.G911R	BRCA1_ENST00000493795.1_Missense_Mutation_p.G864R|BRCA1_ENST00000354071.3_Missense_Mutation_p.G911R|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.G911R|BRCA1_ENST00000471181.2_Missense_Mutation_p.G911R|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.G615R|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000468300.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	911					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TCATTCTTTCCTTGATTTTCT	0.398			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.G911R		.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1-3415	0			c.G2731A						.						132	130	131					17																	41244817		2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		TCTTTCCTTGATT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1100	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 1", "protein phosphatase 1, regulatory subunit 53"	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2731G>A	17.37:g.41244817C>T	ENSP00000350283:p.Gly911Arg	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	146	24	NM_007300	0	0	0	0	0	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.977264	0.34848	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	4.85	2.8	0.32819	.	0.776431	0.11349	N	0.573162	D	0.84188	0.5417	M	0.65320	2	0.09310	N	1	B;B;B;B;D;B	0.59357	0.024;0.065;0.132;0.12;0.985;0.036	B;B;B;B;P;B	0.57371	0.046;0.046;0.261;0.22;0.819;0.043	T	0.71461	-0.4586	10	0.56958	D	0.05	.	8.2084	0.31469	0.0:0.7274:0.0:0.2726	.	911;870;911;911;911;911	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	R	911;911;911;911;615;911;864	ENSP00000350283:G911R;ENSP00000326002:G911R;ENSP00000246907:G911R;ENSP00000310938:G615R;ENSP00000418960:G911R;ENSP00000418775:G864R	ENSP00000310938:G615R	G	-	1	0	BRCA1	38498343	0.001000	0.12720	0.001000	0.08648	0.134000	0.20937	0.961000	0.29267	0.582000	0.29556	0.484000	0.47621	GGA	.		0.398	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		T	41244817	C	T	41244817	3	4	116	1	0	0	0	0	1	0	0	0	1501	690	24	2	2986	2	BRCA1	17	41244817	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	11983608	41244817	39950393	59	10155											
NPEPPS	9520	hgsc.bcm.edu;broad.mit.edu	37	chr17	45668145	45668145	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggattgaatatctgtgtgtAgaccactgcttcccagagta	10	13	10	8	0	1	3	0	1	1	2	2	4	2	4	2	1	1	3	2	1	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:45668145A>G	ENST00000322157.4	+	10	1395	c.1158A>G	c.(1156-1158)gtA>gtG	p.V386V	NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Silent_p.V306V|NPEPPS_ENST00000530173.1_Silent_p.V382V	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	386					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						ATCTGTGTGTAGACCACTGCT	0.393																																					p.V386V		.											.	NPEPPS-90	0			c.A1158G						.						62	55	57					17																	45668145		1791	4055	5846	SO:0001819	synonymous_variant	9520	exon10			GTGTGTAGACCAC	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1158A>G	17.37:g.45668145A>G		Somatic	266	0		WXS	Illumina HiSeq	Phase_I	329	33	NM_006310	0	0	65	71	6	B7Z463|Q6P145|Q9NP16|Q9UEM2	Silent	SNP	ENST00000322157.4	37	CCDS45721.1																																																																																			.		0.393	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		G	45668145	A	G	45668145	2	3	116	1	0	0	0	0	0	0	0	1	10601	407	15	3		3	NPEPPS	17	45668145	Silent	SNP	A	TCGA-G7-6796-01A-11D-1961-08	4423328	45668145	35527065	60	10156											
MSI2	124540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	55754379	55754379	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcaacggcctttacaaatgGataccattgagcaggtgctt	11	11	10	9	1	0	1	0	1	0	0	0	2	0	2	2	3	6	3	2	3	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:55754379G>A	ENST00000284073.2	+	13	1186	c.977G>A	c.(976-978)gGa>gAa	p.G326E	MSI2_ENST00000442934.2_Missense_Mutation_p.G265E|MSI2_ENST00000416426.2_Missense_Mutation_p.G322E	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	326						cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		TTTACAAATGGATACCATTGA	0.458			T	HOXA9	CML																																p.G326E		.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2-658	0			c.G977A						.						234	195	208					17																	55754379		2203	4300	6503	SO:0001583	missense	124540	exon13			CAAATGGATACCA	BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	18585	protein-coding gene	gene with protein product		607897	"musashi homolog 2 (Drosophila)"			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.977G>A	17.37:g.55754379G>A	ENSP00000284073:p.Gly326Glu	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	252	80	NM_138962	0	0	0	0	0	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.739690	0.89573	.	.	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000442934	D;T;T	0.89050	-2.46;0.62;1.01	4.87	4.87	0.63330	.	0.052819	0.85682	D	0.000000	D	0.93605	0.7958	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.94391	0.7614	10	0.87932	D	0	.	18.0345	0.89296	0.0:0.0:1.0:0.0	.	322;326	B4DHE8;Q96DH6	.;MSI2H_HUMAN	E	322;326;265	ENSP00000414671:G322E;ENSP00000284073:G326E;ENSP00000392607:G265E	ENSP00000284073:G326E	G	+	2	0	MSI2	53109378	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.430000	0.97488	2.260000	0.74910	0.462000	0.41574	GGA	.		0.458	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			A	55754379	G	A	55754379	3	1	116	1	0	0	0	0	1	0	0	0	9901	1174	41	2	1122	2	MSI2	17	55754379	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	10086234	55754379	25440831	61	10157											
NACA2	342538	ucsc.edu	37	chr17	59668146	59668146	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctagttgtgcttgctgAgataaatcttggatcttggc	7	15	12	7	0	2	1	0	1	2	1	2	3	2	2	0	2	3	5	0	2	3	6			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:59668146A>G	ENST00000521764.1	-	1	417	c.396T>C	c.(394-396)tcT>tcC	p.S132S		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	132	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					GTGCTTGCTGAGATAAATCTT	0.443																																					p.S132S													.	NACA2-91	0			c.T396C						.						164	162	163					17																	59668146		2203	4300	6503	SO:0001819	synonymous_variant	342538	exon1			TTGCTGAGATAAA	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.396T>C	17.37:g.59668146A>G		Somatic	264	0		WXS	Illumina HiSeq		297	2	NM_199290	0	0	0	0	0	Q2VIR9	Silent	SNP	ENST00000521764.1	37	CCDS11630.1																																																																																			.		0.443	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		G	59668146	A	G	59668146	2	3	116	1	0	0	0	0	0	0	0	1	10159	291	11	3		3	NACA2	17	59668146	Silent	SNP	A	TCGA-G7-6796-01A-11D-1961-08	3913767	59668146	21527064	62	10158											
EXOC7	23265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74081426	74081426	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctggatctgctgctcaaTgtgctcccggtaggagcgct	5	11	14	11	2	3	0	1	0	2	0	4	2	4	2	1	4	4	5	1	4	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:74081426T>A	ENST00000335146.7	-	16	1887	c.1834A>T	c.(1834-1836)Att>Ttt	p.I612F	EXOC7_ENST00000467929.2_Missense_Mutation_p.I533F|EXOC7_ENST00000405575.4_Missense_Mutation_p.I584F|EXOC7_ENST00000411744.2_Missense_Mutation_p.I553F|EXOC7_ENST00000607838.1_Missense_Mutation_p.I584F|EXOC7_ENST00000589210.1_Missense_Mutation_p.I561F|EXOC7_ENST00000332065.5_Missense_Mutation_p.I530F|EXOC7_ENST00000591724.1_5'Flank			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	612					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			TGCTGCTCAATGTGCTCCCGG	0.632																																					p.I612F		.											.	EXOC7-90	0			c.A1834T						.						57	47	50					17																	74081426		2202	4300	6502	SO:0001583	missense	23265	exon16			GCTCAATGTGCTC	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1834A>T	17.37:g.74081426T>A	ENSP00000334100:p.Ile612Phe	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	40	14	NM_001145297	0	0	42	101	59	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	t	27.2	4.809754	0.90707	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.43	4.43	0.53597	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76097	0.3940	M	0.78637	2.42	0.80722	D	1	B;B;P;P;D;B;P	0.58268	0.143;0.014;0.851;0.874;0.982;0.029;0.925	B;B;P;P;D;B;P	0.66497	0.109;0.109;0.635;0.731;0.944;0.043;0.803	T	0.75204	-0.3400	9	0.27082	T	0.32	-17.3693	13.7322	0.62794	0.0:0.0:0.0:1.0	.	553;584;533;498;612;530;561	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	F	530;450;584;612;561;498;553	.	ENSP00000333806:I530F	I	-	1	0	EXOC7	71593021	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	8.037000	0.88933	1.656000	0.50722	0.392000	0.25879	ATT	.		0.632	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74081426	T	A	74081426	3	1	116	1	0	0	0	0	1	0	0	0	5323	1464	51	5	393	5	EXOC7	17	74081426	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	14413280	74081426	7113784	63	10159											
APCDD1	147495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	10487626	10487626	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccccatggatgcggccacagCctcactgctcaacgtcttca	8	8	8	17	2	4	0	3	0	1	0	4	1	4	1	4	2	4	1	4	2	1	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr18:10487626C>G	ENST00000355285.5	+	5	1490	c.1136C>G	c.(1135-1137)gCc>gGc	p.A379G	APCDD1_ENST00000578882.1_Missense_Mutation_p.S175R	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GCGGCCACAGCCTCACTGCTC	0.597																																					p.A379G		.											.	APCDD1-90	0			c.C1136G						.						75	69	71					18																	10487626		2203	4300	6503	SO:0001583	missense	147495	exon5			CCACAGCCTCACT	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1136C>G	18.37:g.10487626C>G	ENSP00000347433:p.Ala379Gly	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	95	15	NM_153000	0	0	0	0	0		Missense_Mutation	SNP	ENST00000355285.5	37	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172736	0.38413	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.18502	2.21	5.06	5.06	0.68205	.	0.162880	0.56097	D	0.000037	T	0.29288	0.0729	M	0.63843	1.955	0.29806	N	0.832069	P	0.46952	0.887	P	0.47044	0.535	T	0.12656	-1.0539	10	0.87932	D	0	-34.4277	18.7893	0.91966	0.0:1.0:0.0:0.0	.	379	Q8J025	APCD1_HUMAN	G	379;430	ENSP00000347433:A379G	ENSP00000347433:A379G	A	+	2	0	APCDD1	10477626	1.000000	0.71417	0.981000	0.43875	0.968000	0.65278	5.655000	0.67981	2.496000	0.84212	0.561000	0.74099	GCC	.		0.597	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		G	10487626	C	G	10487626	3	3	116	1	0	0	0	0	1	0	0	0	765	739	26	4	1154	4	APCDD1	18	10487626	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		10487626	67589622	64	10160											
VAV1	7409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6833546	6833546	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctgcatctcagaggtaccTtctatcagggctaccgctgc	7	10	9	15	1	3	1	2	0	2	1	4	1	3	1	3	2	4	4	3	2	3	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:6833546T>G	ENST00000602142.1	+	17	1700	c.1618T>G	c.(1618-1620)Ttc>Gtc	p.F540V	VAV1_ENST00000304076.2_Missense_Mutation_p.F540V|VAV1_ENST00000596764.1_Missense_Mutation_p.F508V|VAV1_ENST00000539284.1_Missense_Mutation_p.F443V|VAV1_ENST00000599806.1_Missense_Mutation_p.F485V	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	540					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CAGAGGTACCTTCTATCAGGG	0.542																																					p.F540V		.											.	VAV1-1276	0			c.T1618G						.						94	96	95					19																	6833546		2203	4300	6503	SO:0001583	missense	7409	exon17			GGTACCTTCTATC		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1618T>G	19.37:g.6833546T>G	ENSP00000472929:p.Phe540Val	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	203	25	NM_005428	0	0	0	0	0	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.306485	0.60305	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	D;D	0.92647	-3.08;-3.08	4.73	4.73	0.59995	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.055969	0.64402	D	0.000001	D	0.92954	0.7758	L	0.32530	0.975	0.58432	D	0.999999	D;D;D;D	0.89917	0.995;0.998;1.0;0.999	D;D;D;D	0.87578	0.94;0.982;0.998;0.996	D	0.93330	0.6700	10	0.62326	D	0.03	.	12.1658	0.54129	0.0:0.0:0.0:1.0	.	443;540;485;540	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	V	540;443	ENSP00000302269:F540V;ENSP00000443242:F443V	ENSP00000302269:F540V	F	+	1	0	VAV1	6784546	1.000000	0.71417	0.998000	0.56505	0.416000	0.31233	5.489000	0.66875	1.784000	0.52394	0.402000	0.26972	TTC	.		0.542	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			G	6833546	T	G	6833546	3	3	116	1	0	0	0	0	1	0	0	0	17164	1609	56	5	1684	5	VAV1	19	6833546	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08		6833546	52295437	65	10161											
RBM42	79171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36128157	36128157	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatccttccttaaggccaaGgtgatccgtgacaagcgcac	10	8	9	14	2	0	2	0	2	0	0	3	2	3	2	5	2	1	1	5	2	3	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:36128157G>A	ENST00000262633.4	+	9	1338	c.1233G>A	c.(1231-1233)aaG>aaA	p.K411K	RBM42_ENST00000592202.1_Silent_p.K357K|RBM42_ENST00000586618.1_Silent_p.K115K|RBM42_ENST00000360475.4_Silent_p.K382K|RBM42_ENST00000589559.1_Intron|RBM42_ENST00000589871.1_Silent_p.K389K|RBM42_ENST00000588161.1_Silent_p.K381K	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	411	Necessary for interaction with HNRNPK. {ECO:0000250}.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TTAAGGCCAAGGTGATCCGTG	0.577																																					p.K411K		.											.	RBM42-90	0			c.G1233A						.						108	81	90					19																	36128157		2203	4300	6503	SO:0001819	synonymous_variant	79171	exon9			GGCCAAGGTGATC	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"RNA binding motif (RRM) containing"	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.1233G>A	19.37:g.36128157G>A		Somatic	79	1		WXS	Illumina HiSeq	Phase_I	88	14	NM_024321	0	0	103	213	110	O00320|Q8N5R7|Q9BU66	Silent	SNP	ENST00000262633.4	37	CCDS12468.1																																																																																			.		0.577	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321		A	36128157	G	A	36128157	2	1	116	1	0	0	0	0	0	0	0	1	13168	991	35	2		2	RBM42	19	36128157	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08	29294611	36128157	23000826	66	10162											
HNRNPUL1	11100	bcgsc.ca	37	chr19	41807610	41807610	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgcggtcttagaaatgaaagGtaggaaatgagtgcttccca	13	10	12	6	1	1	3	0	2	1	1	2	4	2	4	1	3	2	2	1	3	5	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:41807610G>C	ENST00000392006.3	+	11	1860		c.e11+1		HNRNPUL1_ENST00000263367.3_Splice_Site|HNRNPUL1_ENST00000595018.1_Splice_Site|HNRNPUL1_ENST00000378215.4_Splice_Site|HNRNPUL1_ENST00000593587.1_Splice_Site|HNRNPUL1_ENST00000352456.3_Splice_Site|HNRNPUL1_ENST00000602130.1_Splice_Site	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1						gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						GAAATGAAAGGTAGGAAATGA	0.483																																					.													.	HNRNPUL1-69	0			c.1387+1G>C						.						85	71	76					19																	41807610		2203	4300	6503	SO:0001630	splice_region_variant	11100	exon11			TGAAAGGTAGGAA	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"E1B 55kDa associated protein 5"	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1687+1G>C	19.37:g.41807610G>C		Somatic	62	0		WXS	Illumina HiSeq	Phase_1	61	8	NM_144732	0	0	2	2	0	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Splice_Site	SNP	ENST00000392006.3	37	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968359	0.92855	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1835	0.89786	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPUL1	46499450	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.596000	0.98267	2.833000	0.97629	0.650000	0.86243	.	.		0.483	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	Intron	C	41807610	G	C	41807610	5	2	116	1	0	0	0	0	0	0	1	0	7295	1275	44	4	1730	4	HNRNPUL1	19	41807610	Splice_Site	SNP	G	TCGA-G7-6796-01A-11D-1961-08	5679453	41807610	17321373	67	10163											
IRGC	56269	hgsc.bcm.edu	37	chr19	44223048	44223048	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgaccctctgggacctgcCaggagccggctctccaggct	5	7	13	16	2	2	1	0	1	2	0	3	3	2	3	5	4	2	2	5	4	0	0			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:44223048C>G	ENST00000244314.5	+	2	537	c.338C>G	c.(337-339)cCa>cGa	p.P113R		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	113	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				TGGGACCTGCCAGGAGCCGGC	0.652																																					p.P113R	Colon(189;350 2037 11447 13433 38914)	.											.	IRGC-70	0			c.C338G						.						22	21	21					19																	44223048		2194	4288	6482	SO:0001583	missense	56269	exon2			ACCTGCCAGGAGC	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"immunity-related GTPase family, cinema 1"	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.338C>G	19.37:g.44223048C>G	ENSP00000244314:p.Pro113Arg	Somatic	50	2		WXS	Illumina HiSeq	Phase_I	38	2	NM_019612	0	0	0	0	0	Q05BR8	Missense_Mutation	SNP	ENST00000244314.5	37	CCDS12629.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.785694	0.70337	.	.	ENSG00000124449	ENST00000244314	T	0.56275	0.47	5.71	4.68	0.58851	.	0.067487	0.64402	D	0.000013	T	0.75347	0.3837	M	0.88704	2.975	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	T	0.80185	-0.1487	10	0.87932	D	0	.	12.2899	0.54812	0.0:0.9182:0.0:0.0818	.	113	Q6NXR0	IIGP5_HUMAN	R	113	ENSP00000244314:P113R	ENSP00000244314:P113R	P	+	2	0	IRGC	48914888	1.000000	0.71417	0.878000	0.34440	0.920000	0.55202	6.892000	0.75644	1.421000	0.47157	0.555000	0.69702	CCA	.		0.652	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612		G	44223048	C	G	44223048	3	3	116	1	0	0	0	0	1	0	0	0	7859	594	21	4	340	4	IRGC	19	44223048	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	2415438	44223048	14905935	68	10164											
ERCC1	2067	hgsc.bcm.edu	37	chr19	45926544	45926544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaccactccaggagggaccTcatcctcgtcgaggggtatc	8	8	11	14	2	1	0	1	0	0	0	6	3	3	2	4	4	1	1	4	4	2	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:45926544T>C	ENST00000300853.3	-	2	680	c.89A>G	c.(88-90)gAg>gGg	p.E30G	ERCC1_ENST00000340192.7_Missense_Mutation_p.E30G|ERCC1_ENST00000013807.5_Missense_Mutation_p.E30G|ERCC1_ENST00000589165.1_Missense_Mutation_p.E30G|ERCC1_ENST00000423698.2_Missense_Mutation_p.E30G|ERCC1_ENST00000591636.1_Missense_Mutation_p.E30G	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	30					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		AGGAGGGACCTCATCCTCGTC	0.627								Nucleotide excision repair (NER)																													p.E30G		.											.	ERCC1-659	0			c.A89G						.						64	57	60					19																	45926544		2203	4300	6503	SO:0001583	missense	2067	exon2			GGGACCTCATCCT		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.89A>G	19.37:g.45926544T>C	ENSP00000300853:p.Glu30Gly	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_001983	0	0	18	18	0	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	T	7.316	0.615930	0.14129	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807;ENST00000428893	T;T;T;T	0.50277	0.79;0.77;0.8;0.75	4.82	0.105	0.14535	.	0.649699	0.14042	N	0.345379	T	0.28566	0.0707	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.27823	0.164;0.041;0.099;0.19	B;B;B;B	0.24155	0.04;0.023;0.037;0.051	T	0.12604	-1.0541	10	0.39692	T	0.17	-19.7324	7.1713	0.25721	0.1454:0.0:0.4523:0.4023	.	30;30;30;30	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	G	30	ENSP00000300853:E30G;ENSP00000345203:E30G;ENSP00000394875:E30G;ENSP00000013807:E30G	ENSP00000013807:E30G	E	-	2	0	ERCC1	50618384	0.005000	0.15991	0.003000	0.11579	0.311000	0.27955	-0.194000	0.09559	-0.182000	0.10602	-0.680000	0.03767	GAG	.		0.627	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983		C	45926544	T	C	45926544	3	2	116	1	0	0	0	0	1	0	0	0	5225	1551	54	3	969	3	ERCC1	19	45926544	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	1703496	45926544	13202439	69	10165											
PPP2R1A	5518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52724382	52724382	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgactacgctcttctgcaTcaatgtgagccttccacctg	8	12	7	14	1	3	2	1	2	2	0	4	2	4	2	3	0	3	2	3	0	2	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:52724382T>C	ENST00000322088.6	+	12	1572	c.1514T>C	c.(1513-1515)aTc>aCc	p.I505T	PPP2R1A_ENST00000444322.2_Missense_Mutation_p.I450T|PPP2R1A_ENST00000462990.1_Missense_Mutation_p.I326T|CTD-2525I3.3_ENST00000593857.1_RNA	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	505	PP2A subunit C binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		CTCTTCTGCATCAATGTGAGC	0.597			Mis		clear cell ovarian carcinoma																																p.I505T		.		Dom?	yes		19	19q13.41	5518	"protein phosphatase 2, regulatory subunit A, alpha"		E	.	PPP2R1A-1666	0			c.T1514C						.						150	125	133					19																	52724382		2203	4300	6503	SO:0001583	missense	5518	exon12			TCTGCATCAATGT		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9302	protein-coding gene	gene with protein product	"protein phosphatase 2A, regulatory subunit A, alpha isoform", "protein phosphatase 2, 65kDa regulatory subunit A"	605983	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.1514T>C	19.37:g.52724382T>C	ENSP00000324804:p.Ile505Thr	Somatic	211	2		WXS	Illumina HiSeq	Phase_I	180	43	NM_014225	0	0	0	0	0	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	37	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.028431	0.75390	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000436460;ENST00000444322	T;T	0.37235	1.21;2.1	4.67	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000014	T	0.66954	0.2842	M	0.92555	3.32	0.80722	D	1	D;P	0.57899	0.981;0.93	D;P	0.78314	0.991;0.88	T	0.75314	-0.3361	10	0.87932	D	0	-30.8602	12.4016	0.55416	0.0:0.0:0.0:1.0	.	450;505	F5H3X9;P30153	.;2AAA_HUMAN	T	495;425;505;72;450	ENSP00000324804:I505T;ENSP00000415067:I450T	ENSP00000324804:I505T	I	+	2	0	PPP2R1A	57416194	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.226000	0.78060	2.091000	0.63221	0.533000	0.62120	ATC	.		0.597	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225		C	52724382	T	C	52724382	3	2	116	1	0	0	0	0	1	0	0	0	12411	1435	50	3	1560	3	PPP2R1A	19	52724382	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	6797838	52724382	6404601	70	10166											
ZNF132	7691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58945194	58945194	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacactcgtaaggcttttcTccagtgtgaattctccagtg	8	14	8	11	1	2	1	0	1	2	0	5	1	2	1	2	1	1	2	2	1	3	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:58945194T>A	ENST00000254166.3	-	3	2017	c.1617A>T	c.(1615-1617)ggA>ggT	p.G539G	CTD-2619J13.17_ENST00000594816.1_lincRNA	NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	539					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(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		AAGGCTTTTCTCCAGTGTGAA	0.478																																					p.G539G		.											.	ZNF132-92	0			c.A1617T						.						81	83	82					19																	58945194		2203	4300	6503	SO:0001819	synonymous_variant	7691	exon3			CTTTTCTCCAGTG	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1617A>T	19.37:g.58945194T>A		Somatic	107	0		WXS	Illumina HiSeq	Phase_I	112	22	NM_003433	0	0	0	0	0	Q32MI9	Silent	SNP	ENST00000254166.3	37	CCDS12980.1																																																																																			.		0.478	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		A	58945194	T	A	58945194	2	1	116	1	0	0	0	0	0	0	0	1	17754	1538	54	5		5	ZNF132	19	58945194	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08	6220812	58945194	183789	71	10167											
SEC23B	10483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	18496315	18496315	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctccagcttatggaggcAtatctgaggtgaatcaacct	10	12	9	10	0	2	2	1	2	1	0	4	3	4	3	3	3	2	2	3	3	4	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr20:18496315A>T	ENST00000336714.3	+	4	733	c.301A>T	c.(301-303)Ata>Tta	p.I101L	SEC23B_ENST00000377465.1_Missense_Mutation_p.I101L|SEC23B_ENST00000494645.1_3'UTR|SEC23B_ENST00000377475.3_Missense_Mutation_p.I101L|SEC23B_ENST00000262544.2_Missense_Mutation_p.I101L	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	101					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						TTATGGAGGCATATCTGAGGT	0.348																																					p.I101L		.											.	SEC23B-91	0			c.A301T						.						155	118	130					20																	18496315		2203	4300	6503	SO:0001583	missense	10483	exon4			GGAGGCATATCTG	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"Sec23 (S. cerevisiae) homolog B", "congenital dyserythropoietic anemia, type II"	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.301A>T	20.37:g.18496315A>T	ENSP00000338844:p.Ile101Leu	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	102	14	NM_032985	0	0	2	4	2	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.215314	0.79352	.	.	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.04	5.04	0.67666	Zinc finger, Sec23/Sec24-type (1);	0.000000	0.85682	D	0.000000	D	0.86347	0.5911	M	0.81112	2.525	0.80722	D	1	P;P	0.41041	0.736;0.643	P;B	0.45577	0.486;0.271	D	0.87381	0.2357	10	0.49607	T	0.09	-22.3484	14.4009	0.67044	1.0:0.0:0.0:0.0	.	101;101	B4DJW8;Q15437	.;SC23B_HUMAN	L	101	ENSP00000403971:I101L;ENSP00000338844:I101L;ENSP00000262544:I101L;ENSP00000366695:I101L;ENSP00000366685:I101L	ENSP00000262544:I101L	I	+	1	0	SEC23B	18444315	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	8.929000	0.92859	2.241000	0.73720	0.528000	0.53228	ATA	.		0.348	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			T	18496315	A	T	18496315	3	4	116	1	0	0	0	0	1	0	0	0	14024	217	8	5	311	5	SEC23B	20	18496315	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		18496315	44529205	72	10168											
RPL3	6122	ucsc.edu	37	chr22	39711372	39711372	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaagccaccgcaaagctcAcctttgtagcctttgccctt	8	11	6	16	1	2	0	2	0	0	0	2	0	2	0	5	0	4	3	5	0	3	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr22:39711372A>C	ENST00000216146.4	-	5	862		c.e5+1		SNORD83A_ENST00000386747.1_RNA|SNORD83B_ENST00000386745.1_RNA|RPL3_ENST00000465618.1_Splice_Site|RPL3_ENST00000401609.1_Splice_Site	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3						cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	CGCAAAGCTCACCTTTGTAGC	0.572																																					.													.	RPL3-154	0			c.541+2T>G						.						115	104	108					22																	39711372		2203	4300	6503	SO:0001630	splice_region_variant	6122	exon6			AAGCTCACCTTTG	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"L ribosomal proteins"	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.688+1T>G	22.37:g.39711372A>C		Somatic	171	0		WXS	Illumina HiSeq		138	1	NM_001033853	0	0	0	0	0	B2RDV9|Q15548|Q5I0G0	Splice_Site	SNP	ENST00000216146.4	37	CCDS13988.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.240605	0.79912	.	.	ENSG00000100316	ENST00000401609;ENST00000216146;ENST00000402527;ENST00000453303	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4065	0.74884	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPL3	38041318	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.163000	0.77524	2.051000	0.60960	0.379000	0.24179	.	.		0.572	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967	Intron	C	39711372	A	C	39711372	5	2	116	1	0	0	0	0	0	0	1	0	13611	173	6	5	545	5	RPL3	22	39711372	Splice_Site	SNP	A	TCGA-G7-6796-01A-11D-1961-08		39711372	11593194	73	10169											
FAM132A	388581	ucsc.edu	37	chr1	1179654	1179654	+	Splice_Site	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggggaccgaagagatccCgctggggggagagagaagca	11	3	19	8	2	0	3	0	0	0	3	1	8	1	4	2	5	1	2	2	5	2	0			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	35	32					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	A	1179654	C	A	1179654	5	1	117	1	0	0	0	0	0	0	1	0	5458	666	23	4	636	4	FAM132A	1	1179654	Splice_Site	SNP	C	TCGA-G7-6797-01A-11D-1961-08		1179654	248070967	1	10170											
XKR8	55113	ucsc.edu	37	chr1	28290011	28290011	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtgtgtggtgcctaggtgCgtgcaggagctgcggcaggg	4	10	20	7	2	0	0	0	0	0	0	0	1	0	1	1	5	5	3	1	5	1	2			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	43	43					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		T	28290011	C	T	28290011	2	4	117	1	0	0	0	0	0	0	0	1	17470	776	27	1		1	XKR8	1	28290011	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	27110357	28290011	220960610	2	10171											
ZSCAN20	7579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	33960785	33960785	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtgagcgctccaagctcatCacacaccagagagtgcacac	13	5	9	14	1	2	2	2	1	0	1	3	3	3	2	2	0	3	3	2	0	1	0			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	96	91					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		T	33960785	C	T	33960785	2	4	117	1	0	0	0	0	0	0	0	1	18264	816	29	2		2	ZSCAN20	1	33960785	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	5670774	33960785	215289836	3	10172											
LGTN	1939	ucsc.edu	37	chr1	206785684	206785684	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggacttgacccgaaaggcCttggcaaacatgtctgctgg	9	10	12	10	1	1	1	0	1	1	0	1	3	1	2	2	4	2	2	2	4	2	3			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	103	108					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		T	206785684	C	T	206785684	2	4	117	1	0	0	0	0	0	0	0	1	8782	680	24	2		2	LGTN	1	206785684	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	172824899	206785684	42464937	4	10173											
FAM71A	149647	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	212799448	212799448	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgagtggacagcatggaaGggagcgaacccaggccagcg	11	3	16	11	2	0	1	0	1	0	0	0	5	0	4	3	4	4	1	3	4	2	0	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	59	57					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		T	212799448	G	T	212799448	3	4	117	1	0	0	0	0	1	0	0	0	5626	1000	35	4	1231	4	FAM71A	1	212799448	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	6013764	212799448	36451173	5	10174											
URB2	9816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	229770859	229770859	+	Missense_Mutation	SNP	G	G	C																															agcccgaaggagctgtggtaGcccagttgtttgaggtcatt																										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	55	59					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		C	229770859	G	C	229770859	3	2	117	1	0	0	0	0	1	0	0	0	17058	971	34	4	509	4	URB2	1	229770859	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	16971411	229770859	19479762	6	10175	104	2									
URB2	9816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	229770863	229770863	+	Missense_Mutation	SNP	A	A	G																															cgaaggagctgtggtagcccAgttgtttgaggtcattcacc																										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	55	59					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		G	229770863	A	G	229770863	3	3	117	1	0	0	0	0	1	0	0	0	17058	188	7	3	513	3	URB2	1	229770863	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	4	229770863	19479758	7	10176	104	2									
GEN1	348654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	17955658	17955658	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagaaactctaatcaactaCagccaattcggtaatgtaaa	17	9	6	9	1	2	1	1	0	1	1	3	1	2	1	1	1	4	3	1	1	8	5			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	106	103					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		T	17955658	C	T	17955658	4	4	117	1	0	0	0	0	0	1	0	0	6355	479	17	2	1230	2	GEN1	2	17955658	Nonsense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		17955658	225243715	8	10177											
GPR113	165082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	26532908	26532908	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatctgaaggcagcaactCaccagggagatggtggagct	12	6	15	8	0	2	2	1	1	1	1	2	5	2	4	1	5	3	3	1	5	2	0			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	77	77					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		A	26532908	C	A	26532908	2	1	117	1	0	0	0	0	0	0	0	1	6650	813	29	4		4	GPR113	2	26532908	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	8577250	26532908	216666465	9	10178											
PSME4	23198	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	54147352	54147352	+	Frame_Shift_Del	DEL	C	C	-																															agacatttcaagttttccatCcccacaatgctggagtttga																										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	171	164					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		-	54147352	C	-	54147352	7	5	117	1	0	1	0	1	0	0	0	0	12738	855	30	0	3245	0	PSME4	2	54147352	Frame_Shift_Del	DEL	C	TCGA-G7-6797-01A-11D-1961-08	27614444	54147352	189052021	10	10179											
GFPT1	2673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	69553334	69553334	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattcctcactctacagtcAcagatttggcaagattccgt	11	13	6	11	1	3	2	2	0	1	2	5	2	5	2	2	1	1	1	2	1	3	5			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	90	90					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				T	69553334	A	T	69553334	3	4	117	1	0	0	0	0	1	0	0	0	6365	159	6	5	16	5	GFPT1	2	69553334	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	15405982	69553334	173646039	11	10180											
NCKAP5	344148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	133541732	133541732	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgactcttggggcactggacCcagtccctcctgctgggcat	5	10	12	14	0	1	1	0	1	1	0	3	2	3	2	3	4	1	3	3	4	0	1			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	56	56					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		G	133541732	C	G	133541732	3	3	117	1	0	0	0	0	1	0	0	0	10249	624	22	4	3105	4	NCKAP5	2	133541732	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	63988398	133541732	109657641	12	10181											
TANC1	85461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160084382	160084382	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagtatgccttaagaaagtTtcctcgagaaggattcggag	12	10	11	8	2	0	2	0	0	0	2	3	5	1	4	3	2	1	2	3	2	4	4			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	84	83					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			G	160084382	T	G	160084382	3	3	117	1	0	0	0	0	1	0	0	0	15576	1841	64	5	4046	5	TANC1	2	160084382	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	26542650	160084382	83114991	13	10182											
ITM2C	81618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	231741583	231741583	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctgccagggtctgactgcGtaccatgatatctccctgga	7	11	10	13	1	2	2	0	2	2	0	4	3	3	3	4	2	3	1	4	2	2	2			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	126	133					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		C	231741583	G	C	231741583	2	2	117	1	0	0	0	0	0	0	0	1	7935	1132	40	4		4	ITM2C	2	231741583	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	71657201	231741583	11457790	14	10183											
CCR2	729230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46399085	46399085	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcggtgaagaagtcaccaccTtttttgattatgattacggt	10	14	10	7	2	1	4	1	3	0	1	1	4	1	4	2	2	1	0	2	2	4	5			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	172	179					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		A	46399085	T	A	46399085	3	1	117	1	0	0	0	0	1	0	0	0	2947	1609	56	5	69	5	CCR2	3	46399085	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08		46399085	151623345	15	10184											
SLC26A6	65010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48668741	48668741	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgtggccccgatgagcTgtgggagaggacagagtcag	8	7	17	9	1	1	3	1	1	0	2	1	6	1	4	3	3	2	1	3	3	0	0			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_ENST00000337000.8_Splice_Site|SLC26A6_ENST00000455886.2_Splice_Site|SLC26A6_ENST00000482282.1_5'Flank|SLC26A6_ENST00000420764.2_Splice_Site|SLC26A6_ENST00000383733.3_Splice_Site|SLC26A6_ENST00000358747.6_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	42	41					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	C	48668741	T	C	48668741	5	2	117	1	0	0	0	0	0	0	1	0	14553	1594	55	3	1469	3	SLC26A6	3	48668741	Splice_Site	SNP	T	TCGA-G7-6797-01A-11D-1961-08	2269656	48668741	149353689	16	10185											
GPX1	387	ucsc.edu	37	chr3	49394910	49394910	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcggctgtacctgcgtagggGcacaccgtcagggcccacca	7	5	14	15	3	1	0	1	0	0	0	1	0	1	0	4	4	2	4	4	4	2	2			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_ENST00000496791.1_5'Flank|GPX1_ENST00000419783.1_Missense_Mutation_p.P175S	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	29	28					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		A	49394910	G	A	49394910	1	1	117	0	1	0	0	0	0	0	0	0	6760	1203	42	2		2	GPX1	3	49394910	IGR	SNP	G	TCGA-G7-6797-01A-11D-1961-08	726169	49394910	148627520	17	10186											
ZMYND10	51364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50379017	50379017	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accctcacctgcagcaatacCactcattctggcatcgtgag	10	9	7	15	1	3	1	2	1	1	0	4	1	3	1	3	1	3	3	3	1	2	2			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*	RASSF1_ENST00000357043.2_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA|ZMYND10_ENST00000360165.3_Nonsense_Mutation_p.W407*|RASSF1_ENST00000488024.1_5'Flank|RASSF1_ENST00000359365.4_5'Flank|ZMYND10_ENST00000490675.1_5'UTR	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	129	132					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		T	50379017	C	T	50379017	4	4	117	1	0	0	0	0	0	1	0	0	17737	595	21	2	95	2	ZMYND10	3	50379017	Nonsense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	984107	50379017	147643413	18	10187											
C3orf63	23272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56658883	56658883	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagactatgtgtcgttgctGtatgttctgagcctgaagtc	9	14	11	7	1	1	3	0	2	1	1	3	3	1	3	1	0	2	4	1	0	4	4			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	125	126					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		C	56658883	G	C	56658883	3	2	117	1	0	0	0	0	1	0	0	0	2245	1386	48	4	793	4	C3orf63	3	56658883	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	6279866	56658883	141363547	19	10188											
ACOX2	8309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	58517532	58517532	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	accagggcatgggtggctgaCcgtcccactgagggcagaga	9	5	16	11	1	0	3	0	2	0	1	1	4	1	3	3	4	0	3	3	4	0	0			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	50	52					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			A	58517532	C	A	58517532	2	1	117	1	0	0	0	0	0	0	0	1	159	494	18	4		4	ACOX2	3	58517532	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	1858649	58517532	139504898	20	10189											
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101370105	101370105	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccttgctgttgtgctaataCataattaaccacttgcataa	12	15	5	9	0	0	0	0	0	0	0	1	0	1	0	2	0	5	4	2	0	5	8			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	131	132					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		T	101370105	C	T	101370105	3	4	117	1	0	0	0	0	1	0	0	0	17556	478	17	2	98	2	ZBTB11	3	101370105	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	42852573	101370105	96652325	21	10190											
KIAA2018	205717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113376409	113376409	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagggatctgactgaccaTcatttgagtttggtcagaaa	12	11	12	6	0	3	4	2	3	1	1	3	6	3	6	1	3	0	1	1	3	1	2			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	102	103					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		C	113376409	T	C	113376409	3	2	117	1	0	0	0	0	1	0	0	0	8289	1435	50	3	2621	3	KIAA2018	3	113376409	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	12006304	113376409	84646021	22	10191											
FSTL1	11167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	120122159	120122159	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgagtttccaatcagcAttttcatcagacagttcaat	13	13	6	9	0	4	2	4	1	0	1	5	2	5	2	1	0	2	4	1	0	3	4			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	106	106					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		G	120122159	A	G	120122159	2	3	117	1	0	0	0	0	0	0	0	1	6096	214	8	3		3	FSTL1	3	120122159	Silent	SNP	A	TCGA-G7-6797-01A-11D-1961-08	6745750	120122159	77900271	23	10192											
COL6A6	131873	hgsc.bcm.edu;bcgsc.ca	37	chr3	130311918	130311918	+	Frame_Shift_Del	DEL	A	A	-																															ttttcagggagaagttggggAaaatggaattgacggattaa																										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	259	262					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		-	130311918	A	-	130311918	7	5	117	1	0	1	0	1	0	0	0	0	3709	246	9	0	4443	0	COL6A6	3	130311918	Frame_Shift_Del	DEL	A	TCGA-G7-6797-01A-11D-1961-08	10189759	130311918	67710512	24	10193											
ETV5	2119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	185766603	185766603	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaaagccatggagaagaggGcatctgggtcacagacaaat	15	5	14	7	0	2	3	1	0	1	3	2	5	2	4	1	4	1	1	1	4	3	0			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_ENST00000480706.1_5'UTR|ETV5_ENST00000434744.1_Missense_Mutation_p.A453V|ETV5_ENST00000537818.1_Missense_Mutation_p.A495V	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	61	64					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		A	185766603	G	A	185766603	3	1	117	1	0	0	0	0	1	0	0	0	5295	1203	42	2	178	2	ETV5	3	185766603	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	55454685	185766603	12255827	25	10194											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187539870	187539870	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcggcattggagccctcatCggcatcacttgcaagaactt	9	10	10	12	2	2	1	2	0	0	1	4	2	2	2	1	3	3	3	1	3	2	3			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	59	60					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		A	187539870	C	A	187539870	3	1	117	1	0	0	0	0	1	0	0	0	5708	884	31	4	5968	4	FAT1	4	187539870	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		187539870	3614406	26	10195											
CLPTM1L	81037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1335258	1335258	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgtcgtaggacacggtgAggggcagctcggtggtggag	6	8	19	8	3	0	1	0	1	0	0	2	3	0	3	1	7	1	3	1	7	1	2			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	103	105					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		G	1335258	A	G	1335258	3	3	117	1	0	0	0	0	1	0	0	0	3561	304	11	3	954	3	CLPTM1L	5	1335258	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08		1335258	179580002	27	10196											
RGS7BP	401190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	63905047	63905047	+	Frame_Shift_Del	DEL	T	T	-																															tgagaagacggaagagaaggTtctttgggctgtgttgtctc																										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	148	155					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		-	63905047	T	-	63905047	7	5	117	1	0	1	0	1	0	0	0	0	13343	1725	60	0	764	0	RGS7BP	5	63905047	Frame_Shift_Del	DEL	T	TCGA-G7-6797-01A-11D-1961-08	62569789	63905047	117010213	28	10197											
BHMT	635	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	78426827	78426828	+	Frame_Shift_Ins	INS	-	-	A																															aacccttcaatgtcaaagccINSagatggctggggagtgacca																										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		A	78426828	-	A	78426827	7	5	117	1	0	1	1	0	0	0	0	0	1426	594	21	0	1139	0	BHMT	5	78426827	Frame_Shift_Ins	INS	-	TCGA-G7-6797-01A-11D-1961-08	14521780	78426827	102488433	29	10198											
FBXL21	3950	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	135276238	135276238	+	5'UTR	DEL	A	A	-																															caaaatcattatcatcaatcAaaattgaagatacaccagtg																										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_ENST00000297158.9_RNA|FBXL21_ENST00000467490.1_RNA|LECT2_ENST00000522943.1_Intron			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	71	72					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		-	135276238	A	-	135276238	6	5	117	0	1	1	0	1	0	0	0	0	5737	131	5	0		0	FBXL21	5	135276238	5'UTR	DEL	A	TCGA-G7-6797-01A-11D-1961-08	56849411	135276238	45639022	30	10199											
HLA-G	3135	ucsc.edu	37	chr6	29797394	29797394	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgggcagctgtggtggtGccttctggagaggagcagag	8	8	19	6	0	1	2	0	0	1	2	1	4	1	3	1	5	3	3	1	5	1	1			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_ENST00000376828.2_Silent_p.V278V|HLA-G_ENST00000428701.1_Silent_p.V273V|HLA-G_ENST00000376818.3_Silent_p.V181V|HLA-G_ENST00000376815.3_Intron			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	58	60					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		A	29797394	G	A	29797394	2	1	117	1	0	0	0	0	0	0	0	1	7233	1306	46	2		2	HLA-G	6	29797394	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08		29797394	141317673	31	10200											
AKAP12	9590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	151626981	151626981	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatggccagaaaggagccCtgaacggtcaaggagcccta	14	5	12	10	1	1	2	1	1	0	1	1	4	1	4	3	4	3	0	3	4	6	2			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	46	49					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			G	151626981	C	G	151626981	3	3	117	1	0	0	0	0	1	0	0	0	448	680	24	4	268	4	AKAP12	6	151626981	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	121829587	151626981	19488086	32	10201											
PGAM2	5224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44105125	44105125	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catcacgaggcggtgagtggCcatggtggcagcagggacca	9	5	17	10	2	1	1	1	1	0	0	1	3	1	2	2	6	1	2	2	6	0	0			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	54	57					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			A	44105125	C	A	44105125	3	1	117	1	0	0	0	0	1	0	0	0	11800	739	26	4	769	4	PGAM2	7	44105125	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		44105125	115033538	33	10202											
TMED4	222068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44621125	44621125	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtcaccgggcgtgtgggAggtgaacgtgaagcggccct	7	7	18	9	4	1	2	1	2	0	0	1	3	1	3	2	5	2	0	2	5	2	0			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	89	89					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		G	44621125	A	G	44621125	3	3	117	1	0	0	0	0	1	0	0	0	16038	304	11	3	385	3	TMED4	7	44621125	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	516000	44621125	114517538	34	10203											
ADAM28	10863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	24209520	24209520	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgagtcagatgaagccccaTgtgtatgatctgccagtaga	12	10	11	8	0	2	5	1	3	1	2	2	5	2	5	3	0	2	2	3	0	3	2			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	ADAM28_ENST00000397649.3_Missense_Mutation_p.C482R|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523578.1_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	114	115					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		C	24209520	T	C	24209520	2	2	117	1	0	0	0	0	0	0	0	1	246	1461	51	3		3	ADAM28	8	24209520	Silent	SNP	T	TCGA-G7-6797-01A-11D-1961-08		24209520	122154502	35	10204											
BNIP3L	665	hgsc.bcm.edu	37	chr8	26240664	26240664	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	acaatgtcgtcccacctagtCgagccgccgccgcccctgca	7	6	9	19	5	0	0	0	0	0	0	3	1	1	0	7	0	2	1	7	0	2	1			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	19	18					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		G	26240664	C	G	26240664	2	3	117	1	0	0	0	0	0	0	0	1	1480	871	31	4		4	BNIP3L	8	26240664	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	2031144	26240664	120123358	36	10205											
RAB11FIP1	80223	broad.mit.edu	37	chr8	37729419	37729419	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatctattctttcatcatcCgatgcgacttcaggaatgga	10	14	8	9	2	5	1	3	1	2	0	6	5	6	3	1	2	1	0	1	2	2	4			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_ENST00000524118.1_Intron|RAB11FIP1_ENST00000522727.1_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	128	137					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		A	37729419	C	A	37729419	2	1	117	1	0	0	0	0	0	0	0	1	12925	639	23	4		4	RAB11FIP1	8	37729419	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	11488755	37729419	108634603	37	10206											
XKR4	114786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	56435874	56435874	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttccctcgtgtccctggcCtgggccttggcctcctacca	2	11	10	18	1	0	0	0	0	0	0	4	0	3	0	7	3	1	1	7	3	1	3	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	57	59					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		G	56435874	C	G	56435874	2	3	117	1	0	0	0	0	0	0	0	1	17466	668	24	4		4	XKR4	8	56435874	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	18706455	56435874	89928148	38	10207											
HNF4G	3174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	76465335	76465335	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgttaagaaaattgcaagtaTtggtgatgtctgtgaatcta	13	14	10	4	1	2	3	0	2	2	1	2	3	2	3	0	1	1	3	0	1	7	5			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	109	113					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		C	76465335	T	C	76465335	3	2	117	1	0	0	0	0	1	0	0	0	7275	1493	52	3	536	3	HNF4G	8	76465335	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	20029461	76465335	69898687	39	10208											
PTK2	5747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	141745382	141745382	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttaagttcagtaaacctgggCcgcctgctggggtcataggc	8	10	13	10	1	2	0	2	0	0	0	2	0	2	0	3	4	2	3	3	4	4	4			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_ENST00000538769.1_Silent_p.R334R|PTK2_ENST00000535192.1_Silent_p.R666R|PTK2_ENST00000395218.2_Silent_p.R666R|MIR151A_ENST00000521276.1_RNA|PTK2_ENST00000519419.1_Silent_p.R710R|PTK2_ENST00000517887.1_Silent_p.R710R|PTK2_ENST00000340930.3_Silent_p.R666R|PTK2_ENST00000519465.1_Silent_p.R294R|PTK2_ENST00000521059.1_Silent_p.R666R	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	52	55					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		T	141745382	C	T	141745382	2	4	117	1	0	0	0	0	0	0	0	1	12792	726	26	2		2	PTK2	8	141745382	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	65280047	141745382	4618640	40	10209											
OPLAH	26873	broad.mit.edu	37	chr8	145113801	145113801	+	Splice_Site	DEL	T	T	-																															agcaggtcccccgtgcggccTtccagaaaagcccaggaggc																										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	12	11					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	-	145113801	T	-	145113801	8	5	117	1	0	1	0	1	0	0	1	0	10902	1623	56	0	3498	0	OPLAH	8	145113801	Splice_Site	DEL	T	TCGA-G7-6797-01A-11D-1961-08	3368419	145113801	1250221	41	10210											
C9orf123	90871	broad.mit.edu	37	chr9	7799724	7799724	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcaaaaggctgggacaacCgagaccccatgctctggaac	13	5	10	13	1	2	1	1	0	1	1	2	4	2	3	3	3	3	2	3	3	4	0			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	23	23					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		G	7799724	C	G	7799724	3	3	117	1	0	0	0	0	1	0	0	0	2459	652	23	4	335	4	C9orf123	9	7799724	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		7799724	133413707	42	10211											
SEC61B	10952	bcgsc.ca	37	chr9	101992685	101992685	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtatttatgttgcacatttgGggcaagtacactcgttcgta	9	15	10	7	2	0	0	0	0	0	0	2	0	0	0	0	2	2	7	0	2	5	8			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	251	258					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		T	101992685	G	T	101992685	3	4	117	1	0	0	0	0	1	0	0	0	14034	1241	43	4	284	4	SEC61B	9	101992685	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	94192961	101992685	39220746	43	10212											
TBC1D13	54662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131565636	131565636	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtggagcggatcctgttcatCtacgccaagctcaaccctgg	8	9	11	13	2	3	0	2	0	1	0	4	2	4	2	3	3	4	2	3	3	3	2			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_ENST00000223865.8_Intron|TBC1D13_ENST00000539497.1_Missense_Mutation_p.I36M|TBC1D13_ENST00000466056.1_3'UTR	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	121	131					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		G	131565636	C	G	131565636	3	3	117	1	0	0	0	0	1	0	0	0	15634	903	32	4	681	4	TBC1D13	9	131565636	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	29572951	131565636	9647795	44	10213											
MCM10	55388	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	13222572	13222572	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgggtgacatttggggttAtattgaagaaggttacgcca	11	13	13	4	1	0	3	0	2	0	1	0	3	0	3	1	4	1	2	1	4	5	6			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_ENST00000378714.3_Missense_Mutation_p.I299L|MCM10_ENST00000378694.1_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	230	231					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		C	13222572	A	C	13222572	3	2	117	1	0	0	0	0	1	0	0	0	9410	449	16	5	920	5	MCM10	10	13222572	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08		13222572	122312175	45	10214											
PCBD1	5092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	72643783	72643783	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaaggccggcacactcaTgggtgctcagcgtgatgtgg	8	8	15	10	2	2	2	2	2	0	0	2	2	2	2	1	4	2	2	1	4	1	0			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	76	82					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		C	72643783	T	C	72643783	3	2	117	1	0	0	0	0	1	0	0	0	11524	1464	51	3	79	3	PCBD1	10	72643783	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	59421211	72643783	62890964	46	10215											
ADAM8	101	ucsc.edu	37	chr10	135080899	135080899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agacaggaactgggaagggtGggctggacacagtgaccgga	12	4	18	7	1	0	2	0	1	0	1	0	6	0	6	1	6	1	1	1	6	2	0			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	78	85					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		A	135080899	G	A	135080899	3	1	117	1	0	0	0	0	1	0	0	0	252	1348	47	2	128	2	ADAM8	10	135080899	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	62437116	135080899	453848	47	10216											
OR4C13	283092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	49974076	49974076	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttttctgtcatctacatCaacgccatgataggaaatgt	11	14	8	8	1	4	1	2	1	2	0	4	2	4	2	1	1	2	1	1	1	4	4			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	190	195					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		A	49974076	C	A	49974076	2	1	117	1	0	0	0	0	0	0	0	1	11073	816	29	4		4	OR4C13	11	49974076	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		49974076	85032440	48	10217											
NUMA1	4926	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	71723991	71723991	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaccgctgcctctcctccaGgaccttgaccttggcaccct	6	9	8	18	1	1	1	0	1	1	0	3	3	2	2	7	2	2	2	7	2	1	2			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	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Missense_Mutation_p.L1520M|NUMA1_ENST00000351960.6_Intron	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	100	102					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			T	71723991	G	T	71723991	3	4	117	1	0	0	0	0	1	0	0	0	10776	991	35	4	1841	4	NUMA1	11	71723991	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	21749915	71723991	63282525	49	10218											
HEBP1	50865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	13140120	13140120	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgccttcccgttcctcaaTcttaacgcttttgtcactgg	6	15	7	13	2	3	0	2	0	1	0	5	1	5	0	3	1	2	2	3	1	2	5			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	158	165					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			C	13140120	T	C	13140120	3	2	117	1	0	0	0	0	1	0	0	0	7057	1435	50	3	213	3	HEBP1	12	13140120	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08		13140120	120711775	50	10219											
PPFIBP1	8496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	27809595	27809595	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actagaagaaaaggaatctgAagtaaaaaggctacaagaaa	23	5	9	4	0	1	4	0	1	1	3	1	5	1	5	0	2	1	2	0	2	12	3	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	76	75					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		C	27809595	A	C	27809595	3	2	117	1	0	0	0	0	1	0	0	0	12339	246	9	5	811	5	PPFIBP1	12	27809595	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	14669475	27809595	106042300	51	10220											
GPD1	2819	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	50503242	50503242	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgtgtacaaggtgtgctaCgagggccagccagtgggtga	8	8	17	8	1	0	1	0	1	0	0	0	2	0	1	2	3	4	3	2	3	3	2	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*	RP4-605O3.4_ENST00000552815.1_RNA|COX14_ENST00000317943.2_5'Flank|GPD1_ENST00000548814.1_Nonsense_Mutation_p.Y307*|COX14_ENST00000550654.1_5'Flank|COX14_ENST00000550487.1_5'Flank|COX14_ENST00000548985.1_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	108	118					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			G	50503242	C	G	50503242	4	3	117	1	0	0	0	0	0	1	0	0	6624	547	19	4	1020	4	GPD1	12	50503242	Nonsense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	22693647	50503242	83348653	52	10221											
KRT76	51350	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	53170736	53170736	+	Frame_Shift_Del	DEL	T	T	-																															accagcccctccaaaaccacTacctactcctctgccaccac																										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	276	273					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		-	53170736	T	-	53170736	7	5	117	1	0	1	0	1	0	0	0	0	8510	1522	53	0	1612	0	KRT76	12	53170736	Frame_Shift_Del	DEL	T	TCGA-G7-6797-01A-11D-1961-08	2667494	53170736	80681159	53	10222											
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	59271290	59271290	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccacggctatgatcacgaCacccacagtggcccatccgt	11	6	8	16	3	1	1	1	1	0	0	2	2	2	1	4	2	1	1	4	2	2	1			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	121	152					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		A	59271290	C	A	59271290	3	1	117	1	0	0	0	0	1	0	0	0	8971	478	17	4	951	4	LRIG3	12	59271290	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	6100554	59271290	74580605	54	10223											
ANKRD13A	88455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	110457067	110457067	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagccaaaaagcagggaagTtgagcggcggctcacaagcc	14	3	14	10	2	1	1	1	1	0	0	1	3	1	2	2	3	4	3	2	3	5	1			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	76	76					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		C	110457067	T	C	110457067	3	2	117	1	0	0	0	0	1	0	0	0	641	1725	60	3	690	3	ANKRD13A	12	110457067	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	51185777	110457067	23394828	55	10224											
N4BP2L2	10443	broad.mit.edu	37	chr13	33095588	33095588	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatccttttcctatggccTacacaaaggaaaggaagaaa	15	10	8	8	0	0	1	0	0	0	1	2	3	2	3	3	3	1	1	3	3	7	5			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	63	63					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	C	33095588	T	C	33095588	5	2	117	1	0	0	0	0	0	0	1	0	10137	1536	53	3	2148	3	N4BP2L2	13	33095588	Splice_Site	SNP	T	TCGA-G7-6797-01A-11D-1961-08		33095588	82074290	56	10225											
FREM2	341640	broad.mit.edu	37	chr13	39422803	39422803	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccataaatgactctgtctcCgattgtgagtgtttattaat	10	17	7	7	1	2	2	0	2	2	0	4	3	3	2	2	0	0	1	2	0	4	5	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	51	52					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		G	39422803	C	G	39422803	2	3	117	1	0	0	0	0	0	0	0	1	6064	639	23	4		4	FREM2	13	39422803	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	6327215	39422803	75747075	57	10226											
SIX4	51804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	61190290	61190290	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaagctgtggctctcgaggAtgctgtagagctcggggtag	7	9	17	8	3	1	1	0	0	1	1	3	4	1	2	0	4	3	6	0	4	3	2			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	14	14					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			C	61190290	A	C	61190290	3	2	117	1	0	0	0	0	1	0	0	0	14381	333	12	5	1854	5	SIX4	14	61190290	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08		61190290	46159250	58	10227											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27777872	27777876	+	Frame_Shift_Del	DEL	TTCTT	TTCTT	-																															atggcaaagactgtcagagcTtcttctgctgctatgaagaa																										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			-	27777876	TTCTT	-	27777872	7	5	117	1	0	1	0	1	0	0	0	0	6192	1609	56	0	1287	0	GABRG3	15	27777872	Frame_Shift_Del	DEL	TTCTT	TCGA-G7-6797-01A-11D-1961-08		27777872	74753520	59	10228											
C15orf53	400359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	38988925	38988925	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcatctgtctccaggcGtctgtttggatggctgtaag	7	12	13	9	1	3	0	0	0	3	0	4	1	3	1	1	3	2	5	1	3	1	2	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	95	95					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		C	38988925	G	C	38988925	2	2	117	1	0	0	0	0	0	0	0	1	1805	1132	40	4		4	C15orf53	15	38988925	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	11211053	38988925	63542467	60	10229											
DTWD1	56986	broad.mit.edu	37	chr15	49926740	49926740	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttgttttaggttgcacTcatttttcctggacctcagt	5	20	7	9	0	3	0	2	0	1	0	4	1	4	1	2	2	1	3	2	2	1	7			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_ENST00000558653.1_Missense_Mutation_p.L139R|DTWD1_ENST00000403028.3_Missense_Mutation_p.L139R|DTWD1_ENST00000415425.1_Missense_Mutation_p.L52R|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	46	45					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		G	49926740	T	G	49926740	3	3	117	1	0	0	0	0	1	0	0	0	4802	1551	54	5	426	5	DTWD1	15	49926740	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	10937815	49926740	52604652	61	10230											
IREB2	3658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	78765688	78765689	+	Missense_Mutation	DNP	GT	GT	AC																															ctgggtcatcaaacccttttGttacatccatagatgttgtt																								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	1		WXS	Illumina HiSeq	Phase_I	108	49		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		AC	78765689	GT	AC	78765688	3	1	117	1	0	0	0	0	1	0	0	0	7847	1377	48	2	1018	2	IREB2	15	78765688	Missense_Mutation	DNP	GT	TCGA-G7-6797-01A-11D-1961-08	28838948	78765688	23765704	62	10231											
C16orf59	80178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2511752	2511752	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcttctccgacaggcacCtgctgcggctgcctgcggca	4	7	14	16	4	1	0	0	0	1	0	2	1	1	0	3	4	4	5	3	4	0	1			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_ENST00000483320.1_Silent_p.L37L|C16orf59_ENST00000563531.1_Silent_p.L204L|RP11-715J22.4_ENST00000566085.1_lincRNA	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	56	54					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		T	2511752	C	T	2511752	2	4	117	1	0	0	0	0	0	0	0	1	1827	680	24	2		2	C16orf59	16	2511752	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		2511752	87843001	63	10232											
CES3	23491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67000741	67000741	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttcctcatgggtgtcaacaaCcatgagttcagctggctcat	9	12	9	11	0	4	1	4	1	0	0	5	1	5	1	2	2	3	3	2	2	2	2			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	131	132					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		A	67000741	C	A	67000741	3	1	117	1	0	0	0	0	1	0	0	0	3277	506	18	4	1065	4	CES3	16	67000741	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	64488989	67000741	23354012	64	10233											
FAM65A	79567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67576026	67576026	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggcatgcaccctacagtcGgactctgagccacatcagtg	9	8	11	13	1	2	1	1	1	1	0	3	2	2	2	2	2	3	2	2	2	1	1			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-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.R460Q|CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000540839.3_Missense_Mutation_p.R466Q|CTD-2012K14.4_ENST00000564717.1_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	71	72					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		A	67576026	G	A	67576026	3	1	117	1	0	0	0	0	1	0	0	0	5618	1116	39	1	1383	1	FAM65A	16	67576026	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	575285	67576026	22778727	65	10234											
CHMP1A	5119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89717999	89717999	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcactttggcctgctccGccttggagtccttctccgcc	2	14	8	17	2	3	0	1	0	2	0	6	1	5	1	6	2	1	1	6	2	0	4			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_ENST00000547614.1_5'UTR|CHMP1A_ENST00000253475.5_Silent_p.G21G|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	85	82					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		C	89717999	G	C	89717999	3	2	117	1	0	0	0	0	1	0	0	0	3358	1087	38	4	679	4	CHMP1A	16	89717999	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	22141973	89717999	636754	66	10235											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			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_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y	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	265	268					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		T	15457087	C	T	15457087	3	4	117	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		15457087	65738123	67	10236											
SLC47A2	146802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	19610045	19610045	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agccagggagaagaaggggcCccagtcctgcaggcactggc	10	3	16	12	0	0	2	0	0	0	2	1	3	1	2	4	5	2	2	4	5	2	0			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_ENST00000350657.5_Missense_Mutation_p.G253R|SLC47A2_ENST00000463318.1_5'UTR	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	76	78					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		G	19610045	C	G	19610045	3	3	117	1	0	0	0	0	1	0	0	0	14680	623	22	4	979	4	SLC47A2	17	19610045	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	4152958	19610045	61585165	68	10237											
ZNF207	7756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	30696350	30696350	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttacctaagtatcaacgtAatcttcctcggccaggacag	12	10	8	11	2	2	0	1	0	1	0	4	1	3	1	3	2	2	3	3	2	5	5			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_ENST00000394673.2_Missense_Mutation_p.N370Y|ZNF207_ENST00000577908.1_Missense_Mutation_p.N401Y|ZNF207_ENST00000394670.4_Missense_Mutation_p.N401Y|ZNF207_ENST00000341711.6_Missense_Mutation_p.N302Y|ZNF207_ENST00000342555.6_Missense_Mutation_p.N404Y	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	101	101					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			T	30696350	A	T	30696350	3	4	117	1	0	0	0	0	1	0	0	0	17797	362	13	5	1243	5	ZNF207	17	30696350	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	11086305	30696350	50498860	69	10238											
MPO	4353	ucsc.edu	37	chr17	56355333	56355333	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggttggacatgttgcgCaggttcctggccaggggctc	5	10	16	10	1	0	0	0	0	0	0	2	1	1	1	2	6	2	6	2	6	0	3			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	67	70					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			T	56355333	C	T	56355333	2	4	117	1	0	0	0	0	0	0	0	1	9757	697	25	2		2	MPO	17	56355333	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	25658983	56355333	24839877	70	10239											
PPM1D	8493	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	58740837	58740837	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctgttaaactcaccatgcGacgcagacttaggggccaga	11	8	10	12	2	2	2	1	0	1	2	2	3	2	2	2	2	2	2	2	2	3	2	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	82	83					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		A	58740837	G	A	58740837	3	1	117	1	0	0	0	0	1	0	0	0	12366	1058	37	1	1764	1	PPM1D	17	58740837	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	2385504	58740837	22454373	71	10240											
SMAD7	4092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	46447887	46447887	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taaactcgtggtcattgggcCgctgcaggctgtacgccttc	6	11	12	12	3	1	0	1	0	0	0	3	0	1	0	2	3	3	4	2	3	3	4			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_ENST00000585986.1_5'UTR|SMAD7_ENST00000589634.1_Missense_Mutation_p.R378Q|SMAD7_ENST00000591805.1_Missense_Mutation_p.R164Q	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	77	81					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		T	46447887	C	T	46447887	3	4	117	1	0	0	0	0	1	0	0	0	14795	652	23	1	148	1	SMAD7	18	46447887	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		46447887	31629361	72	10241											
GATAD2A	54815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19613195	19613195	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccgaggtgtcctgcacaCgttcagtccgtcacccaaac	8	7	9	17	3	2	0	2	0	0	0	4	1	4	0	5	1	2	2	5	1	1	1			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_ENST00000404158.1_Missense_Mutation_p.T545M|GATAD2A_ENST00000537887.1_Missense_Mutation_p.T173M|GATAD2A_ENST00000252577.5_Missense_Mutation_p.T519M|GATAD2A_ENST00000429563.2_Missense_Mutation_p.T347M	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	79	78					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		T	19613195	C	T	19613195	3	4	117	1	0	0	0	0	1	0	0	0	6280	536	19	1	1669	1	GATAD2A	19	19613195	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		19613195	39515788	73	10242											
ZNF30	90075	broad.mit.edu	37	chr19	35435141	35435141	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcatcagaggatccatactgGggagaaaccctatgaatgta	14	8	11	8	0	1	3	1	1	0	2	2	5	2	4	2	3	2	2	2	3	5	3			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_ENST00000439785.1_Missense_Mutation_p.G425A|ZNF30_ENST00000426813.2_Missense_Mutation_p.G343A|ZNF30_ENST00000303586.7_Missense_Mutation_p.G425A|ZNF30_ENST00000601957.1_3'UTR			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	62	60					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		C	35435141	G	C	35435141	3	2	117	1	0	0	0	0	1	0	0	0	17862	1232	43	4	1288	4	ZNF30	19	35435141	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	15821946	35435141	23693842	74	10243											
ZNF573	126231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38230139	38230140	+	Nonsense_Mutation	DNP	CC	CC	AA																															gctaaaggcctttccgcattCcttgcattcatagggtttct																										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_ENST00000339503.4_Nonsense_Mutation_p.359_360KE>N*|ZNF573_ENST00000357309.3_Nonsense_Mutation_p.329_330KE>N*|ZNF573_ENST00000392138.1_Nonsense_Mutation_p.330_331KE>N*|ZNF573_ENST00000536220.1_Nonsense_Mutation_p.329_330KE>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		WXS	Illumina HiSeq	Phase_I	296	132		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		AA	38230140	CC	AA	38230139	4	1	117	1	0	0	0	0	0	1	0	0	18037	864	30	4	749	4	ZNF573	19	38230139	Nonsense_Mutation	DNP	CC	TCGA-G7-6797-01A-11D-1961-08	2794998	38230139	20898844	75	10244											
PRR12	57479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50097991	50097991	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccacggagctcttcatctcGggtgccctgccgggttccag	4	9	12	16	3	3	0	1	0	2	0	5	1	4	1	4	3	3	2	4	3	0	2	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	32	31					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		C	50097991	G	C	50097991	2	2	117	1	0	0	0	0	0	0	0	1	12613	1103	39	4		4	PRR12	19	50097991	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	11867852	50097991	9030992	76	10245											
DSN1	79980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	35399580	35399580	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgatcatgagtcttagaCatcactggtcctttttctag	9	16	8	8	0	4	4	2	3	2	1	5	4	5	4	1	1	0	0	1	1	2	4			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	110	110					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		A	35399580	C	A	35399580	3	1	117	1	0	0	0	0	1	0	0	0	4791	478	17	4	1055	4	DSN1	20	35399580	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		35399580	27625940	77	10246											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30051666	30051666	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagcaccgaggccgagccagGtgaggcccattcattgttgg	8	7	15	11	2	1	1	1	1	0	0	1	4	1	1	4	4	2	2	4	4	0	3			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_ENST00000361676.4_Splice_Site|NF2_ENST00000347330.5_Intron|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000413209.2_Intron|NF2_ENST00000361166.4_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	87	85					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	A	30051666	G	A	30051666	5	1	117	1	0	0	0	0	0	0	1	0	10383	1275	44	2	622	2	NF2	22	30051666	Splice_Site	SNP	G	TCGA-G7-6797-01A-11D-1961-08		30051666	21252900	78	10247											
NXF3	56000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	102337711	102337711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtatgttctcttcatggaCgtccagggaggcagccatgc	8	10	13	10	1	2	0	1	0	1	0	4	2	3	2	2	4	2	3	2	4	1	3			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	145	154					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		T	102337711	C	T	102337711	3	4	117	1	0	0	0	0	1	0	0	0	10811	536	19	1	886	1	NXF3	23	102337711	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		102337711	52932849	79	10248											
DOCK11	139818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	117731503	117731503	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttgaatctgaatgatgcAgaatcaagaagggtaggaaa	17	9	11	4	0	2	5	1	3	1	2	2	6	2	6	0	2	2	2	0	2	8	3			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	82	85					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		T	117731503	A	T	117731503	2	4	117	1	0	0	0	0	0	0	0	1	4697	175	7	5		5	DOCK11	23	117731503	Silent	SNP	A	TCGA-G7-6797-01A-11D-1961-08	15393792	117731503	37539057	80	10249											
KIAA1210	57481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	118223094	118223094	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgatcttctaactggAtatgagaaggattcataaac	13	14	7	7	0	4	2	1	2	3	1	4	5	4	4	0	2	2	0	0	2	5	7			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	44	45					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		G	118223094	A	G	118223094	3	3	117	1	0	0	0	0	1	0	0	0	8235	333	12	3	3046	3	KIAA1210	23	118223094	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	491591	118223094	37047466	81	10250											
PLXNA3	55558	ucsc.edu	37	chrX	153696321	153696321	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggacaacctggagtcccGtgtggccctggagtgcaagg	8	7	16	10	1	0	0	0	0	0	0	1	4	1	3	3	5	2	1	3	5	2	0			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	62	64					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		A	153696321	G	A	153696321	3	1	117	1	0	0	0	0	1	0	0	0	12147	1145	40	1	3875	1	PLXNA3	23	153696321	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	35473227	153696321	1574239	82	10251											
C1orf173	127254	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	75114999	75114999	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctattatatgcagcaagtaaCctaaaatacaaaaataaaac	22	9	3	7	0	0	0	0	0	0	0	0	0	0	0	1	0	5	3	1	0	12	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:75114999C>A	ENST00000326665.5	-	2	242	c.24G>T	c.(22-24)ggG>ggT	p.G8G		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		8										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CAGCAAGTAACCTAAAATACA	0.353																																					p.G8G		.											.	C1orf173-94	0			c.G24T						.						71	72	72					1																	75114999		2203	4300	6503	SO:0001630	splice_region_variant	127254	exon2			AAGTAACCTAAAA																												ENST00000326665.5:c.24-1G>T	1.37:g.75114999C>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	76	25	NM_001002912	0	0	0	0	0	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	37	CCDS30755.1																																																																																			.		0.353	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		Silent	A	75114999	C	A	75114999	5	1	118	1	0	0	0	0	0	0	1	0	2020	521	18	4	4620	4	C1orf173	1	75114999	Splice_Site	SNP	C	TCGA-G7-7501-01A-11D-2201-08		75114999	174135622	1	10252											
INTS3	65123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153736638	153736638	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgtccttgcttcctgcctAcaggagctcttcaaggccca	6	12	8	15	0	3	0	1	0	2	0	5	1	5	1	4	2	4	2	4	2	2	4			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:153736638A>G	ENST00000318967.2	+	18	2434	c.1866A>G	c.(1864-1866)ctA>ctG	p.L622L	INTS3_ENST00000435409.2_Silent_p.L622L|INTS3_ENST00000512605.1_Silent_p.L416L|INTS3_ENST00000456435.1_Silent_p.L416L|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	623					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTTCCTGCCTACAGGAGCTCT	0.572																																					p.L622L		.											.	INTS3-93	0			c.A1866G						.						131	122	125					1																	153736638		2203	4300	6503	SO:0001819	synonymous_variant	65123	exon18			CTGCCTACAGGAG	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.1866A>G	1.37:g.153736638A>G		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	107	46	NM_023015	0	0	39	74	35	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			.		0.572	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		G	153736638	A	G	153736638	2	3	118	1	0	0	0	0	0	0	0	1	7800	378	14	3		3	INTS3	1	153736638	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	78621639	153736638	95513983	2	10253											
DCAF6	55827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr1	167962583	167962583	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagatggtcaagagattctcGttagttactcttcagattac	12	14	8	7	1	4	3	2	0	2	3	5	4	4	3	0	1	2	2	0	1	5	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:167962583G>A	ENST00000312263.6	+	7	1012	c.808G>A	c.(808-810)Gtt>Att	p.V270I	DCAF6_ENST00000367840.3_Missense_Mutation_p.V270I|DCAF6_ENST00000367843.3_Missense_Mutation_p.V270I|DCAF6_ENST00000432587.2_Missense_Mutation_p.V239I	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	270					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						AGAGATTCTCGTTAGTTACTC	0.408																																					p.V270I		.											.	DCAF6-516	0			c.G808A						.						107	102	104					1																	167962583		2203	4300	6503	SO:0001583	missense	55827	exon7			ATTCTCGTTAGTT	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	30002	protein-coding gene	gene with protein product		610494	"IQ motif and WD repeats 1"	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.808G>A	1.37:g.167962583G>A	ENSP00000311949:p.Val270Ile	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	56	12	NM_001198956	0	1	17	20	2	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.439538	0.83885	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.86777	0.6014	M	0.61703	1.905	0.43164	D	0.994955	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.80764	0.972;0.991;0.969;0.994	D	0.86770	0.1972	9	0.54805	T	0.06	.	18.9505	0.92640	0.0:0.0:1.0:0.0	.	239;270;270;270	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	I	270;239;270;270	ENSP00000356817:V270I;ENSP00000396238:V239I;ENSP00000311949:V270I;ENSP00000356814:V270I	ENSP00000311949:V270I	V	+	1	0	DCAF6	166229207	1.000000	0.71417	0.986000	0.45419	0.984000	0.73092	9.119000	0.94362	2.547000	0.85894	0.454000	0.30748	GTT	.		0.408	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		A	167962583	G	A	167962583	3	1	118	1	0	0	0	0	1	0	0	0	4280	1145	40	1	834	1	DCAF6	1	167962583	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	14225945	167962583	81288038	3	10254											
FAIM3	9214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207085119	207085119	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggttgtagctgggcgtctgGggcttgagcagcccctccag	4	10	16	11	1	1	1	0	1	1	0	2	1	2	1	3	4	3	5	3	4	1	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:207085119G>C	ENST00000367091.3	-	4	809	c.666C>G	c.(664-666)ccC>ccG	p.P222P	FAIM3_ENST00000420007.2_Silent_p.P222P|FAIM3_ENST00000528654.1_Intron|FAIM3_ENST00000442471.2_Silent_p.P110P	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	222					cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					TGGGCGTCTGGGGCTTGAGCA	0.542											OREG0014185	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P222P		.											.	FAIM3-90	0			c.C666G						.						92	91	91					1																	207085119		2203	4300	6503	SO:0001819	synonymous_variant	9214	exon4			CGTCTGGGGCTTG	AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.666C>G	1.37:g.207085119G>C		Somatic	137	0	2164	WXS	Illumina HiSeq	Phase_I	97	26	NM_005449	0	0	4	4	0	A8K7J2|B7Z6Z0|D9MWM3	Silent	SNP	ENST00000367091.3	37	CCDS1473.1																																																																																			.		0.542	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		C	207085119	G	C	207085119	2	2	118	1	0	0	0	0	0	0	0	1	5393	1219	43	4		4	FAIM3	1	207085119	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08	39122536	207085119	42165502	4	10255											
PIGR	5284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	207105817	207105817	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcaccgacgttcttcctgtgCcgggctctggccacccccac	4	9	9	19	3	3	0	1	0	2	0	4	1	4	0	6	2	1	2	6	2	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:207105817C>G	ENST00000356495.4	-	8	2175	c.1992G>C	c.(1990-1992)cgG>cgC	p.R664R	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	664					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TCTTCCTGTGCCGGGCTCTGG	0.647																																					p.R664R		.											.	PIGR-92	0			c.G1992C						.						72	75	74					1																	207105817		2203	4300	6503	SO:0001819	synonymous_variant	5284	exon8			CCTGTGCCGGGCT		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1992G>C	1.37:g.207105817C>G		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	97	34	NM_002644	0	0	472	985	513	Q68D81|Q8IZY7	Silent	SNP	ENST00000356495.4	37	CCDS1474.1																																																																																			.		0.647	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		G	207105817	C	G	207105817	2	3	118	1	0	0	0	0	0	0	0	1	11923	726	26	4		4	PIGR	1	207105817	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08	20698	207105817	42144804	5	10256											
PLEKHB2	55041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	131897791	131897791	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtacccgccaggaactcaaGttgtctacgctgcgaatggg	9	8	12	12	4	2	0	1	0	1	0	2	2	2	1	2	2	4	3	2	2	5	3	rs143964327		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:131897791G>C	ENST00000403716.1	+	7	1035	c.475G>C	c.(475-477)Gtt>Ctt	p.V159L	PLEKHB2_ENST00000409612.1_Missense_Mutation_p.V159L|PLEKHB2_ENST00000234115.6_Missense_Mutation_p.V158L|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000409158.1_Missense_Mutation_p.V167L|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000409279.1_Missense_Mutation_p.V159L|PLEKHB2_ENST00000438882.2_Intron|PLEKHB2_ENST00000439822.2_Missense_Mutation_p.K114N|PLEKHB2_ENST00000538982.1_Missense_Mutation_p.V111L	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	159						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		AGGAACTCAAGTTGTCTACGC	0.512																																					p.V167L		.											.	PLEKHB2-92	0			c.G499C						.	G	LEU/VAL,LEU/VAL	1,4405	4.2+/-10.8	0,1,2202	62	57	59		475,472	3.9	1	2	dbSNP_134	59	0,8600		0,0,4300	no	missense,missense	PLEKHB2	NM_001100623.1,NM_017958.2	32,32	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	159/223,158/222	131897791	1,13005	2203	4300	6503	SO:0001583	missense	55041	exon7			ACTCAAGTTGTCT		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.475G>C	2.37:g.131897791G>C	ENSP00000385892:p.Val159Leu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	49	20	NM_001267065	0	0	13	24	11	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	SNP	ENST00000403716.1	37	CCDS46413.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.16|16.16	3.043536|3.043536	0.55003|0.55003	2.27E-4|2.27E-4	0.0|0.0	ENSG00000115762|ENSG00000115762	ENST00000439822|ENST00000409158;ENST00000403716;ENST00000234115;ENST00000538982;ENST00000409612;ENST00000409279	.|.	.|.	.|.	4.81|4.81	3.91|3.91	0.45181|0.45181	.|.	.|.	.|.	.|.	.|.	T|T	0.61236|0.61236	0.2331|0.2331	M|M	0.76328|0.76328	2.33|2.33	0.43574|0.43574	D|D	0.995904|0.995904	B|B;B;B;B	0.30482|0.21905	0.281|0.036;0.061;0.036;0.062	B|B;B;B;B	0.32624|0.26094	0.149|0.03;0.066;0.03;0.03	T|T	0.56757|0.56757	-0.7926|-0.7926	8|8	0.17369|0.25106	T|T	0.5|0.35	.|.	12.1112|12.1112	0.53840|0.53840	0.0:0.0:0.8269:0.1731|0.0:0.0:0.8269:0.1731	.|.	114|158;158;159;167	B4DZ66|Q53FF1;Q96CS7-3;Q96CS7;B8ZZN1	.|.;.;PKHB2_HUMAN;.	N|L	114|167;159;158;111;159;159	.|.	ENSP00000389629:K114N|ENSP00000234115:V158L	K|V	+|+	3|1	2|0	PLEKHB2|PLEKHB2	131614261|131614261	0.999000|0.999000	0.42202|0.42202	0.982000|0.982000	0.44146|0.44146	0.843000|0.843000	0.47879|0.47879	1.275000|1.275000	0.33144|0.33144	0.993000|0.993000	0.38866|0.38866	0.650000|0.650000	0.86243|0.86243	AAG|GTT	G|1.000;C|0.000		0.512	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		C	131897791	G	C	131897791	3	2	118	1	0	0	0	0	1	0	0	0	12091	1029	36	4	497	4	PLEKHB2	2	131897791	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		131897791	111301582	6	10257											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179567316	179567316	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcatcaaaggacacttCacactcaaaggtggcagact	14	7	9	11	0	4	1	4	0	0	1	4	2	4	2	0	4	0	2	0	4	2	1			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:179567316C>A	ENST00000591111.1	-	105	29571	c.29347G>T	c.(29347-29349)Gaa>Taa	p.E9783*	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.E8856*|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Nonsense_Mutation_p.E10100*			Q8WZ42	TITIN_HUMAN	titin	13861	Ig-like 79.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGACACTTCACACTCAAAG	0.438																																					p.E10100X		.											.	TTN-636	0			c.G30298T						.						177	174	175					2																	179567316		2019	4185	6204	SO:0001587	stop_gained	7273	exon107			ACACTTCACACTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.29347G>T	2.37:g.179567316C>A	ENSP00000465570:p.Glu9783*	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	89	43	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	60	45.686615	0.99987	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.8805	0.96895	0.0:1.0:0.0:0.0	.	.	.	.	X	8856	.	ENSP00000343764:E8856X	E	-	1	0	TTN	179275561	1.000000	0.71417	0.986000	0.45419	0.981000	0.71138	7.818000	0.86416	2.704000	0.92352	0.655000	0.94253	GAA	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179567316	C	A	179567316	4	1	118	1	0	0	0	0	0	1	0	0	16768	835	29	4	74255	4	TTN	2	179567316	Nonsense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	47669525	179567316	63632057	7	10258											
SLC40A1	30061	broad.mit.edu	37	chr2	190439935	190439935	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcaccgatgatggctcccaGgaccagaacagaccctgcca	11	5	10	15	1	1	3	1	1	0	2	2	5	2	4	5	2	2	1	5	2	1	0			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:190439935G>C	ENST00000261024.2	-	3	649	c.223C>G	c.(223-225)Ctg>Gtg	p.L75V	SLC40A1_ENST00000418714.1_5'UTR	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	75					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			ATGGCTCCCAGGACCAGAACA	0.498																																					p.L75V													.	SLC40A1-91	0			c.C223G						.						201	202	202					2																	190439935		2203	4300	6503	SO:0001583	missense	30061	exon3			CTCCCAGGACCAG	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.223C>G	2.37:g.190439935G>C	ENSP00000261024:p.Leu75Val	Somatic	305	0		WXS	Illumina HiSeq	Phase_I	216	7	NM_014585	0	0	49	49	0	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	37	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.883544	0.72410	.	.	ENSG00000138449	ENST00000261024;ENST00000427241	T;T	0.81247	-1.47;-1.43	5.37	2.54	0.30619	Major facilitator superfamily domain, general substrate transporter (1);	0.074984	0.56097	D	0.000035	D	0.83862	0.5346	L	0.56769	1.78	0.58432	D	0.999994	D;D	0.69078	0.993;0.997	D;D	0.72625	0.951;0.978	T	0.78735	-0.2088	10	0.25751	T	0.34	-10.9426	7.7635	0.28965	0.1396:0.0:0.7272:0.1333	.	75;75	A8K7Y1;Q9NP59	.;S40A1_HUMAN	V	75	ENSP00000261024:L75V;ENSP00000390005:L75V	ENSP00000261024:L75V	L	-	1	2	SLC40A1	190148180	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	2.679000	0.46909	0.377000	0.24735	0.650000	0.86243	CTG	.		0.498	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			C	190439935	G	C	190439935	3	2	118	1	0	0	0	0	1	0	0	0	14660	991	35	4	1516	4	SLC40A1	2	190439935	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	10872619	190439935	52759438	8	10259											
HSPE1	3336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	198365946	198365946	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aacagtagtcgctgttggatCgggttctaaaggaaaggtaa	13	10	13	5	2	1	0	0	0	1	0	3	2	1	2	0	4	1	5	0	4	6	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:198365946C>G	ENST00000233893.5	+	2	595	c.152C>G	c.(151-153)tCg>tGg	p.S51W	HSPE1_ENST00000465573.1_Intron|HSPE1_ENST00000409468.1_Missense_Mutation_p.S51W|HSPD1_ENST00000345042.2_5'Flank|HSPD1_ENST00000388968.3_5'Flank|HSPD1_ENST00000544407.1_5'Flank|HSPE1-MOB4_ENST00000604458.1_Missense_Mutation_p.S51W|HSPE1_ENST00000409729.1_Intron	NM_002157.2	NP_002148.1	P61604	CH10_HUMAN	heat shock 10kDa protein 1	51					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|osteoblast differentiation (GO:0001649)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			lung(1)	1			Epithelial(96;0.225)			GCTGTTGGATCGGGTTCTAAA	0.408																																					p.S51W		.											.	HSPE1-226	0			c.C152G						.						53	55	54					2																	198365946		2203	4300	6503	SO:0001583	missense	3336	exon2			TTGGATCGGGTTC	AF109872	CCDS2320.1	2q33.1	2013-10-17	2013-10-17		ENSG00000115541	ENSG00000115541		"Heat Shock Proteins / Chaperonins"	5269	protein-coding gene	gene with protein product	"chaperonin 10"	600141	"heat shock 10kD protein 1 (chaperonin 10)"			7914093, 7698325	Standard	NM_002157		Approved	CPN10, GROES		P61604	OTTHUMG00000132749	ENST00000233893.5:c.152C>G	2.37:g.198365946C>G	ENSP00000233893:p.Ser51Trp	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_002157	0	0	897	1687	790	O95421|Q04984|Q53X54|Q9UDH0	Missense_Mutation	SNP	ENST00000233893.5	37	CCDS2320.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.710542	0.68730	.	.	ENSG00000115541	ENST00000233893;ENST00000409468	.	.	.	5.37	5.37	0.77165	GroES-like (1);	0.221653	0.39475	U	0.001344	T	0.80813	0.4695	M	0.89214	3.015	0.58432	D	0.999999	D	0.60575	0.988	D	0.65573	0.936	D	0.84237	0.0470	9	0.72032	D	0.01	-11.1967	14.0187	0.64541	0.1511:0.8489:0.0:0.0	.	51	P61604	CH10_HUMAN	W	51	.	ENSP00000233893:S51W	S	+	2	0	HSPE1	198074191	0.720000	0.27996	0.637000	0.29366	0.705000	0.40729	3.596000	0.54024	2.530000	0.85305	0.557000	0.71058	TCG	.		0.408	HSPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256112.1	NM_002157		G	198365946	C	G	198365946	3	3	118	1	0	0	0	0	1	0	0	0	7450	893	31	4	158	4	HSPE1	2	198365946	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	7926011	198365946	44833427	9	10260											
PLCD1	5333	ucsc.edu;bcgsc.ca	37	chr3	38050062	38050062	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacgtacccacaggcccCgttgtcctggaagcggccct	7	6	11	17	3	0	0	0	0	0	0	1	1	1	1	5	3	3	3	5	3	2	2	rs369003040		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr3:38050062C>A	ENST00000334661.4	-	12	2011	c.1789G>T	c.(1789-1791)Ggg>Tgg	p.G597W	PLCD1_ENST00000479619.1_5'Flank|PLCD1_ENST00000463876.1_Missense_Mutation_p.G618W	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	597	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)	p.G618W(1)|p.G597W(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CCACAGGCCCCGTTGTCCTGG	0.662																																					p.G618W													.	PLCD1-226	2	Substitution - Missense(2)	lung(2)	c.G1852T						.						61	64	63					3																	38050062		2203	4300	6503	SO:0001583	missense	5333	exon12			AGGCCCCGTTGTC		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.1789G>T	3.37:g.38050062C>A	ENSP00000335600:p.Gly597Trp	Somatic	81	0		WXS	Illumina HiSeq		26	4	NM_001130964	0	0	2	2	0	B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	37	CCDS2671.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811832	0.90707	.	.	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.71103	-0.54;-0.54	4.71	4.71	0.59529	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	D	0.000000	D	0.90868	0.7131	H	0.98996	4.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94790	0.7961	10	0.87932	D	0	.	17.6247	0.88091	0.0:1.0:0.0:0.0	.	597;618	P51178;B3KR14	PLCD1_HUMAN;.	W	618;597	ENSP00000430344:G618W;ENSP00000335600:G597W	ENSP00000335600:G597W	G	-	1	0	PLCD1	38025066	1.000000	0.71417	0.990000	0.47175	0.980000	0.70556	7.770000	0.85390	2.358000	0.79984	0.561000	0.74099	GGG	.		0.662	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			A	38050062	C	A	38050062	3	1	118	1	0	0	0	0	1	0	0	0	12057	652	23	4	497	4	PLCD1	3	38050062	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		38050062	159972368	10	10261											
DNASE1L3	1776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	58179114	58179114	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctggaagtcaaaaacacTgtttgacttgggaacaacag	14	11	9	7	0	2	1	1	1	1	0	2	3	2	3	0	2	3	1	0	2	5	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr3:58179114T>C	ENST00000394549.2	-	7	1073	c.757A>G	c.(757-759)Agt>Ggt	p.S253G	DNASE1L3_ENST00000318316.3_Missense_Mutation_p.S253G|DNASE1L3_ENST00000486455.1_Missense_Mutation_p.S223G|DNASE1L3_ENST00000483681.1_Missense_Mutation_p.S253G	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	253					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		TCAAAAACACTGTTTGACTTG	0.433																																					p.S253G	Esophageal Squamous(96;1069 1424 4841 43466 52325)	.											.	DNASE1L3-153	0			c.A757G						.						111	99	103					3																	58179114		2203	4300	6503	SO:0001583	missense	1776	exon7			AAACACTGTTTGA	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"DNase gamma"	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.757A>G	3.37:g.58179114T>C	ENSP00000378053:p.Ser253Gly	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	58	20	NM_004944	0	0	5	5	0	B2R8B1|B7Z707|O75803	Missense_Mutation	SNP	ENST00000394549.2	37	CCDS2886.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.327576	0.24080	.	.	ENSG00000163687	ENST00000486455;ENST00000450710;ENST00000318316;ENST00000483681;ENST00000394549	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.7	-7.58	0.01313	Endonuclease/exonuclease/phosphatase (2);	1.174290	0.05847	N	0.620530	T	0.30324	0.0761	N	0.17723	0.515	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.09377	0.003;0.004;0.003	T	0.17684	-1.0361	10	0.21540	T	0.41	.	8.2569	0.31763	0.0:0.3088:0.2525:0.4387	.	223;253;253	B7Z707;E9PES0;Q13609	.;.;DNSL3_HUMAN	G	223;253;253;253;253	ENSP00000419052:S223G;ENSP00000316193:S253G;ENSP00000417047:S253G;ENSP00000378053:S253G	ENSP00000316193:S253G	S	-	1	0	DNASE1L3	58154154	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.785000	0.04628	-1.315000	0.02297	-0.290000	0.09829	AGT	.		0.433	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944		C	58179114	T	C	58179114	3	2	118	1	0	0	0	0	1	0	0	0	4674	1580	55	3	168	3	DNASE1L3	3	58179114	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08	20129052	58179114	139843316	11	10262											
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41748007	41748007	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctgccgccgctgccgcTgccgccgccgccgctgccgc	1	4	13	23	8	0	0	0	0	0	0	0	0	0	0	9	0	5	4	9	0	0	0	rs17884724|rs17879189	byFrequency	TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr4:41748007T>G	ENST00000226382.2	-	3	1121	c.762A>C	c.(760-762)gcA>gcC	p.A254A	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	254	Poly-Ala.		Missing. {ECO:0000269|PubMed:14566559}.		autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						ccgctgccgctgccgccgccg	0.816			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	273	0.0545128	0.093	0.0187	5008	,	,		3561	0.0992		0.008	False		,,,				2504	0.0297				p.A254A		.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B-1970	0			c.A762C						.						2	3	3					4																	41748007		582	1627	2209	SO:0001819	synonymous_variant	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGCCGCTGCCGCC	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"Homeoboxes / PRD class"	9143	protein-coding gene	gene with protein product		603851	"paired mesoderm homeobox 2b"	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.762A>C	4.37:g.41748007T>G		Somatic	5	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_003924	0	0	0	0	0	Q6PJD9	Silent	SNP	ENST00000226382.2	37	CCDS3463.1																																																																																			.		0.816	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			G	41748007	T	G	41748007	2	3	118	1	0	0	0	0	0	0	0	1	11885	1567	55	5		5	PHOX2B	4	41748007	Silent	SNP	T	TCGA-G7-7501-01A-11D-2201-08		41748007	149406269	12	10263											
HERC3	8916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	89575198	89575198	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaatttattctagatcgaGaatctccatgccatgtaaaa	14	15	5	7	1	2	2	0	0	2	2	4	3	2	2	2	0	1	1	2	0	6	7	rs35418561		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr4:89575198G>T	ENST00000402738.1	+	7	930	c.691G>T	c.(691-693)Gaa>Taa	p.E231*	HERC3_ENST00000407637.1_Nonsense_Mutation_p.E231*|HERC3_ENST00000264345.3_Nonsense_Mutation_p.E231*	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	231					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TCTAGATCGAGAATCTCCATG	0.368																																					p.E231X		.											.	HERC3-660	0			c.G691T						.						87	88	88					4																	89575198		2203	4300	6503	SO:0001587	stop_gained	8916	exon7			GATCGAGAATCTC	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.691G>T	4.37:g.89575198G>T	ENSP00000385684:p.Glu231*	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	36	26	NM_014606	0	0	0	0	0	A8K1S5|Q8IXX3	Nonsense_Mutation	SNP	ENST00000402738.1	37	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	G	36	5.963882	0.97151	.	.	ENSG00000138641	ENST00000402738;ENST00000407637;ENST00000264345	.	.	.	5.12	4.24	0.50183	.	0.168861	0.52532	D	0.000072	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	10.4986	0.44791	0.078:0.1468:0.7752:0.0	.	.	.	.	X	231	.	ENSP00000264345:E231X	E	+	1	0	HERC3	89794221	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.005000	0.63972	2.664000	0.90586	0.655000	0.94253	GAA	.		0.368	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		T	89575198	G	T	89575198	4	4	118	1	0	0	0	0	0	1	0	0	7080	943	33	4	709	4	HERC3	4	89575198	Nonsense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	47827191	89575198	101579078	13	10264											
C4orf27	54969	ucsc.edu	37	chr4	170658832	170658832	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atctgtttcagggagctctcGgtacccaacatcatttttat	9	15	7	10	1	4	0	2	0	2	0	5	1	4	1	1	2	3	3	1	2	3	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr4:170658832G>T	ENST00000393381.2	-	6	790	c.715C>A	c.(715-717)Cga>Aga	p.R239R		NM_017867.2	NP_060337.2	Q9NWY4	CD027_HUMAN	chromosome 4 open reading frame 27	239						nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	12		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		GGGAGCTCTCGGTACCCAACA	0.353																																					p.R239R													.	C4orf27-92	0			c.C715A						.						123	122	122					4																	170658832		2203	4300	6503	SO:0001819	synonymous_variant	54969	exon6			GCTCTCGGTACCC	BC010367	CCDS3813.1	4q33	2011-01-25			ENSG00000056050	ENSG00000056050			26051	protein-coding gene	gene with protein product						11230166	Standard	NM_017867		Approved	FLJ20534	uc003isl.4	Q9NWY4	OTTHUMG00000160960	ENST00000393381.2:c.715C>A	4.37:g.170658832G>T		Somatic	127	0		WXS	Illumina HiSeq		40	4	NM_017867	0	0	58	58	0		Silent	SNP	ENST00000393381.2	37	CCDS3813.1																																																																																			.		0.353	C4orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363140.1	NM_017867		T	170658832	G	T	170658832	2	4	118	1	0	0	0	0	0	0	0	1	2264	1124	39	4		4	C4orf27	4	170658832	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08	81083634	170658832	20495444	14	10265											
MYOZ3	91977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	150050078	150050078	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgggcaagaagctgagcGtgccccaggacctgatgatg	10	6	14	11	1	0	4	0	3	0	1	0	5	0	5	4	2	3	2	4	2	2	0	rs370373786		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr5:150050078G>A	ENST00000297130.4	+	3	293	c.94G>A	c.(94-96)Gtg>Atg	p.V32M	MYOZ3_ENST00000517768.1_Missense_Mutation_p.V32M|CTC-345K18.2_ENST00000511626.2_RNA|MYOZ3_ENST00000520112.1_5'Flank	NM_001122853.2|NM_133371.4	NP_001116325.1|NP_588612.2			myozenin 3											large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAAGCTGAGCGTGCCCCAGGA	0.612																																					p.V32M		.											.	MYOZ3-91	0			c.G94A						.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	50	39	43		94,94	2.9	1	5		43	0,8600		0,0,4300	no	missense,missense	MYOZ3	NM_001122853.1,NM_133371.3	21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	32/252,32/252	150050078	1,13005	2203	4300	6503	SO:0001583	missense	91977	exon3			CTGAGCGTGCCCC	AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"calsarcin 3", "FATZ related protein 3"	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000297130.4:c.94G>A	5.37:g.150050078G>A	ENSP00000297130:p.Val32Met	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	23	16	NM_001122853	0	0	0	0	0		Missense_Mutation	SNP	ENST00000297130.4	37	CCDS4309.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.820957	0.50633	2.27E-4	0.0	ENSG00000164591	ENST00000517768;ENST00000297130	T;T	0.70516	-0.49;-0.49	4.74	2.91	0.33838	.	0.542979	0.16126	N	0.228410	T	0.67268	0.2875	M	0.75777	2.31	0.80722	D	1	P	0.51653	0.947	B	0.41946	0.371	T	0.69771	-0.5055	10	0.72032	D	0.01	-16.886	7.231	0.26043	0.277:0.0:0.723:0.0	.	32	Q8TDC0	MYOZ3_HUMAN	M	32	ENSP00000428815:V32M;ENSP00000297130:V32M	ENSP00000297130:V32M	V	+	1	0	MYOZ3	150030271	0.186000	0.23225	0.968000	0.41197	0.985000	0.73830	0.833000	0.27504	1.116000	0.41820	0.555000	0.69702	GTG	.		0.612	MYOZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252369.1	NM_001122853		A	150050078	G	A	150050078	3	1	118	1	0	0	0	0	1	0	0	0	10122	1145	40	1	100	1	MYOZ3	5	150050078	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		150050078	30865182	15	10266											
HLA-DPB1	3115	hgsc.bcm.edu;broad.mit.edu	37	chr6	33048613	33048613	+	Frame_Shift_Del	DEL	A	A	-																															ggcctgctgcggagtactggAacagccagaaggacatcctg																								rs41550319		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:33048613delA	ENST00000418931.2	+	2	381	c.265delA	c.(265-267)aacfs	p.N89fs	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000535465.1_Frame_Shift_Del_p.N89fs	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	89	Beta-1.		N -> H (in allele DPB1*02:03; dbSNP:rs41550319).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGAGTACTGGAACAGCCAGAA	0.657																																					p.N89fs		.											.	HLA-DPB1-515	0			c.265delA						.						54	55	54					6																	33048613		1511	2709	4220	SO:0001589	frameshift_variant	3115	exon2			.		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.265delA	6.37:g.33048613delA	ENSP00000408146:p.Asn89fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	56	12	NM_002121	0	0	0	0	0	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Frame_Shift_Del	DEL	ENST00000418931.2	37	CCDS4765.1																																																																																			.		0.657	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		-	33048613	A	-	33048613	7	5	118	1	0	1	0	1	0	0	0	0	7224	246	9	0	271	0	HLA-DPB1	6	33048613	Frame_Shift_Del	DEL	A	TCGA-G7-7501-01A-11D-2201-08		33048613	138066454	16	10267											
KCNK5	8645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	39159334	39159334	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctgtgctccccttcacctGcagggccttccgggagtgtg	3	10	14	14	1	1	0	1	0	0	0	3	1	3	1	5	3	2	3	5	3	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:39159334G>A	ENST00000359534.3	-	5	1170	c.832C>T	c.(832-834)Cag>Tag	p.Q278*		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	278					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						CCCTTCACCTGCAGGGCCTTC	0.547																																					p.Q278X		.											.	KCNK5-227	0			c.C832T						.						100	105	104					6																	39159334		2203	4300	6503	SO:0001587	stop_gained	8645	exon5			TCACCTGCAGGGC	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.832C>T	6.37:g.39159334G>A	ENSP00000352527:p.Gln278*	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	150	47	NM_003740	0	0	9	14	5	B2RAQ6|B5TJL2|Q5VV76	Nonsense_Mutation	SNP	ENST00000359534.3	37	CCDS4841.1	.	.	.	.	.	.	.	.	.	.	G	35	5.470988	0.96274	.	.	ENSG00000164626	ENST00000359534	.	.	.	5.35	4.47	0.54385	.	1.406490	0.05067	N	0.481046	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	15.979	0.80091	0.0:0.1351:0.8649:0.0	.	.	.	.	X	278	.	ENSP00000352527:Q278X	Q	-	1	0	KCNK5	39267312	0.997000	0.39634	0.848000	0.33437	0.146000	0.21551	4.384000	0.59607	1.233000	0.43693	0.561000	0.74099	CAG	.		0.547	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740		A	39159334	G	A	39159334	4	1	118	1	0	0	0	0	0	1	0	0	8090	1328	46	2	671	2	KCNK5	6	39159334	Nonsense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	6110721	39159334	131955733	17	10268											
C6orf150	115004	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	74135070	74135070	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattgaattcaggaataaaAtaattctcaagtttttctgt	15	16	6	4	0	3	2	2	1	2	1	4	3	3	3	0	1	0	1	0	1	6	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:74135070A>G	ENST00000370315.3	-	5	1543	c.1449T>C	c.(1447-1449)taT>taC	p.Y483Y	MB21D1_ENST00000370318.1_Intron	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	483					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						CAGGAATAAAATAATTCTCAA	0.373																																					p.Y483Y		.											.	MB21D1-90	0			c.T1449C						.						54	54	54					6																	74135070		2203	4300	6503	SO:0001819	synonymous_variant	115004	exon5			AATAAAATAATTC	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1449T>C	6.37:g.74135070A>G		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	39	17	NM_138441	0	0	0	0	0	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Silent	SNP	ENST00000370315.3	37	CCDS4978.1																																																																																			.		0.373	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		G	74135070	A	G	74135070	2	3	118	1	0	0	0	0	0	0	0	1	2343	108	4	3		3	C6orf150	6	74135070	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	34975736	74135070	96979997	18	10269											
AIM1	202	broad.mit.edu	37	chr6	106960616	106960616	+	Frame_Shift_Del	DEL	C	C	-																															ctcccgccaaggagtccccaCccaagagggtgcccgatccc																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:106960616delC	ENST00000369066.3	+	1	887	c.400delC	c.(400-402)cccfs	p.P134fs		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GGAGTCCCCACCCAAGAGGGT	0.761																																					p.P134fs													.	AIM1-139	0			c.400delC						.						4	6	5					6																	106960616		1924	3948	5872	SO:0001589	frameshift_variant	202	exon1			TCCCCACCCAAGA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.400delC	6.37:g.106960616delC	ENSP00000358062:p.Pro134fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	10	3	NM_001624	0	0	0	0	0	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	37	CCDS34506.1																																																																																			.		0.761	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106960616	C	-	106960616	7	5	118	1	0	1	0	1	0	0	0	0	430	507	18	0	402	0	AIM1	6	106960616	Frame_Shift_Del	DEL	C	TCGA-G7-7501-01A-11D-2201-08	32825546	106960616	64154451	19	10270											
TBP	6908	hgsc.bcm.edu;bcgsc.ca	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		.											.	TBP-91	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	6.37:g.170871004G>A		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	71	5	NM_003194	0	0	23	23	0	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	118	1	0	0	0	0	0	0	0	1	15676	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08	63910388	170871004	244063	20	10271											
DNAH11	8701	broad.mit.edu;bcgsc.ca	37	chr7	21630624	21630624	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttagccatcttcaagaaaaGgaacactattttaaaggttt	15	14	6	6	0	2	1	1	0	1	1	2	2	2	2	1	2	2	1	1	2	8	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:21630624G>A	ENST00000409508.3	+	13	2289	c.2258G>A	c.(2257-2259)aGg>aAg	p.R753K	DNAH11_ENST00000328843.6_Missense_Mutation_p.R753K	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	753	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTCAAGAAAAGGAACACTATT	0.264									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						38	37	38					7																	21630624		1781	4050	5831	SO:0001583	missense	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGAAAAGGAACAC	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.2258G>A	7.37:g.21630624G>A	ENSP00000475939:p.Arg753Lys	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	8	6	.	0	0	0	0	0	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	5.689	0.311727	0.10789	.	.	ENSG00000105877	ENST00000328843	T	0.55588	0.51	5.7	4.81	0.61882	Dynein heavy chain, domain-1 (1);	0.507616	0.21149	N	0.079354	T	0.40546	0.1121	.	.	.	0.36491	D	0.868452	B	0.15719	0.014	B	0.16289	0.015	T	0.38178	-0.9673	9	0.19590	T	0.45	.	13.9912	0.64367	0.0747:0.0:0.9253:0.0	.	753	Q96DT5	DYH11_HUMAN	K	753	ENSP00000330671:R753K	ENSP00000330671:R753K	R	+	2	0	DNAH11	21597149	1.000000	0.71417	0.991000	0.47740	0.081000	0.17604	4.275000	0.58927	1.378000	0.46305	0.650000	0.86243	AGG	.		0.264	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21630624	G	A	21630624	3	1	118	1	0	0	0	0	1	0	0	0	4610	1000	35	2	2308	2	DNAH11	7	21630624	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		21630624	137508039	21	10272											
C7orf59	389541	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99746597	99746598	+	Start_Codon_Ins	INS	-	-	G																															ccagcaccgaagactgcgatINSggtgagtgaggacgcatgcg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:99746597_99746598insG	ENST00000341942.5	+	0	68_69				LAMTOR4_ENST00000441173.1_Start_Codon_Ins	NM_001008395.2	NP_001008396.1	Q0VGL1	LTOR4_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4						cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											AAGACTGCGATGGTGAGTGAGG	0.658																																					p.M1fs		.											.	.	0			c.2_3insG						.																																			SO:0001582	initiator_codon_variant	389541	exon1			.		CCDS34702.1	7q22	2012-09-24	2012-09-24	2012-09-24	ENSG00000188186	ENSG00000188186			33772	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 59"	C7orf59		22980980	Standard	NM_001008395		Approved		uc003utq.2	Q0VGL1	OTTHUMG00000154854	ENST00000341942.5:c.3dupG	7.37:g.99746599_99746599dupG		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	86	23	NM_001008395	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000341942.5	37	CCDS34702.1																																																																																			.		0.658	LAMTOR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337373.2	NM_001008395		G	99746598	-	G	99746597	7	5	118	1	0	1	1	0	0	0	0	0	2412	1478	51	0	4	0	C7orf59	7	99746597	Start_Codon_Ins	INS	-	TCGA-G7-7501-01A-11D-2201-08	78115973	99746597	59392066	22	10273											
C7orf58	79974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	120629777	120629777	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcttctaccagactctgacCctccgagggtcgaggaagct	8	9	10	14	2	3	2	0	1	3	1	5	5	4	3	3	2	2	1	3	2	2	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:120629777C>G	ENST00000310396.5	+	2	569	c.102C>G	c.(100-102)acC>acG	p.T34T	CPED1_ENST00000340646.5_Silent_p.T34T|CPED1_ENST00000450913.2_Silent_p.T34T|CPED1_ENST00000495036.1_3'UTR	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	34						endoplasmic reticulum (GO:0005783)											AGACTCTGACCCTCCGAGGGT	0.587																																					p.T34T		.											.	.	0			c.C102G						.						112	107	109					7																	120629777		2203	4300	6503	SO:0001819	synonymous_variant	79974	exon1			TCTGACCCTCCGA		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 58"	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.102C>G	7.37:g.120629777C>G		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	86	36	NM_001105533	0	0	0	0	0	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Silent	SNP	ENST00000310396.5	37	CCDS34739.1																																																																																			.		0.587	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		G	120629777	C	G	120629777	2	3	118	1	0	0	0	0	0	0	0	1	2411	610	22	4		4	C7orf58	7	120629777	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08	20883180	120629777	38508886	23	10274											
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121679512	121679512	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acattttcttttgcagagaaAatgtgatcagtactggcctg	11	14	9	7	0	2	2	1	1	1	1	2	3	2	2	1	1	2	2	1	1	3	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:121679512A>T	ENST00000393386.2	+	20	5918	c.5507A>T	c.(5506-5508)aAa>aTa	p.K1836I	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.K969I	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1836	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTGCAGAGAAAATGTGATCAG	0.423																																					p.K1836I		.											.	PTPRZ1-699	0			c.A5507T						.						84	83	84					7																	121679512		2203	4300	6503	SO:0001583	missense	5803	exon20			AGAGAAAATGTGA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5507A>T	7.37:g.121679512A>T	ENSP00000377047:p.Lys1836Ile	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	65	35	NM_002851	0	0	0	0	0	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.982726	0.93044	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.21361	2.01;2.01	5.88	5.88	0.94601	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.61553	0.2356	H	0.96460	3.825	0.80722	D	1	D;P;P	0.76494	0.999;0.503;0.674	D;P;P	0.85130	0.997;0.843;0.802	T	0.75169	-0.3412	10	0.87932	D	0	.	16.3015	0.82820	1.0:0.0:0.0:0.0	.	975;969;1836	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	I	1836;969	ENSP00000377047:K1836I;ENSP00000410000:K969I	ENSP00000377047:K1836I	K	+	2	0	PTPRZ1	121466748	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.195000	0.72088	2.239000	0.73571	0.533000	0.62120	AAA	.		0.423	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121679512	A	T	121679512	3	4	118	1	0	0	0	0	1	0	0	0	12846	14	1	5	5585	5	PTPRZ1	7	121679512	Missense_Mutation	SNP	A	TCGA-G7-7501-01A-11D-2201-08	1049735	121679512	37459151	24	10275											
DRD4	1815	hgsc.bcm.edu	37	chr11	640253	640253	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gacccgcaggaggcggcgtgCcaagatcaccggccgggagc	8	2	17	14	5	1	1	1	0	0	1	1	4	1	3	4	5	2	1	4	5	1	0	rs200996360	byFrequency	TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr11:640253C>G	ENST00000176183.5	+	3	1016	c.1004C>G	c.(1003-1005)gCc>gGc	p.A335G		NM_000797.3	NP_000788.2	P21917	DRD4_HUMAN	dopamine receptor D4	383	7 X 16 AA approximate tandem repeats of [PA]-A-P-G-L-P-[PQR]-[DG]-P-C-G-P-D-C-A- P.		Missing (in allele D4.2).		activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult locomotory behavior (GO:0008344)|arachidonic acid secretion (GO:0050482)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|cellular calcium ion homeostasis (GO:0006874)|circadian rhythm (GO:0007623)|dopamine metabolic process (GO:0042417)|dopamine receptor signaling pathway (GO:0007212)|fear response (GO:0042596)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein secretion (GO:0050709)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|olfactory learning (GO:0008355)|photoperiodism (GO:0009648)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of kinase activity (GO:0033674)|positive regulation of penile erection (GO:0060406)|positive regulation of sodium:proton antiporter activity (GO:0032417)|regulation of calcium-mediated signaling (GO:0050848)|regulation of circadian rhythm (GO:0042752)|regulation of dopamine metabolic process (GO:0042053)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of neurotransmitter secretion (GO:0046928)|response to amphetamine (GO:0001975)|response to histamine (GO:0034776)|response to steroid hormone (GO:0048545)|retina development in camera-type eye (GO:0060041)|short-term memory (GO:0007614)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)	cell cortex (GO:0005938)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|vesicle membrane (GO:0012506)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)|SH3 domain binding (GO:0017124)			NS(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Ziprasidone(DB00246)	AGGCGGCGTGCCAAGATCACC	0.741													c|||	43	0.00858626	0.0318	0.0014	5008	,	,		6344	0		0	False		,,,				2504	0				p.A335G		.											.	DRD4-90	0			c.C1004G						.						4	6	5					11																	640253		1527	3345	4872	SO:0001583	missense	1815	exon3			GGCGTGCCAAGAT	L12398	CCDS7710.1	11p15.5	2012-08-08			ENSG00000069696	ENSG00000069696		"GPCR / Class A : Dopamine receptors"	3025	protein-coding gene	gene with protein product		126452					Standard	NM_000797		Approved		uc001lqp.2	P21917	OTTHUMG00000133312	ENST00000176183.5:c.1004C>G	11.37:g.640253C>G	ENSP00000176183:p.Ala335Gly	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_000797	0	0	0	0	0	B0M0J7|Q7Z7Q5|Q8NGM5	Missense_Mutation	SNP	ENST00000176183.5	37	CCDS7710.1	24	0.01098901098901099	23	0.046747967479674794	0	0.0	1	0.0017482517482517483	0	0.0	c	15.17	2.754522	0.49362	.	.	ENSG00000069696	ENST00000176183	T	0.37752	1.18	2.76	2.76	0.32466	GPCR, rhodopsin-like superfamily (1);	0.389459	0.24594	N	0.037181	T	0.18467	0.0443	.	.	.	0.53688	D	0.999974	D	0.76494	0.999	D	0.83275	0.996	T	0.45220	-0.9276	9	0.54805	T	0.06	.	12.6971	0.57010	0.0:1.0:0.0:0.0	.	383	P21917	DRD4_HUMAN	G	335	ENSP00000176183:A335G	ENSP00000176183:A335G	A	+	2	0	DRD4	630253	1.000000	0.71417	0.963000	0.40424	0.945000	0.59286	3.113000	0.50376	1.568000	0.49683	0.457000	0.33378	GCC	C|0.989;G|0.011		0.741	DRD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257109.1	NM_000797		G	640253	C	G	640253	3	3	118	1	0	0	0	0	1	0	0	0	4770	739	26	4	1014	4	DRD4	11	640253	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		640253	134366263	25	10276											
SF3B2	10992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65829382	65829382	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aatgcccacaaggtccctccCccatggctgattgccatgca	9	8	8	16	0	0	1	0	1	0	0	2	1	2	1	5	2	3	2	5	2	2	1	rs559206953		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr11:65829382C>A	ENST00000322535.6	+	16	1939	c.1890C>A	c.(1888-1890)ccC>ccA	p.P630P	SF3B2_ENST00000528302.1_Silent_p.P613P	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	630					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AGGTCCCTCCCCCATGGCTGA	0.562																																					p.P630P		.											.	SF3B2-92	0			c.C1890A						.						115	109	111					11																	65829382		2201	4295	6496	SO:0001819	synonymous_variant	10992	exon16			CCCTCCCCCATGG	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1890C>A	11.37:g.65829382C>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	38	20	NM_006842	0	0	162	306	144	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Silent	SNP	ENST00000322535.6	37	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	C	6.177	0.400770	0.11696	.	.	ENSG00000087365	ENST00000530981	.	.	.	5.8	-0.975	0.10289	.	0.105145	0.64402	D	0.000003	T	0.53916	0.1826	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51212	-0.8734	6	0.87932	D	0	-15.3896	2.3521	0.04286	0.1231:0.3008:0.3612:0.2149	.	.	.	.	H	51	.	ENSP00000436757:P51H	P	+	2	0	SF3B2	65585958	0.832000	0.29368	0.923000	0.36655	0.530000	0.34684	-0.126000	0.10563	-0.166000	0.10890	0.650000	0.86243	CCC	.		0.562	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			A	65829382	C	A	65829382	2	1	118	1	0	0	0	0	0	0	0	1	14183	610	22	4		4	SF3B2	11	65829382	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08	65189129	65829382	69177134	26	10277											
ARAP1	116985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	72406598	72406598	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccttcacctgggtcccacTggcagtgccagccacgcgca	7	6	11	17	2	1	0	1	0	0	0	2	0	2	0	5	2	3	2	5	2	0	1			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr11:72406598T>C	ENST00000393609.3	-	25	3698	c.3496A>G	c.(3496-3498)Agt>Ggt	p.S1166G	ARAP1_ENST00000393605.3_Missense_Mutation_p.S926G|ARAP1_ENST00000359373.5_Missense_Mutation_p.S1166G|ARAP1_ENST00000334211.8_Missense_Mutation_p.S921G|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000426523.1_Missense_Mutation_p.S921G|ARAP1_ENST00000455638.2_Missense_Mutation_p.S1166G|ARAP1_ENST00000429686.1_Missense_Mutation_p.S860G|ARAP1-AS1_ENST00000542022.1_RNA	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1166					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						TGGGTCCCACTGGCAGTGCCA	0.647																																					p.S1166G	Ovarian(102;1198 1520 13195 17913 37529)	.											.	ARAP1-91	0			c.A3496G						.						46	44	45					11																	72406598		2200	4293	6493	SO:0001583	missense	116985	exon25			TCCCACTGGCAGT	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.3496A>G	11.37:g.72406598T>C	ENSP00000377233:p.Ser1166Gly	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	30	12	NM_001040118	0	0	0	0	0	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.846485	0.51164	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686	T;T;T;T;T;T;T	0.07327	3.21;3.21;3.22;3.27;3.2;3.27;3.23	4.43	4.43	0.53597	.	0.300288	0.30419	N	0.009674	T	0.07007	0.0178	N	0.08118	0	0.34771	D	0.733746	B;P;P;B;B	0.50943	0.026;0.92;0.94;0.033;0.056	B;B;P;B;B	0.47402	0.01;0.422;0.546;0.028;0.031	T	0.35251	-0.9796	10	0.62326	D	0.03	.	12.6484	0.56748	0.0:0.0:0.0:1.0	.	921;860;1166;1166;926	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	G	1166;1166;926;921;1166;921;860	ENSP00000352332:S1166G;ENSP00000390461:S1166G;ENSP00000377230:S926G;ENSP00000335506:S921G;ENSP00000377233:S1166G;ENSP00000392264:S921G;ENSP00000403127:S860G	ENSP00000335506:S921G	S	-	1	0	ARAP1	72084246	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.593000	0.67550	1.875000	0.54330	0.377000	0.23210	AGT	.		0.647	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		C	72406598	T	C	72406598	3	2	118	1	0	0	0	0	1	0	0	0	838	1580	55	3	900	3	ARAP1	11	72406598	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08	6577216	72406598	62599918	27	10278											
CAPZA3	93661	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	18892035	18892035	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatactctctgacttgaatcTggtgatgtatcctaaattag	11	15	8	7	0	2	3	0	3	2	0	4	4	3	3	1	1	1	1	1	1	6	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr12:18892035T>A	ENST00000317658.3	+	1	991	c.833T>A	c.(832-834)cTg>cAg	p.L278Q	PLCZ1_ENST00000266505.7_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|PLCZ1_ENST00000539875.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	278					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				GACTTGAATCTGGTGATGTAT	0.393																																					p.L278Q		.											.	CAPZA3-91	0			c.T833A						.						51	53	52					12																	18892035		2200	4287	6487	SO:0001583	missense	93661	exon1			TGAATCTGGTGAT	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.833T>A	12.37:g.18892035T>A	ENSP00000326238:p.Leu278Gln	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	83	35	NM_033328	0	0	0	0	0	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.824365	0.50739	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.54	3.39	0.38822	.	0.000000	0.28088	U	0.016650	T	0.34395	0.0896	N	0.08118	0	0.33519	D	0.592145	P	0.49783	0.928	P	0.56612	0.802	T	0.50311	-0.8843	9	0.87932	D	0	-8.2508	7.6761	0.28486	0.0:0.0985:0.0:0.9015	.	278	Q96KX2	CAZA3_HUMAN	Q	278	.	ENSP00000326238:L278Q	L	+	2	0	CAPZA3	18783302	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	4.188000	0.58351	0.778000	0.33520	0.379000	0.24179	CTG	.		0.393	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328		A	18892035	T	A	18892035	3	1	118	1	0	0	0	0	1	0	0	0	2648	1580	55	5	835	5	CAPZA3	12	18892035	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08		18892035	114959860	28	10279											
KRT75	9119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52827640	52827640	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagggtcttgatctgctcgCgctcctcggcccgcacccgc	3	9	12	17	5	2	2	0	2	2	0	5	2	3	2	3	2	1	3	3	2	0	1	rs201256120		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr12:52827640C>T	ENST00000252245.5	-	1	669	c.449G>A	c.(448-450)cGc>cAc	p.R150H		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	150	Coil 1A.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		GATCTGCTCGCGCTCCTCGGC	0.562													C|||	1	0.000199681	0	0	5008	,	,		17797	0.001		0	False		,,,				2504	0				p.R150H		.											.	KRT75-90	0			c.G449A						.						147	148	148					12																	52827640		2203	4300	6503	SO:0001583	missense	9119	exon1			TGCTCGCGCTCCT	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"-", "Intermediate filaments type II, keratins (basic)"	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.449G>A	12.37:g.52827640C>T	ENSP00000252245:p.Arg150His	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	149	60	NM_004693	0	0	0	0	0	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	21.4	4.145521	0.77888	.	.	ENSG00000170454	ENST00000252245	D	0.90133	-2.62	5.74	4.72	0.59763	Filament (1);	0.164522	0.29692	N	0.011442	D	0.94785	0.8316	H	0.94808	3.585	0.30984	N	0.722149	P	0.50943	0.94	P	0.52793	0.709	D	0.94024	0.7295	10	0.87932	D	0	.	9.8904	0.41288	0.0:0.7972:0.0:0.2028	.	150	O95678	K2C75_HUMAN	H	150	ENSP00000252245:R150H	ENSP00000252245:R150H	R	-	2	0	KRT75	51113907	0.984000	0.35163	0.608000	0.28969	0.884000	0.51177	2.211000	0.42825	1.168000	0.42723	0.655000	0.94253	CGC	C|0.999;T|0.000		0.562	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		T	52827640	C	T	52827640	3	4	118	1	0	0	0	0	1	0	0	0	8509	768	27	1	1242	1	KRT75	12	52827640	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	33935605	52827640	81024255	29	10280											
MLXIP	22877	hgsc.bcm.edu;broad.mit.edu	37	chr12	122616846	122616846	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttgtttttcagacctcttCtcttctagccgctccatttt	4	20	5	12	1	4	1	1	0	3	1	6	1	5	1	3	0	1	3	3	0	1	8			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr12:122616846C>T	ENST00000319080.7	+	8	1140	c.1008C>T	c.(1006-1008)ttC>ttT	p.F336F	MLXIP_ENST00000377037.2_5'Flank|MLXIP_ENST00000538698.1_5'Flank					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		CAGACCTCTTCTCTTCTAGCC	0.552																																					p.F336F	Esophageal Squamous(105;787 1493 16200 18566 52466)	.											.	MLXIP-92	0			c.C1008T						.						135	147	143					12																	122616846		1933	4145	6078	SO:0001819	synonymous_variant	22877	exon8			CCTCTTCTCTTCT	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"Basic helix-loop-helix proteins"	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1008C>T	12.37:g.122616846C>T		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	16	8	NM_014938	0	0	0	0	0		Silent	SNP	ENST00000319080.7	37																																																																																				.		0.552	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		T	122616846	C	T	122616846	2	4	118	1	0	0	0	0	0	0	0	1	9661	912	32	2		2	MLXIP	12	122616846	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08	69789206	122616846	11235049	30	10281											
MTUS2	23281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	29600351	29600351	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaaagaggtcaccacatctGttgctgaaaacaggaacctt	14	8	9	10	0	2	2	1	1	1	1	2	3	2	3	2	2	3	3	2	2	4	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr13:29600351G>A	ENST00000431530.3	+	1	1604	c.1546G>A	c.(1546-1548)Gtt>Att	p.V516I		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	506						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CACCACATCTGTTGCTGAAAA	0.507																																					p.V516I		.											.	MTUS2-218	0			c.G1546A						.						85	89	88					13																	29600351		1967	4155	6122	SO:0001583	missense	23281	exon1			ACATCTGTTGCTG	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"+TIP of 150 kDa", "cardiac zipper protein"		"KIAA0774"	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1546G>A	13.37:g.29600351G>A	ENSP00000392057:p.Val516Ile	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	56	25	NM_001033602	0	0	0	0	0	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	11.63	1.695795	0.30052	.	.	ENSG00000132938	ENST00000431530	T	0.14266	2.52	5.39	1.52	0.23074	.	0.415389	0.20061	N	0.100094	T	0.10637	0.0260	L	0.51422	1.61	0.09310	N	1	B	0.23185	0.081	B	0.15484	0.013	T	0.25222	-1.0138	9	.	.	.	.	5.784	0.18322	0.2147:0.2602:0.5251:0.0	.	506	Q5JR59	MTUS2_HUMAN	I	516	ENSP00000392057:V516I	.	V	+	1	0	MTUS2	28498351	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.241000	0.18065	0.388000	0.25054	-0.175000	0.13238	GTT	.		0.507	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		A	29600351	G	A	29600351	3	1	118	1	0	0	0	0	1	0	0	0	9991	1377	48	2	1548	2	MTUS2	13	29600351	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		29600351	85569527	31	10282											
NBEA	26960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	35733740	35733740	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccttcccaatagtagtacAtcatttctctttgataaaat	13	15	4	9	0	2	1	1	1	1	0	4	2	3	1	2	0	1	2	2	0	6	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr13:35733740A>C	ENST00000400445.3	+	22	3966	c.3432A>C	c.(3430-3432)acA>acC	p.T1144T	NBEA_ENST00000379939.2_Silent_p.T1144T|NBEA_ENST00000540320.1_Silent_p.T1144T|NBEA_ENST00000310336.4_Silent_p.T1144T	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1144					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ATAGTAGTACATCATTTCTCT	0.333																																					p.T1144T		.											.	NBEA-144	0			c.A3432C						.						48	44	45					13																	35733740		1841	4085	5926	SO:0001819	synonymous_variant	26960	exon22			TAGTACATCATTT	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.3432A>C	13.37:g.35733740A>C		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	34	5	NM_015678	0	0	2	2	0	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	37	CCDS45026.1																																																																																			.		0.333	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	35733740	A	C	35733740	2	2	118	1	0	0	0	0	0	0	0	1	10212	204	8	5		5	NBEA	13	35733740	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	6133389	35733740	79436138	32	10283											
TXNDC16	57544	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	52907333	52907333	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatttctgctttaccagtGtcaatattgcttttttatac	9	20	5	7	0	2	0	1	0	1	0	2	0	2	0	1	0	4	3	1	0	6	10			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr14:52907333G>C	ENST00000281741.4	-	19	2323	c.1952C>G	c.(1951-1953)aCa>aGa	p.T651R	TXNDC16_ENST00000554399.1_5'UTR	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	651					cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					CTTTACCAGTGTCAATATTGC	0.308																																					p.T651R		.											.	TXNDC16-22	0			c.C1952G						.						81	77	78					14																	52907333		2203	4297	6500	SO:0001583	missense	57544	exon19			ACCAGTGTCAATA	AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"KIAA1344"	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.1952C>G	14.37:g.52907333G>C	ENSP00000281741:p.Thr651Arg	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	39	4	NM_020784	0	0	13	13	0	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	.	.	.	.	.	.	.	.	.	.	G	0.336	-0.953307	0.02285	.	.	ENSG00000087301	ENST00000281741	T	0.28666	1.6	5.29	-2.77	0.05877	.	0.845265	0.10716	N	0.642273	T	0.10121	0.0248	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.29181	-1.0020	10	0.17832	T	0.49	-16.9969	0.0038	0.00000	0.287:0.2064:0.2084:0.2982	.	646;651	B7ZME4;Q9P2K2	.;TXD16_HUMAN	R	651	ENSP00000281741:T651R	ENSP00000281741:T651R	T	-	2	0	TXNDC16	51977083	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-1.373000	0.02568	-0.539000	0.06273	-0.216000	0.12614	ACA	.		0.308	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699		C	52907333	G	C	52907333	3	2	118	1	0	0	0	0	1	0	0	0	16828	1377	48	4	537	4	TXNDC16	14	52907333	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		52907333	54442207	33	10284											
MORF4L1	10933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	79185887	79185887	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttgtcttcatagctctttTatcttcctgccaagaagaat	9	18	5	9	0	4	2	1	0	3	2	5	2	5	2	2	0	2	1	2	0	5	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr15:79185887T>C	ENST00000331268.5	+	10	868	c.664T>C	c.(664-666)Tat>Cat	p.Y222H	MORF4L1_ENST00000559345.1_Missense_Mutation_p.Y95H|MORF4L1_ENST00000379535.4_Missense_Mutation_p.Y208H|MORF4L1_ENST00000426013.2_Missense_Mutation_p.Y183H|MORF4L1_ENST00000561171.1_Intron|MORF4L1_ENST00000558746.1_Missense_Mutation_p.Y156H|MORF4L1_ENST00000558502.1_Missense_Mutation_p.Y95H	NM_206839.2	NP_996670.1	Q9UBU8	MO4L1_HUMAN	mortality factor 4 like 1	222	Interaction with RB1-1.|MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.|Sufficient for interaction with PHF12.|Sufficient for interaction with SIN3A.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|double-strand break repair via homologous recombination (GO:0000724)|histone deacetylation (GO:0016575)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|protein N-terminus binding (GO:0047485)			breast(1)|large_intestine(3)|lung(4)|prostate(1)|urinary_tract(1)	10						ATAGCTCTTTTATCTTCCTGC	0.299																																					p.Y222H		.											.	MORF4L1-90	0			c.T664C						.						67	71	70					15																	79185887		2196	4288	6484	SO:0001583	missense	10933	exon10			CTCTTTTATCTTC	AF100615	CCDS10307.1, CCDS32304.1, CCDS58393.1	15q25.1	2009-07-13			ENSG00000185787	ENSG00000185787			16989	protein-coding gene	gene with protein product	"MORF-related gene on chromosome 15", "Esa1p-associated factor 3 homolog (S. cerevisiae)"	607303				8619474, 9110174	Standard	NM_006791		Approved	MRG15, MORFRG15, HsT17725, Eaf3, MEAF3	uc002bel.4	Q9UBU8	OTTHUMG00000143865	ENST00000331268.5:c.664T>C	15.37:g.79185887T>C	ENSP00000331310:p.Tyr222His	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	96	33	NM_206839	0	0	1	1	0	B4DKN6|B7Z6R1|D3DW88|O95899|Q5QTS1|Q6NVX8|Q86YT7|Q9HBP6|Q9NSW5	Missense_Mutation	SNP	ENST00000331268.5	37	CCDS10307.1	.	.	.	.	.	.	.	.	.	.	T	8.246	0.807960	0.16467	.	.	ENSG00000185787	ENST00000379535;ENST00000426013;ENST00000331268	T;T;T	0.09163	3.01;3.01;3.01	4.72	4.72	0.59763	.	0.113729	0.64402	D	0.000011	T	0.06005	0.0156	N	0.10874	0.06	0.39713	D	0.971363	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.27706	-1.0066	10	0.44086	T	0.13	-22.6224	8.8633	0.35272	0.1672:0.0:0.0:0.8328	.	183;222	Q9UBU8-2;Q9UBU8	.;MO4L1_HUMAN	H	208;183;222	ENSP00000368850:Y208H;ENSP00000408880:Y183H;ENSP00000331310:Y222H	ENSP00000331310:Y222H	Y	+	1	0	MORF4L1	76972942	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.625000	0.61262	1.902000	0.55061	0.459000	0.35465	TAT	.		0.299	MORF4L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000290131.4	NM_006791		C	79185887	T	C	79185887	3	2	118	1	0	0	0	0	1	0	0	0	9731	1754	61	3	702	3	MORF4L1	15	79185887	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08		79185887	23345505	34	10285											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000563630.1_5'UTR|ZNF598_ENST00000562103.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	2	2	NM_178167	0	0	0	1	1	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	118	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08		2059674	88295079	35	10286											
FLYWCH2	114984	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	2946454	2946456	+	In_Frame_Del	DEL	CCC	CCC	-																															aggccctgggtcccgggatgCccctgcccgagcccagcgag																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2946454_2946456delCCC	ENST00000396958.3	+	3	384_386	c.4_6delCCC	c.(4-6)cccdel	p.P2del	FLYWCH2_ENST00000293981.6_In_Frame_Del_p.P2del|FLYWCH2_ENST00000572006.1_In_Frame_Del_p.P2del	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	2							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						TCCCGGGATGCCCCTGCCCGAGC	0.67																																					p.2_2del		.											.	FLYWCH2-22	0			c.4_6del						.																																			SO:0001651	inframe_deletion	114984	exon3			.	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.4_6delCCC	16.37:g.2946454_2946456delCCC	ENSP00000380159:p.Pro2del	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	29	11	NM_001142499	0	0	0	0	0		In_Frame_Del	DEL	ENST00000396958.3	37	CCDS10482.1																																																																																			.		0.67	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		-	2946456	CCC	-	2946454	7	5	118	1	0	1	0	1	0	0	0	0	5967	739	26	0	6	0	FLYWCH2	16	2946454	In_Frame_Del	DEL	CCC	TCGA-G7-7501-01A-11D-2201-08	886780	2946454	87408299	36	10287	105	3									
FLYWCH2	114984	hgsc.bcm.edu;bcgsc.ca	37	chr16	2946458	2946458	+	Missense_Mutation	SNP	T	T	G																															cctgggtcccgggatgccccTgcccgagcccagcgagcagg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2946458T>G	ENST00000396958.3	+	3	388	c.8T>G	c.(7-9)cTg>cGg	p.L3R	FLYWCH2_ENST00000293981.6_Missense_Mutation_p.L3R|FLYWCH2_ENST00000572006.1_Missense_Mutation_p.L3R	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	3							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						GGGATGCCCCTGCCCGAGCCC	0.672																																					p.L3R		.											.	FLYWCH2-22	0			c.T8G						.						28	35	32					16																	2946458		2197	4300	6497	SO:0001583	missense	114984	exon3			TGCCCCTGCCCGA	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.8T>G	16.37:g.2946458T>G	ENSP00000380159:p.Leu3Arg	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	33	11	NM_001142499	0	0	63	63	0		Missense_Mutation	SNP	ENST00000396958.3	37	CCDS10482.1	.	.	.	.	.	.	.	.	.	.	T	8.600	0.886580	0.17540	.	.	ENSG00000162076	ENST00000396958;ENST00000293981	.	.	.	3.6	2.48	0.30137	.	0.351696	0.16312	N	0.219949	T	0.25121	0.0610	L	0.32530	0.975	0.24368	N	0.994842	P	0.44044	0.825	B	0.39935	0.314	T	0.11470	-1.0586	9	0.87932	D	0	.	6.3825	0.21542	0.2172:0.0:0.0:0.7828	.	3	Q96CP2	FWCH2_HUMAN	R	3	.	ENSP00000293981:L3R	L	+	2	0	FLYWCH2	2886459	0.936000	0.31750	0.877000	0.34402	0.638000	0.38207	0.665000	0.25083	0.717000	0.32145	0.334000	0.21626	CTG	.		0.672	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		G	2946458	T	G	2946458	3	3	118	1	0	0	0	0	1	0	0	0	5967	1580	55	5	10	5	FLYWCH2	16	2946458	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08	4	2946458	87408295	37	10288	105	3									
FLYWCH2	114984	hgsc.bcm.edu;bcgsc.ca	37	chr16	2946461	2946461	+	Missense_Mutation	SNP	C	C	A																															gggtcccgggatgcccctgcCcgagcccagcgagcaggagg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2946461C>A	ENST00000396958.3	+	3	391	c.11C>A	c.(10-12)cCc>cAc	p.P4H	FLYWCH2_ENST00000293981.6_Missense_Mutation_p.P4H|FLYWCH2_ENST00000572006.1_Missense_Mutation_p.P4H	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	4							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						ATGCCCCTGCCCGAGCCCAGC	0.672																																					p.P4H		.											.	FLYWCH2-22	0			c.C11A						.						28	36	33					16																	2946461		2197	4300	6497	SO:0001583	missense	114984	exon3			CCCTGCCCGAGCC	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.11C>A	16.37:g.2946461C>A	ENSP00000380159:p.Pro4His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	40	14	NM_001142499	0	0	64	64	0		Missense_Mutation	SNP	ENST00000396958.3	37	CCDS10482.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.050286	0.36181	.	.	ENSG00000162076	ENST00000396958;ENST00000293981	.	.	.	3.6	3.6	0.41247	.	0.236227	0.22090	N	0.064771	T	0.45316	0.1336	L	0.34521	1.04	0.21697	N	0.999582	D	0.65815	0.995	P	0.57468	0.821	T	0.26121	-1.0112	9	0.87932	D	0	.	11.0322	0.47781	0.0:1.0:0.0:0.0	.	4	Q96CP2	FWCH2_HUMAN	H	4	.	ENSP00000293981:P4H	P	+	2	0	FLYWCH2	2886462	0.035000	0.19736	0.510000	0.27712	0.655000	0.38815	1.813000	0.38962	2.322000	0.78497	0.407000	0.27541	CCC	.		0.672	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		A	2946461	C	A	2946461	3	1	118	1	0	0	0	0	1	0	0	0	5967	623	22	4	13	4	FLYWCH2	16	2946461	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	3	2946461	87408292	38	10289	105	3									
RBBP6	5930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	24582258	24582258	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaaacagatacaaagcgaActgtgattaaaacgatggaa	22	6	8	5	2	0	2	0	1	0	1	0	5	0	3	0	1	5	0	0	1	9	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:24582258A>C	ENST00000319715.4	+	18	4303	c.3871A>C	c.(3871-3873)Act>Cct	p.T1291P	RBBP6_ENST00000381039.3_Missense_Mutation_p.T451P|RBBP6_ENST00000348022.2_Missense_Mutation_p.T1257P	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1291					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TACAAAGCGAACTGTGATTAA	0.343																																					p.T1291P		.											.	RBBP6-230	0			c.A3871C						.						44	43	43					16																	24582258		2197	4300	6497	SO:0001583	missense	5930	exon18			AAGCGAACTGTGA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3871A>C	16.37:g.24582258A>C	ENSP00000317872:p.Thr1291Pro	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	63	26	NM_006910	0	0	17	25	8	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.248060	0.59103	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.34667	1.35;1.46;1.36	5.6	5.6	0.85130	.	0.161807	0.42420	D	0.000707	T	0.49406	0.1555	L	0.32530	0.975	0.47621	D	0.999476	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.87578	0.998;0.997;0.994	T	0.40794	-0.9544	10	0.35671	T	0.21	-16.9171	16.0786	0.80985	1.0:0.0:0.0:0.0	.	451;1257;1291	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	P	451;1291;1257	ENSP00000370427:T451P;ENSP00000317872:T1291P;ENSP00000316291:T1257P	ENSP00000317872:T1291P	T	+	1	0	RBBP6	24489759	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.465000	0.80898	2.254000	0.74563	0.460000	0.39030	ACT	.		0.343	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		C	24582258	A	C	24582258	3	2	118	1	0	0	0	0	1	0	0	0	13135	43	2	5	3995	5	RBBP6	16	24582258	Missense_Mutation	SNP	A	TCGA-G7-7501-01A-11D-2201-08	21635797	24582258	65772495	39	10290											
FBXO31	79791	hgsc.bcm.edu	37	chr16	87377237	87377237	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtggggccctttgtggccGtacatgcactccactgtggc	4	11	14	12	1	0	0	0	0	0	0	1	0	1	0	3	5	2	2	3	5	1	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:87377237G>C	ENST00000311635.7	-	4	636	c.624C>G	c.(622-624)taC>taG	p.Y208*		NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	208					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		CTTTGTGGCCGTACATGCACT	0.637																																					p.Y208X		.											.	FBXO31-226	0			c.C624G						.						57	52	54					16																	87377237		2198	4300	6498	SO:0001587	stop_gained	79791	exon4			GTGGCCGTACATG	BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"F-boxes /  "other""	16510	protein-coding gene	gene with protein product		609102	"F-box only protein 31"				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.624C>G	16.37:g.87377237G>C	ENSP00000310841:p.Tyr208*	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_024735	0	0	11	11	0	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Nonsense_Mutation	SNP	ENST00000311635.7	37	CCDS32501.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.648589	0.87958	.	.	ENSG00000103264	ENST00000311635	.	.	.	5.33	-5.65	0.02459	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.2952	15.8179	0.78618	0.859:0.0:0.141:0.0	.	.	.	.	X	208	.	ENSP00000310841:Y208X	Y	-	3	2	FBXO31	85934738	0.054000	0.20591	0.911000	0.35937	0.879000	0.50718	-0.401000	0.07232	-0.907000	0.03862	-0.794000	0.03295	TAC	.		0.637	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735		C	87377237	G	C	87377237	4	2	118	1	0	0	0	0	0	1	0	0	5760	1140	40	4	1019	4	FBXO31	16	87377237	Nonsense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	62794979	87377237	2977516	40	10291											
KIAA0664	23277	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	2601830	2601830	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgatggccatcacgttgcCgtcaatgacggccatggcgc	7	9	13	12	4	2	2	2	2	0	0	2	2	2	2	3	3	1	2	3	3	1	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr17:2601830C>T	ENST00000570628.2	-	10	1312	c.1207G>A	c.(1207-1209)Ggc>Agc	p.G403S	CLUH_ENST00000435359.1_Missense_Mutation_p.G403S|CLUH_ENST00000538975.1_Missense_Mutation_p.G403S			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	403					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											ATCACGTTGCCGTCAATGACG	0.622																																					p.G403S													.	.	0			c.G1207A						.						25	27	26					17																	2601830		2122	4232	6354	SO:0001583	missense	23277	exon10			CGTTGCCGTCAAT	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.1207G>A	17.37:g.2601830C>T	ENSP00000458986:p.Gly403Ser	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	18	5	NM_015229	0	0	48	88	40	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280323	0.95489	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.83075	-1.68;-1.68	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.92899	0.7741	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94006	0.7280	10	0.72032	D	0.01	.	18.1762	0.89762	0.0:1.0:0.0:0.0	.	403;403	O75153;C9J6D7	K0664_HUMAN;.	S	403	ENSP00000388872:G403S;ENSP00000439628:G403S	ENSP00000320468:G403S	G	-	1	0	KIAA0664	2548580	1.000000	0.71417	0.993000	0.49108	0.657000	0.38888	7.482000	0.81143	2.532000	0.85374	0.655000	0.94253	GGC	.		0.622	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		T	2601830	C	T	2601830	3	4	118	1	0	0	0	0	1	0	0	0	8210	652	23	1	2790	1	KIAA0664	17	2601830	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		2601830	78593380	41	10292											
NPTX1	4884	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	78444656	78444656	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgaaggtccacttggtggccCctccgtagatctcgatgtgg	6	10	13	12	3	1	1	0	0	1	1	4	3	3	1	4	4	0	1	4	4	2	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr17:78444656C>A	ENST00000306773.4	-	5	1413	c.1256G>T	c.(1255-1257)gGg>gTg	p.G419V	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	419	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CTTGGTGGCCCCTCCGTAGAT	0.657																																					p.G419V													.	NPTX1-90	0			c.G1256T						.						66	60	62					17																	78444656		2203	4299	6502	SO:0001583	missense	4884	exon5			GTGGCCCCTCCGT	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.1256G>T	17.37:g.78444656C>A	ENSP00000307549:p.Gly419Val	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	73	10	NM_002522	0	0	0	0	0	B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	37	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110877	0.77210	.	.	ENSG00000171246	ENST00000306773;ENST00000535681	T	0.61392	0.11	5.55	5.55	0.83447	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.109437	0.64402	D	0.000008	D	0.82568	0.5065	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86396	0.1739	10	0.72032	D	0.01	-9.2608	19.0994	0.93268	0.0:1.0:0.0:0.0	.	419	Q15818	NPTX1_HUMAN	V	419;181	ENSP00000307549:G419V	ENSP00000307549:G419V	G	-	2	0	NPTX1	76059251	1.000000	0.71417	0.179000	0.23059	0.423000	0.31445	7.541000	0.82084	2.607000	0.88179	0.561000	0.74099	GGG	.		0.657	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			A	78444656	C	A	78444656	3	1	118	1	0	0	0	0	1	0	0	0	10628	623	22	4	46	4	NPTX1	17	78444656	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	75842826	78444656	2750554	42	10293											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558370	11558370	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaagaagaggctgaagaaga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0	rs77563879		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000412601.1_Silent_p.E322E|PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_Silent_p.E322E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	322	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaagaagagg	0.632																																					p.E322E		.											.	PRKCSH-90	1	Deletion - In frame(1)	central_nervous_system(1)	c.G966A						.						27	27	27					19																	11558370		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAAGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.966G>A	19.37:g.11558370G>A		Somatic	19	2		WXS	Illumina HiSeq	Phase_I	13	4	NM_001001329	0	0	50	51	1	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																			.		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558370	G	A	11558370	2	1	118	1	0	0	0	0	0	0	0	1	12545	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08		11558370	47570613	43	10294											
ZNF700	90592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12060128	12060128	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgggaaagccttcagatctgCctcacagcttcgagtgcacg	9	9	11	12	2	3	1	2	0	1	1	4	3	3	2	2	1	4	2	2	1	1	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:12060128C>T	ENST00000254321.5	+	4	1432	c.1289C>T	c.(1288-1290)gCc>gTc	p.A430V	ZNF763_ENST00000591944.1_Intron|ZNF700_ENST00000482090.1_Missense_Mutation_p.A412V|ZNF763_ENST00000590798.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TTCAGATCTGCCTCACAGCTT	0.473																																					p.A433V		.											.	ZNF700-90	0			c.C1298T						.						91	82	85					19																	12060128		2203	4300	6503	SO:0001583	missense	90592	exon4			GATCTGCCTCACA	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"Zinc fingers, C2H2-type", "-"	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.1289C>T	19.37:g.12060128C>T	ENSP00000254321:p.Ala430Val	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	63	24	NM_001271848	1	0	7	14	6	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	c	4.742	0.138029	0.09083	.	.	ENSG00000196757	ENST00000254321	T	0.34072	1.38	0.606	0.606	0.17559	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17450	0.0419	N	0.16708	0.43	0.09310	N	1	B	0.27910	0.193	B	0.21708	0.036	T	0.23868	-1.0176	9	0.17832	T	0.49	.	5.5675	0.17179	0.3178:0.6822:0.0:0.0	.	430	Q9H0M5	ZN700_HUMAN	V	430	ENSP00000254321:A430V	ENSP00000254321:A430V	A	+	2	0	ZNF700	11921128	0.000000	0.05858	0.001000	0.08648	0.090000	0.18270	-0.886000	0.04157	0.577000	0.29470	0.195000	0.17529	GCC	.		0.473	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		T	12060128	C	T	12060128	3	4	118	1	0	0	0	0	1	0	0	0	18136	739	26	2	1303	2	ZNF700	19	12060128	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	501758	12060128	47068855	44	10295											
PLEKHG2	64857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39914552	39914552	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaatttgcctaagcaagacCttccgggcatccacgtttca	10	10	7	14	2	1	1	1	0	0	1	3	1	3	1	5	1	2	3	5	1	3	4			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:39914552C>G	ENST00000409794.3	+	19	3629	c.2779C>G	c.(2779-2781)Ctt>Gtt	p.L927V	PLEKHG2_ENST00000425673.1_Missense_Mutation_p.L898V|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.L868V|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000409797.2_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	927					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TAAGCAAGACCTTCCGGGCAT	0.577																																					p.L927V		.											.	PLEKHG2-274	0			c.C2779G						.						75	73	74					19																	39914552		2203	4300	6503	SO:0001583	missense	64857	exon19			CAAGACCTTCCGG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.2779C>G	19.37:g.39914552C>G	ENSP00000386733:p.Leu927Val	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	80	32	NM_022835	0	0	8	16	8	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	6.255	0.415175	0.11870	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.69306	-0.26;-0.28;-0.39	4.94	2.56	0.30785	.	1.430940	0.04629	N	0.403390	T	0.50905	0.1643	N	0.08118	0	0.41040	D	0.985222	B;B;B	0.12630	0.003;0.002;0.006	B;B;B	0.06405	0.002;0.001;0.001	T	0.27606	-1.0069	10	0.72032	D	0.01	.	11.6779	0.51440	0.0:0.5758:0.4242:0.0	.	898;927;868	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	V	927;898;868	ENSP00000386733:L927V;ENSP00000392906:L898V;ENSP00000408857:L868V	ENSP00000386733:L927V	L	+	1	0	PLEKHG2	44606392	0.001000	0.12720	0.688000	0.30117	0.059000	0.15707	1.112000	0.31172	1.207000	0.43291	0.655000	0.94253	CTT	.		0.577	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		G	39914552	C	G	39914552	3	3	118	1	0	0	0	0	1	0	0	0	12095	681	24	4	2849	4	PLEKHG2	19	39914552	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	27854424	39914552	19214431	45	10296											
ZNF45	7596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44418234	44418234	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atttgaggcctggctgaagcCcttgccacactcctcacatt	8	11	8	14	0	1	2	1	2	0	0	2	2	2	2	4	2	2	1	4	2	1	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:44418234C>T	ENST00000269973.5	-	10	2444	c.1354G>A	c.(1354-1356)Ggc>Agc	p.G452S	RP11-15A1.2_ENST00000586247.1_RNA|ZNF45_ENST00000589703.1_Missense_Mutation_p.G452S	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	452					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						TGGCTGAAGCCCTTGCCACAC	0.483																																					p.G452S		.											.	ZNF45-91	0			c.G1354A						.						62	63	63					19																	44418234		2203	4300	6503	SO:0001583	missense	7596	exon10			TGAAGCCCTTGCC	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"Zinc fingers, C2H2-type", "-"	13111	protein-coding gene	gene with protein product		194554	"zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)", "zinc finger protein 13"	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.1354G>A	19.37:g.44418234C>T	ENSP00000269973:p.Gly452Ser	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	71	23	NM_003425	0	0	2	7	5	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692770	0.48202	.	.	ENSG00000124459	ENST00000269973	T	0.35421	1.31	3.62	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37178	N	0.002211	T	0.17023	0.0409	N	0.01122	-1.005	0.26498	N	0.974814	B	0.34349	0.45	B	0.42995	0.404	T	0.15464	-1.0436	10	0.44086	T	0.13	-11.8092	10.0287	0.42087	0.2022:0.7977:0.0:0.0	.	452	Q02386	ZNF45_HUMAN	S	452	ENSP00000269973:G452S	ENSP00000269973:G452S	G	-	1	0	ZNF45	49110074	0.000000	0.05858	0.984000	0.44739	0.830000	0.47004	0.090000	0.15025	2.030000	0.59900	0.462000	0.41574	GGC	.		0.483	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425		T	44418234	C	T	44418234	3	4	118	1	0	0	0	0	1	0	0	0	17953	623	22	2	698	2	ZNF45	19	44418234	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	4503682	44418234	14710749	46	10297											
SLC8A2	6543	hgsc.bcm.edu;broad.mit.edu	37	chr19	47969527	47969527	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccggctggcagcggtaggacCcctggcagccccctgtgctg	4	6	15	16	2	0	0	0	0	0	0	0	1	0	1	5	5	3	5	5	5	1	1			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:47969527C>T	ENST00000236877.6	-	2	529	c.134G>A	c.(133-135)gGg>gAg	p.G45E	SLC8A2_ENST00000542837.1_Intron|SLC8A2_ENST00000539381.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	45					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GCGGTAGGACCCCTGGCAGCC	0.731																																					p.G45E		.											.	SLC8A2-94	0			c.G134A						.						10	9	9					19																	47969527		2191	4277	6468	SO:0001583	missense	6543	exon2			TAGGACCCCTGGC	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.134G>A	19.37:g.47969527C>T	ENSP00000236877:p.Gly45Glu	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	9	7	NM_015063	0	0	2	2	0	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	37	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.525726	0.44969	.	.	ENSG00000118160	ENST00000236877	T	0.30448	1.53	4.25	3.19	0.36642	.	0.402651	0.22338	N	0.061364	T	0.23611	0.0571	L	0.51914	1.62	0.21782	N	0.999548	B	0.06786	0.001	B	0.06405	0.002	T	0.25433	-1.0132	10	0.10111	T	0.7	.	9.7772	0.40626	0.0:0.7898:0.2102:0.0	.	45	Q9UPR5	NAC2_HUMAN	E	45	ENSP00000236877:G45E	ENSP00000236877:G45E	G	-	2	0	SLC8A2	52661339	0.158000	0.22850	0.999000	0.59377	0.952000	0.60782	1.497000	0.35649	0.979000	0.38497	0.462000	0.41574	GGG	.		0.731	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			T	47969527	C	T	47969527	3	4	118	1	0	0	0	0	1	0	0	0	14739	623	22	2	2667	2	SLC8A2	19	47969527	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	3551293	47969527	11159456	47	10298											
ZNF606	80095	broad.mit.edu	37	chr19	58490170	58490170	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggattttccacatttattAcattcatagggcttaattcc	11	16	5	9	0	1	0	1	0	0	0	3	1	3	1	2	2	1	1	2	2	4	9			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:58490170A>G	ENST00000341164.4	-	7	2498	c.1878T>C	c.(1876-1878)tgT>tgC	p.C626C	ZNF606_ENST00000536132.1_Silent_p.C536C	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	626					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		CACATTTATTACATTCATAGG	0.383																																					p.C626C													.	ZNF606-92	0			c.T1878C						.						87	86	86					19																	58490170		2203	4300	6503	SO:0001819	synonymous_variant	80095	exon7			TTTATTACATTCA	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"Zinc fingers, C2H2-type", "-"	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.1878T>C	19.37:g.58490170A>G		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	123	4	NM_025027	0	0	8	8	0	A8KAN2|Q8NE04|Q96JH5	Silent	SNP	ENST00000341164.4	37	CCDS12968.1																																																																																			.		0.383	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		G	58490170	A	G	58490170	2	3	118	1	0	0	0	0	0	0	0	1	18064	389	14	3		3	ZNF606	19	58490170	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	10520643	58490170	638813	48	10299											
NAPB	63908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	23370612	23370612	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatctcaatggctttctggtActgctcaagctgggcagcat	8	12	11	10	0	3	0	2	0	2	0	4	1	3	0	0	3	4	6	0	3	3	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr20:23370612A>G	ENST00000377026.4	-	7	617	c.532T>C	c.(532-534)Tac>Cac	p.Y178H	NAPB_ENST00000432543.2_Missense_Mutation_p.Y139H|NAPB_ENST00000398425.3_Missense_Mutation_p.Y84H|NAPB_ENST00000472855.1_5'UTR	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	178					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					GCTTTCTGGTACTGCTCAAGC	0.398																																					p.Y178H		.											.	NAPB-91	0			c.T532C						.						101	99	99					20																	23370612		2203	4300	6503	SO:0001583	missense	63908	exon7			TCTGGTACTGCTC	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.532T>C	20.37:g.23370612A>G	ENSP00000366225:p.Tyr178His	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	116	52	NM_022080	0	0	1	2	1	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	37	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.897519	0.91962	.	.	ENSG00000125814	ENST00000377026;ENST00000398425;ENST00000432543;ENST00000431864	T;T;T	0.48201	0.82;0.82;0.82	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.77698	0.4169	H	0.97758	4.07	0.80722	D	1	D;D;D;D	0.65815	0.995;0.983;0.982;0.995	P;P;P;P	0.62435	0.902;0.82;0.848;0.902	D	0.86047	0.1523	10	0.87932	D	0	-17.6345	14.5087	0.67769	1.0:0.0:0.0:0.0	.	139;84;182;178	B4DK44;Q4G0M0;B4DIV0;Q9H115	.;.;.;SNAB_HUMAN	H	178;84;139;135	ENSP00000366225:Y178H;ENSP00000381459:Y84H;ENSP00000413600:Y139H	ENSP00000366225:Y178H	Y	-	1	0	NAPB	23318612	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.251000	0.95483	2.027000	0.59764	0.383000	0.25322	TAC	.		0.398	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080		G	23370612	A	G	23370612	3	3	118	1	0	0	0	0	1	0	0	0	10187	391	14	3	384	3	NAPB	20	23370612	Missense_Mutation	SNP	A	TCGA-G7-7501-01A-11D-2201-08		23370612	39654908	49	10300											
LIPI	149998	hgsc.bcm.edu	37	chr21	15579137	15579137	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagttaaaagagattaccTgatctcaggcacacaactag	16	9	8	8	0	1	3	1	2	1	1	2	4	1	3	1	1	2	2	1	1	6	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr21:15579137T>C	ENST00000536861.1	-	1	46				LIPI_ENST00000344577.2_Splice_Site_p.S36S			Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		agagattacctgatctcaggc	0.348																																					p.S36S		.											.	LIPI-70	0			c.A108G						.						61	63	63					21																	15579137		2203	4300	6503	SO:0001627	intron_variant	149998	exon1			ATTACCTGATCTC	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.46+3983A>G	21.37:g.15579137T>C		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_198996	0	0	0	0	0	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	37																																																																																				.		0.348	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		C	15579137	T	C	15579137	1	2	118	0	1	0	0	0	0	0	0	0	8848	1594	55	3		3	LIPI	21	15579137	Intron	SNP	T	TCGA-G7-7501-01A-11D-2201-08		15579137	32550758	50	10301											
RIPK4	54101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43161570	43161570	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtctgggcgttcacactcaCccccggctgcttggccagca	5	8	11	17	3	3	0	2	0	1	0	3	0	3	0	3	3	2	4	3	3	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr21:43161570C>A	ENST00000352483.2	-	9	1991	c.1927G>T	c.(1927-1929)Gtg>Ttg	p.V643L	RIPK4_ENST00000544709.1_Missense_Mutation_p.V532L|AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000332512.3_Missense_Mutation_p.V595L|RIPK4_ENST00000542057.1_Missense_Mutation_p.V532L			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	643					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTCACACTCACCCCCGGCTGC	0.682																																					p.V595L		.											.	RIPK4-947	0			c.G1783T						.						55	55	55					21																	43161570		2203	4298	6501	SO:0001583	missense	54101	exon8			CACTCACCCCCGG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"Ankyrin repeat domain containing"	496	protein-coding gene	gene with protein product	"protein kinase C-associated kinase", "PKC-delta-interacting protein kinase"	605706	"ankyrin repeat domain 3"	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1927G>T	21.37:g.43161570C>A	ENSP00000330161:p.Val643Leu	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	91	29	NM_020639	0	0	8	26	18	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.44|18.44	3.625278|3.625278	0.66901|0.66901	.|.	.|.	ENSG00000183421|ENSG00000183421	ENST00000330470|ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057	.|T;T;T;T	.|0.65364	.|2.4;2.4;-0.15;-0.15	4.89|4.89	3.99|3.99	0.46301|0.46301	.|.	.|0.235579	.|0.28694	.|N	.|0.014447	T|T	0.51007|0.51007	0.1649|0.1649	L|L	0.28504|0.28504	0.86|0.86	0.35928|0.35928	D|D	0.832337|0.832337	.|B	.|0.33940	.|0.433	.|B	.|0.33454	.|0.164	T|T	0.62101|0.62101	-0.6925|-0.6925	6|10	0.39692|0.62326	T|D	0.17|0.03	-26.51|-26.51	14.2846|14.2846	0.66238|0.66238	0.0:0.8502:0.1498:0.0|0.0:0.8502:0.1498:0.0	.|.	.|595	.|P57078-2	.|.	V|L	331|595;643;532;532	.|ENSP00000332454:V595L;ENSP00000330161:V643L;ENSP00000441754:V532L;ENSP00000442901:V532L	ENSP00000330975:G331V|ENSP00000332454:V595L	G|V	-|-	2|1	0|0	RIPK4|RIPK4	42034639|42034639	0.982000|0.982000	0.34865|0.34865	0.944000|0.944000	0.38274|0.38274	0.671000|0.671000	0.39405|0.39405	4.763000|4.763000	0.62257|0.62257	1.021000|1.021000	0.39600|0.39600	0.591000|0.591000	0.81541|0.81541	GGT|GTG	.		0.682	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		A	43161570	C	A	43161570	3	1	118	1	0	0	0	0	1	0	0	0	13415	507	18	4	575	4	RIPK4	21	43161570	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	27582433	43161570	4968325	51	10302											
CCT8L2	150160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	17073382	17073382	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggactcctcgggctctccCttgggttcagtgccagccgc	3	10	12	16	2	2	0	1	0	1	0	5	1	3	1	4	3	2	2	4	3	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr22:17073382C>T	ENST00000359963.3	-	1	318	c.59G>A	c.(58-60)aGg>aAg	p.R20K		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	20					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CGGGCTCTCCCTTGGGTTCAG	0.657																																					p.R20K		.											.	CCT8L2-69	0			c.G59A						.						39	45	43					22																	17073382		2203	4300	6503	SO:0001583	missense	150160	exon1			CTCTCCCTTGGGT	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.59G>A	22.37:g.17073382C>T	ENSP00000353048:p.Arg20Lys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	32	26	NM_014406	0	0	0	0	0	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	c	0.015	-1.563933	0.00903	.	.	ENSG00000198445	ENST00000359963	T	0.55052	0.54	1.81	-1.91	0.07641	.	1.067860	0.07473	N	0.902516	T	0.23410	0.0566	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	10	0.02654	T	1	-1.1577	5.1497	0.15004	0.0:0.3187:0.0:0.6813	.	20	Q96SF2	TCPQM_HUMAN	K	20	ENSP00000353048:R20K	ENSP00000353048:R20K	R	-	2	0	CCT8L2	15453382	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.440000	0.02412	-0.377000	0.07930	0.393000	0.25936	AGG	.		0.657	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17073382	C	T	17073382	3	4	118	1	0	0	0	0	1	0	0	0	2967	681	24	2	1618	2	CCT8L2	22	17073382	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		17073382	34231184	52	10303											
SHROOM2	357	broad.mit.edu	37	chrX	9863548	9863548	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggatgcccgcgagacaggaCggtgttacccgctggacaaa	10	5	14	12	5	0	1	0	0	0	1	0	5	0	4	2	4	2	2	2	4	2	1	rs548293164		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chrX:9863548C>T	ENST00000380913.3	+	4	1690	c.1600C>T	c.(1600-1602)Cgg>Tgg	p.R534W		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	534					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				CGAGACAGGACGGTGTTACCC	0.692																																					p.R534W													.	SHROOM2-198	0			c.C1600T						.																																			SO:0001583	missense	357	exon4			ACAGGACGGTGTT	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"apical protein, Xenopus laevis-like", "apical protein-like (Xenopus laevis)"	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.1600C>T	X.37:g.9863548C>T	ENSP00000370299:p.Arg534Trp	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	16	6	NM_001649	0	0	0	6	6	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	C	9.756	1.168773	0.21621	.	.	ENSG00000146950	ENST00000380913	T	0.15487	2.42	4.65	-9.3	0.00649	.	1.655670	0.03705	N	0.249200	T	0.08358	0.0208	L	0.34521	1.04	0.09310	N	1	D	0.62365	0.991	B	0.36766	0.232	T	0.33675	-0.9859	10	0.66056	D	0.02	-3.3611	1.8885	0.03243	0.3791:0.3151:0.1513:0.1545	.	534	Q13796	SHRM2_HUMAN	W	534	ENSP00000370299:R534W	ENSP00000370299:R534W	R	+	1	2	SHROOM2	9823548	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.272000	0.02826	-3.964000	0.00086	-2.129000	0.00344	CGG	.		0.692	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		T	9863548	C	T	9863548	3	4	118	1	0	0	0	0	1	0	0	0	14326	527	19	1	1614	1	SHROOM2	23	9863548	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		9863548	145407012	53	10304											
TRPC5	7224	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	111090414	111090416	+	In_Frame_Del	DEL	TCA	TCA	-																															gctcatcgatagctctggttTcataatagaagtaaagctgg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chrX:111090414_111090416delTCA	ENST00000262839.2	-	6	2544_2546	c.1626_1628delTGA	c.(1624-1629)tatgaa>taa	p.542_543YE>*		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	542					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AGCTCTGGTTTCATAATAGAAGT	0.433																																					p.542_543del		.											.	TRPC5-130	0			c.1626_1628del						.																																			SO:0001651	inframe_deletion	7224	exon6			.	AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"Voltage-gated ion channels / Transient receptor potential cation channels"	12337	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 159"	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.1626_1628delTGA	X.37:g.111090414_111090416delTCA	ENSP00000262839:p.Tyr542_Glu543delins*	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	150	72	NM_012471	0	0	0	0	0	B2RP53|O75233|Q5JXY8|Q9Y514	In_Frame_Del	DEL	ENST00000262839.2	37	CCDS14561.1																																																																																			.		0.433	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		-	111090416	TCA	-	111090414	7	5	118	1	0	1	0	1	0	0	0	0	16615	1783	62	0	1317	0	TRPC5	23	111090414	In_Frame_Del	DEL	TCA	TCGA-G7-7501-01A-11D-2201-08	101226866	111090414	44180146	54	10305											
MCF2	4168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	138684576	138684576	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttactgtacctggaaaaatgCgcattctgaatacttcctcc	11	13	6	11	1	1	1	0	1	1	0	3	2	3	2	3	1	4	2	3	1	6	5	rs202133857		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chrX:138684576C>T	ENST00000370576.4	-	16	2034	c.1825G>A	c.(1825-1827)Gca>Aca	p.A609T	MCF2_ENST00000370573.4_Missense_Mutation_p.A609T|MCF2_ENST00000536274.1_Missense_Mutation_p.A570T|MCF2_ENST00000338585.6_Missense_Mutation_p.A625T|MCF2_ENST00000520602.1_Missense_Mutation_p.A669T|MCF2_ENST00000370578.4_Missense_Mutation_p.A754T|MCF2_ENST00000519895.1_Missense_Mutation_p.A685T|MCF2_ENST00000414978.1_Missense_Mutation_p.A669T	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	609	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					TGGAAAAATGCGCATTCTGAA	0.294													C|||	1	0.000264901	0	0.0014	3775	,	,		14097	0		0	False		,,,				2504	0				p.A685T		.											.	MCF2-227	0			c.G2053A						.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	4,3831		0,2,2,1630,569	142	140	141		2005,2053,1708,1825,1873,1825	4.5	1	X		141	0,6727		0,0,0,2428,1871	no	missense,missense,missense,missense,missense,missense	MCF2	NM_001099855.1,NM_001171876.1,NM_001171877.1,NM_001171878.1,NM_001171879.1,NM_005369.4	58,58,58,58,58,58	0,2,2,4058,2440	TT,TC,T,CC,C		0.0,0.1043,0.0379	benign,benign,benign,benign,benign,benign	669/986,685/1002,570/822,609/861,625/942,609/926	138684576	4,10558	2203	4299	6502	SO:0001583	missense	4168	exon20			AAAATGCGCATTC		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"Rho guanine nucleotide exchange factors"	6940	protein-coding gene	gene with protein product	"Oncogene MCF2 (oncogene DBL)"	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.1825G>A	X.37:g.138684576C>T	ENSP00000359608:p.Ala609Thr	Somatic	280	1		WXS	Illumina HiSeq	Phase_I	217	69	NM_001171876	0	0	0	0	0	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Missense_Mutation	SNP	ENST00000370576.4	37	CCDS14667.1	1|1	6.027727546714888E-4|6.027727546714888E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	5.079|5.079	0.200151|0.200151	0.09652|0.09652	0.001043|0.001043	0.0|0.0	ENSG00000101977|ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000446225;ENST00000519895;ENST00000370573;ENST00000338585|ENST00000437564	T;T;T;T;T;T;T;T;T|.	0.41758|.	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99|.	5.35|5.35	4.48|4.48	0.54585|0.54585	Dbl homology (DH) domain (5);|.	0.395304|.	0.30940|.	N|.	0.008571|.	T|T	0.22085|0.22085	0.0532|0.0532	N|N	0.16266|0.16266	0.395|0.395	0.21147|0.21147	N|N	0.999771|0.999771	B;B;B;B;B;B;B;B|.	0.31581|.	0.209;0.175;0.282;0.329;0.282;0.329;0.085;0.04|.	B;B;B;B;B;B;B;B|.	0.29663|.	0.06;0.046;0.036;0.06;0.036;0.105;0.04;0.06|.	T|T	0.11542|0.11542	-1.0583|-1.0583	10|5	0.12430|.	T|.	0.62|.	.|.	5.6306|5.6306	0.17508|0.17508	0.1717:0.668:0.0:0.1603|0.1717:0.668:0.0:0.1603	.|.	685;754;570;609;609;754;625;609|.	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911|.	.;.;.;.;.;.;.;MCF2_HUMAN|.	T|H	669;609;570;754;669;212;685;609;625|112	ENSP00000427745:A669T;ENSP00000359608:A609T;ENSP00000438155:A570T;ENSP00000359610:A754T;ENSP00000397055:A669T;ENSP00000405848:A212T;ENSP00000430276:A685T;ENSP00000359605:A609T;ENSP00000342204:A625T|.	ENSP00000342204:A625T|.	A|R	-|-	1|2	0|0	MCF2|MCF2	138512242|138512242	0.002000|0.002000	0.14202|0.14202	0.955000|0.955000	0.39395|0.39395	0.096000|0.096000	0.18686|0.18686	0.021000|0.021000	0.13489|0.13489	2.242000|2.242000	0.73789|0.73789	0.594000|0.594000	0.82650|0.82650	GCA|CGC	C|0.999;T|0.001		0.294	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369		T	138684576	C	T	138684576	3	4	118	1	0	0	0	0	1	0	0	0	9403	768	27	1	1020	1	MCF2	23	138684576	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	27594162	138684576	16585984	55	10306											
PER3	8863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	7845603	7845603	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcaataaaccaagcactctAgatgccctcaactatgctct	13	9	5	14	1	3	1	1	0	2	1	3	1	3	1	2	0	5	3	2	0	7	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:7845603A>C	ENST00000361923.2	+	2	406	c.231A>C	c.(229-231)ctA>ctC	p.L77L	PER3_ENST00000377541.1_Silent_p.L77L|PER3_ENST00000377532.3_Silent_p.L77L	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	77					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CAAGCACTCTAGATGCCCTCA	0.448																																					p.L77L		.											.	PER3-93	0			c.A231C						.						86	84	84					1																	7845603		2203	4300	6503	SO:0001819	synonymous_variant	8863	exon2			CACTCTAGATGCC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.231A>C	1.37:g.7845603A>C		Somatic	84	1		WXS	Illumina HiSeq	Phase_I	81	19	NM_016831	0	0	8	9	1	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			.		0.448	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		C	7845603	A	C	7845603	2	2	119	1	0	0	0	0	0	0	0	1	11757	407	15	5		5	PER3	1	7845603	Silent	SNP	A	TCGA-G7-7502-01A-11D-2201-08		7845603	241405018	1	10307											
PRAMEF1	65121	broad.mit.edu	37	chr1	12855985	12855985	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggagagtttgaattcctTggttcgtgtcaattgggaga	9	14	14	4	1	1	4	1	2	0	2	3	6	2	4	1	3	0	2	1	3	2	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:12855985T>C	ENST00000332296.7	+	4	1368	c.1265T>C	c.(1264-1266)tTg>tCg	p.L422S	PRAMEF1_ENST00000400814.3_Missense_Mutation_p.L177S	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	422					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTGAATTCCTTGGTTCGTGTC	0.552																																					p.L422S													.	PRAMEF1-22	0			c.T1265C						.						72	71	72					1																	12855985		2203	4296	6499	SO:0001583	missense	65121	exon4			ATTCCTTGGTTCG	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"-"	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.1265T>C	1.37:g.12855985T>C	ENSP00000332134:p.Leu422Ser	Somatic	422	0		WXS	Illumina HiSeq	Phase_I	336	13	NM_023013	0	0	0	0	0	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	0.161	-1.081469	0.01888	.	.	ENSG00000116721	ENST00000332296;ENST00000400814	T;T	0.01464	4.86;4.86	1.56	-3.12	0.05282	.	2.006700	0.02316	N	0.072532	T	0.01222	0.0040	N	0.12637	0.245	0.09310	N	1	P	0.35033	0.481	B	0.33454	0.164	T	0.40136	-0.9579	10	0.21540	T	0.41	.	4.7128	0.12880	0.201:0.0:0.5397:0.2593	.	422	O95521	PRAM1_HUMAN	S	422;177	ENSP00000332134:L422S;ENSP00000383616:L177S	ENSP00000332134:L422S	L	+	2	0	PRAMEF1	12778572	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.829000	0.00744	-2.159000	0.00787	-1.157000	0.01802	TTG	.		0.552	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013		C	12855985	T	C	12855985	3	2	119	1	0	0	0	0	1	0	0	0	12454	1821	63	3	1275	3	PRAMEF1	1	12855985	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	5010382	12855985	236394636	2	10308											
PTAFR	5724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	28477260	28477260	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagaaaaggcagccagccacGttgcacaggaatttggggag	14	5	14	8	1	0	1	0	0	0	1	0	3	0	3	2	4	3	3	2	4	4	2	rs146920734		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:28477260G>A	ENST00000373857.3	-	2	907	c.273C>T	c.(271-273)aaC>aaT	p.N91N	PTAFR_ENST00000539896.1_Silent_p.N91N|PTAFR_ENST00000305392.3_Silent_p.N91N	NM_000952.4|NM_001164722.2|NM_001164723.2	NP_000943.1|NP_001158194.1|NP_001158195.1	P25105	PTAFR_HUMAN	platelet-activating factor receptor	91					chemotaxis (GO:0006935)|cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|inositol trisphosphate biosynthetic process (GO:0032959)|interferon-gamma-mediated signaling pathway (GO:0060333)|phosphatidylinositol-mediated signaling (GO:0048015)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|phospholipid binding (GO:0005543)|platelet activating factor receptor activity (GO:0004992)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|stomach(1)	15		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		AGCCAGCCACGTTGCACAGGA	0.522																																					p.N91N		.											.	PTAFR-90	0			c.C273T						.	G	,,,	3,4403	8.1+/-20.4	0,3,2200	158	133	141		273,273,273,273	-1.6	0.1	1	dbSNP_134	141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTAFR	NM_000952.4,NM_001164721.1,NM_001164722.2,NM_001164723.2	,,,	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	,,,	91/343,91/343,91/343,91/343	28477260	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	5724	exon3			AGCCACGTTGCAC	BC063000	CCDS318.1	1p35-p34.3	2012-08-20			ENSG00000169403	ENSG00000169403		"GPCR / Class A : Platelet-activating factor receptors"	9582	protein-coding gene	gene with protein product		173393				1322356	Standard	NM_001164721		Approved		uc001bpl.3	P25105	OTTHUMG00000003953	ENST00000373857.3:c.273C>T	1.37:g.28477260G>A		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	82	29	NM_001164723	0	0	12	12	0	A3KMC8|A8K2H5	Silent	SNP	ENST00000373857.3	37	CCDS318.1																																																																																			G|1.000;A|0.000		0.522	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011258.1	NM_000952		A	28477260	G	A	28477260	2	1	119	1	0	0	0	0	0	0	0	1	12752	1136	40	1		1	PTAFR	1	28477260	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	15621275	28477260	220773361	3	10309											
MECR	51102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	29520539	29520539	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcttttgggatgatcacaTggtgagaatctgctttgaag	9	14	12	6	0	3	3	1	3	2	1	3	5	3	4	0	2	1	2	0	2	2	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:29520539T>A	ENST00000263702.6	-	10	1142	c.1117A>T	c.(1117-1119)Atg>Ttg	p.M373L	MECR_ENST00000373791.3_Missense_Mutation_p.M297L			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	373				M -> I (in Ref. 2; CAG32984). {ECO:0000305}.	fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		GATGATCACATGGTGAGAATC	0.597																																					p.M373L		.											.	MECR-91	0			c.A1117T						.						87	89	88					1																	29520539		2203	4300	6503	SO:0001583	missense	51102	exon10			ATCACATGGTGAG		CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"nuclear receptor binding factor 1", "mitochondrial 2-enoyl thioester reductase"	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.1117A>T	1.37:g.29520539T>A	ENSP00000263702:p.Met373Leu	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	100	34	NM_016011	0	0	34	42	8	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	ENST00000263702.6	37	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.969746	0.53614	.	.	ENSG00000116353	ENST00000373791;ENST00000263702	T;T	0.03094	4.05;4.12	5.61	5.61	0.85477	.	0.129329	0.64402	D	0.000001	T	0.06325	0.0163	M	0.66939	2.045	0.49798	D	0.999822	B	0.12630	0.006	B	0.14578	0.011	T	0.27226	-1.0080	10	0.19147	T	0.46	.	13.7585	0.62950	0.0:0.0:0.0:1.0	.	373	Q9BV79	MECR_HUMAN	L	297;373	ENSP00000362896:M297L;ENSP00000263702:M373L	ENSP00000263702:M373L	M	-	1	0	MECR	29393126	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.236000	0.32683	2.143000	0.66587	0.533000	0.62120	ATG	.		0.597	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	NM_016011		A	29520539	T	A	29520539	3	1	119	1	0	0	0	0	1	0	0	0	9449	1464	51	5	8	5	MECR	1	29520539	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	1043279	29520539	219730082	4	10310											
TXLNA	200081	hgsc.bcm.edu;broad.mit.edu	37	chr1	32646099	32646099	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcccggcagcagccaggcTcctcggaagccggagggtgt	6	5	17	13	3	0	0	0	0	0	0	3	2	2	2	4	6	3	3	4	6	1	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:32646099T>C	ENST00000373609.1	+	1	434	c.153T>C	c.(151-153)gcT>gcC	p.A51A	TXLNA_ENST00000373610.3_Silent_p.A51A			P40222	TXLNA_HUMAN	taxilin alpha	51					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|exocytosis (GO:0006887)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	cytokine activity (GO:0005125)|high molecular weight B cell growth factor receptor binding (GO:0030372)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCAGCCAGGCTCCTCGGAAGC	0.701																																					p.A51A		.											.	TXLNA-92	0			c.T153C						.						10	13	12					1																	32646099		2197	4291	6488	SO:0001819	synonymous_variant	200081	exon2			CCAGGCTCCTCGG	AF516206	CCDS353.1	1p35	2012-02-21			ENSG00000084652	ENSG00000084652			30685	protein-coding gene	gene with protein product		608676				15184072, 14623251	Standard	NM_175852		Approved	DKFZp451J0118	uc001bui.3	P40222	OTTHUMG00000004423	ENST00000373609.1:c.153T>C	1.37:g.32646099T>C		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	14	4	NM_175852	0	0	3	5	2	D3DPP6|Q5TFJ6|Q66K62|Q86T54|Q86T85|Q86T86|Q86Y86|Q86YW3|Q8N2Y3	Silent	SNP	ENST00000373609.1	37	CCDS353.1																																																																																			.		0.701	TXLNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012844.1	NM_175852		C	32646099	T	C	32646099	2	2	119	1	0	0	0	0	0	0	0	1	16820	1538	54	3		3	TXLNA	1	32646099	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08	3125560	32646099	216604522	5	10311											
CDCA8	55143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38174030	38174030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcagcagcatacggaccCacaaatgagacaccaaagtt	15	6	8	12	1	1	1	0	1	1	1	1	3	1	2	2	1	4	4	2	1	3	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:38174030C>T	ENST00000373055.1	+	10	1108	c.835C>T	c.(835-837)Cac>Tac	p.H279Y	CDCA8_ENST00000327331.2_Missense_Mutation_p.H279Y	NM_001256875.1|NM_018101.3	NP_001243804.1|NP_060571.1	Q53HL2	BOREA_HUMAN	cell division cycle associated 8	279					chromosome organization (GO:0051276)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(1)|stomach(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CATACGGACCCACAAATGAGA	0.483																																					p.H279Y		.											.	CDCA8-90	0			c.C835T						.						131	125	127					1																	38174030		2203	4300	6503	SO:0001583	missense	55143	exon10			CGGACCCACAAAT	BG354581	CCDS424.1	1p34.3	2013-01-17			ENSG00000134690	ENSG00000134690			14629	protein-coding gene	gene with protein product	"borealin"	609977				12188893, 15260989	Standard	NM_001256875		Approved	FLJ12042, MESRGP, BOR, DasraB	uc001cbs.4	Q53HL2	OTTHUMG00000004320	ENST00000373055.1:c.835C>T	1.37:g.38174030C>T	ENSP00000362146:p.His279Tyr	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	67	16	NM_001256875	0	0	2	2	0	D3DPT4|Q53HN1|Q96AM3|Q9NVW5	Missense_Mutation	SNP	ENST00000373055.1	37	CCDS424.1	.	.	.	.	.	.	.	.	.	.	C	6.465	0.453973	0.12283	.	.	ENSG00000134690	ENST00000373055;ENST00000327331	T;T	0.46063	0.88;0.88	5.48	2.55	0.30701	.	1.036760	0.07555	N	0.916095	T	0.26159	0.0638	N	0.22421	0.69	0.25891	N	0.983472	B	0.02656	0.0	B	0.01281	0.0	T	0.27640	-1.0068	10	0.22706	T	0.39	-2.4563	3.8562	0.08976	0.1641:0.5775:0.1703:0.0881	.	279	Q53HL2	BOREA_HUMAN	Y	279	ENSP00000362146:H279Y;ENSP00000316121:H279Y	ENSP00000316121:H279Y	H	+	1	0	CDCA8	37946617	0.989000	0.36119	0.332000	0.25469	0.213000	0.24496	0.321000	0.19558	0.402000	0.25451	0.650000	0.86243	CAC	.		0.483	CDCA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012473.1	NM_018101		T	38174030	C	T	38174030	3	4	119	1	0	0	0	0	1	0	0	0	3098	594	21	2	873	2	CDCA8	1	38174030	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	5527931	38174030	211076591	6	10312											
LRRC40	55631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	70671136	70671136	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgctgccttcaacagccCttggggtaccgaggtaccgc	6	8	11	16	3	1	0	1	0	0	0	2	1	1	0	5	3	5	3	5	3	3	4	rs368762009		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:70671136C>G	ENST00000370952.3	-	1	167	c.88G>C	c.(88-90)Ggg>Cgg	p.G30R	SRSF11_ENST00000454435.2_5'Flank|SRSF11_ENST00000370950.3_5'Flank|SRSF11_ENST00000370951.1_5'Flank|SRSF11_ENST00000405432.1_5'Flank	NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	30						membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						TTCAACAGCCCTTGGGGTACC	0.562																																					p.G30R		.											.	LRRC40-91	0			c.G88C						.						91	82	85					1																	70671136		2203	4300	6503	SO:0001583	missense	55631	exon1			ACAGCCCTTGGGG		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.88G>C	1.37:g.70671136C>G	ENSP00000359990:p.Gly30Arg	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	82	8	NM_017768	0	0	2	3	1	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.858799	0.71834	.	.	ENSG00000066557	ENST00000370952	T	0.25085	1.82	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.26702	0.0653	L	0.35854	1.095	0.58432	D	0.999997	D	0.89917	1.0	D	0.76575	0.988	T	0.01679	-1.1297	10	0.17832	T	0.49	.	14.1132	0.65137	0.0:1.0:0.0:0.0	.	30	Q9H9A6	LRC40_HUMAN	R	30	ENSP00000359990:G30R	ENSP00000359990:G30R	G	-	1	0	LRRC40	70443724	1.000000	0.71417	0.998000	0.56505	0.271000	0.26615	4.265000	0.58865	2.703000	0.92315	0.563000	0.77884	GGG	.		0.562	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		G	70671136	C	G	70671136	3	3	119	1	0	0	0	0	1	0	0	0	9023	681	24	4	1780	4	LRRC40	1	70671136	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	32497106	70671136	178579485	7	10313											
ODF2L	57489	hgsc.bcm.edu	37	chr1	86842001	86842001	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaactttagatgccttttttAaagctacagttttttgccta	11	18	5	7	0	0	1	0	0	0	1	0	1	0	1	2	0	5	2	2	0	6	10			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:86842001A>G	ENST00000359242.3	-	8	1006	c.725T>C	c.(724-726)tTa>tCa	p.L242S	ODF2L_ENST00000370567.1_Missense_Mutation_p.L242S|ODF2L_ENST00000524695.1_5'Flank|ODF2L_ENST00000317336.7_Missense_Mutation_p.L242S|ODF2L_ENST00000394731.1_Missense_Mutation_p.L111S|ODF2L_ENST00000294678.2_Missense_Mutation_p.L242S|ODF2L_ENST00000370566.3_Missense_Mutation_p.L242S	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	242						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TGCCTTTTTTAAAGCTACAGT	0.353																																					p.L242S		.											.	ODF2L-69	0			c.T725C						.						132	121	125					1																	86842001		2201	4300	6501	SO:0001583	missense	57489	exon8			TTTTTTAAAGCTA		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.725T>C	1.37:g.86842001A>G	ENSP00000359600:p.Leu242Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_001007022	0	0	11	11	0	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	37	CCDS41354.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.60|15.60	2.882540|2.882540	0.51908|0.51908	.|.	.|.	ENSG00000122417|ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000460698;ENST00000317336;ENST00000370567;ENST00000394731;ENST00000457680;ENST00000294678;ENST00000479890|ENST00000459999	T;T;T;T;T;T;T;D|.	0.85088|.	0.96;0.91;1.08;0.97;0.98;1.09;0.95;-1.94|.	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.66386|.	0.2784|.	M|M	0.72894|0.72894	2.215|2.215	0.46458|0.46458	D|D	0.999054|0.999054	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.91635|.	0.999;0.999;0.999;0.999;0.999;0.999|.	T|.	0.67654|.	-0.5615|.	10|.	0.72032|.	D|.	0.01|.	-5.523|-5.523	14.3411|14.3411	0.66627|0.66627	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	242;242;242;242;242;242|.	B4E037;B4DZ83;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1|.	.;.;.;.;.;ODF2L_HUMAN|.	S|Q	242;242;242;118;242;242;111;72;242;72|91	ENSP00000359597:L242S;ENSP00000359600:L242S;ENSP00000433092:L118S;ENSP00000320165:L242S;ENSP00000359598:L242S;ENSP00000378219:L111S;ENSP00000294678:L242S;ENSP00000432834:L72S|.	ENSP00000294678:L242S|.	L|X	-|-	2|1	0|0	ODF2L|ODF2L	86614589|86614589	0.996000|0.996000	0.38824|0.38824	0.991000|0.991000	0.47740|0.47740	0.164000|0.164000	0.22412|0.22412	5.973000|5.973000	0.70456|0.70456	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	TTA|TAA	.		0.353	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			G	86842001	A	G	86842001	3	3	119	1	0	0	0	0	1	0	0	0	10854	372	13	3	1405	3	ODF2L	1	86842001	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	16170865	86842001	162408620	8	10314											
NTNG1	22854	hgsc.bcm.edu	37	chr1	107973392	107973392	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgtgaatgcttcggccacTccaatcgatgcagttatatc	10	13	8	10	2	0	1	0	1	0	0	4	2	1	1	2	1	2	3	2	1	4	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:107973392T>C	ENST00000370068.1	+	6	1954	c.1108T>C	c.(1108-1110)Tcc>Ccc	p.S370P	NTNG1_ENST00000370071.2_Intron|NTNG1_ENST00000370072.3_Missense_Mutation_p.S370P|NTNG1_ENST00000370074.4_Intron|NTNG1_ENST00000370073.2_Missense_Mutation_p.S370P|NTNG1_ENST00000370061.3_Intron|NTNG1_ENST00000370065.1_Missense_Mutation_p.S370P|NTNG1_ENST00000370070.2_Intron|NTNG1_ENST00000542803.1_Missense_Mutation_p.S370P|NTNG1_ENST00000370066.1_Intron|NTNG1_ENST00000370067.1_Intron			Q9Y2I2	NTNG1_HUMAN	netrin G1	370	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		CTTCGGCCACTCCAATCGATG	0.428																																					p.S370P		.											.	NTNG1-140	0			c.T1108C						.						96	81	86					1																	107973392		1568	3582	5150	SO:0001583	missense	22854	exon6			GGCCACTCCAATC	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.1108T>C	1.37:g.107973392T>C	ENSP00000359085:p.Ser370Pro	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_001113226	0	0	0	0	0	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	37	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.202136	0.58234	.	.	ENSG00000162631	ENST00000370073;ENST00000542803;ENST00000370072;ENST00000370064;ENST00000370068;ENST00000370065	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	5.47	5.47	0.80525	EGF-like, laminin (3);	0.000000	0.64402	D	0.000017	T	0.81800	0.4899	H	0.95187	3.635	0.80722	D	1	D	0.76494	0.999	D	0.68483	0.958	D	0.86997	0.2114	10	0.56958	D	0.05	.	15.5448	0.76090	0.0:0.0:0.0:1.0	.	370	Q9Y2I2	NTNG1_HUMAN	P	370;370;370;173;370;370	ENSP00000359090:S370P;ENSP00000440561:S370P;ENSP00000359089:S370P;ENSP00000359085:S370P;ENSP00000359082:S370P	ENSP00000359081:S173P	S	+	1	0	NTNG1	107774915	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.030000	0.88816	2.069000	0.61940	0.533000	0.62120	TCC	.		0.428	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		C	107973392	T	C	107973392	3	2	119	1	0	0	0	0	1	0	0	0	10730	1551	54	3	1260	3	NTNG1	1	107973392	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	21131391	107973392	141277229	9	10315											
OR6K2	81448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158669896	158669896	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcaggccagacgcagcaCtgggaggaagtcacagaaga	13	4	15	9	1	1	3	1	0	0	3	1	5	1	5	1	3	2	3	1	3	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:158669896C>T	ENST00000359610.2	-	1	590	c.547G>A	c.(547-549)Gtg>Atg	p.V183M		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					AGACGCAGCACTGGGAGGAAG	0.478																																					p.V183M		.											.	OR6K2-69	0			c.G547A						.						133	112	119					1																	158669896		2203	4300	6503	SO:0001583	missense	81448	exon1			GCAGCACTGGGAG	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"GPCR / Class A : Olfactory receptors"	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.547G>A	1.37:g.158669896C>T	ENSP00000352626:p.Val183Met	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	105	35	NM_001005279	0	0	0	0	0	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.489601	0.44249	.	.	ENSG00000196171	ENST00000359610	T	0.00231	8.49	5.09	3.14	0.36123	GPCR, rhodopsin-like superfamily (1);	0.438834	0.16622	N	0.206443	T	0.00109	0.0003	M	0.66939	2.045	0.09310	N	1	B	0.31893	0.345	B	0.43360	0.417	T	0.34254	-0.9836	10	0.72032	D	0.01	-4.3506	3.0153	0.06058	0.2617:0.4934:0.1539:0.091	.	183	Q8NGY2	OR6K2_HUMAN	M	183	ENSP00000352626:V183M	ENSP00000352626:V183M	V	-	1	0	OR6K2	156936520	0.000000	0.05858	0.982000	0.44146	0.993000	0.82548	-1.509000	0.02264	1.348000	0.45733	0.655000	0.94253	GTG	.		0.478	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		T	158669896	C	T	158669896	3	4	119	1	0	0	0	0	1	0	0	0	11228	565	20	2	431	2	OR6K2	1	158669896	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	50696504	158669896	90580725	10	10316											
PAPPA2	60676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	176740277	176740277	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caaatatgaatgcaaaccagGgtactatgtggcagaaagtg	16	8	11	6	0	0	2	0	1	0	1	0	2	0	2	1	2	3	3	1	2	7	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:176740277G>T	ENST00000367662.3	+	17	5840	c.4676G>T	c.(4675-4677)gGg>gTg	p.G1559V		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1559	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TGCAAACCAGGGTACTATGTG	0.478																																					p.G1559V		.											.	PAPPA2-548	0			c.G4676T						.						96	90	92					1																	176740277		2009	4181	6190	SO:0001583	missense	60676	exon17			AACCAGGGTACTA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4676G>T	1.37:g.176740277G>T	ENSP00000356634:p.Gly1559Val	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	75	18	NM_020318	0	0	6	6	0	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.439678	0.83885	.	.	ENSG00000116183	ENST00000367662	T	0.77358	-1.09	5.53	5.53	0.82687	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.88544	0.6465	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89575	0.3816	10	0.87932	D	0	-23.6151	18.0257	0.89268	0.0:0.0:1.0:0.0	.	1559	Q9BXP8	PAPP2_HUMAN	V	1559	ENSP00000356634:G1559V	ENSP00000356634:G1559V	G	+	2	0	PAPPA2	175006900	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	9.050000	0.93843	2.592000	0.87571	0.655000	0.94253	GGG	.		0.478	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176740277	G	T	176740277	3	4	119	1	0	0	0	0	1	0	0	0	11459	1232	43	4	4791	4	PAPPA2	1	176740277	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	18070381	176740277	72510344	11	10317											
CFHR3	10878	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	196762616	196762617	+	Missense_Mutation	DNP	GA	GA	TT																															caagcagtgtgtcgggaaggGatagtggaataccccagatg																								rs149081467	byFrequency	TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:196762616_196762617GA>TT	ENST00000367425.4	+	6	1058_1059	c.966_967GA>TT	c.(964-969)ggGAta>ggTTta	p.I323L	CFHR3_ENST00000391985.3_Missense_Mutation_p.I262L	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	323	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GTCGGGAAGGGATAGTGGAATA	0.381																																					p.I323L		.											.	CFHR3	0			c.A967T						.																																			SO:0001583	missense	10878	exon6			GAAGGGATAGTGG	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"Complement system"	16980	protein-coding gene	gene with protein product	"complement factor H related 3"	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	Exception_encountered	1.37:g.196762616_196762617delinsTT	ENSP00000356395:p.Ile323Leu	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	124	9		0	0	0	0	0	B4DPR0|Q9UJ16	Missense_Mutation	DNP	ENST00000367425.4	37	CCDS30958.1																																																																																			.		0.381	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023		TT	196762617	GA	TT	196762616	3	4	119	1	0	0	0	0	1	0	0	0	3292	1161	41	4	988	4	CFHR3	1	196762616	Missense_Mutation	DNP	GA	TCGA-G7-7502-01A-11D-2201-08	20022339	196762616	52488005	12	10318											
OTX1	5013	hgsc.bcm.edu	37	chr2	63282948	63282948	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccatctcgccaggctcagcgCccgcgtccgtgtcggtgccg	3	7	13	18	7	2	0	1	0	1	0	5	0	3	0	5	2	2	1	5	2	0	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:63282948C>G	ENST00000282549.2	+	5	838	c.562C>G	c.(562-564)Ccc>Gcc	p.P188A	OTX1_ENST00000366671.3_Missense_Mutation_p.P188A	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	188					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					AGGCTCAGCGCCCGCGTCCGT	0.687																																					p.P188A		.											.	OTX1-70	0			c.C562G						.						13	14	14					2																	63282948		2186	4283	6469	SO:0001583	missense	5013	exon5			TCAGCGCCCGCGT		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"Homeoboxes / PRD class"	8521	protein-coding gene	gene with protein product		600036	"orthodenticle (Drosophila) homolog 1", "orthodenticle homolog 1 (Drosophila)"			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.562C>G	2.37:g.63282948C>G	ENSP00000282549:p.Pro188Ala	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_014562	0	0	0	0	0	A6NHA2|B3KTJ4|Q53TG6	Missense_Mutation	SNP	ENST00000282549.2	37	CCDS1873.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127474	0.56721	.	.	ENSG00000115507	ENST00000366671;ENST00000282549	D;D	0.90900	-2.75;-2.75	3.41	3.41	0.39046	Transcription factor Otx, C-terminal (1);	0.269321	0.29321	N	0.012488	D	0.91730	0.7385	L	0.53249	1.67	0.80722	D	1	D	0.62365	0.991	D	0.66602	0.945	D	0.88527	0.3100	10	0.10377	T	0.69	.	12.6775	0.56903	0.0:1.0:0.0:0.0	.	188	P32242	OTX1_HUMAN	A	188	ENSP00000355631:P188A;ENSP00000282549:P188A	ENSP00000282549:P188A	P	+	1	0	OTX1	63136452	0.997000	0.39634	0.968000	0.41197	0.935000	0.57460	4.214000	0.58527	1.901000	0.55032	0.462000	0.41574	CCC	.		0.687	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			G	63282948	C	G	63282948	3	3	119	1	0	0	0	0	1	0	0	0	11346	739	26	4	572	4	OTX1	2	63282948	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08		63282948	179916425	13	10319											
KDM3A	55818	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	86716748	86716749	+	In_Frame_Ins	INS	-	-	GGG																															tggcacatatatgctgcaaaINSggacacggagaagataaggg																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:86716748_86716749insGGG	ENST00000409556.1	+	24	3904_3905	c.3539_3540insGGG	c.(3538-3543)aaggac>aaGGGggac	p.1180_1181KD>KGD	KDM3A_ENST00000542128.1_In_Frame_Ins_p.1128_1129KD>KGD|KDM3A_ENST00000409064.1_In_Frame_Ins_p.1180_1181KD>KGD|KDM3A_ENST00000312912.5_In_Frame_Ins_p.1180_1181KD>KGD			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	1180	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						TATGCTGCAAAGGACACGGAGA	0.406																																					p.K1180delinsKG	NSCLC(96;1150 1523 6936 46253 49736)	.											.	KDM3A-291	0			c.3539_3540insGGG						.																																			SO:0001652	inframe_insertion	55818	exon23			.	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"Chromatin-modifying enzymes / K-demethylases"	20815	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 2A"	611512	"jumonji domain containing 1", "jumonji domain containing 1A"	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	Exception_encountered	2.37:g.86716748_86716749insGGG	ENSP00000386660:p.Lys1180_Asp1181insGly	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	131	51	NM_018433	0	0	0	0	0	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	In_Frame_Ins	INS	ENST00000409556.1	37	CCDS1990.1																																																																																			.		0.406	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		GGG	86716749	-	GGG	86716748	7	5	119	1	0	1	1	0	0	0	0	0	8147	72	3	0	3625	0	KDM3A	2	86716748	In_Frame_Ins	INS	-	TCGA-G7-7502-01A-11D-2201-08	23433800	86716748	156482625	14	10320											
CIR1	9541	hgsc.bcm.edu;broad.mit.edu	37	chr2	175215408	175215408	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgagaagtttctgtttttgTttggttgttagtgactttaa	7	21	10	3	0	1	2	0	2	1	1	1	3	1	2	0	1	0	5	0	1	3	8			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:175215408T>C	ENST00000342016.3	-	9	749	c.657A>G	c.(655-657)aaA>aaG	p.K219K	CIR1_ENST00000362053.5_3'UTR	NM_004882.3	NP_004873.3	Q86X95	CIR1_HUMAN	corepressor interacting with RBPJ, 1	219	Interaction with RP9. {ECO:0000250}.|Lys/Ser-rich.				mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1)	15						TCTGTTTTTGTTTGGTTGTTA	0.303																																					p.K219K		.											.	CIR1-153	0			c.A657G						.						80	76	78					2																	175215408		2203	4299	6502	SO:0001819	synonymous_variant	9541	exon9			TTTTTGTTTGGTT	AF098297	CCDS2256.1	2q31.1	2009-07-14			ENSG00000138433	ENSG00000138433			24217	protein-coding gene	gene with protein product	"recepin", "CBF1 interacting corepressor"	605228				15652350, 11222720, 9874765	Standard	NM_004882		Approved	CIR	uc002uim.3	Q86X95	OTTHUMG00000132338	ENST00000342016.3:c.657A>G	2.37:g.175215408T>C		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	67	5	NM_004882	0	0	153	156	3	A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2	Silent	SNP	ENST00000342016.3	37	CCDS2256.1																																																																																			.		0.303	CIR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255460.1	NM_004882		C	175215408	T	C	175215408	2	2	119	1	0	0	0	0	0	0	0	1	3438	1722	60	3		3	CIR1	2	175215408	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08	88498660	175215408	67983965	15	10321											
STK36	27148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219556970	219556970	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caggttgtcttggatgggctCcttcatggcttgacagttcc	5	14	12	10	0	2	1	1	1	1	0	4	2	4	2	2	4	0	4	2	4	0	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:219556970C>G	ENST00000295709.3	+	15	2148	c.1869C>G	c.(1867-1869)ctC>ctG	p.L623L	STK36_ENST00000440309.1_Silent_p.L623L|STK36_ENST00000392105.3_Silent_p.L623L|STK36_ENST00000392106.2_Silent_p.L623L	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		TGGATGGGCTCCTTCATGGCT	0.537																																					p.L623L		.											.	STK36-1004	0			c.C1869G						.						90	95	93					2																	219556970		2203	4300	6503	SO:0001819	synonymous_variant	27148	exon15			TGGGCTCCTTCAT	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"fused homolog (Drosophila)"	607652	"serine/threonine kinase 36 (fused homolog, Drosophila)"			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.1869C>G	2.37:g.219556970C>G		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	133	70	NM_015690	0	0	10	24	14		Silent	SNP	ENST00000295709.3	37	CCDS2421.1																																																																																			.		0.537	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			G	219556970	C	G	219556970	2	3	119	1	0	0	0	0	0	0	0	1	15334	842	30	4		4	STK36	2	219556970	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	44341562	219556970	23642403	16	10322											
ECEL1	9427	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	233350797	233350797	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgctcgatctcgcgcatGtcgaggcacgagcggaagaa	10	6	14	11	7	1	1	0	0	1	1	5	5	1	2	0	2	1	3	0	2	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:233350797G>A	ENST00000304546.1	-	2	777	c.567C>T	c.(565-567)gaC>gaT	p.D189D	ECEL1_ENST00000409941.1_Silent_p.D189D	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	189					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TCTCGCGCATGTCGAGGCACG	0.746																																					p.D189D		.											.	ECEL1-90	0			c.C567T						.																																			SO:0001819	synonymous_variant	9427	exon2			GCGCATGTCGAGG	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.567C>T	2.37:g.233350797G>A		Somatic	15	0		WXS	Illumina HiSeq	Phase_I	29	7	NM_004826	0	0	0	0	0	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																			.		0.746	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		A	233350797	G	A	233350797	2	1	119	1	0	0	0	0	0	0	0	1	4902	1368	48	2		2	ECEL1	2	233350797	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	13793827	233350797	9848576	17	10323											
JAGN1	84522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9934676	9934676	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctggttgctaagatgaGcgtgggacacctgaggctct	7	10	15	9	1	1	3	0	2	1	1	1	4	1	4	1	3	3	5	1	3	1	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:9934676G>A	ENST00000307768.4	+	2	336	c.167G>A	c.(166-168)aGc>aAc	p.S56N		NM_032492.3	NP_115881.3			jagunal homolog 1 (Drosophila)											breast(1)|central_nervous_system(1)|endometrium(4)|lung(3)|ovary(1)	10	Medulloblastoma(99;0.227)					GCTAAGATGAGCGTGGGACAC	0.512																																					p.S56N		.											.	JAGN1-91	0			c.G167A						.						158	132	141					3																	9934676		2203	4300	6503	SO:0001583	missense	84522	exon2			AGATGAGCGTGGG	AK074760	CCDS2588.1	3p25.2	2010-03-23			ENSG00000171135	ENSG00000171135			26926	protein-coding gene	gene with protein product						12477932	Standard	NM_032492		Approved	GL009, FLJ14602	uc003btt.4	Q8N5M9	OTTHUMG00000128523	ENST00000307768.4:c.167G>A	3.37:g.9934676G>A	ENSP00000306106:p.Ser56Asn	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	79	20	NM_032492	0	0	64	92	28		Missense_Mutation	SNP	ENST00000307768.4	37	CCDS2588.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434837	0.25813	.	.	ENSG00000171135	ENST00000307768;ENST00000543379	.	.	.	5.24	3.34	0.38264	.	0.446433	0.27754	N	0.017994	T	0.36220	0.0959	L	0.36672	1.1	0.20638	N	0.999878	B	0.17667	0.023	B	0.24541	0.054	T	0.21655	-1.0239	9	0.26408	T	0.33	-15.5227	10.1674	0.42888	0.0:0.1322:0.5948:0.2731	.	56	Q8N5M9	JAGN1_HUMAN	N	56	.	ENSP00000306106:S56N	S	+	2	0	JAGN1	9909676	0.775000	0.28604	0.992000	0.48379	0.966000	0.64601	1.530000	0.36007	0.514000	0.28300	0.313000	0.20887	AGC	.		0.512	JAGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250335.1	NM_032492		A	9934676	G	A	9934676	3	1	119	1	0	0	0	0	1	0	0	0	7957	971	34	2	173	2	JAGN1	3	9934676	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		9934676	188087754	18	10324											
DAG1	1605	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	49568641	49568641	+	Frame_Shift_Del	DEL	A	A	-																															aattagtgccggtggtgaatAacagactatttgacatgtcg																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:49568641delA	ENST00000539901.1	+	3	1255	c.697delA	c.(697-699)aacfs	p.N233fs	DAG1_ENST00000308775.2_Frame_Shift_Del_p.N233fs|DAG1_ENST00000541308.1_Frame_Shift_Del_p.N233fs|DAG1_ENST00000545947.1_Frame_Shift_Del_p.N233fs|DAG1_ENST00000515359.2_Frame_Shift_Del_p.N233fs|DAG1_ENST00000538711.1_Frame_Shift_Del_p.N233fs	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	233	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GGTGGTGAATAACAGACTATT	0.522																																					p.N233fs		.											.	DAG1-92	0			c.697delA						.						72	77	75					3																	49568641		2203	4300	6503	SO:0001589	frameshift_variant	1605	exon4			.	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.697delA	3.37:g.49568641delA	ENSP00000439334:p.Asn233fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	49	10	NM_001177642	0	0	0	0	0	A8K6M7|Q969J9	Frame_Shift_Del	DEL	ENST00000539901.1	37	CCDS2799.1																																																																																			.		0.522	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			-	49568641	A	-	49568641	7	5	119	1	0	1	0	1	0	0	0	0	4231	362	13	0	703	0	DAG1	3	49568641	Frame_Shift_Del	DEL	A	TCGA-G7-7502-01A-11D-2201-08	39633965	49568641	148453789	19	10325											
APEH	327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49720689	49720689	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggctcctgctctatcccaaaAgcacccacgcattatcagag	11	8	7	15	1	2	1	1	0	1	1	4	1	4	1	3	1	2	4	3	1	4	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:49720689A>G	ENST00000296456.5	+	22	2513	c.2113A>G	c.(2113-2115)Agc>Ggc	p.S705G	AC099668.5_ENST00000563780.1_RNA|APEH_ENST00000438011.1_Missense_Mutation_p.S710G	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	705					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CTATCCCAAAAGCACCCACGC	0.557																																					p.S705G		.											.	APEH-91	0			c.A2113G						.						188	196	193					3																	49720689		2203	4300	6503	SO:0001583	missense	327	exon22			CCCAAAAGCACCC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.2113A>G	3.37:g.49720689A>G	ENSP00000296456:p.Ser705Gly	Somatic	332	0		WXS	Illumina HiSeq	Phase_I	353	63	NM_001640	0	0	313	445	132	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180168	0.38511	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.32753	1.44;1.44	5.75	5.75	0.90469	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.129744	0.64402	D	0.000001	T	0.20129	0.0484	N	0.17278	0.47	0.37781	D	0.927029	B;B	0.10296	0.003;0.002	B;B	0.15052	0.012;0.006	T	0.08269	-1.0730	10	0.48119	T	0.1	-38.9892	10.7009	0.45926	0.9202:0.0:0.0798:0.0	.	710;705	C9JIF9;P13798	.;ACPH_HUMAN	G	705;710	ENSP00000296456:S705G;ENSP00000415862:S710G	ENSP00000296456:S705G	S	+	1	0	APEH	49695693	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.552000	0.53705	2.192000	0.70111	0.459000	0.35465	AGC	.		0.557	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			G	49720689	A	G	49720689	3	3	119	1	0	0	0	0	1	0	0	0	768	72	3	3	2199	3	APEH	3	49720689	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	152048	49720689	148301741	20	10326											
ACY1	95	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52022538	52022538	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccattcttcctgtccctcAgaagtggatgcacccccaag	8	10	8	15	0	2	1	1	0	1	1	4	2	4	2	5	1	2	1	5	1	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:52022538A>C	ENST00000404366.2	+	13	1067		c.e13-1		ACY1_ENST00000494103.1_Splice_Site|ACY1_ENST00000476854.1_Splice_Site|ACY1_ENST00000458031.2_Splice_Site|ACY1_ENST00000476351.1_Splice_Site|ABHD14A-ACY1_ENST00000463937.1_Splice_Site	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1						cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CCTGTCCCTCAGAAGTGGATG	0.562																																					.		.											.	ACY1-154	0			c.817-2A>C						.						103	86	92					3																	52022538		2203	4300	6503	SO:0001630	splice_region_variant	95	exon12			TCCCTCAGAAGTG	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.922-1A>C	3.37:g.52022538A>C		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	74	17	NM_001198898	0	0	6	8	2	C9J6I6|C9J9D8|C9JWD4	Splice_Site	SNP	ENST00000404366.2	37	CCDS2844.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.321906	0.41096	.	.	ENSG00000114786;ENSG00000114786;ENSG00000114786;ENSG00000243989;ENSG00000243989;ENSG00000243989;ENSG00000243989	ENST00000458031;ENST00000463937;ENST00000232907;ENST00000476854;ENST00000476351;ENST00000494103;ENST00000404366	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0907	0.72192	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACY1;RP11-155D18.11	51997578	1.000000	0.71417	0.993000	0.49108	0.278000	0.26855	8.943000	0.92975	2.048000	0.60808	0.459000	0.35465	.	.		0.562	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666	Intron	C	52022538	A	C	52022538	5	2	119	1	0	0	0	0	0	0	1	0	226	202	7	5	966	5	ACY1	3	52022538	Splice_Site	SNP	A	TCGA-G7-7502-01A-11D-2201-08	2301849	52022538	145999892	21	10327											
STAB1	23166	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52554291	52554291	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccccatctctttctcctgCagccgaacgcgggccgtgag	6	8	10	17	4	2	1	0	1	2	0	4	2	2	1	5	1	3	1	5	1	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:52554291C>A	ENST00000321725.6	+	52	5560	c.5484C>A	c.(5482-5484)tgC>tgA	p.C1828*		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1828	FAS1 6. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CTTTCTCCTGCAGCCGAACGC	0.632																																					p.C1828X		.											.	STAB1-139	0			c.C5484A						.						82	83	83					3																	52554291		2203	4300	6503	SO:0001587	stop_gained	23166	exon52			CTCCTGCAGCCGA	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"MS-1 antigen", "fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1", "common lymphatic endothelial and vascular endothelial receptor-1"	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.5484C>A	3.37:g.52554291C>A	ENSP00000312946:p.Cys1828*	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	160	17	NM_015136	0	0	0	0	0	A7E297|Q8IUH0|Q8IUH1|Q93072	Nonsense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	40	8.313466	0.98754	.	.	ENSG00000010327	ENST00000321725	.	.	.	6.07	0.741	0.18336	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.5698	0.22533	0.1187:0.5434:0.0:0.3378	.	.	.	.	X	1828	.	ENSP00000312946:C1828X	C	+	3	2	STAB1	52529331	0.999000	0.42202	0.997000	0.53966	0.055000	0.15305	0.493000	0.22451	0.463000	0.27118	-0.126000	0.14955	TGC	.		0.632	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52554291	C	A	52554291	4	1	119	1	0	0	0	0	0	1	0	0	15269	718	25	4	5690	4	STAB1	3	52554291	Nonsense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	531753	52554291	145468139	22	10328											
MYH15	22989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	108110610	108110610	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attacccagactcctaccctGgattctagtttctggatttg	8	15	7	11	0	2	1	0	0	2	1	3	3	3	3	3	2	2	1	3	2	3	6			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:108110610G>A	ENST00000273353.3	-	38	5543	c.5487C>T	c.(5485-5487)tcC>tcT	p.S1829S		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1829						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CTCCTACCCTGGATTCTAGTT	0.473																																					p.S1829S		.											.	MYH15-73	0			c.C5487T						.						183	184	183					3																	108110610		1923	4132	6055	SO:0001819	synonymous_variant	22989	exon38			TACCCTGGATTCT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5487C>T	3.37:g.108110610G>A		Somatic	207	0		WXS	Illumina HiSeq	Phase_I	213	38	NM_014981	0	0	0	0	0		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			.		0.473	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		A	108110610	G	A	108110610	2	1	119	1	0	0	0	0	0	0	0	1	10059	1335	47	2		2	MYH15	3	108110610	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	55556319	108110610	89911820	23	10329											
FAM162A	26355	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122128621	122128621	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagactttaacaagcttgaaCttagaaaagaaagctcgtct	16	10	8	7	1	1	4	0	1	1	3	2	5	1	4	0	0	4	2	0	0	7	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:122128621C>T	ENST00000477892.1	+	5	492	c.408C>T	c.(406-408)aaC>aaT	p.N136N	FAM162A_ENST00000232125.5_Silent_p.N126N	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	136					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						CAAGCTTGAACTTAGAAAAGA	0.438																																					p.N136N		.											.	FAM162A-159	0			c.C408T						.						108	98	101					3																	122128621		1886	4118	6004	SO:0001819	synonymous_variant	26355	exon5			CTTGAACTTAGAA	AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"chromosome 3 open reading frame 28"	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.408C>T	3.37:g.122128621C>T		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	126	55	NM_014367	0	0	82	151	69	Q9NRN6|Q9UJX8	Silent	SNP	ENST00000477892.1	37	CCDS43139.1	.	.	.	.	.	.	.	.	.	.	C	6.587	0.476718	0.12521	.	.	ENSG00000114023	ENST00000440333	.	.	.	5.44	3.65	0.41850	.	.	.	.	.	T	0.64080	0.2566	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64732	-0.6338	5	0.72032	D	0.01	.	8.2172	0.31519	0.0:0.8217:0.0:0.1783	.	.	.	.	F	135	.	ENSP00000405770:L135F	L	+	1	0	FAM162A	123611311	0.995000	0.38212	1.000000	0.80357	0.745000	0.42441	1.364000	0.34171	0.857000	0.35407	0.655000	0.94253	CTT	.		0.438	FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367		T	122128621	C	T	122128621	2	4	119	1	0	0	0	0	0	0	0	1	5490	564	20	2		2	FAM162A	3	122128621	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	14018011	122128621	75893809	24	10330											
PLXNA1	5361	broad.mit.edu	37	chr3	126730880	126730880	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcaccctggccgcacggaAcctgccacagccacagtcag	10	4	9	18	2	2	0	2	0	0	0	2	1	2	1	5	2	3	1	5	2	1	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:126730880A>C	ENST00000393409.2	+	9	2192	c.2192A>C	c.(2191-2193)aAc>aCc	p.N731T	PLXNA1_ENST00000251772.4_Missense_Mutation_p.N708T	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	731					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		GCCGCACGGAACCTGCCACAG	0.627																																					p.N731T													.	PLXNA1-93	0			c.A2192C						.						75	70	72					3																	126730880		2203	4300	6503	SO:0001583	missense	5361	exon9			CACGGAACCTGCC	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"Plexins"	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2192A>C	3.37:g.126730880A>C	ENSP00000377061:p.Asn731Thr	Somatic	109	13		WXS	Illumina HiSeq	Phase_I	93	14	NM_032242	0	0	9	10	1		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	A	16.79	3.221294	0.58560	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.16457	2.34;2.35	3.87	3.87	0.44632	.	0.000000	0.64402	D	0.000004	T	0.45377	0.1339	M	0.87547	2.89	0.58432	D	0.999999	D	0.89917	1.0	D	0.77557	0.99	T	0.54248	-0.8322	10	0.66056	D	0.02	.	12.8542	0.57876	1.0:0.0:0.0:0.0	.	731	Q9UIW2	PLXA1_HUMAN	T	731;708	ENSP00000377061:N731T;ENSP00000251772:N708T	ENSP00000251772:N708T	N	+	2	0	PLXNA1	128213570	1.000000	0.71417	0.996000	0.52242	0.313000	0.28021	7.309000	0.78937	1.633000	0.50488	0.402000	0.26972	AAC	.		0.627	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		C	126730880	A	C	126730880	3	2	119	1	0	0	0	0	1	0	0	0	12145	43	2	5	2226	5	PLXNA1	3	126730880	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	4602259	126730880	71291550	25	10331											
ATR	545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142238533	142238533	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtatttagatgaggttctaGtatttcccgaacatgctcag	10	14	10	7	1	2	2	1	1	1	1	3	3	3	2	1	2	2	4	1	2	5	7			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:142238533G>A	ENST00000350721.4	-	24	4481	c.4360C>T	c.(4360-4362)Cta>Tta	p.L1454L	ATR_ENST00000383101.3_Silent_p.L1390L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1454					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TGAGGTTCTAGTATTTCCCGA	0.363								Other conserved DNA damage response genes																													p.L1454L		.											.	ATR-1139	0			c.C4360T						.						118	118	118					3																	142238533		2203	4300	6503	SO:0001819	synonymous_variant	545	exon24			GTTCTAGTATTTC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4360C>T	3.37:g.142238533G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	152	32	NM_001184	0	0	5	5	0	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			.		0.363	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142238533	G	A	142238533	2	1	119	1	0	0	0	0	0	0	0	1	1205	1020	36	2		2	ATR	3	142238533	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	15507653	142238533	55783897	26	10332											
FXR1	8087	hgsc.bcm.edu	37	chr3	180693192	180693192	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctaaaaacaagaaagaaatGgtaaggagaatttaacctgt	20	8	9	4	0	0	3	0	0	0	3	0	4	0	3	1	2	2	2	1	2	9	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:180693192G>C	ENST00000357559.4	+	16	2079	c.1695G>C	c.(1693-1695)atG>atC	p.M565I	FXR1_ENST00000305586.7_Splice_Site_p.M480I|FXR1_ENST00000468861.1_Intron|FXR1_ENST00000491062.1_Intron|FXR1_ENST00000445140.2_Intron|FXR1_ENST00000480918.1_Splice_Site_p.M552I	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	565					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			AGAAAGAAATGGTAAGGAGAA	0.328																																					p.M565I		.											.	FXR1-153	0			c.G1695C						.						25	26	26					3																	180693192		2182	4290	6472	SO:0001630	splice_region_variant	8087	exon16			AGAAATGGTAAGG	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.1695+1G>C	3.37:g.180693192G>C		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_005087	0	0	2	2	0	A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	ENST00000357559.4	37	CCDS3238.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.11|12.11	1.840212|1.840212	0.32513|0.32513	.|.	.|.	ENSG00000114416|ENSG00000114416	ENST00000357559;ENST00000305586;ENST00000480918|ENST00000482125	T;T;T|.	0.26373|.	1.93;1.74;1.74|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	0.453907|.	0.26987|.	N|.	0.021492|.	T|T	0.47303|0.47303	0.1438|0.1438	N|N	0.08118|0.08118	0|0	0.58432|0.58432	D|D	0.99999|0.99999	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.001|.	T|T	0.43523|0.43523	-0.9386|-0.9386	10|5	0.14252|.	T|.	0.57|.	-25.5339|-25.5339	19.2374|19.2374	0.93866|0.93866	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	552;509;565|.	B4DXZ6;E7ERF5;P51114|.	.;.;FXR1_HUMAN|.	I|S	565;480;552|193	ENSP00000350170:M565I;ENSP00000307633:M480I;ENSP00000418097:M552I|.	ENSP00000307633:M480I|.	M|W	+|+	3|2	0|0	FXR1|FXR1	182175886|182175886	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.220000|9.220000	0.95180|0.95180	2.550000|2.550000	0.86006|0.86006	0.609000|0.609000	0.83330|0.83330	ATG|TGG	.		0.328	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5		Missense_Mutation	C	180693192	G	C	180693192	5	2	119	1	0	0	0	0	0	0	1	0	6134	1362	47	4	1757	4	FXR1	3	180693192	Splice_Site	SNP	G	TCGA-G7-7502-01A-11D-2201-08	38454659	180693192	17329238	27	10333											
N4BP2	55728	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	40122970	40122970	+	Frame_Shift_Del	DEL	A	A	-																															taaaagcacgtttgttgaagAaagtgagcttaccagtgcag																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr4:40122970delA	ENST00000261435.6	+	9	3655	c.3239delA	c.(3238-3240)gaafs	p.E1080fs		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1080					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TTTGTTGAAGAAAGTGAGCTT	0.338																																					p.E1080fs		.											.	N4BP2-602	0			c.3239delA						.						75	81	79					4																	40122970		2201	4300	6501	SO:0001589	frameshift_variant	55728	exon9			.	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.3239delA	4.37:g.40122970delA	ENSP00000261435:p.Glu1080fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	96	25	NM_018177	0	0	0	0	0	A0AVR3|Q9NVK2|Q9P2D4	Frame_Shift_Del	DEL	ENST00000261435.6	37	CCDS3457.1																																																																																			.		0.338	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		-	40122970	A	-	40122970	7	5	119	1	0	1	0	1	0	0	0	0	10135	246	9	0	3265	0	N4BP2	4	40122970	Frame_Shift_Del	DEL	A	TCGA-G7-7502-01A-11D-2201-08		40122970	151031306	28	10334											
LNX1	84708	broad.mit.edu;bcgsc.ca	37	chr4	54362298	54362298	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgtcgatatgccacaccGccatccagcacattgaagat	12	8	7	14	2	0	2	0	1	0	1	2	3	1	2	5	0	2	1	5	0	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr4:54362298G>A	ENST00000263925.7	-	6	1556	c.1242C>T	c.(1240-1242)ggC>ggT	p.G414G	LNX1-AS1_ENST00000502373.1_RNA|FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000306888.2_Silent_p.G318G	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	414	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			ATGCCACACCGCCATCCAGCA	0.502																																					p.G414G													.	LNX1-229	0			c.C1242T						.						159	135	143					4																	54362298		2203	4300	6503	SO:0001819	synonymous_variant	84708	exon6			CACACCGCCATCC	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1242C>T	4.37:g.54362298G>A		Somatic	181	1		WXS	Illumina HiSeq	Phase_I	176	7	NM_001126328	0	0	2	2	0	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Silent	SNP	ENST00000263925.7	37	CCDS47057.1																																																																																			.		0.502	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			A	54362298	G	A	54362298	2	1	119	1	0	0	0	0	0	0	0	1	8888	1074	38	1		1	LNX1	4	54362298	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	14239328	54362298	136791978	29	10335											
ANP32C	55016	broad.mit.edu	37	chr4	165118517	165118517	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggttacctcgcaattgaaaAggtctaagctcttgaggttt	10	14	10	7	1	2	2	0	2	2	0	3	2	2	2	1	3	2	4	1	3	5	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr4:165118517A>G	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GCAATTGAAAAGGTCTAAGCT	0.433																																					p.L116P													.	ANP32C-90	0			c.T347C						.						160	159	159					4																	165118517		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TTGAAAAGGTCTA	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	26077	protein-coding gene	gene with protein product		613331	"membrane-associated ring finger (C3HC4) 1"			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85703T>C	4.37:g.165118517A>G		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	209	3	NM_012403	0	0	162	162	0	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			.		0.433	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		G	165118517	A	G	165118517	1	3	119	0	1	0	0	0	0	0	0	0	707	72	3	3		3	ANP32C	4	165118517	Intron	SNP	A	TCGA-G7-7502-01A-11D-2201-08	110756219	165118517	26035759	30	10336											
SLC9A3	6550	hgsc.bcm.edu	37	chr5	475016	475016	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgtgtgtggactcggggAgggcggcggggggccgctcc	4	6	21	10	4	0	0	0	0	0	0	2	2	1	2	2	8	0	1	2	8	0	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr5:475016A>G	ENST00000264938.3	-	16	2492	c.2483T>C	c.(2482-2484)cTc>cCc	p.L828P	CTD-2228K2.5_ENST00000510604.1_5'Flank|CTD-2228K2.5_ENST00000510714.1_5'Flank|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.5_ENST00000342584.3_5'Flank|CTD-2228K2.7_ENST00000607286.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.L819P|CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	828					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			GGACTCGGGGAGGGCGGCGGG	0.721																																					p.L828P		.											.	SLC9A3-90	0			c.T2483C						.						7	9	8					5																	475016		2156	4230	6386	SO:0001583	missense	6550	exon16			TCGGGGAGGGCGG		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2483T>C	5.37:g.475016A>G	ENSP00000264938:p.Leu828Pro	Somatic	16	1		WXS	Illumina HiSeq	Phase_I	12	2	NM_004174	0	0	14	14	0	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	37	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	A	3.598	-0.082275	0.07141	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.73897	-0.79;-0.79	4.4	-5.74	0.02391	.	10.822200	0.00447	N	0.000092	T	0.54935	0.1889	N	0.14661	0.345	0.09310	N	0.999998	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.43909	-0.9362	10	0.28530	T	0.3	.	7.8835	0.29635	0.3532:0.0:0.5187:0.1281	.	819;828	E9PF67;P48764	.;SL9A3_HUMAN	P	828;819	ENSP00000264938:L828P;ENSP00000422983:L819P	ENSP00000264938:L828P	L	-	2	0	SLC9A3	528016	0.003000	0.15002	0.000000	0.03702	0.014000	0.08584	-0.110000	0.10824	-1.517000	0.01780	-1.542000	0.00909	CTC	.		0.721	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		G	475016	A	G	475016	3	3	119	1	0	0	0	0	1	0	0	0	14745	304	11	3	29	3	SLC9A3	5	475016	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		475016	180440244	31	10337											
NIPAL4	348938	hgsc.bcm.edu	37	chr5	156899851	156899851	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaacccacccccttctccCgccccggaacccactgttat	10	7	4	20	2	1	0	0	0	1	0	2	1	1	1	7	1	2	1	7	1	4	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr5:156899851C>T	ENST00000311946.7	+	6	1400	c.1284C>T	c.(1282-1284)ccC>ccT	p.P428P	ADAM19_ENST00000430702.2_Intron|NIPAL4_ENST00000435489.2_Silent_p.P409P	NM_001099287.1	NP_001092757.1	Q0D2K0	NIPA4_HUMAN	NIPA-like domain containing 4	428						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(3)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|skin(1)	22						CCCCTTCTCCCGCCCCGGAAC	0.512																																					p.P428P		.											.	NIPAL4-68	0			c.C1284T						.						40	39	40					5																	156899851		1923	4135	6058	SO:0001819	synonymous_variant	348938	exon6			TTCTCCCGCCCCG	AK026158	CCDS47328.1, CCDS54944.1	5q33.3	2009-03-24	2009-03-24		ENSG00000172548	ENSG00000172548			28018	protein-coding gene	gene with protein product	"ichthyin"	609383	"NIPA-like 4"			8619474, 9110174, 15317751	Standard	NM_001099287		Approved	ICHYN	uc003lwx.4	Q0D2K0	OTTHUMG00000163497	ENST00000311946.7:c.1284C>T	5.37:g.156899851C>T		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	59	4	NM_001099287	0	0	0	0	0	A8S6F1|A8S6F5|A8S6F8|B4DLF3|Q0D2J8|Q0D2J9	Silent	SNP	ENST00000311946.7	37	CCDS47328.1																																																																																			.		0.512	NIPAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373789.1	NM_001099287		T	156899851	C	T	156899851	2	4	119	1	0	0	0	0	0	0	0	1	10453	639	23	1		1	NIPAL4	5	156899851	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	156424835	156899851	24015409	32	10338											
EHMT2	10919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31864742	31864742	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttccttctccagcagcagcgCccccatctcagcgggggcct	5	8	10	18	2	2	0	1	0	2	0	5	0	3	0	5	2	4	2	5	2	0	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:31864742C>A	ENST00000375537.4	-	2	73	c.67G>T	c.(67-69)Gcg>Tcg	p.A23S	C2_ENST00000469372.1_5'Flank|EHMT2_ENST00000395728.3_Missense_Mutation_p.A80S|EHMT2_ENST00000480912.1_5'Flank|EHMT2_ENST00000375528.4_Missense_Mutation_p.A80S|EHMT2_ENST00000375530.4_Missense_Mutation_p.A23S	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	23					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						AGCAGCAGCGCCCCCATCTCA	0.637																																					p.A23S		.											.	EHMT2-91	0			c.G67T						.						129	130	130					6																	31864742		1511	2709	4220	SO:0001583	missense	10919	exon2			GCAGCGCCCCCAT	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases", "Ankyrin repeat domain containing"	14129	protein-coding gene	gene with protein product		604599	"chromosome 6 open reading frame 30", "HLA-B associated transcript 8"	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.67G>T	6.37:g.31864742C>A	ENSP00000364687:p.Ala23Ser	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	137	37	NM_025256	0	0	7	10	3	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673198	0.29693	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537	T;T;T;T	0.76968	-0.73;-1.06;-0.98;-0.68	3.79	1.93	0.25924	.	0.364320	0.20081	N	0.099658	T	0.38957	0.1060	N	0.08118	0	0.22531	N	0.999013	B;P;B;B	0.50819	0.03;0.939;0.05;0.03	B;B;B;B	0.43867	0.017;0.434;0.025;0.002	T	0.32798	-0.9893	10	0.51188	T	0.08	.	5.6198	0.17451	0.0:0.7389:0.0:0.261	.	80;23;23;23	A2ABF8;Q96KQ7-3;Q96KQ7-2;Q96KQ7	.;.;.;EHMT2_HUMAN	S	80;80;23;23	ENSP00000379078:A80S;ENSP00000364678:A80S;ENSP00000364680:A23S;ENSP00000364687:A23S	ENSP00000364678:A80S	A	-	1	0	EHMT2	31972721	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	1.196000	0.32198	0.735000	0.32537	-0.361000	0.07541	GCG	.		0.637	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		A	31864742	C	A	31864742	3	1	119	1	0	0	0	0	1	0	0	0	4995	739	26	4	3673	4	EHMT2	6	31864742	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08		31864742	139250325	33	10339											
BRD2	6046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32945266	32945266	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcacaggagtttgctgcTgatgtacggcttatgttctc	7	14	12	8	1	1	1	0	1	1	0	2	3	1	2	0	2	4	7	0	2	2	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:32945266T>C	ENST00000374825.4	+	8	2949	c.1248T>C	c.(1246-1248)gcT>gcC	p.A416A	BRD2_ENST00000395289.2_Silent_p.A416A|BRD2_ENST00000443797.2_Silent_p.A296A|BRD2_ENST00000395287.1_Silent_p.A416A|BRD2_ENST00000449085.2_Silent_p.A369A|BRD2_ENST00000374831.4_Silent_p.A416A	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	416	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						AGTTTGCTGCTGATGTACGGC	0.517																																					p.A416A		.											.	BRD2-398	0			c.T1248C						.						279	225	244					6																	32945266		1511	2708	4219	SO:0001819	synonymous_variant	6046	exon8			TGCTGCTGATGTA	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"bromodomain-containing 2"			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1248T>C	6.37:g.32945266T>C		Somatic	228	0		WXS	Illumina HiSeq	Phase_I	158	41	NM_005104	0	0	49	69	20	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	T	9.651	1.141473	0.21205	.	.	ENSG00000204256	ENST00000449025	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	T	0.55337	0.1914	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56360	-0.7992	4	.	.	.	-14.7189	13.1555	0.59514	0.0:0.0:0.0:1.0	.	.	.	.	P	422	.	.	L	+	2	0	BRD2	33053244	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.370000	0.20433	2.205000	0.71048	0.523000	0.50628	CTG	.		0.517	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			C	32945266	T	C	32945266	2	2	119	1	0	0	0	0	0	0	0	1	1505	1567	55	3		3	BRD2	6	32945266	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08	1080524	32945266	138169801	34	10340											
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	38913344	38913344	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctgagtaaacttccacaaTttgcagaaattatgaaccag	16	10	7	8	0	0	3	0	2	0	1	1	3	1	3	2	0	4	3	2	0	6	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:38913344T>C	ENST00000359357.3	+	78	11712	c.11458T>C	c.(11458-11460)Ttt>Ctt	p.F3820L	DNAH8_ENST00000449981.2_Missense_Mutation_p.F4037L|RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000441566.1_Missense_Mutation_p.F3784L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3820					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACTTCCACAATTTGCAGAAAT	0.488																																					p.F4037L		.											.	DNAH8-615	0			c.T12109C						.						96	95	96					6																	38913344		2203	4300	6503	SO:0001583	missense	1769	exon80			CCACAATTTGCAG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11458T>C	6.37:g.38913344T>C	ENSP00000352312:p.Phe3820Leu	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	114	35	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	T	26.7	4.762200	0.89932	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.10382	2.88;2.88;2.88	5.59	5.59	0.84812	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.30634	0.0771	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.20706	-1.0267	10	0.62326	D	0.03	.	15.7453	0.77936	0.0:0.0:0.0:1.0	.	3784;3820	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	L	4025;4025;3820;3784	ENSP00000333363:F4025L;ENSP00000352312:F3820L;ENSP00000402294:F3784L	ENSP00000333363:F4025L	F	+	1	0	DNAH8	39021322	1.000000	0.71417	0.981000	0.43875	0.962000	0.63368	7.948000	0.87774	2.129000	0.65627	0.459000	0.35465	TTT	.		0.488	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38913344	T	C	38913344	3	2	119	1	0	0	0	0	1	0	0	0	4618	1493	52	3	11760	3	DNAH8	6	38913344	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	5968078	38913344	132201723	35	10341											
MRPL2	51069	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43023807	43023820	+	Splice_Site	DEL	GCCATCTCTCACCT	GCCATCTCTCACCT	-																															tccagcccacacatctggtaGccatctctcacctgccattc																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	GCCATCTCTCACCT	GCCATCTCTCACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:43023807_43023820delGCCATCTCTCACCT	ENST00000388752.3	-	4	943_945	c.519_521delAGGTGAGAGATGGC	c.(517-522)gcaggt>gct	p.G174fs	MRPL2_ENST00000489623.1_Intron|CUL7_ENST00000265348.3_5'Flank|CUL7_ENST00000535468.1_5'Flank|MRPL2_ENST00000230413.5_Splice_Site_p.G174fs	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	174					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		ACATCTGGTAGCCATCTCTCACCTGCCATTCGGC	0.533																																					p.173_174del		.											.	MRPL2-90	0			c.519_520del						.																																			SO:0001630	splice_region_variant	51069	exon4			.	AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"Mitochondrial ribosomal proteins / large subunits"	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.520+1AGGTGAGAGATGGC>-	6.37:g.43023807_43023820delGCCATCTCTCACCT		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	45	11	NM_015950	0	0	0	0	0	B2RC56|Q8WUL1|Q96Q56|Q9Y311	Frame_Shift_Del	DEL	ENST00000388752.3	37	CCDS34454.1																																																																																			.		0.533	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2		Frame_Shift_Del	-	43023820	GCCATCTCTCACCT	-	43023807	8	5	119	1	0	1	0	1	0	0	1	0	9810	986	34	0		0	MRPL2	6	43023807	Splice_Site	DEL	GCCATCTCTCACCT	TCGA-G7-7502-01A-11D-2201-08	4110463	43023807	128091260	36	10342											
SLC35B2	347734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	44224125	44224125	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttcagggcctgccacatcGgggtggtctctgccgcctct	3	10	13	15	2	3	0	1	0	2	0	5	0	3	0	4	4	2	1	4	4	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:44224125G>C	ENST00000393812.3	-	3	457	c.314C>G	c.(313-315)cCg>cGg	p.P105R	SLC35B2_ENST00000537814.1_Intron|SLC35B2_ENST00000393810.1_Intron|SLC35B2_ENST00000495706.1_5'UTR|SLC35B2_ENST00000538577.1_Intron|MIR4647_ENST00000583964.1_RNA	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	105					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTGCCACATCGGGGTGGTCTC	0.627																																					p.P105R		.											.	SLC35B2-91	0			c.C314G						.						58	67	64					6																	44224125		2203	4300	6503	SO:0001583	missense	347734	exon3			CACATCGGGGTGG	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"Solute carriers"	16872	protein-coding gene	gene with protein product		610788	"solute carrier family 35, member B2"				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.314C>G	6.37:g.44224125G>C	ENSP00000377401:p.Pro105Arg	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	98	30	NM_178148	0	0	47	100	53	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Missense_Mutation	SNP	ENST00000393812.3	37	CCDS34462.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.752871	0.31046	.	.	ENSG00000157593	ENST00000393812;ENST00000341553	T	0.30714	1.52	4.26	3.35	0.38373	.	0.419213	0.26176	N	0.025884	T	0.08935	0.0221	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.06826	-1.0805	10	0.22109	T	0.4	-29.8524	15.4721	0.75446	0.0:0.1512:0.8488:0.0	.	105	Q8TB61	S35B2_HUMAN	R	105	ENSP00000377401:P105R	ENSP00000342455:P105R	P	-	2	0	SLC35B2	44332103	1.000000	0.71417	0.889000	0.34880	0.859000	0.49053	7.270000	0.78493	2.191000	0.70037	0.561000	0.74099	CCG	.		0.627	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			C	44224125	G	C	44224125	3	2	119	1	0	0	0	0	1	0	0	0	14608	1116	39	4	992	4	SLC35B2	6	44224125	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	1200318	44224125	126890942	37	10343											
MOXD1	26002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	132694134	132694134	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagatcactctcacagtgctAtcctggggatcagacatggg	10	9	11	11	0	3	2	3	0	1	2	5	3	4	3	1	3	1	1	1	3	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:132694134A>C	ENST00000367963.3	-	3	532	c.414T>G	c.(412-414)gaT>gaG	p.D138E	MOXD1_ENST00000336749.3_Missense_Mutation_p.D70E	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	138	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		TCACAGTGCTATCCTGGGGAT	0.458																																					p.D138E		.											.	MOXD1-515	0			c.T414G						.						100	89	92					6																	132694134		2203	4300	6503	SO:0001583	missense	26002	exon3			AGTGCTATCCTGG	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.414T>G	6.37:g.132694134A>C	ENSP00000356940:p.Asp138Glu	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	103	31	NM_015529	0	0	0	0	0	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	A	4.845	0.157121	0.09236	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.77750	-1.12;-1.12	5.3	0.0261	0.14148	DOMON domain (3);	0.440036	0.24074	N	0.041793	T	0.17195	0.0413	N	0.02129	-0.67	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.37842	-0.9688	10	0.02654	T	1	-26.2778	1.3667	0.02202	0.1886:0.3795:0.1103:0.3217	.	138;70	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	E	138;70	ENSP00000356940:D138E;ENSP00000336998:D70E	ENSP00000336998:D70E	D	-	3	2	MOXD1	132735827	0.665000	0.27466	0.999000	0.59377	0.974000	0.67602	-0.336000	0.07863	0.084000	0.17077	0.528000	0.53228	GAT	.		0.458	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		C	132694134	A	C	132694134	3	2	119	1	0	0	0	0	1	0	0	0	9745	446	16	5	1467	5	MOXD1	6	132694134	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	88470009	132694134	38420933	38	10344											
TXLNB	167838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	139563747	139563747	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggcagctcctctgctgcTgctcgtgggggctgcctact	3	11	13	14	1	1	0	0	0	1	0	3	0	2	0	2	3	6	6	2	3	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:139563747T>C	ENST00000358430.3	-	10	2203	c.1971A>G	c.(1969-1971)gcA>gcG	p.A657A	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	657						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		CCTCTGCTGCTGCTCGTGGGG	0.642																																					p.A657A		.											.	TXLNB-91	0			c.A1971G						.						47	53	51					6																	139563747		2203	4300	6503	SO:0001819	synonymous_variant	167838	exon10			TGCTGCTGCTCGT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1971A>G	6.37:g.139563747T>C		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	131	42	NM_153235	0	0	0	0	0	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	37	CCDS34545.1																																																																																			.		0.642	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		C	139563747	T	C	139563747	2	2	119	1	0	0	0	0	0	0	0	1	16821	1567	55	3		3	TXLNB	6	139563747	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08	6869613	139563747	31551320	39	10345											
PHF10	55274	ucsc.edu	37	chr6	170117955	170117955	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagtaatgacatttagctCtctcaggtagagtttctcct	9	16	7	9	0	4	2	2	1	2	1	6	2	4	2	1	1	1	4	1	1	3	6			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:170117955C>A	ENST00000339209.4	-	4	496	c.373G>T	c.(373-375)Gag>Tag	p.E125*	PHF10_ENST00000366780.4_Nonsense_Mutation_p.E123*|PHF10_ENST00000464779.1_5'UTR	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	125	Essential to induce neural progenitor proliferation. {ECO:0000250}.|SAY.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		ACATTTAGCTCTCTCAGGTAG	0.333																																					p.E125X													.	PHF10-226	0			c.G373T						.						48	44	45					6																	170117955		2202	4299	6501	SO:0001587	stop_gained	55274	exon4			TTAGCTCTCTCAG	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"Zinc fingers, PHD-type"	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.373G>T	6.37:g.170117955C>A	ENSP00000341805:p.Glu125*	Somatic	52	0		WXS	Illumina HiSeq		42	4	NM_018288	0	0	36	36	0	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Nonsense_Mutation	SNP	ENST00000339209.4	37	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	C	32	5.117991	0.94385	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-31.5125	19.3504	0.94381	0.0:1.0:0.0:0.0	.	.	.	.	X	123;125	.	ENSP00000341805:E125X	E	-	1	0	PHF10	169859880	1.000000	0.71417	0.967000	0.41034	0.871000	0.50021	7.211000	0.77933	2.885000	0.99019	0.655000	0.94253	GAG	.		0.333	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		A	170117955	C	A	170117955	4	1	119	1	0	0	0	0	0	1	0	0	11847	922	32	4	1159	4	PHF10	6	170117955	Nonsense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	30554208	170117955	997112	40	10346											
TWISTNB	221830	ucsc.edu	37	chr7	19738032	19738032	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttttcttttcttttttttCtttttatggtcactttggta	3	28	5	5	0	4	0	1	0	3	0	4	0	4	0	0	2	0	2	0	2	2	13			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr7:19738032C>T	ENST00000222567.5	-	4	994	c.924G>A	c.(922-924)aaG>aaA	p.K308K		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	308	Lys-rich.				transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						TCTTTTTTTTCTTTTTATGGT	0.378																																					p.K308K													.	TWISTNB-91	0			c.G924A						.						113	126	122					7																	19738032		2200	4298	6498	SO:0001819	synonymous_variant	221830	exon4			TTTTTTCTTTTTA	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.924G>A	7.37:g.19738032C>T		Somatic	241	3		WXS	Illumina HiSeq		304	1	NM_001002926	0	0	29	33	4	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																			.		0.378	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			T	19738032	C	T	19738032	2	4	119	1	0	0	0	0	0	0	0	1	16817	912	32	2		2	TWISTNB	7	19738032	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08		19738032	139400631	41	10347											
HOXA10	3206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	27211695	27211695	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atattgaacagaaactccttCtccagctccagtgtctggtg	10	12	8	11	0	2	2	0	1	2	1	5	2	4	2	3	1	3	1	3	1	3	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr7:27211695C>T	ENST00000283921.4	-	2	1055	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E	HOXA-AS4_ENST00000519694.1_RNA|RP1-170O19.20_ENST00000470747.4_Intron|HOXA-AS4_ENST00000519935.1_RNA|HOXA10_ENST00000396344.4_Silent_p.E36E|HOXA10_ENST00000521421.1_5'UTR|MIR196B_ENST00000384852.1_RNA|HOXA-AS4_ENST00000523790.1_RNA|RP1-170O19.20_ENST00000465941.1_Intron|HOXA9_ENST00000497089.1_5'Flank	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	352					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						GAAACTCCTTCTCCAGCTCCA	0.532																																					p.E352E		.											.	HOXA10-68	0			c.G1056A						.						111	105	107					7																	27211695		2203	4300	6503	SO:0001819	synonymous_variant	3206	exon2			CTCCTTCTCCAGC		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"Homeoboxes / ANTP class : HOXL subclass"	5100	protein-coding gene	gene with protein product		142957	"homeo box A10"	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1056G>A	7.37:g.27211695C>T		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	182	80	NM_018951	0	0	17	52	35	O43370|O43605|Q15949|Q504T1	Silent	SNP	ENST00000283921.4	37	CCDS5410.2																																																																																			.		0.532	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2			T	27211695	C	T	27211695	2	4	119	1	0	0	0	0	0	0	0	1	7310	912	32	2		2	HOXA10	7	27211695	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	7473663	27211695	131926968	42	10348											
PON2	5445	broad.mit.edu	37	chr7	95035516	95035516	+	Frame_Shift_Del	DEL	G	G	-																															cccagatgtcccccgaggaaGgatcaatagataaattatcc																								rs77619496		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr7:95035516delG	ENST00000222572.3	-	8	1067	c.821delC	c.(820-822)cctfs	p.P274fs	PON2_ENST00000536183.1_Frame_Shift_Del_p.P295fs|PON2_ENST00000483292.1_5'UTR|PON2_ENST00000433091.2_Frame_Shift_Del_p.P262fs			Q15165	PON2_HUMAN	paraoxonase 2	274					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			CCCCGAGGAAGGATCAATAGA	0.398																																					p.P274fs	GBM(42;803 823 13649 23368 31463)												.	PON2-90	0			c.821delC						.						128	128	128					7																	95035516		2203	4300	6503	SO:0001589	frameshift_variant	5445	exon8			GAGGAAGGATCAA	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"Paraoxonases"	9205	protein-coding gene	gene with protein product	"paraoxonase nirs", "arylesterase 2"	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.821delC	7.37:g.95035516delG	ENSP00000222572:p.Pro274fs	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	246	13	NM_000305	0	0	0	0	0	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Frame_Shift_Del	DEL	ENST00000222572.3	37	CCDS5640.1																																																																																			.		0.398	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		-	95035516	G	-	95035516	7	5	119	1	0	1	0	1	0	0	0	0	12275	1000	35	0	251	0	PON2	7	95035516	Frame_Shift_Del	DEL	G	TCGA-G7-7502-01A-11D-2201-08	67823821	95035516	64103147	43	10349											
NRG1	3084	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	32463201	32463201	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaccatcgtggaatcaaacGgtaagagatacctacggtat	14	9	9	9	3	2	1	2	0	0	1	3	3	2	2	2	3	3	2	2	3	6	4	rs78513616		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr8:32463201G>A	ENST00000405005.3	+	3	400	c.400G>A	c.(400-402)Gag>Aag	p.E134K	NRG1_ENST00000520407.1_Splice_Site_p.A349T|NRG1_ENST00000523079.1_Splice_Site_p.E134K|NRG1_ENST00000521670.1_Splice_Site_p.E134K|NRG1_ENST00000356819.4_Splice_Site_p.E134K|NRG1_ENST00000287845.5_Splice_Site_p.A134T|NRG1_ENST00000287842.3_Splice_Site_p.E134K|NRG1_ENST00000341377.5_Splice_Site_p.E134K|NRG1_ENST00000519301.1_Splice_Site_p.A113T|NRG1_ENST00000338921.4_Splice_Site_p.E134K			Q02297	NRG1_HUMAN	neuregulin 1	134					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		GGAATCAAACGGTAAGAGATA	0.398																																					p.A349T		.											.	NRG1-525	0			c.G1045A						.	G	LYS/GLU,LYS/GLU,THR/ALA,LYS/GLU,LYS/GLU,THR/ALA,THR/ALA,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,THR/ALA,LYS/GLU	0,4406		0,0,2203	143	129	134		337,337,337,400,400,400,400,400,400,400,400,400,400,1045,400	5	1	8	dbSNP_131	134	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	NRG1	NM_001159995.1,NM_001159999.1,NM_001160001.1,NM_001160002.1,NM_001160004.1,NM_001160005.1,NM_001160007.1,NM_001160008.1,NM_004495.3,NM_013956.3,NM_013957.3,NM_013958.3,NM_013960.3,NM_013962.2,NM_013964.3	56,56,58,56,56,58,58,56,56,56,56,56,56,58,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	113/608,113/625,113/591,134/195,134/460,134/208,134/178,134/421,134/212,134/646,134/638,134/242,134/463,349/423,134/641	32463201	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	3084	exon3			TCAAACGGTAAGA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.400+1G>A	8.37:g.32463201G>A		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	123	21	NM_013962	0	0	0	0	0	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.01|13.01	2.108806|2.108806	0.37242|0.37242	0.0|0.0	1.16E-4|1.16E-4	ENSG00000157168|ENSG00000157168	ENST00000519301;ENST00000520407;ENST00000287845|ENST00000518104;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000341377;ENST00000287842;ENST00000405005;ENST00000521670	T;T;T|T;T;T;T;T;T;T;T;T;T	0.75260|0.39997	-0.92;-0.83;-0.49|1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05	5.03|5.03	5.03|5.03	0.67393|0.67393	.|Immunoglobulin-like fold (1);	.|0.695834	.|0.14318	.|N	.|0.327222	T|T	0.54013|0.54013	0.1832|0.1832	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	B;B;B|P;P;P;P;D;P;P;P;P;D	0.32071|0.59767	0.355;0.11;0.22|0.76;0.776;0.614;0.76;0.986;0.733;0.589;0.857;0.863;0.964	B;B;B|B;B;B;B;D;B;B;B;B;P	0.23852|0.68192	0.049;0.01;0.016|0.038;0.079;0.053;0.038;0.956;0.077;0.054;0.165;0.115;0.454	T|T	0.38478|0.38478	-0.9659|-0.9659	9|10	0.02654|0.24483	T|T	1|0.36	-3.1604|-3.1604	16.914|16.914	0.86147|0.86147	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	134;133;349|134;134;133;134;134;134;134;134;134;134	F8W9E3;B0FWZ3;Q02297-9|E9PHH4;Q7RTW4;B0FYA9;B7Z4Z3;Q02297-4;Q02297-7;Q02297;Q02297-6;Q02297-3;Q02297-8	.;.;.|.;.;.;.;.;.;NRG1_HUMAN;.;.;.	T|K	113;349;134|113;202;134;134;134;134;134;134;134;134	ENSP00000429582:A113T;ENSP00000434640:A349T;ENSP00000287845:A134T|ENSP00000430053:E113K;ENSP00000429067:E202K;ENSP00000430120:E134K;ENSP00000343395:E134K;ENSP00000349275:E134K;ENSP00000287840:E134K;ENSP00000340497:E134K;ENSP00000287842:E134K;ENSP00000384620:E134K;ENSP00000428828:E134K	ENSP00000287845:A134T|ENSP00000287840:E134K	A|E	+|+	1|1	0|0	NRG1|NRG1	32582743|32582743	1.000000|1.000000	0.71417|0.71417	0.953000|0.953000	0.39169|0.39169	0.154000|0.154000	0.21943|0.21943	6.210000|6.210000	0.72176|0.72176	2.485000|2.485000	0.83878|0.83878	0.650000|0.650000	0.86243|0.86243	GCT|GAG	G|1.000;A|0.000		0.398	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		Missense_Mutation	A	32463201	G	A	32463201	5	1	119	1	0	0	0	0	0	0	1	0	10673	1130	39	1	1161	1	NRG1	8	32463201	Splice_Site	SNP	G	TCGA-G7-7502-01A-11D-2201-08		32463201	113900821	44	10350											
GPR124	25960	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	37692907	37692907	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aatgtttctctgtcgtccttCcacatcaaggtgggcgctgg	6	13	11	11	2	2	0	1	0	1	0	6	0	4	0	2	3	0	2	2	3	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr8:37692907C>G	ENST00000412232.2	+	12	1837	c.1824C>G	c.(1822-1824)ttC>ttG	p.F608L	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	608					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			TGTCGTCCTTCCACATCAAGG	0.682																																					p.F608L		.											.	GPR124-157	0			c.C1824G						.						19	23	22					8																	37692907		2201	4298	6499	SO:0001583	missense	25960	exon12			GTCCTTCCACATC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"-", "GPCR / Class B : Orphans", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17849	protein-coding gene	gene with protein product	"tumor endothelial marker 5"	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1824C>G	8.37:g.37692907C>G	ENSP00000406367:p.Phe608Leu	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	29	11	NM_032777	0	0	0	0	0	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	7.845	0.722846	0.15439	.	.	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.53857	0.6	5.29	1.44	0.22558	.	0.251562	0.38778	N	0.001564	T	0.36963	0.0986	N	0.17474	0.49	0.47698	D	0.999493	D	0.62365	0.991	P	0.51266	0.664	T	0.25745	-1.0123	10	0.06625	T	0.88	-18.4995	9.5253	0.39160	0.0:0.7051:0.0:0.2949	.	608	Q96PE1	GP124_HUMAN	L	601;608	ENSP00000406367:F608L	ENSP00000406367:F608L	F	+	3	2	GPR124	37812065	1.000000	0.71417	0.905000	0.35620	0.440000	0.31957	1.327000	0.33746	0.231000	0.21079	-0.140000	0.14226	TTC	.		0.682	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			G	37692907	C	G	37692907	3	3	119	1	0	0	0	0	1	0	0	0	6658	854	30	4	1849	4	GPR124	8	37692907	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	5229706	37692907	108671115	45	10351											
GAPVD1	26130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	128121733	128121733	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atatccagagattgtctaaaGtagtgactgcaaatcacaga	16	10	8	7	0	2	3	1	1	1	2	3	4	3	3	1	0	1	2	1	0	5	4	rs374403416		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr9:128121733G>A	ENST00000495955.1	+	26	4350	c.4060G>A	c.(4060-4062)Gta>Ata	p.V1354I	GAPVD1_ENST00000394104.2_Missense_Mutation_p.V1354I|GAPVD1_ENST00000265956.4_Missense_Mutation_p.V1328I|GAPVD1_ENST00000394105.2_Missense_Mutation_p.V1363I|GAPVD1_ENST00000394083.2_Missense_Mutation_p.V1288I|GAPVD1_ENST00000297933.6_Missense_Mutation_p.V1336I|GAPVD1_ENST00000470056.1_Missense_Mutation_p.V1309I|GAPVD1_ENST00000312123.9_Missense_Mutation_p.V1315I			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1354	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						ATTGTCTAAAGTAGTGACTGC	0.358																																					p.V1363I		.											.	GAPVD1-93	0			c.G4087A						.	G	ILE/VAL	0,4406		0,0,2203	140	141	141		4087	6.2	1	9		141	1,8599	1.2+/-3.3	0,1,4299	no	missense	GAPVD1	NM_015635.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	1363/1488	128121733	1,13005	2203	4300	6503	SO:0001583	missense	26130	exon25			TCTAAAGTAGTGA		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.4060G>A	9.37:g.128121733G>A	ENSP00000419063:p.Val1354Ile	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	158	35	NM_015635	0	0	17	26	9	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	G	26.2	4.716877	0.89205	0.0	1.16E-4	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123;ENST00000438537	T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	6.17	6.17	0.99709	Vacuolar sorting protein 9 (1);	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.30870	0.118;0.23;0.298;0.298;0.298;0.188	B;B;B;B;B;B	0.42692	0.113;0.082;0.225;0.395;0.225;0.277	T	0.05194	-1.0900	10	0.25106	T	0.35	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	1354;369;1309;1315;1336;1363	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	I	1309;1363;1354;1328;1288;1354;1336;1315;47	ENSP00000419767:V1309I;ENSP00000377665:V1363I;ENSP00000377664:V1354I;ENSP00000265956:V1328I;ENSP00000377645:V1288I;ENSP00000419063:V1354I;ENSP00000297933:V1336I;ENSP00000309582:V1315I	ENSP00000265956:V1328I	V	+	1	0	GAPVD1	127161554	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GTA	.		0.358	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128121733	G	A	128121733	3	1	119	1	0	0	0	0	1	0	0	0	6259	1029	36	2	4181	2	GAPVD1	9	128121733	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		128121733	13091698	46	10352											
OLAH	55301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	15107661	15107661	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attaccttatggaatttggaGgcacccccaagcattttgct	10	13	8	10	0	0	0	0	0	0	0	0	2	0	2	3	3	3	3	3	3	4	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr10:15107661G>A	ENST00000378228.3	+	6	735	c.481G>A	c.(481-483)Ggc>Agc	p.G161S	OLAH_ENST00000485251.1_3'UTR|OLAH_ENST00000378217.3_Missense_Mutation_p.G214S	NM_001039702.2	NP_001034791.1	Q9NV23	SAST_HUMAN	oleoyl-ACP hydrolase	161					fatty acid biosynthetic process (GO:0006633)		myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)			endometrium(2)|large_intestine(1)|lung(14)|stomach(1)	18						GGAATTTGGAGGCACCCCCAA	0.408																																					p.G214S		.											.	OLAH-68	0			c.G640A						.						83	77	79					10																	15107661		2203	4300	6503	SO:0001583	missense	55301	exon7			TTTGGAGGCACCC	AK001844	CCDS7106.1, CCDS31152.1	10p13	2010-11-23	2006-07-07	2006-07-07	ENSG00000152463	ENSG00000152463	3.1.2.14		25625	protein-coding gene	gene with protein product			"thioesterase domain containing 1"	THEDC1			Standard	NM_018324		Approved	FLJ11106, SAST	uc001inu.2	Q9NV23	OTTHUMG00000017724	ENST00000378228.3:c.481G>A	10.37:g.15107661G>A	ENSP00000367473:p.Gly161Ser	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	62	17	NM_018324	0	0	0	0	0	Q5VUB6|Q9NUW1	Missense_Mutation	SNP	ENST00000378228.3	37	CCDS31152.1	.	.	.	.	.	.	.	.	.	.	g	16.13	3.036095	0.54896	.	.	ENSG00000152463	ENST00000429028;ENST00000378228;ENST00000378217	.	.	.	5.03	4.12	0.48240	Thioesterase (1);	0.096919	0.64402	D	0.000001	D	0.84552	0.5497	M	0.92122	3.275	0.52099	D	0.999948	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.99	D	0.87441	0.2395	9	0.72032	D	0.01	-5.4247	12.2837	0.54779	0.0:0.0:0.8303:0.1697	.	161;214	Q9NV23;Q9NV23-2	SAST_HUMAN;.	S	161;161;214	.	ENSP00000367462:G214S	G	+	1	0	OLAH	15147667	1.000000	0.71417	0.972000	0.41901	0.162000	0.22319	1.630000	0.37081	1.222000	0.43521	0.557000	0.71058	GGC	.		0.408	OLAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046964.1	NM_018324		A	15107661	G	A	15107661	3	1	119	1	0	0	0	0	1	0	0	0	10877	1000	35	2	662	2	OLAH	10	15107661	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		15107661	120427086	47	10353											
SLC5A12	159963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	26725363	26725363	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatatgtagtcgagatccAtttgttgattgctctaatac	12	16	7	6	1	1	2	0	1	1	1	3	3	2	2	1	0	2	3	1	0	6	8			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:26725363A>C	ENST00000396005.3	-	5	966	c.657T>G	c.(655-657)aaT>aaG	p.N219K	SLC5A12_ENST00000280467.6_Missense_Mutation_p.N219K	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	219					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GTCGAGATCCATTTGTTGATT	0.368																																					p.N219K		.											.	SLC5A12-92	0			c.T657G						.						230	218	222					11																	26725363		2203	4299	6502	SO:0001583	missense	159963	exon5			AGATCCATTTGTT	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"Solute carriers"	28750	protein-coding gene	gene with protein product		612455	"solute carrier family 5 (sodium/glucose cotransporter), member 12"			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.657T>G	11.37:g.26725363A>C	ENSP00000379326:p.Asn219Lys	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	172	56	NM_178498	0	0	0	0	0	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	7.436	0.639686	0.14386	.	.	ENSG00000148942	ENST00000396005;ENST00000280467;ENST00000533617	D;D;D	0.87256	-2.23;-2.23;-2.23	5.07	3.9	0.45041	.	0.177263	0.47852	D	0.000209	T	0.81283	0.4790	L	0.48174	1.505	0.34755	D	0.732193	B;B	0.32467	0.055;0.372	B;B	0.36030	0.037;0.216	T	0.78191	-0.2300	10	0.22109	T	0.4	.	7.1583	0.25649	0.7866:0.0:0.0757:0.1378	.	219;219	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	K	219;219;31	ENSP00000379326:N219K;ENSP00000280467:N219K;ENSP00000435053:N31K	ENSP00000280467:N219K	N	-	3	2	SLC5A12	26681939	1.000000	0.71417	0.997000	0.53966	0.669000	0.39330	1.028000	0.30128	0.834000	0.34852	0.397000	0.26171	AAT	.		0.368	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26725363	A	C	26725363	3	2	119	1	0	0	0	0	1	0	0	0	14696	214	8	5	1243	5	SLC5A12	11	26725363	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		26725363	108281153	48	10354											
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	62293750	62293750	+	Frame_Shift_Del	DEL	G	G	-																															ttgggtcctttcaggtttaaGtcaatatcaggcatggagat																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:62293750delG	ENST00000378024.4	-	5	8413	c.8139delC	c.(8137-8139)gacfs	p.D2713fs	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2713					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCAGGTTTAAGTCAATATCAG	0.463																																					p.D2713fs		.											.	AHNAK-109	0			c.8139delC						.						195	192	193					11																	62293750		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.8139delC	11.37:g.62293750delG	ENSP00000367263:p.Asp2713fs	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	260	83	NM_001620	0	0	0	0	0	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	37	CCDS31584.1																																																																																			.		0.463	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62293750	G	-	62293750	7	5	119	1	0	1	0	1	0	0	0	0	414	1020	36	0	9653	0	AHNAK	11	62293750	Frame_Shift_Del	DEL	G	TCGA-G7-7502-01A-11D-2201-08	35568387	62293750	72712766	49	10355											
LRFN4	78999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66625625	66625625	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctgggccgcatcgcgcCgggagccttcgacgacttcc	5	6	13	17	6	0	0	0	0	0	0	3	3	1	1	5	2	2	2	5	2	0	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:66625625C>T	ENST00000309602.4	+	1	653	c.410C>T	c.(409-411)cCg>cTg	p.P137L	PC_ENST00000393958.2_Intron|PC_ENST00000393960.1_Intron|PC_ENST00000393955.2_Intron|LRFN4_ENST00000393952.3_Missense_Mutation_p.P137L	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	137						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CGCATCGCGCCGGGAGCCTTC	0.692																																					p.P137L		.											.	LRFN4-90	0			c.C410T						.						49	54	52					11																	66625625		2200	4294	6494	SO:0001583	missense	78999	exon1			TCGCGCCGGGAGC	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.410C>T	11.37:g.66625625C>T	ENSP00000312535:p.Pro137Leu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	66	18	NM_024036	0	0	1	1	0	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Missense_Mutation	SNP	ENST00000309602.4	37	CCDS8153.1	.	.	.	.	.	.	.	.	.	.	C	6.081	0.383217	0.11524	.	.	ENSG00000173621	ENST00000393952;ENST00000309602;ENST00000525479	T;T	0.60424	0.19;0.19	4.18	3.26	0.37387	.	0.304296	0.23951	N	0.042954	T	0.51227	0.1662	M	0.69358	2.11	0.24168	N	0.99564	P;B	0.34662	0.462;0.1	B;B	0.29862	0.105;0.108	T	0.50980	-0.8763	10	0.56958	D	0.05	.	9.9013	0.41348	0.0:0.8973:0.0:0.1027	.	137;137	E9PLQ1;Q6PJG9	.;LRFN4_HUMAN	L	137	ENSP00000377524:P137L;ENSP00000312535:P137L	ENSP00000312535:P137L	P	+	2	0	LRFN4	66382201	0.000000	0.05858	0.111000	0.21465	0.012000	0.07955	0.687000	0.25407	1.107000	0.41642	0.313000	0.20887	CCG	.		0.692	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		T	66625625	C	T	66625625	3	4	119	1	0	0	0	0	1	0	0	0	8965	652	23	1	412	1	LRFN4	11	66625625	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	4331875	66625625	68380891	50	10356											
LRP5	4041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	68205929	68205929	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcagaaatcaccaagccgcCctcagacgacagcccggccc	11	2	10	18	3	2	2	2	0	0	2	2	3	2	2	5	2	2	1	5	2	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:68205929C>T	ENST00000294304.7	+	20	4233	c.4127C>T	c.(4126-4128)cCc>cTc	p.P1376L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1376					adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ACCAAGCCGCCCTCAGACGAC	0.592																																					p.P1376L		.											.	LRP5-661	0			c.C4127T						.						95	98	97					11																	68205929		2200	4294	6494	SO:0001583	missense	4041	exon20			AGCCGCCCTCAGA	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.4127C>T	11.37:g.68205929C>T	ENSP00000294304:p.Pro1376Leu	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	90	22	NM_002335	0	0	40	67	27	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065810	0.36470	.	.	ENSG00000162337	ENST00000294304	D	0.94000	-3.33	4.53	4.53	0.55603	.	0.139825	0.31495	U	0.007555	D	0.90889	0.7137	L	0.45137	1.4	0.43787	D	0.996329	B;B	0.24092	0.097;0.097	B;B	0.26094	0.066;0.066	D	0.88780	0.3270	10	0.49607	T	0.09	.	17.5404	0.87845	0.0:1.0:0.0:0.0	.	1376;1376	Q9UES7;O75197	.;LRP5_HUMAN	L	1376	ENSP00000294304:P1376L	ENSP00000294304:P1376L	P	+	2	0	LRP5	67962505	0.649000	0.27322	0.025000	0.17156	0.056000	0.15407	5.269000	0.65542	2.379000	0.81126	0.585000	0.79938	CCC	.		0.592	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68205929	C	T	68205929	3	4	119	1	0	0	0	0	1	0	0	0	8985	623	22	2	4205	2	LRP5	11	68205929	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	1580304	68205929	66800587	51	10357											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49433380	49433380	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggatctgctgccgaatcagCagctctcgtagtcgctggcg	6	10	13	12	4	3	0	1	0	2	0	5	2	3	1	1	2	4	5	1	2	2	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:49433380C>G	ENST00000301067.7	-	32	8066	c.8067G>C	c.(8065-8067)ctG>ctC	p.L2689L	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2689					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GCCGAATCAGCAGCTCTCGTA	0.577																																					p.L2689L		.											.	MLL2-612	0			c.G8067C						.						19	21	20					12																	49433380		1995	4182	6177	SO:0001819	synonymous_variant	8085	exon32			AATCAGCAGCTCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8067G>C	12.37:g.49433380C>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	28	10	NM_003482	0	0	3	4	1	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49433380	C	G	49433380	2	3	119	1	0	0	0	0	0	0	0	1	9646	697	25	4		4	MLL2	12	49433380	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08		49433380	84418515	52	10358											
POLR3B	55703	broad.mit.edu	37	chr12	106889911	106889911	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccggacatcatcatgaaccCacacggcttcccatcacgaa	12	7	6	16	3	3	1	3	1	0	0	5	3	5	2	3	2	1	1	3	2	2	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:106889911C>A	ENST00000228347.4	+	24	3014	c.2792C>A	c.(2791-2793)cCa>cAa	p.P931Q	POLR3B_ENST00000539066.1_Missense_Mutation_p.P873Q|RP11-144F15.1_ENST00000551505.1_3'UTR	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	931					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						ATCATGAACCCACACGGCTTC	0.488																																					p.P931Q													.	POLR3B-91	0			c.C2792A						.						183	156	165					12																	106889911		2203	4300	6503	SO:0001583	missense	55703	exon24			TGAACCCACACGG	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.2792C>A	12.37:g.106889911C>A	ENSP00000228347:p.Pro931Gln	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	144	5	NM_018082	0	0	6	6	0	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	33	5.263308	0.95399	.	.	ENSG00000013503	ENST00000228347;ENST00000539066	D;D	0.92595	-3.07;-3.07	5.4	5.4	0.78164	DNA-directed RNA polymerase, subunit 2, domain 6 (2);	0.000000	0.85682	D	0.000000	D	0.98267	0.9426	H	0.99650	4.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99572	1.0971	10	0.87932	D	0	-13.2872	19.5252	0.95201	0.0:1.0:0.0:0.0	.	931	Q9NW08	RPC2_HUMAN	Q	931;873	ENSP00000228347:P931Q;ENSP00000445721:P873Q	ENSP00000228347:P931Q	P	+	2	0	POLR3B	105414041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.720000	0.84759	2.678000	0.91216	0.655000	0.94253	CCA	.		0.488	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		A	106889911	C	A	106889911	3	1	119	1	0	0	0	0	1	0	0	0	12255	594	21	4	2886	4	POLR3B	12	106889911	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	57456531	106889911	26961984	53	10359											
RPH3A	22895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113306301	113306301	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggtcctcccacagcctatgCctataaagaagaccaagccc	13	6	7	15	0	0	2	0	0	0	2	2	2	2	2	6	1	3	0	6	1	6	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:113306301C>A	ENST00000389385.4	+	8	1008	c.511C>A	c.(511-513)Cct>Act	p.P171T	RPH3A_ENST00000543106.2_Missense_Mutation_p.P171T|RPH3A_ENST00000415485.3_Missense_Mutation_p.P171T|RPH3A_ENST00000548866.1_Missense_Mutation_p.P122T|RPH3A_ENST00000447659.2_Missense_Mutation_p.P122T|RPH3A_ENST00000551052.1_Missense_Mutation_p.P167T|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000420983.2_Missense_Mutation_p.P171T	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	171	Pro-rich.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		ACAGCCTATGCCTATAAAGAA	0.602																																					p.P171T		.											.	RPH3A-519	0			c.C511A						.						60	58	59					12																	113306301		2203	4300	6503	SO:0001583	missense	22895	exon8			CCTATGCCTATAA	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.511C>A	12.37:g.113306301C>A	ENSP00000374036:p.Pro171Thr	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	63	13	NM_001143854	0	0	0	0	0	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	37	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653855	0.88056	.	.	ENSG00000089169	ENST00000543106;ENST00000551593;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T	0.64438	-0.0;-0.0;-0.1;-0.0;-0.0;-0.1;-0.0	4.77	4.77	0.60923	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.64402	D	0.000009	T	0.73521	0.3597	L	0.49126	1.545	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.996;0.996;0.998	T	0.70676	-0.4806	10	0.28530	T	0.3	.	16.5919	0.84767	0.0:1.0:0.0:0.0	.	122;171;171;167	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	T	171;171;171;122;167;171;122;171	ENSP00000440384:P171T;ENSP00000374036:P171T;ENSP00000413254:P122T;ENSP00000448297:P167T;ENSP00000405357:P171T;ENSP00000450347:P122T;ENSP00000408889:P171T	ENSP00000374036:P171T	P	+	1	0	RPH3A	111790684	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.916000	0.75776	2.213000	0.71641	0.655000	0.94253	CCT	.		0.602	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113306301	C	A	113306301	3	1	119	1	0	0	0	0	1	0	0	0	13583	739	26	4	533	4	RPH3A	12	113306301	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	6416390	113306301	20545594	54	10360											
FBXW8	26259	hgsc.bcm.edu	37	chr12	117348921	117348921	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggcgccgaagaagcggCgacggcccgaggctgccgag	8	1	17	15	7	0	1	0	0	0	1	0	5	0	1	4	4	2	1	4	4	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:117348921C>G	ENST00000309909.5	+	1	161	c.79C>G	c.(79-81)Cga>Gga	p.R27G	FBXW8_ENST00000455858.2_Missense_Mutation_p.R27G			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	27					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		GAAGAAGCGGCGACGGCCCGA	0.751																																					p.R27G		.											.	FBXW8-229	0			c.C79G						.						3	4	4					12																	117348921		1164	2768	3932	SO:0001583	missense	26259	exon1			AAGCGGCGACGGC	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"F-boxes / WD-40 domains", "WD repeat domain containing"	13597	protein-coding gene	gene with protein product		609073	"F-box only protein 29", "F-box and WD-40 domain protein 8"	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.79C>G	12.37:g.117348921C>G	ENSP00000310686:p.Arg27Gly	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_012174	0	0	0	0	0	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.482464	0.44147	.	.	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.10477	2.91;2.87	4.11	4.11	0.48088	.	0.440966	0.21290	N	0.076982	T	0.19525	0.0469	L	0.27053	0.805	0.33657	D	0.609235	D;D	0.67145	0.993;0.996	D;D	0.76575	0.972;0.988	T	0.13072	-1.0523	10	0.72032	D	0.01	-20.9936	12.0561	0.53536	0.0:1.0:0.0:0.0	.	27;27	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	G	27	ENSP00000310686:R27G;ENSP00000389144:R27G	ENSP00000310686:R27G	R	+	1	2	FBXW8	115833304	1.000000	0.71417	0.998000	0.56505	0.087000	0.18053	1.536000	0.36072	2.273000	0.75805	0.555000	0.69702	CGA	.		0.751	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174		G	117348921	C	G	117348921	3	3	119	1	0	0	0	0	1	0	0	0	5789	760	27	4	81	4	FBXW8	12	117348921	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	4042620	117348921	16502974	55	10361											
CCDC62	84660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123286278	123286278	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taattgaagccccaggccacAtgtctgacgtggagtggatg	10	9	13	9	1	1	2	0	2	1	0	1	4	1	4	3	3	1	0	3	3	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:123286278A>T	ENST00000253079.6	+	9	1929	c.1585A>T	c.(1585-1587)Atg>Ttg	p.M529L	CCDC62_ENST00000392441.4_Missense_Mutation_p.M529L|CCDC62_ENST00000392440.2_Missense_Mutation_p.M290L|CCDC62_ENST00000537566.1_Missense_Mutation_p.M290L	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	529					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		CCCAGGCCACATGTCTGACGT	0.502																																					p.M529L		.											.	CCDC62-157	0			c.A1585T						.						138	145	143					12																	123286278		2203	4300	6503	SO:0001583	missense	84660	exon9			GGCCACATGTCTG		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"cancer/testis antigen 109"	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.1585A>T	12.37:g.123286278A>T	ENSP00000253079:p.Met529Leu	Somatic	270	0		WXS	Illumina HiSeq	Phase_I	250	59	NM_201435	0	0	0	0	0	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Missense_Mutation	SNP	ENST00000253079.6	37	CCDS9238.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358511	0.41801	.	.	ENSG00000130783	ENST00000253079;ENST00000392441;ENST00000537566;ENST00000392440	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.73	-0.599	0.11645	.	0.206543	0.35805	N	0.002975	T	0.49609	0.1567	L	0.56769	1.78	0.18873	N	0.999988	B;B;B	0.21225	0.053;0.004;0.001	B;B;B	0.15484	0.013;0.006;0.001	T	0.44298	-0.9337	10	0.56958	D	0.05	-8.7087	4.9707	0.14113	0.4874:0.1609:0.3517:0.0	.	529;290;529	Q6P9F0-2;Q6P9F0-3;Q6P9F0	.;.;CCD62_HUMAN	L	529;529;290;290	ENSP00000253079:M529L;ENSP00000376236:M529L;ENSP00000445045:M290L;ENSP00000376235:M290L	ENSP00000253079:M529L	M	+	1	0	CCDC62	121852231	0.575000	0.26692	0.748000	0.31131	0.676000	0.39594	0.351000	0.20096	0.101000	0.17610	0.482000	0.46254	ATG	.		0.502	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		T	123286278	A	T	123286278	3	4	119	1	0	0	0	0	1	0	0	0	2839	217	8	5	1619	5	CCDC62	12	123286278	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	5937357	123286278	10565617	56	10362											
SLC15A4	121260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	129283926	129283926	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccattatggcactctgcAtggacttgggggcagctgag	8	9	14	10	0	1	1	0	1	1	0	1	2	1	2	1	4	3	4	1	4	1	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:129283926A>G	ENST00000266771.5	-	7	1490	c.1451T>C	c.(1450-1452)aTg>aCg	p.M484T	SLC15A4_ENST00000545031.1_Start_Codon_SNP_p.M1T|SLC15A4_ENST00000544112.1_Missense_Mutation_p.M147T	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	484					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		GGCACTCTGCATGGACTTGGG	0.512																																					p.M484T		.											.	SLC15A4-90	0			c.T1451C						.						84	81	82					12																	129283926		2203	4300	6503	SO:0001583	missense	121260	exon7			CTCTGCATGGACT	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"Solute carriers"	23090	protein-coding gene	gene with protein product		615806	"solute carrier family 15, member 4"			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1451T>C	12.37:g.129283926A>G	ENSP00000266771:p.Met484Thr	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	95	36	NM_145648	0	0	15	37	22	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Missense_Mutation	SNP	ENST00000266771.5	37	CCDS9264.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361060	0.82353	.	.	ENSG00000139370	ENST00000266771;ENST00000545031;ENST00000544112	T;T	0.05382	3.45;3.45	5.15	5.15	0.70609	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.28830	0.0715	M	0.85542	2.76	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.08249	-1.0731	10	0.87932	D	0	.	14.985	0.71342	1.0:0.0:0.0:0.0	.	484	Q8N697	S15A4_HUMAN	T	484;1;147	ENSP00000266771:M484T;ENSP00000439946:M147T	ENSP00000266771:M484T	M	-	2	0	SLC15A4	127849879	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.574000	0.90763	1.929000	0.55896	0.533000	0.62120	ATG	.		0.512	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648		G	129283926	A	G	129283926	3	3	119	1	0	0	0	0	1	0	0	0	14433	217	8	3	290	3	SLC15A4	12	129283926	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	5997648	129283926	4567969	57	10363											
SLITRK1	114798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	84453895	84453895	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaacgtgggcgagatcctaGcgtacagctgagggcagatc	10	8	14	9	3	0	3	0	1	0	2	2	4	1	3	1	2	4	3	1	2	3	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr13:84453895G>A	ENST00000377084.2	-	1	2633	c.1748C>T	c.(1747-1749)gCt>gTt	p.A583V		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	583					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		CGAGATCCTAGCGTACAGCTG	0.542																																					p.A583V		.											.	SLITRK1-94	0			c.C1748T						.						94	80	85					13																	84453895		2203	4300	6503	SO:0001583	missense	114798	exon1			ATCCTAGCGTACA	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"leucine rich repeat containing 12"	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1748C>T	13.37:g.84453895G>A	ENSP00000366288:p.Ala583Val	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	35	9	NM_052910	0	0	0	2	2	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	G	7.865	0.726968	0.15439	.	.	ENSG00000178235	ENST00000377084	T	0.58797	0.31	5.22	4.36	0.52297	.	0.190710	0.45126	D	0.000397	T	0.58409	0.2120	M	0.76574	2.34	0.45261	D	0.998262	B	0.22541	0.071	B	0.25987	0.065	T	0.56595	-0.7953	10	0.30854	T	0.27	-10.4812	13.8324	0.63389	0.0:0.1548:0.8452:0.0	.	583	Q96PX8	SLIK1_HUMAN	V	583	ENSP00000366288:A583V	ENSP00000366288:A583V	A	-	2	0	SLITRK1	83351896	1.000000	0.71417	0.958000	0.39756	0.986000	0.74619	3.881000	0.56152	1.320000	0.45209	-0.175000	0.13238	GCT	.		0.542	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84453895	G	A	84453895	3	1	119	1	0	0	0	0	1	0	0	0	14774	971	34	2	346	2	SLITRK1	13	84453895	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		84453895	30715983	58	10364											
UBAC2	337867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99890774	99890774	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactgccagaagctctttgTgtatgaccttcacgcagtca	9	12	8	12	1	4	2	3	1	1	1	4	2	4	2	2	0	2	3	2	0	2	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr13:99890774T>C	ENST00000403766.3	+	2	260	c.125T>C	c.(124-126)gTg>gCg	p.V42A	UBAC2_ENST00000376440.2_Missense_Mutation_p.C84R	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	42					protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAGCTCTTTGTGTATGACCTT	0.547																																					p.C84R		.											.	UBAC2-91	0			c.T250C						.						222	221	222					13																	99890774		2203	4300	6503	SO:0001583	missense	337867	exon2			TCTTTGTGTATGA	AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"phosphoglycerate dehydrogenase like 1"	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.125T>C	13.37:g.99890774T>C	ENSP00000383911:p.Val42Ala	Somatic	442	0		WXS	Illumina HiSeq	Phase_I	334	83	NM_177967	0	0	16	39	23	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Missense_Mutation	SNP	ENST00000403766.3	37	CCDS45064.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.11|13.11	2.139733|2.139733	0.37728|0.37728	.|.	.|.	ENSG00000134882|ENSG00000134882	ENST00000376440|ENST00000403766;ENST00000355700;ENST00000457666	.|T;T;T	.|0.45276	.|0.9;0.9;0.9	5.72|5.72	4.52|4.52	0.55395|0.55395	.|.	.|0.610304	.|0.17766	.|N	.|0.162736	T|T	0.25865|0.25865	0.0630|0.0630	.|.	.|.	.|.	0.37528|0.37528	D|D	0.917816|0.917816	B|B	0.18968|0.13594	0.032|0.008	B|B	0.13407|0.06405	0.009|0.002	T|T	0.12268|0.12268	-1.0554|-1.0554	6|8	.|.	.|.	.|.	-4.5461|-4.5461	5.6483|5.6483	0.17602|0.17602	0.1608:0.0847:0.0:0.7545|0.1608:0.0847:0.0:0.7545	.|.	84|42	Q8NBM4-2|Q8NBM4	.|UBAC2_HUMAN	R|A	84|42;42;48	.|ENSP00000383911:V42A;ENSP00000347928:V42A;ENSP00000402249:V48A	.|.	C|V	+|+	1|2	0|0	UBAC2|UBAC2	98688775|98688775	0.007000|0.007000	0.16637|0.16637	0.998000|0.998000	0.56505|0.56505	0.983000|0.983000	0.72400|0.72400	1.311000|1.311000	0.33562|0.33562	0.960000|0.960000	0.38005|0.38005	0.482000|0.482000	0.46254|0.46254	TGT|GTG	.		0.547	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967		C	99890774	T	C	99890774	3	2	119	1	0	0	0	0	1	0	0	0	16868	1696	59	3	291	3	UBAC2	13	99890774	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	15436879	99890774	15279104	59	10365											
LAMP1	3916	broad.mit.edu	37	chr13	113960803	113960803	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccctggaattgacaggccTcatgcattgtgcgtcagcag	8	11	11	11	1	2	1	2	1	0	0	3	2	3	2	2	2	3	2	2	2	1	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr13:113960803T>C	ENST00000332556.4	+	2	259	c.65T>C	c.(64-66)cTc>cCc	p.L22P	LAMP1_ENST00000397181.3_Missense_Mutation_p.L22P	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	22				LLLLLGLMHCA -> PVAAARPHALS (in Ref. 1; AAA60382). {ECO:0000305}.	autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			TTGACAGGCCTCATGCATTGT	0.473																																					p.L22P													.	LAMP1-514	0			c.T65C						.						168	162	164					13																	113960803		1967	4166	6133	SO:0001583	missense	3916	exon2			CAGGCCTCATGCA	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.65T>C	13.37:g.113960803T>C	ENSP00000333298:p.Leu22Pro	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	178	4	NM_005561	0	0	1	1	0	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	37	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.032500	0.35893	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.34859	1.34;1.45	5.04	5.04	0.67666	.	1.537360	0.04718	N	0.418782	T	0.62877	0.2464	M	0.80028	2.48	0.53005	D	0.99996	D;D	0.71674	0.998;0.983	D;P	0.62955	0.909;0.799	T	0.41980	-0.9478	10	0.44086	T	0.13	-17.283	11.4481	0.50136	0.0:0.0:0.0:1.0	.	22;22	B4DWL3;P11279	.;LAMP1_HUMAN	P	22	ENSP00000333298:L22P;ENSP00000415354:L22P	ENSP00000333298:L22P	L	+	2	0	LAMP1	113008804	0.249000	0.23941	0.861000	0.33841	0.020000	0.10135	3.432000	0.52824	2.026000	0.59711	0.421000	0.28195	CTC	.		0.473	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			C	113960803	T	C	113960803	3	2	119	1	0	0	0	0	1	0	0	0	8638	1551	54	3	71	3	LAMP1	13	113960803	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	14070029	113960803	1209075	60	10366											
FOXG1	2290	hgsc.bcm.edu	37	chr14	29237806	29237806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgccagggccgcgtccTcctccacgtcgccgcaggcc	4	5	13	19	6	0	1	0	1	0	0	4	1	3	1	7	2	1	1	7	2	0	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr14:29237806T>C	ENST00000313071.4	+	1	1520	c.1321T>C	c.(1321-1323)Tcc>Ccc	p.S441P	FOXG1_ENST00000382535.3_Missense_Mutation_p.S441P	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	441					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GGCCGCGTCCTCCTCCACGTC	0.617																																					p.S441P		.											.	FOXG1-660	0			c.T1321C						.						66	62	63					14																	29237806		2203	4300	6503	SO:0001583	missense	2290	exon1			GCGTCCTCCTCCA		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"Forkhead boxes"	3811	protein-coding gene	gene with protein product		164874	"forkhead box G1B", "forkhead box G1C", "forkhead box G1A"	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.1321T>C	14.37:g.29237806T>C	ENSP00000339004:p.Ser441Pro	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	55	3	NM_005249	0	0	0	0	0	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	37	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	T	9.301	1.053132	0.19907	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.93712	-3.27;-3.27	4.14	4.14	0.48551	.	0.394510	0.21935	U	0.066968	D	0.87156	0.6107	N	0.19112	0.55	0.44117	D	0.996893	P	0.44578	0.838	B	0.41813	0.367	D	0.86285	0.1670	10	0.42905	T	0.14	.	10.3384	0.43862	0.0:0.0:0.1649:0.835	.	441	P55316	FOXG1_HUMAN	P	441	ENSP00000371975:S441P;ENSP00000339004:S441P	ENSP00000339004:S441P	S	+	1	0	FOXG1	28307557	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.354000	0.52254	1.633000	0.50488	0.402000	0.26972	TCC	.		0.617	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3			C	29237806	T	C	29237806	3	2	119	1	0	0	0	0	1	0	0	0	6026	1551	54	3	1323	3	FOXG1	14	29237806	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08		29237806	78111734	61	10367											
CASC5	57082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	40914067	40914068	+	Frame_Shift_Del	DEL	TT	TT	-																															gatgggaaaatgaatgtaaaTtgtaactcagttcctcatgt																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:40914067_40914068delTT	ENST00000346991.5	+	11	2073_2074	c.1683_1684delTT	c.(1681-1686)aattgtfs	p.NC561fs	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Frame_Shift_Del_p.NC535fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	561	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TGAATGTAAATTGTAACTCAGT	0.371																																					p.561_562del		.											.	CASC5-660	0			c.1683_1684del						.																																			SO:0001589	frameshift_variant	57082	exon11			.	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.1683_1684delTT	15.37:g.40914067_40914068delTT	ENSP00000335463:p.Asn561fs	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	65	21	NM_170589	0	0	0	0	0	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	37	CCDS42023.1																																																																																			.		0.371	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40914068	TT	-	40914067	7	5	119	1	0	1	0	1	0	0	0	0	2669	1490	52	0	1721	0	CASC5	15	40914067	Frame_Shift_Del	DEL	TT	TCGA-G7-7502-01A-11D-2201-08		40914067	61617325	62	10368											
SPTBN5	51332	broad.mit.edu	37	chr15	42178141	42178141	+	Frame_Shift_Del	DEL	G	G	-																															atccttaaggaaactctcccGgagggctgccttgtgctgga																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:42178141delG	ENST00000320955.6	-	7	1539	c.1312delC	c.(1312-1314)cggfs	p.R438fs		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	438					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		AAACTCTCCCGGAGGGCTGCC	0.667																																					p.R403fs													.	SPTBN5-91	0			c.1207delC						.						13	14	14					15																	42178141		1868	4084	5952	SO:0001589	frameshift_variant	51332	exon7			TCTCCCGGAGGGC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.1312delC	15.37:g.42178141delG	ENSP00000317790:p.Arg438fs	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_016642	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000320955.6	37																																																																																				.		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		-	42178141	G	-	42178141	7	5	119	1	0	1	0	1	0	0	0	0	15154	1115	39	0	9960	0	SPTBN5	15	42178141	Frame_Shift_Del	DEL	G	TCGA-G7-7502-01A-11D-2201-08	1264074	42178141	60353251	63	10369											
NEO1	4756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr15	73428245	73428245	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aacacagctctgaaagattgGtattgctggcaggtggtagc	11	10	13	7	0	1	2	0	1	1	1	1	2	1	2	0	4	4	5	0	4	4	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:73428245G>T	ENST00000339362.5	+	6	1339	c.892G>T	c.(892-894)Gta>Tta	p.V298L	NEO1_ENST00000558964.1_Missense_Mutation_p.V298L|NEO1_ENST00000560262.1_Missense_Mutation_p.V298L|NEO1_ENST00000261908.6_Missense_Mutation_p.V298L			Q92859	NEO1_HUMAN	neogenin 1	298	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TGAAAGATTGGTATTGCTGGC	0.338																																					p.V298L		.											.	NEO1-116	0			c.G892T						.						88	84	85					15																	73428245		2197	4297	6494	SO:0001583	missense	4756	exon5			AGATTGGTATTGC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.892G>T	15.37:g.73428245G>T	ENSP00000341198:p.Val298Leu	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	16	5	NM_001172623	0	0	3	6	3	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	3.964	-0.009769	0.07727	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.66638	-0.22;-0.22	6.04	0.438	0.16560	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.602380	0.17828	N	0.160637	T	0.42877	0.1222	N	0.17872	0.535	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.002	T	0.14896	-1.0456	10	0.27785	T	0.31	-0.8513	4.3015	0.10927	0.3044:0.0:0.443:0.2526	.	298;298;298	B7ZKM9;B7ZKN0;Q92859	.;.;NEO1_HUMAN	L	298;16;298	ENSP00000341198:V298L;ENSP00000261908:V298L	ENSP00000261908:V298L	V	+	1	0	NEO1	71215298	0.026000	0.19158	0.105000	0.21289	0.246000	0.25737	0.203000	0.17315	0.170000	0.19704	-0.219000	0.12488	GTA	.		0.338	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		T	73428245	G	T	73428245	3	4	119	1	0	0	0	0	1	0	0	0	10362	1261	44	4	910	4	NEO1	15	73428245	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	31250104	73428245	29103147	64	10370											
SCAMP2	10066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75142970	75142970	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctgttgcccgagaaccAggccaggcaggcaagcaggt	10	4	16	11	1	0	1	0	0	0	1	0	3	0	2	3	5	4	5	3	5	2	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:75142970A>T	ENST00000268099.9	-	6	626	c.517T>A	c.(517-519)Tgg>Agg	p.W173R		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	173					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						CCCGAGAACCAGGCCAGGCAG	0.562																																					p.W173R		.											.	SCAMP2-91	0			c.T517A						.						123	112	115					15																	75142970		2197	4295	6492	SO:0001583	missense	10066	exon6			AGAACCAGGCCAG	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"Secretory carrier membrane proteins"	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.517T>A	15.37:g.75142970A>T	ENSP00000268099:p.Trp173Arg	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	93	21	NM_005697	0	0	48	87	39	B2RDF0|Q9BQE8	Missense_Mutation	SNP	ENST00000268099.9	37	CCDS10271.1	.	.	.	.	.	.	.	.	.	.	A	7.869	0.727707	0.15439	.	.	ENSG00000140497	ENST00000268099;ENST00000543345	T	0.16597	2.33	4.48	4.48	0.54585	.	0.307839	0.34802	N	0.003680	T	0.22513	0.0543	M	0.71036	2.16	0.30893	N	0.730139	B;B	0.21520	0.049;0.057	B;B	0.29267	0.035;0.1	T	0.10543	-1.0625	10	0.25751	T	0.34	.	13.2599	0.60098	1.0:0.0:0.0:0.0	.	173;142	O15127;B3KU14	SCAM2_HUMAN;.	R	173;142	ENSP00000268099:W173R	ENSP00000268099:W173R	W	-	1	0	SCAMP2	72930023	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	4.332000	0.59279	1.795000	0.52594	0.402000	0.26972	TGG	.		0.562	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697		T	75142970	A	T	75142970	3	4	119	1	0	0	0	0	1	0	0	0	13903	188	7	5	488	5	SCAMP2	15	75142970	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	1714725	75142970	27388422	65	10371											
ZSCAN2	54993	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr15	85159554	85159554	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttccagaaacagcttcctgcGtacatggctgccctgtgtga	8	11	10	12	1	0	2	0	1	0	1	2	2	2	2	3	1	5	3	3	1	2	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:85159554G>A	ENST00000448803.2	+	3	698				ZSCAN2_ENST00000546148.1_Intron|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000327179.6_Intron|ZSCAN2_ENST00000358472.3_Intron|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000379358.3_Missense_Mutation_p.V141I|ZSCAN2_ENST00000485222.2_Intron|RP11-182J1.5_ENST00000542197.1_RNA	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|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)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		agcttcctgcgtacatggctg	0.463																																					p.V141I		.											.	ZSCAN2-91	0			c.G421A						.						170	139	149					15																	85159554		2203	4299	6502	SO:0001627	intron_variant	54993	exon3			TCCTGCGTACATG	BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"-", "Zinc fingers, C2H2-type"	20994	protein-coding gene	gene with protein product			"zinc finger protein 29"	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.407-4279G>A	15.37:g.85159554G>A		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	65	22	NM_001007072	0	0	1	1	0	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Missense_Mutation	SNP	ENST00000448803.2	37	CCDS10329.2	.	.	.	.	.	.	.	.	.	.	G	2.654	-0.281322	0.05642	.	.	ENSG00000176371	ENST00000379358	T	0.05855	3.38	1.85	-3.69	0.04450	.	.	.	.	.	T	0.03434	0.0099	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41787	-0.9489	8	0.38643	T	0.18	.	1.9006	0.03267	0.2148:0.1858:0.4349:0.1645	.	141	Q7Z7L9-4	.	I	141	ENSP00000368663:V141I	ENSP00000368663:V141I	V	+	1	0	ZSCAN2	82960558	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.727000	0.00807	-1.295000	0.02357	-0.414000	0.06135	GTA	.		0.463	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		A	85159554	G	A	85159554	1	1	119	0	1	0	0	0	0	0	0	0	18263	1145	40	1		1	ZSCAN2	15	85159554	Intron	SNP	G	TCGA-G7-7502-01A-11D-2201-08	10016584	85159554	17371838	66	10372											
CHTF18	63922	hgsc.bcm.edu	37	chr16	845697	845697	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccccaggcccagaaccggAtgagccagatgaggaacctg	11	4	13	13	1	0	4	0	2	0	2	0	6	0	6	6	3	4	0	6	3	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:845697A>G	ENST00000262315.9	+	17	2251	c.2188A>G	c.(2188-2190)Atg>Gtg	p.M730V	CHTF18_ENST00000455171.2_Missense_Mutation_p.M758V|CHTF18_ENST00000317063.6_Missense_Mutation_p.M939V	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	730					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CCAGAACCGGATGAGCCAGAT	0.726																																					p.M730V		.											.	CHTF18-227	0			c.A2188G						.						14	18	17					16																	845697		2054	4170	6224	SO:0001583	missense	63922	exon17			AACCGGATGAGCC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"ATPases / AAA-type"	18435	protein-coding gene	gene with protein product		613201	"chromosome 16 open reading frame 41"	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.2188A>G	16.37:g.845697A>G	ENSP00000262315:p.Met730Val	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	35	3	NM_022092	0	0	0	0	0	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	a	4.345	0.063383	0.08388	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.09723	2.95;2.99;2.99	4.41	3.29	0.37713	.	1.148390	0.06406	N	0.719777	T	0.08358	0.0208	L	0.40543	1.245	0.09310	N	1	B;B	0.24675	0.041;0.109	B;B	0.17098	0.017;0.013	T	0.44574	-0.9319	10	0.16896	T	0.51	-0.0122	1.7224	0.02915	0.5608:0.1754:0.0948:0.1689	.	758;730	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	939;758;730	ENSP00000313029:M939V;ENSP00000406252:M758V;ENSP00000262315:M730V	ENSP00000262315:M730V	M	+	1	0	CHTF18	785698	0.012000	0.17670	0.132000	0.22025	0.973000	0.67179	0.965000	0.29319	0.538000	0.28769	0.370000	0.22315	ATG	.		0.726	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		G	845697	A	G	845697	3	3	119	1	0	0	0	0	1	0	0	0	3420	333	12	3	2254	3	CHTF18	16	845697	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		845697	89509056	67	10373											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacgcagctcccgcctTcccgctcaggagctgccgcc	6	5	10	20	4	1	0	1	0	0	0	3	1	3	1	5	1	4	5	5	1	0	1	rs71384660		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1	1	1	5008	,	,		5162	1		1	False		,,,				2504	1				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1	2	2					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"Zinc fingers, C2H2-type"	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	3	3	NM_178167	0	0	0	1	1	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167		C	2059674	T	C	2059674	3	2	119	1	0	0	0	0	1	0	0	0	18060	1770	62	3	2689	3	ZNF598	16	2059674	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	1213977	2059674	88295079	68	10374											
C16orf59	80178	hgsc.bcm.edu	37	chr16	2511166	2511166	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggggcgggcctcagggaccaGcaaatggccccatccgctgc	7	4	15	15	2	1	0	1	0	0	0	2	1	2	1	5	5	2	2	5	5	1	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:2511166G>C	ENST00000361837.4	+	4	611	c.546G>C	c.(544-546)caG>caC	p.Q182H	C16orf59_ENST00000569496.1_Missense_Mutation_p.Q182H|C16orf59_ENST00000483320.1_Missense_Mutation_p.Q15H|C16orf59_ENST00000563531.1_Missense_Mutation_p.Q182H|RP11-715J22.4_ENST00000566085.1_lincRNA	NM_025108.2	NP_079384.2	Q7L2K0	CP059_HUMAN	chromosome 16 open reading frame 59	182										lung(1)|skin(1)|urinary_tract(1)	3		Ovarian(90;0.17)				TCAGGGACCAGCAAATGGCCC	0.667																																					p.Q182H		.											.	C16orf59-90	0			c.G546C						.						10	13	12					16																	2511166		1889	4101	5990	SO:0001583	missense	80178	exon4			GGACCAGCAAATG	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.546G>C	16.37:g.2511166G>C	ENSP00000355022:p.Gln182His	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	21	2	NM_025108	0	0	0	0	0	B4DXD7|Q96H61|Q9H872	Missense_Mutation	SNP	ENST00000361837.4	37	CCDS10468.2	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479988	0.44044	.	.	ENSG00000162062	ENST00000361837	T	0.49432	0.78	3.42	-0.616	0.11583	.	0.610181	0.13837	N	0.359307	T	0.54175	0.1842	M	0.62723	1.935	0.09310	N	1	D;P;P;D	0.60160	0.987;0.95;0.95;0.983	P;P;P;P	0.58391	0.838;0.712;0.712;0.785	T	0.46005	-0.9222	10	0.66056	D	0.02	-1.5097	6.6308	0.22855	0.459:0.0:0.541:0.0	.	15;182;15;15	Q7L2K0-3;Q7L2K0;D3DU95;Q7L2K0-2	.;CP059_HUMAN;.;.	H	182	ENSP00000355022:Q182H	ENSP00000355022:Q182H	Q	+	3	2	C16orf59	2451167	0.001000	0.12720	0.003000	0.11579	0.019000	0.09904	0.419000	0.21247	-0.125000	0.11703	-0.345000	0.07892	CAG	.		0.667	C16orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250802.3	NM_025108		C	2511166	G	C	2511166	3	2	119	1	0	0	0	0	1	0	0	0	1827	962	34	4	560	4	C16orf59	16	2511166	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	451492	2511166	87843587	69	10375											
ACSM2A	123876	hgsc.bcm.edu;broad.mit.edu	37	chr16	20482481	20482481	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tagtgggaccagtggtcttcCcaagatggcagaacattcct	10	10	11	10	0	1	2	0	0	1	2	3	3	3	3	3	3	1	1	3	3	3	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:20482481C>G	ENST00000573854.1	+	5	797	c.683C>G	c.(682-684)cCc>cGc	p.P228R	ACSM2A_ENST00000417235.2_Missense_Mutation_p.P149R|ACSM2A_ENST00000219054.6_Missense_Mutation_p.P228R|ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000536134.1_Intron|ACSM2A_ENST00000575690.1_Missense_Mutation_p.P228R|ACSM2A_ENST00000396104.2_Missense_Mutation_p.P228R	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	228					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						AGTGGTCTTCCCAAGATGGCA	0.507																																					p.P228R		.											.	ACSM2A-91	0			c.C683G						.						88	81	84					16																	20482481		2202	4280	6482	SO:0001583	missense	123876	exon6			GTCTTCCCAAGAT	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"Acyl-CoA synthetase family"	32017	protein-coding gene	gene with protein product		614358	"acyl-CoA synthetase medium-chain family member 2"	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.683C>G	16.37:g.20482481C>G	ENSP00000459451:p.Pro228Arg	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	136	28	NM_001010845	0	0	592	805	213	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977023	0.53720	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000396104	D;D;D	0.85013	-1.93;-1.93;-1.93	4.04	4.04	0.47022	AMP-dependent synthetase/ligase (1);AMP-binding, conserved site (1);	0.000000	0.46758	D	0.000276	D	0.93044	0.7786	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94275	0.7514	10	0.87932	D	0	-15.3933	13.1463	0.59463	0.0:1.0:0.0:0.0	.	149;228	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	R	149;228;228	ENSP00000392169:P149R;ENSP00000219054:P228R;ENSP00000379411:P228R	ENSP00000219054:P228R	P	+	2	0	ACSM2A	20389982	0.994000	0.37717	0.968000	0.41197	0.633000	0.38033	5.357000	0.66058	1.796000	0.52611	0.298000	0.19748	CCC	.		0.507	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		G	20482481	C	G	20482481	3	3	119	1	0	0	0	0	1	0	0	0	183	623	22	4	697	4	ACSM2A	16	20482481	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	17971315	20482481	69872272	70	10376											
KIAA0556	23247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27761006	27761006	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcagtgccttcgaccgcTcccaccggggacgcatctcc	5	7	9	20	4	2	0	1	0	1	0	5	2	3	1	6	2	1	2	6	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:27761006T>A	ENST00000261588.4	+	16	2744	c.2725T>A	c.(2725-2727)Tcc>Acc	p.S909T		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	909						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						CTTCGACCGCTCCCACCGGGG	0.637																																					p.S909T		.											.	KIAA0556-141	0			c.T2725A						.						63	60	61					16																	27761006		2197	4300	6497	SO:0001583	missense	23247	exon16			GACCGCTCCCACC	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2725T>A	16.37:g.27761006T>A	ENSP00000261588:p.Ser909Thr	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	93	22	NM_015202	0	0	2	3	1	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.620080	0.66787	.	.	ENSG00000047578	ENST00000261588	T	0.10382	2.88	4.7	3.58	0.41010	.	0.196895	0.45606	D	0.000352	T	0.10465	0.0256	L	0.53249	1.67	0.25290	N	0.989366	P	0.47545	0.897	P	0.45639	0.488	T	0.06373	-1.0830	10	0.06365	T	0.9	-22.2078	6.7315	0.23385	0.0:0.0832:0.161:0.7558	.	909	O60303	K0556_HUMAN	T	909	ENSP00000261588:S909T	ENSP00000261588:S909T	S	+	1	0	KIAA0556	27668507	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.876000	0.48498	0.738000	0.32606	0.533000	0.62120	TCC	.		0.637	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27761006	T	A	27761006	3	1	119	1	0	0	0	0	1	0	0	0	8204	1551	54	5	2787	5	KIAA0556	16	27761006	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	7278525	27761006	62593747	71	10377											
SEZ6L2	26470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	29884867	29884867	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccccagactcacaggcgcatTtggggaccctatcgctccac	8	7	9	17	2	1	1	1	0	0	1	3	2	2	2	4	3	0	2	4	3	1	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:29884867T>A	ENST00000308713.5	-	13	2815	c.2288A>T	c.(2287-2289)aAa>aTa	p.K763I	SEZ6L2_ENST00000346932.5_Missense_Mutation_p.K649I|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.K693I|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.K719I	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	763	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACAGGCGCATTTGGGGACCCT	0.667																																					p.K763I		.											.	SEZ6L2-92	0			c.A2288T						.						60	55	57					16																	29884867		2197	4300	6497	SO:0001583	missense	26470	exon13			GCGCATTTGGGGA	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"type I transmembrane receptor (seizure related protein)"					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.2288A>T	16.37:g.29884867T>A	ENSP00000312550:p.Lys763Ile	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	61	12	NM_001243332	0	0	0	0	0	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145084	0.77888	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	4.67	4.67	0.58626	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.49916	D	0.000135	T	0.66742	0.2820	L	0.28556	0.865	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.999;1.0	D;D;D;D;D;D	0.91635	0.997;0.999;0.996;0.998;0.998;0.999	T	0.63088	-0.6715	10	0.23891	T	0.37	.	13.1007	0.59218	0.0:0.0:0.0:1.0	.	719;763;649;693;763;693	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	I	693;763;649;719	ENSP00000310206:K693I;ENSP00000312550:K763I;ENSP00000319215:K649I;ENSP00000439412:K719I	ENSP00000312550:K763I	K	-	2	0	SEZ6L2	29792368	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.939000	0.70179	1.737000	0.51674	0.533000	0.62120	AAA	.		0.667	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		A	29884867	T	A	29884867	3	1	119	1	0	0	0	0	1	0	0	0	14176	1841	64	5	507	5	SEZ6L2	16	29884867	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	2123861	29884867	60469886	72	10378											
HEATR3	55027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	50104088	50104088	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcatgatatttggttacaGtgtagtgctggactggattc	10	15	11	5	0	1	1	1	1	0	0	2	3	1	3	0	3	2	3	0	3	4	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:50104088G>A	ENST00000299192.7	+	4	590		c.e4-1		HEATR3_ENST00000285767.4_Splice_Site	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3											cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TTTGGTTACAGTGTAGTGCTG	0.383																																					.		.											.	HEATR3-92	0			c.400-1G>A						.						86	83	84					16																	50104088		2198	4300	6498	SO:0001630	splice_region_variant	55027	exon4			GTTACAGTGTAGT	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.400-1G>A	16.37:g.50104088G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	60	31	NM_182922	0	0	0	0	0	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Splice_Site	SNP	ENST00000299192.7	37	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012741	0.75161	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.545	0.95291	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HEATR3	48661589	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.402000	0.73260	2.861000	0.98227	0.655000	0.94253	.	.		0.383	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922	Intron	A	50104088	G	A	50104088	5	1	119	1	0	0	0	0	0	0	1	0	7050	1043	36	2	413	2	HEATR3	16	50104088	Splice_Site	SNP	G	TCGA-G7-7502-01A-11D-2201-08	20219221	50104088	40250665	73	10379											
AMFR	267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56401438	56401438	+	Splice_Site	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtctgatgctatctgacCgctggaagagaaacagtacc	12	8	11	10	1	2	3	0	2	2	1	2	5	2	4	2	2	3	3	2	2	4	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:56401438C>A	ENST00000290649.5	-	12	1727	c.1517G>T	c.(1516-1518)cGg>cTg	p.R506L		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	506					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						GCTATCTGACCGCTGGAAGAG	0.498																																					p.R506L	Pancreas(2;144 323 39528)	.											.	AMFR-1009	0			c.G1517T						.						248	233	238					16																	56401438		2198	4300	6498	SO:0001630	splice_region_variant	267	exon12			TCTGACCGCTGGA	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1516-1G>T	16.37:g.56401438C>A		Somatic	360	0		WXS	Illumina HiSeq	Phase_I	398	100	NM_001144	0	0	0	0	0	P26442|Q8IZ70	Missense_Mutation	SNP	ENST00000290649.5	37	CCDS10758.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.611801	0.46631	.	.	ENSG00000159461	ENST00000290649	T	0.14391	2.51	5.8	5.8	0.92144	.	0.234971	0.44483	D	0.000455	T	0.15998	0.0385	M	0.63428	1.95	0.80722	D	1	B;P	0.37985	0.415;0.613	B;B	0.28709	0.089;0.093	T	0.02208	-1.1195	10	0.34782	T	0.22	-24.0104	18.2436	0.89977	0.0:1.0:0.0:0.0	.	506;155	Q9UKV5;Q1RN03	AMFR2_HUMAN;.	L	506	ENSP00000290649:R506L	ENSP00000290649:R506L	R	-	2	0	AMFR	54958939	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	3.487000	0.53222	2.735000	0.93741	0.655000	0.94253	CGG	.		0.498	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2		Missense_Mutation	A	56401438	C	A	56401438	5	1	119	1	0	0	0	0	0	0	1	0	571	666	23	4	426	4	AMFR	16	56401438	Splice_Site	SNP	C	TCGA-G7-7502-01A-11D-2201-08	6297350	56401438	33953315	74	10380											
HYDIN	54768	hgsc.bcm.edu;broad.mit.edu	37	chr16	70866949	70866949	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggagaaatgaggctcaaaTtttttgatgtcccatttaaa	14	14	8	5	0	1	3	1	2	0	1	2	4	2	3	1	2	0	1	1	2	4	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:70866949T>A	ENST00000393567.2	-	80	13851	c.13701A>T	c.(13699-13701)aaA>aaT	p.K4567N		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4567					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GAGGCTCAAATTTTTTGATGT	0.413																																					p.K4567N		.											.	HYDIN-92	0			c.A13701T						.						14	14	14					16																	70866949		1811	4061	5872	SO:0001583	missense	54768	exon80			CTCAAATTTTTTG	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13701A>T	16.37:g.70866949T>A	ENSP00000377197:p.Lys4567Asn	Somatic	57	1		WXS	Illumina HiSeq	Phase_I	52	12	NM_001270974	0	0	10	17	7	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.787649	0.49997	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01099	5.34	4.62	-0.806	0.10875	.	0.437992	0.16234	U	0.223455	T	0.02888	0.0086	M	0.74258	2.255	0.09310	N	1	D	0.56968	0.978	P	0.61070	0.883	T	0.40515	-0.9559	10	0.23891	T	0.37	.	1.6269	0.02724	0.1205:0.2403:0.3257:0.3135	.	4566	F8WD23	.	N	4567;4566	ENSP00000377197:K4567N	ENSP00000313052:K4566N	K	-	3	2	HYDIN	69424450	0.181000	0.23161	0.011000	0.14972	0.919000	0.55068	-0.435000	0.06931	-0.520000	0.06435	-0.473000	0.04963	AAA	.		0.413	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70866949	T	A	70866949	3	1	119	1	0	0	0	0	1	0	0	0	7488	1490	52	5	1692	5	HYDIN	16	70866949	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	14465511	70866949	19487804	75	10381											
GRB7	2886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37898588	37898588	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctccacctcatcttagcAgctctccggaagacctttgc	7	12	7	15	1	4	1	1	0	3	1	6	2	4	2	4	1	3	2	4	1	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:37898588A>G	ENST00000309156.4	+	2	291	c.34A>G	c.(34-36)Agc>Ggc	p.S12G	GRB7_ENST00000578702.1_3'UTR|GRB7_ENST00000445327.2_Missense_Mutation_p.S35G|GRB7_ENST00000394211.3_Missense_Mutation_p.S12G|GRB7_ENST00000309185.3_Missense_Mutation_p.S12G|GRB7_ENST00000394204.1_Missense_Mutation_p.S12G|GRB7_ENST00000394209.2_Missense_Mutation_p.S12G	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	12					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCATCTTAGCAGCTCTCCGGA	0.617																																					p.S35G		.											.	GRB7-848	0			c.A103G						.						154	151	152					17																	37898588		2203	4300	6503	SO:0001583	missense	2886	exon2			CTTAGCAGCTCTC	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.34A>G	17.37:g.37898588A>G	ENSP00000310771:p.Ser12Gly	Somatic	295	0		WXS	Illumina HiSeq	Phase_I	250	100	NM_001242442	0	0	14	61	47	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Missense_Mutation	SNP	ENST00000309156.4	37	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	A	7.773	0.707831	0.15239	.	.	ENSG00000141738	ENST00000309185;ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327;ENST00000394204	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	4.61	4.61	0.57282	.	0.366448	0.26349	N	0.024892	T	0.38585	0.1046	L	0.47716	1.5	0.27860	N	0.940439	B;B	0.28971	0.229;0.043	B;B	0.29176	0.099;0.037	T	0.24404	-1.0161	10	0.21540	T	0.41	-25.7351	10.4148	0.44316	1.0:0.0:0.0:0.0	.	12;12	Q14451-2;Q14451	.;GRB7_HUMAN	G	12;12;12;12;35;12	ENSP00000311752:S12G;ENSP00000310771:S12G;ENSP00000377761:S12G;ENSP00000377759:S12G;ENSP00000403459:S35G;ENSP00000377754:S12G	ENSP00000310771:S12G	S	+	1	0	GRB7	35152114	1.000000	0.71417	0.981000	0.43875	0.110000	0.19582	4.739000	0.62080	1.718000	0.51419	0.459000	0.35465	AGC	.		0.617	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310		G	37898588	A	G	37898588	3	3	119	1	0	0	0	0	1	0	0	0	6780	188	7	3	36	3	GRB7	17	37898588	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		37898588	43296622	76	10382											
KRT13	3860	broad.mit.edu	37	chr17	39658827	39658827	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcactccgtctctgccaccGtgttctccagccccgctttc	3	11	8	19	3	2	0	0	0	2	0	6	0	3	0	6	1	2	3	6	1	0	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:39658827G>A	ENST00000246635.3	-	6	1089	c.1043C>T	c.(1042-1044)aCg>aTg	p.T348M	AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000587544.1_Missense_Mutation_p.T348M|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000336861.3_Missense_Mutation_p.T348M	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	348	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				CTCTGCCACCGTGTTCTCCAG	0.632																																					p.T348M													.	KRT13-95	0			c.C1043T						.						85	76	79					17																	39658827		2203	4300	6503	SO:0001583	missense	3860	exon6			GCCACCGTGTTCT		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.1043C>T	17.37:g.39658827G>A	ENSP00000246635:p.Thr348Met	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	149	5	NM_002274	0	0	0	0	0	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	37	CCDS11396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.94|11.94	1.789143|1.789143	0.31685|0.31685	.|.	.|.	ENSG00000171401|ENSG00000171401	ENST00000157775|ENST00000246635;ENST00000336861	.|D;D	.|0.89415	.|-2.51;-2.51	4.45|4.45	4.45|4.45	0.53987|0.53987	.|Filament (1);	.|0.451868	.|0.18101	.|N	.|0.151665	.|D	.|0.93559	.|0.7944	M|M	0.77616|0.77616	2.38|2.38	0.09310|0.09310	N|N	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.999;0.999;0.999	.|D;D;D;D	.|0.67900	.|0.954;0.953;0.921;0.953	.|D	.|0.87051	.|0.2147	.|10	.|0.87932	.|D	.|0	.|.	13.5215|13.5215	0.61569|0.61569	0.0:0.0:0.7766:0.2234|0.0:0.0:0.7766:0.2234	.|.	.|336;348;348;348	.|P13646-2;A1A4E9;P13646-3;P13646	.|.;.;.;K1C13_HUMAN	.|M	-1|348	.|ENSP00000246635:T348M;ENSP00000336604:T348M	.|ENSP00000246635:T348M	.|T	-|-	.|2	.|0	KRT13|KRT13	36912353|36912353	0.254000|0.254000	0.23992|0.23992	0.463000|0.463000	0.27130|0.27130	0.221000|0.221000	0.24807|0.24807	3.044000|3.044000	0.49830|0.49830	2.460000|2.460000	0.83146|0.83146	0.478000|0.478000	0.44815|0.44815	.|ACG	.		0.632	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39658827	G	A	39658827	3	1	119	1	0	0	0	0	1	0	0	0	8471	1145	40	1	345	1	KRT13	17	39658827	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	1760239	39658827	41536383	77	10383											
CDC27	996	hgsc.bcm.edu	37	chr17	45234484	45234484	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agattctaaattcaatctgtTtaattcctgaaacagaaaat	17	14	4	6	0	3	3	1	1	2	2	4	3	4	3	1	0	1	1	1	0	7	6	rs202100614		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:45234484T>C	ENST00000066544.3	-	7	730	c.637A>G	c.(637-639)Aac>Gac	p.N213D	CDC27_ENST00000527547.1_Missense_Mutation_p.N213D|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000446365.2_Missense_Mutation_p.N152D|CDC27_ENST00000531206.1_Missense_Mutation_p.N213D	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	213					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTCAATCTGTTTAATTCCTGA	0.294																																					p.N213D		.											.	CDC27-291	0			c.A637G						.																																			SO:0001583	missense	996	exon7			ATCTGTTTAATTC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1728	protein-coding gene	gene with protein product	"anaphase promoting complex subunit 3"	116946	"cell division cycle 27", "cell division cycle 27 homolog (S. cerevisiae)"	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.637A>G	17.37:g.45234484T>C	ENSP00000066544:p.Asn213Asp	Somatic	42	1		WXS	Illumina HiSeq	Phase_I	26	2	NM_001114091	0	0	0	0	0	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.424821	0.62733	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.67698	-0.24;-0.28;-0.04;-0.24;0.82	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	N	0.24115	0.695	0.58432	D	0.999999	B;B;B;B	0.33379	0.41;0.011;0.006;0.167	B;B;B;B	0.23275	0.045;0.004;0.006;0.045	T	0.50021	-0.8876	10	0.30078	T	0.28	-15.7847	14.1506	0.65381	0.0:0.0:0.0:1.0	.	152;213;213;213	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	213;213;152;213;213	ENSP00000066544:N213D;ENSP00000434614:N213D;ENSP00000392802:N152D;ENSP00000437339:N213D;ENSP00000432105:N213D	ENSP00000066544:N213D	N	-	1	0	CDC27	42589483	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.522000	0.81844	2.227000	0.72691	0.455000	0.32223	AAC	.		0.294	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45234484	T	C	45234484	3	2	119	1	0	0	0	0	1	0	0	0	3072	1841	64	3	1907	3	CDC27	17	45234484	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	5575657	45234484	35960726	78	10384											
CDK5RAP3	80279	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	46058013	46058013	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgaggaggcagatgtcCtgtctgtgagccagttccag	8	10	15	8	0	1	4	0	3	1	1	3	5	3	5	3	2	1	2	3	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:46058013C>T	ENST00000338399.4	+	12	1238	c.1132C>T	c.(1132-1134)Ctg>Ttg	p.L378L	RP11-6N17.10_ENST00000578239.1_RNA|CDK5RAP3_ENST00000536708.2_Silent_p.L403L|CDK5RAP3_ENST00000578663.1_3'UTR	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	378					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						GGCAGATGTCCTGTCTGTGAG	0.527																																					p.L378L		.											.	CDK5RAP3-226	0			c.C1132T						.						182	184	183					17																	46058013		2092	4207	6299	SO:0001819	synonymous_variant	80279	exon12			GATGTCCTGTCTG	AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"ischemic heart CDK5 activator-binding protein C53", "LXXLL/leucine-zipper-containing ARFbinding protein"	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.1132C>T	17.37:g.46058013C>T		Somatic	231	0		WXS	Illumina HiSeq	Phase_I	213	12	NM_176096	0	0	181	197	16	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Silent	SNP	ENST00000338399.4	37	CCDS42356.1																																																																																			.		0.527	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096		T	46058013	C	T	46058013	2	4	119	1	0	0	0	0	0	0	0	1	3153	680	24	2		2	CDK5RAP3	17	46058013	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	823529	46058013	35137197	79	10385											
RANBP3	8498	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	5941706	5941706	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcagtaatttccatctTctctgtcagaatctacagaa	12	12	8	9	0	4	2	1	0	3	2	6	3	5	2	1	1	1	2	1	1	4	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:5941706T>C	ENST00000340578.6	-	5	389	c.332A>G	c.(331-333)gAa>gGa	p.E111G	RANBP3_ENST00000034275.8_Missense_Mutation_p.E43G|RANBP3_ENST00000591124.1_5'UTR|RANBP3_ENST00000439268.2_Missense_Mutation_p.E111G|RANBP3_ENST00000591092.1_Missense_Mutation_p.E43G|RANBP3_ENST00000541471.1_Intron	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3	111					intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						ATTTCCATCTTCTCTGTCAGA	0.423																																					p.E111G		.											.	RANBP3-272	0			c.A332G						.						161	152	155					19																	5941706		1912	4133	6045	SO:0001583	missense	8498	exon5			CCATCTTCTCTGT	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.332A>G	19.37:g.5941706T>C	ENSP00000341483:p.Glu111Gly	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	99	30	NM_007322	0	0	0	0	0	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	.	.	.	.	.	.	.	.	.	.	T	18.44	3.625162	0.66901	.	.	ENSG00000031823	ENST00000340578;ENST00000439268;ENST00000034275;ENST00000324807	T;T;T	0.38887	1.11;1.15;1.83	5.26	5.26	0.73747	.	0.096682	0.64402	D	0.000001	T	0.46171	0.1379	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.58268	0.97;0.982;0.982;0.97	P;P;P;P	0.60345	0.683;0.832;0.873;0.749	T	0.47114	-0.9142	10	0.54805	T	0.06	-17.7103	13.15	0.59484	0.0:0.0:0.0:1.0	.	43;43;111;111	B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4	.;.;.;RANB3_HUMAN	G	111;111;43;42	ENSP00000341483:E111G;ENSP00000404837:E111G;ENSP00000034275:E43G	ENSP00000034275:E43G	E	-	2	0	RANBP3	5892706	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.699000	0.74613	1.996000	0.58369	0.533000	0.62120	GAA	.		0.423	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		C	5941706	T	C	5941706	3	2	119	1	0	0	0	0	1	0	0	0	13061	1783	62	3	1423	3	RANBP3	19	5941706	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08		5941706	53187277	80	10386											
CLEC4M	10332	hgsc.bcm.edu	37	chr19	7830937	7830937	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agatctaccaggagctgacgGagctgaaggctgcagtgggt	10	7	16	8	1	1	3	0	2	1	1	1	5	1	5	1	4	4	4	1	4	2	1	rs59002457	byFrequency	TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:7830937G>C	ENST00000327325.5	+	4	746	c.628G>C	c.(628-630)Gag>Cag	p.E210Q	CLEC4M_ENST00000596363.1_Missense_Mutation_p.E182Q|CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000394122.2_Missense_Mutation_p.E198Q|CLEC4M_ENST00000595496.1_Intron|CLEC4M_ENST00000248228.4_Missense_Mutation_p.E188Q|CLEC4M_ENST00000334806.5_Missense_Mutation_p.E159Q|CLEC4M_ENST00000357361.2_Missense_Mutation_p.E210Q|CLEC4M_ENST00000596707.1_Missense_Mutation_p.E189Q|CLEC4M_ENST00000359059.5_Missense_Mutation_p.E166Q	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	210	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)	p.T209>?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						GGAGCTGACGGAGCTGAAGGC	0.577													C|||	107	0.0213658	0.0015	0.0605	5008	,	,		16155	0.0109		0.0368	False		,,,				2504	0.0153				p.E210Q		.											.	CLEC4M-91	1	Complex(1)	large_intestine(1)	c.G628C						.						118	96	104					19																	7830937		2192	4023	6215	SO:0001583	missense	10332	exon4			CTGACGGAGCTGA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"C-type lectin domain containing", "CD molecules"	13523	protein-coding gene	gene with protein product		605872	"CD299 antigen"	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.628G>C	19.37:g.7830937G>C	ENSP00000316228:p.Glu210Gln	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	2	NM_014257	0	0	0	0	0	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	37	CCDS12187.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.492474	0.00159	.	.	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000334806;ENST00000359059;ENST00000357361;ENST00000358690	T;T;T;T;T;T	0.21734	4.13;1.99;1.99;4.14;2.31;4.01	0.592	0.592	0.17471	.	.	.	.	.	T	0.03263	0.0095	N	0.00142	-2.005	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0;0.0;0.001	B;B;B;B;B;B;B	0.19666	0.001;0.004;0.001;0.001;0.0;0.002;0.026	T	0.40757	-0.9546	8	0.02654	T	1	.	.	.	.	rs59002457	159;182;210;198;187;182;154	B4E2Z5;B4DNV9;Q9H2X3;E7ENS9;Q9H2X3-8;Q9H2X3-9;Q9H2X3-10	.;.;CLC4M_HUMAN;.;.;.;.	Q	210;198;188;159;166;210;154	ENSP00000316228:E210Q;ENSP00000377680:E198Q;ENSP00000248228:E188Q;ENSP00000335228:E159Q;ENSP00000351954:E166Q;ENSP00000349924:E210Q	ENSP00000248228:E188Q	E	+	1	0	CLEC4M	7736937	0.000000	0.05858	0.011000	0.14972	0.006000	0.05464	-1.133000	0.03232	-0.203000	0.10251	-0.463000	0.05309	GAG	.		0.577	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257		C	7830937	G	C	7830937	3	2	119	1	0	0	0	0	1	0	0	0	3524	1175	41	4	663	4	CLEC4M	19	7830937	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	1889231	7830937	51298046	81	10387											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	210	1		WXS	Illumina HiSeq		164	1	NM_031203	0	0	0	0	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	119	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-G7-7502-01A-11D-2201-08	696530	8527467	50601516	82	10388											
DNMT1	1786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	10250732	10250732	+	Frame_Shift_Del	DEL	A	A	-																															acccgtttacctgaggaaggAaaccaccagagagtttttga																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:10250732delA	ENST00000340748.4	-	32	3983	c.3748delT	c.(3748-3750)tccfs	p.S1250fs	DNMT1_ENST00000359526.4_Frame_Shift_Del_p.S1266fs|DNMT1_ENST00000589538.1_Intron|DNMT1_ENST00000540357.1_Frame_Shift_Del_p.S1250fs			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1250	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTGAGGAAGGAAACCACCAGA	0.612																																					p.S1266fs		.											.	DNMT1-660	0			c.3796delT						.						39	40	40					19																	10250732		2203	4300	6503	SO:0001589	frameshift_variant	1786	exon33			.	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.3748delT	19.37:g.10250732delA	ENSP00000345739:p.Ser1250fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	51	10	NM_001130823	0	0	0	0	0	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Frame_Shift_Del	DEL	ENST00000340748.4	37	CCDS12228.1																																																																																			.		0.612	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		-	10250732	A	-	10250732	7	5	119	1	0	1	0	1	0	0	0	0	4686	246	9	0	1138	0	DNMT1	19	10250732	Frame_Shift_Del	DEL	A	TCGA-G7-7502-01A-11D-2201-08	1723265	10250732	48878251	83	10389											
TMED1	11018	hgsc.bcm.edu;bcgsc.ca	37	chr19	10945675	10945675	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agcctctgcccatccttcgaCctcctcgtcatcctggaggc	5	10	8	18	2	2	0	1	0	1	0	7	2	5	1	6	2	2	0	6	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:10945675C>G	ENST00000214869.2	-	3	498	c.400G>C	c.(400-402)Gtc>Ctc	p.V134L	TMED1_ENST00000588289.1_5'UTR|TMED1_ENST00000591695.1_Intron|C19orf38_ENST00000592854.1_5'Flank	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	134					cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						CATCCTTCGACCTCCTCGTCA	0.557																																					p.V134L		.											.	TMED1-155	0			c.G400C						.						160	148	152					19																	10945675		2203	4300	6503	SO:0001583	missense	11018	exon3			CTTCGACCTCCTC	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.400G>C	19.37:g.10945675C>G	ENSP00000214869:p.Val134Leu	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	144	8	NM_006858	0	0	43	43	0		Missense_Mutation	SNP	ENST00000214869.2	37	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	C	7.304	0.613556	0.14066	.	.	ENSG00000099203	ENST00000214869	T	0.40225	1.04	5.02	2.88	0.33553	GOLD (2);	0.765986	0.12157	N	0.494351	T	0.15869	0.0382	N	0.04203	-0.255	0.24941	N	0.991855	B	0.02656	0.0	B	0.11329	0.006	T	0.29822	-0.9999	10	0.09338	T	0.73	-22.7796	2.1997	0.03920	0.156:0.5179:0.1518:0.1743	.	134	Q13445	TMED1_HUMAN	L	134	ENSP00000214869:V134L	ENSP00000214869:V134L	V	-	1	0	TMED1	10806675	0.028000	0.19301	0.524000	0.27887	0.904000	0.53231	1.864000	0.39469	0.520000	0.28426	0.462000	0.41574	GTC	.		0.557	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		G	10945675	C	G	10945675	3	3	119	1	0	0	0	0	1	0	0	0	16034	507	18	4	291	4	TMED1	19	10945675	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	694943	10945675	48183308	84	10390											
ZNF101	94039	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19789581	19789581	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaatctgtaccaaaacctGgggattaagctaaggtaatc	15	9	10	7	0	1	1	0	0	1	1	2	3	1	2	2	3	3	3	2	3	7	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:19789581G>C	ENST00000592502.1	+	3	287	c.177G>C	c.(175-177)ctG>ctC	p.L59L	ZNF101_ENST00000444249.2_Missense_Mutation_p.W58S|ZNF101_ENST00000415784.2_5'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						ACCAAAACCTGGGGATTAAGC	0.333																																					p.L59L		.											.	ZNF101-92	0			c.G177C						.						45	45	45					19																	19789581		2203	4300	6503	SO:0001819	synonymous_variant	94039	exon3			AAACCTGGGGATT	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"Zinc fingers, C2H2-type", "-"	12881	protein-coding gene	gene with protein product		603983	"zinc finger protein 101 (Y2)"			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.177G>C	19.37:g.19789581G>C		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	42	8	NM_033204	0	0	0	0	0	C9JU83|Q0VDG9	Silent	SNP	ENST00000592502.1	37	CCDS32971.1																																																																																			.		0.333	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		C	19789581	G	C	19789581	2	2	119	1	0	0	0	0	0	0	0	1	17746	1335	47	4		4	ZNF101	19	19789581	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	8843906	19789581	39339402	85	10391											
ZFP14	57677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	36831515	36831515	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagctgtgagtaactactaaAggtcttccaacattccatac	14	11	6	10	0	1	1	0	1	1	0	3	1	3	1	2	1	5	2	2	1	7	6			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:36831515A>C	ENST00000270001.7	-	5	1328	c.1213T>G	c.(1213-1215)Ttt>Gtt	p.F405V		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	405					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)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					TAACTACTAAAGGTCTTCCAA	0.408																																					p.F405V		.											.	ZFP14-91	0			c.T1213G						.						115	106	109					19																	36831515		2203	4300	6503	SO:0001583	missense	57677	exon5			TACTAAAGGTCTT	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"Zinc fingers, C2H2-type", "-"	29312	protein-coding gene	gene with protein product			"zinc finger protein 14 homolog (mouse)"			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.1213T>G	19.37:g.36831515A>C	ENSP00000270001:p.Phe405Val	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	118	34	NM_020917	0	0	3	3	0	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	a	18.65	3.668655	0.67814	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.46063	0.88	3.99	3.99	0.46301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000284	T	0.67822	0.2934	M	0.88181	2.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.74919	-0.3500	10	0.87932	D	0	.	12.2842	0.54783	1.0:0.0:0.0:0.0	.	405;405	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	V	405	ENSP00000270001:F405V	ENSP00000270001:F405V	F	-	1	0	ZFP14	41523355	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	5.755000	0.68750	1.794000	0.52575	0.523000	0.50628	TTT	.		0.408	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		C	36831515	A	C	36831515	3	2	119	1	0	0	0	0	1	0	0	0	17671	72	3	5	392	5	ZFP14	19	36831515	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	17041934	36831515	22297468	86	10392											
ZNF776	284309	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	58265245	58265245	+	Frame_Shift_Del	DEL	T	T	-																															aaattcactagcaaaagtaaTagttttaataatcatcaggg																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:58265245delT	ENST00000317178.5	+	3	1010	c.747delT	c.(745-747)aatfs	p.N249fs		NM_173632.3	NP_775903.3	Q68DI1	ZN776_HUMAN	zinc finger protein 776	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|kidney(13)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0256)		GCAAAAGTAATAGTTTTAATA	0.413																																					p.N249fs		.											.	ZNF776-91	0			c.747delT						.						63	64	64					19																	58265245		2203	4300	6503	SO:0001589	frameshift_variant	284309	exon3			.	AK095607	CCDS12962.2	19q13.43	2013-01-08			ENSG00000152443	ENSG00000152443		"Zinc fingers, C2H2-type", "-"	26765	protein-coding gene	gene with protein product							Standard	NM_173632		Approved	FLJ38288		Q68DI1	OTTHUMG00000156943	ENST00000317178.5:c.747delT	19.37:g.58265245delT	ENSP00000321812:p.Asn249fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	65	17	NM_173632	0	0	0	0	0	Q6ZS36|Q8N968	Frame_Shift_Del	DEL	ENST00000317178.5	37	CCDS12962.2																																																																																			.		0.413	ZNF776-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346722.2	NM_173632		-	58265245	T	-	58265245	7	5	119	1	0	1	0	1	0	0	0	0	18181	1403	49	0	757	0	ZNF776	19	58265245	Frame_Shift_Del	DEL	T	TCGA-G7-7502-01A-11D-2201-08	21433730	58265245	863738	87	10393											
CHGB	1114	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr20	5903930	5903930	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacctcagagtgaggagagTtgggatgaggaggacaagag	14	5	18	4	0	1	6	1	2	0	4	1	10	1	9	1	4	0	1	1	4	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr20:5903930T>C	ENST00000378961.4	+	4	1344	c.1140T>C	c.(1138-1140)agT>agC	p.S380S		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	380						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GTGAGGAGAGTTGGGATGAGG	0.547																																					p.S380S		.											.	CHGB-96	0			c.T1140C						.						114	113	113					20																	5903930		2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			GGAGAGTTGGGAT		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"secretogranin B"	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1140T>C	20.37:g.5903930T>C		Somatic	202	2		WXS	Illumina HiSeq	Phase_I	201	48	NM_001819	0	0	7	9	2	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	37	CCDS13092.1																																																																																			.		0.547	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819		C	5903930	T	C	5903930	2	2	119	1	0	0	0	0	0	0	0	1	3345	1722	60	3		3	CHGB	20	5903930	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08		5903930	57121590	88	10394											
PLUNC	51297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31825663	31825663	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gagtcccacaggtcttgcagGaagcttgacaaatggtgagt	11	9	13	8	0	1	2	0	2	1	0	2	4	2	3	1	3	2	2	1	3	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr20:31825663G>A	ENST00000354297.4	+	2	217	c.146G>A	c.(145-147)gGa>gAa	p.G49E	BPIFA1_ENST00000375413.4_Missense_Mutation_p.G49E|BPIFA1_ENST00000375422.2_Missense_Mutation_p.G49E	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	49					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										GGTCTTGCAGGAAGCTTGACA	0.557																																					p.G49E		.											.	.	0			c.G146A						.						84	78	80					20																	31825663		2203	4300	6503	SO:0001583	missense	51297	exon2			TTGCAGGAAGCTT	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.146G>A	20.37:g.31825663G>A	ENSP00000346251:p.Gly49Glu	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	104	39	NM_016583	0	0	0	0	0	A8K9R3|E1P5M9|Q9NZT0	Missense_Mutation	SNP	ENST00000354297.4	37	CCDS13217.1	.	.	.	.	.	.	.	.	.	.	G	9.833	1.189055	0.21954	.	.	ENSG00000198183	ENST00000375422;ENST00000354297;ENST00000375413;ENST00000544328	T;T;T	0.11385	2.78;2.78;2.78	5.11	-0.843	0.10744	.	0.563694	0.17374	N	0.176573	T	0.06826	0.0174	L	0.39245	1.2	0.09310	N	1	B	0.24882	0.113	B	0.23419	0.046	T	0.43702	-0.9375	10	0.02654	T	1	0.4054	9.72	0.40297	0.0869:0.5908:0.3223:0.0	.	49	Q9NP55	BPIA1_HUMAN	E	49;49;49;35	ENSP00000364571:G49E;ENSP00000346251:G49E;ENSP00000364562:G49E	ENSP00000346251:G49E	G	+	2	0	BPIFA1	31289324	0.316000	0.24580	0.019000	0.16419	0.005000	0.04900	0.387000	0.20718	0.087000	0.17167	0.655000	0.94253	GGA	.		0.557	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		A	31825663	G	A	31825663	3	1	119	1	0	0	0	0	1	0	0	0	12141	1174	41	2	148	2	PLUNC	20	31825663	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	25921733	31825663	31199857	89	10395											
TUBB1	81027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	57599037	57599037	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggtggagccctacaacgcGgttctgtctatccaccagct	7	10	11	13	2	2	0	0	0	2	0	3	1	3	1	3	3	4	2	3	3	3	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr20:57599037G>A	ENST00000217133.1	+	4	824	c.555G>A	c.(553-555)gcG>gcA	p.A185A		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	185					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A185A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	CCTACAACGCGGTTCTGTCTA	0.517																																					p.A185A		.											.	TUBB1-227	1	Substitution - coding silent(1)	lung(1)	c.G555A						.						127	121	123					20																	57599037		2203	4300	6503	SO:0001819	synonymous_variant	81027	exon4			CAACGCGGTTCTG	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.555G>A	20.37:g.57599037G>A		Somatic	195	1		WXS	Illumina HiSeq	Phase_I	196	25	NM_030773	0	0	1	1	0		Silent	SNP	ENST00000217133.1	37	CCDS13475.1																																																																																			.		0.517	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		A	57599037	G	A	57599037	2	1	119	1	0	0	0	0	0	0	0	1	16786	1103	39	1		1	TUBB1	20	57599037	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	25773374	57599037	5426483	90	10396											
C21orf7	56911	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	30547133	30547133	+	Frame_Shift_Del	DEL	T	T	-																															tgacggaggagaatcggacgTtgaggttggcccagtctcaa																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr21:30547133delT	ENST00000399947.2	+	9	926	c.649delT	c.(649-651)ttgfs	p.L217fs	MAP3K7CL_ENST00000286791.5_3'UTR|MAP3K7CL_ENST00000339024.4_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000545939.1_Frame_Shift_Del_p.L111fs|MAP3K7CL_ENST00000399926.1_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000399928.1_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000399925.1_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000341618.4_Frame_Shift_Del_p.L217fs|MAP3K7CL_ENST00000399935.2_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000399934.1_Frame_Shift_Del_p.L117fs	NM_020152.2	NP_064537.1	P57077	M3KCL_HUMAN	MAP3K7 C-terminal like	217						cytosol (GO:0005829)|nucleus (GO:0005634)											GAATCGGACGTTGAGGTTGGC	0.488																																					p.L217X		.											.	.	0			c.649delT						.						115	106	109					21																	30547133		2203	4300	6503	SO:0001589	frameshift_variant	56911	exon9			.	AF269161	CCDS13584.1, CCDS68182.1, CCDS74775.1	21q22.3	2013-02-22	2013-02-22	2013-02-22	ENSG00000156265	ENSG00000156265			16457	protein-coding gene	gene with protein product		611110	"chromosome 21 open reading frame 7"	C21orf7			Standard	NM_020152		Approved	TAKL, TAK1L, TAKL-1, TAKL-2, TAKL-4	uc002ynf.3	P57077	OTTHUMG00000078806	ENST00000399947.2:c.649delT	21.37:g.30547133delT	ENSP00000382828:p.Leu217fs	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	65	19	NM_020152	0	0	0	0	0	D3DSE0|Q8TCL9	Nonsense_Mutation	DEL	ENST00000399947.2	37	CCDS13584.1																																																																																			.		0.488	MAP3K7CL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000171865.2	NM_020152		-	30547133	T	-	30547133	7	5	119	1	0	1	0	1	0	0	0	0	2138	1722	60	0	675	0	C21orf7	21	30547133	Frame_Shift_Del	DEL	T	TCGA-G7-7502-01A-11D-2201-08		30547133	17582762	91	10397											
COL6A1	1291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47423886	47423886	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaggccctgctccgcggtGtcttccaccagacagtctcc	6	8	9	18	2	2	1	0	0	2	1	5	1	4	1	6	2	1	1	6	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr21:47423886G>A	ENST00000361866.3	+	35	3160	c.3046G>A	c.(3046-3048)Gtc>Atc	p.V1016I	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	1016	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GCTCCGCGGTGTCTTCCACCA	0.662																																					p.V1016I		.											.	COL6A1-91	0			c.G3046A						.						56	58	58					21																	47423886		2203	4300	6503	SO:0001583	missense	1291	exon35			CGCGGTGTCTTCC	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.3046G>A	21.37:g.47423886G>A	ENSP00000355180:p.Val1016Ile	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	150	63	NM_001848	0	1	160	309	148	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.958303	0.73902	.	.	ENSG00000142156	ENST00000361866	D	0.91464	-2.85	4.83	4.83	0.62350	von Willebrand factor, type A (1);	0.000000	0.64402	D	0.000001	D	0.90376	0.6988	L	0.57536	1.79	0.58432	D	0.99999	D	0.52996	0.957	P	0.49752	0.621	D	0.88044	0.2783	10	0.08381	T	0.77	-40.0397	17.9387	0.89020	0.0:0.0:1.0:0.0	.	1016	P12109	CO6A1_HUMAN	I	1016	ENSP00000355180:V1016I	ENSP00000355180:V1016I	V	+	1	0	COL6A1	46248314	1.000000	0.71417	0.957000	0.39632	0.304000	0.27724	5.907000	0.69908	2.232000	0.73038	0.596000	0.82720	GTC	.		0.662	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		A	47423886	G	A	47423886	3	1	119	1	0	0	0	0	1	0	0	0	3705	1377	48	2	3184	2	COL6A1	21	47423886	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	16876753	47423886	706009	92	10398											
ARVCF	421	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	19966432	19966432	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtccacacctcaggcagcccGacgtgttcttgaagacagtt	9	9	10	13	2	2	2	1	1	1	1	3	3	3	2	3	1	1	3	3	1	1	3	rs542020914	byFrequency	TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:19966432G>A	ENST00000263207.3	-	7	1859	c.1568C>T	c.(1567-1569)tCg>tTg	p.S523L	ARVCF_ENST00000487793.1_5'Flank|ARVCF_ENST00000406522.1_Missense_Mutation_p.S460L|ARVCF_ENST00000401994.1_Missense_Mutation_p.S460L|ARVCF_ENST00000406259.1_Missense_Mutation_p.S523L|ARVCF_ENST00000344269.3_Missense_Mutation_p.S460L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	523					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CAGGCAGCCCGACGTGTTCTT	0.622													G|||	2	0.000399361	0	0	5008	,	,		20460	0		0	False		,,,				2504	0.002				p.S523L		.											.	ARVCF-91	0			c.C1568T						.						136	91	106					22																	19966432		2203	4300	6503	SO:0001583	missense	421	exon7			CAGCCCGACGTGT		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1568C>T	22.37:g.19966432G>A	ENSP00000263207:p.Ser523Leu	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	42	8	NM_001670	0	0	0	0	0	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930425	0.92389	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	4.43	4.43	0.53597	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.64811	0.2632	M	0.75777	2.31	0.80722	D	1	P;D	0.89917	0.906;1.0	P;D	0.79108	0.475;0.992	T	0.66913	-0.5803	9	.	.	.	-14.4434	17.6161	0.88068	0.0:0.0:1.0:0.0	.	523;45	O00192;E7EV58	ARVC_HUMAN;.	L	523;460;460;460;523	ENSP00000263207:S523L;ENSP00000342042:S460L;ENSP00000384341:S460L;ENSP00000384732:S460L;ENSP00000385444:S523L	.	S	-	2	0	ARVCF	18346432	1.000000	0.71417	0.164000	0.22755	0.982000	0.71751	7.455000	0.80726	2.472000	0.83506	0.563000	0.77884	TCG	.		0.622	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19966432	G	A	19966432	3	1	119	1	0	0	0	0	1	0	0	0	1004	1059	37	1	1372	1	ARVCF	22	19966432	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		19966432	31338134	93	10399											
C22orf13	83606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24938994	24938994	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcagctgtccaagtagacaaAgaggatgtcctcatctgtgc	11	10	10	10	0	3	2	2	0	1	2	5	3	5	3	2	1	2	2	2	1	3	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:24938994A>T	ENST00000407471.3	-	6	893	c.703T>A	c.(703-705)Ttt>Att	p.F235I	GUCD1_ENST00000435822.1_Missense_Mutation_p.F234I|GUCD1_ENST00000404664.3_Missense_Mutation_p.F290I|GUCD1_ENST00000402766.1_3'UTR|GUCD1_ENST00000490922.1_Intron|GUCD1_ENST00000447813.2_3'UTR	NM_001284251.1	NP_001271180.1	Q96NT3	GUCD1_HUMAN	guanylyl cyclase domain containing 1	235																	AAGTAGACAAAGAGGATGTCC	0.637																																					p.F235I		.											.	.	0			c.T703A						.						216	165	182					22																	24938994		2203	4300	6503	SO:0001583	missense	83606	exon6			AGACAAAGAGGAT	AK054681	CCDS33621.1, CCDS63426.1, CCDS63427.1, CCDS74831.1, CCDS74832.1, CCDS74833.1	22q11.2	2012-11-13	2012-11-13	2012-11-13	ENSG00000138867	ENSG00000138867			14237	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 13"	C22orf13		12477932	Standard	XM_005261761		Approved	MGC1842, LLN4	uc003aah.2	Q96NT3	OTTHUMG00000150728	ENST00000407471.3:c.703T>A	22.37:g.24938994A>T	ENSP00000386076:p.Phe235Ile	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	106	32	NM_031444	0	0	36	67	31	B5MCB8|B5MCL7|Q96Q79|Q9BU32	Missense_Mutation	SNP	ENST00000407471.3	37	CCDS33621.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.981630	0.93044	.	.	ENSG00000138867	ENST00000407471;ENST00000435822;ENST00000404664	.	.	.	5.37	5.37	0.77165	.	0.104223	0.64402	D	0.000003	T	0.70806	0.3266	M	0.69823	2.125	0.80722	D	1	P;P;P;P	0.47409	0.811;0.885;0.895;0.477	P;P;P;B	0.51324	0.489;0.666;0.629;0.327	T	0.72693	-0.4216	9	0.45353	T	0.12	-8.7496	14.5939	0.68392	1.0:0.0:0.0:0.0	.	290;298;191;235	B5MCL7;B4DH83;B4DL90;Q96NT3	.;.;.;CV013_HUMAN	I	235;234;290	.	ENSP00000381297:F234I	F	-	1	0	C22orf13	23268994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.244000	0.78228	2.037000	0.60232	0.456000	0.33151	TTT	.		0.637	GUCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319819.1	NM_031444		T	24938994	A	T	24938994	3	4	119	1	0	0	0	0	1	0	0	0	2141	72	3	5	23	5	C22orf13	22	24938994	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	4972562	24938994	26365572	94	10400											
OSM	5008	hgsc.bcm.edu	37	chr22	30660245	30660245	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttctccaagtcctcgatgTtcagcccagacctctccaaa	9	10	6	16	1	3	1	1	0	2	1	7	2	4	1	5	0	1	2	5	0	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:30660245T>C	ENST00000215781.2	-	3	426	c.386A>G	c.(385-387)aAc>aGc	p.N129S	OSM_ENST00000403463.1_3'UTR|OSM_ENST00000403389.1_Missense_Mutation_p.N108S	NM_020530.4	NP_065391.1	P13725	ONCM_HUMAN	oncostatin M	129					behavioral response to pain (GO:0048266)|cell proliferation (GO:0008283)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|peripheral nervous system development (GO:0007422)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|response to heat (GO:0009408)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	extracellular space (GO:0005615)|oncostatin-M receptor complex (GO:0005900)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|oncostatin-M receptor binding (GO:0005147)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|skin(3)	11			Epithelial(10;0.206)			GTCCTCGATGTTCAGCCCAGA	0.602																																					p.N129S		.											.	OSM-493	0			c.A386G						.						49	40	43					22																	30660245		2203	4300	6503	SO:0001583	missense	5008	exon3			TCGATGTTCAGCC	AF129855	CCDS13873.1	22q12.2	2011-07-21			ENSG00000099985	ENSG00000099985			8506	protein-coding gene	gene with protein product		165095				1717982	Standard	NM_020530		Approved	MGC20461	uc003ahb.3	P13725	OTTHUMG00000150913	ENST00000215781.2:c.386A>G	22.37:g.30660245T>C	ENSP00000215781:p.Asn129Ser	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_020530	0	0	20	20	0	Q6FHP8|Q9UCP6	Missense_Mutation	SNP	ENST00000215781.2	37	CCDS13873.1	.	.	.	.	.	.	.	.	.	.	T	5.822	0.336000	0.11013	.	.	ENSG00000099985	ENST00000215781;ENST00000403389	T	0.50001	0.76	0.559	-0.762	0.11034	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	.	.	.	.	T	0.25044	0.0608	L	0.29908	0.895	0.09310	N	1	P	0.36909	0.573	B	0.31442	0.13	T	0.17471	-1.0368	8	0.13108	T	0.6	.	.	.	.	.	129	P13725	ONCM_HUMAN	S	129;108	ENSP00000215781:N129S	ENSP00000215781:N129S	N	-	2	0	OSM	28990245	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.028000	0.13644	-0.427000	0.07350	-0.441000	0.05720	AAC	.		0.602	OSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320512.1	NM_020530		C	30660245	T	C	30660245	3	2	119	1	0	0	0	0	1	0	0	0	11317	1725	60	3	376	3	OSM	22	30660245	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	5721251	30660245	20644321	95	10401											
CSF2RB	1439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37334445	37334446	+	Missense_Mutation	DNP	GC	GC	TT																															aagcccccaggccaggctgtGccccaggtgcccgtcattca																								rs554053520		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:37334445_37334446GC>TT	ENST00000403662.3	+	14	2817_2818	c.2595_2596GC>TT	c.(2593-2598)gtGCcc>gtTTcc	p.P866S	CSF2RB_ENST00000262825.5_Missense_Mutation_p.P872S|CSF2RB_ENST00000406230.1_Missense_Mutation_p.P872S|CSF2RB_ENST00000536485.1_Missense_Mutation_p.P813S			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	866					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GCCAGGCTGTGCCCCAGGTGCC	0.589																																					p.P872S		.											.	CSF2RB	0			c.C2596T						.																																			SO:0001583	missense	1439	exon14			GCTGTGCCCCAGG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	Exception_encountered	22.37:g.37334445_37334446delinsTT	ENSP00000384053:p.Pro866Ser	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	165	38		0	0	0	0	0	Q5JZI1|Q6ICE0	Missense_Mutation	DNP	ENST00000403662.3	37	CCDS13936.1																																																																																			.		0.589	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		TT	37334446	GC	TT	37334445	3	4	119	1	0	0	0	0	1	0	0	0	3941	1306	46	4	2645	4	CSF2RB	22	37334445	Missense_Mutation	DNP	GC	TCGA-G7-7502-01A-11D-2201-08	6674200	37334445	13970121	96	10402											
KDM5D	8284	hgsc.bcm.edu	37	chrY	21901510	21901510	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtggggcttgtattccttAtcttttacctcattgtcaaa	7	18	7	9	0	3	0	2	0	1	0	4	0	4	0	2	2	1	2	2	2	4	7			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chrY:21901510A>C	ENST00000317961.4	-	6	832	c.561T>G	c.(559-561)gaT>gaG	p.D187E	KDM5D_ENST00000541639.1_Missense_Mutation_p.D187E|KDM5D_ENST00000382806.2_Missense_Mutation_p.D130E	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	187					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	TGTATTCCTTATCTTTTACCT	0.413																																					p.D187E		.											.	KDM5D-560	0			c.T561G						.						97	112	108					Y																	21901510		597	1932	2529	SO:0001583	missense	8284	exon6			TTCCTTATCTTTT	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11115	protein-coding gene	gene with protein product		426000	"Jumonji, AT rich interactive domain 1D (RBP2-like)", "Smcy homolog, Y-linked (mouse)", "jumonji, AT rich interactive domain 1D"	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.561T>G	Y.37:g.21901510A>C	ENSP00000322408:p.Asp187Glu	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	15	5	NM_001146705	0	0	0	4	4	A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Missense_Mutation	SNP	ENST00000317961.4	37	CCDS14794.1																																																																																			.		0.413	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		C	21901510	A	C	21901510	3	2	119	1	0	0	0	0	1	0	0	0	8157	446	16	5	4243	5	KDM5D	24	21901510	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		21901510	37472056	97	10403											
PAQR7	164091	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	26189753	26189755	+	In_Frame_Del	DEL	TTG	TTG	-																															ggcctggtttctggatgtacTtgttatagcaggagccaatg																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:26189753_26189755delTTG	ENST00000374296.3	-	2	1242_1244	c.576_578delCAA	c.(574-579)aacaag>aag	p.N192del	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	192					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			breast(3)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGATGTACTTGTTATAGCAGG	0.581																																					p.192_193del	Esophageal Squamous(111;1206 1556 18433 19151 38418)	.											.	PAQR7-71	0			c.576_578del						.																																			SO:0001651	inframe_deletion	164091	exon2			.		CCDS267.1	1p35.3	2012-08-10			ENSG00000182749	ENSG00000182749			23146	protein-coding gene	gene with protein product	"membrane progestin receptor alpha"	607779					Standard	NM_178422		Approved	mSR, MPRA	uc001bkx.3	Q86WK9	OTTHUMG00000007373	ENST00000374296.3:c.576_578delCAA	1.37:g.26189753_26189755delTTG	ENSP00000363414:p.Asn192del	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	105	44	NM_178422	0	0	0	0	0	A2A2D3|Q5XKF9|Q86VE4	In_Frame_Del	DEL	ENST00000374296.3	37	CCDS267.1																																																																																			.		0.581	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422		-	26189755	TTG	-	26189753	7	5	120	1	0	1	0	1	0	0	0	0	11466	1609	56	0	466	0	PAQR7	1	26189753	In_Frame_Del	DEL	TTG	TCGA-G7-A4TM-01A-11D-A31X-10		26189753	223060868	1	10404											
WASF2	10163	hgsc.bcm.edu	37	chr1	27736340	27736340	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccccggaggaggaggaggAgggggaggaggaggtgctcc	8	2	24	7	1	0	0	0	0	0	0	1	8	1	8	3	11	1	1	3	11	0	0	rs71584884		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:27736340A>G	ENST00000430629.2	-	8	1400	c.1185T>C	c.(1183-1185)ccT>ccC	p.P395P	WASF2_ENST00000536657.1_Intron	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	395	Poly-Pro.				actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		gaggaggaggagggggaggag	0.642																																					p.P395P		.											.	WASF2-228	0			c.T1185C						.						51	53	52					1																	27736340		2203	4300	6503	SO:0001819	synonymous_variant	10163	exon8			AGGAGGAGGGGGA	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.1185T>C	1.37:g.27736340A>G		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	132	7	NM_006990	0	0	25	25	0	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	37	CCDS304.1																																																																																			A|0.500;T|0.500		0.642	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		G	27736340	A	G	27736340	2	3	120	1	0	0	0	0	0	0	0	1	17286	291	11	3		3	WASF2	1	27736340	Silent	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	1546587	27736340	221514281	2	10405											
AHDC1	27245	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	27876672	27876673	+	Frame_Shift_Del	DEL	GT	GT	-																															ggaagtgggagatgctctggGtgtcgggggcctggtgcacc																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:27876672_27876673delGT	ENST00000247087.5	-	5	2550_2551	c.1954_1955delAC	c.(1954-1956)accfs	p.T652fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.T652fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	652							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GATGCTCTGGGTGTCGGGGGCC	0.703																																					p.652_652del		.											.	AHDC1-90	0			c.1954_1955del						.																																			SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.1954_1955delAC	1.37:g.27876674_27876675delGT	ENSP00000247087:p.Thr652fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	41	16	NM_001029882	0	0	0	0	0	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	37	CCDS30652.1																																																																																			.		0.703	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27876673	GT	-	27876672	7	5	120	1	0	1	0	1	0	0	0	0	412	1261	44	0	2860	0	AHDC1	1	27876672	Frame_Shift_Del	DEL	GT	TCGA-G7-A4TM-01A-11D-A31X-10	140332	27876672	221373949	3	10406											
FOXJ3	22887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	42744042	42744042	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaaccactgccagcctctcTataatatgggaagttatcac	12	10	6	13	0	2	0	1	0	1	0	3	1	2	1	4	1	3	1	4	1	6	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:42744042T>A	ENST00000372572.1	-	5	657	c.346A>T	c.(346-348)Aga>Tga	p.R116*	FOXJ3_ENST00000545068.1_Nonsense_Mutation_p.R116*|FOXJ3_ENST00000372573.1_Nonsense_Mutation_p.R116*|FOXJ3_ENST00000361346.1_Nonsense_Mutation_p.R116*|FOXJ3_ENST00000361776.1_Nonsense_Mutation_p.R116*	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	116					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCAGCCTCTCTATAATATGGG	0.313																																					p.R116X		.											.	FOXJ3-228	0			c.A346T						.						70	71	70					1																	42744042		2203	4300	6503	SO:0001587	stop_gained	22887	exon3			CCTCTCTATAATA	AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"Forkhead boxes"	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.346A>T	1.37:g.42744042T>A	ENSP00000361653:p.Arg116*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	88	34	NM_001198852	0	0	4	4	0	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Nonsense_Mutation	SNP	ENST00000372572.1	37	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	T	40	8.346624	0.98769	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886;ENST00000454417	.	.	.	5.48	5.48	0.80851	.	0.066191	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.527	0.61601	0.0:0.0:0.0:1.0	.	.	.	.	X	116;116;116;116;116;116;73	.	ENSP00000354620:R116X	R	-	1	2	FOXJ3	42516629	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.242000	0.72376	2.082000	0.62665	0.374000	0.22700	AGA	.		0.313	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947		A	42744042	T	A	42744042	4	1	120	1	0	0	0	0	0	1	0	0	6032	1530	53	5	1566	5	FOXJ3	1	42744042	Nonsense_Mutation	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10	14867370	42744042	206506579	4	10407											
RHOC	389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	113244309	113244309	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgatccggttcgccatgtcCcggccttcctcagaccgaac	6	9	9	17	4	1	2	1	1	0	1	5	3	4	2	6	2	1	1	6	2	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:113244309C>G	ENST00000285735.2	-	6	1644	c.435G>C	c.(433-435)cgG>cgC	p.R145R	RHOC_ENST00000369633.2_Silent_p.R145R|RHOC_ENST00000369637.1_Silent_p.R145R|RHOC_ENST00000369636.2_Missense_Mutation_p.G125A|RHOC_ENST00000369638.2_Silent_p.R145R|RHOC_ENST00000369632.2_Silent_p.R145R|RHOC_ENST00000369642.3_Silent_p.R145R|RHOC_ENST00000339083.7_Silent_p.R145R|RP11-426L16.10_ENST00000471038.2_5'Flank			P08134	RHOC_HUMAN	ras homolog family member C	145					apical junction assembly (GO:0043297)|axon guidance (GO:0007411)|cytokinesis (GO:0000910)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCGCCATGTCCCGGCCTTCCT	0.572																																					p.R145R		.											.	RHOC-848	0			c.G435C						.						107	95	99					1																	113244309		2203	4300	6503	SO:0001819	synonymous_variant	389	exon6			CATGTCCCGGCCT	BC052808	CCDS854.1	1p13.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000155366	ENSG00000155366			669	protein-coding gene	gene with protein product		165380	"ras homolog gene family, member C"	ARH9, ARHC		3283705	Standard	NM_001042678		Approved	RhoC	uc001ecp.1	P08134	OTTHUMG00000011905	ENST00000285735.2:c.435G>C	1.37:g.113244309C>G		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	153	59	NM_175744	0	1	255	429	173	B3KSW1|Q6ICN3	Silent	SNP	ENST00000285735.2	37	CCDS854.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.706628	0.30232	.	.	ENSG00000155366	ENST00000369636	T	0.71222	-0.55	5.13	2.24	0.28232	.	0.480686	0.15126	U	0.279101	T	0.46347	0.1388	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37911	-0.9685	7	0.25106	T	0.35	-8.222	4.4249	0.11498	0.0:0.4765:0.1577:0.3659	.	.	.	.	A	125	ENSP00000358650:G125A	ENSP00000358650:G125A	G	-	2	0	RHOC	113045832	0.998000	0.40836	1.000000	0.80357	0.865000	0.49528	0.626000	0.24492	0.196000	0.20367	-1.254000	0.01491	GGG	.		0.572	RHOC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032904.2	NM_175744		G	113244309	C	G	113244309	2	3	120	1	0	0	0	0	0	0	0	1	13368	610	22	4		4	RHOC	1	113244309	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	70500267	113244309	136006312	5	10408											
IVL	3713	broad.mit.edu	37	chr1	152882868	152882868	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctggagctcccagagcagCaggaggggcagctggagctc	9	4	17	11	0	0	1	0	0	0	1	2	4	1	4	1	5	6	7	1	5	0	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:152882868C>G	ENST00000368764.3	+	2	659	c.595C>G	c.(595-597)Cag>Gag	p.Q199E	IVL_ENST00000392667.2_Missense_Mutation_p.Q53E			P07476	INVO_HUMAN	involucrin	199	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cccagagcagcaggaggggca	0.692																																					p.Q199E													.	IVL-93	0			c.C595G						.						1	2	2					1																	152882868		780	1755	2535	SO:0001583	missense	3713	exon2			GAGCAGCAGGAGG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.595C>G	1.37:g.152882868C>G	ENSP00000357753:p.Gln199Glu	Somatic	121	2		WXS	Illumina HiSeq	Phase_I	100	8	NM_005547	0	0	0	0	0	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	C	0.071	-1.202827	0.01581	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.12255	3.0;2.7	3.41	2.47	0.30058	.	.	.	.	.	T	0.10252	0.0251	L	0.59436	1.845	0.09310	N	1	D	0.63046	0.992	P	0.60068	0.868	T	0.06215	-1.0839	9	0.07482	T	0.82	.	10.3906	0.44166	0.0:0.7838:0.2162:0.0	.	199	P07476	INVO_HUMAN	E	199;53	ENSP00000357753:Q199E;ENSP00000376435:Q53E	ENSP00000357753:Q199E	Q	+	1	0	IVL	151149492	0.000000	0.05858	0.015000	0.15790	0.021000	0.10359	0.910000	0.28571	0.766000	0.33244	0.430000	0.28490	CAG	.		0.692	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		G	152882868	C	G	152882868	3	3	120	1	0	0	0	0	1	0	0	0	7950	711	25	4	597	4	IVL	1	152882868	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	39638559	152882868	96367753	6	10409											
CENPF	1063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214815619	214815619	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgaaatactgcaggctgAaaagtatgaactcgtaactg	15	10	10	6	1	0	3	0	3	0	0	1	3	0	3	0	1	4	4	0	1	7	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:214815619A>T	ENST00000366955.3	+	12	4106	c.3938A>T	c.(3937-3939)gAa>gTa	p.E1313V		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CTGCAGGCTGAAAAGTATGAA	0.393																																					p.E1313V	Colon(80;575 1284 11000 14801 43496)	.											.	CENPF-567	0			c.A3938T						.						76	76	76					1																	214815619		2203	4300	6503	SO:0001583	missense	1063	exon12			AGGCTGAAAAGTA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3938A>T	1.37:g.214815619A>T	ENSP00000355922:p.Glu1313Val	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	169	81	NM_016343	0	0	0	0	0	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694781	0.30052	.	.	ENSG00000117724	ENST00000366955	T	0.28255	1.62	4.77	3.61	0.41365	.	0.207947	0.24020	N	0.042296	T	0.51126	0.1656	.	.	.	0.34578	D	0.714136	D	0.89917	1.0	D	0.71414	0.973	T	0.63980	-0.6514	9	0.87932	D	0	.	9.1524	0.36971	0.9148:0.0:0.0852:0.0	.	1313	P49454	CENPF_HUMAN	V	1313	ENSP00000355922:E1313V	ENSP00000355922:E1313V	E	+	2	0	CENPF	212882242	1.000000	0.71417	0.077000	0.20336	0.052000	0.14988	5.178000	0.65037	0.631000	0.30412	0.418000	0.28097	GAA	.		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214815619	A	T	214815619	3	4	120	1	0	0	0	0	1	0	0	0	3237	246	9	5	3980	5	CENPF	1	214815619	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	61932751	214815619	34435002	7	10410											
SLC3A1	6519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44539791	44539791	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatgtcaacgtgatgaacAtgcttcttttcacactccct	10	14	6	11	1	3	2	2	2	1	0	4	2	4	2	1	0	3	2	1	0	3	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr2:44539791A>G	ENST00000260649.6	+	8	1475	c.1399A>G	c.(1399-1401)Atg>Gtg	p.M467V	SLC3A1_ENST00000409229.3_Missense_Mutation_p.M467V|SLC3A1_ENST00000409741.1_Missense_Mutation_p.M467V|SLC3A1_ENST00000409294.1_Missense_Mutation_p.M87V|SLC3A1_ENST00000409380.1_Missense_Mutation_p.M189V|SLC3A1_ENST00000409740.3_Missense_Mutation_p.M98V|SLC3A1_ENST00000409387.1_Missense_Mutation_p.M467V	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	467			M -> K (in CSNU). {ECO:0000269|PubMed:8054986}.|M -> T (in CSNU; loss of 80% of amino acid transport activity). {ECO:0000269|PubMed:11748844, ECO:0000269|PubMed:12234283, ECO:0000269|PubMed:8054986, ECO:0000269|PubMed:9186880}.		amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	CGTGATGAACATGCTTCTTTT	0.408																																					p.M467V		.											.	SLC3A1-90	0			c.A1399G						.						141	128	132					2																	44539791		2203	4300	6503	SO:0001583	missense	6519	exon8			ATGAACATGCTTC		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1399A>G	2.37:g.44539791A>G	ENSP00000260649:p.Met467Val	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	121	45	NM_000341	1	0	213	422	208	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	37	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.955494	0.53293	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000409741;ENST00000409229;ENST00000541289;ENST00000409380;ENST00000409294;ENST00000409740	D;D;D;D;D;D;D	0.99454	-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92	5.82	4.64	0.57946	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.036710	0.85682	D	0.000000	D	0.98710	0.9567	L	0.52364	1.645	0.58432	D	0.999999	B;B;P;P	0.44776	0.387;0.374;0.843;0.716	B;B;P;P	0.48815	0.194;0.194;0.591;0.511	D	0.97965	1.0340	10	0.51188	T	0.08	-23.3976	13.0393	0.58889	0.8655:0.1345:0.0:0.0	.	467;467;467;467	Q07837;B8ZZK1;Q4J6B5;Q4J6B6	SLC31_HUMAN;.;.;.	V	467;467;403;467;467;467;189;87;98	ENSP00000260649:M467V;ENSP00000387308:M467V;ENSP00000386954:M467V;ENSP00000386620:M467V;ENSP00000386709:M189V;ENSP00000386852:M87V;ENSP00000386677:M98V	ENSP00000260649:M467V	M	+	1	0	SLC3A1	44393295	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	5.273000	0.65564	0.987000	0.38709	0.477000	0.44152	ATG	.		0.408	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		G	44539791	A	G	44539791	3	3	120	1	0	0	0	0	1	0	0	0	14658	217	8	3	1429	3	SLC3A1	2	44539791	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		44539791	198659582	8	10411											
DCBLD2	131566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	98600601	98600601	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctagtacagtgtgtccAcatccatcacctttaaaaaa	13	10	7	11	0	1	0	1	0	0	0	3	0	3	0	4	1	1	1	4	1	5	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr3:98600601A>G	ENST00000326840.6	-	2	578	c.216T>C	c.(214-216)tgT>tgC	p.C72C	DCBLD2_ENST00000326857.9_Silent_p.C72C|DCBLD2_ENST00000469648.1_Intron	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	72	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						CAGTGTGTCCACATCCATCAC	0.363																																					p.C72C		.											.	DCBLD2-92	0			c.T216C						.						127	119	121					3																	98600601		1874	4109	5983	SO:0001819	synonymous_variant	131566	exon2			GTGTCCACATCCA		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.216T>C	3.37:g.98600601A>G		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	144	51	NM_080927	0	0	0	0	0	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	37	CCDS46878.1																																																																																			.		0.363	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927		G	98600601	A	G	98600601	2	3	120	1	0	0	0	0	0	0	0	1	4287	157	6	3		3	DCBLD2	3	98600601	Silent	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		98600601	99421829	9	10412											
EXOSC9	5393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	122722615	122722615	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcaaactgcgaacgccgCttcctactccgtgccatcga	8	9	7	17	5	1	0	1	0	1	0	5	2	3	0	4	0	5	1	4	0	3	2	rs150604288		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr4:122722615C>T	ENST00000243498.5	+	1	144	c.36C>T	c.(34-36)cgC>cgT	p.R12R	EXOSC9_ENST00000379663.3_Silent_p.R12R|EXOSC9_ENST00000509980.1_3'UTR|EXOSC9_ENST00000512454.1_5'Flank	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	12	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GCGAACGCCGCTTCCTACTCC	0.582																																					p.R12R		.											.	EXOSC9-90	0			c.C36T						.						84	82	83					4																	122722615		2203	4300	6503	SO:0001819	synonymous_variant	5393	exon1			ACGCCGCTTCCTA	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.36C>T	4.37:g.122722615C>T		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	112	51	NM_001034194	0	0	6	11	5	Q12883|Q4W5P5|Q86Y41|Q86Y48	Silent	SNP	ENST00000243498.5	37	CCDS3722.2																																																																																			C|1.000;G|0.000		0.582	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		T	122722615	C	T	122722615	2	4	120	1	0	0	0	0	0	0	0	1	5334	784	28	2		2	EXOSC9	4	122722615	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		122722615	68431661	10	10413											
RGNEF	64283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	73207182	73207182	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttagtacaaatgtcatttaAcactttcaacaaactgaatc	16	14	3	8	0	2	1	2	1	0	0	3	1	2	1	0	0	4	1	0	0	7	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr5:73207182A>T	ENST00000426542.2	+	34	4750	c.4730A>T	c.(4729-4731)aAc>aTc	p.N1577I	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.N1264I|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.N497I|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.N1533I			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1577	Interaction with microtubules. {ECO:0000250}.|Mediates cytoplasmic retention and interaction with MAPK8IP1. {ECO:0000250}.				central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										ATGTCATTTAACACTTTCAAC	0.363																																					p.N1577I		.											.	.	0			c.A4730T						.						76	70	72					5																	73207182		1930	4126	6056	SO:0001583	missense	64283	exon35			CATTTAACACTTT		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.4730A>T	5.37:g.73207182A>T	ENSP00000412175:p.Asn1577Ile	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	132	45	NM_001080479	0	0	12	26	14	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793921	0.50102	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.36157	2.92;2.93;2.88;2.62;2.93;2.88;2.72;1.27	5.3	5.3	0.74995	.	0.000000	0.35349	U	0.003279	T	0.53481	0.1799	M	0.69823	2.125	0.32983	D	0.52386	P;P;P;D;P	0.62365	0.692;0.916;0.951;0.991;0.95	B;P;P;D;P	0.64042	0.232;0.604;0.626;0.921;0.65	T	0.68356	-0.5430	10	0.87932	D	0	.	8.6768	0.34185	0.9063:0.0:0.0937:0.0	.	1264;1577;1577;497;1577	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	I	1577;1577;1577;1533;1577;1577;1264;497	ENSP00000296794:N1577I;ENSP00000441913:N1577I;ENSP00000441436:N1577I;ENSP00000287898:N1533I;ENSP00000411459:N1577I;ENSP00000412175:N1577I;ENSP00000296799:N1264I;ENSP00000421081:N497I	ENSP00000287898:N1533I	N	+	2	0	RP11-428C6.1	73242938	0.998000	0.40836	0.986000	0.45419	0.532000	0.34746	3.430000	0.52807	2.006000	0.58801	0.443000	0.29094	AAC	.		0.363	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73207182	A	T	73207182	3	4	120	1	0	0	0	0	1	0	0	0	13315	43	2	5	4864	5	RGNEF	5	73207182	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		73207182	107708078	11	10414											
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179201053	179201053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccaacaggaccggggtgtGgctcagttccctggctccca	6	7	14	14	1	1	0	1	0	0	0	3	1	3	1	4	6	1	3	4	6	1	1			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr5:179201053G>A	ENST00000292599.3	+	5	2489	c.2226G>A	c.(2224-2226)gtG>gtA	p.V742V	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACCGGGGTGTGGCTCAGTTCC	0.592																																					p.V742V		.											.	MAML1-848	0			c.G2226A						.						54	55	55					5																	179201053		2203	4300	6503	SO:0001819	synonymous_variant	9794	exon5			GGGTGTGGCTCAG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2226G>A	5.37:g.179201053G>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	43	17	NM_014757	0	0	1	5	4		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																			.		0.592	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		A	179201053	G	A	179201053	2	1	120	1	0	0	0	0	0	0	0	1	9230	1335	47	2		2	MAML1	5	179201053	Silent	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	105993871	179201053	1714207	12	10415											
DSP	1832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	7584156	7584156	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacaacctgtgaccgtcactGagctagtagattctggtata	11	11	10	9	1	2	3	1	2	1	1	2	4	2	3	2	1	2	3	2	1	5	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr6:7584156G>C	ENST00000379802.3	+	24	7002	c.6661G>C	c.(6661-6663)Gag>Cag	p.E2221Q	DSP_ENST00000418664.2_Missense_Mutation_p.E1622Q	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2221	Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GACCGTCACTGAGCTAGTAGA	0.458																																					p.E2221Q		.											.	DSP-518	0			c.G6661C						.						119	109	112					6																	7584156		2203	4300	6503	SO:0001583	missense	1832	exon24			GTCACTGAGCTAG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"desmoplakin (DPI, DPII)"			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.6661G>C	6.37:g.7584156G>C	ENSP00000369129:p.Glu2221Gln	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	54	19	NM_004415	0	0	20	46	26	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015584	0.54468	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.70399	-0.48;-0.48	5.62	5.62	0.85841	.	0.098059	0.45361	D	0.000376	T	0.74114	0.3674	L	0.48877	1.53	0.36056	D	0.841104	P;D	0.76494	0.526;0.999	B;P	0.60886	0.141;0.88	T	0.72440	-0.4293	10	0.41790	T	0.15	.	20.0281	0.97530	0.0:0.0:1.0:0.0	.	1669;2221	Q4LE79;P15924	.;DESP_HUMAN	Q	2221;1622	ENSP00000369129:E2221Q;ENSP00000396591:E1622Q	ENSP00000369129:E2221Q	E	+	1	0	DSP	7529155	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	6.483000	0.73617	2.818000	0.97014	0.655000	0.94253	GAG	.		0.458	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		C	7584156	G	C	7584156	3	2	120	1	0	0	0	0	1	0	0	0	4792	1291	45	4	6755	4	DSP	6	7584156	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		7584156	163530911	13	10416											
ZP3	7784	ucsc.edu	37	chr7	76069823	76069823	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaggctcggctgacatcTgtcaatgctgtaacaaaggt	11	10	12	8	1	2	1	1	1	1	0	3	2	2	2	0	4	2	4	0	4	4	1			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr7:76069823T>A	ENST00000394857.3	+	7	1013	c.955T>A	c.(955-957)Tgt>Agt	p.C319S	ZP3_ENST00000336517.4_Missense_Mutation_p.C268S|ZP3_ENST00000416245.1_Missense_Mutation_p.C143S|ZP3_ENST00000467555.1_3'UTR	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	319					binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						GGCTGACATCTGTCAATGCTG	0.512																																					p.C319S													.	ZP3-90	0			c.T955A						.						91	97	95					7																	76069823		2203	4300	6503	SO:0001583	missense	7784	exon7			GACATCTGTCAAT	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"Zona pellucida glycoproteins"	13189	protein-coding gene	gene with protein product		182889	"zona pellucida glycoprotein 3A (sperm receptor)"	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.955T>A	7.37:g.76069823T>A	ENSP00000378326:p.Cys319Ser	Somatic	218	16		WXS	Illumina HiSeq		347	39	NM_001110354	0	0	3	3	0	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	t	15.09	2.731094	0.48939	.	.	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	T;T;T	0.78924	-0.62;-0.63;-1.22	4.96	4.96	0.65561	.	0.000000	0.85682	U	0.000000	D	0.88403	0.6427	M	0.86864	2.845	0.50467	D	0.999878	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.89966	0.4090	10	0.87932	D	0	-14.8704	11.3228	0.49433	0.0:0.0:0.0:1.0	.	268;319	P21754-3;P21754	.;ZP3_HUMAN	S	268;319;319;143	ENSP00000337310:C268S;ENSP00000378326:C319S;ENSP00000411955:C143S	ENSP00000337310:C268S	C	+	1	0	ZP3	75907759	1.000000	0.71417	0.978000	0.43139	0.083000	0.17756	5.311000	0.65786	2.011000	0.59026	0.459000	0.35465	TGT	.		0.512	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			A	76069823	T	A	76069823	3	1	120	1	0	0	0	0	1	0	0	0	18249	1580	55	5	981	5	ZP3	7	76069823	Missense_Mutation	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10		76069823	83068840	14	10417											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	151874152	151874158	+	Frame_Shift_Del	DEL	TTTTTGG	TTTTTGG	-																															tttgttttcttgttccttttTttttggttcaacagatacac																								rs79763944|rs78116609		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	TTTTTGG	TTTTTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr7:151874152_151874158delTTTTTGG	ENST00000262189.6	-	38	8598_8604	c.8380_8386delCCAAAAA	c.(8380-8388)ccaaaaaaafs	p.PKK2794fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.PKK2794fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2794					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TGTTCCTTTTTTTTTGGTTCAACAGAT	0.357																																					p.2794_2796del		.											.	MLL3-1398	0			c.8380_8386del						.																																			SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8380_8386delCCAAAAA	7.37:g.151874152_151874158delTTTTTGG	ENSP00000262189:p.Pro2794fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	95	30	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.357	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151874158	TTTTTGG	-	151874152	7	5	120	1	0	1	0	1	0	0	0	0	9647	1850	64	0	6437	0	MLL3	7	151874152	Frame_Shift_Del	DEL	TTTTTGG	TCGA-G7-A4TM-01A-11D-A31X-10	75804329	151874152	7264511	15	10418											
RBM33	155435	broad.mit.edu	37	chr7	155532557	155532557	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accccagcacccaccacagcAcccgccgcagcaccagcacc	11	0	6	24	2	0	0	0	0	0	0	0	0	0	0	8	0	4	5	8	0	0	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr7:155532557A>C	ENST00000401878.3	+	12	2084	c.1886A>C	c.(1885-1887)cAc>cCc	p.H629P		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	629	His-rich.|Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		ccaccacagcacccgccgcag	0.706																																					p.H629P													.	RBM33-23	0			c.A1886C						.						12	12	12					7																	155532557		1884	3539	5423	SO:0001583	missense	155435	exon12			CACAGCACCCGCC	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"RNA binding motif (RRM) containing"	27223	protein-coding gene	gene with protein product			"proline rich 8"	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1886A>C	7.37:g.155532557A>C	ENSP00000384160:p.His629Pro	Somatic	26	5		WXS	Illumina HiSeq	Phase_I	58	16	NM_053043	0	0	0	0	0	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Missense_Mutation	SNP	ENST00000401878.3	37	CCDS5941.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.292|7.292	0.611250|0.611250	0.14066|0.14066	.|.	.|.	ENSG00000184863|ENSG00000184863	ENST00000401878|ENST00000392761	T|.	0.45276|.	0.9|.	4.59|4.59	4.59|4.59	0.56863|0.56863	.|.	0.000000|.	0.64402|.	D|.	0.000010|.	T|T	0.33469|0.33469	0.0864|0.0864	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	B;B|.	0.09022|.	0.002;0.002|.	B;B|.	0.11329|.	0.006;0.006|.	T|T	0.14952|0.14952	-1.0454|-1.0454	9|5	.|.	.|.	.|.	.|.	9.2613|9.2613	0.37614|0.37614	0.8184:0.1816:0.0:0.0|0.8184:0.1816:0.0:0.0	.|.	346;629|.	B4DVQ2;Q96EV2|.	.;RBM33_HUMAN|.	P|P	629|401	ENSP00000384160:H629P|.	.|.	H|T	+|+	2|1	0|0	RBM33|RBM33	155225318|155225318	1.000000|1.000000	0.71417|0.71417	0.131000|0.131000	0.22000|0.22000	0.206000|0.206000	0.24218|0.24218	3.795000|3.795000	0.55499|0.55499	1.697000|1.697000	0.51169|0.51169	0.383000|0.383000	0.25322|0.25322	CAC|ACC	.		0.706	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		C	155532557	A	C	155532557	3	2	120	1	0	0	0	0	1	0	0	0	13162	159	6	5	1932	5	RBM33	7	155532557	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	3658405	155532557	3606106	16	10419											
NAT1	9	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	18080420	18080420	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacatggtgatagatttttTactatttagaataaggagta	16	15	8	2	0	0	3	0	1	0	2	0	4	0	4	0	2	2	1	0	2	8	9			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr8:18080420T>C	ENST00000517492.1	+	3	1502	c.864T>C	c.(862-864)ttT>ttC	p.F288F	NAT1_ENST00000518029.1_Silent_p.F288F|NAT1_ENST00000541942.1_Silent_p.F288F|NAT1_ENST00000520546.1_Silent_p.F288F|NAT1_ENST00000535084.1_Silent_p.F288F|NAT1_ENST00000545197.1_Silent_p.F350F|NAT1_ENST00000307719.4_Silent_p.F288F|NAT1_ENST00000539092.1_Silent_p.F288F			Q8IZM9	S38A6_HUMAN	N-acetyltransferase 1 (arylamine N-acetyltransferase)	0					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(2)|urinary_tract(1)	9				Colorectal(111;0.0519)|COAD - Colon adenocarcinoma(73;0.208)		ATAGATTTTTTACTATTTAGA	0.343																																					p.F350F		.											.	NAT1-90	0			c.T1050C						.						28	30	29					8																	18080420		2185	4285	6470	SO:0001819	synonymous_variant	9	exon4			ATTTTTTACTATT	BC047666	CCDS6007.1, CCDS55205.1	8p22	2012-01-18			ENSG00000171428	ENSG00000171428	2.3.1.5		7645	protein-coding gene	gene with protein product		108345		AAC1		7773298	Standard	NM_001160174		Approved		uc003wyt.3	P18440	OTTHUMG00000097001	ENST00000517492.1:c.864T>C	8.37:g.18080420T>C		Somatic	278	1		WXS	Illumina HiSeq	Phase_I	210	83	NM_001160176	0	0	4	6	2	C9JWA6|Q86SY5	Silent	SNP	ENST00000517492.1	37	CCDS6007.1																																																																																			.		0.343	NAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374828.1	NM_000662		C	18080420	T	C	18080420	2	2	120	1	0	0	0	0	0	0	0	1	10198	1751	61	3		3	NAT1	8	18080420	Silent	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10		18080420	128283602	17	10420											
RNF139	11236	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	125487509	125487509	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agccggttctgcatcgtgctCcagatcttcctccggctctt	4	13	9	15	3	3	1	0	0	3	1	7	1	6	1	4	2	3	4	4	2	0	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr8:125487509C>T	ENST00000303545.3	+	1	531	c.159C>T	c.(157-159)ctC>ctT	p.L53L	RNF139-AS1_ENST00000499418.2_lincRNA	NM_007218.3	NP_009149.2			ring finger protein 139											breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(1)	20	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GCATCGTGCTCCAGATCTTCC	0.647																																					p.L53L													.	RNF139-226	0			c.C159T						.						80	83	82					8																	125487509		2203	4300	6503	SO:0001819	synonymous_variant	11236	exon1			CGTGCTCCAGATC	AF064801	CCDS6350.1	8q24	2013-01-09			ENSG00000170881	ENSG00000170881		"RING-type (C3HC4) zinc fingers"	17023	protein-coding gene	gene with protein product		603046				9689122	Standard	NM_007218		Approved	TRC8, RCA1, HRCA1	uc003yrc.3	Q8WU17	OTTHUMG00000165072	ENST00000303545.3:c.159C>T	8.37:g.125487509C>T		Somatic	75	1		WXS	Illumina HiSeq	Phase_I	56	23	NM_007218	0	0	13	19	6		Silent	SNP	ENST00000303545.3	37	CCDS6350.1																																																																																			.		0.647	RNF139-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381692.1	NM_007218		T	125487509	C	T	125487509	2	4	120	1	0	0	0	0	0	0	0	1	13474	842	30	2		2	RNF139	8	125487509	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	107407089	125487509	20876513	18	10421											
ELAVL2	1993	broad.mit.edu	37	chr9	23762097	23762097	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgtcatgttctgaggaaGgtagttgactattaagttgg	9	15	13	4	0	2	2	1	2	1	0	2	3	2	3	0	3	0	4	0	3	4	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr9:23762097G>T	ENST00000397312.2	-	2	410	c.136C>A	c.(136-138)Ctt>Att	p.L46I	ELAVL2_ENST00000380110.4_Missense_Mutation_p.L75I|ELAVL2_ENST00000380117.1_Missense_Mutation_p.L46I|ELAVL2_ENST00000462649.1_5'Flank|ELAVL2_ENST00000223951.6_Missense_Mutation_p.L46I|ELAVL2_ENST00000544538.1_Missense_Mutation_p.L46I	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	46	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)		mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		TTCTGAGGAAGGTAGTTGACT	0.428																																					p.L46I													.	ELAVL2-516	0			c.C136A						.						295	267	277					9																	23762097		2203	4300	6503	SO:0001583	missense	1993	exon2			GAGGAAGGTAGTT	BC030692	CCDS6515.1, CCDS55298.1	9p21	2013-10-03	2013-10-03		ENSG00000107105	ENSG00000107105		"RNA binding motif (RRM) containing"	3313	protein-coding gene	gene with protein product	"Hu antigen B"	601673	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"			8812435	Standard	NM_004432		Approved	HuB, HEL-N1	uc003zpu.3	Q12926	OTTHUMG00000019700	ENST00000397312.2:c.136C>A	9.37:g.23762097G>T	ENSP00000380479:p.Leu46Ile	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	134	4	NM_001171195	0	0	0	0	0	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Missense_Mutation	SNP	ENST00000397312.2	37	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332086	0.81801	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	T;D;D;D;T	0.85861	2.3;-2.04;-2.04;-2.04;2.3	5.92	5.92	0.95590	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.89884	0.6844	L	0.37466	1.105	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.99;0.997	D	0.90202	0.4258	10	0.87932	D	0	.	20.33	0.98713	0.0:0.0:1.0:0.0	.	46;46	Q12926;Q12926-2	ELAV2_HUMAN;.	I	46;46;46;46;46;74;46	ENSP00000223951:L46I;ENSP00000380479:L46I;ENSP00000440998:L46I;ENSP00000369460:L46I;ENSP00000412602:L46I	ENSP00000223951:L46I	L	-	1	0	ELAVL2	23752097	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.813000	0.69201	2.810000	0.96702	0.585000	0.79938	CTT	.		0.428	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		T	23762097	G	T	23762097	3	4	120	1	0	0	0	0	1	0	0	0	5063	1000	35	4	967	4	ELAVL2	9	23762097	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		23762097	117451334	19	10422											
CLTA	1211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	36209297	36209297	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctttctacaaacaacccttCgctgacgtgattggttatgt	9	14	8	10	2	1	2	0	2	1	0	2	2	1	2	1	1	3	3	1	1	4	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr9:36209297C>T	ENST00000242285.6	+	5	639	c.519C>T	c.(517-519)ttC>ttT	p.F173F	CLTA_ENST00000538225.1_Intron|CLTA_ENST00000470744.1_Intron|CLTA_ENST00000396603.2_Silent_p.F173F|CLTA_ENST00000540080.1_Intron|CLTA_ENST00000466396.1_Silent_p.F121F|CLTA_ENST00000433436.2_Silent_p.F173F|CLTA_ENST00000345519.5_Intron			P09496	CLCA_HUMAN	clathrin, light chain A	173					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			AACAACCCTTCGCTGACGTGA	0.403																																					p.F173F		.											.	CLTA-90	0			c.C519T						.						191	165	174					9																	36209297		2203	4300	6503	SO:0001819	synonymous_variant	1211	exon5			ACCCTTCGCTGAC		CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"clathrin, light polypeptide (Lca)"			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.519C>T	9.37:g.36209297C>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	89	38	NM_001076677	0	0	0	0	0	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	37	CCDS6601.1																																																																																			.		0.403	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		T	36209297	C	T	36209297	2	4	120	1	0	0	0	0	0	0	0	1	3570	883	31	1		1	CLTA	9	36209297	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	12447200	36209297	105004134	20	10423											
PRUNE2	158471	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr9	79318374	79318374	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catttcccattcattgtcatGggtgacagcctgcaacgtaa	10	12	8	11	1	2	1	2	1	0	0	3	1	3	1	2	1	3	2	2	1	2	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr9:79318374G>A	ENST00000376718.3	-	9	8278	c.8155C>T	c.(8155-8157)Cat>Tat	p.H2719Y	PRUNE2_ENST00000428286.1_Missense_Mutation_p.H2360Y	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2719					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TCATTGTCATGGGTGACAGCC	0.527																																					p.H2719Y		.											.	PRUNE2-157	0			c.C8155T						.						102	83	89					9																	79318374		1568	3582	5150	SO:0001583	missense	158471	exon9			TGTCATGGGTGAC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"olfaxin"	610691	"chromosome 9 open reading frame 65", "KIAA0367"	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8155C>T	9.37:g.79318374G>A	ENSP00000365908:p.His2719Tyr	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	51	32	NM_015225	0	0	0	12	12	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.75|17.75	3.465272|3.465272	0.63513|0.63513	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.49720|.	0.77;0.78|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.102782|.	0.43747|.	D|.	0.000523|.	T|T	0.71187|0.71187	0.3310|0.3310	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	P;P|.	0.51653|.	0.898;0.947|.	B;B|.	0.43867|.	0.434;0.335|.	T|T	0.68957|0.68957	-0.5272|-0.5272	10|5	0.72032|.	D|.	0.01|.	-6.6465|-6.6465	14.0742|14.0742	0.64880|0.64880	0.0:0.1938:0.8062:0.0|0.0:0.1938:0.8062:0.0	.|.	2719;2719|.	Q8WUY3-3;Q8WUY3|.	.;PRUN2_HUMAN|.	Y|L	2719;2360;2718|2040	ENSP00000365908:H2719Y;ENSP00000397425:H2360Y|.	ENSP00000365908:H2719Y|.	H|P	-|-	1|2	0|0	PRUNE2|PRUNE2	78508194|78508194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.640000|0.640000	0.38277|0.38277	4.226000|4.226000	0.58606|0.58606	2.814000|2.814000	0.96858|0.96858	0.586000|0.586000	0.80456|0.80456	CAT|CCA	.		0.527	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79318374	G	A	79318374	3	1	120	1	0	0	0	0	1	0	0	0	12670	1348	47	2	1155	2	PRUNE2	9	79318374	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	43109077	79318374	61895057	21	10424											
WAPAL	23063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	88227091	88227091	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttcacagagccttcggAttttttctttaattttgttc	7	20	6	8	1	2	1	1	0	1	1	4	2	2	2	1	1	1	2	1	1	1	10			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr10:88227091A>G	ENST00000298767.5	-	9	2787	c.2315T>C	c.(2314-2316)aTc>aCc	p.I772T	WAPAL_ENST00000372075.1_Missense_Mutation_p.I39T|WAPAL_ENST00000263070.7_Missense_Mutation_p.I39T	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	772	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)		p.I772T(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						GAGCCTTCGGATTTTTTCTTT	0.368																																					p.I772T		.											.	WAPAL-91	1	Substitution - Missense(1)	lung(1)	c.T2315C						.						180	167	171					10																	88227091		2203	4300	6503	SO:0001583	missense	23063	exon9			CTTCGGATTTTTT	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.2315T>C	10.37:g.88227091A>G	ENSP00000298767:p.Ile772Thr	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	114	59	NM_015045	0	0	4	8	4	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484052	0.84854	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T	0.48201	0.82	5.99	5.99	0.97316	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67316	0.2880	M	0.64997	1.995	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.99;0.998;0.996	T	0.69537	-0.5119	10	0.72032	D	0.01	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	766;810;772;809	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	T	857;772;857;39;39	ENSP00000298767:I772T	ENSP00000263070:I39T	I	-	2	0	WAPAL	88217071	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.336000	0.96533	2.291000	0.77112	0.533000	0.62120	ATC	.		0.368	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		G	88227091	A	G	88227091	3	3	120	1	0	0	0	0	1	0	0	0	17281	333	12	3	1301	3	WAPAL	10	88227091	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		88227091	47307656	22	10425											
MUC6	4588	bcgsc.ca	37	chr11	1016801	1016801	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgggaagtgtggtctgaggGtgtgatggggttggataggt	6	12	22	1	0	1	2	0	2	1	0	1	4	1	4	0	7	0	1	0	7	2	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr11:1016801G>C	ENST00000421673.2	-	31	6050	c.6000C>G	c.(5998-6000)caC>caG	p.H2000Q		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2000	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGTCTGAGGGTGTGATGGGG	0.542																																					p.H2000Q													.	MUC6-23	0			c.C6000G						.						1371	1357	1362					11																	1016801		2203	4297	6500	SO:0001583	missense	4588	exon31			CTGAGGGTGTGAT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.6000C>G	11.37:g.1016801G>C	ENSP00000406861:p.His2000Gln	Somatic	837	15		WXS	Illumina HiSeq	Phase_1	754	20	NM_005961	0	0	0	0	0	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	6.842	0.524518	0.13066	.	.	ENSG00000184956	ENST00000421673	T	0.17528	2.27	2.76	-5.51	0.02568	.	.	.	.	.	T	0.10337	0.0253	L	0.50333	1.59	0.09310	N	1	B	0.27625	0.183	B	0.21708	0.036	T	0.29610	-1.0006	9	0.27082	T	0.32	.	1.062	0.01603	0.2629:0.2888:0.3017:0.1467	.	2000	Q6W4X9	MUC6_HUMAN	Q	2000	ENSP00000406861:H2000Q	ENSP00000406861:H2000Q	H	-	3	2	MUC6	1006801	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.904000	0.04080	-1.588000	0.01627	0.306000	0.20318	CAC	.		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		C	1016801	G	C	1016801	3	2	120	1	0	0	0	0	1	0	0	0	10005	1252	44	4	1331	4	MUC6	11	1016801	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		1016801	133989715	23	10426											
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62301415	62301415	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacatccacagtgtaggcCgtgacccttctggtcactgt	7	11	10	13	1	3	1	2	1	1	0	4	1	4	1	3	2	0	1	3	2	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr11:62301415C>T	ENST00000378024.4	-	5	748	c.474G>A	c.(472-474)acG>acA	p.T158T	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	158					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CAGTGTAGGCCGTGACCCTTC	0.532																																					p.T158T		.											.	AHNAK-109	0			c.G474A						.						136	119	124					11																	62301415		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			GTAGGCCGTGACC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.474G>A	11.37:g.62301415C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	32	19	NM_001620	0	0	12	23	11	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			.		0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62301415	C	T	62301415	2	4	120	1	0	0	0	0	0	0	0	1	414	639	23	1		1	AHNAK	11	62301415	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	61284614	62301415	72705101	24	10427											
PIWIL4	143689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	94341805	94341805	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagatgcactcagcaaggaCgtgatggttgttggatgcgt	11	10	14	6	2	1	2	1	1	0	1	1	4	1	4	0	3	3	4	0	3	2	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr11:94341805C>T	ENST00000299001.6	+	15	2107	c.1896C>T	c.(1894-1896)gaC>gaT	p.D632D	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	632	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCAGCAAGGACGTGATGGTTG	0.393																																					p.D632D		.											.	PIWIL4-91	0			c.C1896T						.						269	236	247					11																	94341805		2201	4298	6499	SO:0001819	synonymous_variant	143689	exon15			CAAGGACGTGATG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1896C>T	11.37:g.94341805C>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	162	64	NM_152431	0	0	4	5	1	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			.		0.393	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		T	94341805	C	T	94341805	2	4	120	1	0	0	0	0	0	0	0	1	11986	535	19	1		1	PIWIL4	11	94341805	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	32040390	94341805	40664711	25	10428											
PRB1	5542	broad.mit.edu	37	chr12	11506632	11506633	+	Intron	INS	-	-	GGA																															gtggtccttgtggctttcctINSggaggtgggggaccttgagg																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:11506632_11506633insGGA	ENST00000500254.2	-	3	351				PRB1_ENST00000546254.1_Intron|PRB1_ENST00000545626.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GTGGCTTTCCTGGAGGTGGGGG	0.604																																					.													.	PRB1-90	0			.						.																																			SO:0001627	intron_variant	5542	.			CTTTCCTGGAGGT		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.313+90->TCC	12.37:g.11506633_11506635dupGGA		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	79	8	.	0	0	0	0	0	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	In_Frame_Ins	INS	ENST00000500254.2	37	CCDS8642.1																																																																																			.		0.604	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039		GGA	11506633	-	GGA	11506632	6	5	120	0	1	1	1	0	0	0	0	0	12471	1567	55	0		0	PRB1	12	11506632	Intron	INS	-	TCGA-G7-A4TM-01A-11D-A31X-10		11506632	122345263	26	10429			1	33		3	2	24	N	T_-	3.714791e-05
PRB1	5542	broad.mit.edu	37	chr12	11506653	11506653	+	Intron	DEL	T	T	-																															ggaggtgggggaccttgaggTctgttgcctccttgtggggg																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:11506653delT	ENST00000500254.2	-	3	351				PRB1_ENST00000546254.1_Intron|PRB1_ENST00000545626.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GACCTTGAGGTCTGTTGCCTC	0.602																																					.													.	PRB1-90	0			.						.						17	14	15					12																	11506653		1290	2283	3573	SO:0001627	intron_variant	5542	.			TTGAGGTCTGTTG		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.313+70A>-	12.37:g.11506653delT		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	94	7	.	0	0	0	0	0	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Frame_Shift_Del	DEL	ENST00000500254.2	37	CCDS8642.1																																																																																			.		0.602	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039		-	11506653	T	-	11506653	6	5	120	0	1	1	0	1	0	0	0	0	12471	1664	58	0		0	PRB1	12	11506653	Intron	DEL	T	TCGA-G7-A4TM-01A-11D-A31X-10	21	11506653	122345242	27	10430	106	2	1	33		3	2	24	N	T_-	3.714791e-05
PRB1	5542	broad.mit.edu	37	chr12	11506655	11506656	+	Intron	INS	-	-	G																															ggtgggggaccttgaggtctINSgttgcctccttgtgggggtg																								rs371206768		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:11506655_11506656insG	ENST00000500254.2	-	3	351				PRB1_ENST00000546254.1_Intron|PRB1_ENST00000545626.1_Intron	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1							extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			CCTTGAGGTCTGTTGCCTCCTT	0.604																																					.													.	PRB1-90	0			.						.																																			SO:0001627	intron_variant	5542	.			GAGGTCTGTTGCC		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.313+67->C	12.37:g.11506656_11506656dupG		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	94	7	.	0	0	0	0	0	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Frame_Shift_Ins	INS	ENST00000500254.2	37	CCDS8642.1																																																																																			.		0.604	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039		G	11506656	-	G	11506655	6	5	120	0	1	1	1	0	0	0	0	0	12471	1588	55	0		0	PRB1	12	11506655	Intron	INS	-	TCGA-G7-A4TM-01A-11D-A31X-10	2	11506655	122345240	28	10431	106	2	1	33		3	2	24	N	T_-	3.714791e-05
FAM60A	58516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	31448170	31448170	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaagaaagatggactaacatGattccagtttttttttgatc	14	15	7	5	0	0	4	0	2	0	2	2	5	1	5	1	1	1	1	1	1	3	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:31448170G>A	ENST00000337682.4	-	3	594	c.226C>T	c.(226-228)Cat>Tat	p.H76Y	FAM60A_ENST00000395766.1_5'UTR|FAM60A_ENST00000542983.1_5'UTR|FAM60A_ENST00000454658.2_Missense_Mutation_p.H76Y|FAM60A_ENST00000539409.1_Intron	NM_001135812.1	NP_001129284.1	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A	76					negative regulation of cell migration (GO:0030336)	Sin3 complex (GO:0016580)				large_intestine(1)|lung(2)	3	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					GGACTAACATGATTCCAGTTT	0.373																																					p.H76Y		.											.	FAM60A-90	0			c.C226T						.						82	74	77					12																	31448170		2203	4300	6503	SO:0001583	missense	58516	exon4			TAACATGATTCCA	AF212220	CCDS8723.1	12p11.21	2012-11-30	2005-04-07	2005-04-07	ENSG00000139146	ENSG00000139146			30702	protein-coding gene	gene with protein product		615027	"chromosome 12 open reading frame 14"	C12orf14		11042152, 22984288, 22865885	Standard	NM_021238		Approved	TERA	uc001rke.3	Q9NP50	OTTHUMG00000168586	ENST00000337682.4:c.226C>T	12.37:g.31448170G>A	ENSP00000337477:p.His76Tyr	Somatic	440	0		WXS	Illumina HiSeq	Phase_I	439	248	NM_021238	0	0	0	0	0	D3DUV8|Q9BSZ8	Missense_Mutation	SNP	ENST00000337682.4	37	CCDS8723.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261331	0.80246	.	.	ENSG00000139146	ENST00000337682;ENST00000454658;ENST00000398170;ENST00000539004;ENST00000543615	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	4.22	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.80586	0.4651	M	0.82323	2.585	0.80722	D	1	D;D	0.76494	0.989;0.999	D;D	0.76575	0.969;0.988	D	0.84590	0.0666	10	0.87932	D	0	-1.1171	17.1323	0.86729	0.0:0.0:1.0:0.0	.	76;117	Q9NP50;B7Z287	FA60A_HUMAN;.	Y	76;76;117;76;76	ENSP00000337477:H76Y;ENSP00000393279:H76Y;ENSP00000443881:H76Y;ENSP00000437363:H76Y	ENSP00000337477:H76Y	H	-	1	0	FAM60A	31339437	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.457000	0.97630	2.343000	0.79666	0.561000	0.74099	CAT	.		0.373	FAM60A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400347.1	NM_021238		A	31448170	G	A	31448170	3	1	120	1	0	0	0	0	1	0	0	0	5614	1290	45	2	455	2	FAM60A	12	31448170	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	19941515	31448170	102403725	29	10432											
METAP2	10988	broad.mit.edu	37	chr12	95867964	95867964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcgggcaacatggcgggTgtggaggaggtagcggcctc	6	7	18	10	3	1	0	0	0	1	0	3	2	1	2	1	7	2	2	1	7	2	1			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:95867964T>G	ENST00000323666.5	+	1	238	c.9T>G	c.(7-9)ggT>ggG	p.G3G	METAP2_ENST00000261220.9_Silent_p.G3G|METAP2_ENST00000550777.1_Silent_p.G3G|METAP2_ENST00000551840.1_Silent_p.G3G|METAP2_ENST00000546753.1_Silent_p.G3G	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						ACATGGCGGGTGTGGAGGAGG	0.652																																					p.G3G													.	METAP2-90	0			c.T9G						.						34	42	39					12																	95867964		2203	4297	6500	SO:0001819	synonymous_variant	10988	exon1			GGCGGGTGTGGAG	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.9T>G	12.37:g.95867964T>G		Somatic	111	27		WXS	Illumina HiSeq	Phase_I	157	41	NM_006838	0	0	20	23	3		Silent	SNP	ENST00000323666.5	37	CCDS9052.1																																																																																			.		0.652	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		G	95867964	T	G	95867964	2	3	120	1	0	0	0	0	0	0	0	1	9512	1683	59	5		5	METAP2	12	95867964	Silent	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10	64419794	95867964	37983931	30	10433											
KCTD10	83892	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	109889450	109889450	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgcttgatgtggatcctccGcacgcgctcgatccgctccc	4	9	11	17	6	0	1	0	1	0	0	5	3	4	2	4	1	0	4	4	1	0	1			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:109889450G>T	ENST00000228495.6	-	7	1173	c.892C>A	c.(892-894)Cgg>Agg	p.R298R	KCTD10_ENST00000538161.1_5'UTR|KCTD10_ENST00000540089.1_Silent_p.R117R|KCTD10_ENST00000424763.2_Silent_p.R117R|KCTD10_ENST00000540411.1_Silent_p.R272R	NM_031954.3	NP_114160.1	Q9H3F6	BACD3_HUMAN	potassium channel tetramerization domain containing 10	298					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	10						TGGATCCTCCGCACGCGCTCG	0.721																																					p.R298R		.											.	KCTD10-90	0			c.C892A						.						53	49	50					12																	109889450		2203	4300	6503	SO:0001819	synonymous_variant	83892	exon7			TCCTCCGCACGCG	BC040062	CCDS9128.1	12q24.12	2013-06-20	2013-06-20		ENSG00000110906	ENSG00000110906		"BTB/POZ domain containing"	23236	protein-coding gene	gene with protein product		613421	"potassium channel tetramerisation domain containing 10"			12477932	Standard	XM_005253946		Approved	MSTP028, BTBD28	uc001toi.1	Q9H3F6	OTTHUMG00000169253	ENST00000228495.6:c.892C>A	12.37:g.109889450G>T		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	55	4	NM_031954	0	0	28	28	0	Q53HN2|Q59FV1|Q6PL47|Q96SU0	Silent	SNP	ENST00000228495.6	37	CCDS9128.1	.	.	.	.	.	.	.	.	.	.	G	9.426	1.084203	0.20309	.	.	ENSG00000110906	ENST00000538161	.	.	.	4.97	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.5015	11.8876	0.52610	0.0:0.0:0.6832:0.3168	.	.	.	.	X	263	.	.	C	-	3	2	KCTD10	108373833	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	5.414000	0.66405	1.407000	0.46875	0.655000	0.94253	TGC	.		0.721	KCTD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403099.1	NM_031954		T	109889450	G	T	109889450	2	4	120	1	0	0	0	0	0	0	0	1	8118	1086	38	4		4	KCTD10	12	109889450	Silent	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	14021486	109889450	23962445	31	10434											
ELL3	80237	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	44067740	44067740	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctcacttcccactgtgcCatgtgctcccttgaggatcc	6	12	7	16	0	1	1	1	1	0	0	4	2	4	2	5	1	3	1	5	1	1	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr15:44067740C>T	ENST00000319359.3	-	5	1193	c.552G>A	c.(550-552)atG>atA	p.M184I	SERF2_ENST00000381359.1_5'Flank|RP11-296A16.1_ENST00000417761.2_3'UTR|ELL3_ENST00000497465.1_5'Flank	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	184					DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)			cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		CCCACTGTGCCATGTGCTCCC	0.498											OREG0023092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M184I		.											.	ELL3-91	0			c.G552A						.						154	133	140					15																	44067740		2198	4298	6496	SO:0001583	missense	80237	exon5			CTGTGCCATGTGC	AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.552G>A	15.37:g.44067740C>T	ENSP00000320346:p.Met184Ile	Somatic	91	0	921	WXS	Illumina HiSeq	Phase_I	60	8	NM_025165	0	0	9	9	0	B3KQ66|B3KX08|Q6I9Z7|Q9H634	Missense_Mutation	SNP	ENST00000319359.3	37	CCDS10102.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299310	0.40694	.	.	ENSG00000128886	ENST00000319359	T	0.29397	1.57	5.75	2.65	0.31530	.	0.896720	0.09670	N	0.771265	T	0.23492	0.0568	L	0.47716	1.5	0.28997	N	0.887675	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.30707	-0.9969	10	0.19147	T	0.46	-31.8363	4.8606	0.13581	0.1517:0.6198:0.1467:0.0818	.	184;184;138	B3KX08;Q9HB65;B3KQ66	.;ELL3_HUMAN;.	I	184	ENSP00000320346:M184I	ENSP00000320346:M184I	M	-	3	0	ELL3	41855032	0.017000	0.18338	0.948000	0.38648	0.979000	0.70002	-0.179000	0.09768	0.734000	0.32515	0.555000	0.69702	ATG	.		0.498	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165		T	44067740	C	T	44067740	3	4	120	1	0	0	0	0	1	0	0	0	5077	594	21	2	669	2	ELL3	15	44067740	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		44067740	58463652	32	10435											
SGK269	79834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	77450971	77450971	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtgcagcccctgccatCttgcttcccaacaacagttc	9	10	7	15	0	1	1	0	1	1	0	3	1	2	1	4	0	6	3	4	0	3	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr15:77450971C>A	ENST00000560626.2	-	5	3680	c.3205G>T	c.(3205-3207)Gat>Tat	p.D1069Y	PEAK1_ENST00000312493.4_Missense_Mutation_p.D1069Y			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1069					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CCCCTGCCATCTTGCTTCCCA	0.473																																					p.D1069Y		.											.	.	0			c.G3205T						.						127	119	122					15																	77450971		1933	4139	6072	SO:0001583	missense	0	exon6			TGCCATCTTGCTT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3205G>T	15.37:g.77450971C>A	ENSP00000452796:p.Asp1069Tyr	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	59	25	NM_024776	0	0	0	0	0	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826500	0.50739	.	.	ENSG00000173517	ENST00000312493	T	0.69685	-0.42	5.4	4.49	0.54785	.	0.667769	0.14142	N	0.338611	T	0.52092	0.1713	N	0.14661	0.345	0.28725	N	0.902826	P	0.44090	0.826	B	0.41723	0.365	T	0.50717	-0.8795	10	0.59425	D	0.04	-3.0393	12.2917	0.54823	0.0:0.9219:0.0:0.0781	.	1069	Q9H792	PEAK1_HUMAN	Y	1069	ENSP00000309230:D1069Y	ENSP00000309230:D1069Y	D	-	1	0	AC087465.1	75238026	1.000000	0.71417	0.993000	0.49108	0.748000	0.42578	4.715000	0.61909	1.275000	0.44379	0.563000	0.77884	GAT	.		0.473	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77450971	C	A	77450971	3	1	120	1	0	0	0	0	1	0	0	0	14243	913	32	4	2047	4	SGK269	15	77450971	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	33383231	77450971	25080421	33	10436											
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3860637	3860637	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggtgactgaagtattcttGatatctgtagggaaggtggg	9	14	15	3	0	2	3	0	3	2	0	2	4	2	4	0	4	0	2	0	4	5	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:3860637G>A	ENST00000262367.5	-	3	1751	c.942C>T	c.(940-942)atC>atT	p.I314I	CREBBP_ENST00000382070.3_Silent_p.I314I	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	314	Interaction with SRCAP.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AAGTATTCTTGATATCTGTAG	0.517			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.I314I		.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP-1807	0			c.C942T						.						212	196	201					16																	3860637		2197	4300	6497	SO:0001819	synonymous_variant	1387	exon3			ATTCTTGATATCT	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.942C>T	16.37:g.3860637G>A		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	108	36	NM_001079846	0	0	5	5	0	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																			.		0.517	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3860637	G	A	3860637	2	1	120	1	0	0	0	0	0	0	0	1	3867	1280	45	2		2	CREBBP	16	3860637	Silent	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		3860637	86494116	34	10437											
ABCC1	4363	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	16180696	16180696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccagggcgtgaacctgtctGggggccagaagcagcgcgtg	7	5	17	12	3	1	2	0	1	1	1	1	2	1	2	3	3	3	1	3	3	2	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:16180696G>A	ENST00000399410.3	+	18	2483	c.2308G>A	c.(2308-2310)Ggg>Agg	p.G770R	ABCC1_ENST00000351154.5_Missense_Mutation_p.G711R|ABCC1_ENST00000345148.5_Missense_Mutation_p.G770R|ABCC1_ENST00000399408.2_Missense_Mutation_p.G770R|ABCC1_ENST00000346370.5_Intron|ABCC1_ENST00000349029.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	770	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GAACCTGTCTGGGGGCCAGAA	0.587																																					p.G770R		.											.	ABCC1-94	0			c.G2308A						.						60	71	68					16																	16180696		2181	4293	6474	SO:0001583	missense	4363	exon18			CTGTCTGGGGGCC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2308G>A	16.37:g.16180696G>A	ENSP00000382342:p.Gly770Arg	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	35	5	NM_004996	0	0	5	8	3	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	33	5.195409	0.94960	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000351154;ENST00000345148;ENST00000536381	D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64	5.38	5.38	0.77491	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98658	0.9550	H	0.99182	4.46	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.993;0.978;1.0;1.0	D	0.99712	1.1007	10	0.87932	D	0	-31.1556	18.1249	0.89583	0.0:0.0:1.0:0.0	.	770;711;770;770	P33527-4;P33527-2;P33527;P33527-9	.;.;MRP1_HUMAN;.	R	770;770;711;770;444	ENSP00000382342:G770R;ENSP00000382340:G770R;ENSP00000263017:G711R;ENSP00000263014:G770R	ENSP00000263014:G770R	G	+	1	0	ABCC1	16088197	1.000000	0.71417	0.984000	0.44739	0.997000	0.91878	9.697000	0.98697	2.520000	0.84964	0.563000	0.77884	GGG	.		0.587	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16180696	G	A	16180696	3	1	120	1	0	0	0	0	1	0	0	0	49	1348	47	2	2378	2	ABCC1	16	16180696	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	12320059	16180696	74174057	35	10438											
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	24788620	24788620	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagccagtcagaaagcagtgCtttaacaaatcaacagccac	16	6	7	12	0	2	1	2	0	0	1	2	1	2	1	2	0	6	2	2	0	4	2	rs201630200		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:24788620C>G	ENST00000395799.3	+	5	659	c.530C>G	c.(529-531)gCt>gGt	p.A177G	TNRC6A_ENST00000315183.7_Missense_Mutation_p.A177G	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	177	Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GAAAGCAGTGCTTTAACAAAT	0.433																																					p.A177G		.											.	TNRC6A-92	0			c.C530G						.						137	141	140					16																	24788620		2064	4235	6299	SO:0001583	missense	27327	exon5			GCAGTGCTTTAAC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.530C>G	16.37:g.24788620C>G	ENSP00000379144:p.Ala177Gly	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	59	24	NM_014494	0	0	3	8	5	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446741	0.43429	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.12774	2.65;2.65	5.72	4.72	0.59763	.	0.361735	0.29783	N	0.011217	T	0.11110	0.0271	N	0.19112	0.55	0.80722	D	1	B	0.20261	0.043	B	0.19946	0.027	T	0.17228	-1.0376	10	0.26408	T	0.33	-7.991	18.3586	0.90367	0.0:0.8717:0.1283:0.0	.	177	Q8NDV7	TNR6A_HUMAN	G	177	ENSP00000326900:A177G;ENSP00000379144:A177G	ENSP00000326900:A177G	A	+	2	0	TNRC6A	24696121	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.054000	0.49908	2.687000	0.91594	0.591000	0.81541	GCT	.		0.433	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24788620	C	G	24788620	3	3	120	1	0	0	0	0	1	0	0	0	16372	797	28	4	548	4	TNRC6A	16	24788620	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	8607924	24788620	65566133	36	10439											
COG4	25839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	70548271	70548271	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggctgagctcaatgaccgActtgtccaggcacaagtagc	10	8	11	12	2	1	2	1	2	0	0	3	3	2	2	2	2	2	4	2	2	3	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:70548271A>T	ENST00000323786.5	-	4	532	c.511T>A	c.(511-513)Tcg>Acg	p.S171T	COG4_ENST00000393612.4_Missense_Mutation_p.S167T|COG4_ENST00000564653.1_Missense_Mutation_p.S171T	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	167					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				tcaatgaccgACTTGTCCAGG	0.468																																					p.S171T		.											.	COG4-90	0			c.T511A						.						89	75	80					16																	70548271		2198	4300	6498	SO:0001583	missense	25839	exon4			TGACCGACTTGTC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.511T>A	16.37:g.70548271A>T	ENSP00000315775:p.Ser171Thr	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	44	14	NM_015386	0	0	12	24	12	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	37	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.316795	0.81469	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.46819	0.86;0.86;1.12	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.41305	0.1153	L	0.41961	1.31	0.80722	D	1	B;B	0.24368	0.057;0.102	B;B	0.20955	0.032;0.018	T	0.20706	-1.0267	10	0.25751	T	0.34	-5.8107	15.6224	0.76816	1.0:0.0:0.0:0.0	.	166;167	Q6PIW8;Q9H9E3	.;COG4_HUMAN	T	171;167;167;94	ENSP00000315775:S171T;ENSP00000377236:S167T;ENSP00000461912:S94T	ENSP00000315775:S171T	S	-	1	0	COG4	69105772	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.758000	0.91663	2.093000	0.63338	0.459000	0.35465	TCG	.		0.468	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			T	70548271	A	T	70548271	3	4	120	1	0	0	0	0	1	0	0	0	3666	275	10	5	1922	5	COG4	16	70548271	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	45759651	70548271	19806482	37	10440											
KIAA0100	9703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26943696	26943696	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcatcatcttccacacttcGgccaggaaagaaaaagccca	14	8	6	13	1	3	1	2	0	1	1	5	2	4	2	3	2	1	0	3	2	3	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:26943696G>C	ENST00000528896.2	-	35	6171	c.6097C>G	c.(6097-6099)Cga>Gga	p.R2033G	SGK494_ENST00000301037.5_5'Flank|SPAG5-AS1_ENST00000424210.1_RNA|SGK494_ENST00000469832.3_5'Flank|KIAA0100_ENST00000579924.2_5'UTR|SPAG5-AS1_ENST00000414744.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R1890G|SPAG5-AS1_ENST00000554154.1_RNA|RP11-192H23.4_ENST00000577790.1_5'Flank|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R1890G|RP11-192H23.4_ENST00000534850.1_5'Flank	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	2033						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					TCCACACTTCGGCCAGGAAAG	0.448																																					p.R2033G		.											.	KIAA0100-93	0			c.C6097G						.						118	121	120					17																	26943696		2203	4300	6503	SO:0001583	missense	9703	exon35			CACTTCGGCCAGG	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.6097C>G	17.37:g.26943696G>C	ENSP00000436773:p.Arg2033Gly	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	140	85	NM_014680	0	0	29	69	40	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483328	0.63962	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.46819	0.86;0.86	5.87	5.87	0.94306	FMP27,  C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70605	0.3243	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67205	-0.5729	10	0.39692	T	0.17	.	20.1947	0.98239	0.0:0.0:1.0:0.0	.	2033	Q14667	K0100_HUMAN	G	2033;2003;2033;1890	ENSP00000436773:R2033G;ENSP00000446443:R1890G	ENSP00000005905:R2033G	R	-	1	2	KIAA0100	23967823	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	3.682000	0.54656	2.780000	0.95670	0.561000	0.74099	CGA	.		0.448	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26943696	G	C	26943696	3	2	120	1	0	0	0	0	1	0	0	0	8175	1124	39	4	630	4	KIAA0100	17	26943696	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		26943696	54251514	38	10441											
HOXB4	3214	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	46654346	46654346	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcgtgtaggcggtccgaGagcgcttgggctccccgccg	3	6	18	14	7	0	1	0	0	0	1	2	2	2	1	4	4	1	3	4	4	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:46654346G>T	ENST00000332503.5	-	2	2285	c.494C>A	c.(493-495)tCt>tAt	p.S165Y	HOXB3_ENST00000485909.2_5'Flank|HOXB3_ENST00000489475.1_Intron|HOXB3_ENST00000552000.2_Intron|MIR10A_ENST00000385043.1_RNA|HOXB3_ENST00000311626.4_5'Flank|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000490677.1_5'Flank|HOXB3_ENST00000472863.1_Intron|HOXB3_ENST00000476342.1_Intron|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000460160.1_Intron|HOXB-AS3_ENST00000465846.2_RNA	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	165					anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						GGCGGTCCGAGAGCGCTTGGG	0.592																																					p.S165Y		.											.	HOXB4-515	0			c.C494A						.						53	58	56					17																	46654346		2203	4300	6503	SO:0001583	missense	3214	exon2			GTCCGAGAGCGCT		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.494C>A	17.37:g.46654346G>T	ENSP00000328928:p.Ser165Tyr	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	101	57	NM_024015	0	0	5	16	11	Q9NTA0	Missense_Mutation	SNP	ENST00000332503.5	37	CCDS11529.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923509	0.92319	.	.	ENSG00000182742	ENST00000332503	D	0.96365	-3.99	5.27	5.27	0.74061	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96836	0.8967	L	0.33710	1.025	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.97955	1.0334	10	0.87932	D	0	.	18.4966	0.90867	0.0:0.0:1.0:0.0	.	165	P17483	HXB4_HUMAN	Y	165	ENSP00000328928:S165Y	ENSP00000328928:S165Y	S	-	2	0	HOXB4	44009345	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.842000	0.99487	2.456000	0.83038	0.561000	0.74099	TCT	.		0.592	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			T	46654346	G	T	46654346	3	4	120	1	0	0	0	0	1	0	0	0	7324	942	33	4	265	4	HOXB4	17	46654346	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	19710650	46654346	34540864	39	10442											
NOG	9241	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	54672182	54672182	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgtccaagtccgtgcacCtcacggtgctgcggtggcgc	5	7	14	15	5	1	0	1	0	0	0	3	0	3	0	4	3	4	2	4	3	1	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:54672182C>G	ENST00000332822.4	+	1	1123	c.598C>G	c.(598-600)Ctc>Gtc	p.L200V		NM_005450.4	NP_005441.1	Q13253	NOGG_HUMAN	noggin	200					axial mesoderm development (GO:0048318)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal system development (GO:0048706)|endoderm formation (GO:0001706)|epithelial to mesenchymal transition (GO:0001837)|face morphogenesis (GO:0060325)|fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060825)|in utero embryonic development (GO:0001701)|limb development (GO:0060173)|lung morphogenesis (GO:0060425)|mesoderm formation (GO:0001707)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell migration (GO:0030336)|negative regulation of cytokine activity (GO:0060302)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glomerulus development (GO:0090193)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostatic bud formation (GO:0060513)|regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000313)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|somite development (GO:0061053)|spinal cord development (GO:0021510)|ureteric bud formation (GO:0060676)|wound healing (GO:0042060)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)			ovary(1)	1	Breast(9;5.24e-08)					GTCCGTGCACCTCACGGTGCT	0.657																																					p.L200V													.	NOG-90	0			c.C598G						.						27	27	27					17																	54672182		2203	4298	6501	SO:0001583	missense	9241	exon1			GTGCACCTCACGG	U31202	CCDS11589.1	17q22	2006-04-25	2003-03-12		ENSG00000183691	ENSG00000183691			7866	protein-coding gene	gene with protein product		602991	"synostoses (multiple) syndrome 1", "symphalangism 1 (proximal)"	SYNS1, SYM1		7666191, 10080184, 11545688	Standard	NM_005450		Approved		uc002iup.2	Q13253	OTTHUMG00000151770	ENST00000332822.4:c.598C>G	17.37:g.54672182C>G	ENSP00000328181:p.Leu200Val	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	177	105	NM_005450	0	0	0	1	1		Missense_Mutation	SNP	ENST00000332822.4	37	CCDS11589.1	.	.	.	.	.	.	.	.	.	.	C	7.750	0.703154	0.15172	.	.	ENSG00000183691	ENST00000332822	D	0.98207	-4.79	4.85	4.85	0.62838	.	0.163070	0.39146	N	0.001455	D	0.96904	0.8989	L	0.39898	1.24	0.51012	D	0.999903	D	0.56035	0.974	P	0.59703	0.862	D	0.94063	0.7328	10	0.08179	T	0.78	-8.1502	8.5633	0.33525	0.0:0.8257:0.0:0.1743	.	200	Q13253	NOGG_HUMAN	V	200	ENSP00000328181:L200V	ENSP00000328181:L200V	L	+	1	0	NOG	52027181	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.537000	0.23144	2.532000	0.85374	0.561000	0.74099	CTC	.		0.657	NOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323857.1	NM_005450		G	54672182	C	G	54672182	3	3	120	1	0	0	0	0	1	0	0	0	10545	681	24	4	600	4	NOG	17	54672182	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	8017836	54672182	26523028	40	10443											
KIAA0195	9772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73487468	73487468	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgttcttcagcgggaaggtgGagccccctcacagcagccat	8	8	12	13	1	3	0	2	0	1	0	3	2	3	2	3	3	4	2	3	3	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:73487468G>T	ENST00000314256.7	+	13	1712	c.1318G>T	c.(1318-1320)Gag>Tag	p.E440*	KIAA0195_ENST00000579208.1_Nonsense_Mutation_p.E91*|KIAA0195_ENST00000375248.5_Nonsense_Mutation_p.E450*	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	440						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGGAAGGTGGAGCCCCCTCA	0.602																																					p.E440X		.											.	KIAA0195-91	0			c.G1318T						.						102	89	93					17																	73487468		2203	4300	6503	SO:0001587	stop_gained	9772	exon13			AAGGTGGAGCCCC		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.1318G>T	17.37:g.73487468G>T	ENSP00000313885:p.Glu440*	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	74	22	NM_014738	0	0	25	27	2	O75536|Q86XF1	Nonsense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089916	0.94149	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	.	.	.	5.84	4.86	0.63082	.	0.100124	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-25.239	16.9369	0.86205	0.0:0.1279:0.8721:0.0	.	.	.	.	X	440;450	.	ENSP00000313885:E440X	E	+	1	0	KIAA0195	70999063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.741000	0.98843	1.465000	0.48006	0.591000	0.81541	GAG	.		0.602	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		T	73487468	G	T	73487468	4	4	120	1	0	0	0	0	0	1	0	0	8181	1175	41	4	1364	4	KIAA0195	17	73487468	Nonsense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	18815286	73487468	7707742	41	10444											
SS18	6760	ucsc.edu	37	chr18	23658090	23658090	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaatctgctattgtagcaaGgtataccaagtttgtgtgca	12	13	10	6	0	1	1	0	0	1	1	1	1	1	1	1	1	4	6	1	1	7	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr18:23658090G>T	ENST00000415083.2	-	3	236	c.181C>A	c.(181-183)Ctt>Att	p.L61I	SS18_ENST00000542743.1_Missense_Mutation_p.L9I|SS18_ENST00000585241.1_5'UTR|SS18_ENST00000542420.2_Missense_Mutation_p.L38I|SS18_ENST00000539849.1_Intron|SS18_ENST00000269137.7_Missense_Mutation_p.L61I|SS18_ENST00000545952.1_Missense_Mutation_p.L9I	NM_001007559.1|NM_005637.2	NP_001007560.1|NP_005628.2	Q15532	SSXT_HUMAN	synovial sarcoma translocation, chromosome 18	61	Transcriptional activation.				cell morphogenesis (GO:0000902)|ephrin receptor signaling pathway (GO:0048013)|intracellular signal transduction (GO:0035556)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)		SS18/SSX2(706)|SS18/SSX1(1169)|SS18/SSX4(12)	endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(1)	19	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)					ATTGTAGCAAGGTATACCAAG	0.303			T	"SSX1,  SSX2"	synovial sarcoma																																p.L61I				Dom	yes		18	18q11.2	6760	"synovial sarcoma translocation, chromosome 18"		M	.	SS18-1968	0			c.C181A						.						139	132	134					18																	23658090		2203	4298	6501	SO:0001583	missense	6760	exon3			TAGCAAGGTATAC	X79201	CCDS32807.1, CCDS54183.1	18q11.2	2008-07-28				ENSG00000141380			11340	protein-coding gene	gene with protein product		600192		SSXT		8152806, 7951320, 16484776	Standard	XM_005258334		Approved	SYT	uc002kvm.3	Q15532		ENST00000415083.2:c.181C>A	18.37:g.23658090G>T	ENSP00000414516:p.Leu61Ile	Somatic	65	0		WXS	Illumina HiSeq		42	4	NM_001007559	0	0	15	15	0	B0YJ95|Q16404|Q4VAX1|Q9BXC6	Missense_Mutation	SNP	ENST00000415083.2	37	CCDS32807.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.197652	0.38806	.	.	ENSG00000141380	ENST00000415083;ENST00000269138;ENST00000269137;ENST00000542420;ENST00000542743;ENST00000545952	T;T;T;T	0.76060	-0.99;-0.89;0.36;0.36	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.88175	0.6366	M	0.91140	3.18	0.80722	D	1	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.91635	0.987;0.992;0.999	D	0.89906	0.4048	10	0.87932	D	0	-10.1651	12.1087	0.53827	0.0791:0.0:0.9209:0.0	.	9;61;61	B4E2J6;Q4VAX0;Q15532	.;.;SSXT_HUMAN	I	64;61;61;38;9;9	ENSP00000269137:L61I;ENSP00000438066:L38I;ENSP00000444551:L9I;ENSP00000443097:L9I	ENSP00000269137:L61I	L	-	1	0	SS18	21912088	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.519000	0.53458	2.716000	0.92895	0.655000	0.94253	CTT	.		0.303	SS18-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446226.1			T	23658090	G	T	23658090	3	4	120	1	0	0	0	0	1	0	0	0	15207	1000	35	4	1111	4	SS18	18	23658090	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		23658090	54419158	42	10445											
ACER1	125981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6307219	6307219	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagaagctgcaaagcagacGgtcactgatccagctggtca	12	6	11	12	1	2	3	2	1	0	2	3	3	3	3	2	2	4	4	2	2	2	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:6307219G>T	ENST00000301452.4	-	5	648	c.571C>A	c.(571-573)Cgt>Agt	p.R191S		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	191					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						CAAAGCAGACGGTCACTGATC	0.542																																					p.R191S		.											.	ACER1-90	0			c.C571A						.						89	86	87					19																	6307219		2203	4300	6503	SO:0001583	missense	125981	exon5			GCAGACGGTCACT	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.571C>A	19.37:g.6307219G>T	ENSP00000301452:p.Arg191Ser	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	34	9	NM_133492	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301452.4	37	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.037897	0.75617	.	.	ENSG00000167769	ENST00000301452	T	0.47177	0.85	5.58	3.34	0.38264	.	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.87900	2.915	0.80722	D	1	D	0.71674	0.998	D	0.63703	0.917	T	0.75932	-0.3143	10	0.87932	D	0	-21.1368	12.8258	0.57718	0.0:0.0:0.7048:0.2952	.	191	Q8TDN7	ACER1_HUMAN	S	191	ENSP00000301452:R191S	ENSP00000301452:R191S	R	-	1	0	ACER1	6258219	1.000000	0.71417	0.923000	0.36655	0.707000	0.40811	3.467000	0.53078	1.347000	0.45714	0.561000	0.74099	CGT	.		0.542	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		T	6307219	G	T	6307219	3	4	120	1	0	0	0	0	1	0	0	0	138	1116	39	4	231	4	ACER1	19	6307219	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		6307219	52821764	43	10446											
ZNF529	57711	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	37038841	37038841	+	Frame_Shift_Del	DEL	T	T	-																															ggagttatctatcccaaaggTtttccaacattgattacatt																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:37038841delT	ENST00000591340.1	-	5	777	c.619delA	c.(619-621)accfs	p.T207fs	ZNF529_ENST00000334116.7_Frame_Shift_Del_p.T102fs	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	207					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)	1	Esophageal squamous(110;0.198)					ATCCCAAAGGTTTTCCAACAT	0.313																																					p.T207fs		.											.	ZNF529-67	0			c.619delA						.						77	71	73					19																	37038841		1844	4087	5931	SO:0001589	frameshift_variant	57711	exon6			.	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"Zinc fingers, C2H2-type", "-"	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.619delA	19.37:g.37038841delT	ENSP00000465578:p.Thr207fs	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	47	15	NM_001145649	0	0	0	0	0	K7EKE1|Q9H731|Q9HCF7	Frame_Shift_Del	DEL	ENST00000591340.1	37	CCDS54256.1																																																																																			.		0.313	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		-	37038841	T	-	37038841	7	5	120	1	0	1	0	1	0	0	0	0	18002	1725	60	0	1076	0	ZNF529	19	37038841	Frame_Shift_Del	DEL	T	TCGA-G7-A4TM-01A-11D-A31X-10	30731622	37038841	22090142	44	10447											
CAPN12	147968	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	39226808	39226808	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtcagcctcgtcgccggCgtgggcggtgctcggcacca	5	6	16	14	6	1	0	1	0	0	0	4	1	1	0	3	4	2	2	3	4	1	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:39226808C>T	ENST00000328867.4	-	12	1833	c.1525G>A	c.(1525-1527)Gcc>Acc	p.A509T	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Missense_Mutation_p.A360T	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	509	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			TCGTCGCCGGCGTGGGCGGTG	0.731																																					p.A509T		.											.	CAPN12-91	0			c.G1525A						.						5	7	6					19																	39226808		1560	2860	4420	SO:0001583	missense	147968	exon12			CGCCGGCGTGGGC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"EF-hand domain containing"	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1525G>A	19.37:g.39226808C>T	ENSP00000331636:p.Ala509Thr	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	17	8	NM_144691	0	0	5	7	2		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434611	0.43224	.	.	ENSG00000182472	ENST00000328867	D	0.87256	-2.23	3.72	2.48	0.30137	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.544531	0.18591	N	0.136731	T	0.80909	0.4714	L	0.55990	1.75	0.22266	N	0.999247	B	0.19331	0.035	B	0.12156	0.007	T	0.72204	-0.4361	10	0.87932	D	0	.	3.9299	0.09279	0.0:0.5899:0.2287:0.1814	.	509	Q6ZSI9	CAN12_HUMAN	T	509	ENSP00000331636:A509T	ENSP00000331636:A509T	A	-	1	0	CAPN12	43918648	0.987000	0.35691	0.077000	0.20336	0.396000	0.30629	2.272000	0.43373	0.658000	0.30925	0.484000	0.47621	GCC	.		0.731	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39226808	C	T	39226808	3	4	120	1	0	0	0	0	1	0	0	0	2631	768	27	1	674	1	CAPN12	19	39226808	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	2187967	39226808	19902175	45	10448											
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42795850	42795850	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agccactgccactggtgagcCcgcccttctcagtacctgtg	6	9	10	16	1	1	1	1	1	1	0	2	1	1	1	5	1	4	1	5	1	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:42795850C>T	ENST00000575354.2	+	11	2879	c.2839C>T	c.(2839-2841)Ccg>Tcg	p.P947S	CIC_ENST00000572681.2_Missense_Mutation_p.P1856S|CIC_ENST00000160740.3_Missense_Mutation_p.P947S	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	947	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ACTGGTGAGCCCGCCCTTCTC	0.662			"Mis, F, S"		oligodendroglioma																																p.P947S		.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC-591	0			c.C2839T						.						46	52	50					19																	42795850		2048	4111	6159	SO:0001583	missense	23152	exon11			GTGAGCCCGCCCT	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"capicua (Drosophila) homolog", "capicua homolog (Drosophila)"			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.2839C>T	19.37:g.42795850C>T	ENSP00000458663:p.Pro947Ser	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	88	32	NM_015125	0	0	21	39	18	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	9.524	1.109082	0.20714	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.32	3.28	0.37604	.	.	.	.	.	T	0.44138	0.1279	L	0.29908	0.895	0.35299	D	0.782869	B	0.13145	0.007	B	0.12156	0.007	T	0.52200	-0.8607	8	0.87932	D	0	-7.0964	9.1066	0.36701	0.0:0.8892:0.0:0.1108	.	947	Q96RK0	CIC_HUMAN	S	947	.	ENSP00000160740:P947S	P	+	1	0	CIC	47487690	1.000000	0.71417	0.980000	0.43619	0.928000	0.56348	3.631000	0.54280	1.014000	0.39417	0.462000	0.41574	CCG	.		0.662	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			T	42795850	C	T	42795850	3	4	120	1	0	0	0	0	1	0	0	0	3430	623	22	2	2881	2	CIC	19	42795850	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	3569042	42795850	16333133	46	10449											
TMEM145	284339	broad.mit.edu	37	chr19	42819592	42819592	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggccgcagcaggagtagagGgtgaggttccgtgtcccaac	8	7	16	10	2	0	2	0	1	0	1	2	3	2	3	3	4	2	4	3	4	2	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:42819592G>T	ENST00000301204.3	+	8	687	c.646G>T	c.(646-648)Gtc>Ttc	p.V216F	TMEM145_ENST00000598766.1_Splice_Site_p.V240F	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	216					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				Aggagtagagggtgaggttcc	0.537																																					p.V216F													.	TMEM145-90	0			c.G646T						.						96	90	92					19																	42819592		2203	4300	6503	SO:0001630	splice_region_variant	284339	exon8			GTAGAGGGTGAGG	AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.646+1G>T	19.37:g.42819592G>T		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	57	3	NM_173633	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301204.3	37	CCDS12603.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.997506	0.54147	.	.	ENSG00000167619	ENST00000301204	T	0.41758	0.99	3.93	3.93	0.45458	Rhodopsin-like GPCR transmembrane domain (1);	0.000000	0.64402	D	0.000009	T	0.44030	0.1274	L	0.32530	0.975	0.80722	D	1	D	0.67145	0.996	D	0.67382	0.951	T	0.33904	-0.9850	10	0.05436	T	0.98	-29.9471	11.8194	0.52230	0.0:0.0:1.0:0.0	.	216	Q8NBT3	TM145_HUMAN	F	216	ENSP00000301204:V216F	ENSP00000301204:V216F	V	+	1	0	TMEM145	47511432	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.047000	0.76599	1.926000	0.55796	0.455000	0.32223	GTC	.		0.537	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1	NM_173633	Missense_Mutation	T	42819592	G	T	42819592	5	4	120	1	0	0	0	0	0	0	1	0	16091	1246	43	4	676	4	TMEM145	19	42819592	Splice_Site	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	23742	42819592	16309391	47	10450											
ZNF814	730051	bcgsc.ca	37	chr19	58385788	58385788	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccacattctccacattcatAaggtcttttcccagtgtgaa	10	13	5	13	0	3	1	1	1	2	0	5	1	4	1	3	1	0	0	3	1	2	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:58385788A>G	ENST00000435989.2	-	3	1204	c.970T>C	c.(970-972)Tat>Cat	p.Y324H	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	324					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CCACATTCATAAGGTCTTTTC	0.358																																					p.Y324H													.	.	0			c.T970C						.						15	12	13					19																	58385788		688	1564	2252	SO:0001583	missense	730051	exon3			ATTCATAAGGTCT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.970T>C	19.37:g.58385788A>G	ENSP00000410545:p.Tyr324His	Somatic	103	0		WXS	Illumina HiSeq	Phase_1	78	6	NM_001144989	0	0	1	1	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.644	0.896732	0.17686	.	.	ENSG00000204514	ENST00000435989	T	0.21734	1.99	2.27	-1.27	0.09347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13970	0.0338	L	0.33485	1.01	0.09310	N	1	B	0.27498	0.18	B	0.22386	0.039	T	0.24368	-1.0162	9	0.72032	D	0.01	.	7.1587	0.25652	0.6135:0.0:0.3865:0.0	.	324	B7Z6K7	ZN814_HUMAN	H	324	ENSP00000410545:Y324H	ENSP00000410545:Y324H	Y	-	1	0	ZNF814	63077600	0.000000	0.05858	0.008000	0.14137	0.034000	0.12701	0.130000	0.15850	-0.181000	0.10619	0.113000	0.15668	TAT	.		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		G	58385788	A	G	58385788	3	3	120	1	0	0	0	0	1	0	0	0	18208	362	13	3	1601	3	ZNF814	19	58385788	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	15566196	58385788	743195	48	10451											
ARFGEF2	10564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47587774	47587774	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aatgcaatcaagcaatatctCtgtgtggccttgtccaaaaa	14	11	7	9	0	2	0	1	0	1	0	4	0	3	0	2	1	2	2	2	1	7	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr20:47587774C>G	ENST00000371917.4	+	10	1308	c.1308C>G	c.(1306-1308)ctC>ctG	p.L436L		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	436					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGCAATATCTCTGTGTGGCCT	0.458																																					p.L436L	Esophageal Squamous(176;1738 1974 26285 33069 35354)	.											.	ARFGEF2-358	0			c.C1308G						.						213	185	195					20																	47587774		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon10			ATATCTCTGTGTG	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1308C>G	20.37:g.47587774C>G		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	115	47	NM_006420	0	0	2	3	1	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			.		0.458	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		G	47587774	C	G	47587774	2	3	120	1	0	0	0	0	0	0	0	1	853	900	32	4		4	ARFGEF2	20	47587774	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		47587774	15437746	49	10452											
NCAM2	4685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	22710734	22710734	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcacataatacagcttaaAaatgaaactacatatgagaa	20	9	4	8	0	1	2	1	2	0	1	1	3	1	2	1	0	4	1	1	0	9	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr21:22710734A>C	ENST00000400546.1	+	8	1173	c.924A>C	c.(922-924)aaA>aaC	p.K308N	NCAM2_ENST00000535285.1_Missense_Mutation_p.K333N|NCAM2_ENST00000284894.7_Missense_Mutation_p.K166N	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	308	Ig-like C2-type 4.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TACAGCTTAAAAATGAAACTA	0.388																																					p.K308N		.											.	NCAM2-94	0			c.A924C						.						59	58	59					21																	22710734		1859	4085	5944	SO:0001583	missense	4685	exon8			GCTTAAAAATGAA		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.924A>C	21.37:g.22710734A>C	ENSP00000383392:p.Lys308Asn	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	148	61	NM_004540	0	0	0	0	0	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.936147	0.52972	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.69685	-0.42;-0.42;-0.42	5.8	3.37	0.38596	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276736	0.45867	D	0.000323	T	0.67382	0.2887	L	0.39245	1.2	0.53688	D	0.999977	D;P;P	0.55800	0.973;0.776;0.618	P;P;B	0.56474	0.799;0.558;0.374	T	0.64761	-0.6331	10	0.49607	T	0.09	-16.2371	9.6438	0.39855	0.8549:0.0:0.1451:0.0	.	333;166;308	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	N	308;166;333	ENSP00000383392:K308N;ENSP00000284894:K166N;ENSP00000441887:K333N	ENSP00000284894:K166N	K	+	3	2	NCAM2	21632605	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	2.518000	0.45537	0.426000	0.26116	0.482000	0.46254	AAA	.		0.388	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		C	22710734	A	C	22710734	3	2	120	1	0	0	0	0	1	0	0	0	10229	11	1	5	954	5	NCAM2	21	22710734	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		22710734	25419161	50	10453											
RBM3	5935	broad.mit.edu	37	chrX	48434952	48434952	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgacagtcgacctggagggTatggatatggatatggacgt	11	10	15	5	2	0	1	0	1	0	0	1	6	0	5	1	5	0	1	1	5	3	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chrX:48434952T>G	ENST00000376759.3	+	5	436	c.373T>G	c.(373-375)Tat>Gat	p.Y125D	RBM3_ENST00000354480.2_Silent_p.G97G|RBM3_ENST00000430348.2_Silent_p.G97G|RBM3_ENST00000466764.1_3'UTR|RBM3_ENST00000376755.1_Missense_Mutation_p.Y125D|AC115618.1_ENST00000376775.2_5'Flank	NM_006743.4	NP_006734.1	P98179	RBM3_HUMAN	RNA binding motif (RNP1, RRM) protein 3	125	Gly-rich.				positive regulation of translation (GO:0045727)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of translation (GO:0006417)|response to cold (GO:0009409)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						ACCTGGAGGGTATGGATATGG	0.498																																					p.Y125D													.	RBM3-131	0			c.T373G						.						85	72	77					X																	48434952		2198	4293	6491	SO:0001583	missense	5935	exon5			GGAGGGTATGGAT	BC006825	CCDS14301.1	Xp11.2	2014-05-19	2004-04-23		ENSG00000102317	ENSG00000102317		"RNA binding motif (RRM) containing"	9900	protein-coding gene	gene with protein product		300027	"RNA binding motif protein 3"			8634703	Standard	NM_006743		Approved	IS1-RNPL	uc004dkf.2	P98179	OTTHUMG00000024121	ENST00000376759.3:c.373T>G	X.37:g.48434952T>G	ENSP00000365950:p.Tyr125Asp	Somatic	64	12		WXS	Illumina HiSeq	Phase_I	46	15	NM_006743	3	0	306	310	1		Missense_Mutation	SNP	ENST00000376759.3	37	CCDS14301.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.209999	0.39003	.	.	ENSG00000102317	ENST00000376759;ENST00000376755	T;T	0.20598	2.06;2.06	3.86	3.86	0.44501	.	.	.	.	.	T	0.38957	0.1060	M	0.75615	2.305	0.80722	D	1	D	0.58970	0.984	P	0.62435	0.902	T	0.14117	-1.0484	9	0.30078	T	0.28	-5.6672	10.0649	0.42297	0.0:0.0:0.0:1.0	.	125	P98179	RBM3_HUMAN	D	125	ENSP00000365950:Y125D;ENSP00000365946:Y125D	ENSP00000365946:Y125D	Y	+	1	0	RBM3	48319896	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.002000	0.40835	1.735000	0.51646	0.486000	0.48141	TAT	.		0.498	RBM3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060755.1	NM_006743		G	48434952	T	G	48434952	3	3	120	1	0	0	0	0	1	0	0	0	13161	1638	57	5	387	5	RBM3	23	48434952	Missense_Mutation	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10		48434952	106835608	51	10454											
ESPN	83715	ucsc.edu	37	chr1	6512054	6512054	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgtggaggctctcatcccCacgcacgatgagcagggccg	8	5	14	14	4	1	1	1	1	1	0	3	4	2	2	3	3	1	3	3	3	0	0			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:6512054C>T	ENST00000377828.1	+	10	2391	c.2223C>T	c.(2221-2223)ccC>ccT	p.P741P	ESPN_ENST00000475228.1_3'UTR|ESPN_ENST00000416731.1_Silent_p.P175P|ESPN_ENST00000461727.1_Silent_p.P175P	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	741					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		CTCTCATCCCCACGCACGATG	0.657																																					p.P741P													.	ESPN-514	0			c.C2223T						.						22	24	23					1																	6512054		2202	4299	6501	SO:0001819	synonymous_variant	83715	exon10			CATCCCCACGCAC	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"Ankyrin repeat domain containing"	13281	protein-coding gene	gene with protein product		606351	"deafness, autosomal recessive 36"	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.2223C>T	1.37:g.6512054C>T		Somatic	19	0		WXS	Illumina HiSeq		11	4	NM_031475	0	0	4	7	3	Q6XYB2|Q9H0A2|Q9Y329	Silent	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	C	9.229	1.035281	0.19590	.	.	ENSG00000187017	ENST00000434576	.	.	.	5.14	3.25	0.37280	.	.	.	.	.	T	0.55577	0.1929	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47923	-0.9079	4	.	.	.	-29.8002	6.8679	0.24104	0.4151:0.5027:0.0:0.0823	.	.	.	.	Y	85	.	.	H	+	1	0	ESPN	6434641	0.946000	0.32159	0.974000	0.42286	0.733000	0.41908	0.080000	0.14802	0.552000	0.29026	-0.424000	0.05967	CAC	.		0.657	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		T	6512054	C	T	6512054	2	4	121	1	0	0	0	0	0	0	0	1	5267	581	21	2		2	ESPN	1	6512054	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08		6512054	242738567	1	10455											
AGL	178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	100346675	100346675	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccaagtactacaattgtttCtatggcatgttgtgctagtg	9	16	9	7	0	1	0	0	0	1	0	2	0	2	0	1	1	3	5	1	1	6	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:100346675C>G	ENST00000294724.4	+	15	2421	c.1943C>G	c.(1942-1944)tCt>tGt	p.S648C	AGL_ENST00000361522.4_Missense_Mutation_p.S631C|AGL_ENST00000361302.3_Missense_Mutation_p.S632C|AGL_ENST00000370165.3_Missense_Mutation_p.S648C|AGL_ENST00000370163.3_Missense_Mutation_p.S648C|AGL_ENST00000370161.2_Missense_Mutation_p.S632C|AGL_ENST00000361915.3_Missense_Mutation_p.S648C	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	648					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ACAATTGTTTCTATGGCATGT	0.368																																					p.S648C		.											.	AGL-92	0			c.C1943G						.						180	165	170					1																	100346675		2203	4300	6503	SO:0001583	missense	178	exon15			TTGTTTCTATGGC	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"glycogen debranching enzyme", "glycogen storage disease type III"	610860	"amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1943C>G	1.37:g.100346675C>G	ENSP00000294724:p.Ser648Cys	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	96	44	NM_000644	0	0	14	18	4	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.355191	0.41700	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	6.01	6.01	0.97437	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.049923	0.85682	D	0.000000	D	0.89681	0.6785	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.72625	0.978;0.978;0.95	D	0.90138	0.4211	10	0.87932	D	0	.	15.6295	0.76893	0.0:0.9327:0.0:0.0673	.	631;632;648	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	C	648;648;648;648;632;632;631	ENSP00000355106:S648C;ENSP00000359184:S648C;ENSP00000359182:S648C;ENSP00000294724:S648C;ENSP00000354971:S632C;ENSP00000359180:S632C;ENSP00000354635:S631C	ENSP00000294724:S648C	S	+	2	0	AGL	100119263	1.000000	0.71417	0.805000	0.32314	0.062000	0.15995	5.550000	0.67268	2.850000	0.98022	0.655000	0.94253	TCT	.		0.368	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100346675	C	G	100346675	3	3	121	1	0	0	0	0	1	0	0	0	384	913	32	4	2066	4	AGL	1	100346675	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	93834621	100346675	148903946	2	10456											
TMEM79	84283	broad.mit.edu	37	chr1	156256105	156256105	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttctgcccttcggccctttgGggagccacggcgggaggtgg	3	9	17	12	3	1	0	0	0	1	0	2	2	1	2	3	7	2	0	3	7	0	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:156256105G>C	ENST00000405535.2	+	3	983	c.812G>C	c.(811-813)gGg>gCg	p.G271A	TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000295694.5_Missense_Mutation_p.G271A|TMEM79_ENST00000357501.2_Missense_Mutation_p.W32C	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	271					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)		p.G271E(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					CGGCCCTTTGGGGAGCCACGG	0.577																																					p.G271A													.	TMEM79-90	1	Substitution - Missense(1)	lung(1)	c.G812C						.						105	103	104					1																	156256105		2203	4300	6503	SO:0001583	missense	84283	exon3			CCTTTGGGGAGCC	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"mattrin"	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.812G>C	1.37:g.156256105G>C	ENSP00000384748:p.Gly271Ala	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	106	3	NM_032323	0	0	3	3	0	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	37	CCDS1138.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.563|5.563	0.288740|0.288740	0.10513|0.10513	.|.	.|.	ENSG00000163472|ENSG00000163472	ENST00000295694;ENST00000405535|ENST00000357501;ENST00000456810	T;T|.	0.41065|.	1.01;1.01|.	5.93|5.93	0.478|0.478	0.16789|0.16789	.|.	0.639785|.	0.17656|.	N|.	0.166517|.	T|T	0.03564|0.03564	0.0102|0.0102	N|N	0.01352|0.01352	-0.895|-0.895	0.18873|0.18873	N|N	0.999988|0.999988	B|.	0.18863|.	0.031|.	B|.	0.19666|.	0.026|.	T|T	0.35674|0.35674	-0.9779|-0.9779	10|6	0.02654|0.87932	T|D	1|0	-7.6688|-7.6688	7.3474|7.3474	0.26670|0.26670	0.149:0.3975:0.4535:0.0|0.149:0.3975:0.4535:0.0	.|.	271|.	Q9BSE2|.	TMM79_HUMAN|.	A|C	271|32	ENSP00000295694:G271A;ENSP00000384748:G271A|.	ENSP00000295694:G271A|ENSP00000350100:W32C	G|W	+|+	2|3	0|0	TMEM79|TMEM79	154522729|154522729	0.243000|0.243000	0.23878|0.23878	0.081000|0.081000	0.20488|0.20488	0.992000|0.992000	0.81027|0.81027	0.649000|0.649000	0.24843|0.24843	0.100000|0.100000	0.17581|0.17581	0.561000|0.561000	0.74099|0.74099	GGG|TGG	.		0.577	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		C	156256105	G	C	156256105	3	2	121	1	0	0	0	0	1	0	0	0	16235	1232	43	4	818	4	TMEM79	1	156256105	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	55909430	156256105	92994516	3	10457											
BAT2L2	23215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171535917	171535917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggagactaaagcagtctcaGaaatgtctactgaaatagga	17	8	10	6	0	2	3	1	1	2	2	3	5	2	4	0	2	2	1	0	2	6	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:171535917G>A	ENST00000338920.4	+	22	6724	c.6487G>A	c.(6487-6489)Gaa>Aaa	p.E2163K	PRRC2C_ENST00000426496.2_Missense_Mutation_p.E2163K|PRRC2C_ENST00000367742.3_Missense_Mutation_p.E2165K|PRRC2C_ENST00000392078.3_Missense_Mutation_p.E2165K	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2163					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGCAGTCTCAGAAATGTCTAC	0.448																																					p.E2163K		.											.	.	0			c.G6487A						.						77	69	71					1																	171535917		2203	4300	6503	SO:0001583	missense	23215	exon22			GTCTCAGAAATGT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.6487G>A	1.37:g.171535917G>A	ENSP00000343629:p.Glu2163Lys	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	37	11	NM_015172	0	0	18	42	24	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627687	0.66901	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.03124	4.25;4.04;4.27;4.27	5.6	5.6	0.85130	.	0.000000	0.46145	D	0.000303	T	0.10551	0.0258	L	0.59436	1.845	0.58432	D	0.999995	D	0.89917	1.0	D	0.85130	0.997	T	0.12372	-1.0550	10	0.36615	T	0.2	.	19.6251	0.95674	0.0:0.0:1.0:0.0	.	2163	Q9Y520-4	.	K	2165;2117;2163;2165;2163;1920	ENSP00000375928:E2165K;ENSP00000410219:E2163K;ENSP00000356716:E2165K;ENSP00000343629:E2163K	ENSP00000343629:E2163K	E	+	1	0	PRRC2C	169802541	1.000000	0.71417	0.992000	0.48379	0.510000	0.34073	9.236000	0.95360	2.636000	0.89361	0.655000	0.94253	GAA	.		0.448	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		A	171535917	G	A	171535917	3	1	121	1	0	0	0	0	1	0	0	0	1322	943	33	2	6569	2	BAT2L2	1	171535917	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	15279812	171535917	77714704	4	10458											
AGT	183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	230841797	230841797	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggcaggcgctctcagtgaAgggcacttgagtcaccgaga	10	6	14	11	2	2	3	2	2	1	1	3	4	2	3	1	3	0	3	1	3	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:230841797A>T	ENST00000366667.4	-	3	1220	c.1006T>A	c.(1006-1008)Ttc>Atc	p.F336I		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	336					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CTCTCAGTGAAGGGCACTTGA	0.562																																					p.F336I		.											.	AGT-226	0			c.T1006A						.						110	104	106					1																	230841797		2203	4300	6503	SO:0001583	missense	183	exon3			CAGTGAAGGGCAC	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"Serine (or cysteine) peptidase inhibitors", "Endogenous ligands"	333	protein-coding gene	gene with protein product	"alpha-1 antiproteinase, antitrypsin"	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.1006T>A	1.37:g.230841797A>T	ENSP00000355627:p.Phe336Ile	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	126	57	NM_000029	0	0	21	51	30	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	A	8.200	0.797970	0.16327	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.84800	-1.9	5.17	-4.42	0.03579	Serpin domain (3);	0.408163	0.24752	N	0.035897	T	0.66005	0.2746	N	0.14661	0.345	0.09310	N	1	B;B;B	0.26258	0.094;0.145;0.094	B;B;B	0.25140	0.044;0.058;0.044	T	0.54556	-0.8276	10	0.34782	T	0.22	.	7.5483	0.27781	0.1397:0.142:0.6158:0.1025	.	336;336;336	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	I	336;254	ENSP00000355627:F336I	ENSP00000355627:F336I	F	-	1	0	AGT	228908420	0.002000	0.14202	0.012000	0.15200	0.007000	0.05969	-0.319000	0.08039	-0.831000	0.04256	-0.250000	0.11733	TTC	.		0.562	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		T	230841797	A	T	230841797	3	4	121	1	0	0	0	0	1	0	0	0	399	72	3	5	463	5	AGT	1	230841797	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	59305880	230841797	18408824	5	10459											
PUM2	23369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	20518349	20518349	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatccccaagaaatatgcCtttttgtccatcttttgttg	9	17	5	10	0	2	1	1	0	1	1	4	1	4	1	4	0	1	1	4	0	3	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:20518349C>T	ENST00000361078.2	-	2	131	c.109G>A	c.(109-111)Ggc>Agc	p.G37S	PUM2_ENST00000319801.5_Missense_Mutation_p.G37S|PUM2_ENST00000338086.5_Missense_Mutation_p.G37S|PUM2_ENST00000536417.1_Intron|PUM2_ENST00000420234.1_5'UTR|PUM2_ENST00000403432.1_Missense_Mutation_p.G37S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	37	Interaction with SNAPIN.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAAATATGCCTTTTTGTCCA	0.338																																					p.G37S		.											.	PUM2-91	0			c.G109A						.						142	131	135					2																	20518349		2203	4300	6503	SO:0001583	missense	23369	exon2			ATATGCCTTTTTG	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"pumilio (Drosphila) homolog 2", "pumilio homolog 2 (Drosophila)"			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.109G>A	2.37:g.20518349C>T	ENSP00000354370:p.Gly37Ser	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	91	35	NM_015317	0	0	14	25	11	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		.	.	.	.	.	.	.	.	.	.	C	16.75	3.210343	0.58343	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000403432;ENST00000442400	T;T;T;T	0.21031	2.03;2.31;2.21;2.03	5.74	0.167	0.15006	.	0.151206	0.64402	N	0.000016	T	0.17152	0.0412	L	0.49350	1.555	0.80722	D	1	B;B	0.20459	0.0;0.045	B;B	0.20184	0.001;0.028	T	0.05500	-1.0881	10	0.54805	T	0.06	-0.9827	7.59	0.28015	0.1096:0.6213:0.0:0.2691	.	37;37	B7ZL34;Q8TB72-3	.;.	S	37	ENSP00000338173:G37S;ENSP00000354370:G37S;ENSP00000326746:G37S;ENSP00000385992:G37S	ENSP00000326746:G37S	G	-	1	0	PUM2	20381830	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.338000	0.52128	0.071000	0.16664	-0.948000	0.02665	GGC	.		0.338	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		T	20518349	C	T	20518349	3	4	121	1	0	0	0	0	1	0	0	0	12858	681	24	2	3161	2	PUM2	2	20518349	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		20518349	222681024	6	10460											
UNC50	25972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	99232895	99232895	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcgtctcttctggcagAtgttatcctgacagacacat	8	13	9	11	1	3	3	0	1	3	2	5	3	4	3	1	1	1	2	1	1	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:99232895A>T	ENST00000357765.2	+	5	694	c.542A>T	c.(541-543)cAt>cTt	p.H181L	UNC50_ENST00000409975.1_Splice_Site_p.H198L|UNC50_ENST00000409347.1_Splice_Site_p.H198L	NM_014044.5	NP_054763.2	Q53HI1	UNC50_HUMAN	unc-50 homolog (C. elegans)	181					cell surface receptor signaling pathway (GO:0007166)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)	RNA binding (GO:0003723)			breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)	10						CTTCTGGCAGATGTTATCCTG	0.373																																					p.H181L		.											.	UNC50-90	0			c.A542T						.						206	198	201					2																	99232895		2203	4300	6503	SO:0001630	splice_region_variant	25972	exon5			TGGCAGATGTTAT		CCDS2035.1	2q12.2	2008-02-05			ENSG00000115446	ENSG00000115446			16046	protein-coding gene	gene with protein product						10980252	Standard	NM_014044		Approved	URP, UNCL, GMH1	uc002szc.4	Q53HI1	OTTHUMG00000130562	ENST00000357765.2:c.542-1A>T	2.37:g.99232895A>T		Somatic	140	1		WXS	Illumina HiSeq	Phase_I	106	45	NM_014044	0	0	1	3	2	D3DVH4|Q53S98|Q53TD6|Q5U5U2|Q6X7B9|Q9UQF4|Q9Y4S6	Missense_Mutation	SNP	ENST00000357765.2	37	CCDS2035.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.47|10.47	1.358643|1.358643	0.24598|0.24598	.|.	.|.	ENSG00000115446|ENSG00000115446	ENST00000357765;ENST00000409975;ENST00000409347|ENST00000393493	.|.	.|.	.|.	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	0.251636|.	0.46145|.	D|.	0.000306|.	T|T	0.35566|0.35566	0.0936|0.0936	N|N	0.04636|0.04636	-0.2|-0.2	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.08055|.	0.003|.	T|T	0.30504|0.30504	-0.9976|-0.9976	9|5	0.11182|.	T|.	0.66|.	.|.	14.6244|14.6244	0.68611|0.68611	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	181|.	Q53HI1|.	UNC50_HUMAN|.	L|L	181;198;198|48	.|.	ENSP00000350409:H181L|.	H|M	+|+	2|1	0|0	UNC50|UNC50	98599327|98599327	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.713000|0.713000	0.41058|0.41058	8.609000|8.609000	0.90898|0.90898	2.238000|2.238000	0.73509|0.73509	0.477000|0.477000	0.44152|0.44152	CAT|ATG	.		0.373	UNC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252987.1	NM_014044	Missense_Mutation	T	99232895	A	T	99232895	5	4	121	1	0	0	0	0	0	0	1	0	17023	347	12	5	556	5	UNC50	2	99232895	Splice_Site	SNP	A	TCGA-GL-6846-01A-11D-1961-08	78714546	99232895	143966478	7	10461											
TTN	7273	ucsc.edu;bcgsc.ca	37	chr2	179611166	179611166	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcttctcaaattctttaaCgtctttttcacttaattcaa	10	19	2	10	1	5	0	3	0	3	0	6	0	5	0	0	0	2	1	0	0	4	8	rs397517817		TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:179611166C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000359218.5_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.V5321I|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATTCTTTAACGTCTTTTTCA	0.363																																					p.V5321I													.	TTN-636	0			c.G15961A						.						64	58	60					2																	179611166		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			CTTTAACGTCTTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10361-4518G>A	2.37:g.179611166C>T		Somatic	67	0		WXS	Illumina HiSeq		36	10	NM_133379	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	16.24	3.067909	0.55539	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.60040	0.22	5.88	5.88	0.94601	.	.	.	.	.	T	0.70833	0.3269	M	0.63843	1.955	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.64364	-0.6425	9	0.16896	T	0.51	.	14.3978	0.67022	0.0:0.9299:0.0:0.0701	.	5321	Q8WZ42-6	.	I	5321;602	ENSP00000354117:V5321I	ENSP00000304714:V602I	V	-	1	0	TTN	179319411	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.083000	0.71326	2.782000	0.95742	0.655000	0.94253	GTT	.		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179611166	C	T	179611166	1	4	121	0	1	0	0	0	0	0	0	0	16768	536	19	1		1	TTN	2	179611166	Intron	SNP	C	TCGA-GL-6846-01A-11D-1961-08	80378271	179611166	63588207	8	10462											
ANKRD44	91526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197986231	197986231	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccattgtagcaggcgatgTgaagcgctgtatttccatag	9	12	12	8	2	0	1	0	1	0	0	2	2	2	1	2	1	2	4	2	1	4	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:197986231T>C	ENST00000328737.2	-	8	732	c.656A>G	c.(655-657)cAc>cGc	p.H219R	ANKRD44_ENST00000282272.8_Missense_Mutation_p.H236R|ANKRD44_ENST00000450567.1_Missense_Mutation_p.H219R|ANKRD44_ENST00000539527.1_Missense_Mutation_p.H172R|ANKRD44_ENST00000337207.5_Missense_Mutation_p.H219R|ANKRD44_ENST00000409919.1_Missense_Mutation_p.H244R|ANKRD44_ENST00000409153.1_Missense_Mutation_p.H244R			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	244										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GCAGGCGATGTGAAGCGCTGT	0.433																																					p.H244R		.											.	ANKRD44-230	0			c.A731G						.						155	117	130					2																	197986231		2203	4300	6503	SO:0001583	missense	91526	exon8			GCGATGTGAAGCG	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.656A>G	2.37:g.197986231T>C	ENSP00000331516:p.His219Arg	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	50	18	NM_153697	0	0	0	0	0	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		.	.	.	.	.	.	.	.	.	.	T	22.1	4.245633	0.80024	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000409153;ENST00000539527;ENST00000409919	T;T;T;T;T;T;T;T	0.79554	-0.56;-0.56;-1.28;-1.28;-1.28;-0.56;-1.28;-1.28	5.14	5.14	0.70334	.	0.105903	0.64402	D	0.000004	D	0.90287	0.6962	M	0.85630	2.765	0.58432	D	0.999999	D;D	0.89917	1.0;0.99	D;D	0.81914	0.995;0.968	D	0.91903	0.5533	10	0.87932	D	0	.	15.4162	0.74970	0.0:0.0:0.0:1.0	.	172;244	F5H682;Q8N8A2-3	.;.	R	41;236;219;219;219;244;172;244	ENSP00000403415:H41R;ENSP00000282272:H236R;ENSP00000331516:H219R;ENSP00000402420:H219R;ENSP00000338794:H219R;ENSP00000387141:H244R;ENSP00000437825:H172R;ENSP00000387233:H244R	ENSP00000282272:H236R	H	-	2	0	ANKRD44	197694476	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	7.825000	0.86693	2.285000	0.76669	0.533000	0.62120	CAC	.		0.433	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		C	197986231	T	C	197986231	3	2	121	1	0	0	0	0	1	0	0	0	672	1696	59	3	2179	3	ANKRD44	2	197986231	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	18375065	197986231	45213142	9	10463											
FZD5	7855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	208632800	208632800	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgaaggacggctggtagcAgggtaccgcgcagttgggca	9	6	17	9	3	0	1	0	1	0	0	0	2	0	2	1	5	2	7	1	5	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:208632800A>G	ENST00000295417.3	-	2	1217	c.664T>C	c.(664-666)Tgc>Cgc	p.C222R		NM_003468.3	NP_003459.2	Q13467	FZD5_HUMAN	frizzled class receptor 5	222					angiogenesis (GO:0001525)|anterior/posterior axis specification, embryo (GO:0008595)|apoptotic process (GO:0006915)|apoptotic process involved in morphogenesis (GO:0060561)|axonogenesis (GO:0007409)|brain development (GO:0007420)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)|cell maturation (GO:0048469)|cellular response to molecule of bacterial origin (GO:0071219)|chorionic trophoblast cell differentiation (GO:0060718)|embryonic axis specification (GO:0000578)|embryonic camera-type eye development (GO:0031076)|gonad development (GO:0008406)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|neuron differentiation (GO:0030182)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic camera-type eye development (GO:0031077)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of chorionic trophoblast cell proliferation (GO:1901382)|regulation of tight junction assembly (GO:2000810)|Spemann organizer formation (GO:0060061)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell differentiation in thymus (GO:0033077)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	cell projection (GO:0042995)|cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			NS(1)|kidney(1)|lung(1)|ovary(2)|prostate(1)|skin(1)	7				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)		GGCTGGTAGCAGGGTACCGCG	0.632																																					p.C222R		.											.	FZD5-660	0			c.T664C						.						54	52	52					2																	208632800		2203	4300	6503	SO:0001583	missense	7855	exon2			GGTAGCAGGGTAC	U43318	CCDS33366.1	2q33.3	2014-01-29	2014-01-29		ENSG00000163251	ENSG00000163251		"GPCR / Class F : Frizzled receptors"	4043	protein-coding gene	gene with protein product		601723	"frizzled (Drosophila) homolog 5", "chromosome 2 open reading frame 31", "frizzled homolog 5 (Drosophila)", "frizzled 5, seven transmembrane spanning receptor", "frizzled family receptor 5"	C2orf31		8626800, 11408929	Standard	NM_003468		Approved	HFZ5, DKFZP434E2135	uc002vcj.3	Q13467	OTTHUMG00000154790	ENST00000295417.3:c.664T>C	2.37:g.208632800A>G	ENSP00000354607:p.Cys222Arg	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	24	11	NM_003468	0	0	19	37	18	A8K2X1|B2RCZ1|Q53R22	Missense_Mutation	SNP	ENST00000295417.3	37	CCDS33366.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.701621	0.68501	.	.	ENSG00000163251	ENST00000295417	D	0.90197	-2.63	5.05	5.05	0.67936	.	0.051032	0.85682	D	0.000000	D	0.94706	0.8292	M	0.74647	2.275	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.95299	0.8402	10	0.87932	D	0	.	14.4703	0.67512	1.0:0.0:0.0:0.0	.	222	Q13467	FZD5_HUMAN	R	222	ENSP00000354607:C222R	ENSP00000354607:C222R	C	-	1	0	FZD5	208341045	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.339000	0.96797	1.908000	0.55244	0.459000	0.35465	TGC	.		0.632	FZD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337060.1	NM_003468		G	208632800	A	G	208632800	3	3	121	1	0	0	0	0	1	0	0	0	6152	188	7	3	1097	3	FZD5	2	208632800	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	10646569	208632800	34566573	10	10464											
ZNF142	7701	ucsc.edu;bcgsc.ca	37	chr2	219503380	219503380	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcactgtgcttgcgaaggtgGgtgcgcagcaggaagcgcgt	7	8	17	9	4	1	0	1	0	0	0	1	2	1	1	0	3	5	3	0	3	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:219503380G>T	ENST00000449707.1	-	10	5167	c.4746C>A	c.(4744-4746)acC>acA	p.T1582T	ZNF142_ENST00000411696.2_Silent_p.T1582T	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	1582					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(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TGCGAAGGTGGGTGCGCAGCA	0.612																																					p.T1582T	Colon(170;867 1942 8995 15834 18053)												.	ZNF142-137	0			c.C4746A						.						55	62	60					2																	219503380		2183	4274	6457	SO:0001819	synonymous_variant	7701	exon10			AAGGTGGGTGCGC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"Zinc fingers, C2H2-type"	12927	protein-coding gene	gene with protein product		604083	"zinc finger protein 142 (clone pHZ-49)"				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.4746C>A	2.37:g.219503380G>T		Somatic	66	2		WXS	Illumina HiSeq		49	10	NM_001105537	0	0	19	31	12	Q92510	Silent	SNP	ENST00000449707.1	37	CCDS42817.1																																																																																			.		0.612	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		T	219503380	G	T	219503380	2	4	121	1	0	0	0	0	0	0	0	1	17763	1219	43	4		4	ZNF142	2	219503380	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	10870580	219503380	23695993	11	10465											
ZNF620	253639	bcgsc.ca	37	chr3	40553892	40553892	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtttctttctccctgggcaGcattcccattcaccacgcct	5	14	6	16	1	3	0	1	0	2	0	5	0	4	0	4	1	1	3	4	1	0	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:40553892G>C	ENST00000314529.6	+	4	300		c.e4-1		ZNF620_ENST00000418905.1_Intron	NM_175888.3	NP_787084.1	Q6ZNG0	ZN620_HUMAN	zinc finger protein 620						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(1)|urinary_tract(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		TCCCTGGGCAGCATTCCCATT	0.562																																					.													.	ZNF620-91	0			c.152-1G>C						.						75	73	74					3																	40553892		2203	4300	6503	SO:0001630	splice_region_variant	253639	exon4			TGGGCAGCATTCC	AK093599	CCDS33740.1, CCDS58825.1	3p21.33	2013-01-08			ENSG00000177842	ENSG00000177842		"Zinc fingers, C2H2-type", "-"	28742	protein-coding gene	gene with protein product						12477932	Standard	NM_175888		Approved	MGC50836	uc003ckk.4	Q6ZNG0	OTTHUMG00000156044	ENST00000314529.6:c.152-1G>C	3.37:g.40553892G>C		Somatic	36	0		WXS	Illumina HiSeq	Phase_1	57	4	NM_175888	0	0	0	0	0	Q8N223	Splice_Site	SNP	ENST00000314529.6	37	CCDS33740.1	.	.	.	.	.	.	.	.	.	.	G	7.158	0.585110	0.13749	.	.	ENSG00000177842	ENST00000420891;ENST00000314529	.	.	.	2.19	2.19	0.27852	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.8528	0.24024	0.0:0.2925:0.7075:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF620	40528896	0.039000	0.19947	0.010000	0.14722	0.112000	0.19704	1.741000	0.38238	1.517000	0.48917	0.557000	0.71058	.	.		0.562	ZNF620-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342824.1	XM_171060	Intron	C	40553892	G	C	40553892	5	2	121	1	0	0	0	0	0	0	1	0	18076	985	34	4	161	4	ZNF620	3	40553892	Splice_Site	SNP	G	TCGA-GL-6846-01A-11D-1961-08		40553892	157468538	12	10466											
FBXW12	285231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48436087	48436087	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggtgaggaaagtaagtgActccagcattctggtgatgt	11	11	14	5	0	1	3	0	3	1	0	2	4	2	4	1	3	1	2	1	3	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:48436087A>G	ENST00000296438.5	+	11	1544	c.1358A>G	c.(1357-1359)gAc>gGc	p.D453G	FBXW12_ENST00000445170.1_Missense_Mutation_p.D434G|FBXW12_ENST00000415155.1_Missense_Mutation_p.D383G|FBXW12_ENST00000468158.1_Intron|FBXW12_ENST00000436231.1_Missense_Mutation_p.D296G	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	453										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AAAGTAAGTGACTCCAGCATT	0.358																																					p.D453G		.											.	FBXW12-226	0			c.A1358G						.						155	144	147					3																	48436087		2203	4300	6503	SO:0001583	missense	285231	exon11			TAAGTGACTCCAG	AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"F-boxes / WD-40 domains", "WD repeat domain containing"	20729	protein-coding gene	gene with protein product		609075	"F-box only protein 35", "F-box and WD-40 domain protein 12"	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.1358A>G	3.37:g.48436087A>G	ENSP00000296438:p.Asp453Gly	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	197	65	NM_207102	0	0	0	0	0	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	.	.	.	.	.	.	.	.	.	.	A	3.674	-0.066986	0.07273	.	.	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170;ENST00000415155	T;T;T;T	0.27256	2.11;1.69;1.68;1.71	3.33	-3.75	0.04372	.	2.083830	0.03331	N	0.193337	T	0.06690	0.0171	N	0.01874	-0.695	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.21075	-1.0256	10	0.02654	T	1	-4.1095	1.0856	0.01652	0.2988:0.1857:0.3473:0.1683	.	352;434;383;453	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	G	352;453;296;434;383	ENSP00000296438:D453G;ENSP00000413866:D296G;ENSP00000406139:D434G;ENSP00000414683:D383G	ENSP00000296438:D453G	D	+	2	0	FBXW12	48411091	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.770000	0.04705	-0.780000	0.04553	-0.468000	0.05107	GAC	.		0.358	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102		G	48436087	A	G	48436087	3	3	121	1	0	0	0	0	1	0	0	0	5784	275	10	3	1433	3	FBXW12	3	48436087	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	7882195	48436087	149586343	13	10467											
KIAA1407	57577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113721375	113721375	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagctcgttgaattgctctCtcttccatagctagaaaata	11	14	6	10	1	3	2	1	1	2	1	6	2	4	2	1	0	3	4	1	0	6	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:113721375C>A	ENST00000295878.3	-	12	2135	c.1989G>T	c.(1987-1989)gaG>gaT	p.E663D	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	663										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GAATTGCTCTCTCTTCCATAG	0.318																																					p.E663D		.											.	KIAA1407-92	0			c.G1989T						.						90	83	86					3																	113721375		2202	4299	6501	SO:0001583	missense	57577	exon12			TGCTCTCTCTTCC	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.1989G>T	3.37:g.113721375C>A	ENSP00000295878:p.Glu663Asp	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	108	34	NM_020817	0	0	2	4	2	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.887102	0.33348	.	.	ENSG00000163617	ENST00000295878	T	0.35048	1.33	5.35	4.48	0.54585	.	1.585750	0.04130	N	0.317747	T	0.61299	0.2336	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.35101	-0.9802	10	0.59425	D	0.04	.	9.6228	0.39732	0.0:0.8395:0.0:0.1605	.	663	Q8NCU4	K1407_HUMAN	D	663	ENSP00000295878:E663D	ENSP00000295878:E663D	E	-	3	2	KIAA1407	115204065	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.489000	0.22387	1.635000	0.50512	0.655000	0.94253	GAG	.		0.318	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113721375	C	A	113721375	3	1	121	1	0	0	0	0	1	0	0	0	8250	912	32	4	845	4	KIAA1407	3	113721375	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	65285288	113721375	84301055	14	10468											
POLQ	10721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121217327	121217327	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagaccttgacgtttaccttTtatggatggccatttgtcga	8	15	10	8	2	0	2	0	1	0	1	1	5	0	3	3	2	1	1	3	2	2	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:121217327T>G	ENST00000264233.5	-	13	2278	c.2150A>C	c.(2149-2151)aAa>aCa	p.K717T		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	717					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CGTTTACCTTTTATGGATGGC	0.453								DNA polymerases (catalytic subunits)																													p.K717T	Pancreas(152;907 1925 26081 31236 36904)	.											.	POLQ-664	0			c.A2150C						.						164	147	153					3																	121217327		2203	4300	6503	SO:0001583	missense	10721	exon13			TACCTTTTATGGA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"DNA polymerases"	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.2150A>C	3.37:g.121217327T>G	ENSP00000264233:p.Lys717Thr	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	221	118	NM_199420	0	0	0	0	0	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369837	0.82573	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.53857	0.6	5.83	5.83	0.93111	.	0.049703	0.85682	D	0.000000	T	0.69584	0.3127	M	0.85945	2.785	0.49582	D	0.999802	D	0.57257	0.979	P	0.58130	0.833	T	0.75199	-0.3402	10	0.87932	D	0	.	10.5218	0.44922	0.0:0.072:0.0:0.928	.	717	O75417	DPOLQ_HUMAN	T	340;717;853	ENSP00000264233:K717T	ENSP00000264233:K717T	K	-	2	0	POLQ	122700017	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.866000	0.69590	2.212000	0.71576	0.533000	0.62120	AAA	.		0.453	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121217327	T	G	121217327	3	3	121	1	0	0	0	0	1	0	0	0	12234	1841	64	5	5694	5	POLQ	3	121217327	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	7495952	121217327	76805103	15	10469											
SEC62	7095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	169706125	169706125	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcaggctgttttgtagcCagtattcttctccttgctgt	4	17	11	9	0	2	0	0	0	2	0	3	0	2	0	2	2	3	6	2	2	2	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:169706125C>T	ENST00000337002.4	+	7	766	c.708C>T	c.(706-708)gcC>gcT	p.A236A	SEC62-AS1_ENST00000479626.1_RNA|SEC62_ENST00000470355.1_3'UTR|SEC62_ENST00000480708.1_Silent_p.A236A	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	236					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						GTTTTGTAGCCAGTATTCTTC	0.433																																					p.A236A		.											.	SEC62-69	0			c.C708T						.						208	189	195					3																	169706125		2203	4300	6503	SO:0001819	synonymous_variant	7095	exon7			TGTAGCCAGTATT	D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"translocation protein 1"	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.708C>T	3.37:g.169706125C>T		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	180	49	NM_003262	0	0	59	89	30	D3DNQ0|O00682|O00729	Silent	SNP	ENST00000337002.4	37	CCDS3210.1																																																																																			.		0.433	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1			T	169706125	C	T	169706125	2	4	121	1	0	0	0	0	0	0	0	1	14036	581	21	2		2	SEC62	3	169706125	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	48488798	169706125	28316305	16	10470											
ACAP2	23527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	195006526	195006526	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttattagtagaatattgaccTggctgtccataaagtccttc	11	15	7	8	0	0	2	0	1	0	1	3	2	2	2	3	1	0	2	3	1	7	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:195006526T>C	ENST00000326793.6	-	22	2465	c.2235A>G	c.(2233-2235)ccA>ccG	p.P745P		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	745					cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						AATATTGACCTGGCTGTCCAT	0.313																																					p.P745P		.											.	ACAP2-136	0			c.A2235G						.						131	120	124					3																	195006526		2203	4299	6502	SO:0001630	splice_region_variant	23527	exon22			TTGACCTGGCTGT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.2236+1A>G	3.37:g.195006526T>C		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	81	15	NM_012287	0	0	0	1	1	A8K2V4|Q8N5Z8|Q9UQR3	Silent	SNP	ENST00000326793.6	37	CCDS33924.1																																																																																			.		0.313	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287	Silent	C	195006526	T	C	195006526	5	2	121	1	0	0	0	0	0	0	1	0	119	1594	55	3	109	3	ACAP2	3	195006526	Splice_Site	SNP	T	TCGA-GL-6846-01A-11D-1961-08	25300401	195006526	3015904	17	10471											
LMLN	89782	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	197687145	197687145	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgaatggggcggaggagtggGttactcgggctcaggcccgg	6	6	20	9	4	1	0	1	0	0	0	2	3	1	2	1	8	1	2	1	8	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:197687145G>A	ENST00000330198.4	+	1	75	c.53G>A	c.(52-54)gGt>gAt	p.G18D	LMLN_ENST00000420910.2_Missense_Mutation_p.G18D|IQCG_ENST00000480302.1_5'Flank|LMLN_ENST00000332636.5_Silent_p.G6G|IQCG_ENST00000265239.6_5'Flank|LMLN_ENST00000482695.1_Silent_p.G6G	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	18					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GGAGGAGTGGGTTACTCGGGC	0.736																																					p.G18D		.											.	LMLN-91	0			c.G53A						.						21	26	25					3																	197687145		2199	4297	6496	SO:0001583	missense	89782	exon1			GAGTGGGTTACTC	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.53G>A	3.37:g.197687145G>A	ENSP00000328829:p.Gly18Asp	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	61	13	NM_001136049	0	0	9	9	0	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	37	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.349097	0.24426	.	.	ENSG00000185621	ENST00000330198;ENST00000420910	T;T	0.45276	0.92;0.9	3.66	0.764	0.18465	.	0.675595	0.12533	N	0.460640	T	0.22044	0.0531	N	0.19112	0.55	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.16012	-1.0417	10	0.36615	T	0.2	-0.6469	2.1617	0.03827	0.1124:0.1977:0.4859:0.204	.	18;18	Q96KR4;F8WB28	LMLN_HUMAN;.	D	18	ENSP00000328829:G18D;ENSP00000410926:G18D	ENSP00000328829:G18D	G	+	2	0	LMLN	199171542	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	0.016000	0.13377	0.154000	0.19237	0.456000	0.33151	GGT	.		0.736	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197687145	G	A	197687145	3	1	121	1	0	0	0	0	1	0	0	0	8870	1261	44	2	55	2	LMLN	3	197687145	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	2680619	197687145	335285	18	10472											
FRYL	285527	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	48598002	48598003	+	Frame_Shift_Del	DEL	TT	TT	-																															ttccagtgcaactcgagacaTtttcggatctttattctgtt																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:48598002_48598003delTT	ENST00000503238.1	-	11	1049_1050	c.1050_1051delAA	c.(1048-1053)aaaatgfs	p.KM350fs	FRYL_ENST00000507711.1_Frame_Shift_Del_p.KM350fs|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Frame_Shift_Del_p.KM350fs|FRYL_ENST00000537810.1_Frame_Shift_Del_p.KM350fs|FRYL_ENST00000506685.1_Frame_Shift_Del_p.KM56fs			O94915	FRYL_HUMAN	FRY-like	350					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						ACTCGAGACATTTTCGGATCTT	0.302																																					p.350_351del		.											.	FRYL-69	0			c.1050_1051del						.																																			SO:0001589	frameshift_variant	285527	exon14			.	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"KIAA0826", "furry homolog-like (Drosophila)"	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.1050_1051delAA	4.37:g.48598004_48598005delTT	ENSP00000426064:p.Lys350fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	64	18	NM_015030	0	0	0	0	0	O95640|Q8WTZ5|Q9NT40	Frame_Shift_Del	DEL	ENST00000503238.1	37	CCDS43227.1																																																																																			.		0.302	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			-	48598003	TT	-	48598002	7	5	121	1	0	1	0	1	0	0	0	0	6083	1493	52	0	8194	0	FRYL	4	48598002	Frame_Shift_Del	DEL	TT	TCGA-GL-6846-01A-11D-1961-08		48598002	142556274	19	10473											
CWH43	80157	broad.mit.edu	37	chr4	49040168	49040168	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cacctggctccagagattatCtacagctcactgaacatggc	11	9	8	13	0	2	2	1	1	1	1	3	3	3	2	2	2	3	2	2	2	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:49040168C>G	ENST00000226432.4	+	13	1957	c.1774C>G	c.(1774-1776)Cta>Gta	p.L592V	CWH43_ENST00000513409.1_Missense_Mutation_p.L565V	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	592					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						CAGAGATTATCTACAGCTCAC	0.323																																					p.L592V													.	CWH43-93	0			c.C1774G						.						127	136	133					4																	49040168		2203	4300	6503	SO:0001583	missense	80157	exon13			GATTATCTACAGC		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.1774C>G	4.37:g.49040168C>G	ENSP00000226432:p.Leu592Val	Somatic	290	0		WXS	Illumina HiSeq	Phase_I	284	5	NM_025087	0	0	0	0	0	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	37	CCDS3486.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.426451	0.01117	.	.	ENSG00000109182	ENST00000226432;ENST00000513409	T;T	0.29655	1.56;1.56	3.99	1.18	0.20946	Endonuclease/exonuclease/phosphatase (1);	1.583370	0.03606	N	0.234129	T	0.19327	0.0464	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20638	-1.0269	9	.	.	.	.	7.7558	0.28923	0.5584:0.3029:0.1388:0.0	.	592	Q9H720	PG2IP_HUMAN	V	592;565	ENSP00000226432:L592V;ENSP00000422802:L565V	.	L	+	1	2	CWH43	48734925	0.002000	0.14202	0.038000	0.18304	0.945000	0.59286	0.220000	0.17660	0.222000	0.20900	0.555000	0.69702	CTA	.		0.323	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		G	49040168	C	G	49040168	3	3	121	1	0	0	0	0	1	0	0	0	4079	912	32	4	1824	4	CWH43	4	49040168	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	442166	49040168	142114108	20	10474											
TET2	54790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	106157461	106157461	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaagaatgttttcatggtGaaaatcagtattcaaaatca	16	13	8	4	0	4	2	4	1	0	1	4	3	4	3	0	2	0	2	0	2	7	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:106157461G>T	ENST00000540549.1	+	3	3222	c.2362G>T	c.(2362-2364)Gaa>Taa	p.E788*	TET2_ENST00000413648.2_Nonsense_Mutation_p.E788*|TET2_ENST00000394764.1_Nonsense_Mutation_p.E788*|TET2_ENST00000305737.2_Nonsense_Mutation_p.E788*|TET2_ENST00000380013.4_Nonsense_Mutation_p.E788*|TET2_ENST00000513237.1_Nonsense_Mutation_p.E809*|TET2_ENST00000545826.1_Nonsense_Mutation_p.E788*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	788	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.E788K(1)|p.E788*(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TTTTCATGGTGAAAATCAGTA	0.393			"Mis N, F"		MDS																																p.E788X		.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2-4618	2	Substitution - Nonsense(1)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)	c.G2362T						.						57	60	59					4																	106157461		2203	4300	6503	SO:0001587	stop_gained	54790	exon3			CATGGTGAAAATC	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"KIAA1546", "tet oncogene family member 2"	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.2362G>T	4.37:g.106157461G>T	ENSP00000442788:p.Glu788*	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	49	24	NM_001127208	0	0	3	6	3	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	G	42	9.661685	0.99231	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648	.	.	.	5.91	5.91	0.95273	.	16.416400	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	.	.	.	X	788;788;788;809;788;788;788	.	ENSP00000265149:E788X	E	+	1	0	TET2	106376910	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	4.534000	0.60622	2.793000	0.96121	0.655000	0.94253	GAA	.		0.393	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106157461	G	T	106157461	4	4	121	1	0	0	0	0	0	1	0	0	15802	1291	45	4	2364	4	TET2	4	106157461	Nonsense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	57117293	106157461	84996815	21	10475											
TRPC3	7222	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	122853525	122853525	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gacaatgagaggtaagccggGctggccagccccttgtaggc	9	6	15	11	1	0	1	0	1	0	1	0	3	0	1	4	4	2	3	4	4	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:122853525G>A	ENST00000379645.3	-	2	961	c.888C>T	c.(886-888)agC>agT	p.S296S	TRPC3_ENST00000513531.1_Silent_p.S223S|TRPC3_ENST00000264811.5_Silent_p.S223S	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	211					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GGTAAGCCGGGCTGGCCAGCC	0.587																																					p.S296S													.	TRPC3-92	0			c.C888T						.						45	41	42					4																	122853525		2203	4300	6503	SO:0001819	synonymous_variant	7222	exon2			AGCCGGGCTGGCC	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"Voltage-gated ion channels / Transient receptor potential cation channels"	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.888C>T	4.37:g.122853525G>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	29	10	NM_001130698	0	0	0	0	0	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																			.		0.587	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		A	122853525	G	A	122853525	2	1	121	1	0	0	0	0	0	0	0	1	16612	1194	42	2		2	TRPC3	4	122853525	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	16696064	122853525	68300751	22	10476											
CPE	1363	bcgsc.ca	37	chr4	166385584	166385584	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggaatatgcatgggaatgAggctgttggacgagaactgc	11	9	16	5	1	0	2	0	1	0	1	0	6	0	5	0	4	3	3	0	4	4	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:166385584A>G	ENST00000402744.4	+	2	630	c.350A>G	c.(349-351)gAg>gGg	p.E117G		NM_001873.2	NP_001864.1	P16870	CBPE_HUMAN	carboxypeptidase E	117					cardiac left ventricle morphogenesis (GO:0003214)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|insulin processing (GO:0030070)|metabolic process (GO:0008152)|neuropeptide signaling pathway (GO:0007218)|protein localization to membrane (GO:0072657)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)	carboxypeptidase activity (GO:0004180)|cell adhesion molecule binding (GO:0050839)|metallocarboxypeptidase activity (GO:0004181)|neurexin family protein binding (GO:0042043)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CATGGGAATGAGGCTGTTGGA	0.418											OREG0016390	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E117G													.	CPE-155	0			c.A350G						.						171	152	158					4																	166385584		2203	4300	6503	SO:0001583	missense	1363	exon2			GGAATGAGGCTGT	X51405	CCDS3810.1	4q32.3	2012-02-10			ENSG00000109472	ENSG00000109472	3.4.17.10		2303	protein-coding gene	gene with protein product	"carboxypeptidase H", "enkephalin convertase", "insulin granule-associated carboxypeptidase", "cobalt-stimulated chromaffin granule carboxypeptidase"	114855				2334405	Standard	NM_001873		Approved		uc003irg.4	P16870	OTTHUMG00000150252	ENST00000402744.4:c.350A>G	4.37:g.166385584A>G	ENSP00000386104:p.Glu117Gly	Somatic	67	0	1854	WXS	Illumina HiSeq	Phase_1	59	4	NM_001873	0	0	40	40	0	A8K4N1|B3KR42|B4DFN4|D3DP33|Q9UIU9	Missense_Mutation	SNP	ENST00000402744.4	37	CCDS3810.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648987	0.87958	.	.	ENSG00000109472	ENST00000513982;ENST00000402744;ENST00000261510;ENST00000431967;ENST00000511992	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.3	5.3	0.74995	Peptidase M14, carboxypeptidase A (3);	0.000000	0.85682	D	0.000000	T	0.78233	0.4251	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83881	0.0279	10	0.87932	D	0	-24.5917	15.2255	0.73348	1.0:0.0:0.0:0.0	.	117	P16870	CBPE_HUMAN	G	5;117;81;5;5	ENSP00000424830:E5G;ENSP00000386104:E117G;ENSP00000416601:E5G;ENSP00000423699:E5G	ENSP00000261510:E81G	E	+	2	0	CPE	166605034	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.253000	0.95501	2.009000	0.58944	0.477000	0.44152	GAG	.		0.418	CPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317094.2	NM_001873		G	166385584	A	G	166385584	3	3	121	1	0	0	0	0	1	0	0	0	3805	304	11	3	356	3	CPE	4	166385584	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	43532059	166385584	24768692	23	10477											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187530418	187530418	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcttccttggttgccatcTataattgagtagtggatgtg	8	15	12	6	0	1	1	0	1	1	0	2	3	2	2	2	2	2	3	2	2	3	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:187530418T>A	ENST00000441802.2	-	16	10334	c.10125A>T	c.(10123-10125)atA>atT	p.I3375I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3375	Cadherin 31. {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						GGTTGCCATCTATAATTGAGT	0.478										HNSCC(5;0.00058)																											p.I3375I	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.A10125T						.						126	121	123					4																	187530418		1933	4136	6069	SO:0001819	synonymous_variant	2195	exon16			GCCATCTATAATT	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.10125A>T	4.37:g.187530418T>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	82	32	NM_005245	0	0	114	236	122		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187530418	T	A	187530418	2	1	121	1	0	0	0	0	0	0	0	1	5708	1512	53	5		5	FAT1	4	187530418	Silent	SNP	T	TCGA-GL-6846-01A-11D-1961-08	21144834	187530418	3623858	24	10478											
AGGF1	55109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	76344781	76344781	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaaaggatatggaacataCtctccgaatccctgaagttg	15	9	9	8	1	1	2	0	1	1	1	3	5	2	4	2	2	2	1	2	2	7	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:76344781C>A	ENST00000312916.7	+	8	1716	c.1334C>A	c.(1333-1335)aCt>aAt	p.T445N		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	445	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		ATGGAACATACTCTCCGAATC	0.294																																					p.T445N		.											.	AGGF1-117	0			c.C1334A						.						97	106	103					5																	76344781		2203	4295	6498	SO:0001583	missense	55109	exon8			AACATACTCTCCG	AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"G patch domain containing"	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.1334C>A	5.37:g.76344781C>A	ENSP00000316109:p.Thr445Asn	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	179	82	NM_018046	0	0	15	33	18	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028459	0.54790	.	.	ENSG00000164252	ENST00000312916	T	0.39592	1.07	4.64	4.64	0.57946	Forkhead-associated (FHA) domain (4);SMAD/FHA domain (1);	0.105294	0.64402	D	0.000003	T	0.41627	0.1167	N	0.17723	0.515	0.80722	D	1	P	0.51653	0.947	P	0.52424	0.698	T	0.36286	-0.9754	10	0.44086	T	0.13	-4.4424	16.8258	0.85930	0.0:1.0:0.0:0.0	.	445	Q8N302	AGGF1_HUMAN	N	445	ENSP00000316109:T445N	ENSP00000316109:T445N	T	+	2	0	AGGF1	76380537	1.000000	0.71417	0.987000	0.45799	0.743000	0.42351	7.194000	0.77789	2.285000	0.76669	0.305000	0.20034	ACT	.		0.294	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76344781	C	A	76344781	3	1	121	1	0	0	0	0	1	0	0	0	382	565	20	4	1364	4	AGGF1	5	76344781	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		76344781	104570479	25	10479											
NME5	8382	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	137474383	137474383	+	Frame_Shift_Del	DEL	C	C	-																															ctaagaataatatcttgtatCtcctcctctttgtcaacaat																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:137474383delC	ENST00000265191.2	-	2	136	c.87delG	c.(85-87)gagfs	p.E29fs		NM_003551.2	NP_003542.1	P56597	NDK5_HUMAN	NME/NM23 family member 5	29					cilium assembly (GO:0042384)|CTP biosynthetic process (GO:0006241)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|nucleoside metabolic process (GO:0009116)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)|ventricular system development (GO:0021591)	sperm flagellum (GO:0036126)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)			kidney(1)|large_intestine(1)|lung(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TATCTTGTATCTCCTCCTCTT	0.368																																					p.E29fs		.											.	NME5-115	0			c.87delG						.						140	128	132					5																	137474383		2203	4300	6503	SO:0001589	frameshift_variant	8382	exon2			.	Y14992	CCDS4197.1	5q31.2	2012-05-18	2012-05-18		ENSG00000112981	ENSG00000112981			7853	protein-coding gene	gene with protein product	"radial spoke 23 homolog (Chlamydomonas)"	603575	"non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)"			9742940, 19852809	Standard	NM_003551		Approved	nm23-H5, RSPH23	uc003lce.3	P56597	OTTHUMG00000129207	ENST00000265191.2:c.87delG	5.37:g.137474383delC	ENSP00000265191:p.Glu29fs	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	63	32	NM_003551	0	0	0	0	0	B2R5G7	Frame_Shift_Del	DEL	ENST00000265191.2	37	CCDS4197.1																																																																																			.		0.368	NME5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251286.1	NM_003551		-	137474383	C	-	137474383	7	5	121	1	0	1	0	1	0	0	0	0	10520	912	32	0	571	0	NME5	5	137474383	Frame_Shift_Del	DEL	C	TCGA-GL-6846-01A-11D-1961-08	61129602	137474383	43440877	26	10480	107	2									
NME5	8382	hgsc.bcm.edu	37	chr5	137474385	137474386	+	Nonsense_Mutation	DNP	CC	CC	AG																															aagaataatatcttgtatctCctcctctttgtcaacaatat																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:137474385_137474386CC>AG	ENST00000265191.2	-	2	133_134	c.84_85GG>CT	c.(82-87)gaGGag>gaCTag	p.28_29EE>D*		NM_003551.2	NP_003542.1	P56597	NDK5_HUMAN	NME/NM23 family member 5	28					cilium assembly (GO:0042384)|CTP biosynthetic process (GO:0006241)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|nucleoside metabolic process (GO:0009116)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)|ventricular system development (GO:0021591)	sperm flagellum (GO:0036126)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)			kidney(1)|large_intestine(1)|lung(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCTTGTATCTCCTCCTCTTTGT	0.371																																					p.EE28D*		.											.	NME5	0			c.G84C						.																																			SO:0001587	stop_gained	8382	exon2			TATCTCCTCCTCT	Y14992	CCDS4197.1	5q31.2	2012-05-18	2012-05-18		ENSG00000112981	ENSG00000112981			7853	protein-coding gene	gene with protein product	"radial spoke 23 homolog (Chlamydomonas)"	603575	"non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)"			9742940, 19852809	Standard	NM_003551		Approved	nm23-H5, RSPH23	uc003lce.3	P56597	OTTHUMG00000129207	ENST00000265191.2:c.84_85delinsAG	5.37:g.137474385_137474386delinsAG	ENSP00000265191:p.E28_E29delinsD*	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	66	33		0	0	0	0	0	B2R5G7	Nonsense_Mutation	DNP	ENST00000265191.2	37	CCDS4197.1																																																																																			.		0.371	NME5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251286.1	NM_003551		AG	137474386	CC	AG	137474385	4	1	121	1	0	0	0	0	0	1	0	0	10520	864	30	4	573	4	NME5	5	137474385	Nonsense_Mutation	DNP	CC	TCGA-GL-6846-01A-11D-1961-08	2	137474385	43440875	27	10481	107	2									
PCDH12	51294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141336615	141336615	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttggtcagggtctgtggCggtcagttttatgagaagcg	6	12	16	7	2	3	1	2	1	1	1	3	2	3	1	1	4	1	1	1	4	2	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:141336615C>T	ENST00000231484.3	-	1	2012	c.802G>A	c.(802-804)Gcc>Acc	p.A268T	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	268	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A268T(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGTCTGTGGCGGTCAGTTTT	0.527																																					p.A268T		.											.	PCDH12-93	1	Substitution - Missense(1)	large_intestine(1)	c.G802A						.						97	95	96					5																	141336615		2203	4300	6503	SO:0001583	missense	51294	exon1			CTGTGGCGGTCAG	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"Cadherins / Protocadherins : Non-clustered"	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.802G>A	5.37:g.141336615C>T	ENSP00000231484:p.Ala268Thr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	97	37	NM_016580	0	0	5	5	0	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727645	0.89390	.	.	ENSG00000113555	ENST00000231484	T	0.61392	0.11	5.32	5.32	0.75619	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.82190	0.4983	M	0.93283	3.4	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.86437	0.1764	10	0.87932	D	0	.	16.5409	0.84384	0.0:1.0:0.0:0.0	.	268	Q9NPG4	PCD12_HUMAN	T	268	ENSP00000231484:A268T	ENSP00000231484:A268T	A	-	1	0	PCDH12	141316799	1.000000	0.71417	0.991000	0.47740	0.932000	0.56968	7.651000	0.83577	2.767000	0.95098	0.655000	0.94253	GCC	.		0.527	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		T	141336615	C	T	141336615	3	4	121	1	0	0	0	0	1	0	0	0	11536	768	27	1	2768	1	PCDH12	5	141336615	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	3862230	141336615	39578645	28	10482											
AGXT2L2	85007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	177642285	177642285	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccagagcctcacctgacatcCccgacgatgggatgtttgat	9	9	10	13	2	1	3	1	2	0	1	2	6	2	4	5	1	1	1	5	1	0	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:177642285C>T	ENST00000308158.5	-	9	1308	c.1074G>A	c.(1072-1074)ggG>ggA	p.G358G	PHYKPL_ENST00000481811.1_5'UTR	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase	358						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	ACCTGACATCCCCGACGATGG	0.567																																					p.G358G		.											.	AGXT2L2-91	0			c.G1074A						.						42	39	40					5																	177642285		2203	4300	6503	SO:0001819	synonymous_variant	85007	exon9			GACATCCCCGACG	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1074G>A	5.37:g.177642285C>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	53	27	NM_153373	0	0	0	0	0	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Silent	SNP	ENST00000308158.5	37	CCDS4434.1																																																																																			.		0.567	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		T	177642285	C	T	177642285	2	4	121	1	0	0	0	0	0	0	0	1	407	610	22	2		2	AGXT2L2	5	177642285	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	36305670	177642285	3272975	29	10483											
OR2Y1	134083	broad.mit.edu;bcgsc.ca	37	chr5	180166694	180166694	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacgacagacagcagcatagCggtcaaaggccatcaccacc	14	3	10	14	2	2	1	2	0	0	1	2	3	2	1	3	2	3	2	3	2	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:180166694C>T	ENST00000307832.2	-	1	405	c.365G>A	c.(364-366)cGc>cAc	p.R122H		NM_001001657.1	NP_001001657.1	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCAGCATAGCGGTCAAAGGC	0.607																																					p.R122H													.	OR2Y1-68	0			c.G365A						.						77	64	68					5																	180166694		2203	4300	6503	SO:0001583	missense	134083	exon1			GCATAGCGGTCAA	AB065676	CCDS34323.1	5q35	2012-08-09			ENSG00000174339	ENSG00000174339		"GPCR / Class A : Olfactory receptors"	14837	protein-coding gene	gene with protein product							Standard	NM_001001657		Approved		uc003mmf.1	Q8NGV0	OTTHUMG00000162237	ENST00000307832.2:c.365G>A	5.37:g.180166694C>T	ENSP00000312403:p.Arg122His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	35	11	NM_001001657	0	0	0	0	0	B9EIP1|Q6IFB1|Q96R16	Missense_Mutation	SNP	ENST00000307832.2	37	CCDS34323.1	.	.	.	.	.	.	.	.	.	.	c	12.25	1.880972	0.33255	.	.	ENSG00000174339	ENST00000307832	T	0.77489	-1.1	4.41	3.54	0.40534	GPCR, rhodopsin-like superfamily (1);	0.128292	0.36134	N	0.002767	T	0.78755	0.4333	M	0.91249	3.19	0.32000	N	0.603464	P	0.35551	0.509	B	0.28553	0.091	D	0.83720	0.0192	10	0.87932	D	0	.	10.5089	0.44849	0.0:0.903:0.0:0.097	.	122	Q8NGV0	OR2Y1_HUMAN	H	122	ENSP00000312403:R122H	ENSP00000312403:R122H	R	-	2	0	OR2Y1	180099300	1.000000	0.71417	0.997000	0.53966	0.025000	0.11179	3.930000	0.56522	1.197000	0.43143	0.511000	0.50034	CGC	.		0.607	OR2Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368059.2	XM_068682		T	180166694	C	T	180166694	3	4	121	1	0	0	0	0	1	0	0	0	11061	768	27	1	574	1	OR2Y1	5	180166694	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	2524409	180166694	748566	30	10484											
MRS2	57380	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	24418322	24418322	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaattgaagtgaaaagagcAgtgctgggattgaccatgca	14	10	12	5	0	0	4	0	3	0	1	0	5	0	5	1	1	3	3	1	1	4	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:24418322A>T	ENST00000378386.3	+	8	940	c.847A>T	c.(847-849)Agt>Tgt	p.S283C	MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000378353.1_Missense_Mutation_p.S283C|MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000443868.2_Missense_Mutation_p.S286C|MRS2_ENST00000543597.1_5'UTR|MRS2_ENST00000535061.1_Missense_Mutation_p.S233C	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	283						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						TGAAAAGAGCAGTGCTGGGAT	0.388																																					p.S283C		.											.	MRS2-68	0			c.A847T						.						121	112	115					6																	24418322		2203	4300	6503	SO:0001583	missense	57380	exon8			AAGAGCAGTGCTG	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"MRS2-like, magnesium homeostasis factor (S. cerevisiae)", "MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.847A>T	6.37:g.24418322A>T	ENSP00000367637:p.Ser283Cys	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	99	43	NM_020662	0	0	0	0	0	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Missense_Mutation	SNP	ENST00000378386.3	37	CCDS4552.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.390435	0.62066	.	.	ENSG00000124532	ENST00000535061;ENST00000378386;ENST00000378353;ENST00000443868	T;T;T;T	0.50548	1.34;1.32;0.74;1.31	6.06	4.92	0.64577	.	0.084750	0.85682	D	0.000000	T	0.52853	0.1760	M	0.63843	1.955	0.80722	D	1	D;D;P;D	0.89917	1.0;1.0;0.481;0.997	D;D;B;P	0.68353	0.934;0.957;0.164;0.846	T	0.57124	-0.7865	10	0.56958	D	0.05	-22.8995	9.6962	0.40158	0.8692:0.0:0.1308:0.0	.	233;286;283;283	F5GWH3;B4DQL2;Q9HD23;Q9HD23-2	.;.;MRS2_HUMAN;.	C	233;283;283;286	ENSP00000441839:S233C;ENSP00000367637:S283C;ENSP00000367604:S283C;ENSP00000399585:S286C	ENSP00000367604:S283C	S	+	1	0	MRS2	24526301	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	3.503000	0.53340	2.326000	0.78906	0.472000	0.43445	AGT	.		0.388	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			T	24418322	A	T	24418322	3	4	121	1	0	0	0	0	1	0	0	0	9876	188	7	5	877	5	MRS2	6	24418322	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08		24418322	146696745	31	10485											
KCTD20	222658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	36454734	36454734	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcatctataattatgtacaaCgccccttcatccagatgtca	12	13	4	12	1	4	1	3	0	1	1	5	1	5	1	3	0	2	1	3	0	5	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:36454734C>T	ENST00000373731.2	+	8	1433	c.1042C>T	c.(1042-1044)Cgc>Tgc	p.R348C	KCTD20_ENST00000474988.1_3'UTR|KCTD20_ENST00000449081.2_Missense_Mutation_p.R182C|KCTD20_ENST00000536244.1_Missense_Mutation_p.R203C|KCTD20_ENST00000544295.1_Missense_Mutation_p.R102C	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	348					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						TTATGTACAACGCCCCTTCAT	0.463																																					p.R348C		.											.	KCTD20-92	0			c.C1042T						.						90	96	94					6																	36454734		2203	4300	6503	SO:0001583	missense	222658	exon8			GTACAACGCCCCT	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"chromosome 6 open reading frame 69", "potassium channel tetramerisation domain containing 20"	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.1042C>T	6.37:g.36454734C>T	ENSP00000362836:p.Arg348Cys	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	119	45	NM_173562	0	0	17	31	14	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	37	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.701883	0.88924	.	.	ENSG00000112078	ENST00000373731;ENST00000544295;ENST00000449081;ENST00000536244	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.03	6.03	0.97812	.	0.061169	0.64402	N	0.000003	D	0.87148	0.6105	L	0.53561	1.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.87043	0.2142	10	0.56958	D	0.05	-18.2215	15.2928	0.73879	0.14:0.86:0.0:0.0	.	182;348	Q7Z5Y7-2;Q7Z5Y7	.;KCD20_HUMAN	C	348;102;182;203	ENSP00000362836:R348C;ENSP00000440150:R102C;ENSP00000412205:R182C;ENSP00000439118:R203C	ENSP00000362836:R348C	R	+	1	0	KCTD20	36562712	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.971000	0.40530	2.861000	0.98227	0.655000	0.94253	CGC	.		0.463	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		T	36454734	C	T	36454734	3	4	121	1	0	0	0	0	1	0	0	0	8129	536	19	1	1068	1	KCTD20	6	36454734	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	12036412	36454734	134660333	32	10486											
ULBP1	80329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	150289835	150289835	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggcctggtggatgaaaggCcttttcttcactatgactgt	9	13	11	8	0	2	2	1	2	1	0	2	3	2	3	2	4	0	0	2	4	3	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:150289835C>A	ENST00000229708.3	+	2	221	c.178C>A	c.(178-180)Cct>Act	p.P60T		NM_025218.2	NP_079494.1	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	60	MHC class I alpha-1 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			large_intestine(3)|lung(5)|pancreas(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)		GGATGAAAGGCCTTTTCTTCA	0.453																																					p.P60T		.											.	ULBP1-91	0			c.C178A						.						133	133	133					6																	150289835		2203	4300	6503	SO:0001583	missense	80329	exon2			GAAAGGCCTTTTC	AF304377	CCDS5223.1	6q25	2003-04-29			ENSG00000111981	ENSG00000111981			14893	protein-coding gene	gene with protein product		605697				11239445, 11827464	Standard	XM_005267151		Approved	RAET1I	uc003qnp.3	Q9BZM6	OTTHUMG00000015810	ENST00000229708.3:c.178C>A	6.37:g.150289835C>A	ENSP00000229708:p.Pro60Thr	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	192	90	NM_025218	0	0	0	0	0	Q5VY81|Q8IZW3|Q8IZX6	Missense_Mutation	SNP	ENST00000229708.3	37	CCDS5223.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.109641	0.00353	.	.	ENSG00000111981	ENST00000367345;ENST00000229708	T;T	0.00682	5.86;5.86	2.2	-4.39	0.03611	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00144	0.0004	N	0.11927	0.2	0.09310	N	1	B	0.10296	0.003	B	0.17098	0.017	T	0.45101	-0.9284	9	0.72032	D	0.01	.	1.2925	0.02063	0.2296:0.3696:0.2522:0.1487	.	60	Q9BZM6	N2DL1_HUMAN	T	60	ENSP00000356314:P60T;ENSP00000229708:P60T	ENSP00000229708:P60T	P	+	1	0	ULBP1	150331528	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-4.865000	0.00176	-2.597000	0.00453	-0.834000	0.03071	CCT	.		0.453	ULBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042677.2			A	150289835	C	A	150289835	3	1	121	1	0	0	0	0	1	0	0	0	17005	739	26	4	184	4	ULBP1	6	150289835	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	113835101	150289835	20825232	33	10487											
MLLT4	4301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	168344092	168344092	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttgcctaggatggacgtcTagctgcaggtgatcagctcc	8	11	12	10	1	2	1	1	1	1	0	3	3	3	3	2	3	4	3	2	3	2	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:168344092T>A	ENST00000447894.2	+	24	3155	c.3155T>A	c.(3154-3156)cTa>cAa	p.L1052Q	MLLT4_ENST00000392112.1_Missense_Mutation_p.L1035Q|MLLT4_ENST00000392108.3_Missense_Mutation_p.L1052Q|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000344191.4_Missense_Mutation_p.L1052Q|MLLT4_ENST00000400822.3_Missense_Mutation_p.L1051Q|MLLT4_ENST00000366806.2_Missense_Mutation_p.L1052Q|MLLT4_ENST00000351017.4_Missense_Mutation_p.L1059Q			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1052	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GATGGACGTCTAGCTGCAGGT	0.458			T	MLL	AL																																p.L1052Q		.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4-685	0			c.T3155A						.						244	221	229					6																	168344092		2203	4300	6503	SO:0001583	missense	4301	exon24			GACGTCTAGCTGC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3155T>A	6.37:g.168344092T>A	ENSP00000404595:p.Leu1052Gln	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	250	105	NM_001040000	0	0	0	0	0	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	T	23.7	4.441746	0.83993	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.18	5.18	0.71444	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000010	T	0.76751	0.4031	H	0.97983	4.12	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.997	D	0.86288	0.1672	10	0.87932	D	0	-11.2076	15.0548	0.71904	0.0:0.0:0.0:1.0	.	1052;1051;1052;1036	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	Q	1052;1059;1052;1052;1035;1052;1051;1052	ENSP00000341118:L1052Q;ENSP00000252692:L1059Q;ENSP00000375956:L1052Q;ENSP00000355771:L1052Q;ENSP00000375960:L1035Q;ENSP00000383623:L1051Q;ENSP00000404595:L1052Q	ENSP00000345834:L1052Q	L	+	2	0	MLLT4	168086941	1.000000	0.71417	0.015000	0.15790	0.985000	0.73830	7.440000	0.80464	1.954000	0.56735	0.528000	0.53228	CTA	.		0.458	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		A	168344092	T	A	168344092	3	1	121	1	0	0	0	0	1	0	0	0	9654	1522	53	5	3249	5	MLLT4	6	168344092	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	18054257	168344092	2770975	34	10488											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5401235	5401235	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccttactttccgctacTgtggccgctcttccctctct	3	14	6	18	2	2	0	0	0	2	0	5	0	4	0	5	1	3	2	5	1	2	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:5401235T>G	ENST00000430969.1	-	14	4999	c.4651A>C	c.(4651-4653)Agt>Cgt	p.S1551R	TNRC18_ENST00000399537.4_Missense_Mutation_p.S1551R	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1551							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TTTCCGCTACTGTGGCCGCTC	0.716																																					p.S1551R		.											.	TNRC18-46	0			c.A4651C						.						13	15	14					7																	5401235		1511	3484	4995	SO:0001583	missense	84629	exon14			CGCTACTGTGGCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4651A>C	7.37:g.5401235T>G	ENSP00000395538:p.Ser1551Arg	Somatic	6	2		WXS	Illumina HiSeq	Phase_I	15	13	NM_001080495	0	0	0	0	0	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	T	12.54	1.968807	0.34754	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544	T;T	0.12361	2.69;2.69	4.84	2.36	0.29203	.	0.381607	0.19384	N	0.115570	T	0.07908	0.0198	L	0.27053	0.805	0.29152	N	0.878318	B	0.02656	0.0	B	0.01281	0.0	T	0.39603	-0.9606	10	0.10902	T	0.67	.	7.6555	0.28373	0.0:0.0756:0.1472:0.7771	.	1551	O15417	TNC18_HUMAN	R	1551;1551;606	ENSP00000382452:S1551R;ENSP00000395538:S1551R	ENSP00000382452:S1551R	S	-	1	0	TNRC18	5367761	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.920000	0.40025	0.188000	0.20168	0.459000	0.35465	AGT	.		0.716	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5401235	T	G	5401235	3	3	121	1	0	0	0	0	1	0	0	0	16371	1580	55	5	4323	5	TNRC18	7	5401235	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08		5401235	153737428	35	10489											
ACTB	60	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5568236	5568236	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagatgggcacagtgtgggTgaccccgtcaccggagtcca	8	7	15	11	2	1	2	1	1	0	1	2	3	2	3	4	3	0	2	4	3	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:5568236T>C	ENST00000331789.5	-	4	669	c.478A>G	c.(478-480)Acc>Gcc	p.T160A	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	160			T -> I (in dbSNP:rs11549206).		adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		ACAGTGTGGGTGACCCCGTCA	0.607																																					p.T160A		.											.	ACTB-226	0			c.A478G						.						76	76	76					7																	5568236		2203	4300	6503	SO:0001583	missense	60	exon4			TGTGGGTGACCCC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.478A>G	7.37:g.5568236T>C	ENSP00000349960:p.Thr160Ala	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	149	98	NM_001101	4	6	2411	5733	3312	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.609394	0.46527	.	.	ENSG00000075624	ENST00000331789;ENST00000400179;ENST00000320713;ENST00000432588	D;D	0.98296	-4.85;-3.8	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000011	D	0.98040	0.9354	M	0.93016	3.37	0.42954	D	0.994384	B	0.02656	0.0	B	0.11329	0.006	D	0.97321	0.9944	10	0.87932	D	0	.	13.2628	0.60115	0.0:0.0:0.0:1.0	.	160	P60709	ACTB_HUMAN	A	160;132;79;160	ENSP00000349960:T160A;ENSP00000407473:T160A	ENSP00000440549:T79A	T	-	1	0	ACTB	5534762	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.862000	0.69560	2.022000	0.59522	0.529000	0.55759	ACC	.		0.607	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		C	5568236	T	C	5568236	3	2	121	1	0	0	0	0	1	0	0	0	193	1696	59	3	661	3	ACTB	7	5568236	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	167001	5568236	153570427	36	10490											
C7orf26	79034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	6639834	6639834	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcgcctggggctgatcctcTtcgaccacatggtcccgctg	4	9	13	15	3	1	1	0	1	1	0	4	2	3	1	4	4	0	2	4	4	0	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:6639834T>G	ENST00000344417.5	+	4	1222	c.955T>G	c.(955-957)Ttc>Gtc	p.F319V	C7orf26_ENST00000472693.1_3'UTR|C7orf26_ENST00000359073.5_Missense_Mutation_p.F222V	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	319										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		GCTGATCCTCTTCGACCACAT	0.582																																					p.F319V		.											.	C7orf26-91	0			c.T955G						.						59	52	54					7																	6639834		2203	4300	6503	SO:0001583	missense	79034	exon4			ATCCTCTTCGACC	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.955T>G	7.37:g.6639834T>G	ENSP00000340220:p.Phe319Val	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	46	29	NM_024067	0	0	15	33	18	Q9BQ43	Missense_Mutation	SNP	ENST00000344417.5	37	CCDS5353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.95|10.95	1.496091|1.496091	0.26774|0.26774	.|.	.|.	ENSG00000146576|ENSG00000146576	ENST00000344417;ENST00000359073|ENST00000445375	T;T|T	0.39997|0.40756	1.05;1.05|1.02	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.213127|.	0.53938|.	D|.	0.000054|.	T|T	0.30103|0.30103	0.0754|0.0754	N|N	0.19112|0.19112	0.55|0.55	0.29914|0.29914	N|N	0.823337|0.823337	B;B|.	0.17038|.	0.02;0.02|.	B;B|.	0.14023|.	0.004;0.01|.	T|T	0.12344|0.12344	-1.0551|-1.0551	10|7	0.14656|0.09084	T|T	0.56|0.74	-26.1927|-26.1927	13.6493|13.6493	0.62301|0.62301	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	222;319|.	Q96N11-2;Q96N11|.	.;CG026_HUMAN|.	V|R	319;222|56	ENSP00000340220:F319V;ENSP00000351974:F222V|ENSP00000390166:L56R	ENSP00000340220:F319V|ENSP00000390166:L56R	F|L	+|+	1|2	0|0	C7orf26|C7orf26	6606359|6606359	1.000000|1.000000	0.71417|0.71417	0.466000|0.466000	0.27168|0.27168	0.709000|0.709000	0.40893|0.40893	3.987000|3.987000	0.56944|0.56944	2.268000|2.268000	0.75426|0.75426	0.454000|0.454000	0.30748|0.30748	TTC|CTT	.		0.582	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067		G	6639834	T	G	6639834	3	3	121	1	0	0	0	0	1	0	0	0	2387	1609	56	5	969	5	C7orf26	7	6639834	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	1071598	6639834	152498829	37	10491											
ASB4	51666	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	95125264	95125264	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgtgttaagatcctctgtGatcgtggggcaaagctcaat	10	13	11	7	1	2	2	1	1	1	1	4	2	3	2	1	2	1	3	1	2	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:95125264G>A	ENST00000325885.5	+	2	453	c.382G>A	c.(382-384)Gat>Aat	p.D128N	ASB4_ENST00000428113.1_Missense_Mutation_p.D128N|ASB4_ENST00000257621.4_3'UTR	NM_016116.2	NP_057200.1	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box containing 4	128					intracellular signal transduction (GO:0035556)|positive regulation of vasculogenesis (GO:2001214)|protein autoubiquitination (GO:0051865)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|pancreas(1)|prostate(1)|skin(2)	20	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			GATCCTCTGTGATCGTGGGGC	0.458																																					p.D128N		.											.	ASB4-226	0			c.G382A						.						210	156	175					7																	95125264		2203	4300	6503	SO:0001583	missense	51666	exon2			CTCTGTGATCGTG	AF156779	CCDS5641.1, CCDS5642.1	7q21-q22	2013-01-10	2011-01-25		ENSG00000005981	ENSG00000005981		"Ankyrin repeat domain containing"	16009	protein-coding gene	gene with protein product		605761	"ankyrin repeat and SOCS box-containing 4"				Standard	NM_145872		Approved	ASB-4	uc011kij.2	Q9Y574	OTTHUMG00000153960	ENST00000325885.5:c.382G>A	7.37:g.95125264G>A	ENSP00000321388:p.Asp128Asn	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	112	23	NM_016116	0	0	0	0	0	A4D1H6|O14586|Q14D68|Q8TBT2	Missense_Mutation	SNP	ENST00000325885.5	37	CCDS5641.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692526	0.30052	.	.	ENSG00000005981	ENST00000325885;ENST00000428113	T;T	0.65364	-0.15;-0.15	5.35	5.35	0.76521	Ankyrin repeat-containing domain (3);	0.260422	0.44688	D	0.000432	T	0.48822	0.1521	L	0.38531	1.155	0.33932	D	0.642157	B;B	0.15141	0.009;0.012	B;B	0.15052	0.012;0.011	T	0.56062	-0.8041	10	0.45353	T	0.12	-7.733	7.2877	0.26348	0.2046:0.0:0.7954:0.0	.	128;128	Q9Y574;Q14D68	ASB4_HUMAN;.	N	128	ENSP00000321388:D128N;ENSP00000397070:D128N	ENSP00000321388:D128N	D	+	1	0	ASB4	94963200	1.000000	0.71417	1.000000	0.80357	0.292000	0.27327	3.865000	0.56033	2.680000	0.91292	0.655000	0.94253	GAT	.		0.458	ASB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333225.2	NM_016116		A	95125264	G	A	95125264	3	1	121	1	0	0	0	0	1	0	0	0	1026	1290	45	2	388	2	ASB4	7	95125264	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	88485430	95125264	64013399	38	10492											
NRCAM	4897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	107808822	107808822	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagctgcagcagtaagattGctgatcctgggatttactgc	9	11	12	9	0	0	2	0	1	0	1	1	3	1	3	1	1	6	6	1	1	2	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:107808822G>A	ENST00000425651.2	-	26	3212	c.3213C>T	c.(3211-3213)agC>agT	p.S1071S	NRCAM_ENST00000379022.4_Silent_p.S1071S|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000379028.3_Silent_p.S1071S|NRCAM_ENST00000379024.4_Intron	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1071	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CAGTAAGATTGCTGATCCTGG	0.363																																					p.S1071S		.											.	NRCAM-156	0			c.C3213T						.						71	68	69					7																	107808822		1891	4119	6010	SO:0001819	synonymous_variant	4897	exon26			AAGATTGCTGATC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7994	protein-coding gene	gene with protein product	"NgCAM-related cell adhesion molecule"	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3213C>T	7.37:g.107808822G>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	81	27	NM_001037132	0	0	0	0	0	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	G	9.798	1.179809	0.21787	.	.	ENSG00000091129	ENST00000445634	.	.	.	5.75	1.63	0.23807	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49624	-0.8920	4	.	.	.	.	7.8556	0.29480	0.0:0.3328:0.2964:0.3708	.	.	.	.	V	21	.	.	A	-	2	0	NRCAM	107596058	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.272000	0.33109	0.762000	0.33152	0.650000	0.86243	GCA	.		0.363	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107808822	G	A	107808822	2	1	121	1	0	0	0	0	0	0	0	1	10670	1310	46	2		2	NRCAM	7	107808822	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	12683558	107808822	51329841	39	10493											
CHD7	55636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	61654762	61654762	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcggtgcagcagttccaTcaccacccctctactgctct	7	10	6	18	1	3	0	1	0	2	0	5	0	4	0	4	1	4	4	4	1	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr8:61654762T>C	ENST00000423902.2	+	2	1250	c.771T>C	c.(769-771)caT>caC	p.H257H	CHD7_ENST00000524602.1_Silent_p.H257H|CHD7_ENST00000525508.1_Silent_p.H257H	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	257					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AGCAGTTCCATCACCACCCCT	0.582																																					p.H257H		.											.	CHD7-141	0			c.T771C						.						119	122	121					8																	61654762		2099	4221	6320	SO:0001819	synonymous_variant	55636	exon2			GTTCCATCACCAC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"CHARGE association"	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.771T>C	8.37:g.61654762T>C		Somatic	258	1		WXS	Illumina HiSeq	Phase_I	218	89	NM_017780	0	0	3	5	2	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			.		0.582	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		C	61654762	T	C	61654762	2	2	121	1	0	0	0	0	0	0	0	1	3336	1432	50	3		3	CHD7	8	61654762	Silent	SNP	T	TCGA-GL-6846-01A-11D-1961-08		61654762	84709260	40	10494											
PTPRD	5789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	8460558	8460558	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggggtcggagtaagggctgGttgcatacatcttctgagga	8	10	16	7	2	2	1	0	1	2	0	3	3	2	3	0	6	2	4	0	6	2	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:8460558G>T	ENST00000381196.4	-	30	4271	c.3728C>A	c.(3727-3729)aCc>aAc	p.T1243N	PTPRD_ENST00000397617.3_Missense_Mutation_p.T822N|PTPRD_ENST00000540109.1_Missense_Mutation_p.T1243N|PTPRD_ENST00000356435.5_Missense_Mutation_p.T1243N|PTPRD_ENST00000397606.3_Missense_Mutation_p.T822N|PTPRD_ENST00000537002.1_Missense_Mutation_p.T829N|PTPRD_ENST00000360074.4_Missense_Mutation_p.T1230N|PTPRD_ENST00000358503.5_Missense_Mutation_p.T1221N|PTPRD_ENST00000355233.5_Missense_Mutation_p.T832N|PTPRD_ENST00000486161.1_Missense_Mutation_p.T832N|PTPRD_ENST00000397611.3_Missense_Mutation_p.T829N	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1243					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GTAAGGGCTGGTTGCATACAT	0.433										TSP Lung(15;0.13)																											p.T1243N		.											.	PTPRD-912	0			c.C3728A						.						107	100	102					9																	8460558		2203	4300	6503	SO:0001583	missense	5789	exon33			GGGCTGGTTGCAT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3728C>A	9.37:g.8460558G>T	ENSP00000370593:p.Thr1243Asn	Somatic	85	1		WXS	Illumina HiSeq	Phase_I	94	40	NM_002839	0	0	0	0	0	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179248	0.57800	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61	5.89	4.04	0.47022	.	0.255483	0.44483	D	0.000442	T	0.52289	0.1725	L	0.54323	1.7	0.43879	D	0.996492	B;B;B;B;B;P;B;D;B	0.56521	0.244;0.38;0.38;0.38;0.159;0.514;0.213;0.976;0.187	B;B;B;B;B;B;B;P;B	0.53146	0.026;0.137;0.137;0.137;0.358;0.267;0.093;0.719;0.093	T	0.48340	-0.9044	9	.	.	.	.	10.7731	0.46334	0.0681:0.0:0.7999:0.1319	.	822;827;832;832;829;829;1230;1243;1243	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	N	1243;1243;1230;1221;832;822;829;829;714;1243;832;822	ENSP00000370593:T1243N;ENSP00000348812:T1243N;ENSP00000353187:T1230N;ENSP00000351293:T1221N;ENSP00000347373:T832N;ENSP00000380741:T822N;ENSP00000380735:T829N;ENSP00000440515:T829N;ENSP00000438164:T1243N;ENSP00000417093:T832N;ENSP00000380731:T822N	.	T	-	2	0	PTPRD	8450558	1.000000	0.71417	0.999000	0.59377	0.612000	0.37316	9.444000	0.97578	0.812000	0.34326	-0.259000	0.10710	ACC	.		0.433	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8460558	G	T	8460558	3	4	121	1	0	0	0	0	1	0	0	0	12831	1261	44	4	2131	4	PTPRD	9	8460558	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08		8460558	132752873	41	10495											
BNC2	54796	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	16552614	16552615	+	In_Frame_Ins	INS	-	-	GAA																															tcctcttgcttcaggacgctINSgaagagacggtccagcagga																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:16552614_16552615insGAA	ENST00000380672.4	-	5	639_640	c.582_583insTTC	c.(580-585)ttcagc>ttcTTCagc	p.194_195insF	BNC2_ENST00000545497.1_In_Frame_Ins_p.99_100insF|BNC2_ENST00000380667.2_In_Frame_Ins_p.127_128insF|BNC2_ENST00000380666.2_In_Frame_Ins_p.194_195insF	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		TTCAGGACGCTGAAGAGACGGT	0.55																																					p.S195delinsFS		.											.	BNC2-92	0			c.583_584insTTC						.																																			SO:0001652	inframe_insertion	54796	exon5			.	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"Zinc fingers, C2H2-type"	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.580_582dupTTC	9.37:g.16552615_16552617dupGAA	ENSP00000370047:p.Phe194_Phe194dup	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	77	17	NM_017637	0	0	0	0	0		In_Frame_Ins	INS	ENST00000380672.4	37	CCDS6482.2																																																																																			.		0.55	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		GAA	16552615	-	GAA	16552614	7	5	121	1	0	1	1	0	0	0	0	0	1476	1580	55	0	2728	0	BNC2	9	16552614	In_Frame_Ins	INS	-	TCGA-GL-6846-01A-11D-1961-08	8092056	16552614	124660817	42	10496											
GTF3C5	9328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	135917679	135917680	+	Missense_Mutation	DNP	TT	TT	AA																															ccttggcatcatctccaccaTttacaaatttcagggtaact																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:135917679_135917680TT>AA	ENST00000372097.5	+	2	682_683	c.359_360TT>AA	c.(358-360)aTT>aAA	p.I120K	GTF3C5_ENST00000485692.1_Intron|GTF3C5_ENST00000372099.6_Missense_Mutation_p.I111K|GTF3C5_ENST00000372108.5_Missense_Mutation_p.I120K|GTF3C5_ENST00000372095.5_Intron|GTF3C5_ENST00000342018.8_Missense_Mutation_p.I120K	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	120					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		ATCTCCACCATTTACAAATTTC	0.535																																					p.I120K		.											.	GTF3C5	0			c.T360A						.																																			SO:0001583	missense	9328	exon2			CACCATTTACAAA	AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"General transcription factors"	4668	protein-coding gene	gene with protein product	"transcription factor IIIC, 63 kD"	604890	"general transcription factor IIIC, polypeptide 5 (63kD)"			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	Exception_encountered	9.37:g.135917679_135917680delinsAA	ENSP00000361169:p.Ile120Lys	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	94	35		0	0	0	0	0	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation	DNP	ENST00000372097.5	37	CCDS6958.1																																																																																			.		0.535	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823		AA	135917680	TT	AA	135917679	3	1	121	1	0	0	0	0	1	0	0	0	6897	1493	52	5	365	5	GTF3C5	9	135917679	Missense_Mutation	DNP	TT	TCGA-GL-6846-01A-11D-1961-08	119365065	135917679	5295752	43	10497											
CEL	1056	broad.mit.edu	37	chr9	135941956	135941956	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagcacatggccattgcttGggtgaagaggaatatcgcgg	10	9	14	8	2	1	2	1	1	0	1	2	3	1	3	1	4	2	2	1	4	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:135941956G>T	ENST00000372080.4	+	5	603	c.587G>T	c.(586-588)tGg>tTg	p.W196L	CEL_ENST00000351304.7_Missense_Mutation_p.W193L	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	193					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		GCCATTGCTTGGGTGAAGAGG	0.642																																					p.W196L													.	CEL-91	0			c.G587T						.						95	105	102					9																	135941956		1959	4145	6104	SO:0001583	missense	1056	exon5			TTGCTTGGGTGAA	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"bile salt-stimulated lipase"	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.587G>T	9.37:g.135941956G>T	ENSP00000361151:p.Trp196Leu	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	145	9	NM_001807	0	0	0	0	0	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.046582	0.93740	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	D;D	0.84730	-1.89;-1.89	5.31	5.31	0.75309	Carboxylesterase, type B (1);	0.055507	0.85682	D	0.000000	D	0.95733	0.8612	H	0.98682	4.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97548	1.0090	10	0.87932	D	0	.	17.5643	0.87914	0.0:0.0:1.0:0.0	.	193	P19835	CEL_HUMAN	L	196;193;196	ENSP00000361151:W196L;ENSP00000342217:W193L	ENSP00000304021:W196L	W	+	2	0	CEL	134931777	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.317000	0.96327	2.479000	0.83701	0.561000	0.74099	TGG	.		0.642	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			T	135941956	G	T	135941956	3	4	121	1	0	0	0	0	1	0	0	0	3215	1357	47	4	605	4	CEL	9	135941956	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	24277	135941956	5271475	44	10498											
LCN12	286256	broad.mit.edu	37	chr9	139846817	139846819	+	In_Frame_Del	DEL	TGC	TGC	-																															cctgtggctgtggctctcctTgctgaaagtcctgcaggccc																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:139846817_139846819delTGC	ENST00000371633.3	+	1	38_40	c.38_40delTGC	c.(37-42)ttgctg>ttg	p.13_14LL>L		NM_178536.3	NP_848631.2	Q6JVE5	LCN12_HUMAN	lipocalin 12	13					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		TGGCTCTCCTTGCTGAAAGTCCT	0.626																																					p.13_14del													.	LCN12-90	0			c.38_40del						.																																			SO:0001651	inframe_deletion	286256	exon1			TCTCCTTGCTGAA	BC041168	CCDS7018.2	9q34	2011-10-24	2007-12-18		ENSG00000184925	ENSG00000184925		"Lipocalins"	28733	protein-coding gene	gene with protein product		612905				15363845	Standard	XM_005266068		Approved	MGC48935	uc004ckb.3	Q6JVE5	OTTHUMG00000020968	ENST00000371633.3:c.38_40delTGC	9.37:g.139846817_139846819delTGC	ENSP00000360696:p.Leu14del	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	25	7	NM_178536	0	0	0	0	0	A2AMJ7	In_Frame_Del	DEL	ENST00000371633.3	37	CCDS7018.2																																																																																			.		0.626	LCN12-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257990.1	NM_178536		-	139846819	TGC	-	139846817	7	5	121	1	0	1	0	1	0	0	0	0	8703	1821	63	0	40	0	LCN12	9	139846817	In_Frame_Del	DEL	TGC	TCGA-GL-6846-01A-11D-1961-08	3904861	139846817	1366614	45	10499											
CACNA1B	774	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	140943670	140943670	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccctcctagatgatcgacTtgggactgctgcttcaccct	6	12	8	15	1	1	2	1	1	0	1	4	4	3	3	3	1	2	2	3	1	1	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:140943670T>C	ENST00000371372.1	+	24	3758	c.3613T>C	c.(3613-3615)Ttg>Ctg	p.L1205L	CACNA1B_ENST00000371355.4_Silent_p.L1206L|CACNA1B_ENST00000277549.5_Silent_p.L397L|CACNA1B_ENST00000545473.1_3'UTR|CACNA1B_ENST00000277551.2_Silent_p.L1205L|CACNA1B_ENST00000371363.1_Silent_p.L1205L|CACNA1B_ENST00000371357.1_Silent_p.L1206L	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1205					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GATGATCGACTTGGGACTGCT	0.527																																					p.L1205L		.											.	CACNA1B-138	0			c.T3613C						.						177	173	174					9																	140943670		2047	4198	6245	SO:0001819	synonymous_variant	774	exon24			ATCGACTTGGGAC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.3613T>C	9.37:g.140943670T>C		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	88	38	NM_001243812	0	0	0	0	0	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																			.		0.527	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		C	140943670	T	C	140943670	2	2	121	1	0	0	0	0	0	0	0	1	2545	1606	56	3		3	CACNA1B	9	140943670	Silent	SNP	T	TCGA-GL-6846-01A-11D-1961-08	1096853	140943670	269761	46	10500											
DIP2C	22982	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	375449	375449	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagcaaaacgtgtctcggActttgtactgactcacggca	11	9	11	10	3	2	1	1	1	1	0	3	3	2	3	0	3	3	3	0	3	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:375449A>T	ENST00000280886.6	-	30	3764	c.3677T>A	c.(3676-3678)gTc>gAc	p.V1226D		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1226						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CGTGTCTCGGACTTTGTACTG	0.577																																					p.V1226D		.											.	DIP2C-156	0			c.T3677A						.						64	55	58					10																	375449		2203	4300	6503	SO:0001583	missense	22982	exon30			TCTCGGACTTTGT	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3677T>A	10.37:g.375449A>T	ENSP00000280886:p.Val1226Asp	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	54	24	NM_014974	0	0	16	27	11	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	CCDS7054.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.376544|5.376544	0.95945|0.95945	.|.	.|.	ENSG00000151240|ENSG00000151240	ENST00000434695|ENST00000280886;ENST00000535541;ENST00000381503	.|T	.|0.51574	.|0.7	5.84|5.84	5.84|5.84	0.93424|0.93424	.|AMP-dependent synthetase/ligase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67211|0.67211	0.2869|0.2869	M|M	0.67397|0.67397	2.05|2.05	0.80722|0.80722	D|D	1|1	.|D	.|0.60575	.|0.988	.|D	.|0.71656	.|0.974	T|T	0.69749|0.69749	-0.5061|-0.5061	5|10	.|0.66056	.|D	.|0.02	-39.2182|-39.2182	16.2141|16.2141	0.82191|0.82191	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1226	.|Q9Y2E4	.|DIP2C_HUMAN	R|D	31|1226;151;75	.|ENSP00000280886:V1226D	.|ENSP00000280886:V1226D	S|V	-|-	3|2	2|0	DIP2C|DIP2C	365449|365449	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.841000|0.841000	0.47740|0.47740	9.339000|9.339000	0.96797|0.96797	2.230000|2.230000	0.72887|0.72887	0.528000|0.528000	0.53228|0.53228	AGT|GTC	.		0.577	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		T	375449	A	T	375449	3	4	121	1	0	0	0	0	1	0	0	0	4540	275	10	5	1025	5	DIP2C	10	375449	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08		375449	135159298	47	10501											
ZEB1	6935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	31812949	31812949	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accgcccaaaaagaaaatgcGgaagacagaaaatggaatgt	20	4	10	7	2	0	3	0	0	0	3	0	5	0	5	2	2	1	0	2	2	8	0	rs35653460		TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:31812949G>T	ENST00000320985.10	+	8	2800	c.2690G>T	c.(2689-2691)cGg>cTg	p.R897L	ZEB1_ENST00000361642.5_Missense_Mutation_p.R898L|ZEB1_ENST00000560721.2_Missense_Mutation_p.R877L|ZEB1_ENST00000446923.2_Missense_Mutation_p.R881L|ZEB1_ENST00000542815.3_Missense_Mutation_p.R830L			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	897					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R897Q(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				AAGAAAATGCGGAAGACAGAA	0.373																																					p.R898L	Ovarian(40;423 959 14296 36701 49589)	.											.	ZEB1-518	1	Substitution - Missense(1)	large_intestine(1)	c.G2693T						.						111	111	111					10																	31812949		2203	4300	6503	SO:0001583	missense	6935	exon8			AAATGCGGAAGAC	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.2690G>T	10.37:g.31812949G>T	ENSP00000319248:p.Arg897Leu	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	147	59	NM_001174096	0	0	7	13	6	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	37	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.777667	0.70107	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2	5.72	4.8	0.61643	.	0.369405	0.21055	N	0.080939	T	0.15435	0.0372	L	0.27053	0.805	0.41478	D	0.988147	D;P;B;P;P	0.69078	0.997;0.826;0.208;0.826;0.826	D;B;B;B;B	0.69824	0.966;0.334;0.09;0.334;0.177	T	0.02901	-1.1096	10	0.52906	T	0.07	-12.9237	10.1047	0.42526	0.071:0.1383:0.7907:0.0	.	830;881;877;898;897	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	L	679;897;898;892;830;897;877;788;881	ENSP00000444282:R679L;ENSP00000354487:R898L;ENSP00000444891:R830L;ENSP00000319248:R897L;ENSP00000391612:R881L	ENSP00000319248:R897L	R	+	2	0	ZEB1	31852955	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.665000	0.68052	1.410000	0.46936	0.585000	0.79938	CGG	G|0.987;A|0.013		0.373	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		T	31812949	G	T	31812949	3	4	121	1	0	0	0	0	1	0	0	0	17655	1116	39	4	2734	4	ZEB1	10	31812949	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	31437500	31812949	103721798	48	10502											
SLK	9748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105763115	105763115	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaaaataaagaagaaataGgttctttatcaaaaactgaa	22	9	7	3	0	2	4	1	1	1	3	2	5	2	4	0	1	1	1	0	1	11	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:105763115G>A	ENST00000369755.3	+	9	2724	c.2179G>A	c.(2179-2181)Ggt>Agt	p.G727S	SLK_ENST00000335753.4_Missense_Mutation_p.G727S	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	727					apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AGAAGAAATAGGTTCTTTATC	0.393																																					p.G727S	NSCLC(111;540 1651 1927 4474 17706)	.											.	SLK-549	0			c.G2179A						.						47	50	49					10																	105763115		2203	4299	6502	SO:0001583	missense	9748	exon9			GAAATAGGTTCTT		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)", "STE20-like kinase (yeast)"			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.2179G>A	10.37:g.105763115G>A	ENSP00000358770:p.Gly727Ser	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	68	31	NM_014720	0	0	18	35	17	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	G	6.141	0.394210	0.11638	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.70749	-0.5;-0.51	5.71	2.88	0.33553	Protein kinase-like domain (1);	0.453038	0.24499	N	0.037999	T	0.53094	0.1775	L	0.48642	1.525	0.09310	N	1	P;B	0.35872	0.525;0.39	B;B	0.34418	0.182;0.089	T	0.44726	-0.9309	10	0.05833	T	0.94	.	6.1926	0.20532	0.2151:0.1347:0.6502:0.0	.	727;727	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	S	727	ENSP00000336824:G727S;ENSP00000358770:G727S	ENSP00000336824:G727S	G	+	1	0	SLK	105753105	0.842000	0.29525	0.931000	0.37212	0.035000	0.12851	2.556000	0.45862	0.781000	0.33589	0.555000	0.69702	GGT	.		0.393	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		A	105763115	G	A	105763115	3	1	121	1	0	0	0	0	1	0	0	0	14780	1000	35	2	2213	2	SLK	10	105763115	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	73950166	105763115	29771632	49	10503											
SEC23IP	11196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	121692658	121692658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatgaataccttttcgctcTtcagagtcacttatgctatt	10	17	5	9	1	3	2	2	1	1	1	4	2	3	2	1	0	2	2	1	0	5	8			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:121692658T>C	ENST00000369075.3	+	17	2972	c.2900T>C	c.(2899-2901)cTt>cCt	p.L967P	SEC23IP_ENST00000543134.1_Missense_Mutation_p.L756P|SEC23IP_ENST00000475542.1_3'UTR	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	967	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		CTTTTCGCTCTTCAGAGTCAC	0.383																																					p.L967P		.											.	SEC23IP-93	0			c.T2900C						.						128	125	126					10																	121692658		2203	4300	6503	SO:0001583	missense	11196	exon17			TCGCTCTTCAGAG	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2900T>C	10.37:g.121692658T>C	ENSP00000358071:p.Leu967Pro	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	152	68	NM_007190	0	0	13	25	12	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	37	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.667691	0.67814	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.39406	1.08;1.12	5.28	4.14	0.48551	DDHD (2);	0.000000	0.85682	D	0.000000	T	0.65831	0.2729	M	0.86268	2.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.991;0.998	T	0.69254	-0.5193	10	0.62326	D	0.03	-23.9312	11.2264	0.48886	0.0:0.0726:0.0:0.9274	.	756;967	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	P	967;756	ENSP00000358071:L967P;ENSP00000438773:L756P	ENSP00000358071:L967P	L	+	2	0	SEC23IP	121682648	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.655000	0.83696	0.950000	0.37743	-0.256000	0.11100	CTT	.		0.383	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			C	121692658	T	C	121692658	3	2	121	1	0	0	0	0	1	0	0	0	14025	1609	56	3	2966	3	SEC23IP	10	121692658	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	15929543	121692658	13842089	50	10504											
ADAM12	8038	broad.mit.edu;ucsc.edu	37	chr10	127789653	127789653	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccctacctgacaagctgcGcattgtcatgggatttgcga	8	11	10	12	2	1	1	1	1	0	0	2	3	2	2	2	1	4	2	2	1	2	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:127789653G>A	ENST00000368679.4	-	9	1217	c.908C>T	c.(907-909)gCg>gTg	p.A303V	ADAM12_ENST00000368676.4_Missense_Mutation_p.A303V	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	303	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.A303V(3)		biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GACAAGCTGCGCATTGTCATG	0.507																																					p.A303V													.	ADAM12-716	3	Substitution - Missense(3)	central_nervous_system(3)	c.C908T						.						88	77	81					10																	127789653		2203	4300	6503	SO:0001583	missense	8038	exon9			AGCTGCGCATTGT	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.908C>T	10.37:g.127789653G>A	ENSP00000357668:p.Ala303Val	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	62	6	NM_021641	0	0	0	0	0	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.394450	0.83011	.	.	ENSG00000148848	ENST00000368679;ENST00000368676	T;T	0.69040	-0.37;-0.37	5.32	5.32	0.75619	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.79862	0.4519	L	0.56280	1.765	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;0.999;1.0	T	0.80834	-0.1205	10	0.87932	D	0	.	19.1925	0.93672	0.0:0.0:1.0:0.0	.	300;300;303;300;303	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	V	303	ENSP00000357668:A303V;ENSP00000357665:A303V	ENSP00000357665:A303V	A	-	2	0	ADAM12	127779643	1.000000	0.71417	0.205000	0.23548	0.253000	0.25986	7.692000	0.84203	2.767000	0.95098	0.655000	0.94253	GCG	.		0.507	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			A	127789653	G	A	127789653	3	1	121	1	0	0	0	0	1	0	0	0	236	1087	38	1	1989	1	ADAM12	10	127789653	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	6096995	127789653	7745094	51	10505											
DOCK1	1793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	128788791	128788791	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgaatggcgatcacaaattCtttctggaactctgcctcag	10	13	8	10	1	5	1	2	1	3	0	5	3	5	2	1	2	2	0	1	2	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:128788791C>G	ENST00000280333.6	+	6	506	c.397C>G	c.(397-399)Ctt>Gtt	p.L133V		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	133					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		ATCACAAATTCTTTCTGGAAC	0.393																																					p.L133V		.											.	DOCK1-698	0			c.C397G						.						109	103	105					10																	128788791		1909	4134	6043	SO:0001583	missense	1793	exon6			CAAATTCTTTCTG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"DOwnstream of CrK"	601403	"dedicator of cyto-kinesis 1"			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.397C>G	10.37:g.128788791C>G	ENSP00000280333:p.Leu133Val	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_001380	0	0	8	17	9	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	C	14.43	2.532331	0.45073	.	.	ENSG00000150760	ENST00000280333	T	0.47177	0.85	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000001	T	0.47911	0.1471	L	0.61218	1.895	0.53688	D	0.999978	B;B	0.28850	0.122;0.225	B;B	0.26202	0.067;0.061	T	0.52366	-0.8585	10	0.51188	T	0.08	.	17.7282	0.88370	0.0:1.0:0.0:0.0	.	133;133	B2RUU3;Q14185	.;DOCK1_HUMAN	V	133	ENSP00000280333:L133V	ENSP00000280333:L133V	L	+	1	0	DOCK1	128678781	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	4.454000	0.60068	2.510000	0.84645	0.555000	0.69702	CTT	.		0.393	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		G	128788791	C	G	128788791	3	3	121	1	0	0	0	0	1	0	0	0	4695	913	32	4	419	4	DOCK1	10	128788791	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	999138	128788791	6745956	52	10506											
OR56A1	120796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6048449	6048449	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggataggaatgggtgcagtAagaagcgcattccgcaccac	13	6	13	9	2	0	1	0	0	0	1	1	3	1	3	2	3	2	4	2	3	4	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr11:6048449A>G	ENST00000316650.5	-	1	522	c.486T>C	c.(484-486)ctT>ctC	p.L162L		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGGTGCAGTAAGAAGCGCAT	0.498																																					p.L162L		.											.	OR56A1-115	0			c.T486C						.						142	125	131					11																	6048449		2201	4296	6497	SO:0001819	synonymous_variant	120796	exon1			TGCAGTAAGAAGC	AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"GPCR / Class A : Olfactory receptors"	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.486T>C	11.37:g.6048449A>G		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	125	56	NM_001001917	0	0	0	0	0	B2RNI2|Q6IFL0	Silent	SNP	ENST00000316650.5	37	CCDS31405.1																																																																																			.		0.498	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917		G	6048449	A	G	6048449	2	3	121	1	0	0	0	0	0	0	0	1	11159	349	13	3		3	OR56A1	11	6048449	Silent	SNP	A	TCGA-GL-6846-01A-11D-1961-08		6048449	128958067	53	10507											
KIAA1826	84437	broad.mit.edu	37	chr11	105881299	105881299	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgcatcatttcggaatcCaatcttttcatctatctctt	9	19	3	10	1	5	0	2	0	3	0	8	1	6	1	1	1	1	1	1	1	3	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr11:105881299C>G	ENST00000301919.4	-	2	1761	c.346G>C	c.(346-348)Gga>Cga	p.G116R	MSANTD4_ENST00000529805.1_5'Flank	NM_032424.1	NP_115800.1	Q8NCY6	MSD4_HUMAN	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	116						nucleus (GO:0005634)											TTTCGGAATCCAATCTTTTCA	0.443																																					p.G116R													.	.	0			c.G346C						.						141	143	142					11																	105881299		2201	4299	6500	SO:0001583	missense	84437	exon2			GGAATCCAATCTT	AB058729	CCDS31663.1	11q22	2012-03-13	2012-03-13	2012-03-13	ENSG00000170903	ENSG00000170903			29383	protein-coding gene	gene with protein product			"KIAA1826"	KIAA1826			Standard	XM_005271697		Approved		uc001piz.3	Q8NCY6	OTTHUMG00000166240	ENST00000301919.4:c.346G>C	11.37:g.105881299C>G	ENSP00000304713:p.Gly116Arg	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	129	3	NM_032424	0	0	24	24	0	Q96JK1|Q96JZ3|Q9H2N4	Missense_Mutation	SNP	ENST00000301919.4	37	CCDS31663.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.844408	0.51164	.	.	ENSG00000170903	ENST00000301919;ENST00000530788	.	.	.	5.88	4.94	0.65067	.	0.222920	0.45867	D	0.000336	T	0.45856	0.1363	L	0.36672	1.1	0.33135	D	0.543563	B	0.31290	0.318	B	0.33196	0.159	T	0.56938	-0.7896	9	0.37606	T	0.19	-8.0691	16.459	0.84030	0.1316:0.8683:0.0:0.0	.	116	Q8NCY6	K1826_HUMAN	R	116	.	ENSP00000304713:G116R	G	-	1	0	KIAA1826	105386509	1.000000	0.71417	0.998000	0.56505	0.962000	0.63368	3.643000	0.54374	2.782000	0.95742	0.561000	0.74099	GGA	.		0.443	MSANTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388619.1	NM_032424		G	105881299	C	G	105881299	3	3	121	1	0	0	0	0	1	0	0	0	8281	603	21	4	699	4	KIAA1826	11	105881299	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	99832850	105881299	29125217	54	10508											
KIAA0528	9847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	22623804	22623804	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttttgtggtttgtaaagcCtgatttttgtcaaaagtgat	9	19	10	3	0	1	2	1	2	0	0	1	2	1	2	1	1	1	3	1	1	4	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:22623804C>T	ENST00000333957.4	-	21	2655	c.2400G>A	c.(2398-2400)caG>caA	p.Q800Q	C2CD5_ENST00000446597.1_Silent_p.Q800Q|C2CD5_ENST00000542676.1_Silent_p.Q800Q|C2CD5_ENST00000396028.2_Silent_p.Q791Q|C2CD5_ENST00000536386.1_Silent_p.Q802Q|C2CD5_ENST00000544930.1_Silent_p.Q615Q|C2CD5_ENST00000545552.1_Silent_p.Q813Q	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	800					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										TTTGTAAAGCCTGATTTTTGT	0.343																																					p.Q800Q		.											.	.	0			c.G2400A						.						159	149	152					12																	22623804		2203	4299	6502	SO:0001819	synonymous_variant	9847	exon21			TAAAGCCTGATTT	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.2400G>A	12.37:g.22623804C>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	93	27	NM_014802	0	0	26	43	17	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	8.519	0.868292	0.17250	.	.	ENSG00000111731	ENST00000539615	.	.	.	4.99	3.02	0.34903	.	.	.	.	.	T	0.47691	0.1459	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39881	-0.9592	4	.	.	.	-10.4578	4.4442	0.11589	0.0:0.6458:0.0:0.3542	.	.	.	.	K	84	.	.	R	-	2	0	KIAA0528	22515071	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.959000	0.40412	1.338000	0.45544	0.591000	0.81541	AGG	.		0.343	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		T	22623804	C	T	22623804	2	4	121	1	0	0	0	0	0	0	0	1	8203	680	24	2		2	KIAA0528	12	22623804	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08		22623804	111228091	55	10509											
ITGB7	3695	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53586547	53586547	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagtagccgtccaagcacTggcagcggttgcatttgcag	9	9	12	11	2	0	0	0	0	0	0	1	0	1	0	2	2	5	6	2	2	3	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:53586547T>C	ENST00000267082.5	-	13	2105	c.1874A>G	c.(1873-1875)cAg>cGg	p.Q625R	ITGB7_ENST00000338737.4_Intron|ITGB7_ENST00000422257.3_Missense_Mutation_p.Q625R|ITGB7_ENST00000550743.2_Intron	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	625	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCCAAGCACTGGCAGCGGTT	0.597																																					p.Q625R		.											.	ITGB7-231	0			c.A1874G						.						117	95	102					12																	53586547		2203	4300	6503	SO:0001583	missense	3695	exon13			AAGCACTGGCAGC		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1874A>G	12.37:g.53586547T>C	ENSP00000267082:p.Gln625Arg	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	106	65	NM_000889	0	0	11	37	26	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	37	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.372998	0.42105	.	.	ENSG00000139626	ENST00000422257;ENST00000267082	D;D	0.94046	-3.34;-3.34	5.13	5.13	0.70059	EGF, extracellular (1);	0.000000	0.40385	N	0.001119	D	0.87533	0.6201	N	0.20685	0.6	0.80722	D	1	P	0.40515	0.719	B	0.39258	0.295	D	0.86926	0.2070	10	0.30078	T	0.28	.	14.3146	0.66440	0.0:0.0:0.0:1.0	.	625	P26010	ITB7_HUMAN	R	625	ENSP00000408741:Q625R;ENSP00000267082:Q625R	ENSP00000267082:Q625R	Q	-	2	0	ITGB7	51872814	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	1.901000	0.39838	2.087000	0.62958	0.454000	0.30748	CAG	.		0.597	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			C	53586547	T	C	53586547	3	2	121	1	0	0	0	0	1	0	0	0	7921	1580	55	3	538	3	ITGB7	12	53586547	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	30962743	53586547	80265348	56	10510											
TDG	6996	hgsc.bcm.edu	37	chr12	104378526	104378526	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tataaaatgttgtgattctaGctctgctatgttatgccatc	10	17	7	7	0	2	1	0	1	2	0	3	1	2	1	1	0	3	4	1	0	6	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:104378526G>T	ENST00000392872.3	+	8	1026		c.e8-1		TDG_ENST00000544861.1_Splice_Site|TDG_ENST00000266775.9_Splice_Site|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Splice_Site	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase						base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		TGTGATTCTAGCTCTGCTATG	0.323								Base excision repair (BER), DNA glycosylases																													.		.											.	TDG-661	0			c.793-1G>T						.						45	42	43					12																	104378526		2203	4300	6503	SO:0001630	splice_region_variant	6996	exon8			ATTCTAGCTCTGC	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"G/T mismatch-specific thymine DNA glycosylase"	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.793-1G>T	12.37:g.104378526G>T		Somatic	49	1		WXS	Illumina HiSeq	Phase_I	63	5	NM_003211	0	0	0	0	0	Q8IUZ6|Q8IZM3	Splice_Site	SNP	ENST00000392872.3	37	CCDS9095.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099218	0.76983	.	.	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	.	.	.	5.99	5.99	0.97316	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TDG	102902656	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	9.869000	0.99810	2.840000	0.97914	0.655000	0.94253	.	.		0.323	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		Intron	T	104378526	G	T	104378526	5	4	121	1	0	0	0	0	0	0	1	0	15757	985	34	4	822	4	TDG	12	104378526	Splice_Site	SNP	G	TCGA-GL-6846-01A-11D-1961-08	50791979	104378526	29473369	57	10511											
MTIF3	219402	ucsc.edu	37	chr13	28014392	28014392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tattcttttttgtcttttttCcttcattctgggtgtcttca	3	25	5	8	0	6	0	2	0	4	0	7	0	7	0	1	1	0	0	1	1	1	11			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr13:28014392C>T	ENST00000381116.1	-	5	428	c.194G>A	c.(193-195)gGa>gAa	p.G65E	MTIF3_ENST00000431572.2_Missense_Mutation_p.G65E|MTIF3_ENST00000461838.1_5'UTR|MTIF3_ENST00000405591.2_Missense_Mutation_p.G65E|MTIF3_ENST00000381120.3_Missense_Mutation_p.G65E			Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3	65					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		TGTCTTTTTTCCTTCATTCTG	0.403																																					p.G65E													.	MTIF3-92	0			c.G194A						.						106	109	108					13																	28014392		2203	4300	6503	SO:0001583	missense	219402	exon4			TTTTTTCCTTCAT	BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633	ENST00000381116.1:c.194G>A	13.37:g.28014392C>T	ENSP00000370508:p.Gly65Glu	Somatic	149	0		WXS	Illumina HiSeq		139	1	NM_001166263	0	0	29	33	4	Q05BL8|Q5W0V0|Q86X68	Missense_Mutation	SNP	ENST00000381116.1	37	CCDS9322.1	.	.	.	.	.	.	.	.	.	.	C	3.884	-0.025346	0.07589	.	.	ENSG00000122033	ENST00000431572;ENST00000405591;ENST00000381116;ENST00000381120	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.82	-0.823	0.10815	.	0.504141	0.21766	N	0.069438	T	0.15912	0.0383	L	0.36672	1.1	0.09310	N	1	B	0.23806	0.091	B	0.19148	0.024	T	0.09357	-1.0678	10	0.32370	T	0.25	-6.0618	0.9703	0.01414	0.2413:0.3473:0.1435:0.2679	.	65	Q9H2K0	IF3M_HUMAN	E	65	ENSP00000400084:G65E;ENSP00000384659:G65E;ENSP00000370508:G65E;ENSP00000370512:G65E	ENSP00000370508:G65E	G	-	2	0	MTIF3	26912392	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-2.094000	0.01351	0.048000	0.15891	0.655000	0.94253	GGA	.		0.403	MTIF3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044300.1	NM_152912		T	28014392	C	T	28014392	3	4	121	1	0	0	0	0	1	0	0	0	9960	855	30	2	654	2	MTIF3	13	28014392	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		28014392	87155486	58	10512											
FSCB	84075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	44975261	44975261	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaactttaacagaattctcCgcaactgcagtggctgcctc	10	11	8	12	1	1	2	0	1	1	1	3	2	1	2	2	1	5	3	2	1	4	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr14:44975261C>T	ENST00000340446.4	-	1	1221	c.930G>A	c.(928-930)gcG>gcA	p.A310A	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	310						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CAGAATTCTCCGCAACTGCAG	0.527																																					p.A310A		.											.	FSCB-587	0			c.G930A						.						48	51	50					14																	44975261		2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			ATTCTCCGCAACT	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"chromosome 14 open reading frame 155"	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.930G>A	14.37:g.44975261C>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	88	38	NM_032135	0	0	0	0	0	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																			.		0.527	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		T	44975261	C	T	44975261	2	4	121	1	0	0	0	0	0	0	0	1	6085	639	23	1		1	FSCB	14	44975261	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08		44975261	62374279	59	10513											
TDP1	55775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	90429932	90429932	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggacatttgggacatgctGgataaagggaaccccttcca	12	8	11	10	0	0	0	0	0	0	0	1	4	1	4	3	4	2	1	3	4	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr14:90429932G>A	ENST00000335725.4	+	3	724	c.474G>A	c.(472-474)ctG>ctA	p.L158L	TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000555565.1_Intron|TDP1_ENST00000555880.1_Silent_p.L158L|TDP1_ENST00000393452.3_Silent_p.L158L|TDP1_ENST00000393454.2_Silent_p.L158L	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	158					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		GGGACATGCTGGATAAAGGGA	0.512								Repair of DNA-protein crosslinks																													p.L158L		.											.	TDP1-92	0			c.G474A						.						63	59	60					14																	90429932		2203	4300	6503	SO:0001819	synonymous_variant	55775	exon3			CATGCTGGATAAA	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.474G>A	14.37:g.90429932G>A		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	125	51	NM_018319	0	0	2	7	5	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	37	CCDS9888.1																																																																																			.		0.512	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		A	90429932	G	A	90429932	2	1	121	1	0	0	0	0	0	0	0	1	15760	1335	47	2		2	TDP1	14	90429932	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	45454671	90429932	16919608	60	10514											
LRRC49	54839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	71341787	71341787	+	Missense_Mutation	SNP	G	G	A																															aattctgtaaaacatatataGaagaccttgtgaaggaagcc																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr15:71341787G>A	ENST00000260382.5	+	16	2157	c.1897G>A	c.(1897-1899)Gaa>Aaa	p.E633K	LRRC49_ENST00000560158.2_Missense_Mutation_p.E321K|LRRC49_ENST00000560691.1_Missense_Mutation_p.E339K|LRRC49_ENST00000560369.1_Missense_Mutation_p.E638K|LRRC49_ENST00000443425.2_Missense_Mutation_p.E589K|LRRC49_ENST00000544974.2_Missense_Mutation_p.E623K|LRRC49_ENST00000436542.2_3'UTR	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	633						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						AACATATATAGAAGACCTTGT	0.333																																					p.E638K		.											.	LRRC49-91	0			c.G1912A						.						64	69	67					15																	71341787		2199	4297	6496	SO:0001583	missense	54839	exon16			TATATAGAAGACC		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.1897G>A	15.37:g.71341787G>A	ENSP00000260382:p.Glu633Lys	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	121	43	NM_001199017	0	0	10	10	0	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Missense_Mutation	SNP	ENST00000260382.5	37	CCDS32282.1	.	.	.	.	.	.	.	.	.	.	g	6.828	0.521874	0.13005	.	.	ENSG00000137821	ENST00000544974;ENST00000260382;ENST00000443425;ENST00000436542	T;T;T	0.32753	1.45;1.45;1.44	5.11	3.15	0.36227	.	0.337573	0.31381	N	0.007756	T	0.10637	0.0260	N	0.03608	-0.345	0.29353	N	0.865232	B;B;B;B;B	0.13145	0.0;0.001;0.001;0.0;0.007	B;B;B;B;B	0.15484	0.001;0.003;0.003;0.001;0.013	T	0.26780	-1.0093	10	0.08179	T	0.78	-16.1443	6.9842	0.24719	0.0981:0.2677:0.6342:0.0	.	638;605;589;633;623	B7Z366;G5E9Q1;G5E9T5;Q8IUZ0;F5H1J4	.;.;.;LRC49_HUMAN;.	K	623;633;589;605	ENSP00000439600:E623K;ENSP00000260382:E633K;ENSP00000414065:E589K	ENSP00000260382:E633K	E	+	1	0	LRRC49	69128841	0.993000	0.37304	0.824000	0.32777	0.939000	0.58152	2.570000	0.45981	1.386000	0.46466	0.655000	0.94253	GAA	.		0.333	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691		A	71341787	G	A	71341787	3	1	121	1	0	0	0	0	1	0	0	0	9031	943	33	2	1959	2	LRRC49	15	71341787	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08		71341787	31189605	61	10515	108	2									
LRRC49	54839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	71341790	71341790	+	Missense_Mutation	SNP	G	G	A																															tctgtaaaacatatatagaaGaccttgtgaaggaagccaca																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr15:71341790G>A	ENST00000260382.5	+	16	2160	c.1900G>A	c.(1900-1902)Gac>Aac	p.D634N	LRRC49_ENST00000560158.2_Missense_Mutation_p.D322N|LRRC49_ENST00000560691.1_Missense_Mutation_p.D340N|LRRC49_ENST00000560369.1_Missense_Mutation_p.D639N|LRRC49_ENST00000443425.2_Missense_Mutation_p.D590N|LRRC49_ENST00000544974.2_Missense_Mutation_p.D624N|LRRC49_ENST00000436542.2_3'UTR	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	634						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						ATATATAGAAGACCTTGTGAA	0.333																																					p.D639N		.											.	LRRC49-91	0			c.G1915A						.						68	73	72					15																	71341790		2199	4297	6496	SO:0001583	missense	54839	exon16			ATAGAAGACCTTG		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.1900G>A	15.37:g.71341790G>A	ENSP00000260382:p.Asp634Asn	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	125	46	NM_001199017	0	0	5	5	0	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Missense_Mutation	SNP	ENST00000260382.5	37	CCDS32282.1	.	.	.	.	.	.	.	.	.	.	g	12.82	2.053304	0.36181	.	.	ENSG00000137821	ENST00000544974;ENST00000260382;ENST00000443425;ENST00000436542	T;T;T	0.32753	1.44;1.45;1.44	5.11	5.11	0.69529	.	0.112225	0.64402	D	0.000019	T	0.33556	0.0867	N	0.17474	0.49	0.46149	D	0.998895	B;B;B;B;D	0.60575	0.036;0.061;0.061;0.036;0.988	B;B;B;B;P	0.60236	0.01;0.033;0.033;0.015;0.871	T	0.03463	-1.1034	10	0.16420	T	0.52	-22.4388	16.0724	0.80943	0.0:0.0:1.0:0.0	.	639;606;590;634;624	B7Z366;G5E9Q1;G5E9T5;Q8IUZ0;F5H1J4	.;.;.;LRC49_HUMAN;.	N	624;634;590;606	ENSP00000439600:D624N;ENSP00000260382:D634N;ENSP00000414065:D590N	ENSP00000260382:D634N	D	+	1	0	LRRC49	69128844	1.000000	0.71417	0.996000	0.52242	0.959000	0.62525	3.689000	0.54706	2.657000	0.90304	0.655000	0.94253	GAC	.		0.333	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691		A	71341790	G	A	71341790	3	1	121	1	0	0	0	0	1	0	0	0	9031	942	33	2	1962	2	LRRC49	15	71341790	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	3	71341790	31189602	62	10516	108	2									
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2814253	2814253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgaagagttaatggaggtgGtagagaagtctgaagaaccc	15	8	14	4	0	1	5	0	2	1	3	1	7	1	6	1	3	1	2	1	3	6	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:2814253G>A	ENST00000301740.8	+	11	4273	c.3724G>A	c.(3724-3726)Gta>Ata	p.V1242I		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1242	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AATGGAGGTGGTAGAGAAGTC	0.443																																					p.V1242I		.											.	SRRM2-93	0			c.G3724A						.						106	113	111					16																	2814253		2198	4300	6498	SO:0001583	missense	23524	exon11			GAGGTGGTAGAGA	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.3724G>A	16.37:g.2814253G>A	ENSP00000301740:p.Val1242Ile	Somatic	221	0		WXS	Illumina HiSeq	Phase_I	303	72	NM_016333	0	0	60	84	24	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	3.875	-0.027037	0.07589	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24350	1.86	6.17	2.02	0.26589	.	0.793322	0.11547	N	0.553197	T	0.13713	0.0332	N	0.16478	0.41	0.09310	N	0.999996	B	0.06786	0.001	B	0.06405	0.002	T	0.33292	-0.9874	10	0.20519	T	0.43	0.1551	6.7948	0.23719	0.375:0.0:0.625:0.0	.	1242	Q9UQ35	SRRM2_HUMAN	I	1242;1242;494	ENSP00000301740:V1242I	ENSP00000301740:V1242I	V	+	1	0	SRRM2	2754254	0.001000	0.12720	0.868000	0.34077	0.982000	0.71751	-0.011000	0.12721	0.445000	0.26639	0.655000	0.94253	GTA	.		0.443	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2814253	G	A	2814253	3	1	121	1	0	0	0	0	1	0	0	0	15201	1261	44	2	3762	2	SRRM2	16	2814253	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08		2814253	87540500	63	10517											
SRCAP	10847	broad.mit.edu	37	chr16	30735227	30735227	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggacctccctccttggcAccatctggtgcttccccgtc	3	11	8	19	1	1	0	0	0	1	0	5	1	4	1	7	3	1	2	7	3	0	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:30735227A>C	ENST00000262518.4	+	25	4867	c.4482A>C	c.(4480-4482)gcA>gcC	p.A1494A	SRCAP_ENST00000395059.2_Silent_p.A1432A|SRCAP_ENST00000344771.4_Silent_p.A1336A	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1494	Pro-rich.			A -> Q (in Ref. 6; AAD39760). {ECO:0000305}.	histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CCTCCTTGGCACCATCTGGTG	0.587																																					p.A1494A													.	SRCAP-94	0			c.A4482C						.						113	102	106					16																	30735227		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon25			CTTGGCACCATCT	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4482A>C	16.37:g.30735227A>C		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	153	7	NM_006662	0	0	85	86	1	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30735227	A	C	30735227	2	2	121	1	0	0	0	0	0	0	0	1	15167	146	6	5		5	SRCAP	16	30735227	Silent	SNP	A	TCGA-GL-6846-01A-11D-1961-08	27920974	30735227	59619526	64	10518											
C16orf86	388284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67702137	67702137	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcggccgctgtaccagtaCgtcaactattgcaaccctga	9	9	9	14	3	1	1	1	1	0	0	1	1	1	1	3	1	6	4	3	1	5	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:67702137C>G	ENST00000403458.4	+	4	743	c.588C>G	c.(586-588)taC>taG	p.Y196*	ENKD1_ENST00000602409.1_5'Flank|ENKD1_ENST00000602644.1_5'Flank|ENKD1_ENST00000243878.4_5'Flank	NM_001012984.2	NP_001013002.2	Q6ZW13	CP086_HUMAN	chromosome 16 open reading frame 86	196										endometrium(2)|lung(4)	6		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		TGTACCAGTACGTCAACTATT	0.667											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y196X		.											.	.	0			c.C588G						.						15	16	16					16																	67702137		2190	4293	6483	SO:0001587	stop_gained	388284	exon4			CCAGTACGTCAAC		CCDS32468.2	16q22.1	2008-10-30			ENSG00000159761	ENSG00000159761			33755	protein-coding gene	gene with protein product							Standard	NM_001012984		Approved	FLJ41802	uc002ety.3	Q6ZW13	OTTHUMG00000150527	ENST00000403458.4:c.588C>G	16.37:g.67702137C>G	ENSP00000384117:p.Tyr196*	Somatic	25	0	1101	WXS	Illumina HiSeq	Phase_I	32	18	NM_001012984	0	0	9	17	8	B5MCW6	Nonsense_Mutation	SNP	ENST00000403458.4	37	CCDS32468.2	.	.	.	.	.	.	.	.	.	.	C	32	5.154005	0.94645	.	.	ENSG00000159761	ENST00000403458	.	.	.	5.95	2.97	0.34412	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8901	9.6968	0.40163	0.0:0.7838:0.0:0.2162	.	.	.	.	X	196	.	ENSP00000384117:Y196X	Y	+	3	2	C16orf86	66259638	0.998000	0.40836	1.000000	0.80357	0.972000	0.66771	0.259000	0.18405	0.426000	0.26116	0.563000	0.77884	TAC	.		0.667	C16orf86-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318767.2	NM_001012984		G	67702137	C	G	67702137	4	3	121	1	0	0	0	0	0	1	0	0	1843	547	19	4	602	4	C16orf86	16	67702137	Nonsense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	36966910	67702137	22652616	65	10519											
CPNE7	27132	broad.mit.edu	37	chr16	89662976	89662976	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acagccacagaggcctgcccCcgagaagcctgggtgtccct	8	5	12	16	1	0	2	0	0	0	2	1	3	1	2	6	2	3	0	6	2	1	0			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:89662976C>A	ENST00000268720.5	+	17	1979	c.1849C>A	c.(1849-1851)Ccg>Acg	p.P617T	CPNE7_ENST00000319518.8_Missense_Mutation_p.P542T|CPNE7_ENST00000566398.1_3'UTR	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	617					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		AGGCCTGCCCCCGAGAAGCCT	0.667																																					p.P617T													.	CPNE7-90	0			c.C1849A						.						53	54	53					16																	89662976		2197	4299	6496	SO:0001583	missense	27132	exon17			CTGCCCCCGAGAA	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1849C>A	16.37:g.89662976C>A	ENSP00000268720:p.Pro617Thr	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	92	8	NM_014427	0	0	4	4	0		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939497	0.73557	.	.	ENSG00000178773	ENST00000319518;ENST00000268720	T;T	0.33438	1.48;1.41	3.79	3.79	0.43588	.	0.000000	0.85682	D	0.000000	T	0.63200	0.2491	M	0.92026	3.265	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.81914	0.983;0.995	T	0.75102	-0.3436	10	0.87932	D	0	-20.9241	15.6095	0.76704	0.0:1.0:0.0:0.0	.	542;617	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	T	542;617	ENSP00000317374:P542T;ENSP00000268720:P617T	ENSP00000268720:P617T	P	+	1	0	CPNE7	88190477	0.997000	0.39634	0.007000	0.13788	0.005000	0.04900	7.006000	0.76329	1.821000	0.53095	0.561000	0.74099	CCG	.		0.667	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			A	89662976	C	A	89662976	3	1	121	1	0	0	0	0	1	0	0	0	3823	623	22	4	1915	4	CPNE7	16	89662976	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	21960839	89662976	691777	66	10520											
C16orf7	9605	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	89775318	89775318	+	Frame_Shift_Del	DEL	G	G	-																															tggggtgtggcctctggggtGgggcagtagtcttccgcaca																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:89775318delG	ENST00000389386.3	-	13	1768	c.1644delC	c.(1642-1644)cccfs	p.P548fs	VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Frame_Shift_Del_p.P478fs	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	548	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCTCTGGGGTGGGGCAGTAGT	0.682																																					p.P548fs		.											.	.	0			c.1644delC						.						13	16	15					16																	89775318		1928	4125	6053	SO:0001589	frameshift_variant	9605	exon13			.	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1644delC	16.37:g.89775318delG	ENSP00000374037:p.Pro548fs	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_004913	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000389386.3	37	CCDS42220.1																																																																																			.		0.682	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		-	89775318	G	-	89775318	7	5	121	1	0	1	0	1	0	0	0	0	1832	1335	47	0	263	0	C16orf7	16	89775318	Frame_Shift_Del	DEL	G	TCGA-GL-6846-01A-11D-1961-08	112342	89775318	579435	67	10521											
SCARF1	8578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	1538231	1538231	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaccgcttcctctggtcTgactgccataggccctgtgg	4	10	12	15	2	2	1	0	1	2	0	3	2	3	2	5	4	1	1	5	4	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:1538231T>C	ENST00000263071.4	-	11	2363	c.2314A>G	c.(2314-2316)Aga>Gga	p.R772G	SCARF1_ENST00000348987.3_Missense_Mutation_p.R686G|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	772	Gly-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCCTCTGGTCTGACTGCCATA	0.657																																					p.R772G		.											.	SCARF1-91	0			c.A2314G						.						34	39	37					17																	1538231		2203	4298	6501	SO:0001583	missense	8578	exon11			CTGGTCTGACTGC	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.2314A>G	17.37:g.1538231T>C	ENSP00000263071:p.Arg772Gly	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	87	51	NM_003693	1	0	7	11	3	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	t	9.073	0.997418	0.19043	.	.	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.20463	2.07;2.77	4.68	-1.08	0.09936	.	0.960477	0.08537	N	0.931174	T	0.08980	0.0222	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.38993	-0.9635	10	0.24483	T	0.36	-2.2932	9.7539	0.40492	0.0:0.3094:0.0:0.6906	.	686;772	Q14162-2;Q14162	.;SREC_HUMAN	G	772;686	ENSP00000263071:R772G;ENSP00000323964:R686G	ENSP00000263071:R772G	R	-	1	2	SCARF1	1484981	0.000000	0.05858	0.004000	0.12327	0.092000	0.18411	-0.431000	0.06965	-0.332000	0.08489	0.450000	0.29827	AGA	.		0.657	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		C	1538231	T	C	1538231	3	2	121	1	0	0	0	0	1	0	0	0	13915	1588	55	3	182	3	SCARF1	17	1538231	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08		1538231	79656979	68	10522											
CAMKK1	84254	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3788622	3788622	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgttctgccccaccaacCtctgcatctgagatggccac	7	9	7	18	1	3	1	0	1	3	1	4	2	3	1	6	1	3	2	6	1	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:3788622C>G	ENST00000348335.2	-	2	508	c.360G>C	c.(358-360)gaG>gaC	p.E120D	CAMKK1_ENST00000158166.5_Splice_Site_p.E120D|CAMKK1_ENST00000381771.2_Splice_Site_p.E120D|CAMKK1_ENST00000381769.2_Splice_Site_p.E147D	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	120					synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		CCCCACCAACCTCTGCATCTG	0.622																																					p.E120D		.											.	CAMKK1-334	0			c.G360C						.						12	15	14					17																	3788622		2182	4265	6447	SO:0001630	splice_region_variant	84254	exon2			ACCAACCTCTGCA	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.360+1G>C	17.37:g.3788622C>G		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	46	14	NM_032294	0	0	0	0	0	Q9BQH3	Missense_Mutation	SNP	ENST00000348335.2	37	CCDS11038.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.677258	0.29783	.	.	ENSG00000004660	ENST00000381769;ENST00000348335;ENST00000381771;ENST00000158166	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.57	5.57	0.84162	Protein kinase-like domain (1);	0.246503	0.41938	D	0.000799	T	0.31513	0.0799	N	0.19112	0.55	0.44316	D	0.997194	B;B	0.13145	0.007;0.002	B;B	0.14578	0.011;0.005	T	0.11494	-1.0585	9	.	.	.	-39.5364	12.0428	0.53462	0.1724:0.8276:0.0:0.0	.	120;120	F8W9H1;Q8N5S9	.;KKCC1_HUMAN	D	147;120;120;120	ENSP00000371188:E147D;ENSP00000323118:E120D;ENSP00000371190:E120D;ENSP00000158166:E120D	.	E	-	3	2	CAMKK1	3735371	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	2.413000	0.44618	2.632000	0.89209	0.491000	0.48974	GAG	.		0.622	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	Missense_Mutation	G	3788622	C	G	3788622	5	3	121	1	0	0	0	0	0	0	1	0	2612	695	24	4	1339	4	CAMKK1	17	3788622	Splice_Site	SNP	C	TCGA-GL-6846-01A-11D-1961-08	2250391	3788622	77406588	69	10523											
ZNF232	7775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	5009512	5009512	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggacaacaagatgtgagttAtaaatgaaggttttaccaca	16	11	9	5	0	0	3	0	2	0	1	0	4	0	4	1	2	2	2	1	2	7	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:5009512A>G	ENST00000250076.3	-	5	1596	c.942T>C	c.(940-942)taT>taC	p.Y314Y	ZNF232_ENST00000575538.1_5'Flank|ZNF232_ENST00000416429.2_3'UTR|ZNF232_ENST00000575898.1_Silent_p.Y305Y	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	287					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)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						GATGTGAGTTATAAATGAAGG	0.428																																					p.Y314Y		.											.	ZNF232-154	0			c.T942C						.						111	110	111					17																	5009512		2203	4300	6503	SO:0001819	synonymous_variant	7775	exon5			TGAGTTATAAATG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"-", "Zinc fingers, C2H2-type"	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.942T>C	17.37:g.5009512A>G		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	188	47	NM_014519	0	0	2	5	3		Silent	SNP	ENST00000250076.3	37	CCDS11068.1																																																																																			.		0.428	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519		G	5009512	A	G	5009512	2	3	121	1	0	0	0	0	0	0	0	1	17817	456	16	3		3	ZNF232	17	5009512	Silent	SNP	A	TCGA-GL-6846-01A-11D-1961-08	1220890	5009512	76185698	70	10524											
POLDIP2	147007	broad.mit.edu	37	chr17	26684350	26684351	+	5'Flank	DNP	GC	GC	AT																															tccgcgtcgtcgtggtcgacGctggcgagaaggctccagct																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:26684350_26684351GC>AT	ENST00000292114.3	+	0	0				POLDIP2_ENST00000540200.1_Missense_Mutation_p.A41M|CTB-96E2.3_ENST00000591482.1_RNA|TMEM199_ENST00000395404.3_5'Flank|POLDIP2_ENST00000003607.4_5'UTR|TMEM199_ENST00000509083.1_5'Flank	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CGTGGTCGACGCTGGCGAGAAG	0.738																																					.													.	.	0			.						.																																			SO:0001631	upstream_gene_variant	26073	.			TCGACGCTGGCGA	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 32"	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498	Exception_encountered	17.37:g.26684350_26684351delinsAT	Exception_encountered	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	31	18	.	0	0	0	0	0		Missense_Mutation	DNP	ENST00000292114.3	37	CCDS11228.1																																																																																			.		0.738	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464		AT	26684351	GC	AT	26684350	1	1	121	0	1	0	0	0	0	0	0	0	12220	1087	38	1		1	POLDIP2	17	26684350	5'Flank	DNP	GC	TCGA-GL-6846-01A-11D-1961-08	21674838	26684350	54510860	71	10525											
SLC13A2	9058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26818545	26818545	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctcacccagtgcatgaGcctgtgcgtgtgctactccg	6	9	10	16	2	1	1	1	1	0	0	2	1	2	1	5	0	5	2	5	0	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:26818545G>A	ENST00000314669.5	+	5	1085	c.665G>A	c.(664-666)aGc>aAc	p.S222N	SLC13A2_ENST00000537681.1_Missense_Mutation_p.S151N|SLC13A2_ENST00000444914.3_Missense_Mutation_p.S271N|SLC13A2_ENST00000545060.1_Missense_Mutation_p.S179N	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	222					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CAGTGCATGAGCCTGTGCGTG	0.617																																					p.S271N		.											.	SLC13A2-90	0			c.G812A						.						69	64	66					17																	26818545		2203	4300	6503	SO:0001583	missense	9058	exon5			GCATGAGCCTGTG	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.665G>A	17.37:g.26818545G>A	ENSP00000316202:p.Ser222Asn	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	150	46	NM_001145975	0	0	1	1	0	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	37	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265898	0.40095	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000541739;ENST00000537681	T;T;T;T	0.03124	4.04;4.04;4.04;4.04	5.62	4.63	0.57726	.	0.200462	0.64402	D	0.000010	T	0.14227	0.0344	M	0.81341	2.54	0.42186	D	0.991709	D;B;B;B;B	0.65815	0.995;0.007;0.041;0.138;0.041	P;B;B;B;B	0.62560	0.904;0.098;0.081;0.073;0.081	T	0.01621	-1.1310	10	0.35671	T	0.21	-13.5366	9.6615	0.39958	0.0762:0.413:0.5108:0.0	.	179;271;178;151;222	F5GWV6;E7ETH5;B4E1M6;G3V1L2;Q13183	.;.;.;.;S13A2_HUMAN	N	222;271;179;178;151	ENSP00000316202:S222N;ENSP00000392411:S271N;ENSP00000441935:S179N;ENSP00000440802:S151N	ENSP00000316202:S222N	S	+	2	0	SLC13A2	23842672	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	2.293000	0.43558	1.346000	0.45694	0.557000	0.71058	AGC	.		0.617	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		A	26818545	G	A	26818545	3	1	121	1	0	0	0	0	1	0	0	0	14424	971	34	2	830	2	SLC13A2	17	26818545	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	134195	26818545	54376665	72	10526											
SPAG5	10615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26919846	26919846	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatatcatgtcttgttgcTgccccagtggagatggtaca	10	12	10	9	0	2	1	1	0	1	1	2	2	2	1	2	2	3	3	2	2	3	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:26919846T>C	ENST00000321765.5	-	3	748	c.416A>G	c.(415-417)cAg>cGg	p.Q139R		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	139					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					GTCTTGTTGCTGCCCCAGTGG	0.453																																					p.Q139R		.											.	SPAG5-90	0			c.A416G						.						190	176	180					17																	26919846		2203	4300	6503	SO:0001583	missense	10615	exon3			TGTTGCTGCCCCA	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.416A>G	17.37:g.26919846T>C	ENSP00000323300:p.Gln139Arg	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	253	145	NM_006461	0	0	5	5	0	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	T	6.118	0.390021	0.11581	.	.	ENSG00000076382	ENST00000321765	T	0.25912	1.77	5.94	2.35	0.29111	.	0.760636	0.11855	N	0.522906	T	0.23210	0.0561	M	0.67953	2.075	0.25392	N	0.988515	P	0.49090	0.919	B	0.39738	0.308	T	0.32322	-0.9911	10	0.87932	D	0	-0.1373	3.1967	0.06635	0.1858:0.187:0.0:0.6271	.	139	Q96R06	SPAG5_HUMAN	R	139	ENSP00000323300:Q139R	ENSP00000323300:Q139R	Q	-	2	0	SPAG5	23943973	0.917000	0.31117	0.981000	0.43875	0.152000	0.21847	0.898000	0.28404	1.069000	0.40788	0.533000	0.62120	CAG	.		0.453	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26919846	T	C	26919846	3	2	121	1	0	0	0	0	1	0	0	0	15013	1580	55	3	3253	3	SPAG5	17	26919846	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	101301	26919846	54275364	73	10527											
FAM20A	54757	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	66538845	66538846	+	Frame_Shift_Del	DEL	AA	AA	-																															agtactctacctggagagacAaagaaaacactctgcaggat																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:66538845_66538846delAA	ENST00000592554.1	-	6	1639_1640	c.917_918delTT	c.(916-918)tttfs	p.F306fs	AC079210.1_ENST00000600820.1_5'Flank|PRKAR1A_ENST00000588188.2_Intron|FAM20A_ENST00000226094.5_5'UTR	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	306					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					CTGGAGAGACAAAGAAAACACT	0.525																																					p.306_306del		.											.	FAM20A-90	0			c.917_918del						.																																			SO:0001589	frameshift_variant	54757	exon6			.	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.917_918delTT	17.37:g.66538845_66538846delAA	ENSP00000468308:p.Phe306fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	131	30	NM_017565	0	0	0	0	0	B2RN47|B2RN49|Q9UF95	Frame_Shift_Del	DEL	ENST00000592554.1	37	CCDS11679.1																																																																																			.		0.525	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565		-	66538846	AA	-	66538845	7	5	121	1	0	1	0	1	0	0	0	0	5553	127	5	0	731	0	FAM20A	17	66538845	Frame_Shift_Del	DEL	AA	TCGA-GL-6846-01A-11D-1961-08	39618999	66538845	14656365	74	10528											
UNC13D	201294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73831766	73831766	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagctggcagagctccttGaggctgatgtagagctggaa	9	8	15	9	1	0	4	0	2	0	2	1	5	1	5	1	3	3	7	1	3	2	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:73831766G>T	ENST00000207549.4	-	19	2068	c.1689C>A	c.(1687-1689)ctC>ctA	p.L563L	UNC13D_ENST00000412096.2_Silent_p.L563L	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	563	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGAGCTCCTTGAGGCTGATGT	0.637									Familial Hemophagocytic Lymphohistiocytosis																												p.L563L		.											.	UNC13D-92	0			c.C1689A						.						41	38	39					17																	73831766		2203	4300	6503	SO:0001819	synonymous_variant	201294	exon19	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CTCCTTGAGGCTG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.1689C>A	17.37:g.73831766G>T		Somatic	62	1		WXS	Illumina HiSeq	Phase_I	70	23	NM_199242	0	0	1	1	0	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			.		0.637	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73831766	G	T	73831766	2	4	121	1	0	0	0	0	0	0	0	1	17020	1277	45	4		4	UNC13D	17	73831766	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	7292921	73831766	7363444	75	10529											
CTAGE1	64693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	19997258	19997258	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgtatttctatctccaaccGttcttcattcgcttgaaatc	8	18	4	11	2	4	1	1	1	3	0	7	1	4	1	2	0	1	3	2	0	4	8	rs372127240		TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr18:19997258G>A	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.R173W			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					ATCTCCAACCGTTCTTCATTC	0.388																																					p.R173W		.											.	CTAGE1-1	0			c.C517T						.	G	TRP/ARG	0,4314		0,0,2157	95	100	99		517	0.9	0	18		99	2,8574		0,2,4286	no	missense	CTAGE1	NM_172241.2	101	0,2,6443	AA,AG,GG		0.0233,0.0,0.0155	probably-damaging	173/746	19997258	2,12888	2157	4288	6445	SO:0001631	upstream_gene_variant	64693	exon1			CCAACCGTTCTTC	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma-associated antigen 1", "cutaneous T-cell lymphoma-associated antigen 2", "cancer/testis antigen family 21, member 1", "cancer/testis antigen family 21, member 2"	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19997258G>A	Exception_encountered	Somatic	253	0		WXS	Illumina HiSeq	Phase_I	169	71	NM_172241	0	0	0	0	0	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		.	.	.	.	.	.	.	.	.	.	G	12.14	1.849249	0.32699	0.0	2.33E-4	ENSG00000212710	ENST00000391403	T	0.29655	1.56	0.909	0.909	0.19332	.	.	.	.	.	T	0.47581	0.1453	M	0.78637	2.42	0.09310	N	1	D	0.76494	0.999	D	0.64321	0.924	T	0.22941	-1.0202	8	.	.	.	.	5.2011	0.15264	0.0:0.0:1.0:0.0	.	173	Q96RT6	CTGE2_HUMAN	W	173	ENSP00000375220:R173W	.	R	-	1	2	CTAGE1	18251256	0.980000	0.34600	0.003000	0.11579	0.004000	0.04260	0.579000	0.23788	0.776000	0.33473	0.449000	0.29647	CGG	.		0.388	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241		A	19997258	G	A	19997258	1	1	121	0	1	0	0	0	0	0	0	0	3998	1144	40	1		1	CTAGE1	18	19997258	5'Flank	SNP	G	TCGA-GL-6846-01A-11D-1961-08		19997258	58079990	76	10530											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	127	0		WXS	Illumina HiSeq		151	2	NM_031203	0	0	0	0	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	121	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-GL-6846-01A-11D-1961-08		8527467	50601516	77	10531											
ZNF20	7568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	12246707	12246707	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatcctcaaaggccactgAatcctgaaacatctcacata	15	8	4	14	0	2	2	2	2	1	0	5	2	4	2	3	1	1	0	3	1	4	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:12246707A>C	ENST00000334213.5	-	2	240	c.16T>G	c.(16-18)Tca>Gca	p.S6A	ZNF20_ENST00000600335.1_Missense_Mutation_p.S3A|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000485451.1_5'UTR	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	6					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						AAGGCCACTGAATCCTGAAAC	0.468																																					p.S6A		.											.	ZNF20-22	0			c.T16G						.						58	59	59					19																	12246707		2201	4300	6501	SO:0001583	missense	7568	exon2			CCACTGAATCCTG	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"Zinc fingers, C2H2-type", "-"	12992	protein-coding gene	gene with protein product		194557	"zinc finger protein 20 (KOX 13)"				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.16T>G	19.37:g.12246707A>C	ENSP00000335437:p.Ser6Ala	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	87	36	NM_021143	0	0	0	0	0	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	A	7.853	0.724490	0.15439	.	.	ENSG00000132010	ENST00000334213;ENST00000292241;ENST00000418866	T;T	0.00840	5.63;5.63	0.94	-0.185	0.13276	Krueppel-associated box (1);	.	.	.	.	T	0.01092	0.0036	M	0.76328	2.33	0.09310	N	0.999999	P	0.41080	0.737	B	0.33846	0.171	T	0.44636	-0.9315	9	0.23302	T	0.38	.	2.9313	0.05800	0.6786:0.0:0.3214:0.0	.	6	P17024	ZNF20_HUMAN	A	6;6;3	ENSP00000335437:S6A;ENSP00000390115:S3A	ENSP00000292241:S6A	S	-	1	0	ZNF20	12107707	0.000000	0.05858	0.171000	0.22900	0.055000	0.15305	-1.356000	0.02609	-0.137000	0.11455	0.260000	0.18958	TCA	.		0.468	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		C	12246707	A	C	12246707	3	2	121	1	0	0	0	0	1	0	0	0	17793	246	9	5	1594	5	ZNF20	19	12246707	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	3719240	12246707	46882276	78	10532											
LGI4	163175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35617247	35617247	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagtggcgtgtggcatagAcatcctcggcctcggggatg	7	8	17	9	3	0	1	0	0	0	1	3	3	1	3	2	6	0	1	2	6	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:35617247A>G	ENST00000310123.3	-	8	1745	c.1226T>C	c.(1225-1227)gTc>gCc	p.V409A	LGI4_ENST00000392225.3_Missense_Mutation_p.S435P|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	409					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TGTGGCATAGACATCCTCGGC	0.682																																					p.V409A		.											.	LGI4-91	0			c.T1226C						.						35	32	33					19																	35617247		2203	4300	6503	SO:0001583	missense	163175	exon8			GCATAGACATCCT	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1226T>C	19.37:g.35617247A>G	ENSP00000312273:p.Val409Ala	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	36	17	NM_139284	0	0	0	0	0	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	37	CCDS12444.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.097418|4.097418	0.76870|0.76870	.|.	.|.	ENSG00000153902|ENSG00000153902	ENST00000392225|ENST00000310123;ENST00000437421	T|T	0.68331|0.78595	-0.32|-1.19	4.66|4.66	4.66|4.66	0.58398|0.58398	.|.	.|0.000000	.|0.52532	.|D	.|0.000079	D|D	0.84261|0.84261	0.5433|0.5433	L|L	0.58583|0.58583	1.82|1.82	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.85130	.|0.997;0.997	T|T	0.83349|0.83349	-0.0004|-0.0004	7|10	0.87932|0.37606	D|T	0|0.19	.|.	12.0653|12.0653	0.53583|0.53583	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|320;409	.|Q658V8;Q8N135	.|.;LGI4_HUMAN	P|A	435|409	ENSP00000376059:S435P|ENSP00000312273:V409A	ENSP00000376059:S435P|ENSP00000312273:V409A	S|V	-|-	1|2	0|0	LGI4|LGI4	40309087|40309087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.386000|7.386000	0.79775|0.79775	1.745000|1.745000	0.51790|0.51790	0.477000|0.477000	0.44152|0.44152	TCT|GTC	.		0.682	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			G	35617247	A	G	35617247	3	3	121	1	0	0	0	0	1	0	0	0	8776	275	10	3	395	3	LGI4	19	35617247	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	23370540	35617247	23511736	79	10533											
ZNF546	339327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40520846	40520846	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agaaaccctatgaatgtaagGaatgtgggaaggcttttatt	14	12	11	4	0	0	2	0	1	0	1	0	4	0	4	1	3	1	2	1	3	7	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:40520846G>A	ENST00000347077.4	+	7	1885	c.1669G>A	c.(1669-1671)Gaa>Aaa	p.E557K	ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_Missense_Mutation_p.E531K	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	557					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(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TGAATGTAAGGAATGTGGGAA	0.388																																					p.E557K		.											.	ZNF546-155	0			c.G1669A						.						61	59	59					19																	40520846		2203	4300	6503	SO:0001583	missense	339327	exon7			TGTAAGGAATGTG	BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.1669G>A	19.37:g.40520846G>A	ENSP00000339823:p.Glu557Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	84	45	NM_178544	2	0	2	4	0	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	g	15.69	2.907182	0.52333	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.07327	3.2	3.0	-0.424	0.12321	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06781	0.0173	L	0.41415	1.275	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.35624	-0.9781	9	0.56958	D	0.05	.	4.6522	0.12601	0.23:0.1839:0.5862:0.0	.	557	Q86UE3	ZN546_HUMAN	K	557;166	ENSP00000339823:E557K	ENSP00000339823:E557K	E	+	1	0	ZNF546	45212686	0.001000	0.12720	0.990000	0.47175	0.997000	0.91878	0.499000	0.22546	-0.002000	0.14469	0.655000	0.94253	GAA	.		0.388	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		A	40520846	G	A	40520846	3	1	121	1	0	0	0	0	1	0	0	0	18010	1175	41	2	1687	2	ZNF546	19	40520846	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	4903599	40520846	18608137	80	10534											
EGLN2	112398	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41306603	41306603	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagagttacctgccctgTcccctgctcccctcctacca	5	10	8	18	0	0	1	0	0	0	1	3	2	3	1	8	1	4	2	8	1	2	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:41306603T>A	ENST00000593726.1	+	1	1154	c.126T>A	c.(124-126)tgT>tgA	p.C42*	EGLN2_ENST00000594140.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR|EGLN2_ENST00000406058.2_Nonsense_Mutation_p.C42*|EGLN2_ENST00000303961.4_Nonsense_Mutation_p.C42*|CTC-490E21.12_ENST00000601627.1_5'Flank			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	42					cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	ACCTGCCCTGTCCCCTGCTCC	0.652																																					p.C42X		.											.	EGLN2-228	0			c.T126A						.						55	47	50					19																	41306603		2203	4300	6503	SO:0001587	stop_gained	112398	exon2			GCCCTGTCCCCTG	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 1"	606424	"EGL nine (C.elegans) homolog 2", "egl nine homolog 2 (C. elegans)"				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.126T>A	19.37:g.41306603T>A	ENSP00000469686:p.Cys42*	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	52	15	NM_053046	0	0	16	26	10	A8K5S0|Q8WWY4|Q9BV14	Nonsense_Mutation	SNP	ENST00000593726.1	37	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	T	38	6.815813	0.97861	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	.	.	.	4.15	1.91	0.25777	.	0.092299	0.46758	D	0.000268	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0525	7.5512	0.27798	0.0:0.1918:0.0:0.8082	.	.	.	.	X	42	.	ENSP00000307080:C42X	C	+	3	2	EGLN2	45998443	0.372000	0.25064	0.976000	0.42696	0.984000	0.73092	0.337000	0.19841	0.198000	0.20407	0.402000	0.26972	TGT	.		0.652	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			A	41306603	T	A	41306603	4	1	121	1	0	0	0	0	0	1	0	0	4980	1673	58	5	128	5	EGLN2	19	41306603	Nonsense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	785757	41306603	17822380	81	10535											
C19orf41	126123	ucsc.edu;bcgsc.ca	37	chr19	50666348	50666348	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggatgagggcggagcgcAggtgacccagggcctccagc	7	4	19	11	2	0	2	0	2	0	0	1	4	1	4	3	6	2	1	3	6	0	0			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:50666348A>G	ENST00000293405.3	-	1	104	c.104T>C	c.(103-105)cTg>cCg	p.L35P		NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	35						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						GGCGGAGCGCAGGTGACCCAG	0.701																																					p.L35P													.	IZUMO2-90	0			c.T104C						.						19	23	22					19																	50666348		1973	4159	6132	SO:0001583	missense	126123	exon1			GAGCGCAGGTGAC	AY358196	CCDS12792.2	19q13.33	2014-02-17	2010-07-29	2010-07-29	ENSG00000161652	ENSG00000161652		"-"	28518	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 41"	C19orf41		19658160, 22957301	Standard	XM_006723007		Approved	MGC33947, SCRL	uc002prp.1	Q6UXV1	OTTHUMG00000074063	ENST00000293405.3:c.104T>C	19.37:g.50666348A>G	ENSP00000293405:p.Leu35Pro	Somatic	26	0		WXS	Illumina HiSeq		16	4	NM_152358	0	0	0	0	0	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	Missense_Mutation	SNP	ENST00000293405.3	37	CCDS12792.2	.	.	.	.	.	.	.	.	.	.	A	15.79	2.936048	0.52972	.	.	ENSG00000161652	ENST00000293405;ENST00000377000	T	0.38077	1.16	3.39	3.39	0.38822	.	0.727782	0.10719	N	0.641964	T	0.46983	0.1421	L	0.34521	1.04	0.45852	D	0.998715	D	0.89917	1.0	D	0.87578	0.998	T	0.41875	-0.9484	10	0.87932	D	0	.	8.5137	0.33233	1.0:0.0:0.0:0.0	.	35	Q6UXV1	IZUM2_HUMAN	P	35	ENSP00000293405:L35P	ENSP00000293405:L35P	L	-	2	0	IZUMO2	55358160	0.996000	0.38824	0.521000	0.27850	0.005000	0.04900	3.883000	0.56168	1.774000	0.52232	0.533000	0.62120	CTG	.		0.701	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157232.1	NM_152358		G	50666348	A	G	50666348	3	3	121	1	0	0	0	0	1	0	0	0	1930	188	7	3	589	3	C19orf41	19	50666348	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	9359745	50666348	8462635	82	10536											
SLC24A3	57419	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	19665982	19665982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggatgatgatgaaggacCgtacacaccattcgacaccc	13	6	10	12	3	0	3	0	3	0	0	1	7	0	5	3	2	1	1	3	2	2	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:19665982C>T	ENST00000328041.6	+	12	1498	c.1301C>T	c.(1300-1302)cCg>cTg	p.P434L		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	434					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						gatgaagGACCGTACACACCA	0.488																																					p.P434L		.											.	SLC24A3-91	0			c.C1301T						.						166	142	150					20																	19665982		2203	4300	6503	SO:0001583	missense	57419	exon12			AAGGACCGTACAC	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1301C>T	20.37:g.19665982C>T	ENSP00000333519:p.Pro434Leu	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	106	41	NM_020689	0	0	0	1	1	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Missense_Mutation	SNP	ENST00000328041.6	37	CCDS13140.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287750	0.40494	.	.	ENSG00000185052	ENST00000328041	T	0.62498	0.02	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000001	T	0.62036	0.2395	M	0.61703	1.905	0.80722	D	1	B	0.17667	0.023	B	0.12837	0.008	T	0.56486	-0.7971	9	.	.	.	.	19.3646	0.94456	0.0:1.0:0.0:0.0	.	434	Q9HC58	NCKX3_HUMAN	L	434	ENSP00000333519:P434L	.	P	+	2	0	SLC24A3	19613982	1.000000	0.71417	0.833000	0.33012	0.408000	0.30992	7.465000	0.80898	2.668000	0.90789	0.563000	0.77884	CCG	.		0.488	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689		T	19665982	C	T	19665982	3	4	121	1	0	0	0	0	1	0	0	0	14499	652	23	1	1347	1	SLC24A3	20	19665982	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		19665982	43359538	83	10537											
PCIF1	63935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44574469	44574469	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagaacaacgtggtctgcAtccggtataagggagagatg	12	8	15	6	2	1	2	0	0	1	2	2	5	2	3	1	4	3	2	1	4	4	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:44574469A>C	ENST00000372409.3	+	12	1652	c.1288A>C	c.(1288-1290)Atc>Ctc	p.I430L	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	430					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						CGTGGTCTGCATCCGGTATAA	0.602																																					p.I430L		.											.	PCIF1-91	0			c.A1288C						.						105	97	100					20																	44574469		2203	4300	6503	SO:0001583	missense	63935	exon12			GTCTGCATCCGGT	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 121"		"chromosome 20 open reading frame 67"	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1288A>C	20.37:g.44574469A>C	ENSP00000361486:p.Ile430Leu	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	147	51	NM_022104	0	0	25	61	36	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	A	3.545	-0.092801	0.07053	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.01	-1.64	0.08318	.	0.378783	0.26944	N	0.021710	T	0.05914	0.0154	N	0.00823	-1.155	0.28559	N	0.91125	B	0.02656	0.0	B	0.01281	0.0	T	0.37478	-0.9704	9	0.02654	T	1	-2.4041	5.0684	0.14594	0.262:0.3498:0.3882:0.0	.	430	Q9H4Z3	PCIF1_HUMAN	L	430	.	ENSP00000361486:I430L	I	+	1	0	PCIF1	44007876	1.000000	0.71417	0.994000	0.49952	0.897000	0.52465	1.872000	0.39549	-0.182000	0.10602	-0.379000	0.06801	ATC	.		0.602	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		C	44574469	A	C	44574469	3	2	121	1	0	0	0	0	1	0	0	0	11606	217	8	5	1326	5	PCIF1	20	44574469	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	24908487	44574469	18451051	84	10538											
ARFGEF2	10564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47641990	47641990	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaggccttcaactccaattaCgagcagcggactgtcctgtg	10	9	10	12	2	1	0	1	0	0	0	3	2	3	1	3	2	4	1	3	2	4	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:47641990C>T	ENST00000371917.4	+	36	4896	c.4896C>T	c.(4894-4896)taC>taT	p.Y1632Y		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1632					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			ACTCCAATTACGAGCAGCGGA	0.473																																					p.Y1632Y	Esophageal Squamous(176;1738 1974 26285 33069 35354)	.											.	ARFGEF2-358	0			c.C4896T						.						97	80	85					20																	47641990		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon36			CAATTACGAGCAG	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"A-kinase anchor proteins"	15853	protein-coding gene	gene with protein product	"Brefeldin A-inhibited guanine nucleotide-exchange protein 2"	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.4896C>T	20.37:g.47641990C>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_006420	0	0	10	30	20	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			.		0.473	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		T	47641990	C	T	47641990	2	4	121	1	0	0	0	0	0	0	0	1	853	547	19	1		1	ARFGEF2	20	47641990	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	3067521	47641990	15383530	85	10539											
SNAI1	6615	ucsc.edu	37	chr20	48600833	48600833	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctgcgtctgcggaacctgCgggaaggccttctctaggcc	5	8	13	15	3	2	0	0	0	2	0	3	2	2	2	4	4	4	0	4	4	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:48600833C>T	ENST00000244050.2	+	2	616	c.555C>T	c.(553-555)tgC>tgT	p.C185C		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	185	Required for nuclear localization and interaction with KPNB1, NOTCH1 and PARP1.				cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	p.C185*(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			GCGGAACCTGCGGGAAGGCCT	0.622																																					p.C185C													.	SNAI1-227	1	Substitution - Nonsense(1)	lung(1)	c.C555T						.						27	26	26					20																	48600833		2203	4300	6503	SO:0001819	synonymous_variant	6615	exon2			AACCTGCGGGAAG	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"Snail homologs", "Zinc fingers, C2H2-type"	11128	protein-coding gene	gene with protein product		604238	"snail 1 (drosophila homolog), zinc finger protein", "snail homolog 1 (Drosophila)"			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.555C>T	20.37:g.48600833C>T		Somatic	27	0		WXS	Illumina HiSeq		25	4	NM_005985	0	0	1	1	0	B2R842|Q9P113|Q9UBP7|Q9UHH7	Silent	SNP	ENST00000244050.2	37	CCDS13423.1																																																																																			.		0.622	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1			T	48600833	C	T	48600833	2	4	121	1	0	0	0	0	0	0	0	1	14858	776	27	1		1	SNAI1	20	48600833	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	958843	48600833	14424687	86	10540											
LAMA5	3911	ucsc.edu	37	chr20	60891785	60891785	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagtgcagtgctgttggcCaggagctgctgggctcggtc	4	11	16	10	1	1	0	0	0	1	0	3	1	1	1	1	4	4	6	1	4	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:60891785C>T	ENST00000252999.3	-	57	7764	c.7698G>A	c.(7696-7698)ctG>ctA	p.L2566L		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2566	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGCTGTTGGCCAGGAGCTGCT	0.687																																					p.L2566L													.	LAMA5-93	0			c.G7698A						.						26	21	22					20																	60891785		2181	4279	6460	SO:0001819	synonymous_variant	3911	exon57			GTTGGCCAGGAGC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"Laminins"	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7698G>A	20.37:g.60891785C>T		Somatic	24	0		WXS	Illumina HiSeq		31	5	NM_005560	0	0	73	73	0	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			.		0.687	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60891785	C	T	60891785	2	4	121	1	0	0	0	0	0	0	0	1	8630	581	21	2		2	LAMA5	20	60891785	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	12290952	60891785	2133735	87	10541											
KRTAP10-3	386682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45978008	45978008	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gagcacgtggggcggcagagGagggacacgcaggaggccgg	9	1	22	9	4	0	1	0	0	0	1	0	5	0	4	1	8	1	3	1	8	0	0			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr21:45978008G>A	ENST00000391620.1	-	1	635	c.591C>T	c.(589-591)ctC>ctT	p.L197L	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	197	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGCGGCAGAGGAGGGACACGC	0.701																																					p.L197L		.											.	KRTAP10-3-91	0			c.C591T						.						29	35	33					21																	45978008		2199	4295	6494	SO:0001819	synonymous_variant	386682	exon1			GCAGAGGAGGGAC	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"Keratin associated proteins"	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.591C>T	21.37:g.45978008G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	33	16	NM_198696	0	0	0	0	0	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			.		0.701	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			A	45978008	G	A	45978008	2	1	121	1	0	0	0	0	0	0	0	1	8531	1161	41	2		2	KRTAP10-3	21	45978008	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08		45978008	2151887	88	10542											
SMARCB1	6598	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	24175838	24175839	+	Frame_Shift_Ins	INS	-	-	T																															gtgcccactgctggagactcINStgacagacgctgagatggag																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr22:24175838_24175839insT	ENST00000263121.7	+	8	1262_1263	c.1066_1067insT	c.(1066-1068)ctgfs	p.L356fs	SMARCB1_ENST00000407082.3_Frame_Shift_Ins_p.L310fs|DERL3_ENST00000464023.1_5'Flank|SMARCB1_ENST00000344921.6_Frame_Shift_Ins_p.L365fs|SMARCB1_ENST00000407422.3_Frame_Shift_Ins_p.L347fs	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	356					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GCTGGAGACTCTGACAGACGCT	0.629			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.L356fs		.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1-2699	3	Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)	c.1066_1067insT						.																																			SO:0001589	frameshift_variant	6598	exon8			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1067dupT	22.37:g.24175839_24175839dupT	ENSP00000263121:p.Leu356fs	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	111	91	NM_003073	0	0	0	0	0	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Ins	INS	ENST00000263121.7	37	CCDS13817.1																																																																																			.		0.629	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		T	24175839	-	T	24175838	7	5	121	1	0	1	1	0	0	0	0	0	14806	912	32	0	1096	0	SMARCB1	22	24175838	Frame_Shift_Ins	INS	-	TCGA-GL-6846-01A-11D-1961-08		24175838	27128728	89	10543											
GSTT1	2952	broad.mit.edu;bcgsc.ca	37	chr22	24376512	24376512	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttggccttcagaatgacctCatgggcctcctggaagaggt	8	10	12	11	0	2	3	2	1	0	2	3	4	3	4	4	4	0	0	4	4	2	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr22:24376512C>T	ENST00000248935.5	-	5	686	c.634G>A	c.(634-636)Gag>Aag	p.E212K	GSTT1_ENST00000439996.2_Missense_Mutation_p.E94K|KB-226F1.1_ENST00000608619.1_RNA	NM_000853.2	NP_000844.2	P30711	GSTT1_HUMAN		212	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)	6					Carboplatin(DB00958)|Cisplatin(DB00515)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)	AGAATGACCTCATGGGCCTCC	0.632									Myelodysplasia and Acute Myeloid Leukemia (AML), Familial																												p.E212K													.	GSTT1-91	0			c.G634A						.						39	44	42					22																	24376512		1679	3587	5266	SO:0001583	missense	2952	exon5	Familial Cancer Database	incl.: Familial Myelodysplastic syndrome (late-onset), Familial AML, Familial Monocytic Leukemia, Familial Monosomy 7 and AML	TGACCTCATGGGC																												ENST00000248935.5:c.634G>A	22.37:g.24376512C>T	ENSP00000248935:p.Glu212Lys	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	80	7	NM_000853	0	0	227	233	6	O00226|Q5TZY2|Q6IC69|Q969K8|Q96IY3	Missense_Mutation	SNP	ENST00000248935.5	37	CCDS13822.1	.	.	.	.	.	.	.	.	.	.	.	14.79	2.640100	0.47153	.	.	ENSG00000184674	ENST00000436103;ENST00000248935;ENST00000382792;ENST00000439996	T;T;T	0.46451	0.87;2.28;2.28	4.75	4.75	0.60458	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.059936	0.64402	D	0.000004	T	0.30792	0.0776	L	0.42529	1.33	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.08207	-1.0733	10	0.14656	T	0.56	-33.6007	9.1406	0.36901	0.0:0.9024:0.0:0.0976	.	212	P30711	GSTT1_HUMAN	K	80;212;133;94	ENSP00000389481:E80K;ENSP00000248935:E212K;ENSP00000401632:E94K	ENSP00000248935:E212K	E	-	1	0	GSTT1	22706512	0.751000	0.28327	0.997000	0.53966	0.804000	0.45430	0.450000	0.21762	2.648000	0.89879	0.650000	0.86243	GAG	.		0.632	GSTT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320184.2			T	24376512	C	T	24376512	3	4	121	1	0	0	0	0	1	0	0	0	6866	835	29	2	92	2	GSTT1	22	24376512	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	200674	24376512	26928054	90	10544											
SEPT3	55964	hgsc.bcm.edu	37	chr22	42373072	42373072	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacaaaggaggattcatgTccaaaggtagggcggccggc	12	5	16	8	2	1	1	1	0	0	1	2	4	2	3	2	6	0	1	2	6	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr22:42373072T>G	ENST00000396426.3	+	1	259	c.4T>G	c.(4-6)Tcc>Gcc	p.S2A	SEPT3_ENST00000396425.3_Missense_Mutation_p.S2A|SEPT3_ENST00000406029.1_Missense_Mutation_p.S2A|SEPT3_ENST00000291236.11_Missense_Mutation_p.S2A|SEPT3_ENST00000328414.8_Missense_Mutation_p.S2A	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	2					cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)			breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						AGGATTCATGTCCAAAGGTAG	0.751																																					p.S2A		.											.	SEPT3-68	0			c.T4G						.						16	20	18					22																	42373072		1864	4070	5934	SO:0001583	missense	55964	exon1			TTCATGTCCAAAG	AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"Septins"	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.4T>G	22.37:g.42373072T>G	ENSP00000379704:p.Ser2Ala	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	38	3	NM_019106	0	0	0	0	0	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Missense_Mutation	SNP	ENST00000396426.3	37	CCDS14026.2	.	.	.	.	.	.	.	.	.	.	T	12.30	1.895922	0.33442	.	.	ENSG00000100167	ENST00000396426;ENST00000406029;ENST00000328414;ENST00000396425;ENST00000291236	T;T;T;T	0.50813	0.73;0.8;0.74;0.8	3.43	2.36	0.29203	.	1.353170	0.05787	U	0.609675	T	0.30510	0.0767	N	0.08118	0	0.19945	N	0.999949	B;B;B;B	0.06786	0.0;0.001;0.0;0.001	B;B;B;B	0.10450	0.0;0.005;0.001;0.001	T	0.30736	-0.9968	10	0.87932	D	0	.	7.9052	0.29757	0.0:0.0:0.2102:0.7898	.	2;2;2;2	B7Z686;B1AHR1;Q9UH03-2;Q9UH03	.;.;.;SEPT3_HUMAN	A	2	ENSP00000379704:S2A;ENSP00000383956:S2A;ENSP00000379703:S2A;ENSP00000291236:S2A	ENSP00000291236:S2A	S	+	1	0	SEPT3	40703018	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	3.884000	0.56175	0.464000	0.27142	0.165000	0.16767	TCC	.		0.751	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734		G	42373072	T	G	42373072	3	3	121	1	0	0	0	0	1	0	0	0	14097	1667	58	5	6	5	SEPT3	22	42373072	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	17996560	42373072	8931494	91	10545											
CASK	8573	hgsc.bcm.edu	37	chrX	41448782	41448782	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttacctctttggctctctGtactgcatcgcttggaggat	6	15	9	11	1	2	0	0	0	2	0	4	2	2	2	1	3	3	4	1	3	2	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chrX:41448782G>C	ENST00000378163.1	-	13	1693	c.1219C>G	c.(1219-1221)Cag>Gag	p.Q407E	CASK_ENST00000421587.2_Missense_Mutation_p.Q401E|CASK_ENST00000378158.1_Missense_Mutation_p.Q407E|CASK_ENST00000378154.1_Missense_Mutation_p.Q407E|CASK_ENST00000442742.2_Missense_Mutation_p.Q407E|CASK_ENST00000361962.4_Missense_Mutation_p.Q407E|CASK_ENST00000378166.4_Missense_Mutation_p.Q407E|CASK_ENST00000318588.9_Missense_Mutation_p.Q407E			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	407	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						TTGGCTCTCTGTACTGCATCG	0.363																																					p.Q407E	NSCLC(42;104 1086 3090 27189 35040)	.											.	CASK-616	0			c.C1219G						.						159	135	143					X																	41448782		2203	4300	6503	SO:0001583	missense	8573	exon13			CTCTCTGTACTGC	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"trinucleotide repeat containing 8"	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.1219C>G	X.37:g.41448782G>C	ENSP00000367405:p.Gln407Glu	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_001126054	0	0	25	25	0	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Missense_Mutation	SNP	ENST00000378163.1	37		.	.	.	.	.	.	.	.	.	.	G	11.87	1.769092	0.31320	.	.	ENSG00000147044	ENST00000421587;ENST00000318588;ENST00000361962;ENST00000378163;ENST00000378179;ENST00000378158;ENST00000378166;ENST00000442742;ENST00000378154	T;T;T;T;T;T;T;T;T	0.67523	-0.25;-0.26;-0.27;-0.26;3.44;-0.26;-0.26;-0.25;-0.26	5.61	5.61	0.85477	L27, C-terminal (1);L27 (2);	0.000000	0.49305	D	0.000146	T	0.60025	0.2237	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.29805	0.009;0.257;0.02;0.097	B;B;B;B	0.40782	0.008;0.34;0.012;0.028	T	0.55042	-0.8202	10	0.15499	T	0.54	.	18.2422	0.89971	0.0:0.0:1.0:0.0	.	401;407;407;407	O14936-3;O14936-4;O14936-2;O14936	.;.;.;CSKP_HUMAN	E	401;407;407;407;22;407;407;407;407	ENSP00000400526:Q401E;ENSP00000322727:Q407E;ENSP00000354641:Q407E;ENSP00000367405:Q407E;ENSP00000367421:Q22E;ENSP00000367400:Q407E;ENSP00000367408:Q407E;ENSP00000398007:Q407E;ENSP00000367396:Q407E	ENSP00000322727:Q407E	Q	-	1	0	CASK	41333726	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.200000	0.95010	2.346000	0.79739	0.415000	0.27848	CAG	.		0.363	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		C	41448782	G	C	41448782	3	2	121	1	0	0	0	0	1	0	0	0	2671	1386	48	4	1621	4	CASK	23	41448782	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08		41448782	113821778	92	10546											
MAGT1	84061	ucsc.edu;bcgsc.ca	37	chrX	77150838	77150838	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgggcagaggctgagggaaCgtcgcaaacgatgagcagcg	11	5	17	8	4	0	3	0	2	0	1	1	5	0	4	0	3	4	4	0	3	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chrX:77150838C>A	ENST00000373336.3	-	1	99	c.70G>T	c.(70-72)Gtt>Ttt	p.V24F	MAGT1_ENST00000358075.6_Missense_Mutation_p.V56F			Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	24					cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						GCTGAGGGAACGTCGCAAACG	0.552																																					p.V56F													.	MAGT1-63	0			c.G166T						.						133	91	105					X																	77150838		2203	4296	6499	SO:0001583	missense	84061	exon1			AGGGAACGTCGCA		CCDS14436.2	Xq21.1	2014-09-17			ENSG00000102158	ENSG00000102158			28880	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog B (S. cerevisiae)"	300715				15804357	Standard	NM_032121		Approved	DKFZp564K142, IAP, OST3B, MRX95	uc004fof.3	Q9H0U3	OTTHUMG00000021882	ENST00000373336.3:c.70G>T	X.37:g.77150838C>A	ENSP00000362433:p.Val24Phe	Somatic	30	0		WXS	Illumina HiSeq		32	5	NM_032121	0	0	34	34	0	B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	Missense_Mutation	SNP	ENST00000373336.3	37		.	.	.	.	.	.	.	.	.	.	C	6.758	0.508646	0.12883	.	.	ENSG00000102158	ENST00000358075;ENST00000373336	T;T	0.48201	0.82;0.84	4.41	3.47	0.39725	.	0.429903	0.21885	N	0.067680	T	0.24122	0.0584	N	0.04508	-0.205	0.09310	N	1	B;B	0.14805	0.001;0.011	B;B	0.12156	0.003;0.007	T	0.12811	-1.0533	10	0.36615	T	0.2	-16.1902	10.134	0.42695	0.1987:0.8013:0.0:0.0	.	24;56	Q9H0U3;B4DH58	MAGT1_HUMAN;.	F	56;24	ENSP00000354649:V56F;ENSP00000362433:V24F	ENSP00000354649:V56F	V	-	1	0	MAGT1	77037494	0.559000	0.26562	0.837000	0.33122	0.237000	0.25408	0.684000	0.25364	2.165000	0.68154	0.544000	0.68410	GTT	.		0.552	MAGT1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000057302.2	NM_032121		A	77150838	C	A	77150838	3	1	121	1	0	0	0	0	1	0	0	0	9221	536	19	4	977	4	MAGT1	23	77150838	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	35702056	77150838	78119722	93	10547											
NOC2L	26155	bcgsc.ca	37	chr1	887486	887486	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaggaagaggcagtgcaCatactgccagttgtacacag	13	6	11	11	0	0	1	0	0	0	1	0	2	0	2	2	2	4	4	2	2	3	3	rs144707752		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:887486C>G	ENST00000327044.6	-	11	1274	c.1225G>C	c.(1225-1227)Gtg>Ctg	p.V409L	NOC2L_ENST00000487214.1_5'Flank	NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	409					apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		AGGCAGTGCACATACTGCCAG	0.592													C|||	1	0.000199681	8e-04	0	5008	,	,		20190	0		0	False		,,,				2504	0				p.V409L													.	NOC2L-92	0			c.G1225C						.	C	LEU/VAL	2,4404	4.2+/-10.8	0,2,2201	72	67	69		1225	0.3	0.4	1	dbSNP_134	69	0,8600		0,0,4300	no	missense	NOC2L	NM_015658.3	32	0,2,6501	GG,GC,CC		0.0,0.0454,0.0154	benign	409/750	887486	2,13004	2203	4300	6503	SO:0001583	missense	26155	exon11			AGTGCACATACTG	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"novel INHAT repressor", "protein phosphatase 1, regulatory subunit 12"	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.1225G>C	1.37:g.887486C>G	ENSP00000317992:p.Val409Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_1	95	4	NM_015658	0	0	38	38	0	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.584490	0.46110	4.54E-4	0.0	ENSG00000188976	ENST00000327044	T	0.47528	0.84	4.3	0.294	0.15747	Armadillo-type fold (1);	0.432444	0.22891	N	0.054389	T	0.48447	0.1500	L	0.52364	1.645	0.39810	D	0.972687	P;P;P	0.44044	0.825;0.825;0.825	P;P;P	0.51079	0.544;0.544;0.658	T	0.50021	-0.8876	10	0.72032	D	0.01	-16.483	8.3399	0.32237	0.0:0.476:0.0:0.524	.	409;409;176	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	L	409	ENSP00000317992:V409L	ENSP00000317992:V409L	V	-	1	0	NOC2L	877349	0.018000	0.18449	0.441000	0.26858	0.903000	0.53119	0.138000	0.16016	0.165000	0.19558	0.563000	0.77884	GTG	C|1.000;G|0.000		0.592	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658		G	887486	C	G	887486	3	3	122	1	0	0	0	0	1	0	0	0	10539	478	17	4	1060	4	NOC2L	1	887486	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		887486	248363135	1	10548											
MEGF6	1953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	3511980	3511980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtccgggcctccgtggtatAcacctgcctgtagcccatgt	5	10	12	14	2	0	0	0	0	0	0	2	0	2	0	6	3	3	2	6	3	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:3511980A>G	ENST00000356575.4	-	3	524	c.298T>C	c.(298-300)Tat>Cat	p.Y100H		NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	100	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		TCCGTGGTATACACCTGCCTG	0.632																																					p.Y100H	Ovarian(73;978 3658)	.											.	MEGF6-90	0			c.T298C						.						36	44	41					1																	3511980		2027	4179	6206	SO:0001583	missense	1953	exon3			TGGTATACACCTG	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"EGF-like-domain, multiple 3"	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.298T>C	1.37:g.3511980A>G	ENSP00000348982:p.Tyr100His	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	117	41	NM_001409	0	0	0	0	0	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	a	15.35	2.806840	0.50421	.	.	ENSG00000162591	ENST00000356575	D	0.85258	-1.96	3.92	3.92	0.45320	EMI domain (1);	0.000000	0.64402	U	0.000003	D	0.84991	0.5595	M	0.76574	2.34	0.39571	D	0.969271	D	0.53312	0.959	P	0.46076	0.503	D	0.86605	0.1869	10	0.59425	D	0.04	-38.3019	9.703	0.40198	1.0:0.0:0.0:0.0	.	100	O75095	MEGF6_HUMAN	H	100	ENSP00000348982:Y100H	ENSP00000348982:Y100H	Y	-	1	0	MEGF6	3501840	1.000000	0.71417	0.906000	0.35671	0.306000	0.27790	6.186000	0.72026	1.726000	0.51525	0.398000	0.26397	TAT	.		0.632	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		G	3511980	A	G	3511980	3	3	122	1	0	0	0	0	1	0	0	0	9487	391	14	3	4467	3	MEGF6	1	3511980	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	2624494	3511980	245738641	2	10549											
TCEB3	6924	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	24080614	24080614	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcaccccaggaagaagAagaagctggatttactgggc	12	8	11	10	0	2	3	1	0	1	3	2	5	2	5	2	3	2	1	2	3	5	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:24080614A>C	ENST00000418390.2	+	6	1911	c.1640A>C	c.(1639-1641)gAa>gCa	p.E547A	TCEB3_ENST00000609199.1_Missense_Mutation_p.E521A	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	547					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CAGGAAGAAGAAGAAGCTGGA	0.473																																					p.E547A		.											.	TCEB3-91	0			c.A1640C						.						107	99	102					1																	24080614		2203	4300	6503	SO:0001583	missense	6924	exon6			AAGAAGAAGAAGC	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.1640A>C	1.37:g.24080614A>C	ENSP00000395574:p.Glu547Ala	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	120	42	NM_003198	0	0	13	23	10	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	37	CCDS239.2	.	.	.	.	.	.	.	.	.	.	A	23.4	4.405738	0.83230	.	.	ENSG00000011007	ENST00000418390	T	0.10382	2.88	5.71	5.71	0.89125	.	0.243724	0.31936	N	0.006831	T	0.15435	0.0372	M	0.70275	2.135	0.58432	D	0.999995	D	0.54397	0.966	B	0.42462	0.388	T	0.01269	-1.1400	10	0.72032	D	0.01	-23.7872	10.6424	0.45600	0.9197:0.0:0.0803:0.0	.	547	Q14241	ELOA1_HUMAN	A	547	ENSP00000395574:E547A	ENSP00000395574:E547A	E	+	2	0	TCEB3	23953201	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.929000	0.70096	2.179000	0.69175	0.379000	0.24179	GAA	.		0.473	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		C	24080614	A	C	24080614	3	2	122	1	0	0	0	0	1	0	0	0	15713	246	9	5	1662	5	TCEB3	1	24080614	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	20568634	24080614	225170007	3	10550											
PUM1	9698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	31479871	31479871	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccaggcactgtctcgccattGatcacccaggaatattcctt	9	11	7	14	1	2	1	1	1	1	0	4	2	3	2	4	2	0	1	4	2	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:31479871G>C	ENST00000257075.5	-	4	604	c.511C>G	c.(511-513)Caa>Gaa	p.Q171E	PUM1_ENST00000440538.2_Missense_Mutation_p.Q171E|PUM1_ENST00000373747.3_Missense_Mutation_p.Q171E|PUM1_ENST00000423018.2_Intron|PUM1_ENST00000424085.2_Intron|PUM1_ENST00000373741.4_Missense_Mutation_p.Q207E|PUM1_ENST00000426105.2_Missense_Mutation_p.Q171E|PUM1_ENST00000373742.2_Intron	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	171					membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TCTCGCCATTGATCACCCAGG	0.418																																					p.Q171E		.											.	PUM1-92	0			c.C511G						.						301	283	289					1																	31479871		2203	4300	6503	SO:0001583	missense	9698	exon4			GCCATTGATCACC	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"pumilio (Drosophila) homolog 1", "pumilio homolog 1 (Drosophila)"				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.511C>G	1.37:g.31479871G>C	ENSP00000257075:p.Gln171Glu	Somatic	340	0		WXS	Illumina HiSeq	Phase_I	363	122	NM_014676	0	0	27	41	14	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.154|3.154	-0.173618|-0.173618	0.06421|0.06421	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000257075;ENST00000373747;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000543952|ENST00000525843	T;T;T;T;T|.	0.17691|.	2.26;2.53;2.54;2.54;2.53|.	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|.	0.55800|.	0.1943|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.15473|.	0.002;0.013;0.001;0.001|.	B;B;B;B|.	0.12156|.	0.002;0.007;0.001;0.001|.	T|.	0.49513|.	-0.8932|.	10|.	0.05620|.	T|.	0.96|.	-4.9673|-4.9673	19.0513|19.0513	0.93046|0.93046	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	207;171;171;171|.	Q5T1Z8;Q14671-2;Q14671;E9PCJ0|.	.;.;PUM1_HUMAN;.|.	E|X	171;171;171;171;207;171|187	ENSP00000257075:Q171E;ENSP00000362852:Q171E;ENSP00000391723:Q171E;ENSP00000401777:Q171E;ENSP00000362846:Q207E|.	ENSP00000257075:Q171E|.	Q|S	-|-	1|2	0|0	PUM1|PUM1	31252458|31252458	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.482000|4.482000	0.60257|0.60257	2.736000|2.736000	0.93811|0.93811	0.557000|0.557000	0.71058|0.71058	CAA|TCA	.		0.418	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			C	31479871	G	C	31479871	3	2	122	1	0	0	0	0	1	0	0	0	12857	1299	45	4	3131	4	PUM1	1	31479871	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	7399257	31479871	217770750	4	10551											
SLC2A1	6513	hgsc.bcm.edu	37	chr1	43393458	43393458	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggccacgatgctcagatAggacatccagggtagctgct	10	8	13	10	1	1	1	1	0	0	1	2	4	2	2	2	3	3	4	2	3	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:43393458A>G	ENST00000426263.3	-	9	1274	c.1096T>C	c.(1096-1098)Tat>Cat	p.Y366H	SLC2A1_ENST00000475162.1_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	366					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	ATGCTCAGATAGGACATCCAG	0.552																																					p.Y366H		.											.	SLC2A1-94	0			c.T1096C						.						56	54	54					1																	43393458		2203	4300	6503	SO:0001583	missense	6513	exon9			TCAGATAGGACAT	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"Solute carriers"	11005	protein-coding gene	gene with protein product		138140	"human T-cell leukemia virus (I and II) receptor"	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.1096T>C	1.37:g.43393458A>G	ENSP00000416293:p.Tyr366His	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_006516	0	0	142	142	0	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Missense_Mutation	SNP	ENST00000426263.3	37	CCDS477.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.838141	0.71373	.	.	ENSG00000117394	ENST00000426263;ENST00000372501;ENST00000397019	T	0.81247	-1.47	5.31	5.31	0.75309	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.90755	0.7098	H	0.94808	3.585	0.80722	D	1	D	0.59357	0.985	P	0.58391	0.838	D	0.93044	0.6460	10	0.87932	D	0	.	13.1968	0.59743	1.0:0.0:0.0:0.0	.	366	P11166	GTR1_HUMAN	H	366;366;308	ENSP00000416293:Y366H	ENSP00000361579:Y366H	Y	-	1	0	SLC2A1	43166045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.141000	0.77330	2.004000	0.58718	0.533000	0.62120	TAT	.		0.552	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516		G	43393458	A	G	43393458	3	3	122	1	0	0	0	0	1	0	0	0	14570	420	15	3	390	3	SLC2A1	1	43393458	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	11913587	43393458	205857163	5	10552											
CDC20	991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	43828621	43828621	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tactgttctcatttgctccaGgtcacacatcccgggtcctg	6	13	8	14	1	2	0	2	0	1	0	6	0	5	0	3	2	2	2	3	2	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:43828621G>A	ENST00000372462.1	+	10	1524		c.e10-1		ELOVL1_ENST00000470769.1_5'Flank|CDC20_ENST00000310955.6_Splice_Site			Q12834	CDC20_HUMAN	cell division cycle 20						activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATTTGCTCCAGGTCACACATC	0.532																																					.	Esophageal Squamous(137;1154 1759 10362 10401 46925)	.											.	CDC20-227	0			c.1322-1G>A						.						72	70	70					1																	43828621		2203	4300	6503	SO:0001630	splice_region_variant	991	exon11			GCTCCAGGTCACA	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"WD repeat domain containing"	1723	protein-coding gene	gene with protein product		603618	"CDC20 (cell division cycle 20, S. cerevisiae, homolog)", "CDC20 cell division cycle 20 homolog (S. cerevisiae)", "cell division cycle 20 homolog (S. cerevisiae)"			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.1322-1G>A	1.37:g.43828621G>A		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	146	61	NM_001255	0	0	0	0	0	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Splice_Site	SNP	ENST00000372462.1	37	CCDS484.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972600	0.74246	.	.	ENSG00000117399	ENST00000437896;ENST00000310955;ENST00000372462	.	.	.	5.76	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7097	0.69222	0.0697:0.0:0.9303:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC20	43601208	1.000000	0.71417	0.994000	0.49952	0.916000	0.54674	9.338000	0.96553	1.431000	0.47355	0.561000	0.74099	.	.		0.532	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255	Intron	A	43828621	G	A	43828621	5	1	122	1	0	0	0	0	0	0	1	0	3065	1014	35	2	1359	2	CDC20	1	43828621	Splice_Site	SNP	G	TCGA-GL-7773-01A-11D-2136-08	435163	43828621	205422000	6	10553											
STIL	6491	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	47717027	47717027	+	Frame_Shift_Del	DEL	T	T	-																															aggttctttactaagaaagcTggcttttcagtcaactgctg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:47717027delT	ENST00000360380.3	-	18	4008	c.3645delA	c.(3643-3645)ccafs	p.P1215fs	STIL_ENST00000396221.2_Frame_Shift_Del_p.P1198fs|STIL_ENST00000371877.3_Frame_Shift_Del_p.P1216fs|STIL_ENST00000337817.5_Frame_Shift_Del_p.P1215fs|STIL_ENST00000243182.6_Frame_Shift_Del_p.P1215fs	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	1215					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CTAAGAAAGCTGGCTTTTCAG	0.423																																					p.P1216fs		.											.	STIL-659	0			c.3648delA						.						120	121	121					1																	47717027		2203	4300	6503	SO:0001589	frameshift_variant	6491	exon17			.	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.3645delA	1.37:g.47717027delT	ENSP00000353544:p.Pro1215fs	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	175	71	NM_001048166	0	0	0	0	0	Q5T0C5|Q68CN9	Frame_Shift_Del	DEL	ENST00000360380.3	37	CCDS548.1																																																																																			.		0.423	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		-	47717027	T	-	47717027	7	5	122	1	0	1	0	1	0	0	0	0	15314	1567	55	0	222	0	STIL	1	47717027	Frame_Shift_Del	DEL	T	TCGA-GL-7773-01A-11D-2136-08	3888406	47717027	201533594	7	10554											
PRPF38A	84950	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	52881045	52881046	+	In_Frame_Ins	INS	-	-	AGT																															cagacacaggagccactcaaINSagtctcccgaaaggtaatga																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:52881045_52881046insAGT	ENST00000257181.9	+	9	1069_1070	c.883_884insAGT	c.(883-885)aag>aAGTag	p.295_296ins*	PRPF38A_ENST00000474048.1_3'UTR	NM_032864.3	NP_116253.2	Q8NAV1	PR38A_HUMAN	pre-mRNA processing factor 38A	295					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			cervix(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|stomach(1)	9						GAGCCACTCAAAGTCTCCCGAA	0.401																																					p.K295delinsKX		.											.	PRPF38A-90	0			c.883_884insAGT						.																																			SO:0001652	inframe_insertion	84950	exon9			.	AK092038	CCDS567.1	1p32.3	2013-10-03	2013-10-03		ENSG00000134748	ENSG00000134748			25930	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing A"			12477932	Standard	NM_032864		Approved	FLJ14936, Prp38	uc001ctw.4	Q8NAV1	OTTHUMG00000008199	ENST00000257181.9:c.884_886dupAGT	1.37:g.52881046_52881048dupAGT	ENSP00000257181:p.Ser296*	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	51	19	NM_032864	0	0	0	0	0	Q96JW1|Q9BVZ8	Nonsense_Mutation	INS	ENST00000257181.9	37	CCDS567.1																																																																																			.		0.401	PRPF38A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022459.2	NM_032864		AGT	52881046	-	AGT	52881045	7	5	122	1	0	1	1	0	0	0	0	0	12596	15	1	0	917	0	PRPF38A	1	52881045	In_Frame_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08	5164018	52881045	196369576	8	10555											
TTLL7	79739	hgsc.bcm.edu	37	chr1	84383373	84383373	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aagatccaaaatatcttcttCcttcaaaaaatattctaatt	17	15	1	8	0	4	1	1	0	3	1	6	1	6	1	2	0	0	0	2	0	9	8			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:84383373C>G	ENST00000260505.8	-	14	1878	c.1501G>C	c.(1501-1503)Gaa>Caa	p.E501Q	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	501					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		ATATCTTCTTCCTTCAAAAAA	0.343																																					p.E501Q		.											.	TTLL7-91	0			c.G1501C						.						73	71	72					1																	84383373		2202	4300	6502	SO:0001630	splice_region_variant	79739	exon14			CTTCTTCCTTCAA	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.1501-1G>C	1.37:g.84383373C>G		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_024686	0	0	0	0	0	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	ENST00000260505.8	37	CCDS690.2	.	.	.	.	.	.	.	.	.	.	C	27.6	4.842043	0.91197	.	.	ENSG00000137941	ENST00000260505;ENST00000370704;ENST00000370703	T	0.05786	3.39	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.17238	0.0414	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.00160	-1.1973	10	0.52906	T	0.07	.	18.2891	0.90123	0.0:1.0:0.0:0.0	.	501	Q6ZT98	TTLL7_HUMAN	Q	501;278;501	ENSP00000260505:E501Q	ENSP00000260505:E501Q	E	-	1	0	TTLL7	84155961	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.272000	0.78516	2.756000	0.94617	0.563000	0.77884	GAA	.		0.343	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686	Missense_Mutation	G	84383373	C	G	84383373	5	3	122	1	0	0	0	0	0	0	1	0	16765	869	30	4	1194	4	TTLL7	1	84383373	Splice_Site	SNP	C	TCGA-GL-7773-01A-11D-2136-08	31502328	84383373	164867248	9	10556											
DBT	1629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	100680458	100680458	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcggagcttaaccagttcaGtaaggtcaatctcatcacaa	13	10	7	11	1	4	0	4	0	1	0	6	1	4	1	1	2	2	3	1	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:100680458G>T	ENST00000370132.4	-	7	867	c.854C>A	c.(853-855)aCt>aAt	p.T285N	DBT_ENST00000370131.3_Missense_Mutation_p.T285N	NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	285					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		AACCAGTTCAGTAAGGTCAAT	0.373																																					p.T285N		.											.	DBT-91	0			c.C854A						.						77	73	75					1																	100680458		2203	4300	6503	SO:0001583	missense	1629	exon7			AGTTCAGTAAGGT	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.854C>A	1.37:g.100680458G>T	ENSP00000359151:p.Thr285Asn	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	80	29	NM_001918	0	0	3	9	6	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	37	CCDS767.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.275507	0.40294	.	.	ENSG00000137992	ENST00000543138;ENST00000370132;ENST00000370131	T;T	0.51325	0.71;0.71	5.44	4.53	0.55603	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.199950	0.51477	D	0.000096	T	0.38427	0.1040	M	0.81112	2.525	0.45634	D	0.99856	B;B	0.18310	0.002;0.027	B;B	0.24701	0.011;0.055	T	0.41875	-0.9484	10	0.42905	T	0.14	-14.8131	14.2831	0.66226	0.0716:0.0:0.9284:0.0	.	104;285	F5H1F9;P11182	.;ODB2_HUMAN	N	104;285;285	ENSP00000359151:T285N;ENSP00000359150:T285N	ENSP00000359150:T285N	T	-	2	0	DBT	100453046	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	3.303000	0.51858	1.299000	0.44798	0.655000	0.94253	ACT	.		0.373	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918		T	100680458	G	T	100680458	3	4	122	1	0	0	0	0	1	0	0	0	4264	1029	36	4	614	4	DBT	1	100680458	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	16297085	100680458	148570163	10	10557											
CELSR2	1952	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109807126	109807126	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttaacagcctggatcccagCcatggggagagcatcaacgt	11	7	12	11	1	1	1	1	0	0	1	2	3	2	2	3	3	5	2	3	3	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:109807126C>A	ENST00000271332.3	+	11	5401	c.5340C>A	c.(5338-5340)agC>agA	p.S1780R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1780	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGGATCCCAGCCATGGGGAGA	0.617																																					p.S1780R	NSCLC(158;1285 2011 34800 34852 42084)	.											.	CELSR2-526	0			c.C5340A						.						162	141	148					1																	109807126		2203	4300	6503	SO:0001583	missense	1952	exon11			TCCCAGCCATGGG	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.5340C>A	1.37:g.109807126C>A	ENSP00000271332:p.Ser1780Arg	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	184	71	NM_001408	0	0	22	50	28	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.677071	0.29783	.	.	ENSG00000143126	ENST00000271332	T	0.69435	-0.4	4.79	3.85	0.44370	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.34366	0.0895	L	0.36672	1.1	0.41718	D	0.989496	B	0.14438	0.01	B	0.09377	0.004	T	0.17776	-1.0358	9	0.15952	T	0.53	.	10.7084	0.45969	0.1481:0.709:0.1429:0.0	.	1780	Q9HCU4	CELR2_HUMAN	R	1780	ENSP00000271332:S1780R	ENSP00000271332:S1780R	S	+	3	2	CELSR2	109608649	0.905000	0.30787	0.998000	0.56505	0.796000	0.44982	1.567000	0.36407	1.193000	0.43086	0.561000	0.74099	AGC	.		0.617	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109807126	C	A	109807126	3	1	122	1	0	0	0	0	1	0	0	0	3228	738	26	4	5382	4	CELSR2	1	109807126	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	9126668	109807126	139443495	11	10558											
CHIA	27159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	111862962	111862962	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctgtgctgtcagagccaaCggcctctaccccgtggcaaa	8	9	10	14	2	3	1	1	0	2	1	3	1	3	1	4	2	4	2	4	2	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:111862962C>T	ENST00000369740.1	+	12	1408	c.1305C>T	c.(1303-1305)aaC>aaT	p.N435N	CHIA_ENST00000483391.1_Silent_p.N274N|CHIA_ENST00000430615.1_Silent_p.N327N|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000343320.6_Silent_p.N435N|CHIA_ENST00000451398.2_Silent_p.N274N|CHIA_ENST00000353665.6_Silent_p.N274N	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	435	Chitin-binding type-2. {ECO:0000255|PROSITE-ProRule:PRU00144}.				apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCAGAGCCAACGGCCTCTACC	0.597																																					p.N435N		.											.	CHIA-91	0			c.C1305T						.						68	62	64					1																	111862962		2203	4300	6503	SO:0001819	synonymous_variant	27159	exon12			AGCCAACGGCCTC	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.1305C>T	1.37:g.111862962C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	77	31	NM_201653	0	0	0	0	0	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	37	CCDS41368.1																																																																																			.		0.597	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111862962	C	T	111862962	2	4	122	1	0	0	0	0	0	0	0	1	3348	535	19	1		1	CHIA	1	111862962	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2055836	111862962	137387659	12	10559											
RSBN1	54665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	114308975	114308975	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actgatgaatgacatttctaGggatgaagtagatatcattg	14	13	10	4	0	2	5	1	4	1	1	2	6	2	6	0	1	0	1	0	1	5	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:114308975G>C	ENST00000261441.5	-	7	2099	c.2036C>G	c.(2035-2037)cCt>cGt	p.P679R	RSBN1_ENST00000369581.2_5'UTR	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	679						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GACATTTCTAGGGATGAAGTA	0.443																																					p.P679R		.											.	RSBN1-91	0			c.C2036G						.						102	94	97					1																	114308975		2203	4300	6503	SO:0001583	missense	54665	exon7			TTTCTAGGGATGA	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.2036C>G	1.37:g.114308975G>C	ENSP00000261441:p.Pro679Arg	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	177	70	NM_018364	0	0	5	8	3	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	37	CCDS862.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.042164	0.75732	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.81088	0.4750	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82230	-0.0560	9	0.87932	D	0	-8.3576	19.8965	0.96963	0.0:0.0:1.0:0.0	.	679	Q5VWQ0	RSBN1_HUMAN	R	679	.	ENSP00000261441:P679R	P	-	2	0	RSBN1	114110498	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.771000	0.95319	0.563000	0.77884	CCT	.		0.443	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		C	114308975	G	C	114308975	3	2	122	1	0	0	0	0	1	0	0	0	13728	1000	35	4	376	4	RSBN1	1	114308975	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	2446013	114308975	134941646	13	10560											
NBPF10	100132406	broad.mit.edu	37	chr1	145323659	145323659	+	Frame_Shift_Del	DEL	A	A	-																															ctgaatgtattgcaggaattAaaaaggacgaagaagaggaa																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:145323659delA	ENST00000342960.5	+	27	3531	c.3496delA	c.(3496-3498)aaafs	p.K1167fs	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	754						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TGCAGGAATTAAAAAGGACGA	0.473																																					p.K1166fs													.	.	0			c.3496delA						.																																			SO:0001589	frameshift_variant	100132406	exon27			GGAATTAAAAAGG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"neuroblastoma breakpoint family"	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.3496delA	1.37:g.145323659delA	ENSP00000345684:p.Lys1167fs	Somatic	987	0		WXS	Illumina HiSeq	Phase_I	1209	7	NM_001039703	0	0	0	0	0	Q5RHC0|Q9NWN6	Frame_Shift_Del	DEL	ENST00000342960.5	37	CCDS53355.1																																																																																			.		0.473	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703		-	145323659	A	-	145323659	7	5	122	1	0	1	0	1	0	0	0	0	10218	363	13	0	3602	0	NBPF10	1	145323659	Frame_Shift_Del	DEL	A	TCGA-GL-7773-01A-11D-2136-08	31014684	145323659	103926962	14	10561											
FLG	2312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152276023	152276023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaccctgagtgtccagacCtatctaccgattgctcgtgg	7	10	12	12	2	1	2	0	1	1	1	3	4	2	3	4	2	2	1	4	2	2	3	rs367989347		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:152276023C>G	ENST00000368799.1	-	3	11374	c.11339G>C	c.(11338-11340)aGg>aCg	p.R3780T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3780	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGTCCAGACCTATCTACCGA	0.577									Ichthyosis																												p.R3780T		.											.	FLG-106	0			c.G11339C						.						359	347	351					1																	152276023		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCAGACCTATCTA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11339G>C	1.37:g.152276023C>G	ENSP00000357789:p.Arg3780Thr	Somatic	567	0		WXS	Illumina HiSeq	Phase_I	744	264	NM_002016	0	0	1	1	0	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	3.380	-0.126622	0.06795	.	.	ENSG00000143631	ENST00000368799	T	0.01599	4.74	2.62	1.67	0.24075	.	.	.	.	.	T	0.00637	0.0021	L	0.52364	1.645	0.09310	N	1	B	0.18013	0.025	B	0.10450	0.005	T	0.44802	-0.9304	9	0.14656	T	0.56	-2.2716	7.2143	0.25951	0.0:0.6727:0.3273:0.0	.	3780	P20930	FILA_HUMAN	T	3780	ENSP00000357789:R3780T	ENSP00000357789:R3780T	R	-	2	0	FLG	150542647	0.000000	0.05858	0.007000	0.13788	0.002000	0.02628	-0.617000	0.05584	0.644000	0.30656	0.552000	0.68991	AGG	.		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152276023	C	G	152276023	3	3	122	1	0	0	0	0	1	0	0	0	5941	681	24	4	850	4	FLG	1	152276023	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	6952364	152276023	96974598	15	10562											
PBX1	5087	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	164781319	164781320	+	Frame_Shift_Ins	INS	-	-	GTATA																															tttatgctgccaaaacagctINSgtcactgctaccaatgtgtc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:164781319_164781320insGTATA	ENST00000420696.2	+	6	1118_1119	c.930_931insGTATA	c.(931-933)gtcfs	p.-311fs	PBX1_ENST00000367897.1_Frame_Shift_Ins_p.-311fs|PBX1_ENST00000540236.1_Frame_Shift_Ins_p.-311fs|PBX1_ENST00000401534.1_Frame_Shift_Ins_p.-311fs|PBX1_ENST00000560641.1_Frame_Shift_Ins_p.-206fs|PBX1_ENST00000559240.1_Intron|PBX1_ENST00000540246.1_Frame_Shift_Ins_p.-206fs	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1						adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						CCAAAACAGCTGTCACTGCTAC	0.455			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.A310fs		.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1-659	0			c.930_931insGTATA						.																																			SO:0001589	frameshift_variant	5087	exon6			.	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"Homeoboxes / TALE class"	8632	protein-coding gene	gene with protein product		176310	"pre-B-cell leukemia transcription factor 1"				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	Exception_encountered	1.37:g.164781319_164781320insGTATA	ENSP00000405890:p.Val311fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	100	23	NM_001204963	0	0	0	0	0	B4DSC1|F5H4U9|Q5T488	Frame_Shift_Ins	INS	ENST00000420696.2	37	CCDS1246.1																																																																																			.		0.455	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		GTATA	164781320	-	GTATA	164781319	7	5	122	1	0	1	1	0	0	0	0	0	11518	1567	55	0	952	0	PBX1	1	164781319	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08	12505296	164781319	84469302	16	10563											
BAT2L2	23215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171527271	171527271	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagctgtgctgaatgataTctctaagaaatgtaagttgc	13	12	9	7	0	1	3	0	2	1	1	2	3	1	3	1	0	3	4	1	0	5	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:171527271T>C	ENST00000338920.4	+	19	6251	c.6014T>C	c.(6013-6015)aTc>aCc	p.I2005T	PRRC2C_ENST00000367742.3_Missense_Mutation_p.I2007T|PRRC2C_ENST00000392078.3_Missense_Mutation_p.I2007T|PRRC2C_ENST00000426496.2_Missense_Mutation_p.I2005T	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2005					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CTGAATGATATCTCTAAGAAA	0.423																																					p.I2005T		.											.	.	0			c.T6014C						.						63	62	62					1																	171527271		2203	4300	6503	SO:0001583	missense	23215	exon19			ATGATATCTCTAA	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.6014T>C	1.37:g.171527271T>C	ENSP00000343629:p.Ile2005Thr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	85	34	NM_015172	0	0	2	3	1	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.38|16.38	3.105838|3.105838	0.56291|0.56291	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080|ENST00000495585	T;T;T;T|.	0.03035|.	4.11;4.07;4.12;4.12|.	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	0.154856|.	0.29253|.	U|.	0.012694|.	T|T	0.58163|0.58163	0.2103|0.2103	L|L	0.51422|0.51422	1.61|1.61	0.45427|0.45427	D|D	0.998403|0.998403	B|.	0.30361|.	0.277|.	B|.	0.35470|.	0.203|.	T|T	0.58589|0.58589	-0.7610|-0.7610	10|5	0.66056|.	D|.	0.02|.	.|.	15.3486|15.3486	0.74363|0.74363	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2005|.	Q9Y520-4|.	.|.	T|P	2007;1959;2005;2007;2005;1762|553	ENSP00000375928:I2007T;ENSP00000410219:I2005T;ENSP00000356716:I2007T;ENSP00000343629:I2005T|.	ENSP00000343629:I2005T|.	I|S	+|+	2|1	0|0	PRRC2C|PRRC2C	169793895|169793895	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	6.663000|6.663000	0.74431|0.74431	2.013000|2.013000	0.59113|0.59113	0.451000|0.451000	0.29950|0.29950	ATC|TCT	.		0.423	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171527271	T	C	171527271	3	2	122	1	0	0	0	0	1	0	0	0	1322	1435	50	3	6084	3	BAT2L2	1	171527271	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	6745952	171527271	77723350	17	10564											
MRPS14	63931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	174987712	174987712	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagctgatgaaggaaccaTctgaaagacagagacaaggg	17	5	13	6	0	1	6	0	4	1	2	1	8	1	7	1	2	2	1	1	2	5	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:174987712T>C	ENST00000476371.1	-	2	62	c.46A>G	c.(46-48)Atg>Gtg	p.M16V		NM_022100.2	NP_071383.1			mitochondrial ribosomal protein S14											large_intestine(2)|lung(5)|pancreas(1)|prostate(2)	10						GAAGGAACCATCTGAAAGACA	0.448																																					p.M16V		.											.	MRPS14-186	0			c.A46G						.						98	85	89					1																	174987712		2203	4300	6503	SO:0001630	splice_region_variant	63931	exon2			GAACCATCTGAAA	AB051350	CCDS1316.1	1q25.1	2012-09-13			ENSG00000120333	ENSG00000120333		"Mitochondrial ribosomal proteins / small subunits"	14049	protein-coding gene	gene with protein product		611978					Standard	NR_037606		Approved	HSMRPS14	uc001gkk.3	O60783	OTTHUMG00000034878	ENST00000476371.1:c.46-1A>G	1.37:g.174987712T>C		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	88	35	NM_022100	0	0	0	0	0		Missense_Mutation	SNP	ENST00000476371.1	37	CCDS1316.1	.	.	.	.	.	.	.	.	.	.	T	0.064	-1.217425	0.01542	.	.	ENSG00000120333	ENST00000476371	.	.	.	5.67	-1.6	0.08426	.	0.671809	0.15704	N	0.248788	T	0.11707	0.0285	N	0.04043	-0.29	0.22745	N	0.998783	B	0.02656	0.0	B	0.01281	0.0	T	0.34601	-0.9822	9	0.02654	T	1	-0.3997	7.7061	0.28650	0.2345:0.5387:0.0:0.2267	.	16	O60783	RT14_HUMAN	V	16	.	ENSP00000420714:M16V	M	-	1	0	MRPS14	173254335	0.995000	0.38212	0.560000	0.28344	0.318000	0.28184	0.132000	0.15891	-0.280000	0.09154	-0.256000	0.11100	ATG	.		0.448	MRPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084416.2	NM_022100	Missense_Mutation	C	174987712	T	C	174987712	5	2	122	1	0	0	0	0	0	0	1	0	9849	1449	50	3	348	3	MRPS14	1	174987712	Splice_Site	SNP	T	TCGA-GL-7773-01A-11D-2136-08	3460441	174987712	74262909	18	10565											
TNR	7143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	175355248	175355248	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacctcgtatcgggagccaGgccgcagggcctgcactgag	8	5	14	14	3	0	1	0	1	0	0	2	2	0	2	4	3	2	3	4	3	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:175355248G>C	ENST00000367674.2	-	8	2405	c.1697C>G	c.(1696-1698)cCt>cGt	p.P566R	TNR_ENST00000263525.2_Missense_Mutation_p.P566R			Q92752	TENR_HUMAN	tenascin R	566	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCGGGAGCCAGGCCGCAGGGC	0.612																																					p.P566R		.											.	TNR-324	0			c.C1697G						.						63	60	61					1																	175355248		2203	4300	6503	SO:0001583	missense	7143	exon8			GAGCCAGGCCGCA	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11953	protein-coding gene	gene with protein product	"restrictin", "janusin"	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1697C>G	1.37:g.175355248G>C	ENSP00000356646:p.Pro566Arg	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	105	31	NM_003285	0	0	0	0	0	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710158	0.68730	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.68903	-0.36;-0.36	5.58	5.58	0.84498	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84964	0.5589	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86989	0.2109	10	0.72032	D	0.01	.	19.1714	0.93580	0.0:0.0:1.0:0.0	.	566	Q92752	TENR_HUMAN	R	566	ENSP00000356646:P566R;ENSP00000263525:P566R	ENSP00000263525:P566R	P	-	2	0	TNR	173621871	1.000000	0.71417	0.953000	0.39169	0.256000	0.26092	8.911000	0.92721	2.613000	0.88420	0.650000	0.86243	CCT	.		0.612	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175355248	G	C	175355248	3	2	122	1	0	0	0	0	1	0	0	0	16370	1000	35	4	2443	4	TNR	1	175355248	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	367536	175355248	73895373	19	10566											
DHX9	1660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	182856426	182856426	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctatagaggagtttcccgaGgtggctttagaggcaactct	9	11	13	8	1	1	2	0	0	1	2	2	4	2	3	1	4	1	4	1	4	4	5	rs571363823		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:182856426G>C	ENST00000367549.3	+	28	3780	c.3670G>C	c.(3670-3672)Ggt>Cgt	p.G1224R	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1224	NTD.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AGTTTCCCGAGGTGGCTTTAG	0.592																																					p.G1224R	Colon(69;210 1162 3697 13559 39565)	.											.	DHX9-92	0			c.G3670C						.						77	83	81					1																	182856426		1903	4120	6023	SO:0001583	missense	1660	exon28			TCCCGAGGTGGCT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"DEAH-boxes"	2750	protein-coding gene	gene with protein product	"NDH II", "RNA helicase A"	603115	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)", "DEAH (Asp-Glu-Ala-His) box polypeptide 9"	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.3670G>C	1.37:g.182856426G>C	ENSP00000356520:p.Gly1224Arg	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	136	58	NM_001357	0	0	48	114	66	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615017	0.28712	.	.	ENSG00000135829	ENST00000367549	D	0.98329	-4.87	3.88	2.96	0.34315	.	0.241496	0.34725	N	0.003731	D	0.94748	0.8305	L	0.27053	0.805	0.58432	D	0.999996	P;P	0.47106	0.89;0.83	P;P	0.44946	0.465;0.465	D	0.91260	0.5036	10	0.13470	T	0.59	.	9.1231	0.36799	0.1132:0.0:0.8868:0.0	.	503;1224	B3KU66;Q08211	.;DHX9_HUMAN	R	1224	ENSP00000356520:G1224R	ENSP00000356520:G1224R	G	+	1	0	DHX9	181123049	1.000000	0.71417	0.182000	0.23118	0.556000	0.35491	6.067000	0.71193	0.619000	0.30197	0.561000	0.74099	GGT	.		0.592	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		C	182856426	G	C	182856426	3	2	122	1	0	0	0	0	1	0	0	0	4527	1000	35	4	3776	4	DHX9	1	182856426	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	7501178	182856426	66394195	20	10567											
RGS18	64407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	192128419	192128419	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcatgaagacacccgctcCagtagatctgggcacttggc	9	10	10	12	1	2	3	1	1	1	2	3	3	3	3	2	2	0	3	2	2	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:192128419C>T	ENST00000367460.3	+	2	370	c.189C>T	c.(187-189)tcC>tcT	p.S63S	RGS18_ENST00000481707.1_3'UTR	NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	63					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACACCCGCTCCAGTAGATCTG	0.363																																					p.S63S		.											.	RGS18-229	0			c.C189T						.						46	50	48					1																	192128419		2203	4300	6503	SO:0001819	synonymous_variant	64407	exon2			CCGCTCCAGTAGA	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"Regulators of G-protein signaling"	14261	protein-coding gene	gene with protein product		607192	"regulator of G-protein signalling 18"			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.189C>T	1.37:g.192128419C>T		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	83	21	NM_130782	0	0	1	1	0	B2RD23	Silent	SNP	ENST00000367460.3	37	CCDS1374.1																																																																																			.		0.363	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782		T	192128419	C	T	192128419	2	4	122	1	0	0	0	0	0	0	0	1	13332	581	21	2		2	RGS18	1	192128419	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	9271993	192128419	57122202	21	10568											
SIPA1L2	57568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	232649814	232649814	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttggctcgagagagcgcAatccgcctgtcgccttcccc	6	8	12	15	4	0	1	0	0	0	1	4	4	2	1	5	1	1	3	5	1	1	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:232649814A>T	ENST00000366630.1	-	2	1630	c.1272T>A	c.(1270-1272)atT>atA	p.I424I	SIPA1L2_ENST00000262861.4_Silent_p.I424I			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	424					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GAGAGAGCGCAATCCGCCTGT	0.517																																					p.I424I		.											.	SIPA1L2-95	0			c.T1272A						.						138	137	138					1																	232649814		1984	4161	6145	SO:0001819	synonymous_variant	57568	exon1			GAGCGCAATCCGC	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1272T>A	1.37:g.232649814A>T		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	251	101	NM_020808	0	0	2	5	3	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			.		0.517	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232649814	A	T	232649814	2	4	122	1	0	0	0	0	0	0	0	1	14362	126	5	5		5	SIPA1L2	1	232649814	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	40521395	232649814	16600807	22	10569											
LGALS8	3964	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	236702385	236702385	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggtgctgaaggacaaatTccaggtaggttttggagagg	11	11	15	4	0	0	2	0	1	0	1	1	4	1	3	1	6	1	3	1	6	4	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:236702385T>A	ENST00000366584.4	+	4	907	c.341T>A	c.(340-342)tTc>tAc	p.F114Y	LGALS8_ENST00000416919.2_Missense_Mutation_p.F114Y|LGALS8_ENST00000450372.2_Missense_Mutation_p.F114Y|LGALS8_ENST00000341872.6_Missense_Mutation_p.F114Y|LGALS8_ENST00000526634.1_Missense_Mutation_p.F114Y|LGALS8_ENST00000525042.1_Missense_Mutation_p.F114Y|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000352231.2_Missense_Mutation_p.F114Y|LGALS8_ENST00000323938.6_Missense_Mutation_p.F87Y|LGALS8_ENST00000527974.1_Missense_Mutation_p.F114Y|RP11-385F5.5_ENST00000608547.1_RNA|LGALS8_ENST00000526589.1_Missense_Mutation_p.F114Y	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	114	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			AAGGACAAATTCCAGGTAGGT	0.443																																					p.F114Y		.											.	LGALS8-91	0			c.T341A						.						72	69	70					1																	236702385		2203	4300	6503	SO:0001583	missense	3964	exon5			ACAAATTCCAGGT	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"Lectins, galactoside-binding"	6569	protein-coding gene	gene with protein product	"galectin 8"	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.341T>A	1.37:g.236702385T>A	ENSP00000355543:p.Phe114Tyr	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	74	27	NM_006499	0	0	0	0	0	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	37	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.095567	0.56075	.	.	ENSG00000116977	ENST00000454943;ENST00000527974;ENST00000430527;ENST00000352231;ENST00000406509;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000238181;ENST00000356238;ENST00000416919;ENST00000323938;ENST00000526634;ENST00000525042	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.06528	3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29;3.29	4.77	4.77	0.60923	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.159738	0.56097	D	0.000029	T	0.18383	0.0441	L	0.54863	1.705	0.58432	D	0.999999	D;D;P	0.61697	0.99;0.976;0.847	D;D;P	0.64687	0.914;0.928;0.68	T	0.00498	-1.1704	10	0.44086	T	0.13	.	14.4487	0.67370	0.0:0.0:0.0:1.0	.	114;114;114	F6V2D4;O00214;O00214-2	.;LEG8_HUMAN;.	Y	114;114;114;114;114;114;114;114;114;114;114;114;87;114;114	ENSP00000405504:F114Y;ENSP00000431398:F114Y;ENSP00000398630:F114Y;ENSP00000309576:F114Y;ENSP00000385999:F114Y;ENSP00000435460:F114Y;ENSP00000342139:F114Y;ENSP00000408657:F114Y;ENSP00000355543:F114Y;ENSP00000238181:F114Y;ENSP00000410843:F114Y;ENSP00000434860:F87Y;ENSP00000437040:F114Y;ENSP00000431884:F114Y	ENSP00000238181:F114Y	F	+	2	0	LGALS8	234769008	1.000000	0.71417	1.000000	0.80357	0.426000	0.31534	4.655000	0.61476	2.010000	0.58986	0.533000	0.62120	TTC	.		0.443	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499		A	236702385	T	A	236702385	3	1	122	1	0	0	0	0	1	0	0	0	8769	1783	62	5	351	5	LGALS8	1	236702385	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	4052571	236702385	12548236	23	10570											
RASGRP3	25780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	33768640	33768640	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcccaagaggactttgaaaGtatagctgccaattttccct	11	13	7	10	0	0	2	0	1	0	1	2	3	2	3	3	1	2	2	3	1	5	6			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:33768640G>C	ENST00000403687.3	+	13	2080	c.1340G>C	c.(1339-1341)aGt>aCt	p.S447T	RASGRP3_ENST00000402538.3_Missense_Mutation_p.S447T|RASGRP3_ENST00000407811.1_Missense_Mutation_p.S446T|RASGRP3_ENST00000482731.1_3'UTR	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	447	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					GACTTTGAAAGTATAGCTGCC	0.338																																					p.S447T		.											.	RASGRP3-661	0			c.G1340C						.						100	93	95					2																	33768640		1824	4085	5909	SO:0001583	missense	25780	exon14			TTGAAAGTATAGC	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1340G>C	2.37:g.33768640G>C	ENSP00000384192:p.Ser447Thr	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	39	18	NM_170672	0	0	1	3	2	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	37	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250031	0.59212	.	.	ENSG00000152689	ENST00000402538;ENST00000403687;ENST00000407811	T;T;T	0.69175	-0.38;-0.38;-0.38	5.54	5.54	0.83059	EF-hand-like domain (1);	0.096408	0.64402	D	0.000002	T	0.66626	0.2808	N	0.14661	0.345	0.38135	D	0.938277	P;P	0.51240	0.943;0.885	P;P	0.59288	0.855;0.599	T	0.65961	-0.6041	10	0.23302	T	0.38	-3.5489	19.4767	0.94992	0.0:0.0:1.0:0.0	.	446;447	D6W583;Q8IV61	.;GRP3_HUMAN	T	447;447;446	ENSP00000385886:S447T;ENSP00000384192:S447T;ENSP00000383917:S446T	ENSP00000385886:S447T	S	+	2	0	RASGRP3	33622144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.384000	0.52478	2.601000	0.87937	0.563000	0.77884	AGT	.		0.338	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		C	33768640	G	C	33768640	3	2	122	1	0	0	0	0	1	0	0	0	13108	1029	36	4	1382	4	RASGRP3	2	33768640	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		33768640	209430733	24	10571											
STRN	6801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37129786	37129786	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttacaactgagtcctgattTttgtcatcttccctgtccgt	6	18	6	11	1	2	2	1	2	1	0	5	2	5	2	3	0	2	0	3	0	2	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:37129786T>G	ENST00000263918.4	-	5	608	c.600A>C	c.(598-600)aaA>aaC	p.K200N	STRN_ENST00000379213.2_Missense_Mutation_p.K188N	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	200					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				AGTCCTGATTTTTGTCATCTT	0.393																																					p.K200N		.											.	STRN-91	0			c.A600C						.						204	187	193					2																	37129786		2203	4300	6503	SO:0001583	missense	6801	exon5			CTGATTTTTGTCA	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"WD repeat domain containing"	11424	protein-coding gene	gene with protein product		614765	"striatin, calmodulin-binding protein"			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.600A>C	2.37:g.37129786T>G	ENSP00000263918:p.Lys200Asn	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	224	92	NM_003162	0	0	2	4	2	Q3KP65|Q53TQ8|Q9NP38	Missense_Mutation	SNP	ENST00000263918.4	37	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434771	0.43224	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	T;T	0.65732	-0.17;-0.17	5.25	4.1	0.47936	.	0.260012	0.36101	N	0.002786	T	0.52821	0.1758	L	0.47190	1.495	0.36799	D	0.885272	B;B	0.14012	0.009;0.001	B;B	0.12837	0.008;0.004	T	0.52682	-0.8543	10	0.32370	T	0.25	-7.8697	10.7081	0.45966	0.0:0.0746:0.0:0.9254	.	188;200	O43815-2;O43815	.;STRN_HUMAN	N	200;175;188	ENSP00000263918:K200N;ENSP00000368513:K188N	ENSP00000263918:K200N	K	-	3	2	STRN	36983290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.314000	0.43743	0.848000	0.35191	0.533000	0.62120	AAA	.		0.393	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1			G	37129786	T	G	37129786	3	3	122	1	0	0	0	0	1	0	0	0	15361	1838	64	5	1798	5	STRN	2	37129786	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	3361146	37129786	206069587	25	10572											
CNNM4	26504	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97428005	97428005	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatattgtagatattctctaCgtcaaagacttggcctttgt	11	16	7	7	1	2	2	1	0	1	2	3	2	2	2	1	1	1	1	1	1	6	8			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:97428005C>A	ENST00000377075.2	+	1	1367	c.1269C>A	c.(1267-1269)taC>taA	p.Y423*		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	423	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						ATATTCTCTACGTCAAAGACT	0.502																																					p.Y423X		.											.	CNNM4-154	0			c.C1269A						.						149	146	147					2																	97428005		2203	4300	6503	SO:0001587	stop_gained	26504	exon1			TCTCTACGTCAAA	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1269C>A	2.37:g.97428005C>A	ENSP00000366275:p.Tyr423*	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	209	74	NM_020184	0	0	2	3	1	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Nonsense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	C	35	5.425731	0.96131	.	.	ENSG00000158158	ENST00000377075	.	.	.	5.05	-5.28	0.02755	.	0.140382	0.49305	D	0.000151	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	9.3317	0.38025	0.1152:0.5507:0.0:0.3341	.	.	.	.	X	423	.	ENSP00000366275:Y423X	Y	+	3	2	CNNM4	96791732	0.008000	0.16893	0.908000	0.35775	0.975000	0.68041	-0.996000	0.03709	-1.113000	0.02981	-0.302000	0.09304	TAC	.		0.502	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		A	97428005	C	A	97428005	4	1	122	1	0	0	0	0	0	1	0	0	3621	547	19	4	1271	4	CNNM4	2	97428005	Nonsense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	60298219	97428005	145771368	26	10573											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179599140	179599140	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaccaacatctgcactattAaacgaaaagatctccagaca	17	8	4	12	1	3	2	1	0	2	2	4	3	3	2	2	0	3	1	2	0	6	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:179599140A>G	ENST00000591111.1	-	50	14684	c.14460T>C	c.(14458-14460)ttT>ttC	p.F4820F	TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.F5137F|TTN_ENST00000342992.6_Silent_p.F3893F|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12201	Ig-like 28.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCACTATTAAACGAAAAGA	0.373																																					p.F5137F		.											.	TTN-636	0			c.T15411C						.						170	159	162					2																	179599140		1893	4123	6016	SO:0001819	synonymous_variant	7273	exon52			ACTATTAAACGAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.14460T>C	2.37:g.179599140A>G		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	232	81	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179599140	A	G	179599140	2	3	122	1	0	0	0	0	0	0	0	1	16768	359	13	3		3	TTN	2	179599140	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	82171135	179599140	63600233	27	10574											
NEUROD1	4760	broad.mit.edu	37	chr2	182543429	182543429	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctctcccccgttcctCagtgagtcctcctctgcgtt	2	14	6	19	2	3	1	1	1	2	0	9	1	8	1	7	0	1	2	7	0	0	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:182543429C>A	ENST00000295108.3	-	2	616	c.159G>T	c.(157-159)ctG>ctT	p.L53L	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	53					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CCCCGTTCCTCAGTGAGTCCT	0.572																																					p.L53L													.	NEUROD1-91	0			c.G159T						.						127	99	109					2																	182543429		2203	4300	6503	SO:0001819	synonymous_variant	4760	exon2			GTTCCTCAGTGAG	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.159G>T	2.37:g.182543429C>A		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	13	5	NM_002500	0	0	0	0	0	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Silent	SNP	ENST00000295108.3	37	CCDS2283.1																																																																																			.		0.572	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		A	182543429	C	A	182543429	2	1	122	1	0	0	0	0	0	0	0	1	10374	813	29	4		4	NEUROD1	2	182543429	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2944289	182543429	60655944	28	10575											
ANKRD44	91526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197889959	197889959	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagtagcaccagaatctgaTtcttcaaatccactgtttgt	11	15	6	9	0	3	2	1	1	2	1	4	2	4	2	2	0	1	3	2	0	4	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:197889959T>C	ENST00000328737.2	-	17	1684	c.1608A>G	c.(1606-1608)gaA>gaG	p.E536E	ANKRD44_ENST00000450567.1_Silent_p.E536E|ANKRD44_ENST00000282272.8_Silent_p.E553E|ANKRD44_ENST00000337207.5_Silent_p.E536E			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	561										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CAGAATCTGATTCTTCAAATC	0.388																																					p.E561E		.											.	ANKRD44-230	0			c.A1683G						.						133	118	123					2																	197889959		2203	4300	6503	SO:0001819	synonymous_variant	91526	exon17			ATCTGATTCTTCA	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1608A>G	2.37:g.197889959T>C		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	107	39	NM_001195144	0	0	0	1	1	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																				.		0.388	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		C	197889959	T	C	197889959	2	2	122	1	0	0	0	0	0	0	0	1	672	1490	52	3		3	ANKRD44	2	197889959	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	15346530	197889959	45309414	29	10576											
ALS2CR8	79800	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	203848266	203848266	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaccatttctgtgagccaAgttaaacaagaacccaaaga	17	8	7	9	0	1	3	0	1	1	2	1	3	1	3	3	0	4	2	3	0	7	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:203848266A>G	ENST00000402905.3	+	16	2418	c.2097A>G	c.(2095-2097)caA>caG	p.Q699Q	CARF_ENST00000320443.8_Silent_p.Q699Q|CARF_ENST00000545262.1_Silent_p.Q623Q|CARF_ENST00000414439.1_Silent_p.Q597Q|CARF_ENST00000438828.2_Silent_p.Q699Q|CARF_ENST00000545253.1_Silent_p.Q611Q|WDR12_ENST00000477723.1_Intron|CARF_ENST00000428585.1_Silent_p.Q623Q	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	699					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CTGTGAGCCAAGTTAAACAAG	0.328																																					p.Q699Q		.											.	ALS2CR8-136	0			c.A2097G						.						81	78	79					2																	203848266		1801	4076	5877	SO:0001819	synonymous_variant	79800	exon17			GAGCCAAGTTAAA	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"calcium-response factor"	607586	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.2097A>G	2.37:g.203848266A>G		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	93	33	NM_024744	0	0	4	5	1	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Silent	SNP	ENST00000402905.3	37	CCDS42801.1																																																																																			.		0.328	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		G	203848266	A	G	203848266	2	3	122	1	0	0	0	0	0	0	0	1	555	69	3	3		3	ALS2CR8	2	203848266	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	5958307	203848266	39351107	30	10577											
CHL1	10752	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	407694	407695	+	Frame_Shift_Ins	INS	-	-	T																															ccaaattgcatatgcttgaaINSttacattgtgaaagcaaatg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:407694_407695insT	ENST00000256509.2	+	15	2289_2290	c.1647_1648insT	c.(1648-1650)ttafs	p.L550fs	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Frame_Shift_Ins_p.L534fs|CHL1-AS1_ENST00000608098.1_RNA	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		ATATGCTTGAATTACATTGTGA	0.361																																					p.E549fs		.											.	CHL1-583	0			c.1647_1648insT						.																																			SO:0001589	frameshift_variant	10752	exon13			.	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	1939	protein-coding gene	gene with protein product	"neural cell adhesion molecule", "close homolog of L1"	607416	"cell adhesion molecule with homology to L1CAM (close homologue of L1)", "cell adhesion molecule with homology to L1CAM (close homolog of L1)"			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1649dupT	3.37:g.407696_407696dupT	ENSP00000256509:p.Leu550fs	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	87	36	NM_001253388	0	0	0	0	0	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Frame_Shift_Ins	INS	ENST00000256509.2	37	CCDS2556.1																																																																																			.		0.361	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	407695	-	T	407694	7	5	122	1	0	1	1	0	0	0	0	0	3355	98	4	0	1697	0	CHL1	3	407694	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08		407694	197614736	31	10578											
SLC22A13	9390	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38316610	38316610	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaggctccttcagatcacCggcactgcgcctggcttact	6	10	11	14	2	2	1	2	0	0	1	3	2	3	2	3	4	2	3	3	4	1	2	rs200811458		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:38316610C>A	ENST00000311856.4	+	4	817	c.768C>A	c.(766-768)acC>acA	p.T256T	SLC22A13_ENST00000450935.2_Silent_p.R164R	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	256					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		TTCAGATCACCGGCACTGCGC	0.597																																					p.T256T		.											.	SLC22A13-91	0			c.C768A						.						128	126	127					3																	38316610		2203	4300	6503	SO:0001819	synonymous_variant	9390	exon4			GATCACCGGCACT	AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.768C>A	3.37:g.38316610C>A		Somatic	272	2		WXS	Illumina HiSeq	Phase_I	310	107	NM_004256	0	0	0	0	0	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	37	CCDS2676.1																																																																																			C|0.999;T|0.001		0.597	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		A	38316610	C	A	38316610	2	1	122	1	0	0	0	0	0	0	0	1	14476	639	23	4		4	SLC22A13	3	38316610	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	37908916	38316610	159705820	32	10579											
CAMP	820	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48266893	48266893	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggattttttgcggaatctTgtacccaggacagagtccta	11	12	10	8	1	1	1	0	0	1	1	2	4	2	4	2	3	2	1	2	3	4	6			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:48266893T>C	ENST00000576243.1	+	4	632	c.492T>C	c.(490-492)ctT>ctC	p.L164L	CAMP_ENST00000296435.2_Silent_p.L167L			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	164					antibacterial humoral response (GO:0019731)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptidoglycan (GO:0071224)|cellular response to tumor necrosis factor (GO:0071356)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of growth of symbiont on or near host surface (GO:0044140)|phagosome maturation (GO:0090382)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	cell projection (GO:0042995)|cell wall (GO:0005618)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|specific granule (GO:0042581)				endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TGCGGAATCTTGTACCCAGGA	0.453																																					p.L167L		.											.	CAMP-91	0			c.T501C						.						103	113	109					3																	48266893		2203	4300	6503	SO:0001819	synonymous_variant	820	exon4			GAATCTTGTACCC	BC055089	CCDS2762.1, CCDS2762.2	3p21.3	2014-01-30			ENSG00000164047	ENSG00000164047		"Endogenous ligands"	1472	protein-coding gene	gene with protein product		600474				7624374	Standard	NM_004345		Approved	CAP18, FALL39, FALL-39, LL37	uc003csj.3	P49913	OTTHUMG00000133526	ENST00000576243.1:c.492T>C	3.37:g.48266893T>C		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	225	83	NM_004345	0	0	0	0	0	Q71SN9	Silent	SNP	ENST00000576243.1	37																																																																																				.		0.453	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345		C	48266893	T	C	48266893	2	2	122	1	0	0	0	0	0	0	0	1	2616	1799	63	3		3	CAMP	3	48266893	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	9950283	48266893	149755537	33	10580											
IQCF2	389123	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	51897303	51897303	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactggcaatgccacaacTgccagacctgcgctctcctc	8	7	8	18	1	1	1	0	0	1	1	3	1	1	1	5	1	4	2	5	1	2	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:51897303T>C	ENST00000333127.3	+	3	441	c.412T>C	c.(412-414)Tgc>Cgc	p.C138R	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	138										endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ATGCCACAACTGCCAGACCTG	0.577																																					p.C138R		.											.	IQCF2-90	0			c.T412C						.						120	113	116					3																	51897303		2203	4300	6503	SO:0001583	missense	389123	exon3			CACAACTGCCAGA	AK128883	CCDS2835.1	3p21.31	2008-02-05			ENSG00000184345	ENSG00000184345			31815	protein-coding gene	gene with protein product							Standard	NM_203424		Approved		uc003dbt.1	Q8IXL9	OTTHUMG00000156914	ENST00000333127.3:c.412T>C	3.37:g.51897303T>C	ENSP00000329904:p.Cys138Arg	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	180	12	NM_203424	0	0	0	0	0		Missense_Mutation	SNP	ENST00000333127.3	37	CCDS2835.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928595	0.73327	.	.	ENSG00000184345	ENST00000333127	T	0.34859	1.34	5.22	5.22	0.72569	.	0.202993	0.36101	N	0.002800	T	0.52125	0.1715	L	0.58810	1.83	0.48696	D	0.999697	D	0.71674	0.998	D	0.64144	0.922	T	0.54761	-0.8245	10	0.87932	D	0	-16.5932	11.6771	0.51436	0.0:0.0:0.0:1.0	.	138	Q8IXL9	IQCF2_HUMAN	R	138	ENSP00000329904:C138R	ENSP00000329904:C138R	C	+	1	0	IQCF2	51872343	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	3.496000	0.53288	2.311000	0.77944	0.528000	0.53228	TGC	.		0.577	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424		C	51897303	T	C	51897303	3	2	122	1	0	0	0	0	1	0	0	0	7829	1580	55	3	422	3	IQCF2	3	51897303	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	3630410	51897303	146125127	34	10581											
LRTM1	57408	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	54952818	54952823	+	In_Frame_Del	DEL	CAGGAA	CAGGAA	-																															cgaggacactggatcaggagCaggaagagggcagggctggt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	CAGGAA	CAGGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:54952818_54952823delCAGGAA	ENST00000273286.5	-	3	863_868	c.701_706delTTCCTG	c.(700-708)cttcctgct>cct	p.234_236LPA>P	CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000288197.5_Intron|LRTM1_ENST00000493075.1_In_Frame_Del_p.158_160LPA>P	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	234	LRRCT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		GGATCAGGAGCAGGAAGAGGGCAGGG	0.597																																					p.234_236del		.											.	LRTM1-90	0			c.701_706del						.																																			SO:0001651	inframe_deletion	57408	exon3			.	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.701_706delTTCCTG	3.37:g.54952818_54952823delCAGGAA	ENSP00000273286:p.Leu234_Ala236delinsPro	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	43	14	NM_020678	0	0	0	0	0	Q8IUU2	In_Frame_Del	DEL	ENST00000273286.5	37	CCDS2876.1																																																																																			.		0.597	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		-	54952823	CAGGAA	-	54952818	7	5	122	1	0	1	0	1	0	0	0	0	9069	710	25	0	335	0	LRTM1	3	54952818	In_Frame_Del	DEL	CAGGAA	TCGA-GL-7773-01A-11D-2136-08	3055515	54952818	143069612	35	10582											
ARHGEF3	50650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56779418	56779418	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggactcggtgatcttgctTtttgtggtccagcagagctt	5	15	12	9	1	1	2	0	1	1	1	3	3	2	3	1	3	3	3	1	3	0	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:56779418T>G	ENST00000296315.3	-	7	853	c.685A>C	c.(685-687)Aag>Cag	p.K229Q	ARHGEF3_ENST00000496106.1_Missense_Mutation_p.K235Q|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.K261Q|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.K235Q|ARHGEF3_ENST00000495373.1_Missense_Mutation_p.K229Q|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.K200Q	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	229	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		TGATCTTGCTTTTTGTGGTCC	0.478																																					p.K261Q		.											.	ARHGEF3-228	0			c.A781C						.						161	169	166					3																	56779418		2203	4300	6503	SO:0001583	missense	50650	exon10			CTTGCTTTTTGTG	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"Rho guanine nucleotide exchange factors"	683	protein-coding gene	gene with protein product	"exchange factor found in platelets and leukemic and neuronal tissues, XPLN", "RhoGEF protein"	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.685A>C	3.37:g.56779418T>G	ENSP00000296315:p.Lys229Gln	Somatic	229	0		WXS	Illumina HiSeq	Phase_I	238	82	NM_001128615	0	0	11	21	10	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943519	0.92593	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373	T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46	5.85	5.85	0.93711	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.61813	0.2377	M	0.89601	3.045	0.80722	D	1	D;D;D;D;D;D;D	0.69078	0.966;0.968;0.992;0.984;0.98;0.997;0.98	P;P;P;P;P;D;P	0.63192	0.712;0.571;0.591;0.713;0.665;0.912;0.665	T	0.70669	-0.4808	10	0.87932	D	0	-14.323	16.5479	0.84454	0.0:0.0:0.0:1.0	.	235;200;27;229;261;229;235	E9PG37;E7EU49;Q9NR81-4;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;.;ARHG3_HUMAN;.	Q	229;261;235;235;200;229	ENSP00000296315:K229Q;ENSP00000341071:K261Q;ENSP00000410922:K235Q;ENSP00000420420:K235Q;ENSP00000418826:K200Q;ENSP00000417986:K229Q	ENSP00000296315:K229Q	K	-	1	0	ARHGEF3	56754458	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	AAG	.		0.478	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		G	56779418	T	G	56779418	3	3	122	1	0	0	0	0	1	0	0	0	904	1850	64	5	911	5	ARHGEF3	3	56779418	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	1826600	56779418	141243012	36	10583											
C3orf14	57415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	62317065	62317065	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttccacggcctgaggtggtTtctcttgaggtgagcatctt	5	14	12	10	1	2	3	0	3	2	0	4	3	3	3	2	4	1	2	2	4	0	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:62317065T>A	ENST00000494481.1	+	5	557	c.243T>A	c.(241-243)gtT>gtA	p.V81V	PTPRG-AS1_ENST00000490916.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|C3orf14_ENST00000462069.1_Silent_p.V81V|C3orf14_ENST00000542214.1_Silent_p.V81V|C3orf14_ENST00000232519.5_Silent_p.V81V			Q9HBI5	CC014_HUMAN	chromosome 3 open reading frame 14	81										central_nervous_system(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.00023)|KIRC - Kidney renal clear cell carcinoma(15;0.00877)|Kidney(15;0.0101)		CTGAGGTGGTTTCTCTTGAGG	0.393																																					p.V81V		.											.	C3orf14-278	0			c.T243A						.						102	101	102					3																	62317065		2203	4300	6503	SO:0001819	synonymous_variant	57415	exon4			GGTGGTTTCTCTT	AF236158	CCDS2896.1	3p14.2	2011-11-29			ENSG00000114405	ENSG00000114405			25024	protein-coding gene	gene with protein product						12477932	Standard	XM_005265338		Approved	HT021	uc003dlg.3	Q9HBI5	OTTHUMG00000158704	ENST00000494481.1:c.243T>A	3.37:g.62317065T>A		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	147	57	NM_020685	0	0	0	0	0	B2R9U0	Silent	SNP	ENST00000494481.1	37	CCDS2896.1																																																																																			.		0.393	C3orf14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351807.1	NM_020685		A	62317065	T	A	62317065	2	1	122	1	0	0	0	0	0	0	0	1	2214	1828	64	5		5	C3orf14	3	62317065	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	5537647	62317065	135705365	37	10584											
CPOX	1371	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr3	98309567	98309567	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataacagagctcacgcccatAgcacaaaatggcaatttacc	16	7	6	12	1	1	1	1	0	0	1	1	1	1	1	2	1	4	3	2	1	6	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:98309567A>T	ENST00000264193.2	-	3	938	c.720T>A	c.(718-720)gcT>gcA	p.A240A		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	240					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						TCACGCCCATAGCACAAAATG	0.388																																					p.A240A	Esophageal Squamous(75;7 1223 22300 43648 48951)	.											.	CPOX-90	0			c.T720A						.						82	78	79					3																	98309567		2203	4300	6503	SO:0001819	synonymous_variant	1371	exon3			GCCCATAGCACAA	BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"coproporphyria"	612732	"coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.720T>A	3.37:g.98309567A>T		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	88	22	NM_000097	0	0	7	10	3	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Silent	SNP	ENST00000264193.2	37	CCDS2932.1																																																																																			.		0.388	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097		T	98309567	A	T	98309567	2	4	122	1	0	0	0	0	0	0	0	1	3827	407	15	5		5	CPOX	3	98309567	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	35992502	98309567	99712863	38	10585											
ZBTB20	26137	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	114057877	114057878	+	Frame_Shift_Del	DEL	AT	AT	-																															cgtcagacacatgcatcctcAtgtggtcgttgaactgctcg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:114057877_114057878delAT	ENST00000474710.1	-	5	2378_2379	c.2200_2201delAT	c.(2200-2202)atgfs	p.M734fs	ZBTB20_ENST00000464560.1_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000393785.2_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000471418.1_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000462705.1_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000357258.3_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000481632.1_Frame_Shift_Del_p.M661fs	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	734						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		ATGCATCCTCATGTGGTCGTTG	0.48																																					p.734_734del	NSCLC(69;748 1344 9802 11203 30933)	.											.	ZBTB20-95	0			c.2200_2201del						.																																			SO:0001589	frameshift_variant	26137	exon5			.	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.2200_2201delAT	3.37:g.114057877_114057878delAT	ENSP00000419153:p.Met734fs	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	141	56	NM_001164342	0	0	0	0	0	Q63HP6|Q8N6R5|Q9Y410	Frame_Shift_Del	DEL	ENST00000474710.1	37	CCDS54626.1																																																																																			.		0.48	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		-	114057878	AT	-	114057877	7	5	122	1	0	1	0	1	0	0	0	0	17561	217	8	0	28	0	ZBTB20	3	114057877	Frame_Shift_Del	DEL	AT	TCGA-GL-7773-01A-11D-2136-08	15748310	114057877	83964553	39	10586											
MCM2	4171	bcgsc.ca	37	chr3	127340566	127340566	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtgagctcttcaggatgAacaagttcagccacgacctg	12	8	10	11	1	3	2	2	2	1	0	3	4	3	3	2	1	3	2	2	1	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:127340566A>G	ENST00000265056.7	+	16	2909	c.2665A>G	c.(2665-2667)Aac>Gac	p.N889D	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	889					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						CTTCAGGATGAACAAGTTCAG	0.498																																					p.N889D													.	MCM2-230	0			c.A2665G						.						100	95	96					3																	127340566		2203	4300	6503	SO:0001583	missense	4171	exon16			AGGATGAACAAGT	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.2665A>G	3.37:g.127340566A>G	ENSP00000265056:p.Asn889Asp	Somatic	76	0		WXS	Illumina HiSeq	Phase_1	80	4	NM_004526	0	0	12	12	0	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	37	CCDS3043.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.42|19.42	3.824506|3.824506	0.71143|0.71143	.|.	.|.	ENSG00000073111|ENSG00000073111	ENST00000265056;ENST00000539922;ENST00000543142|ENST00000491422	T|.	0.02421|.	4.3|.	5.38|5.38	4.22|4.22	0.49857|0.49857	.|.	0.132166|.	0.64402|.	D|.	0.000002|.	T|.	0.74261|.	0.3693|.	M|M	0.81239|0.81239	2.535|2.535	0.80722|0.80722	D|D	1|1	P;P;B|.	0.38788|.	0.51;0.647;0.419|.	B;P;P|.	0.50896|.	0.282;0.653;0.455|.	T|.	0.74717|.	-0.3571|.	10|.	0.51188|.	T|.	0.08|.	-40.2853|-40.2853	12.3561|12.3561	0.55176|0.55176	0.8518:0.1482:0.0:0.0|0.8518:0.1482:0.0:0.0	.|.	939;759;889|.	F5H1E9;B4DSV5;P49736|.	.;.;MCM2_HUMAN|.	D|W	889;793;939|820	ENSP00000265056:N889D|.	ENSP00000265056:N889D|.	N|X	+|+	1|3	0|0	MCM2|MCM2	128823256|128823256	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.487000|0.487000	0.33371|0.33371	5.837000|5.837000	0.69381|0.69381	0.882000|0.882000	0.36016|0.36016	0.260000|0.260000	0.18958|0.18958	AAC|TGA	.		0.498	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			G	127340566	A	G	127340566	3	3	122	1	0	0	0	0	1	0	0	0	9411	246	9	3	2727	3	MCM2	3	127340566	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	13282689	127340566	70681864	40	10587											
PLSCR2	57047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	146167110	146167110	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttaaaaacccagaccagtgCttagaaatcctgccaaccac	15	7	5	14	0	0	2	0	0	0	2	1	2	1	2	5	0	4	1	5	0	6	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:146167110C>T	ENST00000497985.1	-	8	1186	c.747G>A	c.(745-747)aaG>aaA	p.K249K	PLSCR2_ENST00000336685.2_Silent_p.K176K	NM_001199978.1	NP_001186907.1	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2	249					phospholipid scrambling (GO:0017121)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid scramblase activity (GO:0017128)			endometrium(2)|large_intestine(5)|lung(7)|stomach(1)	15						CAGACCAGTGCTTAGAAATCC	0.328																																					p.K249K		.											.	PLSCR2-90	0			c.G747A						.						128	130	130					3																	146167110		2203	4300	6503	SO:0001819	synonymous_variant	57047	exon8			CCAGTGCTTAGAA		CCDS56284.1, CCDS3134.1, CCDS75029.1	3q24	2008-07-18			ENSG00000163746	ENSG00000163746			16494	protein-coding gene	gene with protein product		607610				10930526	Standard	NM_001199978		Approved		uc003evw.2	Q9NRY7	OTTHUMG00000159429	ENST00000497985.1:c.747G>A	3.37:g.146167110C>T		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	228	90	NM_001199978	0	0	1	1	0	B4DXC3|J3KR76|Q0VAQ1|Q6NSW9|Q7Z4L7	Silent	SNP	ENST00000497985.1	37	CCDS56284.1																																																																																			.		0.328	PLSCR2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000355264.1	NM_020359		T	146167110	C	T	146167110	2	4	122	1	0	0	0	0	0	0	0	1	12136	796	28	2		2	PLSCR2	3	146167110	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	18826544	146167110	51855320	41	10588											
MCCC1	56922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	182789038	182789038	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggctttaatcatgacaggaTagccaattctcctggcgtgt	9	12	10	10	2	2	1	1	1	1	0	3	2	2	2	2	3	1	1	2	3	3	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:182789038T>C	ENST00000265594.4	-	6	745	c.599A>G	c.(598-600)tAt>tGt	p.Y200C	MCCC1_ENST00000492597.1_Missense_Mutation_p.Y91C|MCCC1_ENST00000539926.1_Missense_Mutation_p.Y65C	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	200	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CATGACAGGATAGCCAATTCT	0.463																																					p.Y200C		.											.	MCCC1-92	0			c.A599G						.						100	101	101					3																	182789038		2203	4300	6503	SO:0001583	missense	56922	exon6			ACAGGATAGCCAA	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.599A>G	3.37:g.182789038T>C	ENSP00000265594:p.Tyr200Cys	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	129	30	NM_020166	0	0	14	16	2	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.081996	0.76528	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585;ENST00000541636	D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91	5.9	5.9	0.94986	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.053830	0.85682	D	0.000000	D	0.99242	0.9736	H	0.94698	3.57	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.73708	0.975;0.975;0.981	D	0.99032	1.0821	10	0.87932	D	0	.	16.3322	0.83039	0.0:0.0:0.0:1.0	.	153;91;200	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	C	200;91;50;65;153;153;91	ENSP00000265594:Y200C;ENSP00000419898:Y91C;ENSP00000441253:Y65C;ENSP00000420433:Y153C	ENSP00000265594:Y200C	Y	-	2	0	MCCC1	184271732	1.000000	0.71417	0.605000	0.28930	0.929000	0.56500	5.693000	0.68264	2.251000	0.74343	0.528000	0.53228	TAT	.		0.463	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		C	182789038	T	C	182789038	3	2	122	1	0	0	0	0	1	0	0	0	9399	1406	49	3	1634	3	MCCC1	3	182789038	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	36621928	182789038	15233392	42	10589											
IDUA	3425	hgsc.bcm.edu	37	chr4	980971	980971	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccccgcacctggtgcaTgtggacgcggcccgcgcgct	4	5	16	16	6	0	0	0	0	0	0	0	2	0	1	4	4	1	3	4	4	0	0	rs10794537	byFrequency	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:980971T>G	ENST00000247933.4	+	1	187	c.99T>G	c.(97-99)caT>caG	p.H33Q	SLC26A1_ENST00000398520.2_Intron|IDUA_ENST00000453894.1_Missense_Mutation_p.H33Q	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	33			H -> Q (in dbSNP:rs10794537). {ECO:0000269|PubMed:1362562, ECO:0000269|PubMed:1505961, ECO:0000269|PubMed:1946389, ECO:0000269|PubMed:21394825}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			ACCTGGTGCATGTGGACGCGG	0.801													G|||	4467	0.891973	0.9826	0.8386	5008	,	,		8604	0.8472		0.8042	False		,,,				2504	0.9438				p.H33Q		.											.	IDUA-91	0			c.T99G						.						1	1	1					4																	980971		552	1375	1927	SO:0001583	missense	3425	exon1			GGTGCATGTGGAC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.99T>G	4.37:g.980971T>G	ENSP00000247933:p.His33Gln	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	2	2	NM_000203	0	0	0	5	5	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	1801|1801	0.8246336996336996|0.8246336996336996	464|464	0.943089430894309|0.943089430894309	294|294	0.8121546961325967|0.8121546961325967	448|448	0.7832167832167832|0.7832167832167832	595|595	0.7849604221635884|0.7849604221635884	G|G	3.726|3.726	-0.056533|-0.056533	0.07362|0.07362	.|.	.|.	ENSG00000127415|ENSG00000127415	ENST00000504568|ENST00000247933;ENST00000453894;ENST00000502910	.|D;D;D	.|0.93247	.|-3.18;-3.19;-3.03	3.62|3.62	-0.897|-0.897	0.10553|0.10553	.|.	.|0.728933	.|0.12190	.|N	.|0.491278	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.36817|0.36817	-0.9732|-0.9732	4|9	.|0.10111	.|T	.|0.7	.|.	1.2904|1.2904	0.02059|0.02059	0.1461:0.2669:0.3485:0.2385|0.1461:0.2669:0.3485:0.2385	rs10794537|rs10794537	.|33;33	.|B3KWK6;P35475	.|.;IDUA_HUMAN	G|Q	33|33	.|ENSP00000247933:H33Q;ENSP00000396458:H33Q;ENSP00000422952:H33Q	.|ENSP00000247933:H33Q	C|H	+|+	1|3	0|2	IDUA|IDUA	970971|970971	0.000000|0.000000	0.05858|0.05858	0.992000|0.992000	0.48379|0.48379	0.012000|0.012000	0.07955|0.07955	-2.547000|-2.547000	0.00931|0.00931	-0.253000|-0.253000	0.09514|0.09514	-1.482000|-1.482000	0.00985|0.00985	TGT|CAT	T|0.175;G|0.825		0.801	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203		G	980971	T	G	980971	3	3	122	1	0	0	0	0	1	0	0	0	7525	1461	51	5	101	5	IDUA	4	980971	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		980971	190173305	43	10590											
CPZ	8532	hgsc.bcm.edu	37	chr4	8621334	8621334	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaggccacgctggctgcTcaagtactagccccggcccc	7	5	10	19	2	1	0	1	0	0	0	1	0	1	0	6	3	3	4	6	3	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:8621334T>C	ENST00000360986.4	+	11	2123	c.1949T>C	c.(1948-1950)cTc>cCc	p.L650P	CPZ_ENST00000315782.6_Missense_Mutation_p.L639P|CPZ_ENST00000429646.2_Missense_Mutation_p.L258P|CPZ_ENST00000382480.2_Missense_Mutation_p.L513P	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	650					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CGCTGGCTGCTCAAGTACTAG	0.667																																					p.L650P		.											.	CPZ-93	0			c.T1949C						.						16	15	15					4																	8621334		2198	4295	6493	SO:0001583	missense	8532	exon11			GGCTGCTCAAGTA	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1949T>C	4.37:g.8621334T>C	ENSP00000354255:p.Leu650Pro	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001014447	0	0	16	16	0	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.581338	0.65992	.	.	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782;ENST00000429646	T;T;T;T	0.64085	0.22;1.58;-0.08;1.39	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000013	T	0.77025	0.4070	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.79981	-0.1574	10	0.87932	D	0	-47.5465	12.9665	0.58488	0.0:0.0:0.0:1.0	.	639;650	Q66K79-2;Q66K79	.;CBPZ_HUMAN	P	650;513;639;258	ENSP00000354255:L650P;ENSP00000371920:L513P;ENSP00000315074:L639P;ENSP00000403981:L258P	ENSP00000315074:L639P	L	+	2	0	CPZ	8672234	1.000000	0.71417	1.000000	0.80357	0.437000	0.31866	6.992000	0.76238	1.800000	0.52685	0.379000	0.24179	CTC	.		0.667	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		C	8621334	T	C	8621334	3	2	122	1	0	0	0	0	1	0	0	0	3845	1551	54	3	1991	3	CPZ	4	8621334	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	7640363	8621334	182532942	44	10591											
CDKL2	8999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76529105	76529105	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccagcaaacacaggattttTattaaaaagctcctgatgcc	14	11	6	10	0	0	1	0	1	0	0	2	2	2	2	3	1	4	2	3	1	5	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:76529105T>A	ENST00000429927.2	-	6	1394	c.691A>T	c.(691-693)Aaa>Taa	p.K231*	CDKL2_ENST00000307465.4_Nonsense_Mutation_p.K231*	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ACAGGATTTTTATTAAAAAGC	0.388																																					p.K231X		.											.	CDKL2-454	0			c.A691T						.						86	89	88					4																	76529105		2203	4300	6503	SO:0001587	stop_gained	8999	exon6			GATTTTTATTAAA	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.691A>T	4.37:g.76529105T>A	ENSP00000412365:p.Lys231*	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	113	46	NM_003948	0	0	1	1	0	B2R695	Nonsense_Mutation	SNP	ENST00000429927.2	37	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	T	42	9.693897	0.99240	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	.	.	.	5.14	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.029	11.3921	0.49820	0.0:0.0:0.1508:0.8492	.	.	.	.	X	231	.	ENSP00000306340:K231X	K	-	1	0	CDKL2	76748129	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.829000	0.62737	2.164000	0.68074	0.460000	0.39030	AAA	.		0.388	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		A	76529105	T	A	76529105	4	1	122	1	0	0	0	0	0	1	0	0	3160	1763	61	5	814	5	CDKL2	4	76529105	Nonsense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	67907771	76529105	114625171	45	10592											
USO1	8615	broad.mit.edu	37	chr4	76721515	76721515	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatttcagcttacaggacaAattgcagaaaatcttggaga	16	10	9	6	0	2	3	1	0	1	3	2	5	2	4	0	2	3	2	0	2	4	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:76721515A>T	ENST00000538159.1	+	16	1602	c.1602A>T	c.(1600-1602)caA>caT	p.Q534H	USO1_ENST00000514213.2_Missense_Mutation_p.Q510H			O60763	USO1_HUMAN	USO1 vesicle transport factor	525	Globular head.				ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi vesicle docking (GO:0048211)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|mitotic cell cycle (GO:0000278)|transcytosis (GO:0045056)|vesicle fusion with Golgi apparatus (GO:0048280)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TTACAGGACAAATTGCAGAAA	0.348																																					.													.	USO1-25	0			.						.						78	68	71					4																	76721515		1831	4094	5925	SO:0001583	missense	8615	.			AGGACAAATTGCA	AL832010	CCDS75144.1	4q21.1	2012-12-10	2012-12-10		ENSG00000138768	ENSG00000138768			30904	protein-coding gene	gene with protein product	"vesicle docking protein", "transcytosis associated protein"	603344	"USO1 homolog, vesicle docking protein (yeast)", "USO1 vesicle docking protein homolog (yeast)"			9478999, 9150144, 12077354, 15979508, 14736916	Standard	XM_006714395		Approved	TAP, VDP, p115	uc003hiu.3	O60763	OTTHUMG00000160952	ENST00000538159.1:c.1602A>T	4.37:g.76721515A>T	ENSP00000440586:p.Gln534His	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	13	5	.	0	0	0	0	0	B2RAQ0|Q6PK63|Q86TB8|Q8N592	Missense_Mutation	SNP	ENST00000538159.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.94|18.94	3.730371|3.730371	0.69074|0.69074	.|.	.|.	ENSG00000138768|ENSG00000138768	ENST00000441296|ENST00000508939;ENST00000538159;ENST00000514213;ENST00000264904	.|T;T	.|0.66638	.|-0.22;-0.22	5.83|5.83	1.81|1.81	0.25067|0.25067	.|Vesicle tethering protein Uso1/P115-like , head domain (1);Armadillo-type fold (1);	.|0.053134	.|0.85682	.|D	.|0.000000	T|T	0.63450|0.63450	0.2512|0.2512	L|L	0.48174|0.48174	1.505|1.505	0.58432|0.58432	D|D	0.999992|0.999992	.|B;P	.|0.42483	.|0.059;0.781	.|B;P	.|0.51135	.|0.061;0.66	T|T	0.55289|0.55289	-0.8164|-0.8164	5|10	.|0.13853	.|T	.|0.58	.|.	9.114|9.114	0.36746|0.36746	0.4915:0.0:0.5085:0.0|0.4915:0.0:0.5085:0.0	.|.	.|534;525	.|F5GYR8;O60763	.|.;USO1_HUMAN	I|H	201|360;534;510;453	.|ENSP00000440586:Q534H;ENSP00000444850:Q510H	.|ENSP00000264904:Q453H	K|Q	+|+	2|3	0|2	USO1|USO1	76940539|76940539	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.775000|1.775000	0.38584|0.38584	0.356000|0.356000	0.24157|0.24157	0.460000|0.460000	0.39030|0.39030	AAA|CAA	.		0.348	USO1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003715		T	76721515	A	T	76721515	3	4	122	1	0	0	0	0	1	0	0	0	17072	11	1	5	1474	5	USO1	4	76721515	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	192410	76721515	114432761	46	10593											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123202841	123202841	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttcttaaattcagtgccatGttagatggtatagccattgg	10	15	10	6	0	2	1	1	0	1	1	2	1	2	1	2	2	2	3	2	2	5	7	rs115036597		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:123202841G>C	ENST00000264501.4	+	52	9322	c.8949G>C	c.(8947-8949)atG>atC	p.M2983I	KIAA1109_ENST00000388738.3_Missense_Mutation_p.M2983I|KIAA1109_ENST00000455637.1_Missense_Mutation_p.M2983I			Q2LD37	K1109_HUMAN	KIAA1109	2983					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TCAGTGCCATGTTAGATGGTA	0.383																																					p.M2983I		.											.	KIAA1109-80	0			c.G8949C						.						121	113	116					4																	123202841		1831	4099	5930	SO:0001583	missense	84162	exon50			TGCCATGTTAGAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.8949G>C	4.37:g.123202841G>C	ENSP00000264501:p.Met2983Ile	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	160	57	NM_015312	0	0	0	2	2	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.047|5.047	0.194277|0.194277	0.09599|0.09599	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000419325	T;T;T|.	0.20069|.	2.69;2.69;2.1|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.33990|0.33990	0.0882|0.0882	N|N	0.04090|0.04090	-0.28|-0.28	0.43073|0.43073	D|D	0.994713|0.994713	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.28138|0.28138	-1.0053|-1.0053	10|5	0.05436|.	T|.	0.98|.	.|.	12.6377|12.6377	0.56692|0.56692	0.0759:0.0:0.9241:0.0|0.0759:0.0:0.9241:0.0	.|.	2983;2983|.	Q2LD37-6;Q2LD37|.	.;K1109_HUMAN|.	I|L	2983|941	ENSP00000264501:M2983I;ENSP00000373390:M2983I;ENSP00000389925:M2983I|.	ENSP00000264501:M2983I|.	M|V	+|+	3|1	0|0	KIAA1109|KIAA1109	123422291|123422291	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	6.528000|6.528000	0.73807|0.73807	2.572000|2.572000	0.86782|0.86782	0.591000|0.591000	0.81541|0.81541	ATG|GTT	G|0.999;T|0.001		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123202841	G	C	123202841	3	2	122	1	0	0	0	0	1	0	0	0	8229	1377	48	4	9147	4	KIAA1109	4	123202841	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	46481326	123202841	67951435	47	10594											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159816929	159816929	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcatcttgaagatagactaCaggagatgtaccttaaaagt	15	11	9	6	0	1	4	0	1	1	3	1	5	1	4	1	1	3	2	1	1	6	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:159816929C>G	ENST00000264433.6	+	16	3253	c.3178C>G	c.(3178-3180)Cag>Gag	p.Q1060E	C4orf45_ENST00000434826.2_Intron|C4orf45_ENST00000508011.1_Intron|FNIP2_ENST00000379346.3_Missense_Mutation_p.Q1083E	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	1060					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		AGATAGACTACAGGAGATGTA	0.408																																					p.Q1060E		.											.	FNIP2-68	0			c.C3178G						.						119	118	119					4																	159816929		1905	4126	6031	SO:0001583	missense	57600	exon16			AGACTACAGGAGA	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"O6-methylguanine-induced apoptosis 1"	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.3178C>G	4.37:g.159816929C>G	ENSP00000264433:p.Gln1060Glu	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_020840	0	0	14	14	0	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	37	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	C	31	5.082398	0.94050	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.28069	1.63;1.63	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	M	0.85542	2.76	0.80722	D	1	D	0.69078	0.997	D	0.66602	0.945	T	0.64609	-0.6367	9	.	.	.	.	19.3536	0.94401	0.0:1.0:0.0:0.0	.	1060	Q9P278	FNIP2_HUMAN	E	1060;1083	ENSP00000264433:Q1060E;ENSP00000368651:Q1083E	.	Q	+	1	0	FNIP2	160036379	1.000000	0.71417	0.910000	0.35882	0.996000	0.88848	7.770000	0.85390	2.597000	0.87782	0.591000	0.81541	CAG	.		0.408	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159816929	C	G	159816929	3	3	122	1	0	0	0	0	1	0	0	0	5995	479	17	4	3240	4	FNIP2	4	159816929	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	36614088	159816929	31337347	48	10595											
MTRR	4552	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7878202	7878202	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagaccttgtgaagtcaGagctgctacacattgaatct	12	10	10	9	0	2	4	1	2	1	2	2	5	2	5	1	1	3	2	1	1	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:7878202G>T	ENST00000264668.2	+	5	658	c.628G>T	c.(628-630)Gag>Tag	p.E210*	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Nonsense_Mutation_p.E183*	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	210	Hinge.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	TGTGAAGTCAGAGCTGCTACA	0.478																																					p.E210X		.											.	MTRR-91	0			c.G628T						.						82	77	78					5																	7878202		2203	4300	6503	SO:0001587	stop_gained	4552	exon5			AAGTCAGAGCTGC	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.628G>T	5.37:g.7878202G>T	ENSP00000264668:p.Glu210*	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	57	19	NM_024010	0	0	9	25	16	O60471|Q32MA9|Q7Z4M8	Nonsense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.92|11.92	1.783157|1.783157	0.31593|0.31593	.|.	.|.	ENSG00000124275|ENSG00000124275	ENST00000264668;ENST00000440940|ENST00000514220	.|.	.|.	.|.	5.91|5.91	3.14|3.14	0.36123|0.36123	.|.	1.215660|.	0.05458|.	N|.	0.550635|.	.|T	.|0.49898	.|0.1584	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999986|0.999986	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.38394	.|-0.9663	.|4	0.18276|.	T|.	0.48|.	-19.4083|-19.4083	15.3298|15.3298	0.74200|0.74200	0.0:0.4006:0.5994:0.0|0.0:0.4006:0.5994:0.0	.|.	.|.	.|.	.|.	X|I	210;183|111	.|.	ENSP00000264668:E210X|.	E|R	+|+	1|2	0|0	MTRR|MTRR	7931202|7931202	0.022000|0.022000	0.18835|0.18835	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	1.921000|1.921000	0.40035|0.40035	0.387000|0.387000	0.25024|0.25024	-0.127000|-0.127000	0.14921|0.14921	GAG|AGA	.		0.478	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7878202	G	T	7878202	4	4	122	1	0	0	0	0	0	1	0	0	9986	943	33	4	646	4	MTRR	5	7878202	Nonsense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		7878202	173037058	49	10596											
RNASEN	29102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	31515239	31515239	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccttgattgaggtatagttCttgtctttgccagaactctg	7	17	9	8	0	3	3	0	2	3	1	4	3	4	3	2	1	2	2	2	1	3	7			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:31515239C>G	ENST00000511367.2	-	7	1390	c.1146G>C	c.(1144-1146)aaG>aaC	p.K382N	DROSHA_ENST00000442743.1_Missense_Mutation_p.K345N|DROSHA_ENST00000513349.1_Missense_Mutation_p.K345N|DROSHA_ENST00000344624.3_Missense_Mutation_p.K382N	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	382					defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						AGGTATAGTTCTTGTCTTTGC	0.478																																					p.K382N		.											.	DROSHA-227	0			c.G1146C						.						160	152	154					5																	31515239		1868	4097	5965	SO:0001583	missense	29102	exon7			ATAGTTCTTGTCT	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"drosha, ribonuclease type III", "drosha, double-stranded RNA-specific endoribonuclease"	608828	"ribonuclease type III, nuclear"	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.1146G>C	5.37:g.31515239C>G	ENSP00000425979:p.Lys382Asn	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	178	63	NM_013235	0	0	6	13	7	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.68|16.68	3.189775|3.189775	0.57909|0.57909	.|.	.|.	ENSG00000113360|ENSG00000113360	ENST00000512076|ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000512302	.|T;T;T;T;T	.|0.59083	.|0.29;0.29;0.29;0.29;0.29	5.64|5.64	4.78|4.78	0.61160|0.61160	.|.	.|0.048766	.|0.85682	.|D	.|0.000000	T|T	0.54303|0.54303	0.1850|0.1850	N|N	0.19112|0.19112	0.55|0.55	0.44098|0.44098	D|D	0.996864|0.996864	.|D;B;B	.|0.54964	.|0.969;0.421;0.421	.|P;B;B	.|0.55824	.|0.785;0.154;0.154	T|T	0.55560|0.55560	-0.8122|-0.8122	5|10	.|0.44086	.|T	.|0.13	-27.3211|-27.3211	11.1936|11.1936	0.48700|0.48700	0.0:0.8412:0.0:0.1588|0.0:0.8412:0.0:0.1588	.|.	.|314;345;382	.|Q9NRR4-2;E7EMP9;Q9NRR4	.|.;.;RNC_HUMAN	Q|N	144|382;382;345;345;307;338;149	.|ENSP00000425979:K382N;ENSP00000339845:K382N;ENSP00000409335:K345N;ENSP00000424161:K345N;ENSP00000428782:K149N	.|ENSP00000265075:K307N	E|K	-|-	1|3	0|2	DROSHA|DROSHA	31550996|31550996	0.980000|0.980000	0.34600|0.34600	0.968000|0.968000	0.41197|0.41197	0.798000|0.798000	0.45092|0.45092	0.552000|0.552000	0.23376|0.23376	1.395000|1.395000	0.46643|0.46643	0.561000|0.561000	0.74099|0.74099	GAA|AAG	.		0.478	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		G	31515239	C	G	31515239	3	3	122	1	0	0	0	0	1	0	0	0	13449	912	32	4	3094	4	RNASEN	5	31515239	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	23637037	31515239	149400021	50	10597											
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41017998	41017998	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gagctagcagccgcctgacgGatggtgggcagggtatcaca	9	6	16	10	2	1	1	1	1	0	0	1	3	1	2	2	4	3	4	2	4	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:41017998G>C	ENST00000399564.4	-	28	3288	c.2838C>G	c.(2836-2838)atC>atG	p.I946M	MROH2B_ENST00000506092.2_Missense_Mutation_p.I501M	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	946																	CCGCCTGACGGATGGTGGGCA	0.463																																					p.I946M		.											.	.	0			c.C2838G						.						41	41	41					5																	41017998		1919	4127	6046	SO:0001583	missense	133558	exon28			CTGACGGATGGTG		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"maestro heat-like repeat containing"	26857	protein-coding gene	gene with protein product			"HEAT repeat family member 7B2"	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.2838C>G	5.37:g.41017998G>C	ENSP00000382476:p.Ile946Met	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_173489	0	0	0	0	0	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.186565	0.38609	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.68903	-0.36;-0.36	5.86	4.02	0.46733	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.56097	D	0.000027	T	0.74935	0.3782	L	0.54323	1.7	0.32409	N	0.550956	D	0.76494	0.999	D	0.83275	0.996	T	0.78523	-0.2171	10	0.72032	D	0.01	.	8.1374	0.31063	0.1947:0.0:0.8053:0.0	.	946	Q7Z745	HTRB2_HUMAN	M	501;651;946	ENSP00000441504:I501M;ENSP00000382476:I946M	ENSP00000296803:I651M	I	-	3	3	HEATR7B2	41053755	1.000000	0.71417	1.000000	0.80357	0.279000	0.26890	3.156000	0.50708	0.751000	0.32900	0.591000	0.81541	ATC	.		0.463	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		C	41017998	G	C	41017998	3	2	122	1	0	0	0	0	1	0	0	0	7056	1164	41	4	1979	4	HEATR7B2	5	41017998	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	9502759	41017998	139897262	51	10598											
CHD1	1105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	98192299	98192299	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttgaccggtggtctgaatGtaaccgatgatctgagtgag	10	11	13	7	2	2	5	0	5	2	0	2	6	2	5	2	2	1	1	2	2	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:98192299G>A	ENST00000284049.3	-	35	5067	c.4918C>T	c.(4918-4920)Cat>Tat	p.H1640Y		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1640	3 X 5 AA repeats of H-S-D-H-R.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TGGTCTGAATGTAACCGATGA	0.428																																					p.H1640Y		.											.	CHD1-274	0			c.C4918T						.						136	128	131					5																	98192299		2203	4299	6502	SO:0001583	missense	1105	exon35			CTGAATGTAACCG	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4918C>T	5.37:g.98192299G>A	ENSP00000284049:p.His1640Tyr	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	45	29	NM_001270	0	0	2	15	13	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	G	4.283	0.051605	0.08291	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.89875	-2.58	5.21	5.21	0.72293	.	0.000000	0.34386	U	0.004006	D	0.86079	0.5847	M	0.65498	2.005	0.38271	D	0.942164	B	0.27882	0.192	B	0.22880	0.042	T	0.82969	-0.0193	10	0.02654	T	1	.	18.7493	0.91807	0.0:0.0:1.0:0.0	.	1640	O14646	CHD1_HUMAN	Y	230;1640	ENSP00000284049:H1640Y	ENSP00000284049:H1640Y	H	-	1	0	CHD1	98220199	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	2.914000	0.48797	2.407000	0.81776	0.655000	0.94253	CAT	.		0.428	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		A	98192299	G	A	98192299	3	1	122	1	0	0	0	0	1	0	0	0	3329	1377	48	2	218	2	CHD1	5	98192299	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	57174301	98192299	82722961	52	10599											
PCDHGB2	56103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140741729	140741729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggtattgccagacctcaGcgaccgccgggagccctctg	8	6	13	14	3	2	2	1	0	1	2	2	4	2	3	5	2	3	1	5	2	1	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:140741729G>A	ENST00000522605.1	+	1	2027	c.2027G>A	c.(2026-2028)aGc>aAc	p.S676N	PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	676					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAGACCTCAGCGACCGCCGG	0.602																																					p.S676N		.											.	PCDHGB2-33	0			c.G2027A						.						54	59	57					5																	140741729		2031	4196	6227	SO:0001583	missense	56103	exon1			ACCTCAGCGACCG	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"Cadherins / Protocadherins : Clustered"	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.2027G>A	5.37:g.140741729G>A	ENSP00000429018:p.Ser676Asn	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	68	44	NM_018923	0	0	0	1	1	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	9.065	0.995573	0.19043	.	.	ENSG00000253910	ENST00000522605	T	0.51071	0.72	4.95	3.13	0.36017	.	.	.	.	.	T	0.39937	0.1097	L	0.53617	1.68	0.09310	N	1	B;B	0.24618	0.005;0.107	B;B	0.22601	0.021;0.04	T	0.22977	-1.0201	9	0.21014	T	0.42	.	9.109	0.36716	0.242:0.0:0.758:0.0	.	676;676	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	N	676	ENSP00000429018:S676N	ENSP00000429018:S676N	S	+	2	0	PCDHGB2	140721913	0.000000	0.05858	0.045000	0.18777	0.027000	0.11550	0.655000	0.24933	1.220000	0.43490	0.454000	0.30748	AGC	.		0.602	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		A	140741729	G	A	140741729	3	1	122	1	0	0	0	0	1	0	0	0	11589	971	34	2	2029	2	PCDHGB2	5	140741729	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	42549430	140741729	40173531	53	10600											
DIAPH1	1729	broad.mit.edu	37	chr5	140953588	140953589	+	In_Frame_Ins	INS	-	-	GAT																															aggaggaggaggaggaggagINSgaggaggagtggtactatcc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:140953588_140953589insGAT	ENST00000398557.4	-	16	1968_1969	c.1828_1829insATC	c.(1828-1830)cct>cATCct	p.609_610insH	DIAPH1_ENST00000398566.3_In_Frame_Ins_p.600_601insH|DIAPH1_ENST00000389057.5_In_Frame_Ins_p.600_601insH|DIAPH1_ENST00000518047.1_In_Frame_Ins_p.600_601insH|DIAPH1_ENST00000389054.3_In_Frame_Ins_p.609_610insH|DIAPH1_ENST00000520569.1_In_Frame_Ins_p.555_556insH|DIAPH1_ENST00000253811.6_In_Frame_Ins_p.609_610insH|DIAPH1_ENST00000398562.2_In_Frame_Ins_p.600_601insH	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	609	FH1.			Missing (in Ref. 4; AAI17258). {ECO:0000305}.	actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			aggaggaggaggaggaggagTG	0.584																																					p.P610delinsHP													.	DIAPH1-91	0			c.1829_1830insATC						.																																			SO:0001652	inframe_insertion	1729	exon16			GGAGGAGGAGGAG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1828_1829insATC	5.37:g.140953588_140953589insGAT	ENSP00000381565:p.Pro609_Pro610insHis	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_005219	0	0	0	0	0	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	In_Frame_Ins	INS	ENST00000398557.4	37	CCDS43374.1																																																																																			.		0.584	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		GAT	140953589	-	GAT	140953588	7	5	122	1	0	1	1	0	0	0	0	0	4529	1000	35	0	2041	0	DIAPH1	5	140953588	In_Frame_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08	211859	140953588	39961672	54	10601											
F12	2161	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176829362	176829363	+	Frame_Shift_Del	DEL	GC	GC	-																															gtgtagacgcctggcttgttGcggtcaccacagcccgatcc																								rs375101670		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:176829362_176829363delGC	ENST00000253496.3	-	14	1826_1827	c.1778_1779delGC	c.(1777-1779)cgcfs	p.R593fs	F12_ENST00000514943.1_5'Flank|PFN3_ENST00000358571.2_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	593	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CTGGCTTGTTGCGGTCACCACA	0.619									Hereditary Angioedema																												p.593_593del		.											.	F12-90	0			c.1778_1779del						.																																			SO:0001589	frameshift_variant	2161	exon14	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	.	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.1778_1779delGC	5.37:g.176829362_176829363delGC	ENSP00000253496:p.Arg593fs	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_000505	0	0	0	0	0	P78339	Frame_Shift_Del	DEL	ENST00000253496.3	37	CCDS34302.1																																																																																			.		0.619	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			-	176829363	GC	-	176829362	7	5	122	1	0	1	0	1	0	0	0	0	5352	1306	46	0	72	0	F12	5	176829362	Frame_Shift_Del	DEL	GC	TCGA-GL-7773-01A-11D-2136-08	35875774	176829362	4085898	55	10602											
FLT4	2324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	180030377	180030377	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcacagccacattctggcCaggtcctttacagctgccaa	9	9	9	14	0	2	0	1	0	1	0	3	0	3	0	4	3	4	1	4	3	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:180030377C>T	ENST00000261937.6	-	30	3985	c.3907G>A	c.(3907-3909)Ggc>Agc	p.G1303S		NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1303					blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACATTCTGGCCAGGTCCTTTA	0.617																																					p.G1303S	Colon(97;1075 1466 27033 27547 35871)	.											.	FLT4-1490	0			c.G3907A						.						24	26	25					5																	180030377		2203	4300	6503	SO:0001583	missense	2324	exon30			TCTGGCCAGGTCC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3907G>A	5.37:g.180030377C>T	ENSP00000261937:p.Gly1303Ser	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	47	17	NM_182925	0	0	0	0	0	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	C	9.313	1.056047	0.19907	.	.	ENSG00000037280	ENST00000261937	T	0.75050	-0.9	4.62	2.77	0.32553	.	.	.	.	.	T	0.50292	0.1607	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.42015	-0.9476	9	0.02654	T	1	.	1.1998	0.01882	0.2134:0.4115:0.2083:0.1668	.	1303	P35916	VGFR3_HUMAN	S	1303	ENSP00000261937:G1303S	ENSP00000261937:G1303S	G	-	1	0	FLT4	179962983	0.001000	0.12720	0.010000	0.14722	0.901000	0.52897	0.037000	0.13840	1.051000	0.40369	0.471000	0.43371	GGC	.		0.617	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			T	180030377	C	T	180030377	3	4	122	1	0	0	0	0	1	0	0	0	5963	594	21	2	188	2	FLT4	5	180030377	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	3201015	180030377	884883	56	10603											
CDKAL1	54901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	20548882	20548882	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggttgttctcataataatTcagatggagaatatatggct	12	14	11	4	0	2	2	2	0	1	2	3	3	2	2	0	4	0	3	0	4	5	7			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:20548882T>G	ENST00000378610.1	+	2	242	c.232T>G	c.(232-234)Tca>Gca	p.S78A	CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Missense_Mutation_p.S78A			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	78	MTTase N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00780}.				maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TCATAATAATTCAGATGGAGA	0.294																																					p.S78A		.											.	CDKAL1-92	0			c.T232G						.						80	85	83					6																	20548882		2203	4300	6503	SO:0001583	missense	54901	exon4			AATAATTCAGATG	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.232T>G	6.37:g.20548882T>G	ENSP00000367873:p.Ser78Ala	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	171	68	NM_017774	0	0	2	6	4	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	37	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.515717	0.85389	.	.	ENSG00000145996	ENST00000274695;ENST00000378610	T;T	0.43688	0.94;0.94	5.81	5.81	0.92471	Methylthiotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.49372	0.1553	L	0.52823	1.66	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.83275	0.951;0.996	T	0.39313	-0.9620	10	0.24483	T	0.36	.	16.1708	0.81812	0.0:0.0:0.0:1.0	.	78;78	Q5VV42;Q5VV42-3	CDKAL_HUMAN;.	A	78	ENSP00000274695:S78A;ENSP00000367873:S78A	ENSP00000274695:S78A	S	+	1	0	CDKAL1	20656861	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.400000	0.79949	2.225000	0.72522	0.533000	0.62120	TCA	.		0.294	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		G	20548882	T	G	20548882	3	3	122	1	0	0	0	0	1	0	0	0	3158	1783	62	5	238	5	CDKAL1	6	20548882	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		20548882	150566185	57	10604											
HLA-G	3135	ucsc.edu	37	chr6	29797253	29797253	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gactatgaggccaccctgagGtgctgggccctgggcttcta	6	9	14	12	0	1	2	0	2	1	0	1	3	1	2	3	4	1	2	3	4	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:29797253G>A	ENST00000360323.6	+	4	702	c.678G>A	c.(676-678)agG>agA	p.R226R	HLA-G_ENST00000376828.2_Silent_p.R231R|HLA-G_ENST00000376818.3_Silent_p.R134R|HLA-G_ENST00000428701.1_Silent_p.R226R|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	226	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)	p.R226S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CCACCCTGAGGTGCTGGGCCC	0.592																																					p.R226R													.	HLA-G-517	1	Substitution - Missense(1)	lung(1)	c.G678A						.						92	96	94					6																	29797253		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			CCTGAGGTGCTGG		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.678G>A	6.37:g.29797253G>A		Somatic	277	1		WXS	Illumina HiSeq		295	2	NM_002127	0	3	4889	4893	1		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			.		0.592	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		A	29797253	G	A	29797253	2	1	122	1	0	0	0	0	0	0	0	1	7233	1252	44	2		2	HLA-G	6	29797253	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	9248371	29797253	141317814	58	10605											
COL11A2	1302	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33156195	33156195	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatgatcactccatgggtgtCcaatactggacgagcacttc	10	10	10	11	1	1	1	1	1	0	0	4	4	3	2	2	2	2	1	2	2	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:33156195C>A	ENST00000374708.4	-	4	808	c.550G>T	c.(550-552)Gac>Tac	p.D184Y	COL11A2_ENST00000395194.1_Missense_Mutation_p.D184Y|COL11A2_ENST00000361917.1_Missense_Mutation_p.D184Y|COL11A2_ENST00000341947.2_Missense_Mutation_p.D184Y|COL11A2_ENST00000374713.1_Missense_Mutation_p.D184Y|COL11A2_ENST00000395197.1_Missense_Mutation_p.D184Y|COL11A2_ENST00000374714.1_Missense_Mutation_p.D184Y|COL11A2_ENST00000374712.1_Missense_Mutation_p.D184Y|COL11A2_ENST00000357486.1_Missense_Mutation_p.D184Y	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	184	Laminin G-like.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCATGGGTGTCCAATACTGGA	0.542																																					p.D184Y	Melanoma(1;90 116 3946 5341 17093)	.											.	COL11A2-95	0			c.G550T						.						116	122	120					6																	33156195		1511	2709	4220	SO:0001583	missense	1302	exon4			GGGTGTCCAATAC	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"Collagens"	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.550G>T	6.37:g.33156195C>A	ENSP00000363840:p.Asp184Tyr	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	140	54	NM_080681	0	0	1	1	0	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.551447	0.65311	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917;ENST00000457788;ENST00000395194	T;T;T;T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	3.72	3.72	0.42706	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.000000	0.64402	U	0.000001	D	0.85168	0.5635	M	0.81497	2.545	0.50313	D	0.999863	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.997;0.998	D	0.87424	0.2384	10	0.87932	D	0	.	13.3778	0.60750	0.0:1.0:0.0:0.0	.	184;184;184;184	Q7Z6C3;P13942-8;P13942-6;P13942	.;.;.;COBA2_HUMAN	Y	184	ENSP00000363840:D184Y;ENSP00000339915:D184Y;ENSP00000350079:D184Y;ENSP00000363846:D184Y;ENSP00000363845:D184Y;ENSP00000378623:D184Y;ENSP00000363844:D184Y;ENSP00000355123:D184Y;ENSP00000405520:D184Y;ENSP00000378620:D184Y	ENSP00000339915:D184Y	D	-	1	0	COL11A2	33264173	1.000000	0.71417	0.996000	0.52242	0.652000	0.38707	2.947000	0.49058	2.070000	0.61991	0.453000	0.30009	GAC	.		0.542	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			A	33156195	C	A	33156195	3	1	122	1	0	0	0	0	1	0	0	0	3674	855	30	4	4987	4	COL11A2	6	33156195	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	3358942	33156195	137958872	59	10606											
COL9A1	1297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	71003975	71003975	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagattcaatcctgttgcaGtcaacaaaaagagtagcact	17	9	7	8	0	2	2	2	0	0	2	3	2	3	2	1	0	3	4	1	0	6	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:71003975G>A	ENST00000357250.6	-	5	749	c.591C>T	c.(589-591)gaC>gaT	p.D197D	COL9A1_ENST00000370496.3_Silent_p.D197D	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	197	Laminin G-like.|Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						TCCTGTTGCAGTCAACAAAAA	0.433																																					p.D197D		.											.	COL9A1-94	0			c.C591T						.						128	124	125					6																	71003975		2203	4300	6503	SO:0001819	synonymous_variant	1297	exon5			GTTGCAGTCAACA		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.591C>T	6.37:g.71003975G>A		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	215	73	NM_001851	0	0	0	0	0	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Silent	SNP	ENST00000357250.6	37	CCDS4971.1																																																																																			.		0.433	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	71003975	G	A	71003975	2	1	122	1	0	0	0	0	0	0	0	1	3713	1020	36	2		2	COL9A1	6	71003975	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	37847780	71003975	100111092	60	10607											
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461790	82461790	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgccgccgaagtcgccgccTagggggatgtaggggctgca	6	5	17	13	5	0	0	0	0	0	0	1	2	0	1	5	4	1	3	5	4	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:82461790T>G	ENST00000320172.6	-	2	383	c.69A>C	c.(67-69)ctA>ctC	p.L23L	FAM46A_ENST00000369756.3_Silent_p.L104L|FAM46A_ENST00000369754.3_Silent_p.L42L	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	23					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		agtcgccgccTAGGGGGATGT	0.692																																					p.L23L		.											.	FAM46A-90	0			c.A69C						.						4	5	4					6																	82461790		1435	3404	4839	SO:0001819	synonymous_variant	55603	exon2			GCCGCCTAGGGGG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.69A>C	6.37:g.82461790T>G		Somatic	13	1		WXS	Illumina HiSeq	Phase_I	17	2	NM_017633	0	0	2	2	0	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	37	CCDS34489.1																																																																																			.		0.692	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			G	82461790	T	G	82461790	2	3	122	1	0	0	0	0	0	0	0	1	5584	1509	53	5		5	FAM46A	6	82461790	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	11457815	82461790	88653277	61	10608											
BACH2	60468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90660214	90660214	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcacagagagggaggctgcaGggtgagcccccgctcccgtc	7	5	15	14	2	1	2	1	1	0	1	3	4	2	3	3	3	2	3	3	3	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:90660214G>A	ENST00000257749.4	-	7	2318	c.1611C>T	c.(1609-1611)ccC>ccT	p.P537P	RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000343122.3_Silent_p.P537P|BACH2_ENST00000537989.1_Silent_p.P537P|RP3-512E2.2_ENST00000445838.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	537						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		GGAGGCTGCAGGGTGAGCCCC	0.612																																					p.P537P		.											.	BACH2-231	0			c.C1611T						.						69	68	68					6																	90660214		2203	4300	6503	SO:0001819	synonymous_variant	60468	exon7			GCTGCAGGGTGAG	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"BTB/POZ domain containing", "basic leucine zipper proteins"	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1611C>T	6.37:g.90660214G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	102	40	NM_021813	0	0	0	0	0	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			.		0.612	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90660214	G	A	90660214	2	1	122	1	0	0	0	0	0	0	0	1	1285	987	35	2		2	BACH2	6	90660214	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	8198424	90660214	80454853	62	10609											
PREP	5550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	105776878	105776878	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcataagaccaagaagtTggacctgacacaagctatcc	15	7	9	10	0	0	3	0	1	0	2	1	4	1	4	3	1	2	4	3	1	6	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:105776878T>A	ENST00000369110.3	-	9	1231	c.1039A>T	c.(1039-1041)Aac>Tac	p.N347Y		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	347					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	ACCAAGAAGTTGGACCTGACA	0.413																																					p.N347Y		.											.	PREP-93	0			c.A1039T						.						71	73	73					6																	105776878		2203	4300	6503	SO:0001583	missense	5550	exon9			AGAAGTTGGACCT		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1039A>T	6.37:g.105776878T>A	ENSP00000358106:p.Asn347Tyr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	91	35	NM_002726	0	0	8	18	10	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.627037	0.87560	.	.	ENSG00000085377	ENST00000369110	T	0.47528	0.84	5.48	5.48	0.80851	Peptidase S9A, oligopeptidase, N-terminal (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.123452	0.85682	D	0.000000	T	0.60143	0.2246	M	0.83223	2.63	0.58432	D	0.999996	D	0.54047	0.964	P	0.57009	0.811	T	0.67860	-0.5561	10	0.72032	D	0.01	-30.1871	15.8535	0.78956	0.0:0.0:0.0:1.0	.	347	P48147	PPCE_HUMAN	Y	347	ENSP00000358106:N347Y	ENSP00000358106:N347Y	N	-	1	0	PREP	105883571	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.655000	0.83696	2.207000	0.71202	0.459000	0.35465	AAC	.		0.413	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1			A	105776878	T	A	105776878	3	1	122	1	0	0	0	0	1	0	0	0	12503	1812	63	5	1121	5	PREP	6	105776878	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	15116664	105776878	65338189	63	10610											
CLIP2	7461	broad.mit.edu;bcgsc.ca	37	chr7	73790824	73790824	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcccaggaggagctggctgGgctgcagcggcactggcggg	5	4	21	11	2	0	0	0	0	0	0	0	2	0	2	1	8	3	5	1	8	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr7:73790824G>T	ENST00000395060.1	+	9	2093	c.2093G>T	c.(2092-2094)gGg>gTg	p.G698V	CLIP2_ENST00000223398.6_Missense_Mutation_p.G698V|CLIP2_ENST00000361545.5_Missense_Mutation_p.G663V			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	698						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						GAGCTGGCTGGGCTGCAGCGG	0.687																																					p.G698V													.	CLIP2-93	0			c.G2093T						.						18	23	21					7																	73790824		2200	4297	6497	SO:0001583	missense	7461	exon10			TGGCTGGGCTGCA	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.2093G>T	7.37:g.73790824G>T	ENSP00000378500:p.Gly698Val	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	19	8	NM_003388	0	0	15	32	17	O14527|O43611	Missense_Mutation	SNP	ENST00000395060.1	37	CCDS5569.1	.	.	.	.	.	.	.	.	.	.	G	8.562	0.878099	0.17395	.	.	ENSG00000106665	ENST00000539676;ENST00000223398;ENST00000361545;ENST00000395060	T;T;T	0.58506	0.33;0.33;0.33	5.05	0.538	0.17150	.	0.607950	0.18064	N	0.152849	T	0.35653	0.0939	N	0.24115	0.695	0.09310	N	0.999993	B;P;P	0.42409	0.047;0.779;0.501	B;B;B	0.38616	0.055;0.277;0.143	T	0.17501	-1.0367	10	0.27785	T	0.31	-40.8641	6.4364	0.21825	0.3109:0.1377:0.5514:0.0	.	663;663;698	A7E2F7;Q9UDT6-2;Q9UDT6	.;.;CLIP2_HUMAN	V	698;698;663;698	ENSP00000223398:G698V;ENSP00000355151:G663V;ENSP00000378500:G698V	ENSP00000223398:G698V	G	+	2	0	CLIP2	73428760	0.999000	0.42202	0.372000	0.25991	0.978000	0.69477	2.600000	0.46240	0.174000	0.19809	0.449000	0.29647	GGG	.		0.687	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		T	73790824	G	T	73790824	3	4	122	1	0	0	0	0	1	0	0	0	3539	1232	43	4	2127	4	CLIP2	7	73790824	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		73790824	85347839	64	10611											
SEMA3A	10371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	83631283	83631283	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactcacccgaaaaactgtCatttcttccagcagaacctc	12	9	5	15	1	3	1	2	0	1	1	5	2	4	1	3	0	3	2	3	0	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr7:83631283C>A	ENST00000265362.4	-	12	1754	c.1440G>T	c.(1438-1440)atG>atT	p.M480I	SEMA3A_ENST00000436949.1_Missense_Mutation_p.M480I	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	480	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						GAAAAACTGTCATTTCTTCCA	0.428																																					p.M480I		.											.	SEMA3A-156	0			c.G1440T						.						130	118	122					7																	83631283		2203	4300	6503	SO:0001583	missense	10371	exon12			AACTGTCATTTCT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1440G>T	7.37:g.83631283C>A	ENSP00000265362:p.Met480Ile	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	79	22	NM_006080	0	0	0	0	0		Missense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.665855	0.88251	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.09073	3.02;3.02	5.36	5.36	0.76844	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.09113	0.0225	N	0.10809	0.05	0.80722	D	1	P	0.42039	0.769	P	0.47162	0.54	T	0.46303	-0.9201	10	0.28530	T	0.3	.	19.4559	0.94889	0.0:1.0:0.0:0.0	.	480	Q14563	SEM3A_HUMAN	I	480	ENSP00000265362:M480I;ENSP00000415260:M480I	ENSP00000265362:M480I	M	-	3	0	SEMA3A	83469219	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.722000	0.84778	2.669000	0.90835	0.591000	0.81541	ATG	.		0.428	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83631283	C	A	83631283	3	1	122	1	0	0	0	0	1	0	0	0	14056	826	29	4	899	4	SEMA3A	7	83631283	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	9840459	83631283	75507380	65	10612											
SLC25A13	10165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	95818645	95818645	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttaaagggcagagttccCtcttccagaggagcaatccg	12	8	11	10	1	1	2	0	0	1	2	4	3	4	3	3	2	1	4	3	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr7:95818645C>T	ENST00000265631.5	-	9	1030	c.894G>A	c.(892-894)gaG>gaA	p.E298E	SLC25A13_ENST00000542654.1_Silent_p.E190E|SLC25A13_ENST00000416240.2_Silent_p.E298E			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	298					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	GCAGAGTTCCCTCTTCCAGAG	0.458																																					p.E298E		.											.	SLC25A13-515	0			c.G894A						.						93	91	91					7																	95818645		2203	4300	6503	SO:0001819	synonymous_variant	10165	exon9			AGTTCCCTCTTCC	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"Solute carriers", "EF-hand domain containing"	10983	protein-coding gene	gene with protein product	"mitochondrial aspartate glutamate carrier 2"	603859	"solute carrier family 25, member 13 (citrin)"	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.894G>A	7.37:g.95818645C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	54	23	NM_001160210	0	0	9	13	4	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	37	CCDS5645.1																																																																																			.		0.458	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		T	95818645	C	T	95818645	2	4	122	1	0	0	0	0	0	0	0	1	14507	680	24	2		2	SLC25A13	7	95818645	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	12187362	95818645	63320018	66	10613											
RP1L1	94137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	10466983	10466983	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcaggccccagcgtgctCggagctcagccaccgcactg	6	5	12	18	3	1	0	1	0	0	0	2	1	1	1	5	2	5	4	5	2	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr8:10466983C>A	ENST00000382483.3	-	4	4848	c.4625G>T	c.(4624-4626)cGa>cTa	p.R1542L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1622					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCAGCGTGCTCGGAGCTCAGC	0.647																																					p.R1542L		.											.	RP1L1-139	0			c.G4625T						.						22	26	25					8																	10466983		2119	4242	6361	SO:0001583	missense	94137	exon4			CGTGCTCGGAGCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4625G>T	8.37:g.10466983C>A	ENSP00000371923:p.Arg1542Leu	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_178857	0	0	0	0	0	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	9.421	1.083074	0.20309	.	.	ENSG00000183638	ENST00000382483	T	0.07327	3.2	5.32	-0.24	0.13047	.	0.320649	0.17484	U	0.172610	T	0.03959	0.0111	L	0.29908	0.895	0.09310	N	1	P	0.44309	0.832	B	0.31442	0.13	T	0.40365	-0.9567	10	0.66056	D	0.02	-2.2884	3.8382	0.08903	0.175:0.3157:0.0:0.5092	.	1542	A6NKC6	.	L	1542	ENSP00000371923:R1542L	ENSP00000371923:R1542L	R	-	2	0	RP1L1	10504393	0.988000	0.35896	0.001000	0.08648	0.017000	0.09413	2.285000	0.43487	0.252000	0.21531	0.491000	0.48974	CGA	.		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10466983	C	A	10466983	3	1	122	1	0	0	0	0	1	0	0	0	13565	884	31	4	2581	4	RP1L1	8	10466983	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		10466983	135897039	67	10614											
CA13	377677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	86180770	86180770	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcctgggactactggacaTatcctggttctcttacagtt	8	14	8	11	0	1	0	0	0	1	0	4	2	3	2	2	3	2	2	2	3	3	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr8:86180770T>G	ENST00000321764.3	+	6	885	c.583T>G	c.(583-585)Tat>Gat	p.Y195D	CA13_ENST00000517298.1_3'UTR	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	195					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|myelin sheath (GO:0043209)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)	7					Zonisamide(DB00909)	CTACTGGACATATCCTGGTTC	0.398																																					p.Y195D		.											.	CA13-90	0			c.T583G						.						180	163	169					8																	86180770		2203	4300	6503	SO:0001583	missense	377677	exon6			TGGACATATCCTG	BC052602	CCDS6236.1	8q21	2004-05-10				ENSG00000185015		"Carbonic anhydrases"	14914	protein-coding gene	gene with protein product		611436				14600151	Standard	NM_198584		Approved	CAXIII, FLJ37995, MGC59868	uc003ydg.2	Q8N1Q1		ENST00000321764.3:c.583T>G	8.37:g.86180770T>G	ENSP00000318912:p.Tyr195Asp	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	166	64	NM_198584	0	0	7	9	2		Missense_Mutation	SNP	ENST00000321764.3	37	CCDS6236.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582688	0.86748	.	.	ENSG00000185015	ENST00000321764	D	0.83914	-1.78	5.5	5.5	0.81552	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	H	0.99689	4.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97404	0.9998	10	0.87932	D	0	-19.1625	14.5856	0.68322	0.0:0.0:0.0:1.0	.	195	Q8N1Q1	CAH13_HUMAN	D	195	ENSP00000318912:Y195D	ENSP00000318912:Y195D	Y	+	1	0	CA13	86368022	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.311000	0.78958	2.104000	0.64026	0.383000	0.25322	TAT	.		0.398	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584		G	86180770	T	G	86180770	3	3	122	1	0	0	0	0	1	0	0	0	2520	1406	49	5	605	5	CA13	8	86180770	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	75713787	86180770	60183252	68	10615											
EFR3A	23167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	132982859	132982859	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaagacaatgatgagaaGattgtgcagaatgctatcat	16	10	9	6	0	1	5	1	2	0	4	2	6	2	5	1	0	2	2	1	0	5	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr8:132982859G>T	ENST00000254624.5	+	10	1353	c.1128G>T	c.(1126-1128)aaG>aaT	p.K376N	EFR3A_ENST00000334503.4_Missense_Mutation_p.K376N|EFR3A_ENST00000519656.1_Missense_Mutation_p.K340N	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	376						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATGATGAGAAGATTGTGCAGA	0.378																																					p.K376N		.											.	EFR3A-139	0			c.G1128T						.						124	124	124					8																	132982859		2203	4300	6503	SO:0001583	missense	23167	exon10			TGAGAAGATTGTG	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1128G>T	8.37:g.132982859G>T	ENSP00000254624:p.Lys376Asn	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	182	56	NM_015137	0	0	14	20	6	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	37	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592563	0.46214	.	.	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.67345	3.52;3.52;-0.26	5.56	4.68	0.58851	Armadillo-like helical (1);Armadillo-type fold (1);	0.045081	0.85682	D	0.000000	T	0.58764	0.2145	L	0.47190	1.495	0.38491	D	0.947988	B	0.28512	0.214	B	0.30782	0.12	T	0.59563	-0.7431	10	0.39692	T	0.17	-19.1717	10.108	0.42546	0.073:0.0:0.789:0.138	.	376	Q14156	EFR3A_HUMAN	N	376;376;376;340	ENSP00000254624:K376N;ENSP00000334769:K376N;ENSP00000428086:K340N	ENSP00000254624:K376N	K	+	3	2	EFR3A	133052041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.792000	0.47837	1.342000	0.45619	0.585000	0.79938	AAG	.		0.378	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		T	132982859	G	T	132982859	3	4	122	1	0	0	0	0	1	0	0	0	4969	933	33	4	1166	4	EFR3A	8	132982859	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	46802089	132982859	13381163	69	10616											
KIAA0020	9933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	2810352	2810352	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatagcctaccttctctcCcattttctttcatcttttta	6	21	1	13	0	5	0	2	0	3	0	7	0	6	0	3	0	2	0	3	0	3	10			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:2810352C>G	ENST00000397885.2	-	16	1921	c.1715G>C	c.(1714-1716)gGg>gCg	p.G572A		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	572						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		ACCTTCTCTCCCATTTTCTTT	0.393																																					p.G572A		.											.	KIAA0020-91	0			c.G1715C						.						225	188	201					9																	2810352		2203	4300	6503	SO:0001583	missense	9933	exon16			TCTCTCCCATTTT	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"penguin homolog (Drosophila)", "minor histocompatibility antigen HA-8"	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1715G>C	9.37:g.2810352C>G	ENSP00000380982:p.Gly572Ala	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	91	21	NM_014878	0	0	0	0	0	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731430	0.30684	.	.	ENSG00000080608	ENST00000397885	T	0.50548	0.74	5.95	5.05	0.67936	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.046170	0.85682	D	0.000000	T	0.48607	0.1509	M	0.73962	2.25	0.45528	D	0.998487	B;B	0.12013	0.005;0.001	B;B	0.15870	0.014;0.006	T	0.44682	-0.9312	10	0.21014	T	0.42	-18.5072	14.8914	0.70611	0.0:0.7295:0.2705:0.0	.	432;572	B2RDG4;Q15397	.;K0020_HUMAN	A	572	ENSP00000380982:G572A	ENSP00000380982:G572A	G	-	2	0	KIAA0020	2800352	1.000000	0.71417	0.326000	0.25389	0.569000	0.35902	2.906000	0.48735	1.521000	0.48983	0.650000	0.86243	GGG	.		0.393	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		G	2810352	C	G	2810352	3	3	122	1	0	0	0	0	1	0	0	0	8173	623	22	4	243	4	KIAA0020	9	2810352	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		2810352	138403079	70	10617											
PRSS3	5646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	33798069	33798069	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccggctggggcaacactcTgagctttggtggtgagtggg	5	10	17	9	1	1	2	0	2	1	0	2	2	2	2	1	6	2	3	1	6	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:33798069T>C	ENST00000361005.5	+	3	614	c.614T>C	c.(613-615)cTg>cCg	p.L205P	PRSS3_ENST00000429677.3_Missense_Mutation_p.L141P|PRSS3_ENST00000342836.4_Missense_Mutation_p.L162P|PRSS3_ENST00000379405.3_Missense_Mutation_p.L148P|RP11-133O22.6_ENST00000454429.2_RNA	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	205	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			GGCAACACTCTGAGCTTTGGT	0.572																																					p.L205P		.											.	PRSS3-90	0			c.T614C						.						130	111	117					9																	33798069		2203	4300	6503	SO:0001583	missense	5646	exon3			ACACTCTGAGCTT		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"Serine peptidases / Serine peptidases"	9486	protein-coding gene	gene with protein product	"mesotrypsin"	613578	"protease, serine, 4 (trypsin 4, brain)", "protease, serine, 3 (mesotrypsin)"	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.614T>C	9.37:g.33798069T>C	ENSP00000354280:p.Leu205Pro	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	174	52	NM_007343	0	0	0	0	0	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	37	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	T	10.01	1.233504	0.22626	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41;-2.41	3.61	-1.02	0.10135	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.210916	0.40908	D	0.000985	D	0.83248	0.5213	L	0.27053	0.805	0.58432	D	0.999996	P;P;P	0.52170	0.477;0.951;0.649	P;P;P	0.55785	0.589;0.784;0.485	T	0.76798	-0.2826	10	0.45353	T	0.12	.	2.3719	0.04332	0.3669:0.2296:0.0:0.4035	.	148;205;162	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	P	205;160;162;141;148	ENSP00000354280:L205P;ENSP00000401249:L160P;ENSP00000340889:L162P;ENSP00000401828:L141P;ENSP00000368715:L148P	ENSP00000340889:L162P	L	+	2	0	PRSS3	33788069	0.949000	0.32298	0.976000	0.42696	0.018000	0.09664	1.089000	0.30890	-0.026000	0.13895	-0.753000	0.03488	CTG	.		0.572	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		C	33798069	T	C	33798069	3	2	122	1	0	0	0	0	1	0	0	0	12651	1580	55	3	668	3	PRSS3	9	33798069	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	30987717	33798069	107415362	71	10618											
SEMA4D	10507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	92007357	92007357	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgttcagccaagggattgcAtattctgtcctcagaggact	9	11	10	11	1	3	1	2	0	1	1	4	3	4	3	3	2	2	2	3	2	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:92007357A>T	ENST00000450295.1	-	8	1379	c.603T>A	c.(601-603)taT>taA	p.Y201*	SEMA4D_ENST00000356444.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000339861.4_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000343780.4_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000422704.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000438547.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000420987.1_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000455551.2_Nonsense_Mutation_p.Y201*			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	201	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AAGGGATTGCATATTCTGTCC	0.488																																					p.Y201X		.											.	SEMA4D-92	0			c.T603A						.						125	112	117					9																	92007357		2203	4300	6503	SO:0001587	stop_gained	10507	exon10			GATTGCATATTCT	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.603T>A	9.37:g.92007357A>T	ENSP00000416523:p.Tyr201*	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	139	40	NM_006378	0	0	16	19	3	B2RPM6|Q7Z5S4|Q8N8B0	Nonsense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	G	38	6.945547	0.97956	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	.	.	.	5.92	-9.64	0.00541	.	0.057514	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	23.1558	0.99980	0.8226:0.0:0.1774:0.0	.	.	.	.	X	201	.	ENSP00000344923:Y201X	Y	-	3	2	SEMA4D	91197177	0.023000	0.18921	0.008000	0.14137	0.015000	0.08874	-0.722000	0.04958	-2.623000	0.00438	-1.874000	0.00550	TAT	.		0.488	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		T	92007357	A	T	92007357	4	4	122	1	0	0	0	0	0	1	0	0	14066	224	8	5	2591	5	SEMA4D	9	92007357	Nonsense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	58209288	92007357	49206074	72	10619											
STX17	55014	broad.mit.edu;bcgsc.ca	37	chr9	102730748	102730748	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagctggcagctctgcctgtGgcaggtgcactcatcggggg	6	8	16	11	1	2	0	1	0	1	0	3	0	2	0	1	5	4	5	1	5	1	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:102730748G>A	ENST00000259400.6	+	8	838	c.702G>A	c.(700-702)gtG>gtA	p.V234V	STX17_ENST00000525640.1_Silent_p.V234V|STX17_ENST00000525847.1_3'UTR|STX17_ENST00000534052.1_Silent_p.V234V	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	234	Necessary and sufficient for localization to autophagosome.				autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				CTCTGCCTGTGGCAGGTGCAC	0.488																																					p.V234V													.	STX17-153	0			c.G702A						.						26	30	29					9																	102730748		2175	4250	6425	SO:0001819	synonymous_variant	55014	exon8			GCCTGTGGCAGGT	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.702G>A	9.37:g.102730748G>A		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	62	5	NM_017919	0	0	15	16	1	Q4VXC2	Silent	SNP	ENST00000259400.6	37	CCDS6745.1																																																																																			.		0.488	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919		A	102730748	G	A	102730748	2	1	122	1	0	0	0	0	0	0	0	1	15372	1335	47	2		2	STX17	9	102730748	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	10723391	102730748	38482683	73	10620											
ABL1	25	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr9	133759486	133759486	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accaacttgttcagcgccttGatcaagaagaagaagaagac	16	7	9	9	1	2	6	2	1	0	5	2	6	2	6	2	0	2	1	2	0	6	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:133759486G>A	ENST00000318560.5	+	11	2190	c.1809G>A	c.(1807-1809)ttG>ttA	p.L603L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	603					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TCAGCGCCTTGATCAAGAAGA	0.602			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.L622L		.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1-3810	0			c.G1866A						.						80	91	87					9																	133759486		2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			CGCCTTGATCAAG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1809G>A	9.37:g.133759486G>A		Somatic	225	1		WXS	Illumina HiSeq	Phase_I	232	97	NM_007313	0	0	19	37	18	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.		0.602	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		A	133759486	G	A	133759486	2	1	122	1	0	0	0	0	0	0	0	1	92	1281	45	2		2	ABL1	9	133759486	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	31028738	133759486	7453945	74	10621											
NUP214	8021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134019822	134019822	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcccccactgtgttctccTttggttcttcatctttgaag	5	16	8	12	0	4	1	1	1	3	0	5	2	4	1	3	1	1	2	3	1	1	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:134019822T>A	ENST00000359428.5	+	12	1594	c.1450T>A	c.(1450-1452)Ttt>Att	p.F484I	RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.F484I|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.F484I			P35658	NU214_HUMAN	nucleoporin 214kDa	484	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TGTGTTCTCCTTTGGTTCTTC	0.582			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.F484I	Pancreas(4;24 48 25510 30394 32571)	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214-1131	0			c.T1450A						.						222	224	223					9																	134019822		2203	4300	6503	SO:0001583	missense	8021	exon12			TTCTCCTTTGGTT	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1450T>A	9.37:g.134019822T>A	ENSP00000352400:p.Phe484Ile	Somatic	413	0		WXS	Illumina HiSeq	Phase_I	479	161	NM_005085	0	0	4	9	5	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429164	0.83776	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899	T;T;T	0.79653	-1.29;-1.29;-1.29	5.79	5.79	0.91817	.	0.000000	0.42053	D	0.000772	T	0.72867	0.3514	N	0.08118	0	0.45554	D	0.998503	D;D	0.56287	0.975;0.975	P;P	0.51516	0.591;0.672	T	0.77928	-0.2404	10	0.52906	T	0.07	-18.8096	13.8602	0.63554	0.0:0.0:0.0:1.0	.	484;484	P35658-4;P35658	.;NU214_HUMAN	I	484;484;484;484;77	ENSP00000352400:F484I;ENSP00000396576:F484I;ENSP00000405014:F484I	ENSP00000352400:F484I	F	+	1	0	NUP214	133009643	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.193000	0.50997	2.201000	0.70794	0.533000	0.62120	TTT	.		0.582	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		A	134019822	T	A	134019822	3	1	122	1	0	0	0	0	1	0	0	0	10788	1609	56	5	1496	5	NUP214	9	134019822	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	260336	134019822	7193609	75	10622											
PFKFB3	5209	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr10	6258717	6258717	+	Missense_Mutation	SNP	C	C	A																															agaggagacacatgatccttCattttgccaaagaaaatgac																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:6258717C>A	ENST00000379775.4	+	5	745	c.415C>A	c.(415-417)Cat>Aat	p.H139N	PFKFB3_ENST00000317350.4_Missense_Mutation_p.H139N|PFKFB3_ENST00000379782.3_Missense_Mutation_p.H139N|PFKFB3_ENST00000540253.1_Missense_Mutation_p.H153N|PFKFB3_ENST00000379789.4_Missense_Mutation_p.H119N|PFKFB3_ENST00000360521.2_Missense_Mutation_p.H139N|PFKFB3_ENST00000536985.1_Missense_Mutation_p.H119N|PFKFB3_ENST00000379785.1_Missense_Mutation_p.H139N	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	139	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CATGATCCTTCATTTTGCCAA	0.463																																					p.H139N		.											.	PFKFB3-117	0			c.C415A						.						215	210	211					10																	6258717		2203	4300	6503	SO:0001583	missense	5209	exon5			ATCCTTCATTTTG		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.415C>A	10.37:g.6258717C>A	ENSP00000369100:p.His139Asn	Somatic	254	0		WXS	Illumina HiSeq	Phase_I	206	49	NM_004566	1	0	52	53	0	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	37	CCDS7078.1	.	.	.	.	.	.	.	.	.	.	C	5.826	0.336691	0.11013	.	.	ENSG00000170525	ENST00000536985;ENST00000379789;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.	.	.	5.71	1.54	0.23209	6-phosphofructo-2-kinase (1);	0.496023	0.24935	N	0.034432	T	0.06554	0.0168	N	0.00408	-1.53	0.20403	N	0.999904	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.40905	-0.9538	9	0.05620	T	0.96	-18.1641	9.3897	0.38365	0.3959:0.419:0.1851:0.0	.	153;139;139;119	B7Z955;Q16875-2;Q16875;Q5VX15	.;.;F263_HUMAN;.	N	119;119;153;139;139;139;139;139;139	.	ENSP00000369105:H139N	H	+	1	0	PFKFB3	6298723	0.021000	0.18746	0.983000	0.44433	0.868000	0.49771	0.284000	0.18864	0.716000	0.32124	0.591000	0.81541	CAT	.		0.463	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			A	6258717	C	A	6258717	3	1	122	1	0	0	0	0	1	0	0	0	11788	826	29	4	453	4	PFKFB3	10	6258717	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		6258717	129276030	76	10623	109	2									
PFKFB3	5209	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr10	6258718	6258719	+	Missense_Mutation	DNP	AT	AT	TA																															gaggagacacatgatccttcAttttgccaaagaaaatgact																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:6258718_6258719AT>TA	ENST00000379775.4	+	5	746_747	c.416_417AT>TA	c.(415-417)cAT>cTA	p.H139L	PFKFB3_ENST00000317350.4_Missense_Mutation_p.H139L|PFKFB3_ENST00000379782.3_Missense_Mutation_p.H139L|PFKFB3_ENST00000540253.1_Missense_Mutation_p.H153L|PFKFB3_ENST00000379789.4_Missense_Mutation_p.H119L|PFKFB3_ENST00000360521.2_Missense_Mutation_p.H139L|PFKFB3_ENST00000536985.1_Missense_Mutation_p.H119L|PFKFB3_ENST00000379785.1_Missense_Mutation_p.H139L	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	139	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						ATGATCCTTCATTTTGCCAAAG	0.47																																					p.H153L		.											.	PFKFB3	0			c.T417A						.																																			SO:0001583	missense	5209	exon5			CCTTCATTTTGCC		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	Exception_encountered	10.37:g.6258718_6258719delinsTA	ENSP00000369100:p.His139Leu	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	201	47		0	0	0	0	0	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	DNP	ENST00000379775.4	37	CCDS7078.1																																																																																			.		0.47	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			TA	6258719	AT	TA	6258718	3	4	122	1	0	0	0	0	1	0	0	0	11788	217	8	5	454	5	PFKFB3	10	6258718	Missense_Mutation	DNP	AT	TCGA-GL-7773-01A-11D-2136-08	1	6258718	129276029	77	10624	109	2									
PRPF18	8559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	13653627	13653627	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcaggcgcttggagagTccttagggaaaggcgatgat	9	11	14	7	2	2	2	1	1	1	1	3	5	3	3	1	4	0	1	1	4	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:13653627T>A	ENST00000378572.3	+	6	683	c.523T>A	c.(523-525)Tcc>Acc	p.S175T		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	175					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GCTTGGAGAGTCCTTAGGGAA	0.423																																					p.S175T		.											.	PRPF18-90	0			c.T523A						.						128	119	122					10																	13653627		2203	4300	6503	SO:0001583	missense	8559	exon6			GGAGAGTCCTTAG	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"PRP18 pre-mRNA processing factor 18 homolog (yeast)", "PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.523T>A	10.37:g.13653627T>A	ENSP00000367835:p.Ser175Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	105	39	NM_003675	0	0	0	0	0	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	37	CCDS7100.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.886622	0.33348	.	.	ENSG00000165630	ENST00000378572;ENST00000417658;ENST00000320054;ENST00000378544	.	.	.	5.59	5.59	0.84812	Prp18 (2);	0.105608	0.64402	D	0.000003	T	0.41419	0.1158	N	0.16478	0.41	0.45295	D	0.998291	B	0.06786	0.001	B	0.04013	0.001	T	0.28681	-1.0036	9	0.15499	T	0.54	-14.6828	15.7693	0.78152	0.0:0.0:0.0:1.0	.	175	Q99633	PRP18_HUMAN	T	175;169;160;169	.	ENSP00000367824:S160T	S	+	1	0	PRPF18	13693633	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.281000	0.58965	2.125000	0.65367	0.459000	0.35465	TCC	.		0.423	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			A	13653627	T	A	13653627	3	1	122	1	0	0	0	0	1	0	0	0	12592	1667	58	5	545	5	PRPF18	10	13653627	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	7394909	13653627	121881120	78	10625											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16941136	16941136	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaattctgaggccagtgAggggatctgattgtaccatt	11	11	13	6	0	2	3	0	3	2	0	2	5	2	5	2	4	1	1	2	4	3	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:16941136A>G	ENST00000377833.4	-	54	8522	c.8457T>C	c.(8455-8457)ccT>ccC	p.P2819P		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2819	CUB 21. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAGGCCAGTGAGGGGATCTGA	0.398																																					p.P2819P		.											.	CUBN-166	0			c.T8457C						.						129	121	124					10																	16941136		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon54			CCAGTGAGGGGAT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8457T>C	10.37:g.16941136A>G		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	103	44	NM_001081	0	0	1	1	0	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			.		0.398	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	16941136	A	G	16941136	2	3	122	1	0	0	0	0	0	0	0	1	4057	291	11	3		3	CUBN	10	16941136	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	3287509	16941136	118593611	79	10626											
FBXW4	6468	hgsc.bcm.edu	37	chr10	103454329	103454329	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgccagagcgcaggccccgcGgccgggcgggcagccgactc	5	1	17	18	7	0	1	0	0	0	1	1	2	0	1	5	4	2	2	5	4	0	0	rs61761937	byFrequency	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:103454329G>C	ENST00000331272.7	-	1	687	c.69C>G	c.(67-69)gcC>gcG	p.A23A		NM_022039.3	NP_071322.1	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4	23					cartilage development (GO:0051216)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|positive regulation of mesenchymal cell proliferation (GO:0002053)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	ubiquitin ligase complex (GO:0000151)				breast(3)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	15		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		CAGGCCCCGCGGCCGGGCGGG	0.766													G|||	214	0.0427316	0.0182	0.0648	5008	,	,		9341	0.0853		0.0388	False		,,,				2504	0.0204				p.A23A		.											.	FBXW4-226	0			c.C69G						.						2	2	2					10																	103454329		1212	2761	3973	SO:0001819	synonymous_variant	6468	exon1			CCCCGCGGCCGGG	AF281859	CCDS31271.1	10q24	2013-01-09	2007-02-08	2005-03-12	ENSG00000107829	ENSG00000107829		"F-boxes / WD-40 domains", "WD repeat domain containing"	10847	protein-coding gene	gene with protein product		608071	"split hand/foot malformation (ectrodactyly) type 3", "F-box and WD-40 domain protein 4"	SHFM3		8723077, 7912888	Standard	XM_005270053		Approved	Fbw4, dactylin	uc001kto.3	P57775	OTTHUMG00000018938	ENST00000331272.7:c.69C>G	10.37:g.103454329G>C		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_022039	0	0	14	21	7	Q5SVS1|Q96IM6	Silent	SNP	ENST00000331272.7	37	CCDS31271.1																																																																																			G|0.945;C|0.055		0.766	FBXW4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049979.2	NM_022039		C	103454329	G	C	103454329	2	2	122	1	0	0	0	0	0	0	0	1	5786	1103	39	4		4	FBXW4	10	103454329	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	86513193	103454329	32080418	80	10627											
NRAP	4892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115365937	115365938	+	Splice_Site	DNP	GT	GT	TA																															taagtaacaaaagggcttacGtcactcaggttggctgcatt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:115365937_115365938GT>TA	ENST00000359988.3	-	33	4050_4051	c.3806_3807AC>TA	c.(3805-3807)gAC>gTA	p.D1269V	NRAP_ENST00000360478.3_Splice_Site_p.D1234V|NRAP_ENST00000369360.3_Splice_Site_p.D1242V|NRAP_ENST00000369358.4_Splice_Site_p.D1277V	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AAGGGCTTACGTCACTCAGGTT	0.475																																					p.D1277V		.											.	NRAP	0			c.A3806T						.																																			SO:0001630	splice_region_variant	4892	exon33			CTTACGTCACTCA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3806_3807delinsTA	10.37:g.115365937_115365938delinsTA		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	84	24		0	0	0	0	0		Missense_Mutation	DNP	ENST00000359988.3	37	CCDS7579.1																																																																																			.		0.475	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	Missense_Mutation	TA	115365938	GT	TA	115365937	5	4	122	1	0	0	0	0	0	0	1	0	10664	1159	40	4	1425	4	NRAP	10	115365937	Splice_Site	DNP	GT	TCGA-GL-7773-01A-11D-2136-08	11911608	115365937	20168810	81	10628	110	2									
NRAP	4892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	115365939	115365939	+	Missense_Mutation	SNP	C	C	A																															agtaacaaaagggcttacgtCactcaggttggctgcattcg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:115365939C>A	ENST00000359988.3	-	33	4049	c.3805G>T	c.(3805-3807)Gac>Tac	p.D1269Y	NRAP_ENST00000360478.3_Missense_Mutation_p.D1234Y|NRAP_ENST00000369360.3_Missense_Mutation_p.D1242Y|NRAP_ENST00000369358.4_Missense_Mutation_p.D1277Y	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GGGCTTACGTCACTCAGGTTG	0.473																																					p.D1269Y		.											.	NRAP-522	0			c.G3805T						.						166	157	160					10																	115365939		2203	4300	6503	SO:0001583	missense	4892	exon33			TTACGTCACTCAG		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3805G>T	10.37:g.115365939C>A	ENSP00000353078:p.Asp1269Tyr	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	84	25	NM_001261463	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412753	0.62511	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.64	5.64	0.86602	.	0.155393	0.56097	D	0.000026	T	0.77698	0.4169	M	0.80183	2.485	0.41367	D	0.987468	P;P;P	0.52061	0.95;0.938;0.95	D;D;D	0.67900	0.954;0.923;0.954	T	0.80344	-0.1422	10	0.87932	D	0	.	17.896	0.88888	0.0:1.0:0.0:0.0	.	1269;1234;1269	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	Y	1277;1242;1269;1234	ENSP00000358365:D1277Y;ENSP00000358367:D1242Y;ENSP00000353078:D1269Y;ENSP00000353666:D1234Y	ENSP00000353078:D1269Y	D	-	1	0	NRAP	115355929	1.000000	0.71417	0.998000	0.56505	0.764000	0.43329	2.427000	0.44740	2.664000	0.90586	0.655000	0.94253	GAC	.		0.473	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		A	115365939	C	A	115365939	3	1	122	1	0	0	0	0	1	0	0	0	10664	826	29	4	1427	4	NRAP	10	115365939	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2	115365939	20168808	82	10629	110	2									
KRTAP5-4	387267	bcgsc.ca	37	chr11	1643279	1643279	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacagccggagccacagccCccacagccggagccacagcc	10	0	10	21	2	0	0	0	0	0	0	0	2	0	2	8	2	6	0	8	2	0	0	rs551852315	byFrequency	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:1643279C>T	ENST00000399682.1	-	1	89	c.45G>A	c.(43-45)ggG>ggA	p.G15G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		agccacagcccccacagccgg	0.682																																					p.G15G													.	.	0			c.G45A						.																																			SO:0001819	synonymous_variant	387267	exon1			ACAGCCCCCACAG	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"Keratin associated proteins"	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.45G>A	11.37:g.1643279C>T		Somatic	245	2		WXS	Illumina HiSeq	Phase_1	264	12	NM_001012709	0	0	2	2	0		Silent	SNP	ENST00000399682.1	37																																																																																				.		0.682	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		T	1643279	C	T	1643279	2	4	122	1	0	0	0	0	0	0	0	1	8584	610	22	2		2	KRTAP5-4	11	1643279	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08		1643279	133363237	83	10630											
MPEG1	219972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	58978386	58978386	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagcccctcctgacagAccaccaccatccccatggat	9	6	7	19	0	0	2	0	1	0	1	2	3	2	3	8	1	2	2	8	1	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:58978386A>T	ENST00000361050.3	-	1	2038	c.1953T>A	c.(1951-1953)ggT>ggA	p.G651G		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	651						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				CTCCTGACAGACCACCACCAT	0.577																																					p.G651G		.											.	MPEG1-70	0			c.T1953A						.						100	108	105					11																	58978386		2014	4161	6175	SO:0001819	synonymous_variant	219972	exon1			TGACAGACCACCA	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1953T>A	11.37:g.58978386A>T		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	180	58	NM_001039396	0	0	3	3	0	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.		0.577	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58978386	A	T	58978386	2	4	122	1	0	0	0	0	0	0	0	1	9748	262	10	5		5	MPEG1	11	58978386	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	57335107	58978386	76028130	84	10631											
FLRT1	28992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63885635	63885635	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgtaccgcgccaaagaagaGtacgtggtccacactatctt	11	8	9	13	4	1	2	0	0	1	2	2	2	2	2	4	1	2	2	4	1	5	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:63885635G>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.E632E	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						CCAAAGAAGAGTACGTGGTCC	0.607																																					p.E632E		.											.	FLRT1-90	0			c.G1896A						.						79	69	72					11																	63885635		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AGAAGAGTACGTG	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33075C>T	11.37:g.63885635G>A		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	139	58	NM_013280	0	0	0	0	0	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			.		0.607	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63885635	G	A	63885635	1	1	122	0	1	0	0	0	0	0	0	0	5957	1020	36	2		2	FLRT1	11	63885635	Intron	SNP	G	TCGA-GL-7773-01A-11D-2136-08	4907249	63885635	71120881	85	10632											
PC	5091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66617172	66617172	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcagtgaagtccttgaaGtgggcaaacacatcggggta	11	8	15	7	1	0	2	0	2	0	0	2	2	1	2	1	4	1	3	1	4	4	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:66617172G>C	ENST00000393958.2	-	20	3150	c.3057C>G	c.(3055-3057)caC>caG	p.H1019Q	PC_ENST00000528224.1_5'UTR|PC_ENST00000393955.2_Missense_Mutation_p.H1019Q|PC_ENST00000529047.1_Missense_Mutation_p.H139Q|PC_ENST00000393960.1_Missense_Mutation_p.H1019Q	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1019					biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	AGTCCTTGAAGTGGGCAAACA	0.577																																					p.H1019Q		.											.	PC-228	0			c.C3057G						.						107	86	93					11																	66617172		2200	4295	6495	SO:0001583	missense	5091	exon20			CTTGAAGTGGGCA	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.3057C>G	11.37:g.66617172G>C	ENSP00000377530:p.His1019Gln	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	97	26	NM_000920	0	0	16	34	18	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427583	0.25726	.	.	ENSG00000173599	ENST00000529047;ENST00000393955;ENST00000393958;ENST00000393960	D;D;D;D	0.95377	-1.52;-3.69;-3.69;-3.69	4.89	-4.28	0.03732	Carboxylase, conserved domain (1);	0.231260	0.33515	N	0.004840	T	0.79505	0.4457	N	0.00859	-1.14	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.59568	-0.7430	10	0.34782	T	0.22	-8.0574	7.3499	0.26684	0.0864:0.6092:0.163:0.1415	.	1019	P11498	PYC_HUMAN	Q	139;1019;1019;1019	ENSP00000435905:H139Q;ENSP00000377527:H1019Q;ENSP00000377530:H1019Q;ENSP00000377532:H1019Q	ENSP00000377527:H1019Q	H	-	3	2	PC	66373748	0.988000	0.35896	0.454000	0.27019	0.803000	0.45373	0.243000	0.18106	-0.607000	0.05738	0.462000	0.41574	CAC	.		0.577	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		C	66617172	G	C	66617172	3	2	122	1	0	0	0	0	1	0	0	0	11523	1020	36	4	491	4	PC	11	66617172	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	2731537	66617172	68389344	86	10633											
FUT4	2526	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	94278647	94278649	+	In_Frame_Del	DEL	TTT	TTT	-																															accgtgccaactacgagcgcTttgtgccccgcggcgccttc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:94278647_94278649delTTT	ENST00000358752.2	+	1	1631_1633	c.1348_1350delTTT	c.(1348-1350)tttdel	p.F450del	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_002033.3	NP_002024.1	P22083	FUT4_HUMAN	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific)	450					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	cell periphery (GO:0071944)|cell surface (GO:0009986)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(2)|endometrium(2)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTACGAGCGCTTTGTGCCCCGCG	0.655																																					p.450_450del		.											.	FUT4-91	0			c.1348_1350del						.																																			SO:0001651	inframe_deletion	2526	exon1			.		CCDS8301.1	11q21	2013-02-26			ENSG00000196371	ENSG00000196371		"CD molecules", "Fucosyltransferases"	4015	protein-coding gene	gene with protein product	"ELAM ligand fucosyltransferase", "galactoside 3-L-fucosyltransferase"	104230		CD15, FCT3A, ELFT		1702034	Standard	NM_002033		Approved	FUC-TIV	uc001pez.3	P22083	OTTHUMG00000167795	ENST00000358752.2:c.1348_1350delTTT	11.37:g.94278647_94278649delTTT	ENSP00000351602:p.Phe450del	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	73	25	NM_002033	0	0	0	0	0	B2RMS0	In_Frame_Del	DEL	ENST00000358752.2	37	CCDS8301.1																																																																																			.		0.655	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033		-	94278649	TTT	-	94278647	7	5	122	1	0	1	0	1	0	0	0	0	6125	1609	56	0	1350	0	FUT4	11	94278647	In_Frame_Del	DEL	TTT	TCGA-GL-7773-01A-11D-2136-08	27661475	94278647	40727869	87	10634											
DRD2	1813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113288847	113288847	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaatcctgctgaatttccaCtcacctaccacctggggaca	10	10	7	14	0	1	2	1	2	0	0	3	3	3	3	5	2	2	1	5	2	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:113288847C>T	ENST00000362072.3	-	3	641	c.297G>A	c.(295-297)gaG>gaA	p.E99E	DRD2_ENST00000544518.1_Silent_p.E98E|DRD2_ENST00000346454.3_Silent_p.E99E|DRD2_ENST00000535984.1_5'UTR|DRD2_ENST00000542968.1_Silent_p.E99E|DRD2_ENST00000355319.2_Silent_p.E99E|DRD2_ENST00000538967.1_Silent_p.E99E	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	99					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TGAATTTCCACTCACCTACCA	0.532																																					p.E99E		.											.	DRD2-92	0			c.G297A						.						171	121	138					11																	113288847		2201	4296	6497	SO:0001819	synonymous_variant	1813	exon3			TTTCCACTCACCT	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.297G>A	11.37:g.113288847C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	65	18	NM_016574	0	0	0	0	0	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	37	CCDS8361.1																																																																																			.		0.532	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		T	113288847	C	T	113288847	2	4	122	1	0	0	0	0	0	0	0	1	4768	564	20	2		2	DRD2	11	113288847	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	19010200	113288847	21717669	88	10635											
HINFP	25988	broad.mit.edu;bcgsc.ca	37	chr11	119001504	119001504	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttctgctgacctcatccGccatgtctacttccactgct	6	13	6	16	1	3	1	1	1	2	0	5	1	5	1	4	0	3	3	4	0	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:119001504G>T	ENST00000350777.2	+	3	314	c.251G>T	c.(250-252)cGc>cTc	p.R84L	HINFP_ENST00000527354.1_3'UTR|HINFP_ENST00000527410.1_Missense_Mutation_p.R84L	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	84					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GACCTCATCCGCCATGTCTAC	0.532																																					p.R84L													.	HINFP-320	0			c.G251T						.						140	126	131					11																	119001504		2200	4295	6495	SO:0001583	missense	25988	exon4			TCATCCGCCATGT	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"Zinc fingers, C2H2-type"	17850	protein-coding gene	gene with protein product	"histone nuclear factor P"	607099	"MBD2-interacting zinc finger 1", "MBD2-interacting zinc finger"	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.251G>T	11.37:g.119001504G>T	ENSP00000318085:p.Arg84Leu	Somatic	194	2		WXS	Illumina HiSeq	Phase_I	242	17	NM_015517	0	0	7	10	3	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	37	CCDS8414.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500731	0.85176	.	.	ENSG00000172273	ENST00000350777;ENST00000529988;ENST00000527410;ENST00000532312	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.93	5.93	0.95920	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.64216	0.2578	M	0.66506	2.035	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.979;0.995	T	0.54984	-0.8211	10	0.25751	T	0.34	-38.4882	20.3539	0.98825	0.0:0.0:1.0:0.0	.	84;84	B4DTN3;Q9BQA5	.;HINFP_HUMAN	L	84	ENSP00000318085:R84L;ENSP00000431468:R84L;ENSP00000436815:R84L;ENSP00000434574:R84L	ENSP00000318085:R84L	R	+	2	0	HINFP	118506714	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.444000	0.97578	2.826000	0.97356	0.655000	0.94253	CGC	.		0.532	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517		T	119001504	G	T	119001504	3	4	122	1	0	0	0	0	1	0	0	0	7131	1087	38	4	257	4	HINFP	11	119001504	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	5712657	119001504	16005012	89	10636											
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	133816079	133816079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgtcactgggtggatcaCgtcgcatcgcaggaccacgc	7	7	12	15	5	2	0	2	0	0	0	5	2	3	2	2	3	0	2	2	3	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:133816079C>T	ENST00000321016.8	-	2	369	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	IGSF9B_ENST00000533871.2_Missense_Mutation_p.V47M			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	47	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGGTGGATCACGTCGCATCGC	0.627																																					p.V47M		.											.	IGSF9B-68	0			c.G139A						.						50	57	54					11																	133816079		2145	4233	6378	SO:0001583	missense	22997	exon2			GGATCACGTCGCA	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.139G>A	11.37:g.133816079C>T	ENSP00000317980:p.Val47Met	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_014987	0	0	0	0	0	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	C	32	5.124674	0.94429	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.41	5.41	0.78517	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000025	T	0.82144	0.4973	M	0.75884	2.315	0.58432	D	0.999999	D	0.89917	1.0	D	0.74023	0.982	D	0.84066	0.0377	10	0.87932	D	0	.	18.8177	0.92084	0.0:1.0:0.0:0.0	.	47	Q9UPX0	TUTLB_HUMAN	M	47;47;37;94	ENSP00000317980:V47M;ENSP00000436576:V47M;ENSP00000434026:V37M;ENSP00000435989:V94M	ENSP00000317980:V47M	V	-	1	0	IGSF9B	133321289	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.684000	0.84104	2.544000	0.85801	0.655000	0.94253	GTG	.		0.627	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133816079	C	T	133816079	3	4	122	1	0	0	0	0	1	0	0	0	7627	536	19	1	3982	1	IGSF9B	11	133816079	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	14814575	133816079	1190437	90	10637											
CLEC1B	51266	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	10145838	10145838	+	Frame_Shift_Del	DEL	A	A	-																															gggtgcattttcccattatgAaaataagcacaattcatatt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:10145838delA	ENST00000298527.6	-	6	773	c.594delT	c.(592-594)tttfs	p.F198fs	CLEC1B_ENST00000428126.2_Frame_Shift_Del_p.F165fs|CLEC1B_ENST00000348658.4_Frame_Shift_Del_p.F165fs	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	198	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						TCCCATTATGAAAATAAGCAC	0.373																																					p.F198fs		.											.	CLEC1B-90	0			c.594delT						.						136	123	127					12																	10145838		1852	4085	5937	SO:0001589	frameshift_variant	51266	exon6			.	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.594delT	12.37:g.10145838delA	ENSP00000298527:p.Phe198fs	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	191	72	NM_016509	0	0	0	0	0	Q6UWX7|Q8NHR6	Frame_Shift_Del	DEL	ENST00000298527.6	37	CCDS41752.1																																																																																			.		0.373	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		-	10145838	A	-	10145838	7	5	122	1	0	1	0	1	0	0	0	0	3512	243	9	0	99	0	CLEC1B	12	10145838	Frame_Shift_Del	DEL	A	TCGA-GL-7773-01A-11D-2136-08		10145838	123706057	91	10638											
KLRK1	22914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	10541382	10541382	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaacataccccagctgtgtcGagacctccgaccacgaatcc	12	6	7	16	3	0	1	0	0	0	1	3	4	2	1	6	0	3	1	6	0	3	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:10541382G>A	ENST00000240618.6	-	2	168	c.28C>T	c.(28-30)Cga>Tga	p.R10*	RP11-277P12.20_ENST00000500682.1_RNA|KLRC4-KLRK1_ENST00000539300.1_3'UTR|KLRK1_ENST00000540818.1_Nonsense_Mutation_p.R10*	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	10					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						CAGCTGTGTCGAGACCTCCGA	0.388																																					p.R10X		.											.	.	0			c.C28T						.						101	92	95					12																	10541382		2203	4300	6503	SO:0001587	stop_gained	0	exon7			TGTGTCGAGACCT	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.28C>T	12.37:g.10541382G>A	ENSP00000240618:p.Arg10*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	111	47	NM_001199805	0	0	0	0	0	A8K7K5|A8K7P4|Q9NR41	Nonsense_Mutation	SNP	ENST00000240618.6	37	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601701	0.87055	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	.	.	.	3.92	2.04	0.26737	.	1.508560	0.03947	N	0.287889	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	4.7229	0.12927	0.1127:0.0:0.657:0.2303	.	.	.	.	X	10	.	ENSP00000240618:R10X	R	-	1	2	KLRK1	10432649	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.084000	0.11268	0.589000	0.29677	0.637000	0.83480	CGA	.		0.388	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		A	10541382	G	A	10541382	4	1	122	1	0	0	0	0	0	1	0	0	8444	1066	37	1	650	1	KLRK1	12	10541382	Nonsense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	395544	10541382	123310513	92	10639											
PRB3	5544	broad.mit.edu	37	chr12	11420475	11420475	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacgaggtgggggaccttgAggtttgttgcctccttgtgg	4	12	18	7	1	0	1	0	1	0	0	1	4	1	3	3	6	1	2	3	6	0	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:11420475A>G	ENST00000279573.7	-	3	843	c.708T>C	c.(706-708)ccT>ccC	p.P236P	PRB3_ENST00000440870.3_Intron|PRB3_ENST00000538488.1_Intron|PRB3_ENST00000381842.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	165	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			GGGGACCTTGAGGTTTGTTGC	0.617																																					p.P236P													.	PRB3-1	0			c.T708C						.						10	4	6					12																	11420475		655	1159	1814	SO:0001819	synonymous_variant	5544	exon3			ACCTTGAGGTTTG			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.708T>C	12.37:g.11420475A>G		Somatic	11	0		WXS	Illumina HiSeq	Phase_I	20	4	NM_006249	0	0	0	0	0	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Silent	SNP	ENST00000279573.7	37																																																																																				.		0.617	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249		G	11420475	A	G	11420475	2	3	122	1	0	0	0	0	0	0	0	1	12473	291	11	3		3	PRB3	12	11420475	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	879093	11420475	122431420	93	10640											
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12318144	12318144	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccagtcagtccagtaaacaTagtcacccaacaaagtaaat	17	7	6	11	0	2	0	2	0	0	0	3	0	3	0	3	0	2	2	3	0	7	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:12318144T>A	ENST00000261349.4	-	8	1707	c.1631A>T	c.(1630-1632)tAt>tTt	p.Y544F	LRP6_ENST00000543091.1_Missense_Mutation_p.Y544F	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	544	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CCAGTAAACATAGTCACCCAA	0.433																																					p.Y544F		.											.	LRP6-661	0			c.A1631T						.						149	150	150					12																	12318144		2203	4300	6503	SO:0001583	missense	4040	exon8			TAAACATAGTCAC	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1631A>T	12.37:g.12318144T>A	ENSP00000261349:p.Tyr544Phe	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	215	83	NM_002336	0	0	2	6	4	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	9.879	1.200963	0.22121	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91295	-2.82;-2.82	4.98	3.81	0.43845	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.56097	D	0.000032	T	0.81767	0.4892	N	0.21583	0.68	0.51767	D	0.999935	B;B	0.06786	0.001;0.001	B;B	0.10450	0.001;0.005	T	0.71820	-0.4477	10	0.11794	T	0.64	.	11.3882	0.49798	0.1355:0.0:0.0:0.8645	.	544;544	F5H7J9;O75581	.;LRP6_HUMAN	F	544	ENSP00000261349:Y544F;ENSP00000442472:Y544F	ENSP00000261349:Y544F	Y	-	2	0	LRP6	12209411	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	1.571000	0.36450	0.834000	0.34852	0.377000	0.23210	TAT	.		0.433	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12318144	T	A	12318144	3	1	122	1	0	0	0	0	1	0	0	0	8987	1406	49	5	3274	5	LRP6	12	12318144	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	897669	12318144	121533751	94	10641											
FAR2	55711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	29469910	29469910	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcccctgccattatctaTgactgctatctgcggctcac	6	11	9	15	2	3	1	1	1	2	0	3	1	3	1	3	2	3	2	3	2	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:29469910T>A	ENST00000536681.3	+	9	1338	c.1092T>A	c.(1090-1092)taT>taA	p.Y364*	FAR2_ENST00000547116.1_Nonsense_Mutation_p.Y267*|FAR2_ENST00000182377.4_Nonsense_Mutation_p.Y364*|RP11-996F15.2_ENST00000553105.1_RNA	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	364					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						CCATTATCTATGACTGCTATC	0.502																																					p.Y364X		.											.	FAR2-90	0			c.T1092A						.						133	136	135					12																	29469910		2203	4300	6503	SO:0001587	stop_gained	55711	exon9			TATCTATGACTGC	AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	25531	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 2"		"male sterility domain containing 1"	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.1092T>A	12.37:g.29469910T>A	ENSP00000443291:p.Tyr364*	Somatic	325	0		WXS	Illumina HiSeq	Phase_I	358	142	NM_018099	0	0	1	1	0	F8VV73|Q9H0D5|Q9NVW8	Nonsense_Mutation	SNP	ENST00000536681.3	37	CCDS8717.1	.	.	.	.	.	.	.	.	.	.	T	38	7.075542	0.98048	.	.	ENSG00000064763	ENST00000536681;ENST00000182377;ENST00000547116	.	.	.	4.44	-3.57	0.04612	.	0.075218	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-5.8079	11.3024	0.49314	0.0:0.5138:0.0:0.4862	.	.	.	.	X	364;364;267	.	ENSP00000182377:Y364X	Y	+	3	2	FAR2	29361177	0.039000	0.19947	0.980000	0.43619	0.940000	0.58332	-0.830000	0.04410	-0.596000	0.05821	0.383000	0.25322	TAT	.		0.502	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099		A	29469910	T	A	29469910	4	1	122	1	0	0	0	0	0	1	0	0	5694	1471	51	5	1122	5	FAR2	12	29469910	Nonsense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	17151766	29469910	104381985	95	10642											
LRRK2	120892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	40758851	40758851	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcatgatgacagcacagctAggcaagtttctttcctttag	10	13	9	9	0	2	2	1	2	1	0	3	2	3	2	1	1	2	4	1	1	3	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:40758851A>G	ENST00000298910.7	+	49	7447	c.7389A>G	c.(7387-7389)ctA>ctG	p.L2463L		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2463					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CAGCACAGCTAGGCAAGTTTC	0.343																																					p.L2463L		.											.	LRRK2-533	0			c.A7389G						.						66	63	64					12																	40758851		2203	4298	6501	SO:0001630	splice_region_variant	120892	exon49			ACAGCTAGGCAAG	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.7390+1A>G	12.37:g.40758851A>G		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	96	34	NM_198578	0	0	6	19	13	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			.		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Silent	G	40758851	A	G	40758851	5	3	122	1	0	0	0	0	0	0	1	0	9058	434	15	3	7583	3	LRRK2	12	40758851	Splice_Site	SNP	A	TCGA-GL-7773-01A-11D-2136-08	11288941	40758851	93093044	96	10643											
ANO6	196527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	45803213	45803213	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	taaccccacgatgggaacagGactaccatctgcagcctatg	12	7	9	13	1	1	0	0	0	1	0	1	3	1	2	4	2	5	1	4	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:45803213G>T	ENST00000320560.8	+	16	2156	c.1954G>T	c.(1954-1956)Gac>Tac	p.D652Y	ANO6_ENST00000441606.2_Missense_Mutation_p.D634Y|ANO6_ENST00000423947.3_Missense_Mutation_p.D673Y|ANO6_ENST00000425752.2_Missense_Mutation_p.D652Y|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000435642.1_Missense_Mutation_p.D652Y	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	652					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ATGGGAACAGGACTACCATCT	0.353																																					p.D673Y		.											.	ANO6-516	0			c.G2017T						.						124	124	124					12																	45803213		2203	4300	6503	SO:0001583	missense	196527	exon17			GAACAGGACTACC	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.1954G>T	12.37:g.45803213G>T	ENSP00000320087:p.Asp652Tyr	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	168	58	NM_001204803	0	0	15	43	28	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	37	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.754633	0.89843	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83991	0.5374	M	0.91872	3.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;0.999;1.0;0.995	D	0.87659	0.2533	10	0.87932	D	0	.	19.0047	0.92846	0.0:0.0:1.0:0.0	.	634;673;652;652	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	Y	652;673;652;652;634	ENSP00000391417:D652Y;ENSP00000409126:D673Y;ENSP00000413840:D652Y;ENSP00000320087:D652Y;ENSP00000413137:D634Y	ENSP00000320087:D652Y	D	+	1	0	ANO6	44089480	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.813000	0.99286	2.652000	0.90054	0.655000	0.94253	GAC	.		0.353	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		T	45803213	G	T	45803213	3	4	122	1	0	0	0	0	1	0	0	0	701	1174	41	4	2036	4	ANO6	12	45803213	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	5044362	45803213	88048682	97	10644											
KRT4	3851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53203234	53203234	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccttggcctccaactccAccttgttcaggtaggcagca	8	9	8	16	0	1	0	1	0	0	0	3	0	3	0	6	3	2	4	6	3	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:53203234A>T	ENST00000551956.1	-	4	1259	c.767T>A	c.(766-768)gTg>gAg	p.V256E	KRT4_ENST00000458244.2_Missense_Mutation_p.V236E|KRT4_ENST00000293774.4_Missense_Mutation_p.V330E			P19013	K2C4_HUMAN	keratin 4	270	Coil 1B.|Rod.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CTCCAACTCCACCTTGTTCAG	0.537																																					p.V256E	Pancreas(190;284 2995 41444 45903)	.											.	KRT4-96	0			c.T767A						.						110	116	114					12																	53203234		2191	4299	6490	SO:0001583	missense	3851	exon4			AACTCCACCTTGT		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"-", "Intermediate filaments type II, keratins (basic)"	6441	protein-coding gene	gene with protein product	"cytokeratin 4", "keratin, type II cytoskeletal 4"	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.767T>A	12.37:g.53203234A>T	ENSP00000448220:p.Val256Glu	Somatic	147	1		WXS	Illumina HiSeq	Phase_I	168	41	NM_002272	0	0	0	0	0	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	37	CCDS41787.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.312086	0.81358	.	.	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	D;D;D	0.90563	-2.69;-2.69;-2.69	5.7	4.55	0.56014	Filament (1);	0.000000	0.43260	D	0.000591	D	0.95987	0.8693	H	0.98918	4.37	0.48571	D	0.999672	P	0.46706	0.883	P	0.51297	0.665	D	0.95929	0.8937	10	0.72032	D	0.01	.	11.1001	0.48168	0.9266:0.0:0.0734:0.0	.	270	P19013	K2C4_HUMAN	E	256;330;236	ENSP00000448220:V256E;ENSP00000293774:V330E;ENSP00000387904:V236E	ENSP00000293774:V330E	V	-	2	0	KRT4	51489501	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.371000	0.44248	1.094000	0.41399	0.533000	0.62120	GTG	.		0.537	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272		T	53203234	A	T	53203234	3	4	122	1	0	0	0	0	1	0	0	0	8498	159	6	5	819	5	KRT4	12	53203234	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	7400021	53203234	80648661	98	10645											
ATXN2	6311	hgsc.bcm.edu	37	chr12	112036797	112036797	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgttgctgctgctgctgCtgctgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1	rs4098854	byFrequency	TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:112036797C>T	ENST00000377617.3	-	1	683	c.522G>A	c.(520-522)caG>caA	p.Q174Q	RP11-686G8.2_ENST00000547021.1_RNA|ATXN2_ENST00000535949.1_Intron|ATXN2_ENST00000550104.1_Silent_p.Q174Q|ATXN2_ENST00000549455.1_5'UTR|ATXN2_ENST00000608853.1_Silent_p.Q14Q|ATXN2_ENST00000389153.4_5'Flank|ATXN2_ENST00000542287.2_Intron	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	174	Poly-Gln.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						gctgctgctgctgctgctgct	0.731													C|||	3289	0.656749	0.5734	0.6787	5008	,	,		4944	0.622		0.7167	False		,,,				2504	0.728				p.Q174Q		.											.	ATXN2-136	0			c.G522A						.						1	1	1					12																	112036797		720	1770	2490	SO:0001819	synonymous_variant	6311	exon1			CTGCTGCTGCTGC	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.522G>A	12.37:g.112036797C>T		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	4	4	NM_002973	0	0	178	193	15	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	37	CCDS31902.1																																																																																			C|0.429;T|0.571		0.731	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	112036797	C	T	112036797	2	4	122	1	0	0	0	0	0	0	0	1	1212	796	28	2		2	ATXN2	12	112036797	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	58833563	112036797	21815098	99	10646											
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46549817	46549817	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcacgttccctctctctcTcccgctccctgtctcgttct	1	16	5	19	3	5	0	1	0	4	0	11	0	8	0	3	0	0	4	3	0	0	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr13:46549817T>C	ENST00000242848.4	-	12	2417	c.2069A>G	c.(2068-2070)gAg>gGg	p.E690G	ZC3H13_ENST00000282007.3_Missense_Mutation_p.E690G			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	690	Arg/Glu-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		cctctctctctcccgctccct	0.493																																					p.E690G	Esophageal Squamous(187;747 2077 11056 31291 44172)	.											.	ZC3H13-92	0			c.A2069G						.						205	120	149					13																	46549817		2203	4300	6503	SO:0001583	missense	23091	exon12			TCTCTCTCCCGCT	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"Zinc fingers, CCCH-type domain containing"	20368	protein-coding gene	gene with protein product			"KIAA0853"	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.2069A>G	13.37:g.46549817T>C	ENSP00000242848:p.Glu690Gly	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_015070	0	0	10	10	0	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	T	12.25	1.881313	0.33255	.	.	ENSG00000123200	ENST00000242848;ENST00000282007	T;T	0.37752	2.15;1.18	4.59	4.59	0.56863	.	0.000000	0.56097	D	0.000029	T	0.54208	0.1844	.	.	.	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.78314	0.979;0.991	T	0.50303	-0.8844	9	0.22706	T	0.39	.	14.2792	0.66200	0.0:0.0:0.0:1.0	.	690;690	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	G	690	ENSP00000242848:E690G;ENSP00000282007:E690G	ENSP00000242848:E690G	E	-	2	0	ZC3H13	45447818	1.000000	0.71417	0.901000	0.35422	0.932000	0.56968	6.245000	0.72398	1.822000	0.53115	0.455000	0.32223	GAG	.		0.493	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		C	46549817	T	C	46549817	3	2	122	1	0	0	0	0	1	0	0	0	17597	1551	54	3	2649	3	ZC3H13	13	46549817	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		46549817	68620061	100	10647											
ATP7B	540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	52548876	52548876	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccggaccttgccttcaatGgagctgacacaggactggca	9	9	11	12	1	1	1	1	1	0	0	2	4	2	4	3	4	2	2	3	4	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr13:52548876G>A	ENST00000242839.4	-	2	636	c.480C>T	c.(478-480)tcC>tcT	p.S160S	ATP7B_ENST00000344297.5_Silent_p.S160S|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400366.3_Silent_p.S160S|ATP7B_ENST00000448424.2_Silent_p.S160S|ATP7B_ENST00000542656.1_Silent_p.S128S|ATP7B_ENST00000400370.3_Silent_p.S160S|ATP7B_ENST00000418097.2_Silent_p.S160S	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	160	HMA 2. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCCTTCAATGGAGCTGACAC	0.562									Wilson disease																												p.S160S		.											.	ATP7B-92	0			c.C480T						.						47	49	48					13																	52548876		2045	4186	6231	SO:0001819	synonymous_variant	540	exon2	Familial Cancer Database		TTCAATGGAGCTG	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.480C>T	13.37:g.52548876G>A		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	72	23	NM_001243182	0	0	0	3	3	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	37	CCDS41892.1																																																																																			.		0.562	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		A	52548876	G	A	52548876	2	1	122	1	0	0	0	0	0	0	0	1	1192	1335	47	2		2	ATP7B	13	52548876	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	5999059	52548876	62621002	101	10648											
CDC16	8881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	115022697	115022697	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcggcgtggttgcatttcaGaatggagagtaagtactgga	10	11	15	5	2	1	2	1	0	0	2	2	4	1	3	0	4	2	4	0	4	3	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr13:115022697G>T	ENST00000356221.3	+	13	1350	c.1242G>T	c.(1240-1242)caG>caT	p.Q414H	CDC16_ENST00000252457.5_Missense_Mutation_p.Q413H|CDC16_ENST00000375310.1_Missense_Mutation_p.Q320H|CDC16_ENST00000375312.3_Intron|CDC16_ENST00000252458.6_Intron|CDC16_ENST00000360383.3_Missense_Mutation_p.Q414H|CDC16_ENST00000375308.1_Missense_Mutation_p.Q320H			Q13042	CDC16_HUMAN	cell division cycle 16	414					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TTGCATTTCAGAATGGAGAGT	0.438																																					p.Q414H		.											.	CDC16-226	0			c.G1242T						.						121	114	116					13																	115022697		2203	4300	6503	SO:0001583	missense	8881	exon13			ATTTCAGAATGGA	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.1242G>T	13.37:g.115022697G>T	ENSP00000348554:p.Gln414His	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	166	53	NM_003903	0	0	0	0	0	A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	G	12.89	2.074396	0.36566	.	.	ENSG00000130177	ENST00000360383;ENST00000356221;ENST00000375310;ENST00000252457;ENST00000375308	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	5.94	-2.27	0.06846	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.064378	0.64402	D	0.000003	T	0.27866	0.0686	N	0.12182	0.205	0.80722	D	1	B;B	0.23540	0.018;0.087	B;B	0.11329	0.006;0.006	T	0.07328	-1.0778	9	.	.	.	-19.2092	13.2551	0.60074	0.6016:0.0:0.3984:0.0	.	413;414	Q13042-2;Q13042	.;CDC16_HUMAN	H	414;414;320;413;320	ENSP00000353549:Q414H;ENSP00000348554:Q414H;ENSP00000364459:Q320H;ENSP00000252457:Q413H;ENSP00000364457:Q320H	.	Q	+	3	2	CDC16	114040799	1.000000	0.71417	0.983000	0.44433	0.942000	0.58702	0.794000	0.26958	-0.384000	0.07845	-0.142000	0.14014	CAG	.		0.438	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		T	115022697	G	T	115022697	3	4	122	1	0	0	0	0	1	0	0	0	3064	933	33	4	1292	4	CDC16	13	115022697	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	62473821	115022697	147181	102	10649											
PSME2	5721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24612672	24612672	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgacaattttctccaggttGctgctgatgatatgataaag	11	15	9	6	0	1	4	0	4	1	0	2	4	1	4	1	1	2	3	1	1	4	6			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:24612672G>T	ENST00000216802.5	-	11	1305	c.666C>A	c.(664-666)agC>agA	p.S222R	PSME2_ENST00000471700.2_5'UTR|EMC9_ENST00000419198.2_5'Flank|EMC9_ENST00000558200.1_5'Flank|PSME2_ENST00000560410.1_Missense_Mutation_p.S211R|EMC9_ENST00000560403.1_5'Flank|EMC9_ENST00000216799.4_5'Flank	NM_002818.2	NP_002809.2	Q9UL46	PSME2_HUMAN	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	222					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)				endometrium(1)|lung(3)|prostate(2)	6				GBM - Glioblastoma multiforme(265;0.00839)		TCTCCAGGTTGCTGCTGATGA	0.478																																					p.S222R		.											.	PSME2-90	0			c.C666A						.						104	99	101					14																	24612672		2203	4300	6503	SO:0001583	missense	5721	exon11			CAGGTTGCTGCTG		CCDS9614.1	14q11.2	2010-03-10			ENSG00000100911	ENSG00000100911		"Proteasome (prosome, macropain) subunits"	9569	protein-coding gene	gene with protein product		602161				7789512	Standard	NM_002818		Approved	PA28beta	uc001wmj.3	Q9UL46	OTTHUMG00000028797	ENST00000216802.5:c.666C>A	14.37:g.24612672G>T	ENSP00000216802:p.Ser222Arg	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	118	38	NM_002818	0	0	50	83	33	Q15129	Missense_Mutation	SNP	ENST00000216802.5	37	CCDS9614.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681098	0.47886	.	.	ENSG00000100911	ENST00000216802	T	0.40476	1.03	5.15	5.15	0.70609	Proteasome activator pa28, REG beta subunit (2);	0.142096	0.64402	D	0.000004	T	0.38746	0.1052	L	0.36672	1.1	0.36888	D	0.889745	B	0.19073	0.033	B	0.30105	0.111	T	0.45190	-0.9278	10	0.72032	D	0.01	0.0398	14.4828	0.67594	0.0:0.0:1.0:0.0	.	222	Q9UL46	PSME2_HUMAN	R	222	ENSP00000216802:S222R	ENSP00000216802:S222R	S	-	3	2	PSME2	23682512	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.328000	0.43867	2.570000	0.86706	0.561000	0.74099	AGC	.		0.478	PSME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071918.3	NM_002818		T	24612672	G	T	24612672	3	4	122	1	0	0	0	0	1	0	0	0	12736	1310	46	4	57	4	PSME2	14	24612672	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		24612672	82736868	103	10650											
TINF2	26277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24709984	24709984	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaagatgtgtgccaggcttGgcttttggcaggggattgtg	6	12	18	5	0	0	1	0	0	0	1	0	3	0	3	1	6	1	3	1	6	1	4	rs201135568		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:24709984G>C	ENST00000267415.7	-	6	1043	c.702C>G	c.(700-702)gcC>gcG	p.A234A	TINF2_ENST00000558566.1_3'UTR|TINF2_ENST00000399423.4_Silent_p.A234A|TINF2_ENST00000538777.1_Silent_p.A20A|TINF2_ENST00000540705.1_Silent_p.A199A|TINF2_ENST00000559019.1_3'UTR|TINF2_ENST00000558510.1_5'Flank	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	234					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		TGCCAGGCTTGGCTTTTGGCA	0.552									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome																												p.A234A		.											.	TINF2-227	0			c.C702G						.						149	144	146					14																	24709984		1996	4158	6154	SO:0001819	synonymous_variant	26277	exon6	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	AGGCTTGGCTTTT	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.702C>G	14.37:g.24709984G>C		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	143	35	NM_001099274	0	0	20	37	17	B3W5Q7|Q9H904|Q9UHC2	Silent	SNP	ENST00000267415.7	37	CCDS41936.1																																																																																			G|1.000;A|0.000		0.552	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2			C	24709984	G	C	24709984	2	2	122	1	0	0	0	0	0	0	0	1	15955	1335	47	4		4	TINF2	14	24709984	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	97312	24709984	82639556	104	10651											
HSPA2	3306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	65008125	65008125	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggccatcgcctacggcctGgacaagaagggctgcgcggg	7	4	17	13	5	0	1	0	0	0	1	1	2	0	2	3	5	2	1	3	5	3	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:65008125G>A	ENST00000394709.1	+	2	634	c.558G>A	c.(556-558)ctG>ctA	p.L186L	HSPA2_ENST00000554883.1_3'UTR|HSPA2_ENST00000247207.6_Silent_p.L186L|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	186					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CCTACGGCCTGGACAAGAAGG	0.642																																					p.L186L	Pancreas(136;1211 1835 24894 31984 38227)	.											.	HSPA2-226	0			c.G558A						.						67	75	72					14																	65008125		2203	4300	6503	SO:0001819	synonymous_variant	3306	exon1			CGGCCTGGACAAG	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"Heat shock proteins / HSP70"	5235	protein-coding gene	gene with protein product		140560	"heat shock 70kD protein 2"				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.558G>A	14.37:g.65008125G>A		Somatic	160	0		WXS	Illumina HiSeq	Phase_I	154	45	NM_021979	0	0	13	30	17	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	37	CCDS9766.1																																																																																			.		0.642	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65008125	G	A	65008125	2	1	122	1	0	0	0	0	0	0	0	1	7432	1335	47	2		2	HSPA2	14	65008125	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	40298141	65008125	42341415	105	10652											
HSPA2	3306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	65008173	65008173	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagaacgtgctcatctttgaCctgggcggtggcactttcga	8	11	12	10	3	2	2	1	1	1	1	3	3	2	2	1	3	2	2	1	3	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:65008173C>A	ENST00000394709.1	+	2	682	c.606C>A	c.(604-606)gaC>gaA	p.D202E	HSPA2_ENST00000554883.1_3'UTR|HSPA2_ENST00000247207.6_Missense_Mutation_p.D202E|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	202					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		TCATCTTTGACCTGGGCGGTG	0.642																																					p.D202E	Pancreas(136;1211 1835 24894 31984 38227)	.											.	HSPA2-226	0			c.C606A						.						98	106	103					14																	65008173		2203	4300	6503	SO:0001583	missense	3306	exon1			CTTTGACCTGGGC	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"Heat shock proteins / HSP70"	5235	protein-coding gene	gene with protein product		140560	"heat shock 70kD protein 2"				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.606C>A	14.37:g.65008173C>A	ENSP00000378199:p.Asp202Glu	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	200	58	NM_021979	0	0	10	34	24	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793970	0.70452	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.49720	0.77;0.77	5.22	5.22	0.72569	Heat shock protein 70, conserved site (1);	0.000000	0.56097	U	0.000034	D	0.87026	0.6075	H	0.99998	5.51	0.44736	D	0.997733	D	0.89917	1.0	D	0.91635	0.999	D	0.94368	0.7593	10	0.87932	D	0	-12.6764	18.774	0.91902	0.0:1.0:0.0:0.0	.	202	P54652	HSP72_HUMAN	E	202	ENSP00000378199:D202E;ENSP00000247207:D202E	ENSP00000247207:D202E	D	+	3	2	HSPA2	64077926	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.963000	0.56773	2.422000	0.82143	0.563000	0.77884	GAC	.		0.642	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65008173	C	A	65008173	3	1	122	1	0	0	0	0	1	0	0	0	7432	506	18	4	608	4	HSPA2	14	65008173	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	48	65008173	42341367	106	10653											
ADAM20	8748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	70991146	70991146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctccacataaccatggtagTagcagtcatcctggatgaag	12	9	9	11	0	1	1	1	1	0	0	3	2	3	2	4	2	2	3	4	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:70991146T>C	ENST00000256389.3	-	2	723	c.479A>G	c.(478-480)tAc>tGc	p.Y160C	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	110					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ACCATGGTAGTAGCAGTCATC	0.498																																					p.Y160C		.											.	ADAM20-226	0			c.A479G						.						145	102	117					14																	70991146		2203	4300	6503	SO:0001583	missense	8748	exon2			TGGTAGTAGCAGT	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.479A>G	14.37:g.70991146T>C	ENSP00000256389:p.Tyr160Cys	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	161	71	NM_003814	0	0	0	0	0	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	T	10.77	1.444114	0.25987	.	.	ENSG00000134007	ENST00000256389	T	0.07444	3.19	4.14	1.61	0.23674	Peptidase M12B, propeptide (1);	0.000000	0.35555	N	0.003123	T	0.39600	0.1084	H	0.98133	4.155	0.26202	N	0.979437	D	0.89917	1.0	D	0.79108	0.992	T	0.41179	-0.9523	10	0.87932	D	0	.	9.3882	0.38356	0.4926:0.0:0.0:0.5074	.	110	O43506	ADA20_HUMAN	C	160	ENSP00000256389:Y160C	ENSP00000256389:Y160C	Y	-	2	0	ADAM20	70060899	1.000000	0.71417	0.998000	0.56505	0.115000	0.19883	1.990000	0.40717	0.202000	0.20498	-0.336000	0.08194	TAC	.		0.498	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			C	70991146	T	C	70991146	3	2	122	1	0	0	0	0	1	0	0	0	242	1638	57	3	1855	3	ADAM20	14	70991146	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	5982973	70991146	36358394	107	10654											
NPC2	10577	broad.mit.edu;bcgsc.ca	37	chr14	74959964	74959964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggagcaggaatgtagctGccaggaaacgcatcgcggat	12	5	14	10	3	0	0	0	0	0	0	1	4	0	4	2	4	4	4	2	4	3	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:74959964G>A	ENST00000555619.1	-	1	251	c.14C>T	c.(13-15)gCa>gTa	p.A5V	NPC2_ENST00000238633.2_Missense_Mutation_p.A5V|ISCA2_ENST00000556816.1_5'Flank|ISCA2_ENST00000554924.1_5'Flank|NPC2_ENST00000557510.1_Missense_Mutation_p.A5V|ISCA2_ENST00000298818.8_5'Flank|NPC2_ENST00000434013.2_Missense_Mutation_p.A5V|NPC2_ENST00000541064.1_Missense_Mutation_p.A5V	NM_006432.3	NP_006423.1	P61916	NPC2_HUMAN	Niemann-Pick disease, type C2	5					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|glycolipid transport (GO:0046836)|intracellular cholesterol transport (GO:0032367)|intracellular sterol transport (GO:0032366)|phospholipid transport (GO:0015914)|regulation of isoprenoid metabolic process (GO:0019747)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.00149)		GAATGTAGCTGCCAGGAAACG	0.672																																					p.A5V	Pancreas(93;260 1497 8575 30964 48133)												.	NPC2-90	0			c.C14T						.						32	36	35					14																	74959964		2201	4300	6501	SO:0001583	missense	10577	exon1			GTAGCTGCCAGGA	X67698	CCDS32121.1	14q24.3	2009-09-12				ENSG00000119655			14537	protein-coding gene	gene with protein product	"epididymal protein 1"	601015				8418812, 11125141	Standard	NM_006432		Approved	HE1, NP-C2, EDDM1	uc001xpy.3	P61916		ENST00000555619.1:c.14C>T	14.37:g.74959964G>A	ENSP00000451112:p.Ala5Val	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	24	5	NM_006432	0	0	309	348	39	B4DQV7|Q15668|Q29413	Missense_Mutation	SNP	ENST00000555619.1	37	CCDS32121.1	.	.	.	.	.	.	.	.	.	.	G	6.444	0.449993	0.12223	.	.	ENSG00000119655	ENST00000434013;ENST00000541064;ENST00000555619;ENST00000238633;ENST00000553490;ENST00000557510;ENST00000555592	D;D;D;D;D;D;D	0.89123	-2.45;-2.35;-2.37;-2.38;-2.47;-2.4;-2.35	4.54	-2.02	0.07388	.	1.274000	0.04901	N	0.451378	T	0.75657	0.3879	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.001;0.002	T	0.58532	-0.7620	10	0.15499	T	0.54	-0.5237	1.0393	0.01556	0.1654:0.2592:0.2807:0.2947	.	5;5	B4DQV7;P61916	.;NPC2_HUMAN	V	5	ENSP00000412103:A5V;ENSP00000442488:A5V;ENSP00000451112:A5V;ENSP00000238633:A5V;ENSP00000451180:A5V;ENSP00000451206:A5V;ENSP00000450887:A5V	ENSP00000238633:A5V	A	-	2	0	NPC2	74029717	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.135000	0.15952	-0.374000	0.07967	-0.274000	0.10170	GCA	.		0.672	NPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412346.1	NM_006432		A	74959964	G	A	74959964	3	1	122	1	0	0	0	0	1	0	0	0	10598	1319	46	2	461	2	NPC2	14	74959964	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	3968818	74959964	32389576	108	10655											
C14orf174	161394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	77844646	77844646	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagaggagatgcaaagaaaGgcaactgaggagaaagggac	18	2	15	6	0	0	5	0	1	0	4	0	8	0	6	1	4	2	2	1	4	4	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:77844646G>A	ENST00000216471.4	+	1	1171	c.885G>A	c.(883-885)aaG>aaA	p.K295K	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	295										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						TGCAAAGAAAGGCAACTGAGG	0.493																																					p.K295K		.											.	SAMD15-90	0			c.G885A						.						81	83	82					14																	77844646		2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			AAGAAAGGCAACT	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.885G>A	14.37:g.77844646G>A		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	123	47	NM_001010860	0	0	2	3	1	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			.		0.493	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		A	77844646	G	A	77844646	2	1	122	1	0	0	0	0	0	0	0	1	1763	991	35	2		2	C14orf174	14	77844646	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	2884682	77844646	29504894	109	10656											
NRXN3	9369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	79423648	79423648	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caacgagtggcacaccgttcGggtggtgcggagaggaaaaa	12	5	16	8	4	0	1	0	0	0	1	1	4	0	2	1	5	2	2	1	5	3	1	rs367857290		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:79423648G>A	ENST00000554719.1	+	8	1711	c.1220G>A	c.(1219-1221)cGg>cAg	p.R407Q	NRXN3_ENST00000335750.5_Missense_Mutation_p.R407Q	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	177					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)	p.R407P(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		CACACCGTTCGGGTGGTGCGG	0.473																																					p.R407Q		.											.	NRXN3-587	1	Substitution - Missense(1)	lung(1)	c.G1220A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	276	241	253		1220	3.8	1	14		253	0,8600		0,0,4300	no	missense	NRXN3	NM_004796.4	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	407/1062	79423648	1,13005	2203	4300	6503	SO:0001583	missense	9369	exon8			CCGTTCGGGTGGT	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"chromosome 14 open reading frame 60"	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1220G>A	14.37:g.79423648G>A	ENSP00000451648:p.Arg407Gln	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	172	65	NM_004796	0	0	0	1	1	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774869	0.90108	2.27E-4	0.0	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.77877	-1.13;-1.13	5.64	3.82	0.43975	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.206569	0.42821	N	0.000657	D	0.86772	0.6013	.	.	.	0.54753	D	0.999982	D;D	0.89917	1.0;0.974	D;B	0.87578	0.998;0.406	D	0.86484	0.1793	8	.	.	.	.	12.5919	0.56447	0.135:0.0:0.865:0.0	.	780;407	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	Q	780;769;407;407	ENSP00000451648:R407Q;ENSP00000338349:R407Q	.	R	+	2	0	NRXN3	78493401	1.000000	0.71417	0.985000	0.45067	0.985000	0.73830	4.901000	0.63259	0.860000	0.35481	0.650000	0.86243	CGG	.		0.473	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		A	79423648	G	A	79423648	3	1	122	1	0	0	0	0	1	0	0	0	10693	1116	39	1	1242	1	NRXN3	14	79423648	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	1579002	79423648	27925892	110	10657											
C14orf49	161176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	95903278	95903278	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcctcaggagctgggagAaatcttcatggctcccttct	8	12	10	11	0	4	1	2	0	2	1	6	3	6	2	2	3	1	3	2	3	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:95903278A>G	ENST00000334258.5	-	14	2431	c.2417T>C	c.(2416-2418)tTc>tCc	p.F806S	SYNE3_ENST00000554873.1_Missense_Mutation_p.F563S|SYNE3_ENST00000557275.1_Missense_Mutation_p.F801S	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	806					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						GAGCTGGGAGAAATCTTCATG	0.517																																					p.F806S		.											.	.	0			c.T2417C						.						100	96	97					14																	95903278		2203	4300	6503	SO:0001583	missense	161176	exon14			TGGGAGAAATCTT	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2417T>C	14.37:g.95903278A>G	ENSP00000334308:p.Phe806Ser	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	145	68	NM_152592	0	0	0	0	0	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	A	12.57	1.978684	0.34942	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.15372	3.48;2.43;3.5	5.13	-6.79	0.01715	.	1.951040	0.02897	N	0.134895	T	0.13157	0.0319	M	0.62723	1.935	0.09310	N	1	B;B	0.22211	0.066;0.04	B;B	0.17979	0.02;0.01	T	0.23226	-1.0194	10	0.23891	T	0.37	-0.2886	0.1537	0.00096	0.2263:0.2228:0.217:0.3339	.	801;806	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	S	806;563;801	ENSP00000334308:F806S;ENSP00000452154:F563S;ENSP00000450562:F801S	ENSP00000334308:F806S	F	-	2	0	C14orf49	94973031	0.011000	0.17503	0.000000	0.03702	0.134000	0.20937	0.178000	0.16820	-1.516000	0.01782	0.459000	0.35465	TTC	.		0.517	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		G	95903278	A	G	95903278	3	3	122	1	0	0	0	0	1	0	0	0	1780	246	9	3	526	3	C14orf49	14	95903278	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	16479630	95903278	11446262	111	10658											
BEGAIN	57596	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	101012903	101012903	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagctcgatctccaggtaGtggcgcgtggagtcgaactc	7	8	14	12	5	1	0	0	0	1	0	5	3	1	1	1	3	2	3	1	3	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:101012903G>A	ENST00000355173.2	-	3	182	c.111C>T	c.(109-111)caC>caT	p.H37H	BEGAIN_ENST00000556751.1_5'UTR|BEGAIN_ENST00000443071.2_Silent_p.H37H|BEGAIN_ENST00000554747.1_5'UTR	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	37						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				TCTCCAGGTAGTGGCGCGTGG	0.692																																					p.H37H	NSCLC(159;1889 2010 9965 27479 40101)	.											.	BEGAIN-68	0			c.C111T						.						74	69	71					14																	101012903		2203	4300	6503	SO:0001819	synonymous_variant	57596	exon3			CAGGTAGTGGCGC	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"brain-enriched guanylate kinase-associated homolog (rat)"			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.111C>T	14.37:g.101012903G>A		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	124	44	NM_020836	0	0	0	0	0	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			.		0.692	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836		A	101012903	G	A	101012903	2	1	122	1	0	0	0	0	0	0	0	1	1398	1020	36	2		2	BEGAIN	14	101012903	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	5109625	101012903	6336637	112	10659											
AHNAK2	113146	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	105408067	105408067	+	Frame_Shift_Del	DEL	T	T	-																															ctgcctttgggcctttcaggTccagcttggggcccttgacg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:105408067delT	ENST00000333244.5	-	7	13840	c.13721delA	c.(13720-13722)gacfs	p.D4574fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4574						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCCTTTCAGGTCCAGCTTGGG	0.627																																					p.D4574fs		.											.	AHNAK2-47	0			c.13721delA						.						124	134	131					14																	105408067		1916	4122	6038	SO:0001589	frameshift_variant	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13721delA	14.37:g.105408067delT	ENSP00000353114:p.Asp4574fs	Somatic	307	0		WXS	Illumina HiSeq	Phase_I	302	94	NM_138420	0	0	0	0	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	37	CCDS45177.1																																																																																			.		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		-	105408067	T	-	105408067	7	5	122	1	0	1	0	1	0	0	0	0	415	1667	58	0	3670	0	AHNAK2	14	105408067	Frame_Shift_Del	DEL	T	TCGA-GL-7773-01A-11D-2136-08	4395164	105408067	1941473	113	10660											
HERC2	8924	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	28431846	28431846	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagaccatggattttacaaTcgattcctgagctcctgcac	10	12	8	11	1	0	2	0	2	0	1	3	5	2	3	3	1	3	2	3	1	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:28431846T>A	ENST00000261609.7	-	56	8810	c.8702A>T	c.(8701-8703)gAt>gTt	p.D2901V		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GATTTTACAATCGATTCCTGA	0.423																																					p.D2901V		.											.	HERC2-234	0			c.A8702T						.						84	74	77					15																	28431846		2203	4300	6503	SO:0001583	missense	8924	exon56			TTACAATCGATTC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8702A>T	15.37:g.28431846T>A	ENSP00000261609:p.Asp2901Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	71	27	NM_004667	0	0	2	3	1		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.315805	0.81469	.	.	ENSG00000128731	ENST00000261609	T	0.70164	-0.46	5.0	5.0	0.66597	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.81721	0.4882	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.84597	0.0670	10	0.87932	D	0	.	15.0231	0.71647	0.0:0.0:0.0:1.0	.	2901	O95714	HERC2_HUMAN	V	2901	ENSP00000261609:D2901V	ENSP00000261609:D2901V	D	-	2	0	HERC2	26105441	1.000000	0.71417	0.496000	0.27539	0.859000	0.49053	7.997000	0.88414	2.000000	0.58554	0.528000	0.53228	GAT	.		0.423	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28431846	T	A	28431846	3	1	122	1	0	0	0	0	1	0	0	0	7079	1435	50	5	5954	5	HERC2	15	28431846	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		28431846	74099546	114	10661											
ZNF770	54989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	35274327	35274327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagattgacaagtctttctTattcactgaattatcaatgc	13	15	5	8	0	4	3	2	2	2	1	4	3	4	3	0	0	1	0	0	0	5	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:35274327T>C	ENST00000356321.4	-	3	1653	c.1309A>G	c.(1309-1311)Aag>Gag	p.K437E		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	437					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		AAGTCTTTCTTATTCACTGAA	0.348																																					p.K437E		.											.	ZNF770-91	0			c.A1309G						.						82	84	83					15																	35274327		2201	4297	6498	SO:0001583	missense	54989	exon3			CTTTCTTATTCAC	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"Zinc fingers, C2H2-type"	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.1309A>G	15.37:g.35274327T>C	ENSP00000348673:p.Lys437Glu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	167	65	NM_014106	0	0	11	26	15	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	T	4.829	0.154043	0.09185	.	.	ENSG00000198146	ENST00000356321	T	0.09073	3.02	5.49	5.49	0.81192	.	0.394233	0.25414	N	0.030860	T	0.07052	0.0179	N	0.14661	0.345	0.22996	N	0.998451	B	0.23937	0.094	B	0.22386	0.039	T	0.31194	-0.9952	10	0.87932	D	0	-3.5887	15.7623	0.78096	0.0:0.0:0.0:1.0	.	437	Q6IQ21	ZN770_HUMAN	E	437	ENSP00000348673:K437E	ENSP00000348673:K437E	K	-	1	0	ZNF770	33061619	1.000000	0.71417	0.997000	0.53966	0.123000	0.20343	3.570000	0.53834	2.311000	0.77944	0.533000	0.62120	AAG	.		0.348	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		C	35274327	T	C	35274327	3	2	122	1	0	0	0	0	1	0	0	0	18175	1763	61	3	770	3	ZNF770	15	35274327	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	6842481	35274327	67257065	115	10662											
BAHD1	22893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40758294	40758294	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgccgccatgtctatgacTtccgccacgggcgcatcctt	5	12	9	15	4	1	1	0	1	1	0	3	1	3	1	5	1	1	1	5	1	1	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:40758294T>C	ENST00000416165.1	+	7	2379	c.2308T>C	c.(2308-2310)Ttc>Ctc	p.F770L	BAHD1_ENST00000561234.1_Missense_Mutation_p.F769L|RP11-64K12.8_ENST00000559730.1_RNA|BAHD1_ENST00000560846.1_Missense_Mutation_p.F767L	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	770	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		TGTCTATGACTTCCGCCACGG	0.632																																					p.F770L		.											.	BAHD1-90	0			c.T2308C						.						98	101	100					15																	40758294		2203	4300	6503	SO:0001583	missense	22893	exon7			TATGACTTCCGCC	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.2308T>C	15.37:g.40758294T>C	ENSP00000396976:p.Phe770Leu	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	249	103	NM_014952	0	0	15	34	19	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	37	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.000543	0.93227	.	.	ENSG00000140320	ENST00000416165	D	0.85339	-1.97	5.6	5.6	0.85130	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	D	0.000000	D	0.91965	0.7455	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.87578	0.917;0.998;0.997	D	0.92808	0.6262	10	0.72032	D	0.01	-16.7549	15.7888	0.78332	0.0:0.0:0.0:1.0	.	767;770;769	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	L	770	ENSP00000396976:F770L	ENSP00000396976:F770L	F	+	1	0	BAHD1	38545586	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.040000	0.89188	2.144000	0.66660	0.460000	0.39030	TTC	.		0.632	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		C	40758294	T	C	40758294	3	2	122	1	0	0	0	0	1	0	0	0	1298	1609	56	3	2330	3	BAHD1	15	40758294	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	5483967	40758294	61773098	116	10663											
DMXL2	23312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51790750	51790750	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttagcgagaatatttaccTgagcaactcttatctctgct	10	16	6	9	1	2	2	0	1	2	1	3	3	2	2	1	0	5	2	1	0	6	6			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:51790750T>G	ENST00000251076.5	-	18	4958	c.4671A>C	c.(4669-4671)tcA>tcC	p.S1557S	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Intron|DMXL2_ENST00000543779.2_Splice_Site_p.S1557S	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1557						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AATATTTACCTGAGCAACTCT	0.368																																					p.S1557S		.											.	DMXL2-99	0			c.A4671C						.						47	47	47					15																	51790750		2194	4293	6487	SO:0001630	splice_region_variant	23312	exon18			TTTACCTGAGCAA	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.4672+1A>C	15.37:g.51790750T>G		Somatic	33	1		WXS	Illumina HiSeq	Phase_I	45	16	NM_001174116	0	0	0	0	0	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			.		0.368	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	Silent	G	51790750	T	G	51790750	5	3	122	1	0	0	0	0	0	0	1	0	4606	1594	55	5	4546	5	DMXL2	15	51790750	Splice_Site	SNP	T	TCGA-GL-7773-01A-11D-2136-08	11032456	51790750	50740642	117	10664											
MYO5C	55930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	52498142	52498142	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcaattcttattctgctgtgGactattatgcttcatgaatt	9	18	7	7	0	3	1	1	1	2	0	3	2	3	2	0	1	2	3	0	1	5	7			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:52498142G>T	ENST00000261839.7	-	37	4569	c.4408C>A	c.(4408-4410)Cca>Aca	p.P1470T	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1470	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TTCTGCTGTGGACTATTATGC	0.269																																					p.P1470T		.											.	MYO5C-145	0			c.C4408A						.						57	49	52					15																	52498142		1789	4055	5844	SO:0001583	missense	55930	exon37			GCTGTGGACTATT	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.4408C>A	15.37:g.52498142G>T	ENSP00000261839:p.Pro1470Thr	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	47	19	NM_018728	0	0	5	6	1	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494477	0.64186	.	.	ENSG00000128833	ENST00000261839	T	0.16897	2.31	5.21	4.27	0.50696	Dilute (1);	0.061993	0.64402	D	0.000004	T	0.32010	0.0815	M	0.72118	2.19	0.80722	D	1	D	0.56035	0.974	P	0.52957	0.714	T	0.09228	-1.0684	10	0.33940	T	0.23	.	15.7715	0.78173	0.0:0.1365:0.8635:0.0	.	1470	Q9NQX4	MYO5C_HUMAN	T	1470	ENSP00000261839:P1470T	ENSP00000261839:P1470T	P	-	1	0	MYO5C	50285434	1.000000	0.71417	0.959000	0.39883	0.903000	0.53119	3.298000	0.51818	1.376000	0.46267	0.555000	0.69702	CCA	.		0.269	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		T	52498142	G	T	52498142	3	4	122	1	0	0	0	0	1	0	0	0	10105	1174	41	4	840	4	MYO5C	15	52498142	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	707392	52498142	50033250	118	10665											
C15orf60	283677	hgsc.bcm.edu	37	chr15	73843452	73843452	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccagggcaactgaaagtcaAgggaaggattctgcaaagag	15	5	13	8	0	2	2	1	1	1	1	2	4	2	4	1	3	2	2	1	3	5	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:73843452A>G	ENST00000331090.6	+	4	535	c.507A>G	c.(505-507)caA>caG	p.Q169Q	C15orf60_ENST00000560581.1_Silent_p.Q141Q	NM_001042367.1	NP_001035826.1	Q7Z4M0	RE114_HUMAN		169					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)					endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						CTGAAAGTCAAGGGAAGGATT	0.512																																					p.Q169Q		.											.	C15orf60-46	0			c.A507G						.						43	44	44					15																	73843452		1952	4165	6117	SO:0001819	synonymous_variant	283677	exon4			AAGTCAAGGGAAG																												ENST00000331090.6:c.507A>G	15.37:g.73843452A>G		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	34	2	NM_001042367	0	0	0	0	0		Silent	SNP	ENST00000331090.6	37	CCDS45296.1																																																																																			.		0.512	C15orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419069.1			G	73843452	A	G	73843452	2	3	122	1	0	0	0	0	0	0	0	1	1812	69	3	3		3	C15orf60	15	73843452	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	21345310	73843452	28687940	119	10666											
PML	5371	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr15	74327953	74327953	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	catcctgcccagctgcaaagGggcatcagcccaccccaccg	9	4	9	19	1	1	0	1	0	0	0	2	0	2	0	6	2	4	3	6	2	1	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:74327953G>A	ENST00000268058.3	+	7	1806				PML_ENST00000435786.2_3'UTR|PML_ENST00000354026.6_Silent_p.R669R|PML_ENST00000359928.4_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000563500.1_3'UTR|PML_ENST00000564428.1_Intron|PML_ENST00000268059.6_Silent_p.R717R|PML_ENST00000565898.1_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						AGCTGCAAAGGGGCATCAGCC	0.622			T	"RARA, PAX5"	"APL, ALL"																																p.R717R		.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML-1083	0			c.G2151A						.						64	63	64					15																	74327953		2198	4297	6495	SO:0001627	intron_variant	5371	exon8			GCAAAGGGGCATC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1082G>A	15.37:g.74327953G>A		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	128	39	NM_033239	0	0	36	52	16	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	37	CCDS10255.1																																																																																			.		0.622	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		A	74327953	G	A	74327953	1	1	122	0	1	0	0	0	0	0	0	0	12161	1223	43	2		2	PML	15	74327953	Intron	SNP	G	TCGA-GL-7773-01A-11D-2136-08	484501	74327953	28203439	120	10667											
AXIN1	8312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	338194	338194	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcctcgtcctctcgaacCtcctcaaacaccaccccaca	10	6	4	21	3	2	0	1	0	1	0	6	1	4	0	7	1	2	0	7	1	2	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:338194C>A	ENST00000262320.3	-	11	2888	c.2517G>T	c.(2515-2517)gaG>gaT	p.E839D	AXIN1_ENST00000354866.3_Missense_Mutation_p.E803D	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	839	DIX. {ECO:0000255|PROSITE- ProRule:PRU00069}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCTCTCGAACCTCCTCAAACA	0.587																																					p.E839D		.											.	AXIN1-684	0			c.G2517T						.						233	174	194					16																	338194		2203	4300	6503	SO:0001583	missense	8312	exon11			TCGAACCTCCTCA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.2517G>T	16.37:g.338194C>A	ENSP00000262320:p.Glu839Asp	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	170	47	NM_003502	0	0	27	53	26	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	37	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	c	14.73	2.621324	0.46736	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.61274	0.12;0.12	4.62	-0.702	0.11265	DIX (3);	0.000000	0.85682	D	0.000000	T	0.73528	0.3598	M	0.89534	3.04	0.50171	D	0.999859	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	T	0.70432	-0.4873	10	0.72032	D	0.01	-11.9016	5.4595	0.16610	0.1225:0.5288:0.0:0.3487	.	803;839	O15169-2;O15169	.;AXIN1_HUMAN	D	839;803	ENSP00000262320:E839D;ENSP00000346935:E803D	ENSP00000262320:E839D	E	-	3	2	AXIN1	278195	0.998000	0.40836	0.424000	0.26647	0.122000	0.20287	0.667000	0.25112	-0.105000	0.12132	-0.224000	0.12420	GAG	.		0.587	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	338194	C	A	338194	3	1	122	1	0	0	0	0	1	0	0	0	1237	680	24	4	75	4	AXIN1	16	338194	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		338194	90016559	121	10668											
GLYR1	84656	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4864623	4864623	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgggggttcttcccagacggGccccctcctggatgaacaaa	8	7	12	14	2	1	2	0	1	1	1	3	3	3	3	4	4	1	1	4	4	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:4864623G>C	ENST00000321919.9	-	11	1008	c.932C>G	c.(931-933)gCc>gGc	p.A311G	GLYR1_ENST00000591451.1_Missense_Mutation_p.A305G|GLYR1_ENST00000436648.5_Missense_Mutation_p.A230G|GLYR1_ENST00000381983.3_Missense_Mutation_p.A294G	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	311					pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						TCCCAGACGGGCCCCCTCCTG	0.577																																					p.A311G		.											.	GLYR1-90	0			c.C932G						.						42	41	41					16																	4864623		2197	4300	6497	SO:0001583	missense	84656	exon11			AGACGGGCCCCCT	AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632			24434	protein-coding gene	gene with protein product	"nuclear protein 60kDa"	610660				16352664	Standard	NM_032569		Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.932C>G	16.37:g.4864623G>C	ENSP00000322716:p.Ala311Gly	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	61	17	NM_032569	0	0	12	33	21	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	37	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124490	0.94429	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.73789	-0.49;-0.48;-0.78	5.33	5.33	0.75918	6-phosphogluconate dehydrogenase, NADP-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.86887	0.6041	M	0.79926	2.475	0.80722	D	1	B;P;B;D	0.58620	0.262;0.512;0.173;0.983	B;P;B;D	0.79784	0.418;0.548;0.341;0.993	D	0.86708	0.1934	10	0.46703	T	0.11	-16.0047	18.1572	0.89696	0.0:0.0:1.0:0.0	.	230;305;294;311	Q49A26-5;Q49A26-3;Q49A26-2;Q49A26	.;.;.;GLYR1_HUMAN	G	311;294;230	ENSP00000322716:A311G;ENSP00000371413:A294G;ENSP00000390276:A230G	ENSP00000322716:A311G	A	-	2	0	GLYR1	4804624	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.422000	0.97458	2.654000	0.90174	0.561000	0.74099	GCC	.		0.577	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569		C	4864623	G	C	4864623	3	2	122	1	0	0	0	0	1	0	0	0	6503	1203	42	4	753	4	GLYR1	16	4864623	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	4526429	4864623	85490130	122	10669											
NTAN1	123803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	15133833	15133833	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atttgaaactcactggtcctCctgctaaagttcgcgcagca	10	11	8	12	2	1	1	1	1	0	0	4	1	3	1	2	1	3	4	2	1	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:15133833C>G	ENST00000287706.3	-	8	724	c.632G>C	c.(631-633)gGa>gCa	p.G211A	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	211					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						CACTGGTCCTCCTGCTAAAGT	0.433																																					p.G211A		.											.	NTAN1-90	0			c.G632C						.						112	122	119					16																	15133833		2197	4300	6497	SO:0001583	missense	123803	exon8			GGTCCTCCTGCTA	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.632G>C	16.37:g.15133833C>G	ENSP00000287706:p.Gly211Ala	Somatic	277	0		WXS	Illumina HiSeq	Phase_I	286	106	NM_173474	0	0	0	0	0	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	37	CCDS10558.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344058	0.82022	.	.	ENSG00000157045	ENST00000287706	T	0.29655	1.56	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.62417	0.2426	M	0.85041	2.73	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.67369	-0.5688	10	0.72032	D	0.01	-20.0269	18.5814	0.91172	0.0:1.0:0.0:0.0	.	211	Q96AB6	NTAN1_HUMAN	A	211	ENSP00000287706:G211A	ENSP00000287706:G211A	G	-	2	0	NTAN1	15041334	1.000000	0.71417	0.987000	0.45799	0.810000	0.45777	5.601000	0.67606	2.630000	0.89119	0.650000	0.86243	GGA	.		0.433	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474		G	15133833	C	G	15133833	3	3	122	1	0	0	0	0	1	0	0	0	10721	855	30	4	312	4	NTAN1	16	15133833	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	10269210	15133833	75220920	123	10670											
SH2B1	25970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	28880661	28880661	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagagtctacccagccaggaCctgctgcttggacccagcga	9	6	12	14	1	1	1	0	0	1	1	1	5	1	3	4	2	5	2	4	2	1	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:28880661C>A	ENST00000322610.8	+	7	1705	c.1266C>A	c.(1264-1266)gaC>gaA	p.D422E	SH2B1_ENST00000337120.5_Missense_Mutation_p.D422E|SH2B1_ENST00000538342.1_Missense_Mutation_p.D86E|SH2B1_ENST00000395532.4_Missense_Mutation_p.D422E|SH2B1_ENST00000359285.5_Missense_Mutation_p.D422E|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000545570.1_Missense_Mutation_p.D112E			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	422	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CCAGCCAGGACCTGCTGCTTG	0.632																																					p.D422E		.											.	SH2B1-92	0			c.C1266A						.						50	48	48					16																	28880661		2197	4300	6497	SO:0001583	missense	25970	exon5			CCAGGACCTGCTG	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1266C>A	16.37:g.28880661C>A	ENSP00000321221:p.Asp422Glu	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	96	35	NM_001145796	0	0	20	52	32	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	37	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.420802	0.25639	.	.	ENSG00000178188	ENST00000322610;ENST00000545570;ENST00000359285;ENST00000538342;ENST00000395532;ENST00000337120	T;T;T;T;T;T	0.42131	0.98;1.71;1.01;1.6;1.0;1.0	5.17	-9.53	0.00575	.	0.393219	0.23983	N	0.042660	T	0.11836	0.0288	N	0.03608	-0.345	0.22112	N	0.999357	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.06405	0.0;0.001;0.001;0.002;0.001	T	0.09207	-1.0685	10	0.27082	T	0.32	-14.1712	6.2599	0.20893	0.0853:0.4877:0.1844:0.2426	.	86;112;422;422;422	B4DLN5;F5GXU7;Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;.;.;SH2B1_HUMAN	E	422;112;422;86;422;422	ENSP00000321221:D422E;ENSP00000440354:D112E;ENSP00000352232:D422E;ENSP00000438784:D86E;ENSP00000378903:D422E;ENSP00000337163:D422E	ENSP00000321221:D422E	D	+	3	2	SH2B1	28788162	0.011000	0.17503	0.821000	0.32701	0.889000	0.51656	-2.120000	0.01323	-1.453000	0.01928	-0.373000	0.07131	GAC	.		0.632	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		A	28880661	C	A	28880661	3	1	122	1	0	0	0	0	1	0	0	0	14259	506	18	4	1280	4	SH2B1	16	28880661	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	13746828	28880661	61474092	124	10671											
RABEP2	79874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	28925762	28925762	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggagatggaggcgctgTcatcgcagttgtgagcgaag	10	7	18	6	3	1	2	1	1	0	1	2	6	1	4	0	4	1	3	0	4	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:28925762T>A	ENST00000358201.4	-	5	1277	c.689A>T	c.(688-690)gAc>gTc	p.D230V	RABEP2_ENST00000357573.6_Missense_Mutation_p.D230V|RABEP2_ENST00000544477.1_Missense_Mutation_p.D159V|RABEP2_ENST00000561803.1_5'Flank	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	230					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						GGAGGCGCTGTCATCGCAGTT	0.682																																					p.D230V	Pancreas(66;639 1284 10093 31061 49099)	.											.	RABEP2-137	0			c.A689T						.						24	30	28					16																	28925762		2041	4205	6246	SO:0001583	missense	79874	exon5			GCGCTGTCATCGC	AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.689A>T	16.37:g.28925762T>A	ENSP00000350934:p.Asp230Val	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	48	11	NM_024816	2	0	11	21	8		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.867523	0.72065	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.70516	-0.33;-0.49;-0.27	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.74906	0.3778	L	0.29908	0.895	0.53005	D	0.999965	D;D;D;D	0.89917	0.999;1.0;0.998;0.999	D;D;D;D	0.87578	0.996;0.998;0.994;0.996	T	0.77653	-0.2507	10	0.87932	D	0	-35.9958	11.3244	0.49440	0.0:0.0:0.0:1.0	.	159;230;230;230	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	V	230;230;159	ENSP00000350934:D230V;ENSP00000350186:D230V;ENSP00000442798:D159V	ENSP00000350186:D230V	D	-	2	0	RABEP2	28833263	1.000000	0.71417	0.997000	0.53966	0.848000	0.48234	5.481000	0.66826	1.933000	0.56026	0.379000	0.24179	GAC	.		0.682	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		A	28925762	T	A	28925762	3	1	122	1	0	0	0	0	1	0	0	0	12994	1667	58	5	1056	5	RABEP2	16	28925762	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	45101	28925762	61428991	125	10672											
RNF40	9810	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30775599	30775599	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggaggtggagctggagcTgcaaggccgaatggagttct	9	8	18	6	1	1	1	0	1	1	0	1	6	1	5	1	6	3	4	1	6	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:30775599T>C	ENST00000324685.6	+	5	977	c.542T>C	c.(541-543)cTg>cCg	p.L181P	RNF40_ENST00000563683.1_Missense_Mutation_p.L181P|RNF40_ENST00000357890.5_Missense_Mutation_p.L181P|C16orf93_ENST00000541260.1_5'Flank|C16orf93_ENST00000545825.1_5'Flank|RNF40_ENST00000402121.3_Intron|C16orf93_ENST00000543610.1_5'Flank	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	181					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			GAGCTGGAGCTGCAAGGCCGA	0.632																																					p.L181P		.											.	RNF40-226	0			c.T542C						.						69	56	60					16																	30775599		2197	4300	6497	SO:0001583	missense	9810	exon5			TGGAGCTGCAAGG	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"RING-type (C3HC4) zinc fingers"	16867	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"	607700	"ring finger protein 40"			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.542T>C	16.37:g.30775599T>C	ENSP00000325677:p.Leu181Pro	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	36	11	NM_014771	0	0	9	32	23	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.423101	0.62733	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000452273	T;T	0.60920	0.76;0.15	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000001	T	0.78349	0.4269	M	0.82323	2.585	0.80722	D	1	D;B;B	0.76494	0.999;0.09;0.024	D;B;B	0.85130	0.997;0.06;0.038	T	0.81540	-0.0886	10	0.87932	D	0	-13.9353	15.6114	0.76721	0.0:0.0:0.0:1.0	.	181;181;181	O75150-4;A8K6K1;O75150	.;.;BRE1B_HUMAN	P	181;181;30	ENSP00000325677:L181P;ENSP00000350563:L181P	ENSP00000325677:L181P	L	+	2	0	RNF40	30683100	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	6.959000	0.76031	2.326000	0.78906	0.533000	0.62120	CTG	.		0.632	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		C	30775599	T	C	30775599	3	2	122	1	0	0	0	0	1	0	0	0	13525	1580	55	3	556	3	RNF40	16	30775599	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	1849837	30775599	59579154	126	10673											
ITGAM	3684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31340556	31340556	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttctcccttcagccatgggGtctccactaaatatctcaac	9	13	5	14	0	4	0	2	0	3	0	7	0	4	0	3	2	2	0	3	2	4	4	rs199790913		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:31340556G>T	ENST00000287497.8	+	24	2875	c.2800G>T	c.(2800-2802)Gtc>Ttc	p.V934F	ITGAM_ENST00000544665.3_Missense_Mutation_p.V935F			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	934					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CAGCCATGGGGTCTCCACTAA	0.542																																					p.V935F		.											.	ITGAM-226	0			c.G2803T						.	G	PHE/VAL,PHE/VAL	0,3888		0,0,1944	71	70	70		2803,2800	-6.6	0	16		70	1,8303		0,1,4151	yes	missense,missense	ITGAM	NM_001145808.1,NM_000632.3	50,50	0,1,6095	TT,TG,GG		0.012,0.0,0.0082	benign,benign	935/1154,934/1153	31340556	1,12191	1944	4152	6096	SO:0001583	missense	3684	exon24			CATGGGGTCTCCA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2800G>T	16.37:g.31340556G>T	ENSP00000287497:p.Val934Phe	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	28	10	NM_001145808	0	0	1	1	0	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464821	0.43839	0.0	1.2E-4	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.44083	0.93;0.93	4.87	-6.59	0.01830	Integrin alpha-2 (1);	.	.	.	.	T	0.31513	0.0799	L	0.44542	1.39	0.09310	N	1	B;B	0.34181	0.44;0.44	B;B	0.41619	0.361;0.361	T	0.41574	-0.9501	9	0.59425	D	0.04	.	1.9836	0.03432	0.3427:0.3574:0.1793:0.1206	.	934;934	Q4VAK1;P11215	.;ITAM_HUMAN	F	935;934	ENSP00000441691:V935F;ENSP00000287497:V934F	ENSP00000287497:V934F	V	+	1	0	ITGAM	31248057	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-0.727000	0.04931	-1.560000	0.01686	-0.903000	0.02851	GTC	.		0.542	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31340556	G	T	31340556	3	4	122	1	0	0	0	0	1	0	0	0	7908	1261	44	4	2897	4	ITGAM	16	31340556	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	564957	31340556	59014197	127	10674											
PHKB	5257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	47684490	47684490	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attaaacaatattggaaaatGcatggacgtccacttttcct	14	13	6	8	1	0	0	0	0	0	0	2	2	2	2	2	2	2	1	2	2	6	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:47684490G>T	ENST00000323584.5	+	19	1857	c.1833G>T	c.(1831-1833)atG>atT	p.M611I	PHKB_ENST00000299167.8_Missense_Mutation_p.M611I|PHKB_ENST00000455779.1_Missense_Mutation_p.M604I|PHKB_ENST00000566044.1_Missense_Mutation_p.M604I	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	611					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				ATTGGAAAATGCATGGACGTC	0.408																																					p.M611I		.											.	PHKB-154	0			c.G1833T						.						137	120	126					16																	47684490		2201	4300	6501	SO:0001583	missense	5257	exon19			GAAAATGCATGGA		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1833G>T	16.37:g.47684490G>T	ENSP00000313504:p.Met611Ile	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	120	40	NM_000293	0	0	9	19	10	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.004653	0.74932	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.90900	-2.75;-2.75	5.86	5.86	0.93980	Glycoside hydrolase 15-related (1);	0.036486	0.85682	D	0.000000	D	0.91432	0.7296	M	0.73598	2.24	0.80722	D	1	B;B	0.26902	0.036;0.163	B;B	0.29862	0.098;0.108	D	0.88208	0.2888	10	0.44086	T	0.13	-27.2635	20.1813	0.98205	0.0:0.0:1.0:0.0	.	611;604	Q93100;Q93100-4	KPBB_HUMAN;.	I	604;604;611	ENSP00000414345:M604I;ENSP00000313504:M611I	ENSP00000299167:M604I	M	+	3	0	PHKB	46241991	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.172000	0.94808	2.777000	0.95525	0.591000	0.81541	ATG	.		0.408	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			T	47684490	G	T	47684490	3	4	122	1	0	0	0	0	1	0	0	0	11871	1319	46	4	1966	4	PHKB	16	47684490	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	16343934	47684490	42670263	128	10675											
TMCO7	79613	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	68953020	68953020	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcagcaacattgcagagAgcctgtgcaagcctggccca	11	6	12	12	0	0	1	0	0	0	1	0	2	0	1	3	1	7	5	3	1	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:68953020A>T	ENST00000261778.1	+	12	2037	c.2025A>T	c.(2023-2025)agA>agT	p.R675S		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	675						integral component of membrane (GO:0016021)											CATTGCAGAGAGCCTGTGCAA	0.483																																					p.R675S													.	.	0			c.A2025T						.						85	81	82					16																	68953020		2110	4223	6333	SO:0001583	missense	79613	exon12			GCAGAGAGCCTGT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.2025A>T	16.37:g.68953020A>T	ENSP00000261778:p.Arg675Ser	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	31	12	NM_024562	0	0	5	6	1	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	37	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273473	0.80580	.	.	ENSG00000103047	ENST00000261778	.	.	.	5.36	5.36	0.76844	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65842	0.2730	M	0.72894	2.215	0.52099	D	0.999946	D	0.76494	0.999	D	0.80764	0.994	T	0.68044	-0.5513	9	0.09843	T	0.71	-14.1136	3.9662	0.09433	0.7035:0.0:0.1218:0.1747	.	675	Q9C0B7	TMCO7_HUMAN	S	675	.	ENSP00000261778:R675S	R	+	3	2	TMCO7	67510521	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.365000	0.34182	2.028000	0.59812	0.533000	0.62120	AGA	.		0.483	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68953020	A	T	68953020	3	4	122	1	0	0	0	0	1	0	0	0	16033	301	11	5	2071	5	TMCO7	16	68953020	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	21268530	68953020	21401733	129	10676											
DHX33	56919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	5353590	5353590	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcatgtgatccccctcgctgGatatgaacttcttgcggacc	7	12	9	13	2	2	2	1	2	1	0	4	4	3	4	3	2	2	1	3	2	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:5353590G>T	ENST00000225296.3	-	10	1861	c.1661C>A	c.(1660-1662)tCc>tAc	p.S554Y	DHX33_ENST00000433302.3_Missense_Mutation_p.S330Y	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	554					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CCCCTCGCTGGATATGAACTT	0.542																																					p.S554Y		.											.	DHX33-228	0			c.C1661A						.						153	154	153					17																	5353590		2203	4300	6503	SO:0001583	missense	56919	exon10			TCGCTGGATATGA	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"DEAH-boxes"	16718	protein-coding gene	gene with protein product		614405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1661C>A	17.37:g.5353590G>T	ENSP00000225296:p.Ser554Tyr	Somatic	243	1		WXS	Illumina HiSeq	Phase_I	298	114	NM_020162	0	0	4	5	1	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.816626	0.70912	.	.	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.32272	1.46;1.46	5.69	5.69	0.88448	Helicase-associated domain (2);	0.102611	0.64402	D	0.000001	T	0.58466	0.2124	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.79108	0.992;0.985	T	0.56408	-0.7984	10	0.10902	T	0.67	.	18.8064	0.92038	0.0:0.0:1.0:0.0	.	330;554	Q05BE5;Q9H6R0	.;DHX33_HUMAN	Y	554;330	ENSP00000225296:S554Y;ENSP00000413779:S330Y	ENSP00000225296:S554Y	S	-	2	0	DHX33	5294314	1.000000	0.71417	0.995000	0.50966	0.276000	0.26787	9.333000	0.96459	2.700000	0.92200	0.561000	0.74099	TCC	.		0.542	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		T	5353590	G	T	5353590	3	4	122	1	0	0	0	0	1	0	0	0	4517	1174	41	4	474	4	DHX33	17	5353590	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		5353590	75841620	130	10677											
FLII	2314	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18150014	18150014	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgccagaagtacacgatgCactggaagtcctcctctggc	9	8	10	14	1	1	1	0	0	1	1	3	3	3	2	4	2	3	2	4	2	3	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:18150014C>T	ENST00000327031.4	-	23	3170	c.2945G>A	c.(2944-2946)tGc>tAc	p.C982Y	FLII_ENST00000545457.2_Missense_Mutation_p.C927Y|FLII_ENST00000579294.1_Missense_Mutation_p.C971Y|FLII_ENST00000578558.1_Intron|FLII_ENST00000379450.4_Missense_Mutation_p.C896Y	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	982					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					GTACACGATGCACTGGAAGtc	0.567																																					p.C982Y													.	FLII-91	0			c.G2945A						.						124	90	101					17																	18150014		2203	4300	6503	SO:0001583	missense	2314	exon23			ACGATGCACTGGA	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"flightless I (Drosophila) homolog"			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.2945G>A	17.37:g.18150014C>T	ENSP00000324573:p.Cys982Tyr	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	33	9	NM_002018	0	0	121	235	114	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608402	0.66558	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.15718	2.4;2.4	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.44329	0.1288	M	0.74389	2.26	0.80722	D	1	B;B;D;B;P	0.64830	0.003;0.003;0.994;0.007;0.771	B;B;D;B;B	0.72625	0.007;0.007;0.978;0.035;0.424	T	0.16188	-1.0411	10	0.39692	T	0.17	-29.2534	19.4482	0.94857	0.0:1.0:0.0:0.0	.	896;896;861;982;951	E7EPM0;B4DIL0;F5H407;Q13045;B4DIX0	.;.;.;FLII_HUMAN;.	Y	982;861;896	ENSP00000324573:C982Y;ENSP00000368763:C896Y	ENSP00000324573:C982Y	C	-	2	0	FLII	18090739	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.125000	0.77193	2.601000	0.87937	0.655000	0.94253	TGC	.		0.567	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		T	18150014	C	T	18150014	3	4	122	1	0	0	0	0	1	0	0	0	5944	710	25	2	896	2	FLII	17	18150014	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	12796424	18150014	63045196	131	10678											
C17orf53	78995	hgsc.bcm.edu	37	chr17	42228328	42228328	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctccttccctcccctcttaGcagagtgggagaagtctgga	7	11	10	13	0	3	2	0	0	3	2	6	4	5	3	4	2	1	1	4	2	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:42228328G>C	ENST00000319977.4	+	4	1461		c.e4-1		C17orf53_ENST00000245382.6_Intron|C17orf53_ENST00000585683.1_Splice_Site	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53											NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TCCCCTCTTAGCAGAGTGGGA	0.458																																					.		.											.	C17orf53-90	0			c.1225-1G>C						.						57	46	50					17																	42228328		2203	4300	6503	SO:0001630	splice_region_variant	78995	exon4			CTCTTAGCAGAGT	AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.1225-1G>C	17.37:g.42228328G>C		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_001171251	0	0	0	0	0	A8K7A9|Q9BWM9|Q9HAI1	Splice_Site	SNP	ENST00000319977.4	37	CCDS11477.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.578088	0.45902	.	.	ENSG00000125319	ENST00000319977	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1347	0.93422	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C17orf53	39583854	1.000000	0.71417	0.634000	0.29324	0.261000	0.26267	8.091000	0.89528	2.826000	0.97356	0.561000	0.74099	.	.		0.458	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	Intron	C	42228328	G	C	42228328	5	2	122	1	0	0	0	0	0	0	1	0	1867	985	34	4	1238	4	C17orf53	17	42228328	Splice_Site	SNP	G	TCGA-GL-7773-01A-11D-2136-08	24078314	42228328	38966882	132	10679											
SKAP1	8631	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	46423341	46423341	+	Frame_Shift_Del	DEL	T	T	-																															gagtcccgctgtgattatcaTcagagctgtcctgtccaatg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:46423341delT	ENST00000336915.6	-	4	275	c.206delA	c.(205-207)gatfs	p.D70fs	SKAP1_ENST00000584924.1_Frame_Shift_Del_p.D70fs	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	70					positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						GTGATTATCATCAGAGCTGTC	0.438																																					p.D69fs		.											.	SKAP1-90	0			c.206delA						.						80	70	73					17																	46423341		2203	4300	6503	SO:0001589	frameshift_variant	8631	exon4			.	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.206delA	17.37:g.46423341delT	ENSP00000338171:p.Asp70fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	67	30	NM_003726	0	0	0	0	0	D3DTV1|O15268	Frame_Shift_Del	DEL	ENST00000336915.6	37	CCDS32674.1																																																																																			.		0.438	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726		-	46423341	T	-	46423341	7	5	122	1	0	1	0	1	0	0	0	0	14387	1435	50	0	909	0	SKAP1	17	46423341	Frame_Shift_Del	DEL	T	TCGA-GL-7773-01A-11D-2136-08	4195013	46423341	34771869	133	10680											
HOXB7	3217	broad.mit.edu	37	chr17	46688052	46688052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcggctcgagcccatagcCggccgcgtagacgccggccg	6	4	14	17	8	0	1	0	0	0	1	2	2	0	1	5	3	2	2	5	3	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:46688052C>T	ENST00000239165.7	-	1	327	c.229G>A	c.(229-231)Ggc>Agc	p.G77S	HOXB7_ENST00000567101.2_Intron	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	77					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						AGCCCATAGCCGGCCGCGTAG	0.726																																					p.G77S													.	HOXB7-90	0			c.G229A						.						6	5	5					17																	46688052		1962	3910	5872	SO:0001583	missense	3217	exon1			CATAGCCGGCCGC		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"Homeoboxes / ANTP class : HOXL subclass"	5118	protein-coding gene	gene with protein product		142962	"homeo box B7"	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.229G>A	17.37:g.46688052C>T	ENSP00000239165:p.Gly77Ser	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	13	7	NM_004502	0	0	8	11	3	A8K3N8|Q15957|Q53FN3|Q96BQ6	Missense_Mutation	SNP	ENST00000239165.7	37	CCDS11532.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613350	0.87359	.	.	ENSG00000120087	ENST00000239165	T	0.32272	1.46	4.27	4.27	0.50696	.	0.070609	0.56097	D	0.000039	T	0.27384	0.0672	L	0.46157	1.445	0.45648	D	0.998577	B	0.31503	0.326	B	0.18561	0.022	T	0.16070	-1.0415	10	0.56958	D	0.05	.	16.4843	0.84180	0.0:1.0:0.0:0.0	.	77	P09629	HXB7_HUMAN	S	77	ENSP00000239165:G77S	ENSP00000239165:G77S	G	-	1	0	HOXB7	44043051	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.205000	0.42770	2.212000	0.71576	0.561000	0.74099	GGC	.		0.726	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			T	46688052	C	T	46688052	3	4	122	1	0	0	0	0	1	0	0	0	7327	652	23	1	432	1	HOXB7	17	46688052	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	264711	46688052	34507158	134	10681											
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65134124	65134125	+	Missense_Mutation	DNP	TG	TG	GA																															cagcacgtattctaaacactTgatcagcatatggagtcacc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:65134124_65134125TG>GA	ENST00000358691.5	-	22	3041_3042	c.2875_2876CA>TC	c.(2875-2877)CAa>TCa	p.Q959S	HELZ_ENST00000580168.1_Missense_Mutation_p.Q960S	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	959						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TCTAAACACTTGATCAGCATAT	0.401																																					p.Q959S		.											.	HELZ	0			c.C2875T						.																																			SO:0001583	missense	9931	exon22			ACACTTGATCAGC	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.2875_2876delinsGA	17.37:g.65134124_65134125delinsGA	ENSP00000351524:p.Gln959Ser	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	197	74		0	0	0	0	0	I6L9H4	Missense_Mutation	DNP	ENST00000358691.5	37	CCDS42374.1																																																																																			.		0.401	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		GA	65134125	TG	GA	65134124	3	3	122	1	0	0	0	0	1	0	0	0	7070	1812	63	5	3000	5	HELZ	17	65134124	Missense_Mutation	DNP	TG	TCGA-GL-7773-01A-11D-2136-08	18446072	65134124	16061086	135	10682											
COG1	9382	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	71197359	71197359	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccccttcaaataagcacAtccactttgagtacaacatg	14	10	4	13	0	1	1	1	1	0	0	3	1	3	1	3	0	3	2	3	0	4	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:71197359A>G	ENST00000299886.4	+	7	1473	c.1393A>G	c.(1393-1395)Atc>Gtc	p.I465V		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	465					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			AAATAAGCACATCCACTTTGA	0.522																																					p.I465V		.											.	COG1-91	0			c.A1393G						.						161	147	152					17																	71197359		2203	4300	6503	SO:0001583	missense	9382	exon7			AAGCACATCCACT		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"Components of oligomeric golgi complex"	6545	protein-coding gene	gene with protein product		606973	"low density lipoprotein receptor defect B complementing"	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1393A>G	17.37:g.71197359A>G	ENSP00000299886:p.Ile465Val	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	195	69	NM_018714	0	0	5	11	6	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	A	6.539	0.467704	0.12402	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.19938	2.11;2.11	5.28	-4.74	0.03249	.	0.662686	0.16490	N	0.212142	T	0.08714	0.0216	N	0.17674	0.51	0.09310	N	0.999994	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.40924	-0.9537	10	0.07990	T	0.79	-9.3358	8.8132	0.34981	0.3346:0.2123:0.4531:0.0	.	465;465;465	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	V	465	ENSP00000400111:I465V;ENSP00000299886:I465V	ENSP00000299886:I465V	I	+	1	0	COG1	68708954	0.000000	0.05858	0.363000	0.25875	0.372000	0.29890	-0.711000	0.05019	-0.776000	0.04578	-0.250000	0.11733	ATC	.		0.522	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			G	71197359	A	G	71197359	3	3	122	1	0	0	0	0	1	0	0	0	3663	217	8	3	1419	3	COG1	17	71197359	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	6063235	71197359	9997851	136	10683											
QRICH2	84074	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74277019	74277019	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gatggcactctgcacacggcCcagcagctcctcgtcctgcg	6	7	11	17	3	1	0	0	0	1	0	4	1	3	0	3	2	4	4	3	2	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:74277019C>A	ENST00000262765.5	-	9	3960	c.3781G>T	c.(3781-3783)Ggc>Tgc	p.G1261C		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1261										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						TGCACACGGCCCAGCAGCTCC	0.617																																					p.G1261C													.	QRICH2-94	0			c.G3781T						.						67	54	58					17																	74277019		2203	4300	6503	SO:0001583	missense	84074	exon9			CACGGCCCAGCAG	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.3781G>T	17.37:g.74277019C>A	ENSP00000262765:p.Gly1261Cys	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	42	12	NM_032134	0	0	0	1	1	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808802	0.50421	.	.	ENSG00000129646	ENST00000262765;ENST00000447564;ENST00000301613	T;T	0.47528	2.99;0.84	5.1	5.1	0.69264	.	.	.	.	.	T	0.56499	0.1989	L	0.32530	0.975	0.27664	N	0.946994	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.50110	-0.8866	9	0.72032	D	0.01	-19.5057	10.1929	0.43037	0.0:0.8714:0.0:0.1286	.	1261;1261	B5MD94;Q9H0J4	.;QRIC2_HUMAN	C	1261;269;1261	ENSP00000262765:G1261C;ENSP00000394461:G269C	ENSP00000262765:G1261C	G	-	1	0	QRICH2	71788614	0.555000	0.26530	1.000000	0.80357	0.396000	0.30629	1.806000	0.38892	2.388000	0.81334	0.655000	0.94253	GGC	.		0.617	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74277019	C	A	74277019	3	1	122	1	0	0	0	0	1	0	0	0	12912	623	22	4	1254	4	QRICH2	17	74277019	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	3079660	74277019	6918191	137	10684											
KIAA0802	23255	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	8813134	8813135	+	Frame_Shift_Ins	INS	-	-	T																															atccatcacagcgagaagaaINSctggaaccgggagaaggtgg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr18:8813134_8813135insT	ENST00000306329.11	+	10	3719_3720	c.3719_3720insT	c.(3718-3723)aactggfs	p.W1241fs	SOGA2_ENST00000517570.1_Frame_Shift_Ins_p.W881fs|SOGA2_ENST00000306285.7_Frame_Shift_Ins_p.W275fs|SOGA2_ENST00000518815.1_Frame_Shift_Ins_p.W275fs|SOGA2_ENST00000359865.3_Frame_Shift_Ins_p.W922fs|SOGA2_ENST00000400050.3_Frame_Shift_Ins_p.W881fs																							AGCGAGAAGAACTGGAACCGGG	0.574																																					p.N921fs		.											.	.	0			c.2762_2763insT						.																																			SO:0001589	frameshift_variant	23255	exon12			.																												Exception_encountered	18.37:g.8813134_8813135insT	ENSP00000305027:p.Trp1241fs	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	26	14	NM_015210	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000306329.11	37																																																																																				.		0.574	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8813135	-	T	8813134	7	5	122	1	0	1	1	0	0	0	0	0	8215	43	2	0	2800	0	KIAA0802	18	8813134	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08		8813134	69264114	138	10685	111	2									
KIAA0802	23255	hgsc.bcm.edu;bcgsc.ca	37	chr18	8813135	8813135	+	Silent	SNP	C	C	T																															atccatcacagcgagaagaaCtggaaccgggagaaggtgga																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr18:8813135C>T	ENST00000306329.11	+	10	3720	c.3720C>T	c.(3718-3720)aaC>aaT	p.N1240N	SOGA2_ENST00000517570.1_Silent_p.N880N|SOGA2_ENST00000306285.7_Silent_p.N274N|SOGA2_ENST00000518815.1_Silent_p.N274N|SOGA2_ENST00000359865.3_Silent_p.N921N|SOGA2_ENST00000400050.3_Silent_p.N880N																							GCGAGAAGAACTGGAACCGGG	0.572																																					p.N921N		.											.	.	0			c.C2763T						.						45	44	44					18																	8813135		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon12			GAAGAACTGGAAC																												ENST00000306329.11:c.3720C>T	18.37:g.8813135C>T		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	26	14	NM_015210	0	0	0	0	0		Silent	SNP	ENST00000306329.11	37																																																																																				.		0.572	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8813135	C	T	8813135	2	4	122	1	0	0	0	0	0	0	0	1	8215	564	20	2		2	KIAA0802	18	8813135	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	1	8813135	69264113	139	10686	111	2									
ZNF358	140467	hgsc.bcm.edu;broad.mit.edu	37	chr19	7585576	7585576	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caaacccctccccggctccaGatccacccccagccctactc	8	5	4	24	1	0	1	0	0	0	1	4	1	3	1	9	1	3	1	9	1	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:7585576G>C	ENST00000597229.1	+	2	1618	c.1448G>C	c.(1447-1449)aGa>aCa	p.R483T	ZNF358_ENST00000394341.2_Missense_Mutation_p.R483T|MCOLN1_ENST00000264079.6_5'Flank|CTD-2207O23.11_ENST00000602083.1_RNA	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	483					embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						cccggctccagatccaccccc	0.672																																					p.R483T		.											.	ZNF358-90	0			c.G1448C						.						41	41	41					19																	7585576		2203	4300	6503	SO:0001583	missense	140467	exon2			GCTCCAGATCCAC	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"Zinc fingers, C2H2-type"	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1448G>C	19.37:g.7585576G>C	ENSP00000472305:p.Arg483Thr	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	40	15	NM_018083	0	0	80	136	56	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	37	CCDS32890.2	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350618	0.24512	.	.	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.42131	0.98	2.86	-2.54	0.06307	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16600	-1.0397	9	0.56958	D	0.05	.	3.8533	0.08965	0.2783:0.3607:0.361:0.0	.	483	Q9NW07	ZN358_HUMAN	T	483	ENSP00000377873:R483T	ENSP00000354703:R483T	R	+	2	0	ZNF358	7491576	0.000000	0.05858	0.013000	0.15412	0.546000	0.35178	-0.441000	0.06879	-0.411000	0.07530	0.462000	0.41574	AGA	.		0.672	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1			C	7585576	G	C	7585576	3	2	122	1	0	0	0	0	1	0	0	0	17899	942	33	4	1450	4	ZNF358	19	7585576	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		7585576	51543407	140	10687											
FARSA	2193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13039366	13039366	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccccatctccaggaagatCtgtcggaactgggagcggac	10	6	12	13	2	2	1	0	0	2	1	4	5	2	5	3	4	2	0	3	4	2	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:13039366C>A	ENST00000314606.4	-	6	726	c.708G>T	c.(706-708)caG>caT	p.Q236H	CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000588025.1_Missense_Mutation_p.Q276H|FARSA_ENST00000423140.2_Missense_Mutation_p.Q205H	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	236					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	CCAGGAAGATCTGTCGGAACT	0.652																																					p.Q236H		.											.	FARSA-91	0			c.G708T						.						44	43	43					19																	13039366		2203	4300	6503	SO:0001583	missense	2193	exon6			GAAGATCTGTCGG	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"Aminoacyl tRNA synthetases / Class II"	3592	protein-coding gene	gene with protein product	"phenylalanine tRNA ligase 1, alpha, cytoplasmic"	602918	"phenylalanine-tRNA synthetase-like", "phenylalanyl-tRNA synthetase-like, alpha subunit"	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.708G>T	19.37:g.13039366C>A	ENSP00000320309:p.Gln236His	Somatic	42	1		WXS	Illumina HiSeq	Phase_I	32	20	NM_004461	0	0	21	38	17	B4E363|Q9NSD8|Q9Y4W8	Missense_Mutation	SNP	ENST00000314606.4	37	CCDS12287.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.775233	0.49786	.	.	ENSG00000179115	ENST00000314606;ENST00000423140	T;T	0.64085	-0.08;-0.08	4.79	3.76	0.43208	Aminoacyl-tRNA synthetase, class II (1);Phenylalanyl-tRNA synthetase (1);	0.000000	0.85682	D	0.000000	T	0.76040	0.3932	M	0.81942	2.565	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.74023	0.982;0.963;0.963	T	0.77335	-0.2626	10	0.87932	D	0	-16.1128	7.8931	0.29691	0.0:0.8058:0.0:0.1942	.	205;236;236	B4E363;Q6IBR2;Q9Y285	.;.;SYFA_HUMAN	H	236;205	ENSP00000320309:Q236H;ENSP00000396548:Q205H	ENSP00000320309:Q236H	Q	-	3	2	FARSA	12900366	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.849000	0.48286	1.217000	0.43442	0.563000	0.77884	CAG	.		0.652	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		A	13039366	C	A	13039366	3	1	122	1	0	0	0	0	1	0	0	0	5698	912	32	4	850	4	FARSA	19	13039366	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	5453790	13039366	46089617	141	10688											
CILP2	148113	hgsc.bcm.edu	37	chr19	19656391	19656391	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggacgctggtgaccattAtgccccagggcagctgccgg	8	6	14	13	2	0	1	0	1	0	0	0	2	0	2	4	4	3	3	4	4	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:19656391A>G	ENST00000291495.5	+	8	3122	c.3037A>G	c.(3037-3039)Atg>Gtg	p.M1013V	CILP2_ENST00000586018.1_Missense_Mutation_p.M1019V	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	1013						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						GGTGACCATTATGCCCCAGGG	0.692																																					p.M1013V		.											.	CILP2-91	0			c.A3037G						.						14	16	15					19																	19656391		2201	4298	6499	SO:0001583	missense	148113	exon8			ACCATTATGCCCC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.3037A>G	19.37:g.19656391A>G	ENSP00000291495:p.Met1013Val	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	29	3	NM_153221	0	0	0	0	0	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	A	4.204	0.036578	0.08148	.	.	ENSG00000160161	ENST00000291495	T	0.08458	3.09	5.57	3.45	0.39498	.	0.845319	0.10704	N	0.643671	T	0.02767	0.0083	N	0.01576	-0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.44877	-0.9299	10	0.09590	T	0.72	-10.9758	7.2651	0.26226	0.7759:0.1452:0.0789:0.0	.	1013;1013	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	V	1013	ENSP00000291495:M1013V	ENSP00000291495:M1013V	M	+	1	0	CILP2	19517391	0.000000	0.05858	0.240000	0.24138	0.972000	0.66771	0.481000	0.22260	0.937000	0.37394	-0.501000	0.04562	ATG	.		0.692	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		G	19656391	A	G	19656391	3	3	122	1	0	0	0	0	1	0	0	0	3436	449	16	3	3067	3	CILP2	19	19656391	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	6617025	19656391	39472592	142	10689											
ZNF599	148103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35250173	35250173	+	Missense_Mutation	SNP	T	T	A																															tgggtaaaagcctttccacaTtctctacaaacatagggctt																								rs375598988		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:35250173T>A	ENST00000329285.8	-	4	1906	c.1533A>T	c.(1531-1533)gaA>gaT	p.E511D		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CCTTTCCACATTCTCTACAAA	0.418																																					p.E511D		.											.	ZNF599-92	0			c.A1533T						.						116	117	116					19																	35250173		2203	4300	6503	SO:0001583	missense	148103	exon4			TCCACATTCTCTA	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1533A>T	19.37:g.35250173T>A	ENSP00000333802:p.Glu511Asp	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	173	71	NM_001007248	0	0	0	0	0	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	T	4.110	0.018610	0.07959	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.07444	3.19	2.52	1.45	0.22620	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07143	0.0181	L	0.50993	1.605	0.58432	D	0.999999	B	0.06786	0.001	B	0.11329	0.006	T	0.24905	-1.0147	9	0.45353	T	0.12	.	2.0678	0.03606	0.2607:0.1492:0.0:0.5901	.	511	Q96NL3	ZN599_HUMAN	D	510;511;285	ENSP00000333802:E511D	ENSP00000333802:E511D	E	-	3	2	ZNF599	39942013	0.000000	0.05858	0.906000	0.35671	0.133000	0.20885	-1.206000	0.03011	0.357000	0.24183	0.482000	0.46254	GAA	.		0.418	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35250173	T	A	35250173	3	1	122	1	0	0	0	0	1	0	0	0	18061	1490	52	5	237	5	ZNF599	19	35250173	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	15593782	35250173	23878810	143	10690	112	2									
ZNF599	148103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35250175	35250175	+	Nonsense_Mutation	SNP	C	C	A																															ggtaaaagcctttccacattCtctacaaacatagggcttct																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:35250175C>A	ENST00000329285.8	-	4	1904	c.1531G>T	c.(1531-1533)Gaa>Taa	p.E511*		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTTCCACATTCTCTACAAACA	0.418																																					p.E511X		.											.	ZNF599-92	0			c.G1531T						.						115	117	116					19																	35250175		2203	4300	6503	SO:0001587	stop_gained	148103	exon4			CACATTCTCTACA	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1531G>T	19.37:g.35250175C>A	ENSP00000333802:p.Glu511*	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	176	71	NM_001007248	0	0	0	0	0	Q569K0|Q5PRG1	Nonsense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.544924	0.86022	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	.	.	.	2.52	2.52	0.30459	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999974	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	11.1742	0.48590	0.0:1.0:0.0:0.0	.	.	.	.	X	510;511;285	.	ENSP00000333802:E511X	E	-	1	0	ZNF599	39942015	0.000000	0.05858	0.726000	0.30738	0.087000	0.18053	0.077000	0.14738	1.711000	0.51337	0.591000	0.81541	GAA	.		0.418	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35250175	C	A	35250175	4	1	122	1	0	0	0	0	0	1	0	0	18061	922	32	4	239	4	ZNF599	19	35250175	Nonsense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2	35250175	23878808	144	10691	112	2									
NLRP4	147945	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56370219	56370219	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggaattgctagttgccaAttttgaaaaagcaaggagag	16	9	11	5	0	0	2	0	1	0	1	0	4	0	3	1	2	3	3	1	2	6	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:56370219A>G	ENST00000301295.6	+	3	1882	c.1460A>G	c.(1459-1461)aAt>aGt	p.N487S	NLRP4_ENST00000587891.1_Missense_Mutation_p.N412S|NLRP4_ENST00000346986.5_Missense_Mutation_p.N487S	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	487					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CTAGTTGCCAATTTTGAAAAA	0.418																																					p.N487S		.											.	NLRP4-216	0			c.A1460G						.						134	137	136					19																	56370219		2203	4300	6503	SO:0001583	missense	147945	exon3			TTGCCAATTTTGA	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22943	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4", "cancer/testis antigen 58"	609645	"NACHT, leucine rich repeat and PYD containing 4"	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1460A>G	19.37:g.56370219A>G	ENSP00000301295:p.Asn487Ser	Somatic	167	1		WXS	Illumina HiSeq	Phase_I	193	85	NM_134444	0	0	0	0	0	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	A	5.585	0.292659	0.10567	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.83250	-1.7;-1.7	4.24	-8.48	0.00935	.	.	.	.	.	T	0.52821	0.1758	N	0.04768	-0.165	0.09310	N	1	B;P;P	0.40515	0.005;0.719;0.597	B;B;B	0.38985	0.03;0.287;0.138	T	0.57130	-0.7864	9	0.09843	T	0.71	.	2.0751	0.03623	0.1469:0.1067:0.2674:0.479	.	487;412;487	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	S	487	ENSP00000301295:N487S;ENSP00000344787:N487S	ENSP00000301295:N487S	N	+	2	0	NLRP4	61062031	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.165000	0.09968	-1.965000	0.01010	-0.313000	0.08912	AAT	.		0.418	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		G	56370219	A	G	56370219	3	3	122	1	0	0	0	0	1	0	0	0	10505	101	4	3	1466	3	NLRP4	19	56370219	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	21120044	56370219	2758764	145	10692											
SALL4	57167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	50407897	50407897	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgtagagggccgcctcGtctttgggtttgacatccac	5	13	12	11	2	1	2	0	1	1	1	3	2	2	2	3	2	1	3	3	2	1	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr20:50407897G>C	ENST00000217086.4	-	2	1236	c.1125C>G	c.(1123-1125)gaC>gaG	p.D375E	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Missense_Mutation_p.D375E	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	375					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGGCCGCCTCGTCTTTGGGTT	0.547																																					p.D375E		.											.	SALL4-92	0			c.C1125G						.						78	76	77					20																	50407897		2203	4300	6503	SO:0001583	missense	57167	exon2			CGCCTCGTCTTTG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1125C>G	20.37:g.50407897G>C	ENSP00000217086:p.Asp375Glu	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	128	45	NM_020436	0	0	1	2	1	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	4.854	0.158821	0.09236	.	.	ENSG00000101115	ENST00000217086;ENST00000395997	T;T	0.08807	3.05;3.34	5.29	-5.33	0.02713	.	0.000000	0.47852	D	0.000204	T	0.08044	0.0201	L	0.29908	0.895	0.80722	D	1	B;D	0.69078	0.028;0.997	B;D	0.76575	0.006;0.988	T	0.49781	-0.8903	10	0.02654	T	1	-53.0902	4.1442	0.10209	0.5133:0.168:0.2268:0.0919	.	375;375	A2A2D8;Q9UJQ4	.;SALL4_HUMAN	E	375	ENSP00000217086:D375E;ENSP00000379319:D375E	ENSP00000217086:D375E	D	-	3	2	SALL4	49841304	0.000000	0.05858	0.608000	0.28969	0.091000	0.18340	-1.867000	0.01646	-0.896000	0.03915	-1.581000	0.00855	GAC	.		0.547	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			C	50407897	G	C	50407897	3	2	122	1	0	0	0	0	1	0	0	0	13845	1136	40	4	2048	4	SALL4	20	50407897	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		50407897	12617623	146	10693											
RGL4	266747	hgsc.bcm.edu;bcgsc.ca	37	chr22	24034222	24034222	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagatctggagctttgatgaGgaagctgctcacaaatctgc	11	10	11	9	0	3	3	1	2	2	1	3	5	3	5	0	2	4	3	0	2	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:24034222G>A	ENST00000290691.5	+	1	1175	c.5G>A	c.(4-6)aGg>aAg	p.R2K	KB-1572G7.2_ENST00000421064.1_RNA|AP000347.2_ENST00000417194.1_RNA|GUSBP11_ENST00000455485.1_RNA|RGL4_ENST00000401461.1_Intron	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	2					small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						GCTTTGATGAGGAAGCTGCTC	0.607																																					p.R2K		.											.	RGL4-228	0			c.G5A						.						59	58	58					22																	24034222		2203	4300	6503	SO:0001583	missense	266747	exon1			TGATGAGGAAGCT		CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"RalGDS related oncogene"	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.5G>A	22.37:g.24034222G>A	ENSP00000290691:p.Arg2Lys	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	88	5	NM_153615	0	0	2	2	0	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	37	CCDS13811.1	.	.	.	.	.	.	.	.	.	.	g	8.750	0.921142	0.17982	.	.	ENSG00000159496	ENST00000290691;ENST00000382833;ENST00000423392	T;T	0.32023	1.47;1.47	1.77	-2.54	0.06307	.	7.772780	0.01150	U	0.006397	T	0.18215	0.0437	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.0	T	0.27536	-1.0071	10	0.87932	D	0	.	4.1084	0.10047	0.1754:0.4809:0.3436:0.0	.	2;2	E9PH87;Q8IZJ4	.;RGDSR_HUMAN	K	2	ENSP00000290691:R2K;ENSP00000402142:R2K	ENSP00000290691:R2K	R	+	2	0	RGL4	22364222	0.139000	0.22563	0.000000	0.03702	0.001000	0.01503	-0.102000	0.10956	-0.558000	0.06118	-0.386000	0.06593	AGG	.		0.607	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615		A	24034222	G	A	24034222	3	1	122	1	0	0	0	0	1	0	0	0	13311	1000	35	2	7	2	RGL4	22	24034222	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		24034222	27270344	147	10694											
UQCR10	29796	hgsc.bcm.edu	37	chr22	30163538	30163539	+	Splice_Site	DNP	GT	GT	AA																															acgaccacatcaacgaggggGtgagggcctgtgccatccct																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:30163538_30163539GT>AA	ENST00000330029.6	+	1	180		c.e1+1		ZMAT5_ENST00000397781.3_5'Flank|ZMAT5_ENST00000344318.3_5'Flank|UQCR10_ENST00000401406.3_Missense_Mutation_p.V51K	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X						cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						CAACGAGGGGGTGAGGGCCTGT	0.599																																					p.V51K		.											.	UQCR10	0			c.T152A						.																																			SO:0001630	splice_region_variant	29796	exon1			AGGGGGTGAGGGC	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"Mitochondrial respiratory chain complex / Complex III"	30863	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa", "complex III subunit 9"	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	Exception_encountered	22.37:g.30163538_30163539delinsAA		Somatic	47	2		WXS	Illumina HiSeq	Phase_I	53	7		0	0	0	0	0	B5MCM5|Q9T2V6	Missense_Mutation	DNP	ENST00000330029.6	37	CCDS46680.1																																																																																			.		0.599	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387	Intron	AA	30163539	GT	AA	30163538	5	1	122	1	0	0	0	0	0	0	1	0	17049	1275	44	2	153	2	UQCR10	22	30163538	Splice_Site	DNP	GT	TCGA-GL-7773-01A-11D-2136-08	6129316	30163538	21141028	148	10695											
MICALL1	85377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38328888	38328888	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggcgagagtccgagctcAtctatgtgtgagtccccccg	6	9	13	13	4	2	2	1	1	1	1	4	4	4	2	4	1	2	1	4	1	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:38328888A>G	ENST00000215957.6	+	12	2353	c.2227A>G	c.(2227-2229)Atc>Gtc	p.I743V	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	743	Necessary and sufficient to associate with tubular recycling endosome membranes, mediate phosphatidic acid- binding and membrane tubulation.|RAB-binding domain (RBD); mediates the interaction with RAB13 and RAB35 and intramolecular interaction with the CH domain.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					GTCCGAGCTCATCTATGTGTG	0.582																																					p.I743V		.											.	MICALL1-153	0			c.A2227G						.						68	63	65					22																	38328888		2203	4300	6503	SO:0001583	missense	85377	exon12			GAGCTCATCTATG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"molecule interacting with Rab13"					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.2227A>G	22.37:g.38328888A>G	ENSP00000215957:p.Ile743Val	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	77	31	NM_033386	0	0	0	0	0	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.26|13.26	2.184944|2.184944	0.38609|0.38609	.|.	.|.	ENSG00000100139|ENSG00000100139	ENST00000454685|ENST00000215957;ENST00000402631;ENST00000424008	.|T;T;T	.|0.39406	.|1.08;1.08;1.08	5.47|5.47	4.37|4.37	0.52481|0.52481	.|Domain of unknown function DUF3585 (1);	.|0.102897	.|0.43919	.|D	.|0.000508	T|T	0.16854|0.16854	0.0405|0.0405	N|N	0.02960|0.02960	-0.455|-0.455	0.40194|0.40194	D|D	0.97743|0.97743	.|B	.|0.34329	.|0.449	.|B	.|0.34873	.|0.191	T|T	0.09796|0.09796	-1.0658|-1.0658	5|10	.|0.19147	.|T	.|0.46	.|.	6.8248|6.8248	0.23876|0.23876	0.7709:0.1531:0.076:0.0|0.7709:0.1531:0.076:0.0	.|.	.|743	.|Q8N3F8	.|MILK1_HUMAN	R|V	318|743;170;57	.|ENSP00000215957:I743V;ENSP00000384608:I170V;ENSP00000416766:I57V	.|ENSP00000215957:I743V	H|I	+|+	2|1	0|0	MICALL1|MICALL1	36658834|36658834	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	5.031000|5.031000	0.64134|0.64134	2.070000|2.070000	0.61991|0.61991	0.482000|0.482000	0.46254|0.46254	CAT|ATC	.		0.582	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		G	38328888	A	G	38328888	3	3	122	1	0	0	0	0	1	0	0	0	9598	217	8	3	2273	3	MICALL1	22	38328888	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	8165350	38328888	12975678	149	10696											
MKL1	57591	hgsc.bcm.edu;bcgsc.ca	37	chr22	40816901	40816901	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtggtgctgctgctgctgCtggttgaggatctgcagctg	3	14	16	8	0	1	1	0	1	1	0	1	2	1	2	0	3	7	8	0	3	0	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:40816901C>G	ENST00000355630.3	-	10	1421	c.831G>C	c.(829-831)caG>caC	p.Q277H	MKL1_ENST00000396617.3_Missense_Mutation_p.Q277H|MKL1_ENST00000407029.1_Missense_Mutation_p.Q277H|MKL1_ENST00000402042.1_Missense_Mutation_p.Q227H	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	277	Gln-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GCTGCTGCTGCTGGTTGAGGA	0.657			T	RBM15	acute megakaryocytic leukemia																																p.Q277H		.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1-948	0			c.G831C						.						62	63	62					22																	40816901		2203	4300	6503	SO:0001583	missense	57591	exon10			CTGCTGCTGGTTG	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.831G>C	22.37:g.40816901C>G	ENSP00000347847:p.Gln277His	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	72	4	NM_020831	0	0	16	16	0	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766193	0.69878	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.61859	0.16;0.11;0.07;0.16	5.26	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.77616	2.38	0.48696	D	0.999692	P;D;P	0.67145	0.787;0.996;0.787	B;D;B	0.75484	0.294;0.986;0.294	T	0.75385	-0.3336	10	0.66056	D	0.02	-15.2355	9.9937	0.41887	0.0:0.8449:0.0:0.1551	.	227;277;277	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	H	277;277;227;277	ENSP00000347847:Q277H;ENSP00000379861:Q277H;ENSP00000385584:Q227H;ENSP00000385835:Q277H	ENSP00000347847:Q277H	Q	-	3	2	MKL1	39146847	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.270000	0.51600	1.210000	0.43336	0.462000	0.41574	CAG	.		0.657	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		G	40816901	C	G	40816901	3	3	122	1	0	0	0	0	1	0	0	0	9626	796	28	4	1988	4	MKL1	22	40816901	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2488013	40816901	10487665	150	10697											
ARMCX1	51309	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	100808732	100808733	+	Frame_Shift_Ins	INS	-	-	T																															cttacaatgcccttaataacINSttgagtgtgaacgcagaaaa																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:100808732_100808733insT	ENST00000372829.3	+	4	1190_1191	c.819_820insT	c.(820-822)ttgfs	p.L274fs		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	274						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						CCCTTAATAACTTGAGTGTGAA	0.426																																					p.N273fs		.											.	ARMCX1-134	0			c.819_820insT						.																																			SO:0001589	frameshift_variant	51309	exon4			.	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"Armadillo repeat containing"	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.821dupT	X.37:g.100808734_100808734dupT	ENSP00000361917:p.Leu274fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	103	44	NM_016608	0	0	0	0	0	Q53HK2|Q9H2Q0	Frame_Shift_Ins	INS	ENST00000372829.3	37	CCDS14487.1																																																																																			.		0.426	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		T	100808733	-	T	100808732	7	5	122	1	0	1	1	0	0	0	0	0	960	564	20	0	821	0	ARMCX1	23	100808732	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08		100808732	54461828	151	10698											
PLS3	5358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	114883786	114883786	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagaagaatcggagccagaGtgtatgctctccctgaagac	12	8	11	10	1	1	5	0	1	1	4	3	6	1	6	2	1	2	2	2	1	5	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:114883786G>C	ENST00000420625.2	+	16	1932	c.1798G>C	c.(1798-1800)Gtg>Ctg	p.V600L	PLS3_ENST00000537301.1_Missense_Mutation_p.V587L|PLS3_ENST00000539310.1_Missense_Mutation_p.V555L|PLS3_ENST00000543070.1_Missense_Mutation_p.V194L|PLS3_ENST00000355899.3_Missense_Mutation_p.V600L|PLS3_ENST00000289290.3_Missense_Mutation_p.V564L	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	600	Actin-binding 2.|CH 4. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						CGGAGCCAGAGTGTATGCTCT	0.433																																					p.V600L	Colon(160;1047 1864 8490 12969 29601)	.											.	PLS3-193	0			c.G1798C						.						161	136	145					X																	114883786		2203	4300	6503	SO:0001583	missense	5358	exon16			GCCAGAGTGTATG	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.1798G>C	X.37:g.114883786G>C	ENSP00000398945:p.Val600Leu	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	183	72	NM_005032	0	0	2	36	34	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Missense_Mutation	SNP	ENST00000420625.2	37	CCDS14568.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.840800	0.32513	.	.	ENSG00000102024	ENST00000355899;ENST00000537301;ENST00000289290;ENST00000420625;ENST00000539310;ENST00000543070	D;D;D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58;-3.58;-3.58	5.59	5.59	0.84812	Calponin homology domain (5);	0.053518	0.85682	D	0.000000	D	0.95367	0.8496	M	0.81942	2.565	0.80722	D	1	B;B;B	0.21606	0.02;0.058;0.009	B;B;B	0.39771	0.309;0.306;0.215	D	0.93807	0.7106	10	0.87932	D	0	-7.9383	10.9343	0.47237	0.0886:0.0:0.9114:0.0	.	573;587;600	B4DPW9;B4DGB4;P13797	.;.;PLST_HUMAN	L	600;587;564;600;555;194	ENSP00000348163:V600L;ENSP00000445105:V587L;ENSP00000289290:V564L;ENSP00000398945:V600L;ENSP00000445339:V555L;ENSP00000439260:V194L	ENSP00000289290:V564L	V	+	1	0	PLS3	114790042	1.000000	0.71417	0.983000	0.44433	0.191000	0.23601	7.881000	0.87252	2.494000	0.84150	0.594000	0.82650	GTG	.		0.433	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			C	114883786	G	C	114883786	3	2	122	1	0	0	0	0	1	0	0	0	12134	1029	36	4	1856	4	PLS3	23	114883786	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	14075054	114883786	40386774	152	10699											
WDR44	54521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	117526750	117526750	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggactgttagccatagaTcaagtactaccggaagaatc	13	8	9	11	2	1	2	1	0	0	2	2	4	1	4	3	2	3	2	3	2	7	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:117526750T>G	ENST00000254029.3	+	4	737	c.342T>G	c.(340-342)gaT>gaG	p.D114E	WDR44_ENST00000371822.5_Missense_Mutation_p.D89E|WDR44_ENST00000371825.3_Missense_Mutation_p.D114E|WDR44_ENST00000493448.1_3'UTR	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	114	Binding activity.					endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						TAGCCATAGATCAAGTACTAC	0.403																																					p.D114E		.											.	WDR44-133	0			c.T342G						.						88	83	85					X																	117526750		2203	4300	6503	SO:0001583	missense	54521	exon4			CATAGATCAAGTA	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.342T>G	X.37:g.117526750T>G	ENSP00000254029:p.Asp114Glu	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	190	78	NM_001184965	0	0	8	8	0	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	37	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.058|0.058	-1.232190|-1.232190	0.01505|0.01505	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825|ENST00000371848	T;T;T|.	0.71579|.	-0.58;0.02;0.15|.	5.68|5.68	0.195|0.195	0.15151|0.15151	.|.	0.637812|.	0.17319|.	N|.	0.178592|.	T|T	0.09949|0.09949	0.0244|0.0244	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.0|.	T|T	0.26326|0.26326	-1.0106|-1.0106	10|5	0.08179|.	T|.	0.78|.	-1.0257|-1.0257	1.5608|1.5608	0.02594|0.02594	0.3214:0.0908:0.3459:0.2419|0.3214:0.0908:0.3459:0.2419	.|.	89;114;114|.	F8W913;Q5JSH3-2;Q5JSH3|.	.;.;WDR44_HUMAN|.	E|A	89;114;114|14	ENSP00000360887:D89E;ENSP00000254029:D114E;ENSP00000360890:D114E|.	ENSP00000254029:D114E|.	D|S	+|+	3|1	2|0	WDR44|WDR44	117410778|117410778	0.397000|0.397000	0.25270|0.25270	0.074000|0.074000	0.20217|0.20217	0.110000|0.110000	0.19582|0.19582	0.688000|0.688000	0.25422|0.25422	-0.017000|-0.017000	0.14103|0.14103	0.486000|0.486000	0.48141|0.48141	GAT|TCA	.		0.403	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		G	117526750	T	G	117526750	3	3	122	1	0	0	0	0	1	0	0	0	17329	1432	50	5	356	5	WDR44	23	117526750	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	2642964	117526750	37743810	153	10700											
THOC2	57187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	122801090	122801090	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgccaatcaccaatctttaAtaaggcttccaacaagccaa	15	10	4	12	0	2	0	1	0	1	0	3	0	3	0	4	1	3	1	4	1	7	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:122801090A>G	ENST00000245838.8	-	11	1088	c.1057T>C	c.(1057-1059)Tta>Cta	p.L353L	THOC2_ENST00000491737.1_Silent_p.L238L|THOC2_ENST00000355725.4_Silent_p.L353L	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	353					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CCAATCTTTAATAAGGCTTCC	0.378																																					p.L353L		.											.	THOC2-133	0			c.T1057C						.						138	121	127					X																	122801090		1869	4097	5966	SO:0001819	synonymous_variant	57187	exon11			TCTTTAATAAGGC	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.1057T>C	X.37:g.122801090A>G		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	171	64	NM_001081550	0	0	1	7	6	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																			.		0.378	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			G	122801090	A	G	122801090	2	3	122	1	0	0	0	0	0	0	0	1	15897	98	4	3		3	THOC2	23	122801090	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	5274340	122801090	32469470	154	10701											
ATP2B3	492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	152826336	152826336	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	accatcgttttgggcactttCgggattcaggtaggaggggc	7	11	15	8	2	1	0	1	0	0	0	3	2	1	2	1	6	0	3	1	6	1	5	rs181539158		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:152826336C>T	ENST00000349466.2	+	18	3368	c.3042C>T	c.(3040-3042)ttC>ttT	p.F1014F	ATP2B3_ENST00000263519.4_Silent_p.F1014F|ATP2B3_ENST00000370186.1_Silent_p.F1000F|ATP2B3_ENST00000393842.1_Silent_p.F1000F|ATP2B3_ENST00000370181.2_Silent_p.F1000F|ATP2B3_ENST00000359149.3_Silent_p.F1014F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1014					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.F1014F(5)|p.F1014L(3)|p.F1000F(2)|p.F1000L(1)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGGCACTTTCGGGATTCAGG	0.572													C|||	1	0.000264901	8e-04	0	3775	,	,		13946	0		0	False		,,,				2504	0				p.F1014F		.											.	ATP2B3-109	11	Substitution - coding silent(7)|Substitution - Missense(4)	lung(4)|breast(4)|large_intestine(3)	c.C3042T						.						194	141	159					X																	152826336		2203	4300	6503	SO:0001819	synonymous_variant	492	exon17			CACTTTCGGGATT	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3042C>T	X.37:g.152826336C>T		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	106	50	NM_001001344	0	0	0	0	0	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			C|1.000;A|0.000		0.572	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152826336	C	T	152826336	2	4	122	1	0	0	0	0	0	0	0	1	1142	883	31	1		1	ATP2B3	23	152826336	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	30025246	152826336	2444224	155	10702											
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12919095	12919095	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagacgcttcatctggagccAttgaaagcattgctggaagg	12	9	12	8	1	2	2	1	1	1	1	2	4	2	4	1	3	3	3	1	3	3	3	rs116865587	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:12919095A>C	ENST00000240189.2	+	2	318	c.231A>C	c.(229-231)ccA>ccC	p.P77P		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	77					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATCTGGAGCCATTGAAAGCAT	0.557																																					p.P77P		.											.	PRAMEF2-68	0			c.A231C						.						165	177	173					1																	12919095		2201	4296	6497	SO:0001819	synonymous_variant	65122	exon2			GGAGCCATTGAAA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"-"	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.231A>C	1.37:g.12919095A>C		Somatic	153	1		WXS	Illumina HiSeq	Phase_I	39	2	NM_023014	0	0	0	0	0		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			A|0.974;G|0.026		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		C	12919095	A	C	12919095	2	2	123	1	0	0	0	0	0	0	0	1	12464	204	8	5		5	PRAMEF2	1	12919095	Silent	SNP	A	TCGA-GL-7966-01A-11D-2201-08		12919095	236331526	1	10703											
HFM1	164045	hgsc.bcm.edu	37	chr1	91844675	91844675	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaatagatcatccattactGtatctccagtaagttcttta	13	15	4	9	0	3	1	1	0	2	1	5	1	4	1	2	0	1	3	2	0	6	7			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:91844675G>C	ENST00000370425.3	-	9	1201	c.1103C>G	c.(1102-1104)aCa>aGa	p.T368R	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.T47R	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	368	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		ATCCATTACTGTATCTCCAGT	0.333																																					p.T368R		.											.	HFM1-112	0			c.C1103G						.						85	82	83					1																	91844675		2203	4299	6502	SO:0001583	missense	164045	exon9			ATTACTGTATCTC	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"SEC63 domain containing 1"	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1103C>G	1.37:g.91844675G>C	ENSP00000359454:p.Thr368Arg	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_001017975	0	0	0	0	0	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747630	0.89663	.	.	ENSG00000162669	ENST00000370425;ENST00000370424;ENST00000370421;ENST00000541820	T;T	0.37235	2.43;1.21	5.42	5.42	0.78866	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.40385	U	0.001107	T	0.48352	0.1495	L	0.58669	1.825	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.999	P;D;D	0.79784	0.899;0.993;0.981	T	0.21621	-1.0240	10	0.26408	T	0.33	.	19.2139	0.93768	0.0:0.0:1.0:0.0	.	47;368;368	A6NGI5;B7ZM16;A2PYH4	.;.;HFM1_HUMAN	R	368;47;52;401	ENSP00000359454:T368R;ENSP00000359453:T47R	ENSP00000359450:T52R	T	-	2	0	HFM1	91617263	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.476000	0.97823	2.534000	0.85438	0.563000	0.77884	ACA	.		0.333	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91844675	G	C	91844675	3	2	123	1	0	0	0	0	1	0	0	0	7104	1377	48	4	3328	4	HFM1	1	91844675	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	78925580	91844675	157405946	2	10704											
EVI5	7813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	93160869	93160869	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtctgcccattagcttacctCagacataaagatatcaaata	15	11	5	10	0	3	2	2	0	1	2	3	2	3	2	2	0	3	1	2	0	7	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:93160869C>G	ENST00000370331.1	-	7	1048	c.1039G>C	c.(1039-1041)Gag>Cag	p.E347Q	EVI5_ENST00000543509.1_Missense_Mutation_p.E347Q|EVI5_ENST00000540033.1_Missense_Mutation_p.E347Q	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	347	Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.|Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		TAGCTTACCTCAGACATAAAG	0.423																																					p.E347Q		.											.	EVI5-136	0			c.G1039C						.						107	109	108					1																	93160869		2203	4300	6503	SO:0001583	missense	7813	exon7			TTACCTCAGACAT	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1039G>C	1.37:g.93160869C>G	ENSP00000359356:p.Glu347Gln	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	66	7	NM_005665	0	0	0	0	0	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	37	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	C	31	5.084339	0.94100	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	T;T;T	0.14766	2.48;2.48;2.48	5.94	5.94	0.96194	Rab-GAP/TBC domain (4);	0.045268	0.85682	D	0.000000	T	0.34424	0.0897	M	0.83223	2.63	0.80722	D	1	D;D	0.60575	0.986;0.988	P;P	0.62560	0.844;0.904	T	0.13282	-1.0515	10	0.87932	D	0	-17.0097	20.3552	0.98837	0.0:1.0:0.0:0.0	.	347;347	F5H4R0;O60447	.;EVI5_HUMAN	Q	347	ENSP00000359356:E347Q;ENSP00000440826:E347Q;ENSP00000445019:E347Q	ENSP00000359356:E347Q	E	-	1	0	EVI5	92933457	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.760000	0.85248	2.812000	0.96745	0.557000	0.71058	GAG	.		0.423	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		G	93160869	C	G	93160869	3	3	123	1	0	0	0	0	1	0	0	0	5302	835	29	4	1441	4	EVI5	1	93160869	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08	1316194	93160869	156089752	3	10705											
ASH1L	55870	broad.mit.edu	37	chr1	155451419	155451419	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatctttactgatcagaccTgccaaaggacaactcattag	13	10	7	11	0	3	2	2	1	1	1	3	3	3	3	2	1	3	1	2	1	4	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:155451419T>C	ENST00000368346.3	-	3	1881	c.1242A>G	c.(1240-1242)gcA>gcG	p.A414A	ASH1L_ENST00000548830.1_3'UTR|ASH1L_ENST00000392403.3_Silent_p.A414A			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	414					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TGATCAGACCTGCCAAAGGAC	0.438																																					p.A414A													.	ASH1L-234	0			c.A1242G						.						98	95	96					1																	155451419		2203	4299	6502	SO:0001819	synonymous_variant	55870	exon3			CAGACCTGCCAAA	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.1242A>G	1.37:g.155451419T>C		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	145	3	NM_018489	0	0	8	8	0	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37																																																																																				.		0.438	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155451419	T	C	155451419	2	2	123	1	0	0	0	0	0	0	0	1	1042	1567	55	3		3	ASH1L	1	155451419	Silent	SNP	T	TCGA-GL-7966-01A-11D-2201-08	62290550	155451419	93799202	4	10706											
OR6Y1	391112	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	158517503	158517503	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtagcgtagtggattacaAatggctacatagcggtcaaa	13	9	13	6	2	1	0	1	0	0	0	1	1	1	1	0	4	4	3	0	4	7	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:158517503A>T	ENST00000302617.3	-	1	392	c.393T>A	c.(391-393)atT>atA	p.I131I		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					GTGGATTACAAATGGCTACAT	0.473																																					p.I131I		.											.	OR6Y1-69	0			c.T393A						.						100	85	90					1																	158517503		2202	4300	6502	SO:0001819	synonymous_variant	391112	exon1			ATTACAAATGGCT	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.393T>A	1.37:g.158517503A>T		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	104	8	NM_001005189	0	0	0	0	0	Q6IFS0	Silent	SNP	ENST00000302617.3	37	CCDS30899.1																																																																																			.		0.473	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		T	158517503	A	T	158517503	2	4	123	1	0	0	0	0	0	0	0	1	11239	10	1	5		5	OR6Y1	1	158517503	Silent	SNP	A	TCGA-GL-7966-01A-11D-2201-08	3066084	158517503	90733118	5	10707											
NUAK2	81788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205274389	205274389	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcactaggatcttatggTcatgcccatcaaagggcatg	10	12	10	9	0	4	0	3	0	1	0	4	1	4	1	1	3	1	2	1	3	3	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:205274389T>C	ENST00000367157.3	-	6	887	c.761A>G	c.(760-762)gAc>gGc	p.D254G		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GATCTTATGGTCATGCCCATC	0.572																																					p.D254G		.											.	NUAK2-391	0			c.A761G						.						98	83	88					1																	205274389		2203	4300	6503	SO:0001583	missense	81788	exon6			TTATGGTCATGCC	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.761A>G	1.37:g.205274389T>C	ENSP00000356125:p.Asp254Gly	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	69	17	NM_030952	0	0	32	61	29		Missense_Mutation	SNP	ENST00000367157.3	37	CCDS1453.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.895395	0.91962	.	.	ENSG00000163545	ENST00000367157	T	0.26373	1.74	5.73	5.73	0.89815	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.47093	D	0.000245	T	0.38983	0.1061	L	0.41124	1.26	0.80722	D	1	D	0.63046	0.992	P	0.59056	0.851	T	0.13710	-1.0499	10	0.62326	D	0.03	.	15.683	0.77388	0.0:0.0:0.0:1.0	.	254	Q9H093	NUAK2_HUMAN	G	254	ENSP00000356125:D254G	ENSP00000356125:D254G	D	-	2	0	NUAK2	203541012	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.040000	0.89188	2.188000	0.69820	0.459000	0.35465	GAC	.		0.572	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		C	205274389	T	C	205274389	3	2	123	1	0	0	0	0	1	0	0	0	10739	1667	58	3	1133	3	NUAK2	1	205274389	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	46756886	205274389	43976232	6	10708											
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	216138718	216138718	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttaagagtccattagggCgaaaaggtgcttcccacctc	10	10	11	10	1	0	1	0	0	0	1	3	2	2	1	3	2	1	2	3	2	4	3	rs201386640		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:216138718C>T	ENST00000307340.3	-	37	7447	c.7061G>A	c.(7060-7062)cGc>cAc	p.R2354H	USH2A_ENST00000366943.2_Missense_Mutation_p.R2354H	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2354	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in USH2A). {ECO:0000269|PubMed:17085681}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.R2354H(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCCATTAGGGCGAAAAGGTGC	0.403										HNSCC(13;0.011)			C|||	1	0.000199681	0	0	5008	,	,		16044	0		0.001	False		,,,				2504	0				p.R2354H		.											.	USH2A-115	1	Substitution - Missense(1)	large_intestine(1)	c.G7061A	GRCh37	CM065510	USH2A	M		.						151	149	150					1																	216138718		2203	4300	6503	SO:0001583	missense	7399	exon37			TTAGGGCGAAAAG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7061G>A	1.37:g.216138718C>T	ENSP00000305941:p.Arg2354His	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	166	54	NM_206933	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.917	1.211142	0.22289	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53640	0.61;0.61	5.56	-5.71	0.02413	Fibronectin, type III (3);Immunoglobulin-like fold (1);	1.141870	0.06669	N	0.765866	T	0.13072	0.0317	N	0.00621	-1.32	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21655	-1.0239	10	0.18276	T	0.48	.	5.5397	0.17031	0.0751:0.2583:0.1031:0.5634	.	2354	O75445	USH2A_HUMAN	H	2354	ENSP00000305941:R2354H;ENSP00000355910:R2354H	ENSP00000305941:R2354H	R	-	2	0	USH2A	214205341	0.095000	0.21747	0.000000	0.03702	0.490000	0.33462	0.145000	0.16157	-0.801000	0.04427	-0.136000	0.14681	CGC	C|0.999;T|0.000		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216138718	C	T	216138718	3	4	123	1	0	0	0	0	1	0	0	0	17069	768	27	1	8691	1	USH2A	1	216138718	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08	10864329	216138718	33111903	7	10709											
C1orf55	163859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	226180666	226180666	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgattggttgtcttctcAatctgagcaccaagtgctcg	7	14	9	11	2	4	1	1	1	4	0	7	2	4	1	1	1	2	3	1	1	2	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:226180666A>C	ENST00000272091.7	-	3	294	c.276T>G	c.(274-276)atT>atG	p.I92M		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	92																	TTGTCTTCTCAATCTGAGCAC	0.428																																					p.I92M		.											.	.	0			c.T276G						.						85	76	79					1																	226180666		1868	4101	5969	SO:0001583	missense	163859	exon3			CTTCTCAATCTGA	BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 55"	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.276T>G	1.37:g.226180666A>C	ENSP00000272091:p.Ile92Met	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	69	25	NM_152608	0	0	9	15	6	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	37	CCDS41473.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.5|20.5	3.994098|3.994098	0.74703|0.74703	.|.	.|.	ENSG00000143751|ENSG00000143751	ENST00000272091;ENST00000366818|ENST00000366817	T|T	0.42131|0.49139	0.98|0.79	5.86|5.86	2.21|2.21	0.28008|0.28008	.|.	0.046995|.	0.85682|.	D|.	0.000000|.	T|T	0.41488|0.41488	0.1161|0.1161	L|L	0.41356|0.41356	1.27|1.27	0.29942|0.29942	N|N	0.82101|0.82101	D;D|.	0.89917|.	1.0;0.998|.	D;D|.	0.91635|.	0.999;0.978|.	T|T	0.45071|0.45071	-0.9286|-0.9286	10|7	0.15066|0.87932	T|D	0.55|0	-11.6814|-11.6814	4.9973|4.9973	0.14245|0.14245	0.6408:0.0:0.1288:0.2305|0.6408:0.0:0.1288:0.2305	.|.	80;92|.	Q6IQ49-2;Q6IQ49|.	.;CA055_HUMAN|.	M|W	92;80|41	ENSP00000272091:I92M|ENSP00000355782:L41W	ENSP00000272091:I92M|ENSP00000355782:L41W	I|L	-|-	3|2	3|0	C1orf55|C1orf55	224247289|224247289	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.520000|1.520000	0.35899|0.35899	0.119000|0.119000	0.18210|0.18210	0.529000|0.529000	0.55759|0.55759	ATT|TTG	.		0.428	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1	NM_152608		C	226180666	A	C	226180666	3	2	123	1	0	0	0	0	1	0	0	0	2053	126	5	5	1099	5	C1orf55	1	226180666	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	10041948	226180666	23069955	8	10710											
FH	2271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	241663812	241663812	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatcctttctgtattggcctGgattcccaccacgcagtttt	6	15	8	12	1	1	0	0	0	1	0	3	2	3	1	4	2	0	3	4	2	1	6			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:241663812G>A	ENST00000366560.3	-	9	1353	c.1315C>T	c.(1315-1317)Cag>Tag	p.Q439*		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	439					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		GTATTGGCCTGGATTCCCACC	0.413			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.Q439X	Melanoma(148;1573 2486 7381 46575)	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH-416	0			c.C1315T						.						149	143	145					1																	241663812		2203	4298	6501	SO:0001587	stop_gained	2271	exon9	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TGGCCTGGATTCC	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1315C>T	1.37:g.241663812G>A	ENSP00000355518:p.Gln439*	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	218	91	NM_000143	0	0	42	49	7	B1ANK7	Nonsense_Mutation	SNP	ENST00000366560.3	37	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	G	36	5.942978	0.97128	.	.	ENSG00000091483	ENST00000366560	.	.	.	5.71	5.71	0.89125	.	0.221640	0.47093	D	0.000245	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-13.6944	17.3485	0.87316	0.0:0.0:1.0:0.0	.	.	.	.	X	439	.	ENSP00000355518:Q439X	Q	-	1	0	FH	239730435	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.437000	0.52863	2.697000	0.92050	0.655000	0.94253	CAG	.		0.413	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		A	241663812	G	A	241663812	4	1	123	1	0	0	0	0	0	1	0	0	5894	1357	47	2	225	2	FH	1	241663812	Nonsense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	15483146	241663812	7586809	9	10711											
TAF1B	9014	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	10059757	10059763	+	Frame_Shift_Del	DEL	GCACACT	GCACACT	-																															gaatctacagaaacaatttaGcacactggtcgagtcaacag																								rs59159809		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	GCACACT	GCACACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:10059757_10059763delGCACACT	ENST00000263663.5	+	14	1561_1567	c.1373_1379delGCACACT	c.(1372-1380)agcacactgfs	p.STL458fs	TAF1B_ENST00000396242.3_Frame_Shift_Del_p.STL203fs	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	458					gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AAACAATTTAGCACACTGGTCGAGTCA	0.391																																					p.458_460del		.											.	TAF1B-92	0			c.1373_1379del						.																																			SO:0001589	frameshift_variant	9014	exon14			.	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.1373_1379delGCACACT	2.37:g.10059757_10059763delGCACACT	ENSP00000263663:p.Ser458fs	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	101	17	NM_005680	0	0	0	0	0	B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	ENST00000263663.5	37	CCDS33143.1																																																																																			.		0.391	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		-	10059763	GCACACT	-	10059757	7	5	123	1	0	1	0	1	0	0	0	0	15552	971	34	0	1427	0	TAF1B	2	10059757	Frame_Shift_Del	DEL	GCACACT	TCGA-GL-7966-01A-11D-2201-08		10059757	233139616	10	10712											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32639897	32639897	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataacagcactcagcattcTccaacagccagaaaaacttc	16	8	4	13	0	2	1	1	0	1	1	4	1	2	1	2	0	6	2	2	0	5	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:32639897T>C	ENST00000421745.2	+	10	1672	c.1538T>C	c.(1537-1539)cTc>cCc	p.L513P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	513					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTCAGCATTCTCCAACAGCCA	0.383																																					p.L513P	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.T1538C						.						57	55	56					2																	32639897		2203	4300	6503	SO:0001583	missense	57448	exon10			GCATTCTCCAACA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.1538T>C	2.37:g.32639897T>C	ENSP00000393596:p.Leu513Pro	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	56	3	NM_016252	0	0	13	13	0	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	16.00	2.998429	0.54147	.	.	ENSG00000115760	ENST00000421745	T	0.81078	-1.45	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.85699	0.5757	L	0.44542	1.39	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	D	0.86691	0.1923	10	0.56958	D	0.05	.	15.1339	0.72549	0.0:0.0:0.0:1.0	.	513	Q9NR09	BIRC6_HUMAN	P	513	ENSP00000393596:L513P	ENSP00000393596:L513P	L	+	2	0	BIRC6	32493401	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.948000	0.87774	2.045000	0.60652	0.528000	0.53228	CTC	.		0.383	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32639897	T	C	32639897	3	2	123	1	0	0	0	0	1	0	0	0	1439	1551	54	3	1576	3	BIRC6	2	32639897	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	22580140	32639897	210559476	11	10713											
EIF2AK3	9451	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	88890366	88890366	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattccagatgtcctcccttCttactgaatgccataacttt	9	15	4	13	0	1	2	0	1	1	1	4	2	4	2	4	0	3	0	4	0	3	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:88890366C>T	ENST00000303236.3	-	5	1273	c.972G>A	c.(970-972)aaG>aaA	p.K324K	EIF2AK3_ENST00000419748.1_Silent_p.K173K	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	324					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						GTCCTCCCTTCTTACTGAATG	0.423																																					p.K324K	GBM(138;671 1851 16235 39058 45249)	.											.	EIF2AK3-361	0			c.G972A						.						168	156	160					2																	88890366		2203	4300	6503	SO:0001819	synonymous_variant	9451	exon5			TCCCTTCTTACTG	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.972G>A	2.37:g.88890366C>T		Somatic	191	1		WXS	Illumina HiSeq	Phase_I	170	11	NM_004836	0	0	21	23	2	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Silent	SNP	ENST00000303236.3	37	CCDS33241.1																																																																																			.		0.423	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		T	88890366	C	T	88890366	2	4	123	1	0	0	0	0	0	0	0	1	5009	912	32	2		2	EIF2AK3	2	88890366	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	56250469	88890366	154309007	12	10714											
SCN2A	6326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	166201262	166201262	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atttccaatgattgtgaactCccacgctggcacatgcatga	11	11	8	11	1	0	3	0	3	0	0	2	3	2	3	2	1	2	3	2	1	2	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:166201262C>G	ENST00000375437.2	+	16	3050	c.2760C>G	c.(2758-2760)ctC>ctG	p.L920L	SCN2A_ENST00000283256.6_Silent_p.L920L|SCN2A_ENST00000357398.3_Silent_p.L920L|SCN2A_ENST00000375427.2_Silent_p.L920L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	920					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATTGTGAACTCCCACGCTGGC	0.488																																					p.L920L		.											.	SCN2A-142	0			c.C2760G						.						231	208	216					2																	166201262		2203	4300	6503	SO:0001819	synonymous_variant	6326	exon15			TGAACTCCCACGC	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10588	protein-coding gene	gene with protein product		182390	"sodium channel, voltage-gated, type II, alpha 2 polypeptide", "sodium channel, voltage-gated, type II, alpha 1 polypeptide"	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.2760C>G	2.37:g.166201262C>G		Somatic	199	0		WXS	Illumina HiSeq	Phase_I	182	26	NM_001040143	0	0	3	5	2	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																			.		0.488	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		G	166201262	C	G	166201262	2	3	123	1	0	0	0	0	0	0	0	1	13948	842	30	4		4	SCN2A	2	166201262	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	77310896	166201262	76998111	13	10715											
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	168105759	168105759	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggctctcaaagtaatgctcgGatactaggagtgtgttctga	10	12	12	7	1	2	1	1	1	2	0	4	3	2	3	0	3	2	4	0	3	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:168105759G>A	ENST00000409195.1	+	9	7946	c.7857G>A	c.(7855-7857)cgG>cgA	p.R2619R	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.R2619R|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Silent_p.R2397R|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2444					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GTAATGCTCGGATACTAGGAG	0.458																																					p.R2619R		.											.	XIRP2-104	0			c.G7857A						.						88	85	86					2																	168105759		1909	4120	6029	SO:0001819	synonymous_variant	129446	exon9			TGCTCGGATACTA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7857G>A	2.37:g.168105759G>A		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	147	41	NM_152381	0	0	0	0	0	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			.		0.458	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168105759	G	A	168105759	2	1	123	1	0	0	0	0	0	0	0	1	17463	1161	41	2		2	XIRP2	2	168105759	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08	1904497	168105759	75093614	14	10716											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	179598482	179598482	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctcattttgatttttcCgtcttctctgatgacctctt	7	19	5	10	1	4	3	1	3	3	0	6	3	5	3	2	0	1	1	2	0	1	6	rs377754692		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:179598482C>A	ENST00000591111.1	-	51	14907	c.14683G>T	c.(14683-14685)Gga>Tga	p.G4895*	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.G3968*|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.G5212*|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12287	Ig-like 29.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGATTTTTCCGTCTTCTCTG	0.453																																					p.G5212X		.											.	TTN-636	0			c.G15634T						.						199	188	191					2																	179598482		1906	4138	6044	SO:0001587	stop_gained	7273	exon53			TTTTTCCGTCTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.14683G>T	2.37:g.179598482C>A	ENSP00000465570:p.Gly4895*	Somatic	251	1		WXS	Illumina HiSeq	Phase_I	197	14	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	54	22.899424	0.99951	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	11.0214	0.47720	0.0:0.8884:0.0:0.1116	.	.	.	.	X	3968	.	ENSP00000343764:G3968X	G	-	1	0	TTN	179306727	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.981000	0.56902	2.734000	0.93682	0.655000	0.94253	GGA	.		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179598482	C	A	179598482	4	1	123	1	0	0	0	0	0	1	0	0	16768	661	23	4	89135	4	TTN	2	179598482	Nonsense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08	11492723	179598482	63600891	15	10717											
SESTD1	91404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179986590	179986590	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	catcctttccataggcccagGatgcctgattggagatctga	9	11	10	11	0	1	3	0	2	1	1	3	5	3	4	4	3	1	0	4	3	1	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:179986590G>A	ENST00000428443.3	-	13	1665	c.1349C>T	c.(1348-1350)tCc>tTc	p.S450F		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	450							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			ATAGGCCCAGGATGCCTGATT	0.393																																					p.S450F		.											.	SESTD1-228	0			c.C1349T						.						109	106	107					2																	179986590		2203	4300	6503	SO:0001583	missense	91404	exon13			GCCCAGGATGCCT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1349C>T	2.37:g.179986590G>A	ENSP00000415332:p.Ser450Phe	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	84	26	NM_178123	0	0	17	33	16	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547863	0.86022	.	.	ENSG00000187231	ENST00000428443	T	0.06371	3.31	5.18	5.18	0.71444	.	0.102206	0.64402	D	0.000001	T	0.06280	0.0162	N	0.24115	0.695	0.80722	D	1	P	0.50943	0.94	B	0.41571	0.36	T	0.50268	-0.8848	9	.	.	.	-0.0059	18.0499	0.89344	0.0:0.0:1.0:0.0	.	450	Q86VW0	SESD1_HUMAN	F	450	ENSP00000415332:S450F	.	S	-	2	0	SESTD1	179694835	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.023000	0.93683	2.584000	0.87258	0.467000	0.42956	TCC	.		0.393	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	179986590	G	A	179986590	3	1	123	1	0	0	0	0	1	0	0	0	14159	1174	41	2	765	2	SESTD1	2	179986590	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	388108	179986590	63212783	16	10718											
ICA1L	130026	broad.mit.edu	37	chr2	203693626	203693626	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaagtgctcatcctcttttTttcctgttgctttgataaag	7	18	6	10	0	2	1	1	1	1	0	4	1	4	1	3	0	2	3	3	0	3	6			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:203693626T>G	ENST00000392237.2	-	3	264	c.107A>C	c.(106-108)aAa>aCa	p.K36T	ICA1L_ENST00000425178.1_Missense_Mutation_p.K36T|ICA1L_ENST00000418208.1_Missense_Mutation_p.K36T|ICA1L_ENST00000358299.2_Missense_Mutation_p.K36T	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	36										breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ATCCTCTTTTTTTCCTGTTGC	0.388																																					p.K36T													.	ICA1L-90	0			c.A107C						.						189	175	180					2																	203693626		2203	4300	6503	SO:0001583	missense	130026	exon4			TCTTTTTTTCCTG	AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.107A>C	2.37:g.203693626T>G	ENSP00000376070:p.Lys36Thr	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	161	4	NM_178231	0	0	4	4	0	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Missense_Mutation	SNP	ENST00000392237.2	37	CCDS2354.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.302954	0.60195	.	.	ENSG00000163596	ENST00000392237;ENST00000358299;ENST00000420558;ENST00000425178;ENST00000418208;ENST00000450143;ENST00000435143;ENST00000419460;ENST00000441547;ENST00000412210;ENST00000457524;ENST00000432273;ENST00000416760;ENST00000454326;ENST00000411681;ENST00000421334	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21	6.02	4.84	0.62591	Arfaptin-like (1);	0.046952	0.85682	D	0.000000	D	0.84893	0.5573	M	0.66378	2.025	0.53688	D	0.999973	D;D	0.71674	0.979;0.998	D;D	0.75484	0.925;0.986	D	0.83552	0.0102	10	0.40728	T	0.16	.	10.553	0.45101	0.0:0.0766:0.0:0.9234	.	36;36	Q96Q33;Q8NDH6	.;ICA1L_HUMAN	T	36	ENSP00000376070:K36T;ENSP00000351047:K36T;ENSP00000400249:K36T;ENSP00000404189:K36T;ENSP00000412158:K36T;ENSP00000410747:K36T;ENSP00000405592:K36T;ENSP00000410135:K36T;ENSP00000404618:K36T;ENSP00000387382:K36T;ENSP00000404707:K36T;ENSP00000397827:K36T;ENSP00000392609:K36T;ENSP00000416726:K36T;ENSP00000409741:K36T	ENSP00000351047:K36T	K	-	2	0	ICA1L	203401871	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	6.187000	0.72039	1.064000	0.40671	0.528000	0.53228	AAA	.		0.388	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468		G	203693626	T	G	203693626	3	3	123	1	0	0	0	0	1	0	0	0	7499	1841	64	5	1403	5	ICA1L	2	203693626	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	23707036	203693626	39505747	17	10719											
ABCB6	10058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	220074990	220074990	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cagccatccttgatgacgagGatctggtcagcattgaccac	10	9	10	12	1	2	3	1	3	1	0	3	5	3	4	3	2	2	1	3	2	0	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:220074990G>A	ENST00000265316.3	-	18	2698	c.2382C>T	c.(2380-2382)atC>atT	p.I794I	ABCB6_ENST00000439002.2_Silent_p.I748I	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	794	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGATGACGAGGATCTGGTCAG	0.562																																					p.I794I		.											.	ABCB6-153	0			c.C2382T						.						102	97	99					2																	220074990		2203	4300	6503	SO:0001819	synonymous_variant	10058	exon18			GACGAGGATCTGG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.2382C>T	2.37:g.220074990G>A		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	126	8	NM_005689	0	0	62	63	1	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Silent	SNP	ENST00000265316.3	37	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	G	9.909	1.208939	0.22205	.	.	ENSG00000115657	ENST00000295750	.	.	.	4.83	0.378	0.16204	.	.	.	.	.	T	0.56062	0.1960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49579	-0.8925	4	.	.	.	-23.7644	9.3287	0.38008	0.3743:0.0:0.6257:0.0	.	.	.	.	F	642	.	.	S	-	2	0	ABCB6	219783234	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	0.893000	0.28336	0.171000	0.19730	-0.145000	0.13849	TCC	.		0.562	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220074990	G	A	220074990	2	1	123	1	0	0	0	0	0	0	0	1	45	1164	41	2		2	ABCB6	2	220074990	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08	16381364	220074990	23124383	18	10720											
CNOT10	25904	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	32766999	32766999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgcatccattttgccatgaGcaagcacaatttgggaatat	12	13	8	8	0	0	1	0	1	0	0	1	2	1	2	2	1	4	3	2	1	4	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr3:32766999G>A	ENST00000328834.5	+	9	1236	c.920G>A	c.(919-921)aGc>aAc	p.S307N	CNOT10_ENST00000331889.6_Missense_Mutation_p.S307N|CNOT10_ENST00000463697.1_3'UTR|CNOT10_ENST00000454516.2_Missense_Mutation_p.S367N|CNOT10_ENST00000538368.1_Missense_Mutation_p.S79N	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	307					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						TTTGCCATGAGCAAGCACAAT	0.393																																					p.S367N		.											.	CNOT10-91	0			c.G1100A						.						148	145	146					3																	32766999		2203	4300	6503	SO:0001583	missense	25904	exon9			CCATGAGCAAGCA	BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.920G>A	3.37:g.32766999G>A	ENSP00000330060:p.Ser307Asn	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	133	8	NM_001256742	0	0	19	24	5	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	37	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.689299	0.68271	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000540405;ENST00000538368;ENST00000454516	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.52	5.52	0.82312	Tetratricopeptide-like helical (1);	0.043732	0.85682	D	0.000000	T	0.39279	0.1072	N	0.03608	-0.345	0.47037	D	0.999297	B;B;B;B	0.17465	0.022;0.011;0.019;0.014	B;B;B;B	0.19946	0.027;0.012;0.019;0.02	T	0.23013	-1.0200	10	0.39692	T	0.17	-16.0206	19.4425	0.94827	0.0:0.0:1.0:0.0	.	367;307;306;307	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	N	307;307;207;79;367	ENSP00000329376:S307N;ENSP00000330060:S307N;ENSP00000442552:S79N;ENSP00000399862:S367N	ENSP00000330060:S307N	S	+	2	0	CNOT10	32742003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.348000	0.97062	2.594000	0.87642	0.655000	0.94253	AGC	.		0.393	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		A	32766999	G	A	32766999	3	1	123	1	0	0	0	0	1	0	0	0	3624	971	34	2	954	2	CNOT10	3	32766999	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		32766999	165255431	19	10721											
RAD54L2	23132	hgsc.bcm.edu;bcgsc.ca	37	chr3	51664392	51664392	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggcagtgaggatgaaaaaAgcagtcgagatggtaagatc	15	7	15	4	1	0	4	0	2	0	2	2	6	0	5	0	3	1	3	0	3	4	1	rs562443962	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr3:51664392A>G	ENST00000409535.2	+	5	711	c.586A>G	c.(586-588)Agc>Ggc	p.S196G	RAD54L2_ENST00000296477.3_Intron	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	196						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		GGATGAAAAAAGCAGTCGAGA	0.502																																					p.S196G		.											.	RAD54L2-93	0			c.A586G						.						126	114	118					3																	51664392		2203	4300	6503	SO:0001583	missense	23132	exon5			GAAAAAAGCAGTC	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.586A>G	3.37:g.51664392A>G	ENSP00000386520:p.Ser196Gly	Somatic	105	1		WXS	Illumina HiSeq	Phase_I	79	4	NM_015106	0	0	0	0	0	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	37	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	A	13.31	2.197689	0.38806	.	.	ENSG00000164080	ENST00000409535	T	0.22539	1.95	5.92	4.77	0.60923	.	0.400829	0.31347	N	0.007812	T	0.07458	0.0188	N	0.01352	-0.895	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21586	-1.0241	10	0.22109	T	0.4	-10.2268	11.1025	0.48184	0.9282:0.0:0.0718:0.0	.	196	Q9Y4B4	ARIP4_HUMAN	G	196	ENSP00000386520:S196G	ENSP00000386520:S196G	S	+	1	0	RAD54L2	51639432	1.000000	0.71417	0.997000	0.53966	0.921000	0.55340	3.547000	0.53663	1.069000	0.40788	0.533000	0.62120	AGC	.		0.502	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		G	51664392	A	G	51664392	3	3	123	1	0	0	0	0	1	0	0	0	13026	72	3	3	600	3	RAD54L2	3	51664392	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	18897393	51664392	146358038	20	10722											
CHIC2	26511	hgsc.bcm.edu	37	chr4	54876297	54876297	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcggtgtctttggtaaaaAttctatgaggatgacctgta	12	14	10	5	1	2	2	0	2	2	0	3	3	2	3	1	3	0	2	1	3	6	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr4:54876297A>C	ENST00000263921.3	-	6	852	c.463T>G	c.(463-465)Ttt>Gtt	p.F155V	FIP1L1_ENST00000507166.1_Intron|CHIC2_ENST00000512964.1_Missense_Mutation_p.F136V	NM_012110.3	NP_036242.1	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2	155						Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			TTTGGTAAAAATTCTATGAGG	0.299			T	ETV6	AML																																p.F155V		.		Dom	yes		4	4q11-q12	26511	cysteine-rich hydrophobic domain 2		L	.	CHIC2-1082	0			c.T463G						.						49	51	51					4																	54876297		2203	4299	6502	SO:0001583	missense	26511	exon6			GTAAAAATTCTAT	AF159423	CCDS3493.1	4q12	2013-09-04			ENSG00000109220	ENSG00000109220			1935	protein-coding gene	gene with protein product		604332				10477709	Standard	NM_012110		Approved	BTL	uc003haj.2	Q9UKJ5	OTTHUMG00000102101	ENST00000263921.3:c.463T>G	4.37:g.54876297A>C	ENSP00000263921:p.Phe155Val	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_012110	0	0	9	9	0	B2R639	Missense_Mutation	SNP	ENST00000263921.3	37	CCDS3493.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.06|15.06	2.720392|2.720392	0.48728|0.48728	.|.	.|.	ENSG00000109220|ENSG00000109220	ENST00000263921;ENST00000512964|ENST00000510894	.|.	.|.	.|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72985|0.72985	0.3529|0.3529	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	B|.	0.14012|.	0.009|.	B|.	0.19391|.	0.025|.	T|T	0.72283|0.72283	-0.4339|-0.4339	9|5	0.45353|.	T|.	0.12|.	.|.	16.0516|16.0516	0.80765|0.80765	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	155|.	Q9UKJ5|.	CHIC2_HUMAN|.	V|S	155;136|126	.|.	ENSP00000263921:F155V|.	F|I	-|-	1|2	0|0	CHIC2|CHIC2	54571054|54571054	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.509000|8.509000	0.90529|0.90529	2.181000|2.181000	0.69327|0.69327	0.455000|0.455000	0.32223|0.32223	TTT|ATT	.		0.299	CHIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219937.2			C	54876297	A	C	54876297	3	2	123	1	0	0	0	0	1	0	0	0	3350	101	4	5	38	5	CHIC2	4	54876297	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08		54876297	136277979	21	10723											
FHDC1	85462	bcgsc.ca	37	chr4	153886112	153886112	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcagaaaaattgcatcatgTtcagaagactgctaggtgag	14	11	10	6	0	3	4	3	1	0	3	3	4	3	4	0	1	2	3	0	1	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr4:153886112T>C	ENST00000511601.1	+	9	1273	c.1085T>C	c.(1084-1086)gTt>gCt	p.V362A	FHDC1_ENST00000260008.3_Missense_Mutation_p.V362A			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	362	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					TTGCATCATGTTCAGAAGACT	0.313																																					p.V362A													.	FHDC1-136	0			c.T1085C						.						72	78	76					4																	153886112		2203	4298	6501	SO:0001583	missense	85462	exon8			ATCATGTTCAGAA	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.1085T>C	4.37:g.153886112T>C	ENSP00000427567:p.Val362Ala	Somatic	155	0		WXS	Illumina HiSeq	Phase_1	101	4	NM_033393	0	0	5	5	0		Missense_Mutation	SNP	ENST00000511601.1	37	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305972	0.60305	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.63744	-0.06;-0.06	5.49	5.49	0.81192	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.349721	0.28431	N	0.015377	D	0.82282	0.5003	M	0.88570	2.965	0.58432	D	0.999997	D	0.89917	1.0	D	0.79784	0.993	D	0.85958	0.1468	10	0.87932	D	0	.	15.8895	0.79286	0.0:0.0:0.0:1.0	.	362	Q9C0D6	FHDC1_HUMAN	A	362	ENSP00000427567:V362A;ENSP00000260008:V362A	ENSP00000260008:V362A	V	+	2	0	FHDC1	154105562	1.000000	0.71417	0.969000	0.41365	0.621000	0.37620	7.317000	0.79018	2.207000	0.71202	0.533000	0.62120	GTT	.		0.313	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		C	153886112	T	C	153886112	3	2	123	1	0	0	0	0	1	0	0	0	5895	1725	60	3	1115	3	FHDC1	4	153886112	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	99009815	153886112	37268164	22	10724											
TAS2R1	50834	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	9629374	9629374	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggatgaagaacagaaagatGaaccttctgatgtgaaactt	17	9	10	5	0	1	7	0	4	1	3	1	8	1	8	1	1	3	0	1	1	5	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr5:9629374G>A	ENST00000382492.2	-	1	1089	c.771C>T	c.(769-771)ttC>ttT	p.F257F	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	257					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						ACAGAAAGATGAACCTTCTGA	0.378																																					p.F257F		.											.	TAS2R1-93	0			c.C771T						.						97	101	100					5																	9629374		2203	4300	6503	SO:0001819	synonymous_variant	50834	exon1			AAAGATGAACCTT	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.771C>T	5.37:g.9629374G>A		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	85	7	NM_019599	0	0	0	0	0	Q646G8	Silent	SNP	ENST00000382492.2	37	CCDS3876.1																																																																																			.		0.378	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			A	9629374	G	A	9629374	2	1	123	1	0	0	0	0	0	0	0	1	15597	1281	45	2		2	TAS2R1	5	9629374	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08		9629374	171285886	23	10725											
HCN1	348980	ucsc.edu	37	chr5	45461992	45461992	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaatctggtgggaagtcctGcagtagtggtactaagaact	11	10	13	7	0	1	1	0	0	1	1	2	2	2	2	1	3	3	4	1	3	6	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr5:45461992G>A	ENST00000303230.4	-	3	1024	c.967C>T	c.(967-969)Cag>Tag	p.Q323*		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	323					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GGGAAGTCCTGCAGTAGTGGT	0.428																																					p.Q323X													.	HCN1-91	0			c.C967T						.						75	74	74					5																	45461992		2203	4300	6503	SO:0001587	stop_gained	348980	exon3			AGTCCTGCAGTAG	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.967C>T	5.37:g.45461992G>A	ENSP00000307342:p.Gln323*	Somatic	60	0		WXS	Illumina HiSeq		41	4	NM_021072	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	38	6.874056	0.97901	.	.	ENSG00000164588	ENST00000303230	.	.	.	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.8983	0.96975	0.0:0.0:1.0:0.0	.	.	.	.	X	323	.	ENSP00000307342:Q323X	Q	-	1	0	HCN1	45497749	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.857000	0.99534	2.718000	0.92993	0.650000	0.86243	CAG	.		0.428	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45461992	G	A	45461992	4	1	123	1	0	0	0	0	0	1	0	0	7017	1328	46	2	1729	2	HCN1	5	45461992	Nonsense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	35832618	45461992	135453268	24	10726											
SHROOM1	134549	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	132161119	132161119	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccaggcattcccgcgcCggcccaccgccccgacccac	6	3	8	24	5	1	0	1	0	0	0	2	1	2	0	8	2	0	1	8	2	0	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr5:132161119C>T	ENST00000378679.3	-	4	1518	c.714G>A	c.(712-714)ccG>ccA	p.P238P	SHROOM1_ENST00000378676.1_Silent_p.P238P|SHROOM1_ENST00000319854.3_Silent_p.P238P|SHROOM1_ENST00000488072.1_5'Flank	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	238					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATTCCCGCGCCGGCCCACCGC	0.682																																					p.P238P		.											.	SHROOM1-91	0			c.G714A						.																																			SO:0001819	synonymous_variant	134549	exon1			CCGCGCCGGCCCA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.714G>A	5.37:g.132161119C>T		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	11	8	NM_133456	0	0	1	1	0	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	37	CCDS54902.1																																																																																			.		0.682	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132161119	C	T	132161119	2	4	123	1	0	0	0	0	0	0	0	1	14325	639	23	1		1	SHROOM1	5	132161119	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	86699127	132161119	48754141	25	10727											
PCDHGA2	56113	broad.mit.edu	37	chr5	140720783	140720783	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgtggacggggttcgggctTtcctgcagacctattcccac	5	10	13	13	3	0	1	0	0	0	1	3	2	2	2	3	4	1	3	3	4	1	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr5:140720783T>G	ENST00000394576.2	+	1	2245	c.2245T>G	c.(2245-2247)Ttc>Gtc	p.F749V	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_5'Flank	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	749					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTTCGGGCTTTCCTGCAGAC	0.627																																					p.F749V													.	PCDHGA2-71	0			c.T2245G						.						72	76	75					5																	140720783		2203	4300	6503	SO:0001583	missense	56113	exon1			CGGGCTTTCCTGC	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"Cadherins / Protocadherins : Clustered"	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2245T>G	5.37:g.140720783T>G	ENSP00000378077:p.Phe749Val	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	149	3	NM_018915	0	0	2	2	0	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	14.19	2.460361	0.43736	.	.	ENSG00000081853	ENST00000394576	T	0.44482	0.92	5.39	5.39	0.77823	.	0.000000	0.43579	U	0.000547	T	0.70011	0.3175	H	0.94542	3.55	0.25255	N	0.989647	D;D	0.62365	0.989;0.991	D;P	0.66847	0.947;0.852	T	0.69457	-0.5140	10	0.66056	D	0.02	.	9.5959	0.39573	0.0:0.0792:0.0:0.9208	.	749;749	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	V	749	ENSP00000378077:F749V	ENSP00000378077:F749V	F	+	1	0	PCDHGA2	140700967	0.001000	0.12720	0.914000	0.36105	0.053000	0.15095	0.253000	0.18296	2.051000	0.60960	0.402000	0.26972	TTC	.		0.627	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		G	140720783	T	G	140720783	3	3	123	1	0	0	0	0	1	0	0	0	11580	1841	64	5	2247	5	PCDHGA2	5	140720783	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	8559664	140720783	40194477	26	10728											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390482	45390482	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaacagcagcagcagcagCaggaggcggcggcggcggct	10	1	18	12	4	0	0	0	0	0	0	0	1	0	1	0	6	7	7	0	6	1	0			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr6:45390482C>G	ENST00000371438.1	+	2	569	c.211C>G	c.(211-213)Cag>Gag	p.Q71E	RUNX2_ENST00000371436.6_Missense_Mutation_p.Q71E|RUNX2_ENST00000541979.1_Missense_Mutation_p.Q139E|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q71E|RUNX2_ENST00000371432.3_Missense_Mutation_p.Q57E|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000352853.5_Missense_Mutation_p.Q139E|RUNX2_ENST00000465038.2_Missense_Mutation_p.Q71E|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q57E	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						gcagcagcagcaggaggcggc	0.716																																					p.Q71E		.											.	RUNX2-417	0			c.C211G						.						6	10	9					6																	45390482		1279	2789	4068	SO:0001583	missense	860	exon3			CAGCAGCAGGAGG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.211C>G	6.37:g.45390482C>G	ENSP00000360493:p.Gln71Glu	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	28	3	NM_001024630	0	0	0	0	0	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985548	0.35036	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	3.45	3.45	0.39498	.	1.972660	0.03402	N	0.203449	T	0.19248	0.0462	N	0.14661	0.345	0.27094	N	0.962779	B;B;B	0.23806	0.033;0.055;0.091	B;B;B	0.20384	0.029;0.013;0.029	T	0.13818	-1.0495	10	0.02654	T	1	.	14.8379	0.70197	0.0:1.0:0.0:0.0	.	139;71;57	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	E	71;139;139;71;71;57;57	ENSP00000420707:Q71E;ENSP00000319087:Q139E;ENSP00000446290:Q139E;ENSP00000360493:Q71E;ENSP00000360491:Q71E;ENSP00000352514:Q57E;ENSP00000360486:Q57E	ENSP00000319087:Q139E	Q	+	1	0	RUNX2	45498460	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.268000	0.33062	1.622000	0.50330	0.407000	0.27541	CAG	.		0.716	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390482	C	G	45390482	3	3	123	1	0	0	0	0	1	0	0	0	13780	711	25	4	233	4	RUNX2	6	45390482	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08		45390482	125724585	27	10729											
MTHFD1L	25902	hgsc.bcm.edu	37	chr6	151358132	151358132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgcccatctgcatggcaaAgacccacctttctctatctc	8	13	5	15	0	3	1	0	0	3	1	5	1	3	1	3	1	2	2	3	1	2	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr6:151358132A>G	ENST00000367321.3	+	26	3000	c.2726A>G	c.(2725-2727)aAg>aGg	p.K909R	AL133260.1_ENST00000408542.1_RNA	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	909	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TGCATGGCAAAGACCCACCTT	0.463																																					p.K910R		.											.	MTHFD1L-292	0			c.A2729G						.						85	79	81					6																	151358132		2203	4300	6503	SO:0001583	missense	25902	exon26			TGGCAAAGACCCA	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"10-formyl-THF synthetase", "mitochondrial C1-tetrahydrofolate synthase", "monofunctional C1-tetrahydrofolate synthase, mitochondrial"	611427	"formyltetrahydrofolate synthetase domain containing 1"	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.2726A>G	6.37:g.151358132A>G	ENSP00000356290:p.Lys909Arg	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	87	6	NM_001242767	0	0	71	71	0	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	37	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.951688	0.92660	.	.	ENSG00000120254	ENST00000367321;ENST00000453602;ENST00000450635	T;T;T	0.39787	1.06;1.06;1.06	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.73297	0.3569	H	0.97918	4.105	0.80722	D	1	D;D;D	0.89917	1.0;0.994;1.0	D;D;D	0.91635	0.999;0.914;0.999	D	0.84465	0.0596	10	0.72032	D	0.01	.	15.1893	0.73032	1.0:0.0:0.0:0.0	.	910;664;909	B7ZM99;B2RD24;Q6UB35	.;.;C1TM_HUMAN	R	909;34;8	ENSP00000356290:K909R;ENSP00000391022:K34R;ENSP00000399804:K8R	ENSP00000356290:K909R	K	+	2	0	MTHFD1L	151399825	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	1.974000	0.57490	0.533000	0.62120	AAG	.		0.463	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440		G	151358132	A	G	151358132	3	3	123	1	0	0	0	0	1	0	0	0	9953	72	3	3	2828	3	MTHFD1L	6	151358132	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	105967650	151358132	19756935	28	10730											
EPHB6	2051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142561393	142561393	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttatttctgggcagaggtAttgctggacaccaccggaga	9	11	12	9	1	2	2	0	0	2	2	2	4	2	3	2	4	1	3	2	4	2	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr7:142561393A>T	ENST00000392957.2	+	6	892	c.105A>T	c.(103-105)gtA>gtT	p.V35V	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Silent_p.V35V	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	35	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GGGCAGAGGTATTGCTGGACA	0.582																																					p.V35V		.											.	EPHB6-1489	0			c.A105T						.						79	75	76					7																	142561393		2203	4300	6503	SO:0001819	synonymous_variant	2051	exon6			AGAGGTATTGCTG	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.105A>T	7.37:g.142561393A>T		Somatic	100	1		WXS	Illumina HiSeq	Phase_I	86	37	NM_004445	0	0	0	0	0	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			.		0.582	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142561393	A	T	142561393	2	4	123	1	0	0	0	0	0	0	0	1	5191	436	16	5		5	EPHB6	7	142561393	Silent	SNP	A	TCGA-GL-7966-01A-11D-2201-08		142561393	16577270	29	10731											
COL22A1	169044	broad.mit.edu	37	chr8	139767734	139767734	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgcctcttacctgttccccTttcaagccctcttgctgcac	4	14	6	17	0	3	0	1	0	2	0	4	0	4	0	5	0	5	3	5	0	2	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr8:139767734T>C	ENST00000303045.6	-	20	2414	c.1968A>G	c.(1966-1968)aaA>aaG	p.K656K	COL22A1_ENST00000435777.1_Silent_p.K656K	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	656	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CCTGTTCCCCTTTCAAGCCCT	0.507										HNSCC(7;0.00092)																											p.K656K													.	COL22A1-103	0			c.A1968G						.						327	284	299					8																	139767734		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon20			TTCCCCTTTCAAG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"Collagens"	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1968A>G	8.37:g.139767734T>C		Somatic	299	0		WXS	Illumina HiSeq	Phase_I	268	4	NM_152888	0	0	0	0	0	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			.		0.507	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		C	139767734	T	C	139767734	2	2	123	1	0	0	0	0	0	0	0	1	3687	1606	56	3		3	COL22A1	8	139767734	Silent	SNP	T	TCGA-GL-7966-01A-11D-2201-08		139767734	6596288	30	10732											
KIAA1984	84960	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	139694856	139694856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cccagatcatccgccagctgGagaacaacatcgagaagaca	15	4	9	13	2	1	4	1	0	0	4	3	6	2	4	3	1	3	1	3	1	3	0	rs544497218	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr9:139694856G>A	ENST00000338005.6	+	5	489	c.454G>A	c.(454-456)Gag>Aag	p.E152K	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.E182K|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		152										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CCGCCAGCTGGAGAACAACAT	0.602													G|||	3	0.000599042	0	0	5008	,	,		10479	0		0	False		,,,				2504	0.0031				p.E152K		.											.	KIAA1984-91	0			c.G454A						.																																			SO:0001583	missense	84960	exon5			CAGCTGGAGAACA																												ENST00000338005.6:c.454G>A	9.37:g.139694856G>A	ENSP00000338013:p.Glu152Lys	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	17	6	NM_001039374	0	0	3	3	0	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059818	0.93846	.	.	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.31510	1.49	4.19	4.19	0.49359	.	0.000000	0.41823	U	0.000810	T	0.50086	0.1595	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.49360	-0.8948	10	0.48119	T	0.1	-24.9723	12.0196	0.53336	0.0:0.0:1.0:0.0	.	152	Q5T5S1	K1984_HUMAN	K	152	ENSP00000338013:E152K	ENSP00000338013:E152K	E	+	1	0	KIAA1984	138814677	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	3.494000	0.53273	1.873000	0.54277	0.305000	0.20034	GAG	.		0.602	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			A	139694856	G	A	139694856	3	1	123	1	0	0	0	0	1	0	0	0	8287	1175	41	2	472	2	KIAA1984	9	139694856	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		139694856	1518575	31	10733											
C11orf80	79703	hgsc.bcm.edu;broad.mit.edu	37	chr11	66555634	66555634	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catttcttctcacacagaaaTacagtccatactgcccggaa	13	10	5	13	1	2	1	1	0	2	1	4	2	3	2	2	1	3	0	2	1	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr11:66555634T>C	ENST00000360962.4	+	5	534	c.527T>C	c.(526-528)aTa>aCa	p.I176T	C11orf80_ENST00000527634.1_Intron|C11orf80_ENST00000532565.2_5'UTR|C11orf80_ENST00000540737.1_Missense_Mutation_p.I10T|C11orf80_ENST00000525449.2_Missense_Mutation_p.I21T|C11orf80_ENST00000346672.4_Missense_Mutation_p.I21T|C11orf80_ENST00000527368.1_3'UTR	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	176										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						CACACAGAAATACAGTCCATA	0.433																																					p.I176T		.											.	.	0			c.T527C						.						78	72	74					11																	66555634		1872	4107	5979	SO:0001583	missense	79703	exon5			CAGAAATACAGTC			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.527T>C	11.37:g.66555634T>C	ENSP00000354227:p.Ile176Thr	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_024650	0	0	0	0	0	Q9H677	Missense_Mutation	SNP	ENST00000360962.4	37	CCDS53664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.06|12.06	1.823474|1.823474	0.32237|0.32237	.|.	.|.	ENSG00000173715|ENSG00000173715	ENST00000525908;ENST00000360962;ENST00000346672;ENST00000528340;ENST00000540737;ENST00000525449|ENST00000532089	T;T|.	0.38560|.	1.13;1.14|.	5.38|5.38	4.26|4.26	0.50523|0.50523	.|.	0.346678|.	0.24542|.	N|.	0.037636|.	T|T	0.31513|0.31513	0.0799|0.0799	L|L	0.27053|0.27053	0.805|0.805	0.25537|0.25537	N|N	0.987218|0.987218	P|.	0.46512|.	0.879|.	P|.	0.48677|.	0.586|.	T|T	0.19614|0.19614	-1.0300|-1.0300	10|5	0.72032|.	D|.	0.01|.	.|.	7.6859|7.6859	0.28540|0.28540	0.0:0.0949:0.0:0.9051|0.0:0.0949:0.0:0.9051	.|.	10|.	E9PKZ8|.	.|.	T|H	127;176;21;10;10;21|2	ENSP00000432039:I127T;ENSP00000354227:I176T|.	ENSP00000317408:I21T|.	I|Y	+|+	2|1	0|0	C11orf80|C11orf80	66312210|66312210	0.770000|0.770000	0.28543|0.28543	0.546000|0.546000	0.28166|0.28166	0.821000|0.821000	0.46438|0.46438	2.127000|2.127000	0.42035|0.42035	0.910000|0.910000	0.36722|0.36722	0.533000|0.533000	0.62120|0.62120	ATA|TAC	.		0.433	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		C	66555634	T	C	66555634	3	2	123	1	0	0	0	0	1	0	0	0	1668	1406	49	3	545	3	C11orf80	11	66555634	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08		66555634	68450882	32	10734											
KLHL35	283212	broad.mit.edu	37	chr11	75140917	75140917	+	Frame_Shift_Del	DEL	A	A	-																															cgtccgcctccaccttctccAggaagtaagcgggcgccagt																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr11:75140917delA	ENST00000539798.1	-	1	757	c.758delT	c.(757-759)ctgfs	p.L253fs	KLHL35_ENST00000376292.4_Frame_Shift_Del_p.L33fs	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	253										lung(2)|stomach(1)	3						CACCTTCTCCAGGAAGTAAGC	0.751																																					p.L253fs	Colon(77;683 1691 18820 23811)												.	.	0			c.758delT						.						3	4	4					11																	75140917		1441	3421	4862	SO:0001589	frameshift_variant	283212	exon1			TTCTCCAGGAAGT		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"Kelch-like", "BTB/POZ domain containing"	26597	protein-coding gene	gene with protein product			"kelch-like 35 (Drosophila)"				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.758delT	11.37:g.75140917delA	ENSP00000438526:p.Leu253fs	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001039548	0	0	0	0	0	A2RU06|F5H412|Q86XM7|Q8NBB1	Frame_Shift_Del	DEL	ENST00000539798.1	37	CCDS44685.2																																																																																			.		0.751	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		-	75140917	A	-	75140917	7	5	123	1	0	1	0	1	0	0	0	0	8409	188	7	0	1017	0	KLHL35	11	75140917	Frame_Shift_Del	DEL	A	TCGA-GL-7966-01A-11D-2201-08	8585283	75140917	59865599	33	10735											
PUS3	83480	broad.mit.edu	37	chr11	125766029	125766029	+	Frame_Shift_Del	DEL	T	T	-																															gaaatcaaatgcacgcttagTttttccagctcctgctgaat																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr11:125766029delT	ENST00000530811.1	-	1	196	c.151delA	c.(151-153)actfs	p.T51fs	HYLS1_ENST00000425380.2_Intron|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron|PUS3_ENST00000227474.3_Frame_Shift_Del_p.T51fs			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	51					tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		GCACGCTTAGTTTTTCCAGCT	0.448																																					p.T51fs													.	PUS3-91	0			c.151delA						.						230	226	227					11																	125766029		2201	4299	6500	SO:0001589	frameshift_variant	83480	exon2			GCTTAGTTTTTCC	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.151delA	11.37:g.125766029delT	ENSP00000432386:p.Thr51fs	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	238	18	NM_031307	0	0	0	0	0	B2RAM0|Q96D17|Q96J23|Q96NB4	Frame_Shift_Del	DEL	ENST00000530811.1	37	CCDS8466.1																																																																																			.		0.448	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307		-	125766029	T	-	125766029	7	5	123	1	0	1	0	1	0	0	0	0	12864	1725	60	0	1306	0	PUS3	11	125766029	Frame_Shift_Del	DEL	T	TCGA-GL-7966-01A-11D-2201-08	50625112	125766029	9240487	34	10736											
GLB1L2	89944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	134241359	134241359	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggattcttggactacaagacAacgaagattgctgtccccct	11	10	9	11	1	1	2	0	0	1	2	2	5	2	4	2	2	3	1	2	2	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr11:134241359A>G	ENST00000535456.2	+	14	1589	c.1401A>G	c.(1399-1401)acA>acG	p.T467T	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.T467T|GLB1L2_ENST00000389881.3_Silent_p.T467T	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	467					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ACTACAAGACAACGAAGATTG	0.542																																					p.T467T		.											.	GLB1L2-25	0			c.A1401G						.						161	159	160					11																	134241359		2201	4297	6498	SO:0001819	synonymous_variant	89944	exon14			CAAGACAACGAAG		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.1401A>G	11.37:g.134241359A>G		Somatic	216	0		WXS	Illumina HiSeq	Phase_I	210	79	NM_138342	0	0	31	59	28	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	.	.	.	.	.	.	.	.	.	.	A	4.458	0.084834	0.08583	.	.	ENSG00000149328	ENST00000525089	.	.	.	4.72	-9.38	0.00623	.	.	.	.	.	T	0.13457	0.0326	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.17961	-1.0352	4	.	.	.	-3.4454	0.6104	0.00760	0.3795:0.1978:0.2259:0.1968	.	.	.	.	D	406	.	.	N	+	1	0	GLB1L2	133746569	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.622000	0.00412	-1.622000	0.01560	-1.291000	0.01355	AAC	.		0.542	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342		G	134241359	A	G	134241359	2	3	123	1	0	0	0	0	0	0	0	1	6449	117	5	3		3	GLB1L2	11	134241359	Silent	SNP	A	TCGA-GL-7966-01A-11D-2201-08	8475330	134241359	765157	35	10737											
IPO8	10526	hgsc.bcm.edu;broad.mit.edu	37	chr12	30787080	30787080	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaaggtcaagtggagtacTgaacccctcaagcgcggttt	10	9	12	10	2	3	1	3	1	0	0	3	2	3	2	2	3	3	2	2	3	5	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr12:30787080T>C	ENST00000256079.4	-	23	3174	c.2836A>G	c.(2836-2838)Agt>Ggt	p.S946G	IPO8_ENST00000544829.1_Missense_Mutation_p.S741G	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	946					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					AGTGGAGTACTGAACCCCTCA	0.403																																					p.S946G		.											.	IPO8-227	0			c.A2836G						.						222	173	190					12																	30787080		2203	4300	6503	SO:0001583	missense	10526	exon23			GAGTACTGAACCC	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.2836A>G	12.37:g.30787080T>C	ENSP00000256079:p.Ser946Gly	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	66	5	NM_006390	0	0	53	58	5	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	37	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.098449	0.56183	.	.	ENSG00000133704	ENST00000256079;ENST00000545286;ENST00000544829	T;T	0.65732	-0.17;-0.17	5.22	5.22	0.72569	Armadillo-type fold (1);	0.037226	0.85682	D	0.000000	T	0.62073	0.2398	M	0.64997	1.995	0.58432	D	0.999998	P;P;P	0.46395	0.791;0.877;0.749	B;B;B	0.43194	0.219;0.411;0.194	T	0.62714	-0.6796	10	0.30854	T	0.27	-16.0242	15.3733	0.74584	0.0:0.0:0.0:1.0	.	741;422;946	B7Z7M3;Q59F59;O15397	.;.;IPO8_HUMAN	G	946;422;741	ENSP00000256079:S946G;ENSP00000444520:S741G	ENSP00000256079:S946G	S	-	1	0	IPO8	30678347	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	4.133000	0.57983	2.081000	0.62600	0.533000	0.62120	AGT	.		0.403	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		C	30787080	T	C	30787080	3	2	123	1	0	0	0	0	1	0	0	0	7819	1580	55	3	289	3	IPO8	12	30787080	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08		30787080	103064815	36	10738											
C12orf41	54934	broad.mit.edu	37	chr12	49062988	49062988	+	Frame_Shift_Del	DEL	T	T	-																															tggcggtatcgtcgcagacaTtttaatcgctttaagttctc																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr12:49062988delT	ENST00000420613.2	-	6	824	c.777delA	c.(775-777)aaafs	p.K259fs	KANSL2_ENST00000357861.3_Frame_Shift_Del_p.K64fs|KANSL2_ENST00000553086.1_Frame_Shift_Del_p.K259fs|SNORA2B_ENST00000384583.1_RNA|KANSL2_ENST00000550347.1_Frame_Shift_Del_p.K442fs	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	259					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											GTCGCAGACATTTTAATCGCT	0.502																																					p.K259fs													.	.	0			c.777delA						.						75	68	70					12																	49062988		1932	4130	6062	SO:0001589	frameshift_variant	54934	exon6			CAGACATTTTAAT	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.777delA	12.37:g.49062988delT	ENSP00000415436:p.Lys259fs	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_017822	0	0	0	0	0	Q8N3B5|Q96CV0|Q9NX51	Frame_Shift_Del	DEL	ENST00000420613.2	37	CCDS44869.1																																																																																			.		0.502	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		-	49062988	T	-	49062988	7	5	123	1	0	1	0	1	0	0	0	0	1691	1490	52	0	721	0	C12orf41	12	49062988	Frame_Shift_Del	DEL	T	TCGA-GL-7966-01A-11D-2201-08	18275908	49062988	84788907	37	10739											
ULK1	8408	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132395297	132395297	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtacccaagctcggggtcCggcagcagctccagcagcag	8	5	13	15	3	0	0	0	0	0	0	4	0	2	0	3	3	6	7	3	3	2	1	rs571147302		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr12:132395297C>T	ENST00000321867.4	+	12	1251	c.900C>T	c.(898-900)tcC>tcT	p.S300S		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	300	Interaction with GABARAP and GABARAPL2.|Poly-Ser.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GCTCGGGGTCCGGCAGCAGCT	0.662													T|||	1	0.000199681	8e-04	0	5008	,	,		14232	0		0	False		,,,				2504	0				p.S300S		.											.	ULK1-758	0			c.C900T						.						76	67	70					12																	132395297		2203	4299	6502	SO:0001819	synonymous_variant	8408	exon12			GGGGTCCGGCAGC	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"ATG1 autophagy related 1 homolog (S. cerevisiae)"	603168	"unc-51 (C. elegans)-like kinase 1", "unc-51-like kinase 1 (C. elegans)"			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.900C>T	12.37:g.132395297C>T		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	81	31	NM_003565	0	0	12	22	10	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			.		0.662	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132395297	C	T	132395297	2	4	123	1	0	0	0	0	0	0	0	1	17008	639	23	1		1	ULK1	12	132395297	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	83332309	132395297	1456598	38	10740											
DOCK9	23348	hgsc.bcm.edu	37	chr13	99536093	99536093	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atacactgtagaaaccagatGagtggaaattttcagcagtg	15	10	10	6	0	1	3	1	1	0	2	1	4	1	4	1	1	3	2	1	1	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr13:99536093G>C	ENST00000376460.1	-	22	2523	c.2443C>G	c.(2443-2445)Cat>Gat	p.H815D	DOCK9_ENST00000448493.2_Missense_Mutation_p.H827D|DOCK9_ENST00000442173.1_Missense_Mutation_p.H815D|DOCK9_ENST00000339416.2_Missense_Mutation_p.H816D	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	816	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GAAACCAGATGAGTGGAAATT	0.383																																					p.H816D		.											.	DOCK9-90	0			c.C2446G						.						72	71	71					13																	99536093		1852	4090	5942	SO:0001583	missense	23348	exon22			CCAGATGAGTGGA	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"Pleckstrin homology (PH) domain containing"	14132	protein-coding gene	gene with protein product	"zizimin1"	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2443C>G	13.37:g.99536093G>C	ENSP00000365643:p.His815Asp	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	7	2	NM_001130049	0	0	18	18	0	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.429336	0.83776	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.32315	0.0825	L	0.43152	1.355	0.80722	D	1	P;D;P;B;D	0.89917	0.888;1.0;0.888;0.104;0.996	P;D;P;B;D	0.81914	0.824;0.995;0.579;0.054;0.969	T	0.01508	-1.1337	10	0.62326	D	0.03	.	19.2291	0.93831	0.0:0.0:1.0:0.0	.	816;815;815;815;816	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	D	815;816;816;816;815;816;827;815	ENSP00000365643:H815D;ENSP00000341086:H816D;ENSP00000401958:H827D;ENSP00000406883:H815D	ENSP00000341086:H816D	H	-	1	0	DOCK9	98334094	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.420000	0.97426	2.614000	0.88457	0.655000	0.94253	CAT	.		0.383	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		C	99536093	G	C	99536093	3	2	123	1	0	0	0	0	1	0	0	0	4705	1290	45	4	3964	4	DOCK9	13	99536093	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		99536093	15633785	39	10741											
JKAMP	51528	hgsc.bcm.edu	37	chr14	59965598	59965598	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcttcccaattttaaccgtGcttcaggcagttggtggagg	7	14	11	9	1	2	0	1	0	1	0	3	1	3	1	2	4	2	3	2	4	2	6			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr14:59965598G>C	ENST00000261247.9	+	5	759	c.612G>C	c.(610-612)gtG>gtC	p.V204V	JKAMP_ENST00000425728.2_Silent_p.V198V|JKAMP_ENST00000356057.5_Silent_p.V212V|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000554271.1_Silent_p.V218V	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	219					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						TTTTAACCGTGCTTCAGGCAG	0.348																																					p.V204V		.											.	JKAMP-67	0			c.G612C						.						102	91	95					14																	59965598		1830	4092	5922	SO:0001819	synonymous_variant	51528	exon5			AACCGTGCTTCAG	AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"Jun N-terminal kinase 1-associated membrane protein"	611176	"chromosome 14 open reading frame 100"	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.612G>C	14.37:g.59965598G>C		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_016475	0	0	51	51	0	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Silent	SNP	ENST00000261247.9	37	CCDS45116.1																																																																																			.		0.348	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625		C	59965598	G	C	59965598	2	2	123	1	0	0	0	0	0	0	0	1	7970	1306	46	4		4	JKAMP	14	59965598	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08		59965598	47383942	40	10742											
SNURF	8926	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	25207297	25207297	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgaactacagaacagcaCgtaccagaggtggaagtcca	16	4	11	10	2	0	3	0	0	0	3	1	5	1	4	2	2	5	2	2	2	5	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:25207297C>T	ENST00000577949.1	+	2	114	c.51C>T	c.(49-51)caC>caT	p.H17H	SNURF_ENST00000338094.6_Silent_p.H17H|SNRPN_ENST00000390687.4_5'UTR|SNURF_ENST00000551312.2_Silent_p.H17H|SNRPN_ENST00000400100.1_5'UTR|SNRPN_ENST00000400098.1_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNRPN_ENST00000577565.1_5'UTR|SNRPN_ENST00000554227.2_5'UTR|SNURF_ENST00000338327.4_Silent_p.H17H|SNRPN_ENST00000346403.6_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	17						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		CAGAACAGCACGTACCAGAGG	0.448																																					p.H17H		.											.	SNURF-90	0			c.C51T						.						154	124	134					15																	25207297		2203	4300	6503	SO:0001819	synonymous_variant	8926	exon2			ACAGCACGTACCA		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.51C>T	15.37:g.25207297C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	74	5	NM_005678	0	0	35	35	0	A6NCW2	Silent	SNP	ENST00000577949.1	37	CCDS10016.1																																																																																			.		0.448	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678		T	25207297	C	T	25207297	2	4	123	1	0	0	0	0	0	0	0	1	14910	535	19	1		1	SNURF	15	25207297	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08		25207297	77324095	41	10743											
B2M	567	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	45003781	45003782	+	Frame_Shift_Del	DEL	CT	CT	-																															ccttagctgtgctcgcgctaCtctctctttctggcctggag																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:45003781_45003782delCT	ENST00000558401.1	+	1	107_108	c.37_38delCT	c.(37-39)ctcfs	p.L13fs	B2M_ENST00000559916.1_Frame_Shift_Del_p.L13fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.L13fs|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	13					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L15fs*41(4)|p.A11fs*42(1)|p.L13F(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCTCGCGCTACTCTCTCTTTCT	0.614																																					p.13_13del		.											.	B2M-93	6	Deletion - Frameshift(5)|Substitution - Missense(1)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|skin(1)	c.37_38del						.																																			SO:0001589	frameshift_variant	567	exon1			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.37_38delCT	15.37:g.45003787_45003788delCT	ENSP00000452780:p.Leu13fs	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	58	10	NM_004048	0	0	0	0	0	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.		0.614	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45003782	CT	-	45003781	7	5	123	1	0	1	0	1	0	0	0	0	1245	565	20	0	39	0	B2M	15	45003781	Frame_Shift_Del	DEL	CT	TCGA-GL-7966-01A-11D-2201-08	19796484	45003781	57527611	42	10744											
B2M	567	broad.mit.edu	37	chr15	45007645	45007646	+	Frame_Shift_Ins	INS	-	-	A																															ccaaagattcaggtttactcINSacgtcatccagcagagaatg																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:45007645_45007646insA	ENST00000558401.1	+	2	162_163	c.92_93insA	c.(91-96)tcacgtfs	p.R32fs	B2M_ENST00000559916.1_Frame_Shift_Ins_p.R32fs|B2M_ENST00000544417.1_Frame_Shift_Ins_p.R32fs|B2M_ENST00000559220.1_Intron	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	32	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CAGGTTTACTCACGTCATCCAG	0.411																																					p.S31fs													.	B2M-93	0			c.92_93insA						.																																			SO:0001589	frameshift_variant	567	exon2			TTTACTCACGTCA	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.93dupA	15.37:g.45007646_45007646dupA	ENSP00000452780:p.Arg32fs	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	116	8	NM_004048	0	0	0	0	0	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Ins	INS	ENST00000558401.1	37	CCDS10113.1																																																																																			.		0.411	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		A	45007646	-	A	45007645	7	5	123	1	0	1	1	0	0	0	0	0	1245	838	29	0	98	0	B2M	15	45007645	Frame_Shift_Ins	INS	-	TCGA-GL-7966-01A-11D-2201-08	3864	45007645	57523747	43	10745											
UACA	55075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	70987423	70987423	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaacactcaagattcccCtttgaggtcacaacatggaa	14	10	6	11	0	3	2	3	1	0	1	4	3	4	3	2	2	2	0	2	2	4	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:70987423C>T	ENST00000322954.6	-	3	419	c.234G>A	c.(232-234)aaG>aaA	p.K78K	UACA_ENST00000379983.2_Silent_p.K65K|UACA_ENST00000560441.1_Silent_p.K65K|UACA_ENST00000539319.1_Silent_p.K78K	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	78					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						CAAGATTCCCCTTTGAGGTCA	0.353																																					p.K78K		.											.	UACA-94	0			c.G234A						.						91	83	86					15																	70987423		2199	4297	6496	SO:0001819	synonymous_variant	55075	exon3			ATTCCCCTTTGAG	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.234G>A	15.37:g.70987423C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	27	18	NM_018003	0	0	13	26	13	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			.		0.353	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	70987423	C	T	70987423	2	4	123	1	0	0	0	0	0	0	0	1	16857	680	24	2		2	UACA	15	70987423	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	25979778	70987423	31543969	44	10746											
HCN4	10021	hgsc.bcm.edu	37	chr15	73660576	73660576	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctgctgcgggaggctgtaGagccgcttgcgcatggacgg	6	7	17	11	4	0	1	0	0	0	1	0	3	0	3	2	4	4	5	2	4	1	2	rs201193660	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:73660576G>C	ENST00000261917.3	-	1	1029	c.36C>G	c.(34-36)ctC>ctG	p.L12L		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	12					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GGAGGCTGTAGAGCCGCTTGC	0.761													G|||	18	0.00359425	0	0.0101	5008	,	,		8058	0		0.0109	False		,,,				2504	0				p.L12L		.											.	HCN4-96	0			c.C36G						.	G		5,3709		0,5,1852	3	4	3		36	1.2	1	15		3	36,7592		0,36,3778	no	coding-synonymous	HCN4	NM_005477.2		0,41,5630	CC,CG,GG		0.4719,0.1346,0.3615		12/1204	73660576	41,11301	1857	3814	5671	SO:0001819	synonymous_variant	10021	exon1			GCTGTAGAGCCGC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.36C>G	15.37:g.73660576G>C		Somatic	4	1		WXS	Illumina HiSeq	Phase_I	3	2	NM_005477	0	0	0	0	0	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			G|0.989;C|0.011		0.761	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		C	73660576	G	C	73660576	2	2	123	1	0	0	0	0	0	0	0	1	7020	929	33	4		4	HCN4	15	73660576	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08	2673153	73660576	28870816	45	10747											
KIAA0753	9851	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	6531560	6531560	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acctatcctgggatgaggctGaagtcccggatcatgggtgg	8	9	15	9	1	1	2	1	2	0	0	3	4	3	4	3	5	0	1	3	5	2	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:6531560G>A	ENST00000361413.3	-	3	953	c.595C>T	c.(595-597)Cag>Tag	p.Q199*	KIAA0753_ENST00000542606.1_5'UTR|KIAA0753_ENST00000572370.1_5'UTR	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	199						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		GGATGAGGCTGAAGTCCCGGA	0.483																																					p.Q199X		.											.	KIAA0753-90	0			c.C595T						.						129	131	131					17																	6531560		2023	4175	6198	SO:0001587	stop_gained	9851	exon3			GAGGCTGAAGTCC		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.595C>T	17.37:g.6531560G>A	ENSP00000355250:p.Gln199*	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	157	9	NM_014804	0	0	18	20	2	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Nonsense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	32	5.129961	0.94473	.	.	ENSG00000198920	ENST00000361413	.	.	.	5.34	-0.77	0.11005	.	0.864801	0.09963	N	0.733125	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-2.5116	10.7147	0.46005	0.0:0.5544:0.3039:0.1417	.	.	.	.	X	199	.	ENSP00000355250:Q199X	Q	-	1	0	KIAA0753	6472284	0.004000	0.15560	0.007000	0.13788	0.294000	0.27393	0.211000	0.17474	0.282000	0.22254	0.655000	0.94253	CAG	.		0.483	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		A	6531560	G	A	6531560	4	1	123	1	0	0	0	0	0	1	0	0	8212	1299	45	2	2376	2	KIAA0753	17	6531560	Nonsense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		6531560	74663650	46	10748											
TRPV2	51393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	16340169	16340169	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatggtgcctctgaggaaaActatgtgcccgtccagctcc	8	9	12	12	1	1	1	0	1	1	0	3	3	3	3	4	3	4	1	4	3	3	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:16340169A>G	ENST00000338560.7	+	15	2660	c.2261A>G	c.(2260-2262)aAc>aGc	p.N754S	C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000365172.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|TRPV2_ENST00000577397.1_Missense_Mutation_p.N324S|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000578380.2_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	754					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TCTGAGGAAAACTATGTGCCC	0.562																																					p.N754S		.											.	TRPV2-91	0			c.A2261G						.						154	134	141					17																	16340169		2203	4300	6503	SO:0001583	missense	51393	exon15			AGGAAAACTATGT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.2261A>G	17.37:g.16340169A>G	ENSP00000342222:p.Asn754Ser	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	145	58	NM_016113	0	0	4	4	0	A6NML2|A8K0Z0|Q9Y670	Missense_Mutation	SNP	ENST00000338560.7	37	CCDS32576.1	.	.	.	.	.	.	.	.	.	.	A	5.819	0.335390	0.11013	.	.	ENSG00000187688	ENST00000338560	D	0.87334	-2.24	3.83	3.83	0.44106	.	0.576086	0.16403	N	0.215935	T	0.72740	0.3498	N	0.08118	0	0.19775	N	0.999956	B	0.09022	0.002	B	0.09377	0.004	T	0.61093	-0.7132	10	0.34782	T	0.22	-56.024	9.2873	0.37764	1.0:0.0:0.0:0.0	.	754	Q9Y5S1	TRPV2_HUMAN	S	754	ENSP00000342222:N754S	ENSP00000342222:N754S	N	+	2	0	TRPV2	16280894	0.920000	0.31207	0.964000	0.40570	0.094000	0.18550	2.141000	0.42168	1.972000	0.57404	0.459000	0.35465	AAC	.		0.562	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113		G	16340169	A	G	16340169	3	3	123	1	0	0	0	0	1	0	0	0	16629	43	2	3	2315	3	TRPV2	17	16340169	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	9808609	16340169	64855041	47	10749											
STARD3	10948	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	37809843	37809854	+	In_Frame_Del	DEL	CCTCCCTGGGCT	CCTCCCTGGGCT	-																															gcgcagcctgcctgccgtggCctccctgggctcctcactgt																								rs371019835		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	CCTCCCTGGGCT	CCTCCCTGGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:37809843_37809854delCCTCCCTGGGCT	ENST00000336308.5	+	2	277_288	c.59_70delCCTCCCTGGGCT	c.(58-72)gcctccctgggctcc>gcc	p.SLGS21del	STARD3_ENST00000578232.1_Intron|STARD3_ENST00000544210.2_In_Frame_Del_p.SLGS21del|STARD3_ENST00000580611.1_In_Frame_Del_p.SLGS21del|STARD3_ENST00000394250.4_In_Frame_Del_p.SLGS21del	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	21					cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCTGCCGTGGCCTCCCTGGGCTCCTCACTGTC	0.684											OREG0024381	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.20_24del		.											.	STARD3-90	0			c.59_70del						.																																			SO:0001651	inframe_deletion	10948	exon2			.		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"StAR-related lipid transfer (START) domain containing"	17579	protein-coding gene	gene with protein product		607048	"START domain containing 3"				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.59_70delCCTCCCTGGGCT	17.37:g.37809843_37809854delCCTCCCTGGGCT	ENSP00000337446:p.Ser21_Ser24del	Somatic	76	0	873	WXS	Illumina HiSeq	Phase_I	60	20	NM_006804	0	0	0	0	0	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	In_Frame_Del	DEL	ENST00000336308.5	37	CCDS11341.1																																																																																			.		0.684	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1			-	37809854	CCTCCCTGGGCT	-	37809843	7	5	123	1	0	1	0	1	0	0	0	0	15289	739	26	0	61	0	STARD3	17	37809843	In_Frame_Del	DEL	CCTCCCTGGGCT	TCGA-GL-7966-01A-11D-2201-08	21469674	37809843	43385367	48	10750											
TTC25	83538	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40101470	40101470	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggaaattccagcaagccaTtgacacgtgagtgaccaaga	14	7	11	9	1	0	4	0	3	0	1	1	5	1	5	3	1	2	1	3	1	3	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:40101470T>C	ENST00000591658.1	+	0	1207							Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm (GO:0005737)				endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				CAGCAAGCCATTGACACGTGA	0.458																																					.													.	TTC25-23	0			.						.						44	39	41					17																	40101470		1882	4110	5992			83538	.			AAGCCATTGACAC	AK055498	CCDS74063.1	17q21.2	2014-08-12			ENSG00000204815	ENSG00000204815		"Tetratricopeptide (TTC) repeat domain containing"	25280	protein-coding gene	gene with protein product							Standard	XM_006722129		Approved	DKFZP434H0115	uc002hyj.4	Q96NG3	OTTHUMG00000175837		17.37:g.40101470T>C		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	23	13	.	0	0	0	0	0	Q6NX40|Q6PJ04|Q9H0K5	Missense_Mutation	SNP	ENST00000591658.1	37																																																																																				.		0.458	TTC25-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000449237.1	NM_031421		C	40101470	T	C	40101470	1	2	123	0	1	0	0	0	0	0	0	0	16726	1493	52	3		3	TTC25	17	40101470	RNA	SNP	T	TCGA-GL-7966-01A-11D-2201-08	2291627	40101470	41093740	49	10751											
MYCBPAP	55040	ucsc.edu	37	chr17	48608775	48608775	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaatgtcgaggaggctttgCgcctctgcaggtgactctcg	7	10	14	10	3	2	2	0	1	2	1	4	4	2	3	1	3	2	2	1	3	1	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:48608775C>T	ENST00000268933.3	+	0	0				MYCBPAP_ENST00000323776.5_Missense_Mutation_p.R981C|MYCBPAP_ENST00000436259.2_3'UTR|EPN3_ENST00000541226.1_5'Flank|EPN3_ENST00000537145.1_5'Flank	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3							clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			GGAGGCTTTGCGCCTCTGCAG	0.522																																					p.R981C													.	MYCBPAP-230	0			c.C2941T						.						70	59	63					17																	48608775		2203	4300	6503	SO:0001631	upstream_gene_variant	84073	exon19			GCTTTGCGCCTCT	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201			17.37:g.48608775C>T	Exception_encountered	Somatic	24	0		WXS	Illumina HiSeq		31	4	NM_032133	0	0	0	0	0	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	C	9.729	1.161778	0.21538	.	.	ENSG00000136449	ENST00000323776	T	0.26810	1.71	5.1	1.66	0.24008	.	0.990904	0.08203	N	0.981944	T	0.24353	0.0590	L	0.57536	1.79	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.31779	-0.9931	10	0.72032	D	0.01	0.4844	4.9734	0.14127	0.0:0.6024:0.1803:0.2173	.	944	Q8TBZ2	MYBPP_HUMAN	C	981	ENSP00000323184:R981C	ENSP00000323184:R981C	R	+	1	0	MYCBPAP	45963774	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.063000	0.11655	1.040000	0.40099	0.549000	0.68633	CGC	.		0.522	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		T	48608775	C	T	48608775	1	4	123	0	1	0	0	0	0	0	0	0	10044	768	27	1		1	MYCBPAP	17	48608775	5'Flank	SNP	C	TCGA-GL-7966-01A-11D-2201-08	8507305	48608775	32586435	50	10752											
ENPP7	339221	broad.mit.edu	37	chr17	77710872	77710872	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttcaacaatggggagcaCggctttgacaacaaggacat	14	7	11	9	1	1	1	1	1	0	0	1	3	1	3	0	4	3	3	0	4	4	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:77710872C>T	ENST00000328313.5	+	4	1280	c.1059C>T	c.(1057-1059)caC>caT	p.H353H		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			ATGGGGAGCACGGCTTTGACA	0.607																																					p.H353H													.	ENPP7-92	0			c.C1059T						.						98	81	87					17																	77710872		2203	4300	6503	SO:0001819	synonymous_variant	339221	exon4			GGAGCACGGCTTT	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"alkaline sphingomyelinase"					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.1059C>T	17.37:g.77710872C>T		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	94	5	NM_178543	0	0	0	0	0		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			.		0.607	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77710872	C	T	77710872	2	4	123	1	0	0	0	0	0	0	0	1	5148	535	19	1		1	ENPP7	17	77710872	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	29102097	77710872	3484338	51	10753											
SYT4	6860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	40853736	40853736	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atagaatgtaaaggtctcatCaaaagctggatccaaggttt	15	11	9	6	0	2	1	2	0	1	1	4	2	3	2	1	3	1	3	1	3	7	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr18:40853736C>G	ENST00000255224.3	-	2	1026	c.658G>C	c.(658-660)Gat>Cat	p.D220H	SYT4_ENST00000590752.1_Missense_Mutation_p.D202H|SYT4_ENST00000586678.1_Intron	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	220	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						AAGGTCTCATCAAAAGCTGGA	0.403																																					p.D220H	NSCLC(85;81 1419 2855 22820 35912)	.											.	SYT4-132	0			c.G658C						.						111	108	109					18																	40853736		2203	4300	6503	SO:0001583	missense	6860	exon2			TCTCATCAAAAGC	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.658G>C	18.37:g.40853736C>G	ENSP00000255224:p.Asp220His	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	68	30	NM_020783	0	0	1	1	0	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	37	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319387	0.81469	.	.	ENSG00000132872	ENST00000255224;ENST00000442661	T	0.09163	3.01	5.87	5.87	0.94306	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.043597	0.85682	D	0.000000	T	0.33265	0.0857	M	0.64260	1.97	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.69142	0.962;0.962	T	0.00357	-1.1792	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	202;220	B4DEU3;Q9H2B2	.;SYT4_HUMAN	H	220;25	ENSP00000255224:D220H	ENSP00000255224:D220H	D	-	1	0	SYT4	39107734	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.729000	0.84864	2.941000	0.99782	0.655000	0.94253	GAT	.		0.403	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		G	40853736	C	G	40853736	3	3	123	1	0	0	0	0	1	0	0	0	15508	826	29	4	631	4	SYT4	18	40853736	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08		40853736	37223512	52	10754											
SERPINB10	5273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	61585305	61585305	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttaaaacagccaatgcgaTatatggagagaaaacgtatg	18	8	9	6	2	0	1	0	0	0	1	0	4	0	2	1	1	4	1	1	1	8	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr18:61585305T>A	ENST00000238508.3	+	4	400	c.341T>A	c.(340-342)aTa>aAa	p.I114K		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	114					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				GCCAATGCGATATATGGAGAG	0.363																																					p.I114K		.											.	SERPINB10-227	0			c.T341A						.						103	94	97					18																	61585305		2203	4300	6503	SO:0001583	missense	5273	exon3			ATGCGATATATGG	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"Serine (or cysteine) peptidase inhibitors"	8942	protein-coding gene	gene with protein product	"protease inhibitor 10 (ovalbumin type, bomapin)"	602058	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.341T>A	18.37:g.61585305T>A	ENSP00000238508:p.Ile114Lys	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	44	6	NM_005024	0	0	0	0	0	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	T	9.136	1.012671	0.19277	.	.	ENSG00000242550	ENST00000238508	D	0.84370	-1.84	5.83	3.43	0.39272	Serpin domain (3);	0.694589	0.14087	N	0.342276	D	0.88555	0.6468	H	0.94771	3.58	0.09310	N	1	B	0.27316	0.175	B	0.28465	0.09	T	0.83166	-0.0096	10	0.87932	D	0	.	9.1438	0.36919	0.0:0.1534:0.0:0.8466	.	114	P48595	SPB10_HUMAN	K	114	ENSP00000238508:I114K	ENSP00000238508:I114K	I	+	2	0	SERPINB10	59736285	0.002000	0.14202	0.004000	0.12327	0.109000	0.19521	1.191000	0.32138	1.037000	0.40024	-0.274000	0.10170	ATA	.		0.363	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		A	61585305	T	A	61585305	3	1	123	1	0	0	0	0	1	0	0	0	14129	1406	49	5	351	5	SERPINB10	18	61585305	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	20731569	61585305	16491943	53	10755											
ZSWIM4	65249	broad.mit.edu	37	chr19	13941242	13941242	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctgtgcgagaagaaccactCggccttcgaggcggcctacc	8	6	12	15	4	0	2	0	0	0	2	2	4	0	2	5	3	3	0	5	3	3	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr19:13941242C>T	ENST00000254323.2	+	13	2537	c.2348C>T	c.(2347-2349)tCg>tTg	p.S783L	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.S617L	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	783							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			AAGAACCACTCGGCCTTCGAG	0.697																																					p.S783L													.	ZSWIM4-90	0			c.C2348T						.						78	80	80					19																	13941242		2203	4300	6503	SO:0001583	missense	65249	exon13			ACCACTCGGCCTT	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"Zinc fingers, SWIM-type"	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.2348C>T	19.37:g.13941242C>T	ENSP00000254323:p.Ser783Leu	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	168	7	NM_023072	0	0	12	12	0		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	C	2.142	-0.396521	0.04899	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.41065	1.01;1.01	4.14	4.14	0.48551	.	0.205124	0.32640	N	0.005825	T	0.21761	0.0524	N	0.08118	0	0.23791	N	0.996832	B;B	0.15719	0.014;0.002	B;B	0.09377	0.003;0.004	T	0.08994	-1.0695	10	0.11485	T	0.65	-2.7245	13.8964	0.63775	0.0:1.0:0.0:0.0	.	617;783	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	L	783;617	ENSP00000254323:S783L;ENSP00000405278:S617L	ENSP00000254323:S783L	S	+	2	0	ZSWIM4	13802242	0.980000	0.34600	0.110000	0.21437	0.293000	0.27360	2.803000	0.47924	1.849000	0.53698	0.484000	0.47621	TCG	.		0.697	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		T	13941242	C	T	13941242	3	4	123	1	0	0	0	0	1	0	0	0	18275	893	31	1	2398	1	ZSWIM4	19	13941242	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08		13941242	45187741	54	10756											
C19orf50	79036	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	18679377	18679377	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggacctgtcccatgtccAgcctggctccccagccatca	7	7	9	18	1	1	0	1	0	0	0	4	2	4	1	7	2	2	1	7	2	0	0			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr19:18679377A>T	ENST00000602094.1	+	5	1927	c.467A>T	c.(466-468)cAg>cTg	p.Q156L	KXD1_ENST00000539106.1_Missense_Mutation_p.Q156L|KXD1_ENST00000601630.1_Missense_Mutation_p.Q175L|KXD1_ENST00000599319.1_Missense_Mutation_p.Q156L|KXD1_ENST00000595073.1_Missense_Mutation_p.Q156L|AC005253.4_ENST00000593791.1_RNA|KXD1_ENST00000222307.4_Missense_Mutation_p.Q156L|KXD1_ENST00000540691.1_Missense_Mutation_p.Q156L			Q9BQD3	KXDL1_HUMAN	KxDL motif containing 1	156					vesicle-mediated transport (GO:0016192)	BLOC-1 complex (GO:0031083)											TCCCATGTCCAGCCTGGCTCC	0.657																																					p.Q156L		.											.	.	0			c.A467T						.						96	89	92					19																	18679377		2203	4300	6503	SO:0001583	missense	79036	exon6			ATGTCCAGCCTGG	AK098346	CCDS12381.1	19p13.11	2011-11-24	2011-11-24	2011-11-24	ENSG00000105700	ENSG00000105700			28420	protein-coding gene	gene with protein product		615178	"chromosome 19 open reading frame 50"	C19orf50		21159114	Standard	NM_001171948		Approved	FLJ25480, MGC2749, KXDL	uc002njo.3	Q9BQD3		ENST00000602094.1:c.467A>T	19.37:g.18679377A>T	ENSP00000472836:p.Gln156Leu	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	141	9	NM_001171948	0	0	69	69	0	O76098	Missense_Mutation	SNP	ENST00000602094.1	37	CCDS12381.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.064988	0.36470	.	.	ENSG00000105700	ENST00000540691;ENST00000539106;ENST00000222307	T;T;T	0.45276	0.9;0.9;0.9	4.59	-4.19	0.03835	.	0.517276	0.21501	N	0.073525	T	0.21590	0.0520	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.05699	-1.0869	10	0.59425	D	0.04	-5.0797	6.0241	0.19646	0.4521:0.2352:0.3127:0.0	.	156	Q9BQD3	CS050_HUMAN	L	156	ENSP00000443549:Q156L;ENSP00000438903:Q156L;ENSP00000222307:Q156L	ENSP00000222307:Q156L	Q	+	2	0	C19orf50	18540377	0.002000	0.14202	0.000000	0.03702	0.040000	0.13550	0.014000	0.13333	-0.954000	0.03640	-0.345000	0.07892	CAG	.		0.657	KXD1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465107.1	NM_024069		T	18679377	A	T	18679377	3	4	123	1	0	0	0	0	1	0	0	0	1938	188	7	5	481	5	C19orf50	19	18679377	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	4738135	18679377	40449606	55	10757											
NKPD1	284353	broad.mit.edu	37	chr19	45656458	45656458	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttttcacgcgacaccagccGctcgatcttcttgcgctggc	5	11	9	16	5	3	0	1	0	2	0	4	2	3	0	2	1	2	2	2	1	0	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr19:45656458G>A	ENST00000438936.2	-	3	782	c.571C>T	c.(571-573)Cgg>Tgg	p.R191W	NKPD1_ENST00000589776.1_Missense_Mutation_p.R191W|AC005757.7_ENST00000589594.1_lincRNA|NKPD1_ENST00000317951.4_Missense_Mutation_p.R413W|NKPD1_ENST00000429338.1_Missense_Mutation_p.R191W			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1	191	KAP NTPase.					integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		GACACCAGCCGCTCGATCTTC	0.617																																					p.R413W													.	NKPD1-68	0			c.C1237T						.						11	14	13					19																	45656458		2064	4212	6276	SO:0001583	missense	284353	exon4			CCAGCCGCTCGAT	AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521	ENST00000438936.2:c.571C>T	19.37:g.45656458G>A	ENSP00000401739:p.Arg191Trp	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_198478	0	0	0	0	0	B7ZLG6|D6RH15|Q8N2A2	Missense_Mutation	SNP	ENST00000438936.2	37		.	.	.	.	.	.	.	.	.	.	G	16.16	3.043458	0.55003	.	.	ENSG00000179846	ENST00000317951;ENST00000438936;ENST00000429338	T;T;T	0.51574	0.7;0.7;0.72	4.66	3.57	0.40892	KAP P-loop (1);	0.070935	0.53938	D	0.000059	T	0.62925	0.2468	M	0.61703	1.905	0.34967	D	0.752799	D	0.89917	1.0	D	0.75484	0.986	T	0.74019	-0.3799	10	0.72032	D	0.01	-35.867	11.9149	0.52759	0.0:0.0:0.8259:0.1741	.	191	Q17RQ9	NKPD1_HUMAN	W	413;191;191	ENSP00000321976:R413W;ENSP00000401739:R191W;ENSP00000404706:R191W	ENSP00000321976:R413W	R	-	1	2	NKPD1	50348298	0.999000	0.42202	1.000000	0.80357	0.948000	0.59901	1.046000	0.30354	2.121000	0.65114	0.313000	0.20887	CGG	.		0.617	NKPD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000360950.2	NM_198478		A	45656458	G	A	45656458	3	1	123	1	0	0	0	0	1	0	0	0	10472	1086	38	1	1265	1	NKPD1	19	45656458	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	26977081	45656458	13472525	56	10758											
MYBPC2	4606	broad.mit.edu	37	chr19	50939282	50939282	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgtagggaaggacgcagtGgtcgtggccaaggtgaacgg	10	6	18	7	3	0	1	0	1	0	0	1	3	0	3	1	6	1	2	1	6	4	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr19:50939282G>T	ENST00000357701.5	+	4	261	c.210G>T	c.(208-210)gtG>gtT	p.V70V		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	70	Ig-like C2-type 1.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		AGGACGCAGTGGTCGTGGCCA	0.607																																					p.V70V													.	MYBPC2-67	0			c.G210T						.						33	38	36					19																	50939282		2082	4200	6282	SO:0001819	synonymous_variant	4606	exon4			CGCAGTGGTCGTG		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7550	protein-coding gene	gene with protein product	"fast-type muscle myosin-binding-protein C"	160793	"myosin-binding protein C, fast-type"			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.210G>T	19.37:g.50939282G>T		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_004533	0	0	0	0	0	A1L4G9	Silent	SNP	ENST00000357701.5	37	CCDS46152.1																																																																																			.		0.607	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		T	50939282	G	T	50939282	2	4	123	1	0	0	0	0	0	0	0	1	10037	1335	47	4		4	MYBPC2	19	50939282	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08	5282824	50939282	8189701	57	10759											
TCFL5	10732	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	61490803	61490806	+	Frame_Shift_Del	DEL	AGAA	AGAA	-																															ttcaatttcttgctgataacAgaaagaaaatgctctaggca																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	AGAA	AGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr20:61490803_61490806delAGAA	ENST00000335351.3	-	3	996_999	c.904_907delTTCT	c.(904-909)ttctgtfs	p.FC302fs	TCFL5_ENST00000217162.5_Frame_Shift_Del_p.FC254fs	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	302					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TGCTGATAACAGAAAGAAAATGCT	0.387																																					p.302_303del		.											.	TCFL5-581	0			c.904_907del						.																																			SO:0001589	frameshift_variant	10732	exon3			.	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"Basic helix-loop-helix proteins"	11646	protein-coding gene	gene with protein product	"HPV-16 E2 binding protein 1"	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.904_907delTTCT	20.37:g.61490807_61490810delAGAA	ENSP00000334294:p.Phe302fs	Somatic	228	0		WXS	Illumina HiSeq	Phase_I	210	74	NM_006602	0	0	0	0	0	O94771|Q9BYW0	Frame_Shift_Del	DEL	ENST00000335351.3	37	CCDS13506.1																																																																																			.		0.387	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602		-	61490806	AGAA	-	61490803	7	5	123	1	0	1	0	1	0	0	0	0	15731	188	7	0	611	0	TCFL5	20	61490803	Frame_Shift_Del	DEL	AGAA	TCGA-GL-7966-01A-11D-2201-08		61490803	1534717	58	10760											
LSS	4047	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47615617	47615617	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtaggtctgccccatacagGcgaaggcctccaggccaaac	10	5	12	14	1	1	0	0	0	1	0	2	1	2	0	5	5	3	1	5	5	4	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr21:47615617G>A	ENST00000397728.3	-	19	1868	c.1790C>T	c.(1789-1791)gCc>gTc	p.A597V	AP001468.1_ENST00000594486.1_5'Flank|LSS_ENST00000522411.1_Missense_Mutation_p.A586V|LSS_ENST00000356396.4_Missense_Mutation_p.A597V|LSS_ENST00000457828.2_Missense_Mutation_p.A517V	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	597					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)	p.A597V(1)		cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CCCCATACAGGCGAAGGCCTC	0.582																																					p.A597V	Pancreas(114;955 2313 34923 50507)	.											.	LSS-90	1	Substitution - Missense(1)	skin(1)	c.C1790T						.						127	109	115					21																	47615617		2203	4300	6503	SO:0001583	missense	4047	exon19			ATACAGGCGAAGG	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1790C>T	21.37:g.47615617G>A	ENSP00000380837:p.Ala597Val	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	67	51	NM_001001438	0	0	1	14	13	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.738473	0.69304	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	5.61	5.61	0.85477	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.098347	0.64402	D	0.000001	T	0.31670	0.0804	L	0.39692	1.235	0.80722	D	1	D;D	0.62365	0.979;0.991	B;P	0.49922	0.393;0.626	T	0.01205	-1.1419	10	0.19590	T	0.45	.	19.224	0.93810	0.0:0.0:1.0:0.0	.	586;597	E9PEI9;P48449	.;ERG7_HUMAN	V	597;517;597;586	ENSP00000348762:A597V;ENSP00000409191:A517V;ENSP00000380837:A597V;ENSP00000429133:A586V	ENSP00000348762:A597V	A	-	2	0	LSS	46440045	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	9.232000	0.95325	2.633000	0.89246	0.655000	0.94253	GCC	.		0.582	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47615617	G	A	47615617	3	1	123	1	0	0	0	0	1	0	0	0	9090	1203	42	2	424	2	LSS	21	47615617	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		47615617	514278	59	10761											
PRMT2	3275	bcgsc.ca	37	chr21	48083430	48083430	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgtctgtggctctgagctgGgctgtcacttccagacaaga	8	11	12	10	0	3	3	1	1	2	2	4	3	4	3	1	2	1	3	1	2	1	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr21:48083430G>A	ENST00000397637.1	+	10	2187	c.1233G>A	c.(1231-1233)tgG>tgA	p.W411*	PRMT2_ENST00000451211.2_Intron|PRMT2_ENST00000397638.2_Nonsense_Mutation_p.W411*|PRMT2_ENST00000291705.6_Intron|PRMT2_ENST00000458387.2_Missense_Mutation_p.G264S|PRMT2_ENST00000355680.3_Nonsense_Mutation_p.W411*|PRMT2_ENST00000440086.1_Nonsense_Mutation_p.W309*			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	411	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		CTCTGAGCTGGGCTGTCACTT	0.542																																					p.W411X													.	PRMT2-91	0			c.G1233A						.						136	120	125					21																	48083430		2203	4300	6503	SO:0001587	stop_gained	3275	exon11			GAGCTGGGCTGTC	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"Protein arginine methyltransferases"	5186	protein-coding gene	gene with protein product		601961	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1", "HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.1233G>A	21.37:g.48083430G>A	ENSP00000380759:p.Trp411*	Somatic	89	0		WXS	Illumina HiSeq	Phase_1	49	4	NM_206962	0	0	88	88	0	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Nonsense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	46|46	12.763896|12.763896	0.99694|0.99694	.|.	.|.	ENSG00000160310|ENSG00000160310	ENST00000458387|ENST00000355680;ENST00000397638;ENST00000397637;ENST00000440086	T|.	0.75938|.	-0.98|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.195548	.|0.48767	.|D	.|0.000171	T|.	0.72104|.	0.3419|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.35433|.	0.501|.	B|.	0.22386|.	0.039|.	T|.	0.70722|.	-0.4794|.	7|.	.|.	.|.	.|.	-16.0416|-16.0416	16.504|16.504	0.84264|0.84264	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	264|.	B7U631|.	.|.	S|X	264|411;411;411;309	ENSP00000407463:G264S|.	.|.	G|W	+|+	1|3	0|0	PRMT2|PRMT2	46907858|46907858	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.939000|0.939000	0.58152|0.58152	6.436000|6.436000	0.73417|0.73417	2.583000|2.583000	0.87209|0.87209	0.561000|0.561000	0.74099|0.74099	GGC|TGG	.		0.542	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535		A	48083430	G	A	48083430	4	1	123	1	0	0	0	0	0	1	0	0	12566	1241	43	2	1267	2	PRMT2	21	48083430	Nonsense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	467813	48083430	46465	60	10762											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	30061052	30061052	+	Splice_Site	DEL	T	T	-																															aaagcttcgtgttaataagcTggtaagttgagatcctggtt																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr22:30061052delT	ENST00000338641.4	+	9	1325	c.884delT	c.(883-885)ctg>cg	p.L295fs	NF2_ENST00000403435.1_Splice_Site_p.L295fs|NF2_ENST00000403999.3_Splice_Site_p.L295fs|NF2_ENST00000334961.7_Splice_Site_p.L212fs|NF2_ENST00000347330.5_Splice_Site_p.L136fs|NF2_ENST00000397789.3_Splice_Site_p.L295fs|NF2_ENST00000361452.4_Splice_Site_p.L254fs|NF2_ENST00000361166.4_Splice_Site_p.L295fs|NF2_ENST00000353887.4_Splice_Site_p.L212fs|NF2_ENST00000361676.4_Splice_Site_p.L253fs|NF2_ENST00000413209.2_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	295	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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.?(3)|p.F271_L295del(1)		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						GTTAATAAGCTGGTAAGTTGA	0.333			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.L295fs		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	4	Unknown(3)|Deletion - In frame(1)	central_nervous_system(2)|large_intestine(1)|stomach(1)	c.884delT	GRCh37	CD070492	NF2	D		.						111	103	106					22																	30061052		2202	4300	6502	SO:0001630	splice_region_variant	4771	exon9	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	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.885+1T>-	22.37:g.30061052delT		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	24	18	NM_000268	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	37	CCDS13861.1																																																																																			.		0.333	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Frame_Shift_Del	-	30061052	T	-	30061052	8	5	123	1	0	1	0	1	0	0	1	0	10383	1594	55	0	918	0	NF2	22	30061052	Splice_Site	DEL	T	TCGA-GL-7966-01A-11D-2201-08		30061052	21243514	61	10763											
APOL3	80833	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr22	36556768	36556768	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatccagctgttctgagctGtgtggatcccacctccagcc	7	10	10	14	0	1	2	0	1	1	1	4	3	4	3	5	1	3	3	5	1	0	1	rs11089781	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr22:36556768G>T	ENST00000349314.2	-	1	209	c.172C>A	c.(172-174)Cag>Aag	p.Q58K	APOL3_ENST00000424878.2_5'UTR|APOL3_ENST00000397287.2_5'UTR|APOL3_ENST00000361710.2_5'UTR|APOL3_ENST00000397293.2_5'UTR	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	58					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						GTTCTGAGCTGTGTGGATCCC	0.512																																					p.Q58K		.											.	APOL3-90	0			c.C172A						.						149	122	131					22																	36556768		2203	4300	6503	SO:0001583	missense	80833	exon1			TGAGCTGTGTGGA	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"Apolipoproteins"	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.172C>A	22.37:g.36556768G>T	ENSP00000344577:p.Gln58Lys	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	75	11	NM_145640	0	0	87	87	0	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Missense_Mutation	SNP	ENST00000349314.2	37	CCDS13922.1	.	.	.	.	.	.	.	.	.	.	G	5.735	0.320098	0.10845	.	.	ENSG00000128284	ENST00000349314;ENST00000531095	T;T	0.60672	3.74;0.17	2.76	1.71	0.24356	.	680.984000	0.00751	U	0.001072	T	0.34890	0.0913	N	0.08118	0	0.23879	N	0.99658	P	0.43477	0.808	B	0.33799	0.17	T	0.40040	-0.9584	10	0.51188	T	0.08	.	6.0512	0.19787	0.1475:0.0:0.8525:0.0	.	58	O95236	APOL3_HUMAN	K	58;22	ENSP00000344577:Q58K;ENSP00000432271:Q22K	ENSP00000344577:Q58K	Q	-	1	0	APOL3	34886714	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	-0.640000	0.05440	0.726000	0.32339	0.603000	0.83216	CAG	G|0.932;A|0.068		0.512	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641		T	36556768	G	T	36556768	3	4	123	1	0	0	0	0	1	0	0	0	807	1386	48	4	1048	4	APOL3	22	36556768	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	6495716	36556768	14747798	62	10764											
CACNG2	10369	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	37098492	37098492	+	Frame_Shift_Del	DEL	T	T	-																															ggtttcattctcactgacacTtttggtcttgcaaacccctc																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr22:37098492delT	ENST00000300105.6	-	1	1111	c.130delA	c.(130-132)agtfs	p.S44fs	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	44					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TCACTGACACTTTTGGTCTTG	0.488																																					p.S44fs		.											.	CACNG2-90	0			c.130delA						.						266	225	239					22																	37098492		2203	4300	6503	SO:0001589	frameshift_variant	10369	exon1			.	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.130delA	22.37:g.37098492delT	ENSP00000300105:p.Ser44fs	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	174	120	NM_006078	0	0	0	0	0	Q2M1M1|Q5TGT3|Q9UGZ7	Frame_Shift_Del	DEL	ENST00000300105.6	37	CCDS13931.1																																																																																			.		0.488	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			-	37098492	T	-	37098492	7	5	123	1	0	1	0	1	0	0	0	0	2563	1609	56	0	857	0	CACNG2	22	37098492	Frame_Shift_Del	DEL	T	TCGA-GL-7966-01A-11D-2201-08	541724	37098492	14206074	63	10765											
ATP2B3	492	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	152823737	152823737	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtggctgtgatcgtggcCttcacaggtgcctgcattac	5	12	14	10	1	1	1	1	1	0	0	2	1	1	1	2	4	3	2	2	4	1	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chrX:152823737C>T	ENST00000349466.2	+	16	2927	c.2601C>T	c.(2599-2601)gcC>gcT	p.A867A	ATP2B3_ENST00000359149.3_Silent_p.A867A|ATP2B3_ENST00000263519.4_Silent_p.A867A|ATP2B3_ENST00000370186.1_Silent_p.A853A|ATP2B3_ENST00000370181.2_Silent_p.A853A|ATP2B3_ENST00000393842.1_Silent_p.A853A|ATP2B3_ENST00000460549.1_3'UTR			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	867					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGATCGTGGCCTTCACAGGTG	0.582																																					p.A867A		.											.	ATP2B3-109	0			c.C2601T						.						181	128	146					X																	152823737		2203	4300	6503	SO:0001819	synonymous_variant	492	exon15			CGTGGCCTTCACA	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"ATPases / P-type"	816	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 3", "cilia and flagella associated protein 39"	300014	"spinocerebellar ataxia, X-linked 1", "cerebellar ataxia 2 (X-linked)"	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2601C>T	X.37:g.152823737C>T		Somatic	208	0		WXS	Illumina HiSeq	Phase_I	133	8	NM_001001344	0	0	0	0	0	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			.		0.582	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152823737	C	T	152823737	2	4	123	1	0	0	0	0	0	0	0	1	1142	668	24	2		2	ATP2B3	23	152823737	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08		152823737	2446823	64	10766											
PRAMEF17	391004	hgsc.bcm.edu	37	chr1	13718601	13718601	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctactctcgagatcctcaCgttaaaggactgtcagatcc	10	11	8	12	2	3	2	2	0	1	2	6	4	5	3	2	1	2	2	2	1	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:13718601C>T	ENST00000376098.4	+	3	1090	c.1064C>T	c.(1063-1065)aCg>aTg	p.T355M		NM_001099851.1	NP_001093321.1	Q5VTA0	PRA17_HUMAN	PRAME family member 17	355					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					kidney(1)|lung(2)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAGATCCTCACGTTAAAGGAC	0.537																																					p.T355M		.											.	.	0			c.C1064T						.						9	22	19					1																	13718601		831	2388	3219	SO:0001583	missense	391004	exon3			TCCTCACGTTAAA		CCDS41264.1	1p36.21	2013-01-17			ENSG00000204479	ENSG00000204479		"-"	29485	protein-coding gene	gene with protein product							Standard	NM_001099851		Approved	OTTHUMG00000007909	uc009vnz.1	Q5VTA0	OTTHUMG00000007909	ENST00000376098.4:c.1064C>T	1.37:g.13718601C>T	ENSP00000365266:p.Thr355Met	Somatic	116	2		WXS	Illumina HiSeq	Phase_I	44	4	NM_001099851	0	0	0	0	0	B2RUU4	Missense_Mutation	SNP	ENST00000376098.4	37	CCDS41264.1	.	.	.	.	.	.	.	.	.	.	C	0.396	-0.920692	0.02396	.	.	ENSG00000204479	ENST00000376098	T	0.11821	2.74	1.03	-2.05	0.07321	.	1.024390	0.07732	N	0.945353	T	0.06962	0.0177	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.12837	0.008	T	0.37731	-0.9693	10	0.66056	D	0.02	.	1.9565	0.03377	0.4378:0.2899:0.0:0.2723	.	355	Q5VTA0	PRA17_HUMAN	M	355	ENSP00000365266:T355M	ENSP00000365266:T355M	T	+	2	0	PRAMEF17	13591188	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.801000	0.04550	-1.158000	0.02811	-0.507000	0.04495	ACG	.		0.537	PRAMEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021780.2	NM_001099851		T	13718601	C	T	13718601	3	4	124	1	0	0	0	0	1	0	0	0	12461	536	19	1	1074	1	PRAMEF17	1	13718601	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		13718601	235532020	1	10767											
FAM46B	115572	hgsc.bcm.edu	37	chr1	27332864	27332864	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagccccgcaccaggaggtgGcagtacttgaggaggccacc	10	4	14	13	1	0	1	0	1	0	0	0	3	0	3	5	5	2	3	5	5	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:27332864G>A	ENST00000289166.5	-	2	1014	c.849C>T	c.(847-849)tgC>tgT	p.C283C		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	283										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		CCAGGAGGTGGCAGTACTTGA	0.672																																					p.C283C		.											.	FAM46B-90	0			c.C849T						.						19	22	21					1																	27332864		2202	4295	6497	SO:0001819	synonymous_variant	115572	exon2			GAGGTGGCAGTAC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.849C>T	1.37:g.27332864G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_052943	0	0	1	1	0		Silent	SNP	ENST00000289166.5	37	CCDS294.2																																																																																			.		0.672	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		A	27332864	G	A	27332864	2	1	124	1	0	0	0	0	0	0	0	1	5585	1195	42	2		2	FAM46B	1	27332864	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	13614263	27332864	221917757	2	10768											
IPO13	9670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	44423086	44423086	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccccagcacacagaggccCtcctctacggcttccaatcc	8	8	6	19	1	1	1	0	0	1	1	5	1	5	1	6	2	2	2	6	2	2	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:44423086C>A	ENST00000372343.3	+	7	2067	c.1405C>A	c.(1405-1407)Ctc>Atc	p.L469I	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	469					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				CACAGAGGCCCTCCTCTACGG	0.572																																					p.L469I		.											.	IPO13-226	0			c.C1405A						.						109	99	103					1																	44423086		2203	4300	6503	SO:0001583	missense	9670	exon7			GAGGCCCTCCTCT	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"Importins"	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.1405C>A	1.37:g.44423086C>A	ENSP00000361418:p.Leu469Ile	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	69	54	NM_014652	0	0	0	14	14	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Missense_Mutation	SNP	ENST00000372343.3	37	CCDS503.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818926	0.50633	.	.	ENSG00000117408	ENST00000372343	T	0.66995	-0.24	5.69	4.78	0.61160	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.53351	0.1791	L	0.47716	1.5	0.80722	D	1	P	0.37663	0.604	B	0.35550	0.205	T	0.49312	-0.8953	10	0.22109	T	0.4	16.3773	7.0228	0.24924	0.0:0.7119:0.0:0.2881	.	469	O94829	IPO13_HUMAN	I	469	ENSP00000361418:L469I	ENSP00000361418:L469I	L	+	1	0	IPO13	44195673	0.942000	0.31987	1.000000	0.80357	0.991000	0.79684	1.613000	0.36900	1.420000	0.47138	0.561000	0.74099	CTC	.		0.572	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		A	44423086	C	A	44423086	3	1	124	1	0	0	0	0	1	0	0	0	7815	681	24	4	1431	4	IPO13	1	44423086	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	17090222	44423086	204827535	3	10769											
CSDE1	7812	hgsc.bcm.edu	37	chr1	115280131	115280131	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactccctgttggactctgAcccggggcagctggagattt	7	10	12	12	1	1	2	0	1	1	1	2	4	2	3	2	4	1	3	2	4	0	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:115280131A>G	ENST00000358528.4	-	5	789	c.363T>C	c.(361-363)ggT>ggC	p.G121G	CSDE1_ENST00000530886.1_Intron|CSDE1_ENST00000534699.1_Silent_p.G121G|CSDE1_ENST00000261443.5_Intron|CSDE1_ENST00000438362.2_Silent_p.G167G|CSDE1_ENST00000339438.6_Intron|CSDE1_ENST00000369530.1_Intron	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	121					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTGGACTCTGACCCGGGGCAG	0.423																																					p.G167G		.											.	CSDE1-227	0			c.T501C						.						78	68	71					1																	115280131		2203	4300	6503	SO:0001819	synonymous_variant	7812	exon6			ACTCTGACCCGGG		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.363T>C	1.37:g.115280131A>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_001242891	0	0	15	15	0	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Silent	SNP	ENST00000358528.4	37	CCDS30812.1																																																																																			.		0.423	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		G	115280131	A	G	115280131	2	3	124	1	0	0	0	0	0	0	0	1	3935	262	10	3		3	CSDE1	1	115280131	Silent	SNP	A	TCGA-GL-8500-01A-11D-2396-08	70857045	115280131	133970490	4	10770											
C1orf112	55732	hgsc.bcm.edu	37	chr1	169775219	169775219	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatgccaatacttggaagTttataattaagtaagtttgt	13	17	7	4	0	1	0	1	0	0	0	1	1	1	1	1	1	2	3	1	1	7	9			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:169775219T>C	ENST00000286031.6	+	7	1253	c.553T>C	c.(553-555)Ttt>Ctt	p.F185L	C1orf112_ENST00000413811.2_Missense_Mutation_p.F156L|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000456684.1_Missense_Mutation_p.F243L|C1orf112_ENST00000359326.4_Missense_Mutation_p.F185L	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	185										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TACTTGGAAGTTTATAATTAA	0.269																																					p.F185L		.											.	C1orf112-90	0			c.T553C						.						80	76	77					1																	169775219		2203	4294	6497	SO:0001583	missense	55732	exon7			TGGAAGTTTATAA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.553T>C	1.37:g.169775219T>C	ENSP00000286031:p.Phe185Leu	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_018186	0	0	0	0	0	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849916	0.91277	.	.	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000456684;ENST00000286031	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.62551	0.2437	M	0.78637	2.42	0.53005	D	0.999963	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.87578	0.987;0.998;0.998	T	0.69105	-0.5233	10	0.87932	D	0	-24.8356	14.1068	0.65096	0.0:0.0:0.0:1.0	.	156;127;185	B4E0A9;B4DGF2;Q9NSG2	.;.;CA112_HUMAN	L	156;185;243;185	ENSP00000389257:F156L;ENSP00000352276:F185L;ENSP00000415583:F243L;ENSP00000286031:F185L	ENSP00000286031:F185L	F	+	1	0	C1orf112	168041843	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.055000	0.76656	2.067000	0.61834	0.533000	0.62120	TTT	.		0.269	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		C	169775219	T	C	169775219	3	2	124	1	0	0	0	0	1	0	0	0	1991	1725	60	3	571	3	C1orf112	1	169775219	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	54495088	169775219	79475402	5	10771											
SLC30A1	7779	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	211749303	211749308	+	In_Frame_Del	DEL	ATCTAA	ATCTAA	-																															attacaacacaaagagttggAtctaaatatagcacccagca																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	ATCTAA	ATCTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:211749303_211749308delATCTAA	ENST00000367001.4	-	2	1075_1080	c.946_951delTTAGAT	c.(946-951)ttagatdel	p.LD316del		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	316					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)	p.D317Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		AAAGAGTTGGATCTAAATATAGCACC	0.364																																					p.316_317del		.											.	SLC30A1-93	1	Substitution - Missense(1)	large_intestine(1)	c.946_951del						.																																			SO:0001651	inframe_deletion	7779	exon2			.	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.946_951delTTAGAT	1.37:g.211749303_211749308delATCTAA	ENSP00000355968:p.Leu316_Asp317del	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	95	72	NM_021194	0	0	0	0	0	Q0VAK9|Q9BZF6	In_Frame_Del	DEL	ENST00000367001.4	37	CCDS1499.1																																																																																			.		0.364	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			-	211749308	ATCTAA	-	211749303	7	5	124	1	0	1	0	1	0	0	0	0	14585	330	12	0	576	0	SLC30A1	1	211749303	In_Frame_Del	DEL	ATCTAA	TCGA-GL-8500-01A-11D-2396-08	41974084	211749303	37501318	6	10772											
RRP15	51018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	218480910	218480910	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagatttcatcagtgtttTgagagggatggatggaagta	13	12	14	2	0	2	2	2	1	0	2	2	7	2	5	0	3	0	2	0	3	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:218480910T>G	ENST00000366932.3	+	4	671	c.641T>G	c.(640-642)tTg>tGg	p.L214W		NM_016052.3	NP_057136.2	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog (S. cerevisiae)	214						mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)			ACBD6/RRP15(2)	NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		ATCAGTGTTTTGAGAGGGATG	0.373																																					p.L214W		.											.	RRP15-90	0			c.T641G						.						109	106	107					1																	218480910		2203	4300	6503	SO:0001583	missense	51018	exon4			GTGTTTTGAGAGG		CCDS1520.2	1q41	2008-02-05			ENSG00000067533	ENSG00000067533			24255	protein-coding gene	gene with protein product		611193	"KIAA0507"	KIAA0507		15769876	Standard	NM_016052		Approved	CGI-115	uc001hlj.3	Q9Y3B9	OTTHUMG00000039494	ENST00000366932.3:c.641T>G	1.37:g.218480910T>G	ENSP00000355899:p.Leu214Trp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	28	24	NM_016052	0	0	1	10	9		Missense_Mutation	SNP	ENST00000366932.3	37	CCDS1520.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.883907	0.91814	.	.	ENSG00000067533	ENST00000366932	T	0.56275	0.47	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.78329	0.4266	M	0.90759	3.145	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.83015	-0.0170	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	214	Q9Y3B9	RRP15_HUMAN	W	214	ENSP00000355899:L214W	ENSP00000355899:L214W	L	+	2	0	RRP15	216547533	1.000000	0.71417	0.940000	0.37924	0.987000	0.75469	7.935000	0.87658	2.371000	0.80710	0.533000	0.62120	TTG	.		0.373	RRP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095284.1	NM_016052		G	218480910	T	G	218480910	3	3	124	1	0	0	0	0	1	0	0	0	13719	1821	63	5	655	5	RRP15	1	218480910	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	6731607	218480910	30769711	7	10773											
GALNT2	2590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	230385000	230385000	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agaaggtcccggcaggggaaCccagtcgcccctataaagta	12	5	12	12	2	0	1	0	0	0	1	2	2	1	2	4	4	1	2	4	4	6	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:230385000C>A	ENST00000366672.4	+	9	960	c.888C>A	c.(886-888)aaC>aaA	p.N296K	GALNT2_ENST00000541865.1_Missense_Mutation_p.N206K|GALNT2_ENST00000543760.1_Missense_Mutation_p.N258K	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	296					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				GGCAGGGGAACCCAGTCGCCC	0.567																																					p.N296K		.											.	GALNT2-92	0			c.C888A						.						68	73	71					1																	230385000		2203	4300	6503	SO:0001583	missense	2590	exon9			GGGGAACCCAGTC	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.888C>A	1.37:g.230385000C>A	ENSP00000355632:p.Asn296Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	29	18	NM_004481	0	0	2	13	11	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.038196	0.35989	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291;ENST00000541865	T;T;T	0.59638	0.25;0.25;0.25	4.99	0.378	0.16204	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.39118	0.1066	L	0.28649	0.875	0.80722	D	1	B;B	0.27882	0.192;0.063	B;B	0.20577	0.03;0.018	T	0.21690	-1.0238	10	0.66056	D	0.02	.	8.1747	0.31275	0.0:0.5081:0.0:0.4919	.	296;258	Q10471;G3V1S6	GALT2_HUMAN;.	K	258;296;177;206	ENSP00000445017:N258K;ENSP00000355632:N296K;ENSP00000444346:N206K	ENSP00000355632:N296K	N	+	3	2	GALNT2	228451623	0.998000	0.40836	0.988000	0.46212	0.888000	0.51559	0.520000	0.22878	0.244000	0.21351	-0.373000	0.07131	AAC	.		0.567	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		A	230385000	C	A	230385000	3	1	124	1	0	0	0	0	1	0	0	0	6233	506	18	4	922	4	GALNT2	1	230385000	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	11904090	230385000	18865621	8	10774											
RGS7	6000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	241094065	241094065	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atttgatggccaaaaataggGggtctgcggaatgaaaagaa	16	8	13	4	1	1	3	0	2	1	1	1	4	1	4	1	4	1	0	1	4	7	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:241094065G>C	ENST00000407727.1	-	5	336	c.337C>G	c.(337-339)Ccc>Gcc	p.P113A	RGS7_ENST00000331110.7_Missense_Mutation_p.P87A|RGS7_ENST00000366565.1_Missense_Mutation_p.P113A|RGS7_ENST00000446183.2_Missense_Mutation_p.P29A|RGS7_ENST00000348120.2_Intron|RGS7_ENST00000401882.1_Intron|RGS7_ENST00000366562.4_Missense_Mutation_p.P113A|RGS7_ENST00000366564.1_Missense_Mutation_p.P113A|RGS7_ENST00000366563.1_Missense_Mutation_p.P113A			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	113					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			CAAAAATAGGGGGTCTGCGGA	0.383																																					p.P113A		.											.	RGS7-232	0			c.C337G						.						102	114	110					1																	241094065		2203	4300	6503	SO:0001583	missense	6000	exon6			AATAGGGGGTCTG	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"Regulators of G-protein signaling"	10003	protein-coding gene	gene with protein product		602517	"regulator of G-protein signalling 7"			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.337C>G	1.37:g.241094065G>C	ENSP00000384428:p.Pro113Ala	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	81	68	NM_002924	0	0	0	0	0	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	37		.	.	.	.	.	.	.	.	.	.	G	25.7	4.660563	0.88154	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000446183;ENST00000366562;ENST00000407727	T;T;T;T;T;T;T	0.47177	1.16;1.1;1.14;1.13;0.85;1.14;1.11	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.74604	0.3738	M	0.88640	2.97	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.987;0.998;0.994;0.999;0.996	T	0.78907	-0.2019	10	0.87932	D	0	-3.1678	17.2744	0.87111	0.0:0.0:1.0:0.0	.	29;87;113;113;113	B7Z223;B7Z257;P49802-2;P49802-5;P49802-3	.;.;.;.;.	A	87;113;113;113;29;113;113	ENSP00000331485:P87A;ENSP00000355523:P113A;ENSP00000355522:P113A;ENSP00000355521:P113A;ENSP00000390138:P29A;ENSP00000355520:P113A;ENSP00000384428:P113A	ENSP00000331485:P87A	P	-	1	0	RGS7	239160688	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.000000	0.93564	2.769000	0.95229	0.655000	0.94253	CCC	.		0.383	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		C	241094065	G	C	241094065	3	2	124	1	0	0	0	0	1	0	0	0	13342	1232	43	4	1178	4	RGS7	1	241094065	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	10709065	241094065	8156556	9	10775											
PSME4	23198	broad.mit.edu;ucsc.edu	37	chr2	54176408	54176408	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgctaaattttctcccataAagtcgaatatatctgcaaga	14	14	5	8	1	2	1	0	0	2	1	4	2	2	1	1	0	2	2	1	0	8	7			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:54176408A>G	ENST00000404125.1	-	2	310	c.255T>C	c.(253-255)ctT>ctC	p.L85L	PSME4_ENST00000421748.2_5'Flank	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	85					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)			TTCTCCCATAAAGTCGAatat	0.333																																					p.L85L													.	PSME4-275	0			c.T255C						.						78	64	68					2																	54176408		692	1591	2283	SO:0001819	synonymous_variant	23198	exon2			CCCATAAAGTCGA	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.255T>C	2.37:g.54176408A>G		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_014614	0	0	0	0	0	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			.		0.333	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54176408	A	G	54176408	2	3	124	1	0	0	0	0	0	0	0	1	12738	1	1	3		3	PSME4	2	54176408	Silent	SNP	A	TCGA-GL-8500-01A-11D-2396-08		54176408	189022965	10	10776											
VPS24	51652	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	86790455	86790455	+	Frame_Shift_Del	DEL	T	T	-																															tgggcggcttctcctgggtcTttccaaacagccccatgacg																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:86790455delT	ENST00000263856.4	-	1	145	c.17delA	c.(16-18)aagfs	p.K6fs	CHMP3_ENST00000409727.1_Frame_Shift_Del_p.K6fs|CHMP3_ENST00000439940.2_Intron|AC015971.2_ENST00000439077.1_RNA|RNF103-CHMP3_ENST00000604011.1_Intron|AC015971.2_ENST00000597638.1_RNA|CHMP3_ENST00000409225.2_5'UTR	NM_001193517.1|NM_016079.3	NP_001180446.1|NP_057163.1	Q9Y3E7	CHMP3_HUMAN	charged multivesicular body protein 3	6	Intramolecular interaction with C- terminus.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)											CTCCTGGGTCTTTCCAAACAG	0.632																																					p.K6fs		.											.	.	0			c.17delA						.						120	123	122					2																	86790455		2203	4300	6503	SO:0001589	frameshift_variant	51652	exon1			.	AF219226	CCDS33236.1, CCDS42707.1, CCDS54375.1	2p11.2	2011-09-21	2011-09-21	2011-09-21	ENSG00000115561	ENSG00000115561		"Charged multivesicular body proteins"	29865	protein-coding gene	gene with protein product		610052	"vacuolar protein sorting 24 (yeast)", "vacuolar protein sorting 24 homolog (S. cerevisiae)"	VPS24		11549700, 12878588	Standard	NM_016079		Approved	NEDF, CGI-149		Q9Y3E7	OTTHUMG00000153189	ENST00000263856.4:c.17delA	2.37:g.86790455delT	ENSP00000263856:p.Lys6fs	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	219	93	NM_016079	0	0	0	0	0	A8K3W0|B4DG34|B8ZZM0|B8ZZX5|Q3ZTS9|Q53S71|Q53SU5|Q9NZ51	Frame_Shift_Del	DEL	ENST00000263856.4	37	CCDS33236.1																																																																																			.		0.632	CHMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330015.2	NM_016079		-	86790455	T	-	86790455	7	5	124	1	0	1	0	1	0	0	0	0	17228	1609	56	0	675	0	VPS24	2	86790455	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08	32614047	86790455	156408918	11	10777											
CHRNA1	1134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	175624262	175624262	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccacggtgacctccacgAcctggcggtggtcttccact	5	8	12	16	3	1	1	0	1	1	0	3	2	3	1	5	5	0	0	5	5	0	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:175624262A>T	ENST00000261007.5	-	2	209	c.143T>A	c.(142-144)gTc>gAc	p.V48D	CHRNA1_ENST00000409219.1_Missense_Mutation_p.V48D|CHRNA1_ENST00000348749.5_Missense_Mutation_p.V48D|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_Missense_Mutation_p.V48D|CHRNA1_ENST00000409323.1_Missense_Mutation_p.V48D	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	48					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GACCTCCACGACCTGGCGGTG	0.617																																					p.V48D		.											.	CHRNA1-518	0			c.T143A						.						132	130	130					2																	175624262		2203	4300	6503	SO:0001583	missense	1134	exon2			TCCACGACCTGGC	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1955	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 1 (muscle)"	100690	"cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.143T>A	2.37:g.175624262A>T	ENSP00000261007:p.Val48Asp	Somatic	288	1		WXS	Illumina HiSeq	Phase_I	277	92	NM_001039523	0	0	1	1	0	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	A	19.63	3.863276	0.71949	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19	5.91	-8.16	0.01061	Neurotransmitter-gated ion-channel ligand-binding (3);	0.620936	0.18070	N	0.152675	T	0.67021	0.2849	L	0.61036	1.89	0.09310	N	1	B;B;B	0.24043	0.06;0.074;0.096	B;B;B	0.28305	0.066;0.068;0.088	T	0.50717	-0.8795	10	0.22109	T	0.4	.	11.3745	0.49719	0.6712:0.0:0.2368:0.092	.	48;48;48	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	D	48	ENSP00000261008:V48D;ENSP00000261007:V48D;ENSP00000387026:V48D;ENSP00000386611:V48D;ENSP00000386684:V48D	ENSP00000261007:V48D	V	-	2	0	CHRNA1	175332508	0.000000	0.05858	0.000000	0.03702	0.860000	0.49131	0.097000	0.15168	-1.811000	0.01229	0.379000	0.24179	GTC	.		0.617	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			T	175624262	A	T	175624262	3	4	124	1	0	0	0	0	1	0	0	0	3387	275	10	5	1341	5	CHRNA1	2	175624262	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	88833807	175624262	67575111	12	10778											
SLC40A1	30061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190428363	190428363	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgacagagattatgggcAcagattcaggacttgtctcc	11	10	11	9	0	2	3	1	1	1	2	3	6	2	4	1	2	0	1	1	2	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:190428363A>T	ENST00000261024.2	-	7	1775	c.1349T>A	c.(1348-1350)gTg>gAg	p.V450E		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	450					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			GATTATGGGCACAGATTCAGG	0.368																																					p.V450E		.											.	SLC40A1-91	0			c.T1349A						.						78	80	80					2																	190428363		2203	4300	6503	SO:0001583	missense	30061	exon7			ATGGGCACAGATT	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.1349T>A	2.37:g.190428363A>T	ENSP00000261024:p.Val450Glu	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	95	40	NM_014585	0	0	44	82	38	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	37	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.195338	0.38806	.	.	ENSG00000138449	ENST00000261024	D	0.92397	-3.03	6.02	0.296	0.15757	Major facilitator superfamily domain, general substrate transporter (1);	0.667620	0.15785	N	0.244735	T	0.81245	0.4782	N	0.16368	0.405	0.22827	N	0.998683	B	0.02656	0.0	B	0.06405	0.002	T	0.61237	-0.7103	10	0.02654	T	1	-0.1187	12.0936	0.53742	0.5205:0.0:0.0:0.4795	.	450	Q9NP59	S40A1_HUMAN	E	450	ENSP00000261024:V450E	ENSP00000261024:V450E	V	-	2	0	SLC40A1	190136608	0.973000	0.33851	0.001000	0.08648	0.433000	0.31745	1.091000	0.30915	-0.201000	0.10284	0.528000	0.53228	GTG	.		0.368	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			T	190428363	A	T	190428363	3	4	124	1	0	0	0	0	1	0	0	0	14660	159	6	5	374	5	SLC40A1	2	190428363	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	14804101	190428363	52771010	13	10779											
HECW2	57520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197187250	197187250	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggactggaatggttagtttcCccagaaaacgcttgatgatg	11	11	12	7	1	0	3	0	2	0	1	1	5	1	5	2	3	1	3	2	3	4	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:197187250C>T	ENST00000260983.3	-	7	1018	c.836G>A	c.(835-837)gGg>gAg	p.G279E	HECW2_ENST00000409111.1_5'UTR	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	279	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GGTTAGTTTCCCCAGAAAACG	0.413																																					p.G279E		.											.	HECW2-668	0			c.G836A						.						123	126	125					2																	197187250		2203	4300	6503	SO:0001583	missense	57520	exon7			AGTTTCCCCAGAA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.836G>A	2.37:g.197187250C>T	ENSP00000260983:p.Gly279Glu	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	194	77	NM_020760	0	0	1	1	0	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280284	0.95489	.	.	ENSG00000138411	ENST00000260983	T	0.77489	-1.1	5.49	5.49	0.81192	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.221358	0.47093	D	0.000253	D	0.88496	0.6452	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88816	0.3295	10	0.87932	D	0	.	19.6359	0.95733	0.0:1.0:0.0:0.0	.	279	Q9P2P5	HECW2_HUMAN	E	279	ENSP00000260983:G279E	ENSP00000260983:G279E	G	-	2	0	HECW2	196895495	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.635000	0.83286	2.878000	0.98634	0.650000	0.86243	GGG	.		0.413	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197187250	C	T	197187250	3	4	124	1	0	0	0	0	1	0	0	0	7064	623	22	2	3974	2	HECW2	2	197187250	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	6758887	197187250	46012123	14	10780											
ABCB6	10058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220075814	220075814	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactccaatgtgagaccggAgagaggcctgggtcacctag	11	6	13	11	1	1	2	1	1	0	2	2	5	2	3	4	3	1	0	4	3	3	1	rs387906909		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:220075814A>G	ENST00000265316.3	-	15	2301	c.1985T>C	c.(1984-1986)cTc>cCc	p.L662P	ABCB6_ENST00000439002.2_Missense_Mutation_p.L616P	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	662	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTGAGACCGGAGAGAGGCCTG	0.582																																					p.L662P		.											.	ABCB6-153	0			c.T1985C						.						108	106	106					2																	220075814		2203	4300	6503	SO:0001583	missense	10058	exon15			GACCGGAGAGAGG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1985T>C	2.37:g.220075814A>G	ENSP00000265316:p.Leu662Pro	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	142	55	NM_005689	0	0	34	55	21	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	37	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.065625|4.065625	0.76187|0.76187	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750	D;D|.	0.92299|.	-3.01;-3.01|.	4.7|4.7	4.7|4.7	0.59300|0.59300	ATPase, AAA+ type, core (1);ABC transporter-like (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79885|0.79885	0.4523|0.4523	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.994;0.996|.	D|D	0.83833|0.83833	0.0253|0.0253	10|5	0.87932|.	D|.	0|.	-18.3339|-18.3339	14.286|14.286	0.66247|0.66247	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	616;662|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	P|P	662;616|510	ENSP00000265316:L662P;ENSP00000394333:L616P|.	ENSP00000265316:L662P|.	L|S	-|-	2|1	0|0	ABCB6|ABCB6	219784058|219784058	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.828000|0.828000	0.46876|0.46876	8.912000|8.912000	0.92726|0.92726	2.084000|2.084000	0.62774|0.62774	0.528000|0.528000	0.53228|0.53228	CTC|TCC	.		0.582	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		G	220075814	A	G	220075814	3	3	124	1	0	0	0	0	1	0	0	0	45	304	11	3	563	3	ABCB6	2	220075814	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	22888564	220075814	23123559	15	10781											
SEC13	6396	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	10342967	10342967	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgctcgttctgctggcccTctgtcactgatgctgatacg	5	13	10	13	2	3	2	1	2	2	0	4	2	3	2	1	1	4	4	1	1	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:10342967T>C	ENST00000350697.3	-	9	1072	c.947A>G	c.(946-948)gAg>gGg	p.E316G	SEC13_ENST00000397109.3_Missense_Mutation_p.E302G|SEC13_ENST00000337354.4_Missense_Mutation_p.E319G|SEC13_ENST00000383801.2_Missense_Mutation_p.E362G|SEC13_ENST00000492602.1_Intron|SEC13_ENST00000397117.1_Intron	NM_183352.1	NP_899195.1	P55735	SEC13_HUMAN	SEC13 homolog (S. cerevisiae)	316					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17						CTGCTGGCCCTCTGTCACTGA	0.612																																					p.E316G		.											.	SEC13-91	0			c.A947G						.						120	96	104					3																	10342967		2203	4300	6503	SO:0001583	missense	6396	exon9			TGGCCCTCTGTCA		CCDS2599.1, CCDS46751.1, CCDS63540.1	3p25-p24	2013-01-10	2006-11-07	2006-11-07	ENSG00000157020	ENSG00000157020		"WD repeat domain containing"	10697	protein-coding gene	gene with protein product		600152	"SEC13 (S. cerevisiae)-like 1", "SEC13-like 1 (S. cerevisiae)"	D3S1231E, SEC13L1		7987303	Standard	NM_183352		Approved	SEC13R, npp-20	uc003bvn.3	P55735	OTTHUMG00000128671	ENST00000350697.3:c.947A>G	3.37:g.10342967T>C	ENSP00000312122:p.Glu316Gly	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	98	40	NM_183352	0	0	110	193	83	A8MV37|B4DXJ1|Q5BJF0|Q9BRM6|Q9BUG7	Missense_Mutation	SNP	ENST00000350697.3	37	CCDS2599.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444051	0.63067	.	.	ENSG00000157020	ENST00000397109;ENST00000337354;ENST00000350697;ENST00000383801	T;T;T;T	0.69806	0.84;-0.3;-0.43;-0.37	5.23	5.23	0.72850	.	0.288120	0.41001	D	0.000976	T	0.53706	0.1813	L	0.36672	1.1	0.54753	D	0.999984	P;B	0.34522	0.455;0.0	B;B	0.30105	0.111;0.0	T	0.53229	-0.8468	10	0.27785	T	0.31	.	13.0995	0.59212	0.0:0.0:0.0:1.0	.	362;316	B4DXJ1;P55735	.;SEC13_HUMAN	G	302;319;316;362	ENSP00000380298:E302G;ENSP00000336566:E319G;ENSP00000312122:E316G;ENSP00000373312:E362G	ENSP00000336566:E319G	E	-	2	0	SEC13	10317967	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.914000	0.87478	1.971000	0.57363	0.533000	0.62120	GAG	.		0.612	SEC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250563.3			C	10342967	T	C	10342967	3	2	124	1	0	0	0	0	1	0	0	0	14012	1551	54	3	25	3	SEC13	3	10342967	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08		10342967	187679463	16	10782											
MLH1	4292	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	37042512	37042512	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtcctttgaggatttaGccagtatttctacctatggc	8	15	9	9	0	1	1	0	1	1	0	2	2	2	2	3	2	3	2	3	2	4	7	rs63750133		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:37042512G>A	ENST00000231790.2	+	3	490	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	MLH1_ENST00000435176.1_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000492474.1_3'UTR|MLH1_ENST00000455445.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	92					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)			NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TGAGGATTTAGCCAGTATTTC	0.348		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.A92T		.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	.	MLH1-2559	0			c.G274A						.						152	151	152					3																	37042512		2203	4300	6503	SO:0001583	missense	4292	exon3	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	GATTTAGCCAGTA	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.274G>A	3.37:g.37042512G>A	ENSP00000231790:p.Ala92Thr	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	82	41	NM_000249	0	0	3	11	8	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195561	0.38806	.	.	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937	D	0.94537	-3.45	5.91	4.11	0.48088	DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.269957	0.37669	N	0.001984	D	0.84683	0.5526	N	0.04018	-0.295	0.80722	D	1	B;B	0.16166	0.016;0.009	B;B	0.25405	0.06;0.038	T	0.75434	-0.3319	10	0.20046	T	0.44	-6.4566	8.0469	0.30555	0.0732:0.0:0.6432:0.2836	.	92;92	Q53GX1;P40692	.;MLH1_HUMAN	T	92;58;58	ENSP00000231790:A92T	ENSP00000231790:A92T	A	+	1	0	MLH1	37017516	1.000000	0.71417	0.962000	0.40283	0.992000	0.81027	1.745000	0.38278	0.829000	0.34733	-0.169000	0.13324	GCC	.		0.348	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		A	37042512	G	A	37042512	3	1	124	1	0	0	0	0	1	0	0	0	9642	971	34	2	284	2	MLH1	3	37042512	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	26699545	37042512	160979918	17	10783											
XYLB	9942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38404484	38404484	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ggcttcgacttctctcaagtCctagccttgtccggggcggg	4	11	13	13	3	2	0	1	0	1	0	6	1	4	0	3	4	1	1	3	4	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:38404484C>G	ENST00000207870.3	+	4	357	c.267C>G	c.(265-267)gtC>gtG	p.V89V	XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	89					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TCTCTCAAGTCCTAGCCTTGT	0.532																																					p.V89V		.											.	XYLB-91	0			c.C267G						.						108	108	108					3																	38404484		2203	4300	6503	SO:0001819	synonymous_variant	9942	exon4			TCAAGTCCTAGCC	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.267C>G	3.37:g.38404484C>G		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	109	48	NM_005108	0	0	0	0	0	B2RAW4|B4DDT2|B9EH64	Silent	SNP	ENST00000207870.3	37	CCDS2678.1																																																																																			.		0.532	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		G	38404484	C	G	38404484	2	3	124	1	0	0	0	0	0	0	0	1	17495	842	30	4		4	XYLB	3	38404484	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	1361972	38404484	159617946	18	10784											
SLC38A3	10991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	50257565	50257565	+	RNA	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcttgagcttcatcatcAttgactgggcctcagggacc	8	11	11	11	0	4	3	4	3	0	0	4	4	4	4	2	2	2	2	2	2	0	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:50257565A>G	ENST00000420502.1	+	0	1624									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		CTTCATCATCATTGACTGGGC	0.557																																					p.I491V		.											.	SLC38A3-67	0			c.A1471G						.						93	88	89					3																	50257565		2026	4180	6206			10991	exon16			ATCATCATTGACT	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		3.37:g.50257565A>G		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	13	10	NM_006841	0	0	0	0	0		Missense_Mutation	SNP	ENST00000420502.1	37																																																																																				.		0.557	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		G	50257565	A	G	50257565	1	3	124	0	1	0	0	0	0	0	0	0	14637	217	8	3		3	SLC38A3	3	50257565	RNA	SNP	A	TCGA-GL-8500-01A-11D-2396-08	11853081	50257565	147764865	19	10785											
ABHD10	55347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	111700691	111700691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaccttccaaacctggcttAtaagaagctaaaaggcaaaa	18	7	7	9	0	0	2	0	0	0	2	1	2	1	2	3	2	2	3	3	2	8	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:111700691A>G	ENST00000273359.3	+	2	230	c.203A>G	c.(202-204)tAt>tGt	p.Y68C	ABHD10_ENST00000494817.1_Missense_Mutation_p.Y68C|ABHD10_ENST00000534857.1_Intron	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	68					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						AACCTGGCTTATAAGAAGCTA	0.378																																					p.Y68C		.											.	ABHD10-90	0			c.A203G						.						126	123	124					3																	111700691		2203	4300	6503	SO:0001583	missense	55347	exon2			TGGCTTATAAGAA	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.203A>G	3.37:g.111700691A>G	ENSP00000273359:p.Tyr68Cys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	140	62	NM_001272069	0	0	25	59	34	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	37	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190688	0.78789	.	.	ENSG00000144827	ENST00000273359;ENST00000494817	T	0.48836	0.8	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.69115	0.3075	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.72962	-0.4132	10	0.62326	D	0.03	-30.1278	14.7236	0.69326	1.0:0.0:0.0:0.0	.	68	Q9NUJ1	ABHDA_HUMAN	C	68	ENSP00000273359:Y68C	ENSP00000273359:Y68C	Y	+	2	0	ABHD10	113183381	1.000000	0.71417	0.953000	0.39169	0.988000	0.76386	8.935000	0.92923	2.117000	0.64856	0.459000	0.35465	TAT	.		0.378	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394		G	111700691	A	G	111700691	3	3	124	1	0	0	0	0	1	0	0	0	74	449	16	3	209	3	ABHD10	3	111700691	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	61443126	111700691	86321739	20	10786											
EEFSEC	60678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	127981023	127981023	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaagccggggggaccagagGcccccgaaactgaagctcca	11	2	13	15	2	0	2	0	1	0	1	1	4	1	3	6	4	3	1	6	4	3	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:127981023G>C	ENST00000254730.6	+	3	631	c.577G>C	c.(577-579)Gcc>Ccc	p.A193P	EEFSEC_ENST00000483457.1_Missense_Mutation_p.A193P	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	193	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						GGGACCAGAGGCCCCCGAAAC	0.562																																					p.A193P		.											.	EEFSEC-91	0			c.G577C						.						90	104	100					3																	127981023		2203	4300	6503	SO:0001583	missense	60678	exon3			CCAGAGGCCCCCG		CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"elongation factor for selenoprotein translation"	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.577G>C	3.37:g.127981023G>C	ENSP00000254730:p.Ala193Pro	Somatic	203	2		WXS	Illumina HiSeq	Phase_I	172	75	NM_021937	0	0	9	17	8	Q96HZ6	Missense_Mutation	SNP	ENST00000254730.6	37	CCDS33849.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764626	0.69878	.	.	ENSG00000132394	ENST00000254730;ENST00000483457	T;T	0.56941	0.82;0.43	5.45	5.45	0.79879	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.67439	0.2893	L	0.52905	1.665	0.58432	D	0.999998	D;D	0.71674	0.998;0.997	D;D	0.71184	0.972;0.939	T	0.63134	-0.6705	10	0.31617	T	0.26	2.1892	17.4767	0.87661	0.0:0.0:1.0:0.0	.	193;193	C9J8T0;P57772	.;SELB_HUMAN	P	193	ENSP00000254730:A193P;ENSP00000417660:A193P	ENSP00000254730:A193P	A	+	1	0	EEFSEC	129463713	1.000000	0.71417	1.000000	0.80357	0.124000	0.20399	9.064000	0.93933	2.546000	0.85860	0.650000	0.86243	GCC	.		0.562	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937		C	127981023	G	C	127981023	3	2	124	1	0	0	0	0	1	0	0	0	4942	1203	42	4	587	4	EEFSEC	3	127981023	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	16280332	127981023	70041407	21	10787											
ZMAT3	64393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	178785387	178785387	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccctcccttcgataactCttcttcccctgcaagaggca	7	11	5	18	1	2	1	0	0	2	1	6	2	5	1	5	1	2	2	5	1	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:178785387C>A	ENST00000311417.2	-	2	895	c.154G>T	c.(154-156)Gag>Tag	p.E52*	ZMAT3_ENST00000432729.1_Nonsense_Mutation_p.E52*	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3											breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			TTCGATAACTCTTCTTCCCCT	0.552																																					p.E52X		.											.	ZMAT3-228	0			c.G154T						.						123	116	119					3																	178785387		2203	4300	6503	SO:0001587	stop_gained	64393	exon2			ATAACTCTTCTTC	AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.154G>T	3.37:g.178785387C>A	ENSP00000311221:p.Glu52*	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	123	45	NM_022470	0	0	5	8	3		Nonsense_Mutation	SNP	ENST00000311417.2	37	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	C	44	11.170319	0.99525	.	.	ENSG00000172667	ENST00000311417;ENST00000432729;ENST00000414084	.	.	.	5.86	5.86	0.93980	.	0.278038	0.40554	N	0.001064	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-15.196	20.1931	0.98233	0.0:1.0:0.0:0.0	.	.	.	.	X	52	.	ENSP00000311221:E52X	E	-	1	0	ZMAT3	180268081	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	5.278000	0.65592	2.771000	0.95319	0.563000	0.77884	GAG	.		0.552	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240		A	178785387	C	A	178785387	4	1	124	1	0	0	0	0	0	1	0	0	17725	922	32	4	735	4	ZMAT3	3	178785387	Nonsense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	50804364	178785387	19237043	22	10788											
PDS5A	23244	ucsc.edu	37	chr4	39911931	39911931	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaatttcacactttctaaTctcacaggaacatgaatatc	15	12	4	10	0	3	1	2	1	2	0	5	2	3	2	0	1	1	1	0	1	5	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr4:39911931T>G	ENST00000303538.8	-	10	1559	c.1020A>C	c.(1018-1020)agA>agC	p.R340S	PDS5A_ENST00000503396.1_Missense_Mutation_p.R340S	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						CACTTTCTAATCTCACAGGAA	0.323																																					p.R340S													.	.	0			c.A1020C						.						70	65	67					4																	39911931		1839	4102	5941	SO:0001583	missense	23244	exon10			TTCTAATCTCACA	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1020A>C	4.37:g.39911931T>G	ENSP00000303427:p.Arg340Ser	Somatic	14	0		WXS	Illumina HiSeq		7	1	NM_001100399	0	0	17	28	11		Missense_Mutation	SNP	ENST00000303538.8	37	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860782	0.71834	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.72394	-0.65;-0.64	5.06	1.03	0.20045	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80059	0.4554	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.999	T	0.76561	-0.2914	9	.	.	.	-15.7137	5.7433	0.18106	0.0:0.1556:0.1419:0.7025	.	340;340	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	S	340	ENSP00000303427:R340S;ENSP00000426749:R340S	.	R	-	3	2	PDS5A	39588326	0.996000	0.38824	1.000000	0.80357	0.952000	0.60782	0.297000	0.19101	0.366000	0.24427	-0.263000	0.10527	AGA	.		0.323	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		G	39911931	T	G	39911931	3	3	124	1	0	0	0	0	1	0	0	0	11717	1432	50	5	3122	5	PDS5A	4	39911931	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08		39911931	151242345	23	10789											
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	123229112	123229112	+	Frame_Shift_Del	DEL	T	T	-																															aattatcaaaagctgtgctgTtttggctgaattataaggcc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr4:123229112delT	ENST00000264501.4	+	58	10223	c.9850delT	c.(9850-9852)tttfs	p.F3284fs	KIAA1109_ENST00000455637.1_Frame_Shift_Del_p.F3284fs|KIAA1109_ENST00000388738.3_Frame_Shift_Del_p.F3284fs			Q2LD37	K1109_HUMAN	KIAA1109	3284					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGCTGTGCTGTTTTGGCTGAA	0.343																																					p.F3284fs		.											.	KIAA1109-80	0			c.9850delT						.						132	129	130					4																	123229112		1827	4092	5919	SO:0001589	frameshift_variant	84162	exon56			.	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9850delT	4.37:g.123229112delT	ENSP00000264501:p.Phe3284fs	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	171	65	NM_015312	0	0	0	0	0	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Frame_Shift_Del	DEL	ENST00000264501.4	37	CCDS43267.1																																																																																			.		0.343	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		-	123229112	T	-	123229112	7	5	124	1	0	1	0	1	0	0	0	0	8229	1725	60	0	10072	0	KIAA1109	4	123229112	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08	83317181	123229112	67925164	24	10790											
SPOCK3	50859	hgsc.bcm.edu;bcgsc.ca	37	chr4	167713322	167713322	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaaatttagaaatcttactGcttctctcaggcctcagcaa	12	13	5	11	0	5	1	3	0	2	1	6	1	5	1	1	1	3	2	1	1	5	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr4:167713322G>T	ENST00000357154.3	-	8	854	c.717C>A	c.(715-717)agC>agA	p.S239R	SPOCK3_ENST00000511531.1_Splice_Site_p.S239R|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000512681.1_Splice_Site_p.S141R|SPOCK3_ENST00000541637.1_Splice_Site_p.S141R|SPOCK3_ENST00000511269.1_Splice_Site_p.S236R|SPOCK3_ENST00000502330.1_Splice_Site_p.S239R|SPOCK3_ENST00000541354.1_Splice_Site_p.S119R|SPOCK3_ENST00000512648.1_Splice_Site_p.S236R|SPOCK3_ENST00000421836.2_Splice_Site_p.S188R|SPOCK3_ENST00000535728.1_Intron|SPOCK3_ENST00000506886.1_Splice_Site_p.S239R|SPOCK3_ENST00000510741.1_Intron|SPOCK3_ENST00000504953.1_Splice_Site_p.S236R|SPOCK3_ENST00000534949.1_Splice_Site_p.S143R|SPOCK3_ENST00000357545.4_Splice_Site_p.S236R	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	239					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		AAATCTTACTGCTTCTCTCAG	0.373																																					p.S239R		.											.	SPOCK3-136	0			c.C717A						.						101	84	90					4																	167713322		2203	4300	6503	SO:0001630	splice_region_variant	50859	exon8			CTTACTGCTTCTC	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.718+1C>A	4.37:g.167713322G>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	60	4	NM_016950	0	0	0	0	0	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	37	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504073	0.44558	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000421836;ENST00000541637;ENST00000534949;ENST00000512648;ENST00000510403	T;T;T;T;T;T;T;T;T;T;T;T;T;D	0.87412	1.48;1.49;1.49;1.48;1.48;1.48;1.4;0.92;1.49;1.29;0.92;1.18;2.2;-2.25	5.33	4.47	0.54385	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.410761	0.26800	N	0.022422	D	0.89350	0.6690	L	0.59436	1.845	0.37036	D	0.896894	D;D;D;D;D;D;D	0.64830	0.959;0.967;0.958;0.994;0.967;0.98;0.984	P;P;P;D;P;P;P	0.63192	0.629;0.664;0.821;0.912;0.587;0.711;0.81	D	0.87800	0.2624	10	0.27082	T	0.32	-13.9637	9.7077	0.40225	0.2078:0.0:0.7921:0.0	.	141;143;188;248;239;236;239	B4DGK5;F5H099;B4DHB4;B4DFW5;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;TICN3_HUMAN	R	239;236;236;239;239;239;119;141;236;188;141;143;236;118	ENSP00000349677:S239R;ENSP00000350153:S236R;ENSP00000425570:S236R;ENSP00000420920:S239R;ENSP00000423421:S239R;ENSP00000423606:S239R;ENSP00000444789:S119R;ENSP00000426318:S141R;ENSP00000425502:S236R;ENSP00000411344:S188R;ENSP00000445430:S141R;ENSP00000438142:S143R;ENSP00000426177:S236R;ENSP00000423176:S118R	ENSP00000349677:S239R	S	-	3	2	SPOCK3	167949897	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	2.196000	0.42686	2.650000	0.89964	0.563000	0.77884	AGC	.		0.373	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		Missense_Mutation	T	167713322	G	T	167713322	5	4	124	1	0	0	0	0	0	0	1	0	15113	1333	46	4	613	4	SPOCK3	4	167713322	Splice_Site	SNP	G	TCGA-GL-8500-01A-11D-2396-08	44484210	167713322	23440954	25	10791											
CLPTM1L	81037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1324927	1324927	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagattcgctgtaagtgccaAactgttgtgaaattcaacac	13	11	8	9	1	1	2	1	1	0	1	2	2	1	2	1	0	3	3	1	0	4	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:1324927A>T	ENST00000320895.5	-	11	1405	c.1148T>A	c.(1147-1149)tTt>tAt	p.F383Y	CLPTM1L_ENST00000507807.1_Splice_Site_p.F214Y|CLPTM1L_ENST00000506641.1_5'UTR|CLPTM1L_ENST00000320927.6_Splice_Site_p.F347Y	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	383					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)		GTAAGTGCCAAACTGTTGTGA	0.488																																					p.F383Y		.											.	CLPTM1L-153	0			c.T1148A						.						241	182	202					5																	1324927		2203	4300	6503	SO:0001630	splice_region_variant	81037	exon11			GTGCCAAACTGTT	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.1147-1T>A	5.37:g.1324927A>T		Somatic	100	1		WXS	Illumina HiSeq	Phase_I	94	43	NM_030782	0	0	1	1	0	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	37	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	A	8.846	0.943427	0.18281	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.50277	0.75;0.83;0.81	5.15	3.94	0.45596	.	0.280237	0.41097	D	0.000945	T	0.49983	0.1589	M	0.74389	2.26	0.53005	D	0.999963	B;B	0.23990	0.095;0.06	B;B	0.33568	0.166;0.032	T	0.42085	-0.9472	10	0.26408	T	0.33	-15.2716	11.2025	0.48749	0.8456:0.1544:0.0:0.0	.	383;214	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	Y	383;214;347	ENSP00000313854:F383Y;ENSP00000423321:F214Y;ENSP00000315196:F347Y	ENSP00000313854:F383Y	F	-	2	0	CLPTM1L	1377927	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	5.991000	0.70602	0.856000	0.35383	0.459000	0.35465	TTT	.		0.488	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782	Missense_Mutation	T	1324927	A	T	1324927	5	4	124	1	0	0	0	0	0	0	1	0	3561	28	1	5	496	5	CLPTM1L	5	1324927	Splice_Site	SNP	A	TCGA-GL-8500-01A-11D-2396-08		1324927	179590333	26	10792											
ITGA2	3673	hgsc.bcm.edu	37	chr5	52368456	52368456	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcgtagattcctttccacaAagactgtggtgaggacggac	10	11	11	9	2	0	3	0	1	0	2	3	5	2	5	2	3	0	1	2	3	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:52368456A>C	ENST00000296585.5	+	19	2503	c.2360A>C	c.(2359-2361)aAa>aCa	p.K787T		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	787					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				CCTTTCCACAAAGACTGTGGT	0.343																																					p.K787T		.											.	ITGA2-226	0			c.A2360C						.						82	73	76					5																	52368456		2202	4300	6502	SO:0001583	missense	3673	exon19			TCCACAAAGACTG		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"CD molecules", "Integrins"	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2360A>C	5.37:g.52368456A>C	ENSP00000296585:p.Lys787Thr	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_002203	0	0	0	0	0	Q14595	Missense_Mutation	SNP	ENST00000296585.5	37	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.696313	0.48202	.	.	ENSG00000164171	ENST00000296585	T	0.54675	0.56	5.66	4.5	0.54988	Integrin alpha-2 (1);	0.048740	0.85682	D	0.000000	T	0.57140	0.2033	M	0.69358	2.11	0.54753	D	0.999985	B;P	0.36354	0.314;0.549	B;B	0.43360	0.417;0.364	T	0.58487	-0.7628	10	0.56958	D	0.05	.	11.5138	0.50509	0.93:0.0:0.07:0.0	.	787;787	E7ESP4;P17301	.;ITA2_HUMAN	T	787	ENSP00000296585:K787T	ENSP00000296585:K787T	K	+	2	0	ITGA2	52404213	1.000000	0.71417	0.928000	0.36995	0.683000	0.39861	8.098000	0.89540	0.979000	0.38497	0.460000	0.39030	AAA	.		0.343	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		C	52368456	A	C	52368456	3	2	124	1	0	0	0	0	1	0	0	0	7896	14	1	5	2434	5	ITGA2	5	52368456	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	51043529	52368456	128546804	27	10793											
MOCS2	4338	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	52397195	52397196	+	Frame_Shift_Ins	INS	-	-	T																															aaggaaatcatacccaagtcINStatggaacactgctatgtgt																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:52397195_52397196insT	ENST00000396954.3	-	5	1047_1048	c.370_371insA	c.(370-372)agafs	p.R124fs	MOCS2_ENST00000510818.2_3'UTR|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000361377.4_Intron|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000582677.1_Intron|MOCS2_ENST00000527216.1_3'UTR	NM_004531.3	NP_004522.1			molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				ATACCCAAGTCTATGGAACACT	0.342																																					p.R124fs		.											.	MOCS2-90	0			c.371_372insA						.																																			SO:0001589	frameshift_variant	4338	exon5			.	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000396954.3:c.371dupA	5.37:g.52397196_52397196dupT	ENSP00000380157:p.Arg124fs	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	175	83	NM_004531	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000396954.3	37	CCDS3958.1																																																																																			.		0.342	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418		T	52397196	-	T	52397195	7	5	124	1	0	1	1	0	0	0	0	0	9716	913	32	0	207	0	MOCS2	5	52397195	Frame_Shift_Ins	INS	-	TCGA-GL-8500-01A-11D-2396-08	28739	52397195	128518065	28	10794											
MAST4	375449	hgsc.bcm.edu	37	chr5	66440576	66440576	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacaaaaccaaaagcaccaCcttgccatccacagaaacac	18	3	5	15	0	0	1	0	0	0	1	1	2	1	2	5	1	4	1	5	1	5	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:66440576C>G	ENST00000403625.2	+	22	3105	c.2810C>G	c.(2809-2811)aCc>aGc	p.T937S	MAST4_ENST00000403666.1_Missense_Mutation_p.T748S|MAST4_ENST00000405643.1_Missense_Mutation_p.T758S|MAST4_ENST00000261569.7_Missense_Mutation_p.T743S|MAST4_ENST00000404260.3_Missense_Mutation_p.T940S	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	940						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AAAAGCACCACCTTGCCATCC	0.408																																					p.T937S		.											.	MAST4-647	0			c.C2810G						.						65	70	69					5																	66440576		1870	4117	5987	SO:0001583	missense	375449	exon22			GCACCACCTTGCC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.2810C>G	5.37:g.66440576C>G	ENSP00000385727:p.Thr937Ser	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001164664	0	0	2	2	0	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.57|11.57	1.677412|1.677412	0.29783|0.29783	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	.|T;T;T;T;T	.|0.64803	.|-0.09;-0.09;-0.12;-0.11;-0.09	5.69|5.69	4.82|4.82	0.62117|0.62117	.|.	.|0.745634	.|0.13293	.|N	.|0.398827	T|T	0.39733|0.39733	0.1089|0.1089	N|N	0.12569|0.12569	0.235|0.235	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.18310	.|0.027;0.004;0.006;0.007	.|B;B;B;B	.|0.16289	.|0.011;0.007;0.015;0.007	T|T	0.18147|0.18147	-1.0346|-1.0346	5|10	.|0.07175	.|T	.|0.84	-0.0745|-0.0745	10.3504|10.3504	0.43931|0.43931	0.0:0.7952:0.1342:0.0706|0.0:0.7952:0.1342:0.0706	.|.	.|758;940;743;748	.|E7EWQ5;O15021;O15021-2;O15021-3	.|.;MAST4_HUMAN;.;.	Q|S	60|940;937;748;758;758;743;743	.|ENSP00000385048:T940S;ENSP00000385727:T937S;ENSP00000384313:T748S;ENSP00000384099:T758S;ENSP00000261569:T743S	.|ENSP00000261569:T743S	H|T	+|+	3|2	2|0	MAST4|MAST4	66476332|66476332	0.016000|0.016000	0.18221|0.18221	0.082000|0.082000	0.20525|0.20525	0.950000|0.950000	0.60333|0.60333	2.374000|2.374000	0.44274|0.44274	1.422000|1.422000	0.47177|0.47177	0.591000|0.591000	0.81541|0.81541	CAC|ACC	.		0.408	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			G	66440576	C	G	66440576	3	3	124	1	0	0	0	0	1	0	0	0	9352	507	18	4	3026	4	MAST4	5	66440576	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	14043381	66440576	114474684	29	10795											
RGNEF	64283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	73205322	73205322	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtctctcggccactctaTcctccgaggcggccccttgc	3	10	9	19	3	2	0	0	0	2	0	6	1	4	0	6	3	1	0	6	3	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:73205322T>A	ENST00000426542.2	+	33	4267	c.4247T>A	c.(4246-4248)aTc>aAc	p.I1416N	ARHGEF28_ENST00000296794.6_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.I1103N|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.I1372N|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.I336N			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1416					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GGCCACTCTATCCTCCGAGGC	0.622																																					p.I1416N		.											.	.	0			c.T4247A						.						21	25	24					5																	73205322		2019	4181	6200	SO:0001583	missense	64283	exon34			ACTCTATCCTCCG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.4247T>A	5.37:g.73205322T>A	ENSP00000412175:p.Ile1416Asn	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	20	10	NM_001080479	0	0	17	35	18	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.374983	0.00207	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91	0.55	0.55	0.17219	.	.	.	.	.	T	0.11324	0.0276	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.23990	0.002;0.023;0.04;0.004;0.095	B;B;B;B;B	0.23018	0.0;0.014;0.021;0.006;0.043	T	0.32481	-0.9905	8	0.27082	T	0.32	.	.	.	.	.	1103;1416;1416;336;1416	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	N	1416;1416;1416;1372;1416;1416;1103;336	ENSP00000296794:I1416N;ENSP00000441913:I1416N;ENSP00000441436:I1416N;ENSP00000287898:I1372N;ENSP00000411459:I1416N;ENSP00000412175:I1416N;ENSP00000296799:I1103N;ENSP00000421081:I336N	ENSP00000287898:I1372N	I	+	2	0	RP11-428C6.1	73241078	0.000000	0.05858	0.009000	0.14445	0.029000	0.11900	0.015000	0.13355	0.464000	0.27142	0.454000	0.30748	ATC	.		0.622	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73205322	T	A	73205322	3	1	124	1	0	0	0	0	1	0	0	0	13315	1435	50	5	4377	5	RGNEF	5	73205322	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	6764746	73205322	107709938	30	10796											
SEMA6A	57556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	115822558	115822558	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgagagtctccaggaactgaGcagttcaagcgcgccttcag	10	8	12	11	2	3	2	2	2	1	1	4	4	3	3	2	1	3	2	2	1	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:115822558G>A	ENST00000343348.6	-	10	1636	c.849C>T	c.(847-849)tgC>tgT	p.C283C	SEMA6A_ENST00000257414.8_Silent_p.C283C|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000510263.1_Silent_p.C283C|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000503962.1_5'Flank	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	283	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CAGGAACTGAGCAGTTCAAGC	0.463																																					p.C283C		.											.	SEMA6A-92	0			c.C849T						.						110	110	110					5																	115822558		2009	4214	6223	SO:0001819	synonymous_variant	57556	exon10			AACTGAGCAGTTC	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"Semaphorins"	10738	protein-coding gene	gene with protein product	"sema VIa"	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.849C>T	5.37:g.115822558G>A		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	137	59	NM_020796	0	0	3	7	4	Q9P2H9	Silent	SNP	ENST00000343348.6	37	CCDS47256.1																																																																																			.		0.463	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		A	115822558	G	A	115822558	2	1	124	1	0	0	0	0	0	0	0	1	14071	963	34	2		2	SEMA6A	5	115822558	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	42617236	115822558	65092702	31	10797											
LOC153328	153328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	135178132	135178132	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgtcatcgttggccaccCtctggacacagtcaaggtac	9	9	10	13	1	3	0	2	0	1	0	4	1	3	1	2	3	1	2	2	3	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:135178132C>A	ENST00000420621.1	+	2	246	c.74C>A	c.(73-75)cCt>cAt	p.P25H	SLC25A48_ENST00000274513.5_Missense_Mutation_p.P25H|SLC25A48_ENST00000425402.1_Missense_Mutation_p.P25H|SLC25A48_ENST00000433282.2_5'UTR|SLC25A48_ENST00000412661.2_Missense_Mutation_p.P25H			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	25					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						GTTGGCCACCCTCTGGACACA	0.507																																					p.P25H		.											.	SLC25A48-91	0			c.C74A						.						141	154	150					5																	135178132		2131	4257	6388	SO:0001583	missense	153328	exon2			GCCACCCTCTGGA		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"Solute carriers"	30451	protein-coding gene	gene with protein product	"HCC-down-regulated mitochondrial carrier protein"					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.74C>A	5.37:g.135178132C>A	ENSP00000407973:p.Pro25His	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	204	69	NM_145282	0	0	0	0	0	Q8TAV9	Missense_Mutation	SNP	ENST00000420621.1	37		.	.	.	.	.	.	.	.	.	.	C	18.21	3.574438	0.65878	.	.	ENSG00000145832	ENST00000425402;ENST00000274513;ENST00000420621;ENST00000412661	D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	H	0.98918	4.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98808	1.0742	10	0.87932	D	0	-31.2085	14.3274	0.66530	0.0:1.0:0.0:0.0	.	25;25	Q6ZT89-3;Q6ZT89-2	.;.	H	25	ENSP00000408750:P25H;ENSP00000274513:P25H;ENSP00000407973:P25H;ENSP00000413049:P25H	ENSP00000274513:P25H	P	+	2	0	SLC25A48	135206031	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.217000	0.58547	2.480000	0.83734	0.563000	0.77884	CCT	.		0.507	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282		A	135178132	C	A	135178132	3	1	124	1	0	0	0	0	1	0	0	0	8894	681	24	4	80	4	LOC153328	5	135178132	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	19355574	135178132	45737128	32	10798											
HSPA9	3313	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	137904733	137904733	+	Frame_Shift_Del	DEL	T	T	-																															ggacaattttaaagggaacaTttttactgtaagacacaaaa																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:137904733delT	ENST00000297185.3	-	5	541	c.416delA	c.(415-417)aatfs	p.N139fs	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	139					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAAGGGAACATTTTTACTGTA	0.403																																					p.N139fs		.											.	HSPA9-226	0			c.416delA						.						61	61	61					5																	137904733		2203	4300	6503	SO:0001589	frameshift_variant	3313	exon5			.	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.416delA	5.37:g.137904733delT	ENSP00000297185:p.Asn139fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	103	40	NM_004134	0	0	0	0	0	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Frame_Shift_Del	DEL	ENST00000297185.3	37	CCDS4208.1																																																																																			.		0.403	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		-	137904733	T	-	137904733	7	5	124	1	0	1	0	1	0	0	0	0	7438	1493	52	0	1675	0	HSPA9	5	137904733	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08	2726601	137904733	43010527	33	10799											
RANBP17	64901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	170323085	170323085	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acactgcataataggagtaaTaatcctttctgaattgactc	14	13	6	8	0	1	2	0	2	1	0	3	3	2	3	1	1	1	2	1	1	5	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:170323085T>A	ENST00000523189.1	+	5	619	c.455T>A	c.(454-456)aTa>aAa	p.I152K		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	152					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ATAGGAGTAATAATCCTTTCT	0.388			T	TRD@	ALL																																p.I152K		.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17-524	0			c.T455A						.						116	109	111					5																	170323085		2203	4300	6503	SO:0001583	missense	64901	exon5			GAGTAATAATCCT	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.455T>A	5.37:g.170323085T>A	ENSP00000427975:p.Ile152Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	106	43	NM_022897	0	0	2	2	0	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	.	4.832	0.154664	0.09236	.	.	ENSG00000204764	ENST00000523189	T	0.65916	-0.18	5.14	5.14	0.70334	Armadillo-type fold (1);	0.271232	0.32343	N	0.006225	T	0.29620	0.0739	N	0.02181	-0.65	0.49213	D	0.999766	B;B	0.19583	0.004;0.037	B;B	0.13407	0.007;0.009	T	0.35201	-0.9798	10	0.02654	T	1	-4.1259	11.0057	0.47633	0.0:0.0:0.156:0.844	.	152;202	Q9H2T7;B4DQG2	RBP17_HUMAN;.	K	152	ENSP00000427975:I152K	ENSP00000373770:I152K	I	+	2	0	RANBP17	170255663	0.998000	0.40836	0.997000	0.53966	0.968000	0.65278	3.161000	0.50747	2.072000	0.62099	0.460000	0.39030	ATA	.		0.388	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		A	170323085	T	A	170323085	3	1	124	1	0	0	0	0	1	0	0	0	13059	1406	49	5	473	5	RANBP17	5	170323085	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	32418352	170323085	10592175	34	10800											
RNF44	22838	hgsc.bcm.edu	37	chr5	175957116	175957116	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaagctggggtagtagggtGgtgggggtgggggtgggggc	4	7	28	2	0	0	0	0	0	0	0	0	1	0	1	0	11	1	3	0	11	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:175957116G>T	ENST00000274811.4	-	7	1417	c.893C>A	c.(892-894)cCa>cAa	p.P298Q	RNF44_ENST00000509404.1_5'Flank|RNF44_ENST00000537487.1_Missense_Mutation_p.P217Q	NM_014901.4	NP_055716.1	Q7L0R7	RNF44_HUMAN	ring finger protein 44	298	Pro-rich.						zinc ion binding (GO:0008270)			endometrium(2)|lung(3)|prostate(1)|skin(1)|stomach(1)	8	all_cancers(89;0.0029)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTAGTAGGGTggtgggggtgg	0.622																																					p.P298Q		.											.	RNF44-658	0			c.C893A						.						8	8	8					5																	175957116		2165	4263	6428	SO:0001583	missense	22838	exon7			TAGGGTGGTGGGG	AB029023	CCDS4404.1	5q35.3	2013-01-09			ENSG00000146083	ENSG00000146083		"RING-type (C3HC4) zinc fingers"	19180	protein-coding gene	gene with protein product						10470851	Standard	NM_014901		Approved	KIAA1100	uc003mek.1	Q7L0R7	OTTHUMG00000130664	ENST00000274811.4:c.893C>A	5.37:g.175957116G>T	ENSP00000274811:p.Pro298Gln	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_014901	0	0	0	13	13	B4DYE0|Q8ND05|Q9UPQ2	Missense_Mutation	SNP	ENST00000274811.4	37	CCDS4404.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169154	0.57584	.	.	ENSG00000146083	ENST00000274811;ENST00000537487	D;D	0.86230	-2.09;-2.09	4.21	3.34	0.38264	.	0.516697	0.16329	N	0.219220	D	0.89128	0.6627	M	0.63843	1.955	0.33426	D	0.580514	D	0.53462	0.96	P	0.55871	0.786	D	0.88730	0.3236	10	0.26408	T	0.33	-9.7863	11.602	0.51008	0.0881:0.0:0.9119:0.0	.	298	Q7L0R7	RNF44_HUMAN	Q	298;217	ENSP00000274811:P298Q;ENSP00000440352:P217Q	ENSP00000274811:P298Q	P	-	2	0	RNF44	175889722	1.000000	0.71417	0.069000	0.20011	0.518000	0.34316	8.688000	0.91260	0.995000	0.38917	0.549000	0.68633	CCA	.		0.622	RNF44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253156.2			T	175957116	G	T	175957116	3	4	124	1	0	0	0	0	1	0	0	0	13528	1348	47	4	425	4	RNF44	5	175957116	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	5634031	175957116	4958144	35	10801											
RANBP9	10048	broad.mit.edu	37	chr6	13711709	13711709	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgttgctgctgctgcGgcggcggcggcggcggctgc	0	8	20	13	6	0	0	0	0	0	0	0	0	0	0	0	6	6	7	0	6	0	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:13711709G>T	ENST00000011619.3	-	1	87	c.29C>A	c.(28-30)cCg>cAg	p.P10Q		NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	10	Poly-Pro.				axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			ctgctgctgcggcggcggcgg	0.761																																					p.P10Q													.	RANBP9-414	0			c.C29A						.						4	5	5					6																	13711709		764	1870	2634	SO:0001583	missense	10048	exon1			TGCTGCGGCGGCG	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.29C>A	6.37:g.13711709G>T	ENSP00000011619:p.Pro10Gln	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	10	2	NM_005493	0	0	0	0	0	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Missense_Mutation	SNP	ENST00000011619.3	37	CCDS4529.1	.	.	.	.	.	.	.	.	.	.	g	8.018	0.759040	0.15846	.	.	ENSG00000010017	ENST00000011619;ENST00000283152	T	0.78003	-1.14	1.59	-3.18	0.05186	.	.	.	.	.	T	0.30198	0.0757	N	0.08118	0	0.21416	N	0.999694	B	0.18968	0.032	B	0.10450	0.005	T	0.18555	-1.0333	9	0.30854	T	0.27	.	5.1241	0.14875	0.0:0.0:0.4149:0.5851	.	10	Q96S59	RANB9_HUMAN	Q	10	ENSP00000011619:P10Q	ENSP00000011619:P10Q	P	-	2	0	RANBP9	13819688	0.000000	0.05858	0.967000	0.41034	0.688000	0.40055	-1.054000	0.03496	-0.053000	0.13289	0.154000	0.16183	CCG	.		0.761	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			T	13711709	G	T	13711709	3	4	124	1	0	0	0	0	1	0	0	0	13064	1116	39	4	2216	4	RANBP9	6	13711709	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08		13711709	157403358	36	10802											
SLC17A4	10050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	25773825	25773825	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttttagtctcttatttctgtGaatactggcttttttatacc	7	22	5	7	0	2	1	0	1	2	0	3	1	2	1	1	1	2	1	1	1	6	9			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:25773825G>A	ENST00000377905.4	+	8	1029	c.910G>A	c.(910-912)Gaa>Aaa	p.E304K	SLC17A4_ENST00000397076.2_Missense_Mutation_p.E74K|SLC17A4_ENST00000439485.2_Intron	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	304					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TTATTTCTGTGAATACTGGCT	0.443																																					p.E304K		.											.	SLC17A4-91	0			c.G910A						.						163	144	150					6																	25773825		2203	4300	6503	SO:0001583	missense	10050	exon8			TTCTGTGAATACT	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"Solute carriers"	10932	protein-coding gene	gene with protein product		604216	"solute carrier family 17 (sodium phosphate), member 4"			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.910G>A	6.37:g.25773825G>A	ENSP00000367137:p.Glu304Lys	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	92	36	NM_005495	0	0	1	1	0	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	37	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468242	0.63625	.	.	ENSG00000146039	ENST00000377905;ENST00000397076	T;T	0.58797	0.41;0.31	5.34	0.672	0.17935	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.890844	0.09592	N	0.781378	T	0.40645	0.1125	M	0.73598	2.24	0.09310	N	1	P;B	0.38048	0.616;0.082	B;B	0.40901	0.343;0.158	T	0.40365	-0.9567	10	0.54805	T	0.06	.	7.4701	0.27344	0.1347:0.4004:0.4649:0.0	.	74;304	E7EU17;Q9Y2C5	.;S17A4_HUMAN	K	304;74	ENSP00000367137:E304K;ENSP00000380266:E74K	ENSP00000367137:E304K	E	+	1	0	SLC17A4	25881804	0.000000	0.05858	0.079000	0.20413	0.976000	0.68499	-0.078000	0.11375	0.167000	0.19631	0.655000	0.94253	GAA	.		0.443	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1			A	25773825	G	A	25773825	3	1	124	1	0	0	0	0	1	0	0	0	14451	1291	45	2	936	2	SLC17A4	6	25773825	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	12062116	25773825	145341242	37	10803											
HLA-G	3135	ucsc.edu	37	chr6	29797247	29797247	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtctttgactatgaggccacCctgaggtgctgggccctggg	5	10	15	11	0	1	3	0	3	1	0	1	3	1	3	3	4	1	1	3	4	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:29797247C>T	ENST00000360323.6	+	4	696	c.672C>T	c.(670-672)acC>acT	p.T224T	HLA-G_ENST00000376818.3_Silent_p.T132T|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.T224T|HLA-G_ENST00000376828.2_Silent_p.T229T			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	224	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						ATGAGGCCACCCTGAGGTGCT	0.582																																					p.T224T													.	HLA-G-517	0			c.C672T						.						95	99	98					6																	29797247		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			GGCCACCCTGAGG		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.672C>T	6.37:g.29797247C>T		Somatic	259	0		WXS	Illumina HiSeq		255	1	NM_002127	0	0	3	3	0		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			.		0.582	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797247	C	T	29797247	2	4	124	1	0	0	0	0	0	0	0	1	7233	610	22	2		2	HLA-G	6	29797247	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	4023422	29797247	141317820	38	10804											
MUC21	394263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30955264	30955264	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaacacagccaccaacTctgggtccagtgtgacctct	9	7	10	15	0	2	1	0	1	2	0	3	1	3	1	5	2	3	0	5	2	2	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:30955264T>A	ENST00000376296.3	+	2	1553	c.1312T>A	c.(1312-1314)Tct>Act	p.S438T	MUC21_ENST00000486149.2_De_novo_Start_OutOfFrame	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	438	Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGCCACCAACTCTGGGTCCAG	0.577																																					p.S438T		.											.	MUC21-92	0			c.T1312A						.						124	120	122					6																	30955264		2203	4300	6503	SO:0001583	missense	394263	exon2			ACCAACTCTGGGT	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1312T>A	6.37:g.30955264T>A	ENSP00000365473:p.Ser438Thr	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	179	75	NM_001010909	0	0	0	0	0	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	t	7.419	0.636395	0.14386	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02015	4.5	3.96	-1.72	0.08107	.	.	.	.	.	T	0.00328	0.0010	N	0.12746	0.255	0.09310	N	1	B	0.15473	0.013	B	0.17722	0.019	T	0.42275	-0.9461	9	0.07325	T	0.83	0.2489	4.0719	0.09885	0.5071:0.2625:0.0:0.2303	.	438	Q5SSG8	MUC21_HUMAN	T	288;438	ENSP00000365473:S438T	ENSP00000365473:S438T	S	+	1	0	MUC21	31063243	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.031000	0.13710	-0.390000	0.07774	-0.468000	0.05107	TCT	.		0.577	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		A	30955264	T	A	30955264	3	1	124	1	0	0	0	0	1	0	0	0	10002	1551	54	5	1318	5	MUC21	6	30955264	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	1158017	30955264	140159803	39	10805											
MCM3	4172	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	52141973	52141973	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagcacataccgcagaagctGagacttggcaacggatgggt	13	6	13	9	2	0	2	0	1	0	2	0	4	0	3	1	3	4	4	1	3	4	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:52141973G>C	ENST00000229854.7	-	8	1133	c.1057C>G	c.(1057-1059)Cag>Gag	p.Q353E	MCM3_ENST00000476448.1_5'UTR|MCM3_ENST00000596288.1_Missense_Mutation_p.Q398E|MCM3_ENST00000419835.2_Missense_Mutation_p.Q307E			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	353	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.Q353K(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					CGCAGAAGCTGAGACTTGGCA	0.597																																					p.Q398E		.											.	MCM3-228	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C1192G						.						60	58	59					6																	52141973		2203	4300	6503	SO:0001583	missense	4172	exon8			GAAGCTGAGACTT	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1057C>G	6.37:g.52141973G>C	ENSP00000229854:p.Gln353Glu	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	39	12	NM_002388	0	0	16	31	15	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Missense_Mutation	SNP	ENST00000229854.7	37		.	.	.	.	.	.	.	.	.	.	G	32	5.114750	0.94339	.	.	ENSG00000112118	ENST00000229854;ENST00000419835	T;T	0.10960	2.82;2.82	5.36	5.36	0.76844	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.44726	0.1307	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.63510	-0.6621	10	0.87932	D	0	-17.9504	19.2924	0.94105	0.0:0.0:1.0:0.0	.	307;353	B4DUQ9;P25205	.;MCM3_HUMAN	E	353;307	ENSP00000229854:Q353E;ENSP00000388647:Q307E	ENSP00000229854:Q353E	Q	-	1	0	MCM3	52249932	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.783000	0.95769	0.655000	0.94253	CAG	.		0.597	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			C	52141973	G	C	52141973	3	2	124	1	0	0	0	0	1	0	0	0	9412	1299	45	4	1409	4	MCM3	6	52141973	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	21186709	52141973	118973094	40	10806											
COL19A1	1310	broad.mit.edu	37	chr6	70866589	70866589	+	Frame_Shift_Del	DEL	G	G	-																															aaggagagcggggctaccctGggatacctggggagaaaggc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:70866589delG	ENST00000322773.4	+	34	2368	c.2266delG	c.(2266-2268)gggfs	p.G756fs	COL19A1_ENST00000393344.1_Frame_Shift_Del_p.G378fs	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	756	Collagen-like 7.|Triple-helical region 4 (COL4).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GGGCTACCCTGGGATACCTGG	0.378																																					p.G756fs													.	COL19A1-156	0			c.2266delG						.						78	81	80					6																	70866589		2203	4300	6503	SO:0001589	frameshift_variant	1310	exon34			TACCCTGGGATAC		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2266delG	6.37:g.70866589delG	ENSP00000316030:p.Gly756fs	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	20	7	NM_001858	0	0	0	0	0	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Frame_Shift_Del	DEL	ENST00000322773.4	37	CCDS4970.1																																																																																			.		0.378	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			-	70866589	G	-	70866589	7	5	124	1	0	1	0	1	0	0	0	0	3682	1348	47	0	2396	0	COL19A1	6	70866589	Frame_Shift_Del	DEL	G	TCGA-GL-8500-01A-11D-2396-08	18724616	70866589	100248478	41	10807											
FERD3L	222894	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	19184646	19184646	+	Frame_Shift_Del	DEL	T	T	-																															ggcctcgttgaggttgaacaTccgcttcctttcgcggatgt																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:19184646delT	ENST00000275461.3	-	1	398	c.340delA	c.(340-342)atgfs	p.M114fs	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	114	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						AGGTTGAACATCCGCTTCCTT	0.612																																					p.M114fs		.											.	FERD3L-153	0			c.340delA						.						103	83	90					7																	19184646		2203	4300	6503	SO:0001589	frameshift_variant	222894	exon1			.	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"Basic helix-loop-helix proteins"	16660	protein-coding gene	gene with protein product			"Fer3-like (Drosophila)"			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.340delA	7.37:g.19184646delT	ENSP00000275461:p.Met114fs	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	80	26	NM_152898	0	0	0	0	0	Q495K0	Frame_Shift_Del	DEL	ENST00000275461.3	37	CCDS5368.1																																																																																			.		0.612	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			-	19184646	T	-	19184646	7	5	124	1	0	1	0	1	0	0	0	0	5835	1435	50	0	164	0	FERD3L	7	19184646	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08		19184646	139954017	42	10808											
SEMA3D	223117	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	84636164	84636164	+	Frame_Shift_Del	DEL	G	G	-																															tctggatataccatttaataGttgcttgttgggatttaggt																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:84636164delG	ENST00000284136.6	-	16	1905	c.1862delC	c.(1861-1863)actfs	p.T621fs	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	621	Ig-like C2-type.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CCATTTAATAGTTGCTTGTTG	0.388																																					p.T621fs	Ovarian(63;442 1191 17318 29975 31528)	.											.	SEMA3D-138	0			c.1862delC						.						214	198	203					7																	84636164		2203	4300	6503	SO:0001589	frameshift_variant	223117	exon16			.	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"Semaphorins", "Immunoglobulin superfamily / V-set domain containing"	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1862delC	7.37:g.84636164delG	ENSP00000284136:p.Thr621fs	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	441	305	NM_152754	0	0	0	0	0	A6NK46|Q6UW77|Q8NCQ1	Frame_Shift_Del	DEL	ENST00000284136.6	37	CCDS34676.1																																																																																			.		0.388	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		-	84636164	G	-	84636164	7	5	124	1	0	1	0	1	0	0	0	0	14059	1029	36	0	479	0	SEMA3D	7	84636164	Frame_Shift_Del	DEL	G	TCGA-GL-8500-01A-11D-2396-08	65451518	84636164	74502499	43	10809											
KIAA1549	57670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	138597164	138597164	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatcctcagtacttctttgAttgctgtaatgatgtactcc	9	16	7	9	0	2	2	1	2	1	0	4	3	4	2	2	0	3	4	2	0	4	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:138597164A>C	ENST00000422774.1	-	3	2969	c.2921T>G	c.(2920-2922)aTc>aGc	p.I974S	KIAA1549_ENST00000242365.4_Missense_Mutation_p.I924S|KIAA1549_ENST00000440172.1_Missense_Mutation_p.I974S			Q9HCM3	K1549_HUMAN	KIAA1549	974						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TACTTCTTTGATTGCTGTAAT	0.463			O	BRAF	pilocytic astrocytoma																																p.I974S	NSCLC(119;1534 1718 44213 46230 50068)	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549-369	0			c.T2921G						.						149	145	146					7																	138597164		2032	4201	6233	SO:0001583	missense	57670	exon3			TCTTTGATTGCTG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.2921T>G	7.37:g.138597164A>C	ENSP00000416040:p.Ile974Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	71	43	NM_020910	0	0	2	6	4	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284165	0.80803	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.32515	1.45;1.46;1.46	5.38	5.38	0.77491	.	0.071830	0.56097	D	0.000028	T	0.45994	0.1370	L	0.36672	1.1	0.51482	D	0.999929	D;D	0.89917	1.0;1.0	D;D	0.77004	0.975;0.989	T	0.44544	-0.9321	10	0.87932	D	0	.	14.7359	0.69414	1.0:0.0:0.0:0.0	.	974;974	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	S	974;924;974	ENSP00000406661:I974S;ENSP00000242365:I924S;ENSP00000416040:I974S	ENSP00000242365:I924S	I	-	2	0	KIAA1549	138247704	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	7.162000	0.77515	2.254000	0.74563	0.533000	0.62120	ATC	.		0.463	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			C	138597164	A	C	138597164	3	2	124	1	0	0	0	0	1	0	0	0	8265	333	12	5	3003	5	KIAA1549	7	138597164	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	53961000	138597164	20541499	44	10810											
ATP6V0E2	155066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	149576654	149576654	+	3'UTR	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgtcctgctccaataccCgcactgctctggagtttgcc	6	11	10	14	1	1	0	0	0	1	0	3	2	3	2	4	2	4	4	4	2	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:149576654C>G	ENST00000425642.2	+	0	519				ATP6V0E2-AS1_ENST00000464939.1_RNA|ATP6V0E2_ENST00000421974.2_Missense_Mutation_p.P177R|ATP6V0E2_ENST00000479613.1_Missense_Mutation_p.P151R|ATP6V0E2_ENST00000456496.2_3'UTR|ATP6V0E2_ENST00000606024.1_Missense_Mutation_p.P128R|RP11-445N20.3_ENST00000608912.1_lincRNA			Q8NHE4	VA0E2_HUMAN	ATPase, H+ transporting V0 subunit e2						ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|hydrogen ion transmembrane transporter activity (GO:0015078)			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00256)			CTCCAATACCCGCACTGCTCT	0.637																																					p.P177R		.											.	.	0			c.C530G						.						61	69	66					7																	149576654		1987	4159	6146	SO:0001624	3_prime_UTR_variant	155066	exon3			AATACCCGCACTG	AK057700	CCDS47742.1, CCDS55181.1	7q36.1	2010-04-21	2006-10-12	2006-10-12	ENSG00000171130	ENSG00000171130		"ATPases / V-type"	21723	protein-coding gene	gene with protein product		611019	"chromosome 7 open reading frame 32", "ATPase, H+ transporting V0 subunit E isoform 2-like (rat)"	C7orf32, ATP6V0E2L			Standard	XM_005249958		Approved		uc003wgs.3	Q8NHE4	OTTHUMG00000158094	ENST00000425642.2:c.*250C>G	7.37:g.149576654C>G		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	28	19	NM_001100592	0	0	35	88	53	A2T863|A2T8L7|B5MDP5|J3KQW7|Q6MZW1|Q75L47|Q7Z4R7|Q8N7I8	Missense_Mutation	SNP	ENST00000425642.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.45|12.45	1.941217|1.941217	0.34283|0.34283	.|.	.|.	ENSG00000171130|ENSG00000171130	ENST00000421974;ENST00000425642;ENST00000479613|ENST00000307445	.|.	.|.	.|.	2.78|2.78	1.89|1.89	0.25635|0.25635	.|.	.|.	.|.	.|.	.|.	T|T	0.19725|0.19725	0.0474|0.0474	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P;P|.	0.44090|.	0.826;0.742|.	B;B|.	0.37422|.	0.249;0.238|.	T|T	0.19160|0.19160	-1.0314|-1.0314	8|6	0.72032|0.87932	D|D	0.01|0	.|.	5.6822|5.6822	0.17782|0.17782	0.0:0.8483:0.0:0.1517|0.0:0.8483:0.0:0.1517	.|.	177;151|.	E9PAS2;Q8NHE4-3|.	.;.|.	R|G	177;128;151|96	.|.	ENSP00000411672:P177R|ENSP00000304519:R96G	P|R	+|+	2|1	0|0	ATP6V0E2|ATP6V0E2	149207587|149207587	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.005000|0.005000	0.04900|0.04900	0.044000|0.044000	0.13992|0.13992	0.750000|0.750000	0.32877|0.32877	0.467000|0.467000	0.42956|0.42956	CCG|CGC	.		0.637	ATP6V0E2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470874.1	NM_145230		G	149576654	C	G	149576654	1	3	124	0	1	0	0	0	0	0	0	0	1177	652	23	4		4	ATP6V0E2	7	149576654	3'UTR	SNP	C	TCGA-GL-8500-01A-11D-2396-08	10979490	149576654	9562009	45	10811											
NEIL2	252969	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	11637150	11637150	+	Frame_Shift_Del	DEL	A	A	-																															tagatttgatctagatgaagAaatggggccccctggcagca																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:11637150delA	ENST00000284503.6	+	3	781	c.182delA	c.(181-183)gaafs	p.E61fs	NEIL2_ENST00000436750.3_Frame_Shift_Del_p.E61fs|NEIL2_ENST00000403422.3_5'UTR|NEIL2_ENST00000528323.1_Intron|NEIL2_ENST00000455213.2_Frame_Shift_Del_p.E61fs	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	61					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		CTAGATGAAGAAATGGGGCCC	0.527								Base excision repair (BER), DNA glycosylases																													p.E61fs		.											.	NEIL2-659	0			c.182delA						.						59	75	70					8																	11637150		2203	4300	6503	SO:0001589	frameshift_variant	252969	exon3			.	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"nei like 2 (E. coli)"			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.182delA	8.37:g.11637150delA	ENSP00000284503:p.Glu61fs	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	190	91	NM_001135746	0	0	0	0	0	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Frame_Shift_Del	DEL	ENST00000284503.6	37	CCDS5984.1																																																																																			.		0.527	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		-	11637150	A	-	11637150	7	5	124	1	0	1	0	1	0	0	0	0	10345	246	9	0	193	0	NEIL2	8	11637150	Frame_Shift_Del	DEL	A	TCGA-GL-8500-01A-11D-2396-08		11637150	134726872	46	10812											
GOT1L1	137362	hgsc.bcm.edu	37	chr8	37797478	37797478	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgggtaatcatcttgtttgtAggtctttaacaagctgccct	8	15	9	9	1	3	0	1	0	2	0	3	0	3	0	1	2	3	4	1	2	4	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:37797478A>G	ENST00000307599.4	-	1	169	c.70T>C	c.(70-72)Tac>Cac	p.Y24H		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	24					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			TCTTGTTTGTAGGTCTTTAAC	0.448																																					p.Y24H		.											.	GOT1L1-23	0			c.T70C						.						135	123	127					8																	37797478		1941	4123	6064	SO:0001583	missense	137362	exon1			GTTTGTAGGTCTT	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.70T>C	8.37:g.37797478A>G	ENSP00000303077:p.Tyr24His	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_152413	0	0	0	0	0	A8MWL4	Missense_Mutation	SNP	ENST00000307599.4	37	CCDS47839.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852246	0.51270	.	.	ENSG00000169154	ENST00000307599;ENST00000524298	T	0.23950	1.88	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major domain (1);	0.177963	0.36519	N	0.002544	T	0.52869	0.1761	M	0.86097	2.795	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.60198	-0.7310	10	0.87932	D	0	-8.5012	11.9993	0.53222	1.0:0.0:0.0:0.0	.	24	Q8NHS2	AATC2_HUMAN	H	24;17	ENSP00000303077:Y24H	ENSP00000303077:Y24H	Y	-	1	0	GOT1L1	37916635	1.000000	0.71417	0.965000	0.40720	0.173000	0.22820	4.187000	0.58344	2.094000	0.63399	0.454000	0.30748	TAC	.		0.448	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413		G	37797478	A	G	37797478	3	3	124	1	0	0	0	0	1	0	0	0	6600	420	15	3	1076	3	GOT1L1	8	37797478	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	26160328	37797478	108566544	47	10813											
LYN	4067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	56922610	56922610	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaccaacgtttgactacttaCagagcgtcctggatgatttc	10	12	9	10	2	0	3	0	2	0	1	2	5	1	4	2	1	4	1	2	1	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:56922610C>A	ENST00000519728.1	+	13	1776	c.1480C>A	c.(1480-1482)Cag>Aag	p.Q494K	LYN_ENST00000520220.2_Missense_Mutation_p.Q473K	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	494	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	TGACTACTTACAGAGCGTCCT	0.527																																					p.Q494K		.											.	LYN-1002	0			c.C1480A						.						102	94	96					8																	56922610		2203	4300	6503	SO:0001583	missense	4067	exon13			TACTTACAGAGCG	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"SH2 domain containing"	6735	protein-coding gene	gene with protein product		165120	"v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1480C>A	8.37:g.56922610C>A	ENSP00000428924:p.Gln494Lys	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	103	39	NM_002350	0	0	10	15	5	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672813	0.88445	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	T;T	0.10573	2.86;2.86	5.95	5.95	0.96441	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.13500	0.0327	N	0.12422	0.21	0.80722	D	1	P;P	0.41265	0.744;0.59	P;B	0.48189	0.57;0.415	T	0.08106	-1.0738	10	0.54805	T	0.06	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	564;494	Q6NUK7;P07948	.;LYN_HUMAN	K	494;473	ENSP00000428924:Q494K;ENSP00000428424:Q473K	ENSP00000428924:Q494K	Q	+	1	0	LYN	57085164	1.000000	0.71417	0.967000	0.41034	0.879000	0.50718	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	CAG	.		0.527	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		A	56922610	C	A	56922610	3	1	124	1	0	0	0	0	1	0	0	0	9132	479	17	4	1526	4	LYN	8	56922610	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	19125132	56922610	89441412	48	10814											
GEM	2669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	95262646	95262646	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcctggctttcctgggcatGctctccttccttttctggta	2	16	9	14	1	2	0	0	0	2	0	5	0	4	0	4	3	1	4	4	3	1	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:95262646G>A	ENST00000297596.2	-	5	1047	c.783C>T	c.(781-783)agC>agT	p.S261S	GEM_ENST00000396194.2_Silent_p.S261S	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	261					cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCCTGGGCATGCTCTCCTTCC	0.552																																					p.S261S	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	.											.	GEM-659	0			c.C783T						.						96	87	90					8																	95262646		2203	4300	6503	SO:0001819	synonymous_variant	2669	exon5			GGGCATGCTCTCC		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"kinase-inducible Ras-like protein"	600164	"GTP-binding protein overexpressed in skeletal muscle"			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.783C>T	8.37:g.95262646G>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	67	25	NM_181702	0	0	2	8	6	B2RA31	Silent	SNP	ENST00000297596.2	37	CCDS6261.1																																																																																			.		0.552	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702		A	95262646	G	A	95262646	2	1	124	1	0	0	0	0	0	0	0	1	6349	1310	46	2		2	GEM	8	95262646	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	38340036	95262646	51101376	49	10815											
RAD54B	25788	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	95419720	95419720	+	Frame_Shift_Del	DEL	T	T	-																															tttggaaatcattctgtctaTtttcctttgaacttggttta																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:95419720delT	ENST00000336148.5	-	5	852	c.728delA	c.(727-729)aatfs	p.N243fs		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	243					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			ATTCTGTCTATTTTCCTTTGA	0.353								Direct reversal of damage;Homologous recombination																													p.N243fs		.											.	RAD54B-539	0			c.728delA						.						79	78	79					8																	95419720		2203	4300	6503	SO:0001589	frameshift_variant	25788	exon5			.	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.728delA	8.37:g.95419720delT	ENSP00000336606:p.Asn243fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	116	58	NM_012415	0	0	0	0	0	F6WBS8	Frame_Shift_Del	DEL	ENST00000336148.5	37	CCDS6262.1																																																																																			.		0.353	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		-	95419720	T	-	95419720	7	5	124	1	0	1	0	1	0	0	0	0	13024	1493	52	0	2048	0	RAD54B	8	95419720	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08	157074	95419720	50944302	50	10816											
C8orf38	137682	hgsc.bcm.edu	37	chr8	96037319	96037319	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgccgccggccgcctctggGtctgtacgcgcgcatgcggc	2	7	15	17	7	2	0	0	0	2	0	2	0	2	0	4	3	3	2	4	3	1	1	rs201223057	byFrequency	TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:96037319G>C	ENST00000396124.4	+	1	106	c.83G>C	c.(82-84)gGt>gCt	p.G28A	NDUFAF6_ENST00000286687.4_5'UTR|NDUFAF6_ENST00000542894.1_Intron|NDUFAF6_ENST00000396111.2_Intron|NDUFAF6_ENST00000396113.1_Intron	NM_152416.3	NP_689629.2	Q330K2	NDUF6_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 6	28					biosynthetic process (GO:0009058)|mitochondrial respiratory chain complex I assembly (GO:0032981)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	transferase activity (GO:0016740)										CCGCCTCTGGGTCTGTACGCG	0.766													G|||	3	0.000599042	8e-04	0	5008	,	,		10023	0		0.001	False		,,,				2504	0.001				p.G28A		.											.	.	0			c.G83C						.						2	3	3					8																	96037319		1152	2673	3825	SO:0001583	missense	137682	exon1			CTCTGGGTCTGTA	BC028166	CCDS6266.2	8q22.1	2013-10-21	2012-05-08	2012-05-08	ENSG00000156170	ENSG00000156170		"Mitochondrial respiratory chain complex assembly factors"	28625	protein-coding gene	gene with protein product		612392	"chromosome 8 open reading frame 38"	C8orf38		22019594, 23509070	Standard	NM_152416		Approved	MGC40214	uc003yhj.3	Q330K2	OTTHUMG00000150173	ENST00000396124.4:c.83G>C	8.37:g.96037319G>C	ENSP00000379430:p.Gly28Ala	Somatic	2	1		WXS	Illumina HiSeq	Phase_I	9	2	NM_152416	0	0	0	0	0	A8MT28|A8MWF0|B4DQ45|Q8N6U6	Missense_Mutation	SNP	ENST00000396124.4	37	CCDS6266.2	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593484	0.46214	.	.	ENSG00000156170	ENST00000396124	D	0.82344	-1.6	4.69	-0.395	0.12431	.	4.915100	0.02393	U	0.079907	T	0.66446	0.2790	N	0.19112	0.55	0.29426	N	0.860208	B	0.23591	0.088	B	0.21360	0.034	T	0.57974	-0.7718	10	0.05620	T	0.96	-0.9879	3.6626	0.08244	0.3757:0.0:0.4557:0.1686	.	28	Q330K2	CH038_HUMAN	A	28	ENSP00000379430:G28A	ENSP00000379430:G28A	G	+	2	0	C8orf38	96106495	0.000000	0.05858	0.000000	0.03702	0.416000	0.31233	0.481000	0.22260	-0.303000	0.08856	0.655000	0.94253	GGT	.		0.766	NDUFAF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316700.2	NM_152416		C	96037319	G	C	96037319	3	2	124	1	0	0	0	0	1	0	0	0	2430	1261	44	4	85	4	C8orf38	8	96037319	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	617599	96037319	50326703	51	10817											
PTK2	5747	hgsc.bcm.edu	37	chr8	141684434	141684434	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtcagcagggctgctgAggctggcaaggcttcccaga	8	7	15	11	0	1	2	1	1	0	1	2	2	2	2	1	4	3	7	1	4	1	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:141684434A>G	ENST00000522684.1	-	29	2901	c.2672T>C	c.(2671-2673)cTc>cCc	p.L891P	PTK2_ENST00000430260.2_Missense_Mutation_p.L201P|PTK2_ENST00000340930.3_Missense_Mutation_p.L901P|PTK2_ENST00000521059.1_Missense_Mutation_p.L891P|PTK2_ENST00000538769.1_Missense_Mutation_p.L559P|PTK2_ENST00000535192.1_Missense_Mutation_p.L845P|PTK2_ENST00000395218.2_Missense_Mutation_p.L901P|PTK2_ENST00000517887.1_Missense_Mutation_p.L935P|PTK2_ENST00000519419.1_Missense_Mutation_p.L935P|PTK2_ENST00000519465.1_Missense_Mutation_p.L519P	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	891	Interaction with TGFB1I1.|Pro-rich.				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)			AGGGCTGCTGAGGCTGGCAAG	0.567																																					p.L913P		.											.	PTK2-1517	0			c.T2738C						.						49	41	43					8																	141684434		2203	4300	6503	SO:0001583	missense	5747	exon29			CTGCTGAGGCTGG	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.2672T>C	8.37:g.141684434A>G	ENSP00000429911:p.Leu891Pro	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_005607	0	0	85	85	0	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	A	16.49	3.137373	0.56936	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T	0.77098	-1.02;-1.05;-1.02;-1.04;-1.02;-1.07;-1.01;-1.04;-1.0;-1.04;1.37;-1.04	5.96	5.96	0.96718	.	0.148388	0.45606	D	0.000349	T	0.66177	0.2763	N	0.19112	0.55	0.80722	D	1	P;P;B;B;B;B;B;B;B;P	0.43662	0.814;0.574;0.238;0.303;0.357;0.303;0.375;0.075;0.0;0.736	B;B;B;B;B;B;B;B;B;B	0.43052	0.229;0.406;0.167;0.121;0.167;0.121;0.397;0.265;0.002;0.248	T	0.65586	-0.6132	10	0.27785	T	0.31	.	11.5164	0.50524	0.8663:0.0:0.0:0.1337	.	901;586;811;891;913;845;843;718;559;519	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	P	891;845;519;935;891;843;901;812;586;563;901;559;935;201;589	ENSP00000429911:L891P;ENSP00000438009:L845P;ENSP00000429170:L519P;ENSP00000429082:L935P;ENSP00000429474:L891P;ENSP00000378644:L901P;ENSP00000428492:L563P;ENSP00000341189:L901P;ENSP00000445742:L559P;ENSP00000429129:L935P;ENSP00000403416:L201P;ENSP00000430603:L589P	ENSP00000341189:L901P	L	-	2	0	PTK2	141753616	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.777000	0.68931	2.284000	0.76573	0.528000	0.53228	CTC	.		0.567	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		G	141684434	A	G	141684434	3	3	124	1	0	0	0	0	1	0	0	0	12792	304	11	3	502	3	PTK2	8	141684434	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	45647115	141684434	4679588	52	10818											
PLEC	5339	hgsc.bcm.edu	37	chr8	144997533	144997533	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agctgcagccgcagtgttgtCagctcctgctccacctgcgc	5	9	11	16	2	1	0	1	0	0	0	3	0	3	0	4	0	6	6	4	0	0	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:144997533C>G	ENST00000322810.4	-	31	7144	c.6975G>C	c.(6973-6975)ctG>ctC	p.L2325L	PLEC_ENST00000354958.2_Silent_p.L2166L|PLEC_ENST00000354589.3_Silent_p.L2188L|PLEC_ENST00000345136.3_Silent_p.L2188L|PLEC_ENST00000527096.1_Silent_p.L2211L|PLEC_ENST00000398774.2_Silent_p.L2156L|PLEC_ENST00000436759.2_Silent_p.L2215L|PLEC_ENST00000356346.3_Silent_p.L2174L|PLEC_ENST00000357649.2_Silent_p.L2192L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2325	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCAGTGTTGTCAGCTCCTGCT	0.662																																					p.L2325L		.											.	PLEC-141	0			c.G6975C						.						11	13	12					8																	144997533		2137	4243	6380	SO:0001819	synonymous_variant	5339	exon31			TGTTGTCAGCTCC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.6975G>C	8.37:g.144997533C>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	22	2	NM_201380	0	0	11	11	0	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.		0.662	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		G	144997533	C	G	144997533	2	3	124	1	0	0	0	0	0	0	0	1	12078	813	29	4		4	PLEC	8	144997533	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	3313099	144997533	1366489	53	10819											
GRINA	2907	hgsc.bcm.edu	37	chr8	145066937	145066937	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagagtatgtgtttgctgcGctgaacctgtacacagacat	11	11	11	8	1	0	3	0	1	0	2	0	4	0	3	1	0	4	5	1	0	4	3	rs184930535		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:145066937G>A	ENST00000313269.5	+	7	1322	c.1044G>A	c.(1042-1044)gcG>gcA	p.A348A	GRINA_ENST00000395068.4_Silent_p.A348A	NM_000837.1	NP_000828.1	Q7Z429	LFG1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	348						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	9	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGTTTGCTGCGCTGAACCTGT	0.572													G|||	1	0.000199681	0	0	5008	,	,		22289	0		0.001	False		,,,				2504	0				p.A348A		.											.	GRINA-90	0			c.G1044A						.						199	124	149					8																	145066937		2203	4299	6502	SO:0001819	synonymous_variant	2907	exon7			TGCTGCGCTGAAC	NM_001009184	CCDS34961.1	8q24.3	2010-03-18	2008-04-01						4589	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 3"	138251		NMDARA1		1719427, 8406459	Standard	XM_005250899		Approved	HNRGW, TMBIM3, LFG1	uc003zao.1	Q7Z429		ENST00000313269.5:c.1044G>A	8.37:g.145066937G>A		Somatic	52	1		WXS	Illumina HiSeq	Phase_I	41	3	NM_001009184	0	0	339	339	0	B3KXM7|O43836|Q8IVW7	Silent	SNP	ENST00000313269.5	37	CCDS34961.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	9.946|9.946	1.218930|1.218930	0.22373|0.22373	.|.	.|.	ENSG00000178719|ENSG00000178719	ENST00000533044;ENST00000527194|ENST00000534791	T;T|.	0.59083|.	0.29;0.29|.	4.75|4.75	-9.49|-9.49	0.00587|0.00587	.|.	0.125575|.	0.52532|.	D|.	0.000061|.	T|T	0.42449|0.42449	0.1203|0.1203	.|.	.|.	.|.	0.58432|0.58432	D|D	0.999996|0.999996	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49072|0.49072	-0.8977|-0.8977	7|4	0.46703|.	T|.	0.11|.	-22.2342|-22.2342	5.2211|5.2211	0.15370|0.15370	0.3542:0.4442:0.1201:0.0815|0.3542:0.4442:0.1201:0.0815	.|.	.|.	.|.	.|.	T|H	171;161|327	ENSP00000432095:A171T;ENSP00000431217:A161T|.	ENSP00000431217:A161T|.	A|R	+|+	1|2	0|0	GRINA|GRINA	145138925|145138925	0.000000|0.000000	0.05858|0.05858	0.016000|0.016000	0.15963|0.15963	0.842000|0.842000	0.47809|0.47809	-5.389000|-5.389000	0.00126|0.00126	-2.455000|-2.455000	0.00540|0.00540	-1.354000|-1.354000	0.01226|0.01226	GCT|CGC	G|0.999;A|0.000		0.572	GRINA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384048.1	NM_001009184		A	145066937	G	A	145066937	2	1	124	1	0	0	0	0	0	0	0	1	6806	1074	38	1		1	GRINA	8	145066937	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	69404	145066937	1297085	54	10820											
OR13J1	392309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35869823	35869823	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagtcttcgctgaccgaCgtgttgccgcatgccagctt	7	10	12	12	4	1	1	0	1	1	0	2	3	1	2	3	1	3	4	3	1	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:35869823C>T	ENST00000377981.2	-	1	638	c.576G>A	c.(574-576)acG>acA	p.T192T		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			CGCTGACCGACGTGTTGCCGC	0.597																																					p.T192T		.											.	OR13J1-68	0			c.G576A						.						69	57	61					9																	35869823		2203	4300	6503	SO:0001819	synonymous_variant	392309	exon1			GACCGACGTGTTG		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"GPCR / Class A : Olfactory receptors"	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.576G>A	9.37:g.35869823C>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	56	18	NM_001004487	0	0	0	0	0	B2RN66|Q6IF20|Q96R40	Silent	SNP	ENST00000377981.2	37	CCDS35011.1																																																																																			.		0.597	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1			T	35869823	C	T	35869823	2	4	124	1	0	0	0	0	0	0	0	1	10970	523	19	1		1	OR13J1	9	35869823	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08		35869823	105343608	55	10821											
SECISBP2	79048	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	91965762	91965762	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caactgtgagaagatacagtCaaaaggtaaaggcacagtgt	17	7	11	6	0	1	2	1	1	0	2	1	3	1	2	0	2	2	2	0	2	7	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:91965762C>T	ENST00000375807.3	+	14	2179	c.2108C>T	c.(2107-2109)tCa>tTa	p.S703L	SECISBP2_ENST00000534113.2_Missense_Mutation_p.S635L|SECISBP2_ENST00000339901.4_Missense_Mutation_p.S630L	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	703					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						AAGATACAGTCAAAAGGTAAA	0.498																																					p.S703L		.											.	SECISBP2-93	0			c.C2108T						.						68	69	69					9																	91965762		2203	4300	6503	SO:0001583	missense	79048	exon14			TACAGTCAAAAGG	AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.2108C>T	9.37:g.91965762C>T	ENSP00000364965:p.Ser703Leu	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	67	34	NM_024077	0	0	0	0	0	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299315	0.81136	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113	T;T;T	0.57273	0.41;0.41;0.41	4.84	4.84	0.62591	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	L	0.52905	1.665	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.998	T	0.70695	-0.4801	10	0.59425	D	0.04	-12.0495	18.4955	0.90864	0.0:1.0:0.0:0.0	.	710;630;703	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	L	703;709;630;635	ENSP00000364965:S703L;ENSP00000364959:S630L;ENSP00000436650:S635L	ENSP00000364959:S630L	S	+	2	0	SECISBP2	91155582	1.000000	0.71417	0.991000	0.47740	0.546000	0.35178	7.314000	0.78988	2.686000	0.91538	0.561000	0.74099	TCA	.		0.498	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		T	91965762	C	T	91965762	3	4	124	1	0	0	0	0	1	0	0	0	14038	838	29	2	2162	2	SECISBP2	9	91965762	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	56095939	91965762	49247669	56	10822											
RAD23B	5887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	110091836	110091836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcttccagttaaaggcattaGgatttcctgaaggacttgtg	10	14	10	7	0	1	1	0	1	1	0	3	3	3	3	2	3	0	2	2	3	4	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:110091836G>A	ENST00000358015.3	+	10	1480	c.1129G>A	c.(1129-1131)Gga>Aga	p.G377R	RAD23B_ENST00000416373.2_Missense_Mutation_p.G305R	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	377	UBA 2. {ECO:0000255|PROSITE- ProRule:PRU00212}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAGGCATTAGGATTTCCTGA	0.328								Direct reversal of damage;Nucleotide excision repair (NER)																													p.G377R		.											.	RAD23B-228	0			c.G1129A						.						71	73	72					9																	110091836		2203	4300	6503	SO:0001583	missense	5887	exon10			GCATTAGGATTTC		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.1129G>A	9.37:g.110091836G>A	ENSP00000350708:p.Gly377Arg	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	102	33	NM_002874	0	0	0	0	0	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	37	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086513	0.76642	.	.	ENSG00000119318	ENST00000358015;ENST00000416373	D;D	0.93019	-3.15;-3.15	5.27	5.27	0.74061	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	D	0.97804	0.9279	H	0.94503	3.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.994	D	0.98693	1.0697	10	0.87932	D	0	-3.6232	19.2454	0.93901	0.0:0.0:1.0:0.0	.	356;377	B7Z4W4;P54727	.;RD23B_HUMAN	R	377;305	ENSP00000350708:G377R;ENSP00000405623:G305R	ENSP00000350708:G377R	G	+	1	0	RAD23B	109131657	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.439000	0.97543	2.623000	0.88846	0.563000	0.77884	GGA	.		0.328	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		A	110091836	G	A	110091836	3	1	124	1	0	0	0	0	1	0	0	0	13015	1001	35	2	1167	2	RAD23B	9	110091836	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	18126074	110091836	31121595	57	10823											
RABGAP1	23637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125751642	125751642	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacaaaatcctcttctgtgtCagagggcatgatggaactcc	11	11	9	10	0	3	2	1	1	2	1	5	3	5	3	2	2	2	1	2	2	4	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:125751642C>T	ENST00000373647.4	+	5	791	c.657C>T	c.(655-657)gtC>gtT	p.V219V		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	219	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						TCTTCTGTGTCAGAGGGCATG	0.413																																					p.V219V		.											.	RABGAP1-500	0			c.C657T						.						117	115	116					9																	125751642		2203	4300	6503	SO:0001819	synonymous_variant	23637	exon5			CTGTGTCAGAGGG	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"rab6 GTPase activating protein (GAP and centrosome-associated)", "TBC1 domain family, member 11"	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.657C>T	9.37:g.125751642C>T		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	90	44	NM_012197	0	0	8	11	3	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																			.		0.413	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		T	125751642	C	T	125751642	2	4	124	1	0	0	0	0	0	0	0	1	12996	813	29	2		2	RABGAP1	9	125751642	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	15659806	125751642	15461789	58	10824											
MLLT10	8028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	22022934	22022934	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaactggcaattaatggcAttgtaggagctttaaatggg	13	11	11	6	0	0	0	0	0	0	0	0	1	0	1	1	4	2	4	1	4	6	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr10:22022934A>T	ENST00000307729.7	+	20	2912	c.2734A>T	c.(2734-2736)Att>Ttt	p.I912F	MLLT10_ENST00000377059.3_Missense_Mutation_p.I912F|MLLT10_ENST00000377072.3_Missense_Mutation_p.I928F|MLLT10_ENST00000446906.2_Missense_Mutation_p.I912F			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	912					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						AATTAATGGCATTGTAGGAGC	0.498			T	"MLL, PICALM, CDK6"	AL																																p.I928F		.		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	.	MLLT10-658	0			c.A2782T						.						105	92	96					10																	22022934		2203	4300	6503	SO:0001583	missense	8028	exon21			AATGGCATTGTAG	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.2734A>T	10.37:g.22022934A>T	ENSP00000307411:p.Ile912Phe	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	78	33	NM_004641	0	0	3	6	3	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	37	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.302680	0.60195	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059	T;T;T;T	0.19938	2.21;2.22;2.11;2.22	4.55	4.55	0.56014	.	0.178156	0.48767	D	0.000174	T	0.33731	0.0873	L	0.55481	1.735	0.58432	D	0.999998	D;P;D;P	0.65815	0.96;0.745;0.995;0.883	P;B;P;B	0.56163	0.59;0.169;0.793;0.231	T	0.06954	-1.0798	10	0.56958	D	0.05	.	12.4706	0.55785	1.0:0.0:0.0:0.0	.	607;912;912;928	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	F	928;912;912;747;912	ENSP00000366272:I928F;ENSP00000401406:I912F;ENSP00000307411:I912F;ENSP00000366258:I912F	ENSP00000307411:I912F	I	+	1	0	MLLT10	22062940	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.644000	0.67902	1.686000	0.51046	0.455000	0.32223	ATT	.		0.498	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1			T	22022934	A	T	22022934	3	4	124	1	0	0	0	0	1	0	0	0	9651	217	8	5	2860	5	MLLT10	10	22022934	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		22022934	113511813	59	10825											
ANXA11	311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	81927005	81927005	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctttcatggccttccgcAggacctcggcatctcgcagg	6	9	11	15	3	2	0	1	0	1	0	5	1	3	1	4	4	1	3	4	4	0	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr10:81927005A>C	ENST00000438331.1	-	7	1108	c.626T>G	c.(625-627)cTg>cGg	p.L209R	ANXA11_ENST00000537102.1_Missense_Mutation_p.L176R|ANXA11_ENST00000360615.4_Missense_Mutation_p.L209R|ANXA11_ENST00000535999.1_Missense_Mutation_p.L209R|ANXA11_ENST00000372231.3_Missense_Mutation_p.L209R|ANXA11_ENST00000265447.4_Missense_Mutation_p.L209R|ANXA11_ENST00000422982.3_Missense_Mutation_p.L209R	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	209					cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			GGCCTTCCGCAGGACCTCGGC	0.577																																					p.L209R		.											.	ANXA11-91	0			c.T626G						.						66	61	63					10																	81927005		2203	4300	6503	SO:0001583	missense	311	exon6			TTCCGCAGGACCT	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"Annexins"	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.626T>G	10.37:g.81927005A>C	ENSP00000398610:p.Leu209Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	61	31	NM_145868	0	0	161	286	125	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	.	.	.	.	.	.	.	.	.	.	.	26.1	4.707456	0.89018	.	.	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102	T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000001	T	0.61924	0.2386	H	0.99498	4.595	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.995	T	0.78922	-0.2013	10	0.87932	D	0	.	13.5153	0.61537	1.0:0.0:0.0:0.0	.	309;209;209	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	R	209;209;209;209;209;209;209;116;176	ENSP00000361305:L209R;ENSP00000404412:L209R;ENSP00000398610:L209R;ENSP00000353827:L209R;ENSP00000265447:L209R;ENSP00000441748:L209R;ENSP00000441400:L176R	ENSP00000265447:L209R	L	-	2	0	ANXA11	81916985	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	8.792000	0.91856	2.151000	0.67156	0.459000	0.35465	CTG	.		0.577	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		C	81927005	A	C	81927005	3	2	124	1	0	0	0	0	1	0	0	0	716	188	7	5	935	5	ANXA11	10	81927005	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	59904071	81927005	53607742	60	10826											
PSTK	118672	hgsc.bcm.edu;broad.mit.edu	37	chr10	124740205	124740205	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgccggggcaagagcgcgAccggcggtcagcacggaggg	7	2	19	13	7	1	1	1	0	0	1	2	3	1	2	2	6	2	2	2	6	1	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr10:124740205A>G	ENST00000368887.3	+	1	650	c.210A>G	c.(208-210)cgA>cgG	p.R70R	PSTK_ENST00000405485.1_Silent_p.R70R	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	70					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		CAAGAGCGCGACCGGCGGTCA	0.756											OREG0020597	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R70R		.											.	PSTK-91	0			c.A210G						.						8	7	8					10																	124740205		1998	3971	5969	SO:0001819	synonymous_variant	118672	exon1			AGCGCGACCGGCG	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"chromosome 10 open reading frame 89"	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.210A>G	10.37:g.124740205A>G		Somatic	22	0	1536	WXS	Illumina HiSeq	Phase_I	10	4	NM_153336	0	0	0	0	0	Q6ZSS9	Silent	SNP	ENST00000368887.3	37	CCDS7633.1	.	.	.	.	.	.	.	.	.	.	A	9.597	1.127752	0.20959	.	.	ENSG00000179988	ENST00000406217	.	.	.	4.31	-1.6	0.08426	.	.	.	.	.	T	0.18800	0.0451	.	.	.	0.19300	N	0.999975	.	.	.	.	.	.	T	0.24261	-1.0165	4	.	.	.	0.6253	1.3993	0.02267	0.2116:0.3347:0.3029:0.1508	.	.	.	.	G	71	.	.	D	+	2	0	PSTK	124730195	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.142000	0.10311	-0.157000	0.11059	-0.242000	0.12053	GAC	.		0.756	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336		G	124740205	A	G	124740205	2	3	124	1	0	0	0	0	0	0	0	1	12749	262	10	3		3	PSTK	10	124740205	Silent	SNP	A	TCGA-GL-8500-01A-11D-2396-08	42813200	124740205	10794542	61	10827											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253368	1253368	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaacagctttgaggacccCtgctccctcagtgtggagaa	10	8	12	11	0	1	2	1	1	0	1	2	5	2	4	3	3	3	2	3	3	2	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:1253368C>A	ENST00000529681.1	+	15	1879	c.1821C>A	c.(1819-1821)ccC>ccA	p.P607P	MUC5B_ENST00000447027.1_Silent_p.P610P	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	607	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TTGAGGACCCCTGCTCCCTCA	0.682																																					p.P607P		.											.	.	0			c.C1821A						.						48	57	54					11																	1253368		2100	4195	6295	SO:0001819	synonymous_variant	727897	exon15			GGACCCCTGCTCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1821C>A	11.37:g.1253368C>A		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1253368	C	A	1253368	2	1	124	1	0	0	0	0	0	0	0	1	10004	668	24	4		4	MUC5B	11	1253368	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08		1253368	133753148	62	10828											
INCENP	3619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	61912744	61912744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcagaagtttgctcagatcGacgagaagactgagaaggtg	14	7	14	6	2	1	5	1	1	0	5	2	8	1	5	0	1	2	3	0	1	3	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:61912744G>A	ENST00000394818.3	+	13	2021	c.1819G>A	c.(1819-1821)Gac>Aac	p.D607N	INCENP_ENST00000278849.4_Missense_Mutation_p.D603N	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	607					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTCAGATCGACGAGAAGAC	0.582																																					p.D607N		.											.	INCENP-227	0			c.G1819A						.						103	107	105					11																	61912744		2202	4299	6501	SO:0001583	missense	3619	exon13			CAGATCGACGAGA	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1819G>A	11.37:g.61912744G>A	ENSP00000378295:p.Asp607Asn	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	105	46	NM_001040694	0	0	2	5	3	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141344	0.57044	.	.	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.16457	2.36;2.34	4.7	3.78	0.43462	.	0.232274	0.29916	N	0.010874	T	0.12433	0.0302	L	0.46157	1.445	0.38861	D	0.956484	B;P;B	0.36249	0.436;0.545;0.41	B;B;B	0.23716	0.027;0.048;0.022	T	0.07404	-1.0774	10	0.42905	T	0.14	.	10.2229	0.43207	0.098:0.0:0.902:0.0	.	603;603;607	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	N	607;603	ENSP00000378295:D607N;ENSP00000278849:D603N	ENSP00000278849:D603N	D	+	1	0	INCENP	61669320	1.000000	0.71417	0.303000	0.25071	0.969000	0.65631	5.818000	0.69236	2.522000	0.85027	0.561000	0.74099	GAC	.		0.582	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61912744	G	A	61912744	3	1	124	1	0	0	0	0	1	0	0	0	7754	1058	37	1	1865	1	INCENP	11	61912744	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	60659376	61912744	73093772	63	10829											
DKFZp761E198	91056	hgsc.bcm.edu	37	chr11	65547487	65547487	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccagcagcccgggcttgcaGctctctagctctcgcaggca	6	7	11	17	2	2	0	0	0	2	0	4	0	2	0	2	2	5	7	2	2	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:65547487G>A	ENST00000532090.2	-	2	687	c.477C>T	c.(475-477)agC>agT	p.S159S		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	159	Leu-rich.				endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						CGGGCTTGCAGCTCTCTAGCT	0.716																																					p.S159S		.											.	.	0			c.C477T						.						3	5	4					11																	65547487		1695	3877	5572	SO:0001819	synonymous_variant	91056	exon2			CTTGCAGCTCTCT	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.477C>T	11.37:g.65547487G>A		Somatic	6	1		WXS	Illumina HiSeq	Phase_I	7	3	NM_138368	0	0	1	1	0	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Silent	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			.		0.716	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368		A	65547487	G	A	65547487	2	1	124	1	0	0	0	0	0	0	0	1	4554	962	34	2		2	DKFZp761E198	11	65547487	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	3634743	65547487	69459029	64	10830											
EED	8726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	85956385	85956385	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctctctggagacgagaaTgtaagtgcagcttctggcag	10	9	13	9	1	2	2	0	0	2	2	3	5	2	2	1	2	2	4	1	2	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:85956385T>A	ENST00000263360.6	+	1	800	c.114T>A	c.(112-114)aaT>aaA	p.N38K	EED_ENST00000528180.1_Splice_Site_p.N38K|EED_ENST00000327320.4_Splice_Site_p.N38K|EED_ENST00000351625.6_Splice_Site_p.N38K	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	38					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				GAGACGAGAATGTAAGTGCAG	0.572																																					p.N38K		.											.	EED-227	0			c.T114A						.						52	42	46					11																	85956385		2203	4299	6502	SO:0001630	splice_region_variant	8726	exon1			CGAGAATGTAAGT	AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"WD repeat domain containing"	3188	protein-coding gene	gene with protein product	"WD protein associating with integrin cytoplasmic tails 1"	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.114+1T>A	11.37:g.85956385T>A		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	35	17	NM_003797	0	0	0	0	0	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Missense_Mutation	SNP	ENST00000263360.6	37	CCDS8273.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.68|15.68	2.906014|2.906014	0.52333|0.52333	.|.	.|.	ENSG00000074266|ENSG00000074266	ENST00000534595|ENST00000263360;ENST00000528180;ENST00000351625;ENST00000327320;ENST00000537092	.|T;T;T;T	.|0.79653	.|-0.79;-1.29;-0.71;-0.72	4.73|4.73	2.47|2.47	0.30058|0.30058	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80347|0.80347	0.4606|0.4606	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|B;D;B;B	.|0.57899	.|0.144;0.981;0.022;0.183	.|B;D;B;B	.|0.67900	.|0.055;0.954;0.008;0.028	T|T	0.76203|0.76203	-0.3045|-0.3045	5|9	.|.	.|.	.|.	-22.0933|-22.0933	6.2948|6.2948	0.21079|0.21079	0.0:0.3337:0.0:0.6663|0.0:0.3337:0.0:0.6663	.|.	.|38;38;38;38	.|O75530-3;E9PJK2;O75530-2;O75530	.|.;.;.;EED_HUMAN	N|K	37|38	.|ENSP00000263360:N38K;ENSP00000431778:N38K;ENSP00000338186:N38K;ENSP00000315587:N38K	.|.	I|N	+|+	2|3	0|2	EED|EED	85634033|85634033	0.966000|0.966000	0.33281|0.33281	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	0.057000|0.057000	0.14279|0.14279	0.949000|0.949000	0.37715|0.37715	0.533000|0.533000	0.62120|0.62120	ATT|AAT	.		0.572	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797	Missense_Mutation	A	85956385	T	A	85956385	5	1	124	1	0	0	0	0	0	0	1	0	4933	1478	51	5	116	5	EED	11	85956385	Splice_Site	SNP	T	TCGA-GL-8500-01A-11D-2396-08	20408898	85956385	49050131	65	10831											
SLC35F2	54733	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	107677532	107677532	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacggcgatgaagtggatcActctgtatcttgcatgaaga	11	10	11	9	2	3	3	1	2	2	1	3	5	3	4	1	2	1	2	1	2	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:107677532A>C	ENST00000525815.1	-	4	905	c.485T>G	c.(484-486)gTg>gGg	p.V162G	SLC35F2_ENST00000429869.1_Missense_Mutation_p.V162G|SLC35F2_ENST00000375682.4_Missense_Mutation_p.V115G|SLC35F2_ENST00000265836.7_Missense_Mutation_p.V14G|SLC35F2_ENST00000525071.1_Missense_Mutation_p.V162G	NM_017515.4	NP_059985.2	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	162					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		GAAGTGGATCACTCTGTATCT	0.463																																					p.V162G		.											.	SLC35F2-90	0			c.T485G						.						137	136	136					11																	107677532		1983	4179	6162	SO:0001583	missense	54733	exon4			TGGATCACTCTGT		CCDS41709.1	11q22.3	2013-05-22			ENSG00000110660	ENSG00000110660		"Solute carriers"	23615	protein-coding gene	gene with protein product						9119394	Standard	NM_017515		Approved	FLJ13018	uc001pjq.3	Q8IXU6	OTTHUMG00000166366	ENST00000525815.1:c.485T>G	11.37:g.107677532A>C	ENSP00000436785:p.Val162Gly	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	81	32	NM_017515	0	0	14	24	10	Q14963|Q5JPA8|Q6ZRQ3|Q9H947	Missense_Mutation	SNP	ENST00000525815.1	37	CCDS41709.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.133031	0.56828	.	.	ENSG00000110660	ENST00000525815;ENST00000525071;ENST00000265836;ENST00000375682;ENST00000429869	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	4.86	4.86	0.63082	.	0.341161	0.28140	N	0.016457	T	0.72211	0.3432	L	0.53249	1.67	0.50467	D	0.999875	P;P	0.42296	0.605;0.775	B;P	0.46208	0.405;0.507	T	0.75836	-0.3177	10	0.66056	D	0.02	.	14.4886	0.67634	1.0:0.0:0.0:0.0	.	162;162	E9PJD1;Q8IXU6	.;S35F2_HUMAN	G	162;162;14;115;162	ENSP00000436785:V162G;ENSP00000434307:V162G;ENSP00000364834:V115G;ENSP00000393571:V162G	ENSP00000265836:V14G	V	-	2	0	SLC35F2	107182742	1.000000	0.71417	1.000000	0.80357	0.534000	0.34807	3.837000	0.55820	1.824000	0.53156	0.533000	0.62120	GTG	.		0.463	SLC35F2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389417.1	NM_017515		C	107677532	A	C	107677532	3	2	124	1	0	0	0	0	1	0	0	0	14621	159	6	5	659	5	SLC35F2	11	107677532	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	21721147	107677532	27328984	66	10832											
SIDT2	51092	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	117058116	117058118	+	In_Frame_Del	DEL	TTC	TTC	-																															caccctcgagtcctggctgaTtcttttcctggcagttcccc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:117058116_117058118delTTC	ENST00000324225.4	+	11	1569_1571	c.1038_1040delTTC	c.(1036-1041)gattct>gat	p.S347del	SIDT2_ENST00000431081.2_In_Frame_Del_p.S351del	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	347					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		TCCTGGCTGATTCTTTTCCTGGC	0.517																																					p.346_347del		.											.	SIDT2-90	0			c.1038_1040del						.																																			SO:0001651	inframe_deletion	51092	exon11			.	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1038_1040delTTC	11.37:g.117058116_117058118delTTC	ENSP00000314023:p.Ser347del	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	153	58	NM_001040455	0	0	0	0	0	Q8NBY7|Q9Y357	In_Frame_Del	DEL	ENST00000324225.4	37	CCDS31682.1																																																																																			.		0.517	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		-	117058118	TTC	-	117058116	7	5	124	1	0	1	0	1	0	0	0	0	14335	1490	52	0	1080	0	SIDT2	11	117058116	In_Frame_Del	DEL	TTC	TCGA-GL-8500-01A-11D-2396-08	9380584	117058116	17948400	67	10833											
SLC6A12	6539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	308019	308019	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagtagatgatgccctggtAggctccgggaagggtgacac	9	8	16	8	1	0	3	0	2	0	1	1	4	1	4	2	4	1	4	2	4	4	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:308019A>T	ENST00000428720.1	-	8	1533	c.790T>A	c.(790-792)Tac>Aac	p.Y264N	SLC6A12_ENST00000424061.2_Missense_Mutation_p.Y264N|SLC6A12_ENST00000359674.4_Missense_Mutation_p.Y264N|SLC6A12_ENST00000538272.1_5'UTR|SLC6A12_ENST00000397296.2_Missense_Mutation_p.Y264N|SLC6A12_ENST00000536824.1_Missense_Mutation_p.Y264N	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	264					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			ATGCCCTGGTAGGCTCCGGGA	0.562																																					p.Y264N		.											.	SLC6A12-91	0			c.T790A						.						143	119	127					12																	308019		2203	4300	6503	SO:0001583	missense	6539	exon8			CCTGGTAGGCTCC	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.790T>A	12.37:g.308019A>T	ENSP00000388184:p.Tyr264Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	128	69	NM_001122848	1	0	13	28	14	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	A	8.181	0.793882	0.16327	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	4.44	3.19	0.36642	.	0.450623	0.22962	N	0.053522	T	0.74245	0.3691	L	0.52905	1.665	0.09310	N	1	P	0.34800	0.469	P	0.48901	0.594	T	0.62163	-0.6912	10	0.28530	T	0.3	.	6.6378	0.22893	0.6374:0.2349:0.0:0.1277	.	264	P48065	S6A12_HUMAN	N	264	ENSP00000352702:Y264N;ENSP00000380464:Y264N;ENSP00000388184:Y264N;ENSP00000399136:Y264N;ENSP00000444268:Y264N	ENSP00000352702:Y264N	Y	-	1	0	SLC6A12	178280	0.021000	0.18746	0.919000	0.36401	0.166000	0.22503	0.594000	0.24014	1.762000	0.52044	0.533000	0.62120	TAC	.		0.562	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		T	308019	A	T	308019	3	4	124	1	0	0	0	0	1	0	0	0	14707	420	15	5	1090	5	SLC6A12	12	308019	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		308019	133543876	68	10834											
KDM5A	5927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	401948	401948	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttgcagggcctttggcAgttctgtgctgcgcacacag	5	11	13	12	1	1	0	0	0	1	0	2	0	2	0	2	2	3	5	2	2	0	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:401948A>G	ENST00000399788.2	-	27	5205	c.4843T>C	c.(4843-4845)Tgc>Cgc	p.C1615R	KDM5A_ENST00000540838.1_5'UTR|KDM5A_ENST00000382815.4_Missense_Mutation_p.C1615R	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1615					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GGCCTTTGGCAGTTCTGTGCT	0.468			T	NUP98	AML																																p.C1615R		.		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A-227	0			c.T4843C						.						118	119	119					12																	401948		2033	4195	6228	SO:0001583	missense	5927	exon27			TTTGGCAGTTCTG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4843T>C	12.37:g.401948A>G	ENSP00000382688:p.Cys1615Arg	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	151	48	NM_001042603	0	0	8	15	7	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219116	0.79464	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	D;D	0.99667	-6.34;-3.28	5.48	5.48	0.80851	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.150326	0.64402	D	0.000005	D	0.99354	0.9773	L	0.59436	1.845	0.80722	D	1	D;D	0.64830	0.99;0.994	P;P	0.60682	0.758;0.878	D	0.98834	1.0752	10	0.87932	D	0	-9.1245	15.575	0.76368	1.0:0.0:0.0:0.0	.	1615;1615	P29375;P29375-2	KDM5A_HUMAN;.	R	1615	ENSP00000382688:C1615R;ENSP00000372265:C1615R	ENSP00000372265:C1615R	C	-	1	0	KDM5A	272209	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.313000	0.96297	2.080000	0.62538	0.528000	0.53228	TGC	.		0.468	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		G	401948	A	G	401948	3	3	124	1	0	0	0	0	1	0	0	0	8154	188	7	3	237	3	KDM5A	12	401948	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	93929	401948	133449947	69	10835											
C12orf5	57103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	4461705	4461705	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agtgttccttaccagccactCtgagcagatctgaacttatg	10	12	8	11	0	2	3	0	2	2	1	3	3	3	3	3	0	4	2	3	0	3	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:4461705C>G	ENST00000179259.4	+	6	728	c.661C>G	c.(661-663)Ctg>Gtg	p.L221V		NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	221					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			ACCAGCCACTCTGAGCAGATC	0.423																																					p.L221V	Colon(1;100 192 35375 49454 52532)	.											.	C12orf5-226	0			c.C661G						.						100	89	93					12																	4461705		2203	4300	6503	SO:0001583	missense	57103	exon6			GCCACTCTGAGCA	AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"TP53-induced glycolysis and apoptosis regulator"	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.661C>G	12.37:g.4461705C>G	ENSP00000179259:p.Leu221Val	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	125	49	NM_020375	0	0	4	8	4	B2R840	Missense_Mutation	SNP	ENST00000179259.4	37	CCDS8525.1	.	.	.	.	.	.	.	.	.	.	C	3.030	-0.199744	0.06219	.	.	ENSG00000078237	ENST00000179259	T	0.80738	-1.41	5.86	-2.23	0.06930	.	0.842330	0.10652	N	0.649789	T	0.68659	0.3025	L	0.43152	1.355	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.54609	-0.8268	10	0.40728	T	0.16	-13.6183	6.2439	0.20805	0.0912:0.2965:0.4592:0.1531	.	221	Q9NQ88	TIGAR_HUMAN	V	221	ENSP00000179259:L221V	ENSP00000179259:L221V	L	+	1	2	C12orf5	4331966	0.005000	0.15991	0.000000	0.03702	0.066000	0.16364	-0.080000	0.11339	-0.333000	0.08476	-0.219000	0.12488	CTG	.		0.423	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375		G	4461705	C	G	4461705	3	3	124	1	0	0	0	0	1	0	0	0	1698	912	32	4	683	4	C12orf5	12	4461705	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	4059757	4461705	129390190	70	10836											
GPR162	27239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6933600	6933600	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccaagatcggcctcggctTtggcgtttgcttcagcctct	4	13	10	14	3	2	1	1	0	1	1	5	1	3	1	3	3	2	3	3	3	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:6933600T>C	ENST00000311268.3	+	2	1323	c.536T>C	c.(535-537)tTt>tCt	p.F179S	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GGCCTCGGCTTTGGCGTTTGC	0.597																																					p.F179S		.											.	GPR162-92	0			c.T536C						.						86	82	84					12																	6933600		2203	4300	6503	SO:0001583	missense	27239	exon2			TCGGCTTTGGCGT	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"GPCR / Class A : Orphans"	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.536T>C	12.37:g.6933600T>C	ENSP00000311528:p.Phe179Ser	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	97	39	NM_019858	0	0	0	2	2	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	37	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.910599	0.72983	.	.	ENSG00000250510	ENST00000311268	T	0.72051	-0.62	4.33	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59321	0.2185	L	0.34521	1.04	0.80722	D	1	P;B	0.41624	0.757;0.156	B;B	0.40602	0.334;0.053	T	0.60234	-0.7303	9	0.87932	D	0	.	9.5237	0.39152	0.0:0.0841:0.0:0.9159	.	179;179	B7Z3U3;Q16538	.;GP162_HUMAN	S	179	ENSP00000311528:F179S	ENSP00000311528:F179S	F	+	2	0	GPR162	6803861	1.000000	0.71417	0.747000	0.31113	0.888000	0.51559	7.858000	0.86971	0.722000	0.32252	0.402000	0.26972	TTT	.		0.597	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		C	6933600	T	C	6933600	3	2	124	1	0	0	0	0	1	0	0	0	6686	1841	64	3	557	3	GPR162	12	6933600	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	2471895	6933600	126918295	71	10837											
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	26809443	26809443	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtttatggccagatactggCgatccaagcacatccttgca	10	10	10	11	1	0	1	0	0	0	1	2	2	2	1	3	3	3	3	3	3	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:26809443C>G	ENST00000381340.3	-	19	2647	c.2231G>C	c.(2230-2232)cGc>cCc	p.R744P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	744					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CAGATACTGGCGATCCAAGCA	0.453																																					p.R744P		.											.	ITPR2-542	0			c.G2231C						.						68	70	69					12																	26809443		2001	4179	6180	SO:0001583	missense	3709	exon19			TACTGGCGATCCA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.2231G>C	12.37:g.26809443C>G	ENSP00000370744:p.Arg744Pro	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	85	27	NM_002223	0	0	2	2	0	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.758328	0.89843	.	.	ENSG00000123104	ENST00000381340	D	0.95656	-3.77	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.97949	0.9325	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98818	1.0746	10	0.87932	D	0	.	18.0329	0.89290	0.0:1.0:0.0:0.0	.	744	Q14571	ITPR2_HUMAN	P	744	ENSP00000370744:R744P	ENSP00000370744:R744P	R	-	2	0	ITPR2	26700710	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.596000	0.82721	2.546000	0.85860	0.655000	0.94253	CGC	.		0.453	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26809443	C	G	26809443	3	3	124	1	0	0	0	0	1	0	0	0	7942	768	27	4	6030	4	ITPR2	12	26809443	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	19875843	26809443	107042452	72	10838											
DIP2B	57609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	51092173	51092173	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatgaatggattgagctAtggggtaatacgggtcaata	13	11	12	5	1	2	2	2	2	0	0	2	3	2	3	0	4	2	2	0	4	7	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:51092173A>G	ENST00000301180.5	+	18	2145	c.2111A>G	c.(2110-2112)tAt>tGt	p.Y704C		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	704						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						GGATTGAGCTATGGGGTAATA	0.463																																					p.Y704C		.											.	DIP2B-95	0			c.A2111G						.						108	101	103					12																	51092173		2203	4300	6503	SO:0001583	missense	57609	exon18			TGAGCTATGGGGT	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.2111A>G	12.37:g.51092173A>G	ENSP00000301180:p.Tyr704Cys	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	104	38	NM_173602	0	0	0	2	2	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.896459	0.72639	.	.	ENSG00000066084	ENST00000301180	T	0.23552	1.9	5.2	5.2	0.72013	AMP-dependent synthetase/ligase (1);	0.113362	0.64402	D	0.000011	T	0.45498	0.1345	M	0.71581	2.175	0.42957	D	0.994399	D	0.63880	0.993	D	0.64687	0.928	T	0.38714	-0.9648	10	0.40728	T	0.16	-14.3821	11.1177	0.48270	0.8536:0.0:0.0:0.1464	.	704	Q9P265	DIP2B_HUMAN	C	704	ENSP00000301180:Y704C	ENSP00000301180:Y704C	Y	+	2	0	DIP2B	49378440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.169000	0.77578	2.184000	0.69523	0.482000	0.46254	TAT	.		0.463	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		G	51092173	A	G	51092173	3	3	124	1	0	0	0	0	1	0	0	0	4539	449	16	3	2181	3	DIP2B	12	51092173	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	24282730	51092173	82759722	73	10839											
ESPL1	9700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53680427	53680427	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caccattaataaaaagtgtcCctggctcagagccctctaag	13	9	7	12	0	2	1	1	0	1	1	3	1	3	1	3	1	1	1	3	1	5	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:53680427C>A	ENST00000257934.4	+	18	3998	c.3907C>A	c.(3907-3909)Cct>Act	p.P1303T	ESPL1_ENST00000552462.1_Missense_Mutation_p.P1303T	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1303					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						AAAAAGTGTCCCTGGCTCAGA	0.527																																					p.P1303T	Colon(53;1069 1201 2587 5382)	.											.	ESPL1-228	0			c.C3907A						.						42	44	44					12																	53680427		2203	4300	6503	SO:0001583	missense	9700	exon18			AGTGTCCCTGGCT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.3907C>A	12.37:g.53680427C>A	ENSP00000257934:p.Pro1303Thr	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	79	40	NM_012291	0	0	0	1	1		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.435949	0.01108	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.11385	2.78;2.78	5.26	1.4	0.22301	.	0.405202	0.29501	N	0.011979	T	0.05273	0.0140	N	0.21583	0.68	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42050	-0.9474	10	0.14252	T	0.57	.	3.9836	0.09506	0.1566:0.4565:0.3028:0.0841	.	1303	Q14674	ESPL1_HUMAN	T	1303;978;1303	ENSP00000257934:P1303T;ENSP00000449831:P1303T	ENSP00000257934:P1303T	P	+	1	0	ESPL1	51966694	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.007000	0.12810	0.093000	0.17368	0.561000	0.74099	CCT	.		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		A	53680427	C	A	53680427	3	1	124	1	0	0	0	0	1	0	0	0	5266	623	22	4	3973	4	ESPL1	12	53680427	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	2588254	53680427	80171468	74	10840											
RDH5	5959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56115258	56115258	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggcagccaagtgggtggAgatgcacgttaaggaagcag	12	5	17	7	1	0	1	0	0	0	1	0	3	0	2	1	4	3	5	1	4	3	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:56115258A>G	ENST00000257895.5	+	2	442	c.290A>G	c.(289-291)gAg>gGg	p.E97G	RP11-644F5.10_ENST00000549424.1_Intron|RDH5_ENST00000547072.1_5'UTR|RDH5_ENST00000553160.1_Intron|RP11-644F5.10_ENST00000550412.1_Intron|RDH5_ENST00000548082.1_Missense_Mutation_p.E97G	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	97					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	AAGTGGGTGGAGATGCACGTT	0.612																																					p.E97G		.											.	RDH5-91	0			c.A290G						.						65	55	58					12																	56115258		2203	4300	6503	SO:0001583	missense	5959	exon2			GGGTGGAGATGCA	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	9940	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 5"	601617	"retinol dehydrogenase 5 (11-cis and 9-cis)"	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.290A>G	12.37:g.56115258A>G	ENSP00000257895:p.Glu97Gly	Somatic	132	1		WXS	Illumina HiSeq	Phase_I	103	40	NM_001199771	0	0	24	41	17	O00179|Q8TAI2	Missense_Mutation	SNP	ENST00000257895.5	37	CCDS31829.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.320462	0.23994	.	.	ENSG00000135437	ENST00000257895;ENST00000548082	D;D	0.87650	-2.28;-2.28	5.21	4.04	0.47022	NAD(P)-binding domain (1);	0.327481	0.34700	N	0.003750	T	0.77572	0.4150	N	0.25031	0.7	0.24743	N	0.993021	B	0.06786	0.001	B	0.08055	0.003	T	0.69060	-0.5245	10	0.56958	D	0.05	.	9.7426	0.40427	0.9125:0.0:0.0875:0.0	.	97	Q92781	RDH1_HUMAN	G	97	ENSP00000257895:E97G;ENSP00000447128:E97G	ENSP00000257895:E97G	E	+	2	0	RDH5	54401525	0.003000	0.15002	0.300000	0.25030	0.102000	0.19082	1.965000	0.40471	2.107000	0.64212	0.533000	0.62120	GAG	.		0.612	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905		G	56115258	A	G	56115258	3	3	124	1	0	0	0	0	1	0	0	0	13227	304	11	3	292	3	RDH5	12	56115258	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	2434831	56115258	77736637	75	10841											
PTPRB	5787	hgsc.bcm.edu	37	chr12	70964842	70964842	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaaggctgactgctgtacatCcccgctaatcgtcaagacaa	12	8	9	12	2	1	2	1	1	0	1	3	3	2	2	2	1	2	4	2	1	5	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:70964842C>A	ENST00000261266.5	-	11	2709	c.2680G>T	c.(2680-2682)Gat>Tat	p.D894Y	PTPRB_ENST00000451516.2_Missense_Mutation_p.D804Y|PTPRB_ENST00000538708.1_Missense_Mutation_p.D894Y|PTPRB_ENST00000334414.6_Missense_Mutation_p.D1112Y|PTPRB_ENST00000550358.1_Missense_Mutation_p.D1024Y|PTPRB_ENST00000550857.1_Missense_Mutation_p.D804Y|PTPRB_ENST00000551525.1_Missense_Mutation_p.D1111Y	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	894	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TGCTGTACATCCCCGCTAATC	0.433																																					p.D1112Y		.											.	PTPRB-226	0			c.G3334T						.						76	72	74					12																	70964842		1930	4139	6069	SO:0001583	missense	5787	exon13			GTACATCCCCGCT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.2680G>T	12.37:g.70964842C>A	ENSP00000261266:p.Asp894Tyr	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	60	3	NM_001109754	0	0	1	1	0	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.656809	0.67586	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37	5.9	5.9	0.94986	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.265469	0.44483	D	0.000448	T	0.61311	0.2337	L	0.38838	1.175	0.44523	D	0.997474	P;P;D;B;P;P;D	0.57571	0.937;0.878;0.97;0.25;0.855;0.88;0.98	P;P;P;B;P;P;P	0.62649	0.785;0.785;0.905;0.225;0.69;0.793;0.891	T	0.61686	-0.7012	10	0.62326	D	0.03	.	14.4259	0.67215	0.0:0.9302:0.0:0.0698	.	804;894;991;1111;1112;894;1024	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	Y	1112;804;1024;894;804;894;1111;991	ENSP00000334928:D1112Y;ENSP00000393028:D804Y;ENSP00000448058:D1024Y;ENSP00000438927:D894Y;ENSP00000447302:D804Y;ENSP00000261266:D894Y;ENSP00000448349:D1111Y;ENSP00000446982:D991Y	ENSP00000261266:D894Y	D	-	1	0	PTPRB	69251109	0.997000	0.39634	0.993000	0.49108	0.894000	0.52154	2.145000	0.42207	2.788000	0.95919	0.650000	0.86243	GAT	.		0.433	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			A	70964842	C	A	70964842	3	1	124	1	0	0	0	0	1	0	0	0	12828	855	30	4	3401	4	PTPRB	12	70964842	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	14849584	70964842	62887053	76	10842											
GLIPR1L2	144321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	75785104	75785104	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agctgcggggcgacgtcattCcccgagggtctaacttgcgc	6	8	14	13	5	2	0	1	0	1	0	3	2	3	0	2	3	4	1	2	3	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:75785104C>A	ENST00000550916.1	+	1	255	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	GLIPR1L2_ENST00000320460.4_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000435775.1_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000378692.3_5'UTR|GLIPR1L2_ENST00000441218.1_5'Flank|CAPS2_ENST00000442339.2_5'Flank|GLIPR1L2_ENST00000547164.1_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000378689.2_Missense_Mutation_p.P70T	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	70	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						CGACGTCATTCCCCGAGGGTC	0.567											OREG0021999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P70T		.											.	GLIPR1L2-91	0			c.C208A						.						104	80	88					12																	75785104		2203	4300	6503	SO:0001583	missense	144321	exon1			GTCATTCCCCGAG	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.208C>A	12.37:g.75785104C>A	ENSP00000448248:p.Pro70Thr	Somatic	92	0	1163	WXS	Illumina HiSeq	Phase_I	81	39	NM_152436	0	0	0	0	0	Q6MZS1|Q8N6N0|Q8NA43	Missense_Mutation	SNP	ENST00000550916.1	37	CCDS58258.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.906693	0.33628	.	.	ENSG00000180481	ENST00000550916;ENST00000435775;ENST00000378689;ENST00000320460;ENST00000547164	T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5	3.68	3.68	0.42216	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.41880	0.1178	M	0.90425	3.115	0.48288	D	0.999624	D;D	0.89917	0.997;1.0	P;D	0.87578	0.897;0.998	T	0.49062	-0.8978	10	0.87932	D	0	.	11.1954	0.48709	0.0:1.0:0.0:0.0	.	70;70	Q4G1C9;Q4G1C9-2	GRPL2_HUMAN;.	T	70	ENSP00000448248:P70T;ENSP00000398328:P70T;ENSP00000367960:P70T;ENSP00000317385:P70T;ENSP00000447980:P70T	ENSP00000317385:P70T	P	+	1	0	GLIPR1L2	74071371	0.067000	0.21026	0.025000	0.17156	0.007000	0.05969	2.883000	0.48554	2.352000	0.79861	0.585000	0.79938	CCC	.		0.567	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		A	75785104	C	A	75785104	3	1	124	1	0	0	0	0	1	0	0	0	6463	855	30	4	210	4	GLIPR1L2	12	75785104	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	4820262	75785104	58066791	77	10843											
CUL4A	8451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	113915023	113915023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agatgagaaagactcttggtCataatcttctagtttctgaa	13	14	8	6	0	5	4	1	2	4	3	5	5	5	4	0	1	0	1	0	1	4	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr13:113915023C>G	ENST00000375440.4	+	19	2218	c.2134C>G	c.(2134-2136)Cat>Gat	p.H712D	CUL4A_ENST00000326335.4_Missense_Mutation_p.H612D|CUL4A_ENST00000451881.1_Missense_Mutation_p.H612D|CUL4A_ENST00000375441.3_Missense_Mutation_p.H612D	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	712					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			GACTCTTGGTCATAATCTTCT	0.328																																					p.H712D		.											.	CUL4A-651	0			c.C2134G						.						75	74	74					13																	113915023		2203	4300	6503	SO:0001583	missense	8451	exon19			CTTGGTCATAATC	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.2134C>G	13.37:g.113915023C>G	ENSP00000364589:p.His712Asp	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	31	14	NM_001008895	0	0	18	30	12	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332500	0.81801	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.18	5.52	5.52	0.82312	Cullin protein, neddylation domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.93588	0.7953	H	0.99011	4.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.95979	0.8976	10	0.87932	D	0	-35.2623	19.4327	0.94778	0.0:1.0:0.0:0.0	.	712;712	Q13619;A8MSH7	CUL4A_HUMAN;.	D	612;612;612;712	ENSP00000364590:H612D;ENSP00000389118:H612D;ENSP00000322132:H612D;ENSP00000364589:H712D	ENSP00000322132:H612D	H	+	1	0	CUL4A	112963024	1.000000	0.71417	0.165000	0.22776	0.878000	0.50629	5.612000	0.67681	2.594000	0.87642	0.561000	0.74099	CAT	.		0.328	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		G	113915023	C	G	113915023	3	3	124	1	0	0	0	0	1	0	0	0	4063	826	29	4	2208	4	CUL4A	13	113915023	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		113915023	1254855	78	10844											
LAMP1	3916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	113963979	113963979	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgacctttgacctgccaTcagatgccacagtggtgctc	9	10	9	13	0	1	3	1	2	0	1	2	3	1	3	4	1	3	1	4	1	0	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr13:113963979T>C	ENST00000332556.4	+	3	399	c.205T>C	c.(205-207)Tca>Cca	p.S69P	LAMP1_ENST00000397181.3_Missense_Mutation_p.S69P	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	69	First lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			TGACCTGCCATCAGATGCCAC	0.423																																					p.S69P		.											.	LAMP1-514	0			c.T205C						.						89	92	91					13																	113963979		1960	4142	6102	SO:0001583	missense	3916	exon3			CTGCCATCAGATG	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.205T>C	13.37:g.113963979T>C	ENSP00000333298:p.Ser69Pro	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	115	45	NM_005561	0	0	132	275	143	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	37	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.434683	0.25813	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.32023	1.47;1.88	5.15	-10.3	0.00346	.	1.186920	0.05805	N	0.612961	T	0.19366	0.0465	L	0.51914	1.62	0.09310	N	1	B;B	0.15141	0.012;0.004	B;B	0.14578	0.011;0.004	T	0.10064	-1.0646	10	0.26408	T	0.33	-1.3993	4.2226	0.10565	0.0888:0.4046:0.2957:0.2108	.	69;69	B4DWL3;P11279	.;LAMP1_HUMAN	P	69	ENSP00000333298:S69P;ENSP00000415354:S69P	ENSP00000333298:S69P	S	+	1	0	LAMP1	113011980	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.754000	0.00790	-2.251000	0.00700	-0.479000	0.04858	TCA	.		0.423	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			C	113963979	T	C	113963979	3	2	124	1	0	0	0	0	1	0	0	0	8638	1435	50	3	215	3	LAMP1	13	113963979	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	48956	113963979	1205899	79	10845											
C14orf126	112487	hgsc.bcm.edu	37	chr14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgggcctgaggaatccGgctaccctcagccatggctt	6	7	12	16	3	1	1	1	1	0	0	2	2	2	2	5	4	2	2	5	4	2	2	rs17097904	byFrequency	TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W|DTD2_ENST00000356180.4_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		.											.	.	1	Substitution - Missense(1)	skin(1)	c.C16T						.						12	12	12					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	7	1		WXS	Illumina HiSeq	Phase_I	10	2	NM_080664	0	0	6	11	5	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		A	31926584	G	A	31926584	3	1	124	1	0	0	0	0	1	0	0	0	1747	1115	39	1	502	1	C14orf126	14	31926584	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08		31926584	75422956	80	10846											
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35295323	35295323	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattagcaaaaccattttgAtgtgatggagggaggacttc	12	11	11	7	0	0	2	0	2	0	0	1	5	0	5	2	3	2	1	2	3	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:35295323A>G	ENST00000382422.2	-	3	759	c.432T>C	c.(430-432)caT>caC	p.H144H	BAZ1A_ENST00000360310.1_Silent_p.H144H|BAZ1A_ENST00000553853.1_5'Flank|BAZ1A_ENST00000358716.4_Silent_p.H144H			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	144					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		AACCATTTTGATGTGATGGAG	0.338																																					p.H144H		.											.	BAZ1A-291	0			c.T432C						.						105	87	93					14																	35295323		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon4			ATTTTGATGTGAT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.432T>C	14.37:g.35295323A>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_182648	0	0	0	0	0	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			.		0.338	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35295323	A	G	35295323	2	3	124	1	0	0	0	0	0	0	0	1	1330	330	12	3		3	BAZ1A	14	35295323	Silent	SNP	A	TCGA-GL-8500-01A-11D-2396-08	3368739	35295323	72054217	81	10847											
SDCCAG1	9147	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	50292672	50292672	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttttctgctgacttgaatGcctatttatagaaaagagtt	11	17	7	6	0	2	4	0	2	2	2	2	4	2	4	1	0	2	2	1	0	6	8	rs370101877		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:50292672G>A	ENST00000298310.5	-	16	1939	c.1490C>T	c.(1489-1491)gCa>gTa	p.A497V	NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000546046.1_Splice_Site_p.A497V|NEMF_ENST00000545773.1_Splice_Site_p.A455V|AL627171.2_ENST00000595378.1_3'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	497					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TGACTTGAATGCCTATTTATA	0.269																																					p.A497V		.											.	NEMF-90	0			c.C1490T						.	G	VAL/ALA	0,4400		0,0,2200	96	91	93		1490	5.3	1	14		93	1,8591	1.2+/-3.3	0,1,4295	no	missense-near-splice	NEMF	NM_004713.3	64	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	497/1077	50292672	1,12991	2200	4296	6496	SO:0001630	splice_region_variant	9147	exon16			TTGAATGCCTATT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1489-1C>T	14.37:g.50292672G>A		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	23	17	NM_004713	0	0	0	0	0	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	37	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.985467	0.93044	0.0	1.16E-4	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.34	5.34	0.76211	Fibronectin-binding A, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.73892	0.3645	M	0.86864	2.845	0.80722	D	1	D;D;D;D;D	0.69078	0.997;0.994;0.985;0.997;0.995	D;D;D;D;D	0.73380	0.966;0.966;0.943;0.966;0.98	T	0.77086	-0.2718	10	0.54805	T	0.06	-18.6685	19.4564	0.94892	0.0:0.0:1.0:0.0	.	497;268;472;455;497	O60524-3;F5H639;O60524-5;O60524-4;O60524	.;.;.;.;NEMF_HUMAN	V	497;455;497;268;455	ENSP00000298310:A497V;ENSP00000438309:A455V;ENSP00000441016:A497V;ENSP00000452540:A455V	ENSP00000298310:A497V	A	-	2	0	NEMF	49362422	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.484000	0.90445	2.684000	0.91462	0.644000	0.83932	GCA	.		0.269	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713	Missense_Mutation	A	50292672	G	A	50292672	5	1	124	1	0	0	0	0	0	0	1	0	13989	1333	46	2	1812	2	SDCCAG1	14	50292672	Splice_Site	SNP	G	TCGA-GL-8500-01A-11D-2396-08	14997349	50292672	57056868	82	10848											
DLGAP5	9787	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	55655750	55655751	+	Frame_Shift_Ins	INS	-	-	AT																															tccaaggttggaatgtttacINSatctttcaaaccaaagtgtc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:55655750_55655751insAT	ENST00000247191.2	-	2	363_364	c.147_148insAT	c.(145-150)gatgtafs	p.V50fs	DLGAP5_ENST00000395425.2_Frame_Shift_Ins_p.V50fs	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	50					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						GGAATGTTTACATCTTTCAAAC	0.347																																					p.V50fs		.											.	DLGAP5-92	0			c.148_149insAT						.																																			SO:0001589	frameshift_variant	9787	exon2			.	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.146_147dupAT	14.37:g.55655751_55655752dupAT	ENSP00000247191:p.Val50fs	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	43	28	NM_001146015	0	0	0	0	0	A8MTM6|B4DRM8|Q86T11|Q8NG58	Frame_Shift_Ins	INS	ENST00000247191.2	37	CCDS9723.1																																																																																			.		0.347	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		AT	55655751	-	AT	55655750	7	5	124	1	0	1	1	0	0	0	0	0	4574	478	17	0	2559	0	DLGAP5	14	55655750	Frame_Shift_Ins	INS	-	TCGA-GL-8500-01A-11D-2396-08	5363078	55655750	51693790	83	10849											
PPM1A	5494	hgsc.bcm.edu;broad.mit.edu	37	chr14	60712638	60712638	+	5'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatgaaaagagagaaaagaAgaatggggaagagaagggca	22	3	15	1	0	0	6	0	1	0	5	0	9	0	7	0	3	0	1	0	3	9	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:60712638A>G	ENST00000529574.1	+	0	164				PPM1A_ENST00000325642.3_Missense_Mutation_p.R25G|CTD-2184C24.2_ENST00000529171.1_RNA|CTD-2184C24.2_ENST00000553269.1_RNA|CTD-2184C24.2_ENST00000532515.1_RNA|CTD-2184C24.2_ENST00000553775.1_RNA			P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A						cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		agagaaaagaagaatggggaa	0.408																																					p.R25G		.											.	PPM1A-227	0			c.A73G						.						79	77	78					14																	60712638		1568	3578	5146	SO:0001623	5_prime_UTR_variant	5494	exon1			AAAAGAAGAATGG	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000529574.1:c.-234A>G	14.37:g.60712638A>G		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_177952	0	0	0	0	0	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000529574.1	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415786	0.25552	.	.	ENSG00000100614	ENST00000325642	T	0.33438	1.41	3.86	0.196	0.15159	.	.	.	.	.	T	0.14141	0.0342	N	0.08118	0	0.09310	N	0.999997	.	.	.	.	.	.	T	0.23297	-1.0192	7	0.87932	D	0	.	2.3945	0.04386	0.5595:0.0:0.2316:0.2089	.	.	.	.	G	25	ENSP00000327255:R25G	ENSP00000327255:R25G	R	+	1	2	PPM1A	59782391	0.006000	0.16342	0.001000	0.08648	0.216000	0.24613	-0.020000	0.12525	0.023000	0.15187	0.172000	0.16884	AGA	.		0.408	PPM1A-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		NM_021003		G	60712638	A	G	60712638	1	3	124	0	1	0	0	0	0	0	0	0	12364	64	3	3		3	PPM1A	14	60712638	5'UTR	SNP	A	TCGA-GL-8500-01A-11D-2396-08	5056888	60712638	46636902	84	10850											
GPHB5	122876	broad.mit.edu	37	chr14	63779788	63779788	+	RNA	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctcgttgtaggtacagaCtcgatgatgggcttcaatat	9	13	12	7	2	2	2	1	1	1	1	4	3	2	2	0	3	1	4	0	3	4	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:63779788C>A	ENST00000539258.1	-	0	302							Q86YW7	GPHB5_HUMAN	glycoprotein hormone beta 5						regulation of thyroid hormone mediated signaling pathway (GO:0002155)	extracellular region (GO:0005576)				breast(1)|endometrium(1)|lung(4)|urinary_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(108;0.00372)|all cancers(60;0.0226)|BRCA - Breast invasive adenocarcinoma(234;0.0978)		TAGGTACAGACTCGATGATGG	0.488																																					.													.	GPHB5-67	0			.						.						85	92	90					14																	63779788		1960	4148	6108			122876	.			TACAGACTCGATG	AF467770	CCDS73643.1	14q23.3	2006-09-25				ENSG00000179600			18055	protein-coding gene	gene with protein product		609652					Standard	NM_145171		Approved	ZLUT1, GPB5	uc021rud.1	Q86YW7			14.37:g.63779788C>A		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	9	3	.	0	0	0	0	0	Q6NTD0|Q8NFW2	Missense_Mutation	SNP	ENST00000539258.1	37																																																																																				.		0.488	GPHB5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000400582.1	NM_145171		A	63779788	C	A	63779788	1	1	124	0	1	0	0	0	0	0	0	0	6629	564	20	4		4	GPHB5	14	63779788	RNA	SNP	C	TCGA-GL-8500-01A-11D-2396-08	3067150	63779788	43569752	85	10851											
DISP2	85455	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	40661086	40661086	+	Frame_Shift_Del	DEL	A	A	-																															accagacccagctcttctacAatgaggtcagccactggctg																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr15:40661086delA	ENST00000267889.3	+	8	2860	c.2773delA	c.(2773-2775)aatfs	p.N925fs	RP11-64K12.4_ENST00000558421.1_RNA|LINC00594_ENST00000561261.1_lincRNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	925					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GCTCTTCTACAATGAGGTCAG	0.602																																					p.N925fs		.											.	DISP2-92	0			c.2773delA						.						53	58	56					15																	40661086		2203	4300	6503	SO:0001589	frameshift_variant	85455	exon8			.	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2773delA	15.37:g.40661086delA	ENSP00000267889:p.Asn925fs	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	98	40	NM_033510	0	0	0	0	0	Q6AHW3|Q9C0C1	Frame_Shift_Del	DEL	ENST00000267889.3	37	CCDS10056.1																																																																																			.		0.602	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		-	40661086	A	-	40661086	7	5	124	1	0	1	0	1	0	0	0	0	4551	130	5	0	2803	0	DISP2	15	40661086	Frame_Shift_Del	DEL	A	TCGA-GL-8500-01A-11D-2396-08		40661086	61870306	86	10852											
MYO5A	4644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	52606371	52606371	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcttcaaactcattaacTggagtatacaaattcaacac	15	13	3	10	0	4	0	3	0	1	0	4	1	4	1	0	1	4	1	0	1	6	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr15:52606371T>C	ENST00000399231.3	-	40	5607	c.5364A>G	c.(5362-5364)ccA>ccG	p.P1788P	MYO5A_ENST00000399233.2_Silent_p.P1785P|MYO5A_ENST00000358212.6_Silent_p.P1813P|MYO5A_ENST00000553916.1_Silent_p.P1786P|MYO5A_ENST00000356338.6_Silent_p.P1761P	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1788	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ACTCATTAACTGGAGTATACA	0.348																																					p.P1788P		.											.	MYO5A-93	0			c.A5364G						.						88	81	83					15																	52606371		1810	4082	5892	SO:0001819	synonymous_variant	4644	exon40			ATTAACTGGAGTA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.5364A>G	15.37:g.52606371T>C		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	82	29	NM_000259	0	0	5	6	1	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																			.		0.348	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		C	52606371	T	C	52606371	2	2	124	1	0	0	0	0	0	0	0	1	10103	1567	55	3		3	MYO5A	15	52606371	Silent	SNP	T	TCGA-GL-8500-01A-11D-2396-08	11945285	52606371	49925021	87	10853											
SRRM2	23524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2812806	2812806	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcatttcttcaaggcggagCaggtctctctcttcaccacg	7	11	9	14	3	5	0	2	0	3	0	7	1	5	1	1	3	1	2	1	3	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:2812806C>G	ENST00000301740.8	+	11	2826	c.2277C>G	c.(2275-2277)agC>agG	p.S759R		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	759	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						CAAGGCGGAGCAGGTCTCTCT	0.473																																					p.S759R		.											.	SRRM2-93	0			c.C2277G						.						119	123	122					16																	2812806		2198	4300	6498	SO:0001583	missense	23524	exon11			GCGGAGCAGGTCT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2277C>G	16.37:g.2812806C>G	ENSP00000301740:p.Ser759Arg	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	285	170	NM_016333	0	0	5	21	16	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	8.634	0.894431	0.17613	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.26373	1.74	5.62	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.32526	0.0832	L	0.27053	0.805	0.33222	D	0.554776	D	0.65815	0.995	P	0.59115	0.852	T	0.48747	-0.9008	10	0.87932	D	0	-13.5853	12.4668	0.55764	0.0:0.9183:0.0:0.0817	.	759	Q9UQ35	SRRM2_HUMAN	R	759;759;11;724	ENSP00000301740:S759R	ENSP00000301740:S759R	S	+	3	2	SRRM2	2752807	0.982000	0.34865	1.000000	0.80357	0.796000	0.44982	0.846000	0.27682	1.367000	0.46095	0.655000	0.94253	AGC	.		0.473	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2812806	C	G	2812806	3	3	124	1	0	0	0	0	1	0	0	0	15201	709	25	4	2315	4	SRRM2	16	2812806	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		2812806	87541947	88	10854											
PRKCB	5579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23848699	23848699	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttctgcttttgcaggggCttcgggaagcagggattcca	6	12	13	10	1	1	0	0	0	1	0	4	2	3	2	2	4	3	4	2	4	1	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:23848699C>T	ENST00000321728.7	+	2	352	c.177C>T	c.(175-177)ggC>ggT	p.G59G	PRKCB_ENST00000498058.1_Intron|PRKCB_ENST00000303531.7_Silent_p.G59G	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	59					apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	TTTGCAGGGGCTTCGGGAAGC	0.552																																					p.G59G		.											.	PRKCB-1530	0			c.C177T						.						113	123	120					16																	23848699		2197	4300	6497	SO:0001819	synonymous_variant	5579	exon2			CAGGGGCTTCGGG	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"protein kinase C, beta 1"	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.177C>T	16.37:g.23848699C>T		Somatic	337	1		WXS	Illumina HiSeq	Phase_I	342	202	NM_212535	0	0	0	0	0	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			.		0.552	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		T	23848699	C	T	23848699	2	4	124	1	0	0	0	0	0	0	0	1	12537	784	28	2		2	PRKCB	16	23848699	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	21035893	23848699	66506054	89	10855											
ZNF48	197407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30408740	30408740	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggttcaaggaagaagatttgGctccagatcatgaagtagga	14	9	13	5	0	2	4	2	1	0	3	3	6	3	6	1	4	0	3	1	4	5	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:30408740G>C	ENST00000320159.2	+	2	545	c.169G>C	c.(169-171)Gct>Cct	p.A57P	SEPT1_ENST00000570039.1_5'Flank	NM_001214906.1|NM_001214907.1|NM_001214909.1|NM_152652.2	NP_001201835.1|NP_001201836.1|NP_001201838.1|NP_689865.2	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	57					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(3)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)|pancreas(1)|skin(1)	21						AGAAGATTTGGCTCCAGATCA	0.488																																					p.A57P		.											.	ZNF48-90	0			c.G169C						.						117	119	119					16																	30408740		2197	4300	6497	SO:0001583	missense	197407	exon3			GATTTGGCTCCAG	M88358, AK056313	CCDS10679.1, CCDS73868.1	16p11.2	2013-01-08			ENSG00000180035	ENSG00000180035		"Zinc fingers, C2H2-type"	13114	protein-coding gene	gene with protein product			"zinc finger protein 553"	ZNF553		1505991	Standard	NM_152652		Approved	DKFZp762K013, FLJ31751, MGC43952	uc021tgi.1	Q96MX3	OTTHUMG00000048195	ENST00000320159.2:c.169G>C	16.37:g.30408740G>C	ENSP00000324056:p.Ala57Pro	Somatic	183	1		WXS	Illumina HiSeq	Phase_I	206	46	NM_001214906	0	0	8	16	8	Q15920|Q4G0R3|Q69YP3|Q96IL9	Missense_Mutation	SNP	ENST00000320159.2	37	CCDS10679.1	.	.	.	.	.	.	.	.	.	.	G	9.037	0.988666	0.18966	.	.	ENSG00000180035	ENST00000495929;ENST00000528032;ENST00000524644;ENST00000320159	T;T;T	0.08193	3.42;3.35;3.12	4.61	0.489	0.16854	.	2.071660	0.02505	N	0.090916	T	0.07188	0.0182	N	0.19112	0.55	0.09310	N	1	B	0.22604	0.072	B	0.17433	0.018	T	0.39165	-0.9627	10	0.72032	D	0.01	-5.4461	7.1767	0.25749	0.4784:0.0:0.5216:0.0	.	57	Q96MX3	ZNF48_HUMAN	P	182;57;57;57	ENSP00000435674:A57P;ENSP00000432548:A57P;ENSP00000324056:A57P	ENSP00000324056:A57P	A	+	1	0	ZNF48	30316241	0.815000	0.29118	0.000000	0.03702	0.905000	0.53344	0.926000	0.28804	0.031000	0.15407	-0.251000	0.11542	GCT	.		0.488	ZNF48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255549.2	NM_152652		C	30408740	G	C	30408740	3	2	124	1	0	0	0	0	1	0	0	0	17966	1203	42	4	175	4	ZNF48	16	30408740	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	6560041	30408740	59946013	90	10856											
ZC3H18	124245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	88653085	88653085	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtcccacctgccggttcttCatgaaaggtaattgtctgcg	7	12	10	12	3	3	1	1	1	2	0	4	1	4	1	3	2	2	2	3	2	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:88653085C>T	ENST00000301011.5	+	3	881	c.681C>T	c.(679-681)ttC>ttT	p.F227F	ZC3H18_ENST00000452588.2_Silent_p.F227F	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	227						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GCCGGTTCTTCATGAAAGGTA	0.587																																					p.F227F	Ovarian(121;375 2276 20373 38669)	.											.	ZC3H18-69	0			c.C681T						.						112	88	96					16																	88653085		2198	4300	6498	SO:0001819	synonymous_variant	124245	exon3			GTTCTTCATGAAA	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"Zinc fingers, CCCH-type domain containing"	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.681C>T	16.37:g.88653085C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	74	18	NM_144604	0	0	0	0	0	Q96DG4|Q96MP7	Silent	SNP	ENST00000301011.5	37	CCDS10967.1																																																																																			.		0.587	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88653085	C	T	88653085	2	4	124	1	0	0	0	0	0	0	0	1	17600	825	29	2		2	ZC3H18	16	88653085	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	58244345	88653085	1701668	91	10857											
SAT2	112483	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	7530935	7530935	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctccctccttggcctctcGgatccgcacggaagccatcc	5	9	9	18	3	2	0	0	0	2	0	7	2	5	2	6	3	1	1	6	3	1	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr17:7530935G>A	ENST00000269298.5	-	1	238	c.19C>T	c.(19-21)Cga>Tga	p.R7*	SHBG_ENST00000576478.1_Intron|SHBG_ENST00000576728.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000575314.1_Intron|SHBG_ENST00000572262.1_Intron|SHBG_ENST00000340624.5_5'Flank|SHBG_ENST00000416273.3_5'Flank|SAT2_ENST00000573566.1_Nonsense_Mutation_p.R7*|SAT2_ENST00000380466.2_5'UTR|SHBG_ENST00000575903.1_5'Flank|SHBG_ENST00000441599.2_5'Flank|SHBG_ENST00000380450.4_5'Flank|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000574539.1_Intron	NM_133491.3	NP_597998.1	Q96F10	SAT2_HUMAN	spermidine/spermine N1-acetyltransferase family member 2	7	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				nor-spermidine metabolic process (GO:0046204)|putrescine acetylation (GO:0032920)|putrescine catabolic process (GO:0009447)|spermidine acetylation (GO:0032918)|spermine acetylation (GO:0032919)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	diamine N-acetyltransferase activity (GO:0004145)	p.?(1)		kidney(1)|large_intestine(2)	3				READ - Rectum adenocarcinoma(115;0.166)	Spermine(DB00127)	TTGGCCTCTCGGATCCGCACG	0.632																																					p.R7X		.											.	SAT2-90	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C19T						.						50	45	47					17																	7530935		2203	4300	6503	SO:0001587	stop_gained	112483	exon1			CCTCTCGGATCCG	AF348524	CCDS11116.1	17p13.2	2011-11-16	2008-01-07		ENSG00000141504	ENSG00000141504	2.3.1.57		23160	protein-coding gene	gene with protein product	"diamine N-acetyltransferase 2"	611463	"spermidine/spermine N1-acetyltransferase 2"			15283699, 17558023	Standard	NM_133491		Approved	SSAT2	uc002gic.2	Q96F10	OTTHUMG00000108152	ENST00000269298.5:c.19C>T	17.37:g.7530935G>A	ENSP00000269298:p.Arg7*	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	58	18	NM_133491	0	0	63	102	39		Nonsense_Mutation	SNP	ENST00000269298.5	37	CCDS11116.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.441041|6.441041	0.97568|0.97568	.|.	.|.	ENSG00000141504|ENSG00000141504	ENST00000380466|ENST00000269298	.|.	.|.	.|.	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	0.000000|.	0.31963|.	U|.	0.006786|.	T|.	0.34658|.	0.0905|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.15752|.	-1.0426|.	6|.	0.72032|0.02654	D|T	0.01|1	-13.2823|-13.2823	13.0369|13.0369	0.58877|0.58877	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	80|7	.|.	ENSP00000369833:P80L|ENSP00000269298:R7X	P|R	-|-	2|1	0|2	SAT2|SAT2	7471660|7471660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	3.025000|3.025000	0.49681|0.49681	2.453000|2.453000	0.82957|0.82957	0.655000|0.655000	0.94253|0.94253	CCG|CGA	.		0.632	SAT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440078.1	NM_133491		A	7530935	G	A	7530935	4	1	124	1	0	0	0	0	0	1	0	0	13884	1124	39	1	517	1	SAT2	17	7530935	Nonsense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08		7530935	73664275	92	10858											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7750183	7750183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctccaccaccattaccacCaccaccaccaccaccaccac	12	3	1	25	0	0	0	0	0	0	0	1	0	1	0	12	0	1	0	12	0	1	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr17:7750183C>T	ENST00000448097.2	+	9	1089	c.758C>T	c.(757-759)cCa>cTa	p.P253L	KDM6B_ENST00000254846.5_Missense_Mutation_p.P253L			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	253	Pro-rich.			Missing (in Ref. 1; BAA21572 and 3; AAH09994). {ECO:0000305}.	cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						ccattaccaccaccaccacca	0.607																																					p.P253L		.											.	KDM6B-205	0			c.C758T						.						26	24	25					17																	7750183		2194	4283	6477	SO:0001583	missense	23135	exon9			TACCACCACCACC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.758C>T	17.37:g.7750183C>T	ENSP00000412513:p.Pro253Leu	Somatic	44	1		WXS	Illumina HiSeq	Phase_I	38	2	NM_001080424	0	0	0	0	0	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		.	.	.	.	.	.	.	.	.	.	C	5.495	0.276381	0.10403	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.29397	1.57;1.58	0.584	0.584	0.17422	.	0.532596	0.13901	U	0.354930	T	0.27967	0.0689	N	0.08118	0	0.36960	D	0.893296	P	0.51449	0.945	P	0.59056	0.851	T	0.38542	-0.9656	9	0.62326	D	0.03	.	.	.	.	.	253	O15054-1	.	L	253	ENSP00000254846:P253L;ENSP00000412513:P253L	ENSP00000254846:P253L	P	+	2	0	KDM6B	7690908	0.624000	0.27102	0.831000	0.32960	0.645000	0.38454	0.207000	0.17395	0.612000	0.30071	0.089000	0.15464	CCA	.		0.607	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		T	7750183	C	T	7750183	3	4	124	1	0	0	0	0	1	0	0	0	8159	594	21	2	780	2	KDM6B	17	7750183	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	219248	7750183	73445027	93	10859											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7750211	7750211	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccaccaccaccaccaccAccacccctgcctggcctggc	8	3	5	25	0	0	0	0	0	0	0	0	0	0	0	12	2	1	0	12	2	0	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr17:7750211A>C	ENST00000448097.2	+	9	1117	c.786A>C	c.(784-786)ccA>ccC	p.P262P	KDM6B_ENST00000254846.5_Silent_p.P262P			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	262	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						caccaccaccaccaccCCTGC	0.632																																					p.P262P		.											.	KDM6B-205	0			c.A786C						.						13	14	13					17																	7750211		2187	4288	6475	SO:0001819	synonymous_variant	23135	exon9			ACCACCACCACCC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.786A>C	17.37:g.7750211A>C		Somatic	25	1		WXS	Illumina HiSeq	Phase_I	33	5	NM_001080424	0	0	1	1	0	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				.		0.632	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		C	7750211	A	C	7750211	2	2	124	1	0	0	0	0	0	0	0	1	8159	146	6	5		5	KDM6B	17	7750211	Silent	SNP	A	TCGA-GL-8500-01A-11D-2396-08	28	7750211	73444999	94	10860											
TOP3A	7156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18181411	18181411	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgctttcaccagcagccgtgGgtggtgggagggtctgggcc	4	9	18	10	1	2	0	1	0	1	0	2	1	2	1	3	5	3	2	3	5	0	1	rs201017469		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr17:18181411G>A	ENST00000321105.5	-	18	2619	c.2405C>T	c.(2404-2406)cCc>cTc	p.P802L	TOP3A_ENST00000540524.1_Missense_Mutation_p.P332L|TOP3A_ENST00000542570.1_Missense_Mutation_p.P707L	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	802					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						AGCAGCCGTGGGTGGTGGGAG	0.627													G|||	1	0.000199681	0	0	5008	,	,		16717	0.001		0	False		,,,				2504	0				p.P802L		.											.	TOP3A-228	0			c.C2405T						.						57	61	60					17																	18181411		2203	4300	6503	SO:0001583	missense	7156	exon18			GCCGTGGGTGGTG	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 7"	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.2405C>T	17.37:g.18181411G>A	ENSP00000321636:p.Pro802Leu	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	119	45	NM_004618	0	0	3	5	2	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	37	CCDS11194.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	4.844	0.156908	0.09236	.	.	ENSG00000177302	ENST00000321105;ENST00000540524;ENST00000542570	T;T;T	0.12039	3.12;2.72;3.12	5.55	4.55	0.56014	.	0.389850	0.31404	N	0.007707	T	0.12902	0.0313	L	0.40543	1.245	0.18873	N	0.999988	B;B	0.25441	0.014;0.126	B;B	0.15484	0.005;0.013	T	0.11792	-1.0573	10	0.40728	T	0.16	-15.0687	15.7664	0.78128	0.0:0.0:0.863:0.1369	.	707;802	B4DK80;Q13472	.;TOP3A_HUMAN	L	802;332;707	ENSP00000321636:P802L;ENSP00000446425:P332L;ENSP00000442336:P707L	ENSP00000321636:P802L	P	-	2	0	TOP3A	18122136	0.030000	0.19436	0.015000	0.15790	0.233000	0.25261	2.238000	0.43070	2.621000	0.88768	0.549000	0.68633	CCC	G|0.999;A|0.000		0.627	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			A	18181411	G	A	18181411	3	1	124	1	0	0	0	0	1	0	0	0	16400	1232	43	2	608	2	TOP3A	17	18181411	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	10431200	18181411	63013799	95	10861											
GPS1	2873	hgsc.bcm.edu	37	chr17	80011903	80011903	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgtacgaggagatccacCgcaagctctcagaggccacc	12	5	10	14	2	1	2	1	0	1	2	3	4	2	2	4	2	2	3	4	2	2	1	rs199969665		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr17:80011903C>A	ENST00000306823.6	+	3	309	c.286C>A	c.(286-288)Cgc>Agc	p.R96S	GPS1_ENST00000355130.2_Missense_Mutation_p.R136S|RFNG_ENST00000310496.4_5'Flank|GPS1_ENST00000578552.1_Missense_Mutation_p.R96S|GPS1_ENST00000320548.4_Missense_Mutation_p.R80S|RFNG_ENST00000429557.3_5'Flank|GPS1_ENST00000392358.2_Missense_Mutation_p.R136S			Q13098	CSN1_HUMAN	G protein pathway suppressor 1	96					cell cycle (GO:0007049)|cullin deneddylation (GO:0010388)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)			breast(1)|central_nervous_system(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|skin(2)	13	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			GGAGATCCACCGCAAGCTCTC	0.632																																					p.R136S		.											.	GPS1-226	0			c.C406A						.						46	36	40					17																	80011903		2200	4295	6495	SO:0001583	missense	2873	exon3			ATCCACCGCAAGC		CCDS11800.1, CCDS32774.1	17q25.3	2013-03-14				ENSG00000169727			4549	protein-coding gene	gene with protein product	"COP9 signalosome subunit 1"	601934				9535219	Standard	NM_212492		Approved	COPS1, CSN1	uc002kdl.1	Q13098		ENST00000306823.6:c.286C>A	17.37:g.80011903C>A	ENSP00000302873:p.Arg96Ser	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_212492	0	0	78	78	0	Q8NA10|Q9BWL1	Missense_Mutation	SNP	ENST00000306823.6	37	CCDS32774.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.318714	0.41096	.	.	ENSG00000169727	ENST00000392358;ENST00000306823;ENST00000355130	.	.	.	4.61	3.63	0.41609	.	.	.	.	.	T	0.40546	0.1121	N	0.19112	0.55	0.58432	D	0.999996	B;P;B;P;P	0.49358	0.005;0.874;0.009;0.577;0.923	B;B;B;B;P	0.45276	0.014;0.283;0.031;0.137;0.475	T	0.18209	-1.0344	8	0.31617	T	0.26	.	12.9552	0.58424	0.3093:0.6907:0.0:0.0	.	88;136;96;96;136	B4DND6;A8K070;Q13098-5;Q13098;Q13098-7	.;.;.;CSN1_HUMAN;.	S	136;96;136	.	ENSP00000302873:R96S	R	+	1	0	GPS1	77605192	1.000000	0.71417	0.997000	0.53966	0.904000	0.53231	4.408000	0.59761	1.126000	0.42016	0.563000	0.77884	CGC	C|0.999;T|0.000		0.632	GPS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442176.1	NM_212492		A	80011903	C	A	80011903	3	1	124	1	0	0	0	0	1	0	0	0	6753	652	23	4	453	4	GPS1	17	80011903	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	61830492	80011903	1183307	96	10862											
MRO	83876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	48331527	48331527	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctgatttacttacgtcAtctaataaagtcctggtctg	9	18	6	8	1	4	1	1	1	3	0	5	1	5	1	1	1	2	0	1	1	5	7			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr18:48331527A>G	ENST00000428869.2	-	6	684	c.426T>C	c.(424-426)gaT>gaC	p.D142D	MRO_ENST00000431965.2_Silent_p.D156D|MRO_ENST00000588444.1_Silent_p.D142D|MRO_ENST00000587291.1_5'UTR|MRO_ENST00000256425.2_Silent_p.D142D|MRO_ENST00000436348.2_Silent_p.D156D|MRO_ENST00000398439.3_Silent_p.D142D			Q9BYG7	MSTRO_HUMAN	maestro	142						nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		TACTTACGTCATCTAATAAAG	0.448																																					p.D156D		.											.	MRO-90	0			c.T468C						.						85	81	82					18																	48331527		2203	4300	6503	SO:0001819	synonymous_variant	83876	exon4			TACGTCATCTAAT	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"maestro heat-like repeat containing"	24121	protein-coding gene	gene with protein product	"B29 protein", "beside the Ma29 deletion"	608080	"chromosome 18 open reading frame 3"	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.426T>C	18.37:g.48331527A>G		Somatic	120	1		WXS	Illumina HiSeq	Phase_I	87	34	NM_001127175	0	0	0	0	0	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Silent	SNP	ENST00000428869.2	37	CCDS11947.1																																																																																			.		0.448	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939		G	48331527	A	G	48331527	2	3	124	1	0	0	0	0	0	0	0	1	9797	214	8	3		3	MRO	18	48331527	Silent	SNP	A	TCGA-GL-8500-01A-11D-2396-08		48331527	29745721	97	10863											
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56056373	56056373	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactggagacagcattctatTtacaagaacggctactgccc	12	9	9	11	1	1	2	0	0	1	2	1	4	1	2	1	2	5	2	1	2	5	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr18:56056373T>C	ENST00000400345.3	+	28	2887	c.2604T>C	c.(2602-2604)atT>atC	p.I868I	NEDD4L_ENST00000586263.1_Silent_p.I840I|NEDD4L_ENST00000256830.9_Silent_p.I764I|NEDD4L_ENST00000356462.6_Silent_p.I804I|NEDD4L_ENST00000256832.7_Silent_p.I728I|NEDD4L_ENST00000435432.2_Silent_p.I727I|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000456986.1_Silent_p.I747I|NEDD4L_ENST00000456173.2_Silent_p.I727I|NEDD4L_ENST00000357895.5_Silent_p.I860I|NEDD4L_ENST00000431212.2_Silent_p.I747I|NEDD4L_ENST00000382850.4_Silent_p.I848I	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	868	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						AGCATTCTATTTACAAGAACG	0.522																																					p.I868I		.											.	NEDD4L-658	0			c.T2604C						.						89	89	89					18																	56056373		1976	4155	6131	SO:0001819	synonymous_variant	23327	exon28			TTCTATTTACAAG	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.2604T>C	18.37:g.56056373T>C		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_001144967	0	0	33	33	0	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	37	CCDS45872.1																																																																																			.		0.522	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	56056373	T	C	56056373	2	2	124	1	0	0	0	0	0	0	0	1	10337	1829	64	3		3	NEDD4L	18	56056373	Silent	SNP	T	TCGA-GL-8500-01A-11D-2396-08	7724846	56056373	22020875	98	10864											
LINGO3	645191	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	2290213	2290213	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggatggtggtgaggtcgagCggcgcgcgcagggccgccag	6	4	21	10	6	0	1	0	1	0	0	1	3	0	2	2	6	1	1	2	6	0	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:2290213C>T	ENST00000585527.1	-	1	1810	c.1563G>A	c.(1561-1563)ccG>ccA	p.P521P	LINGO3_ENST00000404279.1_Silent_p.P521P			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	521						integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						TGAGGTCGAGCGGCGCGCGCA	0.706																																					p.P521P		.											.	.	0			c.G1563A						.						20	25	24					19																	2290213		2039	4177	6216	SO:0001819	synonymous_variant	645191	exon2			GTCGAGCGGCGCG	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"Immunoglobulin superfamily / I-set domain containing"	21206	protein-coding gene	gene with protein product		609792	"leucine rich repeat neuronal 6B"	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.1563G>A	19.37:g.2290213C>T		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	59	23	NM_001101391	0	0	0	0	0		Silent	SNP	ENST00000585527.1	37	CCDS45905.1																																																																																			.		0.706	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391		T	2290213	C	T	2290213	2	4	124	1	0	0	0	0	0	0	0	1	8839	755	27	1		1	LINGO3	19	2290213	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08		2290213	56838770	99	10865											
ZNF557	79230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7075688	7075688	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcttccctgttcccagcCtctcagcgagaaggacacac	8	9	8	16	1	2	1	1	0	2	1	5	3	4	2	3	1	2	1	3	1	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:7075688C>G	ENST00000439035.2	+	4	273	c.33C>G	c.(31-33)gcC>gcG	p.A11A	ZNF557_ENST00000252840.6_Silent_p.A18A|ZNF557_ENST00000414706.1_Silent_p.A18A			Q8N988	ZN557_HUMAN	zinc finger protein 557	11					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		TGTTCCCAGCCTCTCAGCGAG	0.532																																					p.A18A		.											.	ZNF557-92	0			c.C54G						.						132	139	136					19																	7075688		2203	4300	6503	SO:0001630	splice_region_variant	79230	exon4			CCCAGCCTCTCAG	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.32-1C>G	19.37:g.7075688C>G		Somatic	140	0		WXS	Illumina HiSeq	Phase_I	108	52	NM_001044387	0	0	4	4	0	Q6PEJ3|Q9BTZ1	Silent	SNP	ENST00000439035.2	37	CCDS45945.1																																																																																			.		0.532	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341	Silent	G	7075688	C	G	7075688	5	3	124	1	0	0	0	0	0	0	1	0	18020	695	24	4	60	4	ZNF557	19	7075688	Splice_Site	SNP	C	TCGA-GL-8500-01A-11D-2396-08	4785475	7075688	52053295	100	10866											
CTXN1	404217	hgsc.bcm.edu	37	chr19	7990272	7990272	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtaggggtcgagcaggatgCgcacgcagcgcaccatcaac	10	5	14	12	4	1	0	1	0	0	0	2	2	1	1	1	3	4	5	1	3	2	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:7990272C>T	ENST00000318978.4	-	2	371	c.152G>A	c.(151-153)cGc>cAc	p.R51H	CTD-3193O13.8_ENST00000594308.1_RNA|TIMM44_ENST00000598968.1_5'Flank	NM_206833.3	NP_996664.1	P60606	CTXN1_HUMAN	cortexin 1	51						integral component of membrane (GO:0016021)				ovary(1)	1						GAGCAGGATGCGCACGCAGCG	0.701																																					p.R51H		.											.	CTXN1-69	0			c.G152A						.						21	22	22					19																	7990272		2178	4290	6468	SO:0001583	missense	404217	exon2			AGGATGCGCACGC	AK098834	CCDS12191.1	19p13.2	2012-10-02			ENSG00000178531	ENSG00000178531			31108	protein-coding gene	gene with protein product		600135					Standard	NM_206833		Approved	FLJ25968	uc002miy.4	P60606		ENST00000318978.4:c.152G>A	19.37:g.7990272C>T	ENSP00000313226:p.Arg51His	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	30	3	NM_206833	0	0	35	35	0		Missense_Mutation	SNP	ENST00000318978.4	37	CCDS12191.1	.	.	.	.	.	.	.	.	.	.	C	35	5.551234	0.96501	.	.	ENSG00000178531	ENST00000318978	T	0.39592	1.07	4.36	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.64789	0.2630	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.70722	-0.4794	9	0.87932	D	0	-4.8528	14.8225	0.70085	0.0:1.0:0.0:0.0	.	51	P60606	CTXN1_HUMAN	H	51	ENSP00000313226:R51H	ENSP00000313226:R51H	R	-	2	0	CTXN1	7896272	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.412000	0.80091	2.167000	0.68274	0.442000	0.29010	CGC	.		0.701	CTXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461614.1			T	7990272	C	T	7990272	3	4	124	1	0	0	0	0	1	0	0	0	4055	768	27	1	100	1	CTXN1	19	7990272	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	914584	7990272	51138711	101	10867											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13318726	13318726	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcgggggccccgagcCgccggccttacggatcacag	5	5	15	16	5	1	0	1	0	0	0	1	2	1	1	5	4	4	1	5	4	1	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:13318726C>T	ENST00000360228.5	-	47	6921	c.6922G>A	c.(6922-6924)Ggc>Agc	p.G2308S	CACNA1A_ENST00000573710.2_3'UTR	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2309					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCCCCGAGCCGCCGGCCTTA	0.756																																					p.G2308S		.											.	CACNA1A-67	0			c.G6922A						.						1	1	1					19																	13318726		584	1526	2110	SO:0001583	missense	773	exon47			CCGAGCCGCCGGC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6922G>A	19.37:g.13318726C>T	ENSP00000353362:p.Gly2308Ser	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	2	NM_001127222	0	0	0	0	0	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	c	6.449	0.451029	0.12223	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018	D	0.95238	-3.65	3.04	-1.56	0.08532	.	0.773330	0.09942	U	0.735832	T	0.78868	0.4351	N	0.01352	-0.895	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.70296	-0.4911	10	0.19590	T	0.45	.	4.3532	0.11165	0.1658:0.4876:0.0:0.3466	.	2314;2308;2297	E9PD31;Q9NS88;E7EVF2	.;.;.	S	2308;2314;2297	ENSP00000353362:G2308S	ENSP00000349520:G2297S	G	-	1	0	CACNA1A	13179726	.	.	0.014000	0.15608	0.880000	0.50808	.	.	-0.118000	0.11851	0.281000	0.19383	GGC	.		0.756	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13318726	C	T	13318726	3	4	124	1	0	0	0	0	1	0	0	0	2544	652	23	1	602	1	CACNA1A	19	13318726	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	5328454	13318726	45810257	102	10868											
CACNA1A	773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	13346025	13346025	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagggacacgacactcacctGcatcccaatgatggcataga	13	7	9	12	1	1	2	1	1	0	1	2	4	2	3	2	2	1	2	2	2	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:13346025G>A	ENST00000360228.5	-	33	5130	c.5131C>T	c.(5131-5133)Cag>Tag	p.Q1711*	CACNA1A_ENST00000574822.1_5'UTR|CACNA1A_ENST00000573710.2_Nonsense_Mutation_p.Q1712*	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1712					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	ACACTCACCTGCATCCCAATG	0.557											OREG0025293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1712X		.											.	CACNA1A-67	0			c.C5134T						.						44	48	47					19																	13346025		2021	4185	6206	SO:0001587	stop_gained	773	exon33			TCACCTGCATCCC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.5131C>T	19.37:g.13346025G>A	ENSP00000353362:p.Gln1711*	Somatic	21	0	686	WXS	Illumina HiSeq	Phase_I	15	5	NM_001127221	0	0	0	0	0	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Nonsense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	48	14.471052	0.99797	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	.	.	.	5.17	5.17	0.71159	.	0.140928	0.48767	D	0.000167	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.4899	0.87700	0.0:0.0:1.0:0.0	.	.	.	.	X	1711;1717;1712;1712	.	ENSP00000317661:Q1712X	Q	-	1	0	CACNA1A	13207025	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.808000	0.99193	2.411000	0.81874	0.644000	0.83932	CAG	.		0.557	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13346025	G	A	13346025	4	1	124	1	0	0	0	0	0	1	0	0	2544	1328	46	2	2550	2	CACNA1A	19	13346025	Nonsense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	27299	13346025	45782958	103	10869											
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15067322	15067322	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catagcggtgatgagggcttGtagcatgcccccaatgaagg	10	8	14	9	1	0	3	0	3	0	0	0	3	0	3	2	3	3	3	2	3	4	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:15067322G>T	ENST00000221742.3	-	6	1142	c.1135C>A	c.(1135-1137)Caa>Aaa	p.Q379K	SLC1A6_ENST00000430939.2_Missense_Mutation_p.Q315K|SLC1A6_ENST00000600144.1_Intron	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	379					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						ATGAGGGCTTGTAGCATGCCC	0.582																																					p.Q379K		.											.	SLC1A6-186	0			c.C1135A						.						162	123	136					19																	15067322		2203	4300	6503	SO:0001583	missense	6511	exon6			GGGCTTGTAGCAT		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"Solute carriers"	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1135C>A	19.37:g.15067322G>T	ENSP00000221742:p.Gln379Lys	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	33	2	NM_005071	0	0	41	41	0	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	g	19.15	3.770991	0.69992	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.58506	0.33;0.34	3.96	3.96	0.45880	.	0.195990	0.47852	D	0.000202	T	0.68531	0.3011	M	0.64676	1.99	0.80722	D	1	D;P	0.56968	0.978;0.88	P;P	0.59012	0.85;0.598	T	0.73347	-0.4011	10	0.87932	D	0	-11.7811	13.8869	0.63714	0.0:0.0:1.0:0.0	.	315;379	E7EV13;P48664	.;EAA4_HUMAN	K	315;379	ENSP00000409386:Q315K;ENSP00000221742:Q379K	ENSP00000221742:Q379K	Q	-	1	0	SLC1A6	14928322	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	7.423000	0.80229	2.225000	0.72522	0.591000	0.81541	CAA	.		0.582	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15067322	G	T	15067322	3	4	124	1	0	0	0	0	1	0	0	0	14468	1386	48	4	575	4	SLC1A6	19	15067322	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	1721297	15067322	44061661	104	10870											
GDF15	9518	hgsc.bcm.edu	37	chr19	18499142	18499142	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgcgtatctctcgggcCgcccttcccgaggggctccc	3	8	11	19	4	1	0	0	0	1	0	5	1	3	0	5	3	1	2	5	3	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:18499142C>A	ENST00000252809.3	+	2	356	c.324C>A	c.(322-324)gcC>gcA	p.A108A	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	108					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						TCTCTCGGGCCGCCCTTCCCG	0.687											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A108A		.											.	GDF15-650	0			c.C324A						.						18	21	20					19																	18499142		2174	4281	6455	SO:0001819	synonymous_variant	9518	exon2			TCGGGCCGCCCTT	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.324C>A	19.37:g.18499142C>A		Somatic	67	0	726	WXS	Illumina HiSeq	Phase_I	48	3	NM_004864	0	1	187	191	3	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																			.		0.687	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		A	18499142	C	A	18499142	2	1	124	1	0	0	0	0	0	0	0	1	6333	639	23	4		4	GDF15	19	18499142	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	3431820	18499142	40629841	105	10871											
ZNF461	92283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	37147417	37147417	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcccttgctccaatgaggaGattacggctggcttagaaac	10	11	10	10	1	0	3	0	1	0	2	2	4	2	3	2	3	3	3	2	3	4	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:37147417G>C	ENST00000588268.1	-	4	392	c.165C>G	c.(163-165)atC>atG	p.I55M	ZNF461_ENST00000360357.4_Missense_Mutation_p.I55M	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CCAATGAGGAGATTACGGCTG	0.443																																					p.I55M		.											.	.	0			c.C165G						.						72	74	73					19																	37147417		2068	4232	6300	SO:0001583	missense	92283	exon4			TGAGGAGATTACG	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"Zinc fingers, C2H2-type", "-"	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.165C>G	19.37:g.37147417G>C	ENSP00000467931:p.Ile55Met	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	78	32	NM_153257	0	0	0	0	0	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306002	0.40795	.	.	ENSG00000197808	ENST00000396893;ENST00000360357	T	0.00912	5.55	3.27	-0.373	0.12516	Krueppel-associated box (3);	.	.	.	.	T	0.05090	0.0136	M	0.88704	2.975	0.09310	N	1	D;D	0.64830	0.994;0.994	D;D	0.76071	0.987;0.987	T	0.14364	-1.0475	9	0.87932	D	0	.	5.9972	0.19501	0.3696:0.0:0.6304:0.0	.	55;55	B4DRP8;Q8TAF7	.;ZN461_HUMAN	M	55	ENSP00000353515:I55M	ENSP00000353515:I55M	I	-	3	3	ZNF461	41839257	0.882000	0.30256	0.011000	0.14972	0.955000	0.61496	0.417000	0.21214	-0.071000	0.12886	0.585000	0.79938	ATC	.		0.443	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		C	37147417	G	C	37147417	3	2	124	1	0	0	0	0	1	0	0	0	17957	932	33	4	1538	4	ZNF461	19	37147417	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	18648275	37147417	21981566	106	10872											
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39058443	39058443	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggagaaggaagaagttccCgagcccacaccagagccccc	12	2	13	14	1	0	3	0	0	0	3	1	6	1	4	5	3	2	1	5	3	3	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:39058443C>T	ENST00000359596.3	+	93	13545	c.13545C>T	c.(13543-13545)ccC>ccT	p.P4515P	RYR1_ENST00000355481.4_Silent_p.P4510P|RYR1_ENST00000360985.3_Silent_p.P4510P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4515	Pro-rich.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AAGAAGTTCCCGAGCCCACAC	0.577																																					p.P4515P		.											.	RYR1-100	0			c.C13545T						.						88	94	92					19																	39058443		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon93			AGTTCCCGAGCCC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.13545C>T	19.37:g.39058443C>T		Somatic	137	2		WXS	Illumina HiSeq	Phase_I	84	24	NM_000540	0	0	1	1	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			.		0.577	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39058443	C	T	39058443	2	4	124	1	0	0	0	0	0	0	0	1	13800	639	23	1		1	RYR1	19	39058443	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	1911026	39058443	20070540	107	10873											
ERCC2	2068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45868315	45868315	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacctcatagaatcggcaGtggggcaggctggtgtcatg	9	9	15	8	1	2	1	2	0	0	1	3	1	2	1	1	5	1	4	1	5	3	2	rs139263710		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:45868315G>A	ENST00000391945.4	-	6	539	c.462C>T	c.(460-462)caC>caT	p.H154H	ERCC2_ENST00000221481.6_Intron|ERCC2_ENST00000391944.3_Intron|ERCC2_ENST00000485403.2_Silent_p.H130H|ERCC2_ENST00000391940.4_Silent_p.H130H	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	154	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AGAATCGGCAGTGGGGCAGGC	0.637			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.H154H		.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"		E	.	ERCC2-848	0			c.C462T						.						61	55	57					19																	45868315		2203	4300	6503	SO:0001819	synonymous_variant	2068	exon6	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCGGCAGTGGGGC		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"General transcription factor IIH complex subunits"	3434	protein-coding gene	gene with protein product	"excision repair cross-complementing rodent repair deficiency, complementation group 2 protein", "TFIIH basal transcription factor complex helicase XPB subunit"	126340	"xeroderma pigmentosum complementary group D", "excision repair cross-complementing rodent repair deficiency, complementation group 2"	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.462C>T	19.37:g.45868315G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	50	23	NM_000400	0	0	9	18	9	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Silent	SNP	ENST00000391945.4	37	CCDS33049.1																																																																																			G|1.000;C|0.000		0.637	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		A	45868315	G	A	45868315	2	1	124	1	0	0	0	0	0	0	0	1	5226	1020	36	2		2	ERCC2	19	45868315	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	6809872	45868315	13260668	108	10874											
BAX	581	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	49464330	49464330	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatcatcagatgtggtctaTaatgcgttttccttacgtgt	9	16	9	7	2	3	2	2	0	1	2	4	2	4	2	1	1	2	1	1	1	3	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:49464330T>C	ENST00000345358.7	+	5	526				BAX_ENST00000354470.3_Intron|CTD-2639E6.9_ENST00000599784.1_lincRNA|BAX_ENST00000539787.1_Intron|BAX_ENST00000391871.3_Intron|BAX_ENST00000415969.2_Intron|BAX_ENST00000293288.8_Silent_p.Y211Y	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		ATGTGGTCTATAATGCGTTTT	0.567																																					p.Y211Y		.											.	BAX-1271	0			c.T633C						.						89	63	72					19																	49464330		2176	4278	6454	SO:0001627	intron_variant	581	exon5			GGTCTATAATGCG		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.474+159T>C	19.37:g.49464330T>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	96	45	NM_004324	0	0	7	13	6	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Silent	SNP	ENST00000345358.7	37	CCDS12742.1																																																																																			.		0.567	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		C	49464330	T	C	49464330	1	2	124	0	1	0	0	0	0	0	0	0	1329	1413	49	3		3	BAX	19	49464330	Intron	SNP	T	TCGA-GL-8500-01A-11D-2396-08	3596015	49464330	9664653	109	10875											
ZNF321	399669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53432286	53432286	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaattctttgggatgtcAaaattaaggaggcattgatg	15	12	11	3	0	2	2	1	1	1	1	2	4	2	4	0	3	0	1	0	3	5	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:53432286A>G	ENST00000391777.3	-	4	693	c.572T>C	c.(571-573)tTg>tCg	p.L191S	ZNF816_ENST00000434371.2_Missense_Mutation_p.L191S|ZNF816-ZNF321P_ENST00000313956.4_RNA|ZNF816_ENST00000549216.1_Missense_Mutation_p.L122S			Q8N8H1	ZN321_HUMAN	zinc finger protein 321, pseudogene	122										endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TTGGGATGTCAAAATTAAGGA	0.373																																					p.L191S		.											.	.	0			c.T572C						.						94	100	98					19																	53432286		2185	4293	6478	SO:0001583	missense	100529240	exon4			GATGTCAAAATTA	AK096828		19q13.4	2013-01-08	2011-04-19	2011-04-19	ENSG00000221874	ENSG00000221874			13827	pseudogene	pseudogene			"zinc finger protein 321"	ZNF321			Standard	NR_037805		Approved	MGC35402		Q8N8H1	OTTHUMG00000167760	ENST00000391777.3:c.572T>C	19.37:g.53432286A>G	ENSP00000375656:p.Leu191Ser	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	200	89	NM_001202473	0	0	3	4	1	B7ZB38|Q68DZ0|Q86SS5	Missense_Mutation	SNP	ENST00000391777.3	37	CCDS56101.1	.	.	.	.	.	.	.	.	.	.	g	0.886	-0.727124	0.03158	.	.	ENSG00000180257;ENSG00000180257;ENSG00000221874	ENST00000549216;ENST00000434371;ENST00000391777	T;T;T	0.01252	5.1;5.95;5.95	1.78	-0.553	0.11815	.	.	.	.	.	T	0.00412	0.0013	N	0.00337	-1.62	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46512	-0.9186	9	0.02654	T	1	.	4.0322	0.09714	0.4322:0.0:0.5678:0.0	.	122	Q8N8H1	ZN321_HUMAN	S	122;191;191	ENSP00000449832:L122S;ENSP00000438519:L191S;ENSP00000375656:L191S	ENSP00000375656:L191S	L	-	2	0	ZNF321P;ZNF816	58124098	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.088000	0.14979	0.107000	0.17824	-1.981000	0.00455	TTG	.		0.373	ZNF321P-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000396130.1	NR_037805		G	53432286	A	G	53432286	3	3	124	1	0	0	0	0	1	0	0	0	17872	131	5	3	133	3	ZNF321	19	53432286	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	3967956	53432286	5696697	110	10876											
NLRP9	338321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56244868	56244868	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacaggtttccttctcccatAtgagttgaaatgtttccttc	8	16	7	10	0	1	2	0	2	1	0	5	3	3	2	3	1	0	3	3	1	2	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:56244868A>T	ENST00000332836.2	-	2	356	c.329T>A	c.(328-330)aTa>aAa	p.I110K		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	110						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		CTTCTCCCATATGAGTTGAAA	0.363																																					p.I110K		.											.	NLRP9-294	0			c.T329A						.						122	122	122					19																	56244868		2203	4300	6503	SO:0001583	missense	338321	exon2			TCCCATATGAGTT	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"Nucleotide-binding domain and leucine rich repeat containing"	22941	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"	609663	"NACHT, leucine rich repeat and PYD containing 9"	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.329T>A	19.37:g.56244868A>T	ENSP00000331857:p.Ile110Lys	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	124	57	NM_176820	0	0	0	0	0	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559517	0.45590	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.73897	-0.79	3.4	3.4	0.38934	.	.	.	.	.	T	0.60996	0.2312	L	0.39898	1.24	0.18873	N	0.999985	P	0.42827	0.791	B	0.36719	0.231	T	0.49925	-0.8887	9	0.29301	T	0.29	.	8.4613	0.32929	1.0:0.0:0.0:0.0	.	110	Q7RTR0	NALP9_HUMAN	K	110	ENSP00000331857:I110K	ENSP00000331857:I110K	I	-	2	0	NLRP9	60936680	0.004000	0.15560	0.004000	0.12327	0.074000	0.17049	1.274000	0.33132	1.588000	0.49971	0.524000	0.50904	ATA	.		0.363	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56244868	A	T	56244868	3	4	124	1	0	0	0	0	1	0	0	0	10510	449	16	5	2678	5	NLRP9	19	56244868	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	2812582	56244868	2884115	111	10877											
ZNF749	388567	hgsc.bcm.edu	37	chr19	57954667	57954667	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttcttacaggttgttggCatggagccaaggatgaggag	9	11	15	6	0	1	1	0	1	1	0	1	4	1	4	1	5	2	4	1	5	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:57954667C>G	ENST00000334181.4	+	3	401	c.151C>G	c.(151-153)Cat>Gat	p.H51D	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|lung(3)|prostate(1)	13		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		AGGTTGTTGGCATGGAGCCAA	0.507																																					p.H51D		.											.	.	0			c.C151G						.						67	64	65					19																	57954667		2203	4300	6503	SO:0001583	missense	388567	exon3			TGTTGGCATGGAG	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"Zinc fingers, C2H2-type", "-"	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.151C>G	19.37:g.57954667C>G	ENSP00000333980:p.His51Asp	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_001023561	0	0	0	0	0		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	C	12.76	2.033661	0.35893	.	.	ENSG00000186230	ENST00000334181	T	0.00801	5.68	2.07	-0.28	0.12886	Krueppel-associated box (3);	.	.	.	.	T	0.00815	0.0027	L	0.34521	1.04	0.09310	N	1	P	0.47409	0.895	B	0.38156	0.266	T	0.53683	-0.8404	9	0.35671	T	0.21	.	6.3111	0.21164	0.0:0.7049:0.0:0.2951	.	51	O43361	ZN749_HUMAN	D	51	ENSP00000333980:H51D	ENSP00000333980:H51D	H	+	1	0	ZNF749	62646479	0.000000	0.05858	0.014000	0.15608	0.316000	0.28119	-1.407000	0.02488	0.007000	0.14760	0.313000	0.20887	CAT	.		0.507	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561		G	57954667	C	G	57954667	3	3	124	1	0	0	0	0	1	0	0	0	18163	710	25	4	161	4	ZNF749	19	57954667	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	1709799	57954667	1174316	112	10878											
MZF1	7593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr19	59073766	59073766	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggccgcactcaccgcaGtggtagggcttttcgccggt	5	8	13	15	4	1	0	1	0	0	0	2	0	1	0	4	4	0	4	4	4	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:59073766G>T	ENST00000215057.2	-	6	2438	c.1878C>A	c.(1876-1878)caC>caA	p.H626Q	AC016629.8_ENST00000600534.1_RNA|AC016629.8_ENST00000593642.1_RNA|MZF1_ENST00000599369.1_Missense_Mutation_p.H626Q|AC016629.8_ENST00000600726.1_RNA|MZF1_ENST00000594234.1_3'UTR	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	626					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		ACTCACCGCAGTGGTAGGGCT	0.682																																					p.H626Q		.											.	MZF1-91	0			c.C1878A						.						33	25	28					19																	59073766		2201	4300	6501	SO:0001583	missense	7593	exon6			ACCGCAGTGGTAG	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.1878C>A	19.37:g.59073766G>T	ENSP00000215057:p.His626Gln	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	17	11	NM_198055	0	0	6	15	9	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	G	8.359	0.832673	0.16820	.	.	ENSG00000099326	ENST00000215057	T	0.16073	2.37	3.21	2.17	0.27698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.732947	0.11236	N	0.585150	T	0.04272	0.0118	N	0.00315	-1.66	0.25952	N	0.982731	B	0.27286	0.174	B	0.34722	0.188	T	0.43540	-0.9385	10	0.15499	T	0.54	-9.8517	4.7075	0.12856	0.1258:0.2248:0.6494:0.0	.	626	P28698	MZF1_HUMAN	Q	626	ENSP00000215057:H626Q	ENSP00000215057:H626Q	H	-	3	2	MZF1	63765578	0.000000	0.05858	0.908000	0.35775	0.900000	0.52787	-0.753000	0.04792	0.925000	0.37094	-0.379000	0.06801	CAC	.		0.682	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		T	59073766	G	T	59073766	3	4	124	1	0	0	0	0	1	0	0	0	10133	1020	36	4	330	4	MZF1	19	59073766	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	1119099	59073766	55217	113	10879											
SIRPA	140885	hgsc.bcm.edu	37	chr20	1895835	1895835	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccactctgcgctgcactgCgacctctctgatccctgtgg	5	10	10	16	2	2	1	0	1	2	0	4	2	3	1	3	1	4	2	3	1	0	0	rs17855612	byFrequency	TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr20:1895835C>T	ENST00000358771.4	+	2	322	c.170C>T	c.(169-171)gCg>gTg	p.A57V	SIRPA_ENST00000356025.3_Missense_Mutation_p.A57V|SIRPA_ENST00000400068.3_Missense_Mutation_p.A57V	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	57	Ig-like V-type.		A -> V (in dbSNP:rs17855612). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CGCTGCACTGCGACCTCTCTG	0.582													C|||	1319	0.263379	0.1445	0.304	5008	,	,		11273	0.4474		0.1849	False		,,,				2504	0.2863				p.A57V	GBM(155;1668 1920 5945 42733 48121)	.											.	SIRPA-227	0			c.C170T						.	C	VAL/ALA,VAL/ALA,VAL/ALA	91,4161		1,89,2036	54	48	50		170,170,170	0.1	0	20	dbSNP_123	50	318,7874		0,318,3778	yes	missense,missense,missense	SIRPA	NM_001040022.1,NM_001040023.1,NM_080792.2	64,64,64	1,407,5814	TT,TC,CC		3.8818,2.1402,3.2867	benign,benign,benign	57/505,57/505,57/505	1895835	409,12035	2126	4096	6222	SO:0001583	missense	140885	exon3			GCACTGCGACCTC	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	9662	protein-coding gene	gene with protein product		602461	"protein tyrosine phosphatase, non-receptor type substrate 1"	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.170C>T	20.37:g.1895835C>T	ENSP00000351621:p.Ala57Val	Somatic	53	2		WXS	Illumina HiSeq	Phase_I	41	5	NM_001040022	0	0	10	10	0	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	706	0.3232600732600733	88	0.17886178861788618	117	0.32320441988950277	308	0.5384615384615384	193	0.2546174142480211	C	0.148	-1.095121	0.01858	0.021402	0.038818	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.63913	-0.07;-0.07;-0.07	5.11	0.0951	0.14484	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.016370	0.07877	N	0.968974	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.42344	-0.9457	9	0.02654	T	1	.	8.9342	0.35688	0.0:0.2455:0.0:0.7545	rs17855612	37;57;57	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	V	57	ENSP00000382941:A57V;ENSP00000348307:A57V;ENSP00000351621:A57V	ENSP00000348307:A57V	A	+	2	0	SIRPA	1843835	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.221000	0.09202	0.089000	0.17243	-2.077000	0.00380	GCG	C|0.677;T|0.323		0.582	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		T	1895835	C	T	1895835	3	4	124	1	0	0	0	0	1	0	0	0	14364	768	27	1	176	1	SIRPA	20	1895835	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		1895835	61129685	114	10880											
CPXM1	56265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	2776796	2776796	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccctcggcccagcccacCagctctgaaccctgccgggc	5	4	11	21	3	1	1	0	1	1	0	2	1	1	1	6	3	4	1	6	3	1	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr20:2776796C>G	ENST00000380605.2	-	10	1318	c.1254G>C	c.(1252-1254)ctG>ctC	p.L418L		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	418					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CCCAGCCCACCAGCTCTGAAC	0.602																																					p.L418L		.											.	CPXM1-94	0			c.G1254C						.						56	59	58					20																	2776796		2203	4300	6503	SO:0001819	synonymous_variant	56265	exon10			GCCCACCAGCTCT	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"carboxypeptidase-like protein X1"	609555	"carboxypeptidase X (M14 family)"	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.1254G>C	20.37:g.2776796C>G		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	83	32	NM_001184699	0	0	0	0	0	Q6P4G8|Q6UW65|Q9NUB5	Silent	SNP	ENST00000380605.2	37	CCDS13033.1																																																																																			.		0.602	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		G	2776796	C	G	2776796	2	3	124	1	0	0	0	0	0	0	0	1	3843	581	21	4		4	CPXM1	20	2776796	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	880961	2776796	60248724	115	10881											
MACROD2	140733	hgsc.bcm.edu	37	chr20	14066372	14066372	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggtagatgctatagtcaatgCcggtgagtagttgattttcc	9	14	12	6	1	1	3	1	2	0	1	2	3	2	3	2	2	2	4	2	2	5	7			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr20:14066372C>T	ENST00000310348.4	+	3	269	c.269C>T	c.(268-270)gCc>gTc	p.A90V	MACROD2_ENST00000217246.4_Missense_Mutation_p.A90V			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	90	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.|Substrate binding.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ATAGTCAATGCCGGTGAGTAG	0.308																																					p.A90V		.											.	MACROD2-22	0			c.C269T						.						86	80	81					20																	14066372		1830	4077	5907	SO:0001583	missense	140733	exon3			TCAATGCCGGTGA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"chromosome 20 open reading frame 133"	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.269C>T	20.37:g.14066372C>T	ENSP00000309809:p.Ala90Val	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_080676	0	0	0	0	0	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650091	0.87958	.	.	ENSG00000172264	ENST00000217246;ENST00000310348	T;T	0.44083	0.93;0.93	5.97	5.97	0.96955	Appr-1-p processing (3);	0.064305	0.64402	D	0.000009	T	0.79488	0.4454	H	0.98559	4.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	D	0.86855	0.2026	10	0.87932	D	0	-7.7929	17.9263	0.88985	0.0:1.0:0.0:0.0	.	90;90	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	V	90	ENSP00000217246:A90V;ENSP00000309809:A90V	ENSP00000217246:A90V	A	+	2	0	MACROD2	14014372	1.000000	0.71417	0.992000	0.48379	0.876000	0.50452	5.209000	0.65208	2.833000	0.97629	0.585000	0.79938	GCC	.		0.308	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		T	14066372	C	T	14066372	3	4	124	1	0	0	0	0	1	0	0	0	9171	739	26	2	279	2	MACROD2	20	14066372	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	11289576	14066372	48959148	116	10882											
HUNK	30811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	33371363	33371363	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgatgggcatcggacagAtgttaaggaagcgccatcag	12	8	13	8	2	1	2	1	1	0	1	2	4	1	4	1	3	1	2	1	3	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr21:33371363A>C	ENST00000270112.2	+	11	2371	c.2011A>C	c.(2011-2013)Atg>Ctg	p.M671L		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	671					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						CATCGGACAGATGTTAAGGAA	0.617																																					p.M671L		.											.	HUNK-334	0			c.A2011C						.						54	60	58					21																	33371363		2203	4300	6503	SO:0001583	missense	30811	exon11			GGACAGATGTTAA	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"hormonally upregulated Neu-associated kinase"			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.2011A>C	21.37:g.33371363A>C	ENSP00000270112:p.Met671Leu	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	114	36	NM_014586	0	0	2	3	1		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935668	0.52972	.	.	ENSG00000142149	ENST00000270112	T	0.68181	-0.31	4.21	4.21	0.49690	.	0.165227	0.51477	D	0.000092	T	0.64148	0.2572	L	0.29908	0.895	0.45354	D	0.998345	P	0.40970	0.734	P	0.50825	0.651	T	0.60727	-0.7206	10	0.25751	T	0.34	-32.4647	13.4793	0.61326	1.0:0.0:0.0:0.0	.	671	P57058	HUNK_HUMAN	L	671	ENSP00000270112:M671L	ENSP00000270112:M671L	M	+	1	0	HUNK	32293234	1.000000	0.71417	0.997000	0.53966	0.204000	0.24138	5.843000	0.69424	1.767000	0.52121	0.482000	0.46254	ATG	.		0.617	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		C	33371363	A	C	33371363	3	2	124	1	0	0	0	0	1	0	0	0	7479	333	12	5	2053	5	HUNK	21	33371363	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		33371363	14758532	117	10883											
TTC3	7267	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	38568034	38568035	+	Frame_Shift_Ins	INS	-	-	T																															ggccaagggcttgtgacttcINStgcaagcgacgtgactggaa																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr21:38568034_38568035insT	ENST00000399017.2	+	42	8023_8024	c.5276_5277insT	c.(5275-5280)tctgcafs	p.A1760fs	TTC3_ENST00000479930.1_3'UTR|TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000355666.1_Frame_Shift_Ins_p.A1760fs|TTC3_ENST00000354749.2_Frame_Shift_Ins_p.A1760fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1760					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CTTGTGACTTCTGCAAGCGACG	0.569																																					p.S1759fs	Ovarian(38;194 1649 35661)	.											.	TTC3-590	0			c.5276_5277insT						.																																			SO:0001589	frameshift_variant	7267	exon42			.	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5277dupT	21.37:g.38568035_38568035dupT	ENSP00000381981:p.Ala1760fs	Somatic	340	0		WXS	Illumina HiSeq	Phase_I	305	129	NM_003316	0	0	0	0	0	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Ins	INS	ENST00000399017.2	37	CCDS13651.1																																																																																			.		0.569	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38568035	-	T	38568034	7	5	124	1	0	1	1	0	0	0	0	0	16730	913	32	0	5438	0	TTC3	21	38568034	Frame_Shift_Ins	INS	-	TCGA-GL-8500-01A-11D-2396-08	5196671	38568034	9561861	118	10884											
MICAL3	57553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18293513	18293513	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctcctgcttggcctgtcTccgagctgccttttgcacac	3	13	8	17	1	1	0	0	0	1	0	4	1	3	0	5	1	4	3	5	1	0	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:18293513T>C	ENST00000441493.2	-	28	5864	c.5512A>G	c.(5512-5514)Aga>Gga	p.R1838G	XXbac-B461K10.4_ENST00000476405.1_RNA|MICAL3_ENST00000580469.1_5'UTR	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1838					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		TTGGCCTGTCTCCGAGCTGCC	0.572																																					p.R1838G		.											.	MICAL3-68	0			c.A5512G						.						92	98	96					22																	18293513		2184	4283	6467	SO:0001583	missense	57553	exon28			CCTGTCTCCGAGC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.5512A>G	22.37:g.18293513T>C	ENSP00000416015:p.Arg1838Gly	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	76	26	NM_015241	0	0	17	21	4	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.051801	0.55218	.	.	ENSG00000093100	ENST00000441493	T	0.68025	-0.3	4.81	4.81	0.61882	.	0.102956	0.64402	D	0.000009	T	0.70631	0.3246	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	T	0.69146	-0.5222	9	.	.	.	.	11.1121	0.48239	0.0:0.0:0.1547:0.8453	.	1838	Q7RTP6	MICA3_HUMAN	G	1838	ENSP00000416015:R1838G	.	R	-	1	2	XXbac-B461K10.4	16673513	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.991000	0.49409	1.799000	0.52666	0.379000	0.24179	AGA	.		0.572	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			C	18293513	T	C	18293513	3	2	124	1	0	0	0	0	1	0	0	0	9596	1559	54	3	516	3	MICAL3	22	18293513	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08		18293513	33011053	119	10885											
MTMR3	8897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30413918	30413918	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctcccccctcctcaggtGctgtaccctgtgtgccatgt	3	12	9	17	0	1	0	1	0	0	0	4	0	4	0	7	1	3	2	7	1	1	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:30413918G>T	ENST00000401950.2	+	16	2019	c.1677G>T	c.(1675-1677)gtG>gtT	p.V559V	MTMR3_ENST00000333027.3_Silent_p.V559V|MTMR3_ENST00000351488.3_Silent_p.V559V|CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000323630.5_Silent_p.V423V|MTMR3_ENST00000406629.1_Silent_p.V559V|CTA-85E5.10_ENST00000429350.1_RNA	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	559	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CTCCTCAGGTGCTGTACCCTG	0.552																																					p.V559V		.											.	MTMR3-292	0			c.G1677T						.						194	153	167					22																	30413918		2203	4300	6503	SO:0001819	synonymous_variant	8897	exon16			TCAGGTGCTGTAC	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.1677G>T	22.37:g.30413918G>T		Somatic	193	1		WXS	Illumina HiSeq	Phase_I	171	55	NM_153050	0	0	1	1	0	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			.		0.552	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		T	30413918	G	T	30413918	2	4	124	1	0	0	0	0	0	0	0	1	9970	1306	46	4		4	MTMR3	22	30413918	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	12120405	30413918	20890648	120	10886											
POLR2F	5435	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38355418	38355418	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caggccaaccagaagcgaatCaccacaccatacatgaccaa	17	3	6	15	1	1	2	1	1	0	1	1	3	1	2	5	1	3	0	5	1	5	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:38355418C>G	ENST00000442738.2	+	3	281	c.156C>G	c.(154-156)atC>atG	p.I52M	POLR2F_ENST00000407936.1_Missense_Mutation_p.I52M|POLR2F_ENST00000405557.1_Missense_Mutation_p.I52M|POLR2F_ENST00000488684.1_Nonsense_Mutation_p.S72*|POLR2F_ENST00000606538.1_Missense_Mutation_p.I52M|POLR2F_ENST00000460648.1_Intron|POLR2F_ENST00000470701.1_Missense_Mutation_p.I47M	NM_021974.3	NP_068809.1	P61218	RPAB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide F	52					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|urinary_tract(2)	3	Melanoma(58;0.045)					AGAAGCGAATCACCACACCAT	0.577																																					p.I52M		.											.	POLR2F-153	0			c.C156G						.						187	170	176					22																	38355418		2203	4300	6503	SO:0001583	missense	5435	exon3			GCGAATCACCACA		CCDS13963.1	22q13.1	2013-01-21			ENSG00000100142	ENSG00000100142		"RNA polymerase subunits"	9193	protein-coding gene	gene with protein product	"DNA directed RNA polymerase II 14.4 kda polypeptide"	604414				8786150	Standard	XR_112241		Approved	RPB6, HRBP14.4	uc010gxi.3	P61218	OTTHUMG00000151160	ENST00000442738.2:c.156C>G	22.37:g.38355418C>G	ENSP00000403852:p.Ile52Met	Somatic	294	0		WXS	Illumina HiSeq	Phase_I	230	99	NM_021974	0	0	90	209	119	P41584|Q6IAY3	Missense_Mutation	SNP	ENST00000442738.2	37	CCDS13963.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242366	0.79912	.	.	ENSG00000100142	ENST00000442738;ENST00000407936;ENST00000405557	.	.	.	4.98	4.98	0.66077	RNA polymerase subunit, RPB6/omega (1);	0.000000	0.85682	D	0.000000	T	0.67353	0.2884	L	0.60455	1.87	0.80722	D	1	B	0.11235	0.004	B	0.25140	0.058	T	0.65656	-0.6115	9	0.54805	T	0.06	.	18.6213	0.91322	0.0:1.0:0.0:0.0	.	52	P61218	RPAB2_HUMAN	M	52	.	ENSP00000384112:I52M	I	+	3	3	POLR2F	36685364	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.564000	0.53791	2.467000	0.83353	0.655000	0.94253	ATC	.		0.577	POLR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321570.1	NM_021974		G	38355418	C	G	38355418	3	3	124	1	0	0	0	0	1	0	0	0	12245	816	29	4	166	4	POLR2F	22	38355418	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	7941500	38355418	12949148	121	10887											
KDELR3	11015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38875733	38875733	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggcctttccttccttgaaAactacagtttcactctgctg	7	16	6	12	0	2	1	1	1	1	0	4	1	4	1	3	1	3	2	3	1	3	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:38875733A>G	ENST00000216014.4	+	3	500	c.328A>G	c.(328-330)Aac>Gac	p.N110D	KDELR3_ENST00000409006.3_Missense_Mutation_p.N110D|KDELR3_ENST00000471268.1_3'UTR	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	110					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					CTTCCTTGAAAACTACAGTTT	0.473																																					p.N110D	Ovarian(11;103 529 24120 28493 32980)	.											.	KDELR3-92	0			c.A328G						.						226	234	231					22																	38875733		2203	4300	6503	SO:0001583	missense	11015	exon3			CTTGAAAACTACA	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.328A>G	22.37:g.38875733A>G	ENSP00000216014:p.Asn110Asp	Somatic	418	0		WXS	Illumina HiSeq	Phase_I	386	171	NM_016657	0	0	52	110	58	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	37	CCDS13972.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824209	0.90955	.	.	ENSG00000100196	ENST00000216014;ENST00000409006	T;T	0.29142	1.58;1.58	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.89287	3.02	0.80722	D	1	D;D	0.58970	0.984;0.98	D;P	0.64410	0.925;0.823	T	0.66937	-0.5797	10	0.54805	T	0.06	.	13.8085	0.63248	1.0:0.0:0.0:0.0	.	110;110	O43731;O43731-2	ERD23_HUMAN;.	D	110	ENSP00000216014:N110D;ENSP00000386918:N110D	ENSP00000216014:N110D	N	+	1	0	KDELR3	37205679	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	8.916000	0.92745	1.854000	0.53819	0.533000	0.62120	AAC	.		0.473	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			G	38875733	A	G	38875733	3	3	124	1	0	0	0	0	1	0	0	0	8142	14	1	3	338	3	KDELR3	22	38875733	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	520315	38875733	12428833	122	10888											
ZXDB	158586	hgsc.bcm.edu	37	chrX	57619097	57619097	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgctcctgcccagcagcccGggtgtctgatcgccccgcaa	5	6	11	19	4	1	1	0	1	1	0	3	1	2	1	6	1	3	3	6	1	1	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chrX:57619097G>A	ENST00000374888.1	+	1	829	c.616G>A	c.(616-618)Ggg>Agg	p.G206R		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.G206R(2)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						CCAGCAGCCCGGGTGTCTGAT	0.711																																					p.G206R		.											.	ZXDB-130	2	Substitution - Missense(2)	lung(1)|prostate(1)	c.G616A						.						12	14	13					X																	57619097		2186	4257	6443	SO:0001583	missense	158586	exon1			CAGCCCGGGTGTC	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.616G>A	X.37:g.57619097G>A	ENSP00000364023:p.Gly206Arg	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	13	2	NM_007157	0	0	0	4	4	A8K151|Q9UBB3	Missense_Mutation	SNP	ENST00000374888.1	37	CCDS35313.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.654782	0.00108	.	.	ENSG00000198455	ENST00000374888	T	0.11063	2.81	2.65	1.78	0.24846	.	0.160870	0.29602	N	0.011697	T	0.04452	0.0122	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41787	-0.9489	10	0.15952	T	0.53	.	4.3042	0.10938	0.3435:0.0:0.6565:0.0	.	206	P98169	ZXDB_HUMAN	R	206	ENSP00000364023:G206R	ENSP00000364023:G206R	G	+	1	0	ZXDB	57635822	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-0.287000	0.08388	0.520000	0.28426	0.556000	0.70494	GGG	.		0.711	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		A	57619097	G	A	57619097	3	1	124	1	0	0	0	0	1	0	0	0	18283	1116	39	1	618	1	ZXDB	23	57619097	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08		57619097	97651463	123	10889											
MTOR	2475	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11270889	11270889	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accttgacaattctgcagatGagcacatcatagcgctgatg	12	10	9	10	1	2	4	1	3	1	1	2	4	2	4	1	0	3	3	1	0	2	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:11270889G>A	ENST00000361445.4	-	24	3712	c.3636C>T	c.(3634-3636)ctC>ctT	p.L1212L		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1212					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTCTGCAGATGAGCACATCAT	0.403																																					p.L1212L													.	MTOR-1439	0			c.C3636T						.						105	94	98					1																	11270889		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon24			GCAGATGAGCACA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3636C>T	1.37:g.11270889G>A		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	64	8	NM_004958	0	0	3	8	5	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			.		0.403	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		A	11270889	G	A	11270889	2	1	125	1	0	0	0	0	0	0	0	1	9979	1277	45	2		2	MTOR	1	11270889	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		11270889	237979732	1	10890											
MTF1	4520	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38288352	38288352	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcggaacatcactgactGactctgcatcaccattaaaa	14	9	7	11	1	3	2	2	2	1	0	3	3	3	3	1	2	2	1	1	2	3	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:38288352G>T	ENST00000373036.4	-	9	1348	c.1208C>A	c.(1207-1209)tCa>tAa	p.S403*		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	403					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ATCACTGACTGACTCTGCATC	0.438																																					p.S403X													.	MTF1-92	0			c.C1208A						.						59	66	64					1																	38288352		2203	4300	6503	SO:0001587	stop_gained	4520	exon9			CTGACTGACTCTG	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1208C>A	1.37:g.38288352G>T	ENSP00000362127:p.Ser403*	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	42	8	NM_005955	0	0	1	1	0	B2RAK6|Q96CB1	Nonsense_Mutation	SNP	ENST00000373036.4	37	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	G	37	6.559377	0.97663	.	.	ENSG00000188786	ENST00000373036	.	.	.	6.11	6.11	0.99139	.	0.399758	0.26776	N	0.022551	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	.	18.9147	0.92501	0.0:0.0:1.0:0.0	.	.	.	.	X	403	.	ENSP00000362127:S403X	S	-	2	0	MTF1	38060939	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.613000	0.67688	2.906000	0.99361	0.655000	0.94253	TCA	.		0.438	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		T	38288352	G	T	38288352	4	4	125	1	0	0	0	0	0	1	0	0	9947	1294	45	4	1065	4	MTF1	1	38288352	Nonsense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	27017463	38288352	210962269	2	10891											
RIMS3	9783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	41107442	41107442	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcccacgatggccaccatCttggcacccaggctgctccg	7	6	11	17	2	1	0	0	0	1	0	2	1	2	0	5	4	1	3	5	4	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:41107442C>T	ENST00000372684.3	-	3	625	c.156G>A	c.(154-156)aaG>aaA	p.K52K	RIMS3_ENST00000372683.1_Silent_p.K52K	NM_014747.2	NP_055562.2	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	52					calcium ion-dependent exocytosis (GO:0017156)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			TGGCCACCATCTTGGCACCCA	0.662																																					p.K52K		.											.	RIMS3-90	0			c.G156A						.						50	46	47					1																	41107442		2203	4300	6503	SO:0001819	synonymous_variant	9783	exon3			CACCATCTTGGCA	BC003103	CCDS30687.1	1p34.2	2013-09-19			ENSG00000117016	ENSG00000117016			21292	protein-coding gene	gene with protein product		611600				12620390, 10748113	Standard	NM_014747		Approved	RIM3, NIM3	uc001cfu.1	Q9UJD0	OTTHUMG00000007453	ENST00000372684.3:c.156G>A	1.37:g.41107442C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	88	18	NM_014747	0	0	0	1	1	D3DPV8|Q92511|X5D7U7	Silent	SNP	ENST00000372684.3	37	CCDS30687.1																																																																																			.		0.662	RIMS3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019585.1	NM_014747		T	41107442	C	T	41107442	2	4	125	1	0	0	0	0	0	0	0	1	13401	912	32	2		2	RIMS3	1	41107442	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	2819090	41107442	208143179	3	10892											
LRRC42	115353	broad.mit.edu;bcgsc.ca	37	chr1	54417869	54417876	+	Frame_Shift_Del	DEL	AAGAGAAG	AAGAGAAG	-																															ggaagacgacactgcacggaAagagaagactgatcatttca																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	AAGAGAAG	AAGAGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:54417869_54417876delAAGAGAAG	ENST00000371370.3	+	3	718_725	c.197_204delAAGAGAAG	c.(196-204)aaagagaagfs	p.KEK66fs	LRRC42_ENST00000319223.4_Frame_Shift_Del_p.KEK66fs	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	66										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						ACTGCACGGAAAGAGAAGACTGATCATT	0.514																																					p.66_68del													.	LRRC42-90	0			c.197_204del						.																																			SO:0001589	frameshift_variant	115353	exon2			CACGGAAAGAGAA	AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.197_204delAAGAGAAG	1.37:g.54417869_54417876delAAGAGAAG	ENSP00000360421:p.Lys66fs	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	111	13	NM_052940	0	0	0	0	0	D3DQ46|Q8N2Q8	Frame_Shift_Del	DEL	ENST00000371370.3	37	CCDS585.1																																																																																			.		0.514	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1	NM_052940		-	54417876	AAGAGAAG	-	54417869	7	5	125	1	0	1	0	1	0	0	0	0	9025	14	1	0	199	0	LRRC42	1	54417869	Frame_Shift_Del	DEL	AAGAGAAG	TCGA-GL-A4EM-01A-11D-A25F-10	13310427	54417869	194832752	4	10893											
MCL1	4170	broad.mit.edu	37	chr1	150551617	150551617	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttcccgagaggctccggCtcgtacccgtccagctcctc	4	8	10	19	5	0	1	0	0	0	1	6	2	4	1	5	2	2	5	5	2	1	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:150551617C>T	ENST00000369026.2	-	1	449	c.390G>A	c.(388-390)gaG>gaA	p.E130E	MCL1_ENST00000464132.1_5'Flank|MCL1_ENST00000307940.3_Silent_p.E130E	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	130	PEST-like.				apoptotic mitochondrial changes (GO:0008637)|cell fate determination (GO:0001709)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|protein transmembrane transport (GO:0071806)|regulation of response to DNA damage stimulus (GO:2001020)|response to cytokine (GO:0034097)	Bcl-2 family protein complex (GO:0097136)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	BH3 domain binding (GO:0051434)|protein channel activity (GO:0015266)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GAGGCTCCGGCTCGTACCCGT	0.672																																					p.E130E													.	MCL1-227	0			c.G390A						.						20	24	23					1																	150551617		2167	4235	6402	SO:0001819	synonymous_variant	4170	exon1			CTCCGGCTCGTAC	BC017197	CCDS956.1, CCDS957.1, CCDS72909.1	1q21	2014-03-07	2014-03-07		ENSG00000143384	ENSG00000143384			6943	protein-coding gene	gene with protein product		159552	"myeloid cell leukemia sequence 1 (BCL2-related)"			7682708, 7835896	Standard	NM_021960		Approved	BCL2L3, Mcl-1	uc001euz.3	Q07820	OTTHUMG00000034867	ENST00000369026.2:c.390G>A	1.37:g.150551617C>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	18	3	NM_021960	0	0	10	17	7	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Silent	SNP	ENST00000369026.2	37	CCDS957.1																																																																																			.		0.672	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		T	150551617	C	T	150551617	2	4	125	1	0	0	0	0	0	0	0	1	9409	796	28	2		2	MCL1	1	150551617	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	96133748	150551617	98699004	5	10894											
PSMB4	5692	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151372469	151372469	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctttaggaaccccatggtGaccgggacctcagtcctcgg	7	9	11	14	2	2	1	1	1	1	0	4	3	3	3	5	4	1	0	5	4	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:151372469G>A	ENST00000290541.6	+	2	207	c.153G>A	c.(151-153)gtG>gtA	p.V51V		NM_002796.2	NP_002787.2	P28070	PSB4_HUMAN	proteasome (prosome, macropain) subunit, beta type, 4	51					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	lipopolysaccharide binding (GO:0001530)|threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|lung(9)|ovary(2)|prostate(1)|skin(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			ACCCCATGGTGACCGGGACCT	0.577																																					p.V51V													.	PSMB4-92	0			c.G153A						.						73	76	75					1																	151372469		2203	4300	6503	SO:0001819	synonymous_variant	5692	exon2			CATGGTGACCGGG	D26600	CCDS996.1	1q21	2008-02-05			ENSG00000159377	ENSG00000159377		"Proteasome (prosome, macropain) subunits"	9541	protein-coding gene	gene with protein product		602177				7918633	Standard	NM_002796		Approved	HN3, PROS26	uc001eyc.1	P28070	OTTHUMG00000012494	ENST00000290541.6:c.153G>A	1.37:g.151372469G>A		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	65	7	NM_002796	0	0	0	0	0	B2R9L3|P31148|Q5SZS5|Q6IBI4|Q969L6	Silent	SNP	ENST00000290541.6	37	CCDS996.1																																																																																			.		0.577	PSMB4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034885.1	NM_002796		A	151372469	G	A	151372469	2	1	125	1	0	0	0	0	0	0	0	1	12708	1277	45	2		2	PSMB4	1	151372469	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	820852	151372469	97878152	6	10895											
SLC25A44	9673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156169658	156169658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaggacaaacgcaacaTccagatcatcgagtgggaac	15	5	11	10	2	1	1	1	0	0	1	3	5	2	4	1	3	3	1	1	3	3	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:156169658T>C	ENST00000359511.4	+	2	192	c.20T>C	c.(19-21)aTc>aCc	p.I7T	SLC25A44_ENST00000423538.2_Missense_Mutation_p.I7T|SLC25A44_ENST00000469537.1_3'UTR	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	7					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Hepatocellular(266;0.158)					AAACGCAACATCCAGATCATC	0.507																																					p.I7T		.											.	SLC25A44-91	0			c.T20C						.						153	142	146					1																	156169658		2203	4300	6503	SO:0001583	missense	9673	exon2			GCAACATCCAGAT	AB007915	CCDS1133.1, CCDS72943.1	1q22	2013-05-22			ENSG00000160785	ENSG00000160785		"Solute carriers"	29036	protein-coding gene	gene with protein product		610824				16949250	Standard	NM_001286184		Approved	FLJ90431, KIAA0446	uc001fnp.3	Q96H78	OTTHUMG00000014816	ENST00000359511.4:c.20T>C	1.37:g.156169658T>C	ENSP00000352497:p.Ile7Thr	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	123	16	NM_014655	0	0	6	11	5	O75034	Missense_Mutation	SNP	ENST00000359511.4	37	CCDS1133.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365339	0.82463	.	.	ENSG00000160785	ENST00000359511;ENST00000423538;ENST00000412949	T;T	0.80824	-1.42;-1.34	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.85517	0.5715	M	0.79123	2.44	0.80722	D	1	D;D;D	0.63046	0.992;0.986;0.986	P;P;P	0.61477	0.858;0.889;0.889	D	0.87847	0.2655	10	0.72032	D	0.01	-27.8219	13.6089	0.62063	0.0:0.0:0.0:1.0	.	7;7;7	E9PGQ0;B4DGC4;Q96H78	.;.;S2544_HUMAN	T	7	ENSP00000352497:I7T;ENSP00000407560:I7T	ENSP00000352497:I7T	I	+	2	0	SLC25A44	154436282	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.778000	0.85637	2.108000	0.64289	0.528000	0.53228	ATC	.		0.507	SLC25A44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040856.1	NM_014655		C	156169658	T	C	156169658	3	2	125	1	0	0	0	0	1	0	0	0	14541	1435	50	3	22	3	SLC25A44	1	156169658	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	4797189	156169658	93080963	7	10896											
OR6K6	128371	broad.mit.edu;bcgsc.ca	37	chr1	158724869	158724869	+	Frame_Shift_Del	DEL	T	T	-																															gccctgcacacccctttgtaTttctttatcagtgtcctctc																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:158724869delT	ENST00000368144.2	+	1	360	c.264delT	c.(262-264)tatfs	p.Y88fs		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					CCCCTTTGTATTTCTTTATCA	0.463																																					p.Y88fs													.	OR6K6-69	0			c.264delT						.						156	157	157					1																	158724869		2203	4300	6503	SO:0001589	frameshift_variant	128371	exon1			TTTGTATTTCTTT	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"GPCR / Class A : Olfactory receptors"	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.264delT	1.37:g.158724869delT	ENSP00000357126:p.Tyr88fs	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	153	16	NM_001005184	0	0	0	0	0	B9EIM8|Q5VUU9|Q6IFR4	Frame_Shift_Del	DEL	ENST00000368144.2	37	CCDS30904.1																																																																																			.		0.463	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184		-	158724869	T	-	158724869	7	5	125	1	0	1	0	1	0	0	0	0	11230	1500	52	0	266	0	OR6K6	1	158724869	Frame_Shift_Del	DEL	T	TCGA-GL-A4EM-01A-11D-A25F-10	2555211	158724869	90525752	8	10897											
HMCN1	83872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	186024754	186024754	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggccgttatgtgtgtgtTgctgtgaatgtagcaggaat	9	13	14	5	1	0	1	0	1	0	0	0	2	0	2	1	2	2	5	1	2	4	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:186024754T>A	ENST00000271588.4	+	45	7321	c.7092T>A	c.(7090-7092)gtT>gtA	p.V2364V	HMCN1_ENST00000367492.2_Silent_p.V2364V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2364	Ig-like C2-type 21.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATGTGTGTGTTGCTGTGAATG	0.418																																					p.V2364V		.											.	HMCN1-113	0			c.T7092A						.						152	137	142					1																	186024754		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon45			GTGTGTTGCTGTG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7092T>A	1.37:g.186024754T>A		Somatic	331	0		WXS	Illumina HiSeq	Phase_I	258	43	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.		0.418	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186024754	T	A	186024754	2	1	125	1	0	0	0	0	0	0	0	1	7241	1799	63	5		5	HMCN1	1	186024754	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	27299885	186024754	63225867	9	10898											
PPP1R15B	84919	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	204379087	204379089	+	In_Frame_Del	DEL	CTA	CTA	-																															gttctggggattataaggatCtacactgcagaaagagttcc																								rs200631983		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	CTA	CTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:204379087_204379089delCTA	ENST00000367188.4	-	1	1830_1832	c.1451_1453delTAG	c.(1450-1455)gtagat>gat	p.V484del	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	484					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			TTATAAGGATCTACACTGCAGAA	0.448																																					p.484_485del		.											.	PPP1R15B-652	0			c.1451_1453del						.																																			SO:0001651	inframe_deletion	84919	exon1			.	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1451_1453delTAG	1.37:g.204379087_204379089delCTA	ENSP00000356156:p.Val484del	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	67	12	NM_032833	0	0	0	0	0	Q53GQ4|Q658M2|Q6P156|Q96SN1	In_Frame_Del	DEL	ENST00000367188.4	37	CCDS1445.1																																																																																			.		0.448	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		-	204379089	CTA	-	204379087	7	5	125	1	0	1	0	1	0	0	0	0	12393	913	32	0	696	0	PPP1R15B	1	204379087	In_Frame_Del	DEL	CTA	TCGA-GL-A4EM-01A-11D-A25F-10	18354333	204379087	44871534	10	10899											
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	215820886	215820886	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttttgggtggtgaaactGatccactcggaagccgtact	8	13	11	9	2	1	2	0	2	1	0	3	3	2	3	2	3	3	1	2	3	3	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:215820886G>T	ENST00000307340.3	-	67	15155	c.14769C>A	c.(14767-14769)atC>atA	p.I4923I	USH2A_ENST00000366943.2_Silent_p.I4923I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4923	Fibronectin type-III 34. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGGTGAAACTGATCCACTCGG	0.532										HNSCC(13;0.011)																											p.I4923I		.											.	USH2A-115	0			c.C14769A						.						93	76	81					1																	215820886		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon67			GAAACTGATCCAC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"Fibronectin type III domain containing"	12601	protein-coding gene	gene with protein product	"usherin"	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.14769C>A	1.37:g.215820886G>T		Somatic	196	0		WXS	Illumina HiSeq	Phase_I	165	25	NM_206933	0	0	0	0	0	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			.		0.532	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	215820886	G	T	215820886	2	4	125	1	0	0	0	0	0	0	0	1	17069	1280	45	4		4	USH2A	1	215820886	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	11441799	215820886	33429735	11	10900											
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228462497	228462497	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacgcgggccagatcaccGtggaggctgagggcgcctca	8	4	17	12	4	2	2	2	1	0	1	2	4	2	4	3	5	0	1	3	5	0	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:228462497G>C	ENST00000422127.1	+	20	5952	c.5908G>C	c.(5908-5910)Gtg>Ctg	p.V1970L	RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.V2345L|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000366707.4_5'UTR|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000284548.11_Missense_Mutation_p.V1970L|OBSCN_ENST00000359599.6_Missense_Mutation_p.V817L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1970	Ig-like 19.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCAGATCACCGTGGAGGCTGA	0.652																																					p.V2345L		.											.	OBSCN-403	0			c.G7033C						.						27	33	31					1																	228462497		2133	4237	6370	SO:0001583	missense	84033	exon24			ATCACCGTGGAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.5908G>C	1.37:g.228462497G>C	ENSP00000409493:p.Val1970Leu	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	104	18	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331260	0.24167	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.76448	1.01;1.01;-1.02	5.49	3.61	0.41365	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.425981	0.22964	N	0.053513	T	0.73393	0.3581	L	0.51914	1.62	0.48571	D	0.999671	B;P	0.44816	0.002;0.844	B;B	0.44085	0.005;0.44	T	0.69339	-0.5171	10	0.36615	T	0.2	.	11.1091	0.48221	0.0696:0.129:0.8014:0.0	.	1970;1970	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	L	1970;1970;817	ENSP00000284548:V1970L;ENSP00000409493:V1970L;ENSP00000352613:V817L	ENSP00000284548:V1970L	V	+	1	0	OBSCN	226529120	0.981000	0.34729	0.000000	0.03702	0.005000	0.04900	6.186000	0.72026	0.679000	0.31345	0.555000	0.69702	GTG	.		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228462497	G	C	228462497	3	2	125	1	0	0	0	0	1	0	0	0	10838	1145	40	4	5982	4	OBSCN	1	228462497	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	12641611	228462497	20788124	12	10901											
PKDCC	91461	broad.mit.edu;bcgsc.ca	37	chr2	42281437	42281445	+	In_Frame_Del	DEL	AATGCCTAC	AATGCCTAC	-																															acgagaagcggaacctctatAatgcctacaggtgacctcca																								rs55733961|rs371967754	byFrequency	TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	AATGCCTAC	AATGCCTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:42281437_42281445delAATGCCTAC	ENST00000294964.5	+	3	1204_1212	c.1024_1032delAATGCCTAC	c.(1024-1032)aatgcctacdel	p.NAY342del		NM_138370.2	NP_612379.2			protein kinase domain containing, cytoplasmic											breast(2)|kidney(1)|lung(5)	8						GAACCTCTATAATGCCTACAGGTGACCTC	0.617																																					p.342_344del													.	PKDCC-67	0			c.1024_1032del						.																																			SO:0001651	inframe_deletion	91461	exon3			CTCTATAATGCCT		CCDS33186.2	2p21	2014-01-28	2012-12-07		ENSG00000162878	ENSG00000162878			25123	protein-coding gene	gene with protein product	"vertebrate lonesome kinase"	614150	"protein kinase domain containing, cytoplasmic homolog (mouse)"			19097194, 19465597	Standard	NM_138370		Approved	SgK493, Vlk	uc002rsg.3	Q504Y2	OTTHUMG00000152303	ENST00000294964.5:c.1024_1032delAATGCCTAC	2.37:g.42281437_42281445delAATGCCTAC	ENSP00000294964:p.Asn342_Tyr344del	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	201	16	NM_138370	0	0	0	0	0		In_Frame_Del	DEL	ENST00000294964.5	37	CCDS33186.2																																																																																			.		0.617	PKDCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325745.3			-	42281445	AATGCCTAC	-	42281437	7	5	125	1	0	1	0	1	0	0	0	0	11995	362	13	0	1034	0	PKDCC	2	42281437	In_Frame_Del	DEL	AATGCCTAC	TCGA-GL-A4EM-01A-11D-A25F-10		42281437	200917936	13	10902											
MSH6	2956	broad.mit.edu;bcgsc.ca	37	chr2	48025884	48025885	+	Frame_Shift_Ins	INS	-	-	G																															gaagggtcatatcagattctINSgagagtgacattggtggctc																								rs267608072		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:48025884_48025885insG	ENST00000234420.5	+	4	914_915	c.762_763insG	c.(763-765)gagfs	p.E255fs	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_5'UTR|MSH6_ENST00000540021.1_Frame_Shift_Ins_p.E125fs	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	255					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TATCAGATTCTGAGAGTGACAT	0.436			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.S254fs			yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6-3014	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.762_763insG						.																																			SO:0001589	frameshift_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AGATTCTGAGAGT	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"mutS (E. coli) homolog 6", "mutS homolog 6 (E. coli)"	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.763dupG	2.37:g.48025885_48025885dupG	ENSP00000234420:p.Glu255fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	57	8	NM_000179	0	0	0	0	0	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Frame_Shift_Ins	INS	ENST00000234420.5	37	CCDS1836.1																																																																																			.		0.436	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		G	48025885	-	G	48025884	7	5	125	1	0	1	1	0	0	0	0	0	9899	1567	55	0	776	0	MSH6	2	48025884	Frame_Shift_Ins	INS	-	TCGA-GL-A4EM-01A-11D-A25F-10	5744447	48025884	195173489	14	10903											
MFSD9	84804	broad.mit.edu	37	chr2	103343361	103343361	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtggctgctccgagaaggaGatagcccagagcactgagta	11	6	15	9	1	0	4	0	1	0	3	1	6	1	4	2	3	3	4	2	3	3	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:103343361G>A	ENST00000258436.5	-	4	413	c.370C>T	c.(370-372)Ctc>Ttc	p.L124F		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	124					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CCGAGAAGGAGATAGCCCAGA	0.488																																					p.L124F													.	MFSD9-155	0			c.C370T						.						81	79	80					2																	103343361		2203	4300	6503	SO:0001583	missense	84804	exon4			GAAGGAGATAGCC		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.370C>T	2.37:g.103343361G>A	ENSP00000258436:p.Leu124Phe	Somatic	251	4		WXS	Illumina HiSeq	Phase_I	257	7	NM_032718	0	0	1	1	0	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Missense_Mutation	SNP	ENST00000258436.5	37	CCDS2063.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035350	0.54896	.	.	ENSG00000135953	ENST00000258436	T	0.61627	0.09	5.34	4.45	0.53987	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.326073	0.30704	N	0.009046	T	0.48732	0.1516	M	0.69248	2.105	0.27141	N	0.96166	B	0.16802	0.019	B	0.19391	0.025	T	0.27773	-1.0064	10	0.22706	T	0.39	-21.7696	4.4903	0.11810	0.1674:0.2193:0.6133:0.0	.	124	Q8NBP5	MFSD9_HUMAN	F	124	ENSP00000258436:L124F	ENSP00000258436:L124F	L	-	1	0	MFSD9	102709793	1.000000	0.71417	0.495000	0.27527	0.664000	0.39144	4.031000	0.57267	2.663000	0.90544	0.655000	0.94253	CTC	.		0.488	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718		A	103343361	G	A	103343361	3	1	125	1	0	0	0	0	1	0	0	0	9564	942	33	2	1066	2	MFSD9	2	103343361	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	55317477	103343361	139856012	15	10904											
ZEB2	9839	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	145157390	145157390	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgtacctcacttaaattaCtattcatggtgggaaaccca	12	14	6	9	0	2	0	2	0	0	0	2	1	2	1	2	2	3	1	2	2	6	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:145157390C>T	ENST00000558170.2	-	8	2548	c.1364G>A	c.(1363-1365)aGt>aAt	p.S455N	ZEB2_ENST00000409487.3_Missense_Mutation_p.S455N|ZEB2_ENST00000303660.4_Missense_Mutation_p.S455N|ZEB2_ENST00000539609.3_Missense_Mutation_p.S431N	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	455	SMAD-MH2 binding domain. {ECO:0000250}.				cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		ACTTAAATTACTATTCATGGT	0.438																																					p.S455N	Melanoma(33;1235 1264 5755 16332)												.	ZEB2-297	0			c.G1364A						.						75	78	77					2																	145157390		2203	4300	6503	SO:0001583	missense	9839	exon8			AAATTACTATTCA	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	14881	protein-coding gene	gene with protein product	"SMAD interacting protein 1"	605802	"zinc finger homeobox 1b"	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.1364G>A	2.37:g.145157390C>T	ENSP00000454157:p.Ser455Asn	Somatic	137	1		WXS	Illumina HiSeq	Phase_I	99	13	NM_014795	0	0	0	1	1	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	0.218	-1.030702	0.02045	.	.	ENSG00000169554	ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902	T;T;T;T	0.11495	2.79;2.77;2.77;2.88	5.53	5.53	0.82687	.	0.037192	0.85682	D	0.000000	T	0.06962	0.0177	N	0.11927	0.2	0.48135	D	0.999594	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.10450	0.005;0.001;0.001;0.005	T	0.14254	-1.0479	10	0.02654	T	1	-8.897	19.4645	0.94932	0.0:1.0:0.0:0.0	.	431;320;454;455	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	N	431;455;455;455	ENSP00000443792:S431N;ENSP00000302501:S455N;ENSP00000386854:S455N;ENSP00000395496:S455N	ENSP00000302501:S455N	S	-	2	0	ZEB2	144873860	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.709000	0.61867	2.587000	0.87381	0.655000	0.94253	AGT	.		0.438	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		T	145157390	C	T	145157390	3	4	125	1	0	0	0	0	1	0	0	0	17656	565	20	2	2292	2	ZEB2	2	145157390	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	41814029	145157390	98041983	16	10905											
IKZF2	22807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	213872808	213872808	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgaatcgcatgagcttttccCctggaagggagtgggaggtg	8	10	16	7	1	0	2	0	2	0	0	2	5	1	5	2	4	1	2	2	4	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:213872808C>A	ENST00000434687.1	-	9	1166	c.857G>T	c.(856-858)gGg>gTg	p.G286V	IKZF2_ENST00000421754.2_Splice_Site_p.G212V|IKZF2_ENST00000457361.1_Splice_Site_p.G286V|IKZF2_ENST00000342002.2_Splice_Site_p.G292V|IKZF2_ENST00000374327.4_Splice_Site_p.G141V|IKZF2_ENST00000451136.2_Splice_Site_p.G214V|AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000374319.4_Splice_Site_p.G260V|IKZF2_ENST00000413091.3_3'UTR			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	286					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GAGCTTTTCCCCTGGAAGGGA	0.373																																					p.G286V		.											.	IKZF2-226	0			c.G857T						.						35	35	35					2																	213872808		2203	4300	6503	SO:0001630	splice_region_variant	22807	exon8			TTTTCCCCTGGAA	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13177	protein-coding gene	gene with protein product		606234	"zinc finger protein, subfamily 1A, 2 (Helios)"	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.857-1G>T	2.37:g.213872808C>A		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	71	12	NM_016260	0	0	0	0	0	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Missense_Mutation	SNP	ENST00000434687.1	37	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.154388	0.57259	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327	T;T;T;T;T;T;T	0.24350	2.74;2.71;2.74;2.88;2.86;3.06;1.86	5.83	5.83	0.93111	.	0.072285	0.64402	D	0.000018	T	0.60090	0.2242	M	0.88979	2.995	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.998;0.999;0.999	T	0.66248	-0.5971	10	0.87932	D	0	.	18.2957	0.90145	0.0:1.0:0.0:0.0	.	214;212;141;260;286;64	C9JCG7;C9JTM9;F5H8M1;Q9UKS7-2;Q9UKS7;Q96LD7	.;.;.;.;IKZF2_HUMAN;.	V	286;292;286;260;214;212;141	ENSP00000410447:G286V;ENSP00000342876:G292V;ENSP00000412869:G286V;ENSP00000363439:G260V;ENSP00000395203:G214V;ENSP00000399574:G212V;ENSP00000363447:G141V	ENSP00000342876:G292V	G	-	2	0	IKZF2	213581053	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	5.731000	0.68554	2.750000	0.94351	0.655000	0.94253	GGG	.		0.373	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260	Missense_Mutation	A	213872808	C	A	213872808	5	1	125	1	0	0	0	0	0	0	1	0	7636	637	22	4	727	4	IKZF2	2	213872808	Splice_Site	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	68715418	213872808	29326565	17	10906											
PER2	8864	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	239162231	239162231	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacacgggccccccagatccGgtgctctcagatgagtctcg	7	7	12	15	3	2	3	1	1	2	2	5	4	3	3	4	2	1	1	4	2	0	0	rs566281173	byFrequency	TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:239162231G>A	ENST00000254657.3	-	19	2712	c.2433C>T	c.(2431-2433)acC>acT	p.T811T	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	811					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CCCCAGATCCGGTGCTCTCAG	0.572													g|||	2	0.000399361	0	0	5008	,	,		14310	0		0	False		,,,				2504	0.002				p.T811T		.											.	PER2-154	0			c.C2433T						.						12	15	14					2																	239162231		2199	4298	6497	SO:0001819	synonymous_variant	8864	exon19			AGATCCGGTGCTC	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2433C>T	2.37:g.239162231G>A		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	53	12	NM_022817	0	0	1	2	1	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			.		0.572	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239162231	G	A	239162231	2	1	125	1	0	0	0	0	0	0	0	1	11756	1103	39	1		1	PER2	2	239162231	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	25289423	239162231	4037142	18	10907											
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52429465	52429465	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaaaagctctctgccatcTccctgggccaggggcaggtc	8	7	11	15	0	2	0	0	0	2	0	5	0	2	0	4	4	2	2	4	4	2	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:52429465T>A	ENST00000420323.2	+	69	11371	c.11110T>A	c.(11110-11112)Tcc>Acc	p.S3704T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3769					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CTCTGCCATCTCCCTGGGCCA	0.627																																					p.S3704T		.											.	DNAH1-67	0			c.T11110A						.						36	38	37					3																	52429465		1924	4124	6048	SO:0001583	missense	25981	exon69			GCCATCTCCCTGG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11110T>A	3.37:g.52429465T>A	ENSP00000401514:p.Ser3704Thr	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	199	36	NM_015512	0	0	1	1	0	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.840907	0.71488	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.14022	2.54	4.38	4.38	0.52667	.	0.000000	0.64402	D	0.000005	T	0.57110	0.2031	H	0.99435	4.565	0.45366	D	0.998355	D;D	0.89917	1.0;0.99	D;D	0.85130	0.997;0.979	T	0.76963	-0.2764	10	0.87932	D	0	.	13.7712	0.63026	0.0:0.0:0.0:1.0	.	3704;3769	C9JXH6;Q9P2D7-2	.;.	T	3704;457	ENSP00000401514:S3704T	ENSP00000273600:S457T	S	+	1	0	DNAH1	52404505	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.531000	0.81973	1.837000	0.53436	0.533000	0.62120	TCC	.		0.627	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52429465	T	A	52429465	3	1	125	1	0	0	0	0	1	0	0	0	4608	1551	54	5	11380	5	DNAH1	3	52429465	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		52429465	145592965	19	10908											
LRIG1	26018	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	66436541	66436541	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactccatcacttccccgtcCtgcgcgtggacgtggacaaa	8	9	9	15	4	1	0	1	0	0	0	4	2	4	2	4	2	2	0	4	2	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:66436541C>G	ENST00000273261.3	-	13	2177	c.1653G>C	c.(1651-1653)caG>caC	p.Q551H	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Missense_Mutation_p.Q575H|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	551	Ig-like C2-type 1.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		CTTCCCCGTCCTGCGCGTGGA	0.567																																					p.Q551H													.	LRIG1-230	0			c.G1653C						.						230	196	207					3																	66436541		2203	4300	6503	SO:0001583	missense	26018	exon13			CCCGTCCTGCGCG	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1653G>C	3.37:g.66436541C>G	ENSP00000273261:p.Gln551His	Somatic	407	1		WXS	Illumina HiSeq	Phase_I	339	52	NM_015541	0	0	5	8	3	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.748197	0.30955	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.39229	1.09;1.09	6.17	6.17	0.99709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.293434	0.33075	N	0.005306	T	0.32675	0.0837	L	0.39898	1.24	0.45995	D	0.998806	B;P;B	0.38148	0.095;0.62;0.116	B;B;B	0.33568	0.045;0.166;0.044	T	0.15178	-1.0446	10	0.62326	D	0.03	.	10.391	0.44168	0.0:0.7956:0.1354:0.0689	.	575;551;551	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	H	551;575;454	ENSP00000273261:Q551H;ENSP00000373208:Q575H	ENSP00000273261:Q551H	Q	-	3	2	LRIG1	66519231	0.970000	0.33590	1.000000	0.80357	0.068000	0.16541	0.512000	0.22755	2.941000	0.99782	0.655000	0.94253	CAG	.		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		G	66436541	C	G	66436541	3	3	125	1	0	0	0	0	1	0	0	0	8969	680	24	4	1656	4	LRIG1	3	66436541	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	14007076	66436541	131585889	20	10909											
EPHA3	2042	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	89478285	89478285	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatgattgtcacagaatacAtggagaatggttccttggat	12	14	10	5	0	1	3	1	1	0	2	2	5	2	4	1	3	1	1	1	3	4	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:89478285A>C	ENST00000336596.2	+	12	2329	c.2104A>C	c.(2104-2106)Atg>Ctg	p.M702L	EPHA3_ENST00000494014.1_Missense_Mutation_p.M702L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	702	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CACAGAATACATGGAGAATGG	0.299										TSP Lung(6;0.00050)																											p.M702L		.											.	EPHA3-1500	0			c.A2104C						.						111	116	114					3																	89478285		2203	4299	6502	SO:0001583	missense	2042	exon12			GAATACATGGAGA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2104A>C	3.37:g.89478285A>C	ENSP00000337451:p.Met702Leu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	77	11	NM_005233	0	0	0	0	0	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.781520	0.90282	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.62639	0.01;0.01	5.68	5.68	0.88126	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70228	0.3200	L	0.39020	1.185	0.80722	D	1	P	0.50710	0.938	D	0.65773	0.938	T	0.67964	-0.5534	9	.	.	.	.	16.2237	0.82280	1.0:0.0:0.0:0.0	.	702	P29320	EPHA3_HUMAN	L	702	ENSP00000337451:M702L;ENSP00000419190:M702L	.	M	+	1	0	EPHA3	89560975	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.287000	0.95975	2.289000	0.77006	0.482000	0.46254	ATG	.		0.299	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89478285	A	C	89478285	3	2	125	1	0	0	0	0	1	0	0	0	5181	217	8	5	2176	5	EPHA3	3	89478285	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	23041744	89478285	108544145	21	10910											
ATR	545	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	142279142	142279142	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacaatgaacagtacacaGagcagtcagttgtaagacaa	19	6	9	7	0	1	4	1	1	0	3	1	4	1	4	0	0	4	4	0	0	6	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:142279142G>T	ENST00000350721.4	-	6	1625	c.1504C>A	c.(1504-1506)Ctg>Atg	p.L502M	ATR_ENST00000383101.3_Intron	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	502					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						ACAGTACACAGAGCAGTCAGT	0.378								Other conserved DNA damage response genes																													p.L502M													.	ATR-1139	0			c.C1504A						.						141	138	139					3																	142279142		2203	4300	6503	SO:0001583	missense	545	exon6			TACACAGAGCAGT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"	601215	"ataxia telangiectasia and Rad3 related"			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1504C>A	3.37:g.142279142G>T	ENSP00000343741:p.Leu502Met	Somatic	244	2		WXS	Illumina HiSeq	Phase_I	224	29	NM_001184	0	0	0	1	1	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.493824	0.64186	.	.	ENSG00000175054	ENST00000350721	T	0.03982	3.74	5.71	2.98	0.34508	Armadillo-type fold (1);	0.445732	0.20701	N	0.087280	T	0.10680	0.0261	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.65233	0.933	T	0.02625	-1.1132	10	0.59425	D	0.04	-8.5525	10.5221	0.44924	0.2672:0.0:0.7328:0.0	.	502	Q13535	ATR_HUMAN	M	502	ENSP00000343741:L502M	ENSP00000343741:L502M	L	-	1	2	ATR	143761832	0.999000	0.42202	0.998000	0.56505	0.979000	0.70002	0.525000	0.22956	0.358000	0.24211	0.585000	0.79938	CTG	.		0.378	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142279142	G	T	142279142	3	4	125	1	0	0	0	0	1	0	0	0	1205	933	33	4	6598	4	ATR	3	142279142	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	52800857	142279142	55743288	22	10911											
CP	1356	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	148924070	148924070	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacatgcttcccacggatatTatcctttgatgaagacttgt	11	14	7	9	1	0	3	0	2	0	1	2	4	2	4	2	1	2	1	2	1	4	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:148924070T>G	ENST00000264613.6	-	6	1355	c.1093A>C	c.(1093-1095)Aat>Cat	p.N365H		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	365					cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CCACGGATATTATCCTTTGAT	0.408																																					p.N365H		.											.	CP-515	0			c.A1093C						.						140	137	138					3																	148924070		2203	4300	6503	SO:0001583	missense	1356	exon6			GGATATTATCCTT	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1093A>C	3.37:g.148924070T>G	ENSP00000264613:p.Asn365His	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	112	10	NM_000096	0	0	3	3	0	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.511691	0.27036	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.99239	-5.04;-5.61	5.81	-5.54	0.02544	.	1.443030	0.03609	N	0.234542	D	0.97785	0.9273	L	0.53249	1.67	0.09310	N	1	B;B;B;B	0.28128	0.0;0.201;0.0;0.0	B;B;B;B	0.24848	0.0;0.056;0.0;0.0	D	0.94485	0.7696	10	0.39692	T	0.17	0.0553	13.1324	0.59391	0.0:0.1357:0.1004:0.7639	.	365;365;365;365	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	H	365;148	ENSP00000264613:N365H;ENSP00000420545:N148H	ENSP00000264613:N365H	N	-	1	0	CP	150406760	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.776000	0.04674	-1.021000	0.03350	-0.242000	0.12053	AAT	.		0.408	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		G	148924070	T	G	148924070	3	3	125	1	0	0	0	0	1	0	0	0	3793	1754	61	5	2160	5	CP	3	148924070	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	6644928	148924070	49098360	23	10912											
NDUFB5	4711	broad.mit.edu	37	chr3	179322628	179322629	+	Frame_Shift_Ins	INS	-	-	G																															ggccatgagtttgttgcggcINSgggtttcggttactgcggtg																								rs144873631|rs11539673		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:179322628_179322629insG	ENST00000259037.3	+	1	139_140	c.25_26insG	c.(25-27)cggfs	p.R9fs	MRPL47_ENST00000476781.1_5'Flank|NDUFB5_ENST00000472629.1_Frame_Shift_Ins_p.R9fs|MRPL47_ENST00000259038.2_5'Flank|NDUFB5_ENST00000493866.1_Frame_Shift_Ins_p.R9fs|MRPL47_ENST00000392659.2_5'Flank	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	9					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R9P(1)		endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			TTTGTTGCGGCGGGTTTCGGTT	0.609																																					p.R9fs													.	NDUFB5-91	1	Substitution - Missense(1)	lung(1)	c.25_26insG						.																																			SO:0001589	frameshift_variant	4711	exon1			TTGCGGCGGGTTT	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"Mitochondrial respiratory chain complex / Complex I"	7700	protein-coding gene	gene with protein product	"complex I SGDH subunit"	603841	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.28dupG	3.37:g.179322631_179322631dupG	ENSP00000259037:p.Arg9fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	100	16	NM_002492	0	0	0	0	0	Q561V6	Frame_Shift_Ins	INS	ENST00000259037.3	37	CCDS3234.1																																																																																			.		0.609	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492		G	179322629	-	G	179322628	7	5	125	1	0	1	1	0	0	0	0	0	10310	759	27	0	27	0	NDUFB5	3	179322628	Frame_Shift_Ins	INS	-	TCGA-GL-A4EM-01A-11D-A25F-10	30398558	179322628	18699802	24	10913											
ABCC5	10057	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183732125	183732125	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggttctctccctcacaCttctatacccaggactgggg	6	12	9	14	0	3	0	1	0	2	0	5	1	4	1	2	4	2	2	2	4	2	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:183732125C>G	ENST00000334444.6	-	2	296	c.56G>C	c.(55-57)aGt>aCt	p.S19T	ABCC5_ENST00000446941.2_Missense_Mutation_p.S19T|ABCC5_ENST00000427120.2_Missense_Mutation_p.S19T|ABCC5_ENST00000392579.2_Missense_Mutation_p.S19T|ABCC5_ENST00000382494.2_Missense_Mutation_p.S19T|ABCC5_ENST00000265586.6_Missense_Mutation_p.S19T|ABCC5-AS1_ENST00000422946.1_RNA	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	19					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CTCCCTCACACTTCTATACCC	0.483																																					p.S19T													.	ABCC5-137	0			c.G56C						.						141	126	131					3																	183732125		2203	4300	6503	SO:0001583	missense	10057	exon2			CTCACACTTCTAT	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.56G>C	3.37:g.183732125C>G	ENSP00000333926:p.Ser19Thr	Somatic	164	2		WXS	Illumina HiSeq	Phase_I	174	37	NM_005688	0	0	4	6	2	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	C	6.516	0.463419	0.12402	.	.	ENSG00000114770	ENST00000334444;ENST00000265586;ENST00000427120;ENST00000392579;ENST00000382494;ENST00000437341;ENST00000446941	D;D;T;T;T	0.91577	-2.66;-2.87;1.37;1.38;1.41	5.28	2.0	0.26442	.	0.201917	0.34133	N	0.004231	T	0.81422	0.4819	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.31817	0.341;0.287;0.002;0.021;0.016	B;B;B;B;B	0.28011	0.059;0.085;0.008;0.033;0.011	T	0.66376	-0.5939	10	0.21014	T	0.42	-4.7806	6.1229	0.20164	0.0:0.3249:0.0:0.6751	.	19;19;19;19;19	A5PKY6;Q29ZA9;Q86UX3;Q86W30;O15440	.;.;.;.;MRP5_HUMAN	T	19	ENSP00000333926:S19T;ENSP00000265586:S19T;ENSP00000404809:S19T;ENSP00000376358:S19T;ENSP00000371934:S19T	ENSP00000265586:S19T	S	-	2	0	ABCC5	185214819	0.254000	0.23992	0.002000	0.10522	0.091000	0.18340	0.507000	0.22675	0.190000	0.20209	-0.136000	0.14681	AGT	.		0.483	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		G	183732125	C	G	183732125	3	3	125	1	0	0	0	0	1	0	0	0	56	565	20	4	4413	4	ABCC5	3	183732125	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	4409497	183732125	14290305	25	10914											
CPZ	8532	hgsc.bcm.edu	37	chr4	8621250	8621250	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcccgacccgctccgggcgcGcaggcagccctcggccgacg	4	2	15	20	8	0	0	0	0	0	0	2	2	1	0	5	3	1	3	5	3	0	0	rs144042196		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr4:8621250G>A	ENST00000360986.4	+	11	2039	c.1865G>A	c.(1864-1866)cGc>cAc	p.R622H	CPZ_ENST00000315782.6_Missense_Mutation_p.R611H|CPZ_ENST00000382480.2_Missense_Mutation_p.R485H|CPZ_ENST00000429646.2_Missense_Mutation_p.R230H	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	622					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CTCCGGGCGCGCAGGCAGCCC	0.672																																					p.R622H		.											.	CPZ-93	0			c.G1865A						.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4402		0,0,2201	28	31	30		1865,1454,1832	2.1	0.1	4	dbSNP_134	30	1,8595	1.2+/-3.3	0,1,4297	yes	missense,missense,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	29,29,29	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	622/653,485/516,611/642	8621250	1,12997	2201	4298	6499	SO:0001583	missense	8532	exon11			GGGCGCGCAGGCA	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1865G>A	4.37:g.8621250G>A	ENSP00000354255:p.Arg622His	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	8	5	NM_001014447	0	0	2	2	0	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.677115	0.47886	0.0	1.16E-4	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782;ENST00000429646	T;T;T;T	0.58940	0.62;1.98;0.3;1.86	4.82	2.09	0.27110	.	0.624251	0.13588	U	0.376803	T	0.51873	0.1700	M	0.62723	1.935	0.09310	N	0.999999	B;B	0.18013	0.025;0.006	B;B	0.10450	0.005;0.001	T	0.46610	-0.9179	10	0.46703	T	0.11	-25.7306	8.9438	0.35747	0.2406:0.0:0.7594:0.0	.	611;622	Q66K79-2;Q66K79	.;CBPZ_HUMAN	H	622;485;611;230	ENSP00000354255:R622H;ENSP00000371920:R485H;ENSP00000315074:R611H;ENSP00000403981:R230H	ENSP00000315074:R611H	R	+	2	0	CPZ	8672150	0.003000	0.15002	0.094000	0.20943	0.121000	0.20230	0.793000	0.26944	0.448000	0.26722	0.462000	0.41574	CGC	G|1.000;A|0.000		0.672	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		A	8621250	G	A	8621250	3	1	125	1	0	0	0	0	1	0	0	0	3845	1087	38	1	1907	1	CPZ	4	8621250	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		8621250	182533026	26	10915											
GBA3	57733	broad.mit.edu	37	chr4	22737642	22737642	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaaaaggcccttgtgtctggGacacatttactcatcaggga	11	10	11	9	0	3	0	2	0	1	0	3	3	3	2	1	3	1	0	1	3	3	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr4:22737642G>T	ENST00000503442.1	+	0	188				GBA3_ENST00000508166.1_RNA|GBA3_ENST00000511446.2_RNA	NM_001128432.2	NP_001121904.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)						carbohydrate metabolic process (GO:0005975)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide catabolic process (GO:0046477)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	beta-galactosidase activity (GO:0004565)|beta-glucosidase activity (GO:0008422)|glycosylceramidase activity (GO:0017042)			breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TTGTGTCTGGGACACATTTAC	0.448																																					.													.	GBA3-1	0			.						.						112	115	114					4																	22737642		1931	4143	6074			57733	.			GTCTGGGACACAT	AB017913		4p15.2	2013-05-09	2013-05-09		ENSG00000249948	ENSG00000249948	3.2.1.21		19069	protein-coding gene	gene with protein product	"klotho-related protein"	606619	"glucosidase, beta, acid 3 (cytosolic)"			11389701	Standard	NM_020973		Approved	GLUC, KLrP	uc031sdv.1	Q9H227	OTTHUMG00000160448		4.37:g.22737642G>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	106	4	.	0	0	14	14	0	Q32LY7|Q3MIH4|Q53GG8|Q6NSF4|Q8NHT8|Q9H3T4|Q9H4C6	Missense_Mutation	SNP	ENST00000503442.1	37																																																																																				.		0.448	GBA3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000360620.2			T	22737642	G	T	22737642	1	4	125	0	1	0	0	0	0	0	0	0	6288	1174	41	4		4	GBA3	4	22737642	RNA	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	14116392	22737642	168416634	27	10916											
SEC31A	22872	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	83769958	83769958	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggaccatatcactcacaTggggataatattgttgagtt	11	14	9	7	0	3	1	2	1	1	0	3	3	3	3	1	3	0	2	1	3	3	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr4:83769958T>G	ENST00000395310.2	-	20	2683	c.2501A>C	c.(2500-2502)cAt>cCt	p.H834P	SEC31A_ENST00000500777.2_Splice_Site_p.H795P|SEC31A_ENST00000508479.1_Splice_Site_p.H834P|SEC31A_ENST00000505984.1_Splice_Site_p.H795P|SEC31A_ENST00000509142.1_Splice_Site_p.H834P|SEC31A_ENST00000508502.1_Splice_Site_p.H834P|SEC31A_ENST00000311785.7_Splice_Site_p.H834P|SEC31A_ENST00000513858.1_Splice_Site_p.H795P|SEC31A_ENST00000505472.1_Splice_Site_p.H834P|SEC31A_ENST00000355196.2_Splice_Site_p.H834P|SEC31A_ENST00000348405.4_Splice_Site_p.H795P|SEC31A_ENST00000326950.5_Splice_Site_p.H795P|SEC31A_ENST00000443462.2_Splice_Site_p.H829P|SEC31A_ENST00000432794.1_Splice_Site_p.H834P|SEC31A_ENST00000448323.1_Splice_Site_p.H834P|SEC31A_ENST00000264405.5_Splice_Site_p.H567P	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	834	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				ATCACTCACATGGGGATAATA	0.448																																					p.H834P													.	SEC31A-268	0			c.A2501C						.						84	81	82					4																	83769958		2203	4300	6503	SO:0001630	splice_region_variant	22872	exon20			CTCACATGGGGAT	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.2502+1A>C	4.37:g.83769958T>G		Somatic	155	1		WXS	Illumina HiSeq	Phase_I	154	25	NM_001077206	0	0	0	0	0	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Missense_Mutation	SNP	ENST00000395310.2	37	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985948	0.53934	.	.	ENSG00000138674	ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984;ENST00000508479	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.36520	1.43;1.25;2.49;2.45;1.3;2.39;2.49;1.43;1.3;1.27;1.25;2.46;2.49;3.37;2.42;2.36	5.72	5.72	0.89469	.	0.270404	0.40640	N	0.001049	T	0.31482	0.0798	N	0.12182	0.205	0.45118	D	0.998132	B;B;B;B;B;B;P;B;P	0.37038	0.357;0.167;0.357;0.0;0.0;0.0;0.49;0.238;0.579	B;B;B;B;B;B;B;B;P	0.46975	0.232;0.123;0.232;0.001;0.002;0.001;0.409;0.125;0.533	T	0.17806	-1.0357	10	0.30078	T	0.28	-7.7203	14.2292	0.65879	0.0:0.0:0.0:1.0	.	829;795;834;795;795;834;834;834;567	B4DIW6;B7ZL00;D6RHZ5;O94979-6;O94979-4;O94979-3;O94979-2;O94979;O94979-7	.;.;.;.;.;.;.;SC31A_HUMAN;.	P	795;795;834;829;834;834;834;795;834;834;795;834;834;567;795;834	ENSP00000337602:H795P;ENSP00000426886:H795P;ENSP00000378721:H834P;ENSP00000408027:H829P;ENSP00000426569:H834P;ENSP00000407944:H834P;ENSP00000400926:H834P;ENSP00000325087:H795P;ENSP00000309070:H834P;ENSP00000421633:H834P;ENSP00000421464:H795P;ENSP00000424635:H834P;ENSP00000347329:H834P;ENSP00000264405:H567P;ENSP00000424451:H795P;ENSP00000425999:H834P	ENSP00000264405:H567P	H	-	2	0	SEC31A	83988982	1.000000	0.71417	1.000000	0.80357	0.300000	0.27592	5.132000	0.64758	2.184000	0.69523	0.383000	0.25322	CAT	.		0.448	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211	Missense_Mutation	G	83769958	T	G	83769958	5	3	125	1	0	0	0	0	0	0	1	0	14030	1478	51	5	1193	5	SEC31A	4	83769958	Splice_Site	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	61032316	83769958	107384318	28	10917											
GRID2	2895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	94690404	94690404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgacatggacatcctgaagCacaaatggtggcctaagaat	14	8	11	8	0	0	3	0	2	0	1	1	4	1	4	2	3	1	1	2	3	4	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr4:94690404C>T	ENST00000282020.4	+	15	2662	c.2404C>T	c.(2404-2406)Cac>Tac	p.H802Y	GRID2_ENST00000510992.1_Missense_Mutation_p.H707Y	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	802					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		CATCCTGAAGCACAAATGGTG	0.483																																					p.H802Y		.											.	GRID2-159	0			c.C2404T						.						124	117	119					4																	94690404		2203	4300	6503	SO:0001583	missense	2895	exon15			CTGAAGCACAAAT	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2404C>T	4.37:g.94690404C>T	ENSP00000282020:p.His802Tyr	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	156	21	NM_001510	0	0	0	0	0	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.829280	0.71258	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.26957	1.7;1.7	5.17	5.17	0.71159	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.054536	0.64402	D	0.000001	T	0.16514	0.0397	N	0.08118	0	0.58432	D	0.999992	B;B	0.30584	0.286;0.286	B;B	0.26693	0.072;0.072	T	0.11324	-1.0592	10	0.87932	D	0	.	18.7052	0.91635	0.0:1.0:0.0:0.0	.	707;802	E9PH24;O43424	.;GRID2_HUMAN	Y	802;707	ENSP00000282020:H802Y;ENSP00000421257:H707Y	ENSP00000282020:H802Y	H	+	1	0	GRID2	94909427	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.713000	0.54882	2.415000	0.81967	0.650000	0.86243	CAC	.		0.483	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	94690404	C	T	94690404	3	4	125	1	0	0	0	0	1	0	0	0	6793	710	25	2	2462	2	GRID2	4	94690404	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	10920446	94690404	96463872	29	10918											
ZCCHC10	54819	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	132342536	132342536	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggcctatgtaggtattttcTttttcctgtgcattcataag	7	18	9	7	0	2	0	1	0	1	0	3	0	3	0	2	2	1	3	2	2	4	9			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr5:132342536T>G	ENST00000509437.1	-	3	191	c.184A>C	c.(184-186)Aga>Cga	p.R62R	ZCCHC10_ENST00000508080.1_5'UTR|ZCCHC10_ENST00000509008.1_Silent_p.R40R|ZCCHC10_ENST00000513848.1_Silent_p.R40R|ZCCHC10_ENST00000355372.2_Silent_p.R62R|ZCCHC10_ENST00000513541.1_Silent_p.R62R|ZCCHC10_ENST00000324170.3_Silent_p.R40R			Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	62							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGGTATTTTCTTTTTCCTGTG	0.338																																					p.R40R		.											.	ZCCHC10-90	0			c.A118C						.						91	83	85					5																	132342536		2201	4298	6499	SO:0001819	synonymous_variant	54819	exon2			ATTTTCTTTTTCC	BC005211	CCDS4165.1, CCDS75300.1, CCDS75301.1, CCDS75302.1	5q31.1	2008-05-02			ENSG00000155329	ENSG00000155329		"Zinc fingers, CCHC domain containing"	25954	protein-coding gene	gene with protein product						12477932	Standard	XM_005272024		Approved	FLJ20094	uc003kyg.3	Q8TBK6	OTTHUMG00000129013	ENST00000509437.1:c.184A>C	5.37:g.132342536T>G		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	153	16	NM_017665	0	0	4	10	6	Q9NXR4	Silent	SNP	ENST00000509437.1	37																																																																																				.		0.338	ZCCHC10-004	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000370163.1	NM_017665		G	132342536	T	G	132342536	2	3	125	1	0	0	0	0	0	0	0	1	17611	1617	56	5		5	ZCCHC10	5	132342536	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		132342536	48572724	30	10919											
DDX41	51428	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176943931	176943931	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctcctaccttccgttcggGttccgactcctccattcttt	3	16	5	17	3	2	0	0	0	2	0	8	1	6	0	6	1	1	2	6	1	1	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr5:176943931G>T	ENST00000507955.1	-	1	539	c.16C>A	c.(16-18)Ccc>Acc	p.P6T	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	6					apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TTCCGTTCGGGTTCCGACTCC	0.657																																					p.P6T													.	DDX41-226	0			c.C16A						.						73	61	65					5																	176943931		2202	4300	6502	SO:0001583	missense	51428	exon1			GTTCGGGTTCCGA	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"DEAD-boxes"	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.16C>A	5.37:g.176943931G>T	ENSP00000422753:p.Pro6Thr	Somatic	174	1		WXS	Illumina HiSeq	Phase_I	227	52	NM_016222	0	0	0	0	0	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	37	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547551	0.45383	.	.	ENSG00000183258	ENST00000507955	T	0.26518	1.73	4.65	3.71	0.42584	.	1.216860	0.06063	N	0.658641	T	0.20333	0.0489	N	0.22421	0.69	0.34597	D	0.716069	B	0.25904	0.137	B	0.23018	0.043	T	0.05289	-1.0894	10	0.30854	T	0.27	-19.3593	12.3624	0.55211	0.0:0.1709:0.8291:0.0	.	6	Q9UJV9	DDX41_HUMAN	T	6	ENSP00000422753:P6T	ENSP00000422753:P6T	P	-	1	0	DDX41	176876537	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	1.870000	0.39529	2.571000	0.86741	0.591000	0.81541	CCC	.		0.657	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		T	176943931	G	T	176943931	3	4	125	1	0	0	0	0	1	0	0	0	4367	1261	44	4	1920	4	DDX41	5	176943931	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	44601395	176943931	3971329	31	10920											
COL12A1	1303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	75860944	75860944	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atctgccacattgtatgcatGggtatcatcaggatcagttg	10	13	10	8	0	4	0	3	0	1	0	4	1	4	1	1	2	2	4	1	2	2	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:75860944G>T	ENST00000322507.8	-	21	4369	c.4060C>A	c.(4060-4062)Cat>Aat	p.H1354N	COL12A1_ENST00000483888.2_Missense_Mutation_p.H1354N|COL12A1_ENST00000416123.2_Missense_Mutation_p.H1354N|COL12A1_ENST00000345356.6_Missense_Mutation_p.H190N	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1354	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTGTATGCATGGGTATCATCA	0.368																																					p.H1354N		.											.	COL12A1-142	0			c.C4060A						.						171	170	170					6																	75860944		1901	4128	6029	SO:0001583	missense	1303	exon21			ATGCATGGGTATC	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4060C>A	6.37:g.75860944G>T	ENSP00000325146:p.His1354Asn	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	100	16	NM_004370	0	0	0	0	0	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.98|18.98	3.738638|3.738638	0.69304|0.69304	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888|ENST00000419671	D;D;D;D|.	0.84516|.	-1.86;-1.86;-1.86;-1.86|.	5.6|5.6	5.6|5.6	0.85130|0.85130	von Willebrand factor, type A (3);|.	0.072196|.	0.64402|.	D|.	0.000020|.	T|T	0.57548|0.57548	0.2061|0.2061	M|M	0.63169|0.63169	1.94|1.94	0.49915|0.49915	D|D	0.999831|0.999831	B;D|.	0.60575|.	0.345;0.988|.	B;D|.	0.64237|.	0.199;0.923|.	T|T	0.57289|0.57289	-0.7837|-0.7837	10|5	0.66056|.	D|.	0.02|.	.|.	12.886|12.886	0.58045|0.58045	0.0744:0.0:0.9256:0.0|0.0744:0.0:0.9256:0.0	.|.	190;1354|.	Q99715-2;Q99715|.	.;COCA1_HUMAN|.	N|Q	1354;1354;190;1354;1354|95	ENSP00000325146:H1354N;ENSP00000305147:H190N;ENSP00000412864:H1354N;ENSP00000421216:H1354N|.	ENSP00000325146:H1354N|.	H|P	-|-	1|2	0|0	COL12A1|COL12A1	75917664|75917664	1.000000|1.000000	0.71417|0.71417	0.509000|0.509000	0.27700|0.27700	0.925000|0.925000	0.55904|0.55904	7.690000|7.690000	0.84178|0.84178	2.631000|2.631000	0.89168|0.89168	0.655000|0.655000	0.94253|0.94253	CAT|CCA	.		0.368	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75860944	G	T	75860944	3	4	125	1	0	0	0	0	1	0	0	0	3675	1348	47	4	5315	4	COL12A1	6	75860944	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		75860944	95254123	32	10921											
MYO6	4646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76602272	76602272	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	agtggaggcacagctggcccGacagaaggaggaggaatccc	12	3	16	10	1	0	1	0	0	0	1	1	6	1	5	2	6	1	2	2	6	2	0	rs529167250		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:76602272G>C	ENST00000369977.3	+	28	3111	c.2972G>C	c.(2971-2973)cGa>cCa	p.R991P	MYO6_ENST00000369975.1_Missense_Mutation_p.R991P|MYO6_ENST00000369981.3_Missense_Mutation_p.R991P|MYO6_ENST00000369985.4_Missense_Mutation_p.R991P	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	991	Glu-rich.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CAGCTGGCCCGACAGAAGGAG	0.532																																					p.R991P		.											.	MYO6-92	0			c.G2972C						.						100	109	106					6																	76602272		2203	4300	6503	SO:0001583	missense	4646	exon28			TGGCCCGACAGAA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"Myosins / Myosin superfamily : Class VI"	7605	protein-coding gene	gene with protein product		600970	"deafness, autosomal recessive 37"	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2972G>C	6.37:g.76602272G>C	ENSP00000358994:p.Arg991Pro	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	97	15	NM_004999	0	0	6	14	8	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	9.868	1.198055	0.22037	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975;ENST00000430435	T;T;T;T;T	0.58060	2.07;2.59;2.59;2.07;0.36	5.75	3.97	0.46021	.	0.350255	0.33477	N	0.004873	T	0.55210	0.1906	L	0.61218	1.895	0.09310	N	1	B;D	0.62365	0.086;0.991	B;D	0.67548	0.049;0.952	T	0.50939	-0.8768	10	0.72032	D	0.01	.	11.8787	0.52562	0.1401:0.0:0.8599:0.0	.	991;991	Q9UM54-2;Q9UM54-1	.;.	P	991;991;991;991;991;54	ENSP00000358998:R991P;ENSP00000359002:R991P;ENSP00000358994:R991P;ENSP00000358992:R991P;ENSP00000399406:R54P	ENSP00000358992:R991P	R	+	2	0	MYO6	76658992	0.031000	0.19500	0.018000	0.16275	0.286000	0.27126	0.655000	0.24933	1.448000	0.47680	0.491000	0.48974	CGA	.		0.532	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		C	76602272	G	C	76602272	3	2	125	1	0	0	0	0	1	0	0	0	10106	1058	37	4	3078	4	MYO6	6	76602272	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	741328	76602272	94512795	33	10922											
C6orf167	253714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	97629854	97629854	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcccaaccaaaaagttgAataattgatataactggctg	16	11	6	8	0	1	2	1	2	0	0	2	2	2	2	2	1	2	2	2	1	7	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:97629854A>T	ENST00000275053.4	-	16	2575	c.2310T>A	c.(2308-2310)atT>atA	p.I770I	MMS22L_ENST00000369251.2_Silent_p.I730I	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	770					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CAAAAAGTTGAATAATTGATA	0.373																																					p.I770I		.											.	MMS22L-92	0			c.T2310A						.						174	169	171					6																	97629854		2203	4300	6503	SO:0001819	synonymous_variant	253714	exon16			AAGTTGAATAATT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"chromosome 6 open reading frame 167"	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.2310T>A	6.37:g.97629854A>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	67	10	NM_198468	0	0	1	1	0	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Silent	SNP	ENST00000275053.4	37	CCDS5039.1																																																																																			.		0.373	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		T	97629854	A	T	97629854	2	4	125	1	0	0	0	0	0	0	0	1	2348	242	9	5		5	C6orf167	6	97629854	Silent	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	21027582	97629854	73485213	34	10923											
SERINC1	57515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	122777747	122777747	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacagctttatagccaaccaAaatgttacaagggacaacac	17	8	6	10	0	0	0	0	0	0	0	0	1	0	1	2	1	6	2	2	1	9	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:122777747A>G	ENST00000339697.4	-	3	334	c.250T>C	c.(250-252)Ttg>Ctg	p.L84L		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	84					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		TAGCCAACCAAAATGTTACAA	0.333																																					p.L84L		.											.	SERINC1-91	0			c.T250C						.						125	110	115					6																	122777747		2203	4300	6503	SO:0001819	synonymous_variant	57515	exon3			CAACCAAAATGTT	AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"tumor differentially expressed 2"	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.250T>C	6.37:g.122777747A>G		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	74	13	NM_020755	0	0	26	49	23	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Silent	SNP	ENST00000339697.4	37	CCDS5125.1																																																																																			.		0.333	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		G	122777747	A	G	122777747	2	3	125	1	0	0	0	0	0	0	0	1	14111	11	1	3		3	SERINC1	6	122777747	Silent	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	25147893	122777747	48337320	35	10924											
SP4	6671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	21469335	21469335	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaattcaaatcaatccaacTagtagttcatctctacagga	16	11	4	10	0	4	0	3	0	1	0	6	1	5	1	1	1	2	2	1	1	7	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr7:21469335T>C	ENST00000222584.3	+	3	770	c.552T>C	c.(550-552)acT>acC	p.T184T		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	184					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						TCAATCCAACTAGTAGTTCAT	0.398																																					p.T184T		.											.	SP4-95	0			c.T552C						.						77	74	75					7																	21469335		2203	4300	6503	SO:0001819	synonymous_variant	6671	exon3			TCCAACTAGTAGT		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.552T>C	7.37:g.21469335T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	71	15	NM_003112	0	0	0	0	0	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																			.		0.398	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		C	21469335	T	C	21469335	2	2	125	1	0	0	0	0	0	0	0	1	14998	1509	53	3		3	SP4	7	21469335	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		21469335	137669328	36	10925											
MYO1G	64005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	45010552	45010552	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agcggagcacgaggtcccggGgtgtggccgtcagctcagcc	6	5	17	13	4	2	0	2	0	0	0	3	2	3	1	3	5	4	2	3	5	0	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr7:45010552G>T	ENST00000258787.7	-	8	1089	c.953C>A	c.(952-954)cCc>cAc	p.P318H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	318	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						GAGGTCCCGGGGTGTGGCCGT	0.657																																					p.P318H		.											.	MYO1G-137	0			c.C953A						.						57	47	50					7																	45010552		2202	4300	6502	SO:0001583	missense	64005	exon8			TCCCGGGGTGTGG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"Myosins / Myosin superfamily : Class I"	13880	protein-coding gene	gene with protein product	"minor histocompatibility antigen HA-2"	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.953C>A	7.37:g.45010552G>T	ENSP00000258787:p.Pro318His	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	87	12	NM_033054	0	0	6	6	0	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.075212	0.55646	.	.	ENSG00000136286	ENST00000258787	D	0.87029	-2.2	5.3	4.36	0.52297	Myosin head, motor domain (2);	0.183757	0.26598	N	0.023498	D	0.86871	0.6037	L	0.42744	1.35	0.09310	N	1	P;P	0.50528	0.936;0.848	P;P	0.53401	0.725;0.722	T	0.79472	-0.1789	10	0.46703	T	0.11	.	11.939	0.52890	0.0:0.2921:0.7079:0.0	.	318;318	B0I1T2-4;B0I1T2	.;MYO1G_HUMAN	H	318	ENSP00000258787:P318H	ENSP00000258787:P318H	P	-	2	0	MYO1G	44977077	0.000000	0.05858	0.428000	0.26697	0.808000	0.45660	0.514000	0.22786	2.649000	0.89929	0.655000	0.94253	CCC	.		0.657	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45010552	G	T	45010552	3	4	125	1	0	0	0	0	1	0	0	0	10099	1232	43	4	2163	4	MYO1G	7	45010552	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	23541217	45010552	114128111	37	10926											
NUP205	23165	broad.mit.edu	37	chr7	135269748	135269748	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agatttccttgcacttatgcCaatgaaggtaagtgtaataa	14	13	8	6	0	0	2	0	1	0	1	1	2	1	2	2	1	2	3	2	1	6	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr7:135269748C>A	ENST00000285968.6	+	8	1237	c.1211C>A	c.(1210-1212)cCa>cAa	p.P404Q	NUP205_ENST00000440390.2_Missense_Mutation_p.P198Q	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	404					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GCACTTATGCCAATGAAGGTA	0.299																																					p.P404Q													.	NUP205-207	0			c.C1211A						.						42	41	41					7																	135269748		2203	4300	6503	SO:0001583	missense	23165	exon8			TTATGCCAATGAA	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1211C>A	7.37:g.135269748C>A	ENSP00000285968:p.Pro404Gln	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	30	4	NM_015135	0	0	0	0	0	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700331	0.88924	.	.	ENSG00000155561	ENST00000285968;ENST00000440390	T;T	0.33438	1.41;1.41	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.56920	0.2018	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.57441	-0.7811	10	0.62326	D	0.03	-2.9094	19.44	0.94815	0.0:1.0:0.0:0.0	.	404	Q92621	NU205_HUMAN	Q	404;198	ENSP00000285968:P404Q;ENSP00000401983:P198Q	ENSP00000285968:P404Q	P	+	2	0	NUP205	134920288	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.586000	0.87340	0.591000	0.81541	CCA	.		0.299	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			A	135269748	C	A	135269748	3	1	125	1	0	0	0	0	1	0	0	0	10785	594	21	4	1241	4	NUP205	7	135269748	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	90259196	135269748	23868915	38	10927											
ARMC1	55156	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	66534565	66534565	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catcttttctctgtttgcacGgcattctgccaagtatcgaa	8	15	7	11	2	3	0	0	0	3	0	5	1	3	0	1	1	2	4	1	1	3	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr8:66534565G>C	ENST00000276569.3	-	3	452	c.208C>G	c.(208-210)Cgt>Ggt	p.R70G	ARMC1_ENST00000523384.1_Intron|ARMC1_ENST00000458464.2_Missense_Mutation_p.P31R	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	70					metal ion transport (GO:0030001)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(1)|lung(8)|skin(1)	14			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			CTGTTTGCACGGCATTCTGCC	0.348																																					p.R70G													.	ARMC1-91	0			c.C208G						.						151	144	146					8																	66534565		2203	4300	6503	SO:0001583	missense	55156	exon3			TTGCACGGCATTC	BC011607	CCDS6181.1, CCDS69490.1	8q12.3	2013-02-14			ENSG00000104442	ENSG00000104442		"Armadillo repeat containing"	17684	protein-coding gene	gene with protein product							Standard	XM_005251264		Approved	FLJ10511, Arcp	uc003xvl.3	Q9NVT9	OTTHUMG00000164374	ENST00000276569.3:c.208C>G	8.37:g.66534565G>C	ENSP00000276569:p.Arg70Gly	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	84	14	NM_018120	0	0	6	6	0	B4E2W7|Q9H018|Q9H820	Missense_Mutation	SNP	ENST00000276569.3	37	CCDS6181.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.91|16.91	3.252602|3.252602	0.59212|0.59212	.|.	.|.	ENSG00000104442|ENSG00000104442	ENST00000458464|ENST00000276569;ENST00000518908;ENST00000519352	.|T;T;T	.|0.50277	.|0.75;0.75;0.75	4.97|4.97	4.97|4.97	0.65823|0.65823	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.054393	.|0.85682	.|D	.|0.000000	T|T	0.45875|0.45875	0.1364|0.1364	L|L	0.57536|0.57536	1.79|1.79	0.37913|0.37913	D|D	0.931434|0.931434	D|B	0.55385|0.02656	0.971|0.0	P|B	0.54629|0.04013	0.757|0.001	T|T	0.46190|0.46190	-0.9209|-0.9209	8|10	0.54805|0.17369	T|T	0.06|0.5	-15.0047|-15.0047	18.5949|18.5949	0.91226|0.91226	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	31|70	B4E2W7|Q9NVT9	.|ARMC1_HUMAN	R|G	31|70	.|ENSP00000276569:R70G;ENSP00000429191:R70G;ENSP00000429715:R70G	ENSP00000388572:P31R|ENSP00000276569:R70G	P|R	-|-	2|1	0|0	ARMC1|ARMC1	66697119|66697119	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.383000|9.383000	0.97214|0.97214	2.478000|2.478000	0.83669|0.83669	0.467000|0.467000	0.42956|0.42956	CCG|CGT	.		0.348	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120		C	66534565	G	C	66534565	3	2	125	1	0	0	0	0	1	0	0	0	950	1116	39	4	660	4	ARMC1	8	66534565	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		66534565	79829457	39	10928											
TMC1	117531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	75355127	75355127	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagatgatgatggccaaggTaggtatttttatagttgtct	11	16	11	3	0	1	3	0	2	1	1	1	3	1	3	1	3	0	3	1	3	6	8			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr9:75355127T>C	ENST00000297784.5	+	9	993		c.e9+2		TMC1_ENST00000340019.3_Splice_Site|TMC1_ENST00000396237.3_Splice_Site	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1						auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						ATGGCCAAGGTAGGTATTTTT	0.358																																					.	Pancreas(75;173 1345 14232 34245 43413)	.											.	TMC1-91	0			c.453+2T>C						.						105	108	107					9																	75355127		2203	4300	6503	SO:0001630	splice_region_variant	117531	exon9			CCAAGGTAGGTAT	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"transmembrane, cochlear expressed, 1"	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.453+2T>C	9.37:g.75355127T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	73	16	NM_138691	0	0	0	0	0	A8MVZ2|B1AM91	Splice_Site	SNP	ENST00000297784.5	37	CCDS6643.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.251532	0.39797	.	.	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000396235;ENST00000537917;ENST00000538054;ENST00000542143;ENST00000396237	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2221	0.54439	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMC1	74544947	1.000000	0.71417	0.998000	0.56505	0.532000	0.34746	3.240000	0.51368	2.133000	0.65898	0.533000	0.62120	.	.		0.358	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		Intron	C	75355127	T	C	75355127	5	2	125	1	0	0	0	0	0	0	1	0	16016	1652	57	3	473	3	TMC1	9	75355127	Splice_Site	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		75355127	65858304	40	10929											
NOTCH1	4851	broad.mit.edu	37	chr9	139391937	139391937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatccgtgatgtcccggttgGcaaagtggtccagcagcacc	8	8	13	12	2	0	1	0	1	0	0	3	2	3	1	4	3	2	4	4	3	1	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr9:139391937G>A	ENST00000277541.6	-	34	6329	c.6254C>T	c.(6253-6255)gCc>gTc	p.A2085V		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2085					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTCCCGGTTGGCAAAGTGGTC	0.652			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.A2085V				Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1-5459	0			c.C6254T						.						30	32	32					9																	139391937		2185	4275	6460	SO:0001583	missense	4851	exon34			CGGTTGGCAAAGT	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"Ankyrin repeat domain containing"	7881	protein-coding gene	gene with protein product		190198	"Notch (Drosophila) homolog 1 (translocation-associated)", "Notch homolog 1, translocation-associated (Drosophila)"	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6254C>T	9.37:g.139391937G>A	ENSP00000277541:p.Ala2085Val	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	82	4	NM_017617	0	0	4	4	0	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824283	0.90955	.	.	ENSG00000148400	ENST00000277541	T	0.61510	0.1	5.42	5.42	0.78866	Ankyrin repeat-containing domain (4);	0.115232	0.64402	D	0.000017	T	0.78329	0.4266	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.68483	0.958	T	0.81241	-0.1022	10	0.87932	D	0	.	18.5525	0.91071	0.0:0.0:1.0:0.0	.	2085	P46531	NOTC1_HUMAN	V	2085	ENSP00000277541:A2085V	ENSP00000277541:A2085V	A	-	2	0	NOTCH1	138511758	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	9.598000	0.98277	2.703000	0.92315	0.561000	0.74099	GCC	.		0.652	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139391937	G	A	139391937	3	1	125	1	0	0	0	0	1	0	0	0	10573	1203	42	2	1417	2	NOTCH1	9	139391937	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	64036810	139391937	1821494	41	10930											
COBRA1	25920	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	140158762	140158762	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaagagggcgcgggagctGcaggggtttctcgatggcgt	7	7	19	8	4	1	1	0	0	1	1	2	3	1	2	0	5	3	4	0	5	1	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr9:140158762G>A	ENST00000343053.4	+	6	1186	c.849G>A	c.(847-849)ctG>ctA	p.L283L		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	283					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGCGGGAGCTGCAGGGGTTTC	0.672																																					p.L283L		.											.	.	0			c.G849A						.						63	61	62					9																	140158762		2201	4299	6500	SO:0001819	synonymous_variant	25920	exon6			GGAGCTGCAGGGG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"cofactor of BRCA1"	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.849G>A	9.37:g.140158762G>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	37	8	NM_015456	0	0	25	41	16	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	37	CCDS7040.1																																																																																			.		0.672	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		A	140158762	G	A	140158762	2	1	125	1	0	0	0	0	0	0	0	1	3661	1306	46	2		2	COBRA1	9	140158762	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	766825	140158762	1054669	42	10931											
C10orf18	54906	hgsc.bcm.edu;broad.mit.edu	37	chr10	5781661	5781661	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggattagcataaatagtgttCaaccagaaaataccacagcg	17	8	8	8	1	1	1	1	0	0	1	1	2	1	2	2	1	4	2	2	1	8	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:5781661C>T	ENST00000328090.5	+	13	2153	c.1528C>T	c.(1528-1530)Caa>Taa	p.Q510*	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	510																	AAATAGTGTTCAACCAGAAAA	0.383																																					p.Q510X		.											.	.	0			c.C1528T						.						99	93	95					10																	5781661		1895	4126	6021	SO:0001587	stop_gained	54906	exon13			AGTGTTCAACCAG	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.1528C>T	10.37:g.5781661C>T	ENSP00000328426:p.Gln510*	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	112	6	NM_017782	0	0	1	1	0	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Nonsense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.453755|6.453755	0.97581|0.97581	.|.	.|.	ENSG00000108021|ENSG00000108021	ENST00000328090|ENST00000380270	.|.	.|.	.|.	5.72|5.72	3.81|3.81	0.43845|0.43845	.|.	0.212671|.	0.33144|.	N|.	0.005222|.	.|T	.|0.63920	.|0.2552	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69379	.|-0.5161	.|3	0.25106|.	T|.	0.35|.	.|.	13.9222|13.9222	0.63940|0.63940	0.0:0.556:0.444:0.0|0.0:0.556:0.444:0.0	.|.	.|.	.|.	.|.	X|L	510|208	.|.	ENSP00000328426:Q510X|.	Q|S	+|+	1|2	0|0	C10orf18|C10orf18	5821667|5821667	0.722000|0.722000	0.28017|0.28017	0.029000|0.029000	0.17559|0.17559	0.010000|0.010000	0.07245|0.07245	1.851000|1.851000	0.39338|0.39338	0.699000|0.699000	0.31761|0.31761	-0.274000|-0.274000	0.10170|0.10170	CAA|TCA	.		0.383	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5781661	C	T	5781661	4	4	125	1	0	0	0	0	0	1	0	0	1600	827	29	2	1566	2	C10orf18	10	5781661	Nonsense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		5781661	129753086	43	10932											
EPC1	80314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	32573863	32573863	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatttgtccgaggtatttgTttctgaggtattggcaaact	9	16	11	5	1	1	2	0	1	1	1	2	3	2	2	1	3	1	4	1	3	3	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:32573863T>A	ENST00000263062.8	-	10	1776	c.1507A>T	c.(1507-1509)Aca>Tca	p.T503S	EPC1_ENST00000319778.6_Missense_Mutation_p.T503S|EPC1_ENST00000375110.2_Missense_Mutation_p.T453S|RP11-166N17.3_ENST00000419441.1_RNA	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	503					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GAGGTATTTGTTTCTGAGGTA	0.423																																					p.T503S		.											.	EPC1-93	0			c.A1507T						.						145	139	141					10																	32573863		2203	4300	6503	SO:0001583	missense	80314	exon10			TATTTGTTTCTGA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.1507A>T	10.37:g.32573863T>A	ENSP00000263062:p.Thr503Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	119	21	NM_025209	0	0	1	5	4	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	37	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.240893	0.58995	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.16743	2.32;2.32;2.32	6.07	4.93	0.64822	.	0.132659	0.64402	D	0.000002	T	0.19485	0.0468	L	0.56769	1.78	0.37213	D	0.904872	B;B;B	0.26512	0.019;0.003;0.151	B;B;B	0.27796	0.031;0.027;0.083	T	0.06391	-1.0829	10	0.25106	T	0.35	-3.2229	13.751	0.62908	0.0:0.0:0.1278:0.8721	.	453;503;503	Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;EPC1_HUMAN	S	453;503;503	ENSP00000364251:T453S;ENSP00000318559:T503S;ENSP00000263062:T503S	ENSP00000263062:T503S	T	-	1	0	EPC1	32613869	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.783000	0.68982	1.080000	0.41073	0.533000	0.62120	ACA	.		0.423	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			A	32573863	T	A	32573863	3	1	125	1	0	0	0	0	1	0	0	0	5173	1725	60	5	1027	5	EPC1	10	32573863	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	26792202	32573863	102960884	44	10933											
MBL2	4153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	54527970	54527970	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccactggccatttttcagtAgcaatacacaatcttcatca	12	13	4	12	0	4	0	3	0	1	0	5	0	5	0	2	1	2	2	2	1	4	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:54527970A>G	ENST00000373968.3	-	4	738	c.674T>C	c.(673-675)cTa>cCa	p.L225P		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	225	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						ATTTTTCAGTAGCAATACACA	0.502																																					p.L225P		.											.	MBL2-91	0			c.T674C						.						379	337	351					10																	54527970		2202	4300	6502	SO:0001583	missense	4153	exon4			TTCAGTAGCAATA	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"Collectins"	6922	protein-coding gene	gene with protein product		154545	"mannose-binding lectin (protein C) 2, soluble (opsonic defect)"	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.674T>C	10.37:g.54527970A>G	ENSP00000363079:p.Leu225Pro	Somatic	263	0		WXS	Illumina HiSeq	Phase_I	219	39	NM_000242	0	0	0	0	0	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	CCDS7247.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.444961	0.63178	.	.	ENSG00000165471	ENST00000373968	T	0.24350	1.86	5.13	5.13	0.70059	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	1.028080	0.07735	N	0.945891	T	0.66137	0.2759	H	0.95611	3.695	0.22811	N	0.99871	D	0.89917	1.0	D	0.85130	0.997	T	0.56805	-0.7918	10	0.87932	D	0	-1.5247	13.1902	0.59706	1.0:0.0:0.0:0.0	.	225	P11226	MBL2_HUMAN	P	225	ENSP00000363079:L225P	ENSP00000363079:L225P	L	-	2	0	MBL2	54197976	0.066000	0.20996	0.003000	0.11579	0.002000	0.02628	4.043000	0.57354	2.048000	0.60808	0.482000	0.46254	CTA	.		0.502	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242		G	54527970	A	G	54527970	3	3	125	1	0	0	0	0	1	0	0	0	9375	420	15	3	76	3	MBL2	10	54527970	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	21954107	54527970	81006777	45	10934											
HHEX	3087	broad.mit.edu	37	chr10	94450034	94450038	+	Frame_Shift_Del	DEL	GGGCC	GGGCC	-																															tacggacccggcggcttcggGggccctctgtaccccttccc																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	GGGCC	GGGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:94450034_94450038delGGGCC	ENST00000282728.5	+	1	2090_2094	c.291_295delGGGCC	c.(289-297)gggggccctfs	p.GP98fs	HHEX_ENST00000472590.2_5'Flank|HHEX_ENST00000492654.2_5'Flank	NM_002729.4	NP_002720.1	Q03014	HHEX_HUMAN	hematopoietically expressed homeobox	98	Pro-rich.				anterior/posterior pattern specification (GO:0009952)|B cell differentiation (GO:0030183)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|DNA conformation change (GO:0071103)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|forebrain morphogenesis (GO:0048853)|gall bladder development (GO:0061010)|hepatic duct development (GO:0061011)|hepatoblast differentiation (GO:0061017)|hepatocyte differentiation (GO:0070365)|in utero embryonic development (GO:0001701)|interkinetic nuclear migration (GO:0022027)|mRNA export from nucleus (GO:0006406)|multicellular organism growth (GO:0035264)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|pancreas development (GO:0031016)|poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|primary lung bud formation (GO:0060431)|primitive streak formation (GO:0090009)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|eukaryotic initiation factor 4E binding (GO:0008190)|protein homodimerization activity (GO:0042803)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(2)|lung(5)|ovary(1)	10						GCGGCTTCGGGGGCCCTCTGTACCC	0.737																																					p.97_99del													.	HHEX-227	0			c.291_295del						.																																			SO:0001589	frameshift_variant	3087	exon1			CTTCGGGGGCCCT	Z21533	CCDS7423.1	10q23.33	2011-06-20	2007-02-15		ENSG00000152804	ENSG00000152804		"Homeoboxes / ANTP class : NKL subclass"	4901	protein-coding gene	gene with protein product		604420		PRHX		8096636, 8103988	Standard	NM_002729		Approved	HEX, HOX11L-PEN	uc001kid.3	Q03014	OTTHUMG00000018762	ENST00000282728.5:c.291_295delGGGCC	10.37:g.94450034_94450038delGGGCC	ENSP00000282728:p.Gly98fs	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	10	3	NM_002729	0	0	0	0	0	B1AQ17|Q96CE9	Frame_Shift_Del	DEL	ENST00000282728.5	37	CCDS7423.1																																																																																			.		0.737	HHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049402.2			-	94450038	GGGCC	-	94450034	7	5	125	1	0	1	0	1	0	0	0	0	7112	1219	43	0	293	0	HHEX	10	94450034	Frame_Shift_Del	DEL	GGGCC	TCGA-GL-A4EM-01A-11D-A25F-10	39922064	94450034	41084713	46	10935											
MUC6	4588	broad.mit.edu	37	chr11	1019461	1019462	+	Frame_Shift_Ins	INS	-	-	T																															ggaggcagccctgatgtggcINSttgtggggtgacggccgtgg																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:1019461_1019462insT	ENST00000421673.2	-	30	3893_3894	c.3843_3844insA	c.(3841-3846)caagccfs	p.A1282fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1282	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCTGATGTGGCTTGTGGGGTGA	0.639																																					p.A1282fs													.	MUC6-23	0			c.3844_3845insA						.																																			SO:0001589	frameshift_variant	4588	exon30			ATGTGGCTTGTGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3844dupA	11.37:g.1019463_1019463dupT	ENSP00000406861:p.Ala1282fs	Somatic	304	0		WXS	Illumina HiSeq	Phase_I	439	7	NM_005961	0	0	0	0	0	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Ins	INS	ENST00000421673.2	37	CCDS44513.1																																																																																			.		0.639	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1019462	-	T	1019461	7	5	125	1	0	1	1	0	0	0	0	0	10005	797	28	0	3491	0	MUC6	11	1019461	Frame_Shift_Ins	INS	-	TCGA-GL-A4EM-01A-11D-A25F-10		1019461	133987055	47	10936											
MUC2	4583	broad.mit.edu	37	chr11	1092953	1092953	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccatcaccaccaccactaCggtgaccccaaccccaacac	13	3	3	22	1	1	1	1	1	0	0	1	1	1	1	8	1	3	0	8	1	3	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:1092953C>T	ENST00000441003.2	+	30	4799	c.4772C>T	c.(4771-4773)aCg>aTg	p.T1591M	MUC2_ENST00000359061.5_Splice_Site_p.T1592M|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1592M(1)|p.T1591M(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccactacggtgacccca	0.627																																					p.T1591M													.	MUC2-90	2	Substitution - Missense(2)	endometrium(2)	c.C4772T						.						54	86	74					11																	1092953		1812	3313	5125	SO:0001583	missense	4583	exon30			CCACTACGGTGAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4772C>T	11.37:g.1092953C>T	ENSP00000415183:p.Thr1591Met	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	101	8	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.179	-0.168424	0.06461	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.16743	2.32;2.56	1.75	-0.619	0.11572	.	6.725620	0.00827	U	0.001636	T	0.08846	0.0219	.	.	.	0.09310	N	1	D	0.60575	0.988	B	0.34489	0.184	T	0.24548	-1.0157	9	0.32370	T	0.25	.	3.3423	0.07123	0.2481:0.5888:0.0:0.163	.	1591	E7EUV1	.	M	1591;1592	ENSP00000415183:T1591M;ENSP00000351956:T1592M	ENSP00000351956:T1592M	T	+	2	0	MUC2	1082953	0.064000	0.20934	0.000000	0.03702	0.189000	0.23516	1.615000	0.36922	-0.313000	0.08728	0.121000	0.15741	ACG	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092953	C	T	1092953	3	4	125	1	0	0	0	0	1	0	0	0	10000	536	19	1	4890	1	MUC2	11	1092953	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	73492	1092953	133913563	48	10937											
CCDC86	79080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	60609627	60609627	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccgttaaggcgcagccgacgGctgggaggcctaaggcccga	8	4	16	13	5	0	0	0	0	0	0	0	3	0	1	4	5	1	3	4	5	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:60609627G>T	ENST00000227520.5	+	1	84	c.30G>T	c.(28-30)cgG>cgT	p.R10R	RP11-804A23.4_ENST00000538705.1_RNA|RP11-804A23.2_ENST00000539897.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	10					viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						GCAGCCGACGGCTGGGAGGCC	0.642																																					p.R10R		.											.	CCDC86-90	0			c.G30T						.						15	16	15					11																	60609627		2187	4274	6461	SO:0001819	synonymous_variant	79080	exon1			CCGACGGCTGGGA	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.30G>T	11.37:g.60609627G>T		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	98	18	NM_024098	0	0	13	28	15	B4DY99	Silent	SNP	ENST00000227520.5	37	CCDS7993.1																																																																																			.		0.642	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098		T	60609627	G	T	60609627	2	4	125	1	0	0	0	0	0	0	0	1	2867	1190	42	4		4	CCDC86	11	60609627	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	59516674	60609627	74396889	49	10938											
FERMT3	83706	broad.mit.edu	37	chr11	63978789	63978789	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggggatgccagctcacttctCggacagcgcccagactgagg	8	6	14	13	2	2	2	1	1	1	1	3	4	2	4	2	4	3	1	2	4	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:63978789C>T	ENST00000279227.5	+	5	652	c.557C>T	c.(556-558)tCg>tTg	p.S186L	FERMT3_ENST00000345728.5_Missense_Mutation_p.S186L	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	186					integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						GCTCACTTCTCGGACAGCGCC	0.701																																					p.S186L													.	FERMT3-23	0			c.C557T						.						32	28	29					11																	63978789		2199	4296	6495	SO:0001583	missense	83706	exon5			ACTTCTCGGACAG	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"Fermitins", "Pleckstrin homology (PH) domain containing"	23151	protein-coding gene	gene with protein product	"kindlin-3"	607901	"fermitin family homolog 3 (Drosophila)"				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.557C>T	11.37:g.63978789C>T	ENSP00000279227:p.Ser186Leu	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	58	4	NM_031471	0	0	21	21	0	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.272987	0.23221	.	.	ENSG00000149781	ENST00000544997;ENST00000345728;ENST00000279227;ENST00000541252	T;T;T;T	0.48836	1.46;0.87;0.88;0.8	3.37	3.37	0.38596	Band 4.1 domain (1);	0.235735	0.34750	N	0.003715	T	0.25457	0.0619	N	0.11427	0.14	0.39553	D	0.969006	B;B	0.19706	0.012;0.038	B;B	0.10450	0.005;0.005	T	0.10042	-1.0647	10	0.39692	T	0.17	-11.0265	8.147	0.31117	0.0:0.8833:0.0:0.1167	.	186;186	Q86UX7-2;Q86UX7	.;URP2_HUMAN	L	186;186;186;6	ENSP00000445778:S186L;ENSP00000339950:S186L;ENSP00000279227:S186L;ENSP00000438885:S6L	ENSP00000279227:S186L	S	+	2	0	FERMT3	63735365	0.997000	0.39634	0.998000	0.56505	0.122000	0.20287	3.722000	0.54948	1.915000	0.55452	0.561000	0.74099	TCG	.		0.701	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		T	63978789	C	T	63978789	3	4	125	1	0	0	0	0	1	0	0	0	5838	893	31	1	571	1	FERMT3	11	63978789	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	3369162	63978789	71027727	50	10939											
RNASEH2C	84153	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	65487867	65487867	+	Frame_Shift_Del	DEL	C	C	-																															cctctccccgtagacagcggCcccgaaacgacacttcgagt																								rs554234154		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:65487867delC	ENST00000308418.4	-	2	382	c.194delG	c.(193-195)ggcfs	p.G65fs	RNASEH2C_ENST00000528220.1_5'UTR|RNASEH2C_ENST00000527610.1_Frame_Shift_Del_p.G65fs	NM_032193.3	NP_115569.2	Q8TDP1	RNH2C_HUMAN	ribonuclease H2, subunit C	65					RNA catabolic process (GO:0006401)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)				cervix(1)	1						TAGACAGCGGCCCCGAAACGA	0.677																																					p.G65fs		.											.	RNASEH2C-90	0			c.194delG						.						41	48	46					11																	65487867		2201	4296	6497	SO:0001589	frameshift_variant	84153	exon2			.	AF312034	CCDS8111.1	11q13.1	2014-09-17							24116	protein-coding gene	gene with protein product	"Aicardi-Goutieres syndrome 3"	610330				8244390, 16845400	Standard	NM_032193		Approved	AYP1, AGS3	uc001ofn.3	Q8TDP1		ENST00000308418.4:c.194delG	11.37:g.65487867delC	ENSP00000308193:p.Gly65fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	76	16	NM_032193	0	0	0	0	0	Q9H7F5	Frame_Shift_Del	DEL	ENST00000308418.4	37	CCDS8111.1																																																																																			.		0.677	RNASEH2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390693.2	NM_032193		-	65487867	C	-	65487867	7	5	125	1	0	1	0	1	0	0	0	0	13446	739	26	0	312	0	RNASEH2C	11	65487867	Frame_Shift_Del	DEL	C	TCGA-GL-A4EM-01A-11D-A25F-10	1509078	65487867	69518649	51	10940											
PANX1	24145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	93911576	93911576	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctctttgcgatcctcctgtaCctgcccccgctgttctggcg	2	13	9	17	3	2	0	0	0	2	0	4	1	4	0	5	1	3	3	5	1	1	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:93911576C>G	ENST00000227638.3	+	3	748	c.363C>G	c.(361-363)taC>taG	p.Y121*	PANX1_ENST00000436171.2_Nonsense_Mutation_p.Y121*	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	121					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	TCCTCCTGTACCTGCCCCCGC	0.463																																					p.Y121X		.											.	PANX1-68	0			c.C363G						.						167	127	141					11																	93911576		2201	4298	6499	SO:0001587	stop_gained	24145	exon3			CCTGTACCTGCCC	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"Ion channels / Pannexins"	8599	protein-coding gene	gene with protein product	"innexin"	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.363C>G	11.37:g.93911576C>G	ENSP00000227638:p.Tyr121*	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	184	41	NM_015368	0	0	2	3	1	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Nonsense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	.	.	.	.	.	.	.	.	.	.	C	38	6.963806	0.97967	.	.	ENSG00000110218	ENST00000227638;ENST00000436171	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.6852	13.9642	0.64199	0.0:0.9245:0.0:0.0755	.	.	.	.	X	121	.	ENSP00000227638:Y121X	Y	+	3	2	PANX1	93551224	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	0.922000	0.28734	2.402000	0.81655	0.563000	0.77884	TAC	.		0.463	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368		G	93911576	C	G	93911576	4	3	125	1	0	0	0	0	0	1	0	0	11446	518	18	4	373	4	PANX1	11	93911576	Nonsense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	28423709	93911576	41094940	52	10941											
LPCAT3	10162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7125633	7125633	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgacgcgcccagggacgtCgccaacttgttaaggctcag	8	8	12	13	4	2	1	1	1	1	0	3	2	2	2	2	2	1	2	2	2	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:7125633C>T	ENST00000261407.4	-	1	181	c.96G>A	c.(94-96)gcG>gcA	p.A32A	C1S_ENST00000406697.1_Intron	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	32					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						CCAGGGACGTCGCCAACTTGT	0.662																																					p.A32A		.											.	LPCAT3-91	0			c.G96A						.						49	48	49					12																	7125633		2202	4299	6501	SO:0001819	synonymous_variant	10162	exon1			GGACGTCGCCAAC	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"O-acyltransferase (membrane bound) domain containing 5", "membrane bound O-acyltransferase domain containing 5"	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.96G>A	12.37:g.7125633C>T		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	143	39	NM_005768	0	0	67	153	86	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Silent	SNP	ENST00000261407.4	37	CCDS8572.1																																																																																			.		0.662	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768		T	7125633	C	T	7125633	2	4	125	1	0	0	0	0	0	0	0	1	8937	871	31	1		1	LPCAT3	12	7125633	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		7125633	126726262	53	10942											
SCN8A	6334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52188171	52188171	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaacaaaatccaaggaaTcgtctttgattttgtcactc	13	12	6	10	1	2	2	1	1	1	1	5	3	3	3	2	1	1	0	2	1	5	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:52188171T>A	ENST00000354534.6	+	26	4719	c.4541T>A	c.(4540-4542)aTc>aAc	p.I1514N	SCN8A_ENST00000545061.1_Missense_Mutation_p.I1473N	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1514					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	ATCCAAGGAATCGTCTTTGAT	0.428																																					p.I1514N		.											.	SCN8A-29	0			c.T4541A						.						132	127	129					12																	52188171		1982	4186	6168	SO:0001583	missense	6334	exon26			AAGGAATCGTCTT	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10596	protein-coding gene	gene with protein product		600702	"sodium channel, voltage gated, type VIII, alpha polypeptide"	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.4541T>A	12.37:g.52188171T>A	ENSP00000346534:p.Ile1514Asn	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	72	25	NM_014191	0	0	0	0	0	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	t	11.59	1.684148	0.29872	.	.	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133	D;D;D	0.96073	-3.9;-3.87;-3.75	4.96	4.96	0.65561	.	0.387189	0.31821	N	0.007009	D	0.92051	0.7481	L	0.60455	1.87	0.23050	N	0.998375	B	0.06786	0.001	B	0.01281	0.0	D	0.83764	0.0216	10	0.66056	D	0.02	.	3.8457	0.08934	0.0:0.1628:0.1988:0.6384	.	1514	Q9UQD0	SCN8A_HUMAN	N	1514;1473;1473	ENSP00000346534:I1514N;ENSP00000440360:I1473N;ENSP00000347255:I1473N	ENSP00000346534:I1514N	I	+	2	0	SCN8A	50474438	0.009000	0.17119	0.680000	0.29994	0.997000	0.91878	1.516000	0.35856	2.228000	0.72767	0.524000	0.50904	ATC	.		0.428	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		A	52188171	T	A	52188171	3	1	125	1	0	0	0	0	1	0	0	0	13956	1435	50	5	4639	5	SCN8A	12	52188171	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	45062538	52188171	81663724	54	10943											
KRT84	3890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	52779218	52779218	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggtgatgacactccgactaCcaaagctgccaaggccccgg	11	5	11	14	2	0	2	0	2	0	0	1	3	1	2	5	3	3	1	5	3	3	1	rs148258545		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:52779218C>G	ENST00000257951.3	-	1	218	c.152G>C	c.(151-153)gGt>gCt	p.G51A	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	51	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		ACTCCGACTACCAAAGCTGCC	0.582																																					p.G51A		.											.	KRT84-91	0			c.G152C						.						75	80	78					12																	52779218		2203	4300	6503	SO:0001583	missense	3890	exon1			CGACTACCAAAGC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"-", "Intermediate filaments type II, keratins (basic)"	6461	protein-coding gene	gene with protein product	"hard keratin type II 4"	602766	"keratin, hair, basic, 4"	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.152G>C	12.37:g.52779218C>G	ENSP00000257951:p.Gly51Ala	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	164	35	NM_033045	0	0	0	0	0	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.370922	0.42003	.	.	ENSG00000161849	ENST00000257951	D	0.84944	-1.92	5.06	4.15	0.48705	.	0.143814	0.32563	N	0.005926	D	0.87269	0.6135	M	0.86420	2.815	0.34114	D	0.663369	B	0.15141	0.012	B	0.12156	0.007	D	0.89533	0.3787	10	0.66056	D	0.02	.	15.849	0.78912	0.0:0.864:0.136:0.0	.	51	Q9NSB2	KRT84_HUMAN	A	51	ENSP00000257951:G51A	ENSP00000257951:G51A	G	-	2	0	KRT84	51065485	0.946000	0.32159	0.968000	0.41197	0.853000	0.48598	2.037000	0.41174	1.466000	0.48025	0.543000	0.68304	GGT	C|1.000;T|0.000		0.582	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		G	52779218	C	G	52779218	3	3	125	1	0	0	0	0	1	0	0	0	8519	507	18	4	1686	4	KRT84	12	52779218	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	591047	52779218	81072677	55	10944											
C12orf29	91298	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	88442035	88442035	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgccatcatcttggcttaTgctggccaattccagatact	9	13	7	12	1	2	1	1	0	1	1	4	1	3	1	3	2	2	2	3	2	3	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:88442035T>A	ENST00000356891.3	+	7	1017	c.814T>A	c.(814-816)Tgc>Agc	p.C272S		NM_001009894.2	NP_001009894.2	Q8N999	CL029_HUMAN	chromosome 12 open reading frame 29	272					hematopoietic progenitor cell differentiation (GO:0002244)					large_intestine(3)|lung(1)|ovary(1)	5						TCTTGGCTTATGCTGGCCAAT	0.363																																					p.C272S		.											.	C12orf29-90	0			c.T814A						.						126	108	114					12																	88442035		2203	4300	6503	SO:0001583	missense	91298	exon7			GGCTTATGCTGGC	AL137488	CCDS31866.1	12q21.32	2012-05-30			ENSG00000133641	ENSG00000133641			25322	protein-coding gene	gene with protein product						14702039	Standard	NM_001009894		Approved	DKFZp434N2030	uc001tao.3	Q8N999	OTTHUMG00000169870	ENST00000356891.3:c.814T>A	12.37:g.88442035T>A	ENSP00000349358:p.Cys272Ser	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	141	41	NM_001009894	0	0	1	2	1	Q569K5|Q6AWA8|Q6PEK5|Q8IYQ5|Q9NT75	Missense_Mutation	SNP	ENST00000356891.3	37	CCDS31866.1	.	.	.	.	.	.	.	.	.	.	.	3.780	-0.045871	0.07452	.	.	ENSG00000133641	ENST00000356891	T	0.50001	0.76	5.41	1.98	0.26296	.	0.784752	0.12584	N	0.456148	T	0.27278	0.0669	L	0.34521	1.04	0.26278	N	0.978315	B	0.02656	0.0	B	0.04013	0.001	T	0.32851	-0.9891	10	0.02654	T	1	0.2767	4.1297	0.10143	0.1564:0.353:0.0:0.4906	.	272	Q8N999	CL029_HUMAN	S	272	ENSP00000349358:C272S	ENSP00000349358:C272S	C	+	1	0	C12orf29	86966166	0.225000	0.23685	0.998000	0.56505	0.994000	0.84299	0.223000	0.17719	0.109000	0.17891	0.533000	0.62120	TGC	.		0.363	C12orf29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406335.1	NM_001009894		A	88442035	T	A	88442035	3	1	125	1	0	0	0	0	1	0	0	0	1684	1464	51	5	840	5	C12orf29	12	88442035	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	35662817	88442035	45409860	56	10945											
RPH3A	22895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113333603	113333603	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtttttctatgacatcaaaCacagtgacctggcaaagaag	15	10	8	8	0	2	3	1	2	1	1	2	3	2	3	1	1	1	2	1	1	4	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:113333603C>A	ENST00000389385.4	+	21	2376	c.1879C>A	c.(1879-1881)Cac>Aac	p.H627N	RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000420983.2_Missense_Mutation_p.H627N|RPH3A_ENST00000551052.1_Missense_Mutation_p.H623N|RPH3A_ENST00000415485.3_Missense_Mutation_p.H627N|RPH3A_ENST00000548866.1_Missense_Mutation_p.H578N|RPH3A_ENST00000447659.2_Missense_Mutation_p.H578N|RPH3A_ENST00000543106.2_Missense_Mutation_p.H627N	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	627	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		TGACATCAAACACAGTGACCT	0.473																																					p.H627N		.											.	RPH3A-519	0			c.C1879A						.						97	78	84					12																	113333603		2203	4300	6503	SO:0001583	missense	22895	exon21			ATCAAACACAGTG	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1879C>A	12.37:g.113333603C>A	ENSP00000374036:p.His627Asn	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	101	11	NM_001143854	0	0	0	0	0	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	37	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599097	0.87055	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983;ENST00000549913	T;T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.42	5.42	0.78866	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.64402	D	0.000007	T	0.70684	0.3252	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.997	D;D;D	0.77004	0.989;0.972;0.977	T	0.68637	-0.5356	10	0.27785	T	0.31	.	18.006	0.89209	0.0:1.0:0.0:0.0	.	578;627;623	F8VP47;Q9Y2J0;Q9Y2J0-2	.;RP3A_HUMAN;.	N	627;627;578;623;627;578;627;279	ENSP00000440384:H627N;ENSP00000374036:H627N;ENSP00000413254:H578N;ENSP00000448297:H623N;ENSP00000405357:H627N;ENSP00000450347:H578N;ENSP00000408889:H627N	ENSP00000374036:H627N	H	+	1	0	RPH3A	111817986	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.703000	0.68340	2.550000	0.86006	0.655000	0.94253	CAC	.		0.473	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113333603	C	A	113333603	3	1	125	1	0	0	0	0	1	0	0	0	13583	478	17	4	1953	4	RPH3A	12	113333603	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	24891568	113333603	20518292	57	10946											
FREM2	341640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	39262352	39262352	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggagctgcgttcacgagggGctcctgtgggcagccctgct	4	9	16	12	2	1	0	1	0	0	0	2	2	2	1	2	4	4	5	2	4	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr13:39262352G>C	ENST00000280481.7	+	1	1087	c.871G>C	c.(871-873)Gct>Cct	p.A291P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	291					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)		TTCACGAGGGGCTCCTGTGGG	0.617																																					p.A291P		.											.	FREM2-100	0			c.G871C						.						57	56	56					13																	39262352		2203	4300	6503	SO:0001583	missense	341640	exon1			CGAGGGGCTCCTG	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.871G>C	13.37:g.39262352G>C	ENSP00000280481:p.Ala291Pro	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	107	22	NM_207361	0	0	0	1	1	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.909632	0.33721	.	.	ENSG00000150893	ENST00000280481	T	0.19532	2.14	5.93	0.756	0.18421	.	0.690381	0.13204	N	0.405691	T	0.16685	0.0401	L	0.39898	1.24	0.22675	N	0.998866	B	0.10296	0.003	B	0.10450	0.005	T	0.21655	-1.0239	10	0.62326	D	0.03	.	8.0541	0.30596	0.138:0.0:0.6112:0.2508	.	291	Q5SZK8	FREM2_HUMAN	P	291	ENSP00000280481:A291P	ENSP00000280481:A291P	A	+	1	0	FREM2	38160352	0.752000	0.28338	0.027000	0.17364	0.945000	0.59286	1.457000	0.35212	-0.207000	0.10187	0.555000	0.69702	GCT	.		0.617	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39262352	G	C	39262352	3	2	125	1	0	0	0	0	1	0	0	0	6064	1203	42	4	873	4	FREM2	13	39262352	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		39262352	75907526	58	10947											
RAB15	376267	broad.mit.edu;bcgsc.ca	37	chr14	65418357	65418362	+	In_Frame_Del	DEL	GTATCT	GTATCT	-																															tactgctttgtgatggtctgGtatctctcctgccctgcagt																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	GTATCT	GTATCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:65418357_65418362delGTATCT	ENST00000533601.2	-	3	542_547	c.205_210delAGATAC	c.(205-210)agatacdel	p.RY69del	FNTB_ENST00000542227.1_Intron|RAB15_ENST00000426039.3_In_Frame_Del_p.RY23del|CHURC1-FNTB_ENST00000549987.1_Intron|RAB15_ENST00000436278.2_In_Frame_Del_p.RY23del|FNTB_ENST00000447296.2_Intron|RAB15_ENST00000267512.5_In_Frame_Del_p.RY69del			P59190	RAB15_HUMAN	RAB15, member RAS oncogene family	69					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	8				all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102)		TGATGGTCTGGTATCTCTCCTGCCCT	0.592																																					p.69_70del													.	RAB15-228	0			c.205_210del						.																																			SO:0001651	inframe_deletion	376267	exon3			GGTCTGGTATCTC	BC014511	CCDS9768.1	14q23.2	2012-02-28	2012-02-28		ENSG00000139998	ENSG00000139998		"RAB, member RAS oncogene"	20150	protein-coding gene	gene with protein product						11697911	Standard	NM_198686		Approved		uc001xhz.2	P59190	OTTHUMG00000142810	ENST00000533601.2:c.205_210delAGATAC	14.37:g.65418357_65418362delGTATCT	ENSP00000434103:p.Arg69_Tyr70del	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	154	19	NM_198686	0	0	0	0	0	G5EMR7|Q86TX7|Q8IW89	In_Frame_Del	DEL	ENST00000533601.2	37																																																																																				.		0.592	RAB15-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000390443.2	NM_198686		-	65418362	GTATCT	-	65418357	7	5	125	1	0	1	0	1	0	0	0	0	12933	1256	44	0	436	0	RAB15	14	65418357	In_Frame_Del	DEL	GTATCT	TCGA-GL-A4EM-01A-11D-A25F-10		65418357	41931183	59	10948											
PLEKHH1	57475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	68038953	68038953	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcctgagcacaaactgcagCgcacctcatcctactccacc	11	6	6	18	1	1	1	1	1	0	0	3	1	3	1	5	0	6	3	5	0	2	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:68038953C>A	ENST00000329153.5	+	11	1819	c.1687C>A	c.(1687-1689)Cgc>Agc	p.R563S		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	563						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CAAACTGCAGCGCACCTCATC	0.662																																					p.R563S		.											.	PLEKHH1-22	0			c.C1687A						.						29	32	31					14																	68038953		2079	4209	6288	SO:0001583	missense	57475	exon11			CTGCAGCGCACCT	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"Pleckstrin homology (PH) domain containing"	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.1687C>A	14.37:g.68038953C>A	ENSP00000330278:p.Arg563Ser	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_020715	0	0	0	0	0	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966478	0.74131	.	.	ENSG00000054690	ENST00000329153	T	0.73789	-0.78	4.61	3.68	0.42216	.	0.000000	0.85682	D	0.000000	T	0.79650	0.4482	M	0.64997	1.995	0.80722	D	1	P;D	0.61080	0.911;0.989	P;P	0.60012	0.486;0.867	T	0.76963	-0.2764	10	0.30854	T	0.27	.	11.6328	0.51185	0.2994:0.7006:0.0:0.0	.	78;563	Q9ULM0-2;Q9ULM0	.;PKHH1_HUMAN	S	563	ENSP00000330278:R563S	ENSP00000330278:R563S	R	+	1	0	PLEKHH1	67108706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.483000	0.45233	2.387000	0.81309	0.555000	0.69702	CGC	.		0.662	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		A	68038953	C	A	68038953	3	1	125	1	0	0	0	0	1	0	0	0	12102	768	27	4	1725	4	PLEKHH1	14	68038953	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	2620596	68038953	39310587	60	10949											
EML5	161436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	89105224	89105224	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggcacagaatatcatcaTtatgttcctgataaaaactc	15	12	6	8	0	2	3	2	2	0	1	4	3	3	3	1	1	1	2	1	1	6	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:89105224T>G	ENST00000380664.5	-	30	4240	c.4241A>C	c.(4240-4242)aAt>aCt	p.N1414T	EML5_ENST00000554922.1_Missense_Mutation_p.N1422T|EML5_ENST00000352093.5_Missense_Mutation_p.N1376T			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1414						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AATATCATCATTATGTTCCTG	0.333																																					p.N1422T		.											.	EML5-93	0			c.A4265C						.						81	71	74					14																	89105224		1809	4079	5888	SO:0001583	missense	161436	exon31			TCATCATTATGTT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.4241A>C	14.37:g.89105224T>G	ENSP00000370039:p.Asn1414Thr	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	72	12	NM_183387	0	0	0	0	0	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	2.398	-0.338242	0.05278	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.04234	3.67;3.67;3.67	5.38	3.04	0.35103	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.114168	0.64402	D	0.000016	T	0.01029	0.0034	N	0.00332	-1.63	0.31575	N	0.655785	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38112	-0.9676	10	0.02654	T	1	-24.3174	5.3744	0.16156	0.0:0.1523:0.1491:0.6985	.	1422;1414	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	T	1422;1376;1414	ENSP00000451998:N1422T;ENSP00000298315:N1376T;ENSP00000370039:N1414T	ENSP00000298315:N1376T	N	-	2	0	EML5	88174977	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.975000	0.40569	0.884000	0.36064	0.482000	0.46254	AAT	.		0.333	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			G	89105224	T	G	89105224	3	3	125	1	0	0	0	0	1	0	0	0	5113	1493	52	5	1720	5	EML5	14	89105224	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	21066271	89105224	18244316	61	10950											
WDR20	91833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102689211	102689211	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagttctccaggtggaacTgtagtgtagcgacctcactg	8	10	12	11	1	2	0	1	0	1	0	3	2	2	1	3	2	2	3	3	2	3	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:102689211T>A	ENST00000335263.5	+	4	1817	c.1737T>A	c.(1735-1737)acT>acA	p.T579T	WDR20_ENST00000556807.1_Silent_p.T518T	NM_181291.2	NP_851808.1	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	0										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						CAGGTGGAACTGTAGTGTAGC	0.602																																					p.T579T		.											.	WDR20-90	0			c.T1737A						.						148	116	126					14																	102689211		2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			TGGAACTGTAGTG	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000335263.5:c.1737T>A	14.37:g.102689211T>A		Somatic	221	0		WXS	Illumina HiSeq	Phase_I	232	42	NM_181291	0	0	0	4	4	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000335263.5	37	CCDS9968.1																																																																																			.		0.602	WDR20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414960.1	NM_181291		A	102689211	T	A	102689211	2	1	125	1	0	0	0	0	0	0	0	1	17313	1567	55	5		5	WDR20	14	102689211	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	13583987	102689211	4660329	62	10951											
EIF2AK4	440275	ucsc.edu	37	chr15	40284411	40284411	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacgatcagacaggagacttGattaagtcagacccttcagg	13	8	11	9	1	3	4	3	1	0	3	3	7	3	4	1	2	0	0	1	2	1	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:40284411G>A	ENST00000263791.5	+	17	2710	c.2667G>A	c.(2665-2667)ttG>ttA	p.L889L	EIF2AK4_ENST00000382727.2_Silent_p.L861L	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	889	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		CAGGAGACTTGATTAAGTCAG	0.353																																					p.L889L													.	EIF2AK4-757	0			c.G2667A						.						109	103	105					15																	40284411		1813	4073	5886	SO:0001819	synonymous_variant	440275	exon17			AGACTTGATTAAG	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.2667G>A	15.37:g.40284411G>A		Somatic	48	0		WXS	Illumina HiSeq		46	4	NM_001013703	0	0	6	6	0	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	37	CCDS42016.1																																																																																			.		0.353	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			A	40284411	G	A	40284411	2	1	125	1	0	0	0	0	0	0	0	1	5010	1281	45	2		2	EIF2AK4	15	40284411	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		40284411	62246981	63	10952											
BAHD1	22893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40751142	40751142	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagccgtgaccgtgatcgtgCtactgggggctggtcctcct	4	10	14	13	3	0	2	0	2	0	0	3	2	2	2	4	3	3	2	4	3	1	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:40751142C>A	ENST00000416165.1	+	2	550	c.479C>A	c.(478-480)gCt>gAt	p.A160D	BAHD1_ENST00000561234.1_Missense_Mutation_p.A160D|BAHD1_ENST00000560846.1_Missense_Mutation_p.A160D	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	160					heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CGTGATCGTGCTACTGGGGGC	0.672																																					p.A160D		.											.	BAHD1-90	0			c.C479A						.						22	29	26					15																	40751142		2197	4296	6493	SO:0001583	missense	22893	exon2			ATCGTGCTACTGG	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.479C>A	15.37:g.40751142C>A	ENSP00000396976:p.Ala160Asp	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	44	10	NM_014952	0	0	10	13	3	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	37	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	C	9.014	0.983230	0.18889	.	.	ENSG00000140320	ENST00000416165	T	0.18338	2.22	5.11	0.82	0.18793	.	0.394096	0.23881	N	0.043645	T	0.09291	0.0229	N	0.08118	0	0.09310	N	1	P;B;P	0.36909	0.573;0.437;0.573	B;B;B	0.41894	0.369;0.203;0.369	T	0.26121	-1.0112	10	0.36615	T	0.2	-3.895	7.9432	0.29971	0.0:0.6539:0.1214:0.2247	.	160;160;160	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	D	160	ENSP00000396976:A160D	ENSP00000396976:A160D	A	+	2	0	BAHD1	38538434	0.840000	0.29493	0.037000	0.18230	0.004000	0.04260	1.548000	0.36201	0.311000	0.23014	-0.182000	0.12963	GCT	.		0.672	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40751142	C	A	40751142	3	1	125	1	0	0	0	0	1	0	0	0	1298	797	28	4	481	4	BAHD1	15	40751142	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	466731	40751142	61780250	64	10953											
UBR1	197131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43378432	43378432	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ataaaaatcaacttgctgatCccaccactaaaagaaaagaa	21	7	4	9	0	1	3	1	1	0	2	2	3	2	3	2	0	2	1	2	0	9	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:43378432C>T	ENST00000290650.4	-	2	166	c.88G>A	c.(88-90)Gat>Aat	p.D30N	UBR1_ENST00000382177.2_Missense_Mutation_p.D30N	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	30					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACTTGCTGATCCCACCACTAA	0.358																																					p.D30N		.											.	UBR1-91	0			c.G88A						.						47	50	49					15																	43378432		2203	4299	6502	SO:0001583	missense	197131	exon2			GCTGATCCCACCA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"Ubiquitin protein ligase E3 component n-recognins"	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.88G>A	15.37:g.43378432C>T	ENSP00000290650:p.Asp30Asn	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	30	6	NM_174916	0	0	0	0	0	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.442186	0.25987	.	.	ENSG00000159459	ENST00000290650;ENST00000382177;ENST00000546274	T;T	0.70045	0.39;-0.45	5.41	3.39	0.38822	.	0.425163	0.24730	N	0.036070	T	0.42539	0.1207	N	0.08118	0	0.32678	N	0.515941	B;P	0.35433	0.147;0.501	B;B	0.25140	0.045;0.058	T	0.48958	-0.8988	10	0.17832	T	0.49	-13.2485	17.5354	0.87829	0.0:0.7515:0.2485:0.0	.	30;30	B4DYL2;Q8IWV7	.;UBR1_HUMAN	N	30	ENSP00000290650:D30N;ENSP00000371612:D30N	ENSP00000290650:D30N	D	-	1	0	UBR1	41165724	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.711000	0.37930	1.277000	0.44412	0.561000	0.74099	GAT	.		0.358	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		T	43378432	C	T	43378432	3	4	125	1	0	0	0	0	1	0	0	0	16934	855	30	2	5345	2	UBR1	15	43378432	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	2627290	43378432	59152960	65	10954											
SLC24A5	283652	broad.mit.edu	37	chr15	48431306	48431306	+	Frame_Shift_Del	DEL	T	T	-																															aaaactactttgtgataaccTttttcatgtctgcaatatgg																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:48431306delT	ENST00000341459.3	+	7	1085	c.1012delT	c.(1012-1014)tttfs	p.F339fs	SLC24A5_ENST00000449382.2_Frame_Shift_Del_p.F279fs	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	339					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TGTGATAACCTTTTTCATGTC	0.308																																					p.F338fs													.	SLC24A5-90	0			c.1012delT						.						101	99	100					15																	48431306		2198	4287	6485	SO:0001589	frameshift_variant	283652	exon7			ATAACCTTTTTCA	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"Solute carriers"	20611	protein-coding gene	gene with protein product	"oculocutaneous albinism 6 (autosomal recessive)"	609802	"solute carrier family 24, member 5"			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.1012delT	15.37:g.48431306delT	ENSP00000341550:p.Phe339fs	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	78	7	NM_205850	0	0	0	0	0	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Frame_Shift_Del	DEL	ENST00000341459.3	37	CCDS10128.1																																																																																			.		0.308	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850		-	48431306	T	-	48431306	7	5	125	1	0	1	0	1	0	0	0	0	14501	1609	56	0	1038	0	SLC24A5	15	48431306	Frame_Shift_Del	DEL	T	TCGA-GL-A4EM-01A-11D-A25F-10	5052874	48431306	54100086	66	10955											
C15orf60	283677	broad.mit.edu	37	chr15	73735652	73735652	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacccacctgggccatgcctGgaagctgggacagccccctg	7	5	13	16	0	0	0	0	0	0	0	0	3	0	2	6	3	3	1	6	3	1	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:73735652G>T	ENST00000331090.6	+	1	154	c.126G>T	c.(124-126)ctG>ctT	p.L42L	C15orf60_ENST00000560581.1_Silent_p.L42L	NM_001042367.1	NP_001035826.1	Q7Z4M0	RE114_HUMAN		42					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)					endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|pancreas(1)|prostate(2)	17						GGCCATGCCTGGAAGCTGGGA	0.652																																					p.L42L													.	C15orf60-46	0			c.G126T						.						17	23	21					15																	73735652		1995	4151	6146	SO:0001819	synonymous_variant	283677	exon1			ATGCCTGGAAGCT																												ENST00000331090.6:c.126G>T	15.37:g.73735652G>T		Somatic	39	2		WXS	Illumina HiSeq	Phase_I	43	6	NM_001042367	0	0	0	0	0		Silent	SNP	ENST00000331090.6	37	CCDS45296.1																																																																																			.		0.652	C15orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419069.1			T	73735652	G	T	73735652	2	4	125	1	0	0	0	0	0	0	0	1	1812	1335	47	4		4	C15orf60	15	73735652	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	25304346	73735652	28795740	67	10956											
POLG	5428	broad.mit.edu;bcgsc.ca	37	chr15	89872222	89872222	+	Frame_Shift_Del	DEL	G	G	-																															gacttctggccttgctttgtGgggggctggaccttgtgttt																								rs551973680		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:89872222delG	ENST00000268124.5	-	4	1308	c.975delC	c.(973-975)cccfs	p.P325fs	POLG_ENST00000442287.2_Frame_Shift_Del_p.P325fs	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	325					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			CTTGCTTTGTGGGGGGCTGGA	0.602								DNA polymerases (catalytic subunits)																													p.P325fs	Colon(73;648 1203 11348 18386 27782)												.	POLG-228	0			c.975delC						.						91	80	83					15																	89872222		2200	4299	6499	SO:0001589	frameshift_variant	5428	exon4			CTTTGTGGGGGGC	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"DNA polymerases"	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.975delC	15.37:g.89872222delG	ENSP00000268124:p.Pro325fs	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	150	19	NM_002693	0	0	0	0	0	Q8NFM2|Q92515	Frame_Shift_Del	DEL	ENST00000268124.5	37	CCDS10350.1																																																																																			.		0.602	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		-	89872222	G	-	89872222	7	5	125	1	0	1	0	1	0	0	0	0	12226	1335	47	0	2824	0	POLG	15	89872222	Frame_Shift_Del	DEL	G	TCGA-GL-A4EM-01A-11D-A25F-10	16136570	89872222	12659170	68	10957											
MMP25	64386	hgsc.bcm.edu	37	chr16	3100091	3100091	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggggctggtcaggcggcGtcgccggtacgctctgagcg	3	6	20	12	7	2	1	1	1	1	0	3	1	2	1	1	7	2	3	1	7	1	1	rs146181243		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr16:3100091G>A	ENST00000336577.4	+	3	551	c.314G>A	c.(313-315)cGt>cAt	p.R105H	MMP25_ENST00000570755.1_3'UTR|RP11-473M20.7_ENST00000576250.1_RNA	NM_022468.4	NP_071913.1	Q9H239	MMP28_HUMAN	matrix metallopeptidase 25	120					negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	14					Marimastat(DB00786)	GTCAGGCGGCGTCGCCGGTAC	0.701																																					p.R105H	NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336)	.											.	MMP25-226	0			c.G314A						.	G	HIS/ARG	1,4393	2.1+/-5.4	0,1,2196	54	59	57		314	5.1	0.1	16	dbSNP_134	57	0,8596		0,0,4298	no	missense	MMP25	NM_022468.4	29	0,1,6494	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	105/563	3100091	1,12989	2197	4298	6495	SO:0001583	missense	64386	exon3			GGCGGCGTCGCCG	AF145442	CCDS10492.1	16p13.3	2008-02-05	2005-08-08			ENSG00000008516			14246	protein-coding gene	gene with protein product		608482	"matrix metalloproteinase 25", "matrix metallopeptidase-like 1"	MMPL1, MMP20		10628838, 10706098	Standard	NM_022468		Approved	MT6-MMP	uc002cth.3	Q9NPA2		ENST00000336577.4:c.314G>A	16.37:g.3100091G>A	ENSP00000337816:p.Arg105His	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	22	9	NM_022468	0	0	0	0	0	Q96F04|Q96TE2	Missense_Mutation	SNP	ENST00000336577.4	37	CCDS10492.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085309	0.36758	2.28E-4	0.0	ENSG00000008516	ENST00000336577;ENST00000325800	T	0.19105	2.17	5.06	5.06	0.68205	Metallopeptidase, catalytic domain (1);	0.000000	0.34802	U	0.003670	T	0.19725	0.0474	M	0.62088	1.915	0.09310	N	0.999994	P;D	0.57571	0.796;0.98	B;B	0.37833	0.124;0.259	T	0.39820	-0.9595	10	0.72032	D	0.01	.	9.5362	0.39224	0.0975:0.0:0.9025:0.0	.	29;105	O43923;Q9NPA2	.;MMP25_HUMAN	H	105;32	ENSP00000337816:R105H	ENSP00000324953:R32H	R	+	2	0	MMP25	3040092	0.997000	0.39634	0.093000	0.20910	0.166000	0.22503	5.754000	0.68743	2.356000	0.79943	0.655000	0.94253	CGT	G|1.000;A|0.000		0.701	MMP25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437116.1	NM_022468		A	3100091	G	A	3100091	3	1	125	1	0	0	0	0	1	0	0	0	9687	1145	40	1	324	1	MMP25	16	3100091	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		3100091	87254662	69	10958											
ANKS4B	257629	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	21245180	21245180	+	Frame_Shift_Del	DEL	A	A	-																															tcctactctcttggcagcctAccatgggaacttggaagccc																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr16:21245180delA	ENST00000311620.5	+	1	195	c.122delA	c.(121-123)tacfs	p.Y41fs		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	41					response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|lung(11)|ovary(2)	20				GBM - Glioblastoma multiforme(48;0.0565)		TTGGCAGCCTACCATGGGAAC	0.463																																					p.Y41fs		.											.	ANKS4B-92	0			c.122delA						.						128	125	126					16																	21245180		1902	4118	6020	SO:0001589	frameshift_variant	257629	exon1			.	AK096138	CCDS42130.1	16p12.2	2013-01-10				ENSG00000175311		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26795	protein-coding gene	gene with protein product		609901					Standard	NM_145865		Approved	FLJ38819, HARP	uc010bwp.1	Q8N8V4		ENST00000311620.5:c.122delA	16.37:g.21245180delA	ENSP00000308772:p.Tyr41fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	144	47	NM_145865	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000311620.5	37	CCDS42130.1																																																																																			.		0.463	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865		-	21245180	A	-	21245180	7	5	125	1	0	1	0	1	0	0	0	0	691	391	14	0	124	0	ANKS4B	16	21245180	Frame_Shift_Del	DEL	A	TCGA-GL-A4EM-01A-11D-A25F-10	18145089	21245180	69109573	70	10959											
COG8	84342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	69368509	69368509	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagatcattgaaggcaaccAgaatattgttgagaaagcag	16	8	11	6	0	1	4	1	2	0	3	1	5	1	4	1	1	2	4	1	1	5	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr16:69368509A>T	ENST00000306875.4	-	3	1442	c.1328T>A	c.(1327-1329)cTg>cAg	p.L443Q	RP11-343C2.12_ENST00000562949.1_Missense_Mutation_p.L89Q|COG8_ENST00000562081.1_Missense_Mutation_p.L443Q	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	443					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						GAAGGCAACCAGAATATTGTT	0.597																																					p.L443Q		.											.	COG8-91	0			c.T1328A						.						68	65	66					16																	69368509		2198	4300	6498	SO:0001583	missense	84342	exon3			GCAACCAGAATAT	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.1328T>A	16.37:g.69368509A>T	ENSP00000305459:p.Leu443Gln	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	153	27	NM_032382	0	0	16	24	8	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	ENST00000306875.4	37	CCDS10876.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556094	0.86231	.	.	ENSG00000213380	ENST00000306875	T	0.61859	0.07	5.86	5.86	0.93980	.	0.085303	0.56097	D	0.000029	T	0.73860	0.3641	M	0.74881	2.28	0.80722	D	1	D;D	0.61080	0.989;0.989	P;P	0.61328	0.887;0.887	T	0.76305	-0.3008	10	0.56958	D	0.05	-1.8093	16.2605	0.82541	1.0:0.0:0.0:0.0	.	470;443	B4DYU2;Q96MW5	.;COG8_HUMAN	Q	443	ENSP00000305459:L443Q	ENSP00000305459:L443Q	L	-	2	0	COG8	67926010	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.903000	0.92573	2.237000	0.73441	0.460000	0.39030	CTG	.		0.597	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		T	69368509	A	T	69368509	3	4	125	1	0	0	0	0	1	0	0	0	3670	188	7	5	522	5	COG8	16	69368509	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	48123329	69368509	20986244	71	10960											
GPR172B	55065	ucsc.edu;bcgsc.ca	37	chr17	4937403	4937403	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggaaagtgacattagaGgtacaacaggccattgccaa	15	6	12	8	0	0	2	0	1	0	1	0	3	0	3	2	4	3	2	2	4	5	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:4937403G>T	ENST00000424747.1	-	3	1093	c.381C>A	c.(379-381)acC>acA	p.T127T	SLC52A1_ENST00000512825.2_Silent_p.T127T|SLC52A1_ENST00000254853.5_Silent_p.T127T	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	127					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										TGACATTAGAGGTACAACAGG	0.597																																					p.T127T													.	.	0			c.C381A						.						145	143	144					17																	4937403		2203	4300	6503	SO:0001819	synonymous_variant	55065	exon3			ATTAGAGGTACAA	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.381C>A	17.37:g.4937403G>T		Somatic	111	2		WXS	Illumina HiSeq		158	46	NM_017986	0	0	2	3	1	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	37	CCDS11066.1																																																																																			.		0.597	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		T	4937403	G	T	4937403	2	4	125	1	0	0	0	0	0	0	0	1	6690	987	35	4		4	GPR172B	17	4937403	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		4937403	76257807	72	10961											
CHRNB1	1140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7350850	7350850	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttccccttcgactggcagaAttgcactatggtgttcagct	7	13	9	12	1	1	1	1	0	0	1	3	2	2	1	2	2	2	4	2	2	2	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:7350850A>T	ENST00000306071.2	+	6	558	c.491A>T	c.(490-492)aAt>aTt	p.N164I	CHRNB1_ENST00000536404.2_Missense_Mutation_p.N92I|RP11-104H15.10_ENST00000575331.1_RNA|CHRNB1_ENST00000576360.1_Missense_Mutation_p.N92I	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	164					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	GACTGGCAGAATTGCACTATG	0.567																																					p.N164I		.											.	CHRNB1-92	0			c.A491T						.						126	112	117					17																	7350850		2203	4300	6503	SO:0001583	missense	1140	exon6			GGCAGAATTGCAC	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1961	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 1 (muscle)"	100710	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.491A>T	17.37:g.7350850A>T	ENSP00000304290:p.Asn164Ile	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	166	21	NM_000747	0	0	2	6	4	B7Z5H1|Q8IZ46|Q96FB8	Missense_Mutation	SNP	ENST00000306071.2	37	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331856	0.81801	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	T;T	0.80480	-1.38;-1.38	4.96	4.96	0.65561	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.86335	0.5908	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86860	0.2029	10	0.87932	D	0	.	7.3997	0.26956	0.9015:0.0:0.0985:0.0	.	164	P11230	ACHB_HUMAN	I	164;92	ENSP00000304290:N164I;ENSP00000439209:N92I	ENSP00000304290:N164I	N	+	2	0	CHRNB1	7291574	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.939000	0.92951	1.863000	0.54032	0.459000	0.35465	AAT	.		0.567	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3			T	7350850	A	T	7350850	3	4	125	1	0	0	0	0	1	0	0	0	3396	101	4	5	513	5	CHRNB1	17	7350850	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	2413447	7350850	73844360	73	10962											
AMAC1L3	643664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7386013	7386013	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctgctgggctctgtgccagGcctctttgtgctgcagcccc	2	11	13	15	0	2	0	0	0	2	0	2	0	2	0	4	2	5	5	4	2	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:7386013G>C	ENST00000412468.2	+	2	825	c.710G>C	c.(709-711)gGc>gCc	p.G237A	POLR2A_ENST00000572844.1_5'Flank|POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	237						integral component of membrane (GO:0016021)											TCTGTGCCAGGCCTCTTTGTG	0.612																																					p.G237A		.											.	.	0			c.G710C						.						52	52	52					17																	7386013		2203	4297	6500	SO:0001583	missense	643664	exon2			TGCCAGGCCTCTT		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.710G>C	17.37:g.7386013G>C	ENSP00000396523:p.Gly237Ala	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	183	25	NM_001102614	0	0	0	0	0		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	3.103	-0.184272	0.06340	.	.	ENSG00000181222	ENST00000412468	T	0.49720	0.77	4.06	3.07	0.35406	.	.	.	.	.	T	0.21631	0.0521	N	0.08118	0	0.25938	N	0.982908	B	0.09022	0.002	B	0.14578	0.011	T	0.27468	-1.0073	9	0.02654	T	1	-1.8186	7.3041	0.26436	0.0:0.1871:0.6199:0.193	.	237	P0C7Q6	S35G6_HUMAN	A	237	ENSP00000396523:G237A	ENSP00000396523:G237A	G	+	2	0	SLC35G6	7326737	0.975000	0.34042	0.271000	0.24616	0.720000	0.41350	2.298000	0.43602	0.827000	0.34685	0.467000	0.42956	GGC	.		0.612	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		C	7386013	G	C	7386013	3	2	125	1	0	0	0	0	1	0	0	0	561	1203	42	4	716	4	AMAC1L3	17	7386013	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	35163	7386013	73809197	74	10963											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	349	16		WXS	Illumina HiSeq		420	30	NM_145301	0	0	4	32	28	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		T	15457087	C	T	15457087	3	4	125	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	8071074	15457087	65738123	75	10964											
UTP6	55813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	30219812	30219812	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccaaagttgaacatcgTcctgcaagaaaagcaatgta	17	7	9	8	1	0	3	0	1	0	2	2	3	1	3	2	0	4	4	2	0	7	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:30219812T>C	ENST00000261708.4	-	5	451	c.314A>G	c.(313-315)gAc>gGc	p.D105G	UTP6_ENST00000490218.2_5'UTR	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	105					rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				TTGAACATCGTCCTGCAAGAA	0.378																																					p.D105G		.											.	UTP6-91	0			c.A314G						.						116	93	101					17																	30219812		2203	4300	6503	SO:0001630	splice_region_variant	55813	exon5			ACATCGTCCTGCA	AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated antigen 66"		"chromosome 17 open reading frame 40"	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.313-1A>G	17.37:g.30219812T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	76	10	NM_018428	0	0	0	0	0	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.111575	0.37242	.	.	ENSG00000108651	ENST00000261708	T	0.36699	1.24	5.44	5.44	0.79542	.	0.233979	0.51477	D	0.000100	T	0.24084	0.0583	N	0.21617	0.685	0.54753	D	0.999983	B;B	0.29766	0.129;0.256	B;B	0.24155	0.021;0.051	T	0.06698	-1.0812	10	0.15952	T	0.53	-22.7625	15.1464	0.72657	0.0:0.0:0.0:1.0	.	105;105	B4DSL9;Q9NYH9	.;UTP6_HUMAN	G	105	ENSP00000261708:D105G	ENSP00000261708:D105G	D	-	2	0	UTP6	27243925	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	3.602000	0.54066	2.057000	0.61298	0.454000	0.30748	GAC	.		0.378	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428	Missense_Mutation	C	30219812	T	C	30219812	5	2	125	1	0	0	0	0	0	0	1	0	17135	1681	58	3	1539	3	UTP6	17	30219812	Splice_Site	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	14762725	30219812	50975398	76	10965											
CLTC	1213	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	57760151	57760152	+	Frame_Shift_Del	DEL	AG	AG	-																															aacagtactcgaacatggaaAgaggtaatctaaacccaagt																								rs111452880		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:57760151_57760152delAG	ENST00000269122.3	+	23	4036_4037	c.3762_3763delAG	c.(3760-3765)aaagagfs	p.E1255fs	CLTC_ENST00000579456.1_Frame_Shift_Del_p.E192fs|CLTC_ENST00000393043.1_Frame_Shift_Del_p.E1255fs	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1255	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAACATGGAAAGAGGTAATCTA	0.386			T	"ALK, TFE3"	"ALCL, renal "																																p.1254_1255del		.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC-835	0			c.3762_3763del						.																																			SO:0001589	frameshift_variant	1213	exon23			.	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.3762_3763delAG	17.37:g.57760153_57760154delAG	ENSP00000269122:p.Glu1255fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	90	21	NM_004859	0	0	0	0	0	D3DU00|Q6N0A0|Q86TF2	Frame_Shift_Del	DEL	ENST00000269122.3	37	CCDS32696.1																																																																																			.		0.386	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		-	57760152	AG	-	57760151	7	5	125	1	0	1	0	1	0	0	0	0	3572	69	3	0	3852	0	CLTC	17	57760151	Frame_Shift_Del	DEL	AG	TCGA-GL-A4EM-01A-11D-A25F-10	27540339	57760151	23435059	77	10966											
SLC25A19	60386	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73273550	73273550	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctccactgccacaaagcaGgttttggaggttctctgaac	10	10	10	11	0	1	1	0	1	1	0	3	2	2	2	2	3	4	4	2	3	2	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:73273550G>C	ENST00000402418.3	-	5	1567	c.658C>G	c.(658-660)Ctg>Gtg	p.L220V	SLC25A19_ENST00000375261.4_Missense_Mutation_p.L163V|SLC25A19_ENST00000416858.2_Missense_Mutation_p.L220V|SLC25A19_ENST00000442286.2_Missense_Mutation_p.L220V|SLC25A19_ENST00000580994.1_Missense_Mutation_p.L220V|SLC25A19_ENST00000320362.3_Missense_Mutation_p.L220V			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	220					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			CCACAAAGCAGGTTTTGGAGG	0.512																																					p.L220V		.											.	SLC25A19-91	0			c.C658G						.						83	75	78					17																	73273550		2203	4300	6503	SO:0001583	missense	60386	exon6			AAAGCAGGTTTTG		CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"Solute carriers"	14409	protein-coding gene	gene with protein product		606521	"solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19", "microcephaly, Amish"	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.658C>G	17.37:g.73273550G>C	ENSP00000385312:p.Leu220Val	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	105	27	NM_001126122	0	0	16	22	6	E9PF74|Q6V9R7	Missense_Mutation	SNP	ENST00000402418.3	37	CCDS11720.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.031943	0.54790	.	.	ENSG00000125454	ENST00000416858;ENST00000442286;ENST00000320362;ENST00000402418;ENST00000375261	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	5.35	2.3	0.28687	Mitochondrial carrier domain (2);	0.067029	0.64402	D	0.000011	D	0.82435	0.5036	L	0.45581	1.43	0.45930	D	0.998765	D;P	0.61697	0.99;0.935	P;P	0.62014	0.897;0.513	T	0.81187	-0.1047	10	0.62326	D	0.03	-13.3282	9.0336	0.36273	0.3003:0.0:0.6997:0.0	.	163;220	E9PF74;Q9HC21	.;TPC_HUMAN	V	220;220;220;220;163	ENSP00000397818:L220V;ENSP00000402202:L220V;ENSP00000319574:L220V;ENSP00000385312:L220V;ENSP00000364410:L163V	ENSP00000319574:L220V	L	-	1	2	SLC25A19	70785145	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.657000	0.61490	0.648000	0.30732	-0.157000	0.13467	CTG	.		0.512	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734		C	73273550	G	C	73273550	3	2	125	1	0	0	0	0	1	0	0	0	14513	991	35	4	312	4	SLC25A19	17	73273550	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	15513399	73273550	7921660	78	10967											
RNF213	57674	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	78321624	78321624	+	Frame_Shift_Del	DEL	C	C	-																															gtgtacaaacactttcccatCcccctcattaaccggctgga																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:78321624delC	ENST00000582970.1	+	29	9632	c.9489delC	c.(9487-9489)atcfs	p.I3163fs	RNF213_ENST00000336301.6_Frame_Shift_Del_p.I1236fs|RNF213_ENST00000508628.2_Frame_Shift_Del_p.I3212fs	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3163					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ACTTTCCCATCCCCCTCATTA	0.542																																					p.I3163fs		.											.	RNF213-577	0			c.9489delC						.						67	62	63					17																	78321624		2203	4300	6503	SO:0001589	frameshift_variant	57674	exon29			.	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.9489delC	17.37:g.78321624delC	ENSP00000464087:p.Ile3163fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	180	48	NM_001256071	0	0	0	0	0	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Frame_Shift_Del	DEL	ENST00000582970.1	37	CCDS58606.1																																																																																			.		0.542	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		-	78321624	C	-	78321624	7	5	125	1	0	1	0	1	0	0	0	0	13509	845	30	0	9918	0	RNF213	17	78321624	Frame_Shift_Del	DEL	C	TCGA-GL-A4EM-01A-11D-A25F-10	5048074	78321624	2873586	79	10968											
PIGN	23556	bcgsc.ca	37	chr18	59807700	59807700	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aataagggaagtcatcaatgGtgcaatatcagcctacaaat	17	9	8	7	0	3	0	3	0	0	0	3	1	3	1	1	2	3	1	1	2	8	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr18:59807700G>A	ENST00000357637.5	-	12	1391	c.976C>T	c.(976-978)Cca>Tca	p.P326S	PIGN_ENST00000400334.3_Missense_Mutation_p.P326S	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	326					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				GTCATCAATGGTGCAATATCA	0.303																																					p.P326S													.	PIGN-227	0			c.C976T						.						57	51	53					18																	59807700		1828	4080	5908	SO:0001583	missense	23556	exon12			TCAATGGTGCAAT	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"Phosphatidylinositol glycan anchor biosynthesis"	8967	protein-coding gene	gene with protein product		606097	"phosphatidylinositol glycan, class N"			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.976C>T	18.37:g.59807700G>A	ENSP00000350263:p.Pro326Ser	Somatic	97	0		WXS	Illumina HiSeq	Phase_1	99	6	NM_176787	0	0	0	0	0	Q7L8F8|Q8TC01|Q9NT05	Missense_Mutation	SNP	ENST00000357637.5	37	CCDS45879.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569012	0.86439	.	.	ENSG00000197563	ENST00000357637;ENST00000400334	T;T	0.46063	0.88;0.88	5.72	5.72	0.89469	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.054258	0.85682	D	0.000000	T	0.62060	0.2397	L	0.58583	1.82	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.69479	0.946;0.964	T	0.56141	-0.8028	9	.	.	.	-11.9738	19.8454	0.96706	0.0:0.0:1.0:0.0	.	326;326	B2RCI8;O95427	.;PIGN_HUMAN	S	326	ENSP00000350263:P326S;ENSP00000383188:P326S	.	P	-	1	0	PIGN	57958680	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.060000	0.64312	2.850000	0.98022	0.650000	0.86243	CCA	.		0.303	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787		A	59807700	G	A	59807700	3	1	125	1	0	0	0	0	1	0	0	0	11919	1261	44	2	1899	2	PIGN	18	59807700	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		59807700	18269548	80	10969											
CC2D1A	54862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	14028999	14028999	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccgctagacacttccgcGtggctaaggtgcgtccagcc	6	8	12	15	4	0	1	0	0	0	1	2	1	2	1	4	2	3	2	4	2	2	3	rs368763604		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:14028999G>T	ENST00000318003.7	+	7	1106	c.865G>T	c.(865-867)Gtg>Ttg	p.V289L	CC2D1A_ENST00000589606.1_Missense_Mutation_p.V289L	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	289	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ACACTTCCGCGTGGCTAAGGT	0.632																																					p.V289L		.											.	CC2D1A-90	0			c.G865T						.						9	11	10					19																	14028999		2035	4174	6209	SO:0001583	missense	54862	exon7			TTCCGCGTGGCTA	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"mental retardation, nonsyndromic, autosomal recessive, 3"	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.865G>T	19.37:g.14028999G>T	ENSP00000313601:p.Val289Leu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	156	32	NM_017721	0	0	0	0	0	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760509	0.31137	.	.	ENSG00000132024	ENST00000318003;ENST00000397486	T	0.23147	1.92	5.38	4.32	0.51571	Domain of unknown function DM14 (1);	0.244121	0.35291	N	0.003314	T	0.20007	0.0481	L	0.47716	1.5	0.34644	D	0.72099	P;B;P	0.43909	0.543;0.33;0.821	B;B;B	0.36719	0.198;0.126;0.231	T	0.30679	-0.9970	10	0.30854	T	0.27	-20.8199	10.4966	0.44780	0.0918:0.0:0.9082:0.0	.	289;289;43	Q6P1N0-2;Q6P1N0;C9J1T8	.;C2D1A_HUMAN;.	L	289;43	ENSP00000313601:V289L	ENSP00000313601:V289L	V	+	1	0	CC2D1A	13889999	0.936000	0.31750	0.936000	0.37596	0.192000	0.23643	1.812000	0.38952	1.235000	0.43724	0.655000	0.94253	GTG	.		0.632	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		T	14028999	G	T	14028999	3	4	125	1	0	0	0	0	1	0	0	0	2732	1145	40	4	891	4	CC2D1A	19	14028999	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		14028999	45099984	81	10970											
GRAMD1A	57655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35505160	35505160	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagccagacagtgacccCggtggctgaacccccgagca	9	4	11	17	2	0	3	0	2	0	1	1	4	1	3	6	2	3	2	6	2	1	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:35505160C>G	ENST00000317991.5	+	10	1130	c.938C>G	c.(937-939)cCg>cGg	p.P313R	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.P306R|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.P79R|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.P400R	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	313						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			ACAGTGACCCCGGTGGCTGAA	0.652																																					p.P313R		.											.	GRAMD1A-90	0			c.C938G						.						48	61	57					19																	35505160		2097	4240	6337	SO:0001583	missense	57655	exon10			TGACCCCGGTGGC	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.938C>G	19.37:g.35505160C>G	ENSP00000441032:p.Pro313Arg	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	168	21	NM_020895	0	0	61	85	24	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536733	0.65085	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.47177	0.85;1.89;1.9	4.44	4.44	0.53790	.	0.367080	0.24580	N	0.037308	T	0.54647	0.1871	L	0.34521	1.04	0.50039	D	0.999843	P;D;D;D;D	0.76494	0.484;0.997;0.999;0.964;0.997	B;P;D;P;D	0.75484	0.215;0.901;0.986;0.694;0.963	T	0.44174	-0.9345	10	0.18276	T	0.48	.	14.5907	0.68362	0.0:1.0:0.0:0.0	.	313;313;79;306;400	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	R	400;79;313;306	ENSP00000423728:P79R;ENSP00000441032:P313R;ENSP00000439267:P306R	ENSP00000441032:P313R	P	+	2	0	GRAMD1A	40197000	0.272000	0.24172	0.963000	0.40424	0.951000	0.60555	1.956000	0.40382	2.309000	0.77851	0.491000	0.48974	CCG	.		0.652	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		G	35505160	C	G	35505160	3	3	125	1	0	0	0	0	1	0	0	0	6768	652	23	4	976	4	GRAMD1A	19	35505160	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	21476161	35505160	23623823	82	10971											
FCGBP	8857	bcgsc.ca	37	chr19	40374023	40374023	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgttcctggcacaccaCgactttacccacatggcacg	8	9	9	15	2	0	0	0	0	0	0	1	1	1	0	3	2	1	4	3	2	1	3	rs561293450	byFrequency	TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:40374023C>T	ENST00000221347.6	-	26	12062	c.12055G>A	c.(12055-12057)Gtg>Atg	p.V4019M	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4019	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGGCACACCACGACTTTACCC	0.642													C|||	36	0.0071885	0.0121	0.0029	5008	,	,		23567	0.004		0.0119	False		,,,				2504	0.002				p.V4019M													.	FCGBP-98	0			c.G12055A						.						13	14	13					19																	40374023		2141	4205	6346	SO:0001583	missense	8857	exon26			ACACCACGACTTT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12055G>A	19.37:g.40374023C>T	ENSP00000221347:p.Val4019Met	Somatic	826	6		WXS	Illumina HiSeq	Phase_1	1115	22	NM_003890	0	0	1	1	0	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	6.436	0.448534	0.12223	.	.	ENSG00000090920	ENST00000221347	T	0.06608	3.28	2.99	-5.98	0.02220	von Willebrand factor, type C (1);	.	.	.	.	T	0.03520	0.0101	L	0.31476	0.935	0.09310	N	1	B	0.29766	0.256	B	0.14578	0.011	T	0.30060	-0.9991	9	0.34782	T	0.22	.	6.2908	0.21059	0.0:0.3427:0.2739:0.3834	.	4019	Q9Y6R7	FCGBP_HUMAN	M	4019	ENSP00000221347:V4019M	ENSP00000221347:V4019M	V	-	1	0	FCGBP	45065863	0.000000	0.05858	0.010000	0.14722	0.077000	0.17291	-1.245000	0.02899	-1.918000	0.01072	-0.680000	0.03767	GTG	CGA|0.500;TGC|0.500		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40374023	C	T	40374023	3	4	125	1	0	0	0	0	1	0	0	0	5797	536	19	1	4206	1	FCGBP	19	40374023	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	4868863	40374023	18754960	83	10972											
CYP2A6	1548	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41350548	41350548	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctcttaccgatggaaaaggGcacaaaagcatcactcttct	13	10	7	11	1	4	0	1	0	3	0	5	2	4	1	1	2	2	2	1	2	5	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:41350548G>T	ENST00000301141.5	-	8	1311	c.1291C>A	c.(1291-1293)Ccc>Acc	p.P431T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	431					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	ATGGAAAAGGGCACAAAAGCA	0.567																																					p.P431T													.	CYP2A6-92	0			c.C1291A						.						160	150	153					19																	41350548		2203	4300	6503	SO:0001583	missense	1548	exon8			AAAAGGGCACAAA	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1291C>A	19.37:g.41350548G>T	ENSP00000301141:p.Pro431Thr	Somatic	385	2		WXS	Illumina HiSeq	Phase_I	360	49	NM_000762	0	0	0	0	0	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	13.72	2.322377	0.41096	.	.	ENSG00000255974	ENST00000301141	D	0.83591	-1.74	3.16	1.88	0.25563	.	0.000000	0.85682	U	0.000000	D	0.88343	0.6411	M	0.70595	2.14	0.26111	N	0.980682	D	0.89917	1.0	D	0.81914	0.995	T	0.79165	-0.1916	10	0.72032	D	0.01	.	10.5837	0.45269	0.0:0.3621:0.6378:0.0	.	431	P11509	CP2A6_HUMAN	T	431	ENSP00000301141:P431T	ENSP00000301141:P431T	P	-	1	0	CYP2A6	46042388	1.000000	0.71417	0.646000	0.29493	0.731000	0.41821	3.222000	0.51223	1.487000	0.48415	0.379000	0.24179	CCC	.		0.567	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		T	41350548	G	T	41350548	3	4	125	1	0	0	0	0	1	0	0	0	4168	1203	42	4	201	4	CYP2A6	19	41350548	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	976525	41350548	17778435	84	10973											
ZNF235	9310	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44792844	44792844	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctacgctgggtaagaggtgaTacctttagggtatctttacc	9	13	11	8	1	1	2	0	1	1	1	1	2	1	2	2	3	3	3	2	3	6	8			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:44792844T>C	ENST00000291182.4	-	5	846	c.744A>G	c.(742-744)gtA>gtG	p.V248V	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	248					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)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				TAAGAGGTGATACCTTTAGGG	0.378																																					p.V248V													.	ZNF235-137	0			c.A744G						.						107	107	107					19																	44792844		2203	4300	6503	SO:0001819	synonymous_variant	9310	exon5			AGGTGATACCTTT	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"Zinc fingers, C2H2-type", "-"	12866	protein-coding gene	gene with protein product		604749	"zinc finger protein homologous to Zfp93 in mouse"	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.744A>G	19.37:g.44792844T>C		Somatic	133	1		WXS	Illumina HiSeq	Phase_I	167	41	NM_004234	0	0	0	0	0	B4DTQ7|O14898|O14899|Q17RR8	Silent	SNP	ENST00000291182.4	37	CCDS33048.1																																																																																			.		0.378	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			C	44792844	T	C	44792844	2	2	125	1	0	0	0	0	0	0	0	1	17820	1393	49	3		3	ZNF235	19	44792844	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	3442296	44792844	14336139	85	10974											
ZNF154	7710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58213806	58213806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgagactgtagcttttgcTaaaggatttcccacattcac	11	14	7	9	0	1	1	1	1	0	1	2	3	2	2	1	1	2	3	1	1	3	7			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:58213806T>C	ENST00000512439.2	-	3	707	c.511A>G	c.(511-513)Agc>Ggc	p.S171G	ZNF154_ENST00000426889.1_Missense_Mutation_p.S171G|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	171					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)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TAGCTTTTGCTAAAGGATTTC	0.433																																					p.S171G		.											.	ZNF154-90	0			c.A511G						.						215	215	215					19																	58213806		2165	4285	6450	SO:0001583	missense	7710	exon3			TTTTGCTAAAGGA	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"Zinc fingers, C2H2-type", "-"	12939	protein-coding gene	gene with protein product		604085	"zinc finger protein 154 (pHZ-92)"			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.511A>G	19.37:g.58213806T>C	ENSP00000421258:p.Ser171Gly	Somatic	335	0		WXS	Illumina HiSeq	Phase_I	296	41	NM_001085384	0	0	0	0	0	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.953447	0.53293	.	.	ENSG00000179909	ENST00000512439;ENST00000426889;ENST00000396157	T;T	0.07688	3.17;3.17	3.03	2.0	0.26442	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08044	0.0201	L	0.55834	1.745	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.34825	-0.9813	9	0.52906	T	0.07	.	2.5259	0.04691	0.2336:0.1338:0.0:0.6326	.	171	Q13106	ZN154_HUMAN	G	171;171;42	ENSP00000421258:S171G;ENSP00000442370:S171G	ENSP00000440907:S42G	S	-	1	0	ZNF154	62905618	0.001000	0.12720	0.015000	0.15790	0.941000	0.58515	0.218000	0.17622	0.559000	0.29153	0.459000	0.35465	AGC	.		0.433	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			C	58213806	T	C	58213806	3	2	125	1	0	0	0	0	1	0	0	0	17767	1522	53	3	806	3	ZNF154	19	58213806	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	13420962	58213806	915177	86	10975											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		.											.	.	0			c.G965A						.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	106	14	NM_001144989	0	0	2	2	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	125	1	0	0	0	0	1	0	0	0	18208	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	171987	58385793	743190	87	10976	113	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385799	58385799	+	Missense_Mutation	SNP	C	C	T																															cacattcataaggtcttttcCcagtgtgaactctctgatga																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:58385799C>T	ENST00000435989.2	-	3	1193	c.959G>A	c.(958-960)gGg>gAg	p.G320E	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	320					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G320E(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AGGTCTTTTCCCAGTGTGAAC	0.358																																					p.G320E		.											.	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G959A						.						14	11	12					19																	58385799		687	1560	2247	SO:0001583	missense	730051	exon3			CTTTTCCCAGTGT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.959G>A	19.37:g.58385799C>T	ENSP00000410545:p.Gly320Glu	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	96	14	NM_001144989	0	0	2	2	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	7.488	0.650166	0.14516	.	.	ENSG00000204514	ENST00000435989	T	0.25749	1.78	2.37	-4.23	0.03789	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29389	0.0732	L	0.41824	1.3	0.09310	N	0.999992	D	0.76494	0.999	D	0.65573	0.936	T	0.23261	-1.0193	9	0.66056	D	0.02	.	2.112	0.03705	0.1507:0.4859:0.1487:0.2147	.	320	B7Z6K7	ZN814_HUMAN	E	320	ENSP00000410545:G320E	ENSP00000410545:G320E	G	-	2	0	ZNF814	63077611	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.267000	0.08619	-0.341000	0.08376	-3.844000	0.00018	GGG	.		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385799	C	T	58385799	3	4	125	1	0	0	0	0	1	0	0	0	18208	623	22	2	1612	2	ZNF814	19	58385799	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	6	58385799	743184	88	10977	113	2									
IDH3B	3420	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	2639397	2639398	+	Nonstop_Mutation	DNP	CT	CT	TA																															gttggaagaaataaagggctCtagctccctttagtctgcag																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr20:2639397_2639398CT>TA	ENST00000380843.4	-	12	1187_1188	c.1157_1158AG>TA	c.(1156-1158)tAG>tTA	p.*386L	SNORD86_ENST00000391196.1_RNA|IDH3B_ENST00000380851.5_Intron|SNORD56_ENST00000413522.1_RNA|IDH3B_ENST00000488299.1_5'UTR|SNORD57_ENST00000448188.1_RNA	NM_006899.3	NP_008830.2	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3 (NAD+) beta	0					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|NADH metabolic process (GO:0006734)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(1)|endometrium(3)|kidney(2)|lung(7)|prostate(1)	14						ATAAAGGGCTCTAGCTCCCTTT	0.55																																					.		.											.	IDH3B-226	0			c.A1157T						.																																			SO:0001578	stop_lost	3420	exon12			GGGCTCTAGCTCC		CCDS13031.1, CCDS13032.1, CCDS74696.1	20p13	2013-02-14			ENSG00000101365	ENSG00000101365	1.1.1.41		5385	protein-coding gene	gene with protein product		604526				10575215	Standard	NM_006899		Approved	RP46	uc002wgp.4	O43837	OTTHUMG00000031699	ENST00000380843.4:c.1156_1156delinsTA	20.37:g.2639397_2639398delinsTA	Exception_encountered	Somatic	278	0		WXS	Illumina HiSeq	Phase_I	210	20	NM_006899	0	0	0	0	0	B2RDR1|D3DVX2|D3DVX3|O95106|Q5JXS8|Q9NQ06|Q9NQ07|Q9NUZ0|Q9UEX0|Q9UG99	Missense_Mutation	DNP	ENST00000380843.4	37	CCDS13032.1																																																																																			.		0.55	IDH3B-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077613.1			TA	2639398	CT	TA	2639397	4	4	125	1	0	0	0	0	0	0	0	0	7518	924	32	2	88	2	IDH3B	20	2639397	Nonstop_Mutation	DNP	CT	TCGA-GL-A4EM-01A-11D-A25F-10		2639397	60386123	89	10978	114	2									
IDH3B	3420	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	2639399	2639399	+	Nonstop_Mutation	SNP	A	A	C																															tggaagaaataaagggctctAgctccctttagtctgcaggt																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr20:2639399A>C	ENST00000380843.4	-	12	1186	c.1156T>G	c.(1156-1158)Tag>Gag	p.*386E	SNORD86_ENST00000391196.1_RNA|IDH3B_ENST00000380851.5_Intron|SNORD56_ENST00000413522.1_RNA|IDH3B_ENST00000488299.1_5'UTR|SNORD57_ENST00000448188.1_RNA	NM_006899.3	NP_008830.2	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3 (NAD+) beta	0					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|NADH metabolic process (GO:0006734)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(1)|endometrium(3)|kidney(2)|lung(7)|prostate(1)	14						AAAGGGCTCTAGCTCCCTTTA	0.552																																					p.X386E		.											.	IDH3B-226	0			c.T1156G						.						177	154	162					20																	2639399		2203	4300	6503	SO:0001578	stop_lost	3420	exon12			GGCTCTAGCTCCC		CCDS13031.1, CCDS13032.1, CCDS74696.1	20p13	2013-02-14			ENSG00000101365	ENSG00000101365	1.1.1.41		5385	protein-coding gene	gene with protein product		604526				10575215	Standard	NM_006899		Approved	RP46	uc002wgp.4	O43837	OTTHUMG00000031699	ENST00000380843.4:c.1156T>G	20.37:g.2639399A>C	ENSP00000370223:p.*386Glnext*29	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	212	18	NM_006899	0	0	79	80	1	B2RDR1|D3DVX2|D3DVX3|O95106|Q5JXS8|Q9NQ06|Q9NQ07|Q9NUZ0|Q9UEX0|Q9UG99	Missense_Mutation	SNP	ENST00000380843.4	37	CCDS13032.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.913714	0.52439	.	.	ENSG00000101365	ENST00000380843;ENST00000435594	.	.	.	5.69	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.5939	0.33703	0.9128:0.0:0.0872:0.0	.	.	.	.	E	386;234	.	.	X	-	1	0	IDH3B	2587399	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.484000	0.60271	0.979000	0.38497	0.477000	0.44152	TAG	.		0.552	IDH3B-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077613.1			C	2639399	A	C	2639399	4	2	125	1	0	0	0	0	0	0	0	0	7518	433	15	5	90	5	IDH3B	20	2639399	Nonstop_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	2	2639399	60386121	90	10979	114	2									
C20orf117	140710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	35443624	35443624	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgagaaggactcctgctgttCcttgacagagcacccgagga	10	8	12	11	1	0	3	0	2	0	2	2	7	2	5	3	2	2	3	3	2	1	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr20:35443624C>T	ENST00000357779.3	-	5	1833	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K	SOGA1_ENST00000237536.4_Missense_Mutation_p.E741K|SOGA1_ENST00000456801.2_Missense_Mutation_p.E344K|SOGA1_ENST00000279034.6_Missense_Mutation_p.E503K			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	503					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						TCCTGCTGTTCCTTGACAGAG	0.577																																					p.E741K		.											.	.	0			c.G2221A						.						84	95	91					20																	35443624		2173	4275	6448	SO:0001583	missense	140710	exon5			GCTGTTCCTTGAC	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1507G>A	20.37:g.35443624C>T	ENSP00000350424:p.Glu503Lys	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	85	17	NM_080627	0	0	0	0	0	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	C	18.14	3.556991	0.65425	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.22743	1.99;1.94;1.98;1.98	5.72	5.72	0.89469	.	0.594212	0.17064	N	0.188438	T	0.45677	0.1354	M	0.63843	1.955	0.52501	D	0.999954	D	0.89917	1.0	D	0.87578	0.998	T	0.04991	-1.0913	10	0.27082	T	0.32	-37.714	18.6578	0.91460	0.0:1.0:0.0:0.0	.	503	O94964-4	.	K	741;503;344;503	ENSP00000237536:E741K;ENSP00000279034:E503K;ENSP00000413886:E344K;ENSP00000350424:E503K	ENSP00000237536:E741K	E	-	1	0	KIAA0889	34877038	1.000000	0.71417	0.999000	0.59377	0.042000	0.13812	3.774000	0.55341	2.706000	0.92434	0.561000	0.74099	GAA	.		0.577	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35443624	C	T	35443624	3	4	125	1	0	0	0	0	1	0	0	0	2089	864	30	2	2870	2	C20orf117	20	35443624	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	32804225	35443624	27581896	91	10980											
ZSWIM3	140831	bcgsc.ca	37	chr20	44486494	44486501	+	Frame_Shift_Del	DEL	TGAGGACT	TGAGGACT	-																															ggcagctgcttcaagacctaTgaggacttcaaggagtgctt																								rs199725190		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	TGAGGACT	TGAGGACT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr20:44486494_44486501delTGAGGACT	ENST00000255152.2	+	1	239_246	c.30_37delTGAGGACT	c.(28-39)tatgaggacttcfs	p.EDF11fs	ACOT8_ENST00000217455.4_5'Flank|ZSWIM3_ENST00000454862.2_5'UTR	NM_080752.3	NP_542790.2	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM-type containing 3	11							zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	35		Myeloproliferative disorder(115;0.0122)				TCAAGACCTATGAGGACTTCAAGGAGTG	0.601																																					p.10_13del													.	ZSWIM3-92	0			c.30_37del						.																																			SO:0001589	frameshift_variant	140831	exon1			GACCTATGAGGAC	AL008726	CCDS13381.1	20q13.12	2014-06-13	2003-12-17	2003-12-19	ENSG00000132801	ENSG00000132801		"Zinc fingers, SWIM-type"	16157	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 174"		"chromosome 20 open reading frame 164"	C20orf164			Standard	NM_080752		Approved	dJ337O18.7, PPP1R174	uc002xqd.3	Q96MP5	OTTHUMG00000032627	ENST00000255152.2:c.30_37delTGAGGACT	20.37:g.44486494_44486501delTGAGGACT	ENSP00000255152:p.Glu11fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_1	101	6	NM_080752	0	0	0	0	0	Q9BR13	Frame_Shift_Del	DEL	ENST00000255152.2	37	CCDS13381.1																																																																																			.		0.601	ZSWIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079540.1	NM_080752		-	44486501	TGAGGACT	-	44486494	7	5	125	1	0	1	0	1	0	0	0	0	18274	1471	51	0	32	0	ZSWIM3	20	44486494	Frame_Shift_Del	DEL	TGAGGACT	TCGA-GL-A4EM-01A-11D-A25F-10	9042870	44486494	18539026	92	10981											
RPS6KA3	6197	broad.mit.edu	37	chrX	20222171	20222171	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccttcttcaataccttcatGgcataaagctgcctagcatc	10	12	6	13	0	3	0	2	0	1	0	4	0	3	0	3	1	4	3	3	1	5	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:20222171G>A	ENST00000379565.3	-	4	501	c.294C>T	c.(292-294)gcC>gcT	p.A98A	RPS6KA3_ENST00000540702.1_Silent_p.A70A|RPS6KA3_ENST00000544447.1_Silent_p.A70A|RPS6KA3_ENST00000379548.4_Silent_p.A69A	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	98	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	ATACCTTCATGGCATAAAGCT	0.338																																					p.A98A													.	RPS6KA3-1504	0			c.C294T						.						139	126	130					X																	20222171		2203	4300	6503	SO:0001819	synonymous_variant	6197	exon4			CTTCATGGCATAA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.294C>T	X.37:g.20222171G>A		Somatic	105	1		WXS	Illumina HiSeq	Phase_I	102	4	NM_004586	0	0	8	8	0	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Silent	SNP	ENST00000379565.3	37	CCDS14197.1																																																																																			.		0.338	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		A	20222171	G	A	20222171	2	1	125	1	0	0	0	0	0	0	0	1	13684	1335	47	2		2	RPS6KA3	23	20222171	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		20222171	135048389	93	10982											
FOXO4	4303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	70316474	70316474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgtccccgctcctgcacCtggccccttccccgaccaga	5	6	8	22	3	0	1	0	0	0	1	3	2	3	1	10	1	2	2	10	1	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:70316474C>T	ENST00000374259.3	+	1	428	c.96C>T	c.(94-96)acC>acT	p.T32T	FOXO4_ENST00000466874.1_3'UTR|FOXO4_ENST00000341558.3_Silent_p.T32T	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	32				QSRPRSCTWP -> RAVPLLHLA (in Ref. 1; CAA72156). {ECO:0000305}.	cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					GCTCCTGCACCTGGCCCCTTC	0.637																																					p.T32T		.											.	FOXO4-986	0			c.C96T						.						24	27	26					X																	70316474		1951	4125	6076	SO:0001819	synonymous_variant	4303	exon1			CTGCACCTGGCCC		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.96C>T	X.37:g.70316474C>T		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	96	23	NM_005938	0	0	3	3	0	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Silent	SNP	ENST00000374259.3	37	CCDS43969.1																																																																																			.		0.637	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		T	70316474	C	T	70316474	2	4	125	1	0	0	0	0	0	0	0	1	6044	668	24	2		2	FOXO4	23	70316474	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	50094303	70316474	84954086	94	10983											
ALG13	79868	ucsc.edu	37	chrX	110987897	110987897	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttttgtttctttgttagtGattgcctcaccatcctatcc	5	20	6	10	0	2	1	1	1	1	0	4	1	4	1	4	0	1	3	4	0	2	7			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:110987897G>T	ENST00000394780.3	+	24	2709	c.2697G>T	c.(2695-2697)gtG>gtT	p.V899V	ALG13_ENST00000251943.4_Intron|ALG13_ENST00000470971.1_3'UTR	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	899	Pro-rich.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						CTTTGTTAGTGATTGCCTCAC	0.458																																					p.V899V													.	ALG13-130	0			c.G2697T						.						89	61	70					X																	110987897		1567	3574	5141	SO:0001630	splice_region_variant	79868	exon24			GTTAGTGATTGCC	AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"Tudor domain containing", "OTU domain containing"	30881	protein-coding gene	gene with protein product	"tudor domain containing 13", "N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"	300776	"glycosyltransferase 28 domain containing 1", "chromosome X open reading frame 45", "asparagine-linked glycosylation 13 homolog (S. cerevisiae)"	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2696-1G>T	X.37:g.110987897G>T		Somatic	37	0		WXS	Illumina HiSeq		39	4	NM_001099922	0	0	0	0	0	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Silent	SNP	ENST00000394780.3	37	CCDS55477.1																																																																																			.		0.458	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466	Silent	T	110987897	G	T	110987897	5	4	125	1	0	0	0	0	0	0	1	0	515	1304	45	4	2933	4	ALG13	23	110987897	Splice_Site	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	40671423	110987897	44282663	95	10984											
STAG2	10735	broad.mit.edu	37	chrX	123190070	123190070	+	Frame_Shift_Del	DEL	A	A	-																															agtagcagtagcagctggagAatttctctacaaaaagtaaa																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:123190070delA	ENST00000371160.1	+	14	1579	c.1289delA	c.(1288-1290)gaafs	p.E430fs	STAG2_ENST00000371157.3_Frame_Shift_Del_p.E430fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.E430fs|STAG2_ENST00000371145.3_Frame_Shift_Del_p.E430fs|STAG2_ENST00000354548.5_Frame_Shift_Del_p.E361fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Del_p.E430fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	430					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GCAGCTGGAGAATTTCTCTAC	0.333																																					p.E430fs													.	STAG2-134	0			c.1289delA						.						71	69	70					X																	123190070		2203	4300	6503	SO:0001589	frameshift_variant	10735	exon14			CTGGAGAATTTCT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1289delA	X.37:g.123190070delA	ENSP00000360202:p.Glu430fs	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	25	9	NM_001042749	0	0	0	0	0	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	37	CCDS14607.1																																																																																			.		0.333	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123190070	A	-	123190070	7	5	125	1	0	1	0	1	0	0	0	0	15275	246	9	0	1335	0	STAG2	23	123190070	Frame_Shift_Del	DEL	A	TCGA-GL-A4EM-01A-11D-A25F-10	12202173	123190070	32080490	96	10985											
OCRL	4952	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	128678970	128678970	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatgagaaggaacagcatgTtcaagatatcattcctataa	16	10	8	7	0	2	2	2	1	0	2	3	4	3	3	1	1	2	3	1	1	6	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:128678970T>G	ENST00000371113.4	+	3	320	c.155T>G	c.(154-156)gTt>gGt	p.V52G	OCRL_ENST00000486673.1_3'UTR|OCRL_ENST00000357121.5_Missense_Mutation_p.V52G	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	52	PH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						GAACAGCATGTTCAAGATATC	0.348																																					p.V52G		.											.	OCRL-206	0			c.T155G						.						178	153	162					X																	128678970		2203	4300	6503	SO:0001583	missense	4952	exon3			AGCATGTTCAAGA	U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126			8108	protein-coding gene	gene with protein product		300535					Standard	NM_001587		Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.155T>G	X.37:g.128678970T>G	ENSP00000360154:p.Val52Gly	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	37	14	NM_000276	0	0	1	5	4	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.946658	0.34377	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.94376	-3.41;-3.41	5.36	3.03	0.35002	.	0.751295	0.12380	N	0.473987	D	0.84938	0.5583	N	0.14661	0.345	0.47341	D	0.999398	B;B	0.19200	0.034;0.02	B;B	0.19946	0.027;0.019	T	0.80174	-0.1492	10	0.42905	T	0.14	.	5.7638	0.18215	0.0:0.1888:0.0:0.8112	.	52;52	Q01968-2;Q01968	.;OCRL_HUMAN	G	52	ENSP00000360154:V52G;ENSP00000349635:V52G	ENSP00000349635:V52G	V	+	2	0	OCRL	128506651	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.736000	0.26130	1.780000	0.52325	0.417000	0.27973	GTT	.		0.348	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		G	128678970	T	G	128678970	3	3	125	1	0	0	0	0	1	0	0	0	10849	1725	60	5	165	5	OCRL	23	128678970	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	5488900	128678970	26591590	97	10986											
GRIK3	2899	broad.mit.edu	37	chr1	37271815	37271815	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggactccatgagcagcGcgtagtcggccgtcagggcc	6	7	16	12	4	1	1	1	1	0	0	3	2	2	2	3	4	2	2	3	4	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:37271815G>A	ENST00000373091.3	-	14	2220	c.2204C>T	c.(2203-2205)gCg>gTg	p.A735V	GRIK3_ENST00000373093.4_Missense_Mutation_p.A735V	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	735					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CATGAGCAGCGCGTAGTCGGC	0.612																																					p.A735V													.	GRIK3-158	0			c.C2204T						.						170	131	144					1																	37271815		2203	4300	6503	SO:0001583	missense	2899	exon14			AGCAGCGCGTAGT	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.2204C>T	1.37:g.37271815G>A	ENSP00000362183:p.Ala735Val	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	159	5	NM_000831	0	0	0	0	0	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	G	32	5.189769	0.94923	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.18810	2.19;2.19	5.48	5.48	0.80851	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.48692	-0.9013	10	0.72032	D	0.01	.	19.3336	0.94306	0.0:0.0:1.0:0.0	.	735;735	A9Z1Z8;Q13003	.;GRIK3_HUMAN	V	735	ENSP00000362183:A735V;ENSP00000362185:A735V	ENSP00000362183:A735V	A	-	2	0	GRIK3	37044402	1.000000	0.71417	0.953000	0.39169	0.785000	0.44390	9.790000	0.99075	2.566000	0.86566	0.549000	0.68633	GCG	.		0.612	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		A	37271815	G	A	37271815	3	1	126	1	0	0	0	0	1	0	0	0	6796	1087	38	1	567	1	GRIK3	1	37271815	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		37271815	211978806	1	10987											
TTC4	7268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	55183223	55183223	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttaaagaaaaagactacaaGaaagctgtaatttcatacac	20	10	5	6	0	1	3	1	0	0	3	1	3	1	3	0	0	3	2	0	0	9	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:55183223G>C	ENST00000371281.3	+	3	375	c.288G>C	c.(286-288)aaG>aaC	p.K96N	MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.R1332T|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	96										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AAGACTACAAGAAAGCTGTAA	0.368																																					p.K96N		.											.	TTC4-90	0			c.G288C						.						64	63	64					1																	55183223		2203	4300	6503	SO:0001583	missense	7268	exon3			CTACAAGAAAGCT		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"Tetratricopeptide (TTC) repeat domain containing"	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.288G>C	1.37:g.55183223G>C	ENSP00000360329:p.Lys96Asn	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	156	55	NM_004623	0	0	5	9	4	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	37	CCDS596.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.424330	0.43020	.	.	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.61040	0.14	3.97	1.82	0.25136	Elongated TPR repeat-containing domain (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.42877	0.1222	L	0.38838	1.175	0.46185	D	0.998919	B;P	0.34977	0.058;0.478	B;B	0.34824	0.056;0.19	T	0.19549	-1.0302	9	0.45353	T	0.12	-17.6511	6.6318	0.22861	0.303:0.0:0.697:0.0	.	96;107	O95801;Q5TA95	TTC4_HUMAN;.	N	96;107	ENSP00000360329:K96N	ENSP00000360329:K96N	K	+	3	2	TTC4	54955811	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.484000	0.45242	0.311000	0.23014	0.563000	0.77884	AAG	.		0.368	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		C	55183223	G	C	55183223	3	2	126	1	0	0	0	0	1	0	0	0	16743	933	33	4	298	4	TTC4	1	55183223	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	17911408	55183223	194067398	2	10988											
ALG6	29929	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	63868011	63868011	+	Frame_Shift_Del	DEL	A	A	-																															tcatagtctcctatgtgcatAtgtgtaagtttttctttctt																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:63868011delA	ENST00000371108.4	+	4	559	c.254delA	c.(253-255)tatfs	p.Y85fs	ALG6_ENST00000263440.4_Frame_Shift_Del_p.Y85fs	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	85					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CTATGTGCATATGTGTAAGTT	0.353																																					p.Y85fs		.											.	ALG6-90	0			c.254delA						.						118	114	116					1																	63868011		2202	4300	6502	SO:0001589	frameshift_variant	29929	exon4			.	AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"	604566	"asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)", "asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.254delA	1.37:g.63868011delA	ENSP00000360149:p.Tyr85fs	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	37	19	NM_013339	0	0	0	0	0	B3KMU2|Q5SXR9|Q9H3I0	Frame_Shift_Del	DEL	ENST00000371108.4	37	CCDS30735.1																																																																																			.		0.353	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339		-	63868011	A	-	63868011	7	5	126	1	0	1	0	1	0	0	0	0	522	449	16	0	264	0	ALG6	1	63868011	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10	8684788	63868011	185382610	3	10989											
CHD1L	9557	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	146747123	146747123	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccagggctcatcgcattggCcaaaacaagtaagtgatttt	12	10	10	9	1	1	1	1	1	0	0	2	1	1	1	2	2	1	3	2	2	4	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:146747123C>A	ENST00000369258.4	+	13	1397	c.1377C>A	c.(1375-1377)ggC>ggA	p.G459G	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000369259.3_Silent_p.G255G|CHD1L_ENST00000431239.1_Silent_p.G365G|CHD1L_ENST00000361293.5_Silent_p.G178G	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	459	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					ATCGCATTGGCCAAAACAAGT	0.443																																					p.G459G													.	CHD1L-231	0			c.C1377A						.						122	119	120					1																	146747123		2203	4300	6503	SO:0001819	synonymous_variant	9557	exon13			CATTGGCCAAAAC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1377C>A	1.37:g.146747123C>A		Somatic	90	1		WXS	Illumina HiSeq	Phase_I	82	27	NM_004284	0	0	0	0	0	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Silent	SNP	ENST00000369258.4	37	CCDS927.1																																																																																			.		0.443	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		A	146747123	C	A	146747123	2	1	126	1	0	0	0	0	0	0	0	1	3330	726	26	4		4	CHD1L	1	146747123	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	82879112	146747123	102503498	4	10990											
ASH1L	55870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155313421	155313421	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttccaaagcttctcaatGcgaaagatgtcaagtttatc	12	14	6	9	1	3	1	2	0	2	1	6	2	4	1	1	0	2	2	1	0	5	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:155313421G>A	ENST00000368346.3	-	23	8748	c.8109C>T	c.(8107-8109)cgC>cgT	p.R2703R	MIR555_ENST00000384987.1_RNA|ASH1L_ENST00000392403.3_Silent_p.R2698R			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2703	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GCTTCTCAATGCGAAAGATGT	0.493																																					p.R2698R		.											.	ASH1L-234	0			c.C8094T						.						114	109	110					1																	155313421		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon23			CTCAATGCGAAAG	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.8109C>T	1.37:g.155313421G>A		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	177	64	NM_018489	0	0	2	5	3	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37																																																																																				.		0.493	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155313421	G	A	155313421	2	1	126	1	0	0	0	0	0	0	0	1	1042	1306	46	2		2	ASH1L	1	155313421	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	8566298	155313421	93937200	5	10991											
LMNA	4000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156107474	156107474	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcgcaagctggtgcgctcAgtgactgtggttgaggacga	8	9	16	8	3	1	2	1	2	0	0	1	4	1	3	0	3	3	4	0	3	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:156107474A>C	ENST00000368300.4	+	10	1850	c.1638A>C	c.(1636-1638)tcA>tcC	p.S546S	LMNA_ENST00000361308.4_Silent_p.S546S|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Silent_p.S447S|LMNA_ENST00000347559.2_Intron|LMNA_ENST00000368299.3_Silent_p.S546S|LMNA_ENST00000392353.3_Silent_p.S465S|LMNA_ENST00000368297.1_Silent_p.S465S|LMNA_ENST00000368301.2_Silent_p.S546S|LMNA_ENST00000448611.2_Silent_p.S434S	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	546	Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TGGTGCGCTCAGTGACTGTGG	0.622									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.S546S		.											.	LMNA-228	0			c.A1638C						.						64	45	51					1																	156107474		2174	4254	6428	SO:0001819	synonymous_variant	4000	exon10	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GCGCTCAGTGACT	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1638A>C	1.37:g.156107474A>C		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	77	29	NM_170707	0	1	272	503	230	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			.		0.622	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		C	156107474	A	C	156107474	2	2	126	1	0	0	0	0	0	0	0	1	8871	175	7	5		5	LMNA	1	156107474	Silent	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	794053	156107474	93143147	6	10992											
C1orf125	126859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	179339155	179339155	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	atgtctggcatcaccctgttCgaaggaataaattcaaatac	14	11	7	9	1	3	0	2	0	1	0	4	2	3	1	1	2	1	2	1	2	6	4	rs577148644		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:179339155C>G	ENST00000367618.3	+	4	703	c.316C>G	c.(316-318)Cga>Gga	p.R106G	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.R106G	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	106										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						TCACCCTGTTCGAAGGAATAA	0.438																																					p.R106G		.											.	AXDND1-93	0			c.C316G						.						80	72	75					1																	179339155		2203	4300	6503	SO:0001583	missense	126859	exon4			CCTGTTCGAAGGA	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 125"	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.316C>G	1.37:g.179339155C>G	ENSP00000356590:p.Arg106Gly	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	106	44	NM_144696	0	0	0	0	0	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720207	0.30503	.	.	ENSG00000162779	ENST00000509175;ENST00000367618;ENST00000360322;ENST00000507383;ENST00000457238;ENST00000508285;ENST00000511889;ENST00000434088	T;T;T	0.52057	1.9;0.68;2.02	5.39	3.47	0.39725	.	0.176693	0.38605	N	0.001628	T	0.45256	0.1333	L	0.41710	1.295	0.19775	N	0.99996	D;D	0.53619	0.961;0.961	P;P	0.51453	0.67;0.67	T	0.34279	-0.9835	10	0.87932	D	0	0.9492	6.752	0.23491	0.1744:0.7348:0.0:0.0909	.	64;106	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	G	64;106;64;64;106;106;64;40	ENSP00000356590:R106G;ENSP00000416712:R106G;ENSP00000391716:R40G	ENSP00000353471:R64G	R	+	1	2	AXDND1	177605778	0.879000	0.30193	0.432000	0.26747	0.923000	0.55619	1.441000	0.35035	0.605000	0.29947	0.453000	0.30009	CGA	.		0.438	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		G	179339155	C	G	179339155	3	3	126	1	0	0	0	0	1	0	0	0	1999	876	31	4	326	4	C1orf125	1	179339155	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	23231681	179339155	69911466	7	10993											
NFASC	23114	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204948503	204948504	+	Missense_Mutation	DNP	GT	GT	AG																															cactcagactacgtcgtccaGtttgaagaagaccagttcca																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:204948503_204948504GT>AG	ENST00000401399.1	+	18	2191_2192	c.1992_1993GT>AG	c.(1990-1995)caGTtt>caAGtt	p.F665V	NFASC_ENST00000360049.4_Missense_Mutation_p.F661V|NFASC_ENST00000339876.6_Missense_Mutation_p.F665V|NFASC_ENST00000367169.4_Missense_Mutation_p.F665V|NFASC_ENST00000539706.1_Missense_Mutation_p.F661V|NFASC_ENST00000338586.6_Missense_Mutation_p.F665V|NFASC_ENST00000404907.1_Missense_Mutation_p.F661V|NFASC_ENST00000338515.6_Missense_Mutation_p.F665V|NFASC_ENST00000404076.1_Missense_Mutation_p.F644V|NFASC_ENST00000513543.1_Missense_Mutation_p.F661V|NFASC_ENST00000367172.4_Missense_Mutation_p.F665V|NFASC_ENST00000367171.4_Missense_Mutation_p.F650V|NFASC_ENST00000367170.4_Missense_Mutation_p.F665V			O94856	NFASC_HUMAN	neurofascin	665	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ACGTCGTCCAGTTTGAAGAAGA	0.52																																					p.F665V													.	NFASC-139	0			c.T2026G						.																																			SO:0001583	missense	23114	exon17			GTCCAGTTTGAAG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	Exception_encountered	1.37:g.204948503_204948504delinsAG	ENSP00000385637:p.Phe665Val	Somatic	289	3		WXS	Illumina HiSeq	Phase_I	327	119	NM_001160331	0	0	0	0	0	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	DNP	ENST00000401399.1	37	CCDS53460.1																																																																																			.		0.52	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		AG	204948504	GT	AG	204948503	3	1	126	1	0	0	0	0	1	0	0	0	10385	1020	36	2	2142	2	NFASC	1	204948503	Missense_Mutation	DNP	GT	TCGA-GL-A59R-01A-11D-A26P-10	25609348	204948503	44302118	8	10994											
CAPN13	92291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	30987162	30987162	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagtgcagatcggaataggAtccgagcagcctgggaggga	12	6	16	7	2	0	1	0	0	0	1	2	6	1	5	2	4	3	2	2	4	3	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:30987162A>G	ENST00000295055.8	-	6	711	c.535T>C	c.(535-537)Tcc>Ccc	p.S179P	CAPN13_ENST00000534090.2_Missense_Mutation_p.S179P|CAPN13_ENST00000465960.2_5'UTR	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	179	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TCGGAATAGGATCCGAGCAGC	0.577																																					p.S179P		.											.	CAPN13-136	0			c.T535C						.						50	51	51					2																	30987162		2104	4217	6321	SO:0001583	missense	92291	exon6			AATAGGATCCGAG		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.535T>C	2.37:g.30987162A>G	ENSP00000295055:p.Ser179Pro	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	136	55	NM_144575	0	0	0	0	0	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	37	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	A	18.41	3.618329	0.66787	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	D;D	0.89552	-2.53;-2.53	5.22	5.22	0.72569	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.96439	0.8838	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97655	1.0157	10	0.72032	D	0.01	.	14.0703	0.64856	1.0:0.0:0.0:0.0	.	179	Q6MZZ7	CAN13_HUMAN	P	179	ENSP00000295055:S179P;ENSP00000431298:S179P	ENSP00000295055:S179P	S	-	1	0	CAPN13	30840666	1.000000	0.71417	0.951000	0.38953	0.450000	0.32258	4.956000	0.63645	1.970000	0.57323	0.379000	0.24179	TCC	.		0.577	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		G	30987162	A	G	30987162	3	3	126	1	0	0	0	0	1	0	0	0	2632	333	12	3	1542	3	CAPN13	2	30987162	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10		30987162	212212211	9	10995											
MAP4K3	8491	ucsc.edu;bcgsc.ca	37	chr2	39553361	39553361	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgattcccactgcccagagAtcacagagttgattgtaacc	11	10	9	11	0	1	4	1	2	0	2	2	5	2	4	3	0	2	2	3	0	1	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:39553361A>T	ENST00000263881.3	-	9	912	c.588T>A	c.(586-588)gaT>gaA	p.D196E	MAP4K3_ENST00000341681.5_Missense_Mutation_p.D196E|RP11-449G16.1_ENST00000609671.1_RNA|MAP4K3_ENST00000536018.1_5'Flank|MAP4K3_ENST00000437545.1_Missense_Mutation_p.D133E	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	196	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				CTGCCCAGAGATCACAGAGTT	0.423																																					p.D196E													.	MAP4K3-550	0			c.T588A						.						121	123	122					2																	39553361		2203	4300	6503	SO:0001583	missense	8491	exon9			CCAGAGATCACAG	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.588T>A	2.37:g.39553361A>T	ENSP00000263881:p.Asp196Glu	Somatic	168	4		WXS	Illumina HiSeq		164	68	NM_001270425	0	0	0	1	1	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.917943	0.92249	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	T;T;T	0.75367	-0.93;0.71;-0.93	5.68	-6.03	0.02185	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	H	0.99312	4.51	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.999	D	0.91678	0.5356	9	.	.	.	.	18.1275	0.89590	0.3452:0.0:0.6548:0.0	.	196;196	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	E	196;133;196	ENSP00000263881:D196E;ENSP00000416958:D133E;ENSP00000345434:D196E	.	D	-	3	2	MAP4K3	39406865	0.999000	0.42202	0.906000	0.35671	0.966000	0.64601	0.619000	0.24388	-1.116000	0.02969	0.477000	0.44152	GAT	.		0.423	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		T	39553361	A	T	39553361	3	4	126	1	0	0	0	0	1	0	0	0	9286	330	12	5	2200	5	MAP4K3	2	39553361	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	8566199	39553361	203646012	10	10996											
XPO1	7514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	61705989	61705989	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctggaatctcatgtggaTtaaagatgccagggacagac	12	10	11	8	0	2	2	1	0	2	2	3	5	2	5	1	3	1	0	1	3	3	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:61705989T>C	ENST00000401558.2	-	25	3909	c.3182A>G	c.(3181-3183)aAt>aGt	p.N1061S	XPO1_ENST00000404992.2_Missense_Mutation_p.N1061S|XPO1_ENST00000406957.1_Missense_Mutation_p.N1061S|RP11-355B11.2_ENST00000603652.1_RNA|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000603199.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	1061					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			CTCATGTGGATTAAAGATGCC	0.393			Mis		CLL																																p.N1061S		.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1-229	0			c.A3182G						.						137	137	137					2																	61705989		2203	4300	6503	SO:0001583	missense	7514	exon25			TGTGGATTAAAGA	Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"Exportins"	12825	protein-coding gene	gene with protein product	"chromosome region maintenance 1 homolog (yeast)"	602559	"exportin 1 (CRM1, yeast, homolog)", "exportin 1 (CRM1 homolog, yeast)"			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.3182A>G	2.37:g.61705989T>C	ENSP00000384863:p.Asn1061Ser	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	42	20	NM_003400	0	0	40	61	21	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120462	0.77323	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.78007	0.4216	M	0.79258	2.445	0.58432	D	0.999996	D;D	0.76494	0.994;0.999	P;D	0.69307	0.888;0.963	T	0.76534	-0.2924	9	0.28530	T	0.3	-21.4772	15.9952	0.80234	0.0:0.0:0.0:1.0	.	708;1061	B3KWD0;O14980	.;XPO1_HUMAN	S	1061	.	ENSP00000384863:N1061S	N	-	2	0	XPO1	61559493	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.005000	0.88553	2.172000	0.68678	0.533000	0.62120	AAT	.		0.393	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		C	61705989	T	C	61705989	3	2	126	1	0	0	0	0	1	0	0	0	17478	1493	52	3	37	3	XPO1	2	61705989	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	22152628	61705989	181493384	11	10997											
FAM161A	84140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	62067237	62067237	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctccgttcttctttttgcTtgactaaatcatggtaaagg	8	18	7	8	1	4	1	1	1	3	0	5	1	4	1	1	2	1	3	1	2	4	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:62067237T>C	ENST00000405894.3	-	3	1003	c.902A>G	c.(901-903)aAg>aGg	p.K301R	FAM161A_ENST00000404929.1_Missense_Mutation_p.K301R	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	301					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTCTTTTTGCTTGACTAAATC	0.418																																					p.K301R		.											.	FAM161A-136	0			c.A902G						.						166	149	154					2																	62067237		1847	4095	5942	SO:0001583	missense	84140	exon3			TTTTGCTTGACTA		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.902A>G	2.37:g.62067237T>C	ENSP00000385893:p.Lys301Arg	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	46	21	NM_032180	0	0	0	1	1	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322375	0.41096	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.22336	1.96;1.96	5.41	4.26	0.50523	.	0.176973	0.44902	D	0.000408	T	0.22205	0.0535	L	0.52573	1.65	0.29380	N	0.863369	B;B	0.30563	0.285;0.074	B;B	0.34931	0.192;0.064	T	0.10314	-1.0635	10	0.44086	T	0.13	-18.3941	10.8689	0.46872	0.0:0.0746:0.0:0.9254	.	301;301	Q3B820;Q3B820-3	F161A_HUMAN;.	R	301	ENSP00000385158:K301R;ENSP00000385893:K301R	ENSP00000385158:K301R	K	-	2	0	FAM161A	61920741	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	2.205000	0.42770	0.884000	0.36064	0.533000	0.62120	AAG	.		0.418	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		C	62067237	T	C	62067237	3	2	126	1	0	0	0	0	1	0	0	0	5488	1609	56	3	1096	3	FAM161A	2	62067237	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	361248	62067237	181132136	12	10998											
RTKN	6242	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74656034	74656034	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcactgctgccagggtgAgtgtggtgtgagccaagagg	7	9	17	8	0	0	3	0	2	0	1	0	3	0	3	2	3	4	2	2	3	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:74656034A>G	ENST00000233330.6	-	7	958	c.641T>C	c.(640-642)cTc>cCc	p.L214P	RTKN_ENST00000305557.5_Missense_Mutation_p.L251P|RTKN_ENST00000272430.5_Missense_Mutation_p.L264P	NM_001015056.1	NP_001015056.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						TGCCAGGGTGAGTGTGGTGTG	0.552																																					p.L264P		.											.	RTKN-91	0			c.T791C						.						192	128	150					2																	74656034		2203	4300	6503	SO:0001583	missense	6242	exon7			AGGGTGAGTGTGG	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.641T>C	2.37:g.74656034A>G	ENSP00000233330:p.Leu214Pro	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	232	68	NM_001015055	1	0	62	98	35		Missense_Mutation	SNP	ENST00000233330.6	37	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.545730	0.86022	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.65178	-0.14;-0.14;-0.14	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.78291	0.4260	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.81055	-0.1106	10	0.87932	D	0	.	13.6415	0.62253	1.0:0.0:0.0:0.0	.	264;251	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	P	251;264;214	ENSP00000305298:L251P;ENSP00000272430:L264P;ENSP00000233330:L214P	ENSP00000233330:L214P	L	-	2	0	RTKN	74509542	1.000000	0.71417	0.991000	0.47740	0.971000	0.66376	8.673000	0.91186	2.128000	0.65567	0.459000	0.35465	CTC	.		0.552	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		G	74656034	A	G	74656034	3	3	126	1	0	0	0	0	1	0	0	0	13754	304	11	3	924	3	RTKN	2	74656034	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	12588797	74656034	168543339	13	10999											
DNAH6	1768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	84846836	84846836	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttgtcaaatgatgaactTctggagattttggcccagac	10	14	9	8	0	3	4	1	2	2	2	3	5	3	4	1	2	1	0	1	2	2	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:84846836T>G	ENST00000237449.6	+	23	3608	c.3600T>G	c.(3598-3600)ctT>ctG	p.L1200L	DNAH6_ENST00000398278.2_Silent_p.L1200L|DNAH6_ENST00000389394.3_Silent_p.L1200L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1200	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						ATGATGAACTTCTGGAGATTT	0.383																																					p.L1200L		.											.	DNAH6-69	0			c.T3600G						.						138	114	121					2																	84846836		692	1591	2283	SO:0001819	synonymous_variant	1768	exon24			TGAACTTCTGGAG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3600T>G	2.37:g.84846836T>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	54	23	NM_001370	0	0	0	0	0	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			.		0.383	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84846836	T	G	84846836	2	3	126	1	0	0	0	0	0	0	0	1	4616	1770	62	5		5	DNAH6	2	84846836	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	10190802	84846836	158352537	14	11000											
DNAH6	1768	broad.mit.edu	37	chr2	84896615	84896615	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcattccgtgttgtttactgGaataactggagtgggcaagg	9	12	14	6	1	0	0	0	0	0	0	1	2	1	2	1	4	2	4	1	4	4	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:84896615G>A	ENST00000237449.6	+	37	6295	c.6287G>A	c.(6286-6288)gGa>gAa	p.G2096E	DNAH6_ENST00000602588.1_Missense_Mutation_p.G117E|DNAH6_ENST00000398278.2_Missense_Mutation_p.G2096E|DNAH6_ENST00000389394.3_Missense_Mutation_p.G2096E			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2096	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTGTTTACTGGAATAACTGGA	0.428																																					p.G2096E													.	DNAH6-69	0			c.G6287A						.						101	87	91					2																	84896615		692	1591	2283	SO:0001583	missense	1768	exon38			TTACTGGAATAAC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.6287G>A	2.37:g.84896615G>A	ENSP00000237449:p.Gly2096Glu	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	77	3	NM_001370	0	0	0	0	0	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321420	0.81580	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	D;D;D	0.93604	-3.25;-3.25;-3.25	5.16	5.16	0.70880	ATPase, AAA+ type, core (1);	.	.	.	.	D	0.98485	0.9495	H	0.99609	4.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99719	1.1009	9	0.87932	D	0	.	17.7668	0.88481	0.0:0.0:1.0:0.0	.	2096;2096	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	E	2096	ENSP00000374045:G2096E;ENSP00000381326:G2096E;ENSP00000237449:G2096E	ENSP00000237449:G2096E	G	+	2	0	DNAH6	84750126	1.000000	0.71417	0.900000	0.35374	0.881000	0.50899	7.775000	0.85489	2.548000	0.85928	0.579000	0.79373	GGA	.		0.428	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84896615	G	A	84896615	3	1	126	1	0	0	0	0	1	0	0	0	4616	1174	41	2	6433	2	DNAH6	2	84896615	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	49779	84896615	158302758	15	11001											
NEB	4703	hgsc.bcm.edu;bcgsc.ca	37	chr2	152390040	152390040	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatgttgcagaaacatcttGgcactagatttatattttct	11	16	6	8	0	2	2	0	0	2	2	2	2	2	2	1	1	2	3	1	1	4	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:152390040G>T	ENST00000172853.10	-	115	16462				NEB_ENST00000603639.1_Silent_p.A7111A|NEB_ENST00000427231.2_Intron|NEB_ENST00000604864.1_Intron|NEB_ENST00000397345.3_Silent_p.A7111A|NEB_ENST00000409198.1_Intron			P20929	NEBU_HUMAN	nebulin						muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GAAACATCTTGGCACTAGATT	0.413																																					p.A7146A		.											.	NEB-145	0			c.C21438A						.						182	146	157					2																	152390040		692	1591	2283	SO:0001627	intron_variant	4703	exon144			CATCTTGGCACTA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16314+688C>A	2.37:g.152390040G>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_001271208	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152390040	G	T	152390040	1	4	126	0	1	0	0	0	0	0	0	0	10328	1335	47	4		4	NEB	2	152390040	Intron	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	67493425	152390040	90809333	16	11002											
NEB	4703	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152536245	152536245	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggacttacgtcactcgccGcctgcctggcagctttggca	5	10	11	15	3	1	0	1	0	0	0	2	1	1	1	3	3	3	3	3	3	1	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:152536245G>C	ENST00000172853.10	-	32	3392	c.3245C>G	c.(3244-3246)gCg>gGg	p.A1082G	NEB_ENST00000603639.1_Missense_Mutation_p.A1082G|NEB_ENST00000427231.2_Missense_Mutation_p.A1082G|NEB_ENST00000604864.1_Missense_Mutation_p.A1082G|NEB_ENST00000397345.3_Missense_Mutation_p.A1082G|NEB_ENST00000409198.1_Missense_Mutation_p.A1082G			P20929	NEBU_HUMAN	nebulin	1082					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTCACTCGCCGCCTGCCTGGC	0.512																																					p.A1082G													.	NEB-145	0			c.C3245G						.						80	76	77					2																	152536245		1927	4134	6061	SO:0001583	missense	4703	exon32			CTCGCCGCCTGCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.3245C>G	2.37:g.152536245G>C	ENSP00000172853:p.Ala1082Gly	Somatic	55	1		WXS	Illumina HiSeq	Phase_I	53	31	NM_004543	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	17.50	3.405701	0.62288	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.74	5.74	0.90152	.	0.120440	0.56097	D	0.000033	T	0.64962	0.2646	L	0.51422	1.61	0.80722	D	1	D	0.64830	0.994	D	0.71414	0.973	T	0.65224	-0.6220	10	0.72032	D	0.01	.	18.7041	0.91631	0.0:0.0:1.0:0.0	.	1082	P20929	NEBU_HUMAN	G	1082	ENSP00000386259:A1082G;ENSP00000380505:A1082G;ENSP00000416578:A1082G;ENSP00000172853:A1082G	ENSP00000172853:A1082G	A	-	2	0	NEB	152244491	0.029000	0.19370	0.964000	0.40570	0.434000	0.31775	1.739000	0.38217	2.720000	0.93068	0.650000	0.86243	GCG	.		0.512	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152536245	G	C	152536245	3	2	126	1	0	0	0	0	1	0	0	0	10328	1087	38	4	23045	4	NEB	2	152536245	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	146205	152536245	90663128	17	11003											
AGPS	8540	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	178257747	178257747	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacggccactcccgccgCgcaggagtcgggcaccatcc	6	3	12	20	5	0	0	0	0	0	0	3	1	2	1	6	3	0	2	6	3	0	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:178257747C>T	ENST00000264167.4	+	1	376	c.230C>T	c.(229-231)gCg>gTg	p.A77V	AC074286.1_ENST00000397057.2_RNA|NFE2L2_ENST00000464747.1_5'Flank|AGPS_ENST00000409888.1_Missense_Mutation_p.A77V	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	77					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			ACTCCCGCCGCGCAGGAGTCG	0.692																																					p.A77V		.											.	AGPS-92	0			c.C230T						.						2	2	2					2																	178257747		1370	2704	4074	SO:0001583	missense	8540	exon1			CCGCCGCGCAGGA	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.230C>T	2.37:g.178257747C>T	ENSP00000264167:p.Ala77Val	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	53	31	NM_003659	0	0	3	5	2	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	37	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589519	0.66105	.	.	ENSG00000018510	ENST00000264167;ENST00000409888	D	0.97328	-4.34	4.57	3.7	0.42460	.	0.000000	0.45126	D	0.000391	D	0.91543	0.7329	L	0.38531	1.155	0.23751	N	0.996949	P	0.38745	0.645	B	0.22386	0.039	D	0.84254	0.0479	10	0.29301	T	0.29	.	9.702	0.40192	0.0:0.902:0.0:0.098	.	77	O00116	ADAS_HUMAN	V	77	ENSP00000264167:A77V	ENSP00000264167:A77V	A	+	2	0	AGPS	177965993	0.089000	0.21612	0.781000	0.31783	0.978000	0.69477	0.687000	0.25407	1.138000	0.42230	0.655000	0.94253	GCG	.		0.692	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			T	178257747	C	T	178257747	3	4	126	1	0	0	0	0	1	0	0	0	394	768	27	1	232	1	AGPS	2	178257747	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	25721502	178257747	64941626	18	11004											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179598544	179598545	+	Missense_Mutation	DNP	AC	AC	CA																															aaatgggctctgaccctctcAcagcagcttgcagggtaacg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:179598544_179598545AC>CA	ENST00000591111.1	-	51	14844_14845	c.14620_14621GT>TG	c.(14620-14622)GTg>TGg	p.V4874W	TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.V3947W|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V5191W|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12256	Ig-like 29.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGACCCTCTCACAGCAGCTTGC	0.426																																					p.V3947W		.											.	TTN-636	0			c.G15571T						.																																			SO:0001583	missense	7273	exon53			CTCTCACAGCAGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.14620_14621delinsCA	2.37:g.179598544_179598545delinsCA	ENSP00000465570:p.Val4874Trp	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	151	65	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	DNP	ENST00000591111.1	37																																																																																				.		0.426	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		CA	179598545	AC	CA	179598544	3	2	126	1	0	0	0	0	1	0	0	0	16768	159	6	5	89197	5	TTN	2	179598544	Missense_Mutation	DNP	AC	TCGA-GL-A59R-01A-11D-A26P-10	1340797	179598544	63600829	19	11005											
FSIP2	401024	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	186672719	186672719	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttatctccaaaagtaagaTtaaacttgtaccacccacca	16	11	3	11	0	1	1	0	0	1	1	2	1	1	1	4	0	2	2	4	0	7	6	rs377239551		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:186672719T>C	ENST00000424728.1	+	17	18686	c.18686T>C	c.(18685-18687)aTt>aCt	p.I6229T	FSIP2_ENST00000343098.5_Missense_Mutation_p.I6318T			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6229										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AAAAGTAAGATTAAACTTGTA	0.308																																					p.I6318T		.											.	FSIP2-90	0			c.T18953C						.	T	THR/ILE	0,3640		0,0,1820	32	29	30		18953	5.1	1	2		30	1,8109		0,1,4054	no	missense	FSIP2	NM_173651.2	89	0,1,5874	CC,CT,TT		0.0123,0.0,0.0085	probably-damaging	6318/6997	186672719	1,11749	1820	4055	5875	SO:0001583	missense	401024	exon17			GTAAGATTAAACT	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18686T>C	2.37:g.186672719T>C	ENSP00000401306:p.Ile6229Thr	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	152	14	NM_173651	0	0	0	0	0	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	T	15.95	2.984130	0.53827	0.0	1.23E-4	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.60797	0.16;0.16	5.07	5.07	0.68467	.	0.235594	0.29737	N	0.011328	T	0.61825	0.2378	L	0.52011	1.625	0.34264	D	0.680189	.	.	.	.	.	.	T	0.74544	-0.3630	8	0.72032	D	0.01	.	11.132	0.48351	0.0:0.0:0.0:1.0	.	.	.	.	T	6318;6229	ENSP00000344403:I6318T;ENSP00000401306:I6229T	ENSP00000344403:I6318T	I	+	2	0	FSIP2	186380964	1.000000	0.71417	0.983000	0.44433	0.928000	0.56348	3.872000	0.56085	2.130000	0.65690	0.397000	0.26171	ATT	.		0.308	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		C	186672719	T	C	186672719	3	2	126	1	0	0	0	0	1	0	0	0	6094	1493	52	3	19019	3	FSIP2	2	186672719	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	7074175	186672719	56526654	20	11006											
SF3B1	23451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198265131	198265131	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaagagcattaaccactgTgccaaagccgttcaacatta	14	8	7	12	1	1	1	1	0	0	1	1	1	1	1	4	0	5	2	4	0	5	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:198265131T>C	ENST00000335508.6	-	19	2837	c.2746A>G	c.(2746-2748)Aca>Gca	p.T916A	SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	916					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TTAACCACTGTGCCAAAGCCG	0.358			Mis		myelodysplastic syndrome																																p.T916A		.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.A2746G						.						97	95	95					2																	198265131		2203	4300	6503	SO:0001583	missense	23451	exon19			CCACTGTGCCAAA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2746A>G	2.37:g.198265131T>C	ENSP00000335321:p.Thr916Ala	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	176	77	NM_012433	0	0	58	106	48	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.851230	0.51270	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57695	0.2071	L	0.48174	1.505	0.80722	D	1	B	0.14012	0.009	B	0.21360	0.034	T	0.51903	-0.8646	9	0.29301	T	0.29	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	916	O75533	SF3B1_HUMAN	A	916	.	ENSP00000335321:T916A	T	-	1	0	SF3B1	197973376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.910000	0.87451	2.371000	0.80710	0.533000	0.62120	ACA	.		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198265131	T	C	198265131	3	2	126	1	0	0	0	0	1	0	0	0	14181	1696	59	3	1196	3	SF3B1	2	198265131	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	11592412	198265131	44934242	21	11007											
RAF1	5894	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	12653543	12653543	+	Frame_Shift_Del	DEL	T	T	-																															aaggcagtcatgcaagctcaTtccatttcgcacattgacct																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:12653543delT	ENST00000251849.4	-	3	665	c.226delA	c.(226-228)atgfs	p.M76fs	RAF1_ENST00000534997.1_5'Flank|RAF1_ENST00000442415.2_Frame_Shift_Del_p.M76fs|RAF1_ENST00000542177.1_Intron	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	76	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	TGCAAGCTCATTCCATTTCGC	0.498			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.M76X		.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1-1404	0			c.226delA						.						154	137	143					3																	12653543		2203	4300	6503	SO:0001589	frameshift_variant	5894	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	.	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"C-Raf proto-oncogene, serine/threonine kinase"	164760	"v-raf-1 murine leukemia viral oncogene homolog 1"			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.226delA	3.37:g.12653543delT	ENSP00000251849:p.Met76fs	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	118	55	NM_002880	0	0	0	0	0	B0LPH8|B2R5N3|Q15278|Q9UC20	Nonsense_Mutation	DEL	ENST00000251849.4	37	CCDS2612.1																																																																																			.		0.498	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		-	12653543	T	-	12653543	7	5	126	1	0	1	0	1	0	0	0	0	13034	1493	52	0	1780	0	RAF1	3	12653543	Frame_Shift_Del	DEL	T	TCGA-GL-A59R-01A-11D-A26P-10		12653543	185368887	22	11008											
GRIP2	80852	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	14559362	14559362	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggctgtggcaggagggcacGcaggggtcccagcggtgcag	6	4	21	10	2	0	0	0	0	0	0	1	1	1	1	1	7	2	5	1	7	0	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:14559362G>A	ENST00000273083.3	-	0	1138							Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2						synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				endometrium(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	25						AGGAGGGCACGCAGGGGTCCC	0.652																																					.													.	GRIP2-69	0			.						.																																					80852	.			GGGCACGCAGGGG	AB051506		3p24-p23	2012-02-08			ENSG00000144596	ENSG00000144596			23841	protein-coding gene	gene with protein product							Standard	NM_001080423		Approved	KIAA1719	uc021wtn.1	Q9C0E4	OTTHUMG00000155544		3.37:g.14559362G>A		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	36	24	.	0	0	0	0	0	Q8TEH9|Q9H7H3	Silent	SNP	ENST00000273083.3	37																																																																																				.		0.652	GRIP2-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000340582.2	NM_001080423		A	14559362	G	A	14559362	1	1	126	0	1	0	0	0	0	0	0	0	6809	1079	38	1		1	GRIP2	3	14559362	RNA	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	1905819	14559362	183463068	23	11009											
SCN11A	11280	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38966961	38966961	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacggaaggtacgcaggggCaatagtttgatggtgattcc	11	9	14	7	2	0	2	0	2	0	0	1	3	1	3	1	5	1	4	1	5	4	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:38966961C>G	ENST00000302328.3	-	5	855	c.657G>C	c.(655-657)ttG>ttC	p.L219F	SCN11A_ENST00000456224.3_Missense_Mutation_p.L219F|SCN11A_ENST00000444237.2_Missense_Mutation_p.L219F|SCN11A_ENST00000450244.1_Missense_Mutation_p.L219F	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	219					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TACGCAGGGGCAATAGTTTGA	0.463																																					p.L219F		.											.	SCN11A-99	0			c.G657C						.						162	136	145					3																	38966961		2203	4300	6503	SO:0001583	missense	11280	exon5			CAGGGGCAATAGT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.657G>C	3.37:g.38966961C>G	ENSP00000307599:p.Leu219Phe	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	141	53	NM_014139	0	0	0	0	0	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808991	0.50421	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	4.79	-4.0	0.04057	Ion transport (1);	0.225617	0.39210	N	0.001423	D	0.94515	0.8234	L	0.55481	1.735	0.09310	N	1	P	0.50819	0.939	P	0.49192	0.602	D	0.89878	0.4028	10	0.87932	D	0	.	5.7293	0.18030	0.0:0.2152:0.3973:0.3874	.	219	Q9UI33	SCNBA_HUMAN	F	219	ENSP00000307599:L219F;ENSP00000400945:L219F;ENSP00000416757:L219F;ENSP00000408028:L219F	ENSP00000307599:L219F	L	-	3	2	SCN11A	38941965	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	-1.047000	0.03521	-0.513000	0.06496	0.467000	0.42956	TTG	.		0.463	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		G	38966961	C	G	38966961	3	3	126	1	0	0	0	0	1	0	0	0	13945	709	25	4	4806	4	SCN11A	3	38966961	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	24407599	38966961	159055469	24	11010											
NME6	10201	ucsc.edu	37	chr3	48338260	48338260	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcaatcttcctttctccaCagtagttctctcattcgtac	7	16	5	13	1	4	0	1	0	3	0	8	0	5	0	2	1	1	4	2	1	3	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:48338260C>T	ENST00000452211.1	-	4	387	c.150G>A	c.(148-150)ctG>ctA	p.L50L	NME6_ENST00000421967.1_Silent_p.L58L|NME6_ENST00000447314.1_Silent_p.L5L|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000415644.1_Silent_p.L50L|NME6_ENST00000451657.1_Silent_p.L50L|NME6_ENST00000415053.1_Silent_p.L50L|NME6_ENST00000426689.2_Silent_p.L50L|NME6_ENST00000444069.1_Intron|NME6_ENST00000442597.1_Silent_p.L50L|NME6_ENST00000426723.1_Silent_p.L50L|NME6_ENST00000450160.1_Silent_p.L50L|NME6_ENST00000435684.1_Silent_p.L50L			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	50					apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		CCTTTCTCCACAGTAGTTCTC	0.433																																					p.L58L													.	NME6-115	0			c.G174A						.						170	150	157					3																	48338260		2203	4300	6503	SO:0001819	synonymous_variant	10201	exon3			TCTCCACAGTAGT	AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113			20567	protein-coding gene	gene with protein product		608294	"non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)"			10453732, 19852809	Standard	NM_005793		Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000452211.1:c.150G>A	3.37:g.48338260C>T		Somatic	55	0		WXS	Illumina HiSeq		66	2	NM_005793	0	0	3	3	0	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Silent	SNP	ENST00000452211.1	37																																																																																				.		0.433	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793		T	48338260	C	T	48338260	2	4	126	1	0	0	0	0	0	0	0	1	10521	465	17	2		2	NME6	3	48338260	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	9371299	48338260	149684170	25	11011											
PLXNB1	5364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48465285	48465285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacactcgagatacataggCacgaaaagctctagactgag	16	6	9	10	2	1	3	0	1	1	2	2	5	1	3	0	1	2	2	0	1	5	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:48465285C>T	ENST00000358536.4	-	3	1005	c.736G>A	c.(736-738)Gcc>Acc	p.A246T	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Missense_Mutation_p.A246T|PLXNB1_ENST00000456774.1_Missense_Mutation_p.A246T|PLXNB1_ENST00000296440.6_Missense_Mutation_p.A246T	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	246	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GATACATAGGCACGAAAAGCT	0.607																																					p.A246T		.											.	PLXNB1-293	0			c.G736A						.						62	58	59					3																	48465285		2202	4300	6502	SO:0001583	missense	5364	exon3			CATAGGCACGAAA	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.736G>A	3.37:g.48465285C>T	ENSP00000351338:p.Ala246Thr	Somatic	218	0		WXS	Illumina HiSeq	Phase_I	188	81	NM_001130082	0	0	25	54	29	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.836487	0.00579	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.02944	4.1;4.1;4.1;4.1	4.41	2.58	0.30949	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.176749	0.38436	N	0.001699	T	0.00666	0.0022	N	0.00201	-1.865	0.80722	D	1	B;B	0.12013	0.001;0.005	B;B	0.10450	0.005;0.004	T	0.41324	-0.9515	10	0.07325	T	0.83	.	4.5893	0.12299	0.0:0.2937:0.3661:0.3403	.	246;246	O43157;O43157-2	PLXB1_HUMAN;.	T	246	ENSP00000296440:A246T;ENSP00000351242:A246T;ENSP00000351338:A246T;ENSP00000414199:A246T	ENSP00000296440:A246T	A	-	1	0	PLXNB1	48440289	0.995000	0.38212	0.188000	0.23233	0.006000	0.05464	2.590000	0.46154	0.308000	0.22923	-0.229000	0.12294	GCC	.		0.607	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		T	48465285	C	T	48465285	3	4	126	1	0	0	0	0	1	0	0	0	12149	710	25	2	5815	2	PLXNB1	3	48465285	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	127025	48465285	149557145	26	11012											
CACNA2D2	9254	broad.mit.edu;bcgsc.ca	37	chr3	50513567	50513567	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcacggagctgctggacGcctccaaaaatccgcatcac	11	6	8	16	3	2	0	2	0	0	0	4	2	4	2	4	2	2	3	4	2	2	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:50513567G>T	ENST00000479441.1	-	2	269	c.270C>A	c.(268-270)ggC>ggA	p.G90G	CACNA2D2_ENST00000435965.1_Silent_p.G90G|CACNA2D2_ENST00000424201.2_Silent_p.G90G|CACNA2D2_ENST00000395083.1_Silent_p.G90G|CACNA2D2_ENST00000487413.1_5'UTR|CACNA2D2_ENST00000423994.2_Silent_p.G90G|CACNA2D2_ENST00000429770.1_Silent_p.G90G|CACNA2D2_ENST00000266039.3_Silent_p.G90G|CACNA2D2_ENST00000360963.3_Silent_p.G21G			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	90					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GCTGCTGGACGCCTCCAAAAA	0.597																																					p.G90G													.	CACNA2D2-278	0			c.C270A						.						61	57	58					3																	50513567		2201	4299	6500	SO:0001819	synonymous_variant	9254	exon2			CTGGACGCCTCCA	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"Calcium channel subunits"	1400	protein-coding gene	gene with protein product	"gene 26"	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.270C>A	3.37:g.50513567G>T		Somatic	50	2		WXS	Illumina HiSeq	Phase_I	31	10	NM_001174051	0	0	0	0	0	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Silent	SNP	ENST00000479441.1	37	CCDS54588.1																																																																																			.		0.597	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		T	50513567	G	T	50513567	2	4	126	1	0	0	0	0	0	0	0	1	2555	1074	38	4		4	CACNA2D2	3	50513567	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	2048282	50513567	147508863	27	11013											
NISCH	11188	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	52505969	52505969	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcgggcacatcctggacttCacctgtcgccttaagtacct	7	11	8	15	2	1	0	1	0	0	0	4	1	2	1	4	2	1	2	4	2	2	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:52505969C>T	ENST00000479054.1	+	6	621	c.549C>T	c.(547-549)ttC>ttT	p.F183F	NISCH_ENST00000488380.1_Silent_p.F183F|NISCH_ENST00000420808.2_Silent_p.F183F|NISCH_ENST00000345716.4_Silent_p.F183F			Q9Y2I1	NISCH_HUMAN	nischarin	183	Necessary for homooligomerization and targeting to endosomes.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	TCCTGGACTTCACCTGTCGCC	0.632											OREG0015615	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F183F		.											.	NISCH-93	0			c.C549T						.						59	60	60					3																	52505969		2203	4300	6503	SO:0001819	synonymous_variant	11188	exon5			GGACTTCACCTGT	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"imidazoline receptor candidate", "I-1 receptor candidate protein", "imidazoline receptor antisera selected"	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.549C>T	3.37:g.52505969C>T		Somatic	323	0	985	WXS	Illumina HiSeq	Phase_I	284	18	NM_001276293	0	0	11	12	1	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	37	CCDS33767.1																																																																																			.		0.632	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52505969	C	T	52505969	2	4	126	1	0	0	0	0	0	0	0	1	10458	825	29	2		2	NISCH	3	52505969	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	1992402	52505969	145516461	28	11014											
DNAJC13	23317	bcgsc.ca	37	chr3	132196969	132196969	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagataccagatatatcatTggaatgttagagagggtaag	16	10	11	4	0	1	3	1	0	0	3	1	5	1	4	1	2	1	2	1	2	6	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:132196969T>C	ENST00000260818.6	+	24	2942	c.2694T>C	c.(2692-2694)atT>atC	p.I898I		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	898					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						GATATATCATTGGAATGTTAG	0.303																																					p.I898I													.	DNAJC13-272	0			c.T2694C						.						78	82	81					3																	132196969		2203	4300	6503	SO:0001819	synonymous_variant	23317	exon24			TATCATTGGAATG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.2694T>C	3.37:g.132196969T>C		Somatic	37	0		WXS	Illumina HiSeq	Phase_1	46	4	NM_015268	0	0	3	3	0	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																			.		0.303	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132196969	T	C	132196969	2	2	126	1	0	0	0	0	0	0	0	1	4643	1800	63	3		3	DNAJC13	3	132196969	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	79691000	132196969	65825461	29	11015											
SKIL	6498	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	170078913	170078913	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtgcctttgaagtggAgcatgaatgcctaggcaaat	11	10	13	7	0	0	2	0	2	0	0	0	3	0	3	2	3	3	3	2	3	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:170078913A>T	ENST00000458537.3	+	1	1503	c.794A>T	c.(793-795)gAg>gTg	p.E265V	SKIL_ENST00000259119.4_Missense_Mutation_p.E265V|SKIL_ENST00000426052.2_Missense_Mutation_p.E245V|SKIL_ENST00000413427.2_Missense_Mutation_p.E265V	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	265					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TTTGAAGTGGAGCATGAATGC	0.453																																					p.E265V		.											.	SKIL-228	0			c.A794T						.						147	129	135					3																	170078913		2203	4300	6503	SO:0001583	missense	6498	exon1			AAGTGGAGCATGA	X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.794A>T	3.37:g.170078913A>T	ENSP00000415243:p.Glu265Val	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	190	66	NM_001248008	0	0	2	2	0	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	37	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.312956	0.60414	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.91464	-2.85;-2.85;-2.83;-2.85	5.51	5.51	0.81932	SAND domain-like (2);c-SKI Smad4-binding (1);	0.221987	0.48286	D	0.000184	D	0.92038	0.7477	L	0.33485	1.01	0.52099	D	0.999943	D;D	0.89917	0.998;1.0	D;D	0.97110	0.969;1.0	D	0.90522	0.4489	10	0.25751	T	0.34	-22.9066	15.6712	0.77279	1.0:0.0:0.0:0.0	.	265;265	P12757-3;P12757	.;SKIL_HUMAN	V	265;245;265;265	ENSP00000259119:E265V;ENSP00000406520:E245V;ENSP00000400193:E265V;ENSP00000415243:E265V	ENSP00000259119:E265V	E	+	2	0	SKIL	171561607	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	8.962000	0.93254	2.111000	0.64477	0.524000	0.50904	GAG	.		0.453	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		T	170078913	A	T	170078913	3	4	126	1	0	0	0	0	1	0	0	0	14390	304	11	5	796	5	SKIL	3	170078913	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	37881944	170078913	27943517	30	11016											
LRPAP1	4043	broad.mit.edu;bcgsc.ca	37	chr4	3534063	3534077	+	In_Frame_Del	DEL	CAGGGCCCGAGGAAG	CAGGGCCCGAGGAAG	-																															cgccgtggctcgcagcgggcCagggcccgaggaagagcagc																								rs541409658|rs572340534	byFrequency	TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	CAGGGCCCGAGGAAG	CAGGGCCCGAGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr4:3534063_3534077delCAGGGCCCGAGGAAG	ENST00000500728.2	-	1	209_223	c.63_77delCTTCCTCGGGCCCTG	c.(61-78)ctcttcctcgggccctgg>ctg	p.FLGPW22del	LRPAP1_ENST00000296325.5_5'Flank	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	22					extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CGCAGCGGGCCAGGGCCCGAGGAAGAGCAGCAGCA	0.674																																					p.21_26del													.	LRPAP1-92	0			c.63_77del						.																																			SO:0001651	inframe_deletion	4043	exon1			GCGGGCCAGGGCC		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.63_77delCTTCCTCGGGCCCTG	4.37:g.3534063_3534077delCAGGGCCCGAGGAAG	ENSP00000421922:p.Phe22_Trp26del	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	31	7	NM_002337	0	0	0	0	0	D3DVR9|Q2M310|Q53HQ3|Q53HS6	In_Frame_Del	DEL	ENST00000500728.2	37	CCDS3371.1																																																																																			.		0.674	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			-	3534077	CAGGGCCCGAGGAAG	-	3534063	7	5	126	1	0	1	0	1	0	0	0	0	8989	595	21	0	1028	0	LRPAP1	4	3534063	In_Frame_Del	DEL	CAGGGCCCGAGGAAG	TCGA-GL-A59R-01A-11D-A26P-10		3534063	187620213	31	11017											
RUFY3	22902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	71629308	71629308	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acaaaataaatccttctgggGgcctctagaactggtagaaa	15	9	9	8	0	2	2	0	0	2	2	3	2	3	2	2	3	1	1	2	3	8	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr4:71629308G>A	ENST00000226328.4	+	3	955	c.392G>A	c.(391-393)gGg>gAg	p.G131E	RUFY3_ENST00000381006.3_Missense_Mutation_p.G131E|RUFY3_ENST00000502653.1_Missense_Mutation_p.G78E|RUFY3_ENST00000417478.2_Missense_Mutation_p.G191E|RUFY3_ENST00000536664.1_Missense_Mutation_p.G115E	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	131	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TCCTTCTGGGGGCCTCTAGAA	0.368																																					p.G191E		.											.	RUFY3-90	0			c.G572A						.						37	41	40					4																	71629308		2195	4298	6493	SO:0001583	missense	22902	exon3			TCTGGGGGCCTCT	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.392G>A	4.37:g.71629308G>A	ENSP00000226328:p.Gly131Glu	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	104	50	NM_001130709	0	0	3	6	3	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907015	0.92107	.	.	ENSG00000018189	ENST00000503876;ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75;2.75	5.13	5.13	0.70059	RUN (2);	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	M	0.64997	1.995	0.80722	D	1	D;P;B;P	0.59767	0.986;0.498;0.397;0.956	D;P;P;D	0.76071	0.987;0.744;0.679;0.95	T	0.02093	-1.1215	10	0.72032	D	0.01	-9.749	18.944	0.92615	0.0:0.0:1.0:0.0	.	115;131;131;191	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	E	67;191;131;131;115;67;78	ENSP00000426734:G67E;ENSP00000399771:G191E;ENSP00000370394:G131E;ENSP00000226328:G131E;ENSP00000443652:G115E;ENSP00000425574:G67E;ENSP00000425400:G78E	ENSP00000226328:G131E	G	+	2	0	RUFY3	71848172	1.000000	0.71417	0.979000	0.43373	0.957000	0.61999	9.744000	0.98853	2.569000	0.86673	0.591000	0.81541	GGG	.		0.368	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		A	71629308	G	A	71629308	3	1	126	1	0	0	0	0	1	0	0	0	13772	1232	43	2	764	2	RUFY3	4	71629308	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	68095245	71629308	119524968	32	11018											
DSPP	1834	bcgsc.ca	37	chr4	88536953	88536953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgatagcagtgacagcagcGatagcagtgacagcagtgac	13	5	14	9	2	0	3	0	3	0	0	0	5	0	3	0	0	5	4	0	0	2	2	rs200486992		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr4:88536953G>A	ENST00000282478.7	+	4	3172	c.3139G>A	c.(3139-3141)Gat>Aat	p.D1047N	DSPP_ENST00000399271.1_Missense_Mutation_p.D1047N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1047	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.527																																					p.D1047N													.	DSPP-90	0			c.G3139A						.						46	57	53					4																	88536953		1537	2773	4310	SO:0001583	missense	1834	exon5			AGCAGCGATAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3139G>A	4.37:g.88536953G>A	ENSP00000282478:p.Asp1047Asn	Somatic	227	0		WXS	Illumina HiSeq	Phase_1	307	12	NM_014208	0	0	0	0	0	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	3.566	-0.088574	0.07097	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88201	-2.35;-2.35	1.51	-1.84	0.07809	.	.	.	.	.	T	0.78355	0.4270	L	0.34521	1.04	0.09310	N	1	B	0.26708	0.157	B	0.08055	0.003	T	0.61637	-0.7022	9	0.38643	T	0.18	.	5.2365	0.15448	0.5606:0.0:0.4394:0.0	.	1047	Q9NZW4	DSPP_HUMAN	N	1047	ENSP00000382213:D1047N;ENSP00000282478:D1047N	ENSP00000282478:D1047N	D	+	1	0	DSPP	88755977	0.032000	0.19561	0.079000	0.20413	0.006000	0.05464	0.451000	0.21779	-0.607000	0.05738	-0.791000	0.03333	GAT	.		0.527	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88536953	G	A	88536953	3	1	126	1	0	0	0	0	1	0	0	0	4793	1058	37	1	3153	1	DSPP	4	88536953	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	16907645	88536953	102617323	33	11019											
NSUN2	54888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	6600168	6600168	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgtcattgtctggctgtccGgtgctggctgcactctcatt	4	14	11	12	2	3	0	2	0	2	0	5	0	4	0	1	3	2	4	1	3	0	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:6600168G>A	ENST00000264670.6	-	19	2486	c.2175C>T	c.(2173-2175)acC>acT	p.T725T	NSUN2_ENST00000506139.1_Silent_p.T690T|NSUN2_ENST00000539938.1_Silent_p.T489T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	725					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTGGCTGTCCGGTGCTGGCTG	0.537																																					p.T725T		.											.	NSUN2-91	0			c.C2175T						.						182	148	160					5																	6600168		2203	4300	6503	SO:0001819	synonymous_variant	54888	exon19			CTGTCCGGTGCTG	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"NOP2/Sun domain containing"	25994	protein-coding gene	gene with protein product	"tRNA methyltransferase 4 homolog (S. cerevisiae)", "Myc-induced SUN-domain-containing protein"	610916	"NOL1/NOP2/Sun domain family, member 2", "NOP2/Sun domain family, member 2", "mental retardation, non-syndromic, autosomal recessive, 5"	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.2175C>T	5.37:g.6600168G>A		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	146	64	NM_017755	0	0	16	29	13	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			.		0.537	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		A	6600168	G	A	6600168	2	1	126	1	0	0	0	0	0	0	0	1	10704	1103	39	1		1	NSUN2	5	6600168	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		6600168	174315092	34	11020											
FASTKD3	79072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7867451	7867451	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcctccggggtaaatgttTccaatttttcaccttgaagt	9	16	7	9	1	1	1	1	1	0	0	4	1	4	1	4	2	0	2	4	2	5	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:7867451T>C	ENST00000264669.5	-	2	882	c.746A>G	c.(745-747)gAa>gGa	p.E249G	MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	249					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGTAAATGTTTCCAATTTTTC	0.368																																					p.E249G		.											.	FASTKD3-156	0			c.A746G						.						80	85	83					5																	7867451		2203	4300	6503	SO:0001583	missense	79072	exon2			AATGTTTCCAATT	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.746A>G	5.37:g.7867451T>C	ENSP00000264669:p.Glu249Gly	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	32	11	NM_024091	0	0	0	2	2	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	37	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.275390	0.59649	.	.	ENSG00000124279	ENST00000264669	T	0.29142	1.58	4.85	3.65	0.41850	.	0.369914	0.32055	N	0.006643	T	0.31327	0.0793	M	0.72118	2.19	0.23421	N	0.997719	P	0.40144	0.704	B	0.36719	0.231	T	0.14531	-1.0469	10	0.38643	T	0.18	-20.1472	11.6008	0.51001	0.0:0.0:0.1494:0.8506	.	249	Q14CZ7	FAKD3_HUMAN	G	249	ENSP00000264669:E249G	ENSP00000264669:E249G	E	-	2	0	FASTKD3	7920451	0.203000	0.23435	0.094000	0.20943	0.730000	0.41778	2.603000	0.46266	0.835000	0.34877	0.528000	0.53228	GAA	.		0.368	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		C	7867451	T	C	7867451	3	2	126	1	0	0	0	0	1	0	0	0	5706	1783	62	3	1266	3	FASTKD3	5	7867451	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	1267283	7867451	173047809	35	11021											
DNAH5	1767	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	13814812	13814812	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgtcaatgttatgaggctCgaaaatgatcttgcagtttg	11	15	10	5	1	2	2	1	2	1	0	3	3	2	2	0	1	1	4	0	1	4	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:13814812C>A	ENST00000265104.4	-	43	7236	c.7132G>T	c.(7132-7134)Gag>Tag	p.E2378*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2378	AAA 2. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TTATGAGGCTCGAAAATGATC	0.418									Kartagener syndrome																												p.E2378X													.	DNAH5-182	0			c.G7132T						.						102	87	92					5																	13814812		2203	4300	6503	SO:0001587	stop_gained	1767	exon43	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GAGGCTCGAAAAT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.7132G>T	5.37:g.13814812C>A	ENSP00000265104:p.Glu2378*	Somatic	104	2		WXS	Illumina HiSeq	Phase_I	128	57	NM_001369	0	0	0	0	0	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	49	15.754211	0.99844	.	.	ENSG00000039139	ENST00000265104	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.9238	0.92537	0.0:1.0:0.0:0.0	.	.	.	.	X	2378	.	ENSP00000265104:E2378X	E	-	1	0	DNAH5	13867812	1.000000	0.71417	0.972000	0.41901	0.830000	0.47004	7.770000	0.85390	2.468000	0.83385	0.650000	0.86243	GAG	.		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13814812	C	A	13814812	4	1	126	1	0	0	0	0	0	1	0	0	4615	893	31	4	6890	4	DNAH5	5	13814812	Nonsense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	5947361	13814812	167100448	36	11022											
ANKHD1	54882	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	139906526	139906526	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttagacttgaaggtgaaGtgactcctaattccttgtca	10	15	8	8	0	2	4	1	3	1	1	4	4	4	4	2	1	0	0	2	1	4	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:139906526G>A	ENST00000360839.2	+	27	5108	c.4954G>A	c.(4954-4956)Gtg>Atg	p.V1652M	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.V1652M|SNORD45_ENST00000363181.1_RNA|ANKHD1_ENST00000544120.1_Missense_Mutation_p.V35M|ANKHD1_ENST00000297183.6_Missense_Mutation_p.V1652M	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1652						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAAGGTGAAGTGACTCCTAA	0.383																																					p.V1652M													.	ANKHD1-185	0			c.G4954A						.						109	103	105					5																	139906526		2203	4300	6503	SO:0001583	missense	54882	exon27			GGTGAAGTGACTC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4954G>A	5.37:g.139906526G>A	ENSP00000354085:p.Val1652Met	Somatic	167	1		WXS	Illumina HiSeq	Phase_I	149	63	NM_017747	0	0	0	0	0	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.27|14.27	2.486213|2.486213	0.44147|0.44147	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000435794;ENST00000432301|ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000536646;ENST00000433049;ENST00000544120;ENST00000532219	.|T;T;T;T;T;T	.|0.24350	.|1.86;1.86;1.86;1.86;1.86;1.86	5.67|5.67	1.83|1.83	0.25207|0.25207	.|.	.|0.707951	.|0.14055	.|N	.|0.344496	T|T	0.14356|0.14356	0.0347|0.0347	N|N	0.22421|0.22421	0.69|0.69	0.20196|0.20196	N|N	0.999927|0.999927	.|B;B;B;B;B	.|0.28026	.|0.198;0.001;0.001;0.004;0.001	.|B;B;B;B;B	.|0.25614	.|0.062;0.001;0.002;0.004;0.002	T|T	0.21381|0.21381	-1.0247|-1.0247	5|10	.|0.38643	.|T	.|0.18	.|.	5.067|5.067	0.14587|0.14587	0.2909:0.0:0.5765:0.1325|0.2909:0.0:0.5765:0.1325	.|.	.|35;82;1652;1652;1652	.|Q8IWG5;Q9H059;E9PF56;Q8IWZ2;Q8IWZ3	.|.;.;.;.;ANKH1_HUMAN	N|M	142;102|1652;1652;1652;308;87;174;35;1652	.|ENSP00000354085:V1652M;ENSP00000297183:V1652M;ENSP00000393204:V308M;ENSP00000390034:V174M;ENSP00000437687:V35M;ENSP00000432016:V1652M	.|ENSP00000432016:V1652M	S|V	+|+	2|1	0|0	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139886710|139886710	0.881000|0.881000	0.30235|0.30235	0.462000|0.462000	0.27118|0.27118	0.979000|0.979000	0.70002|0.70002	0.839000|0.839000	0.27586|0.27586	0.057000|0.057000	0.16193|0.16193	-0.145000|-0.145000	0.13849|0.13849	AGT|GTG	.		0.383	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		A	139906526	G	A	139906526	3	1	126	1	0	0	0	0	1	0	0	0	628	1029	36	2	5166	2	ANKHD1	5	139906526	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	126091714	139906526	41008734	37	11023											
PCDHB10	56126	bcgsc.ca	37	chr5	140573408	140573411	+	Frame_Shift_Del	DEL	CACC	CACC	-																															caccgtcactgacttggggaCacccaggctgaaaaccgagc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	CACC	CACC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:140573408_140573411delCACC	ENST00000239446.4	+	1	1467_1470	c.1283_1286delCACC	c.(1282-1287)acacccfs	p.TP428fs		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	428	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GACTTGGGGACACCCAGGCTGAAA	0.539																																					p.428_429del													.	PCDHB10-92	0			c.1283_1286del						.																																			SO:0001589	frameshift_variant	56126	exon1			TGGGGACACCCAG	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1283_1286delCACC	5.37:g.140573408_140573411delCACC	ENSP00000239446:p.Thr428fs	Somatic	193	1		WXS	Illumina HiSeq	Phase_1	146	33	NM_018930	0	0	0	0	0	Q96T99	Frame_Shift_Del	DEL	ENST00000239446.4	37	CCDS4252.1																																																																																			.		0.539	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		-	140573411	CACC	-	140573408	7	5	126	1	0	1	0	1	0	0	0	0	11561	478	17	0	1285	0	PCDHB10	5	140573408	Frame_Shift_Del	DEL	CACC	TCGA-GL-A59R-01A-11D-A26P-10	666882	140573408	40341852	38	11024	115	3									
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573409	140573413	+	Frame_Shift_Del	DEL	ACCCA	ACCCA	-																															accgtcactgacttggggacAcccaggctgaaaaccgagca																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	ACCCA	ACCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:140573409_140573413delACCCA	ENST00000239446.4	+	1	1468_1472	c.1284_1288delACCCA	c.(1282-1290)acacccaggfs	p.PR429fs		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	429	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACTTGGGGACACCCAGGCTGAAAAC	0.532																																					p.428_430del		.											.	PCDHB10-92	0			c.1284_1288del						.																																			SO:0001589	frameshift_variant	56126	exon1			.	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1284_1288delACCCA	5.37:g.140573409_140573413delACCCA	ENSP00000239446:p.Pro429fs	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	145	23	NM_018930	0	0	0	0	0	Q96T99	Frame_Shift_Del	DEL	ENST00000239446.4	37	CCDS4252.1																																																																																			.		0.532	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		-	140573413	ACCCA	-	140573409	7	5	126	1	0	1	0	1	0	0	0	0	11561	146	6	0	1286	0	PCDHB10	5	140573409	Frame_Shift_Del	DEL	ACCCA	TCGA-GL-A59R-01A-11D-A26P-10	1	140573409	40341851	39	11025	115	3									
PCDHB10	56126	bcgsc.ca	37	chr5	140573413	140573413	+	Missense_Mutation	SNP	A	A	T																															tcactgacttggggacacccAggctgaaaaccgagcacaac																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:140573413A>T	ENST00000239446.4	+	1	1472	c.1288A>T	c.(1288-1290)Agg>Tgg	p.R430W		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	430	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGGACACCCAGGCTGAAAAC	0.532																																					p.R430W													.	PCDHB10-92	0			c.A1288T						.						94	91	92					5																	140573413		2203	4300	6503	SO:0001583	missense	56126	exon1			ACACCCAGGCTGA	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1288A>T	5.37:g.140573413A>T	ENSP00000239446:p.Arg430Trp	Somatic	186	1		WXS	Illumina HiSeq	Phase_1	143	33	NM_018930	0	0	3	3	0	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.581987	0.46006	.	.	ENSG00000120324	ENST00000239446	T	0.53206	0.63	3.22	3.22	0.36961	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.76212	0.3956	H	0.96833	3.89	0.20489	N	0.999896	D	0.89917	1.0	D	0.87578	0.998	T	0.65952	-0.6043	9	0.72032	D	0.01	.	8.63	0.33913	0.6649:0.3351:0.0:0.0	.	430	Q9UN67	PCDBA_HUMAN	W	430	ENSP00000239446:R430W	ENSP00000239446:R430W	R	+	1	2	PCDHB10	140553597	0.014000	0.17966	0.985000	0.45067	0.725000	0.41563	1.685000	0.37659	1.485000	0.48380	0.449000	0.29647	AGG	.		0.532	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140573413	A	T	140573413	3	4	126	1	0	0	0	0	1	0	0	0	11561	179	7	5	1290	5	PCDHB10	5	140573413	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	4	140573413	40341847	40	11026	115	3									
PHACTR1	221692	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	13230366	13230366	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaaaagaacatccttccCaggcagacggatgaggagcg	15	4	13	9	2	0	4	0	1	0	3	2	7	2	6	2	3	2	1	2	3	4	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:13230366C>A	ENST00000379350.1	+	9	1461	c.1332C>A	c.(1330-1332)ccC>ccA	p.P444P	PHACTR1_ENST00000457702.2_Silent_p.P299P|PHACTR1_ENST00000332995.7_Silent_p.P444P|PHACTR1_ENST00000379345.2_Intron			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	444					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			ACATCCTTCCCAGGCAGACGG	0.597																																					p.P444P													.	.	0			c.C1332A						.						34	35	35					6																	13230366		2041	4189	6230	SO:0001819	synonymous_variant	221692	exon10			CCTTCCCAGGCAG	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379350.1:c.1332C>A	6.37:g.13230366C>A		Somatic	169	1		WXS	Illumina HiSeq	Phase_I	185	87	NM_030948	0	0	0	0	0	A8K1V2|Q3MJ93|Q5JSJ2	Silent	SNP	ENST00000379350.1	37		.	.	.	.	.	.	.	.	.	.	C	9.674	1.147561	0.21288	.	.	ENSG00000112137	ENST00000415087	T	0.35421	1.31	5.47	0.497	0.16902	.	0.000000	0.85682	D	0.000000	T	0.26738	0.0654	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07121	-1.0789	7	0.49607	T	0.09	-19.1306	8.3007	0.32012	0.0:0.5638:0.2478:0.1885	.	.	.	.	Q	279	ENSP00000395948:P279Q	ENSP00000395948:P279Q	P	+	2	0	PHACTR1	13338345	0.809000	0.29036	0.788000	0.31933	0.996000	0.88848	0.088000	0.14979	-0.127000	0.11661	0.557000	0.71058	CCA	.		0.597	PHACTR1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039876.1	XM_166420		A	13230366	C	A	13230366	2	1	126	1	0	0	0	0	0	0	0	1	11835	581	21	4		4	PHACTR1	6	13230366	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		13230366	157884701	41	11027											
DPCR1	135656	ucsc.edu;bcgsc.ca	37	chr6	30917934	30917934	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctacagaaaatggagacAggactcctttggccaatgag	14	7	11	9	0	0	3	0	1	0	2	1	5	1	4	3	3	2	0	3	3	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:30917934A>G	ENST00000462446.1	+	2	1721	c.1693A>G	c.(1693-1695)Agg>Ggg	p.R565G	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	117						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AAATGGAGACAGGACTCCTTT	0.502																																					p.R565G													.	DPCR1-90	0			c.A1693G						.						78	76	77					6																	30917934		692	1591	2283	SO:0001583	missense	135656	exon2			GGAGACAGGACTC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1693A>G	6.37:g.30917934A>G	ENSP00000417182:p.Arg565Gly	Somatic	196	2		WXS	Illumina HiSeq		218	74	NM_080870	0	0	0	0	0	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	7.360	0.624745	0.14193	.	.	ENSG00000168631	ENST00000462446	T	0.47869	0.83	1.97	-3.94	0.04130	.	.	.	.	.	T	0.15003	0.0362	L	0.47716	1.5	0.09310	N	0.999999	B	0.06786	0.001	B	0.10450	0.005	T	0.31280	-0.9949	9	0.23891	T	0.37	.	8.1341	0.31043	0.5066:0.0:0.4934:0.0	.	565	E9PEI6	.	G	565	ENSP00000417182:R565G	ENSP00000417182:R565G	R	+	1	2	DPCR1	31025913	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.739000	0.04866	-0.979000	0.03529	0.000000	0.15137	AGG	.		0.502	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		G	30917934	A	G	30917934	3	3	126	1	0	0	0	0	1	0	0	0	4723	179	7	3	1699	3	DPCR1	6	30917934	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	17687568	30917934	140197133	42	11028											
MUC21	394263	bcgsc.ca	37	chr6	30954603	30954603	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	accaactctgagtccagaacGacctccaatggggctggcac	11	6	10	14	1	1	2	0	1	1	1	3	3	3	2	4	3	2	2	4	3	3	0	rs532108366	byFrequency	TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:30954603G>A	ENST00000376296.3	+	2	892	c.651G>A	c.(649-651)acG>acA	p.T217T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	217	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTCCAGAACGACCTCCAATG	0.617													G|||	17	0.00339457	0.0023	0.0101	5008	,	,		21494	0.003		0.003	False		,,,				2504	0.001				p.T217T													.	MUC21-92	0			c.G651A						.						153	151	152					6																	30954603		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CAGAACGACCTCC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"Mucins"	21661	protein-coding gene	gene with protein product	"epiglycanin"		"chromosome 6 open reading frame 205"	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.651G>A	6.37:g.30954603G>A		Somatic	178	8		WXS	Illumina HiSeq	Phase_1	180	13	NM_001010909	0	0	0	0	0	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		A	30954603	G	A	30954603	2	1	126	1	0	0	0	0	0	0	0	1	10002	1045	37	1		1	MUC21	6	30954603	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	36669	30954603	140160464	43	11029											
DOM3Z	1797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31938842	31938842	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggctgccagctgccagccctCctgccgctcatacggtgtcg	4	8	12	17	3	1	0	1	0	0	0	3	0	2	0	5	2	6	3	5	2	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:31938842C>T	ENST00000375349.3	-	3	850	c.439G>A	c.(439-441)Gag>Aag	p.E147K	DXO_ENST00000478221.1_5'UTR|STK19_ENST00000375333.2_5'Flank|DXO_ENST00000337523.5_Missense_Mutation_p.E147K|STK19_ENST00000375331.2_5'Flank|DXO_ENST00000375356.3_Missense_Mutation_p.E147K			O77932	DXO_HUMAN	decapping exoribonuclease	147					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										TGCCAGCCCTCCTGCCGCTCA	0.642																																					p.E147K		.											.	DOM3Z-90	0			c.G439A						.						81	91	88					6																	31938842		1508	2708	4216	SO:0001583	missense	1797	exon3			AGCCCTCCTGCCG	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"DOM-3 (C. elegans) homolog Z", "dom-3 homolog Z (C. elegans)"	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.439G>A	6.37:g.31938842C>T	ENSP00000364498:p.Glu147Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	88	34	NM_005510	0	0	14	30	16	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568158	0.86439	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	T;T;T	0.19532	2.14;2.14;2.14	4.91	4.03	0.46877	.	0.054459	0.64402	D	0.000001	T	0.24547	0.0595	L	0.53249	1.67	0.49483	D	0.999795	P;D	0.76494	0.951;0.999	P;P	0.62298	0.487;0.9	T	0.01591	-1.1317	10	0.29301	T	0.29	-10.6299	14.2192	0.65815	0.0:0.849:0.151:0.0	.	147;147	F8WC68;O77932	.;DOM3Z_HUMAN	K	147	ENSP00000337759:E147K;ENSP00000364498:E147K;ENSP00000364505:E147K	ENSP00000337759:E147K	E	-	1	0	DOM3Z	32046821	1.000000	0.71417	0.983000	0.44433	0.793000	0.44817	7.160000	0.77495	1.266000	0.44231	-0.305000	0.09177	GAG	.		0.642	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3			T	31938842	C	T	31938842	3	4	126	1	0	0	0	0	1	0	0	0	4716	864	30	2	771	2	DOM3Z	6	31938842	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	984239	31938842	139176225	44	11030											
PGK2	5232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	49753793	49753793	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgtctccaccccctataaCagtgatgcagcccttggaag	10	9	9	13	0	1	1	0	1	1	0	2	2	1	2	4	1	3	1	4	1	3	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:49753793C>G	ENST00000304801.3	-	1	1260	c.1108G>C	c.(1108-1110)Gtt>Ctt	p.V370L		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	370					glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			autonomic_ganglia(1)|endometrium(3)|large_intestine(12)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	47	Lung NSC(77;0.0402)					CCCCCTATAACAGTGATGCAG	0.498																																					p.V370L		.											.	PGK2-91	0			c.G1108C						.						155	152	153					6																	49753793		2203	4300	6503	SO:0001583	missense	5232	exon1			CTATAACAGTGAT	K03019	CCDS4930.1	6p12.3	2012-09-20		2002-04-19	ENSG00000170950	ENSG00000170950			8898	protein-coding gene	gene with protein product		172270				3839763, 3453121	Standard	NM_138733		Approved	PGKPS, PGK-2	uc003ozu.3	P07205	OTTHUMG00000014824	ENST00000304801.3:c.1108G>C	6.37:g.49753793C>G	ENSP00000305995:p.Val370Leu	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	189	53	NM_138733	0	0	0	0	0	B2R6Y8|Q9H107	Missense_Mutation	SNP	ENST00000304801.3	37	CCDS4930.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243598	0.39697	.	.	ENSG00000170950	ENST00000304801	D	0.93712	-3.27	4.81	2.39	0.29439	Phosphoglycerate kinase, C-terminal (1);	0.100392	0.64402	D	0.000003	D	0.84347	0.5452	L	0.56199	1.76	0.22719	N	0.998819	B	0.14805	0.011	B	0.28553	0.091	T	0.79105	-0.1940	10	0.87932	D	0	-12.902	7.2513	0.26150	0.0:0.2024:0.0:0.7976	.	370	P07205	PGK2_HUMAN	L	370	ENSP00000305995:V370L	ENSP00000305995:V370L	V	-	1	0	PGK2	49861752	1.000000	0.71417	0.998000	0.56505	0.921000	0.55340	3.605000	0.54088	0.407000	0.25591	-0.295000	0.09555	GTT	.		0.498	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			G	49753793	C	G	49753793	3	3	126	1	0	0	0	0	1	0	0	0	11817	478	17	4	149	4	PGK2	6	49753793	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	17814951	49753793	121361274	45	11031											
MDN1	23195	broad.mit.edu	37	chr6	90466095	90466095	+	Frame_Shift_Del	DEL	T	T	-																															tgctttctaattcttctacaTaaagttctgtgaacctgtaa																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:90466095delT	ENST00000369393.3	-	20	2832	c.2717delA	c.(2716-2718)tatfs	p.Y906fs	MDN1_ENST00000428876.1_Frame_Shift_Del_p.Y906fs			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	906					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTCTTCTACATAAAGTTCTGT	0.299																																					p.Y906fs													.	MDN1-100	0			c.2717delA						.						137	136	136					6																	90466095		2203	4296	6499	SO:0001589	frameshift_variant	23195	exon20			TCTACATAAAGTT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.2717delA	6.37:g.90466095delT	ENSP00000358400:p.Tyr906fs	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	39	8	NM_014611	0	0	0	0	0	O15019|Q5T794	Frame_Shift_Del	DEL	ENST00000369393.3	37	CCDS5024.1																																																																																			.		0.299	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			-	90466095	T	-	90466095	7	5	126	1	0	1	0	1	0	0	0	0	9440	1406	49	0	14405	0	MDN1	6	90466095	Frame_Shift_Del	DEL	T	TCGA-GL-A59R-01A-11D-A26P-10	40712302	90466095	80648972	46	11032											
TRAF3IP2	10758	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	111912891	111912891	+	Frame_Shift_Del	DEL	A	A	-																															cattgattacgtttttccatAaatgaaaactgatgctctgc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:111912891delA	ENST00000340026.6	-	3	1020	c.426delT	c.(424-426)tttfs	p.F142fs	TRAF3IP2_ENST00000359831.4_Frame_Shift_Del_p.F133fs|TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000368761.5_Frame_Shift_Del_p.F133fs|TRAF3IP2_ENST00000392556.4_5'UTR			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	142	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		GTTTTTCCATAAATGAAAACT	0.512																																					p.F133fs		.											.	TRAF3IP2-228	0			c.399delT						.						51	50	50					6																	111912891		2203	4300	6503	SO:0001589	frameshift_variant	10758	exon2			.	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.426delT	6.37:g.111912891delA	ENSP00000345984:p.Phe142fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	86	32	NM_147686	0	0	0	0	0	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Frame_Shift_Del	DEL	ENST00000340026.6	37																																																																																				.		0.512	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			-	111912891	A	-	111912891	7	5	126	1	0	1	0	1	0	0	0	0	16474	359	13	0	1330	0	TRAF3IP2	6	111912891	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10	21446796	111912891	59202176	47	11033											
ABCA13	154664	bcgsc.ca	37	chr7	48685099	48685099	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcaccacacacatcacttGcccatctgagcactaaagaa	15	7	5	14	0	3	2	2	1	1	1	3	2	3	2	2	0	2	1	2	0	3	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:48685099G>T	ENST00000435803.1	+	62	15192	c.15168G>T	c.(15166-15168)ttG>ttT	p.L5056F	ABCA13_ENST00000544596.1_Missense_Mutation_p.L786F	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	5056					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CACATCACTTGCCCATCTGAG	0.393																																					p.L5056F													.	ABCA13-521	0			c.G15168T						.						59	58	58					7																	48685099		2040	4209	6249	SO:0001583	missense	154664	exon62			TCACTTGCCCATC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.15168G>T	7.37:g.48685099G>T	ENSP00000411096:p.Leu5056Phe	Somatic	72	0		WXS	Illumina HiSeq	Phase_1	76	4	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745617	0.49151	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.88201	-2.27;-2.35;-2.31	5.43	2.0	0.26442	.	1.053260	0.07599	N	0.923389	D	0.85575	0.5728	N	0.22421	0.69	0.09310	N	1	P;D;D	0.59767	0.835;0.96;0.986	P;P;P	0.53649	0.499;0.731;0.708	T	0.74112	-0.3770	10	0.45353	T	0.12	.	5.0829	0.14666	0.2265:0.1633:0.6102:0.0	.	786;2758;5056	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	F	5056;829;786	ENSP00000411096:L5056F;ENSP00000391042:L829F;ENSP00000442634:L786F	ENSP00000391042:L829F	L	+	3	2	ABCA13	48655645	0.774000	0.28592	0.024000	0.17045	0.012000	0.07955	0.619000	0.24388	0.490000	0.27771	0.655000	0.94253	TTG	.		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48685099	G	T	48685099	3	4	126	1	0	0	0	0	1	0	0	0	31	1310	46	4	15243	4	ABCA13	7	48685099	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		48685099	110453564	48	11034											
GIGYF1	64599	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	100279805	100279805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggcaggaacggatataatCgtggacatcatagggggatt	13	8	14	6	2	1	0	1	0	0	0	2	4	1	4	0	6	1	1	0	6	4	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:100279805C>T	ENST00000275732.5	-	22	4024	c.2815G>A	c.(2815-2817)Gat>Aat	p.D939N	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	939					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					CGGATATAATCGTGGACATCA	0.597																																					p.D939N		.											.	GIGYF1-136	0			c.G2815A						.						74	79	77					7																	100279805		2203	4300	6503	SO:0001583	missense	64599	exon22			TATAATCGTGGAC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"GYF domain containing 1"	612064	"PERQ amino acid rich, with GYF domain 1"	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.2815G>A	7.37:g.100279805C>T	ENSP00000275732:p.Asp939Asn	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	81	5	NM_022574	0	0	32	32	0	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	37	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	17.25	3.341351	0.60963	.	.	ENSG00000146830	ENST00000539430;ENST00000275732	D	0.84223	-1.82	5.14	5.14	0.70334	.	0.053328	0.64402	D	0.000001	T	0.78748	0.4332	L	0.59912	1.85	0.51482	D	0.999924	P	0.47409	0.895	B	0.25506	0.061	D	0.83414	0.0029	10	0.59425	D	0.04	-21.0708	16.146	0.81569	0.0:1.0:0.0:0.0	.	939	O75420	PERQ1_HUMAN	N	658;939	ENSP00000275732:D939N	ENSP00000275732:D939N	D	-	1	0	GIGYF1	100117741	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	4.780000	0.62382	2.672000	0.90937	0.555000	0.69702	GAT	.		0.597	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		T	100279805	C	T	100279805	3	4	126	1	0	0	0	0	1	0	0	0	6397	884	31	1	304	1	GIGYF1	7	100279805	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	51594706	100279805	58858858	49	11035											
FOXP2	93986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	114302186	114302186	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagaaaatgttaaaggagcaGtatggactgtggatgaagta	16	10	13	2	0	0	2	0	1	0	1	0	5	0	5	0	3	1	4	0	3	8	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:114302186G>A	ENST00000393494.2	+	14	1993	c.1714G>A	c.(1714-1716)Gta>Ata	p.V572I	FOXP2_ENST00000393491.3_Missense_Mutation_p.V387I|FOXP2_ENST00000350908.4_Missense_Mutation_p.V572I|FOXP2_ENST00000393489.3_Missense_Mutation_p.V480I|FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000403559.4_Missense_Mutation_p.V589I|FOXP2_ENST00000393498.2_Missense_Mutation_p.V551I|FOXP2_ENST00000408937.3_Missense_Mutation_p.V597I			O15409	FOXP2_HUMAN	forkhead box P2	572					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						TAAAGGAGCAGTATGGACTGT	0.393																																					p.V597I		.											.	FOXP2-295	0			c.G1789A						.						139	129	133					7																	114302186		2203	4300	6503	SO:0001583	missense	93986	exon15			GGAGCAGTATGGA	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1714G>A	7.37:g.114302186G>A	ENSP00000377132:p.Val572Ile	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	245	53	NM_148898	0	0	2	4	2	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967741	0.74131	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	D;D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71;-3.71;-3.71	5.65	5.65	0.86999	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.97692	0.9243	M	0.76838	2.35	0.80722	D	1	P;P;D;P;P	0.67145	0.92;0.92;0.996;0.92;0.902	D;D;D;D;D	0.70227	0.935;0.956;0.968;0.935;0.927	D	0.97929	1.0319	10	0.87932	D	0	.	20.0965	0.97849	0.0:0.0:1.0:0.0	.	571;589;387;572;597	B7ZLK5;B4DLD9;Q0PRL4;O15409;O15409-4	.;.;.;FOXP2_HUMAN;.	I	572;597;589;572;549;480;387	ENSP00000377132:V572I;ENSP00000386200:V597I;ENSP00000385069:V589I;ENSP00000265436:V572I;ENSP00000377129:V480I;ENSP00000377130:V387I	ENSP00000265436:V572I	V	+	1	0	FOXP2	114089422	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.813000	0.99286	2.824000	0.97209	0.655000	0.94253	GTA	.		0.393	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		A	114302186	G	A	114302186	3	1	126	1	0	0	0	0	1	0	0	0	6046	1029	36	2	1931	2	FOXP2	7	114302186	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	14022381	114302186	44836477	50	11036											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116415114	116415115	+	Missense_Mutation	DNP	GT	GT	AG																															tccaggcagtgcagcatgtaGtgattgggcccagtagcctg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:116415114_116415115GT>AG	ENST00000318493.6	+	15	3449_3450	c.3262_3263GT>AG	c.(3262-3264)GTg>AGg	p.V1088R	MET_ENST00000539704.1_5'Flank|MET_ENST00000397752.3_Missense_Mutation_p.V1070R			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V1088E(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GCAGCATGTAGTGATTGGGCCC	0.431			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1088R		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.T3209G						.																																			SO:0001583	missense	4233	exon15	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATGTAGTGATTGG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	Exception_encountered	7.37:g.116415114_116415115delinsAG	ENSP00000317272:p.Val1088Arg	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	202	125	NM_000245	0	0	0	0	0	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	DNP	ENST00000318493.6	37	CCDS47689.1																																																																																			.		0.431	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			AG	116415115	GT	AG	116415114	3	1	126	1	0	0	0	0	1	0	0	0	9510	1029	36	2	3316	2	MET	7	116415114	Missense_Mutation	DNP	GT	TCGA-GL-A59R-01A-11D-A26P-10	2112928	116415114	42723549	51	11037											
AASS	10157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	121717970	121717971	+	Missense_Mutation	DNP	CA	CA	AG																															tgaaaagccattgatgtcccCataagccacaagatcaatcg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:121717970_121717971CA>AG	ENST00000393376.1	-	22	2678_2679	c.2583_2584TG>CT	c.(2581-2586)taTGgg>taCTgg	p.G862W	AASS_ENST00000473553.1_5'UTR|AASS_ENST00000417368.2_Missense_Mutation_p.G862W			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	862	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTGATGTCCCCATAAGCCACAA	0.436																																					p.G862W		.											.	AASS-92	0			c.T2583C						.																																			SO:0001583	missense	10157	exon23			GTCCCCATAAGCC	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.2583_2584delinsAG	7.37:g.121717970_121717971delinsAG	ENSP00000377040:p.Gly862Trp	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	222	21	NM_005763	0	0	0	0	0	O95462	Missense_Mutation	DNP	ENST00000393376.1	37	CCDS5783.1																																																																																			.		0.436	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		AG	121717971	CA	AG	121717970	3	1	126	1	0	0	0	0	1	0	0	0	24	594	21	4	204	4	AASS	7	121717970	Missense_Mutation	DNP	CA	TCGA-GL-A59R-01A-11D-A26P-10	5302856	121717970	37420693	52	11038											
KIAA1549	57670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	138566237	138566237	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cttcagaggtcctggcagtgGcgctggctcatgaataatca	9	10	12	10	1	3	2	3	1	0	1	4	2	4	2	1	4	0	3	1	4	2	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:138566237G>T	ENST00000422774.1	-	11	4174	c.4126C>A	c.(4126-4128)Cca>Aca	p.P1376T	KIAA1549_ENST00000242365.4_Missense_Mutation_p.P1326T|KIAA1549_ENST00000440172.1_Missense_Mutation_p.P1376T			Q9HCM3	K1549_HUMAN	KIAA1549	1376						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCTGGCAGTGGCGCTGGCTCA	0.512			O	BRAF	pilocytic astrocytoma																																p.P1376T	NSCLC(119;1534 1718 44213 46230 50068)	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549-369	0			c.C4126A						.						115	121	119					7																	138566237		2083	4214	6297	SO:0001583	missense	57670	exon11			GCAGTGGCGCTGG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4126C>A	7.37:g.138566237G>T	ENSP00000416040:p.Pro1376Thr	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	259	71	NM_020910	0	0	4	5	1	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.101871	0.76983	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25912	1.77;1.77;1.79	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.51227	0.1662	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	T	0.38067	-0.9678	10	0.41790	T	0.15	.	18.5236	0.90963	0.0:0.0:1.0:0.0	.	1376;160;1376;160	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	T	1376;1326;1376	ENSP00000406661:P1376T;ENSP00000242365:P1326T;ENSP00000416040:P1376T	ENSP00000242365:P1326T	P	-	1	0	KIAA1549	138216777	1.000000	0.71417	0.686000	0.30086	0.849000	0.48306	7.124000	0.77185	2.716000	0.92895	0.655000	0.94253	CCA	.		0.512	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138566237	G	T	138566237	3	4	126	1	0	0	0	0	1	0	0	0	8265	1203	42	4	1766	4	KIAA1549	7	138566237	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	16848267	138566237	20572426	53	11039											
ANK1	286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	41547822	41547822	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtacttcatcgccttgcgcaGaaacgacagggaccctcccg	9	7	10	15	4	1	1	1	0	0	1	3	3	2	2	3	1	3	2	3	1	2	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:41547822G>A	ENST00000347528.4	-	33	4110	c.4027C>T	c.(4027-4029)Ctg>Ttg	p.L1343L	ANK1_ENST00000396942.1_Silent_p.L1343L|ANK1_ENST00000379758.2_Silent_p.L1343L|ANK1_ENST00000289734.7_Silent_p.L1343L|ANK1_ENST00000352337.4_Silent_p.L1343L|ANK1_ENST00000265709.8_Silent_p.L1384L|ANK1_ENST00000396945.1_Silent_p.L1343L	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1343	UPA domain. {ECO:0000250}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCCTTGCGCAGAAACGACAGG	0.597																																					p.L1384L		.											.	ANK1-716	0			c.C4150T						.						133	112	119					8																	41547822		2203	4300	6503	SO:0001819	synonymous_variant	286	exon34			TGCGCAGAAACGA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.4027C>T	8.37:g.41547822G>A		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	136	57	NM_001142446	0	0	2	4	2	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	G	8.890	0.953747	0.18431	.	.	ENSG00000029534	ENST00000520299	.	.	.	5.08	4.2	0.49525	.	.	.	.	.	T	0.55210	0.1906	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52734	-0.8536	4	.	.	.	.	6.0089	0.19562	0.1621:0.0:0.6843:0.1536	.	.	.	.	F	664	.	.	S	-	2	0	ANK1	41666979	1.000000	0.71417	0.884000	0.34674	0.838000	0.47535	1.678000	0.37586	1.352000	0.45808	0.563000	0.77884	TCT	.		0.597	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41547822	G	A	41547822	2	1	126	1	0	0	0	0	0	0	0	1	620	933	33	2		2	ANK1	8	41547822	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		41547822	104816200	54	11040											
ZBTB10	65986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	81412103	81412103	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagctatcttcaaatgagTgaagttgttcaaacttgccg	11	12	9	9	1	3	2	2	2	1	0	3	2	3	2	2	0	3	3	2	0	4	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:81412103T>C	ENST00000430430.1	+	3	2126	c.1347T>C	c.(1345-1347)agT>agC	p.S449S	ZBTB10_ENST00000426744.2_Silent_p.S449S|ZBTB10_ENST00000455036.3_Silent_p.S449S|ZBTB10_ENST00000379091.4_Silent_p.S157S	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	449					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)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			TTCAAATGAGTGAAGTTGTTC	0.373																																					p.S449S		.											.	ZBTB10-522	0			c.T1347C						.						88	81	83					8																	81412103		1826	4092	5918	SO:0001819	synonymous_variant	65986	exon2			AATGAGTGAAGTT	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1347T>C	8.37:g.81412103T>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	67	21	NM_023929	0	0	3	5	2	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Silent	SNP	ENST00000430430.1	37	CCDS47880.1																																																																																			.		0.373	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		C	81412103	T	C	81412103	2	2	126	1	0	0	0	0	0	0	0	1	17555	1693	59	3		3	ZBTB10	8	81412103	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	39864281	81412103	64951919	55	11041											
WWP1	11059	broad.mit.edu;bcgsc.ca	37	chr8	87447714	87447715	+	Frame_Shift_Ins	INS	-	-	AATTTTT																															cacaaattgcttatgaacgcINSggctttaggtggaagcttgc																								rs139712565		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:87447714_87447715insAATTTTT	ENST00000517970.1	+	15	1942_1943	c.1635_1636insAATTTTT	c.(1636-1638)ggcfs	p.G546fs	WWP1_ENST00000341922.2_Frame_Shift_Ins_p.G416fs|WWP1_ENST00000349423.2_Frame_Shift_Ins_p.G328fs|WWP1_ENST00000265428.4_Frame_Shift_Ins_p.G546fs	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	546					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						CTTATGAACGCGGCTTTAGGTG	0.302																																					p.R545fs													.	WWP1-659	0			c.1635_1636insAATTTTT						.																																			SO:0001589	frameshift_variant	11059	exon15			TGAACGCGGCTTT	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	Exception_encountered	8.37:g.87447714_87447715insAATTTTT	ENSP00000427793:p.Gly546fs	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	120	18	NM_007013	0	0	0	0	0	O00307|Q5YLC1|Q96BP4	Frame_Shift_Ins	INS	ENST00000517970.1	37	CCDS6242.1																																																																																			.		0.302	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		AATTTTT	87447715	-	AATTTTT	87447714	7	5	126	1	0	1	1	0	0	0	0	0	17448	755	27	0	1685	0	WWP1	8	87447714	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10	6035611	87447714	58916308	56	11042	116	2									
WWP1	11059	bcgsc.ca	37	chr8	87447715	87447715	+	Missense_Mutation	SNP	G	G	T																															cacaaattgcttatgaacgcGgctttaggtggaagcttgct																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:87447715G>T	ENST00000517970.1	+	15	1943	c.1636G>T	c.(1636-1638)Ggc>Tgc	p.G546C	WWP1_ENST00000341922.2_Missense_Mutation_p.G416C|WWP1_ENST00000349423.2_Missense_Mutation_p.G328C|WWP1_ENST00000265428.4_Missense_Mutation_p.G546C	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	546					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TTATGAACGCGGCTTTAGGTG	0.303																																					p.G546C													.	WWP1-659	0			c.G1636T						.						90	91	91					8																	87447715		2203	4300	6503	SO:0001583	missense	11059	exon15			GAACGCGGCTTTA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1636G>T	8.37:g.87447715G>T	ENSP00000427793:p.Gly546Cys	Somatic	171	0		WXS	Illumina HiSeq	Phase_1	116	18	NM_007013	0	0	4	4	0	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.88|14.88	2.667429|2.667429	0.47677|0.47677	.|.	.|.	ENSG00000123124|ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423|ENST00000520453	T;T;T;T|T	0.43688|0.59502	0.94;0.94;0.95;0.94|0.26	5.58|5.58	4.42|4.42	0.53409|0.53409	HECT (1);|.	0.131459|.	0.64402|.	D|.	0.000002|.	T|T	0.36193|0.36193	0.0958|0.0958	N|N	0.02011|0.02011	-0.69|-0.69	0.34971|0.34971	D|D	0.753122|0.753122	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.10450|.	0.005;0.0|.	T|T	0.55256|0.55256	-0.8169|-0.8169	10|7	0.66056|0.87932	D|D	0.02|0	.|.	11.6939|11.6939	0.51532|0.51532	0.9304:0.0:0.0696:0.0|0.9304:0.0:0.0696:0.0	.|.	328;546|.	Q9H0M0-6;Q9H0M0|.	.;WWP1_HUMAN|.	C|L	546;546;416;328|10	ENSP00000427793:G546C;ENSP00000265428:G546C;ENSP00000340564:G416C;ENSP00000342665:G328C|ENSP00000429076:R10L	ENSP00000265428:G546C|ENSP00000429076:R10L	G|R	+|+	1|2	0|0	WWP1|WWP1	87516831|87516831	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	5.936000|5.936000	0.70153|0.70153	0.931000|0.931000	0.37242|0.37242	-0.417000|-0.417000	0.06048|0.06048	GGC|CGG	.		0.303	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		T	87447715	G	T	87447715	3	4	126	1	0	0	0	0	1	0	0	0	17448	1116	39	4	1686	4	WWP1	8	87447715	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	1	87447715	58916307	57	11043	116	2									
JAK2	3717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	5078361	5078361	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaaatattctgcttatcaGagaagaagacaggaagacag	19	7	9	6	0	2	4	1	0	1	4	2	6	2	5	0	1	1	1	0	1	7	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:5078361G>T	ENST00000381652.3	+	16	2542	c.2048G>T	c.(2047-2049)aGa>aTa	p.R683I	JAK2_ENST00000544510.1_Missense_Mutation_p.R534I|JAK2_ENST00000539801.1_Missense_Mutation_p.R683I|AL161450.1_ENST00000601793.1_Intron	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	683	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.R683T(2)|p.I682_R683insTG(1)|p.R683K(1)|p.I682_D686>(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CTGCTTATCAGAGAAGAAGAC	0.363		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.R683I		.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2-75307	5	Substitution - Missense(3)|Insertion - In frame(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.G2048T						.						149	163	158					9																	5078361		2203	4300	6503	SO:0001583	missense	3717	exon16	Familial Cancer Database		TTATCAGAGAAGA		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.2048G>T	9.37:g.5078361G>T	ENSP00000371067:p.Arg683Ile	Somatic	66	1		WXS	Illumina HiSeq	Phase_I	71	25	NM_004972	0	0	4	6	2	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	32	5.158488	0.94686	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	D;D;D	0.83163	-1.69;-1.69;-1.69	5.55	5.55	0.83447	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92381	0.7582	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92930	0.6363	10	0.87932	D	0	-24.9121	19.4912	0.95050	0.0:0.0:1.0:0.0	.	683	O60674	JAK2_HUMAN	I	683;683;534	ENSP00000440387:R683I;ENSP00000371067:R683I;ENSP00000443103:R534I	ENSP00000371067:R683I	R	+	2	0	JAK2	5068361	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.371000	0.97162	2.771000	0.95319	0.561000	0.74099	AGA	.		0.363	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5078361	G	T	5078361	3	4	126	1	0	0	0	0	1	0	0	0	7959	942	33	4	2102	4	JAK2	9	5078361	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		5078361	136135070	58	11044											
DDX58	23586	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	32459420	32459420	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaaggctttgcactttctGcagagcagttttttattttc	7	17	8	9	0	1	1	0	0	1	1	2	1	1	1	1	1	3	5	1	1	2	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:32459420G>T	ENST00000379883.2	-	17	2587	c.2430C>A	c.(2428-2430)tgC>tgA	p.C810*	DDX58_ENST00000379868.1_Nonsense_Mutation_p.C607*|DDX58_ENST00000379882.1_Nonsense_Mutation_p.C765*|DDX58_ENST00000542096.1_Nonsense_Mutation_p.C739*	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	810	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TGCACTTTCTGCAGAGCAGTT	0.388																																					p.C810X		.											.	DDX58-230	0			c.C2430A						.						184	166	172					9																	32459420		2203	4300	6503	SO:0001587	stop_gained	23586	exon17			CTTTCTGCAGAGC	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"DEAD-boxes"	19102	protein-coding gene	gene with protein product	"RNA helicase RIG-I", "retinoic acid inducible gene I"	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2430C>A	9.37:g.32459420G>T	ENSP00000369213:p.Cys810*	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	47	4	NM_014314	0	0	6	9	3	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Nonsense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	G	38	7.254024	0.98168	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096	.	.	.	4.79	-0.4	0.12411	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.0038	9.3509	0.38138	0.719:0.0:0.281:0.0	.	.	.	.	X	765;810;607;739	.	ENSP00000369197:C607X	C	-	3	2	DDX58	32449420	0.540000	0.26410	0.928000	0.36995	0.005000	0.04900	0.443000	0.21644	0.069000	0.16605	0.655000	0.94253	TGC	.		0.388	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		T	32459420	G	T	32459420	4	4	126	1	0	0	0	0	0	1	0	0	4381	1311	46	4	355	4	DDX58	9	32459420	Nonsense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	27381059	32459420	108754011	59	11045											
VPS13A	23230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	79820297	79820297	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgaagccgtattggaagaaAtttatttacttatagtgcct	12	16	8	5	1	0	2	0	1	0	1	0	3	0	3	2	1	3	1	2	1	8	9			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:79820297A>G	ENST00000360280.3	+	4	516	c.256A>G	c.(256-258)Att>Gtt	p.I86V	VPS13A_ENST00000357409.5_Missense_Mutation_p.I86V|VPS13A_ENST00000376636.3_Missense_Mutation_p.I86V|VPS13A_ENST00000376634.4_Missense_Mutation_p.I86V	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	86					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATTGGAAGAAATTTATTTACT	0.229																																					p.I86V		.											.	VPS13A-161	0			c.A256G						.						38	44	42					9																	79820297		2194	4279	6473	SO:0001583	missense	23230	exon4			GAAGAAATTTATT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"chorein"	605978	"chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)"	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.256A>G	9.37:g.79820297A>G	ENSP00000353422:p.Ile86Val	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	55	34	NM_001018038	0	0	0	0	0	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	8.130	0.782854	0.16189	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36	5.62	4.48	0.54585	.	0.063343	0.64402	D	0.000008	T	0.55593	0.1930	N	0.04880	-0.145	0.80722	D	1	B;B;B;B	0.24882	0.012;0.113;0.046;0.046	B;B;B;B	0.25614	0.018;0.062;0.027;0.027	T	0.51980	-0.8636	10	0.02654	T	1	.	7.951	0.30014	0.7743:0.0:0.2257:0.0	.	86;86;86;86	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	V	86	ENSP00000365821:I86V;ENSP00000365823:I86V;ENSP00000353422:I86V;ENSP00000349985:I86V	ENSP00000349985:I86V	I	+	1	0	VPS13A	79010117	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.485000	0.60279	0.952000	0.37798	0.477000	0.44152	ATT	.		0.229	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79820297	A	G	79820297	3	3	126	1	0	0	0	0	1	0	0	0	17222	101	4	3	270	3	VPS13A	9	79820297	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	47360877	79820297	61393134	60	11046											
CTSL2	1515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	99799669	99799669	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caacccatcatctgcctgaaTtcttcattggtcttcaagga	10	13	6	12	0	6	1	3	1	3	0	6	2	6	2	2	2	2	0	2	2	3	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:99799669T>G	ENST00000259470.5	-	4	510	c.261A>C	c.(259-261)gaA>gaC	p.E87D	CTSV_ENST00000538255.1_Missense_Mutation_p.E87D|CTSV_ENST00000479932.1_5'UTR	NM_001333.3	NP_001324.2	O60911	CATL2_HUMAN	cathepsin V	87					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic cell death (GO:0048102)|catagen (GO:0042637)|cellular response to starvation (GO:0009267)|decidualization (GO:0046697)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|multicellular organismal aging (GO:0010259)|negative regulation of keratinocyte proliferation (GO:0010839)|nerve development (GO:0021675)|protein autoprocessing (GO:0016540)|regulation of actin cytoskeleton reorganization (GO:2000249)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to gonadotropin (GO:0034698)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	aminopeptidase activity (GO:0004177)|cysteine-type carboxypeptidase activity (GO:0016807)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptide binding (GO:0042277)										TCTGCCTGAATTCTTCATTGG	0.418																																					p.E87D		.											.	CTSL2-90	0			c.A261C						.						100	100	100					9																	99799669		2203	4300	6503	SO:0001583	missense	1515	exon4			CCTGAATTCTTCA	Y14734	CCDS6723.1	9q22.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000136943	ENSG00000136943		"Cathepsins"	2538	protein-coding gene	gene with protein product		603308	"cathepsin L2"	CTSL2		9563472, 10029531	Standard	NM_001201575		Approved	CTSU	uc004awt.3	O60911	OTTHUMG00000020314	ENST00000259470.5:c.261A>C	9.37:g.99799669T>G	ENSP00000259470:p.Glu87Asp	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	114	55	NM_001201575	0	0	0	0	0	O60233|Q2TB86|Q5T1U0	Missense_Mutation	SNP	ENST00000259470.5	37	CCDS6723.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.776996	0.70107	.	.	ENSG00000136943	ENST00000259470;ENST00000538255	D;D	0.94092	-3.35;-3.35	3.81	2.68	0.31781	Proteinase inhibitor I29, cathepsin propeptide (2);	0.000000	0.85682	D	0.000000	D	0.97356	0.9135	H	0.97365	3.99	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96055	0.9034	9	.	.	.	.	7.4637	0.27310	0.0:0.1067:0.0:0.8933	.	87;87	B2R717;O60911	.;CATL2_HUMAN	D	87	ENSP00000259470:E87D;ENSP00000445052:E87D	.	E	-	3	2	CTSL2	98839490	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	0.938000	0.28965	0.848000	0.35191	0.459000	0.35465	GAA	.		0.418	CTSV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053301.2	NM_001333		G	99799669	T	G	99799669	3	3	126	1	0	0	0	0	1	0	0	0	4045	1490	52	5	763	5	CTSL2	9	99799669	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	19979372	99799669	41413762	61	11047											
DHTKD1	55526	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	12162862	12162863	+	Frame_Shift_Ins	INS	-	-	T																															cacttgcaccagcatgaagaINStatcctcgccaagaccttcg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:12162862_12162863insT	ENST00000263035.4	+	17	2797_2798	c.2735_2736insT	c.(2734-2739)gatatcfs	p.I913fs		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	913					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CAGCATGAAGATATCCTCGCCA	0.5																																					p.D912fs		.											.	DHTKD1-515	0			c.2735_2736insT						.																																			SO:0001589	frameshift_variant	55526	exon17			.	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2736dupT	10.37:g.12162863_12162863dupT	ENSP00000263035:p.Ile913fs	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	90	37	NM_018706	0	0	0	0	0	Q68CU5|Q9BUM8|Q9HCE2	Frame_Shift_Ins	INS	ENST00000263035.4	37	CCDS7087.1																																																																																			.		0.5	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		T	12162863	-	T	12162862	7	5	126	1	0	1	1	0	0	0	0	0	4511	333	12	0	2801	0	DHTKD1	10	12162862	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10		12162862	123371885	62	11048											
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	64968540	64968540	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagaccgtaatggttccatAaaagcttttctttctaattc	12	15	5	9	1	2	1	0	0	2	1	4	1	3	1	2	1	1	3	2	1	4	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:64968540A>G	ENST00000399262.2	-	10	3107	c.2889T>C	c.(2887-2889)ttT>ttC	p.F963F	JMJD1C_ENST00000402544.1_Silent_p.F744F|JMJD1C_ENST00000542921.1_Silent_p.F781F|JMJD1C_ENST00000399251.1_Silent_p.F744F	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	963					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					ATGGTTCCATAAAAGCTTTTC	0.348																																					p.F963F		.											.	JMJD1C-275	0			c.T2889C						.						49	45	46					10																	64968540		1815	4081	5896	SO:0001819	synonymous_variant	221037	exon10			TTCCATAAAAGCT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.2889T>C	10.37:g.64968540A>G		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	28	11	NM_032776	0	0	1	2	1	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	37	CCDS41532.1																																																																																			.		0.348	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		G	64968540	A	G	64968540	2	3	126	1	0	0	0	0	0	0	0	1	7971	359	13	3		3	JMJD1C	10	64968540	Silent	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	52805678	64968540	70566207	63	11049											
P4HA1	5033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74810906	74810906	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttctttggtgtagttttctGatcagattggtcatctgaag	7	19	10	5	0	5	3	2	2	3	1	5	3	5	3	0	2	0	2	0	2	2	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:74810906G>A	ENST00000307116.2	-	7	921	c.805C>T	c.(805-807)Cag>Tag	p.Q269*	P4HA1_ENST00000412021.2_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000394890.2_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000440381.1_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000373008.2_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000263556.3_Nonsense_Mutation_p.Q269*			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	269					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GTAGTTTTCTGATCAGATTGG	0.388																																					p.Q269X	Colon(147;367 2405 2662 52127)	.											.	P4HA1-69	0			c.C805T						.						217	213	214					10																	74810906		2203	4300	6503	SO:0001587	stop_gained	5033	exon7			TTTTCTGATCAGA		CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.805C>T	10.37:g.74810906G>A	ENSP00000307318:p.Gln269*	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	65	34	NM_001142596	0	0	14	14	0	C9JL12|Q15082|Q15083|Q5VSQ5	Nonsense_Mutation	SNP	ENST00000307116.2	37		.	.	.	.	.	.	.	.	.	.	G	38	6.748289	0.97809	.	.	ENSG00000122884	ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381	.	.	.	5.67	4.75	0.60458	.	0.628969	0.17058	N	0.188667	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-9.1782	14.0861	0.64957	0.0:0.0:0.6736:0.3264	.	.	.	.	X	269	.	ENSP00000263556:Q269X	Q	-	1	0	P4HA1	74480912	0.668000	0.27493	1.000000	0.80357	0.995000	0.86356	0.893000	0.28336	1.363000	0.46019	0.557000	0.71058	CAG	.		0.388	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		A	74810906	G	A	74810906	4	1	126	1	0	0	0	0	0	1	0	0	11382	1299	45	2	910	2	P4HA1	10	74810906	Nonsense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	9842366	74810906	60723841	64	11050											
FAM35A	54537	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	88911776	88911776	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcgaacgcagtagataagtCaaggtctgaagcagcagtta	14	8	11	8	2	2	2	1	1	1	1	3	3	2	2	0	1	3	5	0	1	6	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:88911776C>G	ENST00000298784.1	+	3	779	c.665C>G	c.(664-666)tCa>tGa	p.S222*	RN7SL733P_ENST00000582253.1_RNA|FAM35A_ENST00000298786.4_Nonsense_Mutation_p.S222*	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	222										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						GTAGATAAGTCAAGGTCTGAA	0.398																																					p.S222X	Ovarian(175;703 2004 25460 32514 43441)	.											.	FAM35A-94	0			c.C665G						.						34	35	35					10																	88911776		2197	4290	6487	SO:0001587	stop_gained	54537	exon3			ATAAGTCAAGGTC	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.665C>G	10.37:g.88911776C>G	ENSP00000298784:p.Ser222*	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	113	40	NM_019054	0	0	17	23	6	O95885|Q9H991	Nonsense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	c	26.2	4.712906	0.89112	.	.	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	.	.	.	4.09	4.09	0.47781	.	0.374206	0.21967	N	0.066511	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-1.042	14.7247	0.69336	0.0:1.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000298784:S222X	S	+	2	0	FAM35A	88901756	0.031000	0.19500	0.008000	0.14137	0.139000	0.21198	3.315000	0.51951	2.134000	0.65973	0.537000	0.68136	TCA	.		0.398	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054		G	88911776	C	G	88911776	4	3	126	1	0	0	0	0	0	1	0	0	5572	838	29	4	667	4	FAM35A	10	88911776	Nonsense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	14100870	88911776	46622971	65	11051											
TDRD1	56165	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	115947630	115947635	+	In_Frame_Del	DEL	AATTTG	AATTTG	-																															ttaatgtgatgtcaagaaatAatttggaagcacctccttgt																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	AATTTG	AATTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:115947630_115947635delAATTTG	ENST00000369280.1	+	2	500_505	c.40_45delAATTTG	c.(40-45)aatttgdel	p.NL14del	TDRD1_ENST00000369281.2_In_Frame_Del_p.NL14del|TDRD1_ENST00000369282.1_In_Frame_Del_p.NL14del|TDRD1_ENST00000422662.1_5'UTR|TDRD1_ENST00000251864.2_In_Frame_Del_p.NL14del			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	14					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		GTCAAGAAATAATTTGGAAGCACCTC	0.345																																					p.14_15del		.											.	TDRD1-90	0			c.40_45del						.																																			SO:0001651	inframe_deletion	56165	exon2			.	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.40_45delAATTTG	10.37:g.115947630_115947635delAATTTG	ENSP00000358286:p.Asn14_Leu15del	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_198795	0	0	0	0	0	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	In_Frame_Del	DEL	ENST00000369280.1	37																																																																																				.		0.345	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			-	115947635	AATTTG	-	115947630	7	5	126	1	0	1	0	1	0	0	0	0	15762	362	13	0	42	0	TDRD1	10	115947630	In_Frame_Del	DEL	AATTTG	TCGA-GL-A59R-01A-11D-A26P-10	27035854	115947630	19587117	66	11052											
ACCSL	390110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	44079985	44079985	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacaaccgcagctctggcctCtatgtctggatcaacttgaa	10	10	8	13	1	4	1	1	1	3	0	4	2	4	2	2	2	3	2	2	2	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:44079985C>T	ENST00000378832.1	+	12	1502	c.1446C>T	c.(1444-1446)ctC>ctT	p.L482L		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	482					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						GCTCTGGCCTCTATGTCTGGA	0.532																																					p.L482L		.											.	ACCSL-95	0			c.C1446T						.						134	136	135					11																	44079985		1985	4152	6137	SO:0001819	synonymous_variant	390110	exon12			TGGCCTCTATGTC		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.1446C>T	11.37:g.44079985C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	128	60	NM_001031854	0	0	0	0	0		Silent	SNP	ENST00000378832.1	37	CCDS41636.1																																																																																			.		0.532	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		T	44079985	C	T	44079985	2	4	126	1	0	0	0	0	0	0	0	1	134	900	32	2		2	ACCSL	11	44079985	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		44079985	90926531	67	11053											
CNTF	1270	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	58391968	58391968	+	Frame_Shift_Del	DEL	T	T	-																															atcccagcacgtgggagccaTtatattgctaacaacaagaa																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:58391968delT	ENST00000361987.4	+	2	656	c.576delT	c.(574-576)catfs	p.H192fs	ZFP91-CNTF_ENST00000389919.4_3'UTR	NM_000614.3	NP_000605.1	P26441	CNTF_HUMAN	ciliary neurotrophic factor	192					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|growth (GO:0040007)|muscle organ morphogenesis (GO:0048644)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of photoreceptor cell differentiation (GO:0046533)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of retinal cell programmed cell death (GO:0046668)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			NS(1)|breast(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)	10		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				GTGGGAGCCATTATATTGCTA	0.468																																					p.H192fs		.											.	CNTF-91	0			c.576delT						.						84	88	86					11																	58391968		2201	4295	6496	SO:0001589	frameshift_variant	1270	exon2			.	BC068030	CCDS31554.1	11q12	2011-07-21			ENSG00000242689	ENSG00000242689			2169	protein-coding gene	gene with protein product		118945				1840538, 1714745	Standard	NM_000614		Approved	HCNTF	uc001nna.4	P26441	OTTHUMG00000137476	ENST00000361987.4:c.576delT	11.37:g.58391968delT	ENSP00000355370:p.His192fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	68	28	NM_000614	0	0	0	0	0	B2RAB2	Frame_Shift_Del	DEL	ENST00000361987.4	37	CCDS31554.1																																																																																			.		0.468	CNTF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268673.1	NM_000614		-	58391968	T	-	58391968	7	5	126	1	0	1	0	1	0	0	0	0	3643	1490	52	0	582	0	CNTF	11	58391968	Frame_Shift_Del	DEL	T	TCGA-GL-A59R-01A-11D-A26P-10	14311983	58391968	76614548	68	11054											
RELA	5970	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	65425828	65425840	+	Frame_Shift_Del	DEL	GGAGACACGCACA	GGAGACACGCACA	-																															gaaggccgccgcagctgcatGgagacacgcacaggagcctg																								rs375033007		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	GGAGACACGCACA	GGAGACACGCACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:65425828_65425840delGGAGACACGCACA	ENST00000406246.3	-	8	1056_1068	c.795_807delTGTGCGTGTCTCC	c.(793-807)cctgtgcgtgtctccfs	p.PVRVS265fs	RELA_ENST00000308639.9_Frame_Shift_Del_p.PVRVS262fs|RELA_ENST00000525693.1_Frame_Shift_Del_p.PVRVS265fs	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	265	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						GCAGCTGCATGGAGACACGCACAGGAGCCTGCA	0.634																																					p.265_269del		.											.	RELA-872	0			c.795_807del						.																																			SO:0001589	frameshift_variant	5970	exon8			.	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.795_807delTGTGCGTGTCTCC	11.37:g.65425828_65425840delGGAGACACGCACA	ENSP00000384273:p.Pro265fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	78	18	NM_021975	0	0	0	0	0	Q6GTV1|Q6SLK1	Frame_Shift_Del	DEL	ENST00000406246.3	37	CCDS31609.1																																																																																			.		0.634	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		-	65425840	GGAGACACGCACA	-	65425828	7	5	126	1	0	1	0	1	0	0	0	0	13248	1335	47	0	864	0	RELA	11	65425828	Frame_Shift_Del	DEL	GGAGACACGCACA	TCGA-GL-A59R-01A-11D-A26P-10	7033860	65425828	69580688	69	11055											
TSKU	25987	broad.mit.edu;bcgsc.ca	37	chr11	76507649	76507654	+	In_Frame_Del	DEL	GCTCCA	GCTCCA	-																															cacctacccccggaggcctgGctccagccccaaggtggccc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	GCTCCA	GCTCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:76507649_76507654delGCTCCA	ENST00000527881.1	+	2	2015_2020	c.989_994delGCTCCA	c.(988-996)ggctccagc>ggc	p.SS331del	TSKU_ENST00000333090.4_In_Frame_Del_p.SS331del			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	331					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					CGGAGGCCTGGCTCCAGCCCCAAGGT	0.689																																					p.330_332del													.	TSKU-90	0			c.989_994del						.																																			SO:0001651	inframe_deletion	25987	exon2			GGCCTGGCTCCAG	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"leucine rich repeat containing 54", "tsukushin", "tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.989_994delGCTCCA	11.37:g.76507649_76507654delGCTCCA	ENSP00000434847:p.Ser331_Ser332del	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_015516	0	0	0	0	0	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	In_Frame_Del	DEL	ENST00000527881.1	37	CCDS8246.1																																																																																			.		0.689	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516		-	76507654	GCTCCA	-	76507649	7	5	126	1	0	1	0	1	0	0	0	0	16660	1203	42	0	991	0	TSKU	11	76507649	In_Frame_Del	DEL	GCTCCA	TCGA-GL-A59R-01A-11D-A26P-10	11081821	76507649	58498867	70	11056											
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	108381026	108381026	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttccctgaggctggtgaaTgtgatgggtgatggggctcc	5	11	17	8	0	0	4	0	4	0	0	2	4	2	4	2	5	0	3	2	5	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:108381026T>G	ENST00000265843.4	-	6	5318	c.5208A>C	c.(5206-5208)acA>acC	p.T1736T	EXPH5_ENST00000443411.1_Silent_p.T1548T|EXPH5_ENST00000428840.1_Silent_p.T1660T|EXPH5_ENST00000525344.1_Silent_p.T1729T	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1736					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GGCTGGTGAATGTGATGGGTG	0.468																																					p.T1736T		.											.	EXPH5-95	0			c.A5208C						.						85	91	89					11																	108381026		2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			GGTGAATGTGATG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5208A>C	11.37:g.108381026T>G		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	108	41	NM_015065	0	0	0	0	0	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			.		0.468	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		G	108381026	T	G	108381026	2	3	126	1	0	0	0	0	0	0	0	1	5335	1451	51	5		5	EXPH5	11	108381026	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	31873377	108381026	26625490	71	11057											
MCAM	4162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	119182661	119182661	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccagcacctggcctgtcTgggatgagagatgggtcaga	8	10	14	9	0	2	3	1	1	1	2	3	5	3	4	3	3	1	1	3	3	0	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:119182661T>A	ENST00000264036.4	-	10	1158		c.e10-2		MCAM_ENST00000530144.2_5'Flank|MCAM_ENST00000392814.1_Splice_Site	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule						anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CTGGCCTGTCTGGGATGAGAG	0.632																																					.		.											.	MCAM-137	0			c.1144-2A>T						.						90	93	92					11																	119182661		2199	4295	6494	SO:0001630	splice_region_variant	4162	exon11			CCTGTCTGGGATG	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.1144-2A>T	11.37:g.119182661T>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	29	15	NM_006500	0	0	0	0	0	O95812|Q59E86|Q6PHR3|Q6ZTR2	Splice_Site	SNP	ENST00000264036.4	37	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.776310	0.49786	.	.	ENSG00000076706	ENST00000264036;ENST00000392814	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4953	0.33125	0.0:0.0:0.1965:0.8035	.	.	.	.	.	-1	.	.	.	-	.	.	MCAM	118687871	1.000000	0.71417	0.979000	0.43373	0.886000	0.51366	4.238000	0.58688	1.973000	0.57446	0.379000	0.24179	.	.		0.632	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2		Intron	A	119182661	T	A	119182661	5	1	126	1	0	0	0	0	0	0	1	0	9393	1594	55	5	826	5	MCAM	11	119182661	Splice_Site	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	10801635	119182661	15823855	72	11058											
SLC2A14	144195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7984344	7984344	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccgtcaaagttttattgAtaaattcctttatgatctgc	10	18	6	7	1	2	2	1	2	1	0	4	2	4	2	2	0	1	1	2	0	5	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:7984344A>T	ENST00000543909.1	-	9	956	c.197T>A	c.(196-198)aTc>aAc	p.I66N	SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000542546.1_Intron|SLC2A14_ENST00000396589.2_Missense_Mutation_p.I66N|SLC2A14_ENST00000431042.2_Missense_Mutation_p.I43N|SLC2A14_ENST00000340749.5_Missense_Mutation_p.I43N|SLC2A14_ENST00000535295.1_Intron|SLC2A14_ENST00000539924.1_Missense_Mutation_p.I81N			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	66					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		AGTTTTATTGATAAATTCCTT	0.458											OREG0021654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I66N		.											.	SLC2A14-91	0			c.T197A						.						89	86	87					12																	7984344		2203	4300	6503	SO:0001583	missense	144195	exon5			TTATTGATAAATT	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"Solute carriers"	18301	protein-coding gene	gene with protein product		611039	"solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.197T>A	12.37:g.7984344A>T	ENSP00000440480:p.Ile66Asn	Somatic	129	0	645	WXS	Illumina HiSeq	Phase_I	191	61	NM_153449	0	0	0	0	0	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337198	0.41398	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000396589;ENST00000539924;ENST00000546234;ENST00000542782;ENST00000535344;ENST00000537557;ENST00000535266;ENST00000542916;ENST00000535383	T;T;T;T;T;T;T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-0.83;-0.83	3.6	3.6	0.41247	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.322524	0.33496	N	0.004853	D	0.84325	0.5447	M	0.70595	2.14	0.31524	N	0.662021	P;P;B	0.45428	0.858;0.81;0.093	P;P;B	0.57009	0.811;0.575;0.102	D	0.84462	0.0594	10	0.72032	D	0.01	.	6.4066	0.21668	0.781:0.0:0.0:0.219	.	81;43;66	B7ZAC3;Q8TDB8-2;Q8TDB8	.;.;GTR14_HUMAN	N	43;66;43;66;81;43;43;43;66;66;43;43	ENSP00000340450:I43N;ENSP00000440480:I66N;ENSP00000407287:I43N;ENSP00000379834:I66N;ENSP00000445929:I81N;ENSP00000440043:I43N;ENSP00000438312:I43N;ENSP00000443217:I43N;ENSP00000440044:I66N;ENSP00000437653:I66N;ENSP00000442402:I43N;ENSP00000443076:I43N	ENSP00000340450:I43N	I	-	2	0	SLC2A14	7875611	0.995000	0.38212	0.015000	0.15790	0.012000	0.07955	1.901000	0.39838	1.391000	0.46566	0.477000	0.44152	ATC	.		0.458	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		T	7984344	A	T	7984344	3	4	126	1	0	0	0	0	1	0	0	0	14575	333	12	5	1397	5	SLC2A14	12	7984344	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10		7984344	125867551	73	11059											
BCL2L14	79370	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	12247627	12247628	+	Frame_Shift_Del	DEL	CT	CT	-																															gataaggctttgatgggccaCttccaggatgggctgtccta																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:12247627_12247628delCT	ENST00000308721.5	+	5	914_915	c.708_709delCT	c.(706-711)cacttcfs	p.F237fs	BCL2L14_ENST00000586576.1_Frame_Shift_Del_p.F270fs|BCL2L14_ENST00000396369.1_Intron|BCL2L14_ENST00000266434.4_3'UTR|BCL2L14_ENST00000396367.1_Frame_Shift_Del_p.F237fs|BCL2L14_ENST00000589718.1_Frame_Shift_Del_p.F237fs	NM_138723.1	NP_620049.1	Q9BZR8	B2L14_HUMAN	BCL2-like 14 (apoptosis facilitator)	237					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular organelle (GO:0043229)|membrane (GO:0016020)	protein kinase binding (GO:0019901)			large_intestine(1)|lung(2)|skin(3)	6		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		TGATGGGCCACTTCCAGGATGG	0.49																																					p.236_237del		.											.	BCL2L14-227	0			c.708_709del						.																																			SO:0001589	frameshift_variant	79370	exon5			.	AF281254	CCDS8645.1, CCDS8646.1	12p13-p12	2014-03-07			ENSG00000121380	ENSG00000121380			16657	protein-coding gene	gene with protein product		606126				11054413	Standard	NM_030766		Approved	BCLG, BCL-G	uc001rac.3	Q9BZR8	OTTHUMG00000159528	ENST00000308721.5:c.708_709delCT	12.37:g.12247627_12247628delCT	ENSP00000309132:p.Phe237fs	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	276	71	NM_138723	0	0	0	0	0	A8KAD0|Q96QR5|Q9BZR7	Frame_Shift_Del	DEL	ENST00000308721.5	37	CCDS8645.1																																																																																			.		0.49	BCL2L14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355994.3	NM_030766		-	12247628	CT	-	12247627	7	5	126	1	0	1	0	1	0	0	0	0	1373	564	20	0	807	0	BCL2L14	12	12247627	Frame_Shift_Del	DEL	CT	TCGA-GL-A59R-01A-11D-A26P-10	4263283	12247627	121604268	74	11060											
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	12274330	12274330	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtggtggggggtgcaaaGtgccggtagctatatggcct	6	10	19	6	1	0	0	0	0	0	0	0	0	0	0	2	7	3	3	2	7	4	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:12274330G>C	ENST00000261349.4	-	23	4648	c.4572C>G	c.(4570-4572)caC>caG	p.H1524Q	BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.H1479Q	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1524					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				GGGGTGCAAAGTGCCGGTAGC	0.463																																					p.H1524Q		.											.	LRP6-661	0			c.C4572G						.						99	103	101					12																	12274330		2203	4300	6503	SO:0001583	missense	4040	exon23			TGCAAAGTGCCGG	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"Low density lipoprotein receptors"	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4572C>G	12.37:g.12274330G>C	ENSP00000261349:p.His1524Gln	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	166	37	NM_002336	0	0	1	2	1	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.088550	0.36855	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.92911	-3.07;-3.13	5.86	4.96	0.65561	.	0.000000	0.64402	D	0.000004	D	0.89663	0.6780	L	0.43152	1.355	0.54753	D	0.999989	D;P	0.54207	0.965;0.607	P;B	0.47981	0.563;0.177	D	0.88842	0.3313	10	0.52906	T	0.07	.	9.8375	0.40977	0.2372:0.0:0.7628:0.0	.	1479;1524	F5H7J9;O75581	.;LRP6_HUMAN	Q	1524;1479	ENSP00000261349:H1524Q;ENSP00000442472:H1479Q	ENSP00000261349:H1524Q	H	-	3	2	LRP6	12165597	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.704000	0.37857	2.780000	0.95670	0.643000	0.83706	CAC	.		0.463	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12274330	G	C	12274330	3	2	126	1	0	0	0	0	1	0	0	0	8987	1020	36	4	273	4	LRP6	12	12274330	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	26703	12274330	121577565	75	11061											
ARID2	196528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46244883	46244883	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgccatgtcgtcgtcctctAcccctcaatcacagggacca	8	9	7	17	2	3	0	2	0	1	0	6	1	4	1	5	1	2	0	5	1	2	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:46244883A>T	ENST00000334344.6	+	15	3149	c.2977A>T	c.(2977-2979)Acc>Tcc	p.T993S	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Missense_Mutation_p.T603S|ARID2_ENST00000422737.1_Missense_Mutation_p.T844S|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	993	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GTCGTCCTCTACCCCTCAATC	0.498			"N, S, F"		hepatocellular carcinoma																																p.T993S		.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2-100	0			c.A2977T						.						246	213	224					12																	46244883		2203	4300	6503	SO:0001583	missense	196528	exon15			TCCTCTACCCCTC		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2977A>T	12.37:g.46244883A>T	ENSP00000335044:p.Thr993Ser	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	393	114	NM_152641	0	0	2	2	0	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	5.023	0.189957	0.09547	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.33438	1.41	5.66	2.06	0.26882	.	0.394387	0.30593	N	0.009288	T	0.17746	0.0426	N	0.19112	0.55	0.80722	D	1	B;B;B	0.26147	0.143;0.143;0.104	B;B;B	0.30572	0.117;0.075;0.039	T	0.06041	-1.0849	10	0.31617	T	0.26	-1.4259	6.2264	0.20710	0.6727:0.124:0.2032:0.0	.	993;603;993	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	S	993;110;110;844;603	ENSP00000335044:T993S	ENSP00000335044:T993S	T	+	1	0	ARID2	44531150	0.976000	0.34144	0.996000	0.52242	0.380000	0.30137	1.302000	0.33459	0.425000	0.26087	0.379000	0.24179	ACC	.		0.498	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46244883	A	T	46244883	3	4	126	1	0	0	0	0	1	0	0	0	915	391	14	5	3035	5	ARID2	12	46244883	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	33970553	46244883	87607012	76	11062											
KRT6B	3854	broad.mit.edu;bcgsc.ca	37	chr12	52845508	52845508	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggcccccaaagccaccagCaaggccggctccaccaccca	11	1	9	20	1	0	0	0	0	0	0	1	0	1	0	8	3	2	2	8	3	2	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:52845508C>G	ENST00000252252.3	-	1	402	c.355G>C	c.(355-357)Gct>Cct	p.A119P		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	119	Head.			AGG -> LC (in Ref. 2; AAA59466). {ECO:0000305}.	ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		AAGCCACCAGCAAGGCCGGCT	0.627																																					p.A119P													.	KRT6B-92	0			c.G355C						.						18	29	25					12																	52845508		2173	4289	6462	SO:0001583	missense	3854	exon1			CACCAGCAAGGCC	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"-", "Intermediate filaments type II, keratins (basic)"	6444	protein-coding gene	gene with protein product		148042	"keratin-like 1 (a type II keratin sequence)"	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.355G>C	12.37:g.52845508C>G	ENSP00000252252:p.Ala119Pro	Somatic	759	1		WXS	Illumina HiSeq	Phase_I	1117	165	NM_005555	0	0	0	0	0	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729920	0.48833	.	.	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.91740	-2.9	3.19	3.19	0.36642	.	0.434509	0.19735	N	0.107247	D	0.86506	0.5949	L	0.39898	1.24	0.27998	N	0.935415	B	0.27882	0.192	B	0.20384	0.029	T	0.78001	-0.2375	10	0.29301	T	0.29	.	12.7094	0.57082	0.0:1.0:0.0:0.0	.	119	P04259	K2C6B_HUMAN	P	119	ENSP00000252252:A119P	ENSP00000252252:A119P	A	-	1	0	KRT6B	51131775	0.651000	0.27340	0.984000	0.44739	0.868000	0.49771	5.122000	0.64697	2.107000	0.64212	0.298000	0.19748	GCT	.		0.627	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555		G	52845508	C	G	52845508	3	3	126	1	0	0	0	0	1	0	0	0	8502	710	25	4	1375	4	KRT6B	12	52845508	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	6600625	52845508	81006387	77	11063											
SRGAP1	57522	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64521384	64521384	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcagggatgatacgttttCagacactctgagccaaaaag	13	10	9	9	1	3	3	2	2	1	1	3	4	3	4	1	1	2	1	1	1	3	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:64521384C>G	ENST00000355086.3	+	20	2944	c.2420C>G	c.(2419-2421)tCa>tGa	p.S807*	SRGAP1_ENST00000357825.3_Nonsense_Mutation_p.S784*|SRGAP1_ENST00000543397.1_Nonsense_Mutation_p.S744*	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	807					axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		GATACGTTTTCAGACACTCTG	0.438																																					p.S807X													.	SRGAP1-653	0			c.C2420G						.						69	60	63					12																	64521384		2203	4300	6503	SO:0001587	stop_gained	57522	exon20			CGTTTTCAGACAC	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"Rho GTPase activating proteins"	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2420C>G	12.37:g.64521384C>G	ENSP00000347198:p.Ser807*	Somatic	220	2		WXS	Illumina HiSeq	Phase_I	243	149	NM_020762	0	0	0	0	0	Q9H8A3|Q9P2P2	Nonsense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	51	18.575766	0.99907	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	.	.	.	5.46	5.46	0.80206	.	0.000000	0.30890	U	0.008668	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6651	0.95890	0.0:1.0:0.0:0.0	.	.	.	.	X	807;784;744	.	.	S	+	2	0	SRGAP1	62807651	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	7.525000	0.81892	2.722000	0.93159	0.650000	0.86243	TCA	.		0.438	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			G	64521384	C	G	64521384	4	3	126	1	0	0	0	0	0	1	0	0	15177	838	29	4	2498	4	SRGAP1	12	64521384	Nonsense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	11675876	64521384	69330511	78	11064											
NAV3	89795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	78591182	78591182	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aattgtaaatacaacaaatgGtatgcttatcaaatattctg	17	14	5	5	0	2	0	1	0	1	0	2	0	2	0	0	1	3	3	0	1	10	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:78591182G>C	ENST00000397909.2	+	35	6619		c.e35+1		NAV3_ENST00000266692.7_Splice_Site|NAV3_ENST00000541270.1_5'Flank|NAV3_ENST00000228327.6_Splice_Site|NAV3_ENST00000536525.2_Splice_Site			Q8IVL0	NAV3_HUMAN	neuron navigator 3							membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						ACAACAAATGGTATGCTTATC	0.284										HNSCC(70;0.22)																											.		.											.	NAV3-279	0			c.6380+1G>C						.						83	73	76					12																	78591182		1798	4068	5866	SO:0001630	splice_region_variant	89795	exon34			CAAATGGTATGCT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 1", "steerin 3"	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6446+1G>C	12.37:g.78591182G>C		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	27	13	NM_014903	0	0	0	0	0	Q8NFW7|Q9Y2E7	Splice_Site	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	25.5	4.648927	0.87958	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000552895;ENST00000550788	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8339	0.96646	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NAV3	77115313	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.813000	0.99286	2.751000	0.94390	0.655000	0.94253	.	.		0.284	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	Intron	C	78591182	G	C	78591182	5	2	126	1	0	0	0	0	0	0	1	0	10210	1275	44	4	6515	4	NAV3	12	78591182	Splice_Site	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	14069798	78591182	55260713	79	11065											
UBE2N	7334	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	93804921	93804921	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttaggggctgccattgggTattcttctggaaggaatagt	8	14	13	6	0	2	0	0	0	2	0	2	2	2	2	1	5	1	2	1	5	5	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:93804921T>A	ENST00000318066.2	-	2	562	c.185A>T	c.(184-186)tAc>tTc	p.Y62F	UBE2N_ENST00000550657.1_Missense_Mutation_p.Y62F|UBE2N_ENST00000549833.1_5'UTR|UBE2N_ENST00000552442.1_Missense_Mutation_p.Y62F	NM_003348.3	NP_003339.1	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	62					cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						TGCCATTGGGTATTCTTCTGG	0.413								Direct reversal of damage;Rad6 pathway																													p.Y62F	Pancreas(197;738 2228 30225 32034 33454)												.	UBE2N-659	0			c.A185T						.						93	93	93					12																	93804921		2203	4300	6503	SO:0001583	missense	7334	exon2			ATTGGGTATTCTT	D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889		"Ubiquitin-conjugating enzymes E2"	12492	protein-coding gene	gene with protein product		603679	"ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13)", "ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)"			8902611	Standard	NM_003348		Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000318066.2:c.185A>T	12.37:g.93804921T>A	ENSP00000316176:p.Tyr62Phe	Somatic	309	1		WXS	Illumina HiSeq	Phase_I	346	72	NM_003348	0	0	57	77	20	Q16781|Q53Y81	Missense_Mutation	SNP	ENST00000318066.2	37	CCDS31875.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.722514	0.89298	.	.	ENSG00000177889	ENST00000318066;ENST00000550657;ENST00000552442	D;D;D	0.85861	-2.04;-2.04;-2.04	5.94	5.94	0.96194	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.41194	U	0.000927	D	0.92567	0.7639	M	0.80028	2.48	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.93404	0.6763	10	0.87932	D	0	.	16.4075	0.83691	0.0:0.0:0.0:1.0	.	62	P61088	UBE2N_HUMAN	F	62	ENSP00000316176:Y62F;ENSP00000449352:Y62F;ENSP00000448352:Y62F	ENSP00000316176:Y62F	Y	-	2	0	UBE2N	92329052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.153000	0.71819	2.275000	0.75901	0.528000	0.53228	TAC	.		0.413	UBE2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407710.1	NM_003348		A	93804921	T	A	93804921	3	1	126	1	0	0	0	0	1	0	0	0	16899	1638	57	5	285	5	UBE2N	12	93804921	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	15213739	93804921	40046974	80	11066											
ATXN2	6311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	111926345	111926345	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgctgggctggaagtctgAaccccttgggaagtgacctc	8	9	13	11	0	1	2	0	2	1	0	2	4	1	4	3	3	2	2	3	3	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:111926345A>G	ENST00000377617.3	-	15	2816	c.2655T>C	c.(2653-2655)gtT>gtC	p.V885V	ATXN2_ENST00000550104.1_Silent_p.V885V|ATXN2_ENST00000608853.1_Silent_p.V725V|ATXN2_ENST00000389153.4_Silent_p.V620V|ATXN2_ENST00000535949.1_Silent_p.V596V|ATXN2_ENST00000542287.2_Silent_p.V620V|AC002395.1_ENST00000581907.1_RNA	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	885					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TGGAAGTCTGAACCCCTTGGG	0.498																																					p.V885V		.											.	ATXN2-136	0			c.T2655C						.						122	117	119					12																	111926345		2203	4300	6503	SO:0001819	synonymous_variant	6311	exon15			AGTCTGAACCCCT	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"Ataxins"	10555	protein-coding gene	gene with protein product	"trinucleotide repeat containing 13"	601517	"spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.2655T>C	12.37:g.111926345A>G		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	154	85	NM_002973	0	0	6	27	21	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	37	CCDS31902.1																																																																																			.		0.498	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		G	111926345	A	G	111926345	2	3	126	1	0	0	0	0	0	0	0	1	1212	233	9	3		3	ATXN2	12	111926345	Silent	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	18121424	111926345	21925550	81	11067											
CIT	11113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120158284	120158284	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaaacactttgactcaccTttttctttttagcaggttgg	8	18	6	9	0	3	1	2	1	1	0	3	1	3	1	1	2	2	2	1	2	2	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:120158284T>C	ENST00000261833.7	-	29	3765	c.3713A>G	c.(3712-3714)aAg>aGg	p.K1238R	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Splice_Site_p.K1280R	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1238	Interaction with Rho/Rac.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TTGACTCACCTTTTTCTTTTT	0.373																																					p.K1280R		.											.	CIT-399	0			c.A3839G						.						136	130	132					12																	120158284		2203	4299	6502	SO:0001630	splice_region_variant	11113	exon30			CTCACCTTTTTCT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"serine/threonine kinase 21"	605629	"citron (rho-interacting, serine/threonine kinase 21)"			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3714+1A>G	12.37:g.120158284T>C		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	163	88	NM_001206999	0	0	0	0	0	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.70|18.70	3.680696|3.680696	0.68042|0.68042	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392521;ENST00000261833|ENST00000392520	T;T|.	0.69806|.	-0.42;-0.43|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72070|0.72070	0.3415|0.3415	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	B;D;P|.	0.69078|.	0.355;0.997;0.734|.	B;D;B|.	0.73380|.	0.1;0.98;0.203|.	T|T	0.70880|0.70880	-0.4752|-0.4752	10|5	0.24483|.	T|.	0.36|.	.|.	16.1193|16.1193	0.81336|0.81336	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1280;1238;771|.	Q2M5E1;O14578;O14578-3|.	.;CTRO_HUMAN;.|.	R|G	1280;1238|866	ENSP00000376306:K1280R;ENSP00000261833:K1238R|.	ENSP00000261833:K1238R|.	K|R	-|-	2|1	0|2	CIT|CIT	118642667|118642667	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	2.204000|2.204000	0.70986|0.70986	0.528000|0.528000	0.53228|0.53228	AAG|AGG	.		0.373	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	Missense_Mutation	C	120158284	T	C	120158284	5	2	126	1	0	0	0	0	0	0	1	0	3444	1623	56	3	2446	3	CIT	12	120158284	Splice_Site	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	8231939	120158284	13693611	82	11068											
KIAA0564	23078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	42440068	42440068	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attaaacatatatctttaacCatgtgagactgcatcatttc	14	15	4	8	0	2	1	1	1	1	1	3	2	2	1	1	0	3	1	1	0	5	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr13:42440068C>T	ENST00000379310.3	-	11	1385	c.1317G>A	c.(1315-1317)atG>atA	p.M439I	VWA8_ENST00000281496.6_Missense_Mutation_p.M439I	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	439						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										TATCTTTAACCATGTGAGACT	0.418																																					p.M439I		.											.	.	0			c.G1317A						.						146	148	147					13																	42440068		2203	4300	6503	SO:0001583	missense	23078	exon11			TTTAACCATGTGA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1317G>A	13.37:g.42440068C>T	ENSP00000368612:p.Met439Ile	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	73	36	NM_015058	0	0	3	4	1	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040196	0.35989	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.38401	1.14;1.14	5.3	5.3	0.74995	ATPase, AAA+ type, core (1);	0.109015	0.64402	D	0.000017	T	0.33381	0.0861	L	0.46157	1.445	0.43467	D	0.995671	B	0.02656	0.0	B	0.09377	0.004	T	0.17471	-1.0368	10	0.11182	T	0.66	.	19.3149	0.94208	0.0:1.0:0.0:0.0	.	439	A3KMH1	K0564_HUMAN	I	343;439;439;439	ENSP00000368612:M439I;ENSP00000281496:M439I	ENSP00000251030:M343I	M	-	3	0	KIAA0564	41338068	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.386000	0.52492	2.631000	0.89168	0.563000	0.77884	ATG	.		0.418	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42440068	C	T	42440068	3	4	126	1	0	0	0	0	1	0	0	0	8206	594	21	2	4544	2	KIAA0564	13	42440068	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		42440068	72729810	83	11069											
TDRD3	81550	broad.mit.edu	37	chr13	61060035	61060035	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaatgataatgatgaatttGaaaagcaaaggacggctgct	17	9	10	5	1	0	4	0	4	0	0	0	5	0	5	0	2	2	3	0	2	6	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr13:61060035G>A	ENST00000196169.3	+	7	1179	c.391G>A	c.(391-393)Gaa>Aaa	p.E131K	TDRD3_ENST00000377881.2_Missense_Mutation_p.E131K|TDRD3_ENST00000535286.1_Missense_Mutation_p.E224K|TDRD3_ENST00000377894.2_Missense_Mutation_p.E131K	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	131					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		TGATGAATTTGAAAAGCAAAG	0.348																																					p.E224K	Colon(36;164 906 35820 50723)												.	TDRD3-516	0			c.G670A						.						94	88	90					13																	61060035		2203	4300	6503	SO:0001583	missense	81550	exon7			GAATTTGAAAAGC	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.391G>A	13.37:g.61060035G>A	ENSP00000196169:p.Glu131Lys	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	49	4	NM_001146070	0	0	8	8	0	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	37	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.142203	0.77775	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.47	5.54	3.83	0.44106	.	0.099836	0.64402	D	0.000002	D	0.95452	0.8523	M	0.70275	2.135	0.54753	D	0.999989	P;P;P	0.51653	0.947;0.734;0.911	P;B;B	0.55508	0.777;0.301;0.376	D	0.94368	0.7593	10	0.54805	T	0.06	-12.0039	11.7911	0.52070	0.141:0.0:0.859:0.0	.	224;130;131	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	K	131;131;131;224	ENSP00000196169:E131K;ENSP00000367113:E131K;ENSP00000367126:E131K;ENSP00000440190:E224K	ENSP00000196169:E131K	E	+	1	0	TDRD3	59958036	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.581000	0.82535	0.719000	0.32188	0.655000	0.94253	GAA	.		0.348	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61060035	G	A	61060035	3	1	126	1	0	0	0	0	1	0	0	0	15764	1291	45	2	696	2	TDRD3	13	61060035	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	18619967	61060035	54109843	84	11070											
AP1G2	8906	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24030557	24030557	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgtaccagggcacctccTggggaggggtccagatgggg	7	6	19	9	0	0	1	0	0	0	1	2	2	2	2	4	8	1	2	4	8	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:24030557T>C	ENST00000308724.5	-	18	2696	c.1941A>G	c.(1939-1941)ccA>ccG	p.P647P	RP11-66N24.4_ENST00000553985.1_RNA|RP11-66N24.3_ENST00000555968.1_RNA|RP11-66N24.4_ENST00000555446.1_RNA|AP1G2_ENST00000397120.3_Silent_p.P647P|RP11-66N24.4_ENST00000556354.1_RNA	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	647					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		GGGCACCTCCTGGGGAGGGGT	0.577																																					p.P647P													.	AP1G2-45	0			c.A1941G						.						58	57	57					14																	24030557		2203	4299	6502	SO:0001819	synonymous_variant	8906	exon19			ACCTCCTGGGGAG	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1941A>G	14.37:g.24030557T>C		Somatic	73	1		WXS	Illumina HiSeq	Phase_I	92	37	NM_003917	0	0	29	58	29	D3DS51|O75504	Silent	SNP	ENST00000308724.5	37	CCDS9602.1																																																																																			.		0.577	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		C	24030557	T	C	24030557	2	2	126	1	0	0	0	0	0	0	0	1	733	1567	55	3		3	AP1G2	14	24030557	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10		24030557	83318983	85	11071											
SIX4	51804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	61186919	61186919	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactccactgggtccctgaaTaaaagaatttccattaagga	15	10	7	9	0	0	2	0	1	0	1	3	3	3	3	3	2	1	0	3	2	6	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:61186919T>A	ENST00000216513.4	-	2	1167	c.1108A>T	c.(1108-1110)Att>Ttt	p.I370F		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	370					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)		GGTCCCTGAATAAAAGAATTT	0.398																																					p.I370F		.											.	SIX4-154	0			c.A1108T						.						79	76	77					14																	61186919		2203	4300	6503	SO:0001583	missense	51804	exon2			CCTGAATAAAAGA	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.1108A>T	14.37:g.61186919T>A	ENSP00000216513:p.Ile370Phe	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	103	37	NM_017420	0	0	0	0	0	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	T	13.45	2.239521	0.39598	.	.	ENSG00000100625	ENST00000216513;ENST00000554079;ENST00000556952	D;T	0.91792	-2.91;0.56	5.72	5.72	0.89469	.	0.297103	0.34178	N	0.004182	D	0.86464	0.5939	N	0.19112	0.55	0.47698	D	0.999492	P;P	0.49090	0.919;0.454	B;B	0.43575	0.424;0.153	D	0.86816	0.2001	10	0.41790	T	0.15	.	12.7402	0.57249	0.0:0.0:0.146:0.854	.	362;370	G3V2N2;Q9UIU6	.;SIX4_HUMAN	F	370;43;362	ENSP00000216513:I370F;ENSP00000451537:I43F	ENSP00000216513:I370F	I	-	1	0	SIX4	60256672	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.761000	0.55242	2.194000	0.70268	0.533000	0.62120	ATT	.		0.398	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			A	61186919	T	A	61186919	3	1	126	1	0	0	0	0	1	0	0	0	14381	1406	49	5	1245	5	SIX4	14	61186919	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	37156362	61186919	46162621	86	11072											
GPHN	10243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	67647539	67647539	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtaatcaaatgagcagccGtctgatgagcatgcgcagtg	12	8	13	8	2	2	3	1	3	1	0	2	3	2	3	1	1	4	4	1	1	2	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:67647539G>A	ENST00000315266.5	+	22	3217	c.2096G>A	c.(2095-2097)cGt>cAt	p.R699H	GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000543237.1_Missense_Mutation_p.R745H|GPHN_ENST00000478722.1_Missense_Mutation_p.R732H|GPHN_ENST00000305960.9_Missense_Mutation_p.R668H	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	699	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		ATGAGCAGCCGTCTGATGAGC	0.458			T	MLL	AL																																p.R732H		.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN-228	0			c.G2195A						.						128	105	113					14																	67647539		2203	4300	6503	SO:0001583	missense	10243	exon23			GCAGCCGTCTGAT	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.2096G>A	14.37:g.67647539G>A	ENSP00000312771:p.Arg699His	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	125	58	NM_020806	0	0	6	12	6	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934351	0.73442	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.83	4.93	0.64822	MoeA, C-terminal, domain IV (3);	0.102725	0.64402	D	0.000004	T	0.79476	0.4452	M	0.81112	2.525	0.80722	D	1	P;D;D;D	0.89917	0.953;1.0;0.978;1.0	B;D;P;D	0.87578	0.379;0.998;0.75;0.998	T	0.80308	-0.1437	9	0.51188	T	0.08	-7.1864	15.3438	0.74317	0.0681:0.0:0.9319:0.0	.	668;745;699;732	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	H	699;732;745;668	.	ENSP00000303019:R668H	R	+	2	0	GPHN	66717292	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.843000	0.86859	2.768000	0.95171	0.467000	0.42956	CGT	.		0.458	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		A	67647539	G	A	67647539	3	1	126	1	0	0	0	0	1	0	0	0	6630	1145	40	1	2285	1	GPHN	14	67647539	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	6460620	67647539	39702001	87	11073											
EML5	161436	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	89171882	89171883	+	Frame_Shift_Ins	INS	-	-	T																															tcagaatccagttctggaacINSatcagacagatctgaatctg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:89171882_89171883insT	ENST00000380664.5	-	12	1874_1875	c.1875_1876insA	c.(1873-1878)gatgttfs	p.V626fs	EML5_ENST00000352093.5_Frame_Shift_Ins_p.V626fs|EML5_ENST00000554922.1_Frame_Shift_Ins_p.V626fs			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	626						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AGTTCTGGAACATCAGACAGAT	0.337																																					p.V626fs		.											.	EML5-93	0			c.1876_1877insA						.																																			SO:0001589	frameshift_variant	161436	exon12			.	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.1875_1876insA	14.37:g.89171882_89171883insT	ENSP00000370039:p.Val626fs	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	41	18	NM_183387	0	0	0	0	0	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Frame_Shift_Ins	INS	ENST00000380664.5	37	CCDS45148.1																																																																																			.		0.337	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89171883	-	T	89171882	7	5	126	1	0	1	1	0	0	0	0	0	5113	478	17	0	4185	0	EML5	14	89171882	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10	21524343	89171882	18177658	88	11074											
RYR3	6263	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	34130027	34130027	+	Frame_Shift_Del	DEL	A	A	-																															agaattccagaaggccatggAagggcaaaaacagtacacgc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr15:34130027delA	ENST00000389232.4	+	89	11916	c.11846delA	c.(11845-11847)gaafs	p.E3949fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.E3944fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3949					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAGGCCATGGAAGGGCAAAAA	0.403																																					p.E3949fs		.											.	RYR3-520	0			c.11846delA						.						108	103	104					15																	34130027		1895	4111	6006	SO:0001589	frameshift_variant	6263	exon89			.		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.11846delA	15.37:g.34130027delA	ENSP00000373884:p.Glu3949fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	83	45	NM_001036	0	0	0	0	0	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	37	CCDS45210.1																																																																																			.		0.403	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			-	34130027	A	-	34130027	7	5	126	1	0	1	0	1	0	0	0	0	13802	246	9	0	12200	0	RYR3	15	34130027	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10		34130027	68401365	89	11075											
CASKIN1	57524	hgsc.bcm.edu;bcgsc.ca	37	chr16	2239295	2239295	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtcttccccgagttgtccaCcatgcacgggttagactggt	6	11	11	13	3	1	1	0	0	1	1	3	2	3	1	4	2	1	3	4	2	1	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:2239295C>A	ENST00000343516.6	-	5	522	c.430G>T	c.(430-432)Gtg>Ttg	p.V144L		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	144					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						GAGTTGTCCACCATGCACGGG	0.697																																					p.V144L		.											.	CASKIN1-92	0			c.G430T						.						39	52	47					16																	2239295		2114	4208	6322	SO:0001583	missense	57524	exon5			TGTCCACCATGCA	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.430G>T	16.37:g.2239295C>A	ENSP00000345436:p.Val144Leu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_020764	0	0	0	0	0	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	37	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032936	0.54790	.	.	ENSG00000167971	ENST00000343516	T	0.64438	-0.1	3.46	3.46	0.39613	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.42291	0.1196	N	0.13327	0.33	0.42422	D	0.992647	B	0.25105	0.118	B	0.29353	0.101	T	0.44190	-0.9344	9	0.56958	D	0.05	-19.1703	5.5157	0.16906	0.0:0.7694:0.0:0.2306	.	144	Q8WXD9	CSKI1_HUMAN	L	144	ENSP00000345436:V144L	ENSP00000345436:V144L	V	-	1	0	CASKIN1	2179296	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.807000	0.38902	1.954000	0.56735	0.561000	0.74099	GTG	.		0.697	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		A	2239295	C	A	2239295	3	1	126	1	0	0	0	0	1	0	0	0	2672	507	18	4	3929	4	CASKIN1	16	2239295	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		2239295	88115458	90	11076											
ACSM1	116285	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	20681301	20681301	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatgtcttcaggctccgtaAtttcctactaactccaaaat	12	13	5	11	1	2	1	1	0	1	1	5	1	5	1	3	1	2	2	3	1	5	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:20681301A>T	ENST00000307493.4	-	5	827	c.760T>A	c.(760-762)Tta>Ata	p.L254I	ACSM1_ENST00000219151.4_5'UTR|ACSM1_ENST00000520010.1_Missense_Mutation_p.L254I	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	254					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						AGGCTCCGTAATTTCCTACTA	0.512																																					p.L254I													.	ACSM1-91	0			c.T760A						.						112	102	106					16																	20681301		2201	4300	6501	SO:0001583	missense	116285	exon5			TCCGTAATTTCCT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.760T>A	16.37:g.20681301A>T	ENSP00000301956:p.Leu254Ile	Somatic	208	1		WXS	Illumina HiSeq	Phase_I	198	76	NM_052956	0	0	0	0	0	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	37	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	A	3.836	-0.034884	0.07543	.	.	ENSG00000166743	ENST00000307493;ENST00000520010	T;T	0.49432	0.78;0.78	5.05	-5.32	0.02722	AMP-dependent synthetase/ligase (1);	2.926740	0.01433	N	0.014801	T	0.37758	0.1015	L	0.42581	1.335	0.35230	D	0.776841	B	0.06786	0.001	B	0.12837	0.008	T	0.14090	-1.0485	10	0.72032	D	0.01	-11.3632	5.3284	0.15918	0.4297:0.4004:0.0762:0.0937	.	254	Q08AH1	ACSM1_HUMAN	I	254	ENSP00000301956:L254I;ENSP00000428047:L254I	ENSP00000301956:L254I	L	-	1	2	ACSM1	20588802	0.000000	0.05858	0.004000	0.12327	0.027000	0.11550	-0.352000	0.07701	-1.132000	0.02907	-2.194000	0.00310	TTA	.		0.512	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		T	20681301	A	T	20681301	3	4	126	1	0	0	0	0	1	0	0	0	182	98	4	5	1009	5	ACSM1	16	20681301	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	18442006	20681301	69673452	91	11077											
TMEM159	57146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21185458	21185458	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccagcctcatcagctgctgGttttctcccaggtaaataca	9	12	7	13	0	3	0	2	0	1	0	5	0	4	0	3	2	4	4	3	2	3	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:21185458G>C	ENST00000233047.4	+	4	861	c.393G>C	c.(391-393)tgG>tgC	p.W131C	TMEM159_ENST00000261388.3_Missense_Mutation_p.W131C|TMEM159_ENST00000451578.2_Missense_Mutation_p.W155C|TMEM159_ENST00000572599.1_Missense_Mutation_p.W131C|TMEM159_ENST00000572258.1_Intron			Q96B96	TM159_HUMAN	transmembrane protein 159	131						integral component of membrane (GO:0016021)				large_intestine(3)|lung(2)|ovary(1)	6				GBM - Glioblastoma multiforme(48;0.0972)		TCAGCTGCTGGTTTTCTCCCA	0.428																																					p.W131C		.											.	TMEM159-69	0			c.G393C						.						121	98	106					16																	21185458		2200	4300	6500	SO:0001583	missense	57146	exon4			CTGCTGGTTTTCT	AF070596	CCDS10595.1	16p12.2	2008-02-05			ENSG00000011638	ENSG00000011638			30136	protein-coding gene	gene with protein product		611304				8619474, 9110174, 15589683	Standard	NM_020422		Approved	promethin	uc002dif.4	Q96B96	OTTHUMG00000131559	ENST00000233047.4:c.393G>C	16.37:g.21185458G>C	ENSP00000233047:p.Trp131Cys	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	127	59	NM_020422	0	0	0	0	0	A6NMA9|B4DEC1|O00323	Missense_Mutation	SNP	ENST00000233047.4	37	CCDS10595.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.059590	0.36373	.	.	ENSG00000011638	ENST00000233047;ENST00000261388;ENST00000451578	T;T;T	0.25579	1.8;1.8;1.79	6.07	6.07	0.98685	.	0.371511	0.26467	N	0.024208	T	0.49338	0.1551	M	0.64997	1.995	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.65874	0.939;0.912	T	0.38950	-0.9637	10	0.72032	D	0.01	-19.3257	18.139	0.89633	0.0:0.0:1.0:0.0	.	155;131	B4DEC1;Q96B96	.;TM159_HUMAN	C	131;131;155	ENSP00000233047:W131C;ENSP00000261388:W131C;ENSP00000409879:W155C	ENSP00000233047:W131C	W	+	3	0	TMEM159	21092959	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	3.746000	0.55127	2.885000	0.99019	0.650000	0.86243	TGG	.		0.428	TMEM159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254421.1	NM_020422		C	21185458	G	C	21185458	3	2	126	1	0	0	0	0	1	0	0	0	16106	1270	44	4	403	4	TMEM159	16	21185458	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	504157	21185458	69169295	92	11078											
ZP2	7783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21214557	21214557	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taagtagaactgatggagtaGgcatttttcagataactgaa	15	12	10	4	0	1	4	1	2	0	2	1	5	1	5	0	2	2	3	0	2	6	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:21214557G>T	ENST00000574002.1	-	11	1470	c.988C>A	c.(988-990)Cta>Ata	p.L330I	ZP2_ENST00000219593.4_Missense_Mutation_p.L330I|ZP2_ENST00000574091.1_Missense_Mutation_p.L330I|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	330					binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TGATGGAGTAGGCATTTTTCA	0.483																																					p.L330I		.											.	ZP2-91	0			c.C988A						.						107	102	103					16																	21214557		2200	4300	6500	SO:0001583	missense	7783	exon10			GGAGTAGGCATTT	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"Zona pellucida glycoproteins"	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.988C>A	16.37:g.21214557G>T	ENSP00000460971:p.Leu330Ile	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	54	31	NM_003460	0	0	0	0	0	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523709	0.44866	.	.	ENSG00000103310	ENST00000219593	T	0.76316	-1.01	5.97	2.76	0.32466	.	0.485326	0.18994	N	0.125524	T	0.77267	0.4105	M	0.75447	2.3	0.19575	N	0.999964	P;P	0.51351	0.944;0.944	P;P	0.47981	0.563;0.563	T	0.66685	-0.5861	10	0.32370	T	0.25	-6.6445	7.7511	0.28898	0.1328:0.292:0.5752:0.0	.	330;330	Q4VAP1;Q05996	.;ZP2_HUMAN	I	330	ENSP00000219593:L330I	ENSP00000219593:L330I	L	-	1	2	ZP2	21122058	0.879000	0.30193	0.975000	0.42487	0.291000	0.27294	0.880000	0.28159	1.513000	0.48852	0.655000	0.94253	CTA	.		0.483	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			T	21214557	G	T	21214557	3	4	126	1	0	0	0	0	1	0	0	0	18248	991	35	4	1289	4	ZP2	16	21214557	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	29099	21214557	69140196	93	11079											
SETD1A	9739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30976286	30976286	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgagcgcttcccaccttCttacacctcctacctgcccc	6	10	5	20	1	1	1	0	1	1	0	3	1	3	1	7	0	5	2	7	0	2	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:30976286C>A	ENST00000262519.8	+	7	1909	c.1223C>A	c.(1222-1224)tCt>tAt	p.S408Y		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	408	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						TTCCCACCTTCTTACACCTCC	0.662																																					p.S408Y		.											.	SETD1A-93	0			c.C1223A						.						57	66	63					16																	30976286		2197	4300	6497	SO:0001583	missense	9739	exon7			CACCTTCTTACAC	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.1223C>A	16.37:g.30976286C>A	ENSP00000262519:p.Ser408Tyr	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	63	19	NM_014712	0	0	2	5	3	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	37	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.182646	0.38511	.	.	ENSG00000099381	ENST00000262519	D	0.94497	-3.44	5.64	5.64	0.86602	.	0.197187	0.45361	D	0.000366	D	0.93979	0.8072	L	0.36672	1.1	0.26055	N	0.981439	D	0.67145	0.996	P	0.56700	0.804	D	0.89234	0.3579	10	0.72032	D	0.01	.	12.5755	0.56362	0.0:0.92:0.0:0.08	.	408	O15047	SET1A_HUMAN	Y	408	ENSP00000262519:S408Y	ENSP00000262519:S408Y	S	+	2	0	SETD1A	30883787	1.000000	0.71417	1.000000	0.80357	0.548000	0.35241	3.742000	0.55097	2.648000	0.89879	0.561000	0.74099	TCT	.		0.662	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30976286	C	A	30976286	3	1	126	1	0	0	0	0	1	0	0	0	14162	913	32	4	1245	4	SETD1A	16	30976286	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	9761729	30976286	59378467	94	11080											
ATP6V0D1	9114	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67487539	67487539	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctccttgagccggtcatcGatgactgacaccgtcagagg	8	10	11	12	3	3	4	2	3	1	1	5	5	3	4	3	2	1	0	3	2	0	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:67487539G>A	ENST00000290949.3	-	2	360	c.210C>T	c.(208-210)atC>atT	p.I70I	ATP6V0D1_ENST00000602876.1_5'UTR|ATP6V0D1_ENST00000540149.1_Silent_p.I70I	NM_004691.4	NP_004682.2	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1	70					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP hydrolysis coupled proton transport (GO:0015991)|brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|cellular protein metabolic process (GO:0044267)|cilium assembly (GO:0042384)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|synaptic vesicle (GO:0008021)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			large_intestine(3)|lung(3)|urinary_tract(2)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		GCCGGTCATCGATGACTGACA	0.532																																					p.I70I													.	ATP6V0D1-90	0			c.C210T						.						176	135	149					16																	67487539		2198	4300	6498	SO:0001819	synonymous_variant	9114	exon2			GTCATCGATGACT	X71490	CCDS10838.1	16q22	2010-04-21	2006-01-20	2002-05-10	ENSG00000159720	ENSG00000159720		"ATPases / V-type"	13724	protein-coding gene	gene with protein product		607028	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1", "ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D1"	ATP6D		8250920	Standard	NM_004691		Approved	ATP6DV, VATX, VPATPD, P39, Vma6	uc002ete.1	P61421	OTTHUMG00000137515	ENST00000290949.3:c.210C>T	16.37:g.67487539G>A		Somatic	140	2		WXS	Illumina HiSeq	Phase_I	144	63	NM_004691	0	0	46	70	24	P12953|Q02547	Silent	SNP	ENST00000290949.3	37	CCDS10838.1																																																																																			.		0.532	ATP6V0D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268835.1	NM_004691		A	67487539	G	A	67487539	2	1	126	1	0	0	0	0	0	0	0	1	1174	1048	37	1		1	ATP6V0D1	16	67487539	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	36511253	67487539	22867214	95	11081											
THAP11	57215	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	67876718	67876718	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctgcgcggcgtcaatgaGcgcaaagtagcgcgcagacc	9	4	14	14	7	1	2	1	1	0	1	1	2	1	2	2	1	3	4	2	1	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:67876718G>T	ENST00000303596.1	+	1	506	c.261G>T	c.(259-261)gaG>gaT	p.E87D	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	87					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		GCGTCAATGAGCGCAAAGTAG	0.687																																					p.E87D		.											.	THAP11-90	0			c.G261T						.						18	19	18					16																	67876718		2197	4296	6493	SO:0001583	missense	57215	exon1			CAATGAGCGCAAA	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"THAP (C2CH-type zinc finger) domain containing"	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.261G>T	16.37:g.67876718G>T	ENSP00000304689:p.Glu87Asp	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	28	12	NM_020457	0	0	4	10	6	A4UCT5|A8K002|O94795	Missense_Mutation	SNP	ENST00000303596.1	37	CCDS10847.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368381	0.61513	.	.	ENSG00000168286	ENST00000303596	T	0.33216	1.42	5.4	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.41880	0.1178	L	0.32530	0.975	0.51767	D	0.999939	D	0.63880	0.993	D	0.70016	0.967	T	0.26121	-1.0112	10	0.54805	T	0.06	-16.1311	11.7789	0.52001	0.1059:0.0:0.8941:0.0	.	87	Q96EK4	THA11_HUMAN	D	87	ENSP00000304689:E87D	ENSP00000304689:E87D	E	+	3	2	THAP11	66434219	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.044000	0.57361	1.155000	0.42497	0.563000	0.77884	GAG	.		0.687	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457		T	67876718	G	T	67876718	3	4	126	1	0	0	0	0	1	0	0	0	15875	962	34	4	263	4	THAP11	16	67876718	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	389179	67876718	22478035	96	11082											
TBC1D26	353149	broad.mit.edu	37	chr17	15641610	15641610	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagctgtctcaaagagtatAcaaagtcattcccctggcgg	11	10	10	10	1	2	1	2	0	1	1	4	1	3	1	2	2	2	3	2	2	5	4	rs202131240		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr17:15641610A>G	ENST00000437605.2	+	7	546	c.296A>G	c.(295-297)tAc>tGc	p.Y99C	TBC1D26_ENST00000579428.1_Missense_Mutation_p.Y99C|AC005324.6_ENST00000580194.1_RNA|AC005324.6_ENST00000434017.1_RNA|AC005324.6_ENST00000433873.1_RNA|ZNF286A_ENST00000413242.2_3'UTR	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	99							Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		CAAAGAGTATACAAAGTCATT	0.527																																					p.Y99C													.	TBC1D26-90	0			c.A296G						.						94	90	91					17																	15641610		1953	4139	6092	SO:0001583	missense	353149	exon7			GAGTATACAAAGT		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.296A>G	17.37:g.15641610A>G	ENSP00000410111:p.Tyr99Cys	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	229	6	NM_178571	0	0	0	0	0	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1	.	.	.	.	.	.	.	.	.	.	a	6.884	0.532498	0.13127	.	.	ENSG00000214946	ENST00000437605	T	0.40756	1.02	1.44	-0.0271	0.13927	Rab-GAP/TBC domain (2);	0.436109	0.22940	U	0.053784	T	0.48943	0.1528	L	0.58583	1.82	0.19945	N	0.999948	D;D	0.76494	0.999;0.981	D;D	0.67231	0.95;0.914	T	0.36601	-0.9741	10	0.52906	T	0.07	.	3.1782	0.06576	0.6204:0.0:0.0:0.3796	.	99;99	Q86UD7;Q86UD7-2	TBC26_HUMAN;.	C	99	ENSP00000410111:Y99C	ENSP00000410111:Y99C	Y	+	2	0	TBC1D26	15582335	0.952000	0.32445	0.008000	0.14137	0.029000	0.11900	1.676000	0.37565	-0.258000	0.09446	0.338000	0.21704	TAC	.		0.527	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571		G	15641610	A	G	15641610	3	3	126	1	0	0	0	0	1	0	0	0	15648	391	14	3	314	3	TBC1D26	17	15641610	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10		15641610	65553600	97	11083											
LGALS9	3965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	25967635	25967635	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agactggcttcagtggaaatGacattgccttccacttcaac	11	11	8	11	0	2	2	2	1	0	1	3	3	3	3	2	2	2	1	2	2	2	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr17:25967635G>A	ENST00000395473.2	+	3	1637	c.169G>A	c.(169-171)Gac>Aac	p.D57N	LGALS9_ENST00000313648.6_Missense_Mutation_p.D57N|AC015688.3_ENST00000584605.1_3'UTR|LGALS9_ENST00000310394.5_Missense_Mutation_p.D57N|LGALS9_ENST00000302228.5_Missense_Mutation_p.D57N|LGALS9_ENST00000448970.2_3'UTR|LGALS9_ENST00000413914.2_Intron	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	57	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		CAGTGGAAATGACATTGCCTT	0.527																																					p.D57N	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	.											.	LGALS9-226	0			c.G169A						.						124	118	120					17																	25967635		2203	4300	6503	SO:0001583	missense	3965	exon3			GGAAATGACATTG	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"Lectins, galactoside-binding"	6570	protein-coding gene	gene with protein product	"galectin 9"	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.169G>A	17.37:g.25967635G>A	ENSP00000378856:p.Asp57Asn	Somatic	609	0		WXS	Illumina HiSeq	Phase_I	819	207	NM_009587	0	0	12	13	1	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	.	.	.	.	.	.	.	.	.	.	G	9.418	1.082274	0.20309	.	.	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394;ENST00000313648;ENST00000448970	T;T;T;T	0.14022	2.54;2.54;2.54;2.54	3.94	0.839	0.18907	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.459334	0.24325	N	0.039518	T	0.12774	0.0310	L	0.50993	1.605	0.58432	D	0.999995	B;P;P	0.42871	0.1;0.792;0.624	B;B;B	0.42319	0.084;0.383;0.203	T	0.06570	-1.0819	10	0.42905	T	0.14	.	7.4254	0.27096	0.3157:0.0:0.6843:0.0	.	57;57;57	F8W9W4;Q3B8N1;O00182	.;.;LEG9_HUMAN	N	57	ENSP00000378856:D57N;ENSP00000306228:D57N;ENSP00000312259:D57N;ENSP00000318214:D57N	ENSP00000306228:D57N	D	+	1	0	LGALS9	22991762	0.637000	0.27216	0.459000	0.27081	0.622000	0.37654	0.741000	0.26202	0.460000	0.27045	0.586000	0.80456	GAC	.		0.527	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587		A	25967635	G	A	25967635	3	1	126	1	0	0	0	0	1	0	0	0	8770	1290	45	2	179	2	LGALS9	17	25967635	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	10326025	25967635	55227575	98	11084											
SMARCD2	6603	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61910338	61910338	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctgttccagttcctgcCttcgctgctgcacctggaga	5	11	10	15	1	0	1	0	0	0	1	3	2	2	1	5	1	3	6	5	1	0	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr17:61910338C>A	ENST00000448276.2	-	13	1821	c.1556G>T	c.(1555-1557)aGg>aTg	p.R519M	SMARCD2_ENST00000323347.10_Missense_Mutation_p.R471M|FTSJ3_ENST00000580295.1_5'Flank|SMARCD2_ENST00000225742.9_Missense_Mutation_p.R444M	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	519					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						CAGTTCCTGCCTTCGCTGCTG	0.587																																					p.R519M													.	SMARCD2-227	0			c.G1556T						.						40	47	45					17																	61910338		1971	4165	6136	SO:0001583	missense	6603	exon13			TCCTGCCTTCGCT	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"mammalian chromatin remodeling complex BRG1-associated factor 60B", "Swp73-like protein", "chromatin remodeling complex BAF60B subunit", "SWI/SNF complex 60 kDa subunit B"	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.1556G>T	17.37:g.61910338C>A	ENSP00000392617:p.Arg519Met	Somatic	150	1		WXS	Illumina HiSeq	Phase_I	210	113	NM_001098426	0	0	32	72	40	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	37	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	13.60	2.284333	0.40394	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T	0.57107	0.42;0.53	5.87	5.87	0.94306	.	0.044796	0.85682	D	0.000000	T	0.79919	0.4529	M	0.92122	3.275	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.993;0.997;0.997	D	0.84078	0.0383	10	0.87932	D	0	-10.7028	17.6998	0.88291	0.0:1.0:0.0:0.0	.	471;482;519	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	M	519;461;482;471	ENSP00000392617:R519M;ENSP00000318451:R471M	ENSP00000225742:R461M	R	-	2	0	SMARCD2	59264070	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.968000	0.56809	2.785000	0.95823	0.655000	0.94253	AGG	.		0.587	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426		A	61910338	C	A	61910338	3	1	126	1	0	0	0	0	1	0	0	0	14810	681	24	4	43	4	SMARCD2	17	61910338	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	35942703	61910338	19284872	99	11085											
WIPI1	55062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	66440668	66440668	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaatatccaggagggtcttCaacagcttcatgtctttaat	11	13	9	8	0	4	0	2	0	2	0	5	2	5	2	1	3	2	1	1	3	4	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr17:66440668C>T	ENST00000262139.5	-	4	395	c.396G>A	c.(394-396)ttG>ttA	p.L132L	WIPI1_ENST00000589459.1_5'UTR|WIPI1_ENST00000546360.1_Silent_p.L50L	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	132					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						GGAGGGTCTTCAACAGCTTCA	0.433																																					p.L132L		.											.	WIPI1-90	0			c.G396A						.						150	137	142					17																	66440668		2203	4300	6503	SO:0001819	synonymous_variant	55062	exon4			GGTCTTCAACAGC		CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"WD repeat domain containing"	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.396G>A	17.37:g.66440668C>T		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	119	31	NM_017983	0	0	26	44	18	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																			.		0.433	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983		T	66440668	C	T	66440668	2	4	126	1	0	0	0	0	0	0	0	1	17403	825	29	2		2	WIPI1	17	66440668	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	4530330	66440668	14754542	100	11086											
RBBP8	5932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	20562277	20562277	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcattttctggcgttaaccgGctacgaagaaaggagaaccc	12	9	10	10	3	2	2	1	0	1	2	2	4	2	2	2	3	3	2	2	3	5	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr18:20562277G>A	ENST00000399722.2	+	7	876	c.525G>A	c.(523-525)cgG>cgA	p.R175R	RBBP8_ENST00000360790.5_Silent_p.R175R|RBBP8_ENST00000399725.2_Silent_p.R175R|RBBP8_ENST00000327155.5_Silent_p.R175R	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	175					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GCGTTAACCGGCTACGAAGAA	0.433								Homologous recombination																													p.R175R		.											.	RBBP8-659	0			c.G525A						.						174	154	161					18																	20562277		2203	4300	6503	SO:0001819	synonymous_variant	5932	exon7			TAACCGGCTACGA	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.525G>A	18.37:g.20562277G>A		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	138	44	NM_203292	0	0	3	10	7	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Silent	SNP	ENST00000399722.2	37	CCDS11875.1																																																																																			.		0.433	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		A	20562277	G	A	20562277	2	1	126	1	0	0	0	0	0	0	0	1	13137	1190	42	2		2	RBBP8	18	20562277	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		20562277	57514971	101	11087											
REXO1	57455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	1817252	1817252	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggcgtagatccccgggtggGtgtctcctgagagctctttc	4	11	15	11	2	2	2	0	1	2	2	5	3	3	2	3	3	1	2	3	3	1	2	rs200984356		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:1817252G>C	ENST00000170168.4	-	12	3261	c.3167C>G	c.(3166-3168)aCc>aGc	p.T1056S	MIR1909_ENST00000411312.1_RNA|CTB-31O20.3_ENST00000586259.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	1056						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)	p.T1056I(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCGGGTGGGTGTCTCCTGA	0.642													.|||	1	0.000199681	0	0.0014	5008	,	,		14977	0		0	False		,,,				2504	0				p.T1056S		.											.	REXO1-90	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C3167G						.						71	66	67					19																	1817252		2202	4300	6502	SO:0001583	missense	57455	exon12			GGGTGGGTGTCTC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"elongin A binding protein 1"	609614	"transcription elongation factor B polypeptide 3 binding protein 1"	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.3167C>G	19.37:g.1817252G>C	ENSP00000170168:p.Thr1056Ser	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	68	25	NM_020695	0	0	9	18	9	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	.	3.519	-0.098262	0.07010	.	.	ENSG00000079313	ENST00000170168;ENST00000543452	T	0.11063	2.81	3.94	1.53	0.23141	.	0.450432	0.22206	N	0.063169	T	0.04407	0.0121	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.15141	0.012;0.001;0.001	B;B;B	0.15870	0.014;0.002;0.002	T	0.43245	-0.9403	10	0.16896	T	0.51	-7.696	11.7661	0.51930	0.0:0.5977:0.4023:0.0	.	42;365;1056	B4DVD3;B4DWY3;Q8N1G1	.;.;REXO1_HUMAN	S	1056;328	ENSP00000170168:T1056S	ENSP00000170168:T1056S	T	-	2	0	REXO1	1768252	0.323000	0.24643	0.001000	0.08648	0.001000	0.01503	4.178000	0.58284	0.819000	0.34492	0.561000	0.74099	ACC	G|1.000;C|0.000		0.642	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		C	1817252	G	C	1817252	3	2	126	1	0	0	0	0	1	0	0	0	13273	1261	44	4	518	4	REXO1	19	1817252	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		1817252	57311731	102	11088											
LIPE	3991	broad.mit.edu;bcgsc.ca	37	chr19	42911843	42911843	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggggtgagatggtgaccGtgagcgtggggtcggcagtc	5	8	22	6	3	0	3	0	3	0	1	2	4	0	3	1	6	1	1	1	6	0	0	rs377288315		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:42911843G>T	ENST00000244289.4	-	5	2033	c.1757C>A	c.(1756-1758)aCg>aAg	p.T586K	LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE_ENST00000602000.1_5'UTR|LIPE-AS1_ENST00000594624.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	586					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				GATGGTGACCGTGAGCGTGGG	0.642																																					p.T586K													.	LIPE-154	0			c.C1757A						.						82	71	75					19																	42911843		2203	4300	6503	SO:0001583	missense	3991	exon5			GTGACCGTGAGCG	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.1757C>A	19.37:g.42911843G>T	ENSP00000244289:p.Thr586Lys	Somatic	166	1		WXS	Illumina HiSeq	Phase_I	103	45	NM_005357	0	0	1	2	1	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806842	0.31961	.	.	ENSG00000079435	ENST00000244289	T	0.30714	1.52	3.67	2.6	0.31112	Hormone-sensitive lipase, N-terminal (1);	0.404770	0.23048	N	0.052531	T	0.42630	0.1211	L	0.50333	1.59	0.38251	D	0.941615	D	0.89917	1.0	D	0.91635	0.999	T	0.35276	-0.9795	10	0.11182	T	0.66	-5.0497	11.0161	0.47689	0.0995:0.0:0.9005:0.0	.	586	Q05469	LIPS_HUMAN	K	586	ENSP00000244289:T586K	ENSP00000244289:T586K	T	-	2	0	LIPE	47603683	0.847000	0.29606	0.608000	0.28969	0.006000	0.05464	1.042000	0.30303	0.839000	0.34971	0.561000	0.74099	ACG	.		0.642	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		T	42911843	G	T	42911843	3	4	126	1	0	0	0	0	1	0	0	0	8844	1145	40	4	1497	4	LIPE	19	42911843	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	41094591	42911843	16217140	103	11089											
TRPM4	54795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	49714007	49714007	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgagcggaagctgctaacGtgggaatcggtgcataagga	11	6	16	8	4	0	0	0	0	0	0	1	4	0	3	1	4	5	3	1	4	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:49714007G>T	ENST00000252826.5	+	22	3495	c.3369G>T	c.(3367-3369)acG>acT	p.T1123T	TRPM4_ENST00000355712.5_Silent_p.T769T|TRPM4_ENST00000427978.2_Silent_p.T978T	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	1123	Calmodulin-binding.				calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		AGCTGCTAACGTGGGAATCGG	0.622																																					p.T1123T		.											.	TRPM4-91	0			c.G3369T						.						38	44	42					19																	49714007		2203	4300	6503	SO:0001819	synonymous_variant	54795	exon22			GCTAACGTGGGAA	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.3369G>T	19.37:g.49714007G>T		Somatic	186	0		WXS	Illumina HiSeq	Phase_I	125	41	NM_017636	0	0	12	31	19	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	37	CCDS33073.1																																																																																			.		0.622	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49714007	G	T	49714007	2	4	126	1	0	0	0	0	0	0	0	1	16621	1132	40	4		4	TRPM4	19	49714007	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	6802164	49714007	9414976	104	11090											
SIGLEC10	89790	broad.mit.edu;bcgsc.ca	37	chr19	51918318	51918318	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggagcagctgcagtgcagacCctcagcctcccaggagcagg	9	4	14	14	0	1	1	1	0	0	1	2	3	2	3	3	3	6	5	3	3	0	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:51918318C>G	ENST00000339313.5	-	8	1491	c.1375G>C	c.(1375-1377)Ggt>Cgt	p.G459R	SIGLEC10_ENST00000439889.2_Missense_Mutation_p.G401R|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.G459R|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000436984.2_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000353836.5_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	459					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CAGTGCAGACCCTCAGCCTCC	0.692																																					p.G459R													.	SIGLEC10-91	0			c.G1375C						.						11	14	13					19																	51918318		2193	4272	6465	SO:0001583	missense	89790	exon8			GCAGACCCTCAGC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15620	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 10 Ig-like lectin 7", "siglec-like gene 2"	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1375G>C	19.37:g.51918318C>G	ENSP00000345243:p.Gly459Arg	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	19	7	NM_033130	0	0	0	0	0	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	12.97	2.096586	0.36952	.	.	ENSG00000142512	ENST00000356298;ENST00000439889;ENST00000339313	D;D;D	0.86030	-2.06;-2.06;-2.06	4.83	3.8	0.43715	.	0.448137	0.21198	N	0.078518	D	0.91153	0.7214	M	0.85099	2.735	0.09310	N	0.999998	D;P	0.67145	0.996;0.925	D;P	0.65233	0.933;0.85	D	0.83608	0.0132	10	0.72032	D	0.01	.	9.2804	0.37725	0.0:0.8986:0.0:0.1014	.	401;459	Q96LC7-3;Q96LC7	.;SIG10_HUMAN	R	459;401;459	ENSP00000348646:G459R;ENSP00000389132:G401R;ENSP00000345243:G459R	ENSP00000345243:G459R	G	-	1	0	SIGLEC10	56610130	0.188000	0.23250	0.078000	0.20375	0.354000	0.29330	1.416000	0.34759	1.036000	0.39998	-0.254000	0.11334	GGT	.		0.692	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		G	51918318	C	G	51918318	3	3	126	1	0	0	0	0	1	0	0	0	14338	623	22	4	734	4	SIGLEC10	19	51918318	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	2204311	51918318	7210665	105	11091											
TMC4	147798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54669261	54669261	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtagctggtcagagcctcGgactccgccagcagtgtctg	6	9	13	13	2	2	1	1	0	1	1	4	2	3	2	3	2	3	3	3	2	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:54669261G>T	ENST00000376591.4	-	6	986	c.855C>A	c.(853-855)tcC>tcA	p.S285S	TMC4_ENST00000476013.2_Intron|TMC4_ENST00000301187.4_Silent_p.S279S|TMC4_ENST00000416963.1_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	285					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCAGAGCCTCGGACTCCGCCA	0.652																																					p.S285S		.											.	TMC4-91	0			c.C855A						.						32	30	31					19																	54669261		2202	4299	6501	SO:0001819	synonymous_variant	147798	exon6			AGCCTCGGACTCC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.855C>A	19.37:g.54669261G>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	52	25	NM_001145303	0	0	10	14	4	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	37	CCDS46174.1																																																																																			.		0.652	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			T	54669261	G	T	54669261	2	4	126	1	0	0	0	0	0	0	0	1	16019	1103	39	4		4	TMC4	19	54669261	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	2750943	54669261	4459722	106	11092											
CSE1L	1434	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	47705894	47705895	+	Frame_Shift_Ins	INS	-	-	TT																															taaattttgaggaggctttgINStttttggtgtttactgaaat																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr20:47705894_47705895insTT	ENST00000262982.2	+	18	2055_2056	c.1932_1933insTT	c.(1933-1935)tttfs	p.F645fs	CSE1L_ENST00000396192.3_Frame_Shift_Ins_p.F589fs|CSE1L_ENST00000542325.1_Frame_Shift_Ins_p.F428fs	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	645					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AGGAGGCTTTGTTTTTGGTGTT	0.312																																					p.L644fs		.											.	CSE1L-290	0			c.1932_1933insTT						.																																			SO:0001589	frameshift_variant	1434	exon18			.	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.1935_1936dupTT	20.37:g.47705897_47705898dupTT	ENSP00000262982:p.Phe645fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	64	15	NM_001316	0	0	0	0	0	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Frame_Shift_Ins	INS	ENST00000262982.2	37	CCDS13412.1																																																																																			.		0.312	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		TT	47705895	-	TT	47705894	7	5	126	1	0	1	1	0	0	0	0	0	3936	1368	48	0	1998	0	CSE1L	20	47705894	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10		47705894	15319626	107	11093											
CASS4	57091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	55033659	55033659	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcctccgtggcagcagtcaCctctgcagcctgctcaagga	8	8	10	15	1	3	0	2	0	1	0	5	1	5	1	4	2	4	4	4	2	1	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr20:55033659C>A	ENST00000360314.3	+	7	2442	c.2217C>A	c.(2215-2217)caC>caA	p.H739Q	CASS4_ENST00000371336.3_Missense_Mutation_p.H739Q|CASS4_ENST00000434344.1_Missense_Mutation_p.H302Q|AL121914.1_ENST00000390795.2_RNA	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	739					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						GCAGCAGTCACCTCTGCAGCC	0.642																																					p.H739Q		.											.	CASS4-25	0			c.C2217A						.						61	50	53					20																	55033659		2203	4300	6503	SO:0001583	missense	57091	exon6			CAGTCACCTCTGC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"Cas scaffolding proteins"	15878	protein-coding gene	gene with protein product	"HEF-like protein", "HEF1-Efs-p130Cas-like"		"chromosome 20 open reading frame 32"	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.2217C>A	20.37:g.55033659C>A	ENSP00000353462:p.His739Gln	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	94	11	NM_020356	0	0	0	0	0	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.631149	0.28978	.	.	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.22336	1.96;1.96;1.96	5.91	1.54	0.23209	CAS family, DUF3513 (1);	0.511945	0.22918	N	0.054044	T	0.15305	0.0369	L	0.32530	0.975	0.32062	N	0.595525	B;B;B	0.22983	0.078;0.023;0.065	B;B;B	0.23275	0.045;0.013;0.033	T	0.18650	-1.0330	10	0.12430	T	0.62	-9.0912	15.118	0.72419	0.0882:0.3522:0.5595:0.0	.	685;302;739	B4DII4;Q9NQ75-3;Q9NQ75	.;.;CASS4_HUMAN	Q	739;739;302	ENSP00000353462:H739Q;ENSP00000360387:H739Q;ENSP00000410027:H302Q	ENSP00000353462:H739Q	H	+	3	2	CASS4	54467066	1.000000	0.71417	0.288000	0.24862	0.859000	0.49053	1.083000	0.30815	0.372000	0.24591	0.655000	0.94253	CAC	.		0.642	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		A	55033659	C	A	55033659	3	1	126	1	0	0	0	0	1	0	0	0	2689	506	18	4	2239	4	CASS4	20	55033659	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	7327765	55033659	7991861	108	11094											
SLCO4A1	28231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	61300283	61300283	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agtgggcttctctccgcaggGggcatcccggggcccatcgc	4	7	15	15	3	1	0	0	0	1	0	5	0	3	0	3	5	0	3	3	5	0	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr20:61300283G>A	ENST00000370507.1	+	10	1974	c.1878G>A	c.(1876-1878)ggG>ggA	p.G626G	RP11-93B14.5_ENST00000433126.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|SLCO4A1_ENST00000217159.1_Splice_Site_p.G626G|SLCO4A1_ENST00000470412.1_3'UTR|RP11-93B14.5_ENST00000451648.1_RNA			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	626					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TCTCCGCAGGGGGCATCCCGG	0.662											OREG0026115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G626G	Pancreas(168;741 2006 10379 40139 45334)	.											.	SLCO4A1-91	0			c.G1878A						.						29	32	31					20																	61300283		2202	4299	6501	SO:0001630	splice_region_variant	28231	exon11			CGCAGGGGGCATC	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"Solute carriers"	10953	protein-coding gene	gene with protein product		612436	"solute carrier family 21 (organic anion transporter), member 12"	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.1877-1G>A	20.37:g.61300283G>A		Somatic	19	0	1052	WXS	Illumina HiSeq	Phase_I	20	14	NM_016354	0	0	0	4	4	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Silent	SNP	ENST00000370507.1	37	CCDS13501.1																																																																																			.		0.662	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	Silent	A	61300283	G	A	61300283	5	1	126	1	0	0	0	0	0	0	1	0	14761	1246	43	2	1916	2	SLCO4A1	20	61300283	Splice_Site	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	6266624	61300283	1725237	109	11095											
KRTAP19-7	337974	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr21	31933587	31933587	+	Frame_Shift_Del	DEL	A	A	-																															gccgtagcctaggcctccatAgtagctgccggagtagctca																								rs149420565		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr21:31933587delA	ENST00000334849.2	-	1	46	c.22delT	c.(22-24)tatfs	p.Y8fs		NM_181614.1	NP_853645.1	Q3SYF9	KR197_HUMAN	keratin associated protein 19-7	8						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	11						AGGCCTCCATAGTAGCTGCCG	0.522																																					p.Y8fs		.											.	KRTAP19-7-68	0			c.22delT						.						123	106	111					21																	31933587		2203	4300	6503	SO:0001589	frameshift_variant	337974	exon1			.	AP001708	CCDS13599.1	21q22.1	2006-03-13			ENSG00000244362	ENSG00000244362		"Keratin associated proteins"	18942	protein-coding gene	gene with protein product						12359730	Standard	NM_181614		Approved	KAP19.7	uc011adb.2	Q3SYF9	OTTHUMG00000057785	ENST00000334849.2:c.22delT	21.37:g.31933587delA	ENSP00000334696:p.Tyr8fs	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	220	104	NM_181614	0	0	0	0	0	Q08EP7	Frame_Shift_Del	DEL	ENST00000334849.2	37	CCDS13599.1																																																																																			.		0.522	KRTAP19-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128237.2			-	31933587	A	-	31933587	7	5	126	1	0	1	0	1	0	0	0	0	8555	420	15	0	172	0	KRTAP19-7	21	31933587	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10		31933587	16196308	110	11096											
UMODL1	89766	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43547904	43547904	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacctgcactgcaaactccGcgtctgcatggaatcccccg	8	8	8	17	3	1	0	0	0	1	0	3	1	3	1	4	1	5	3	4	1	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr21:43547904G>T	ENST00000408910.2	+	20	3653	c.3653G>T	c.(3652-3654)cGc>cTc	p.R1218L	UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400427.1_Missense_Mutation_p.R1274L|UMODL1_ENST00000400424.2_Missense_Mutation_p.R1146L|UMODL1_ENST00000408989.2_Missense_Mutation_p.R1346L	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1218	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						TGCAAACTCCGCGTCTGCATG	0.468																																					p.R1346L	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)												.	UMODL1-93	0			c.G4037T						.						121	118	119					21																	43547904		1990	4169	6159	SO:0001583	missense	89766	exon19			AACTCCGCGTCTG		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"olfactorin"	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.3653G>T	21.37:g.43547904G>T	ENSP00000386147:p.Arg1218Leu	Somatic	201	1		WXS	Illumina HiSeq	Phase_I	245	103	NM_173568	0	0	0	0	0	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920955	0.33908	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000434156	D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7	3.56	3.56	0.40772	Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	0.157726	0.27052	N	0.021161	D	0.88514	0.6457	M	0.74881	2.28	0.09310	N	1	D;D	0.71674	0.996;0.998	P;D	0.69824	0.891;0.966	T	0.79004	-0.1980	9	.	.	.	-25.27	9.3757	0.38281	0.1022:0.0:0.8978:0.0	.	1346;1218	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	L	1274;1146;1346;1218;103	ENSP00000383279:R1274L;ENSP00000383276:R1146L;ENSP00000386126:R1346L;ENSP00000386147:R1218L	.	R	+	2	0	UMODL1	42420973	0.756000	0.28383	0.009000	0.14445	0.228000	0.25075	3.036000	0.49767	2.290000	0.77057	0.561000	0.74099	CGC	.		0.468	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43547904	G	T	43547904	3	4	126	1	0	0	0	0	1	0	0	0	17013	1087	38	4	4111	4	UMODL1	21	43547904	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	11614317	43547904	4581991	111	11097											
COL18A1	80781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46875643	46875643	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccacacacgtgacccccCggaatggttccacagagcca	11	4	8	18	2	0	2	0	1	0	1	1	3	1	3	7	2	1	1	7	2	1	1	rs375087150		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr21:46875643C>G	ENST00000359759.4	+	1	220	c.199C>G	c.(199-201)Cgg>Ggg	p.R67G	COL18A1_ENST00000355480.5_Missense_Mutation_p.R67G|COL18A1_ENST00000400337.2_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	67					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CGTGACCCCCCGGAATGGTTC	0.647																																					p.R67G		.											.	COL18A1-90	0			c.C199G						.						53	68	63					21																	46875643		2077	4200	6277	SO:0001583	missense	80781	exon1			ACCCCCCGGAATG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"Collagens"	2195	protein-coding gene	gene with protein product	"endostatin"	120328	"Knobloch syndrome, type 1"	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.199C>G	21.37:g.46875643C>G	ENSP00000352798:p.Arg67Gly	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	131	60	NM_030582	0	0	0	1	1	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		.	.	.	.	.	.	.	.	.	.	C	10.16	1.275053	0.23307	.	.	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.38077	1.16;1.16	3.61	0.181	0.15073	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	1.949970	0.03091	N	0.159750	T	0.22627	0.0546	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.28522	-1.0041	10	0.72032	D	0.01	.	4.007	0.09605	0.0:0.3657:0.3946:0.2397	.	67;67	P39060;P39060-1	COIA1_HUMAN;.	G	67	ENSP00000347665:R67G;ENSP00000352798:R67G	ENSP00000347665:R67G	R	+	1	2	COL18A1	45700071	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.084000	0.14891	0.253000	0.21552	-0.339000	0.08088	CGG	.		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			G	46875643	C	G	46875643	3	3	126	1	0	0	0	0	1	0	0	0	3681	643	23	4	315	4	COL18A1	21	46875643	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	3327739	46875643	1254252	112	11098											
GAB4	128954	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	17488934	17488934	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggggccacttccgggccacGaagacaaaggcgcaaatgcc	11	3	13	14	4	0	1	0	0	0	1	1	2	1	1	4	4	1	1	4	4	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr22:17488934G>A	ENST00000400588.1	-	1	178	c.71C>T	c.(70-72)tCg>tTg	p.S24L	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	24										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				TCCGGGCCACGAAGACAAAGG	0.682																																					p.S24L		.											.	GAB4-91	0			c.C71T						.						16	19	18					22																	17488934		2097	4219	6316	SO:0001583	missense	128954	exon1			GGCCACGAAGACA	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"Pleckstrin homology (PH) domain containing"	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.71C>T	22.37:g.17488934G>A	ENSP00000383431:p.Ser24Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	46	14	NM_001037814	0	0	0	0	0		Missense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.290327	0.23478	.	.	ENSG00000215568	ENST00000400588	T	0.10288	2.89	0.637	0.637	0.17735	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	P	0.44241	0.829	B	0.40134	0.32	T	0.37244	-0.9714	8	0.14656	T	0.56	.	.	.	.	.	24	Q2WGN9	GAB4_HUMAN	L	24	ENSP00000383431:S24L	ENSP00000383431:S24L	S	-	2	0	GAB4	15868934	0.001000	0.12720	0.007000	0.13788	0.022000	0.10575	-0.092000	0.11129	0.591000	0.29711	0.313000	0.20887	TCG	.		0.682	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		A	17488934	G	A	17488934	3	1	126	1	0	0	0	0	1	0	0	0	6170	1059	37	1	1693	1	GAB4	22	17488934	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		17488934	33815632	113	11099											
EP300	2033	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	41558757	41558757	+	Frame_Shift_Del	DEL	A	A	-																															aaagaacaattttccaagagAaaaaatgacacactggatcc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr22:41558757delA	ENST00000263253.7	+	21	4921	c.3702delA	c.(3700-3702)agafs	p.R1234fs		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1234					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.Y1198_L1243del(1)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TTTCCAAGAGAAAAAATGACA	0.368			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.R1234fs		.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300-2011	1	Deletion - In frame(1)	breast(1)	c.3702delA						.						120	114	116					22																	41558757		2203	4300	6503	SO:0001589	frameshift_variant	2033	exon21	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3702delA	22.37:g.41558757delA	ENSP00000263253:p.Arg1234fs	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	132	51	NM_001429	0	0	0	0	0	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	37	CCDS14010.1																																																																																			.		0.368	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41558757	A	-	41558757	7	5	126	1	0	1	0	1	0	0	0	0	5161	243	9	0	3784	0	EP300	22	41558757	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10	24069823	41558757	9745809	114	11100											
PADI4	23569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	17674521	17674521	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaacagaggcctgaaggAgtttcccatcaaacgcgtga	14	6	12	9	2	1	3	1	2	0	1	2	5	2	5	2	3	2	1	2	3	4	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:17674521A>T	ENST00000375448.4	+	10	1159	c.1133A>T	c.(1132-1134)gAg>gTg	p.E378V	AC004824.2_ENST00000602074.1_Intron|PADI4_ENST00000487048.1_3'UTR	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	378					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	GGCCTGAAGGAGTTTCCCATC	0.567																																					p.E378V		.											.	PADI4-70	0			c.A1133T						.						99	89	92					1																	17674521		2203	4300	6503	SO:0001583	missense	23569	exon10			TGAAGGAGTTTCC	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"Peptidyl arginine deiminases"	18368	protein-coding gene	gene with protein product		605347	"peptidyl arginine deiminase, type V"	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1133A>T	1.37:g.17674521A>T	ENSP00000364597:p.Glu378Val	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_012387	0	0	0	0	0	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	.	.	.	.	.	.	.	.	.	.	-	15.98	2.991445	0.54041	.	.	ENSG00000159339	ENST00000375448	T	0.25414	1.8	4.85	4.85	0.62838	Protein-arginine deiminase, C-terminal (1);	0.357378	0.28883	N	0.013830	T	0.23649	0.0572	N	0.13235	0.315	0.39431	D	0.967088	B;P	0.47191	0.04;0.891	B;P	0.51550	0.091;0.673	T	0.05920	-1.0856	10	0.41790	T	0.15	-11.7468	11.9518	0.52959	1.0:0.0:0.0:0.0	.	378;378	A8K392;Q9UM07	.;PADI4_HUMAN	V	378	ENSP00000364597:E378V	ENSP00000364597:E378V	E	+	2	0	PADI4	17547108	1.000000	0.71417	0.970000	0.41538	0.890000	0.51754	6.131000	0.71670	2.042000	0.60477	0.423000	0.28283	GAG	.		0.567	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		T	17674521	A	T	17674521	3	4	127	1	0	0	0	0	1	0	0	0	11406	304	11	5	1171	5	PADI4	1	17674521	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		17674521	231576100	1	11101											
ORC1L	4998	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	52849239	52849239	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgtgagtccacagaaggtcGagctgccagggcaaaggaga	12	6	15	8	1	0	3	0	1	0	2	2	5	1	3	2	3	2	2	2	3	2	1	rs201622141		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:52849239G>A	ENST00000371568.3	-	13	2084	c.1866C>T	c.(1864-1866)ctC>ctT	p.L622L	ORC1_ENST00000371566.1_Silent_p.L622L	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	622	Necessary and sufficient for ORC complex assembly.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ACAGAAGGTCGAGCTGCCAGG	0.493													G|||	1	0.000199681	0	0	5008	,	,		19901	0.001		0	False		,,,				2504	0				p.L622L													.	ORC1-206	0			c.C1866T						.						63	60	61					1																	52849239		2203	4300	6503	SO:0001819	synonymous_variant	4998	exon13			AAGGTCGAGCTGC		CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"ATPases / AAA-type"	8487	protein-coding gene	gene with protein product	"origin recognition complex, subunit 1, S. cerevisiae, homolog-like", "origin recognition complex 1", "replication control protein 1"	601902	"origin recognition complex, subunit 1 (yeast homolog)-like", "origin recognition complex, subunit 1-like (yeast)", "origin recognition complex, subunit 1 homolog (S. cerevisiae)"	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.1866C>T	1.37:g.52849239G>A		Somatic	196	1		WXS	Illumina HiSeq	Phase_I	152	47	NM_004153	0	0	0	0	0	D3DQ34|Q13471|Q5T0F5	Silent	SNP	ENST00000371568.3	37	CCDS566.1																																																																																			G|0.999;A|0.000		0.493	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		A	52849239	G	A	52849239	2	1	127	1	0	0	0	0	0	0	0	1	11287	1045	37	1		1	ORC1L	1	52849239	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	35174718	52849239	196401382	2	11102											
RWDD3	25950	ucsc.edu;bcgsc.ca	37	chr1	95710051	95710051	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccagaaactggcagtggcAgtgaaaagtgtactttttca	14	10	10	7	0	1	2	1	1	0	1	1	2	1	2	1	2	3	3	1	2	5	3	rs138509057		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:95710051A>T	ENST00000370202.4	+	2	446	c.370A>T	c.(370-372)Agt>Tgt	p.S124C	RP11-57H12.5_ENST00000444665.1_RNA|RP11-57H12.6_ENST00000604534.1_3'UTR|RWDD3_ENST00000429514.2_Missense_Mutation_p.S109C|RWDD3_ENST00000263893.6_Missense_Mutation_p.S124C|RWDD3_ENST00000495272.1_3'UTR	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	124					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S124R(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		TGGCAGTGGCAGTGAAAAGTG	0.438																																					p.S124C													.	RWDD3-91	1	Substitution - Missense(1)	large_intestine(1)	c.A370T						.						107	102	104					1																	95710051		1947	4130	6077	SO:0001583	missense	25950	exon2			AGTGGCAGTGAAA	BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.370A>T	1.37:g.95710051A>T	ENSP00000359221:p.Ser124Cys	Somatic	133	2		WXS	Illumina HiSeq		111	32	NM_001128142	0	0	11	19	8	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	37	CCDS41357.1	.	.	.	.	.	.	.	.	.	.	A	3.798	-0.042270	0.07452	.	.	ENSG00000122481	ENST00000370202;ENST00000429514;ENST00000263893	T;T;T	0.34859	1.34;1.38;1.35	5.38	-5.53	0.02552	.	1.677590	0.02325	N	0.073392	T	0.09202	0.0227	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B	0.11235	0.001;0.001;0.0;0.004;0.0	B;B;B;B;B	0.09377	0.001;0.001;0.0;0.004;0.001	T	0.27191	-1.0081	10	0.52906	T	0.07	0.4062	0.9194	0.01311	0.2608:0.2714:0.1228:0.345	.	109;124;124;109;124	E7ES73;Q9Y3V2;D3DT49;Q9Y3V2-3;Q9Y3V2-2	.;RWDD3_HUMAN;.;.;.	C	124;109;124	ENSP00000359221:S124C;ENSP00000397398:S109C;ENSP00000263893:S124C	ENSP00000263893:S124C	S	+	1	0	RWDD3	95482639	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.566000	0.05922	-0.478000	0.06823	-0.274000	0.10170	AGT	.		0.438	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485		T	95710051	A	T	95710051	3	4	127	1	0	0	0	0	1	0	0	0	13789	188	7	5	376	5	RWDD3	1	95710051	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	42860812	95710051	153540570	3	11103											
LPPR4	9890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	99764611	99764611	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttcatgtatttggattaTgctctacagctctcattaca	9	17	7	8	0	3	0	2	0	2	0	4	1	3	1	0	1	4	4	0	1	4	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:99764611T>C	ENST00000370185.3	+	4	1056	c.559T>C	c.(559-561)Tgc>Cgc	p.C187R	LPPR4_ENST00000457765.1_Missense_Mutation_p.C187R|LPPR4_ENST00000370184.1_Missense_Mutation_p.C29R	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		187					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		ATTTGGATTATGCTCTACAGC	0.363																																					p.C187R		.											.	LPPR4-93	0			c.T559C						.						150	133	138					1																	99764611		2203	4300	6503	SO:0001583	missense	0	exon4			GGATTATGCTCTA																												ENST00000370185.3:c.559T>C	1.37:g.99764611T>C	ENSP00000359204:p.Cys187Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	103	39	NM_001166252	0	0	0	0	0	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012287	0.75046	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178;ENST00000370184	T;T;T	0.52057	0.68;0.68;0.68	5.41	5.41	0.78517	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63920	0.2552	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.69636	-0.5092	10	0.72032	D	0.01	-30.56	15.7585	0.78058	0.0:0.0:0.0:1.0	.	187;187	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	R	187;187;187;29	ENSP00000359204:C187R;ENSP00000394913:C187R;ENSP00000359203:C29R	ENSP00000263178:C187R	C	+	1	0	RP4-788L13.1	99537199	1.000000	0.71417	0.955000	0.39395	0.578000	0.36192	6.235000	0.72332	2.191000	0.70037	0.528000	0.53228	TGC	.		0.363	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			C	99764611	T	C	99764611	3	2	127	1	0	0	0	0	1	0	0	0	8952	1464	51	3	573	3	LPPR4	1	99764611	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	4054560	99764611	149486010	4	11104											
NUP210L	91181	bcgsc.ca	37	chr1	154033034	154033034	+	Silent	SNP	T	T	C																															acctcaacagagctttctgcTtccatgtaagtgatggtgac																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154033034T>C	ENST00000368559.3	-	20	2903	c.2832A>G	c.(2830-2832)gaA>gaG	p.E944E	NUP210L_ENST00000271854.3_Silent_p.E944E	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	944					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			AGCTTTCTGCTTCCATGTAAG	0.433																																					p.E944E													.	NUP210L-77	0			c.A2832G						.						120	111	114					1																	154033034		1909	4135	6044	SO:0001819	synonymous_variant	91181	exon20			TTCTGCTTCCATG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2832A>G	1.37:g.154033034T>C		Somatic	100	0		WXS	Illumina HiSeq	Phase_1	64	14	NM_001159484	0	0	0	0	0	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Silent	SNP	ENST00000368559.3	37	CCDS41399.1																																																																																			.		0.433	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		C	154033034	T	C	154033034	2	2	127	1	0	0	0	0	0	0	0	1	10787	1606	56	3		3	NUP210L	1	154033034	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	54268423	154033034	95217587	5	11105	117	2									
NUP210L	91181	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	154033038	154033049	+	In_Frame_Del	DEL	ATGTAAGTGATG	ATGTAAGTGATG	-																															caacagagctttctgcttccAtgtaagtgatggtgacaaca																								rs368673993		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	ATGTAAGTGATG	ATGTAAGTGATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154033038_154033049delATGTAAGTGATG	ENST00000368559.3	-	20	2888_2899	c.2817_2828delCATCACTTACAT	c.(2815-2829)accatcacttacatg>acg	p.ITYM940del	NUP210L_ENST00000271854.3_In_Frame_Del_p.ITYM940del	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	940					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TTCTGCTTCCATGTAAGTGATGGTGACAACAC	0.415																																					p.939_943del		.											.	NUP210L-77	0			c.2817_2828del						.																																			SO:0001651	inframe_deletion	91181	exon20			.	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2817_2828delCATCACTTACAT	1.37:g.154033038_154033049delATGTAAGTGATG	ENSP00000357547:p.Ile940_Met943del	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	64	14	NM_001159484	0	0	0	0	0	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	In_Frame_Del	DEL	ENST00000368559.3	37	CCDS41399.1																																																																																			.		0.415	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		-	154033049	ATGTAAGTGATG	-	154033038	7	5	127	1	0	1	0	1	0	0	0	0	10787	217	8	0	2922	0	NUP210L	1	154033038	In_Frame_Del	DEL	ATGTAAGTGATG	TCGA-GL-A59T-01A-21D-A28G-10	4	154033038	95217583	6	11106	117	2									
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842253	154842253	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgctgaagctgcggaGgctgaggctgcagcgagggt	6	7	19	9	2	0	2	0	2	0	0	0	4	0	3	0	4	6	7	0	4	1	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		.											.	KCNN3-91	0			c.C188A						.						6	4	5					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	1.37:g.154842253G>T	ENSP00000271915:p.Pro63His	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	62	15	NM_001204087	0	0	0	0	0	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842253	G	T	154842253	3	4	127	1	0	0	0	0	1	0	0	0	8101	1000	35	4	2061	4	KCNN3	1	154842253	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	809215	154842253	94408368	7	11107											
THBS3	7059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155172114	155172114	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgtgtgcccttgtaccctcGaggacaggcctcacagtgga	7	9	12	13	1	1	0	1	0	0	0	2	3	1	2	3	3	2	1	3	3	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:155172114G>A	ENST00000368378.3	-	9	1056	c.1036C>T	c.(1036-1038)Cga>Tga	p.R346*	THBS3_ENST00000457183.2_Nonsense_Mutation_p.R226*|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000541990.1_5'UTR|THBS3_ENST00000541576.1_5'Flank|RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000453136.1_RNA	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	346	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TTGTACCCTCGAGGACAGGCC	0.602																																					p.R346X		.											.	THBS3-222	0			c.C1036T						.						96	90	92					1																	155172114		2203	4300	6503	SO:0001587	stop_gained	7059	exon9			ACCCTCGAGGACA	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1036C>T	1.37:g.155172114G>A	ENSP00000357362:p.Arg346*	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	151	41	NM_007112	0	0	4	5	1	B1AVR8|B4DQ20|Q8WV34	Nonsense_Mutation	SNP	ENST00000368378.3	37	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316567	0.95655	.	.	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	.	.	.	5.44	5.44	0.79542	.	0.674441	0.14773	N	0.299266	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	3.2614	16.8112	0.85720	0.0:0.0:1.0:0.0	.	.	.	.	X	346;226;196	.	ENSP00000357362:R346X	R	-	1	2	THBS3	153438738	0.461000	0.25783	0.082000	0.20525	0.937000	0.57800	3.403000	0.52615	2.837000	0.97791	0.655000	0.94253	CGA	.		0.602	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		A	155172114	G	A	155172114	4	1	127	1	0	0	0	0	0	1	0	0	15887	1066	37	1	1894	1	THBS3	1	155172114	Nonsense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	329861	155172114	94078507	8	11108											
NIT1	4817	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161089159	161089159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggtgggaaacttttggaaGaatacacccagcttgccagg	11	9	13	8	0	0	1	0	0	0	1	0	3	0	3	2	4	4	1	2	4	4	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:161089159G>A	ENST00000368009.2	+	3	410	c.334G>A	c.(334-336)Gaa>Aaa	p.E112K	PFDN2_ENST00000368010.3_5'Flank|NIT1_ENST00000496861.1_3'UTR|NIT1_ENST00000368007.4_Missense_Mutation_p.E97K|PFDN2_ENST00000468311.1_5'Flank|DEDD_ENST00000489249.1_5'Flank|NIT1_ENST00000392190.5_Missense_Mutation_p.E76K|NIT1_ENST00000368008.1_Missense_Mutation_p.E112K	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	112	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			ACTTTTGGAAGAATACACCCA	0.532											OREG0013937	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E112K													.	NIT1-90	0			c.G334A						.						49	51	50					1																	161089159		2203	4300	6503	SO:0001583	missense	4817	exon3			TTGGAAGAATACA	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.334G>A	1.37:g.161089159G>A	ENSP00000356988:p.Glu112Lys	Somatic	101	3	1814	WXS	Illumina HiSeq	Phase_I	64	20	NM_001185092	0	0	11	17	6	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	37	CCDS1218.1	.	.	.	.	.	.	.	.	.	.	G	8.049	0.765654	0.15983	.	.	ENSG00000158793	ENST00000368009;ENST00000368007;ENST00000368008;ENST00000392190	D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23	5.11	1.87	0.25490	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.588133	0.17579	N	0.169205	T	0.48732	0.1516	N	0.11845	0.185	0.20196	N	0.999928	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.12156	0.004;0.007;0.004	T	0.47381	-0.9122	10	0.05833	T	0.94	-0.6996	8.6096	0.33795	0.0961:0.5513:0.3526:0.0	.	97;112;112	Q86X76-4;B1AQP4;Q86X76	.;.;NIT1_HUMAN	K	112;97;112;76	ENSP00000356988:E112K;ENSP00000356986:E97K;ENSP00000356987:E112K;ENSP00000376028:E76K	ENSP00000356986:E97K	E	+	1	0	NIT1	159355783	0.124000	0.22315	0.998000	0.56505	0.944000	0.59088	0.460000	0.21924	0.629000	0.30376	0.655000	0.94253	GAA	.		0.532	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			A	161089159	G	A	161089159	3	1	127	1	0	0	0	0	1	0	0	0	10459	943	33	2	401	2	NIT1	1	161089159	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	5917045	161089159	88161462	9	11109											
PAPPA2	60676	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	176525851	176525851	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccggctgccccatgggtaggGgatagtcctattgggcaatc	7	9	14	11	1	0	0	0	0	0	0	2	1	1	1	4	5	1	3	4	5	4	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:176525851G>A	ENST00000367662.3	+	2	1557	c.393G>A	c.(391-393)ggG>ggA	p.G131G	PAPPA2_ENST00000367661.3_Silent_p.G131G	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	131					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CATGGGTAGGGGATAGTCCTA	0.537																																					p.G131G		.											.	PAPPA2-548	0			c.G393A						.						114	115	114					1																	176525851		2073	4228	6301	SO:0001819	synonymous_variant	60676	exon2			GGTAGGGGATAGT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"placenta-specific 3"	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.393G>A	1.37:g.176525851G>A		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	152	12	NM_021936	0	0	0	0	0	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																			.		0.537	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176525851	G	A	176525851	2	1	127	1	0	0	0	0	0	0	0	1	11459	1219	43	2		2	PAPPA2	1	176525851	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	15436692	176525851	72724770	10	11110											
SYT2	127833	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	202566051	202566052	+	Frame_Shift_Del	DEL	AG	AG	-																															ctatggcttcgttcttgcccAgcttgtcatagtccagcacg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:202566051_202566052delAG	ENST00000367267.1	-	9	1285_1286	c.1093_1094delCT	c.(1093-1095)ctgfs	p.L365fs	SYT2_ENST00000367268.4_Frame_Shift_Del_p.L365fs	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	365	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GTTCTTGCCCAGCTTGTCATAG	0.584																																					p.365_365del		.											.	SYT2-93	0			c.1093_1094del						.																																			SO:0001589	frameshift_variant	127833	exon9			.	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"Synaptotagmins"	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.1093_1094delCT	1.37:g.202566051_202566052delAG	ENSP00000356236:p.Leu365fs	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	122	32	NM_177402	0	0	0	0	0	Q496K5|Q8NBE5	Frame_Shift_Del	DEL	ENST00000367267.1	37	CCDS1427.1																																																																																			.		0.584	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		-	202566052	AG	-	202566051	7	5	127	1	0	1	0	1	0	0	0	0	15506	188	7	0	169	0	SYT2	1	202566051	Frame_Shift_Del	DEL	AG	TCGA-GL-A59T-01A-21D-A28G-10	26040200	202566051	46684570	11	11111											
AHCTF1	25909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247053281	247053281	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actataccttgataaacgctCaaacttctgtcgacgactgg	12	11	7	11	3	2	1	1	1	1	0	3	3	2	1	1	1	3	1	1	1	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:247053281C>T	ENST00000391829.2	-	17	2254	c.2131G>A	c.(2131-2133)Gag>Aag	p.E711K	AHCTF1_ENST00000326225.3_Missense_Mutation_p.E720K|AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Missense_Mutation_p.E746K			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	711	Necessary for cytoplasmic localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E711Q(1)		NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GATAAACGCTCAAACTTCTGT	0.338																																					p.E720K	Colon(145;197 1800 4745 15099 26333)	.											.	AHCTF1-97	1	Substitution - Missense(1)	urinary_tract(1)	c.G2158A						.						114	120	118					1																	247053281		2203	4300	6503	SO:0001583	missense	25909	exon17			AACGCTCAAACTT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.2131G>A	1.37:g.247053281C>T	ENSP00000375705:p.Glu711Lys	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	47	13	NM_015446	0	0	0	0	0	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		.	.	.	.	.	.	.	.	.	.	C	10.35	1.327003	0.24080	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.33438	1.41;1.41;1.41	5.61	3.62	0.41486	.	0.132552	0.52532	D	0.000063	T	0.33323	0.0859	M	0.63428	1.95	0.40661	D	0.982126	P;P	0.48503	0.911;0.605	B;B	0.43867	0.434;0.121	T	0.21211	-1.0252	10	0.34782	T	0.22	-9.9643	12.8931	0.58082	0.0:0.8042:0.1258:0.07	.	746;711	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	K	746;720;711	ENSP00000355464:E746K;ENSP00000355465:E720K;ENSP00000375705:E711K	ENSP00000355465:E720K	E	-	1	0	AHCTF1	245119904	1.000000	0.71417	0.890000	0.34922	0.002000	0.02628	3.403000	0.52615	1.379000	0.46325	0.579000	0.79373	GAG	.		0.338	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247053281	C	T	247053281	3	4	127	1	0	0	0	0	1	0	0	0	408	835	29	2	4749	2	AHCTF1	1	247053281	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	44487230	247053281	2197340	12	11112											
TTC15	51112	ucsc.edu;bcgsc.ca	37	chr2	3392363	3392363	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtggagtcctgcgggccgtGgccacccagcagcgcggcgc	4	4	17	16	6	0	0	0	0	0	0	1	1	1	1	4	4	3	1	4	4	0	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:3392363G>C	ENST00000324266.5	+	2	1164	c.969G>C	c.(967-969)gtG>gtC	p.V323V	TRAPPC12_ENST00000382110.2_Silent_p.V323V	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	323					vesicle-mediated transport (GO:0016192)												TGCGGGCCGTGGCCACCCAGC	0.682																																					p.V323V													.	.	0			c.G969C						.						26	24	25					2																	3392363		2200	4294	6494	SO:0001819	synonymous_variant	51112	exon2			GGCCGTGGCCACC	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"Trafficking protein particle complex", "Tetratricopeptide (TTC) repeat domain containing"	24284	protein-coding gene	gene with protein product		614139	"tetratricopeptide repeat domain 15"	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.969G>C	2.37:g.3392363G>C		Somatic	226	2		WXS	Illumina HiSeq		199	97	NM_016030	0	0	5	17	12	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1																																																																																			.		0.682	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		C	3392363	G	C	3392363	2	2	127	1	0	0	0	0	0	0	0	1	16715	1335	47	4		4	TTC15	2	3392363	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		3392363	239807010	13	11113											
DNMT3A	1788	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	25505312	25505312	+	Frame_Shift_Del	DEL	G	G	-																															ctggtgctgaggactcacccGcttctgcaggggctcctcgg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:25505312delG	ENST00000264709.3	-	4	783	c.446delC	c.(445-447)gcgfs	p.A149fs	DNMT3A_ENST00000406659.3_Frame_Shift_Del_p.A149fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.A149fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	149					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGACTCACCCGCTTCTGCAGG	0.637			"Mis, F, N, S"		AML																																p.A149fs		.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A-1924	0			c.446delC						.						14	17	16					2																	25505312		2202	4299	6501	SO:0001589	frameshift_variant	1788	exon4			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.446delC	2.37:g.25505312delG	ENSP00000264709:p.Ala149fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	146	67	NM_175630	0	0	0	0	0	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	37	CCDS33157.1																																																																																			.		0.637	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		-	25505312	G	-	25505312	7	5	127	1	0	1	0	1	0	0	0	0	4687	1087	38	0	2505	0	DNMT3A	2	25505312	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	22112949	25505312	217694061	14	11114											
ZC3H6	376940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	113089251	113089251	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagattatggaatacaaaaaGtgatcttcatcaaaatacag	19	11	6	5	0	3	2	2	1	1	1	3	3	3	3	0	1	2	0	0	1	9	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:113089251G>C	ENST00000409871.1	+	12	3157	c.2756G>C	c.(2755-2757)aGt>aCt	p.S919T	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Missense_Mutation_p.S919T	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	919							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AATACAAAAAGTGATCTTCAT	0.388																																					p.S919T		.											.	ZC3H6-93	0			c.G2756C						.						65	59	61					2																	113089251		1855	4101	5956	SO:0001583	missense	376940	exon12			CAAAAAGTGATCT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2756G>C	2.37:g.113089251G>C	ENSP00000386764:p.Ser919Thr	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	74	26	NM_198581	0	0	0	0	0	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	9.984	1.229069	0.22542	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.15487	2.42;2.42	5.94	5.06	0.68205	.	0.469384	0.26776	N	0.022560	T	0.14485	0.0350	L	0.54323	1.7	0.22389	N	0.999144	P	0.35433	0.501	B	0.26770	0.073	T	0.19679	-1.0298	10	0.39692	T	0.17	-2.4342	9.1318	0.36850	0.2286:0.0:0.7714:0.0	.	919	P61129	ZC3H6_HUMAN	T	919	ENSP00000386764:S919T;ENSP00000340298:S919T	ENSP00000340298:S919T	S	+	2	0	ZC3H6	112805722	0.931000	0.31567	0.994000	0.49952	0.985000	0.73830	1.552000	0.36244	1.512000	0.48834	0.591000	0.81541	AGT	.		0.388	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		C	113089251	G	C	113089251	3	2	127	1	0	0	0	0	1	0	0	0	17603	1029	36	4	2802	4	ZC3H6	2	113089251	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	87583939	113089251	130110122	15	11115											
FAP	2191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	163046173	163046173	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaagatcttactaatttcAtctacttcaagtttcttaat	14	18	2	7	0	5	1	2	0	3	1	5	1	5	1	0	0	2	1	0	0	7	8			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:163046173A>G	ENST00000188790.4	-	18	1749	c.1542T>C	c.(1540-1542)gaT>gaC	p.D514D	FAP_ENST00000443424.1_Silent_p.D489D	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TACTAATTTCATCTACTTCAA	0.284																																					p.D514D		.											.	FAP-93	0			c.T1542C						.						58	59	58					2																	163046173		2190	4274	6464	SO:0001819	synonymous_variant	2191	exon18			AATTTCATCTACT	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1542T>C	2.37:g.163046173A>G		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	84	50	NM_004460	0	0	0	0	0		Silent	SNP	ENST00000188790.4	37	CCDS33311.1																																																																																			.		0.284	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			G	163046173	A	G	163046173	2	3	127	1	0	0	0	0	0	0	0	1	5692	214	8	3		3	FAP	2	163046173	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	49956922	163046173	80153200	16	11116											
LRP2	4036	broad.mit.edu	37	chr2	170096143	170096143	+	Frame_Shift_Del	DEL	A	A	-																															tgctggctacaagagcctagAatatcacattcatctatgtc																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:170096143delA	ENST00000263816.3	-	26	4473	c.4188delT	c.(4186-4188)attfs	p.I1396fs		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1396	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AAGAGCCTAGAATATCACATT	0.438																																					p.I1396fs													.	LRP2-175	0			c.4188delT						.						145	138	141					2																	170096143		2203	4300	6503	SO:0001589	frameshift_variant	4036	exon26			GCCTAGAATATCA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.4188delT	2.37:g.170096143delA	ENSP00000263816:p.Ile1396fs	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	213	15	NM_004525	0	0	0	0	0	O00711|Q16215	Frame_Shift_Del	DEL	ENST00000263816.3	37	CCDS2232.1																																																																																			.		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170096143	A	-	170096143	7	5	127	1	0	1	0	1	0	0	0	0	8981	242	9	0	9995	0	LRP2	2	170096143	Frame_Shift_Del	DEL	A	TCGA-GL-A59T-01A-21D-A28G-10	7049970	170096143	73103230	17	11117											
FN1	2335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	216232592	216232592	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcaactactcactagatgAatcacatctgaaatgaccac	17	8	5	11	0	3	4	2	3	1	1	3	4	3	4	1	0	3	1	1	0	6	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:216232592A>G	ENST00000359671.1	-	41	7004	c.6739T>C	c.(6739-6741)Tca>Cca	p.S2247P	FN1_ENST00000357867.4_Missense_Mutation_p.S2037P|FN1_ENST00000356005.4_Missense_Mutation_p.S2157P|FN1_ENST00000443816.1_Missense_Mutation_p.S2126P|FN1_ENST00000323926.6_Missense_Mutation_p.S2307P|FN1_ENST00000354785.4_Missense_Mutation_p.S2338P|FN1_ENST00000336916.4_Missense_Mutation_p.S2216P|FN1_ENST00000432072.2_Missense_Mutation_p.S2128P|FN1_ENST00000346544.3_Intron|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000421182.1_Missense_Mutation_p.S2101P|FN1_ENST00000345488.5_Missense_Mutation_p.S2045P|FN1_ENST00000446046.1_Missense_Mutation_p.S2191P			P02751	FINC_HUMAN	fibronectin 1	2247	Fibrin-binding 2.|Fibronectin type-I 10. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TCACTAGATGAATCACATCTG	0.458																																					p.S2338P		.											.	FN1-584	0			c.T7012C						.						115	90	98					2																	216232592		2203	4300	6503	SO:0001583	missense	2335	exon42			TAGATGAATCACA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6739T>C	2.37:g.216232592A>G	ENSP00000352696:p.Ser2247Pro	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	155	50	NM_212482	0	0	0	3	3	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	A	20.4	3.977481	0.74360	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000345488;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T	0.66638	-0.22;1.16;1.37;-0.05;1.65;1.31;1.1;1.08;0.57;-0.11;0.61;0.54	5.67	5.67	0.87782	Fibronectin, type I (2);Complement control module (1);	0.000000	0.56097	D	0.000034	T	0.79811	0.4510	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;0.992;1.0;0.992;0.995;0.995;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.998;0.989;0.998;0.993;0.985;0.999;0.985;0.993;0.993;0.998;0.995	T	0.80269	-0.1453	10	0.49607	T	0.09	.	15.8986	0.79356	1.0:0.0:0.0:0.0	.	2128;2307;2037;2157;2191;2216;2248;2101;2126;2338;2247	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15;P02751	.;.;.;.;.;.;.;.;.;.;FINC_HUMAN	P	2101;2307;2216;2037;2338;2248;2247;2045;2191;2126;2128;2157;964	ENSP00000394423:S2101P;ENSP00000323534:S2307P;ENSP00000338200:S2216P;ENSP00000350534:S2037P;ENSP00000346839:S2338P;ENSP00000352696:S2247P;ENSP00000273049:S2045P;ENSP00000410422:S2191P;ENSP00000415018:S2126P;ENSP00000399538:S2128P;ENSP00000348285:S2157P;ENSP00000416139:S964P	ENSP00000265313:S2248P	S	-	1	0	FN1	215940837	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.156000	0.67533	0.477000	0.44152	TCA	.		0.458	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		G	216232592	A	G	216232592	3	3	127	1	0	0	0	0	1	0	0	0	5981	246	9	3	441	3	FN1	2	216232592	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	46136449	216232592	26966781	18	11118											
CHPF	79586	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220406754	220406754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccatgccaggtggggcccGgcggccccgtgcgcccgtca	3	5	16	17	5	1	0	1	0	0	0	1	0	1	0	6	5	3	0	6	5	0	0	rs571316585		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:220406754G>A	ENST00000243776.6	-	2	720	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	CHPF_ENST00000535926.1_5'UTR|TMEM198_ENST00000344458.2_5'Flank|TMEM198_ENST00000373883.3_5'Flank|CHPF_ENST00000373891.2_Missense_Mutation_p.R158W	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	158					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GGTGGGGCCCGGCGGCCCCGT	0.721											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R158W													.	CHPF-90	0			c.C472T						.						12	12	12					2																	220406754		2186	4288	6474	SO:0001583	missense	79586	exon2			GGGCCCGGCGGCC	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.472C>T	2.37:g.220406754G>A	ENSP00000243776:p.Arg158Trp	Somatic	103	0	2266	WXS	Illumina HiSeq	Phase_I	83	6	NM_024536	0	0	33	39	6	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Missense_Mutation	SNP	ENST00000243776.6	37	CCDS2443.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332252	0.81801	.	.	ENSG00000123989	ENST00000243776;ENST00000373891	T	0.12672	2.66	4.28	2.28	0.28536	.	0.155094	0.42294	D	0.000738	T	0.16128	0.0388	N	0.12182	0.205	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.63488	0.915;0.908	T	0.07139	-1.0788	10	0.66056	D	0.02	-28.0341	10.855	0.46794	0.0:0.0:0.4172:0.5828	.	158;158	F8W6H2;Q8IZ52	.;CHSS2_HUMAN	W	158	ENSP00000243776:R158W	ENSP00000243776:R158W	R	-	1	2	CHPF	220114998	1.000000	0.71417	0.993000	0.49108	0.976000	0.68499	3.858000	0.55979	1.135000	0.42183	0.448000	0.29417	CGG	.		0.721	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		A	220406754	G	A	220406754	3	1	127	1	0	0	0	0	1	0	0	0	3374	1115	39	1	1867	1	CHPF	2	220406754	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	4174162	220406754	22792619	19	11119											
EFHD1	80303	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	233498655	233498656	+	Frame_Shift_Ins	INS	-	-	AC																															ctgcagggtcttcaacccctINSacacggagttcccggagttc																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:233498655_233498656insAC	ENST00000264059.3	+	1	718_719	c.241_242insAC	c.(241-243)tacfs	p.Y81fs	EFHD1_ENST00000409613.1_Intron	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	81					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		CTTCAACCCCTACACGGAGTTC	0.708																																					p.Y81fs		.											.	EFHD1-90	0			c.241_242insAC						.																																			SO:0001589	frameshift_variant	80303	exon1			.		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"EF-hand domain containing"	29556	protein-coding gene	gene with protein product	"swiprosin-2"	611617	"EF hand domain containing 1"			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.244_245dupAC	2.37:g.233498658_233498659dupAC	ENSP00000264059:p.Tyr81fs	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	28	13	NM_025202	0	0	0	0	0	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Frame_Shift_Ins	INS	ENST00000264059.3	37	CCDS2497.1																																																																																			.		0.708	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202		AC	233498656	-	AC	233498655	7	5	127	1	0	1	1	0	0	0	0	0	4959	1522	53	0	243	0	EFHD1	2	233498655	Frame_Shift_Ins	INS	-	TCGA-GL-A59T-01A-21D-A28G-10	13091901	233498655	9700718	20	11120											
HJURP	55355	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234749356	234749356	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattgccctggcgtccggaGccctggggttctgatagcct	5	10	14	12	2	1	1	0	1	1	0	2	3	2	2	4	4	3	1	4	4	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:234749356G>C	ENST00000411486.2	-	8	2135	c.2070C>G	c.(2068-2070)ggC>ggG	p.G690G	HJURP_ENST00000441687.1_Silent_p.G605G|HJURP_ENST00000432087.1_Silent_p.G636G|HJURP_ENST00000434039.1_5'Flank	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	690					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GGCGTCCGGAGCCCTGGGGTT	0.592																																					p.G690G													.	HJURP-69	0			c.C2070G						.						83	86	85					2																	234749356		2203	4300	6503	SO:0001819	synonymous_variant	55355	exon8			TCCGGAGCCCTGG		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.2070C>G	2.37:g.234749356G>C		Somatic	85	1		WXS	Illumina HiSeq	Phase_I	113	57	NM_018410	0	0	0	0	0	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Silent	SNP	ENST00000411486.2	37	CCDS33406.1																																																																																			.		0.592	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		C	234749356	G	C	234749356	2	2	127	1	0	0	0	0	0	0	0	1	7210	958	34	4		4	HJURP	2	234749356	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	1250701	234749356	8450017	21	11121											
CNTN4	152330	broad.mit.edu	37	chr3	3080674	3080675	+	Frame_Shift_Ins	INS	-	-	TA																															ggcagcaaatctgaactggtINStataacctgggaggtaaatg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:3080674_3080675insTA	ENST00000397461.1	+	18	2534_2535	c.2150_2151insTA	c.(2149-2154)gttatafs	p.VI717fs	CNTN4_ENST00000427331.1_Frame_Shift_Ins_p.VI717fs|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000448906.2_Frame_Shift_Ins_p.VI389fs|CNTN4_ENST00000397459.2_Frame_Shift_Ins_p.VI389fs|CNTN4_ENST00000418658.1_Frame_Shift_Ins_p.VI717fs|CNTN4_ENST00000358480.3_Frame_Shift_Ins_p.VI498fs	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	717	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TCTGAACTGGTTATAACCTGGG	0.45																																					p.V717fs													.	CNTN4-344	0			c.2150_2151insTA						.																																			SO:0001589	frameshift_variant	152330	exon19			AACTGGTTATAAC	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2153_2154dupTA	3.37:g.3080677_3080678dupTA	ENSP00000380602:p.Val717fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	158	10	NM_175607	0	0	0	0	0	B2RAX3|Q8IX14|Q8TC35	Frame_Shift_Ins	INS	ENST00000397461.1	37	CCDS43041.1																																																																																			.		0.45	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			TA	3080675	-	TA	3080674	7	5	127	1	0	1	1	0	0	0	0	0	3649	1725	60	0	2212	0	CNTN4	3	3080674	Frame_Shift_Ins	INS	-	TCGA-GL-A59T-01A-21D-A28G-10		3080674	194941756	22	11122											
FBXL2	25827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	33415410	33415410	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcctcaacttgcagtcctgCtcagtaagtagcgtgccttt	8	12	9	12	1	2	0	2	0	0	0	3	0	3	0	3	0	6	4	3	0	3	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:33415410C>T	ENST00000484457.1	+	9	745	c.654C>T	c.(652-654)tgC>tgT	p.C218C	FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000538892.1_Silent_p.C150C|FBXL2_ENST00000446237.3_5'UTR|FBXL2_ENST00000507198.1_Silent_p.C150C|FBXL2_ENST00000542085.1_5'UTR|FBXL2_ENST00000538181.1_Silent_p.C134C	NM_012157.3	NP_036289.3			F-box and leucine-rich repeat protein 2											endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|urinary_tract(1)	15						TGCAGTCCTGCTCAGTAAGTA	0.498																																					p.C218C		.											.	FBXL2-289	0			c.C654T						.						152	145	147					3																	33415410		2203	4300	6503	SO:0001819	synonymous_variant	25827	exon9			GTCCTGCTCAGTA	AF174589	CCDS2658.1, CCDS54560.1	3p22.3	2011-06-09			ENSG00000153558	ENSG00000153558		"F-boxes / Leucine-rich repeats"	13598	protein-coding gene	gene with protein product		605652				10508920, 10531035	Standard	NM_012157		Approved	FBL2, FBL3	uc003cfp.3	Q9UKC9	OTTHUMG00000130745	ENST00000484457.1:c.654C>T	3.37:g.33415410C>T		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	139	64	NM_012157	0	0	0	0	0		Silent	SNP	ENST00000484457.1	37	CCDS2658.1																																																																																			.		0.498	FBXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253245.2	NM_012157		T	33415410	C	T	33415410	2	4	127	1	0	0	0	0	0	0	0	1	5735	805	28	2		2	FBXL2	3	33415410	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	30334736	33415410	164607020	23	11123											
CCDC66	285331	broad.mit.edu	37	chr3	56649978	56649978	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacaaatggaatataatgcAtctaacatttcaaattcaag	19	12	4	6	0	3	0	2	0	1	0	3	1	3	1	0	1	3	1	0	1	8	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:56649978A>C	ENST00000394672.3	+	13	1810	c.1740A>C	c.(1738-1740)gcA>gcC	p.A580A	CCDC66_ENST00000436465.2_Silent_p.A580A|CCDC66_ENST00000326595.7_Silent_p.A546A	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	580					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		AATATAATGCATCTAACATTT	0.294																																					p.A580A													.	CCDC66-135	0			c.A1740C						.						73	78	76					3																	56649978		2203	4294	6497	SO:0001819	synonymous_variant	285331	exon13			TAATGCATCTAAC	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1740A>C	3.37:g.56649978A>C		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	46	7	NM_001141947	0	0	1	3	2	B3KWL8|Q4VC34|Q8N949	Silent	SNP	ENST00000394672.3	37	CCDS46852.1																																																																																			.		0.294	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		C	56649978	A	C	56649978	2	2	127	1	0	0	0	0	0	0	0	1	2844	204	8	5		5	CCDC66	3	56649978	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	23234568	56649978	141372452	24	11124											
QTRTD1	79691	broad.mit.edu	37	chr3	113795754	113795754	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctagactacgcttgctgtcAtcagtcactgcagagctgcc	8	10	10	13	1	3	2	3	0	0	2	3	2	3	2	1	0	5	5	1	0	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:113795754A>G	ENST00000493014.1	+	3	461	c.393A>G	c.(391-393)tcA>tcG	p.S131S	QTRTD1_ENST00000479882.1_Silent_p.S114S|QTRTD1_ENST00000485050.1_Silent_p.S249S|QTRTD1_ENST00000281273.4_Silent_p.S237S	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						GCTTGCTGTCATCAGTCACTG	0.577																																					p.S249S													.	QTRTD1-91	0			c.A747G						.						68	55	59					3																	113795754		2203	4300	6503	SO:0001819	synonymous_variant	79691	exon6			GCTGTCATCAGTC	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.393A>G	3.37:g.113795754A>G		Somatic	190	1		WXS	Illumina HiSeq	Phase_I	226	4	NM_001256835	0	0	3	3	0		Silent	SNP	ENST00000493014.1	37	CCDS58845.1																																																																																			.		0.577	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638		G	113795754	A	G	113795754	2	3	127	1	0	0	0	0	0	0	0	1	12918	204	8	3		3	QTRTD1	3	113795754	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	57145776	113795754	84226676	25	11125											
PARP14	54625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122437696	122437696	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagagaaaagaaaaaaacAgttgatgtcaaaattaatca	23	7	8	3	0	2	3	2	1	0	2	2	5	2	4	0	1	1	1	0	1	8	2	rs377210300		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:122437696A>G	ENST00000474629.2	+	14	4964	c.4698A>G	c.(4696-4698)acA>acG	p.T1566T	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1566	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		AGAAAAAAACAGTTGATGTCA	0.373																																					p.T1566T		.											.	PARP14-525	0			c.A4698G						.	A		0,3790		0,0,1895	88	87	87		4698	-5.7	0	3		87	1,8247		0,1,4123	no	coding-synonymous	PARP14	NM_017554.2		0,1,6018	GG,GA,AA		0.0121,0.0,0.0083		1566/1802	122437696	1,12037	1895	4124	6019	SO:0001819	synonymous_variant	54625	exon14			AAAAACAGTTGAT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4698A>G	3.37:g.122437696A>G		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	150	39	NM_017554	0	0	11	15	4	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			.		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122437696	A	G	122437696	2	3	127	1	0	0	0	0	0	0	0	1	11484	175	7	3		3	PARP14	3	122437696	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	8641942	122437696	75584734	26	11126											
UBA5	79876	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132379518	132379518	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcgagaagatgagctcagAggtggtggattcgaatccct	11	9	13	8	2	1	4	1	1	0	3	4	7	2	5	1	3	1	1	1	3	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:132379518A>T	ENST00000356232.4	+	1	1209	c.137A>T	c.(136-138)gAg>gTg	p.E46V	UBA5_ENST00000473651.1_Missense_Mutation_p.E46V|ACAD11_ENST00000355458.3_5'Flank|UBA5_ENST00000493720.2_Missense_Mutation_p.E46V|ACAD11_ENST00000481970.2_5'Flank|UBA5_ENST00000480955.1_3'UTR|ACAD11_ENST00000489991.1_5'Flank|UBA5_ENST00000494238.2_De_novo_Start_OutOfFrame|ACAD11_ENST00000545291.1_5'Flank|ACAD11_ENST00000264990.6_5'UTR|UBA5_ENST00000264991.4_Intron	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	46					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|UFM1 activating enzyme activity (GO:0071566)			breast(2)|endometrium(4)|kidney(4)|large_intestine(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						ATGAGCTCAGAGGTGGTGGAT	0.672																																					p.E46V													.	UBA5-226	0			c.A137T						.						35	36	36					3																	132379518		2177	4271	6448	SO:0001583	missense	79876	exon1			GCTCAGAGGTGGT	AY253672	CCDS3076.1, CCDS3077.1	3q22	2007-11-30	2007-11-30	2007-11-30	ENSG00000081307	ENSG00000081307		"Ubiquitin-like modifier activating enzymes"	23230	protein-coding gene	gene with protein product	"UBA5, ubiquitin-activating enzyme E1 homolog (yeast)"	610552	"ubiquitin-activating enzyme E1-domain containing 1"	UBE1DC1		11230166, 15071506	Standard	NM_198329		Approved	FLJ23251	uc003epa.4	Q9GZZ9	OTTHUMG00000159759	ENST00000356232.4:c.137A>T	3.37:g.132379518A>T	ENSP00000348565:p.Glu46Val	Somatic	264	2		WXS	Illumina HiSeq	Phase_I	359	171	NM_024818	0	0	7	17	10	A6NJL3|D3DNC8|Q96ST1	Missense_Mutation	SNP	ENST00000356232.4	37	CCDS3076.1	.	.	.	.	.	.	.	.	.	.	A	32	5.173474	0.94807	.	.	ENSG00000081307	ENST00000356232;ENST00000493720;ENST00000473651	D;D;D	0.85171	-1.95;-1.93;-1.89	4.83	4.83	0.62350	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.82453	0.5040	M	0.67700	2.07	0.80722	D	1	B;P	0.38922	0.196;0.651	B;B	0.35039	0.141;0.194	D	0.84018	0.0352	10	0.52906	T	0.07	-8.3735	13.1245	0.59346	1.0:0.0:0.0:0.0	.	46;46	E7EWE1;Q9GZZ9	.;UBA5_HUMAN	V	46	ENSP00000348565:E46V;ENSP00000417879:E46V;ENSP00000424984:E46V	ENSP00000348565:E46V	E	+	2	0	UBA5	133862208	1.000000	0.71417	0.998000	0.56505	0.918000	0.54935	7.126000	0.77201	2.029000	0.59856	0.459000	0.35465	GAG	.		0.672	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818		T	132379518	A	T	132379518	3	4	127	1	0	0	0	0	1	0	0	0	16863	304	11	5	139	5	UBA5	3	132379518	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	9941822	132379518	65642912	27	11127											
STAG1	10274	broad.mit.edu	37	chr3	136183765	136183765	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccacagcaacagggcgaTgtgccgagtacaccaagtgg	11	5	13	12	2	0	0	0	0	0	0	0	2	0	0	3	2	5	2	3	2	3	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:136183765T>C	ENST00000383202.2	-	13	1527	c.1271A>G	c.(1270-1272)cAt>cGt	p.H424R	STAG1_ENST00000236698.5_Missense_Mutation_p.H424R|STAG1_ENST00000536929.1_Intron|STAG1_ENST00000434713.2_Missense_Mutation_p.H198R	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	424					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						AACAGGGCGATGTGCCGAGTA	0.393																																					p.H424R													.	STAG1-228	0			c.A1271G						.						75	69	71					3																	136183765		2203	4300	6503	SO:0001583	missense	10274	exon13			GGGCGATGTGCCG	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.1271A>G	3.37:g.136183765T>C	ENSP00000372689:p.His424Arg	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	60	4	NM_005862	0	0	0	0	0	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.922940	0.73213	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713	T;T;T	0.32753	1.44;1.44;1.44	5.51	5.51	0.81932	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.47358	0.1441	M	0.70903	2.155	0.80722	D	1	B;D;B	0.52996	0.386;0.957;0.386	B;P;B	0.54499	0.175;0.754;0.175	T	0.40459	-0.9562	10	0.32370	T	0.25	.	15.615	0.76760	0.0:0.0:0.0:1.0	.	441;424;424	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	R	424;424;198	ENSP00000372689:H424R;ENSP00000236698:H424R;ENSP00000404396:H198R	ENSP00000236698:H424R	H	-	2	0	STAG1	137666455	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.036000	0.88901	2.091000	0.63221	0.477000	0.44152	CAT	.		0.393	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		C	136183765	T	C	136183765	3	2	127	1	0	0	0	0	1	0	0	0	15274	1464	51	3	2593	3	STAG1	3	136183765	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	3804247	136183765	61838665	28	11128											
SMC4	10051	bcgsc.ca	37	chr3	160119803	160119803	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaatgaagctggagctccTcggcttatgataactcatat	12	11	8	10	1	1	2	1	2	0	0	3	3	2	3	2	2	3	3	2	2	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:160119803T>C	ENST00000357388.3	+	3	691	c.240T>C	c.(238-240)ccT>ccC	p.P80P	SMC4_ENST00000469762.1_Silent_p.P55P|MIR16-2_ENST00000362117.1_RNA|SMC4_ENST00000344722.5_Silent_p.P80P|IFT80_ENST00000477495.1_5'Flank|SMC4_ENST00000462787.1_Silent_p.P80P|IFT80_ENST00000496589.1_5'Flank|IFT80_ENST00000326448.7_5'Flank|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000360111.2_Silent_p.P80P|MIR15B_ENST00000385045.1_RNA	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	80					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CTGGAGCTCCTCGGCTTATGA	0.413																																					p.P80P													.	SMC4-291	0			c.T240C						.						70	79	76					3																	160119803		2203	4300	6503	SO:0001819	synonymous_variant	10051	exon2			AGCTCCTCGGCTT	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"Structural maintenance of chromosomes proteins"	14013	protein-coding gene	gene with protein product		605575	"SMC4 (structural maintenance of chromosomes 4, yeast)-like 1", "SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.240T>C	3.37:g.160119803T>C		Somatic	47	0		WXS	Illumina HiSeq	Phase_1	51	4	NM_005496	0	0	0	0	0	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Silent	SNP	ENST00000357388.3	37	CCDS3189.1																																																																																			.		0.413	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			C	160119803	T	C	160119803	2	2	127	1	0	0	0	0	0	0	0	1	14817	1538	54	3		3	SMC4	3	160119803	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	23936038	160119803	37902627	29	11129											
NDUFB5	4711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179322636	179322636	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtttgttgcggcgggtttcGgttactgcggtggcagctct	3	14	16	8	4	1	0	0	0	1	0	2	0	1	0	0	5	4	6	0	5	1	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:179322636G>A	ENST00000259037.3	+	1	147	c.33G>A	c.(31-33)tcG>tcA	p.S11S	NDUFB5_ENST00000493866.1_Silent_p.S11S|NDUFB5_ENST00000472629.1_Silent_p.S11S|MRPL47_ENST00000392659.2_5'Flank|MRPL47_ENST00000476781.1_5'Flank|MRPL47_ENST00000259038.2_5'Flank	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	11					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			GGCGGGTTTCGGTTACTGCGG	0.617																																					p.S11S		.											.	NDUFB5-91	0			c.G33A						.						36	36	36					3																	179322636		2203	4300	6503	SO:0001819	synonymous_variant	4711	exon1			GGTTTCGGTTACT	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"Mitochondrial respiratory chain complex / Complex I"	7700	protein-coding gene	gene with protein product	"complex I SGDH subunit"	603841	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.33G>A	3.37:g.179322636G>A		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	107	34	NM_002492	0	0	1	20	19	Q561V6	Silent	SNP	ENST00000259037.3	37	CCDS3234.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903796	0.52333	.	.	ENSG00000136521	ENST00000482604	.	.	.	5.75	1.95	0.26073	.	.	.	.	.	T	0.56093	0.1962	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48340	-0.9044	5	0.40728	T	0.16	-3.1698	6.2744	0.20973	0.2212:0.1325:0.6463:0.0	.	.	.	.	Q	8	.	ENSP00000419099:R3Q	R	+	2	0	NDUFB5	180805330	0.998000	0.40836	0.993000	0.49108	0.016000	0.09150	0.145000	0.16157	0.148000	0.19059	-0.133000	0.14855	CGG	.		0.617	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492		A	179322636	G	A	179322636	2	1	127	1	0	0	0	0	0	0	0	1	10310	1103	39	1		1	NDUFB5	3	179322636	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	19202833	179322636	18699794	30	11130											
KLHL6	89857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183226047	183226047	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacccagctcatcacggtctCaaacacctgagcctcctcgg	9	7	8	17	2	3	1	3	1	1	0	6	2	4	1	4	2	3	1	4	2	1	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:183226047C>T	ENST00000341319.3	-	3	744	c.709G>A	c.(709-711)Gag>Aag	p.E237K		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	237	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			ATCACGGTCTCAAACACCTGa	0.547																																					p.E237K		.											.	KLHL6-93	0			c.G709A						.						135	114	121					3																	183226047		2203	4300	6503	SO:0001583	missense	89857	exon3			CGGTCTCAAACAC	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"Kelch-like", "BTB/POZ domain containing"	18653	protein-coding gene	gene with protein product	"kelch-like protein KLHL6"	614214	"kelch-like 6 (Drosophila)"			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.709G>A	3.37:g.183226047C>T	ENSP00000341342:p.Glu237Lys	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	277	69	NM_130446	0	0	0	0	0	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	36	5.904004	0.97087	.	.	ENSG00000172578	ENST00000341319	T	0.69685	-0.42	5.87	5.87	0.94306	BTB/Kelch-associated (2);	0.043908	0.85682	D	0.000000	D	0.83083	0.5177	M	0.79343	2.45	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.82400	-0.0476	10	0.54805	T	0.06	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	237	Q8WZ60	KLHL6_HUMAN	K	237	ENSP00000341342:E237K	ENSP00000341342:E237K	E	-	1	0	KLHL6	184708741	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.941000	0.99782	0.655000	0.94253	GAG	.		0.547	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		T	183226047	C	T	183226047	3	4	127	1	0	0	0	0	1	0	0	0	8414	835	29	2	1176	2	KLHL6	3	183226047	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	3903411	183226047	14796383	31	11131											
TMPRSS11F	389208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	68930403	68930403	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attaggttgaaactgctcacCatcatctacaatggatccaa	14	11	6	10	0	3	1	2	1	1	0	4	2	4	2	2	2	3	2	2	2	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:68930403C>A	ENST00000356291.2	-	8	1074	c.1015G>T	c.(1015-1017)Gga>Tga	p.G339*	RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	339	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						AACTGCTCACCATCATCTACA	0.363																																					p.G339X		.											.	TMPRSS11F-91	0			c.G1015T						.						68	68	68					4																	68930403		2203	4300	6503	SO:0001630	splice_region_variant	389208	exon8			GCTCACCATCATC	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"Serine peptidases / Transmembrane"	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.1015+1G>T	4.37:g.68930403C>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	40	14	NM_207407	0	0	0	0	0	A8MXX2	Nonsense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	37	6.372005	0.97515	.	.	ENSG00000198092	ENST00000356291	.	.	.	5.92	5.92	0.95590	.	0.000000	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8344	0.78787	0.0:1.0:0.0:0.0	.	.	.	.	X	339	.	.	G	-	1	0	TMPRSS11F	68612998	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	4.819000	0.62664	2.822000	0.97130	0.650000	0.86243	GGA	.		0.363	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	Nonsense_Mutation	A	68930403	C	A	68930403	5	1	127	1	0	0	0	0	0	0	1	0	16275	608	21	4	313	4	TMPRSS11F	4	68930403	Splice_Site	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		68930403	122223873	32	11132											
WWC2	80014	broad.mit.edu;bcgsc.ca	37	chr4	184129218	184129218	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggacacagaaggaactgtaCcatgtgaaggagcagaggct	14	5	14	8	1	0	3	0	1	0	2	0	6	0	6	1	4	3	3	1	4	4	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:184129218C>T	ENST00000403733.3	+	3	553	c.354C>T	c.(352-354)taC>taT	p.Y118Y	WWC2_ENST00000378925.3_Silent_p.Y20Y|WWC2_ENST00000448232.2_Silent_p.Y118Y|WWC2_ENST00000513834.1_Silent_p.Y118Y|WWC2_ENST00000504005.1_5'Flank	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	118					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		AGGAACTGTACCATGTGAAGG	0.493																																					p.Y118Y													.	WWC2-93	0			c.C354T						.						65	71	69					4																	184129218		2090	4229	6319	SO:0001819	synonymous_variant	80014	exon3			ACTGTACCATGTG	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"WW, C2 and coiled-coil domain containing"	24148	protein-coding gene	gene with protein product			"WW, C2 and coiled-coil domain containing 2"			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.354C>T	4.37:g.184129218C>T		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	154	6	NM_024949	0	0	0	0	0	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Silent	SNP	ENST00000403733.3	37	CCDS34109.2																																																																																			.		0.493	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		T	184129218	C	T	184129218	2	4	127	1	0	0	0	0	0	0	0	1	17445	518	18	2		2	WWC2	4	184129218	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	115198815	184129218	7025058	33	11133											
CASP3	836	broad.mit.edu	37	chr4	185552222	185552222	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtatgcatacaagaagtcGgcctccactggtattttatg	11	12	10	8	1	0	1	0	0	0	1	2	2	1	1	2	2	2	3	2	2	6	5	rs200014759	byFrequency	TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:185552222G>T	ENST00000308394.4	-	7	835	c.573C>A	c.(571-573)gcC>gcA	p.A191A	CASP3_ENST00000517513.1_Intron|CASP3_ENST00000393588.4_Intron|CASP3_ENST00000393585.2_Intron|CASP3_ENST00000523916.1_Silent_p.A191A	NM_004346.3	NP_004337.2	P42574	CASP3_HUMAN	caspase 3, apoptosis-related cysteine peptidase	191					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell homeostasis (GO:0001782)|cell fate commitment (GO:0045165)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte differentiation (GO:0030218)|execution phase of apoptosis (GO:0097194)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|heart development (GO:0007507)|hippo signaling (GO:0035329)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|keratinocyte differentiation (GO:0030216)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|proteolysis (GO:0006508)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|release of cytochrome c from mitochondria (GO:0001836)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097200)|peptidase activity (GO:0008233)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00139)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.057)|all_hematologic(60;0.0592)		all cancers(43;2.05e-27)|Epithelial(43;4.27e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.04e-11)|Colorectal(24;2e-05)|STAD - Stomach adenocarcinoma(60;2.35e-05)|GBM - Glioblastoma multiforme(59;4.94e-05)|COAD - Colon adenocarcinoma(29;0.00017)|BRCA - Breast invasive adenocarcinoma(30;0.000218)|LUSC - Lung squamous cell carcinoma(40;0.00904)|READ - Rectum adenocarcinoma(43;0.161)	Minocycline(DB01017)	ACAAGAAGTCGGCCTCCACTG	0.443																																					p.A191A													.	CASP3-659	0			c.C573A						.						119	100	107					4																	185552222		2203	4300	6503	SO:0001819	synonymous_variant	836	exon7			GAAGTCGGCCTCC	BC016926	CCDS3836.1	4q34	2008-02-05	2005-08-17		ENSG00000164305	ENSG00000164305		"Caspases"	1504	protein-coding gene	gene with protein product		600636	"caspase 3, apoptosis-related cysteine protease"			8780721	Standard	NM_004346		Approved	CPP32, CPP32B, Yama, apopain	uc003iwi.3	P42574	OTTHUMG00000133681	ENST00000308394.4:c.573C>A	4.37:g.185552222G>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	90	3	NM_004346	0	0	10	10	0	A8K5M2|D3DP53|Q96AN1|Q96KP2	Silent	SNP	ENST00000308394.4	37	CCDS3836.1																																																																																			G|0.999;A|0.001		0.443	CASP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257885.2	NM_004346		T	185552222	G	T	185552222	2	4	127	1	0	0	0	0	0	0	0	1	2678	1103	39	4		4	CASP3	4	185552222	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	1423004	185552222	5602054	34	11134											
FAT1	2195	bcgsc.ca	37	chr4	187628814	187628818	+	Frame_Shift_Del	DEL	CCAGT	CCAGT	-																															ggttttcctttacctgaataCcagtcggaagagtgcttcta																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	CCAGT	CCAGT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:187628814_187628818delCCAGT	ENST00000441802.2	-	2	2373_2377	c.2164_2168delACTGG	c.(2164-2169)actggtfs	p.TG722fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	722	Cadherin 6. {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						TACCTGAATACCAGTCGGAAGAGTG	0.444										HNSCC(5;0.00058)																											p.722_723del	Colon(197;1040 2055 4143 4984 49344)												.	FAT1-34	0			c.2164_2168del						.																																			SO:0001589	frameshift_variant	2195	exon2			TGAATACCAGTCG	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.2164_2168delACTGG	4.37:g.187628814_187628818delCCAGT	ENSP00000406229:p.Thr722fs	Somatic	119	0		WXS	Illumina HiSeq	Phase_1	77	6	NM_005245	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.444	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187628818	CCAGT	-	187628814	7	5	127	1	0	1	0	1	0	0	0	0	5708	507	18	0	11702	0	FAT1	4	187628814	Frame_Shift_Del	DEL	CCAGT	TCGA-GL-A59T-01A-21D-A28G-10	2076592	187628814	3525462	35	11135											
SLC12A7	10723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1093744	1093744	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttgttgagcagcgaggaCaccatggggttactgtccat	9	10	13	9	1	0	1	0	1	0	0	1	3	1	2	2	3	4	4	2	3	1	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:1093744C>A	ENST00000264930.5	-	3	289	c.246G>T	c.(244-246)gtG>gtT	p.V82V		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	82					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GCAGCGAGGACACCATGGGGT	0.682																																					p.V82V		.											.	SLC12A7-138	0			c.G246T						.						111	75	87					5																	1093744		2202	4299	6501	SO:0001819	synonymous_variant	10723	exon3			CGAGGACACCATG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"Solute carriers"	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.246G>T	5.37:g.1093744C>A		Somatic	235	0		WXS	Illumina HiSeq	Phase_I	163	47	NM_006598	0	0	2	4	2	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1																																																																																			.		0.682	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		A	1093744	C	A	1093744	2	1	127	1	0	0	0	0	0	0	0	1	14420	465	17	4		4	SLC12A7	5	1093744	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		1093744	179821516	36	11136											
LOX	4015	broad.mit.edu	37	chr5	121412648	121412648	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatggacatcttctgcacgTacgtggacgcctggatgtag	9	10	12	10	3	2	0	0	0	2	0	2	3	2	3	1	3	2	3	1	3	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:121412648T>C	ENST00000231004.4	-	2	979	c.680A>G	c.(679-681)tAc>tGc	p.Y227C	LOX_ENST00000513319.1_Intron	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	227	Lysyl-oxidase like.				blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		CTTCTGCACGTACGTGGACGC	0.632											OREG0016741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y227C													.	LOX-650	0			c.A680G						.						103	98	100					5																	121412648		2203	4300	6503	SO:0001583	missense	4015	exon2			TGCACGTACGTGG		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.680A>G	5.37:g.121412648T>C	ENSP00000231004:p.Tyr227Cys	Somatic	108	0	1511	WXS	Illumina HiSeq	Phase_I	109	3	NM_002317	0	0	1	1	0	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	37	CCDS4129.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.139164	0.77775	.	.	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.45276	0.9	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.70753	0.3260	M	0.90542	3.125	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.78173	-0.2307	10	0.87932	D	0	.	14.9742	0.71257	0.0:0.0:0.0:1.0	.	227	P28300	LYOX_HUMAN	C	227;187	ENSP00000231004:Y227C	ENSP00000231004:Y227C	Y	-	2	0	LOX	121440547	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.993000	0.88291	2.014000	0.59158	0.374000	0.22700	TAC	.		0.632	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			C	121412648	T	C	121412648	3	2	127	1	0	0	0	0	1	0	0	0	8923	1638	57	3	597	3	LOX	5	121412648	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	120318904	121412648	59502612	37	11137											
RBM27	54439	broad.mit.edu;bcgsc.ca	37	chr5	145638017	145638017	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttttttccaacagctgctAacattgtgatccagactgaa	11	15	6	9	0	0	3	0	2	0	1	2	3	2	3	2	0	4	2	2	0	3	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:145638017A>G	ENST00000265271.5	+	11	1766	c.1600A>G	c.(1600-1602)Aac>Gac	p.N534D	RBM27_ENST00000506502.1_Missense_Mutation_p.N479D	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	534					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AACAGCTGCTAACATTGTGAT	0.343																																					p.N534D													.	RBM27-70	0			c.A1600G						.						103	91	94					5																	145638017		1568	3582	5150	SO:0001583	missense	54439	exon11			GCTGCTAACATTG	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1600A>G	5.37:g.145638017A>G	ENSP00000265271:p.Asn534Asp	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	66	4	NM_018989	0	0	0	0	0	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.549076	0.86127	.	.	ENSG00000091009	ENST00000265271	T	0.47177	0.85	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	N	0.19112	0.55	0.43874	D	0.996481	D;D	0.63880	0.993;0.993	D;D	0.68192	0.956;0.956	T	0.41893	-0.9483	10	0.12103	T	0.63	-15.369	15.8844	0.79232	1.0:0.0:0.0:0.0	.	534;479	Q9P2N5;B3KY61	RBM27_HUMAN;.	D	534	ENSP00000265271:N534D	ENSP00000265271:N534D	N	+	1	0	RBM27	145618210	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.413000	0.90235	2.147000	0.66899	0.402000	0.26972	AAC	.		0.343	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		G	145638017	A	G	145638017	3	3	127	1	0	0	0	0	1	0	0	0	13159	362	13	3	1642	3	RBM27	5	145638017	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	24225369	145638017	35277243	38	11138											
NSD1	64324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176562915	176562915	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acattacaatagaagagcaaTtaaactcaataaatttatct	20	12	3	6	0	2	2	1	0	1	2	2	2	2	2	0	0	3	1	0	0	11	6	rs374083142		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:176562915T>G	ENST00000439151.2	+	2	856	c.811T>G	c.(811-813)Tta>Gta	p.L271V	NSD1_ENST00000361032.4_Missense_Mutation_p.L271V|NSD1_ENST00000347982.4_Intron|NSD1_ENST00000511258.1_Intron|NSD1_ENST00000354179.4_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	271					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGAAGAGCAATTAAACTCAAT	0.383			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.L271V		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.T811G						.						66	67	67					5																	176562915		2203	4300	6503	SO:0001583	missense	64324	exon2	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GAGCAATTAAACT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.811T>G	5.37:g.176562915T>G	ENSP00000395929:p.Leu271Val	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	91	31	NM_022455	0	0	0	0	0	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.841288	0.32513	.	.	ENSG00000165671	ENST00000439151;ENST00000361032	D;D	0.94576	-3.23;-3.46	5.19	5.19	0.71726	.	0.186195	0.26485	N	0.024119	D	0.88633	0.6489	N	0.14661	0.345	0.80722	D	1	B;B;B	0.30634	0.288;0.19;0.137	B;B;B	0.30572	0.117;0.055;0.051	D	0.88112	0.2826	10	0.72032	D	0.01	.	12.6728	0.56876	0.0:0.0:0.0:1.0	.	271;271;271	Q96L73-3;Q96L73;Q6PJ64	.;NSD1_HUMAN;.	V	271	ENSP00000395929:L271V;ENSP00000354310:L271V	ENSP00000354310:L271V	L	+	1	2	NSD1	176495521	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.025000	0.57225	2.189000	0.69895	0.533000	0.62120	TTA	.		0.383	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		G	176562915	T	G	176562915	3	3	127	1	0	0	0	0	1	0	0	0	10695	1490	52	5	813	5	NSD1	5	176562915	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	30924898	176562915	4352345	39	11139											
KIF6	221458	broad.mit.edu	37	chr6	39607523	39607523	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagatggtaccattgtaacCtgccaggacactgcaataaa	16	8	8	9	0	0	1	0	0	0	1	0	2	0	2	3	2	4	3	3	2	6	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:39607523C>T	ENST00000287152.7	-	4	356	c.262G>A	c.(262-264)Ggt>Agt	p.G88S	KIF6_ENST00000373215.3_Missense_Mutation_p.G88S|KIF6_ENST00000538893.1_Missense_Mutation_p.G88S|KIF6_ENST00000373216.3_Missense_Mutation_p.G88S	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	88	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						CCATTGTAACCTGCCAGGACA	0.408																																					p.G88S													.	KIF6-713	0			c.G262A						.						139	107	118					6																	39607523		2203	4300	6503	SO:0001583	missense	221458	exon4			TGTAACCTGCCAG	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"Kinesins"	21202	protein-coding gene	gene with protein product		613919	"chromosome 6 open reading frame 102"	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.262G>A	6.37:g.39607523C>T	ENSP00000287152:p.Gly88Ser	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	84	8	NM_145027	0	0	0	0	0	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	C	35	5.542203	0.96474	.	.	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373215;ENST00000538893	D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91	5.82	5.82	0.92795	Kinesin, motor domain (5);	.	.	.	.	D	0.96494	0.8856	H	0.99758	4.755	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98057	1.0391	9	0.87932	D	0	.	19.6904	0.95998	0.0:1.0:0.0:0.0	.	88;88;88	E7EUN7;F6VGH2;Q6ZMV9	.;.;KIF6_HUMAN	S	88	ENSP00000287152:G88S;ENSP00000362312:G88S;ENSP00000362311:G88S;ENSP00000441435:G88S	ENSP00000287152:G88S	G	-	1	0	KIF6	39715501	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.696000	0.84270	2.767000	0.95098	0.655000	0.94253	GGT	.		0.408	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		T	39607523	C	T	39607523	3	4	127	1	0	0	0	0	1	0	0	0	8329	681	24	2	2262	2	KIF6	6	39607523	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		39607523	131507544	40	11140											
MRPS10	55173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	42176601	42176601	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaattcaagctatacctttgTtacttccatggcaacccctt	11	14	4	12	0	1	0	1	0	0	0	2	0	2	0	4	1	4	3	4	1	6	7			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:42176601T>A	ENST00000053468.3	-	6	532	c.517A>T	c.(517-519)Aca>Tca	p.T173S		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	173						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			TATACCTTTGTTACTTCCATG	0.443																																					p.T173S		.											.	MRPS10-90	0			c.A517T						.						103	98	100					6																	42176601		2203	4300	6503	SO:0001583	missense	55173	exon6			CCTTTGTTACTTC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"Mitochondrial ribosomal proteins / small subunits"	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.517A>T	6.37:g.42176601T>A	ENSP00000053468:p.Thr173Ser	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	152	45	NM_018141	0	0	0	0	0	B2RE89|Q9H3E5|Q9NVR3	Missense_Mutation	SNP	ENST00000053468.3	37	CCDS4866.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.906883	0.72868	.	.	ENSG00000048544	ENST00000053468	.	.	.	5.78	5.78	0.91487	.	0.094475	0.64402	D	0.000001	T	0.49047	0.1534	L	0.41415	1.275	0.46901	D	0.999243	D	0.53462	0.96	P	0.52454	0.699	T	0.46456	-0.9190	9	0.32370	T	0.25	-7.8115	15.0972	0.72244	0.0:0.0:0.0:1.0	.	173	P82664	RT10_HUMAN	S	173	.	ENSP00000053468:T173S	T	-	1	0	MRPS10	42284579	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.043000	0.76572	2.200000	0.70718	0.460000	0.39030	ACA	.		0.443	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1			A	42176601	T	A	42176601	3	1	127	1	0	0	0	0	1	0	0	0	9846	1725	60	5	96	5	MRPS10	6	42176601	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	2569078	42176601	128938466	41	11141											
SLC29A1	2030	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	44197513	44197513	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gttattcacctacctcaactCcttcctgcatcagaggtgag	9	12	7	13	0	3	2	3	1	0	1	5	2	5	2	4	1	3	2	4	1	3	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:44197513C>A	ENST00000393841.1	+	5	790	c.299C>A	c.(298-300)tCc>tAc	p.S100Y	SLC29A1_ENST00000371724.1_Missense_Mutation_p.S100Y|SLC29A1_ENST00000371731.1_Missense_Mutation_p.S100Y|SLC29A1_ENST00000371713.1_Missense_Mutation_p.S100Y|SLC29A1_ENST00000427851.2_Missense_Mutation_p.S100Y|SLC29A1_ENST00000313248.7_Missense_Mutation_p.S179Y|SLC29A1_ENST00000371755.3_Missense_Mutation_p.S100Y|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000371740.5_Missense_Mutation_p.S100Y|SLC29A1_ENST00000393844.1_Missense_Mutation_p.S100Y|SLC29A1_ENST00000371708.1_Missense_Mutation_p.S100Y	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	100					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	TACCTCAACTCCTTCCTGCAT	0.597																																					p.S100Y													.	SLC29A1-154	0			c.C299A						.						130	119	123					6																	44197513		2203	4300	6503	SO:0001583	missense	2030	exon4			TCAACTCCTTCCT	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.299C>A	6.37:g.44197513C>A	ENSP00000377424:p.Ser100Tyr	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	89	30	NM_004955	0	0	12	17	5	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Missense_Mutation	SNP	ENST00000393841.1	37	CCDS4908.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403214	0.62288	.	.	ENSG00000112759	ENST00000544345;ENST00000393844;ENST00000313248;ENST00000427851;ENST00000371755;ENST00000371740;ENST00000371731;ENST00000393841;ENST00000371724;ENST00000371713;ENST00000371708	T;T;T;T;T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	5.1	4.22	0.49857	.	0.000000	0.85682	D	0.000000	D	0.83769	0.5326	M	0.86420	2.815	0.54753	D	0.999988	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.991;0.987;0.982	D	0.87111	0.2185	10	0.02654	T	1	-14.8574	13.9988	0.64419	0.0:0.8486:0.1514:0.0	.	100;119;179;100	B7Z1J8;B7Z914;B3KQV7;Q99808	.;.;.;S29A1_HUMAN	Y	119;100;179;100;100;100;100;100;100;100;100	ENSP00000377427:S100Y;ENSP00000319152:S179Y;ENSP00000392668:S100Y;ENSP00000360820:S100Y;ENSP00000360805:S100Y;ENSP00000360796:S100Y;ENSP00000377424:S100Y;ENSP00000360789:S100Y;ENSP00000360778:S100Y;ENSP00000360773:S100Y	ENSP00000319152:S179Y	S	+	2	0	SLC29A1	44305491	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.007000	0.76335	1.360000	0.45960	0.563000	0.77884	TCC	.		0.597	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			A	44197513	C	A	44197513	3	1	127	1	0	0	0	0	1	0	0	0	14566	855	30	4	309	4	SLC29A1	6	44197513	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	2020912	44197513	126917554	42	11142											
EEF1A1	1915	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	74227601	74227601	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcagccttcttgtccaCtgctttgatgacacccaccg	7	11	7	16	1	1	2	0	2	1	0	3	2	3	2	5	0	3	2	5	0	0	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:74227601C>T	ENST00000316292.9	-	7	2312	c.1321G>A	c.(1321-1323)Gtg>Atg	p.V441M	EEF1A1_ENST00000331523.2_Missense_Mutation_p.V441M|EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.V441M	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	441					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						TTCTTGTCCACTGCTTTGATG	0.443											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V441M		.											.	EEF1A1-226	0			c.G1321A						.						29	30	30					6																	74227601		2203	4296	6499	SO:0001583	missense	1915	exon8			TGTCCACTGCTTT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1321G>A	6.37:g.74227601C>T	ENSP00000339063:p.Val441Met	Somatic	172	0	1151	WXS	Illumina HiSeq	Phase_I	101	25	NM_001402	1	0	6399	11366	4966	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352587	0.82132	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.52526	0.66;0.66;0.66	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.072938	0.53938	U	0.000048	T	0.68229	0.2978	H	0.94462	3.54	0.80722	D	1	D;D;D	0.55172	0.97;0.97;0.97	P;P;P	0.54590	0.756;0.756;0.756	T	0.79850	-0.1629	10	0.87932	D	0	.	18.3119	0.90203	0.0:1.0:0.0:0.0	.	441;441;441	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	M	441;441;441;420	ENSP00000339063:V441M;ENSP00000339053:V441M;ENSP00000330054:V441M	ENSP00000339053:V441M	V	-	1	0	EEF1A1	74284322	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.405000	0.80007	2.381000	0.81170	0.556000	0.70494	GTG	.		0.443	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		T	74227601	C	T	74227601	3	4	127	1	0	0	0	0	1	0	0	0	4934	565	20	2	71	2	EEF1A1	6	74227601	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	30030088	74227601	96887466	43	11143											
RIPPLY2	134701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	84563845	84563845	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctggaatgaccgcagcCtcaggaaagctttaccaatt	11	8	10	12	1	1	1	1	1	0	0	1	3	1	3	4	3	3	2	4	3	4	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:84563845C>T	ENST00000369689.1	+	3	355	c.204C>T	c.(202-204)gcC>gcT	p.A68A	RIPPLY2_ENST00000369687.1_Silent_p.A10A	NM_001009994.1	NP_001009994.1	Q5TAB7	RIPP2_HUMAN	ripply transcriptional repressor 2	68					bone morphogenesis (GO:0060349)|determination of left/right symmetry (GO:0007368)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression (GO:0010468)|somite rostral/caudal axis specification (GO:0032525)|somitogenesis (GO:0001756)	nucleus (GO:0005634)				large_intestine(2)|lung(4)|urinary_tract(1)	7						TGACCGCAGCCTCAGGAAAGC	0.592																																					p.A68A		.											.	RIPPLY2-90	0			c.C204T						.						102	96	98					6																	84563845		2203	4300	6503	SO:0001819	synonymous_variant	134701	exon3			CGCAGCCTCAGGA	BC130460	CCDS34493.1	6q14.2	2013-07-23	2013-07-23	2008-05-07	ENSG00000203877	ENSG00000203877			21390	protein-coding gene	gene with protein product		609891	"chromosome 6 open reading frame 159", "ripply2 homolog (zebrafish)"	C6orf159			Standard	NM_001009994		Approved	dJ237I15.1	uc003pke.3	Q5TAB7	OTTHUMG00000015117	ENST00000369689.1:c.204C>T	6.37:g.84563845C>T		Somatic	163	0		WXS	Illumina HiSeq	Phase_I	132	13	NM_001009994	0	0	0	0	0	Q5TAB6	Silent	SNP	ENST00000369689.1	37	CCDS34493.1																																																																																			.		0.592	RIPPLY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041360.1	NM_001009994		T	84563845	C	T	84563845	2	4	127	1	0	0	0	0	0	0	0	1	13417	668	24	2		2	RIPPLY2	6	84563845	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	10336244	84563845	86551222	44	11144											
IGF2R	3482	hgsc.bcm.edu;bcgsc.ca	37	chr6	160494272	160494272	+	Frame_Shift_Del	DEL	G	G	-																															ctttggacagaccaggattaGcgtgggcaaggccaacaaga																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:160494272delG	ENST00000356956.1	+	34	4866	c.4718delG	c.(4717-4719)agcfs	p.S1573fs		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1573					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ACCAGGATTAGCGTGGGCAAG	0.547																																					p.S1573fs		.											.	IGF2R-118	0			c.4718delG						.						146	128	134					6																	160494272		2203	4300	6503	SO:0001589	frameshift_variant	3482	exon34			.	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4718delG	6.37:g.160494272delG	ENSP00000349437:p.Ser1573fs	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	226	54	NM_000876	0	0	0	0	0	Q7Z7G9|Q96PT5	Frame_Shift_Del	DEL	ENST00000356956.1	37	CCDS5273.1																																																																																			.		0.547	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		-	160494272	G	-	160494272	7	5	127	1	0	1	0	1	0	0	0	0	7597	971	34	0	4852	0	IGF2R	6	160494272	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	75930427	160494272	10620795	45	11145											
ACTB	60	broad.mit.edu	37	chr7	5568199	5568199	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccagacgcaggatggcatggGggagggcatacccctcgtag	9	5	16	11	2	0	1	0	0	0	1	1	3	0	3	3	5	1	4	3	5	2	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:5568199G>C	ENST00000331789.5	-	4	706	c.515C>G	c.(514-516)cCc>cGc	p.P172R	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	172					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GATGGCATGGGGGAGGGCATA	0.637																																					p.P172R													.	ACTB-226	0			c.C515G						.						62	62	62					7																	5568199		2203	4300	6503	SO:0001583	missense	60	exon4			GCATGGGGGAGGG	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.515C>G	7.37:g.5568199G>C	ENSP00000349960:p.Pro172Arg	Somatic	274	0		WXS	Illumina HiSeq	Phase_I	303	8	NM_001101	1	0	1882	1925	42	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978194	0.53720	.	.	ENSG00000075624	ENST00000331789;ENST00000400179;ENST00000320713	D	0.94138	-3.36	5.37	4.47	0.54385	.	0.000000	0.56097	U	0.000026	D	0.96586	0.8886	M	0.84773	2.715	0.51233	D	0.999913	P	0.38729	0.644	P	0.60886	0.88	D	0.96792	0.9583	10	0.87932	D	0	.	12.3856	0.55330	0.0848:0.0:0.9152:0.0	.	172	P60709	ACTB_HUMAN	R	172;144;91	ENSP00000349960:P172R	ENSP00000440549:P91R	P	-	2	0	ACTB	5534725	1.000000	0.71417	0.929000	0.37066	0.984000	0.73092	7.659000	0.83766	2.514000	0.84764	0.650000	0.86243	CCC	.		0.637	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		C	5568199	G	C	5568199	3	2	127	1	0	0	0	0	1	0	0	0	193	1232	43	4	624	4	ACTB	7	5568199	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		5568199	153570464	46	11146											
C7orf65	401335	broad.mit.edu;bcgsc.ca	37	chr7	47698325	47698325	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagaagttaagcaacttGcccaggccacacagctattc	13	8	8	12	0	1	1	1	0	0	1	2	2	1	1	2	1	4	3	2	1	4	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:47698325G>A	ENST00000408988.2	+	2	140	c.105G>A	c.(103-105)ttG>ttA	p.L35L		NM_001123065.1	NP_001116537.1	Q6ZTY9	CG065_HUMAN	chromosome 7 open reading frame 65	35										endometrium(1)|lung(2)	3						taagcaacttgcccaggccac	0.423																																					p.L35L													.	.	0			c.G105A						.						55	52	53					7																	47698325		1568	3582	5150	SO:0001819	synonymous_variant	401335	exon2			CAACTTGCCCAGG		CCDS43580.1	7p12.3	2009-02-11			ENSG00000221845	ENSG00000221845			34432	protein-coding gene	gene with protein product							Standard	NM_001123065		Approved	FLJ44108	uc010kyp.1	Q6ZTY9	OTTHUMG00000155550	ENST00000408988.2:c.105G>A	7.37:g.47698325G>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	98	6	NM_001123065	0	0	0	0	0	A4D2F8	Silent	SNP	ENST00000408988.2	37	CCDS43580.1																																																																																			.		0.423	C7orf65-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340616.1	NM_001123065		A	47698325	G	A	47698325	2	1	127	1	0	0	0	0	0	0	0	1	2417	1310	46	2		2	C7orf65	7	47698325	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	42130126	47698325	111440338	47	11147											
GATAD1	57798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	92083893	92083893	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctactatgctcaaatcagAggttttatccaggaccagta	12	11	7	11	0	2	1	2	0	0	1	3	2	3	2	3	2	2	3	3	2	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:92083893A>G	ENST00000287957.3	+	4	790	c.513A>G	c.(511-513)agA>agG	p.R171R	AC007566.10_ENST00000427458.1_RNA	NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	171						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTCAAATCAGAGGTTTTATCC	0.458																																					p.R171R		.											.	GATAD1-514	0			c.A513G						.						193	183	186					7																	92083893		2203	4300	6503	SO:0001819	synonymous_variant	57798	exon4			AATCAGAGGTTTT		CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259		"GATA zinc finger domain containing"	29941	protein-coding gene	gene with protein product	"ocular development associated gene"	614518				12062807	Standard	NM_021167		Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.513A>G	7.37:g.92083893A>G		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	136	63	NM_021167	0	0	5	13	8	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	Silent	SNP	ENST00000287957.3	37	CCDS5625.1																																																																																			.		0.458	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253929.2	NM_021167		G	92083893	A	G	92083893	2	3	127	1	0	0	0	0	0	0	0	1	6279	301	11	3		3	GATAD1	7	92083893	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	44385568	92083893	67054770	48	11148											
LRCH4	4034	broad.mit.edu;bcgsc.ca	37	chr7	100176068	100176068	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggggccaggtcccccagggCcgacccacgctgcccggcct	5	3	14	19	3	0	0	0	0	0	0	1	1	1	0	7	5	1	1	7	5	0	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:100176068C>A	ENST00000310300.6	-	6	854	c.802G>T	c.(802-804)Gcc>Tcc	p.A268S	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	268					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCCCCCAGGGCCGACCCACGC	0.632																																					p.A268S													.	LRCH4-136	0			c.G802T						.						32	41	38					7																	100176068		2202	4298	6500	SO:0001583	missense	4034	exon6			CCAGGGCCGACCC	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.802G>T	7.37:g.100176068C>A	ENSP00000309689:p.Ala268Ser	Somatic	408	1		WXS	Illumina HiSeq	Phase_I	461	35	NM_002319	0	0	16	16	0	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	.	.	.	.	.	.	.	.	.	.	c	0.115	-1.133361	0.01756	.	.	ENSG00000077454	ENST00000310300	T	0.29917	1.55	5.19	3.32	0.38043	.	0.339915	0.30762	N	0.008934	T	0.16342	0.0393	N	0.24115	0.695	0.20638	N	0.999871	B	0.20164	0.042	B	0.19946	0.027	T	0.31280	-0.9949	10	0.07813	T	0.8	-4.3266	7.8558	0.29480	0.161:0.7528:0.0:0.0862	.	268	O75427	LRCH4_HUMAN	S	268	ENSP00000309689:A268S	ENSP00000309689:A268S	A	-	1	0	LRCH4	100014004	0.257000	0.24022	0.083000	0.20561	0.265000	0.26407	2.031000	0.41117	0.547000	0.28938	0.538000	0.68166	GCC	.		0.632	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319		A	100176068	C	A	100176068	3	1	127	1	0	0	0	0	1	0	0	0	8960	739	26	4	1301	4	LRCH4	7	100176068	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	8092175	100176068	58962595	49	11149											
DOCK5	80005	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	25224425	25224425	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttggcagttgcatttctcAcccatgagtcccttcagctt	7	15	7	12	0	2	1	2	1	1	0	4	1	3	1	2	1	2	4	2	1	0	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:25224425A>G	ENST00000276440.7	+	31	3207	c.3163A>G	c.(3163-3165)Acc>Gcc	p.T1055A		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1055					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TGCATTTCTCACCCATGAGTC	0.383																																					p.T1055A	Pancreas(145;34 1887 3271 10937 30165)												.	DOCK5-71	0			c.A3163G						.						99	91	94					8																	25224425		2203	4300	6503	SO:0001583	missense	80005	exon31			TTTCTCACCCATG		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3163A>G	8.37:g.25224425A>G	ENSP00000276440:p.Thr1055Ala	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	53	5	NM_024940	0	0	0	0	0	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.59|18.59	3.657437|3.657437	0.67586|0.67586	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000444569|ENST00000276440	.|T	.|0.25749	.|1.78	5.95|5.95	4.79|4.79	0.61399|0.61399	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.35451|0.35451	0.0932|0.0932	M|M	0.73430|0.73430	2.235|2.235	0.58432|0.58432	D|D	0.999999|0.999999	.|B;B;B	.|0.28082	.|0.2;0.2;0.2	.|B;B;B	.|0.36030	.|0.167;0.216;0.167	T|T	0.18618|0.18618	-1.0331|-1.0331	5|10	.|0.72032	.|D	.|0.01	.|.	12.0589|12.0589	0.53550|0.53550	0.933:0.0:0.067:0.0|0.933:0.0:0.067:0.0	.|.	.|1045;830;1055	.|D3DSS6;Q68DL4;Q9H7D0	.|.;.;DOCK5_HUMAN	R|A	826|1055	.|ENSP00000276440:T1055A	.|ENSP00000276440:T1055A	H|T	+|+	2|1	0|0	DOCK5|DOCK5	25280342|25280342	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.442000|7.442000	0.80503|0.80503	1.075000|1.075000	0.40932|0.40932	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.		0.383	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		G	25224425	A	G	25224425	3	3	127	1	0	0	0	0	1	0	0	0	4701	159	6	3	3285	3	DOCK5	8	25224425	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		25224425	121139597	50	11150											
KIF13B	23303	broad.mit.edu;bcgsc.ca	37	chr8	28984648	28984650	+	In_Frame_Del	DEL	CTC	CTC	-																															tagaaacttacatggaaggtCtcatgtgttctgggggctct																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984648_28984650delCTC	ENST00000524189.1	-	25	3249_3251	c.3211_3213delGAG	c.(3211-3213)gagdel	p.E1071del	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1071					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CATGGAAGGTCTCATGTGTTCTG	0.424																																					p.1071_1071del													.	KIF13B-22	0			c.3211_3213del						.																																			SO:0001651	inframe_deletion	23303	exon25			GAAGGTCTCATGT	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3211_3213delGAG	8.37:g.28984648_28984650delCTC	ENSP00000427900:p.Glu1071del	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	99	0	NM_015254	0	0	0	0	0	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	In_Frame_Del	DEL	ENST00000524189.1	37	CCDS55217.1																																																																																			.		0.424	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			-	28984650	CTC	-	28984648	7	5	127	1	0	1	0	1	0	0	0	0	8296	912	32	0	2331	0	KIF13B	8	28984648	In_Frame_Del	DEL	CTC	TCGA-GL-A59T-01A-21D-A28G-10	3760223	28984648	117379374	51	11151	118	2									
KIF13B	23303	broad.mit.edu;bcgsc.ca	37	chr8	28984652	28984654	+	In_Frame_Del	DEL	TGT	TGT	-																															aacttacatggaaggtctcaTgtgttctgggggctctgagc																								rs536929811		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984652_28984654delTGT	ENST00000524189.1	-	25	3245_3247	c.3207_3209delACA	c.(3205-3210)acacat>act	p.H1070del	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1070					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		GAAGGTCTCATGTGTTCTGGGGG	0.429																																					p.1069_1070del													.	KIF13B-22	0			c.3207_3209del						.																																			SO:0001651	inframe_deletion	23303	exon25			GTCTCATGTGTTC	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3207_3209delACA	8.37:g.28984652_28984654delTGT	ENSP00000427900:p.His1070del	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	99	10	NM_015254	0	0	0	0	0	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	In_Frame_Del	DEL	ENST00000524189.1	37	CCDS55217.1																																																																																			.		0.429	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			-	28984654	TGT	-	28984652	7	5	127	1	0	1	0	1	0	0	0	0	8296	1464	51	0	2335	0	KIF13B	8	28984652	In_Frame_Del	DEL	TGT	TCGA-GL-A59T-01A-21D-A28G-10	4	28984652	117379370	52	11152	118	2									
WHSC1L1	54904	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr8	38175506	38175506	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctcaatcgctgcggagaCggagctgtcactgaatctga	9	10	11	11	3	3	3	2	2	1	1	5	5	4	4	1	2	2	2	1	2	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:38175506C>T	ENST00000317025.8	-	9	2373				WHSC1L1_ENST00000525081.1_5'UTR|WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.V636I|WHSC1L1_ENST00000433384.2_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1						histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			GCTGCGGAGACGGAGCTGTCA	0.537			T	NUP98	AML																																p.V636I		.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1-658	0			c.G1906A						.						90	82	85					8																	38175506		2203	4300	6503	SO:0001627	intron_variant	54904	exon10			CGGAGACGGAGCT	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1855+906G>A	8.37:g.38175506C>T		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	79	28	NM_017778	0	0	7	8	1	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	37	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835251	0.50951	.	.	ENSG00000147548	ENST00000316985	T	0.64438	-0.1	6.17	5.29	0.74685	.	.	.	.	.	T	0.50752	0.1634	.	.	.	0.21499	N	0.999666	B	0.14805	0.011	B	0.10450	0.005	T	0.33033	-0.9884	8	0.40728	T	0.16	.	11.9912	0.53176	0.0:0.9189:0.0:0.0811	.	636	Q9BZ95-3	.	I	636	ENSP00000313410:V636I	ENSP00000313410:V636I	V	-	1	0	WHSC1L1	38294663	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.355000	0.44107	2.941000	0.99782	0.655000	0.94253	GTC	.		0.537	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		T	38175506	C	T	38175506	1	4	127	0	1	0	0	0	0	0	0	0	17396	536	19	1		1	WHSC1L1	8	38175506	Intron	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	9190854	38175506	108188516	53	11153											
INTS8	55656	ucsc.edu	37	chr8	95884142	95884142	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggactttgaagctgtggcAatcacagtgaaagagctagt	12	10	13	6	0	1	3	1	2	0	1	1	4	1	4	0	2	2	3	0	2	4	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:95884142A>G	ENST00000523731.1	+	21	2578	c.2445A>G	c.(2443-2445)gcA>gcG	p.A815A	INTS8_ENST00000447247.1_Silent_p.A815A	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	815					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					AAGCTGTGGCAATCACAGTGA	0.343																																					p.A815A													.	INTS8-90	0			c.A2445G						.						112	106	108					8																	95884142		2203	4300	6503	SO:0001819	synonymous_variant	55656	exon21			TGTGGCAATCACA	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2445A>G	8.37:g.95884142A>G		Somatic	64	0		WXS	Illumina HiSeq		41	4	NM_017864	0	0	22	22	0	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Silent	SNP	ENST00000523731.1	37	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	A	10.56	1.384319	0.25031	.	.	ENSG00000164941	ENST00000520526	.	.	.	5.57	-5.85	0.02311	.	.	.	.	.	T	0.35799	0.0944	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44605	-0.9317	4	.	.	.	-16.3704	1.5279	0.02529	0.1785:0.3688:0.1616:0.2912	.	.	.	.	R	637	.	.	Q	+	2	0	INTS8	95953318	0.394000	0.25246	0.989000	0.46669	0.989000	0.77384	-0.262000	0.08682	-0.448000	0.07128	-0.435000	0.05868	CAA	.		0.343	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		G	95884142	A	G	95884142	2	3	127	1	0	0	0	0	0	0	0	1	7805	117	5	3		3	INTS8	8	95884142	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	57708636	95884142	50479880	54	11154											
JAK2	3717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	5126752	5126752	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcctttagggatctagcTcttcgagtggatcaaataag	10	12	9	10	1	3	0	1	0	2	0	5	3	4	2	2	2	1	1	2	2	4	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:5126752T>C	ENST00000381652.3	+	25	3854	c.3360T>C	c.(3358-3360)gcT>gcC	p.A1120A	JAK2_ENST00000539801.1_Silent_p.A1120A|JAK2_ENST00000544510.1_Silent_p.A971A|JAK2_ENST00000487310.1_3'UTR	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	1120	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGGATCTAGCTCTTCGAGTGG	0.348		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.A1120A		.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2-75307	0			c.T3360C						.						79	74	76					9																	5126752		2203	4299	6502	SO:0001819	synonymous_variant	3717	exon25	Familial Cancer Database		TCTAGCTCTTCGA		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"SH2 domain containing"	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.3360T>C	9.37:g.5126752T>C		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	58	45	NM_004972	0	0	1	2	1	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			.		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5126752	T	C	5126752	2	2	127	1	0	0	0	0	0	0	0	1	7959	1538	54	3		3	JAK2	9	5126752	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10		5126752	136086679	55	11155											
IFT74	80173	ucsc.edu	37	chr9	27055739	27055739	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatatataatgatttgccagCtttaaaatcatcaggtgaag	15	13	8	5	0	2	2	2	2	0	0	2	3	2	2	1	1	2	1	1	1	6	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:27055739C>T	ENST00000443698.1	+	17	1637	c.1466C>T	c.(1465-1467)gCt>gTt	p.A489V	IFT74_ENST00000380062.5_Missense_Mutation_p.A489V|IFT74_ENST00000433700.1_Missense_Mutation_p.A489V	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	489					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		GATTTGCCAGCTTTAAAATCA	0.294																																					p.A489V													.	IFT74-515	0			c.C1466T						.						64	61	62					9																	27055739		1803	4063	5866	SO:0001583	missense	80173	exon17			TGCCAGCTTTAAA	AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872		"Intraflagellar transport homologs"	21424	protein-coding gene	gene with protein product	"capillary morphogenesis protein 1"	608040	"coiled-coil domain containing 2", "intraflagellar transport 74 homolog (Chlamydomonas)"	CCDC2		11683410	Standard	NM_001099223		Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.1466C>T	9.37:g.27055739C>T	ENSP00000404122:p.Ala489Val	Somatic	139	0		WXS	Illumina HiSeq		91	1	NM_001099222	0	0	23	25	2	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.115265	0.56505	.	.	ENSG00000096872	ENST00000433700;ENST00000443698;ENST00000380062;ENST00000544022	T;T;T	0.12672	2.66;2.66;2.66	5.24	4.32	0.51571	.	0.182103	0.45361	D	0.000363	T	0.19087	0.0458	M	0.62723	1.935	0.47123	D	0.999325	B	0.31548	0.328	B	0.36134	0.218	T	0.02059	-1.1221	10	0.30078	T	0.28	-3.3595	15.0187	0.71609	0.1437:0.8563:0.0:0.0	.	489	Q96LB3	IFT74_HUMAN	V	489	ENSP00000389224:A489V;ENSP00000404122:A489V;ENSP00000369402:A489V	ENSP00000369402:A489V	A	+	2	0	IFT74	27045739	1.000000	0.71417	0.842000	0.33263	0.948000	0.59901	4.045000	0.57368	1.152000	0.42452	0.563000	0.77884	GCT	.		0.294	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103		T	27055739	C	T	27055739	3	4	127	1	0	0	0	0	1	0	0	0	7584	797	28	2	1597	2	IFT74	9	27055739	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	21928987	27055739	114157692	56	11156											
DAPK1	1612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	90321821	90321821	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggggggtacaaggaaagcTtcagcagcatcatgtgcttc	10	9	14	8	0	2	0	2	0	0	0	3	1	2	1	0	4	5	5	0	4	3	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:90321821T>G	ENST00000408954.3	+	26	4170	c.3835T>G	c.(3835-3837)Ttc>Gtc	p.F1279V	DAPK1_ENST00000469640.2_Missense_Mutation_p.F1304V|DAPK1_ENST00000472284.1_Missense_Mutation_p.F1279V|DAPK1_ENST00000358077.5_Missense_Mutation_p.F1279V|DAPK1_ENST00000491893.1_Missense_Mutation_p.F1213V	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1279					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CAAGGAAAGCTTCAGCAGCAT	0.567									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.F1279V		.											.	DAPK1-359	0			c.T3835G						.						54	62	60					9																	90321821		2131	4237	6368	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	GAAAGCTTCAGCA	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"Ankyrin repeat domain containing"	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3835T>G	9.37:g.90321821T>G	ENSP00000386135:p.Phe1279Val	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	108	79	NM_004938	0	0	3	21	18	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	T	18.91	3.723375	0.68959	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.63255	0.05;0.05;0.03;0.05;-0.03	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000040	T	0.77552	0.4147	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.83275	0.987;0.996;0.987	T	0.77534	-0.2552	10	0.45353	T	0.12	.	16.2026	0.82095	0.0:0.0:0.0:1.0	.	1213;1279;1279	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	V	1279;1279;1304;1279;1213	ENSP00000350785:F1279V;ENSP00000417076:F1279V;ENSP00000418885:F1304V;ENSP00000386135:F1279V;ENSP00000419026:F1213V	ENSP00000350785:F1279V	F	+	1	0	DAPK1	89511641	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.997000	0.88414	2.285000	0.76669	0.533000	0.62120	TTC	.		0.567	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		G	90321821	T	G	90321821	3	3	127	1	0	0	0	0	1	0	0	0	4241	1609	56	5	3933	5	DAPK1	9	90321821	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	63266082	90321821	50891610	57	11157											
SPTAN1	6709	broad.mit.edu	37	chr9	131370209	131370209	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacagcagctgttggctcacGgacactatgccagccctgag	9	7	12	13	1	1	1	1	1	0	0	1	3	1	2	2	2	4	4	2	2	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:131370209G>T	ENST00000372731.4	+	33	4335	c.4225G>T	c.(4225-4227)Gga>Tga	p.G1409*	SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.G1409*|SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.G1409*	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1409					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.G1409R(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GTTGGCTCACGGACACTATGC	0.547																																					p.G1409X	NSCLC(120;833 1744 2558 35612 37579)												.	SPTAN1-158	1	Substitution - Missense(1)	large_intestine(1)	c.G4225T						.						78	74	75					9																	131370209		2203	4300	6503	SO:0001587	stop_gained	6709	exon33			GCTCACGGACACT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4225G>T	9.37:g.131370209G>T	ENSP00000361816:p.Gly1409*	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	134	5	NM_003127	0	0	54	54	0	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Nonsense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	42	9.687602	0.99238	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	.	.	.	5.54	4.65	0.58169	.	0.048617	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.7251	0.69339	0.0699:0.0:0.9301:0.0	.	.	.	.	X	1409;1409;1409;1389	.	ENSP00000350882:G1409X	G	+	1	0	SPTAN1	130410030	1.000000	0.71417	0.996000	0.52242	0.938000	0.57974	6.594000	0.74104	1.488000	0.48433	0.591000	0.81541	GGA	.		0.547	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131370209	G	T	131370209	4	4	127	1	0	0	0	0	0	1	0	0	15149	1117	39	4	4351	4	SPTAN1	9	131370209	Nonsense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	41048388	131370209	9843222	58	11158											
ABL1	25	ucsc.edu;bcgsc.ca	37	chr9	133738297	133738297	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atggtgtgtcccccaactacGacaagtgggagatggaacgc	11	7	13	10	2	0	1	0	0	0	1	1	4	1	2	2	3	3	0	2	3	4	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:133738297G>A	ENST00000318560.5	+	4	1078	c.697G>A	c.(697-699)Gac>Aac	p.D233N		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	233					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCCCAACTACGACAAGTGGGA	0.577			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.D252N				Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1-3810	0			c.G754A						.						131	104	113					9																	133738297		2203	4300	6503	SO:0001583	missense	25	exon4			AACTACGACAAGT	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"SH2 domain containing"	76	protein-coding gene	gene with protein product		189980	"v-abl Abelson murine leukemia viral oncogene homolog 1", "c-abl oncogene 1, receptor tyrosine kinase", "c-abl oncogene 1, non-receptor tyrosine kinase"	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.697G>A	9.37:g.133738297G>A	ENSP00000323315:p.Asp233Asn	Somatic	198	2		WXS	Illumina HiSeq		172	119	NM_007313	0	0	0	8	8	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	5.978409|5.978409	0.97168|0.97168	.|.	.|.	ENSG00000097007|ENSG00000097007	ENST00000372348;ENST00000318560|ENST00000444970	T;T|.	0.62232|.	0.04;0.04|.	6.03|6.03	6.03|6.03	0.97812|0.97812	Protein kinase-like domain (1);SH2 motif (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85952|0.85952	0.5817|0.5817	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.75484|.	0.986;0.986|.	D|D	0.87424|0.87424	0.2384|0.2384	10|6	0.87932|0.72032	D|D	0|0.01	.|.	19.6124|19.6124	0.95613|0.95613	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	233;270|.	P00519;Q59FK4|.	ABL1_HUMAN;.|.	N|Q	252;233|49	ENSP00000361423:D252N;ENSP00000323315:D233N|.	ENSP00000323315:D233N|ENSP00000400412:R49Q	D|R	+|+	1|2	0|0	ABL1|ABL1	132728118|132728118	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.812000|9.812000	0.99227|0.99227	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	GAC|CGA	.		0.577	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		A	133738297	G	A	133738297	3	1	127	1	0	0	0	0	1	0	0	0	92	1058	37	1	851	1	ABL1	9	133738297	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	2368088	133738297	7475134	59	11159											
RAPGEF1	2889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134505712	134505712	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtgagcctgaccagctcCtacccccacaagaaaaaggc	13	5	9	14	0	0	3	0	2	0	1	1	3	1	3	5	2	3	1	5	2	4	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:134505712C>T	ENST00000372189.3	-	6	724		c.e6-1		RAPGEF1_ENST00000372195.1_Splice_Site|RAPGEF1_ENST00000481260.1_Intron|RAPGEF1_ENST00000372190.3_Splice_Site	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1						activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		TGACCAGCTCCTACCCCCACA	0.592																																					.		.											.	RAPGEF1-849	0			c.601-1G>A						.						57	65	62					9																	134505712		2074	4208	6282	SO:0001630	splice_region_variant	2889	exon7			CAGCTCCTACCCC	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.601-1G>A	9.37:g.134505712C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	97	9	NM_005312	0	0	0	0	0	Q5JUE4|Q8IV73	Splice_Site	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.006457	0.74932	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000357686	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0057	0.80362	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAPGEF1	133495533	1.000000	0.71417	0.996000	0.52242	0.758000	0.43043	6.814000	0.75236	2.549000	0.85964	0.655000	0.94253	.	.		0.592	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	Intron	T	134505712	C	T	134505712	5	4	127	1	0	0	0	0	0	0	1	0	13075	695	24	2	2709	2	RAPGEF1	9	134505712	Splice_Site	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	767415	134505712	6707719	60	11160											
KIN	22944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	7811178	7811178	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacgcaatccataaactgtaCctccatgatttcatccagtg	12	11	5	13	1	1	1	1	1	0	0	4	1	4	1	4	0	2	2	4	0	4	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:7811178C>T	ENST00000379562.4	-	8	846		c.e8+1		KIN_ENST00000535925.1_Splice_Site|KIN_ENST00000463666.1_5'Flank|KIN_ENST00000543003.1_Splice_Site	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						ATAAACTGTACCTCCATGATT	0.343																																					.		.											.	KIN-230	0			c.798+1G>A						.						99	99	99					10																	7811178		2203	4300	6503	SO:0001630	splice_region_variant	22944	exon9			ACTGTACCTCCAT	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.798+1G>A	10.37:g.7811178C>T		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	23	8	NM_012311	0	0	0	0	0		Splice_Site	SNP	ENST00000379562.4	37	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955761	0.73902	.	.	ENSG00000151657	ENST00000535925;ENST00000379562;ENST00000543003	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.75	0.85483	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIN	7851184	1.000000	0.71417	0.995000	0.50966	0.891000	0.51852	5.846000	0.69444	2.363000	0.80096	0.650000	0.86243	.	.		0.343	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311	Intron	T	7811178	C	T	7811178	5	4	127	1	0	0	0	0	0	0	1	0	8336	521	18	2	406	2	KIN	10	7811178	Splice_Site	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		7811178	127723569	61	11161											
KIAA1217	56243	broad.mit.edu;bcgsc.ca	37	chr10	24834831	24834831	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctgcttctaagattccaGccctttctcccagctctggg	6	13	7	15	0	3	1	0	0	3	1	5	1	4	1	4	1	4	2	4	1	2	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:24834831G>A	ENST00000376454.3	+	21	5440	c.5410G>A	c.(5410-5412)Gcc>Acc	p.A1804T	KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A1235T|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376462.1_Missense_Mutation_p.A1125T|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A1210T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1804	Ser-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TAAGATTCCAGCCCTTTCTCC	0.493																																					p.A1804T													.	KIAA1217-98	0			c.G5410A						.						147	146	147					10																	24834831		2203	4300	6503	SO:0001583	missense	56243	exon21			ATTCCAGCCCTTT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5410G>A	10.37:g.24834831G>A	ENSP00000365637:p.Ala1804Thr	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	161	6	NM_019590	0	0	15	15	0	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.675129	0.88445	.	.	ENSG00000120549	ENST00000376462;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000450158	T;T;T;T	0.53640	0.89;0.61;1.05;0.71	5.67	5.67	0.87782	.	0.060496	0.64402	D	0.000004	T	0.66655	0.2811	M	0.63843	1.955	0.33399	D	0.57704	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.77004	0.952;0.989;0.984;0.952	T	0.67573	-0.5636	10	0.24483	T	0.36	.	19.7685	0.96352	0.0:0.0:1.0:0.0	.	1210;1235;1804;1205	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	T	1125;1210;1804;1235;1393	ENSP00000365645:A1125T;ENSP00000392625:A1210T;ENSP00000365637:A1804T;ENSP00000365635:A1235T	ENSP00000365635:A1235T	A	+	1	0	KIAA1217	24874837	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.503000	0.81632	2.679000	0.91253	0.650000	0.86243	GCC	.		0.493	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		A	24834831	G	A	24834831	3	1	127	1	0	0	0	0	1	0	0	0	8237	971	34	2	5492	2	KIAA1217	10	24834831	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	17023653	24834831	110699916	62	11162											
PLCE1	51196	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	96005839	96005839	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccttggtacgtgctgtccAtccaagccgatgtgcaccag	7	10	10	14	2	0	0	0	0	0	0	3	1	3	0	5	1	4	3	5	1	2	2	rs200483837	byFrequency	TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:96005839A>G	ENST00000371380.3	+	7	2792	c.2557A>G	c.(2557-2559)Atc>Gtc	p.I853V	PLCE1_ENST00000371375.1_Missense_Mutation_p.I545V|PLCE1_ENST00000260766.3_Missense_Mutation_p.I853V|PLCE1_ENST00000371385.3_Missense_Mutation_p.I545V			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	853					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				CGTGCTGTCCATCCAAGCCGA	0.572																																					p.I853V													.	PLCE1-229	0			c.A2557G						.						64	70	68					10																	96005839		2152	4256	6408	SO:0001583	missense	51196	exon8			CTGTCCATCCAAG		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"nephrosis type 3"	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.2557A>G	10.37:g.96005839A>G	ENSP00000360431:p.Ile853Val	Somatic	214	2		WXS	Illumina HiSeq	Phase_I	219	21	NM_016341	0	0	0	0	0	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	A	13.50	2.254909	0.39896	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	6.04	3.71	0.42584	Ras guanine nucleotide exchange factor, domain (1);	0.297710	0.33712	N	0.004639	T	0.21022	0.0506	N	0.19112	0.55	0.24609	N	0.99373	B;B;B	0.27380	0.177;0.008;0.036	B;B;B	0.24394	0.053;0.023;0.03	T	0.12630	-1.0540	10	0.39692	T	0.17	.	7.7436	0.28856	0.8078:0.0:0.0667:0.1255	.	853;545;853	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	V	853;853;545;545	ENSP00000260766:I853V;ENSP00000360431:I853V;ENSP00000360438:I545V;ENSP00000360426:I545V	ENSP00000260766:I853V	I	+	1	0	PLCE1	95995829	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.444000	0.60001	1.085000	0.41206	0.477000	0.44152	ATC	A|0.999;T|0.000		0.572	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		G	96005839	A	G	96005839	3	3	127	1	0	0	0	0	1	0	0	0	12060	217	8	3	2869	3	PLCE1	10	96005839	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	71171008	96005839	39528908	63	11163											
HPS1	3257	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	100177417	100177417	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggatgacagacaggtgcagGgccagcagctcgtagcacct	10	5	15	11	1	0	2	0	1	0	1	1	3	0	3	2	3	4	5	2	3	1	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:100177417G>A	ENST00000325103.6	-	20	2240	c.2007C>T	c.(2005-2007)gcC>gcT	p.A669A	PYROXD2_ENST00000370575.4_5'Flank|HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Silent_p.A669A	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	669					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		ACAGGTGCAGGGCCAGCAGCT	0.662									Hermansky-Pudlak syndrome																												p.A669A													.	HPS1-91	0			c.C2007T						.						69	62	65					10																	100177417		2203	4300	6503	SO:0001819	synonymous_variant	3257	exon20	Familial Cancer Database	HPS, HPS1-8	GTGCAGGGCCAGC	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"Hermansky-Pudlak syndrome"	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.2007C>T	10.37:g.100177417G>A		Somatic	260	1		WXS	Illumina HiSeq	Phase_I	217	61	NM_000195	0	0	50	76	26	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1																																																																																			.		0.662	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639		A	100177417	G	A	100177417	2	1	127	1	0	0	0	0	0	0	0	1	7360	1219	43	2		2	HPS1	10	100177417	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	4171578	100177417	35357330	64	11164											
ABCC2	1244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101559080	101559080	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcctgaaatcattcctactGaagctagtgaatgacatctt	12	13	6	10	0	2	4	1	4	1	0	4	4	4	4	2	0	2	1	2	0	5	4	rs181542662		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:101559080G>A	ENST00000370449.4	+	8	1097	c.984G>A	c.(982-984)ctG>ctA	p.L328L		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	328	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CATTCCTACTGAAGCTAGTGA	0.463													G|||	1	0.000199681	8e-04	0	5008	,	,		18381	0		0	False		,,,				2504	0				p.L328L		.											.	ABCC2-91	0			c.G984A						.						292	300	297					10																	101559080		2203	4300	6503	SO:0001819	synonymous_variant	1244	exon8			CCTACTGAAGCTA	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.984G>A	10.37:g.101559080G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	52	10	NM_000392	0	0	0	0	0	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																			G|0.999;A|0.000		0.463	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101559080	G	A	101559080	2	1	127	1	0	0	0	0	0	0	0	1	53	1277	45	2		2	ABCC2	10	101559080	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	1381663	101559080	33975667	65	11165											
OAT	4942	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	126100644	126100644	+	Frame_Shift_Del	DEL	T	T	-																															ggttggagggccttggactgTttttttagttgcaacagatg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:126100644delT	ENST00000368845.5	-	2	189	c.97delA	c.(97-99)acafs	p.T33fs	OAT_ENST00000539214.1_Intron	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	33					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	CCTTGGACTGTTTTTTTAGTT	0.433																																					p.T33fs		.											.	OAT-68	0			c.97delA						.						88	81	83					10																	126100644		2203	4300	6503	SO:0001589	frameshift_variant	4942	exon2			.	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"Ornithine aminotransferase", "ornithine aminotransferase precursor", "gyrate atrophy"	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.97delA	10.37:g.126100644delT	ENSP00000357838:p.Thr33fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	96	27	NM_000274	0	0	0	0	0	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Frame_Shift_Del	DEL	ENST00000368845.5	37	CCDS7639.1																																																																																			.		0.433	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274		-	126100644	T	-	126100644	7	5	127	1	0	1	0	1	0	0	0	0	10829	1725	60	0	1258	0	OAT	10	126100644	Frame_Shift_Del	DEL	T	TCGA-GL-A59T-01A-21D-A28G-10	24541564	126100644	9434103	66	11166											
AP2A2	161	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	985477	985477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgagtgcctggagaccaTcctgaacaaagcccaagaac	14	5	10	12	0	0	4	0	2	0	2	1	6	1	4	4	1	4	0	4	1	4	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:985477T>C	ENST00000448903.2	+	8	998	c.857T>C	c.(856-858)aTc>aCc	p.I286T	AP2A2_ENST00000534328.1_Missense_Mutation_p.I286T|AP2A2_ENST00000332231.5_Missense_Mutation_p.I287T	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	286					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTGGAGACCATCCTGAACAAA	0.592																																					p.I287T													.	AP2A2-90	0			c.T860C						.						102	108	106					11																	985477		2101	4232	6333	SO:0001583	missense	161	exon8			AGACCATCCTGAA	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.857T>C	11.37:g.985477T>C	ENSP00000413234:p.Ile286Thr	Somatic	148	1		WXS	Illumina HiSeq	Phase_I	148	54	NM_001242837	0	0	22	38	16	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	37	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.425714	0.83667	.	.	ENSG00000183020	ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000329626	T;T;T	0.31510	1.49;1.49;1.49	3.89	3.89	0.44902	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.062577	0.64402	D	0.000008	T	0.53012	0.1770	M	0.73753	2.245	0.80722	D	1	D;D	0.64830	0.991;0.994	P;D	0.69142	0.874;0.962	T	0.59096	-0.7518	10	0.72032	D	0.01	-38.971	13.0543	0.58971	0.0:0.0:0.0:1.0	.	287;286	O94973-2;O94973	.;AP2A2_HUMAN	T	286;286;286;287;287;159	ENSP00000436059:I286T;ENSP00000413234:I286T;ENSP00000327694:I287T	ENSP00000328024:I159T	I	+	2	0	AP2A2	975477	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	7.863000	0.87023	1.552000	0.49463	0.533000	0.62120	ATC	.		0.592	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		C	985477	T	C	985477	3	2	127	1	0	0	0	0	1	0	0	0	740	1435	50	3	887	3	AP2A2	11	985477	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10		985477	134021039	67	11167											
MUC2	4583	hgsc.bcm.edu;broad.mit.edu	37	chr11	1093292	1093292	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcgacacccatcaccaccaCcactacggtgaccccaaccc	12	4	4	21	2	1	1	1	1	0	0	2	2	1	1	7	1	2	0	7	1	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:1093292C>T	ENST00000441003.2	+	30	5138	c.5111C>T	c.(5110-5112)aCc>aTc	p.T1704I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1671I|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	atcaccaccaccactacggtg	0.637																																					p.T1704I		.											.	MUC2-90	0			c.C5111T						.						107	156	138					11																	1093292		1878	3453	5331	SO:0001583	missense	4583	exon30			CCACCACCACTAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5111C>T	11.37:g.1093292C>T	ENSP00000415183:p.Thr1704Ile	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	107	7	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.150	-0.394632	0.04899	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11063	2.81;2.84	1.6	-2.66	0.06077	.	2.760050	0.04005	U	0.297091	T	0.06416	0.0165	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.36286	-0.9754	9	0.36615	T	0.2	.	2.477	0.04578	0.4942:0.3128:0.0:0.1931	.	1704	E7EUV1	.	I	1704;1671	ENSP00000415183:T1704I;ENSP00000351956:T1671I	ENSP00000351956:T1671I	T	+	2	0	MUC2	1083292	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.330000	0.19715	-0.514000	0.06488	0.184000	0.17185	ACC	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093292	C	T	1093292	3	4	127	1	0	0	0	0	1	0	0	0	10000	507	18	2	5229	2	MUC2	11	1093292	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	107815	1093292	133913224	68	11168											
MPEG1	219972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	58978564	58978564	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgggtgaaaggtgggagcCtggcagggggcagggaccct	7	4	21	9	1	0	1	0	1	0	0	0	3	0	3	3	7	1	2	3	7	1	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:58978564C>T	ENST00000361050.3	-	1	1860	c.1775G>A	c.(1774-1776)aGg>aAg	p.R592K		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	592						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				AGGTGGGAGCCTGGCAGGGGG	0.582																																					p.R592K		.											.	MPEG1-70	0			c.G1775A						.						87	97	93					11																	58978564		1945	4123	6068	SO:0001583	missense	219972	exon1			GGGAGCCTGGCAG	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"macrophage expressed gene 1"	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1775G>A	11.37:g.58978564C>T	ENSP00000354335:p.Arg592Lys	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	104	39	NM_001039396	0	0	6	6	0	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648686	0.47258	.	.	ENSG00000197629	ENST00000361050	T	0.23147	1.92	5.69	5.69	0.88448	.	0.109255	0.64402	D	0.000015	T	0.42154	0.1190	L	0.61387	1.9	0.34323	D	0.686779	D	0.60575	0.988	P	0.54759	0.76	T	0.52601	-0.8554	10	0.44086	T	0.13	-27.9243	16.7224	0.85413	0.0:1.0:0.0:0.0	.	592	Q2M385	MPEG1_HUMAN	K	592	ENSP00000354335:R592K	ENSP00000354335:R592K	R	-	2	0	MPEG1	58735140	0.678000	0.27586	1.000000	0.80357	0.942000	0.58702	0.292000	0.19011	2.682000	0.91365	0.655000	0.94253	AGG	.		0.582	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58978564	C	T	58978564	3	4	127	1	0	0	0	0	1	0	0	0	9748	681	24	2	379	2	MPEG1	11	58978564	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	57885272	58978564	76027952	69	11169											
PYGM	5837	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64517951	64517951	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacattggccccgtccatggTgccaatggtcagagccccgt	7	8	11	15	2	1	1	1	0	0	1	2	1	2	1	6	3	2	0	6	3	1	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:64517951T>A	ENST00000164139.3	-	17	2472	c.2074A>T	c.(2074-2076)Acc>Tcc	p.T692S	PYGM_ENST00000377432.3_Missense_Mutation_p.T604S|PYGM_ENST00000462303.1_5'Flank	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	692					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCGTCCATGGTGCCAATGGTC	0.567																																					p.T692S		.											.	PYGM-92	0			c.A2074T						.						167	151	157					11																	64517951		2201	4297	6498	SO:0001583	missense	5837	exon17			CCATGGTGCCAAT		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"Glycogen phosphorylases"	9726	protein-coding gene	gene with protein product	"McArdle syndrome", "glycogen storage disease type V", "glycogen phosphorylase, muscle form"	608455	"phosphorylase, glycogen; muscle"				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.2074A>T	11.37:g.64517951T>A	ENSP00000164139:p.Thr692Ser	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	114	38	NM_005609	0	0	0	0	0	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	37	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.903517	0.92035	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.95342	-3.68;-3.68	4.91	4.91	0.64330	.	0.000000	0.52532	D	0.000074	D	0.96895	0.8986	M	0.93854	3.465	0.80722	D	1	P;P	0.48407	0.91;0.91	P;P	0.52386	0.697;0.697	D	0.97609	1.0128	10	0.87932	D	0	-39.6172	12.5412	0.56172	0.0:0.0:0.0:1.0	.	604;692	A6NDY6;P11217	.;PYGM_HUMAN	S	604;692;673	ENSP00000366650:T604S;ENSP00000164139:T692S	ENSP00000164139:T692S	T	-	1	0	PYGM	64274527	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.832000	0.86757	2.073000	0.62155	0.454000	0.30748	ACC	.		0.567	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		A	64517951	T	A	64517951	3	1	127	1	0	0	0	0	1	0	0	0	12894	1696	59	5	470	5	PYGM	11	64517951	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	5539387	64517951	70488565	70	11170											
NUMA1	4926	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	71733436	71733436	+	Frame_Shift_Del	DEL	G	G	-																															ctgggacttttggagctcatGgtagagtggtataagagcag																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:71733436delG	ENST00000393695.3	-	7	652	c.321delC	c.(319-321)accfs	p.T107fs	NUMA1_ENST00000351960.6_Frame_Shift_Del_p.T107fs|NUMA1_ENST00000358965.6_Frame_Shift_Del_p.T107fs|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						TGGAGCTCATGGTAGAGTGGT	0.517			T	RARA	APL																																p.T107fs		.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1-633	0			c.321delC						.						155	158	157					11																	71733436		2200	4293	6493	SO:0001589	frameshift_variant	4926	exon7			.	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.321delC	11.37:g.71733436delG	ENSP00000377298:p.Thr107fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	68	21	NM_006185	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000393695.3	37	CCDS31633.1																																																																																			.		0.517	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			-	71733436	G	-	71733436	7	5	127	1	0	1	0	1	0	0	0	0	10776	1335	47	0	6110	0	NUMA1	11	71733436	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	7215485	71733436	63273080	71	11171											
CHCHD8	51287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	73584202	73584202	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgcctcctctgcagctcCtcttgccgcctcgcctgctg	1	13	8	19	2	3	0	0	0	3	0	6	0	5	0	6	0	5	3	6	0	0	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:73584202C>A	ENST00000355693.4	-	2	469	c.222G>T	c.(220-222)gaG>gaT	p.E74D	COA4_ENST00000545127.1_Missense_Mutation_p.E74D|COA4_ENST00000541455.1_Missense_Mutation_p.E83D|COA4_ENST00000537581.1_5'Flank|COA4_ENST00000537289.1_Missense_Mutation_p.E74D	NM_016565.2	NP_057649.2	Q9NYJ1	COA4_HUMAN	cytochrome c oxidase assembly factor 4 homolog (S. cerevisiae)	74						mitochondrion (GO:0005739)											TCTGCAGCTCCTCTTGCCGCC	0.612																																					p.E74D		.											.	.	0			c.G222T						.						108	81	90					11																	73584202		2200	4293	6493	SO:0001583	missense	51287	exon2			CAGCTCCTCTTGC	AF242180	CCDS8225.1	11q13.4	2013-10-18	2012-10-15	2012-10-15		ENSG00000181924		"Coiled-coil-helix-coiled-coil-helix domain containing", "Mitochondrial respiratory chain complex assembly factors"	24604	protein-coding gene	gene with protein product		608016	"coiled-coil-helix-coiled-coil-helix domain containing 8"	CHCHD8		11085516, 20624914	Standard	NM_016565		Approved	E2IG2, CMC3	uc001ouj.3	Q9NYJ1		ENST00000355693.4:c.222G>T	11.37:g.73584202C>A	ENSP00000347919:p.Glu74Asp	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	77	9	NM_016565	0	0	80	107	27	B2RAA0|Q69YU4	Missense_Mutation	SNP	ENST00000355693.4	37	CCDS8225.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273202	0.59649	.	.	ENSG00000181924	ENST00000355693;ENST00000545127;ENST00000541455;ENST00000537289	.	.	.	6.02	2.73	0.32206	.	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	.	.	.	0.33160	D	0.546821	P	0.39665	0.682	B	0.34038	0.174	T	0.50890	-0.8774	8	0.59425	D	0.04	-24.9482	8.1718	0.31260	0.0:0.6617:0.0:0.3383	.	74	Q9NYJ1	CHCH8_HUMAN	D	74;74;83;74	.	ENSP00000347919:E74D	E	-	3	2	CHCHD8	73261850	0.857000	0.29778	0.996000	0.52242	0.388000	0.30384	0.299000	0.19138	0.879000	0.35944	0.655000	0.94253	GAG	.		0.612	COA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397878.1	NM_016565		A	73584202	C	A	73584202	3	1	127	1	0	0	0	0	1	0	0	0	3328	680	24	4	45	4	CHCHD8	11	73584202	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	1850766	73584202	61422314	72	11172											
PRCP	5547	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82560214	82560214	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatgtcctgagaagttaaTgggctgcataagtgaagggc	11	10	15	5	0	0	2	0	2	0	1	1	4	1	3	1	3	1	3	1	3	4	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:82560214T>C	ENST00000313010.3	-	6	992	c.798A>G	c.(796-798)ccA>ccG	p.P266P	PRCP_ENST00000393399.2_Silent_p.P287P|PRCP_ENST00000535099.1_Silent_p.P161P	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	266	SKS domain.				angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GAGAAGTTAATGGGCTGCATA	0.443																																					p.P287P		.											.	PRCP-91	0			c.A861G						.						115	108	110					11																	82560214		2203	4300	6503	SO:0001819	synonymous_variant	5547	exon7			AGTTAATGGGCTG	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.798A>G	11.37:g.82560214T>C		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	88	18	NM_199418	0	0	54	69	15	A8MU24|B2R7B7|B3KRK5|B5BU34	Silent	SNP	ENST00000313010.3	37	CCDS8262.1																																																																																			.		0.443	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040		C	82560214	T	C	82560214	2	2	127	1	0	0	0	0	0	0	0	1	12478	1451	51	3		3	PRCP	11	82560214	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	8976012	82560214	52446302	73	11173											
DDX10	1662	hgsc.bcm.edu	37	chr11	108559718	108559718	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgagctgcagcaaaaaataAgtgtgctgtattcctttttg	11	14	10	6	0	0	1	0	1	0	0	1	1	1	1	1	0	4	5	1	0	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:108559718A>G	ENST00000322536.3	+	7	1033	c.904A>G	c.(904-906)Agt>Ggt	p.S302G	DDX10_ENST00000526794.1_Missense_Mutation_p.S302G	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	302	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		GCAAAAAATAAGTGTGCTGTA	0.373			T	NUP98	AML*																																p.S302G		.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10-1145	0			c.A904G						.						194	193	193					11																	108559718		2201	4298	6499	SO:0001583	missense	1662	exon7			AAAATAAGTGTGC	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.904A>G	11.37:g.108559718A>G	ENSP00000314348:p.Ser302Gly	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_004398	0	0	9	9	0	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	37	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	A	8.380	0.837213	0.16891	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.04809	3.55;3.55	5.61	5.61	0.85477	Helicase, C-terminal (1);	0.171976	0.64402	D	0.000008	T	0.04092	0.0114	N	0.16130	0.375	0.30844	N	0.735378	B;B	0.20887	0.049;0.049	B;B	0.16722	0.016;0.016	T	0.20505	-1.0273	10	0.27082	T	0.32	-11.3262	15.8096	0.78547	1.0:0.0:0.0:0.0	.	302;302	Q13206;E9PIF2	DDX10_HUMAN;.	G	302;208;302	ENSP00000314348:S302G;ENSP00000432032:S302G	ENSP00000314348:S302G	S	+	1	0	DDX10	108064928	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	6.272000	0.72575	2.132000	0.65825	0.533000	0.62120	AGT	.		0.373	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		G	108559718	A	G	108559718	3	3	127	1	0	0	0	0	1	0	0	0	4348	72	3	3	930	3	DDX10	11	108559718	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	25999504	108559718	26446798	74	11174											
SLC37A4	51399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118895661	118895661	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcccatcttggtgcggaTgtttcgtaggaggaagaagg	8	10	16	7	3	1	1	0	0	1	1	3	4	1	4	1	6	1	2	1	6	3	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:118895661T>C	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000525102.1_5'UTR|SLC37A4_ENST00000330775.7_Missense_Mutation_p.I438V|SLC37A4_ENST00000538950.1_Missense_Mutation_p.I344V|SLC37A4_ENST00000357590.5_Missense_Mutation_p.I439V|SLC37A4_ENST00000545985.1_Missense_Mutation_p.I417V|TRAPPC4_ENST00000533058.1_Missense_Mutation_p.C226R	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		TTGGTGCGGATGTTTCGTAGG	0.597																																					p.I439V		.											.	SLC37A4-67	0			c.A1315G						.						43	51	48					11																	118895661		2020	4175	6195	SO:0001628	intergenic_variant	2542	exon12			TGCGGATGTTTCG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"Trafficking protein particle complex"	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			11.37:g.118895661T>C		Somatic	180	0		WXS	Illumina HiSeq	Phase_I	125	41	NM_001164278	0	0	72	147	75	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	37	CCDS8407.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560807	0.45590	.	.	ENSG00000196655	ENST00000533058	T	0.50001	0.76	5.27	5.27	0.74061	.	.	.	.	.	T	0.52370	0.1730	L	0.36672	1.1	0.50171	D	0.999855	.	.	.	.	.	.	T	0.56147	-0.8027	7	0.87932	D	0	-22.4876	15.3661	0.74523	0.0:0.0:0.0:1.0	.	.	.	.	R	226	ENSP00000432920:C226R	ENSP00000432920:C226R	C	+	1	0	TRAPPC4	118400871	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.309000	0.78937	2.226000	0.72624	0.459000	0.35465	TGT	.		0.597	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146		C	118895661	T	C	118895661	1	2	127	0	1	0	0	0	0	0	0	0	14632	1464	51	3		3	SLC37A4	11	118895661	IGR	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	10335943	118895661	16110855	75	11175											
NCAPD2	9918	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6637492	6637492	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggactcctcatctgtatgcTcggtaagagacccctcacaa	10	10	8	13	1	3	1	2	0	1	1	5	3	4	2	3	2	1	3	3	2	3	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:6637492T>C	ENST00000315579.5	+	25	4096	c.3297T>C	c.(3295-3297)gcT>gcC	p.A1099A	NCAPD2_ENST00000545962.1_Silent_p.A1054A	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1099					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						ATCTGTATGCTCGGTAAGAGA	0.577																																					p.A1099A		.											.	NCAPD2-660	0			c.T3297C						.						139	143	142					12																	6637492		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon25			GTATGCTCGGTAA	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"chromosome condensation related SMC associated protein 1"	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.3297T>C	12.37:g.6637492T>C		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	134	31	NM_014865	0	0	0	0	0	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			.		0.577	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		C	6637492	T	C	6637492	2	2	127	1	0	0	0	0	0	0	0	1	10231	1538	54	3		3	NCAPD2	12	6637492	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10		6637492	127214403	76	11176											
LARP4	113251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	50847398	50847398	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caccaacagtactcggtctaTagtattgtgcctcagtcttg	9	13	8	11	1	3	0	1	0	2	0	4	0	3	0	2	1	3	2	2	1	5	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:50847398T>C	ENST00000398473.2	+	9	1072	c.960T>C	c.(958-960)taT>taC	p.Y320Y	LARP4_ENST00000518444.1_Silent_p.Y319Y|LARP4_ENST00000347328.5_Intron|LARP4_ENST00000518561.1_Silent_p.Y250Y|LARP4_ENST00000429001.3_Silent_p.Y326Y|LARP4_ENST00000522085.1_Silent_p.Y320Y|LARP4_ENST00000293618.8_Silent_p.Y320Y	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	320					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						ACTCGGTCTATAGTATTGTGC	0.373																																					p.Y320Y		.											.	LARP4-91	0			c.T960C						.						208	181	190					12																	50847398		1906	4126	6032	SO:0001819	synonymous_variant	113251	exon9			GGTCTATAGTATT	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.960T>C	12.37:g.50847398T>C		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	178	44	NM_001170808	0	0	1	2	1	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	37	CCDS41782.1																																																																																			.		0.373	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		C	50847398	T	C	50847398	2	2	127	1	0	0	0	0	0	0	0	1	8651	1413	49	3		3	LARP4	12	50847398	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	44209906	50847398	83004497	77	11177											
NPFF	8620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53900627	53900627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aattcagcccctctccagccCggggactcagccattcattc	8	9	7	17	1	4	0	3	0	1	0	6	1	4	1	5	2	3	0	5	2	1	3	rs199569723		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:53900627C>T	ENST00000267017.3	-	3	438	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	RP11-793H13.10_ENST00000591834.1_3'UTR|NPFF_ENST00000609999.1_Missense_Mutation_p.R95Q	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor	92					acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						CTCTCCAGCCCGGGGACTCAG	0.552																																					p.R92Q		.											.	NPFF-90	0			c.G275A						.						111	114	113					12																	53900627		2203	4300	6503	SO:0001583	missense	8620	exon3			CCAGCCCGGGGAC	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856	ENST00000267017.3:c.275G>A	12.37:g.53900627C>T	ENSP00000267017:p.Arg92Gln	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	76	10	NM_003717	0	0	7	7	0	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	37	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.306772	0.23821	.	.	ENSG00000139574	ENST00000267017	T	0.54279	0.58	4.52	-1.46	0.08800	.	0.173981	0.36555	N	0.002528	T	0.36441	0.0967	L	0.49126	1.545	0.09310	N	1	B	0.23490	0.086	B	0.17722	0.019	T	0.13737	-1.0498	10	0.38643	T	0.18	-7.5784	3.979	0.09487	0.3493:0.371:0.0:0.2797	.	92	O15130	NPFF_HUMAN	Q	92	ENSP00000267017:R92Q	ENSP00000267017:R92Q	R	-	2	0	NPFF	52186894	0.048000	0.20356	0.008000	0.14137	0.980000	0.70556	0.139000	0.16036	-0.071000	0.12886	0.491000	0.48974	CGG	.		0.552	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		T	53900627	C	T	53900627	3	4	127	1	0	0	0	0	1	0	0	0	10602	652	23	1	70	1	NPFF	12	53900627	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	3053229	53900627	79951268	78	11178											
CEP290	80184	broad.mit.edu;bcgsc.ca	37	chr12	88474150	88474150	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcttttacttttttcacttCatcttcatggttttcttgaa	6	22	4	9	1	5	1	3	1	2	0	5	1	5	1	0	1	1	2	0	1	2	10			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:88474150C>T	ENST00000552810.1	-	38	5378	c.5035G>A	c.(5035-5037)Gaa>Aaa	p.E1679K	CEP290_ENST00000397838.3_Missense_Mutation_p.E739K|CEP290_ENST00000547691.2_Missense_Mutation_p.E739K|CEP290_ENST00000309041.7_Missense_Mutation_p.E1681K	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1679					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTTTCACTTCATCTTCATGG	0.348																																					p.E1679K													.	CEP290-96	0			c.G5035A						.						125	111	115					12																	88474150		1818	4077	5895	SO:0001583	missense	80184	exon38			TCACTTCATCTTC	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5035G>A	12.37:g.88474150C>T	ENSP00000448012:p.Glu1679Lys	Somatic	52	1		WXS	Illumina HiSeq	Phase_I	56	24	NM_025114	0	0	2	2	0	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.241191	0.39598	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93	4.53	4.53	0.55603	.	0.238715	0.41938	D	0.000800	D	0.88058	0.6335	L	0.29908	0.895	0.44635	D	0.997619	B	0.34399	0.452	B	0.36567	0.228	D	0.86549	0.1833	10	0.30078	T	0.28	.	17.6111	0.88053	0.0:1.0:0.0:0.0	.	1679	O15078	CE290_HUMAN	K	739;1679;1681;739	ENSP00000446905:E739K;ENSP00000448012:E1679K;ENSP00000308021:E1681K;ENSP00000380938:E739K	ENSP00000308021:E1681K	E	-	1	0	CEP290	86998281	1.000000	0.71417	0.921000	0.36526	0.187000	0.23431	5.327000	0.65881	2.226000	0.72624	0.460000	0.39030	GAA	.		0.348	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88474150	C	T	88474150	3	4	127	1	0	0	0	0	1	0	0	0	3259	835	29	2	2472	2	CEP290	12	88474150	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	34573523	88474150	45377745	79	11179											
CEP290	80184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	88514780	88514780	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaaaatacataccgattcAtaatcttttaacctcttcag	16	14	2	9	1	4	0	2	0	2	0	4	1	4	0	2	0	3	0	2	0	7	8			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:88514780A>C	ENST00000552810.1	-	14	1696	c.1353T>G	c.(1351-1353)taT>taG	p.Y451*	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Nonsense_Mutation_p.Y451*	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	451					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATACCGATTCATAATCTTTTA	0.363																																					p.Y451X		.											.	CEP290-96	0			c.T1353G						.						89	86	87					12																	88514780		1837	4077	5914	SO:0001587	stop_gained	80184	exon14			CGATTCATAATCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4"	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1353T>G	12.37:g.88514780A>C	ENSP00000448012:p.Tyr451*	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	18	10	NM_025114	0	0	0	0	0	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Nonsense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	41	8.542306	0.98857	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	.	.	.	5.61	4.42	0.53409	.	0.147782	0.46758	D	0.000264	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	5.4776	0.16704	0.7324:0.0:0.1371:0.1305	.	.	.	.	X	451;451;451;353	.	ENSP00000308021:Y451X	Y	-	3	2	CEP290	87038911	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.199000	0.58426	2.137000	0.66172	0.482000	0.46254	TAT	.		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88514780	A	C	88514780	4	2	127	1	0	0	0	0	0	1	0	0	3259	224	8	5	6250	5	CEP290	12	88514780	Nonsense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	40630	88514780	45337115	80	11180											
ANKS1B	56899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	99640158	99640158	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actcttgatgttttctcattGgaaggataggcaatgagatc	11	14	10	6	0	2	2	1	2	2	1	4	5	2	4	0	3	0	2	0	3	3	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:99640158G>A	ENST00000547776.2	-	13	2240	c.2241C>T	c.(2239-2241)tcC>tcT	p.S747S	ANKS1B_ENST00000329257.7_Silent_p.S747S|ANKS1B_ENST00000547010.1_Silent_p.S327S|ANKS1B_ENST00000550833.1_5'Flank	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	747						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TTTTCTCATTGGAAGGATAGG	0.413																																					p.S747S		.											.	.	0			c.C2241T						.						92	87	89					12																	99640158		1912	4102	6014	SO:0001819	synonymous_variant	56899	exon13			CTCATTGGAAGGA	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.2241C>T	12.37:g.99640158G>A		Somatic	198	0		WXS	Illumina HiSeq	Phase_I	231	112	NM_152788	0	0	0	0	0	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	7.433	0.639208	0.14386	.	.	ENSG00000185046	ENST00000550778	.	.	.	5.21	-7.15	0.01521	.	.	.	.	.	T	0.38401	0.1039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45977	-0.9224	4	.	.	.	-6.1946	3.8547	0.08970	0.0906:0.3375:0.3258:0.2461	.	.	.	.	L	19	.	.	P	-	2	0	ANKS1B	98164289	0.194000	0.23325	0.127000	0.21898	0.969000	0.65631	-1.051000	0.03507	-0.833000	0.04245	0.462000	0.41574	CCA	.		0.413	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		A	99640158	G	A	99640158	2	1	127	1	0	0	0	0	0	0	0	1	689	1335	47	2		2	ANKS1B	12	99640158	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	11125378	99640158	34211737	81	11181											
CCDC64	92558	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120428098	120428098	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaggagctgacagacaagctCgaggtgaggacctccctcca	12	5	12	12	1	0	3	0	2	0	1	3	6	2	5	3	3	2	2	3	3	2	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:120428098C>T	ENST00000397558.2	+	1	426	c.426C>T	c.(424-426)ctC>ctT	p.L142L		NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	142					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAGACAAGCTCGAGGTGAGGA	0.657																																					p.L142L													.	CCDC64-92	0			c.C426T						.						8	9	9					12																	120428098		2031	4193	6224	SO:0001819	synonymous_variant	92558	exon1			CAAGCTCGAGGTG	U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.426C>T	12.37:g.120428098C>T		Somatic	208	1		WXS	Illumina HiSeq	Phase_I	269	64	NM_207311	0	0	0	0	0	A8MUC8|B4DWL0|B5MDJ0|O95000	Silent	SNP	ENST00000397558.2	37	CCDS41845.1																																																																																			.		0.657	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311		T	120428098	C	T	120428098	2	4	127	1	0	0	0	0	0	0	0	1	2841	871	31	1		1	CCDC64	12	120428098	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	20787940	120428098	13423797	82	11182											
GPC6	10082	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	94938687	94938687	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagatgtcaagatttctgAagccattatgaacatgcaag	15	11	9	6	0	2	4	1	2	1	2	2	5	2	4	1	0	3	1	1	0	6	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr13:94938687A>C	ENST00000377047.4	+	5	1577	c.962A>C	c.(961-963)gAa>gCa	p.E321A		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	321					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				AAGATTTCTGAAGCCATTATG	0.423																																					p.E321A													.	GPC6-90	0			c.A962C						.						100	91	94					13																	94938687		2203	4300	6503	SO:0001583	missense	10082	exon5			TTTCTGAAGCCAT	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.962A>C	13.37:g.94938687A>C	ENSP00000366246:p.Glu321Ala	Somatic	105	1		WXS	Illumina HiSeq	Phase_I	91	34	NM_005708	0	0	0	1	1	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684752	0.88639	.	.	ENSG00000183098	ENST00000377047	T	0.58506	0.33	5.64	5.64	0.86602	.	0.063315	0.64402	D	0.000008	T	0.78502	0.4293	M	0.85710	2.77	0.58432	D	0.999997	P;D	0.71674	0.74;0.998	P;D	0.77557	0.641;0.99	T	0.81402	-0.0949	10	0.54805	T	0.06	.	15.8646	0.79055	1.0:0.0:0.0:0.0	.	321;321	B4E2M1;Q9Y625	.;GPC6_HUMAN	A	321	ENSP00000366246:E321A	ENSP00000366246:E321A	E	+	2	0	GPC6	93736688	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.950000	0.93019	2.149000	0.67028	0.477000	0.44152	GAA	.		0.423	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		C	94938687	A	C	94938687	3	2	127	1	0	0	0	0	1	0	0	0	6622	246	9	5	980	5	GPC6	13	94938687	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		94938687	20231191	83	11183											
FAM161B	145483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	74409353	74409353	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actagaggaggcgataggggAagaggccatctggagcatgt	12	6	17	6	1	1	2	0	0	1	2	1	6	1	5	1	6	1	1	1	6	3	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr14:74409353A>T	ENST00000534936.1	-	4	1096	c.991T>A	c.(991-993)Tcc>Acc	p.S331T	FAM161B_ENST00000286544.3_Missense_Mutation_p.S394T			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	331										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						GCGATAGGGGAAGAGGCCATC	0.532																																					p.S394T		.											.	FAM161B-91	0			c.T1180A						.						88	96	94					14																	74409353		2203	4300	6503	SO:0001583	missense	145483	exon4			TAGGGGAAGAGGC	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 44"	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.991T>A	14.37:g.74409353A>T	ENSP00000445326:p.Ser331Thr	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	72	18	NM_152445	0	0	0	5	5	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	37		.	.	.	.	.	.	.	.	.	.	A	16.34	3.096005	0.56075	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.21361	2.01;2.01	5.5	4.34	0.51931	.	0.392302	0.25786	N	0.028306	T	0.38719	0.1051	M	0.79475	2.455	0.29528	N	0.852984	D	0.61697	0.99	P	0.61722	0.893	T	0.35475	-0.9787	10	0.09843	T	0.71	-10.2675	12.0316	0.53401	0.5426:0.4574:0.0:0.0	.	331	Q96MY7	F161B_HUMAN	T	394;331	ENSP00000286544:S394T;ENSP00000445326:S331T	ENSP00000286544:S394T	S	-	1	0	FAM161B	73479106	0.652000	0.27349	1.000000	0.80357	0.874000	0.50279	1.334000	0.33827	1.081000	0.41110	0.533000	0.62120	TCC	.		0.532	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445		T	74409353	A	T	74409353	3	4	127	1	0	0	0	0	1	0	0	0	5489	246	9	5	976	5	FAM161B	14	74409353	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		74409353	32940187	84	11184											
C14orf49	161176	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	95906070	95906070	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaccagccagccctgcgCttccaccagggacagctggg	8	5	11	17	1	1	0	1	0	0	0	2	1	2	1	5	2	4	2	5	2	0	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr14:95906070C>T	ENST00000334258.5	-	12	2139	c.2125G>A	c.(2125-2127)Gcg>Acg	p.A709T	SYNE3_ENST00000557275.1_Missense_Mutation_p.A709T|SYNE3_ENST00000554873.1_Missense_Mutation_p.A466T	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	709					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CAGCCCTGCGCTTCCACCAGG	0.637																																					p.A709T		.											.	.	0			c.G2125A						.						44	47	46					14																	95906070		2203	4300	6503	SO:0001583	missense	161176	exon12			CCTGCGCTTCCAC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"chromosome 14 open reading frame 49"	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2125G>A	14.37:g.95906070C>T	ENSP00000334308:p.Ala709Thr	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	137	7	NM_152592	0	0	0	0	0	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.663059	0.47572	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.52295	0.67;0.67;0.67	5.34	5.34	0.76211	.	0.171047	0.27932	N	0.017272	T	0.46034	0.1372	L	0.50333	1.59	0.80722	D	1	P;P	0.50369	0.919;0.934	P;P	0.48598	0.447;0.583	T	0.26573	-1.0099	10	0.12430	T	0.62	-23.2732	11.6332	0.51187	0.1774:0.8226:0.0:0.0	.	709;709	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	T	709;466;709	ENSP00000334308:A709T;ENSP00000452154:A466T;ENSP00000450562:A709T	ENSP00000334308:A709T	A	-	1	0	C14orf49	94975823	0.218000	0.23608	0.039000	0.18376	0.023000	0.10783	1.454000	0.35178	2.507000	0.84556	0.561000	0.74099	GCG	.		0.637	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95906070	C	T	95906070	3	4	127	1	0	0	0	0	1	0	0	0	1780	797	28	2	826	2	C14orf49	14	95906070	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	21496717	95906070	11443470	85	11185											
RAB26	25837	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2201715	2201715	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtgggacacagctggtcAggagcggttccgcagtgtta	8	9	16	8	2	1	0	1	0	0	0	2	3	2	2	1	4	2	4	1	4	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr16:2201715A>G	ENST00000210187.6	+	4	528	c.368A>G	c.(367-369)cAg>cGg	p.Q123R	RAB26_ENST00000541451.1_Missense_Mutation_p.Q57R	NM_014353.4	NP_055168.2	Q9ULW5	RAB26_HUMAN	RAB26, member RAS oncogene family	123					exocrine system development (GO:0035272)|Golgi to plasma membrane protein transport (GO:0043001)|regulated secretory pathway (GO:0045055)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	Golgi membrane (GO:0000139)|intrinsic component of plasma membrane (GO:0031226)|secretory granule membrane (GO:0030667)	GMP binding (GO:0019002)|GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(3)	5						ACAGCTGGTCAGGAGCGGTTC	0.642																																					p.Q123R													.	RAB26-227	0			c.A368G						.						104	87	93					16																	2201715		2197	4300	6497	SO:0001583	missense	25837	exon4			CTGGTCAGGAGCG	AB027137	CCDS10460.1	16p13.3	2008-07-28			ENSG00000167964	ENSG00000167964		"RAB, member RAS oncogene"	14259	protein-coding gene	gene with protein product		605455				11043516	Standard	NM_014353		Approved		uc002cou.3	Q9ULW5	OTTHUMG00000128829	ENST00000210187.6:c.368A>G	16.37:g.2201715A>G	ENSP00000210187:p.Gln123Arg	Somatic	280	1		WXS	Illumina HiSeq	Phase_I	347	93	NM_014353	0	0	0	0	0	B2RAA6|Q3L6K5|Q6NXS7	Missense_Mutation	SNP	ENST00000210187.6	37	CCDS10460.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279466	0.59758	.	.	ENSG00000167964	ENST00000541451;ENST00000210187	D;D	0.83673	-1.75;-1.75	3.93	3.93	0.45458	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000003	D	0.92616	0.7654	H	0.95539	3.685	0.80722	D	1	P	0.50943	0.94	D	0.64410	0.925	D	0.94013	0.7286	10	0.87932	D	0	.	11.7693	0.51949	1.0:0.0:0.0:0.0	.	123	Q9ULW5	RAB26_HUMAN	R	57;123	ENSP00000441580:Q57R;ENSP00000210187:Q123R	ENSP00000210187:Q123R	Q	+	2	0	RAB26	2141716	1.000000	0.71417	1.000000	0.80357	0.362000	0.29581	8.398000	0.90195	1.657000	0.50732	0.254000	0.18369	CAG	.		0.642	RAB26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250767.2			G	2201715	A	G	2201715	3	3	127	1	0	0	0	0	1	0	0	0	12945	188	7	3	382	3	RAB26	16	2201715	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		2201715	88153038	86	11186											
TBC1D24	57465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2550436	2550436	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgctcgccacttcaacctGccctccaagaccgagtccat	8	7	7	19	3	1	1	1	0	0	1	4	2	3	1	7	0	2	1	7	0	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr16:2550436G>T	ENST00000293970.5	+	7	1603	c.1470G>T	c.(1468-1470)ctG>ctT	p.L490L	TBC1D24_ENST00000567020.1_Silent_p.L484L|TBC1D24_ENST00000434757.2_Silent_p.L490L|RP11-20I23.1_ENST00000564543.1_Intron	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	490	TLD.				neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|terminal bouton (GO:0043195)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(4)|large_intestine(3)|lung(4)	13						ACTTCAACCTGCCCTCCAAGA	0.692																																					p.L490L		.											.	TBC1D24-90	0			c.G1470T						.						12	17	15					16																	2550436		2057	4196	6253	SO:0001819	synonymous_variant	57465	exon7			CAACCTGCCCTCC	AB032997	CCDS42107.1, CCDS55980.1	16p13.3	2014-05-07				ENSG00000162065			29203	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 6"	613577	"deafness, autosomal recessive 86"	DFNB86		10574461, 24387994, 24729539	Standard	NM_001199107		Approved	KIAA1171, TLDC6, DFNA65	uc002cql.3	Q9ULP9		ENST00000293970.5:c.1470G>T	16.37:g.2550436G>T		Somatic	314	0		WXS	Illumina HiSeq	Phase_I	269	58	NM_001199107	0	0	0	2	2	A0JNW3|B9A6M6|Q2KJ08	Silent	SNP	ENST00000293970.5	37	CCDS55980.1																																																																																			.		0.692	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705		T	2550436	G	T	2550436	2	4	127	1	0	0	0	0	0	0	0	1	15646	1306	46	4		4	TBC1D24	16	2550436	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	348721	2550436	87804317	87	11187											
CHD9	80205	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	53288491	53288491	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgtgttacagagcatgAgtggaagagaaagtaatgtt	15	10	13	3	0	0	3	0	1	0	2	0	5	0	4	0	1	3	5	0	1	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr16:53288491A>G	ENST00000398510.3	+	17	4090	c.4003A>G	c.(4003-4005)Agt>Ggt	p.S1335G	CHD9_ENST00000447540.1_Missense_Mutation_p.S1335G|CHD9_ENST00000564845.1_Missense_Mutation_p.S1335G|CHD9_ENST00000566029.1_Missense_Mutation_p.S1335G			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1335	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ACAGAGCATGAGTGGAAGAGA	0.378																																					p.S1335G													.	CHD9-272	0			c.A4003G						.						258	254	255					16																	53288491		1881	4105	5986	SO:0001583	missense	80205	exon18			AGCATGAGTGGAA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.4003A>G	16.37:g.53288491A>G	ENSP00000381522:p.Ser1335Gly	Somatic	145	1		WXS	Illumina HiSeq	Phase_I	148	41	NM_025134	0	0	0	0	0	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	A	21.2	4.107119	0.77096	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	D;D	0.86865	-2.1;-2.18	5.39	5.39	0.77823	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000002	D	0.90535	0.7034	L	0.42581	1.335	0.80722	D	1	B;P;P;D	0.56035	0.417;0.923;0.956;0.974	B;P;D;D	0.70487	0.206;0.79;0.931;0.969	D	0.90634	0.4569	10	0.48119	T	0.1	-16.5693	15.4021	0.74849	1.0:0.0:0.0:0.0	.	861;1335;1335;1335	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	G	1335;1335;861	ENSP00000396345:S1335G;ENSP00000381522:S1335G	ENSP00000219084:S861G	S	+	1	0	CHD9	51845992	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.281000	0.95811	2.049000	0.60858	0.477000	0.44152	AGT	.		0.378	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53288491	A	G	53288491	3	3	127	1	0	0	0	0	1	0	0	0	3338	304	11	3	4069	3	CHD9	16	53288491	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	50738055	53288491	37066262	88	11188											
SDR42E1	93517	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	82033252	82033252	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aaactcaaccaggctcctggGgtccccgtagacaaacttga	12	7	9	13	1	1	2	1	1	0	1	3	2	3	2	4	3	3	2	4	3	4	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr16:82033252G>T	ENST00000328945.5	-	3	773	c.646C>A	c.(646-648)Ccc>Acc	p.P216T	SDR42E1_ENST00000534209.1_5'Flank	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	216					steroid biosynthetic process (GO:0006694)	integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)			NS(2)|endometrium(1)|lung(4)|skin(3)	10						AGGCTCCTGGGGTCCCCGTAG	0.547																																					p.P216T													.	SDR42E1-90	0			c.C646A						.						108	110	109					16																	82033252		1902	4115	6017	SO:0001583	missense	93517	exon3			TCCTGGGGTCCCC	AF161368	CCDS42205.1	16q23.3	2011-09-14				ENSG00000184860	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	29834	protein-coding gene	gene with protein product						19027726	Standard	NM_145168		Approved	HSPC105	uc002fgu.3	Q8WUS8		ENST00000328945.5:c.646C>A	16.37:g.82033252G>T	ENSP00000332407:p.Pro216Thr	Somatic	125	1		WXS	Illumina HiSeq	Phase_I	142	41	NM_145168	0	0	0	2	2	B2RDS1|Q9P0D1	Missense_Mutation	SNP	ENST00000328945.5	37	CCDS42205.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870740	0.72065	.	.	ENSG00000184860	ENST00000328945	D	0.88664	-2.41	5.58	4.6	0.57074	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.153104	0.64402	N	0.000011	D	0.91922	0.7442	M	0.75447	2.3	0.54753	D	0.999988	P	0.51240	0.943	P	0.57204	0.815	D	0.90190	0.4249	10	0.27082	T	0.32	-14.8805	13.0466	0.58931	0.0:0.0:0.8391:0.1609	.	216	Q8WUS8	D42E1_HUMAN	T	216	ENSP00000332407:P216T	ENSP00000332407:P216T	P	-	1	0	SDR42E1	80590753	1.000000	0.71417	0.742000	0.31022	0.950000	0.60333	6.302000	0.72788	1.301000	0.44836	0.655000	0.94253	CCC	.		0.547	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168		T	82033252	G	T	82033252	3	4	127	1	0	0	0	0	1	0	0	0	14005	1232	43	4	539	4	SDR42E1	16	82033252	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	28744761	82033252	8321501	89	11189											
FBXW10	10517	bcgsc.ca	37	chr17	18653384	18653384	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agccagcactgggccgccatGgctcaacaggtcaagatgga	11	5	13	12	1	2	1	2	0	0	1	2	2	2	2	3	4	3	2	3	4	2	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:18653384G>T	ENST00000395665.4	+	4	1154	c.933G>T	c.(931-933)atG>atT	p.M311I	FBXW10_ENST00000301938.4_Missense_Mutation_p.M311I|FBXW10_ENST00000395667.1_Missense_Mutation_p.M311I|FBXW10_ENST00000308799.4_Missense_Mutation_p.M340I			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	311	F-box.									NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GGGCCGCCATGGCTCAACAGG	0.517																																					p.M311I													.	FBXW10-91	0			c.G933T						.						16	18	17					17																	18653384		2040	4094	6134	SO:0001583	missense	10517	exon4			CGCCATGGCTCAA	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"F-boxes / WD-40 domains", "WD repeat domain containing"	1211	protein-coding gene	gene with protein product		611679	"chromosome 17 open reading frame 1A", "F-box and WD-40 domain protein 10"	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.933G>T	17.37:g.18653384G>T	ENSP00000379025:p.Met311Ile	Somatic	511	1		WXS	Illumina HiSeq	Phase_1	682	84	NM_001267585	0	0	0	0	0	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	G	3.163	-0.171623	0.06421	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.27256	2.15;1.68;2.15;2.15	2.49	0.244	0.15507	F-box domain, Skp2-like (1);	0.296938	0.17883	U	0.158818	T	0.11665	0.0284	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.19706	0.038;0.015;0.022;0.017	B;B;B;B	0.13407	0.009;0.009;0.004;0.009	T	0.16335	-1.0406	10	0.51188	T	0.08	.	3.6229	0.08103	0.1637:0.2623:0.574:0.0	.	311;340;311;311	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	I	311;340;311;311	ENSP00000379026:M311I;ENSP00000310382:M340I;ENSP00000306937:M311I;ENSP00000379025:M311I	ENSP00000306937:M311I	M	+	3	0	FBXW10	18594109	0.159000	0.22864	0.083000	0.20561	0.238000	0.25445	0.459000	0.21908	-0.034000	0.13713	0.405000	0.27470	ATG	.		0.517	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		T	18653384	G	T	18653384	3	4	127	1	0	0	0	0	1	0	0	0	5782	1348	47	4	947	4	FBXW10	17	18653384	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		18653384	62541826	90	11190											
TCAP	8557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37821723	37821723	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccacacggcccgaggagggGtgagtgtgggtctgctagag	7	7	18	9	2	1	2	0	1	1	1	2	4	2	3	2	5	1	1	2	5	1	1	rs113187448		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:37821723G>A	ENST00000309889.2	+	1	1283		c.e1+1		TCAP_ENST00000578283.1_Splice_Site|PNMT_ENST00000269582.2_5'Flank|PNMT_ENST00000394246.1_5'Flank|PNMT_ENST00000581428.1_5'Flank			O15273	TELT_HUMAN	titin-cap						adult heart development (GO:0007512)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of mechanical stimulus (GO:0050982)|detection of muscle stretch (GO:0035995)|muscle filament sliding (GO:0030049)|otic vesicle formation (GO:0030916)|protein complex assembly (GO:0006461)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle contraction (GO:0003009)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)	cytosol (GO:0005829)|I band (GO:0031674)|Z disc (GO:0030018)	FATZ binding (GO:0051373)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			kidney(1)|lung(1)	2	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCGAGGAGGGGTGAGTGTGGG	0.627																																					.		.											.	TCAP-90	0			c.110+1G>A						.						67	64	65					17																	37821723		2203	4300	6503	SO:0001630	splice_region_variant	8557	exon1			GGAGGGGTGAGTG	AJ000491	CCDS11342.1	17q12	2014-09-17	2012-09-20		ENSG00000173991	ENSG00000173991			11610	protein-coding gene	gene with protein product	"19 kDa sarcomeric protein"	604488	"limb girdle muscular dystrophy 2G (autosomal recessive)", "titin-cap (telethonin)"	LGMD2G		9350988, 9817758	Standard	NM_003673		Approved	T-cap, TELE, telethonin, CMD1N	uc002hsh.3	O15273	OTTHUMG00000133215	ENST00000309889.2:c.110+1G>A	17.37:g.37821723G>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	134	32	NM_003673	0	0	0	2	2	Q96L27	Splice_Site	SNP	ENST00000309889.2	37	CCDS11342.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.194985	0.38806	.	.	ENSG00000173991	ENST00000309889	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5082	0.95130	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TCAP	35075249	1.000000	0.71417	1.000000	0.80357	0.117000	0.20001	7.443000	0.80521	2.710000	0.92621	0.563000	0.77884	.	.		0.627	TCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256942.1	NM_003673	Intron	A	37821723	G	A	37821723	5	1	127	1	0	0	0	0	0	0	1	0	15698	1275	44	2	113	2	TCAP	17	37821723	Splice_Site	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	19168339	37821723	43373487	91	11191											
KRT10	3858	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38978229	38978229	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acctgatttttaaggtcatcGatggttttgtagtatttgct	8	19	9	5	1	1	1	1	1	0	0	2	2	1	1	1	2	1	4	1	2	3	8			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:38978229G>A	ENST00000269576.5	-	1	618	c.609C>T	c.(607-609)atC>atT	p.I203I	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	203	Coil 1B.|Gly-rich.|Rod.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				TAAGGTCATCGATGGTTTTGT	0.393																																					p.I203I													.	KRT10-90	0			c.C609T						.						170	155	160					17																	38978229		2203	4300	6503	SO:0001819	synonymous_variant	3858	exon1			GTCATCGATGGTT	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.609C>T	17.37:g.38978229G>A		Somatic	144	1		WXS	Illumina HiSeq	Phase_I	186	113	NM_000421	0	0	0	0	0	Q14664|Q8N175	Silent	SNP	ENST00000269576.5	37	CCDS11377.1																																																																																			.		0.393	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		A	38978229	G	A	38978229	2	1	127	1	0	0	0	0	0	0	0	1	8469	1048	37	1		1	KRT10	17	38978229	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	1156506	38978229	42216981	92	11192											
EME1	146956	bcgsc.ca	37	chr17	48457701	48457701	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagatgaaactaccttctccTtctgtctggagagtgactgg	9	12	11	9	0	3	4	0	2	3	2	4	6	3	4	2	2	2	0	2	2	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:48457701T>C	ENST00000338165.4	+	8	1457	c.1375T>C	c.(1375-1377)Ttc>Ctc	p.F459L	EME1_ENST00000393271.2_Missense_Mutation_p.F472L|EME1_ENST00000511648.2_Missense_Mutation_p.F472L	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	459					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TACCTTCTCCTTCTGTCTGGA	0.542								Direct reversal of damage;Homologous recombination																													p.F472L													.	EME1-227	0			c.T1414C						.						74	58	63					17																	48457701		2203	4300	6503	SO:0001583	missense	146956	exon8			TTCTCCTTCTGTC	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"	610885	"essential meiotic endonuclease 1 homolog 1 (S. pombe)"			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.1375T>C	17.37:g.48457701T>C	ENSP00000339897:p.Phe459Leu	Somatic	126	3		WXS	Illumina HiSeq	Phase_1	170	99	NM_001166131	0	0	0	1	1	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	33|33	5.264539|5.264539	0.95399|0.95399	.|.	.|.	ENSG00000154920|ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648|ENST00000510246	T;T;T|.	0.47869|.	0.83;0.83;0.83|.	5.72|5.72	5.72|5.72	0.89469|0.89469	ERCC4 domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80149|0.80149	0.4570|0.4570	M|M	0.86420|0.86420	2.815|2.815	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	T|T	0.82859|0.82859	-0.0249|-0.0249	10|5	0.87932|.	D|.	0|.	-15.4409|-15.4409	16.0037|16.0037	0.80327|0.80327	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	472;459|.	Q96AY2-2;Q96AY2|.	.;EME1_HUMAN|.	L|P	459;472;472|270	ENSP00000339897:F459L;ENSP00000376952:F472L;ENSP00000421700:F472L|.	ENSP00000339897:F459L|.	F|L	+|+	1|2	0|0	EME1|EME1	45812700|45812700	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.911000|0.911000	0.54048|0.54048	7.536000|7.536000	0.82023|0.82023	2.184000|2.184000	0.69523|0.69523	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.		0.542	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		C	48457701	T	C	48457701	3	2	127	1	0	0	0	0	1	0	0	0	5101	1609	56	3	1440	3	EME1	17	48457701	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	9479472	48457701	32737509	93	11193											
RPTOR	57521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	78811724	78811724	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgttctctccgcaggcAagcctgggacctggctgttg	4	11	12	14	1	2	0	0	0	2	0	4	1	3	1	4	3	1	5	4	3	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:78811724A>C	ENST00000306801.3	+	10	1501	c.1139A>C	c.(1138-1140)cAa>cCa	p.Q380P	RPTOR_ENST00000544334.2_Missense_Mutation_p.Q380P|RPTOR_ENST00000537330.1_Missense_Mutation_p.Q195P|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	380					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CTCCGCAGGCAAGCCTGGGAC	0.612																																					p.Q380P		.											.	RPTOR-847	0			c.A1139C						.						111	77	89					17																	78811724		2203	4300	6503	SO:0001583	missense	57521	exon10			GCAGGCAAGCCTG		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"WD repeat domain containing"	30287	protein-coding gene	gene with protein product	"regulatory associated protein of mTOR"	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1139A>C	17.37:g.78811724A>C	ENSP00000307272:p.Gln380Pro	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	174	36	NM_001163034	0	0	0	0	0	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.260139	0.59321	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T	0.46819	0.86;0.86	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.79475	2.455	0.80722	D	1	D;B;D	0.56521	0.96;0.168;0.976	D;B;B	0.64237	0.923;0.086;0.438	T	0.68526	-0.5385	10	0.46703	T	0.11	.	13.1464	0.59463	1.0:0.0:0.0:0.0	.	380;195;380	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	P	195;380;380	ENSP00000307272:Q380P;ENSP00000442479:Q380P	ENSP00000307272:Q380P	Q	+	2	0	RPTOR	76426319	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.087000	0.89521	1.990000	0.58119	0.455000	0.32223	CAA	.		0.612	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		C	78811724	A	C	78811724	3	2	127	1	0	0	0	0	1	0	0	0	13697	130	5	5	1177	5	RPTOR	17	78811724	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	30354023	78811724	2383486	94	11194											
ACTG1	71	ucsc.edu	37	chr17	79478136	79478136	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgccgcaagattccataccTaggggacagagccctccctt	10	8	9	14	1	0	2	0	0	0	2	2	3	2	3	5	2	3	1	5	2	3	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:79478136T>C	ENST00000575842.1	-	4	1229		c.e4-2		ACTG1_ENST00000573283.1_Splice_Site|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000575087.1_Splice_Site|ACTG1_ENST00000331925.2_Splice_Site|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1						adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			ATTCCATACCTAGGGGACAGA	0.537																																					.													.	ACTG1-91	0			c.803-2A>G						.						86	76	80					17																	79478136		2203	4300	6503	SO:0001630	splice_region_variant	71	exon6			CATACCTAGGGGA		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"deafness, autosomal dominant 20; deafness, autosomal dominant 26"	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.803-2A>G	17.37:g.79478136T>C		Somatic	343	0		WXS	Illumina HiSeq		395	2	NM_001199954	0	0	9	9	0	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Splice_Site	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	t	3.884	-0.025353	0.07589	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	.	.	.	3.61	2.53	0.30540	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.8977	0.29717	0.0:0.1028:0.0:0.8972	.	.	.	.	.	-1	.	.	.	-	.	.	ACTG1	77092731	1.000000	0.71417	0.355000	0.25773	0.171000	0.22731	7.434000	0.80377	0.501000	0.28013	0.450000	0.29827	.	.		0.537	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	Intron	C	79478136	T	C	79478136	5	2	127	1	0	0	0	0	0	0	1	0	196	1536	53	3	334	3	ACTG1	17	79478136	Splice_Site	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	666412	79478136	1717074	95	11195											
IMPACT	55364	broad.mit.edu	37	chr18	22020564	22020564	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaaagcattggattttgatAtcagtgaaactcggacaggt	13	13	10	5	1	1	2	1	2	0	0	2	4	1	4	0	3	2	1	0	3	4	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr18:22020564A>G	ENST00000284202.4	+	6	613	c.472A>G	c.(472-474)Atc>Gtc	p.I158V	RP11-178F10.1_ENST00000579049.1_RNA	NM_018439.3	NP_060909	Q9P2X3	IMPCT_HUMAN	impact RWD domain protein	158					negative regulation of protein phosphorylation (GO:0001933)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00018)|all_epithelial(16;1.5e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)					GGATTTTGATATCAGTGAAAC	0.343																																					p.I158V													.	IMPACT-90	0			c.A472G						.						154	149	151					18																	22020564		2203	4300	6503	SO:0001583	missense	55364	exon6			TTTGATATCAGTG	AB026264	CCDS11886.1	18q11.2-q12.1	2012-12-07	2012-12-07		ENSG00000154059	ENSG00000154059			20387	protein-coding gene	gene with protein product	"RWD domain containing 5"	615319	"Impact homolog (mouse)"			11116084	Standard	NM_018439		Approved	RWDD5	uc002kvh.4	Q9P2X3	OTTHUMG00000131943	ENST00000284202.4:c.472A>G	18.37:g.22020564A>G	ENSP00000284202:p.Ile158Val	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	100	3	NM_018439	0	0	3	3	0	A8MXG0|Q49AM0|Q9H2X4	Missense_Mutation	SNP	ENST00000284202.4	37	CCDS11886.1	.	.	.	.	.	.	.	.	.	.	A	1.262	-0.615672	0.03663	.	.	ENSG00000154059	ENST00000284202	T	0.28454	1.61	5.29	-3.87	0.04218	.	1.325790	0.04559	N	0.391367	T	0.19046	0.0457	L	0.28556	0.865	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21075	-1.0256	10	0.20519	T	0.43	.	6.1062	0.20075	0.4272:0.0:0.4388:0.134	.	158	Q9P2X3	IMPCT_HUMAN	V	158	ENSP00000284202:I158V	ENSP00000284202:I158V	I	+	1	0	IMPACT	20274562	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.200000	0.09478	-0.630000	0.05567	-0.371000	0.07208	ATC	.		0.343	IMPACT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254901.1	NM_018439		G	22020564	A	G	22020564	3	3	127	1	0	0	0	0	1	0	0	0	7745	449	16	3	494	3	IMPACT	18	22020564	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		22020564	56056684	96	11196											
MUC16	94025	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9048182	9048182	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgaccagagaggtcaccattCctggtacctcaggtgaaaca	12	8	10	11	0	2	3	2	2	0	1	3	4	3	3	4	3	2	1	4	3	2	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:9048182C>T	ENST00000397910.4	-	5	33652	c.33449G>A	c.(33448-33450)gGa>gAa	p.G11150E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11152	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGTCACCATTCCTGGTACCTC	0.468																																					p.G11150E													.	MUC16-566	0			c.G33449A						.						88	80	83					19																	9048182		1909	4131	6040	SO:0001583	missense	94025	exon5			ACCATTCCTGGTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33449G>A	19.37:g.9048182C>T	ENSP00000381008:p.Gly11150Glu	Somatic	140	1		WXS	Illumina HiSeq	Phase_I	118	32	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	5.752	0.323183	0.10900	.	.	ENSG00000181143	ENST00000397910	T	0.03553	3.89	3.11	-6.22	0.02058	.	.	.	.	.	T	0.03095	0.0091	L	0.45581	1.43	.	.	.	P	0.37101	0.582	B	0.32583	0.148	T	0.18967	-1.0320	8	0.87932	D	0	.	5.7136	0.17948	0.152:0.2213:0.0:0.6267	.	11150	B5ME49	.	E	11150	ENSP00000381008:G11150E	ENSP00000381008:G11150E	G	-	2	0	MUC16	8909182	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.020000	0.00312	-1.359000	0.02174	-1.173000	0.01734	GGA	.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9048182	C	T	9048182	3	4	127	1	0	0	0	0	1	0	0	0	9998	855	30	2	10394	2	MUC16	19	9048182	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		9048182	50080801	97	11197											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558370	11558370	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaagaagaggctgaagaaga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0	rs77563879		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000412601.1_Silent_p.E322E|PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	322	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaagaagagg	0.632																																					p.E322E		.											.	PRKCSH-90	1	Deletion - In frame(1)	central_nervous_system(1)	c.G966A						.						27	27	27					19																	11558370		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAAGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.966G>A	19.37:g.11558370G>A		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	115	6	NM_001001329	0	0	15	15	0	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																			.		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558370	G	A	11558370	2	1	127	1	0	0	0	0	0	0	0	1	12545	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	2510188	11558370	47570613	98	11198											
GIPC1	10755	broad.mit.edu	37	chr19	14591257	14591257	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatcatgtcgcccacgctgAtgaggtggatgtggtcgatc	7	10	14	10	4	1	2	1	2	0	0	4	5	1	3	1	3	0	1	1	3	0	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:14591257A>T	ENST00000393033.4	-	6	784	c.515T>A	c.(514-516)aTc>aAc	p.I172N	GIPC1_ENST00000345425.2_Missense_Mutation_p.I172N|GIPC1_ENST00000586027.1_Missense_Mutation_p.I172N|GIPC1_ENST00000393029.3_Missense_Mutation_p.I75N|GIPC1_ENST00000591349.1_Missense_Mutation_p.I75N|GIPC1_ENST00000393028.1_Missense_Mutation_p.I75N	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	172	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						GCCCACGCTGATGAGGTGGAT	0.677											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I172N	Pancreas(33;78 923 2910 41023 52850)												.	GIPC1-226	0			c.T515A						.						81	81	81					19																	14591257		2203	4300	6503	SO:0001583	missense	10755	exon5			ACGCTGATGAGGT	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"chromosome 19 open reading frame 3", "regulator of G-protein signalling 19 interacting protein 1"	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.515T>A	19.37:g.14591257A>T	ENSP00000376753:p.Ile172Asn	Somatic	197	0	696	WXS	Illumina HiSeq	Phase_I	208	6	NM_202468	0	0	138	139	1	A8K4I3|A8MZG3|Q9BTC9	Missense_Mutation	SNP	ENST00000393033.4	37	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.778354	0.90195	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.96	4.96	0.65561	PDZ/DHR/GLGF (4);	0.105541	0.64402	D	0.000006	T	0.68293	0.2985	M	0.88241	2.94	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.75172	-0.3411	10	0.87932	D	0	-6.4705	12.5539	0.56242	1.0:0.0:0.0:0.0	.	172	O14908	GIPC1_HUMAN	N	172;172;75;75;172	ENSP00000376753:I172N;ENSP00000340698:I172N;ENSP00000376749:I75N;ENSP00000376748:I75N	ENSP00000340698:I172N	I	-	2	0	GIPC1	14452257	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.736000	0.74811	1.871000	0.54225	0.459000	0.35465	ATC	.		0.677	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2			T	14591257	A	T	14591257	3	4	127	1	0	0	0	0	1	0	0	0	6412	333	12	5	502	5	GIPC1	19	14591257	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	3032887	14591257	44537726	99	11199											
GRWD1	83743	hgsc.bcm.edu	37	chr19	48953775	48953775	+	Frame_Shift_Del	DEL	G	G	-																															tgcccttgactggtccccccGggtgaccggtgagtccctgg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:48953775delG	ENST00000253237.5	+	4	907	c.674delG	c.(673-675)cggfs	p.R225fs		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	225						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		TGGTCCCCCCGGGTGACCGGT	0.667																																					p.R225fs		.											.	GRWD1-91	0			c.674delG						.						34	37	36					19																	48953775		2203	4300	6503	SO:0001589	frameshift_variant	83743	exon4			.	AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"WD repeat domain containing"	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.674delG	19.37:g.48953775delG	ENSP00000253237:p.Arg225fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	54	12	NM_031485	0	0	0	0	0	Q8TF59	Frame_Shift_Del	DEL	ENST00000253237.5	37	CCDS12720.1																																																																																			.		0.667	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485		-	48953775	G	-	48953775	7	5	127	1	0	1	0	1	0	0	0	0	6832	1116	39	0	688	0	GRWD1	19	48953775	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	34362518	48953775	10175208	100	11200											
FAM71E1	112703	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50970983	50970983	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtctcgggtcttgagtggggCccgcagctgcaagtagaagg	7	8	17	9	2	2	2	0	1	2	1	3	2	2	2	1	4	2	4	1	4	3	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:50970983C>T	ENST00000600100.1	-	4	1007	c.643G>A	c.(643-645)Gcc>Acc	p.A215T	FAM71E1_ENST00000595790.1_Missense_Mutation_p.A199T			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	215										breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		TTGAGTGGGGCCCGCAGCTGC	0.602																																					p.A199T													.	FAM71E1-44	0			c.G595A						.						32	31	31					19																	50970983		2203	4299	6502	SO:0001583	missense	112703	exon4			GTGGGGCCCGCAG		CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.643G>A	19.37:g.50970983C>T	ENSP00000472421:p.Ala215Thr	Somatic	175	1		WXS	Illumina HiSeq	Phase_I	140	45	NM_138411	0	0	2	10	8	Q96EJ5|Q9BSM9	Missense_Mutation	SNP	ENST00000600100.1	37		.	.	.	.	.	.	.	.	.	.	C	7.100	0.573879	0.13623	.	.	ENSG00000142530	ENST00000391816;ENST00000270620	T;T	0.18810	2.19;2.19	4.0	0.357	0.16079	.	0.572956	0.13647	N	0.372543	T	0.17066	0.0410	M	0.61703	1.905	0.09310	N	1	P;B	0.39094	0.659;0.22	B;B	0.38921	0.285;0.101	T	0.13575	-1.0504	10	0.28530	T	0.3	-4.065	1.7219	0.02913	0.1668:0.4764:0.1626:0.1943	.	215;199	Q6IPT2;Q6IPT2-2	F71E1_HUMAN;.	T	215;199	ENSP00000375692:A215T;ENSP00000270620:A199T	ENSP00000270620:A199T	A	-	1	0	FAM71E1	55662795	0.005000	0.15991	0.001000	0.08648	0.017000	0.09413	0.570000	0.23653	0.060000	0.16281	0.462000	0.41574	GCC	.		0.602	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2			T	50970983	C	T	50970983	3	4	127	1	0	0	0	0	1	0	0	0	5630	739	26	2	104	2	FAM71E1	19	50970983	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	2017208	50970983	8158000	101	11201											
ZNF615	284370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52496371	52496372	+	Missense_Mutation	DNP	GC	GC	AT																															attttccacattcagtacatGcaaaggaagtctttcctgtg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:52496371_52496372GC>AT	ENST00000602063.1	-	6	2306_2307	c.1957_1958GC>AT	c.(1957-1959)GCa>ATa	p.A653I	ZNF615_ENST00000594083.1_Missense_Mutation_p.A664I|ZNF615_ENST00000598071.1_Missense_Mutation_p.A664I|ZNF615_ENST00000376716.5_Missense_Mutation_p.A653I|ZNF615_ENST00000391795.3_Missense_Mutation_p.A658I			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	653					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)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TTCAGTACATGCAAAGGAAGTC	0.406																																					p.A663I		.											.	ZNF615-95	0			c.G1957A						.																																			SO:0001583	missense	284370	exon6			TACATGCAAAGGA	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1957_1958delinsAT	19.37:g.52496371_52496372delinsAT	ENSP00000473089:p.Ala653Ile	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	134	41	NM_198480	0	0	0	0	0	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	DNP	ENST00000602063.1	37	CCDS12846.1																																																																																			.		0.406	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		AT	52496372	GC	AT	52496371	3	1	127	1	0	0	0	0	1	0	0	0	18072	1319	46	2	241	2	ZNF615	19	52496371	Missense_Mutation	DNP	GC	TCGA-GL-A59T-01A-21D-A28G-10	1525388	52496371	6632612	102	11202											
ZNF160	90338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53572249	53572249	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgaaggctttcccacacTcattacacttgtaaggtttc	10	13	6	12	0	1	1	1	1	0	0	3	1	2	1	1	2	1	3	1	2	3	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:53572249T>C	ENST00000429604.1	-	7	1953	c.1538A>G	c.(1537-1539)gAg>gGg	p.E513G	ZNF160_ENST00000601421.1_Missense_Mutation_p.E477G|ZNF160_ENST00000418871.1_Missense_Mutation_p.E513G|ZNF160_ENST00000599056.1_Missense_Mutation_p.E513G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	513					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TTTCCCACACTCATTACACTT	0.403																																					p.E513G		.											.	ZNF160-90	0			c.A1538G						.						103	103	103					19																	53572249		2203	4300	6503	SO:0001583	missense	90338	exon7			CCACACTCATTAC	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1538A>G	19.37:g.53572249T>C	ENSP00000406201:p.Glu513Gly	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	49	16	NM_001102603	0	0	4	5	1	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.552720	0.27739	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.07444	3.19;3.19	2.47	0.0174	0.14112	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20780	0.0500	M	0.64080	1.96	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.07908	-1.0748	9	0.87932	D	0	.	6.7782	0.23630	0.363:0.0:0.0:0.637	.	513	Q9HCG1	ZN160_HUMAN	G	513	ENSP00000406201:E513G;ENSP00000409597:E513G	ENSP00000409597:E513G	E	-	2	0	ZNF160	58264061	0.000000	0.05858	0.002000	0.10522	0.354000	0.29330	0.114000	0.15520	-0.237000	0.09739	0.459000	0.35465	GAG	.		0.403	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		C	53572249	T	C	53572249	3	2	127	1	0	0	0	0	1	0	0	0	17771	1551	54	3	922	3	ZNF160	19	53572249	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	1075878	53572249	5556734	103	11203											
ZNF416	55659	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58084873	58084873	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcctggtgaaagaccgcAcatgccccagtcaagtatag	11	8	11	11	1	1	2	1	1	0	1	2	2	2	2	4	2	1	2	4	2	4	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:58084873A>T	ENST00000196489.3	-	4	621	c.399T>A	c.(397-399)tgT>tgA	p.C133*		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	133					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(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		GAAAGACCGCACATGCCCCAG	0.507																																					p.C133X													.	ZNF416-90	0			c.T399A						.						108	87	94					19																	58084873		2203	4300	6503	SO:0001587	stop_gained	55659	exon4			GACCGCACATGCC	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"Zinc fingers, C2H2-type", "-"	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.399T>A	19.37:g.58084873A>T	ENSP00000196489:p.Cys133*	Somatic	174	1		WXS	Illumina HiSeq	Phase_I	160	63	NM_017879	0	0	0	2	2	Q9NWW8	Nonsense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	A	19.65	3.866781	0.72065	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	.	.	.	3.34	2.32	0.28847	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1875	0.15191	0.8617:0.0:0.1383:0.0	.	.	.	.	X	133;119;113	.	ENSP00000196489:C133X	C	-	3	2	ZNF416	62776685	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.535000	0.23114	0.501000	0.28013	0.496000	0.49642	TGT	.		0.507	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		T	58084873	A	T	58084873	4	4	127	1	0	0	0	0	0	1	0	0	17925	157	6	5	1389	5	ZNF416	19	58084873	Nonsense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	4512624	58084873	1044110	104	11204											
TBC1D20	128637	broad.mit.edu	37	chr20	422661	422661	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaatcagttcttcctggaGcccttctctctgttcctctg	4	16	7	14	0	6	0	2	0	4	0	9	1	8	1	3	1	1	2	3	1	1	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:422661G>T	ENST00000354200.4	-	4	511	c.364C>A	c.(364-366)Ctc>Atc	p.L122I	TBC1D20_ENST00000461188.1_5'Flank	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	122	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				TCTTCCTGGAGCCCTTCTCTC	0.517																																					p.L122I													.	TBC1D20-90	0			c.C364A						.						93	91	92					20																	422661		2203	4300	6503	SO:0001583	missense	128637	exon4			CCTGGAGCCCTTC	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.364C>A	20.37:g.422661G>T	ENSP00000346139:p.Leu122Ile	Somatic	83	1		WXS	Illumina HiSeq	Phase_I	69	5	NM_144628	0	0	4	4	0	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	37	CCDS13002.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310040	0.81247	.	.	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.04275	3.66	6.03	6.03	0.97812	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.22437	0.0541	M	0.86097	2.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00137	-1.2004	10	0.46703	T	0.11	-10.3698	10.8765	0.46915	0.1422:0.0:0.8578:0.0	.	122	Q96BZ9	TBC20_HUMAN	I	122;147	ENSP00000346139:L122I	ENSP00000246077:L147I	L	-	1	0	TBC1D20	370661	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.393000	0.59665	2.854000	0.98071	0.655000	0.94253	CTC	.		0.517	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		T	422661	G	T	422661	3	4	127	1	0	0	0	0	1	0	0	0	15641	971	34	4	867	4	TBC1D20	20	422661	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		422661	62602859	105	11205											
SRXN1	140809	broad.mit.edu	37	chr20	633661	633661	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcaccttggcggggtccaAcacggacggcagcggccgga	7	4	16	14	5	0	0	0	0	0	0	1	2	1	2	3	7	3	2	3	7	1	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:633661A>G	ENST00000381962.3	-	1	353	c.169T>C	c.(169-171)Ttg>Ctg	p.L57L	RP5-850E9.3_ENST00000488788.2_Intron	NM_080725.1	NP_542763.1	Q9BYN0	SRXN1_HUMAN	sulfiredoxin 1	57					response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	ATP binding (GO:0005524)|oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)|sulfiredoxin activity (GO:0032542)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5						GCGGGGTCCAACACGGACGGC	0.731																																					p.L57L													.	SRXN1-91	0			c.T169C						.						12	12	12					20																	633661		2174	4259	6433	SO:0001819	synonymous_variant	140809	exon1			GGTCCAACACGGA	AF075053	CCDS13005.1	20p13	2013-05-22	2010-06-24	2005-05-10	ENSG00000271303	ENSG00000271303			16132	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 139", "sulfiredoxin 1 homolog (S. cerevisiae)"	C20orf139			Standard	NM_080725		Approved	Npn3, SRX1, YKL086W, dJ850E9.2	uc002wea.4	Q9BYN0	OTTHUMG00000031644	ENST00000381962.3:c.169T>C	20.37:g.633661A>G		Somatic	144	0		WXS	Illumina HiSeq	Phase_I	93	3	NM_080725	0	0	8	8	0	B2R543|Q8NDM3|Q96AK6	Silent	SNP	ENST00000381962.3	37	CCDS13005.1																																																																																			.		0.731	SRXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077479.2	NM_080725		G	633661	A	G	633661	2	3	127	1	0	0	0	0	0	0	0	1	15205	40	2	3		3	SRXN1	20	633661	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	211000	633661	62391859	106	11206											
C20orf30	29058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	5086868	5086868	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcctgacagcaggagggagCctataataatgagaaaggcg	15	5	14	7	1	0	2	0	2	0	1	0	5	0	4	2	3	3	1	2	3	4	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:5086868C>T	ENST00000379286.2	-	4	608	c.188G>A	c.(187-189)gGc>gAc	p.G63D	TMEM230_ENST00000202834.7_Missense_Mutation_p.G63D|TMEM230_ENST00000342308.5_Missense_Mutation_p.G126D|TMEM230_ENST00000379283.2_Missense_Mutation_p.G63D|TMEM230_ENST00000379277.2_Missense_Mutation_p.G63D|TMEM230_ENST00000379279.2_Missense_Mutation_p.G63D|TMEM230_ENST00000492419.1_5'UTR	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	63						integral component of membrane (GO:0016021)											CAGGAGGGAGCCTATAATAAT	0.453																																					p.G126D		.											.	.	0			c.G377A						.						66	66	66					20																	5086868		2203	4300	6503	SO:0001583	missense	29058	exon4			AGGGAGCCTATAA	AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 30"	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.188G>A	20.37:g.5086868C>T	ENSP00000368588:p.Gly63Asp	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	93	6	NM_001009923	0	0	71	85	14	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Missense_Mutation	SNP	ENST00000379286.2	37	CCDS13086.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.392086	0.83011	.	.	ENSG00000089063	ENST00000379283;ENST00000342308;ENST00000379299;ENST00000202834;ENST00000379286;ENST00000379279;ENST00000379277;ENST00000379276	T	0.60299	0.2	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.80879	0.4708	M	0.90145	3.09	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.81914	0.964;0.995;0.993	D	0.84375	0.0546	10	0.87932	D	0	-27.0491	17.8394	0.88711	0.0:1.0:0.0:0.0	.	63;63;126	Q5JWB9;Q96A57;Q96A57-2	.;CT030_HUMAN;.	D	63;126;63;63;63;63;63;63	ENSP00000341364:G126D	ENSP00000202834:G63D	G	-	2	0	C20orf30	5034868	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	7.104000	0.77024	2.854000	0.98071	0.655000	0.94253	GGC	.		0.453	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1			T	5086868	C	T	5086868	3	4	127	1	0	0	0	0	1	0	0	0	2116	739	26	2	182	2	C20orf30	20	5086868	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	4453207	5086868	57938652	107	11207											
PLCB4	5332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	9440354	9440354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccacagtgctgaggagcaaGaaatccgagacctgcacctc	12	5	10	14	1	0	3	0	1	0	2	2	5	1	4	4	1	3	3	4	1	2	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:9440354G>A	ENST00000378493.1	+	31	3124	c.3109G>A	c.(3109-3111)Gaa>Aaa	p.E1037K	PLCB4_ENST00000378473.3_Missense_Mutation_p.E1049K|PLCB4_ENST00000414679.2_Missense_Mutation_p.E1049K|PLCB4_ENST00000492632.1_Intron|PLCB4_ENST00000378501.2_Missense_Mutation_p.E1037K|PLCB4_ENST00000278655.4_Missense_Mutation_p.E1037K|PLCB4_ENST00000334005.3_Missense_Mutation_p.E1037K			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	1037					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						TGAGGAGCAAGAAATCCGAGA	0.502																																					p.E1049K		.											.	PLCB4-274	0			c.G3145A						.						64	53	57					20																	9440354		2203	4300	6503	SO:0001583	missense	5332	exon34			GAGCAAGAAATCC		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.3109G>A	20.37:g.9440354G>A	ENSP00000367754:p.Glu1037Lys	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	71	23	NM_001172646	0	0	7	11	4	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565149	0.65651	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.51	5.51	0.81932	.	0.055638	0.64402	D	0.000001	T	0.44829	0.1312	L	0.50333	1.59	0.53688	D	0.999974	B;B;B;P	0.37824	0.042;0.021;0.083;0.609	B;B;B;P	0.44860	0.013;0.014;0.011;0.462	T	0.29027	-1.0025	10	0.35671	T	0.21	.	12.7258	0.57170	0.0753:0.0:0.9247:0.0	.	1049;884;1037;1037	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	K	1037;1049;1037;1037;1037;885	ENSP00000334105:E1037K;ENSP00000367734:E1049K;ENSP00000278655:E1037K;ENSP00000367754:E1037K;ENSP00000367762:E1037K;ENSP00000390616:E885K	ENSP00000278655:E1037K	E	+	1	0	PLCB4	9388354	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	7.421000	0.80204	2.578000	0.87016	0.561000	0.74099	GAA	.		0.502	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9440354	G	A	9440354	3	1	127	1	0	0	0	0	1	0	0	0	12056	943	33	2	3271	2	PLCB4	20	9440354	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	4353486	9440354	53585166	108	11208											
MYH7B	57644	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	33567508	33567512	+	Frame_Shift_Del	DEL	TCGCT	TCGCT	-																															ctgcagcccatgaacccgccTcgcttcgacttactggagga																								rs539864476|rs572570454	byFrequency	TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TCGCT	TCGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:33567508_33567512delTCGCT	ENST00000262873.7	+	5	461_465	c.369_373delTCGCT	c.(367-375)cctcgcttcfs	p.RF124fs		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	82	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			TGAACCCGCCTCGCTTCGACTTACT	0.629																																					p.123_125del		.											.	MYH7B-136	0			c.369_373del						.																																			SO:0001589	frameshift_variant	57644	exon7			.	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"Myosins / Myosin superfamily : Class II"	15906	protein-coding gene	gene with protein product		609928	"myosin, heavy polypeptide 7B, cardiac muscle, beta"			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.369_373delTCGCT	20.37:g.33567508_33567512delTCGCT	ENSP00000262873:p.Arg124fs	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	76	29	NM_020884	0	0	0	0	0	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Frame_Shift_Del	DEL	ENST00000262873.7	37	CCDS42869.1																																																																																			.		0.629	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		-	33567512	TCGCT	-	33567508	7	5	127	1	0	1	0	1	0	0	0	0	10065	1538	54	0	387	0	MYH7B	20	33567508	Frame_Shift_Del	DEL	TCGCT	TCGA-GL-A59T-01A-21D-A28G-10	24127154	33567508	29458012	109	11209											
APP	351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	27328004	27328004	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acatgctcgaaatgctttagGgtgtgctgtctgtccttctg	6	15	11	9	1	2	0	0	0	2	0	4	1	3	0	1	1	3	3	1	1	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:27328004G>C	ENST00000346798.3	-	12	1557	c.1524C>G	c.(1522-1524)acC>acG	p.T508T	APP_ENST00000359726.3_Silent_p.T452T|APP_ENST00000440126.3_Silent_p.T484T|APP_ENST00000439274.2_Silent_p.T452T|APP_ENST00000358918.3_Silent_p.T508T|APP_ENST00000448388.2_Silent_p.T398T|APP_ENST00000357903.3_Silent_p.T489T|APP_ENST00000354192.3_Silent_p.T377T|APP_ENST00000348990.5_Silent_p.T433T	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	508	Heparin-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				AATGCTTTAGGGTGTGCTGTC	0.483																																					p.T508T		.											.	APP-91	0			c.C1524G						.						229	180	196					21																	27328004		2203	4300	6503	SO:0001819	synonymous_variant	351	exon12			CTTTAGGGTGTGC	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"Endogenous ligands"	620	protein-coding gene	gene with protein product	"peptidase nexin-II"	104760	"Alzheimer disease"	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1524C>G	21.37:g.27328004G>C		Somatic	202	0		WXS	Illumina HiSeq	Phase_I	168	43	NM_000484	0	0	305	697	392	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	G	8.763	0.923954	0.18056	.	.	ENSG00000142192	ENST00000448850	.	.	.	5.45	3.65	0.41850	.	.	.	.	.	T	0.55970	0.1954	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50816	-0.8783	4	.	.	.	-24.9633	7.0758	0.25203	0.3229:0.0:0.6771:0.0	.	.	.	.	A	411	.	.	P	-	1	0	APP	26249875	0.782000	0.28689	0.975000	0.42487	0.811000	0.45836	-0.105000	0.10907	0.869000	0.35703	0.655000	0.94253	CCT	.		0.483	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27328004	G	C	27328004	2	2	127	1	0	0	0	0	0	0	0	1	815	1219	43	4		4	APP	21	27328004	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		27328004	20801891	110	11210											
BRWD1	54014	bcgsc.ca	37	chr21	40646393	40646393	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccatctctgctaccacttAggaaccttaaaacattcaga	13	12	4	12	0	2	1	1	0	1	1	4	2	3	2	3	1	4	1	3	1	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:40646393A>G	ENST00000333229.2	-	13	1478	c.1151T>C	c.(1150-1152)cTa>cCa	p.L384P	BRWD1_ENST00000380800.3_Missense_Mutation_p.L384P|BRWD1_ENST00000342449.3_Missense_Mutation_p.L384P	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	384					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				GCTACCACTTAGGAACCTTAA	0.378																																					p.L384P	Melanoma(170;988 1986 4794 16843 39731)												.	BRWD1-94	0			c.T1151C						.						174	144	154					21																	40646393		2203	4300	6503	SO:0001583	missense	54014	exon13			CCACTTAGGAACC	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.1151T>C	21.37:g.40646393A>G	ENSP00000330753:p.Leu384Pro	Somatic	94	0		WXS	Illumina HiSeq	Phase_1	65	4	NM_018963	0	0	0	0	0	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.382783	0.82792	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.62232	0.04;0.04;0.04	5.35	5.35	0.76521	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.229595	0.29660	N	0.011536	D	0.82430	0.5035	M	0.89904	3.07	0.80722	D	1	D;D;D	0.76494	0.989;0.997;0.999	P;D;D	0.72075	0.883;0.976;0.972	D	0.86479	0.1790	10	0.87932	D	0	-5.2723	15.3221	0.74129	1.0:0.0:0.0:0.0	.	95;384;384	Q5R2U6;Q9NSI6-2;Q9NSI6	.;.;BRWD1_HUMAN	P	384	ENSP00000330753:L384P;ENSP00000344333:L384P;ENSP00000370178:L384P	ENSP00000330753:L384P	L	-	2	0	BRWD1	39568263	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.798000	0.91888	2.031000	0.59945	0.397000	0.26171	CTA	.		0.378	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		G	40646393	A	G	40646393	3	3	127	1	0	0	0	0	1	0	0	0	1528	420	15	3	6170	3	BRWD1	21	40646393	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	13318389	40646393	7483502	111	11211											
DIP2A	23181	hgsc.bcm.edu;bcgsc.ca	37	chr21	47985760	47985761	+	Frame_Shift_Del	DEL	TG	TG	-																															tgggcaaggaccggctacctTggcttccttcggcgaacaga																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:47985760_47985761delTG	ENST00000417564.2	+	36	4320_4321	c.4299_4300delTG	c.(4297-4302)cttggcfs	p.G1434fs	DIP2A_ENST00000318711.7_Frame_Shift_Del_p.G1435fs|DIP2A_ENST00000479654.1_3'UTR|DIP2A_ENST00000400274.1_Frame_Shift_Del_p.G1430fs			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1434					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		CCGGCTACCTTGGCTTCCTTCG	0.614																																					p.1433_1434del		.											.	DIP2A-24	0			c.4299_4300del						.																																			SO:0001589	frameshift_variant	23181	exon36			.	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.4299_4300delTG	21.37:g.47985760_47985761delTG	ENSP00000392066:p.Gly1434fs	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	117	27	NM_015151	0	0	0	0	0	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Frame_Shift_Del	DEL	ENST00000417564.2	37	CCDS46655.1																																																																																			.		0.614	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		-	47985761	TG	-	47985760	7	5	127	1	0	1	0	1	0	0	0	0	4538	1799	63	0	4554	0	DIP2A	21	47985760	Frame_Shift_Del	DEL	TG	TCGA-GL-A59T-01A-21D-A28G-10	7339367	47985760	144135	112	11212											
ARVCF	421	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	19967613	19967613	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccgccagcgcggctccttgCgggcgctatccactgagggc	4	6	14	17	5	0	1	0	1	0	0	2	1	2	1	4	3	2	2	4	3	1	2	rs376884775		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:19967613C>A	ENST00000263207.3	-	6	1340	c.1049G>T	c.(1048-1050)cGc>cTc	p.R350L	ARVCF_ENST00000406259.1_Missense_Mutation_p.R350L|ARVCF_ENST00000401994.1_Missense_Mutation_p.R287L|ARVCF_ENST00000406522.1_Missense_Mutation_p.R287L|ARVCF_ENST00000344269.3_Missense_Mutation_p.R287L|ARVCF_ENST00000487793.1_5'Flank	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	350					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CGGCTCCTTGCGGGCGCTATC	0.726																																					p.R350L		.											.	ARVCF-91	0			c.G1049T						.						5	7	6					22																	19967613		2043	3993	6036	SO:0001583	missense	421	exon6			TCCTTGCGGGCGC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1049G>T	22.37:g.19967613C>A	ENSP00000263207:p.Arg350Leu	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_001670	0	0	1	2	1	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120544	0.94385	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.69435	-0.4;-0.34;-0.34;-0.34;-0.4	5.35	4.33	0.51752	Armadillo-like helical (1);	0.049736	0.85682	D	0.000000	T	0.61788	0.2375	L	0.38838	1.175	0.80722	D	1	P	0.49090	0.919	P	0.46850	0.529	T	0.60747	-0.7202	9	.	.	.	-18.2472	14.2537	0.66038	0.0:0.9281:0.0:0.0719	.	350	O00192	ARVC_HUMAN	L	350;287;287;287;350	ENSP00000263207:R350L;ENSP00000342042:R287L;ENSP00000384341:R287L;ENSP00000384732:R287L;ENSP00000385444:R350L	.	R	-	2	0	ARVCF	18347613	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.598000	0.67585	1.406000	0.46857	0.655000	0.94253	CGC	.		0.726	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19967613	C	A	19967613	3	1	127	1	0	0	0	0	1	0	0	0	1004	768	27	4	1895	4	ARVCF	22	19967613	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		19967613	31336953	113	11213											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	305	0		WXS	Illumina HiSeq	Phase_I	192	25	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	127	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	9917949	29885562	21419004	114	11214											
CACNA1I	8911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40055466	40055466	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgcatatttttggctgcAagttcagcctccgcacggac	8	11	11	11	2	1	0	1	0	0	0	2	2	2	2	2	3	3	5	2	3	2	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:40055466A>G	ENST00000402142.3	+	13	2359	c.2359A>G	c.(2359-2361)Aag>Gag	p.K787E	CACNA1I_ENST00000404898.1_Missense_Mutation_p.K752E|CACNA1I_ENST00000336649.4_Missense_Mutation_p.K793E|CACNA1I_ENST00000401624.1_Missense_Mutation_p.K787E|CACNA1I_ENST00000407673.1_Missense_Mutation_p.K752E|CACNA1I_ENST00000400164.3_Missense_Mutation_p.K752E	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	787					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TTTTGGCTGCAAGTTCAGCCT	0.552																																					p.K787E		.											.	CACNA1I-135	0			c.A2359G						.						51	52	52					22																	40055466		2095	4208	6303	SO:0001583	missense	8911	exon13			GGCTGCAAGTTCA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.2359A>G	22.37:g.40055466A>G	ENSP00000385019:p.Lys787Glu	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	179	64	NM_021096	0	0	0	0	0	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813895	0.90790	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91;-4.91	4.3	4.3	0.51218	Ion transport (1);	0.048588	0.85682	D	0.000000	D	0.98544	0.9514	M	0.69185	2.1	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.85130	0.995;0.948;0.997;0.996	D	0.99593	1.0976	10	0.87932	D	0	.	13.8843	0.63699	1.0:0.0:0.0:0.0	.	752;787;752;787	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	E	787;752;787;752;793;752	ENSP00000385019:K787E;ENSP00000384093:K752E;ENSP00000383887:K787E;ENSP00000385680:K752E;ENSP00000337829:K793E;ENSP00000383028:K752E	ENSP00000337829:K793E	K	+	1	0	CACNA1I	38385412	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.849000	0.92178	1.920000	0.55613	0.459000	0.35465	AAG	.		0.552	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		G	40055466	A	G	40055466	3	3	127	1	0	0	0	0	1	0	0	0	2552	131	5	3	2409	3	CACNA1I	22	40055466	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	10169904	40055466	11249100	115	11215											
PKDREJ	10343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46654194	46654194	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctcggattcggacgatctGgtcatgtatcctctgcattt	6	14	10	11	3	3	0	1	0	2	0	6	3	4	2	2	3	1	2	2	3	1	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46654194G>A	ENST00000253255.5	-	1	5025	c.5026C>T	c.(5026-5028)Cag>Tag	p.Q1676*		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1676					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CGGACGATCTGGTCATGTATC	0.418																																					p.Q1676X		.											.	PKDREJ-156	0			c.C5026T						.						200	166	178					22																	46654194		2203	4300	6503	SO:0001587	stop_gained	10343	exon1			CGATCTGGTCATG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like", "polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like", "polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5026C>T	22.37:g.46654194G>A	ENSP00000253255:p.Gln1676*	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_006071	0	0	0	0	0	B1AJY3|O95850	Nonsense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	g	42	9.331670	0.99138	.	.	ENSG00000130943	ENST00000253255	.	.	.	4.95	-3.76	0.04359	.	1.756340	0.02965	N	0.143633	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-0.9396	3.1764	0.06570	0.1516:0.388:0.2844:0.1761	.	.	.	.	X	1676	.	ENSP00000253255:Q1676X	Q	-	1	0	PKDREJ	45032858	0.000000	0.05858	0.000000	0.03702	0.449000	0.32228	0.053000	0.14184	-0.308000	0.08792	0.298000	0.19748	CAG	.		0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46654194	G	A	46654194	4	1	127	1	0	0	0	0	0	1	0	0	11996	1357	47	2	1739	2	PKDREJ	22	46654194	Nonsense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	6598728	46654194	4650372	116	11216											
TTC38	55020	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46677589	46677589	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaggatgggttggaattcAtgcagcactcagagaccttc	11	10	11	9	0	3	1	3	0	0	1	4	4	3	3	1	3	2	3	1	3	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46677589A>G	ENST00000381031.3	+	7	785	c.709A>G	c.(709-711)Atg>Gtg	p.M237V	TTC38_ENST00000445282.2_Missense_Mutation_p.M179V	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	237						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GTTGGAATTCATGCAGCACTC	0.512																																					p.M237V		.											.	TTC38-91	0			c.A709G						.						125	128	127					22																	46677589		2092	4220	6312	SO:0001583	missense	55020	exon7			GAATTCATGCAGC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"Tetratricopeptide (TTC) repeat domain containing"	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.709A>G	22.37:g.46677589A>G	ENSP00000370419:p.Met237Val	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	88	31	NM_017931	0	0	8	13	5	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079821	0.76528	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.75704	1.62;-0.96	5.79	5.79	0.91817	Tetratricopeptide-like helical (1);	0.072520	0.85682	D	0.000000	D	0.84320	0.5446	M	0.79693	2.465	0.58432	D	0.999992	D;D	0.62365	0.991;0.962	P;P	0.59171	0.853;0.523	D	0.84956	0.0874	10	0.42905	T	0.14	-12.5636	15.3166	0.74085	1.0:0.0:0.0:0.0	.	179;237	E7ES35;Q5R3I4	.;TTC38_HUMAN	V	237;179	ENSP00000370419:M237V;ENSP00000393960:M179V	ENSP00000370419:M237V	M	+	1	0	TTC38	45056253	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	4.319000	0.59197	2.207000	0.71202	0.533000	0.62120	ATG	.		0.512	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		G	46677589	A	G	46677589	3	3	127	1	0	0	0	0	1	0	0	0	16739	217	8	3	735	3	TTC38	22	46677589	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	23395	46677589	4626977	117	11217											
WWC3	55841	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	10062249	10062249	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggacttccctcaccatgtAggcgtgcctggcgatgctgg	5	10	14	12	2	1	0	1	0	0	0	2	2	2	1	3	4	2	2	3	4	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chrX:10062249A>T	ENST00000380861.4	+	7	976	c.585A>T	c.(583-585)gtA>gtT	p.V195V	WWC3_ENST00000454666.1_Silent_p.V195V	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	195					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CTCACCATGTAGGCGTGCCTG	0.577																																					p.V195V		.											.	WWC3-134	0			c.A585T						.						144	125	132					X																	10062249		2203	4300	6503	SO:0001819	synonymous_variant	55841	exon7			CCATGTAGGCGTG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.585A>T	X.37:g.10062249A>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	80	8	NM_015691	0	0	3	3	0	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			.		0.577	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		T	10062249	A	T	10062249	2	4	127	1	0	0	0	0	0	0	0	1	17446	407	15	5		5	WWC3	23	10062249	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		10062249	145208311	118	11218											
HUWE1	10075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53584383	53584383	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtcatttgacttagatgcAgtacactgcaaaaagaaggg	15	9	11	6	0	1	3	1	1	0	2	1	4	1	3	0	1	3	3	0	1	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chrX:53584383A>G	ENST00000342160.3	-	59	8623	c.8166T>C	c.(8164-8166)acT>acC	p.T2722T	MIR98_ENST00000606724.1_RNA|MIRLET7F2_ENST00000385277.1_RNA|HUWE1_ENST00000262854.6_Silent_p.T2722T			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2722					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						ACTTAGATGCAGTACACTGCA	0.428																																					p.T2722T		.											.	HUWE1-280	0			c.T8166C						.						137	122	127					X																	53584383		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon60			AGATGCAGTACAC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8166T>C	X.37:g.53584383A>G		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	41	31	NM_031407	0	0	0	0	0	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	8.337	0.827732	0.16749	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.64	0.708	0.18144	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22695	-1.0209	4	.	.	.	.	3.0889	0.06286	0.3857:0.0:0.3048:0.3095	.	.	.	.	R	1756	.	.	C	-	1	0	HUWE1	53601108	0.001000	0.12720	0.177000	0.23020	0.915000	0.54546	0.717000	0.25851	0.266000	0.21894	0.486000	0.48141	TGC	.		0.428	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		G	53584383	A	G	53584383	2	3	127	1	0	0	0	0	0	0	0	1	7482	175	7	3		3	HUWE1	23	53584383	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	43522134	53584383	101686177	119	11219											
DDI2	84301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15956850	15956850	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatagatttcagtagtatagCtgtgcctggcacatcaagtc	12	12	9	8	0	2	1	2	0	0	1	3	1	2	1	1	1	2	4	1	1	6	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr1:15956850C>A	ENST00000480945.1	+	3	470	c.299C>A	c.(298-300)gCt>gAt	p.A100D		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	100							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AGTAGTATAGCTGTGCCTGGC	0.473																																					p.A100D		.											.	DDI2-44	0			c.C299A						.						86	88	87					1																	15956850		2203	4300	6503	SO:0001583	missense	84301	exon3			GTATAGCTGTGCC		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.299C>A	1.37:g.15956850C>A	ENSP00000417748:p.Ala100Asp	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	112	24	NM_032341	0	0	5	6	1	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	37	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182624	0.78677	.	.	ENSG00000197312	ENST00000480945	T	0.23552	1.9	5.9	5.9	0.94986	.	0.130770	0.51477	U	0.000091	T	0.34774	0.0909	M	0.71036	2.16	0.80722	D	1	P	0.44946	0.846	B	0.40101	0.319	T	0.19321	-1.0309	10	0.56958	D	0.05	-28.9484	19.873	0.96856	0.0:1.0:0.0:0.0	.	100	Q5TDH0	DDI2_HUMAN	D	100	ENSP00000417748:A100D	ENSP00000417748:A100D	A	+	2	0	DDI2	15829437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.971000	0.76105	2.802000	0.96397	0.650000	0.86243	GCT	.		0.473	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		A	15956850	C	A	15956850	3	1	128	1	0	0	0	0	1	0	0	0	4335	797	28	4	309	4	DDI2	1	15956850	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		15956850	233293771	1	11220											
NRXN1	9378	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	50149203	50149203	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttactgatgtagtttcgaCtctcgtccacatggtatgag	9	14	10	8	2	1	2	0	2	1	0	4	3	2	2	1	1	1	4	1	1	3	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:50149203C>G	ENST00000406316.2	-	22	5789	c.4313G>C	c.(4312-4314)aGt>aCt	p.S1438T	NRXN1_ENST00000406859.3_Missense_Mutation_p.S1438T|NRXN1_ENST00000401710.1_Missense_Mutation_p.S456T|NRXN1_ENST00000405472.3_Missense_Mutation_p.S1460T|NRXN1_ENST00000401669.2_Missense_Mutation_p.S1468T|NRXN1_ENST00000402717.3_Missense_Mutation_p.S1460T|NRXN1_ENST00000342183.5_Missense_Mutation_p.S403T|NRXN1_ENST00000404971.1_Missense_Mutation_p.S1508T	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1438					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTAGTTTCGACTCTCGTCCAC	0.478																																					p.S1508T		.											.	NRXN1-92	0			c.G4523C						.						230	185	200					2																	50149203		2203	4300	6503	SO:0001583	missense	9378	exon24			TTTCGACTCTCGT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.4313G>C	2.37:g.50149203C>G	ENSP00000384311:p.Ser1438Thr	Somatic	130	1		WXS	Illumina HiSeq	Phase_I	111	16	NM_001135659	0	0	0	0	0	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	12.73|12.73|12.73	2.026044|2.026044|2.026044	0.35701|0.35701|0.35701	.|.|.	.|.|.	ENSG00000179915|ENSG00000179915|ENSG00000179915	ENST00000378262|ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859|ENST00000412315	T|T;T;T;T;T;T;T;T|.	0.70869|0.72615|.	-0.52|0.82;2.08;0.04;0.05;-0.67;-0.56;-0.27;-0.09|.	5.44|5.44|5.44	5.44|5.44|5.44	0.79542|0.79542|0.79542	.|Neurexin/syndecan/glycophorin C (1);|.	.|0.000000|.	.|0.64402|.	.|U|.	.|0.000011|.	T|T|T	0.60457|0.60457|0.60457	0.2270|0.2270|0.2270	L|L|L	0.33245|0.33245|0.33245	0.995|0.995|0.995	0.51012|0.51012|0.51012	D|D|D	0.999905|0.999905|0.999905	.|P;B;B;D;P;B|.	.|0.61697|.	.|0.877;0.296;0.172;0.99;0.946;0.452|.	.|D;B;B;D;P;P|.	.|0.72982|.	.|0.916;0.101;0.145;0.979;0.77;0.762|.	T|T|T	0.52779|0.52779|0.52779	-0.8530|-0.8530|-0.8530	7|10|5	0.72032|0.29301|.	D|T|.	0.01|0.29|.	.|.|.	19.4587|19.4587|19.4587	0.94906|0.94906|0.94906	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|103;1508;403;1438;1457;100|.	.|B4DIT5;Q9ULB1-3;P58400;F8WB18;A7E294;Q5HYI0|.	.|.;.;NRX1B_HUMAN;.;.;.|.	D|T|L	104|403;357;456;1508;1438;1460;1468;1509;1460;1438|171	ENSP00000367510:E104D|ENSP00000341184:S403T;ENSP00000385580:S456T;ENSP00000385142:S1508T;ENSP00000384311:S1438T;ENSP00000434015:S1460T;ENSP00000385017:S1468T;ENSP00000385434:S1460T;ENSP00000385681:S1438T|.	ENSP00000367510:E104D|ENSP00000341184:S403T|.	E|S|V	-|-|-	3|2|1	2|0|0	NRXN1|NRXN1|NRXN1	50002707|50002707|50002707	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.651000|7.651000|7.651000	0.83577|0.83577|0.83577	2.828000|2.828000|2.828000	0.97474|0.97474|0.97474	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAG|AGT|GTC	.		0.478	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			G	50149203	C	G	50149203	3	3	128	1	0	0	0	0	1	0	0	0	10691	565	20	4	124	4	NRXN1	2	50149203	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		50149203	193050170	2	11221											
CCDC88A	55704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55523606	55523606	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcatggtcatgaagcaggcTaaattctccactgctgtggc	9	11	10	11	0	3	1	2	1	1	0	4	1	3	1	1	3	2	3	1	3	3	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:55523606T>C	ENST00000436346.1	-	30	5720	c.4879A>G	c.(4879-4881)Agc>Ggc	p.S1627G	CCDC88A_ENST00000422883.2_Missense_Mutation_p.S128G|CCDC88A_ENST00000263630.8_Missense_Mutation_p.S1599G|CCDC88A_ENST00000413716.2_Missense_Mutation_p.S1626G|CCDC88A_ENST00000336838.6_Missense_Mutation_p.S1626G	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1627					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						TGAAGCAGGCTAAATTCTCCA	0.453																																					p.S1626G		.											.	CCDC88A-94	0			c.A4876G						.						119	105	110					2																	55523606		2203	4300	6503	SO:0001583	missense	55704	exon30			GCAGGCTAAATTC	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.4879A>G	2.37:g.55523606T>C	ENSP00000410608:p.Ser1627Gly	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	68	19	NM_001254943	0	0	24	25	1	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.68|14.68	2.606920|2.606920	0.46527|0.46527	.|.	.|.	ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000456975	T;T;T;T;T;T|.	0.52295|.	2.4;2.38;2.62;0.67;2.4;1.32|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.56097|.	U|.	0.000024|.	T|.	0.69024|.	0.3065|.	L|L	0.54323|0.54323	1.7|1.7	0.58432|0.58432	D|D	0.999998|0.999998	B;D;D;D;B;D;D|.	0.63046|.	0.005;0.99;0.982;0.982;0.05;0.992;0.99|.	B;D;D;D;B;D;D|.	0.74674|.	0.012;0.979;0.952;0.961;0.019;0.984;0.979|.	T|.	0.67436|.	-0.5671|.	10|.	0.27082|.	T|.	0.32|.	-9.3716|-9.3716	15.4218|15.4218	0.75018|0.75018	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1626;1599;1544;128;1627;1626;1598|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.	.;.;.;.;GRDN_HUMAN;.;.|.	G|W	1626;1599;1627;128;644;1626;802|579	ENSP00000338728:S1626G;ENSP00000263630:S1599G;ENSP00000410608:S1627G;ENSP00000390012:S644G;ENSP00000404431:S1626G;ENSP00000405080:S802G|.	ENSP00000263630:S1599G|.	S|X	-|-	1|2	0|0	CCDC88A|CCDC88A	55377110|55377110	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.274000|7.274000	0.78538|0.78538	2.051000|2.051000	0.60960|0.60960	0.383000|0.383000	0.25322|0.25322	AGC|TAG	.		0.453	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55523606	T	C	55523606	3	2	128	1	0	0	0	0	1	0	0	0	2869	1522	53	3	748	3	CCDC88A	2	55523606	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	5374403	55523606	187675767	3	11222											
FAM161A	84140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	62067675	62067675	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggctctgaaaatgatgtcAttaatgagacagggtgatag	14	10	12	5	0	2	4	1	4	1	1	2	5	2	4	0	2	0	1	0	2	4	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:62067675A>T	ENST00000405894.3	-	3	565	c.464T>A	c.(463-465)aTg>aAg	p.M155K	FAM161A_ENST00000404929.1_Missense_Mutation_p.M155K	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	155					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AAATGATGTCATTAATGAGAC	0.363																																					p.M155K		.											.	FAM161A-136	0			c.T464A						.						104	91	95					2																	62067675		1846	4096	5942	SO:0001583	missense	84140	exon3			GATGTCATTAATG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"retinitis pigmentosa 28 (autosomal recessive)"	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.464T>A	2.37:g.62067675A>T	ENSP00000385893:p.Met155Lys	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	67	8	NM_032180	0	0	1	2	1	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	A	12.65	2.002006	0.35320	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.20598	2.87;2.06	5.3	-0.661	0.11417	.	1.199220	0.05573	N	0.571416	T	0.17323	0.0416	L	0.51422	1.61	0.09310	N	1	B;B	0.28233	0.204;0.018	B;B	0.21708	0.036;0.013	T	0.29119	-1.0022	9	.	.	.	-6.764	4.6748	0.12706	0.4925:0.0:0.1664:0.3411	.	155;155	Q3B820;Q3B820-3	F161A_HUMAN;.	K	155	ENSP00000385158:M155K;ENSP00000385893:M155K	.	M	-	2	0	FAM161A	61921179	0.001000	0.12720	0.000000	0.03702	0.743000	0.42351	0.901000	0.28445	-0.003000	0.14444	-0.490000	0.04691	ATG	.		0.363	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		T	62067675	A	T	62067675	3	4	128	1	0	0	0	0	1	0	0	0	5488	217	8	5	1534	5	FAM161A	2	62067675	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	6544069	62067675	181131698	4	11223											
WDR92	116143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	68368907	68368907	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggatcatctttttgccttgGgtcccacaccttcacagttc	7	14	7	13	0	3	0	2	0	1	0	5	1	4	1	3	2	1	1	3	2	0	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:68368907G>T	ENST00000295121.6	-	4	552	c.436C>A	c.(436-438)Cca>Aca	p.P146T	WDR92_ENST00000492039.2_5'UTR|WDR92_ENST00000406245.2_Missense_Mutation_p.P45T|RP11-474G23.1_ENST00000406334.3_3'UTR|WDR92_ENST00000409164.1_Missense_Mutation_p.P146T	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	146					apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)			endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						TTTTGCCTTGGGTCCCACACC	0.373																																					p.P146T		.											.	WDR92-68	0			c.C436A						.						196	186	189					2																	68368907		2203	4300	6503	SO:0001583	missense	116143	exon4			GCCTTGGGTCCCA	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"WD repeat domain containing"	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.436C>A	2.37:g.68368907G>T	ENSP00000295121:p.Pro146Thr	Somatic	248	2		WXS	Illumina HiSeq	Phase_I	201	31	NM_001256476	0	0	3	4	1	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	37	CCDS1884.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.216136	0.39201	.	.	ENSG00000243667	ENST00000295121;ENST00000406245;ENST00000409164	T;T;T	0.64991	1.64;1.64;-0.13	5.71	5.71	0.89125	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000002	T	0.55114	0.1900	L	0.38953	1.18	0.80722	D	1	B	0.12013	0.005	B	0.08055	0.003	T	0.45991	-0.9223	10	0.22706	T	0.39	.	20.2245	0.98337	0.0:0.0:1.0:0.0	.	146	Q96MX6	WDR92_HUMAN	T	146;45;146	ENSP00000295121:P146T;ENSP00000384518:P45T;ENSP00000386746:P146T	ENSP00000295121:P146T	P	-	1	0	WDR92	68222411	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.656000	0.74396	2.861000	0.98227	0.650000	0.86243	CCA	.		0.373	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458		T	68368907	G	T	68368907	3	4	128	1	0	0	0	0	1	0	0	0	17372	1232	43	4	657	4	WDR92	2	68368907	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	6301232	68368907	174830466	5	11224											
MAT2A	4144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	85770091	85770091	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccattatggtacctctcagaAgagtgagagagagctattag	13	10	11	7	0	1	4	1	1	1	4	2	6	1	4	2	1	2	2	2	1	5	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:85770091A>T	ENST00000306434.3	+	8	1142	c.1019A>T	c.(1018-1020)aAg>aTg	p.K340M	MAT2A_ENST00000409017.1_Missense_Mutation_p.K277M	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	340					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	ACCTCTCAGAAGAGTGAGAGA	0.398																																					p.K340M		.											.	MAT2A-90	0			c.A1019T						.						153	156	155					2																	85770091		2203	4300	6503	SO:0001583	missense	4144	exon8			CTCAGAAGAGTGA		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.1019A>T	2.37:g.85770091A>T	ENSP00000303147:p.Lys340Met	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	143	28	NM_005911	0	0	38	50	12	A8K511|B4DN45|D6W5L1|Q53SP5	Missense_Mutation	SNP	ENST00000306434.3	37	CCDS1977.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.358960	0.41801	.	.	ENSG00000168906	ENST00000306434;ENST00000424323;ENST00000409017	D;D	0.97688	-4.49;-4.49	5.8	5.8	0.92144	S-adenosylmethionine synthetase, C-terminal (1);S-adenosylmethionine synthetase superfamily (1);	0.000000	0.85682	D	0.000000	D	0.95230	0.8453	L	0.39692	1.235	0.58432	D	0.999993	B;B	0.16802	0.019;0.019	B;B	0.18263	0.021;0.021	D	0.92657	0.6138	10	0.31617	T	0.26	-9.6104	14.0949	0.65013	1.0:0.0:0.0:0.0	.	340;340	B4DEX8;P31153	.;METK2_HUMAN	M	340;121;277	ENSP00000303147:K340M;ENSP00000386353:K277M	ENSP00000303147:K340M	K	+	2	0	MAT2A	85623602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.899000	0.69846	2.209000	0.71365	0.460000	0.39030	AAG	.		0.398	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911		T	85770091	A	T	85770091	3	4	128	1	0	0	0	0	1	0	0	0	9355	72	3	5	1049	5	MAT2A	2	85770091	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	17401184	85770091	157429282	6	11225											
PHOSPHO2	493911	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	170557930	170557930	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcaatagatgcccaaagaAtctttgcaaaaaggtagttt	15	12	8	6	0	1	2	0	0	1	2	1	2	1	2	1	1	3	4	1	1	7	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:170557930A>G	ENST00000359744.3	+	4	837	c.449A>G	c.(448-450)aAt>aGt	p.N150S	KLHL23_ENST00000602521.1_Intron|KLHL23_ENST00000272797.4_Intron	NM_001008489.3|NM_001199285.1|NM_001199286.1|NM_001199288.1	NP_001008489.1|NP_001186214.1|NP_001186215.1|NP_001186217.1	Q8TCD6	PHOP2_HUMAN	phosphatase, orphan 2	150							metal ion binding (GO:0046872)|pyridoxal phosphatase activity (GO:0033883)			breast(1)|large_intestine(1)|lung(6)|skin(2)	10						TGCCCAAAGAATCTTTGCAAA	0.308																																					p.N150S		.											.	PHOSPHO2-91	0			c.A449G						.						64	65	64					2																	170557930		2203	4299	6502	SO:0001583	missense	493911	exon4			CAAAGAATCTTTG	BC022324	CCDS33319.1	2q31.1	2008-02-05			ENSG00000144362	ENSG00000144362			28316	protein-coding gene	gene with protein product						16054448	Standard	NM_001199285		Approved	MGC22679	uc021vsh.1	Q8TCD6	OTTHUMG00000153981	ENST00000359744.3:c.449A>G	2.37:g.170557930A>G	ENSP00000352782:p.Asn150Ser	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	75	13	NM_001199286	0	0	1	1	0	B2RC30|D3DPC7	Missense_Mutation	SNP	ENST00000359744.3	37	CCDS33319.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082674	0.76528	.	.	ENSG00000144362	ENST00000359744	T	0.61980	0.06	5.96	5.96	0.96718	HAD-like domain (2);	0.000000	0.85682	U	0.000000	D	0.82508	0.5052	M	0.89353	3.025	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.84925	0.0856	10	0.52906	T	0.07	.	16.4219	0.83766	1.0:0.0:0.0:0.0	.	150	Q8TCD6	PHOP2_HUMAN	S	150	ENSP00000352782:N150S	ENSP00000352782:N150S	N	+	2	0	PHOSPHO2	170266176	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.155000	0.89643	2.282000	0.76494	0.533000	0.62120	AAT	.		0.308	PHOSPHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333304.1	NM_001008489		G	170557930	A	G	170557930	3	3	128	1	0	0	0	0	1	0	0	0	11883	101	4	3	451	3	PHOSPHO2	2	170557930	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	84787839	170557930	72641443	7	11226											
PSMD1	5707	broad.mit.edu;bcgsc.ca	37	chr2	231943417	231943417	+	Frame_Shift_Del	DEL	A	A	-																															catactgcaaccgttatagcAaactcttttatgcactgtgg																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:231943417delA	ENST00000308696.6	+	10	1278	c.1116delA	c.(1114-1116)gcafs	p.A372fs	PSMD1_ENST00000373635.4_Frame_Shift_Del_p.A372fs|PSMD1_ENST00000409643.1_Frame_Shift_Del_p.A372fs	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	372					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CCGTTATAGCAAACTCTTTTA	0.343																																					p.A372fs													.	PSMD1-92	0			c.1116delA						.						126	120	122					2																	231943417		2203	4300	6503	SO:0001589	frameshift_variant	5707	exon10			TATAGCAAACTCT	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.1116delA	2.37:g.231943417delA	ENSP00000309474:p.Ala372fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	78	12	NM_002807	0	0	0	0	0	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Frame_Shift_Del	DEL	ENST00000308696.6	37	CCDS2482.1																																																																																			.		0.343	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			-	231943417	A	-	231943417	7	5	128	1	0	1	0	1	0	0	0	0	12721	117	5	0	1154	0	PSMD1	2	231943417	Frame_Shift_Del	DEL	A	TCGA-HE-7128-01A-11D-1961-08	61385487	231943417	11255956	8	11227											
OR6B2	389090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	240969643	240969643	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gacacgtaccagatctccagGaaagacatggagctcagaaa	16	5	10	10	1	2	3	1	0	1	3	3	6	2	5	2	2	2	2	2	2	3	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:240969643G>C	ENST00000402971.2	-	1	263	c.204C>G	c.(202-204)ttC>ttG	p.F68L		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		AGATCTCCAGGAAAGACATGG	0.557																																					p.F68L		.											.	.	0			c.C204G						.						117	127	124					2																	240969643		2117	4242	6359	SO:0001583	missense	389090	exon1			CTCCAGGAAAGAC		CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"GPCR / Class A : Olfactory receptors"	15041	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 2 pseudogene"	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.204C>G	2.37:g.240969643G>C	ENSP00000384563:p.Phe68Leu	Somatic	242	0		WXS	Illumina HiSeq	Phase_I	168	20	NM_001005853	0	0	0	0	0	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	37	CCDS46559.1	.	.	.	.	.	.	.	.	.	.	N	4.356	0.065626	0.08388	.	.	ENSG00000182083	ENST00000402971	T	0.00966	5.49	4.35	0.501	0.16925	GPCR, rhodopsin-like superfamily (1);	0.813827	0.10478	N	0.669897	T	0.00967	0.0032	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.22601	0.04	T	0.45818	-0.9235	10	0.38643	T	0.18	.	8.2409	0.31660	0.3395:0.0:0.6605:0.0	.	68	Q6IFH4	OR6B2_HUMAN	L	68	ENSP00000384563:F68L	ENSP00000384563:F68L	F	-	3	2	OR6B2	240618316	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.228000	0.09114	-0.029000	0.13827	-0.237000	0.12165	TTC	.		0.557	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853		C	240969643	G	C	240969643	3	2	128	1	0	0	0	0	1	0	0	0	11214	1165	41	4	736	4	OR6B2	2	240969643	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	9026226	240969643	2229730	9	11228											
RPL14	9045	hgsc.bcm.edu	37	chr3	40503557	40503557	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgctaaagTtccagcaaaaaagatcaccg	12	9	9	11	1	1	1	1	0	0	1	2	1	2	1	2	0	6	7	2	0	5	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr3:40503557T>C	ENST00000396203.2	+	6	614	c.482T>C	c.(481-483)gTt>gCt	p.V161A	RPL14_ENST00000338970.6_Missense_Mutation_p.V161A|RPL14_ENST00000416518.1_3'UTR	NM_001034996.2	NP_001030168.1	P50914	RL14_HUMAN	ribosomal protein L14	161					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)								KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		gctgctAAAGTTCCAGCAAAA	0.532																																					p.V161A		.											.	RPL14-90	0			c.T482C						.						12	12	12					3																	40503557		2196	4288	6484	SO:0001583	missense	9045	exon6			CTAAAGTTCCAGC	D87735	CCDS33739.1, CCDS43070.1	3p22-p21.2	2008-07-18			ENSG00000188846	ENSG00000188846		"L ribosomal proteins"	10305	protein-coding gene	gene with protein product	"CAG-ISL 7", "60S ribosomal protein L14"					9480843	Standard	NM_003973		Approved	L14, hRL14, RL14, CTG-B33	uc003ckg.4	P50914	OTTHUMG00000156046	ENST00000396203.2:c.482T>C	3.37:g.40503557T>C	ENSP00000379506:p.Val161Ala	Somatic	49	2		WXS	Illumina HiSeq	Phase_I	37	2	NM_003973	0	3	729	733	1	Q45RF0|Q53G20|Q8TBD5|Q8WUT0|Q92579|Q96GR0|Q9BSB8|Q9BW65|Q9BYF6	Missense_Mutation	SNP	ENST00000396203.2	37	CCDS43070.1	.	.	.	.	.	.	.	.	.	.	T	7.353	0.623248	0.14193	.	.	ENSG00000188846	ENST00000338970;ENST00000396203	T;T	0.42513	0.97;0.97	4.43	0.773	0.18516	.	1.064700	0.07443	N	0.897726	T	0.23806	0.0576	N	0.17082	0.46	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16541	-1.0399	10	0.16896	T	0.51	.	5.9465	0.19221	0.0:0.3206:0.0:0.6794	.	161	P50914	RL14_HUMAN	A	161	ENSP00000345156:V161A;ENSP00000379506:V161A	ENSP00000345156:V161A	V	+	2	0	RPL14	40478561	0.562000	0.26586	0.855000	0.33649	0.302000	0.27658	0.600000	0.24104	0.211000	0.20683	0.519000	0.50382	GTT	.		0.532	RPL14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342889.2	NM_003973		C	40503557	T	C	40503557	3	2	128	1	0	0	0	0	1	0	0	0	13593	1725	60	3	511	3	RPL14	3	40503557	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08		40503557	157518873	10	11229											
DZIP3	9666	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	108324275	108324275	+	Frame_Shift_Del	DEL	T	T	-																															tggattctctaccagatgaaTtttttgtgaggtaaggccac																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr3:108324275delT	ENST00000361582.3	+	2	252	c.22delT	c.(22-24)tttfs	p.F9fs	DZIP3_ENST00000463306.1_Frame_Shift_Del_p.F9fs	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	9					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						ACCAGATGAATTTTTTGTGAG	0.443																																					p.F8fs		.											.	DZIP3-91	0			c.22delT						.						111	116	114					3																	108324275		2203	4300	6503	SO:0001589	frameshift_variant	9666	exon2			.	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.22delT	3.37:g.108324275delT	ENSP00000355028:p.Phe9fs	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	96	20	NM_014648	0	0	0	0	0	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Frame_Shift_Del	DEL	ENST00000361582.3	37	CCDS2952.1																																																																																			.		0.443	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		-	108324275	T	-	108324275	7	5	128	1	0	1	0	1	0	0	0	0	4876	1493	52	0	24	0	DZIP3	3	108324275	Frame_Shift_Del	DEL	T	TCGA-HE-7128-01A-11D-1961-08	67820718	108324275	89698155	11	11230											
LIPH	200879	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	185241864	185241865	+	Frame_Shift_Del	DEL	AA	AA	-																															aatataaaggcttacctcccAatattgttttggggcagcca																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr3:185241864_185241865delAA	ENST00000296252.4	-	5	853_854	c.712_713delTT	c.(712-714)ttgfs	p.L238fs	LIPH_ENST00000424591.2_Frame_Shift_Del_p.L204fs	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	238					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CTTACCTCCCAATATTGTTTTG	0.436																																					p.238_238del		.											.	LIPH-92	0			c.712_713del						.																																			SO:0001589	frameshift_variant	200879	exon5			.	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.712_713delTT	3.37:g.185241864_185241865delAA	ENSP00000296252:p.Leu238fs	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	63	24	NM_139248	0	0	0	0	0	A2IBA7|Q8TEC7	Frame_Shift_Del	DEL	ENST00000296252.4	37	CCDS3272.1																																																																																			.		0.436	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1			-	185241865	AA	-	185241864	7	5	128	1	0	1	0	1	0	0	0	0	8847	131	5	0	666	0	LIPH	3	185241864	Frame_Shift_Del	DEL	AA	TCGA-HE-7128-01A-11D-1961-08	76917589	185241864	12780566	12	11231											
THAP9	79725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	83839493	83839493	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcattactagacctgtcaGatcataggcgaaatctcatc	13	10	8	10	1	3	2	3	0	1	2	5	3	3	2	1	2	1	1	1	2	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr4:83839493G>A	ENST00000302236.5	+	5	2179	c.2128G>A	c.(2128-2130)Gat>Aat	p.D710N	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	710					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AGACCTGTCAGATCATAGGCG	0.423																																					p.D710N		.											.	THAP9-156	0			c.G2128A						.						117	101	106					4																	83839493		2203	4300	6503	SO:0001583	missense	79725	exon5			CTGTCAGATCATA	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.2128G>A	4.37:g.83839493G>A	ENSP00000305533:p.Asp710Asn	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	107	26	NM_024672	0	0	2	2	0	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	G	3.185	-0.167102	0.06461	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.90069	-2.61	3.87	3.02	0.34903	.	0.462748	0.18401	N	0.142355	T	0.77805	0.4185	N	0.22421	0.69	0.09310	N	0.999994	B	0.23058	0.079	B	0.21546	0.035	T	0.62124	-0.6920	10	0.22706	T	0.39	-12.7397	5.7567	0.18176	0.1093:0.218:0.6727:0.0	.	710	Q9H5L6	THAP9_HUMAN	N	710	ENSP00000305533:D710N	ENSP00000305533:D710N	D	+	1	0	THAP9	84058517	0.016000	0.18221	0.085000	0.20634	0.025000	0.11179	1.445000	0.35079	1.203000	0.43233	0.655000	0.94253	GAT	.		0.423	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		A	83839493	G	A	83839493	3	1	128	1	0	0	0	0	1	0	0	0	15883	942	33	2	2146	2	THAP9	4	83839493	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08		83839493	107314783	13	11232											
NR3C2	4306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	149075914	149075914	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gaaccagtgctgtgttgaccGagggttcttttgcaggagcg	7	11	15	8	2	1	1	0	1	1	0	1	4	1	2	2	2	4	4	2	2	1	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr4:149075914G>C	ENST00000358102.3	-	5	2515	c.2153C>G	c.(2152-2154)tCg>tGg	p.S718W	NR3C2_ENST00000355292.3_Missense_Mutation_p.S722W|NR3C2_ENST00000511528.1_Missense_Mutation_p.S722W|NR3C2_ENST00000344721.4_Missense_Mutation_p.S718W|NR3C2_ENST00000503313.1_5'UTR|RP11-76G10.1_ENST00000514843.1_RNA|NR3C2_ENST00000512865.1_Intron	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	718	Hinge.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S718L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	TGTGTTGACCGAGGGTTCTTT	0.567																																					p.S718W	Melanoma(27;428 957 40335 51025 51111)	.											.	NR3C2-154	1	Substitution - Missense(1)	large_intestine(1)	c.C2153G						.						192	172	179					4																	149075914		2203	4300	6503	SO:0001583	missense	4306	exon5			TTGACCGAGGGTT	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.2153C>G	4.37:g.149075914G>C	ENSP00000350815:p.Ser718Trp	Somatic	289	0		WXS	Illumina HiSeq	Phase_I	177	30	NM_000901	0	0	2	3	1	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	37	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.928892	0.52759	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000511528	D;D;D;D	0.90676	-2.71;-2.71;-2.71;-2.71	5.57	5.57	0.84162	.	0.406531	0.27932	N	0.017264	D	0.94318	0.8174	M	0.77313	2.365	0.52501	D	0.99995	D	0.63880	0.993	P	0.56514	0.8	D	0.93801	0.7101	9	.	.	.	.	19.5581	0.95361	0.0:0.0:1.0:0.0	.	718	B0ZBF6	.	W	718;722;718;722	ENSP00000341390:S718W;ENSP00000347441:S722W;ENSP00000350815:S718W;ENSP00000421481:S722W	.	S	-	2	0	NR3C2	149295364	0.985000	0.35326	0.611000	0.29010	0.430000	0.31655	3.814000	0.55643	2.614000	0.88457	0.655000	0.94253	TCG	.		0.567	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			C	149075914	G	C	149075914	3	2	128	1	0	0	0	0	1	0	0	0	10657	1059	37	4	821	4	NR3C2	4	149075914	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	65236421	149075914	42078362	14	11233											
SFRS12	140890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	65466769	65466769	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atcgcgaagatctcgtagttCcagcaggtttgataatgctt	10	13	10	8	3	1	2	0	1	1	1	4	3	2	2	1	1	2	5	1	1	3	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr5:65466769C>T	ENST00000380918.3	+	10	1790	c.1130C>T	c.(1129-1131)tCc>tTc	p.S377F	SREK1_ENST00000334121.6_Missense_Mutation_p.S493F|SREK1_ENST00000284041.3_3'UTR	NM_139168.3	NP_631907.1	Q8WXA9	SREK1_HUMAN	splicing regulatory glutamine/lysine-rich protein 1	377	Arg/Glu/Lys/Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(3)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)	9						TCTCGTAGTTCCAGCAGGTTT	0.368																																					p.S493F	GBM(10;31 347 27684 38976 41583)	.											.	SREK1-91	0			c.C1478T						.						60	66	64					5																	65466769		2200	4297	6497	SO:0001583	missense	140890	exon9			GTAGTTCCAGCAG	AF459094	CCDS3991.1, CCDS43323.1, CCDS75253.1	5q11.2-q12.1	2013-02-12	2010-09-08	2010-09-08	ENSG00000153914	ENSG00000153914		"RNA binding motif (RRM) containing"	17882	protein-coding gene	gene with protein product	"serine-arginine-rich splicing regulatory protein 508"	609268	"splicing factor, arginine/serine-rich 12"	SFRS12		12043562	Standard	NM_001077199		Approved	DKFZp564B176, SRrp86, SRrp508	uc003jun.4	Q8WXA9	OTTHUMG00000097809	ENST00000380918.3:c.1130C>T	5.37:g.65466769C>T	ENSP00000370305:p.Ser377Phe	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	69	17	NM_001077199	0	0	0	1	1	A4FTW3|Q2M1J0|Q86X37	Missense_Mutation	SNP	ENST00000380918.3	37	CCDS3991.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.67|16.67	3.186680|3.186680	0.57909|0.57909	.|.	.|.	ENSG00000153914|ENSG00000153914	ENST00000537482|ENST00000334121;ENST00000380918	.|T;T	.|0.11821	.|2.74;2.74	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.330683	.|0.31167	.|N	.|0.008136	T|T	0.11580|0.11580	0.0282|0.0282	N|N	0.19112|0.19112	0.55|0.55	0.31022|0.31022	N|N	0.718059|0.718059	.|P;P	.|0.40794	.|0.61;0.729	.|B;B	.|0.38056	.|0.135;0.264	T|T	0.02269|0.02269	-1.1185|-1.1185	6|10	0.44086|0.56958	T|D	0.13|0.05	.|.	18.2481|18.2481	0.89993|0.89993	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|377;493	.|Q8WXA9;Q8WXA9-2	.|SREK1_HUMAN;.	S|F	493|493;377	.|ENSP00000334538:S493F;ENSP00000370305:S377F	ENSP00000445557:P493S|ENSP00000334538:S493F	P|S	+|+	1|2	0|0	SREK1|SREK1	65502525|65502525	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.322000|4.322000	0.59215|0.59215	2.409000|2.409000	0.81822|0.81822	0.650000|0.650000	0.86243|0.86243	CCA|TCC	.		0.368	SREK1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381118.1	NM_001077199		T	65466769	C	T	65466769	3	4	128	1	0	0	0	0	1	0	0	0	14199	855	30	2	1512	2	SFRS12	5	65466769	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		65466769	115448491	15	11234											
PTK7	5754	broad.mit.edu	37	chr6	43112987	43112987	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaggctcagggcttggaGgagggagtggcagagaccct	10	5	18	8	0	1	1	1	0	0	1	1	5	1	4	1	6	0	4	1	6	1	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:43112987G>A	ENST00000230419.4	+	16	2678	c.2457G>A	c.(2455-2457)gaG>gaA	p.E819E	PTK7_ENST00000349241.2_Silent_p.E689E|PTK7_ENST00000352931.2_Silent_p.E763E|PTK7_ENST00000345201.2_Silent_p.E779E|PTK7_ENST00000481273.1_Silent_p.E827E	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	819	Interaction with CTNNB1.|Protein kinase; inactive. {ECO:0000255|PROSITE-ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGGGCTTGGAGGAGGGAGTGG	0.597																																					p.E827E													.	PTK7-1493	0			c.G2481A						.						87	85	86					6																	43112987		2203	4300	6503	SO:0001819	synonymous_variant	5754	exon16			CTTGGAGGAGGGA	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.2457G>A	6.37:g.43112987G>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	103	4	NM_001270398	0	0	31	31	0	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1	.	.	.	.	.	.	.	.	.	.	G	8.784	0.929057	0.18131	.	.	ENSG00000112655	ENST00000489707	.	.	.	5.71	2.47	0.30058	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28267	-1.0049	4	.	.	.	.	5.8526	0.18701	0.3389:0.0:0.5272:0.1338	.	.	.	.	K	114	.	.	R	+	2	0	PTK7	43220965	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.999000	0.29757	0.737000	0.32582	0.655000	0.94253	AGG	.		0.597	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			A	43112987	G	A	43112987	2	1	128	1	0	0	0	0	0	0	0	1	12795	991	35	2		2	PTK7	6	43112987	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08		43112987	128002080	16	11235											
SLC22A7	10864	ucsc.edu	37	chr6	43270500	43270500	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttgtaccctacggtgctcAggtgaggaagcctgcaactg	9	9	13	10	1	1	1	1	1	0	0	1	2	1	2	2	3	6	4	2	3	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:43270500A>G	ENST00000372585.5	+	9	1479	c.1384A>G	c.(1384-1386)Aga>Gga	p.R462G	SLC22A7_ENST00000372589.3_Splice_Site_p.R460G|SLC22A7_ENST00000372574.3_Splice_Site_p.R460G	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	462					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	TACGGTGCTCAGGTGAGGAAG	0.527																																					p.R462G													.	SLC22A7-90	0			c.A1384G						.						57	47	50					6																	43270500		2203	4300	6503	SO:0001630	splice_region_variant	10864	exon8			GTGCTCAGGTGAG	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.1385+1A>G	6.37:g.43270500A>G		Somatic	21	0		WXS	Illumina HiSeq		13	2	NM_153320	0	0	0	6	6	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	37	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	A	15.13	2.741588	0.49151	.	.	ENSG00000137204	ENST00000372589;ENST00000372585;ENST00000372574;ENST00000436107	T;T;T;D	0.87650	-0.09;-0.09;-0.09;-2.28	5.17	5.17	0.71159	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.95172	0.8435	H	0.97659	4.05	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96489	0.9362	10	0.87932	D	0	.	12.8168	0.57669	1.0:0.0:0.0:0.0	.	462;460;460	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	G	460;462;460;155	ENSP00000361670:R460G;ENSP00000361666:R462G;ENSP00000361655:R460G;ENSP00000393836:R155G	ENSP00000361655:R460G	R	+	1	2	SLC22A7	43378478	1.000000	0.71417	1.000000	0.80357	0.125000	0.20455	3.882000	0.56160	2.089000	0.63090	0.379000	0.24179	AGA	.		0.527	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		Missense_Mutation	G	43270500	A	G	43270500	5	3	128	1	0	0	0	0	0	0	1	0	14491	202	7	3	1414	3	SLC22A7	6	43270500	Splice_Site	SNP	A	TCGA-HE-7128-01A-11D-1961-08	157513	43270500	127844567	17	11236											
NT5DC1	221294	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	116429548	116429548	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaaaggtttggcattggaTctagaagatgggaacttcct	11	12	12	6	0	1	2	0	0	1	2	2	4	2	4	1	4	2	3	1	4	4	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:116429548T>A	ENST00000319550.4	+	3	289	c.207T>A	c.(205-207)gaT>gaA	p.D69E		NM_152729.2	NP_689942.2	Q5TFE4	NT5D1_HUMAN	5'-nucleotidase domain containing 1	69							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|stomach(1)	8		all_cancers(87;0.00367)|all_epithelial(87;0.00449)|Colorectal(196;0.0469)		all cancers(137;0.0327)|OV - Ovarian serous cystadenocarcinoma(136;0.0445)|GBM - Glioblastoma multiforme(226;0.0719)|Epithelial(106;0.112)		TGGCATTGGATCTAGAAGATG	0.323																																					p.D69E	Colon(128;1440 1664 38087 41475 42869)												.	NT5DC1-226	0			c.T207A						.						104	104	104					6																	116429548		2203	4299	6502	SO:0001583	missense	221294	exon3			ATTGGATCTAGAA	BC015138	CCDS5104.1	6q22.31	2008-02-05	2006-01-27	2006-01-27	ENSG00000178425	ENSG00000178425			21556	protein-coding gene	gene with protein product			"5'-nucleotidase, cytosolic II-like 1"	NT5C2L1			Standard	NM_152729		Approved	dJ486I3.1, MGC24302	uc003pwj.3	Q5TFE4	OTTHUMG00000015428	ENST00000319550.4:c.207T>A	6.37:g.116429548T>A	ENSP00000326858:p.Asp69Glu	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	71	10	NM_152729	0	0	30	36	6	B2RND9|B3KR35|Q6XYD5	Missense_Mutation	SNP	ENST00000319550.4	37	CCDS5104.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.666737	0.67814	.	.	ENSG00000178425	ENST00000368618;ENST00000319550;ENST00000419791	T;T	0.53206	0.63;0.63	5.15	2.74	0.32292	HAD-like domain (1);	0.097795	0.64402	D	0.000002	T	0.58552	0.2130	M	0.85041	2.73	0.46131	D	0.998888	D;D	0.89917	0.998;1.0	D;D	0.97110	0.994;1.0	T	0.62964	-0.6742	10	0.66056	D	0.02	-14.0759	8.9428	0.35740	0.0:0.1569:0.0:0.8431	.	69;69	A8K2Z3;Q5TFE4	.;NT5D1_HUMAN	E	69	ENSP00000326858:D69E;ENSP00000393578:D69E	ENSP00000326858:D69E	D	+	3	2	NT5DC1	116536241	1.000000	0.71417	1.000000	0.80357	0.758000	0.43043	0.994000	0.29693	0.383000	0.24910	-0.256000	0.11100	GAT	.		0.323	NT5DC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041931.3	NM_152729		A	116429548	T	A	116429548	3	1	128	1	0	0	0	0	1	0	0	0	10716	1432	50	5	217	5	NT5DC1	6	116429548	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	73159048	116429548	54685519	18	11237											
SGK1	6446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	134495704	134495704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataaagtcgttcagacccaTcctcctctgcttcatgaaag	12	11	6	12	1	3	2	2	1	1	1	6	2	5	2	3	0	1	2	3	0	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:134495704T>C	ENST00000237305.7	-	2	185	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	SGK1_ENST00000475719.2_Missense_Mutation_p.M33V|SGK1_ENST00000413996.3_Missense_Mutation_p.M47V|SGK1_ENST00000367858.5_Missense_Mutation_p.M128V|SGK1_ENST00000528577.1_Missense_Mutation_p.M61V|SGK1_ENST00000367857.5_Missense_Mutation_p.M23V|SGK1_ENST00000489458.2_5'Flank	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	33	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCAGACCCATCCTCCTCTGC	0.423											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M128V		.											.	SGK1-981	0			c.A382G						.						81	81	81					6																	134495704		2203	4300	6503	SO:0001583	missense	6446	exon4			GACCCATCCTCCT	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"serum/glucocorticoid regulated kinase"	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.97A>G	6.37:g.134495704T>C	ENSP00000237305:p.Met33Val	Somatic	70	0	1611	WXS	Illumina HiSeq	Phase_I	51	7	NM_001143676	0	0	253	303	50	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.121060	0.56613	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38401	1.66;1.66;1.66;1.66;1.66;1.66;1.14	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.47488	0.1448	M	0.62723	1.935	0.80722	D	1	B;P;B;B;B;B	0.48911	0.01;0.917;0.004;0.001;0.019;0.002	B;D;B;B;B;B	0.63488	0.018;0.915;0.008;0.01;0.032;0.008	T	0.38628	-0.9652	10	0.41790	T	0.15	.	16.3127	0.82898	0.0:0.0:0.0:1.0	.	61;47;33;23;128;33	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	128;47;33;23;61;33;97	ENSP00000356832:M128V;ENSP00000396242:M47V;ENSP00000237305:M33V;ENSP00000356831:M23V;ENSP00000434450:M61V;ENSP00000434302:M33V;ENSP00000435577:M97V	ENSP00000237305:M33V	M	-	1	0	SGK1	134537397	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.246000	0.74042	0.533000	0.62120	ATG	.		0.423	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134495704	T	C	134495704	3	2	128	1	0	0	0	0	1	0	0	0	14239	1435	50	3	1242	3	SGK1	6	134495704	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	18066156	134495704	36619363	19	11238											
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137245094	137245094	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggtgctggtgcacgctgccTacctggtgctcatccagaag	6	9	13	13	2	1	1	1	0	0	1	2	1	2	1	3	3	5	4	3	3	2	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:137245094T>C	ENST00000331858.4	+	2	676	c.511T>C	c.(511-513)Tac>Cac	p.Y171H		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	171					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		GCACGCTGCCTACCTGGTGCT	0.706																																					p.Y171H		.											.	SLC35D3-91	0			c.T511C						.						17	15	15					6																	137245094		2183	4273	6456	SO:0001583	missense	340146	exon2			GCTGCCTACCTGG		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"Solute carriers"	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.511T>C	6.37:g.137245094T>C	ENSP00000333591:p.Tyr171His	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	10	6	NM_001008783	0	0	0	0	0	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644042	0.87859	.	.	ENSG00000182747	ENST00000331858	T	0.63096	-0.02	5.67	5.67	0.87782	Domain of unknown function DUF250 (1);	0.000000	0.85682	D	0.000000	T	0.71584	0.3357	L	0.61218	1.895	0.58432	D	0.999999	D	0.89917	1.0	D	0.77557	0.99	T	0.74791	-0.3545	10	0.59425	D	0.04	-16.1043	15.9193	0.79547	0.0:0.0:0.0:1.0	.	171	Q5M8T2	S35D3_HUMAN	H	171	ENSP00000333591:Y171H	ENSP00000333591:Y171H	Y	+	1	0	SLC35D3	137286787	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.900000	0.87376	2.176000	0.68965	0.454000	0.30748	TAC	.		0.706	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		C	137245094	T	C	137245094	3	2	128	1	0	0	0	0	1	0	0	0	14615	1522	53	3	517	3	SLC35D3	6	137245094	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	2749390	137245094	33869973	20	11239											
MLL5	55904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	104748161	104748161	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaactccaacttgagggAcctgacaccctcgcatcagt	11	8	9	13	1	1	3	1	3	0	0	3	4	2	4	3	1	2	1	3	1	2	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr7:104748161A>T	ENST00000311117.3	+	22	3802	c.3257A>T	c.(3256-3258)gAc>gTc	p.D1086V	CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334914.7_Missense_Mutation_p.D141V|SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000334877.4_Missense_Mutation_p.D1086V|KMT2E_ENST00000257745.4_Missense_Mutation_p.D1086V	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1086					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AACTTGAGGGACCTGACACCC	0.498																																					p.D1086V		.											.	MLL5-93	0			c.A3257T						.						83	82	82					7																	104748161		2203	4300	6503	SO:0001583	missense	55904	exon21			TGAGGGACCTGAC	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3257A>T	7.37:g.104748161A>T	ENSP00000312379:p.Asp1086Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	65	22	NM_018682	0	0	8	17	9	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704341	0.88924	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.96136	-3.92;-3.2;-3.92;-0.21	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.96222	0.8768	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97101	0.9797	10	0.87932	D	0	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	1086	Q8IZD2	MLL5_HUMAN	V	1086;1086;1086;1006;1086;141	ENSP00000312379:D1086V;ENSP00000335599:D1086V;ENSP00000257745:D1086V;ENSP00000333986:D141V	ENSP00000257745:D1086V	D	+	2	0	MLL5	104535397	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	8.690000	0.91272	2.302000	0.77476	0.533000	0.62120	GAC	.		0.498	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104748161	A	T	104748161	3	4	128	1	0	0	0	0	1	0	0	0	9649	275	10	5	3335	5	MLL5	7	104748161	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		104748161	54390502	21	11240											
TTC26	79989	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	138822639	138822639	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggatactaatttgtggaTtggatattgtgcctttcacc	10	15	10	6	0	1	1	1	0	0	1	1	4	1	4	2	3	2	0	2	3	3	7			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr7:138822639T>C	ENST00000464848.1	+	3	268	c.188T>C	c.(187-189)aTt>aCt	p.I63T	TTC26_ENST00000474035.2_Missense_Mutation_p.I63T|TTC26_ENST00000478836.2_Missense_Mutation_p.I63T|TTC26_ENST00000481482.1_3'UTR|TTC26_ENST00000495038.1_Missense_Mutation_p.I63T|TTC26_ENST00000343187.4_Intron|TTC26_ENST00000430935.1_Missense_Mutation_p.I63T			A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26	63					cilium assembly (GO:0042384)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle B (GO:0030992)|primary cilium (GO:0072372)				breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	24						AATTTGTGGATTGGATATTGT	0.323																																					p.I63T		.											.	TTC26-91	0			c.T188C						.						154	153	153					7																	138822639		2203	4300	6503	SO:0001583	missense	79989	exon3			TGTGGATTGGATA	AK022633	CCDS5852.1, CCDS55172.1, CCDS55173.1, CCDS75665.1	7q34	2013-01-11			ENSG00000105948	ENSG00000105948		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	21882	protein-coding gene	gene with protein product							Standard	NM_001144920		Approved	FLJ12571, dyf-13, DYF13	uc003vus.2	A0AVF1	OTTHUMG00000157472	ENST00000464848.1:c.188T>C	7.37:g.138822639T>C	ENSP00000419279:p.Ile63Thr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	110	7	NM_001144920	0	0	11	12	1	A4D1S3|B7Z5M0|C9J2N7|F8W724|Q9H9S8|Q9NTC0	Missense_Mutation	SNP	ENST00000464848.1	37	CCDS5852.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.717383	0.48622	.	.	ENSG00000105948	ENST00000430935;ENST00000495038;ENST00000474035;ENST00000478836;ENST00000464848	T;T;T;T;T	0.77229	-1.08;1.52;-1.08;1.15;-1.08	6.05	6.05	0.98169	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.287285	0.37761	N	0.001947	T	0.76550	0.4003	L	0.39245	1.2	0.58432	D	0.999996	P;B;P;B;B	0.41188	0.605;0.012;0.741;0.004;0.137	P;B;P;B;B	0.45660	0.489;0.018;0.489;0.012;0.062	T	0.77720	-0.2482	10	0.52906	T	0.07	.	15.5826	0.76455	0.0:0.0:0.0:1.0	.	63;63;63;63;63	B7Z2T3;C9J2N7;B7Z6R6;A0AVF1;Q96CU4	.;.;.;TTC26_HUMAN;.	T	63	ENSP00000410655:I63T;ENSP00000418788:I63T;ENSP00000443253:I63T;ENSP00000419178:I63T;ENSP00000419279:I63T	ENSP00000410655:I63T	I	+	2	0	TTC26	138473179	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.353000	0.59411	2.323000	0.78572	0.533000	0.62120	ATT	.		0.323	TTC26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348919.2	NM_024926		C	138822639	T	C	138822639	3	2	128	1	0	0	0	0	1	0	0	0	16727	1493	52	3	198	3	TTC26	7	138822639	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	34074478	138822639	20316024	22	11241											
AGPAT6	137964	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	41467379	41467379	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtcctggaacctgctgagCagaaccaattataacttcca	13	9	8	11	0	0	2	0	1	0	1	2	4	2	3	4	1	5	2	4	1	5	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr8:41467379C>T	ENST00000396987.3	+	4	1368	c.441C>T	c.(439-441)agC>agT	p.S147S	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	147					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			ACCTGCTGAGCAGAACCAATT	0.493																																					p.S147S		.											.	AGPAT6-90	0			c.C441T						.						98	96	97					8																	41467379		2203	4300	6503	SO:0001819	synonymous_variant	137964	exon4			GCTGAGCAGAACC	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.441C>T	8.37:g.41467379C>T		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	124	30	NM_178819	1	0	34	45	10	Q86V89	Silent	SNP	ENST00000396987.3	37	CCDS6117.1																																																																																			.		0.493	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		T	41467379	C	T	41467379	2	4	128	1	0	0	0	0	0	0	0	1	391	709	25	2		2	AGPAT6	8	41467379	Silent	SNP	C	TCGA-HE-7128-01A-11D-1961-08		41467379	104896643	23	11242											
CDC37L1	55664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	4706079	4706079	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactcggtggtacataaagaAgatgatgaacccaaaatgat	18	8	9	6	1	0	5	0	3	0	2	1	5	0	5	1	2	3	1	1	2	8	2	rs200977934		TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:4706079A>G	ENST00000381854.3	+	7	1183	c.981A>G	c.(979-981)gaA>gaG	p.E327E		NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	327	Interaction with Hsp70.|Required for interaction with STIP1.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		TACATAAAGAAGATGATGAAC	0.393																																					p.E327E		.											.	CDC37L1-90	0			c.A981G						.						130	112	118					9																	4706079		2203	4300	6503	SO:0001819	synonymous_variant	55664	exon7			TAAAGAAGATGAT	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1", "cell division cycle 37 homolog (S. cerevisiae)-like 1"				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.981A>G	9.37:g.4706079A>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	46	6	NM_017913	0	0	11	14	3	B1AL70|Q9NWS3|Q9NX16	Silent	SNP	ENST00000381854.3	37	CCDS6454.1																																																																																			.		0.393	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913		G	4706079	A	G	4706079	2	3	128	1	0	0	0	0	0	0	0	1	3075	69	3	3		3	CDC37L1	9	4706079	Silent	SNP	A	TCGA-HE-7128-01A-11D-1961-08		4706079	136507352	24	11243											
OGN	4969	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	95148550	95148550	+	Frame_Shift_Del	DEL	A	A	-																															attccagggcattatggtccAagtagaggaaggtgaggtta																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:95148550delA	ENST00000262551.4	-	6	1079	c.659delT	c.(658-660)ttgfs	p.L220fs	CENPP_ENST00000375587.3_Intron|OGN_ENST00000375561.5_Frame_Shift_Del_p.L220fs	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	220					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						ATTATGGTCCAAGTAGAGGAA	0.368																																					p.L220fs		.											.	OGN-492	0			c.659delT						.						195	188	190					9																	95148550		2203	4300	6503	SO:0001589	frameshift_variant	4969	exon6			.	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.659delT	9.37:g.95148550delA	ENSP00000262551:p.Leu220fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	50	16	NM_033014	0	0	0	0	0	Q6FIB0|Q9UF90|Q9UNK5	Frame_Shift_Del	DEL	ENST00000262551.4	37	CCDS6695.1																																																																																			.		0.368	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		-	95148550	A	-	95148550	7	5	128	1	0	1	0	1	0	0	0	0	10872	131	5	0	245	0	OGN	9	95148550	Frame_Shift_Del	DEL	A	TCGA-HE-7128-01A-11D-1961-08	90442471	95148550	46064881	25	11244											
TOR2A	27433	ucsc.edu	37	chr9	130494938	130494938	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcgccacgcctccaatGccacctggttgatctgcttg	5	10	11	15	2	1	1	0	1	1	0	2	1	2	1	5	2	3	3	5	2	1	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:130494938G>A	ENST00000373284.5	-	4	672	c.626C>T	c.(625-627)gCa>gTa	p.A209V	TOR2A_ENST00000336067.6_Intron|TOR2A_ENST00000458505.3_3'UTR|TOR2A_ENST00000373281.5_3'UTR|TOR2A_ENST00000472723.1_5'UTR	NM_001085347.2	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A	209					chaperone mediated protein folding requiring cofactor (GO:0051085)|protein homooligomerization (GO:0051260)	endoplasmic reticulum lumen (GO:0005788)	ATP binding (GO:0005524)			NS(1)|endometrium(2)	3						CGCCTCCAATGCCACCTGGTT	0.657																																					p.A209V													.	TOR2A-90	0			c.C626T						.						14	19	17					9																	130494938		2115	4225	6340	SO:0001583	missense	27433	exon4			TCCAATGCCACCT	AA873275	CCDS6876.1, CCDS43879.1, CCDS48024.1	9q34.11	2010-08-20			ENSG00000160404	ENSG00000160404			11996	protein-coding gene	gene with protein product		608052				10644435	Standard	NM_001085347		Approved	FLJ14771, TORP1	uc004brs.4	Q5JU69	OTTHUMG00000020706	ENST00000373284.5:c.626C>T	9.37:g.130494938G>A	ENSP00000362381:p.Ala209Val	Somatic	12	0		WXS	Illumina HiSeq		4	1	NM_001085347	0	0	16	19	3	A4FU12|A4FU13|Q3ZCN9|Q3ZCP0|Q5JU68|Q66K87|Q6UXW6|Q8NAN5|Q96SL7	Missense_Mutation	SNP	ENST00000373284.5	37	CCDS43879.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.585931	0.46110	.	.	ENSG00000160404	ENST00000373284	T	0.29397	1.57	5.72	-3.4	0.04853	ATPase, AAA+ type, core (1);	0.302598	0.39687	N	0.001290	T	0.16428	0.0395	L	0.27053	0.805	0.54753	D	0.999988	B	0.12630	0.006	B	0.12156	0.007	T	0.28459	-1.0043	10	0.10111	T	0.7	-1.6228	13.502	0.61462	0.236:0.0:0.764:0.0	.	209	Q5JU69	TOR2A_HUMAN	V	209	ENSP00000362381:A209V	ENSP00000362381:A209V	A	-	2	0	TOR2A	129534759	0.011000	0.17503	0.012000	0.15200	0.862000	0.49288	0.317000	0.19487	-0.535000	0.06307	-1.036000	0.02392	GCA	.		0.657	TOR2A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054205.1	NM_130459		A	130494938	G	A	130494938	3	1	128	1	0	0	0	0	1	0	0	0	16408	1319	46	2	347	2	TOR2A	9	130494938	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	35346388	130494938	10718493	26	11245											
C9orf7	11094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	136333115	136333115	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgccatcgcctttgctacGggggtgctgtacggactctc	6	10	12	13	4	1	0	0	0	1	0	3	1	1	1	2	3	5	3	2	3	3	3	rs150411088		TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:136333115G>A	ENST00000316948.4	+	4	473	c.393G>A	c.(391-393)acG>acA	p.T131T	CACFD1_ENST00000542192.1_Silent_p.T89T|CACFD1_ENST00000291722.7_Silent_p.T89T|CACFD1_ENST00000540581.1_Silent_p.T131T	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1	131					synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										CCTTTGCTACGGGGGTGCTGT	0.657																																					p.T131T		.											.	.	0			c.G393A						.	G	,,,	1,4405	2.1+/-5.4	0,1,2202	76	68	70		267,393,267,393	-10.8	0.2	9	dbSNP_134	70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C9orf7	NM_001135775.2,NM_001242369.1,NM_001242370.1,NM_017586.3	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	89/131,131/234,89/192,131/173	136333115	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11094	exon4			TGCTACGGGGGTG		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"chromosome 9 open reading frame 7"	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.393G>A	9.37:g.136333115G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	59	16	NM_017586	0	0	8	19	11	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Silent	SNP	ENST00000316948.4	37	CCDS6974.1																																																																																			G|1.000;A|0.000		0.657	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586		A	136333115	G	A	136333115	2	1	128	1	0	0	0	0	0	0	0	1	2499	1103	39	1		1	C9orf7	9	136333115	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08	5838177	136333115	4880316	27	11246											
SLC16A12	387700	bcgsc.ca	37	chr10	91203549	91203549	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaatctacaatggaatggaTccatgccgtttgtgcgtaat	12	12	9	8	2	1	0	0	0	1	0	2	2	2	2	2	2	3	2	2	2	5	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr10:91203549T>C	ENST00000341233.4	-	4	568	c.178A>G	c.(178-180)Atc>Gtc	p.I60V	SLC16A12_ENST00000371790.4_Missense_Mutation_p.I90V	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|skin(1)|stomach(1)	14						ATGGAATGGATCCATGCCGTT	0.378																																					p.I90V													.	SLC16A12-69	0			c.A268G						.						124	108	114					10																	91203549		2203	4300	6503	SO:0001583	missense	387700	exon4			AATGGATCCATGC		CCDS7404.1, CCDS7404.2	10q23.32	2013-07-18	2013-07-18		ENSG00000152779	ENSG00000152779		"Solute carriers"	23094	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 12"	611910	"solute carrier family 16 (monocarboxylic acid transporters), member 12", "solute carrier family 16, member 12 (monocarboxylic acid transporter 12)"				Standard	NM_213606		Approved	MCT12	uc001kgm.3	Q6ZSM3	OTTHUMG00000018714	ENST00000341233.4:c.178A>G	10.37:g.91203549T>C	ENSP00000343022:p.Ile60Val	Somatic	56	0		WXS	Illumina HiSeq	Phase_1	60	4	NM_213606	0	0	22	22	0	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	37		.	.	.	.	.	.	.	.	.	.	T	18.13	3.554819	0.65425	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	T;T	0.55413	0.52;0.52	5.47	5.47	0.80525	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.098147	0.64402	D	0.000002	T	0.46658	0.1404	L	0.37850	1.14	0.80722	D	1	P	0.37612	0.602	B	0.42214	0.38	T	0.33163	-0.9879	10	0.14252	T	0.57	.	14.7418	0.69461	0.0:0.0:0.0:1.0	.	60	Q6ZSM3	MOT12_HUMAN	V	60;90	ENSP00000343022:I60V;ENSP00000360855:I90V	ENSP00000343022:I60V	I	-	1	0	SLC16A12	91193529	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.223000	0.72257	2.087000	0.62958	0.482000	0.46254	ATC	.		0.378	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		C	91203549	T	C	91203549	3	2	128	1	0	0	0	0	1	0	0	0	14437	1435	50	3	1302	3	SLC16A12	10	91203549	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08		91203549	44331198	28	11247											
OR51A7	119687	broad.mit.edu;bcgsc.ca	37	chr11	4928976	4928976	+	Frame_Shift_Del	DEL	T	T	-																															tttggaccgctttcttgccaTtcacaatcccttaagataca																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:4928976delT	ENST00000359350.4	+	1	377	c.377delT	c.(376-378)attfs	p.I126fs	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTTCTTGCCATTCACAATCCC	0.393																																					p.I126fs													.	OR51A7-70	0			c.377delT						.						102	98	99					11																	4928976		2201	4298	6499	SO:0001589	frameshift_variant	119687	exon1			TTGCCATTCACAA	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.377delT	11.37:g.4928976delT	ENSP00000352305:p.Ile126fs	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	112	15	NM_001004749	0	0	0	0	0	Q6IFH8	Frame_Shift_Del	DEL	ENST00000359350.4	37	CCDS31364.1																																																																																			.		0.393	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		-	4928976	T	-	4928976	7	5	128	1	0	1	0	1	0	0	0	0	11114	1493	52	0	379	0	OR51A7	11	4928976	Frame_Shift_Del	DEL	T	TCGA-HE-7128-01A-11D-1961-08		4928976	130077540	29	11248											
NDUFS3	4722	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47604000	47604000	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atcctttccggaaagactttCctctatctggctatgttgag	8	15	8	10	1	2	2	0	1	2	1	5	3	5	3	3	2	0	2	3	2	3	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:47604000C>T	ENST00000263774.4	+	6	689	c.607C>T	c.(607-609)Cct>Tct	p.P203S	NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	203					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	GAAAGACTTTCCTCTATCTGG	0.512																																					p.P203S	Pancreas(15;551 601 22438 23457 52512)	.											.	NDUFS3-90	0			c.C607T						.						261	270	267					11																	47604000		2201	4298	6499	SO:0001583	missense	4722	exon6			GACTTTCCTCTAT	AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7710	protein-coding gene	gene with protein product	"complex I 30kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"	603846	"NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.607C>T	11.37:g.47604000C>T	ENSP00000263774:p.Pro203Ser	Somatic	512	1		WXS	Illumina HiSeq	Phase_I	378	86	NM_004551	0	0	60	79	19	B2R9J1|B4DFM8|Q9UNQ8	Missense_Mutation	SNP	ENST00000263774.4	37	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	C	33	5.261674	0.95368	.	.	ENSG00000213619	ENST00000263774	D	0.88124	-2.34	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.972;0.979	D	0.95909	0.8921	10	0.87932	D	0	-17.4651	20.206	0.98277	0.0:1.0:0.0:0.0	.	203;129	O75489;Q9UF24	NDUS3_HUMAN;.	S	203	ENSP00000263774:P203S	ENSP00000263774:P203S	P	+	1	0	NDUFS3	47560576	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	7.474000	0.81024	2.785000	0.95823	0.655000	0.94253	CCT	.		0.512	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551		T	47604000	C	T	47604000	3	4	128	1	0	0	0	0	1	0	0	0	10319	855	30	2	629	2	NDUFS3	11	47604000	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	42675024	47604000	87402516	30	11249											
ARHGEF17	9828	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	73020521	73020521	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctcgggcagtgacgacGaccgagacggtgagggcggc	8	4	17	12	6	0	3	0	2	0	1	2	6	1	3	2	4	0	1	2	4	0	0			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:73020521G>T	ENST00000263674.3	+	1	1188	c.838G>T	c.(838-840)Gac>Tac	p.D280Y	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	280					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CAGTGACGACGACCGAGACGG	0.697																																					p.D280Y		.											.	ARHGEF17-227	0			c.G838T						.						16	21	20					11																	73020521		2151	4242	6393	SO:0001583	missense	9828	exon1			GACGACGACCGAG	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"Rho guanine nucleotide exchange factors"	21726	protein-coding gene	gene with protein product	"Rho-specific guanine-nucleotide exchange factor 164 kDa", "tumor endothelial marker 4"					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.838G>T	11.37:g.73020521G>T	ENSP00000263674:p.Asp280Tyr	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	50	13	NM_014786	0	0	9	12	3	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.677629	0.47886	.	.	ENSG00000110237	ENST00000263674	T	0.68181	-0.31	4.72	4.72	0.59763	.	0.000000	0.40554	N	0.001072	T	0.60495	0.2273	L	0.27053	0.805	0.09310	N	0.999994	P	0.49447	0.924	P	0.46419	0.516	T	0.60239	-0.7302	10	0.87932	D	0	-17.9023	15.1972	0.73100	0.0:0.0:1.0:0.0	.	280	Q96PE2	ARHGH_HUMAN	Y	280	ENSP00000263674:D280Y	ENSP00000263674:D280Y	D	+	1	0	ARHGEF17	72698169	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	4.087000	0.57671	2.179000	0.69175	0.313000	0.20887	GAC	.		0.697	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73020521	G	T	73020521	3	4	128	1	0	0	0	0	1	0	0	0	900	1058	37	4	840	4	ARHGEF17	11	73020521	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	25416521	73020521	61985995	31	11250											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49446075	49446075	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtggtgacaggcgtgatGcctcaggtggtggggacgtg	5	9	21	6	2	1	2	1	2	0	0	1	3	1	3	1	7	1	0	1	7	0	0			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:49446075G>A	ENST00000301067.7	-	10	1390	c.1391C>T	c.(1390-1392)gCa>gTa	p.A464V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	464	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CAGGCGTGATGCCTCAGGTGG	0.657																																					p.A464V		.											.	MLL2-612	0			c.C1391T						.						88	98	94					12																	49446075		2162	4235	6397	SO:0001583	missense	8085	exon10			CGTGATGCCTCAG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.1391C>T	12.37:g.49446075G>A	ENSP00000301067:p.Ala464Val	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	180	48	NM_003482	0	0	7	10	3	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	7.479	0.648310	0.14516	.	.	ENSG00000167548	ENST00000301067	T	0.80393	-1.37	3.73	2.82	0.32997	.	.	.	.	.	T	0.58807	0.2148	N	0.08118	0	0.21841	N	0.999512	P	0.38395	0.629	B	0.29440	0.102	T	0.53844	-0.8381	9	0.87932	D	0	.	8.8235	0.35041	0.0:0.0:0.5915:0.4085	.	464	O14686	MLL2_HUMAN	V	464	ENSP00000301067:A464V	ENSP00000301067:A464V	A	-	2	0	MLL2	47732342	0.989000	0.36119	0.999000	0.59377	0.673000	0.39480	0.945000	0.29056	1.130000	0.42092	0.313000	0.20887	GCA	.		0.657	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49446075	G	A	49446075	3	1	128	1	0	0	0	0	1	0	0	0	9646	1319	46	2	15402	2	MLL2	12	49446075	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08		49446075	84405820	32	11251											
UTP20	27340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	101684601	101684601	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggagaaacactcaaaaacAtggtcaaatccactgtatcc	16	9	6	10	0	2	1	2	0	0	1	4	2	4	1	2	2	2	1	2	2	5	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:101684601A>G	ENST00000261637.4	+	8	1000	c.826A>G	c.(826-828)Atg>Gtg	p.M276V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	276					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						ACTCAAAAACATGGTCAAATC	0.373																																					p.M276V		.											.	UTP20-155	0			c.A826G						.						165	146	153					12																	101684601		2203	4300	6503	SO:0001583	missense	27340	exon8			AAAAACATGGTCA	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.826A>G	12.37:g.101684601A>G	ENSP00000261637:p.Met276Val	Somatic	65	1		WXS	Illumina HiSeq	Phase_I	95	28	NM_014503	0	0	2	4	2	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	a	11.01	1.513057	0.27123	.	.	ENSG00000120800	ENST00000261637	T	0.63096	-0.02	5.36	5.36	0.76844	Armadillo-type fold (1);	0.044796	0.85682	D	0.000000	T	0.53449	0.1797	M	0.65975	2.015	0.41134	D	0.9859	B	0.13145	0.007	B	0.08055	0.003	T	0.49523	-0.8931	10	0.02654	T	1	-27.2237	10.5826	0.45265	0.8563:0.0:0.0:0.1437	.	276	O75691	UTP20_HUMAN	V	276	ENSP00000261637:M276V	ENSP00000261637:M276V	M	+	1	0	UTP20	100208732	1.000000	0.71417	0.999000	0.59377	0.862000	0.49288	5.005000	0.63972	2.031000	0.59945	0.528000	0.53228	ATG	.		0.373	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101684601	A	G	101684601	3	3	128	1	0	0	0	0	1	0	0	0	17132	217	8	3	856	3	UTP20	12	101684601	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	52238526	101684601	32167294	33	11252											
PTPN11	5781	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112892482	112892482	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtacagtactacaactcaagCaggtgagcagattggaaagc	15	7	11	8	0	1	2	1	1	0	1	1	3	1	3	0	2	7	4	0	2	6	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:112892482C>A	ENST00000351677.2	+	5	838	c.640C>A	c.(640-642)Cag>Aag	p.Q214K	PTPN11_ENST00000392597.1_Missense_Mutation_p.Q214K	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	214	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						ACAACTCAAGCAGGTGAGCAG	0.378			Mis		"JMML, AML, MDS"		Noonan Syndrome		Noonan syndrome																												p.Q214K				Dom	yes		12	12q24.1	5781	"protein tyrosine phosphatase, non-receptor type 11"	yes	L	.	PTPN11-7239	0			c.C640A						.						72	67	69					12																	112892482		2203	4300	6503	SO:0001583	missense	5781	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CTCAAGCAGGTGA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor", "SH2 domain containing"	9644	protein-coding gene	gene with protein product		176876	"Noonan syndrome 1"	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.640C>A	12.37:g.112892482C>A	ENSP00000340944:p.Gln214Lys	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	50	7	NM_080601	0	0	0	0	0	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.04|17.04	3.287636|3.287636	0.59976|0.59976	.|.	.|.	ENSG00000179295|ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596|ENST00000530818	T;T|.	0.75938|.	-0.98;-0.98|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68531|0.68531	0.3011|0.3011	L|L	0.42744|0.42744	1.35|1.35	0.80722|0.80722	D|D	1|1	B;B|.	0.19583|.	0.016;0.037|.	B;B|.	0.23150|.	0.036;0.044|.	T|T	0.63296|0.63296	-0.6669|-0.6669	10|5	0.40728|.	T|.	0.16|.	.|.	19.717|19.717	0.96124|0.96124	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	214;214|.	Q06124-2;Q06124-3|.	.;.|.	K|R	214|58	ENSP00000376376:Q214K;ENSP00000340944:Q214K|.	ENSP00000340944:Q214K|.	Q|S	+|+	1|3	0|2	PTPN11|PTPN11	111376865|111376865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.431000|0.431000	0.31685|0.31685	7.468000|7.468000	0.80943|0.80943	2.654000|2.654000	0.90174|0.90174	0.484000|0.484000	0.47621|0.47621	CAG|AGC	.		0.378	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			A	112892482	C	A	112892482	3	1	128	1	0	0	0	0	1	0	0	0	12810	711	25	4	658	4	PTPN11	12	112892482	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	11207881	112892482	20959413	34	11253											
ABCB9	23457	broad.mit.edu	37	chr12	123444428	123444428	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgtacgtccacacgaacaGggcccaaaaccaggggtccc	13	4	10	14	2	0	0	0	0	0	0	2	1	2	0	4	3	3	1	4	3	5	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:123444428G>T	ENST00000542678.1	-	2	3193	c.355C>A	c.(355-357)Ctg>Atg	p.L119M	ABCB9_ENST00000344275.7_Missense_Mutation_p.L119M|ABCB9_ENST00000392439.3_Missense_Mutation_p.L119M|ABCB9_ENST00000280560.8_Missense_Mutation_p.L119M|ABCB9_ENST00000540285.1_Missense_Mutation_p.L119M|ABCB9_ENST00000442028.2_Missense_Mutation_p.L119M|ABCB9_ENST00000442833.2_Missense_Mutation_p.L119M|ABCB9_ENST00000346530.5_Missense_Mutation_p.L119M			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	119					peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CACACGAACAGGGCCCAAAAC	0.647																																					p.L119M	Ovarian(49;786 1333 9175 38236)												.	ABCB9-90	0			c.C355A						.						35	38	37					12																	123444428		2203	4300	6503	SO:0001583	missense	23457	exon2			CGAACAGGGCCCA	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.355C>A	12.37:g.123444428G>T	ENSP00000440288:p.Leu119Met	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	35	6	NM_019625	0	0	6	11	5	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.707845	0.48412	.	.	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028;ENST00000539502	D;D;D;D;D;D	0.90732	-2.41;-2.72;-2.6;-2.41;-2.41;-2.39	5.53	3.63	0.41609	.	0.159060	0.42053	D	0.000776	D	0.92570	0.7640	L	0.55481	1.735	0.45777	D	0.998666	P;D;D;D;D	0.89917	0.822;1.0;1.0;0.961;1.0	P;D;D;P;D	0.91635	0.54;0.999;0.991;0.774;0.987	D	0.90410	0.4409	10	0.44086	T	0.13	-30.2529	8.7879	0.34832	0.07:0.0:0.6597:0.2704	.	119;119;119;119;119	B4E2J0;F5GX63;Q9NP78-3;Q9NP78-2;Q9NP78	.;.;.;.;ABCB9_HUMAN	M	119	ENSP00000280560:L119M;ENSP00000441734:L119M;ENSP00000280559:L119M;ENSP00000376234:L119M;ENSP00000440288:L119M;ENSP00000394898:L119M	ENSP00000280560:L119M	L	-	1	2	ABCB9	122010381	0.994000	0.37717	0.991000	0.47740	0.938000	0.57974	1.935000	0.40173	0.642000	0.30620	0.561000	0.74099	CTG	.		0.647	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		T	123444428	G	T	123444428	3	4	128	1	0	0	0	0	1	0	0	0	48	991	35	4	1989	4	ABCB9	12	123444428	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	10551946	123444428	10407467	35	11254											
OGFOD2	79676	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123463804	123463804	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctctgtcccatgtgctgcCgtgagcccgacctggtggac	4	9	13	15	2	1	1	0	1	1	0	2	3	2	2	5	2	3	1	5	2	0	0			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:123463804C>G	ENST00000228922.7	+	7	996	c.964C>G	c.(964-966)Cgt>Ggt	p.R322G	ARL6IP4_ENST00000315580.5_5'Flank|ARL6IP4_ENST00000439686.2_5'Flank|RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000357866.4_5'Flank|ARL6IP4_ENST00000426960.2_5'Flank|ARL6IP4_ENST00000453766.2_5'Flank|OGFOD2_ENST00000454694.2_Missense_Mutation_p.R158G|ABCB9_ENST00000542678.1_5'UTR|ARL6IP4_ENST00000392435.2_5'Flank|OGFOD2_ENST00000545612.1_Missense_Mutation_p.R158G|OGFOD2_ENST00000397389.2_Missense_Mutation_p.R262G|OGFOD2_ENST00000538755.1_Missense_Mutation_p.R158G|OGFOD2_ENST00000536150.1_Missense_Mutation_p.R158G|ARL6IP4_ENST00000543566.1_5'Flank|ARL6IP4_ENST00000412505.2_5'Flank|OGFOD2_ENST00000538628.1_Missense_Mutation_p.R158G|ARL6IP4_ENST00000454885.2_5'Flank|OGFOD2_ENST00000545317.1_Missense_Mutation_p.R158G			Q6N063	OGFD2_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 2	322							iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			breast(1)|endometrium(2)|lung(4)|pancreas(1)	8	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.11e-05)|Epithelial(86;0.000127)|BRCA - Breast invasive adenocarcinoma(302;0.107)	Vitamin C(DB00126)	CATGTGCTGCCGTGAGCCCGA	0.647																																					p.R262G		.											.	OGFOD2-69	0			c.C784G						.						42	49	47					12																	123463804		2166	4249	6415	SO:0001583	missense	79676	exon8			TGCTGCCGTGAGC	AK094820	CCDS41855.1	12q24.31	2010-11-23			ENSG00000111325	ENSG00000111325			25823	protein-coding gene	gene with protein product						12477932	Standard	NM_024623		Approved	FLJ13491, FLJ37501	uc001udz.1	Q6N063		ENST00000228922.7:c.964C>G	12.37:g.123463804C>G	ENSP00000228922:p.Arg322Gly	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	70	13	NM_024623	0	0	13	29	16	B3KT24|Q4KN13|Q6N023|Q9H8K6	Missense_Mutation	SNP	ENST00000228922.7	37		.	.	.	.	.	.	.	.	.	.	C	2.311	-0.357912	0.05138	.	.	ENSG00000111325	ENST00000397389;ENST00000538755;ENST00000536150;ENST00000545056;ENST00000545612;ENST00000538628;ENST00000545317;ENST00000454694;ENST00000228922;ENST00000536439	D;D	0.86432	-2.12;-2.12	5.07	2.15	0.27550	.	0.765042	0.12924	N	0.427954	D	0.83691	0.5309	M	0.62723	1.935	0.09310	N	1	B;B	0.13594	0.008;0.003	B;B	0.10450	0.005;0.005	T	0.74976	-0.3480	10	0.62326	D	0.03	-12.262	8.1428	0.31093	0.2533:0.6406:0.0:0.1061	.	322;262	Q6N063;Q6N063-2	OGFD2_HUMAN;.	G	262;158;158;158;158;158;158;158;322;158	ENSP00000380544:R262G;ENSP00000228922:R322G	ENSP00000228922:R322G	R	+	1	0	OGFOD2	122029757	0.007000	0.16637	0.378000	0.26068	0.008000	0.06430	0.512000	0.22755	0.560000	0.29169	-0.954000	0.02651	CGT	.		0.647	OGFOD2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000400984.1	NM_024623		G	123463804	C	G	123463804	3	3	128	1	0	0	0	0	1	0	0	0	10868	652	23	4	806	4	OGFOD2	12	123463804	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	19376	123463804	10388091	36	11255											
FARP1	10160	ucsc.edu	37	chr13	98865556	98865556	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggggccccggaaaattcGgggatcagtaccttggaacg	9	7	15	10	3	1	0	1	0	0	0	2	3	1	3	3	6	2	1	3	6	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr13:98865556G>A	ENST00000319562.6	+	2	325	c.60G>A	c.(58-60)tcG>tcA	p.S20S	FARP1_ENST00000376586.2_Silent_p.S20S|FARP1_ENST00000376581.5_Silent_p.S20S|FARP1_ENST00000595437.1_Silent_p.S20S	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	20					dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S20S(6)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CGGAAAATTCGGGGATCAGTA	0.542																																					p.S20S													.	FARP1-290	6	Substitution - coding silent(6)	lung(3)|endometrium(3)	c.G60A						.						109	126	120					13																	98865556		2203	4300	6503	SO:0001819	synonymous_variant	10160	exon2			AAATTCGGGGATC	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.60G>A	13.37:g.98865556G>A		Somatic	249	0		WXS	Illumina HiSeq		153	5	NM_001001715	0	0	81	89	8	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1																																																																																			.		0.542	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		A	98865556	G	A	98865556	2	1	128	1	0	0	0	0	0	0	0	1	5695	1103	39	1		1	FARP1	13	98865556	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08		98865556	16304322	37	11256											
BTBD7	55727	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	93730186	93730186	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtctttgctgagttcataaAaaacatccgaagtcatgacc	13	11	8	9	1	3	2	2	2	1	0	4	3	4	2	2	1	2	2	2	1	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr14:93730186A>C	ENST00000334746.5	-	4	1623	c.1316T>G	c.(1315-1317)tTt>tGt	p.F439C	BTBD7_ENST00000393170.2_Intron|BTBD7_ENST00000554565.1_Missense_Mutation_p.F88C	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	439	BACK.				multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GAGTTCATAAAAAACATCCGA	0.428																																					p.F439C		.											.	BTBD7-91	0			c.T1316G						.						121	113	116					14																	93730186		2203	4300	6503	SO:0001583	missense	55727	exon4			TCATAAAAAACAT	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"BTB/POZ domain containing"	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.1316T>G	14.37:g.93730186A>C	ENSP00000335615:p.Phe439Cys	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	75	16	NM_001002860	0	0	7	13	6	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	37	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453818	0.84209	.	.	ENSG00000011114	ENST00000334746;ENST00000554565	D;D	0.82526	-1.62;-1.62	4.99	4.99	0.66335	BTB/Kelch-associated (2);	0.049285	0.85682	D	0.000000	D	0.90758	0.7099	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.65443	0.935;0.819	D	0.92297	0.5846	10	0.87932	D	0	.	14.7279	0.69357	1.0:0.0:0.0:0.0	.	88;439	Q9P203-5;Q9P203	.;BTBD7_HUMAN	C	439;88	ENSP00000335615:F439C;ENSP00000451010:F88C	ENSP00000335615:F439C	F	-	2	0	BTBD7	92799939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	1.904000	0.55121	0.456000	0.33151	TTT	.		0.428	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		C	93730186	A	C	93730186	3	2	128	1	0	0	0	0	1	0	0	0	1549	14	1	5	2114	5	BTBD7	14	93730186	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		93730186	13619354	38	11257											
SLC27A2	11001	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	50528292	50528292	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctaaaaccctgaaactctGaatattcccaggaggataac	15	9	7	10	0	1	2	0	2	1	0	2	4	2	4	2	2	4	1	2	2	6	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr15:50528292G>A	ENST00000267842.5	+	10	2094	c.1862G>A	c.(1861-1863)tGa>tAa	p.*621*	SLC27A2_ENST00000380902.4_Silent_p.*568*|SLC27A2_ENST00000544960.1_Silent_p.*386*	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	0					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)|very long-chain fatty acid catabolic process (GO:0042760)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of peroxisomal membrane (GO:0005779)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|phytanate-CoA ligase activity (GO:0050197)|pristanate-CoA ligase activity (GO:0070251)|receptor binding (GO:0005102)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		CTGAAACTCTGAATATTCCCA	0.363																																					p.X621X													.	SLC27A2-92	0			c.G1862A						.						104	100	102					15																	50528292		2196	4295	6491	SO:0001819	synonymous_variant	11001	exon10			AACTCTGAATATT	D88308	CCDS10133.1, CCDS53943.1	15q21.2	2013-05-22			ENSG00000140284	ENSG00000140284		"Acyl-CoA synthetase family", "Solute carriers"	10996	protein-coding gene	gene with protein product		603247		FACVL1		9730624	Standard	NM_003645		Approved	FATP2, hFACVL1, VLACS, VLCS, HsT17226, ACSVL1	uc001zxw.3	O14975	OTTHUMG00000131643	ENST00000267842.5:c.1862G>A	15.37:g.50528292G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	75	15	NM_003645	1	0	3	11	7	A8K2J7|Q53FY6|Q6PF09	Silent	SNP	ENST00000267842.5	37	CCDS10133.1																																																																																			.		0.363	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645		A	50528292	G	A	50528292	2	1	128	1	0	0	0	0	0	0	0	1	14558	1285	45	2		2	SLC27A2	15	50528292	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08		50528292	52003100	39	11258											
CDH16	1014	ucsc.edu	37	chr16	66949283	66949283	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagaggaaggggatgccTggttcacggtgggagggcaa	11	5	20	5	1	1	1	1	0	0	1	1	5	1	5	1	8	1	2	1	8	3	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr16:66949283T>A	ENST00000299752.4	-	6	618		c.e6-2		CDH16_ENST00000394055.3_Splice_Site|CDH16_ENST00000570262.1_Splice_Site|CDH16_ENST00000565796.1_Splice_Site|CDH16_ENST00000568632.1_Intron	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin						calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		AGGGGATGCCTGGTTCACGGT	0.562																																					.													.	CDH16-93	0			c.425-2A>T						.						54	55	55					16																	66949283		2200	4300	6500	SO:0001630	splice_region_variant	1014	exon7			GATGCCTGGTTCA	AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"Cadherins / Major cadherins"	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.425-2A>T	16.37:g.66949283T>A		Somatic	60	0		WXS	Illumina HiSeq		65	1	NM_004062	0	0	4	4	0	B4DPA8|H3BPD3|Q6UW93	Splice_Site	SNP	ENST00000299752.4	37	CCDS10823.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094037	0.76870	.	.	ENSG00000166589	ENST00000394055;ENST00000299752;ENST00000544875	.	.	.	4.82	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0694	0.47995	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDH16	65506784	1.000000	0.71417	0.850000	0.33497	0.589000	0.36550	5.069000	0.64370	1.930000	0.55929	0.460000	0.39030	.	.		0.562	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062	Intron	A	66949283	T	A	66949283	5	1	128	1	0	0	0	0	0	0	1	0	3107	1594	55	5	2118	5	CDH16	16	66949283	Splice_Site	SNP	T	TCGA-HE-7128-01A-11D-1961-08		66949283	23405470	40	11259											
PIK3R6	146850	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	8731475	8731475	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agagctgcaggctgagtctgGgagtgaggcagaacttctgg	9	8	17	7	0	2	4	0	2	2	2	2	5	2	5	0	4	3	4	0	4	1	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr17:8731475G>A	ENST00000311434.9	-	12	1585	c.1346C>T	c.(1345-1347)cCc>cTc	p.P449L	PIK3R6_ENST00000434064.2_5'UTR	NM_001010855.2	NP_001010855.1	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	449					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										GCTGAGTCTGGGAGTGAGGCA	0.642																																					.													.	.	0			.						.						94	98	96					17																	8731475		1991	4163	6154	SO:0001583	missense	146850	.			AGTCTGGGAGTGA	AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"chromosome 17 open reading frame 38"	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000311434.9:c.1346C>T	17.37:g.8731475G>A	ENSP00000475670:p.Pro449Leu	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	80	9	.	0	0	13	13	0	Q658R3	Missense_Mutation	SNP	ENST00000311434.9	37																																																																																				.		0.642	PIK3R6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001010855		A	8731475	G	A	8731475	3	1	128	1	0	0	0	0	1	0	0	0	11949	1232	43	2	953	2	PIK3R6	17	8731475	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08		8731475	72463735	41	11260											
NOL11	25926	broad.mit.edu	37	chr17	65732103	65732103	+	Frame_Shift_Del	DEL	G	G	-																															gtgaagtgtcatcattagcaGgtgctcttggaaaactcaag																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr17:65732103delG	ENST00000253247.4	+	9	1133	c.1018delG	c.(1018-1020)ggtfs	p.G340fs	NOL11_ENST00000535137.1_Frame_Shift_Del_p.G158fs	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	340					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATCATTAGCAGGTGCTCTTGG	0.338																																					p.G340fs													.	NOL11-90	0			c.1018delG						.						115	105	108					17																	65732103		2203	4300	6503	SO:0001589	frameshift_variant	25926	exon9			TTAGCAGGTGCTC	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1018delG	17.37:g.65732103delG	ENSP00000253247:p.Gly340fs	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	81	8	NM_015462	0	0	0	0	0	B7Z5V9|Q7L5S1|Q9UG18	Frame_Shift_Del	DEL	ENST00000253247.4	37	CCDS11671.1																																																																																			.		0.338	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		-	65732103	G	-	65732103	7	5	128	1	0	1	0	1	0	0	0	0	10547	1000	35	0	1052	0	NOL11	17	65732103	Frame_Shift_Del	DEL	G	TCGA-HE-7128-01A-11D-1961-08	57000628	65732103	15463107	42	11261											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31318454	31318454	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctaatttctgtacaggctGggcatgtcaagagaggaatc	11	12	11	7	0	3	1	1	0	2	1	4	3	3	2	0	3	1	3	0	3	4	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr18:31318454G>C	ENST00000269197.5	+	11	1086	c.1086G>C	c.(1084-1086)ctG>ctC	p.L362L		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	362					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(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						TGTACAGGCTGGGCATGTCAA	0.408																																					p.L362L		.											.	ASXL3-49	0			c.G1086C						.						50	48	49					18																	31318454		1880	4118	5998	SO:0001819	synonymous_variant	80816	exon11			CAGGCTGGGCATG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"KIAA1713", "additional sex combs like 3 (Drosophila)"	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.1086G>C	18.37:g.31318454G>C		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_030632	0	0	0	0	0	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	37	CCDS45847.1																																																																																			.		0.408	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			C	31318454	G	C	31318454	2	2	128	1	0	0	0	0	0	0	0	1	1069	1335	47	4		4	ASXL3	18	31318454	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08		31318454	46758794	43	11262											
KIAA1632	57724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	43440155	43440155	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctggcaggctgctgttaaaAggggcagcaccaccagccca	10	6	12	13	0	1	0	0	0	1	0	1	0	1	0	3	4	3	6	3	4	2	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr18:43440155A>G	ENST00000282041.5	-	40	6957	c.6923T>C	c.(6922-6924)cTt>cCt	p.L2308P	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2308					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TGCTGTTAAAAGGGGCAGCAC	0.537																																					p.L2308P		.											.	EPG5-580	0			c.T6923C						.						76	79	78					18																	43440155		1977	4156	6133	SO:0001583	missense	57724	exon40			GTTAAAAGGGGCA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"KIAA1632"	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.6923T>C	18.37:g.43440155A>G	ENSP00000282041:p.Leu2308Pro	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	90	18	NM_020964	0	0	10	12	2	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	16.85	3.237609	0.58886	.	.	ENSG00000152223	ENST00000282041;ENST00000540322;ENST00000308403	T	0.12672	2.66	5.59	5.59	0.84812	.	.	.	.	.	T	0.36082	0.0954	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.08106	-1.0738	9	0.87932	D	0	-10.9784	15.7665	0.78131	1.0:0.0:0.0:0.0	.	2308	Q9HCE0	EPG5_HUMAN	P	2308;236;1183	ENSP00000282041:L2308P	ENSP00000282041:L2308P	L	-	2	0	EPG5	41694153	1.000000	0.71417	0.897000	0.35233	0.053000	0.15095	9.225000	0.95219	2.108000	0.64289	0.533000	0.62120	CTT	.		0.537	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		G	43440155	A	G	43440155	3	3	128	1	0	0	0	0	1	0	0	0	8270	72	3	3	836	3	KIAA1632	18	43440155	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	12121701	43440155	34637093	44	11263											
ZNF532	55205	ucsc.edu	37	chr18	56586955	56586955	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacaccacggtgaaagccaCggtcatatctgctgcctctg	10	8	9	14	2	3	1	1	1	2	0	3	1	3	1	3	2	4	1	3	2	3	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr18:56586955C>T	ENST00000336078.4	+	4	2212	c.1436C>T	c.(1435-1437)aCg>aTg	p.T479M	ZNF532_ENST00000589288.1_Missense_Mutation_p.T479M|ZNF532_ENST00000591808.1_Missense_Mutation_p.T479M|ZNF532_ENST00000591230.1_Missense_Mutation_p.T479M|ZNF532_ENST00000591083.1_Missense_Mutation_p.T479M	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	479					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(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GTGAAAGCCACGGTCATATCT	0.552																																					p.T479M													.	ZNF532-154	0			c.C1436T						.						33	29	30					18																	56586955		2203	4300	6503	SO:0001583	missense	55205	exon4			AAGCCACGGTCAT	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"Zinc fingers, C2H2-type"	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.1436C>T	18.37:g.56586955C>T	ENSP00000338217:p.Thr479Met	Somatic	50	0		WXS	Illumina HiSeq		32	3	NM_018181	0	0	5	5	0	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	c	15.70	2.909737	0.52439	.	.	ENSG00000074657	ENST00000336078	T	0.01787	4.64	5.6	5.6	0.85130	.	0.104215	0.64402	D	0.000004	T	0.08670	0.0215	L	0.58101	1.795	0.48395	D	0.999646	D	0.89917	1.0	D	0.63957	0.92	T	0.01114	-1.1447	10	0.72032	D	0.01	-4.1959	19.3114	0.94188	0.0:1.0:0.0:0.0	.	479	Q9HCE3	ZN532_HUMAN	M	479	ENSP00000338217:T479M	ENSP00000338217:T479M	T	+	2	0	ZNF532	54737935	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.840000	0.62817	2.663000	0.90544	0.544000	0.68410	ACG	.		0.552	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56586955	C	T	56586955	3	4	128	1	0	0	0	0	1	0	0	0	18004	536	19	1	1438	1	ZNF532	18	56586955	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	13146800	56586955	21490293	45	11264											
MIDN	90007	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	1257046	1257048	+	In_Frame_Del	DEL	GCT	GCT	-																															acgcgctgcaaggtggaacgGctgcagctgcttctgcagca																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:1257046_1257048delGCT	ENST00000591446.2	+	7	1591_1593	c.1182_1184delGCT	c.(1180-1185)cggctg>cgg	p.L395del	CIRBP_ENST00000588030.1_5'Flank|MIDN_ENST00000300952.2_In_Frame_Del_p.L395del			Q504T8	MIDN_HUMAN	midnolin	395						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGTGGAACGGCTGCAGCTGCTT	0.67																																					p.394_395del		.											.	MIDN-90	0			c.1182_1184del						.																																			SO:0001651	inframe_deletion	90007	exon8			.	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.1182_1184delGCT	19.37:g.1257046_1257048delGCT	ENSP00000467679:p.Leu395del	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	40	10	NM_177401	0	0	0	0	0	Q96BW8	In_Frame_Del	DEL	ENST00000591446.2	37	CCDS32864.1																																																																																			.		0.67	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			-	1257048	GCT	-	1257046	7	5	128	1	0	1	0	1	0	0	0	0	9604	1190	42	0	1208	0	MIDN	19	1257046	In_Frame_Del	DEL	GCT	TCGA-HE-7128-01A-11D-1961-08		1257046	57871937	46	11265											
LPHN1	22859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	14263148	14263148	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgaagacagggggcgaggAgggattgaagcccactgact	11	6	17	7	1	0	4	0	3	0	1	0	7	0	6	1	4	1	1	1	4	2	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:14263148A>G	ENST00000340736.6	-	22	3934	c.3637T>C	c.(3637-3639)Tcc>Ccc	p.S1213P	CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.S1208P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1213					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGGGGCGAGGAGGGATTGAAG	0.617																																					p.S1213P		.											.	LPHN1-523	0			c.T3637C						.						96	103	101					19																	14263148		2203	4300	6503	SO:0001583	missense	22859	exon22			GCGAGGAGGGATT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.3637T>C	19.37:g.14263148A>G	ENSP00000340688:p.Ser1213Pro	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	69	7	NM_001008701	0	0	2	5	3	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	37	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	A	5.267	0.234643	0.09969	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.66099	-0.19;-0.19	4.99	4.99	0.66335	GPCR, family 2, latrophilin, C-terminal (1);	0.061997	0.64402	D	0.000003	T	0.28797	0.0714	N	0.01235	-0.94	0.45747	D	0.998642	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.36672	-0.9738	10	0.02654	T	1	.	12.6626	0.56822	1.0:0.0:0.0:0.0	.	1208;1213	O94910-2;O94910	.;LPHN1_HUMAN	P	1213;1208	ENSP00000340688:S1213P;ENSP00000355328:S1208P	ENSP00000340688:S1213P	S	-	1	0	LPHN1	14124148	0.998000	0.40836	1.000000	0.80357	0.928000	0.56348	0.694000	0.25512	1.881000	0.54492	0.459000	0.35465	TCC	.		0.617	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		G	14263148	A	G	14263148	3	3	128	1	0	0	0	0	1	0	0	0	8940	304	11	3	799	3	LPHN1	19	14263148	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	13006102	14263148	44865835	47	11266											
EMR2	30817	ucsc.edu	37	chr19	14884819	14884819	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggattgcagcgacaggCggtggcattgacacacgagg	9	6	15	11	3	0	1	0	1	0	0	0	4	0	2	1	5	2	2	1	5	0	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:14884819C>T	ENST00000315576.3	-	4	581	c.130G>A	c.(130-132)Gcc>Acc	p.A44T	EMR2_ENST00000353876.1_Missense_Mutation_p.A44T|EMR2_ENST00000594294.1_Missense_Mutation_p.A44T|EMR2_ENST00000346057.1_Missense_Mutation_p.A44T|EMR2_ENST00000392964.3_5'Flank|EMR2_ENST00000353005.1_Missense_Mutation_p.A44T|EMR2_ENST00000392967.2_Missense_Mutation_p.A44T|EMR2_ENST00000595839.1_Missense_Mutation_p.A44T|EMR2_ENST00000596991.2_Missense_Mutation_p.A44T|EMR2_ENST00000601345.1_Missense_Mutation_p.A44T|EMR2_ENST00000599423.1_5'UTR|EMR2_ENST00000392965.3_Missense_Mutation_p.A44T|EMR2_ENST00000594076.1_Missense_Mutation_p.A44T	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	44	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						CAGCGACAGGCGGTGGCATTG	0.582																																					p.A44T													.	EMR2-524	0			c.G130A						.						128	117	120					19																	14884819		2203	4300	6503	SO:0001583	missense	30817	exon3			GACAGGCGGTGGC	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"CD molecules", "-", "GPCR / Class B : Orphans"	3337	protein-coding gene	gene with protein product		606100	"egf-like module containing, mucin-like, hormone receptor-like sequence 2"				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.130G>A	19.37:g.14884819C>T	ENSP00000319883:p.Ala44Thr	Somatic	210	0		WXS	Illumina HiSeq		142	1	NM_001271052	0	0	47	74	27	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.827492	0.32329	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000360222;ENST00000392965;ENST00000392962	T;T;T;T;T;T;D	0.86694	-0.93;-1.05;-0.43;0.39;1.13;-1.22;-2.16	3.87	-7.75	0.01236	.	.	.	.	.	T	0.70456	0.3226	L	0.43554	1.36	0.09310	N	1	P;B;P;B;B;B;P	0.43477	0.808;0.278;0.466;0.001;0.037;0.341;0.668	B;B;B;B;B;B;B	0.32022	0.139;0.032;0.016;0.0;0.021;0.035;0.112	T	0.63633	-0.6593	9	0.17369	T	0.5	.	4.0651	0.09856	0.439:0.1847:0.0:0.3763	.	44;44;44;44;44;44;44	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;.;.;.;EMR2_HUMAN;.	T	44	ENSP00000319883:A44T;ENSP00000376694:A44T;ENSP00000263380:A44T;ENSP00000319454:A44T;ENSP00000319838:A44T;ENSP00000376692:A44T;ENSP00000376689:A44T	ENSP00000319883:A44T	A	-	1	0	EMR2	14745819	0.000000	0.05858	0.004000	0.12327	0.275000	0.26752	-3.623000	0.00411	-1.229000	0.02564	-0.507000	0.04495	GCC	.		0.582	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			T	14884819	C	T	14884819	3	4	128	1	0	0	0	0	1	0	0	0	5118	768	27	1	2413	1	EMR2	19	14884819	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	621671	14884819	44244164	48	11267											
CYP4F2	8529	broad.mit.edu;bcgsc.ca	37	chr19	16003152	16003153	+	Frame_Shift_Ins	INS	-	-	ATAT																															cactctcattgaaaatcttcINSatatagggcttcaggatgtt																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:16003152_16003153insATAT	ENST00000221700.6	-	5	586_587	c.491_492insATAT	c.(490-492)atgfs	p.M164fs	CYP4F2_ENST00000011989.7_Frame_Shift_Ins_p.M15fs	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TGAAAATCTTCATATAGGGCTT	0.52																																					p.M164fs													.	CYP4F2-92	0			c.492_493insATAT						.																																			SO:0001589	frameshift_variant	8529	exon5			AATCTTCATATAG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"Cytochrome P450s"	2645	protein-coding gene	gene with protein product		604426	"cytochrome P450, subfamily IVF, polypeptide 2"			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.488_491dupATAT	19.37:g.16003153_16003156dupATAT	ENSP00000221700:p.Met164fs	Somatic	258	0		WXS	Illumina HiSeq	Phase_I	186	22	NM_001082	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000221700.6	37	CCDS12336.1																																																																																			.		0.52	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082		ATAT	16003153	-	ATAT	16003152	7	5	128	1	0	1	1	0	0	0	0	0	4194	826	29	0	1106	0	CYP4F2	19	16003152	Frame_Shift_Ins	INS	-	TCGA-HE-7128-01A-11D-1961-08	1118333	16003152	43125831	49	11268											
LPAR2	9170	broad.mit.edu	37	chr19	19735163	19735163	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtatagtggacagactcgcGggtggactggcggaggcacg	8	7	18	8	4	0	1	0	0	0	1	1	4	0	4	0	6	0	2	0	6	2	2	rs144007983		TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:19735163G>A	ENST00000542587.1	-	6	1860	c.958C>T	c.(958-960)Cgc>Tgc	p.R320C	LPAR2_ENST00000586703.1_Missense_Mutation_p.R320C|LPAR2_ENST00000407877.3_Missense_Mutation_p.R320C			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	320					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						ACAGACTCGCGGGTGGACTGG	0.617																																					p.R320C													.	LPAR2-501	0			c.C958T						.	G	CYS/ARG	0,4406		0,0,2203	102	93	96		958	3.9	0	19	dbSNP_134	96	1,8599	1.2+/-3.3	0,1,4299	no	missense	LPAR2	NM_004720.5	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	320/352	19735163	1,13005	2203	4300	6503	SO:0001583	missense	9170	exon3			ACTCGCGGGTGGA	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3168	protein-coding gene	gene with protein product		605110	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.958C>T	19.37:g.19735163G>A	ENSP00000443256:p.Arg320Cys	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	75	6	NM_004720	0	0	3	3	0	O00543|O43431	Missense_Mutation	SNP	ENST00000542587.1	37	CCDS12407.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.896393	0.33442	0.0	1.16E-4	ENSG00000064547	ENST00000407877;ENST00000542587	T;T	0.38887	1.11;1.11	3.92	3.92	0.45320	.	1.007880	0.07969	N	0.983676	T	0.25644	0.0624	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.04976	-1.0914	10	0.59425	D	0.04	.	9.1791	0.37129	0.0:0.0:0.7833:0.2167	.	320	Q9HBW0	LPAR2_HUMAN	C	320	ENSP00000384665:R320C;ENSP00000443256:R320C	ENSP00000384665:R320C	R	-	1	0	LPAR2	19596163	0.032000	0.19561	0.013000	0.15412	0.023000	0.10783	1.904000	0.39868	2.480000	0.83734	0.561000	0.74099	CGC	G|1.000;A|0.000		0.617	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720		A	19735163	G	A	19735163	3	1	128	1	0	0	0	0	1	0	0	0	8930	1116	39	1	101	1	LPAR2	19	19735163	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	3732011	19735163	39393820	50	11269											
MIA	8190	ucsc.edu	37	chr19	41282923	41282924	+	Missense_Mutation	DNP	CC	CC	AA																															tgctcgcctgggctatttccCcagtagcattgtccgagagg																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:41282923_41282924CC>AA	ENST00000263369.3	+	3	477_478	c.311_312CC>AA	c.(310-312)cCC>cAA	p.P104Q	MIA-RAB4B_ENST00000600729.1_Missense_Mutation_p.P104Q|MIA_ENST00000597784.1_Missense_Mutation_p.P104Q|RAB4B_ENST00000594800.1_5'Flank|MIA_ENST00000594436.1_Missense_Mutation_p.P104Q|RAB4B-EGLN2_ENST00000594136.1_5'Flank|RAB4B_ENST00000357052.2_5'Flank	NM_006533.3	NP_006524.1	Q16674	MIA_HUMAN	melanoma inhibitory activity	104	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell proliferation (GO:0008283)	extracellular space (GO:0005615)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)	GBM - Glioblastoma multiforme(1328;0.0199)		GGCTATTTCCCCAGTAGCATTG	0.545																																					p.P104Q													.	MIA-651	0			c.C312A						.																																			SO:0001583	missense	8190	exon4			TTTCCCCAGTAGC	X75450	CCDS12566.1	19q13.2	2012-10-15			ENSG00000261857	ENSG00000261857			7076	protein-coding gene	gene with protein product		601340				7923218, 8661134	Standard	NM_006533		Approved	CD-RAP	uc021uuu.1	Q16674		Exception_encountered	19.37:g.41282923_41282924delinsAA	ENSP00000263369:p.Pro104Gln	Somatic	65	2		WXS	Illumina HiSeq		37	4	NM_001202553	0	0	0	0	0	Q6FHV3	Missense_Mutation	DNP	ENST00000263369.3	37	CCDS12566.1																																																																																			.		0.545	MIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463162.1			AA	41282924	CC	AA	41282923	3	1	128	1	0	0	0	0	1	0	0	0	9588	623	22	4	321	4	MIA	19	41282923	Missense_Mutation	DNP	CC	TCGA-HE-7128-01A-11D-1961-08	21547760	41282923	17846060	51	11270											
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50462728	50462728	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgcagctccagccccagggTtctggggccccaggggtggg	5	5	17	14	1	1	0	0	0	1	0	2	0	2	0	5	6	2	3	5	6	0	1	rs550818529	byFrequency	TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:50462728T>G	ENST00000447370.2	-	5	1036	c.946A>C	c.(946-948)Acc>Ccc	p.T316P	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Missense_Mutation_p.T316P	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	316	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		AGCCCCAGGGTTCTGGGGCCC	0.692													T|||	2	0.000399361	0.0015	0	5008	,	,		12019	0		0	False		,,,				2504	0				p.T316P		.											.	SIGLEC11-94	0			c.A946C						.						6	10	9					19																	50462728		1815	4163	5978	SO:0001583	missense	114132	exon5			CCAGGGTTCTGGG	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.946A>C	19.37:g.50462728T>G	ENSP00000412361:p.Thr316Pro	Somatic	57	1		WXS	Illumina HiSeq	Phase_I	35	3	NM_052884	0	0	5	5	0		Missense_Mutation	SNP	ENST00000447370.2	37	CCDS12790.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.500|0.500	-0.871393|-0.871393	0.02570|0.02570	.|.	.|.	ENSG00000161640|ENSG00000161640	ENST00000426971|ENST00000447370;ENST00000458019	.|T	.|0.67523	.|-0.27	1.61|1.61	-1.27|-1.27	0.09347|0.09347	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|1.785050	.|0.02815	.|N	.|0.124869	T|T	0.72211|0.72211	0.3432|0.3432	M|M	0.91972|0.91972	3.26|3.26	0.09310|0.09310	N|N	1|1	.|B;B	.|0.20368	.|0.044;0.02	.|B;B	.|0.25405	.|0.045;0.06	T|T	0.47535|0.47535	-0.9110|-0.9110	5|10	.|0.34782	.|T	.|0.22	.|.	5.7793|5.7793	0.18297|0.18297	0.0:0.0:0.5751:0.4249|0.0:0.0:0.5751:0.4249	.|.	.|316;316	.|Q96RL6-2;Q96RL6	.|.;SIG11_HUMAN	D|P	305|316	.|ENSP00000412361:T316P	.|ENSP00000412361:T316P	E|T	-|-	3|1	2|0	SIGLEC11|SIGLEC11	55154540|55154540	0.001000|0.001000	0.12720|0.12720	0.036000|0.036000	0.18154|0.18154	0.195000|0.195000	0.23768|0.23768	-0.655000|-0.655000	0.05348|0.05348	-0.403000|-0.403000	0.07622|0.07622	0.529000|0.529000	0.55759|0.55759	GAA|ACC	.		0.692	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		G	50462728	T	G	50462728	3	3	128	1	0	0	0	0	1	0	0	0	14339	1725	60	5	1178	5	SIGLEC11	19	50462728	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	9179805	50462728	8666255	52	11271											
SYT3	84258	hgsc.bcm.edu	37	chr19	51135725	51135725	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcctctggatacgagtcCatgtccaagtaggagggctc	9	8	13	11	1	1	0	0	0	1	0	4	3	3	2	3	3	2	3	3	3	3	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:51135725C>G	ENST00000338916.4	-	2	1125	c.492G>C	c.(490-492)atG>atC	p.M164I	SYT3_ENST00000593901.1_Missense_Mutation_p.M164I|SYT3_ENST00000544769.1_Missense_Mutation_p.M164I|SYT3_ENST00000600079.1_Missense_Mutation_p.M164I	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	164					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GATACGAGTCCATGTCCAAGT	0.647																																					p.M164I		.											.	SYT3-155	0			c.G492C						.						26	26	26					19																	51135725		2202	4299	6501	SO:0001583	missense	84258	exon2			CGAGTCCATGTCC	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.492G>C	19.37:g.51135725C>G	ENSP00000340914:p.Met164Ile	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_032298	0	0	0	0	0	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	37	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.350361	0.41599	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.59502	0.26;0.26	4.59	4.59	0.56863	.	0.067275	0.53938	U	0.000047	T	0.58104	0.2099	L	0.27053	0.805	0.80722	D	1	P	0.45126	0.851	P	0.55391	0.775	T	0.50065	-0.8871	10	0.17832	T	0.49	.	16.6764	0.85280	0.0:1.0:0.0:0.0	.	164	Q9BQG1	SYT3_HUMAN	I	164	ENSP00000340914:M164I;ENSP00000438883:M164I	ENSP00000340914:M164I	M	-	3	0	SYT3	55827537	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.982000	0.63825	2.536000	0.85505	0.563000	0.77884	ATG	.		0.647	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		G	51135725	C	G	51135725	3	3	128	1	0	0	0	0	1	0	0	0	15507	594	21	4	1308	4	SYT3	19	51135725	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	672997	51135725	7993258	53	11272											
C20orf72	27131	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	17950811	17950811	+	5'Flank	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaaaactggtttcctatCttcaatccagagagaagtga	14	10	7	10	0	2	3	1	1	1	2	4	4	4	3	3	1	1	1	3	1	5	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr20:17950811C>A	ENST00000377768.3	-	0	0				SNX5_ENST00000486039.1_5'Flank|SNX5_ENST00000377759.4_5'Flank|SNX5_ENST00000606602.1_5'Flank|SNX5_ENST00000481323.1_5'Flank|SNX5_ENST00000606557.1_5'Flank|MGME1_ENST00000377704.4_Silent_p.I103I|MGME1_ENST00000377709.1_Intron|MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377710.5_Silent_p.I103I	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5						intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						GGTTTCCTATCTTCAATCCAG	0.478																																					p.I103I													.	.	0			c.C309A						.						68	71	70					20																	17950811		2203	4300	6503	SO:0001631	upstream_gene_variant	92667	exon2			TCCTATCTTCAAT	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"Sorting nexins"	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953		20.37:g.17950811C>A	Exception_encountered	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	96	14	NM_052865	0	1	20	24	3	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			.		0.478	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			A	17950811	C	A	17950811	1	1	128	0	1	0	0	0	0	0	0	0	2124	903	32	4		4	C20orf72	20	17950811	5'Flank	SNP	C	TCGA-HE-7128-01A-11D-1961-08		17950811	45074709	54	11273											
C20orf132	140699	bcgsc.ca	37	chr20	35769661	35769661	+	Frame_Shift_Del	DEL	A	A	-																															ttcagggttttcagggtatcAaatgtagtcattataaactg																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr20:35769661delA	ENST00000400441.3	-	12	1391	c.1392delT	c.(1390-1392)tttfs	p.F464fs	MROH8_ENST00000441008.2_Frame_Shift_Del_p.F450fs|MROH8_ENST00000217333.8_Intron			Q9H579	MROH8_HUMAN	maestro heat-like repeat family member 8	349																	TCAGGGTATCAAATGTAGTCA	0.378																																					.													.	.	0			.						.						91	79	83					20																	35769661		1849	4093	5942	SO:0001589	frameshift_variant	140699	.			GGTATCAAATGTA	AL136172		20q11.22	2012-12-19	2012-12-19	2012-12-19	ENSG00000101353	ENSG00000101353		"maestro heat-like repeat containing"	16125	protein-coding gene	gene with protein product	"hypothetical protein LOC140699"		"chromosome 20 open reading frame 131", "chromosome 20 open reading frame 132"	C20orf131, C20orf132		11780052, 15635413	Standard	NM_152503		Approved	dJ621N11.4, dJ621N11.3	uc010zvu.2	Q9H579	OTTHUMG00000032407	ENST00000400441.3:c.1392delT	20.37:g.35769661delA	ENSP00000383291:p.Phe464fs	Somatic	34	0		WXS	Illumina HiSeq	Phase_1	19	5	.	0	0	0	0	0	Q5JYQ6	Frame_Shift_Del	DEL	ENST00000400441.3	37																																																																																				.		0.378	MROH8-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152503		-	35769661	A	-	35769661	7	5	128	1	0	1	0	1	0	0	0	0	2092	127	5	0	1800	0	C20orf132	20	35769661	Frame_Shift_Del	DEL	A	TCGA-HE-7128-01A-11D-1961-08	17818850	35769661	27255859	55	11274											
KCNQ2	3785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62070959	62070959	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggacttactgcaggcaGcgcgaagaaggagacaccga	13	4	14	10	3	0	2	0	0	0	2	0	6	0	3	1	3	4	3	1	3	3	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr20:62070959G>A	ENST00000359125.2	-	6	1093	c.919C>T	c.(919-921)Ctg>Ttg	p.L307L	KCNQ2_ENST00000344425.5_Silent_p.L307L|KCNQ2_ENST00000344462.4_Silent_p.L307L|KCNQ2_ENST00000370224.1_Silent_p.L307L|KCNQ2_ENST00000354587.3_Silent_p.L307L|KCNQ2_ENST00000359689.1_Silent_p.L307L|KCNQ2_ENST00000357249.2_Silent_p.L307L|KCNQ2_ENST00000360480.3_Silent_p.L307L	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	307					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	ACTGCAGGCAGCGCGAAGAAG	0.637																																					p.L307L		.											.	KCNQ2-92	0			c.C919T						.						152	116	128					20																	62070959		2203	4300	6503	SO:0001819	synonymous_variant	3785	exon6			CAGGCAGCGCGAA	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.919C>T	20.37:g.62070959G>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	75	28	NM_172106	0	0	0	0	0	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			.		0.637	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62070959	G	A	62070959	2	1	128	1	0	0	0	0	0	0	0	1	8104	962	34	2		2	KCNQ2	20	62070959	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08	26301298	62070959	954561	56	11275											
L3MBTL2	83746	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	41621916	41621916	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccggccaccttctgtcagaAgaatgacattgagctcacac	11	8	8	14	1	3	4	2	2	1	2	3	4	3	4	3	1	1	1	3	1	2	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr22:41621916A>G	ENST00000216237.5	+	12	1633	c.1475A>G	c.(1474-1476)aAg>aGg	p.K492R		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	492					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTCTGTCAGAAGAATGACATT	0.592																																					p.K492R		.											.	L3MBTL2-92	0			c.A1475G						.						94	69	78					22																	41621916		2203	4300	6503	SO:0001583	missense	83746	exon12			GTCAGAAGAATGA	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.1475A>G	22.37:g.41621916A>G	ENSP00000216237:p.Lys492Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	70	6	NM_031488	0	0	25	26	1	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Missense_Mutation	SNP	ENST00000216237.5	37	CCDS14011.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.711335	0.30322	.	.	ENSG00000100395	ENST00000216237	T	0.31769	1.48	5.23	4.17	0.49024	.	0.233465	0.50627	D	0.000106	T	0.27663	0.0680	L	0.54965	1.715	0.35928	D	0.832306	B;B	0.14438	0.004;0.01	B;B	0.21151	0.003;0.033	T	0.19484	-1.0304	10	0.46703	T	0.11	.	7.1971	0.25860	0.7961:0.0:0.0731:0.1308	.	492;492	Q969R5-3;Q969R5	.;LMBL2_HUMAN	R	492	ENSP00000216237:K492R	ENSP00000216237:K492R	K	+	2	0	L3MBTL2	39951862	1.000000	0.71417	0.987000	0.45799	0.906000	0.53458	2.599000	0.46231	0.792000	0.33850	0.459000	0.35465	AAG	.		0.592	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		G	41621916	A	G	41621916	3	3	128	1	0	0	0	0	1	0	0	0	8613	72	3	3	1521	3	L3MBTL2	22	41621916	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		41621916	9682650	57	11276											
DMD	1756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	31152282	31152282	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctctaaccctgtgcttgtgtCctggggaggactgagaagat	8	11	13	9	0	1	2	0	1	1	2	2	5	2	4	2	3	2	1	2	3	2	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chrX:31152282C>G	ENST00000357033.4	-	77	11157	c.10951G>C	c.(10951-10953)Gac>Cac	p.D3651H	DMD_ENST00000378723.3_Missense_Mutation_p.D583H|DMD_ENST00000343523.2_Missense_Mutation_p.D1081H|DMD_ENST00000541735.1_Missense_Mutation_p.D1081H|DMD_ENST00000361471.4_Missense_Mutation_p.D570H|DMD_ENST00000474231.1_Missense_Mutation_p.D1191H|DMD_ENST00000359836.1_Missense_Mutation_p.D1178H|DMD_ENST00000378702.4_Missense_Mutation_p.D583H|DMD_ENST00000378677.2_Missense_Mutation_p.D3647H|DMD_ENST00000378707.3_Missense_Mutation_p.D1191H|DMD_ENST00000378680.2_Missense_Mutation_p.D473H	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3651					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTGCTTGTGTCCTGGGGAGGA	0.408																																					p.D3651H		.											.	DMD-265	0			c.G10951C						.						189	119	143					X																	31152282		2202	4300	6502	SO:0001583	missense	1756	exon77			TTGTGTCCTGGGG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10951G>C	X.37:g.31152282C>G	ENSP00000354923:p.Asp3651His	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	39	13	NM_004006	0	0	4	7	3	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.136863|4.136863	0.77662|0.77662	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680|ENST00000465285	T;T;T;T;T;T;T;T;T;T;T;T|.	0.65178|.	2.06;3.8;-0.14;-0.14;3.72;3.74;3.68;3.48;2.04;3.74;2.08;2.1|.	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.000000|.	0.36740|.	U|.	0.002431|.	T|T	0.73992|0.73992	0.3658|0.3658	M|M	0.68317|0.68317	2.08|2.08	0.45621|0.45621	D|D	0.998554|0.998554	D;D;D;D;D;D;B;B;B;D;D;P;P;B;B;B|.	0.89917|.	0.996;0.996;0.999;0.999;0.999;0.996;0.098;0.059;0.059;0.999;1.0;0.86;0.729;0.003;0.001;0.38|.	D;D;D;D;D;D;B;B;B;D;D;P;P;B;B;B|.	0.83275|.	0.926;0.955;0.974;0.995;0.945;0.926;0.077;0.035;0.052;0.99;0.996;0.661;0.526;0.003;0.005;0.326|.	T|T	0.73379|0.73379	-0.4001|-0.4001	10|5	0.52906|.	T|.	0.07|.	.|.	17.7643|17.7643	0.88473|0.88473	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	473;3643;3651;3647;2310;2307;1178;1191;1191;1081;1081;3528;570;583;570;583|.	B4DSV7;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1|.	.;.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.|.	H|A	3643;2310;2307;583;1334;3647;3651;1178;1081;3651;3528;1191;1081;583;1191;570;473|1379	ENSP00000367997:D583H;ENSP00000350765:D1334H;ENSP00000367948:D3647H;ENSP00000354923:D3651H;ENSP00000352894:D1178H;ENSP00000340057:D1081H;ENSP00000367979:D1191H;ENSP00000444119:D1081H;ENSP00000367974:D583H;ENSP00000417123:D1191H;ENSP00000354464:D570H;ENSP00000367951:D473H|.	ENSP00000340057:D1081H|.	D|G	-|-	1|2	0|0	DMD|DMD	31062203|31062203	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	6.271000|6.271000	0.72569|0.72569	2.470000|2.470000	0.83445|0.83445	0.600000|0.600000	0.82982|0.82982	GAC|GGA	.		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	31152282	C	G	31152282	3	3	128	1	0	0	0	0	1	0	0	0	4591	855	30	4	204	4	DMD	23	31152282	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		31152282	124118278	58	11277											
GLUD2	2747	ucsc.edu	37	chrX	120182436	120182436	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggaatgacaccagggtttAgagataaaacatttgttgtt	14	13	10	4	0	0	2	0	1	0	1	0	4	0	3	1	2	1	3	1	2	5	7			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chrX:120182436A>G	ENST00000328078.1	+	1	975	c.898A>G	c.(898-900)Aga>Gga	p.R300G		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	300					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						ACCAGGGTTTAGAGATAAAAC	0.413																																					p.R300G													.	GLUD2-131	0			c.A898G						.						189	170	177					X																	120182436		2203	4300	6503	SO:0001583	missense	2747	exon1			GGGTTTAGAGATA	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.898A>G	X.37:g.120182436A>G	ENSP00000327589:p.Arg300Gly	Somatic	109	0		WXS	Illumina HiSeq		92	1	NM_012084	0	0	1	150	149	B2R8G0|Q9UDQ4	Missense_Mutation	SNP	ENST00000328078.1	37	CCDS14603.1	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.462215	0.01062	.	.	ENSG00000182890	ENST00000328078	D	0.95272	-3.66	2.3	-1.33	0.09172	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (2);NAD(P)-binding domain (1);	0.376526	0.30093	N	0.010424	T	0.76983	0.4064	N	0.02247	-0.625	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.70048	-0.4979	10	0.02654	T	1	-8.2867	4.1877	0.10405	0.2739:0.2268:0.4994:0.0	.	300	P49448	DHE4_HUMAN	G	300	ENSP00000327589:R300G	ENSP00000327589:R300G	R	+	1	2	GLUD2	120010117	1.000000	0.71417	0.578000	0.28575	0.925000	0.55904	2.644000	0.46613	-0.680000	0.05211	-0.386000	0.06593	AGA	.		0.413	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		G	120182436	A	G	120182436	3	3	128	1	0	0	0	0	1	0	0	0	6497	412	15	3	900	3	GLUD2	23	120182436	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	89030154	120182436	35088124	59	11278											
PRDM2	7799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	14068533	14068533	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgggatggatgtgcattGatgccactgatccagagaag	11	11	13	6	0	0	3	0	2	0	1	1	6	1	5	2	2	2	1	2	2	1	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:14068533G>T	ENST00000235372.7	+	5	1121	c.265G>T	c.(265-267)Gat>Tat	p.D89Y	PRDM2_ENST00000502727.1_3'UTR|PRDM2_ENST00000311066.5_Missense_Mutation_p.D89Y|PRDM2_ENST00000376048.5_Missense_Mutation_p.D89Y	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	89	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GATGTGCATTGATGCCACTGA	0.383																																					p.D89Y		.											.	PRDM2-116	0			c.G265T						.						78	72	74					1																	14068533		2203	4300	6503	SO:0001583	missense	7799	exon5			TGCATTGATGCCA	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.265G>T	1.37:g.14068533G>T	ENSP00000235372:p.Asp89Tyr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	65	35	NM_015866	0	0	1	4	3	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160930	0.57368	.	.	ENSG00000116731	ENST00000484063;ENST00000376048;ENST00000235372;ENST00000311066;ENST00000400800	D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4	5.95	5.95	0.96441	SET domain (2);	0.000000	0.85682	D	0.000000	D	0.97826	0.9286	H	0.94620	3.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98389	1.0562	10	0.87932	D	0	.	18.957	0.92662	0.0:0.0:1.0:0.0	.	89;89;89	Q13029;Q13029-2;B1AJZ4	PRDM2_HUMAN;.;.	Y	80;89;89;89;89	ENSP00000423010:D80Y;ENSP00000365216:D89Y;ENSP00000235372:D89Y;ENSP00000312352:D89Y	ENSP00000235372:D89Y	D	+	1	0	PRDM2	13941120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.957000	0.93082	2.824000	0.97209	0.655000	0.94253	GAT	.		0.383	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14068533	G	T	14068533	3	4	129	1	0	0	0	0	1	0	0	0	12487	1290	45	4	279	4	PRDM2	1	14068533	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		14068533	235182088	1	11279											
INSRR	3645	broad.mit.edu	37	chr1	156818724	156818724	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcactcacgactccttgtaGtacacgatgaagctgagcag	11	8	11	11	2	1	2	1	2	0	0	2	4	2	2	1	1	3	5	1	1	3	3	rs544109301		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:156818724G>A	ENST00000368195.3	-	7	1956	c.1560C>T	c.(1558-1560)taC>taT	p.Y520Y	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	520	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACTCCTTGTAGTACACGATGA	0.672																																					p.Y520Y													.	INSRR-1403	0			c.C1560T						.						13	14	13					1																	156818724		2194	4295	6489	SO:0001819	synonymous_variant	3645	exon7			CTTGTAGTACACG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.1560C>T	1.37:g.156818724G>A		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	8	3	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			.		0.672	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156818724	G	A	156818724	2	1	129	1	0	0	0	0	0	0	0	1	7795	1024	36	2		2	INSRR	1	156818724	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08	142750191	156818724	92431897	2	11280											
NEK2	4751	broad.mit.edu	37	chr1	211843673	211843673	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attcaattcatcagagtaacGgtatggaattcgcctgaatt	13	13	8	7	2	3	2	3	1	0	1	4	3	3	3	1	2	1	2	1	2	5	6			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:211843673G>C	ENST00000366999.4	-	5	853	c.715C>G	c.(715-717)Cgt>Ggt	p.R239G	NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000366998.3_Missense_Mutation_p.R239G|NEK2_ENST00000540251.1_Missense_Mutation_p.R196G	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)	p.R239S(2)		breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		TCAGAGTAACGGTATGGAATT	0.363																																					p.R239G													.	NEK2-765	2	Substitution - Missense(2)	lung(2)	c.C715G						.						156	163	160					1																	211843673		2203	4300	6503	SO:0001583	missense	4751	exon5			AGTAACGGTATGG	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.715C>G	1.37:g.211843673G>C	ENSP00000355966:p.Arg239Gly	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	218	5	NM_002497	0	0	2	2	0	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.914393	0.52546	.	.	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	T;T;T	0.65364	-0.15;-0.15;-0.15	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47875	0.1469	N	0.13168	0.305	0.80722	D	1	B;B;B	0.13145	0.007;0.006;0.003	B;B;B	0.13407	0.005;0.009;0.005	T	0.36648	-0.9739	10	0.36615	T	0.2	.	17.4884	0.87694	0.0:0.0:1.0:0.0	.	239;239;239	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	G	239;196;239	ENSP00000355966:R239G;ENSP00000440237:R196G;ENSP00000355965:R239G	ENSP00000355965:R239G	R	-	1	0	NEK2	209910296	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.507000	0.97996	2.550000	0.86006	0.655000	0.94253	CGT	.		0.363	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		C	211843673	G	C	211843673	3	2	129	1	0	0	0	0	1	0	0	0	10350	1116	39	4	638	4	NEK2	1	211843673	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	55024949	211843673	37406948	3	11281											
SFRS7	6432	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	38978383	38978384	+	Missense_Mutation	DNP	GC	GC	AA																															cttcttacctcctccgtaccGcccgtaacgcgacatgatga																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:38978383_38978384GC>AA	ENST00000313117.6	-	1	252_253	c.15_16GC>TT	c.(13-18)ggGCgg>ggTTgg	p.R6W	GEMIN6_ENST00000409011.1_5'Flank|SRSF7_ENST00000446327.2_Missense_Mutation_p.R6W|SRSF7_ENST00000409276.1_Missense_Mutation_p.R6W	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	6					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CCTCCGTACCGCCCGTAACGCG	0.624																																					p.R6W		.											.	SRSF7	0			c.G15T						.																																			SO:0001583	missense	6432	exon1			GTACCGCCCGTAA	L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"Zinc fingers, CCHC domain containing", "Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10789	protein-coding gene	gene with protein product	"SR splicing factor 7"	600572	"splicing factor, arginine/serine-rich 7 (35kD)", "splicing factor, arginine/serine-rich 7, 35kDa"	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.15_16delinsAA	2.37:g.38978383_38978384delinsAA	ENSP00000325905:p.Arg6Trp	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	87	32		0	0	0	0	0	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	DNP	ENST00000313117.6	37	CCDS33183.1																																																																																			.		0.624	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		AA	38978384	GC	AA	38978383	3	1	129	1	0	0	0	0	1	0	0	0	14214	1086	38	1	732	1	SFRS7	2	38978383	Missense_Mutation	DNP	GC	TCGA-HE-7129-01A-11D-1961-08		38978383	204220990	4	11282											
C2orf55	343990	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	99413866	99413867	+	Frame_Shift_Del	DEL	GT	GT	-																															tggttcagacttcagggtccGtgccccaggcttgtcttcct																								rs201196594		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:99413866_99413867delGT	ENST00000397899.2	-	8	2881_2882	c.2550_2551delAC	c.(2548-2553)gcacggfs	p.R851fs		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	851																	TTCAGGGTCCGTGCCCCAGGCT	0.619																																					p.850_851del		.											.	.	0			c.2550_2551del						.																																			SO:0001589	frameshift_variant	343990	exon8			.	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 55"	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.2550_2551delAC	2.37:g.99413866_99413867delGT	ENSP00000380996:p.Arg851fs	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	102	42	NM_207362	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000397899.2	37	CCDS42720.1																																																																																			.		0.619	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		-	99413867	GT	-	99413866	7	5	129	1	0	1	0	1	0	0	0	0	2182	1144	40	0	349	0	C2orf55	2	99413866	Frame_Shift_Del	DEL	GT	TCGA-HE-7129-01A-11D-1961-08	60435483	99413866	143785507	5	11283											
ANKZF1	55139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr2	220099828	220099828	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctggtcagccagagctctgGaatgcactgcttgctgcttg	6	11	12	12	0	2	1	1	0	1	1	2	2	2	2	2	2	6	5	2	2	1	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:220099828G>T	ENST00000323348.5	+	10	1659	c.1485G>T	c.(1483-1485)tgG>tgT	p.W495C	GLB1L_ENST00000497855.1_5'Flank|ANKZF1_ENST00000410034.3_Missense_Mutation_p.W495C|ANKZF1_ENST00000409849.1_Missense_Mutation_p.W285C	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	495						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGAGCTCTGGAATGCACTGC	0.587																																					p.W495C		.											.	ANKZF1-92	0			c.G1485T						.						51	55	53					2																	220099828		2017	4171	6188	SO:0001583	missense	55139	exon10			GCTCTGGAATGCA	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1485G>T	2.37:g.220099828G>T	ENSP00000321617:p.Trp495Cys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	57	22	NM_001042410	0	0	18	28	10	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	37	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.709332	0.30322	.	.	ENSG00000163516	ENST00000323348;ENST00000409849;ENST00000410034	T;T;T	0.52983	0.64;0.64;0.64	5.41	4.51	0.55191	Ankyrin repeat-containing domain (2);	0.253027	0.37955	N	0.001878	T	0.43942	0.1270	M	0.65975	2.015	0.53005	D	0.999964	B	0.15141	0.012	B	0.17722	0.019	T	0.38265	-0.9669	10	0.37606	T	0.19	-6.7572	8.4061	0.32616	0.0:0.1513:0.5358:0.313	.	495	Q9H8Y5	ANKZ1_HUMAN	C	495;285;495	ENSP00000321617:W495C;ENSP00000386815:W285C;ENSP00000386337:W495C	ENSP00000321617:W495C	W	+	3	0	ANKZF1	219808072	1.000000	0.71417	0.983000	0.44433	0.353000	0.29299	1.765000	0.38481	1.473000	0.48159	0.591000	0.81541	TGG	.		0.587	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		T	220099828	G	T	220099828	3	4	129	1	0	0	0	0	1	0	0	0	693	1183	41	4	1519	4	ANKZF1	2	220099828	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	120685962	220099828	23099545	6	11284											
PLCL2	23228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	17051783	17051783	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcttaagttcaaagaattGcataaatcaaaggacaaagc	19	8	8	6	0	2	1	2	0	0	1	2	3	2	2	0	1	3	3	0	1	7	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:17051783G>T	ENST00000418129.2	+	2	1032	c.567G>T	c.(565-567)ttG>ttT	p.L189F	PLCL2_ENST00000460467.1_Intron|PLCL2_ENST00000396755.2_Missense_Mutation_p.L189F|PLCL2_ENST00000432376.1_Missense_Mutation_p.L189F	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	315	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						TCAAAGAATTGCATAAATCAA	0.348																																					p.L189F		.											.	PLCL2-229	0			c.G567T						.						61	64	63					3																	17051783		2203	4300	6503	SO:0001583	missense	23228	exon2			AGAATTGCATAAA	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"phospholipase C, epsilon 2"	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.567G>T	3.37:g.17051783G>T	ENSP00000409637:p.Leu189Phe	Somatic	102	1		WXS	Illumina HiSeq	Phase_I	161	53	NM_015184	0	0	10	14	4	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	37	CCDS33713.1	.	.	.	.	.	.	.	.	.	.	G	6.609	0.480810	0.12581	.	.	ENSG00000154822	ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376	T;T;T	0.45276	0.9;0.9;0.9	5.54	5.54	0.83059	EF-hand-like domain (1);	0.063928	0.64402	D	0.000008	T	0.53142	0.1778	.	.	.	0.54753	D	0.999982	D	0.52996	0.957	P	0.57502	0.822	T	0.51980	-0.8636	8	.	.	.	.	9.7379	0.40399	0.1594:0.0:0.8406:0.0	.	315	Q9UPR0	PLCL2_HUMAN	F	189;316;189;189	ENSP00000409637:L189F;ENSP00000379979:L189F;ENSP00000412836:L189F	.	L	+	3	2	PLCL2	17026787	0.998000	0.40836	0.999000	0.59377	0.977000	0.68977	0.452000	0.21795	2.600000	0.87896	0.563000	0.77884	TTG	.		0.348	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			T	17051783	G	T	17051783	3	4	129	1	0	0	0	0	1	0	0	0	12066	1310	46	4	945	4	PLCL2	3	17051783	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		17051783	180970647	7	11285											
TRAK1	22906	ucsc.edu	37	chr3	42251523	42251523	+	Intron	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtctcaggcagcagaagttAcccgagccggcctcaggctt	8	8	12	13	2	2	1	2	0	1	1	3	2	2	1	3	3	3	4	3	3	2	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:42251523A>C	ENST00000327628.5	+	14	2363				TRAK1_ENST00000487159.1_Intron|TRAK1_ENST00000341421.3_Missense_Mutation_p.Y612S|TRAK1_ENST00000396175.1_Intron	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1						endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						AGCAGAAGTTACCCGAGCCGG	0.637																																					p.Y670S	GBM(44;195 884 22595 31865 41850)												.	TRAK1-91	0			c.A2009C						.						53	51	52					3																	42251523		2203	4300	6503	SO:0001627	intron_variant	22906	exon14			GAAGTTACCCGAG		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"OGT(O Glc NAc transferase) interacting protein 106 KDa", "O-linked N-acetylglucosamine transferase interacting protein 106", "milton homolog 1 (Drosophila)"	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1963+46A>C	3.37:g.42251523A>C		Somatic	75	3		WXS	Illumina HiSeq		65	3	NM_001265608	0	0	9	11	2	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	A	9.834	1.189127	0.21954	.	.	ENSG00000182606	ENST00000341421	T	0.07688	3.17	4.97	-3.01	0.05463	.	.	.	.	.	T	0.03305	0.0096	N	0.14661	0.345	0.21256	N	0.999741	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.45920	-0.9228	8	.	.	.	.	0.4311	0.00471	0.3368:0.2619:0.1475:0.2538	.	596;670;612	B7Z218;B7Z347;Q9UPV9-2	.;.;.	S	612	ENSP00000340702:Y612S	.	Y	+	2	0	TRAK1	42226527	0.992000	0.36948	0.952000	0.39060	0.981000	0.71138	0.277000	0.18734	-0.288000	0.09051	-0.290000	0.09829	TAC	.		0.637	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		C	42251523	A	C	42251523	1	2	129	0	1	0	0	0	0	0	0	0	16482	391	14	5		5	TRAK1	3	42251523	Intron	SNP	A	TCGA-HE-7129-01A-11D-1961-08	25199740	42251523	155770907	8	11286											
C3orf27	23434	broad.mit.edu	37	chr3	128292497	128292497	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccctggaggcgggagaCgctgagtctaggcaggctcg	6	6	19	10	3	1	2	0	1	1	1	3	4	2	3	1	6	0	3	1	6	1	1	rs141693917		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:128292497C>T	ENST00000356020.2	-	3	1042	c.76G>A	c.(76-78)Gtc>Atc	p.V26I		NM_007354.2	NP_031380.1	O15544	GR6_HUMAN	chromosome 3 open reading frame 27	26								p.V26I(2)		large_intestine(2)|lung(5)|prostate(1)	8				GBM - Glioblastoma multiforme(114;0.176)		AGGCGGGAGACGCTGAGTCTA	0.592																																					p.V26I													.	C3orf27-90	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G76A						.	C	ILE/VAL	0,4402		0,0,2201	28	29	29		76	-1.2	0	3	dbSNP_134	29	1,8597		0,1,4298	no	missense	C3orf27	NM_007354.2	29	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	26/150	128292497	1,12999	2201	4299	6500	SO:0001583	missense	23434	exon3			GGGAGACGCTGAG	AF008192	CCDS3050.1	3q21	2005-12-19			ENSG00000198685	ENSG00000198685			17099	protein-coding gene	gene with protein product						9307271	Standard	NR_125802		Approved	GR6	uc003ekq.3	O15544	OTTHUMG00000159688	ENST00000356020.2:c.76G>A	3.37:g.128292497C>T	ENSP00000348302:p.Val26Ile	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	58	10	NM_007354	0	0	0	0	0		Missense_Mutation	SNP	ENST00000356020.2	37	CCDS3050.1	.	.	.	.	.	.	.	.	.	.	C	9.932	1.215195	0.22373	0.0	1.16E-4	ENSG00000198685	ENST00000356020	.	.	.	2.35	-1.23	0.09465	.	.	.	.	.	T	0.11750	0.0286	N	0.08118	0	0.09310	N	1	P	0.39404	0.672	B	0.29942	0.109	T	0.16158	-1.0412	8	0.87932	D	0	.	6.0846	0.19960	0.157:0.6855:0.0:0.1575	.	26	O15544	GR6_HUMAN	I	26	.	ENSP00000348302:V26I	V	-	1	0	C3orf27	129775187	0.000000	0.05858	0.001000	0.08648	0.388000	0.30384	-0.996000	0.03709	-0.054000	0.13266	0.313000	0.20887	GTC	C|1.000;T|0.000		0.592	C3orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356924.1	NM_007354		T	128292497	C	T	128292497	3	4	129	1	0	0	0	0	1	0	0	0	2225	536	19	1	377	1	C3orf27	3	128292497	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	86040974	128292497	69729933	9	11287											
KY	339855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr3	134323200	134323200	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catggttggagggtacacctCcaacttcatcccattcttcc	8	12	7	14	0	2	0	1	0	1	0	5	1	5	1	4	3	2	2	4	3	2	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:134323200C>A	ENST00000423778.2	-	11	1268	c.1207G>T	c.(1207-1209)Gag>Tag	p.E403*	KY_ENST00000508956.1_Nonsense_Mutation_p.E382*|KY_ENST00000503669.1_3'UTR	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	403					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGGTACACCTCCAACTTCATC	0.542																																					p.E403X		.											.	KY-24	0			c.G1207T						.						87	86	86					3																	134323200		2128	4244	6372	SO:0001587	stop_gained	339855	exon11			ACACCTCCAACTT	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1207G>T	3.37:g.134323200C>A	ENSP00000397598:p.Glu403*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	143	104	NM_178554	0	0	4	6	2	B7Z1S4|Q6ZT15	Nonsense_Mutation	SNP	ENST00000423778.2	37	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	36	5.846292	0.97016	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000310263	.	.	.	5.48	5.48	0.80851	.	0.368781	0.27393	N	0.019579	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-14.9747	19.3474	0.94370	0.0:1.0:0.0:0.0	.	.	.	.	X	382;403;403	.	ENSP00000309520:E403X	E	-	1	0	KY	135805890	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.042000	0.57347	2.578000	0.87016	0.561000	0.74099	GAG	.		0.542	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		A	134323200	C	A	134323200	4	1	129	1	0	0	0	0	0	1	0	0	8607	864	30	4	782	4	KY	3	134323200	Nonsense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	6030703	134323200	63699230	10	11288											
HPS3	84343	hgsc.bcm.edu;broad.mit.edu	37	chr3	148885021	148885021	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcatgaactgaaagaagaGaaccgggtatgctttttcag	15	10	10	6	1	2	4	2	2	0	2	2	5	2	4	1	1	3	2	1	1	6	3	rs551986971		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:148885021G>T	ENST00000296051.2	+	15	2930	c.2790G>T	c.(2788-2790)gaG>gaT	p.E930D	HPS3_ENST00000460120.1_Missense_Mutation_p.E765D	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	930					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGAAAGAAGAGAACCGGGTAT	0.403									Hermansky-Pudlak syndrome																												p.E930D		.											.	HPS3-158	0			c.G2790T						.						74	75	75					3																	148885021		2203	4300	6503	SO:0001583	missense	84343	exon15	Familial Cancer Database	HPS, HPS1-8	AGAAGAGAACCGG	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2790G>T	3.37:g.148885021G>T	ENSP00000296051:p.Glu930Asp	Somatic	29	1		WXS	Illumina HiSeq	Phase_I	45	26	NM_032383	0	0	1	1	0	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	G	9.373	1.071040	0.20147	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.63417	-0.03;-0.04	6.01	0.327	0.15913	.	0.542522	0.23534	N	0.047155	T	0.32466	0.0830	N	0.15975	0.35	0.49582	D	0.999804	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.14448	-1.0472	10	0.06494	T	0.89	-9.9199	4.0764	0.09906	0.1806:0.318:0.4022:0.0992	.	765;930	G5E9V4;Q969F9	.;HPS3_HUMAN	D	930;765	ENSP00000296051:E930D;ENSP00000418230:E765D	ENSP00000296051:E930D	E	+	3	2	HPS3	150367711	0.080000	0.21391	0.995000	0.50966	0.991000	0.79684	-0.222000	0.09190	0.105000	0.17753	0.650000	0.86243	GAG	.		0.403	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		T	148885021	G	T	148885021	3	4	129	1	0	0	0	0	1	0	0	0	7361	933	33	4	2848	4	HPS3	3	148885021	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	14561821	148885021	49137409	11	11289											
VPS8	23355	ucsc.edu	37	chr3	184603940	184603940	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attactgccttctgctgcagCgaaagtgagtatgcgttgcc	8	12	11	10	2	1	1	0	1	1	0	1	2	1	1	2	0	7	4	2	0	3	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:184603940C>T	ENST00000437079.3	+	22	1948	c.1777C>T	c.(1777-1779)Cga>Tga	p.R593*	VPS8_ENST00000446204.2_Intron|VPS8_ENST00000287546.4_Nonsense_Mutation_p.R593*|VPS8_ENST00000436792.2_Nonsense_Mutation_p.R591*	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	593							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TCTGCTGCAGCGAAAGTGAGT	0.433																																					p.R593X													.	VPS8-91	0			c.C1777T						.						194	190	191					3																	184603940		1977	4153	6130	SO:0001587	stop_gained	23355	exon21			CTGCAGCGAAAGT	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.1777C>T	3.37:g.184603940C>T	ENSP00000397879:p.Arg593*	Somatic	21	0		WXS	Illumina HiSeq		40	4	NM_001009921	0	0	0	0	0	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Nonsense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	C	41	8.738117	0.98935	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792	.	.	.	5.83	3.99	0.46301	.	0.053175	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-8.1278	15.0324	0.71717	0.2602:0.7397:0.0:0.0	.	.	.	.	X	593;593;591	.	ENSP00000287546:R593X	R	+	1	2	VPS8	186086634	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	2.885000	0.48570	0.761000	0.33130	-0.181000	0.13052	CGA	.		0.433	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		T	184603940	C	T	184603940	4	4	129	1	0	0	0	0	0	1	0	0	17251	760	27	1	1855	1	VPS8	3	184603940	Nonsense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	35718919	184603940	13418490	12	11290											
CRIPAK	285464	broad.mit.edu	37	chr4	1388729	1388729	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcacacgtgcccatgcGgagtgcccgcctgctcacac	6	7	10	18	3	2	0	2	0	0	0	2	1	2	1	3	1	5	2	3	1	0	0			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr4:1388729G>C	ENST00000324803.4	+	1	3390	c.430G>C	c.(430-432)Gga>Cga	p.G144R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	144					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GTGCCCATGCGGAGTGCCCGC	0.701																																					p.G144R													.	CRIPAK-90	0			c.G430C						.						37	37	37					4																	1388729		2033	3881	5914	SO:0001583	missense	285464	exon1			CCATGCGGAGTGC	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.430G>C	4.37:g.1388729G>C	ENSP00000323978:p.Gly144Arg	Somatic	394	1		WXS	Illumina HiSeq	Phase_I	254	4	NM_175918	0	0	19	19	0	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	10.33|10.33	1.320122|1.320122	0.23994|0.23994	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.17370|.	2.28|.	0.948|0.948	0.948|0.948	0.19561|0.19561	Post-SET domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.18841|0.18841	0.0452|0.0452	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	D|.	0.76494|.	0.999|.	D|.	0.70487|.	0.969|.	T|T	0.25082|0.25082	-1.0142|-1.0142	9|6	0.19147|0.32370	T|T	0.46|0.25	.|.	7.86|7.86	0.29504|0.29504	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	144|.	Q8N1N5|.	CRPAK_HUMAN|.	R|P	144|127	ENSP00000323978:G144R|.	ENSP00000323978:G144R|ENSP00000372402:R127P	G|R	+|+	1|2	0|0	CRIPAK|CRIPAK	1378729|1378729	0.000000|0.000000	0.05858|0.05858	0.032000|0.032000	0.17829|0.17829	0.031000|0.031000	0.12232|0.12232	-2.156000|-2.156000	0.01283|0.01283	0.840000|0.840000	0.34995|0.34995	0.121000|0.121000	0.15741|0.15741	GGA|CGG	.		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		C	1388729	G	C	1388729	3	2	129	1	0	0	0	0	1	0	0	0	3883	1117	39	4	432	4	CRIPAK	4	1388729	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		1388729	189765547	13	11291											
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr4	155256161	155256161	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggtgacatcggcattaaTgacagctgtgagcccaccac	11	9	10	11	1	0	3	0	3	0	0	1	3	0	3	2	2	2	2	2	2	2	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr4:155256161T>G	ENST00000357232.4	-	8	1074	c.1075A>C	c.(1075-1077)Att>Ctt	p.I359L	DCHS2_ENST00000339452.1_Missense_Mutation_p.I858L|DCHS2_ENST00000507542.1_5'UTR	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	359	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TCGGCATTAATGACAGCTGTG	0.433																																					p.I858L		.											.	DCHS2-94	0			c.A2572C						.						110	109	109					4																	155256161		2203	4300	6503	SO:0001583	missense	54798	exon4			CATTAATGACAGC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.1075A>C	4.37:g.155256161T>G	ENSP00000349768:p.Ile359Leu	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	108	55	NM_001142552	0	0	0	0	0	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	2.461	-0.324065	0.05350	.	.	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	T;T	0.52983	0.64;0.73	6.17	-3.98	0.04082	Cadherin (2);	1.778240	0.02970	N	0.144240	T	0.35128	0.0921	L	0.31926	0.97	0.09310	N	1	B;B	0.20887	0.049;0.024	B;B	0.20955	0.032;0.014	T	0.16660	-1.0395	10	0.23302	T	0.38	.	8.8965	0.35467	0.0:0.4543:0.2232:0.3226	.	858;359	E9PC11;Q6V1P9	.;PCD23_HUMAN	L	359;858;858	ENSP00000349768:I359L;ENSP00000345062:I858L	ENSP00000345062:I858L	I	-	1	0	DCHS2	155475611	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-0.719000	0.04974	-0.924000	0.03780	-0.408000	0.06270	ATT	.		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155256161	T	G	155256161	3	3	129	1	0	0	0	0	1	0	0	0	4294	1464	51	5	7843	5	DCHS2	4	155256161	Missense_Mutation	SNP	T	TCGA-HE-7129-01A-11D-1961-08	153867432	155256161	35898115	14	11292											
SLC27A6	28965	ucsc.edu	37	chr5	128302311	128302311	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagccctagtggtgggcgcaGgtagagtatggggtgtggtc	6	9	20	6	1	0	1	0	0	0	1	1	2	0	1	1	6	1	3	1	6	3	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:128302311G>A	ENST00000262462.4	+	1	1491	c.481G>A	c.(481-483)Gat>Aat	p.D161N	SLC27A6_ENST00000395266.1_Splice_Site_p.D161N|SLC27A6_ENST00000506176.1_Splice_Site_p.D161N			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	161					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		GGTGGGCGCAGGTAGAGTATG	0.517																																					p.D161N													.	SLC27A6-90	0			c.G481A						.						27	22	24					5																	128302311		2203	4300	6503	SO:0001630	splice_region_variant	28965	exon1			GGCGCAGGTAGAG	AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"Acyl-CoA synthetase family", "Solute carriers"	11000	protein-coding gene	gene with protein product	"fatty-acid-Coenzyme A ligase, very long-chain 2"	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.481+1G>A	5.37:g.128302311G>A		Somatic	37	0		WXS	Illumina HiSeq		21	4	NM_001017372	0	0	0	0	0	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862321	0.71949	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.50548	0.74;0.74;0.74	4.04	4.04	0.47022	AMP-dependent synthetase/ligase (1);	0.145674	0.64402	N	0.000010	T	0.53254	0.1785	M	0.79258	2.445	0.80722	D	1	B	0.18968	0.032	B	0.24848	0.056	T	0.58741	-0.7583	10	0.51188	T	0.08	-12.852	17.5013	0.87732	0.0:0.0:1.0:0.0	.	161	Q9Y2P4	S27A6_HUMAN	N	161	ENSP00000262462:D161N;ENSP00000378684:D161N;ENSP00000421024:D161N	ENSP00000262462:D161N	D	+	1	0	SLC27A6	128330210	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.984000	0.93482	2.536000	0.85505	0.561000	0.74099	GAT	.		0.517	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	Missense_Mutation	A	128302311	G	A	128302311	5	1	129	1	0	0	0	0	0	0	1	0	14562	1014	35	2	483	2	SLC27A6	5	128302311	Splice_Site	SNP	G	TCGA-HE-7129-01A-11D-1961-08		128302311	52612949	15	11293											
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140625665	140625665	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcaaaactacaatatttcTcccaattctcatttccatgt	12	16	2	11	0	3	0	2	0	2	0	6	0	4	0	2	0	2	1	2	0	6	6			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:140625665T>C	ENST00000231173.3	+	1	519	c.519T>C	c.(517-519)tcT>tcC	p.S173S		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	173	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAATATTTCTCCCAATTCTC	0.502																																					p.S173S		.											.	PCDHB15-156	0			c.T519C						.						44	47	46					5																	140625665		2203	4300	6503	SO:0001819	synonymous_variant	56121	exon1			TATTTCTCCCAAT	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"Cadherins / Protocadherins : Clustered"	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.519T>C	5.37:g.140625665T>C		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	27	2	NM_018935	0	0	36	36	0	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			.		0.502	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		C	140625665	T	C	140625665	2	2	129	1	0	0	0	0	0	0	0	1	11566	1538	54	3		3	PCDHB15	5	140625665	Silent	SNP	T	TCGA-HE-7129-01A-11D-1961-08	12323354	140625665	40289595	16	11294											
HNRNPAB	85007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr5	177632984	177632984	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagggtttgggtttatcctGttcaaagatgcagccagtgt	9	13	13	6	0	1	2	1	0	0	2	2	2	2	2	2	2	2	4	2	2	2	4	rs201431713		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:177632984G>A	ENST00000308158.5	-	0	2038				HNRNPAB_ENST00000355836.5_Silent_p.L117L|HNRNPAB_ENST00000506339.1_Silent_p.L117L|HNRNPAB_ENST00000506259.1_Silent_p.L117L|PHYKPL_ENST00000481811.1_5'Flank|HNRNPAB_ENST00000514633.1_Silent_p.L117L|HNRNPAB_ENST00000515193.1_Silent_p.L117L|HNRNPAB_ENST00000504898.1_Silent_p.L117L|HNRNPAB_ENST00000358344.3_Silent_p.L117L	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	GGTTTATCCTGTTCAAAGATG	0.408																																					p.L117L		.											.	HNRNPAB-22	0			c.G351A						.						129	126	127					5																	177632984		2203	4300	6503	SO:0001628	intergenic_variant	3182	exon3			TATCCTGTTCAAA	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892		5.37:g.177632984G>A		Somatic	193	0		WXS	Illumina HiSeq	Phase_I	198	104	NM_031266	0	1	108	193	84	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Silent	SNP	ENST00000308158.5	37	CCDS4434.1																																																																																			G|0.999;C|0.001		0.408	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		A	177632984	G	A	177632984	1	1	129	0	1	0	0	0	0	0	0	0	7282	1364	48	2		2	HNRNPAB	5	177632984	IGR	SNP	G	TCGA-HE-7129-01A-11D-1961-08	37007319	177632984	3282276	17	11295											
CCDC90A	63933	broad.mit.edu;ucsc.edu	37	chr6	13800602	13800602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgttttaactgatgtagttCgagttttattttctaaaaac	11	20	6	4	1	1	1	0	1	1	0	2	2	1	1	0	0	2	4	0	0	6	10	rs556879787		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:13800602C>T	ENST00000379170.4	-	5	892	c.754G>A	c.(754-756)Gaa>Aaa	p.E252K		NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	252					calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)											TGATGTAGTTCGAGTTTTATT	0.244													C|||	1	0.000199681	0	0	5008	,	,		16997	0		0	False		,,,				2504	0.001				p.E252K													.	CCDC90A-90	0			c.G754A						.						35	36	36					6																	13800602		2198	4287	6485	SO:0001583	missense	63933	exon5			GTAGTTCGAGTTT	BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 79", "coiled-coil domain containing 90A"	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.754G>A	6.37:g.13800602C>T	ENSP00000368468:p.Glu252Lys	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	26	9	NM_001031713	0	0	0	0	0	Q96JS7|Q9H7F8	Missense_Mutation	SNP	ENST00000379170.4	37	CCDS35495.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279411	0.80692	.	.	ENSG00000050393	ENST00000379170	T	0.45668	0.89	5.16	5.16	0.70880	.	0.050117	0.85682	D	0.000000	T	0.55955	0.1953	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.68943	0.961	T	0.59064	-0.7524	10	0.62326	D	0.03	-18.5219	15.9312	0.79659	0.0:1.0:0.0:0.0	.	252	Q96AQ8	CC90A_HUMAN	K	252	ENSP00000368468:E252K	ENSP00000368468:E252K	E	-	1	0	CCDC90A	13908581	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	3.018000	0.49625	2.561000	0.86390	0.655000	0.94253	GAA	.		0.244	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102		T	13800602	C	T	13800602	3	4	129	1	0	0	0	0	1	0	0	0	2874	893	31	1	345	1	CCDC90A	6	13800602	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		13800602	157314465	18	11296											
MDFI	4188	broad.mit.edu;ucsc.edu	37	chr6	41614025	41614025	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacagcactgacctcgacGtccccacagaagctgtgaca	11	6	10	14	2	0	3	0	2	0	1	2	5	1	4	3	1	2	2	3	1	1	0	rs367874076		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:41614025G>A	ENST00000373050.4	+	3	263							Q99750	MDFI_HUMAN	MyoD family inhibitor						activation of JUN kinase activity (GO:0007257)|cytoplasmic sequestering of transcription factor (GO:0042994)|dorsal/ventral axis specification (GO:0009950)|embryo development (GO:0009790)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|prostate(2)|skin(1)|urinary_tract(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)			TGACCTCGACGTCCCCACAGA	0.627													G|||	1	0.000199681	0	0	5008	,	,		18391	0.001		0	False		,,,				2504	0				p.V80I													.	MDFI-90	0			c.G238A						.						36	34	35					6																	41614025		2203	4300	6503	SO:0001627	intron_variant	4188	exon3			CTCGACGTCCCCA	U78313	CCDS4857.1, CCDS75451.1	6p21	2008-08-29			ENSG00000112559	ENSG00000112559			6967	protein-coding gene	gene with protein product	"inhibitor of MyoD family a"	604971				9250874, 17289077	Standard	NM_005586		Approved	I-mfa	uc003oqq.4	Q99750	OTTHUMG00000014681	ENST00000373050.4:c.77-3332G>A	6.37:g.41614025G>A		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	32	15	NM_005586	0	0	0	0	0		Missense_Mutation	SNP	ENST00000373050.4	37		.	.	.	.	.	.	.	.	.	.	G	11.01	1.512898	0.27123	.	.	ENSG00000112559	ENST00000432027;ENST00000419164;ENST00000373051;ENST00000441667;ENST00000230321;ENST00000543326;ENST00000446650	.	.	.	5.56	1.13	0.20643	.	0.618193	0.15698	N	0.249098	T	0.11153	0.0272	L	0.33485	1.01	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.29427	-1.0012	9	0.30078	T	0.28	-23.2738	6.7381	0.23421	0.2547:0.1343:0.611:0.0	.	80	Q99750	MDFI_HUMAN	I	80	.	ENSP00000230321:V80I	V	+	1	0	MDFI	41722003	0.117000	0.22190	0.791000	0.31998	0.989000	0.77384	1.430000	0.34914	0.280000	0.22209	0.655000	0.94253	GTC	.		0.627	MDFI-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000040519.2	NM_005586		A	41614025	G	A	41614025	1	1	129	0	1	0	0	0	0	0	0	0	9429	1145	40	1		1	MDFI	6	41614025	Intron	SNP	G	TCGA-HE-7129-01A-11D-1961-08	27813423	41614025	129501042	19	11297											
ICK	22858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr6	52878690	52878690	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgggcctgccttttccaGgatgcctttctgtggttttt	3	17	12	9	0	1	0	0	0	1	0	2	1	2	1	4	4	2	1	4	4	0	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:52878690G>C	ENST00000350082.5	-	9	1268	c.922C>G	c.(922-924)Ctg>Gtg	p.L308V	ICK_ENST00000356971.3_Missense_Mutation_p.L308V	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	308					intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GCCTTTTCCAGGATGCCTTTC	0.512																																					p.L308V		.											.	ICK-421	0			c.C922G						.						137	113	121					6																	52878690		2203	4300	6503	SO:0001583	missense	22858	exon10			TTTCCAGGATGCC	AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.922C>G	6.37:g.52878690G>C	ENSP00000263043:p.Leu308Val	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	48	23	NM_016513	0	0	6	10	4	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Missense_Mutation	SNP	ENST00000350082.5	37	CCDS4949.1	.	.	.	.	.	.	.	.	.	.	G	3.787	-0.044509	0.07452	.	.	ENSG00000112144	ENST00000350082;ENST00000356971	T;T	0.72282	-0.64;-0.64	6.06	5.18	0.71444	Protein kinase-like domain (1);	1.200720	0.05905	N	0.630645	T	0.33498	0.0865	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.26677	-1.0096	10	0.15499	T	0.54	5.3033	15.6578	0.77155	0.0661:0.0:0.9339:0.0	.	308	Q9UPZ9	ICK_HUMAN	V	308	ENSP00000263043:L308V;ENSP00000349458:L308V	ENSP00000263043:L308V	L	-	1	2	ICK	52986649	0.844000	0.29557	0.232000	0.24009	0.396000	0.30629	3.921000	0.56454	1.551000	0.49450	0.655000	0.94253	CTG	.		0.512	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513		C	52878690	G	C	52878690	3	2	129	1	0	0	0	0	1	0	0	0	7505	991	35	4	1000	4	ICK	6	52878690	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	11264665	52878690	118236377	20	11298											
CCM2	83605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	45112359	45112359	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtggacattaaggagacCtacgaggtggaagccagcac	15	5	13	8	1	0	1	0	0	0	1	0	5	0	3	2	4	3	1	2	4	4	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:45112359C>T	ENST00000258781.6	+	7	929	c.780C>T	c.(778-780)acC>acT	p.T260T	CCM2_ENST00000475551.1_Silent_p.T254T|CCM2_ENST00000544363.1_Silent_p.T169T|CCM2_ENST00000381112.3_Silent_p.T281T|CCM2_ENST00000541586.1_Silent_p.T202T|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000474617.1_Silent_p.T163T	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	260					blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TTAAGGAGACCTACGAGGTGG	0.507																																					p.T281T		.											.	CCM2-90	0			c.C843T						.						102	87	92					7																	45112359		2203	4300	6503	SO:0001819	synonymous_variant	83605	exon7			GGAGACCTACGAG	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.780C>T	7.37:g.45112359C>T		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	174	41	NM_001029835	0	0	79	101	22	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Silent	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	C	7.888	0.731770	0.15507	.	.	ENSG00000136280	ENST00000480382	.	.	.	5.55	-2.66	0.06077	.	.	.	.	.	T	0.41328	0.1154	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28235	-1.0050	4	.	.	.	-0.5904	2.9764	0.05939	0.3625:0.1562:0.3533:0.128	.	.	.	.	L	127	.	.	P	+	2	0	CCM2	45078884	0.004000	0.15560	0.000000	0.03702	0.904000	0.53231	-0.395000	0.07287	-0.809000	0.04381	-0.165000	0.13383	CCT	.		0.507	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443		T	45112359	C	T	45112359	2	4	129	1	0	0	0	0	0	0	0	1	2914	668	24	2		2	CCM2	7	45112359	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		45112359	114026304	21	11299											
HIP1	3092	broad.mit.edu	37	chr7	75168684	75168684	+	Frame_Shift_Del	DEL	T	T	-																															caccagcaagctcgtagtgcTttttccgaagctctcccagt																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:75168684delT	ENST00000336926.6	-	30	3046	c.3020delA	c.(3019-3021)aagfs	p.K1007fs	HIP1_ENST00000434438.2_Frame_Shift_Del_p.K956fs	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	1007	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CTCGTAGTGCTTTTTCCGAAG	0.507			T	PDGFRB	CMML																																p.K1007fs				Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1-1085	0			c.3020delA						.						303	294	297					7																	75168684		2203	4300	6503	SO:0001589	frameshift_variant	3092	exon30			TAGTGCTTTTTCC	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.3020delA	7.37:g.75168684delT	ENSP00000336747:p.Lys1007fs	Somatic	554	0		WXS	Illumina HiSeq	Phase_I	805	8	NM_005338	0	0	0	0	0	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Frame_Shift_Del	DEL	ENST00000336926.6	37	CCDS34669.1																																																																																			.		0.507	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		-	75168684	T	-	75168684	7	5	129	1	0	1	0	1	0	0	0	0	7135	1609	56	0	101	0	HIP1	7	75168684	Frame_Shift_Del	DEL	T	TCGA-HE-7129-01A-11D-1961-08	30056325	75168684	83969979	22	11300											
PDK4	5166	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	95221864	95221872	+	In_Frame_Del	DEL	CCAATGTGG	CCAATGTGG	-																															cacagttaggatcaatgcttCcaatgtggcttgggtttcct																								rs138077797		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	CCAATGTGG	CCAATGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:95221864_95221872delCCAATGTGG	ENST00000005178.5	-	5	764_772	c.567_575delCCACATTGG	c.(565-576)agccacattgga>aga	p.189_192SHIG>R		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	189	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			ATCAATGCTTCCAATGTGGCTTGGGTTTC	0.321																																					p.189_192del		.											.	PDK4-358	0			c.567_575del						.																																			SO:0001651	inframe_deletion	5166	exon5			.	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.567_575delCCACATTGG	7.37:g.95221864_95221872delCCAATGTGG	ENSP00000005178:p.Ser189_Gly192delinsArg	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	204	78	NM_002612	0	0	0	0	0		In_Frame_Del	DEL	ENST00000005178.5	37	CCDS5643.1																																																																																			.		0.321	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		-	95221872	CCAATGTGG	-	95221864	7	5	129	1	0	1	0	1	0	0	0	0	11704	855	30	0	688	0	PDK4	7	95221864	In_Frame_Del	DEL	CCAATGTGG	TCGA-HE-7129-01A-11D-1961-08	20053180	95221864	63916799	23	11301											
ZKSCAN5	23660	broad.mit.edu	37	chr7	99123898	99123898	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgcggaaaggctttccGggtgagttcccacctggttc	5	11	15	10	2	0	1	0	1	0	0	3	2	2	2	3	5	1	3	3	5	1	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:99123898G>T	ENST00000394170.2	+	6	1486	c.1235G>T	c.(1234-1236)cGg>cTg	p.R412L	ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.R412L|ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.R412L	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AAGGCTTTCCGGGTGAGTTCC	0.582																																					p.R412L													.	ZKSCAN5-91	0			c.G1235T						.						144	141	142					7																	99123898		2203	4300	6503	SO:0001583	missense	23660	exon6			CTTTCCGGGTGAG	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"Zinc fingers, C2H2-type", "-", "-", "-"	12867	protein-coding gene	gene with protein product		611272	"zinc finger protein homologous to Zfp95 in mouse", "zinc finger protein 95 homolog (mouse)"	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.1235G>T	7.37:g.99123898G>T	ENSP00000377725:p.Arg412Leu	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	299	7	NM_145102	0	0	16	16	0	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099745	0.56183	.	.	ENSG00000196652	ENST00000537357;ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.05925	3.37;3.37;3.37	4.63	4.63	0.57726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.261790	0.27567	N	0.018793	T	0.06735	0.0172	N	0.16266	0.395	0.25005	N	0.991449	D;D	0.53619	0.961;0.961	P;P	0.51866	0.682;0.682	T	0.39603	-0.9606	10	0.15952	T	0.53	.	11.117	0.48266	0.0:0.1871:0.8129:0.0	.	412;412	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	L	412	ENSP00000322872:R412L;ENSP00000392104:R412L;ENSP00000377725:R412L	ENSP00000322872:R412L	R	+	2	0	ZKSCAN5	98961834	0.000000	0.05858	0.965000	0.40720	0.996000	0.88848	0.225000	0.17757	2.581000	0.87130	0.655000	0.94253	CGG	.		0.582	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		T	99123898	G	T	99123898	3	4	129	1	0	0	0	0	1	0	0	0	17722	1116	39	4	1253	4	ZKSCAN5	7	99123898	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	3902034	99123898	60014765	24	11302											
ZKSCAN1	7586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	99621201	99621201	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggagaaggatggtatcgtAatagtgaaggtggaagagga	15	7	17	2	1	0	3	0	1	0	2	1	7	0	6	0	6	0	2	0	6	6	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:99621201A>G	ENST00000324306.6	+	2	306	c.72A>G	c.(70-72)gtA>gtG	p.V24V	ZKSCAN1_ENST00000535170.1_Intron|ZKSCAN1_ENST00000426572.1_5'UTR	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	24					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(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ATGGTATCGTAATAGTGAAGG	0.542																																					p.V24V		.											.	ZKSCAN1-93	0			c.A72G						.						94	83	87					7																	99621201		2203	4300	6503	SO:0001819	synonymous_variant	7586	exon2			TATCGTAATAGTG	X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"Zinc fingers, C2H2-type", "-", "-", "-"	13101	protein-coding gene	gene with protein product		601260	"zinc finger protein 36 (KOX 18)"	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.72A>G	7.37:g.99621201A>G		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	191	48	NM_003439	0	0	27	36	9	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Silent	SNP	ENST00000324306.6	37	CCDS34698.1																																																																																			.		0.542	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439		G	99621201	A	G	99621201	2	3	129	1	0	0	0	0	0	0	0	1	17718	349	13	3		3	ZKSCAN1	7	99621201	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08	497303	99621201	59517462	25	11303											
SLC4A2	6522	broad.mit.edu	37	chr7	150769158	150769158	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcgtctcccgcttcaccCaggagatcttcgccttcttg	4	13	8	16	3	4	1	1	0	3	1	7	2	4	1	3	1	0	2	3	1	0	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:150769158C>A	ENST00000485713.1	+	16	3510	c.2470C>A	c.(2470-2472)Cag>Aag	p.Q824K	SLC4A2_ENST00000461735.1_Missense_Mutation_p.Q810K|SLC4A2_ENST00000310317.5_Missense_Mutation_p.Q742K|SLC4A2_ENST00000413384.2_Missense_Mutation_p.Q824K|SLC4A2_ENST00000392826.2_Missense_Mutation_p.Q815K|RP11-148K1.12_ENST00000485974.1_RNA	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	824	Membrane (anion exchange).			Q -> R (in Ref. 1; CAA44067 and 7; CAA27556). {ECO:0000305}.	anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGCTTCACCCAGGAGATCTT	0.617																																					p.Q824K													.	SLC4A2-90	0			c.C2470A						.						171	173	172					7																	150769158		2203	4300	6503	SO:0001583	missense	6522	exon16			TTCACCCAGGAGA		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"Solute carriers"	11028	protein-coding gene	gene with protein product	"anion exchanger 2 type a", "anion exchanger 2 type b1", "anion exchanger 2 type b2"	109280	"erythrocyte membrane protein band 3-like 1", "solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.2470C>A	7.37:g.150769158C>A	ENSP00000419412:p.Gln824Lys	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	376	12	NM_003040	0	0	266	266	0	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442592	0.83993	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31	4.85	4.85	0.62838	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91593	0.7344	M	0.93106	3.38	0.80722	D	1	D;D;D	0.69078	0.982;0.997;0.997	D;D;D	0.74674	0.954;0.973;0.984	D	0.93451	0.6802	10	0.87932	D	0	.	15.534	0.75986	0.0:1.0:0.0:0.0	.	815;810;824	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	K	824;824;742;815;810	ENSP00000419412:Q824K;ENSP00000405600:Q824K;ENSP00000311402:Q742K;ENSP00000376571:Q815K;ENSP00000419164:Q810K	ENSP00000311402:Q742K	Q	+	1	0	SLC4A2	150400091	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.604000	0.82830	2.524000	0.85096	0.561000	0.74099	CAG	.		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150769158	C	A	150769158	3	1	129	1	0	0	0	0	1	0	0	0	14686	595	21	4	2528	4	SLC4A2	7	150769158	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	51147957	150769158	8369505	26	11304											
ASB10	136371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	150878302	150878302	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaaagcagcaagctgcaCagctgcaggcagcgggcggt	10	4	16	11	2	0	1	0	1	0	0	0	1	0	1	0	3	7	8	0	3	2	0			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:150878302C>G	ENST00000420175.2	-	3	852	c.828G>C	c.(826-828)ctG>ctC	p.L276L	ASB10_ENST00000275838.1_Silent_p.L276L|ASB10_ENST00000377867.3_Silent_p.L261L|ASB10_ENST00000422024.1_Silent_p.L321L|ASB10_ENST00000434669.1_Silent_p.L321L			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	276					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAAGCTGCACAGCTGCAGGC	0.682																																					p.L276L		.											.	ASB10-226	0			c.G828C						.						29	31	30					7																	150878302		2202	4297	6499	SO:0001819	synonymous_variant	136371	exon3			GCTGCACAGCTGC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.828G>C	7.37:g.150878302C>G		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	64	17	NM_001142459	0	0	0	0	0	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	37	CCDS47750.2																																																																																			.		0.682	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		G	150878302	C	G	150878302	2	3	129	1	0	0	0	0	0	0	0	1	1015	465	17	4		4	ASB10	7	150878302	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	109144	150878302	8260361	27	11305											
WISP1	8840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr8	134225321	134225321	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggaggctgccatctgtgaccCccaccggggcctctactgtg	5	8	13	15	1	2	1	0	1	2	0	2	2	2	2	5	4	2	1	5	4	1	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr8:134225321C>T	ENST00000250160.6	+	2	390	c.284C>T	c.(283-285)cCc>cTc	p.P95L	WISP1_ENST00000377863.2_Intron|WISP1_ENST00000220856.6_Missense_Mutation_p.P95L|WISP1_ENST00000519433.1_Intron|WISP1_ENST00000517423.1_Missense_Mutation_p.P95L	NM_003882.3	NP_003873.1	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	95	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			ATCTGTGACCCCCACCGGGGC	0.612																																					p.P95L		.											.	WISP1-610	0			c.C284T						.						57	59	58					8																	134225321		2203	4300	6503	SO:0001583	missense	8840	exon2			GTGACCCCCACCG	AF100779	CCDS6371.1, CCDS6372.1, CCDS56555.1, CCDS56556.1	8q24.22	2007-05-14			ENSG00000104415	ENSG00000104415			12769	protein-coding gene	gene with protein product		603398				9843955	Standard	NM_003882		Approved	CCN4	uc003yub.3	O95388	OTTHUMG00000164440	ENST00000250160.6:c.284C>T	8.37:g.134225321C>T	ENSP00000250160:p.Pro95Leu	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	82	41	NM_003882	0	0	0	0	0	A8KAG6|E7EMM5|Q5JBS6|Q5JBS7|Q5JBS8|Q9HCS3	Missense_Mutation	SNP	ENST00000250160.6	37	CCDS6371.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895808	0.52121	.	.	ENSG00000104415	ENST00000250160;ENST00000517423;ENST00000220856	T;T;T	0.64618	-0.11;-0.11;-0.11	5.27	4.33	0.51752	Insulin-like growth factor-binding protein, IGFBP (3);	0.467062	0.24962	N	0.034202	T	0.57961	0.2089	M	0.63843	1.955	0.80722	D	1	P;P;B	0.45176	0.852;0.458;0.27	B;B;B	0.42462	0.388;0.137;0.089	T	0.62315	-0.6880	10	0.56958	D	0.05	-27.7812	7.9781	0.30166	0.0:0.7412:0.1659:0.0928	.	95;95;95	E7EMM5;O95388-2;O95388	.;.;WISP1_HUMAN	L	95	ENSP00000250160:P95L;ENSP00000427744:P95L;ENSP00000220856:P95L	ENSP00000220856:P95L	P	+	2	0	WISP1	134294503	0.959000	0.32827	1.000000	0.80357	0.965000	0.64279	1.247000	0.32815	2.460000	0.83146	0.542000	0.68232	CCC	.		0.612	WISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378794.2	NM_003882		T	134225321	C	T	134225321	3	4	129	1	0	0	0	0	1	0	0	0	17405	623	22	2	290	2	WISP1	8	134225321	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		134225321	12138701	28	11306											
COL27A1	85301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr9	117047026	117047026	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acacaaaggcattgtgggacCccttggacctcctggaccaa	11	7	10	13	0	0	0	0	0	0	0	1	3	1	3	5	4	0	1	5	4	2	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr9:117047026C>G	ENST00000356083.3	+	41	4347	c.3956C>G	c.(3955-3957)cCc>cGc	p.P1319R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1319	Collagen-like 12.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						ATTGTGGGACCCCTTGGACCT	0.557																																					p.P1319R		.											.	COL27A1-94	0			c.C3956G						.						142	119	127					9																	117047026		2203	4300	6503	SO:0001583	missense	85301	exon41			TGGGACCCCTTGG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3956C>G	9.37:g.117047026C>G	ENSP00000348385:p.Pro1319Arg	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	98	35	NM_032888	0	1	13	36	22	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	c	12.60	1.986411	0.35036	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.93366	-3.21	4.71	3.82	0.43975	.	.	.	.	.	D	0.93779	0.8011	L	0.55017	1.72	0.38600	D	0.950644	P	0.52577	0.954	P	0.60012	0.867	D	0.91884	0.5518	9	0.22706	T	0.39	.	10.6899	0.45864	0.0:0.9065:0.0:0.0935	.	1319	Q8IZC6	CORA1_HUMAN	R	1319	ENSP00000348385:P1319R	ENSP00000348385:P1319R	P	+	2	0	COL27A1	116086847	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.396000	0.66297	1.205000	0.43262	-0.265000	0.10407	CCC	.		0.557	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		G	117047026	C	G	117047026	3	3	129	1	0	0	0	0	1	0	0	0	3691	623	22	4	4118	4	COL27A1	9	117047026	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		117047026	24166405	29	11307											
TMEM203	94107	broad.mit.edu;ucsc.edu	37	chr9	140099503	140099503	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcagctgcaggagaatgaAgagcggggacgtaatgaggc	13	4	18	6	2	0	4	0	2	0	2	0	7	0	5	0	4	4	4	0	4	3	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr9:140099503A>T	ENST00000343666.5	-	1	587	c.364T>A	c.(364-366)Ttc>Atc	p.F122I	TPRN_ENST00000541945.1_5'Flank|TMEM203_ENST00000537254.1_Missense_Mutation_p.F122I|NDOR1_ENST00000371521.4_5'Flank|NDOR1_ENST00000427047.2_5'Flank|NDOR1_ENST00000458322.2_5'Flank|NDOR1_ENST00000344894.5_5'Flank	NM_053045.1	NP_444273.1	Q969S6	TM203_HUMAN	transmembrane protein 203	122						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)	2	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		AGGAGAATGAAGAGCGGGGAC	0.587																																					p.F122I													.	TMEM203-22	0			c.T364A						.						42	41	41					9																	140099503		2200	4294	6494	SO:0001583	missense	94107	exon1			GAATGAAGAGCGG	BC009283	CCDS35185.1	9q34.3	2007-12-18			ENSG00000187713	ENSG00000187713			28217	protein-coding gene	gene with protein product	"HBeAg-binding protein 1"					12477932	Standard	NM_053045		Approved	MGC14327, HBEBP1	uc004clv.3	Q969S6	OTTHUMG00000020985	ENST00000343666.5:c.364T>A	9.37:g.140099503A>T	ENSP00000375053:p.Phe122Ile	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	44	24	NM_053045	0	0	33	76	43	Q6NW08	Missense_Mutation	SNP	ENST00000343666.5	37	CCDS35185.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394143	0.83011	.	.	ENSG00000187713	ENST00000343666;ENST00000537254	.	.	.	4.31	4.31	0.51392	.	0.158722	0.42053	U	0.000772	T	0.68860	0.3047	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.71334	-0.4624	9	0.59425	D	0.04	.	12.4385	0.55612	1.0:0.0:0.0:0.0	.	122	Q969S6	TM203_HUMAN	I	122	.	ENSP00000375053:F122I	F	-	1	0	TMEM203	139219324	1.000000	0.71417	0.992000	0.48379	0.369000	0.29798	8.717000	0.91425	1.799000	0.52666	0.533000	0.62120	TTC	.		0.587	TMEM203-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055325.2	NM_053045		T	140099503	A	T	140099503	3	4	129	1	0	0	0	0	1	0	0	0	16160	72	3	5	50	5	TMEM203	9	140099503	Missense_Mutation	SNP	A	TCGA-HE-7129-01A-11D-1961-08	23052477	140099503	1113928	30	11308											
PCDH15	65217	broad.mit.edu;ucsc.edu	37	chr10	55568839	55568839	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcttgcaagcacaatgttTttccttgctttttctccttc	5	20	4	12	0	2	0	0	0	2	0	5	0	3	0	2	0	3	4	2	0	2	8			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr10:55568839T>A	ENST00000395445.1	-	36	5365	c.4971A>T	c.(4969-4971)aaA>aaT	p.K1657N	PCDH15_ENST00000409834.1_3'UTR|PCDH15_ENST00000395438.1_3'UTR|PCDH15_ENST00000395442.1_Missense_Mutation_p.K522N|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395446.1_Missense_Mutation_p.K853N|PCDH15_ENST00000395440.1_Missense_Mutation_p.K591N|PCDH15_ENST00000414778.1_Intron	NM_001142769.1	NP_001136241.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	0					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCACAATGTTTTTCCTTGCTT	0.473										HNSCC(58;0.16)																											.													.	PCDH15-193	0			.						.						123	94	103					10																	55568839		1568	3582	5150	SO:0001583	missense	65217	.			AATGTTTTTCCTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000395445.1:c.4971A>T	10.37:g.55568839T>A	ENSP00000378832:p.Lys1657Asn	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	27	13	.	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000395445.1	37		.	.	.	.	.	.	.	.	.	.	T	12.19	1.863009	0.32884	.	.	ENSG00000150275	ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440	T;D;D;D	0.97089	-0.31;-4.24;-4.24;-4.24	5.55	-4.49	0.03504	.	.	.	.	.	D	0.89656	0.6778	N	0.14661	0.345	0.21841	N	0.99951	P;P	0.38922	0.651;0.501	B;B	0.29785	0.107;0.107	T	0.82623	-0.0366	9	0.62326	D	0.03	.	9.0437	0.36333	0.1044:0.4727:0.0:0.4229	.	1655;1657	C6ZEF5;A2A3E2	.;.	N	1657;853;522;591	ENSP00000378832:K1657N;ENSP00000378833:K853N;ENSP00000378829:K522N;ENSP00000378827:K591N	ENSP00000378827:K591N	K	-	3	2	PCDH15	55238845	0.945000	0.32115	0.056000	0.19401	0.489000	0.33432	0.441000	0.21611	-0.418000	0.07450	-0.290000	0.09829	AAA	.		0.473	PCDH15-007	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000291335.1	NM_033056		A	55568839	T	A	55568839	3	1	129	1	0	0	0	0	1	0	0	0	11537	1838	64	5	945	5	PCDH15	10	55568839	Missense_Mutation	SNP	T	TCGA-HE-7129-01A-11D-1961-08		55568839	79965908	31	11309											
AP3M1	26985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	75898090	75898090	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgctcttccagtgcttctcTagaaatatgtcaccggaaca	11	11	7	12	2	3	1	1	0	2	1	5	2	4	2	2	1	2	2	2	1	4	4	rs147488745		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr10:75898090T>C	ENST00000355264.4	-	2	359	c.48A>G	c.(46-48)ctA>ctG	p.L16L	AP3M1_ENST00000487653.1_5'UTR|AP3M1_ENST00000372745.1_Silent_p.L16L	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	16					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|protein targeting to lysosome (GO:0006622)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	Rab GTPase binding (GO:0017137)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13	Prostate(51;0.0112)					AGTGCTTCTCTAGAAATATGT	0.358																																					p.L16L		.											.	AP3M1-90	0			c.A48G						.						76	76	76					10																	75898090		2203	4300	6503	SO:0001819	synonymous_variant	26985	exon3			CTTCTCTAGAAAT	AF092092	CCDS7342.1	10q22.1-q22.3	2008-07-07			ENSG00000185009	ENSG00000185009			569	protein-coding gene	gene with protein product		610366				10024875	Standard	NM_207012		Approved		uc001jwh.3	Q9Y2T2	OTTHUMG00000018497	ENST00000355264.4:c.48A>G	10.37:g.75898090T>C		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	93	50	NM_207012	0	0	4	14	10	Q5JQ12|Q9H5L2	Silent	SNP	ENST00000355264.4	37	CCDS7342.1																																																																																			T|1.000;G|0.000		0.358	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1			C	75898090	T	C	75898090	2	2	129	1	0	0	0	0	0	0	0	1	747	1509	53	3		3	AP3M1	10	75898090	Silent	SNP	T	TCGA-HE-7129-01A-11D-1961-08	20329251	75898090	59636657	32	11310											
MUC2	4583	broad.mit.edu	37	chr11	1098668	1098668	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagtgccacgcactggtGcccccgcagcactactacga	8	5	10	18	3	0	0	0	0	0	0	0	1	0	0	4	1	5	3	4	1	2	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:1098668G>A	ENST00000441003.2	+	37	7065	c.7038G>A	c.(7036-7038)gtG>gtA	p.V2346V	MUC2_ENST00000361558.6_3'UTR	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4708					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACGCACTGGTGCCCCCGCAGC	0.652																																					p.V2342V													.	MUC2-90	0			c.G7026A						.						21	26	24					11																	1098668		2108	4219	6327	SO:0001819	synonymous_variant	4583	exon38			ACTGGTGCCCCCG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.7038G>A	11.37:g.1098668G>A		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	25	8	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1098668	G	A	1098668	2	1	129	1	0	0	0	0	0	0	0	1	10000	1306	46	2		2	MUC2	11	1098668	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08		1098668	133907848	33	11311											
OR8I2	120586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	55861472	55861472	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catcctgaggatccagtcagCagcaggcaggcagaaggcct	11	5	13	12	0	1	2	1	1	0	1	3	3	3	3	3	4	2	4	3	4	1	0			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:55861472C>G	ENST00000302124.2	+	1	720	c.689C>G	c.(688-690)gCa>gGa	p.A230G		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A230E(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					ATCCAGTCAGCAGCAGGCAGG	0.468																																					p.A230G		.											.	OR8I2-113	1	Substitution - Missense(1)	lung(1)	c.C689G						.						148	133	138					11																	55861472		2201	4296	6497	SO:0001583	missense	120586	exon1			AGTCAGCAGCAGG	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.689C>G	11.37:g.55861472C>G	ENSP00000303864:p.Ala230Gly	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	91	26	NM_001003750	0	0	0	0	0	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	C	7.367	0.625989	0.14257	.	.	ENSG00000172154	ENST00000302124	T	0.00207	8.55	4.33	3.41	0.39046	GPCR, rhodopsin-like superfamily (1);	0.410674	0.17770	U	0.162617	T	0.00241	0.0007	L	0.60904	1.88	0.09310	N	1	B	0.19935	0.04	B	0.25614	0.062	T	0.31613	-0.9937	10	0.62326	D	0.03	-0.4958	11.6945	0.51536	0.0:0.9111:0.0:0.0889	.	230	Q8N0Y5	OR8I2_HUMAN	G	230	ENSP00000303864:A230G	ENSP00000303864:A230G	A	+	2	0	OR8I2	55618048	0.000000	0.05858	0.014000	0.15608	0.555000	0.35460	0.408000	0.21065	0.934000	0.37316	0.440000	0.28878	GCA	.		0.468	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		G	55861472	C	G	55861472	3	3	129	1	0	0	0	0	1	0	0	0	11266	710	25	4	691	4	OR8I2	11	55861472	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	54762804	55861472	79145044	34	11312											
TNKS1BP1	85456	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	57076186	57076186	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccactccacatccccgtagCccctgagaacctccagagtc	9	6	6	20	1	0	2	0	1	0	2	4	3	3	2	8	0	2	1	8	0	2	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:57076186C>T	ENST00000532437.1	-	5	4310	c.3999G>A	c.(3997-3999)ggG>ggA	p.G1333G	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Silent_p.G1333G			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1333	Acidic.|Gly-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				ATCCCCGTAGCCCCTGAGAAC	0.607																																					p.G1333G		.											.	TNKS1BP1-91	0			c.G3999A						.						134	146	142					11																	57076186		2201	4296	6497	SO:0001819	synonymous_variant	85456	exon6			CCGTAGCCCCTGA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.3999G>A	11.37:g.57076186C>T		Somatic	404	2		WXS	Illumina HiSeq	Phase_I	244	100	NM_033396	0	0	17	39	22	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			.		0.607	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57076186	C	T	57076186	2	4	129	1	0	0	0	0	0	0	0	1	16352	726	26	2		2	TNKS1BP1	11	57076186	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	1214714	57076186	77930330	35	11313											
SLC3A2	6520	ucsc.edu	37	chr11	62648666	62648666	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggcggaggcggcagccgcGgctaagttcacgggcctgtc	6	5	18	12	5	1	0	1	0	0	0	2	2	1	1	2	6	1	3	2	6	1	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:62648666G>A	ENST00000377890.2	+	4	642	c.474G>A	c.(472-474)gcG>gcA	p.A158A	SLC3A2_ENST00000536981.1_5'Flank|SLC3A2_ENST00000377889.2_Silent_p.A96A|SLC3A2_ENST00000338663.7_Silent_p.A57A|SLC3A2_ENST00000377892.1_Silent_p.A189A|SLC3A2_ENST00000535296.1_Silent_p.A127A|SLC3A2_ENST00000377891.2_Silent_p.A159A	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	158				A -> P (in Ref. 3; AAA51540). {ECO:0000305}.	amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CGGCAGCCGCGGCTAAGTTCA	0.677											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A159A													.	SLC3A2-90	0			c.G477A						.						15	19	18					11																	62648666		2193	4292	6485	SO:0001819	synonymous_variant	6520	exon4			AGCCGCGGCTAAG		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"Solute carriers"	11026	protein-coding gene	gene with protein product	"antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43", "antigen defined by monoclonal antibody 4F2", "heavy chain", "4F2 heavy chain", "CD98 heavy chain", "monoclonal antibody 44D7", "4F2 cell-surface antigen heavy chain", "lymphocyte activation antigen 4F2 large subunit"	158070	"solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.474G>A	11.37:g.62648666G>A		Somatic	25	0	1062	WXS	Illumina HiSeq		18	4	NM_001012662	1	0	248	249	0	Q13543	Silent	SNP	ENST00000377890.2	37	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	G	0.757	-0.770850	0.02974	.	.	ENSG00000168003	ENST00000538084	.	.	.	4.22	-1.89	0.07689	.	.	.	.	.	T	0.43166	0.1235	.	.	.	0.41309	D	0.987096	.	.	.	.	.	.	T	0.29274	-1.0017	4	.	.	.	-2.3345	4.2588	0.10730	0.0792:0.3374:0.3594:0.224	.	.	.	.	Q	129	.	.	R	+	2	0	SLC3A2	62405242	0.017000	0.18338	0.015000	0.15790	0.058000	0.15608	-0.108000	0.10857	-0.509000	0.06532	-1.268000	0.01426	CGG	.		0.677	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		A	62648666	G	A	62648666	2	1	129	1	0	0	0	0	0	0	0	1	14659	1103	39	1		1	SLC3A2	11	62648666	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08	5572480	62648666	72357850	36	11314											
DSCAML1	57453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	117375681	117375681	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttgggtggggggtagccgtCcaccgagcagttgagcacac	7	7	16	11	2	0	1	0	1	0	0	1	2	1	1	3	4	3	4	3	4	1	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:117375681C>T	ENST00000321322.6	-	10	2321	c.2320G>A	c.(2320-2322)Gac>Aac	p.D774N	DSCAML1_ENST00000527706.1_Missense_Mutation_p.D504N	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	714	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGTAGCCGTCCACCGAGCAG	0.602																																					p.D774N		.											.	DSCAML1-159	0			c.G2320A						.						88	77	81					11																	117375681		2201	4296	6497	SO:0001583	missense	57453	exon10			AGCCGTCCACCGA		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2320G>A	11.37:g.117375681C>T	ENSP00000315465:p.Asp774Asn	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	67	27	NM_020693	0	0	13	23	10	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.813851	0.70912	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66995	-0.24;-0.24	4.32	4.32	0.51571	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54727	0.1876	N	0.21097	0.63	0.58432	D	0.999999	B	0.18013	0.025	B	0.21360	0.034	T	0.52358	-0.8586	9	0.38643	T	0.18	.	16.5931	0.84781	0.0:1.0:0.0:0.0	.	714	Q8TD84	DSCL1_HUMAN	N	504;774;481	ENSP00000434335:D504N;ENSP00000315465:D774N	ENSP00000315465:D774N	D	-	1	0	DSCAML1	116880891	1.000000	0.71417	0.939000	0.37840	0.852000	0.48524	7.559000	0.82265	2.222000	0.72286	0.313000	0.20887	GAC	.		0.602	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117375681	C	T	117375681	3	4	129	1	0	0	0	0	1	0	0	0	4780	855	30	2	4117	2	DSCAML1	11	117375681	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	54727015	117375681	17630835	37	11315											
LIMA1	51474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	50571511	50571511	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ccaaggcacttcctgaacttCcaagttcagtggggggtggc	8	9	13	11	0	1	1	1	1	0	0	3	1	3	1	3	5	1	2	3	5	3	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr12:50571511C>G	ENST00000341247.4	-	11	1765	c.1616G>C	c.(1615-1617)gGa>gCa	p.G539A	LIMA1_ENST00000552783.1_Missense_Mutation_p.G380A|LIMA1_ENST00000394943.3_Missense_Mutation_p.G540A|LIMA1_ENST00000552823.1_Missense_Mutation_p.G379A|LIMA1_ENST00000547825.1_Missense_Mutation_p.G237A|LIMA1_ENST00000552909.1_Missense_Mutation_p.G378A|LIMA1_ENST00000552491.1_Missense_Mutation_p.G236A	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	539					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						TCCTGAACTTCCAAGTTCAGT	0.532																																					p.G540A		.											.	LIMA1-91	0			c.G1619C						.						113	118	116					12																	50571511		2203	4300	6503	SO:0001583	missense	51474	exon11			GAACTTCCAAGTT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1616G>C	12.37:g.50571511C>G	ENSP00000340184:p.Gly539Ala	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	193	89	NM_001113546	0	0	35	66	31	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.467708	0.63625	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.84800	-1.15;-1.15;-1.49;-1.9;-1.16;-1.49;-1.49	5.73	4.83	0.62350	.	0.635701	0.18245	N	0.147130	D	0.82779	0.5111	L	0.44542	1.39	0.30474	N	0.773064	B;B;P	0.38129	0.072;0.293;0.619	B;B;B	0.39339	0.067;0.078;0.297	T	0.81895	-0.0723	10	0.49607	T	0.09	.	17.0525	0.86523	0.0:0.8729:0.1271:0.0	.	549;539;378	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	A	236;237;379;540;539;380;378;458	ENSP00000448463:G236A;ENSP00000448706:G237A;ENSP00000450266:G379A;ENSP00000378400:G540A;ENSP00000340184:G539A;ENSP00000448779:G380A;ENSP00000450087:G378A	ENSP00000340184:G539A	G	-	2	0	LIMA1	48857778	0.928000	0.31464	0.969000	0.41365	0.973000	0.67179	4.892000	0.63193	1.530000	0.49136	0.655000	0.94253	GGA	.		0.532	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		G	50571511	C	G	50571511	3	3	129	1	0	0	0	0	1	0	0	0	8818	855	30	4	667	4	LIMA1	12	50571511	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		50571511	83280384	38	11316											
LAMP1	3916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr13	113964011	113964011	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgctcaaccgcagctcCtgtggaaaagagaacacttc	11	8	11	11	1	1	1	1	0	0	1	3	3	2	2	2	2	4	3	2	2	4	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr13:113964011C>T	ENST00000332556.4	+	3	431	c.237C>T	c.(235-237)tcC>tcT	p.S79S	LAMP1_ENST00000397181.3_Silent_p.S79S	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	79	First lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			ACCGCAGCTCCTGTGGAAAAG	0.448																																					p.S79S		.											.	LAMP1-514	0			c.C237T						.						110	114	113					13																	113964011		1968	4157	6125	SO:0001819	synonymous_variant	3916	exon3			CAGCTCCTGTGGA	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.237C>T	13.37:g.113964011C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	117	64	NM_005561	0	0	275	546	271	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	37	CCDS41909.1																																																																																			.		0.448	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			T	113964011	C	T	113964011	2	4	129	1	0	0	0	0	0	0	0	1	8638	668	24	2		2	LAMP1	13	113964011	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		113964011	1205867	39	11317											
BAZ1A	11177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	35242930	35242930	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccagatatgtcgatctgtAacctgtaacaaaattcaaac	15	11	5	10	1	2	1	1	0	1	1	4	2	3	1	2	0	3	2	2	0	6	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:35242930A>G	ENST00000382422.2	-	19	3327	c.3000T>C	c.(2998-3000)gtT>gtC	p.V1000V	BAZ1A_ENST00000360310.1_Silent_p.V1000V|BAZ1A_ENST00000358716.4_Silent_p.V968V			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1000					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		GTCGATCTGTAACCTGTAACA	0.323																																					p.V1000V		.											.	BAZ1A-291	0			c.T3000C						.						87	78	81					14																	35242930		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon20			ATCTGTAACCTGT	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.3000T>C	14.37:g.35242930A>G		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	46	26	NM_013448	0	0	0	0	0	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			.		0.323	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35242930	A	G	35242930	2	3	129	1	0	0	0	0	0	0	0	1	1330	349	13	3		3	BAZ1A	14	35242930	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08		35242930	72106610	40	11318											
ARID4A	5926	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	58827698	58827698	+	Frame_Shift_Del	DEL	C	C	-																															gggacgacctcctttaaaatCaaccctctcatcaaacatgc																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:58827698delC	ENST00000355431.3	+	19	2391	c.2018delC	c.(2017-2019)tcafs	p.S673fs	ARID4A_ENST00000395168.3_Frame_Shift_Del_p.S673fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.S673fs|ARID4A_ENST00000348476.3_Frame_Shift_Del_p.S673fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	673					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						CCTTTAAAATCAACCCTCTCA	0.433																																					p.S673X		.											.	ARID4A-231	0			c.2018delC						.						169	155	159					14																	58827698		2203	4300	6503	SO:0001589	frameshift_variant	5926	exon19			.	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"-"	9885	protein-coding gene	gene with protein product		180201	"retinoblastoma-binding protein 1"	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2018delC	14.37:g.58827698delC	ENSP00000347602:p.Ser673fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	132	59	NM_002892	0	0	0	0	0	Q15991|Q15992|Q15993	Nonsense_Mutation	DEL	ENST00000355431.3	37	CCDS9732.1																																																																																			.		0.433	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		-	58827698	C	-	58827698	7	5	129	1	0	1	0	1	0	0	0	0	919	838	29	0	2088	0	ARID4A	14	58827698	Frame_Shift_Del	DEL	C	TCGA-HE-7129-01A-11D-1961-08	23584768	58827698	48521842	41	11319											
ESR2	2100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	64746749	64746749	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atccttcacacgaccagactCcatagtgatatcccgatgcg	11	9	7	14	3	1	2	1	1	0	1	4	4	4	2	4	0	1	0	4	0	2	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:64746749C>G	ENST00000341099.4	-	3	902	c.485G>C	c.(484-486)gGa>gCa	p.G162A	ESR2_ENST00000353772.3_Missense_Mutation_p.G162A|ESR2_ENST00000555483.1_Intron|ESR2_ENST00000542956.1_Missense_Mutation_p.G162A|ESR2_ENST00000554572.1_Missense_Mutation_p.G162A|ESR2_ENST00000267525.6_Missense_Mutation_p.G162A|ESR2_ENST00000358599.5_Missense_Mutation_p.G162A|ESR2_ENST00000557772.1_Missense_Mutation_p.G162A|ESR2_ENST00000553796.1_Missense_Mutation_p.G162A|ESR2_ENST00000357782.2_Missense_Mutation_p.G162A|ESR2_ENST00000555278.1_Missense_Mutation_p.G162A	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	162					brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CGACCAGACTCCATAGTGATA	0.453																																					p.G162A		.											.	ESR2-611	0			c.G485C						.						236	229	232					14																	64746749		2203	4300	6503	SO:0001583	missense	2100	exon2			CAGACTCCATAGT	X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"Nuclear hormone receptors"	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.485G>C	14.37:g.64746749C>G	ENSP00000343925:p.Gly162Ala	Somatic	426	1		WXS	Illumina HiSeq	Phase_I	345	152	NM_001214902	0	0	0	0	0	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	37	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148027	0.94603	.	.	ENSG00000140009	ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525	D;D;D;D;D;D;D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44	5.56	5.56	0.83823	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99312	0.9759	H	0.99425	4.56	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.98376	1.0556	10	0.87932	D	0	.	19.5206	0.95183	0.0:1.0:0.0:0.0	.	162;162;162;162;162	Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3	.;ESR2_HUMAN;.;.;.	A	162	ENSP00000452485:G162A;ENSP00000441792:G162A;ENSP00000450699:G162A;ENSP00000335551:G162A;ENSP00000351412:G162A;ENSP00000450488:G162A;ENSP00000452426:G162A;ENSP00000350427:G162A;ENSP00000451582:G162A;ENSP00000343925:G162A;ENSP00000267525:G162A	ENSP00000267525:G162A	G	-	2	0	ESR2	63816502	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.647000	0.83462	2.623000	0.88846	0.557000	0.71058	GGA	.		0.453	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			G	64746749	C	G	64746749	3	3	129	1	0	0	0	0	1	0	0	0	5270	855	30	4	1221	4	ESR2	14	64746749	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	5919051	64746749	42602791	42	11320											
HERC1	8925	ucsc.edu	37	chr15	63901303	63901303	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtagtcagtgtcggagccctCggcgttgtccacgtttctcg	4	12	13	12	5	2	0	1	0	1	0	6	1	3	1	2	2	1	3	2	2	1	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr15:63901303C>T	ENST00000443617.2	-	78	14650	c.14563G>A	c.(14563-14565)Gag>Aag	p.E4855K		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4855					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TCGGAGCCCTCGGCGTTGTCC	0.537																																					p.E4855K													.	HERC1-666	0			c.G14563A						.						71	79	76					15																	63901303		2131	4230	6361	SO:0001583	missense	8925	exon78			AGCCCTCGGCGTT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"WD repeat domain containing"	4867	protein-coding gene	gene with protein product		605109	"hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.14563G>A	15.37:g.63901303C>T	ENSP00000390158:p.Glu4855Lys	Somatic	34	0		WXS	Illumina HiSeq		36	4	NM_003922	0	0	17	17	0	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	36	5.744559	0.96882	.	.	ENSG00000103657	ENST00000443617	T	0.25250	1.81	5.42	5.42	0.78866	.	0.073125	0.51477	U	0.000085	T	0.12817	0.0311	N	0.08118	0	0.80722	D	1	P	0.44006	0.824	B	0.27500	0.08	T	0.09422	-1.0675	10	0.46703	T	0.11	.	19.2521	0.93929	0.0:1.0:0.0:0.0	.	4855	Q15751	HERC1_HUMAN	K	4855	ENSP00000390158:E4855K	ENSP00000390158:E4855K	E	-	1	0	HERC1	61688356	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	7.703000	0.84585	2.542000	0.85734	0.655000	0.94253	GAG	.		0.537	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63901303	C	T	63901303	3	4	129	1	0	0	0	0	1	0	0	0	7078	893	31	1	26	1	HERC1	15	63901303	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		63901303	38630089	43	11321											
CP110	9738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	19548870	19548870	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gataccctaagggatctggcTtcgttaacaagaataaaatg	15	10	9	7	1	1	1	0	0	1	1	2	3	1	2	1	2	2	2	1	2	7	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:19548870T>A	ENST00000381396.5	+	4	2126	c.1879T>A	c.(1879-1881)Ttc>Atc	p.F627I	CCP110_ENST00000396208.2_Missense_Mutation_p.F627I|CCP110_ENST00000396212.2_Missense_Mutation_p.F627I	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	627					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						GGGATCTGGCTTCGTTAACAA	0.348																																					p.F627I		.											.	CCP110-90	0			c.T1879A						.						40	42	42					16																	19548870		2197	4300	6497	SO:0001583	missense	9738	exon4			TCTGGCTTCGTTA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1879T>A	16.37:g.19548870T>A	ENSP00000370803:p.Phe627Ile	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	62	25	NM_001199022	0	0	4	11	7	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901950	0.33535	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.13307	2.6;2.6;2.6	5.39	1.56	0.23342	.	0.876000	0.09983	N	0.730791	T	0.05318	0.0141	N	0.03608	-0.345	0.22213	N	0.999282	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.39251	-0.9623	10	0.37606	T	0.19	-0.0461	3.164	0.06529	0.1377:0.0766:0.1437:0.642	.	627;627	O43303;O43303-2	CP110_HUMAN;.	I	627	ENSP00000379515:F627I;ENSP00000370803:F627I;ENSP00000379511:F627I	ENSP00000370803:F627I	F	+	1	0	CCP110	19456371	0.389000	0.25205	0.861000	0.33841	0.927000	0.56198	0.910000	0.28571	0.291000	0.22468	0.460000	0.39030	TTC	.		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		A	19548870	T	A	19548870	3	1	129	1	0	0	0	0	1	0	0	0	3794	1609	56	5	1889	5	CP110	16	19548870	Missense_Mutation	SNP	T	TCGA-HE-7129-01A-11D-1961-08		19548870	70805883	44	11322											
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	24826534	24826534	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctatgactttatgaacagcaGtacttcaccagccagtcctc	11	11	6	13	0	1	2	1	2	0	0	3	2	2	2	3	0	4	2	3	0	4	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:24826534G>A	ENST00000395799.3	+	19	4868	c.4739G>A	c.(4738-4740)aGt>aAt	p.S1580N	TNRC6A_ENST00000432286.2_Missense_Mutation_p.S58N|TNRC6A_ENST00000315183.7_Missense_Mutation_p.S1531N|CTD-2515A14.1_ENST00000568895.1_RNA	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1580					cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ATGAACAGCAGTACTTCACCA	0.458																																					p.S1580N		.											.	TNRC6A-92	0			c.G4739A						.						89	87	88					16																	24826534		2197	4300	6497	SO:0001583	missense	27327	exon19			ACAGCAGTACTTC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"Trinucleotide (CAG) repeat containing"	11969	protein-coding gene	gene with protein product		610739	"trinucleotide repeat containing 6"	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.4739G>A	16.37:g.24826534G>A	ENSP00000379144:p.Ser1580Asn	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	136	36	NM_014494	0	0	14	17	3	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561278	0.86335	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.14022	2.58;2.54	5.92	5.92	0.95590	.	0.042755	0.85682	D	0.000000	T	0.29458	0.0734	L	0.59436	1.845	0.58432	D	0.999998	P;B;B;D	0.63880	0.718;0.427;0.392;0.993	B;B;B;P	0.54629	0.366;0.254;0.315;0.757	T	0.00097	-1.2072	10	0.33141	T	0.24	-13.8994	20.3206	0.98668	0.0:0.0:1.0:0.0	.	247;719;1531;1580	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7	.;.;.;TNR6A_HUMAN	N	1531;1580;58	ENSP00000326900:S1531N;ENSP00000379144:S1580N	ENSP00000326900:S1531N	S	+	2	0	TNRC6A	24734035	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.423000	0.90264	2.809000	0.96659	0.655000	0.94253	AGT	.		0.458	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24826534	G	A	24826534	3	1	129	1	0	0	0	0	1	0	0	0	16372	1029	36	2	4813	2	TNRC6A	16	24826534	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	5277664	24826534	65528219	45	11323											
CNOT1	23019	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	58585134	58585134	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattctctcagtttgatctgTggccacaagcaacgtatcta	11	13	7	10	1	4	1	1	1	3	0	5	1	4	1	1	1	2	3	1	1	5	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:58585134T>C	ENST00000317147.5	-	24	3576	c.3244A>G	c.(3244-3246)Aca>Gca	p.T1082A	CNOT1_ENST00000569732.1_5'Flank|CNOT1_ENST00000441024.2_Missense_Mutation_p.T1082A|CNOT1_ENST00000569240.1_Missense_Mutation_p.T1077A|CNOT1_ENST00000245138.4_5'UTR|SNORA46_ENST00000384762.1_RNA	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1082					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GTTTGATCTGTGGCCACAAGC	0.323																																					p.T1082A		.											.	CNOT1-95	0			c.A3244G						.						106	124	118					16																	58585134		2197	4300	6497	SO:0001583	missense	23019	exon24			GATCTGTGGCCAC	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3244A>G	16.37:g.58585134T>C	ENSP00000320949:p.Thr1082Ala	Somatic	226	0		WXS	Illumina HiSeq	Phase_I	464	292	NM_206999	1	1	14	57	41	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.669566	0.88348	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000394200;ENST00000441024	T;T	0.45668	0.93;0.89	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.51449	0.1675	L	0.37561	1.115	0.80722	D	1	D;P;P	0.56035	0.974;0.851;0.939	D;B;P	0.70487	0.969;0.253;0.625	T	0.39522	-0.9610	10	0.13470	T	0.59	.	15.4218	0.75018	0.0:0.0:0.0:1.0	.	1082;1082;1077	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	A	1082;511;1077;1082	ENSP00000320949:T1082A;ENSP00000413113:T1082A	ENSP00000320949:T1082A	T	-	1	0	CNOT1	57142635	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.051000	0.60960	0.383000	0.25322	ACA	.		0.323	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58585134	T	C	58585134	3	2	129	1	0	0	0	0	1	0	0	0	3623	1696	59	3	4212	3	CNOT1	16	58585134	Missense_Mutation	SNP	T	TCGA-HE-7129-01A-11D-1961-08	33758600	58585134	31769619	46	11324											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|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	265	268					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	334	49		WXS	Illumina HiSeq		632	81	NM_145301	0	0	12	89	77	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		T	15457087	C	T	15457087	3	4	129	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		15457087	65738123	47	11325											
UBB	7314	broad.mit.edu	37	chr17	16285476	16285476	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcttcgtgaagaccctgacCggcaagaccatcaccctgga	11	7	9	14	2	2	4	1	2	1	2	3	5	2	5	4	2	0	1	4	2	2	1	rs370706400		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:16285476C>G	ENST00000395837.1	+	2	436	c.255C>G	c.(253-255)acC>acG	p.T85T	UBB_ENST00000535788.1_Intron|UBB_ENST00000578649.1_Intron|UBB_ENST00000302182.3_Silent_p.T85T|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000395839.1_Silent_p.T85T	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	85	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|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 type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCCTGACCGGCAAGACCA	0.552																																					p.T85T	Melanoma(163;1126 3406 34901)												.	UBB-47	0			c.C255G						.						69	69	69					17																	16285476		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CCTGACCGGCAAG		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"polyubiquitin B"	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.255C>G	17.37:g.16285476C>G		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	189	4	NM_018955	2	8	6944	6957	3	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			.		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955		G	16285476	C	G	16285476	2	3	129	1	0	0	0	0	0	0	0	1	16874	639	23	4		4	UBB	17	16285476	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	828389	16285476	64909734	48	11326											
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28525539	28525565	+	Splice_Site	DEL	TAATAATACGCTATTGGGAAGAAAATA	TAATAATACGCTATTGGGAAGAAAATA	-																															tgtttctggggtaatactttTaataatacgctattgggaag																								rs202181933|rs201520429|rs200015551		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	TAATAATACGCTATTGGGAAGAAAATA	TAATAATACGCTATTGGGAAGAAAATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:28525539_28525565delTAATAATACGCTATTGGGAAGAAAATA	ENST00000401766.2	-	14	2331_2340	c.1819_1828delTATTTTCTTCCCAATAGCGTATTATTA	c.(1819-1830)tattttcttccc>cc	p.YFLP607del	SLC6A4_ENST00000261707.3_Splice_Site_p.YFLP607del			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	607					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	GTAATACTTTTAATAATACGCTATTGGGAAGAAAATACAATGTTATA	0.335																																					p.607_610del		.											.	SLC6A4-94	0			c.1819_1828del						.																																			SO:0001630	splice_region_variant	6532	exon15			.	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1819-1TATTTTCTTCCCAATAGCGTATTATTA>-	17.37:g.28525539_28525565delTAATAATACGCTATTGGGAAGAAAATA		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	89	18	NM_001045	0	0	0	0	0	Q5EE02	Frame_Shift_Del	DEL	ENST00000401766.2	37	CCDS11256.1																																																																																			.		0.335	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045	In_Frame_Del	-	28525565	TAATAATACGCTATTGGGAAGAAAATA	-	28525539	8	5	129	1	0	1	0	1	0	0	1	0	14718	1763	61	0	68	0	SLC6A4	17	28525539	Splice_Site	DEL	TAATAATACGCTATTGGGAAGAAAATA	TCGA-HE-7129-01A-11D-1961-08	12240063	28525539	52669671	49	11327											
BLMH	642	hgsc.bcm.edu;broad.mit.edu	37	chr17	28601215	28601215	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcacaccactcggaataTctggaagagaggaggaggaa	15	5	14	7	1	1	1	0	0	1	1	2	8	1	6	1	5	1	1	1	5	4	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:28601215T>C	ENST00000261714.6	-	7	820	c.646A>G	c.(646-648)Ata>Gta	p.I216V	BLMH_ENST00000394819.3_Splice_Site_p.I129V|BLMH_ENST00000582669.1_5'UTR	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	216					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	ACTCGGAATATCTGGAAGAGA	0.408																																					p.I216V	Pancreas(127;628 1772 12912 33293 36203)	.											.	BLMH-91	0			c.A646G						.						52	52	52					17																	28601215		2203	4300	6503	SO:0001630	splice_region_variant	642	exon7			GGAATATCTGGAA	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.646-1A>G	17.37:g.28601215T>C		Somatic	58	1		WXS	Illumina HiSeq	Phase_I	85	14	NM_000386	0	0	0	0	0	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.634591	0.29068	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.47869	0.83;0.83	5.91	3.38	0.38709	.	0.142143	0.64402	N	0.000007	T	0.21631	0.0521	N	0.04820	-0.15	0.39774	D	0.972206	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.005	T	0.05818	-1.0862	10	0.16896	T	0.51	-15.4969	6.3794	0.21525	0.0:0.3117:0.0:0.6883	.	129;216	E7EMN3;Q13867	.;BLMH_HUMAN	V	216;129	ENSP00000261714:I216V;ENSP00000378296:I129V	ENSP00000261714:I216V	I	-	1	0	BLMH	25625341	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.118000	0.50414	1.064000	0.40671	0.533000	0.62120	ATA	.		0.408	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386	Missense_Mutation	C	28601215	T	C	28601215	5	2	129	1	0	0	0	0	0	0	1	0	1447	1449	50	3	745	3	BLMH	17	28601215	Splice_Site	SNP	T	TCGA-HE-7129-01A-11D-1961-08	75676	28601215	52593995	50	11328											
MED24	9862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	38182477	38182477	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctggcggatcatctgcagCgacttctcacgctcatccag	8	9	10	14	3	4	0	3	0	2	0	6	2	5	1	1	2	3	3	1	2	0	1	rs572516214		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:38182477C>T	ENST00000394128.2	-	19	1998	c.1917G>A	c.(1915-1917)tcG>tcA	p.S639S	MED24_ENST00000394127.2_Silent_p.S626S|MED24_ENST00000356271.3_Silent_p.S626S|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000501516.3_Silent_p.S658S|MED24_ENST00000394126.1_Silent_p.S664S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	639					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					TCATCTGCAGCGACTTCTCAC	0.567																																					p.S639S		.											.	MED24-187	0			c.G1917A						.						143	129	134					17																	38182477		2203	4300	6503	SO:0001819	synonymous_variant	9862	exon19			CTGCAGCGACTTC	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1917G>A	17.37:g.38182477C>T		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	200	45	NM_014815	0	0	62	95	33	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			.		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38182477	C	T	38182477	2	4	129	1	0	0	0	0	0	0	0	1	9467	755	27	1		1	MED24	17	38182477	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	9581262	38182477	43012733	51	11329											
ITGB3	3690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	45369560	45369560	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccccaggagaaggagaagtCctttaccataaagcccgtgg	12	7	11	11	1	0	2	0	0	0	2	2	4	2	2	5	3	2	0	5	3	5	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:45369560C>T	ENST00000559488.1	+	10	1332	c.1316C>T	c.(1315-1317)tCc>tTc	p.S439F	ITGB3_ENST00000560629.1_Silent_p.V427V|ITGB3_ENST00000435993.2_Missense_Mutation_p.S392F	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	439					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	AAGGAGAAGTCCTTTACCATA	0.522																																					p.S439F		.											.	ITGB3-714	0			c.C1316T						.						94	78	84					17																	45369560		2203	4300	6503	SO:0001583	missense	3690	exon10			AGAAGTCCTTTAC		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"CD molecules", "Integrins"	6156	protein-coding gene	gene with protein product	"platelet glycoprotein IIIa"	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1316C>T	17.37:g.45369560C>T	ENSP00000452786:p.Ser439Phe	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	104	67	NM_000212	0	0	52	145	93	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558922	0.86231	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	T	0.67171	-0.25	5.4	5.4	0.78164	Integrin beta subunit, N-terminal (2);	0.153255	0.56097	D	0.000025	T	0.78960	0.4366	L	0.60455	1.87	0.51233	D	0.99991	D	0.64830	0.994	D	0.65573	0.936	T	0.80324	-0.1430	10	0.66056	D	0.02	.	17.9137	0.88942	0.0:1.0:0.0:0.0	.	439	P05106	ITB3_HUMAN	F	439;392	ENSP00000407801:S392F	ENSP00000262017:S439F	S	+	2	0	C17orf57	42724559	0.998000	0.40836	1.000000	0.80357	0.953000	0.61014	3.315000	0.51951	2.531000	0.85337	0.462000	0.41574	TCC	.		0.522	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45369560	C	T	45369560	3	4	129	1	0	0	0	0	1	0	0	0	7916	855	30	2	1354	2	ITGB3	17	45369560	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	7187083	45369560	35825650	52	11330											
HSF5	124535	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	56540550	56540550	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaggaatgcaactcatcaaCtatctgaaagacagcctcta	15	8	8	10	0	4	2	2	1	2	1	4	4	4	4	1	2	4	1	1	2	6	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:56540550C>G	ENST00000323777.3	-	4	1244	c.1135G>C	c.(1135-1137)Gtt>Ctt	p.V379L		NM_001080439.1	NP_001073908.1	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	379					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	16	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AACTCATCAACTATCTGAAAG	0.438																																					p.V379L		.											.	HSF5-71	0			c.G1135C						.						101	97	98					17																	56540550		2203	4300	6503	SO:0001583	missense	124535	exon4			CATCAACTATCTG	BC033020	CCDS32690.1	17q23.2	2006-04-25				ENSG00000176160			26862	protein-coding gene	gene with protein product							Standard	NM_001080439		Approved	FLJ40311	uc002iwi.1	Q4G112		ENST00000323777.3:c.1135G>C	17.37:g.56540550C>G	ENSP00000313243:p.Val379Leu	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	227	69	NM_001080439	0	0	0	0	0	Q08EH7|Q8N7V2	Missense_Mutation	SNP	ENST00000323777.3	37	CCDS32690.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396051	0.42512	.	.	ENSG00000176160	ENST00000412540;ENST00000323777	T	0.43294	0.95	5.47	4.49	0.54785	.	0.247257	0.28754	N	0.014249	T	0.30448	0.0765	L	0.27053	0.805	0.38062	D	0.936116	B	0.06786	0.001	B	0.08055	0.003	T	0.11372	-1.0590	10	0.34782	T	0.22	.	12.6737	0.56882	0.1654:0.8346:0.0:0.0	.	379	Q4G112	HSF5_HUMAN	L	279;379	ENSP00000313243:V379L	ENSP00000313243:V379L	V	-	1	0	HSF5	53895549	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.377000	0.44300	1.273000	0.44346	0.650000	0.86243	GTT	.		0.438	HSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444719.1	XM_064190		G	56540550	C	G	56540550	3	3	129	1	0	0	0	0	1	0	0	0	7420	565	20	4	667	4	HSF5	17	56540550	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	11170990	56540550	24654660	53	11331											
TEX14	56155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	56663339	56663339	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggctgcagcagggcgtcggGctcattttcagcctcgctct	4	10	14	13	3	3	0	2	0	1	0	5	0	3	0	1	3	3	5	1	3	0	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:56663339G>C	ENST00000240361.8	-	18	2996	c.2911C>G	c.(2911-2913)Ccc>Gcc	p.P971A	TEX14_ENST00000389934.3_Missense_Mutation_p.P965A|TEX14_ENST00000349033.5_Missense_Mutation_p.P965A			Q8IWB6	TEX14_HUMAN	testis expressed 14	971					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGGCGTCGGGCTCATTTTCA	0.512																																					p.P971A		.											.	TEX14-810	0			c.C2911G						.						145	146	146					17																	56663339		2203	4300	6503	SO:0001583	missense	56155	exon18			CGTCGGGCTCATT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2911C>G	17.37:g.56663339G>C	ENSP00000240361:p.Pro971Ala	Somatic	209	1		WXS	Illumina HiSeq	Phase_I	257	74	NM_001201457	0	0	0	0	0	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.349191	0.41599	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.78126	-1.15;-1.15;-1.1	5.38	-0.87	0.10646	.	1.113020	0.06645	N	0.761719	T	0.69450	0.3112	L	0.57536	1.79	0.09310	N	1	B;B;B	0.12630	0.006;0.002;0.002	B;B;B	0.14023	0.003;0.01;0.01	T	0.55648	-0.8108	10	0.45353	T	0.12	-3.8719	2.7702	0.05332	0.3122:0.0:0.3257:0.3621	.	971;965;965	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	A	971;965;965	ENSP00000240361:P971A;ENSP00000374584:P965A;ENSP00000268910:P965A	ENSP00000240361:P971A	P	-	1	0	TEX14	54018338	0.000000	0.05858	0.003000	0.11579	0.431000	0.31685	-0.152000	0.10159	0.220000	0.20860	0.561000	0.74099	CCC	.		0.512	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			C	56663339	G	C	56663339	3	2	129	1	0	0	0	0	1	0	0	0	15810	1203	42	4	1646	4	TEX14	17	56663339	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	122789	56663339	24531871	54	11332											
METTL2A	339175	broad.mit.edu	37	chr17	60501296	60501296	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccctgaaggtgcacctgcAgtcctcgccgataagaggca	10	7	11	13	2	0	2	0	1	0	1	2	3	1	2	4	2	3	3	4	2	3	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:60501296A>G	ENST00000311506.5	+	1	69	c.33A>G	c.(31-33)gcA>gcG	p.A11A		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	11					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			GTGCACCTGCAGTCCTCGCCG	0.597											OREG0024635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A11A													.	METTL2A-248	0			c.A33G						.						57	67	64					17																	60501296		692	1591	2283	SO:0001819	synonymous_variant	339175	exon1			ACCTGCAGTCCTC	AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.33A>G	17.37:g.60501296A>G		Somatic	47	0	1046	WXS	Illumina HiSeq	Phase_I	63	21	NM_181725	0	0	42	67	25	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Silent	SNP	ENST00000311506.5	37	CCDS45752.1																																																																																			.		0.597	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725		G	60501296	A	G	60501296	2	3	129	1	0	0	0	0	0	0	0	1	9524	175	7	3		3	METTL2A	17	60501296	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08	3837957	60501296	20693914	55	11333											
CYB561	1534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	61511913	61511913	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccagcagcaggcccagcacGttggccaggacaccctcggg	8	3	14	16	2	0	0	0	0	0	0	1	1	0	1	4	4	3	4	4	4	0	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:61511913G>A	ENST00000392976.1	-	6	905	c.606C>T	c.(604-606)aaC>aaT	p.N202N	CYB561_ENST00000582997.1_Silent_p.N209N|CYB561_ENST00000582297.1_Intron|CYB561_ENST00000582034.1_Silent_p.N173N|CYB561_ENST00000542042.1_Silent_p.N269N|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000448884.2_3'UTR|CYB561_ENST00000581573.1_Silent_p.N202N|CYB561_ENST00000360793.3_Silent_p.N202N|CYB561_ENST00000584031.1_3'UTR|RP11-269G24.4_ENST00000584608.1_lincRNA|CYB561_ENST00000392975.2_Silent_p.N202N	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	202	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				electron transport chain (GO:0022900)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|transmembrane electron transfer carrier (GO:0022865)			lung(2)|ovary(1)|prostate(1)	4				READ - Rectum adenocarcinoma(1115;0.0689)		GGCCCAGCACGTTGGCCAGGA	0.642																																					p.N202N		.											.	CYB561-91	0			c.C606T						.						48	48	48					17																	61511913		2203	4300	6503	SO:0001819	synonymous_variant	1534	exon6			CAGCACGTTGGCC		CCDS11636.1	17q23.3	2013-03-14	2013-03-14		ENSG00000008283	ENSG00000008283		"Cytochrome b genes"	2571	protein-coding gene	gene with protein product	"ferric-chelate reductase 2", "cytochrome b561 family, member A1"	600019				7959749, 23249217	Standard	XM_005257091		Approved	FRRS2, CYB561A1	uc002jas.3	P49447		ENST00000392976.1:c.606C>T	17.37:g.61511913G>A		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	50	33	NM_001915	0	0	57	142	85	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Silent	SNP	ENST00000392976.1	37	CCDS11636.1																																																																																			.		0.642	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915		A	61511913	G	A	61511913	2	1	129	1	0	0	0	0	0	0	0	1	4125	1136	40	1		1	CYB561	17	61511913	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08	1010617	61511913	19683297	56	11334											
ABCA5	23461	hgsc.bcm.edu;broad.mit.edu	37	chr17	67303077	67303077	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgactccagctccttccaaaGagaaacattggtcttcaact	12	11	6	12	0	2	2	1	1	1	1	5	3	5	2	3	1	3	1	3	1	3	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:67303077G>A	ENST00000392676.3	-	6	641	c.577C>T	c.(577-579)Ctt>Ttt	p.L193F	ABCA5_ENST00000588877.1_Missense_Mutation_p.L193F|ABCA5_ENST00000392677.2_Missense_Mutation_p.L193F			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	193					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TCCTTCCAAAGAGAAACATTG	0.348																																					p.L193F		.											.	ABCA5-93	0			c.C577T						.						56	60	59					17																	67303077		2198	4294	6492	SO:0001583	missense	23461	exon5			TCCAAAGAGAAAC	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.577C>T	17.37:g.67303077G>A	ENSP00000376443:p.Leu193Phe	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	113	39	NM_018672	0	0	2	4	2	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836993	0.50951	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.87966	-2.32;-2.32	5.22	-9.14	0.00701	.	1.842040	0.03300	N	0.188828	T	0.60625	0.2283	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.57452	-0.7809	9	.	.	.	.	6.752	0.23491	0.1697:0.5331:0.2205:0.0768	.	193;193	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	F	193	ENSP00000376444:L193F;ENSP00000376443:L193F	.	L	-	1	0	ABCA5	64814672	0.090000	0.21635	0.839000	0.33178	0.999000	0.98932	0.440000	0.21592	-1.239000	0.02532	0.650000	0.86243	CTT	.		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		A	67303077	G	A	67303077	3	1	129	1	0	0	0	0	1	0	0	0	35	942	33	2	4487	2	ABCA5	17	67303077	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	5791164	67303077	13892133	57	11335											
NOTUM	147111	broad.mit.edu	37	chr17	79913365	79913365	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctgccccgtcaggtgcacGttgtccaccgtcagctgtgc	4	9	13	15	3	2	0	2	0	0	0	3	0	3	0	4	2	4	4	4	2	0	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:79913365G>A	ENST00000409678.3	-	9	1427	c.1044C>T	c.(1042-1044)aaC>aaT	p.N348N		NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)	348						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	15	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			TCAGGTGCACGTTGTCCACCG	0.687																																					p.N348N													.	NOTUM-22	0			c.C1044T						.						23	20	21					17																	79913365		2202	4285	6487	SO:0001819	synonymous_variant	147111	exon9			GTGCACGTTGTCC	BC060882	CCDS32771.2	17q25.3	2008-02-05			ENSG00000185269	ENSG00000185269			27106	protein-coding gene	gene with protein product		609847					Standard	NM_178493		Approved		uc010wvg.2	Q6P988	OTTHUMG00000154416	ENST00000409678.3:c.1044C>T	17.37:g.79913365G>A		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	54	20	NM_178493	0	0	0	0	0	Q8N410|Q8NI82	Silent	SNP	ENST00000409678.3	37	CCDS32771.2																																																																																			.		0.687	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335123.2	NM_178493		A	79913365	G	A	79913365	2	1	129	1	0	0	0	0	0	0	0	1	10578	1136	40	1		1	NOTUM	17	79913365	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08	12610288	79913365	1281845	58	11336											
HCN2	610	broad.mit.edu	37	chr19	615935	615935	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccgagctgggtcagcgcGtgggcctcttcccgccgccg	3	6	16	16	6	2	0	1	0	1	0	3	1	3	0	5	3	2	1	5	3	0	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr19:615935G>C	ENST00000251287.2	+	8	2184	c.2131G>C	c.(2131-2133)Gtg>Ctg	p.V711L	AC005559.2_ENST00000591847.1_RNA	NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	711					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGTCAGCGCGTGGGCCTCTT	0.692																																					p.V711L	Melanoma(145;1175 2427 8056 36306)												.	HCN2-90	0			c.G2131C						.						26	22	23					19																	615935		2198	4296	6494	SO:0001583	missense	610	exon8			CAGCGCGTGGGCC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.2131G>C	19.37:g.615935G>C	ENSP00000251287:p.Val711Leu	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_001194	0	0	0	0	0	O60742|O60743|O75267|Q9UBS2	Missense_Mutation	SNP	ENST00000251287.2	37	CCDS12035.1	.	.	.	.	.	.	.	.	.	.	.	9.846	1.192309	0.21954	.	.	ENSG00000099822	ENST00000251287	T	0.42900	0.96	3.52	3.52	0.40303	.	.	.	.	.	T	0.19485	0.0468	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.12837	0.008	T	0.19679	-1.0298	9	0.07325	T	0.83	.	8.5564	0.33483	0.1283:0.0:0.8717:0.0	.	711	Q9UL51	HCN2_HUMAN	L	711	ENSP00000251287:V711L	ENSP00000251287:V711L	V	+	1	0	HCN2	566935	0.009000	0.17119	0.104000	0.21259	0.845000	0.48019	0.661000	0.25023	1.697000	0.51169	0.478000	0.44815	GTG	.		0.692	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194		C	615935	G	C	615935	3	2	129	1	0	0	0	0	1	0	0	0	7018	1145	40	4	2161	4	HCN2	19	615935	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		615935	58513048	59	11337											
ZNF284	342909	broad.mit.edu	37	chr19	44590761	44590761	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atataattgtaatgtatgtgGgaagggcttcaggtggtcct	10	14	13	4	0	1	0	1	0	0	0	2	1	2	1	1	4	0	3	1	4	5	6			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr19:44590761G>C	ENST00000421176.3	+	5	1346	c.1130G>C	c.(1129-1131)gGg>gCg	p.G377A	ZNF223_ENST00000591793.1_3'UTR|RNU6-902P_ENST00000517212.1_RNA	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				AATGTATGTGGGAAGGGCTTC	0.428																																					p.G377A													.	.	0			c.G1130C						.						100	106	104					19																	44590761		2104	4238	6342	SO:0001583	missense	342909	exon5			TATGTGGGAAGGG	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"Zinc fingers, C2H2-type", "-"	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1130G>C	19.37:g.44590761G>C	ENSP00000411032:p.Gly377Ala	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	110	4	NM_001037813	0	0	2	2	0	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	37	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.707297	0.48412	.	.	ENSG00000186026	ENST00000421176	T	0.07114	3.22	2.15	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28962	0.0719	M	0.87827	2.91	0.29133	N	0.879512	D	0.89917	1.0	D	0.97110	1.0	T	0.06607	-1.0817	9	0.87932	D	0	.	7.7642	0.28970	0.1413:0.0:0.8587:0.0	.	377	Q2VY69	ZN284_HUMAN	A	377	ENSP00000411032:G377A	ENSP00000411032:G377A	G	+	2	0	ZNF284	49282601	1.000000	0.71417	0.015000	0.15790	0.070000	0.16714	3.579000	0.53900	0.228000	0.21019	0.462000	0.41574	GGG	.		0.428	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		C	44590761	G	C	44590761	3	2	129	1	0	0	0	0	1	0	0	0	17853	1232	43	4	1144	4	ZNF284	19	44590761	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	43974826	44590761	14538222	60	11338											
RIN2	54453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr20	19955386	19955386	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gacggtgtctgtcctgcctcCctgcgtcagctctgccttat	3	13	10	15	2	3	0	1	0	2	0	5	1	5	0	4	1	4	1	4	1	1	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr20:19955386C>T	ENST00000255006.6	+	8	1013	c.864C>T	c.(862-864)tcC>tcT	p.S288S	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	239					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						GTCCTGCCTCCCTGCGTCAGC	0.547																																					p.S288S		.											.	RIN2-660	0			c.C864T						.						73	77	75					20																	19955386		1935	4144	6079	SO:0001819	synonymous_variant	54453	exon8			TGCCTCCCTGCGT	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.864C>T	20.37:g.19955386C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	68	33	NM_001242581	0	0	11	18	7	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			.		0.547	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19955386	C	T	19955386	2	4	129	1	0	0	0	0	0	0	0	1	13404	610	22	2		2	RIN2	20	19955386	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		19955386	43070134	61	11339											
RBM9	23543	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr22	36206007	36206007	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaatgggatggtagtaaaAggctgaaccattgcgtcagg	13	8	15	5	1	1	1	1	1	0	0	1	3	1	3	1	5	2	3	1	5	5	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr22:36206007A>G	ENST00000438146.2	-	3	281	c.282T>C	c.(280-282)ccT>ccC	p.P94P	RBFOX2_ENST00000416721.2_Silent_p.P24P|RBFOX2_ENST00000262829.7_Silent_p.P24P|RBFOX2_ENST00000359369.4_Silent_p.P4P|RBFOX2_ENST00000414461.2_Silent_p.P24P|RBFOX2_ENST00000405409.2_Silent_p.P24P|RBFOX2_ENST00000449924.2_Silent_p.P24P|RBFOX2_ENST00000397303.2_Silent_p.P4P	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	34					dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						TGGTAGTAAAAGGCTGAACCA	0.473																																					p.P94P		.											.	RBFOX2-90	0			c.T282C						.						148	133	138					22																	36206007		2203	4300	6503	SO:0001819	synonymous_variant	23543	exon3			AGTAAAAGGCTGA	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"RNA binding motif (RRM) containing"	9906	protein-coding gene	gene with protein product	"hexaribonucleotide binding protein 2"	612149	"RNA binding motif protein 9"	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.282T>C	22.37:g.36206007A>G		Somatic	172	1		WXS	Illumina HiSeq	Phase_I	131	58	NM_001082579	0	0	25	49	24	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Silent	SNP	ENST00000438146.2	37	CCDS43013.1																																																																																			.		0.473	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3			G	36206007	A	G	36206007	2	3	129	1	0	0	0	0	0	0	0	1	13179	59	3	3		3	RBM9	22	36206007	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08		36206007	15098559	62	11340											
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu	37	chrX	44920581	44920581	+	Frame_Shift_Del	DEL	A	A	-																															ttcctcagaatacttctgacAattggagtggtggacatgct																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chrX:44920581delA	ENST00000377967.4	+	14	1383	c.1342delA	c.(1342-1344)aatfs	p.N448fs	KDM6A_ENST00000543216.1_Frame_Shift_Del_p.N403fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.N455fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.N403fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	448	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TACTTCTGACAATTGGAGTGG	0.348			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.N448fs	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.1342delA						.						58	47	51					X																	44920581		2203	4300	6503	SO:0001589	frameshift_variant	7403	exon14			.	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.1342delA	X.37:g.44920581delA	ENSP00000367203:p.Asn448fs	Somatic	11	0		WXS	Illumina HiSeq	Phase_I	15	14	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																			.		0.348	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44920581	A	-	44920581	7	5	129	1	0	1	0	1	0	0	0	0	8158	130	5	0	1396	0	KDM6A	23	44920581	Frame_Shift_Del	DEL	A	TCGA-HE-7129-01A-11D-1961-08		44920581	110349979	63	11341											
EMD	2010	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	153609241	153609241	+	Splice_Site	DEL	G	G	-																															tgctcccctcttttgcctcaGggaacgccccatgtacggcc																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chrX:153609241delG	ENST00000369842.4	+	6	737		c.e6-1		EMD_ENST00000369835.3_Splice_Site|EMD_ENST00000492448.1_Splice_Site	NM_000117.2	NP_000108.1	P50402	EMD_HUMAN	emerin						cellular response to growth factor stimulus (GO:0071363)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fibroblast proliferation (GO:0048147)|positive regulation of protein export from nucleus (GO:0046827)|regulation of canonical Wnt signaling pathway (GO:0060828)|skeletal muscle cell differentiation (GO:0035914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	actin binding (GO:0003779)|beta-tubulin binding (GO:0048487)			lung(5)	5	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)					TTTTGCCTCAGGGAACGCCCC	0.622																																					.		.											.	EMD-130	0			c.450-1G>-						.						77	67	71					X																	153609241		2203	4300	6503	SO:0001630	splice_region_variant	2010	exon6			.	X82434	CCDS14745.1	Xq27.3-q28	2014-09-17	2008-07-29		ENSG00000102119	ENSG00000102119			3331	protein-coding gene	gene with protein product	"LEM domain containing 5"	300384	"Emery-Dreifuss muscular dystrophy"				Standard	NM_000117		Approved	STA, LEMD5	uc004fkl.3	P50402	OTTHUMG00000033186	ENST00000369842.4:c.450-1G>-	X.37:g.153609241delG		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	45	40	NM_000117	0	0	0	0	0	Q6FI02	Splice_Site	DEL	ENST00000369842.4	37	CCDS14745.1																																																																																			.		0.622	EMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080921.1		Intron	-	153609241	G	-	153609241	8	5	129	1	0	1	0	1	0	0	1	0	5100	1014	35	0	471	0	EMD	23	153609241	Splice_Site	DEL	G	TCGA-HE-7129-01A-11D-1961-08	108688660	153609241	1661319	64	11342											
PEX10	5192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	2341814	2341814	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgggagcttctacctgcAagtgtggtgaggccaaagta	9	9	14	9	1	1	1	0	1	1	0	1	2	1	2	3	3	3	3	3	3	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:2341814A>C	ENST00000447513.2	-	2	257	c.189T>G	c.(187-189)ctT>ctG	p.L63L	PEX10_ENST00000288774.3_Silent_p.L63L|PEX10_ENST00000515760.1_5'Flank|PEX10_ENST00000507596.1_Silent_p.L63L	NM_002617.3	NP_002608.1	O60683	PEX10_HUMAN	peroxisomal biogenesis factor 10	63					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	integral component of peroxisomal membrane (GO:0005779)|intracellular (GO:0005622)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	7	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		TTCTACCTGCAAGTGTGGTGA	0.597																																					p.L63L	GBM(12;9 508 1649 13619)	.											.	PEX10-90	0			c.T189G						.						99	86	91					1																	2341814		2203	4300	6503	SO:0001819	synonymous_variant	5192	exon2			ACCTGCAAGTGTG	AF060502	CCDS41.1, CCDS44045.1	1p36.32	2013-01-09	2008-08-26		ENSG00000157911	ENSG00000157911		"RING-type (C3HC4) zinc fingers"	8851	protein-coding gene	gene with protein product		602859	"peroxisome biogenesis factor 10"			9683594	Standard	NM_002617		Approved	RNF69	uc001ajg.3	O60683	OTTHUMG00000001637	ENST00000447513.2:c.189T>G	1.37:g.2341814A>C		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	61	25	NM_002617	0	0	1	1	0	B3KWD8|Q5T095|Q9BW90	Silent	SNP	ENST00000447513.2	37	CCDS44045.1																																																																																			.		0.597	PEX10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367454.1	NM_153818		C	2341814	A	C	2341814	2	2	130	1	0	0	0	0	0	0	0	1	11762	117	5	5		5	PEX10	1	2341814	Silent	SNP	A	TCGA-HE-7130-01A-11D-1961-08		2341814	246908807	1	11343											
KIF1B	23095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10431203	10431203	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcggtttgcttccagttgtCtgatatctctccaattggac	6	17	8	10	1	2	1	0	1	2	0	6	2	4	2	2	2	1	3	2	2	2	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:10431203C>T	ENST00000377086.1	+	45	5031	c.4829C>T	c.(4828-4830)tCt>tTt	p.S1610F	KIF1B_ENST00000263934.6_Missense_Mutation_p.S1564F|KIF1B_ENST00000377081.1_Missense_Mutation_p.S1610F			O60333	KIF1B_HUMAN	kinesin family member 1B	1610					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TTCCAGTTGTCTGATATCTCT	0.488																																					p.S1564F		.											.	KIF1B-93	0			c.C4691T						.						139	121	127					1																	10431203		2203	4300	6503	SO:0001583	missense	23095	exon43			AGTTGTCTGATAT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.4829C>T	1.37:g.10431203C>T	ENSP00000366290:p.Ser1610Phe	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	180	45	NM_015074	0	0	0	0	0	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	C	26.3	4.719966	0.89205	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.11712	2.75;2.75;2.75	5.53	5.53	0.82687	.	0.060274	0.64402	D	0.000002	T	0.22126	0.0533	N	0.19112	0.55	0.80722	D	1	D;P;D;D;P;D	0.76494	0.966;0.744;0.999;0.972;0.952;0.994	P;B;D;P;B;D	0.74348	0.641;0.289;0.959;0.845;0.288;0.983	T	0.02868	-1.1100	10	0.72032	D	0.01	.	19.8228	0.96604	0.0:1.0:0.0:0.0	.	1596;1570;1610;1584;1610;1564	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	F	1610;1564;1610;1610	ENSP00000263934:S1564F;ENSP00000366290:S1610F;ENSP00000366284:S1610F	ENSP00000263934:S1564F	S	+	2	0	KIF1B	10353790	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	7.445000	0.80570	2.759000	0.94783	0.650000	0.86243	TCT	.		0.488	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10431203	C	T	10431203	3	4	130	1	0	0	0	0	1	0	0	0	8305	913	32	2	6346	2	KIF1B	1	10431203	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	8089389	10431203	238819418	2	11344											
C1orf187	374946	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11775243	11775243	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcctcaacaacaaatgcttCgatgactgcatgtgtgtgga	11	10	11	9	1	1	1	1	1	0	0	2	3	1	2	1	2	4	2	1	2	3	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:11775243C>T	ENST00000294485.5	+	6	1050	c.915C>T	c.(913-915)ttC>ttT	p.F305F		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		ACAAATGCTTCGATGACTGCA	0.582																																					p.F305F		.											.	.	0			c.C915T						.						180	135	150					1																	11775243		2203	4300	6503	SO:0001819	synonymous_variant	374946	exon6			ATGCTTCGATGAC	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"dorsal repulsive axon guidance protein", "neural tissue-specific cysteine-rich protein"	612682	"chromosome 1 open reading frame 187"	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.915C>T	1.37:g.11775243C>T		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	171	29	NM_198545	0	0	2	2	0		Silent	SNP	ENST00000294485.5	37	CCDS135.1																																																																																			.		0.582	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545		T	11775243	C	T	11775243	2	4	130	1	0	0	0	0	0	0	0	1	2027	883	31	1		1	C1orf187	1	11775243	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1344040	11775243	237475378	3	11345											
CASP9	842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15844625	15844625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgacatcaccaaatcctccaGaaccaatgtccactggtctg	12	8	6	15	1	2	1	1	0	1	1	5	2	5	1	5	1	1	0	5	1	3	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:15844625G>A	ENST00000333868.5	-	2	492	c.398C>T	c.(397-399)tCt>tTt	p.S133F	CASP9_ENST00000546424.1_Missense_Mutation_p.S133F|CASP9_ENST00000348549.5_Missense_Mutation_p.S133F|CASP9_ENST00000469637.1_5'Flank|CASP9_ENST00000375890.4_Missense_Mutation_p.S50F	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	133					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		AAATCCTCCAGAACCAATGTC	0.517																																					p.S133F		.											.	CASP9-1083	0			c.C398T						.						114	100	105					1																	15844625		2203	4300	6503	SO:0001583	missense	842	exon2			CCTCCAGAACCAA	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"Caspases", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 56"	602234	"caspase 9, apoptosis-related cysteine protease"			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.398C>T	1.37:g.15844625G>A	ENSP00000330237:p.Ser133Phe	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	203	36	NM_001229	0	0	43	55	12	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	.	.	.	.	.	.	.	.	.	.	G	8.539	0.872713	0.17322	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000375890;ENST00000447522;ENST00000440484	T;T;T;T;T;T	0.09445	4.56;4.58;2.98;4.47;3.81;3.51	4.77	3.83	0.44106	.	1.470630	0.03659	N	0.242280	T	0.24586	0.0596	L	0.50333	1.59	0.09310	N	1	D;P;B	0.54207	0.965;0.695;0.137	P;B;B	0.54312	0.748;0.231;0.087	T	0.20042	-1.0287	10	0.66056	D	0.02	.	10.9008	0.47051	0.0:0.1903:0.8097:0.0	.	133;133;133	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	F	133;133;133;50;50;133	ENSP00000449584:S133F;ENSP00000330237:S133F;ENSP00000255256:S133F;ENSP00000365051:S50F;ENSP00000396540:S50F;ENSP00000411304:S133F	ENSP00000330237:S133F	S	-	2	0	CASP9	15717212	0.022000	0.18835	0.150000	0.22450	0.099000	0.18886	1.320000	0.33666	1.330000	0.45394	0.563000	0.77884	TCT	.		0.517	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996		A	15844625	G	A	15844625	3	1	130	1	0	0	0	0	1	0	0	0	2685	942	33	2	884	2	CASP9	1	15844625	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	4069382	15844625	233405996	4	11346											
EIF4G3	8672	hgsc.bcm.edu;broad.mit.edu	37	chr1	21188793	21188793	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttctttctttcacaattttCtccatctgattaaagtactg	9	20	3	9	0	5	1	1	1	4	0	6	1	5	1	1	0	1	1	1	0	4	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:21188793C>G	ENST00000264211.8	-	17	3065	c.2871G>C	c.(2869-2871)gaG>gaC	p.E957D	EIF4G3_ENST00000536266.1_Missense_Mutation_p.E561D|EIF4G3_ENST00000537738.1_Missense_Mutation_p.E447D|EIF4G3_ENST00000374937.3_Missense_Mutation_p.E963D|EIF4G3_ENST00000400422.1_Missense_Mutation_p.E957D|EIF4G3_ENST00000602326.1_Missense_Mutation_p.E963D|EIF4G3_ENST00000374935.3_Missense_Mutation_p.E677D	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	957	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.|eIF3/EIF4A-binding. {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TCACAATTTTCTCCATCTGAT	0.353																																					p.E993D		.											.	EIF4G3-91	0			c.G2979C						.						123	119	121					1																	21188793		2203	4300	6503	SO:0001583	missense	8672	exon21			AATTTTCTCCATC	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.2871G>C	1.37:g.21188793C>G	ENSP00000264211:p.Glu957Asp	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	83	6	NM_001198801	0	0	21	22	1	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240150	0.58995	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81	5.56	1.54	0.23209	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.122140	0.56097	D	0.000022	T	0.34454	0.0898	L	0.37561	1.115	0.80722	D	1	D;B;B;D;B	0.89917	1.0;0.035;0.0;0.999;0.392	D;B;B;D;B	0.85130	0.997;0.05;0.011;0.994;0.173	T	0.01484	-1.1343	10	0.27785	T	0.31	-16.9367	9.6933	0.40143	0.0:0.7145:0.0:0.2855	.	1152;677;561;963;957	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	D	957;1153;957;677;447;963;561	ENSP00000264211:E957D;ENSP00000383274:E957D;ENSP00000364071:E677D;ENSP00000442010:E447D;ENSP00000364073:E963D;ENSP00000444693:E561D	ENSP00000264211:E957D	E	-	3	2	EIF4G3	21061380	0.678000	0.27586	0.998000	0.56505	0.983000	0.72400	-0.070000	0.11523	0.025000	0.15241	-0.808000	0.03180	GAG	.		0.353	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		G	21188793	C	G	21188793	3	3	130	1	0	0	0	0	1	0	0	0	5051	912	32	4	1946	4	EIF4G3	1	21188793	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5344168	21188793	228061828	5	11347											
EIF4G3	8672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	21226358	21226358	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggtcagaggggtctctttCaggatgaaacccctggctca	9	10	12	10	0	4	2	3	1	1	1	5	3	4	3	2	5	1	1	2	5	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:21226358C>A	ENST00000264211.8	-	10	1857	c.1663G>T	c.(1663-1665)Gaa>Taa	p.E555*	EIF4G3_ENST00000536266.1_Nonsense_Mutation_p.E159*|EIF4G3_ENST00000537738.1_Nonsense_Mutation_p.E8*|EIF4G3_ENST00000374937.3_Nonsense_Mutation_p.E561*|EIF4G3_ENST00000400422.1_Nonsense_Mutation_p.E555*|EIF4G3_ENST00000602326.1_Nonsense_Mutation_p.E561*|EIF4G3_ENST00000544689.1_Nonsense_Mutation_p.E98*|EIF4G3_ENST00000374935.3_Nonsense_Mutation_p.E275*|EIF4G3_ENST00000374933.3_5'UTR	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	555					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GGGTCTCTTTCAGGATGAAAC	0.403																																					p.E561X		.											.	EIF4G3-91	0			c.G1681T						.						163	174	170					1																	21226358		2203	4300	6503	SO:0001587	stop_gained	8672	exon14			CTCTTTCAGGATG	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.1663G>T	1.37:g.21226358C>A	ENSP00000264211:p.Glu555*	Somatic	300	1		WXS	Illumina HiSeq	Phase_I	212	50	NM_001198802	0	0	17	17	0	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Nonsense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	37	6.423410	0.97555	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266;ENST00000374933;ENST00000544689	.	.	.	5.72	5.72	0.89469	.	0.733486	0.13569	N	0.378186	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-6.563	12.2565	0.54627	0.0:0.9228:0.0:0.0772	.	.	.	.	X	555;751;555;275;8;561;159;98;98	.	ENSP00000264211:E555X	E	-	1	0	EIF4G3	21098945	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	5.084000	0.64462	2.711000	0.92665	0.644000	0.83932	GAA	.		0.403	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		A	21226358	C	A	21226358	4	1	130	1	0	0	0	0	0	1	0	0	5051	835	29	4	3182	4	EIF4G3	1	21226358	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	37565	21226358	228024263	6	11348											
EIF4G3	8672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	21226427	21226427	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtcaatggaaagctcctcttCagctttaagctaaataataa	15	12	6	8	0	3	0	2	0	1	0	4	1	4	1	1	1	3	3	1	1	7	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:21226427C>T	ENST00000264211.8	-	10	1788	c.1594G>A	c.(1594-1596)Gaa>Aaa	p.E532K	EIF4G3_ENST00000536266.1_Missense_Mutation_p.E136K|EIF4G3_ENST00000537738.1_5'Flank|EIF4G3_ENST00000374937.3_Missense_Mutation_p.E538K|EIF4G3_ENST00000400422.1_Missense_Mutation_p.E532K|EIF4G3_ENST00000602326.1_Missense_Mutation_p.E538K|EIF4G3_ENST00000544689.1_Missense_Mutation_p.E75K|EIF4G3_ENST00000374935.3_Missense_Mutation_p.E252K|EIF4G3_ENST00000374933.3_5'UTR	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	532					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		AGCTCCTCTTCAGCTTTAAGC	0.358																																					p.E538K		.											.	EIF4G3-91	0			c.G1612A						.						95	103	100					1																	21226427		2202	4300	6502	SO:0001583	missense	8672	exon14			CCTCTTCAGCTTT	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.1594G>A	1.37:g.21226427C>T	ENSP00000264211:p.Glu532Lys	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	164	38	NM_001198802	0	0	0	0	0	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854237	0.51270	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000374937;ENST00000536266;ENST00000374933;ENST00000544689	T;T;T;T;T;D	0.87412	2.05;2.05;1.94;2.05;2.05;-2.25	4.98	4.06	0.47325	.	0.426295	0.27143	N	0.020740	T	0.74809	0.3765	N	0.08118	0	0.80722	D	1	P;P;B;P;B	0.47762	0.9;0.651;0.007;0.546;0.376	B;B;B;B;B	0.40285	0.325;0.115;0.006;0.049;0.099	T	0.78458	-0.2196	10	0.52906	T	0.07	-18.3664	13.2326	0.59951	0.0:0.9233:0.0:0.0767	.	727;252;136;538;532	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	K	532;728;532;252;538;136;75;75	ENSP00000264211:E532K;ENSP00000383274:E532K;ENSP00000364071:E252K;ENSP00000364073:E538K;ENSP00000444693:E136K;ENSP00000444401:E75K	ENSP00000264211:E532K	E	-	1	0	EIF4G3	21099014	0.999000	0.42202	0.967000	0.41034	0.284000	0.27059	5.276000	0.65580	1.325000	0.45301	0.644000	0.83932	GAA	.		0.358	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		T	21226427	C	T	21226427	3	4	130	1	0	0	0	0	1	0	0	0	5051	835	29	2	3251	2	EIF4G3	1	21226427	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	69	21226427	228024194	7	11349											
CDC42	998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22413230	22413230	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttgggactcaaattgatctCagagatgacccctctactat	11	12	8	10	0	3	3	2	2	2	1	4	5	3	4	2	1	1	1	2	1	3	4	rs143448220		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:22413230C>G	ENST00000344548.3	+	6	608	c.357C>G	c.(355-357)ctC>ctG	p.L119L	CDC42_ENST00000315554.8_Silent_p.L119L|CDC42_ENST00000421089.2_Silent_p.L161L|CDC42_ENST00000400259.1_Silent_p.L119L|CDC42_ENST00000498236.1_3'UTR	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	119					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		AAATTGATCTCAGAGATGACC	0.438																																					p.L119L		.											.	CDC42-1084	0			c.C357G						.						167	181	177					1																	22413230		2203	4300	6503	SO:0001819	synonymous_variant	998	exon6			TGATCTCAGAGAT	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.357C>G	1.37:g.22413230C>G		Somatic	383	0		WXS	Illumina HiSeq	Phase_I	285	72	NM_001039802	0	0	207	304	97	P21181|P25763|Q7L8R5|Q9UDI2	Silent	SNP	ENST00000344548.3	37	CCDS221.1																																																																																			C|1.000;T|0.000		0.438	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		G	22413230	C	G	22413230	2	3	130	1	0	0	0	0	0	0	0	1	3077	813	29	4		4	CDC42	1	22413230	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1186803	22413230	226837391	8	11350											
CDC42	998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22413329	22413329	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcccgtgacctgaaggctgtCaagtatgtggagtgttctgc	7	11	14	9	1	2	2	1	2	1	0	2	3	2	3	2	2	1	3	2	2	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:22413329C>G	ENST00000344548.3	+	6	707	c.456C>G	c.(454-456)gtC>gtG	p.V152V	CDC42_ENST00000315554.8_Silent_p.V152V|CDC42_ENST00000421089.2_Silent_p.V194V|CDC42_ENST00000400259.1_Silent_p.V152V|CDC42_ENST00000498236.1_3'UTR	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	152					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		TGAAGGCTGTCAAGTATGTGG	0.448																																					p.V152V		.											.	CDC42-1084	0			c.C456G						.						148	150	149					1																	22413329		2203	4300	6503	SO:0001819	synonymous_variant	998	exon6			GGCTGTCAAGTAT	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.456C>G	1.37:g.22413329C>G		Somatic	306	0		WXS	Illumina HiSeq	Phase_I	245	62	NM_001039802	0	0	173	236	63	P21181|P25763|Q7L8R5|Q9UDI2	Silent	SNP	ENST00000344548.3	37	CCDS221.1																																																																																			.		0.448	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		G	22413329	C	G	22413329	2	3	130	1	0	0	0	0	0	0	0	1	3077	813	29	4		4	CDC42	1	22413329	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	99	22413329	226837292	9	11351											
INPP5B	3633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38328025	38328025	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaactggtgaataaattcttGagccttcttcttctctgtca	9	16	7	9	0	5	2	1	2	4	0	6	3	5	2	1	1	2	0	1	1	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:38328025G>C	ENST00000373026.1	-	23	2944	c.2944C>G	c.(2944-2946)Caa>Gaa	p.Q982E	INPP5B_ENST00000373027.1_Missense_Mutation_p.Q738E|MTF1_ENST00000373036.4_5'Flank|INPP5B_ENST00000373024.3_Missense_Mutation_p.Q902E|INPP5B_ENST00000373023.2_Missense_Mutation_p.Q982E|RP11-109P14.10_ENST00000419993.1_RNA			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	982	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ATAAATTCTTGAGCCTTCTTC	0.453																																					p.Q902E		.											.	INPP5B-227	0			c.C2704G						.						121	118	119					1																	38328025		1860	4104	5964	SO:0001583	missense	3633	exon24			ATTCTTGAGCCTT	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"inositol polyphosphate-5-phosphatase, 75kD"			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.2944C>G	1.37:g.38328025G>C	ENSP00000362117:p.Gln982Glu	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	131	19	NM_005540	0	0	6	10	4	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		.	.	.	.	.	.	.	.	.	.	G	14.26	2.482316	0.44147	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373026;ENST00000373024	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.45637	0.1352	L	0.56769	1.78	0.80722	D	1	P	0.44241	0.829	B	0.43274	0.414	T	0.23368	-1.0190	10	0.17832	T	0.49	.	20.054	0.97641	0.0:0.0:1.0:0.0	.	902	P32019-2	.	E	738;982;982;902	ENSP00000362118:Q738E;ENSP00000362114:Q982E;ENSP00000362117:Q982E;ENSP00000362115:Q902E	ENSP00000362114:Q982E	Q	-	1	0	INPP5B	38100612	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.101000	0.89546	2.808000	0.96608	0.655000	0.94253	CAA	.		0.453	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		C	38328025	G	C	38328025	3	2	130	1	0	0	0	0	1	0	0	0	7776	1299	45	4	41	4	INPP5B	1	38328025	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	15914696	38328025	210922596	10	11352											
INPP5B	3633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38338748	38338748	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgtccaagtgcagaaccaGaatgtcctcaattttgtctt	10	13	7	11	0	2	2	1	0	1	2	4	2	4	2	4	0	2	1	4	0	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:38338748G>A	ENST00000373026.1	-	18	2281	c.2281C>T	c.(2281-2283)Ctg>Ttg	p.L761L	INPP5B_ENST00000373027.1_Silent_p.L517L|INPP5B_ENST00000373024.3_Silent_p.L681L|INPP5B_ENST00000373023.2_Silent_p.L761L			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	761	ASH. {ECO:0000250}.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TGCAGAACCAGAATGTCCTCA	0.438																																					p.L681L		.											.	INPP5B-227	0			c.C2041T						.						207	193	198					1																	38338748		1876	4120	5996	SO:0001819	synonymous_variant	3633	exon19			GAACCAGAATGTC	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"inositol polyphosphate-5-phosphatase, 75kD"			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.2281C>T	1.37:g.38338748G>A		Somatic	207	0		WXS	Illumina HiSeq	Phase_I	188	31	NM_005540	0	0	8	9	1	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37																																																																																				.		0.438	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		A	38338748	G	A	38338748	2	1	130	1	0	0	0	0	0	0	0	1	7776	933	33	2		2	INPP5B	1	38338748	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10723	38338748	210911873	11	11353											
BMP8A	353500	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	39991443	39991443	+	Frame_Shift_Del	DEL	G	G	-																															ctgcgcaagcaccgcaacatGgtggtcaaggcctgcggctg																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:39991443delG	ENST00000331593.5	+	7	1528	c.1182delG	c.(1180-1182)atgfs	p.M394fs	RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000417869.1_RNA|RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000440190.1_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	394					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|diet induced thermogenesis (GO:0002024)|growth (GO:0040007)|negative regulation of insulin secretion (GO:0046676)|ossification (GO:0001503)|regulation of energy homeostasis (GO:2000505)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(1)|skin(1)	5	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACCGCAACATGGTGGTCAAGG	0.612																																					p.M394fs		.											.	BMP8A-90	0			c.1182delG						.						135	111	119					1																	39991443		2203	4300	6503	SO:0001589	frameshift_variant	353500	exon7			.	AY303954	CCDS437.1	1p35-p32	2014-01-30			ENSG00000183682	ENSG00000183682		"Bone morphogenetic proteins", "Endogenous ligands"	21650	protein-coding gene	gene with protein product							Standard	NM_181809		Approved		uc001cdi.3	Q7Z5Y6	OTTHUMG00000008394	ENST00000331593.5:c.1182delG	1.37:g.39991443delG	ENSP00000327440:p.Met394fs	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	171	35	NM_181809	0	0	0	0	0	Q5T3A5	Frame_Shift_Del	DEL	ENST00000331593.5	37	CCDS437.1																																																																																			.		0.612	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809		-	39991443	G	-	39991443	7	5	130	1	0	1	0	1	0	0	0	0	1467	1348	47	0	1208	0	BMP8A	1	39991443	Frame_Shift_Del	DEL	G	TCGA-HE-7130-01A-11D-1961-08	1652695	39991443	209259178	12	11354											
PTPRF	5792	broad.mit.edu;bcgsc.ca	37	chr1	44063474	44063474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agcatgggctccaccacggtCcgggtaagttgggtcccgcc	6	7	14	14	3	0	0	0	0	0	0	3	0	3	0	5	4	1	4	5	4	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:44063474C>T	ENST00000359947.4	+	12	2209	c.1869C>T	c.(1867-1869)gtC>gtT	p.V623V	PTPRF_ENST00000438120.1_Silent_p.V623V|PTPRF_ENST00000422171.2_Intron|PTPRF_ENST00000372414.3_Silent_p.V623V|PTPRF_ENST00000372413.3_Silent_p.V623V	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	623	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCACCACGGTCCGGGTAAGTT	0.687																																					p.V623V													.	PTPRF-232	0			c.C1869T						.						23	23	23					1																	44063474		2203	4299	6502	SO:0001819	synonymous_variant	5792	exon12			CACGGTCCGGGTA	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.1869C>T	1.37:g.44063474C>T		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	27	15	NM_002840	0	0	159	348	189	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	.	.	.	.	.	.	.	.	.	.	C	9.661	1.144186	0.21205	.	.	ENSG00000142949	ENST00000429895	.	.	.	3.36	2.43	0.29744	.	.	.	.	.	T	0.59649	0.2209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54403	-0.8299	4	.	.	.	.	10.5636	0.45161	0.0:0.9017:0.0:0.0983	.	.	.	.	F	280	.	.	S	+	2	0	PTPRF	43836061	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	1.537000	0.36083	0.544000	0.28883	0.313000	0.20887	TCC	.		0.687	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44063474	C	T	44063474	2	4	130	1	0	0	0	0	0	0	0	1	12833	842	30	2		2	PTPRF	1	44063474	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4072031	44063474	205187147	13	11355											
PTPRF	5792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	44063522	44063522	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacagccgcaacggcgttatCacccagtactccgtggccta	9	7	10	15	4	1	0	1	0	0	0	2	1	2	0	4	2	3	3	4	2	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:44063522C>T	ENST00000359947.4	+	12	2257	c.1917C>T	c.(1915-1917)atC>atT	p.I639I	PTPRF_ENST00000438120.1_Silent_p.I639I|PTPRF_ENST00000422171.2_Intron|PTPRF_ENST00000372414.3_Silent_p.I639I|PTPRF_ENST00000372413.3_Silent_p.I639I	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	639	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACGGCGTTATCACCCAGTACT	0.682																																					p.I639I		.											.	PTPRF-232	0			c.C1917T						.						36	35	35					1																	44063522		2203	4299	6502	SO:0001819	synonymous_variant	5792	exon12			CGTTATCACCCAG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.1917C>T	1.37:g.44063522C>T		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	30	17	NM_002840	0	1	193	428	234	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	.	.	.	.	.	.	.	.	.	.	C	6.416	0.444943	0.12164	.	.	ENSG00000142949	ENST00000429895	.	.	.	3.36	2.39	0.29439	.	.	.	.	.	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50101	-0.8867	4	.	.	.	.	6.7821	0.23652	0.1746:0.725:0.0:0.1004	.	.	.	.	L	296	.	.	S	+	2	0	PTPRF	43836109	0.931000	0.31567	0.996000	0.52242	0.537000	0.34900	0.201000	0.17276	1.613000	0.50231	0.313000	0.20887	TCA	.		0.682	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44063522	C	T	44063522	2	4	130	1	0	0	0	0	0	0	0	1	12833	816	29	2		2	PTPRF	1	44063522	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	48	44063522	205187099	14	11356											
CCDC18	343099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	93705376	93705376	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttaagacaactccaggaattGagagatgtactacagaaggc	16	8	10	7	0	0	4	0	1	0	3	1	6	1	5	1	2	3	1	1	2	6	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:93705376G>C	ENST00000343253.7	+	21	3403	c.2901G>C	c.(2899-2901)ttG>ttC	p.L967F	CCDC18_ENST00000334652.5_Missense_Mutation_p.E261Q|CCDC18_ENST00000401026.3_Missense_Mutation_p.L968F|CCDC18_ENST00000338949.4_Missense_Mutation_p.L723F|CCDC18_ENST00000557479.1_Missense_Mutation_p.L1086F			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	967										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TCCAGGAATTGAGAGATGTAC	0.343																																					p.L968F		.											.	CCDC18-138	0			c.G2904C						.						100	91	94					1																	93705376		1815	4083	5898	SO:0001583	missense	343099	exon21			GGAATTGAGAGAT			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.2901G>C	1.37:g.93705376G>C	ENSP00000343377:p.Leu967Phe	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	53	8	NM_206886	0	0	3	3	0	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	17.75|17.75|17.75	3.466942|3.466942|3.466942	0.63625|0.63625|0.63625	.|.|.	.|.|.	ENSG00000122483|ENSG00000122483|ENSG00000122483	ENST00000334652|ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267|ENST00000370276	.|T;T|.	.|0.78707|.	.|-1.2;-1.2|.	5.83|5.83|5.83	5.83|5.83|5.83	0.93111|0.93111|0.93111	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000002|.	T|T|.	0.41534|0.41534|.	0.1163|0.1163|.	L|L|L	0.58101|0.58101|0.58101	1.795|1.795|1.795	0.22066|0.22066|0.22066	N|N|N	0.999385|0.999385|0.999385	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.91635|.	.|0.999;0.999|.	T|T|.	0.36986|0.36986|.	-0.9725|-0.9725|.	6|10|.	0.87932|0.62326|.	D|D|.	0|0.03|.	.|.|.	13.3361|13.3361|13.3361	0.60518|0.60518|0.60518	0.0719:0.0:0.9281:0.0|0.0719:0.0:0.9281:0.0|0.0719:0.0:0.9281:0.0	.|.|.	.|967;1086|.	.|Q5T9S5;G3V388|.	.|CCD18_HUMAN;.|.	Q|F|S	261|967;968;1086;723;643|1021	.|ENSP00000383808:L968F;ENSP00000451099:L1086F|.	ENSP00000334084:E261Q|ENSP00000344380:L723F|.	E|L|X	+|+|+	1|3|2	0|2|2	CCDC18|CCDC18|CCDC18	93477964|93477964|93477964	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.996000|0.996000|0.996000	0.88848|0.88848|0.88848	1.479000|1.479000|1.479000	0.35453|0.35453|0.35453	2.749000|2.749000|2.749000	0.94314|0.94314|0.94314	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	GAG|TTG|TGA	.		0.343	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		C	93705376	G	C	93705376	3	2	130	1	0	0	0	0	1	0	0	0	2800	1281	45	4	3340	4	CCDC18	1	93705376	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	49641854	93705376	155545245	15	11357											
DDX20	11218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	112309171	112309171	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagtgacacccccaatccaGagaaatatcaagaatcacct	17	6	6	12	0	2	3	2	1	0	2	3	5	3	3	4	0	0	0	4	0	6	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:112309171G>A	ENST00000369702.4	+	11	2745	c.2125G>A	c.(2125-2127)Gag>Aag	p.E709K	DDX20_ENST00000475700.1_Missense_Mutation_p.E317K	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	709					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCCCAATCCAGAGAAATATCA	0.478																																					p.E709K		.											.	DDX20-227	0			c.G2125A						.						68	71	70					1																	112309171		2203	4299	6502	SO:0001583	missense	11218	exon11			AATCCAGAGAAAT	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2125G>A	1.37:g.112309171G>A	ENSP00000358716:p.Glu709Lys	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	123	38	NM_007204	0	0	6	8	2	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	.	.	.	.	.	.	.	.	.	.	G	4.428	0.079164	0.08533	.	.	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.35048	1.33;1.89	5.71	5.71	0.89125	.	1.938660	0.01863	N	0.036737	T	0.13457	0.0326	N	0.19112	0.55	0.23893	N	0.996542	B;B	0.30973	0.302;0.09	B;B	0.33620	0.167;0.016	T	0.19289	-1.0310	9	.	.	.	0.764	8.6694	0.34140	0.0762:0.0:0.7714:0.1524	.	317;709	E9PJ60;Q9UHI6	.;DDX20_HUMAN	K	709;317	ENSP00000358716:E709K;ENSP00000435660:E317K	.	E	+	1	0	DDX20	112110694	0.080000	0.21391	0.034000	0.17996	0.052000	0.14988	2.490000	0.45294	2.703000	0.92315	0.655000	0.94253	GAG	.		0.478	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		A	112309171	G	A	112309171	3	1	130	1	0	0	0	0	1	0	0	0	4354	943	33	2	2167	2	DDX20	1	112309171	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	18603795	112309171	136941450	16	11358											
DDX20	11218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	112309315	112309315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccaggaagatgattggtatGactgtcatagggaaatacgt	13	10	12	6	1	1	3	1	2	0	1	1	5	1	5	1	3	1	1	1	3	5	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:112309315G>A	ENST00000369702.4	+	11	2889	c.2269G>A	c.(2269-2271)Gac>Aac	p.D757N	DDX20_ENST00000475700.1_Missense_Mutation_p.D365N	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	757					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATTGGTATGACTGTCATAG	0.478																																					p.D757N		.											.	DDX20-227	0			c.G2269A						.						101	100	100					1																	112309315		2203	4300	6503	SO:0001583	missense	11218	exon11			TGGTATGACTGTC	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"DEAD-boxes"	2743	protein-coding gene	gene with protein product		606168	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2269G>A	1.37:g.112309315G>A	ENSP00000358716:p.Asp757Asn	Somatic	70	2		WXS	Illumina HiSeq	Phase_I	132	39	NM_007204	0	0	10	10	0	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512691	0.44660	.	.	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.35789	1.29;1.76	5.6	3.73	0.42828	.	0.820184	0.11606	N	0.547319	T	0.17238	0.0414	L	0.56769	1.78	0.44694	D	0.997688	B;B	0.29085	0.232;0.028	B;B	0.29176	0.099;0.018	T	0.04678	-1.0934	9	.	.	.	-7.2593	7.781	0.29064	0.144:0.1328:0.7233:0.0	.	365;757	E9PJ60;Q9UHI6	.;DDX20_HUMAN	N	757;365	ENSP00000358716:D757N;ENSP00000435660:D365N	.	D	+	1	0	DDX20	112110838	0.454000	0.25728	0.673000	0.29887	0.131000	0.20780	1.414000	0.34736	0.738000	0.32606	0.655000	0.94253	GAC	.		0.478	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		A	112309315	G	A	112309315	3	1	130	1	0	0	0	0	1	0	0	0	4354	1290	45	2	2311	2	DDX20	1	112309315	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	144	112309315	136941306	17	11359											
ST7L	54879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	113124686	113124686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagtgattctaagagattttCatggatgttcaacatggtaa	14	14	9	4	0	3	2	2	1	1	1	3	4	3	3	0	2	1	2	0	2	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:113124686C>T	ENST00000358039.4	-	9	1301	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	ST7L_ENST00000490067.1_Missense_Mutation_p.E316K|ST7L_ENST00000538187.1_Missense_Mutation_p.E277K|ST7L_ENST00000369668.2_Missense_Mutation_p.E333K|ST7L_ENST00000544629.1_Missense_Mutation_p.E268K|ST7L_ENST00000343210.7_Missense_Mutation_p.E333K|ST7L_ENST00000360743.4_Missense_Mutation_p.E333K|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000543570.1_Missense_Mutation_p.E316K|ST7L_ENST00000369669.1_Missense_Mutation_p.E150K|ST7L_ENST00000369666.1_Missense_Mutation_p.E316K	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	333					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGAGATTTTCATGGATGTTC	0.343																																					p.E333K		.											.	ST7L-90	0			c.G997A						.						107	107	107					1																	113124686		2203	4299	6502	SO:0001583	missense	54879	exon9			GATTTTCATGGAT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.997G>A	1.37:g.113124686C>T	ENSP00000350734:p.Glu333Lys	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	129	35	NM_138728	0	0	2	2	0	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	C	34	5.381617	0.95967	.	.	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187;ENST00000543570;ENST00000369665	T;T;T;T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98	5.56	5.56	0.83823	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.45895	0.1365	M	0.82630	2.6	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.997;0.999;0.996;0.996;0.996;0.997;0.999	T	0.48980	-0.8986	10	0.62326	D	0.03	-13.6675	19.1265	0.93386	0.0:1.0:0.0:0.0	.	316;277;268;333;316;316;333;333	B7Z8V6;B7Z7D4;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;.;.;.;ST7L_HUMAN	K	333;333;268;150;316;333;333;316;277;316;211	ENSP00000350734:E333K;ENSP00000353972:E333K;ENSP00000445499:E268K;ENSP00000358683:E150K;ENSP00000417140:E316K;ENSP00000358682:E333K;ENSP00000345312:E333K;ENSP00000358680:E316K;ENSP00000444021:E277K;ENSP00000444088:E316K	ENSP00000345312:E333K	E	-	1	0	ST7L	112926209	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.618000	0.88619	0.462000	0.41574	GAA	.		0.343	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			T	113124686	C	T	113124686	3	4	130	1	0	0	0	0	1	0	0	0	15262	835	29	2	797	2	ST7L	1	113124686	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	815371	113124686	136125935	18	11360											
TXNIP	10628	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	145440057	145440059	+	In_Frame_Del	DEL	AAG	AAG	-																															ggcacctgtgtctgctaaaaAagaaaagaaagtttcctgca																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:145440057_145440059delAAG	ENST00000369317.4	+	4	825_827	c.491_493delAAG	c.(490-495)aaagaa>aaa	p.E165del	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	165					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCTGCTAAAAAAGAAAAGAAAGT	0.414																																					p.164_165del		.											.	TXNIP-92	0			c.491_493del						.																																			SO:0001651	inframe_deletion	10628	exon4			.	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"upregulated by 1,25-dihydroxyvitamin D-3", "thioredoxin binding protein 2"	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.491_493delAAG	1.37:g.145440057_145440059delAAG	ENSP00000358323:p.Glu165del	Somatic	453	0		WXS	Illumina HiSeq	Phase_I	684	383	NM_006472	0	0	0	0	0	B4E3D3|Q16226|Q6PML0|Q9BXG9	In_Frame_Del	DEL	ENST00000369317.4	37	CCDS913.1																																																																																			.		0.414	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		-	145440059	AAG	-	145440057	7	5	130	1	0	1	0	1	0	0	0	0	16836	14	1	0	505	0	TXNIP	1	145440057	In_Frame_Del	DEL	AAG	TCGA-HE-7130-01A-11D-1961-08	32315371	145440057	103810564	19	11361											
POGZ	23126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151377387	151377387	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggctcaattgtctcttcaGgagatgatctgggtcgtgga	8	12	13	8	1	4	2	2	1	2	1	6	4	4	3	0	4	0	1	0	4	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:151377387G>A	ENST00000271715.2	-	19	4438	c.4124C>T	c.(4123-4125)cCt>cTt	p.P1375L	POGZ_ENST00000531094.1_Missense_Mutation_p.P1313L|POGZ_ENST00000392723.1_Missense_Mutation_p.P1322L|POGZ_ENST00000540984.1_Missense_Mutation_p.P737L|POGZ_ENST00000361398.3_Missense_Mutation_p.P1322L|POGZ_ENST00000368863.2_Missense_Mutation_p.P1280L|POGZ_ENST00000409503.1_Missense_Mutation_p.P1366L|POGZ_ENST00000491586.1_Missense_Mutation_p.P1331L	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	1375					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGTCTCTTCAGGAGATGATCT	0.488											OREG0003905	type=REGULATORY REGION|Gene=POGZ|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.P1375L		.											.	POGZ-93	0			c.C4124T						.						101	96	98					1																	151377387		2203	4300	6503	SO:0001583	missense	23126	exon19			TCTTCAGGAGATG	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.4124C>T	1.37:g.151377387G>A	ENSP00000271715:p.Pro1375Leu	Somatic	144	0	1739	WXS	Illumina HiSeq	Phase_I	190	44	NM_015100	0	0	19	30	11	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	37	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607106	0.46527	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586	T;T;T;T;T;T;T;T	0.24908	5.79;5.82;5.79;5.76;5.8;5.8;1.83;5.28	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000003	T	0.20007	0.0481	N	0.19112	0.55	0.58432	D	0.999999	B;D;P;P;B;B	0.58268	0.164;0.982;0.763;0.465;0.253;0.267	B;P;B;B;B;B	0.53006	0.04;0.715;0.173;0.124;0.087;0.058	T	0.02098	-1.1214	10	0.66056	D	0.02	-14.1248	17.4919	0.87707	0.0:0.0:1.0:0.0	.	1313;1366;1280;1331;1322;1375	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	L	1322;1375;1322;1280;1366;1313;737;1331	ENSP00000376484:P1322L;ENSP00000271715:P1375L;ENSP00000354467:P1322L;ENSP00000357856:P1280L;ENSP00000386836:P1366L;ENSP00000431259:P1313L;ENSP00000443547:P737L;ENSP00000418408:P1331L	ENSP00000271715:P1375L	P	-	2	0	POGZ	149644011	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	6.397000	0.73239	2.780000	0.95670	0.655000	0.94253	CCT	.		0.488	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151377387	G	A	151377387	3	1	130	1	0	0	0	0	1	0	0	0	12212	1000	35	2	112	2	POGZ	1	151377387	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	5937330	151377387	97873234	20	11362											
FLG	2312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152281276	152281276	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtccactgtctctgactgcaGatgaagcttgtccatgccca	8	11	9	13	0	1	3	0	2	1	1	4	3	3	3	3	0	3	2	3	0	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:152281276G>C	ENST00000368799.1	-	3	6121	c.6086C>G	c.(6085-6087)tCt>tGt	p.S2029C	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2029	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTGACTGCAGATGAAGCTTG	0.542									Ichthyosis																												p.S2029C		.											.	FLG-106	0			c.C6086G						.						601	507	539					1																	152281276		2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTGCAGATGAAG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6086C>G	1.37:g.152281276G>C	ENSP00000357789:p.Ser2029Cys	Somatic	1055	0		WXS	Illumina HiSeq	Phase_I	1229	541	NM_002016	0	0	0	0	0	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	5.168	0.216596	0.09810	.	.	ENSG00000143631	ENST00000368799	T	0.04083	3.71	3.44	2.51	0.30379	.	.	.	.	.	T	0.07052	0.0179	M	0.61703	1.905	0.09310	N	1	D	0.76494	0.999	D	0.65684	0.937	T	0.17440	-1.0369	9	0.56958	D	0.05	.	8.6711	0.34152	0.0:0.2608:0.7392:0.0	.	2029	P20930	FILA_HUMAN	C	2029	ENSP00000357789:S2029C	ENSP00000357789:S2029C	S	-	2	0	FLG	150547900	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.118000	0.10692	0.748000	0.32831	0.485000	0.47835	TCT	.		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152281276	G	C	152281276	3	2	130	1	0	0	0	0	1	0	0	0	5941	942	33	4	6103	4	FLG	1	152281276	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	903889	152281276	96969345	21	11363											
CHRNB2	1141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154544111	154544111	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagatgacgttgtgcatctCagtgctgctggcgctcacgg	7	10	14	10	3	2	2	2	1	1	1	3	3	2	2	0	2	3	5	0	2	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:154544111C>A	ENST00000368476.3	+	5	1076	c.812C>A	c.(811-813)tCa>tAa	p.S271*		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	271					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)	p.S271*(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TTGTGCATCTCAGTGCTGCTG	0.577																																					p.S271X		.											.	CHRNB2-90	1	Substitution - Nonsense(1)	lung(1)	c.C812A						.						280	208	233					1																	154544111		2203	4300	6503	SO:0001587	stop_gained	1141	exon5			GCATCTCAGTGCT	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.812C>A	1.37:g.154544111C>A	ENSP00000357461:p.Ser271*	Somatic	225	1		WXS	Illumina HiSeq	Phase_I	281	167	NM_000748	0	0	0	0	0	Q9UEH9	Nonsense_Mutation	SNP	ENST00000368476.3	37	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	C	39	7.470747	0.98306	.	.	ENSG00000160716	ENST00000368476	.	.	.	4.1	4.1	0.47936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1089	0.81244	0.0:1.0:0.0:0.0	.	.	.	.	X	271	.	ENSP00000357461:S271X	S	+	2	0	CHRNB2	152810735	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.608000	0.82898	2.095000	0.63458	0.467000	0.42956	TCA	.		0.577	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		A	154544111	C	A	154544111	4	1	130	1	0	0	0	0	0	1	0	0	3397	838	29	4	830	4	CHRNB2	1	154544111	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2262835	154544111	94706510	22	11364											
GON4L	54856	broad.mit.edu;bcgsc.ca	37	chr1	155723185	155723185	+	Silent	SNP	G	G	A																															tcatggggctccttgctcttGtaggatttgctgtcacagac																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:155723185G>A	ENST00000368331.1	-	29	5700	c.5652C>T	c.(5650-5652)taC>taT	p.Y1884Y	GON4L_ENST00000271883.5_Silent_p.Y1884Y|GON4L_ENST00000437809.1_Silent_p.Y1884Y	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1884					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCTTGCTCTTGTAGGATTTGC	0.572																																					p.Y1884Y													.	GON4L-93	0			c.C5652T						.						111	109	110					1																	155723185		1934	4136	6070	SO:0001819	synonymous_variant	54856	exon29			GCTCTTGTAGGAT	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5652C>T	1.37:g.155723185G>A		Somatic	239	0		WXS	Illumina HiSeq	Phase_I	278	13	NM_001037533	0	0	12	12	0	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Silent	SNP	ENST00000368331.1	37																																																																																				.		0.572	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155723185	G	A	155723185	2	1	130	1	0	0	0	0	0	0	0	1	6592	1372	48	2		2	GON4L	1	155723185	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1179074	155723185	93527436	23	11365	119	2									
GON4L	54856	broad.mit.edu;bcgsc.ca	37	chr1	155723194	155723194	+	Missense_Mutation	SNP	G	G	C																															tccttgctcttgtaggatttGctgtcacagacctgcaggga																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:155723194G>C	ENST00000368331.1	-	29	5691	c.5643C>G	c.(5641-5643)agC>agG	p.S1881R	GON4L_ENST00000271883.5_Missense_Mutation_p.S1881R|GON4L_ENST00000437809.1_Missense_Mutation_p.S1881R	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1881					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TGTAGGATTTGCTGTCACAGA	0.582																																					p.S1881R													.	GON4L-93	0			c.C5643G						.						107	105	106					1																	155723194		1950	4137	6087	SO:0001583	missense	54856	exon29			GGATTTGCTGTCA	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5643C>G	1.37:g.155723194G>C	ENSP00000357315:p.Ser1881Arg	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	251	13	NM_001037533	0	0	0	0	0	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	G	15.41	2.824139	0.50739	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.10668	2.85;2.85;2.85	5.15	4.23	0.50019	.	0.195098	0.45867	D	0.000333	T	0.04770	0.0129	L	0.44542	1.39	0.34449	D	0.70051	P;P	0.38048	0.481;0.616	B;B	0.35312	0.098;0.2	T	0.23655	-1.0182	10	0.45353	T	0.12	.	13.8128	0.63273	0.0753:0.0:0.9247:0.0	.	1881;1881	Q3T8J9;Q3T8J9-3	GON4L_HUMAN;.	R	1881	ENSP00000396117:S1881R;ENSP00000357315:S1881R;ENSP00000271883:S1881R	ENSP00000271883:S1881R	S	-	3	2	GON4L	153989818	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.844000	0.62846	1.377000	0.46286	0.455000	0.32223	AGC	.		0.582	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		C	155723194	G	C	155723194	3	2	130	1	0	0	0	0	1	0	0	0	6592	1310	46	4	1095	4	GON4L	1	155723194	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	9	155723194	93527427	24	11366	119	2									
OR10Z1	128368	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158576303	158576303	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agttctggggagttgcagctCcttctctttgccttgttcct	3	17	10	11	0	2	0	0	0	2	0	5	1	4	1	3	2	3	5	3	2	0	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:158576303C>T	ENST00000361284.1	+	1	75	c.75C>T	c.(73-75)ctC>ctT	p.L25L		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AGTTGCAGCTCCTTCTCTTTG	0.498																																					p.L25L		.											.	OR10Z1-70	0			c.C75T						.						179	173	175					1																	158576303		2203	4300	6503	SO:0001819	synonymous_variant	128368	exon1			GCAGCTCCTTCTC	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"GPCR / Class A : Olfactory receptors"	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.75C>T	1.37:g.158576303C>T		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	239	34	NM_001004478	0	0	0	0	0	Q5VYL0|Q6IFR7	Silent	SNP	ENST00000361284.1	37	CCDS30901.1																																																																																			.		0.498	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576303	C	T	158576303	2	4	130	1	0	0	0	0	0	0	0	1	10949	842	30	2		2	OR10Z1	1	158576303	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2853109	158576303	90674318	25	11367											
OR6N1	128372	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158735810	158735810	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attctgagcactgtgcagatGatctgcacataggagcagag	12	9	12	8	0	2	4	0	2	2	2	2	5	2	5	0	1	4	4	0	1	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:158735810G>A	ENST00000335094.2	-	1	682	c.663C>T	c.(661-663)atC>atT	p.I221I		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					CTGTGCAGATGATCTGCACAT	0.488																																					p.I221I		.											.	OR6N1-69	0			c.C663T						.						125	124	125					1																	158735810		2203	4300	6503	SO:0001819	synonymous_variant	128372	exon1			GCAGATGATCTGC	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"GPCR / Class A : Olfactory receptors"	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.663C>T	1.37:g.158735810G>A		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	231	119	NM_001005185	0	0	0	0	0	Q5VUU8|Q96R35	Silent	SNP	ENST00000335094.2	37	CCDS30905.1																																																																																			.		0.488	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		A	158735810	G	A	158735810	2	1	130	1	0	0	0	0	0	0	0	1	11232	1280	45	2		2	OR6N1	1	158735810	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	159507	158735810	90514811	26	11368											
PYHIN1	149628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158943473	158943473	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggagcacagtcatcgcctGcaaactttagaatcacctca	13	8	7	13	1	3	1	3	0	0	1	4	2	3	2	2	1	3	2	2	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:158943473G>A	ENST00000368140.1	+	8	1641	c.1396G>A	c.(1396-1398)Gca>Aca	p.A466T	PYHIN1_ENST00000392252.3_Intron|PYHIN1_ENST00000392254.2_Intron|PYHIN1_ENST00000368138.3_Missense_Mutation_p.A457T	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	466					cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					GTCATCGCCTGCAAACTTTAG	0.448																																					p.A466T		.											.	PYHIN1-94	0			c.G1396A						.						162	144	150					1																	158943473		2203	4300	6503	SO:0001583	missense	149628	exon8			TCGCCTGCAAACT	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.1396G>A	1.37:g.158943473G>A	ENSP00000357122:p.Ala466Thr	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	105	54	NM_152501	0	0	0	0	0	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	37	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	G	1.474	-0.558987	0.03967	.	.	ENSG00000163564	ENST00000368140;ENST00000368138	T;T	0.06294	3.33;3.32	1.95	-2.27	0.06846	.	.	.	.	.	T	0.00724	0.0024	N	0.08118	0	0.09310	N	1	B;B	0.22604	0.072;0.043	B;B	0.16289	0.015;0.007	T	0.46512	-0.9186	9	0.16420	T	0.52	.	6.2156	0.20653	0.668:0.0:0.332:0.0	.	457;466	Q6K0P9-2;Q6K0P9	.;IFIX_HUMAN	T	466;457	ENSP00000357122:A466T;ENSP00000357120:A457T	ENSP00000357120:A457T	A	+	1	0	PYHIN1	157210097	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.349000	0.02627	-0.729000	0.04875	-0.143000	0.13931	GCA	.		0.448	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		A	158943473	G	A	158943473	3	1	130	1	0	0	0	0	1	0	0	0	12897	1319	46	2	1422	2	PYHIN1	1	158943473	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	207663	158943473	90307148	27	11369											
F5	2153	broad.mit.edu	37	chr1	169493136	169493136	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcttgctaatctgggctccCagtaacctaaactcaaggga	12	10	8	11	0	3	0	1	0	2	0	4	1	4	1	2	2	3	3	2	2	5	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:169493136C>A	ENST00000367797.3	-	20	5996	c.5795G>T	c.(5794-5796)tGg>tTg	p.W1932L	F5_ENST00000367796.3_Missense_Mutation_p.W1937L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1932	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCTGGGCTCCCAGTAACCTAA	0.373																																					p.W1932L													.	F5-157	0			c.G5795T						.						110	117	114					1																	169493136		2203	4300	6503	SO:0001583	missense	2153	exon20			GGCTCCCAGTAAC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.5795G>T	1.37:g.169493136C>A	ENSP00000356771:p.Trp1932Leu	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	254	9	NM_000130	0	0	0	0	0	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436127	0.62955	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98937	-5.25;-5.25	5.81	5.81	0.92471	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.98551	0.9516	M	0.67517	2.055	0.45554	D	0.998506	P	0.49307	0.922	P	0.54060	0.741	D	0.99150	1.0858	9	0.59425	D	0.04	-6.5618	20.0826	0.97783	0.0:1.0:0.0:0.0	.	1932	P12259	FA5_HUMAN	L	1932;1937	ENSP00000356771:W1932L;ENSP00000356770:W1937L	ENSP00000356770:W1937L	W	-	2	0	F5	167759760	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	6.987000	0.76206	2.746000	0.94184	0.655000	0.94253	TGG	.		0.373	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169493136	C	A	169493136	3	1	130	1	0	0	0	0	1	0	0	0	5361	595	21	4	903	4	F5	1	169493136	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	10549663	169493136	79757485	28	11370											
FASLG	356	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	172634825	172634825	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctatggaattgtcctgctttCtggagtgaagtataagaagg	11	13	12	5	0	1	2	0	1	1	1	2	4	2	4	1	3	1	2	1	3	6	5	rs80358236		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:172634825C>T	ENST00000367721.2	+	4	699	c.515C>T	c.(514-516)tCt>tTt	p.S172F	FASLG_ENST00000340030.3_3'UTR	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	172					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						GTCCTGCTTTCTGGAGTGAAG	0.433																																					p.S172F	Ovarian(28;486 876 30334 44033)	.											.	FASLG-618	0			c.C515T						.						136	120	126					1																	172634825		2203	4300	6503	SO:0001583	missense	356	exon4			TGCTTTCTGGAGT	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"Tumor necrosis factor (ligand) superfamily", "CD molecules", "Endogenous ligands"	11936	protein-coding gene	gene with protein product		134638	"tumor necrosis factor (ligand) superfamily, member 6"	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.515C>T	1.37:g.172634825C>T	ENSP00000356694:p.Ser172Phe	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	139	11	NM_000639	0	0	0	0	0	Q9BZP9	Missense_Mutation	SNP	ENST00000367721.2	37	CCDS1304.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374699	0.61735	.	.	ENSG00000117560	ENST00000367721	T	0.65732	-0.17	5.24	5.24	0.73138	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.277042	0.34046	N	0.004302	T	0.74496	0.3724	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.78064	-0.2350	10	0.72032	D	0.01	-19.152	13.9766	0.64277	0.0:0.8471:0.1529:0.0	.	172	P48023	TNFL6_HUMAN	F	172	ENSP00000356694:S172F	ENSP00000356694:S172F	S	+	2	0	FASLG	170901448	0.930000	0.31532	0.910000	0.35882	0.880000	0.50808	2.041000	0.41213	2.455000	0.83008	0.650000	0.86243	TCT	.		0.433	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1			T	172634825	C	T	172634825	3	4	130	1	0	0	0	0	1	0	0	0	5701	913	32	2	529	2	FASLG	1	172634825	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3141689	172634825	76615796	29	11371											
CEP350	9857	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	180044161	180044161	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catggtgtgaccataggtttCtgacaaagcgggagcaaaaa	14	8	12	7	1	1	2	0	2	1	0	1	3	1	3	1	3	2	2	1	3	4	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:180044161C>T	ENST00000367607.3	+	28	5990	c.5572C>T	c.(5572-5574)Ctg>Ttg	p.L1858L		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1858					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						CCATAGGTTTCTGACAAAGCG	0.438																																					p.L1858L													.	CEP350-26	0			c.C5572T						.						47	42	44					1																	180044161		2203	4300	6503	SO:0001819	synonymous_variant	9857	exon28			AGGTTTCTGACAA	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.5572C>T	1.37:g.180044161C>T		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	34	8	NM_014810	0	0	0	0	0	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	C	9.568	1.120365	0.20877	.	.	ENSG00000135837	ENST00000429851	.	.	.	5.81	3.95	0.45737	.	.	.	.	.	T	0.60405	0.2266	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58177	-0.7682	4	.	.	.	.	10.2361	0.43284	0.0:0.7933:0.0:0.2067	.	.	.	.	F	32	.	.	S	+	2	0	CEP350	178310784	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	0.989000	0.29629	1.467000	0.48044	0.591000	0.81541	TCT	.		0.438	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180044161	C	T	180044161	2	4	130	1	0	0	0	0	0	0	0	1	3260	912	32	2		2	CEP350	1	180044161	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	7409336	180044161	69206460	30	11372											
OR2L8	391190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	248112585	248112585	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcaaaagagtgtgtgtgctGatgataacagggtcttggat	12	11	14	4	0	1	3	0	2	1	1	1	4	1	4	0	2	3	2	0	2	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:248112585G>A	ENST00000357191.3	+	1	426	c.426G>A	c.(424-426)ctG>ctA	p.L142L	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TGTGTGTGCTGATGATAACAG	0.438																																					p.L142L		.											.	OR2L8-70	0			c.G426A						.						295	240	258					1																	248112585		2203	4300	6503	SO:0001819	synonymous_variant	391190	exon1			TGTGCTGATGATA	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.426G>A	1.37:g.248112585G>A		Somatic	253	0		WXS	Illumina HiSeq	Phase_I	270	24	NM_001001963	0	0	0	0	0	Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																			.		0.438	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112585	G	A	248112585	2	1	130	1	0	0	0	0	0	0	0	1	11035	1277	45	2		2	OR2L8	1	248112585	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	68068424	248112585	1138036	31	11373											
CAPN13	92291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	30976059	30976059	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgttggaaatcttgacacGacatcctgttaaaaacagat	14	12	7	8	1	2	2	0	1	2	1	3	4	3	3	1	1	1	2	1	1	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:30976059G>A	ENST00000295055.8	-	10	1123	c.947C>T	c.(946-948)tCg>tTg	p.S316L	CAPN13_ENST00000534090.2_Missense_Mutation_p.S316L	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	316	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					ATCTTGACACGACATCCTGTT	0.473																																					p.S316L		.											.	CAPN13-136	0			c.C947T						.						146	131	136					2																	30976059		1917	4122	6039	SO:0001583	missense	92291	exon10			TGACACGACATCC		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.947C>T	2.37:g.30976059G>A	ENSP00000295055:p.Ser316Leu	Somatic	106	2		WXS	Illumina HiSeq	Phase_I	102	32	NM_144575	0	0	0	0	0	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	37	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.802500	0.70682	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	D;D	0.91843	-2.92;-2.92	5.27	5.27	0.74061	Peptidase C2, calpain, catalytic domain (3);	0.325611	0.33364	N	0.004988	D	0.97483	0.9176	H	0.97340	3.985	0.58432	D	0.999994	D	0.89917	1.0	D	0.85130	0.997	D	0.98552	1.0637	10	0.87932	D	0	.	14.3858	0.66942	0.0:0.0:1.0:0.0	.	316	Q6MZZ7	CAN13_HUMAN	L	316	ENSP00000295055:S316L;ENSP00000431298:S316L	ENSP00000295055:S316L	S	-	2	0	CAPN13	30829563	1.000000	0.71417	0.999000	0.59377	0.588000	0.36517	5.259000	0.65485	2.462000	0.83206	0.561000	0.74099	TCG	.		0.473	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		A	30976059	G	A	30976059	3	1	130	1	0	0	0	0	1	0	0	0	2632	1059	37	1	1114	1	CAPN13	2	30976059	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		30976059	212223314	32	11374											
BIRC6	57448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	32626579	32626579	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgatccagcaattgtacaaCagcttattctatcaggagac	14	11	7	9	0	2	2	1	1	1	1	3	3	3	2	1	1	4	3	1	1	5	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:32626579C>T	ENST00000421745.2	+	8	1440	c.1306C>T	c.(1306-1308)Cag>Tag	p.Q436*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	436					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					AATTGTACAACAGCTTATTCT	0.378																																					p.Q436X	Pancreas(94;175 1509 16028 18060 45422)	.											.	BIRC6-233	0			c.C1306T						.						105	107	106					2																	32626579		2203	4300	6503	SO:0001587	stop_gained	57448	exon8			GTACAACAGCTTA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"Baculoviral IAP repeat containing", "Ubiquitin-conjugating enzymes E2"	13516	protein-coding gene	gene with protein product	"apollon"	605638	"baculoviral IAP repeat-containing 6"			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.1306C>T	2.37:g.32626579C>T	ENSP00000393596:p.Gln436*	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	106	38	NM_016252	0	0	6	7	1	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	36	5.679441	0.96774	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.92	5.92	0.95590	.	0.157867	0.40908	D	0.000998	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	.	13.5098	0.61504	0.0:0.929:0.0:0.071	.	.	.	.	X	436	.	ENSP00000393596:Q436X	Q	+	1	0	BIRC6	32480083	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.615000	0.61190	2.813000	0.96785	0.561000	0.74099	CAG	.		0.378	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32626579	C	T	32626579	4	4	130	1	0	0	0	0	0	1	0	0	1439	479	17	2	1336	2	BIRC6	2	32626579	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1650520	32626579	210572794	33	11375											
SOS1	6654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	39281894	39281894	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagtttgttctcctgaggtgGaaggctcttcgtcagttaaa	9	14	11	7	1	3	1	1	1	2	0	5	2	3	2	1	3	0	4	1	3	4	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:39281894G>A	ENST00000426016.1	-	6	667	c.581C>T	c.(580-582)tCc>tTc	p.S194F	SOS1_ENST00000428721.2_Missense_Mutation_p.S137F|SOS1_ENST00000402219.2_Missense_Mutation_p.S194F|SOS1_ENST00000395038.2_Missense_Mutation_p.S194F			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	194					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TCCTGAGGTGGAAGGCTCTTC	0.284									Noonan syndrome																												p.S194F		.											.	SOS1-851	0			c.C581T						.						86	99	94					2																	39281894		2203	4297	6500	SO:0001583	missense	6654	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	GAGGTGGAAGGCT	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.581C>T	2.37:g.39281894G>A	ENSP00000387784:p.Ser194Phe	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	166	68	NM_005633	0	0	5	8	3	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.921771	0.52653	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721	T;T;T;D	0.96334	-1.08;-1.08;-1.21;-3.98	5.88	5.88	0.94601	.	0.063359	0.64402	D	0.000004	D	0.93575	0.7949	L	0.27053	0.805	0.58432	D	0.999995	B	0.12013	0.005	B	0.15484	0.013	D	0.88675	0.3198	10	0.59425	D	0.04	.	20.2187	0.98312	0.0:0.0:1.0:0.0	.	194	Q07889	SOS1_HUMAN	F	194;194;194;194;137	ENSP00000387784:S194F;ENSP00000384675:S194F;ENSP00000378479:S194F;ENSP00000399992:S137F	ENSP00000263879:S194F	S	-	2	0	SOS1	39135398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.200000	0.51051	2.780000	0.95670	0.655000	0.94253	TCC	.		0.284	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		A	39281894	G	A	39281894	3	1	130	1	0	0	0	0	1	0	0	0	14968	1174	41	2	3496	2	SOS1	2	39281894	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	6655315	39281894	203917479	34	11376											
MDH1	4190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	63826356	63826356	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgcctgactgcttccaagtCagctccatccatccccaagg	8	9	7	17	0	1	1	1	1	0	0	5	1	5	1	6	1	3	2	6	1	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:63826356C>G	ENST00000233114.8	+	5	863	c.428C>G	c.(427-429)tCa>tGa	p.S143*	MDH1_ENST00000409476.1_Nonsense_Mutation_p.S19*|MDH1_ENST00000539945.1_Nonsense_Mutation_p.S161*|MDH1_ENST00000544381.1_Nonsense_Mutation_p.S54*|MDH1_ENST00000409908.1_Intron|MDH1_ENST00000394423.1_Nonsense_Mutation_p.S143*	NM_005917.3	NP_005908.1	P40925	MDHC_HUMAN	malate dehydrogenase 1, NAD (soluble)	143					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	diiodophenylpyruvate reductase activity (GO:0047860)|L-malate dehydrogenase activity (GO:0030060)|malic enzyme activity (GO:0004470)|NAD binding (GO:0051287)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(4)	13						GCTTCCAAGTCAGCTCCATCC	0.418																																					p.S161X		.											.	MDH1-537	0			c.C482G						.						103	95	97					2																	63826356		2203	4300	6503	SO:0001587	stop_gained	4190	exon5			CCAAGTCAGCTCC		CCDS1874.1, CCDS56121.1, CCDS56122.1	2p23	2012-10-02			ENSG00000014641	ENSG00000014641	1.1.1.37		6970	protein-coding gene	gene with protein product		154200					Standard	NM_005917		Approved		uc010ypv.2	P40925	OTTHUMG00000129512	ENST00000233114.8:c.428C>G	2.37:g.63826356C>G	ENSP00000233114:p.Ser143*	Somatic	85	1		WXS	Illumina HiSeq	Phase_I	93	11	NM_001199111	0	0	170	172	2	B2R5V5|B4DUN2|B7Z3I7|F5H098|Q6I9V0	Nonsense_Mutation	SNP	ENST00000233114.8	37	CCDS1874.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.291876	0.80914	.	.	ENSG00000014641	ENST00000233114;ENST00000409476;ENST00000436321;ENST00000432309;ENST00000539945;ENST00000544381;ENST00000394423	.	.	.	5.2	4.31	0.51392	.	0.267927	0.38837	N	0.001542	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-0.539	12.967	0.58490	0.0:0.9202:0.0:0.0798	.	.	.	.	X	143;19;98;161;161;54;143	.	ENSP00000233114:S143X	S	+	2	0	MDH1	63679860	1.000000	0.71417	0.958000	0.39756	0.942000	0.58702	4.937000	0.63513	2.564000	0.86499	0.585000	0.79938	TCA	.		0.418	MDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251687.1			G	63826356	C	G	63826356	4	3	130	1	0	0	0	0	0	1	0	0	9433	838	29	4	446	4	MDH1	2	63826356	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	24544462	63826356	179373017	35	11377											
ACTR2	10097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	65492181	65492181	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattgtgcctttctagatctGaattctacaaacacattgtg	11	15	6	9	0	3	2	0	1	3	1	3	2	3	2	1	0	3	0	1	0	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:65492181G>A	ENST00000260641.5	+	8	1043	c.886G>A	c.(886-888)Gaa>Aaa	p.E296K	ACTR2_ENST00000542850.1_Missense_Mutation_p.E241K|ACTR2_ENST00000377982.4_Missense_Mutation_p.E301K	NM_005722.3	NP_005713.1	P61160	ARP2_HUMAN	ARP2 actin-related protein 2 homolog (yeast)	296					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium assembly (GO:0042384)|cytoplasmic transport (GO:0016482)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|spindle localization (GO:0051653)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	12						TTCTAGATCTGAATTCTACAA	0.428																																					p.E301K		.											.	ACTR2-278	0			c.G901A						.						179	168	171					2																	65492181		2203	4300	6503	SO:0001583	missense	10097	exon9			AGATCTGAATTCT	AF006082	CCDS1881.1, CCDS46307.1	2p14	2008-05-20	2001-11-28		ENSG00000138071	ENSG00000138071			169	protein-coding gene	gene with protein product		604221	"ARP2 (actin-related protein 2, yeast) homolog"			9230079	Standard	NM_001005386		Approved	ARP2	uc002sdp.3	P61160	OTTHUMG00000129540	ENST00000260641.5:c.886G>A	2.37:g.65492181G>A	ENSP00000260641:p.Glu296Lys	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	176	70	NM_001005386	0	0	0	0	0	B2RCP5|D6W5F4|E9PF41|O15142|Q96C82	Missense_Mutation	SNP	ENST00000260641.5	37	CCDS1881.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.731091	0.69189	.	.	ENSG00000138071	ENST00000260641;ENST00000542850;ENST00000377982;ENST00000535303	D;D;D	0.94576	-3.46;-3.46;-3.46	5.98	5.1	0.69264	.	0.120167	0.53938	U	0.000057	D	0.93841	0.8030	M	0.70275	2.135	0.58432	D	0.999999	B;B;B	0.13594	0.005;0.008;0.004	B;B;B	0.13407	0.009;0.007;0.007	D	0.91169	0.4967	10	0.62326	D	0.03	-23.7201	17.2991	0.87177	0.0:0.1254:0.8746:0.0	.	241;296;301	F5H6T1;P61160;E9PF41	.;ARP2_HUMAN;.	K	296;241;301;241	ENSP00000260641:E296K;ENSP00000437383:E241K;ENSP00000367220:E301K	ENSP00000260641:E296K	E	+	1	0	ACTR2	65345685	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	9.476000	0.97823	1.525000	0.49052	0.591000	0.81541	GAA	.		0.428	ACTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251730.1	NM_001005386		A	65492181	G	A	65492181	3	1	130	1	0	0	0	0	1	0	0	0	211	1291	45	2	935	2	ACTR2	2	65492181	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1665825	65492181	177707192	36	11378											
CLEC4F	165530	broad.mit.edu;bcgsc.ca	37	chr2	71043525	71043525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctttttaacacgtgaatttCatcaccagctctttccaaat	11	15	3	12	1	3	1	2	1	1	0	4	1	4	1	3	0	2	1	3	0	3	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:71043525C>T	ENST00000272367.2	-	4	1064	c.988G>A	c.(988-990)Gaa>Aaa	p.E330K	CLEC4F_ENST00000426626.1_Missense_Mutation_p.E330K	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	330					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						ACGTGAATTTCATCACCAGCT	0.423																																					p.E330K	Colon(107;10 2157 6841 26035)												.	CLEC4F-95	0			c.G988A						.						93	90	91					2																	71043525		2203	4300	6503	SO:0001583	missense	165530	exon4			GAATTTCATCACC	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"C-type lectin domain containing"	25357	protein-coding gene	gene with protein product			"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.988G>A	2.37:g.71043525C>T	ENSP00000272367:p.Glu330Lys	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	128	10	NM_173535	0	0	0	0	0	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576506	0.28092	.	.	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.78246	-1.16;-1.16	3.99	3.1	0.35709	.	0.390460	0.18739	N	0.132519	T	0.69233	0.3088	L	0.55481	1.735	0.09310	N	1	B;B	0.22541	0.071;0.071	B;B	0.21360	0.034;0.034	T	0.56768	-0.7924	10	0.30078	T	0.28	.	8.148	0.31124	0.0:0.8884:0.0:0.1116	.	330;330	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	K	330	ENSP00000272367:E330K;ENSP00000390581:E330K	ENSP00000272367:E330K	E	-	1	0	CLEC4F	70897033	0.004000	0.15560	0.004000	0.12327	0.012000	0.07955	0.746000	0.26275	1.234000	0.43709	0.467000	0.42956	GAA	.		0.423	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		T	71043525	C	T	71043525	3	4	130	1	0	0	0	0	1	0	0	0	3522	835	29	2	797	2	CLEC4F	2	71043525	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5551344	71043525	172155848	37	11379											
CNGA3	1261	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	99012521	99012522	+	Frame_Shift_Ins	INS	-	-	GT																															gcacagagacaaggaccaacINStaccccaatatgttcaggat																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:99012521_99012522insGT	ENST00000272602.2	+	7	927_928	c.888_889insGT	c.(889-891)tacfs	p.Y297fs	CNGA3_ENST00000436404.2_Frame_Shift_Ins_p.Y279fs|CNGA3_ENST00000409937.1_Frame_Shift_Ins_p.Y301fs|CNGA3_ENST00000393504.1_Frame_Shift_Ins_p.Y297fs			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	297					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						CAAGGACCAACTACCCCAATAT	0.45																																					p.N296fs		.											.	CNGA3-96	0			c.888_889insGT						.																																			SO:0001589	frameshift_variant	1261	exon8			.	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	Exception_encountered	2.37:g.99012521_99012522insGT	ENSP00000272602:p.Tyr297fs	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	92	20	NM_001298	0	0	0	0	0	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Frame_Shift_Ins	INS	ENST00000272602.2	37	CCDS2034.1																																																																																			.		0.45	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		GT	99012522	-	GT	99012521	7	5	130	1	0	1	1	0	0	0	0	0	3604	564	20	0	914	0	CNGA3	2	99012521	Frame_Shift_Ins	INS	-	TCGA-HE-7130-01A-11D-1961-08	27968996	99012521	144186852	38	11380											
SULT1C2	6819	broad.mit.edu;ucsc.edu	37	chr2	108921890	108921890	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggacccaaagcatgaaattcGgaaggtgatgcagttcatgg	13	8	13	7	1	1	2	1	2	0	0	2	4	1	4	1	4	2	3	1	4	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:108921890G>T	ENST00000437390.2	+	7	836	c.659G>T	c.(658-660)cGg>cTg	p.R220L	SULT1C2_ENST00000326853.5_Missense_Mutation_p.R217L|SULT1C2_ENST00000409880.1_Missense_Mutation_p.R169L|SULT1C2_ENST00000251481.6_Missense_Mutation_p.R206L			O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 2	212					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						CATGAAATTCGGAAGGTGATG	0.403																																					p.R217L													.	SULT1C2-91	0			c.G650T						.						93	92	93					2																	108921890		2203	4300	6503	SO:0001583	missense	6819	exon8			AAATTCGGAAGGT	U66036, AF186255	CCDS2075.1, CCDS2076.1	2q12.3	2010-09-30	2007-03-16	2007-03-16	ENSG00000198203	ENSG00000198203		"Sulfotransferases, cytosolic"	11456	protein-coding gene	gene with protein product		602385	"sulfotransferase family, cytosolic, 1C, member 1"	SULT1C1		9169148, 10783263	Standard	NM_001056		Approved	ST1C1	uc002tdx.3	O00338	OTTHUMG00000153215	ENST00000437390.2:c.659G>T	2.37:g.108921890G>T	ENSP00000399651:p.Arg220Leu	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	50	5	NM_176825	0	0	0	0	0	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000437390.2	37		.	.	.	.	.	.	.	.	.	.	G	12.27	1.888899	0.33348	.	.	ENSG00000198203	ENST00000251481;ENST00000326853;ENST00000409880;ENST00000437390	D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63	4.66	-4.12	0.03916	Sulfotransferase domain (1);	0.750429	0.12255	N	0.485245	T	0.69913	0.3164	L	0.27053	0.805	0.22330	N	0.9992	B;B;B;B	0.15473	0.004;0.006;0.013;0.01	B;B;B;B	0.25759	0.038;0.003;0.063;0.037	T	0.54708	-0.8253	10	0.30078	T	0.28	.	11.0503	0.47882	0.6167:0.0:0.3833:0.0	.	220;121;206;217	B4DLP0;B4DPE8;O00338;O00338-2	.;.;ST1C2_HUMAN;.	L	206;217;169;220	ENSP00000251481:R206L;ENSP00000319622:R217L;ENSP00000387054:R169L;ENSP00000399651:R220L	ENSP00000251481:R206L	R	+	2	0	SULT1C2	108288322	0.001000	0.12720	0.945000	0.38365	0.789000	0.44602	0.233000	0.17911	-0.811000	0.04369	-1.044000	0.02363	CGG	.		0.403	SULT1C2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000329969.2	NM_176825		T	108921890	G	T	108921890	3	4	130	1	0	0	0	0	1	0	0	0	15409	1116	39	4	738	4	SULT1C2	2	108921890	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	9909369	108921890	134277483	39	11381											
FSIP2	401024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	186678413	186678413	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgtatttggaaaattacAtaaaagaggaacgagattct	18	11	9	3	1	1	2	0	0	1	2	1	5	1	4	0	2	2	1	0	2	8	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:186678413A>T	ENST00000424728.1	+	18	19969	c.19969A>T	c.(19969-19971)Ata>Tta	p.I6657L	FSIP2_ENST00000343098.5_Missense_Mutation_p.I6746L			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6657										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						GGAAAATTACATAAAAGAGGA	0.308																																					p.I6746L		.											.	FSIP2-90	0			c.A20236T						.						60	58	59					2																	186678413		1815	4082	5897	SO:0001583	missense	401024	exon18			AATTACATAAAAG	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.19969A>T	2.37:g.186678413A>T	ENSP00000401306:p.Ile6657Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	40	11	NM_173651	0	0	0	0	0	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		.	.	.	.	.	.	.	.	.	.	A	8.432	0.848829	0.17034	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.39787	1.06;1.07	4.74	-6.09	0.02145	.	2.291920	0.01415	N	0.014178	T	0.16557	0.0398	N	0.03608	-0.345	0.09310	N	1	.	.	.	.	.	.	T	0.11567	-1.0582	8	0.17369	T	0.5	.	5.0483	0.14496	0.3028:0.0:0.4212:0.2761	.	.	.	.	L	6746;6657	ENSP00000344403:I6746L;ENSP00000401306:I6657L	ENSP00000344403:I6746L	I	+	1	0	FSIP2	186386658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.003000	0.13083	-1.474000	0.01879	-1.412000	0.01120	ATA	.		0.308	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186678413	A	T	186678413	3	4	130	1	0	0	0	0	1	0	0	0	6094	217	8	5	20306	5	FSIP2	2	186678413	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	77756523	186678413	56520960	40	11382											
MSTN	2660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190922196	190922196	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctctccagagcagtaattggCcttatatcttttaggagcga	10	13	9	9	1	2	1	0	0	2	1	3	3	2	2	2	2	2	2	2	2	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:190922196C>T	ENST00000260950.4	-	3	1048	c.916G>A	c.(916-918)Gcc>Acc	p.A306T	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	306					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			CAGTAATTGGCCTTATATCTT	0.423																																					p.A306T		.											.	MSTN-650	0			c.G916A						.						85	83	84					2																	190922196		2203	4300	6503	SO:0001583	missense	2660	exon3			AATTGGCCTTATA	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.916G>A	2.37:g.190922196C>T	ENSP00000260950:p.Ala306Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	69	34	NM_005259	0	0	0	0	0	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	37	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497799	0.85069	.	.	ENSG00000138379	ENST00000260950	D	0.86497	-2.13	5.79	5.79	0.91817	Transforming growth factor beta, conserved site (1);Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.95604	0.8571	H	0.94886	3.595	0.80722	D	1	P	0.48089	0.905	D	0.65140	0.932	D	0.96037	0.9021	10	0.87932	D	0	-9.1744	20.0308	0.97536	0.0:1.0:0.0:0.0	.	306	O14793	GDF8_HUMAN	T	306	ENSP00000260950:A306T	ENSP00000260950:A306T	A	-	1	0	MSTN	190630441	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.732000	0.93576	0.585000	0.79938	GCC	.		0.423	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		T	190922196	C	T	190922196	3	4	130	1	0	0	0	0	1	0	0	0	9918	739	26	2	215	2	MSTN	2	190922196	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4243783	190922196	52277177	41	11383											
ALS2CR12	130540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	202172265	202172265	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttctcttgaatgaagttctCaaagacagcactgcaggatt	12	12	8	9	0	2	3	1	2	2	1	4	4	2	4	0	1	2	3	0	1	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:202172265C>G	ENST00000286190.5	-	10	902	c.856G>C	c.(856-858)Gag>Cag	p.E286Q	ALS2CR12_ENST00000405148.2_Missense_Mutation_p.E286Q|ALS2CR12_ENST00000448967.1_5'Flank|ALS2CR12_ENST00000392257.3_Missense_Mutation_p.E286Q|ALS2CR12_ENST00000439709.1_Missense_Mutation_p.E286Q			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	286					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						ATGAAGTTCTCAAAGACAGCA	0.438																																					p.E286Q		.											.	ALS2CR12-154	0			c.G856C						.						223	220	221					2																	202172265		2203	4299	6502	SO:0001583	missense	130540	exon11			AGTTCTCAAAGAC	AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.856G>C	2.37:g.202172265C>G	ENSP00000286190:p.Glu286Gln	Somatic	265	1		WXS	Illumina HiSeq	Phase_I	275	53	NM_001127391	0	0	0	0	0	G5E9S3|Q53TT6|Q8N1B6	Missense_Mutation	SNP	ENST00000286190.5	37	CCDS2346.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.237379|5.237379	0.95240|0.95240	.|.	.|.	ENSG00000155749|ENSG00000155749	ENST00000286190;ENST00000405148;ENST00000392257;ENST00000439709|ENST00000415745	T;T;T;T|.	0.44482|.	0.92;0.92;0.92;0.92|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.216156|.	0.32970|.	N|.	0.005435|.	T|T	0.57873|0.57873	0.2083|0.2083	L|L	0.60455|0.60455	1.87|1.87	0.26519|0.26519	N|N	0.974462|0.974462	D;D|.	0.67145|.	0.996;0.996|.	P;P|.	0.62298|.	0.9;0.9|.	T|T	0.52756|0.52756	-0.8533|-0.8533	10|5	0.33141|.	T|.	0.24|.	-10.1129|-10.1129	16.749|16.749	0.85480|0.85480	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	286;286|.	Q96Q35;G5E9S3|.	AL2SB_HUMAN;.|.	Q|F	286|60	ENSP00000286190:E286Q;ENSP00000385098:E286Q;ENSP00000376086:E286Q;ENSP00000412073:E286Q|.	ENSP00000286190:E286Q|.	E|L	-|-	1|3	0|2	ALS2CR12|ALS2CR12	201880510|201880510	0.991000|0.991000	0.36638|0.36638	0.738000|0.738000	0.30950|0.30950	0.804000|0.804000	0.45430|0.45430	3.681000|3.681000	0.54648|0.54648	2.773000|2.773000	0.95371|0.95371	0.650000|0.650000	0.86243|0.86243	GAG|TTG	.		0.438	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163		G	202172265	C	G	202172265	3	3	130	1	0	0	0	0	1	0	0	0	553	835	29	4	501	4	ALS2CR12	2	202172265	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	11250069	202172265	41027108	42	11384											
KIF1A	547	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	241661280	241661280	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtactctctgttgaatgTgtgcgtgagcaggcgcaagc	7	12	14	8	2	1	2	0	2	1	0	2	2	1	2	0	1	4	4	0	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:241661280T>C	ENST00000320389.7	-	42	4542	c.4384A>G	c.(4384-4386)Aca>Gca	p.T1462A	KIF1A_ENST00000498729.2_Missense_Mutation_p.T1563A	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1462					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CTGTTGAATGTGTGCGTGAGC	0.657																																					p.T1563A		.											.	KIF1A-91	0			c.A4687G						.						75	81	79					2																	241661280		2148	4248	6396	SO:0001583	missense	547	exon44			TGAATGTGTGCGT	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.4384A>G	2.37:g.241661280T>C	ENSP00000322791:p.Thr1462Ala	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	11	8	NM_001244008	0	0	0	2	2	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.630002	0.46944	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308	T;T	0.72167	-0.55;-0.63	4.33	3.14	0.36123	.	0.120608	0.53938	U	0.000050	T	0.64483	0.2602	L	0.46157	1.445	0.41290	D	0.986977	P;B	0.39737	0.685;0.032	P;B	0.46299	0.511;0.014	T	0.57159	-0.7859	10	0.08599	T	0.76	.	9.5613	0.39371	0.165:0.0:0.0:0.835	.	1563;1462	F5H045;Q12756	.;KIF1A_HUMAN	A	1462;1563;1571	ENSP00000322791:T1462A;ENSP00000438388:T1563A	ENSP00000322791:T1462A	T	-	1	0	KIF1A	241309953	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	1.446000	0.35090	0.517000	0.28361	0.528000	0.53228	ACA	.		0.657	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		C	241661280	T	C	241661280	3	2	130	1	0	0	0	0	1	0	0	0	8304	1696	59	3	712	3	KIF1A	2	241661280	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	39489015	241661280	1538093	43	11385											
OXSM	54995	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	25833175	25833175	+	Frame_Shift_Del	DEL	T	T	-																															ctgtgggagactcatttagaTttatagcccatggtgatgct																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:25833175delT	ENST00000280701.3	+	2	763	c.664delT	c.(664-666)tttfs	p.F222fs	OXSM_ENST00000420173.2_Frame_Shift_Del_p.F222fs|OXSM_ENST00000449808.1_Intron|NGLY1_ENST00000417874.2_5'Flank	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	222					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						CTCATTTAGATTTATAGCCCA	0.498																																					p.F222fs		.											.	OXSM-132	0			c.664delT						.						121	119	120					3																	25833175		2203	4300	6503	SO:0001589	frameshift_variant	54995	exon2			.	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.664delT	3.37:g.25833175delT	ENSP00000280701:p.Phe222fs	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	178	86	NM_017897	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000280701.3	37	CCDS2643.1																																																																																			.		0.498	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		-	25833175	T	-	25833175	7	5	130	1	0	1	0	1	0	0	0	0	11361	1493	52	0	666	0	OXSM	3	25833175	Frame_Shift_Del	DEL	T	TCGA-HE-7130-01A-11D-1961-08		25833175	172189255	44	11386											
SEMA3F	6405	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50220896	50220896	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtgtgtctactccatggctGatattcgcatggtcttcaac	7	15	9	10	1	3	1	1	1	2	0	5	1	4	1	1	2	2	2	1	2	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:50220896G>C	ENST00000002829.3	+	12	1616	c.1132G>C	c.(1132-1134)Gat>Cat	p.D378H	SEMA3F_ENST00000413852.1_Missense_Mutation_p.D279H|SEMA3F_ENST00000434342.1_Missense_Mutation_p.D347H	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	378	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CTCCATGGCTGATATTCGCAT	0.632																																					p.D378H		.											.	SEMA3F-279	0			c.G1132C						.						86	74	78					3																	50220896		2203	4300	6503	SO:0001583	missense	6405	exon12			ATGGCTGATATTC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1132G>C	3.37:g.50220896G>C	ENSP00000002829:p.Asp378His	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	71	7	NM_004186	0	0	157	180	23	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Missense_Mutation	SNP	ENST00000002829.3	37	CCDS2811.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151596	0.94645	.	.	ENSG00000001617	ENST00000450338;ENST00000413852;ENST00000002829;ENST00000434342	T;T;T;T	0.27720	1.65;1.65;1.65;1.65	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.67590	0.2909	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.981	T	0.77096	-0.2714	10	0.87932	D	0	.	18.8886	0.92389	0.0:0.0:1.0:0.0	.	347;378	C9JQ85;Q13275	.;SEM3F_HUMAN	H	347;279;378;347	ENSP00000398399:D347H;ENSP00000388931:D279H;ENSP00000002829:D378H;ENSP00000409859:D347H	ENSP00000002829:D378H	D	+	1	0	SEMA3F	50195900	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.651000	0.98493	2.542000	0.85734	0.511000	0.50034	GAT	.		0.632	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		C	50220896	G	C	50220896	3	2	130	1	0	0	0	0	1	0	0	0	14061	1290	45	4	1174	4	SEMA3F	3	50220896	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	24387721	50220896	147801534	45	11387											
CCDC80	151887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	112324296	112324296	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccatggtgataactctcatGatgacggtagtcatcctggt	9	13	10	9	1	2	3	2	3	1	0	5	3	4	3	2	3	1	1	2	3	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:112324296G>A	ENST00000206423.3	-	8	3774	c.2821C>T	c.(2821-2823)Cat>Tat	p.H941Y	CCDC80_ENST00000439685.2_Missense_Mutation_p.H941Y	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	941					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(21)|ovary(3)|pancreas(2)|prostate(4)	51						TAACTCTCATGATGACGGTAG	0.483																																					p.H941Y		.											.	CCDC80-92	0			c.C2821T						.						97	89	92					3																	112324296		2203	4300	6503	SO:0001583	missense	151887	exon8			TCTCATGATGACG	AY333429	CCDS2968.1	3q13.2	2010-12-24			ENSG00000091986	ENSG00000091986			30649	protein-coding gene	gene with protein product	"steroid sensitive gene 1"	608298				15325258, 18178152	Standard	XM_005247135		Approved	URB, SSG1, DRO1	uc003dzf.3	Q76M96	OTTHUMG00000159265	ENST00000206423.3:c.2821C>T	3.37:g.112324296G>A	ENSP00000206423:p.His941Tyr	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	99	27	NM_199511	0	0	0	0	0	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	37	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211797	0.79240	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000444594	T;T	0.52754	0.65;0.65	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.37571	0.1008	N	0.19112	0.55	0.46317	D	0.998989	B;B	0.31931	0.347;0.236	B;B	0.26416	0.069;0.031	T	0.29058	-1.0024	10	0.87932	D	0	-20.2625	20.4324	0.99085	0.0:0.0:1.0:0.0	.	952;941	Q76M96-2;Q76M96	.;CCD80_HUMAN	Y	941;941;542	ENSP00000206423:H941Y;ENSP00000411814:H941Y	ENSP00000206423:H941Y	H	-	1	0	CCDC80	113806986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.764000	0.74960	2.833000	0.97629	0.585000	0.79938	CAT	.		0.483	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		A	112324296	G	A	112324296	3	1	130	1	0	0	0	0	1	0	0	0	2860	1290	45	2	35	2	CCDC80	3	112324296	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	62103400	112324296	85698134	46	11388											
KALRN	8997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	124103778	124103778	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaccccgaggagatctacaaGgcagctcgacacctggaggt	11	5	13	12	2	1	1	0	0	1	1	2	6	1	2	3	4	2	2	3	4	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:124103778G>C	ENST00000240874.3	+	11	2008	c.1851G>C	c.(1849-1851)aaG>aaC	p.K617N	KALRN_ENST00000460856.1_Missense_Mutation_p.K617N|KALRN_ENST00000360013.3_Missense_Mutation_p.K617N	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	617					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AGATCTACAAGGCAGCTCGAC	0.567																																					p.K617N		.											.	KALRN-738	0			c.G1851C						.						108	88	95					3																	124103778		2203	4300	6503	SO:0001583	missense	8997	exon11			CTACAAGGCAGCT	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1851G>C	3.37:g.124103778G>C	ENSP00000240874:p.Lys617Asn	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	84	38	NM_003947	0	0	1	1	0	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.01|15.01	2.706440|2.706440	0.48412|0.48412	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013;ENST00000439170|ENST00000354186	T;T;T;T|.	0.41758|.	0.99;0.99;0.99;0.99|.	5.0|5.0	4.09|4.09	0.47781|0.47781	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.38214|0.38214	0.1032|0.1032	N|N	0.21373|0.21373	0.66|0.66	0.80722|0.80722	D|D	1|1	P;P;P|.	0.48089|.	0.542;0.905;0.486|.	B;P;B|.	0.50314|.	0.388;0.637;0.268|.	T|T	0.15065|0.15065	-1.0450|-1.0450	10|5	0.18276|.	T|.	0.48|.	.|.	5.048|5.048	0.14494|0.14494	0.4066:0.0:0.5934:0.0|0.4066:0.0:0.5934:0.0	.|.	617;617;617|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	N|T	617;617;617;93|595	ENSP00000418611:K617N;ENSP00000240874:K617N;ENSP00000353109:K617N;ENSP00000402950:K93N|.	ENSP00000240874:K617N|.	K|R	+|+	3|2	2|0	KALRN|KALRN	125586468|125586468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.890000|1.890000	0.39728|0.39728	1.232000|1.232000	0.43678|0.43678	0.563000|0.563000	0.77884|0.77884	AAG|AGG	.		0.567	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		C	124103778	G	C	124103778	3	2	130	1	0	0	0	0	1	0	0	0	7996	991	35	4	1893	4	KALRN	3	124103778	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	11779482	124103778	73918652	47	11389											
KY	339855	ucsc.edu	37	chr3	134322978	134322978	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgatggagcagcgcccgtCgctggtgtggatgatagggt	6	9	18	8	3	0	2	0	2	0	0	1	4	0	4	1	4	2	3	1	4	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:134322978C>T	ENST00000423778.2	-	11	1490	c.1429G>A	c.(1429-1431)Gac>Aac	p.D477N	KY_ENST00000508956.1_Missense_Mutation_p.D456N|KY_ENST00000503669.1_3'UTR	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	477					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						CAGCGCCCGTCGCTGGTGTGG	0.637																																					p.D477N													.	KY-24	0			c.G1429A						.						24	26	25					3																	134322978		2064	4179	6243	SO:0001583	missense	339855	exon11			GCCCGTCGCTGGT	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1429G>A	3.37:g.134322978C>T	ENSP00000397598:p.Asp477Asn	Somatic	18	0		WXS	Illumina HiSeq		13	4	NM_178554	0	0	0	0	0	B7Z1S4|Q6ZT15	Missense_Mutation	SNP	ENST00000423778.2	37	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506252	0.85282	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000310263	.	.	.	5.63	5.63	0.86233	.	0.272187	0.36101	N	0.002796	T	0.79329	0.4427	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.978;0.999	T	0.80434	-0.1384	9	0.87932	D	0	-5.6797	19.6704	0.95910	0.0:1.0:0.0:0.0	.	456;477	Q8NBH2-3;Q8NBH2-4	.;.	N	456;477;477	.	ENSP00000309520:D477N	D	-	1	0	KY	135805668	0.999000	0.42202	0.876000	0.34364	0.985000	0.73830	5.677000	0.68142	2.659000	0.90383	0.561000	0.74099	GAC	.		0.637	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		T	134322978	C	T	134322978	3	4	130	1	0	0	0	0	1	0	0	0	8607	884	31	1	560	1	KY	3	134322978	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	10219200	134322978	63699452	48	11390											
TTC14	151613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	180324303	180324303	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaagtttgaacaaagcaataGaagattttgagcttgcatta	16	12	9	4	0	0	4	0	2	0	2	0	5	0	4	0	0	4	4	0	0	7	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:180324303G>C	ENST00000296015.4	+	9	1216	c.1084G>C	c.(1084-1086)Gaa>Caa	p.E362Q	TTC14_ENST00000382584.4_Missense_Mutation_p.E362Q|TTC14_ENST00000412756.2_Missense_Mutation_p.E362Q	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	362							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CAAAGCAATAGAAGATTTTGA	0.383																																					p.E362Q		.											.	TTC14-91	0			c.G1084C						.						117	124	121					3																	180324303		2203	4300	6503	SO:0001583	missense	151613	exon9			GCAATAGAAGATT	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.1084G>C	3.37:g.180324303G>C	ENSP00000296015:p.Glu362Gln	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	214	119	NM_001042601	0	0	6	11	5	G5E9X0|Q6UWJ7|Q8TF22	Missense_Mutation	SNP	ENST00000296015.4	37	CCDS3237.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.396059	0.62177	.	.	ENSG00000163728	ENST00000296015;ENST00000412756;ENST00000382584	T;T;T	0.62232	0.04;0.04;0.04	5.93	5.93	0.95920	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.482695	0.24828	N	0.035263	T	0.64778	0.2629	L	0.42529	1.33	0.33985	D	0.648465	D;P;P	0.71674	0.998;0.787;0.912	P;B;P	0.55615	0.78;0.419;0.575	T	0.70063	-0.4975	10	0.30854	T	0.27	-20.8298	11.6377	0.51213	0.1367:0.0:0.8633:0.0	.	362;362;362	Q96N46-2;G5E9X0;Q96N46	.;.;TTC14_HUMAN	Q	362	ENSP00000296015:E362Q;ENSP00000413743:E362Q;ENSP00000372027:E362Q	ENSP00000296015:E362Q	E	+	1	0	TTC14	181806997	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.915000	0.48805	2.798000	0.96311	0.655000	0.94253	GAA	.		0.383	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		C	180324303	G	C	180324303	3	2	130	1	0	0	0	0	1	0	0	0	16714	943	33	4	1118	4	TTC14	3	180324303	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	46001325	180324303	17698127	49	11391											
CCDC39	339829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	180337752	180337752	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgaagttcttctttttcttGagcagcctatgaagtacaga	10	16	8	7	0	3	4	0	3	3	1	3	4	3	4	1	0	3	3	1	0	4	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:180337752G>C	ENST00000442201.2	-	15	2124	c.2005C>G	c.(2005-2007)Caa>Gaa	p.Q669E	CCDC39_ENST00000273654.4_Intron	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	669					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TCTTTTTCTTGAGCAGCCTAT	0.383																																					p.Q669E		.											.	CCDC39-72	0			c.C2005G						.						64	53	57					3																	180337752		1829	4079	5908	SO:0001583	missense	339829	exon15			TTTCTTGAGCAGC	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.2005C>G	3.37:g.180337752G>C	ENSP00000405708:p.Gln669Glu	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	55	9	NM_181426	0	0	0	0	0	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263405	0.80358	.	.	ENSG00000145075	ENST00000442201	T	0.77620	-1.11	5.25	5.25	0.73442	.	.	.	.	.	D	0.87446	0.6179	M	0.83953	2.67	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	D	0.84150	0.0422	9	0.13108	T	0.6	.	19.205	0.93726	0.0:0.0:1.0:0.0	.	669	Q9UFE4	CCD39_HUMAN	E	669	ENSP00000405708:Q669E	ENSP00000405708:Q669E	Q	-	1	0	CCDC39	181820446	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.762000	0.91711	2.596000	0.87737	0.563000	0.77884	CAA	.		0.383	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		C	180337752	G	C	180337752	3	2	130	1	0	0	0	0	1	0	0	0	2817	1299	45	4	844	4	CCDC39	3	180337752	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	13449	180337752	17684678	50	11392											
C3orf59	151963	broad.mit.edu	37	chr3	192516239	192516239	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgtcaggattgataaagacaGagattgactttcccgggttc	11	11	11	8	2	1	4	1	2	0	2	3	6	2	5	1	2	0	1	1	2	2	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:192516239G>C	ENST00000392452.2	-	2	1732	c.1412C>G	c.(1411-1413)tCt>tGt	p.S471C		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	471							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						GATAAAGACAGAGATTGACTT	0.453																																					p.S471C													.	MB21D2-70	0			c.C1412G						.						106	112	110					3																	192516239		2203	4300	6503	SO:0001583	missense	151963	exon2			AAGACAGAGATTG	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 59"	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.1412C>G	3.37:g.192516239G>C	ENSP00000376246:p.Ser471Cys	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	210	5	NM_178496	0	0	4	4	0	Q86VD8	Missense_Mutation	SNP	ENST00000392452.2	37	CCDS3302.2	.	.	.	.	.	.	.	.	.	.	G	17.93	3.508051	0.64410	.	.	ENSG00000180611	ENST00000392452	T	0.61742	0.08	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.69115	0.3075	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.71932	-0.4443	10	0.87932	D	0	-6.8519	18.2207	0.89901	0.0:0.0:1.0:0.0	.	471	Q8IYB1	M21D2_HUMAN	C	471	ENSP00000376246:S471C	ENSP00000376246:S471C	S	-	2	0	MB21D2	193998933	1.000000	0.71417	0.994000	0.49952	0.921000	0.55340	9.567000	0.98161	2.538000	0.85594	0.650000	0.86243	TCT	.		0.453	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		C	192516239	G	C	192516239	3	2	130	1	0	0	0	0	1	0	0	0	2243	942	33	4	67	4	C3orf59	3	192516239	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	12178487	192516239	5506191	51	11393											
PDE6B	5158	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	619524	619524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaatgtggccgcggcctgcGaggacgggtgcccgccggac	6	4	18	13	6	0	1	0	0	0	1	0	4	0	3	4	5	2	0	4	5	1	0	rs376908835		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:619524G>A	ENST00000496514.1	+	1	130	c.109G>A	c.(109-111)Gag>Aag	p.E37K	PDE6B_ENST00000255622.6_Missense_Mutation_p.E37K			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	37					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	CGCGGCCTGCGAGGACGGGTG	0.647																																					p.E37K	GBM(71;463 1194 9848 25922 46834)												.	PDE6B-90	0			c.G109A						.	G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	46	49	48		109,109	5	0	4		48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PDE6B	NM_000283.3,NM_001145291.1	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	37/855,37/854	619524	1,13005	2203	4300	6503	SO:0001583	missense	5158	exon1			GCCTGCGAGGACG	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"Phosphodiesterases"	8786	protein-coding gene	gene with protein product	"congenital stationary night blindness 3, autosomal dominant"	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.109G>A	4.37:g.619524G>A	ENSP00000420295:p.Glu37Lys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	62	15	NM_001145291	0	0	0	0	0	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	37	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	G	4.307	0.056193	0.08291	0.0	1.16E-4	ENSG00000133256	ENST00000255622;ENST00000496514	T;T	0.62639	0.01;0.01	4.98	4.98	0.66077	.	0.434210	0.23720	N	0.045237	T	0.49150	0.1540	L	0.38531	1.155	0.80722	D	1	B;B	0.13145	0.007;0.005	B;B	0.08055	0.001;0.003	T	0.44574	-0.9319	10	0.06494	T	0.89	.	15.7244	0.77743	0.0:0.0:1.0:0.0	.	37;37	P35913;P35913-2	PDE6B_HUMAN;.	K	37	ENSP00000255622:E37K;ENSP00000420295:E37K	ENSP00000255622:E37K	E	+	1	0	PDE6B	609524	0.010000	0.17322	0.010000	0.14722	0.110000	0.19582	1.168000	0.31859	2.326000	0.78906	0.561000	0.74099	GAG	.		0.647	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		A	619524	G	A	619524	3	1	130	1	0	0	0	0	1	0	0	0	11672	1059	37	1	111	1	PDE6B	4	619524	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		619524	190534752	52	11394											
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1806099	1806099	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacgaggcgggcagtgtgtAtgcaggcatcctcagctacg	8	8	15	10	3	1	1	1	1	0	0	2	2	2	1	1	3	3	5	1	3	2	2	rs121913485		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:1806099A>G	ENST00000260795.2	+	8	1220	c.1118A>G	c.(1117-1119)tAt>tGt	p.Y373C	FGFR3_ENST00000481110.2_Missense_Mutation_p.Y373C|FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000340107.4_Missense_Mutation_p.Y375C|FGFR3_ENST00000412135.2_Intron|FGFR3_ENST00000440486.2_Missense_Mutation_p.Y373C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	373			Y -> C (in KERSEB and TD1; disulfide- linked dimer with constitutive kinase activation). {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9207791}.		alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.Y373C(395)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	GGCAGTGTGTATGCAGGCATC	0.682	Y373C(KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.Y375C		.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	395	Substitution - Missense(395)	urinary_tract(371)|skin(16)|haematopoietic_and_lymphoid_tissue(8)	c.A1124G	GRCh37	CM960657	FGFR3	M	rs121913485	.						141	134	137					4																	1806099		2203	4300	6503	SO:0001583	missense	2261	exon9	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GTGTGTATGCAGG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1118A>G	4.37:g.1806099A>G	ENSP00000260795:p.Tyr373Cys	Somatic	304	1		WXS	Illumina HiSeq	Phase_I	201	172	NM_001163213	0	0	0	406	406	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	a	12.61	1.990190	0.35131	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000260795	D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35	4.68	1.93	0.25924	.	0.343855	0.31061	N	0.008340	D	0.93148	0.7818	M	0.82517	2.595	0.80722	A	1	D;D;D	0.76494	0.992;0.994;0.999	D;P;D	0.72625	0.94;0.896;0.978	D	0.94049	0.7316	9	0.72032	D	0.01	.	8.9873	0.36001	0.7079:0.0:0.0:0.2921	.	375;373;373	P22607-2;P22607;F8W9L4	.;FGFR3_HUMAN;.	C	373;375;373;373	ENSP00000420533:Y373C;ENSP00000339824:Y375C;ENSP00000414914:Y373C;ENSP00000260795:Y373C	ENSP00000260795:Y373C	Y	+	2	0	FGFR3	1775897	0.999000	0.42202	0.495000	0.27527	0.084000	0.17831	4.274000	0.58921	0.715000	0.32103	0.379000	0.24179	TAT	.		0.682	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1806099	A	G	1806099	3	3	130	1	0	0	0	0	1	0	0	0	5886	449	16	3	1303	3	FGFR3	4	1806099	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	1186575	1806099	189348177	53	11395											
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1807891	1807891	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacctcgactactacaagaaGacgaccaacgtgagcccggc	14	4	9	14	4	0	3	0	1	0	2	1	5	0	3	3	1	5	0	3	1	6	2	rs28928868		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:1807891G>C	ENST00000260795.2	+	13	2052	c.1950G>C	c.(1948-1950)aaG>aaC	p.K650N	FGFR3_ENST00000481110.2_Missense_Mutation_p.K651N|FGFR3_ENST00000352904.1_Missense_Mutation_p.K538N|FGFR3_ENST00000340107.4_Missense_Mutation_p.K652N|FGFR3_ENST00000412135.2_Missense_Mutation_p.K538N|FGFR3_ENST00000440486.2_Missense_Mutation_p.K650N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	650	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in KERSEB, TD2, TGCT and bladder cancer samples; bladder transitional cell carcinoma; somatic mutation; constitutively activated kinase with impaired internalization and degradation, resulting in prolonged FGFR3 signaling). {ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:19855393, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:9207791}.|K -> M (in KERSEB, ACH and TD1; constitutively activated kinase with impaired internalization and degradation, resulting in prolonged FGFR3 signaling). {ECO:0000269|PubMed:10671061, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:9207791}.|K -> Q (in hypochondroplasia and bladder cancer; in hypochondroplasia the form is milder than that seen in individuals with the K-540 or M-650 mutations; constitutively activated kinase). {ECO:0000269|PubMed:11055896, ECO:0000269|PubMed:11314002}.		alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	ACTACAAGAAGACGACCAACG	0.662		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.K652N		.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	0			c.G1956C	GRCh37	CM002965|CM002966	FGFR3	M	rs28928868	.						31	32	31					4																	1807891		2203	4299	6502	SO:0001583	missense	2261	exon14	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CAAGAAGACGACC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1950G>C	4.37:g.1807891G>C	ENSP00000260795:p.Lys650Asn	Somatic	50	1		WXS	Illumina HiSeq	Phase_I	18	16	NM_001163213	0	0	0	0	0	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	g	13.74	2.328521	0.41197	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	4.35	3.48	0.39840	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86100	0.5852	L	0.53671	1.685	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.98;1.0;1.0	D	0.85665	0.1291	10	0.87932	D	0	.	5.6966	0.17859	0.3256:0.0:0.6744:0.0	.	652;538;650;651	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	N	651;652;650;538;650;538	ENSP00000420533:K651N;ENSP00000339824:K652N;ENSP00000414914:K650N;ENSP00000412903:K538N;ENSP00000260795:K650N;ENSP00000231803:K538N	ENSP00000260795:K650N	K	+	3	2	FGFR3	1777689	1.000000	0.71417	1.000000	0.80357	0.396000	0.30629	2.106000	0.41835	2.127000	0.65507	0.448000	0.29417	AAG	G|1.000		0.662	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		C	1807891	G	C	1807891	3	2	130	1	0	0	0	0	1	0	0	0	5886	933	33	4	2155	4	FGFR3	4	1807891	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1792	1807891	189346385	54	11396											
FGFR3	2261	broad.mit.edu;bcgsc.ca	37	chr4	1808562	1808562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgccctgcccgcaggtacatGatcatgcgggagtgctggca	7	7	14	13	3	1	1	1	1	0	0	1	2	1	2	2	3	4	4	2	3	1	1	rs377402598		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:1808562G>A	ENST00000260795.2	+	16	2277	c.2175G>A	c.(2173-2175)atG>atA	p.M725I	FGFR3_ENST00000481110.2_Missense_Mutation_p.D703N|FGFR3_ENST00000352904.1_Missense_Mutation_p.M613I|FGFR3_ENST00000340107.4_Missense_Mutation_p.M727I|FGFR3_ENST00000412135.2_Missense_Mutation_p.M613I|FGFR3_ENST00000440486.2_Missense_Mutation_p.M725I			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	725	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	GCAGGTACATGATCATGCGGG	0.687		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.M727I				Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	0			c.G2181A						.	G	ILE/MET,ILE/MET,ILE/MET	1,4395		0,1,2197	23	25	24		2175,2181,1839	3.9	1	4		24	0,8598		0,0,4299	no	missense,missense,missense	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	10,10,10	0,1,6496	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign	725/807,727/809,613/695	1808562	1,12993	2198	4299	6497	SO:0001583	missense	2261	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GTACATGATCATG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.2175G>A	4.37:g.1808562G>A	ENSP00000260795:p.Met725Ile	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	13	10	NM_001163213	0	0	0	1	1	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.8|20.8	4.049321|4.049321	0.75846|0.75846	2.27E-4|2.27E-4	0.0|0.0	ENSG00000068078|ENSG00000068078	ENST00000481110|ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	T|D;D;D;D;D	0.80738|0.91180	-1.41|-2.8;-2.8;-2.8;-2.8;-2.8	4.88|4.88	3.88|3.88	0.44766|0.44766	.|Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.213818|.	0.46758|.	D|.	0.000263|.	D|D	0.83381|0.83381	0.5242|0.5242	N|N	0.20685|0.20685	0.6|0.6	0.80722|0.80722	D|D	1|1	B|B;P;B	0.25007|0.42409	0.116|0.015;0.779;0.354	B|B;B;B	0.24155|0.40165	0.051|0.047;0.313;0.321	T|T	0.83259|0.83259	-0.0049|-0.0049	10|9	0.87932|0.72032	D|D	0|0.01	.|.	11.1768|11.1768	0.48603|0.48603	0.1118:0.0:0.8882:0.0|0.1118:0.0:0.8882:0.0	.|.	703|727;613;725	F8W9L4|P22607-2;P22607-3;P22607	.|.;.;FGFR3_HUMAN	N|I	703|727;725;613;725;613	ENSP00000420533:D703N|ENSP00000339824:M727I;ENSP00000414914:M725I;ENSP00000412903:M613I;ENSP00000260795:M725I;ENSP00000231803:M613I	ENSP00000420533:D703N|ENSP00000260795:M725I	D|M	+|+	1|3	0|0	FGFR3|FGFR3	1778360|1778360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	6.445000|6.445000	0.73456|0.73456	0.925000|0.925000	0.37094|0.37094	0.561000|0.561000	0.74099|0.74099	GAT|ATG	.		0.687	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		A	1808562	G	A	1808562	3	1	130	1	0	0	0	0	1	0	0	0	5886	1290	45	2	2392	2	FGFR3	4	1808562	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	671	1808562	189345714	55	11397											
JAKMIP1	152789	broad.mit.edu;ucsc.edu	37	chr4	6052355	6052355	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagagcgctgctgtggttctCggggaaggtggtgatttgga	6	11	19	5	2	1	2	0	1	1	1	2	5	1	4	0	6	2	3	0	6	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:6052355C>T	ENST00000409021.3	-	14	2307	c.1858G>A	c.(1858-1860)Gag>Aag	p.E620K	JAKMIP1_ENST00000409371.3_Missense_Mutation_p.E435K	NM_001099433.1	NP_001092903.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	0	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTGTGGTTCTCGGGGAAGGTG	0.542																																					p.E620K													.	JAKMIP1-292	0			c.G1858A						.						91	99	96					4																	6052355		2026	4154	6180	SO:0001583	missense	152789	exon14			GGTTCTCGGGGAA	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000409021.3:c.1858G>A	4.37:g.6052355C>T	ENSP00000386711:p.Glu620Lys	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	11	7	NM_001099433	0	0	0	0	0	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000409021.3	37	CCDS47005.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598874	0.66332	.	.	ENSG00000152969	ENST00000409021;ENST00000409371	T;T	0.36157	1.7;1.27	5.1	5.1	0.69264	.	.	.	.	.	T	0.27731	0.0682	.	.	.	0.80722	D	1	P;D	0.56287	0.899;0.975	B;B	0.38225	0.268;0.206	T	0.04976	-1.0914	8	0.35671	T	0.21	.	13.3054	0.60349	0.0:0.8416:0.1584:0.0	.	435;620	Q96N16-5;Q96N16-2	.;.	K	620;435	ENSP00000386711:E620K;ENSP00000387042:E435K	ENSP00000386711:E620K	E	-	1	0	JAKMIP1	6103256	1.000000	0.71417	0.998000	0.56505	0.876000	0.50452	6.374000	0.73132	2.375000	0.81037	0.555000	0.69702	GAG	.		0.542	JAKMIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329747.1	NM_144720		T	6052355	C	T	6052355	3	4	130	1	0	0	0	0	1	0	0	0	7961	893	31	1	669	1	JAKMIP1	4	6052355	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4243793	6052355	185101921	56	11398											
PPARGC1A	10891	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	23830149	23830149	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgtggtcagatatttgaGaagctccgagcagggacgtc	9	11	14	7	2	1	2	1	1	0	2	3	5	2	3	1	2	2	3	1	2	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:23830149G>T	ENST00000264867.2	-	5	750	c.631C>A	c.(631-633)Ctc>Atc	p.L211I	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	211					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				AGATATTTGAGAAGCTCCGAG	0.443																																					p.L211I	Esophageal Squamous(29;694 744 13796 34866 44181)	.											.	PPARGC1A-230	0			c.C631A						.						373	340	351					4																	23830149		2203	4300	6503	SO:0001583	missense	10891	exon5			ATTTGAGAAGCTC	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.631C>A	4.37:g.23830149G>T	ENSP00000264867:p.Leu211Ile	Somatic	210	1		WXS	Illumina HiSeq	Phase_I	198	70	NM_013261	0	0	0	0	0	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	37	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.209026	0.58343	.	.	ENSG00000109819	ENST00000264867	T	0.27104	1.69	6.17	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.52789	0.1756	M	0.79475	2.455	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.58487	-0.7628	10	0.66056	D	0.02	-1.9376	15.7894	0.78343	0.065:0.0:0.935:0.0	.	211	Q9UBK2	PRGC1_HUMAN	I	211	ENSP00000264867:L211I	ENSP00000264867:L211I	L	-	1	0	PPARGC1A	23439247	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.637000	0.91014	1.626000	0.50381	0.655000	0.94253	CTC	.		0.443	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		T	23830149	G	T	23830149	3	4	130	1	0	0	0	0	1	0	0	0	12326	942	33	4	1801	4	PPARGC1A	4	23830149	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	17777794	23830149	167324127	57	11399											
HOPX	84525	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr4	57514941	57514941	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgagcgccgccactttGccaggcgctgcttaaaccat	7	10	9	15	3	1	1	0	1	1	0	1	1	1	1	4	1	4	2	4	1	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:57514941G>A	ENST00000337881.7	-	3	823	c.167C>T	c.(166-168)gCa>gTa	p.A56V	HOPX_ENST00000503639.3_Missense_Mutation_p.A56V|HOPX_ENST00000381260.3_3'UTR|HOPX_ENST00000556376.2_Missense_Mutation_p.A56V|HOPX_ENST00000555760.2_Missense_Mutation_p.A56V|HOPX_ENST00000556614.2_Missense_Mutation_p.A56V|HOPX_ENST00000381255.3_Missense_Mutation_p.A56V|HOPX_ENST00000553379.2_Missense_Mutation_p.A56V|HOPX_ENST00000420433.1_Missense_Mutation_p.A74V|HOPX_ENST00000554144.1_3'UTR|HOPX_ENST00000508121.1_Missense_Mutation_p.A74V|HOPX_ENST00000317745.7_Missense_Mutation_p.A56V	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox	56					heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					CCGCCACTTTGCCAGGCGCTG	0.478																																					p.A74V		.											.	HOPX-22	0			c.C221T						.						78	77	77					4																	57514941		2203	4300	6503	SO:0001583	missense	84525	exon4			CACTTTGCCAGGC		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"Homeoboxes / PRD class"	24961	protein-coding gene	gene with protein product	"homeobox only domain"	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.167C>T	4.37:g.57514941G>A	ENSP00000337330:p.Ala56Val	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	145	61	NM_032495	0	0	178	321	143	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Missense_Mutation	SNP	ENST00000337881.7	37	CCDS3507.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.103343	0.76983	.	.	ENSG00000171476	ENST00000420433;ENST00000508121;ENST00000556376;ENST00000553379;ENST00000381255;ENST00000317745;ENST00000503639;ENST00000337881;ENST00000555760;ENST00000556614;ENST00000514890;ENST00000506661	D;D;D;D;D;D;D;D;D;D	0.97161	-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27	5.93	5.93	0.95920	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	.	.	.	.	D	0.98298	0.9436	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.995	D;D	0.69824	0.966;0.927	D	0.98808	1.0742	8	0.87932	D	0	.	15.8335	0.78778	0.0:0.0:1.0:0.0	.	74;56	E9PB55;Q9BPY8	.;HOP_HUMAN	V	74;74;56;56;56;56;56;56;56;56;56;56	ENSP00000396275:A74V;ENSP00000422175:A74V;ENSP00000451794:A56V;ENSP00000452340:A56V;ENSP00000370654:A56V;ENSP00000315198:A56V;ENSP00000424101:A56V;ENSP00000337330:A56V;ENSP00000452098:A56V;ENSP00000452003:A56V	ENSP00000315198:A56V	A	-	2	0	HOPX	57209698	1.000000	0.71417	0.996000	0.52242	0.528000	0.34623	5.302000	0.65733	2.818000	0.97014	0.591000	0.81541	GCA	.		0.478	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4			A	57514941	G	A	57514941	3	1	130	1	0	0	0	0	1	0	0	0	7306	1319	46	2	58	2	HOPX	4	57514941	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	33684792	57514941	133639335	58	11400											
PLK4	10733	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	128813651	128813651	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attctcctggtgctgattttGaggtttggttttatgatggt	5	20	12	4	0	1	3	0	3	1	0	2	3	1	3	1	4	1	3	1	4	1	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:128813651G>C	ENST00000270861.5	+	10	2444	c.2170G>C	c.(2170-2172)Gag>Cag	p.E724Q	PLK4_ENST00000507249.1_Missense_Mutation_p.E663Q|PLK4_ENST00000515069.1_Missense_Mutation_p.E646Q|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000514379.1_Missense_Mutation_p.E683Q|PLK4_ENST00000513090.1_Missense_Mutation_p.E692Q	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	724					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						TGCTGATTTTGAGGTTTGGTT	0.318																																					p.E724Q	Colon(135;508 1718 19061 31832 42879)	.											.	PLK4-333	0			c.G2170C						.						145	132	137					4																	128813651		2202	4300	6502	SO:0001583	missense	10733	exon10			GATTTTGAGGTTT	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"serine/threonine kinase 18", "polo-like kinase 4 (Drosophila)"	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2170G>C	4.37:g.128813651G>C	ENSP00000270861:p.Glu724Gln	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	53	7	NM_014264	0	0	2	4	2	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561758	0.86335	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.66723	0.2818	M	0.86178	2.8	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.72239	-0.4351	10	0.87932	D	0	-7.7549	19.2043	0.93723	0.0:0.0:1.0:0.0	.	692;724	O00444-2;O00444	.;PLK4_HUMAN	Q	724;646;692;663;683	ENSP00000270861:E724Q;ENSP00000421774:E646Q;ENSP00000427554:E692Q;ENSP00000423412:E663Q;ENSP00000423582:E683Q	ENSP00000270861:E724Q	E	+	1	0	PLK4	129033101	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.502000	0.97981	2.536000	0.85505	0.313000	0.20887	GAG	.		0.318	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			C	128813651	G	C	128813651	3	2	130	1	0	0	0	0	1	0	0	0	12124	1291	45	4	2208	4	PLK4	4	128813651	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	71298710	128813651	62340625	59	11401											
MAP3K1	4214	ucsc.edu	37	chr5	56155606	56155606	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacttagcagctgagtctcCaggagaggtccaggcaagtg	10	8	13	10	0	2	2	1	1	1	1	4	3	3	2	2	3	2	3	2	3	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:56155606C>T	ENST00000399503.3	+	3	698	c.698C>T	c.(697-699)cCa>cTa	p.P233L	AC008937.2_ENST00000415589.1_RNA|snoU13_ENST00000459264.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	233					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GCTGAGTCTCCAGGAGAGGTC	0.463																																					p.P233L													.	MAP3K1-956	0			c.C698T						.						43	43	43					5																	56155606		1915	4137	6052	SO:0001583	missense	4214	exon3			AGTCTCCAGGAGA	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.698C>T	5.37:g.56155606C>T	ENSP00000382423:p.Pro233Leu	Somatic	37	0		WXS	Illumina HiSeq		35	4	NM_005921	0	0	10	10	0		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	C	8.286	0.816620	0.16607	.	.	ENSG00000095015	ENST00000399503	T	0.66099	-0.19	5.72	-1.09	0.09904	.	0.679571	0.15209	N	0.274585	T	0.38374	0.1038	N	0.08118	0	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.18209	-1.0344	10	0.35671	T	0.21	.	12.3505	0.55144	0.2871:0.6121:0.0:0.1008	.	233	Q13233	M3K1_HUMAN	L	233	ENSP00000382423:P233L	ENSP00000382423:P233L	P	+	2	0	MAP3K1	56191363	0.348000	0.24861	0.010000	0.14722	0.155000	0.21991	0.666000	0.25097	-0.319000	0.08652	-0.150000	0.13652	CCA	.		0.463	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		T	56155606	C	T	56155606	3	4	130	1	0	0	0	0	1	0	0	0	9268	594	21	2	708	2	MAP3K1	5	56155606	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		56155606	124759654	60	11402											
MAP1B	4131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	71495628	71495628	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgatgaaacccctcccacctCagtcagcgagtcagccccat	10	7	7	17	1	3	2	3	2	0	0	4	3	4	2	6	0	3	0	6	0	1	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:71495628C>G	ENST00000296755.7	+	5	6744	c.6446C>G	c.(6445-6447)tCa>tGa	p.S2149*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2149					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CCTCCCACCTCAGTCAGCGAG	0.587																																					p.S2149X	Melanoma(17;367 822 11631 31730 47712)	.											.	MAP1B-155	0			c.C6446G						.						90	81	84					5																	71495628		2203	4300	6503	SO:0001587	stop_gained	4131	exon5			CCACCTCAGTCAG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 102"	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6446C>G	5.37:g.71495628C>G	ENSP00000296755:p.Ser2149*	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	73	8	NM_005909	0	0	3	3	0	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	48	14.809369	0.99811	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.82	5.82	0.92795	.	0.000000	0.52532	D	0.000072	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.7908	20.0953	0.97838	0.0:1.0:0.0:0.0	.	.	.	.	X	2149	.	ENSP00000296755:S2149X	S	+	2	0	MAP1B	71531384	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.767000	0.95098	0.655000	0.94253	TCA	.		0.587	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		G	71495628	C	G	71495628	4	3	130	1	0	0	0	0	0	1	0	0	9253	838	29	4	6464	4	MAP1B	5	71495628	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	15340022	71495628	109419632	61	11403											
CMYA5	202333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	79027353	79027353	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaagaaattgtccatagatCtctaaatctaaaaggtgcat	16	11	8	6	0	2	2	0	0	2	2	4	3	3	3	1	2	1	1	1	2	7	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79027353C>T	ENST00000446378.2	+	2	2796	c.2765C>T	c.(2764-2766)tCt>tTt	p.S922F		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	922					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GTCCATAGATCTCTAAATCTA	0.413																																					p.S922F		.											.	CMYA5-77	0			c.C2765T						.						103	100	101					5																	79027353		1924	4135	6059	SO:0001583	missense	202333	exon2			ATAGATCTCTAAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.2765C>T	5.37:g.79027353C>T	ENSP00000394770:p.Ser922Phe	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	94	51	NM_153610	0	0	4	15	11	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	C	7.587	0.669858	0.14776	.	.	ENSG00000164309	ENST00000446378	T	0.59502	0.26	5.54	2.7	0.31948	.	1.759930	0.02782	N	0.121104	T	0.67239	0.2872	M	0.78456	2.415	0.09310	N	1	D	0.56035	0.974	P	0.49752	0.621	T	0.40813	-0.9543	10	0.72032	D	0.01	.	4.9024	0.13781	0.178:0.5938:0.0:0.2282	.	922	Q8N3K9	CMYA5_HUMAN	F	922	ENSP00000394770:S922F	ENSP00000394770:S922F	S	+	2	0	CMYA5	79063109	0.035000	0.19736	0.003000	0.11579	0.048000	0.14542	0.437000	0.21543	0.358000	0.24211	-0.302000	0.09304	TCT	.		0.413	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79027353	C	T	79027353	3	4	130	1	0	0	0	0	1	0	0	0	3596	913	32	2	2771	2	CMYA5	5	79027353	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	7531725	79027353	101887907	62	11404			1	34		5	5	5227	N	G_C	8.857889e-08
CMYA5	202333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	79030983	79030983	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agtaaaaatacccacacaaaGaaaacccatctcctcaatcc	19	6	2	14	0	2	1	1	0	1	1	4	1	3	1	4	0	2	1	4	0	8	2	rs79193094	byFrequency	TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79030983G>C	ENST00000446378.2	+	2	6426	c.6395G>C	c.(6394-6396)aGa>aCa	p.R2132T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2132					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CCCACACAAAGAAAACCCATC	0.448																																					p.R2132T		.											.	CMYA5-77	0			c.G6395C						.						84	81	82					5																	79030983		1882	4113	5995	SO:0001583	missense	202333	exon2			CACAAAGAAAACC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6395G>C	5.37:g.79030983G>C	ENSP00000394770:p.Arg2132Thr	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	84	38	NM_153610	0	0	9	24	15	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	6.577	0.474842	0.12521	.	.	ENSG00000164309	ENST00000446378	T	0.04015	3.73	5.96	1.21	0.21127	.	1.390360	0.04325	N	0.351334	T	0.02047	0.0064	N	0.03608	-0.345	0.09310	N	1	B	0.14805	0.011	B	0.11329	0.006	T	0.44877	-0.9299	10	0.13108	T	0.6	.	0.325	0.00309	0.2677:0.1408:0.3029:0.2886	.	2132	Q8N3K9	CMYA5_HUMAN	T	2132	ENSP00000394770:R2132T	ENSP00000394770:R2132T	R	+	2	0	CMYA5	79066739	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.548000	0.23314	0.297000	0.22615	0.650000	0.86243	AGA	G|0.999;A|0.001		0.448	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79030983	G	C	79030983	3	2	130	1	0	0	0	0	1	0	0	0	3596	942	33	4	6401	4	CMYA5	5	79030983	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3630	79030983	101884277	63	11405			1	34		5	5	5227	N	G_C	8.857889e-08
CMYA5	202333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	79031337	79031337	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taaaactgctgatgaacccaGaggtactttagtaaaatctg	15	11	8	7	0	1	3	0	2	1	1	1	3	1	3	1	1	4	3	1	1	7	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79031337G>A	ENST00000446378.2	+	2	6780	c.6749G>A	c.(6748-6750)aGa>aAa	p.R2250K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2250					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GATGAACCCAGAGGTACTTTA	0.343																																					p.R2250K		.											.	CMYA5-77	0			c.G6749A						.						84	86	85					5																	79031337		1802	4075	5877	SO:0001583	missense	202333	exon2			AACCCAGAGGTAC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6749G>A	5.37:g.79031337G>A	ENSP00000394770:p.Arg2250Lys	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	140	75	NM_153610	0	0	11	24	13	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	4.593	0.110236	0.08780	.	.	ENSG00000164309	ENST00000446378	T	0.15718	2.4	5.74	-0.131	0.13494	.	1.286200	0.05079	N	0.483194	T	0.15046	0.0363	L	0.48362	1.52	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.33599	-0.9862	10	0.33940	T	0.23	.	4.6556	0.12615	0.2976:0.3196:0.3827:0.0	.	2250	Q8N3K9	CMYA5_HUMAN	K	2250	ENSP00000394770:R2250K	ENSP00000394770:R2250K	R	+	2	0	CMYA5	79067093	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.363000	0.07593	0.328000	0.23435	0.650000	0.86243	AGA	.		0.343	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79031337	G	A	79031337	3	1	130	1	0	0	0	0	1	0	0	0	3596	942	33	2	6755	2	CMYA5	5	79031337	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	354	79031337	101883923	64	11406			1	34		5	5	5227	N	G_C	8.857889e-08
CMYA5	202333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	79031882	79031882	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtgaagacagactcaagaaaGaaatgcaaaatcctacttcc	18	7	7	9	0	1	5	1	1	0	4	3	5	3	5	2	0	2	1	2	0	7	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79031882G>C	ENST00000446378.2	+	2	7325	c.7294G>C	c.(7294-7296)Gaa>Caa	p.E2432Q		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2432					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ACTCAAGAAAGAAATGCAAAA	0.333																																					p.E2432Q		.											.	CMYA5-77	0			c.G7294C						.						38	38	38					5																	79031882		1818	4082	5900	SO:0001583	missense	202333	exon2			AAGAAAGAAATGC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7294G>C	5.37:g.79031882G>C	ENSP00000394770:p.Glu2432Gln	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	58	24	NM_153610	0	0	3	9	6	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.484254	0.63962	.	.	ENSG00000164309	ENST00000446378	T	0.24723	1.84	5.87	4.09	0.47781	.	0.121012	0.37483	N	0.002068	T	0.37100	0.0991	M	0.71581	2.175	0.28279	N	0.924047	D	0.59767	0.986	P	0.53954	0.738	T	0.32877	-0.9890	10	0.66056	D	0.02	.	6.9428	0.24502	0.2444:0.0:0.7556:0.0	.	2432	Q8N3K9	CMYA5_HUMAN	Q	2432	ENSP00000394770:E2432Q	ENSP00000394770:E2432Q	E	+	1	0	CMYA5	79067638	0.992000	0.36948	0.963000	0.40424	0.963000	0.63663	1.287000	0.33284	1.493000	0.48517	0.655000	0.94253	GAA	.		0.333	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79031882	G	C	79031882	3	2	130	1	0	0	0	0	1	0	0	0	3596	943	33	4	7300	4	CMYA5	5	79031882	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	545	79031882	101883378	65	11407			1	34		5	5	5227	N	G_C	8.857889e-08
CMYA5	202333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	79032579	79032579	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtattagaaaagtcaagcaGagatatgccagatcacagtg	17	8	10	6	0	2	3	2	0	0	3	2	4	2	3	1	0	2	2	1	0	6	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79032579G>A	ENST00000446378.2	+	2	8022	c.7991G>A	c.(7990-7992)aGa>aAa	p.R2664K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2664					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAGTCAAGCAGAGATATGCCA	0.403																																					p.R2664K		.											.	CMYA5-77	0			c.G7991A						.						49	49	49					5																	79032579		1848	4092	5940	SO:0001583	missense	202333	exon2			CAAGCAGAGATAT	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7991G>A	5.37:g.79032579G>A	ENSP00000394770:p.Arg2664Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	50	25	NM_153610	0	0	19	35	16	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.448897	0.26074	.	.	ENSG00000164309	ENST00000446378	T	0.36340	1.26	3.85	2.95	0.34219	.	.	.	.	.	T	0.25419	0.0618	L	0.34521	1.04	0.09310	N	1	B	0.26483	0.15	B	0.23419	0.046	T	0.17349	-1.0372	9	0.39692	T	0.17	.	6.834	0.23925	0.1396:0.0:0.8604:0.0	.	2664	Q8N3K9	CMYA5_HUMAN	K	2664	ENSP00000394770:R2664K	ENSP00000394770:R2664K	R	+	2	0	CMYA5	79068335	0.000000	0.05858	0.016000	0.15963	0.089000	0.18198	0.577000	0.23758	0.699000	0.31761	0.393000	0.25936	AGA	.		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79032579	G	A	79032579	3	1	130	1	0	0	0	0	1	0	0	0	3596	942	33	2	7997	2	CMYA5	5	79032579	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	697	79032579	101882681	66	11408			1	34		5	5	5227	N	G_C	8.857889e-08
MTX3	345778	hgsc.bcm.edu	37	chr5	79284404	79284404	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcaaaggaaaaggaatttGtgaagcaaaccatggctttg	16	9	10	6	0	1	1	1	1	0	0	1	3	1	3	1	3	2	2	1	3	6	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79284404G>C	ENST00000512528.1	-	5	405	c.385C>G	c.(385-387)Caa>Gaa	p.Q129E	MTX3_ENST00000509852.1_Missense_Mutation_p.Q129E|MTX3_ENST00000512560.1_Missense_Mutation_p.Q68E			Q5HYI7	MTX3_HUMAN	metaxin 3	129					protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		AAAGGAATTTGTGAAGCAAAC	0.438																																					p.Q129E		.											.	.	0			c.C385G						.						52	48	49					5																	79284404		1886	4117	6003	SO:0001583	missense	345778	exon5			GAATTTGTGAAGC	BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.385C>G	5.37:g.79284404G>C	ENSP00000424798:p.Gln129Glu	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	18	2	NM_001010891	0	0	3	3	0	B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	37		.	.	.	.	.	.	.	.	.	.	G	12.57	1.978410	0.34942	.	.	ENSG00000177034	ENST00000512560;ENST00000328496;ENST00000509852;ENST00000512528;ENST00000418095	T;T;T	0.40476	1.05;1.03;1.03	5.58	5.58	0.84498	.	0.238382	0.42548	D	0.000688	T	0.26376	0.0644	N	0.19112	0.55	0.23386	N	0.997788	B;B	0.13594	0.004;0.008	B;B	0.23275	0.009;0.045	T	0.14699	-1.0463	10	0.02654	T	1	-2.1197	14.3221	0.66493	0.0:0.0:0.8155:0.1845	.	129;129	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	E	68;129;129;129;129	ENSP00000423600:Q68E;ENSP00000423302:Q129E;ENSP00000424798:Q129E	ENSP00000331672:Q129E	Q	-	1	0	MTX3	79320160	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	4.897000	0.63231	2.627000	0.88993	0.655000	0.94253	CAA	.		0.438	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971		C	79284404	G	C	79284404	3	2	130	1	0	0	0	0	1	0	0	0	9994	1386	48	4	573	4	MTX3	5	79284404	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	251825	79284404	101630856	67	11409											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82786054	82786054	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatcaaatggtctaagattGaagtggacaaaaatggaaaa	19	8	10	4	0	2	2	1	1	1	1	2	4	2	4	0	3	0	1	0	3	7	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:82786054G>T	ENST00000265077.3	+	3	773	c.208G>T	c.(208-210)Gaa>Taa	p.E70*	VCAN_ENST00000343200.5_Nonsense_Mutation_p.E70*|VCAN_ENST00000513984.1_Nonsense_Mutation_p.E70*|VCAN_ENST00000502527.2_Nonsense_Mutation_p.E70*|VCAN_ENST00000342785.4_Nonsense_Mutation_p.E70*|VCAN_ENST00000512590.2_Nonsense_Mutation_p.E22*	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	70	Ig-like V-type.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GTCTAAGATTGAAGTGGACAA	0.418																																					p.E70X		.											.	VCAN-238	0			c.G208T						.						104	102	103					5																	82786054		2203	4300	6503	SO:0001587	stop_gained	1462	exon3			AAGATTGAAGTGG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.208G>T	5.37:g.82786054G>T	ENSP00000265077:p.Glu70*	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	99	23	NM_004385	0	0	8	8	0	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Nonsense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	40	8.125073	0.98665	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000513960;ENST00000513984;ENST00000502527	.	.	.	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	19.9898	0.97362	0.0:0.0:1.0:0.0	.	.	.	.	X	70;70;70;22;70;70;70	.	ENSP00000265077:E70X	E	+	1	0	VCAN	82821810	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.034000	0.64152	2.733000	0.93635	0.655000	0.94253	GAA	.		0.418	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82786054	G	T	82786054	4	4	130	1	0	0	0	0	0	1	0	0	17171	1291	45	4	214	4	VCAN	5	82786054	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3501650	82786054	98129206	68	11410											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	82817031	82817031	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcctactacttatgtagactCttcccataccattcctcttt	8	16	3	14	0	2	1	0	0	2	1	4	1	4	1	4	0	3	1	4	0	5	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:82817031C>G	ENST00000265077.3	+	7	3471	c.2906C>G	c.(2905-2907)tCt>tGt	p.S969C	VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.S969C|VCAN_ENST00000512590.2_Missense_Mutation_p.S921C	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	969	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TATGTAGACTCTTCCCATACC	0.433																																					p.S969C		.											.	VCAN-238	0			c.C2906G						.						113	112	112					5																	82817031		2203	4300	6503	SO:0001583	missense	1462	exon7			TAGACTCTTCCCA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2906C>G	5.37:g.82817031C>G	ENSP00000265077:p.Ser969Cys	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	105	9	NM_004385	0	0	0	0	0	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	10.39	1.337475	0.24253	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.20332	2.08;2.08;2.08	5.26	-0.324	0.12706	.	1.069220	0.07230	N	0.862281	T	0.21718	0.0523	L	0.44542	1.39	0.09310	N	1	P;P	0.51653	0.904;0.947	P;P	0.47981	0.563;0.453	T	0.19257	-1.0311	10	0.62326	D	0.03	.	4.5464	0.12083	0.0:0.4105:0.2996:0.29	.	969;969	P13611-3;P13611	.;CSPG2_HUMAN	C	969;969;921	ENSP00000265077:S969C;ENSP00000342768:S969C;ENSP00000425959:S921C	ENSP00000265077:S969C	S	+	2	0	VCAN	82852787	0.000000	0.05858	0.022000	0.16811	0.689000	0.40095	-0.838000	0.04372	-0.249000	0.09569	0.591000	0.81541	TCT	.		0.433	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82817031	C	G	82817031	3	3	130	1	0	0	0	0	1	0	0	0	17171	913	32	4	2928	4	VCAN	5	82817031	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	30977	82817031	98098229	69	11411											
APBB3	10307	hgsc.bcm.edu	37	chr5	139940335	139940335	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcctcgttcagcacatcCatgcctgggggaacataccc	9	8	10	14	1	1	0	1	0	0	0	3	1	2	1	4	3	4	2	4	3	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:139940335C>G	ENST00000357560.4	-	11	1364	c.921G>C	c.(919-921)atG>atC	p.M307I	APBB3_ENST00000507279.1_5'Flank|APBB3_ENST00000354402.5_Missense_Mutation_p.M314I|SRA1_ENST00000336283.6_5'Flank|APBB3_ENST00000356738.2_Missense_Mutation_p.M312I|APBB3_ENST00000508496.2_Missense_Mutation_p.M84I|APBB3_ENST00000511201.2_Intron|APBB3_ENST00000412920.3_Missense_Mutation_p.M305I|APBB3_ENST00000358580.5_Intron	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	307	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGCACATCCATGCCTGGGG	0.572																																					p.M314I		.											.	APBB3-92	0			c.G942C						.						43	44	44					5																	139940335		2203	4300	6503	SO:0001583	missense	10307	exon10			CACATCCATGCCT	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.921G>C	5.37:g.139940335C>G	ENSP00000350171:p.Met307Ile	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_006051	0	0	0	0	0	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180314	0.57800	.	.	ENSG00000113108	ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920	T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	L	0.38175	1.15	0.80722	D	1	D;P	0.54601	0.967;0.803	P;B	0.46940	0.532;0.27	T	0.00822	-1.1552	9	.	.	.	-17.4445	15.5267	0.75915	0.0:0.862:0.138:0.0	.	305;312	O95704-2;O95704-3	.;.	I	312;314;307;84;305	ENSP00000349177:M312I;ENSP00000346378:M314I;ENSP00000350171:M307I;ENSP00000444013:M84I;ENSP00000402591:M305I	.	M	-	3	0	APBB3	139920519	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.658000	0.61497	2.579000	0.87056	0.655000	0.94253	ATG	.		0.572	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051		G	139940335	C	G	139940335	3	3	130	1	0	0	0	0	1	0	0	0	762	594	21	4	551	4	APBB3	5	139940335	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	57123304	139940335	40974925	70	11412											
PCDHGC3	5098	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140856910	140856910	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcaagaattacttcactttGaaaaccagtgcagacctgga	14	10	7	10	0	2	3	2	1	0	2	2	4	2	4	2	1	3	1	2	1	5	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:140856910G>A	ENST00000308177.3	+	1	1331	c.1227G>A	c.(1225-1227)ttG>ttA	p.L409L	PCDHGB7_ENST00000398594.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA11_ENST00000518882.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	409	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTTCACTTTGAAAACCAGTG	0.552																																					p.L409L													.	PCDHGC3-24	0			c.G1227A						.						55	56	56					5																	140856910		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			CACTTTGAAAACC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"Cadherins / Protocadherins : Clustered"	8716	other	protocadherin	"cadherin-like 2", "protocadherin 2", "protocadherin 43"	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.1227G>A	5.37:g.140856910G>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	59	14	NM_032402	0	0	3	6	3	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			.		0.552	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		A	140856910	G	A	140856910	2	1	130	1	0	0	0	0	0	0	0	1	11595	1281	45	2		2	PCDHGC3	5	140856910	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	916575	140856910	40058350	71	11413											
GRIA1	2890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	153078520	153078520	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagagctggcggcagagattGccaagcacgtgggctactcc	9	7	14	11	2	0	2	0	0	0	2	1	3	1	2	2	3	4	4	2	3	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:153078520G>C	ENST00000285900.5	+	10	1682	c.1339G>C	c.(1339-1341)Gcc>Ccc	p.A447P	GRIA1_ENST00000340592.5_Missense_Mutation_p.A447P|GRIA1_ENST00000518142.1_Missense_Mutation_p.A367P|GRIA1_ENST00000521843.2_Missense_Mutation_p.A378P|GRIA1_ENST00000448073.4_Missense_Mutation_p.A457P|GRIA1_ENST00000518783.1_Missense_Mutation_p.A457P	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	447					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GGCAGAGATTGCCAAGCACGT	0.537																																					p.A457P		.											.	GRIA1-96	0			c.G1369C						.						115	102	106					5																	153078520		2203	4300	6503	SO:0001583	missense	2890	exon10			GAGATTGCCAAGC		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1339G>C	5.37:g.153078520G>C	ENSP00000285900:p.Ala447Pro	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	82	19	NM_001258021	0	0	0	0	0	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	34	5.344853	0.95807	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;D;T;T;T;D	0.81821	1.03;1.03;-1.54;1.03;1.03;1.03;-1.54	5.44	5.44	0.79542	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.93514	0.7930	H	0.96996	3.92	0.80722	D	1	D;D;D;D;D;D	0.71674	0.987;0.987;0.998;0.987;0.984;0.998	D;D;D;D;P;D	0.91635	0.931;0.931;0.999;0.931;0.887;0.984	D	0.95457	0.8539	10	0.87932	D	0	.	18.2393	0.89961	0.0:0.0:1.0:0.0	.	457;457;367;457;447;447	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	P	447;447;367;401;447;378;378;457;457	ENSP00000285900:A447P;ENSP00000427920:A367P;ENSP00000339343:A447P;ENSP00000427864:A378P;ENSP00000442108:A378P;ENSP00000428994:A457P;ENSP00000415569:A457P	ENSP00000285900:A447P	A	+	1	0	GRIA1	153058713	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.640000	0.98453	2.548000	0.85928	0.655000	0.94253	GCC	.		0.537	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			C	153078520	G	C	153078520	3	2	130	1	0	0	0	0	1	0	0	0	6788	1319	46	4	1377	4	GRIA1	5	153078520	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	12221610	153078520	27836740	72	11414											
SGCD	6444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156186311	156186311	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaacgaggcagaaggtcttCgagatctgcgtctgcgccaa	10	7	14	10	4	3	2	0	0	3	2	4	5	3	3	1	3	3	1	1	3	3	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:156186311C>T	ENST00000435422.3	+	8	1267	c.780C>T	c.(778-780)ttC>ttT	p.F260F	SGCD_ENST00000337851.4_Silent_p.F261F	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	260					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.F261L(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGAAGGTCTTCGAGATCTGCG	0.488																																					p.F261F		.											.	.	1	Substitution - Missense(1)	lung(1)	c.C783T						.						130	125	127					5																	156186311		1968	4175	6143	SO:0001819	synonymous_variant	6444	exon9			GGTCTTCGAGATC	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.780C>T	5.37:g.156186311C>T		Somatic	171	1		WXS	Illumina HiSeq	Phase_I	131	44	NM_000337	0	0	0	0	0	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	37	CCDS47327.1																																																																																			.		0.488	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3			T	156186311	C	T	156186311	2	4	130	1	0	0	0	0	0	0	0	1	14233	883	31	1		1	SGCD	5	156186311	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3107791	156186311	24728949	73	11415											
HLA-B	3106	broad.mit.edu	37	chr6	31324628	31324628	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggactcgcggcgtcgctgtcGaacctcacgaactgggtgtc	6	8	14	13	6	1	0	1	0	0	0	5	3	1	1	1	3	2	1	1	3	2	0	rs151341114		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:31324628G>A	ENST00000412585.2	-	2	208	c.180C>T	c.(178-180)ttC>ttT	p.F60F		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	60	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGTCGCTGTCGAACCTCACGA	0.652									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.F60F													.	HLA-B-90	0			c.C180T						.						39	33	35					6																	31324628		2158	4201	6359	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GCTGTCGAACCTC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4932	protein-coding gene	gene with protein product		142830	"ankylosing spondylitis"	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.180C>T	6.37:g.31324628G>A		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	12	7	NM_005514	1	0	164	871	705	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			.		0.652	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		A	31324628	G	A	31324628	2	1	130	1	0	0	0	0	0	0	0	1	7217	1049	37	1		1	HLA-B	6	31324628	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		31324628	139790439	74	11416											
FOXP4	116113	bcgsc.ca	37	chr6	41533574	41533574	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgggcagcctctctgggCaagccgatggcagcagcggc	6	5	17	13	3	1	0	0	0	1	0	2	1	1	0	2	4	4	4	2	4	1	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:41533574C>A	ENST00000307972.4	+	1	88	c.76C>A	c.(76-78)Caa>Aaa	p.Q26K	FOXP4_ENST00000409208.1_Missense_Mutation_p.Q26K|FOXP4_ENST00000373063.3_Missense_Mutation_p.Q26K|FOXP4_ENST00000373060.1_Missense_Mutation_p.Q26K|FOXP4_ENST00000373057.3_Missense_Mutation_p.Q26K			Q8IVH2	FOXP4_HUMAN	forkhead box P4	26					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CCTCTCTGGGCAAGCCGATGG	0.627																																					p.Q26K													.	FOXP4-289	0			c.C76A						.						83	84	84					6																	41533574		2201	4292	6493	SO:0001583	missense	116113	exon2			TCTGGGCAAGCCG	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"Forkhead boxes"	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.76C>A	6.37:g.41533574C>A	ENSP00000309823:p.Gln26Lys	Somatic	170	16		WXS	Illumina HiSeq	Phase_1	81	18	NM_001012427	0	0	6	6	0	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.547854	0.45383	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.91464	-2.85;-2.81;-2.81;-2.8;-2.85	5.35	5.35	0.76521	.	0.000000	0.50627	D	0.000103	D	0.82715	0.5097	M	0.70595	2.14	0.58432	D	0.999996	B;B;B	0.29037	0.231;0.231;0.231	B;B;B	0.24848	0.056;0.056;0.056	T	0.82694	-0.0330	10	0.02654	T	1	.	19.0777	0.93169	0.0:1.0:0.0:0.0	.	26;26;26	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	K	26	ENSP00000362151:Q26K;ENSP00000362154:Q26K;ENSP00000386958:Q26K;ENSP00000362148:Q26K;ENSP00000309823:Q26K	ENSP00000309823:Q26K	Q	+	1	0	FOXP4	41641552	1.000000	0.71417	0.999000	0.59377	0.155000	0.21991	7.077000	0.76814	2.529000	0.85273	0.655000	0.94253	CAA	.		0.627	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		A	41533574	C	A	41533574	3	1	130	1	0	0	0	0	1	0	0	0	6048	711	25	4	78	4	FOXP4	6	41533574	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	10208946	41533574	129581493	75	11417											
CUL7	9820	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43008726	43008726	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcttgcaggcattgctgcaGctgtgccagcctctccattt	6	12	10	13	0	1	0	0	0	1	0	2	0	1	0	3	1	7	6	3	1	0	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:43008726G>A	ENST00000265348.3	-	20	3818	c.3733C>T	c.(3733-3735)Ctg>Ttg	p.L1245L	CUL7_ENST00000535468.1_Silent_p.L1329L			Q14999	CUL7_HUMAN	cullin 7	1245					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CATTGCTGCAGCTGTGCCAGC	0.572																																					p.L1329L													.	CUL7-229	0			c.C3985T						.						40	31	34					6																	43008726		2203	4300	6503	SO:0001819	synonymous_variant	9820	exon20			GCTGCAGCTGTGC	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"KIAA0076"	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3733C>T	6.37:g.43008726G>A		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	12	4	NM_001168370	0	0	4	7	3	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																			.		0.572	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		A	43008726	G	A	43008726	2	1	130	1	0	0	0	0	0	0	0	1	4066	962	34	2		2	CUL7	6	43008726	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1475152	43008726	128106341	76	11418											
CUL9	23113	hgsc.bcm.edu	37	chr6	43181268	43181268	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacctcagggaatggcccTttgaccctgcatgagggcca	8	8	11	14	0	2	2	2	2	0	0	2	3	2	3	4	3	1	1	4	3	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:43181268T>C	ENST00000252050.4	+	28	5535	c.5451T>C	c.(5449-5451)ccT>ccC	p.P1817P	CUL9_ENST00000354495.3_Silent_p.P1707P|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000502937.1_3'UTR|CUL9_ENST00000372647.2_Silent_p.P1817P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1817					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGAATGGCCCTTTGACCCTGC	0.632																																					p.P1817P		.											.	CUL9-529	0			c.T5451C						.						50	51	51					6																	43181268		2203	4300	6503	SO:0001819	synonymous_variant	23113	exon28			TGGCCCTTTGACC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5451T>C	6.37:g.43181268T>C		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_015089	0	0	4	4	0	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			.		0.632	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		C	43181268	T	C	43181268	2	2	130	1	0	0	0	0	0	0	0	1	4067	1596	56	3		3	CUL9	6	43181268	Silent	SNP	T	TCGA-HE-7130-01A-11D-1961-08	172542	43181268	127933799	77	11419											
TJAP1	93643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43468508	43468508	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgactgatgcagaaaggatGaagtgagtatctgctacctg	12	10	12	7	0	1	5	0	4	1	1	1	6	1	6	1	1	3	3	1	1	4	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:43468508G>T	ENST00000372445.5	+	5	502	c.126G>T	c.(124-126)atG>atT	p.M42I	TJAP1_ENST00000372444.2_Missense_Mutation_p.M42I|TJAP1_ENST00000372449.1_Missense_Mutation_p.M42I|TJAP1_ENST00000436109.2_Missense_Mutation_p.M42I|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000259751.1_Missense_Mutation_p.M42I|TJAP1_ENST00000438588.2_Missense_Mutation_p.M42I|TJAP1_ENST00000372452.1_Missense_Mutation_p.M42I	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	42					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CAGAAAGGATGAAGTGAGTAT	0.537																																					p.M42I		.											.	TJAP1-90	0			c.G126T						.						170	152	158					6																	43468508		2203	4300	6503	SO:0001583	missense	93643	exon5			AAGGATGAAGTGA	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.126G>T	6.37:g.43468508G>T	ENSP00000361522:p.Met42Ile	Somatic	170	2		WXS	Illumina HiSeq	Phase_I	82	59	NM_080604	0	0	0	1	1	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	37	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814511	0.70912	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.9	5.9	0.94986	.	0.048207	0.85682	D	0.000000	T	0.71134	0.3304	N	0.17082	0.46	0.37379	D	0.911945	B;D;P	0.53745	0.001;0.962;0.664	B;D;B	0.66716	0.003;0.946;0.203	T	0.68017	-0.5520	10	0.15066	T	0.55	-26.5245	17.4349	0.87548	0.0:0.0:1.0:0.0	.	42;42;42	E2QRK7;Q5JTD0;Q5JTD0-2	.;TJAP1_HUMAN;.	I	42	ENSP00000361521:M42I;ENSP00000361522:M42I;ENSP00000407080:M42I;ENSP00000390981:M42I;ENSP00000259751:M42I;ENSP00000361530:M42I;ENSP00000361527:M42I;ENSP00000408769:M42I	ENSP00000259751:M42I	M	+	3	0	TJAP1	43576486	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.402000	0.59722	2.788000	0.95919	0.650000	0.86243	ATG	.		0.537	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		T	43468508	G	T	43468508	3	4	130	1	0	0	0	0	1	0	0	0	15960	1290	45	4	132	4	TJAP1	6	43468508	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	287240	43468508	127646559	78	11420											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152557320	152557320	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgttacttagccagcactctCcaagttgatttagttggctt	8	16	8	9	0	1	1	0	1	1	0	2	1	1	1	2	1	3	5	2	1	4	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:152557320C>T	ENST00000367255.5	-	110	20919	c.20318G>A	c.(20317-20319)gGa>gAa	p.G6773E	SYNE1_ENST00000341594.5_Missense_Mutation_p.G6385E|SYNE1_ENST00000265368.4_Missense_Mutation_p.G6773E|SYNE1_ENST00000448038.1_Missense_Mutation_p.G6702E|SYNE1_ENST00000423061.1_Missense_Mutation_p.G6702E|SYNE1_ENST00000356820.4_Missense_Mutation_p.G1297E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6773					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCAGCACTCTCCAAGTTGATT	0.373										HNSCC(10;0.0054)																											p.G6773E		.											.	SYNE1-607	0			c.G20318A						.						170	166	167					6																	152557320		2203	4300	6503	SO:0001583	missense	23345	exon110			CACTCTCCAAGTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.20318G>A	6.37:g.152557320C>T	ENSP00000356224:p.Gly6773Glu	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	81	58	NM_182961	0	0	2	2	0	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	12.94	2.087720	0.36855	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50548	0.83;0.81;0.74;0.82;0.92;2.82	5.56	5.56	0.83823	.	0.000000	0.56097	D	0.000029	T	0.53498	0.1800	L	0.33710	1.025	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.55147	-0.8186	10	0.54805	T	0.06	.	19.5353	0.95251	0.0:1.0:0.0:0.0	.	6773;6773;6702	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	E	6773;6702;6773;6702;6385;1297	ENSP00000356224:G6773E;ENSP00000396024:G6702E;ENSP00000265368:G6773E;ENSP00000390975:G6702E;ENSP00000341887:G6385E;ENSP00000349276:G1297E	ENSP00000265368:G6773E	G	-	2	0	SYNE1	152599013	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	6.073000	0.71245	2.607000	0.88179	0.655000	0.94253	GGA	.		0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152557320	C	T	152557320	3	4	130	1	0	0	0	0	1	0	0	0	15477	855	30	2	6296	2	SYNE1	6	152557320	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	109088812	152557320	18557747	79	11421											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152560730	152560730	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttcagtacagcagaagcctGagccatcagctctgtatgga	11	10	10	10	0	3	2	2	1	1	1	3	3	3	3	2	1	5	4	2	1	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:152560730G>C	ENST00000367255.5	-	108	20606	c.20005C>G	c.(20005-20007)Cag>Gag	p.Q6669E	SYNE1_ENST00000341594.5_Missense_Mutation_p.Q6281E|SYNE1_ENST00000265368.4_Missense_Mutation_p.Q6669E|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q6598E|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q6598E|SYNE1_ENST00000356820.4_Missense_Mutation_p.Q1193E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6669					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCAGAAGCCTGAGCCATCAGC	0.468										HNSCC(10;0.0054)																											p.Q6669E		.											.	SYNE1-607	0			c.C20005G						.						136	112	120					6																	152560730		2203	4300	6503	SO:0001583	missense	23345	exon108			AAGCCTGAGCCAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.20005C>G	6.37:g.152560730G>C	ENSP00000356224:p.Gln6669Glu	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	61	47	NM_182961	0	0	0	1	1	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	2.493	-0.316916	0.05386	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34	5.7	4.81	0.61882	.	0.210406	0.33438	N	0.004910	T	0.14787	0.0357	L	0.36672	1.1	0.30220	N	0.796918	B;B;B	0.26876	0.101;0.101;0.162	B;B;B	0.22386	0.017;0.017;0.039	T	0.10428	-1.0630	10	0.66056	D	0.02	.	12.7363	0.57225	0.0:0.1256:0.7439:0.1305	.	6669;6669;6598	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	E	6669;6598;6669;6598;6281;1193	ENSP00000356224:Q6669E;ENSP00000396024:Q6598E;ENSP00000265368:Q6669E;ENSP00000390975:Q6598E;ENSP00000341887:Q6281E;ENSP00000349276:Q1193E	ENSP00000265368:Q6669E	Q	-	1	0	SYNE1	152602423	0.999000	0.42202	0.997000	0.53966	0.994000	0.84299	2.850000	0.48294	1.368000	0.46115	0.655000	0.94253	CAG	.		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152560730	G	C	152560730	3	2	130	1	0	0	0	0	1	0	0	0	15477	1299	45	4	6617	4	SYNE1	6	152560730	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3410	152560730	18554337	80	11422											
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	152730280	152730280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actgtgaattttcttcagctCagataacaagtgttttcctt	10	17	6	8	0	3	2	2	1	1	1	4	2	4	2	1	0	2	2	1	0	3	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:152730280C>T	ENST00000367255.5	-	44	7064	c.6463G>A	c.(6463-6465)Gag>Aag	p.E2155K	SYNE1_ENST00000341594.5_Missense_Mutation_p.E2192K|SYNE1_ENST00000265368.4_Missense_Mutation_p.E2155K|SYNE1_ENST00000448038.1_Missense_Mutation_p.E2162K|RNA5SP223_ENST00000365174.1_RNA|SYNE1_ENST00000423061.1_Missense_Mutation_p.E2162K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2155					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCTTCAGCTCAGATAACAAG	0.383										HNSCC(10;0.0054)																											p.E2162K		.											.	SYNE1-607	0			c.G6484A						.						147	142	143					6																	152730280		2203	4300	6503	SO:0001583	missense	23345	exon44			TCAGCTCAGATAA	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"myocyte nuclear envelope protein 1", "nuclear envelope spectrin repeat-1"	608441	"chromosome 6 open reading frame 98"	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.6463G>A	6.37:g.152730280C>T	ENSP00000356224:p.Glu2155Lys	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	55	45	NM_033071	0	0	0	1	1	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	18.72	3.684114	0.68157	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52295	1.38;1.38;1.38;1.38;0.67	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000013	T	0.49115	0.1538	M	0.61703	1.905	0.80722	D	1	D;D;D;D	0.58620	0.982;0.983;0.983;0.978	P;P;P;P	0.59424	0.791;0.678;0.678;0.857	T	0.46582	-0.9181	10	0.06891	T	0.86	.	19.5527	0.95328	0.0:1.0:0.0:0.0	.	2138;2155;2155;2162	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	K	2155;2162;2155;2162;2192	ENSP00000356224:E2155K;ENSP00000396024:E2162K;ENSP00000265368:E2155K;ENSP00000390975:E2162K;ENSP00000341887:E2192K	ENSP00000265368:E2155K	E	-	1	0	SYNE1	152771973	1.000000	0.71417	0.991000	0.47740	0.194000	0.23727	7.794000	0.85869	2.630000	0.89119	0.655000	0.94253	GAG	.		0.383	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152730280	C	T	152730280	3	4	130	1	0	0	0	0	1	0	0	0	15477	835	29	2	20415	2	SYNE1	6	152730280	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	169550	152730280	18384787	81	11423											
MLLT4	4301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	168347543	168347543	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggtgatgacagactgatgaAaaatagagctgatcaccgtt	14	10	11	6	1	1	7	1	5	0	2	1	7	1	7	1	1	1	2	1	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:168347543A>C	ENST00000447894.2	+	26	3494	c.3494A>C	c.(3493-3495)aAa>aCa	p.K1165T	MLLT4_ENST00000392108.3_Missense_Mutation_p.K1165T|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000366806.2_Missense_Mutation_p.K1165T|MLLT4_ENST00000351017.4_Missense_Mutation_p.K1172T|MLLT4_ENST00000392112.1_Missense_Mutation_p.K1148T|MLLT4_ENST00000400822.3_Missense_Mutation_p.K1164T|MLLT4_ENST00000344191.4_Missense_Mutation_p.K1165T			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1165					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		AGACTGATGAAAAATAGAGCT	0.433			T	MLL	AL																																p.K1165T		.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.	MLLT4-685	0			c.A3494C						.						115	116	116					6																	168347543		2203	4300	6503	SO:0001583	missense	4301	exon26			TGATGAAAAATAG	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3494A>C	6.37:g.168347543A>C	ENSP00000404595:p.Lys1165Thr	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	77	60	NM_001040000	0	0	0	18	18	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	A	22.4	4.286695	0.80803	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.04970	3.73;3.62;3.72;3.71;3.52;3.62;3.62	5.36	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.12347	0.0300	M	0.73962	2.25	0.52501	D	0.999956	P;D;P;P	0.67145	0.586;0.996;0.817;0.843	B;D;B;P	0.63703	0.263;0.917;0.345;0.63	T	0.00800	-1.1561	10	0.59425	D	0.04	-31.0185	11.4921	0.50387	0.929:0.0:0.071:0.0	.	1165;1164;1165;1149	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	T	1165;1172;1165;1165;1148;1165;1164;1165	ENSP00000341118:K1165T;ENSP00000252692:K1172T;ENSP00000375956:K1165T;ENSP00000355771:K1165T;ENSP00000375960:K1148T;ENSP00000383623:K1164T;ENSP00000404595:K1165T	ENSP00000345834:K1165T	K	+	2	0	MLLT4	168090392	1.000000	0.71417	0.812000	0.32479	0.904000	0.53231	8.548000	0.90669	0.965000	0.38133	0.533000	0.62120	AAA	.		0.433	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		C	168347543	A	C	168347543	3	2	130	1	0	0	0	0	1	0	0	0	9654	14	1	5	3596	5	MLLT4	6	168347543	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	15617263	168347543	2767524	82	11424											
FRMD1	79981	hgsc.bcm.edu;broad.mit.edu	37	chr6	168457843	168457843	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcgagacagttgctggacctCttgctggggagagtggccct	6	9	16	10	1	1	2	0	0	1	2	1	5	1	3	2	4	2	3	2	4	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:168457843C>G	ENST00000283309.6	-	11	1648	c.1584G>C	c.(1582-1584)aaG>aaC	p.K528N	FRMD1_ENST00000440994.2_Missense_Mutation_p.K460N|FRMD1_ENST00000537786.1_Missense_Mutation_p.K299N|FRMD1_ENST00000432403.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	528						cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		TGCTGGACCTCTTGCTGGGGA	0.672																																					p.K528N	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	.											.	FRMD1-91	0			c.G1584C						.						42	35	37					6																	168457843		2201	4298	6499	SO:0001583	missense	79981	exon11			GGACCTCTTGCTG		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1584G>C	6.37:g.168457843C>G	ENSP00000283309:p.Lys528Asn	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	10	8	NM_024919	0	0	0	0	0	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	.	.	.	.	.	.	.	.	.	.	C	9.261	1.043138	0.19748	.	.	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.46451	0.87;0.87;0.87	3.29	-0.146	0.13432	.	0.376195	0.16637	U	0.205782	T	0.10078	0.0247	L	0.28115	0.83	0.22280	N	0.999235	B;B;B;B	0.20261	0.043;0.043;0.04;0.043	B;B;B;B	0.23419	0.02;0.02;0.046;0.03	T	0.20438	-1.0275	10	0.72032	D	0.01	.	2.0231	0.03513	0.1548:0.5026:0.152:0.1906	.	463;528;460;423	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	N	528;460;299	ENSP00000283309:K528N;ENSP00000414115:K460N;ENSP00000440078:K299N	ENSP00000283309:K528N	K	-	3	2	FRMD1	168200692	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.243000	0.08915	0.339000	0.23719	-0.463000	0.05309	AAG	.		0.672	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		G	168457843	C	G	168457843	3	3	130	1	0	0	0	0	1	0	0	0	6068	912	32	4	69	4	FRMD1	6	168457843	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	110300	168457843	2657224	83	11425											
SBDS	51119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	66456129	66456129	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atatttgactcttacgatttCtaactgttggccataatctt	10	18	5	8	1	3	1	0	1	3	0	3	2	3	1	1	1	2	1	1	1	4	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:66456129C>G	ENST00000246868.2	-	4	802	c.619G>C	c.(619-621)Gaa>Caa	p.E207Q		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	207					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						CTTACGATTTCTAACTGTTGG	0.353			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.E207Q		.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS-523	0			c.G619C						.						150	125	133					7																	66456129		2203	4300	6503	SO:0001583	missense	51119	exon4	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	CGATTTCTAACTG	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.619G>C	7.37:g.66456129C>G	ENSP00000246868:p.Glu207Gln	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	84	33	NM_016038	0	0	0	0	0	A8K0P4|Q96FX0|Q9NV53	Missense_Mutation	SNP	ENST00000246868.2	37	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.189067	0.78789	.	.	ENSG00000126524	ENST00000246868	D	0.96745	-4.11	5.04	5.04	0.67666	Ribosome maturation protein SBDS, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96929	0.8997	M	0.87381	2.88	0.80722	D	1	P	0.37594	0.601	P	0.44394	0.448	D	0.96222	0.9161	10	0.30854	T	0.27	-19.3899	15.9306	0.79656	0.0:1.0:0.0:0.0	.	207	Q9Y3A5	SBDS_HUMAN	Q	207	ENSP00000246868:E207Q	ENSP00000246868:E207Q	E	-	1	0	SBDS	66093564	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.965000	0.76067	2.641000	0.89580	0.555000	0.69702	GAA	.		0.353	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038		G	66456129	C	G	66456129	3	3	130	1	0	0	0	0	1	0	0	0	13889	922	32	4	141	4	SBDS	7	66456129	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		66456129	92682534	84	11426											
PHTF2	57157	hgsc.bcm.edu;broad.mit.edu	37	chr7	77539715	77539715	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gatctctggcatgctgctttCtttttatcagggtttgtatt	5	20	9	7	0	3	0	1	0	2	0	4	1	3	0	0	2	2	5	0	2	2	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:77539715C>G	ENST00000248550.7	+	8	841	c.765C>G	c.(763-765)ttC>ttG	p.F255L	PHTF2_ENST00000415251.2_Missense_Mutation_p.F217L|PHTF2_ENST00000424760.1_Missense_Mutation_p.F217L|PHTF2_ENST00000450574.1_Missense_Mutation_p.F221L|PHTF2_ENST00000307305.8_Missense_Mutation_p.F217L|PHTF2_ENST00000275575.7_Missense_Mutation_p.F217L|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000422959.2_Missense_Mutation_p.F221L|PHTF2_ENST00000416283.2_Missense_Mutation_p.F221L			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	255					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						ATGCTGCTTTCTTTTTATCAG	0.413																																					p.F221L		.											.	PHTF2-23	0			c.C663G						.						82	78	79					7																	77539715		1912	4141	6053	SO:0001583	missense	57157	exon7			TGCTTTCTTTTTA	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.765C>G	7.37:g.77539715C>G	ENSP00000248550:p.Phe255Leu	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	51	7	NM_001127359	0	0	0	0	0	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	C	13.99	2.400678	0.42613	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000415251;ENST00000275575;ENST00000450574;ENST00000416283;ENST00000248550	.	.	.	5.5	5.5	0.81552	.	0.050270	0.85682	D	0.000000	T	0.53238	0.1784	N	0.24115	0.695	0.50313	D	0.999866	P;B;B;B;B;B;B;B;B	0.46859	0.885;0.114;0.105;0.066;0.105;0.447;0.141;0.172;0.172	P;B;B;B;B;B;B;B;B	0.48189	0.57;0.022;0.03;0.008;0.03;0.067;0.045;0.045;0.02	T	0.46247	-0.9205	9	0.23302	T	0.38	-12.6236	19.4005	0.94627	0.0:1.0:0.0:0.0	.	59;217;80;221;255;221;217;217;217	Q8WVD6;Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;G5E9H7;Q8N3S3-3;B3KQZ2;E9PEE3	.;.;.;.;PHTF2_HUMAN;.;.;.;.	L	221;221;217;217;217;217;221;221;255	.	ENSP00000248550:F255L	F	+	3	2	PHTF2	77377651	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.493000	0.66899	2.591000	0.87537	0.655000	0.94253	TTC	.		0.413	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		G	77539715	C	G	77539715	3	3	130	1	0	0	0	0	1	0	0	0	11889	912	32	4	689	4	PHTF2	7	77539715	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	11083586	77539715	81598948	85	11427											
MAGI2	9863	hgsc.bcm.edu;broad.mit.edu	37	chr7	77885410	77885410	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gccagggcatccctgaatgtCaagtatttgtttcacccgct	8	12	9	12	1	2	1	2	1	0	0	3	1	3	1	3	1	0	4	3	1	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:77885410C>G	ENST00000354212.4	-	10	2150	c.1897G>C	c.(1897-1899)Gac>Cac	p.D633H	MAGI2_ENST00000419488.1_Missense_Mutation_p.D633H|MAGI2_ENST00000522391.1_Missense_Mutation_p.D633H|MAGI2_ENST00000536571.1_Missense_Mutation_p.D465H|MAGI2_ENST00000535697.1_Missense_Mutation_p.D470H	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	633	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CCCTGAATGTCAAGTATTTGT	0.488																																					p.D633H		.											.	MAGI2-461	0			c.G1897C						.						71	60	64					7																	77885410		2203	4300	6503	SO:0001583	missense	9863	exon10			GAATGTCAAGTAT	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1897G>C	7.37:g.77885410C>G	ENSP00000346151:p.Asp633His	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	41	6	NM_012301	0	0	0	0	0	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198609	0.79015	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	5.74	5.74	0.90152	PDZ/DHR/GLGF (4);	0.000000	0.38381	U	0.001709	T	0.58133	0.2101	M	0.85710	2.77	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.961;0.987;0.987;1.0;0.998	D;D;D;D;D;D	0.76575	0.979;0.94;0.93;0.93;0.988;0.944	T	0.63152	-0.6701	10	0.87932	D	0	.	18.9145	0.92499	0.0:1.0:0.0:0.0	.	470;465;633;633;633;633	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	H	633;633;633;633;465;470	ENSP00000405766:D633H;ENSP00000346151:D633H;ENSP00000428389:D633H;ENSP00000441584:D465H;ENSP00000441603:D470H	ENSP00000346151:D633H	D	-	1	0	MAGI2	77723346	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.550000	0.82173	2.700000	0.92200	0.561000	0.74099	GAC	.		0.488	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		G	77885410	C	G	77885410	3	3	130	1	0	0	0	0	1	0	0	0	9216	826	29	4	2522	4	MAGI2	7	77885410	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	345695	77885410	81253253	86	11428											
COL1A2	1278	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	94035021	94035021	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggaactcctggacttcctGgcttcaaaggcattagggtg	8	11	12	10	0	1	0	1	0	0	0	3	2	3	2	2	5	1	2	2	5	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:94035021G>A	ENST00000297268.6	+	11	994	c.523G>A	c.(523-525)Ggc>Agc	p.G175S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	175					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TGGACTTCCTGGCTTCAAAGG	0.373										HNSCC(75;0.22)																											p.G175S		.											.	COL1A2-521	0			c.G523A						.						158	155	156					7																	94035021		2203	4299	6502	SO:0001583	missense	1278	exon11			CTTCCTGGCTTCA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"Collagens"	2198	protein-coding gene	gene with protein product	"alpha 2(I)-collagen", "alpha-2 collagen type I", "type I procollagen", "collagen I, alpha-2 polypeptide", "collagen of skin, tendon and bone, alpha-2 chain"	120160	"osteogenesis imperfecta type IV"	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.523G>A	7.37:g.94035021G>A	ENSP00000297268:p.Gly175Ser	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	264	56	NM_000089	0	0	50	50	0	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.343237	0.82022	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93659	-3.26	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98330	0.9446	H	0.98833	4.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99501	1.0953	10	0.87932	D	0	.	19.1584	0.93520	0.0:0.0:1.0:0.0	.	175	P08123	CO1A2_HUMAN	S	175;176	ENSP00000297268:G175S	ENSP00000297268:G175S	G	+	1	0	COL1A2	93872957	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.420000	0.97426	2.697000	0.92050	0.591000	0.81541	GGC	.		0.373	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		A	94035021	G	A	94035021	3	1	130	1	0	0	0	0	1	0	0	0	3684	1348	47	2	565	2	COL1A2	7	94035021	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	16149611	94035021	65103642	87	11429											
TFR2	7036	broad.mit.edu	37	chr7	100239125	100239125	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggaatagaccccaaagcCgctccatgcttgtgtcccct	8	10	8	15	1	1	1	0	0	1	1	3	2	3	2	6	1	2	2	6	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:100239125C>T	ENST00000462107.1	-	2	295	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	TFR2_ENST00000431692.1_Missense_Mutation_p.R3Q|TFR2_ENST00000223051.3_Missense_Mutation_p.R3Q			Q9UP52	TFR2_HUMAN	transferrin receptor 2	3					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	ACCCCAAAGCCGCTCCATGCT	0.587																																					p.R3Q													.	TFR2-92	0			c.G8A						.						83	73	76					7																	100239125		2203	4300	6503	SO:0001583	missense	7036	exon1			CAAAGCCGCTCCA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.8G>A	7.37:g.100239125C>T	ENSP00000420525:p.Arg3Gln	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	40	5	NM_003227	0	0	0	0	0	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	37	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010438	0.35511	.	.	ENSG00000106327	ENST00000223051;ENST00000431692;ENST00000462107	T;T;T	0.56444	0.55;0.46;0.55	4.63	-1.77	0.07982	.	0.842939	0.09703	N	0.766751	T	0.25606	0.0623	N	0.12182	0.205	0.22710	N	0.998822	B	0.13145	0.007	B	0.04013	0.001	T	0.22661	-1.0210	10	0.09338	T	0.73	-4.8853	5.2345	0.15439	0.0:0.3478:0.167:0.4852	.	3	Q9UP52	TFR2_HUMAN	Q	3	ENSP00000223051:R3Q;ENSP00000413905:R3Q;ENSP00000420525:R3Q	ENSP00000223051:R3Q	R	-	2	0	TFR2	100077061	0.937000	0.31787	0.826000	0.32828	0.792000	0.44763	-0.050000	0.11904	-0.621000	0.05633	-0.327000	0.08410	CGG	.		0.587	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		T	100239125	C	T	100239125	3	4	130	1	0	0	0	0	1	0	0	0	15843	652	23	1	2469	1	TFR2	7	100239125	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	6204104	100239125	58899538	88	11430											
TAS2R41	259287	broad.mit.edu;bcgsc.ca	37	chr7	143175820	143175820	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catcccttcatcctcatcttCagcaacctcaagcttcgaag	10	11	4	16	1	5	0	4	0	1	0	8	1	7	0	3	0	3	2	3	0	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:143175820C>T	ENST00000408916.1	+	1	855	c.855C>T	c.(853-855)ttC>ttT	p.F285F	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	285					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F285F(1)		endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					TCCTCATCTTCAGCAACCTCA	0.502																																					p.F285F													.	TAS2R41-92	1	Substitution - coding silent(1)	lung(1)	c.C855T						.						135	124	128					7																	143175820		2068	4201	6269	SO:0001819	synonymous_variant	259287	exon1			CATCTTCAGCAAC	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.855C>T	7.37:g.143175820C>T		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	85	14	NM_176883	0	0	0	0	0	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Silent	SNP	ENST00000408916.1	37	CCDS43663.1																																																																																			.		0.502	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175820	C	T	143175820	2	4	130	1	0	0	0	0	0	0	0	1	15611	825	29	2		2	TAS2R41	7	143175820	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	42936695	143175820	15962843	89	11431											
ATG9B	285973	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	150720230	150720230	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttacttggttggttggcaaaGagaacattgtaatccacgca	12	12	10	7	1	0	1	0	0	0	1	1	2	1	1	1	3	2	5	1	3	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:150720230G>A	ENST00000377974.2	-	4	798	c.723C>T	c.(721-723)ctC>ctT	p.L241L	ATG9B_ENST00000444312.1_5'UTR|ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000605952.1_Silent_p.L241L|ATG9B_ENST00000605938.1_Silent_p.L241L			Q674R7	ATG9B_HUMAN	autophagy related 9B	241					autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGTTGGCAAAGAGAACATTGT	0.532																																					.													.	ATG9B-91	0			.						.						266	270	269					7																	150720230		2036	4201	6237	SO:0001819	synonymous_variant	285973	.			GGCAAAGAGAACA	AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652			21899	protein-coding gene	gene with protein product		612205	"nitric oxide synthase 3 antisense", "ATG9 autophagy related 9 homolog B (S. cerevisiae)"	NOS3AS		15234981, 15755735	Standard	NM_173681		Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000377974.2:c.723C>T	7.37:g.150720230G>A		Somatic	369	0		WXS	Illumina HiSeq	Phase_I	349	66	.	0	0	5	5	0	A1A5D3|Q6JRW5|Q8N8I8	Silent	SNP	ENST00000377974.2	37																																																																																				.		0.532	ATG9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173681		A	150720230	G	A	150720230	2	1	130	1	0	0	0	0	0	0	0	1	1104	929	33	2		2	ATG9B	7	150720230	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	7544410	150720230	8418433	90	11432											
RP1L1	94137	hgsc.bcm.edu;broad.mit.edu	37	chr8	10468873	10468873	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accccgcaccctggctggcaCtgcttctccttgatgcccct	4	10	8	19	1	1	1	0	1	1	0	2	1	1	1	6	2	2	4	6	2	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:10468873C>T	ENST00000382483.3	-	4	2958	c.2735G>A	c.(2734-2736)aGt>aAt	p.S912N		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	912					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTGGCTGGCACTGCTTCTCCT	0.716																																					p.S912N		.											.	RP1L1-139	0			c.G2735A						.						12	16	15					8																	10468873		1930	4102	6032	SO:0001583	missense	94137	exon4			CTGGCACTGCTTC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2735G>A	8.37:g.10468873C>T	ENSP00000371923:p.Ser912Asn	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_178857	0	0	0	0	0	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	6.313	0.425815	0.11987	.	.	ENSG00000183638	ENST00000382483	T	0.04156	3.69	4.6	2.64	0.31445	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	P	0.49961	0.93	P	0.44860	0.462	T	0.42949	-0.9421	9	0.38643	T	0.18	0.111	4.4393	0.11566	0.1583:0.6002:0.1536:0.0879	.	912	A6NKC6	.	N	912	ENSP00000371923:S912N	ENSP00000371923:S912N	S	-	2	0	RP1L1	10506283	0.001000	0.12720	0.001000	0.08648	0.060000	0.15804	1.033000	0.30191	1.107000	0.41642	0.313000	0.20887	AGT	.		0.716	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10468873	C	T	10468873	3	4	130	1	0	0	0	0	1	0	0	0	13565	565	20	2	4471	2	RP1L1	8	10468873	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		10468873	135895149	91	11433											
PCM1	5108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	17885162	17885162	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagaaacggtgggagcccaGagtatatgagatgtcttcag	12	9	13	7	1	3	3	2	1	1	3	3	5	3	4	1	2	2	1	1	2	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:17885162G>C	ENST00000519253.1	+	39	6293	c.6042G>C	c.(6040-6042)caG>caC	p.Q2014H	PCM1_ENST00000327578.8_Missense_Mutation_p.Q721H|PCM1_ENST00000325083.8_Missense_Mutation_p.Q2022H|PCM1_ENST00000524226.1_Missense_Mutation_p.Q1858H			Q15154	PCM1_HUMAN	pericentriolar material 1	2022	Interaction with BBS4.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TGGGAGCCCAGAGTATATGAG	0.303			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.Q2022H		.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1-742	0			c.G6066C						.						52	51	51					8																	17885162		1794	4062	5856	SO:0001583	missense	5108	exon39			AGCCCAGAGTATA		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.6042G>C	8.37:g.17885162G>C	ENSP00000431099:p.Gln2014His	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	62	10	NM_006197	0	0	15	22	7	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.24|10.24	1.296731|1.296731	0.23650|0.23650	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578|ENST00000522275	T;T;T;T|.	0.22945|.	3.3;3.3;3.0;1.93|.	5.51|5.51	-6.77|-6.77	0.01727|0.01727	.|.	0.261946|.	0.40302|.	N|.	0.001133|.	T|T	0.25195|0.25195	0.0612|0.0612	N|N	0.20986|0.20986	0.625|0.625	0.29276|0.29276	N|N	0.870346|0.870346	B;B;B;B;B;B;B|.	0.06786|.	0.001;0.001;0.001;0.001;0.001;0.001;0.001|.	B;B;B;B;B;B;B|.	0.08055|.	0.003;0.003;0.003;0.003;0.003;0.003;0.003|.	T|T	0.35101|0.35101	-0.9802|-0.9802	10|5	0.87932|.	D|.	0|.	-2.5298|-2.5298	8.8371|8.8371	0.35119|0.35119	0.2748:0.2274:0.4978:0.0|0.2748:0.2274:0.4978:0.0	.|.	2014;2022;821;2014;1967;1858;2022|.	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154|.	.;.;.;.;.;.;PCM1_HUMAN|.	H|T	2022;2014;1858;721|762	ENSP00000327077:Q2022H;ENSP00000431099:Q2014H;ENSP00000430521:Q1858H;ENSP00000328332:Q721H|.	ENSP00000327077:Q2022H|.	Q|R	+|+	3|2	2|0	PCM1|PCM1	17929442|17929442	0.944000|0.944000	0.32072|0.32072	0.012000|0.012000	0.15200|0.15200	0.629000|0.629000	0.37895|0.37895	-0.012000|-0.012000	0.12699|0.12699	-1.249000|-1.249000	0.02500|0.02500	-0.302000|-0.302000	0.09304|0.09304	CAG|AGA	.		0.303	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		C	17885162	G	C	17885162	3	2	130	1	0	0	0	0	1	0	0	0	11610	933	33	4	6212	4	PCM1	8	17885162	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	7416289	17885162	128478860	92	11434											
EBF2	64641	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	25890622	25890622	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgtcaattatgactgggtccGatggagtctcatttcggttt	7	16	11	7	2	2	1	2	1	1	0	5	3	3	2	1	3	0	1	1	3	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:25890622G>C	ENST00000520164.1	-	6	1067	c.530C>G	c.(529-531)tCg>tGg	p.S177W	EBF2_ENST00000408929.3_Missense_Mutation_p.S29W	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	177					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GACTGGGTCCGATGGAGTCTC	0.388																																					p.S177W	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	.											.	EBF2-26	0			c.C530G						.						139	138	138					8																	25890622		1949	4188	6137	SO:0001583	missense	64641	exon6			GGGTCCGATGGAG	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.530C>G	8.37:g.25890622G>C	ENSP00000430241:p.Ser177Trp	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	155	20	NM_022659	0	0	0	0	0	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281973	0.80692	.	.	ENSG00000221818	ENST00000520164;ENST00000408929	T;T	0.57273	0.47;0.41	6.17	5.27	0.74061	.	0.000000	0.64402	U	0.000001	T	0.76234	0.3959	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79232	-0.1888	10	0.87932	D	0	-4.121	17.6654	0.88201	0.0:0.1224:0.8776:0.0	.	177	Q9HAK2	COE2_HUMAN	W	177;29	ENSP00000430241:S177W;ENSP00000386178:S29W	ENSP00000386178:S29W	S	-	2	0	EBF2	25946539	1.000000	0.71417	0.917000	0.36280	0.772000	0.43724	7.624000	0.83124	2.941000	0.99782	0.655000	0.94253	TCG	.		0.388	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		C	25890622	G	C	25890622	3	2	130	1	0	0	0	0	1	0	0	0	4892	1059	37	4	1241	4	EBF2	8	25890622	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	8005460	25890622	120473400	93	11435											
MATN2	4147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	99019720	99019720	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttgcaggggtggattactgCctgctgagtgaccatggttg	6	13	15	7	0	0	2	0	2	0	0	0	3	0	3	2	4	4	3	2	4	1	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:99019720C>T	ENST00000520016.1	+	9	1588	c.1464C>T	c.(1462-1464)tgC>tgT	p.C488C	MATN2_ENST00000521689.1_Silent_p.C488C|MATN2_ENST00000524308.1_Silent_p.C447C|MATN2_ENST00000522025.2_Silent_p.C204C|MATN2_ENST00000254898.5_Silent_p.C488C			O00339	MATN2_HUMAN	matrilin 2	488	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGGATTACTGCCTGCTGAGTG	0.547																																					p.C488C		.											.	MATN2-24	0			c.C1464T						.						131	130	131					8																	99019720		2069	4211	6280	SO:0001819	synonymous_variant	4147	exon10			TTACTGCCTGCTG	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1464C>T	8.37:g.99019720C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	72	30	NM_002380	0	0	0	0	0	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	9.120	1.008646	0.19199	.	.	ENSG00000132561	ENST00000518154	.	.	.	5.65	4.77	0.60923	.	.	.	.	.	T	0.63827	0.2544	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62407	-0.6861	4	.	.	.	-23.2752	12.1976	0.54307	0.0:0.9189:0.0:0.0811	.	.	.	.	S	271	.	.	P	+	1	0	MATN2	99088896	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.602000	0.36783	1.393000	0.46605	0.655000	0.94253	CCT	.		0.547	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99019720	C	T	99019720	2	4	130	1	0	0	0	0	0	0	0	1	9359	747	26	2		2	MATN2	8	99019720	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	73129098	99019720	47344302	94	11436											
TG	7038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133945814	133945814	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggtgcttgcagattgcacaGaggacgaggcctgcagcttc	8	9	14	10	1	0	2	0	0	0	2	1	4	0	3	1	3	5	5	1	3	0	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:133945814G>A	ENST00000220616.4	+	24	4865	c.4825G>A	c.(4825-4827)Gag>Aag	p.E1609K	TG_ENST00000377869.1_Missense_Mutation_p.E1552K|TG_ENST00000542445.1_Missense_Mutation_p.E43K	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1609					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGATTGCACAGAGGACGAGGC	0.582																																					p.E1609K		.											.	TG-145	0			c.G4825A						.						237	176	197					8																	133945814		2203	4300	6503	SO:0001583	missense	7038	exon24			TGCACAGAGGACG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4825G>A	8.37:g.133945814G>A	ENSP00000220616:p.Glu1609Lys	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	113	12	NM_003235	0	0	0	0	0	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.015|0.015	-1.564449|-1.564449	0.00903|0.00903	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	T;T;T|.	0.63417|.	-0.04;-0.04;-0.04|.	5.3|5.3	-6.81|-6.81	0.01704|0.01704	.|.	2.263600|.	0.01555|.	N|.	0.019854|.	T|T	0.14056|0.14056	0.0340|0.0340	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.24764|0.24764	-1.0151|-1.0151	10|5	0.06099|.	T|.	0.92|.	.|.	1.784|1.784	0.03038|0.03038	0.3015:0.2787:0.305:0.1148|0.3015:0.2787:0.305:0.1148	.|.	43;1609|.	F5GWW5;P01266|.	.;THYG_HUMAN|.	K|K	1552;415;1609;43|128	ENSP00000367100:E1552K;ENSP00000220616:E1609K;ENSP00000441693:E43K|.	ENSP00000220616:E1609K|.	E|R	+|+	1|2	0|0	TG|TG	134014996|134014996	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.841000|-0.841000	0.04359|0.04359	-0.900000|-0.900000	0.03896|0.03896	-0.154000|-0.154000	0.13518|0.13518	GAG|AGA	.		0.582	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133945814	G	A	133945814	3	1	130	1	0	0	0	0	1	0	0	0	15845	943	33	2	4919	2	TG	8	133945814	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	34926094	133945814	12418208	95	11437											
BAI1	575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	143603450	143603450	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctccggaaccgcctcatccGcaagcgcttcctctgcctgg	5	8	9	19	4	2	0	1	0	1	0	5	1	5	1	7	2	3	2	7	2	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:143603450G>A	ENST00000517894.1	+	21	4043	c.3149G>A	c.(3148-3150)cGc>cAc	p.R1050H	BAI1_ENST00000323289.5_Missense_Mutation_p.R1050H			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1050					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CGCCTCATCCGCAAGCGCTTC	0.652																																					p.R1050H		.											.	BAI1-1129	0			c.G3149A						.						30	40	37					8																	143603450		2200	4299	6499	SO:0001583	missense	575	exon20			TCATCCGCAAGCG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"-", "GPCR / Class B : Orphans"	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.3149G>A	8.37:g.143603450G>A	ENSP00000430945:p.Arg1050His	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	78	30	NM_001702	0	0	0	0	0		Missense_Mutation	SNP	ENST00000517894.1	37		.	.	.	.	.	.	.	.	.	.	G	28.6	4.933063	0.92458	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.39787	1.06;1.06	3.78	3.78	0.43462	.	0.156800	0.43110	U	0.000612	T	0.51024	0.1650	L	0.46947	1.48	0.58432	D	0.999997	D	0.60160	0.987	P	0.56648	0.803	T	0.57493	-0.7802	10	0.87932	D	0	.	14.6053	0.68475	0.0:0.0:1.0:0.0	.	1050	E9PBK0	.	H	1050	ENSP00000430945:R1050H;ENSP00000313046:R1050H	ENSP00000313046:R1050H	R	+	2	0	BAI1	143600452	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.618000	0.83043	1.641000	0.50575	0.305000	0.20034	CGC	.		0.652	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		A	143603450	G	A	143603450	3	1	130	1	0	0	0	0	1	0	0	0	1299	1087	38	1	3227	1	BAI1	8	143603450	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	9657636	143603450	2760572	96	11438											
FRMPD1	22844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	37729833	37729833	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggctgcacctgctgcacgaaGaggaactcatccagcaggta	11	6	12	12	1	1	1	1	0	0	1	2	3	2	2	2	3	5	6	2	3	3	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:37729833G>A	ENST00000539465.1	+	8	1314	c.721G>A	c.(721-723)Gag>Aag	p.E241K	FRMPD1_ENST00000377765.3_Missense_Mutation_p.E241K|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000541302.1_Missense_Mutation_p.E110K|FRMPD1_ENST00000536622.1_Missense_Mutation_p.E63K			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	241	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GCTGCACGAAGAGGAACTCAT	0.602																																					p.E241K		.											.	FRMPD1-159	0			c.G721A						.						93	75	81					9																	37729833		2203	4300	6503	SO:0001583	missense	22844	exon8			CACGAAGAGGAAC	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.721G>A	9.37:g.37729833G>A	ENSP00000444411:p.Glu241Lys	Somatic	102	2		WXS	Illumina HiSeq	Phase_I	44	34	NM_014907	0	0	0	0	0	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.020484	0.93462	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	5.64	5.64	0.86602	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.105447	0.64402	D	0.000005	D	0.88973	0.6583	L	0.39898	1.24	0.80722	D	1	D;D	0.71674	0.982;0.998	P;D	0.71870	0.871;0.975	D	0.88259	0.2922	10	0.44086	T	0.13	-21.3858	17.1917	0.86881	0.0:0.0:1.0:0.0	.	110;241	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	K	241;241;63;110	ENSP00000366995:E241K;ENSP00000444411:E241K;ENSP00000437762:E63K;ENSP00000444804:E110K	ENSP00000366995:E241K	E	+	1	0	FRMPD1	37719833	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.301000	0.96167	2.666000	0.90696	0.655000	0.94253	GAG	.		0.602	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37729833	G	A	37729833	3	1	130	1	0	0	0	0	1	0	0	0	6076	943	33	2	747	2	FRMPD1	9	37729833	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		37729833	103483598	97	11439											
TRPM3	80036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	73151243	73151243	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagttctgcttctcgctctgGatggcagcaagttaagtcct	7	13	10	11	1	3	0	0	0	3	0	5	1	4	1	1	2	2	6	1	2	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:73151243G>C	ENST00000377110.3	-	25	4993	c.4750C>G	c.(4750-4752)Cca>Gca	p.P1584A	TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000423814.3_Missense_Mutation_p.P1611A|TRPM3_ENST00000360823.2_Missense_Mutation_p.P1446A|TRPM3_ENST00000357533.2_Missense_Mutation_p.P1588A|TRPM3_ENST00000396285.1_Missense_Mutation_p.P1443A|TRPM3_ENST00000396292.4_Missense_Mutation_p.P1456A|TRPM3_ENST00000377106.1_Missense_Mutation_p.P1456A|TRPM3_ENST00000377105.1_Missense_Mutation_p.P1443A|TRPM3_ENST00000396280.5_Missense_Mutation_p.P1433A|TRPM3_ENST00000358082.3_Missense_Mutation_p.P1446A|TRPM3_ENST00000408909.2_Missense_Mutation_p.P1443A			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1609					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TCTCGCTCTGGATGGCAGCAA	0.542																																					p.P1584A		.											.	TRPM3-521	0			c.C4750G						.						128	119	122					9																	73151243		2203	4300	6503	SO:0001583	missense	80036	exon25			GCTCTGGATGGCA	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4750C>G	9.37:g.73151243G>C	ENSP00000366314:p.Pro1584Ala	Somatic	189	2		WXS	Illumina HiSeq	Phase_I	91	65	NM_001007471	0	0	0	0	0	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	37	CCDS43835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.42|13.42	2.233192|2.233192	0.39498|0.39498	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T|.	0.57107|.	0.54;0.45;0.44;0.43;0.54;0.43;0.42;0.45;0.44;0.54|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61236|0.61236	0.2331|0.2331	L|L	0.32530|0.32530	0.975|0.975	0.58432|0.58432	D|D	0.999999|0.999999	D;B;D;D;D;D;D|.	0.76494|.	0.999;0.311;0.999;0.999;0.999;0.999;0.999|.	D;B;D;D;D;D;D|.	0.83275|.	0.996;0.147;0.991;0.991;0.996;0.996;0.991|.	T|T	0.52909|0.52909	-0.8512|-0.8512	10|5	0.10636|.	T|.	0.68|.	-14.3964|-14.3964	20.2181|20.2181	0.98305|0.98305	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1584;1574;1588;1446;1443;1556;1443|.	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.|.	A|C	1584;1456;1446;1443;1588;1443;1443;1456;1446;1611|1432	ENSP00000366314:P1584A;ENSP00000366310:P1456A;ENSP00000354066:P1446A;ENSP00000366309:P1443A;ENSP00000350140:P1588A;ENSP00000386127:P1443A;ENSP00000379581:P1443A;ENSP00000379587:P1456A;ENSP00000350791:P1446A;ENSP00000389542:P1611A|.	ENSP00000350140:P1588A|.	P|S	-|-	1|2	0|0	TRPM3|TRPM3	72341063|72341063	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.972000|0.972000	0.66771|0.66771	9.230000|9.230000	0.95299|0.95299	2.785000|2.785000	0.95823|0.95823	0.655000|0.655000	0.94253|0.94253	CCA|TCC	.		0.542	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		C	73151243	G	C	73151243	3	2	130	1	0	0	0	0	1	0	0	0	16620	1174	41	4	377	4	TRPM3	9	73151243	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	35421410	73151243	68062188	98	11440											
C5	727	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	123783919	123783919	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acatcaattgtttgtgcattCagtgttactgggactcctcc	8	15	8	10	0	2	0	2	0	0	0	4	1	4	1	2	1	2	3	2	1	2	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:123783919C>G	ENST00000223642.1	-	11	1199	c.1170G>C	c.(1168-1170)ctG>ctC	p.L390L		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	390					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TTTGTGCATTCAGTGTTACTG	0.403																																					p.L390L		.											.	C5-92	0			c.G1170C						.						201	182	188					9																	123783919		2203	4300	6503	SO:0001819	synonymous_variant	727	exon11			TGCATTCAGTGTT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"Complement system", "Endogenous ligands"	1331	protein-coding gene	gene with protein product	"prepro-C5", "C5a anaphylatoxin"	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.1170G>C	9.37:g.123783919C>G		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	61	6	NM_001735	0	0	0	0	0	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			.		0.403	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		G	123783919	C	G	123783919	2	3	130	1	0	0	0	0	0	0	0	1	2286	813	29	4		4	C5	9	123783919	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	50632676	123783919	17429512	99	11441											
DDX31	64794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	135545615	135545615	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaagctctctgaatgcctctGagaagcgagatccggcgcca	10	7	12	12	3	2	3	0	2	2	2	4	6	3	3	3	1	3	1	3	1	3	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:135545615G>C	ENST00000372159.3	-	1	173	c.22C>G	c.(22-24)Cag>Gag	p.Q8E	GTF3C4_ENST00000372146.4_5'UTR|DDX31_ENST00000544003.1_5'Flank|DDX31_ENST00000372153.1_Missense_Mutation_p.Q8E|DDX31_ENST00000480876.1_5'UTR|DDX31_ENST00000310532.2_Missense_Mutation_p.Q8E|GTF3C4_ENST00000483873.2_5'UTR	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	8						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		GAATGCCTCTGAGAAGCGAGA	0.622																																					p.Q8E		.											.	DDX31-226	0			c.C22G						.						24	22	23					9																	135545615		2163	4206	6369	SO:0001583	missense	64794	exon1			GCCTCTGAGAAGC	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"DEAD-boxes", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	16715	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 25"		"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.22C>G	9.37:g.135545615G>C	ENSP00000361232:p.Gln8Glu	Somatic	47	1		WXS	Illumina HiSeq	Phase_I	24	17	NM_022779	0	0	1	1	0	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Missense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582024	0.28180	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000372153;ENST00000310532	T;T;T	0.05199	4.34;3.88;3.48	3.16	-1.78	0.07957	.	.	.	.	.	T	0.03220	0.0094	N	0.14661	0.345	0.20638	N	0.999874	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.43637	-0.9379	9	0.34782	T	0.22	.	3.7708	0.08640	0.2994:0.3994:0.3012:0.0	.	8;8;8	Q9H8H2-2;Q9H8H2-3;Q9H8H2	.;.;DDX31_HUMAN	E	8	ENSP00000361232:Q8E;ENSP00000361226:Q8E;ENSP00000310539:Q8E	ENSP00000310539:Q8E	Q	-	1	0	DDX31	134535436	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.320000	0.19540	-0.347000	0.08299	0.462000	0.41574	CAG	.		0.622	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		C	135545615	G	C	135545615	3	2	130	1	0	0	0	0	1	0	0	0	4362	1299	45	4	2620	4	DDX31	9	135545615	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	11761696	135545615	5667816	100	11442											
KCNT1	402381	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	138594186	138594186	+	5'Flank	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gctacaccaaccggaccttcGagtttgacgacggccaatgc	10	7	10	14	4	0	1	0	1	0	0	1	4	0	2	4	2	3	2	4	2	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:138594186G>C	ENST00000298466.5	-	0	0				KCNT1_ENST00000298480.5_Missense_Mutation_p.E28Q|KCNT1_ENST00000371757.2_Missense_Mutation_p.E28Q|SOHLH1_ENST00000425225.1_5'Flank|KCNT1_ENST00000487664.1_Missense_Mutation_p.E28Q	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		CCGGACCTTCGAGTTTGACGA	0.726																																					p.E28Q		.											.	KCNT1-137	0			c.G82C						.						22	27	25					9																	138594186		2200	4297	6497	SO:0001631	upstream_gene_variant	57582	exon1			ACCTTCGAGTTTG	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915		9.37:g.138594186G>C	Exception_encountered	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	19	9	NM_001272003	0	0	0	0	0	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Missense_Mutation	SNP	ENST00000298466.5	37	CCDS35174.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.270987	0.23221	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757	T;T;T	0.22336	1.98;1.96;1.96	2.17	2.17	0.27698	.	.	.	.	.	T	0.08582	0.0213	N	0.08118	0	0.80722	D	1	B;P	0.34757	0.315;0.467	B;B	0.26517	0.049;0.07	T	0.21861	-1.0233	9	0.41790	T	0.15	.	7.9137	0.29806	0.0:0.0:1.0:0.0	.	28;28	B9EGP2;G5E9V0	.;.	Q	28	ENSP00000417851:E28Q;ENSP00000298480:E28Q;ENSP00000360822:E28Q	ENSP00000298480:E28Q	E	+	1	0	KCNT1	137734007	0.552000	0.26505	0.891000	0.34965	0.007000	0.05969	1.839000	0.39220	1.514000	0.48869	0.650000	0.86243	GAG	.		0.726	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		C	138594186	G	C	138594186	1	2	130	0	1	0	0	0	0	0	0	0	8112	1059	37	4		4	KCNT1	9	138594186	5'Flank	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3048571	138594186	2619245	101	11443											
CLIC3	9022	broad.mit.edu;bcgsc.ca	37	chr9	139890192	139890192	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaggggcagtgacccacgctCtccccgtcctcactcgcctg	5	7	11	18	3	2	1	1	1	1	0	5	2	3	1	5	2	0	2	5	2	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:139890192C>G	ENST00000494426.1	-	2	310	c.51G>C	c.(49-51)gaG>gaC	p.E17D	CLIC3_ENST00000480181.1_5'UTR	NM_004669.2	NP_004660.2	O95833	CLIC3_HUMAN	chloride intracellular channel 3	17	GST N-terminal.|Required for insertion into the membrane. {ECO:0000250}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|signal transduction (GO:0007165)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			lung(1)|skin(1)	2	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GACCCACGCTCTCCCCGTCCT	0.706																																					p.E17D													.	CLIC3-90	0			c.G51C						.						37	32	33					9																	139890192		2179	4283	6462	SO:0001583	missense	9022	exon2			CACGCTCTCCCCG	AF102166	CCDS7021.1	9q34.3	2012-09-26			ENSG00000169583	ENSG00000169583		"Ion channels / Chloride channels : Intracellular"	2064	protein-coding gene	gene with protein product		606533				9880541	Standard	NM_004669		Approved		uc004ckj.1	O95833	OTTHUMG00000020954	ENST00000494426.1:c.51G>C	9.37:g.139890192C>G	ENSP00000419378:p.Glu17Asp	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	7	4	NM_004669	0	0	66	91	25	Q5SPZ7	Missense_Mutation	SNP	ENST00000494426.1	37	CCDS7021.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.541433	0.45280	.	.	ENSG00000169583	ENST00000494426	T	0.25749	1.78	3.99	3.99	0.46301	Thioredoxin-like fold (2);	0.052675	0.64402	D	0.000001	T	0.29061	0.0722	M	0.63428	1.95	0.45676	D	0.998592	B	0.10296	0.003	B	0.06405	0.002	T	0.19484	-1.0304	10	0.66056	D	0.02	.	15.014	0.71570	0.0:1.0:0.0:0.0	.	17	O95833	CLIC3_HUMAN	D	17	ENSP00000419378:E17D	ENSP00000419378:E17D	E	-	3	2	CLIC3	139010013	0.995000	0.38212	1.000000	0.80357	0.969000	0.65631	0.393000	0.20817	2.045000	0.60652	0.561000	0.74099	GAG	.		0.706	CLIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055173.2	NM_004669		G	139890192	C	G	139890192	3	3	130	1	0	0	0	0	1	0	0	0	3533	912	32	4	679	4	CLIC3	9	139890192	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1296006	139890192	1323239	102	11444											
FAM171A1	221061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	15256140	15256140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtaactacccctgtagtcatCattgcccgaggactcgtagc	9	10	9	13	2	2	0	2	0	0	0	3	2	2	1	3	1	4	3	3	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:15256140C>T	ENST00000378116.4	-	8	1453	c.1447G>A	c.(1447-1449)Gat>Aat	p.D483N	FAM171A1_ENST00000477161.1_5'Flank	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	483						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						CTGTAGTCATCATTGCCCGAG	0.483																																					p.D483N		.											.	FAM171A1-138	0			c.G1447A						.						126	107	113					10																	15256140		2203	4300	6503	SO:0001583	missense	221061	exon8			AGTCATCATTGCC	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 38"	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1447G>A	10.37:g.15256140C>T	ENSP00000367356:p.Asp483Asn	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	244	27	NM_001010924	0	0	3	3	0	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.660|1.660	-0.511725|-0.511725	0.04200|0.04200	.|.	.|.	ENSG00000148468|ENSG00000148468	ENST00000378116|ENST00000396781	T|.	0.33438|.	1.41|.	5.25|5.25	2.22|2.22	0.28083|0.28083	.|.	0.813268|.	0.11427|.	N|.	0.565243|.	T|T	0.38161|0.38161	0.1030|0.1030	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.26467|0.26467	-1.0102|-1.0102	10|6	0.32370|0.18276	T|T	0.25|0.48	-0.8277|-0.8277	7.3007|7.3007	0.26418|0.26418	0.0:0.692:0.0:0.308|0.0:0.692:0.0:0.308	.|.	483|.	Q5VUB5|.	F1711_HUMAN|.	N|I	483|482	ENSP00000367356:D483N|.	ENSP00000367356:D483N|ENSP00000380001:M482I	D|M	-|-	1|3	0|0	FAM171A1|FAM171A1	15296146|15296146	0.000000|0.000000	0.05858|0.05858	0.006000|0.006000	0.13384|0.13384	0.058000|0.058000	0.15608|0.15608	-0.109000|-0.109000	0.10840|0.10840	0.272000|0.272000	0.22027|0.22027	0.563000|0.563000	0.77884|0.77884	GAT|ATG	.		0.483	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		T	15256140	C	T	15256140	3	4	130	1	0	0	0	0	1	0	0	0	5506	826	29	2	1229	2	FAM171A1	10	15256140	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		15256140	120278607	103	11445											
ANKRD30A	91074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	37451603	37451603	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggggaagccatctgccttcGaggtatttagttttatgatt	8	15	11	7	2	1	1	0	1	1	0	2	3	1	2	2	3	2	2	2	3	4	7	rs376283553		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:37451603G>A	ENST00000602533.1	+	16	1858	c.1759G>A	c.(1759-1761)Gag>Aag	p.E587K	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.E587K|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.E587K			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	643					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						ATCTGCCTTCGAGGTATTTAG	0.333													.|||	1	0.000199681	8e-04	0	5008	,	,		17442	0		0	False		,,,				2504	0				p.E587K		.											.	ANKRD30A-161	0			c.G1759A						.	G	LYS/GLU	1,3617		0,1,1808	162	135	143		1759	-1	0	10		143	0,8130		0,0,4065	no	missense	ANKRD30A	NM_052997.2	56	0,1,5873	AA,AG,GG		0.0,0.0276,0.0085	benign	587/1342	37451603	1,11747	1809	4065	5874	SO:0001583	missense	91074	exon16			GCCTTCGAGGTAT	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1759G>A	10.37:g.37451603G>A	ENSP00000473551:p.Glu587Lys	Somatic	164	1		WXS	Illumina HiSeq	Phase_I	254	51	NM_052997	0	0	0	0	0	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	0.014	-1.579776	0.00879	2.76E-4	0.0	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05139	3.49;3.49	0.731	-1.01	0.10169	.	.	.	.	.	T	0.01189	0.0039	N	0.00413	-1.525	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.44528	-0.9322	9	0.02654	T	1	.	2.925	0.05781	0.6458:0.0:0.3542:0.0	.	643	Q9BXX3	AN30A_HUMAN	K	587	ENSP00000354432:E587K;ENSP00000363792:E587K	ENSP00000354432:E587K	E	+	1	0	ANKRD30A	37491609	0.071000	0.21146	0.009000	0.14445	0.199000	0.23934	-0.207000	0.09384	-0.240000	0.09696	0.089000	0.15464	GAG	.		0.333	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37451603	G	A	37451603	3	1	130	1	0	0	0	0	1	0	0	0	658	1059	37	1	1821	1	ANKRD30A	10	37451603	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	22195463	37451603	98083144	104	11446											
CSGALNACT2	55454	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	43654255	43654255	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagacatgtgaccctcttcCgcccttttggacctctcatg	7	13	7	14	1	2	2	1	1	2	1	4	3	3	3	4	1	0	0	4	1	1	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:43654255C>T	ENST00000374466.3	+	3	1089	c.754C>T	c.(754-756)Cgc>Tgc	p.R252C	CSGALNACT2_ENST00000374464.1_Missense_Mutation_p.R252C	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	252					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GACCCTCTTCCGCCCTTTTGG	0.393																																					p.R252C													.	CSGALNACT2-69	0			c.C754T						.						98	93	95					10																	43654255		2203	4300	6503	SO:0001583	missense	55454	exon3			CTCTTCCGCCCTT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.754C>T	10.37:g.43654255C>T	ENSP00000363590:p.Arg252Cys	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	67	10	NM_018590	0	0	9	14	5	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053268	0.55218	.	.	ENSG00000169826	ENST00000374466;ENST00000374464	T;T	0.23950	1.88;1.88	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.39226	0.1070	M	0.85630	2.765	0.80722	D	1	B;B	0.26081	0.141;0.108	B;B	0.20184	0.028;0.016	T	0.39921	-0.9590	10	0.87932	D	0	-9.3537	19.5366	0.95255	0.0:1.0:0.0:0.0	.	252;252	Q8N6G5;Q8N6G5-2	CGAT2_HUMAN;.	C	252	ENSP00000363590:R252C;ENSP00000363588:R252C	ENSP00000363588:R252C	R	+	1	0	CSGALNACT2	42974261	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.581000	0.60949	2.622000	0.88805	0.591000	0.81541	CGC	.		0.393	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43654255	C	T	43654255	3	4	130	1	0	0	0	0	1	0	0	0	3945	652	23	1	760	1	CSGALNACT2	10	43654255	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	6202652	43654255	91880492	105	11447											
C10orf10	11067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	45472882	45472882	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggtgcgagtagagtgttctGaggacactgctggggcgggg	7	8	20	6	2	1	2	0	1	1	1	1	4	1	3	0	6	2	3	0	6	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:45472882G>A	ENST00000298295.3	-	2	814	c.597C>T	c.(595-597)ctC>ctT	p.L199L	RASSF4_ENST00000334940.6_Intron|RASSF4_ENST00000374417.2_Intron|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000472561.1_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	199						mitochondrion (GO:0005739)				lung(1)	1						AGAGTGTTCTGAGGACACTGC	0.607																																					p.L199L		.											.	C10orf10-90	0			c.C597T						.						59	71	67					10																	45472882		2197	4298	6495	SO:0001819	synonymous_variant	11067	exon2			TGTTCTGAGGACA	AB022718	CCDS7210.1	10q11.21	2014-07-31			ENSG00000165507	ENSG00000165507			23355	protein-coding gene	gene with protein product	"decidual protein induced by progesterone", "fasting induced", "fat-specific expressed gene"	611309				24530860, 19937567, 16123073	Standard	NM_007021		Approved	DEPP, FIG, Fseg	uc001jbr.4	Q9NTK1	OTTHUMG00000018063	ENST00000298295.3:c.597C>T	10.37:g.45472882G>A		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	100	24	NM_007021	0	0	70	92	22	B2R6A1|O94997|Q5T735|Q76MX8	Silent	SNP	ENST00000298295.3	37	CCDS7210.1																																																																																			.		0.607	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021		A	45472882	G	A	45472882	2	1	130	1	0	0	0	0	0	0	0	1	1583	1277	45	2		2	C10orf10	10	45472882	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1818627	45472882	90061865	106	11448											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61830133	61830133	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtctgccttccagtgtgaaGaactgggcccctgacttctg	6	12	11	12	0	2	3	0	2	2	1	3	3	3	3	4	1	2	0	4	1	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:61830133G>A	ENST00000280772.2	-	37	10697	c.10506C>T	c.(10504-10506)ttC>ttT	p.F3502F	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3502					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CCAGTGTGAAGAACTGGGCCC	0.438																																					p.F3502F		.											.	ANK3-107	0			c.C10506T						.						85	84	84					10																	61830133		2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TGTGAAGAACTGG	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.10506C>T	10.37:g.61830133G>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	65	16	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			.		0.438	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61830133	G	A	61830133	2	1	130	1	0	0	0	0	0	0	0	1	622	933	33	2		2	ANK3	10	61830133	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	16357251	61830133	73704614	107	11449											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61830689	61830689	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaatagattcgtcatcgcttGaatcactgacgtctgccccg	10	11	8	12	4	3	3	2	2	1	1	5	3	3	3	2	0	1	1	2	0	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:61830689G>C	ENST00000280772.2	-	37	10141	c.9950C>G	c.(9949-9951)tCa>tGa	p.S3317*	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3317					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GTCATCGCTTGAATCACTGAC	0.443																																					p.S3317X		.											.	ANK3-107	0			c.C9950G						.						130	132	131					10																	61830689		2203	4300	6503	SO:0001587	stop_gained	288	exon37			TCGCTTGAATCAC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.9950C>G	10.37:g.61830689G>C	ENSP00000280772:p.Ser3317*	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	157	41	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Nonsense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	51	17.357246	0.99884	.	.	ENSG00000151150	ENST00000280772	.	.	.	5.48	5.48	0.80851	.	0.000000	0.38326	N	0.001738	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.359	0.94428	0.0:0.0:1.0:0.0	.	.	.	.	X	3317	.	ENSP00000280772:S3317X	S	-	2	0	ANK3	61500695	1.000000	0.71417	0.256000	0.24389	0.293000	0.27360	7.876000	0.87215	2.584000	0.87258	0.561000	0.74099	TCA	.		0.443	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61830689	G	C	61830689	4	2	130	1	0	0	0	0	0	1	0	0	622	1294	45	4	3524	4	ANK3	10	61830689	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	556	61830689	73704058	108	11450											
PRF1	5551	ucsc.edu;bcgsc.ca	37	chr10	72360284	72360284	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccgaccttccagtcgttgcgGatgctacgagccgcatcccg	6	8	11	16	6	0	0	0	0	0	0	3	3	2	1	5	1	4	3	5	1	1	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:72360284G>A	ENST00000441259.1	-	2	535	c.375C>T	c.(373-375)atC>atT	p.I125I	PRF1_ENST00000373209.2_Silent_p.I125I	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	125	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						AGTCGTTGCGGATGCTACGAG	0.627			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.I125I			yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1-578	0			c.C375T						.						48	45	46					10																	72360284		2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTTGCGGATGCTA	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"Perforin", "perforin 1 (preforming protein)"	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.375C>T	10.37:g.72360284G>A		Somatic	38	0		WXS	Illumina HiSeq		39	6	NM_001083116	0	0	0	0	0	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			.		0.627	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		A	72360284	G	A	72360284	2	1	130	1	0	0	0	0	0	0	0	1	12507	1164	41	2		2	PRF1	10	72360284	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10529595	72360284	63174463	109	11451											
CHST3	9469	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	73765714	73765714	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gtgatagtttttgtcttcatCgaaaaggaaaataaaatcat	16	14	7	4	1	3	1	2	1	1	0	4	3	3	2	0	1	0	1	0	1	7	5	rs374590185		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:73765714C>G	ENST00000373115.4	+	2	551	c.114C>G	c.(112-114)atC>atG	p.I38M		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	38					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TTGTCTTCATCGAAAAGGAAA	0.478																																					p.I38M		.											.	CHST3-90	0			c.C114G						.						182	168	173					10																	73765714		2203	4300	6503	SO:0001583	missense	9469	exon2			CTTCATCGAAAAG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.114C>G	10.37:g.73765714C>G	ENSP00000362207:p.Ile38Met	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	147	9	NM_004273	0	0	3	3	0	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	37	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072133	0.55646	.	.	ENSG00000122863	ENST00000373115	D	0.98044	-4.68	5.66	0.325	0.15903	.	0.000000	0.85682	D	0.000000	D	0.97445	0.9164	L	0.59436	1.845	0.47214	D	0.999359	D	0.89917	1.0	D	0.87578	0.998	D	0.95229	0.8341	10	0.87932	D	0	-10.7332	5.8588	0.18734	0.1406:0.4405:0.0:0.4189	.	38	Q7LGC8	CHST3_HUMAN	M	38	ENSP00000362207:I38M	ENSP00000362207:I38M	I	+	3	3	CHST3	73435720	0.992000	0.36948	0.997000	0.53966	0.982000	0.71751	0.179000	0.16840	-0.128000	0.11641	-1.202000	0.01658	ATC	.		0.478	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		G	73765714	C	G	73765714	3	3	130	1	0	0	0	0	1	0	0	0	3411	874	31	4	116	4	CHST3	10	73765714	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1405430	73765714	61769033	110	11452											
CDHR1	92211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	85956359	85956359	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctagaagcgtcttttctgttGaccccacttttggaaacatc	9	14	7	11	1	2	2	0	1	2	1	3	3	2	3	2	1	2	1	2	1	3	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:85956359G>A	ENST00000372117.3	+	3	353	c.250G>A	c.(250-252)Gac>Aac	p.D84N	CDHR1_ENST00000332904.3_Missense_Mutation_p.D84N	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	84	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CTTTTCTGTTGACCCCACTTT	0.562																																					p.D84N		.											.	CDHR1-91	0			c.G250A						.						138	124	129					10																	85956359		2203	4300	6503	SO:0001583	missense	92211	exon3			TCTGTTGACCCCA	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"Cadherins / Cadherin-related"	14550	protein-coding gene	gene with protein product		609502	"protocadherin 21"	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.250G>A	10.37:g.85956359G>A	ENSP00000361189:p.Asp84Asn	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	109	66	NM_001171971	0	0	0	0	0	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237685	0.79800	.	.	ENSG00000148600	ENST00000332904;ENST00000372117	T;T	0.62788	-0.0;-0.0	5.57	5.57	0.84162	Cadherin (5);Cadherin-like (1);	0.095350	0.64402	D	0.000001	T	0.54191	0.1843	L	0.37630	1.12	0.80722	D	1	B;B	0.30542	0.284;0.148	B;B	0.34722	0.188;0.186	T	0.53215	-0.8470	10	0.39692	T	0.17	-36.6578	12.4369	0.55604	0.0811:0.0:0.9189:0.0	.	84;84	Q96JP9-2;Q96JP9	.;CDHR1_HUMAN	N	84	ENSP00000331063:D84N;ENSP00000361189:D84N	ENSP00000331063:D84N	D	+	1	0	CDHR1	85946339	1.000000	0.71417	0.770000	0.31555	0.782000	0.44232	5.695000	0.68279	2.630000	0.89119	0.561000	0.74099	GAC	.		0.562	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		A	85956359	G	A	85956359	3	1	130	1	0	0	0	0	1	0	0	0	3124	1290	45	2	260	2	CDHR1	10	85956359	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	12190645	85956359	49578388	111	11453											
CALHM1	255022	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105215149	105215149	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgcatttgtgccagctcGtgagcagcctgttcatggtg	5	14	13	9	1	1	1	1	1	0	0	2	1	1	1	2	1	5	5	2	1	0	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:105215149G>A	ENST00000329905.5	-	2	1047	c.911C>T	c.(910-912)aCg>aTg	p.T304M	RP11-225H22.4_ENST00000411906.1_RNA|CALHM2_ENST00000393235.1_5'Flank|CALHM2_ENST00000369788.3_5'Flank	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	304					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						GTGCCAGCTCGTGAGCAGCCT	0.677																																					p.T304M													.	CALHM1-91	0			c.C911T						.						67	52	57					10																	105215149		2203	4300	6503	SO:0001583	missense	255022	exon2			CAGCTCGTGAGCA	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"family with sequence similarity 26, member C"	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.911C>T	10.37:g.105215149G>A	ENSP00000329926:p.Thr304Met	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	54	18	NM_001001412	0	0	0	0	0	Q5W091	Missense_Mutation	SNP	ENST00000329905.5	37	CCDS7550.1	.	.	.	.	.	.	.	.	.	.	G	9.572	1.121186	0.20877	.	.	ENSG00000185933	ENST00000329905	T	0.18016	2.24	4.8	1.28	0.21552	.	0.231983	0.45867	D	0.000331	T	0.07728	0.0194	N	0.14661	0.345	0.26966	N	0.96569	B	0.06786	0.001	B	0.04013	0.001	T	0.18681	-1.0329	10	0.48119	T	0.1	-15.6045	2.9522	0.05865	0.0963:0.1134:0.4129:0.3775	.	304	Q8IU99	CAHM1_HUMAN	M	304	ENSP00000329926:T304M	ENSP00000329926:T304M	T	-	2	0	CALHM1	105205139	0.405000	0.25336	0.635000	0.29338	0.188000	0.23474	1.119000	0.31258	0.546000	0.28920	0.462000	0.41574	ACG	.		0.677	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412		A	105215149	G	A	105215149	3	1	130	1	0	0	0	0	1	0	0	0	2588	1145	40	1	133	1	CALHM1	10	105215149	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	19258790	105215149	30319598	112	11454											
TRUB1	142940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	116734920	116734920	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtgctagagctgacccgaAccaaacagggaccatttacg	13	7	10	11	2	0	2	0	1	0	1	0	4	0	3	3	1	5	2	3	1	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:116734920A>G	ENST00000298746.3	+	8	893	c.832A>G	c.(832-834)Acc>Gcc	p.T278A		NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	278					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		GCTGACCCGAACCAAACAGGG	0.408																																					p.T278A		.											.	TRUB1-90	0			c.A832G						.						157	145	149					10																	116734920		2203	4300	6503	SO:0001583	missense	142940	exon8			ACCCGAACCAAAC	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"TruB pseudouridine (psi) synthase homolog 1 (E. coli)"			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.832A>G	10.37:g.116734920A>G	ENSP00000298746:p.Thr278Ala	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	112	24	NM_139169	0	0	15	18	3	B2R716|Q53ES2	Missense_Mutation	SNP	ENST00000298746.3	37	CCDS7591.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.696609	0.88830	.	.	ENSG00000165832	ENST00000298746	T	0.16196	2.36	5.7	5.7	0.88788	Pseudouridine synthase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	M	0.93062	3.375	0.80722	D	1	D	0.55605	0.972	P	0.62740	0.906	T	0.61048	-0.7141	10	0.66056	D	0.02	-16.4514	14.82	0.70065	1.0:0.0:0.0:0.0	.	278	Q8WWH5	TRUB1_HUMAN	A	278	ENSP00000298746:T278A	ENSP00000298746:T278A	T	+	1	0	TRUB1	116724910	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.785000	0.85724	2.287000	0.76781	0.533000	0.62120	ACC	.		0.408	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169		G	116734920	A	G	116734920	3	3	130	1	0	0	0	0	1	0	0	0	16635	43	2	3	862	3	TRUB1	10	116734920	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	11519771	116734920	18799827	113	11455											
MKI67	4288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	129910532	129910532	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccctcctctcttaggaacctCtgtctgagatttgctgctgg	5	14	9	13	0	3	1	0	1	3	1	5	3	4	2	3	2	3	2	3	2	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:129910532C>T	ENST00000368654.3	-	9	2209	c.1834G>A	c.(1834-1836)Gag>Aag	p.E612K	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.E252K	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	612					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTAGGAACCTCTGTCTGAGAT	0.488																																					p.E612K		.											.	MKI67-519	0			c.G1834A						.						111	102	105					10																	129910532		2203	4300	6503	SO:0001583	missense	4288	exon9			GAACCTCTGTCTG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1834G>A	10.37:g.129910532C>T	ENSP00000357643:p.Glu612Lys	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	84	11	NM_002417	0	0	21	22	1	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117442	0.37339	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01335	5.04;5.0	3.15	2.24	0.28232	.	0.534998	0.18473	N	0.140147	T	0.01592	0.0051	N	0.22421	0.69	0.09310	N	1	P;P;P	0.50528	0.73;0.936;0.61	B;P;B	0.47673	0.205;0.554;0.101	T	0.55276	-0.8166	10	0.33141	T	0.24	.	8.3147	0.32093	0.0:0.8808:0.0:0.1192	.	612;252;612	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	K	612;252;612;187	ENSP00000357643:E612K;ENSP00000357642:E252K	ENSP00000357641:E187K	E	-	1	0	MKI67	129800522	0.000000	0.05858	0.031000	0.17742	0.069000	0.16628	0.316000	0.19469	0.889000	0.36185	0.655000	0.94253	GAG	.		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129910532	C	T	129910532	3	4	130	1	0	0	0	0	1	0	0	0	9623	922	32	2	7964	2	MKI67	10	129910532	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	13175612	129910532	5624215	114	11456											
MTG1	92170	broad.mit.edu;bcgsc.ca	37	chr10	135209677	135209677	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attttgccacatcccactttCaggccgcaaccctctgtttc	7	13	5	16	1	2	0	1	0	1	0	4	0	3	0	4	1	2	2	4	1	1	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:135209677C>T	ENST00000317502.6	+	3	238	c.188C>T	c.(187-189)tCa>tTa	p.S63L	MTG1_ENST00000477902.2_Missense_Mutation_p.S22L|RP11-108K14.8_ENST00000468317.2_Missense_Mutation_p.S68L	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	63	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		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)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		ATCCCACTTTCAGGCCGCAAC	0.468																																					p.S63L													.	MTG1-91	0			c.C188T						.						199	209	205					10																	135209677		2203	4300	6503	SO:0001583	missense	92170	exon3			CACTTTCAGGCCG		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"GTP-binding protein 7", "GTP-binding protein 7 (putative)", "mitochondrial GTPase 1 homolog (S. cerevisiae)"	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	ENST00000317502.6:c.188C>T	10.37:g.135209677C>T	ENSP00000323047:p.Ser63Leu	Somatic	368	0		WXS	Illumina HiSeq	Phase_I	233	15	NM_138384	0	0	0	0	0	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Missense_Mutation	SNP	ENST00000317502.6	37	CCDS31320.1	.	.	.	.	.	.	.	.	.	.	c	29.2	4.990134	0.93106	.	.	ENSG00000254536;ENSG00000148824;ENSG00000148824;ENSG00000148824	ENST00000468317;ENST00000317502;ENST00000432508;ENST00000537620	T;T;T	0.12984	2.63;2.63;2.63	5.4	5.4	0.78164	.	4.888220	0.00424	N	0.000066	T	0.38825	0.1055	M	0.88181	2.935	0.58432	D	0.999999	P	0.36577	0.558	B	0.41723	0.365	T	0.46965	-0.9153	10	0.87932	D	0	-1.9895	16.6591	0.85236	0.0:1.0:0.0:0.0	.	63	Q9BT17	MTG1_HUMAN	L	68;63;63;22	ENSP00000436767:S68L;ENSP00000323047:S63L;ENSP00000393480:S63L	ENSP00000323047:S63L	S	+	2	0	AL360181.1;MTG1	135059667	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.217000	0.72218	2.535000	0.85469	0.478000	0.44815	TCA	.		0.468	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384		T	135209677	C	T	135209677	3	4	130	1	0	0	0	0	1	0	0	0	9951	838	29	2	198	2	MTG1	10	135209677	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5299145	135209677	325070	115	11457											
OR51G2	81282	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4936273	4936273	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atacccactgtagagacgatGacaaacatgccgtagatgct	14	8	9	10	2	0	3	0	1	0	2	0	5	0	3	2	0	4	3	2	0	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:4936273G>A	ENST00000322013.3	-	1	649	c.621C>T	c.(619-621)gtC>gtT	p.V207V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	207						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)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TAGAGACGATGACAAACATGC	0.512																																					p.V207V													.	OR51G2-70	0			c.C621T						.						133	108	117					11																	4936273		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			GACGATGACAAAC	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.621C>T	11.37:g.4936273G>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	27	11	NM_001005238	0	0	0	0	0	Q6IFH7	Silent	SNP	ENST00000322013.3	37	CCDS31365.1																																																																																			.		0.512	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		A	4936273	G	A	4936273	2	1	130	1	0	0	0	0	0	0	0	1	11125	1277	45	2		2	OR51G2	11	4936273	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		4936273	130070243	116	11458											
IPO7	10527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	9451343	9451343	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgatctgtgaatatagtgaaGaagttactcctattgcagta	13	14	9	5	0	1	4	0	3	1	1	2	4	2	4	1	0	2	3	1	0	8	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:9451343G>A	ENST00000379719.3	+	15	1856	c.1714G>A	c.(1714-1716)Gaa>Aaa	p.E572K	SNORA23_ENST00000365128.1_RNA|CTD-2371O3.2_ENST00000531111.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	572					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		ATATAGTGAAGAAGTTACTCC	0.353																																					p.E572K		.											.	IPO7-271	0			c.G1714A						.						71	61	65					11																	9451343		2201	4294	6495	SO:0001583	missense	10527	exon15			AGTGAAGAAGTTA	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"Importins"	9852	protein-coding gene	gene with protein product		605586	"RAN binding protein 7"	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.1714G>A	11.37:g.9451343G>A	ENSP00000369042:p.Glu572Lys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	26	12	NM_006391	0	0	7	19	12	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743031	0.89663	.	.	ENSG00000205339	ENST00000379719	T	0.44881	0.91	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	M	0.80183	2.485	0.80722	D	1	B	0.31989	0.35	B	0.36335	0.222	T	0.55049	-0.8201	10	0.51188	T	0.08	.	20.1772	0.98182	0.0:0.0:1.0:0.0	.	572	O95373	IPO7_HUMAN	K	572	ENSP00000369042:E572K	ENSP00000369042:E572K	E	+	1	0	IPO7	9407919	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.778000	0.95560	0.655000	0.94253	GAA	.		0.353	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		A	9451343	G	A	9451343	3	1	130	1	0	0	0	0	1	0	0	0	7818	943	33	2	1772	2	IPO7	11	9451343	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	4515070	9451343	125555173	117	11459											
COPB1	1315	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	14501121	14501121	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tattttaaacctacttgacaGatttaatagcatgaaagact	16	14	5	6	0	0	4	0	2	0	2	0	4	0	4	1	0	3	1	1	0	7	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:14501121G>C	ENST00000249923.3	-	11	1652	c.1352C>G	c.(1351-1353)tCt>tGt	p.S451C	COPB1_ENST00000439561.2_Missense_Mutation_p.S451C|RNU7-49P_ENST00000516182.1_RNA	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	451					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						CTACTTGACAGATTTAATAGC	0.343																																					p.S451C		.											.	COPB1-91	0			c.C1352G						.						76	78	77					11																	14501121		2200	4293	6493	SO:0001583	missense	1315	exon11			TTGACAGATTTAA	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"coatomer protein complex, subunit beta"	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.1352C>G	11.37:g.14501121G>C	ENSP00000249923:p.Ser451Cys	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	100	73	NM_001144062	0	0	0	0	0	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070302	0.93950	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234	T;T;T	0.14893	2.47;2.47;2.47	5.83	5.83	0.93111	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.049398	0.85682	D	0.000000	T	0.48589	0.1508	M	0.87971	2.92	0.80722	D	1	P	0.45768	0.866	P	0.60117	0.869	T	0.47302	-0.9128	10	0.56958	D	0.05	-0.5739	20.127	0.97984	0.0:0.0:1.0:0.0	.	451	P53618	COPB_HUMAN	C	451	ENSP00000249923:S451C;ENSP00000397873:S451C;ENSP00000436383:S451C	ENSP00000249923:S451C	S	-	2	0	COPB1	14457697	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.775000	0.95449	0.585000	0.79938	TCT	.		0.343	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		C	14501121	G	C	14501121	3	2	130	1	0	0	0	0	1	0	0	0	3734	942	33	4	1557	4	COPB1	11	14501121	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	5049778	14501121	120505395	118	11460											
RAG2	5897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	36614896	36614896	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attttcaagctgatagccacCaacaataacaaattcatcat	17	11	3	10	0	3	1	3	1	0	0	3	1	3	1	2	0	4	1	2	0	6	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:36614896C>T	ENST00000311485.3	-	2	984	c.823G>A	c.(823-825)Ggt>Agt	p.G275S	C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank|C11orf74_ENST00000347206.4_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000446510.2_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	275					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				TGATAGCCACCAACAATAACA	0.428									Familial Hemophagocytic Lymphohistiocytosis																												p.G275S		.											.	RAG2-95	0			c.G823A						.						86	87	86					11																	36614896		2202	4298	6500	SO:0001583	missense	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGCCACCAACAAT	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.823G>A	11.37:g.36614896C>T	ENSP00000308620:p.Gly275Ser	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	44	22	NM_001243785	0	0	0	0	0	A8K9E9|Q8TBL4	Missense_Mutation	SNP	ENST00000311485.3	37	CCDS7903.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473990	0.84640	.	.	ENSG00000175097	ENST00000311485	D	0.93906	-3.31	5.69	5.69	0.88448	Galactose oxidase/kelch, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.98027	0.9350	H	0.96048	3.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98794	1.0737	10	0.87932	D	0	-12.4322	19.8052	0.96529	0.0:1.0:0.0:0.0	.	275	P55895	RAG2_HUMAN	S	275	ENSP00000308620:G275S	ENSP00000308620:G275S	G	-	1	0	RAG2	36571472	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.487000	0.81328	2.692000	0.91855	0.650000	0.86243	GGT	.		0.428	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		T	36614896	C	T	36614896	3	4	130	1	0	0	0	0	1	0	0	0	13037	594	21	2	764	2	RAG2	11	36614896	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	22113775	36614896	98391620	119	11461											
OR9G1	390174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	56468116	56468116	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagatcctagtgacctgcAtctctgaagacaaaagcatc	15	8	7	11	0	1	4	0	2	1	2	4	4	2	4	2	0	2	2	2	0	5	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:56468116A>G	ENST00000312153.1	+	1	253	c.253A>G	c.(253-255)Atc>Gtc	p.I85V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						AGTGACCTGCATCTCTGAAGA	0.507																																					p.I85V		.											.	.	0			c.A253G						.						127	124	125					11																	56468116		2201	4293	6494	SO:0001583	missense	504191	exon1			ACCTGCATCTCTG	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"GPCR / Class A : Olfactory receptors"	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.253A>G	11.37:g.56468116A>G	ENSP00000309012:p.Ile85Val	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	174	22	NM_001013358	0	0	0	0	0	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	A	0.852	-0.738253	0.03111	.	.	ENSG00000174914	ENST00000312153	T	0.02236	4.38	4.54	4.54	0.55810	GPCR, rhodopsin-like superfamily (1);	0.251802	0.29178	N	0.012920	T	0.01661	0.0053	N	0.15975	0.35	0.24579	N	0.993886	B	0.06786	0.001	B	0.10450	0.005	T	0.48592	-0.9022	10	0.19590	T	0.45	-19.0486	10.2627	0.43436	0.721:0.279:0.0:0.0	.	85	Q8NH87	OR9G1_HUMAN	V	85	ENSP00000309012:I85V	ENSP00000309012:I85V	I	+	1	0	OR9G1	56224692	0.000000	0.05858	0.995000	0.50966	0.171000	0.22731	-0.467000	0.06664	2.013000	0.59113	0.477000	0.44152	ATC	.		0.507	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		G	56468116	A	G	56468116	3	3	130	1	0	0	0	0	1	0	0	0	11276	217	8	3	255	3	OR9G1	11	56468116	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	19853220	56468116	78538400	120	11462											
LPXN	9404	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	58295114	58295114	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccatggcagagcgttcccCggcggtgatggtaatggagc	8	7	15	11	3	0	2	0	1	0	1	1	3	1	3	3	5	2	3	3	5	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:58295114C>T	ENST00000395074.2	-	9	1062	c.974G>A	c.(973-975)cGg>cAg	p.R325Q	LPXN_ENST00000528954.1_Missense_Mutation_p.R330Q|LPXN_ENST00000528489.1_Missense_Mutation_p.R305Q	NM_004811.2	NP_004802.1	O60711	LPXN_HUMAN	leupaxin	325	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell adhesion (GO:0007162)|protein complex assembly (GO:0006461)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|podosome (GO:0002102)	transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				GAGCGTTCCCCGGCGGTGATG	0.542																																					p.R330Q													.	LPXN-91	0			c.G989A						.						77	67	70					11																	58295114		2201	4295	6496	SO:0001583	missense	9404	exon9			GTTCCCCGGCGGT	AF062075	CCDS7969.1, CCDS53635.1	11q12.1	2013-09-20			ENSG00000110031	ENSG00000110031			14061	protein-coding gene	gene with protein product		605390				9565592	Standard	NM_004811		Approved	LDPL	uc001nmw.3	O60711	OTTHUMG00000167466	ENST00000395074.2:c.974G>A	11.37:g.58295114C>T	ENSP00000378512:p.Arg325Gln	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	38	6	NM_001143995	0	0	3	4	1	B2R8B4|B4DV71|Q53FW6|Q6FI07	Missense_Mutation	SNP	ENST00000395074.2	37	CCDS7969.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883091	0.72410	.	.	ENSG00000110031	ENST00000528954;ENST00000395074	D;D	0.87029	-2.2;-2.2	6.03	2.1	0.27182	Zinc finger, LIM-type (2);	0.221957	0.39274	N	0.001420	T	0.70842	0.3270	N	0.02973	-0.45	0.44042	D	0.996771	P;B;B	0.36990	0.577;0.097;0.25	B;B;B	0.40038	0.317;0.013;0.089	T	0.68750	-0.5326	10	0.38643	T	0.18	.	9.295	0.37811	0.0:0.6642:0.0:0.3358	.	305;330;325	B7Z5P7;B4DV71;O60711	.;.;LPXN_HUMAN	Q	330;325	ENSP00000431284:R330Q;ENSP00000378512:R325Q	ENSP00000378512:R325Q	R	-	2	0	LPXN	58051690	0.002000	0.14202	0.998000	0.56505	0.756000	0.42949	0.015000	0.13355	0.885000	0.36088	0.557000	0.71058	CGG	.		0.542	LPXN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394709.1	NM_004811		T	58295114	C	T	58295114	3	4	130	1	0	0	0	0	1	0	0	0	8954	652	23	1	190	1	LPXN	11	58295114	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1826998	58295114	76711402	121	11463											
OR4D11	219986	hgsc.bcm.edu;broad.mit.edu	37	chr11	59271133	59271133	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	accagagtttggtcttgtttCtttttttatgtcttgtgtac	5	22	8	6	0	3	1	0	0	3	1	3	1	3	1	1	1	1	3	1	1	2	9			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:59271133C>G	ENST00000313253.1	+	1	85	c.85C>G	c.(85-87)Ctt>Gtt	p.L29V		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						GGTCTTGTTTCTTTTTTTATG	0.433																																					p.L29V		.											.	OR4D11-70	0			c.C85G						.						103	96	98					11																	59271133		2201	4295	6496	SO:0001583	missense	219986	exon1			TTGTTTCTTTTTT	AB065810	CCDS31563.1	11q12.1	2012-08-09		2004-03-10	ENSG00000176200	ENSG00000176200		"GPCR / Class A : Olfactory receptors"	15174	protein-coding gene	gene with protein product				OR4D11P			Standard	NM_001004706		Approved		uc001noa.1	Q8NGI4	OTTHUMG00000167342	ENST00000313253.1:c.85C>G	11.37:g.59271133C>G	ENSP00000320077:p.Leu29Val	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	99	5	NM_001004706	0	0	0	0	0		Missense_Mutation	SNP	ENST00000313253.1	37	CCDS31563.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.816889	0.00072	.	.	ENSG00000176200	ENST00000313253	T	0.00418	7.49	5.45	-1.74	0.08056	.	0.332667	0.21503	N	0.073498	T	0.00144	0.0004	N	0.16233	0.39	0.20638	N	0.999875	B	0.02656	0.0	B	0.06405	0.002	T	0.46176	-0.9210	10	0.02654	T	1	-9.7981	2.6212	0.04917	0.2091:0.3651:0.287:0.1389	.	29	Q8NGI4	OR4DB_HUMAN	V	29	ENSP00000320077:L29V	ENSP00000320077:L29V	L	+	1	0	OR4D11	59027709	0.000000	0.05858	0.184000	0.23157	0.091000	0.18340	-1.215000	0.02985	-0.006000	0.14370	-0.311000	0.09066	CTT	.		0.433	OR4D11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394236.1	NM_001004706		G	59271133	C	G	59271133	3	3	130	1	0	0	0	0	1	0	0	0	11081	913	32	4	87	4	OR4D11	11	59271133	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	976019	59271133	75735383	122	11464											
GSTP1	2950	ucsc.edu	37	chr11	67352042	67352042	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcactcaaagcctcctgcGtaagtgaccatgcccgggca	9	7	10	15	2	2	1	2	1	0	0	3	1	3	1	4	1	3	3	4	1	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:67352042G>C	ENST00000398606.3	+	3	393		c.e3+1		GSTP1_ENST00000398603.1_Splice_Site|GSTP1_ENST00000498765.1_Splice_Site	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1						cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	AGCCTCCTGCGTAAGTGACCA	0.672																																					.													.	GSTP1-91	0			c.144+1G>C						.						14	18	17					11																	67352042		1959	4140	6099	SO:0001630	splice_region_variant	2950	exon3			TCCTGCGTAAGTG	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"Glutathione S-transferases / Soluble"	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.144+1G>C	11.37:g.67352042G>C		Somatic	43	0		WXS	Illumina HiSeq		61	1	NM_000852	0	0	12	12	0	O00460|Q15690|Q5TZY3	Splice_Site	SNP	ENST00000398606.3	37	CCDS41679.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.811907	0.50527	.	.	ENSG00000084207	ENST00000398606;ENST00000398603	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5527	0.68078	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GSTP1	67108618	1.000000	0.71417	0.998000	0.56505	0.369000	0.29798	4.707000	0.61852	2.505000	0.84491	0.561000	0.74099	.	.		0.672	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852	Intron	C	67352042	G	C	67352042	5	2	130	1	0	0	0	0	0	0	1	0	6865	1159	40	4	155	4	GSTP1	11	67352042	Splice_Site	SNP	G	TCGA-HE-7130-01A-11D-1961-08	8080909	67352042	67654474	123	11465											
LRP5	4041	broad.mit.edu;bcgsc.ca	37	chr11	68197137	68197137	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgctcatgcccagtccacctCgtgctcctgcagaacctgct	6	10	8	17	1	1	1	1	0	0	1	4	1	3	1	5	0	6	4	5	0	1	0	rs556919142		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:68197137C>T	ENST00000294304.7	+	17	3838	c.3732C>T	c.(3730-3732)ctC>ctT	p.L1244L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1244	EGF-like 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGTCCACCTCGTGCTCCTGC	0.592													C|||	1	0.000199681	0	0	5008	,	,		21123	0		0	False		,,,				2504	0.001				p.L1244L													.	LRP5-661	0			c.C3732T						.						147	108	122					11																	68197137		2200	4294	6494	SO:0001819	synonymous_variant	4041	exon17			CCACCTCGTGCTC	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3732C>T	11.37:g.68197137C>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	502	19	NM_002335	0	0	333	340	7	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																			.		0.592	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68197137	C	T	68197137	2	4	130	1	0	0	0	0	0	0	0	1	8985	871	31	1		1	LRP5	11	68197137	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	845095	68197137	66809379	124	11466											
NARS2	79731	hgsc.bcm.edu	37	chr11	78154732	78154732	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taagcgctcctctaagaaatGgtatcgttcttctctgaggc	9	13	9	10	2	3	2	0	1	3	1	6	2	4	2	1	2	1	3	1	2	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:78154732G>C	ENST00000281038.5	-	12	1612	c.1237C>G	c.(1237-1239)Cat>Gat	p.H413D	NARS2_ENST00000528850.1_Missense_Mutation_p.H186D|RP11-452H21.1_ENST00000534168.1_RNA	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	413					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TCTAAGAAATGGTATCGTTCT	0.423																																					p.H413D		.											.	NARS2-92	0			c.C1237G						.						96	91	93					11																	78154732		2200	4292	6492	SO:0001583	missense	79731	exon12			AGAAATGGTATCG	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"Aminoacyl tRNA synthetases / Class II"	26274	protein-coding gene	gene with protein product	"asparagine tRNA ligase 2, mitochondrial (putative)"	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.1237C>G	11.37:g.78154732G>C	ENSP00000281038:p.His413Asp	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_024678	0	0	7	7	0	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.65|15.65	2.895206|2.895206	0.52121|0.52121	.|.	.|.	ENSG00000137513|ENSG00000137513	ENST00000281038;ENST00000528850|ENST00000529771	T;T|.	0.77229|.	-1.08;-1.08|.	4.96|4.96	4.96|4.96	0.65561|0.65561	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);|.	0.189082|.	0.56097|.	D|.	0.000031|.	T|T	0.10551|0.10551	0.0258|0.0258	N|N	0.00106|0.00106	-2.12|-2.12	0.35491|0.35491	D|D	0.798978|0.798978	B|.	0.06786|.	0.001|.	B|.	0.10450|.	0.005|.	T|T	0.29579|0.29579	-1.0007|-1.0007	10|5	0.02654|.	T|.	1|.	-6.0659|-6.0659	15.1595|15.1595	0.72771|0.72771	0.0:0.1415:0.8585:0.0|0.0:0.1415:0.8585:0.0	.|.	413|.	Q96I59|.	SYNM_HUMAN|.	D|R	413;186|25	ENSP00000281038:H413D;ENSP00000432635:H186D|.	ENSP00000281038:H413D|.	H|P	-|-	1|2	0|0	NARS2|NARS2	77832380|77832380	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.992000|0.992000	0.81027|0.81027	2.432000|2.432000	0.44784|0.44784	2.734000|2.734000	0.93682|0.93682	0.591000|0.591000	0.81541|0.81541	CAT|CCA	.		0.423	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		C	78154732	G	C	78154732	3	2	130	1	0	0	0	0	1	0	0	0	10196	1348	47	4	208	4	NARS2	11	78154732	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	9957595	78154732	56851784	125	11467											
FAM181B	220382	broad.mit.edu	37	chr11	82444012	82444012	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctccgcgcccttctccaggtCgcccaagctcacgtccggcc	4	7	9	21	5	2	0	1	0	1	0	6	0	4	0	6	2	1	1	6	2	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:82444012C>T	ENST00000329203.3	-	1	894	c.760G>A	c.(760-762)Gac>Aac	p.D254N		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	254	Gly-rich.									large_intestine(1)|lung(2)|prostate(1)	4						TTCTCCAGGTCGCCCAAGCTC	0.731																																					p.D254N													.	FAM181B-135	0			c.G760A						.						5	6	5					11																	82444012		1957	3912	5869	SO:0001583	missense	220382	exon1			CCAGGTCGCCCAA	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.760G>A	11.37:g.82444012C>T	ENSP00000365295:p.Asp254Asn	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	10	4	NM_175885	0	0	1	1	0	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087202	0.94100	.	.	ENSG00000182103	ENST00000329203	T	0.33654	1.4	4.36	4.36	0.52297	.	0.175158	0.37906	U	0.001900	T	0.42177	0.1191	L	0.29908	0.895	0.43885	D	0.996506	D	0.71674	0.998	P	0.57548	0.823	T	0.23655	-1.0182	9	.	.	.	.	16.4743	0.84128	0.0:1.0:0.0:0.0	.	254	A6NEQ2	F181B_HUMAN	N	254	ENSP00000365295:D254N	.	D	-	1	0	FAM181B	82121660	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.269000	0.58890	1.969000	0.57287	0.462000	0.41574	GAC	.		0.731	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885		T	82444012	C	T	82444012	3	4	130	1	0	0	0	0	1	0	0	0	5525	884	31	1	524	1	FAM181B	11	82444012	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4289280	82444012	52562504	126	11468											
CREBZF	58487	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	85375684	85375684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctcctccatctcctcggggGagggcgcgcgcacggccacg	4	5	14	18	6	1	0	0	0	1	0	5	1	3	1	5	4	0	1	5	4	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:85375684G>A	ENST00000527447.1	-	1	462	c.236C>T	c.(235-237)tCc>tTc	p.S79F	CREBZF_ENST00000398294.2_5'UTR|CREBZF_ENST00000531515.1_Intron|CREBZF_ENST00000534224.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	79					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				CTCCTCGGGGGAGGGCGCGCG	0.701																																					p.S79F	NSCLC(172;674 2044 9050 18334 41735)	.											.	CREBZF-91	0			c.C236T						.						35	42	40					11																	85375684		1861	4083	5944	SO:0001583	missense	58487	exon1			TCGGGGGAGGGCG	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"basic leucine zipper proteins"	24905	protein-coding gene	gene with protein product	"Zhangfei"	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.236C>T	11.37:g.85375684G>A	ENSP00000433459:p.Ser79Phe	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	78	41	NM_001039618	0	0	4	14	10	B2R8Q9|Q0P5U9|Q52LT3	Missense_Mutation	SNP	ENST00000527447.1	37	CCDS41697.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.635626	0.47049	.	.	ENSG00000137504	ENST00000527447	.	.	.	3.72	3.72	0.42706	.	0.000000	0.33217	U	0.005143	T	0.29749	0.0743	N	0.08118	0	0.80722	D	1	B	0.31910	0.346	B	0.35550	0.205	T	0.09443	-1.0674	8	.	.	.	-19.421	8.7689	0.34719	0.0:0.0:0.7748:0.2252	.	79	Q9NS37	ZHANG_HUMAN	F	79	.	.	S	-	2	0	CREBZF	85053332	0.998000	0.40836	0.998000	0.56505	0.982000	0.71751	2.082000	0.41605	2.068000	0.61886	0.561000	0.74099	TCC	.		0.701	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618		A	85375684	G	A	85375684	3	1	130	1	0	0	0	0	1	0	0	0	3869	1174	41	2	832	2	CREBZF	11	85375684	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2931672	85375684	49630832	127	11469											
MTMR2	8898	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	95621408	95621408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtatgcactgaattctctGaatgagaagtggaggcacta	12	12	11	6	0	1	3	0	3	1	1	2	5	1	4	0	2	1	3	0	2	5	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:95621408G>A	ENST00000346299.5	-	2	438	c.98C>T	c.(97-99)tCa>tTa	p.S33L	MTMR2_ENST00000409459.1_5'UTR|MTMR2_ENST00000393223.3_5'UTR|MTMR2_ENST00000484818.1_5'UTR|MTMR2_ENST00000352297.7_5'UTR	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	33	Ser-rich.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGAATTCTCTGAATGAGAAGT	0.358																																					p.S33L													.	MTMR2-91	0			c.C98T						.						75	71	72					11																	95621408		2201	4298	6499	SO:0001583	missense	8898	exon2			TTCTCTGAATGAG	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.98C>T	11.37:g.95621408G>A	ENSP00000345752:p.Ser33Leu	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	19	7	NM_016156	0	0	3	7	4	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	37	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348120	0.82132	.	.	ENSG00000087053	ENST00000346299;ENST00000546018	D	0.95069	-3.6	5.81	5.81	0.92471	.	0.282561	0.35291	N	0.003307	D	0.94185	0.8134	L	0.32530	0.975	0.80722	D	1	P;D	0.54601	0.791;0.967	B;P	0.60789	0.15;0.879	D	0.91270	0.5043	10	0.12103	T	0.63	.	16.9897	0.86350	0.0:0.0:1.0:0.0	.	33;33	A8K5G2;Q13614	.;MTMR2_HUMAN	L	33;16	ENSP00000345752:S33L	ENSP00000345752:S33L	S	-	2	0	MTMR2	95261056	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	5.703000	0.68340	2.750000	0.94351	0.655000	0.94253	TCA	.		0.358	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		A	95621408	G	A	95621408	3	1	130	1	0	0	0	0	1	0	0	0	9969	1294	45	2	1889	2	MTMR2	11	95621408	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10245724	95621408	39385108	128	11470											
YAP1	10413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102080284	102080284	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atcccagcacagcaaattctCcaaaatgtcaggtaggctct	13	9	7	12	0	3	0	1	0	2	0	5	0	4	0	2	2	2	4	2	2	4	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:102080284C>G	ENST00000282441.5	+	6	1409	c.1021C>G	c.(1021-1023)Cca>Gca	p.P341A	YAP1_ENST00000345877.2_Intron|YAP1_ENST00000526343.1_Intron|YAP1_ENST00000531439.1_Intron|YAP1_ENST00000537274.1_Intron|YAP1_ENST00000524575.1_Missense_Mutation_p.P163A	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	341	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		AGCAAATTCTCCAAAATGTCA	0.368																																					p.P341A	Colon(50;247 1103 7861 28956)	.											.	YAP1-659	0			c.C1021G						.						142	126	131					11																	102080284		1568	3581	5149	SO:0001583	missense	10413	exon6			AATTCTCCAAAAT		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"Yes-associated protein 1, 65kDa"			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1021C>G	11.37:g.102080284C>G	ENSP00000282441:p.Pro341Ala	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	114	62	NM_001130145	0	0	0	2	2	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Missense_Mutation	SNP	ENST00000282441.5	37	CCDS44716.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138326	0.56936	.	.	ENSG00000137693	ENST00000282441;ENST00000445250;ENST00000524575	T	0.39592	1.07	6.17	6.17	0.99709	.	0.226095	0.38720	N	0.001598	T	0.46386	0.1390	N	0.08118	0	0.80722	D	1	D;D;D	0.69078	0.993;0.996;0.997	D;D;D	0.73708	0.956;0.981;0.98	T	0.49399	-0.8944	10	0.35671	T	0.21	.	19.0599	0.93085	0.0:1.0:0.0:0.0	.	163;258;341	B4DTY1;F5GWC5;P46937	.;.;YAP1_HUMAN	A	341;258;163	ENSP00000435602:P163A	ENSP00000282441:P341A	P	+	1	0	YAP1	101585494	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.770000	0.62309	2.941000	0.99782	0.655000	0.94253	CCA	.		0.368	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		G	102080284	C	G	102080284	3	3	130	1	0	0	0	0	1	0	0	0	17499	855	30	4	1055	4	YAP1	11	102080284	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	6458876	102080284	32926232	129	11471											
YAP1	10413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102098224	102098224	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctatcactctcgagatgaGagtacagacagtggactaag	14	8	10	9	1	2	3	1	1	1	3	3	6	2	4	1	1	1	1	1	1	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:102098224G>C	ENST00000282441.5	+	8	1576	c.1188G>C	c.(1186-1188)gaG>gaC	p.E396D	YAP1_ENST00000345877.2_Missense_Mutation_p.E346D|YAP1_ENST00000526343.1_Missense_Mutation_p.E342D|YAP1_ENST00000528834.1_3'UTR|YAP1_ENST00000531439.1_Missense_Mutation_p.E380D|YAP1_ENST00000537274.1_Missense_Mutation_p.E384D|RP11-864G5.3_ENST00000526310.1_RNA|YAP1_ENST00000524575.1_Missense_Mutation_p.E218D	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	396	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		CTCGAGATGAGAGTACAGACA	0.408																																					p.E396D	Colon(50;247 1103 7861 28956)	.											.	YAP1-659	0			c.G1188C						.						155	119	131					11																	102098224		2203	4299	6502	SO:0001583	missense	10413	exon8			AGATGAGAGTACA		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"Yes-associated protein 1, 65kDa"			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1188G>C	11.37:g.102098224G>C	ENSP00000282441:p.Glu396Asp	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	50	12	NM_001130145	0	0	46	62	16	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Missense_Mutation	SNP	ENST00000282441.5	37	CCDS44716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.43|19.43	3.825846|3.825846	0.71143|0.71143	.|.	.|.	ENSG00000137693|ENSG00000137693	ENST00000526343;ENST00000282441;ENST00000537274;ENST00000345877;ENST00000445250;ENST00000531439;ENST00000524575|ENST00000529029	T;T;T|.	0.56103|.	0.48;0.5;0.6|.	5.28|5.28	1.34|1.34	0.21922|0.21922	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61527|0.61527	0.2354|0.2354	M|M	0.65975|0.65975	2.015|2.015	0.48632|0.48632	D|D	0.999686|0.999686	P;D;D;D;D;D|.	0.71674|.	0.956;0.998;0.991;0.97;0.991;0.998|.	D;D;P;P;P;P|.	0.68353|.	0.931;0.957;0.82;0.774;0.82;0.875|.	T|T	0.55354|0.55354	-0.8154|-0.8154	10|5	0.32370|.	T|.	0.25|.	.|.	9.06|9.06	0.36429|0.36429	0.4715:0.0:0.5285:0.0|0.4715:0.0:0.5285:0.0	.|.	218;313;342;380;396;346|.	B4DTY1;F5GWC5;E9PRV2;P46937-2;P46937;P46937-3|.	.;.;.;.;YAP1_HUMAN;.|.	D|T	342;396;384;346;313;380;218|150	ENSP00000434134:E342D;ENSP00000331023:E346D;ENSP00000435602:E218D|.	ENSP00000282441:E396D|.	E|R	+|+	3|2	2|0	YAP1|YAP1	101603434|101603434	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.980000|0.980000	0.70556|0.70556	2.046000|2.046000	0.41260|0.41260	-0.001000|-0.001000	0.14495|0.14495	0.650000|0.650000	0.86243|0.86243	GAG|AGA	.		0.408	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		C	102098224	G	C	102098224	3	2	130	1	0	0	0	0	1	0	0	0	17499	933	33	4	1230	4	YAP1	11	102098224	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	17940	102098224	32908292	130	11472											
HTR3A	3359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113856896	113856896	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatgcagaaatgaagttctAtgtgagtgggagtgaatgtg	12	12	14	3	0	1	4	0	3	1	1	1	5	1	5	0	1	1	2	0	1	5	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:113856896A>G	ENST00000504030.2	+	6	1149	c.704A>G	c.(703-705)tAt>tGt	p.Y235C	HTR3A_ENST00000355556.2_Splice_Site_p.Y241C|HTR3A_ENST00000535865.1_Intron|HTR3A_ENST00000506841.2_Splice_Site_p.Y235C|HTR3A_ENST00000375498.2_Splice_Site_p.Y241C|HTR3A_ENST00000299961.5_Splice_Site_p.Y220C			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	235					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	ATGAAGTTCTATGTGAGTGGG	0.463																																					p.Y241C		.											.	HTR3A-90	0			c.A722G						.						127	129	128					11																	113856896		2201	4296	6497	SO:0001630	splice_region_variant	3359	exon6			AGTTCTATGTGAG	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.705+1A>G	11.37:g.113856896A>G		Somatic	217	1		WXS	Illumina HiSeq	Phase_I	132	82	NM_000869	0	0	0	0	0	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	A	14.92	2.678107	0.47886	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33	5.19	5.19	0.71726	.	0.238980	0.43579	D	0.000549	D	0.87390	0.6165	M	0.73598	2.24	0.80722	D	1	D;D;D	0.71674	0.996;0.998;0.998	P;P;D	0.66351	0.905;0.887;0.943	D	0.87931	0.2710	10	0.54805	T	0.06	-11.3278	11.1542	0.48478	0.8621:0.0:0.0:0.1379	.	220;241;241	B4DSY6;G5E986;Q7KZM7	.;.;.	C	235;241;241;235;220	ENSP00000424189:Y235C;ENSP00000347754:Y241C;ENSP00000364648:Y241C;ENSP00000424776:Y235C;ENSP00000299961:Y220C	ENSP00000299961:Y220C	Y	+	2	0	HTR3A	113362106	1.000000	0.71417	0.987000	0.45799	0.454000	0.32378	4.949000	0.63596	2.079000	0.62486	0.533000	0.62120	TAT	.		0.463	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	Missense_Mutation	G	113856896	A	G	113856896	5	3	130	1	0	0	0	0	0	0	1	0	7465	463	16	3	770	3	HTR3A	11	113856896	Splice_Site	SNP	A	TCGA-HE-7130-01A-11D-1961-08	11758672	113856896	21149620	131	11473											
PCSK7	9159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117097976	117097976	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggtggttgccattctcCacatccgggtggggcatggg	5	10	15	11	1	1	0	0	0	1	0	3	0	2	0	4	6	1	2	4	6	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:117097976C>A	ENST00000320934.3	-	5	1296	c.666G>T	c.(664-666)gtG>gtT	p.V222V		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	222	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		TGCCATTCTCCACATCCGGGT	0.582			T	IGH@	MLCLS																																p.V222V		.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7-658	0			c.G666T						.						117	108	111					11																	117097976		2201	4296	6497	SO:0001819	synonymous_variant	9159	exon5			ATTCTCCACATCC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.666G>T	11.37:g.117097976C>A		Somatic	231	2		WXS	Illumina HiSeq	Phase_I	138	41	NM_004716	0	0	11	16	5	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			.		0.582	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		A	117097976	C	A	117097976	2	1	130	1	0	0	0	0	0	0	0	1	11631	581	21	4		4	PCSK7	11	117097976	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3241080	117097976	17908540	132	11474											
HSPA8	3312	bcgsc.ca	37	chr11	122929378	122929379	+	In_Frame_Ins	INS	-	-	TACTCT																															aatcttgttctcttttcccgINStactcttgtccacagcagag																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:122929378_122929379insTACTCT	ENST00000532636.1	-	7	1602_1603	c.1483_1484insAGAGTA	c.(1483-1485)acg>aAGAGTAcg	p.494_495insKS	HSPA8_ENST00000526110.1_In_Frame_Ins_p.475_476insKS|HSPA8_ENST00000534319.1_In_Frame_Ins_p.258_259insKS|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_In_Frame_Ins_p.494_495insKS|HSPA8_ENST00000533540.1_In_Frame_Ins_p.348_349insKS|HSPA8_ENST00000534624.1_In_Frame_Ins_p.494_495insKS|SNORD14C_ENST00000365382.1_RNA|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000453788.2_Intron			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	494					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CTCTTTTCCCGTACTCTTGTCC	0.446																																					p.T495delinsKST	Colon(21;486 594 5900 6733 14272)												.	HSPA8-654	0			c.1484_1485insAGAGTA						.																																			SO:0001652	inframe_insertion	3312	exon7			TTTCCCGTACTCT	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"Heat shock proteins / HSP70"	5241	protein-coding gene	gene with protein product		600816	"heat shock 70kD protein 8"	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1478_1483dupAGAGTA	11.37:g.122929379_122929384dupTACTCT	ENSP00000437125:p.Lys493_Ser494dup	Somatic	121	0		WXS	Illumina HiSeq	Phase_1	88	6	NM_006597	0	0	0	0	0	Q9H3R6	In_Frame_Ins	INS	ENST00000532636.1	37	CCDS8440.1																																																																																			.		0.446	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			TACTCT	122929379	-	TACTCT	122929378	7	5	130	1	0	1	1	0	0	0	0	0	7437	1145	40	0	468	0	HSPA8	11	122929378	In_Frame_Ins	INS	-	TCGA-HE-7130-01A-11D-1961-08	5831402	122929378	12077138	133	11475											
VWF	7450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6167128	6167128	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccggggctccgccagcccaGagggggtaaggaagtcgtcg	7	4	17	13	4	0	1	0	0	0	1	3	2	1	2	4	5	1	2	4	5	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:6167128G>C	ENST00000261405.5	-	14	1870	c.1616C>G	c.(1615-1617)tCt>tGt	p.S539C		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	539	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CGCCAGCCCAGAGGGGGTAAG	0.662																																					p.S539C		.											.	VWF-163	0			c.C1616G						.						56	59	58					12																	6167128		2203	4299	6502	SO:0001583	missense	7450	exon14			AGCCCAGAGGGGG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1616C>G	12.37:g.6167128G>C	ENSP00000261405:p.Ser539Cys	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	105	31	NM_000552	0	0	42	44	2	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.911404	0.33721	.	.	ENSG00000110799	ENST00000261405	T	0.62498	0.02	4.94	4.03	0.46877	von Willebrand factor, type D domain (3);	0.650601	0.12694	N	0.446915	T	0.80889	0.4710	M	0.87617	2.895	0.47214	D	0.999357	D;P	0.64830	0.994;0.794	D;P	0.64687	0.928;0.694	T	0.82458	-0.0447	10	0.87932	D	0	.	14.3887	0.66963	0.0:0.1485:0.8515:0.0	.	539;539	B4DNX0;P04275	.;VWF_HUMAN	C	539	ENSP00000261405:S539C	ENSP00000261405:S539C	S	-	2	0	VWF	6037389	0.891000	0.30450	0.007000	0.13788	0.010000	0.07245	4.866000	0.63005	1.267000	0.44247	0.491000	0.48974	TCT	.		0.662	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		C	6167128	G	C	6167128	3	2	130	1	0	0	0	0	1	0	0	0	17279	942	33	4	6981	4	VWF	12	6167128	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		6167128	127684767	134	11476											
CAPRIN2	65981	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	30906661	30906661	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cttttccacagaagtgagctCgaaacccaatgatgcttgag	12	10	9	10	1	0	4	0	3	0	1	2	5	1	4	2	0	3	2	2	0	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:30906661C>G	ENST00000395805.2	-	1	584	c.37G>C	c.(37-39)Gag>Cag	p.E13Q	CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.E13Q|RP11-77I22.2_ENST00000500076.2_lincRNA|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.E13Q|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.E13Q	NM_001206856.1	NP_001193785.1			caprin family member 2									p.E13K(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GAAGTGAGCTCGAAACCCAAT	0.408											OREG0021723	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E13Q		.											.	CAPRIN2-92	2	Substitution - Missense(2)	large_intestine(2)	c.G37C						.						103	104	104					12																	30906661		2202	4299	6501	SO:0001583	missense	65981	exon1			TGAGCTCGAAACC	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"C1q domain containing 1"	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.37G>C	12.37:g.30906661C>G	ENSP00000379150:p.Glu13Gln	Somatic	179	0	820	WXS	Illumina HiSeq	Phase_I	169	15	NM_023925	0	0	1	1	0		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165966	0.57476	.	.	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045	T;T;T;T	0.73363	-0.74;2.74;-0.69;2.74	3.72	2.83	0.33086	.	.	.	.	.	T	0.48978	0.1530	N	0.08118	0	0.19575	N	0.999963	B;P;B;B	0.35226	0.358;0.491;0.218;0.325	B;B;B;B	0.32805	0.073;0.153;0.03;0.067	T	0.31833	-0.9929	8	.	.	.	0.5218	5.7801	0.18301	0.0:0.7584:0.0:0.2416	.	13;13;13;13	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2	.;.;CAPR2_HUMAN;.	Q	13	ENSP00000298892:E13Q;ENSP00000379150:E13Q;ENSP00000251071:E13Q;ENSP00000391479:E13Q	.	E	-	1	0	CAPRIN2	30797928	0.001000	0.12720	0.056000	0.19401	0.500000	0.33767	0.235000	0.17948	0.783000	0.33636	0.563000	0.77884	GAG	.		0.408	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		G	30906661	C	G	30906661	3	3	130	1	0	0	0	0	1	0	0	0	2642	893	31	4	3418	4	CAPRIN2	12	30906661	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	24739533	30906661	102945234	135	11477											
SLC2A13	114134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	40422219	40422219	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tacgggccttctgagtctgtCctttctgaataagccatcga	8	13	9	11	2	3	2	0	2	3	0	5	3	4	2	3	1	2	0	3	1	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:40422219C>T	ENST00000280871.4	-	3	859	c.809G>A	c.(808-810)gGa>gAa	p.G270E	SLC2A13_ENST00000380858.1_Missense_Mutation_p.G270E	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	270					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CTGAGTCTGTCCTTTCTGAAT	0.438										HNSCC(50;0.14)																											p.G270E		.											.	SLC2A13-515	0			c.G809A						.						101	106	104					12																	40422219		2203	4300	6503	SO:0001583	missense	114134	exon3			GTCTGTCCTTTCT	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.809G>A	12.37:g.40422219C>T	ENSP00000280871:p.Gly270Glu	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	184	39	NM_052885	0	0	2	2	0	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	37	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781378	0.90282	.	.	ENSG00000151229	ENST00000280871;ENST00000380858	T;T	0.76839	-1.05;-1.05	5.54	5.54	0.83059	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099482	0.64402	D	0.000001	D	0.88403	0.6427	M	0.82323	2.585	0.80722	D	1	P;D	0.60575	0.933;0.988	P;P	0.61722	0.838;0.893	D	0.88848	0.3317	10	0.59425	D	0.04	-17.57	19.8499	0.96734	0.0:1.0:0.0:0.0	.	270;270	Q96QE2;E9PE47	MYCT_HUMAN;.	E	270	ENSP00000280871:G270E;ENSP00000370239:G270E	ENSP00000280871:G270E	G	-	2	0	SLC2A13	38708486	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.290000	0.78711	2.779000	0.95612	0.591000	0.81541	GGA	.		0.438	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			T	40422219	C	T	40422219	3	4	130	1	0	0	0	0	1	0	0	0	14574	855	30	2	1169	2	SLC2A13	12	40422219	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	9515558	40422219	93429676	136	11478											
DDX23	9416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49231830	49231830	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgccgtcgctttagagcttCagcctctcgttctgctttag	4	15	9	13	3	3	1	1	0	2	1	5	1	3	1	2	0	4	4	2	0	2	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:49231830C>T	ENST00000308025.3	-	6	593	c.514G>A	c.(514-516)Gaa>Aaa	p.E172K	DDX23_ENST00000553182.1_5'UTR	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	172	Glu-rich.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|kidney(4)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(3)	36						TTTAGAGCTTCAGCCTCTCGT	0.498																																					p.E172K		.											.	DDX23-539	0			c.G514A						.						149	140	143					12																	49231830		2203	4300	6503	SO:0001583	missense	9416	exon6			GAGCTTCAGCCTC	AF026402	CCDS8770.1	12q13.11	2013-07-16				ENSG00000174243		"DEAD-boxes"	17347	protein-coding gene	gene with protein product		612172	"PRP28 homolog, yeast"			9409622, 9539711	Standard	NM_004818		Approved	prp28, U5-100K, PRPF28, SNRNP100	uc001rsm.3	Q9BUQ8		ENST00000308025.3:c.514G>A	12.37:g.49231830C>T	ENSP00000310723:p.Glu172Lys	Somatic	241	0		WXS	Illumina HiSeq	Phase_I	232	92	NM_004818	0	0	42	86	44	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450245	0.84101	.	.	ENSG00000174243	ENST00000550834;ENST00000308025;ENST00000552512	T	0.22945	1.93	5.15	5.15	0.70609	.	0.055638	0.64402	D	0.000001	T	0.20333	0.0489	L	0.36672	1.1	0.58432	D	0.999999	P	0.39480	0.675	B	0.34093	0.175	T	0.03231	-1.1058	10	0.21014	T	0.42	-10.372	17.5534	0.87884	0.0:1.0:0.0:0.0	.	172	Q9BUQ8	DDX23_HUMAN	K	16;172;172	ENSP00000310723:E172K	ENSP00000310723:E172K	E	-	1	0	DDX23	47518097	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	7.411000	0.80078	2.676000	0.91093	0.563000	0.77884	GAA	.		0.498	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		T	49231830	C	T	49231830	3	4	130	1	0	0	0	0	1	0	0	0	4356	835	29	2	1996	2	DDX23	12	49231830	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	8809611	49231830	84620065	137	11479											
SPATS2	65244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49916614	49916614	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gatgtagagaccctaaagaaGagcattgattcatttggaca	15	10	10	6	0	1	4	1	1	0	3	1	7	1	5	1	1	1	2	1	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:49916614G>C	ENST00000553127.1	+	13	1602	c.1089G>C	c.(1087-1089)aaG>aaC	p.K363N	SPATS2_ENST00000552918.1_Missense_Mutation_p.K363N|SPATS2_ENST00000321898.6_Missense_Mutation_p.K363N			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	363						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						CCCTAAAGAAGAGCATTGATT	0.448																																					p.K363N		.											.	SPATS2-135	0			c.G1089C						.						145	125	132					12																	49916614		2203	4300	6503	SO:0001583	missense	65244	exon12			AAAGAAGAGCATT	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.1089G>C	12.37:g.49916614G>C	ENSP00000448228:p.Lys363Asn	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	80	37	NM_023071	0	0	10	18	8	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	37	CCDS31794.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725778	0.69074	.	.	ENSG00000123352	ENST00000553127;ENST00000321898;ENST00000552918;ENST00000395063	.	.	.	5.84	5.84	0.93424	.	0.215681	0.51477	D	0.000085	T	0.62097	0.2400	L	0.56769	1.78	0.80722	D	1	P	0.42161	0.772	P	0.49528	0.614	T	0.59139	-0.7510	9	0.38643	T	0.18	-13.4976	11.3109	0.49364	0.0822:0.0:0.9178:0.0	.	363	Q86XZ4	SPAS2_HUMAN	N	363	.	ENSP00000326841:K363N	K	+	3	2	SPATS2	48202881	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.162000	0.42367	2.937000	0.99478	0.650000	0.86243	AAG	.		0.448	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071		C	49916614	G	C	49916614	3	2	130	1	0	0	0	0	1	0	0	0	15051	933	33	4	1127	4	SPATS2	12	49916614	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	684784	49916614	83935281	138	11480											
RARG	5916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53607847	53607847	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagggcctaacttaccaggAtatctaggcaggcagctttg	11	9	11	10	0	1	0	0	0	1	0	1	1	1	1	2	4	3	3	2	4	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:53607847A>G	ENST00000425354.2	-	7	1296	c.809T>C	c.(808-810)aTc>aCc	p.I270T	RARG_ENST00000338561.5_Missense_Mutation_p.I259T|RARG_ENST00000327550.3_Missense_Mutation_p.I198T|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000394426.1_Missense_Mutation_p.I270T|RARG_ENST00000543726.1_Missense_Mutation_p.I248T	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	270	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	ACTTACCAGGATATCTAGGCA	0.532											OREG0021862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I270T		.											.	RARG-722	0			c.T809C						.						185	185	185					12																	53607847		2203	4300	6503	SO:0001583	missense	5916	exon7			ACCAGGATATCTA	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"Nuclear hormone receptors"	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.809T>C	12.37:g.53607847A>G	ENSP00000388510:p.Ile270Thr	Somatic	412	0	993	WXS	Illumina HiSeq	Phase_I	365	139	NM_000966	0	0	2	2	0	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	37	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.906612	0.72868	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000538479;ENST00000327550;ENST00000338561;ENST00000543726;ENST00000550265	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.37	5.37	0.77165	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	T	0.65657	0.2712	M	0.79258	2.445	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;1.0;1.0	D;D;D;D	0.97110	1.0;0.993;1.0;0.999	T	0.70447	-0.4869	10	0.87932	D	0	.	14.6593	0.68858	1.0:0.0:0.0:0.0	.	307;248;270;259	F8VR45;B7Z4F1;P13631;F1D8P1	.;.;RARG_HUMAN;.	T	270;270;32;198;259;248;307	ENSP00000388510:I270T;ENSP00000377947:I270T;ENSP00000332695:I198T;ENSP00000343698:I259T;ENSP00000444335:I248T	ENSP00000332695:I198T	I	-	2	0	RARG	51894114	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	9.034000	0.93747	2.171000	0.68590	0.460000	0.39030	ATC	.		0.532	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		G	53607847	A	G	53607847	3	3	130	1	0	0	0	0	1	0	0	0	13086	333	12	3	571	3	RARG	12	53607847	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	3691233	53607847	80244048	139	11481											
DPY19L2	283417	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	64061939	64061939	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacgaactggaaggggccgaGaagaaaggtcttggccacca	13	4	15	9	2	1	2	0	0	1	2	1	6	1	3	3	5	1	0	3	5	4	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:64061939G>A	ENST00000324472.4	-	1	418	c.235C>T	c.(235-237)Ctc>Ttc	p.L79F	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	79					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AAGGGGCCGAGAAGAAAGGTC	0.602																																					p.L79F		.											.	DPY19L2-515	0			c.C235T						.						74	80	78					12																	64061939		2203	4300	6503	SO:0001583	missense	283417	exon1			GGCCGAGAAGAAA		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"spermatogenesis associated 34"	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.235C>T	12.37:g.64061939G>A	ENSP00000315988:p.Leu79Phe	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	133	22	NM_173812	0	0	0	0	0	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	G	3.843	-0.033397	0.07543	.	.	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.45668	0.95;0.89	1.61	0.631	0.17699	.	.	.	.	.	T	0.26231	0.0640	L	0.32530	0.975	0.09310	N	0.999999	B	0.32653	0.379	B	0.30029	0.11	T	0.14643	-1.0465	8	.	.	.	.	5.6322	0.17516	0.0:0.3487:0.6513:0.0	.	79	Q6NUT2	D19L2_HUMAN	F	79	ENSP00000315988:L79F;ENSP00000444932:L79F	.	L	-	1	0	DPY19L2	62348206	0.000000	0.05858	0.010000	0.14722	0.121000	0.20230	0.247000	0.18179	0.202000	0.20498	0.195000	0.17529	CTC	.		0.602	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		A	64061939	G	A	64061939	3	1	130	1	0	0	0	0	1	0	0	0	4752	942	33	2	2129	2	DPY19L2	12	64061939	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10454092	64061939	69789956	140	11482											
LLPH	84298	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	66522754	66522754	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caccacagttgctatctcttGaacatctttcattaaaacat	13	14	3	11	0	3	1	1	1	2	0	4	1	3	1	1	0	3	2	1	0	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:66522754G>A	ENST00000266604.2	-	2	203	c.133C>T	c.(133-135)Caa>Taa	p.Q45*	TMBIM4_ENST00000556010.1_3'UTR|TMBIM4_ENST00000539652.1_3'UTR|LLPH_ENST00000446587.2_Nonsense_Mutation_p.Q45*|RP11-745O10.2_ENST00000510317.2_RNA	NM_032338.3	NP_115714.1	Q9BRT6	LLPH_HUMAN	LLP homolog, long-term synaptic facilitation (Aplysia)	45	Lys-rich.						poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|skin(1)	5						GCTATCTCTTGAACATCTTTC	0.403																																					p.Q45X		.											.	LLPH-514	0			c.C133T						.						122	112	115					12																	66522754		2203	4297	6500	SO:0001587	stop_gained	84298	exon2			TCTCTTGAACATC	AK057947	CCDS8974.1	12q14.3	2014-05-09	2008-10-02	2008-10-02	ENSG00000139233	ENSG00000139233			28229	protein-coding gene	gene with protein product	"human LAPS18-like protein"		"chromosome 12 open reading frame 31"	C12orf31		12477932	Standard	NM_032338		Approved	MGC14817, hLLP	uc010ssw.2	Q9BRT6	OTTHUMG00000168959	ENST00000266604.2:c.133C>T	12.37:g.66522754G>A	ENSP00000266604:p.Gln45*	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	228	34	NM_032338	0	0	47	51	4	Q3B766	Nonsense_Mutation	SNP	ENST00000266604.2	37	CCDS8974.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127434	0.94473	.	.	ENSG00000139233	ENST00000266604;ENST00000446587	.	.	.	4.13	-0.482	0.12078	.	0.626869	0.17801	N	0.161575	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.9384	6.7866	0.23677	0.0:0.1983:0.3284:0.4734	.	.	.	.	X	45	.	.	Q	-	1	0	LLPH	64809021	0.974000	0.33945	0.987000	0.45799	0.865000	0.49528	0.701000	0.25616	0.090000	0.17273	0.467000	0.42956	CAA	.		0.403	LLPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401752.1	NM_032338		A	66522754	G	A	66522754	4	1	130	1	0	0	0	0	0	1	0	0	8858	1299	45	2	264	2	LLPH	12	66522754	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2460815	66522754	67329141	141	11483											
AMDHD1	144193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	96354342	96354342	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggattcttcaacgtggaaaaGatatagggttacagattaac	15	11	10	5	1	2	2	1	0	1	2	2	4	2	4	0	3	3	1	0	3	7	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:96354342G>C	ENST00000266736.2	+	5	860	c.754G>C	c.(754-756)Gat>Cat	p.D252H		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	252					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						ACGTGGAAAAGATATAGGGTT	0.428																																					p.D252H		.											.	AMDHD1-90	0			c.G754C						.						122	117	118					12																	96354342		2203	4300	6503	SO:0001583	missense	144193	exon5			GGAAAAGATATAG	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.754G>C	12.37:g.96354342G>C	ENSP00000266736:p.Asp252His	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	178	65	NM_152435	0	0	0	0	0	A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	37	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.540809	0.45280	.	.	ENSG00000139344	ENST00000266736	T	0.46063	0.88	5.55	4.65	0.58169	Metal-dependent hydrolase, composite domain (1);	0.384940	0.33235	N	0.005136	T	0.49660	0.1570	L	0.60957	1.885	0.34446	D	0.700188	P	0.40107	0.703	P	0.47528	0.549	T	0.65340	-0.6192	10	0.54805	T	0.06	-0.0155	13.7543	0.62926	0.0749:0.0:0.9251:0.0	.	252	Q96NU7	HUTI_HUMAN	H	252	ENSP00000266736:D252H	ENSP00000266736:D252H	D	+	1	0	AMDHD1	94878473	1.000000	0.71417	0.605000	0.28930	0.004000	0.04260	4.953000	0.63624	1.447000	0.47661	0.655000	0.94253	GAT	.		0.428	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435		C	96354342	G	C	96354342	3	2	130	1	0	0	0	0	1	0	0	0	567	942	33	4	772	4	AMDHD1	12	96354342	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	29831588	96354342	37497553	142	11484											
C12orf42	374470	broad.mit.edu	37	chr12	103699754	103699754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccacaacatgatacttaccaGaatttttcttgggactgctc	11	13	6	11	0	1	2	0	1	1	1	2	3	1	3	2	1	4	1	2	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:103699754G>A	ENST00000378113.2	-	5	854	c.629C>T	c.(628-630)tCt>tTt	p.S210F	C12orf42_ENST00000315192.8_Intron|C12orf42_ENST00000548048.1_Missense_Mutation_p.S143F|C12orf42_ENST00000548883.1_Missense_Mutation_p.S210F|C12orf42_ENST00000548789.1_5'UTR	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	210										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						ATACTTACCAGAATTTTTCTT	0.418																																					p.S210F													.	C12orf42-91	0			c.C629T						.						166	160	162					12																	103699754		1885	4107	5992	SO:0001583	missense	374470	exon5			TTACCAGAATTTT	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.629C>T	12.37:g.103699754G>A	ENSP00000367353:p.Ser210Phe	Somatic	286	0		WXS	Illumina HiSeq	Phase_I	358	7	NM_001099336	0	0	0	0	0	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	37	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441683	0.43326	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113	T;T;T	0.59083	0.29;0.29;0.29	4.02	2.18	0.27775	.	0.916854	0.08987	N	0.864952	T	0.43144	0.1234	L	0.32530	0.975	0.09310	N	1	B	0.32031	0.352	B	0.29176	0.099	T	0.40117	-0.9580	10	0.87932	D	0	-2.6865	5.0246	0.14378	0.1071:0.0:0.6868:0.2061	.	210	Q96LP6	CL042_HUMAN	F	210;143;210	ENSP00000447908:S210F;ENSP00000449362:S143F;ENSP00000367353:S210F	ENSP00000367353:S210F	S	-	2	0	C12orf42	102223884	0.055000	0.20627	0.009000	0.14445	0.065000	0.16274	0.795000	0.26972	0.653000	0.30826	0.555000	0.69702	TCT	.		0.418	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521		A	103699754	G	A	103699754	3	1	130	1	0	0	0	0	1	0	0	0	1692	942	33	2	461	2	C12orf42	12	103699754	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	7345412	103699754	30152141	143	11485											
KSR2	283455	broad.mit.edu	37	chr12	118293234	118293234	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccccggggcctgctcaccTgacatgtggacattcctgag	7	8	12	14	1	1	2	1	2	0	0	2	4	2	3	5	3	1	1	5	3	0	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:118293234T>C	ENST00000339824.5	-	3	1198	c.471A>G	c.(469-471)tcA>tcG	p.S157S	KSR2_ENST00000425217.1_Splice_Site_p.S128S			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	157					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCTGCTCACCTGACATGTGGA	0.652																																					p.S128S													.	KSR2-1449	0			c.A384G						.						66	75	72					12																	118293234		2058	4195	6253	SO:0001630	splice_region_variant	283455	exon3			CTCACCTGACATG	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.472+1A>G	12.37:g.118293234T>C		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	100	3	NM_173598	0	0	1	1	0	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																				.		0.652	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	Silent	C	118293234	T	C	118293234	5	2	130	1	0	0	0	0	0	0	1	0	8603	1594	55	3	2453	3	KSR2	12	118293234	Splice_Site	SNP	T	TCGA-HE-7130-01A-11D-1961-08	14593480	118293234	15558661	144	11486											
P2RX4	5025	broad.mit.edu;bcgsc.ca	37	chr12	121648006	121648006	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgctggcggccttcctgttCgagtacgacacgccgcgcat	5	8	13	15	7	0	0	0	0	0	0	2	2	1	0	3	2	1	4	3	2	1	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:121648006C>T	ENST00000337233.4	+	1	347	c.39C>T	c.(37-39)ttC>ttT	p.F13F	P2RX4_ENST00000540930.1_3'UTR|P2RX4_ENST00000543171.1_5'UTR|P2RX4_ENST00000541532.1_Silent_p.F13F|P2RX4_ENST00000359949.7_Silent_p.F13F	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	13					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTTCCTGTTCGAGTACGACA	0.706																																					p.F13F													.	P2RX4-68	0			c.C39T						.						16	16	16					12																	121648006		2195	4290	6485	SO:0001819	synonymous_variant	5025	exon1			CCTGTTCGAGTAC	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.39C>T	12.37:g.121648006C>T		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	23	9	NM_001261398	0	0	4	4	0	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Silent	SNP	ENST00000337233.4	37	CCDS9214.1																																																																																			.		0.706	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567		T	121648006	C	T	121648006	2	4	130	1	0	0	0	0	0	0	0	1	11368	883	31	1		1	P2RX4	12	121648006	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3354772	121648006	12203889	145	11487											
UTP14C	9724	hgsc.bcm.edu;broad.mit.edu	37	chr13	52603705	52603705	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaaaagtatcacaaagtcgtGaagaaaggaaaggccaagaa	22	4	10	5	1	1	3	1	1	0	2	2	4	1	4	1	2	0	1	1	2	9	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:52603705G>C	ENST00000521776.2	+	2	1498	c.765G>C	c.(763-765)gtG>gtC	p.V255V	ALG11_ENST00000523764.1_3'UTR|ALG11_ENST00000521508.1_3'UTR	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	255					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		ACAAAGTCGTGAAGAAAGGAA	0.433																																					p.V255V		.											.	UTP14C-138	0			c.G765C						.						89	88	88					13																	52603705		2203	4300	6503	SO:0001819	synonymous_variant	9724	exon2			AGTCGTGAAGAAA	D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.765G>C	13.37:g.52603705G>C		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	83	5	NM_021645	0	0	25	25	0	Q5FWG3|Q92555	Silent	SNP	ENST00000521776.2	37	CCDS31978.1																																																																																			.		0.433	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		C	52603705	G	C	52603705	2	2	130	1	0	0	0	0	0	0	0	1	17129	1277	45	4		4	UTP14C	13	52603705	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		52603705	62566173	146	11488											
OLFM4	10562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	53624805	53624805	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcataagatgcaggaaaaaGtgcagagcattaactataac	18	8	9	6	0	0	2	0	0	0	2	0	3	0	3	0	1	6	4	0	1	6	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:53624805G>C	ENST00000219022.2	+	5	1510	c.1432G>C	c.(1432-1434)Gtg>Ctg	p.V478L		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	478	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		GCAGGAAAAAGTGCAGAGCAT	0.368																																					p.V478L		.											.	OLFM4-69	0			c.G1432C						.						108	108	108					13																	53624805		2203	4300	6503	SO:0001583	missense	10562	exon5			GAAAAAGTGCAGA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.1432G>C	13.37:g.53624805G>C	ENSP00000219022:p.Val478Leu	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	129	18	NM_006418	0	0	0	0	0	O95362|Q5VWG0|Q86T22	Missense_Mutation	SNP	ENST00000219022.2	37	CCDS9440.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.362917	0.24684	.	.	ENSG00000102837	ENST00000219022	T	0.14022	2.54	5.64	-2.23	0.06930	Olfactomedin-like (3);	0.818724	0.11361	N	0.571904	T	0.03959	0.0111	N	0.03268	-0.37	0.18873	N	0.999988	B	0.06786	0.001	B	0.15484	0.013	T	0.43426	-0.9392	10	0.15499	T	0.54	.	2.2285	0.03991	0.2383:0.3579:0.2837:0.1201	.	478	Q6UX06	OLFM4_HUMAN	L	478	ENSP00000219022:V478L	ENSP00000219022:V478L	V	+	1	0	OLFM4	52522806	0.000000	0.05858	0.030000	0.17652	0.978000	0.69477	-0.374000	0.07484	-0.094000	0.12374	0.585000	0.79938	GTG	.		0.368	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		C	53624805	G	C	53624805	3	2	130	1	0	0	0	0	1	0	0	0	10881	1029	36	4	1450	4	OLFM4	13	53624805	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1021100	53624805	61545073	147	11489											
PCDH20	64881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	61986466	61986467	+	Missense_Mutation	DNP	CC	CC	TT																															gagtagaaactgtcagaattCctgtgacactgtctaaggaa																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:61986466_61986467CC>TT	ENST00000409186.1	-	5	3870_3871	c.1765_1766GG>AA	c.(1765-1767)GGa>AAa	p.G589K	PCDH20_ENST00000409204.4_Missense_Mutation_p.G589K			Q8N6Y1	PCD20_HUMAN	protocadherin 20	589	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TGTCAGAATTCCTGTGACACTG	0.455																																					p.G589K		.											.	PCDH20	0			c.G1765A						.																																			SO:0001583	missense	64881	exon2			GAATTCCTGTGAC	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1765_1766delinsTT	13.37:g.61986466_61986467delinsTT	ENSP00000386653:p.Gly589Lys	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	121	25		0	0	0	0	0	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	DNP	ENST00000409186.1	37	CCDS9442.2																																																																																			.		0.455	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		TT	61986467	CC	TT	61986466	3	4	130	1	0	0	0	0	1	0	0	0	11541	855	30	2	1093	2	PCDH20	13	61986466	Missense_Mutation	DNP	CC	TCGA-HE-7130-01A-11D-1961-08	8361661	61986466	53183412	148	11490											
RBM26	64062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	79945132	79945132	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgcttctatctctgtccctCtcacgaagcctctctttact	5	16	4	16	1	4	0	1	0	4	0	8	1	5	0	2	0	3	1	2	0	3	4	rs199797508		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:79945132C>T	ENST00000438737.2	-	5	1022	c.582G>A	c.(580-582)gaG>gaA	p.E194E	RBM26_ENST00000267229.7_Silent_p.E194E|RBM26_ENST00000438724.1_Silent_p.E194E			Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	194	Arg-rich.				mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		CTCTGTCCCTCTCACGAAGCC	0.428													C|||	1	0.000199681	0	0	5008	,	,		15718	0.001		0	False		,,,				2504	0				p.E194E		.											.	RBM26-91	0			c.G582A						.						167	171	170					13																	79945132		2203	4300	6503	SO:0001819	synonymous_variant	64062	exon5			GTCCCTCTCACGA	AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	20327	protein-coding gene	gene with protein product	"acidic rich RS domain containing 2", "protein phosphatase 1, regulatory 132"		"chromosome 13 open reading frame 10"	C13orf10		11149944, 15741184	Standard	XM_005266497		Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000438737.2:c.582G>A	13.37:g.79945132C>T		Somatic	266	0		WXS	Illumina HiSeq	Phase_I	352	47	NM_022118	0	0	31	34	3	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	Silent	SNP	ENST00000438737.2	37																																																																																				C|0.999;T|0.000		0.428	RBM26-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045373.4	NM_022118		T	79945132	C	T	79945132	2	4	130	1	0	0	0	0	0	0	0	1	13158	912	32	2		2	RBM26	13	79945132	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	17958666	79945132	35224746	149	11491											
CIDEB	27141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24775203	24775203	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagtcacaactcatagagtaGagcccgtagaatgtggcttt	13	10	10	8	1	2	3	2	0	0	3	2	3	2	3	1	1	2	3	1	1	6	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:24775203G>C	ENST00000336557.5	-	7	1779	c.477C>G	c.(475-477)ctC>ctG	p.L159L	LTB4R2_ENST00000528054.1_5'Flank|NOP9_ENST00000267425.3_3'UTR|CIDEB_ENST00000258807.5_Silent_p.L159L|CIDEB_ENST00000554411.1_Silent_p.L159L			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	159					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TCATAGAGTAGAGCCCGTAGA	0.488																																					p.L159L		.											.	CIDEB-90	0			c.C477G						.						141	134	136					14																	24775203		2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			AGAGTAGAGCCCG	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.477C>G	14.37:g.24775203G>C		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	104	24	NM_014430	0	0	29	33	4	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																			.		0.488	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			C	24775203	G	C	24775203	2	2	130	1	0	0	0	0	0	0	0	1	3432	929	33	4		4	CIDEB	14	24775203	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		24775203	82574337	150	11492											
FANCM	57697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	45642339	45642339	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atcatcctttgcctacacatCaagttgatcactcagatcga	12	12	5	12	1	4	2	4	1	0	1	6	3	5	2	2	0	2	1	2	0	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:45642339C>G	ENST00000267430.5	+	13	2327	c.2242C>G	c.(2242-2244)Caa>Gaa	p.Q748E	FANCM_ENST00000542564.2_Missense_Mutation_p.Q722E	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	748					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GCCTACACATCAAGTTGATCA	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Q748E		.											.	FANCM-569	0			c.C2242G						.						160	144	150					14																	45642339		2203	4300	6503	SO:0001583	missense	57697	exon13	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ACACATCAAGTTG	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2242C>G	14.37:g.45642339C>G	ENSP00000267430:p.Gln748Glu	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	88	55	NM_020937	0	0	1	1	0	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	2.703	-0.270591	0.05716	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18338	2.83;2.83;2.22	5.79	5.79	0.91817	.	1.031910	0.07642	N	0.930388	T	0.18841	0.0452	L	0.60455	1.87	0.09310	N	1	B;B	0.28233	0.204;0.204	B;B	0.21708	0.036;0.033	T	0.21999	-1.0229	10	0.23302	T	0.38	.	9.037	0.36293	0.1484:0.7768:0.0:0.0748	.	722;748	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	E	748;722;264	ENSP00000267430:Q748E;ENSP00000442493:Q722E;ENSP00000452033:Q264E	ENSP00000267430:Q748E	Q	+	1	0	FANCM	44712089	0.001000	0.12720	0.103000	0.21229	0.402000	0.30811	1.154000	0.31688	2.746000	0.94184	0.561000	0.74099	CAA	.		0.398	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45642339	C	G	45642339	3	3	130	1	0	0	0	0	1	0	0	0	5690	827	29	4	2292	4	FANCM	14	45642339	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	20867136	45642339	61707201	151	11493											
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64989477	64989477	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtccagtacaagaggatgctGaaaatgcatcttgtgagctg	12	10	12	7	0	1	3	0	2	1	1	2	4	2	4	1	1	4	4	1	1	4	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:64989477G>C	ENST00000554015.1	+	4	1686	c.1255G>C	c.(1255-1257)Gaa>Caa	p.E419Q	ZBTB1_ENST00000358738.3_Missense_Mutation_p.E419Q|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Missense_Mutation_p.E419Q			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	419					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		AGAGGATGCTGAAAATGCATC	0.423																																					p.E419Q		.											.	ZBTB1-91	0			c.G1255C						.						61	59	60					14																	64989477		2203	4300	6503	SO:0001583	missense	22890	exon2			GATGCTGAAAATG	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1255G>C	14.37:g.64989477G>C	ENSP00000451000:p.Glu419Gln	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	38	3	NM_014950	0	0	39	39	0	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	37	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.714837	0.30413	.	.	ENSG00000126804	ENST00000554015;ENST00000358738;ENST00000394712	T;T;T	0.10960	2.82;3.36;2.82	6.17	6.17	0.99709	.	0.000000	0.43110	D	0.000615	T	0.15003	0.0362	N	0.24115	0.695	0.21822	N	0.999521	D;P	0.52996	0.957;0.818	P;B	0.48454	0.578;0.255	T	0.02758	-1.1114	10	0.87932	D	0	-29.409	20.8794	0.99867	0.0:0.0:1.0:0.0	.	419;419	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	Q	419	ENSP00000451000:E419Q;ENSP00000351587:E419Q;ENSP00000378201:E419Q	ENSP00000351587:E419Q	E	+	1	0	ZBTB1	64059230	1.000000	0.71417	0.278000	0.24718	0.995000	0.86356	5.210000	0.65214	2.941000	0.99782	0.655000	0.94253	GAA	.		0.423	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			C	64989477	G	C	64989477	3	2	130	1	0	0	0	0	1	0	0	0	17554	1291	45	4	1257	4	ZBTB1	14	64989477	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	19347138	64989477	42360063	152	11494											
SLC8A3	6547	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	70633987	70633987	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggctcatcggtgtgcacctCgctcatgctggaggccttct	5	11	12	13	2	3	0	2	0	1	0	5	1	3	1	2	4	2	4	2	4	0	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:70633987C>T	ENST00000381269.2	-	2	1906	c.1153G>A	c.(1153-1155)Gag>Aag	p.E385K	SLC8A3_ENST00000534137.1_Missense_Mutation_p.E385K|SLC8A3_ENST00000528359.1_Missense_Mutation_p.E385K|SLC8A3_ENST00000356921.2_Missense_Mutation_p.E385K|SLC8A3_ENST00000357887.3_Missense_Mutation_p.E385K	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	385					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GTGTGCACCTCGCTCATGCTG	0.512																																					p.E385K		.											.	SLC8A3-225	0			c.G1153A						.						126	116	119					14																	70633987		2203	4300	6503	SO:0001583	missense	6547	exon2			GCACCTCGCTCAT	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"Solute carriers"	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1153G>A	14.37:g.70633987C>T	ENSP00000370669:p.Glu385Lys	Somatic	205	2		WXS	Illumina HiSeq	Phase_I	149	87	NM_183002	0	0	0	1	1	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.764362	0.31228	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.36699	1.33;1.24;1.38;1.33;1.38	5.83	5.83	0.93111	Na-Ca exchanger/integrin-beta4 (1);	0.054654	0.64402	D	0.000001	T	0.55386	0.1917	L	0.55990	1.75	0.80722	D	1	P;P;D;D	0.61080	0.811;0.843;0.989;0.989	B;B;P;P	0.62740	0.146;0.228;0.906;0.874	T	0.44143	-0.9347	10	0.37606	T	0.19	.	20.1242	0.97973	0.0:1.0:0.0:0.0	.	385;385;385;385	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	K	385	ENSP00000349392:E385K;ENSP00000370669:E385K;ENSP00000350560:E385K;ENSP00000436688:E385K;ENSP00000433531:E385K	ENSP00000349392:E385K	E	-	1	0	SLC8A3	69703740	1.000000	0.71417	0.979000	0.43373	0.631000	0.37964	4.942000	0.63547	2.744000	0.94065	0.643000	0.83706	GAG	.		0.512	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70633987	C	T	70633987	3	4	130	1	0	0	0	0	1	0	0	0	14740	893	31	1	1769	1	SLC8A3	14	70633987	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5644510	70633987	36715553	153	11495											
PAPLN	89932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	73720491	73720491	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agggccatgggcaccctgctCagcctcctgtggaggaggct	6	7	15	13	0	1	0	1	0	0	0	2	2	2	2	4	5	2	3	4	5	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:73720491C>T	ENST00000554301.1	+	11	1287	c.1124C>T	c.(1123-1125)tCa>tTa	p.S375L	PAPLN_ENST00000381166.3_Missense_Mutation_p.S375L|PAPLN_ENST00000427855.1_Missense_Mutation_p.S375L|PAPLN_ENST00000340738.5_Missense_Mutation_p.S348L|PAPLN_ENST00000555445.1_Missense_Mutation_p.S375L			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	375	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GCACCCTGCTCAGCCTCCTGT	0.672																																					p.S348L		.											.	PAPLN-70	0			c.C1043T						.						44	47	46					14																	73720491		2202	4299	6501	SO:0001583	missense	89932	exon11			CCTGCTCAGCCTC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1124C>T	14.37:g.73720491C>T	ENSP00000451803:p.Ser375Leu	Somatic	157	1		WXS	Illumina HiSeq	Phase_I	135	30	NM_173462	0	0	1	1	0	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		.	.	.	.	.	.	.	.	.	.	C	17.90	3.503048	0.64298	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	4.57	4.57	0.56435	.	.	.	.	.	D	0.89111	0.6622	H	0.98351	4.21	0.53005	D	0.999967	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.994	D	0.93625	0.6951	9	0.87932	D	0	.	17.5437	0.87855	0.0:1.0:0.0:0.0	.	375;375;348	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	L	348;375;375;375;375	ENSP00000345395:S348L;ENSP00000403403:S375L;ENSP00000370558:S375L;ENSP00000451803:S375L;ENSP00000451729:S375L	ENSP00000216658:S375L	S	+	2	0	PAPLN	72790244	1.000000	0.71417	0.939000	0.37840	0.046000	0.14306	7.385000	0.79763	2.385000	0.81259	0.462000	0.41574	TCA	.		0.672	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		T	73720491	C	T	73720491	3	4	130	1	0	0	0	0	1	0	0	0	11454	838	29	2	1081	2	PAPLN	14	73720491	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3086504	73720491	33629049	154	11496											
FLRT2	23768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	86088747	86088747	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgctgactcaaggggtttttGataatctctccaacctgaag	10	13	9	9	0	2	3	1	3	1	0	4	3	3	3	2	2	2	2	2	2	4	3	rs199966508		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:86088747G>C	ENST00000330753.4	+	2	1656	c.889G>C	c.(889-891)Gat>Cat	p.D297H	FLRT2_ENST00000554746.1_Missense_Mutation_p.D297H	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	297					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		AGGGGTTTTTGATAATCTCTC	0.448																																					p.D297H		.											.	FLRT2-94	0			c.G889C						.						169	178	175					14																	86088747		2203	4300	6503	SO:0001583	missense	23768	exon2			GTTTTTGATAATC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"Fibronectin type III domain containing"	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.889G>C	14.37:g.86088747G>C	ENSP00000332879:p.Asp297His	Somatic	367	1		WXS	Illumina HiSeq	Phase_I	405	57	NM_013231	0	0	0	0	0	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355620	0.61293	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.58210	0.35;0.35	5.97	5.97	0.96955	.	0.048069	0.85682	D	0.000000	T	0.64316	0.2587	L	0.32530	0.975	0.80722	D	1	D	0.65815	0.995	D	0.65233	0.933	T	0.63747	-0.6567	10	0.59425	D	0.04	-19.3382	20.4238	0.99064	0.0:0.0:1.0:0.0	.	297	O43155	FLRT2_HUMAN	H	297	ENSP00000332879:D297H;ENSP00000451050:D297H	ENSP00000332879:D297H	D	+	1	0	FLRT2	85158500	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.061000	0.89467	2.828000	0.97474	0.655000	0.94253	GAT	G|0.999;T|0.000		0.448	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			C	86088747	G	C	86088747	3	2	130	1	0	0	0	0	1	0	0	0	5958	1290	45	4	891	4	FLRT2	14	86088747	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	12368256	86088747	21260793	155	11497											
EML5	161436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	89161727	89161727	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctattgaaagtttctctcCtttcttccagtcccagagca	8	15	6	12	0	2	2	0	1	2	1	6	2	5	2	3	0	2	3	3	0	2	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:89161727C>T	ENST00000380664.5	-	16	2415	c.2416G>A	c.(2416-2418)Gga>Aga	p.G806R	EML5_ENST00000352093.5_Missense_Mutation_p.G806R|EML5_ENST00000554922.1_Missense_Mutation_p.G806R			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	806						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AGTTTCTCTCCTTTCTTCCAG	0.338																																					p.G806R		.											.	EML5-93	0			c.G2416A						.						88	79	82					14																	89161727		1843	4083	5926	SO:0001583	missense	161436	exon16			TCTCTCCTTTCTT	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"WD repeat domain containing"	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.2416G>A	14.37:g.89161727C>T	ENSP00000370039:p.Gly806Arg	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	77	17	NM_183387	0	0	1	1	0	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.718501	0.89205	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.65916	-0.18;1.86;-0.18	4.86	4.86	0.63082	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80391	0.4614	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81899	-0.0721	10	0.51188	T	0.08	-15.3073	17.7789	0.88517	0.0:1.0:0.0:0.0	.	806	Q05BV3	EMAL5_HUMAN	R	806	ENSP00000451998:G806R;ENSP00000298315:G806R;ENSP00000370039:G806R	ENSP00000298315:G806R	G	-	1	0	EML5	88231480	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.320000	0.79064	2.526000	0.85167	0.467000	0.42956	GGA	.		0.338	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89161727	C	T	89161727	3	4	130	1	0	0	0	0	1	0	0	0	5113	690	24	2	3629	2	EML5	14	89161727	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3072980	89161727	18187813	156	11498											
MARK3	4140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	103932113	103932113	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagtggctcacttccctttGatgggcaaaacctaaaggta	11	11	9	10	0	2	1	2	1	0	0	3	1	3	1	2	3	1	3	2	3	5	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:103932113G>C	ENST00000429436.2	+	8	1270	c.760G>C	c.(760-762)Gat>Cat	p.D254H	MARK3_ENST00000216288.7_Missense_Mutation_p.D254H|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000440884.3_Intron|MARK3_ENST00000416682.2_Missense_Mutation_p.D277H|MARK3_ENST00000303622.9_Missense_Mutation_p.D254H|MARK3_ENST00000553942.1_Missense_Mutation_p.D254H|MARK3_ENST00000335102.5_Missense_Mutation_p.D277H	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			ACTTCCCTTTGATGGGCAAAA	0.403																																					p.D254H		.											.	MARK3-360	0			c.G760C						.						64	65	65					14																	103932113		1975	4183	6158	SO:0001583	missense	4140	exon8			CCCTTTGATGGGC	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.760G>C	14.37:g.103932113G>C	ENSP00000411397:p.Asp254His	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	56	9	NM_001128919	0	0	23	31	8	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.1|26.1	4.702752|4.702752	0.88924|0.88924	.|.	.|.	ENSG00000075413|ENSG00000075413	ENST00000335102;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942|ENST00000554627	T;T;T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61185|0.61185	0.2327|0.2327	L|L	0.33189|0.33189	0.99|0.99	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	0.997;0.996;0.999;0.998;1.0;0.995|.	T|T	0.53208|0.53208	-0.8471|-0.8471	10|5	0.87932|.	D|.	0|.	.|.	20.1454|20.1454	0.98074|0.98074	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	277;277;254;254;254;254|.	P27448-7;P27448-2;P27448-6;P27448;P27448-4;P27448-3|.	.;.;.;MARK3_HUMAN;.;.|.	H|F	277;277;254;254;254;254|21	ENSP00000335347:D277H;ENSP00000408092:D277H;ENSP00000411397:D254H;ENSP00000303698:D254H;ENSP00000216288:D254H;ENSP00000450772:D254H|.	ENSP00000216288:D254H|.	D|L	+|+	1|3	0|2	MARK3|MARK3	103001866|103001866	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.996000|0.996000	0.88848|0.88848	9.807000|9.807000	0.99171|0.99171	2.748000|2.748000	0.94277|0.94277	0.650000|0.650000	0.86243|0.86243	GAT|TTG	.		0.403	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		C	103932113	G	C	103932113	3	2	130	1	0	0	0	0	1	0	0	0	9339	1290	45	4	790	4	MARK3	14	103932113	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	14770386	103932113	3417427	157	11499											
MARK3	4140	ucsc.edu	37	chr14	103932725	103932725	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgcagggcatgaagaagatGaactcaaaccatttgttgaa	16	9	10	6	0	1	5	1	3	0	2	1	5	1	5	1	1	3	3	1	1	5	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:103932725G>A	ENST00000429436.2	+	10	1453	c.943G>A	c.(943-945)Gaa>Aaa	p.E315K	MARK3_ENST00000216288.7_Missense_Mutation_p.E315K|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000440884.3_Missense_Mutation_p.E236K|MARK3_ENST00000416682.2_Missense_Mutation_p.E338K|MARK3_ENST00000303622.9_Missense_Mutation_p.E315K|MARK3_ENST00000553942.1_Missense_Mutation_p.E315K|MARK3_ENST00000335102.5_Missense_Mutation_p.E338K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	315						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			TGAAGAAGATGAACTCAAACC	0.373																																					p.E315K													.	MARK3-360	0			c.G943A						.						109	97	101					14																	103932725		1910	4129	6039	SO:0001583	missense	4140	exon10			GAAGATGAACTCA	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.943G>A	14.37:g.103932725G>A	ENSP00000411397:p.Glu315Lys	Somatic	46	0		WXS	Illumina HiSeq		19	3	NM_001128919	0	0	38	50	12	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.634428|5.634428	0.96682|0.96682	.|.	.|.	ENSG00000075413|ENSG00000075413	ENST00000335102;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942|ENST00000554627	T;T;T;T;T;T;T|.	0.74002|.	-0.8;3.14;-0.74;-0.76;-0.75;1.85;-0.76|.	5.69|5.69	5.69|5.69	0.88448|0.88448	Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.66567|0.66567	0.2802|0.2802	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	P;D;P;B;D;D;B|.	0.63046|.	0.749;0.981;0.849;0.446;0.986;0.992;0.392|.	P;P;B;B;D;P;B|.	0.64776|.	0.511;0.876;0.375;0.138;0.929;0.868;0.058|.	T|T	0.60777|0.60777	-0.7196|-0.7196	10|5	0.41790|.	T|.	0.15|.	.|.	19.8215|19.8215	0.96599|0.96599	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	338;338;315;315;236;315;315|.	P27448-7;P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3|.	.;.;.;MARK3_HUMAN;.;.;.|.	K|I	338;236;338;315;315;315;315|82	ENSP00000335347:E338K;ENSP00000402104:E236K;ENSP00000408092:E338K;ENSP00000411397:E315K;ENSP00000303698:E315K;ENSP00000216288:E315K;ENSP00000450772:E315K|.	ENSP00000216288:E315K|.	E|M	+|+	1|3	0|0	MARK3|MARK3	103002478|103002478	1.000000|1.000000	0.71417|0.71417	0.927000|0.927000	0.36925|0.36925	0.971000|0.971000	0.66376|0.66376	7.645000|7.645000	0.83430|0.83430	2.679000|2.679000	0.91253|0.91253	0.650000|0.650000	0.86243|0.86243	GAA|ATG	.		0.373	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		A	103932725	G	A	103932725	3	1	130	1	0	0	0	0	1	0	0	0	9339	1291	45	2	981	2	MARK3	14	103932725	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	612	103932725	3416815	158	11500											
AHNAK2	113146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	105409722	105409722	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctggacctccaggtcagcGgaagggggctgaacgctgag	8	5	17	11	2	1	2	1	2	0	0	2	4	2	4	3	5	2	2	3	5	2	0	rs372712364	byFrequency	TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:105409722G>A	ENST00000333244.5	-	7	12185	c.12066C>T	c.(12064-12066)tcC>tcT	p.S4022S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4022						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCAGGTCAGCGGAAGGGGGCT	0.657													.|||	2	0.000399361	8e-04	0.0014	5008	,	,		17513	0		0	False		,,,				2504	0				p.S4022S		.											.	AHNAK2-47	0			c.C12066T						.						109	115	113					14																	105409722		1954	4133	6087	SO:0001819	synonymous_variant	113146	exon7			GTCAGCGGAAGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12066C>T	14.37:g.105409722G>A		Somatic	333	0		WXS	Illumina HiSeq	Phase_I	126	88	NM_138420	0	0	4	4	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.		0.657	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105409722	G	A	105409722	2	1	130	1	0	0	0	0	0	0	0	1	415	1103	39	1		1	AHNAK2	14	105409722	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1476997	105409722	1939818	159	11501											
ZFYVE19	84936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41099974	41099974	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcccaggacttggccggcgtGatctcagctctgcagaccct	6	8	12	15	2	2	2	1	1	2	1	3	3	2	3	3	3	2	2	3	3	0	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:41099974G>A	ENST00000355341.4	+	1	688	c.187G>A	c.(187-189)Gat>Aat	p.D63N	ZFYVE19_ENST00000564258.1_Intron|ZFYVE19_ENST00000570108.1_Intron|DNAJC17_ENST00000220496.4_5'Flank|ZFYVE19_ENST00000299173.10_Missense_Mutation_p.D63N|ZFYVE19_ENST00000563530.1_3'UTR|ZFYVE19_ENST00000336455.5_Intron	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	63					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		TGGCCGGCGTGATCTCAGCTC	0.672																																					p.D63N		.											.	ZFYVE19-91	0			c.G187A						.						36	46	42					15																	41099974		2053	4206	6259	SO:0001583	missense	84936	exon1			CGGCGTGATCTCA	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"Zinc fingers, FYVE domain containing"	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.187G>A	15.37:g.41099974G>A	ENSP00000347498:p.Asp63Asn	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	30	18	NM_001077268	0	0	8	15	7	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	37	CCDS42025.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756051	0.49362	.	.	ENSG00000166140	ENST00000355341;ENST00000299173	T;T	0.37058	1.23;1.22	4.57	1.69	0.24217	.	1.328960	0.05087	N	0.484506	T	0.25680	0.0625	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.29610	-1.0006	10	0.72032	D	0.01	1.3232	6.5318	0.22332	0.2972:0.0:0.7028:0.0	.	63;63	Q96K21-3;Q96K21	.;ZFY19_HUMAN	N	63	ENSP00000347498:D63N;ENSP00000299173:D63N	ENSP00000299173:D63N	D	+	1	0	ZFYVE19	38887266	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	1.012000	0.29924	0.425000	0.26087	0.603000	0.83216	GAT	.		0.672	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850		A	41099974	G	A	41099974	3	1	130	1	0	0	0	0	1	0	0	0	17697	1290	45	2	189	2	ZFYVE19	15	41099974	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		41099974	61431418	160	11502											
ZFYVE19	84936	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41100015	41100015	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggtgctgggagccaccatGgagagtaggtgctacggctg	7	7	18	9	2	0	1	0	0	0	1	0	3	0	2	2	5	4	4	2	5	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:41100015G>A	ENST00000355341.4	+	1	729	c.228G>A	c.(226-228)atG>atA	p.M76I	ZFYVE19_ENST00000564258.1_Intron|ZFYVE19_ENST00000570108.1_Missense_Mutation_p.M53I|DNAJC17_ENST00000220496.4_5'Flank|ZFYVE19_ENST00000299173.10_Missense_Mutation_p.M76I|ZFYVE19_ENST00000563530.1_3'UTR|ZFYVE19_ENST00000336455.5_Intron	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	76					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GAGCCACCATGGAGAGTAGGT	0.657																																					p.M76I													.	ZFYVE19-91	0			c.G228A						.						40	49	46					15																	41100015		2070	4201	6271	SO:0001583	missense	84936	exon1			CACCATGGAGAGT	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"Zinc fingers, FYVE domain containing"	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.228G>A	15.37:g.41100015G>A	ENSP00000347498:p.Met76Ile	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_001077268	0	0	2	5	3	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	37	CCDS42025.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220228	0.95139	.	.	ENSG00000166140	ENST00000355341;ENST00000299173	T;T	0.41065	1.01;1.01	5.5	5.5	0.81552	Zinc finger, FYVE-type (1);Zinc finger, FYVE/PHD-type (1);	171.812000	0.00166	N	0.000000	T	0.72827	0.3509	M	0.77486	2.375	0.54753	D	0.999986	D;D	0.71674	0.998;0.998	D;D	0.80764	0.991;0.994	T	0.54860	-0.8230	10	0.45353	T	0.12	-2.0204	18.3837	0.90459	0.0:0.0:1.0:0.0	.	76;76	Q96K21-3;Q96K21	.;ZFY19_HUMAN	I	76	ENSP00000347498:M76I;ENSP00000299173:M76I	ENSP00000299173:M76I	M	+	3	0	ZFYVE19	38887307	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	8.435000	0.90297	2.866000	0.98385	0.650000	0.86243	ATG	.		0.657	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850		A	41100015	G	A	41100015	3	1	130	1	0	0	0	0	1	0	0	0	17697	1348	47	2	230	2	ZFYVE19	15	41100015	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	41	41100015	61431377	161	11503											
INO80	54617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41384347	41384347	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtcttcactctgagaatCagcctcgctggattcatcac	9	12	7	13	2	6	1	4	1	2	1	8	3	6	2	1	1	1	1	1	1	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:41384347C>A	ENST00000361937.3	-	5	839	c.415G>T	c.(415-417)Gat>Tat	p.D139Y	INO80_ENST00000401393.3_Missense_Mutation_p.D139Y			Q9ULG1	INO80_HUMAN	INO80 complex subunit	139	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTCTGAGAATCAGCCTCGCTG	0.378																																					p.D139Y		.											.	INO80-72	0			c.G415T						.						123	114	117					15																	41384347		2203	4300	6503	SO:0001583	missense	54617	exon5			GAGAATCAGCCTC	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"INO80 complex subunits"	26956	protein-coding gene	gene with protein product	"INO80 complex subunit A"	610169	"INO80 complex homolog 1 (S. cerevisiae)", "INO80 homolog (S. cerevisiae)"	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.415G>T	15.37:g.41384347C>A	ENSP00000355205:p.Asp139Tyr	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	42	19	NM_017553	0	0	2	8	6	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	37	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.111190	0.56398	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.92752	-3.1;-3.1	5.37	5.37	0.77165	.	0.099076	0.64402	D	0.000002	D	0.92612	0.7653	L	0.59436	1.845	0.80722	D	1	P	0.51791	0.948	P	0.47626	0.552	D	0.93222	0.6609	10	0.72032	D	0.01	.	19.3098	0.94182	0.0:1.0:0.0:0.0	.	139	Q9ULG1	INO80_HUMAN	Y	139	ENSP00000355205:D139Y;ENSP00000384686:D139Y	ENSP00000355205:D139Y	D	-	1	0	INO80	39171639	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	6.847000	0.75404	2.800000	0.96347	0.455000	0.32223	GAT	.		0.378	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		A	41384347	C	A	41384347	3	1	130	1	0	0	0	0	1	0	0	0	7767	826	29	4	4383	4	INO80	15	41384347	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	284332	41384347	61147045	162	11504											
TRPM7	54822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	50906430	50906430	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacaagtcctatatcaatcaGagtgatcttatatcctggag	14	12	7	8	0	3	2	2	1	1	1	5	3	5	3	2	1	1	0	2	1	7	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:50906430G>C	ENST00000313478.7	-	14	1806	c.1525C>G	c.(1525-1527)Ctg>Gtg	p.L509V	TRPM7_ENST00000560955.1_Missense_Mutation_p.L509V	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	509					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		ATATCAATCAGAGTGATCTTA	0.363																																					p.L509V		.											.	TRPM7-392	0			c.C1525G						.						77	73	74					15																	50906430		1819	4082	5901	SO:0001583	missense	54822	exon14			CAATCAGAGTGAT	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"Voltage-gated ion channels / Transient receptor potential cation channels"	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.1525C>G	15.37:g.50906430G>C	ENSP00000320239:p.Leu509Val	Somatic	80	2		WXS	Illumina HiSeq	Phase_I	50	24	NM_017672	0	0	5	13	8	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149746	0.57151	.	.	ENSG00000092439	ENST00000313478	T	0.69685	-0.42	4.99	3.08	0.35506	.	0.079472	0.51477	D	0.000082	T	0.71091	0.3299	M	0.77712	2.385	0.47511	D	0.999449	D	0.58620	0.983	P	0.51016	0.656	T	0.70615	-0.4823	10	0.49607	T	0.09	-10.3651	8.4541	0.32888	0.3035:0.0:0.6965:0.0	.	509	Q96QT4	TRPM7_HUMAN	V	509	ENSP00000320239:L509V	ENSP00000320239:L509V	L	-	1	2	TRPM7	48693722	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	2.080000	0.41586	0.667000	0.31107	0.563000	0.77884	CTG	.		0.363	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		C	50906430	G	C	50906430	3	2	130	1	0	0	0	0	1	0	0	0	16624	933	33	4	4176	4	TRPM7	15	50906430	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	9522083	50906430	51624962	163	11505											
DMXL2	23312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51773559	51773559	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctttttttgcagataaggcaGatgttttggttacttttgga	8	19	10	4	0	0	2	0	0	0	2	0	3	0	3	0	3	2	4	0	3	2	9			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:51773559G>A	ENST00000251076.5	-	24	6031	c.5744C>T	c.(5743-5745)tCt>tTt	p.S1915F	DMXL2_ENST00000543779.2_Missense_Mutation_p.S1915F|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Missense_Mutation_p.S1279F	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1915						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AGATAAGGCAGATGTTTTGGT	0.383																																					p.S1915F		.											.	DMXL2-99	0			c.C5744T						.						190	183	185					15																	51773559		2196	4293	6489	SO:0001583	missense	23312	exon24			AAGGCAGATGTTT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.5744C>T	15.37:g.51773559G>A	ENSP00000251076:p.Ser1915Phe	Somatic	195	1		WXS	Illumina HiSeq	Phase_I	185	88	NM_001174116	0	0	1	4	3	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.745636	0.30955	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.26660	1.85;1.85;1.72	5.65	4.68	0.58851	.	0.408961	0.29624	N	0.011623	T	0.23289	0.0563	L	0.48986	1.54	0.30040	N	0.812686	B;B;B	0.18863	0.001;0.031;0.0	B;B;B	0.10450	0.004;0.005;0.002	T	0.08806	-1.0704	10	0.56958	D	0.05	.	9.5634	0.39383	0.0741:0.1436:0.7824:0.0	.	1915;1279;1915	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	F	1915;1915;1279	ENSP00000251076:S1915F;ENSP00000441858:S1915F;ENSP00000400855:S1279F	ENSP00000251076:S1915F	S	-	2	0	DMXL2	49560851	0.996000	0.38824	0.872000	0.34217	0.993000	0.82548	3.716000	0.54904	2.665000	0.90641	0.650000	0.86243	TCT	.		0.383	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51773559	G	A	51773559	3	1	130	1	0	0	0	0	1	0	0	0	4606	942	33	2	3449	2	DMXL2	15	51773559	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	867129	51773559	50757833	164	11506											
AKAP13	11214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	86269660	86269660	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaggttcaagcagttcttctCactgacattttagttttcct	8	17	7	9	0	3	1	2	1	2	0	5	2	4	1	1	1	1	4	1	1	2	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:86269660C>G	ENST00000394518.2	+	27	6860	c.6765C>G	c.(6763-6765)ctC>ctG	p.L2255L	AKAP13_ENST00000361243.2_Silent_p.L2259L|RP11-158M2.2_ENST00000561417.1_RNA|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Silent_p.L500L	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2255	Interaction with ESR1.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CAGTTCTTCTCACTGACATTT	0.338																																					p.L2259L	Melanoma(94;603 1453 3280 32295 32951)	.											.	AKAP13-258	0			c.C6777G						.						184	186	186					15																	86269660		2202	4298	6500	SO:0001819	synonymous_variant	11214	exon27			TCTTCTCACTGAC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"A-kinase anchor proteins", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	371	protein-coding gene	gene with protein product		604686	"lymphoid blast crisis oncogene"	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.6765C>G	15.37:g.86269660C>G		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	130	31	NM_006738	0	0	18	23	5	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			.		0.338	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86269660	C	G	86269660	2	3	130	1	0	0	0	0	0	0	0	1	449	813	29	4		4	AKAP13	15	86269660	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	34496101	86269660	16261732	165	11507											
PRC1	9055	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	91524227	91524227	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatttgagtacgcagcccctCacacactgcttcattttgtg	8	13	8	12	1	2	1	2	1	0	0	2	2	2	1	2	0	3	3	2	0	1	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:91524227C>T	ENST00000361188.5	-	6	1920	c.709G>A	c.(709-711)Gag>Aag	p.E237K	PRC1_ENST00000361919.3_Missense_Mutation_p.E237K|PRC1_ENST00000442656.2_Missense_Mutation_p.E196K|PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000394249.3_Missense_Mutation_p.E237K					protein regulator of cytokinesis 1									p.E237Q(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					CGCAGCCCCTCACACACTGCT	0.507																																					p.E237K													.	PRC1-92	1	Substitution - Missense(1)	ovary(1)	c.G709A						.						110	107	108					15																	91524227		2198	4298	6496	SO:0001583	missense	9055	exon6			GCCCCTCACACAC	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"anaphase spindle elongation 1 homolog (S. cerevisiae)"	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.709G>A	15.37:g.91524227C>T	ENSP00000354679:p.Glu237Lys	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	125	15	NM_199413	0	0	41	54	13		Missense_Mutation	SNP	ENST00000361188.5	37	CCDS45352.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.253520	0.39797	.	.	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000442656;ENST00000556982	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.19	5.19	0.71726	.	0.240235	0.41605	D	0.000850	T	0.49012	0.1532	M	0.74258	2.255	0.41448	D	0.987967	P;P;P;P	0.51933	0.936;0.936;0.936;0.949	P;P;P;P	0.57960	0.738;0.811;0.738;0.83	T	0.42085	-0.9472	10	0.08381	T	0.77	.	18.5027	0.90888	0.0:1.0:0.0:0.0	.	196;237;237;237	O43663-3;F8W9B5;O43663-2;O43663	.;.;.;PRC1_HUMAN	K	237;237;237;196;11	ENSP00000377793:E237K;ENSP00000354618:E237K;ENSP00000354679:E237K;ENSP00000409549:E196K	ENSP00000354679:E237K	E	-	1	0	PRC1	89325231	0.608000	0.26966	0.998000	0.56505	0.023000	0.10783	1.659000	0.37387	2.711000	0.92665	0.655000	0.94253	GAG	.		0.507	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		T	91524227	C	T	91524227	3	4	130	1	0	0	0	0	1	0	0	0	12475	835	29	2	1193	2	PRC1	15	91524227	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5254567	91524227	11007165	166	11508											
ZNF689	115509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30616559	30616559	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccacagtctgggcaagggtAaggcttttttagattctggg	8	12	13	8	0	2	1	0	0	2	1	2	1	2	1	1	4	0	3	1	4	3	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:30616559A>G	ENST00000287461.3	-	3	866	c.529T>C	c.(529-531)Tac>Cac	p.Y177H	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	177					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GGGCAAGGGTAAGGCTTTTTT	0.617																																					p.Y177H		.											.	ZNF689-68	0			c.T529C						.						73	78	77					16																	30616559		2197	4300	6497	SO:0001583	missense	115509	exon3			AAGGGTAAGGCTT	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"Zinc fingers, C2H2-type", "-"	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.529T>C	16.37:g.30616559A>G	ENSP00000287461:p.Tyr177His	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_138447	0	0	7	9	2	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	37	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	a	10.15	1.270760	0.23221	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.60040	0.22	4.94	3.8	0.43715	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35495	N	0.003162	T	0.43567	0.1253	N	0.25332	0.735	0.32189	N	0.579329	B	0.18166	0.026	B	0.25614	0.062	T	0.54227	-0.8325	10	0.62326	D	0.03	-23.399	9.3707	0.38252	0.8409:0.0:0.0:0.159	.	177	Q96CS4	ZN689_HUMAN	H	177	ENSP00000287461:Y177H	ENSP00000287461:Y177H	Y	-	1	0	ZNF689	30524060	0.355000	0.24921	0.997000	0.53966	0.194000	0.23727	2.424000	0.44714	2.074000	0.62210	0.455000	0.32223	TAC	.		0.617	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		G	30616559	A	G	30616559	3	3	130	1	0	0	0	0	1	0	0	0	18126	362	13	3	977	3	ZNF689	16	30616559	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08		30616559	59738194	167	11509											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30749163	30749163	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtgtcagagaagaacctttCtctcaccccttctgcaccca	9	11	6	15	0	4	2	2	0	2	2	5	3	4	2	4	0	2	1	4	0	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:30749163C>G	ENST00000262518.4	+	34	8187	c.7802C>G	c.(7801-7803)tCt>tGt	p.S2601C	SRCAP_ENST00000344771.4_Missense_Mutation_p.S2443C|RP11-2C24.4_ENST00000483578.1_lincRNA|SRCAP_ENST00000395059.2_Missense_Mutation_p.S2539C	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2601	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AAGAACCTTTCTCTCACCCCT	0.552																																					p.S2601C		.											.	SRCAP-94	0			c.C7802G						.						79	68	72					16																	30749163		2197	4300	6497	SO:0001583	missense	10847	exon34			ACCTTTCTCTCAC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.7802C>G	16.37:g.30749163C>G	ENSP00000262518:p.Ser2601Cys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	84	24	NM_006662	0	0	15	24	9	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	7.548	0.662079	0.14645	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91792	-2.9;-2.91;-2.91	4.88	3.85	0.44370	.	0.294453	0.24843	N	0.035160	D	0.83594	0.5288	N	0.08118	0	0.22728	N	0.9988	P;P	0.50156	0.932;0.758	P;B	0.46479	0.518;0.319	T	0.76427	-0.2963	10	0.62326	D	0.03	-9.0E-4	7.2792	0.26302	0.0:0.8786:0.0:0.1214	.	2539;2601	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	C	2601;2539;2443	ENSP00000262518:S2601C;ENSP00000378499:S2539C;ENSP00000343042:S2443C	ENSP00000262518:S2601C	S	+	2	0	SRCAP	30656664	0.483000	0.25956	0.998000	0.56505	0.666000	0.39218	0.172000	0.16704	2.543000	0.85770	0.467000	0.42956	TCT	.		0.552	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30749163	C	G	30749163	3	3	130	1	0	0	0	0	1	0	0	0	15167	913	32	4	7928	4	SRCAP	16	30749163	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	132604	30749163	59605590	168	11510											
BBS2	583	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56518732	56518732	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtgttgatgttattgcttcGaattgcatcccgacaagcag	9	14	10	8	2	0	1	0	1	0	0	2	3	1	1	1	0	3	5	1	0	3	5	rs567573386		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:56518732G>A	ENST00000245157.5	-	17	2527	c.2107C>T	c.(2107-2109)Cga>Tga	p.R703*	BBS2_ENST00000568104.1_Nonsense_Mutation_p.R657*	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	703					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						TTATTGCTTCGAATTGCATCC	0.398									Bardet-Biedl syndrome				G|||	1	0.000199681	0	0	5008	,	,		18568	0.001		0	False		,,,				2504	0				p.R703X													.	BBS2-91	0			c.C2107T						.						154	123	133					16																	56518732		2198	4300	6498	SO:0001587	stop_gained	583	exon17	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TGCTTCGAATTGC	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.2107C>T	16.37:g.56518732G>A	ENSP00000245157:p.Arg703*	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	75	19	NM_031885	0	0	5	7	2	Q96CM0|Q96SN9	Nonsense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	.	.	.	.	.	.	.	.	.	.	G	43	9.864671	0.99283	.	.	ENSG00000125124	ENST00000245157	.	.	.	5.3	5.3	0.74995	.	0.126809	0.49305	D	0.000144	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	-6.8024	14.1321	0.65260	0.0:0.0:0.8135:0.1864	.	.	.	.	X	703	.	ENSP00000245157:R703X	R	-	1	2	BBS2	55076233	1.000000	0.71417	0.992000	0.48379	0.991000	0.79684	5.120000	0.64685	2.629000	0.89072	0.591000	0.81541	CGA	.		0.398	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		A	56518732	G	A	56518732	4	1	130	1	0	0	0	0	0	1	0	0	1339	1066	37	1	62	1	BBS2	16	56518732	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	25769569	56518732	33836021	169	11511											
CMTM2	146225	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	66614056	66614056	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtacagctttgccattcataGatacatacccttcatcctgt	10	14	5	12	0	2	1	2	0	0	1	3	1	3	1	3	0	5	2	3	0	4	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:66614056G>C	ENST00000268595.2	+	2	564	c.413G>C	c.(412-414)aGa>aCa	p.R138T	RP11-403P17.2_ENST00000568430.1_RNA|CMTM2_ENST00000379486.2_Intron	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	138	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		GCCATTCATAGATACATACCC	0.483																																					p.R138T		.											.	CMTM2-91	0			c.G413C						.						258	204	223					16																	66614056		2201	4300	6501	SO:0001583	missense	146225	exon2			TTCATAGATACAT	BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"chemokine-like factor super family 2", "chemokine-like factor superfamily 2"	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.413G>C	16.37:g.66614056G>C	ENSP00000268595:p.Arg138Thr	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	114	8	NM_144673	0	0	0	0	0	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416443	0.83449	.	.	ENSG00000140932	ENST00000268595	T	0.35605	1.3	4.51	4.51	0.55191	Marvel (1);	0.000000	0.56097	D	0.000029	T	0.52661	0.1748	L	0.54323	1.7	0.35958	D	0.834422	D	0.89917	1.0	D	0.87578	0.998	T	0.57219	-0.7849	10	0.40728	T	0.16	20.5482	13.0353	0.58867	0.0:0.0:1.0:0.0	.	138	Q8TAZ6	CKLF2_HUMAN	T	138	ENSP00000268595:R138T	ENSP00000268595:R138T	R	+	2	0	CMTM2	65171557	1.000000	0.71417	0.997000	0.53966	0.404000	0.30871	2.341000	0.43983	2.786000	0.95864	0.561000	0.74099	AGA	.		0.483	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			C	66614056	G	C	66614056	3	2	130	1	0	0	0	0	1	0	0	0	3589	942	33	4	419	4	CMTM2	16	66614056	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10095324	66614056	23740697	170	11512											
AARS	16	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	70316659	70316659	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttcacttgctgttagagtaGagtccatcttgaaagtcacc	10	14	8	9	0	3	3	2	1	1	2	4	3	4	3	2	0	1	3	2	0	3	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:70316659G>C	ENST00000261772.8	-	2	151	c.8C>G	c.(7-9)tCt>tGt	p.S3C		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		TGTTAGAGTAGAGTCCATCTT	0.388																																					p.S3C		.											.	AARS-91	0			c.C8G						.						119	117	118					16																	70316659		2198	4300	6498	SO:0001583	missense	16	exon2			AGAGTAGAGTCCA	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.8C>G	16.37:g.70316659G>C	ENSP00000261772:p.Ser3Cys	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	141	76	NM_001605	0	0	9	22	13		Missense_Mutation	SNP	ENST00000261772.8	37	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.270776	0.59540	.	.	ENSG00000090861	ENST00000261772	T	0.64991	-0.13	5.56	1.06	0.20224	.	0.309320	0.37012	N	0.002288	T	0.54334	0.1852	L	0.39898	1.24	0.30179	N	0.800544	B	0.29085	0.232	B	0.38921	0.285	T	0.57353	-0.7826	10	0.66056	D	0.02	0.0292	8.518	0.33257	0.3543:0.0:0.6457:0.0	.	3	P49588	SYAC_HUMAN	C	3	ENSP00000261772:S3C	ENSP00000261772:S3C	S	-	2	0	AARS	68874160	0.401000	0.25303	0.169000	0.22859	0.874000	0.50279	3.302000	0.51849	0.212000	0.20703	0.591000	0.81541	TCT	.		0.388	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		C	70316659	G	C	70316659	3	2	130	1	0	0	0	0	1	0	0	0	19	942	33	4	2978	4	AARS	16	70316659	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3702603	70316659	20038094	171	11513											
HYDIN	54768	broad.mit.edu;bcgsc.ca	37	chr16	70896078	70896078	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagggctgtggggaaccctCggcccagtggtccatggtgc	6	7	17	11	1	0	0	0	0	0	0	2	2	1	1	3	6	2	1	3	6	2	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:70896078C>T	ENST00000393567.2	-	69	11800	c.11650G>A	c.(11650-11652)Gag>Aag	p.E3884K		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3884					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGGGAACCCTCGGCCCAGTGG	0.562																																					p.E3884K													.	HYDIN-92	0			c.G11650A						.						37	39	39					16																	70896078		1932	4139	6071	SO:0001583	missense	54768	exon69			AACCCTCGGCCCA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11650G>A	16.37:g.70896078C>T	ENSP00000377197:p.Glu3884Lys	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	34	9	NM_001270974	0	0	0	0	0	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.189687	0.38707	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00912	5.55	5.97	5.97	0.96955	.	1.190440	0.06746	U	0.779107	T	0.01222	0.0040	L	0.34521	1.04	0.80722	D	1	B	0.33964	0.434	B	0.28916	0.096	T	0.63301	-0.6668	10	0.06365	T	0.9	.	17.1497	0.86774	0.0:1.0:0.0:0.0	.	3883	F8WD23	.	K	3884;3883	ENSP00000377197:E3884K	ENSP00000313052:E3883K	E	-	1	0	HYDIN	69453579	0.003000	0.15002	0.315000	0.25238	0.202000	0.24057	1.389000	0.34453	2.838000	0.97847	0.511000	0.50034	GAG	.		0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70896078	C	T	70896078	3	4	130	1	0	0	0	0	1	0	0	0	7488	893	31	1	3787	1	HYDIN	16	70896078	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	579419	70896078	19458675	172	11514											
PRPF8	10594	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	1586885	1586885	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggtcatgtctccatggtctcGaatgatcttcctgacatgtt	7	15	9	10	1	4	2	1	2	3	0	7	3	5	2	2	2	0	1	2	2	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:1586885G>C	ENST00000572621.1	-	2	476	c.211C>G	c.(211-213)Cga>Gga	p.R71G	PRPF8_ENST00000304992.6_Missense_Mutation_p.R71G			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	71					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CCATGGTCTCGAATGATCTTC	0.478																																					p.R71G		.											.	PRPF8-525	0			c.C211G						.						210	180	190					17																	1586885		2203	4300	6503	SO:0001583	missense	10594	exon3			GGTCTCGAATGAT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.211C>G	17.37:g.1586885G>C	ENSP00000460348:p.Arg71Gly	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	79	5	NM_006445	0	0	55	60	5	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914983	0.72983	.	.	ENSG00000174231	ENST00000304992	T	0.44881	0.91	5.41	4.42	0.53409	Pre-mRNA-processing-splicing factor 8 (2);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	L	0.61218	1.895	0.80722	D	1	P	0.44241	0.829	P	0.45310	0.476	T	0.54510	-0.8283	10	0.72032	D	0.01	.	15.2921	0.73872	0.0:0.0:0.8586:0.1413	.	71	Q6P2Q9	PRP8_HUMAN	G	71	ENSP00000304350:R71G	ENSP00000304350:R71G	R	-	1	2	PRPF8	1533635	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.592000	0.61027	1.237000	0.43756	0.467000	0.42956	CGA	.		0.478	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			C	1586885	G	C	1586885	3	2	130	1	0	0	0	0	1	0	0	0	12604	1066	37	4	6960	4	PRPF8	17	1586885	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		1586885	79608325	173	11515											
ZZEF1	23140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3926086	3926086	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caacttcagcaaatcggtctGaaggaaagtagcacggatct	14	8	10	9	2	3	1	1	1	2	0	4	3	3	3	0	3	3	3	0	3	5	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:3926086G>C	ENST00000381638.2	-	44	7253	c.7129C>G	c.(7129-7131)Cag>Gag	p.Q2377E		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2377							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						AAATCGGTCTGAAGGAAAGTA	0.498																																					p.Q2377E		.											.	ZZEF1-93	0			c.C7129G						.						95	85	88					17																	3926086		2203	4300	6503	SO:0001583	missense	23140	exon44			CGGTCTGAAGGAA	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.7129C>G	17.37:g.3926086G>C	ENSP00000371051:p.Gln2377Glu	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	40	12	NM_015113	0	0	7	14	7	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	G	7.212	0.595598	0.13875	.	.	ENSG00000074755	ENST00000381638	T	0.19938	2.11	5.96	4.94	0.65067	.	0.473334	0.24301	N	0.039721	T	0.09598	0.0236	N	0.08118	0	0.27680	N	0.946471	B	0.02656	0.0	B	0.01281	0.0	T	0.15896	-1.0421	10	0.02654	T	1	-4.1226	13.6249	0.62159	0.0:0.1251:0.7598:0.1151	.	2377	O43149	ZZEF1_HUMAN	E	2377	ENSP00000371051:Q2377E	ENSP00000371051:Q2377E	Q	-	1	0	ZZEF1	3872835	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.220000	0.51207	2.832000	0.97577	0.655000	0.94253	CAG	.		0.498	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		C	3926086	G	C	3926086	3	2	130	1	0	0	0	0	1	0	0	0	18287	1299	45	4	1804	4	ZZEF1	17	3926086	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2339201	3926086	77269124	174	11516											
TRPV2	51393	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	16330054	16330054	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaccgacaccgaatggtcGttttggagcccctgaacaaa	12	7	10	12	3	0	1	0	1	0	0	1	4	0	2	4	2	3	2	4	2	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:16330054G>A	ENST00000338560.7	+	7	1513	c.1114G>A	c.(1114-1116)Gtt>Att	p.V372I	TRPV2_ENST00000577397.1_Intron|AC093484.4_ENST00000441875.1_RNA	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	372	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		CCGAATGGTCGTTTTGGAGCC	0.507																																					p.V372I													.	TRPV2-91	0			c.G1114A						.						89	74	79					17																	16330054		2203	4300	6503	SO:0001583	missense	51393	exon7			ATGGTCGTTTTGG	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1114G>A	17.37:g.16330054G>A	ENSP00000342222:p.Val372Ile	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	40	14	NM_016113	0	0	3	3	0	A6NML2|A8K0Z0|Q9Y670	Missense_Mutation	SNP	ENST00000338560.7	37	CCDS32576.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.105678	0.56291	.	.	ENSG00000187688	ENST00000338560	D	0.89617	-2.54	5.29	2.95	0.34219	.	0.314085	0.34133	N	0.004239	D	0.83418	0.5250	M	0.72479	2.2	0.28997	N	0.887687	P	0.48694	0.914	B	0.29785	0.107	T	0.79077	-0.1951	10	0.37606	T	0.19	-30.5063	12.2162	0.54408	0.1653:0.0:0.8347:0.0	.	372	Q9Y5S1	TRPV2_HUMAN	I	372	ENSP00000342222:V372I	ENSP00000342222:V372I	V	+	1	0	TRPV2	16270779	0.014000	0.17966	1.000000	0.80357	0.953000	0.61014	0.888000	0.28268	1.248000	0.43934	-0.232000	0.12228	GTT	.		0.507	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113		A	16330054	G	A	16330054	3	1	130	1	0	0	0	0	1	0	0	0	16629	1145	40	1	1136	1	TRPV2	17	16330054	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	12403968	16330054	64865156	175	11517											
MPRIP	23164	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	17046031	17046031	+	Frame_Shift_Del	DEL	C	C	-																															gtggggccctcaccatccagCgacacacgccagggccgcag																								rs146439071		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:17046031delC	ENST00000341712.4	+	8	987	c.987delC	c.(985-987)agcfs	p.S329fs	MPRIP_ENST00000395804.3_Frame_Shift_Del_p.S329fs|MPRIP_ENST00000395811.5_Frame_Shift_Del_p.S329fs|MPRIP_ENST00000444976.1_Frame_Shift_Del_p.S329fs			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	329	Interaction with F-actin. {ECO:0000250}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CACCATCCAGCGACACACGCC	0.632																																					p.S329fs		.											.	MPRIP-90	0			c.987delC						.						85	77	80					17																	17046031		2203	4300	6503	SO:0001589	frameshift_variant	23164	exon8			.	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.987delC	17.37:g.17046031delC	ENSP00000342379:p.Ser329fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	55	16	NM_015134	0	0	0	0	0	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Frame_Shift_Del	DEL	ENST00000341712.4	37	CCDS32578.1																																																																																			.		0.632	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		-	17046031	C	-	17046031	7	5	130	1	0	1	0	1	0	0	0	0	9768	767	27	0	1017	0	MPRIP	17	17046031	Frame_Shift_Del	DEL	C	TCGA-HE-7130-01A-11D-1961-08	715977	17046031	64149179	176	11518											
ZNF286B	729288	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18565401	18565401	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atgaatgaatgaaggcttttCcacactcactacatttgtac	13	13	6	9	0	1	3	1	3	0	0	2	3	2	3	1	1	2	2	1	1	5	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:18565401C>T	ENST00000545289.1	-	5	1668	c.1418G>A	c.(1417-1419)gGa>gAa	p.G473E	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	473					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)			endometrium(1)|lung(1)	2						GAAGGCTTTTCCACACTCACT	0.393																																					p.G473E													.	.	0			c.G1418A						.						171	159	162					17																	18565401		692	1591	2283	SO:0001583	missense	729288	exon5			GCTTTTCCACACT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"Zinc fingers, C2H2-type"	33241	protein-coding gene	gene with protein product	"zinc finger protein 590"		"zinc finger protein 286-like", "zinc finger 286C pseudogene"	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1418G>A	17.37:g.18565401C>T	ENSP00000461413:p.Gly473Glu	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	16	5	NM_001145045	0	0	0	0	0		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			.		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		T	18565401	C	T	18565401	3	4	130	1	0	0	0	0	1	0	0	0	17856	855	30	2	154	2	ZNF286B	17	18565401	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1519370	18565401	62629809	177	11519			2	35		2	2	13	C		8.837772e-05
ZNF286B	729288	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18565413	18565413	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggcttttccacactcactaCatttgtacggtttctttcca	8	16	5	12	1	2	0	1	0	1	0	4	0	4	0	2	2	2	3	2	2	2	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:18565413C>T	ENST00000545289.1	-	5	1656	c.1406G>A	c.(1405-1407)tGt>tAt	p.C469Y	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	469					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)			endometrium(1)|lung(1)	2						ACACTCACTACATTTGTACGG	0.393																																					p.C469Y													.	.	0			c.G1406A						.						154	144	147					17																	18565413		692	1591	2283	SO:0001583	missense	729288	exon5			TCACTACATTTGT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"Zinc fingers, C2H2-type"	33241	protein-coding gene	gene with protein product	"zinc finger protein 590"		"zinc finger protein 286-like", "zinc finger 286C pseudogene"	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1406G>A	17.37:g.18565413C>T	ENSP00000461413:p.Cys469Tyr	Somatic	35	1		WXS	Illumina HiSeq	Phase_I	14	6	NM_001145045	0	0	0	0	0		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			.		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		T	18565413	C	T	18565413	3	4	130	1	0	0	0	0	1	0	0	0	17856	478	17	2	166	2	ZNF286B	17	18565413	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	12	18565413	62629797	178	11520			2	35		2	2	13	C		8.837772e-05
IKZF3	22806	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	37949078	37949078	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttcatattcattatattctCttgaatagctgtaagggatt	11	19	6	5	0	3	1	2	1	1	0	4	2	3	2	0	1	1	2	0	1	6	10			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:37949078C>T	ENST00000346872.3	-	4	333	c.272G>A	c.(271-273)aGa>aAa	p.R91K	IKZF3_ENST00000377958.2_Intron|IKZF3_ENST00000346243.3_Missense_Mutation_p.R91K|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000350532.3_Missense_Mutation_p.R91K|IKZF3_ENST00000535189.1_Missense_Mutation_p.R57K|IKZF3_ENST00000377944.3_Intron|IKZF3_ENST00000377952.2_Intron|IKZF3_ENST00000351680.3_Missense_Mutation_p.R91K|IKZF3_ENST00000467757.1_Missense_Mutation_p.R91K|IKZF3_ENST00000377945.3_Missense_Mutation_p.R91K|IKZF3_ENST00000439016.2_Missense_Mutation_p.R91K|IKZF3_ENST00000439167.2_Missense_Mutation_p.R57K	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	91					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E92fs*29(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			ATTATATTCTCTTGAATAGCT	0.383																																					p.R91K		.											.	IKZF3-971	1	Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.G272A						.						127	118	121					17																	37949078		2203	4300	6503	SO:0001583	missense	22806	exon4			TATTCTCTTGAAT	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13178	protein-coding gene	gene with protein product		606221	"zinc finger protein, subfamily 1A, 3 (Aiolos)"	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.272G>A	17.37:g.37949078C>T	ENSP00000344544:p.Arg91Lys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	88	12	NM_012481	0	0	2	4	2	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	37	CCDS11346.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.24|18.24	3.579420|3.579420	0.65878|0.65878	.|.	.|.	ENSG00000161405|ENSG00000161405	ENST00000439167;ENST00000439016|ENST00000488188;ENST00000346872;ENST00000377945;ENST00000535189;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	.|T;T;T;T;T;T;T	.|0.05855	.|3.45;3.52;3.43;3.48;3.52;3.38;4.4	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.10594|0.10594	0.0259|0.0259	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999992|0.999992	.|P;B;P;D;P;P;P;P;P	.|0.59357	.|0.794;0.317;0.864;0.985;0.57;0.93;0.864;0.798;0.786	.|B;B;P;D;B;P;P;B;B	.|0.70716	.|0.31;0.228;0.523;0.97;0.341;0.798;0.523;0.384;0.323	T|T	0.22661|0.22661	-1.0210|-1.0210	5|10	.|0.02654	.|T	.|1	-18.7806|-18.7806	10.1431|10.1431	0.42747|0.42747	0.0:0.7917:0.1376:0.0707|0.0:0.7917:0.1376:0.0707	.|.	.|91;57;91;91;91;91;91;57;91	.|Q9UKT9-13;Q9UKT9-7;Q9UKT9-6;Q9UKT9-5;Q9UKT9-4;Q9UKT9-2;Q9UKT9-3;Q9UKT9-8;Q9UKT9	.|.;.;.;.;.;.;.;.;IKZF3_HUMAN	K|K	45|91;91;91;57;91;91;91;91	.|ENSP00000344544:R91K;ENSP00000367180:R91K;ENSP00000438972:R57K;ENSP00000345622:R91K;ENSP00000341977:R91K;ENSP00000344471:R91K;ENSP00000420463:R91K	.|ENSP00000341977:R91K	E|R	-|-	1|2	0|0	IKZF3|IKZF3	35202604|35202604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.918000|1.918000	0.40006|0.40006	2.832000|2.832000	0.97577|0.97577	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.		0.383	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		T	37949078	C	T	37949078	3	4	130	1	0	0	0	0	1	0	0	0	7637	913	32	2	1277	2	IKZF3	17	37949078	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	19383665	37949078	43246132	179	11521											
HAP1	9001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39887800	39887800	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcctcatcctcaagagtgtcGagttgagaggcctggaggga	9	9	14	9	1	2	2	2	1	0	2	5	6	4	4	3	3	0	1	3	3	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:39887800G>A	ENST00000310778.5	-	6	1023	c.1014C>T	c.(1012-1014)ctC>ctT	p.L338L	RN7SL399P_ENST00000471648.2_RNA|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Silent_p.L338L|HAP1_ENST00000341193.5_Silent_p.L346L|HAP1_ENST00000393939.2_Silent_p.L338L			P54257	HAP1_HUMAN	huntingtin-associated protein 1	338	Glu-rich.|HAP1 N-terminal.				anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CAAGAGTGTCGAGTTGAGAGG	0.557																																					p.L346L		.											.	HAP1-92	0			c.C1038T						.						142	116	125					17																	39887800		2203	4300	6503	SO:0001819	synonymous_variant	9001	exon6			AGTGTCGAGTTGA	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"neuroan 1"	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.1014C>T	17.37:g.39887800G>A		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	103	66	NM_001079870	0	0	0	0	0	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Silent	SNP	ENST00000310778.5	37																																																																																				.		0.557	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		A	39887800	G	A	39887800	2	1	130	1	0	0	0	0	0	0	0	1	6974	1045	37	1		1	HAP1	17	39887800	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1938722	39887800	41307410	180	11522											
UBTF	7343	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42293042	42293042	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttcttcttctccggaagctCcttgtatttcttggacagaa	7	16	7	11	1	4	1	0	0	4	1	6	3	5	3	2	2	1	2	2	2	3	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:42293042C>T	ENST00000302904.4	-	5	946	c.454G>A	c.(454-456)Gag>Aag	p.E152K	UBTF_ENST00000436088.1_Missense_Mutation_p.E152K|UBTF_ENST00000529383.1_Missense_Mutation_p.E152K|UBTF_ENST00000393606.3_Missense_Mutation_p.E152K|UBTF_ENST00000537550.1_5'UTR|UBTF_ENST00000343638.5_Missense_Mutation_p.E152K|UBTF_ENST00000526094.1_Missense_Mutation_p.E152K|UBTF_ENST00000533177.1_Missense_Mutation_p.E152K|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000527034.1_Missense_Mutation_p.E152K			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	152					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TCCGGAAGCTCCTTGTATTTC	0.547																																					p.E152K													.	UBTF-90	0			c.G454A						.						112	116	115					17																	42293042		2203	4300	6503	SO:0001583	missense	7343	exon5			GAAGCTCCTTGTA	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.454G>A	17.37:g.42293042C>T	ENSP00000302640:p.Glu152Lys	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	120	13	NM_014233	0	0	41	46	5	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	c	26.9	4.784023	0.90282	.	.	ENSG00000108312	ENST00000343638;ENST00000302904;ENST00000527034;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383;ENST00000530828	D;D;D;D;D;D;D;D;D	0.98060	-4.69;-4.69;-4.69;-4.69;-4.69;-4.69;-4.69;-4.69;-4.69	4.27	4.27	0.50696	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	L	0.35854	1.095	0.80722	D	1	D;P;D	0.76494	0.999;0.553;0.999	D;B;D	0.91635	0.998;0.331;0.999	D	0.96841	0.9618	10	0.26408	T	0.33	-30.3629	16.6665	0.85254	0.0:1.0:0.0:0.0	.	152;152;152	E9PKP7;P17480-2;P17480	.;.;UBF1_HUMAN	K	152;152;152;152;152;152;152;152;124	ENSP00000345297:E152K;ENSP00000302640:E152K;ENSP00000431539:E152K;ENSP00000437180:E152K;ENSP00000390669:E152K;ENSP00000377231:E152K;ENSP00000432925:E152K;ENSP00000435708:E152K;ENSP00000433046:E124K	ENSP00000302640:E152K	E	-	1	0	UBTF	39648568	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.713000	0.84693	2.082000	0.62665	0.467000	0.42956	GAG	.		0.547	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		T	42293042	C	T	42293042	3	4	130	1	0	0	0	0	1	0	0	0	16942	864	30	2	1908	2	UBTF	17	42293042	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2405242	42293042	38902168	181	11523											
KIAA1267	284058	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	44248974	44248974	+	Frame_Shift_Del	DEL	C	C	-																															atgaagtgagagcccgttttCccccattgagggaagtggaa																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:44248974delC	ENST00000262419.6	-	2	1006	c.536delG	c.(535-537)ggafs	p.G179fs	KANSL1_ENST00000572904.1_Frame_Shift_Del_p.G179fs|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000575318.1_Frame_Shift_Del_p.G179fs|KANSL1_ENST00000432791.1_Frame_Shift_Del_p.G179fs|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Frame_Shift_Del_p.G179fs	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	179					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AGCCCGTTTTCCCCCATTGAG	0.473																																					p.G179fs		.											.	.	0			c.536delG						.						104	138	127					17																	44248974		2203	4300	6503	SO:0001589	frameshift_variant	284058	exon2			.	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"centromere protein 36"	612452	"KIAA1267"	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.536delG	17.37:g.44248974delC	ENSP00000262419:p.Gly179fs	Somatic	304	0		WXS	Illumina HiSeq	Phase_I	277	119	NM_001193466	0	0	0	0	0	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Frame_Shift_Del	DEL	ENST00000262419.6	37	CCDS11503.1																																																																																			.		0.473	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		-	44248974	C	-	44248974	7	5	130	1	0	1	0	1	0	0	0	0	8240	855	30	0	2837	0	KIAA1267	17	44248974	Frame_Shift_Del	DEL	C	TCGA-HE-7130-01A-11D-1961-08	1955932	44248974	36946236	182	11524											
C17orf57	124989	ucsc.edu	37	chr17	45452155	45452155	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaaacattcagagaagggtGaaattcatgactcaaagtct	18	9	8	6	0	4	3	3	2	1	1	4	4	4	3	0	1	1	0	0	1	5	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:45452155G>A	ENST00000331493.2	+	12	1606	c.1195G>A	c.(1195-1197)Gaa>Aaa	p.E399K	EFCAB13_ENST00000517484.1_Missense_Mutation_p.E303K	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	399						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										AGAGAAGGGTGAAATTCATGA	0.363																																					p.E399K													.	.	0			c.G1195A						.						60	63	62					17																	45452155		2203	4300	6503	SO:0001583	missense	124989	exon12			AAGGGTGAAATTC	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1195G>A	17.37:g.45452155G>A	ENSP00000332111:p.Glu399Lys	Somatic	39	0		WXS	Illumina HiSeq		44	5	NM_152347	0	0	0	0	0	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769226	0.69992	.	.	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.68025	0.06;-0.3	3.69	3.69	0.42338	.	0.488035	0.20086	N	0.099559	T	0.70107	0.3186	L	0.42245	1.32	0.09310	N	1	D;D;D	0.64830	0.994;0.994;0.994	P;P;P	0.60173	0.82;0.87;0.87	T	0.59783	-0.7389	9	.	.	.	5.8359	11.0933	0.48130	0.0:0.0:1.0:0.0	.	351;399;303	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	K	399;303;351	ENSP00000332111:E399K;ENSP00000430048:E303K	.	E	+	1	0	C17orf57	42807154	0.622000	0.27085	0.114000	0.21550	0.916000	0.54674	2.027000	0.41078	2.045000	0.60652	0.585000	0.79938	GAA	.		0.363	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		A	45452155	G	A	45452155	3	1	130	1	0	0	0	0	1	0	0	0	1870	1291	45	2	1229	2	C17orf57	17	45452155	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1203181	45452155	35743055	183	11525											
SKAP1	8631	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	46239837	46239837	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctttctgtccttaccttgctCagaatacggatgaggtcacc	8	13	8	12	1	3	2	2	1	1	1	4	3	4	3	3	2	3	1	3	2	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:46239837C>G	ENST00000336915.6	-	11	1041	c.972G>C	c.(970-972)ctG>ctC	p.L324L	SKAP1_ENST00000584924.1_Silent_p.L324L	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	324	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.L324L(1)		large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						TTACCTTGCTCAGAATACGGA	0.433																																					p.L324L		.											.	SKAP1-90	1	Substitution - coding silent(1)	urinary_tract(1)	c.G972C						.						93	79	84					17																	46239837		2203	4300	6503	SO:0001819	synonymous_variant	8631	exon11			CTTGCTCAGAATA	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.972G>C	17.37:g.46239837C>G		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	70	6	NM_003726	0	0	0	0	0	D3DTV1|O15268	Silent	SNP	ENST00000336915.6	37	CCDS32674.1																																																																																			.		0.433	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726		G	46239837	C	G	46239837	2	3	130	1	0	0	0	0	0	0	0	1	14387	813	29	4		4	SKAP1	17	46239837	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	787682	46239837	34955373	184	11526											
KIF19	124602	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72338804	72338804	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gccaccaccaagagcctcatCgagggcgtcatctcaggcta	10	6	10	15	2	3	1	3	0	1	1	5	2	3	1	4	2	1	1	4	2	2	1	rs368432623		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:72338804C>G	ENST00000389916.4	+	4	405	c.267C>G	c.(265-267)atC>atG	p.I89M		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	89	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						AGAGCCTCATCGAGGGCGTCA	0.622																																					p.I89M		.											.	KIF19-90	0			c.C267G						.						140	112	121					17																	72338804		2203	4300	6503	SO:0001583	missense	124602	exon4			CCTCATCGAGGGC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.267C>G	17.37:g.72338804C>G	ENSP00000374566:p.Ile89Met	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	81	41	NM_153209	0	0	0	0	0	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611793	0.66558	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.75821	-0.97;-0.97	5.5	-11.0	0.00169	Kinesin, motor domain (4);	.	.	.	.	T	0.77916	0.4202	M	0.79805	2.47	0.28548	N	0.91179	D;D;P;D	0.64830	0.99;0.981;0.93;0.994	D;D;P;D	0.67382	0.932;0.916;0.803;0.951	T	0.72581	-0.4250	9	0.87932	D	0	.	2.1205	0.03724	0.1636:0.208:0.163:0.4655	.	89;89;89;89	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	M	89	ENSP00000449134:I89M;ENSP00000374566:I89M	ENSP00000374566:I89M	I	+	3	3	KIF19	69850399	0.000000	0.05858	0.008000	0.14137	0.981000	0.71138	-2.329000	0.01111	-1.540000	0.01730	0.456000	0.33151	ATC	.		0.622	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		G	72338804	C	G	72338804	3	3	130	1	0	0	0	0	1	0	0	0	8303	874	31	4	281	4	KIF19	17	72338804	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	26098967	72338804	8856406	185	11527											
EIF4A3	9775	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	78120725	78120725	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagcagccgctttcgcgcCgagcccgaggtcgccatcgt	5	8	13	15	7	0	1	0	1	0	0	3	3	0	1	4	1	3	2	4	1	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:78120725C>G	ENST00000269349.3	-	1	257	c.36G>C	c.(34-36)tcG>tcC	p.S12S		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	12					ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			GCTTTCGCGCCGAGCCCGAGG	0.652																																					p.S12S		.											.	EIF4A3-227	0			c.G36C						.						33	28	30					17																	78120725		2203	4292	6495	SO:0001819	synonymous_variant	9775	exon1			TCGCGCCGAGCCC	BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"DEAD-boxes"	18683	protein-coding gene	gene with protein product		608546	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 48", "eukaryotic translation initiation factor 4A, isoform 3"	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.36G>C	17.37:g.78120725C>G		Somatic	55	1		WXS	Illumina HiSeq	Phase_I	42	9	NM_014740	0	0	47	59	12	Q15033|Q6IBQ2|Q96A18	Silent	SNP	ENST00000269349.3	37	CCDS11767.1																																																																																			.		0.652	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740		G	78120725	C	G	78120725	2	3	130	1	0	0	0	0	0	0	0	1	5039	639	23	4		4	EIF4A3	17	78120725	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5781921	78120725	3074485	186	11528											
MIB1	57534	broad.mit.edu;bcgsc.ca	37	chr18	19399507	19399507	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caataagtaagaaacgtgatGatatcctagcagttcttttg	14	13	8	6	1	1	3	0	2	1	1	2	3	2	3	1	0	2	3	1	0	6	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr18:19399507G>A	ENST00000261537.6	+	12	1993	c.1729G>A	c.(1729-1731)Gat>Aat	p.D577N	SNORA73_ENST00000363107.1_RNA|MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	577					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			GAAACGTGATGATATCCTAGC	0.368																																					p.D577N													.	MIB1-526	0			c.G1729A						.						151	143	145					18																	19399507		2203	4300	6503	SO:0001583	missense	57534	exon12			CGTGATGATATCC	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.1729G>A	18.37:g.19399507G>A	ENSP00000261537:p.Asp577Asn	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	218	13	NM_020774	0	0	20	20	0	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	G	31	5.088114	0.94100	.	.	ENSG00000101752	ENST00000261537	T	0.67171	-0.25	5.1	5.1	0.69264	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.74884	0.3775	L	0.37630	1.12	0.80722	D	1	D	0.53885	0.963	D	0.68621	0.959	T	0.72717	-0.4209	10	0.35671	T	0.21	-20.3959	18.8792	0.92350	0.0:0.0:1.0:0.0	.	577	Q86YT6	MIB1_HUMAN	N	577	ENSP00000261537:D577N	ENSP00000261537:D577N	D	+	1	0	MIB1	17653505	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.544000	0.85801	0.563000	0.77884	GAT	.		0.368	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		A	19399507	G	A	19399507	3	1	130	1	0	0	0	0	1	0	0	0	9591	1290	45	2	1775	2	MIB1	18	19399507	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		19399507	58677741	187	11529											
HRH4	59340	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	22048831	22048831	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaaatctgtgtattttggctCactactgactatctgttatg	9	17	8	7	0	3	1	1	1	2	0	3	2	3	1	0	1	1	3	0	1	5	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr18:22048831C>T	ENST00000256906.4	+	2	373	c.273C>T	c.(271-273)ctC>ctT	p.L91L	HRH4_ENST00000426880.2_Intron	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	91					inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	TATTTTGGCTCACTACTGACT	0.403																																					p.L91L													.	HRH4-92	0			c.C273T						.						228	186	200					18																	22048831		2203	4300	6503	SO:0001819	synonymous_variant	59340	exon2			TTGGCTCACTACT	AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"GPCR / Class A : Histamine receptors"	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.273C>T	18.37:g.22048831C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	105	12	NM_021624	0	0	0	0	0	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Silent	SNP	ENST00000256906.4	37	CCDS11887.1																																																																																			.		0.403	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1			T	22048831	C	T	22048831	2	4	130	1	0	0	0	0	0	0	0	1	7379	813	29	2		2	HRH4	18	22048831	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2649324	22048831	56028417	188	11530											
TAF4B	6875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	23866009	23866009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcaagccagtctgaaaagtCaattattgtttctggagcaa	13	12	8	8	0	4	1	2	1	2	0	4	2	4	2	1	1	2	2	1	1	6	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr18:23866009C>T	ENST00000269142.5	+	7	2134	c.1136C>T	c.(1135-1137)tCa>tTa	p.S379L	TAF4B_ENST00000578121.1_Missense_Mutation_p.S379L|TAF4B_ENST00000400466.2_Missense_Mutation_p.S379L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	379					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TCTGAAAAGTCAATTATTGTT	0.463																																					p.S379L		.											.	TAF4B-71	0			c.C1136T						.						100	97	98					18																	23866009		1925	4142	6067	SO:0001583	missense	6875	exon7			AAAAGTCAATTAT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1136C>T	18.37:g.23866009C>T	ENSP00000269142:p.Ser379Leu	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	82	64	NM_005640	0	0	1	2	1	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	c	2.722	-0.266371	0.05754	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.22945	1.93;1.93;1.93	5.35	4.47	0.54385	.	1.607940	0.03022	N	0.150849	T	0.16685	0.0401	N	0.08118	0	0.09310	N	1	B;B	0.13594	0.001;0.008	B;B	0.14578	0.001;0.011	T	0.23797	-1.0178	10	0.20519	T	0.43	0.3248	9.9174	0.41444	0.1569:0.6917:0.1514:0.0	.	379;379	Q92750;A4PBF7	TAF4B_HUMAN;.	L	379	ENSP00000389365:S379L;ENSP00000269142:S379L;ENSP00000383314:S379L	ENSP00000269142:S379L	S	+	2	0	TAF4B	22120007	0.028000	0.19301	0.092000	0.20876	0.014000	0.08584	2.845000	0.48254	1.228000	0.43614	0.558000	0.71614	TCA	.		0.463	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		T	23866009	C	T	23866009	3	4	130	1	0	0	0	0	1	0	0	0	15559	838	29	2	1162	2	TAF4B	18	23866009	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1817178	23866009	54211239	189	11531											
DOK6	220164	hgsc.bcm.edu;broad.mit.edu	37	chr18	67266711	67266711	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	catctttcacgatgaaacatCgaagacatttgcctgtgagt	12	12	8	9	2	2	3	1	2	1	1	3	5	2	3	1	0	2	0	1	0	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr18:67266711C>G	ENST00000382713.5	+	3	456	c.266C>G	c.(265-267)tCg>tGg	p.S89W	RP11-465I4.2_ENST00000583991.1_RNA	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	89	PH.									central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				GATGAAACATCGAAGACATTT	0.448																																					p.S89W		.											.	DOK6-92	0			c.C266G						.						101	78	86					18																	67266711		2203	4300	6503	SO:0001583	missense	220164	exon3			AAACATCGAAGAC	AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"Pleckstrin homology (PH) domain containing"	28301	protein-coding gene	gene with protein product		611402	"docking protein 5-like"	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.266C>G	18.37:g.67266711C>G	ENSP00000372160:p.Ser89Trp	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	25	3	NM_152721	0	0	0	0	0	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	37	CCDS32841.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.295543	0.60086	.	.	ENSG00000206052	ENST00000382713	T	0.79352	-1.26	5.91	5.91	0.95273	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.85548	0.5722	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.85609	0.1257	10	0.66056	D	0.02	-2.6428	19.2865	0.94077	0.0:1.0:0.0:0.0	.	89	Q6PKX4	DOK6_HUMAN	W	89	ENSP00000372160:S89W	ENSP00000372160:S89W	S	+	2	0	DOK6	65417691	1.000000	0.71417	0.262000	0.24481	0.116000	0.19942	7.786000	0.85741	2.802000	0.96397	0.655000	0.94253	TCG	.		0.448	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721		G	67266711	C	G	67266711	3	3	130	1	0	0	0	0	1	0	0	0	4712	893	31	4	276	4	DOK6	18	67266711	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	43400702	67266711	10810537	190	11532											
MED16	10025	hgsc.bcm.edu	37	chr19	879943	879943	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcagctcaccttcccGtggctgtcaatccccaccag	7	7	7	20	1	2	0	2	0	0	0	4	0	4	0	7	1	2	3	7	1	1	1	rs201392672|rs76403059	byFrequency	TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000325464.1_Missense_Mutation_p.H449Q|MED16_ENST00000395808.3_Missense_Mutation_p.H449Q|MED16_ENST00000606828.1_Intron|MED16_ENST00000312090.6_Missense_Mutation_p.H449Q|MED16_ENST00000269814.4_Missense_Mutation_p.H449Q			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	449					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACCTTCCCGTGGCTGTCAA	0.672																																					p.H449Q		.											.	MED16-186	0			c.C1347G						.						13	11	12					19																	879943		2152	4247	6399	SO:0001583	missense	10025	exon8			CTTCCCGTGGCTG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"WD repeat domain containing"	17556	protein-coding gene	gene with protein product		604062	"thyroid hormone receptor associated protein 5"	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1347C>G	19.37:g.879943G>C	ENSP00000464810:p.His449Gln	Somatic	36	1		WXS	Illumina HiSeq	Phase_I	25	3	NM_005481	0	0	1	1	0	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	3.376	-0.127462	0.06753	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000424039	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.21	-7.89	0.01174	WD40 repeat-like-containing domain (1);	0.323237	0.32357	N	0.006220	T	0.21307	0.0513	L	0.37850	1.14	0.37741	D	0.925623	B;B;B;B;B	0.13145	0.006;0.007;0.002;0.001;0.001	B;B;B;B;B	0.14023	0.006;0.006;0.003;0.006;0.01	T	0.20009	-1.0288	10	0.15066	T	0.55	-14.2411	8.1092	0.30905	0.4704:0.1904:0.3392:0.0	.	449;449;449;449;449	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	Q	449;449;449;449;449;305;210;208;449	ENSP00000325612:H449Q;ENSP00000308528:H449Q;ENSP00000379153:H449Q;ENSP00000269814:H449Q	ENSP00000269814:H449Q	H	-	3	2	MED16	830943	0.000000	0.05858	0.886000	0.34754	0.057000	0.15508	-3.404000	0.00482	-1.779000	0.01280	-2.326000	0.00250	CAC	.		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		C	879943	G	C	879943	3	2	130	1	0	0	0	0	1	0	0	0	9459	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		879943	58249040	191	11533											
ATP8B3	148229	ucsc.edu;bcgsc.ca	37	chr19	1811677	1811677	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccaggtcctggtggggcaGggcttggctcagggccagct	4	7	17	13	0	1	0	1	0	0	0	2	0	2	0	4	7	1	4	4	7	0	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:1811677G>T	ENST00000310127.6	-	2	297	c.59C>A	c.(58-60)cCt>cAt	p.P20H	ATP8B3_ENST00000539485.1_Missense_Mutation_p.P20H|ATP8B3_ENST00000525591.1_Intron|ATP8B3_ENST00000526092.2_Intron	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	20					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGTGGGGCAGGGCTTGGCTC	0.647																																					p.P20H													.	.	0			c.C59A						.						31	35	34					19																	1811677		2002	4160	6162	SO:0001583	missense	148229	exon2			GGGGCAGGGCTTG	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"ATPases / P-type"	13535	protein-coding gene	gene with protein product	"aminophospholipid translocase ATP8B3", "potential phospholipid-transporting ATPase IK"	605866	"ATPase, Class I, type 8B, member 3", "ATPase, class I, type 8B, member 3"			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.59C>A	19.37:g.1811677G>T	ENSP00000311336:p.Pro20His	Somatic	36	0		WXS	Illumina HiSeq		29	10	NM_138813	0	0	0	0	0	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	c	3.042	-0.197318	0.06259	.	.	ENSG00000130270	ENST00000310127;ENST00000539485	T;T	0.75477	-0.94;-0.94	1.78	-3.56	0.04626	.	.	.	.	.	T	0.45637	0.1352	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13308	-1.0514	9	0.39692	T	0.17	.	1.204	0.01891	0.1366:0.3313:0.1985:0.3336	.	20	O60423	AT8B3_HUMAN	H	20	ENSP00000311336:P20H;ENSP00000443574:P20H	ENSP00000311336:P20H	P	-	2	0	ATP8B3	1762677	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.066000	0.03454	-1.603000	0.01597	-0.465000	0.05216	CCT	.		0.647	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		T	1811677	G	T	1811677	3	4	130	1	0	0	0	0	1	0	0	0	1197	1000	35	4	4003	4	ATP8B3	19	1811677	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	931734	1811677	57317306	192	11534											
NFIC	4782	ucsc.edu	37	chr19	3435161	3435161	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttactacacttcgcccagctCgcccacgagtagcagccgca	9	7	8	17	4	0	0	0	0	0	0	2	1	0	0	3	0	5	4	3	0	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:3435161C>T	ENST00000443272.2	+	6	965	c.914C>T	c.(913-915)tCg>tTg	p.S305L	NFIC_ENST00000341919.3_Missense_Mutation_p.S305L|NFIC_ENST00000586919.1_Missense_Mutation_p.S272L|NFIC_ENST00000589123.1_Missense_Mutation_p.S296L|NFIC_ENST00000346156.5_Missense_Mutation_p.S272L|NFIC_ENST00000395111.3_Missense_Mutation_p.S296L|NFIC_ENST00000590282.1_Missense_Mutation_p.S305L	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	305					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		TCGCCCAGCTCGCCCACGAGT	0.662																																					p.S305L													.	NFIC-226	0			c.C914T						.						28	24	25					19																	3435161		2200	4298	6498	SO:0001583	missense	4782	exon6			CCAGCTCGCCCAC	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.914C>T	19.37:g.3435161C>T	ENSP00000396843:p.Ser305Leu	Somatic	40	0		WXS	Illumina HiSeq		29	4	NM_001245004	0	0	42	42	0	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	37	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159672	0.78226	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.58506	0.33;0.33;0.33	4.69	3.64	0.41730	.	0.287773	0.33813	N	0.004531	T	0.46308	0.1386	L	0.50333	1.59	0.44402	D	0.997317	P;P;P;P;P	0.49862	0.716;0.929;0.668;0.531;0.531	B;B;B;B;B	0.37267	0.092;0.245;0.055;0.055;0.055	T	0.51616	-0.8683	10	0.40728	T	0.16	.	11.87	0.52515	0.0:0.9119:0.0:0.0881	.	305;305;296;305;296	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	L	296;296;272;305;305;305	ENSP00000378543:S296L;ENSP00000301935:S272L;ENSP00000342194:S305L	ENSP00000269778:S305L	S	+	2	0	NFIC	3386161	0.999000	0.42202	0.990000	0.47175	0.984000	0.73092	4.572000	0.60886	2.152000	0.67230	0.561000	0.74099	TCG	.		0.662	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3435161	C	T	3435161	3	4	130	1	0	0	0	0	1	0	0	0	10398	893	31	1	943	1	NFIC	19	3435161	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1623484	3435161	55693822	193	11535											
TRIP10	9322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	6743264	6743264	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aatggctttaaacagctggaGaatgtgagtttgcagaggta	13	11	13	4	0	0	3	0	1	0	2	0	4	0	3	0	3	3	5	0	3	5	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:6743264G>C	ENST00000313244.9	+	5	440	c.405G>C	c.(403-405)gaG>gaC	p.E135D	TRIP10_ENST00000313285.8_Missense_Mutation_p.E135D|TRIP10_ENST00000600428.1_Missense_Mutation_p.E27D|TRIP10_ENST00000596758.1_Missense_Mutation_p.E135D			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	135	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						AACAGCTGGAGAATGTGAGTT	0.582																																					p.E135D		.											.	TRIP10-228	0			c.G405C						.						53	55	54					19																	6743264		2203	4300	6503	SO:0001583	missense	9322	exon5			GCTGGAGAATGTG	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"Cdc42-interacting protein"	604504	"salt tolerator"	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.405G>C	19.37:g.6743264G>C	ENSP00000320117:p.Glu135Asp	Somatic	59	1		WXS	Illumina HiSeq	Phase_I	39	4	NM_004240	0	0	0	0	0	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	37		.	.	.	.	.	.	.	.	.	.	G	5.067	0.198081	0.09652	.	.	ENSG00000125733	ENST00000313285;ENST00000313244;ENST00000420690	T;T	0.17528	2.27;2.27	3.97	1.76	0.24704	.	0.279702	0.33309	N	0.005060	T	0.05914	0.0154	N	0.10760	0.04	0.37681	D	0.9235	B;P;B	0.39424	0.003;0.673;0.008	B;B;B	0.34536	0.019;0.185;0.012	T	0.43523	-0.9386	10	0.12103	T	0.63	-23.3165	6.6451	0.22931	0.2321:0.0:0.7679:0.0	.	135;135;135	G5E9U1;Q15642;Q15642-2	.;CIP4_HUMAN;.	D	135	ENSP00000320493:E135D;ENSP00000320117:E135D	ENSP00000320117:E135D	E	+	3	2	TRIP10	6694264	1.000000	0.71417	0.999000	0.59377	0.854000	0.48673	0.793000	0.26944	0.174000	0.19809	0.462000	0.41574	GAG	.		0.582	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			C	6743264	G	C	6743264	3	2	130	1	0	0	0	0	1	0	0	0	16587	933	33	4	423	4	TRIP10	19	6743264	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3308103	6743264	52385719	194	11536											
NR2F6	2063	broad.mit.edu	37	chr19	17355929	17355929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgctggcggcaccggggggcGaggccgagtcgtcctcggcc	3	4	19	15	7	0	0	0	0	0	0	3	2	1	0	4	7	0	2	4	7	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:17355929G>A	ENST00000291442.3	-	1	820	c.101C>T	c.(100-102)tCg>tTg	p.S34L	AC010646.3_ENST00000594059.1_Intron	NM_005234.3	NP_005225.2	P10588	NR2F6_HUMAN	nuclear receptor subfamily 2, group F, member 6	34					detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|entrainment of circadian clock by photoperiod (GO:0043153)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						ACCGGGGGGCGAGGCCGAGTC	0.771																																					p.S34L													.	NR2F6-186	0			c.C101T						.						6	7	6					19																	17355929		1976	3706	5682	SO:0001583	missense	2063	exon1			GGGGGCGAGGCCG	X12794	CCDS12352.1	19p13.11	2013-09-20			ENSG00000160113	ENSG00000160113		"Nuclear hormone receptors"	7977	protein-coding gene	gene with protein product		132880		ERBAL2		2905047	Standard	NM_005234		Approved	EAR-2	uc002nfq.3	P10588	OTTHUMG00000182728	ENST00000291442.3:c.101C>T	19.37:g.17355929G>A	ENSP00000291442:p.Ser34Leu	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_005234	0	0	0	0	0	B2RC68|Q5XGA0|Q6P586|Q9BUE8	Missense_Mutation	SNP	ENST00000291442.3	37	CCDS12352.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144482	0.57044	.	.	ENSG00000160113	ENST00000291442	D	0.93307	-3.2	2.97	2.97	0.34412	.	0.363501	0.24793	N	0.035544	D	0.86397	0.5923	L	0.46157	1.445	0.80722	D	1	P	0.49253	0.921	B	0.24974	0.057	D	0.87361	0.2344	10	0.59425	D	0.04	.	11.8123	0.52189	0.0:0.0:1.0:0.0	.	34	P10588	NR2F6_HUMAN	L	34	ENSP00000291442:S34L	ENSP00000291442:S34L	S	-	2	0	NR2F6	17216929	1.000000	0.71417	0.966000	0.40874	0.092000	0.18411	3.656000	0.54467	1.686000	0.51046	0.298000	0.19748	TCG	.		0.771	NR2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463325.1			A	17355929	G	A	17355929	3	1	130	1	0	0	0	0	1	0	0	0	10655	1059	37	1	1129	1	NR2F6	19	17355929	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10612665	17355929	41773054	195	11537											
WDR88	126248	hgsc.bcm.edu	37	chr19	33635808	33635808	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggcccaaagctcctgttgTagagtgcagcatcaccggcg	9	7	12	13	2	1	1	1	0	0	1	2	1	2	1	3	2	3	5	3	2	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:33635808T>C	ENST00000355868.3	+	3	522	c.446T>C	c.(445-447)gTa>gCa	p.V149A	WDR88_ENST00000361680.2_Missense_Mutation_p.V149A|WDR88_ENST00000592765.1_Missense_Mutation_p.V149A	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	149										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					GCTCCTGTTGTAGAGTGCAGC	0.552																																					p.V149A		.											.	WDR88-154	0			c.T446C						.						117	91	100					19																	33635808		2203	4300	6503	SO:0001583	missense	126248	exon3			CTGTTGTAGAGTG	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"WD repeat domain containing"	26999	protein-coding gene	gene with protein product			"PQQ repeat and WD repeat domain containing"	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.446T>C	19.37:g.33635808T>C	ENSP00000348129:p.Val149Ala	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_173479	0	0	0	0	0	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	T	2.527	-0.309490	0.05458	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.39406	1.08;1.08	5.09	1.36	0.22044	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	44.246300	0.00166	N	0.000000	T	0.28928	0.0718	N	0.24115	0.695	0.09310	N	1	B	0.22480	0.07	B	0.16722	0.016	T	0.11891	-1.0569	10	0.16896	T	0.51	.	5.9601	0.19295	0.0:0.4463:0.0:0.5537	.	149	Q6ZMY6	WDR88_HUMAN	A	149	ENSP00000348129:V149A;ENSP00000355148:V149A	ENSP00000348129:V149A	V	+	2	0	WDR88	38327648	0.001000	0.12720	0.026000	0.17262	0.171000	0.22731	0.476000	0.22180	0.366000	0.24427	0.459000	0.35465	GTA	.		0.552	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		C	33635808	T	C	33635808	3	2	130	1	0	0	0	0	1	0	0	0	17368	1638	57	3	456	3	WDR88	19	33635808	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	16279879	33635808	25493175	196	11538											
NCCRP1	342897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39691364	39691364	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcggcggacacgggtgaccGactcctccgtgtctgtgcag	5	8	15	13	5	1	1	0	1	1	0	3	3	3	2	3	3	2	1	3	3	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:39691364G>A	ENST00000339852.4	+	6	818	c.796G>A	c.(796-798)Gac>Aac	p.D266N		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	266	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						ACGGGTGACCGACTCCTCCGT	0.617																																					p.D266N	Melanoma(107;1207 1556 14956 29427 52130)	.											.	NCCRP1-91	0			c.G796A						.						152	148	149					19																	39691364		2203	4300	6503	SO:0001583	missense	342897	exon6			GTGACCGACTCCT	AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.796G>A	19.37:g.39691364G>A	ENSP00000342137:p.Asp266Asn	Somatic	385	0		WXS	Illumina HiSeq	Phase_I	303	60	NM_001001414	0	0	442	553	111	Q6NVV5	Missense_Mutation	SNP	ENST00000339852.4	37	CCDS12529.1	.	.	.	.	.	.	.	.	.	.	G	9.500	1.103019	0.20632	.	.	ENSG00000188505	ENST00000339852	T	0.24350	1.86	4.96	4.96	0.65561	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	0.050217	0.85682	D	0.000000	T	0.22898	0.0553	N	0.11201	0.11	0.50313	D	0.999862	D	0.61697	0.99	P	0.57057	0.812	T	0.02728	-1.1118	10	0.07030	T	0.85	-30.2767	15.693	0.77469	0.0:0.0:1.0:0.0	.	266	Q6ZVX7	NCRP1_HUMAN	N	266	ENSP00000342137:D266N	ENSP00000342137:D266N	D	+	1	0	NCCRP1	44383204	1.000000	0.71417	0.955000	0.39395	0.144000	0.21451	4.099000	0.57755	2.319000	0.78375	0.484000	0.47621	GAC	.		0.617	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463829.1	NM_001001414		A	39691364	G	A	39691364	3	1	130	1	0	0	0	0	1	0	0	0	10239	1058	37	1	818	1	NCCRP1	19	39691364	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	6055556	39691364	19437619	197	11539											
AKT2	208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40741033	40741033	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtcgacctcggacgtgacctGaggtttgaagggtggcagga	8	8	17	8	3	0	3	0	3	0	0	2	6	0	5	2	5	0	2	2	5	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:40741033G>C	ENST00000392038.2	-	13	1583	c.1285C>G	c.(1285-1287)Cag>Gag	p.Q429E	AKT2_ENST00000579047.1_Missense_Mutation_p.Q367E|AKT2_ENST00000424901.1_Missense_Mutation_p.Q429E|AKT2_ENST00000311278.6_Missense_Mutation_p.Q386E	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	429	AGC-kinase C-terminal.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			GACGTGACCTGAGGTTTGAAG	0.617			A		"ovarian, pancreatic "																																p.Q429E		.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2-978	0			c.C1285G						.						131	117	122					19																	40741033		2203	4300	6503	SO:0001583	missense	208	exon13			TGACCTGAGGTTT	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"Pleckstrin homology (PH) domain containing"	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.1285C>G	19.37:g.40741033G>C	ENSP00000375892:p.Gln429Glu	Somatic	108	1		WXS	Illumina HiSeq	Phase_I	82	38	NM_001626	0	0	71	154	83	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	37	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.720332	0.48728	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278	T;T;T	0.56611	0.45;0.45;0.45	5.39	4.36	0.52297	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.51941	0.1704	M	0.69823	2.125	0.80722	D	1	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.15870	0.001;0.014;0.006	T	0.52162	-0.8612	10	0.41790	T	0.15	.	12.9122	0.58187	0.0788:0.0:0.9212:0.0	.	367;386;429	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	E	429;330;429;386	ENSP00000375892:Q429E;ENSP00000399532:Q429E;ENSP00000309428:Q386E	ENSP00000309428:Q386E	Q	-	1	0	AKT2	45432873	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.329000	0.96413	1.513000	0.48852	0.655000	0.94253	CAG	.		0.617	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		C	40741033	G	C	40741033	3	2	130	1	0	0	0	0	1	0	0	0	480	1299	45	4	168	4	AKT2	19	40741033	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1049669	40741033	18387950	198	11540											
C19orf47	126526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40832303	40832303	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtggtgcctttgggcatgTtgatgacgtacttcccctcc	4	14	12	11	1	0	2	0	2	0	0	2	2	2	2	4	2	2	3	4	2	1	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:40832303T>C	ENST00000582783.1	-	7	653	c.641A>G	c.(640-642)aAc>aGc	p.N214S	C19orf47_ENST00000392035.2_Missense_Mutation_p.N147S	NM_001256440.1	NP_001243369.1	Q8N9M1	CS047_HUMAN	chromosome 19 open reading frame 47	214						nucleus (GO:0005634)				endometrium(5)|kidney(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20			Lung(22;0.000636)			TTTGGGCATGTTGATGACGTA	0.662																																					p.N214S		.											.	C19orf47-92	0			c.A641G						.						132	102	112					19																	40832303		2203	4300	6503	SO:0001583	missense	126526	exon7			GGCATGTTGATGA	AL834131	CCDS58662.1	19q13.2	2012-07-20			ENSG00000160392	ENSG00000160392			26723	protein-coding gene	gene with protein product						12477932	Standard	NM_001256440		Approved	FLJ36888	uc002oni.5	Q8N9M1	OTTHUMG00000179028	ENST00000582783.1:c.641A>G	19.37:g.40832303T>C	ENSP00000463159:p.Asn214Ser	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	55	26	NM_001256440	0	0	7	12	5	Q8IZ33|Q8N0V9	Missense_Mutation	SNP	ENST00000582783.1	37	CCDS58662.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356248	0.61293	.	.	ENSG00000160392	ENST00000357884;ENST00000392035	.	.	.	5.54	4.44	0.53790	.	0.086607	0.85682	D	0.000000	T	0.51329	0.1668	L	0.59436	1.845	0.50632	D	0.999884	B	0.32753	0.383	B	0.33521	0.165	T	0.46803	-0.9165	9	0.14656	T	0.56	1.1855	13.0399	0.58893	0.0:0.0:0.1429:0.8571	.	214	Q8N9M1	CS047_HUMAN	S	214;147	.	ENSP00000350556:N214S	N	-	2	0	C19orf47	45524143	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.596000	0.54024	2.115000	0.64714	0.379000	0.24179	AAC	.		0.662	C19orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444488.1	NM_178830		C	40832303	T	C	40832303	3	2	130	1	0	0	0	0	1	0	0	0	1936	1725	60	3	639	3	C19orf47	19	40832303	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	91270	40832303	18296680	199	11541											
LYPD3	27076	hgsc.bcm.edu	37	chr19	43967362	43967362	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcacgaccggcggcgatgTaccctggcacgcctcccggc	5	5	13	18	6	1	0	1	0	0	0	2	2	2	0	4	4	1	3	4	4	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:43967362T>C	ENST00000244333.3	-	4	548	c.460A>G	c.(460-462)Aca>Gca	p.T154A		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	154	UPAR/Ly6 2.				cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				GGCGGCGATGTACCCTGGCAC	0.647																																					p.T154A		.											.	LYPD3-91	0			c.A460G						.						73	65	68					19																	43967362		2203	4300	6503	SO:0001583	missense	27076	exon4			GCGATGTACCCTG	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.460A>G	19.37:g.43967362T>C	ENSP00000244333:p.Thr154Ala	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	99	7	NM_014400	1	1	832	834	0	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	.	.	.	.	.	.	.	.	.	.	T	4.370	0.068265	0.08436	.	.	ENSG00000124466	ENST00000244333	T	0.69435	-0.4	4.67	-1.43	0.08884	CD59 antigen (1);	1.302740	0.05157	N	0.497038	T	0.32763	0.0840	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.12400	-1.0549	10	0.10636	T	0.68	.	3.1389	0.06448	0.4169:0.1813:0.0:0.4018	.	154	O95274	LYPD3_HUMAN	A	154	ENSP00000244333:T154A	ENSP00000244333:T154A	T	-	1	0	LYPD3	48659202	0.000000	0.05858	0.000000	0.03702	0.485000	0.33311	-0.246000	0.08878	-0.637000	0.05516	0.374000	0.22700	ACA	.		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		C	43967362	T	C	43967362	3	2	130	1	0	0	0	0	1	0	0	0	9136	1638	57	3	588	3	LYPD3	19	43967362	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	3135059	43967362	15161621	200	11542											
ALDH16A1	126133	ucsc.edu	37	chr19	49969068	49969068	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgaagctccaggcccatcCgggattcgtctggcaacctc	7	7	10	17	3	1	0	0	0	1	0	5	2	3	1	5	3	2	2	5	3	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:49969068C>T	ENST00000293350.4	+	13	1805	c.1642C>T	c.(1642-1644)Cgg>Tgg	p.R548W	ALDH16A1_ENST00000455361.2_Missense_Mutation_p.R497W|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.R383W|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.R385W	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	548						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CAGGCCCATCCGGGATTCGTC	0.652																																					p.R548W													.	ALDH16A1-91	0			c.C1642T						.						38	41	40					19																	49969068		2203	4300	6503	SO:0001583	missense	126133	exon13			CCCATCCGGGATT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"Aldehyde dehydrogenases"	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1642C>T	19.37:g.49969068C>T	ENSP00000293350:p.Arg548Trp	Somatic	57	0		WXS	Illumina HiSeq		33	4	NM_153329	0	0	23	23	0	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	C	4.227	0.041032	0.08196	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	4.77	-1.69	0.08186	Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	1.480900	0.04153	N	0.321619	T	0.21962	0.0529	L	0.37800	1.135	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.20940	-1.0260	10	0.36615	T	0.2	-21.3384	3.6231	0.08103	0.2686:0.3861:0.0:0.3453	.	385;497;548	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	W	548;497;385;383	ENSP00000293350:R548W;ENSP00000410142:R497W;ENSP00000445088:R385W;ENSP00000398675:R383W	ENSP00000293350:R548W	R	+	1	2	ALDH16A1	54660880	0.000000	0.05858	0.070000	0.20053	0.014000	0.08584	-1.814000	0.01723	-0.156000	0.11079	-0.254000	0.11334	CGG	.		0.652	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		T	49969068	C	T	49969068	3	4	130	1	0	0	0	0	1	0	0	0	488	643	23	1	1692	1	ALDH16A1	19	49969068	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	6001706	49969068	9159915	201	11543											
KLK10	5655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	51518766	51518766	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcacactctttagggctcagGatagtgatgctggagcaggt	9	11	13	8	0	3	1	2	1	1	0	3	3	3	3	0	4	2	3	0	4	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:51518766G>T	ENST00000309958.3	-	5	803	c.585C>A	c.(583-585)atC>atA	p.I195I	KLK10_ENST00000391805.1_Silent_p.I195I|CTC-518B2.12_ENST00000596286.1_RNA|KLK10_ENST00000358789.3_Silent_p.I195I	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	195	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		TAGGGCTCAGGATAGTGATGC	0.567																																					p.I195I		.											.	KLK10-650	0			c.C585A						.						273	256	262					19																	51518766		2203	4300	6503	SO:0001819	synonymous_variant	5655	exon5			GCTCAGGATAGTG	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.585C>A	19.37:g.51518766G>T		Somatic	468	0		WXS	Illumina HiSeq	Phase_I	385	66	NM_145888	0	0	0	0	0	A6NC12|Q53YL3|Q99920|Q9GZW9	Silent	SNP	ENST00000309958.3	37	CCDS12817.1																																																																																			.		0.567	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		T	51518766	G	T	51518766	2	4	130	1	0	0	0	0	0	0	0	1	8419	1164	41	4		4	KLK10	19	51518766	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1549698	51518766	7610217	202	11544											
ZNF347	84671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53643875	53643875	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acactcattgcatttgtaagGtttttttccagtatggattg	9	18	8	6	0	1	0	1	0	0	0	2	1	2	1	1	2	1	4	1	2	2	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:53643875G>T	ENST00000334197.7	-	5	2274	c.2206C>A	c.(2206-2208)Cct>Act	p.P736T	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.P737T|ZNF347_ENST00000452676.2_Missense_Mutation_p.P737T	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	736					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CATTTGTAAGGTTTTTTTCCA	0.423																																					p.P737T	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.C2209A						.						167	155	159					19																	53643875		2203	4300	6503	SO:0001583	missense	84671	exon5			TGTAAGGTTTTTT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2206C>A	19.37:g.53643875G>T	ENSP00000334146:p.Pro736Thr	Somatic	232	0		WXS	Illumina HiSeq	Phase_I	172	28	NM_001172675	0	0	5	5	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.486058	0.44147	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.16897	2.31;2.31	2.64	-0.0406	0.13871	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36054	0.0953	M	0.76574	2.34	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.981	T	0.11036	-1.0604	9	0.87932	D	0	.	6.5531	0.22446	0.3119:0.0:0.6881:0.0	.	737;736	G5E9N4;Q96SE7	.;ZN347_HUMAN	T	736;737	ENSP00000334146:P736T;ENSP00000405218:P737T	ENSP00000334146:P736T	P	-	1	0	ZNF347	58335687	0.348000	0.24861	0.000000	0.03702	0.251000	0.25915	1.732000	0.38146	-0.074000	0.12820	0.655000	0.94253	CCT	.		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53643875	G	T	53643875	3	4	130	1	0	0	0	0	1	0	0	0	17893	1261	44	4	317	4	ZNF347	19	53643875	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2125109	53643875	5485108	203	11545											
MYADM	91663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54377552	54377552	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctatgccaccgcccttgttCtctggcccctctaccagttc	4	13	6	18	1	3	0	0	0	3	0	5	0	3	0	6	1	2	2	6	1	2	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:54377552C>T	ENST00000391769.2	+	3	1049	c.769C>T	c.(769-771)Ctc>Ttc	p.L257F	MYADM_ENST00000391768.2_Missense_Mutation_p.L257F|MYADM_ENST00000391771.1_Missense_Mutation_p.L257F|AC008440.5_ENST00000413496.2_RNA|MYADM_ENST00000391770.4_Missense_Mutation_p.L257F|MYADM_ENST00000336967.3_Missense_Mutation_p.L257F	NM_001020821.1	NP_001018657.1	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	257	MARVEL 2. {ECO:0000255|PROSITE- ProRule:PRU00581}.				establishment of endothelial barrier (GO:0061028)|membrane raft organization (GO:0031579)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of gene expression (GO:0010629)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of protein kinase C signaling (GO:0090038)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell migration (GO:0030335)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein targeting to plasma membrane (GO:0072661)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|ruffle (GO:0001726)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		CGCCCTTGTTCTCTGGCCCCT	0.622																																					p.L257F		.											.	MYADM-91	0			c.C769T						.						84	77	79					19																	54377552		2203	4300	6503	SO:0001583	missense	91663	exon3			CTTGTTCTCTGGC	AF087882	CCDS12866.1	19q13.33-q13.4	2004-07-23			ENSG00000179820	ENSG00000179820			7544	protein-coding gene	gene with protein product		609959				10733104, 12075932	Standard	NM_001020818		Approved		uc002qcl.3	Q96S97	OTTHUMG00000060775	ENST00000391769.2:c.769C>T	19.37:g.54377552C>T	ENSP00000375649:p.Leu257Phe	Somatic	146	1		WXS	Illumina HiSeq	Phase_I	103	23	NM_138373	0	0	4	4	0	B2RE58|Q542Z1|Q7Z507|Q8N9R4|Q96CS6|Q96SK9	Missense_Mutation	SNP	ENST00000391769.2	37	CCDS12866.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.957420	0.34565	.	.	ENSG00000179820	ENST00000336967;ENST00000391770;ENST00000439000;ENST00000391771;ENST00000415619;ENST00000391769;ENST00000391768	T;T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77;1.77	4.3	0.655	0.17839	Marvel (1);MARVEL-like domain (1);	0.516121	0.18617	N	0.135981	T	0.48187	0.1486	M	0.85542	2.76	0.44447	D	0.997374	D	0.71674	0.998	D	0.71656	0.974	T	0.45527	-0.9255	10	0.87932	D	0	-12.2374	7.6235	0.28200	0.472:0.3744:0.1536:0.0	.	257	Q96S97	MYADM_HUMAN	F	257;257;257;257;220;257;257	ENSP00000337222:L257F;ENSP00000375650:L257F;ENSP00000416919:L257F;ENSP00000375651:L257F;ENSP00000375649:L257F;ENSP00000375648:L257F	ENSP00000337222:L257F	L	+	1	0	MYADM	59069364	0.029000	0.19370	0.419000	0.26584	0.201000	0.24016	-0.708000	0.05035	0.027000	0.15297	0.305000	0.20034	CTC	.		0.622	MYADM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134337.1	NM_138373		T	54377552	C	T	54377552	3	4	130	1	0	0	0	0	1	0	0	0	10031	913	32	2	771	2	MYADM	19	54377552	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	733677	54377552	4751431	204	11546											
NLRP7	199713	broad.mit.edu	37	chr19	55450843	55450843	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cggaggatgtctccgtccagGaacagacggaggtcggactc	9	6	15	11	4	1	1	0	0	1	1	5	6	2	6	2	6	1	0	2	6	1	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:55450843G>A	ENST00000590030.1	-	3	1384	c.1344C>T	c.(1342-1344)ttC>ttT	p.F448F	NLRP7_ENST00000328092.5_Silent_p.F448F|NLRP7_ENST00000446217.1_Silent_p.F476F|NLRP7_ENST00000592784.1_Silent_p.F448F|NLRP7_ENST00000588756.1_Silent_p.F448F|NLRP7_ENST00000448121.2_Silent_p.F448F|NLRP7_ENST00000340844.2_Silent_p.F448F			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	448	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CTCCGTCCAGGAACAGACGGA	0.627																																					p.F448F													.	NLRP7-291	0			c.C1344T						.						35	32	33					19																	55450843		2203	4298	6501	SO:0001819	synonymous_variant	199713	exon4			GTCCAGGAACAGA	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"Nucleotide-binding domain and leucine rich repeat containing"	22947	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"	609661	"NACHT, leucine rich repeat and PYD containing 7"	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1344C>T	19.37:g.55450843G>A		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	46	6	NM_001127255	0	0	2	2	0	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			.		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55450843	G	A	55450843	2	1	130	1	0	0	0	0	0	0	0	1	10508	1165	41	2		2	NLRP7	19	55450843	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1073291	55450843	3678140	205	11547											
GALP	85569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56694579	56694579	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gtttgccaaaccagagattgGaggtaaagccaggaaacaca	16	6	11	8	0	0	1	0	0	0	1	0	4	0	3	3	3	4	2	3	3	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:56694579G>C	ENST00000357330.2	+	5	375	c.293G>C	c.(292-294)gGa>gCa	p.G98A	GALP_ENST00000440823.1_3'UTR	NM_033106.3	NP_149097.1	Q9UBC7	GALP_HUMAN	galanin-like peptide	98					behavioral response to starvation (GO:0042595)|defense response to bacterium (GO:0042742)|neuropeptide signaling pathway (GO:0007218)|regulation of appetite (GO:0032098)|response to insulin (GO:0032868)	extracellular region (GO:0005576)				lung(4)	4		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)		CCAGAGATTGGAGGTAAAGCC	0.507																																					p.G98A		.											.	GALP-90	0			c.G293C						.						94	88	90					19																	56694579		2203	4300	6503	SO:0001583	missense	85569	exon5			AGATTGGAGGTAA	AF188493	CCDS12940.1, CCDS46202.1	19q13.42	2013-02-26	2007-08-24			ENSG00000197487		"Endogenous ligands"	24840	protein-coding gene	gene with protein product		611178				10601261	Standard	NM_033106		Approved		uc002qmo.1	Q9UBC7		ENST00000357330.2:c.293G>C	19.37:g.56694579G>C	ENSP00000349884:p.Gly98Ala	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	96	32	NM_033106	0	0	0	0	0	A1KXL3	Missense_Mutation	SNP	ENST00000357330.2	37	CCDS12940.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.687848	0.29962	.	.	ENSG00000197487	ENST00000357330	T	0.60797	0.16	2.07	0.986	0.19784	.	.	.	.	.	T	0.35508	0.0934	L	0.32530	0.975	0.80722	D	1	B	0.33266	0.404	B	0.18561	0.022	T	0.07597	-1.0764	9	0.25106	T	0.35	-6.1554	6.4753	0.22033	0.0:0.3481:0.6519:0.0	.	98	Q9UBC7	GALP_HUMAN	A	98	ENSP00000349884:G98A	ENSP00000349884:G98A	G	+	2	0	GALP	61386391	0.945000	0.32115	0.166000	0.22797	0.024000	0.10985	0.450000	0.21762	0.410000	0.25675	0.591000	0.81541	GGA	.		0.507	GALP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457832.1	NM_033106		C	56694579	G	C	56694579	3	2	130	1	0	0	0	0	1	0	0	0	6246	1174	41	4	307	4	GALP	19	56694579	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1243736	56694579	2434404	206	11548											
USP29	57663	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57641187	57641187	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agtttttaggtcagtgtttaGaccagctgaaagaagacatg	13	12	11	5	0	1	4	1	1	0	3	1	4	1	4	1	1	1	3	1	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:57641187G>C	ENST00000254181.4	+	4	1598	c.1144G>C	c.(1144-1146)Gac>Cac	p.D382H	USP29_ENST00000598197.1_Missense_Mutation_p.D382H	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	382	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCAGTGTTTAGACCAGCTGAA	0.368																																					p.D382H		.											.	USP29-661	0			c.G1144C						.						58	58	58					19																	57641187		2203	4298	6501	SO:0001583	missense	57663	exon4			TGTTTAGACCAGC		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"Ubiquitin-specific peptidases"	18563	protein-coding gene	gene with protein product		609546	"ubiquitin specific protease 29"			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1144G>C	19.37:g.57641187G>C	ENSP00000254181:p.Asp382His	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	106	42	NM_020903	0	0	0	0	0		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588551	0.46110	.	.	ENSG00000131864	ENST00000254181	T	0.78595	-1.19	2.44	2.44	0.29823	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.617223	0.13416	U	0.389500	D	0.87688	0.6240	M	0.85630	2.765	0.29467	N	0.857365	D	0.89917	1.0	D	0.76575	0.988	T	0.80843	-0.1201	10	0.87932	D	0	-5.0112	11.0121	0.47669	0.0:0.0:1.0:0.0	.	382	Q9HBJ7	UBP29_HUMAN	H	382	ENSP00000254181:D382H	ENSP00000254181:D382H	D	+	1	0	USP29	62332999	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.330000	0.52068	1.646000	0.50622	0.591000	0.81541	GAC	.		0.368	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			C	57641187	G	C	57641187	3	2	130	1	0	0	0	0	1	0	0	0	17092	942	33	4	1146	4	USP29	19	57641187	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	946608	57641187	1487796	207	11549											
C20orf46	55321	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	1161561	1161561	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttctccaccagggcctggccCccatccccattgagctgtct	5	10	8	18	0	2	1	0	1	2	0	4	1	3	1	7	2	1	1	7	2	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:1161561C>T	ENST00000381894.3	-	2	1373	c.702G>A	c.(700-702)ggG>ggA	p.G234G	TMEM74B_ENST00000481747.1_5'Flank	NM_018354.1	NP_060824.1	Q9NUR3	TM74B_HUMAN	transmembrane protein 74B	234						integral component of membrane (GO:0016021)											GGGCCTGGCCCCCATCCCCAT	0.592																																					p.G234G													.	.	0			c.G702A						.						80	73	75					20																	1161561		2203	4300	6503	SO:0001819	synonymous_variant	55321	exon2			CTGGCCCCCATCC	AK002052	CCDS13011.1	20p13	2011-11-23	2011-11-23	2011-11-23	ENSG00000125895	ENSG00000125895			15893	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 46"	C20orf46			Standard	XM_005260748		Approved	FLJ11190	uc002weq.1	Q9NUR3	OTTHUMG00000031655	ENST00000381894.3:c.702G>A	20.37:g.1161561C>T		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	99	12	NM_018354	0	0	6	12	6	D3DVW5	Silent	SNP	ENST00000381894.3	37	CCDS13011.1																																																																																			.		0.592	TMEM74B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077496.2	NM_018354		T	1161561	C	T	1161561	2	4	130	1	0	0	0	0	0	0	0	1	2119	610	22	2		2	C20orf46	20	1161561	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08		1161561	61863959	208	11550											
CHD6	84181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	40033767	40033767	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtggttgccatgggtggactGaggagtcccccaacaccaaa	10	7	13	11	0	0	1	0	1	0	0	1	3	1	3	4	4	2	1	4	4	2	1	rs559201396		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:40033767G>A	ENST00000373233.3	-	37	7791	c.7614C>T	c.(7612-7614)ctC>ctT	p.L2538L	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2538					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TGGGTGGACTGAGGAGTCCCC	0.557																																					p.L2538L		.											.	CHD6-238	0			c.C7614T						.						90	83	85					20																	40033767		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon37			TGGACTGAGGAGT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.7614C>T	20.37:g.40033767G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	156	23	NM_032221	0	0	19	19	0	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	37	CCDS13317.1																																																																																			.		0.557	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40033767	G	A	40033767	2	1	130	1	0	0	0	0	0	0	0	1	3335	1277	45	2		2	CHD6	20	40033767	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	38872206	40033767	22991753	209	11551											
CHD6	84181	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	40050320	40050320	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttcattttcaagggactctGaagtcctactcatttgagaa	11	14	8	8	0	4	2	3	2	1	1	5	4	5	3	1	1	1	1	1	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:40050320G>A	ENST00000373233.3	-	31	5132	c.4955C>T	c.(4954-4956)tCa>tTa	p.S1652L		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1652					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AAGGGACTCTGAAGTCCTACT	0.398																																					p.S1652L													.	CHD6-238	0			c.C4955T						.						59	61	60					20																	40050320		2203	4300	6503	SO:0001583	missense	84181	exon31			GACTCTGAAGTCC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.4955C>T	20.37:g.40050320G>A	ENSP00000362330:p.Ser1652Leu	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	75	16	NM_032221	0	0	7	7	0	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	G	11.57	1.677648	0.29783	.	.	ENSG00000124177	ENST00000373233	T	0.70164	-0.46	6.17	4.2	0.49525	.	0.656538	0.13852	N	0.358262	T	0.48003	0.1476	L	0.27053	0.805	0.58432	D	0.999999	B	0.02656	0.0	B	0.08055	0.003	T	0.41070	-0.9529	10	0.23891	T	0.37	-2.5172	4.8034	0.13308	0.0851:0.301:0.5012:0.1128	.	1652	Q8TD26	CHD6_HUMAN	L	1652	ENSP00000362330:S1652L	ENSP00000362330:S1652L	S	-	2	0	CHD6	39483734	0.819000	0.29175	1.000000	0.80357	0.984000	0.73092	1.588000	0.36633	1.633000	0.50488	0.655000	0.94253	TCA	.		0.398	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40050320	G	A	40050320	3	1	130	1	0	0	0	0	1	0	0	0	3335	1294	45	2	3220	2	CHD6	20	40050320	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	16553	40050320	22975200	210	11552											
PTPN1	5770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49195155	49195155	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctgtctggctgataccTgcctcttgctggtaaggagg	5	13	12	11	0	3	1	0	1	3	0	3	2	3	2	3	4	3	3	3	4	2	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:49195155T>G	ENST00000371621.3	+	6	865	c.691T>G	c.(691-693)Tgc>Ggc	p.C231G	PTPN1_ENST00000541713.1_Missense_Mutation_p.C158G|RP4-530I15.9_ENST00000431019.1_RNA	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	231	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	GGCTGATACCTGCCTCTTGCT	0.597																																					p.C231G		.											.	PTPN1-1082	0			c.T691G						.						47	48	48					20																	49195155		2203	4300	6503	SO:0001583	missense	5770	exon6			GATACCTGCCTCT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.691T>G	20.37:g.49195155T>G	ENSP00000360683:p.Cys231Gly	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	56	18	NM_002827	0	0	0	0	0	Q5TGD8|Q9BQV9|Q9NQQ4	Missense_Mutation	SNP	ENST00000371621.3	37	CCDS13430.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.457273	0.84317	.	.	ENSG00000196396	ENST00000371621;ENST00000541713	D;D	0.83250	-1.7;-1.7	5.24	5.24	0.73138	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.91408	0.7289	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92757	0.6221	10	0.87932	D	0	.	15.139	0.72595	0.0:0.0:0.0:1.0	.	231	P18031	PTN1_HUMAN	G	231;158	ENSP00000360683:C231G;ENSP00000437732:C158G	ENSP00000360683:C231G	C	+	1	0	PTPN1	48628562	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	7.977000	0.88081	1.979000	0.57680	0.379000	0.24179	TGC	.		0.597	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2			G	49195155	T	G	49195155	3	3	130	1	0	0	0	0	1	0	0	0	12809	1580	55	5	713	5	PTPN1	20	49195155	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	9144835	49195155	13830365	211	11553											
HRH3	11255	broad.mit.edu	37	chr20	60791561	60791561	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctcagcgcctacggccGcctcacccaccccatacctg	6	5	8	22	4	2	0	2	0	0	0	2	0	2	0	8	2	3	0	8	2	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:60791561G>A	ENST00000340177.5	-	3	1123	c.839C>T	c.(838-840)gCg>gTg	p.A280V	HRH3_ENST00000317393.6_Missense_Mutation_p.A280V	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	280			A -> V (in one Shy-Drager syndrome patient; rare variant with unknown pathological significance). {ECO:0000269|PubMed:11956964}.		brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	GCCTACGGCCGCCTCACCCAC	0.756																																					p.A280V													.	HRH3-90	0			c.C839T						.						4	5	5					20																	60791561		1932	3885	5817	SO:0001583	missense	11255	exon3			ACGGCCGCCTCAC	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"GPCR / Class A : Histamine receptors"	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.839C>T	20.37:g.60791561G>A	ENSP00000342560:p.Ala280Val	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	11	7	NM_007232	0	0	0	0	0	Q4QRI7|Q9GZX2|Q9H4K8	Missense_Mutation	SNP	ENST00000340177.5	37	CCDS13493.1	.	.	.	.	.	.	.	.	.	.	G	2.089	-0.408938	0.04799	.	.	ENSG00000101180	ENST00000340177;ENST00000317393;ENST00000370797	T;T	0.67171	-0.22;-0.25	3.29	-2.86	0.05717	GPCR, rhodopsin-like superfamily (1);	0.819050	0.10671	U	0.647521	T	0.51958	0.1705	L	0.54323	1.7	0.09310	N	1	B;B	0.13594	0.007;0.008	B;B	0.10450	0.003;0.005	T	0.37126	-0.9719	10	0.28530	T	0.3	-9.5065	3.3454	0.07133	0.2806:0.0:0.4203:0.2991	.	280;280	Q9Y5N1-2;Q9Y5N1	.;HRH3_HUMAN	V	280;280;250	ENSP00000342560:A280V;ENSP00000321482:A280V	ENSP00000321482:A280V	A	-	2	0	HRH3	60224956	0.000000	0.05858	0.005000	0.12908	0.076000	0.17211	-0.457000	0.06745	-0.559000	0.06110	0.205000	0.17691	GCG	.		0.756	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232		A	60791561	G	A	60791561	3	1	130	1	0	0	0	0	1	0	0	0	7378	1087	38	1	502	1	HRH3	20	60791561	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	11596406	60791561	2233959	212	11554											
DIP2A	23181	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47978259	47978259	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggcctgccggcccgcgccGtaagcaccacgttcgggtgc	4	6	15	16	6	0	0	0	0	0	0	1	0	0	0	5	3	3	3	5	3	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr21:47978259G>A	ENST00000417564.2	+	32	3943	c.3922G>A	c.(3922-3924)Gta>Ata	p.V1308I	DIP2A_ENST00000400274.1_Missense_Mutation_p.V1304I|DIP2A_ENST00000318711.7_Missense_Mutation_p.V1309I			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1308					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GGCCCGCGCCGTAAGCACCAC	0.657																																					p.V1308I													.	DIP2A-24	0			c.G3922A						.						14	19	17					21																	47978259		2050	4184	6234	SO:0001583	missense	23181	exon32			CGCGCCGTAAGCA	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"chromosome 21 open reading frame 106"	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.3922G>A	21.37:g.47978259G>A	ENSP00000392066:p.Val1308Ile	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	24	7	NM_015151	0	0	8	12	4	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.832722	0.91036	.	.	ENSG00000160305	ENST00000400274;ENST00000318711;ENST00000417564	T;T;T	0.38887	1.11;1.11;1.11	5.2	5.2	0.72013	AMP-dependent synthetase/ligase (1);	0.000000	0.64402	D	0.000001	T	0.56202	0.1969	L	0.52011	1.625	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.984	D;D;D	0.87578	0.998;0.993;0.938	T	0.47649	-0.9101	10	0.08599	T	0.76	-22.8966	17.7235	0.88359	0.0:0.0:1.0:0.0	.	1309;99;1308	E9PER1;Q9NSX6;Q14689	.;.;DIP2A_HUMAN	I	1304;1309;1308	ENSP00000383133:V1304I;ENSP00000323633:V1309I;ENSP00000392066:V1308I	ENSP00000323633:V1309I	V	+	1	0	DIP2A	46802687	1.000000	0.71417	0.986000	0.45419	0.838000	0.47535	9.680000	0.98651	2.430000	0.82344	0.557000	0.71058	GTA	.		0.657	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		A	47978259	G	A	47978259	3	1	130	1	0	0	0	0	1	0	0	0	4538	1145	40	1	4161	1	DIP2A	21	47978259	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		47978259	151636	213	11555											
SERPIND1	3053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	21140297	21140297	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccttttctgtctagaactcGagaagtgcttctgccgaaat	9	14	8	10	2	3	2	0	0	3	2	5	4	4	2	2	0	3	1	2	0	4	4	rs368023291		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:21140297G>A	ENST00000215727.5	+	4	1452	c.1169G>A	c.(1168-1170)cGa>cAa	p.R390Q	PI4KA_ENST00000572273.1_Intron|PI4KA_ENST00000255882.6_Intron|PI4KA_ENST00000466162.1_Intron|SERPIND1_ENST00000406799.1_Missense_Mutation_p.R390Q	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	390					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	TCTAGAACTCGAGAAGTGCTT	0.423																																					p.R390Q		.											.	SERPIND1-414	0			c.G1169A						.	G	GLN/ARG,	0,4406		0,0,2203	130	134	132		1169,	5.3	1	22		132	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	43,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	390/500,	21140297	1,13005	2203	4300	6503	SO:0001583	missense	3053	exon4			GAACTCGAGAAGT	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"Serine (or cysteine) peptidase inhibitors"	4838	protein-coding gene	gene with protein product	"heparin cofactor II"	142360	"serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.1169G>A	22.37:g.21140297G>A	ENSP00000215727:p.Arg390Gln	Somatic	249	0		WXS	Illumina HiSeq	Phase_I	187	20	NM_000185	0	0	0	0	0	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	37	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164332	0.94727	0.0	1.16E-4	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.87650	-2.28;-2.28	5.28	5.28	0.74379	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.93032	0.7782	M	0.73962	2.25	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66979	0.948;0.948	D	0.92954	0.6383	10	0.56958	D	0.05	.	19.0957	0.93249	0.0:0.0:1.0:0.0	.	390;390	Q8IVC0;P05546	.;HEP2_HUMAN	Q	390	ENSP00000215727:R390Q;ENSP00000384050:R390Q	ENSP00000215727:R390Q	R	+	2	0	SERPIND1	19470297	1.000000	0.71417	0.988000	0.46212	0.855000	0.48748	8.835000	0.92100	2.755000	0.94549	0.655000	0.94253	CGA	.		0.423	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21140297	G	A	21140297	3	1	130	1	0	0	0	0	1	0	0	0	14142	1058	37	1	1179	1	SERPIND1	22	21140297	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		21140297	30164269	214	11556											
SERPIND1	3053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	21140328	21140328	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgccgaaattcaagctggaGaagaactacaatctagtgga	15	8	10	8	1	2	2	1	0	1	2	2	5	2	3	1	2	4	1	1	2	7	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:21140328G>A	ENST00000215727.5	+	4	1483	c.1200G>A	c.(1198-1200)gaG>gaA	p.E400E	PI4KA_ENST00000572273.1_Intron|PI4KA_ENST00000255882.6_Intron|PI4KA_ENST00000466162.1_Intron|SERPIND1_ENST00000406799.1_Silent_p.E400E	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	400					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	TCAAGCTGGAGAAGAACTACA	0.448																																					p.E400E		.											.	SERPIND1-414	0			c.G1200A						.						171	164	166					22																	21140328		2203	4300	6503	SO:0001819	synonymous_variant	3053	exon4			GCTGGAGAAGAAC	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"Serine (or cysteine) peptidase inhibitors"	4838	protein-coding gene	gene with protein product	"heparin cofactor II"	142360	"serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.1200G>A	22.37:g.21140328G>A		Somatic	254	0		WXS	Illumina HiSeq	Phase_I	199	24	NM_000185	0	0	1	2	1	B2RAI1|D3DX34|Q6IBZ5	Silent	SNP	ENST00000215727.5	37	CCDS13783.1																																																																																			.		0.448	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21140328	G	A	21140328	2	1	130	1	0	0	0	0	0	0	0	1	14142	933	33	2		2	SERPIND1	22	21140328	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	31	21140328	30164238	215	11557											
SEZ6L	23544	broad.mit.edu	37	chr22	26702084	26702084	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagctgcacctgcactttgaGaggctgttgctgcatgacaa	10	10	11	10	0	0	2	0	2	0	1	0	3	0	2	1	1	5	7	1	1	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:26702084G>A	ENST00000248933.6	+	6	1583	c.1488G>A	c.(1486-1488)gaG>gaA	p.E496E	SEZ6L_ENST00000529632.2_Silent_p.E496E|SEZ6L_ENST00000343706.4_Silent_p.E496E|SEZ6L_ENST00000404234.3_Silent_p.E496E|SEZ6L_ENST00000360929.3_Silent_p.E496E|SEZ6L_ENST00000402979.1_Silent_p.E269E|SEZ6L_ENST00000403121.1_Silent_p.E269E			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	496	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TGCACTTTGAGAGGCTGTTGC	0.517																																					p.E496E													.	SEZ6L-95	0			c.G1488A						.						58	56	57					22																	26702084		2203	4300	6503	SO:0001819	synonymous_variant	23544	exon6			CTTTGAGAGGCTG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1488G>A	22.37:g.26702084G>A		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	81	5	NM_021115	0	0	0	0	0	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			.		0.517	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26702084	G	A	26702084	2	1	130	1	0	0	0	0	0	0	0	1	14175	933	33	2		2	SEZ6L	22	26702084	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	5561756	26702084	24602482	216	11558											
MCM5	4174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	35806777	35806777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctgggaacagggttaccAtcatgggcatctactccatc	9	10	9	13	0	2	0	1	0	1	0	5	1	4	1	3	3	3	2	3	3	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:35806777A>G	ENST00000216122.4	+	7	947	c.793A>G	c.(793-795)Atc>Gtc	p.I265V	MCM5_ENST00000382011.5_Missense_Mutation_p.I222V	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	265					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						CAGGGTTACCATCATGGGCAT	0.557																																					p.I265V		.											.	MCM5-228	0			c.A793G						.						166	144	151					22																	35806777		2203	4300	6503	SO:0001583	missense	4174	exon7			GTTACCATCATGG		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.793A>G	22.37:g.35806777A>G	ENSP00000216122:p.Ile265Val	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	176	54	NM_006739	0	0	24	50	26	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	37	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	A	7.703	0.693600	0.15039	.	.	ENSG00000100297	ENST00000216122;ENST00000382011;ENST00000444582;ENST00000444778	T;T;T	0.03413	3.94;3.94;3.94	5.32	5.32	0.75619	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.046124	0.85682	D	0.000000	T	0.02727	0.0082	N	0.11789	0.175	0.58432	D	0.999999	B;B;B;B	0.11235	0.004;0.004;0.004;0.004	B;B;B;B	0.17979	0.009;0.009;0.02;0.009	T	0.48115	-0.9063	10	0.08837	T	0.75	-32.0355	15.5601	0.76237	1.0:0.0:0.0:0.0	.	265;265;222;265	B1AHB0;Q53FG5;B1AHB1;P33992	.;.;.;MCM5_HUMAN	V	265;222;174;122	ENSP00000216122:I265V;ENSP00000371441:I222V;ENSP00000408705:I122V	ENSP00000216122:I265V	I	+	1	0	MCM5	34136777	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.001000	0.57046	2.142000	0.66516	0.459000	0.35465	ATC	.		0.557	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			G	35806777	A	G	35806777	3	3	130	1	0	0	0	0	1	0	0	0	9415	217	8	3	815	3	MCM5	22	35806777	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	9104693	35806777	15497789	217	11559											
MYH9	4627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	36696256	36696256	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cgcctcggtggtcaccttctCcagctgcagcttctgccggg	3	10	12	16	3	3	0	1	0	2	0	5	0	3	0	4	3	4	3	4	3	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:36696256C>G	ENST00000216181.5	-	23	3123	c.2893G>C	c.(2893-2895)Gag>Cag	p.E965Q		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	965					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GTCACCTTCTCCAGCTGCAGC	0.632			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.E965Q		.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9-292	0			c.G2893C						.						76	71	73					22																	36696256		2203	4300	6503	SO:0001583	missense	4627	exon23	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTTCTCCAGCTG		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.2893G>C	22.37:g.36696256C>G	ENSP00000216181:p.Glu965Gln	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	113	50	NM_002473	0	0	253	445	192	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	35	5.458931	0.96240	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	D	0.92911	-3.13	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.97517	0.9187	H	0.96889	3.9	0.80722	D	1	D	0.62365	0.991	D	0.65773	0.938	D	0.98548	1.0635	10	0.87932	D	0	.	19.3857	0.94555	0.0:1.0:0.0:0.0	.	965	P35579	MYH9_HUMAN	Q	829;965	ENSP00000216181:E965Q	ENSP00000216181:E965Q	E	-	1	0	MYH9	35026202	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.781000	0.85668	2.665000	0.90641	0.655000	0.94253	GAG	.		0.632	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		G	36696256	C	G	36696256	3	3	130	1	0	0	0	0	1	0	0	0	10067	864	30	4	3065	4	MYH9	22	36696256	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	889479	36696256	14608310	218	11560											
HDAC10	83933	hgsc.bcm.edu;broad.mit.edu	37	chr22	50687534	50687534	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agccctccgtgcagtcacctCaaaggccagtgggagcagca	10	5	12	14	1	2	0	2	0	0	0	3	1	3	1	4	2	4	3	4	2	1	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:50687534C>G	ENST00000216271.5	-	8	1106	c.754G>C	c.(754-756)Gag>Cag	p.E252Q	HDAC10_ENST00000498366.1_5'UTR|MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000349505.4_Missense_Mutation_p.E252Q|HDAC10_ENST00000448072.1_Missense_Mutation_p.E252Q	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	252	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCAGTCACCTCAAAGGCCAGT	0.642																																					p.E252Q		.											.	HDAC10-226	0			c.G754C						.						41	26	31					22																	50687534		2190	4291	6481	SO:0001583	missense	83933	exon8			TCACCTCAAAGGC	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.754G>C	22.37:g.50687534C>G	ENSP00000216271:p.Glu252Gln	Somatic	19	1		WXS	Illumina HiSeq	Phase_I	19	9	NM_032019	0	0	1	2	1	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.847077	0.91277	.	.	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.69685	-0.42;-0.23;0.57	4.54	4.54	0.55810	Histone deacetylase domain (2);	0.062472	0.64402	D	0.000005	T	0.78033	0.4220	L	0.49455	1.56	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.96	D;D;P	0.85130	0.97;0.997;0.856	T	0.80369	-0.1411	10	0.66056	D	0.02	-26.0078	17.069	0.86568	0.0:1.0:0.0:0.0	.	252;252;252	Q969S8-2;C9J8B8;Q969S8	.;.;HDA10_HUMAN	Q	252	ENSP00000216271:E252Q;ENSP00000397542:E252Q;ENSP00000343540:E252Q	ENSP00000216271:E252Q	E	-	1	0	HDAC10	49029661	1.000000	0.71417	0.997000	0.53966	0.899000	0.52679	5.208000	0.65203	2.342000	0.79632	0.561000	0.74099	GAG	.		0.642	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019		G	50687534	C	G	50687534	3	3	130	1	0	0	0	0	1	0	0	0	7026	835	29	4	1307	4	HDAC10	22	50687534	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	13991278	50687534	617032	219	11561											
MAOB	4129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	43655117	43655117	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcactcacttgaccagatcCgcccacaaatttcctctcct	9	11	3	18	1	3	2	2	1	1	1	6	2	5	2	5	0	0	0	5	0	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:43655117C>T	ENST00000378069.4	-	7	784	c.637G>A	c.(637-639)Gga>Aga	p.G213R	MAOB_ENST00000536181.1_Missense_Mutation_p.G197R|MAOB_ENST00000487544.1_5'Flank|MAOB_ENST00000538942.1_Missense_Mutation_p.G197R	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	213					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TGACCAGATCCGCCCACAAAT	0.458																																					p.G213R		.											.	MAOB-555	0			c.G637A						.						82	69	74					X																	43655117		2203	4300	6503	SO:0001583	missense	4129	exon7			CAGATCCGCCCAC		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.637G>A	X.37:g.43655117C>T	ENSP00000367309:p.Gly213Arg	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	125	46	NM_000898	0	0	0	4	4	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	37	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778441	0.90195	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	T;T;T	0.25085	1.82;1.82;1.82	5.42	5.42	0.78866	Amine oxidase (1);	0.000000	0.85682	D	0.000000	T	0.67306	0.2879	H	0.96861	3.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80054	-0.1543	10	0.87932	D	0	-15.4168	18.5254	0.90969	0.0:1.0:0.0:0.0	.	197;213	B7Z5H3;P27338	.;AOFB_HUMAN	R	213;197;197	ENSP00000367309:G213R;ENSP00000441613:G197R;ENSP00000442240:G197R	ENSP00000367309:G213R	G	-	1	0	MAOB	43540061	1.000000	0.71417	0.991000	0.47740	0.950000	0.60333	7.104000	0.77024	2.404000	0.81709	0.600000	0.82982	GGA	.		0.458	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43655117	C	T	43655117	3	4	130	1	0	0	0	0	1	0	0	0	9251	661	23	1	961	1	MAOB	23	43655117	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		43655117	111615443	220	11562											
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	44870205	44870205	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctttttcccttcctttacaGaatgctgcctttttatatgg	6	20	5	10	0	1	1	0	0	1	1	3	1	3	1	3	1	3	1	3	1	4	9			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:44870205G>C	ENST00000377967.4	+	5	425		c.e5-1		KDM6A_ENST00000543216.1_Splice_Site|KDM6A_ENST00000382899.4_Splice_Site|KDM6A_ENST00000536777.1_Splice_Site	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A						canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0(10)|p.0?(6)|p.?(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TTCCTTTACAGAATGCTGCCT	0.299			"D, N, F, S"		"renal, oesophageal SCC, MM"																																.	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	17	No detectable mRNA/protein(10)|Whole gene deletion(6)|Unknown(1)	haematopoietic_and_lymphoid_tissue(11)|oesophagus(2)|breast(2)|pancreas(2)	c.385-1G>C						.						121	102	108					X																	44870205		2203	4299	6502	SO:0001630	splice_region_variant	7403	exon5			TTTACAGAATGCT	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.385-1G>C	X.37:g.44870205G>C		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	67	30	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Splice_Site	SNP	ENST00000377967.4	37	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994801	0.35226	.	.	ENSG00000147050	ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000542299	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2912	0.90131	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KDM6A	44755149	1.000000	0.71417	0.995000	0.50966	0.078000	0.17371	9.225000	0.95219	2.258000	0.74832	0.506000	0.49869	.	.		0.299	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	Intron	C	44870205	G	C	44870205	5	2	130	1	0	0	0	0	0	0	1	0	8158	956	33	4	402	4	KDM6A	23	44870205	Splice_Site	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1215088	44870205	110400355	221	11563											
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	44969446	44969447	+	Frame_Shift_Del	DEL	AC	AC	-																															gaaaactttgtggtgctagaAcagtacaaaatggaggacct																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:44969446_44969447delAC	ENST00000377967.4	+	28	4169_4170	c.4128_4129delAC	c.(4126-4131)gaacagfs	p.Q1377fs	KDM6A_ENST00000543216.1_Frame_Shift_Del_p.Q1298fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.Q1384fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.Q1332fs|KDM6A_ENST00000479423.1_3'UTR	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1377					canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.Q1377*(1)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						TGGTGCTAGAACAGTACAAAAT	0.386			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.1376_1377del	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	7	Whole gene deletion(6)|Substitution - Nonsense(1)	oesophagus(2)|breast(2)|pancreas(2)|urinary_tract(1)	c.4128_4129del						.																																			SO:0001589	frameshift_variant	7403	exon28			.	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.4128_4129delAC	X.37:g.44969446_44969447delAC	ENSP00000367203:p.Gln1377fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	106	36	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																			.		0.386	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44969447	AC	-	44969446	7	5	130	1	0	1	0	1	0	0	0	0	8158	40	2	0	4238	0	KDM6A	23	44969446	Frame_Shift_Del	DEL	AC	TCGA-HE-7130-01A-11D-1961-08	99241	44969446	110301114	222	11564											
HUWE1	10075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53641559	53641559	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgcatggcctgtacttcctCttcctcctcatcctcactag	5	14	5	17	0	3	0	2	0	1	0	7	0	7	0	5	1	2	2	5	1	2	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:53641559C>T	ENST00000342160.3	-	22	2654	c.2197G>A	c.(2197-2199)Gag>Aag	p.E733K	HUWE1_ENST00000218328.8_Missense_Mutation_p.E733K|HUWE1_ENST00000262854.6_Missense_Mutation_p.E733K			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	733					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TGTACTTCCTCTTCCTCCTCA	0.473																																					p.E733K		.											.	HUWE1-280	0			c.G2197A						.						246	208	221					X																	53641559		2203	4300	6503	SO:0001583	missense	10075	exon23			CTTCCTCTTCCTC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2197G>A	X.37:g.53641559C>T	ENSP00000340648:p.Glu733Lys	Somatic	251	1		WXS	Illumina HiSeq	Phase_I	337	116	NM_031407	0	0	4	41	37	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	34	5.381036	0.95945	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.42900	0.96;0.96;0.96	5.46	5.46	0.80206	E3 ubiquitin ligase, domain of unknown function DUF913 (1);	0.137022	0.48286	D	0.000191	T	0.49047	0.1534	L	0.41236	1.265	0.80722	D	1	D	0.53619	0.961	P	0.54544	0.755	T	0.33904	-0.9850	10	0.29301	T	0.29	.	16.9953	0.86366	0.0:1.0:0.0:0.0	.	733	Q7Z6Z7	HUWE1_HUMAN	K	733	ENSP00000340648:E733K;ENSP00000262854:E733K;ENSP00000218328:E733K	ENSP00000218328:E733K	E	-	1	0	HUWE1	53658284	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.068000	0.76748	2.275000	0.75901	0.600000	0.82982	GAG	.		0.473	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53641559	C	T	53641559	3	4	130	1	0	0	0	0	1	0	0	0	7482	922	32	2	11175	2	HUWE1	23	53641559	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	8672113	53641559	101629001	223	11565											
ERCC6L	54821	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	71426809	71426809	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagtagtttgtcttattaatGagtccttgaaaacctgtctt	10	17	7	7	0	2	2	0	2	2	0	3	2	3	2	2	0	1	2	2	0	5	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:71426809G>C	ENST00000334463.3	-	2	1943	c.1808C>G	c.(1807-1809)tCa>tGa	p.S603*	ERCC6L_ENST00000373657.1_Nonsense_Mutation_p.S480*|PIN4_ENST00000423432.2_Intron	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	603	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					TCTTATTAATGAGTCCTTGAA	0.348																																					p.S603X		.											.	ERCC6L-93	0			c.C1808G						.						101	99	99					X																	71426809		2203	4300	6503	SO:0001587	stop_gained	54821	exon2			ATTAATGAGTCCT	AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871			20794	protein-coding gene	gene with protein product	"PLK1-interacting checkpoint helicase"	300687	"excision repair cross-complementing rodent repair deficiency, complementation group 6-like"			17218258	Standard	NM_017669		Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000334463.3:c.1808C>G	X.37:g.71426809G>C	ENSP00000334675:p.Ser603*	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	175	12	NM_017669	0	0	2	3	1	Q8NCI1|Q96H93|Q9NXQ8	Nonsense_Mutation	SNP	ENST00000334463.3	37	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	G	42	9.316536	0.99135	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-9.103	15.597	0.76590	0.0:0.0:1.0:0.0	.	.	.	.	X	480;603	.	ENSP00000334675:S603X	S	-	2	0	ERCC6L	71343534	1.000000	0.71417	0.937000	0.37676	0.994000	0.84299	7.739000	0.84976	2.279000	0.76181	0.594000	0.82650	TCA	.		0.348	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		C	71426809	G	C	71426809	4	2	130	1	0	0	0	0	0	1	0	0	5231	1294	45	4	1948	4	ERCC6L	23	71426809	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	17785250	71426809	83843751	224	11566											
PHKA1	5255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	71886083	71886083	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcagggaaggaaaccactGagagtagactagcatcaacc	16	4	12	9	0	1	2	1	1	0	2	1	5	1	4	2	3	3	3	2	3	5	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:71886083G>A	ENST00000373542.4	-	8	941	c.782C>T	c.(781-783)tCa>tTa	p.S261L	PHKA1_ENST00000373539.3_Missense_Mutation_p.S261L|PHKA1_ENST00000541944.1_Missense_Mutation_p.S261L|PHKA1_ENST00000373545.3_Missense_Mutation_p.S261L|PHKA1_ENST00000339490.3_Missense_Mutation_p.S261L	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	261					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GGAAACCACTGAGAGTAGACT	0.423																																					p.S261L		.											.	PHKA1-134	0			c.C782T						.						109	91	97					X																	71886083		2203	4300	6503	SO:0001583	missense	5255	exon8			ACCACTGAGAGTA		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.782C>T	X.37:g.71886083G>A	ENSP00000362643:p.Ser261Leu	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	92	48	NM_001172436	0	0	3	3	0	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	35	5.514712	0.96402	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29	5.78	5.78	0.91487	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.059029	0.64402	D	0.000002	D	0.96349	0.8809	M	0.80746	2.51	0.58432	D	0.999999	P;D;D	0.67145	0.916;0.989;0.996	P;P;D	0.65773	0.515;0.897;0.938	D	0.95897	0.8912	10	0.42905	T	0.14	-12.5655	16.1536	0.81640	0.0:0.0:1.0:0.0	.	261;261;261	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	L	261	ENSP00000362646:S261L;ENSP00000362643:S261L;ENSP00000441251:S261L;ENSP00000342469:S261L;ENSP00000362640:S261L	ENSP00000342469:S261L	S	-	2	0	PHKA1	71802808	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.296000	0.96104	2.417000	0.82017	0.600000	0.82982	TCA	.		0.423	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71886083	G	A	71886083	3	1	130	1	0	0	0	0	1	0	0	0	11869	1294	45	2	2989	2	PHKA1	23	71886083	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	459274	71886083	83384477	225	11567											
GPRASP2	114928	broad.mit.edu;bcgsc.ca	37	chrX	101971025	101971025	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcagcaatctgtgaatctGagccaggaactgaggagggg	11	8	14	8	0	3	3	1	3	2	0	3	5	3	5	1	4	3	1	1	4	3	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:101971025G>C	ENST00000535209.1	+	4	2059	c.1228G>C	c.(1228-1230)Gag>Cag	p.E410Q	GPRASP2_ENST00000332262.5_Missense_Mutation_p.E410Q|GPRASP2_ENST00000543253.1_Missense_Mutation_p.E410Q			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	410						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						CTGTGAATCTGAGCCAGGAAC	0.562																																					p.E410Q													.	GPRASP2-131	0			c.G1228C						.						60	64	62					X																	101971025		2203	4300	6503	SO:0001583	missense	114928	exon4			GAATCTGAGCCAG	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"Armadillo repeat containing"	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.1228G>C	X.37:g.101971025G>C	ENSP00000437394:p.Glu410Gln	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	176	7	NM_138437	0	0	4	4	0	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	.	.	.	.	.	.	.	.	.	.	G	3.485	-0.105101	0.06967	.	.	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.07021	3.23;3.23;3.23	4.44	0.0818	0.14426	.	1.880220	0.02612	N	0.102273	T	0.08714	0.0216	L	0.44542	1.39	0.09310	N	1	B	0.28128	0.201	B	0.22386	0.039	T	0.38520	-0.9657	10	0.21014	T	0.42	.	8.4458	0.32841	0.345:0.0:0.655:0.0	.	410	Q96D09	GASP2_HUMAN	Q	410	ENSP00000437872:E410Q;ENSP00000437394:E410Q;ENSP00000339057:E410Q	ENSP00000339057:E410Q	E	+	1	0	GPRASP2	101857681	0.000000	0.05858	0.000000	0.03702	0.968000	0.65278	0.558000	0.23469	-0.104000	0.12154	0.600000	0.82982	GAG	.		0.562	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		C	101971025	G	C	101971025	3	2	130	1	0	0	0	0	1	0	0	0	6744	1291	45	4	1230	4	GPRASP2	23	101971025	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	30084942	101971025	53299535	226	11568											
PGRMC1	10857	broad.mit.edu;bcgsc.ca	37	chrX	118370497	118370497	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccggcggccagcggcgacagCgacgacgacgagccgccccc	7	0	15	19	9	0	0	0	0	0	0	0	5	0	0	5	3	3	0	5	3	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:118370497C>T	ENST00000217971.7	+	1	282	c.171C>T	c.(169-171)agC>agT	p.S57S	PGRMC1_ENST00000535419.1_Silent_p.S57S	NM_006667.3	NP_006658.1	O00264	PGRC1_HUMAN	progesterone receptor membrane component 1	57					axon guidance (GO:0007411)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	heme binding (GO:0020037)|steroid binding (GO:0005496)			lung(6)	6					Dextromethorphan(DB00514)|Nortriptyline(DB00540)	GCGGCGACAGCGACGACGACG	0.692																																					p.S57S													.	PGRMC1-130	0			c.C171T						.						18	14	16					X																	118370497		2148	4187	6335	SO:0001819	synonymous_variant	10857	exon1			CGACAGCGACGAC		CCDS14576.1, CCDS65313.1	Xq22-q24	2005-11-29			ENSG00000101856	ENSG00000101856			16090	protein-coding gene	gene with protein product		300435				9705155	Standard	NM_006667		Approved	HPR6.6	uc004erb.3	O00264	OTTHUMG00000022268	ENST00000217971.7:c.171C>T	X.37:g.118370497C>T		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	52	9	NM_006667	0	0	50	50	0	B7Z1L3|Q9UGJ9	Silent	SNP	ENST00000217971.7	37	CCDS14576.1																																																																																			.		0.692	PGRMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058024.1	NM_006667		T	118370497	C	T	118370497	2	4	130	1	0	0	0	0	0	0	0	1	11832	767	27	1		1	PGRMC1	23	118370497	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	16399472	118370497	36900063	227	11569											
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123202456	123202456	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacaaatgagagtattttgtCagatatgtcaacattacctg	15	13	7	6	0	2	2	2	1	0	2	2	3	2	2	1	0	3	1	1	0	6	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:123202456C>T	ENST00000371160.1	+	24	2598	c.2308C>T	c.(2308-2310)Cag>Tag	p.Q770*	STAG2_ENST00000371145.3_Nonsense_Mutation_p.Q770*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.Q701*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.Q770*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.Q770*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.Q770*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	770					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AGTATTTTGTCAGATATGTCA	0.284																																					p.Q770X		.											.	STAG2-134	0			c.C2308T						.						75	70	72					X																	123202456		2203	4285	6488	SO:0001587	stop_gained	10735	exon24			TTTTGTCAGATAT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.2308C>T	X.37:g.123202456C>T	ENSP00000360202:p.Gln770*	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	183	57	NM_001042749	0	0	1	4	3	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	41	8.670079	0.98908	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.19	5.19	0.71726	.	0.185733	0.49305	D	0.000159	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-2.5759	18.1116	0.89538	0.0:1.0:0.0:0.0	.	.	.	.	X	770;701;770;770;770;770	.	ENSP00000218089:Q770X	Q	+	1	0	STAG2	123030137	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	3.356000	0.52269	2.301000	0.77427	0.534000	0.68092	CAG	.		0.284	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123202456	C	T	123202456	4	4	130	1	0	0	0	0	0	1	0	0	15275	827	29	2	2394	2	STAG2	23	123202456	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4831959	123202456	32068104	228	11570											
ODZ1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	123680889	123680889	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctggcagagaggacttataTaacagttgctttgttgacaa	12	12	10	7	0	0	2	0	1	0	1	0	4	0	3	1	2	2	4	1	2	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:123680889T>A	ENST00000371130.3	-	15	2549	c.2486A>T	c.(2485-2487)tAt>tTt	p.Y829F	TENM1_ENST00000422452.2_Missense_Mutation_p.Y829F	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	829					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGGACTTATATAACAGTTGCT	0.403																																					p.Y829F		.											.	.	0			c.A2486T						.						119	102	108					X																	123680889		2203	4300	6503	SO:0001583	missense	10178	exon15			CTTATATAACAGT	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"tenascin M", "odz, odd Oz/ten-m homolog 1 (Drosophila)"	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.2486A>T	X.37:g.123680889T>A	ENSP00000360171:p.Tyr829Phe	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	201	112	NM_001163278	0	0	0	0	0	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641329	0.29157	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.11169	2.8;2.8	5.32	5.32	0.75619	.	0.304797	0.31772	N	0.007082	T	0.05090	0.0136	N	0.08118	0	0.32290	N	0.566467	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.001;0.002	T	0.23332	-1.0191	10	0.10902	T	0.67	.	9.7127	0.40256	0.1566:0.0:0.0:0.8434	.	828;829;829	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	F	829	ENSP00000360171:Y829F;ENSP00000403954:Y829F	ENSP00000360171:Y829F	Y	-	2	0	ODZ1	123508570	1.000000	0.71417	0.954000	0.39281	0.787000	0.44495	3.654000	0.54453	1.955000	0.56771	0.481000	0.45027	TAT	.		0.403	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123680889	T	A	123680889	3	1	130	1	0	0	0	0	1	0	0	0	10860	1406	49	5	5784	5	ODZ1	23	123680889	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	478433	123680889	31589671	229	11571											
AGRN	375790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	957703	957703	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtgacaaccaggtgtcCactggggacaccaggatctt	10	9	11	11	0	2	1	0	1	2	0	3	3	3	3	3	4	1	0	3	4	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:957703C>A	ENST00000379370.2	+	2	374	c.324C>A	c.(322-324)tcC>tcA	p.S108S		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	108	NtA. {ECO:0000255|PROSITE- ProRule:PRU00443}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		ACCAGGTGTCCACTGGGGACA	0.602																																					p.S108S		.											.	AGRN-136	0			c.C324A						.						131	137	135					1																	957703		2203	4300	6503	SO:0001819	synonymous_variant	375790	exon2			GGTGTCCACTGGG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"Proteoglycans / Extracellular Matrix : Other"	329	protein-coding gene	gene with protein product	"agrin proteoglycan"	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.324C>A	1.37:g.957703C>A		Somatic	160	0		WXS	Illumina HiSeq	Phase_I	216	38	NM_198576	0	0	9	21	12	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			.		0.602	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		A	957703	C	A	957703	2	1	131	1	0	0	0	0	0	0	0	1	397	581	21	4		4	AGRN	1	957703	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		957703	248292918	1	11572											
OTUD3	23252	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	20233031	20233031	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggaaatcagggcttaaaTgaaggcaggaccgaaaacaa	17	7	11	6	1	1	1	1	1	0	0	1	4	1	3	1	4	1	2	1	4	7	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:20233031T>C	ENST00000375120.3	+	7	943	c.942T>C	c.(940-942)aaT>aaC	p.N314N		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	314					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGCTTAAATGAAGGCAGGA	0.488																																					p.N314N		.											.	.	0			c.T942C						.						107	112	110					1																	20233031		1980	4166	6146	SO:0001819	synonymous_variant	23252	exon7			CTTAAATGAAGGC	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.942T>C	1.37:g.20233031T>C		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	138	23	NM_015207	0	0	2	2	0	O75047	Silent	SNP	ENST00000375120.3	37	CCDS41279.1																																																																																			.		0.488	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			C	20233031	T	C	20233031	2	2	131	1	0	0	0	0	0	0	0	1	11339	1461	51	3		3	OTUD3	1	20233031	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	19275328	20233031	229017590	2	11573											
KANK4	163782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	62739262	62739262	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggcctccttcctgttcagtgCctgcttcttcaatcctgagt	4	15	8	14	0	3	1	2	1	1	0	6	1	6	1	5	1	2	2	5	1	1	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:62739262C>T	ENST00000371153.4	-	3	1892	c.1514G>A	c.(1513-1515)gGc>gAc	p.G505D	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	505						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						CTGTTCAGTGCCTGCTTCTTC	0.602																																					p.G505D		.											.	KANK4-74	0			c.G1514A						.						74	76	75					1																	62739262		2203	4300	6503	SO:0001583	missense	163782	exon3			TCAGTGCCTGCTT	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	27263	protein-coding gene	gene with protein product		614612	"ankyrin repeat domain 38"	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1514G>A	1.37:g.62739262C>T	ENSP00000360195:p.Gly505Asp	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	133	18	NM_181712	0	0	0	0	0	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	.	.	.	.	.	.	.	.	.	.	C	6.119	0.390267	0.11581	.	.	ENSG00000132854	ENST00000371153	T	0.45668	0.89	5.0	-4.67	0.03319	.	0.629621	0.13219	N	0.404541	T	0.18173	0.0436	N	0.20685	0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	10	0.14656	T	0.56	-0.895	4.4402	0.11570	0.4045:0.2134:0.0:0.382	.	505	Q5T7N3	KANK4_HUMAN	D	505	ENSP00000360195:G505D	ENSP00000360195:G505D	G	-	2	0	KANK4	62511850	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.315000	0.08081	-0.487000	0.06735	-0.880000	0.02959	GGC	.		0.602	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		T	62739262	C	T	62739262	3	4	131	1	0	0	0	0	1	0	0	0	8000	739	26	2	1505	2	KANK4	1	62739262	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	42506231	62739262	186511359	3	11574											
SYDE2	84144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	85648463	85648463	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggtgagtctccatcactaAggtaaccacctttgcaggaa	12	9	9	11	0	2	1	1	1	1	0	3	2	2	2	3	3	2	2	3	3	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:85648463A>T	ENST00000341460.5	-	3	1911	c.1862T>A	c.(1861-1863)cTt>cAt	p.L621H		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	621					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		TCCATCACTAAGGTAACCACC	0.378																																					p.L621H		.											.	SYDE2-70	0			c.T1862A						.						86	80	82					1																	85648463		1853	4086	5939	SO:0001583	missense	84144	exon3			TCACTAAGGTAAC	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1862T>A	1.37:g.85648463A>T	ENSP00000340594:p.Leu621His	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	84	13	NM_032184	0	0	0	0	0	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737544	0.69304	.	.	ENSG00000097096	ENST00000341460	T	0.25749	1.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.46502	0.1396	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.54125	-0.8340	10	0.87932	D	0	.	15.6946	0.77484	1.0:0.0:0.0:0.0	.	621;621	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	H	621	ENSP00000340594:L621H	ENSP00000340594:L621H	L	-	2	0	SYDE2	85421051	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.923000	0.92808	2.116000	0.64780	0.454000	0.30748	CTT	.		0.378	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			T	85648463	A	T	85648463	3	4	131	1	0	0	0	0	1	0	0	0	15468	72	3	5	1742	5	SYDE2	1	85648463	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	22909201	85648463	163602158	4	11575											
NTRK1	4914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156851384	156851384	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaggatgtgcacgcccggCtgcaagccctggcccaggca	8	5	13	15	2	1	0	1	0	0	0	1	1	1	1	3	4	3	4	3	4	2	0			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:156851384C>T	ENST00000524377.1	+	17	2382	c.2341C>T	c.(2341-2343)Ctg>Ttg	p.L781L	NTRK1_ENST00000368196.3_Silent_p.L775L|NTRK1_ENST00000392302.2_Silent_p.L745L|NTRK1_ENST00000358660.3_Silent_p.L778L|NTRK1_ENST00000531606.1_3'UTR	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	781	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GCACGCCCGGCTGCAAGCCCT	0.697			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.L781L		.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1-1393	0			c.C2341T						.						23	24	24					1																	156851384		2202	4297	6499	SO:0001819	synonymous_variant	4914	exon17			GCCCGGCTGCAAG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8031	protein-coding gene	gene with protein product	"high affinity nerve growth factor receptor"	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.2341C>T	1.37:g.156851384C>T		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_002529	0	0	0	0	0	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	37	CCDS1161.1																																																																																			.		0.697	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156851384	C	T	156851384	2	4	131	1	0	0	0	0	0	0	0	1	10732	796	28	2		2	NTRK1	1	156851384	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	71202921	156851384	92399237	5	11576											
HSPA6	3310	broad.mit.edu	37	chr1	161495204	161495204	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaattccggcggaagcatggGaaggacctgagcgggaacaa	13	4	16	8	3	0	1	0	1	0	0	1	6	1	5	2	5	3	1	2	5	5	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:161495204G>A	ENST00000309758.4	+	1	1169	c.756G>A	c.(754-756)ggG>ggA	p.G252G	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	252					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GGAAGCATGGGAAGGACCTGA	0.627																																					p.G252G													.	HSPA6-226	0			c.G756A						.																																			SO:0001819	synonymous_variant	3310	exon1			GCATGGGAAGGAC		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"Heat shock proteins / HSP70"	5239	protein-coding gene	gene with protein product		140555	"heat shock 70kD protein 6 (HSP70B')"			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.756G>A	1.37:g.161495204G>A		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	176	16	NM_002155	0	0	6	6	0	Q1HBA8|Q8IYK7|Q9BT95	Silent	SNP	ENST00000309758.4	37	CCDS1231.1																																																																																			.		0.627	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155		A	161495204	G	A	161495204	2	1	131	1	0	0	0	0	0	0	0	1	7436	1161	41	2		2	HSPA6	1	161495204	Silent	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	4643820	161495204	87755417	6	11577											
ARHGEF4	50649	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	131801154	131801154	+	Frame_Shift_Del	DEL	A	A	-																															accagctcatctactgtaagAaggtaccagagctgctctgc																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:131801154delA	ENST00000326016.5	+	11	2116	c.1597delA	c.(1597-1599)aagfs	p.K533fs	ARHGEF4_ENST00000525839.1_Frame_Shift_Del_p.K533fs|ARHGEF4_ENST00000409303.1_Frame_Shift_Del_p.K473fs|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000355771.3_Frame_Shift_Del_p.K462fs|ARHGEF4_ENST00000392953.3_Frame_Shift_Del_p.K533fs	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	533	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CTACTGTAAGAAGGTACCAGA	0.572																																					p.K533fs		.											.	ARHGEF4-292	0			c.1597delA						.						97	87	90					2																	131801154		2203	4300	6503	SO:0001589	frameshift_variant	50649	exon11			.	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	684	protein-coding gene	gene with protein product	"APC-stimulated guanine nucleotide exchange factor"	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1597delA	2.37:g.131801154delA	ENSP00000316845:p.Lys533fs	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	202	54	NM_032995	0	0	0	0	0	Q9HDC6|Q9UPP0	Frame_Shift_Del	DEL	ENST00000326016.5	37	CCDS2165.1																																																																																			.		0.572	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			-	131801154	A	-	131801154	7	5	131	1	0	1	0	1	0	0	0	0	908	247	9	0	1631	0	ARHGEF4	2	131801154	Frame_Shift_Del	DEL	A	TCGA-HE-A5NF-01A-11D-A26P-10		131801154	111398219	7	11578											
ERMN	57471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	158178038	158178038	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaaattctatcactcgaacTtcatcttcatcattattgca	12	17	2	10	1	6	0	4	0	2	0	7	1	6	0	0	0	2	1	0	0	5	7			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:158178038T>A	ENST00000410096.1	-	3	891	c.600A>T	c.(598-600)gaA>gaT	p.E200D	ERMN_ENST00000397283.2_Missense_Mutation_p.E213D|ERMN_ENST00000535935.1_Missense_Mutation_p.E94D|ERMN_ENST00000420719.2_Missense_Mutation_p.E180D	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein	200					actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						TCACTCGAACTtcatcttcat	0.383																																					p.E213D		.											.	ERMN-92	0			c.A639T						.						122	118	119					2																	158178038		1908	4131	6039	SO:0001583	missense	57471	exon4			TCGAACTTCATCT	AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"juxtanodin", "ermin"	610072	"KIAA1189"	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.600A>T	2.37:g.158178038T>A	ENSP00000387047:p.Glu200Asp	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	73	12	NM_001009959	0	0	0	0	0	B4DKA6|Q9ULN1	Missense_Mutation	SNP	ENST00000410096.1	37	CCDS46431.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290199	0.40494	.	.	ENSG00000136541	ENST00000410096;ENST00000397283;ENST00000535935;ENST00000420719	.	.	.	5.81	4.66	0.58398	.	0.162184	0.43416	D	0.000573	T	0.48021	0.1477	L	0.36672	1.1	0.28039	N	0.933847	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.66602	0.945;0.945;0.945	T	0.37549	-0.9701	9	0.38643	T	0.18	.	8.1808	0.31309	0.0:0.1976:0.0:0.8024	.	180;213;200	B4DIZ1;Q8TAM6-2;Q8TAM6	.;.;ERMIN_HUMAN	D	200;213;94;180	.	ENSP00000380453:E213D	E	-	3	2	ERMN	157886284	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	0.434000	0.21494	1.031000	0.39867	0.533000	0.62120	GAA	.		0.383	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959		A	158178038	T	A	158178038	3	1	131	1	0	0	0	0	1	0	0	0	5248	1606	56	5	258	5	ERMN	2	158178038	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	26376884	158178038	85021335	8	11579											
UBR3	130507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170762609	170762609	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcagacctactatgctgccTttgctgctgaacttgaggcc	7	12	9	13	0	1	3	1	2	0	1	1	3	1	3	3	1	6	3	3	1	3	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:170762609T>A	ENST00000272793.5	+	10	1764	c.1714T>A	c.(1714-1716)Ttt>Att	p.F572I	UBR3_ENST00000418381.1_Missense_Mutation_p.F572I			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	572					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						CTATGCTGCCTTTGCTGCTGA	0.388																																					p.F572I		.											.	UBR3-68	0			c.T1714A						.						116	103	107					2																	170762609		692	1591	2283	SO:0001583	missense	130507	exon10			GCTGCCTTTGCTG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"Ubiquitin protein ligase E3 component n-recognins"	30467	protein-coding gene	gene with protein product		613831	"zinc finger protein 650"	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1714T>A	2.37:g.170762609T>A	ENSP00000272793:p.Phe572Ile	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	101	29	NM_172070	0	0	3	4	1	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.	.	.	.	.	.	.	.	.	.	T	34	5.361453	0.95877	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	T;T	0.58060	0.36;0.36	5.58	5.58	0.84498	.	.	.	.	.	T	0.64316	0.2587	L	0.43923	1.385	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.60835	-0.7184	9	0.30854	T	0.27	.	15.7431	0.77918	0.0:0.0:0.0:1.0	.	572	Q6ZT12	UBR3_HUMAN	I	572	ENSP00000272793:F572I;ENSP00000396068:F572I	ENSP00000272793:F572I	F	+	1	0	UBR3	170470855	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.116000	0.64780	0.482000	0.46254	TTT	.		0.388	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		A	170762609	T	A	170762609	3	1	131	1	0	0	0	0	1	0	0	0	16936	1609	56	5	1752	5	UBR3	2	170762609	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	12584571	170762609	72436764	9	11580											
OBSL1	23363	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220416332	220416332	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcctcaggtcgaacgtcatGgatgaccaggctgtgggtgg	7	9	16	9	2	2	1	2	1	0	0	4	3	3	2	2	5	1	1	2	5	1	0			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:220416332G>T	ENST00000404537.1	-	20	5658	c.5602C>A	c.(5602-5604)Cat>Aat	p.H1868N	OBSL1_ENST00000265318.4_3'UTR|MIR3132_ENST00000581997.1_RNA|OBSL1_ENST00000373876.1_Missense_Mutation_p.H1776N	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1868	Ig-like 14.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CGAACGTCATGGATGACCAGG	0.657																																					p.H1868N		.											.	OBSL1-71	0			c.C5602A						.						32	37	36					2																	220416332		2086	4208	6294	SO:0001583	missense	23363	exon20			CGTCATGGATGAC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.5602C>A	2.37:g.220416332G>T	ENSP00000385636:p.His1868Asn	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	209	53	NM_015311	0	0	1	5	4	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.174528	0.38413	.	.	ENSG00000124006	ENST00000404537;ENST00000373876	T;T	0.65916	-0.18;-0.18	5.32	3.38	0.38709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53449	0.1797	L	0.28344	0.845	0.80722	D	1	B	0.27192	0.171	B	0.41691	0.364	T	0.43798	-0.9369	9	0.21540	T	0.41	.	9.4425	0.38677	0.0:0.1395:0.5724:0.2881	.	1868	O75147	OBSL1_HUMAN	N	1868;1776	ENSP00000385636:H1868N;ENSP00000362983:H1776N	ENSP00000362983:H1776N	H	-	1	0	OBSL1	220124576	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.056000	0.57448	1.220000	0.43490	0.655000	0.94253	CAT	.		0.657	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			T	220416332	G	T	220416332	3	4	131	1	0	0	0	0	1	0	0	0	10839	1348	47	4	96	4	OBSL1	2	220416332	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	49653723	220416332	22783041	10	11581											
SNED1	25992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242026825	242026825	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtataaaagagtctaccgAgttcaccaagacatctgctt	14	10	8	9	1	3	2	1	0	2	2	3	3	3	2	2	1	2	3	2	1	5	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:242026825A>T	ENST00000310397.8	+	30	4140	c.4140A>T	c.(4138-4140)cgA>cgT	p.R1380R	SNED1_ENST00000342631.6_Silent_p.R1347R|SNED1_ENST00000405547.3_Intron|MTERFD2_ENST00000464344.2_Intron	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1380					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GAGTCTACCGAGTTCACCAAG	0.488																																					p.R1380R		.											.	SNED1-72	0			c.A4140T						.						50	46	47					2																	242026825		1886	4111	5997	SO:0001819	synonymous_variant	25992	exon30			CTACCGAGTTCAC	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"Fibronectin type III domain containing"	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.4140A>T	2.37:g.242026825A>T		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	196	70	NM_001080437	0	0	0	2	2	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			.		0.488	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	242026825	A	T	242026825	2	4	131	1	0	0	0	0	0	0	0	1	14877	291	11	5		5	SNED1	2	242026825	Silent	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	21610493	242026825	1172548	11	11582											
SRGAP3	9901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9100033	9100033	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgtcacttcgggaatccaGgttgtccactgcattctcaa	8	13	8	12	1	2	0	2	0	1	0	6	1	4	1	2	2	1	2	2	2	2	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:9100033G>T	ENST00000383836.3	-	7	1352	c.925C>A	c.(925-927)Ctg>Atg	p.L309M	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.L309M	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	309	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CGGGAATCCAGGTTGTCCACT	0.552			T	RAF1	pilocytic astrocytoma																																p.L309M		.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3-344	0			c.C925A						.						246	203	218					3																	9100033		2203	4300	6503	SO:0001583	missense	9901	exon7			AATCCAGGTTGTC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"Rho GTPase activating proteins"	19744	protein-coding gene	gene with protein product		606525	"SLIT-ROBO Rho GTPase activating protein 2"	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.925C>A	3.37:g.9100033G>T	ENSP00000373347:p.Leu309Met	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	178	29	NM_014850	0	0	0	0	0	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.927507	0.52759	.	.	ENSG00000196220	ENST00000383836;ENST00000360413;ENST00000544908	T;T	0.14893	2.47;2.47	5.54	4.66	0.58398	.	0.000000	0.64402	D	0.000001	T	0.18800	0.0451	M	0.67397	2.05	0.58432	D	0.999993	B;B;B	0.30937	0.074;0.301;0.2	B;B;B	0.27796	0.083;0.083;0.038	T	0.01956	-1.1240	10	0.45353	T	0.12	.	10.889	0.46984	0.1445:0.0:0.8555:0.0	.	178;309;309	Q9ULR4;O43295-2;O43295	.;.;SRGP2_HUMAN	M	309;309;189	ENSP00000373347:L309M;ENSP00000353587:L309M	ENSP00000353587:L309M	L	-	1	2	SRGAP3	9075033	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.275000	0.43399	2.606000	0.88127	0.655000	0.94253	CTG	.		0.552	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			T	9100033	G	T	9100033	3	4	131	1	0	0	0	0	1	0	0	0	15179	991	35	4	2473	4	SRGAP3	3	9100033	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		9100033	188922397	12	11583											
TBC1D5	9779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	17550057	17550057	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagtttcagataaggaatgAtacattgtgggaactggaca	14	11	11	5	0	1	2	1	1	0	1	1	5	1	5	0	3	2	1	0	3	5	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:17550057A>G	ENST00000253692.7	-	3	1670	c.6T>C	c.(4-6)taT>taC	p.Y2Y	TBC1D5_ENST00000414318.2_Intron|TBC1D5_ENST00000429383.4_Silent_p.Y2Y|TBC1D5_ENST00000446818.2_Silent_p.Y2Y	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	2						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						ATAAGGAATGATACATTGTGG	0.403																																					p.Y2Y		.											.	TBC1D5-91	0			c.T6C						.						142	122	129					3																	17550057		2203	4300	6503	SO:0001819	synonymous_variant	9779	exon3			GGAATGATACATT	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.6T>C	3.37:g.17550057A>G		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	109	32	NM_014744	0	0	1	4	3	A6NP25|C9JP52	Silent	SNP	ENST00000253692.7	37	CCDS33714.1																																																																																			.		0.403	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		G	17550057	A	G	17550057	2	3	131	1	0	0	0	0	0	0	0	1	15655	340	12	3		3	TBC1D5	3	17550057	Silent	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	8450024	17550057	180472373	13	11584											
ZNF445	353274	ucsc.edu;bcgsc.ca	37	chr3	44492934	44492934	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagatcgcagggctcctgtaCccatccaatgcacatctggg	9	8	10	14	1	1	1	0	0	1	1	4	1	3	1	3	2	2	4	3	2	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:44492934C>T	ENST00000396077.2	-	4	817	c.470G>A	c.(469-471)gGt>gAt	p.G157D	ZNF445_ENST00000425708.2_Missense_Mutation_p.G157D	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	157					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		GGCTCCTGTACCCATCCAATG	0.542																																					p.G157D													.	ZNF445-91	0			c.G470A						.						81	82	82					3																	44492934		2203	4300	6503	SO:0001583	missense	353274	exon4			CCTGTACCCATCC	AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"Zinc fingers, C2H2-type", "-", "-", "-"	21018	protein-coding gene	gene with protein product			"zinc finger protein 168"	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.470G>A	3.37:g.44492934C>T	ENSP00000379387:p.Gly157Asp	Somatic	164	2		WXS	Illumina HiSeq		200	42	NM_181489	0	0	2	2	0	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	37	CCDS2713.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.157033	0.78114	.	.	ENSG00000185219	ENST00000425708;ENST00000396077	T;T	0.06068	3.35;3.35	5.07	4.18	0.49190	Transcription regulator SCAN (1);	0.141093	0.33217	N	0.005158	T	0.08980	0.0222	N	0.08118	0	0.39350	D	0.965742	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.29458	-1.0011	10	0.52906	T	0.07	.	8.7795	0.34783	0.0:0.8979:0.0:0.1021	.	157;157	B7ZKX2;P59923	.;ZN445_HUMAN	D	157	ENSP00000413073:G157D;ENSP00000379387:G157D	ENSP00000379387:G157D	G	-	2	0	ZNF445	44467938	0.999000	0.42202	0.998000	0.56505	0.995000	0.86356	2.097000	0.41748	2.537000	0.85549	0.491000	0.48974	GGT	.		0.542	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489		T	44492934	C	T	44492934	3	4	131	1	0	0	0	0	1	0	0	0	17950	507	18	2	2645	2	ZNF445	3	44492934	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	26942877	44492934	153529496	14	11585											
MST1	327	broad.mit.edu	37	chr3	49723112	49723112	+	IGR	DEL	T	T	-																															catggctatccccatctgggTtccggcagaagttctcctcc																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:49723112delT	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Frame_Shift_Del_p.N435fs	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCCATCTGGGTTCCGGCAGAA	0.587																																					p.N435fs													.	MST1-278	0			c.1304delA						.						43	42	43					3																	49723112		2203	4300	6503	SO:0001628	intergenic_variant	4485	exon11			TCTGGGTTCCGGC	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723112delT		Somatic	254	0		WXS	Illumina HiSeq	Phase_I	406	8	NM_020998	0	0	0	0	0	Q9BQ33|Q9P0Y2	Frame_Shift_Del	DEL	ENST00000296456.5	37	CCDS2801.1																																																																																			.		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			-	49723112	T	-	49723112	6	5	131	0	1	1	0	1	0	0	0	0	9915	1725	60	0		0	MST1	3	49723112	IGR	DEL	T	TCGA-HE-A5NF-01A-11D-A26P-10	5230178	49723112	148299318	15	11586											
RPL24	6152	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101404668	101404668	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtattccacttaccgactgTccctttttgtgcttccttct	4	18	5	14	2	1	0	0	0	1	0	4	1	4	0	4	0	2	2	4	0	2	7			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:101404668T>C	ENST00000394077.3	-	3	291	c.186A>G	c.(184-186)ggA>ggG	p.G62G	RPL24_ENST00000469605.1_Silent_p.G62G|RPL24_ENST00000495401.1_Silent_p.G62G	NM_000986.3	NP_000977.1	P83731	RL24_HUMAN	ribosomal protein L24	62					cellular protein metabolic process (GO:0044267)|exit from mitosis (GO:0010458)|gene expression (GO:0010467)|mitotic cell cycle checkpoint (GO:0007093)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|optic nerve development (GO:0021554)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|ribosomal large subunit assembly (GO:0000027)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(2)|urinary_tract(1)	4						TTACCGACTGTCCCTTTTTGT	0.443																																					p.G62G													.	RPL24-90	0			c.A186G						.						89	78	81					3																	101404668		2203	4300	6503	SO:0001819	synonymous_variant	6152	exon3			CGACTGTCCCTTT	AB007177	CCDS33809.1	3q12	2011-04-06			ENSG00000114391	ENSG00000114391		"L ribosomal proteins"	10325	protein-coding gene	gene with protein product		604180				9582194	Standard	NM_000986		Approved	L24	uc003dvh.1	P83731	OTTHUMG00000159146	ENST00000394077.3:c.186A>G	3.37:g.101404668T>C		Somatic	127	1		WXS	Illumina HiSeq	Phase_I	161	50	NM_000986	0	0	0	0	0	B2R4Y3|P38663|Q6IBS3	Silent	SNP	ENST00000394077.3	37	CCDS33809.1																																																																																			.		0.443	RPL24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353487.1	NM_000986		C	101404668	T	C	101404668	2	2	131	1	0	0	0	0	0	0	0	1	13604	1654	58	3		3	RPL24	3	101404668	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	51681556	101404668	96617762	16	11587											
ZBTB20	26137	broad.mit.edu	37	chr3	114070690	114070690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttgtgaaggttgatgctgtGaatgcgctcggtcatcccct	6	13	13	9	2	1	3	1	3	0	0	3	3	2	3	2	2	2	4	2	2	2	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:114070690G>A	ENST00000474710.1	-	4	413	c.235C>T	c.(235-237)Cac>Tac	p.H79Y	ZBTB20_ENST00000357258.3_Missense_Mutation_p.H6Y|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000464560.1_Missense_Mutation_p.H6Y|ZBTB20_ENST00000481632.1_Missense_Mutation_p.H6Y|ZBTB20_ENST00000462705.1_Missense_Mutation_p.H6Y|ZBTB20_ENST00000471418.1_Missense_Mutation_p.H6Y|ZBTB20_ENST00000393785.2_Missense_Mutation_p.H6Y|ZBTB20-AS1_ENST00000475939.1_RNA	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	79						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		TTGATGCTGTGAATGCGCTCG	0.547																																					p.H79Y	NSCLC(69;748 1344 9802 11203 30933)												.	ZBTB20-95	0			c.C235T						.						75	77	76					3																	114070690		2203	4299	6502	SO:0001583	missense	26137	exon4			TGCTGTGAATGCG	AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13503	protein-coding gene	gene with protein product		606025	"zinc finger protein 288"	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.235C>T	3.37:g.114070690G>A	ENSP00000419153:p.His79Tyr	Somatic	140	2		WXS	Illumina HiSeq	Phase_I	251	22	NM_001164342	0	0	0	0	0	Q63HP6|Q8N6R5|Q9Y410	Missense_Mutation	SNP	ENST00000474710.1	37	CCDS54626.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559799	0.65538	.	.	ENSG00000181722	ENST00000462705;ENST00000393785;ENST00000481632;ENST00000471418;ENST00000474710;ENST00000357258;ENST00000464560;ENST00000470311	T;T;T;T;T;T;T;T	0.45276	2.94;2.94;2.94;2.94;2.91;2.94;2.94;0.9	6.1	5.23	0.72850	BTB/POZ fold (1);	0.049382	0.85682	N	0.000000	T	0.53706	0.1813	L	0.39085	1.19	0.80722	D	1	D	0.57899	0.981	D	0.65140	0.932	T	0.57636	-0.7777	10	0.87932	D	0	.	15.4094	0.74905	0.0662:0.0:0.9338:0.0	.	79	Q9HC78	ZBT20_HUMAN	Y	6;6;6;6;79;6;6;6	ENSP00000420324:H6Y;ENSP00000377375:H6Y;ENSP00000418092:H6Y;ENSP00000419902:H6Y;ENSP00000419153:H79Y;ENSP00000349803:H6Y;ENSP00000417307:H6Y;ENSP00000420684:H6Y	ENSP00000349803:H6Y	H	-	1	0	ZBTB20	115553380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	1.601000	0.50113	0.650000	0.86243	CAC	.		0.547	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		A	114070690	G	A	114070690	3	1	131	1	0	0	0	0	1	0	0	0	17561	1290	45	2	1998	2	ZBTB20	3	114070690	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	12666022	114070690	83951740	17	11588											
STAG1	10274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	136060303	136060303	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcatgcctcactccagtTctcactttcatgtagttcat	9	14	5	13	0	4	0	4	0	1	0	6	0	5	0	2	0	2	4	2	0	1	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:136060303T>A	ENST00000383202.2	-	31	3793	c.3537A>T	c.(3535-3537)agA>agT	p.R1179S	STAG1_ENST00000434713.2_Missense_Mutation_p.R919S|STAG1_ENST00000536929.1_Missense_Mutation_p.R763S|STAG1_ENST00000236698.5_Intron	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1179					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TCACTCCAGTTCTCACTTTCA	0.423																																					p.R1179S		.											.	STAG1-228	0			c.A3537T						.						273	206	228					3																	136060303		2203	4300	6503	SO:0001583	missense	10274	exon31			TCCAGTTCTCACT	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3537A>T	3.37:g.136060303T>A	ENSP00000372689:p.Arg1179Ser	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	115	31	NM_005862	0	0	3	3	0	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970648	0.74246	.	.	ENSG00000118007	ENST00000383202;ENST00000434713;ENST00000536929	T;T;T	0.50277	1.31;0.75;0.97	5.91	3.52	0.40303	.	0.100808	0.64402	D	0.000003	T	0.50633	0.1627	M	0.63843	1.955	0.54753	D	0.999983	D	0.60160	0.987	P	0.54174	0.744	T	0.47724	-0.9095	10	0.13108	T	0.6	.	8.6846	0.34229	0.0:0.2062:0.0:0.7938	.	1179	Q8WVM7	STAG1_HUMAN	S	1179;919;763	ENSP00000372689:R1179S;ENSP00000404396:R919S;ENSP00000445787:R763S	ENSP00000372689:R1179S	R	-	3	2	STAG1	137542993	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.775000	0.26689	0.483000	0.27608	0.528000	0.53228	AGA	.		0.423	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		A	136060303	T	A	136060303	3	1	131	1	0	0	0	0	1	0	0	0	15274	1780	62	5	255	5	STAG1	3	136060303	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	21989613	136060303	61962127	18	11589											
UBE2K	3093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39757353	39757353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtttggatatcctgaaagAtcaatggtaagagattttga	13	15	10	3	0	1	4	1	2	0	2	2	6	2	5	1	2	0	2	1	2	4	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:39757353A>G	ENST00000261427.5	+	4	577	c.293A>G	c.(292-294)gAt>gGt	p.D98G	UBE2K_ENST00000503368.1_Missense_Mutation_p.D47G|UBE2K_ENST00000295963.6_Intron|UBE2K_ENST00000438068.2_3'UTR|UBE2K_ENST00000445950.2_Missense_Mutation_p.D98G	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	98					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						ATCCTGAAAGATCAATGGTAA	0.343																																					p.D98G	NSCLC(101;689 1592 16105 29682 31745)	.											.	UBE2K-23	0			c.A293G						.						152	150	151					4																	39757353		2203	4300	6503	SO:0001583	missense	3093	exon4			TGAAAGATCAATG	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.293A>G	4.37:g.39757353A>G	ENSP00000261427:p.Asp98Gly	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	57	8	NM_005339	0	0	0	0	0	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	37	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885370	0.91814	.	.	ENSG00000078140	ENST00000261427;ENST00000503368;ENST00000445950	T;T;T	0.72835	-0.69;-0.69;-0.69	5.98	5.98	0.97165	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	D	0.82935	0.5145	M	0.74467	2.265	0.80722	D	1	D;D;B	0.61697	0.97;0.99;0.034	D;D;B	0.66497	0.925;0.944;0.131	D	0.84525	0.0630	10	0.62326	D	0.03	-22.3267	15.4553	0.75308	1.0:0.0:0.0:0.0	.	98;47;98	P61086;P61086-2;C9JGP1	UBE2K_HUMAN;.;.	G	98;47;98	ENSP00000261427:D98G;ENSP00000421203:D47G;ENSP00000390483:D98G	ENSP00000261427:D98G	D	+	2	0	UBE2K	39433748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.872000	0.92352	2.296000	0.77279	0.482000	0.46254	GAT	.		0.343	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		G	39757353	A	G	39757353	3	3	131	1	0	0	0	0	1	0	0	0	16895	333	12	3	307	3	UBE2K	4	39757353	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10		39757353	151396923	19	11590											
OCIAD2	132299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48887522	48887522	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaagctgaaggctgagaGtctcccttctcacttaatcc	10	11	9	11	0	2	2	1	2	2	1	5	4	3	3	2	2	1	2	2	2	4	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:48887522G>T	ENST00000508632.1	-	7	676	c.444C>A	c.(442-444)gaC>gaA	p.D148E	OCIAD2_ENST00000508069.2_5'UTR|OCIAD2_ENST00000273860.4_3'UTR	NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2	148						endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						AAGGCTGAGAGTCTCCCTTCT	0.368																																					p.D148E		.											.	OCIAD2-68	0			c.C444A						.						185	180	182					4																	48887522		2203	4300	6503	SO:0001583	missense	132299	exon7			CTGAGAGTCTCCC	BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247			28685	protein-coding gene	gene with protein product						17054434	Standard	NM_001286774		Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.444C>A	4.37:g.48887522G>T	ENSP00000423014:p.Asp148Glu	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	195	42	NM_001014446	0	0	109	216	107	B4DPE7|Q8N544	Missense_Mutation	SNP	ENST00000508632.1	37	CCDS33981.1	.	.	.	.	.	.	.	.	.	.	G	5.308	0.242112	0.10077	.	.	ENSG00000145247	ENST00000508632	T	0.41758	0.99	5.25	-4.51	0.03483	.	0.562361	0.17338	N	0.177837	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18178	-1.0345	9	.	.	.	1.3177	6.0446	0.19752	0.3698:0.2579:0.3723:0.0	.	148	Q56VL3	OCAD2_HUMAN	E	148	ENSP00000423014:D148E	.	D	-	3	2	OCIAD2	48582279	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	-0.089000	0.11180	-1.031000	0.03308	-0.302000	0.09304	GAC	.		0.368	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361984.5	NM_152398		T	48887522	G	T	48887522	3	4	131	1	0	0	0	0	1	0	0	0	10844	1020	36	4	24	4	OCIAD2	4	48887522	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	9130169	48887522	142266754	20	11591											
DSPP	1834	bcgsc.ca	37	chr4	88536953	88536953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgatagcagtgacagcagcGatagcagtgacagcagtgac	13	5	14	9	2	0	3	0	3	0	0	0	5	0	3	0	0	5	4	0	0	2	2	rs200486992		TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:88536953G>A	ENST00000282478.7	+	4	3172	c.3139G>A	c.(3139-3141)Gat>Aat	p.D1047N	DSPP_ENST00000399271.1_Missense_Mutation_p.D1047N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1047	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.527																																					p.D1047N													.	DSPP-90	0			c.G3139A						.						46	57	53					4																	88536953		1537	2773	4310	SO:0001583	missense	1834	exon5			AGCAGCGATAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3139G>A	4.37:g.88536953G>A	ENSP00000282478:p.Asp1047Asn	Somatic	178	0		WXS	Illumina HiSeq	Phase_1	211	13	NM_014208	0	0	0	0	0	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	3.566	-0.088574	0.07097	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88201	-2.35;-2.35	1.51	-1.84	0.07809	.	.	.	.	.	T	0.78355	0.4270	L	0.34521	1.04	0.09310	N	1	B	0.26708	0.157	B	0.08055	0.003	T	0.61637	-0.7022	9	0.38643	T	0.18	.	5.2365	0.15448	0.5606:0.0:0.4394:0.0	.	1047	Q9NZW4	DSPP_HUMAN	N	1047	ENSP00000382213:D1047N;ENSP00000282478:D1047N	ENSP00000282478:D1047N	D	+	1	0	DSPP	88755977	0.032000	0.19561	0.079000	0.20413	0.006000	0.05464	0.451000	0.21779	-0.607000	0.05738	-0.791000	0.03333	GAT	.		0.527	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88536953	G	A	88536953	3	1	131	1	0	0	0	0	1	0	0	0	4793	1058	37	1	3153	1	DSPP	4	88536953	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	39649431	88536953	102617323	21	11592											
ADH1B	125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100231924	100231924	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactaacttaaaatctacctTttcccagagtgaagcaggtc	14	11	6	10	0	1	2	0	1	1	1	3	2	2	2	2	1	4	1	2	1	6	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:100231924T>C	ENST00000305046.8	-	8	1168	c.1101A>G	c.(1099-1101)aaA>aaG	p.K367K	ADH1B_ENST00000394887.3_Silent_p.K327K			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	367					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	AAATCTACCTTTTCCCAGAGT	0.333																																					p.K367K		.											.	ADH1B-136	0			c.A1101G						.						72	72	72					4																	100231924		2202	4300	6502	SO:0001819	synonymous_variant	125	exon8			CTACCTTTTCCCA	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"Alcohol dehydrogenases"	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.1101A>G	4.37:g.100231924T>C		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	90	13	NM_000668	0	0	0	0	0	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																			.		0.333	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		C	100231924	T	C	100231924	2	2	131	1	0	0	0	0	0	0	0	1	308	1838	64	3		3	ADH1B	4	100231924	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	11694971	100231924	90922352	22	11593											
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	126408614	126408614	+	Frame_Shift_Del	DEL	A	A	-																															ggcacacttttctaattgggAaaaatggaacagcaacagta																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:126408614delA	ENST00000394329.3	+	16	12944	c.12931delA	c.(12931-12933)aaafs	p.K4311fs	FAT4_ENST00000335110.5_Frame_Shift_Del_p.K2552fs	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4311	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCTAATTGGGAAAAATGGAAC	0.403																																					p.K4311fs		.											.	FAT4-108	0			c.12931delA						.						82	83	83					4																	126408614		2203	4300	6503	SO:0001589	frameshift_variant	79633	exon16			.	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12931delA	4.37:g.126408614delA	ENSP00000377862:p.Lys4311fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	65	15	NM_024582	0	0	0	0	0	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Frame_Shift_Del	DEL	ENST00000394329.3	37	CCDS3732.3																																																																																			.		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		-	126408614	A	-	126408614	7	5	131	1	0	1	0	1	0	0	0	0	5711	247	9	0	12993	0	FAT4	4	126408614	Frame_Shift_Del	DEL	A	TCGA-HE-A5NF-01A-11D-A26P-10	26176690	126408614	64745662	23	11594											
SLC6A3	6531	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	1394869	1394869	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacaccttgagccagtggCggagctggaaagaaaacagg	13	6	13	9	1	1	2	0	1	1	1	1	4	1	4	2	4	4	1	2	4	4	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:1394869C>T	ENST00000270349.9	-	15	1971	c.1844G>A	c.(1843-1845)cGc>cAc	p.R615H	SLC6A3_ENST00000453492.2_Missense_Mutation_p.R615H	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	615					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)	p.R615P(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GAGCCAGTGGCGGAGCTGGAA	0.522																																					p.R615H		.											.	SLC6A3-157	1	Substitution - Missense(1)	lung(1)	c.G1844A						.						101	100	100					5																	1394869		2203	4300	6503	SO:0001583	missense	6531	exon15			CAGTGGCGGAGCT		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"Solute carriers"	11049	protein-coding gene	gene with protein product	"dopamine transporter"	126455	"solute carrier family 6 (neurotransmitter transporter, dopamine), member 3", "dopamine transporter 1"	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1844G>A	5.37:g.1394869C>T	ENSP00000270349:p.Arg615His	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	83	5	NM_001044	0	0	0	0	0	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	37	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627534	0.28978	.	.	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.74632	-0.86;-0.86	4.79	2.97	0.34412	.	0.585459	0.14305	N	0.328004	T	0.53834	0.1821	N	0.12182	0.205	0.32012	N	0.60198	B	0.16802	0.019	B	0.13407	0.009	T	0.56643	-0.7945	10	0.49607	T	0.09	.	6.8118	0.23809	0.0:0.7896:0.0:0.2104	.	615	Q01959	SC6A3_HUMAN	H	615	ENSP00000270349:R615H;ENSP00000399806:R615H	ENSP00000270349:R615H	R	-	2	0	SLC6A3	1447869	1.000000	0.71417	0.999000	0.59377	0.917000	0.54804	0.574000	0.23714	1.139000	0.42245	0.655000	0.94253	CGC	.		0.522	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1394869	C	T	1394869	3	4	131	1	0	0	0	0	1	0	0	0	14717	768	27	1	22	1	SLC6A3	5	1394869	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		1394869	179520391	24	11595											
MEGF10	84466	hgsc.bcm.edu;ucsc.edu	37	chr5	126790286	126790286	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggacttgacagaagctatatGggaaaatccttaaaaggtat	16	10	10	5	0	0	2	0	1	0	1	1	4	1	4	1	3	1	2	1	3	8	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:126790286G>T	ENST00000274473.6	+	24	3276	c.3009G>T	c.(3007-3009)atG>atT	p.M1003I	MEGF10_ENST00000503335.2_Missense_Mutation_p.M1003I|MEGF10_ENST00000510828.1_3'UTR	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	1003	Necessary for formation of large intracellular vacuoles.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GAAGCTATATGGGAAAATCCT	0.328																																					p.M1003I		.											.	MEGF10-94	0			c.G3009T						.						71	73	72					5																	126790286		2203	4300	6503	SO:0001583	missense	84466	exon24			CTATATGGGAAAA	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.3009G>T	5.37:g.126790286G>T	ENSP00000274473:p.Met1003Ile	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	26	4	NM_032446	0	0	0	0	0	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.130925	0.37630	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	T;T	0.79940	-1.32;-1.32	6.03	5.16	0.70880	.	0.346611	0.28847	N	0.013959	T	0.62925	0.2468	N	0.08118	0	0.37163	D	0.902706	B	0.02656	0.0	B	0.04013	0.001	T	0.61461	-0.7058	10	0.24483	T	0.36	-5.9793	12.4451	0.55647	0.1344:0.0:0.8656:0.0	.	1003	Q96KG7	MEG10_HUMAN	I	1003	ENSP00000423354:M1003I;ENSP00000274473:M1003I	ENSP00000274473:M1003I	M	+	3	0	MEGF10	126818185	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.346000	0.52190	1.558000	0.49541	0.655000	0.94253	ATG	.		0.328	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126790286	G	T	126790286	3	4	131	1	0	0	0	0	1	0	0	0	9485	1348	47	4	3095	4	MEGF10	5	126790286	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	125395417	126790286	54124974	25	11596											
CTNNA1	1495	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	138118896	138118897	+	Frame_Shift_Del	DEL	GG	GG	-																															ttgtaaacaccaatagtaaaGggccctctaataagaagaga																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:138118896_138118897delGG	ENST00000302763.7	+	3	226_227	c.136_137delGG	c.(136-138)gggfs	p.G46fs	CTNNA1_ENST00000518825.1_Frame_Shift_Del_p.G46fs|CTNNA1_ENST00000355078.5_Intron	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	46	Involved in homodimerization.				adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CAATAGTAAAGGGCCCTCTAAT	0.356																																					p.46_46del		.											.	CTNNA1-671	0			c.136_137del						.																																			SO:0001589	frameshift_variant	1495	exon3			.	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.136_137delGG	5.37:g.138118896_138118897delGG	ENSP00000304669:p.Gly46fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	104	18	NM_001903	0	0	0	0	0	Q12795|Q8N1C0	Frame_Shift_Del	DEL	ENST00000302763.7	37	CCDS34243.1																																																																																			.		0.356	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		-	138118897	GG	-	138118896	7	5	131	1	0	1	0	1	0	0	0	0	4018	1000	35	0	142	0	CTNNA1	5	138118896	Frame_Shift_Del	DEL	GG	TCGA-HE-A5NF-01A-11D-A26P-10	11328610	138118896	42796364	26	11597											
SPINK13	153218	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	147661756	147661756	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgtgcctcaaatggccaCactttccagaatgagtgttt	9	14	9	9	0	1	2	1	1	0	1	2	2	2	2	3	1	1	2	3	1	2	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:147661756C>T	ENST00000512953.1	+	5	729	c.198C>T	c.(196-198)caC>caT	p.H66H	RP11-373N22.3_ENST00000501695.3_RNA|SPINK13_ENST00000511106.1_Silent_p.H26H|SPINK13_ENST00000398450.4_Silent_p.H66H			Q1W4C9	ISK13_HUMAN	serine peptidase inhibitor, Kazal type 13 (putative)	66	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of acrosome reaction (GO:1902225)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|lung(3)	5						CAAATGGCCACACTTTCCAGA	0.403																																					p.H66H													.	SPINK13-22	0			c.C198T						.						159	144	149					5																	147661756		1920	4136	6056	SO:0001819	synonymous_variant	153218	exon4			TGGCCACACTTTC		CCDS43383.1	5q32	2011-08-31			ENSG00000214510	ENSG00000214510		"Serine peptidase inhibitors, Kazal type"	27200	protein-coding gene	gene with protein product		615205					Standard	NM_001040129		Approved	SPINK5L3, LiESP6, HESPINTOR, MGC149260, HBVDNAPTP1	uc003lpc.3	Q1W4C9	OTTHUMG00000163426	ENST00000512953.1:c.198C>T	5.37:g.147661756C>T		Somatic	130	1		WXS	Illumina HiSeq	Phase_I	161	25	NM_001040129	0	0	0	0	0	A1A4Y2	Silent	SNP	ENST00000512953.1	37	CCDS43383.1																																																																																			.		0.403	SPINK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373337.1	NM_001040129.2		T	147661756	C	T	147661756	2	4	131	1	0	0	0	0	0	0	0	1	15090	477	17	2		2	SPINK13	5	147661756	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	9542860	147661756	33253504	27	11598											
ADAM19	8728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156908922	156908922	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggtttgccgggagtgcCttctggggcggccgaggcct	3	9	18	11	3	1	0	0	0	1	0	1	2	1	1	4	6	2	1	4	6	0	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:156908922C>A	ENST00000517905.1	-	22	2624	c.2580G>T	c.(2578-2580)aaG>aaT	p.K860N	ADAM19_ENST00000394020.1_Missense_Mutation_p.K862N|ADAM19_ENST00000257527.4_Missense_Mutation_p.K860N|ADAM19_ENST00000430702.2_Intron			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	860					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCGGGAGTGCCTTCTGGGGCG	0.622																																					p.K860N		.											.	ADAM19-294	0			c.G2580T						.						12	15	14					5																	156908922		2201	4297	6498	SO:0001583	missense	8728	exon22			GAGTGCCTTCTGG	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"ADAM metallopeptidase domain containing"	197	protein-coding gene	gene with protein product	"meltrin beta"	603640	"a disintegrin and metalloproteinase domain 19 (meltrin beta)"			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.2580G>T	5.37:g.156908922C>A	ENSP00000428654:p.Lys860Asn	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	64	16	NM_033274	0	0	0	0	0	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.047583|4.047583	0.75846|0.75846	.|.	.|.	ENSG00000135074|ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905|ENST00000517374	T;T;T|.	0.01854|.	4.61;4.62;4.6|.	5.51|5.51	1.19|1.19	0.21007|0.21007	.|.	0.184073|.	0.37809|.	N|.	0.001925|.	T|T	0.50205|0.50205	0.1602|0.1602	L|L	0.50333|0.50333	1.59|1.59	0.35227|0.35227	D|D	0.776606|0.776606	D;D|.	0.76494|.	0.999;0.997|.	D;P|.	0.69479|.	0.964;0.888|.	T|T	0.54827|0.54827	-0.8235|-0.8235	10|5	0.87932|.	D|.	0|.	.|.	7.8|7.8	0.29168|0.29168	0.0:0.5227:0.0:0.4773|0.0:0.5227:0.0:0.4773	.|.	860;860|.	Q9H013-2;Q9H013|.	.;ADA19_HUMAN|.	N|M	860;862;860|431	ENSP00000257527:K860N;ENSP00000377588:K862N;ENSP00000428654:K860N|.	ENSP00000257527:K860N|.	K|R	-|-	3|2	2|0	ADAM19|ADAM19	156841500|156841500	0.995000|0.995000	0.38212|0.38212	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	0.140000|0.140000	0.16056|0.16056	0.304000|0.304000	0.22809|0.22809	0.561000|0.561000	0.74099|0.74099	AAG|AGG	.		0.622	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		A	156908922	C	A	156908922	3	1	131	1	0	0	0	0	1	0	0	0	240	680	24	4	184	4	ADAM19	5	156908922	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	9247166	156908922	24006338	28	11599											
FLT4	2324	broad.mit.edu	37	chr5	180055903	180055903	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggaactcgggcggggggTacgctgccagcttcacgggc	6	6	17	12	4	1	0	1	0	0	0	2	1	1	1	1	6	4	3	1	6	2	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:180055903T>G	ENST00000261937.6	-	8	1160	c.1082A>C	c.(1081-1083)tAc>tCc	p.Y361S	FLT4_ENST00000502649.1_Missense_Mutation_p.Y361S|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000393347.3_Missense_Mutation_p.Y361S	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	361	Ig-like C2-type 4.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGGCGGGGGGTACGCTGCCAG	0.632																																					p.Y361S	Colon(97;1075 1466 27033 27547 35871)												.	FLT4-1490	0			c.A1082C						.						29	31	30					5																	180055903		2200	4295	6495	SO:0001583	missense	2324	exon8			GGGGGGTACGCTG	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.1082A>C	5.37:g.180055903T>G	ENSP00000261937:p.Tyr361Ser	Somatic	37	5		WXS	Illumina HiSeq	Phase_I	40	7	NM_182925	0	0	0	0	0	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	T	12.69	2.015069	0.35511	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868	T;T;T	0.11712	2.75;2.75;2.75	4.68	4.68	0.58851	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.27866	0.0686	L	0.56280	1.765	0.49389	D	0.999784	D;D;D	0.89917	1.0;0.997;0.997	D;D;D	0.74023	0.982;0.979;0.979	T	0.01561	-1.1324	9	0.87932	D	0	.	14.4436	0.67336	0.0:0.0:0.0:1.0	.	361;361;361	P35916-3;E9PD35;P35916	.;.;VGFR3_HUMAN	S	361;361;361;171	ENSP00000261937:Y361S;ENSP00000377016:Y361S;ENSP00000426057:Y361S	ENSP00000261937:Y361S	Y	-	2	0	FLT4	179988509	1.000000	0.71417	0.646000	0.29493	0.040000	0.13550	2.726000	0.47302	1.875000	0.54330	0.459000	0.35465	TAC	.		0.632	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			G	180055903	T	G	180055903	3	3	131	1	0	0	0	0	1	0	0	0	5963	1638	57	5	3109	5	FLT4	5	180055903	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	23146981	180055903	859357	29	11600											
UNC5CL	222643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	41000635	41000635	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctcaccctctgagatgtAcgtgagcttcaggcactggt	7	11	10	13	1	3	2	2	2	1	1	4	3	4	2	2	2	2	3	2	2	1	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:41000635A>G	ENST00000373164.1	-	3	997	c.937T>C	c.(937-939)Tac>Cac	p.Y313H	UNC5CL_ENST00000470102.1_5'UTR|UNC5CL_ENST00000244565.3_Missense_Mutation_p.Y313H			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	313	Interaction with RELA and NFKB1.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTGAGATGTACGTGAGCTTC	0.632																																					p.Y313H		.											.	UNC5CL-92	0			c.T937C						.						19	21	20					6																	41000635		2201	4299	6500	SO:0001583	missense	222643	exon4			AGATGTACGTGAG	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.937T>C	6.37:g.41000635A>G	ENSP00000362258:p.Tyr313His	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	77	10	NM_173561	0	0	0	0	0	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	37	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	A	7.812	0.716007	0.15306	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	T;T	0.52526	0.66;0.66	5.43	5.43	0.79202	.	0.000000	0.40554	N	0.001066	T	0.16342	0.0393	N	0.24115	0.695	0.33409	D	0.578337	B	0.14438	0.01	B	0.12156	0.007	T	0.08785	-1.0705	10	0.19590	T	0.45	-29.4271	11.8914	0.52630	1.0:0.0:0.0:0.0	.	313	Q8IV45	UN5CL_HUMAN	H	313	ENSP00000244565:Y313H;ENSP00000362258:Y313H	ENSP00000244565:Y313H	Y	-	1	0	UNC5CL	41108613	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	4.569000	0.60865	2.042000	0.60477	0.533000	0.62120	TAC	.		0.632	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		G	41000635	A	G	41000635	3	3	131	1	0	0	0	0	1	0	0	0	17027	391	14	3	643	3	UNC5CL	6	41000635	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10		41000635	130114432	30	11601											
DEFB110	245913	hgsc.bcm.edu;broad.mit.edu	37	chr6	49986835	49986835	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catactcaggatatttctttTtggctgtaagaagggaagaa	13	13	10	5	0	2	2	1	0	1	2	2	4	2	4	0	3	1	2	0	3	6	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:49986835T>G	ENST00000371148.2	-	2	104	c.59A>C	c.(58-60)aAa>aCa	p.K20T	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	20					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					ATATTTCTTTTTGGCTGTAAG	0.353																																					p.K20T		.											.	DEFB110-45	0			c.A59C						.						129	126	127					6																	49986835		2203	4300	6503	SO:0001583	missense	245913	exon2			TTCTTTTTGGCTG	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"Defensins, beta"	18091	protein-coding gene	gene with protein product			"defensin, beta 110"			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.59A>C	6.37:g.49986835T>G	ENSP00000360190:p.Lys20Thr	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	102	6	NM_001037497	0	0	0	0	0	Q30KR0	Missense_Mutation	SNP	ENST00000371148.2	37	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.622246	0.28889	.	.	ENSG00000203970	ENST00000371148	.	.	.	4.77	-6.13	0.02118	.	0.904575	0.09377	N	0.810521	T	0.07954	0.0199	.	.	.	0.23882	N	0.996572	B	0.12630	0.006	B	0.12837	0.008	T	0.34700	-0.9818	7	.	.	.	-4.2088	9.1953	0.37224	0.0:0.6424:0.1253:0.2323	.	20	Q30KQ9	DB110_HUMAN	T	20	.	.	K	-	2	0	DEFB110	50094794	0.245000	0.23899	0.575000	0.28536	0.857000	0.48899	-1.073000	0.03430	-1.040000	0.03271	-0.408000	0.06270	AAA	.		0.353	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		G	49986835	T	G	49986835	3	3	131	1	0	0	0	0	1	0	0	0	4410	1841	64	5	284	5	DEFB110	6	49986835	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	8986200	49986835	121128232	31	11602											
SERINC1	57515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	122766258	122766258	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	acatacagcacgatgccaatCcaactggaagagattttcac	15	8	7	11	1	1	1	1	0	0	1	2	4	2	2	2	1	4	1	2	1	4	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:122766258C>G	ENST00000339697.4	-	10	1377	c.1293G>C	c.(1291-1293)tgG>tgC	p.W431C		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	431					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		CGATGCCAATCCAACTGGAAG	0.428																																					p.W431C		.											.	SERINC1-91	0			c.G1293C						.						107	96	99					6																	122766258		2203	4300	6503	SO:0001583	missense	57515	exon10			GCCAATCCAACTG	AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"tumor differentially expressed 2"	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.1293G>C	6.37:g.122766258C>G	ENSP00000342962:p.Trp431Cys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	92	19	NM_020755	0	0	105	175	70	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Missense_Mutation	SNP	ENST00000339697.4	37	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569369	0.86439	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	T;T	0.25579	1.79;1.79	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.62405	0.2425	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75502	-0.3295	10	0.87932	D	0	-7.4299	19.5937	0.95526	0.0:1.0:0.0:0.0	.	431	Q9NRX5	SERC1_HUMAN	C	431	ENSP00000342962:W431C;ENSP00000357439:W431C	ENSP00000342962:W431C	W	-	3	0	SERINC1	122807957	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.798000	0.85924	2.629000	0.89072	0.655000	0.94253	TGG	.		0.428	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		G	122766258	C	G	122766258	3	3	131	1	0	0	0	0	1	0	0	0	14111	856	30	4	72	4	SERINC1	6	122766258	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	72779423	122766258	48348809	32	11603											
AEBP1	165	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	44150535	44150535	+	Frame_Shift_Del	DEL	G	G	-																															tttcatgggaacgtggacaaGgacacacccgtgctgagtga																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr7:44150535delG	ENST00000223357.3	+	13	1814	c.1509delG	c.(1507-1509)aagfs	p.K503fs	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Frame_Shift_Del_p.K46fs	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	503	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						ACGTGGACAAGGACACACCCG	0.627																																					p.K503fs		.											.	AEBP1-90	0			c.1509delG						.						88	81	83					7																	44150535		2203	4300	6503	SO:0001589	frameshift_variant	165	exon13			.	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"aortic carboxypeptidase-like protein", "adipocyte enhancer binding protein 1"	602981	"AE-binding protein 1"			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.1509delG	7.37:g.44150535delG	ENSP00000223357:p.Lys503fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	105	30	NM_001129	0	0	0	0	0	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Frame_Shift_Del	DEL	ENST00000223357.3	37	CCDS5476.1																																																																																			.		0.627	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		-	44150535	G	-	44150535	7	5	131	1	0	1	0	1	0	0	0	0	349	991	35	0	1559	0	AEBP1	7	44150535	Frame_Shift_Del	DEL	G	TCGA-HE-A5NF-01A-11D-A26P-10		44150535	114988128	33	11604											
POM121C	100101267	broad.mit.edu;bcgsc.ca	37	chr7	75054953	75054953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actccttgtctgctgccaatGgagttgaagaactggaatga	11	11	11	8	0	1	3	0	2	1	1	2	5	2	5	2	2	3	2	2	2	4	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr7:75054953G>A	ENST00000257665.5	-	7	1336	c.1337C>T	c.(1336-1338)cCa>cTa	p.P446L	POM121C_ENST00000473168.1_5'UTR|POM121C_ENST00000453279.2_Missense_Mutation_p.P204L			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	446	Pore side. {ECO:0000255}.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						TGCTGCCAATGGAGTTGAAGA	0.453																																					p.P204L													.	.	0			c.C611T						.						38	47	44					7																	75054953		2201	4296	6497	SO:0001583	missense	100101267	exon9			GCCAATGGAGTTG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"POM121 membrane glycoprotein C"			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.1337C>T	7.37:g.75054953G>A	ENSP00000257665:p.Pro446Leu	Somatic	234	2		WXS	Illumina HiSeq	Phase_I	312	41	NM_001099415	0	0	6	7	1	O75115|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000257665.5	37		.	.	.	.	.	.	.	.	.	.	G	11.84	1.759509	0.31137	.	.	ENSG00000135213	ENST00000257665;ENST00000453279;ENST00000439629	T;T;T	0.15834	2.39;2.39;2.39	3.46	3.46	0.39613	.	0.000000	0.39146	N	0.001448	T	0.34193	0.0889	M	0.72118	2.19	0.09310	N	0.999998	D	0.64830	0.994	P	0.59221	0.854	T	0.08785	-1.0705	10	0.87932	D	0	.	12.0262	0.53371	0.0:0.0:1.0:0.0	.	446	A8CG34	P121C_HUMAN	L	446;204;76	ENSP00000257665:P446L;ENSP00000414208:P204L;ENSP00000410033:P76L	ENSP00000257665:P446L	P	-	2	0	POM121C	74892889	0.998000	0.40836	0.086000	0.20670	0.054000	0.15201	5.673000	0.68109	1.641000	0.50575	0.195000	0.17529	CCA	.		0.453	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415		A	75054953	G	A	75054953	3	1	131	1	0	0	0	0	1	0	0	0	12266	1348	47	2	2380	2	POM121C	7	75054953	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	30904418	75054953	84083710	34	11605											
DUSP26	78986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	33454873	33454873	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttacaggctgtcttgcctGtgtagaggagccgctccaac	7	10	13	11	1	1	1	0	0	1	1	2	2	2	2	3	3	4	4	3	3	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:33454873G>T	ENST00000256261.4	-	2	678	c.161C>A	c.(160-162)aCa>aAa	p.T54K	DUSP26_ENST00000523956.1_Missense_Mutation_p.T54K	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	54					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		TGTCTTGCCTGTGTAGAGGAG	0.572																																					p.T54K		.											.	DUSP26-90	0			c.C161A						.						69	52	58					8																	33454873		2203	4300	6503	SO:0001583	missense	78986	exon2			TTGCCTGTGTAGA	AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.161C>A	8.37:g.33454873G>T	ENSP00000256261:p.Thr54Lys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	93	16	NM_024025	0	0	0	0	0	D3DSV8|Q9BTW0	Missense_Mutation	SNP	ENST00000256261.4	37	CCDS6092.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638232	0.47153	.	.	ENSG00000133878	ENST00000256261;ENST00000523956;ENST00000522982	T;T;T	0.60040	0.22;0.22;0.22	5.5	5.5	0.81552	.	0.146976	0.64402	D	0.000010	T	0.43765	0.1262	L	0.27053	0.805	0.54753	D	0.999983	B	0.21520	0.057	B	0.20955	0.032	T	0.40776	-0.9545	10	0.05436	T	0.98	-14.8884	18.9825	0.92760	0.0:0.0:1.0:0.0	.	54	Q9BV47	DUS26_HUMAN	K	54	ENSP00000256261:T54K;ENSP00000429176:T54K;ENSP00000430922:T54K	ENSP00000256261:T54K	T	-	2	0	DUSP26	33574415	1.000000	0.71417	0.962000	0.40283	0.975000	0.68041	7.744000	0.85034	2.590000	0.87494	0.561000	0.74099	ACA	.		0.572	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025		T	33454873	G	T	33454873	3	4	131	1	0	0	0	0	1	0	0	0	4834	1377	48	4	486	4	DUSP26	8	33454873	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		33454873	112909149	35	11606											
EFCAB1	79645	broad.mit.edu	37	chr8	49647656	49647656	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actacattcttacttacaatGcttgcaatttttggttaagg	11	17	6	7	0	1	0	0	0	1	0	1	0	1	0	0	2	5	3	0	2	6	8			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:49647656G>A	ENST00000262103.3	-	1	135	c.55C>T	c.(55-57)Cat>Tat	p.H19Y	EFCAB1_ENST00000521002.1_5'UTR|EFCAB1_ENST00000523092.1_Missense_Mutation_p.H19Y|EFCAB1_ENST00000433756.1_Missense_Mutation_p.H19Y	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	19							calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				TACTTACAATGCTTGCAATTT	0.602																																					p.H19Y													.	EFCAB1-90	0			c.C55T						.						179	160	167					8																	49647656		2203	4300	6503	SO:0001583	missense	79645	exon1			TACAATGCTTGCA		CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.55C>T	8.37:g.49647656G>A	ENSP00000262103:p.His19Tyr	Somatic	63	1		WXS	Illumina HiSeq	Phase_I	90	8	NM_024593	0	0	0	0	0	B4DSB4|E7EVN7	Missense_Mutation	SNP	ENST00000262103.3	37	CCDS6145.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397676	0.62177	.	.	ENSG00000034239	ENST00000433756;ENST00000262103;ENST00000450553;ENST00000523092	T;T;T	0.68025	-0.3;-0.29;-0.3	5.04	4.15	0.48705	EF-hand-like domain (1);	0.193761	0.53938	D	0.000052	T	0.76564	0.4005	M	0.77103	2.36	0.52099	D	0.99994	B;D	0.59357	0.05;0.985	B;P	0.56788	0.024;0.806	T	0.76637	-0.2886	10	0.35671	T	0.21	.	12.9599	0.58451	0.0:0.0:0.8368:0.1632	.	19;19	Q9HAE3-2;Q9HAE3	.;EFCB1_HUMAN	Y	19	ENSP00000400873:H19Y;ENSP00000262103:H19Y;ENSP00000430765:H19Y	ENSP00000262103:H19Y	H	-	1	0	EFCAB1	49810209	1.000000	0.71417	0.994000	0.49952	0.568000	0.35870	3.938000	0.56583	1.247000	0.43917	0.462000	0.41574	CAT	.		0.602	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		A	49647656	G	A	49647656	3	1	131	1	0	0	0	0	1	0	0	0	4944	1319	46	2	604	2	EFCAB1	8	49647656	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	16192783	49647656	96716366	36	11607											
CA13	377677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	86162972	86162972	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcctatatatttaaggtcCtattcactggaaggaatttt	11	16	8	6	0	1	0	1	0	0	0	3	2	3	2	2	4	0	0	2	4	7	9			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:86162972C>T	ENST00000321764.3	+	2	343	c.41C>T	c.(40-42)cCt>cTt	p.P14L	RP11-219B4.6_ENST00000551479.1_5'Flank|CA13_ENST00000517298.1_3'UTR	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	14					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|myelin sheath (GO:0043209)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)	7					Zonisamide(DB00909)	ATTTAAGGTCCTATTCACTGG	0.338																																					p.P14L		.											.	CA13-90	0			c.C41T						.						62	64	63					8																	86162972		2203	4300	6503	SO:0001583	missense	377677	exon2			AAGGTCCTATTCA	BC052602	CCDS6236.1	8q21	2004-05-10				ENSG00000185015		"Carbonic anhydrases"	14914	protein-coding gene	gene with protein product		611436				14600151	Standard	NM_198584		Approved	CAXIII, FLJ37995, MGC59868	uc003ydg.2	Q8N1Q1		ENST00000321764.3:c.41C>T	8.37:g.86162972C>T	ENSP00000318912:p.Pro14Leu	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	91	11	NM_198584	0	0	0	0	0		Missense_Mutation	SNP	ENST00000321764.3	37	CCDS6236.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887731	0.91814	.	.	ENSG00000185015	ENST00000321764	T	0.68624	-0.34	5.48	5.48	0.80851	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.89361	0.6693	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93109	0.6515	10	0.87932	D	0	-23.2453	19.3527	0.94395	0.0:1.0:0.0:0.0	.	14	Q8N1Q1	CAH13_HUMAN	L	14	ENSP00000318912:P14L	ENSP00000318912:P14L	P	+	2	0	CA13	86350224	1.000000	0.71417	0.973000	0.42090	0.987000	0.75469	7.044000	0.76578	2.567000	0.86603	0.563000	0.77884	CCT	.		0.338	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584		T	86162972	C	T	86162972	3	4	131	1	0	0	0	0	1	0	0	0	2520	681	24	2	47	2	CA13	8	86162972	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	36515316	86162972	60201050	37	11608											
ADCY8	114	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	132002781	132002781	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acatgaatagcactgcctggGccacaacctaaaataaacac	17	6	6	12	0	0	1	0	1	0	0	0	1	0	1	3	1	4	1	3	1	7	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:132002781G>A	ENST00000286355.5	-	2	3060	c.968C>T	c.(967-969)gCc>gTc	p.A323V	ADCY8_ENST00000377928.3_Missense_Mutation_p.A323V	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	323					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CACTGCCTGGGCCACAACCTA	0.428										HNSCC(32;0.087)																											p.A323V		.											.	ADCY8-157	0			c.C968T						.						96	106	103					8																	132002781		2203	4300	6503	SO:0001583	missense	114	exon2			GCCTGGGCCACAA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.968C>T	8.37:g.132002781G>A	ENSP00000286355:p.Ala323Val	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	91	8	NM_001115	0	0	0	0	0		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767301	0.90020	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.81163	-1.46;-1.45	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.89326	0.6683	M	0.76002	2.32	0.58432	D	0.999991	D;P	0.63880	0.993;0.455	D;B	0.70227	0.968;0.214	D	0.88311	0.2956	10	0.44086	T	0.13	.	18.7877	0.91961	0.0:0.0:1.0:0.0	.	323;323	E7EVL1;P40145	.;ADCY8_HUMAN	V	323	ENSP00000286355:A323V;ENSP00000367161:A323V	ENSP00000286355:A323V	A	-	2	0	ADCY8	132071963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.792000	0.99085	2.751000	0.94390	0.650000	0.86243	GCC	.		0.428	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132002781	G	A	132002781	3	1	131	1	0	0	0	0	1	0	0	0	300	1203	42	2	2855	2	ADCY8	8	132002781	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	45839809	132002781	14361241	38	11609											
TG	7038	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	133899726	133899727	+	Frame_Shift_Ins	INS	-	-	TA																															agtgcttcaactcagagtgcINStactgtgttgatgctgaggg																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:133899726_133899727insTA	ENST00000220616.4	+	9	2149_2150	c.2109_2110insTA	c.(2110-2112)tacfs	p.Y704fs	TG_ENST00000377869.1_Frame_Shift_Ins_p.Y704fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	704	Thyroglobulin type-1 6. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ACTCAGAGTGCTACTGTGTTGA	0.515																																					p.C703fs		.											.	TG-145	0			c.2109_2110insTA						.																																			SO:0001589	frameshift_variant	7038	exon9			.	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2110_2111dupTA	8.37:g.133899727_133899728dupTA	ENSP00000220616:p.Tyr704fs	Somatic	416	0		WXS	Illumina HiSeq	Phase_I	497	91	NM_003235	0	0	0	0	0	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Frame_Shift_Ins	INS	ENST00000220616.4	37	CCDS34944.1																																																																																			.		0.515	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		TA	133899727	-	TA	133899726	7	5	131	1	0	1	1	0	0	0	0	0	15845	805	28	0	2143	0	TG	8	133899726	Frame_Shift_Ins	INS	-	TCGA-HE-A5NF-01A-11D-A26P-10	1896945	133899726	12464296	39	11610											
RMI1	80010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	86617525	86617525	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatggtactgcatatctaGatgtagactttgtggatgaa	11	14	11	5	0	1	4	0	2	1	2	1	5	1	5	0	2	2	3	0	2	5	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:86617525G>T	ENST00000325875.3	+	3	1956	c.1624G>T	c.(1624-1626)Gat>Tat	p.D542Y		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	542					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)				biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						TGCATATCTAGATGTAGACTT	0.368																																					p.D542Y		.											.	RMI1-90	0			c.G1624T						.						197	193	194					9																	86617525		2203	4300	6503	SO:0001583	missense	80010	exon3			TATCTAGATGTAG	AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"BLM-Associated Polypeptide, 75 kDa"	610404	"chromosome 9 open reading frame 76", "RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.1624G>T	9.37:g.86617525G>T	ENSP00000317039:p.Asp542Tyr	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	97	19	NM_024945	0	0	1	1	0	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	37	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935730	0.52972	.	.	ENSG00000178966	ENST00000325875	T	0.47177	0.85	5.29	5.29	0.74685	.	0.104013	0.64402	D	0.000005	T	0.61198	0.2328	L	0.55481	1.735	0.47659	D	0.999484	D	0.89917	1.0	D	0.70487	0.969	T	0.58702	-0.7590	9	.	.	.	-9.5894	12.6452	0.56731	0.0762:0.0:0.9238:0.0	.	542	Q9H9A7	RMI1_HUMAN	Y	542	ENSP00000317039:D542Y	.	D	+	1	0	RMI1	85807345	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.827000	0.75303	2.620000	0.88729	0.563000	0.77884	GAT	.		0.368	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945		T	86617525	G	T	86617525	3	4	131	1	0	0	0	0	1	0	0	0	13427	942	33	4	1626	4	RMI1	9	86617525	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		86617525	54595906	40	11611											
LPAR1	1902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	113704022	113704022	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacccgccggttgctcatccGtgtgtggagctgcatgcgga	5	10	14	12	4	1	0	1	0	0	0	2	2	2	2	3	3	5	4	3	3	1	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:113704022G>A	ENST00000374431.3	-	4	855	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	LPAR1_ENST00000541779.1_Missense_Mutation_p.R159W|LPAR1_ENST00000358883.4_Missense_Mutation_p.R158W|LPAR1_ENST00000538760.1_Missense_Mutation_p.R159W|LPAR1_ENST00000374430.2_Missense_Mutation_p.R158W	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	158					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.R158W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						TTGCTCATCCGTGTGTGGAGC	0.542																																					p.R158W	NSCLC(115;661 2323 9836 34256)	.											.	LPAR1-24	1	Substitution - Missense(1)	large_intestine(1)	c.C472T						.						117	104	109					9																	113704022		2203	4300	6503	SO:0001583	missense	1902	exon3			TCATCCGTGTGTG	U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3166	protein-coding gene	gene with protein product		602282	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.472C>T	9.37:g.113704022G>A	ENSP00000363553:p.Arg158Trp	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	180	28	NM_001401	0	0	0	5	5	B4DK36|O00656|O00722|P78351	Missense_Mutation	SNP	ENST00000374431.3	37	CCDS6777.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017060	0.75161	.	.	ENSG00000198121	ENST00000374431;ENST00000541779;ENST00000374430;ENST00000358883;ENST00000449490;ENST00000538760;ENST00000441240	T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07	5.53	4.64	0.57946	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60301	0.2258	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.983;0.983	T	0.63189	-0.6693	10	0.72032	D	0.01	.	8.4744	0.33005	0.0771:0.0:0.7707:0.1522	.	159;159;158	B4DQ18;B4DK36;Q92633	.;.;LPAR1_HUMAN	W	158;159;158;158;140;159;158	ENSP00000363553:R158W;ENSP00000445697:R159W;ENSP00000363552:R158W;ENSP00000351755:R158W;ENSP00000440201:R159W;ENSP00000401810:R158W	ENSP00000351755:R158W	R	-	1	2	LPAR1	112743843	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.528000	0.73807	1.357000	0.45904	0.655000	0.94253	CGG	.		0.542	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159		A	113704022	G	A	113704022	3	1	131	1	0	0	0	0	1	0	0	0	8929	1144	40	1	630	1	LPAR1	9	113704022	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	27086497	113704022	27509409	41	11612											
SPTAN1	6709	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	131362363	131362363	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctttctttgaataggatgAaactgattccaagacagcct	12	13	7	9	0	2	4	0	3	2	1	3	5	3	5	2	1	2	0	2	1	4	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:131362363A>T	ENST00000372731.4	+	27	3658	c.3548A>T	c.(3547-3549)gAa>gTa	p.E1183V	SPTAN1_ENST00000358161.5_Missense_Mutation_p.E1183V|SPTAN1_ENST00000372739.3_Missense_Mutation_p.E1183V	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1183					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GAATAGGATGAAACTGATTCC	0.433																																					p.E1183V	NSCLC(120;833 1744 2558 35612 37579)	.											.	SPTAN1-158	0			c.A3548T						.						125	114	118					9																	131362363		2203	4300	6503	SO:0001583	missense	6709	exon27			AGGATGAAACTGA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3548A>T	9.37:g.131362363A>T	ENSP00000361816:p.Glu1183Val	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	94	9	NM_003127	0	0	0	0	0	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.305120	0.60305	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.51574	0.7;0.72;0.7	6.08	6.08	0.98989	.	0.142496	0.64402	D	0.000006	T	0.40398	0.1115	N	0.19112	0.55	0.80722	D	1	P;B;B;B	0.36733	0.567;0.384;0.384;0.265	B;B;B;B	0.39840	0.18;0.311;0.311;0.165	T	0.42103	-0.9471	10	0.87932	D	0	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	1183;1163;1183;1183	A6NG51;Q13813-3;Q13813-2;Q13813	.;.;.;SPTA2_HUMAN	V	1183;1183;1183;1163	ENSP00000350882:E1183V;ENSP00000361816:E1183V;ENSP00000361824:E1183V	ENSP00000350882:E1183V	E	+	2	0	SPTAN1	130402184	1.000000	0.71417	0.945000	0.38365	0.557000	0.35523	8.593000	0.90832	2.333000	0.79357	0.533000	0.62120	GAA	.		0.433	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131362363	A	T	131362363	3	4	131	1	0	0	0	0	1	0	0	0	15149	246	9	5	3650	5	SPTAN1	9	131362363	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	17658341	131362363	9851068	42	11613											
LCN10	414332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139633991	139633991	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctctcatggcaggatggTgtgtgtacgggacgctgtgg	5	11	18	7	2	1	0	1	0	1	0	2	2	1	2	0	6	1	4	0	6	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:139633991T>C	ENST00000474369.1	-	5	549	c.550A>G	c.(550-552)Acc>Gcc	p.T184A	LCN6_ENST00000435202.1_3'UTR|LCN10_ENST00000527229.1_Missense_Mutation_p.T161A|LCN6_ENST00000480584.1_5'Flank|LCN10_ENST00000497771.1_Missense_Mutation_p.T197A			Q6JVE6	LCN10_HUMAN	lipocalin 10	184					transport (GO:0006810)	extracellular region (GO:0005576)				breast(2)|cervix(1)|large_intestine(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		GGCAGGATGGTGTGTGTACGG	0.617																																					p.T197A		.											.	LCN10-67	0			c.A589G						.						92	76	81					9																	139633991		2199	4295	6494	SO:0001583	missense	414332	exon6			GGATGGTGTGTGT	AY301271	CCDS35182.2	9q34.3	2011-10-24			ENSG00000187922	ENSG00000187922		"Lipocalins"	20892	protein-coding gene	gene with protein product		612904				15363845	Standard	NM_001001712		Approved		uc004civ.3	Q6JVE6	OTTHUMG00000150428	ENST00000474369.1:c.550A>G	9.37:g.139633991T>C	ENSP00000420564:p.Thr184Ala	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	196	24	NM_001001712	0	0	0	0	0	A2RUU3|B0QZ79	Missense_Mutation	SNP	ENST00000474369.1	37	CCDS35182.2	.	.	.	.	.	.	.	.	.	.	T	13.52	2.260996	0.39995	.	.	ENSG00000187922	ENST00000527229;ENST00000497771;ENST00000474369	T;T	0.33865	1.39;1.41	3.17	2.04	0.26737	.	0.000000	0.36002	U	0.002855	T	0.39655	0.1086	.	.	.	0.27101	N	0.962612	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.63957	0.92;0.92;0.92	T	0.17410	-1.0370	9	0.19147	T	0.46	-7.4152	4.3041	0.10938	0.0:0.1588:0.0:0.8412	.	161;184;197	E9PK15;Q6JVE6;Q6JVE6-2	.;LCN10_HUMAN;.	A	161;197;184	ENSP00000418491:T197A;ENSP00000420564:T184A	ENSP00000420564:T184A	T	-	1	0	LCN10	138753812	0.530000	0.26330	1.000000	0.80357	0.718000	0.41266	1.557000	0.36299	1.410000	0.46936	0.451000	0.29950	ACC	.		0.617	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712		C	139633991	T	C	139633991	3	2	131	1	0	0	0	0	1	0	0	0	8702	1696	59	3	17	3	LCN10	9	139633991	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	8271628	139633991	1579440	43	11614											
CUBN	8029	broad.mit.edu	37	chr10	16941145	16941145	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgaggccagtgaggggatctGattgtaccattatcagaatg	11	11	13	6	0	2	4	1	3	1	1	2	5	2	5	2	3	1	1	2	3	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:16941145G>C	ENST00000377833.4	-	54	8513	c.8448C>G	c.(8446-8448)atC>atG	p.I2816M		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2816	CUB 21. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAGGGGATCTGATTGTACCAT	0.403																																					p.I2816M													.	CUBN-166	0			c.C8448G						.						118	112	114					10																	16941145		2203	4300	6503	SO:0001583	missense	8029	exon54			GGATCTGATTGTA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8448C>G	10.37:g.16941145G>C	ENSP00000367064:p.Ile2816Met	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	100	4	NM_001081	0	0	9	9	0	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.139005	0.21123	.	.	ENSG00000107611	ENST00000377833	T	0.40476	1.03	5.63	0.557	0.17260	CUB (5);	0.137522	0.33057	N	0.005332	T	0.64494	0.2603	M	0.93150	3.385	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.64782	-0.6326	10	0.66056	D	0.02	.	7.5405	0.27735	0.1201:0.0:0.4925:0.3874	.	2816	O60494	CUBN_HUMAN	M	2816	ENSP00000367064:I2816M	ENSP00000367064:I2816M	I	-	3	3	CUBN	16981151	1.000000	0.71417	0.001000	0.08648	0.014000	0.08584	3.071000	0.50041	-0.070000	0.12908	-0.940000	0.02684	ATC	.		0.403	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16941145	G	C	16941145	3	2	131	1	0	0	0	0	1	0	0	0	4057	1280	45	4	2479	4	CUBN	10	16941145	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		16941145	118593602	44	11615											
NUDT13	25961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74879794	74879794	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtatttatttgaactgaaGgaagatgatgatgcatgtaa	15	13	11	2	0	0	5	0	4	0	1	0	6	0	6	0	2	2	3	0	2	6	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:74879794G>T	ENST00000357321.4	+	3	220	c.102G>T	c.(100-102)aaG>aaT	p.K34N	NUDT13_ENST00000372997.3_Missense_Mutation_p.K34N|NUDT13_ENST00000349051.5_Missense_Mutation_p.K34N|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000537969.1_5'UTR|NUDT13_ENST00000544879.1_5'UTR	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					TTGAACTGAAGGAAGATGATG	0.403																																					p.K34N		.											.	NUDT13-90	0			c.G102T						.						134	144	141					10																	74879794		2203	4300	6503	SO:0001583	missense	25961	exon3			ACTGAAGGAAGAT	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.102G>T	10.37:g.74879794G>T	ENSP00000349874:p.Lys34Asn	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	43	15	NM_015901	0	0	0	1	1		Missense_Mutation	SNP	ENST00000357321.4	37	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.736917	0.69304	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.58797	1.36;0.36;0.31	5.18	-2.34	0.06704	.	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.992;0.993	T	0.59862	-0.7374	10	0.72032	D	0.01	-2.5729	12.2089	0.54369	0.6313:0.0:0.3687:0.0	.	34;34;34	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	N	34	ENSP00000349874:K34N;ENSP00000335326:K34N;ENSP00000362088:K34N	ENSP00000335326:K34N	K	+	3	2	NUDT13	74549800	0.999000	0.42202	0.977000	0.42913	0.998000	0.95712	0.456000	0.21859	-0.547000	0.06207	0.655000	0.94253	AAG	.		0.403	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		T	74879794	G	T	74879794	3	4	131	1	0	0	0	0	1	0	0	0	10755	991	35	4	108	4	NUDT13	10	74879794	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	57938649	74879794	60654953	45	11616											
LZTS2	84445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102763858	102763858	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcctggaaggaaagctccgaGaccgggaggcagagcttcag	11	5	15	10	2	1	2	1	0	0	2	3	6	3	5	3	4	2	3	3	4	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:102763858G>C	ENST00000370220.1	+	2	4066	c.1003G>C	c.(1003-1005)Gac>Cac	p.D335H	LZTS2_ENST00000370223.3_Missense_Mutation_p.D335H					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		AAAGCTCCGAGACCGGGAGGC	0.637																																					p.D335H	Esophageal Squamous(8;38 437 13604 19902 37640)	.											.	LZTS2-155	0			c.G1003C						.						43	47	46					10																	102763858		2202	4297	6499	SO:0001583	missense	84445	exon3			CTCCGAGACCGGG	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.1003G>C	10.37:g.102763858G>C	ENSP00000359240:p.Asp335His	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	156	33	NM_032429	0	0	25	32	7		Missense_Mutation	SNP	ENST00000370220.1	37	CCDS7507.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123472	0.56613	.	.	ENSG00000107816	ENST00000370223;ENST00000315797;ENST00000370220	T;T	0.41065	1.01;1.01	5.12	4.19	0.49359	.	0.157325	0.56097	D	0.000028	T	0.42494	0.1205	L	0.39898	1.24	0.43222	D	0.995102	P	0.40398	0.716	P	0.45946	0.498	T	0.20405	-1.0276	9	.	.	.	-23.6803	15.3201	0.74115	0.0:0.1408:0.8592:0.0	.	335	Q9BRK4	LZTS2_HUMAN	H	335	ENSP00000359243:D335H;ENSP00000359240:D335H	.	D	+	1	0	LZTS2	102753848	1.000000	0.71417	0.732000	0.30844	0.655000	0.38815	7.542000	0.82095	1.243000	0.43853	0.561000	0.74099	GAC	.		0.637	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743		C	102763858	G	C	102763858	3	2	131	1	0	0	0	0	1	0	0	0	9164	942	33	4	1009	4	LZTS2	10	102763858	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	27884064	102763858	32770889	46	11617											
TIAL1	7073	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	121338280	121338280	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggtttacgagtggcccAattggttcggatttgacgac	8	12	14	7	3	0	1	0	1	0	0	1	4	0	2	1	5	1	2	1	5	2	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:121338280A>C	ENST00000436547.2	-	7	558	c.514T>G	c.(514-516)Tgg>Ggg	p.W172G	TIAL1_ENST00000369092.4_Missense_Mutation_p.W49G|TIAL1_ENST00000369093.2_Missense_Mutation_p.W189G|TIAL1_ENST00000463089.2_5'Flank	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	172	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		CGAGTGGCCCAATTGGTTCGG	0.398																																					p.W189G		.											.	TIAL1-91	0			c.T565G						.						160	141	147					10																	121338280		2203	4300	6503	SO:0001583	missense	7073	exon7			TGGCCCAATTGGT	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.514T>G	10.37:g.121338280A>C	ENSP00000394902:p.Trp172Gly	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	183	39	NM_001033925	0	0	8	21	13	A8K3T0|A8K4L9	Missense_Mutation	SNP	ENST00000436547.2	37	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385753	0.82792	.	.	ENSG00000151923	ENST00000369093;ENST00000369092;ENST00000436547	T;T;T	0.75367	3.33;-0.93;-0.93	5.61	5.61	0.85477	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	D	0.85008	0.5599	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	0.993;1.0;1.0;0.999	D;D;D;D	0.91635	0.968;0.999;0.994;0.966	D	0.86674	0.1912	10	0.87932	D	0	-1.9553	15.8113	0.78568	1.0:0.0:0.0:0.0	.	49;49;189;172	B4DHS3;Q49AS9;A8K4L9;Q01085	.;.;.;TIAR_HUMAN	G	189;49;172	ENSP00000358089:W189G;ENSP00000358088:W49G;ENSP00000394902:W172G	ENSP00000358088:W49G	W	-	1	0	TIAL1	121328270	1.000000	0.71417	0.993000	0.49108	0.863000	0.49368	9.125000	0.94402	2.137000	0.66172	0.482000	0.46254	TGG	.		0.398	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		C	121338280	A	C	121338280	3	2	131	1	0	0	0	0	1	0	0	0	15921	130	5	5	637	5	TIAL1	10	121338280	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	18574422	121338280	14196467	47	11618											
WDR11	55717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	122664157	122664157	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaaaccgtttctcttactaGacagacagagctgtgcagtt	13	11	8	9	1	1	3	0	0	1	3	2	3	1	3	1	0	4	4	1	0	4	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:122664157G>A	ENST00000263461.6	+	25	3273		c.e25-1		WDR11_ENST00000604509.1_Intron	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11						cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TCTCTTACTAGACAGACAGAG	0.358																																					.		.											.	WDR11-226	0			c.3028-1G>A						.						93	89	90					10																	122664157		2203	4300	6503	SO:0001630	splice_region_variant	55717	exon25			TTACTAGACAGAC	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"WD repeat domain containing"	13831	protein-coding gene	gene with protein product		606417	"bromodomain and WD repeat domain containing 2"	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3028-1G>A	10.37:g.122664157G>A		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	98	15	NM_018117	0	0	0	0	0	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Splice_Site	SNP	ENST00000263461.6	37	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566439	0.86439	.	.	ENSG00000120008	ENST00000263461	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR11	122654147	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.434000	0.97515	2.836000	0.97738	0.655000	0.94253	.	.		0.358	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		Intron	A	122664157	G	A	122664157	5	1	131	1	0	0	0	0	0	0	1	0	17306	956	33	2	3125	2	WDR11	10	122664157	Splice_Site	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	1325877	122664157	12870590	48	11619											
C11orf40	143501	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	4592781	4592781	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagtgttttgtaatcagtgcGgtccaattcaatggcccagt	10	13	10	8	1	2	0	2	0	0	0	3	0	3	0	2	2	1	2	2	2	4	4	rs573632085	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:4592781G>C	ENST00000307616.1	-	4	525	c.526C>G	c.(526-528)Cgc>Ggc	p.R176G		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	176										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		taatcagtgcggtccaattca	0.433																																					p.R176G		.											.	C11orf40-92	0			c.C526G						.						81	73	76					11																	4592781		2201	4298	6499	SO:0001583	missense	143501	exon4			CAGTGCGGTCCAA		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.526C>G	11.37:g.4592781G>C	ENSP00000302918:p.Arg176Gly	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	86	14	NM_144663	0	0	0	0	0		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.039801	0.00402	.	.	ENSG00000171987	ENST00000307616	T	0.55930	0.49	0.832	-1.66	0.08265	.	.	.	.	.	T	0.26774	0.0655	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.08743	-1.0707	9	0.87932	D	0	.	3.0485	0.06161	0.2412:0.0:0.4837:0.275	.	176	Q8WZ69	CK040_HUMAN	G	176	ENSP00000302918:R176G	ENSP00000302918:R176G	R	-	1	0	C11orf40	4549357	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.923000	0.04000	-1.894000	0.01105	-1.561000	0.00884	CGC	.		0.433	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		C	4592781	G	C	4592781	3	2	131	1	0	0	0	0	1	0	0	0	1643	1116	39	4	130	4	C11orf40	11	4592781	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		4592781	130413735	49	11620											
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6646473	6646473	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aggtgcattgtcattgacatCctccacaagcactgtgaggt	10	11	10	10	0	1	2	1	2	0	0	3	2	3	2	2	2	2	2	2	2	1	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:6646473C>G	ENST00000299441.3	-	19	7513	c.7102G>C	c.(7102-7104)Gat>Cat	p.D2368H	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2368	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATTGACATCCTCCACAAGC	0.587																																					p.D2368H		.											.	DCHS1-73	0			c.G7102C						.						101	92	95					11																	6646473		2201	4296	6497	SO:0001583	missense	8642	exon19			TGACATCCTCCAC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.7102G>C	11.37:g.6646473C>G	ENSP00000299441:p.Asp2368His	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	136	20	NM_003737	0	0	2	2	0	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	c	22.9	4.351321	0.82132	.	.	ENSG00000166341	ENST00000299441	T	0.76186	-1.0	4.94	4.94	0.65067	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.43747	D	0.000525	D	0.91202	0.7228	H	0.97682	4.055	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94164	0.7417	10	0.87932	D	0	.	16.9335	0.86197	0.0:1.0:0.0:0.0	.	2368	Q96JQ0	PCD16_HUMAN	H	2368	ENSP00000299441:D2368H	ENSP00000299441:D2368H	D	-	1	0	DCHS1	6603049	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.632000	0.83247	2.560000	0.86352	0.651000	0.88453	GAT	.		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		G	6646473	C	G	6646473	3	3	131	1	0	0	0	0	1	0	0	0	4293	855	30	4	2806	4	DCHS1	11	6646473	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	2053692	6646473	128360043	50	11621											
LRP4	4038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46898795	46898795	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggtgttcttcatggtaaTgttgattggtaccaccacat	10	15	9	7	0	2	1	1	1	1	0	2	1	2	1	2	3	1	4	2	3	3	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:46898795T>C	ENST00000378623.1	-	23	3474	c.3232A>G	c.(3232-3234)Att>Gtt	p.I1078V	LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1078					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TTCATGGTAATGTTGATTGGT	0.507																																					p.I1078V		.											.	LRP4-94	0			c.A3232G						.						250	187	208					11																	46898795		2201	4299	6500	SO:0001583	missense	4038	exon23			TGGTAATGTTGAT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"Low density lipoprotein receptors"	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3232A>G	11.37:g.46898795T>C	ENSP00000367888:p.Ile1078Val	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	176	25	NM_002334	0	0	1	1	0	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.991485	0.35131	.	.	ENSG00000134569	ENST00000378623	D	0.90955	-2.76	6.17	-1.45	0.08828	Six-bladed beta-propeller, TolB-like (1);	0.729507	0.14357	N	0.324711	T	0.70850	0.3271	N	0.00926	-1.1	0.20926	N	0.999826	B	0.02656	0.0	B	0.01281	0.0	T	0.58440	-0.7636	10	0.14656	T	0.56	.	13.3945	0.60843	0.0:0.5812:0.0:0.4188	.	1078	O75096	LRP4_HUMAN	V	1078	ENSP00000367888:I1078V	ENSP00000367888:I1078V	I	-	1	0	LRP4	46855371	1.000000	0.71417	0.959000	0.39883	0.998000	0.95712	0.814000	0.27239	-0.251000	0.09542	0.533000	0.62120	ATT	.		0.507	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		C	46898795	T	C	46898795	3	2	131	1	0	0	0	0	1	0	0	0	8984	1464	51	3	2549	3	LRP4	11	46898795	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	40252322	46898795	88107721	51	11622											
AMOTL1	154810	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	94533391	94533391	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccgggatgctccacgagatGgtcaagccctaccctgctcc	7	7	10	17	2	1	1	1	0	0	1	3	3	3	2	5	2	4	2	5	2	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:94533391G>T	ENST00000433060.2	+	3	1176	c.1035G>T	c.(1033-1035)atG>atT	p.M345I	AMOTL1_ENST00000317837.9_Missense_Mutation_p.M345I|AMOTL1_ENST00000317829.8_Missense_Mutation_p.M295I	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	345					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				TCCACGAGATGGTCAAGCCCT	0.562																																					p.M345I		.											.	AMOTL1-91	0			c.G1035T						.						115	116	116					11																	94533391		2016	4172	6188	SO:0001583	missense	154810	exon3			CGAGATGGTCAAG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"junction-enriched and associated protein"	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1035G>T	11.37:g.94533391G>T	ENSP00000387739:p.Met345Ile	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	127	22	NM_130847	0	0	1	3	2	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471025	0.43942	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000317837;ENST00000433060	T;T;T	0.13307	2.6;2.6;2.6	5.13	4.15	0.48705	.	0.155049	0.44688	D	0.000423	T	0.10380	0.0254	L	0.40543	1.245	0.30008	N	0.815444	B;B	0.16802	0.013;0.019	B;B	0.13407	0.009;0.006	T	0.06127	-1.0844	9	.	.	.	-21.0972	7.6609	0.28402	0.0937:0.2865:0.6198:0.0	.	295;345	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	I	295;351;345;345	ENSP00000320968:M295I;ENSP00000323474:M345I;ENSP00000387739:M345I	.	M	+	3	0	AMOTL1	94173039	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.997000	0.29731	2.395000	0.81488	0.555000	0.69702	ATG	.		0.562	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		T	94533391	G	T	94533391	3	4	131	1	0	0	0	0	1	0	0	0	583	1348	47	4	1045	4	AMOTL1	11	94533391	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	47634596	94533391	40473125	52	11623											
TMBIM4	51643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	66546147	66546147	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgagggcaaacagcaaaatTaaggcaggactgaaagacat	18	4	11	8	1	0	2	0	1	0	1	0	4	0	3	1	3	2	3	1	3	5	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:66546147T>C	ENST00000358230.3	-	3	336	c.216A>G	c.(214-216)ttA>ttG	p.L72L	TMBIM4_ENST00000556010.1_Silent_p.L72L|TMBIM4_ENST00000286424.7_Silent_p.L119L|TMBIM4_ENST00000539652.1_Silent_p.L72L|TMBIM4_ENST00000542724.1_Silent_p.L41L|TMBIM4_ENST00000398033.4_Silent_p.L72L|TMBIM4_ENST00000544599.1_5'UTR	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	72					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		ACAGCAAAATTAAGGCAGGAC	0.303																																					p.L72L		.											.	TMBIM4-515	0			c.A216G						.						79	75	76					12																	66546147		1821	4077	5898	SO:0001819	synonymous_variant	51643	exon3			CAAAATTAAGGCA	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.216A>G	12.37:g.66546147T>C		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	123	20	NM_016056	0	0	0	0	0	Q542Z6|Q9UHY5|Q9Y3C2	Silent	SNP	ENST00000358230.3	37	CCDS41805.1																																																																																			.		0.303	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056		C	66546147	T	C	66546147	2	2	131	1	0	0	0	0	0	0	0	1	16014	1751	61	3		3	TMBIM4	12	66546147	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		66546147	67305748	53	11624											
HPD	3242	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	122281677	122281677	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcagcttctcccgcagtTgtttgtagtacgtggaggga	6	14	12	9	2	3	0	1	0	2	0	4	2	3	2	1	2	2	6	1	2	2	6	rs201305943		TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:122281677T>G	ENST00000289004.4	-	12	928	c.893A>C	c.(892-894)cAa>cCa	p.Q298P	HPD_ENST00000543163.1_Missense_Mutation_p.Q259P	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	298					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	CTCCCGCAGTTGTTTGTAGTA	0.557													T|||	1	0.000199681	0	0	5008	,	,		16317	0.001		0	False		,,,				2504	0				p.Q298P													.	HPD-90	0			c.A893C						.						154	133	140					12																	122281677		2203	4300	6503	SO:0001583	missense	3242	exon12			CGCAGTTGTTTGT	BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"glyoxalase domain containing 3"	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.893A>C	12.37:g.122281677T>G	ENSP00000289004:p.Gln298Pro	Somatic	153	1		WXS	Illumina HiSeq	Phase_I	202	59	NM_002150	0	0	6	11	5	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	37	CCDS9224.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	10.24	1.295797	0.23564	.	.	ENSG00000158104	ENST00000289004;ENST00000545969;ENST00000543163	T;T	0.69926	-0.44;-0.44	4.32	3.14	0.36123	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.521328	0.20860	N	0.084365	T	0.67268	0.2875	M	0.78456	2.415	0.28564	N	0.910987	B	0.15719	0.014	B	0.35770	0.21	T	0.61983	-0.6950	10	0.38643	T	0.18	-13.4789	5.2654	0.15595	0.3145:0.0:0.1519:0.5335	.	298	P32754	HPPD_HUMAN	P	298;295;259	ENSP00000289004:Q298P;ENSP00000441677:Q259P	ENSP00000289004:Q298P	Q	-	2	0	HPD	120766060	0.995000	0.38212	0.652000	0.29579	0.773000	0.43773	1.628000	0.37060	0.668000	0.31126	0.418000	0.28097	CAA	T|0.999;G|0.000		0.557	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150		G	122281677	T	G	122281677	3	3	131	1	0	0	0	0	1	0	0	0	7353	1812	63	5	300	5	HPD	12	122281677	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	55735530	122281677	11570218	54	11625											
ZNF140	7699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	133683062	133683062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcagccggagcttttcccTcattctacatcagagaactc	9	12	6	14	1	4	1	3	0	1	1	6	3	5	2	2	1	4	1	2	1	2	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:133683062T>C	ENST00000355557.2	+	5	2482	c.1199T>C	c.(1198-1200)cTc>cCc	p.L400P	ZNF140_ENST00000440550.2_3'UTR|ZNF140_ENST00000544426.1_Missense_Mutation_p.L297P	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	400					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)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AGCTTTTCCCTCATTCTACAT	0.448																																					p.L400P		.											.	ZNF140-90	0			c.T1199C						.						90	91	91					12																	133683062		2203	4300	6503	SO:0001583	missense	7699	exon5			TTTCCCTCATTCT	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1199T>C	12.37:g.133683062T>C	ENSP00000347755:p.Leu400Pro	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	47	7	NM_003440	0	0	3	9	6	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	37	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.296703	0.60086	.	.	ENSG00000196387	ENST00000355557;ENST00000544426;ENST00000433577	T;T	0.14266	2.52;2.52	3.85	3.85	0.44370	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31859	N	0.006952	T	0.39627	0.1085	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36672	-0.9738	10	0.87932	D	0	.	7.0829	0.25241	0.0:0.1065:0.0:0.8935	.	400	P52738	ZN140_HUMAN	P	400;297;191	ENSP00000347755:L400P;ENSP00000445411:L297P	ENSP00000347755:L400P	L	+	2	0	ZNF140	132193135	0.996000	0.38824	0.998000	0.56505	0.958000	0.62258	5.435000	0.66532	1.736000	0.51660	0.460000	0.39030	CTC	.		0.448	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		C	133683062	T	C	133683062	3	2	131	1	0	0	0	0	1	0	0	0	17761	1551	54	3	1213	3	ZNF140	12	133683062	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	11401385	133683062	168833	55	11626											
KCTD12	115207	hgsc.bcm.edu	37	chr13	77460122	77460122	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcagcgagtcgggcacCgacaccaccgtgcagcgccg	9	2	14	16	6	0	1	0	0	0	1	1	3	0	1	4	1	4	3	4	1	0	0	rs371800969		TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr13:77460122C>G	ENST00000377474.2	-	1	403	c.162G>C	c.(160-162)tcG>tcC	p.S54S	AC000403.1_ENST00000579275.1_RNA|KCTD12_ENST00000317765.2_Silent_p.S54S	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	54					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		AGTCGGGCACCGACACCACCG	0.692																																					p.S54S		.											.	KCTD12-91	0			c.G162C						.	C		0,4356		0,0,2178	16	15	15		162	0.4	1	13		15	2,8550		0,2,4274	no	coding-synonymous	KCTD12	NM_138444.3		0,2,6452	GG,GC,CC		0.0234,0.0,0.0155		54/326	77460122	2,12906	2178	4276	6454	SO:0001819	synonymous_variant	115207	exon1			GGGCACCGACACC	AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"predominantly fetal expressed T1 domain"	610521	"chromosome 13 open reading frame 2", "potassium channel tetramerisation domain containing 12"	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.162G>C	13.37:g.77460122C>G		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_138444	0	0	5	7	2		Silent	SNP	ENST00000377474.2	37	CCDS9455.1																																																																																			.		0.692	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444		G	77460122	C	G	77460122	2	3	131	1	0	0	0	0	0	0	0	1	8120	639	23	4		4	KCTD12	13	77460122	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		77460122	37709756	56	11627											
TEP1	7011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20845648	20845648	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgaccctgagccccctggGaacctagagaatgagagaga	12	5	12	12	0	0	5	0	3	0	3	0	9	0	6	5	1	2	0	5	1	3	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:20845648G>T	ENST00000262715.5	-	41	5919	c.5879C>A	c.(5878-5880)tCc>tAc	p.S1960Y	TEP1_ENST00000545983.1_Missense_Mutation_p.S298Y|TEP1_ENST00000556935.1_Missense_Mutation_p.S1852Y	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1960					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGCCCCCTGGGAACCTAGAGA	0.582																																					p.S1960Y		.											.	TEP1-95	0			c.C5879A						.						53	54	54					14																	20845648		2203	4300	6503	SO:0001583	missense	7011	exon41			CCCTGGGAACCTA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"WD repeat domain containing"	11726	protein-coding gene	gene with protein product	"TROVE domain family, member 1"	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5879C>A	14.37:g.20845648G>T	ENSP00000262715:p.Ser1960Tyr	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	76	17	NM_007110	0	0	0	0	0	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164956	0.78339	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.71461	0.73;-0.57;1.23	5.33	5.33	0.75918	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.606102	0.17469	N	0.173149	T	0.80639	0.4661	M	0.71036	2.16	0.38057	D	0.935966	D;D;D;D	0.59767	0.976;0.983;0.986;0.971	P;P;P;P	0.57152	0.556;0.804;0.814;0.641	D	0.83486	0.0067	10	0.59425	D	0.04	-4.4509	15.9418	0.79758	0.0:0.0:1.0:0.0	.	298;1852;1303;1960	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	Y	1960;1960;1852;298	ENSP00000262715:S1960Y;ENSP00000452574:S1852Y;ENSP00000438849:S298Y	ENSP00000262715:S1960Y	S	-	2	0	TEP1	19915488	0.983000	0.35010	0.894000	0.35097	0.940000	0.58332	4.982000	0.63825	2.502000	0.84385	0.563000	0.77884	TCC	.		0.582	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20845648	G	T	20845648	3	4	131	1	0	0	0	0	1	0	0	0	15791	1174	41	4	2064	4	TEP1	14	20845648	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		20845648	86503892	57	11628											
CDH24	64403	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23524349	23524349	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgttgatgtcttgcacttTgatgatgaactctgatgggg	7	15	13	6	1	2	5	0	5	2	0	3	5	2	5	0	2	2	2	0	2	1	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:23524349T>A	ENST00000267383.5	-	2	507	c.415A>T	c.(415-417)Aaa>Taa	p.K139*	CDH24_ENST00000487137.2_Nonsense_Mutation_p.K139*|CDH24_ENST00000397359.3_Nonsense_Mutation_p.K139*|CDH24_ENST00000554034.1_Nonsense_Mutation_p.K139*			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	139	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TCTTGCACTTTGATGATGAAC	0.587											OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K139X		.											.	CDH24-90	0			c.A415T						.						86	90	88					14																	23524349		2203	4300	6503	SO:0001587	stop_gained	64403	exon3			GCACTTTGATGAT	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"Cadherins / Major cadherins"	14265	protein-coding gene	gene with protein product			"cadherin-like 24"			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.415A>T	14.37:g.23524349T>A	ENSP00000267383:p.Lys139*	Somatic	118	0	764	WXS	Illumina HiSeq	Phase_I	138	23	NM_022478	0	0	0	0	0	D3DS44|Q86UP1|Q9NT84	Nonsense_Mutation	SNP	ENST00000267383.5	37	CCDS9585.1	.	.	.	.	.	.	.	.	.	.	T	36	5.772834	0.96922	.	.	ENSG00000139880	ENST00000397359;ENST00000487137;ENST00000422751;ENST00000554034;ENST00000267383	.	.	.	3.72	3.72	0.42706	.	0.061985	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8066	0.52158	0.0:0.0:0.0:1.0	.	.	.	.	X	139	.	ENSP00000267383:K139X	K	-	1	0	CDH24	22594189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	1.689000	0.51079	0.459000	0.35465	AAA	.		0.587	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478		A	23524349	T	A	23524349	4	1	131	1	0	0	0	0	0	1	0	0	3115	1821	63	5	2088	5	CDH24	14	23524349	Nonsense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	2678701	23524349	83825191	58	11629											
NYNRIN	57523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24885037	24885037	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctggcagccgtggcctgcgGcctggagcgctttggccagt	3	8	16	14	3	0	0	0	0	0	0	0	1	0	1	5	5	3	2	5	5	0	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:24885037G>T	ENST00000382554.3	+	9	4400	c.4082G>T	c.(4081-4083)gGc>gTc	p.G1361V		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1361					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GTGGCCTGCGGCCTGGAGCGC	0.627																																					p.G1361V		.											.	NYNRIN-3	0			c.G4082T						.						68	73	71					14																	24885037		1961	4143	6104	SO:0001583	missense	57523	exon9			CCTGCGGCCTGGA	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"Cousin of GIN1"		"KIAA1305"	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.4082G>T	14.37:g.24885037G>T	ENSP00000371994:p.Gly1361Val	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	85	27	NM_025081	0	0	0	0	0	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.597704	0.46318	.	.	ENSG00000205978	ENST00000382554	T	0.10668	2.85	4.93	4.02	0.46733	Ribonuclease H-like (1);	.	.	.	.	T	0.12603	0.0306	N	0.24115	0.695	0.49582	D	0.999804	P	0.50066	0.931	P	0.50860	0.652	T	0.03555	-1.1025	9	0.87932	D	0	.	11.5825	0.50900	0.0:0.3481:0.6519:0.0	.	1361	Q9P2P1	NYNRI_HUMAN	V	1361	ENSP00000371994:G1361V	ENSP00000371994:G1361V	G	+	2	0	NYNRIN	23954877	0.997000	0.39634	0.949000	0.38748	0.982000	0.71751	2.871000	0.48459	1.254000	0.44035	0.655000	0.94253	GGC	.		0.627	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			T	24885037	G	T	24885037	3	4	131	1	0	0	0	0	1	0	0	0	10822	1203	42	4	4112	4	NYNRIN	14	24885037	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	1360688	24885037	82464503	59	11630											
C14orf126	112487	ucsc.edu	37	chr14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgggcctgaggaatccGgctaccctcagccatggctt	6	7	12	16	3	1	1	1	1	0	0	2	2	2	2	5	4	2	2	5	4	2	2	rs17097904	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	DTD2_ENST00000356180.4_Missense_Mutation_p.R6W|RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W													.	.	1	Substitution - Missense(1)	skin(1)	c.C16T						.						12	12	12					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 126"	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	21	3		WXS	Illumina HiSeq		40	6	NM_080664	0	0	8	14	6	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664		A	31926584	G	A	31926584	3	1	131	1	0	0	0	0	1	0	0	0	1747	1115	39	1	502	1	C14orf126	14	31926584	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	7041547	31926584	75422956	60	11631											
MLH3	27030	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	75516201	75516205	+	Frame_Shift_Del	DEL	TGAAC	TGAAC	-																															caaatccattgtctatcactTgaacttggaaggtttccata																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	TGAAC	TGAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:75516201_75516205delTGAAC	ENST00000556740.1	-	1	189_193	c.154_158delGTTCA	c.(154-159)gttcaafs	p.VQ52fs	MLH3_ENST00000556257.1_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000238662.7_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000355774.2_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000555671.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	52					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GTCTATCACTTGAACTTGGAAGGTT	0.444								Mismatch excision repair (MMR)																													p.52_53del		.											.	MLH3-228	0			c.154_158del						.																																			SO:0001589	frameshift_variant	27030	exon2			.	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.154_158delGTTCA	14.37:g.75516201_75516205delTGAAC	ENSP00000452316:p.Val52fs	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	169	28	NM_014381	0	0	0	0	0	P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	37	CCDS32123.1																																																																																			.		0.444	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		-	75516205	TGAAC	-	75516201	7	5	131	1	0	1	0	1	0	0	0	0	9643	1812	63	0	4251	0	MLH3	14	75516201	Frame_Shift_Del	DEL	TGAAC	TCGA-HE-A5NF-01A-11D-A26P-10	43589617	75516201	31833339	61	11632											
ATXN3	4287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	92549507	92549507	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctaattcttctccaataaGttttggtcgatgcatctgtt	8	18	7	8	1	3	0	0	0	3	0	5	1	3	0	1	1	2	4	1	1	3	7			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:92549507G>C	ENST00000532032.1	-	7	580	c.571C>G	c.(571-573)Ctt>Gtt	p.L191V	ATXN3_ENST00000340660.6_Missense_Mutation_p.L136V|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000503767.1_Missense_Mutation_p.L176V|ATXN3_ENST00000429774.2_Missense_Mutation_p.L176V|ATXN3_ENST00000545170.1_Missense_Mutation_p.L191V|ATXN3_ENST00000393287.5_Missense_Mutation_p.L191V|ATXN3_ENST00000502250.1_Missense_Mutation_p.L12V			P54252	ATX3_HUMAN	ataxin 3	191					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		TCTCCAATAAGTTTTGGTCGA	0.368																																					p.L191V	Esophageal Squamous(190;752 2094 29897 44875 49530)	.											.	ATXN3-522	0			c.C571G						.						146	138	141					14																	92549507		2203	4300	6503	SO:0001583	missense	4287	exon7			CAATAAGTTTTGG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"Ataxins"	7106	protein-coding gene	gene with protein product		607047	"Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.571C>G	14.37:g.92549507G>C	ENSP00000437157:p.Leu191Val	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	47	7	NM_004993	0	0	4	4	0	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		.	.	.	.	.	.	.	.	.	.	G	25.0	4.587229	0.86851	.	.	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220;ENST00000506466	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.55760	2.13;2.17;2.16;0.72;2.16;1.82;1.81;1.42;0.5;1.85;1.41;1.39;1.38;1.45	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.71592	0.3358	M	0.65498	2.005	0.58432	D	0.999997	D;D;D;D;D	0.71674	0.974;0.993;0.97;0.998;0.996	P;P;P;D;D	0.75484	0.829;0.901;0.804;0.986;0.966	T	0.71866	-0.4463	10	0.46703	T	0.11	.	18.7593	0.91843	0.0:0.0:1.0:0.0	.	191;176;191;136;191	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	V	191;191;191;191;191;191;191;176;190;191;12;176;136;191;121;12;190;93;140;85;125	ENSP00000445618:L191V;ENSP00000389376:L176V;ENSP00000376965:L191V;ENSP00000425322:L12V;ENSP00000426697:L176V;ENSP00000339110:L136V;ENSP00000437157:L191V;ENSP00000451001:L121V;ENSP00000450642:L12V;ENSP00000451385:L190V;ENSP00000451417:L93V;ENSP00000451996:L140V;ENSP00000450641:L85V;ENSP00000435571:L125V	ENSP00000339110:L136V	L	-	1	0	ATXN3	91619260	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.235000	0.51328	2.450000	0.82876	0.478000	0.44815	CTT	.		0.368	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993		C	92549507	G	C	92549507	3	2	131	1	0	0	0	0	1	0	0	0	1214	1029	36	4	534	4	ATXN3	14	92549507	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	17033306	92549507	14800033	62	11633											
ASPG	374569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	104565246	104565246	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccgggcaaccaaggtagaCgctcggaggttcgcagcttt	10	7	13	11	4	0	1	0	0	0	1	2	2	0	2	2	4	3	6	2	4	4	3	rs200662335	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:104565246C>T	ENST00000551177.1	+	6	662	c.570C>T	c.(568-570)gaC>gaT	p.D190D	ASPG_ENST00000455920.2_Silent_p.D190D|ASPG_ENST00000546892.2_Silent_p.D190D	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	190	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.				asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						CCAAGGTAGACGCTCGGAGGT	0.622													C|||	5	0.000998403	0.0038	0	5008	,	,		18268	0		0	False		,,,				2504	0				p.D190D		.											.	.	0			c.C570T						.	C		3,4013		0,3,2005	47	55	52		570	-0.9	0.1	14		52	0,8346		0,0,4173	no	coding-synonymous	ASPG	NM_001080464.2		0,3,6178	TT,TC,CC		0.0,0.0747,0.0243		190/574	104565246	3,12359	2008	4173	6181	SO:0001819	synonymous_variant	374569	exon6			GGTAGACGCTCGG		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"Ankyrin repeat domain containing"	20123	protein-coding gene	gene with protein product	"60-kDa-lysophospholipase"		"chromosome 14 open reading frame 76", "asparaginase homolog (S. cerevisiae)"	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.570C>T	14.37:g.104565246C>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	68	15	NM_001080464	0	0	0	0	0	B9EGQ2|Q8IV80	Silent	SNP	ENST00000551177.1	37	CCDS45170.2																																																																																			C|0.999;T|0.001		0.622	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464		T	104565246	C	T	104565246	2	4	131	1	0	0	0	0	0	0	0	1	1053	535	19	1		1	ASPG	14	104565246	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	12015739	104565246	2784294	63	11634											
TLE3	7090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	70368460	70368460	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacaggaaaggcatgatcTgtgctaaaattgtgttcagt	12	12	12	5	0	2	2	1	2	1	0	2	3	2	3	0	2	1	3	0	2	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:70368460T>A	ENST00000558939.1	-	5	1649	c.272A>T	c.(271-273)cAg>cTg	p.Q91L	TLE3_ENST00000440567.3_Missense_Mutation_p.Q84L|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000560939.1_Missense_Mutation_p.Q97L|TLE3_ENST00000559929.1_Missense_Mutation_p.Q91L|TLE3_ENST00000557907.1_Missense_Mutation_p.Q91L|TLE3_ENST00000560589.1_Missense_Mutation_p.Q35L|TLE3_ENST00000539550.1_Missense_Mutation_p.Q25L|TLE3_ENST00000558201.1_Missense_Mutation_p.Q97L|TLE3_ENST00000442299.2_Missense_Mutation_p.Q91L|TLE3_ENST00000557997.1_Missense_Mutation_p.Q91L|TLE3_ENST00000558379.1_Missense_Mutation_p.Q91L|TLE3_ENST00000559048.1_Missense_Mutation_p.Q97L|TLE3_ENST00000317509.8_Missense_Mutation_p.Q91L|TLE3_ENST00000451782.2_Missense_Mutation_p.Q91L	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	91	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGGCATGATCTGTGCTAAAAT	0.438																																					p.Q91L		.											.	TLE3-522	0			c.A272T						.						170	166	167					15																	70368460		1956	4138	6094	SO:0001583	missense	7090	exon5			ATGATCTGTGCTA	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"WD repeat domain containing"	11839	protein-coding gene	gene with protein product		600190	"transducin-like enhancer of split 3, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.272A>T	15.37:g.70368460T>A	ENSP00000452871:p.Gln91Leu	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	57	7	NM_001105192	0	0	6	6	0	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	T	33	5.250170	0.95305	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.63913	0.26;0.29;0.34;0.26;-0.07	5.85	5.85	0.93711	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.81635	0.4864	M	0.93854	3.465	0.80722	D	1	P;P;D;P;P;P;P;P	0.54397	0.851;0.927;0.966;0.877;0.748;0.877;0.62;0.911	B;P;P;P;P;P;P;P	0.56216	0.419;0.794;0.783;0.72;0.575;0.72;0.46;0.786	D	0.86775	0.1975	10	0.87932	D	0	-17.3549	16.2303	0.82332	0.0:0.0:0.0:1.0	.	84;91;91;91;91;91;97;25	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	L	91;91;91;84;25	ENSP00000390007:Q91L;ENSP00000394717:Q91L;ENSP00000319233:Q91L;ENSP00000415057:Q84L;ENSP00000442594:Q25L	ENSP00000319233:Q91L	Q	-	2	0	TLE3	68155514	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.924000	0.87555	2.233000	0.73108	0.533000	0.62120	CAG	.		0.438	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		A	70368460	T	A	70368460	3	1	131	1	0	0	0	0	1	0	0	0	15972	1580	55	5	2110	5	TLE3	15	70368460	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		70368460	32162932	64	11635											
CYP11A1	1583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	74640247	74640247	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccaggactcacttcaacAggactcctatgggtctctgg	8	9	11	13	0	3	0	2	0	1	0	5	2	4	2	2	5	1	0	2	5	2	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:74640247A>T	ENST00000268053.6	-	2	573	c.419T>A	c.(418-420)cTg>cAg	p.L140Q	CYP11A1_ENST00000358632.4_5'UTR|CYP11A1_ENST00000541301.1_Missense_Mutation_p.L140Q|CYP11A1_ENST00000419019.2_Intron	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	140					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	TCACTTCAACAGGACTCCTAT	0.622																																					p.L140Q	Esophageal Squamous(87;818 1337 4093 9268 37314)	.											.	CYP11A1-92	0			c.T419A						.						45	42	43					15																	74640247		2197	4296	6493	SO:0001583	missense	1583	exon2			TTCAACAGGACTC	AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"Cytochrome P450s"	2590	protein-coding gene	gene with protein product	"cholesterol monooxygenase (side-chain-cleaving)"	118485	"cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.419T>A	15.37:g.74640247A>T	ENSP00000268053:p.Leu140Gln	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	102	15	NM_000781	0	0	0	0	0	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Missense_Mutation	SNP	ENST00000268053.6	37	CCDS32291.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040820	0.55003	.	.	ENSG00000140459	ENST00000268053;ENST00000541301;ENST00000450547;ENST00000433240;ENST00000416978	T;T;T	0.71222	-0.55;-0.55;-0.55	4.46	4.46	0.54185	.	0.000000	0.64402	D	0.000001	T	0.81917	0.4924	M	0.71871	2.18	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.79108	0.929;0.992;0.929	T	0.83072	-0.0142	10	0.51188	T	0.08	-0.0287	13.4211	0.60998	1.0:0.0:0.0:0.0	.	140;140;140	E7EPP8;B4DTE5;P05108	.;.;CP11A_HUMAN	Q	140;140;52;140;140	ENSP00000268053:L140Q;ENSP00000439750:L140Q;ENSP00000388018:L140Q	ENSP00000268053:L140Q	L	-	2	0	CYP11A1	72427300	1.000000	0.71417	0.556000	0.28293	0.404000	0.30871	7.439000	0.80444	1.642000	0.50584	0.523000	0.50628	CTG	.		0.622	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1			T	74640247	A	T	74640247	3	4	131	1	0	0	0	0	1	0	0	0	4150	188	7	5	1178	5	CYP11A1	15	74640247	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	4271787	74640247	27891145	65	11636											
CHD2	1106	broad.mit.edu	37	chr15	93480801	93480801	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaggaacaaggcaccagtgCagagagtgagccagaacaaa	18	2	12	9	0	0	3	0	1	0	2	0	5	0	4	2	2	4	2	2	2	4	0			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:93480801C>T	ENST00000394196.4	+	6	1565	c.497C>T	c.(496-498)gCa>gTa	p.A166V	CHD2_ENST00000420239.2_Missense_Mutation_p.A166V|CHD2_ENST00000557381.1_Missense_Mutation_p.A166V|CHD2_ENST00000536619.1_Missense_Mutation_p.A179V	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	166					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GGCACCAGTGCAGAGAGTGAG	0.403																																					p.A166V													.	CHD2-229	0			c.C497T						.						101	99	99					15																	93480801		2197	4298	6495	SO:0001583	missense	1106	exon6			CCAGTGCAGAGAG	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.497C>T	15.37:g.93480801C>T	ENSP00000377747:p.Ala166Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	88	3	NM_001042572	0	0	4	4	0	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	C	16.04	3.008892	0.54361	.	.	ENSG00000173575	ENST00000556722;ENST00000394196;ENST00000557381;ENST00000420239;ENST00000536619	D;D;T;T	0.90004	-2.6;-2.6;0.88;0.87	5.07	5.07	0.68467	.	0.000000	0.33916	U	0.004434	T	0.78572	0.4304	N	0.14661	0.345	0.43179	D	0.994992	B;B;B;P	0.37781	0.075;0.099;0.16;0.608	B;B;B;B	0.30401	0.026;0.027;0.059;0.115	T	0.80120	-0.1515	10	0.39692	T	0.17	-32.1826	15.4022	0.74849	0.1394:0.8606:0.0:0.0	.	179;166;166;166	B7Z3I4;O14647;O14647-2;Q6AI05	.;CHD2_HUMAN;.;.	V	166;166;166;166;179	ENSP00000377747:A166V;ENSP00000451366:A166V;ENSP00000406581:A166V;ENSP00000443618:A179V	ENSP00000377747:A166V	A	+	2	0	CHD2	91281805	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.498000	0.60373	2.798000	0.96311	0.650000	0.86243	GCA	.		0.403	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		T	93480801	C	T	93480801	3	4	131	1	0	0	0	0	1	0	0	0	3331	710	25	2	515	2	CHD2	15	93480801	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	18840554	93480801	9050591	66	11637											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30734928	30734928	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcccccggagctgcccccTtgaccatctcttctcctctc	4	10	6	21	1	3	1	0	1	3	0	6	2	3	2	6	1	3	1	6	1	0	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:30734928T>C	ENST00000262518.4	+	25	4568	c.4183T>C	c.(4183-4185)Ttg>Ctg	p.L1395L	SRCAP_ENST00000344771.4_Silent_p.L1237L|SRCAP_ENST00000395059.2_Silent_p.L1333L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1395	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AGCTGCCCCCTTGACCATCTC	0.567																																					p.L1395L		.											.	SRCAP-94	0			c.T4183C						.						149	141	144					16																	30734928		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon25			GCCCCCTTGACCA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.4183T>C	16.37:g.30734928T>C		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	123	30	NM_006662	0	0	4	6	2	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.567	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30734928	T	C	30734928	2	2	131	1	0	0	0	0	0	0	0	1	15167	1606	56	3		3	SRCAP	16	30734928	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		30734928	59619825	67	11638											
AMFR	267	broad.mit.edu	37	chr16	56396896	56396896	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacgcagggtcacggggtcAgaggacgcaccttccgaggg	8	4	17	12	5	2	1	2	0	0	1	3	4	3	2	2	5	0	2	2	5	0	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:56396896A>G	ENST00000290649.5	-	14	2067	c.1857T>C	c.(1855-1857)tcT>tcC	p.S619S		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	619	VCP/p97-interacting motif (VIM).				aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						TCACGGGGTCAGAGGACGCAC	0.567																																					p.S619S	Pancreas(2;144 323 39528)												.	AMFR-1009	0			c.T1857C						.						49	44	45					16																	56396896		2198	4300	6498	SO:0001819	synonymous_variant	267	exon14			GGGGTCAGAGGAC	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1857T>C	16.37:g.56396896A>G		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	77	5	NM_001144	0	0	36	36	0	P26442|Q8IZ70	Silent	SNP	ENST00000290649.5	37	CCDS10758.1																																																																																			.		0.567	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			G	56396896	A	G	56396896	2	3	131	1	0	0	0	0	0	0	0	1	571	175	7	3		3	AMFR	16	56396896	Silent	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	25661968	56396896	33957857	68	11639											
SLC12A3	6559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	56919183	56919183	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccttgctctcccagaggtaaAttggggctcctcggtacagg	7	10	12	12	1	1	1	0	0	1	1	4	1	2	1	3	5	2	4	3	5	3	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:56919183A>C	ENST00000563236.1	+	15	1857	c.1832A>C	c.(1831-1833)aAt>aCt	p.N611T	SLC12A3_ENST00000262502.5_Missense_Mutation_p.N610T|SLC12A3_ENST00000566786.1_Missense_Mutation_p.N610T|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N611T			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	611					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CCAGAGGTAAATTGGGGCTCC	0.567																																					p.N611T		.											.	SLC12A3-155	0			c.A1832C	GRCh37	CM075008	SLC12A3	M		.						85	63	70					16																	56919183		2156	4234	6390	SO:0001583	missense	6559	exon15			AGGTAAATTGGGG		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"Solute carriers"	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1832A>C	16.37:g.56919183A>C	ENSP00000456149:p.Asn611Thr	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	99	35	NM_001126108	0	0	0	0	0	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	37	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386422	0.82902	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.4	5.4	0.78164	Amino acid permease domain (1);	0.088014	0.85682	D	0.000000	T	0.77478	0.4136	M	0.71296	2.17	0.80722	D	1	P;D;D	0.76494	0.735;0.999;0.999	B;D;D	0.74674	0.426;0.984;0.973	T	0.80415	-0.1392	9	0.87932	D	0	.	14.4174	0.67160	1.0:0.0:0.0:0.0	.	610;611;611	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	T	610;611	.	ENSP00000262502:N611T	N	+	2	0	SLC12A3	55476684	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.060000	0.93907	2.048000	0.60808	0.533000	0.62120	AAT	.		0.567	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			C	56919183	A	C	56919183	3	2	131	1	0	0	0	0	1	0	0	0	14416	101	4	5	1890	5	SLC12A3	16	56919183	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	522287	56919183	33435570	69	11640											
KIAA0753	9851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	6526336	6526336	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaagtggatgctcccctcGgtcagtaaactgagtgacaa	12	8	12	9	1	1	2	1	2	0	0	3	4	2	4	2	3	2	2	2	3	4	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:6526336G>C	ENST00000361413.3	-	6	1328	c.970C>G	c.(970-972)Cga>Gga	p.R324G	KIAA0753_ENST00000542606.1_Missense_Mutation_p.R25G|KIAA0753_ENST00000589033.1_5'Flank|KIAA0753_ENST00000572370.1_Missense_Mutation_p.R25G	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	324						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TGCTCCCCTCGGTCAGTAAAC	0.517																																					p.R324G		.											.	KIAA0753-90	0			c.C970G						.						62	60	60					17																	6526336		1915	4127	6042	SO:0001583	missense	9851	exon6			CCCCTCGGTCAGT		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.970C>G	17.37:g.6526336G>C	ENSP00000355250:p.Arg324Gly	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	256	68	NM_014804	0	0	1	1	0	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533928	0.27387	.	.	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86230	-2.09;-2.09	5.7	-0.0324	0.13905	.	0.841046	0.10770	N	0.636068	T	0.79052	0.4381	L	0.42245	1.32	0.80722	D	1	B	0.18013	0.025	B	0.17098	0.017	T	0.65903	-0.6055	10	0.30078	T	0.28	-0.3706	5.2141	0.15332	0.0698:0.1147:0.3462:0.4694	.	324	Q2KHM9	K0753_HUMAN	G	324;25	ENSP00000355250:R324G;ENSP00000444634:R25G	ENSP00000355250:R324G	R	-	1	2	KIAA0753	6467060	1.000000	0.71417	0.995000	0.50966	0.396000	0.30629	2.647000	0.46639	0.118000	0.18165	-1.035000	0.02400	CGA	.		0.517	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		C	6526336	G	C	6526336	3	2	131	1	0	0	0	0	1	0	0	0	8212	1124	39	4	1989	4	KIAA0753	17	6526336	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		6526336	74668874	70	11641											
SHBG	6462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7534128	7534128	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgagatccaactgcacaatCactgggcccagcttacggtg	10	8	10	13	1	1	1	1	1	0	1	2	2	2	1	2	2	4	2	2	2	3	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:7534128C>G	ENST00000380450.4	+	3	365	c.334C>G	c.(334-336)Cac>Gac	p.H112D	SHBG_ENST00000576478.1_Missense_Mutation_p.H54D|SHBG_ENST00000441599.2_Missense_Mutation_p.H112D|SHBG_ENST00000575314.1_Missense_Mutation_p.H54D|SHBG_ENST00000570547.1_Missense_Mutation_p.H54D|SAT2_ENST00000380466.2_5'Flank|SAT2_ENST00000269298.5_5'Flank|SHBG_ENST00000575903.1_Missense_Mutation_p.H112D|SHBG_ENST00000340624.5_Missense_Mutation_p.H54D|SHBG_ENST00000572182.1_Missense_Mutation_p.H54D|SHBG_ENST00000576728.1_Missense_Mutation_p.H54D|SHBG_ENST00000572262.1_Missense_Mutation_p.H54D|SHBG_ENST00000416273.3_Missense_Mutation_p.H112D|SHBG_ENST00000574539.1_Missense_Mutation_p.H54D	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	112	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	ACTGCACAATCACTGGGCCCA	0.567																																					p.H112D		.											.	SHBG-90	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C334G						.						81	77	78					17																	7534128		2203	4300	6503	SO:0001583	missense	6462	exon3			CACAATCACTGGG		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"androgen binding protein"	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.334C>G	17.37:g.7534128C>G	ENSP00000369816:p.His112Asp	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	202	59	NM_001040	0	0	1	1	0	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	C	8.055	0.766779	0.15983	.	.	ENSG00000129214	ENST00000340624;ENST00000441599;ENST00000416273;ENST00000441313;ENST00000452698;ENST00000380450	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	5.04	-0.0208	0.13954	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	2.361970	0.01468	N	0.016151	T	0.71592	0.3358	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B;B;B;B;B;B;B	0.25007	0.01;0.045;0.023;0.001;0.013;0.116;0.116;0.03;0.007;0.013;0.013	B;B;B;B;B;B;B;B;B;B;B	0.28011	0.011;0.03;0.044;0.001;0.042;0.085;0.085;0.045;0.038;0.031;0.013	T	0.49194	-0.8965	10	0.12103	T	0.63	2.7497	9.104	0.36687	0.0:0.6418:0.1148:0.2435	.	112;107;85;112;112;112;85;85;85;112;54	F5H5Z8;P04278-2;B0FWH6;E9PH59;E9PGW1;E9PGQ3;B0FWH7;B0FWH5;B0FWH4;P04278;B4DYU0	.;.;.;.;.;.;.;.;.;SHBG_HUMAN;.	D	54;112;112;112;112;112	ENSP00000345675:H54D;ENSP00000393426:H112D;ENSP00000388867:H112D;ENSP00000369816:H112D	ENSP00000345675:H54D	H	+	1	0	SHBG	7474853	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	-0.109000	0.10840	-0.068000	0.12953	-1.134000	0.01955	CAC	.		0.567	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		G	7534128	C	G	7534128	3	3	131	1	0	0	0	0	1	0	0	0	14301	826	29	4	344	4	SHBG	17	7534128	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	1007792	7534128	73661082	71	11642											
SOCS7	30837	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	36508826	36508826	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccggcggtggggatgggacCggcaagaggccttctggaga	7	6	19	9	3	1	2	0	0	1	2	2	5	2	4	3	8	0	1	3	8	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:36508826C>A	ENST00000577233.1	+	1	699	c.699C>A	c.(697-699)acC>acA	p.T233T	SOCS7_ENST00000331159.5_Silent_p.T233T	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	233	Mediates interaction with SORBS3.				fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					GGGATGGGACCGGCAAGAGGC	0.667																																					p.T233T		.											.	SOCS7-227	0			c.C699A						.						7	10	9					17																	36508826		2166	4235	6401	SO:0001819	synonymous_variant	30837	exon1			TGGGACCGGCAAG	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"Suppressors of cytokine signaling", "SH2 domain containing"	29846	protein-coding gene	gene with protein product	"Nck, Ash and phospholipase C binding protein", "NCK-associated protein 4"	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.699C>A	17.37:g.36508826C>A		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	47	10	NM_014598	0	0	1	6	5	A2VCU2|Q0IJ63	Silent	SNP	ENST00000577233.1	37	CCDS32637.1																																																																																			.		0.667	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052		A	36508826	C	A	36508826	2	1	131	1	0	0	0	0	0	0	0	1	14951	639	23	4		4	SOCS7	17	36508826	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	28974698	36508826	44686384	72	11643											
KRTAP4-7	100132476	hgsc.bcm.edu;ucsc.edu	37	chr17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcccacctgctgccgccccaGctgctgccgcccctgctgct	2	7	10	22	2	0	0	0	0	0	0	0	0	0	0	8	0	7	5	8	0	0	0	rs553572799|rs199957151	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:39240796G>C	ENST00000391417.4	+	1	338	c.338G>C	c.(337-339)aGc>aCc	p.S113T		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						tgccgccccagctgctgccgc	0.667																																					p.S113T		.											.	.	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						.																																			SO:0001583	missense	100132476	exon1			GCCCCAGCTGCTG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"Keratin associated proteins"	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.338G>C	17.37:g.39240796G>C	ENSP00000375236:p.Ser113Thr	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	14	9	NM_033061	0	0	0	0	0	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.047	-1.263726	0.01433	.	.	ENSG00000240871	ENST00000391417	T	0.00627	6.12	2.73	1.66	0.24008	.	2.038930	0.02697	N	0.111300	T	0.00552	0.0018	.	.	.	0.21290	N	0.999731	B	0.13145	0.007	B	0.12837	0.008	T	0.47222	-0.9134	9	0.17832	T	0.49	.	5.1702	0.15107	0.0:0.2319:0.5315:0.2367	.	168	Q9BYR0	KRA47_HUMAN	T	113	ENSP00000375236:S113T	ENSP00000375236:S113T	S	+	2	0	KRTAP4-7	36494322	0.010000	0.17322	0.067000	0.19924	0.024000	0.10985	-0.517000	0.06275	0.191000	0.20236	0.289000	0.19496	AGC	.		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			C	39240796	G	C	39240796	3	2	131	1	0	0	0	0	1	0	0	0	8576	971	34	4	340	4	KRTAP4-7	17	39240796	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	2731970	39240796	41954414	73	11644											
TOB1	10140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48940734	48940734	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atggctttctgcttcaagagGtcattcacattcaagccgag	10	12	9	10	1	5	1	4	0	1	1	5	2	5	1	1	2	2	2	1	2	2	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:48940734G>C	ENST00000268957.3	-	3	1073	c.645C>G	c.(643-645)gaC>gaG	p.D215E	TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Missense_Mutation_p.D215E	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	215					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GCTTCAAGAGGTCATTCACAT	0.527																																					p.D215E	NSCLC(144;643 1919 24513 29423 40686)	.											.	TOB1-226	0			c.C645G						.						98	100	99					17																	48940734		2203	4300	6503	SO:0001583	missense	10140	exon2			CAAGAGGTCATTC	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.645C>G	17.37:g.48940734G>C	ENSP00000268957:p.Asp215Glu	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	230	64	NM_005749	0	0	90	177	87	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	37	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	G	6.571	0.473717	0.12521	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.39229	1.09;1.09	6.07	6.07	0.98685	.	0.168901	0.51477	D	0.000081	T	0.21550	0.0519	N	0.02539	-0.55	0.38296	D	0.94283	B	0.16396	0.017	B	0.12156	0.007	T	0.14254	-1.0479	10	0.38643	T	0.18	.	14.7663	0.69642	0.0684:0.0:0.9316:0.0	.	215	P50616	TOB1_HUMAN	E	215	ENSP00000427695:D215E;ENSP00000268957:D215E	ENSP00000268957:D215E	D	-	3	2	TOB1	46295733	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.185000	0.32065	2.885000	0.99019	0.655000	0.94253	GAC	.		0.527	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			C	48940734	G	C	48940734	3	2	131	1	0	0	0	0	1	0	0	0	16379	1252	44	4	396	4	TOB1	17	48940734	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	9699938	48940734	32254476	74	11645											
ABCA8	10351	broad.mit.edu;bcgsc.ca	37	chr17	66878037	66878037	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggagacatttctcgtggCtatcttattcttcctcttgg	7	16	9	9	1	4	1	0	0	4	1	6	3	5	1	1	3	0	1	1	3	3	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:66878037C>A	ENST00000269080.2	-	29	3930	c.3793G>T	c.(3793-3795)Gcc>Tcc	p.A1265S	ABCA8_ENST00000586539.1_Missense_Mutation_p.A1305S|ABCA8_ENST00000430352.2_Missense_Mutation_p.A1305S	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1265	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TTTCTCGTGGCTATCTTATTC	0.473																																					p.A1265S													.	ABCA8-93	0			c.G3793T						.						171	157	161					17																	66878037		2203	4300	6503	SO:0001583	missense	10351	exon29			TCGTGGCTATCTT	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"ATP binding cassette transporters / subfamily A"	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3793G>T	17.37:g.66878037C>A	ENSP00000269080:p.Ala1265Ser	Somatic	100	2		WXS	Illumina HiSeq	Phase_I	124	29	NM_007168	0	0	1	1	0	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.875492	0.91664	.	.	ENSG00000141338	ENST00000269080;ENST00000430352	T;T	0.16743	2.32;2.32	4.75	4.75	0.60458	ABC transporter-like (1);	0.000000	0.52532	D	0.000066	T	0.46464	0.1394	M	0.83603	2.65	0.51767	D	0.999932	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.77557	0.99;0.94;0.94	T	0.51764	-0.8664	10	0.72032	D	0.01	.	17.2614	0.87071	0.0:1.0:0.0:0.0	.	1305;1305;1265	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	S	1265;1305	ENSP00000269080:A1265S;ENSP00000402814:A1305S	ENSP00000269080:A1265S	A	-	1	0	ABCA8	64389632	1.000000	0.71417	0.923000	0.36655	0.874000	0.50279	6.725000	0.74752	2.623000	0.88846	0.563000	0.77884	GCC	.		0.473	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		A	66878037	C	A	66878037	3	1	131	1	0	0	0	0	1	0	0	0	38	797	28	4	992	4	ABCA8	17	66878037	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	17937303	66878037	14317173	75	11646											
TOMM40	10452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	45397281	45397281	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcggggctctgacttcacaGcagccgtcaccctggggaac	8	7	12	14	2	3	1	2	1	1	0	4	2	3	2	2	4	3	2	2	4	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr19:45397281G>A	ENST00000426677.2	+	5	781	c.601G>A	c.(601-603)Gca>Aca	p.A201T	TOMM40_ENST00000405636.2_Missense_Mutation_p.A201T|TOMM40_ENST00000592434.1_Missense_Mutation_p.A201T|TOMM40_ENST00000252487.5_Missense_Mutation_p.A201T	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	201					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		TGACTTCACAGCAGCCGTCAC	0.617																																					p.A201T		.											.	TOMM40-90	0			c.G601A						.						45	44	45					19																	45397281		2203	4300	6503	SO:0001583	missense	10452	exon5			TTCACAGCAGCCG	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.601G>A	19.37:g.45397281G>A	ENSP00000410339:p.Ala201Thr	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	106	12	NM_001128917	1	0	25	45	19	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Missense_Mutation	SNP	ENST00000426677.2	37	CCDS12646.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176405	0.57692	.	.	ENSG00000130204	ENST00000426677;ENST00000405636;ENST00000252487	T;T;T	0.45668	0.89;0.89;0.89	4.76	4.76	0.60689	.	0.122142	0.53938	D	0.000046	T	0.39145	0.1067	L	0.49571	1.57	0.46701	D	0.999162	B;B	0.26975	0.165;0.037	B;B	0.28139	0.086;0.05	T	0.20306	-1.0279	10	0.28530	T	0.3	1.0773	15.2511	0.73545	0.0:0.0:1.0:0.0	.	201;201	O96008-2;O96008	.;TOM40_HUMAN	T	201	ENSP00000410339:A201T;ENSP00000385184:A201T;ENSP00000252487:A201T	ENSP00000252487:A201T	A	+	1	0	TOMM40	50089121	1.000000	0.71417	0.016000	0.15963	0.939000	0.58152	5.430000	0.66501	2.191000	0.70037	0.561000	0.74099	GCA	.		0.617	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1			A	45397281	G	A	45397281	3	1	131	1	0	0	0	0	1	0	0	0	16390	971	34	2	619	2	TOMM40	19	45397281	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		45397281	13731702	76	11647											
CNOT3	4849	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54648053	54648053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagtgcagacacgcaagaaGaagggcgacaaggatgtgag	15	4	15	7	2	1	4	1	1	0	3	1	6	1	5	0	2	1	2	0	2	4	0			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr19:54648053G>A	ENST00000406403.1	+	6	2071	c.468G>A	c.(466-468)aaG>aaA	p.K156K	CNOT3_ENST00000358389.3_5'UTR|CNOT3_ENST00000221232.5_Silent_p.K156K			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	156					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(7)|urinary_tract(3)	28	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CACGCAAGAAGAAGGGCGACA	0.557																																					p.K156K													.	CNOT3-93	0			c.G468A						.						136	103	114					19																	54648053		2203	4300	6503	SO:0001819	synonymous_variant	4849	exon7			CAAGAAGAAGGGC	AF180474	CCDS12880.1	19q13.4	2011-02-14			ENSG00000088038	ENSG00000088038			7879	protein-coding gene	gene with protein product	"NOT3 (negative regulator of transcription 3, yeast) homolog"	604910		NOT3		10637334, 9734811	Standard	NM_014516		Approved	NOT3H, KIAA0691, LENG2	uc002qdj.2	O75175	OTTHUMG00000066468	ENST00000406403.1:c.468G>A	19.37:g.54648053G>A		Somatic	323	1		WXS	Illumina HiSeq	Phase_I	402	67	NM_014516	0	0	3	11	8	Q9NZN7|Q9UF76	Silent	SNP	ENST00000406403.1	37	CCDS12880.1	.	.	.	.	.	.	.	.	.	.	G	9.574	1.121845	0.20877	.	.	ENSG00000088038	ENST00000440571	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	T	0.74512	0.3726	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72686	-0.4218	4	.	.	.	-30.9714	18.2928	0.90136	0.0:0.0:1.0:0.0	.	.	.	.	K	77	.	.	R	+	2	0	CNOT3	59339865	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.854000	0.69503	2.697000	0.92050	0.655000	0.94253	AGA	.		0.557	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		A	54648053	G	A	54648053	2	1	131	1	0	0	0	0	0	0	0	1	3626	933	33	2		2	CNOT3	19	54648053	Silent	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	9250772	54648053	4480930	77	11648											
NKX2-2	4821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	21492814	21492814	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggggcgtcacctccatacctTtctcggcccgggcgcgcttc	3	9	12	17	5	2	0	1	0	1	0	5	0	3	0	4	4	1	1	4	4	1	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr20:21492814T>G	ENST00000377142.4	-	2	925	c.569A>C	c.(568-570)aAa>aCa	p.K190T	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	190					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						CTCCATACCTTTCTCGGCCCG	0.667																																					p.K190T		.											.	NKX2-2-92	0			c.A569C						.						38	40	39					20																	21492814		2202	4300	6502	SO:0001583	missense	4821	exon2			ATACCTTTCTCGG	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"Homeoboxes / ANTP class : NKL subclass"	7835	protein-coding gene	gene with protein product		604612	"NK-2 (Drosophila) homolog B", "NK2 transcription factor related, locus 2 (Drosophila)"	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.569A>C	20.37:g.21492814T>G	ENSP00000366347:p.Lys190Thr	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	48	5	NM_002509	0	0	0	0	0		Missense_Mutation	SNP	ENST00000377142.4	37	CCDS13145.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.724176	0.89298	.	.	ENSG00000125820	ENST00000377142	D	0.91996	-2.95	5.35	5.35	0.76521	Homeobox (1);	0.000000	0.85682	D	0.000000	D	0.94499	0.8229	M	0.73217	2.22	0.80722	D	1	D	0.57257	0.979	P	0.57620	0.824	D	0.94718	0.7898	10	0.56958	D	0.05	.	15.3169	0.74089	0.0:0.0:0.0:1.0	.	190	O95096	NKX22_HUMAN	T	190	ENSP00000366347:K190T	ENSP00000366347:K190T	K	-	2	0	NKX2-2	21440814	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.002000	0.88514	2.014000	0.59158	0.379000	0.24179	AAA	.		0.667	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9			G	21492814	T	G	21492814	3	3	131	1	0	0	0	0	1	0	0	0	10476	1841	64	5	256	5	NKX2-2	20	21492814	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		21492814	41532706	78	11649											
KCNG1	3755	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49621336	49621336	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgttgtggcacatctgggaaCagtggccctgggagagaggg	8	7	18	8	1	1	1	0	0	1	1	1	4	1	3	1	5	1	2	1	5	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr20:49621336C>T	ENST00000371571.4	-	3	1067	c.782G>A	c.(781-783)tGt>tAt	p.C261Y	KCNG1_ENST00000506387.1_5'UTR|RP5-955M13.4_ENST00000424566.1_RNA	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	261					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						CATCTGGGAACAGTGGCCCTG	0.652																																					p.C261Y													.	KCNG1-515	0			c.G782A						.						12	12	12					20																	49621336		2198	4293	6491	SO:0001583	missense	3755	exon3			TGGGAACAGTGGC	AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.782G>A	20.37:g.49621336C>T	ENSP00000360626:p.Cys261Tyr	Somatic	103	1		WXS	Illumina HiSeq	Phase_I	144	31	NM_002237	0	0	0	0	0	A8K3S4|O43528|Q5JXL5|Q9BRC1	Missense_Mutation	SNP	ENST00000371571.4	37	CCDS13436.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.903278	0.52333	.	.	ENSG00000026559	ENST00000371571	D	0.97924	-4.61	5.0	5.0	0.66597	.	0.090523	0.85682	D	0.000000	D	0.97232	0.9095	M	0.85945	2.785	0.80722	D	1	B	0.27316	0.175	B	0.24269	0.052	D	0.96618	0.9457	9	.	.	.	.	18.6442	0.91405	0.0:1.0:0.0:0.0	.	261	Q9UIX4	KCNG1_HUMAN	Y	261	ENSP00000360626:C261Y	.	C	-	2	0	KCNG1	49054743	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.776000	0.85560	2.477000	0.83638	0.313000	0.20887	TGT	.		0.652	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		T	49621336	C	T	49621336	3	4	131	1	0	0	0	0	1	0	0	0	8048	478	17	2	763	2	KCNG1	20	49621336	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	28128522	49621336	13404184	79	11650											
SETD4	54093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	37408418	37408418	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgcgcttcggtgaaatcaGgtaaaagctgtttgcaaact	13	11	10	7	2	1	1	1	1	0	0	2	1	1	1	0	2	4	5	0	2	5	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr21:37408418G>C	ENST00000399215.1	-	10	2692	c.1320C>G	c.(1318-1320)acC>acG	p.T440T	SETD4_ENST00000399212.1_Silent_p.T416T|SETD4_ENST00000332131.4_Silent_p.T440T|AP000688.1_ENST00000600312.1_Intron|SETD4_ENST00000481477.1_5'UTR			Q9NVD3	SETD4_HUMAN	SET domain containing 4	440				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GGTGAAATCAGGTAAAAGCTG	0.433																																					p.T440T		.											.	SETD4-154	0			c.C1320G						.						147	146	146					21																	37408418		2203	4300	6503	SO:0001819	synonymous_variant	54093	exon11			AAATCAGGTAAAA	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.1320C>G	21.37:g.37408418G>C		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	65	13	NM_017438	0	0	0	3	3	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Silent	SNP	ENST00000399215.1	37	CCDS13640.1																																																																																			.		0.433	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		C	37408418	G	C	37408418	2	2	131	1	0	0	0	0	0	0	0	1	14165	987	35	4		4	SETD4	21	37408418	Silent	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		37408418	10721477	80	11651											
MCM3AP	8888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47664760	47664760	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgcggaagctggaaccCgagcacagcctgcttcagcc	9	6	11	15	2	2	0	1	0	1	0	2	3	2	2	3	2	7	3	3	2	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr21:47664760C>T	ENST00000397708.1	-	24	5253	c.4999G>A	c.(4999-5001)Ggg>Agg	p.G1667R	MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP_ENST00000291688.1_Missense_Mutation_p.G1667R|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1667	Acetyltransferase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AGCTGGAACCCGAGCACAGCC	0.642																																					p.G1667R		.											.	MCM3AP-291	0			c.G4999A						.						38	38	38					21																	47664760		2203	4300	6503	SO:0001583	missense	8888	exon23			GGAACCCGAGCAC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"germinal-centre associated nuclear protein"	603294	"minichromosome maintenance deficient (S. cerevisiae) 3-associated protein", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4999G>A	21.37:g.47664760C>T	ENSP00000380820:p.Gly1667Arg	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	138	32	NM_003906	0	0	6	16	10	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146050	0.37923	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03468	3.92;3.92	5.55	2.48	0.30137	.	0.335736	0.36409	N	0.002607	T	0.05456	0.0144	L	0.47716	1.5	0.29780	N	0.834087	B;D	0.59767	0.022;0.986	B;P	0.49421	0.005;0.61	T	0.14699	-1.0463	10	0.56958	D	0.05	-13.7278	5.035	0.14430	0.3494:0.4672:0.0:0.1834	.	1667;162	O60318;B3KT88	MCM3A_HUMAN;.	R	1667;1667;162	ENSP00000380820:G1667R;ENSP00000291688:G1667R	ENSP00000291688:G1667R	G	-	1	0	MCM3AP	46489188	0.922000	0.31269	0.682000	0.30024	0.188000	0.23474	1.789000	0.38724	0.711000	0.32018	-0.136000	0.14681	GGG	.		0.642	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		T	47664760	C	T	47664760	3	4	131	1	0	0	0	0	1	0	0	0	9413	652	23	1	967	1	MCM3AP	21	47664760	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	10256342	47664760	465135	81	11652											
PI4KA	5297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	21119517	21119517	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccctcgtaccattcttctggCcagagtcctgcaataaagtg	9	11	8	13	1	2	1	0	0	2	1	4	1	3	1	4	1	2	2	4	1	4	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr22:21119517C>T	ENST00000572273.1	-	21	2501	c.2271G>A	c.(2269-2271)tgG>tgA	p.W757*	PI4KA_ENST00000255882.6_Nonsense_Mutation_p.W815*|PI4KA_ENST00000466162.1_5'UTR			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	757					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATTCTTCTGGCCAGAGTCCTG	0.493																																					p.W815X	GBM(136;1332 1831 3115 23601 50806)	.											.	PI4KA-454	0			c.G2445A						.						93	97	96					22																	21119517		2203	4300	6503	SO:0001587	stop_gained	5297	exon21			TTCTGGCCAGAGT	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2271G>A	22.37:g.21119517C>T	ENSP00000458238:p.Trp757*	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	145	28	NM_058004	0	0	0	0	0	Q7Z625|Q9UPG2	Nonsense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	C	40	8.059858	0.98632	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5831	19.2017	0.93713	0.0:1.0:0.0:0.0	.	.	.	.	X	757	.	ENSP00000255882:W757X	W	-	3	0	PI4KA	19449517	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	7.539000	0.82063	2.770000	0.95276	0.650000	0.86243	TGG	.		0.493	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		T	21119517	C	T	21119517	4	4	131	1	0	0	0	0	0	1	0	0	11899	740	26	2	4003	2	PI4KA	22	21119517	Nonsense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		21119517	30185049	82	11653											
ZNF436	80818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	23693623	23693623	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agaggtctccattcttcccgGgtgagatacatggccatatc	9	11	10	11	1	2	2	0	1	2	2	5	3	3	2	3	3	1	0	3	3	2	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:23693623G>A	ENST00000314011.4	-	3	208	c.72C>T	c.(70-72)acC>acT	p.T24T	ZNF436_ENST00000374608.3_Silent_p.T24T|C1orf213_ENST00000437367.2_5'Flank|C1orf213_ENST00000454117.1_5'Flank|C1orf213_ENST00000335648.3_5'Flank|C1orf213_ENST00000518821.1_5'Flank	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|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(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		ATTCTTCCCGGGTGAGATACA	0.438																																					p.T24T		.											.	ZNF436-153	0			c.C72T						.						136	129	132					1																	23693623		2203	4300	6503	SO:0001819	synonymous_variant	80818	exon3			TTCCCGGGTGAGA	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.72C>T	1.37:g.23693623G>A		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	131	47	NM_001077195	0	0	1	3	2	Q658I9	Silent	SNP	ENST00000314011.4	37	CCDS233.1																																																																																			.		0.438	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		A	23693623	G	A	23693623	2	1	132	1	0	0	0	0	0	0	0	1	17941	1219	43	2		2	ZNF436	1	23693623	Silent	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		23693623	225556998	1	11654											
KLF17	128209	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	44595405	44595405	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgggaatctaaggatgccCcccaatgggctgccagtctc	8	8	13	12	0	2	0	0	0	2	0	3	2	2	2	4	4	2	1	4	4	3	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:44595405C>G	ENST00000372299.3	+	2	520	c.462C>G	c.(460-462)ccC>ccG	p.P154P	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	154					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TAAGGATGCCCCCCAATGGGC	0.562																																					p.P154P		.											.	KLF17-92	0			c.C462G						.						33	37	35					1																	44595405		2203	4300	6503	SO:0001819	synonymous_variant	128209	exon2			GATGCCCCCCAAT	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	18830	protein-coding gene	gene with protein product		609602	"zinc finger protein 393"	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.462C>G	1.37:g.44595405C>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	43	16	NM_173484	0	0	0	0	0	Q86VQ7|Q8N805	Silent	SNP	ENST00000372299.3	37	CCDS508.1																																																																																			.		0.562	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484		G	44595405	C	G	44595405	2	3	132	1	0	0	0	0	0	0	0	1	8366	610	22	4		4	KLF17	1	44595405	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	20901782	44595405	204655216	2	11655											
LRRC8C	84230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90179946	90179946	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacctggagcgtattcctcAtgctgtgttcagcctactca	7	13	9	12	1	3	1	3	1	0	0	4	2	4	2	3	1	4	3	3	1	2	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:90179946A>C	ENST00000370454.4	+	3	2072	c.1817A>C	c.(1816-1818)cAt>cCt	p.H606P	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	606					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CGTATTCCTCATGCTGTGTTC	0.448																																					p.H606P		.											.	LRRC8C-97	0			c.A1817C						.						57	55	56					1																	90179946		2203	4300	6503	SO:0001583	missense	84230	exon3			TTCCTCATGCTGT		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1817A>C	1.37:g.90179946A>C	ENSP00000359483:p.His606Pro	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	121	40	NM_032270	0	0	1	1	0	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.754041	0.49362	.	.	ENSG00000171488	ENST00000370454	T	0.54866	0.55	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.31199	0.0789	N	0.00656	-1.285	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	T	0.63730	-0.6571	10	0.39692	T	0.17	.	16.5441	0.84409	1.0:0.0:0.0:0.0	.	606	Q8TDW0	LRC8C_HUMAN	P	606	ENSP00000359483:H606P	ENSP00000359483:H606P	H	+	2	0	LRRC8C	89952534	1.000000	0.71417	0.397000	0.26308	0.684000	0.39900	9.284000	0.95882	2.364000	0.80123	0.524000	0.50904	CAT	.		0.448	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90179946	A	C	90179946	3	2	132	1	0	0	0	0	1	0	0	0	9048	217	8	5	1823	5	LRRC8C	1	90179946	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	45584541	90179946	159070675	3	11656											
EVI5	7813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	93073196	93073196	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaattgagtaaggagtcctTtgttctgtgcagaaagatac	12	14	10	5	0	1	3	0	1	1	2	2	4	2	4	1	1	2	3	1	1	4	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:93073196T>A	ENST00000370331.1	-	15	1877	c.1868A>T	c.(1867-1869)aAa>aTa	p.K623I	EVI5_ENST00000543509.1_Missense_Mutation_p.K634I|EVI5_ENST00000540033.1_Missense_Mutation_p.K623I|EVI5_ENST00000491940.1_5'UTR	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	623	Dimerization.|Interaction with AURKB and INCENP.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		AAGGAGTCCTTTGTTCTGTGC	0.358																																					p.K623I		.											.	EVI5-136	0			c.A1868T						.						166	149	154					1																	93073196		2202	4299	6501	SO:0001583	missense	7813	exon15			AGTCCTTTGTTCT	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1868A>T	1.37:g.93073196T>A	ENSP00000359356:p.Lys623Ile	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	88	45	NM_005665	0	0	0	2	2	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	37	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.656843	0.88154	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	T;T;T	0.37584	1.19;1.19;1.19	5.59	4.26	0.50523	.	0.052940	0.85682	D	0.000000	T	0.44286	0.1286	M	0.79123	2.44	0.51767	D	0.999936	P;P	0.49696	0.927;0.88	P;P	0.55455	0.776;0.602	T	0.51124	-0.8745	10	0.87932	D	0	-27.0804	12.0805	0.53667	0.0:0.0783:0.0:0.9217	.	634;623	F5H4R0;O60447	.;EVI5_HUMAN	I	623;623;634	ENSP00000359356:K623I;ENSP00000440826:K623I;ENSP00000445019:K634I	ENSP00000359356:K623I	K	-	2	0	EVI5	92845784	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.949000	0.70257	2.132000	0.65825	0.533000	0.62120	AAA	.		0.358	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		A	93073196	T	A	93073196	3	1	132	1	0	0	0	0	1	0	0	0	5302	1841	64	5	580	5	EVI5	1	93073196	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	2893250	93073196	156177425	4	11657											
GPSM2	29899	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109439646	109439646	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccagttgggcaatgcttatTtctatttgcatgattatgcc	8	16	9	8	0	1	1	0	1	1	0	1	1	1	1	2	1	3	4	2	1	4	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:109439646T>G	ENST00000406462.2	+	4	990	c.217T>G	c.(217-219)Ttc>Gtc	p.F73V	GPSM2_ENST00000264126.3_Missense_Mutation_p.F73V|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	73					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CAATGCTTATTTCTATTTGCA	0.378																																					p.F73V													.	GPSM2-227	0			c.T217G						.						122	126	125					1																	109439646		2203	4300	6503	SO:0001583	missense	29899	exon3			GCTTATTTCTATT	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"Tetratricopeptide (TTC) repeat domain containing"	29501	protein-coding gene	gene with protein product		609245	"G-protein signalling modulator 2 (AGS3-like, C. elegans)", "deafness, autosomal recessive 82"	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.217T>G	1.37:g.109439646T>G	ENSP00000385510:p.Phe73Val	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	67	29	NM_013296	0	0	0	1	1	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.	.	.	.	.	.	.	.	.	.	T	31	5.083858	0.94050	.	.	ENSG00000121957	ENST00000406462;ENST00000435987;ENST00000264126;ENST00000435475	T;T;T	0.65916	-0.18;-0.18;-0.18	5.61	5.61	0.85477	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	L	0.58810	1.83	0.80722	D	1	P	0.50617	0.937	D	0.64877	0.93	T	0.72603	-0.4243	10	0.59425	D	0.04	-7.2819	15.7996	0.78443	0.0:0.0:0.0:1.0	.	73	P81274	GPSM2_HUMAN	V	73	ENSP00000385510:F73V;ENSP00000408664:F73V;ENSP00000264126:F73V	ENSP00000264126:F73V	F	+	1	0	GPSM2	109241169	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.133000	0.65898	0.533000	0.62120	TTC	.		0.378	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		G	109439646	T	G	109439646	3	3	132	1	0	0	0	0	1	0	0	0	6756	1841	64	5	223	5	GPSM2	1	109439646	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	16366450	109439646	139810975	5	11658											
EDEM3	80267	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	184723718	184723718	+	Frame_Shift_Del	DEL	T	T	-																															aacgcggccgtcgccgccacTagtctccatcgcgctcgctg																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:184723718delT	ENST00000318130.8	-	1	329	c.63delA	c.(61-63)ctafs	p.L21fs	EDEM3_ENST00000367512.3_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	21					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCGCCGCCACTAGTCTCCATC	0.716																																					p.L21fs		.											.	EDEM3-91	0			c.63delA						.						5	10	9					1																	184723718		667	1557	2224	SO:0001589	frameshift_variant	80267	exon1			.	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.63delA	1.37:g.184723718delT	ENSP00000318147:p.Leu21fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	54	13	NM_025191	0	0	0	0	0	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Frame_Shift_Del	DEL	ENST00000318130.8	37	CCDS1363.2																																																																																			.		0.716	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		-	184723718	T	-	184723718	7	5	132	1	0	1	0	1	0	0	0	0	4924	1509	53	0	2815	0	EDEM3	1	184723718	Frame_Shift_Del	DEL	T	TCGA-HE-A5NH-01A-11D-A26P-10	75284072	184723718	64526903	6	11659											
HMCN1	83872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	186082053	186082053	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgccagcaacattgcaggaaAgactacaagagaatttattc	16	9	8	8	0	0	2	0	0	0	2	1	4	0	3	1	1	5	2	1	1	6	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:186082053A>G	ENST00000271588.4	+	72	11328	c.11099A>G	c.(11098-11100)aAg>aGg	p.K3700R	HMCN1_ENST00000367492.2_Missense_Mutation_p.K3700R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3700	Ig-like C2-type 35.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATTGCAGGAAAGACTACAAGA	0.393																																					p.K3700R		.											.	HMCN1-113	0			c.A11099G						.						106	101	103					1																	186082053		2203	4300	6503	SO:0001583	missense	83872	exon72			CAGGAAAGACTAC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11099A>G	1.37:g.186082053A>G	ENSP00000271588:p.Lys3700Arg	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	69	24	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607517	0.46527	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.69561	-0.41;-0.41	4.91	3.77	0.43336	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.134451	0.64402	D	0.000003	T	0.62527	0.2435	N	0.12637	0.245	0.45747	D	0.99864	D	0.69078	0.997	D	0.80764	0.994	T	0.58278	-0.7664	10	0.21014	T	0.42	.	10.2014	0.43087	0.921:0.0:0.079:0.0	.	3700	Q96RW7	HMCN1_HUMAN	R	3700	ENSP00000271588:K3700R;ENSP00000356462:K3700R	ENSP00000271588:K3700R	K	+	2	0	HMCN1	184348676	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.263000	0.58853	1.957000	0.56846	0.533000	0.62120	AAG	.		0.393	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186082053	A	G	186082053	3	3	132	1	0	0	0	0	1	0	0	0	7241	72	3	3	11385	3	HMCN1	1	186082053	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	1358335	186082053	63168568	7	11660											
NBAS	51594	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	15519770	15519770	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaggttggtagaagaattGaagtactctctgctggcagc	10	11	14	6	0	1	4	0	2	1	2	2	4	1	4	0	3	3	5	0	3	5	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:15519770G>T	ENST00000281513.5	-	30	3571	c.3546C>A	c.(3544-3546)ttC>ttA	p.F1182L	NBAS_ENST00000441750.1_Missense_Mutation_p.F1062L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1182					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TAGAAGAATTGAAGTACTCTC	0.443																																					p.F1182L		.											.	NBAS-94	0			c.C3546A						.						115	113	114					2																	15519770		2203	4300	6503	SO:0001583	missense	51594	exon30			AGAATTGAAGTAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.3546C>A	2.37:g.15519770G>T	ENSP00000281513:p.Phe1182Leu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	150	61	NM_015909	0	0	3	6	3	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.8|27.8	4.863074|4.863074	0.91511|0.91511	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000441755|ENST00000442506	T;T;T|.	0.32272|.	1.46;1.46;1.46|.	5.79|5.79	4.92|4.92	0.64577|0.64577	Secretory pathway Sec39 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.75258|.	0.3825|.	M|M	0.78637|0.78637	2.42|2.42	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	0.992;1.0|.	D;D|.	0.91635|.	0.965;0.999|.	T|.	0.76699|.	-0.2863|.	10|.	0.87932|.	D|.	0|.	.|.	14.7925|14.7925	0.69854|0.69854	0.0691:0.0:0.9309:0.0|0.0691:0.0:0.9309:0.0	.|.	1062;1182|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	L|X	1062;1182;229|230	ENSP00000413201:F1062L;ENSP00000281513:F1182L;ENSP00000396501:F229L|.	ENSP00000281513:F1182L|.	F|S	-|-	3|2	2|0	NBAS|NBAS	15437221|15437221	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.815000|4.815000	0.62634|0.62634	1.461000|1.461000	0.47929|0.47929	0.563000|0.563000	0.77884|0.77884	TTC|TCA	.		0.443	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15519770	G	T	15519770	3	4	132	1	0	0	0	0	1	0	0	0	10211	1281	45	4	3661	4	NBAS	2	15519770	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		15519770	227679603	8	11661											
RIF1	55183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152320162	152320162	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actaatactgtagaggagaaAaatgtagaaattaatttgga	19	11	9	2	0	0	3	0	0	0	3	0	5	0	4	0	2	1	2	0	2	8	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:152320162A>T	ENST00000243326.5	+	29	4611	c.4128A>T	c.(4126-4128)aaA>aaT	p.K1376N	RIF1_ENST00000428287.2_Missense_Mutation_p.K1376N|RIF1_ENST00000453091.2_Missense_Mutation_p.K1376N|RIF1_ENST00000430328.2_Missense_Mutation_p.K1376N|RIF1_ENST00000444746.2_Missense_Mutation_p.K1376N			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TAGAGGAGAAAAATGTAGAAA	0.348																																					p.K1376N		.											.	RIF1-300	0			c.A4128T						.						72	78	76					2																	152320162		2203	4300	6503	SO:0001583	missense	55183	exon30			GGAGAAAAATGTA	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"RAP1 interacting factor homolog (yeast)"			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.4128A>T	2.37:g.152320162A>T	ENSP00000243326:p.Lys1376Asn	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	25	11	NM_018151	0	0	1	4	3	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	0.921	-0.715998	0.03206	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.45	1.54	0.23209	.	0.844182	0.10956	N	0.615469	T	0.20210	0.0486	L	0.41710	1.295	0.09310	N	1	B;B	0.28512	0.078;0.214	B;B	0.21546	0.015;0.035	T	0.21895	-1.0232	10	0.39692	T	0.17	-9.694	3.1462	0.06472	0.5289:0.0:0.2045:0.2666	.	1376;1376	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	N	1376	ENSP00000390181:K1376N;ENSP00000414615:K1376N;ENSP00000415691:K1376N;ENSP00000243326:K1376N;ENSP00000416123:K1376N	ENSP00000243326:K1376N	K	+	3	2	RIF1	152028408	0.003000	0.15002	0.001000	0.08648	0.192000	0.23643	0.898000	0.28404	0.384000	0.24942	0.455000	0.32223	AAA	.		0.348	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152320162	A	T	152320162	3	4	132	1	0	0	0	0	1	0	0	0	13391	11	1	5	4242	5	RIF1	2	152320162	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	136800392	152320162	90879211	9	11662											
PLA2R1	22925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160825863	160825863	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtatatcactggtgttccatCtctccagctgtgggaagatt	8	14	10	9	0	2	1	1	0	1	1	5	2	4	2	2	2	1	3	2	2	3	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:160825863C>G	ENST00000283243.7	-	19	2874	c.2668G>C	c.(2668-2670)Gat>Cat	p.D890H	PLA2R1_ENST00000392771.1_Missense_Mutation_p.D890H	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	890	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GGTGTTCCATCTCTCCAGCTG	0.408																																					p.D890H		.											.	PLA2R1-93	0			c.G2668C						.						116	110	112					2																	160825863		2203	4300	6503	SO:0001583	missense	22925	exon19			TTCCATCTCTCCA	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"C-type lectin domain containing"	9042	protein-coding gene	gene with protein product		604939	"phospholipase A2 receptor 1, 180kD"			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.2668G>C	2.37:g.160825863C>G	ENSP00000283243:p.Asp890His	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	59	15	NM_001195641	0	0	0	0	0	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867614	0.72065	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15834	2.39;2.39	5.8	4.92	0.64577	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.107665	0.64402	D	0.000009	T	0.51143	0.1657	H	0.95365	3.66	0.47994	D	0.999564	B;D;D	0.89917	0.372;1.0;0.999	B;D;D	0.71414	0.309;0.973;0.966	T	0.62604	-0.6819	10	0.51188	T	0.08	.	11.2567	0.49058	0.0:0.9128:0.0:0.0872	.	890;890;890	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	H	890	ENSP00000283243:D890H;ENSP00000376524:D890H	ENSP00000283243:D890H	D	-	1	0	PLA2R1	160534109	0.976000	0.34144	0.999000	0.59377	0.993000	0.82548	1.512000	0.35812	1.426000	0.47256	0.650000	0.86243	GAT	.		0.408	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160825863	C	G	160825863	3	3	132	1	0	0	0	0	1	0	0	0	12036	913	32	4	1779	4	PLA2R1	2	160825863	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	8505701	160825863	82373510	10	11663											
TTLL4	9654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219611762	219611762	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcattccagattgggaggAaggaccggctatggcggaac	10	7	15	9	2	1	1	1	0	0	1	2	5	2	5	2	6	1	2	2	6	3	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:219611762A>C	ENST00000392102.1	+	9	2351	c.2011A>C	c.(2011-2013)Aag>Cag	p.K671Q	TTLL4_ENST00000442769.1_Intron|TTLL4_ENST00000258398.4_Missense_Mutation_p.K671Q|TTLL4_ENST00000457313.1_Missense_Mutation_p.K506Q	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	671	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GATTGGGAGGAAGGACCGGCT	0.537																																					p.K671Q	GBM(172;1818 2053 15407 20943 49753)	.											.	TTLL4-93	0			c.A2011C						.						135	125	128					2																	219611762		2203	4300	6503	SO:0001583	missense	9654	exon9			GGGAGGAAGGACC		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"Tubulin tyrosine ligase-like family"	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.2011A>C	2.37:g.219611762A>C	ENSP00000375951:p.Lys671Gln	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	197	73	NM_014640	0	0	7	11	4	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.973585	0.92919	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000258398	T;T;T	0.09255	3.0;3.0;3.0	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	H	0.97918	4.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69982	-0.4997	10	0.87932	D	0	.	15.3584	0.74448	1.0:0.0:0.0:0.0	.	506;671	E9PH58;Q14679	.;TTLL4_HUMAN	Q	506;671;671	ENSP00000393332:K506Q;ENSP00000375951:K671Q;ENSP00000258398:K671Q	ENSP00000258398:K671Q	K	+	1	0	TTLL4	219320006	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.904000	0.92590	2.217000	0.71921	0.482000	0.46254	AAG	.		0.537	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		C	219611762	A	C	219611762	3	2	132	1	0	0	0	0	1	0	0	0	16762	247	9	5	2037	5	TTLL4	2	219611762	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	58785899	219611762	23587611	11	11664											
CCDC108	255101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219878079	219878079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccggcttcactgtcacacCtatgaaatttagctggaaat	11	12	7	11	1	2	1	2	1	0	0	3	2	3	2	2	2	1	2	2	2	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:219878079C>T	ENST00000341552.5	-	24	3942	c.3859G>A	c.(3859-3861)Ggt>Agt	p.G1287S	CCDC108_ENST00000441968.1_Missense_Mutation_p.G1287S|AC097468.4_ENST00000441450.1_RNA|CCDC108_ENST00000453220.1_Missense_Mutation_p.G1287S	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1287						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACTGTCACACCTATGAAATTT	0.542																																					p.G1287S		.											.	CCDC108-94	0			c.G3859A						.						96	86	89					2																	219878079		2202	4299	6501	SO:0001583	missense	255101	exon24			TCACACCTATGAA	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.3859G>A	2.37:g.219878079C>T	ENSP00000340776:p.Gly1287Ser	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	179	76	NM_194302	0	0	0	0	0	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	31	5.066292	0.93898	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.13307	2.6;2.6;2.6	5.11	5.11	0.69529	.	0.000000	0.42420	D	0.000714	T	0.40222	0.1108	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.31081	-0.9956	10	0.72032	D	0.01	-14.6861	18.1538	0.89686	0.0:1.0:0.0:0.0	.	1287	Q6ZU64	CC108_HUMAN	S	1287	ENSP00000340776:G1287S;ENSP00000413377:G1287S;ENSP00000409117:G1287S	ENSP00000340776:G1287S	G	-	1	0	CCDC108	219586323	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	6.610000	0.74178	2.372000	0.80975	0.650000	0.86243	GGT	.		0.542	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219878079	C	T	219878079	3	4	132	1	0	0	0	0	1	0	0	0	2749	681	24	2	1966	2	CCDC108	2	219878079	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	266317	219878079	23321294	12	11665											
SPEG	10290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220349151	220349151	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaggcagcagtctcagtagCagcatcgaaaacttggagtc	12	7	11	11	1	1	0	1	0	1	0	4	2	1	1	1	2	4	5	1	2	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:220349151C>T	ENST00000312358.7	+	30	7098	c.6966C>T	c.(6964-6966)agC>agT	p.S2322S	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2322					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GTCTCAGTAGCAGCATCGAAA	0.692																																					p.S2322S		.											.	SPEG-383	0			c.C6966T						.						15	19	18					2																	220349151		1916	4034	5950	SO:0001819	synonymous_variant	10290	exon30			CAGTAGCAGCATC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.6966C>T	2.37:g.220349151C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	52	15	NM_005876	0	0	0	0	0	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			.		0.692	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220349151	C	T	220349151	2	4	132	1	0	0	0	0	0	0	0	1	15068	709	25	2		2	SPEG	2	220349151	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	471072	220349151	22850222	13	11666											
STK11IP	114790	hgsc.bcm.edu	37	chr2	220470428	220470428	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgggggtcctgatactGcgaggcaatgagcttcggag	7	9	16	9	2	1	2	0	2	1	0	3	4	2	3	1	4	3	3	1	4	2	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:220470428G>T	ENST00000456909.1	+	8	807	c.717G>T	c.(715-717)ctG>ctT	p.L239L	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Silent_p.L250L			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	250					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCCTGATACTGCGAGGCAATG	0.602																																					p.L250L		.											.	STK11IP-91	0			c.G750T						.						32	32	32					2																	220470428		1964	4137	6101	SO:0001819	synonymous_variant	114790	exon8			GATACTGCGAGGC	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"LKB1 interacting protein"	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.717G>T	2.37:g.220470428G>T		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_052902	0	0	4	4	0	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	37																																																																																				.		0.602	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220470428	G	T	220470428	2	4	132	1	0	0	0	0	0	0	0	1	15320	1306	46	4		4	STK11IP	2	220470428	Silent	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	121277	220470428	22728945	14	11667											
IL5RA	3568	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	3139630	3139630	+	Frame_Shift_Del	DEL	A	A	-																															gagccgttaacaagcaccgcAagccagtcacgccctttgct																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:3139630delA	ENST00000446632.2	-	7	1207	c.633delT	c.(631-633)cttfs	p.L211fs	IL5RA_ENST00000383846.1_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000438560.1_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000456302.1_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000256452.3_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000430514.2_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000418488.2_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000311981.8_Frame_Shift_Del_p.L211fs	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	211					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		CAAGCACCGCAAGCCAGTCAC	0.507																																					p.L211fs	GBM(169;430 2801 24955 28528)	.											.	IL5RA-91	0			c.633delT						.						112	97	102					3																	3139630		2203	4300	6503	SO:0001589	frameshift_variant	3568	exon7			.	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"Interleukins and interleukin receptors", "CD molecules"	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.633delT	3.37:g.3139630delA	ENSP00000412209:p.Leu211fs	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	217	86	NM_001243099	0	0	0	0	0	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Frame_Shift_Del	DEL	ENST00000446632.2	37	CCDS2559.1																																																																																			.		0.507	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			-	3139630	A	-	3139630	7	5	132	1	0	1	0	1	0	0	0	0	7721	117	5	0	679	0	IL5RA	3	3139630	Frame_Shift_Del	DEL	A	TCGA-HE-A5NH-01A-11D-A26P-10		3139630	194882800	15	11668											
IL17RC	84818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9971714	9971714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctctcaccccttccagacTccctggggcctctcaaagac	7	8	7	19	0	2	2	2	0	2	2	6	2	4	2	6	2	0	0	6	2	1	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:9971714T>C	ENST00000295981.3	+	14	1590	c.1372T>C	c.(1372-1374)Tcc>Ccc	p.S458P	IL17RC_ENST00000413608.1_Missense_Mutation_p.S387P|IL17RC_ENST00000383812.4_Missense_Mutation_p.S372P|IL17RC_ENST00000455057.1_Missense_Mutation_p.S355P|IL17RC_ENST00000416074.2_Missense_Mutation_p.S226P|IL17RC_ENST00000403601.3_Missense_Mutation_p.S387P|IL17RC_ENST00000498214.1_Intron	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	458					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CCTTCCAGACTCCCTGGGGCC	0.597																																					p.S458P		.											.	IL17RC-92	0			c.T1372C						.						62	66	65					3																	9971714		2203	4300	6503	SO:0001583	missense	84818	exon14			CCAGACTCCCTGG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1372T>C	3.37:g.9971714T>C	ENSP00000295981:p.Ser458Pro	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	116	44	NM_153461	0	0	0	0	0	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.526941	0.64860	.	.	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.84	1.78	0.24846	.	0.258488	0.27223	N	0.020354	T	0.25269	0.0614	L	0.59436	1.845	0.26156	N	0.980074	D;D;P;P;P;P;P;D;D;D	0.59357	0.98;0.967;0.93;0.93;0.883;0.883;0.944;0.958;0.966;0.985	P;P;B;P;P;P;B;P;P;P	0.56916	0.731;0.642;0.368;0.462;0.462;0.462;0.439;0.663;0.543;0.809	T	0.03148	-1.1067	10	0.72032	D	0.01	-27.1927	5.0209	0.14361	0.2862:0.0:0.2374:0.4764	.	372;226;355;370;387;387;226;372;458;387	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;B4E008;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;.;I17RC_HUMAN;.	P	372;458;362;387;226;355;387	ENSP00000373323:S372P;ENSP00000295981:S458P;ENSP00000401128:S362P;ENSP00000384969:S387P;ENSP00000395315:S226P;ENSP00000407894:S355P;ENSP00000396064:S387P	ENSP00000295981:S458P	S	+	1	0	IL17RC	9946714	0.275000	0.24201	1.000000	0.80357	0.836000	0.47400	0.499000	0.22546	1.000000	0.39049	0.459000	0.35465	TCC	.		0.597	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		C	9971714	T	C	9971714	3	2	132	1	0	0	0	0	1	0	0	0	7662	1551	54	3	1426	3	IL17RC	3	9971714	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	6832084	9971714	188050716	16	11669											
EOMES	8320	broad.mit.edu;bcgsc.ca	37	chr3	27760357	27760358	+	Frame_Shift_Ins	INS	-	-	T																															atatgcagtcggggttggtaINStttgtgtaaggattgtaaga																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:27760357_27760358insT	ENST00000295743.4	-	4	1388_1389	c.1185_1186insA	c.(1183-1188)aaatacfs	p.Y396fs	EOMES_ENST00000461503.1_5'UTR|EOMES_ENST00000537516.1_Frame_Shift_Ins_p.Y101fs|EOMES_ENST00000449599.1_Frame_Shift_Ins_p.Y396fs			O95936	EOMES_HUMAN	eomesodermin	396					brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						CGGGGTTGGTATTTGTGTAAGG	0.381																																					p.Y396fs													.	EOMES-156	0			c.1186_1187insA						.																																			SO:0001589	frameshift_variant	8320	exon4			GTTGGTATTTGTG	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"T-boxes"	3372	protein-coding gene	gene with protein product	"T-box brain2"	604615	"eomesodermin (Xenopus laevis) homolog"			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.1186dupA	3.37:g.27760360_27760360dupT	ENSP00000295743:p.Tyr396fs	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	38	11	NM_005442	0	0	0	0	0	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Frame_Shift_Ins	INS	ENST00000295743.4	37	CCDS2646.1																																																																																			.		0.381	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		T	27760358	-	T	27760357	7	5	132	1	0	1	1	0	0	0	0	0	5160	449	16	0	886	0	EOMES	3	27760357	Frame_Shift_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10	17788643	27760357	170262073	17	11670											
SCAP	22937	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47460314	47460314	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggagcgtgactgggatgaCgggcagcaggctgatgtacc	8	6	18	9	3	0	3	0	3	0	0	0	5	0	5	1	4	3	4	1	4	1	1	rs199794833		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:47460314C>A	ENST00000265565.5	-	14	2372	c.1960G>T	c.(1960-1962)Gtc>Ttc	p.V654F	SCAP_ENST00000465628.1_5'Flank|SCAP_ENST00000441517.2_Missense_Mutation_p.V399F|SCAP_ENST00000545718.1_Missense_Mutation_p.V262F	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	654					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		ACTGGGATGACGGGCAGCAGG	0.706																																					p.V654F	Pancreas(149;978 1908 29304 37806 46700)												.	SCAP-91	0			c.G1960T						.						23	22	23					3																	47460314		2201	4297	6498	SO:0001583	missense	22937	exon14			GGATGACGGGCAG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.1960G>T	3.37:g.47460314C>A	ENSP00000265565:p.Val654Phe	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	23	4	NM_012235	0	0	19	38	19	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	14.87	2.664257	0.47572	.	.	ENSG00000114650	ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	T;T;T	0.80393	-1.37;-1.33;0.81	4.65	3.78	0.43462	.	0.205924	0.41500	D	0.000872	T	0.72391	0.3454	L	0.44542	1.39	0.47905	D	0.999548	P;B	0.39094	0.659;0.429	B;B	0.38327	0.271;0.124	T	0.72462	-0.4286	10	0.56958	D	0.05	-31.8419	8.9911	0.36024	0.0:0.8289:0.0:0.1711	.	399;654	F8W921;Q12770	.;SCAP_HUMAN	F	281;654;399;262	ENSP00000265565:V654F;ENSP00000416847:V399F;ENSP00000438956:V262F	ENSP00000265565:V654F	V	-	1	0	SCAP	47435318	1.000000	0.71417	0.975000	0.42487	0.422000	0.31414	4.644000	0.61397	1.182000	0.42928	0.561000	0.74099	GTC	.		0.706	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		A	47460314	C	A	47460314	3	1	132	1	0	0	0	0	1	0	0	0	13909	536	19	4	1919	4	SCAP	3	47460314	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	19699957	47460314	150562116	18	11671											
RFT1	91869	ucsc.edu;bcgsc.ca	37	chr3	53126088	53126088	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcacagcagaggaataccTggggaaagaaaccattgtca	15	6	11	9	0	2	2	2	0	0	2	2	4	2	4	2	3	3	2	2	3	4	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:53126088T>A	ENST00000296292.3	-	13	1520		c.e13-2		RFT1_ENST00000394738.3_Splice_Site|RP11-894J14.5_ENST00000607203.1_Intron	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)						carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		GAGGAATACCTGGGGAAAGAA	0.557																																					.													.	RFT1-91	0			c.1459-2A>T						.						52	45	47					3																	53126088		2203	4300	6503	SO:0001630	splice_region_variant	91869	exon14			AATACCTGGGGAA	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"congenital disorder of glycosylation 1N"	611908	"RFT1, requiring fifty three 1 homolog (S. cerevisiae)"			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1459-2A>T	3.37:g.53126088T>A		Somatic	132	1		WXS	Illumina HiSeq		161	80	NM_052859	0	0	0	1	1	Q96J03	Splice_Site	SNP	ENST00000296292.3	37	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.292549	0.40594	.	.	ENSG00000163933	ENST00000296292;ENST00000394738	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4957	0.33127	0.1725:0.0:0.0:0.8275	.	.	.	.	.	-1	.	.	.	-	.	.	RFT1	53101128	1.000000	0.71417	0.976000	0.42696	0.457000	0.32468	7.337000	0.79256	2.219000	0.72066	0.459000	0.35465	.	.		0.557	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	Intron	A	53126088	T	A	53126088	5	1	132	1	0	0	0	0	0	0	1	0	13289	1594	55	5	172	5	RFT1	3	53126088	Splice_Site	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	5665774	53126088	144896342	19	11672											
ARL13B	200894	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	93761993	93761993	+	Frame_Shift_Del	DEL	T	T	-																															aatcacaatggccaaaaaaaTaatgaatttggactagtaga																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:93761993delT	ENST00000394222.3	+	7	1208	c.933delT	c.(931-933)aatfs	p.N312fs	ARL13B_ENST00000471138.1_Frame_Shift_Del_p.N312fs|ARL13B_ENST00000535334.1_Frame_Shift_Del_p.N209fs|ARL13B_ENST00000539730.1_Frame_Shift_Del_p.N33fs|ARL13B_ENST00000303097.7_Frame_Shift_Del_p.N205fs	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	312					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						GCCAAAAAAATAATGAATTTG	0.373																																					p.N311fs		.											.	ARL13B-91	0			c.933delT						.						81	80	81					3																	93761993		2203	4300	6503	SO:0001589	frameshift_variant	200894	exon7			.	AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	25419	protein-coding gene	gene with protein product		608922	"ADP-ribosylation factor-like 2-like 1"	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.933delT	3.37:g.93761993delT	ENSP00000377769:p.Asn312fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	164	56	NM_182896	0	0	0	0	0	D3DN29|G3V1S8|Q504W8|Q8TCL5	Frame_Shift_Del	DEL	ENST00000394222.3	37	CCDS2925.1																																																																																			.		0.373	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		-	93761993	T	-	93761993	7	5	132	1	0	1	0	1	0	0	0	0	929	1403	49	0	959	0	ARL13B	3	93761993	Frame_Shift_Del	DEL	T	TCGA-HE-A5NH-01A-11D-A26P-10	40635905	93761993	104260437	20	11673											
DZIP1L	199221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	137813760	137813760	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagctccccttgggtccActttagcttggcccgtagct	4	13	9	15	1	0	0	0	0	0	0	3	0	3	0	5	2	3	4	5	2	2	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:137813760A>T	ENST00000327532.2	-	4	1014	c.652T>A	c.(652-654)Tgg>Agg	p.W218R	DZIP1L_ENST00000488595.1_5'Flank|DZIP1L_ENST00000469243.1_Missense_Mutation_p.W218R	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	218					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CCTTGGGTCCACTTTAGCTTG	0.567																																					p.W218R		.											.	DZIP1L-92	0			c.T652A						.						204	183	190					3																	137813760		2203	4300	6503	SO:0001583	missense	199221	exon5			GGGTCCACTTTAG	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.652T>A	3.37:g.137813760A>T	ENSP00000332148:p.Trp218Arg	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	166	58	NM_001170538	0	0	0	2	2	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	A	2.056	-0.416478	0.04766	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.58940	0.3;0.3	4.85	0.616	0.17613	.	0.838115	0.10499	N	0.667430	T	0.49287	0.1548	L	0.57536	1.79	0.24258	N	0.995292	B;B	0.16166	0.016;0.007	B;B	0.15870	0.01;0.014	T	0.44967	-0.9293	10	0.49607	T	0.09	-4.0524	5.9081	0.19012	0.3628:0.38:0.0:0.2572	.	218;218	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	R	218	ENSP00000332148:W218R;ENSP00000419486:W218R	ENSP00000332148:W218R	W	-	1	0	DZIP1L	139296450	0.994000	0.37717	0.993000	0.49108	0.676000	0.39594	0.188000	0.17018	0.280000	0.22209	0.460000	0.39030	TGG	.		0.567	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		T	137813760	A	T	137813760	3	4	132	1	0	0	0	0	1	0	0	0	4875	159	6	5	1712	5	DZIP1L	3	137813760	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	44051767	137813760	60208670	21	11674											
ARAP2	116984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	36069579	36069579	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttggaagggttcttgaccGttgtagaaccacattaagtt	10	15	10	6	1	1	2	0	1	1	1	1	3	1	3	2	2	1	4	2	2	4	8	rs377015356		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr4:36069579G>A	ENST00000303965.4	-	33	5554	c.5065C>T	c.(5065-5067)Cgg>Tgg	p.R1689W		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1689					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						GTTCTTGACCGTTGTAGAACC	0.358																																					p.R1689W		.											.	ARAP2-93	0			c.C5065T						.						97	98	98					4																	36069579		2203	4300	6503	SO:0001583	missense	116984	exon33			TTGACCGTTGTAG	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.5065C>T	4.37:g.36069579G>A	ENSP00000302895:p.Arg1689Trp	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	79	33	NM_015230	0	0	2	7	5	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069954	0.55539	.	.	ENSG00000047365	ENST00000303965	T	0.10573	2.86	5.79	2.62	0.31277	.	0.081885	0.48286	D	0.000197	T	0.19327	0.0464	L	0.32530	0.975	0.26832	N	0.968552	D	0.89917	1.0	D	0.65573	0.936	T	0.02391	-1.1166	10	0.87932	D	0	.	12.1751	0.54180	0.0:0.0:0.5359:0.4641	.	1689	Q8WZ64	ARAP2_HUMAN	W	1689	ENSP00000302895:R1689W	ENSP00000302895:R1689W	R	-	1	2	ARAP2	35745974	0.543000	0.26434	0.703000	0.30354	0.768000	0.43524	1.288000	0.33296	0.691000	0.31592	0.650000	0.86243	CGG	.		0.358	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36069579	G	A	36069579	3	1	132	1	0	0	0	0	1	0	0	0	839	1144	40	1	53	1	ARAP2	4	36069579	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		36069579	155084697	22	11675											
GABRB1	2560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	47427723	47427723	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtaacattctcctcagcacCctggaaatccggaatgagac	12	8	9	12	1	2	1	1	1	1	1	4	4	3	3	3	3	2	2	3	3	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr4:47427723C>G	ENST00000295454.3	+	9	1405	c.1113C>G	c.(1111-1113)acC>acG	p.T371T	GABRB1_ENST00000538619.1_Silent_p.T301T	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	371					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|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)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					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)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|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)	TCCTCAGCACCCTGGAAATCC	0.547																																					p.T371T		.											.	GABRB1-92	0			c.C1113G						.						77	75	76					4																	47427723		2203	4300	6503	SO:0001819	synonymous_variant	2560	exon9			CAGCACCCTGGAA		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4081	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 1"	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.1113C>G	4.37:g.47427723C>G		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	128	50	NM_000812	0	0	0	0	0	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			.		0.547	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			G	47427723	C	G	47427723	2	3	132	1	0	0	0	0	0	0	0	1	6185	610	22	4		4	GABRB1	4	47427723	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	11358144	47427723	143726553	23	11676											
MTRR	4552	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	7895903	7895903	+	Frame_Shift_Del	DEL	C	C	-																															ttaccagatgacccctcaatCcccatcataatggtgggtcc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:7895903delC	ENST00000264668.2	+	12	1725	c.1695delC	c.(1693-1695)atcfs	p.I565fs	MTRR_ENST00000440940.2_Frame_Shift_Del_p.I538fs	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	565					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ACCCCTCAATCCCCATCATAA	0.403																																					p.I565fs		.											.	MTRR-91	0			c.1695delC						.						137	138	138					5																	7895903		2203	4300	6503	SO:0001589	frameshift_variant	4552	exon12			.	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1695delC	5.37:g.7895903delC	ENSP00000264668:p.Ile565fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	81	39	NM_024010	0	0	0	0	0	O60471|Q32MA9|Q7Z4M8	Frame_Shift_Del	DEL	ENST00000264668.2	37	CCDS3874.1																																																																																			.		0.403	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			-	7895903	C	-	7895903	7	5	132	1	0	1	0	1	0	0	0	0	9986	845	30	0	1741	0	MTRR	5	7895903	Frame_Shift_Del	DEL	C	TCGA-HE-A5NH-01A-11D-A26P-10		7895903	173019357	24	11677											
PRR16	51334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	120021685	120021685	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaccctgacctctgacctaCagctggaggatgagatgact	11	8	10	12	0	1	4	0	4	1	1	1	7	1	6	3	2	2	1	3	2	1	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:120021685C>A	ENST00000407149.2	+	2	405	c.196C>A	c.(196-198)Cag>Aag	p.Q66K	PRR16_ENST00000505123.1_5'UTR|PRR16_ENST00000379551.2_Missense_Mutation_p.Q43K|PRR16_ENST00000446965.1_5'UTR			Q569H4	LARGN_HUMAN	proline rich 16	66					positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CTCTGACCTACAGCTGGAGGA	0.463																																					p.Q43K		.											.	PRR16-71	0			c.C127A						.						97	88	91					5																	120021685		2203	4300	6503	SO:0001583	missense	51334	exon3			GACCTACAGCTGG	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.196C>A	5.37:g.120021685C>A	ENSP00000385118:p.Gln66Lys	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	87	37	NM_016644	0	0	0	0	0	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	37		.	.	.	.	.	.	.	.	.	.	C	22.1	4.240061	0.79912	.	.	ENSG00000184838	ENST00000407149;ENST00000379551	T;T	0.45668	0.89;0.89	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	L	0.43152	1.355	0.80722	D	1	D;D	0.67145	0.988;0.996	P;P	0.57911	0.829;0.829	T	0.44190	-0.9344	9	.	.	.	-0.1775	17.7817	0.88526	0.0:1.0:0.0:0.0	.	66;43	Q569H4;Q569H4-3	PRR16_HUMAN;.	K	66;43	ENSP00000385118:Q66K;ENSP00000368869:Q43K	.	Q	+	1	0	PRR16	120049584	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.383000	0.79741	2.568000	0.86640	0.555000	0.69702	CAG	.		0.463	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		A	120021685	C	A	120021685	3	1	132	1	0	0	0	0	1	0	0	0	12618	479	17	4	133	4	PRR16	5	120021685	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	112125782	120021685	60893575	25	11678											
CCNI2	645121	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	132088594	132088594	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagctgctgcaaggaacttGtaatgcagcaactgagaagt	14	8	11	8	0	0	1	0	1	0	1	0	3	0	2	0	1	7	6	0	1	5	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:132088594G>A	ENST00000378731.1	+	6	1093	c.1042G>A	c.(1042-1044)Gta>Ata	p.V348I	SEPT8_ENST00000481030.1_Intron|SEPT8_ENST00000378719.2_Intron	NM_001039780.2	NP_001034869.1	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2	348					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAAGGAACTTGTAATGCAGCA	0.478																																					p.V348I		.											.	CCNI2-68	0			c.G1042A						.						122	105	111					5																	132088594		2203	4300	6503	SO:0001583	missense	645121	exon6			GAACTTGTAATGC	BC132837	CCDS34236.1, CCDS75297.1	5q31.1	2014-07-03			ENSG00000205089	ENSG00000205089			33869	protein-coding gene	gene with protein product						23707792	Standard	NM_001287252		Approved	FLJ16793	uc003kxq.1	Q6ZMN8	OTTHUMG00000059737	ENST00000378731.1:c.1042G>A	5.37:g.132088594G>A	ENSP00000368005:p.Val348Ile	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	98	38	NM_001039780	0	0	0	0	0	B2RNE2|B7ZMB7|B7ZMB8	Missense_Mutation	SNP	ENST00000378731.1	37	CCDS34236.1	.	.	.	.	.	.	.	.	.	.	g	15.24	2.775517	0.49786	.	.	ENSG00000205089	ENST00000378731	T	0.42131	0.98	5.35	2.54	0.30619	.	0.252001	0.38959	N	0.001518	T	0.43055	0.1230	M	0.66297	2.02	0.09310	N	0.999999	B;B;P	0.41710	0.261;0.261;0.76	B;B;P	0.45232	0.03;0.052;0.474	T	0.31194	-0.9952	10	0.52906	T	0.07	.	6.9365	0.24468	0.1591:0.1432:0.6976:0.0	.	349;364;348	B7ZMB7;B7ZMB8;Q6ZMN8	.;.;CCNI2_HUMAN	I	348	ENSP00000368005:V348I	ENSP00000368005:V348I	V	+	1	0	CCNI2	132116493	0.435000	0.25577	0.001000	0.08648	0.003000	0.03518	1.780000	0.38634	0.434000	0.26340	-0.144000	0.13903	GTA	.		0.478	CCNI2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132833.1	NM_001039780		A	132088594	G	A	132088594	3	1	132	1	0	0	0	0	1	0	0	0	2933	1377	48	2	1064	2	CCNI2	5	132088594	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	12066909	132088594	48826666	26	11679											
FAM13B	51306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	137354741	137354741	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatcaagtggaattccaaaTattttgttagcaagaacgga	15	12	8	6	1	2	1	2	0	0	1	3	3	3	3	1	2	2	2	1	2	7	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:137354741T>C	ENST00000033079.3	-	3	511	c.60A>G	c.(58-60)atA>atG	p.I20M	FAM13B_ENST00000425075.2_Intron|FAM13B_ENST00000420893.2_Missense_Mutation_p.I20M	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	20					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						GAATTCCAAATATTTTGTTAG	0.448																																					p.I20M		.											.	.	0			c.A60G						.						102	99	100					5																	137354741		2203	4300	6503	SO:0001583	missense	51306	exon3			TCCAAATATTTTG	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"Rho GTPase activating proteins"	1335	protein-coding gene	gene with protein product		609371	"chromosome 5 open reading frame 5", "family with sequence similarity 13, member B1"	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.60A>G	5.37:g.137354741T>C	ENSP00000033079:p.Ile20Met	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	256	120	NM_001101800	0	0	1	1	0	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	T	17.19	3.327093	0.60743	.	.	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310;ENST00000502471;ENST00000509596;ENST00000508403;ENST00000505961	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.87	5.87	0.94306	Rho GTPase-activating protein domain (1);Rho GTPase activation protein (1);	0.045544	0.85682	D	0.000000	T	0.48874	0.1524	N	0.14661	0.345	0.43394	D	0.995515	D;D	0.76494	0.999;0.998	D;D	0.74023	0.952;0.982	T	0.56986	-0.7888	10	0.87932	D	0	-9.9548	16.27	0.82612	0.0:0.0:0.0:1.0	.	20;20	Q9NYF5-2;Q9NYF5	.;FA13B_HUMAN	M	20	ENSP00000033079:I20M;ENSP00000388521:I20M;ENSP00000425326:I20M;ENSP00000424785:I20M;ENSP00000422311:I20M;ENSP00000426863:I20M;ENSP00000422673:I20M	ENSP00000033079:I20M	I	-	3	3	FAM13B	137382640	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.908000	0.56355	2.248000	0.74166	0.533000	0.62120	ATA	.		0.448	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			C	137354741	T	C	137354741	3	2	132	1	0	0	0	0	1	0	0	0	5469	1396	49	3	2841	3	FAM13B	5	137354741	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	5266147	137354741	43560519	27	11680											
C6orf146	222826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	4069042	4069042	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acactatattttgtcggtaaAgtttctttttggtcccaaag	10	17	7	7	1	1	0	0	0	1	0	3	0	2	0	1	2	0	2	1	2	5	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:4069042A>G	ENST00000274673.3	-	7	1818	c.1415T>C	c.(1414-1416)cTt>cCt	p.L472P	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	472																	TTGTCGGTAAAGTTTCTTTTT	0.403																																					p.L472P		.											.	.	0			c.T1415C						.						87	92	90					6																	4069042		2203	4300	6503	SO:0001583	missense	222826	exon7			CGGTAAAGTTTCT	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.1415T>C	6.37:g.4069042A>G	ENSP00000274673:p.Leu472Pro	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	97	35	NM_173563	0	0	0	0	0	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	A	9.632	1.136613	0.21123	.	.	ENSG00000145975	ENST00000274673;ENST00000538080	T	0.19806	2.12	4.94	1.19	0.21007	.	0.439613	0.19414	N	0.114873	T	0.04724	0.0128	L	0.27053	0.805	0.38087	D	0.936832	B	0.22683	0.073	B	0.25884	0.064	T	0.21586	-1.0241	10	0.45353	T	0.12	.	3.9837	0.09506	0.6123:0.1915:0.1961:0.0	.	472	Q8IXS0	CF146_HUMAN	P	472;319	ENSP00000274673:L472P	ENSP00000274673:L472P	L	-	2	0	C6orf146	4014041	0.583000	0.26757	0.264000	0.24511	0.732000	0.41865	1.295000	0.33377	0.055000	0.16094	0.477000	0.44152	CTT	.		0.403	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563		G	4069042	A	G	4069042	3	3	132	1	0	0	0	0	1	0	0	0	2341	72	3	3	115	3	C6orf146	6	4069042	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10		4069042	167046025	28	11681											
MYLIP	29116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	16143330	16143330	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgcagattgtgtcggcaAtggaaaactatggcatagaa	13	12	11	5	1	0	2	0	0	0	2	1	3	0	3	0	3	2	3	0	3	6	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:16143330A>G	ENST00000356840.3	+	4	742	c.544A>G	c.(544-546)Atg>Gtg	p.M182V	MIR4639_ENST00000584938.1_RNA|MYLIP_ENST00000349606.4_Start_Codon_SNP_p.M1V	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	182	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			TGTGTCGGCAATGGAAAACTA	0.473																																					p.M182V		.											.	MYLIP-91	0			c.A544G						.						130	122	125					6																	16143330		2203	4300	6503	SO:0001583	missense	29116	exon4			TCGGCAATGGAAA	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.544A>G	6.37:g.16143330A>G	ENSP00000349298:p.Met182Val	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	158	77	NM_013262	0	0	8	20	12	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Missense_Mutation	SNP	ENST00000356840.3	37	CCDS4536.1	.	.	.	.	.	.	.	.	.	.	A	11.61	1.689703	0.29962	.	.	ENSG00000007944	ENST00000356840;ENST00000349606	T;T	0.76839	-1.05;1.32	5.57	5.57	0.84162	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.135191	0.64402	D	0.000002	T	0.57548	0.2061	L	0.38175	1.15	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.63125	-0.6707	10	0.87932	D	0	.	11.5381	0.50651	0.7336:0.2664:0.0:0.0	.	182	Q8WY64	MYLIP_HUMAN	V	182;1	ENSP00000349298:M182V;ENSP00000008686:M1V	ENSP00000008686:M1V	M	+	1	0	MYLIP	16251309	0.995000	0.38212	0.927000	0.36925	0.499000	0.33736	3.374000	0.52402	2.230000	0.72887	0.533000	0.62120	ATG	.		0.473	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262		G	16143330	A	G	16143330	3	3	132	1	0	0	0	0	1	0	0	0	10080	101	4	3	558	3	MYLIP	6	16143330	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	12074288	16143330	154971737	29	11682											
SLC17A1	6568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	25811999	25811999	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agggaagacaagaacccattCtgaagaggaaacattattct	17	8	9	7	0	2	4	0	1	2	3	2	6	2	6	1	2	2	0	1	2	6	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:25811999C>T	ENST00000244527.4	-	9	1013		c.e9-1		SLC17A1_ENST00000476801.1_Splice_Site|SLC17A1_ENST00000468082.1_Splice_Site|SLC17A1_ENST00000427328.1_Splice_Site	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1						ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						AGAACCCATTCTGAAGAGGAA	0.403																																					.		.											.	SLC17A1-94	0			c.898-1G>A						.						87	79	82					6																	25811999		2203	4300	6503	SO:0001630	splice_region_variant	6568	exon10			CCCATTCTGAAGA		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"Solute carriers"	10929	protein-coding gene	gene with protein product		182308	"solute carrier family 17 (sodium phosphate), member 1"	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.898-1G>A	6.37:g.25811999C>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	73	26	NM_005074	0	0	1	4	3	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Splice_Site	SNP	ENST00000244527.4	37	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	C	7.361	0.624846	0.14193	.	.	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	.	.	.	3.38	3.38	0.38709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5584	0.45131	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC17A1	25919978	1.000000	0.71417	0.946000	0.38457	0.079000	0.17450	4.214000	0.58527	2.191000	0.70037	0.650000	0.86243	.	.		0.403	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2		Intron	T	25811999	C	T	25811999	5	4	132	1	0	0	0	0	0	0	1	0	14448	927	32	2	522	2	SLC17A1	6	25811999	Splice_Site	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	9668669	25811999	145303068	30	11683											
GCLC	2729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	53370243	53370243	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaaaggatcactctggtgaGcagtaccacaaacaccacat	15	6	9	11	0	2	1	1	1	1	0	2	3	2	3	2	3	3	2	2	3	3	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:53370243G>C	ENST00000229416.6	-	12	1825	c.1342C>G	c.(1342-1344)Ctc>Gtc	p.L448V	RP1-27K12.4_ENST00000508884.1_RNA	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	448					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	ACTCTGGTGAGCAGTACCACA	0.403																																					p.L448V		.											.	GCLC-515	0			c.C1342G						.						98	90	93					6																	53370243		2203	4300	6503	SO:0001583	missense	2729	exon12			TGGTGAGCAGTAC	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.1342C>G	6.37:g.53370243G>C	ENSP00000229416:p.Leu448Val	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	178	72	NM_001498	0	0	7	11	4	Q14399	Missense_Mutation	SNP	ENST00000229416.6	37	CCDS4952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.15|17.15	3.315237|3.315237	0.60524|0.60524	.|.	.|.	ENSG00000001084|ENSG00000001084	ENST00000514373|ENST00000229416	.|T	.|0.77358	.|-1.09	5.94|5.94	5.94|5.94	0.96194|0.96194	.|.	.|0.055897	.|0.85682	.|D	.|0.000000	T|T	0.71787|0.71787	0.3381|0.3381	M|M	0.66297|0.66297	2.02|2.02	0.80722|0.80722	D|D	1|1	.|B	.|0.18968	.|0.032	.|B	.|0.22152	.|0.038	T|T	0.66779|0.66779	-0.5837|-0.5837	5|10	.|0.42905	.|T	.|0.14	.|.	20.3594|20.3594	0.98849|0.98849	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|448	.|P48506	.|GSH1_HUMAN	W|V	49|448	.|ENSP00000229416:L448V	.|ENSP00000229416:L448V	C|L	-|-	3|1	2|0	GCLC|GCLC	53478202|53478202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.830000|0.830000	0.47004|0.47004	8.018000|8.018000	0.88722|0.88722	2.816000|2.816000	0.96949|0.96949	0.563000|0.563000	0.77884|0.77884	TGC|CTC	.		0.403	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			C	53370243	G	C	53370243	3	2	132	1	0	0	0	0	1	0	0	0	6315	971	34	4	591	4	GCLC	6	53370243	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	27558244	53370243	117744824	31	11684											
C6orf162	57150	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	88046811	88046811	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccaaagagaaagagtttcAaagcccagggctcagagggg	15	4	13	9	0	2	3	2	0	0	3	2	4	2	3	2	3	1	2	2	3	3	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:88046811A>C	ENST00000392863.1	+	3	151	c.62A>C	c.(61-63)cAa>cCa	p.Q21P	SMIM8_ENST00000608353.1_Missense_Mutation_p.Q21P|SMIM8_ENST00000229570.5_Missense_Mutation_p.Q21P|RP1-102H19.8_ENST00000448282.2_Missense_Mutation_p.Q21P|SMIM8_ENST00000608525.1_Missense_Mutation_p.Q21P|SMIM8_ENST00000608868.1_Missense_Mutation_p.Q21P	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	21						integral component of membrane (GO:0016021)											AAAGAGTTTCAAAGCCCAGGG	0.398																																					p.Q21P		.											.	.	0			c.A62C						.						89	91	90					6																	88046811		2203	4300	6503	SO:0001583	missense	57150	exon3			AGTTTCAAAGCCC	AL050201	CCDS34496.1, CCDS75493.1	6q15	2013-06-21	2012-11-20	2012-11-20	ENSG00000111850	ENSG00000111850			21401	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 162"	C6orf162			Standard	NM_001287445		Approved	DKFZP586E1923, dJ102H19.2	uc003plq.1	Q96KF7	OTTHUMG00000015168	ENST00000392863.1:c.62A>C	6.37:g.88046811A>C	ENSP00000376603:p.Gln21Pro	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	64	31	NM_001042493	0	0	2	3	1	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Missense_Mutation	SNP	ENST00000392863.1	37	CCDS34496.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015538	0.35511	.	.	ENSG00000111850	ENST00000392863;ENST00000229570	.	.	.	5.69	-0.263	0.12954	.	0.368122	0.29501	N	0.011965	T	0.08044	0.0201	.	.	.	0.25064	N	0.991047	B	0.02656	0.0	B	0.04013	0.001	T	0.35475	-0.9787	8	0.25106	T	0.35	0.3915	5.1987	0.15252	0.2411:0.3105:0.4483:0.0	.	21	Q96KF7	CF162_HUMAN	P	21	.	ENSP00000229570:Q21P	Q	+	2	0	C6orf162	88103530	0.489000	0.26004	0.812000	0.32479	0.823000	0.46562	0.679000	0.25291	-0.373000	0.07979	0.533000	0.62120	CAA	.		0.398	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425		C	88046811	A	C	88046811	3	2	132	1	0	0	0	0	1	0	0	0	2346	130	5	5	64	5	C6orf162	6	88046811	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	34676568	88046811	83068256	32	11685											
MET	4233	hgsc.bcm.edu	37	chr7	116411633	116411634	+	In_Frame_Ins	INS	-	-	TTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT																															cacaggattgattgctggtgINSttgtctcaatatcaacagca																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:116411633_116411634insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	ENST00000318493.6	+	13	3053_3054	c.2866_2867insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	c.(2866-2868)gtt>gTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGTtt	p.969_970insVSISTALLLLLGF	MET_ENST00000397752.3_In_Frame_Ins_p.951_952insVSISTALLLLLGF			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GATTGCTGGTGTTGTCTCAATA	0.347			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V956delinsVVSISTALLLLLGF		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.2866_2867insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT						.																																			SO:0001652	inframe_insertion	4233	exon13	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	.	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.2867_2905dupTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	7.37:g.116411633_116411634insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	ENSP00000317272:p.Val957_Phe969dup	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	110	20	NM_001127500	0	0	0	0	0	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	In_Frame_Ins	INS	ENST00000318493.6	37	CCDS47689.1																																																																																			.		0.347	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			TTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	116411634	-	TTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	116411633	7	5	132	1	0	1	1	0	0	0	0	0	9510	1377	48	0	2912	0	MET	7	116411633	In_Frame_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10		116411633	42727030	33	11686											
MET	4233	hgsc.bcm.edu;bcgsc.ca	37	chr7	116411675	116411675	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttattactacttgggtttTtcctgtggctgaaaaagaga	10	16	10	5	0	0	2	0	1	0	1	1	3	1	2	1	2	2	3	1	2	5	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:116411675T>G	ENST00000318493.6	+	13	3095	c.2908T>G	c.(2908-2910)Ttc>Gtc	p.F970V	MET_ENST00000397752.3_Missense_Mutation_p.F952V			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			ACTTGGGTTTTTCCTGTGGCT	0.348			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.F970V		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.T2908G						.						117	110	112					7																	116411675		1845	4085	5930	SO:0001583	missense	4233	exon13	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGGTTTTTCCTGT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.2908T>G	7.37:g.116411675T>G	ENSP00000317272:p.Phe970Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	97	15	NM_001127500	0	0	124	124	0	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.377141	0.42105	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000454623	T;T	0.72167	-0.63;-0.63	5.76	5.76	0.90799	.	0.096961	0.64402	D	0.000001	T	0.67420	0.2891	M	0.73598	2.24	0.80722	D	1	P;B	0.38129	0.619;0.349	B;B	0.35510	0.204;0.185	T	0.67428	-0.5673	10	0.31617	T	0.26	.	10.6767	0.45789	0.0:0.0713:0.0:0.9287	.	970;952	P08581-2;P08581	.;MET_HUMAN	V	952;970;84	ENSP00000380860:F952V;ENSP00000317272:F970V	ENSP00000317272:F970V	F	+	1	0	MET	116198911	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	2.954000	0.49113	2.324000	0.78689	0.533000	0.62120	TTC	.		0.348	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116411675	T	G	116411675	3	3	132	1	0	0	0	0	1	0	0	0	9510	1841	64	5	2954	5	MET	7	116411675	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	42	116411675	42726988	34	11687											
PLXNA4	91584	hgsc.bcm.edu;bcgsc.ca	37	chr7	131859582	131859583	+	Frame_Shift_Ins	INS	-	-	AA																															cttcaattcctgggaacagcINSacccgcatggtgtaagttct																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:131859582_131859583insAA	ENST00000359827.3	-	21	4933_4934	c.3971_3972insTT	c.(3970-3972)gtgfs	p.V1324fs	PLXNA4_ENST00000321063.4_Frame_Shift_Ins_p.V1324fs			Q9HCM2	PLXA4_HUMAN	plexin A4	1324					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CTGGGAACAGCACCCGCATGGT	0.569																																					p.V1324fs		.											.	PLXNA4-91	0			c.3972_3973insTT						.																																			SO:0001589	frameshift_variant	91584	exon21			.	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"Plexins"	9102	protein-coding gene	gene with protein product		604280	"plexin A4, A", "plexin A4, B"	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3971_3972insTT	7.37:g.131859582_131859583insAA	ENSP00000352882:p.Val1324fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	172	55	NM_020911	0	0	0	0	0	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Frame_Shift_Ins	INS	ENST00000359827.3	37	CCDS43646.1																																																																																			.		0.569	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		AA	131859583	-	AA	131859582	7	5	132	1	0	1	1	0	0	0	0	0	12148	697	25	0	1760	0	PLXNA4	7	131859582	Frame_Shift_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10	15447907	131859582	27279081	35	11688											
GBX1	2636	broad.mit.edu	37	chr7	150864527	150864529	+	In_Frame_Del	DEL	GCG	GCG	-																															gtacagcaagtggccggagcGcggcggcggcggcccgatta																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	GCG	GCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:150864527_150864529delGCG	ENST00000297537.4	-	1	106_108	c.107_109delCGC	c.(106-111)ccgcgc>cgc	p.P36del	GBX1_ENST00000475831.1_Intron	NM_001098834.1	NP_001092304.1	Q14549	GBX1_HUMAN	gastrulation brain homeobox 1	36	Pro-rich.				adult walking behavior (GO:0007628)|neuron fate commitment (GO:0048663)|proprioception (GO:0019230)|regulation of transcription, DNA-templated (GO:0006355)|sensory neuron axon guidance (GO:0097374)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(5)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGCCGGAGCGCGGCGGCGGCGG	0.773																																					p.36_37del													.	GBX1-68	0			c.107_109del						.			5,2199		0,5,1097						2.6	0.7			3	12,4672		2,8,2332	no	coding	GBX1	NM_001098834.1		2,13,3429	A1A1,A1R,RR		0.2562,0.2269,0.2468				17,6871				SO:0001651	inframe_deletion	2636	exon1			CGGAGCGCGGCGG	L11239	CCDS43682.1	7q36.1	2012-03-09	2005-12-22		ENSG00000164900	ENSG00000164900		"Homeoboxes / ANTP class : HOXL subclass"	4185	protein-coding gene	gene with protein product		603354	"gastrulation brain homeo box 1"			7903253	Standard	NM_001098834		Approved		uc011kvg.2	Q14549	OTTHUMG00000158751	ENST00000297537.4:c.107_109delCGC	7.37:g.150864536_150864538delGCG	ENSP00000297537:p.Pro36del	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001098834	0	0	0	0	0		In_Frame_Del	DEL	ENST00000297537.4	37	CCDS43682.1																																																																																			.		0.773	GBX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352029.1			-	150864529	GCG	-	150864527	7	5	132	1	0	1	0	1	0	0	0	0	6300	1087	38	0	989	0	GBX1	7	150864527	In_Frame_Del	DEL	GCG	TCGA-HE-A5NH-01A-11D-A26P-10	19004945	150864527	8274136	36	11689											
MTUS1	57509	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr8	17579357	17579357	+	Intron	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgtagaattgataaagatTtttgaagaaatatcagtttc	16	15	8	2	0	1	5	1	2	0	3	2	5	1	5	0	0	0	2	0	0	7	7			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:17579357T>A	ENST00000262102.6	-	4	2674				MTUS1_ENST00000381861.3_Missense_Mutation_p.K18N|MTUS1_ENST00000519263.1_Intron|MTUS1_ENST00000544260.1_Intron|MTUS1_ENST00000381869.3_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1						cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TGATAAAGATTTTTGAAGAAA	0.428																																					p.K18N		.											.	MTUS1-92	0			c.A54T						.						86	86	86					8																	17579357		1840	4094	5934	SO:0001627	intron_variant	57509	exon1			AAAGATTTTTGAA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2449+1823A>T	8.37:g.17579357T>A		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	74	35	NM_001001931	0	0	0	0	0	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.116072	0.37339	.	.	ENSG00000129422	ENST00000381861	T	0.15487	2.42	5.48	1.4	0.22301	.	.	.	.	.	T	0.07234	0.0183	.	.	.	0.23602	N	0.997312	B	0.09022	0.002	B	0.11329	0.006	T	0.39860	-0.9593	8	0.16896	T	0.51	.	0.4383	0.00482	0.2369:0.2954:0.15:0.3178	.	18	Q9ULD2-6	.	N	18	ENSP00000371285:K18N	ENSP00000371285:K18N	K	-	3	2	MTUS1	17623637	0.479000	0.25925	0.804000	0.32291	0.992000	0.81027	0.640000	0.24705	0.443000	0.26582	0.533000	0.62120	AAA	.		0.428	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17579357	T	A	17579357	1	1	132	0	1	0	0	0	0	0	0	0	9990	1838	64	5		5	MTUS1	8	17579357	Intron	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10		17579357	128784665	37	11690											
LPL	4023	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	19811710	19811710	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgatgcagattttgtagaCgtcttacacacattcaccag	12	12	8	9	1	2	3	1	1	1	2	2	4	2	3	1	0	2	2	1	0	2	5	rs118204076		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:19811710C>T	ENST00000311322.8	+	5	1091	c.621C>T	c.(619-621)gaC>gaT	p.D207D		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	207			D -> E (in LPL deficiency). {ECO:0000269|PubMed:8288243}.		chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	ATTTTGTAGACGTCTTACACA	0.483																																					p.D207D		.											.	LPL-92	0			c.C621T	GRCh37	CM930483	LPL	M	rs118204076	.						139	134	135					8																	19811710		2203	4300	6503	SO:0001819	synonymous_variant	4023	exon5			TGTAGACGTCTTA		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.621C>T	8.37:g.19811710C>T		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	155	73	NM_000237	0	0	1	1	0	B2R5T9|Q16282|Q16283|Q96FC4	Silent	SNP	ENST00000311322.8	37	CCDS6012.1																																																																																			.		0.483	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			T	19811710	C	T	19811710	2	4	132	1	0	0	0	0	0	0	0	1	8946	535	19	1		1	LPL	8	19811710	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	2232353	19811710	126552312	38	11691											
PPP2R2A	5520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	26211991	26211991	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttcattttagaacaaaaTccagtctcatagcagaggag	14	12	8	7	0	2	2	2	0	1	2	4	3	3	3	1	1	2	2	1	1	5	5	rs373174942		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:26211991T>C	ENST00000380737.3	+	4	517	c.188T>C	c.(187-189)aTc>aCc	p.I63T	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.I73T	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	63					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(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;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		TAGAACAAAATCCAGTCTCAT	0.318																																					p.I73T		.											.	PPP2R2A-659	0			c.T218C						.	T	THR/ILE,THR/ILE	0,4406		0,0,2203	70	73	72		218,188	4.8	1	8		72	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	PPP2R2A	NM_001177591.1,NM_002717.3	89,89	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	,	73/458,63/448	26211991	1,13003	2203	4299	6502	SO:0001583	missense	5520	exon4			ACAAAATCCAGTC	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.188T>C	8.37:g.26211991T>C	ENSP00000370113:p.Ile63Thr	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	38	12	NM_001177591	0	0	0	0	0	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	37	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	T	6.035	0.374882	0.11409	0.0	1.16E-4	ENSG00000221914	ENST00000380737;ENST00000315985	T;T	0.29142	1.59;1.58	5.97	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.287722	0.32204	U	0.006432	T	0.08358	0.0208	N	0.01576	-0.805	0.37304	D	0.908831	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28522	-1.0041	10	0.09843	T	0.71	-14.6536	2.6676	0.05057	0.0:0.1705:0.291:0.5384	.	73;63	B4E1T7;P63151	.;2ABA_HUMAN	T	63;73	ENSP00000370113:I63T;ENSP00000325074:I73T	ENSP00000325074:I73T	I	+	2	0	PPP2R2A	26267908	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.834000	0.39171	2.285000	0.76669	0.528000	0.53228	ATC	.		0.318	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		C	26211991	T	C	26211991	3	2	132	1	0	0	0	0	1	0	0	0	12413	1435	50	3	243	3	PPP2R2A	8	26211991	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	6400281	26211991	120152031	39	11692											
ADAM9	8754	broad.mit.edu	37	chr8	38854664	38854670	+	Frame_Shift_Del	DEL	GGTGCGG	GGTGCGG	-																															gcctggtgggcccagtcctcGgtgcggcgcggccaggtggg																								rs576406930		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	GGTGCGG	GGTGCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:38854664_38854670delGGTGCGG	ENST00000487273.2	+	1	160_166	c.82_88delGGTGCGG	c.(82-90)ggtgcggcgfs	p.GAA28fs	ADAM9_ENST00000466936.1_Frame_Shift_Del_p.GAA28fs|TM2D2_ENST00000412303.1_5'Flank|TM2D2_ENST00000456397.2_5'Flank|TM2D2_ENST00000522434.1_5'Flank|ADAM9_ENST00000481513.1_Frame_Shift_Del_p.GAA28fs|TM2D2_ENST00000456845.2_5'Flank|TM2D2_ENST00000397070.2_5'Flank	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	28				Missing (in Ref. 2; no nucleotide entry). {ECO:0000305}.	activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			CCCAGTCCTCGGTGCGGCGCGGCCAGG	0.715																																					p.28_30del													.	ADAM9-227	0			c.82_88del						.																																			SO:0001589	frameshift_variant	8754	exon1			GTCCTCGGTGCGG	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.82_88delGGTGCGG	8.37:g.38854664_38854670delGGTGCGG	ENSP00000419446:p.Gly28fs	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_003816	0	0	0	0	0	B7ZLN7|Q10718|Q8NFM6	Frame_Shift_Del	DEL	ENST00000487273.2	37	CCDS6112.1																																																																																			.		0.715	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			-	38854670	GGTGCGG	-	38854664	7	5	132	1	0	1	0	1	0	0	0	0	253	1116	39	0	84	0	ADAM9	8	38854664	Frame_Shift_Del	DEL	GGTGCGG	TCGA-HE-A5NH-01A-11D-A26P-10	12642673	38854664	107509358	40	11693											
ASPH	444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	62460750	62460750	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtcctctcttgtgcccaagCtcataccacttatatgcctg	7	14	6	14	0	2	0	1	0	1	0	4	0	3	0	4	0	4	1	4	0	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:62460750C>T	ENST00000379454.4	-	21	1831	c.1644G>A	c.(1642-1644)gaG>gaA	p.E548E	ASPH_ENST00000541428.1_Silent_p.E519E	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	548					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)	p.E548E(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	TGTGCCCAAGCTCATACCACT	0.403																																					p.E548E		.											.	ASPH-93	1	Substitution - coding silent(1)	large_intestine(1)	c.G1644A						.						119	102	108					8																	62460750		2203	4300	6503	SO:0001819	synonymous_variant	444	exon21			CCCAAGCTCATAC	AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"junctin", "humbug", "junctate"	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.1644G>A	8.37:g.62460750C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	134	54	NM_004318	0	0	7	16	9	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Silent	SNP	ENST00000379454.4	37	CCDS34898.1																																																																																			.		0.403	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		T	62460750	C	T	62460750	2	4	132	1	0	0	0	0	0	0	0	1	1054	796	28	2		2	ASPH	8	62460750	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	23606086	62460750	83903272	41	11694											
TRAPPC9	83696	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	141301159	141301159	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gctgaacttcacacacatctCcttgaacccactggaaatct	12	10	5	14	0	3	2	1	2	2	0	4	3	3	3	2	1	2	1	2	1	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:141301159C>G	ENST00000438773.2	-	12	1920	c.1787G>C	c.(1786-1788)gGa>gCa	p.G596A	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.G694A|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.G587A	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	596					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						ACACACATCTCCTTGAACCCA	0.368																																					p.G694A													.	TRAPPC9-228	0			c.G2081C						.						158	138	145					8																	141301159		2203	4300	6503	SO:0001583	missense	83696	exon12			ACATCTCCTTGAA	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.1787G>C	8.37:g.141301159C>G	ENSP00000405060:p.Gly596Ala	Somatic	139	1		WXS	Illumina HiSeq	Phase_I	184	81	NM_031466	0	0	6	9	3	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	37	CCDS55278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.9|23.9	4.474358|4.474358	0.84640|0.84640	.|.	.|.	ENSG00000167632|ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773|ENST00000520857	.|.	.|.	.|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73598|0.73598	0.3607|0.3607	M|M	0.63843|0.63843	1.955|1.955	0.58432|0.58432	D|D	0.999994|0.999994	D;D;D;D|.	0.71674|.	0.998;0.998;0.996;0.998|.	D;D;D;D|.	0.73708|.	0.977;0.964;0.919;0.981|.	T|T	0.71856|0.71856	-0.4466|-0.4466	9|5	0.72032|.	D|.	0.01|.	.|.	18.9153|18.9153	0.92503|0.92503	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	694;596;587;694|.	A6NIF0;Q96Q05;Q96Q05-3;Q96Q05-2|.	.;TPPC9_HUMAN;.;.|.	A|S	694;587;596|439	.|.	ENSP00000373978:G587A|.	G|R	-|-	2|3	0|2	TRAPPC9|TRAPPC9	141370341|141370341	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.995000|0.995000	0.86356|0.86356	4.423000|4.423000	0.59861|0.59861	2.484000|2.484000	0.83849|0.83849	0.561000|0.561000	0.74099|0.74099	GGA|AGG	.		0.368	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		G	141301159	C	G	141301159	3	3	132	1	0	0	0	0	1	0	0	0	16498	855	30	4	1707	4	TRAPPC9	8	141301159	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	78840409	141301159	5062863	42	11695											
LRRC14	9684	broad.mit.edu	37	chr8	145745730	145745730	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgctgccgtagctcgcacAtgcattgcccagcagcaggg	8	7	12	14	2	0	0	0	0	0	0	1	0	0	0	2	1	7	7	2	1	1	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:145745730A>G	ENST00000292524.1	+	3	584	c.438A>G	c.(436-438)acA>acG	p.T146T	LRRC14_ENST00000529022.1_Silent_p.T146T|RECQL4_ENST00000428558.2_5'Flank|RECQL4_ENST00000532237.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	146										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TAGCTCGCACATGCATTGCCC	0.662																																					p.T146T													.	LRRC14-90	0			c.A438G						.						71	75	74					8																	145745730		2203	4300	6503	SO:0001819	synonymous_variant	9684	exon4			TCGCACATGCATT	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.438A>G	8.37:g.145745730A>G		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	29	4	NM_001272036	0	0	2	3	1	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			.		0.662	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		G	145745730	A	G	145745730	2	3	132	1	0	0	0	0	0	0	0	1	8993	204	8	3		3	LRRC14	8	145745730	Silent	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	4444571	145745730	618292	43	11696											
FOXD4L3	286380	hgsc.bcm.edu;broad.mit.edu	37	chr9	70919081	70919082	+	Frame_Shift_Del	DEL	GG	GG	-																															tgcgctcccaccaagggcgcGgtgctgggcgggcacctgtc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr9:70919081_70919082delGG	ENST00000342833.2	+	1	1806_1807	c.1214_1215delGG	c.(1213-1215)cggfs	p.R405fs		NM_199135.4	NP_954586.4	Q6VB84	FX4L3_HUMAN	forkhead box D4-like 3	405						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			ovary(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CCAAGGGCGCGGTGCTGGGCGG	0.668																																					p.405_405del		.											.	FOXD4L3-40	0			c.1214_1215del						.																																			SO:0001589	frameshift_variant	286380	exon1			.	AY344642	CCDS43833.1	9q13	2008-05-13				ENSG00000187559			18523	protein-coding gene	gene with protein product		611086				12421752	Standard	NM_199135		Approved	OTTHUMG00000019959, FOXD6	uc004agm.1	Q6VB84	OTTHUMG00000019959	ENST00000342833.2:c.1214_1215delGG	9.37:g.70919081_70919082delGG	ENSP00000341961:p.Arg405fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	144	27	NM_199135	0	0	0	0	0	Q5JTX9	Frame_Shift_Del	DEL	ENST00000342833.2	37	CCDS43833.1																																																																																			.		0.668	FOXD4L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052539.2	NM_199358		-	70919082	GG	-	70919081	7	5	132	1	0	1	0	1	0	0	0	0	6020	1116	39	0	1216	0	FOXD4L3	9	70919081	Frame_Shift_Del	DEL	GG	TCGA-HE-A5NH-01A-11D-A26P-10		70919081	70294350	44	11697											
ODF2	4957	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131256869	131256869	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacggaggcgaagctggcTgagtgccaagaccaactgca	12	5	13	11	2	1	2	1	1	0	1	1	4	1	3	2	3	4	3	2	3	3	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr9:131256869T>C	ENST00000434106.3	+	17	2196	c.1833T>C	c.(1831-1833)gcT>gcC	p.A611A	ODF2_ENST00000372807.5_Silent_p.A606A|ODF2_ENST00000393527.3_Silent_p.A587A|ODF2_ENST00000372791.3_Silent_p.A592A|ODF2_ENST00000393533.2_Silent_p.A611A|ODF2_ENST00000604420.1_Silent_p.A611A|ODF2_ENST00000546203.1_Silent_p.A592A|ODF2_ENST00000372814.3_Silent_p.A655A|ODF2_ENST00000444119.2_Silent_p.A587A|ODF2_ENST00000448249.3_Silent_p.A530A|ODF2_ENST00000351030.3_Silent_p.A606A	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	611					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						CGAAGCTGGCTGAGTGCCAAG	0.572																																					p.A675A													.	ODF2-69	0			c.T2025C						.						74	64	68					9																	131256869		2203	4300	6503	SO:0001819	synonymous_variant	4957	exon17			GCTGGCTGAGTGC	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"cancer/testis antigen 134"	602015	"outer dense fibre of sperm tails 2"			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.1833T>C	9.37:g.131256869T>C		Somatic	194	1		WXS	Illumina HiSeq	Phase_I	228	88	NM_153435	0	0	4	8	4	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																			.		0.572	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			C	131256869	T	C	131256869	2	2	132	1	0	0	0	0	0	0	0	1	10853	1567	55	3		3	ODF2	9	131256869	Silent	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	60337788	131256869	9956562	45	11698											
NUP214	8021	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	134019825	134019825	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccccactgtgttctcctttGgttcttcatctttgaagtca	5	17	6	13	0	5	1	2	1	3	0	6	1	5	1	3	1	0	2	3	1	1	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr9:134019825G>C	ENST00000359428.5	+	12	1597	c.1453G>C	c.(1453-1455)Ggt>Cgt	p.G485R	RP11-544A12.4_ENST00000587264.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.G485R|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.G485R|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	485	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GTTCTCCTTTGGTTCTTCATC	0.577			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.G485R	Pancreas(4;24 48 25510 30394 32571)			Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214-1131	0			c.G1453C						.						217	219	218					9																	134019825		2203	4300	6503	SO:0001583	missense	8021	exon12			TCCTTTGGTTCTT	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"nuclear pore complex protein Nup214", "CAN protein, putative oncogene"	114350	"nucleoporin 214kD (CAIN)"			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1453G>C	9.37:g.134019825G>C	ENSP00000352400:p.Gly485Arg	Somatic	65	1		WXS	Illumina HiSeq	Phase_I	77	30	NM_005085	0	0	1	2	1	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.861397	0.71949	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899	T;T;T	0.80738	-1.41;-1.41;-1.41	5.79	5.79	0.91817	.	0.000000	0.41823	D	0.000813	T	0.72170	0.3427	N	0.08118	0	0.28472	N	0.915369	D;D	0.57571	0.98;0.98	P;P	0.56700	0.804;0.804	T	0.64672	-0.6352	10	0.20046	T	0.44	-17.3717	10.2889	0.43584	0.093:0.0:0.907:0.0	.	485;485	P35658-4;P35658	.;NU214_HUMAN	R	485;485;485;485;78	ENSP00000352400:G485R;ENSP00000396576:G485R;ENSP00000405014:G485R	ENSP00000352400:G485R	G	+	1	0	NUP214	133009646	0.876000	0.30132	1.000000	0.80357	0.916000	0.54674	1.801000	0.38843	2.726000	0.93360	0.655000	0.94253	GGT	.		0.577	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		C	134019825	G	C	134019825	3	2	132	1	0	0	0	0	1	0	0	0	10788	1348	47	4	1499	4	NUP214	9	134019825	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	2762956	134019825	7193606	46	11699											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16941145	16941145	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgaggccagtgaggggatctGattgtaccattatcagaatg	11	11	13	6	0	2	4	1	3	1	1	2	5	2	5	2	3	1	1	2	3	3	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:16941145G>C	ENST00000377833.4	-	54	8513	c.8448C>G	c.(8446-8448)atC>atG	p.I2816M		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2816	CUB 21. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAGGGGATCTGATTGTACCAT	0.403																																					p.I2816M		.											.	CUBN-166	0			c.C8448G						.						118	112	114					10																	16941145		2203	4300	6503	SO:0001583	missense	8029	exon54			GGATCTGATTGTA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.8448C>G	10.37:g.16941145G>C	ENSP00000367064:p.Ile2816Met	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	88	38	NM_001081	0	0	5	12	7	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.139005	0.21123	.	.	ENSG00000107611	ENST00000377833	T	0.40476	1.03	5.63	0.557	0.17260	CUB (5);	0.137522	0.33057	N	0.005332	T	0.64494	0.2603	M	0.93150	3.385	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.64782	-0.6326	10	0.66056	D	0.02	.	7.5405	0.27735	0.1201:0.0:0.4925:0.3874	.	2816	O60494	CUBN_HUMAN	M	2816	ENSP00000367064:I2816M	ENSP00000367064:I2816M	I	-	3	3	CUBN	16981151	1.000000	0.71417	0.001000	0.08648	0.014000	0.08584	3.071000	0.50041	-0.070000	0.12908	-0.940000	0.02684	ATC	.		0.403	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16941145	G	C	16941145	3	2	132	1	0	0	0	0	1	0	0	0	4057	1280	45	4	2479	4	CUBN	10	16941145	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		16941145	118593602	47	11700											
JMJD1C	221037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	64974605	64974605	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctgcttcttcatgttttTtatcttcctgtatttgatcc	4	23	4	10	0	4	1	1	1	3	0	7	1	6	1	2	0	1	3	2	0	2	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:64974605T>G	ENST00000399262.2	-	8	1540	c.1322A>C	c.(1321-1323)aAa>aCa	p.K441T	JMJD1C_ENST00000399251.1_Missense_Mutation_p.K222T|JMJD1C_ENST00000542921.1_Missense_Mutation_p.K259T|JMJD1C_ENST00000489372.2_5'Flank|JMJD1C_ENST00000402544.1_Missense_Mutation_p.K222T	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	441					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TTCATGTTTTTTATCTTCCTG	0.388																																					p.K441T		.											.	JMJD1C-275	0			c.A1322C						.						148	131	136					10																	64974605		1826	4079	5905	SO:0001583	missense	221037	exon8			TGTTTTTTATCTT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"thyroid hormone receptor interactor 8"	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.1322A>C	10.37:g.64974605T>G	ENSP00000382204:p.Lys441Thr	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_032776	0	0	1	2	1	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356618	0.61293	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.55930	0.84;0.49;2.4;0.84	5.85	4.71	0.59529	.	0.256048	0.33290	U	0.005078	T	0.44159	0.1280	L	0.51422	1.61	0.44012	D	0.99672	P;P	0.39282	0.666;0.666	B;B	0.33339	0.162;0.115	T	0.51631	-0.8681	10	0.62326	D	0.03	-15.2085	12.0787	0.53659	0.0:0.0679:0.0:0.9321	.	441;259	Q15652;A0T124	JHD2C_HUMAN;.	T	441;222;222;259	ENSP00000382204:K441T;ENSP00000384990:K222T;ENSP00000382195:K222T;ENSP00000444682:K259T	ENSP00000382195:K222T	K	-	2	0	JMJD1C	64644611	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	2.933000	0.48948	2.237000	0.73441	0.459000	0.35465	AAA	.		0.388	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		G	64974605	T	G	64974605	3	3	132	1	0	0	0	0	1	0	0	0	7971	1841	64	5	6376	5	JMJD1C	10	64974605	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	48033460	64974605	70560142	48	11701											
LDB1	8861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103871028	103871028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacccaatccctggctccAggtatgtaggcggatacatg	9	10	10	12	1	0	0	0	0	0	0	2	1	2	1	3	4	2	3	3	4	5	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:103871028A>G	ENST00000425280.1	-	3	500	c.158T>C	c.(157-159)cTg>cCg	p.L53P	LDB1_ENST00000361198.5_Missense_Mutation_p.L17P|LDB1_ENST00000490751.1_5'UTR	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	53					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		CCCTGGCTCCAGGTATGTAGG	0.577																																					p.L53P		.											.	LDB1-289	0			c.T158C						.						98	98	98					10																	103871028		2203	4300	6503	SO:0001583	missense	8861	exon3			GGCTCCAGGTATG	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.158T>C	10.37:g.103871028A>G	ENSP00000392466:p.Leu53Pro	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	155	68	NM_001113407	0	0	13	19	6	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	37	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.149912	0.57151	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.73	5.73	0.89815	.	0.148563	0.46442	D	0.000281	T	0.39733	0.1089	N	0.19112	0.55	0.80722	D	1	P;B	0.48407	0.91;0.0	B;B	0.41135	0.348;0.001	T	0.26503	-1.0101	9	0.31617	T	0.26	-13.3126	15.6898	0.77442	1.0:0.0:0.0:0.0	.	53;17	Q86U70;Q86U70-3	LDB1_HUMAN;.	P	17;53	.	ENSP00000354616:L17P	L	-	2	0	LDB1	103861018	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.008000	0.76341	2.199000	0.70637	0.459000	0.35465	CTG	.		0.577	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		G	103871028	A	G	103871028	3	3	132	1	0	0	0	0	1	0	0	0	8716	188	7	3	1113	3	LDB1	10	103871028	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	38896423	103871028	31663719	49	11702											
FAM53B	9679	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	126311947	126311947	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtccagggcgcagctgtctGactcctcacaggacaggtcc	7	7	12	15	2	2	1	1	1	1	0	5	2	5	2	3	3	1	2	3	3	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:126311947G>A	ENST00000337318.3	-	5	1344	c.1133C>T	c.(1132-1134)tCa>tTa	p.S378L	RP11-12J10.3_ENST00000494792.1_Intron|FAM53B_ENST00000392754.3_Missense_Mutation_p.S378L	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	378										cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		GCAGCTGTCTGACTCCTCACA	0.711																																					p.S378L		.											.	FAM53B-91	0			c.C1133T						.						21	22	21					10																	126311947		2200	4294	6494	SO:0001583	missense	9679	exon5			CTGTCTGACTCCT	D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319			28968	protein-coding gene	gene with protein product			"KIAA0140"	KIAA0140		8590280	Standard	NM_014661		Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000337318.3:c.1133C>T	10.37:g.126311947G>A	ENSP00000338532:p.Ser378Leu	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	38	23	NM_014661	0	0	2	4	2	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Missense_Mutation	SNP	ENST00000337318.3	37	CCDS7641.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.688447	0.29962	.	.	ENSG00000189319	ENST00000337318;ENST00000392754	.	.	.	4.78	3.86	0.44501	.	0.743799	0.11858	N	0.522697	T	0.30978	0.0782	L	0.34521	1.04	0.19945	N	0.999948	B	0.26809	0.16	B	0.31337	0.128	T	0.21793	-1.0235	9	0.06365	T	0.9	-7.9821	11.3285	0.49463	0.0:0.0:0.6724:0.3276	.	378	Q14153	FA53B_HUMAN	L	378	.	ENSP00000338532:S378L	S	-	2	0	FAM53B	126301937	0.742000	0.28228	0.299000	0.25016	0.686000	0.39977	2.551000	0.45820	1.213000	0.43380	0.655000	0.94253	TCA	.		0.711	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661		A	126311947	G	A	126311947	3	1	132	1	0	0	0	0	1	0	0	0	5599	1294	45	2	139	2	FAM53B	10	126311947	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	22440919	126311947	9222800	50	11703											
ADAM12	8038	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	127806755	127806755	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttgcacttttcattggtTctaagacatagctttcattt	8	19	7	7	0	3	1	2	0	1	1	3	1	3	1	0	2	2	4	0	2	2	9			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:127806755T>G	ENST00000368679.4	-	6	773	c.464A>C	c.(463-465)gAa>gCa	p.E155A	ADAM12_ENST00000368676.4_Missense_Mutation_p.E155A	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	155					cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TTTCATTGGTTCTAAGACATA	0.383																																					p.E155A													.	ADAM12-716	0			c.A464C						.						114	99	104					10																	127806755		2203	4300	6503	SO:0001583	missense	8038	exon6			ATTGGTTCTAAGA	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"ADAM metallopeptidase domain containing"	190	protein-coding gene	gene with protein product	"meltrin alpha"	602714	"a disintegrin and metalloproteinase domain 12 (meltrin alpha)"			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.464A>C	10.37:g.127806755T>G	ENSP00000357668:p.Glu155Ala	Somatic	56	2		WXS	Illumina HiSeq	Phase_I	92	36	NM_021641	0	0	0	0	0	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.666850	0.67814	.	.	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	T;T;T	0.10288	2.89;2.89;2.89	5.03	5.03	0.67393	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.40767	0.1130	M	0.91140	3.18	0.52501	D	0.999957	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.97110	0.999;0.998;0.998;0.998;1.0	T	0.50931	-0.8769	10	0.87932	D	0	.	13.1591	0.59535	0.0:0.0:0.0:1.0	.	152;152;155;152;155	A8K6G4;O43184-3;O43184-2;O43184-4;O43184	.;.;.;.;ADA12_HUMAN	A	155;155;152	ENSP00000357668:E155A;ENSP00000357665:E155A;ENSP00000391268:E152A	ENSP00000357665:E155A	E	-	2	0	ADAM12	127796745	0.999000	0.42202	0.598000	0.28837	0.711000	0.40976	2.805000	0.47939	2.118000	0.64928	0.533000	0.62120	GAA	.		0.383	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			G	127806755	T	G	127806755	3	3	132	1	0	0	0	0	1	0	0	0	236	1783	62	5	2445	5	ADAM12	10	127806755	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	1494808	127806755	7727992	51	11704											
TRPM5	29850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	2428360	2428360	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctcacccaggtgctccCgcttgtgctcagcctccttc	3	10	9	19	2	2	0	2	0	0	0	5	0	4	0	5	2	3	3	5	2	0	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:2428360C>T	ENST00000155858.6	-	20	3115	c.3107G>A	c.(3106-3108)cGg>cAg	p.R1036Q	TRPM5_ENST00000528453.1_Missense_Mutation_p.R1036Q|TRPM5_ENST00000452833.1_Missense_Mutation_p.R1038Q|AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000533060.1_Missense_Mutation_p.R1036Q	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		CAGGTGCTCCCGCTTGTGCTC	0.706																																					p.R1036Q	NSCLC(1;49 61 17205 18850 43201)	.											.	TRPM5-137	0			c.G3107A						.						26	25	26					11																	2428360		2193	4288	6481	SO:0001583	missense	29850	exon20			TGCTCCCGCTTGT	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"Voltage-gated ion channels / Transient receptor potential cation channels"	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.3107G>A	11.37:g.2428360C>T	ENSP00000155858:p.Arg1036Gln	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	24	15	NM_014555	0	0	0	0	0		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	1.660	-0.511828	0.04200	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453	T;T;T;T;T	0.61627	0.27;0.21;0.21;0.09;0.21	3.21	1.21	0.21127	.	0.630612	0.15729	N	0.247507	T	0.33644	0.0870	N	0.15975	0.35	0.21553	N	0.999642	B;B;B	0.17465	0.022;0.022;0.006	B;B;B	0.13407	0.007;0.007;0.009	T	0.15065	-1.0450	10	0.25751	T	0.34	-7.4235	6.0447	0.19753	0.0:0.6066:0.0:0.3934	.	1036;1038;1036	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	1030;1036;1038;1036;1036	ENSP00000434383:R1030Q;ENSP00000155858:R1036Q;ENSP00000387965:R1038Q;ENSP00000434121:R1036Q;ENSP00000436809:R1036Q	ENSP00000155858:R1036Q	R	-	2	0	TRPM5	2384936	0.007000	0.16637	0.005000	0.12908	0.300000	0.27592	1.127000	0.31357	0.058000	0.16222	0.134000	0.15878	CGG	.		0.706	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2428360	C	T	2428360	3	4	132	1	0	0	0	0	1	0	0	0	16622	652	23	1	410	1	TRPM5	11	2428360	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10		2428360	132578156	52	11705											
CALCB	797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	15096663	15096663	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtaaagaggacgcgcgccTcctgctggctgcactggtgc	7	7	14	13	3	0	1	0	0	0	1	1	2	1	2	2	3	3	4	2	3	2	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:15096663T>A	ENST00000533448.1	+	3	254	c.143T>A	c.(142-144)cTc>cAc	p.L48H	CALCB_ENST00000324229.6_Missense_Mutation_p.L48H|CALCB_ENST00000523376.1_Missense_Mutation_p.L59H			P10092	CALCB_HUMAN	calcitonin-related polypeptide beta	48					cellular calcium ion homeostasis (GO:0006874)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			endometrium(1)|large_intestine(1)|lung(1)|skin(2)	5						GACGCGCGCCTCCTGCTGGCT	0.627											OREG0020793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L48H		.											.	CALCB-90	0			c.T143A						.						58	61	60					11																	15096663		2200	4294	6494	SO:0001583	missense	797	exon3			CGCGCCTCCTGCT		CCDS7820.1	11p14.2-p12	2013-02-25	2008-02-20			ENSG00000175868		"Endogenous ligands"	1438	protein-coding gene	gene with protein product		114160	"calcitonin 2"	CALC2			Standard	NM_000728		Approved	FLJ30166, CGRP-II	uc001mlx.1	P10092		ENST00000533448.1:c.143T>A	11.37:g.15096663T>A	ENSP00000433490:p.Leu48His	Somatic	343	0	700	WXS	Illumina HiSeq	Phase_I	419	177	NM_000728	0	0	0	0	0	A8K573|D3DQX4|Q569I0|Q9UCN9	Missense_Mutation	SNP	ENST00000533448.1	37	CCDS7820.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370035	0.82573	.	.	ENSG00000175868	ENST00000523376;ENST00000324229;ENST00000533448	T;T;T	0.24151	1.87;1.87;1.87	5.4	3.0	0.34707	.	0.000000	0.46442	D	0.000284	T	0.28267	0.0698	M	0.81239	2.535	0.27438	N	0.953794	B	0.30686	0.29	B	0.32022	0.139	T	0.17077	-1.0381	10	0.44086	T	0.13	-26.0769	6.6446	0.22929	0.1187:0.0:0.3692:0.512	.	48	P10092	CALCB_HUMAN	H	59;48;48	ENSP00000428882:L59H;ENSP00000346017:L48H;ENSP00000433490:L48H	ENSP00000346017:L48H	L	+	2	0	CALCB	15053239	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.094000	0.64523	2.176000	0.68965	0.454000	0.30748	CTC	.		0.627	CALCB-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387433.1	NM_000728		A	15096663	T	A	15096663	3	1	132	1	0	0	0	0	1	0	0	0	2582	1551	54	5	149	5	CALCB	11	15096663	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	12668303	15096663	119909853	53	11706											
PIK3C2A	5286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	17150900	17150900	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaagcttctggtcccttTctctgcttattagaatcagg	8	14	7	12	0	3	1	1	0	2	1	5	1	4	1	2	2	2	2	2	2	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:17150900T>G	ENST00000265970.7	-	12	2345	c.2346A>C	c.(2344-2346)agA>agC	p.R782S	PIK3C2A_ENST00000540361.1_Missense_Mutation_p.R402S|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	782	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						CTGGTCCCTTTCTCTGCTTAT	0.388																																					p.R782S		.											.	PIK3C2A-1310	0			c.A2346C						.						90	96	94					11																	17150900		2200	4293	6493	SO:0001583	missense	5286	exon12			TCCCTTTCTCTGC	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"phosphoinositide-3-kinase, class 2, alpha polypeptide"			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.2346A>C	11.37:g.17150900T>G	ENSP00000265970:p.Arg782Ser	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	153	55	NM_002645	0	0	7	8	1	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.807327	0.70797	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.77229	-1.08;-1.08	6.17	3.81	0.43845	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	D	0.82834	0.5123	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79967	-0.1580	10	0.33940	T	0.23	-23.3516	5.1651	0.15081	0.1256:0.1839:0.0:0.6905	.	782	O00443	P3C2A_HUMAN	S	782;402	ENSP00000265970:R782S;ENSP00000438687:R402S	ENSP00000265970:R782S	R	-	3	2	PIK3C2A	17107476	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.962000	0.29280	1.126000	0.42016	0.533000	0.62120	AGA	.		0.388	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17150900	T	G	17150900	3	3	132	1	0	0	0	0	1	0	0	0	11935	1780	62	5	2798	5	PIK3C2A	11	17150900	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	2054237	17150900	117855616	54	11707											
OR5AR1	219493	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	56432020	56432028	+	In_Frame_Del	DEL	CCCTTGATC	CCCTTGATC	-																															ttatcatccccatgttaaatCccttgatctacagtttgcgg																								rs139654321		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	CCCTTGATC	CCCTTGATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:56432020_56432028delCCCTTGATC	ENST00000302969.2	+	1	883_891	c.859_867delCCCTTGATC	c.(859-867)cccttgatcdel	p.PLI287del		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	287						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CATGTTAAATCCCTTGATCTACAGTTTGC	0.407																																					p.287_289del		.											.	OR5AR1-68	0			c.859_867del						.																																			SO:0001651	inframe_deletion	219493	exon1			.	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"GPCR / Class A : Olfactory receptors"	15260	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily AR, member 1"				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.859_867delCCCTTGATC	11.37:g.56432020_56432028delCCCTTGATC	ENSP00000302639:p.Pro287_Ile289del	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	169	27	NM_001004730	0	0	0	0	0	Q6IF61	In_Frame_Del	DEL	ENST00000302969.2	37	CCDS31535.1																																																																																			.		0.407	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730		-	56432028	CCCTTGATC	-	56432020	7	5	132	1	0	1	0	1	0	0	0	0	11171	855	30	0	861	0	OR5AR1	11	56432020	In_Frame_Del	DEL	CCCTTGATC	TCGA-HE-A5NH-01A-11D-A26P-10	39281120	56432020	78574496	55	11708											
PPFIA1	8500	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	70202285	70202285	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggtgtttccgagacggAtaactcatctcaggatgcct	9	11	11	10	2	2	1	2	0	1	1	4	4	3	3	2	3	3	2	2	3	1	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:70202285A>T	ENST00000253925.7	+	19	2722	c.2507A>T	c.(2506-2508)gAt>gTt	p.D836V	AP000487.6_ENST00000528607.1_RNA|AP000487.4_ENST00000324630.5_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.D836V	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	836					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TCCGAGACGGATAACTCATCT	0.398																																					p.D836V													.	PPFIA1-228	0			c.A2507T						.						139	145	143					11																	70202285		2200	4294	6494	SO:0001583	missense	8500	exon19			AGACGGATAACTC	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"Sterile alpha motif (SAM) domain containing"	9245	protein-coding gene	gene with protein product	"Liprin-alpha1"	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2507A>T	11.37:g.70202285A>T	ENSP00000253925:p.Asp836Val	Somatic	136	1		WXS	Illumina HiSeq	Phase_I	144	55	NM_177423	0	0	8	16	8	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.01|14.01	2.407640|2.407640	0.42715|0.42715	.|.	.|.	ENSG00000131626|ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950|ENST00000528750	T;T|.	0.19250|.	2.16;2.16|.	5.01|5.01	5.01|5.01	0.66863|0.66863	.|.	0.411876|.	0.24172|.	U|.	0.040892|.	T|T	0.56337|0.56337	0.1978|0.1978	L|L	0.34521|0.34521	1.04|1.04	0.54753|0.54753	D|D	0.999981|0.999981	B;B|.	0.25105|.	0.004;0.118|.	B;B|.	0.24541|.	0.027;0.054|.	T|T	0.53570|0.53570	-0.8420|-0.8420	10|5	0.87932|.	D|.	0|.	.|.	15.0281|15.0281	0.71684|0.71684	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	836;836|.	Q13136;Q13136-2|.	LIPA1_HUMAN;.|.	V|L	836;836;333|279	ENSP00000253925:D836V;ENSP00000374198:D836V|.	ENSP00000253925:D836V|.	D|I	+|+	2|1	0|0	PPFIA1|PPFIA1	69879933|69879933	1.000000|1.000000	0.71417|0.71417	0.048000|0.048000	0.18961|0.18961	0.016000|0.016000	0.09150|0.09150	4.706000|4.706000	0.61845|0.61845	2.004000|2.004000	0.58718|0.58718	0.533000|0.533000	0.62120|0.62120	GAT|ATA	.		0.398	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		T	70202285	A	T	70202285	3	4	132	1	0	0	0	0	1	0	0	0	12335	333	12	5	2577	5	PPFIA1	11	70202285	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	13770265	70202285	64804231	56	11709											
MOGAT2	80168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	75431106	75431106	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctcctcactgtcctgtatgCggcctggtggtatctggacc	4	12	12	13	1	2	0	1	0	1	0	4	1	4	1	4	4	1	3	4	4	2	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:75431106C>A	ENST00000198801.5	+	2	231	c.161C>A	c.(160-162)gCg>gAg	p.A54E	MOGAT2_ENST00000526712.1_5'UTR	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	54					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)			NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					GTCCTGTATGCGGCCTGGTGG	0.567																																					p.A54E		.											.	MOGAT2-228	0			c.C161A						.						175	164	168					11																	75431106		2200	4293	6493	SO:0001583	missense	80168	exon2			TGTATGCGGCCTG	AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391			23248	protein-coding gene	gene with protein product		610270				14970677	Standard	NM_025098		Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.161C>A	11.37:g.75431106C>A	ENSP00000198801:p.Ala54Glu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	131	47	NM_025098	0	0	0	0	0	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	37	CCDS8240.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.230712	0.58777	.	.	ENSG00000166391	ENST00000198801	T	0.15487	2.42	5.14	3.25	0.37280	.	0.175147	0.49916	D	0.000127	T	0.40595	0.1123	M	0.87180	2.865	0.37511	D	0.917131	D;D	0.67145	0.983;0.996	P;D	0.65233	0.815;0.933	T	0.47071	-0.9145	10	0.62326	D	0.03	.	8.4411	0.32816	0.0:0.6272:0.2933:0.0795	.	54;54	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	E	54	ENSP00000198801:A54E	ENSP00000198801:A54E	A	+	2	0	MOGAT2	75108754	0.114000	0.22134	0.003000	0.11579	0.143000	0.21401	2.008000	0.40893	0.732000	0.32470	-0.215000	0.12644	GCG	.		0.567	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098		A	75431106	C	A	75431106	3	1	132	1	0	0	0	0	1	0	0	0	9720	768	27	4	167	4	MOGAT2	11	75431106	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	5228821	75431106	59575410	57	11710											
ARCN1	372	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118464375	118464375	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatgagctacaagaagataaTttagaactgaatgatgtggt	16	12	10	3	0	0	6	0	3	0	3	0	6	0	6	0	1	3	1	0	1	8	5	rs546784519		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:118464375T>G	ENST00000264028.4	+	8	1298	c.1203T>G	c.(1201-1203)aaT>aaG	p.N401K	RNU6-1157P_ENST00000384456.1_RNA|ARCN1_ENST00000392859.3_Missense_Mutation_p.N313K|ARCN1_ENST00000534182.2_Intron|ARCN1_ENST00000359415.4_Missense_Mutation_p.N442K	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	401	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		AAGAAGATAATTTAGAACTGA	0.438													T|||	1	0.000199681	0	0	5008	,	,		20456	0.001		0	False		,,,				2504	0				p.N401K		.											.	ARCN1-90	0			c.T1203G						.						118	100	106					11																	118464375		2200	4295	6495	SO:0001583	missense	372	exon8			AGATAATTTAGAA	X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"coatomer protein complex, subunit delta"	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.1203T>G	11.37:g.118464375T>G	ENSP00000264028:p.Asn401Lys	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	98	42	NM_001655	0	0	10	19	9	B4E1X2|E9PEU4|Q52M80	Missense_Mutation	SNP	ENST00000264028.4	37	CCDS8400.1	.	.	.	.	.	.	.	.	.	.	T	9.897	1.205804	0.22205	.	.	ENSG00000095139	ENST00000392859;ENST00000359415;ENST00000264028	T;T;T	0.17528	2.27;2.27;2.27	5.95	1.01	0.19927	Clathrin adaptor, mu subunit, C-terminal (3);	0.266986	0.47455	D	0.000229	T	0.10121	0.0248	L	0.29908	0.895	0.29104	N	0.881303	B;B;B	0.14438	0.003;0.01;0.002	B;B;B	0.17979	0.006;0.02;0.005	T	0.18085	-1.0348	10	0.30078	T	0.28	-13.078	5.5305	0.16983	0.0:0.491:0.1917:0.3174	.	313;442;401	E9PEU4;B0YIW6;P48444	.;.;COPD_HUMAN	K	313;442;401	ENSP00000376599:N313K;ENSP00000352385:N442K;ENSP00000264028:N401K	ENSP00000264028:N401K	N	+	3	2	ARCN1	117969585	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.769000	0.26604	0.173000	0.19788	0.460000	0.39030	AAT	.		0.438	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1			G	118464375	T	G	118464375	3	3	132	1	0	0	0	0	1	0	0	0	842	1490	52	5	1233	5	ARCN1	11	118464375	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	43033269	118464375	16542141	58	11711											
SORL1	6653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	121475939	121475939	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcttgtgtatataatgTctactacaggtaggtcccat	9	16	8	8	0	2	0	0	0	2	0	3	0	3	0	1	2	3	3	1	2	6	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:121475939T>G	ENST00000260197.7	+	34	4898	c.4769T>G	c.(4768-4770)gTc>gGc	p.V1590G	SORL1_ENST00000534286.1_Missense_Mutation_p.V500G|SORL1_ENST00000527934.1_Missense_Mutation_p.V205G|SORL1_ENST00000525532.1_Missense_Mutation_p.V534G|SORL1_ENST00000532694.1_Missense_Mutation_p.V436G	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1590	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GTATATAATGTCTACTACAGG	0.443																																					p.V1590G		.											.	SORL1-228	0			c.T4769G						.						121	119	120					11																	121475939		2203	4299	6502	SO:0001583	missense	6653	exon34			ATAATGTCTACTA	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"Fibronectin type III domain containing"	11185	protein-coding gene	gene with protein product	"LDLR relative with 11 ligand-binding repeats"	602005	"chromosome 11 open reading frame 32", "sortilin-related receptor, L(DLR class) A repeats-containing"	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4769T>G	11.37:g.121475939T>G	ENSP00000260197:p.Val1590Gly	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	79	30	NM_003105	0	0	0	0	0	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.133710	0.56828	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.3	4.17	0.49024	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.537145	0.18359	N	0.143626	T	0.61185	0.2327	N	0.19112	0.55	0.51012	D	0.999904	P;P	0.51933	0.942;0.949	P;P	0.52386	0.697;0.659	T	0.60984	-0.7154	10	0.52906	T	0.07	.	10.8817	0.46942	0.0:0.0749:0.0:0.9251	.	205;1590	E9PKB0;Q92673	.;SORL_HUMAN	G	1590;534;436;500;205	ENSP00000260197:V1590G;ENSP00000434634:V534G;ENSP00000432131:V436G;ENSP00000436447:V500G;ENSP00000435405:V205G	ENSP00000260197:V1590G	V	+	2	0	SORL1	120981149	0.992000	0.36948	0.699000	0.30290	0.670000	0.39368	7.698000	0.84413	0.854000	0.35336	0.533000	0.62120	GTC	.		0.443	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		G	121475939	T	G	121475939	3	3	132	1	0	0	0	0	1	0	0	0	14966	1667	58	5	4903	5	SORL1	11	121475939	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	3011564	121475939	13530577	59	11712											
IGSF9B	22997	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	133789844	133789844	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcccactgcggctgctctggGagggggagcctgtggacggc	4	7	18	12	2	1	0	0	0	1	0	2	3	2	3	2	6	3	2	2	6	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:133789844G>A	ENST00000321016.8	-	18	4006	c.3776C>T	c.(3775-3777)tCc>tTc	p.S1259F	IGSF9B_ENST00000533871.2_Missense_Mutation_p.S1259F			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1259	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GCTGCTCTGGGAGGGGGAGCC	0.687																																					p.S1259F		.											.	IGSF9B-68	0			c.C3776T						.						19	25	23					11																	133789844		1888	4098	5986	SO:0001583	missense	22997	exon18			CTCTGGGAGGGGG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.3776C>T	11.37:g.133789844G>A	ENSP00000317980:p.Ser1259Phe	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	62	27	NM_014987	0	0	0	0	0	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	10.57	1.386761	0.25031	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.68479	-0.0;-0.33	5.29	4.38	0.52667	.	0.164446	0.29119	N	0.013091	T	0.47414	0.1444	N	0.08118	0	0.33398	D	0.577033	B	0.06786	0.001	B	0.04013	0.001	T	0.56402	-0.7985	10	0.66056	D	0.02	.	13.4086	0.60929	0.0768:0.0:0.9232:0.0	.	1259	Q9UPX0	TUTLB_HUMAN	F	1259;1101	ENSP00000317980:S1259F;ENSP00000436552:S1101F	ENSP00000317980:S1259F	S	-	2	0	IGSF9B	133295054	1.000000	0.71417	0.411000	0.26484	0.307000	0.27823	7.382000	0.79729	1.243000	0.43853	0.555000	0.69702	TCC	.		0.687	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133789844	G	A	133789844	3	1	132	1	0	0	0	0	1	0	0	0	7627	1174	41	2	281	2	IGSF9B	11	133789844	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	12313905	133789844	1216672	60	11713											
ING4	51147	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	6760401	6760401	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagcagcgtgggcaaaacCtgaaacagagaaggggagag	15	2	18	6	1	0	3	0	1	0	2	0	6	0	4	1	4	4	2	1	4	4	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:6760401C>T	ENST00000396807.4	-	8	749		c.e8-1		ING4_ENST00000486287.1_Splice_Site|ING4_ENST00000446105.2_Splice_Site|ING4_ENST00000444704.2_Splice_Site|ING4_ENST00000412586.2_Splice_Site|ING4_ENST00000423703.2_Splice_Site|ING4_ENST00000341550.4_Splice_Site	NM_001127582.1|NM_001127585.1|NM_001127586.1|NM_016162.3	NP_001121054.1|NP_001121057.1|NP_001121058.1|NP_057246.2	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4						apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|protein acetylation (GO:0006473)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(3)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	10						TGGGCAAAACCTGAAACAGAG	0.512																																					.		.											.	ING4-515	0			c.563-1G>A						.						112	96	102					12																	6760401		2203	4300	6503	SO:0001630	splice_region_variant	51147	exon8			CAAAACCTGAAAC	AF063594	CCDS8555.1, CCDS44812.1, CCDS44813.1, CCDS44814.1, CCDS44815.1, CCDS44816.1	12p13.32	2013-01-28			ENSG00000111653	ENSG00000111653		"Zinc fingers, PHD-type"	19423	protein-coding gene	gene with protein product		608524				12750254	Standard	NM_001127582		Approved	p29ING4, my036	uc001qpw.4	Q9UNL4	OTTHUMG00000141274	ENST00000396807.4:c.711-1G>A	12.37:g.6760401C>T		Somatic	162	0		WXS	Illumina HiSeq	Phase_I	238	90	NM_001127586	0	0	0	0	0	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Splice_Site	SNP	ENST00000396807.4	37	CCDS44813.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842434	0.71488	.	.	ENSG00000111653	ENST00000341550;ENST00000396807;ENST00000446105;ENST00000444704;ENST00000412586	.	.	.	4.63	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5782	0.84706	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ING4	6630662	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	6.445000	0.73456	2.556000	0.86216	0.561000	0.74099	.	.		0.512	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287	Intron	T	6760401	C	T	6760401	5	4	132	1	0	0	0	0	0	0	1	0	7759	695	24	2	43	2	ING4	12	6760401	Splice_Site	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10		6760401	127091494	61	11714											
BHLHE41	79365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	26276658	26276658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccaagactacagctttcTccagatgtcccagagtctgc	10	11	7	13	0	2	3	0	0	2	3	5	3	4	3	3	0	3	1	3	0	2	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:26276658T>C	ENST00000242728.4	-	4	598	c.251A>G	c.(250-252)gAg>gGg	p.E84G	RP11-283G6.3_ENST00000535914.1_RNA|RP11-283G6.3_ENST00000545819.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	84	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						TACAGCTTTCTCCAGATGTCC	0.408																																					p.E84G		.											.	BHLHE41-226	0			c.A251G						.						93	92	92					12																	26276658		2202	4300	6502	SO:0001583	missense	79365	exon4			GCTTTCTCCAGAT	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"Basic helix-loop-helix proteins"	16617	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 2", "Enhancer-of-split and hairy-related protein 1"	606200	"basic helix-loop-helix domain containing, class B, 3"	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.251A>G	12.37:g.26276658T>C	ENSP00000242728:p.Glu84Gly	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_030762	0	0	9	18	9	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	37	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.546283	0.65198	.	.	ENSG00000123095	ENST00000242728;ENST00000540731	D	0.98120	-4.73	4.15	4.15	0.48705	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	U	0.000000	D	0.98172	0.9396	M	0.67569	2.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98797	1.0738	10	0.87932	D	0	-16.7562	12.4813	0.55844	0.0:0.0:0.0:1.0	.	84	Q9C0J9	BHE41_HUMAN	G	84	ENSP00000242728:E84G	ENSP00000242728:E84G	E	-	2	0	BHLHE41	26167925	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.709000	0.84645	1.876000	0.54355	0.528000	0.53228	GAG	.		0.408	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		C	26276658	T	C	26276658	3	2	132	1	0	0	0	0	1	0	0	0	1425	1551	54	3	1205	3	BHLHE41	12	26276658	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	19516257	26276658	107575237	62	11715											
ERGIC2	51290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	29502995	29502995	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgaccacgaggatgtggAattgccctgaaaggagaaaa	15	6	13	7	1	0	3	0	2	0	1	0	7	0	5	2	3	1	1	2	3	4	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:29502995A>T	ENST00000360150.4	-	9	654	c.579T>A	c.(577-579)atT>atA	p.I193I		NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2	193					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)				endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)					GAGGATGTGGAATTGCCCTGA	0.303																																					p.I193I		.											.	ERGIC2-91	0			c.T579A						.						57	53	54					12																	29502995		1824	4085	5909	SO:0001819	synonymous_variant	51290	exon9			ATGTGGAATTGCC	AF216751	CCDS41765.1	12p11.22	2006-02-08							30208	protein-coding gene	gene with protein product		612236				11445006, 12932305	Standard	NM_016570		Approved	PTX1, Erv41	uc001riv.3	Q96RQ1		ENST00000360150.4:c.579T>A	12.37:g.29502995A>T		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	214	77	NM_016570	0	0	0	0	0	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	Silent	SNP	ENST00000360150.4	37	CCDS41765.1	.	.	.	.	.	.	.	.	.	.	a	11.11	1.541269	0.27563	.	.	ENSG00000087502	ENST00000548909	.	.	.	5.78	0.983	0.19767	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45556	-0.9253	4	.	.	.	.	8.0069	0.30329	0.655:0.0:0.345:0.0	.	.	.	.	T	3	.	.	S	-	1	0	ERGIC2	29394262	0.982000	0.34865	1.000000	0.80357	0.989000	0.77384	0.257000	0.18369	0.143000	0.18926	0.524000	0.50904	TCC	.		0.303	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403489.1	NM_016570		T	29502995	A	T	29502995	2	4	132	1	0	0	0	0	0	0	0	1	5237	242	9	5		5	ERGIC2	12	29502995	Silent	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	3226337	29502995	104348900	63	11716											
C12orf64	283310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	80730767	80730767	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatacataaaataattgtcAatcggttggcaagaaaggta	17	10	8	6	1	1	1	1	0	0	1	2	1	1	1	1	3	1	3	1	3	8	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:80730767A>T	ENST00000547103.1	+	41	4786	c.4780A>T	c.(4780-4782)Aat>Tat	p.N1594Y	OTOGL_ENST00000458043.2_Missense_Mutation_p.N1606Y			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1594	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						AATAATTGTCAATCGGTTGGC	0.279																																					p.N1606Y		.											.	.	0			c.A4816T						.						28	26	26					12																	80730767		1788	4046	5834	SO:0001583	missense	283310	exon41			ATTGTCAATCGGT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"chromosome 12 open reading frame 64"	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.4780A>T	12.37:g.80730767A>T	ENSP00000447211:p.Asn1594Tyr	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	12	5	NM_173591	0	0	0	0	0	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		.	.	.	.	.	.	.	.	.	.	A	14.88	2.668809	0.47677	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.58652	0.32;0.32	4.92	3.72	0.42706	.	.	.	.	.	T	0.65428	0.2690	M	0.72118	2.19	0.28910	N	0.892741	.	.	.	.	.	.	T	0.61888	-0.6970	7	0.59425	D	0.04	.	10.9776	0.47475	0.8598:0.0:0.0:0.1402	.	.	.	.	Y	1594;1606	ENSP00000447211:N1594Y;ENSP00000400895:N1606Y	ENSP00000400895:N1606Y	N	+	1	0	OTOGL	79254898	1.000000	0.71417	0.989000	0.46669	0.943000	0.58893	4.208000	0.58486	0.757000	0.33036	0.482000	0.46254	AAT	.		0.279	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80730767	A	T	80730767	3	4	132	1	0	0	0	0	1	0	0	0	1711	130	5	5	4978	5	C12orf64	12	80730767	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	51227772	80730767	53121128	64	11717											
PPP1CC	5501	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	111168372	111168372	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaattctgttgatgctggcaCattcatggttccctctgaga	9	14	9	9	0	3	2	1	2	2	1	4	3	4	2	1	2	1	4	1	2	1	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:111168372C>T	ENST00000335007.5	-	3	570	c.380G>A	c.(379-381)tGt>tAt	p.C127Y	PPP1CC_ENST00000551690.1_5'Flank|PPP1CC_ENST00000546933.1_Missense_Mutation_p.C136Y|PPP1CC_ENST00000550991.1_Missense_Mutation_p.C127Y|PPP1CC_ENST00000340766.5_Missense_Mutation_p.C127Y|PPP1CC_ENST00000551676.1_Missense_Mutation_p.C127Y	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	127					cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|large_intestine(2)|lung(3)	6						GATGCTGGCACATTCATGGTT	0.338																																					p.C127Y		.											.	PPP1CC-1082	0			c.G380A						.						62	67	65					12																	111168372		2203	4300	6503	SO:0001583	missense	5501	exon3			CTGGCACATTCAT		CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9283	protein-coding gene	gene with protein product		176914	"protein phosphatase 1, catalytic subunit, gamma isoform"				Standard	NM_002710		Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.380G>A	12.37:g.111168372C>T	ENSP00000335084:p.Cys127Tyr	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	19	7	NM_002710	0	0	18	35	17		Missense_Mutation	SNP	ENST00000335007.5	37	CCDS9150.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520313	0.85495	.	.	ENSG00000186298	ENST00000335007;ENST00000340766;ENST00000546933;ENST00000550991;ENST00000551676	D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87	5.61	5.61	0.85477	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.039374	0.85682	D	0.000000	D	0.93015	0.7777	H	0.95611	3.695	0.80722	D	1	P	0.51240	0.943	P	0.50231	0.635	D	0.94583	0.7781	10	0.87932	D	0	-4.8814	19.998	0.97395	0.0:1.0:0.0:0.0	.	127	P36873	PP1G_HUMAN	Y	127;127;136;127;127	ENSP00000335084:C127Y;ENSP00000341779:C127Y;ENSP00000447122:C136Y;ENSP00000448981:C127Y;ENSP00000448437:C127Y	ENSP00000335084:C127Y	C	-	2	0	PPP1CC	109652755	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	2.804000	0.96469	0.462000	0.41574	TGT	.		0.338	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404659.1			T	111168372	C	T	111168372	3	4	132	1	0	0	0	0	1	0	0	0	12380	478	17	2	611	2	PPP1CC	12	111168372	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	30437605	111168372	22683523	65	11718											
SSTR1	6751	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	38678806	38678806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctactccgtggtgtgcctggTggggctgtgtgggaactcta	4	12	16	9	1	1	0	0	0	1	0	2	1	2	1	2	5	3	1	2	5	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr14:38678806T>C	ENST00000267377.2	+	3	829	c.212T>C	c.(211-213)gTg>gCg	p.V71A		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	71					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)|Pasireotide(DB06663)	GTGTGCCTGGTGGGGCTGTGT	0.562																																					p.V71A		.											.	SSTR1-947	0			c.T212C						.						144	130	135					14																	38678806		2203	4300	6503	SO:0001583	missense	6751	exon3			GCCTGGTGGGGCT		CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"GPCR / Class A : Somatostatin receptors"	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.212T>C	14.37:g.38678806T>C	ENSP00000267377:p.Val71Ala	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	133	48	NM_001049	0	0	0	0	0		Missense_Mutation	SNP	ENST00000267377.2	37	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.664028	0.47572	.	.	ENSG00000139874	ENST00000267377	T	0.20598	2.06	4.74	3.58	0.41010	.	0.000000	0.48767	D	0.000167	T	0.16685	0.0401	L	0.32530	0.975	0.49687	D	0.99981	B	0.31581	0.329	B	0.32090	0.14	T	0.04427	-1.0952	10	0.52906	T	0.07	.	10.861	0.46827	0.0:0.0:0.1584:0.8416	.	71	P30872	SSR1_HUMAN	A	71	ENSP00000267377:V71A	ENSP00000267377:V71A	V	+	2	0	SSTR1	37748557	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.841000	0.86834	0.828000	0.34709	0.533000	0.62120	GTG	.		0.562	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			C	38678806	T	C	38678806	3	2	132	1	0	0	0	0	1	0	0	0	15229	1696	59	3	214	3	SSTR1	14	38678806	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10		38678806	68670734	66	11719											
ZBTB1	22890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64988346	64988346	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcaagcacacaaggcagttCtagctgcctgtagctcctat	10	11	8	12	0	2	0	1	0	1	0	3	0	3	0	2	1	4	6	2	1	5	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr14:64988346C>G	ENST00000554015.1	+	4	555	c.124C>G	c.(124-126)Cta>Gta	p.L42V	ZBTB1_ENST00000358738.3_Missense_Mutation_p.L42V|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Missense_Mutation_p.L42V			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	42	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		CAAGGCAGTTCTAGCTGCCTG	0.393																																					p.L42V		.											.	ZBTB1-91	0			c.C124G						.						106	98	101					14																	64988346		2203	4300	6503	SO:0001583	missense	22890	exon2			GCAGTTCTAGCTG	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.124C>G	14.37:g.64988346C>G	ENSP00000451000:p.Leu42Val	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	87	27	NM_014950	0	0	4	7	3	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	37	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937405	0.73557	.	.	ENSG00000126804	ENST00000553583;ENST00000556965;ENST00000554015;ENST00000358738;ENST00000394712	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52	6.16	2.42	0.29668	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.250565	0.28219	N	0.016157	D	0.95385	0.8502	H	0.95043	3.615	0.46203	D	0.998929	D;D	0.76494	0.999;0.997	D;D	0.85130	0.994;0.997	D	0.94162	0.7415	10	0.87932	D	0	-10.7701	9.9144	0.41425	0.0:0.6811:0.0:0.3189	.	42;42	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	V	42	ENSP00000451584:L42V;ENSP00000450689:L42V;ENSP00000451000:L42V;ENSP00000351587:L42V;ENSP00000378201:L42V	ENSP00000351587:L42V	L	+	1	2	ZBTB1	64058099	0.970000	0.33590	0.892000	0.35008	0.997000	0.91878	1.715000	0.37971	0.195000	0.20347	0.650000	0.86243	CTA	.		0.393	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			G	64988346	C	G	64988346	3	3	132	1	0	0	0	0	1	0	0	0	17554	912	32	4	126	4	ZBTB1	14	64988346	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	26309540	64988346	42361194	67	11720											
WDR20	91833	hgsc.bcm.edu;bcgsc.ca	37	chr14	102674963	102674964	+	Frame_Shift_Ins	INS	-	-	A																															taatagacaagtcacgagttINSacctgtgtcaaatgggttcc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr14:102674963_102674964insA	ENST00000342702.3	+	3	487_488	c.456_457insA	c.(457-459)accfs	p.T153fs	WDR20_ENST00000545563.1_5'UTR|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000335263.5_Frame_Shift_Ins_p.T153fs|WDR20_ENST00000424963.2_Frame_Shift_Ins_p.T29fs|WDR20_ENST00000499851.2_Intron|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000454394.2_Frame_Shift_Ins_p.T184fs|WDR20_ENST00000556511.2_Frame_Shift_Ins_p.T92fs|WDR20_ENST00000556807.1_Frame_Shift_Ins_p.T92fs	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	153										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AGTCACGAGTTACCTGTGTCAA	0.45																																					p.V183fs		.											.	WDR20-90	0			c.549_550insA						.																																			SO:0001589	frameshift_variant	91833	exon4			.	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.457dupA	14.37:g.102674964_102674964dupA	ENSP00000341037:p.Thr153fs	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	60	14	NM_001242417	0	0	0	0	0	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Frame_Shift_Ins	INS	ENST00000342702.3	37	CCDS9969.1																																																																																			.		0.45	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		A	102674964	-	A	102674963	7	5	132	1	0	1	1	0	0	0	0	0	17313	1741	61	0	483	0	WDR20	14	102674963	Frame_Shift_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10	37686617	102674963	4674577	68	11721											
C15orf2	23742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	24921405	24921405	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcctgctgccttcaccaCgtgagccggcggtcaaggcc	5	8	11	17	3	3	1	2	1	1	0	4	1	3	1	5	3	3	1	5	3	1	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:24921405C>T	ENST00000329468.2	+	1	865	c.391C>T	c.(391-393)Cgt>Tgt	p.R131C		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	131					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R131C(1)									GCCTTCACCACGTGAGCCGGC	0.627																																					p.R131C		.											.	.	1	Substitution - Missense(1)	endometrium(1)	c.C391T						.						51	43	46					15																	24921405		2203	4300	6503	SO:0001583	missense	23742	exon1			TCACCACGTGAGC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.391C>T	15.37:g.24921405C>T	ENSP00000333735:p.Arg131Cys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_018958	0	0	0	0	0		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	7.490	0.650540	0.14516	.	.	ENSG00000185823	ENST00000329468	T	0.06294	3.32	2.27	1.33	0.21861	.	4.968620	0.00575	N	0.000313	T	0.05410	0.0143	N	0.14661	0.345	0.09310	N	1	P	0.43094	0.799	B	0.37780	0.258	T	0.39643	-0.9604	10	0.56958	D	0.05	.	8.6687	0.34137	0.2269:0.7731:0.0:0.0	.	131	Q9NZP6	CO002_HUMAN	C	131	ENSP00000333735:R131C	ENSP00000333735:R131C	R	+	1	0	C15orf2	22472498	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.028000	0.13644	0.082000	0.17018	-2.175000	0.00321	CGT	.		0.627	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921405	C	T	24921405	3	4	132	1	0	0	0	0	1	0	0	0	1788	536	19	1	393	1	C15orf2	15	24921405	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10		24921405	77609987	69	11722											
TJP1	7082	ucsc.edu;bcgsc.ca	37	chr15	30010892	30010892	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcgtgccgcagggcggatgCtctaggtgcctgttcgtaac	5	11	14	11	4	1	0	0	0	1	0	3	1	1	1	2	3	4	4	2	3	2	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:30010892C>A	ENST00000346128.6	-	21	3928	c.3454G>T	c.(3454-3456)Gca>Tca	p.A1152S	TJP1_ENST00000356107.6_Missense_Mutation_p.A1152S|TJP1_ENST00000400011.2_Missense_Mutation_p.A1076S|TJP1_ENST00000545208.2_Missense_Mutation_p.A1072S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1152					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		AGGGCGGATGCTCTAGGTGCC	0.597																																					p.A1152S	Melanoma(77;681 1843 6309 6570)												.	TJP1-95	0			c.G3454T						.						101	106	104					15																	30010892		2100	4228	6328	SO:0001583	missense	7082	exon21			CGGATGCTCTAGG		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.3454G>T	15.37:g.30010892C>A	ENSP00000281537:p.Ala1152Ser	Somatic	182	2		WXS	Illumina HiSeq		230	76	NM_003257	0	0	8	20	12	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	1.722	-0.496273	0.04291	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.05786	3.39;3.5	6.05	2.57	0.30868	.	0.392909	0.28612	N	0.014722	T	0.02380	0.0073	N	0.03608	-0.345	0.80722	D	1	B;B;B;B	0.14438	0.0;0.0;0.0;0.01	B;B;B;B	0.17098	0.001;0.002;0.001;0.017	T	0.49041	-0.8980	10	0.13108	T	0.6	.	5.5402	0.17033	0.0:0.2831:0.1345:0.5823	.	1145;1072;1152;1076	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	S	1152;1076;1152;1072;1072	ENSP00000281537:A1152S;ENSP00000382890:A1076S	ENSP00000281537:A1152S	A	-	1	0	TJP1	27798184	1.000000	0.71417	0.134000	0.22075	0.106000	0.19336	2.424000	0.44714	0.191000	0.20236	-0.312000	0.09012	GCA	.		0.597	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		A	30010892	C	A	30010892	3	1	132	1	0	0	0	0	1	0	0	0	15961	797	28	4	1824	4	TJP1	15	30010892	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	5089487	30010892	72520500	70	11723											
C15orf52	388115	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40631768	40631768	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggctggaggagtgctggtGtggtcacagccatccccccc	6	7	14	14	0	1	0	1	0	0	0	2	2	2	2	4	5	2	2	4	5	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:40631768G>A	ENST00000559313.1	-	3	323	c.308C>T	c.(307-309)aCa>aTa	p.T103I	C15orf52_ENST00000557973.1_5'Flank|C15orf52_ENST00000397536.2_5'Flank	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	103							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GAGTGCTGGTGTGGTCACAGC	0.662																																					p.T103I													.	C15orf52-153	0			c.C308T						.						85	94	91					15																	40631768		2140	4235	6375	SO:0001583	missense	388115	exon3			GCTGGTGTGGTCA	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.308C>T	15.37:g.40631768G>A	ENSP00000453969:p.Thr103Ile	Somatic	109	1		WXS	Illumina HiSeq	Phase_I	108	49	NM_207380	0	0	4	5	1	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	.	.	.	.	.	.	.	.	.	.	G	17.63	3.436789	0.62955	.	.	ENSG00000188549	ENST00000382688	.	.	.	5.17	4.24	0.50183	.	0.513303	0.17847	N	0.160005	T	0.61098	0.2320	M	0.67953	2.075	0.19575	N	0.999964	D	0.63046	0.992	P	0.59357	0.856	T	0.54443	-0.8293	9	0.72032	D	0.01	-2.0548	11.0227	0.47728	0.0:0.0:0.8139:0.1861	.	103	Q6ZUT6	CO052_HUMAN	I	103	.	ENSP00000372135:T103I	T	-	2	0	C15orf52	38419060	0.145000	0.22656	0.060000	0.19600	0.492000	0.33523	2.204000	0.42761	1.152000	0.42452	0.563000	0.77884	ACA	.		0.662	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380		A	40631768	G	A	40631768	3	1	132	1	0	0	0	0	1	0	0	0	1804	1377	48	2	1332	2	C15orf52	15	40631768	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	10620876	40631768	61899624	71	11724											
UNC13C	440279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	54557623	54557623	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatatgttacagttcaagtTggaaagaacaaaagaagaac	19	8	8	6	0	1	3	1	0	0	3	1	4	1	4	1	1	3	3	1	1	9	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:54557623T>A	ENST00000260323.11	+	9	3747	c.3747T>A	c.(3745-3747)gtT>gtA	p.V1249V	UNC13C_ENST00000537900.1_Silent_p.V1247V|UNC13C_ENST00000545554.1_Silent_p.V1249V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1249	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAGTTCAAGTTGGAAAGAACA	0.318																																					p.V1249V		.											.	UNC13C-51	0			c.T3747A						.						54	50	51					15																	54557623		1800	4067	5867	SO:0001819	synonymous_variant	440279	exon8			TCAAGTTGGAAAG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.3747T>A	15.37:g.54557623T>A		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	174	70	NM_001080534	0	0	0	0	0	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			.		0.318	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54557623	T	A	54557623	2	1	132	1	0	0	0	0	0	0	0	1	17019	1799	63	5		5	UNC13C	15	54557623	Silent	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	13925855	54557623	47973769	72	11725											
SNX1	6642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	64424017	64424017	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aaattgagcagctccaccagGaacaggccaacaatgacttc	15	6	8	12	0	0	2	0	2	0	0	2	3	1	3	3	2	4	2	3	2	4	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:64424017G>C	ENST00000559844.1	+	11	1161	c.1147G>C	c.(1147-1149)Gaa>Caa	p.E383Q	SNX1_ENST00000561026.1_Missense_Mutation_p.E318Q|SNX1_ENST00000560829.1_Missense_Mutation_p.E165Q|SNX1_ENST00000261889.5_Missense_Mutation_p.E383Q|SNX1_ENST00000353874.4_Missense_Mutation_p.E383Q			Q13596	SNX1_HUMAN	sorting nexin 1	383	BAR.				early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						GCTCCACCAGGAACAGGCCAA	0.537																																					p.E383Q		.											.	SNX1-226	0			c.G1147C						.						125	118	120					15																	64424017		2203	4300	6503	SO:0001583	missense	6642	exon11			CACCAGGAACAGG	BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.1147G>C	15.37:g.64424017G>C	ENSP00000453785:p.Glu383Gln	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	174	69	NM_003099	0	0	48	75	27	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Missense_Mutation	SNP	ENST00000559844.1	37	CCDS32266.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180341	0.78677	.	.	ENSG00000028528	ENST00000380285;ENST00000353874;ENST00000261889	T	0.32023	1.47	5.2	5.2	0.72013	Vps5 C-terminal (1);	0.092925	0.64402	D	0.000001	T	0.38532	0.1044	L	0.45137	1.4	0.80722	D	1	P;B;P;P;B;P;P	0.47106	0.89;0.167;0.74;0.74;0.365;0.475;0.571	P;B;P;P;B;B;B	0.48952	0.596;0.34;0.513;0.457;0.142;0.411;0.378	T	0.09885	-1.0654	10	0.52906	T	0.07	-19.057	17.8936	0.88879	0.0:0.0:1.0:0.0	.	383;293;383;383;318;383;383	Q6ZRJ8;Q59GU6;Q53HL9;Q53GY8;Q13596-2;A6NKH4;Q13596	.;.;.;.;.;.;SNX1_HUMAN	Q	383;383;318	ENSP00000326668:E383Q	ENSP00000261889:E318Q	E	+	1	0	SNX1	62211070	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.657000	0.98554	2.693000	0.91896	0.561000	0.74099	GAA	.		0.537	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		C	64424017	G	C	64424017	3	2	132	1	0	0	0	0	1	0	0	0	14912	1175	41	4	1189	4	SNX1	15	64424017	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	9866394	64424017	38107375	73	11726											
ANP32A	8125	ucsc.edu	37	chr15	69072440	69072440	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagtcatcatcttctccctCatcttcaggttctcgttttc	5	19	4	13	1	8	0	4	0	4	0	11	0	8	0	1	1	0	2	1	1	1	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:69072440C>A	ENST00000465139.2	-	7	873	c.730G>T	c.(730-732)Gag>Tag	p.E244*	ANP32A_ENST00000483551.2_5'UTR	NM_006305.3	NP_006296.1	P39687	AN32A_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	244	Asp/Glu-rich (highly acidic).|Interaction with E4F1. {ECO:0000250}.				gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|nucleocytoplasmic transport (GO:0006913)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						TCTTCTCCCTCATCTTCAGGT	0.408																																					p.E244X													.	.	0			c.G730T						.						64	71	69					15																	69072440		2199	4298	6497	SO:0001587	stop_gained	8125	exon7			CTCCCTCATCTTC	AF025684	CCDS45292.1	15q23	2008-05-14			ENSG00000140350	ENSG00000140350		"ANP32 acidic nuclear phosphoproteins"	13233	protein-coding gene	gene with protein product		600832		C15orf1		8970164, 9144194	Standard	NM_006305		Approved	LANP, PP32, I1PP2A, PHAPI, MAPM, mapmodulin	uc002arl.3	P39687	OTTHUMG00000154502	ENST00000465139.2:c.730G>T	15.37:g.69072440C>A	ENSP00000417864:p.Glu244*	Somatic	54	3		WXS	Illumina HiSeq		48	22	NM_006305	0	0	26	44	18	B2R6T4|Q53FK4|Q5J8L8|Q7M4N6	Nonsense_Mutation	SNP	ENST00000465139.2	37	CCDS45292.1	.	.	.	.	.	.	.	.	.	.	C	36	5.661156	0.96734	.	.	ENSG00000140350	ENST00000465139	.	.	.	5.11	5.11	0.69529	.	0.138458	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	17.8884	0.88864	0.0:1.0:0.0:0.0	.	.	.	.	X	244	.	ENSP00000417864:E244X	E	-	1	0	ANP32A	66859494	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.769000	0.74985	2.537000	0.85549	0.561000	0.74099	GAG	.		0.408	ANP32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335525.2			A	69072440	C	A	69072440	4	1	132	1	0	0	0	0	0	1	0	0	705	835	29	4	23	4	ANP32A	15	69072440	Nonsense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	4648423	69072440	33458952	74	11727											
ALPK3	57538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	85411510	85411510	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagagtccatctgctggcagGaaaggctcccagctgagtcc	10	7	12	12	0	1	2	0	1	1	1	4	3	4	3	3	3	2	4	3	3	2	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:85411510G>C	ENST00000258888.5	+	14	5714	c.5547G>C	c.(5545-5547)agG>agC	p.R1849S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1849					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTGCTGGCAGGAAAGGCTCCC	0.627																																					p.R1849S		.											.	ALPK3-337	0			c.G5547C						.						56	65	62					15																	85411510		2203	4299	6502	SO:0001583	missense	57538	exon14			TGGCAGGAAAGGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17574	protein-coding gene	gene with protein product	"myocyte induction differentiation originator", "muscle alpha-kinase"					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.5547G>C	15.37:g.85411510G>C	ENSP00000258888:p.Arg1849Ser	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	92	41	NM_020778	0	0	0	6	6	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.610641	0.66558	.	.	ENSG00000136383	ENST00000258888	T	0.68903	-0.36	3.93	1.99	0.26369	.	0.271361	0.27778	N	0.017892	T	0.76307	0.3969	M	0.74258	2.255	0.37283	D	0.907916	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.996	T	0.75625	-0.3253	10	0.54805	T	0.06	-23.6009	5.715	0.17954	0.3613:0.0:0.6387:0.0	.	150;1849	B4DU37;Q96L96	.;ALPK3_HUMAN	S	1849	ENSP00000258888:R1849S	ENSP00000258888:R1849S	R	+	3	2	ALPK3	83212514	1.000000	0.71417	0.996000	0.52242	0.906000	0.53458	0.646000	0.24797	0.408000	0.25621	0.313000	0.20887	AGG	.		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		C	85411510	G	C	85411510	3	2	132	1	0	0	0	0	1	0	0	0	546	1165	41	4	5601	4	ALPK3	15	85411510	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	16339070	85411510	17119882	75	11728											
BTBD12	84464	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	3645657	3645657	+	Frame_Shift_Del	DEL	C	C	-																															tcctgcgatggcaccacaaaCccagtcagaggaaggccgcc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr16:3645657delC	ENST00000294008.3	-	9	2602	c.1962delG	c.(1960-1962)gggfs	p.G654fs		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	654	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GCACCACAAACCCAGTCAGAG	0.627								Direct reversal of damage																													p.G654fs		.											.	SLX4-94	0			c.1962delG						.						63	65	64					16																	3645657		2197	4300	6497	SO:0001589	frameshift_variant	84464	exon9			.	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"Fanconi anemia, complementation groups", "BTB/POZ domain containing"	23845	protein-coding gene	gene with protein product	"Fanconi anemia, complementation group P"	613278	"BTB (POZ) domain containing 12", "SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1962delG	16.37:g.3645657delC	ENSP00000294008:p.Gly654fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	103	41	NM_032444	0	0	0	0	0	Q69YT8|Q8TF15|Q96JP1	Frame_Shift_Del	DEL	ENST00000294008.3	37	CCDS10506.2																																																																																			.		0.627	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		-	3645657	C	-	3645657	7	5	132	1	0	1	0	1	0	0	0	0	1543	494	18	0	3570	0	BTBD12	16	3645657	Frame_Shift_Del	DEL	C	TCGA-HE-A5NH-01A-11D-A26P-10		3645657	86709096	76	11729											
LOC100132247	100132247	broad.mit.edu;bcgsc.ca	37	chr16	22545906	22545906	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gataatatcaagacacctgcCgagcgtctgcgggggccgct	9	7	13	12	4	2	1	1	0	1	1	2	3	2	1	3	2	3	1	3	2	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr16:22545906C>T	ENST00000517539.1	+	8	1677	c.1602C>T	c.(1600-1602)gcC>gcT	p.A534A	NPIPB5_ENST00000424340.1_Silent_p.A534A|NPIPB5_ENST00000415654.1_3'UTR			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	534	Pro-rich.					integral component of membrane (GO:0016021)											AGACACCTGCCGAGCGTCTGC	0.592																																					p.A534A													.	.	0			c.C1602T						.						4	4	4					16																	22545906		650	1439	2089	SO:0001819	synonymous_variant	0	exon7			ACCTGCCGAGCGT		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1602C>T	16.37:g.22545906C>T		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	71	14	NM_001135865	0	0	322	345	23	B4DK13	Silent	SNP	ENST00000517539.1	37	CCDS45443.1																																																																																			.		0.592	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374343.2	NM_001135865		T	22545906	C	T	22545906	2	4	132	1	0	0	0	0	0	0	0	1	8891	639	23	1		1	LOC100132247	16	22545906	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	18900249	22545906	67808847	77	11730											
ZNF668	79759	broad.mit.edu;bcgsc.ca	37	chr16	31072415	31072415	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccctcttcaggcattcCtagcaaagccaccaggggct	8	7	10	16	1	2	0	1	0	1	0	3	0	3	0	5	4	2	3	5	4	2	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr16:31072415C>G	ENST00000538906.1	-	3	2618	c.1834G>C	c.(1834-1836)Gga>Cga	p.G612R	ZNF668_ENST00000426488.2_Missense_Mutation_p.G635R|ZNF668_ENST00000535577.1_Missense_Mutation_p.G612R|ZNF668_ENST00000539836.3_Missense_Mutation_p.G635R|ZNF668_ENST00000417110.2_5'Flank|ZNF668_ENST00000394983.2_Missense_Mutation_p.G612R|ZNF668_ENST00000300849.4_Missense_Mutation_p.G612R	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	612					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(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						TCAGGCATTCCTAGCAAAGCC	0.657																																					p.G635R	Colon(181;1111 1980 5060 10512 25785)												.	ZNF668-585	0			c.G1903C						.						32	40	37					16																	31072415		2158	4276	6434	SO:0001583	missense	79759	exon4			GCATTCCTAGCAA		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"Zinc fingers, C2H2-type"	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1834G>C	16.37:g.31072415C>G	ENSP00000440149:p.Gly612Arg	Somatic	93	2		WXS	Illumina HiSeq	Phase_I	93	34	NM_001172669	0	0	4	7	3	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004650	0.74932	.	.	ENSG00000167394	ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	T;T;T;T;T	0.07327	3.2;3.22;3.22;3.22;3.22	5.05	5.05	0.67936	.	0.417562	0.21039	N	0.081215	T	0.10078	0.0247	N	0.14661	0.345	0.42318	D	0.992244	D	0.54207	0.965	P	0.51016	0.656	T	0.40021	-0.9585	10	0.29301	T	0.29	-5.1861	17.3426	0.87301	0.0:1.0:0.0:0.0	.	612	Q96K58	ZN668_HUMAN	R	635;612;612;612;612	ENSP00000442573:G635R;ENSP00000441349:G612R;ENSP00000440149:G612R;ENSP00000378434:G612R;ENSP00000300849:G612R	ENSP00000300849:G612R	G	-	1	0	ZNF668	30979916	0.358000	0.24947	1.000000	0.80357	0.908000	0.53690	2.421000	0.44688	2.640000	0.89533	0.561000	0.74099	GGA	.		0.657	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		G	31072415	C	G	31072415	3	3	132	1	0	0	0	0	1	0	0	0	18107	690	24	4	29	4	ZNF668	16	31072415	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	8526509	31072415	59282338	78	11731											
CES3	23491	broad.mit.edu	37	chr16	66997181	66997181	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccttgtgaatgtctttcTgggcattccatttgcccagc	5	14	9	13	1	2	1	0	1	2	0	3	1	3	1	4	1	2	1	4	1	1	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr16:66997181T>G	ENST00000303334.4	+	2	253	c.182T>G	c.(181-183)cTg>cGg	p.L61R	RP11-361L15.4_ENST00000566869.1_RNA|CES3_ENST00000394037.1_Missense_Mutation_p.L61R	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	61						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)		AATGTCTTTCTGGGCATTCCA	0.662																																					p.L61R													.	CES3-517	0			c.T182G						.						59	62	61					16																	66997181		2200	4300	6500	SO:0001583	missense	23491	exon2			TCTTTCTGGGCAT	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.182T>G	16.37:g.66997181T>G	ENSP00000304782:p.Leu61Arg	Somatic	64	3		WXS	Illumina HiSeq	Phase_I	91	10	NM_024922	0	0	3	3	0	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Missense_Mutation	SNP	ENST00000303334.4	37	CCDS10826.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.887142	0.52014	.	.	ENSG00000172828	ENST00000303334;ENST00000394037	T;T	0.70749	-0.51;-0.51	4.31	3.19	0.36642	Carboxylesterase, type B (1);	0.000000	0.30752	N	0.008957	T	0.74504	0.3725	L	0.48260	1.515	0.80722	D	1	D	0.65815	0.995	P	0.61722	0.893	T	0.74682	-0.3583	10	0.87932	D	0	.	9.289	0.37775	0.1615:0.0:0.0:0.8385	.	61	Q6UWW8	EST3_HUMAN	R	61	ENSP00000304782:L61R;ENSP00000377602:L61R	ENSP00000304782:L61R	L	+	2	0	CES3	65554682	1.000000	0.71417	1.000000	0.80357	0.163000	0.22366	6.725000	0.74752	0.748000	0.32831	0.533000	0.62120	CTG	.		0.662	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922		G	66997181	T	G	66997181	3	3	132	1	0	0	0	0	1	0	0	0	3277	1580	55	5	188	5	CES3	16	66997181	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	35924766	66997181	23357572	79	11732											
PKD1L2	114780	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81193369	81193369	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaccacagtcaaatagtagaCcccttctccaaaacgcaggt	14	7	7	13	1	2	1	1	0	1	1	3	2	2	1	4	1	1	2	4	1	5	3	rs566575678	byFrequency	TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr16:81193369C>G	ENST00000525539.1	-	0	3753				PKD1L2_ENST00000533478.1_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AAATAGTAGACCCCTTCTCCA	0.587																																					.													.	PKD1L2-92	0			.						.						47	49	48					16																	81193369		1997	4182	6179			114780	.			AGTAGACCCCTTC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81193369C>G		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	125	52	.	0	0	0	0	0	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37																																																																																				.		0.587	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			G	81193369	C	G	81193369	1	3	132	0	1	0	0	0	0	0	0	0	11991	507	18	4		4	PKD1L2	16	81193369	RNA	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	14196188	81193369	9161384	80	11733											
SSH2	85464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27959441	27959441	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaatcattctttgaattcTtacgagtggacaatgaggta	14	13	9	5	1	3	3	1	2	2	1	3	5	3	4	0	2	1	1	0	2	6	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr17:27959441T>A	ENST00000269033.3	-	15	2841	c.2690A>T	c.(2689-2691)aAg>aTg	p.K897M	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.K924M	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	897					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTTTGAATTCTTACGAGTGGA	0.502																																					p.K897M		.											.	SSH2-92	0			c.A2690T						.						184	192	189					17																	27959441		2203	4300	6503	SO:0001583	missense	85464	exon15			GAATTCTTACGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2690A>T	17.37:g.27959441T>A	ENSP00000269033:p.Lys897Met	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	189	106	NM_033389	0	0	0	2	2	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.585604	0.66105	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.19806	2.14;2.12	5.97	4.89	0.63831	.	0.456816	0.25546	N	0.029933	T	0.43809	0.1264	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.36407	-0.9749	10	0.87932	D	0	-19.645	11.9775	0.53100	0.0:0.0675:0.0:0.9325	.	924;897	F5H527;Q76I76	.;SSH2_HUMAN	M	897;924	ENSP00000269033:K897M;ENSP00000444743:K924M	ENSP00000269033:K897M	K	-	2	0	SSH2	24983567	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.807000	0.69157	1.089000	0.41292	0.472000	0.43445	AAG	.		0.502	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		A	27959441	T	A	27959441	3	1	132	1	0	0	0	0	1	0	0	0	15217	1609	56	5	1585	5	SSH2	17	27959441	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10		27959441	53235769	81	11734											
TGIF1	7050	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	3452341	3452341	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccccatcccagggcgcacagGgtccagctcctcggcgccga	6	4	12	19	4	0	0	0	0	0	0	4	1	3	0	6	3	1	2	6	3	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr18:3452341G>C	ENST00000330513.5	+	1	667	c.364G>C	c.(364-366)Ggt>Cgt	p.G122R	TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000401449.1_Intron|TGIF1_ENST00000345133.5_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	122					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GGGCGCACAGGGTCCAGCTCC	0.687																																					p.G122R		.											.	TGIF1-227	0			c.G364C						.						14	16	15					18																	3452341		2171	4257	6428	SO:0001583	missense	7050	exon1			GCACAGGGTCCAG	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"Homeoboxes / TALE class"	11776	protein-coding gene	gene with protein product		602630	"TGFB-induced factor (TALE family homeobox)"	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.364G>C	18.37:g.3452341G>C	ENSP00000327959:p.Gly122Arg	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	99	50	NM_170695	0	0	0	0	0	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	37	CCDS11834.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.037731	0.54896	.	.	ENSG00000177426	ENST00000330513	T	0.52295	0.67	3.89	3.01	0.34805	.	.	.	.	.	T	0.37348	0.1000	L	0.38175	1.15	0.21473	N	0.999675	P	0.44877	0.845	B	0.41813	0.367	T	0.15235	-1.0444	9	0.52906	T	0.07	3.9769	7.1745	0.25736	0.1232:0.0:0.8768:0.0	.	122	Q15583	TGIF1_HUMAN	R	122	ENSP00000327959:G122R	ENSP00000327959:G122R	G	+	1	0	TGIF1	3442341	0.004000	0.15560	0.040000	0.18447	0.018000	0.09664	1.238000	0.32707	0.855000	0.35359	0.655000	0.94253	GGT	.		0.687	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		C	3452341	G	C	3452341	3	2	132	1	0	0	0	0	1	0	0	0	15857	1232	43	4	448	4	TGIF1	18	3452341	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		3452341	74624907	82	11735											
PTPRM	5797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	8378412	8378412	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagattaaagaggaattccgGgtaagtgatgcctaagggag	14	8	14	5	1	0	3	0	1	0	2	1	5	1	5	2	3	1	1	2	3	5	4	rs374669816		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr18:8378412G>T	ENST00000332175.8	+	25	4610	c.3573G>T	c.(3571-3573)cgG>cgT	p.R1191R	PTPRM_ENST00000580170.1_Splice_Site_p.R1204R|PTPRM_ENST00000400053.4_Splice_Site_p.R1129R|PTPRM_ENST00000444013.1_Splice_Site_p.R978R|PTPRM_ENST00000400060.4_Splice_Site_p.R1205R	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1191	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AGGAATTCCGGGTAAGTGATG	0.493																																					p.R1204R		.											.	PTPRM-228	0			c.G3612T						.						116	97	103					18																	8378412		2203	4300	6503	SO:0001630	splice_region_variant	5797	exon27			ATTCCGGGTAAGT	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3573+1G>T	18.37:g.8378412G>T		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	150	57	NM_001105244	0	0	0	0	0	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	37	CCDS11840.1																																																																																			.		0.493	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Silent	T	8378412	G	T	8378412	5	4	132	1	0	0	0	0	0	0	1	0	12838	1246	43	4	3718	4	PTPRM	18	8378412	Splice_Site	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	4926071	8378412	69698836	83	11736											
KIAA1468	57614	bcgsc.ca	37	chr18	59954615	59954615	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catttgcataagttagccttGgtgaacaacttacagattgt	12	14	8	7	0	0	2	0	1	0	1	0	2	0	2	1	1	5	2	1	1	5	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr18:59954615G>T	ENST00000398130.2	+	26	3517	c.3285G>T	c.(3283-3285)ttG>ttT	p.L1095F	KIAA1468_ENST00000256858.6_Missense_Mutation_p.L1129F	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	1095										autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				AGTTAGCCTTGGTGAACAACT	0.353																																					p.L1095F													.	KIAA1468-158	0			c.G3285T						.						165	151	156					18																	59954615		2203	4300	6503	SO:0001583	missense	57614	exon26			AGCCTTGGTGAAC	BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444			29289	protein-coding gene	gene with protein product						11973628	Standard	NM_020854		Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.3285G>T	18.37:g.59954615G>T	ENSP00000381198:p.Leu1095Phe	Somatic	74	0		WXS	Illumina HiSeq	Phase_1	82	5	NM_020854	0	0	14	14	0		Missense_Mutation	SNP	ENST00000398130.2	37	CCDS11979.2	.	.	.	.	.	.	.	.	.	.	G	12.76	2.035142	0.35893	.	.	ENSG00000134444	ENST00000398130;ENST00000256858	T;T	0.74421	-0.84;-0.84	5.71	4.84	0.62591	Armadillo-type fold (1);	0.063705	0.64402	D	0.000003	T	0.51736	0.1692	N	0.08118	0	0.51233	D	0.999914	B;B	0.15141	0.007;0.012	B;B	0.18561	0.022;0.015	T	0.45702	-0.9243	9	.	.	.	-5.9435	9.7506	0.40473	0.0702:0.0:0.7902:0.1396	.	1129;1095	Q9P260-2;Q9P260	.;K1468_HUMAN	F	1095;1129	ENSP00000381198:L1095F;ENSP00000256858:L1129F	.	L	+	3	2	KIAA1468	58105595	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.414000	0.59802	1.558000	0.49541	0.650000	0.86243	TTG	.		0.353	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854		T	59954615	G	T	59954615	3	4	132	1	0	0	0	0	1	0	0	0	8257	1339	47	4	3387	4	KIAA1468	18	59954615	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	51576203	59954615	18122633	84	11737											
FUT6	2528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	5832530	5832530	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaacagcagcgtggtcaGacagcagcgccacgaccact	12	4	11	14	3	1	2	1	1	0	1	1	3	1	2	2	1	5	2	2	1	1	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:5832530G>T	ENST00000318336.4	-	3	1243	c.49C>A	c.(49-51)Ctg>Atg	p.L17M	FUT6_ENST00000286955.5_Missense_Mutation_p.L17M|FUT6_ENST00000524754.1_Missense_Mutation_p.L17M|FUT6_ENST00000592563.1_Missense_Mutation_p.L17M|FUT6_ENST00000527106.1_Missense_Mutation_p.L17M	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	17					fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						AGCGTGGTCAGACAGCAGCGC	0.572																																					p.L17M		.											.	FUT6-90	0			c.C49A						.						35	30	32					19																	5832530		2203	4300	6503	SO:0001583	missense	2528	exon3			TGGTCAGACAGCA		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"Fucosyltransferases"	4017	protein-coding gene	gene with protein product	"alpha-(1,3)-fucosyltransferase", "galactoside 3-L-fucosyltransferase"	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.49C>A	19.37:g.5832530G>T	ENSP00000313398:p.Leu17Met	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	139	61	NM_000150	0	0	6	17	11	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.377927	0.24944	.	.	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530;ENST00000529165;ENST00000531085;ENST00000531199;ENST00000532464;ENST00000528505	T;T;T;T;T;T;T;T;T	0.61859	1.81;1.81;1.81;1.81;1.81;0.81;0.24;0.07;0.19	3.7	1.52	0.23074	.	0.960505	0.08559	U	0.927769	T	0.72803	0.3506	M	0.77616	2.38	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.55068	-0.8198	10	0.54805	T	0.06	.	6.2965	0.21089	0.1124:0.195:0.6925:0.0	.	17;17	C9J8A2;P51993	.;FUT6_HUMAN	M	17	ENSP00000431708:L17M;ENSP00000432954:L17M;ENSP00000313398:L17M;ENSP00000286955:L17M;ENSP00000436547:L17M;ENSP00000432161:L17M;ENSP00000436413:L17M;ENSP00000431880:L17M;ENSP00000433811:L17M	ENSP00000286955:L17M	L	-	1	2	FUT6	5783530	0.017000	0.18338	0.005000	0.12908	0.033000	0.12548	1.348000	0.33987	0.849000	0.35215	0.436000	0.28706	CTG	.		0.572	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150		T	5832530	G	T	5832530	3	4	132	1	0	0	0	0	1	0	0	0	6127	933	33	4	1034	4	FUT6	19	5832530	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		5832530	53296453	85	11738											
CYP4F8	11283	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15739650	15739650	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tattcctttctcggcggggcCcaggtgaggccagggggtgt	4	10	17	10	2	1	1	0	1	1	0	3	1	2	1	3	7	0	0	3	7	1	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:15739650C>G	ENST00000441682.2	+	0	1455							P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 8						icosanoid metabolic process (GO:0006690)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alkane 1-monooxygenase activity (GO:0018685)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(1)	26						TCGGCGGGGCCCAGGTGAGGC	0.582																																					.													.	CYP4F8-90	0			.						.						40	45	43					19																	15739650		2016	4203	6219			11283	.			CGGGGCCCAGGTG	AF133298	CCDS74303.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186526	ENSG00000186526		"Cytochrome P450s"	2648	protein-coding gene	gene with protein product		611545	"cytochrome P450, subfamily IVF, polypeptide 8"			10405341	Standard	NM_007253		Approved		uc002nbi.3	P98187	OTTHUMG00000182386		19.37:g.15739650C>G		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	66	30	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000441682.2	37		.	.	.	.	.	.	.	.	.	.	.	17.80	3.477280	0.63849	.	.	ENSG00000186526	ENST00000441682;ENST00000325723	.	.	.	3.32	3.32	0.38043	Cytochrome P450, conserved site (1);	0.000000	0.64402	U	0.000001	T	0.71459	0.3342	.	.	.	0.49051	D	0.999743	P;D	0.61697	0.566;0.99	P;D	0.63877	0.624;0.919	T	0.81393	-0.0953	7	0.87932	D	0	.	12.1517	0.54053	0.0:1.0:0.0:0.0	.	277;465	B4DU85;P98187	.;CP4F8_HUMAN	R	464;277	.	ENSP00000314398:P277R	P	+	2	0	CYP4F8	15600650	1.000000	0.71417	0.998000	0.56505	0.722000	0.41435	4.681000	0.61663	1.681000	0.50988	0.436000	0.28706	CCC	.		0.582	CYP4F8-201	KNOWN	basic	processed_transcript	processed_transcript		NM_007253		G	15739650	C	G	15739650	1	3	132	0	1	0	0	0	0	0	0	0	4197	623	22	4		4	CYP4F8	19	15739650	RNA	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	9907120	15739650	43389333	86	11739											
IL28B	282617	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	39735444	39735444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactaaggcatctttggccCtcttaaaggcctgcagctcc	8	11	8	14	0	3	0	1	0	2	0	4	0	4	0	3	3	2	3	3	3	3	3	rs201018323	byFrequency	TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:39735444C>T	ENST00000413851.2	-	1	202	c.164G>A	c.(163-165)aGg>aAg	p.R55K	IFNL4_ENST00000606380.1_RNA	NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	55					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of viral genome replication (GO:0045071)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											ATCTTTGGCCCTCTTAAAGGC	0.622													C|||	3	0.000599042	8e-04	0	5008	,	,		19948	0		0.001	False		,,,				2504	0.001				p.R55K		.											.	.	0			c.G164A						.						21	24	23					19																	39735444		2203	4292	6495	SO:0001583	missense	282617	exon1			TTGGCCCTCTTAA	AY129149	CCDS12530.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000197110	ENSG00000197110		"Interferons"	18365	protein-coding gene	gene with protein product		607402	"interleukin 28B", "interleukin 28B (interferon, lambda 3)"	IL28B			Standard	NM_172139		Approved	IL-28B, IL28C	uc010xut.2	Q8IZI9	OTTHUMG00000182805	ENST00000413851.2:c.164G>A	19.37:g.39735444C>T	ENSP00000409000:p.Arg55Lys	Somatic	266	0		WXS	Illumina HiSeq	Phase_I	347	107	NM_172139	0	0	0	0	0	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Missense_Mutation	SNP	ENST00000413851.2	37	CCDS12530.1	.	.	.	.	.	.	.	.	.	.	C	0.482	-0.879400	0.02550	.	.	ENSG00000197110	ENST00000413851	T	0.26223	1.75	2.97	-4.43	0.03568	.	0.765632	0.12009	N	0.508070	T	0.03739	0.0106	N	0.00521	-1.4	0.18873	N	0.999982	B	0.06786	0.001	B	0.04013	0.001	T	0.37197	-0.9716	10	0.06757	T	0.87	2.9441	0.3638	0.00368	0.1912:0.2524:0.1896:0.3668	.	55	Q8IZI9	IL28B_HUMAN	K	55	ENSP00000409000:R55K	ENSP00000409000:R55K	R	-	2	0	IL28B	44427284	0.000000	0.05858	0.388000	0.26195	0.653000	0.38743	-1.727000	0.01860	-0.398000	0.07679	0.194000	0.17425	AGG	.		0.622	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139		T	39735444	C	T	39735444	3	4	132	1	0	0	0	0	1	0	0	0	7704	681	24	2	445	2	IL28B	19	39735444	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	23995794	39735444	19393539	87	11740											
PSG4	5672	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	43708130	43708130	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatcctgcatcctcctgcGtgacattctggatcagcagg	8	10	11	12	1	2	1	1	1	1	0	5	3	5	3	3	3	3	2	3	3	0	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:43708130G>A	ENST00000405312.3	-	2	575	c.338C>T	c.(337-339)aCg>aTg	p.T113M	PSG4_ENST00000244295.9_Missense_Mutation_p.T113M|PSG4_ENST00000433626.2_Missense_Mutation_p.T113M	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	113	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				ATCCTCCTGCGTGACATTCTG	0.458																																					p.P113L													.	PSG4-91	0			c.C338T						.						272	278	276					19																	43708130		2140	4271	6411	SO:0001583	missense	5672	exon2			TCCTGCGTGACAT		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9521	protein-coding gene	gene with protein product	"pregnancy-specific beta-1-glycoprotein 4"	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.338C>T	19.37:g.43708130G>A	ENSP00000384770:p.Thr113Met	Somatic	236	1		WXS	Illumina HiSeq	Phase_I	302	95	NM_002780	0	0	0	0	0	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	N	11.42	1.632906	0.29068	.	.	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626;ENST00000451895	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	1.65	1.65	0.23941	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82300	0.5007	M	0.91038	3.17	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.994;1.0	T	0.67569	-0.5637	9	0.87932	D	0	.	6.8053	0.23774	0.0:0.0:1.0:0.0	.	113;113;113	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	M	113;113;113;129	ENSP00000244295:T113M;ENSP00000384770:T113M;ENSP00000387864:T113M;ENSP00000388134:T129M	ENSP00000244295:T113M	T	-	2	0	PSG4	48399970	0.000000	0.05858	0.009000	0.14445	0.003000	0.03518	-0.474000	0.06607	1.251000	0.43983	0.173000	0.16961	ACG	.		0.458	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633		A	43708130	G	A	43708130	3	1	132	1	0	0	0	0	1	0	0	0	12686	1145	40	1	941	1	PSG4	19	43708130	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	3972686	43708130	15420853	88	11741											
CCDC9	26093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	47767895	47767895	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcaggcagaacattgagaaGatgaatgaggagatggagaa	17	5	15	4	1	0	7	0	3	0	5	0	10	0	7	0	3	1	2	0	3	4	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:47767895G>T	ENST00000221922.6	+	6	720	c.498G>T	c.(496-498)aaG>aaT	p.K166N		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	166							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		ACATTGAGAAGATGAATGAGG	0.617																																					p.K166N		.											.	CCDC9-90	0			c.G498T						.						80	63	69					19																	47767895		2202	4299	6501	SO:0001583	missense	26093	exon6			TGAGAAGATGAAT	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.498G>T	19.37:g.47767895G>T	ENSP00000221922:p.Lys166Asn	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	52	17	NM_015603	0	0	5	7	2		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	g	16.68	3.191307	0.58017	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.27890	1.64	4.63	4.63	0.57726	.	0.356482	0.30667	N	0.009121	T	0.53769	0.1817	M	0.67953	2.075	0.44694	D	0.997682	D	0.89917	1.0	D	0.77004	0.989	T	0.55477	-0.8135	10	0.52906	T	0.07	-46.2641	16.3937	0.83548	0.0:0.0:1.0:0.0	.	166	Q9Y3X0	CCDC9_HUMAN	N	166;148	ENSP00000221922:K166N	ENSP00000221922:K166N	K	+	3	2	CCDC9	52459735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.672000	0.54583	2.416000	0.81992	0.561000	0.74099	AAG	.		0.617	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		T	47767895	G	T	47767895	3	4	132	1	0	0	0	0	1	0	0	0	2873	933	33	4	516	4	CCDC9	19	47767895	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	4059765	47767895	11361088	89	11742											
ZNF600	162966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53269420	53269420	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgaaggtcttgctgcacTcattacacttgtaaggtttc	9	14	9	9	0	2	1	1	1	1	0	3	2	2	1	0	2	3	4	0	2	3	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:53269420T>A	ENST00000338230.3	-	3	1856	c.1589A>T	c.(1588-1590)gAg>gTg	p.E530V		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	530					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(2)|endometrium(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		CTTGCTGCACTCATTACACTT	0.458																																					p.E530V	Esophageal Squamous(196;1235 2112 2375 33339 34207)	.											.	ZNF600-90	0			c.A1589T						.						220	195	204					19																	53269420		2203	4300	6503	SO:0001583	missense	162966	exon3			CTGCACTCATTAC	U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"Zinc fingers, C2H2-type"	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.1589A>T	19.37:g.53269420T>A	ENSP00000344791:p.Glu530Val	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	109	37	NM_198457	0	0	10	12	2	Q6MZR0	Missense_Mutation	SNP	ENST00000338230.3	37	CCDS12856.1	.	.	.	.	.	.	.	.	.	.	.	12.82	2.052449	0.36181	.	.	ENSG00000189190	ENST00000338230	T	0.17528	2.27	1.51	0.278	0.15673	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18593	0.0446	N	0.11789	0.175	0.09310	N	1	D	0.55172	0.97	D	0.74348	0.983	T	0.16928	-1.0386	9	0.45353	T	0.12	.	5.4227	0.16409	0.251:0.0:0.0:0.749	.	530	Q6ZNG1	ZN600_HUMAN	V	530	ENSP00000344791:E530V	ENSP00000344791:E530V	E	-	2	0	ZNF600	57961232	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	0.274000	0.18680	-0.139000	0.11414	0.163000	0.16589	GAG	.		0.458	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457		A	53269420	T	A	53269420	3	1	132	1	0	0	0	0	1	0	0	0	18062	1551	54	5	583	5	ZNF600	19	53269420	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	5501525	53269420	5859563	90	11743											
ZNF761	388561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53959526	53959526	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagtgacaaagcttacagtTtcaaatcaaaccttgaaata	18	11	5	7	0	2	2	2	2	0	0	2	2	2	2	1	0	3	2	1	0	7	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:53959526T>G	ENST00000454407.1	+	0	2218							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AGCTTACAGTTTCAAATCAAA	0.403																																					p.F589V		.											.	ZNF761-91	0			c.T1765G						.						98	102	101					19																	53959526		2203	4299	6502			388561	exon7			TACAGTTTCAAAT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959526T>G		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	103	47	NM_001008401	0	0	1	3	2	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				.		0.403	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		G	53959526	T	G	53959526	1	3	132	0	1	0	0	0	0	0	0	0	18168	1841	64	5		5	ZNF761	19	53959526	RNA	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	690106	53959526	5169457	91	11744											
CRNKL1	51340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	20026023	20026023	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catatgttcatctccaaagaAttccacagctctctcataca	13	12	3	13	0	4	1	2	0	2	1	7	1	5	1	2	0	2	2	2	0	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr20:20026023A>T	ENST00000377340.2	-	7	1244	c.1213T>A	c.(1213-1215)Ttc>Atc	p.F405I	CRNKL1_ENST00000377327.4_Missense_Mutation_p.F393I|CRNKL1_ENST00000536226.1_Missense_Mutation_p.F244I	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	405					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TCTCCAAAGAATTCCACAGCT	0.398																																					p.F405I		.											.	CRNKL1-137	0			c.T1213A						.						175	173	173					20																	20026023		2203	4300	6503	SO:0001583	missense	51340	exon7			CAAAGAATTCCAC	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.1213T>A	20.37:g.20026023A>T	ENSP00000366557:p.Phe405Ile	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	153	54	NM_016652	0	0	5	7	2	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.764213	0.69878	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.08984	3.03;3.03;3.03	5.8	5.8	0.92144	Tetratricopeptide-like helical (1);	0.091092	0.85682	D	0.000000	T	0.13114	0.0318	M	0.70787	2.145	0.80722	D	1	B	0.29716	0.255	B	0.26517	0.07	T	0.02301	-1.1180	10	0.33141	T	0.24	-21.9403	16.1384	0.81506	1.0:0.0:0.0:0.0	.	405	Q9BZJ0	CRNL1_HUMAN	I	393;405;244	ENSP00000366544:F393I;ENSP00000366557:F405I;ENSP00000440733:F244I	ENSP00000366544:F393I	F	-	1	0	CRNKL1	19974023	1.000000	0.71417	0.976000	0.42696	0.987000	0.75469	9.339000	0.96797	2.203000	0.70933	0.460000	0.39030	TTC	.		0.398	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			T	20026023	A	T	20026023	3	4	132	1	0	0	0	0	1	0	0	0	3897	101	4	5	1369	5	CRNKL1	20	20026023	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10		20026023	42999497	92	11745											
KIAA1755	85449	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	36841970	36841970	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctggcccaggcctgccCggctcagggaggccacctgc	4	5	14	18	1	1	0	1	0	0	0	2	1	2	1	6	5	2	2	6	5	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr20:36841970C>T	ENST00000279024.4	-	14	3348	c.3077G>A	c.(3076-3078)cGg>cAg	p.R1026Q		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1026										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CAGGCCTGCCCGGCTCAGGGA	0.677																																					p.R1026Q		.											.	KIAA1755-95	0			c.G3077A						.						25	25	25					20																	36841970		2200	4297	6497	SO:0001583	missense	85449	exon14			CCTGCCCGGCTCA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.3077G>A	20.37:g.36841970C>T	ENSP00000279024:p.Arg1026Gln	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	51	23	NM_001029864	0	0	0	0	0	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421251	0.25639	.	.	ENSG00000149633	ENST00000279024	T	0.05717	3.4	5.29	-4.25	0.03766	.	0.891096	0.09443	N	0.801481	T	0.03011	0.0089	N	0.11064	0.09	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.48692	-0.9013	10	0.10902	T	0.67	.	11.6604	0.51343	0.0:0.3634:0.0:0.6366	.	1026	Q5JYT7	K1755_HUMAN	Q	1026	ENSP00000279024:R1026Q	ENSP00000279024:R1026Q	R	-	2	0	KIAA1755	36275384	0.000000	0.05858	0.002000	0.10522	0.669000	0.39330	-2.684000	0.00835	-1.072000	0.03141	-0.224000	0.12420	CGG	.		0.677	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36841970	C	T	36841970	3	4	132	1	0	0	0	0	1	0	0	0	8278	652	23	1	529	1	KIAA1755	20	36841970	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	16815947	36841970	26183550	93	11746											
CABLES2	81928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	60967982	60967982	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagagggcactcaccatgtaCgacgcaaagatgaggacacg	14	4	13	10	3	1	3	1	1	0	2	1	6	1	4	1	2	1	3	1	2	2	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr20:60967982C>G	ENST00000279101.5	-	7	986	c.978G>C	c.(976-978)tcG>tcC	p.S326S		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	326					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCACCATGTACGACGCAAAGA	0.657																																					p.S326S		.											.	CABLES2-91	0			c.G978C						.						140	122	128					20																	60967982		2203	4300	6503	SO:0001819	synonymous_variant	81928	exon7			CATGTACGACGCA	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 150"	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.978G>C	20.37:g.60967982C>G		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	147	52	NM_031215	0	0	0	0	0	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	37	CCDS33503.1	.	.	.	.	.	.	.	.	.	.	C	0.070	-1.204574	0.01568	.	.	ENSG00000149679	ENST00000453274	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.30448	0.0765	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39742	-0.9599	4	.	.	.	-34.41	0.1912	0.00134	0.2752:0.1684:0.22:0.3364	.	.	.	.	P	120	.	.	R	-	2	0	CABLES2	60401377	0.000000	0.05858	0.020000	0.16555	0.052000	0.14988	-2.225000	0.01212	-2.475000	0.00527	-1.774000	0.00658	CGT	.		0.657	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265		G	60967982	C	G	60967982	2	3	132	1	0	0	0	0	0	0	0	1	2536	523	19	4		4	CABLES2	20	60967982	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	24126012	60967982	2057538	94	11747											
DGCR8	54487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	20077782	20077782	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgcaaagatgaatccgttgGtgagtttttgaaggactctt	10	14	12	5	1	1	4	0	3	1	1	2	5	2	5	1	2	1	3	1	2	3	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr22:20077782G>C	ENST00000351989.3	+	5	1735		c.e5+1		DGCR8_ENST00000407755.1_Splice_Site|DGCR8_ENST00000383024.2_Splice_Site	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit						gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					GAATCCGTTGGTGAGTTTTTG	0.532																																					.		.											.	DGCR8-90	0			c.1306+1G>C						.						34	41	38					22																	20077782		2198	4297	6495	SO:0001630	splice_region_variant	54487	exon5			CCGTTGGTGAGTT	AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"chromosome 22 open reading frame 12", "DiGeorge syndrome critical region gene 8"	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.1306+1G>C	22.37:g.20077782G>C		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	57	25	NM_001190326	0	0	0	0	0	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Splice_Site	SNP	ENST00000351989.3	37	CCDS13773.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002878	0.35320	.	.	ENSG00000128191	ENST00000351989;ENST00000383024;ENST00000407755	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.878	0.88830	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DGCR8	18457782	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	9.225000	0.95219	2.618000	0.88619	0.467000	0.42956	.	.		0.532	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1		Intron	C	20077782	G	C	20077782	5	2	132	1	0	0	0	0	0	0	1	0	4475	1275	44	4	1321	4	DGCR8	22	20077782	Splice_Site	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		20077782	31226784	95	11748											
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	46931730	46931730	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctcgtcctccacctcgatGtacacggtggccgtggcact	5	11	10	15	4	1	0	0	0	1	0	5	1	3	0	4	3	1	2	4	3	1	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr22:46931730G>A	ENST00000262738.3	-	1	1337	c.1338C>T	c.(1336-1338)taC>taT	p.Y446Y	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Silent_p.Y446Y	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	446	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CCACCTCGATGTACACGGTGG	0.672																																					p.Y446Y		.											.	CELSR1-525	0			c.C1338T						.						64	39	47					22																	46931730		2198	4295	6493	SO:0001819	synonymous_variant	9620	exon1			CTCGATGTACACG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.1338C>T	22.37:g.46931730G>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	28	9	NM_014246	0	0	3	4	1	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			.		0.672	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46931730	G	A	46931730	2	1	132	1	0	0	0	0	0	0	0	1	3227	1372	48	2		2	CELSR1	22	46931730	Silent	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	26853948	46931730	4372836	96	11749											
KDM5C	8242	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53245084	53245084	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggaaggtcttaggcgatgTtgactccaccttcacatccc	9	10	9	13	1	2	1	1	1	1	0	4	3	4	2	3	3	0	1	3	3	2	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chrX:53245084T>C	ENST00000375401.3	-	7	1388	c.856A>G	c.(856-858)Aca>Gca	p.T286A	KDM5C_ENST00000375383.3_Missense_Mutation_p.T245A|KDM5C_ENST00000452825.3_Missense_Mutation_p.T219A|KDM5C_ENST00000375379.3_Missense_Mutation_p.T286A|KDM5C_ENST00000404049.3_Missense_Mutation_p.T285A|KDM5C-IT1_ENST00000412242.1_RNA	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	286					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						TTAGGCGATGTTGACTCCACC	0.547			"N, F, S"		clear cell renal carcinoma								T|||	1	0.000264901	0	0	3775	,	,		14662	0		0	False		,,,				2504	0.001				p.T286A				Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C-1272	0			c.A856G						.						216	158	177					X																	53245084		2203	4300	6503	SO:0001583	missense	8242	exon7			GCGATGTTGACTC	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	11114	protein-coding gene	gene with protein product		314690	"Jumonji, AT rich interactive domain 1C (RBP2-like)", "Smcy homolog, X-linked (mouse)", "jumonji, AT rich interactive domain 1C", "mental retardation, X-linked 13"	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.856A>G	X.37:g.53245084T>C	ENSP00000364550:p.Thr286Ala	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	106	84	NM_004187	0	0	0	16	16	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	T	0.018	-1.484126	0.01027	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.85629	-2.01;-1.7;-1.7;-1.7;-1.84	5.25	-8.15	0.01065	.	1.077560	0.07053	N	0.832366	T	0.55737	0.1939	N	0.01800	-0.715	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.54886	-0.8226	10	0.07482	T	0.82	0.2577	7.9029	0.29744	0.1202:0.6219:0.1198:0.1381	.	219;285;286	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	A	219;286;285;286;245	ENSP00000445176:T219A;ENSP00000364550:T286A;ENSP00000385394:T285A;ENSP00000364528:T286A;ENSP00000364532:T245A	ENSP00000364528:T286A	T	-	1	0	KDM5C	53261809	0.000000	0.05858	0.222000	0.23844	0.453000	0.32348	-1.761000	0.01805	-1.875000	0.01132	0.430000	0.28490	ACA	.		0.547	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		C	53245084	T	C	53245084	3	2	132	1	0	0	0	0	1	0	0	0	8156	1725	60	3	4004	3	KDM5C	23	53245084	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10		53245084	102025476	97	11750											
ATP11C	286410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	138880882	138880882	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtagctcctttcagcaagAgattttcaggtcccaaagac	11	10	9	11	1	2	2	2	0	0	2	4	3	4	2	2	1	2	3	2	1	3	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chrX:138880882A>C	ENST00000327569.3	-	9	838	c.740T>G	c.(739-741)cTc>cGc	p.L247R	ATP11C_ENST00000460773.1_5'Flank|ATP11C_ENST00000359686.2_Missense_Mutation_p.L247R|ATP11C_ENST00000361648.2_Missense_Mutation_p.L247R|ATP11C_ENST00000370543.1_Missense_Mutation_p.L247R|ATP11C_ENST00000370557.1_Missense_Mutation_p.L244R	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	247					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TTTCAGCAAGAGATTTTCAGG	0.368																																					p.L247R		.											.	ATP11C-198	0			c.T740G						.						61	56	58					X																	138880882		2203	4300	6503	SO:0001583	missense	286410	exon9			AGCAAGAGATTTT	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.740T>G	X.37:g.138880882A>C	ENSP00000332756:p.Leu247Arg	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	59	49	NM_001010986	0	0	0	3	3	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.355898	0.82243	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75	5.62	5.62	0.85841	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.96911	0.8991	H	0.96748	3.875	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.98001	1.0360	10	0.87932	D	0	.	13.8743	0.63643	1.0:0.0:0.0:0.0	.	247;247	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	R	244;247;247;247;247	ENSP00000359588:L244R;ENSP00000355165:L247R;ENSP00000332756:L247R;ENSP00000359574:L247R;ENSP00000352715:L247R	ENSP00000332756:L247R	L	-	2	0	ATP11C	138708548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	1.873000	0.54277	0.481000	0.45027	CTC	.		0.368	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		C	138880882	A	C	138880882	3	2	132	1	0	0	0	0	1	0	0	0	1122	304	11	5	2809	5	ATP11C	23	138880882	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	85635798	138880882	16389678	98	11751											
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	8422784	8422784	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgctttactgtcattgcTggaggtactggcagcgctgg	5	13	13	10	1	2	0	1	0	1	0	2	1	2	1	0	4	5	5	0	4	2	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:8422784T>C	ENST00000337907.3	-	17	2495	c.1861A>G	c.(1861-1863)Agc>Ggc	p.S621G	RERE_ENST00000400907.2_Intron|RERE_ENST00000400908.2_Missense_Mutation_p.S621G|RERE_ENST00000377464.1_Missense_Mutation_p.S353G|RERE_ENST00000476556.1_Missense_Mutation_p.S67G	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	621					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		CTGTCATTGCTGGAGGTACTG	0.577																																					p.S621G		.											.	RERE-515	0			c.A1861G						.						137	114	122					1																	8422784		2203	4300	6503	SO:0001583	missense	473	exon17			CATTGCTGGAGGT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1861A>G	1.37:g.8422784T>C	ENSP00000338629:p.Ser621Gly	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	201	70	NM_012102	0	0	6	7	1	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.838657	0.91117	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T;T	0.64260	-0.09;3.35;1.89;-0.09	5.7	5.7	0.88788	.	.	.	.	.	T	0.77226	0.4099	M	0.67953	2.075	0.80722	D	1	D;D	0.63046	0.992;0.979	D;D	0.76071	0.987;0.982	T	0.78347	-0.2239	9	0.52906	T	0.07	-23.6318	15.138	0.72583	0.0:0.0:0.0:1.0	.	353;621	B1AKN3;Q9P2R6	.;RERE_HUMAN	G	621;353;67;621;41	ENSP00000338629:S621G;ENSP00000366684:S353G;ENSP00000422246:S67G;ENSP00000383700:S621G	ENSP00000338629:S621G	S	-	1	0	RERE	8345371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.644000	0.83416	2.158000	0.67659	0.460000	0.39030	AGC	.		0.577	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			C	8422784	T	C	8422784	3	2	133	1	0	0	0	0	1	0	0	0	13263	1580	55	3	2871	3	RERE	1	8422784	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		8422784	240827837	1	11752											
MFN2	9927	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	12052666	12052667	+	Frame_Shift_Del	DEL	AC	AC	-																															cacagaagaacaggttctggAcgtcaaaggttacctatcca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:12052666_12052667delAC	ENST00000235329.5	+	4	552_553	c.230_231delAC	c.(229-231)gacfs	p.D77fs	MFN2_ENST00000497302.1_3'UTR|MFN2_ENST00000444836.1_Frame_Shift_Del_p.D77fs	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	77					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		CAGGTTCTGGACGTCAAAGGTT	0.525																																					p.77_77del		.											.	MFN2-91	0			c.230_231del						.																																			SO:0001589	frameshift_variant	9927	exon4			.	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.230_231delAC	1.37:g.12052666_12052667delAC	ENSP00000235329:p.Asp77fs	Somatic	472	0		WXS	Illumina HiSeq	Phase_I	347	129	NM_014874	0	0	0	0	0	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Frame_Shift_Del	DEL	ENST00000235329.5	37	CCDS30587.1																																																																																			.		0.525	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		-	12052667	AC	-	12052666	7	5	133	1	0	1	0	1	0	0	0	0	9549	275	10	0	236	0	MFN2	1	12052666	Frame_Shift_Del	DEL	AC	TCGA-HE-A5NI-01A-11D-A26P-10	3629882	12052666	237197955	2	11753											
SPEN	23013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	16260463	16260463	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccccgcccccgccagtTgactctaaaaagcctttaga	10	7	9	15	2	1	2	0	1	1	1	1	3	1	2	6	1	1	1	6	1	4	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:16260463T>G	ENST00000375759.3	+	11	7932	c.7728T>G	c.(7726-7728)gtT>gtG	p.V2576V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2576	RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCCCGCCAGTTGACTCTAAAA	0.527																																					p.V2576V		.											.	SPEN-298	0			c.T7728G						.						72	83	79					1																	16260463		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			GCCAGTTGACTCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.7728T>G	1.37:g.16260463T>G		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	25	10	NM_015001	0	0	2	2	0	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	37	CCDS164.1																																																																																			.		0.527	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16260463	T	G	16260463	2	3	133	1	0	0	0	0	0	0	0	1	15070	1799	63	5		5	SPEN	1	16260463	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	4207797	16260463	232990158	3	11754											
AKR7A3	22977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19611546	19611546	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcatagaacctcagtccAaagtgcctgaggcaggggaa	14	5	13	9	0	1	2	1	1	0	1	2	3	2	3	3	4	2	2	3	4	5	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:19611546A>G	ENST00000361640.4	-	4	1110	c.570T>C	c.(568-570)ttT>ttC	p.F190F		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	190					cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACCTCAGTCCAAAGTGCCTGA	0.612																																					p.F190F		.											.	AKR7A3-90	0			c.T570C						.						94	96	95					1																	19611546		2199	4300	6499	SO:0001819	synonymous_variant	22977	exon4			CAGTCCAAAGTGC	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"Aldo-keto reductases"	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.570T>C	1.37:g.19611546A>G		Somatic	338	0		WXS	Illumina HiSeq	Phase_I	296	116	NM_012067	0	0	64	119	55	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	37	CCDS193.1																																																																																			.		0.612	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067		G	19611546	A	G	19611546	2	3	133	1	0	0	0	0	0	0	0	1	476	127	5	3		3	AKR7A3	1	19611546	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	3351083	19611546	229639075	4	11755											
RAP1GAP	5909	bcgsc.ca	37	chr1	21952821	21952821	+	5'UTR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtagagtgaaggagtataGgagggaactaagttcactcg	13	8	16	4	1	1	2	1	1	0	1	2	5	1	5	0	4	1	3	0	4	6	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:21952821G>T	ENST00000374765.4	-	0	158				RAP1GAP_ENST00000290101.4_Silent_p.S50S|RAP1GAP_ENST00000542643.2_5'UTR|RAP1GAP_ENST00000374757.3_5'UTR	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein						GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		AAGGAGTATAGGAGGGAACTA	0.577																																					p.S50S													.	RAP1GAP-245	0			c.C150A						.						131	128	129					1																	21952821		1568	3582	5150	SO:0001623	5_prime_UTR_variant	5909	exon3			AGTATAGGAGGGA	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"RAP1, GTPase activating protein 1"	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.-43C>A	1.37:g.21952821G>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_1	47	4	NM_001145658	0	0	1	1	0	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			.		0.577	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		T	21952821	G	T	21952821	1	4	133	0	1	0	0	0	0	0	0	0	13069	987	35	4		4	RAP1GAP	1	21952821	5'UTR	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	2341275	21952821	227297800	5	11756											
ZMYM1	79830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	35569920	35569920	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attttaaatccaaaggatgtGattagtgtccagctggaaga	14	12	10	5	0	0	2	0	1	0	1	2	4	2	4	2	2	1	1	2	2	5	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:35569920G>C	ENST00000373330.1	+	6	618	c.444G>C	c.(442-444)gtG>gtC	p.V148V	ZMYM1_ENST00000373329.1_3'UTR|ZMYM1_ENST00000359858.4_Silent_p.V148V			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	148						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CAAAGGATGTGATTAGTGTCC	0.308																																					p.V148V		.											.	ZMYM1-90	0			c.G444C						.						41	40	41					1																	35569920		1830	4087	5917	SO:0001819	synonymous_variant	79830	exon5			GGATGTGATTAGT	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.444G>C	1.37:g.35569920G>C		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	78	31	NM_024772	0	0	1	3	2	D3DPR7|Q7Z3Q4	Silent	SNP	ENST00000373330.1	37	CCDS41302.1																																																																																			.		0.308	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		C	35569920	G	C	35569920	2	2	133	1	0	0	0	0	0	0	0	1	17731	1277	45	4		4	ZMYM1	1	35569920	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	13617099	35569920	213680701	6	11757											
EPS15	2060	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	51946986	51946986	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacaggattcccacttgataActgaaataaacacattaata	18	11	4	8	0	0	2	0	2	0	0	1	3	1	3	1	1	3	0	1	1	7	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:51946986A>C	ENST00000371733.3	-	2	130	c.34T>G	c.(34-36)Tta>Gta	p.L12V	EPS15_ENST00000371730.2_Splice_Site_p.L12V	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	12	Interaction with DAB2. {ECO:0000250}.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)			endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						CCACTTGATAACTGAAATAAA	0.274			T	MLL	ALL																																p.L12V				Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	EPS15-1082	0			c.T34G						.						52	53	53					1																	51946986		2200	4296	6496	SO:0001630	splice_region_variant	2060	exon2			TTGATAACTGAAA	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.34-1T>G	1.37:g.51946986A>C		Somatic	126	1		WXS	Illumina HiSeq	Phase_I	88	31	NM_001981	0	0	0	0	0	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	.	.	.	.	.	.	.	.	.	.	A	11.39	1.624296	0.28889	.	.	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000371727	T;T	0.25749	1.87;1.78	5.0	3.81	0.43845	EPS15 homology (EH) (1);	0.000000	0.26478	N	0.024144	T	0.39655	0.1086	M	0.75264	2.295	0.80722	D	1	D;D	0.67145	0.993;0.996	D;D	0.75484	0.967;0.986	T	0.56080	-0.8038	10	0.02654	T	1	.	6.4196	0.21736	0.7757:0.0:0.2243:0.0	.	12;12	B1AUU8;P42566	.;EPS15_HUMAN	V	12	ENSP00000360795:L12V;ENSP00000360798:L12V	ENSP00000360792:L12V	L	-	1	2	EPS15	51719574	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.897000	0.39799	0.930000	0.37217	0.533000	0.62120	TTA	.		0.274	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	Missense_Mutation	C	51946986	A	C	51946986	5	2	133	1	0	0	0	0	0	0	1	0	5205	57	2	5	2850	5	EPS15	1	51946986	Splice_Site	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	16377066	51946986	197303635	7	11758											
ATG4C	84938	broad.mit.edu;bcgsc.ca	37	chr1	63284805	63284806	+	Frame_Shift_Ins	INS	-	-	A																															agagaattcaaaaccccaacINSaatttctctgaaggaaacaa																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:63284805_63284806insA	ENST00000317868.4	+	5	731_732	c.524_525insA	c.(523-528)acaattfs	p.I176fs	ATG4C_ENST00000371120.3_Frame_Shift_Ins_p.I176fs	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	176					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						AAAACCCCAACAATTTCTCTGA	0.366																																					p.T175fs													.	ATG4C-91	0			c.524_525insA						.																																			SO:0001589	frameshift_variant	84938	exon5			CCCCAACAATTTC	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog C (S. cerevisiae)", "ATG4 autophagy related 4 homolog C (S. cerevisiae)"	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.526dupA	1.37:g.63284807_63284807dupA	ENSP00000322159:p.Ile176fs	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	34	9	NM_178221	0	0	0	0	0	A6NLR8|D3DQ58|Q96K04	Frame_Shift_Ins	INS	ENST00000317868.4	37	CCDS623.1																																																																																			.		0.366	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		A	63284806	-	A	63284805	7	5	133	1	0	1	1	0	0	0	0	0	1099	478	17	0	538	0	ATG4C	1	63284805	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	11337819	63284805	185965816	8	11759											
FAM46C	54855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	118165851	118165851	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttcccttctgaacttcctgCcagagggtgtgaacaagctc	8	11	10	12	0	1	3	0	2	1	1	4	3	3	3	3	1	4	2	3	1	3	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:118165851C>G	ENST00000369448.3	+	2	608	c.361C>G	c.(361-363)Cca>Gca	p.P121A		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	121										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		GAACTTCCTGCCAGAGGGTGT	0.502			"Mis, F, O"		MM					Multiple Myeloma(3;1.13e-06)																											p.P121A		.		Rec	yes		1	1p12	54855	"family with sequence similarity 46, member C"		L	.	FAM46C-90	0			c.C361G						.						104	106	105					1																	118165851		2203	4300	6503	SO:0001583	missense	54855	exon2			TTCCTGCCAGAGG	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.361C>G	1.37:g.118165851C>G	ENSP00000358458:p.Pro121Ala	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	146	64	NM_017709	0	0	0	0	0	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.877619	0.72294	.	.	ENSG00000183508	ENST00000369448	T	0.46819	0.86	5.75	5.75	0.90469	Domain of unknown function DUF1693 (1);	0.000000	0.64402	D	0.000002	T	0.70456	0.3226	M	0.87971	2.92	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.74850	-0.3524	10	0.72032	D	0.01	-31.2719	18.9258	0.92544	0.0:1.0:0.0:0.0	.	121	Q5VWP2	FA46C_HUMAN	A	121	ENSP00000358458:P121A	ENSP00000358458:P121A	P	+	1	0	FAM46C	117967374	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.818000	0.86416	2.711000	0.92665	0.655000	0.94253	CCA	.		0.502	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709		G	118165851	C	G	118165851	3	3	133	1	0	0	0	0	1	0	0	0	5586	739	26	4	363	4	FAM46C	1	118165851	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	54881046	118165851	131084770	9	11760											
ZC3H11A	9877	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	203819761	203819761	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgccgctgtgaagccactCagctccagcagtgtcctaca	9	9	9	14	1	1	1	1	1	0	0	3	1	3	1	4	0	5	3	4	0	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:203819761C>T	ENST00000545588.1	+	15	5885	c.2058C>T	c.(2056-2058)ctC>ctT	p.L686L	ZC3H11A_ENST00000367214.1_Silent_p.L686L|ZC3H11A_ENST00000367210.1_Silent_p.L686L|ZC3H11A_ENST00000367212.3_Silent_p.L686L|ZC3H11A_ENST00000332127.4_Silent_p.L686L	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	686					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TGAAGCCACTCAGCTCCAGCA	0.502																																					p.L686L		.											.	ZC3H11A-515	0			c.C2058T						.						80	80	80					1																	203819761		2203	4300	6503	SO:0001819	synonymous_variant	9877	exon18			GCCACTCAGCTCC		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"Zinc fingers, CCCH-type domain containing"	29093	protein-coding gene	gene with protein product		613513	"zinc finger CCCH-type domain containing 11A"	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.2058C>T	1.37:g.203819761C>T		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	142	62	NM_014827	0	0	22	43	21	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Silent	SNP	ENST00000545588.1	37	CCDS30978.1																																																																																			.		0.502	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827		T	203819761	C	T	203819761	2	4	133	1	0	0	0	0	0	0	0	1	17592	813	29	2		2	ZC3H11A	1	203819761	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	85653910	203819761	45430860	10	11761											
NUAK2	81788	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	205272646	205272646	+	Frame_Shift_Del	DEL	G	G	-																															cacctcctggcagtctgtcaGggaaaagcagctgtccccca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:205272646delG	ENST00000367157.3	-	7	1945	c.1819delC	c.(1819-1821)ctgfs	p.L607fs		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CAGTCTGTCAGGGAAAAGCAG	0.642																																					p.L607X		.											.	NUAK2-391	0			c.1819delC						.						55	53	54					1																	205272646		2203	4300	6503	SO:0001589	frameshift_variant	81788	exon7			.	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"SNF1/AMP activated protein kinase"	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1819delC	1.37:g.205272646delG	ENSP00000356125:p.Leu607fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	85	32	NM_030952	0	0	0	0	0		Nonsense_Mutation	DEL	ENST00000367157.3	37	CCDS1453.1																																																																																			.		0.642	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		-	205272646	G	-	205272646	7	5	133	1	0	1	0	1	0	0	0	0	10739	991	35	0	71	0	NUAK2	1	205272646	Frame_Shift_Del	DEL	G	TCGA-HE-A5NI-01A-11D-A26P-10	1452885	205272646	43977975	11	11762											
PLXNA2	5362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	208213052	208213052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtgatggcatcaatggggcCcttctccatctgctgcttga	6	12	11	12	1	3	2	1	2	2	0	4	2	3	2	2	3	2	3	2	3	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:208213052C>T	ENST00000367033.3	-	24	5171	c.4414G>A	c.(4414-4416)Ggc>Agc	p.G1472S		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1472					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TCAATGGGGCCCTTCTCCATC	0.622																																					p.G1472S		.											.	PLXNA2-92	0			c.G4414A						.						96	88	91					1																	208213052		2203	4300	6503	SO:0001583	missense	5362	exon24			TGGGGCCCTTCTC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4414G>A	1.37:g.208213052C>T	ENSP00000356000:p.Gly1472Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	111	31	NM_025179	0	0	2	2	0	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.938808	0.97122	.	.	ENSG00000076356	ENST00000367033	T	0.35789	1.29	5.51	5.51	0.81932	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.71745	0.3376	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79752	-0.1671	10	0.87932	D	0	.	19.4545	0.94882	0.0:1.0:0.0:0.0	.	1472	O75051	PLXA2_HUMAN	S	1472	ENSP00000356000:G1472S	ENSP00000356000:G1472S	G	-	1	0	PLXNA2	206279675	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.538000	0.82048	2.590000	0.87494	0.650000	0.86243	GGC	.		0.622	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208213052	C	T	208213052	3	4	133	1	0	0	0	0	1	0	0	0	12146	623	22	2	1306	2	PLXNA2	1	208213052	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	2940406	208213052	41037569	12	11763											
CAPN2	824	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	223900487	223900487	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgggacgctcttccaggacCcgtccttcccggccatcccc	4	7	9	21	4	1	0	0	0	1	0	5	2	5	2	8	3	0	1	8	3	0	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:223900487C>A	ENST00000295006.5	+	1	454	c.145C>A	c.(145-147)Ccg>Acg	p.P49T	CAPN2_ENST00000433674.2_Intron	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	49	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CTTCCAGGACCCGTCCTTCCC	0.672																																					p.P49T		.											.	CAPN2-523	0			c.C145A						.						24	24	24					1																	223900487		2201	4297	6498	SO:0001583	missense	824	exon1			CAGGACCCGTCCT	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"EF-hand domain containing"	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.145C>A	1.37:g.223900487C>A	ENSP00000295006:p.Pro49Thr	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	71	30	NM_001748	0	0	5	9	4	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.935915	0.52972	.	.	ENSG00000162909	ENST00000295006;ENST00000366869	T	0.49432	0.78	3.88	3.88	0.44766	Peptidase C2, calpain, catalytic domain (3);	0.526246	0.19489	U	0.113025	T	0.54046	0.1834	M	0.81112	2.525	0.24034	N	0.996105	B	0.34214	0.442	B	0.39094	0.29	T	0.54556	-0.8276	10	0.54805	T	0.06	.	12.5002	0.55952	0.0:0.6877:0.3123:0.0	.	49	P17655	CAN2_HUMAN	T	49;78	ENSP00000295006:P49T	ENSP00000295006:P49T	P	+	1	0	CAPN2	221967110	0.000000	0.05858	0.913000	0.36048	0.489000	0.33432	0.484000	0.22308	1.862000	0.54008	0.491000	0.48974	CCG	.		0.672	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		A	223900487	C	A	223900487	3	1	133	1	0	0	0	0	1	0	0	0	2633	623	22	4	154	4	CAPN2	1	223900487	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	15687435	223900487	25350134	13	11764											
ASXL2	55252	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	25972919	25972919	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgtggtgagatggttcttCtcagattcctgttcagcaga	7	14	12	8	0	3	3	2	1	2	3	5	4	4	3	1	2	1	4	1	2	0	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:25972919C>T	ENST00000435504.4	-	12	1799	c.1506G>A	c.(1504-1506)gaG>gaA	p.E502E	ASXL2_ENST00000272341.4_Silent_p.E242E|ASXL2_ENST00000404843.1_Silent_p.E242E|ASXL2_ENST00000336112.4_Silent_p.E474E			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	502					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGGTTCTTCTCAGATTCCT	0.443																																					p.E502E		.											.	ASXL2-23	0			c.G1506A						.						148	136	140					2																	25972919		1903	4132	6035	SO:0001819	synonymous_variant	55252	exon11			GTTCTTCTCAGAT			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"additional sex combs like 2 (Drosophila)"			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.1506G>A	2.37:g.25972919C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	57	29	NM_018263	0	0	0	0	0	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Silent	SNP	ENST00000435504.4	37																																																																																				.		0.443	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		T	25972919	C	T	25972919	2	4	133	1	0	0	0	0	0	0	0	1	1068	912	32	2		2	ASXL2	2	25972919	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10		25972919	217226454	14	11765											
HADHA	3030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	26427053	26427053	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatcagccctgcaccaagAatagccagatgcctgcaagg	12	5	9	15	0	1	2	1	0	0	2	1	2	1	2	5	1	5	2	5	1	4	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:26427053A>C	ENST00000380649.3	-	12	1227	c.1098T>G	c.(1096-1098)atT>atG	p.I366M		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	366					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGCACCAAGAATAGCCAGAT	0.468																																					p.I366M		.											.	HADHA-91	0			c.T1098G						.						223	216	219					2																	26427053		2203	4300	6503	SO:0001583	missense	3030	exon12			ACCAAGAATAGCC	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1098T>G	2.37:g.26427053A>C	ENSP00000370023:p.Ile366Met	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	131	36	NM_000182	0	0	0	0	0	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	37	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521115	0.64747	.	.	ENSG00000084754	ENST00000380649	T	0.81163	-1.46	5.0	3.85	0.44370	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.398782	0.28834	N	0.013995	D	0.83454	0.5258	M	0.65677	2.01	0.80722	D	1	P;P	0.40731	0.728;0.728	P;P	0.57057	0.812;0.812	T	0.81743	-0.0793	10	0.66056	D	0.02	-14.6089	1.9477	0.03360	0.5809:0.166:0.0927:0.1603	.	366;366	E9KL44;P40939	.;ECHA_HUMAN	M	366	ENSP00000370023:I366M	ENSP00000370023:I366M	I	-	3	3	HADHA	26280557	0.998000	0.40836	0.972000	0.41901	0.988000	0.76386	0.641000	0.24720	0.867000	0.35654	0.533000	0.62120	ATT	.		0.468	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26427053	A	C	26427053	3	2	133	1	0	0	0	0	1	0	0	0	6964	242	9	5	1229	5	HADHA	2	26427053	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	454134	26427053	216772320	15	11766											
TET3	200424	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74320721	74320721	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaaggacggcccttcgcgggGgtcacggcctgcatggactt	6	7	16	12	4	1	0	1	0	0	0	2	3	1	2	2	6	1	1	2	6	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:74320721G>T	ENST00000409262.3	+	7	2790	c.2790G>T	c.(2788-2790)ggG>ggT	p.G930G		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	930					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCTTCGCGGGGGTCACGGCCT	0.597																																					p.G930G		.											.	.	0			c.G2790T						.						71	76	74					2																	74320721		2052	4226	6278	SO:0001819	synonymous_variant	200424	exon7			CGCGGGGGTCACG		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"tet oncogene family member 3"			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.2790G>T	2.37:g.74320721G>T		Somatic	159	0		WXS	Illumina HiSeq	Phase_I	152	46	NM_144993	0	0	2	2	0	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																			.		0.597	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74320721	G	T	74320721	2	4	133	1	0	0	0	0	0	0	0	1	15803	1219	43	4		4	TET3	2	74320721	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	47893668	74320721	168878652	16	11767											
MAP4K4	9448	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	102493592	102493592	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtacttgagggcttgaatgtCttggtgacaatatctggtga	9	14	13	5	0	2	4	0	4	2	0	2	4	2	4	0	3	1	2	0	3	4	5	rs575144210		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:102493592C>G	ENST00000347699.4	+	24	2934	c.2934C>G	c.(2932-2934)gtC>gtG	p.V978V	MAP4K4_ENST00000324219.4_Silent_p.V1059V|MAP4K4_ENST00000350198.4_Silent_p.V897V|MAP4K4_ENST00000302217.5_Silent_p.V781V|MAP4K4_ENST00000413150.2_Silent_p.V893V|MAP4K4_ENST00000456652.1_Silent_p.V777V|MAP4K4_ENST00000350878.4_Silent_p.V1018V|MAP4K4_ENST00000425019.1_Silent_p.V1011V	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	978	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.|Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GCTTGAATGTCTTGGTGACAA	0.418													C|||	1	0.000199681	0	0	5008	,	,		22716	0.001		0	False		,,,				2504	0				p.V1012V		.											.	MAP4K4-547	0			c.C3036G						.						180	173	175					2																	102493592		1970	4164	6134	SO:0001819	synonymous_variant	9448	exon25			GAATGTCTTGGTG	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6866	protein-coding gene	gene with protein product	"HPK/GCK-like kinase", "hepatocyte progenitor kinase-like/germinal center kinase-like kinase"	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2934C>G	2.37:g.102493592C>G		Somatic	311	0		WXS	Illumina HiSeq	Phase_I	420	124	NM_145686	0	0	7	7	0	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	8.328	0.825853	0.16749	.	.	ENSG00000071054	ENST00000421882	.	.	.	5.48	1.44	0.22558	.	.	.	.	.	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43972	-0.9358	4	.	.	.	.	6.5872	0.22626	0.1267:0.6675:0.0:0.2057	.	.	.	.	V	795	.	.	L	+	1	0	MAP4K4	101860024	1.000000	0.71417	0.986000	0.45419	0.981000	0.71138	1.591000	0.36665	0.368000	0.24481	-0.136000	0.14681	CTT	.		0.418	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		G	102493592	C	G	102493592	2	3	133	1	0	0	0	0	0	0	0	1	9287	900	32	4		4	MAP4K4	2	102493592	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	28172871	102493592	140705781	17	11768											
NPHP1	4867	broad.mit.edu	37	chr2	110936067	110936067	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgggtaagcttgtccaaaaGagtatgctcctcttcttttc	8	16	8	9	0	2	1	0	0	2	1	5	1	4	1	2	1	2	4	2	1	4	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:110936067G>A	ENST00000393272.3	-	4	359	c.262C>T	c.(262-264)Ctt>Ttt	p.L88F	NPHP1_ENST00000316534.4_Missense_Mutation_p.L88F|NPHP1_ENST00000418527.1_Missense_Mutation_p.L88F|NPHP1_ENST00000445609.2_Missense_Mutation_p.L88F|NPHP1_ENST00000355301.4_Intron|NPHP1_ENST00000417665.1_Missense_Mutation_p.L88F	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	88					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						TTGTCCAAAAGAGTATGCTCC	0.358																																					p.L88F													.	NPHP1-92	0			c.C262T						.						165	149	154					2																	110936067		2203	4300	6503	SO:0001583	missense	4867	exon4			CCAAAAGAGTATG	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.262C>T	2.37:g.110936067G>A	ENSP00000376953:p.Leu88Phe	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_207181	0	0	5	5	0	O14837	Missense_Mutation	SNP	ENST00000393272.3	37	CCDS46385.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.916016	0.52546	.	.	ENSG00000144061	ENST00000316534;ENST00000445609;ENST00000393272;ENST00000417665;ENST00000418527	T;T;T;T	0.62639	0.01;0.04;0.01;0.04	5.57	2.59	0.31030	.	0.325851	0.28488	N	0.015164	T	0.69815	0.3153	L	0.56769	1.78	0.19575	N	0.999963	P;P;D;P;P;D	0.71674	0.868;0.947;0.998;0.868;0.919;0.977	B;P;D;B;B;P	0.69142	0.23;0.642;0.962;0.383;0.406;0.847	T	0.57860	-0.7738	10	0.39692	T	0.17	-10.1049	8.3457	0.32272	0.0775:0.0:0.6507:0.2718	.	88;88;88;88;88;88	B4DQY0;C9JNM7;C9J082;O15259;O15259-2;O15259-4	.;.;.;NPHP1_HUMAN;.;.	F	88	ENSP00000313169:L88F;ENSP00000389879:L88F;ENSP00000376953:L88F;ENSP00000402176:L88F	ENSP00000313169:L88F	L	-	1	0	NPHP1	110293356	0.499000	0.26083	0.400000	0.26346	0.901000	0.52897	1.117000	0.31234	0.800000	0.34041	0.655000	0.94253	CTT	.		0.358	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		A	110936067	G	A	110936067	3	1	133	1	0	0	0	0	1	0	0	0	10605	942	33	2	2007	2	NPHP1	2	110936067	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	8442475	110936067	132263306	18	11769											
ZC3H6	376940	broad.mit.edu;bcgsc.ca	37	chr2	113067649	113067649	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caatcagctgaaacaatacaGgcaagctaaagaaacctcaa	20	5	6	10	0	2	2	2	1	0	1	2	2	2	2	1	1	5	3	1	1	9	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:113067649G>A	ENST00000409871.1	+	4	925	c.524G>A	c.(523-525)aGg>aAg	p.R175K	ZC3H6_ENST00000343936.4_Missense_Mutation_p.R175K	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	175							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AAACAATACAGGCAAGCTAAA	0.378																																					p.R175K													.	ZC3H6-93	0			c.G524A						.						81	75	77					2																	113067649		1854	4104	5958	SO:0001583	missense	376940	exon4			AATACAGGCAAGC	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.524G>A	2.37:g.113067649G>A	ENSP00000386764:p.Arg175Lys	Somatic	270	1		WXS	Illumina HiSeq	Phase_I	321	31	NM_198581	0	0	0	0	0	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	37	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805777	0.70682	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.15603	2.41;2.41	5.86	5.86	0.93980	.	0.213150	0.44285	D	0.000480	T	0.39172	0.1068	M	0.62016	1.91	0.37302	D	0.908746	D	0.61697	0.99	P	0.61070	0.883	T	0.10636	-1.0621	10	0.46703	T	0.11	-26.5479	20.1828	0.98210	0.0:0.0:1.0:0.0	.	175	P61129	ZC3H6_HUMAN	K	175;175;152	ENSP00000386764:R175K;ENSP00000340298:R175K	ENSP00000340298:R175K	R	+	2	0	ZC3H6	112784120	1.000000	0.71417	0.998000	0.56505	0.939000	0.58152	4.052000	0.57420	2.767000	0.95098	0.561000	0.74099	AGG	.		0.378	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		A	113067649	G	A	113067649	3	1	133	1	0	0	0	0	1	0	0	0	17603	1000	35	2	538	2	ZC3H6	2	113067649	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	2131582	113067649	130131724	19	11770											
CCDC74B	91409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	130899739	130899739	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggacttgacagactggaagcTtgacgtggagaggctgtctg	9	9	16	7	1	1	4	0	2	1	2	1	7	1	6	0	4	1	2	0	4	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:130899739T>G	ENST00000310463.6	-	3	648	c.511A>C	c.(511-513)Agc>Cgc	p.S171R	CCDC74B_ENST00000409128.1_Missense_Mutation_p.S147R|CCDC74B_ENST00000409943.3_Missense_Mutation_p.S105R|MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000392984.3_Missense_Mutation_p.S273R	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	171										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					GACTGGAAGCTTGACGTGGAG	0.647																																					p.S171R		.											.	CCDC74B-90	0			c.A511C						.						98	73	81					2																	130899739		2201	4298	6499	SO:0001583	missense	91409	exon3			GGAAGCTTGACGT		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.511A>C	2.37:g.130899739T>G	ENSP00000308873:p.Ser171Arg	Somatic	383	1		WXS	Illumina HiSeq	Phase_I	433	205	NM_207310	0	0	0	2	2	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	37	CCDS2155.1	.	.	.	.	.	.	.	.	.	.	.	13.91	2.377052	0.42105	.	.	ENSG00000152076	ENST00000409943;ENST00000310463;ENST00000392984;ENST00000409488;ENST00000409128	T;T;T;T	0.57273	1.77;1.86;1.79;0.41	2.21	2.21	0.28008	.	0.538074	0.15538	U	0.257135	T	0.62134	0.2403	M	0.69823	2.125	0.09310	N	1	D;D;D	0.71674	0.995;0.998;0.991	P;P;P	0.61070	0.763;0.862;0.883	T	0.48822	-0.9001	10	0.42905	T	0.14	-14.6217	6.277	0.20987	0.0:0.0:0.0:1.0	.	273;105;171	E7ESC5;Q96LY2-2;Q96LY2	.;.;CC74B_HUMAN	R	105;171;273;105;147	ENSP00000386294:S105R;ENSP00000308873:S171R;ENSP00000376710:S273R;ENSP00000386644:S147R	ENSP00000308873:S171R	S	-	1	0	CCDC74B	130616209	0.427000	0.25514	0.007000	0.13788	0.018000	0.09664	2.792000	0.47837	1.010000	0.39314	0.248000	0.18094	AGC	.		0.647	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		G	130899739	T	G	130899739	3	3	133	1	0	0	0	0	1	0	0	0	2854	1609	56	5	655	5	CCDC74B	2	130899739	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	17832090	130899739	112299634	20	11771											
SF3B1	23451	broad.mit.edu;bcgsc.ca	37	chr2	198285209	198285209	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggtccgcctatgcttttTgtattcatcttcccggtctg	4	17	8	12	2	3	0	1	0	2	0	5	0	5	0	3	2	1	2	3	2	2	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:198285209T>G	ENST00000335508.6	-	4	449	c.358A>C	c.(358-360)Aaa>Caa	p.K120Q	SF3B1_ENST00000487698.1_Missense_Mutation_p.K120Q|SF3B1_ENST00000409915.4_Missense_Mutation_p.K120Q|SF3B1_ENST00000414963.2_Missense_Mutation_p.K120Q	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	120					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTATGCTTTTTGTATTCATCT	0.368			Mis		myelodysplastic syndrome																																p.K120Q				Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.A358C						.						178	174	175					2																	198285209		2203	4300	6503	SO:0001583	missense	23451	exon4			GCTTTTTGTATTC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.358A>C	2.37:g.198285209T>G	ENSP00000335321:p.Lys120Gln	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	242	9	NM_012433	0	0	30	30	0	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	13.16	2.153467	0.38021	.	.	ENSG00000115524	ENST00000335508;ENST00000409915;ENST00000414963;ENST00000487698	.	.	.	6.06	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.26955	0.0660	N	0.02539	-0.55	0.58432	D	0.999998	D;D;B	0.54964	0.969;0.969;0.001	P;P;B	0.50314	0.556;0.637;0.002	T	0.25467	-1.0131	9	0.02654	T	1	.	12.5268	0.56091	0.1251:0.0:0.0:0.8749	.	120;120;120	B4DGZ4;E9PCH3;O75533	.;.;SF3B1_HUMAN	Q	120	.	ENSP00000335321:K120Q	K	-	1	0	SF3B1	197993454	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.111000	0.71541	1.076000	0.40961	0.523000	0.50628	AAA	.		0.368	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			G	198285209	T	G	198285209	3	3	133	1	0	0	0	0	1	0	0	0	14181	1821	63	5	3668	5	SF3B1	2	198285209	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	67385470	198285209	44914164	21	11772											
C2orf69	205327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	200790075	200790075	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatcaaagaaaagtttgaaTgtttggaataaggactccat	16	13	8	4	0	1	2	1	1	0	1	2	4	2	4	1	2	0	2	1	2	7	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:200790075T>A	ENST00000319974.5	+	2	807	c.624T>A	c.(622-624)aaT>aaA	p.N208K	C2orf69_ENST00000491721.1_Intron	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	208						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						AAAGTTTGAATGTTTGGAATA	0.348																																					p.N208K		.											.	C2orf69-23	0			c.T624A						.						52	52	52					2																	200790075		1819	4078	5897	SO:0001583	missense	205327	exon2			TTTGAATGTTTGG		CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"hypothetical protein FLJ38973"					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.624T>A	2.37:g.200790075T>A	ENSP00000312770:p.Asn208Lys	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_153689	0	0	0	0	0	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	37	CCDS46482.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.923247	0.00498	.	.	ENSG00000178074	ENST00000319974	.	.	.	5.5	-1.14	0.09741	.	0.634163	0.16276	N	0.221571	T	0.06050	0.0157	N	0.01048	-1.04	0.09310	N	0.999996	B	0.06786	0.001	B	0.08055	0.003	T	0.29518	-1.0009	9	0.05620	T	0.96	-2.3723	1.9048	0.03275	0.1333:0.2218:0.111:0.5339	.	208	Q8N8R5	CB069_HUMAN	K	208	.	ENSP00000312770:N208K	N	+	3	2	C2orf69	200498320	0.999000	0.42202	0.155000	0.22561	0.064000	0.16182	0.773000	0.26661	-0.325000	0.08577	-0.250000	0.11733	AAT	.		0.348	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689		A	200790075	T	A	200790075	3	1	133	1	0	0	0	0	1	0	0	0	2194	1461	51	5	630	5	C2orf69	2	200790075	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	2504866	200790075	42409298	22	11773											
CLK1	1195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	201721517	201721517	+	Frame_Shift_Del	DEL	G	G	-																															ttaatatctggatttattaaGgtgcgttcatcacgtttctg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:201721517delG	ENST00000321356.4	-	9	1080	c.945delC	c.(943-945)accfs	p.T315fs	CLK1_ENST00000409769.2_Frame_Shift_Del_p.T138fs|CLK1_ENST00000434813.2_Frame_Shift_Del_p.T357fs	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	315	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GATTTATTAAGGTGCGTTCAT	0.328																																					p.T357fs		.											.	CLK1-784	0			c.1071delC						.						163	159	161					2																	201721517		2202	4300	6502	SO:0001589	frameshift_variant	1195	exon9			.	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.945delC	2.37:g.201721517delG	ENSP00000326830:p.Thr315fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	164	98	NM_001162407	0	0	0	0	0	B4DFW7|Q0P694|Q8N5V8	Frame_Shift_Del	DEL	ENST00000321356.4	37	CCDS2331.1																																																																																			.		0.328	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			-	201721517	G	-	201721517	7	5	133	1	0	1	0	1	0	0	0	0	3542	987	35	0	529	0	CLK1	2	201721517	Frame_Shift_Del	DEL	G	TCGA-HE-A5NI-01A-11D-A26P-10	931442	201721517	41477856	23	11774											
ORC2L	4999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	201778083	201778083	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcccggagtgtcagatcacTattgacgaggaatgcctccc	9	8	12	12	2	2	2	2	1	0	1	3	5	3	4	3	3	1	0	3	3	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:201778083T>A	ENST00000234296.2	-	17	1831	c.1582A>T	c.(1582-1584)Agt>Tgt	p.S528C		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	528					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						GTCAGATCACTATTGACGAGG	0.428																																					p.S528C		.											.	ORC2-209	0			c.A1582T						.						101	95	97					2																	201778083		2203	4300	6503	SO:0001583	missense	4999	exon17			GATCACTATTGAC		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1582A>T	2.37:g.201778083T>A	ENSP00000234296:p.Ser528Cys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	76	42	NM_006190	0	0	3	12	9	Q13204|Q53TX5	Missense_Mutation	SNP	ENST00000234296.2	37	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.506382	0.85282	.	.	ENSG00000115942	ENST00000234296	T	0.52057	0.68	5.6	5.6	0.85130	.	0.091390	0.85682	D	0.000000	T	0.76190	0.3953	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82835	-0.0261	10	0.87932	D	0	-13.9094	15.7889	0.78338	0.0:0.0:0.0:1.0	.	528	Q13416	ORC2_HUMAN	C	528	ENSP00000234296:S528C	ENSP00000234296:S528C	S	-	1	0	ORC2	201486328	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.057000	0.71119	2.116000	0.64780	0.482000	0.46254	AGT	.		0.428	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		A	201778083	T	A	201778083	3	1	133	1	0	0	0	0	1	0	0	0	11288	1522	53	5	159	5	ORC2L	2	201778083	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	56566	201778083	41421290	24	11775											
FN1	2335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	216271073	216271073	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtgacttctgcaaaggtgttCctgctgatgggcagcctctg	6	12	13	10	0	2	2	0	2	2	0	3	2	3	2	2	2	3	4	2	2	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:216271073C>T	ENST00000359671.1	-	19	3139	c.2874G>A	c.(2872-2874)agG>agA	p.R958R	FN1_ENST00000443816.1_Silent_p.R958R|FN1_ENST00000446046.1_Silent_p.R958R|FN1_ENST00000357009.2_Silent_p.R958R|FN1_ENST00000356005.4_Silent_p.R958R|FN1_ENST00000357867.4_Silent_p.R958R|FN1_ENST00000336916.4_Silent_p.R958R|FN1_ENST00000346544.3_Silent_p.R958R|FN1_ENST00000421182.1_Silent_p.R958R|FN1_ENST00000345488.5_Silent_p.R958R|FN1_ENST00000354785.4_Silent_p.R958R|FN1_ENST00000323926.6_Silent_p.R958R|FN1_ENST00000432072.2_Silent_p.R958R			P02751	FINC_HUMAN	fibronectin 1	958	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CAAAGGTGTTCCTGCTGATGG	0.597																																					p.R958R		.											.	FN1-584	0			c.G2874A						.						63	62	63					2																	216271073		2203	4300	6503	SO:0001819	synonymous_variant	2335	exon19			GGTGTTCCTGCTG		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2874G>A	2.37:g.216271073C>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	144	24	NM_212476	0	0	7	7	0	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																				.		0.597	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216271073	C	T	216271073	2	4	133	1	0	0	0	0	0	0	0	1	5981	854	30	2		2	FN1	2	216271073	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	14492990	216271073	26928300	25	11776											
TRNT1	51095	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	3182301	3182309	+	In_Frame_Del	DEL	CAGAGATCT	CAGAGATCT	-																															tggcagaaagatgcggaacgCagagatctcactataaattc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CAGAGATCT	CAGAGATCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:3182301_3182309delCAGAGATCT	ENST00000251607.6	+	4	552_560	c.450_458delCAGAGATCT	c.(448-459)cgcagagatctc>cgc	p.RDL151del	TRNT1_ENST00000280591.6_In_Frame_Del_p.RDL151del	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	151					protein targeting to mitochondrion (GO:0006626)|tRNA 3'-end processing (GO:0042780)|tRNA 3'-terminal CCA addition (GO:0001680)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity (GO:0052929)|CTP:3'-cytidine-tRNA cytidylyltransferase activity (GO:0052928)|CTP:tRNA cytidylyltransferase activity (GO:0052927)|tRNA adenylyltransferase activity (GO:0004810)|tRNA binding (GO:0000049)			breast(2)|endometrium(3)|large_intestine(4)|lung(2)|urinary_tract(1)	12				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)		ATGCGGAACGCAGAGATCTCACTATAAAT	0.354																																					p.150_153del		.											.	TRNT1-90	0			c.450_458del						.																																			SO:0001651	inframe_deletion	51095	exon4			.	AF151805	CCDS2561.2	3p25.1	2002-05-30			ENSG00000072756	ENSG00000072756	2.7.7.25		17341	protein-coding gene	gene with protein product		612907				10810093, 11504732	Standard	NM_182916		Approved	MtCCA, CGI-47, CCA1	uc003bpp.4	Q96Q11	OTTHUMG00000090259	ENST00000251607.6:c.450_458delCAGAGATCT	3.37:g.3182301_3182309delCAGAGATCT	ENSP00000251607:p.Arg151_Leu153del	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	104	24	NM_182916	0	0	0	0	0	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	In_Frame_Del	DEL	ENST00000251607.6	37	CCDS2561.2																																																																																			.		0.354	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			-	3182309	CAGAGATCT	-	3182301	7	5	133	1	0	1	0	1	0	0	0	0	16606	697	25	0	460	0	TRNT1	3	3182301	In_Frame_Del	DEL	CAGAGATCT	TCGA-HE-A5NI-01A-11D-A26P-10		3182301	194840129	26	11777											
FBLN2	2199	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	13671374	13671374	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgccagcacacgtgtgagaAcacactcggctcctaccgct	9	7	10	15	3	0	1	0	1	0	1	2	2	1	1	3	1	4	3	3	1	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:13671374A>G	ENST00000295760.7	+	13	2825	c.2756A>G	c.(2755-2757)aAc>aGc	p.N919S	FBLN2_ENST00000492059.1_Missense_Mutation_p.N966S|FBLN2_ENST00000404922.3_Missense_Mutation_p.N966S|FBLN2_ENST00000535798.1_Missense_Mutation_p.N945S	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	919	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			ACGTGTGAGAACACACTCGGC	0.642																																					p.N966S													.	FBLN2-91	0			c.A2897G						.						22	26	24					3																	13671374		2135	4244	6379	SO:0001583	missense	2199	exon14			GTGAGAACACACT	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2756A>G	3.37:g.13671374A>G	ENSP00000295760:p.Asn919Ser	Somatic	347	1		WXS	Illumina HiSeq	Phase_I	226	44	NM_001004019	0	0	4	4	0	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	37	CCDS46762.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.908264	0.72868	.	.	ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059	D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39	5.1	5.1	0.69264	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96371	0.8816	H	0.96943	3.91	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.996;0.997;0.997	D	0.97757	1.0218	10	0.87932	D	0	.	14.8854	0.70564	1.0:0.0:0.0:0.0	.	919;966;945	P98095;P98095-2;F5H1F3	FBLN2_HUMAN;.;.	S	945;966;919;966	ENSP00000445705:N945S;ENSP00000384169:N966S;ENSP00000295760:N919S;ENSP00000420042:N966S	ENSP00000295760:N919S	N	+	2	0	FBLN2	13646375	1.000000	0.71417	0.998000	0.56505	0.400000	0.30750	7.469000	0.80959	1.920000	0.55613	0.383000	0.25322	AAC	.		0.642	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		G	13671374	A	G	13671374	3	3	133	1	0	0	0	0	1	0	0	0	5718	43	2	3	1637	3	FBLN2	3	13671374	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	10489073	13671374	184351056	27	11778											
TGFBR2	7048	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	30713426	30713426	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgagctggacaccctggtgGggaaaggtcgctttgctgag	7	10	16	8	1	0	2	0	2	0	0	1	4	0	4	1	5	2	3	1	5	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:30713426G>A	ENST00000295754.5	+	4	1133	c.751G>A	c.(751-753)Ggg>Agg	p.G251R	TGFBR2_ENST00000359013.4_Missense_Mutation_p.G276R	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CACCCTGGTGGGGAAAGGTCG	0.517																																					p.G276R													.	TGFBR2-1698	0			c.G826A						.						119	101	107					3																	30713426		2203	4300	6503	SO:0001583	missense	7048	exon5			CTGGTGGGGAAAG		CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"transforming growth factor, beta receptor II (70-80kD)"	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.751G>A	3.37:g.30713426G>A	ENSP00000295754:p.Gly251Arg	Somatic	274	1		WXS	Illumina HiSeq	Phase_I	405	106	NM_001024847	0	0	4	4	0	B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	ENST00000295754.5	37	CCDS2648.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957609	0.92726	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	D;D	0.82984	-1.67;-1.67	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93759	0.8005	M	0.94063	3.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95033	0.8171	10	0.87932	D	0	.	19.2452	0.93899	0.0:0.0:1.0:0.0	.	251;276	P37173;D2JYI1	TGFR2_HUMAN;.	R	251;276;117	ENSP00000295754:G251R;ENSP00000351905:G276R	ENSP00000295754:G251R	G	+	1	0	TGFBR2	30688430	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.864000	0.99589	2.536000	0.85505	0.591000	0.81541	GGG	.		0.517	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2			A	30713426	G	A	30713426	3	1	133	1	0	0	0	0	1	0	0	0	15854	1232	43	2	844	2	TGFBR2	3	30713426	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	17042052	30713426	167309004	28	11779											
OSBPL10	114884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	31705657	31705657	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgcttctcctccaggtgccGcttctgctcggtggctgcgt	1	14	12	14	3	2	0	0	0	2	0	5	0	3	0	3	3	4	4	3	3	0	3	rs375455808		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:31705657G>A	ENST00000396556.2	-	11	2286	c.2164C>T	c.(2164-2166)Cgg>Tgg	p.R722W	OSBPL10_ENST00000438237.2_Missense_Mutation_p.R658W	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	722					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		TCCAGGTGCCGCTTCTGCTCG	0.607																																					p.R722W		.											.	OSBPL10-69	0			c.C2164T						.	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	110	100	103		1972,2164	5.2	1	3		103	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	OSBPL10	NM_001174060.1,NM_017784.4	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	658/701,722/765	31705657	1,13005	2203	4300	6503	SO:0001583	missense	114884	exon11			GGTGCCGCTTCTG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.2164C>T	3.37:g.31705657G>A	ENSP00000379804:p.Arg722Trp	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	183	58	NM_017784	0	0	4	4	0	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	34	5.329303	0.95733	0.0	1.16E-4	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.31247	1.5;1.5	5.25	5.25	0.73442	.	0.051590	0.85682	D	0.000000	T	0.57989	0.2091	M	0.77103	2.36	0.48696	D	0.999691	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.70935	0.971;0.93;0.969	T	0.57412	-0.7816	10	0.42905	T	0.14	-24.6464	19.2246	0.93814	0.0:0.0:1.0:0.0	.	658;722;490	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	W	722;658	ENSP00000379804:R722W;ENSP00000406124:R658W	ENSP00000379804:R722W	R	-	1	2	OSBPL10	31680661	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.694000	0.74587	2.635000	0.89317	0.655000	0.94253	CGG	.		0.607	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	31705657	G	A	31705657	3	1	133	1	0	0	0	0	1	0	0	0	11301	1086	38	1	138	1	OSBPL10	3	31705657	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	992231	31705657	166316773	29	11780											
TRIM71	131405	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	32915387	32915387	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccggcatgggggccacagCttcatctacctccaggaggc	7	6	14	14	1	2	0	1	0	1	0	3	1	3	1	4	6	2	2	4	6	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:32915387C>A	ENST00000383763.5	+	2	993	c.930C>A	c.(928-930)agC>agA	p.S310R		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	310					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGGGCCACAGCTTCATCTACC	0.607																																					p.S310R													.	TRIM71-92	0			c.C930A						.						166	176	173					3																	32915387		2112	4227	6339	SO:0001583	missense	131405	exon2			CCACAGCTTCATC		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.930C>A	3.37:g.32915387C>A	ENSP00000373272:p.Ser310Arg	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	173	35	NM_001039111	0	0	0	0	0		Missense_Mutation	SNP	ENST00000383763.5	37	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.659417	0.29515	.	.	ENSG00000206557	ENST00000383763	T	0.40756	1.02	5.83	3.08	0.35506	Zinc finger, B-box (3);	0.090053	0.85682	D	0.000000	T	0.32436	0.0829	N	0.24115	0.695	0.58432	D	0.999999	P	0.51147	0.942	P	0.49999	0.628	T	0.03374	-1.1043	10	0.13470	T	0.59	-46.6103	9.4738	0.38858	0.0:0.7713:0.0:0.2287	.	310	Q2Q1W2	LIN41_HUMAN	R	310	ENSP00000373272:S310R	ENSP00000373272:S310R	S	+	3	2	TRIM71	32890391	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.122000	0.41987	0.817000	0.34445	0.655000	0.94253	AGC	.		0.607	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		A	32915387	C	A	32915387	3	1	133	1	0	0	0	0	1	0	0	0	16577	796	28	4	936	4	TRIM71	3	32915387	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	1209730	32915387	165107043	30	11781											
PRKCD	5580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	53220041	53220041	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcaaaggcagcttcgggAaggtgagggctgtgagccgg	8	6	20	7	2	0	2	0	2	0	0	1	3	0	3	1	6	2	4	1	6	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:53220041A>T	ENST00000394729.2	+	11	1412	c.1084A>T	c.(1084-1086)Aag>Tag	p.K362*	PRKCD_ENST00000330452.3_Nonsense_Mutation_p.K362*	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	362	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	CAGCTTCGGGAAGGTGAGGGC	0.602																																					p.K362X		.											.	PRKCD-1378	0			c.A1084T						.						72	66	68					3																	53220041		2203	4300	6503	SO:0001587	stop_gained	5580	exon11			TTCGGGAAGGTGA		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.1084A>T	3.37:g.53220041A>T	ENSP00000378217:p.Lys362*	Somatic	371	0		WXS	Illumina HiSeq	Phase_I	450	235	NM_212539	0	0	0	0	0	B0KZ81|B2R834|Q15144|Q86XJ6	Nonsense_Mutation	SNP	ENST00000394729.2	37	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	A	41	8.637830	0.98895	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9599	0.64172	1.0:0.0:0.0:0.0	.	.	.	.	X	362	.	ENSP00000331602:K362X	K	+	1	0	PRKCD	53195081	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.283000	0.95860	1.990000	0.58119	0.482000	0.46254	AAG	.		0.602	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1			T	53220041	A	T	53220041	4	4	133	1	0	0	0	0	0	1	0	0	12538	247	9	5	1122	5	PRKCD	3	53220041	Nonsense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	20304654	53220041	144802389	31	11782											
C3orf63	23272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56667344	56667344	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgaggctggttcatttctaCttcagttaaagccgaagtgg	9	14	11	7	1	3	1	2	1	1	0	3	2	3	1	1	3	2	3	1	3	4	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:56667344C>G	ENST00000493960.2	-	18	3485	c.3475G>C	c.(3475-3477)Gta>Cta	p.V1159L	FAM208A_ENST00000355628.5_Missense_Mutation_p.V1098L|FAM208A_ENST00000431842.2_Missense_Mutation_p.V722L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1159							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						TTCATTTCTACTTCAGTTAAA	0.423																																					p.V1159L		.											.	.	0			c.G3475C						.						161	153	156					3																	56667344		2203	4300	6503	SO:0001583	missense	23272	exon18			TTTCTACTTCAGT	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.3475G>C	3.37:g.56667344C>G	ENSP00000417509:p.Val1159Leu	Somatic	255	1		WXS	Illumina HiSeq	Phase_I	282	153	NM_001112736	0	0	0	5	5	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.233960	0.22626	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.11930	2.73;2.92;2.92	5.71	2.97	0.34412	.	0.560812	0.17265	N	0.180629	T	0.14141	0.0342	L	0.59436	1.845	0.33043	D	0.531757	B;B;B;B	0.29481	0.052;0.082;0.046;0.245	B;B;B;B	0.26202	0.067;0.053;0.045;0.049	T	0.07731	-1.0757	10	0.49607	T	0.09	0.2694	9.0639	0.36451	0.0:0.7733:0.0:0.2267	.	1159;1098;722;1159	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	L	722;1159;1098	ENSP00000399410:V722L;ENSP00000417509:V1159L;ENSP00000347845:V1098L	ENSP00000347845:V1098L	V	-	1	0	C3orf63	56642384	0.810000	0.29049	0.970000	0.41538	0.807000	0.45602	0.627000	0.24506	0.444000	0.26612	-0.145000	0.13849	GTA	.		0.423	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		G	56667344	C	G	56667344	3	3	133	1	0	0	0	0	1	0	0	0	2245	565	20	4	1625	4	C3orf63	3	56667344	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	3447303	56667344	141355086	32	11783											
FRMD4B	23150	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	69247894	69247894	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaattttttctcacggaaaTataagttctccagctgtttc	11	16	5	9	1	2	0	1	0	2	0	5	1	2	1	1	1	1	3	1	1	4	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:69247894T>C	ENST00000398540.3	-	12	991	c.908A>G	c.(907-909)tAt>tGt	p.Y303C	FRMD4B_ENST00000478263.1_De_novo_Start_OutOfFrame|FRMD4B_ENST00000542259.1_Missense_Mutation_p.Y249C	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	303	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CTCACGGAAATATAAGTTCTC	0.333																																					p.Y303C													.	FRMD4B-72	0			c.A908G						.						49	44	45					3																	69247894		1798	4063	5861	SO:0001583	missense	23150	exon12			CGGAAATATAAGT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.908A>G	3.37:g.69247894T>C	ENSP00000381549:p.Tyr303Cys	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	98	57	NM_015123	0	0	0	0	0	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.628228	0.87560	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000462512	D;D;D	0.87334	-2.24;-2.24;-2.24	5.73	5.73	0.89815	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.93360	0.7883	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;0.973	D;D	0.97110	1.0;0.934	D	0.94028	0.7298	10	0.72032	D	0.01	-14.0669	16.026	0.80545	0.0:0.0:0.0:1.0	.	147;303	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	C	303;249;14	ENSP00000381549:Y303C;ENSP00000437658:Y249C;ENSP00000419869:Y14C	ENSP00000381549:Y303C	Y	-	2	0	FRMD4B	69330584	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	8.040000	0.89188	2.191000	0.70037	0.533000	0.62120	TAT	.		0.333	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			C	69247894	T	C	69247894	3	2	133	1	0	0	0	0	1	0	0	0	6071	1406	49	3	2244	3	FRMD4B	3	69247894	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	12580550	69247894	128774536	33	11784											
CEP97	79598	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	101450739	101450739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagaatggcacctgcttaccTacccagaagtcttgctatac	11	11	7	12	0	1	2	0	0	1	2	1	2	1	2	3	1	5	3	3	1	7	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:101450739T>C	ENST00000341893.3	+	5	1255	c.503T>C	c.(502-504)cTa>cCa	p.L168P	CEP97_ENST00000494050.1_Missense_Mutation_p.L168P|CEP97_ENST00000327230.4_Missense_Mutation_p.L168P			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	168					cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						CCTGCTTACCTACCCAGAAGT	0.358																																					p.L168P		.											.	CEP97-70	0			c.T503C						.						175	171	172					3																	101450739		2203	4300	6503	SO:0001583	missense	79598	exon5			CTTACCTACCCAG	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"leucine-rich repeats and IQ motif containing 2"	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.503T>C	3.37:g.101450739T>C	ENSP00000342510:p.Leu168Pro	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	72	15	NM_024548	0	0	0	0	0	B5MDY8|Q8NA71|Q9H5T9	Missense_Mutation	SNP	ENST00000341893.3	37	CCDS2944.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.711642	0.89112	.	.	ENSG00000182504	ENST00000341893;ENST00000327230;ENST00000494050	T;T;T	0.54866	0.55;0.55;0.55	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.78220	0.4249	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.83115	-0.0121	10	0.87932	D	0	-9.0356	16.2507	0.82485	0.0:0.0:0.0:1.0	.	168;168;168	E9PG22;Q8IW35-2;Q8IW35	.;.;CEP97_HUMAN	P	168	ENSP00000342510:L168P;ENSP00000325881:L168P;ENSP00000418185:L168P	ENSP00000325881:L168P	L	+	2	0	CEP97	102933429	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.867000	0.87062	2.237000	0.73441	0.528000	0.53228	CTA	.		0.358	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		C	101450739	T	C	101450739	3	2	133	1	0	0	0	0	1	0	0	0	3269	1522	53	3	521	3	CEP97	3	101450739	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	32202845	101450739	96571691	34	11785											
ITGB5	3693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	124536482	124536482	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttacattgtatgcattaaTaatcagttgaataatatttt	15	18	4	4	0	1	1	1	1	0	0	1	1	1	1	0	0	2	3	0	0	7	10			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:124536482T>A	ENST00000296181.4	-	8	1410	c.1114A>T	c.(1114-1116)Att>Ttt	p.I372F		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	372	VWFA.				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)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		TATGCATTAATAATCAGTTGA	0.463																																					p.I372F		.											.	ITGB5-227	0			c.A1114T						.						90	93	92					3																	124536482		2203	4300	6503	SO:0001583	missense	3693	exon8			CATTAATAATCAG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1114A>T	3.37:g.124536482T>A	ENSP00000296181:p.Ile372Phe	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	60	33	NM_002213	0	0	0	0	0	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	37	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.39|10.39	1.336008|1.336008	0.24253|0.24253	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000296181|ENST00000481591	D|.	0.97731|.	-4.51|.	5.91|5.91	3.56|3.56	0.40772|0.40772	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);|.	0.258920|.	0.37761|.	N|.	0.001959|.	T|T	0.58177|0.58177	0.2104|0.2104	M|M	0.62723|0.62723	1.935|1.935	0.48087|0.48087	D|D	0.99958|0.99958	D|.	0.53745|.	0.962|.	P|.	0.54401|.	0.751|.	T|T	0.55829|0.55829	-0.8079|-0.8079	10|5	0.87932|.	D|.	0|.	.|.	4.6147|4.6147	0.12420|0.12420	0.0:0.4306:0.0:0.5694|0.0:0.4306:0.0:0.5694	.|.	372|.	P18084|.	ITB5_HUMAN|.	F|F	372|106	ENSP00000296181:I372F|.	ENSP00000296181:I372F|.	I|L	-|-	1|3	0|2	ITGB5|ITGB5	126019172|126019172	0.989000|0.989000	0.36119|0.36119	0.981000|0.981000	0.43875|0.43875	0.079000|0.079000	0.17450|0.17450	2.520000|2.520000	0.45554|0.45554	1.062000|1.062000	0.40625|0.40625	-0.290000|-0.290000	0.09829|0.09829	ATT|TTA	.		0.463	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		A	124536482	T	A	124536482	3	1	133	1	0	0	0	0	1	0	0	0	7919	1406	49	5	1317	5	ITGB5	3	124536482	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	23085743	124536482	73485948	35	11786											
IFT122	55764	hgsc.bcm.edu;bcgsc.ca	37	chr3	129200472	129200472	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgcctcccgtaagaagctgGccgtggtagatgaaaatgac	11	8	13	9	2	0	4	0	2	0	2	1	4	1	4	3	2	2	3	3	2	5	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:129200472G>C	ENST00000348417.2	+	14	1665	c.1588G>C	c.(1588-1590)Gcc>Ccc	p.A530P	IFT122_ENST00000440957.2_Missense_Mutation_p.A321P|IFT122_ENST00000296266.3_Missense_Mutation_p.A581P|IFT122_ENST00000347300.2_Missense_Mutation_p.A471P|IFT122_ENST00000431818.2_Missense_Mutation_p.A380P|IFT122_ENST00000349441.2_Missense_Mutation_p.A419P|IFT122_ENST00000507564.1_Missense_Mutation_p.A522P|IFT122_ENST00000504021.1_Missense_Mutation_p.A424P	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	530					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						TAAGAAGCTGGCCGTGGTAGA	0.537																																					p.A581P		.											.	IFT122-92	0			c.G1741C						.						36	37	36					3																	129200472		2202	4280	6482	SO:0001583	missense	55764	exon15			AAGCTGGCCGTGG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.1588G>C	3.37:g.129200472G>C	ENSP00000324005:p.Ala530Pro	Somatic	829	2		WXS	Illumina HiSeq	Phase_I	1002	371	NM_052985	0	0	2	5	3	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058399	0.93846	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522	T;T;T;D;T;T;T;D;T	0.91237	2.88;0.84;0.84;-2.81;1.18;1.18;0.84;-2.81;0.28	5.5	5.5	0.81552	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.052903	0.85682	D	0.000000	D	0.96676	0.8915	M	0.92507	3.315	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D	0.97110	0.998;0.991;1.0;1.0;0.999;1.0;0.996;0.998	D	0.97335	0.9953	10	0.87932	D	0	-22.9133	19.3987	0.94619	0.0:0.0:1.0:0.0	.	321;522;424;370;419;471;530;581	E9PDG2;E7EQF4;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;IF122_HUMAN;.	P	471;581;522;471;380;424;419;530;370;321;45	ENSP00000323973:A471P;ENSP00000296266:A581P;ENSP00000425536:A522P;ENSP00000410946:A380P;ENSP00000422179:A424P;ENSP00000324165:A419P;ENSP00000324005:A530P;ENSP00000401569:A321P;ENSP00000424727:A45P	ENSP00000296266:A581P	A	+	1	0	IFT122	130683162	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.113000	0.94321	2.553000	0.86117	0.585000	0.79938	GCC	.		0.537	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		C	129200472	G	C	129200472	3	2	133	1	0	0	0	0	1	0	0	0	7576	1203	42	4	1799	4	IFT122	3	129200472	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	4663990	129200472	68821958	36	11787											
DZIP1L	199221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	137790541	137790541	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattctcctgtctctccttcGctctgctggtgacttccttg	2	17	7	15	1	3	1	0	1	3	0	8	1	5	1	3	1	1	2	3	1	0	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:137790541G>A	ENST00000327532.2	-	12	1921	c.1559C>T	c.(1558-1560)gCg>gTg	p.A520V	DZIP1L_ENST00000488595.1_Intron|DZIP1L_ENST00000469243.1_Missense_Mutation_p.A520V	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	520					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						TCTCTCCTTCGCTCTGCTGGT	0.582																																					p.A520V		.											.	DZIP1L-92	0			c.C1559T						.						90	92	91					3																	137790541		2203	4300	6503	SO:0001583	missense	199221	exon13			TCCTTCGCTCTGC	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"DAZ interacting protein 1-like"			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1559C>T	3.37:g.137790541G>A	ENSP00000332148:p.Ala520Val	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	112	65	NM_001170538	0	0	1	5	4	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	G	4.821	0.152566	0.09185	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.38240	1.15;1.55	4.86	-3.99	0.04069	.	0.809238	0.10642	N	0.650958	T	0.12263	0.0298	N	0.03324	-0.35	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.001	T	0.38351	-0.9665	10	0.02654	T	1	-4.7251	11.046	0.47859	0.5108:0.0:0.4892:0.0	.	520;520	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	V	520	ENSP00000332148:A520V;ENSP00000419486:A520V	ENSP00000332148:A520V	A	-	2	0	DZIP1L	139273231	0.009000	0.17119	0.025000	0.17156	0.009000	0.06853	0.410000	0.21098	-0.777000	0.04572	-1.004000	0.02495	GCG	.		0.582	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		A	137790541	G	A	137790541	3	1	133	1	0	0	0	0	1	0	0	0	4875	1087	38	1	773	1	DZIP1L	3	137790541	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	8590069	137790541	60231889	37	11788											
KNG1	3827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186445075	186445075	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctactcaattgtgcaaacgaAttgttccaaagagaattttc	14	13	6	8	1	1	1	1	0	0	1	3	3	2	1	1	0	3	2	1	0	6	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:186445075A>C	ENST00000265023.4	+	5	826	c.614A>C	c.(613-615)aAt>aCt	p.N205T	KNG1_ENST00000287611.2_Missense_Mutation_p.N205T|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000599314.1_RNA	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	205	Cystatin kininogen-type 2. {ECO:0000255|PROSITE-ProRule:PRU00979}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		GTGCAAACGAATTGTTCCAAA	0.348																																					p.N205T		.											.	KNG1-92	0			c.A614C						.						105	109	108					3																	186445075		2203	4300	6503	SO:0001583	missense	3827	exon5			AAACGAATTGTTC		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.614A>C	3.37:g.186445075A>C	ENSP00000265023:p.Asn205Thr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	77	27	NM_000893	0	0	0	0	0	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.353296	0.61293	.	.	ENSG00000113889	ENST00000287611;ENST00000265023;ENST00000432028	T;T	0.26067	1.76;1.76	4.98	3.82	0.43975	Proteinase inhibitor I25, cystatin (2);	0.085672	0.49916	D	0.000134	T	0.40473	0.1118	L	0.52011	1.625	0.80722	D	1	D;D	0.89917	0.974;1.0	D;D	0.85130	0.961;0.997	T	0.15263	-1.0443	10	0.54805	T	0.06	-28.4834	7.9142	0.29808	0.9039:0.0:0.0961:0.0	.	205;205	P01042;P01042-2	KNG1_HUMAN;.	T	205;205;193	ENSP00000287611:N205T;ENSP00000265023:N205T	ENSP00000265023:N205T	N	+	2	0	KNG1	187927769	0.996000	0.38824	0.989000	0.46669	0.901000	0.52897	4.757000	0.62213	0.998000	0.38996	0.528000	0.53228	AAT	.		0.348	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		C	186445075	A	C	186445075	3	2	133	1	0	0	0	0	1	0	0	0	8448	101	4	5	632	5	KNG1	3	186445075	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	48654534	186445075	11577355	38	11789											
RNF168	165918	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	196214285	196214286	+	Frame_Shift_Ins	INS	-	-	T																															ttacaatatcaatgcttagcINStttcttgccagttcctcatc																								rs375146769		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:196214285_196214286insT	ENST00000318037.3	-	3	1136_1137	c.542_543insA	c.(541-543)aagfs	p.K181fs		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	181					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		CAATGCTTAGCTTTCTTGCCAG	0.47																																					p.K181fs		.											.	RNF168-90	0			c.543_544insA						.																																			SO:0001589	frameshift_variant	165918	exon3			.	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.543dupA	3.37:g.196214288_196214288dupT	ENSP00000320898:p.Lys181fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	180	89	NM_152617	0	0	0	0	0	Q8NA67|Q96NS4	Frame_Shift_Ins	INS	ENST00000318037.3	37	CCDS3317.1																																																																																			.		0.47	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		T	196214286	-	T	196214285	7	5	133	1	0	1	1	0	0	0	0	0	13491	796	28	0	1188	0	RNF168	3	196214285	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	9769210	196214285	1808145	39	11790											
TIGD4	201798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	153690653	153690653	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagttaataaaattttcaaGgtctgctaaagaattttgaa	17	14	7	3	0	2	3	1	1	1	2	2	3	2	3	0	1	1	2	0	1	8	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr4:153690653G>C	ENST00000304337.2	-	2	2324	c.1504C>G	c.(1504-1506)Ctt>Gtt	p.L502V		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	502						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					AAATTTTCAAGGTCTGCTAAA	0.284																																					p.L502V		.											.	TIGD4-91	0			c.C1504G						.						34	39	38					4																	153690653		2202	4299	6501	SO:0001583	missense	201798	exon2			TTTCAAGGTCTGC	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.1504C>G	4.37:g.153690653G>C	ENSP00000355162:p.Leu502Val	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	51	13	NM_145720	0	0	0	0	0	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	37	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	G	4.593	0.110214	0.08780	.	.	ENSG00000169989	ENST00000304337	T	0.17854	2.25	6.08	2.33	0.28932	Centromere protein Cenp-B, dimerisation domain (1);	0.493860	0.17134	N	0.185704	T	0.10981	0.0268	L	0.29908	0.895	0.26016	N	0.981923	B	0.06786	0.001	B	0.06405	0.002	T	0.24048	-1.0171	10	0.56958	D	0.05	-8.793	4.401	0.11386	0.0666:0.2372:0.3299:0.3663	.	502	Q8IY51	TIGD4_HUMAN	V	502	ENSP00000355162:L502V	ENSP00000355162:L502V	L	-	1	0	TIGD4	153910103	0.997000	0.39634	0.991000	0.47740	0.706000	0.40770	0.275000	0.18698	0.118000	0.18165	-0.293000	0.09583	CTT	.		0.284	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		C	153690653	G	C	153690653	3	2	133	1	0	0	0	0	1	0	0	0	15930	1000	35	4	38	4	TIGD4	4	153690653	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		153690653	37463623	40	11791											
MFAP3L	9848	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	170913188	170913189	+	Frame_Shift_Ins	INS	-	-	A																															ttctctgcaccttcggtcctINSaaagaactcattgatggcct																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr4:170913188_170913189insA	ENST00000361618.3	-	3	877_878	c.570_571insT	c.(568-573)tttaggfs	p.R191fs	RP11-6E9.4_ENST00000508955.1_RNA|MFAP3L_ENST00000393704.3_Frame_Shift_Ins_p.R88fs	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		CCTTCGGTCCTAAAGAACTCAT	0.525																																					p.R191_T192delinsX		.											.	MFAP3L-91	0			c.571_572insT						.																																			SO:0001589	frameshift_variant	9848	exon3			.	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"Immunoglobulin superfamily / I-set domain containing"	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.571dupT	4.37:g.170913191_170913191dupA	ENSP00000354583:p.Arg191fs	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	162	52	NM_021647	0	0	0	0	0	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Nonsense_Mutation	INS	ENST00000361618.3	37	CCDS34103.1																																																																																			.		0.525	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		A	170913189	-	A	170913188	7	5	133	1	0	1	1	0	0	0	0	0	9541	1521	53	0	662	0	MFAP3L	4	170913188	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	17222535	170913188	20241088	41	11792											
SEMA5A	9037	broad.mit.edu	37	chr5	9063125	9063125	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgcccctgctgcagtcacGgctgcactgtgaccacgacg	8	7	11	15	3	1	1	1	1	0	0	1	2	1	1	3	1	4	4	3	1	1	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:9063125G>C	ENST00000382496.5	-	18	3057	c.2392C>G	c.(2392-2394)Cgt>Ggt	p.R798G		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	798	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						CTGCAGTCACGGCTGCACTGT	0.597																																					p.R798G													.	SEMA5A-91	0			c.C2392G						.						82	65	71					5																	9063125		2203	4300	6503	SO:0001583	missense	9037	exon18			AGTCACGGCTGCA	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"Semaphorins"	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2392C>G	5.37:g.9063125G>C	ENSP00000371936:p.Arg798Gly	Somatic	335	1		WXS	Illumina HiSeq	Phase_I	265	4	NM_003966	0	0	1	1	0	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959722	0.74016	.	.	ENSG00000112902	ENST00000382496	T	0.52754	0.65	5.65	3.75	0.43078	.	0.000000	0.85682	D	0.000000	T	0.68997	0.3062	M	0.85197	2.74	0.53005	D	0.999964	D	0.65815	0.995	D	0.69307	0.963	T	0.74399	-0.3678	10	0.62326	D	0.03	.	12.7069	0.57065	0.0:0.0:0.6934:0.3066	.	798	Q13591	SEM5A_HUMAN	G	798	ENSP00000371936:R798G	ENSP00000371936:R798G	R	-	1	0	SEMA5A	9116125	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	4.915000	0.63355	1.323000	0.45263	0.655000	0.94253	CGT	.		0.597	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			C	9063125	G	C	9063125	3	2	133	1	0	0	0	0	1	0	0	0	14069	1116	39	4	856	4	SEMA5A	5	9063125	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		9063125	171852135	42	11793											
CARD6	84674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	40852818	40852818	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcttttgtgcgtctaggaTactgtagcttctctaagtcc	6	17	8	10	1	3	0	0	0	3	0	6	1	4	1	1	1	3	2	1	1	4	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:40852818T>C	ENST00000254691.5	+	3	1583	c.1384T>C	c.(1384-1386)Tac>Cac	p.Y462H	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	462					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						GCGTCTAGGATACTGTAGCTT	0.433																																					p.Y462H		.											.	CARD6-230	0			c.T1384C						.						87	91	89					5																	40852818		2203	4300	6503	SO:0001583	missense	84674	exon3			CTAGGATACTGTA	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1384T>C	5.37:g.40852818T>C	ENSP00000254691:p.Tyr462His	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	145	64	NM_032587	0	0	0	0	0	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	T	4.601	0.111736	0.08831	.	.	ENSG00000132357	ENST00000254691	T	0.11169	2.8	5.48	-5.23	0.02798	.	1.493650	0.03820	N	0.267293	T	0.04724	0.0128	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34950	-0.9808	10	0.35671	T	0.21	3.1866	3.3078	0.07006	0.209:0.5204:0.1052:0.1655	.	462	Q9BX69	CARD6_HUMAN	H	462	ENSP00000254691:Y462H	ENSP00000254691:Y462H	Y	+	1	0	CARD6	40888575	0.000000	0.05858	0.002000	0.10522	0.968000	0.65278	-0.582000	0.05814	-1.244000	0.02516	-0.248000	0.11899	TAC	.		0.433	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			C	40852818	T	C	40852818	3	2	133	1	0	0	0	0	1	0	0	0	2656	1406	49	3	1394	3	CARD6	5	40852818	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	31789693	40852818	140062442	43	11794											
MSH3	4437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	80037368	80037368	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggaaatcctacagaatcagGtcaggcaaatacaagggcta	16	7	10	8	0	2	1	2	0	0	1	3	2	3	2	1	4	2	2	1	4	7	3	rs550626088		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:80037368G>C	ENST00000265081.6	+	11	1733		c.e11+1		MSH3_ENST00000512258.1_Splice_Site	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3						ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		ACAGAATCAGGTCAGGCAAAT	0.333								Mismatch excision repair (MMR)																													.	Melanoma(88;1010 1399 13793 26548 36275)	.											.	MSH3-661	0			c.1653+1G>C						.						53	58	57					5																	80037368		2203	4297	6500	SO:0001630	splice_region_variant	4437	exon11			AATCAGGTCAGGC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1653+1G>C	5.37:g.80037368G>C		Somatic	166	0		WXS	Illumina HiSeq	Phase_I	103	34	NM_002439	0	0	0	0	0	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Splice_Site	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770243	0.69992	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9659	0.86285	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MSH3	80073124	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.767000	0.74975	2.369000	0.80426	0.650000	0.86243	.	.		0.333	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	Intron	C	80037368	G	C	80037368	5	2	133	1	0	0	0	0	0	0	1	0	9896	1275	44	4	1696	4	MSH3	5	80037368	Splice_Site	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	39184550	80037368	100877892	44	11795											
PAM	5066	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	102203042	102203042	+	Frame_Shift_Del	DEL	T	T	-																															caccagacccgtagttcctaTtgattcatcagattttgcat																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:102203042delT	ENST00000438793.3	+	2	625	c.155delT	c.(154-156)attfs	p.I52fs	PAM_ENST00000348126.2_Frame_Shift_Del_p.I52fs|PAM_ENST00000274392.9_De_novo_Start_OutOfFrame|PAM_ENST00000513648.1_3'UTR|PAM_ENST00000379787.4_De_novo_Start_InFrame|PAM_ENST00000304400.7_Frame_Shift_Del_p.I52fs|PAM_ENST00000455264.2_Frame_Shift_Del_p.I52fs|PAM_ENST00000346918.2_Frame_Shift_Del_p.I52fs	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	52	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GTAGTTCCTATTGATTCATCA	0.373																																					p.I52fs		.											.	PAM-68	0			c.155delT						.						168	148	155					5																	102203042		2203	4300	6503	SO:0001589	frameshift_variant	5066	exon2			.	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.155delT	5.37:g.102203042delT	ENSP00000396493:p.Ile52fs	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	79	21	NM_138822	0	0	0	0	0	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Frame_Shift_Del	DEL	ENST00000438793.3	37	CCDS54885.1																																																																																			.		0.373	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		-	102203042	T	-	102203042	7	5	133	1	0	1	0	1	0	0	0	0	11438	1493	52	0	161	0	PAM	5	102203042	Frame_Shift_Del	DEL	T	TCGA-HE-A5NI-01A-11D-A26P-10	22165674	102203042	78712218	45	11796	120	3									
PAM	5066	hgsc.bcm.edu	37	chr5	102203043	102203044	+	Frame_Shift_Del	DEL	TG	TG	-																															accagacccgtagttcctatTgattcatcagattttgcatt																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:102203043_102203044delTG	ENST00000438793.3	+	2	626_627	c.156_157delTG	c.(154-159)attgatfs	p.D53fs	PAM_ENST00000348126.2_Frame_Shift_Del_p.D53fs|PAM_ENST00000274392.9_5'UTR|PAM_ENST00000513648.1_3'UTR|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000304400.7_Frame_Shift_Del_p.D53fs|PAM_ENST00000455264.2_Frame_Shift_Del_p.D53fs|PAM_ENST00000346918.2_Frame_Shift_Del_p.D53fs	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	53	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TAGTTCCTATTGATTCATCAGA	0.376																																					p.52_53del		.											.	PAM-68	0			c.156_157del						.																																			SO:0001589	frameshift_variant	5066	exon2			.	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.156_157delTG	5.37:g.102203043_102203044delTG	ENSP00000396493:p.Asp53fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	80	17	NM_138822	0	0	0	0	0	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Frame_Shift_Del	DEL	ENST00000438793.3	37	CCDS54885.1																																																																																			.		0.376	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		-	102203044	TG	-	102203043	7	5	133	1	0	1	0	1	0	0	0	0	11438	1800	63	0	162	0	PAM	5	102203043	Frame_Shift_Del	DEL	TG	TCGA-HE-A5NI-01A-11D-A26P-10	1	102203043	78712217	46	11797	120	3									
PAM	5066	hgsc.bcm.edu;bcgsc.ca	37	chr5	102203044	102203044	+	Missense_Mutation	SNP	G	G	A																															ccagacccgtagttcctattGattcatcagattttgcattg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:102203044G>A	ENST00000438793.3	+	2	627	c.157G>A	c.(157-159)Gat>Aat	p.D53N	PAM_ENST00000348126.2_Missense_Mutation_p.D53N|PAM_ENST00000274392.9_5'UTR|PAM_ENST00000513648.1_3'UTR|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000304400.7_Missense_Mutation_p.D53N|PAM_ENST00000455264.2_Missense_Mutation_p.D53N|PAM_ENST00000346918.2_Missense_Mutation_p.D53N	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	53	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	AGTTCCTATTGATTCATCAGA	0.373																																					p.D53N		.											.	PAM-68	0			c.G157A						.						166	147	153					5																	102203044		2203	4300	6503	SO:0001583	missense	5066	exon2			CCTATTGATTCAT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.157G>A	5.37:g.102203044G>A	ENSP00000396493:p.Asp53Asn	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	80	22	NM_138822	0	0	3	3	0	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	37	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.347969	0.41599	.	.	ENSG00000145730	ENST00000511839;ENST00000509832;ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T;T;T	0.64085	0.66;-0.08;1.36;1.36;1.36;1.36;1.36	5.68	5.68	0.88126	Copper type II, ascorbate-dependent monooxygenase, N-terminal (1);PHM/PNGase F domain (1);	0.264128	0.41396	D	0.000899	T	0.54481	0.1861	L	0.29908	0.895	0.80722	D	1	B;B;B;B;B	0.12630	0.004;0.006;0.006;0.006;0.006	B;B;B;B;B	0.12156	0.003;0.006;0.006;0.006;0.007	T	0.45760	-0.9239	10	0.39692	T	0.17	.	19.791	0.96456	0.0:0.0:1.0:0.0	.	53;53;53;53;53	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	N	53	ENSP00000426448:D53N;ENSP00000423763:D53N;ENSP00000396493:D53N;ENSP00000282992:D53N;ENSP00000314638:D53N;ENSP00000306100:D53N;ENSP00000403461:D53N	ENSP00000306100:D53N	D	+	1	0	PAM	102230943	1.000000	0.71417	0.985000	0.45067	0.013000	0.08279	5.413000	0.66399	2.677000	0.91161	0.491000	0.48974	GAT	.		0.373	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102203044	G	A	102203044	3	1	133	1	0	0	0	0	1	0	0	0	11438	1290	45	2	163	2	PAM	5	102203044	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	1	102203044	78712216	47	11798	120	3									
ARHGAP26	23092	broad.mit.edu	37	chr5	142281511	142281511	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcattacagctgctggccttCctgcaaggactcttcacttt	7	14	7	13	0	3	0	2	0	1	0	4	1	4	1	2	2	4	3	2	2	2	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:142281511C>A	ENST00000274498.4	+	7	987	c.609C>A	c.(607-609)ttC>ttA	p.F203L	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.F203L	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	203					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCTGGCCTTCCTGCAAGGAC	0.458																																					p.F203L													.	ARHGAP26-660	0			c.C609A						.						149	125	133					5																	142281511		2203	4300	6503	SO:0001583	missense	23092	exon7			GGCCTTCCTGCAA	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.609C>A	5.37:g.142281511C>A	ENSP00000274498:p.Phe203Leu	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	163	6	NM_015071	0	0	0	0	0	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063007	0.76187	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.04551	3.6;3.6	5.79	3.03	0.35002	IRSp53/MIM homology domain (IMD) (2);	0.000000	0.85682	D	0.000000	T	0.15955	0.0384	M	0.85462	2.755	0.58432	D	0.999998	P;P	0.49307	0.655;0.922	P;P	0.55667	0.557;0.781	T	0.00363	-1.1788	10	0.54805	T	0.06	.	8.3362	0.32217	0.0:0.6617:0.0:0.3383	.	203;203	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	L	203	ENSP00000274498:F203L;ENSP00000367243:F203L	ENSP00000274498:F203L	F	+	3	2	ARHGAP26	142261695	0.926000	0.31397	1.000000	0.80357	0.990000	0.78478	0.065000	0.14466	0.784000	0.33661	0.563000	0.77884	TTC	.		0.458	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		A	142281511	C	A	142281511	3	1	133	1	0	0	0	0	1	0	0	0	875	854	30	4	635	4	ARHGAP26	5	142281511	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	40078467	142281511	38633749	48	11799											
SYCP2L	221711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	10931696	10931696	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgccagttttccctcccagtAgtggcagtggccatgagaaa	9	10	11	11	0	0	1	0	1	0	1	2	2	2	1	4	2	1	3	4	2	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:10931696A>G	ENST00000283141.6	+	20	1953	c.1657A>G	c.(1657-1659)Agt>Ggt	p.S553G		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	553						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			CCCTCCCAGTAGTGGCAGTGG	0.398																																					p.S553G		.											.	SYCP2L-24	0			c.A1657G						.						162	153	156					6																	10931696		1894	4121	6015	SO:0001583	missense	221711	exon20			CCCAGTAGTGGCA	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 177"	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.1657A>G	6.37:g.10931696A>G	ENSP00000283141:p.Ser553Gly	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	104	37	NM_001040274	0	0	0	0	0	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	37	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.964123	0.34659	.	.	ENSG00000153157	ENST00000283141	T	0.31247	1.5	4.54	3.37	0.38596	.	0.357110	0.31648	N	0.007296	T	0.19327	0.0464	L	0.52011	1.625	0.24843	N	0.992458	D	0.60160	0.987	P	0.50270	0.636	T	0.03325	-1.1048	10	0.59425	D	0.04	.	8.5559	0.33480	0.7752:0.2248:0.0:0.0	.	553	Q5T4T6	SYC2L_HUMAN	G	553	ENSP00000283141:S553G	ENSP00000283141:S553G	S	+	1	0	SYCP2L	11039682	0.004000	0.15560	0.006000	0.13384	0.043000	0.13939	0.576000	0.23744	0.822000	0.34565	0.460000	0.39030	AGT	.		0.398	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		G	10931696	A	G	10931696	3	3	133	1	0	0	0	0	1	0	0	0	15465	420	15	3	1735	3	SYCP2L	6	10931696	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		10931696	160183371	49	11800											
GPLD1	2822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	24450018	24450018	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatccagcagcagccttactTtgtaggtgagctgctcggag	8	11	12	10	1	0	1	0	1	0	0	2	2	1	2	2	2	6	5	2	2	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:24450018T>C	ENST00000230036.1	-	15	1555	c.1445A>G	c.(1444-1446)aAa>aGa	p.K482R		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	482					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						CAGCCTTACTTTGTAGGTGAG	0.632																																					p.K482R		.											.	GPLD1-228	0			c.A1445G						.						67	71	69					6																	24450018		2203	4300	6503	SO:0001630	splice_region_variant	2822	exon15			CTTACTTTGTAGG	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1446+1A>G	6.37:g.24450018T>C		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	69	32	NM_001503	0	0	0	0	0	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	T	9.926	1.213638	0.22289	.	.	ENSG00000112293	ENST00000230036	T	0.66995	-0.24	5.5	-3.95	0.04118	.	0.800408	0.11589	N	0.548920	T	0.20455	0.0492	N	0.12527	0.23	0.53005	D	0.999964	B	0.09022	0.002	B	0.14578	0.011	T	0.12142	-1.0559	10	0.12766	T	0.61	-0.5038	9.3674	0.38232	0.0:0.1973:0.5455:0.2572	.	482	P80108	PHLD_HUMAN	R	482	ENSP00000230036:K482R	ENSP00000230036:K482R	K	-	2	0	GPLD1	24557997	0.006000	0.16342	0.147000	0.22382	0.634000	0.38068	-0.438000	0.06905	-0.534000	0.06315	0.482000	0.46254	AAA	.		0.632	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	Missense_Mutation	C	24450018	T	C	24450018	5	2	133	1	0	0	0	0	0	0	1	0	6634	1855	64	3	1121	3	GPLD1	6	24450018	Splice_Site	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	13518322	24450018	146665049	50	11801											
NOTCH4	4855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32169043	32169043	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccctgccatcacgatccttCcttacccagagtcctaccct	7	11	4	19	1	1	1	1	0	0	1	5	2	5	1	7	0	3	0	7	0	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:32169043C>T	ENST00000375023.3	-	22	4128	c.3990G>A	c.(3988-3990)agG>agA	p.R1330R		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1330					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CACGATCCTTCCTTACCCAGA	0.622																																					p.R1330R		.											.	NOTCH4-1321	0			c.G3990A						.						59	65	63					6																	32169043		1511	2709	4220	SO:0001819	synonymous_variant	4855	exon22			ATCCTTCCTTACC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"Ankyrin repeat domain containing"	7884	protein-coding gene	gene with protein product		164951	"Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)"	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.3990G>A	6.37:g.32169043C>T		Somatic	229	0		WXS	Illumina HiSeq	Phase_I	142	53	NM_004557	0	0	0	0	0	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			.		0.622	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			T	32169043	C	T	32169043	2	4	133	1	0	0	0	0	0	0	0	1	10577	854	30	2		2	NOTCH4	6	32169043	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	7719025	32169043	138946024	51	11802											
C6orf106	64771	hgsc.bcm.edu;broad.mit.edu	37	chr6	34664262	34664262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaggcgcaaccggcaggaTtgagctggaagccgagcagc	12	3	16	10	3	0	2	0	1	0	1	0	5	0	4	2	4	5	4	2	4	3	1	rs369638409		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:34664262T>C	ENST00000374023.3	-	1	362	c.119A>G	c.(118-120)aAt>aGt	p.N40S	RP11-140K17.3_ENST00000606971.1_RNA|C6orf106_ENST00000374026.3_Missense_Mutation_p.N40S|RP11-140K17.3_ENST00000606496.1_RNA	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	40										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						ACCGGCAGGATTGAGCTGGAA	0.662																																					p.N40S		.											.	C6orf106-93	0			c.A119G						.	T	SER/ASN,SER/ASN	0,4406		0,0,2203	62	43	49		119,119	1.8	1	6		49	1,8599		0,1,4299	no	missense,missense	C6orf106	NM_022758.4,NM_024294.2	46,46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	40/233,40/299	34664262	1,13005	2203	4300	6503	SO:0001583	missense	64771	exon1			GCAGGATTGAGCT	AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821			21215	protein-coding gene	gene with protein product		612217					Standard	XM_005249298		Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.119A>G	6.37:g.34664262T>C	ENSP00000363135:p.Asn40Ser	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	50	7	NM_024294	0	0	3	4	1	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	Missense_Mutation	SNP	ENST00000374023.3	37	CCDS4796.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.399579	0.25291	0.0	1.16E-4	ENSG00000196821	ENST00000374023;ENST00000374026	.	.	.	2.99	1.78	0.24846	UBA-like (1);	0.185370	0.46442	D	0.000288	T	0.21186	0.0510	L	0.46670	1.46	0.80722	D	1	B;P	0.46142	0.207;0.873	B;B	0.44163	0.219;0.443	T	0.04178	-1.0971	9	0.33940	T	0.23	-7.2216	2.9531	0.05868	0.2121:0.1602:0.0:0.6277	.	40;40	Q9H6K1-2;Q9H6K1	.;CF106_HUMAN	S	40	.	ENSP00000363135:N40S	N	-	2	0	C6orf106	34772240	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	3.873000	0.56093	0.535000	0.28714	-0.669000	0.03829	AAT	.		0.662	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040251.1	NM_022758		C	34664262	T	C	34664262	3	2	133	1	0	0	0	0	1	0	0	0	2325	1493	52	3	797	3	C6orf106	6	34664262	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	2495219	34664262	136450805	52	11803											
DST	667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	56501422	56501422	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctgtaagatccagctcCactgcgtctgcattgccgct	8	10	10	13	2	1	2	0	0	1	2	3	2	3	2	3	0	5	5	3	0	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:56501422C>T	ENST00000361203.3	-	19	2367	c.2360G>A	c.(2359-2361)tGg>tAg	p.W787*	DST_ENST00000370788.2_Nonsense_Mutation_p.W787*|DST_ENST00000370769.4_Nonsense_Mutation_p.W787*|DST_ENST00000312431.6_Nonsense_Mutation_p.W787*|DST_ENST00000244364.6_Nonsense_Mutation_p.W461*|DST_ENST00000421834.2_Nonsense_Mutation_p.W787*|DST_ENST00000446842.2_Nonsense_Mutation_p.W461*|DST_ENST00000370754.5_Nonsense_Mutation_p.W965*|DST_ENST00000518935.1_Nonsense_Mutation_p.W461*|DST_ENST00000370765.6_Nonsense_Mutation_p.W461*			Q03001	DYST_HUMAN	dystonin	787					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GATCCAGCTCCACTGCGTCTG	0.453																																					p.W461X		.											.	DST-523	0			c.G1382A						.						171	142	152					6																	56501422		2203	4300	6503	SO:0001587	stop_gained	667	exon9			CAGCTCCACTGCG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"EF-hand domain containing"	1090	protein-coding gene	gene with protein product		113810	"bullous pemphigoid antigen 1, 230/240kDa"	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.2360G>A	6.37:g.56501422C>T	ENSP00000354508:p.Trp787*	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	40	23	NM_001723	0	0	0	0	0	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	38	6.731382	0.97796	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	.	.	.	5.25	5.25	0.73442	.	0.000000	0.46145	D	0.000304	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.029	0.92948	0.0:1.0:0.0:0.0	.	.	.	.	X	461;965;787;787;461;787;787;787;461;827;461;461	.	ENSP00000244364:W461X	W	-	2	0	DST	56609381	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.644000	0.83416	2.726000	0.93360	0.579000	0.79373	TGG	.		0.453	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56501422	C	T	56501422	4	4	133	1	0	0	0	0	0	1	0	0	4794	595	21	2	19077	2	DST	6	56501422	Nonsense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	21837160	56501422	114613645	53	11804											
KIAA1009	22832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	84872967	84872967	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcagtcttttgatgtctTccaataaactgtctttttct	7	21	5	8	0	5	1	1	1	4	0	6	1	6	1	1	0	1	1	1	0	3	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:84872967T>G	ENST00000403245.3	-	19	2522	c.2408A>C	c.(2407-2409)gAa>gCa	p.E803A	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Missense_Mutation_p.E727A	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTTGATGTCTTCCAATAAACT	0.318																																					p.E803A		.											.	KIAA1009-91	0			c.A2408C						.						180	165	170					6																	84872967		2203	4300	6503	SO:0001583	missense	22832	exon19			ATGTCTTCCAATA																												ENST00000403245.3:c.2408A>C	6.37:g.84872967T>G	ENSP00000385215:p.Glu803Ala	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	31	11	NM_014895	0	0	0	4	4		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	T	18.77	3.694256	0.68386	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.33216	1.42;1.42	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000005	T	0.43523	0.1251	M	0.66506	2.035	0.46437	D	0.999046	D	0.71674	0.998	D	0.81914	0.995	T	0.37686	-0.9695	10	0.44086	T	0.13	-22.1089	14.6743	0.68967	0.0:0.0:0.0:1.0	.	803	Q5TB80	QN1_HUMAN	A	727;803	ENSP00000257766:E727A;ENSP00000385215:E803A	ENSP00000257766:E727A	E	-	2	0	KIAA1009	84929686	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	6.642000	0.74329	1.912000	0.55364	0.460000	0.39030	GAA	.		0.318	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			G	84872967	T	G	84872967	3	3	133	1	0	0	0	0	1	0	0	0	8224	1783	62	5	1839	5	KIAA1009	6	84872967	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	28371545	84872967	86242100	54	11805											
ZNF292	23036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	87943085	87943085	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcccatcttgttggataTgagaattaaacatctaatca	13	13	8	7	0	3	1	1	1	2	1	4	3	4	2	1	2	1	1	1	2	5	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:87943085T>A	ENST00000369577.3	+	5	624	c.581T>A	c.(580-582)aTg>aAg	p.M194K	ZNF292_ENST00000339907.4_Missense_Mutation_p.M189K	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	194						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TTGTTGGATATGAGAATTAAA	0.313																																					p.M194K		.											.	ZNF292-72	0			c.T581A						.						81	77	78					6																	87943085		1825	4076	5901	SO:0001583	missense	23036	exon5			TGGATATGAGAAT	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.581T>A	6.37:g.87943085T>A	ENSP00000358590:p.Met194Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	85	24	NM_015021	0	0	0	0	0	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.376146	0.82682	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.10860	2.83;2.85	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	M	0.72894	2.215	0.58432	D	0.999993	D	0.76494	0.999	D	0.79784	0.993	T	0.01524	-1.1333	10	0.87932	D	0	.	15.658	0.77158	0.0:0.0:0.0:1.0	.	194	O60281	ZN292_HUMAN	K	194;189	ENSP00000358590:M194K;ENSP00000342847:M189K	ENSP00000342847:M189K	M	+	2	0	ZNF292	87999804	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.183000	0.77697	2.158000	0.67659	0.460000	0.39030	ATG	.		0.313	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		A	87943085	T	A	87943085	3	1	133	1	0	0	0	0	1	0	0	0	17858	1464	51	5	599	5	ZNF292	6	87943085	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	3070118	87943085	83171982	55	11806											
PNRC1	10957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	89793801	89793801	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagtgatccaccttctccTagtgttcttccaaagcctcc	7	15	5	14	0	2	1	0	1	2	0	6	1	5	1	6	0	1	1	6	0	3	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:89793801T>C	ENST00000336032.3	+	2	987	c.870T>C	c.(868-870)ccT>ccC	p.P290P	PNRC1_ENST00000354922.3_Silent_p.P105P|PNRC1_ENST00000369472.1_Silent_p.P105P	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		CACCTTCTCCTAGTGTTCTTC	0.413										Multiple Myeloma(7;0.094)																											p.P290P		.											.	PNRC1-186	0			c.T870C						.						81	83	83					6																	89793801		2203	4300	6503	SO:0001819	synonymous_variant	10957	exon2			TTCTCCTAGTGTT	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"proline rich 2"	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.870T>C	6.37:g.89793801T>C		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	105	43	NM_006813	0	0	48	82	34	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Silent	SNP	ENST00000336032.3	37	CCDS5018.1																																																																																			.		0.413	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813		C	89793801	T	C	89793801	2	2	133	1	0	0	0	0	0	0	0	1	12200	1509	53	3		3	PNRC1	6	89793801	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	1850716	89793801	81321266	56	11807											
MCM9	254394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	119245294	119245294	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggacagacaggcaaaccTgatggagaaaacaaaaaaac	21	3	9	8	0	1	3	1	1	0	2	1	5	1	4	1	3	3	1	1	3	6	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:119245294T>C	ENST00000316316.6	-	3	591		c.e3-2		MCM9_ENST00000316068.3_Splice_Site	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9						cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		CAGGCAAACCTGATGGAGAAA	0.393																																					.		.											.	MCM9-515	0			c.305-2A>G						.						118	126	124					6																	119245294		2201	4300	6501	SO:0001630	splice_region_variant	254394	exon3			CAAACCTGATGGA	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"minichromosome maintenance deficient domain containing 1", "chromosome 6 open reading frame 61"	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.305-2A>G	6.37:g.119245294T>C		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	54	21	NM_017696	0	0	0	0	0	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Splice_Site	SNP	ENST00000316316.6	37	CCDS56447.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073982	0.55646	.	.	ENSG00000111877	ENST00000316316;ENST00000316068;ENST00000425154	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5716	0.76341	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MCM9	119286993	1.000000	0.71417	0.963000	0.40424	0.735000	0.41995	7.499000	0.81566	2.072000	0.62099	0.460000	0.39030	.	.		0.393	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	Intron	C	119245294	T	C	119245294	5	2	133	1	0	0	0	0	0	0	1	0	9419	1594	55	3	892	3	MCM9	6	119245294	Splice_Site	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	29451493	119245294	51869773	57	11808											
FGFR1OP	11116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	167435950	167435950	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtctccttgtcagaaccCaagagcaaaagcagccttca	13	8	8	12	0	3	2	2	0	1	2	4	2	3	2	3	0	4	2	3	0	4	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:167435950C>A	ENST00000366847.4	+	8	864	c.633C>A	c.(631-633)ccC>ccA	p.P211P	FGFR1OP_ENST00000349556.4_Silent_p.P191P|RP11-517H2.6_ENST00000609590.1_RNA	NM_007045.2	NP_008976.1	O95684	FR1OP_HUMAN	FGFR1 oncogene partner	211					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292)			large_intestine(2)|ovary(1)|stomach(1)	4		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		TGTCAGAACCCAAGAGCAAAA	0.428			T	FGFR1	"MPD, NHL"																																p.P211P		.		Dom	yes		6	6q27	11116	FGFR1 oncogene partner (FOP)		L	.	FGFR1OP-683	0			c.C633A						.						96	92	93					6																	167435950		2203	4300	6503	SO:0001819	synonymous_variant	11116	exon8			AGAACCCAAGAGC	Y18046	CCDS5296.1, CCDS5297.1, CCDS75550.1	6q27	2008-02-05			ENSG00000213066	ENSG00000213066			17012	protein-coding gene	gene with protein product		605392				9949182, 10373756	Standard	NM_007045		Approved	FOP	uc003qvj.3	O95684	OTTHUMG00000016011	ENST00000366847.4:c.633C>A	6.37:g.167435950C>A		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	38	11	NM_007045	0	0	5	9	4	A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1	Silent	SNP	ENST00000366847.4	37	CCDS5296.1																																																																																			.		0.428	FGFR1OP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043099.2	NM_007045		A	167435950	C	A	167435950	2	1	133	1	0	0	0	0	0	0	0	1	5883	581	21	4		4	FGFR1OP	6	167435950	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	48190656	167435950	3679117	58	11809											
WBSCR27	155368	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	73249148	73249148	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaagccatccttggcagAgatgccggataccacctcca	11	7	10	13	1	0	2	0	1	0	1	2	5	2	3	6	2	3	1	6	2	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr7:73249148A>C	ENST00000297873.4	-	6	712	c.663T>G	c.(661-663)tcT>tcG	p.S221S		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	221										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				TCCTTGGCAGAGATGCCGGAT	0.637																																					p.S221S		.											.	WBSCR27-90	0			c.T663G						.						68	61	63					7																	73249148		2203	4300	6503	SO:0001819	synonymous_variant	155368	exon6			TGGCAGAGATGCC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.663T>G	7.37:g.73249148A>C		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	117	42	NM_152559	0	0	26	43	17		Silent	SNP	ENST00000297873.4	37	CCDS5561.1																																																																																			.		0.637	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559		C	73249148	A	C	73249148	2	2	133	1	0	0	0	0	0	0	0	1	17299	291	11	5		5	WBSCR27	7	73249148	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		73249148	85889515	59	11810											
HTR5A	3361	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	154862732	154862732	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctctcggtcttcggagtGcttattctcaccttgctggg	3	15	11	12	2	3	0	1	0	3	0	6	1	3	1	1	3	3	3	1	3	1	4	rs372855479		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr7:154862732G>T	ENST00000287907.2	+	1	699	c.123G>T	c.(121-123)gtG>gtT	p.V41V	HTR5A-AS1_ENST00000543018.1_Intron|HTR5A-AS1_ENST00000493904.1_Intron|HTR5A-AS1_ENST00000395731.2_Intron	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	41					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	TCTTCGGAGTGCTTATTCTCA	0.642																																					p.V41V													.	HTR5A-155	0			c.G123T						.						103	89	94					7																	154862732		2203	4300	6503	SO:0001819	synonymous_variant	3361	exon1			CGGAGTGCTTATT		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5300	protein-coding gene	gene with protein product		601305	"5-hydroxytryptamine (serotonin) receptor 5A"			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.123G>T	7.37:g.154862732G>T		Somatic	109	1		WXS	Illumina HiSeq	Phase_I	125	49	NM_024012	0	0	0	0	0	Q2M2D2	Silent	SNP	ENST00000287907.2	37	CCDS5936.1																																																																																			.		0.642	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012		T	154862732	G	T	154862732	2	4	133	1	0	0	0	0	0	0	0	1	7471	1306	46	4		4	HTR5A	7	154862732	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	81613584	154862732	4275931	60	11811											
TRIM35	23087	bcgsc.ca	37	chr8	27145422	27145422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcagcgcccgagtcctggCgcacacgtaccacgcccacc	7	4	9	21	5	1	0	1	0	0	0	2	1	2	0	6	1	2	2	6	1	1	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr8:27145422C>T	ENST00000305364.4	-	6	1210	c.1127G>A	c.(1126-1128)cGc>cAc	p.R376H	TRIM35_ENST00000521253.1_3'UTR	NM_171982.3	NP_741983.2	Q9UPQ4	TRI35_HUMAN	tripartite motif containing 35	376	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	14		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|Epithelial(17;9.34e-10)|Colorectal(74;0.141)		CGAGTCCTGGCGCACACGTAC	0.697																																					p.R376H													.	TRIM35-226	0			c.G1127A						.						35	31	32					8																	27145422		2201	4297	6498	SO:0001583	missense	23087	exon6			TCCTGGCGCACAC	AB029021	CCDS6056.2	8p21.2	2013-01-09	2011-01-25		ENSG00000104228	ENSG00000104228		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16285	protein-coding gene	gene with protein product			"tripartite motif-containing 35"			11331580, 14662771, 12692137	Standard	XM_005273451		Approved	KIAA1098, MAIR, HLS5	uc003xfl.1	Q9UPQ4	OTTHUMG00000102047	ENST00000305364.4:c.1127G>A	8.37:g.27145422C>T	ENSP00000301924:p.Arg376His	Somatic	22	0		WXS	Illumina HiSeq	Phase_1	11	3	NM_171982	0	0	3	3	0	Q86XQ0|Q8WVA4	Missense_Mutation	SNP	ENST00000305364.4	37	CCDS6056.2	.	.	.	.	.	.	.	.	.	.	C	13.92	2.380304	0.42207	.	.	ENSG00000104228	ENST00000305364;ENST00000380544	T	0.61040	0.14	5.42	2.27	0.28462	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.406842	0.21274	N	0.077274	T	0.31979	0.0814	N	0.14661	0.345	0.09310	N	1	P	0.38167	0.621	B	0.36534	0.227	T	0.08932	-1.0698	10	0.33141	T	0.24	.	2.7059	0.05162	0.2211:0.5064:0.0:0.2725	.	376	Q9UPQ4	TRI35_HUMAN	H	376	ENSP00000301924:R376H	ENSP00000301924:R376H	R	-	2	0	TRIM35	27201339	0.024000	0.19004	0.005000	0.12908	0.427000	0.31564	0.264000	0.18497	0.556000	0.29098	0.313000	0.20887	CGC	.		0.697	TRIM35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219848.2	NM_171982		T	27145422	C	T	27145422	3	4	133	1	0	0	0	0	1	0	0	0	16542	768	27	1	358	1	TRIM35	8	27145422	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10		27145422	119218600	61	11812											
GDAP1	54332	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	75274164	75274164	+	Frame_Shift_Del	DEL	A	A	-																															gctgaagaaacttgctgaagAaaacccagatttacaagaag																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr8:75274164delA	ENST00000220822.7	+	4	610	c.530delA	c.(529-531)gaafs	p.E177fs	GDAP1_ENST00000521096.1_3'UTR|GDAP1_ENST00000434412.2_Frame_Shift_Del_p.E109fs	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	177	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CTTGCTGAAGAAAACCCAGAT	0.373																																					p.E177fs		.											.	GDAP1-90	0			c.530delA						.						118	110	113					8																	75274164		2203	4300	6503	SO:0001589	frameshift_variant	54332	exon4			.		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.530delA	8.37:g.75274164delA	ENSP00000220822:p.Glu177fs	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	31	16	NM_018972	0	0	0	0	0	A8K957|E7FJF3|E7FJF4	Frame_Shift_Del	DEL	ENST00000220822.7	37	CCDS34911.1																																																																																			.		0.373	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		-	75274164	A	-	75274164	7	5	133	1	0	1	0	1	0	0	0	0	6327	246	9	0	544	0	GDAP1	8	75274164	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	48128742	75274164	71089858	62	11813											
SQLE	6713	ucsc.edu;bcgsc.ca	37	chr8	126033029	126033029	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttacaattttattttagattCcctgcatcaactaagaaaag	15	15	4	7	0	1	2	1	0	0	2	2	2	2	2	1	0	3	1	1	0	8	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr8:126033029C>T	ENST00000265896.5	+	10	2346	c.1448C>T	c.(1447-1449)tCc>tTc	p.S483F	SQLE_ENST00000523430.1_Missense_Mutation_p.S388F	NM_003129.3	NP_003120.2	Q14534	ERG1_HUMAN	squalene epoxidase	483					cellular aromatic compound metabolic process (GO:0006725)|cholesterol biosynthetic process (GO:0006695)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|squalene monooxygenase activity (GO:0004506)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	ATTTTAGATTCCCTGCATCAA	0.348																																					p.S483F													.	SQLE-523	0			c.C1448T						.						75	73	74					8																	126033029		1841	4086	5927	SO:0001583	missense	6713	exon10			TAGATTCCCTGCA	D78130	CCDS47918.1	8q24.1	2014-06-23			ENSG00000104549	ENSG00000104549	1.14.13.132		11279	protein-coding gene	gene with protein product	"squalene monooxygenase"	602019				9286711	Standard	NM_003129		Approved		uc011liq.2	Q14534	OTTHUMG00000164990	ENST00000265896.5:c.1448C>T	8.37:g.126033029C>T	ENSP00000265896:p.Ser483Phe	Somatic	54	0		WXS	Illumina HiSeq		40	4	NM_003129	0	0	1	1	0	Q9UEK6	Missense_Mutation	SNP	ENST00000265896.5	37	CCDS47918.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429507	0.62844	.	.	ENSG00000104549	ENST00000523430;ENST00000265896;ENST00000541193;ENST00000518931	T;T;T	0.40476	1.03;1.03;1.03	5.87	3.0	0.34707	Squalene epoxidase (1);	0.096455	0.85682	D	0.000000	T	0.61602	0.2360	M	0.83012	2.62	0.58432	D	0.99999	D	0.53462	0.96	P	0.61003	0.882	T	0.63413	-0.6643	10	0.51188	T	0.08	-7.9375	12.0916	0.53730	0.2455:0.6365:0.118:0.0	.	483	Q14534	ERG1_HUMAN	F	388;483;288;135	ENSP00000430331:S388F;ENSP00000265896:S483F;ENSP00000429916:S135F	ENSP00000265896:S483F	S	+	2	0	SQLE	126102211	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	3.631000	0.54280	0.425000	0.26087	0.655000	0.94253	TCC	.		0.348	SQLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381362.1	NM_003129		T	126033029	C	T	126033029	3	4	133	1	0	0	0	0	1	0	0	0	15160	855	30	2	1385	2	SQLE	8	126033029	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	50758865	126033029	20330993	63	11814											
ACER2	340485	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	19435060	19435060	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggagttccttgcactgcaCtgctcatcgcagagctaaag	9	10	11	11	1	1	1	1	0	0	1	3	2	2	2	1	1	4	6	1	1	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:19435060C>T	ENST00000340967.2	+	4	507	c.481C>T	c.(481-483)Ctg>Ttg	p.L161L	ACER2_ENST00000380376.1_Silent_p.L112L	NM_001010887.2	NP_001010887.2	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	161					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to drug (GO:0035690)|ceramide metabolic process (GO:0006672)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of protein glycosylation in Golgi (GO:0090285)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	13						TTGCACTGCACTGCTCATCGC	0.557																																					p.L161L		.											.	ACER2-516	0			c.C481T						.						219	164	182					9																	19435060		2203	4300	6503	SO:0001819	synonymous_variant	340485	exon4			ACTGCACTGCTCA	AK123581	CCDS34992.1	9p21.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000177076	ENSG00000177076	3.5.1.23	"Alkaline ceramidase"	23675	protein-coding gene	gene with protein product		613492	"N-acylsphingosine amidohydrolase 3-like"	ASAH3L		18945876	Standard	XM_005251447		Approved	FLJ41587	uc003zny.1	Q5QJU3	OTTHUMG00000019644	ENST00000340967.2:c.481C>T	9.37:g.19435060C>T		Somatic	243	0		WXS	Illumina HiSeq	Phase_I	212	50	NM_001010887	0	0	0	0	0	A2A3R8|Q569G5|Q5VZR7|Q71RD2	Silent	SNP	ENST00000340967.2	37	CCDS34992.1																																																																																			.		0.557	ACER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051864.1	XM_294540		T	19435060	C	T	19435060	2	4	133	1	0	0	0	0	0	0	0	1	139	564	20	2		2	ACER2	9	19435060	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10		19435060	121778371	64	11815											
FAM22F	54754	bcgsc.ca	37	chr9	97081337	97081337	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agtgcgcactctgccctgtcCctgagggtcctgggcagctg	4	9	14	14	1	1	1	0	1	1	0	3	1	3	1	3	2	3	3	3	2	0	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:97081337C>A	ENST00000253262.4	-	7	1701	c.1681G>T	c.(1681-1683)Gga>Tga	p.G561*	NUTM2F_ENST00000335456.7_Intron|NUTM2F_ENST00000341207.4_Nonsense_Mutation_p.G546*	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	561																	CTGCCCTGTCCCTGAGGGTCC	0.632																																					p.G561X													.	FAM22F-68	0			c.G1681T						.						9	15	13					9																	97081337		1825	4044	5869	SO:0001587	stop_gained	54754	exon7			CCTGTCCCTGAGG		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1681G>T	9.37:g.97081337C>A	ENSP00000253262:p.Gly561*	Somatic	144	2		WXS	Illumina HiSeq	Phase_1	127	56	NM_017561	0	0	0	0	0	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Nonsense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524387	0.44969	.	.	ENSG00000130950	ENST00000253262;ENST00000341207;ENST00000375347	.	.	.	1.45	-0.439	0.12264	.	0.767987	0.11801	N	0.528127	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	3.6141	0.08071	0.0:0.3681:0.0:0.6319	.	.	.	.	X	561;546;395	.	ENSP00000253262:G561X	G	-	1	0	FAM22F	96121158	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.318000	0.08050	-0.110000	0.12022	0.400000	0.26472	GGA	.		0.632	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		A	97081337	C	A	97081337	4	1	133	1	0	0	0	0	0	1	0	0	5561	632	22	4	593	4	FAM22F	9	97081337	Nonsense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	77646277	97081337	44132094	65	11816											
FAM22G	441457	bcgsc.ca	37	chr9	99700841	99700841	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggctgcccaggaccctcagGgacagggcagagtgcgcact	8	4	15	14	2	1	1	1	0	0	1	1	3	1	3	2	4	2	3	2	4	0	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:99700841G>T	ENST00000372322.3	+	7	1657	c.1636G>T	c.(1636-1638)Gga>Tga	p.G546*	NUTM2G_ENST00000354649.3_Intron|HIATL2_ENST00000506067.1_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	546																	GGACCCTCAGGGACAGGGCAG	0.642																																					p.G546X													.	FAM22G-69	0			c.G1636T						.						62	71	68					9																	99700841		692	1591	2283	SO:0001587	stop_gained	441457	exon7			CCTCAGGGACAGG		CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"family with sequence similarity 22, member G"	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.1636G>T	9.37:g.99700841G>T	ENSP00000361397:p.Gly546*	Somatic	659	3		WXS	Illumina HiSeq	Phase_1	444	73	NM_001170741	0	0	0	0	0	A6NNI5|Q5VZR3	Nonsense_Mutation	SNP	ENST00000372322.3	37	CCDS55329.1	.	.	.	.	.	.	.	.	.	.	.	14.35	2.510637	0.44660	.	.	ENSG00000188152	ENST00000372322;ENST00000417159;ENST00000375230	.	.	.	1.01	-1.15	0.09709	.	0.767987	0.11801	N	0.528127	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	3.5235	0.07751	0.5622:0.0:0.4378:0.0	.	.	.	.	X	546;395;427	.	ENSP00000361397:G546X	G	+	1	0	FAM22G	98740662	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.006000	0.13152	-0.335000	0.08451	0.473000	0.43528	GGA	.		0.642	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741		T	99700841	G	T	99700841	4	4	133	1	0	0	0	0	0	1	0	0	5562	1233	43	4	1662	4	FAM22G	9	99700841	Nonsense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	2619504	99700841	41512590	66	11817											
PTGR1	22949	broad.mit.edu;bcgsc.ca	37	chr9	114332439	114332439	+	Frame_Shift_Del	DEL	C	C	-																															tccttgccagcggtagacgaCaaaagcttccatgcgaagct																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:114332439delC	ENST00000407693.2	-	9	1073	c.811delG	c.(811-813)gtcfs	p.V272fs	PTGR1_ENST00000538962.1_Frame_Shift_Del_p.V272fs|PTGR1_ENST00000238248.3_Frame_Shift_Del_p.V149fs|ZNF483_ENST00000358151.4_Intron|PTGR1_ENST00000309195.5_Frame_Shift_Del_p.V272fs	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	272					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						CGGTAGACGACAAAAGCTTCC	0.547																																					p.V271fs	Ovarian(200;132 2151 7551 19220 46064)												.	PTGR1-90	0			c.811delG						.						53	52	52					9																	114332439		2203	4300	6503	SO:0001589	frameshift_variant	22949	exon9			AGACGACAAAAGC	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.811delG	9.37:g.114332439delC	ENSP00000385763:p.Val272fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	61	7	NM_001146108	0	0	0	0	0	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Frame_Shift_Del	DEL	ENST00000407693.2	37	CCDS6779.1																																																																																			.		0.547	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			-	114332439	C	-	114332439	7	5	133	1	0	1	0	1	0	0	0	0	12783	478	17	0	217	0	PTGR1	9	114332439	Frame_Shift_Del	DEL	C	TCGA-HE-A5NI-01A-11D-A26P-10	14631598	114332439	26880992	67	11818	121	2									
PTGR1	22949	bcgsc.ca	37	chr9	114332440	114332440	+	Silent	SNP	A	A	G																															ccttgccagcggtagacgacAaaagcttccatgcgaagctc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:114332440A>G	ENST00000407693.2	-	9	1072	c.810T>C	c.(808-810)ttT>ttC	p.F270F	PTGR1_ENST00000538962.1_Silent_p.F270F|PTGR1_ENST00000238248.3_Silent_p.F147F|ZNF483_ENST00000358151.4_Intron|PTGR1_ENST00000309195.5_Silent_p.F270F	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	270					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						GGTAGACGACAAAAGCTTCCA	0.547																																					p.F270F	Ovarian(200;132 2151 7551 19220 46064)												.	PTGR1-90	0			c.T810C						.						53	52	52					9																	114332440		2203	4300	6503	SO:0001819	synonymous_variant	22949	exon9			GACGACAAAAGCT	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.810T>C	9.37:g.114332440A>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_1	64	7	NM_001146108	0	0	31	31	0	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Silent	SNP	ENST00000407693.2	37	CCDS6779.1																																																																																			.		0.547	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			G	114332440	A	G	114332440	2	3	133	1	0	0	0	0	0	0	0	1	12783	127	5	3		3	PTGR1	9	114332440	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	1	114332440	26880991	68	11819	121	2									
GPR21	2844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	125797664	125797664	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatatatcatctacttcttGttggaaagctccactggcca	10	13	6	12	0	3	0	1	0	2	0	4	1	4	1	3	2	2	2	3	2	4	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:125797664G>T	ENST00000373642.1	+	1	859	c.819G>T	c.(817-819)ttG>ttT	p.L273F	RABGAP1_ENST00000373647.4_Intron|RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373643.5_Intron	NM_005294.1	NP_005285.1	Q99679	GPR21_HUMAN	G protein-coupled receptor 21	273					G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|negative regulation of insulin receptor signaling pathway (GO:0046627)|positive regulation of multicellular organism growth (GO:0040018)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	15						TCTACTTCTTGTTGGAAAGCT	0.458																																					p.L273F		.											.	GPR21-91	0			c.G819T						.						148	128	135					9																	125797664		2203	4300	6503	SO:0001583	missense	2844	exon2			CTTCTTGTTGGAA	BC066885	CCDS6849.1	9q33	2012-08-21			ENSG00000188394	ENSG00000188394		"GPCR / Class A : Orphans"	4476	protein-coding gene	gene with protein product		601909					Standard	NM_005294		Approved		uc011lzk.3	Q99679	OTTHUMG00000020631	ENST00000373642.1:c.819G>T	9.37:g.125797664G>T	ENSP00000362746:p.Leu273Phe	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	129	49	NM_005294	0	0	0	0	0	B2R8W9|Q6NXU2	Missense_Mutation	SNP	ENST00000373642.1	37	CCDS6849.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365299	0.24684	.	.	ENSG00000188394	ENST00000373642	T	0.41758	0.99	5.93	1.91	0.25777	GPCR, rhodopsin-like superfamily (1);	0.281802	0.23228	U	0.050493	T	0.33352	0.0860	M	0.64630	1.985	0.80722	D	1	P	0.41232	0.743	B	0.36244	0.22	T	0.05099	-1.0906	10	0.44086	T	0.13	-6.8862	5.7514	0.18148	0.2774:0.2257:0.4969:0.0	.	273	Q99679	GPR21_HUMAN	F	273	ENSP00000362746:L273F	ENSP00000362746:L273F	L	+	3	2	GPR21	124837485	0.993000	0.37304	0.989000	0.46669	0.976000	0.68499	0.535000	0.23114	0.080000	0.16959	-0.218000	0.12543	TTG	.		0.458	GPR21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053965.1	NM_005294		T	125797664	G	T	125797664	3	4	133	1	0	0	0	0	1	0	0	0	6701	1368	48	4	821	4	GPR21	9	125797664	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	11465224	125797664	15415767	69	11820											
SPTAN1	6709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131386741	131386741	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccttcagttcaactggaaGgcggacgtggtggagtcctg	7	11	14	9	2	2	0	2	0	0	0	4	3	4	3	2	5	1	1	2	5	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:131386741G>A	ENST00000372731.4	+	45	6062	c.5952G>A	c.(5950-5952)aaG>aaA	p.K1984K	SPTAN1_ENST00000372739.3_Silent_p.K1989K|SPTAN1_ENST00000358161.5_Silent_p.K1989K	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1984					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TCAACTGGAAGGCGGACGTGG	0.562																																					p.K1989K	NSCLC(120;833 1744 2558 35612 37579)	.											.	SPTAN1-158	0			c.G5967A						.						64	53	57					9																	131386741		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon46			CTGGAAGGCGGAC	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"EF-hand domain containing"	11273	protein-coding gene	gene with protein product	"alpha-fodrin"	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.5952G>A	9.37:g.131386741G>A		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	159	68	NM_001130438	0	0	19	32	13	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			.		0.562	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131386741	G	A	131386741	2	1	133	1	0	0	0	0	0	0	0	1	15149	991	35	2		2	SPTAN1	9	131386741	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	5589077	131386741	9826690	70	11821											
DNAJC1	64215	ucsc.edu	37	chr10	22208842	22208842	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttttcttttctctcttttttCtacttagtagttcatcctta	5	25	2	9	0	5	0	1	0	4	0	7	0	6	0	1	0	1	2	1	0	4	12			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:22208842C>G	ENST00000376980.3	-	5	844	c.554G>C	c.(553-555)aGa>aCa	p.R185T		NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	185					negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				TCTCTTTTTTCTACTTAGTAG	0.333																																					p.R185T													.	DNAJC1-226	0			c.G554C						.						82	87	85					10																	22208842		2201	4293	6494	SO:0001583	missense	64215	exon5			TTTTTTCTACTTA	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.554G>C	10.37:g.22208842C>G	ENSP00000366179:p.Arg185Thr	Somatic	24	0		WXS	Illumina HiSeq		5	1	NM_022365	0	0	3	11	8	B0YIZ8|Q5VX89|Q9H6B8	Missense_Mutation	SNP	ENST00000376980.3	37	CCDS7136.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077825	0.36662	.	.	ENSG00000136770	ENST00000376980	T	0.45668	0.89	5.7	4.79	0.61399	.	0.126969	0.64402	D	0.000001	T	0.30603	0.0770	L	0.38531	1.155	0.80722	D	1	P	0.40144	0.704	B	0.38378	0.272	T	0.02813	-1.1107	10	0.17832	T	0.49	-7.7676	11.1524	0.48466	0.0:0.8588:0.0:0.1412	.	185	Q96KC8	DNJC1_HUMAN	T	185	ENSP00000366179:R185T	ENSP00000366179:R185T	R	-	2	0	DNAJC1	22248848	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.912000	0.28597	2.695000	0.91970	0.650000	0.86243	AGA	.		0.333	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		G	22208842	C	G	22208842	3	3	133	1	0	0	0	0	1	0	0	0	4639	913	32	4	1142	4	DNAJC1	10	22208842	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10		22208842	113325905	71	11822											
KIF5B	3799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	32320043	32320043	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaagcaattcatattccttAgttttgtcttcaacttcctg	9	18	4	10	0	3	0	2	0	1	0	5	0	5	0	2	0	2	2	2	0	5	9			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:32320043A>G	ENST00000302418.4	-	14	1996	c.1539T>C	c.(1537-1539)acT>acC	p.T513T		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	513					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				CATATTCCTTAGTTTTGTCTT	0.313			T	"RET, ALK"	NSCLC																																p.T513T		.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B-399	0			c.T1539C						.						103	101	102					10																	32320043		2203	4300	6503	SO:0001819	synonymous_variant	3799	exon14			TTCCTTAGTTTTG	X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"Kinesins"	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.1539T>C	10.37:g.32320043A>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	37	10	NM_004521	0	0	2	2	0	A0AVB2|Q5VZ85	Silent	SNP	ENST00000302418.4	37	CCDS7171.1																																																																																			.		0.313	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		G	32320043	A	G	32320043	2	3	133	1	0	0	0	0	0	0	0	1	8327	407	15	3		3	KIF5B	10	32320043	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	10111201	32320043	103214704	72	11823											
CYP26A1	1592	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	94834101	94834101	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatgaagcgcaggaaatacGgcttcatctacaagacgcat	15	7	10	9	3	2	3	1	1	1	2	2	4	2	4	0	2	3	3	0	2	5	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:94834101G>A	ENST00000224356.4	+	2	271	c.226G>A	c.(226-228)Ggc>Agc	p.G76S	CYP26A1_ENST00000394139.1_Missense_Mutation_p.G7S|CYP26A1_ENST00000371531.1_Missense_Mutation_p.G7S	NM_000783.3	NP_000774.2	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A, polypeptide 1	76					anterior/posterior pattern specification (GO:0009952)|cellular response to retinoic acid (GO:0071300)|central nervous system development (GO:0007417)|metabolic process (GO:0008152)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Colorectal(252;0.122)			Acitretin(DB00459)|Ketoconazole(DB01026)|Vitamin A(DB00162)	CAGGAAATACGGCTTCATCTA	0.657																																					p.G76S		.											.	CYP26A1-155	0			c.G226A						.						53	56	55					10																	94834101		2203	4300	6503	SO:0001583	missense	1592	exon2			AAATACGGCTTCA	AF005418	CCDS7426.1, CCDS7427.1	10q23-q24	2003-10-06	2003-01-14		ENSG00000095596	ENSG00000095596		"Cytochrome P450s"	2603	protein-coding gene	gene with protein product		602239	"cytochrome P450, subfamily XXVIA, polypeptide 1"			9228017, 9521883	Standard	NM_000783		Approved	P450RAI, CP26, CYP26, P450RAI1	uc001kil.2	O43174	OTTHUMG00000018765	ENST00000224356.4:c.226G>A	10.37:g.94834101G>A	ENSP00000224356:p.Gly76Ser	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	51	17	NM_000783	0	0	0	0	0	B3KNI4|Q5VXH9|Q5VXI0	Missense_Mutation	SNP	ENST00000224356.4	37	CCDS7426.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324133	0.95708	.	.	ENSG00000095596	ENST00000371531;ENST00000224356;ENST00000394139	T;T;T	0.78003	-1.14;-1.14;-1.14	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.85504	0.5712	L	0.52759	1.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84672	0.0712	10	0.45353	T	0.12	-21.1018	18.8725	0.92320	0.0:0.0:1.0:0.0	.	76	O43174	CP26A_HUMAN	S	7;76;7	ENSP00000360586:G7S;ENSP00000224356:G76S;ENSP00000377695:G7S	ENSP00000224356:G76S	G	+	1	0	CYP26A1	94824091	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.187000	0.94912	2.711000	0.92665	0.561000	0.74099	GGC	.		0.657	CYP26A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049408.3			A	94834101	G	A	94834101	3	1	133	1	0	0	0	0	1	0	0	0	4161	1116	39	1	232	1	CYP26A1	10	94834101	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	62514058	94834101	40700646	73	11824											
LGI1	9211	hgsc.bcm.edu	37	chr10	95549895	95549895	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccagacactcccaaaagaTattttcaaaggcctggattc	13	10	6	12	0	1	2	1	0	0	2	4	3	3	3	3	2	0	0	3	2	4	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:95549895T>C	ENST00000371418.4	+	5	731	c.471T>C	c.(469-471)gaT>gaC	p.D157D	LGI1_ENST00000371413.3_Silent_p.D157D|LGI1_ENST00000542308.1_Silent_p.D109D	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	157					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				TCCCAAAAGATATTTTCAAAG	0.328																																					p.D157D		.											.	LGI1-517	0			c.T471C						.						54	57	56					10																	95549895		2203	4299	6502	SO:0001819	synonymous_variant	9211	exon5			AAAAGATATTTTC	AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"epilepsy, partial"	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.471T>C	10.37:g.95549895T>C		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	10	5	NM_005097	0	0	0	0	0	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Silent	SNP	ENST00000371418.4	37	CCDS7431.1																																																																																			.		0.328	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		C	95549895	T	C	95549895	2	2	133	1	0	0	0	0	0	0	0	1	8773	1403	49	3		3	LGI1	10	95549895	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	715794	95549895	39984852	74	11825											
SEMA4G	57715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	102738660	102738660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagcaaggccagtgcagtggGtgatgatgacaaggtgtact	11	8	16	6	0	0	3	0	3	0	0	0	4	0	3	1	3	3	3	1	3	3	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:102738660G>A	ENST00000370250.4	+	7	1071	c.698G>A	c.(697-699)gGt>gAt	p.G233D	SEMA4G_ENST00000519756.1_Intron|MRPL43_ENST00000318325.2_3'UTR|MRPL43_ENST00000370241.3_3'UTR|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000517724.1_Missense_Mutation_p.G233D|SEMA4G_ENST00000210633.3_Missense_Mutation_p.G233D	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	233	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		AGTGCAGTGGGTGATGATGAC	0.587																																					p.G233D		.											.	SEMA4G-154	0			c.G698A						.						84	65	71					10																	102738660		2203	4300	6503	SO:0001583	missense	57715	exon7			CAGTGGGTGATGA	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.698G>A	10.37:g.102738660G>A	ENSP00000359270:p.Gly233Asp	Somatic	370	0		WXS	Illumina HiSeq	Phase_I	288	106	NM_001203244	0	0	0	0	0	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		.	.	.	.	.	.	.	.	.	.	G	23.0	4.363918	0.82353	.	.	ENSG00000095539	ENST00000519649;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.74	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.050938	0.85682	D	0.000000	T	0.52805	0.1757	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.984	D;D;P	0.97110	1.0;1.0;0.907	T	0.53049	-0.8493	10	0.45353	T	0.12	.	13.9543	0.64137	0.0731:0.0:0.9269:0.0	.	233;233;233	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	D	233	ENSP00000428896:G233D;ENSP00000359270:G233D;ENSP00000430175:G233D;ENSP00000210633:G233D	ENSP00000210633:G233D	G	+	2	0	SEMA4G	102728650	1.000000	0.71417	0.959000	0.39883	0.876000	0.50452	7.636000	0.83301	1.433000	0.47394	0.484000	0.47621	GGT	.		0.587	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			A	102738660	G	A	102738660	3	1	133	1	0	0	0	0	1	0	0	0	14068	1261	44	2	724	2	SEMA4G	10	102738660	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	7188765	102738660	32796087	75	11826											
PPRC1	23082	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103899235	103899235	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgcccaacctcacccacctgGcatcacttgaggatgagctt	9	9	8	15	0	2	2	2	2	0	0	2	3	2	3	4	2	3	2	4	2	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:103899235G>A	ENST00000278070.2	+	5	1009	c.970G>A	c.(970-972)Gca>Aca	p.A324T	PPRC1_ENST00000370012.1_5'Flank|PPRC1_ENST00000413464.2_Missense_Mutation_p.A324T	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	324					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CACCCACCTGGCATCACTTGA	0.602																																					p.A324T													.	PPRC1-227	0			c.G970A						.						90	77	81					10																	103899235		2203	4300	6503	SO:0001583	missense	23082	exon5			CACCTGGCATCAC	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.970G>A	10.37:g.103899235G>A	ENSP00000278070:p.Ala324Thr	Somatic	133	1		WXS	Illumina HiSeq	Phase_I	134	43	NM_015062	0	0	1	1	0	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	G	7.563	0.665151	0.14710	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.53857	0.6;0.6	5.87	1.18	0.20946	.	0.908110	0.09536	N	0.788858	T	0.27205	0.0667	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.20773	-1.0265	10	0.20519	T	0.43	.	4.8401	0.13485	0.2462:0.0:0.584:0.1699	.	324;204;324	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	T	324	ENSP00000278070:A324T;ENSP00000399743:A324T	ENSP00000278070:A324T	A	+	1	0	PPRC1	103889225	0.825000	0.29262	0.862000	0.33874	0.407000	0.30961	1.093000	0.30939	0.240000	0.21263	-0.350000	0.07774	GCA	.		0.602	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		A	103899235	G	A	103899235	3	1	133	1	0	0	0	0	1	0	0	0	12439	1203	42	2	988	2	PPRC1	10	103899235	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	1160575	103899235	31635512	76	11827											
DMBT1	1755	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	124339398	124339398	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgtggccatagtgaagaCgctggtgtcatctgctcagg	9	10	13	9	1	3	2	2	1	1	1	3	2	3	2	1	3	2	2	1	3	3	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:124339398C>G	ENST00000338354.3	+	10	1090	c.984C>G	c.(982-984)gaC>gaG	p.D328E	DMBT1_ENST00000344338.3_Missense_Mutation_p.D328E|DMBT1_ENST00000368909.3_Missense_Mutation_p.D328E|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Missense_Mutation_p.D328E|DMBT1_ENST00000330163.4_Missense_Mutation_p.D328E|DMBT1_ENST00000368956.2_Missense_Mutation_p.D328E			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	328	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				ATAGTGAAGACGCTGGTGTCA	0.532																																					p.D328E	Ovarian(182;93 2026 18125 22222 38972)												.	DMBT1-494	0			c.C984G						.						82	81	81					10																	124339398		1908	4138	6046	SO:0001583	missense	1755	exon10			TGAAGACGCTGGT		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.984C>G	10.37:g.124339398C>G	ENSP00000342210:p.Asp328Glu	Somatic	127	1		WXS	Illumina HiSeq	Phase_I	101	25	NM_007329	0	0	0	0	0	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	c	16.17	3.046172	0.55110	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.52526	0.66;0.66;0.66;0.66;0.66;0.66	3.94	-7.88	0.01178	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.74741	0.3756	H	0.95504	3.68	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;1.0	D;D;D;D;D	0.97110	1.0;0.996;0.98;0.997;0.999	D	0.85967	0.1474	9	0.66056	D	0.02	.	19.1418	0.93449	0.0:0.092:0.0:0.908	.	328;328;328;328;328	Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	E	328	ENSP00000342210:D328E;ENSP00000343175:D328E;ENSP00000327747:D328E;ENSP00000357905:D328E;ENSP00000357951:D328E;ENSP00000357952:D328E	ENSP00000331522:D328E	D	+	3	2	DMBT1	124329388	0.017000	0.18338	0.000000	0.03702	0.118000	0.20060	-1.037000	0.03557	-3.153000	0.00230	-1.386000	0.01163	GAC	.		0.532	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124339398	C	G	124339398	3	3	133	1	0	0	0	0	1	0	0	0	4588	535	19	4	1022	4	DMBT1	10	124339398	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	20440163	124339398	11195349	77	11828											
C2CD3	26005	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	73748552	73748561	+	Frame_Shift_Del	DEL	AGGTTACTGG	AGGTTACTGG	-																															aggagctgacttgcaacaccAggttactggatttctccagg																								rs146977583		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AGGTTACTGG	AGGTTACTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr11:73748552_73748561delAGGTTACTGG	ENST00000334126.7	-	30	6069_6078	c.5843_5852delCCAGTAACCT	c.(5842-5853)tccagtaacctgfs	p.SSNL1948fs	C2CD3_ENST00000313663.7_Frame_Shift_Del_p.SSNL1948fs			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1948					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTGCAACACCAGGTTACTGGATTTCTCCAG	0.49																																					p.1948_1951del		.											.	C2CD3-75	0			c.5843_5852del						.																																			SO:0001589	frameshift_variant	26005	exon30			.	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5843_5852delCCAGTAACCT	11.37:g.73748552_73748561delAGGTTACTGG	ENSP00000334379:p.Ser1948fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	97	31	NM_015531	0	0	0	0	0	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Frame_Shift_Del	DEL	ENST00000334126.7	37																																																																																				.		0.49	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		-	73748561	AGGTTACTGG	-	73748552	7	5	133	1	0	1	0	1	0	0	0	0	2160	188	7	0	47	0	C2CD3	11	73748552	Frame_Shift_Del	DEL	AGGTTACTGG	TCGA-HE-A5NI-01A-11D-A26P-10		73748552	61257964	78	11829											
NAALAD2	10003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	89896525	89896525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggactcctgggtatttggaGctattgacccaaccagtggg	8	10	14	9	0	0	1	0	1	0	0	1	3	1	3	3	4	2	2	3	4	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr11:89896525G>A	ENST00000534061.1	+	10	1353	c.1123G>A	c.(1123-1125)Gct>Act	p.A375T	NAALAD2_ENST00000321955.4_Missense_Mutation_p.A342T|NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000525171.1_Missense_Mutation_p.A282T	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	375	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GGTATTTGGAGCTATTGACCC	0.403																																					p.A375T		.											.	NAALAD2-92	0			c.G1123A						.						122	129	126					11																	89896525		2201	4299	6500	SO:0001583	missense	10003	exon10			TTTGGAGCTATTG	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1123G>A	11.37:g.89896525G>A	ENSP00000432481:p.Ala375Thr	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_005467	0	0	0	0	0	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	37	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688939	0.68271	.	.	ENSG00000077616	ENST00000534061;ENST00000321955;ENST00000525171	T;T;T	0.65364	-0.15;-0.15;-0.15	5.51	4.61	0.57282	Peptidase M28 (1);	0.502085	0.19690	N	0.108285	T	0.69975	0.3171	M	0.83012	2.62	0.80722	D	1	P;B	0.45283	0.855;0.001	P;B	0.45753	0.492;0.004	T	0.73726	-0.3892	9	.	.	.	-1.5086	14.2116	0.65769	0.0725:0.0:0.9275:0.0	.	375;282	Q9Y3Q0;E9PKX5	NALD2_HUMAN;.	T	375;342;282	ENSP00000432481:A375T;ENSP00000320083:A342T;ENSP00000435249:A282T	.	A	+	1	0	NAALAD2	89536173	1.000000	0.71417	0.972000	0.41901	0.993000	0.82548	7.040000	0.76551	1.467000	0.48044	-0.218000	0.12543	GCT	.		0.403	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		A	89896525	G	A	89896525	3	1	133	1	0	0	0	0	1	0	0	0	10153	971	34	2	1161	2	NAALAD2	11	89896525	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	16147973	89896525	45109991	79	11830											
GPRC5D	55507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	13102558	13102558	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggacgatgtacagcagcAggaaaacccatgcgttggtg	12	6	14	9	2	0	0	0	0	0	0	0	3	0	2	1	3	5	4	1	3	3	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:13102558A>T	ENST00000228887.1	-	1	760	c.761T>A	c.(760-762)cTg>cAg	p.L254Q	RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000545914.1_RNA|GPRC5D_ENST00000396333.3_Missense_Mutation_p.L254Q|RP11-392P7.6_ENST00000540198.1_RNA|RP11-392P7.6_ENST00000542078.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	254						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		GTACAGCAGCAGGAAAACCCA	0.577																																					p.L254Q		.											.	GPRC5D-90	0			c.T761A						.						144	132	136					12																	13102558		2203	4300	6503	SO:0001583	missense	55507	exon1			AGCAGCAGGAAAA	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"GPCR / Class C : Orphans"	13310	protein-coding gene	gene with protein product		607437	"G protein-coupled receptor, family C, group 5, member D"				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.761T>A	12.37:g.13102558A>T	ENSP00000228887:p.Leu254Gln	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	245	129	NM_018654	0	0	0	0	0	Q3KNV3|Q7Z5J9|Q8TDS6	Missense_Mutation	SNP	ENST00000228887.1	37	CCDS8658.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684961	0.88639	.	.	ENSG00000111291	ENST00000228887;ENST00000396333	D;D	0.94793	-3.52;-3.52	6.03	6.03	0.97812	GPCR, family 3, C-terminal (1);	0.000000	0.56097	D	0.000037	D	0.97269	0.9107	M	0.80183	2.485	0.51767	D	0.999936	D	0.89917	1.0	D	0.97110	1.0	D	0.97842	1.0269	10	0.87932	D	0	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	254	Q9NZD1	GPC5D_HUMAN	Q	254	ENSP00000228887:L254Q;ENSP00000379624:L254Q	ENSP00000228887:L254Q	L	-	2	0	GPRC5D	12993825	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.300000	0.96151	2.302000	0.77476	0.533000	0.62120	CTG	.		0.577	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1			T	13102558	A	T	13102558	3	4	133	1	0	0	0	0	1	0	0	0	6748	188	7	5	286	5	GPRC5D	12	13102558	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		13102558	120749337	80	11831											
PDZRN4	29951	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	41966603	41966603	+	Frame_Shift_Del	DEL	A	A	-																															ttgcttaatgaagaactgagAaacattgagcttgagtgtca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:41966603delA	ENST00000402685.2	+	10	2030	c.2022delA	c.(2020-2022)agafs	p.R674fs	PDZRN4_ENST00000539469.2_Frame_Shift_Del_p.R416fs|PDZRN4_ENST00000298919.7_Frame_Shift_Del_p.R414fs	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	674							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AAGAACTGAGAAACATTGAGC	0.458																																					p.R674fs		.											.	PDZRN4-296	0			c.2022delA						.						112	100	104					12																	41966603		2203	4300	6503	SO:0001589	frameshift_variant	29951	exon10			.	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"RING-type (C3HC4) zinc fingers"	30552	protein-coding gene	gene with protein product	"similar to semaF cytoplasmic domain associated protein 3"	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2022delA	12.37:g.41966603delA	ENSP00000384197:p.Arg674fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	212	64	NM_001164595	0	0	0	0	0	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Frame_Shift_Del	DEL	ENST00000402685.2	37	CCDS53777.1																																																																																			.		0.458	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		-	41966603	A	-	41966603	7	5	133	1	0	1	0	1	0	0	0	0	11736	243	9	0	2133	0	PDZRN4	12	41966603	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	28864045	41966603	91885292	81	11832											
GALNT6	11226	broad.mit.edu;bcgsc.ca	37	chr12	51751976	51751982	+	Frame_Shift_Del	DEL	ACCAGGA	ACCAGGA	-																															tgggtagacattgtgcaggtAccaggaaaagttgtgacagt																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	ACCAGGA	ACCAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:51751976_51751982delACCAGGA	ENST00000543196.2	-	8	1637_1643	c.1432_1438delTCCTGGT	c.(1432-1440)tcctggtacfs	p.SWY478fs	GALNT6_ENST00000356317.3_Frame_Shift_Del_p.SWY478fs			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	478					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TTGTGCAGGTACCAGGAAAAGTTGTGA	0.517																																					p.478_480del													.	GALNT6-92	0			c.1432_1438del						.																																			SO:0001589	frameshift_variant	11226	exon9			GCAGGTACCAGGA	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.1432_1438delTCCTGGT	12.37:g.51751976_51751982delACCAGGA	ENSP00000444171:p.Ser478fs	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	245	33	NM_007210	0	0	0	0	0	Q8IYH4|Q9H6G2|Q9UIV5	Frame_Shift_Del	DEL	ENST00000543196.2	37	CCDS8813.1																																																																																			.		0.517	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		-	51751982	ACCAGGA	-	51751976	7	5	133	1	0	1	0	1	0	0	0	0	6237	391	14	0	446	0	GALNT6	12	51751976	Frame_Shift_Del	DEL	ACCAGGA	TCGA-HE-A5NI-01A-11D-A26P-10	9785373	51751976	82099919	82	11833											
SP7	121340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53722359	53722359	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagctgtggatgggcttcttCcgcagcccagccgctgctgc	4	9	13	15	2	1	0	0	0	1	0	2	1	2	1	3	2	5	5	3	2	0	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:53722359C>T	ENST00000536324.2	-	3	1150	c.867G>A	c.(865-867)cgG>cgA	p.R289R	SP7_ENST00000303846.3_Silent_p.R289R|SP7_ENST00000537210.2_Silent_p.R271R	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	289					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						TGGGCTTCTTCCGCAGCCCAG	0.657																																					p.R289R		.											.	.	0			c.G867A						.						17	22	20					12																	53722359		2187	4292	6479	SO:0001819	synonymous_variant	121340	exon2			CTTCTTCCGCAGC	AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.867G>A	12.37:g.53722359C>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	43	17	NM_152860	0	0	0	0	0	B3KY26|Q3MJ72|Q7Z718	Silent	SNP	ENST00000536324.2	37	CCDS44897.1																																																																																			.		0.657	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			T	53722359	C	T	53722359	2	4	133	1	0	0	0	0	0	0	0	1	15001	842	30	2		2	SP7	12	53722359	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	1970383	53722359	80129536	83	11834											
DNAJC14	85406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56216194	56216194	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcctggaatccgagaaccaaAtgagatgtgataggggactc	13	7	13	8	1	0	3	0	2	0	2	2	7	1	5	3	3	1	0	3	3	4	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:56216194A>G	ENST00000357606.3	-	7	2150	c.1861T>C	c.(1861-1863)Ttt>Ctt	p.F621L	RP11-762I7.5_ENST00000552719.1_5'UTR|RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.I250T|DNAJC14_ENST00000317287.5_Missense_Mutation_p.F621L|DNAJC14_ENST00000317269.3_Missense_Mutation_p.F621L			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	621					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						CGAGAACCAAATGAGATGTGA	0.463											OREG0021910	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F621L		.											.	DNAJC14-229	0			c.T1861C						.						107	112	110					12																	56216194		2203	4300	6503	SO:0001583	missense	85406	exon6			AACCAAATGAGAT	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.1861T>C	12.37:g.56216194A>G	ENSP00000350223:p.Phe621Leu	Somatic	104	0	1013	WXS	Illumina HiSeq	Phase_I	120	62	NM_032364	0	0	3	9	6	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Missense_Mutation	SNP	ENST00000357606.3	37	CCDS8894.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.5|23.5	4.424150|4.424150	0.83667|0.83667	.|.	.|.	ENSG00000135392|ENSG00000257390	ENST00000357606;ENST00000317269;ENST00000537962;ENST00000317287;ENST00000540330|ENST00000546837	T;T;T|.	0.33216|.	1.42;1.42;1.42|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53481|0.53481	0.1799|0.1799	L|L	0.28014|0.28014	0.82|0.82	0.58432|0.58432	D|D	0.999997|0.999997	D;D|.	0.71674|.	0.998;0.998|.	D;D|.	0.72625|.	0.978;0.978|.	T|T	0.50285|0.50285	-0.8846|-0.8846	10|5	0.29301|.	T|.	0.29|.	-12.4258|-12.4258	14.2815|14.2815	0.66216|0.66216	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	621;621|.	Q6Y2X3;A8K5A7|.	DJC14_HUMAN;.|.	L|T	621;621;331;621;117|250	ENSP00000350223:F621L;ENSP00000316240:F621L;ENSP00000317500:F621L|.	ENSP00000316240:F621L|.	F|I	-|-	1|2	0|0	DNAJC14|RP11-762I7.5	54502461|54502461	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	8.512000|8.512000	0.90538|0.90538	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	TTT|ATT	.		0.463	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		G	56216194	A	G	56216194	3	3	133	1	0	0	0	0	1	0	0	0	4644	101	4	3	255	3	DNAJC14	12	56216194	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	2493835	56216194	77635701	84	11835											
DPY19L2	283417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	63991615	63991615	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttccatgaagtcaaattcggGagcacaggtatatattaaag	15	11	9	6	1	1	1	1	1	0	0	3	2	2	2	1	2	1	2	1	2	7	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:63991615G>A	ENST00000324472.4	-	14	1618	c.1435C>T	c.(1435-1437)Ccc>Tcc	p.P479S		NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	479					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		TCAAATTCGGGAGCACAGGTA	0.323																																					p.P479S		.											.	DPY19L2-515	0			c.C1435T						.						53	58	56					12																	63991615		2202	4287	6489	SO:0001583	missense	283417	exon14			ATTCGGGAGCACA		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"spermatogenesis associated 34"	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.1435C>T	12.37:g.63991615G>A	ENSP00000315988:p.Pro479Ser	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	129	29	NM_173812	0	0	0	0	0	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769090	0.49680	.	.	ENSG00000177990	ENST00000324472	T	0.54071	0.59	3.15	2.22	0.28083	.	0.062767	0.64402	U	0.000008	T	0.51991	0.1707	M	0.71581	2.175	0.58432	D	0.999999	B	0.25272	0.122	B	0.36186	0.219	T	0.44050	-0.9353	9	.	.	.	.	8.3442	0.32263	0.0:0.2427:0.7573:0.0	.	479	Q6NUT2	D19L2_HUMAN	S	479	ENSP00000315988:P479S	.	P	-	1	0	DPY19L2	62277882	1.000000	0.71417	0.698000	0.30274	0.953000	0.61014	2.632000	0.46511	0.619000	0.30197	0.586000	0.80456	CCC	.		0.323	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		A	63991615	G	A	63991615	3	1	133	1	0	0	0	0	1	0	0	0	4752	1174	41	2	877	2	DPY19L2	12	63991615	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	7775421	63991615	69860280	85	11836											
TMPO	7112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	98925573	98925573	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagcagaaaatacaaggcaGaatggaagtaatgattctga	18	8	10	5	0	2	4	1	2	1	2	2	5	2	5	0	2	2	3	0	2	7	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:98925573G>C	ENST00000556029.1	+	3	878	c.522G>C	c.(520-522)caG>caC	p.Q174H	TMPO_ENST00000343315.5_Missense_Mutation_p.Q174H|TMPO_ENST00000266732.4_Missense_Mutation_p.Q174H|TMPO_ENST00000393053.2_Missense_Mutation_p.Q174H|TMPO_ENST00000261210.5_Missense_Mutation_p.Q174H	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	174	NAKAP95-binding N.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						ATACAAGGCAGAATGGAAGTA	0.323																																					p.Q174H		.											.	TMPO-93	0			c.G522C						.						70	70	70					12																	98925573		2203	4300	6503	SO:0001583	missense	7112	exon3			AAGGCAGAATGGA		CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802			11875	protein-coding gene	gene with protein product	"LEM domain containing 4"	188380				7517549	Standard	NM_003276		Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.522G>C	12.37:g.98925573G>C	ENSP00000450627:p.Gln174His	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	160	36	NM_003276	0	0	4	4	0	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	37	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562332	0.65538	.	.	ENSG00000120802	ENST00000556029;ENST00000343315;ENST00000266732;ENST00000393053;ENST00000261210;ENST00000556678	T;T;T;T;T;T	0.74421	0.18;0.22;1.55;-0.23;-0.84;-0.8	5.4	2.51	0.30379	.	0.053524	0.85682	D	0.000000	T	0.78046	0.4222	L	0.46157	1.445	0.49687	D	0.999819	D;P;D;D	0.71674	0.997;0.604;0.998;0.997	D;B;D;D	0.79784	0.991;0.204;0.993;0.99	T	0.75611	-0.3258	10	0.59425	D	0.04	.	6.5002	0.22164	0.2145:0.1293:0.6561:0.0	.	207;174;174;174	Q59G12;P42167;A2T926;P42166	.;LAP2B_HUMAN;.;LAP2A_HUMAN	H	174;174;174;174;174;81	ENSP00000450627:Q174H;ENSP00000340251:Q174H;ENSP00000266732:Q174H;ENSP00000376773:Q174H;ENSP00000261210:Q174H;ENSP00000451552:Q81H	ENSP00000261210:Q174H	Q	+	3	2	TMPO	97449704	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.511000	0.45476	0.634000	0.30469	0.655000	0.94253	CAG	.		0.323	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		C	98925573	G	C	98925573	3	2	133	1	0	0	0	0	1	0	0	0	16269	933	33	4	532	4	TMPO	12	98925573	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	34933958	98925573	34926322	86	11837											
POLR3B	55703	broad.mit.edu	37	chr12	106890644	106890644	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atgtgtgtgaggacctcgttCgccatggttataactacttg	8	14	11	8	2	0	1	0	1	0	0	2	2	0	2	2	2	2	2	2	2	3	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:106890644C>T	ENST00000228347.4	+	25	3154	c.2932C>T	c.(2932-2934)Cgc>Tgc	p.R978C	RP11-144F15.1_ENST00000551505.1_Intron|POLR3B_ENST00000539066.1_Missense_Mutation_p.R920C	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	978				R -> C (in Ref. 2; BAA91527). {ECO:0000305}.	defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GGACCTCGTTCGCCATGGTTA	0.488																																					p.R978C													.	POLR3B-91	0			c.C2932T						.						215	170	185					12																	106890644		2203	4300	6503	SO:0001583	missense	55703	exon25			CTCGTTCGCCATG	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"RNA polymerase subunits"	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.2932C>T	12.37:g.106890644C>T	ENSP00000228347:p.Arg978Cys	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	116	4	NM_018082	0	0	4	4	0	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	C	35	5.566002	0.96540	.	.	ENSG00000013503	ENST00000228347;ENST00000539066	T;T	0.73047	-0.71;-0.71	5.56	5.56	0.83823	DNA-directed RNA polymerase, subunit 2, domain 6 (2);	0.046314	0.85682	D	0.000000	T	0.82226	0.4991	M	0.71036	2.16	0.80722	D	1	D	0.65815	0.995	P	0.58970	0.849	D	0.83970	0.0326	10	0.87932	D	0	-12.8497	19.5302	0.95226	0.0:1.0:0.0:0.0	.	978	Q9NW08	RPC2_HUMAN	C	978;920	ENSP00000228347:R978C;ENSP00000445721:R920C	ENSP00000228347:R978C	R	+	1	0	POLR3B	105414774	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	7.786000	0.85741	2.592000	0.87571	0.655000	0.94253	CGC	.		0.488	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082		T	106890644	C	T	106890644	3	4	133	1	0	0	0	0	1	0	0	0	12255	884	31	1	3030	1	POLR3B	12	106890644	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	7965071	106890644	26961251	87	11838											
RNF34	80196	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	121855373	121855374	+	Frame_Shift_Del	DEL	AG	AG	-																															tcttacaagaaaatctccgtAgatgttctacttgtcactta																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:121855373_121855374delAG	ENST00000392464.2	+	3	361_362	c.292_293delAG	c.(292-294)agafs	p.R98fs	RNF34_ENST00000361234.5_Frame_Shift_Del_p.R98fs|RNF34_ENST00000555076.1_Intron|RNF34_ENST00000392465.3_Frame_Shift_Del_p.R99fs					ring finger protein 34, E3 ubiquitin protein ligase											breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		AAATCTCCGTAGATGTTCTACT	0.416																																					p.99_99del		.											.	RNF34-226	0			c.295_296del						.																																			SO:0001589	frameshift_variant	80196	exon4			.	AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633		"RING-type (C3HC4) zinc fingers"	17297	protein-coding gene	gene with protein product		608299	"ring finger protein 34"			12118383	Standard	NM_025126		Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.292_293delAG	12.37:g.121855373_121855374delAG	ENSP00000376257:p.Arg98fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	82	44	NM_194271	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000392464.2	37																																																																																				.		0.416	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271		-	121855374	AG	-	121855373	7	5	133	1	0	1	0	1	0	0	0	0	13521	412	15	0	315	0	RNF34	12	121855373	Frame_Shift_Del	DEL	AG	TCGA-HE-A5NI-01A-11D-A26P-10	14964729	121855373	11996522	88	11839											
SACS	26278	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	23906370	23906371	+	Frame_Shift_Ins	INS	-	-	A																															tagactcctgaacagaccagINSaaactactctcttaactgta																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr13:23906370_23906371insA	ENST00000382292.3	-	9	11917_11918	c.11644_11645insT	c.(11644-11646)tctfs	p.S3882fs	SACS_ENST00000382298.3_Frame_Shift_Ins_p.S3882fs|SACS_ENST00000402364.1_Frame_Shift_Ins_p.S3132fs			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3882					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAACAGACCAGAAACTACTCTC	0.416																																					p.S3882fs		.											.	SACS-298	0			c.11645_11646insT						.																																			SO:0001589	frameshift_variant	26278	exon10			.	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"Heat shock proteins / DNAJ (HSP40)"	10519	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 138"	604490	"spastic ataxia of Charlevoix-Saguenay (sacsin)"			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.11645dupT	13.37:g.23906373_23906373dupA	ENSP00000371729:p.Ser3882fs	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	46	14	NM_014363	0	0	0	0	0	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Frame_Shift_Ins	INS	ENST00000382292.3	37	CCDS9300.2																																																																																			.		0.416	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23906371	-	A	23906370	7	5	133	1	0	1	1	0	0	0	0	0	13836	942	33	0	2098	0	SACS	13	23906370	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10		23906370	91263508	89	11840											
IPO4	79711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24654679	24654679	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcacctgtaggttttctgAgaactggcccagggcaaaca	10	10	11	10	0	2	1	1	1	1	1	2	2	2	1	2	3	2	4	2	3	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:24654679A>T	ENST00000354464.6	-	13	1440	c.1264T>A	c.(1264-1266)Tca>Aca	p.S422T	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	422					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		AGGTTTTCTGAGAACTGGCCC	0.562																																					p.S422T		.											.	IPO4-226	0			c.T1264A						.						85	91	89					14																	24654679		2042	4182	6224	SO:0001583	missense	79711	exon13			TTTCTGAGAACTG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1264T>A	14.37:g.24654679A>T	ENSP00000346453:p.Ser422Thr	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	141	60	NM_024658	0	0	0	0	0	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.007813	0.93287	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.05513	3.43	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.21962	0.0529	M	0.69185	2.1	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	T	0.00138	-1.2003	10	0.72032	D	0.01	-9.0334	13.1234	0.59340	1.0:0.0:0.0:0.0	.	422	Q8TEX9	IPO4_HUMAN	T	422;98	ENSP00000346453:S422T	ENSP00000346453:S422T	S	-	1	0	IPO4	23724519	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.283000	0.65621	2.288000	0.76882	0.533000	0.62120	TCA	.		0.562	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		T	24654679	A	T	24654679	3	4	133	1	0	0	0	0	1	0	0	0	7816	304	11	5	2053	5	IPO4	14	24654679	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		24654679	82694861	90	11841											
BRMS1L	84312	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	36300676	36300676	+	Frame_Shift_Del	DEL	T	T	-																															tttggatgaaatgtccaatcTtgaaaaacagtttaccgatc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:36300676delT	ENST00000216807.7	+	2	402	c.203delT	c.(202-204)cttfs	p.L68fs	BRMS1L_ENST00000543183.1_Frame_Shift_Del_p.L20fs	NM_032352.3	NP_115728.2	Q5PSV4	BRM1L_HUMAN	breast cancer metastasis-suppressor 1-like	68					regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Breast(36;0.137)|Hepatocellular(127;0.158)		Lung(8;1.7e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.00467)|all cancers(34;0.0157)|BRCA - Breast invasive adenocarcinoma(188;0.158)	GBM - Glioblastoma multiforme(112;0.0333)		ATGTCCAATCTTGAAAAACAG	0.333																																					p.L68fs		.											.	BRMS1L-226	0			c.203delT						.						116	117	116					14																	36300676		2203	4300	6503	SO:0001589	frameshift_variant	84312	exon2			.	AK096496	CCDS32066.1	14q13.1	2005-09-22	2003-12-02	2003-12-03		ENSG00000100916			20512	protein-coding gene	gene with protein product			"breast cancer metastasis-suppressor 1"	BRMS1			Standard	XM_005268128		Approved	MGC11296, FLJ39177	uc001wtl.3	Q5PSV4		ENST00000216807.7:c.203delT	14.37:g.36300676delT	ENSP00000216807:p.Leu68fs	Somatic	242	0		WXS	Illumina HiSeq	Phase_I	203	80	NM_032352	0	0	0	0	0	A6NFW5|A6NH45|B2RD65|Q9BRI4	Frame_Shift_Del	DEL	ENST00000216807.7	37	CCDS32066.1																																																																																			.		0.333	BRMS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409601.2	NM_032352		-	36300676	T	-	36300676	7	5	133	1	0	1	0	1	0	0	0	0	1520	1609	56	0	209	0	BRMS1L	14	36300676	Frame_Shift_Del	DEL	T	TCGA-HE-A5NI-01A-11D-A26P-10	11645997	36300676	71048864	91	11842											
NIN	51199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	51223359	51223359	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccttcaacttcctagtcagCtcctgtaactttgttttctc	6	18	4	13	0	3	0	2	0	1	0	7	0	6	0	3	0	3	3	3	0	3	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:51223359C>G	ENST00000382041.3	-	18	4579	c.4389G>C	c.(4387-4389)gaG>gaC	p.E1463D	NIN_ENST00000245441.5_Missense_Mutation_p.E1463D|NIN_ENST00000453196.1_Missense_Mutation_p.E1463D|NIN_ENST00000382043.4_Intron|NIN_ENST00000389868.3_Intron|NIN_ENST00000530997.2_Missense_Mutation_p.E1463D|NIN_ENST00000324330.9_Missense_Mutation_p.E1463D	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1463					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					tcctagtcagctcctgtaact	0.418			T	PDGFRB	MPD																																p.E1463D		.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN-229	0			c.G4389C						.						113	88	96					14																	51223359		2194	4286	6480	SO:0001583	missense	51199	exon18			AGTCAGCTCCTGT	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.4389G>C	14.37:g.51223359C>G	ENSP00000371472:p.Glu1463Asp	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	81	27	NM_020921	0	0	4	5	1	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.37|16.37	3.103971|3.103971	0.56291|0.56291	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853|ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	.|T;T;T;T	.|0.10192	.|3.17;2.91;2.9;2.91	5.59|5.59	4.7|4.7	0.59300|0.59300	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.20170|0.20170	0.0485|0.0485	M|M	0.62723|0.62723	1.935|1.935	0.31457|0.31457	N|N	0.670061|0.670061	.|P;D;P;P	.|0.59767	.|0.873;0.986;0.852;0.8	.|B;P;B;B	.|0.53224	.|0.291;0.721;0.275;0.416	T|T	0.11842|0.11842	-1.0571|-1.0571	5|10	.|0.48119	.|T	.|0.1	-1.0688|-1.0688	10.3959|10.3959	0.44201|0.44201	0.0:0.9099:0.0:0.0901|0.0:0.9099:0.0:0.0901	.|.	.|1469;1463;1463;1463	.|Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7	.|.;.;NIN_HUMAN;.	P|D	954|1463;1446;1469;1463;1463;1463	.|ENSP00000245441:E1463D;ENSP00000371472:E1463D;ENSP00000324210:E1463D;ENSP00000412391:E1463D	.|ENSP00000245441:E1463D	A|E	-|-	1|3	0|2	NIN|NIN	50293109|50293109	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	0.415000|0.415000	0.21181|0.21181	1.366000|1.366000	0.46076|0.46076	0.655000|0.655000	0.94253|0.94253	GCT|GAG	.		0.418	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		G	51223359	C	G	51223359	3	3	133	1	0	0	0	0	1	0	0	0	10443	796	28	4	2216	4	NIN	14	51223359	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	14922683	51223359	56126181	92	11843											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493794	77493794	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgctgctgTtgctgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1	rs377151545|rs28718623|rs71125518	byFrequency	TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:77493794T>C	ENST00000238647.3	-	1	1240	c.342A>G	c.(340-342)caA>caG	p.Q114Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	114	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgttgctgctgct	0.697													T|||	1146	0.228834	0.1649	0.1758	5008	,	,		5976	0.2659		0.2614	False		,,,				2504	0.2812				p.Q114Q		.											.	IRF2BPL-90	0			c.A342G						.	-		160,2330		6,148,1091	2	2	2		342	0.6	0	14	dbSNP_125	2	324,4012		7,310,1851	no	coding-synonymous	IRF2BPL	NM_024496.2		13,458,2942	CC,CT,TT		7.4723,6.4257,7.0905		114/797	77493794	484,6342	1245	2168	3413	SO:0001819	synonymous_variant	64207	exon1			CTGCTGTTGCTGC	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.342A>G	14.37:g.77493794T>C		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	5	5	NM_024496	1	1	18	4841	4821	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			.		0.697	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		C	77493794	T	C	77493794	2	2	133	1	0	0	0	0	0	0	0	1	1777	1722	60	3		3	C14orf4	14	77493794	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	26270435	77493794	29855746	93	11844											
CHGA	1113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	93397675	93397675	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagaaaagtggtgaagccAcagacggagccaggccccag	14	2	14	11	1	0	3	0	1	0	2	0	5	0	4	4	3	2	0	4	3	3	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:93397675A>G	ENST00000216492.5	+	6	716	c.436A>G	c.(436-438)Aca>Gca	p.T146A	CHGA_ENST00000553866.1_3'UTR|CHGA_ENST00000334654.4_Intron	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	146					regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		TGGTGAAGCCACAGACGGAGC	0.597																																					p.T146A	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	.											.	CHGA-516	0			c.A436G						.						33	40	37					14																	93397675		2203	4300	6503	SO:0001583	missense	1113	exon6			GAAGCCACAGACG		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"vasostatin", "pancreastatin", "parastatin"	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.436A>G	14.37:g.93397675A>G	ENSP00000216492:p.Thr146Ala	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	118	43	NM_001275	0	0	0	0	0	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	37	CCDS9906.1	.	.	.	.	.	.	.	.	.	.	A	5.459	0.269804	0.10349	.	.	ENSG00000100604	ENST00000216492	T	0.01647	4.71	4.7	-9.4	0.00616	.	2.536240	0.01191	N	0.007328	T	0.01061	0.0035	N	0.16656	0.425	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45862	-0.9232	10	0.11182	T	0.66	6.9295	4.398	0.11372	0.216:0.2247:0.4493:0.11	.	146	P10645	CMGA_HUMAN	A	146	ENSP00000216492:T146A	ENSP00000216492:T146A	T	+	1	0	CHGA	92467428	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.711000	0.05019	-2.936000	0.00299	-0.441000	0.05720	ACA	.		0.597	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275		G	93397675	A	G	93397675	3	3	133	1	0	0	0	0	1	0	0	0	3344	159	6	3	458	3	CHGA	14	93397675	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	15903881	93397675	13951865	94	11845											
C15orf29	79768	broad.mit.edu;bcgsc.ca	37	chr15	34445066	34445072	+	Frame_Shift_Del	DEL	ATATGTT	ATATGTT	-																															gaatcactggagttaaccaaAtatgttcgactatcatggtg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	ATATGTT	ATATGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:34445066_34445072delATATGTT	ENST00000256544.3	-	4	499_505	c.357_363delAACATAT	c.(355-363)cgaacatatfs	p.RTY119fs		NM_024713.2	NP_078989.1	Q9H079	KTBL1_HUMAN	katanin p80 subunit B-like 1	119						nucleolus (GO:0005730)											AGTTAACCAAATATGTTCGACTATCAT	0.411																																					p.119_121del													.	.	0			c.357_363del						.																																			SO:0001589	frameshift_variant	79768	exon4			AACCAAATATGTT	AL136908	CCDS10034.1	15q13.2	2012-09-27	2012-09-27	2012-09-27	ENSG00000134152	ENSG00000134152			26199	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 29"	C15orf29		11230166	Standard	NM_024713		Approved	FLJ22557	uc001zhp.3	Q9H079	OTTHUMG00000129368	ENST00000256544.3:c.357_363delAACATAT	15.37:g.34445066_34445072delATATGTT	ENSP00000256544:p.Arg119fs	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	45	9	NM_024713	0	0	0	0	0	A8KAF6|Q2TAC0|Q9H670	Frame_Shift_Del	DEL	ENST00000256544.3	37	CCDS10034.1																																																																																			.		0.411	KATNBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251520.1	NM_024713		-	34445072	ATATGTT	-	34445066	7	5	133	1	0	1	0	1	0	0	0	0	1793	108	4	0	579	0	C15orf29	15	34445066	Frame_Shift_Del	DEL	ATATGTT	TCGA-HE-A5NI-01A-11D-A26P-10		34445066	68086326	95	11846											
GCNT3	9245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	59911000	59911000	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcttcccaaatgtcttcaTagccagtaagctggttcggg	8	13	10	10	1	2	0	1	0	1	0	4	0	3	0	2	2	3	4	2	2	3	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:59911000T>C	ENST00000396065.1	+	3	1011	c.563T>C	c.(562-564)aTa>aCa	p.I188T	GCNT3_ENST00000560585.1_Missense_Mutation_p.I188T	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	188					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AATGTCTTCATAGCCAGTAAG	0.498																																					p.I188T		.											.	GCNT3-91	0			c.T563C						.						117	110	112					15																	59911000		2190	4290	6480	SO:0001583	missense	9245	exon3			TCTTCATAGCCAG	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.563T>C	15.37:g.59911000T>C	ENSP00000379377:p.Ile188Thr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	72	31	NM_004751	0	0	1	1	0		Missense_Mutation	SNP	ENST00000396065.1	37	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311833	0.60414	.	.	ENSG00000140297	ENST00000396065	T	0.11712	2.75	6.13	6.13	0.99165	.	0.536118	0.20374	N	0.093586	T	0.20210	0.0486	M	0.80183	2.485	0.45035	D	0.998058	P	0.36354	0.549	B	0.35182	0.197	T	0.01249	-1.1406	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	188	O95395	GCNT3_HUMAN	T	188	ENSP00000379377:I188T	ENSP00000379377:I188T	I	+	2	0	GCNT3	57698292	1.000000	0.71417	0.948000	0.38648	0.868000	0.49771	7.955000	0.87856	2.367000	0.80283	0.529000	0.55759	ATA	.		0.498	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		C	59911000	T	C	59911000	3	2	133	1	0	0	0	0	1	0	0	0	6322	1406	49	3	565	3	GCNT3	15	59911000	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	25465934	59911000	42620392	96	11847											
DENND4A	10260	hgsc.bcm.edu;bcgsc.ca	37	chr15	65956990	65956991	+	Frame_Shift_Ins	INS	-	-	T																															ttttaatgctttttaccataINScttttcaacagttcctggtt																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:65956990_65956991insT	ENST00000431932.2	-	30	5505_5506	c.5297_5298insA	c.(5296-5298)agtfs	p.S1766fs	DENND4A_ENST00000443035.3_Frame_Shift_Ins_p.S1809fs	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1766					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TTTTTACCATACTTTTCAACAG	0.337																																					p.S1809fs		.											.	DENND4A-229	0			c.5427_5428insA						.																																			SO:0001589	frameshift_variant	10260	exon31			.	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"DENN/MADD domain containing"	24321	protein-coding gene	gene with protein product		600382	"c-myc promoter binding protein"	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.5297_5298insA	15.37:g.65956990_65956991insT	ENSP00000396830:p.Ser1766fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	53	15	NM_001144823	0	0	0	0	0	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Frame_Shift_Ins	INS	ENST00000431932.2	37	CCDS45285.1																																																																																			.		0.337	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	65956991	-	T	65956990	7	5	133	1	0	1	1	0	0	0	0	0	4444	388	14	0	305	0	DENND4A	15	65956990	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	6045990	65956990	36574402	97	11848											
UACA	55075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	70991969	70991969	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctgctgctttcatcaatcGgtcatcatatttattccaat	9	18	4	10	1	5	0	4	0	1	0	7	0	6	0	1	1	2	2	1	1	4	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:70991969G>A	ENST00000322954.6	-	2	294	c.109C>T	c.(109-111)Cga>Tga	p.R37*	UACA_ENST00000379983.2_Nonsense_Mutation_p.R24*|UACA_ENST00000560441.1_Nonsense_Mutation_p.R24*|UACA_ENST00000539319.1_Nonsense_Mutation_p.R37*	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	37					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TTCATCAATCGGTCATCATAT	0.363																																					p.R37X		.											.	UACA-94	0			c.C109T						.						145	125	132					15																	70991969		2199	4297	6496	SO:0001587	stop_gained	55075	exon2			TCAATCGGTCATC	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"Ankyrin repeat domain containing"	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.109C>T	15.37:g.70991969G>A	ENSP00000314556:p.Arg37*	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	58	20	NM_018003	0	0	0	0	0	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Nonsense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	G	37	6.366924	0.97511	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362;ENST00000539319	.	.	.	5.28	3.23	0.37069	.	0.000000	0.48286	D	0.000192	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.7105	14.3737	0.66860	0.0:0.0:0.6557:0.3443	.	.	.	.	X	37;24;24;37	.	ENSP00000314556:R37X	R	-	1	2	UACA	68779023	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	4.021000	0.57196	1.312000	0.45043	0.491000	0.48974	CGA	.		0.363	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			A	70991969	G	A	70991969	4	1	133	1	0	0	0	0	0	1	0	0	16857	1124	39	1	4213	1	UACA	15	70991969	Nonsense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	5034979	70991969	31539423	98	11849											
ST8SIA2	8128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	92973323	92973323	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatcagctgtgaacagctTacatagcaaatctaataggt	15	10	8	8	0	2	2	1	1	1	1	2	2	2	2	0	1	5	3	0	1	6	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:92973323T>C	ENST00000268164.3	+	2	380	c.143T>C	c.(142-144)tTa>tCa	p.L48S	ST8SIA2_ENST00000539113.1_Intron	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	48					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			GTGAACAGCTTACATAGCAAA	0.393																																					p.L48S		.											.	ST8SIA2-90	0			c.T143C						.						143	133	136					15																	92973323		2198	4298	6496	SO:0001583	missense	8128	exon2			ACAGCTTACATAG	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.143T>C	15.37:g.92973323T>C	ENSP00000268164:p.Leu48Ser	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	82	30	NM_006011	0	0	0	0	0	Q4VAZ0|Q92470|Q92746	Missense_Mutation	SNP	ENST00000268164.3	37	CCDS10372.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.239532	0.22711	.	.	ENSG00000140557	ENST00000268164;ENST00000555434	T;T	0.27720	1.95;1.65	5.55	5.55	0.83447	.	0.179000	0.35436	N	0.003205	T	0.23054	0.0557	L	0.27053	0.805	0.80722	D	1	B	0.12630	0.006	B	0.09377	0.004	T	0.05053	-1.0909	10	0.20046	T	0.44	0.2846	15.71	0.77620	0.0:0.0:0.0:1.0	.	48	Q92186	SIA8B_HUMAN	S	48	ENSP00000268164:L48S;ENSP00000450851:L48S	ENSP00000268164:L48S	L	+	2	0	ST8SIA2	90774327	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.306000	0.65756	2.105000	0.64084	0.533000	0.62120	TTA	.		0.393	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		C	92973323	T	C	92973323	3	2	133	1	0	0	0	0	1	0	0	0	15264	1764	61	3	149	3	ST8SIA2	15	92973323	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	21981354	92973323	9558069	99	11850											
ASB7	140460	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	101152488	101152488	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgcagattcaggccgcggtgGctgctggggatgtccacaca	7	8	15	11	2	1	1	1	0	0	1	2	2	2	2	2	5	2	3	2	5	0	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:101152488G>A	ENST00000332783.7	+	4	852	c.67G>A	c.(67-69)Gct>Act	p.A23T	ASB7_ENST00000343276.4_Missense_Mutation_p.A23T|ASB7_ENST00000558747.1_Missense_Mutation_p.A23T	NM_198243.2	NP_937886.1	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box containing 7	23					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)	16	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)			GGCCGCGGTGGCTGCTGGGGA	0.512																																					p.A23T													.	ASB7-227	0			c.G67A						.						106	95	99					15																	101152488		2203	4300	6503	SO:0001583	missense	140460	exon4			GCGGTGGCTGCTG		CCDS10387.1, CCDS10388.1	15q26.3	2013-01-10	2011-01-25		ENSG00000183475	ENSG00000183475		"Ankyrin repeat domain containing"	17182	protein-coding gene	gene with protein product		615052	"ankyrin repeat and SOCS box-containing 7"				Standard	NM_024708		Approved		uc002bwk.3	Q9H672	OTTHUMG00000149868	ENST00000332783.7:c.67G>A	15.37:g.101152488G>A	ENSP00000328327:p.Ala23Thr	Somatic	157	1		WXS	Illumina HiSeq	Phase_I	153	58	NM_024708	0	0	1	1	0	A8K1E5|Q6GSJ6|Q7Z4S3	Missense_Mutation	SNP	ENST00000332783.7	37	CCDS10387.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969229	0.74246	.	.	ENSG00000183475	ENST00000332783;ENST00000343276	T;T	0.65364	-0.15;-0.11	5.9	5.9	0.94986	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.76828	0.4042	L	0.56280	1.765	0.80722	D	1	D;P	0.62365	0.991;0.867	D;B	0.77004	0.989;0.445	T	0.72679	-0.4220	10	0.38643	T	0.18	-7.1712	20.2822	0.98520	0.0:0.0:1.0:0.0	.	23;23	Q9H672;Q9H672-2	ASB7_HUMAN;.	T	23	ENSP00000328327:A23T;ENSP00000339819:A23T	ENSP00000328327:A23T	A	+	1	0	ASB7	98970011	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.296000	0.96104	2.806000	0.96561	0.655000	0.94253	GCT	.		0.512	ASB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313617.1	NM_024708		A	101152488	G	A	101152488	3	1	133	1	0	0	0	0	1	0	0	0	1029	1203	42	2	69	2	ASB7	15	101152488	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	8179165	101152488	1378904	100	11851											
PCSK6	5046	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	101865152	101865152	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagacaggcactgcgtcgcAgctctgctggagcaggtctc	8	7	13	13	2	2	1	0	0	2	1	4	2	2	2	0	3	4	5	0	3	1	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:101865152A>G	ENST00000348070.1	-	18	2276	c.2277T>C	c.(2275-2277)gcT>gcC	p.A759A	PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000358417.3_Silent_p.A746A	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	760	CRM (Cys-rich motif).				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACTGCGTCGCAGCTCTGCTGG	0.587																																					.													.	PCSK6-46	0			.						.						45	50	48					15																	101865152		2042	4184	6226	SO:0001819	synonymous_variant	5046	.			CGTCGCAGCTCTG		CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"subtilisin-like protease", "subtilisin-like proprotein convertase 4", "subtilisin/kexin-like protease PACE4"	167405	"paired basic amino acid cleaving system 4"	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.2277T>C	15.37:g.101865152A>G		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	54	12	.	0	0	0	0	0	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Silent	SNP	ENST00000348070.1	37																																																																																				.		0.587	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570		G	101865152	A	G	101865152	2	3	133	1	0	0	0	0	0	0	0	1	11630	175	7	3		3	PCSK6	15	101865152	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	712664	101865152	666240	101	11852											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30733555	30733555	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagggcaacaagctgactttGactggtgcccaggtgcgcca	9	7	13	12	1	0	2	0	2	0	0	0	2	0	2	2	3	4	2	2	3	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:30733555G>C	ENST00000262518.4	+	22	4039	c.3654G>C	c.(3652-3654)ttG>ttC	p.L1218F	SRCAP_ENST00000395059.2_Missense_Mutation_p.L1218F|SRCAP_ENST00000344771.4_Missense_Mutation_p.L1122F	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1218	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AGCTGACTTTGACTGGTGCCC	0.587																																					p.L1218F		.											.	SRCAP-94	0			c.G3654C						.						113	96	102					16																	30733555		2197	4300	6497	SO:0001583	missense	10847	exon22			GACTTTGACTGGT	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3654G>C	16.37:g.30733555G>C	ENSP00000262518:p.Leu1218Phe	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	267	72	NM_006662	0	0	8	8	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673750	0.47781	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.96913	-4.07;-4.17;-3.98	4.68	4.68	0.58851	.	0.000000	0.40064	N	0.001186	D	0.96522	0.8865	L	0.29908	0.895	0.27411	N	0.954569	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	D	0.92402	0.5930	10	0.72032	D	0.01	-5.1815	16.5291	0.84353	0.0:0.0:1.0:0.0	.	1122;1218;1218	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	F	1218;1218;1122	ENSP00000262518:L1218F;ENSP00000378499:L1218F;ENSP00000343042:L1122F	ENSP00000262518:L1218F	L	+	3	2	SRCAP	30641056	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	2.423000	0.44705	2.414000	0.81942	0.462000	0.41574	TTG	.		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30733555	G	C	30733555	3	2	133	1	0	0	0	0	1	0	0	0	15167	1281	45	4	3732	4	SRCAP	16	30733555	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		30733555	59621198	102	11853											
ITGAX	3687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31371302	31371302	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cactttcgaggaattcaggcGcagctcaaaccccctcagcc	10	7	8	16	2	3	0	3	0	0	0	4	2	3	1	3	2	3	2	3	2	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:31371302G>A	ENST00000268296.4	+	7	744	c.623G>A	c.(622-624)cGc>cAc	p.R208H	ITGAX_ENST00000562522.1_Missense_Mutation_p.R208H	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	208	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GAATTCAGGCGCAGCTCAAAC	0.517																																					p.R208H		.											.	ITGAX-229	0			c.G623A						.						101	103	102					16																	31371302		2197	4300	6497	SO:0001583	missense	3687	exon7			TCAGGCGCAGCTC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.623G>A	16.37:g.31371302G>A	ENSP00000268296:p.Arg208His	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	71	43	NM_000887	0	0	1	1	0	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.616950	0.28801	.	.	ENSG00000140678	ENST00000268296	T	0.78246	-1.16	4.88	-5.48	0.02592	von Willebrand factor, type A (3);	.	.	.	.	T	0.64800	0.2631	L	0.41492	1.28	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.54002	-0.8358	9	0.56958	D	0.05	.	8.8842	0.35394	0.176:0.46:0.364:0.0	.	208	P20702	ITAX_HUMAN	H	208	ENSP00000268296:R208H	ENSP00000268296:R208H	R	+	2	0	ITGAX	31278803	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.940000	0.01543	-0.882000	0.03987	-0.670000	0.03821	CGC	.		0.517	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31371302	G	A	31371302	3	1	133	1	0	0	0	0	1	0	0	0	7910	1087	38	1	649	1	ITGAX	16	31371302	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	637747	31371302	58983451	103	11854											
ZNF319	57567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	58031774	58031774	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcttgcagaccccacagacGaagggcttctgctcagcctg	9	8	10	14	1	3	2	1	0	2	2	3	3	3	2	3	1	3	3	3	1	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:58031774G>A	ENST00000299237.2	-	2	1018	c.396C>T	c.(394-396)ttC>ttT	p.F132F	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	132					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						CCCCACAGACGAAGGGCTTCT	0.572																																					p.F132F		.											.	ZNF319-90	0			c.C396T						.						59	57	57					16																	58031774		2198	4300	6498	SO:0001819	synonymous_variant	57567	exon2			ACAGACGAAGGGC	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"Zinc fingers, C2H2-type"	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.396C>T	16.37:g.58031774G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	98	46	NM_020807	0	0	0	0	0	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			.		0.572	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1			A	58031774	G	A	58031774	2	1	133	1	0	0	0	0	0	0	0	1	17869	1049	37	1		1	ZNF319	16	58031774	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	26660472	58031774	32322979	104	11855											
AP1G1	164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	71772895	71772895	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcatatctagctctgtgcTgttggaggcctgtatcgtta	6	15	11	9	2	3	0	1	0	2	0	4	1	3	1	1	2	2	5	1	2	4	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:71772895T>A	ENST00000299980.4	-	21	2659	c.2218A>T	c.(2218-2220)Agc>Tgc	p.S740C	AP1G1_ENST00000564155.1_Missense_Mutation_p.S165C|AP1G1_ENST00000433195.2_Missense_Mutation_p.S763C|AP1G1_ENST00000423132.2_Missense_Mutation_p.S743C|AP1G1_ENST00000569748.1_Missense_Mutation_p.S740C|AP1G1_ENST00000393512.3_Missense_Mutation_p.S743C	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	740	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				AGCTCTGTGCTGTTGGAGGCC	0.418																																					p.S743C		.											.	AP1G1-92	0			c.A2227T						.						208	183	191					16																	71772895		2198	4300	6498	SO:0001583	missense	164	exon22			CTGTGCTGTTGGA	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2218A>T	16.37:g.71772895T>A	ENSP00000299980:p.Ser740Cys	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	348	94	NM_001030007	0	0	9	13	4	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	37	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307011	0.40795	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.29	5.29	0.74685	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.135369	0.64402	D	0.000002	T	0.38878	0.1057	L	0.52905	1.665	0.49687	D	0.999819	B;B;B	0.12013	0.005;0.002;0.002	B;B;B	0.19666	0.026;0.017;0.023	T	0.26608	-1.0098	10	0.48119	T	0.1	-8.7323	10.4684	0.44622	0.1451:0.0:0.0:0.8549	.	740;763;743	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	C	740;743;743;763	ENSP00000299980:S740C;ENSP00000377148:S743C;ENSP00000409153:S743C;ENSP00000403259:S763C	ENSP00000299980:S740C	S	-	1	0	AP1G1	70330396	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	3.020000	0.49643	1.996000	0.58369	0.528000	0.53228	AGC	.		0.418	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71772895	T	A	71772895	3	1	133	1	0	0	0	0	1	0	0	0	732	1580	55	5	262	5	AP1G1	16	71772895	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	13741121	71772895	18581858	105	11856											
PRPF8	10594	broad.mit.edu	37	chr17	1585300	1585301	+	Frame_Shift_Ins	INS	-	-	T																															cttgaaatgcctcctatctcINSttttttctcggcgcatcata																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:1585300_1585301insT	ENST00000572621.1	-	4	731_732	c.466_467insA	c.(466-468)agafs	p.R156fs	PRPF8_ENST00000304992.6_Frame_Shift_Ins_p.R156fs			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	156					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CCTCCTATCTCTTTTTTCTCGG	0.51																																					p.R156fs													.	PRPF8-525	0			c.467_468insA						.																																			SO:0001589	frameshift_variant	10594	exon5			CTATCTCTTTTTT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.467dupA	17.37:g.1585306_1585306dupT	ENSP00000460348:p.Arg156fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	123	10	NM_006445	0	0	0	0	0	O14547|O75965	Frame_Shift_Ins	INS	ENST00000572621.1	37	CCDS11010.1																																																																																			.		0.51	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			T	1585301	-	T	1585300	7	5	133	1	0	1	1	0	0	0	0	0	12604	913	32	0	6696	0	PRPF8	17	1585300	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10		1585300	79609910	106	11857											
ACACA	31	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	35615281	35615281	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttgattctatatagaggAatccccatggcaatctgaaa	13	12	7	9	0	2	3	0	2	2	1	4	4	4	4	3	2	0	1	3	2	6	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:35615281A>T	ENST00000394406.2	-	13	1594	c.1404T>A	c.(1402-1404)atT>atA	p.I468I	ACACA_ENST00000353139.5_Silent_p.I505I|ACACA_ENST00000335166.5_Silent_p.I390I|ACACA_ENST00000360679.3_Silent_p.I410I	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	468	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TATATAGAGGAATCCCCATGG	0.368																																					p.I505I	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	.											.	ACACA-154	0			c.T1515A						.						67	66	66					17																	35615281		2203	4300	6503	SO:0001819	synonymous_variant	31	exon13			TAGAGGAATCCCC	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1404T>A	17.37:g.35615281A>T		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	108	61	NM_198834	0	0	0	1	1	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																			.		0.368	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35615281	A	T	35615281	2	4	133	1	0	0	0	0	0	0	0	1	106	242	9	5		5	ACACA	17	35615281	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	34029981	35615281	45579929	107	11858											
KRT23	25984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39092459	39092459	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagggtcacccagcatcttaCctgctcctgcaggtgtgtga	7	10	11	13	0	2	1	1	1	1	0	3	1	3	1	3	2	4	3	3	2	1	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:39092459C>G	ENST00000209718.3	-	2	821		c.e2+1		KRT23_ENST00000582283.1_5'Flank|AC004231.2_ENST00000418393.1_RNA|KRT23_ENST00000436344.3_Intron	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)							intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				CAGCATCTTACCTGCTCCTGC	0.517																																					.		.											.	KRT23-91	0			c.396+1G>C						.						55	57	56					17																	39092459		2203	4300	6503	SO:0001630	splice_region_variant	25984	exon3			ATCTTACCTGCTC	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"-", "Intermediate filaments type I, keratins (acidic)"	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.396+1G>C	17.37:g.39092459C>G		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	63	32	NM_015515	0	0	0	0	0	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Splice_Site	SNP	ENST00000209718.3	37	CCDS11380.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.205300	0.39003	.	.	ENSG00000108244	ENST00000209718	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8915	0.96931	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT23	36345985	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	7.797000	0.85911	2.707000	0.92482	0.557000	0.71058	.	.		0.517	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		Intron	G	39092459	C	G	39092459	5	3	133	1	0	0	0	0	0	0	1	0	8481	521	18	4	903	4	KRT23	17	39092459	Splice_Site	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	3477178	39092459	42102751	108	11859											
PSMD12	5718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65362549	65362549	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggctagcttcgcacactcGggtaggcgctgatccaccgt	6	10	12	13	4	0	1	0	1	0	0	3	1	1	1	2	3	1	5	2	3	2	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:65362549G>C	ENST00000356126.3	-	1	194	c.87C>G	c.(85-87)ccC>ccG	p.P29P	PSMD12_ENST00000581618.1_5'UTR|PSMD12_ENST00000357146.4_Silent_p.P29P	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	29					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TCGCACACTCGGGTAGGCGCT	0.706																																					p.P29P		.											.	PSMD12-90	0			c.C87G						.						40	31	34					17																	65362549		2203	4299	6502	SO:0001819	synonymous_variant	5718	exon1			ACACTCGGGTAGG	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.87C>G	17.37:g.65362549G>C		Somatic	31	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_174871	0	0	0	0	0	A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	37	CCDS11669.1																																																																																			.		0.706	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65362549	G	C	65362549	2	2	133	1	0	0	0	0	0	0	0	1	12724	1103	39	4		4	PSMD12	17	65362549	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	26270090	65362549	15832661	109	11860											
TRIM47	91107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73872839	73872839	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctggactgtgcaatgccaGcacccagctcgtccatgcgg	7	7	12	15	2	0	0	0	0	0	0	2	1	1	1	4	2	5	3	4	2	1	0	rs377764139		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:73872839G>A	ENST00000254816.2	-	2	757	c.731C>T	c.(730-732)gCt>gTt	p.A244V	TRIM47_ENST00000587339.1_Missense_Mutation_p.A6V|RP11-552F3.9_ENST00000586076.1_RNA	NM_033452.2	NP_258411.2	Q96LD4	TRI47_HUMAN	tripartite motif containing 47	244						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22			Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCAATGCCAGCACCCAGCTC	0.587																																					p.A244V		.											.	TRIM47-659	0			c.C731T						.						170	119	136					17																	73872839		2203	4300	6503	SO:0001583	missense	91107	exon2			ATGCCAGCACCCA	AY026763	CCDS32737.1	17q25	2013-01-09	2011-01-25			ENSG00000132481		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19020	protein-coding gene	gene with protein product		611041	"tripartite motif-containing 47"				Standard	NM_033452		Approved	GOA, RNF100	uc002jpw.3	Q96LD4		ENST00000254816.2:c.731C>T	17.37:g.73872839G>A	ENSP00000254816:p.Ala244Val	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	167	106	NM_033452	0	0	5	18	13	Q96AD0|Q96GU5|Q9BRN7	Missense_Mutation	SNP	ENST00000254816.2	37	CCDS32737.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.404309	0.42613	.	.	ENSG00000132481	ENST00000254816	T	0.45276	0.9	4.91	4.91	0.64330	.	0.105328	0.42682	D	0.000664	T	0.27524	0.0676	N	0.24115	0.695	0.37335	D	0.910149	B	0.02656	0.0	B	0.06405	0.002	T	0.14783	-1.0460	10	0.39692	T	0.17	.	9.121	0.36786	0.097:0.0:0.903:0.0	.	244	Q96LD4	TRI47_HUMAN	V	244	ENSP00000254816:A244V	ENSP00000254816:A244V	A	-	2	0	TRIM47	71384434	0.747000	0.28283	0.927000	0.36925	0.785000	0.44390	3.752000	0.55172	2.560000	0.86352	0.511000	0.50034	GCT	.		0.587	TRIM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448934.1			A	73872839	G	A	73872839	3	1	133	1	0	0	0	0	1	0	0	0	16555	971	34	2	1205	2	TRIM47	17	73872839	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	8510290	73872839	7322371	110	11861											
OSBPL1A	114876	ucsc.edu;bcgsc.ca	37	chr18	21914248	21914248	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttgccttctcttgctgcTgctaaaagtaattcttcaag	8	17	7	9	0	3	0	1	0	2	0	4	0	3	0	1	0	4	5	1	0	4	8			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr18:21914248T>C	ENST00000319481.3	-	6	647	c.441A>G	c.(439-441)gcA>gcG	p.A147A		NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	147	Interaction with RAB7A.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					CTCTTGCTGCTGCTAAAAGTA	0.363																																					p.A147A													.	OSBPL1A-94	0			c.A441G						.						138	125	129					18																	21914248		2203	4297	6500	SO:0001819	synonymous_variant	114876	exon6			TGCTGCTGCTAAA	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.441A>G	18.37:g.21914248T>C		Somatic	44	1		WXS	Illumina HiSeq		19	6	NM_080597	0	0	0	0	0	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			.		0.363	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		C	21914248	T	C	21914248	2	2	133	1	0	0	0	0	0	0	0	1	11303	1567	55	3		3	OSBPL1A	18	21914248	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		21914248	56163000	111	11862											
B4GALT6	9331	bcgsc.ca	37	chr18	29218694	29218694	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaaattggaagatgttcatgGcgattacggaaaggaatgag	16	9	13	3	2	1	2	1	1	0	1	1	6	1	5	0	4	1	1	0	4	6	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr18:29218694G>A	ENST00000306851.5	-	5	797	c.501C>T	c.(499-501)cgC>cgT	p.R167R	B4GALT6_ENST00000237019.7_Silent_p.R128R|B4GALT6_ENST00000383131.3_Intron	NM_004775.3	NP_004766.2	Q9UBX8	B4GT6_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6	167	UDP-alpha-D-galactose binding. {ECO:0000250}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(6)|pancreas(1)	20			OV - Ovarian serous cystadenocarcinoma(10;0.00791)			GATGTTCATGGCGATTACGGA	0.353																																					p.R167R													.	B4GALT6-90	0			c.C501T						.						85	84	84					18																	29218694		2203	4300	6503	SO:0001819	synonymous_variant	9331	exon5			TTCATGGCGATTA	AF038664	CCDS11900.1	18q11	2013-02-19			ENSG00000118276	ENSG00000118276		"Beta 4-glycosyltransferases"	929	protein-coding gene	gene with protein product	"UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase"	604017				9597550, 12180132	Standard	NM_004775		Approved	beta4GalT-VI	uc002kwz.4	Q9UBX8	OTTHUMG00000131980	ENST00000306851.5:c.501C>T	18.37:g.29218694G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_1	69	4	NM_004775	0	0	0	0	0	O60514|Q6NT09	Silent	SNP	ENST00000306851.5	37	CCDS11900.1																																																																																			.		0.353	B4GALT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254942.2	NM_004775		A	29218694	G	A	29218694	2	1	133	1	0	0	0	0	0	0	0	1	1276	1190	42	2		2	B4GALT6	18	29218694	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	7304446	29218694	48858554	112	11863											
MADCAM1	8174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	504882	504883	+	Missense_Mutation	DNP	CC	CC	AT																															ctgaggacgacacccacccaCcagcttctctgaggcttctg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:504882_504883CC>AT	ENST00000215637.3	+	5	1112_1113	c.1066_1067CC>AT	c.(1066-1068)CCa>ATa	p.P356I	MADCAM1_ENST00000382683.4_Missense_Mutation_p.P174I|TPGS1_ENST00000359315.5_5'Flank|MADCAM1_ENST00000346144.4_Missense_Mutation_p.P269I|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P137I	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	356					aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCCACCCACCAGCTTCTCTG	0.673																																					p.P380I		.											.	MADCAM1-90	0			c.C806T						.																																			SO:0001583	missense	8174	exon4			ACCCACCAGCTTC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6765	protein-coding gene	gene with protein product	"mucosal addressin cell adhesion molecule-1"	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	Exception_encountered	19.37:g.504882_504883delinsAT	ENSP00000215637:p.Pro356Ile	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	66	22	NM_130762	0	0	0	0	0	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	DNP	ENST00000215637.3	37	CCDS12028.1																																																																																			.		0.673	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760		AT	504883	CC	AT	504882	3	1	133	1	0	0	0	0	1	0	0	0	9176	507	18	4	1084	4	MADCAM1	19	504882	Missense_Mutation	DNP	CC	TCGA-HE-A5NI-01A-11D-A26P-10		504882	58624101	113	11864											
PLIN4	729359	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	4511773	4511773	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaccggtcaccccactgcaGacggtgtccttggtaccagt	7	8	11	15	2	1	1	1	0	0	1	2	1	2	1	5	3	2	3	5	3	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:4511773G>A	ENST00000301286.3	-	3	2156	c.2157C>T	c.(2155-2157)gtC>gtT	p.V719V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	719	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCCCACTGCAGACGGTGTCCT	0.572																																					p.V719V		.											.	PLIN4-68	0			c.C2157T						.						210	212	211					19																	4511773		2098	4206	6304	SO:0001819	synonymous_variant	729359	exon3			ACTGCAGACGGTG	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"Perilipins"	29393	protein-coding gene	gene with protein product		613247	"KIAA1881"	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2157C>T	19.37:g.4511773G>A		Somatic	293	0		WXS	Illumina HiSeq	Phase_I	234	37	NM_001080400	0	0	0	0	0	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			.		0.572	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4511773	G	A	4511773	2	1	133	1	0	0	0	0	0	0	0	1	12118	929	33	2		2	PLIN4	19	4511773	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	4006891	4511773	54617210	114	11865											
PLIN3	10226	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	4839279	4839279	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agccacgtgacaggtgtgttCtgggccacatattccaccat	9	10	10	12	1	1	1	0	1	1	0	2	1	2	1	4	2	1	1	4	2	1	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:4839279C>G	ENST00000221957.4	-	8	1406	c.1230G>C	c.(1228-1230)caG>caC	p.Q410H	PLIN3_ENST00000585479.1_Missense_Mutation_p.Q409H|PLIN3_ENST00000592528.1_Missense_Mutation_p.Q398H|CTC-518P12.6_ENST00000591657.1_RNA	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	410					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	CAGGTGTGTTCTGGGCCACAT	0.632																																					p.Q410H		.											.	PLIN3-90	0			c.G1230C						.						66	70	69					19																	4839279		2203	4300	6503	SO:0001583	missense	10226	exon8			TGTGTTCTGGGCC	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"Perilipins"	16893	protein-coding gene	gene with protein product	"cargo selection protein (mannose 6 phosphate receptor binding protein)", "placental protein 17", "MPR-BINDING PROTEIN, 47-KD"	602702	"mannose-6-phosphate receptor binding protein 1"	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.1230G>C	19.37:g.4839279C>G	ENSP00000221957:p.Gln410His	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	80	7	NM_005817	0	0	9	9	0	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	C	7.106	0.575129	0.13623	.	.	ENSG00000105355	ENST00000221957	T	0.18960	2.18	4.97	2.65	0.31530	.	0.938934	0.08920	N	0.874576	T	0.19287	0.0463	L	0.28192	0.835	0.34333	D	0.68787	B;B;B	0.23249	0.027;0.082;0.033	B;B;B	0.25140	0.022;0.058;0.038	T	0.21690	-1.0238	10	0.37606	T	0.19	-13.9129	16.1339	0.81465	0.0:0.4858:0.5141:0.0	.	409;227;410	O60664-3;O60664-2;O60664	.;.;PLIN3_HUMAN	H	410	ENSP00000221957:Q410H	ENSP00000221957:Q410H	Q	-	3	2	PLIN3	4790279	1.000000	0.71417	0.992000	0.48379	0.108000	0.19459	0.655000	0.24933	1.042000	0.40150	0.561000	0.74099	CAG	.		0.632	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		G	4839279	C	G	4839279	3	3	133	1	0	0	0	0	1	0	0	0	12117	912	32	4	78	4	PLIN3	19	4839279	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	327506	4839279	54289704	115	11866											
PLIN3	10226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4839466	4839466	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattggtggggaggccctgaAtgctggaccccagggaggta	8	7	17	9	0	0	1	0	1	0	0	0	4	0	4	3	7	1	2	3	7	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:4839466A>C	ENST00000221957.4	-	8	1219	c.1043T>G	c.(1042-1044)aTt>aGt	p.I348S	PLIN3_ENST00000585479.1_Missense_Mutation_p.I347S|PLIN3_ENST00000592528.1_Missense_Mutation_p.I336S|CTC-518P12.6_ENST00000591657.1_RNA	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	348					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GAGGCCCTGAATGCTGGACCC	0.647																																					p.I348S		.											.	PLIN3-90	0			c.T1043G						.						37	31	33					19																	4839466		2203	4300	6503	SO:0001583	missense	10226	exon8			CCCTGAATGCTGG	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"Perilipins"	16893	protein-coding gene	gene with protein product	"cargo selection protein (mannose 6 phosphate receptor binding protein)", "placental protein 17", "MPR-BINDING PROTEIN, 47-KD"	602702	"mannose-6-phosphate receptor binding protein 1"	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.1043T>G	19.37:g.4839466A>C	ENSP00000221957:p.Ile348Ser	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	89	27	NM_005817	0	0	10	18	8	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.433232	0.43224	.	.	ENSG00000105355	ENST00000221957	T	0.20332	2.08	4.85	4.85	0.62838	.	422.645000	0.01670	U	0.025543	T	0.50120	0.1597	M	0.78637	2.42	0.27909	N	0.93868	D;P;D	0.56746	0.971;0.937;0.977	P;P;D	0.64506	0.879;0.698;0.926	T	0.06881	-1.0802	10	0.87932	D	0	-13.3555	9.052	0.36383	0.9163:0.0:0.0837:0.0	.	347;165;348	O60664-3;O60664-2;O60664	.;.;PLIN3_HUMAN	S	348	ENSP00000221957:I348S	ENSP00000221957:I348S	I	-	2	0	PLIN3	4790466	0.801000	0.28930	0.975000	0.42487	0.034000	0.12701	3.474000	0.53129	1.817000	0.53016	0.454000	0.30748	ATT	.		0.647	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		C	4839466	A	C	4839466	3	2	133	1	0	0	0	0	1	0	0	0	12117	101	4	5	265	5	PLIN3	19	4839466	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	187	4839466	54289517	116	11867											
DCAF15	90379	hgsc.bcm.edu;broad.mit.edu	37	chr19	14070072	14070072	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcttccgccgggccaaagagGccaagggcggggtccctgag	7	5	16	13	3	1	2	0	1	1	1	3	2	3	2	5	5	0	0	5	5	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:14070072G>A	ENST00000254337.6	+	7	1021	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T		NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	334					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						GGCCAAAGAGGCCAAGGGCGG	0.682																																					p.A334T		.											.	DCAF15-90	0			c.G1000A						.						27	35	32					19																	14070072		2203	4300	6503	SO:0001583	missense	90379	exon7			AAAGAGGCCAAGG	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"DDB1 and CUL4 associated factors"	25095	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 72"	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.1000G>A	19.37:g.14070072G>A	ENSP00000254337:p.Ala334Thr	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_138353	0	0	5	9	4	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	37	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	g	32	5.112699	0.94339	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.46	4.46	0.54185	.	0.085620	0.44097	D	0.000488	T	0.60470	0.2271	L	0.29908	0.895	0.41151	D	0.986027	D	0.54207	0.965	P	0.55871	0.786	T	0.65998	-0.6032	9	0.62326	D	0.03	-24.0048	15.8605	0.79017	0.0:0.0:1.0:0.0	.	334	Q66K64	DCA15_HUMAN	T	334	.	ENSP00000254337:A334T	A	+	1	0	DCAF15	13931072	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.504000	0.66968	2.043000	0.60533	0.491000	0.48974	GCC	.		0.682	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353		A	14070072	G	A	14070072	3	1	133	1	0	0	0	0	1	0	0	0	4273	1203	42	2	1026	2	DCAF15	19	14070072	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	9230606	14070072	45058911	117	11868											
TECR	9524	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	14674655	14674657	+	In_Frame_Del	DEL	CGT	CGT	-																															gatgttctgcagaagctgccCgtgggcaccacggccacact																								rs367952165|rs201634024		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CGT	CGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:14674655_14674657delCGT	ENST00000215567.5	+	5	344_346	c.207_209delCGT	c.(205-210)cccgtg>ccg	p.V70del	TECR_ENST00000600083.1_5'UTR|TECR_ENST00000596073.1_5'UTR|TECR_ENST00000436007.2_In_Frame_Del_p.V85del|TECR_ENST00000596164.1_3'UTR	NM_138501.5	NP_612510.1	Q9NZ01	TECR_HUMAN	trans-2,3-enoyl-CoA reductase	70					cellular lipid metabolic process (GO:0044255)|fatty acid elongation (GO:0030497)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|nucleus (GO:0005634)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|large_intestine(1)|ovary(1)	3						AGAAGCTGCCCGTGGGCACCACG	0.66																																					p.69_70del		.											.	TECR-90	0			c.207_209del						.																																			SO:0001651	inframe_deletion	9524	exon5			.	AK001416	CCDS12313.1	19p13.12	2014-05-27	2009-07-21	2009-07-21	ENSG00000099797	ENSG00000099797			4551	protein-coding gene	gene with protein product		610057	"glycoprotein, synaptic 2"	SC2, GPSN2		9653160, 12482854	Standard	NM_138501		Approved	TER, MRT14	uc002mza.3	Q9NZ01		ENST00000215567.5:c.207_209delCGT	19.37:g.14674655_14674657delCGT	ENSP00000215567:p.Val70del	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	87	35	NM_138501	0	0	0	0	0	B2RD55|O75350|Q6IBB2|Q9BWK3|Q9Y6P0	In_Frame_Del	DEL	ENST00000215567.5	37	CCDS12313.1																																																																																			.		0.66	TECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466000.1	NM_138501		-	14674657	CGT	-	14674655	7	5	133	1	0	1	0	1	0	0	0	0	15777	639	23	0	225	0	TECR	19	14674655	In_Frame_Del	DEL	CGT	TCGA-HE-A5NI-01A-11D-A26P-10	604583	14674655	44454328	118	11869											
NAPA	8775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	47996229	47996229	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccccacctgttcgtagaTgtcaatggccttctgatact	7	14	8	12	1	2	2	1	1	1	1	4	2	3	2	4	1	1	2	4	1	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:47996229T>C	ENST00000263354.3	-	7	849	c.550A>G	c.(550-552)Atc>Gtc	p.I184V	NAPA_ENST00000595227.1_Missense_Mutation_p.I145V|NAPA-AS1_ENST00000593284.1_RNA|NAPA-AS1_ENST00000594367.1_RNA|NAPA_ENST00000593785.1_5'Flank	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	184					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		TGTTCGTAGATGTCAATGGCC	0.607																																					p.I184V	Ovarian(185;1135 2042 27703 31345 42493)	.											.	NAPA-90	0			c.A550G						.						113	101	105					19																	47996229		2203	4300	6503	SO:0001583	missense	8775	exon7			CGTAGATGTCAAT	U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"alpha SNAP"	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.550A>G	19.37:g.47996229T>C	ENSP00000263354:p.Ile184Val	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	186	74	NM_003827	0	0	23	31	8	A8K879|Q96IK3|Q9BVJ3	Missense_Mutation	SNP	ENST00000263354.3	37	CCDS12702.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.323538	0.41096	.	.	ENSG00000105402	ENST00000263354	T	0.76448	-1.02	5.16	5.16	0.70880	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.77605	0.4155	M	0.76170	2.325	0.80722	D	1	B	0.16603	0.018	B	0.20577	0.03	T	0.75190	-0.3405	10	0.45353	T	0.12	-33.228	14.1002	0.65049	0.0:0.0:0.0:1.0	.	184	P54920	SNAA_HUMAN	V	184	ENSP00000263354:I184V	ENSP00000263354:I184V	I	-	1	0	NAPA	52688041	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	7.585000	0.82584	2.168000	0.68352	0.496000	0.49642	ATC	.		0.607	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827		C	47996229	T	C	47996229	3	2	133	1	0	0	0	0	1	0	0	0	10186	1464	51	3	357	3	NAPA	19	47996229	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	33321574	47996229	11132754	119	11870											
ZNF836	162962	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	52658860	52658860	+	Frame_Shift_Del	DEL	T	T	-																															aactcattacaattgtaaggTttctctccagtatgaattat																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:52658860delT	ENST00000322146.8	-	5	2597	c.2076delA	c.(2074-2076)aaafs	p.K692fs	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Frame_Shift_Del_p.K692fs	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	692					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)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						AATTGTAAGGTTTCTCTCCAG	0.393																																					p.K692fs		.											.	ZNF836-46	0			c.2076delA						.						71	76	74					19																	52658860		2071	4245	6316	SO:0001589	frameshift_variant	162962	exon5			.	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"Zinc fingers, C2H2-type", "-"	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.2076delA	19.37:g.52658860delT	ENSP00000325038:p.Lys692fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	36	20	NM_001102657	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000322146.8	37	CCDS46162.1																																																																																			.		0.393	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		-	52658860	T	-	52658860	7	5	133	1	0	1	0	1	0	0	0	0	18219	1722	60	0	736	0	ZNF836	19	52658860	Frame_Shift_Del	DEL	T	TCGA-HE-A5NI-01A-11D-A26P-10	4662631	52658860	6470123	120	11871											
BRSK1	84446	broad.mit.edu	37	chr19	55805597	55805597	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaggtccccccattatgcGtgtccagaggtgattaaggt	8	11	11	11	1	1	2	1	1	0	1	3	2	3	2	4	3	1	0	4	3	2	2	rs374051558		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:55805597G>T	ENST00000309383.1	+	6	868	c.591G>T	c.(589-591)gcG>gcT	p.A197A	BRSK1_ENST00000585418.1_Silent_p.A197A|BRSK1_ENST00000590333.1_Silent_p.A213A	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	197	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.A197A(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CCCATTATGCGTGTCCAGAGG	0.617																																					p.A197A													.	BRSK1-759	2	Substitution - coding silent(2)	large_intestine(2)	c.G591T						.						82	84	83					19																	55805597		2203	4300	6503	SO:0001819	synonymous_variant	84446	exon6			TTATGCGTGTCCA	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.591G>T	19.37:g.55805597G>T		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	133	4	NM_032430	0	0	7	7	0	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			.		0.617	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		T	55805597	G	T	55805597	2	4	133	1	0	0	0	0	0	0	0	1	1526	1132	40	4		4	BRSK1	19	55805597	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	3146737	55805597	3323386	121	11872											
ZNF274	10782	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	58723654	58723658	+	Frame_Shift_Del	DEL	TACCT	TACCT	-																															ttgtcctctacattagaagaTaccttgcagggtggggtcca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	TACCT	TACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:58723654_58723658delTACCT	ENST00000326804.4	+	9	1563_1567	c.1104_1108delTACCT	c.(1102-1110)gataccttgfs	p.TL369fs	ZNF274_ENST00000345813.3_Frame_Shift_Del_p.TL337fs|ZNF274_ENST00000424679.2_Frame_Shift_Del_p.TL264fs|ZNF274_ENST00000597818.1_3'UTR	NM_001278734.1|NM_133502.1	NP_001265663.1|NP_598009.1	Q96GC6	ZN274_HUMAN	zinc finger protein 274	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)|skin(1)	21		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		CATTAGAAGATACCTTGCAGGGTGG	0.483																																					.		.											.	ZNF274-91	0			.						.																																			SO:0001589	frameshift_variant	10782	.			.	AB029149	CCDS74473.1, CCDS74474.1, CCDS74475.1, CCDS74476.1	19q13.43	2013-01-09				ENSG00000171606		"Zinc fingers, C2H2-type", "-", "-", "-"	13068	protein-coding gene	gene with protein product		605467				10777669	Standard	NM_133502		Approved	ZKSCAN19, ZSCAN51	uc002qrs.1	Q96GC6		ENST00000326804.4:c.1104_1108delTACCT	19.37:g.58723654_58723658delTACCT	ENSP00000321209:p.Thr369fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	50	12	.	0	0	0	0	0	Q53XU4|Q6MZG1|Q8WY37|Q8WY38|Q92969|Q9UII0|Q9UII1	Targeted_Region	DEL	ENST00000326804.4	37																																																																																				.		0.483	ZNF274-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_133502		-	58723658	TACCT	-	58723654	7	5	133	1	0	1	0	1	0	0	0	0	17841	1403	49	0	1132	0	ZNF274	19	58723654	Frame_Shift_Del	DEL	TACCT	TCGA-HE-A5NI-01A-11D-A26P-10	2918057	58723654	405329	122	11873											
ZNF274	10782	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58724017	58724017	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgtaggaaaaccttcagtcgGagtactaaacagattacgtt	14	11	9	7	2	1	1	1	0	0	1	2	3	1	3	1	2	4	3	1	2	7	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:58724017G>C	ENST00000326804.4	+	9	1926	c.1467G>C	c.(1465-1467)cgG>cgC	p.R489R	ZNF274_ENST00000345813.3_Silent_p.R457R|ZNF274_ENST00000424679.2_Silent_p.R384R|ZNF274_ENST00000597818.1_3'UTR	NM_001278734.1|NM_133502.1	NP_001265663.1|NP_598009.1	Q96GC6	ZN274_HUMAN	zinc finger protein 274	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)|skin(1)	21		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		CCTTCAGTCGGAGTACTAAAC	0.388																																					.													.	ZNF274-91	0			.						.						91	91	91					19																	58724017		1893	4106	5999	SO:0001819	synonymous_variant	10782	.			CAGTCGGAGTACT	AB029149	CCDS74473.1, CCDS74474.1, CCDS74475.1, CCDS74476.1	19q13.43	2013-01-09				ENSG00000171606		"Zinc fingers, C2H2-type", "-", "-", "-"	13068	protein-coding gene	gene with protein product		605467				10777669	Standard	NM_133502		Approved	ZKSCAN19, ZSCAN51	uc002qrs.1	Q96GC6		ENST00000326804.4:c.1467G>C	19.37:g.58724017G>C		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	41	23	.	0	0	6	11	5	Q53XU4|Q6MZG1|Q8WY37|Q8WY38|Q92969|Q9UII0|Q9UII1	Silent	SNP	ENST00000326804.4	37																																																																																				.		0.388	ZNF274-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_133502		C	58724017	G	C	58724017	2	2	133	1	0	0	0	0	0	0	0	1	17841	1161	41	4		4	ZNF274	19	58724017	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	363	58724017	404966	123	11874											
MZF1	7593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	59082640	59082640	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgcaggcgtgcagcttcaggGcctgggtcccataaggcagc	7	6	15	13	2	1	0	1	0	0	0	2	0	2	0	2	4	3	4	2	4	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:59082640G>A	ENST00000215057.2	-	2	677	c.117C>T	c.(115-117)ggC>ggT	p.G39G	MZF1_ENST00000594108.1_Silent_p.G39G|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000599369.1_Silent_p.G39G|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|MZF1_ENST00000594234.1_Silent_p.G39G	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	39					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CAGCTTCAGGGCCTGGGTCCC	0.657																																					p.G39G		.											.	MZF1-91	0			c.C117T						.						26	29	28					19																	59082640		2203	4300	6503	SO:0001819	synonymous_variant	7593	exon2			TTCAGGGCCTGGG	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.117C>T	19.37:g.59082640G>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	50	16	NM_198055	0	0	2	6	4	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Silent	SNP	ENST00000215057.2	37	CCDS12988.1																																																																																			.		0.657	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		A	59082640	G	A	59082640	2	1	133	1	0	0	0	0	0	0	0	1	10133	1190	42	2		2	MZF1	19	59082640	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	358623	59082640	46343	124	11875											
PLCB1	23236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	8608961	8608961	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaccccaaattacgtgaactTttggatgtggggaacatcgg	11	10	12	8	2	0	1	0	1	0	0	1	4	0	3	2	4	3	0	2	4	4	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:8608961T>G	ENST00000338037.6	+	4	294	c.267T>G	c.(265-267)ctT>ctG	p.L89L	PLCB1_ENST00000378641.3_Silent_p.L89L|PLCB1_ENST00000378637.2_Silent_p.L89L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	89					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TACGTGAACTTTTGGATGTGG	0.443																																					p.N89K		.											.	PLCB1-297	0			c.C267G						.						78	78	78					20																	8608961		2203	4300	6503	SO:0001819	synonymous_variant	23236	exon4			TGAACTTTTGGAT	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.267T>G	20.37:g.8608961T>G		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	116	34	NM_015192	0	0	0	0	0	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			.		0.443	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			G	8608961	T	G	8608961	2	3	133	1	0	0	0	0	0	0	0	1	12053	1828	64	5		5	PLCB1	20	8608961	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		8608961	54416559	125	11876											
ASIP	434	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	32856797	32856797	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccggcgtttcccacgcagAaggaggcttcgatgaagaaa	11	6	12	12	4	0	3	0	1	0	2	2	5	1	4	3	3	0	3	3	3	3	2	rs538816237		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:32856797A>G	ENST00000568305.1	+	4	425	c.223A>G	c.(223-225)Aag>Gag	p.K75E	RP4-785G19.5_ENST00000512005.1_RNA|ASIP_ENST00000374954.3_Splice_Site_p.K75E			P42127	ASIP_HUMAN	agouti signaling protein	75	Arg/Lys-rich (basic).				adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|generation of precursor metabolites and energy (GO:0006091)|genetic imprinting (GO:0071514)|hormone-mediated signaling pathway (GO:0009755)|melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|regulation of molecular function, epigenetic (GO:0040030)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(2)	3						TCCCACGCAGAAGGAGGCTTC	0.697													A|||	1	0.000199681	0	0	5008	,	,		12806	0.001		0	False		,,,				2504	0				p.K75E		.											.	ASIP-90	0			c.A223G						.						8	11	10					20																	32856797		2188	4282	6470	SO:0001630	splice_region_variant	434	exon3			ACGCAGAAGGAGG		CCDS13232.1	20q11.2-q12	2010-06-24	2010-06-24		ENSG00000101440	ENSG00000101440			745	protein-coding gene	gene with protein product	"nonagouti homolog (mouse)"	600201	"agouti (mouse)-signaling protein", "agouti signaling protein, nonagouti homolog (mouse)"	AGTIL		7937887, 7757071	Standard	NM_001672		Approved	ASP	uc002xah.1	P42127	OTTHUMG00000032289	ENST00000568305.1:c.223-1A>G	20.37:g.32856797A>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	67	33	NM_001672	0	0	0	0	0	Q3SXL2	Missense_Mutation	SNP	ENST00000568305.1	37	CCDS13232.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744523	0.49151	.	.	ENSG00000101440	ENST00000374954	T	0.31769	1.48	4.61	4.61	0.57282	.	0.063957	0.64402	D	0.000013	T	0.48660	0.1512	M	0.82323	2.585	0.40299	D	0.978584	P	0.51240	0.943	P	0.54346	0.749	T	0.54970	-0.8213	9	.	.	.	.	10.3603	0.43989	1.0:0.0:0.0:0.0	.	75	P42127	ASIP_HUMAN	E	75	ENSP00000364092:K75E	.	K	+	1	0	ASIP	32320458	1.000000	0.71417	1.000000	0.80357	0.127000	0.20565	3.560000	0.53763	1.942000	0.56320	0.397000	0.26171	AAG	.		0.697	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1		Missense_Mutation	G	32856797	A	G	32856797	5	3	133	1	0	0	0	0	0	0	1	0	1044	260	9	3	233	3	ASIP	20	32856797	Splice_Site	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	24247836	32856797	30168723	126	11877											
C20orf152	140894	ucsc.edu;bcgsc.ca	37	chr20	34618475	34618475	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agacgactaaacctcgttatCctatttttatggcaccccag	11	12	6	12	2	0	1	0	0	0	1	2	2	1	1	4	1	1	2	4	1	5	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:34618475C>A	ENST00000373973.3	+	12	1809	c.1636C>A	c.(1636-1638)Cct>Act	p.P546T	CNBD2_ENST00000538900.1_3'UTR|CNBD2_ENST00000349339.1_Missense_Mutation_p.P542T			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	546																	ACCTCGTTATCCTATTTTTAT	0.468																																					p.P542T													.	.	0			c.C1624A						.						232	221	225					20																	34618475		2203	4300	6503	SO:0001583	missense	140894	exon12			CGTTATCCTATTT	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 152", "cyclic nucleotide (cNMP) binding domain containing 1"	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.1636C>A	20.37:g.34618475C>A	ENSP00000363084:p.Pro546Thr	Somatic	260	4		WXS	Illumina HiSeq		279	68	NM_080834	0	0	0	0	0	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		.	.	.	.	.	.	.	.	.	.	C	13.10	2.134926	0.37728	.	.	ENSG00000149646	ENST00000373973;ENST00000349339	T;T	0.25250	1.81;1.81	5.26	4.31	0.51392	.	0.000000	0.56097	D	0.000033	T	0.39963	0.1098	L	0.46157	1.445	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.13308	-1.0514	10	0.72032	D	0.01	-16.0468	9.1274	0.36824	0.0:0.9017:0.0:0.0983	.	542	Q96M20-2	.	T	546;542	ENSP00000363084:P546T;ENSP00000340954:P542T	ENSP00000340954:P542T	P	+	1	0	C20orf152	34081889	0.002000	0.14202	0.900000	0.35374	0.020000	0.10135	0.206000	0.17375	2.634000	0.89283	0.561000	0.74099	CCT	.		0.468	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834		A	34618475	C	A	34618475	3	1	133	1	0	0	0	0	1	0	0	0	2098	855	30	4	1670	4	C20orf152	20	34618475	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	1761678	34618475	28407045	127	11878											
SALL4	57167	hgsc.bcm.edu;bcgsc.ca	37	chr20	50401006	50401006	+	Frame_Shift_Del	DEL	A	A	-																															ccccactctggatcacagagAtctcattggtcttcacggcc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:50401006delA	ENST00000217086.4	-	4	3071	c.2960delT	c.(2959-2961)atcfs	p.I987fs	SALL4_ENST00000371539.3_Frame_Shift_Del_p.I210fs|SALL4_ENST00000395997.3_Frame_Shift_Del_p.I550fs	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	987					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GATCACAGAGATCTCATTGGT	0.572																																					p.I987fs		.											.	SALL4-92	0			c.2960delT						.						85	78	80					20																	50401006		2203	4300	6503	SO:0001589	frameshift_variant	57167	exon4			.	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2960delT	20.37:g.50401006delA	ENSP00000217086:p.Ile987fs	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	211	66	NM_020436	0	0	0	0	0	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Del	DEL	ENST00000217086.4	37	CCDS13438.1																																																																																			.		0.572	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			-	50401006	A	-	50401006	7	5	133	1	0	1	0	1	0	0	0	0	13845	333	12	0	205	0	SALL4	20	50401006	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	15782531	50401006	12624514	128	11879											
ARVCF	421	hgsc.bcm.edu	37	chr22	19967432	19967432	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgcacctcagcccgcgggtgGtccagcagtgccacaagcag	8	4	13	16	3	1	0	1	0	0	0	2	0	2	0	4	2	4	3	4	2	1	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr22:19967432G>T	ENST00000263207.3	-	6	1521	c.1230C>A	c.(1228-1230)gaC>gaA	p.D410E	ARVCF_ENST00000344269.3_Missense_Mutation_p.D347E|ARVCF_ENST00000406522.1_Missense_Mutation_p.D347E|ARVCF_ENST00000401994.1_Missense_Mutation_p.D347E|ARVCF_ENST00000487793.1_5'Flank|ARVCF_ENST00000406259.1_Missense_Mutation_p.D410E	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	410					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CCCGCGGGTGGTCCAGCAGTG	0.682																																					p.D410E		.											.	ARVCF-91	0			c.C1230A						.						19	19	19					22																	19967432		2178	4274	6452	SO:0001583	missense	421	exon6			CGGGTGGTCCAGC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"Armadillo repeat containing"	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1230C>A	22.37:g.19967432G>T	ENSP00000263207:p.Asp410Glu	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_001670	0	0	3	6	3	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167282	0.57476	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	4.51	-0.0128	0.13987	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.42040	0.1185	L	0.28115	0.83	0.50171	D	0.999858	P	0.39601	0.68	P	0.51742	0.678	T	0.11966	-1.0566	9	.	.	.	-21.2014	9.1754	0.37109	0.4923:0.0:0.5077:0.0	.	410	O00192	ARVC_HUMAN	E	410;347;347;347;410	ENSP00000263207:D410E;ENSP00000342042:D347E;ENSP00000384341:D347E;ENSP00000384732:D347E;ENSP00000385444:D410E	.	D	-	3	2	ARVCF	18347432	0.997000	0.39634	0.997000	0.53966	0.684000	0.39900	0.345000	0.19979	0.012000	0.14892	-0.131000	0.14894	GAC	.		0.682	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		T	19967432	G	T	19967432	3	4	133	1	0	0	0	0	1	0	0	0	1004	1252	44	4	1714	4	ARVCF	22	19967432	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		19967432	31337134	129	11880											
YPEL1	29799	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	22064932	22064932	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgccttggagatgagctcGtcatgattggccaggtgtgc	6	12	14	9	1	1	3	1	2	0	1	2	4	1	3	2	3	3	1	2	3	0	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr22:22064932G>C	ENST00000339468.3	-	2	485	c.102C>G	c.(100-102)gaC>gaG	p.D34E	YPEL1_ENST00000403503.1_Missense_Mutation_p.D34E	NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)	34						nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					AGATGAGCTCGTCATGATTGG	0.438																																					p.D34E													.	YPEL1-90	0			c.C102G						.						317	269	285					22																	22064932		2203	4300	6503	SO:0001583	missense	29799	exon2			GAGCTCGTCATGA	AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027			12845	protein-coding gene	gene with protein product		608082	"yippee (Drosophila) homolog-like 1"			11473580	Standard	NM_013313		Approved		uc002zvl.3	O60688	OTTHUMG00000150830	ENST00000339468.3:c.102C>G	22.37:g.22064932G>C	ENSP00000342832:p.Asp34Glu	Somatic	309	2		WXS	Illumina HiSeq	Phase_I	263	81	NM_013313	0	0	3	3	0	Q65ZA1|Q6GLI6	Missense_Mutation	SNP	ENST00000339468.3	37	CCDS13794.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432950	0.43224	.	.	ENSG00000100027	ENST00000339468;ENST00000403503	.	.	.	4.86	-7.17	0.01511	.	0.000000	0.85682	D	0.000000	T	0.45175	0.1329	L	0.31065	0.9	0.53688	D	0.999971	B	0.15930	0.015	B	0.19666	0.026	T	0.02721	-1.1119	9	0.36615	T	0.2	.	16.9342	0.86199	0.6194:0.0:0.3806:0.0	.	34	O60688	YPEL1_HUMAN	E	34	.	ENSP00000342832:D34E	D	-	3	2	YPEL1	20394932	0.300000	0.24435	0.368000	0.25939	0.764000	0.43329	-0.146000	0.10250	-2.011000	0.00952	-2.069000	0.00389	GAC	.		0.438	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320245.1	NM_013313		C	22064932	G	C	22064932	3	2	133	1	0	0	0	0	1	0	0	0	17522	1136	40	4	273	4	YPEL1	22	22064932	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	2097500	22064932	29239634	130	11881											
LARGE	9215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	33679190	33679190	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcagctagagccactcacctGaatgtgaagagggtccccat	11	7	11	12	0	1	4	1	2	0	2	2	4	2	4	4	1	2	2	4	1	3	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr22:33679190G>A	ENST00000354992.2	-	14	2446	c.1875C>T	c.(1873-1875)ttC>ttT	p.F625F	LARGE_ENST00000402320.1_Silent_p.F573F|LARGE_ENST00000452586.2_Silent_p.F424F|LARGE_ENST00000437602.2_Intron|LARGE_ENST00000397394.2_Silent_p.F625F|LARGE_ENST00000337431.2_Silent_p.F573F	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	625					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CCACTCACCTGAATGTGAAGA	0.552																																					p.F625F	Colon(70;397 1175 4573 19089 45288)	.											.	LARGE-92	0			c.C1875T						.						140	124	129					22																	33679190		2203	4300	6503	SO:0001819	synonymous_variant	9215	exon14			TCACCTGAATGTG	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"Glycosyltransferase family 8 domain containing"	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1875C>T	22.37:g.33679190G>A		Somatic	224	0		WXS	Illumina HiSeq	Phase_I	187	61	NM_004737	0	0	0	0	0	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																			.		0.552	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	33679190	G	A	33679190	2	1	133	1	0	0	0	0	0	0	0	1	8648	1281	45	2		2	LARGE	22	33679190	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	11614258	33679190	17625376	131	11882											
SFRS17A	8227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	1714402	1714403	+	Missense_Mutation	DNP	GG	GG	AA																															cgcagagagaaggaagcggaGgagaggcagcgagcggagga																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:1714402_1714403GG>AA	ENST00000313871.3	+	3	1084_1085	c.888_889GG>AA	c.(886-891)gaGGag>gaAAag	p.E297K	AKAP17A_ENST00000381261.3_Missense_Mutation_p.E297K	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	297					B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						AGGAAGCGGAGGAGAGGCAGCG	0.604																																					p.E297K		.											.	AKAP17A-40	0			c.G889A						.																																			SO:0001583	missense	8227	exon3			GCGGAGGAGAGGC	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	Exception_encountered	X.37:g.1714402_1714403delinsAA	ENSP00000324827:p.Glu297Lys	Somatic	152	1		WXS	Illumina HiSeq	Phase_I	89	73	NM_005088	0	0	0	0	0	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	DNP	ENST00000313871.3	37	CCDS14116.1																																																																																			.		0.604	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		AA	1714403	GG	AA	1714402	3	1	133	1	0	0	0	0	1	0	0	0	14205	991	35	2	894	2	SFRS17A	23	1714402	Missense_Mutation	DNP	GG	TCGA-HE-A5NI-01A-11D-A26P-10		1714402	153556158	132	11883											
BCOR	54880	hgsc.bcm.edu;bcgsc.ca	37	chrX	39923132	39923132	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaatgcacaccttcaggttGgtcagctcactataatgtgg	10	12	9	10	0	4	0	4	0	0	0	4	0	4	0	1	3	2	3	1	3	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:39923132G>T	ENST00000378444.4	-	8	3804	c.3576C>A	c.(3574-3576)acC>acA	p.T1192T	BCOR_ENST00000397354.3_Intron|BCOR_ENST00000378455.4_Intron|BCOR_ENST00000342274.4_Intron|BCOR_ENST00000378463.1_Intron	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1192					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						CCTTCAGGTTGGTCAGCTCAC	0.453			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.T1192T		.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR-229	0			c.C3576A						.						57	55	55					X																	39923132		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon8			CAGGTTGGTCAGC	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.3576C>A	X.37:g.39923132G>T		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_001123385	0	0	0	0	0	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			.		0.453	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39923132	G	T	39923132	2	4	133	1	0	0	0	0	0	0	0	1	1387	1335	47	4		4	BCOR	23	39923132	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	38208730	39923132	115347428	133	11884											
GATA1	2623	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	48650855	48650855	+	Frame_Shift_Del	DEL	A	A	-																															atgggcagaacaggcccctcAtccggcccaagaagcgcctg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:48650855delA	ENST00000376670.3	+	4	835	c.724delA	c.(724-726)atcfs	p.I242fs	GATA1_ENST00000376665.3_Frame_Shift_Del_p.I242fs	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	242					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						CAGGCCCCTCATCCGGCCCAA	0.562			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.I242fs	Pancreas(9;429 505 11287 29617)	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1-1315	0			c.724delA						.						62	58	59					X																	48650855		2203	4300	6503	SO:0001589	frameshift_variant	2623	exon4			.	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.724delA	X.37:g.48650855delA	ENSP00000365858:p.Ile242fs	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	132	99	NM_002049	0	0	0	0	0	Q96GB8	Frame_Shift_Del	DEL	ENST00000376670.3	37	CCDS14305.1																																																																																			.		0.562	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		-	48650855	A	-	48650855	7	5	133	1	0	1	0	1	0	0	0	0	6273	217	8	0	734	0	GATA1	23	48650855	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	8727723	48650855	106619705	134	11885											
DCX	1641	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	110654011	110654011	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcctatcaaattggaacttCgggctaaatacattaaaact	15	12	5	9	1	1	0	1	0	0	0	3	1	2	1	1	2	3	1	1	2	8	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:110654011C>T	ENST00000338081.3	-	1	363	c.192G>A	c.(190-192)ccG>ccA	p.P64P	DCX_ENST00000496551.1_Intron|DCX_ENST00000488120.1_Intron|DCX_ENST00000371993.2_Intron|DCX_ENST00000356915.2_Intron|DCX_ENST00000356220.3_Intron	NM_000555.3	NP_000546.2	O43602	DCX_HUMAN	doublecortin	64					axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						ATTGGAACTTCGGGCTAAATA	0.433																																					p.P64P													.	DCX-554	0			c.G192A						.						167	158	161					X																	110654011		2203	4300	6503	SO:0001819	synonymous_variant	1641	exon1			GAACTTCGGGCTA	AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279			2714	protein-coding gene	gene with protein product	"doublecortex"	300121	"doublecortex; lissencephaly, X-linked (doublecortin)"			9489699, 9489700	Standard	NM_178151		Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000338081.3:c.192G>A	X.37:g.110654011C>T		Somatic	129	2		WXS	Illumina HiSeq	Phase_I	97	74	NM_000555	0	0	0	0	0	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	Silent	SNP	ENST00000338081.3	37	CCDS14556.1	.	.	.	.	.	.	.	.	.	.	c	4.746	0.138661	0.09083	.	.	ENSG00000077279	ENST00000358070	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	T	0.60287	0.2257	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57688	-0.7768	4	.	.	.	.	9.6932	0.40141	0.0:0.7737:0.2263:0.0	.	.	.	.	Q	56	.	.	R	-	2	0	DCX	110540667	0.959000	0.32827	1.000000	0.80357	0.995000	0.86356	1.431000	0.34925	2.442000	0.82660	0.509000	0.49947	CGA	.		0.433	DCX-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357058.1	NM_178153		T	110654011	C	T	110654011	2	4	133	1	0	0	0	0	0	0	0	1	4324	871	31	1		1	DCX	23	110654011	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	62003156	110654011	44616549	135	11886											
PRRG3	79057	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	150869380	150869380	+	Frame_Shift_Del	DEL	C	C	-																															gactgtccagcaccacccctCccccctcctacgaggaggtg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:150869380delC	ENST00000370353.3	+	4	961	c.571delC	c.(571-573)cccfs	p.P192fs	PRRG3_ENST00000538575.1_Frame_Shift_Del_p.P192fs			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	192						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					CACCACCCCTCCCCCCTCCTA	0.647																																					p.P191fs		.											.	PRRG3-134	0			c.571delC						.						55	44	48					X																	150869380		2203	4300	6503	SO:0001589	frameshift_variant	79057	exon4			.	AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.571delC	X.37:g.150869380delC	ENSP00000359378:p.Pro192fs	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	154	102	NM_024082	0	0	0	0	0	A1A523|A1A575|Q8N2N6	Frame_Shift_Del	DEL	ENST00000370353.3	37	CCDS14699.1																																																																																			.		0.647	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	NM_024082		-	150869380	C	-	150869380	7	5	133	1	0	1	0	1	0	0	0	0	12636	855	30	0	581	0	PRRG3	23	150869380	Frame_Shift_Del	DEL	C	TCGA-HE-A5NI-01A-11D-A26P-10	40215369	150869380	4401180	136	11887											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	27106015	27106015	+	Frame_Shift_Del	DEL	C	C	-																															ggcctcacgcaccctgcccaCcagcccctcggaagcatgtg																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:27106015delC	ENST00000324856.7	+	20	5997	c.5626delC	c.(5626-5628)ccafs	p.P1876fs	ARID1A_ENST00000457599.2_Frame_Shift_Del_p.P1659fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.P204fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.P1493fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1876					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		ACCCTGCCCACCAGCCCCTCG	0.622			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.P1876fs		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.5626delC						.						64	70	68					1																	27106015		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5626delC	1.37:g.27106015delC	ENSP00000320485:p.Pro1876fs	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	122	49	NM_006015	0	0	0	0	0	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																			.		0.622	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27106015	C	-	27106015	7	5	134	1	0	1	0	1	0	0	0	0	913	507	18	0	5704	0	ARID1A	1	27106015	Frame_Shift_Del	DEL	C	TCGA-HE-A5NJ-01A-11D-A26P-10		27106015	222144606	1	11888											
TMEM125	128218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	43739036	43739036	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacgagaccacatccagcAttgccagcctcatctgacgg	10	7	9	15	2	3	2	2	1	1	1	4	3	4	2	4	1	3	1	4	1	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:43739036A>G	ENST00000432792.2	+	4	1213	c.643A>G	c.(643-645)Att>Gtt	p.I215V	TMEM125_ENST00000439858.1_Missense_Mutation_p.I215V			Q96AQ2	TM125_HUMAN	transmembrane protein 125	215						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CACATCCAGCATTGCCAGCCT	0.627																																					p.I215V		.											.	TMEM125-153	0			c.A643G						.						35	29	31					1																	43739036		2203	4300	6503	SO:0001583	missense	128218	exon4			TCCAGCATTGCCA	BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178			28275	protein-coding gene	gene with protein product							Standard	NM_144626		Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.643A>G	1.37:g.43739036A>G	ENSP00000429275:p.Ile215Val	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	150	80	NM_144626	0	0	15	23	8	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	37	CCDS480.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340390	0.41498	.	.	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.44482	0.92;0.92	4.91	4.91	0.64330	.	0.123297	0.53938	D	0.000057	T	0.28599	0.0708	N	0.19112	0.55	0.29819	N	0.830963	P	0.34462	0.454	B	0.31337	0.128	T	0.19844	-1.0293	10	0.36615	T	0.2	.	14.5656	0.68173	1.0:0.0:0.0:0.0	.	215	Q96AQ2	TM125_HUMAN	V	215	ENSP00000429775:I215V;ENSP00000429275:I215V	ENSP00000429275:I215V	I	+	1	0	TMEM125	43511623	1.000000	0.71417	0.997000	0.53966	0.784000	0.44337	2.906000	0.48735	1.842000	0.53543	0.460000	0.39030	ATT	.		0.627	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626		G	43739036	A	G	43739036	3	3	134	1	0	0	0	0	1	0	0	0	16069	217	8	3	645	3	TMEM125	1	43739036	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	16633021	43739036	205511585	2	11889											
RPTN	126638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152127305	152127305	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttcatgggtttgcctgtctCgtctctgatggctctgctca	3	16	10	12	1	5	1	2	1	3	0	7	1	5	1	1	2	2	3	1	2	0	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:152127305C>T	ENST00000316073.3	-	3	2334	c.2270G>A	c.(2269-2271)cGa>cAa	p.R757Q		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	757	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TTGCCTGTCTCGTCTCTGATG	0.512																																					p.R757Q		.											.	RPTN-68	0			c.G2270A						.						835	660	713					1																	152127305		1568	3582	5150	SO:0001583	missense	126638	exon3			CTGTCTCGTCTCT	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.2270G>A	1.37:g.152127305C>T	ENSP00000317895:p.Arg757Gln	Somatic	367	1		WXS	Illumina HiSeq	Phase_I	399	158	NM_001122965	0	0	0	0	0	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	4.873	0.162231	0.09287	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.12569	2.67	5.46	-6.92	0.01644	.	1.609200	0.05690	N	0.591997	T	0.02688	0.0081	N	0.25286	0.73	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.25187	-1.0139	10	0.29301	T	0.29	0.289	14.9735	0.71251	0.0:0.6643:0.0:0.3357	.	757	Q6XPR3	RPTN_HUMAN	Q	757;412	ENSP00000317895:R757Q	ENSP00000317895:R757Q	R	-	2	0	RPTN	150393929	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-1.478000	0.02329	-2.128000	0.00818	-1.183000	0.01708	CGA	.		0.512	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		T	152127305	C	T	152127305	3	4	134	1	0	0	0	0	1	0	0	0	13696	884	31	1	88	1	RPTN	1	152127305	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	108388269	152127305	97123316	3	11890											
NUP210L	91181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154108401	154108401	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacccgttaagtgcaactcTatggtcttgcaattccagta	11	12	8	10	1	2	1	0	0	2	1	3	1	3	1	2	1	3	4	2	1	5	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:154108401T>C	ENST00000368559.3	-	7	969	c.898A>G	c.(898-900)Aga>Gga	p.R300G	NUP210L_ENST00000271854.3_Missense_Mutation_p.R300G	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	300					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			AGTGCAACTCTATGGTCTTGC	0.418																																					p.R300G		.											.	NUP210L-77	0			c.A898G						.						108	99	102					1																	154108401		1876	4103	5979	SO:0001583	missense	91181	exon7			CAACTCTATGGTC	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.898A>G	1.37:g.154108401T>C	ENSP00000357547:p.Arg300Gly	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	94	29	NM_001159484	0	0	0	0	0	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.410097	0.25465	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.05447	3.44;3.44	5.0	2.53	0.30540	.	0.593551	0.16379	N	0.216995	T	0.01387	0.0045	L	0.44542	1.39	0.09310	N	1	B;B	0.31125	0.201;0.309	B;B	0.21917	0.037;0.037	T	0.48714	-0.9011	10	0.23302	T	0.38	-11.1939	4.5019	0.11869	0.0:0.1237:0.3878:0.4885	.	300;300	E7EP56;Q5VU65	.;P210L_HUMAN	G	300	ENSP00000357547:R300G;ENSP00000271854:R300G	ENSP00000271854:R300G	R	-	1	2	NUP210L	152375025	0.003000	0.15002	0.002000	0.10522	0.896000	0.52359	1.475000	0.35409	0.321000	0.23259	0.533000	0.62120	AGA	.		0.418	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		C	154108401	T	C	154108401	3	2	134	1	0	0	0	0	1	0	0	0	10787	1530	53	3	4904	3	NUP210L	1	154108401	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	1981096	154108401	95142220	4	11891											
TMEM9	252839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201123024	201123024	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggcaccagcaaacacccgaCcacagccaccaaagataaga	17	1	8	15	1	0	2	0	0	0	2	0	3	0	2	5	1	3	2	5	1	3	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:201123024C>T	ENST00000367330.1	-	1	544	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	TMEM9_ENST00000485839.2_Missense_Mutation_p.V10I|TMEM9_ENST00000367332.1_Missense_Mutation_p.V10I|TMEM9_ENST00000367334.5_Missense_Mutation_p.V10I|TMEM9_ENST00000367333.2_Missense_Mutation_p.V10I			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	10					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)				liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				AAACACCCGACCACAGCCACC	0.582																																					p.V10I		.											.	TMEM9-90	0			c.G28A						.						70	66	67					1																	201123024		2203	4300	6503	SO:0001583	missense	252839	exon2			ACCCGACCACAGC		CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.28G>A	1.37:g.201123024C>T	ENSP00000356299:p.Val10Ile	Somatic	275	0		WXS	Illumina HiSeq	Phase_I	251	89	NM_016456	0	0	12	21	9	B1ALM6|Q96NQ9|Q9BQF5	Missense_Mutation	SNP	ENST00000367330.1	37	CCDS1408.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198740	0.58126	.	.	ENSG00000116857	ENST00000367334;ENST00000367332;ENST00000367330;ENST00000367329;ENST00000367333;ENST00000455367;ENST00000435310;ENST00000414605	.	.	.	4.66	3.75	0.43078	.	0.790844	0.10935	N	0.617956	T	0.20210	0.0486	N	0.19112	0.55	0.19300	N	0.999979	B;B;B;B	0.31581	0.329;0.049;0.008;0.003	B;B;B;B	0.25987	0.065;0.039;0.003;0.004	T	0.11641	-1.0579	9	0.08599	T	0.76	-18.4909	9.8146	0.40844	0.0:0.9026:0.0:0.0974	.	10;10;10;10	B4DJZ4;B4E1H4;B1ALM5;Q9P0T7	.;.;.;TMEM9_HUMAN	I	10	.	ENSP00000356298:V10I	V	-	1	0	TMEM9	199389647	0.000000	0.05858	0.772000	0.31596	0.991000	0.79684	0.133000	0.15912	1.175000	0.42826	0.557000	0.71058	GTC	.		0.582	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456		T	201123024	C	T	201123024	3	4	134	1	0	0	0	0	1	0	0	0	16249	507	18	2	543	2	TMEM9	1	201123024	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	47014623	201123024	48127597	5	11892											
GPN1	11321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27858007	27858007	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgatttttttgtggctttagGcatcctcatttccaacagtt	7	19	7	8	0	1	1	1	1	0	0	3	1	3	1	2	2	1	3	2	2	2	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:27858007G>A	ENST00000610189.1	+	7	437	c.430G>A	c.(430-432)Gca>Aca	p.A144T	GPN1_ENST00000458167.2_Splice_Site_p.A49T|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000503738.1_Splice_Site_p.A49T|GPN1_ENST00000424214.1_Splice_Site_p.A65T|GPN1_ENST00000461249.1_3'UTR|GPN1_ENST00000264718.3_Splice_Site_p.A158T|GPN1_ENST00000407583.3_Splice_Site_p.A132T|ZNF512_ENST00000556601.1_3'UTR|GPN1_ENST00000515877.1_Splice_Site_p.A65T	NM_007266.3	NP_009197.2			GPN-loop GTPase 1											endometrium(1)|large_intestine(1)|lung(12)	14						GTGGCTTTAGGCATCCTCATT	0.443																																					p.A158T		.											.	GPN1-159	0			c.G472A						.						209	190	196					2																	27858007		2203	4300	6503	SO:0001630	splice_region_variant	11321	exon7			CTTTAGGCATCCT	AB044661	CCDS1760.2, CCDS46248.1, CCDS46249.1, CCDS46250.1	2p23.3	2011-11-04	2008-04-30	2008-04-30	ENSG00000198522	ENSG00000198522		"GPN-loop GTPases"	17030	protein-coding gene	gene with protein product	"RNA polymerase II associated protein 4"	611479	"XPA binding protein 1", "XPA binding protein 1, GTPase"	XAB1		11058119, 11124703	Standard	NM_007266		Approved	NTPBP, MBDIN, ATPBD1A, RPAP4	uc010ymc.2	Q9HCN4	OTTHUMG00000097784	ENST00000610189.1:c.430-1G>A	2.37:g.27858007G>A		Somatic	209	0		WXS	Illumina HiSeq	Phase_I	189	73	NM_007266	0	0	0	1	1		Missense_Mutation	SNP	ENST00000610189.1	37		.	.	.	.	.	.	.	.	.	.	G	36	5.660616	0.96734	.	.	ENSG00000198522	ENST00000515877;ENST00000503738;ENST00000458167;ENST00000424214;ENST00000407583;ENST00000264718	T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9	5.96	5.96	0.96718	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	M	0.77616	2.38	0.80722	D	1	P;D;D;D	0.89917	0.792;1.0;0.98;0.992	P;D;P;D	0.81914	0.9;0.995;0.876;0.92	T	0.50039	-0.8874	9	.	.	.	-8.5718	17.1122	0.86679	0.0:0.0:1.0:0.0	.	144;158;49;132	Q9HCN4;B4DQM4;B4DXU4;B5MBZ5	GPN1_HUMAN;.;.;.	T	65;49;49;65;132;158	ENSP00000424678:A65T;ENSP00000427269:A49T;ENSP00000412170:A49T;ENSP00000398115:A65T;ENSP00000384255:A132T;ENSP00000264718:A158T	.	A	+	1	0	GPN1	27711511	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.896000	0.92521	2.820000	0.97059	0.655000	0.94253	GCA	.		0.443	GPN1-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473126.1	NM_007266	Missense_Mutation	A	27858007	G	A	27858007	5	1	134	1	0	0	0	0	0	0	1	0	6637	1217	42	2	581	2	GPN1	2	27858007	Splice_Site	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		27858007	215341366	6	11893											
RTN4	57142	bcgsc.ca	37	chr2	55254453	55254453	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcttgaagtgttccttcaGtgggtaatactgttgacaaa	10	16	9	6	0	2	2	1	2	1	0	3	2	3	2	1	1	1	3	1	1	4	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:55254453G>T	ENST00000337526.6	-	3	1025	c.782C>A	c.(781-783)aCt>aAt	p.T261N	RTN4_ENST00000357376.3_Missense_Mutation_p.T55N|RTN4_ENST00000354474.6_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000394611.2_Missense_Mutation_p.T55N|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.T55N|RTN4_ENST00000404909.1_Missense_Mutation_p.T55N	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	261					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						TGTTCCTTCAGTGGGTAATAC	0.398																																					p.T261N													.	RTN4-155	0			c.C782A						.						76	78	77					2																	55254453		2203	4300	6503	SO:0001583	missense	57142	exon3			CCTTCAGTGGGTA	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.782C>A	2.37:g.55254453G>T	ENSP00000337838:p.Thr261Asn	Somatic	49	0		WXS	Illumina HiSeq	Phase_1	62	4	NM_020532	0	0	0	0	0	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	G	9.097	1.003103	0.19121	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000427710	T;T;T;T;T	0.20463	2.07;2.07;2.3;2.07;2.07	6.02	3.28	0.37604	.	0.837760	0.10740	N	0.639616	T	0.21718	0.0523	L	0.56769	1.78	0.53688	D	0.99997	P	0.34462	0.454	B	0.30251	0.113	T	0.01951	-1.1241	10	0.72032	D	0.01	-0.0569	9.4715	0.38844	0.1281:0.1192:0.7527:0.0	.	261	Q9NQC3	RTN4_HUMAN	N	55;55;261;55;55;55	ENSP00000384471:T55N;ENSP00000349944:T55N;ENSP00000337838:T261N;ENSP00000378109:T55N;ENSP00000385650:T55N	ENSP00000337838:T261N	T	-	2	0	RTN4	55107957	0.920000	0.31207	0.045000	0.18777	0.578000	0.36192	2.530000	0.45641	0.438000	0.26450	-0.156000	0.13503	ACT	.		0.398	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			T	55254453	G	T	55254453	3	4	134	1	0	0	0	0	1	0	0	0	13760	1029	36	4	2862	4	RTN4	2	55254453	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	27396446	55254453	187944920	7	11894											
ALMS1	7840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	73836707	73836707	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctacagagagtgaccaatCaacttctggggagaaaagtt	14	10	10	7	0	3	3	1	1	2	2	3	5	3	3	1	2	2	1	1	2	5	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:73836707C>T	ENST00000264448.6	+	23	12583	c.12472C>T	c.(12472-12474)Caa>Taa	p.Q4158*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Q4116*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4158	ALMS motif.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGTGACCAATCAACTTCTGGG	0.433																																					p.Q4158X		.											.	ALMS1-142	0			c.C12472T						.						117	116	116					2																	73836707		1850	4083	5933	SO:0001587	stop_gained	7840	exon23			ACCAATCAACTTC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.12472C>T	2.37:g.73836707C>T	ENSP00000264448:p.Gln4158*	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	53	15	NM_015120	0	0	0	0	0	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	53	21.012144	0.99936	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	.	.	.	5.34	5.34	0.76211	.	0.658065	0.14442	N	0.319301	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	14.4071	0.67090	0.0:1.0:0.0:0.0	.	.	.	.	X	4116;4158	.	ENSP00000264448:Q4158X	Q	+	1	0	ALMS1	73690215	0.984000	0.35163	0.996000	0.52242	0.780000	0.44128	2.387000	0.44389	2.779000	0.95612	0.591000	0.81541	CAA	.		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73836707	C	T	73836707	4	4	134	1	0	0	0	0	0	1	0	0	535	827	29	2	12562	2	ALMS1	2	73836707	Nonsense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	18582254	73836707	169362666	8	11895											
ACVR2A	92	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	148676153	148676153	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggccacaaacctgccatAtctcacaggtagactaaatt	14	9	7	11	0	1	1	1	0	1	1	2	2	1	1	3	2	2	1	3	2	5	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:148676153A>G	ENST00000241416.7	+	7	1590	c.954A>G	c.(952-954)atA>atG	p.I318M	ACVR2A_ENST00000404590.1_Missense_Mutation_p.I318M|ACVR2A_ENST00000535787.1_Missense_Mutation_p.I210M	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AACCTGCCATATCTCACAGGT	0.348																																					p.I318M		.											.	ACVR2A-831	0			c.A954G						.						42	44	43					2																	148676153		2202	4300	6502	SO:0001583	missense	92	exon7			TGCCATATCTCAC		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.954A>G	2.37:g.148676153A>G	ENSP00000241416:p.Ile318Met	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	56	22	NM_001616	0	0	0	0	0	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	37	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	17.99	3.524183	0.64747	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.73789	-0.78;-0.78;-0.78	5.63	0.102	0.14522	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050216	0.85682	D	0.000000	D	0.84465	0.5478	M	0.86178	2.8	0.54753	D	0.999987	P	0.42827	0.791	P	0.56514	0.8	D	0.85693	0.1308	10	0.59425	D	0.04	.	15.9363	0.79712	0.3896:0.6104:0.0:0.0	.	318	P27037	AVR2A_HUMAN	M	318;210;318	ENSP00000241416:I318M;ENSP00000439988:I210M;ENSP00000384338:I318M	ENSP00000241416:I318M	I	+	3	3	ACVR2A	148392623	0.981000	0.34729	0.995000	0.50966	0.986000	0.74619	0.307000	0.19296	-0.207000	0.10187	0.460000	0.39030	ATA	.		0.348	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		G	148676153	A	G	148676153	3	3	134	1	0	0	0	0	1	0	0	0	223	439	16	3	980	3	ACVR2A	2	148676153	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	74839446	148676153	94523220	9	11896											
SH3BP4	23677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	235949726	235949726	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaccgaaatgggctacatcCcctcctcctatgtgcagccc	8	8	7	18	1	0	0	0	0	0	0	3	1	3	0	7	1	3	2	7	1	3	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:235949726C>G	ENST00000409212.1	+	4	820	c.313C>G	c.(313-315)Ccc>Gcc	p.P105A	SH3BP4_ENST00000392011.2_Missense_Mutation_p.P105A|SH3BP4_ENST00000344528.4_Missense_Mutation_p.P105A			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	105	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GGGCTACATCCCCTCCTCCTA	0.537																																					p.P105A		.											.	SH3BP4-94	0			c.C313G						.						171	144	153					2																	235949726		2203	4300	6503	SO:0001583	missense	23677	exon4			TACATCCCCTCCT	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.313C>G	2.37:g.235949726C>G	ENSP00000386862:p.Pro105Ala	Somatic	321	0		WXS	Illumina HiSeq	Phase_I	320	127	NM_014521	0	0	2	5	3	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.895268	0.91962	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000446904	D;D;D;D;D	0.99454	-5.92;-5.92;-5.92;-5.92;-5.92	5.24	5.24	0.73138	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97817	1.0254	10	0.72032	D	0.01	-9.9278	17.3901	0.87427	0.0:1.0:0.0:0.0	.	105;105	A8K594;Q9P0V3	.;SH3B4_HUMAN	A	105	ENSP00000375867:P105A;ENSP00000403251:P105A;ENSP00000386862:P105A;ENSP00000340237:P105A;ENSP00000415391:P105A	ENSP00000340237:P105A	P	+	1	0	SH3BP4	235614465	1.000000	0.71417	0.996000	0.52242	0.940000	0.58332	7.571000	0.82399	2.442000	0.82660	0.655000	0.94253	CCC	.		0.537	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			G	235949726	C	G	235949726	3	3	134	1	0	0	0	0	1	0	0	0	14278	623	22	4	319	4	SH3BP4	2	235949726	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	87273573	235949726	7249647	10	11897											
ITPR1	3708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	4859771	4859771	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttgtctcatttttaggcttgGaaagagacaagtttgacaac	12	14	9	6	0	1	2	1	1	1	1	2	4	1	3	0	2	1	2	0	2	4	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:4859771G>A	ENST00000443694.2	+	57	7828	c.7828G>A	c.(7828-7830)Gaa>Aaa	p.E2610K	AC018816.3_ENST00000441894.1_Intron|ITPR1_ENST00000423119.2_Missense_Mutation_p.E2577K|AC018816.3_ENST00000489771.1_Intron|ITPR1_ENST00000544951.1_Missense_Mutation_p.E588K|ITPR1_ENST00000354582.6_Missense_Mutation_p.E2610K|ITPR1_ENST00000302640.8_Missense_Mutation_p.E2610K|ITPR1_ENST00000357086.4_Missense_Mutation_p.E2577K|ITPR1_ENST00000456211.2_Missense_Mutation_p.E2562K|ITPR1_ENST00000463980.1_3'UTR|AC018816.3_ENST00000449914.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2625					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTTAGGCTTGGAAAGAGACAA	0.448																																					p.E2610K		.											.	ITPR1-710	0			c.G7828A						.						52	48	49					3																	4859771		1897	4121	6018	SO:0001583	missense	3708	exon59			GGCTTGGAAAGAG	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"Ion channels / Inositol triphosphate receptors"	6180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 94"	147265	"spinocerebellar ataxia 15", "spinocerebellar ataxia 16", "spinocerebellar ataxia 29"	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7828G>A	3.37:g.4859771G>A	ENSP00000401671:p.Glu2610Lys	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	126	45	NM_001168272	0	0	2	2	0	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	g	32	5.120856	0.94385	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	L	0.57536	1.79	0.80722	D	1	D;B;B	0.62365	0.991;0.102;0.226	P;B;B	0.61201	0.885;0.07;0.425	T	0.56147	-0.8027	10	0.35671	T	0.21	.	18.3362	0.90288	0.0:0.0:1.0:0.0	.	588;2625;2577	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	K	2625;2610;2610;2577;1071;2577;2562;588;2610	ENSP00000306253:E2610K;ENSP00000346595:E2610K;ENSP00000405934:E2577K;ENSP00000349597:E2577K;ENSP00000397885:E2562K;ENSP00000440564:E588K;ENSP00000401671:E2610K	ENSP00000306253:E2610K	E	+	1	0	ITPR1	4834771	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.709000	0.98729	2.311000	0.77944	0.461000	0.40582	GAA	.		0.448	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4859771	G	A	4859771	3	1	134	1	0	0	0	0	1	0	0	0	7941	1175	41	2	8103	2	ITPR1	3	4859771	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		4859771	193162659	11	11898											
THUMPD3	25917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9406849	9406849	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaaagtgacctcggaagtGaatctgagcttctagtcact	12	10	10	9	1	3	4	1	3	2	1	4	5	3	5	1	1	1	1	1	1	4	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:9406849G>A	ENST00000345094.3	+	2	431	c.97G>A	c.(97-99)Gaa>Aaa	p.E33K	SETD5-AS1_ENST00000468186.1_RNA|RP11-380O24.1_ENST00000517846.1_RNA|RP11-380O24.1_ENST00000518331.1_RNA|THUMPD3_ENST00000515662.2_Missense_Mutation_p.E33K|RP11-380O24.1_ENST00000517687.1_RNA|THUMPD3_ENST00000452837.2_Missense_Mutation_p.E33K|RP11-380O24.1_ENST00000466431.2_RNA|RP11-380O24.1_ENST00000491930.2_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	33						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		CCTCGGAAGTGAATCTGAGCT	0.443																																					p.E33K		.											.	THUMPD3-227	0			c.G97A						.						94	95	94					3																	9406849		2203	4300	6503	SO:0001583	missense	25917	exon2			GGAAGTGAATCTG	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.97G>A	3.37:g.9406849G>A	ENSP00000339532:p.Glu33Lys	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	128	51	NM_001114092	0	0	0	0	0	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	37	CCDS2573.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044109	0.75732	.	.	ENSG00000134077	ENST00000452837;ENST00000417036;ENST00000419437;ENST00000345094;ENST00000515662	T;T;T	0.44083	0.93;0.93;0.93	5.57	4.47	0.54385	.	0.949351	0.08920	N	0.874534	T	0.35595	0.0937	L	0.51422	1.61	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.11494	-1.0585	10	0.40728	T	0.16	.	5.2477	0.15506	0.1312:0.2026:0.6662:0.0	.	33	Q9BV44	THUM3_HUMAN	K	33	ENSP00000395893:E33K;ENSP00000339532:E33K;ENSP00000424064:E33K	ENSP00000339532:E33K	E	+	1	0	THUMPD3	9381849	0.049000	0.20398	0.085000	0.20634	0.888000	0.51559	2.198000	0.42705	2.785000	0.95823	0.655000	0.94253	GAA	.		0.443	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453		A	9406849	G	A	9406849	3	1	134	1	0	0	0	0	1	0	0	0	15916	1291	45	2	99	2	THUMPD3	3	9406849	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	4547078	9406849	188615581	12	11899											
COL7A1	1294	hgsc.bcm.edu;bcgsc.ca	37	chr3	48610131	48610131	+	Frame_Shift_Del	DEL	T	T	-																															ggggcccccgtggggccaggTtctcctttaggtccgacagg																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:48610131delT	ENST00000328333.8	-	87	6980	c.6873delA	c.(6871-6873)gaafs	p.E2291fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.E2259fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2291	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGGGCCAGGTTCTCCTTTAG	0.632																																					p.E2291fs		.											.	COL7A1-160	0			c.6873delA						.						24	30	28					3																	48610131		2200	4297	6497	SO:0001589	frameshift_variant	1294	exon87			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6873delA	3.37:g.48610131delT	ENSP00000332371:p.Glu2291fs	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	114	31	NM_000094	0	0	0	0	0	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	37	CCDS2773.1																																																																																			.		0.632	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		-	48610131	T	-	48610131	7	5	134	1	0	1	0	1	0	0	0	0	3710	1722	60	0	2089	0	COL7A1	3	48610131	Frame_Shift_Del	DEL	T	TCGA-HE-A5NJ-01A-11D-A26P-10	39203282	48610131	149412299	13	11900											
IL17RD	54756	hgsc.bcm.edu;bcgsc.ca	37	chr3	57144293	57144293	+	Frame_Shift_Del	DEL	C	C	-																															tggcactgtcttccctccgaCttcagctcctccagtattac																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:57144293delC	ENST00000296318.7	-	4	445	c.357delG	c.(355-357)aagfs	p.K119fs	IL17RD_ENST00000427856.2_Frame_Shift_Del_p.K95fs|IL17RD_ENST00000463523.1_5'UTR|IL17RD_ENST00000320057.5_5'UTR	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	119					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TTCCCTCCGACTTCAGCTCCT	0.438																																					p.K119fs		.											.	IL17RD-500	0			c.357delG						.						121	109	113					3																	57144293		1911	4137	6048	SO:0001589	frameshift_variant	54756	exon4			.	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.357delG	3.37:g.57144293delC	ENSP00000296318:p.Lys119fs	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	90	27	NM_017563	0	0	0	0	0	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Frame_Shift_Del	DEL	ENST00000296318.7	37	CCDS2880.2																																																																																			.		0.438	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		-	57144293	C	-	57144293	7	5	134	1	0	1	0	1	0	0	0	0	7663	564	20	0	1902	0	IL17RD	3	57144293	Frame_Shift_Del	DEL	C	TCGA-HE-A5NJ-01A-11D-A26P-10	8534162	57144293	140878137	14	11901											
IGSF10	285313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151155196	151155196	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctatcagatactgataacTttgtggtccattggaaaatc	12	14	8	7	0	1	2	1	1	0	1	3	3	2	3	1	2	3	1	1	2	5	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:151155196T>G	ENST00000282466.3	-	6	7152	c.7153A>C	c.(7153-7155)Agt>Cgt	p.S2385R	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2385	Ig-like C2-type 10.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TACTGATAACTTTGTGGTCCA	0.408																																					p.S2385R		.											.	IGSF10-102	0			c.A7153C						.						125	125	125					3																	151155196		2203	4300	6503	SO:0001583	missense	285313	exon6			GATAACTTTGTGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.7153A>C	3.37:g.151155196T>G	ENSP00000282466:p.Ser2385Arg	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	77	41	NM_178822	0	0	0	0	0	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	4.176	0.031261	0.08101	.	.	ENSG00000152580	ENST00000282466	T	0.63580	-0.05	5.59	0.331	0.15933	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.945401	0.08716	N	0.904233	T	0.42607	0.1210	L	0.28115	0.83	0.09310	N	1	P;B	0.41080	0.737;0.141	B;B	0.36845	0.234;0.066	T	0.18681	-1.0329	10	0.22706	T	0.39	.	6.415	0.21712	0.0:0.1304:0.2469:0.6227	.	2385;412	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	R	2385	ENSP00000282466:S2385R	ENSP00000282466:S2385R	S	-	1	0	IGSF10	152637886	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	1.061000	0.30542	-0.160000	0.11002	-0.316000	0.08728	AGT	.		0.408	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		G	151155196	T	G	151155196	3	3	134	1	0	0	0	0	1	0	0	0	7618	1609	56	5	722	5	IGSF10	3	151155196	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	94010903	151155196	46867234	15	11902											
UGT2B28	54490	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	70146322	70146322	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaccggtgaatacagccAttggatgaatatgaagacaa	15	8	12	6	1	0	4	0	3	0	1	0	6	0	6	2	3	2	0	2	3	6	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr4:70146322A>T	ENST00000335568.5	+	1	106	c.104A>T	c.(103-105)cAt>cTt	p.H35L	UGT2B28_ENST00000511240.1_Missense_Mutation_p.H35L	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	35					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						GAATACAGCCATTGGATGAAT	0.458																																					p.H35L													.	UGT2B28-91	0			c.A104T						.						160	185	177					4																	70146322		2067	4246	6313	SO:0001583	missense	54490	exon1			ACAGCCATTGGAT	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"UDP glucuronosyltransferases"	13479	protein-coding gene	gene with protein product		606497	"UDP glycosyltransferase 2 family, polypeptide B28"			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.104A>T	4.37:g.70146322A>T	ENSP00000334276:p.His35Leu	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	170	74	NM_053039	0	0	0	0	0	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	.	.	.	.	.	.	.	.	.	.	-	7.966	0.747929	0.15710	.	.	ENSG00000135226	ENST00000335568;ENST00000511240	T;T	0.75704	-0.96;-0.96	2.18	2.18	0.27775	.	0.076639	0.51477	U	0.000092	T	0.80560	0.4646	M	0.90595	3.13	0.31529	N	0.661439	B;B	0.25007	0.004;0.116	B;B	0.39935	0.015;0.314	T	0.81614	-0.0853	10	0.66056	D	0.02	.	7.9497	0.30008	1.0:0.0:0.0:0.0	.	35;35	Q9BY64-2;Q9BY64	.;UDB28_HUMAN	L	35	ENSP00000334276:H35L;ENSP00000427399:H35L	ENSP00000334276:H35L	H	+	2	0	UGT2B28	70180911	0.998000	0.40836	0.173000	0.22940	0.039000	0.13416	5.193000	0.65120	1.012000	0.39366	0.155000	0.16302	CAT	.		0.458	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039		T	70146322	A	T	70146322	3	4	134	1	0	0	0	0	1	0	0	0	16993	217	8	5	106	5	UGT2B28	4	70146322	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10		70146322	121007954	16	11903											
NPFFR2	10886	bcgsc.ca	37	chr4	73012838	73012838	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaagaagaaaaatattaccGagtgagactcaactcccaga	18	6	8	9	1	1	4	1	1	0	4	2	6	2	4	2	0	2	1	2	0	7	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr4:73012838G>A	ENST00000308744.6	+	4	976	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000395999.1_Missense_Mutation_p.R194Q|NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000358749.3_Missense_Mutation_p.R191Q	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	293					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			AAATATTACCGAGTGAGACTC	0.433																																					p.R293Q													.	NPFFR2-92	0			c.G878A						.						140	138	138					4																	73012838		2203	4300	6503	SO:0001583	missense	10886	exon4			ATTACCGAGTGAG	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"GPCR / Class A :  Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors"	4525	protein-coding gene	gene with protein product	"neuropeptide FF 2"	607449	"G protein-coupled receptor 74"	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.878G>A	4.37:g.73012838G>A	ENSP00000307822:p.Arg293Gln	Somatic	83	0		WXS	Illumina HiSeq	Phase_1	89	5	NM_004885	0	0	0	0	0	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	37	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	G	8.617	0.890562	0.17613	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.71817	-0.6;-0.6;-0.6	5.67	0.868	0.19090	GPCR, rhodopsin-like superfamily (1);	0.487974	0.17420	N	0.174879	T	0.57519	0.2059	L	0.48174	1.505	0.47659	D	0.99948	B;B	0.31655	0.108;0.334	B;B	0.29524	0.024;0.103	T	0.40515	-0.9559	10	0.17832	T	0.49	.	9.92	0.41459	0.3518:0.0:0.6482:0.0	.	194;293	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	Q	293;194;191	ENSP00000307822:R293Q;ENSP00000379321:R194Q;ENSP00000351599:R191Q	ENSP00000307822:R293Q	R	+	2	0	NPFFR2	73231702	0.252000	0.23972	0.933000	0.37362	0.106000	0.19336	0.370000	0.20433	-0.165000	0.10908	-0.136000	0.14681	CGA	.		0.433	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		A	73012838	G	A	73012838	3	1	134	1	0	0	0	0	1	0	0	0	10604	1058	37	1	898	1	NPFFR2	4	73012838	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	2866516	73012838	118141438	17	11904											
ENPEP	2028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	111397929	111397929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctacacgggcaccgtgaGcatctccatcaacctgagcg	10	6	9	16	3	2	2	1	2	1	0	3	2	2	2	4	1	4	2	4	1	2	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr4:111397929G>A	ENST00000265162.5	+	1	701	c.359G>A	c.(358-360)aGc>aAc	p.S120N		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	120					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		GGCACCGTGAGCATCTCCATC	0.627																																					p.S120N		.											.	ENPEP-157	0			c.G359A						.						96	100	99					4																	111397929		2203	4300	6503	SO:0001583	missense	2028	exon1			CCGTGAGCATCTC	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"CD molecules"	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.359G>A	4.37:g.111397929G>A	ENSP00000265162:p.Ser120Asn	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	143	38	NM_001977	0	0	0	2	2	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	G	4.521	0.096620	0.08681	.	.	ENSG00000138792	ENST00000265162	T	0.02709	4.19	5.83	-6.19	0.02078	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.193580	0.05705	N	0.594848	T	0.02342	0.0072	N	0.12443	0.215	0.20489	N	0.999897	B	0.09022	0.002	B	0.14023	0.01	T	0.41270	-0.9518	10	0.17832	T	0.49	.	18.7095	0.91651	0.2671:0.1216:0.6113:0.0	.	120	Q07075	AMPE_HUMAN	N	120	ENSP00000265162:S120N	ENSP00000265162:S120N	S	+	2	0	ENPEP	111617378	0.004000	0.15560	0.072000	0.20136	0.026000	0.11368	-0.722000	0.04958	-1.974000	0.00998	-0.305000	0.09177	AGC	.		0.627	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			A	111397929	G	A	111397929	3	1	134	1	0	0	0	0	1	0	0	0	5141	971	34	2	361	2	ENPEP	4	111397929	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	38385091	111397929	79756347	18	11905											
CCT5	22948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	10263419	10263419	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atcgactgtttgcacaagggGacaaatggtgaggagctgtc	11	9	14	7	1	0	1	0	1	0	0	2	4	0	3	0	4	2	3	0	4	2	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:10263419G>A	ENST00000280326.4	+	10	1911	c.1491G>A	c.(1489-1491)ggG>ggA	p.G497G	CCT5_ENST00000515676.1_Silent_p.G459G|CCT5_ENST00000503026.1_Silent_p.G476G|CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000506600.1_Silent_p.G404G|CCT5_ENST00000515390.1_Silent_p.G442G	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	497					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TGCACAAGGGGACAAATGGTG	0.512																																					p.G497G		.											.	CCT5-92	0			c.G1491A						.						59	55	56					5																	10263419		2203	4300	6503	SO:0001819	synonymous_variant	22948	exon10			CAAGGGGACAAAT	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"Heat Shock Proteins / Chaperonins"	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1491G>A	5.37:g.10263419G>A		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	111	50	NM_012073	0	0	1	2	1	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																			.		0.512	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			A	10263419	G	A	10263419	2	1	134	1	0	0	0	0	0	0	0	1	2962	1161	41	2		2	CCT5	5	10263419	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		10263419	170651841	19	11906											
ZNF366	167465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	71739709	71739709	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgccgggtactctgaaaagcCctgagactgagacactcatc	11	7	10	13	2	2	3	1	3	1	2	3	5	2	3	2	1	2	1	2	1	3	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:71739709C>T	ENST00000318442.5	-	5	2599	c.2109G>A	c.(2107-2109)agG>agA	p.R703R	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	703	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TCTGAAAAGCCCTGAGACTGA	0.517																																					p.R703R		.											.	ZNF366-91	0			c.G2109A						.						102	107	105					5																	71739709		2203	4300	6503	SO:0001819	synonymous_variant	167465	exon5			AAAAGCCCTGAGA	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"Zinc fingers, C2H2-type"	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.2109G>A	5.37:g.71739709C>T		Somatic	36	0		WXS	Illumina HiSeq	Phase_I	42	13	NM_152625	0	0	0	0	0	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																			.		0.517	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			T	71739709	C	T	71739709	2	4	134	1	0	0	0	0	0	0	0	1	17902	622	22	2		2	ZNF366	5	71739709	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	61476290	71739709	109175551	20	11907											
SLC12A2	6558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	127477532	127477532	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctttaggttcttgtgtTgttcgagatgccactggaaa	7	16	12	6	1	1	1	0	0	1	1	2	3	1	2	1	2	2	4	1	2	2	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:127477532T>A	ENST00000262461.2	+	10	1821	c.1632T>A	c.(1630-1632)gtT>gtA	p.V544V	SLC12A2_ENST00000343225.4_Silent_p.V544V	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	544					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	GTTCTTGTGTTGTTCGAGATG	0.308																																					p.V544V		.											.	SLC12A2-94	0			c.T1632A						.						171	162	165					5																	127477532		2203	4300	6503	SO:0001819	synonymous_variant	6558	exon10			TTGTGTTGTTCGA		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1632T>A	5.37:g.127477532T>A		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	74	25	NM_001046	0	0	0	0	0	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	37	CCDS4144.1																																																																																			.		0.308	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		A	127477532	T	A	127477532	2	1	134	1	0	0	0	0	0	0	0	1	14415	1799	63	5		5	SLC12A2	5	127477532	Silent	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	55737823	127477532	53437728	21	11908											
SLC26A2	1836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149361289	149361289	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaccttctcttctatagTgtgtatgaagcgatggcttt	10	15	9	7	1	2	1	0	1	2	0	3	3	2	1	1	1	2	2	1	1	6	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:149361289T>C	ENST00000286298.4	+	3	2401	c.2133T>C	c.(2131-2133)agT>agC	p.S711S		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	711	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TCTTCTATAGTGTGTATGAAG	0.413																																					p.S711S		.											.	SLC26A2-90	0			c.T2133C						.						57	63	61					5																	149361289		2203	4299	6502	SO:0001819	synonymous_variant	1836	exon3			CTATAGTGTGTAT	U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.2133T>C	5.37:g.149361289T>C		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	41	17	NM_000112	0	0	2	2	0	A8K2U3|B2R6J1|Q6N051	Silent	SNP	ENST00000286298.4	37	CCDS4300.1																																																																																			.		0.413	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		C	149361289	T	C	149361289	2	2	134	1	0	0	0	0	0	0	0	1	14549	1693	59	3		3	SLC26A2	5	149361289	Silent	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	21883757	149361289	31553971	22	11909											
C6orf108	23113	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	43193768	43193768	+	IGR	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagggaggcttggggtgctCaccgcggccagactgcgggc	5	5	20	11	3	1	1	1	0	0	1	1	3	1	3	2	7	2	2	2	7	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr6:43193768C>A	ENST00000252050.4	+	0	7780				RP3-330M21.5_ENST00000500590.1_RNA|DNPH1_ENST00000230431.6_Intron|DNPH1_ENST00000393987.2_Nonsense_Mutation_p.E127*	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TTGGGGTGCTCACCGCGGCCA	0.647																																					p.E127X		.											.	.	0			c.G379T						.						27	26	26					6																	43193768		2203	4298	6501	SO:0001628	intergenic_variant	10591	exon3			GGTGCTCACCGCG	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723		6.37:g.43193768C>A		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	72	25	NM_199184	0	0	2	9	7	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Nonsense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.539836	0.27563	.	.	ENSG00000112667	ENST00000393987	.	.	.	4.24	2.38	0.29361	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.999974	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	6.7563	0.23516	0.0:0.7731:0.0:0.2269	.	.	.	.	X	127	.	ENSP00000377556:E127X	E	-	1	0	C6orf108	43301746	0.036000	0.19791	0.992000	0.48379	0.353000	0.29299	0.002000	0.13061	0.989000	0.38761	0.462000	0.41574	GAG	.		0.647	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43193768	C	A	43193768	1	1	134	0	1	0	0	0	0	0	0	0	2326	835	29	4		4	C6orf108	6	43193768	IGR	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		43193768	127921299	23	11910											
HCRTR2	3062	ucsc.edu;bcgsc.ca	37	chr6	55113587	55113587	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gacctggttttttggacagtCcctttgcaaagtgattcctt	7	16	9	9	0	0	1	0	1	0	0	2	3	2	2	3	2	1	2	3	2	1	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr6:55113587C>G	ENST00000370862.3	+	2	710	c.374C>G	c.(373-375)tCc>tGc	p.S125C		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	125					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)	p.S125C(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TTTGGACAGTCCCTTTGCAAA	0.423																																					p.S125C													.	HCRTR2-525	1	Substitution - Missense(1)	lung(1)	c.C374G						.						251	234	240					6																	55113587		2203	4299	6502	SO:0001583	missense	3062	exon2			GACAGTCCCTTTG	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.374C>G	6.37:g.55113587C>G	ENSP00000359899:p.Ser125Cys	Somatic	176	2		WXS	Illumina HiSeq		181	73	NM_001526	0	0	0	0	0	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	37	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	C	16.63	3.177419	0.57692	.	.	ENSG00000137252	ENST00000370862	T	0.72167	-0.63	4.65	4.65	0.58169	GPCR, rhodopsin-like superfamily (1);	0.230889	0.43416	D	0.000566	T	0.64821	0.2633	L	0.41492	1.28	0.32294	N	0.565959	P;P	0.40931	0.733;0.733	P;P	0.56343	0.796;0.796	T	0.64774	-0.6328	10	0.39692	T	0.17	.	11.1333	0.48360	0.1407:0.723:0.1364:0.0	.	125;125	Q548Y0;O43614	.;OX2R_HUMAN	C	125	ENSP00000359899:S125C	ENSP00000359899:S125C	S	+	2	0	HCRTR2	55221546	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.695000	0.54749	2.282000	0.76494	0.555000	0.69702	TCC	.		0.423	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			G	55113587	C	G	55113587	3	3	134	1	0	0	0	0	1	0	0	0	7023	855	30	4	380	4	HCRTR2	6	55113587	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	11919819	55113587	116001480	24	11911											
IGF2R	3482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	160467594	160467594	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tataaagttgagacaaagaaGtatgacttttatataaatgt	18	14	7	2	0	0	3	0	2	0	2	0	4	0	3	0	0	0	2	0	0	10	8			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr6:160467594G>C	ENST00000356956.1	+	15	2116	c.1968G>C	c.(1966-1968)aaG>aaC	p.K656N		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	656					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AGACAAAGAAGTATGACTTTT	0.413																																					p.K656N		.											.	IGF2R-118	0			c.G1968C						.						81	88	86					6																	160467594		2203	4300	6503	SO:0001583	missense	3482	exon15			AAAGAAGTATGAC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"CD molecules"	5467	protein-coding gene	gene with protein product	"cation-independent mannose-6 phosphate receptor"	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1968G>C	6.37:g.160467594G>C	ENSP00000349437:p.Lys656Asn	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_000876	0	0	3	7	4	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.287371	0.23478	.	.	ENSG00000197081	ENST00000356956	T	0.11277	2.79	5.07	3.25	0.37280	Mannose-6-phosphate receptor, binding (1);	0.269818	0.41500	D	0.000876	T	0.04770	0.0129	L	0.58354	1.805	0.45995	D	0.998804	P	0.45396	0.857	P	0.45377	0.478	T	0.37798	-0.9690	10	0.19147	T	0.46	-5.8683	3.1762	0.06569	0.2087:0.1255:0.5372:0.1286	.	656	P11717	MPRI_HUMAN	N	656	ENSP00000349437:K656N	ENSP00000349437:K656N	K	+	3	2	IGF2R	160387584	0.158000	0.22850	0.965000	0.40720	0.840000	0.47671	-0.185000	0.09684	1.262000	0.44165	0.655000	0.94253	AAG	.		0.413	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160467594	G	C	160467594	3	2	134	1	0	0	0	0	1	0	0	0	7597	1020	36	4	2026	4	IGF2R	6	160467594	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	105354007	160467594	10647473	25	11912											
ISPD	729920	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	16255771	16255771	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaattctctaatctgcattaGgttttccattttctgactgg	9	18	6	8	0	3	1	0	1	3	0	5	1	4	1	1	2	1	2	1	2	3	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:16255771G>C	ENST00000407010.2	-	9	1170	c.1171C>G	c.(1171-1173)Cta>Gta	p.L391V	ISPD-AS1_ENST00000582683.1_RNA|ISPD-AS1_ENST00000438573.1_RNA|ISPD_ENST00000399310.3_Missense_Mutation_p.L341V|ISPD-AS1_ENST00000579293.1_RNA|ISPD-AS1_ENST00000457112.1_RNA	NM_001101426.3	NP_001094896.1	A4D126	ISPD_HUMAN	isoprenoid synthase domain containing	391					axon guidance (GO:0007411)|isoprenoid biosynthetic process (GO:0008299)|protein O-linked mannosylation (GO:0035269)		nucleotidyltransferase activity (GO:0016779)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9						ATCTGCATTAGGTTTTCCATT	0.303										Multiple Myeloma(15;0.18)																											p.L391V		.											.	ISPD-23	0			c.C1171G						.						64	60	61					7																	16255771		1786	4057	5843	SO:0001583	missense	729920	exon9			GCATTAGGTTTTC	AK124805		7p21.2	2010-03-19			ENSG00000214960	ENSG00000214960			37276	protein-coding gene	gene with protein product	"notch1-induced protein", "4-diphosphocytidyl-2C-methyl-D-erythritol synthase homolog (Arabidopsis)"	614631				11181995	Standard	NM_001101417		Approved	hCG_1745121, IspD, Nip	uc010ktx.2	A4D126	OTTHUMG00000152447	ENST00000407010.2:c.1171C>G	7.37:g.16255771G>C	ENSP00000385478:p.Leu391Val	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	50	28	NM_001101426	0	0	0	1	1	A8MU35|H9KVB2	Missense_Mutation	SNP	ENST00000407010.2	37		.	.	.	.	.	.	.	.	.	.	G	5.747	0.322274	0.10900	.	.	ENSG00000214960	ENST00000407010;ENST00000399310	D;D	0.87729	-2.23;-2.29	5.22	3.4	0.38934	.	.	.	.	.	T	0.77711	0.4171	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.65857	-0.6066	9	0.48119	T	0.1	-18.4993	7.3675	0.26781	0.0916:0.1697:0.7388:0.0	.	391	A4D126	ISPD_HUMAN	V	391;341	ENSP00000385478:L391V;ENSP00000382249:L341V	ENSP00000382249:L341V	L	-	1	2	ISPD	16222296	0.250000	0.23951	0.038000	0.18304	0.431000	0.31685	0.794000	0.26958	0.685000	0.31468	0.591000	0.81541	CTA	.		0.303	ISPD-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000326252.4	NM_001101426		C	16255771	G	C	16255771	3	2	134	1	0	0	0	0	1	0	0	0	7885	991	35	4	192	4	ISPD	7	16255771	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		16255771	142882892	26	11913											
HIP1	3092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	75183809	75183809	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctggaaatggatgtgacCgtggagaggaggtgatctgt	10	9	17	5	1	1	3	0	2	1	1	1	7	1	6	1	5	1	1	1	5	1	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:75183809C>T	ENST00000336926.6	-	20	2006	c.1980G>A	c.(1978-1980)acG>acA	p.T660T	HIP1_ENST00000434438.2_Silent_p.T660T	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	660					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TGGATGTGACCGTGGAGAGGA	0.527			T	PDGFRB	CMML																																p.T660T		.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1-1085	0			c.G1980A						.						98	90	92					7																	75183809		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon20			TGTGACCGTGGAG	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.1980G>A	7.37:g.75183809C>T		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	105	63	NM_005338	0	0	2	7	5	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			.		0.527	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		T	75183809	C	T	75183809	2	4	134	1	0	0	0	0	0	0	0	1	7135	639	23	1		1	HIP1	7	75183809	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	58928038	75183809	83954854	27	11914											
CD36	948	broad.mit.edu;bcgsc.ca	37	chr7	80302113	80302113	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattcactttacaatttgcaAaacggctgcaggtcaaccta	13	11	7	10	1	2	0	2	0	0	0	2	1	2	0	1	2	5	3	1	2	6	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:80302113A>T	ENST00000435819.1	+	15	1837	c.1153A>T	c.(1153-1155)Aaa>Taa	p.K385*	CD36_ENST00000447544.2_Nonsense_Mutation_p.K385*|CD36_ENST00000394788.3_Nonsense_Mutation_p.K385*|CD36_ENST00000432207.1_Nonsense_Mutation_p.K385*|CD36_ENST00000433696.2_Nonsense_Mutation_p.K346*|CD36_ENST00000538969.1_Nonsense_Mutation_p.K325*|CD36_ENST00000309881.7_Nonsense_Mutation_p.K385*|CD36_ENST00000534394.1_Nonsense_Mutation_p.K309*|CD36_ENST00000544133.1_3'UTR			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	385					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 cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						ACAATTTGCAAAACGGCTGCA	0.289																																					p.K385X													.	CD36-69	0			c.A1153T						.						63	64	64					7																	80302113		2200	4298	6498	SO:0001587	stop_gained	948	exon10			TTTGCAAAACGGC	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"CD molecules"	1663	protein-coding gene	gene with protein product		173510	"CD36 antigen (collagen type I receptor, thrombospondin receptor)"			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.1153A>T	7.37:g.80302113A>T	ENSP00000399421:p.Lys385*	Somatic	81	2		WXS	Illumina HiSeq	Phase_I	166	108	NM_001127444	0	0	1	1	0	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Nonsense_Mutation	SNP	ENST00000435819.1	37	CCDS34673.1	.	.	.	.	.	.	.	.	.	.	A	38	6.792769	0.97841	.	.	ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000534394;ENST00000394788;ENST00000447544;ENST00000432207;ENST00000419819;ENST00000538969;ENST00000433696	.	.	.	5.06	5.06	0.68205	.	0.043359	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.73	14.7706	0.69675	1.0:0.0:0.0:0.0	.	.	.	.	X	385;385;309;385;385;385;385;325;346	.	.	K	+	1	0	CD36	80140049	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	4.318000	0.59190	2.016000	0.59253	0.482000	0.46254	AAA	.		0.289	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547		T	80302113	A	T	80302113	4	4	134	1	0	0	0	0	0	1	0	0	3013	15	1	5	1191	5	CD36	7	80302113	Nonsense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	5118304	80302113	78836550	28	11915											
HIPK2	28996	ucsc.edu;bcgsc.ca	37	chr7	139305166	139305166	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggttgtggacagtggtcAgctggttgttaaaggtcatg	7	13	15	6	0	2	0	2	0	0	0	2	1	2	1	1	5	1	4	1	5	2	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:139305166A>T	ENST00000406875.3	-	7	1857	c.1763T>A	c.(1762-1764)cTg>cAg	p.L588Q	HIPK2_ENST00000428878.2_Missense_Mutation_p.L588Q|HIPK2_ENST00000342645.6_Missense_Mutation_p.L588Q	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	588	Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GACAGTGGTCAGCTGGTTGTT	0.527																																					p.L588Q													.	HIPK2-785	0			c.T1763A						.						204	197	199					7																	139305166		2096	4234	6330	SO:0001583	missense	28996	exon7			GTGGTCAGCTGGT	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1763T>A	7.37:g.139305166A>T	ENSP00000385571:p.Leu588Gln	Somatic	348	3		WXS	Illumina HiSeq		663	290	NM_022740	0	0	5	8	3	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	37		.	.	.	.	.	.	.	.	.	.	A	21.8	4.199947	0.79015	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.56776	0.46;0.44;0.51	4.79	4.79	0.61399	.	.	.	.	.	T	0.72179	0.3428	.	.	.	0.58432	D	0.999999	D;D	0.71674	0.998;0.997	D;D	0.80764	0.991;0.994	T	0.76490	-0.2940	8	0.66056	D	0.02	.	14.3492	0.66688	1.0:0.0:0.0:0.0	.	588;588	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	Q	588	ENSP00000385571:L588Q;ENSP00000413724:L588Q;ENSP00000343108:L588Q	ENSP00000343108:L588Q	L	-	2	0	HIPK2	138955706	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.907000	0.92634	1.780000	0.52325	0.533000	0.62120	CTG	.		0.527	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		T	139305166	A	T	139305166	3	4	134	1	0	0	0	0	1	0	0	0	7138	188	7	5	1869	5	HIPK2	7	139305166	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	59003053	139305166	19833497	29	11916											
PAXIP1	22976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	154767474	154767474	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtaatattcctcagtgtccGtacagctggactccaggtag	10	11	10	10	1	1	0	1	0	0	0	4	1	4	1	3	2	2	4	3	2	4	5	rs540417697		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:154767474G>A	ENST00000404141.1	-	6	1160	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	PAXIP1_ENST00000397192.1_Missense_Mutation_p.R336W|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	336					adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		CTCAGTGTCCGTACAGCTGGA	0.433																																					p.R336W		.											.	PAXIP1-228	0			c.C1006T						.						45	44	44					7																	154767474		1947	4167	6114	SO:0001583	missense	22976	exon6			GTGTCCGTACAGC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1006C>T	7.37:g.154767474G>A	ENSP00000384048:p.Arg336Trp	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	202	86	NM_007349	0	0	0	2	2	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486598	0.63962	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.48836	0.8;0.8	5.04	4.16	0.48862	.	0.000000	0.50627	U	0.000119	T	0.63141	0.2486	M	0.68952	2.095	0.40826	D	0.983548	B;D;B;D	0.89917	0.225;1.0;0.333;1.0	B;D;B;D	0.91635	0.028;0.999;0.061;0.998	T	0.66040	-0.6022	10	0.72032	D	0.01	-63.4587	8.8578	0.35238	0.0761:0.0:0.7761:0.1478	.	289;245;302;336	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	W	336;336;284;289	ENSP00000384048:R336W;ENSP00000380376:R336W	ENSP00000319149:R289W	R	-	1	2	PAXIP1	154398407	1.000000	0.71417	0.985000	0.45067	0.878000	0.50629	3.274000	0.51631	1.250000	0.43966	0.305000	0.20034	CGG	.		0.433	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		A	154767474	G	A	154767474	3	1	134	1	0	0	0	0	1	0	0	0	11513	1144	40	1	2267	1	PAXIP1	7	154767474	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	15462308	154767474	4371189	30	11917											
SGK223	157285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	8235300	8235300	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcagccagtttctggcggaAgctctcctgggtggagggcc	5	8	17	11	1	2	0	0	0	2	0	3	2	2	2	3	6	2	3	3	6	1	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:8235300A>G	ENST00000520004.1	-	3	883	c.619T>C	c.(619-621)Ttc>Ctc	p.F207L	SGK223_ENST00000330777.4_Missense_Mutation_p.F207L			Q86YV5	SG223_HUMAN		207							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TTCTGGCGGAAGCTCTCCTGG	0.602																																					p.F207L	GBM(34;731 755 10259 33573 33867)	.											.	.	0			c.T619C						.						88	97	94					8																	8235300		1951	4139	6090	SO:0001583	missense	0	exon2			GGCGGAAGCTCTC																												ENST00000520004.1:c.619T>C	8.37:g.8235300A>G	ENSP00000428054:p.Phe207Leu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	94	43	NM_001080826	0	0	3	4	1	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.466943	0.26335	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.56103	0.48;0.48	5.2	5.2	0.72013	.	0.099877	0.41605	D	0.000844	T	0.38188	0.1031	L	0.32530	0.975	0.30179	N	0.800576	B	0.27351	0.176	B	0.25884	0.064	T	0.37150	-0.9718	10	0.37606	T	0.19	.	7.5573	0.27831	0.8992:0.0:0.1008:0.0	.	207	Q86YV5	SG223_HUMAN	L	207	ENSP00000330930:F207L;ENSP00000428054:F207L	ENSP00000330930:F207L	F	-	1	0	AC068353.1	8272710	0.988000	0.35896	1.000000	0.80357	0.426000	0.31534	1.270000	0.33086	2.089000	0.63090	0.533000	0.62120	TTC	.		0.602	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			G	8235300	A	G	8235300	3	3	134	1	0	0	0	0	1	0	0	0	14242	72	3	3	3605	3	SGK223	8	8235300	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10		8235300	138128722	31	11918											
PXDNL	137902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	52359698	52359698	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggagagaactgtatgcTggccttccacagggagctgc	10	7	14	10	0	0	2	0	0	0	2	1	5	1	4	2	3	4	3	2	3	2	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:52359698T>A	ENST00000356297.4	-	12	1491	c.1391A>T	c.(1390-1392)cAg>cTg	p.Q464L	PXDNL_ENST00000543296.1_Missense_Mutation_p.Q464L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	464	Ig-like C2-type 3.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				AACTGTATGCTGGCCTTCCAC	0.512																																					p.Q464L		.											.	PXDNL-70	0			c.A1391T						.						109	107	108					8																	52359698		2028	4190	6218	SO:0001583	missense	137902	exon12			GTATGCTGGCCTT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"Immunoglobulin superfamily / I-set domain containing"	26359	protein-coding gene	gene with protein product	"polysomal ribonuclease 1 homolog (Xenopus)"	615904	"peroxidasin homolog-like (Drosophila)"			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1391A>T	8.37:g.52359698T>A	ENSP00000348645:p.Gln464Leu	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	108	44	NM_144651	0	0	0	0	0	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	T	5.421	0.262910	0.10294	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.81659	-1.52;-1.52	4.02	-7.16	0.01516	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65450	0.2692	L	0.43701	1.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.49523	-0.8931	9	0.36615	T	0.2	.	4.0424	0.09758	0.3721:0.1572:0.0:0.4707	.	464	A1KZ92	PXDNL_HUMAN	L	464	ENSP00000348645:Q464L;ENSP00000444865:Q464L	ENSP00000348645:Q464L	Q	-	2	0	PXDNL	52522251	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.100000	0.15231	-1.355000	0.02186	-0.375000	0.07067	CAG	.		0.512	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52359698	T	A	52359698	3	1	134	1	0	0	0	0	1	0	0	0	12880	1580	55	5	3048	5	PXDNL	8	52359698	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	44124398	52359698	94004324	32	11919											
RB1CC1	9821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	53555097	53555097	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactgacttcttcttcaagcTttttcttttcctcaagcaaa	9	18	3	11	0	5	1	2	1	3	0	6	1	6	1	1	0	3	2	1	0	4	8			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:53555097T>G	ENST00000025008.5	-	18	4674	c.4151A>C	c.(4150-4152)aAg>aCg	p.K1384T	RB1CC1_ENST00000539297.1_Missense_Mutation_p.K1384T|RB1CC1_ENST00000435644.2_Missense_Mutation_p.K1384T|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1384					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				TTCTTCAAGCTTTTTCTTTTC	0.383																																					p.K1384T	GBM(180;1701 2102 13475 42023 52570)	.											.	RB1CC1-170	0			c.A4151C						.						96	91	93					8																	53555097		2203	4300	6503	SO:0001583	missense	9821	exon18			TCAAGCTTTTTCT	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"200 kDa FAK family kinase-interacting protein", "phosphatase 1, regulatory subunit 131"	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.4151A>C	8.37:g.53555097T>G	ENSP00000025008:p.Lys1384Thr	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	93	39	NM_001083617	0	0	2	6	4	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.040807	0.55003	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.18338	2.22;2.22;2.22	5.61	4.46	0.54185	.	0.235291	0.44097	D	0.000482	T	0.12561	0.0305	L	0.27053	0.805	0.34041	D	0.654965	B;B	0.30361	0.277;0.181	B;B	0.33042	0.157;0.075	T	0.22941	-1.0202	10	0.26408	T	0.33	-15.3958	10.1369	0.42712	0.0:0.0806:0.0:0.9194	.	1384;1384	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	T	1384	ENSP00000025008:K1384T;ENSP00000396067:K1384T;ENSP00000445960:K1384T	ENSP00000025008:K1384T	K	-	2	0	RB1CC1	53717650	0.999000	0.42202	0.825000	0.32803	0.998000	0.95712	3.259000	0.51515	0.950000	0.37743	0.533000	0.62120	AAG	.		0.383	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		G	53555097	T	G	53555097	3	3	134	1	0	0	0	0	1	0	0	0	13131	1609	56	5	661	5	RB1CC1	8	53555097	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	1195399	53555097	92808925	33	11920											
UTP23	84294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	117782585	117782585	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgaagagggaaatcctcatCattattttgtggcaacacag	13	12	9	7	0	2	2	2	1	0	1	3	3	3	3	1	2	1	1	1	2	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:117782585C>T	ENST00000309822.2	+	2	444	c.343C>T	c.(343-345)Cat>Tat	p.H115Y	UTP23_ENST00000517820.1_Intron|UTP23_ENST00000520733.1_Missense_Mutation_p.H9Y|UTP23_ENST00000357148.3_Missense_Mutation_p.H115Y	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	115					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						AAATCCTCATCATTATTTTGT	0.353																																					p.H115Y		.											.	UTP23-226	0			c.C343T						.						112	105	107					8																	117782585		2203	4300	6503	SO:0001583	missense	84294	exon2			CCTCATCATTATT		CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 53"	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.343C>T	8.37:g.117782585C>T	ENSP00000308332:p.His115Tyr	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	87	30	NM_032334	0	0	4	8	4	B2RE25|Q96NJ8	Missense_Mutation	SNP	ENST00000309822.2	37	CCDS6320.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351801	0.82132	.	.	ENSG00000147679	ENST00000309822;ENST00000357148;ENST00000517814;ENST00000520733	T	0.24151	1.87	5.9	5.9	0.94986	.	0.093959	0.64402	D	0.000001	T	0.54935	0.1889	M	0.79011	2.435	0.58432	D	0.999998	D	0.71674	0.998	D	0.69142	0.962	T	0.54662	-0.8260	10	0.62326	D	0.03	-17.3326	20.2789	0.98501	0.0:1.0:0.0:0.0	.	115	Q9BRU9	UTP23_HUMAN	Y	115;115;115;9	ENSP00000308332:H115Y	ENSP00000308332:H115Y	H	+	1	0	UTP23	117851766	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.525000	0.67110	2.788000	0.95919	0.650000	0.86243	CAT	.		0.353	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334		T	117782585	C	T	117782585	3	4	134	1	0	0	0	0	1	0	0	0	17133	826	29	2	349	2	UTP23	8	117782585	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	64227488	117782585	28581437	34	11921											
NFKBIL2	4796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145668588	145668588	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtgcctgcagcaaagcatcCctcgactggcagtggtcata	9	9	11	12	1	1	0	1	0	0	0	3	1	2	0	2	2	4	4	2	2	2	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:145668588C>G	ENST00000409379.3	-	4	410	c.381G>C	c.(379-381)agG>agC	p.R127S		NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	127					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GCAAAGCATCCCTCGACTGGC	0.622																																					p.R127S		.											.	TONSL-92	0			c.G381C						.						78	80	79					8																	145668588		692	1591	2283	SO:0001583	missense	4796	exon4			AGCATCCCTCGAC		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.381G>C	8.37:g.145668588C>G	ENSP00000386239:p.Arg127Ser	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	160	50	NM_013432	0	0	0	1	1	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	C	3.081	-0.189045	0.06299	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.75367	-0.93	4.66	2.56	0.30785	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.56630	0.1998	L	0.36672	1.1	0.09310	N	0.999996	B	0.29716	0.255	B	0.19148	0.024	T	0.36040	-0.9764	9	0.10111	T	0.7	.	7.8666	0.29541	0.1718:0.7237:0.0:0.1045	.	127	Q96HA7	TONSL_HUMAN	S	127	ENSP00000386239:R127S	ENSP00000386239:R127S	R	-	3	2	TONSL	145639396	0.079000	0.21365	0.105000	0.21289	0.613000	0.37349	0.816000	0.27267	0.930000	0.37217	0.462000	0.41574	AGG	.		0.622	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		G	145668588	C	G	145668588	3	3	134	1	0	0	0	0	1	0	0	0	10408	622	22	4	3847	4	NFKBIL2	8	145668588	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	27886003	145668588	695434	35	11922											
FAM22F	54754	bcgsc.ca	37	chr9	97082579	97082579	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccgtcctcttcctgcggctGctccactttgcccttttccc	1	14	6	20	2	1	0	0	0	1	0	5	0	5	0	6	1	3	2	6	1	0	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr9:97082579G>A	ENST00000253262.4	-	5	1299	c.1279C>T	c.(1279-1281)Cag>Tag	p.Q427*	NUTM2F_ENST00000341207.4_Nonsense_Mutation_p.Q412*|NUTM2F_ENST00000335456.7_Nonsense_Mutation_p.Q412*	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	427																	TCCTGCGGCTGCTCCACTTTG	0.592																																					p.Q427X													.	FAM22F-68	0			c.C1279T						.						82	96	92					9																	97082579		1957	4131	6088	SO:0001587	stop_gained	54754	exon5			GCGGCTGCTCCAC		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"family with sequence similarity 22, member F"	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1279C>T	9.37:g.97082579G>A	ENSP00000253262:p.Gln427*	Somatic	295	2		WXS	Illumina HiSeq	Phase_1	314	105	NM_017561	0	0	0	0	0	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Nonsense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	.	12.92	2.081550	0.36758	.	.	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207;ENST00000375347	.	.	.	1.2	1.2	0.21068	.	2.955810	0.00957	N	0.003056	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8356	0.18605	0.0:0.0:1.0:0.0	.	.	.	.	X	412;427;412;261	.	ENSP00000253262:Q427X	Q	-	1	0	FAM22F	96122400	0.024000	0.19004	0.001000	0.08648	0.006000	0.05464	1.009000	0.29886	0.992000	0.38840	0.456000	0.33151	CAG	.		0.592	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		A	97082579	G	A	97082579	4	1	134	1	0	0	0	0	0	1	0	0	5561	1328	46	2	1003	2	FAM22F	9	97082579	Nonsense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		97082579	44130852	36	11923											
KIAA1529	100499483	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	100128909	100128909	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtgacacctttgaccagtgCgccgagaacattagcaaaaa	14	8	9	10	2	0	3	0	2	0	1	0	4	0	3	3	0	3	1	3	0	4	2	rs575555258		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr9:100128909C>T	ENST00000357054.1	+	43	5018	c.4083C>T	c.(4081-4083)tgC>tgT	p.C1361C	CCDC180_ENST00000375202.2_Silent_p.C1416C|RP11-23J9.4_ENST00000534123.1_RNA|MIR1302-8_ENST00000408342.1_RNA|CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000529487.1_Silent_p.C1416C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1361						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.C1361C(1)									TTGACCAGTGCGCCGAGAACA	0.532													C|||	1	0.000199681	0	0	5008	,	,		20527	0		0	False		,,,				2504	0.001				p.C1416C													.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4248T						.						108	90	96					9																	100128909		2203	4300	6503	SO:0001819	synonymous_variant	0	exon31			CCAGTGCGCCGAG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"Behcet's Disease Associated Gene 1"		"KIAA1529", "chromosome 9 open reading frame 174"	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.4083C>T	9.37:g.100128909C>T		Somatic	300	2		WXS	Illumina HiSeq	Phase_I	336	119	NM_020893	0	0	5	6	1	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				.		0.532	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100128909	C	T	100128909	2	4	134	1	0	0	0	0	0	0	0	1	8261	776	27	1		1	KIAA1529	9	100128909	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	3046330	100128909	41084522	37	11924											
IDI2	91734	broad.mit.edu	37	chr10	1066741	1066741	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccagctctgcttgcagaCgcctctgggctgccctcctc	3	11	9	18	1	2	1	0	0	2	1	5	1	4	1	4	1	4	4	4	1	0	2	rs368608756		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:1066741C>T	ENST00000277517.1	-	4	396	c.332G>A	c.(331-333)cGt>cAt	p.R111H	IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000437374.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000420381.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	111	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		TGCTTGCAGACGCCTCTGGGC	0.572													C|||	1	0.000199681	0	0.0014	5008	,	,		16338	0		0	False		,,,				2504	0				p.R111H													.	IDI2-90	0			c.G332A						.						100	86	91					10																	1066741		2203	4300	6503	SO:0001583	missense	91734	exon4			TGCAGACGCCTCT	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.332G>A	10.37:g.1066741C>T	ENSP00000277517:p.Arg111His	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_033261	0	0	0	0	0		Missense_Mutation	SNP	ENST00000277517.1	37	CCDS7055.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673904	0.47781	.	.	ENSG00000148377	ENST00000277517	T	0.08193	3.12	4.09	-1.8	0.07907	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.116280	0.53938	U	0.000051	T	0.25568	0.0622	M	0.88979	2.995	0.20403	N	0.999907	D	0.71674	0.998	D	0.65573	0.936	T	0.05354	-1.0890	10	0.87932	D	0	-4.7047	8.2637	0.31801	0.0:0.6495:0.1046:0.246	.	111	Q9BXS1	IDI2_HUMAN	H	111	ENSP00000277517:R111H	ENSP00000277517:R111H	R	-	2	0	IDI2	1056741	0.103000	0.21917	0.000000	0.03702	0.001000	0.01503	2.002000	0.40835	-1.050000	0.03230	-2.005000	0.00442	CGT	.		0.572	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261		T	1066741	C	T	1066741	3	4	134	1	0	0	0	0	1	0	0	0	7521	536	19	1	359	1	IDI2	10	1066741	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		1066741	134468006	38	11925											
FAM21C	253725	broad.mit.edu	37	chr10	46282636	46282644	+	In_Frame_Del	DEL	GAGGCCGGT	GAGGCCGGT	-																															ctgtccttcccgggagtgggGaggccggtgtgagttttgat																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	GAGGCCGGT	GAGGCCGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:46282636_46282644delGAGGCCGGT	ENST00000336378.4	+	27	3077_3085	c.2959_2967delGAGGCCGGT	c.(2959-2967)gaggccggtdel	p.EAG987del	FAM21C_ENST00000540872.1_In_Frame_Del_p.EAG948del|FAM21C_ENST00000374362.2_In_Frame_Del_p.EAG989del|FAM21C_ENST00000537517.1_In_Frame_Del_p.EAG914del|FAM21C_ENST00000359860.4_In_Frame_Del_p.EAG931del	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	987					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CGGGAGTGGGGAGGCCGGTGTGAGTTTTG	0.488																																					p.989_991del													.	FAM21C-91	0			c.2965_2973del						.																																			SO:0001651	inframe_deletion	253725	exon27			AGTGGGGAGGCCG		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.2959_2967delGAGGCCGGT	10.37:g.46282636_46282644delGAGGCCGGT	ENSP00000337541:p.Glu987_Gly989del	Somatic	620	0		WXS	Illumina HiSeq	Phase_I	516	27	NM_015262	0	0	0	0	0	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	In_Frame_Del	DEL	ENST00000336378.4	37																																																																																				.		0.488	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				-	46282644	GAGGCCGGT	-	46282636	7	5	134	1	0	1	0	1	0	0	0	0	5558	1175	41	0	3071	0	FAM21C	10	46282636	In_Frame_Del	DEL	GAGGCCGGT	TCGA-HE-A5NJ-01A-11D-A26P-10	45215895	46282636	89252111	39	11926											
MYPN	84665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	69959137	69959137	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttattaggtgagtggtttaCcgcccccggagctgacatgg	7	12	13	9	2	0	2	0	2	0	0	0	3	0	3	3	4	2	2	3	4	3	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:69959137C>T	ENST00000358913.5	+	17	3786	c.3298C>T	c.(3298-3300)Ccg>Tcg	p.P1100S	MYPN_ENST00000354393.2_Missense_Mutation_p.P825S|MYPN_ENST00000540630.1_Missense_Mutation_p.P1100S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1100	Ig-like 4.|Interaction with ACTN.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						GAGTGGTTTACCGCCCCCGGA	0.507																																					p.P1100S		.											.	MYPN-95	0			c.C3298T						.						56	48	50					10																	69959137		2203	4300	6503	SO:0001583	missense	84665	exon17			GGTTTACCGCCCC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"Immunoglobulin superfamily / I-set domain containing"	23246	protein-coding gene	gene with protein product	"sarcomeric protein myopalladin, 145 kDa"	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.3298C>T	10.37:g.69959137C>T	ENSP00000351790:p.Pro1100Ser	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	129	47	NM_032578	0	0	0	0	0	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053409	0.93793	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.80393	-1.37;-1.37;-1.37	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94072	0.8100	H	0.97806	4.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	D	0.95767	0.8805	9	.	.	.	.	19.3311	0.94288	0.0:1.0:0.0:0.0	.	1100;825;1100	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	S	825;825;1100;1100	ENSP00000346369:P825S;ENSP00000351790:P1100S;ENSP00000441668:P1100S	.	P	+	1	0	MYPN	69629143	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	7.595000	0.82710	2.813000	0.96785	0.655000	0.94253	CCG	.		0.507	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69959137	C	T	69959137	3	4	134	1	0	0	0	0	1	0	0	0	10123	507	18	2	3360	2	MYPN	10	69959137	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	23676501	69959137	65575610	40	11927											
TRIM8	81603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104416093	104416093	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacctgaactccaagctcttCctgaacgaagtggccaagaa	13	7	8	13	1	1	3	0	2	1	1	3	4	3	3	4	1	3	1	4	1	6	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:104416093C>A	ENST00000302424.7	+	5	1121	c.999C>A	c.(997-999)ttC>ttA	p.F333L	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	333					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CCAAGCTCTTCCTGAACGAAG	0.607																																					p.F333L		.											.	TRIM8-227	0			c.C999A						.						59	46	50					10																	104416093		2203	4300	6503	SO:0001583	missense	81603	exon5			GCTCTTCCTGAAC	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.999C>A	10.37:g.104416093C>A	ENSP00000302120:p.Phe333Leu	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	200	86	NM_030912	0	0	24	55	31	A6NI31|Q9C028	Missense_Mutation	SNP	ENST00000302424.7	37	CCDS31274.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940287	0.52972	.	.	ENSG00000171206	ENST00000302424;ENST00000369896	T	0.77489	-1.1	5.67	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.76205	0.3955	L	0.29908	0.895	0.58432	D	0.99999	P	0.52842	0.956	P	0.62184	0.899	T	0.69525	-0.5122	10	0.08837	T	0.75	.	12.1033	0.53796	0.0:0.8608:0.0:0.1392	.	333	Q9BZR9	TRIM8_HUMAN	L	333;332	ENSP00000302120:F333L	ENSP00000302120:F333L	F	+	3	2	TRIM8	104406083	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.588000	0.36633	0.753000	0.32945	0.555000	0.69702	TTC	.		0.607	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		A	104416093	C	A	104416093	3	1	134	1	0	0	0	0	1	0	0	0	16581	854	30	4	1017	4	TRIM8	10	104416093	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	34456956	104416093	31118654	41	11928											
GPR83	10888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	94113422	94113422	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagccctctggccatcatTcttctctgtccaggccaccc	5	10	9	17	0	4	0	1	0	3	0	6	1	5	1	5	3	1	0	5	3	0	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr11:94113422T>A	ENST00000243673.2	-	4	1336	c.1165A>T	c.(1165-1167)Aat>Tat	p.N389Y	GPR83_ENST00000539203.2_Missense_Mutation_p.N347Y	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	389					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGGCCATCATTCTTCTCTGTC	0.562																																					p.N389Y		.											.	GPR83-92	0			c.A1165T						.						83	82	82					11																	94113422		2201	4298	6499	SO:0001583	missense	10888	exon4			CATCATTCTTCTC	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.1165A>T	11.37:g.94113422T>A	ENSP00000243673:p.Asn389Tyr	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	175	76	NM_016540	0	0	0	0	0	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	37	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.689837	0.00100	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.61392	0.11;0.22	5.75	0.538	0.17150	.	0.659318	0.17607	N	0.168232	T	0.31544	0.0800	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17319	-1.0373	10	0.21014	T	0.42	.	9.6421	0.39846	0.0:0.4117:0.0:0.5883	.	389	Q9NYM4	GPR83_HUMAN	Y	389;347	ENSP00000243673:N389Y;ENSP00000441550:N347Y	ENSP00000243673:N389Y	N	-	1	0	GPR83	93753070	0.772000	0.28567	0.077000	0.20336	0.003000	0.03518	0.384000	0.20668	0.096000	0.17463	-0.250000	0.11733	AAT	.		0.562	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		A	94113422	T	A	94113422	3	1	134	1	0	0	0	0	1	0	0	0	6733	1783	62	5	110	5	GPR83	11	94113422	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		94113422	40893094	42	11929											
PIWIL4	143689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	94340737	94340737	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacagggcatgatgatgagtAtcgccaccaagatcgctatg	13	8	11	9	2	0	4	0	3	0	1	2	4	0	4	2	1	1	3	2	1	4	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr11:94340737A>G	ENST00000299001.6	+	14	1982	c.1771A>G	c.(1771-1773)Atc>Gtc	p.I591V	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	591	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GATGATGAGTATCGCCACCAA	0.453																																					p.I591V		.											.	PIWIL4-91	0			c.A1771G						.						89	82	84					11																	94340737		2201	4298	6499	SO:0001583	missense	143689	exon14			ATGAGTATCGCCA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"Argonaute/PIWI family"	18444	protein-coding gene	gene with protein product		610315	"piwi-like 4 (Drosophila)"			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1771A>G	11.37:g.94340737A>G	ENSP00000299001:p.Ile591Val	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	95	37	NM_152431	0	0	0	0	0	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	A	0.557	-0.846779	0.02671	.	.	ENSG00000134627	ENST00000299001	T	0.30448	1.53	4.75	-9.49	0.00587	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	1.548280	0.03817	N	0.266847	T	0.10337	0.0253	N	0.03881	-0.34	0.40307	D	0.978677	B	0.14438	0.01	B	0.21546	0.035	T	0.24621	-1.0155	10	0.06099	T	0.92	0.1986	8.5103	0.33213	0.4048:0.3269:0.2683:0.0	.	591	Q7Z3Z4	PIWL4_HUMAN	V	591	ENSP00000299001:I591V	ENSP00000299001:I591V	I	+	1	0	PIWIL4	93980385	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	-0.634000	0.05477	-2.120000	0.00826	-0.472000	0.04984	ATC	.		0.453	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		G	94340737	A	G	94340737	3	3	134	1	0	0	0	0	1	0	0	0	11986	449	16	3	1825	3	PIWIL4	11	94340737	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	227315	94340737	40665779	43	11930											
ARHGAP32	9743	broad.mit.edu	37	chr11	128936739	128936739	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacccgaaaatcttcataacTtcttttaacaatccaacttt	14	15	1	11	1	3	0	1	0	2	0	4	1	4	0	2	0	4	0	2	0	7	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr11:128936739T>A	ENST00000310343.9	-	6	513	c.514A>T	c.(514-516)Agt>Tgt	p.S172C	ARHGAP32_ENST00000524655.1_Missense_Mutation_p.S98C	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	172	PX; atypical.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TCTTCATAACTTCTTTTAACA	0.348																																					p.S172C													.	ARHGAP32-231	0			c.A514T						.						58	54	55					11																	128936739		1566	3578	5144	SO:0001583	missense	9743	exon6			CATAACTTCTTTT	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.514A>T	11.37:g.128936739T>A	ENSP00000310561:p.Ser172Cys	Somatic	24	1		WXS	Illumina HiSeq	Phase_I	25	13	NM_001142685	0	0	2	2	0	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.529999	0.85706	.	.	ENSG00000134909	ENST00000310343;ENST00000524655;ENST00000457677;ENST00000525234	T;T;T	0.32515	1.45;1.45;1.45	5.04	5.04	0.67666	Phox homologous domain (3);	.	.	.	.	T	0.58452	0.2123	M	0.82716	2.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.961	T	0.65195	-0.6227	9	0.87932	D	0	.	13.8913	0.63740	0.0:0.0:0.0:1.0	.	106;172	Q86T64;A7KAX9	.;RHG32_HUMAN	C	172;98;106;146	ENSP00000310561:S172C;ENSP00000432468:S98C;ENSP00000432303:S146C	ENSP00000310561:S172C	S	-	1	0	ARHGAP32	128441949	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.647000	0.67923	2.123000	0.65237	0.455000	0.32223	AGT	.		0.348	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		A	128936739	T	A	128936739	3	1	134	1	0	0	0	0	1	0	0	0	881	1609	56	5	5817	5	ARHGAP32	11	128936739	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	34596002	128936739	6069777	44	11931											
XPOT	11260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	64827226	64827226	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtttttacaacagatgttCatgcccctgcttcatgcaat	9	14	6	12	1	2	1	2	0	0	1	2	1	2	1	3	0	5	4	3	0	3	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:64827226C>A	ENST00000332707.5	+	19	2824	c.2295C>A	c.(2293-2295)ttC>ttA	p.F765L		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	765	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		AACAGATGTTCATGCCCCTGC	0.383																																					p.F765L		.											.	XPOT-652	0			c.C2295A						.						142	139	140					12																	64827226		2203	4300	6503	SO:0001583	missense	11260	exon19			GATGTTCATGCCC	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2295C>A	12.37:g.64827226C>A	ENSP00000327821:p.Phe765Leu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	126	74	NM_007235	0	0	3	17	14	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	37	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	C	9.351	1.065624	0.20067	.	.	ENSG00000184575	ENST00000332707	T	0.35048	1.33	4.99	1.1	0.20463	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.25121	0.0610	L	0.43923	1.385	0.58432	D	0.999994	B	0.26483	0.15	B	0.19946	0.027	T	0.05632	-1.0873	9	.	.	.	.	8.7565	0.34648	0.0:0.4567:0.0:0.5433	.	765	O43592	XPOT_HUMAN	L	765	ENSP00000327821:F765L	.	F	+	3	2	XPOT	63113493	1.000000	0.71417	0.998000	0.56505	0.566000	0.35808	0.960000	0.29253	-0.000000	0.14550	0.650000	0.86243	TTC	.		0.383	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		A	64827226	C	A	64827226	3	1	134	1	0	0	0	0	1	0	0	0	17483	825	29	4	2365	4	XPOT	12	64827226	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		64827226	69024669	45	11932											
UHRF1BP1L	23074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	100453199	100453199	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aagcttctaggtcagaatgtCgacagtttggacagtgcctt	10	12	11	8	1	2	1	1	0	1	1	3	3	2	2	1	2	2	2	1	2	3	4	rs374748413		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:100453199C>G	ENST00000279907.7	-	14	2068	c.1856G>C	c.(1855-1857)cGa>cCa	p.R619P	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.R269P	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	619								p.R619Q(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GTCAGAATGTCGACAGTTTGG	0.353																																					p.R619P		.											.	UHRF1BP1L-24	1	Substitution - Missense(1)	large_intestine(1)	c.G1856C						.						47	50	49					12																	100453199		2203	4300	6503	SO:0001583	missense	23074	exon14			GAATGTCGACAGT		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1856G>C	12.37:g.100453199C>G	ENSP00000279907:p.Arg619Pro	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	103	22	NM_015054	0	0	0	2	2	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.110310	0.56398	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.10960	2.83;2.82	5.56	5.56	0.83823	.	0.071690	0.56097	D	0.000028	T	0.26159	0.0638	L	0.51422	1.61	0.80722	D	1	D	0.63046	0.992	P	0.59115	0.852	T	0.00102	-1.2063	10	0.48119	T	0.1	-7.7813	19.5255	0.95203	0.0:1.0:0.0:0.0	.	619	A0JNW5	UH1BL_HUMAN	P	619;269	ENSP00000279907:R619P;ENSP00000444824:R269P	ENSP00000279907:R619P	R	-	2	0	UHRF1BP1L	98977330	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	4.740000	0.62087	2.624000	0.88883	0.650000	0.86243	CGA	.		0.353	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		G	100453199	C	G	100453199	3	3	134	1	0	0	0	0	1	0	0	0	17002	884	31	4	2570	4	UHRF1BP1L	12	100453199	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	35625973	100453199	33398696	46	11933											
SCYL2	55681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	100707272	100707272	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacatgtaaagctactgttaAatgtaactccgactgtaaga	16	11	7	7	1	0	1	0	0	0	1	1	2	1	1	1	0	4	5	1	0	8	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:100707272A>T	ENST00000360820.2	+	7	1362	c.925A>T	c.(925-927)Aat>Tat	p.N309Y		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						GCTACTGTTAAATGTAACTCC	0.363																																					p.N309Y		.											.	SCYL2-336	0			c.A925T						.						94	84	87					12																	100707272		2203	4300	6503	SO:0001583	missense	55681	exon7			CTGTTAAATGTAA	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.925A>T	12.37:g.100707272A>T	ENSP00000354061:p.Asn309Tyr	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	102	27	NM_017988	0	0	8	11	3	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	A	29.9	5.046858	0.93740	.	.	ENSG00000136021	ENST00000549687;ENST00000258506;ENST00000360820	T;T	0.66815	-0.23;-0.23	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.039673	0.85682	D	0.000000	T	0.78349	0.4269	M	0.68952	2.095	0.80722	D	1	P	0.45240	0.854	P	0.57009	0.811	T	0.79680	-0.1702	10	0.62326	D	0.03	.	16.2736	0.82632	1.0:0.0:0.0:0.0	.	309	Q6P3W7	SCYL2_HUMAN	Y	309;136;309	ENSP00000448366:N309Y;ENSP00000354061:N309Y	ENSP00000258506:N136Y	N	+	1	0	SCYL2	99231403	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	8.769000	0.91742	2.247000	0.74100	0.477000	0.44152	AAT	.		0.363	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		T	100707272	A	T	100707272	3	4	134	1	0	0	0	0	1	0	0	0	13980	14	1	5	947	5	SCYL2	12	100707272	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	254073	100707272	33144623	47	11934											
IFT81	28981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	110565896	110565896	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccagagcagacagccaaaCgaatgttgagccttcttggt	11	9	11	10	1	1	3	0	1	1	2	1	4	1	3	3	1	5	2	3	1	2	3	rs372027811		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:110565896C>T	ENST00000242591.5	+	3	696	c.190C>T	c.(190-192)Cga>Tga	p.R64*	IFT81_ENST00000361948.4_Nonsense_Mutation_p.R64*|IFT81_ENST00000552912.1_Nonsense_Mutation_p.R64*	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	64	CH (calponin-homology)-like region.				cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						GACAGCCAAACGAATGTTGAG	0.343																																					p.R64X		.											.	IFT81-91	0			c.C190T						.	C	stop/ARG,stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	125	120	122		190,190,190	2.9	1	12		122	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained	IFT81	NM_001143779.1,NM_014055.3,NM_031473.3	,,	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	,,	64/677,64/677,64/432	110565896	3,13003	2203	4300	6503	SO:0001587	stop_gained	28981	exon3			GCCAAACGAATGT	AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"Intraflagellar transport homologs"	14313	protein-coding gene	gene with protein product		605489	"carnitine deficiency-associated, expressed in ventricle 1", "intraflagellar transport 81 homolog (Chlamydomonas)"	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.190C>T	12.37:g.110565896C>T	ENSP00000242591:p.Arg64*	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	119	36	NM_014055	0	0	7	7	0	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Nonsense_Mutation	SNP	ENST00000242591.5	37	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830743	0.91036	4.54E-4	1.16E-4	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	.	.	.	5.96	2.88	0.33553	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.6056	16.1793	0.81889	0.5747:0.4253:0.0:0.0	.	.	.	.	X	64	.	ENSP00000242591:R64X	R	+	1	2	IFT81	109050279	0.998000	0.40836	0.997000	0.53966	0.972000	0.66771	1.423000	0.34837	0.248000	0.21435	0.655000	0.94253	CGA	.		0.343	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		T	110565896	C	T	110565896	4	4	134	1	0	0	0	0	0	1	0	0	7586	528	19	1	196	1	IFT81	12	110565896	Nonsense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	9858624	110565896	23285999	48	11935											
OLFM4	10562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	53624827	53624827	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagcattaactataaccCttttgaccagaaactttatg	14	12	6	9	0	0	3	0	1	0	2	0	3	0	3	2	0	4	2	2	0	5	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr13:53624827C>A	ENST00000219022.2	+	5	1532	c.1454C>A	c.(1453-1455)cCt>cAt	p.P485H		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	485	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		AACTATAACCCTTTTGACCAG	0.378																																					p.P485H		.											.	OLFM4-69	0			c.C1454A						.						99	100	100					13																	53624827		2203	4300	6503	SO:0001583	missense	10562	exon5			ATAACCCTTTTGA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.1454C>A	13.37:g.53624827C>A	ENSP00000219022:p.Pro485His	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	72	43	NM_006418	0	0	0	0	0	O95362|Q5VWG0|Q86T22	Missense_Mutation	SNP	ENST00000219022.2	37	CCDS9440.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.816222	0.90790	.	.	ENSG00000102837	ENST00000219022	T	0.19669	2.13	5.64	5.64	0.86602	Olfactomedin-like (3);	0.049423	0.85682	D	0.000000	T	0.58409	0.2120	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67465	-0.5664	10	0.87932	D	0	.	19.7082	0.96082	0.0:1.0:0.0:0.0	.	485	Q6UX06	OLFM4_HUMAN	H	485	ENSP00000219022:P485H	ENSP00000219022:P485H	P	+	2	0	OLFM4	52522828	1.000000	0.71417	0.882000	0.34594	0.914000	0.54420	6.095000	0.71439	2.651000	0.90000	0.585000	0.79938	CCT	.		0.378	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		A	53624827	C	A	53624827	3	1	134	1	0	0	0	0	1	0	0	0	10881	681	24	4	1472	4	OLFM4	13	53624827	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		53624827	61545051	49	11936											
C14orf105	55195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	57960296	57960296	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcctgcagtcttgccagTgaatatgaagtcttttcttc	7	16	9	9	0	3	2	0	2	3	0	5	2	4	2	2	1	2	1	2	1	3	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:57960296T>A	ENST00000216445.3	-	1	274	c.138A>T	c.(136-138)tcA>tcT	p.S46S	C14orf105_ENST00000422976.2_Silent_p.S46S|C14orf105_ENST00000526336.1_Silent_p.S46S|C14orf105_ENST00000534126.1_Silent_p.S46S	NM_001283057.1|NM_018168.2	NP_001269986.1|NP_060638.2	Q9NVL8	CN105_HUMAN	chromosome 14 open reading frame 105	46										breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						GTCTTGCCAGTGAATATGAAG	0.438																																					p.S46S		.											.	C14orf105-90	0			c.A138T						.						126	127	127					14																	57960296		2203	4300	6503	SO:0001819	synonymous_variant	55195	exon1			TGCCAGTGAATAT	AK001512	CCDS9730.1, CCDS61458.1, CCDS61459.1	14q22.2	2012-09-25			ENSG00000100557	ENSG00000100557			20189	protein-coding gene	gene with protein product							Standard	XM_005267806		Approved	FLJ10650	uc001xcy.2	Q9NVL8	OTTHUMG00000140317	ENST00000216445.3:c.138A>T	14.37:g.57960296T>A		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	75	35	NM_018168	0	0	5	14	9	Q53G04	Silent	SNP	ENST00000216445.3	37	CCDS9730.1																																																																																			.		0.438	C14orf105-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276921.2	NM_018168		A	57960296	T	A	57960296	2	1	134	1	0	0	0	0	0	0	0	1	1741	1683	59	5		5	C14orf105	14	57960296	Silent	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		57960296	49389244	50	11937											
PAPLN	89932	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	73712877	73712877	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtatcggtggctgccctacTacagcggtgagcgcggccgg	5	7	17	12	5	0	1	0	1	0	0	1	1	0	1	2	6	5	2	2	6	3	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:73712877T>G	ENST00000554301.1	+	4	491	c.328T>G	c.(328-330)Tac>Gac	p.Y110D	PAPLN_ENST00000381166.3_Missense_Mutation_p.Y110D|PAPLN_ENST00000427855.1_Missense_Mutation_p.Y110D|RNU6-419P_ENST00000517030.1_RNA|RP4-647C14.2_ENST00000554614.1_RNA|PAPLN_ENST00000340738.5_Missense_Mutation_p.Y110D|PAPLN_ENST00000555445.1_Missense_Mutation_p.Y110D			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	110						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GCTGCCCTACTACAGCGGTGA	0.642																																					p.Y110D		.											.	PAPLN-70	0			c.T328G						.						8	10	10					14																	73712877		2163	4255	6418	SO:0001583	missense	89932	exon5			CCCTACTACAGCG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"Immunoglobulin superfamily / I-set domain containing"	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.328T>G	14.37:g.73712877T>G	ENSP00000451803:p.Tyr110Asp	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	60	20	NM_173462	0	0	0	0	0	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		.	.	.	.	.	.	.	.	.	.	T	23.3	4.398999	0.83120	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000394134;ENST00000554301;ENST00000555445	T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93	4.26	4.26	0.50523	.	.	.	.	.	T	0.17662	0.0424	M	0.82132	2.575	0.47698	D	0.999491	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.72625	0.978;0.951;0.975	T	0.00593	-1.1654	9	0.62326	D	0.03	.	13.222	0.59894	0.0:0.0:0.0:1.0	.	110;110;110	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	D	110	ENSP00000345395:Y110D;ENSP00000403403:Y110D;ENSP00000370558:Y110D;ENSP00000451803:Y110D;ENSP00000451729:Y110D	ENSP00000216658:Y110D	Y	+	1	0	PAPLN	72782630	1.000000	0.71417	0.997000	0.53966	0.671000	0.39405	4.002000	0.57053	1.789000	0.52484	0.379000	0.24179	TAC	.		0.642	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		G	73712877	T	G	73712877	3	3	134	1	0	0	0	0	1	0	0	0	11454	1522	53	5	342	5	PAPLN	14	73712877	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	15752581	73712877	33636663	51	11938											
TDP1	55775	bcgsc.ca	37	chr14	90459808	90459808	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccagacttcagtaaaattGcttggttccttgtcacaagg	10	13	8	10	0	2	1	2	0	0	1	4	1	4	1	2	2	1	3	2	2	3	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:90459808G>T	ENST00000335725.4	+	14	1772	c.1522G>T	c.(1522-1524)Gct>Tct	p.A508S	TDP1_ENST00000393452.3_Missense_Mutation_p.A508S|TDP1_ENST00000393454.2_Missense_Mutation_p.A508S|TDP1_ENST00000357382.3_Missense_Mutation_p.A269S|TDP1_ENST00000555880.1_Missense_Mutation_p.A508S	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	508					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		CAGTAAAATTGCTTGGTTCCT	0.403								Repair of DNA-protein crosslinks																													p.A508S													.	TDP1-92	0			c.G1522T						.						98	90	93					14																	90459808		2203	4300	6503	SO:0001583	missense	55775	exon14			AAAATTGCTTGGT	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1522G>T	14.37:g.90459808G>T	ENSP00000337353:p.Ala508Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_1	106	6	NM_018319	0	0	5	5	0	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.5|20.5	4.002048|4.002048	0.74932|0.74932	.|.	.|.	ENSG00000042088|ENSG00000042088	ENST00000393452;ENST00000393454;ENST00000335725;ENST00000357382;ENST00000555880|ENST00000556063	T;T;T;T;T|.	0.42131|.	0.98;0.98;0.98;0.98;0.98|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74359|0.74359	0.3706|0.3706	M|M	0.65320|0.65320	2|2	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.76494|.	0.999;0.999;0.999;0.981;0.999|.	D;D;D;D;D|.	0.83275|.	0.986;0.992;0.996;0.949;0.996|.	T|T	0.71504|0.71504	-0.4573|-0.4573	10|5	0.25751|.	T|.	0.34|.	-9.0E-4|-9.0E-4	19.4362|19.4362	0.94796|0.94796	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	508;508;508;269;508|.	G3V2F4;E7EPD8;B2RDI0;Q86TV8;Q9NUW8|.	.;.;.;.;TYDP1_HUMAN|.	S|F	508;508;508;269;508|148	ENSP00000377098:A508S;ENSP00000377099:A508S;ENSP00000337353:A508S;ENSP00000349952:A269S;ENSP00000450628:A508S|.	ENSP00000337353:A508S|.	A|C	+|+	1|2	0|0	TDP1|TDP1	89529561|89529561	1.000000|1.000000	0.71417|0.71417	0.128000|0.128000	0.21923|0.21923	0.978000|0.978000	0.69477|0.69477	6.611000|6.611000	0.74183|0.74183	2.683000|2.683000	0.91414|0.91414	0.655000|0.655000	0.94253|0.94253	GCT|TGC	.		0.403	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		T	90459808	G	T	90459808	3	4	134	1	0	0	0	0	1	0	0	0	15760	1319	46	4	1568	4	TDP1	14	90459808	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	16746931	90459808	16889732	52	11939											
SERPINA6	866	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	94780584	94780584	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcaactccaggctgccAtcaagaaacaaggcattgcc	13	6	8	14	0	1	1	1	0	0	1	3	1	3	1	4	2	5	3	4	2	4	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:94780584A>T	ENST00000341584.3	-	2	548	c.402T>A	c.(400-402)gaT>gaA	p.D134E		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	134					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	CCAGGCTGCCATCAAGAAACA	0.502																																					p.D134E													.	SERPINA6-653	0			c.T402A						.						92	87	89					14																	94780584		2203	4300	6503	SO:0001583	missense	866	exon2			GCTGCCATCAAGA	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"Serine (or cysteine) peptidase inhibitors"	1540	protein-coding gene	gene with protein product	"corticosteroid binding globulin", "transcortin"	122500	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.402T>A	14.37:g.94780584A>T	ENSP00000342850:p.Asp134Glu	Somatic	106	1		WXS	Illumina HiSeq	Phase_I	89	34	NM_001756	0	0	3	4	1	A8K456|Q7Z2Q9	Missense_Mutation	SNP	ENST00000341584.3	37	CCDS9924.1	.	.	.	.	.	.	.	.	.	.	A	0.415	-0.911384	0.02434	.	.	ENSG00000170099	ENST00000341584;ENST00000557225	D;D	0.87966	-2.32;-1.66	4.85	1.84	0.25277	Serpin domain (3);	1.049680	0.07521	N	0.910514	T	0.76140	0.3946	L	0.28192	0.835	0.09310	N	1	B	0.20164	0.042	B	0.25759	0.063	T	0.59595	-0.7425	10	0.17369	T	0.5	.	2.1492	0.03795	0.2204:0.2403:0.4165:0.1227	.	134	P08185	CBG_HUMAN	E	134	ENSP00000342850:D134E;ENSP00000452018:D134E	ENSP00000342850:D134E	D	-	3	2	SERPINA6	93850337	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	0.022000	0.13511	0.581000	0.29539	-0.242000	0.12053	GAT	.		0.502	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756		T	94780584	A	T	94780584	3	4	134	1	0	0	0	0	1	0	0	0	14125	214	8	5	831	5	SERPINA6	14	94780584	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	4320776	94780584	12568956	53	11940											
NUSAP1	51203	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41669495	41669495	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacaaacaaccccatctcCagacaaagtaagtacataat	18	8	3	12	0	1	1	0	0	1	1	2	1	1	1	3	0	4	2	3	0	7	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr15:41669495C>T	ENST00000559596.1	+	10	1312	c.1225C>T	c.(1225-1227)Cag>Tag	p.Q409*	NUSAP1_ENST00000450318.1_Nonsense_Mutation_p.Q370*|NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000560177.1_Nonsense_Mutation_p.Q408*|NUSAP1_ENST00000414849.2_Nonsense_Mutation_p.Q408*|NUSAP1_ENST00000560747.1_Nonsense_Mutation_p.Q407*|NUSAP1_ENST00000260359.6_Nonsense_Mutation_p.Q394*|NUSAP1_ENST00000450592.2_Nonsense_Mutation_p.Q346*			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	409					establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		ACCCCATCTCCAGACAAAGTA	0.333																																					p.Q409X		.											.	.	0			c.C1225T						.						16	14	15					15																	41669495		1771	4000	5771	SO:0001587	stop_gained	51203	exon10			CATCTCCAGACAA	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.1225C>T	15.37:g.41669495C>T	ENSP00000453403:p.Gln409*	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	56	20	NM_016359	0	0	0	0	0	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Nonsense_Mutation	SNP	ENST00000559596.1	37	CCDS45234.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761477	0.49468	.	.	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318;ENST00000450592	.	.	.	5.65	4.71	0.59529	.	0.367085	0.31922	N	0.006860	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	12.8916	0.58073	0.1626:0.8374:0.0:0.0	.	.	.	.	X	409;408;370;346	.	ENSP00000260359:Q409X	Q	+	1	0	NUSAP1	39456787	1.000000	0.71417	0.756000	0.31282	0.567000	0.35839	2.988000	0.49386	1.561000	0.49584	0.655000	0.94253	CAG	.		0.333	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359		T	41669495	C	T	41669495	4	4	134	1	0	0	0	0	0	1	0	0	10804	595	21	2	1263	2	NUSAP1	15	41669495	Nonsense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		41669495	60861897	54	11941											
SHF	90525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	45491143	45491143	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggcgtgagcatccaggaatGgggctgggcggaactcagac	9	5	17	10	3	1	2	1	1	0	1	2	4	2	4	1	6	2	2	1	6	2	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr15:45491143G>T	ENST00000290894.8	-	2	624	c.130C>A	c.(130-132)Cat>Aat	p.H44N	SHF_ENST00000318390.6_Missense_Mutation_p.H101N|CTD-2651B20.6_ENST00000563103.1_RNA|CTD-2651B20.7_ENST00000568314.1_RNA|RP11-519G16.2_ENST00000560034.1_RNA	NM_138356.2	NP_612365			Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		ATCCAGGAATGGGGCTGGGCG	0.632											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H44N		.											.	SHF-69	0			c.C130A						.						50	54	53					15																	45491143		1969	4159	6128	SO:0001583	missense	90525	exon2			AGGAATGGGGCTG	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"SH2 domain containing"	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.130C>A	15.37:g.45491143G>T	ENSP00000290894:p.His44Asn	Somatic	123	0	932	WXS	Illumina HiSeq	Phase_I	137	68	NM_138356	0	0	0	0	0		Missense_Mutation	SNP	ENST00000290894.8	37	CCDS10120.2	.	.	.	.	.	.	.	.	.	.	G	11.94	1.788761	0.31685	.	.	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390	T;T	0.38240	1.57;1.15	3.04	-6.08	0.02151	.	7739.210000	0.00166	N	0.000000	T	0.23886	0.0578	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15578	-1.0432	10	0.37606	T	0.19	3.8664	8.6801	0.34203	0.0:0.4794:0.1588:0.3618	.	44	Q7M4L6	SHF_HUMAN	N	44;44;101	ENSP00000290894:H44N;ENSP00000315978:H101N	ENSP00000290894:H44N	H	-	1	0	SHF	43278435	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.536000	0.02208	-1.992000	0.00975	0.655000	0.94253	CAT	.		0.632	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356		T	45491143	G	T	45491143	3	4	134	1	0	0	0	0	1	0	0	0	14309	1348	47	4	1169	4	SHF	15	45491143	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3821648	45491143	57040249	55	11942											
C15orf39	56905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75499667	75499667	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgccagcgagccagccctgCtcagagcctgtgaggcctgc	6	7	13	15	1	1	2	1	1	0	1	1	3	1	2	5	1	7	1	5	1	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr15:75499667C>T	ENST00000360639.2	+	2	1598	c.1278C>T	c.(1276-1278)tgC>tgT	p.C426C	C15orf39_ENST00000394987.4_Silent_p.C426C|C15orf39_ENST00000567617.1_Silent_p.C426C			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	426						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						GCCAGCCCTGCTCAGAGCCTG	0.642																																					p.C426C		.											.	C15orf39-90	0			c.C1278T						.						37	42	40					15																	75499667		2197	4295	6492	SO:0001819	synonymous_variant	56905	exon2			GCCCTGCTCAGAG	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1278C>T	15.37:g.75499667C>T		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	150	64	NM_015492	0	0	4	8	4	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Silent	SNP	ENST00000360639.2	37	CCDS10276.1																																																																																			.		0.642	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		T	75499667	C	T	75499667	2	4	134	1	0	0	0	0	0	0	0	1	1797	805	28	2		2	C15orf39	15	75499667	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	30008524	75499667	27031725	56	11943											
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3901001	3901001	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattttccaagtcaaacaatGatccaaaatctagaaattaa	19	11	3	8	0	2	2	1	1	1	1	4	2	4	2	2	0	1	0	2	0	8	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:3901001G>A	ENST00000262367.5	-	2	904	c.95C>T	c.(94-96)tCa>tTa	p.S32L	CREBBP_ENST00000382070.3_Missense_Mutation_p.S32L	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	32					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GTCAAACAATGATCCAAAATC	0.403			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.S32L		.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP-1807	0			c.C95T						.						55	54	55					16																	3901001		2195	4291	6486	SO:0001583	missense	1387	exon2			AACAATGATCCAA	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.95C>T	16.37:g.3901001G>A	ENSP00000262367:p.Ser32Leu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	78	22	NM_001079846	0	0	0	0	0	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054063	0.75960	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.86562	-2.14;-2.12	5.92	5.92	0.95590	.	0.086452	0.49916	D	0.000127	D	0.92172	0.7518	M	0.72894	2.215	0.80722	D	1	P;D	0.58620	0.949;0.983	P;P	0.57101	0.719;0.813	D	0.92259	0.5815	10	0.87932	D	0	-4.3311	20.3206	0.98668	0.0:0.0:1.0:0.0	.	100;32	Q4LE28;Q92793	.;CBP_HUMAN	L	32;100;32	ENSP00000262367:S32L;ENSP00000371502:S32L	ENSP00000262367:S32L	S	-	2	0	CREBBP	3841002	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.390000	0.79816	2.809000	0.96659	0.655000	0.94253	TCA	.		0.403	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3901001	G	A	3901001	3	1	134	1	0	0	0	0	1	0	0	0	3867	1294	45	2	7353	2	CREBBP	16	3901001	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		3901001	86453752	57	11944											
UBN1	29855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	4908004	4908004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttacagaagaaagatctgtCagatcctttcaatgacgaag	15	11	8	7	1	3	5	2	1	1	4	4	6	4	5	1	0	1	0	1	0	5	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:4908004C>T	ENST00000396658.4	+	2	966	c.263C>T	c.(262-264)tCa>tTa	p.S88L	UBN1_ENST00000590769.1_Missense_Mutation_p.S88L|UBN1_ENST00000545171.1_Missense_Mutation_p.S88L|UBN1_ENST00000262376.6_Missense_Mutation_p.S88L	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	88	Sufficient for interaction with HIRA.				chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						AAAGATCTGTCAGATCCTTTC	0.338																																					p.S88L		.											.	UBN1-92	0			c.C263T						.						70	77	75					16																	4908004		2197	4300	6497	SO:0001583	missense	29855	exon3			ATCTGTCAGATCC	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.263C>T	16.37:g.4908004C>T	ENSP00000379894:p.Ser88Leu	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	32	9	NM_001079514	0	0	1	1	0	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	37	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	C	10.11	1.260216	0.23051	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.44083	1.51;0.93;1.51	5.37	-2.3	0.06785	.	1.211730	0.05673	N	0.589051	T	0.27313	0.0670	N	0.16266	0.395	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.26258	-1.0108	10	0.27785	T	0.31	1.4387	11.8692	0.52511	0.0:0.4651:0.0:0.5349	.	88;88	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	L	88	ENSP00000262376:S88L;ENSP00000442379:S88L;ENSP00000379894:S88L	ENSP00000262376:S88L	S	+	2	0	UBN1	4848005	0.000000	0.05858	0.017000	0.16124	0.976000	0.68499	-1.157000	0.03157	-0.259000	0.09432	0.655000	0.94253	TCA	.		0.338	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		T	4908004	C	T	4908004	3	4	134	1	0	0	0	0	1	0	0	0	16925	838	29	2	269	2	UBN1	16	4908004	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	1007003	4908004	85446749	58	11945											
DNAH3	55567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	21051260	21051260	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcatggccactgtccggaaCaaggcctggaaaagaaacaa	16	5	10	10	1	1	1	1	0	0	1	2	3	2	3	3	4	2	0	3	4	6	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:21051260C>A	ENST00000261383.3	-	33	4643	c.4644G>T	c.(4642-4644)ttG>ttT	p.L1548F	DNAH3_ENST00000415178.1_Missense_Mutation_p.L1548F	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1548	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTGTCCGGAACAAGGCCTGGA	0.488																																					p.L1548F		.											.	DNAH3-167	0			c.G4644T						.						114	103	107					16																	21051260		2201	4300	6501	SO:0001583	missense	55567	exon33			CCGGAACAAGGCC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.4644G>T	16.37:g.21051260C>A	ENSP00000261383:p.Leu1548Phe	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	236	59	NM_017539	0	0	0	0	0	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	c	19.21	3.783406	0.70222	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.40756	1.02;1.02	5.48	-3.63	0.04529	ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000008	T	0.71787	0.3381	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76408	-0.2970	10	0.87932	D	0	.	11.9329	0.52857	0.0:0.4256:0.0:0.5744	.	1548	Q8TD57	DYH3_HUMAN	F	1548	ENSP00000261383:L1548F;ENSP00000394245:L1548F	ENSP00000261383:L1548F	L	-	3	2	DNAH3	20958761	0.014000	0.17966	0.915000	0.36163	0.963000	0.63663	-0.900000	0.04097	-0.896000	0.03915	-0.753000	0.03488	TTG	.		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21051260	C	A	21051260	3	1	134	1	0	0	0	0	1	0	0	0	4614	477	17	4	7825	4	DNAH3	16	21051260	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	16143256	21051260	69303493	59	11946											
MBTPS1	8720	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	84094306	84094306	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccttccatcctctctggagtGactgagcctgctccactggg	5	11	10	15	0	1	2	0	2	1	0	5	3	4	3	5	2	2	1	5	2	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:84094306G>C	ENST00000343411.3	-	20	3180	c.2685C>G	c.(2683-2685)gtC>gtG	p.V895V		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	895					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCTCTGGAGTGACTGAGCCTG	0.592																																					p.V895V		.											.	MBTPS1-92	0			c.C2685G						.						65	53	57					16																	84094306		2200	4300	6500	SO:0001819	synonymous_variant	8720	exon20			TGGAGTGACTGAG	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"membrane-bound transcription factor protease, site 1"			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.2685C>G	16.37:g.84094306G>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	126	55	NM_003791	0	0	17	42	25	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			.		0.592	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		C	84094306	G	C	84094306	2	2	134	1	0	0	0	0	0	0	0	1	9386	1277	45	4		4	MBTPS1	16	84094306	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	63043046	84094306	6260447	60	11947											
ZCCHC14	23174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	87445209	87445209	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacaagataggttcccgcTctttttgtgactggaaccat	10	13	9	9	1	1	2	0	1	1	1	2	3	2	3	2	2	2	3	2	2	4	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:87445209T>A	ENST00000268616.4	-	12	2924	c.2707A>T	c.(2707-2709)Agc>Tgc	p.S903C		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	903							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGGTTCCCGCTCTTTTTGTGA	0.597																																					p.S903C		.											.	ZCCHC14-154	0			c.A2707T						.						85	74	78					16																	87445209		2198	4300	6498	SO:0001583	missense	23174	exon12			TCCCGCTCTTTTT	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2707A>T	16.37:g.87445209T>A	ENSP00000268616:p.Ser903Cys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	165	56	NM_015144	0	0	7	10	3	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	37	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.654553	0.47467	.	.	ENSG00000140948	ENST00000268616	T	0.76968	-1.06	5.55	5.55	0.83447	.	0.169858	0.53938	D	0.000059	T	0.79375	0.4435	L	0.27053	0.805	0.33555	D	0.596683	D;D	0.67145	0.996;0.993	P;P	0.59288	0.855;0.72	D	0.85907	0.1438	10	0.87932	D	0	-19.183	15.975	0.80057	0.0:0.0:0.0:1.0	.	903;903	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	C	903	ENSP00000268616:S903C	ENSP00000268616:S903C	S	-	1	0	ZCCHC14	86002710	0.998000	0.40836	0.998000	0.56505	0.927000	0.56198	1.668000	0.37481	2.223000	0.72356	0.533000	0.62120	AGC	.		0.597	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		A	87445209	T	A	87445209	3	1	134	1	0	0	0	0	1	0	0	0	17615	1551	54	5	150	5	ZCCHC14	16	87445209	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	3350903	87445209	2909544	61	11948											
FXR2	9513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7497319	7497319	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacaaaaatgaagggaaccaTtccctagagaacagagagca	20	4	9	8	0	0	3	0	1	0	2	1	6	1	4	2	1	4	1	2	1	7	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:7497319T>G	ENST00000250113.7	-	11	1358	c.1024A>C	c.(1024-1026)Atg>Ctg	p.M342L	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	342						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		AAGGGAACCATTCCCTAGAGA	0.532																																					p.M342L		.											.	.	0			c.A1024C						.						60	59	59					17																	7497319		1905	4126	6031	SO:0001583	missense	9513	exon11			GAACCATTCCCTA	U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1024A>C	17.37:g.7497319T>G	ENSP00000250113:p.Met342Leu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	63	18	NM_004860	0	0	0	2	2	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	T	9.196	1.027335	0.19512	.	.	ENSG00000129245	ENST00000250113	T	0.27720	1.65	5.52	5.52	0.82312	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.122387	0.64402	D	0.000001	T	0.18299	0.0439	N	0.12746	0.255	0.42425	D	0.992651	B	0.06786	0.001	B	0.09377	0.004	T	0.08932	-1.0698	10	0.22706	T	0.39	1.2613	13.6401	0.62246	0.0:0.0:0.0:1.0	.	342	P51116	FXR2_HUMAN	L	342	ENSP00000250113:M342L	ENSP00000250113:M342L	M	-	1	0	FXR2	7438044	1.000000	0.71417	1.000000	0.80357	0.081000	0.17604	5.842000	0.69417	2.317000	0.78254	0.460000	0.39030	ATG	.		0.532	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			G	7497319	T	G	7497319	3	3	134	1	0	0	0	0	1	0	0	0	6135	1493	52	5	925	5	FXR2	17	7497319	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		7497319	73697891	62	11949											
WDR16	146845	broad.mit.edu	37	chr17	9503401	9503402	+	Frame_Shift_Ins	INS	-	-	T																															aggtggatgatgatgatagcINStttttctaccttggcaccac																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:9503401_9503402insT	ENST00000352665.5	+	6	723_724	c.654_655insT	c.(655-657)tttfs	p.F219fs	WDR16_ENST00000396219.3_Frame_Shift_Ins_p.F151fs|WDR16_ENST00000299764.5_Frame_Shift_Ins_p.F229fs	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						ATGATGATAGCTTTTTCTACCT	0.485																																					p.S218fs													.	WDR16-71	0			c.654_655insT						.																																			SO:0001589	frameshift_variant	146845	exon6			TGATAGCTTTTTC	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"WD repeat domain containing"	16053	protein-coding gene	gene with protein product	"WD40-repeat protein upregulated in HCC"	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.659dupT	17.37:g.9503406_9503406dupT	ENSP00000339449:p.Phe219fs	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	168	7	NM_145054	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000352665.5	37	CCDS11149.2																																																																																			.		0.485	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		T	9503402	-	T	9503401	7	5	134	1	0	1	1	0	0	0	0	0	17309	796	28	0	676	0	WDR16	17	9503401	Frame_Shift_Ins	INS	-	TCGA-HE-A5NJ-01A-11D-A26P-10	2006082	9503401	71691809	63	11950											
MYH4	4622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10366950	10366950	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagcactgatgatttgatctTcaagggtccccttaagagaa	12	12	9	8	0	2	4	1	3	1	1	3	5	3	4	2	1	1	1	2	1	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:10366950T>G	ENST00000255381.2	-	8	769	c.659A>C	c.(658-660)gAa>gCa	p.E220A	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	220	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GATTTGATCTTCAAGGGTCCC	0.448																																					p.E220A		.											.	MYH4-102	0			c.A659C						.						73	73	73					17																	10366950		2203	4300	6503	SO:0001583	missense	4622	exon8			TGATCTTCAAGGG		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.659A>C	17.37:g.10366950T>G	ENSP00000255381:p.Glu220Ala	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	72	55	NM_017533	0	0	0	0	0		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567354	0.86439	.	.	ENSG00000141048	ENST00000255381	D	0.89050	-2.46	5.14	5.14	0.70334	Myosin head, motor domain (2);	0.000000	0.38005	U	0.001849	D	0.96503	0.8859	H	0.97707	4.06	0.80722	D	1	D	0.63880	0.993	D	0.77557	0.99	D	0.97990	1.0354	10	0.87932	D	0	.	15.2278	0.73364	0.0:0.0:0.0:1.0	.	220	Q9Y623	MYH4_HUMAN	A	220	ENSP00000255381:E220A	ENSP00000255381:E220A	E	-	2	0	MYH4	10307675	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.966000	0.87956	2.052000	0.61016	0.455000	0.32223	GAA	.		0.448	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		G	10366950	T	G	10366950	3	3	134	1	0	0	0	0	1	0	0	0	10062	1783	62	5	5292	5	MYH4	17	10366950	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	863549	10366950	70828260	64	11951											
STAC2	342667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37373422	37373422	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catcgcaagccctgtttggaGtttcctaggaagaatttggg	9	12	12	8	1	0	1	0	0	0	1	2	3	1	3	2	3	1	3	2	3	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:37373422G>A	ENST00000333461.5	-	3	771	c.402C>T	c.(400-402)aaC>aaT	p.N134N		NM_198993.3	NP_945344.1	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	134					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			NS(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(2)	17						CCTGTTTGGAGTTTCCTAGGA	0.562																																					p.N134N		.											.	STAC2-91	0			c.C402T						.						59	56	57					17																	37373422		2203	4300	6503	SO:0001819	synonymous_variant	342667	exon3			TTTGGAGTTTCCT	AJ608762	CCDS11335.1	17q21.2	2012-11-19			ENSG00000141750	ENSG00000141750			23990	protein-coding gene	gene with protein product							Standard	NM_198993		Approved	24b2	uc002hrs.3	Q6ZMT1	OTTHUMG00000179039	ENST00000333461.5:c.402C>T	17.37:g.37373422G>A		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	115	60	NM_198993	0	0	0	0	0	Q32MA3	Silent	SNP	ENST00000333461.5	37	CCDS11335.1																																																																																			.		0.562	STAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444533.2	NM_198993		A	37373422	G	A	37373422	2	1	134	1	0	0	0	0	0	0	0	1	15272	1020	36	2		2	STAC2	17	37373422	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	27006472	37373422	43821788	65	11952											
LLGL2	3993	broad.mit.edu	37	chr17	73565071	73565071	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacaggcacgaggacggCacggtgcggttctgggatgc	7	5	17	12	4	1	0	0	0	1	0	1	3	1	2	1	6	2	3	1	6	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:73565071C>A	ENST00000392550.3	+	13	1452	c.1335C>A	c.(1333-1335)ggC>ggA	p.G445G	LLGL2_ENST00000577200.1_Silent_p.G445G|LLGL2_ENST00000167462.5_Silent_p.G445G	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	445					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			ACGAGGACGGCACGGTGCGGT	0.667																																					p.G445G													.	LLGL2-251	0			c.C1335A						.						41	42	41					17																	73565071		2203	4300	6503	SO:0001819	synonymous_variant	3993	exon13			GGACGGCACGGTG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"WD repeat domain containing"	6629	protein-coding gene	gene with protein product			"lethal giant larvae (Drosophila) homolog 2"				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1335C>A	17.37:g.73565071C>A		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	36	5	NM_004524	0	0	0	0	0	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			.		0.667	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		A	73565071	C	A	73565071	2	1	134	1	0	0	0	0	0	0	0	1	8857	697	25	4		4	LLGL2	17	73565071	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	36191649	73565071	7630139	66	11953											
NEDD4L	23327	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	56033337	56033337	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	accagatgtcctaaaagctaGactgtggattgagtttgaat	13	12	10	6	0	0	4	0	2	0	2	1	5	1	5	2	1	1	2	2	1	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr18:56033337G>C	ENST00000400345.3	+	21	2223	c.1940G>C	c.(1939-1941)aGa>aCa	p.R647T	NEDD4L_ENST00000456986.1_Missense_Mutation_p.R526T|NEDD4L_ENST00000456173.2_Missense_Mutation_p.R506T|NEDD4L_ENST00000586263.1_Missense_Mutation_p.R619T|NEDD4L_ENST00000356462.6_Missense_Mutation_p.R583T|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Missense_Mutation_p.R639T|NEDD4L_ENST00000256830.9_Missense_Mutation_p.R543T|NEDD4L_ENST00000435432.2_Missense_Mutation_p.R506T|NEDD4L_ENST00000431212.2_Missense_Mutation_p.R526T|NEDD4L_ENST00000382850.4_Missense_Mutation_p.R627T|NEDD4L_ENST00000256832.7_Missense_Mutation_p.R507T	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	647	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						CTAAAAGCTAGACTGTGGATT	0.408																																					p.R647T		.											.	NEDD4L-658	0			c.G1940C						.						122	114	117					18																	56033337		1867	4102	5969	SO:0001583	missense	23327	exon21			AAGCTAGACTGTG	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"neural precursor cell expressed, developmentally down-regulated 4-like"			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1940G>C	18.37:g.56033337G>C	ENSP00000383199:p.Arg647Thr	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	132	9	NM_001144967	0	0	9	9	0	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	37	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	30	5.052900	0.93793	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.75938	0.97;0.97;0.97;0.97;-0.98;-0.98;0.97;-0.98;-0.98;-0.98	5.54	5.54	0.83059	HECT (3);	0.000000	0.85682	D	0.000000	D	0.86727	0.6002	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.999;0.966;0.985;0.999;0.999	D;D;P;D;D;D	0.77004	0.989;0.985;0.574;0.955;0.977;0.985	D	0.87407	0.2373	10	0.87932	D	0	.	19.8487	0.96730	0.0:0.0:1.0:0.0	.	619;639;506;583;647;627	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;NED4L_HUMAN;.	T	647;627;583;543;507;526;639;506;506;526	ENSP00000383199:R647T;ENSP00000372301:R627T;ENSP00000348847:R583T;ENSP00000256830:R543T;ENSP00000256832:R507T;ENSP00000411947:R526T;ENSP00000350569:R639T;ENSP00000393395:R506T;ENSP00000405440:R506T;ENSP00000389406:R526T	ENSP00000256830:R543T	R	+	2	0	NEDD4L	54184317	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.813000	0.99286	2.748000	0.94277	0.650000	0.86243	AGA	.		0.408	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	56033337	G	C	56033337	3	2	134	1	0	0	0	0	1	0	0	0	10337	942	33	4	2050	4	NEDD4L	18	56033337	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		56033337	22043911	67	11954											
LPPR3	79948	hgsc.bcm.edu	37	chr19	815207	815207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacaaaccgcaccgtacgccGcaggaaggagttgaagttgc	12	5	12	12	4	0	1	0	1	0	0	0	3	0	3	3	2	3	5	3	2	4	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:815207G>A	ENST00000520876.3	-	4	460	c.382C>T	c.(382-384)Cgg>Tgg	p.R128W	LPPR3_ENST00000359894.2_Missense_Mutation_p.R128W|MIR3187_ENST00000583431.1_RNA	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		128						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										ACCGTACGCCGCAGGAAGGAG	0.716																																					p.R128W		.											.	.	0			c.C382T						.						23	28	26					19																	815207		2181	4286	6467	SO:0001583	missense	0	exon4			TACGCCGCAGGAA																												ENST00000520876.3:c.382C>T	19.37:g.815207G>A	ENSP00000430297:p.Arg128Trp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_001270366	0	0	0	0	0	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	37	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790052	0.70337	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876;ENST00000521445	T;T	0.52526	0.66;0.66	4.33	3.27	0.37495	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.68339	0.2990	M	0.82517	2.595	0.52501	D	0.999955	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.71712	-0.4510	10	0.87932	D	0	-9.9087	11.2342	0.48931	0.0:0.0:0.8149:0.1851	.	128;128;128	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	W	128	ENSP00000352962:R128W;ENSP00000430297:R128W	ENSP00000300947:R128W	R	-	1	2	AC006273.1	766207	0.599000	0.26891	0.997000	0.53966	0.459000	0.32528	0.345000	0.19979	0.788000	0.33755	0.462000	0.41574	CGG	.		0.716	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			A	815207	G	A	815207	3	1	134	1	0	0	0	0	1	0	0	0	8951	1086	38	1	1874	1	LPPR3	19	815207	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		815207	58313776	68	11955											
STK11	6794	ucsc.edu	37	chr19	1220643	1220643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agggctccccggctttccagCcgcccgagattgccaacggc	6	6	12	17	4	0	1	0	0	0	1	2	2	2	1	6	3	3	2	6	3	1	2	rs587782546		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:1220643C>T	ENST00000326873.7	+	5	1834	c.661C>T	c.(661-663)Ccg>Tcg	p.P221S		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	221	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(2)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCTTTCCAGCCGCCCGAGAT	0.711		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.P221S			yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	.	STK11-5227	22	Whole gene deletion(20)|Unknown(2)	cervix(14)|lung(4)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C661T						.						13	19	17					19																	1220643		1945	4124	6069	SO:0001583	missense	6794	exon5	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	TTCCAGCCGCCCG	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"polarization-related protein LKB1"	602216	"serine/threonine kinase 11 (Peutz-Jeghers syndrome)"			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.661C>T	19.37:g.1220643C>T	ENSP00000324856:p.Pro221Ser	Somatic	18	0		WXS	Illumina HiSeq		24	4	NM_000455	0	0	32	32	0	B2RBX7|E7EW76	Missense_Mutation	SNP	ENST00000326873.7	37	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.963262	0.92791	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	T	0.81163	-1.46	5.6	5.6	0.85130	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76335	0.3973	N	0.04335	-0.225	0.80722	D	1	D	0.62365	0.991	P	0.58660	0.843	T	0.79298	-0.1861	10	0.34782	T	0.22	-28.8932	18.5988	0.91240	0.0:1.0:0.0:0.0	.	221	Q15831	STK11_HUMAN	S	221	ENSP00000324856:P221S	ENSP00000324856:P221S	P	+	1	0	STK11	1171643	1.000000	0.71417	0.999000	0.59377	0.684000	0.39900	7.712000	0.84684	2.644000	0.89710	0.561000	0.74099	CCG	.		0.711	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1220643	C	T	1220643	3	4	134	1	0	0	0	0	1	0	0	0	15319	739	26	2	679	2	STK11	19	1220643	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	405436	1220643	57908340	69	11956											
ZNF57	126295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2915555	2915555	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaggatgtggctgtggacttCaccctggaggagtgggcttt	6	11	17	7	0	1	0	1	0	0	0	1	5	1	4	1	6	0	2	1	6	0	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:2915555C>T	ENST00000306908.5	+	2	187	c.39C>T	c.(37-39)ttC>ttT	p.F13F	AC006277.2_ENST00000520090.2_RNA|ZNF57_ENST00000523428.1_5'UTR	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	13	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGTGGACTTCACCCTGGAGG	0.542																																					p.F13F	NSCLC(150;910 1964 4303 10464 26498)	.											.	ZNF57-71	0			c.C39T						.						160	141	147					19																	2915555		2203	4300	6503	SO:0001819	synonymous_variant	126295	exon2			GGACTTCACCCTG	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"Zinc fingers, C2H2-type", "-"	13125	protein-coding gene	gene with protein product			"zinc finger protein 424"	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.39C>T	19.37:g.2915555C>T		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	170	76	NM_173480	0	0	0	0	0	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																			.		0.542	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		T	2915555	C	T	2915555	2	4	134	1	0	0	0	0	0	0	0	1	18033	825	29	2		2	ZNF57	19	2915555	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	1694912	2915555	56213428	70	11957											
ZFR2	23217	hgsc.bcm.edu;broad.mit.edu	37	chr19	3808936	3808936	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcatccccggggcccagggGcccagccgcactgctcacag	6	4	13	18	2	1	0	1	0	0	0	2	0	2	0	5	4	3	3	5	4	0	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:3808936G>A	ENST00000262961.4	-	17	2489	c.2479C>T	c.(2479-2481)Ccc>Tcc	p.P827S		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	827	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GGGCCCAGGGGCCCAGCCGCA	0.697																																					p.P827S		.											.	ZFR2-70	0			c.C2479T						.						10	15	14					19																	3808936		2017	4182	6199	SO:0001583	missense	23217	exon17			CCAGGGGCCCAGC	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.2479C>T	19.37:g.3808936G>A	ENSP00000262961:p.Pro827Ser	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	33	15	NM_015174	0	0	0	0	0		Missense_Mutation	SNP	ENST00000262961.4	37	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588474	0.46110	.	.	ENSG00000105278	ENST00000262961	T	0.42131	0.98	3.97	3.97	0.46021	DZF (2);	0.084158	0.48767	U	0.000179	T	0.62962	0.2471	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.65668	-0.6112	10	0.48119	T	0.1	-16.1842	11.3964	0.49845	0.0:0.0:1.0:0.0	.	827	Q9UPR6	ZFR2_HUMAN	S	827	ENSP00000262961:P827S	ENSP00000262961:P827S	P	-	1	0	ZFR2	3759936	1.000000	0.71417	0.677000	0.29947	0.009000	0.06853	5.975000	0.70475	2.053000	0.61076	0.484000	0.47621	CCC	.		0.697	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		A	3808936	G	A	3808936	3	1	134	1	0	0	0	0	1	0	0	0	17692	1203	42	2	352	2	ZFR2	19	3808936	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	893381	3808936	55320047	71	11958											
LOC55908	55908	broad.mit.edu;bcgsc.ca	37	chr19	11350388	11350388	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcagcggcccccatgggCggcccagaactggcacagca	8	3	13	17	2	1	1	1	0	0	1	1	1	1	1	4	4	3	2	4	4	1	0	rs376063419		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:11350388C>T	ENST00000252453.8	+	1	94	c.75C>T	c.(73-75)ggC>ggT	p.G25G	C19orf80_ENST00000591200.1_Intron|DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	25					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CCCCCATGGGCGGCCCAGAAC	0.652																																					p.G25G													.	.	0			c.C75T						.	C	,	0,3918		0,0,1959	24	26	25		75,	-8.4	0	19		25	2,8282		0,2,4140	no	coding-synonymous,intron	C19orf80,DOCK6	NM_018687.6,NM_020812.2	,	0,2,6099	TT,TC,CC		0.0241,0.0,0.0164	,	25/199,	11350388	2,12200	1959	4142	6101	SO:0001819	synonymous_variant	55908	exon1			CATGGGCGGCCCA		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"lipasin", "betatrophin"					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.75C>T	19.37:g.11350388C>T		Somatic	48	1		WXS	Illumina HiSeq	Phase_I	104	46	NM_018687	0	0	0	0	0	Q9NQZ1	Silent	SNP	ENST00000252453.8	37	CCDS54220.1																																																																																			.		0.652	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		T	11350388	C	T	11350388	2	4	134	1	0	0	0	0	0	0	0	1	8906	755	27	1		1	LOC55908	19	11350388	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	7541452	11350388	47778595	72	11959											
IL27RA	9466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	14150421	14150421	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgacaaactccttgtctgggGcactaaggcaggccagcctc	9	8	11	13	0	1	1	0	1	1	0	3	1	2	1	3	4	2	2	3	4	2	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:14150421G>A	ENST00000263379.2	+	3	445	c.320G>A	c.(319-321)gGc>gAc	p.G107D		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	107					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						CTTGTCTGGGGCACTAAGGCA	0.612																																					p.G107D	Colon(164;1849 1896 4443 37792 47834)	.											.	IL27RA-90	0			c.G320A						.						66	61	63					19																	14150421		2203	4300	6503	SO:0001583	missense	9466	exon3			TCTGGGGCACTAA	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	17290	protein-coding gene	gene with protein product	"T-cell cytokine receptor type 1"	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.320G>A	19.37:g.14150421G>A	ENSP00000263379:p.Gly107Asp	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	190	61	NM_004843	0	0	4	6	2	A0N0L1|O60624	Missense_Mutation	SNP	ENST00000263379.2	37	CCDS12303.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314782	0.40996	.	.	ENSG00000104998	ENST00000263379	T	0.61627	0.09	4.54	-2.12	0.07165	.	0.705821	0.12338	N	0.477779	T	0.46073	0.1374	L	0.32530	0.975	0.09310	N	0.999991	P	0.52316	0.952	P	0.49140	0.601	T	0.43718	-0.9374	10	0.23891	T	0.37	-20.1299	7.3547	0.26713	0.0:0.2745:0.2642:0.4613	.	107	Q6UWB1	I27RA_HUMAN	D	107	ENSP00000263379:G107D	ENSP00000263379:G107D	G	+	2	0	IL27RA	14011421	0.006000	0.16342	0.097000	0.21041	0.288000	0.27193	-0.354000	0.07681	-0.030000	0.13804	0.555000	0.69702	GGC	.		0.612	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		A	14150421	G	A	14150421	3	1	134	1	0	0	0	0	1	0	0	0	7702	1203	42	2	330	2	IL27RA	19	14150421	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	2800033	14150421	44978562	73	11960											
MYO9B	4650	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	17322846	17322846	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggacccccatcatgcccacGgccaacatcaagctcccacc	10	4	6	21	2	2	0	2	0	0	0	3	1	3	1	6	2	3	1	6	2	2	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:17322846G>A	ENST00000594824.1	+	40	6348	c.6201G>A	c.(6199-6201)acG>acA	p.T2067T	MYO9B_ENST00000595618.1_3'UTR|MYO9B_ENST00000397274.2_3'UTR			Q13459	MYO9B_HUMAN	myosin IXB	2067	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						TCATGCCCACGGCCAACATCA	0.736																																					p.T2067T		.											.	MYO9B-67	0			c.G6201A						.						9	11	10					19																	17322846		1808	4035	5843	SO:0001819	synonymous_variant	4650	exon40			GCCCACGGCCAAC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"Myosins / Myosin superfamily : Class IX"	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.6201G>A	19.37:g.17322846G>A		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	59	36	NM_004145	0	0	2	3	1	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				.		0.736	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17322846	G	A	17322846	2	1	134	1	0	0	0	0	0	0	0	1	10110	1103	39	1		1	MYO9B	19	17322846	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3172425	17322846	41806137	74	11961											
USF2	7392	bcgsc.ca	37	chr19	35761401	35761402	+	In_Frame_Ins	INS	-	-	TCAGCGGGGAGGCACGATTTGCCT																															cagtccggcggccgaggctgINStcagcggggaggcacgattt																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:35761401_35761402insTCAGCGGGGAGGCACGATTTGCCT	ENST00000222305.3	+	5	518_519	c.481_482insTCAGCGGGGAGGCACGATTTGCCT	c.(481-483)gtc>gTCAGCGGGGAGGCACGATTTGCCTtc	p.161_162insSGEARFAF	USF2_ENST00000594064.1_In_Frame_Ins_p.159_160insSGEARFAF|USF2_ENST00000343550.5_In_Frame_Ins_p.94_95insSGEARFAF|USF2_ENST00000379134.3_Intron|USF2_ENST00000595068.1_In_Frame_Ins_p.161_162insSGEARFAF	NM_003367.2	NP_003358.1	Q15853	USF2_HUMAN	upstream transcription factor 2, c-fos interacting	161					lactation (GO:0007595)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|urinary_tract(1)	13	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GGCCGAGGCTGTCAGCGGGGAG	0.589																																					p.V161delinsVSGEARFAF	NSCLC(103;173 2832 8890)												.	USF2-514	0			c.481_482insTCAGCGGGGAGGCACGATTTGCCT						.																																			SO:0001652	inframe_insertion	7392	exon5			GAGGCTGTCAGCG	AY007087	CCDS12452.1, CCDS12453.1	19q13	2013-05-21				ENSG00000105698		"Basic helix-loop-helix proteins"	12594	protein-coding gene	gene with protein product		600390				8954795	Standard	NM_003367		Approved	FIP, bHLHb12	uc002nyq.1	Q15853		ENST00000222305.3:c.482_505dupTCAGCGGGGAGGCACGATTTGCCT	19.37:g.35761401_35761402insTCAGCGGGGAGGCACGATTTGCCT	ENSP00000222305:p.Val161_Ser162insSerGlyGluAlaArgPheAlaPhe	Somatic	288	0		WXS	Illumina HiSeq	Phase_1	209	10	NM_003367	0	0	0	0	0	O00671|O00709|Q05750|Q07952|Q15851|Q15852|Q6FI33|Q6YI47	In_Frame_Ins	INS	ENST00000222305.3	37	CCDS12452.1																																																																																			.		0.589	USF2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466056.1	NM_003367		TCAGCGGGGAGGCACGATTTGCCT	35761402	-	TCAGCGGGGAGGCACGATTTGCCT	35761401	7	5	134	1	0	1	1	0	0	0	0	0	17066	1377	48	0	499	0	USF2	19	35761401	In_Frame_Ins	INS	-	TCGA-HE-A5NJ-01A-11D-A26P-10	18438555	35761401	23367582	75	11962											
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40698281	40698281	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gctttggcaaggtctatcggGccctgtggcgtggcgaggag	5	9	18	9	3	1	0	0	0	1	0	2	2	1	1	1	6	0	2	1	6	2	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:40698281G>T	ENST00000253055.3	+	1	631	c.343G>T	c.(343-345)Gcc>Tcc	p.A115S	MAP3K10_ENST00000593906.1_3'UTR	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GGTCTATCGGGCCCTGTGGCG	0.687																																					p.A115S		.											.	MAP3K10-981	0			c.G343T						.						33	38	36					19																	40698281		2202	4298	6500	SO:0001583	missense	4294	exon1			TATCGGGCCCTGT	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6849	protein-coding gene	gene with protein product	"MKN28 kinase", "mixed lineage kinase 2", "MKN28 derived nonreceptor_type serine/threonine kinase"	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.343G>T	19.37:g.40698281G>T	ENSP00000253055:p.Ala115Ser	Somatic	9	0		WXS	Illumina HiSeq	Phase_I	28	4	NM_002446	0	0	6	6	0	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	37	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976122	0.92982	.	.	ENSG00000130758	ENST00000253055	D	0.84944	-1.92	4.3	4.3	0.51218	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.207947	0.38897	N	0.001532	D	0.89223	0.6654	M	0.63428	1.95	0.39678	D	0.970865	P	0.51933	0.949	P	0.58660	0.843	D	0.91138	0.4943	10	0.87932	D	0	.	14.3128	0.66426	0.0:0.0:1.0:0.0	.	115	Q02779	M3K10_HUMAN	S	115	ENSP00000253055:A115S	ENSP00000253055:A115S	A	+	1	0	MAP3K10	45390121	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.646000	0.98474	2.232000	0.73038	0.655000	0.94253	GCC	.		0.687	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		T	40698281	G	T	40698281	3	4	134	1	0	0	0	0	1	0	0	0	9269	1203	42	4	345	4	MAP3K10	19	40698281	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	4936880	40698281	18430702	76	11963											
CYP2A6	1548	ucsc.edu;bcgsc.ca	37	chr19	41349763	41349763	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcaaagcccacgtgtttggGggacacgtcaatgtccttag	9	9	13	10	2	1	0	1	0	0	0	2	1	2	1	2	3	1	2	2	3	3	2	rs561053481	byFrequency	TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:41349763G>T	ENST00000301141.5	-	9	1443	c.1423C>A	c.(1423-1425)Ccc>Acc	p.P475T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	475					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	ACGTGTTTGGGGGACACGTCA	0.602																																					p.P475T													.	CYP2A6-92	0			c.C1423A						.						213	159	177					19																	41349763		2202	4300	6502	SO:0001583	missense	1548	exon9			GTTTGGGGGACAC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"Cytochrome P450s"	2610	protein-coding gene	gene with protein product		122720	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1423C>A	19.37:g.41349763G>T	ENSP00000301141:p.Pro475Thr	Somatic	1557	5		WXS	Illumina HiSeq		1723	501	NM_000762	0	0	0	0	0	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	22.8	4.342732	0.82022	.	.	ENSG00000255974	ENST00000301141	T	0.68624	-0.34	3.02	1.92	0.25849	.	0.064020	0.64402	U	0.000006	T	0.75140	0.3809	L	0.56340	1.77	0.33079	D	0.536371	D	0.89917	1.0	D	0.97110	1.0	T	0.79995	-0.1568	10	0.87932	D	0	.	10.8431	0.46728	0.0:0.1951:0.8049:0.0	.	475	P11509	CP2A6_HUMAN	T	475	ENSP00000301141:P475T	ENSP00000301141:P475T	P	-	1	0	CYP2A6	46041603	0.999000	0.42202	0.036000	0.18154	0.855000	0.48748	2.893000	0.48633	0.364000	0.24374	0.386000	0.25728	CCC	.		0.602	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		T	41349763	G	T	41349763	3	4	134	1	0	0	0	0	1	0	0	0	4168	1232	43	4	65	4	CYP2A6	19	41349763	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	651482	41349763	17779220	77	11964											
ZNF221	7638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44471195	44471195	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgtgaagagtgtggaaagaGatttactcagagttcacaac	15	10	11	5	0	2	4	2	1	0	3	2	6	2	5	0	1	2	1	0	1	4	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:44471195G>C	ENST00000251269.5	+	6	1869	c.1541G>C	c.(1540-1542)aGa>aCa	p.R514T	ZNF221_ENST00000587682.1_Missense_Mutation_p.R514T|ZNF221_ENST00000592350.1_Missense_Mutation_p.R514T	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				TGTGGAAAGAGATTTACTCAG	0.428																																					p.R514T		.											.	ZNF221-91	0			c.G1541C						.						94	89	91					19																	44471195		2203	4300	6503	SO:0001583	missense	7638	exon6			GAAAGAGATTTAC	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1541G>C	19.37:g.44471195G>C	ENSP00000251269:p.Arg514Thr	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	51	15	NM_013359	0	0	0	0	0	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	12.16	1.853235	0.32699	.	.	ENSG00000159905	ENST00000251269	T	0.16597	2.33	2.63	-1.52	0.08637	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10895	0.0266	N	0.11870	0.19	0.09310	N	1	P	0.51240	0.943	P	0.48873	0.593	T	0.25152	-1.0140	9	0.38643	T	0.18	.	5.5077	0.16864	0.1145:0.0:0.5338:0.3517	.	514	Q9UK13	ZN221_HUMAN	T	514	ENSP00000251269:R514T	ENSP00000251269:R514T	R	+	2	0	ZNF221	49163035	0.000000	0.05858	0.000000	0.03702	0.888000	0.51559	0.114000	0.15520	-0.005000	0.14395	0.313000	0.20887	AGA	.		0.428	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			C	44471195	G	C	44471195	3	2	134	1	0	0	0	0	1	0	0	0	17807	942	33	4	1555	4	ZNF221	19	44471195	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3121432	44471195	14657788	78	11965											
SEPT5	5413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	19709430	19709430	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacctcaaggacgtgacgtgCgacgtgcactacgagaacta	12	6	12	11	5	1	2	1	1	0	1	1	6	1	3	1	1	4	1	1	1	4	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr22:19709430C>T	ENST00000455784.2	+	10	1025	c.900C>T	c.(898-900)tgC>tgT	p.C300C	SEPT5_ENST00000406395.1_Nonsense_Mutation_p.R297*|SEPT5_ENST00000383045.3_Silent_p.C309C|SEPT5_ENST00000438754.2_Nonsense_Mutation_p.R306*|GP1BB_ENST00000366425.3_5'Flank	NM_002688.5	NP_002679.2	Q99719	SEPT5_HUMAN	septin 5	300	Septin-type G.				cytokinesis (GO:0000910)|GTP catabolic process (GO:0006184)|regulation of exocytosis (GO:0017157)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic vesicle targeting (GO:0016080)	plasma membrane (GO:0005886)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			lung(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					ACGTGACGTGCGACGTGCACT	0.662																																					p.R306X		.											.	SEPT5-636	0			c.C916T						.						58	52	54					22																	19709430		2203	4299	6502	SO:0001819	synonymous_variant	5413	exon9			GACGTGCGACGTG	Y11593	CCDS13764.1, CCDS56224.1	22q11.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000184702	ENSG00000184702		"Septins"	9164	protein-coding gene	gene with protein product		602724	"peanut-like 1 (Drosophila)"	PNUTL1		9385360, 9611266	Standard	NM_002688		Approved	HCDCREL-1, H5		Q99719	OTTHUMG00000150399	ENST00000455784.2:c.900C>T	22.37:g.19709430C>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	119	43	NM_001009939	0	0	6	12	6	O15251|Q96MY5	Nonsense_Mutation	SNP	ENST00000455784.2	37	CCDS13764.1	.	.	.	.	.	.	.	.	.	.	C	35	5.483869	0.96307	.	.	ENSG00000184702	ENST00000406395;ENST00000438754	.	.	.	3.66	-2.26	0.06867	.	.	.	.	.	.	.	.	.	.	.	0.58432	A	0.999992	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	5.9818	0.19411	0.0:0.3259:0.1386:0.5355	.	.	.	.	X	297;306	.	ENSP00000384535:R297X	R	+	1	2	SEPT5	18089430	0.020000	0.18652	0.802000	0.32245	0.983000	0.72400	-0.876000	0.04201	-0.201000	0.10284	0.297000	0.19635	CGA	.		0.662	SEPT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317937.1	NM_002688		T	19709430	C	T	19709430	2	4	134	1	0	0	0	0	0	0	0	1	14099	776	27	1		1	SEPT5	22	19709430	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		19709430	31595136	79	11966											
MTMR3	8897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30416249	30416249	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caaggtcatcatagatcttgCcttgtaaatagtggcaagga	13	11	10	7	0	3	1	2	0	1	1	3	2	3	2	1	3	1	2	1	3	6	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr22:30416249C>T	ENST00000401950.2	+	17	2943	c.2601C>T	c.(2599-2601)tgC>tgT	p.C867C	CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000333027.3_Silent_p.C867C|MTMR3_ENST00000351488.3_Silent_p.C867C|MTMR3_ENST00000406629.1_Silent_p.C867C|MTMR3_ENST00000323630.5_Silent_p.C731C|CTA-85E5.10_ENST00000429350.1_RNA	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	867					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			ATAGATCTTGCCTTGTAAATA	0.512																																					p.C867C		.											.	MTMR3-292	0			c.C2601T						.						69	65	66					22																	30416249		2203	4300	6503	SO:0001819	synonymous_variant	8897	exon17			ATCTTGCCTTGTA	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"Zinc fingers, FYVE domain containing", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.2601C>T	22.37:g.30416249C>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	145	60	NM_153050	0	0	10	11	1	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			.		0.512	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		T	30416249	C	T	30416249	2	4	134	1	0	0	0	0	0	0	0	1	9970	747	26	2		2	MTMR3	22	30416249	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	10706819	30416249	20888317	80	11967											
POLA1	5422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	24750526	24750526	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtccatcacagttttgcaTtggataaagcagccccaaag	12	10	9	10	0	1	0	1	0	0	0	2	1	2	1	3	2	3	3	3	2	3	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chrX:24750526T>A	ENST00000379059.3	+	16	1723	c.1708T>A	c.(1708-1710)Ttg>Atg	p.L570M	POLA1_ENST00000379068.3_Missense_Mutation_p.L576M|POLA1_ENST00000493342.1_3'UTR	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	570					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	CAGTTTTGCATTGGATAAAGC	0.398																																					p.L570M		.											.	POLA1-229	0			c.T1708A						.						189	158	168					X																	24750526		2203	4300	6503	SO:0001583	missense	5422	exon16			TTTGCATTGGATA		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"DNA polymerases"	9173	protein-coding gene	gene with protein product		312040	"polymerase (DNA directed), alpha", "polymerase (DNA directed), alpha 1", "N syndrome (mental retardation, malformations, chromosome breakage)"	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1708T>A	X.37:g.24750526T>A	ENSP00000368349:p.Leu570Met	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	26	23	NM_016937	0	0	0	3	3	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.534808	0.45073	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.45276	0.9;0.9	5.42	0.376	0.16193	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.268948	0.37483	N	0.002076	T	0.45357	0.1338	M	0.82323	2.585	0.33032	D	0.530339	B	0.32283	0.362	B	0.36244	0.22	T	0.54675	-0.8258	10	0.54805	T	0.06	-6.8741	9.4781	0.38884	0.0:0.4038:0.0:0.5962	.	570	P09884	DPOLA_HUMAN	M	576;570	ENSP00000368358:L576M;ENSP00000368349:L570M	ENSP00000368349:L570M	L	+	1	2	POLA1	24660447	0.321000	0.24625	0.054000	0.19295	0.938000	0.57974	0.682000	0.25335	-0.193000	0.10415	0.417000	0.27973	TTG	.		0.398	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24750526	T	A	24750526	3	1	134	1	0	0	0	0	1	0	0	0	12213	1490	52	5	1770	5	POLA1	23	24750526	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		24750526	130520034	81	11968											
GATA1	2623	hgsc.bcm.edu	37	chrX	48652221	48652221	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaaccggccactgaccatgCggaaggatggtattcagact	11	8	12	10	2	1	3	1	2	0	1	1	5	1	5	3	4	2	1	3	4	3	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chrX:48652221C>T	ENST00000376670.3	+	6	1003	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	GATA1_ENST00000376665.3_Intron	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	298					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						ACTGACCATGCGGAAGGATGG	0.582			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.R298W	Pancreas(9;429 505 11287 29617)	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1-1315	0			c.C892T						.						21	20	21					X																	48652221		2203	4299	6502	SO:0001583	missense	2623	exon6			ACCATGCGGAAGG	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.892C>T	X.37:g.48652221C>T	ENSP00000365858:p.Arg298Trp	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	75	4	NM_002049	0	0	0	0	0	Q96GB8	Missense_Mutation	SNP	ENST00000376670.3	37	CCDS14305.1	.	.	.	.	.	.	.	.	.	.	c	18.07	3.540683	0.65085	.	.	ENSG00000102145	ENST00000376670	D	0.99667	-6.34	4.21	-2.43	0.06522	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (2);	0.068357	0.56097	U	0.000034	D	0.99007	0.9661	L	0.28694	0.88	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96825	0.9607	10	0.87932	D	0	-11.8489	14.9001	0.70672	0.8239:0.1761:0.0:0.0	.	298	P15976	GATA1_HUMAN	W	298	ENSP00000365858:R298W	ENSP00000365858:R298W	R	+	1	2	GATA1	48537165	0.693000	0.27728	0.976000	0.42696	0.976000	0.68499	-0.187000	0.09656	-1.041000	0.03266	0.365000	0.22127	CGG	.		0.582	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		T	48652221	C	T	48652221	3	4	134	1	0	0	0	0	1	0	0	0	6273	759	27	1	910	1	GATA1	23	48652221	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	23901695	48652221	106618339	82	11969											
FAM155B	27112	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	68748896	68748896	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgacccagcaggaatgccagCgctgggtgccctgcaagcaa	10	5	13	13	1	0	1	0	1	0	0	0	2	0	2	3	2	6	4	3	2	3	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chrX:68748896C>T	ENST00000252338.4	+	2	964	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C		NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	308						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						GGAATGCCAGCGCTGGGTGCC	0.597																																					p.R308C													.	FAM155B-131	0			c.C922T						.						57	44	48					X																	68748896		2203	4300	6503	SO:0001583	missense	27112	exon2			TGCCAGCGCTGGG	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"transmembrane protein 28", "chromosome X open reading frame 63"	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.922C>T	X.37:g.68748896C>T	ENSP00000252338:p.Arg308Cys	Somatic	103	1		WXS	Illumina HiSeq	Phase_I	96	84	NM_015686	0	0	0	0	0	B1ALV6|B9EGK1|D3DVU1	Missense_Mutation	SNP	ENST00000252338.4	37	CCDS35317.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482094	0.63849	.	.	ENSG00000130054	ENST00000252338	T	0.12569	2.67	5.31	4.44	0.53790	.	0.417992	0.21811	N	0.068766	T	0.12220	0.0297	N	0.19112	0.55	0.38759	D	0.954299	D	0.57571	0.98	P	0.46049	0.502	T	0.06661	-1.0814	10	0.72032	D	0.01	-4.1926	12.3103	0.54925	0.1695:0.8305:0.0:0.0	.	308	O75949-2	.	C	308	ENSP00000252338:R308C	ENSP00000252338:R308C	R	+	1	0	FAM155B	68665621	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.899000	0.48679	0.993000	0.38866	0.523000	0.50628	CGC	.		0.597	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057037.1	NM_015686		T	68748896	C	T	68748896	3	4	134	1	0	0	0	0	1	0	0	0	5482	768	27	1	928	1	FAM155B	23	68748896	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	20096675	68748896	86521664	83	11970											
TBC1D8B	54885	broad.mit.edu	37	chrX	106109170	106109170	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgagtccctgggctcattctGcaaataaagactcactagct	11	11	8	11	0	3	2	2	1	1	1	4	2	4	2	1	1	2	3	1	1	4	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chrX:106109170G>A	ENST00000357242.5	+	16	2743	c.2569G>A	c.(2569-2571)Gca>Aca	p.A857T	TBC1D8B_ENST00000276175.3_Missense_Mutation_p.A851T	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	857							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GGCTCATTCTGCAAATAAAGA	0.408																																					p.A857T													.	TBC1D8B-133	0			c.G2569A						.						136	119	125					X																	106109170		2203	4300	6503	SO:0001583	missense	54885	exon16			CATTCTGCAAATA	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"EF-hand domain containing"	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.2569G>A	X.37:g.106109170G>A	ENSP00000349781:p.Ala857Thr	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_017752	0	0	0	0	0	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Missense_Mutation	SNP	ENST00000357242.5	37	CCDS14522.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.04|10.04	1.241609|1.241609	0.22711|0.22711	.|.	.|.	ENSG00000133138|ENSG00000133138	ENST00000357242;ENST00000276175;ENST00000394972|ENST00000431860	T;T|.	0.30182|.	1.54;1.54|.	5.71|5.71	4.83|4.83	0.62350|0.62350	EF-hand-like domain (1);|.	0.116831|.	0.64402|.	D|.	0.000017|.	T|T	0.59595|0.59595	0.2205|0.2205	L|L	0.43598|0.43598	1.365|1.365	0.44282|0.44282	D|D	0.997149|0.997149	B|.	0.18461|.	0.028|.	B|.	0.15870|.	0.014|.	T|T	0.55496|0.55496	-0.8132|-0.8132	10|5	0.07175|.	T|.	0.84|.	-8.178|-8.178	14.2281|14.2281	0.65873|0.65873	0.0:0.1465:0.8535:0.0|0.0:0.1465:0.8535:0.0	.|.	857|.	Q0IIM8|.	TBC8B_HUMAN|.	T|Y	857;851;119|119	ENSP00000349781:A857T;ENSP00000276175:A851T|.	ENSP00000276175:A851T|.	A|C	+|+	1|2	0|0	TBC1D8B|TBC1D8B	105995826|105995826	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.899000|0.899000	0.52679|0.52679	3.852000|3.852000	0.55934|0.55934	1.125000|1.125000	0.41998|0.41998	0.594000|0.594000	0.82650|0.82650	GCA|TGC	.		0.408	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		A	106109170	G	A	106109170	3	1	134	1	0	0	0	0	1	0	0	0	15658	1319	46	2	2697	2	TBC1D8B	23	106109170	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	37360274	106109170	49161390	84	11971											
DDI2	84301	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15956933	15956933	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctggagaaataacttcaTctcctcagggcttggacaat	11	11	8	11	0	3	1	2	0	1	1	5	3	4	2	2	3	1	1	2	3	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:15956933T>G	ENST00000480945.1	+	3	553	c.382T>G	c.(382-384)Tct>Gct	p.S128A		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	128							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AATAACTTCATCTCCTCAGGG	0.552																																					p.S128A													.	DDI2-44	0			c.T382G						.						95	87	90					1																	15956933		2203	4300	6503	SO:0001583	missense	84301	exon3			ACTTCATCTCCTC		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.382T>G	1.37:g.15956933T>G	ENSP00000417748:p.Ser128Ala	Somatic	116	1		WXS	Illumina HiSeq	Phase_I	129	36	NM_032341	0	0	0	0	0	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	37	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.463776	0.43736	.	.	ENSG00000197312	ENST00000480945	T	0.23348	1.91	5.67	4.53	0.55603	.	0.259165	0.39341	U	0.001400	T	0.13030	0.0316	N	0.12182	0.205	0.31118	N	0.709206	B	0.02656	0.0	B	0.01281	0.0	T	0.17776	-1.0358	10	0.08381	T	0.77	-21.6366	11.9893	0.53166	0.1297:0.0:0.0:0.8703	.	128	Q5TDH0	DDI2_HUMAN	A	128	ENSP00000417748:S128A	ENSP00000449475:S13A	S	+	1	0	DDI2	15829520	1.000000	0.71417	0.774000	0.31636	0.995000	0.86356	4.722000	0.61958	0.949000	0.37715	0.528000	0.53228	TCT	.		0.552	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		G	15956933	T	G	15956933	3	3	135	1	0	0	0	0	1	0	0	0	4335	1435	50	5	392	5	DDI2	1	15956933	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10		15956933	233293688	1	11972											
C1orf213	80818	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	23696043	23696043	+	5'Flank	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagacttgcaggcgaagcccAgatatcgtaggctgatccta	11	9	11	10	2	0	3	0	1	0	2	2	4	1	3	2	2	2	3	2	2	5	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:23696043A>C	ENST00000314011.4	-	0	0				ZNF436_ENST00000374608.3_5'Flank|C1orf213_ENST00000454117.1_Intron|C1orf213_ENST00000335648.3_Silent_p.R85R|C1orf213_ENST00000518821.1_Intron|C1orf213_ENST00000458053.1_Intron|Y_RNA_ENST00000364535.1_RNA|C1orf213_ENST00000437367.2_Intron	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|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(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		GGCGAAGCCCAGATATCGTAG	0.562																																					.													.	C1orf213-68	0			.						.						66	67	67					1																	23696043		2203	4300	6503	SO:0001631	upstream_gene_variant	148898	.			AAGCCCAGATATC	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"Zinc fingers, C2H2-type", "-"	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232		1.37:g.23696043A>C	Exception_encountered	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	135	36	.	0	0	0	0	0	Q658I9	RNA	SNP	ENST00000314011.4	37	CCDS233.1																																																																																			.		0.562	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		C	23696043	A	C	23696043	1	2	135	0	1	0	0	0	0	0	0	0	2036	180	7	5		5	C1orf213	1	23696043	5'Flank	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	7739110	23696043	225554578	2	11973											
C1orf173	127254	broad.mit.edu	37	chr1	75038719	75038719	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaccctgttccccttcagaaGctgctttgtctgtctcaagc	7	13	7	14	0	3	1	2	0	2	1	5	1	4	1	3	0	4	3	3	0	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:75038719G>A	ENST00000326665.5	-	14	2893	c.2675C>T	c.(2674-2676)gCt>gTt	p.A892V	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		892	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CCCTTCAGAAGCTGCTTTGTC	0.498																																					p.A892V													.	C1orf173-94	0			c.C2675T						.						248	246	247					1																	75038719		2203	4300	6503	SO:0001583	missense	127254	exon14			TCAGAAGCTGCTT																												ENST00000326665.5:c.2675C>T	1.37:g.75038719G>A	ENSP00000322609:p.Ala892Val	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	132	4	NM_001002912	0	0	0	0	0	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413575	0.25465	.	.	ENSG00000178965	ENST00000326665	T	0.12984	2.63	5.37	-7.67	0.01272	.	.	.	.	.	T	0.01835	0.0058	L	0.36672	1.1	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.44605	-0.9317	9	0.22109	T	0.4	-0.0472	0.526	0.00620	0.2864:0.2006:0.3108:0.2021	.	892	Q5RHP9	CA173_HUMAN	V	892	ENSP00000322609:A892V	ENSP00000322609:A892V	A	-	2	0	C1orf173	74811307	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.399000	0.02506	-1.229000	0.02564	0.563000	0.77884	GCT	.		0.498	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75038719	G	A	75038719	3	1	135	1	0	0	0	0	1	0	0	0	2020	971	34	2	1921	2	C1orf173	1	75038719	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	51342676	75038719	174211902	3	11974											
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	78414969	78414969	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggaggagccccagtcggAgcaggaactgcctgaccttt	8	7	13	13	1	0	1	0	1	0	0	1	5	0	5	5	4	4	1	5	4	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:78414969A>G	ENST00000370768.2	-	19	1878	c.1797T>C	c.(1795-1797)gcT>gcC	p.A599A	FUBP1_ENST00000489495.1_5'Flank|FUBP1_ENST00000370767.1_Silent_p.A599A|FUBP1_ENST00000436586.2_Silent_p.A620A	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	599					positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						CCCCAGTCGGAGCAGGAACTG	0.448			"F, N"		oligodendroglioma																																p.A599A		.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1-227	0			c.T1797C						.						64	69	67					1																	78414969		2203	4300	6503	SO:0001819	synonymous_variant	8880	exon19			AGTCGGAGCAGGA	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1797T>C	1.37:g.78414969A>G		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	69	14	NM_003902	0	0	5	26	21	Q12828	Silent	SNP	ENST00000370768.2	37	CCDS683.1																																																																																			.		0.448	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		G	78414969	A	G	78414969	2	3	135	1	0	0	0	0	0	0	0	1	6111	291	11	3		3	FUBP1	1	78414969	Silent	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	3376250	78414969	170835652	4	11975											
RBMXL1	494115	broad.mit.edu	37	chr1	89449426	89449426	+	Frame_Shift_Del	DEL	A	A	-																															actattcgtccatatttgccAaatactgtttcaagagcttt																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:89449426delA	ENST00000321792.5	-	2	511	c.84delT	c.(82-84)tttfs	p.F28fs	RBMXL1_ENST00000399794.2_Frame_Shift_Del_p.F28fs|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	28	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CATATTTGCCAAATACTGTTT	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F28fs													.	.	0			c.84delT						.						191	187	188					1																	89449426		2203	4300	6503	SO:0001589	frameshift_variant	494115	exon2			TTTGCCAAATACT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"RNA binding motif (RRM) containing"	25073	protein-coding gene	gene with protein product	"kynurenine aminotransferase III"					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.84delT	1.37:g.89449426delA	ENSP00000318415:p.Phe28fs	Somatic	525	0	1267	WXS	Illumina HiSeq	Phase_I	504	53	NM_019610	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000321792.5	37	CCDS716.1																																																																																			.		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		-	89449426	A	-	89449426	7	5	135	1	0	1	0	1	0	0	0	0	13185	127	5	0	1092	0	RBMXL1	1	89449426	Frame_Shift_Del	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	11034457	89449426	159801195	5	11976											
LRRC8C	84230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90179188	90179188	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggaatattcctttgagtaTgtccgtcaggagactggaat	10	12	12	7	2	1	2	1	1	0	1	3	5	3	4	2	3	0	1	2	3	4	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:90179188T>C	ENST00000370454.4	+	3	1314	c.1059T>C	c.(1057-1059)taT>taC	p.Y353Y	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	353					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CCTTTGAGTATGTCCGTCAGG	0.388																																					p.Y353Y		.											.	LRRC8C-97	0			c.T1059C						.						54	50	51					1																	90179188		2203	4299	6502	SO:0001819	synonymous_variant	84230	exon3			TGAGTATGTCCGT		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1059T>C	1.37:g.90179188T>C		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	146	36	NM_032270	0	0	0	0	0	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	37	CCDS725.1																																																																																			.		0.388	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90179188	T	C	90179188	2	2	135	1	0	0	0	0	0	0	0	1	9048	1471	51	3		3	LRRC8C	1	90179188	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	729762	90179188	159071433	6	11977											
IQGAP3	128239	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	156517916	156517917	+	Frame_Shift_Del	DEL	AG	AG	-																															ctcagaaagtgggaatgctcAgcaaacttctgccgaactag																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:156517916_156517917delAG	ENST00000361170.2	-	19	2262_2263	c.2252_2253delCT	c.(2251-2253)gctfs	p.A751fs		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	751	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGAATGCTCAGCAAACTTCTG	0.579																																					p.751_751del		.											.	IQGAP3-96	0			c.2252_2253del						.																																			SO:0001589	frameshift_variant	128239	exon19			.	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.2252_2253delCT	1.37:g.156517916_156517917delAG	ENSP00000354451:p.Ala751fs	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	131	33	NM_178229	0	0	0	0	0	Q5T3H8	Frame_Shift_Del	DEL	ENST00000361170.2	37	CCDS1144.1																																																																																			.		0.579	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		-	156517917	AG	-	156517916	7	5	135	1	0	1	0	1	0	0	0	0	7837	175	7	0	2722	0	IQGAP3	1	156517916	Frame_Shift_Del	DEL	AG	TCGA-HE-A5NK-01A-11D-A26P-10	66338728	156517916	92732705	7	11978											
LY9	4063	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	160786562	160786562	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcaatgtctcatggagAagcagtgaaaatcaccccaa	15	7	7	12	0	3	2	3	1	1	1	4	3	3	2	3	1	1	1	3	1	5	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:160786562A>C	ENST00000263285.6	+	5	1281	c.1251A>C	c.(1249-1251)agA>agC	p.R417S	LY9_ENST00000341032.4_Intron|LY9_ENST00000392203.4_Intron|LY9_ENST00000368040.1_Missense_Mutation_p.R69S|LY9_ENST00000368037.5_Missense_Mutation_p.R417S|LY9_ENST00000368041.2_Intron			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	417	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TCTCATGGAGAAGCAGTGAAA	0.527																																					p.R417S													.	LY9-91	0			c.A1251C						.						159	138	145					1																	160786562		2203	4300	6503	SO:0001583	missense	4063	exon5			ATGGAGAAGCAGT	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.1251A>C	1.37:g.160786562A>C	ENSP00000263285:p.Arg417Ser	Somatic	246	1		WXS	Illumina HiSeq	Phase_I	233	59	NM_001261456	0	0	1	1	0	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	37	CCDS30916.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.295086	0.23564	.	.	ENSG00000122224	ENST00000368041;ENST00000368040;ENST00000263285;ENST00000368037;ENST00000368035	T;T;T	0.37235	1.21;1.21;1.21	4.75	-0.968	0.10313	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.07818	0.0196	L	0.41573	1.285	0.09310	N	1	B;B;B	0.22909	0.024;0.063;0.077	B;B;B	0.25405	0.06;0.022;0.038	T	0.37979	-0.9682	9	0.14252	T	0.57	-1.3404	2.8809	0.05647	0.461:0.0:0.1909:0.3481	.	69;417;417	Q5VYI1;Q9HBG7-2;Q9HBG7	.;.;LY9_HUMAN	S	417;69;417;377;69	ENSP00000357019:R69S;ENSP00000263285:R417S;ENSP00000357014:R69S	ENSP00000263285:R417S	R	+	3	2	LY9	159053186	0.000000	0.05858	0.003000	0.11579	0.128000	0.20619	0.088000	0.14979	-0.120000	0.11809	0.455000	0.32223	AGA	.		0.527	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		C	160786562	A	C	160786562	3	2	135	1	0	0	0	0	1	0	0	0	9126	243	9	5	1401	5	LY9	1	160786562	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	4268646	160786562	88464059	8	11979											
SLC19A2	10560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	169446750	169446750	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actttctggtacatgcccagGtccaccacactgtagatata	11	11	7	12	0	1	1	0	0	1	1	2	1	2	1	3	2	2	2	3	2	4	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:169446750G>A	ENST00000236137.5	-	2	686	c.450C>T	c.(448-450)gaC>gaT	p.D150D	SLC19A2_ENST00000367804.4_Intron	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	150					folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|thiamine transport (GO:0015888)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid transporter activity (GO:0008517)|thiamine transmembrane transporter activity (GO:0015234)|thiamine uptake transmembrane transporter activity (GO:0015403)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.208)				Thiamine(DB00152)	ACATGCCCAGGTCCACCACAC	0.478																																					p.D150D		.											.	SLC19A2-90	0			c.C450T						.						93	96	95					1																	169446750		2203	4300	6503	SO:0001819	synonymous_variant	10560	exon2			GCCCAGGTCCACC	AF135488	CCDS1280.1	1q23.3	2013-05-22			ENSG00000117479	ENSG00000117479		"Solute carriers"	10938	protein-coding gene	gene with protein product		603941		TRMA		9399900, 10391221	Standard	NM_006996		Approved	THTR1	uc001gge.4	O60779	OTTHUMG00000035452	ENST00000236137.5:c.450C>T	1.37:g.169446750G>A		Somatic	179	0		WXS	Illumina HiSeq	Phase_I	176	52	NM_006996	0	0	0	0	0	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Silent	SNP	ENST00000236137.5	37	CCDS1280.1																																																																																			.		0.478	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996		A	169446750	G	A	169446750	2	1	135	1	0	0	0	0	0	0	0	1	14461	1252	44	2		2	SLC19A2	1	169446750	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	8660188	169446750	79803871	9	11980											
CACNA1E	777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	181701628	181701628	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctcaacagagaggaggcGccgaccatgaacccgctcaa	12	3	11	15	3	2	2	2	1	0	1	2	5	2	3	4	2	2	1	4	2	3	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:181701628G>A	ENST00000367573.2	+	20	2406	c.2406G>A	c.(2404-2406)gcG>gcA	p.A802A	CACNA1E_ENST00000526775.1_Silent_p.A783A|CACNA1E_ENST00000367567.4_Silent_p.A409A|CACNA1E_ENST00000360108.3_Silent_p.A783A|CACNA1E_ENST00000367570.1_Silent_p.A802A|CACNA1E_ENST00000357570.5_Silent_p.A753A|CACNA1E_ENST00000358338.5_Silent_p.A734A	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	802					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GAGAGGAGGCGCCGACCATGa	0.657																																					p.A802A		.											.	CACNA1E-95	0			c.G2406A						.						39	57	51					1																	181701628		1759	3301	5060	SO:0001819	synonymous_variant	777	exon20			GGAGGCGCCGACC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2406G>A	1.37:g.181701628G>A		Somatic	328	0		WXS	Illumina HiSeq	Phase_I	380	44	NM_001205293	0	0	0	0	0	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			.		0.657	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181701628	G	A	181701628	2	1	135	1	0	0	0	0	0	0	0	1	2548	1074	38	1		1	CACNA1E	1	181701628	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	12254878	181701628	67548993	10	11981											
CABC1	56997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	227172964	227172964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctctccccagatcatcaggGctgctgccgacagggacagg	8	6	12	15	1	3	1	2	0	1	1	4	3	3	2	4	3	2	2	4	3	0	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:227172964G>A	ENST00000366779.1	+	19	4353	c.1582G>A	c.(1582-1584)Gct>Act	p.A528T	ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000458507.2_Missense_Mutation_p.A249T|ADCK3_ENST00000433743.2_Missense_Mutation_p.A202T|ADCK3_ENST00000366778.1_Missense_Mutation_p.A476T|ADCK3_ENST00000366777.3_Missense_Mutation_p.A528T			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	528					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						GATCATCAGGGCTGCTGCCGA	0.632																																					p.A528T		.											.	ADCK3-361	0			c.G1582A						.						119	116	117					1																	227172964		2203	4300	6503	SO:0001583	missense	56997	exon14			ATCAGGGCTGCTG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"coenzyme Q8 homolog (yeast)"	606980	"chaperone-ABC1 (activity of bc1 complex, S.pombe)-like", "chaperone, ABC1 activity of bc1 complex like (S. pombe)", "chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.1582G>A	1.37:g.227172964G>A	ENSP00000355741:p.Ala528Thr	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	62	17	NM_020247	0	0	0	0	0	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Missense_Mutation	SNP	ENST00000366779.1	37	CCDS1557.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.998025	0.93227	.	.	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000458507;ENST00000366775;ENST00000405743;ENST00000433743	T;T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1;0.1	5.69	5.69	0.88448	.	0.105243	0.64402	D	0.000005	D	0.82554	0.5062	H	0.94847	3.59	0.58432	D	0.999995	D;D	0.64830	0.982;0.994	P;D	0.63033	0.796;0.91	D	0.87070	0.2159	10	0.87932	D	0	-11.9896	19.815	0.96564	0.0:0.0:1.0:0.0	.	202;528	E7EVZ8;Q8NI60	.;ADCK3_HUMAN	T	528;476;528;453;249;373;479;202	ENSP00000355741:A528T;ENSP00000355740:A476T;ENSP00000355739:A528T;ENSP00000355738:A453T;ENSP00000403704:A249T;ENSP00000355737:A373T;ENSP00000404550:A202T	ENSP00000355737:A373T	A	+	1	0	ADCK3	225239587	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.953000	0.56699	2.681000	0.91329	0.561000	0.74099	GCT	.		0.632	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247		A	227172964	G	A	227172964	3	1	135	1	0	0	0	0	1	0	0	0	2533	1203	42	2	1632	2	CABC1	1	227172964	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	45471336	227172964	22077657	11	11982											
FMN2	56776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	240370577	240370577	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctgtggtctgctgggcAaggacagcctgggtcacagc	6	9	14	12	0	3	0	1	0	2	0	3	1	3	1	2	4	3	2	2	4	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:240370577A>T	ENST00000319653.9	+	5	2695	c.2465A>T	c.(2464-2466)cAa>cTa	p.Q822L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	822	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TCTGCTGGGCAAGGACAGCCT	0.537																																					p.Q822L		.											.	FMN2-145	0			c.A2465T						.						74	71	72					1																	240370577		2203	4300	6503	SO:0001583	missense	56776	exon5			CTGGGCAAGGACA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2465A>T	1.37:g.240370577A>T	ENSP00000318884:p.Gln822Leu	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	121	32	NM_020066	0	0	0	0	0	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	A	7.760	0.705185	0.15172	.	.	ENSG00000155816	ENST00000319653	T	0.31510	1.49	4.09	4.09	0.47781	Actin-binding FH2/DRF autoregulatory (1);	0.425372	0.19864	N	0.104352	T	0.30823	0.0777	L	0.57536	1.79	0.80722	D	1	B	0.30482	0.281	B	0.32533	0.147	T	0.07849	-1.0751	9	.	.	.	.	12.1017	0.53788	1.0:0.0:0.0:0.0	.	822	Q9NZ56	FMN2_HUMAN	L	822	ENSP00000318884:Q822L	.	Q	+	2	0	FMN2	238437200	0.247000	0.23920	0.447000	0.26932	0.071000	0.16799	1.728000	0.38105	1.842000	0.53543	0.454000	0.30748	CAA	.		0.537	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240370577	A	T	240370577	3	4	135	1	0	0	0	0	1	0	0	0	5969	130	5	5	2483	5	FMN2	1	240370577	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	13197613	240370577	8880044	12	11983											
KIDINS220	57498	broad.mit.edu	37	chr2	8919107	8919107	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgcttagtccacgactatTaaggaacacaggcaagtgga	14	9	10	8	1	0	0	0	0	0	0	1	3	1	2	1	3	2	2	1	3	5	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:8919107T>A	ENST00000256707.3	-	19	2714	c.2533A>T	c.(2533-2535)Aat>Tat	p.N845Y	KIDINS220_ENST00000473731.1_Missense_Mutation_p.N845Y|KIDINS220_ENST00000418530.1_Missense_Mutation_p.N803Y|KIDINS220_ENST00000427284.1_Missense_Mutation_p.N845Y|KIDINS220_ENST00000319688.5_Missense_Mutation_p.N846Y	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	845	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCACGACTATTAAGGAACACA	0.418																																					p.N845Y													.	KIDINS220-93	0			c.A2533T						.						220	199	206					2																	8919107		1903	4132	6035	SO:0001583	missense	57498	exon19			GACTATTAAGGAA	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2533A>T	2.37:g.8919107T>A	ENSP00000256707:p.Asn845Tyr	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	115	3	NM_020738	0	0	1	1	0	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.128451	0.56721	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.64	5.64	0.86602	KAP P-loop (1);	0.000000	0.85682	D	0.000000	T	0.54143	0.1840	M	0.63428	1.95	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.999;0.986;1.0;1.0	T	0.56251	-0.8010	10	0.72032	D	0.01	.	16.1617	0.81721	0.0:0.0:0.0:1.0	.	846;846;803;845	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	Y	592;529;845;845;803;845;846;846	ENSP00000420364:N592Y;ENSP00000256707:N845Y;ENSP00000411849:N845Y;ENSP00000414923:N803Y;ENSP00000418974:N845Y;ENSP00000419964:N846Y;ENSP00000319947:N846Y	ENSP00000256707:N845Y	N	-	1	0	KIDINS220	8836558	1.000000	0.71417	0.313000	0.25210	0.057000	0.15508	7.948000	0.87774	2.275000	0.75901	0.528000	0.53228	AAT	.		0.418	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		A	8919107	T	A	8919107	3	1	135	1	0	0	0	0	1	0	0	0	8292	1754	61	5	2830	5	KIDINS220	2	8919107	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10		8919107	234280266	13	11984											
VWA3B	200403	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	98907042	98907042	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagatcccctcaaaggacaGaaggttattgcaagatgtga	14	8	10	9	0	1	4	1	1	0	3	2	5	2	5	3	2	1	2	3	2	4	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:98907042G>A	ENST00000477737.1	+	23	3318	c.3114G>A	c.(3112-3114)caG>caA	p.Q1038Q	VWA3B_ENST00000490947.2_3'UTR	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1038										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TCAAAGGACAGAAGGTTATTG	0.323																																					p.Q1038Q													.	VWA3B-139	0			c.G3114A						.						109	101	103					2																	98907042		1815	4071	5886	SO:0001819	synonymous_variant	200403	exon23			AGGACAGAAGGTT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.3114G>A	2.37:g.98907042G>A		Somatic	324	1		WXS	Illumina HiSeq	Phase_I	353	59	NM_144992	0	0	0	0	0	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	7.644	0.681410	0.14907	.	.	ENSG00000168658	ENST00000473149	.	.	.	4.52	4.52	0.55395	.	.	.	.	.	T	0.58466	0.2124	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55366	-0.8152	4	.	.	.	.	8.6822	0.34216	0.1025:0.0:0.8975:0.0	.	.	.	.	K	449	.	.	E	+	1	0	VWA3B	98273474	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.549000	0.45803	2.499000	0.84300	0.557000	0.71058	GAA	.		0.323	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98907042	G	A	98907042	2	1	135	1	0	0	0	0	0	0	0	1	17274	933	33	2		2	VWA3B	2	98907042	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	89987935	98907042	144292331	14	11985											
NEB	4703	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152426612	152426612	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacatcgctctgcagttcgtAggccttcttggcctgaatca	7	12	9	13	2	3	1	1	1	2	0	5	1	3	1	2	2	1	4	2	2	2	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:152426612A>T	ENST00000172853.10	-	81	12457	c.12310T>A	c.(12310-12312)Tac>Aac	p.Y4104N	NEB_ENST00000409198.1_Missense_Mutation_p.Y4104N|NEB_ENST00000427231.2_Missense_Mutation_p.Y5805N|NEB_ENST00000604864.1_Missense_Mutation_p.Y5805N|NEB_ENST00000603639.1_Missense_Mutation_p.Y5805N|NEB_ENST00000397345.3_Missense_Mutation_p.Y5805N			P20929	NEBU_HUMAN	nebulin	4104					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGCAGTTCGTAGGCCTTCTTG	0.507																																					p.Y5805N													.	NEB-145	0			c.T17413A						.						40	40	40					2																	152426612		2059	4189	6248	SO:0001583	missense	4703	exon109			GTTCGTAGGCCTT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.12310T>A	2.37:g.152426612A>T	ENSP00000172853:p.Tyr4104Asn	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	148	32	NM_001271208	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	A	19.45	3.830650	0.71258	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.66626	0.2808	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.999	T	0.69003	-0.5260	10	0.54805	T	0.06	.	16.4101	0.83708	1.0:0.0:0.0:0.0	.	4104;535	P20929;Q14215	NEBU_HUMAN;.	N	4104;5805;5805;153;535;4104	ENSP00000386259:Y4104N;ENSP00000380505:Y5805N;ENSP00000416578:Y5805N;ENSP00000410961:Y535N;ENSP00000172853:Y4104N	ENSP00000172853:Y4104N	Y	-	1	0	NEB	152134858	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.339000	0.96797	2.280000	0.76307	0.460000	0.39030	TAC	.		0.507	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152426612	A	T	152426612	3	4	135	1	0	0	0	0	1	0	0	0	10328	420	15	5	8569	5	NEB	2	152426612	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	53519570	152426612	90772761	15	11986											
CCDC141	285025	broad.mit.edu	37	chr2	179701995	179701995	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatgctctctggatgttcAgcactgattctgtgtaaggc	8	14	10	9	0	4	1	2	1	2	0	5	2	4	2	0	2	2	4	0	2	1	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:179701995A>T	ENST00000420890.2	-	23	4068	c.3951T>A	c.(3949-3951)gcT>gcA	p.A1317A	CCDC141_ENST00000295723.5_Silent_p.A742A|CCDC141_ENST00000480419.1_5'UTR	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1317										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CTGGATGTTCAGCACTGATTC	0.493																																					p.A1317A													.	CCDC141-78	0			c.T3951A						.						120	105	110					2																	179701995		2203	4300	6503	SO:0001819	synonymous_variant	285025	exon23			ATGTTCAGCACTG	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3951T>A	2.37:g.179701995A>T		Somatic	190	0		WXS	Illumina HiSeq	Phase_I	228	4	NM_173648	0	0	0	0	0	H7C0P1|J3KNW6|Q8N8H3	Silent	SNP	ENST00000420890.2	37																																																																																				.		0.493	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		T	179701995	A	T	179701995	2	4	135	1	0	0	0	0	0	0	0	1	2781	175	7	5		5	CCDC141	2	179701995	Silent	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	27275383	179701995	63497378	16	11987											
PLCL1	5334	ucsc.edu;bcgsc.ca	37	chr2	198949559	198949559	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gagctttgaaaatgggctgtCgaagcgttgaactcgatgta	11	11	13	6	3	0	2	0	2	0	0	2	5	0	2	0	1	3	4	0	1	5	3	rs376872615		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:198949559C>G	ENST00000428675.1	+	2	1716	c.1318C>G	c.(1318-1320)Cga>Gga	p.R440G	PLCL1_ENST00000437704.2_Missense_Mutation_p.R342G	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	440	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	AATGGGCTGTCGAAGCGTTGA	0.408																																					p.R440G													.	PLCL1-228	0			c.C1318G						.						61	59	59					2																	198949559		2203	4300	6503	SO:0001583	missense	5334	exon2			GGCTGTCGAAGCG	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"phospholipase C related, but catalytically inactive protein", "protein phosphatase 1, regulatory subunit 127"	600597	"phospholipase C, epsilon"	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1318C>G	2.37:g.198949559C>G	ENSP00000402861:p.Arg440Gly	Somatic	238	3		WXS	Illumina HiSeq		282	62	NM_006226	0	0	0	0	0	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	C	13.17	2.158059	0.38119	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.81415	-1.49;-1.49	5.94	2.89	0.33648	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.000000	0.53938	D	0.000051	D	0.93449	0.7910	H	0.98466	4.24	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96190	0.9137	9	.	.	.	.	15.4712	0.75441	0.4363:0.5637:0.0:0.0	.	440;366	Q15111;B4DYZ4	PLCL1_HUMAN;.	G	440;342	ENSP00000402861:R440G;ENSP00000414138:R342G	.	R	+	1	2	PLCL1	198657804	0.997000	0.39634	1.000000	0.80357	0.930000	0.56654	1.426000	0.34870	1.501000	0.48654	0.561000	0.74099	CGA	.		0.408	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		G	198949559	C	G	198949559	3	3	135	1	0	0	0	0	1	0	0	0	12065	876	31	4	1324	4	PLCL1	2	198949559	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	19247564	198949559	44249814	17	11988											
CPS1	1373	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	211471605	211471605	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctacctcaatggaatactGcatcattgaagtgaatgcca	13	11	7	10	0	2	2	2	2	0	0	3	3	3	3	3	1	4	1	3	1	6	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:211471605G>T	ENST00000233072.5	+	18	2328	c.2132G>T	c.(2131-2133)tGc>tTc	p.C711F	CPS1_ENST00000451903.2_Missense_Mutation_p.C260F|CPS1_ENST00000430249.2_Missense_Mutation_p.C717F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	711	ATP-grasp 1.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ATGGAATACTGCATCATTGAA	0.458																																					p.C717F													.	CPS1-162	0			c.G2150T						.						129	110	116					2																	211471605		2203	4300	6503	SO:0001583	missense	1373	exon19			AATACTGCATCAT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"carbamoyl-phosphate synthetase 1, mitochondrial"				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2132G>T	2.37:g.211471605G>T	ENSP00000233072:p.Cys711Phe	Somatic	214	1		WXS	Illumina HiSeq	Phase_I	276	51	NM_001122633	0	0	2	2	0	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245638	0.59103	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.96967	-4.19;-4.19;-4.19	5.83	5.83	0.93111	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.152323	0.64402	D	0.000009	D	0.94712	0.8294	L	0.35341	1.055	0.41705	D	0.989423	D;D	0.53151	0.958;0.958	P;P	0.54060	0.741;0.741	D	0.93061	0.6474	10	0.41790	T	0.15	-24.117	8.7971	0.34885	0.0797:0.0:0.7691:0.1511	.	721;711	Q59HF8;P31327	.;CPSM_HUMAN	F	717;719;711;260	ENSP00000402608:C717F;ENSP00000233072:C711F;ENSP00000406136:C260F	ENSP00000233072:C711F	C	+	2	0	CPS1	211179850	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.300000	0.65721	2.781000	0.95711	0.586000	0.80456	TGC	.		0.458	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			T	211471605	G	T	211471605	3	4	135	1	0	0	0	0	1	0	0	0	3829	1319	46	4	2224	4	CPS1	2	211471605	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	12522046	211471605	31727768	18	11989											
IKZF2	22807	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	213872649	213872649	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgattgtgcttggcgggTgctgcatcagagggtgaagg	7	9	18	7	2	1	2	1	1	0	1	1	3	1	2	0	4	4	3	0	4	1	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:213872649T>C	ENST00000434687.1	-	9	1325	c.1016A>G	c.(1015-1017)cAc>cGc	p.H339R	IKZF2_ENST00000451136.2_Missense_Mutation_p.H267R|IKZF2_ENST00000457361.1_Missense_Mutation_p.H339R|IKZF2_ENST00000342002.2_Missense_Mutation_p.H345R|IKZF2_ENST00000421754.2_Missense_Mutation_p.H265R|AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000374327.4_Missense_Mutation_p.H194R|IKZF2_ENST00000413091.3_3'UTR|IKZF2_ENST00000374319.4_Missense_Mutation_p.H313R			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	339					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GCTTGGCGGGTGCTGCATCAG	0.498																																					p.H339R													.	IKZF2-226	0			c.A1016G						.						106	97	100					2																	213872649		2203	4300	6503	SO:0001583	missense	22807	exon8			GGCGGGTGCTGCA	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	13177	protein-coding gene	gene with protein product		606234	"zinc finger protein, subfamily 1A, 2 (Helios)"	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.1016A>G	2.37:g.213872649T>C	ENSP00000412869:p.His339Arg	Somatic	173	1		WXS	Illumina HiSeq	Phase_I	221	40	NM_016260	0	0	0	0	0	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Missense_Mutation	SNP	ENST00000434687.1	37	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.391634	0.25118	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327	T;T;T;T;T;T;T	0.13901	3.3;3.27;3.3;3.33;3.27;3.31;2.55	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.33411	0.0862	M	0.64997	1.995	0.80722	D	1	D;D;D;B;D;D	0.89917	0.993;0.996;1.0;0.092;0.997;0.989	D;D;D;B;D;D	0.85130	0.943;0.99;0.997;0.07;0.989;0.978	T	0.01966	-1.1238	10	0.45353	T	0.12	-8.9537	12.3172	0.54964	0.0:0.0:0.1409:0.859	.	267;265;194;313;339;117	C9JCG7;C9JTM9;F5H8M1;Q9UKS7-2;Q9UKS7;Q96LD7	.;.;.;.;IKZF2_HUMAN;.	R	339;345;339;313;267;265;194	ENSP00000410447:H339R;ENSP00000342876:H345R;ENSP00000412869:H339R;ENSP00000363439:H313R;ENSP00000395203:H267R;ENSP00000399574:H265R;ENSP00000363447:H194R	ENSP00000342876:H345R	H	-	2	0	IKZF2	213580894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.696000	0.61774	2.288000	0.76882	0.533000	0.62120	CAC	.		0.498	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260		C	213872649	T	C	213872649	3	2	135	1	0	0	0	0	1	0	0	0	7636	1696	59	3	568	3	IKZF2	2	213872649	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	2401044	213872649	29326724	19	11990											
ABCB6	10058	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220075010	220075011	+	Missense_Mutation	DNP	CA	CA	AG																															gatctggtcagcattgaccaCagttgagagcctgagaagtc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:220075010_220075011CA>AG	ENST00000265316.3	-	18	2677_2678	c.2361_2362TG>CT	c.(2359-2364)acTGtg>acCTtg	p.V788L	ABCB6_ENST00000439002.2_Missense_Mutation_p.V742L	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	788	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCATTGACCACAGTTGAGAGCC	0.55																																					p.V788L													.	ABCB6-153	0			c.T2361C						.																																			SO:0001583	missense	10058	exon18			GACCACAGTTGAG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.2361_2362delinsAG	2.37:g.220075010_220075011delinsAG	ENSP00000265316:p.Val788Leu	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	178	28	NM_005689	0	0	0	0	0	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	DNP	ENST00000265316.3	37	CCDS2436.1																																																																																			.		0.55	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		AG	220075011	CA	AG	220075010	3	1	135	1	0	0	0	0	1	0	0	0	45	478	17	4	174	4	ABCB6	2	220075010	Missense_Mutation	DNP	CA	TCGA-HE-A5NK-01A-11D-A26P-10	6202361	220075010	23124363	20	11991											
EIF4E2	9470	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233428989	233428989	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggaggttttatagccacatGgtacgtcctggggacctgac	8	11	13	9	1	0	1	0	1	0	0	1	3	1	3	3	5	2	2	3	5	3	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:233428989G>T	ENST00000258416.3	+	4	976	c.303G>T	c.(301-303)atG>atT	p.M101I	EIF4E2_ENST00000409394.1_Missense_Mutation_p.M56I|EIF4E2_ENST00000409322.1_Missense_Mutation_p.M56I|EIF4E2_ENST00000409514.1_Missense_Mutation_p.M101I|EIF4E2_ENST00000409167.3_Missense_Mutation_p.M56I|EIF4E2_ENST00000409495.1_Missense_Mutation_p.M101I|EIF4E2_ENST00000409098.1_Missense_Mutation_p.M101I	NM_004846.2	NP_004837.1	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E family member 2	101					cytokine-mediated signaling pathway (GO:0019221)|in utero embryonic development (GO:0001701)|negative regulation of translation (GO:0017148)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATAGCCACATGGTACGTCCTG	0.458																																					p.M101I													.	EIF4E2-90	0			c.G303T						.						48	45	46					2																	233428989		2203	4300	6503	SO:0001583	missense	9470	exon4			CCACATGGTACGT	AF038957	CCDS2496.1, CCDS63158.1, CCDS63159.1, CCDS74671.1	2q37.1	2008-02-05	2006-11-13	2004-10-30	ENSG00000135930	ENSG00000135930			3293	protein-coding gene	gene with protein product		605895	"eukaryotic translation initiation factor 4E-like 3"	EIF4EL3		9653160, 9582349	Standard	XM_005246975		Approved	IF4e, 4EHP	uc002vta.3	O60573	OTTHUMG00000133256	ENST00000258416.3:c.303G>T	2.37:g.233428989G>T	ENSP00000258416:p.Met101Ile	Somatic	178	1		WXS	Illumina HiSeq	Phase_I	256	49	NM_004846	0	0	12	28	16	B8ZZJ9|O75349	Missense_Mutation	SNP	ENST00000258416.3	37	CCDS2496.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970766	0.53614	.	.	ENSG00000135930	ENST00000258416;ENST00000409514;ENST00000409098;ENST00000409495;ENST00000409167;ENST00000409322;ENST00000409394;ENST00000454501	T;T;T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31;1.31;1.31	5.65	5.65	0.86999	Translation Initiation factor eIF- 4e-like  domain (2);	0.000000	0.85682	D	0.000000	T	0.16257	0.0391	N	0.01618	-0.8	0.53005	D	0.999961	B;B;B	0.15473	0.013;0.003;0.002	B;B;B	0.24974	0.018;0.057;0.004	T	0.18587	-1.0332	10	0.08599	T	0.76	-10.3692	17.2336	0.86991	0.0:0.0:1.0:0.0	.	56;101;101	B4E1E4;B8ZZJ9;O60573	.;.;IF4E2_HUMAN	I	101;101;101;101;56;56;56;96	ENSP00000258416:M101I;ENSP00000387336:M101I;ENSP00000386996:M101I;ENSP00000386876:M101I;ENSP00000387328:M56I;ENSP00000386424:M56I;ENSP00000386983:M56I;ENSP00000390904:M96I	ENSP00000258416:M101I	M	+	3	0	EIF4E2	233137233	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.876000	0.87215	2.660000	0.90430	0.655000	0.94253	ATG	.		0.458	EIF4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257033.2	NM_004846		T	233428989	G	T	233428989	3	4	135	1	0	0	0	0	1	0	0	0	5043	1348	47	4	317	4	EIF4E2	2	233428989	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	13353979	233428989	9770384	21	11992											
TMEM43	79188	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	14183165	14183165	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgccttctgtgtggccacctCgctgaccctgctgaccgtgg	3	11	12	15	2	1	2	0	2	1	0	2	2	1	2	5	2	2	2	5	2	0	1	rs63750743		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:14183165C>T	ENST00000306077.4	+	12	1327	c.1073C>T	c.(1072-1074)tCg>tTg	p.S358L	RP11-434D12.1_ENST00000608606.1_Intron|RP11-434D12.1_ENST00000601399.1_Intron	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	358			S -> L (in ARVD5). {ECO:0000269|PubMed:18313022}.		nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						GTGGCCACCTCGCTGACCCTG	0.602																																					p.S358L		.											.	TMEM43-91	0			c.C1073T	GRCh37	CM081452	TMEM43	M	rs63750743	.						135	110	119					3																	14183165		2203	4300	6503	SO:0001583	missense	79188	exon12			CCACCTCGCTGAC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.1073C>T	3.37:g.14183165C>T	ENSP00000303992:p.Ser358Leu	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	155	14	NM_024334	0	0	25	34	9	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	C	35	5.493272	0.96339	.	.	ENSG00000170876	ENST00000306077	T	0.35973	1.28	5.71	5.71	0.89125	.	0.066812	0.64402	D	0.000008	T	0.58293	0.2112	L	0.57536	1.79	0.80722	A	1	D	0.89917	1.0	D	0.69142	0.962	T	0.55711	-0.8098	9	0.52906	T	0.07	-15.2636	19.8516	0.96743	0.0:1.0:0.0:0.0	rs63750743	358	Q9BTV4	TMM43_HUMAN	L	358	ENSP00000303992:S358L	ENSP00000303992:S358L	S	+	2	0	TMEM43	14158166	1.000000	0.71417	0.940000	0.37924	0.911000	0.54048	7.205000	0.77881	2.685000	0.91497	0.585000	0.79938	TCG	.		0.602	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		T	14183165	C	T	14183165	3	4	135	1	0	0	0	0	1	0	0	0	16199	893	31	1	1119	1	TMEM43	3	14183165	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		14183165	183839265	22	11993											
SMARCC1	6599	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	47718172	47718172	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagggggtatcagctaataCattaaaatgaggagtaggag	16	8	14	3	0	1	2	1	1	0	1	1	4	1	4	0	4	2	3	0	4	6	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:47718172C>A	ENST00000254480.5	-	17	1791	c.1672G>T	c.(1672-1674)Gta>Tta	p.V558L	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	558					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		TCAGCTAATACATTAAAATGA	0.463																																					p.V558L		.											.	SMARCC1-228	0			c.G1672T						.						73	70	71					3																	47718172		2203	4300	6503	SO:0001583	missense	6599	exon17			CTAATACATTAAA	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1672G>T	3.37:g.47718172C>A	ENSP00000254480:p.Val558Leu	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	131	19	NM_003074	0	0	0	1	1	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	37	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	C	35	5.457122	0.96223	.	.	ENSG00000173473	ENST00000254480	T	0.55760	0.5	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.77294	0.4109	M	0.85099	2.735	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.78959	-0.1998	10	0.87932	D	0	-21.3909	19.4236	0.94732	0.0:1.0:0.0:0.0	.	558	Q92922	SMRC1_HUMAN	L	558	ENSP00000254480:V558L	ENSP00000254480:V558L	V	-	1	0	SMARCC1	47693176	1.000000	0.71417	0.995000	0.50966	0.958000	0.62258	7.580000	0.82523	2.937000	0.99478	0.650000	0.86243	GTA	.		0.463	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			A	47718172	C	A	47718172	3	1	135	1	0	0	0	0	1	0	0	0	14807	478	17	4	1693	4	SMARCC1	3	47718172	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	33535007	47718172	150304258	23	11994											
COL7A1	1294	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48604393	48604393	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accaacactgccaggtggccCtgggggaccagcagagccat	10	4	13	14	0	0	1	0	0	0	1	0	2	0	2	5	4	4	1	5	4	1	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:48604393C>A	ENST00000328333.8	-	110	8280	c.8173G>T	c.(8173-8175)Ggg>Tgg	p.G2725W	COL7A1_ENST00000470076.1_5'Flank|COL7A1_ENST00000454817.1_Missense_Mutation_p.G2693W	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2725	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCAGGTGGCCCTGGGGGACCA	0.617																																					p.G2725W													.	COL7A1-160	0			c.G8173T						.						24	27	26					3																	48604393		2203	4299	6502	SO:0001583	missense	1294	exon110			GTGGCCCTGGGGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.8173G>T	3.37:g.48604393C>A	ENSP00000332371:p.Gly2725Trp	Somatic	87	1		WXS	Illumina HiSeq	Phase_I	79	15	NM_000094	0	0	3	6	3	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	9.532	1.111099	0.20714	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.99369	-5.78;-5.78	4.86	4.86	0.63082	.	0.000000	0.41938	D	0.000791	D	0.99664	0.9875	H	0.98005	4.125	0.53005	D	0.999962	D	0.89917	1.0	D	0.97110	1.0	D	0.97321	0.9944	10	0.87932	D	0	.	16.16	0.81698	0.0:1.0:0.0:0.0	.	2725	Q02388	CO7A1_HUMAN	W	2725;2693	ENSP00000332371:G2725W;ENSP00000412569:G2693W	ENSP00000332371:G2725W	G	-	1	0	COL7A1	48579397	1.000000	0.71417	0.985000	0.45067	0.058000	0.15608	6.966000	0.76073	2.260000	0.74910	0.467000	0.42956	GGG	.		0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48604393	C	A	48604393	3	1	135	1	0	0	0	0	1	0	0	0	3710	681	24	4	697	4	COL7A1	3	48604393	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	886221	48604393	149418037	24	11995											
APEH	327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49718019	49718019	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcacaattgaccaggaccTcatggtggcacagttttcca	10	10	9	12	0	2	1	2	1	0	0	3	2	3	2	3	3	0	3	3	3	1	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:49718019T>C	ENST00000296456.5	+	14	1656	c.1256T>C	c.(1255-1257)cTc>cCc	p.L419P	APEH_ENST00000438011.1_Missense_Mutation_p.L419P	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	419					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GACCAGGACCTCATGGTGGCA	0.572																																					p.L419P		.											.	APEH-91	0			c.T1256C						.						136	107	117					3																	49718019		2203	4300	6503	SO:0001583	missense	327	exon14			AGGACCTCATGGT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1256T>C	3.37:g.49718019T>C	ENSP00000296456:p.Leu419Pro	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	269	67	NM_001640	0	0	48	84	36	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.573571	0.86542	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.39787	1.06;1.06	5.44	5.44	0.79542	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.59074	0.2167	M	0.66939	2.045	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.61201	0.885;0.885	T	0.58228	-0.7673	10	0.36615	T	0.2	-28.7761	15.1365	0.72572	0.0:0.0:0.0:1.0	.	419;419	C9JIF9;P13798	.;ACPH_HUMAN	P	419	ENSP00000296456:L419P;ENSP00000415862:L419P	ENSP00000296456:L419P	L	+	2	0	APEH	49693023	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.147000	0.77382	2.056000	0.61249	0.459000	0.35465	CTC	.		0.572	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			C	49718019	T	C	49718019	3	2	135	1	0	0	0	0	1	0	0	0	768	1551	54	3	1310	3	APEH	3	49718019	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	1113626	49718019	148304411	25	11996											
CACNA1D	776	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	53844325	53844325	+	Splice_Site	DEL	A	A	-																															gcggacagcttggtggaggcAgtgagtacggttcttggccg																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:53844325delA	ENST00000350061.5	+	47	6703	c.6192delA	c.(6190-6192)gca>gc	p.A2064fs	CACNA1D_ENST00000544977.1_3'UTR|CACNA1D_ENST00000288139.4_Splice_Site_p.A2084fs|CACNA1D_ENST00000422281.2_Splice_Site_p.A2040fs	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2064					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGTGGAGGCAGTGAGTACGG	0.612																																					p.A2084fs		.											.	CACNA1D-100	0			c.6252delA						.						53	60	57					3																	53844325		2203	4300	6503	SO:0001630	splice_region_variant	776	exon48			.	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6192+1A>-	3.37:g.53844325delA		Somatic	376	0		WXS	Illumina HiSeq	Phase_I	472	86	NM_000720	0	0	0	0	0	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Frame_Shift_Del	DEL	ENST00000350061.5	37	CCDS46848.1																																																																																			.		0.612	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	Frame_Shift_Del	-	53844325	A	-	53844325	8	5	135	1	0	1	0	1	0	0	1	0	2547	202	7	0	6550	0	CACNA1D	3	53844325	Splice_Site	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	4126306	53844325	144178105	26	11997											
SLC15A2	6565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121649781	121649781	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggtgtgtctgcttatagaActgtgcaaagaggagagtaa	13	11	13	4	0	1	3	0	0	1	3	1	4	1	3	0	2	3	3	0	2	5	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:121649781A>G	ENST00000489711.1	+	18	2036	c.1648A>G	c.(1648-1650)Act>Gct	p.T550A	SLC15A2_ENST00000465060.1_3'UTR|SLC15A2_ENST00000295605.2_Missense_Mutation_p.T519A	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	550					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TGCTTATAGAACTGTGCAAAG	0.388																																					p.T550A		.											.	SLC15A2-91	0			c.A1648G						.						196	183	187					3																	121649781		2203	4300	6503	SO:0001583	missense	6565	exon18			TATAGAACTGTGC	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1648A>G	3.37:g.121649781A>G	ENSP00000417085:p.Thr550Ala	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	199	31	NM_021082	0	0	3	3	0	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	A	0.388	-0.925105	0.02377	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.02656	4.5;4.21	5.42	1.6	0.23607	.	0.546824	0.20900	N	0.083650	T	0.02156	0.0067	L	0.45228	1.405	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.49051	-0.8979	10	0.08599	T	0.76	-1.3387	3.1896	0.06613	0.5309:0.0:0.1062:0.3628	.	519;550	B4E2A7;Q16348	.;S15A2_HUMAN	A	550;512;519	ENSP00000417085:T550A;ENSP00000295605:T519A	ENSP00000295605:T519A	T	+	1	0	SLC15A2	123132471	0.000000	0.05858	0.036000	0.18154	0.509000	0.34042	0.828000	0.27435	0.109000	0.17891	0.528000	0.53228	ACT	.		0.388	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		G	121649781	A	G	121649781	3	3	135	1	0	0	0	0	1	0	0	0	14431	43	2	3	1718	3	SLC15A2	3	121649781	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	67805456	121649781	76372649	27	11998											
HEG1	57493	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	124748131	124748131	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttctacttgaagagccgCtccttcctctagcatctgct	6	15	7	13	1	3	2	0	1	3	1	5	2	5	2	3	0	4	4	3	0	3	6			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:124748131C>T	ENST00000311127.4	-	2	585	c.518G>A	c.(517-519)aGc>aAc	p.S173N		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	173					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						TGAAGAGCCGCTCCTTCCTCT	0.512																																					p.S173N		.											.	HEG1-70	0			c.G518A						.						92	89	90					3																	124748131		1958	4173	6131	SO:0001583	missense	57493	exon2			GAGCCGCTCCTTC	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.518G>A	3.37:g.124748131C>T	ENSP00000311502:p.Ser173Asn	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	241	56	NM_020733	0	0	0	0	0	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	C	0.917	-0.717219	0.03182	.	.	ENSG00000173706	ENST00000311127	T	0.44482	0.92	5.38	-10.8	0.00216	.	.	.	.	.	T	0.09158	0.0226	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13361	-1.0512	9	0.02654	T	1	.	5.997	0.19499	0.0926:0.2061:0.5365:0.1648	.	173;173	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	N	173	ENSP00000311502:S173N	ENSP00000311502:S173N	S	-	2	0	HEG1	126230821	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.000000	0.03693	-1.869000	0.01141	-1.298000	0.01336	AGC	.		0.512	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		T	124748131	C	T	124748131	3	4	135	1	0	0	0	0	1	0	0	0	7065	797	28	2	3691	2	HEG1	3	124748131	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	3098350	124748131	73274299	28	11999											
COL6A5	256076	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	130095526	130095526	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctccgtgggggtgcagaaaGcttctgaggaaaatctgaag	11	9	14	7	1	3	3	0	2	3	1	4	4	3	4	1	3	2	2	1	3	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:130095526G>T	ENST00000432398.2	+	3	1008	c.514G>T	c.(514-516)Gct>Tct	p.A172S	COL6A5_ENST00000265379.6_Missense_Mutation_p.A172S	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	172	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GGTGCAGAAAGCTTCTGAGGA	0.502																																					p.A172S		.											.	.	0			c.G514T						.						81	81	81					3																	130095526		692	1591	2283	SO:0001583	missense	256076	exon3			CAGAAAGCTTCTG	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"Collagens"	26674	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 4"	611916	"collagen, type XXIX, alpha 1"	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.514G>T	3.37:g.130095526G>T	ENSP00000390895:p.Ala172Ser	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	155	20	NM_153264	0	0	0	0	0	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	G	6.971	0.549091	0.13312	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.80214	-1.35;-1.35	5.14	3.34	0.38264	.	.	.	.	.	T	0.80989	0.4730	M	0.72479	2.2	0.09310	N	0.99999	P	0.38582	0.638	P	0.45577	0.486	T	0.69379	-0.5161	9	0.38643	T	0.18	.	6.3024	0.21119	0.1591:0.0:0.6941:0.1469	.	172	A8TX70-2	.	S	172	ENSP00000390895:A172S;ENSP00000265379:A172S	ENSP00000265379:A172S	A	+	1	0	COL6A5	131578216	0.445000	0.25657	0.010000	0.14722	0.017000	0.09413	2.715000	0.47210	0.671000	0.31185	-0.259000	0.10710	GCT	.		0.502	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130095526	G	T	130095526	3	4	135	1	0	0	0	0	1	0	0	0	3708	971	34	4	520	4	COL6A5	3	130095526	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	5347395	130095526	67926904	29	12000											
TBL1XR1	79718	broad.mit.edu;bcgsc.ca	37	chr3	176771657	176771657	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcaccatttatattggaCtgactgatatggctttctat	10	15	9	7	0	1	2	0	2	1	0	1	3	1	3	1	3	0	2	1	3	4	7			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:176771657C>G	ENST00000430069.1	-	4	367	c.108G>C	c.(106-108)caG>caC	p.Q36H	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.Q36H			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	36	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTATATTGGACTGACTGATAT	0.378																																					p.Q36H													.	TBL1XR1-187	0			c.G108C						.						104	97	100					3																	176771657		1867	4107	5974	SO:0001583	missense	79718	exon4			ATTGGACTGACTG	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"WD repeat domain containing"	29529	protein-coding gene	gene with protein product		608628	"transducin (beta)-like 1X-linked receptor 1"			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.108G>C	3.37:g.176771657C>G	ENSP00000405574:p.Gln36His	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	158	6	NM_024665	0	0	1	1	0	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	37	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698324	0.68386	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000352800;ENST00000437738;ENST00000450267;ENST00000431674;ENST00000422066;ENST00000443315;ENST00000422442;ENST00000427349	T;T	0.54279	0.58;0.58	5.21	4.27	0.50696	LisH dimerisation motif (2);	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	L	0.54323	1.7	0.58432	D	0.999999	B	0.32731	0.382	B	0.28553	0.091	T	0.49283	-0.8956	10	0.62326	D	0.03	-20.5183	11.9894	0.53166	0.0:0.9084:0.0:0.0916	.	36	Q9BZK7	TBL1R_HUMAN	H	36	ENSP00000405574:Q36H;ENSP00000413251:Q36H	ENSP00000263964:Q36H	Q	-	3	2	TBL1XR1	178254351	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.260000	0.51523	1.202000	0.43218	0.655000	0.94253	CAG	.		0.378	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		G	176771657	C	G	176771657	3	3	135	1	0	0	0	0	1	0	0	0	15672	564	20	4	1488	4	TBL1XR1	3	176771657	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	46676131	176771657	21250773	30	12001											
KLHL24	54800	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183381404	183381404	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcagagtatgcagtctgtgCtctaaggaatgacattcttg	11	13	10	7	0	4	2	1	1	3	1	4	3	4	3	0	1	2	3	0	1	3	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:183381404C>A	ENST00000454652.2	+	5	1465	c.1079C>A	c.(1078-1080)gCt>gAt	p.A360D	KLHL24_ENST00000242810.6_Missense_Mutation_p.A360D|KLHL24_ENST00000476808.1_Missense_Mutation_p.A360D	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	360						cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			GCAGTCTGTGCTCTAAGGAAT	0.353																																					p.A360D		.											.	KLHL24-91	0			c.C1079A						.						104	99	101					3																	183381404		2203	4300	6503	SO:0001583	missense	54800	exon4			TCTGTGCTCTAAG		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"Kelch-like", "BTB/POZ domain containing"	25947	protein-coding gene	gene with protein product		611295	"kelch-like 24 (Drosophila)"				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.1079C>A	3.37:g.183381404C>A	ENSP00000395012:p.Ala360Asp	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	107	11	NM_017644	0	0	4	4	0	A5PLN8|Q9H620|Q9NXT9	Missense_Mutation	SNP	ENST00000454652.2	37	CCDS3246.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086083	0.76642	.	.	ENSG00000114796	ENST00000242810;ENST00000454652;ENST00000476808	T;T;T	0.79352	-1.26;-1.26;-1.26	5.34	5.34	0.76211	Galactose oxidase, beta-propeller (1);	0.047926	0.85682	D	0.000000	D	0.85048	0.5608	M	0.80847	2.515	0.80722	D	1	B;B	0.30146	0.131;0.27	B;B	0.42593	0.04;0.392	D	0.84947	0.0869	10	0.66056	D	0.02	.	19.4149	0.94690	0.0:1.0:0.0:0.0	.	360;360	Q6TFL4-2;Q6TFL4	.;KLH24_HUMAN	D	360	ENSP00000242810:A360D;ENSP00000395012:A360D;ENSP00000419010:A360D	ENSP00000242810:A360D	A	+	2	0	KLHL24	184864098	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.445000	0.80570	2.675000	0.91044	0.462000	0.41574	GCT	.		0.353	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644		A	183381404	C	A	183381404	3	1	135	1	0	0	0	0	1	0	0	0	8400	797	28	4	1085	4	KLHL24	3	183381404	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	6609747	183381404	14641026	31	12002											
YEATS2	55689	broad.mit.edu;bcgsc.ca	37	chr3	183476664	183476664	+	Frame_Shift_Del	DEL	A	A	-																															tatcaggaagtcctacaaacAagatctccacggcttctcag																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:183476664delA	ENST00000305135.5	+	13	1762	c.1567delA	c.(1567-1569)aagfs	p.K523fs		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	523					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TCCTACAAACAAGATCTCCAC	0.373																																					p.K523fs													.	YEATS2-138	0			c.1567delA						.						138	126	129					3																	183476664		1834	4080	5914	SO:0001589	frameshift_variant	55689	exon13			ACAAACAAGATCT	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1567delA	3.37:g.183476664delA	ENSP00000306983:p.Lys523fs	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	388	55	NM_018023	0	0	0	0	0	A7E2B9|D3DNS9|Q641P6|Q9NW96	Frame_Shift_Del	DEL	ENST00000305135.5	37	CCDS43175.1																																																																																			.		0.373	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		-	183476664	A	-	183476664	7	5	135	1	0	1	0	1	0	0	0	0	17505	131	5	0	1613	0	YEATS2	3	183476664	Frame_Shift_Del	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	95260	183476664	14545766	32	12003											
CNGA1	1259	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	47938977	47938977	+	Frame_Shift_Del	DEL	T	T	-																															aatgtacatctctcgtccgaTatcccctttcttgcaaatat																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:47938977delT	ENST00000514170.1	-	11	1853	c.1534delA	c.(1534-1536)atcfs	p.I512fs	CNGA1_ENST00000544810.1_Frame_Shift_Del_p.I512fs|CNGA1_ENST00000420489.2_Frame_Shift_Del_p.I512fs|CNGA1_ENST00000402813.3_Frame_Shift_Del_p.I581fs|CNGA1_ENST00000358519.4_Frame_Shift_Del_p.I512fs			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	512					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TCTCGTCCGATATCCCCTTTC	0.463																																					p.I581fs		.											.	CNGA1-92	0			c.1741delA						.						111	112	111					4																	47938977		2138	4277	6415	SO:0001589	frameshift_variant	1259	exon10			.	M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.1534delA	4.37:g.47938977delT	ENSP00000426862:p.Ile512fs	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	176	29	NM_001142564	0	0	0	0	0	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Frame_Shift_Del	DEL	ENST00000514170.1	37	CCDS43226.1																																																																																			.		0.463	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		-	47938977	T	-	47938977	7	5	135	1	0	1	0	1	0	0	0	0	3602	1406	49	0	542	0	CNGA1	4	47938977	Frame_Shift_Del	DEL	T	TCGA-HE-A5NK-01A-11D-A26P-10		47938977	143215299	33	12004											
USO1	8615	broad.mit.edu	37	chr4	76726384	76726384	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtagattgcgagaagagatAgaagaattaaaacgtaatca	19	8	11	3	2	1	5	1	0	0	5	1	7	1	5	0	1	2	2	0	1	8	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:76726384A>G	ENST00000538159.1	+	20	2244	c.2244A>G	c.(2242-2244)atA>atG	p.I748M	USO1_ENST00000514213.2_Missense_Mutation_p.I724M			O60763	USO1_HUMAN	USO1 vesicle transport factor	739					ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi vesicle docking (GO:0048211)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|mitotic cell cycle (GO:0000278)|transcytosis (GO:0045056)|vesicle fusion with Golgi apparatus (GO:0048280)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAGAAGAGATAGAAGAATTAA	0.363																																					.													.	USO1-25	0			.						.						62	59	60					4																	76726384		1844	4090	5934	SO:0001583	missense	8615	.			AGAGATAGAAGAA	AL832010	CCDS75144.1	4q21.1	2012-12-10	2012-12-10		ENSG00000138768	ENSG00000138768			30904	protein-coding gene	gene with protein product	"vesicle docking protein", "transcytosis associated protein"	603344	"USO1 homolog, vesicle docking protein (yeast)", "USO1 vesicle docking protein homolog (yeast)"			9478999, 9150144, 12077354, 15979508, 14736916	Standard	XM_006714395		Approved	TAP, VDP, p115	uc003hiu.3	O60763	OTTHUMG00000160952	ENST00000538159.1:c.2244A>G	4.37:g.76726384A>G	ENSP00000440586:p.Ile748Met	Somatic	264	0		WXS	Illumina HiSeq	Phase_I	307	6	.	0	0	11	11	0	B2RAQ0|Q6PK63|Q86TB8|Q8N592	Missense_Mutation	SNP	ENST00000538159.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.94|10.94	1.493406|1.493406	0.26774|0.26774	.|.	.|.	ENSG00000138768|ENSG00000138768	ENST00000508939;ENST00000538159;ENST00000514213;ENST00000264904|ENST00000441296	.|.	.|.	.|.	5.7|5.7	1.58|1.58	0.23477|0.23477	Armadillo-type fold (1);|.	0.332013|.	0.36815|.	N|.	0.002383|.	T|.	0.34077|.	0.0885|.	L|L	0.47716|0.47716	1.5|1.5	0.29331|0.29331	N|N	0.866689|0.866689	P;P|.	0.48089|.	0.905;0.664|.	B;B|.	0.42555|.	0.391;0.115|.	T|.	0.32428|.	-0.9907|.	9|.	0.45353|.	T|.	0.12|.	.|.	1.9891|1.9891	0.03442|0.03442	0.4271:0.254:0.0733:0.2456|0.4271:0.254:0.0733:0.2456	.|.	748;739|.	F5GYR8;O60763|.	.;USO1_HUMAN|.	M|W	574;748;724;667|415	.|.	ENSP00000264904:I667M|.	I|X	+|+	3|2	3|0	USO1|USO1	76945408|76945408	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.316000|0.316000	0.28119|0.28119	0.503000|0.503000	0.22610|0.22610	0.399000|0.399000	0.25367|0.25367	-0.757000|-0.757000	0.03467|0.03467	ATA|TAG	.		0.363	USO1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003715		G	76726384	A	G	76726384	3	3	135	1	0	0	0	0	1	0	0	0	17072	410	15	3	2132	3	USO1	4	76726384	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	28787407	76726384	114427892	34	12005											
WDFY3	23001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	85716095	85716095	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtgacggtattatttgtagGagcattatgaggggccaaac	11	12	13	5	1	0	2	0	2	0	0	0	3	0	3	1	4	2	3	1	4	5	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:85716095G>T	ENST00000295888.4	-	20	3612	c.3205C>A	c.(3205-3207)Cct>Act	p.P1069T	WDFY3_ENST00000322366.6_Missense_Mutation_p.P1069T	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1069					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TTATTTGTAGGAGCATTATGA	0.378																																					p.P1069T		.											.	WDFY3-93	0			c.C3205A						.						72	69	70					4																	85716095		2203	4300	6503	SO:0001583	missense	23001	exon20			TTGTAGGAGCATT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3205C>A	4.37:g.85716095G>T	ENSP00000295888:p.Pro1069Thr	Somatic	357	0		WXS	Illumina HiSeq	Phase_I	404	105	NM_014991	0	0	0	0	0	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	3.505	-0.100986	0.06967	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.40476	1.03;1.03	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.30417	0.0764	N	0.24115	0.695	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.14643	-1.0465	10	0.07325	T	0.83	.	19.6264	0.95679	0.0:0.0:1.0:0.0	.	1069	Q8IZQ1	WDFY3_HUMAN	T	1069	ENSP00000318466:P1069T;ENSP00000295888:P1069T	ENSP00000295888:P1069T	P	-	1	0	WDFY3	85935119	1.000000	0.71417	0.996000	0.52242	0.219000	0.24729	7.424000	0.80242	2.717000	0.92951	0.655000	0.94253	CCT	.		0.378	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85716095	G	T	85716095	3	4	135	1	0	0	0	0	1	0	0	0	17303	1174	41	4	7571	4	WDFY3	4	85716095	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	8989711	85716095	105438181	35	12006											
C4orf37	285555	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	98893529	98893529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcacttttcttctgtttctTtgagcagatatttctaacac	8	19	5	9	0	4	2	0	1	4	1	4	2	4	2	0	0	3	3	0	0	2	8			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:98893529T>C	ENST00000295268.3	-	7	924	c.835A>G	c.(835-837)Aag>Gag	p.K279E		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	279			K -> R (in dbSNP:rs7654193).														TTCTGTTTCTTTGAGCAGATA	0.358																																					p.K279E		.											.	.	0			c.A835G						.						71	71	71					4																	98893529		2203	4300	6503	SO:0001583	missense	285555	exon7			GTTTCTTTGAGCA	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.835A>G	4.37:g.98893529T>C	ENSP00000295268:p.Lys279Glu	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	220	41	NM_174952	0	0	0	0	0		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.723977	0.00694	.	.	ENSG00000163116	ENST00000295268	T	0.11604	2.76	5.45	1.74	0.24563	.	0.432965	0.22937	N	0.053831	T	0.06005	0.0156	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.34800	-0.9814	9	.	.	.	-8.5472	4.1354	0.10169	0.0:0.3996:0.2191:0.3813	.	279	Q8N412	CD037_HUMAN	E	279	ENSP00000295268:K279E	.	K	-	1	0	C4orf37	99112552	0.115000	0.22152	0.080000	0.20451	0.292000	0.27327	0.392000	0.20801	0.901000	0.36495	0.455000	0.32223	AAG	.		0.358	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		C	98893529	T	C	98893529	3	2	135	1	0	0	0	0	1	0	0	0	2273	1850	64	3	564	3	C4orf37	4	98893529	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	13177434	98893529	92260747	36	12007											
PDE5A	8654	ucsc.edu;bcgsc.ca	37	chr4	120528177	120528177	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactggtccccttcatcaTgatcaaaccttggaggggtt	9	11	10	11	0	3	1	3	1	0	0	4	2	4	2	3	4	2	2	3	4	1	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:120528177T>A	ENST00000354960.3	-	2	747	c.428A>T	c.(427-429)cAt>cTt	p.H143L	PDE5A_ENST00000394439.1_Missense_Mutation_p.H91L|PDE5A_ENST00000264805.5_Missense_Mutation_p.H101L	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	143					blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	CCCTTCATCATGATCAAACCT	0.428																																					p.H143L													.	PDE5A-90	0			c.A428T						.						119	112	114					4																	120528177		2203	4300	6503	SO:0001583	missense	8654	exon2			TCATCATGATCAA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"Phosphodiesterases"	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.428A>T	4.37:g.120528177T>A	ENSP00000347046:p.His143Leu	Somatic	193	2		WXS	Illumina HiSeq		194	20	NM_001083	0	0	0	0	0	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	T	0.029	-1.349473	0.01266	.	.	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805;ENST00000420633	T;T;T;T	0.08193	3.12;3.12;3.12;3.12	5.51	0.545	0.17190	.	1.839920	0.02500	N	0.090345	T	0.03608	0.0103	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30851	-0.9964	10	0.02654	T	1	.	2.3607	0.04307	0.1028:0.1584:0.2143:0.5245	.	143;101	O76074;O76074-2	PDE5A_HUMAN;.	L	143;91;101;91	ENSP00000347046:H143L;ENSP00000377957:H91L;ENSP00000264805:H101L;ENSP00000416309:H91L	ENSP00000264805:H101L	H	-	2	0	PDE5A	120747625	0.000000	0.05858	0.019000	0.16419	0.569000	0.35902	0.454000	0.21827	0.076000	0.16826	0.459000	0.35465	CAT	.		0.428	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		A	120528177	T	A	120528177	3	1	135	1	0	0	0	0	1	0	0	0	11670	1464	51	5	2279	5	PDE5A	4	120528177	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	21634648	120528177	70626099	37	12008											
NR3C2	4306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	149356416	149356416	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccgatcgtgataaagataTtgtaccttgagcaccaatcc	13	10	8	10	2	0	3	0	2	0	1	2	4	1	3	4	0	3	2	4	0	5	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:149356416T>C	ENST00000358102.3	-	2	1959	c.1597A>G	c.(1597-1599)Ata>Gta	p.I533V	NR3C2_ENST00000512865.1_Missense_Mutation_p.I533V|NR3C2_ENST00000355292.3_Missense_Mutation_p.I533V|NR3C2_ENST00000511528.1_Missense_Mutation_p.I533V|NR3C2_ENST00000344721.4_Missense_Mutation_p.I533V	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	533	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	GATAAAGATATTGTACCTTGA	0.483																																					p.I533V	Melanoma(27;428 957 40335 51025 51111)	.											.	NR3C2-154	0			c.A1597G						.						121	112	115					4																	149356416		2203	4300	6503	SO:0001583	missense	4306	exon2			AAGATATTGTACC	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"Nuclear hormone receptors"	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.1597A>G	4.37:g.149356416T>C	ENSP00000350815:p.Ile533Val	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	216	54	NM_001166104	0	0	2	2	0	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	37	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234464	0.39498	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	D;D;D;D;D;D	0.90069	-2.6;-2.61;-2.6;-2.17;-2.18;-2.61	5.51	5.51	0.81932	.	0.037872	0.85682	D	0.000000	T	0.80839	0.4700	N	0.24115	0.695	0.45806	D	0.998684	B;P	0.41524	0.144;0.753	B;B	0.35550	0.035;0.205	T	0.80576	-0.1321	9	.	.	.	.	15.9104	0.79470	0.0:0.0:0.0:1.0	.	533;533	B0ZBF5;B0ZBF6	.;.	V	533	ENSP00000341390:I533V;ENSP00000347441:I533V;ENSP00000350815:I533V;ENSP00000423510:I533V;ENSP00000343907:I533V;ENSP00000421481:I533V	.	I	-	1	0	NR3C2	149575866	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.615000	0.83006	2.210000	0.71456	0.533000	0.62120	ATA	.		0.483	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			C	149356416	T	C	149356416	3	2	135	1	0	0	0	0	1	0	0	0	10657	1493	52	3	1389	3	NR3C2	4	149356416	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	28828239	149356416	41797860	38	12009											
NAF1	92345	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	164061509	164061509	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtaacacataaaatggatgTgcaacaggtccaaatatctc	16	9	7	9	1	1	0	0	0	1	0	3	1	2	1	1	2	3	2	1	2	6	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:164061509T>C	ENST00000274054.2	-	5	937	c.744A>G	c.(742-744)gcA>gcG	p.A248A	NAF1_ENST00000509434.1_5'Flank|NAF1_ENST00000422287.2_Silent_p.A248A	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	248					pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				AAAATGGATGTGCAACAGGTC	0.299																																					p.A248A													.	NAF1-70	0			c.A744G						.						82	90	87					4																	164061509		2203	4291	6494	SO:0001819	synonymous_variant	92345	exon5			TGGATGTGCAACA		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"nuclear assembly factor 1 homolog (S. cerevisiae)"			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.744A>G	4.37:g.164061509T>C		Somatic	49	1		WXS	Illumina HiSeq	Phase_I	45	7	NM_138386	0	0	5	5	0	D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	37	CCDS3803.1																																																																																			.		0.299	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		C	164061509	T	C	164061509	2	2	135	1	0	0	0	0	0	0	0	1	10165	1683	59	3		3	NAF1	4	164061509	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	14705093	164061509	27092767	39	12010											
C5orf42	65250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	37121780	37121780	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggctgggtttgttaggcaAtggtttctgtggtagagttg	6	15	17	3	0	1	1	0	0	1	1	1	1	1	1	0	5	0	7	0	5	3	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:37121780A>G	ENST00000508244.1	-	47	9055	c.8962T>C	c.(8962-8964)Ttg>Ctg	p.L2988L	C5orf42_ENST00000425232.2_Silent_p.L2988L|C5orf42_ENST00000274258.7_Silent_p.L1886L|C5orf42_ENST00000512288.1_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2988						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TTGTTAGGCAATGGTTTCTGT	0.463																																					p.L2988L		.											.	C5orf42-94	0			c.T8962C						.						308	265	280					5																	37121780		2203	4300	6503	SO:0001819	synonymous_variant	65250	exon48			TAGGCAATGGTTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.8962T>C	5.37:g.37121780A>G		Somatic	445	1		WXS	Illumina HiSeq	Phase_I	701	235	NM_023073	0	0	3	7	4	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			.		0.463	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37121780	A	G	37121780	2	3	135	1	0	0	0	0	0	0	0	1	2307	98	4	3		3	C5orf42	5	37121780	Silent	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		37121780	143793480	40	12011											
ADAMTS6	11174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	64587271	64587271	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtcacgcttgggaggctcaTtatcaaggcaagtaccacgg	11	8	12	10	2	3	0	3	0	0	0	3	1	3	1	1	4	1	4	1	4	4	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:64587271T>A								ADAMTS6 (92679 upstream) : ADAMTS6 (5763 downstream)																							GGGAGGCTCATTATCAAGGCA	0.458																																					p.N466I		.											.	ADAMTS6-226	0			c.A1397T						.						107	97	101					5																	64587271		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon11			GGCTCATTATCAA																													5.37:g.64587271T>A		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	326	50	NM_197941	0	0	0	0	0		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	T	18.48	3.633123	0.67015	.	.	ENSG00000049192	ENST00000381055;ENST00000464680	D;D	0.90004	-2.6;-2.6	5.26	5.26	0.73747	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.92854	0.7727	L	0.53249	1.67	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.987;0.997	D	0.93648	0.6970	10	0.87932	D	0	.	15.4604	0.75353	0.0:0.0:0.0:1.0	.	466;466	D6R9L6;Q9UKP5	.;ATS6_HUMAN	I	466	ENSP00000370443:N466I;ENSP00000423551:N466I	ENSP00000370443:N466I	N	-	2	0	ADAMTS6	64623027	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.578000	0.82498	2.117000	0.64856	0.533000	0.62120	AAT	.	0	0.458									A	64587271	T	A	64587271	1	1	135	0	1	0	0	0	0	0	0	0	270	1493	52	5		5	ADAMTS6	5	64587271	IGR	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	27465491	64587271	116327989	41	12012											
UTP15	84135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	72864379	72864379	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagatggtggagttcaactTtttgatataagtgggagggc	11	12	15	3	0	1	2	1	1	0	1	1	5	1	4	0	4	1	1	0	4	4	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:72864379T>A	ENST00000296792.4	+	4	573	c.318T>A	c.(316-318)ctT>ctA	p.L106L	UTP15_ENST00000508491.1_Silent_p.L87L|ANKRA2_ENST00000296785.3_5'Flank|UTP15_ENST00000543251.1_5'UTR	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	106					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GAGTTCAACTTTTTGATATAA	0.413																																					p.L106L		.											.	UTP15-90	0			c.T318A						.						101	103	102					5																	72864379		2203	4300	6503	SO:0001819	synonymous_variant	84135	exon4			TCAACTTTTTGAT	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.318T>A	5.37:g.72864379T>A		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	187	33	NM_032175	0	0	4	4	0	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	37	CCDS34186.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454530	0.26161	.	.	ENSG00000164338	ENST00000509005	.	.	.	5.55	-2.87	0.05700	.	.	.	.	.	T	0.51500	0.1678	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49735	-0.8908	4	.	.	.	.	7.9204	0.29843	0.0:0.4287:0.3982:0.1731	.	.	.	.	Y	133	.	.	F	+	2	0	UTP15	72900135	0.042000	0.20092	0.996000	0.52242	0.996000	0.88848	-1.057000	0.03486	-0.143000	0.11334	0.533000	0.62120	TTT	.		0.413	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		A	72864379	T	A	72864379	2	1	135	1	0	0	0	0	0	0	0	1	17130	1828	64	5		5	UTP15	5	72864379	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	8277108	72864379	108050881	42	12013											
CCDC112	153733	broad.mit.edu;bcgsc.ca	37	chr5	114603580	114603581	+	Frame_Shift_Ins	INS	-	-	TT																															aatttgattatctcatactcINSttctctgtattccttgtctc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:114603580_114603581insTT	ENST00000512261.1	-	11	1749_1750	c.1333_1334insAA	c.(1333-1335)agafs	p.R445fs	CCDC112_ENST00000379611.5_Frame_Shift_Ins_p.R528fs|CCDC112_ENST00000395557.4_Frame_Shift_Ins_p.R445fs|CCDC112_ENST00000506442.1_Frame_Shift_Ins_p.R413fs			Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112	445										endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|skin(1)	20		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)		ATCTCATACTCTTCTCTGTATT	0.327																																					p.R528fs													.	CCDC112-90	0			c.1583_1584insAA						.																																			SO:0001589	frameshift_variant	153733	exon10			CATACTCTTCTCT	BC031242	CCDS4117.1, CCDS34213.1	5q22.3	2009-04-17			ENSG00000164221	ENSG00000164221			28599	protein-coding gene	gene with protein product						12477932	Standard	NM_001040440		Approved	MGC39633	uc003kqz.2	Q8NEF3	OTTHUMG00000128894	ENST00000512261.1:c.1332_1333dupAA	5.37:g.114603581_114603582dupTT	ENSP00000423712:p.Arg445fs	Somatic	238	0		WXS	Illumina HiSeq	Phase_I	238	31	NM_001040440	0	0	0	0	0	Q6A334	Frame_Shift_Ins	INS	ENST00000512261.1	37	CCDS4117.1																																																																																			.		0.327	CCDC112-003	PUTATIVE	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370999.1	NM_152549		TT	114603581	-	TT	114603580	7	5	135	1	0	1	1	0	0	0	0	0	2755	913	32	0	10	0	CCDC112	5	114603580	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	41739201	114603580	66311680	43	12014											
ARSI	340075	bcgsc.ca	37	chr5	149678111	149678111	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtgtcacctggtccaGgggcaggcagttgggctgct	5	9	17	10	0	1	0	1	0	0	0	2	0	2	0	2	6	1	6	2	6	0	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:149678111G>C	ENST00000328668.7	-	2	955	c.376C>G	c.(376-378)Ctg>Gtg	p.L126V		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	126					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACCTGGTCCAGGGGCAGGCAG	0.612																																					p.L126V													.	ARSI-92	0			c.C376G						.						50	56	54					5																	149678111		2186	4287	6473	SO:0001583	missense	340075	exon2			GGTCCAGGGGCAG	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"Arylsulfatase family"	32521	protein-coding gene	gene with protein product		610009	"arylsulfatase I"			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.376C>G	5.37:g.149678111G>C	ENSP00000333395:p.Leu126Val	Somatic	190	0		WXS	Illumina HiSeq	Phase_1	301	9	NM_001012301	0	0	0	0	0	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	37	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101429	0.37048	.	.	ENSG00000183876	ENST00000328668	D	0.98717	-5.09	4.58	2.64	0.31445	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.068615	0.64402	D	0.000011	D	0.97561	0.9201	M	0.71036	2.16	0.80722	D	1	B	0.26147	0.143	B	0.33121	0.158	D	0.94605	0.7799	10	0.59425	D	0.04	.	11.2155	0.48823	0.2441:0.0:0.7559:0.0	.	126	Q5FYB1	ARSI_HUMAN	V	126	ENSP00000333395:L126V	ENSP00000333395:L126V	L	-	1	2	ARSI	149658304	0.998000	0.40836	0.997000	0.53966	0.952000	0.60782	0.925000	0.28791	0.124000	0.18369	-1.134000	0.01955	CTG	.		0.612	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		C	149678111	G	C	149678111	3	2	135	1	0	0	0	0	1	0	0	0	995	991	35	4	1337	4	ARSI	5	149678111	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	35074531	149678111	31237149	44	12015											
MRPL22	29093	broad.mit.edu	37	chr5	154346429	154346429	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagtatattcagcagcttcGcagccggaccatcgttcaca	11	9	9	12	3	2	1	2	0	0	1	4	2	2	2	2	1	3	5	2	1	2	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:154346429G>A	ENST00000523037.1	+	7	634	c.593G>A	c.(592-594)cGc>cAc	p.R198H	MRPL22_ENST00000518364.1_3'UTR|MRPL22_ENST00000265229.8_Missense_Mutation_p.R118H|MRPL22_ENST00000439747.3_Missense_Mutation_p.R224H|MRPL22_ENST00000522038.1_Missense_Mutation_p.R204H	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	198					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CAGCAGCTTCGCAGCCGGACC	0.438																																					p.R198H													.	MRPL22-90	0			c.G593A						.						54	47	50					5																	154346429		2203	4300	6503	SO:0001583	missense	29093	exon7			AGCTTCGCAGCCG	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.593G>A	5.37:g.154346429G>A	ENSP00000431040:p.Arg198His	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	129	5	NM_014180	0	0	46	46	0	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Missense_Mutation	SNP	ENST00000523037.1	37	CCDS4331.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506467	0.64410	.	.	ENSG00000082515	ENST00000523037;ENST00000265229;ENST00000439747;ENST00000522038	T;T;T;T	0.59772	0.28;0.4;0.24;0.27	5.8	5.8	0.92144	.	0.579484	0.18168	N	0.149546	T	0.74574	0.3734	M	0.79926	2.475	0.58432	D	0.999999	D	0.60575	0.988	P	0.55303	0.773	T	0.75958	-0.3134	10	0.54805	T	0.06	-1.2567	20.0415	0.97592	0.0:0.0:1.0:0.0	.	198	Q9NWU5	RM22_HUMAN	H	198;118;224;204	ENSP00000431040:R198H;ENSP00000265229:R118H;ENSP00000411177:R224H;ENSP00000429039:R204H	ENSP00000265229:R118H	R	+	2	0	MRPL22	154326622	0.996000	0.38824	0.800000	0.32199	0.138000	0.21146	4.728000	0.62000	2.745000	0.94114	0.563000	0.77884	CGC	.		0.438	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			A	154346429	G	A	154346429	3	1	135	1	0	0	0	0	1	0	0	0	9813	1087	38	1	619	1	MRPL22	5	154346429	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	4668318	154346429	26568831	45	12016											
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35182249	35182249	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttgtcctgctggtccacgcCcgcgccgcccagtacagcaa	6	7	10	18	4	0	0	0	0	0	0	2	0	2	0	5	1	3	3	5	1	2	2	rs113302940	byFrequency	TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:35182249C>T	ENST00000274938.7	+	1	54	c.54C>T	c.(52-54)gcC>gcT	p.A18A	SCUBE3_ENST00000394681.1_Silent_p.A18A	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						TGGTCCACGCCCGCGCCGCCC	0.736													C|||	30	0.00599042	0.0045	0.0072	5008	,	,		9874	0		0.0189	False		,,,				2504	0				p.A18A		.											.	SCUBE3-91	0			c.C54T						.	C		15,4025		0,15,2005	4	5	5		54	1	1	6	dbSNP_132	5	139,7901		0,139,3881	no	coding-synonymous	SCUBE3	NM_152753.2		0,154,5886	TT,TC,CC		1.7289,0.3713,1.2748		18/994	35182249	154,11926	2020	4020	6040	SO:0001819	synonymous_variant	222663	exon1			CCACGCCCGCGCC	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.54C>T	6.37:g.35182249C>T		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_152753	0	0	0	0	0		Silent	SNP	ENST00000274938.7	37	CCDS4800.1																																																																																			C|0.992;T|0.008		0.736	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		T	35182249	C	T	35182249	2	4	135	1	0	0	0	0	0	0	0	1	13978	610	22	2		2	SCUBE3	6	35182249	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		35182249	135932818	46	12017											
DEFB113	245927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	49936558	49936558	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctttttctctctgcaacTtctcttgtttttttctgtgg	2	24	5	10	0	5	0	0	0	5	0	8	0	5	0	0	1	2	2	0	1	1	7			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:49936558T>C	ENST00000398718.1	-	2	80	c.81A>G	c.(79-81)gaA>gaG	p.E27E		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	27					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					TCTCTGCAACTTCTCTTGTTT	0.363																																					p.E27E		.											.	DEFB113-90	0			c.A81G						.						95	92	93					6																	49936558		1859	4093	5952	SO:0001819	synonymous_variant	245927	exon2			TGCAACTTCTCTT	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"Defensins, beta"	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.81A>G	6.37:g.49936558T>C		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	85	15	NM_001037729	0	0	0	0	0		Silent	SNP	ENST00000398718.1	37	CCDS43472.1																																																																																			.		0.363	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1			C	49936558	T	C	49936558	2	2	135	1	0	0	0	0	0	0	0	1	4412	1606	56	3		3	DEFB113	6	49936558	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	14754309	49936558	121178509	47	12018											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51750667	51750667	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacaacaaaaaagcttacctGggcaccacctgcactttccc	14	7	5	15	0	0	0	0	0	0	0	1	0	1	0	4	1	5	3	4	1	6	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:51750667G>T	ENST00000371117.3	-	45	7488	c.7213C>A	c.(7213-7215)Cag>Aag	p.Q2405K	PKHD1_ENST00000340994.4_Missense_Mutation_p.Q2405K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2405					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AAGCTTACCTGGGCACCACCT	0.383																																					p.Q2405K		.											.	PKHD1-603	0			c.C7213A						.						43	41	42					6																	51750667		2203	4300	6503	SO:0001583	missense	5314	exon45			TTACCTGGGCACC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.7213C>A	6.37:g.51750667G>T	ENSP00000360158:p.Gln2405Lys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	130	29	NM_170724	0	0	0	0	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.841905	0.51057	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.79653	-1.29;-1.29	5.81	5.81	0.92471	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.147468	0.48286	D	0.000193	T	0.69797	0.3151	M	0.67953	2.075	0.34697	D	0.726304	P;B;P	0.40000	0.698;0.313;0.698	B;B;B	0.35353	0.201;0.104;0.167	T	0.72704	-0.4213	10	0.27082	T	0.32	.	17.2257	0.86970	0.0:0.0:1.0:0.0	.	2405;2405;2405	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	K	2405	ENSP00000360158:Q2405K;ENSP00000341097:Q2405K	ENSP00000341097:Q2405K	Q	-	1	0	PKHD1	51858626	0.998000	0.40836	0.941000	0.38009	0.505000	0.33919	3.052000	0.49893	2.756000	0.94617	0.650000	0.86243	CAG	.		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51750667	G	T	51750667	3	4	135	1	0	0	0	0	1	0	0	0	11997	1357	47	4	5142	4	PKHD1	6	51750667	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	1814109	51750667	119364400	48	12019											
COL9A1	1297	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	70926682	70926682	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagaaaccgggaagcccaGgaggtcccgggggtccaggc	10	2	16	13	2	0	1	0	0	0	1	2	3	2	3	4	6	2	0	4	6	2	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:70926682G>T	ENST00000357250.6	-	38	2842	c.2684C>A	c.(2683-2685)cCt>cAt	p.P895H	COL9A1_ENST00000320755.7_Missense_Mutation_p.P652H|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Missense_Mutation_p.P652H	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	895	Collagen-like 10.|Triple-helical region (COL1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGGAAGCCCAGGAGGTCCCGG	0.632																																					p.P895H													.	COL9A1-94	0			c.C2684A						.						36	44	41					6																	70926682		2203	4300	6503	SO:0001583	missense	1297	exon38			AGCCCAGGAGGTC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens"	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.2684C>A	6.37:g.70926682G>T	ENSP00000349790:p.Pro895His	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	176	44	NM_001851	0	0	0	0	0	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.820329	0.32145	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.94280	-3.39;-3.39;-3.39	5.87	5.87	0.94306	.	0.341840	0.28577	N	0.014857	D	0.96009	0.8700	M	0.84773	2.715	0.51482	D	0.999929	P;B;D	0.60575	0.619;0.218;0.988	B;B;P	0.57057	0.245;0.055;0.812	D	0.94708	0.7889	10	0.41790	T	0.15	.	20.1935	0.98237	0.0:0.0:1.0:0.0	.	895;652;444	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	H	895;652;652	ENSP00000349790:P895H;ENSP00000315252:P652H;ENSP00000359530:P652H	ENSP00000315252:P652H	P	-	2	0	COL9A1	70983403	1.000000	0.71417	0.924000	0.36721	0.411000	0.31082	8.196000	0.89725	2.779000	0.95612	0.591000	0.81541	CCT	.		0.632	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			T	70926682	G	T	70926682	3	4	135	1	0	0	0	0	1	0	0	0	3713	1000	35	4	85	4	COL9A1	6	70926682	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	19176015	70926682	100188385	49	12020											
ALDH8A1	64577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	135260502	135260502	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcagccatcgctggagctAtcttccaggtcagcaagtag	9	9	11	12	1	2	0	1	0	1	0	4	1	3	1	2	2	4	5	2	2	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:135260502A>G	ENST00000265605.2	-	4	562	c.494T>C	c.(493-495)aTa>aCa	p.I165T	RP11-349J5.2_ENST00000416448.2_RNA|ALDH8A1_ENST00000367847.2_Intron|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.I165T	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	165					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		CGCTGGAGCTATCTTCCAGGT	0.542																																					p.I165T		.											.	ALDH8A1-94	0			c.T494C						.						100	87	91					6																	135260502		2203	4300	6503	SO:0001583	missense	64577	exon4			GGAGCTATCTTCC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"Aldehyde dehydrogenases"	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.494T>C	6.37:g.135260502A>G	ENSP00000265605:p.Ile165Thr	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	128	17	NM_022568	0	0	6	8	2	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.654610	0.67472	.	.	ENSG00000118514	ENST00000265605;ENST00000367845	T;T	0.78364	-1.17;-1.17	5.45	4.29	0.51040	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.097324	0.64402	D	0.000001	T	0.79805	0.4509	M	0.72118	2.19	0.80722	D	1	D;D	0.54397	0.958;0.966	P;D	0.64687	0.881;0.928	T	0.78919	-0.2014	10	0.35671	T	0.21	.	11.1526	0.48469	0.9277:0.0:0.0723:0.0	.	165;165	Q9H2A2-2;Q9H2A2	.;AL8A1_HUMAN	T	165	ENSP00000265605:I165T;ENSP00000356819:I165T	ENSP00000265605:I165T	I	-	2	0	ALDH8A1	135302195	1.000000	0.71417	0.338000	0.25549	0.733000	0.41908	7.522000	0.81844	0.909000	0.36697	0.460000	0.39030	ATA	.		0.542	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			G	135260502	A	G	135260502	3	3	135	1	0	0	0	0	1	0	0	0	505	449	16	3	985	3	ALDH8A1	6	135260502	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	64333820	135260502	35854565	50	12021											
RBM16	22828	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	155154048	155154048	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggttctaccggtctatggtgGtccaaaaggcttacatgaag	10	11	12	8	1	2	1	0	1	2	0	3	1	3	1	2	5	2	2	2	5	6	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:155154048G>A	ENST00000367178.3	+	20	3911	c.3335G>A	c.(3334-3336)gGt>gAt	p.G1112D	SCAF8_ENST00000417268.1_Missense_Mutation_p.G1112D|TIAM2_ENST00000461783.3_5'UTR|SCAF8_ENST00000367186.4_Missense_Mutation_p.G1178D	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	1112					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						GTCTATGGTGGTCCAAAAGGC	0.468																																					p.G1112D		.											.	SCAF8-91	0			c.G3335A						.						66	72	70					6																	155154048		2203	4300	6503	SO:0001583	missense	22828	exon20			ATGGTGGTCCAAA	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.3335G>A	6.37:g.155154048G>A	ENSP00000356146:p.Gly1112Asp	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	216	40	NM_014892	0	0	4	5	1	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784709	0.70222	.	.	ENSG00000213079;ENSG00000213079;ENSG00000213079;ENSG00000146426	ENST00000367178;ENST00000417268;ENST00000367186;ENST00000528928	T;T;T	0.61274	0.18;0.18;0.12	5.97	5.97	0.96955	.	0.000000	0.64402	U	0.000001	T	0.63534	0.2519	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.66388	-0.5936	10	0.87932	D	0	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	1157;1178;1112	B7Z876;B7Z888;Q9UPN6	.;.;SCAF8_HUMAN	D	1112;1112;1178;73	ENSP00000356146:G1112D;ENSP00000413098:G1112D;ENSP00000356154:G1178D	ENSP00000356146:G1112D	G	+	2	0	TIAM2;SCAF8	155195740	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	5.774000	0.68906	2.828000	0.97474	0.655000	0.94253	GGT	.		0.468	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		A	155154048	G	A	155154048	3	1	135	1	0	0	0	0	1	0	0	0	13150	1261	44	2	3413	2	RBM16	6	155154048	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	19893546	155154048	15961019	51	12022											
LPA	4018	hgsc.bcm.edu;bcgsc.ca	37	chr6	161071523	161071523	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaccacatggctttgctcaGgtgctgctaaaattaaaaca	13	10	9	9	0	1	0	1	0	0	0	1	1	1	1	1	3	4	4	1	3	4	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:161071523G>T	ENST00000316300.5	-	2	100	c.56C>A	c.(55-57)cCt>cAt	p.P19H	LPA_ENST00000447678.1_Missense_Mutation_p.P19H			P08519	APOA_HUMAN	lipoprotein, Lp(a)	2527					blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GCTTTGCTCAGGTGCTGCTAA	0.433																																					p.P19H		.											.	LPA-74	0			c.C56A						.						129	134	132					6																	161071523		2186	4297	6483	SO:0001583	missense	4018	exon3			TGCTCAGGTGCTG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.56C>A	6.37:g.161071523G>T	ENSP00000321334:p.Pro19His	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	109	16	NM_005577	0	0	0	0	0	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	g	7.332	0.619100	0.14129	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.61627	0.09;0.09	2.71	2.71	0.32032	.	.	.	.	.	T	0.32164	0.0820	L	0.43152	1.355	0.09310	N	1	.	.	.	.	.	.	T	0.16719	-1.0393	7	0.20519	T	0.43	.	9.0216	0.36204	0.0:0.0:1.0:0.0	.	.	.	.	H	19	ENSP00000321334:P19H;ENSP00000395608:P19H	ENSP00000321334:P19H	P	-	2	0	LPA	160991513	0.652000	0.27349	0.137000	0.22149	0.005000	0.04900	4.568000	0.60857	1.519000	0.48950	0.499000	0.49734	CCT	.		0.433	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161071523	G	T	161071523	3	4	135	1	0	0	0	0	1	0	0	0	8928	1000	35	4	6218	4	LPA	6	161071523	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	5917475	161071523	10043544	52	12023											
SEPT7	989	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	35923576	35923576	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagggtcagaggaaggcagTatccttggggtgttgctgaa	11	9	16	5	0	1	2	1	1	0	1	2	3	2	3	1	5	1	4	1	5	4	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:35923576T>A	ENST00000435235.1	+	8	1072	c.640T>A	c.(640-642)Tat>Aat	p.Y214N	SEPT7_ENST00000494488.2_Missense_Mutation_p.Y253N|SEPT7_ENST00000399034.2_Missense_Mutation_p.Y268N|SEPT7_ENST00000432293.2_Intron|SEPT7_ENST00000350320.6_Missense_Mutation_p.Y266N|SEPT7_ENST00000399035.3_Missense_Mutation_p.Y266N|SEPT7_ENST00000469679.2_Intron			Q16181	SEPT7_HUMAN	septin 7	267	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						AGGAAGGCAGTATCCTTGGGG	0.343																																					p.Y266N													.	.	0			c.T796A						.						131	122	125					7																	35923576		1847	4086	5933	SO:0001583	missense	989	exon8			AGGCAGTATCCTT	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.640T>A	7.37:g.35923576T>A	ENSP00000413507:p.Tyr214Asn	Somatic	119	1		WXS	Illumina HiSeq	Phase_I	166	32	NM_001011553	0	0	22	40	18	Q52M76|Q6NX50	Missense_Mutation	SNP	ENST00000435235.1	37		.	.	.	.	.	.	.	.	.	.	T	24.2	4.503094	0.85176	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1	4.88	4.88	0.63580	.	0.000000	0.64402	U	0.000001	T	0.78168	0.4241	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.82587	-0.0383	10	0.87932	D	0	.	14.8193	0.70059	0.0:0.0:0.0:1.0	.	212;266;267	B4DNE4;E7EPK1;Q16181	.;.;SEPT7_HUMAN	N	214;268;266;266;212;214;253	ENSP00000413507:Y214N;ENSP00000381992:Y268N;ENSP00000344868:Y266N;ENSP00000381993:Y266N;ENSP00000438395:Y253N	ENSP00000344868:Y266N	Y	+	1	0	SEPT7	35890101	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.037000	0.88933	1.960000	0.56953	0.456000	0.33151	TAT	.		0.343	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		A	35923576	T	A	35923576	3	1	135	1	0	0	0	0	1	0	0	0	14101	1638	57	5	827	5	SEPT7	7	35923576	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10		35923576	123215087	53	12024											
AUTS2	26053	broad.mit.edu	37	chr7	70255120	70255120	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtgagccggcctacgagaAccccaagaagagctccgagg	11	3	15	12	3	0	4	0	1	0	3	1	6	1	4	5	3	4	1	5	3	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:70255120A>T	ENST00000342771.4	+	19	3239	c.2918A>T	c.(2917-2919)aAc>aTc	p.N973I	AUTS2_ENST00000406775.2_Missense_Mutation_p.N949I	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	973										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GCCTACGAGAACCCCAAGAAG	0.697																																					p.N973I													.	AUTS2-92	0			c.A2918T						.						19	17	18					7																	70255120		2184	4284	6468	SO:0001583	missense	26053	exon19			ACGAGAACCCCAA	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2918A>T	7.37:g.70255120A>T	ENSP00000344087:p.Asn973Ile	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	62	5	NM_015570	0	0	0	0	0	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	A	14.15	2.448589	0.43531	.	.	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.31769	1.48;1.48	4.63	4.63	0.57726	.	0.318337	0.36665	N	0.002467	T	0.34366	0.0895	L	0.42245	1.32	0.80722	D	1	B;B;B	0.33857	0.429;0.429;0.429	B;B;B	0.43478	0.241;0.421;0.421	T	0.09378	-1.0677	9	.	.	.	-17.0461	14.0636	0.64815	1.0:0.0:0.0:0.0	.	425;949;973	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	I	949;973	ENSP00000385263:N949I;ENSP00000344087:N973I	.	N	+	2	0	AUTS2	69893056	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.386000	0.52492	1.723000	0.51488	0.533000	0.62120	AAC	.		0.697	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70255120	A	T	70255120	3	4	135	1	0	0	0	0	1	0	0	0	1226	43	2	5	3137	5	AUTS2	7	70255120	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	34331544	70255120	88883543	54	12025											
AKAP9	10142	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	91631221	91631221	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataatttaggcattcactatAaacagcagatagatggttta	16	13	7	5	0	1	2	1	0	0	2	1	2	1	2	0	2	2	3	0	2	7	9			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:91631221A>T	ENST00000359028.2	+	9	2251	c.2026A>T	c.(2026-2028)Aaa>Taa	p.K676*	AKAP9_ENST00000358100.2_Nonsense_Mutation_p.K676*|AKAP9_ENST00000356239.3_Nonsense_Mutation_p.K664*			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	676	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CATTCACTATAAACAGCAGAT	0.289			T	BRAF	papillary thyroid																																p.K664X				Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9-755	0			c.A1990T						.						41	45	44					7																	91631221		2197	4281	6478	SO:0001587	stop_gained	10142	exon8			CACTATAAACAGC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.2026A>T	7.37:g.91631221A>T	ENSP00000351922:p.Lys676*	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	53	6	NM_005751	0	0	0	0	0	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Nonsense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	38	7.134461	0.98085	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	.	.	.	5.73	4.58	0.56647	.	0.000000	0.44483	D	0.000455	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4971	0.50415	0.93:0.0:0.07:0.0	.	.	.	.	X	664;676;676;676;676	.	ENSP00000348573:K664X	K	+	1	0	AKAP9	91469157	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.891000	0.56227	2.323000	0.78572	0.529000	0.55759	AAA	.		0.289	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		T	91631221	A	T	91631221	4	4	135	1	0	0	0	0	0	1	0	0	459	363	13	5	2020	5	AKAP9	7	91631221	Nonsense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	21376101	91631221	67507442	55	12026											
NPTX2	4885	bcgsc.ca	37	chr7	98257767	98257767	+	Frame_Shift_Del	DEL	C	C	-																															gcatttgtcggggagctcagCcagttcaacatatgggaccg																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:98257767delC	ENST00000265634.3	+	5	1287	c.1122delC	c.(1120-1122)agcfs	p.S374fs		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	374	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			GGGAGCTCAGCCAGTTCAACA	0.567																																					p.S374fs													.	NPTX2-515	0			c.1122delC						.						89	70	76					7																	98257767		2203	4300	6503	SO:0001589	frameshift_variant	4885	exon5			GCTCAGCCAGTTC		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1122delC	7.37:g.98257767delC	ENSP00000265634:p.Ser374fs	Somatic	168	1		WXS	Illumina HiSeq	Phase_1	246	43	NM_002523	0	0	0	0	0	A4D267|Q86XV7|Q96G70	Frame_Shift_Del	DEL	ENST00000265634.3	37	CCDS5657.1																																																																																			.		0.567	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		-	98257767	C	-	98257767	7	5	135	1	0	1	0	1	0	0	0	0	10629	738	26	0	1140	0	NPTX2	7	98257767	Frame_Shift_Del	DEL	C	TCGA-HE-A5NK-01A-11D-A26P-10	6626546	98257767	60880896	56	12027											
METTL2B	55798	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	128119287	128119287	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgggtttttcaaggataGacattggctttttaccgaat	12	15	9	5	1	1	1	1	0	0	1	1	3	1	2	1	3	1	2	1	3	5	7			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:128119287G>T	ENST00000262432.8	+	3	315	c.278G>T	c.(277-279)aGa>aTa	p.R93I	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Missense_Mutation_p.R28I	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	93					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TTCAAGGATAGACATTGGCTT	0.348																																					p.R93I		.											.	METTL2B-23	0			c.G278T						.						46	48	47					7																	128119287		2202	4296	6498	SO:0001583	missense	55798	exon3			AGGATAGACATTG	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.278G>T	7.37:g.128119287G>T	ENSP00000262432:p.Arg93Ile	Somatic	390	0		WXS	Illumina HiSeq	Phase_I	481	67	NM_018396	0	0	8	8	0	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	37	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.704511	0.48412	.	.	ENSG00000165055	ENST00000462662;ENST00000262432;ENST00000480046	T;T;T	0.04654	3.58;3.58;3.58	2.86	1.97	0.26223	.	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	M	0.94021	3.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01583	-1.1319	10	0.87932	D	0	-0.8843	7.7593	0.28942	0.1338:0.0:0.8662:0.0	.	28;93	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	I	87;93;28	ENSP00000418634:R87I;ENSP00000262432:R93I;ENSP00000418402:R28I	ENSP00000262432:R93I	R	+	2	0	METTL2B	127906523	1.000000	0.71417	0.984000	0.44739	0.344000	0.29017	9.445000	0.97587	0.540000	0.28808	-0.491000	0.04670	AGA	.		0.348	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		T	128119287	G	T	128119287	3	4	135	1	0	0	0	0	1	0	0	0	9525	942	33	4	288	4	METTL2B	7	128119287	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	29861520	128119287	31019376	57	12028											
TAS2R39	259285	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	142880641	142880641	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttttagcagttttacttgctGaatacctcattggtatcatt	9	19	6	7	0	2	1	2	1	0	0	2	1	2	1	1	1	4	4	1	1	5	9			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:142880641G>A	ENST00000446620.1	+	1	130	c.130G>A	c.(130-132)Gaa>Aaa	p.E44K		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	44					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	Melanoma(164;0.059)					TTTACTTGCTGAATACCTCAT	0.413																																					p.E44K		.											.	TAS2R39-1	0			c.G130A						.						145	132	136					7																	142880641		1939	4149	6088	SO:0001583	missense	259285	exon1			CTTGCTGAATACC	AF494230	CCDS47729.1	7q34	2012-08-22			ENSG00000236398	ENSG00000236398		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18886	protein-coding gene	gene with protein product						12379855	Standard	NM_176881		Approved		uc011ksw.2	P59534	OTTHUMG00000152636	ENST00000446620.1:c.130G>A	7.37:g.142880641G>A	ENSP00000405095:p.Glu44Lys	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	188	13	NM_176881	0	0	0	0	0	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	37	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.876777	0.51801	.	.	ENSG00000236398	ENST00000446620	T	0.37411	1.2	4.66	4.66	0.58398	.	.	.	.	.	T	0.65196	0.2668	M	0.89478	3.035	0.29517	N	0.853797	D	0.71674	0.998	D	0.68765	0.96	T	0.65676	-0.6110	9	0.72032	D	0.01	.	14.7561	0.69567	0.0:0.0:1.0:0.0	.	44	P59534	T2R39_HUMAN	K	44	ENSP00000405095:E44K	ENSP00000405095:E44K	E	+	1	0	TAS2R39	142590763	0.321000	0.24625	0.437000	0.26809	0.026000	0.11368	1.677000	0.37576	2.583000	0.87209	0.557000	0.71058	GAA	.		0.413	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881		A	142880641	G	A	142880641	3	1	135	1	0	0	0	0	1	0	0	0	15608	1291	45	2	132	2	TAS2R39	7	142880641	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	14761354	142880641	16258022	58	12029											
KRBA1	84626	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	149430813	149430813	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	acgctcccccggcagaacctCctgggctccactgcagctct	6	7	9	19	2	1	1	0	0	1	1	4	1	4	1	5	2	3	5	5	2	1	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:149430813C>G	ENST00000485033.2	+	15	2587	c.2587C>G	c.(2587-2589)Cct>Gct	p.P863A	KRBA1_ENST00000479560.1_3'UTR|KRBA1_ENST00000319551.8_Missense_Mutation_p.P863A|KRBA1_ENST00000255992.10_Missense_Mutation_p.P923A			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	924										breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(17)|ovary(1)|prostate(1)	27	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCAGAACCTCCTGGGCTCCA	0.692																																					.													.	KRBA1-91	0			.						.						9	12	11					7																	149430813		2163	4252	6415	SO:0001583	missense	84626	.			GAACCTCCTGGGC	AB058765	CCDS75674.1	7q36	2014-02-12	2006-08-15		ENSG00000133619	ENSG00000133619		"-"	22228	protein-coding gene	gene with protein product			"KRAB A domain containing 1"				Standard	NM_001290187		Approved	KIAA1862	uc003wfz.3	A5PL33	OTTHUMG00000157886	ENST00000485033.2:c.2587C>G	7.37:g.149430813C>G	ENSP00000420112:p.Pro863Ala	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	50	10	.	0	0	3	5	2	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Missense_Mutation	SNP	ENST00000485033.2	37		.	.	.	.	.	.	.	.	.	.	C	10.09	1.254707	0.22965	.	.	ENSG00000133619	ENST00000255992;ENST00000319551;ENST00000485033	T;T;T	0.28069	1.63;1.63;1.63	5.37	0.334	0.15948	.	0.552042	0.15405	N	0.264109	T	0.11750	0.0286	.	.	.	0.09310	N	1	B;B	0.20780	0.048;0.048	B;B	0.24541	0.054;0.054	T	0.36529	-0.9744	9	0.05436	T	0.98	-1.0704	7.65	0.28342	0.0:0.3639:0.0:0.6361	.	863;924	E7ENE9;A5PL33	.;KRBA1_HUMAN	A	923;863;863	ENSP00000255992:P923A;ENSP00000317165:P863A;ENSP00000420112:P863A	ENSP00000255992:P923A	P	+	1	0	KRBA1	149061746	0.003000	0.15002	0.032000	0.17829	0.084000	0.17831	0.213000	0.17521	-0.172000	0.10779	-0.320000	0.08662	CCT	.		0.692	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534		G	149430813	C	G	149430813	3	3	135	1	0	0	0	0	1	0	0	0	8460	855	30	4	2831	4	KRBA1	7	149430813	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	6550172	149430813	9707850	59	12030											
REPIN1	29803	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	150069172	150069172	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caataagccctatctgacttCgcaccggcgcatccacaccg	10	7	7	17	4	1	1	0	1	1	0	3	1	2	1	4	1	1	2	4	1	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:150069172C>A	ENST00000425389.2	+	1	920	c.842C>A	c.(841-843)tCg>tAg	p.S281*	REPIN1_ENST00000489432.2_Nonsense_Mutation_p.S338*|REPIN1_ENST00000444957.1_Nonsense_Mutation_p.S281*|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000540729.1_Nonsense_Mutation_p.S281*|REPIN1_ENST00000397281.2_Nonsense_Mutation_p.S281*|REPIN1_ENST00000479668.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	281					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TATCTGACTTCGCACCGGCGC	0.637																																					p.S338X		.											.	REPIN1-69	0			c.C1013A						.						18	23	22					7																	150069172		2160	4279	6439	SO:0001587	stop_gained	29803	exon3			TGACTTCGCACCG	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"Zinc fingers, C2H2-type"	17922	protein-coding gene	gene with protein product	"replication initiation region protein (60kD)", "zinc finger protein AP4", "zinc finger protein 464 (RIP60)"		"zinc finger protein 464 (RIP60)"	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.842C>A	7.37:g.150069172C>A	ENSP00000388287:p.Ser281*	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	52	9	NM_001099695	0	0	4	6	2	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Nonsense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.090002	0.76756	.	.	ENSG00000214022	ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000425389	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.22017	N	0.999416	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-5.8606	11.3408	0.49531	0.0:0.8167:0.1833:0.0	.	.	.	.	X	281;281;281;338;340;341;281	.	ENSP00000380451:S281X	S	+	2	0	REPIN1	149700105	0.000000	0.05858	0.985000	0.45067	0.853000	0.48598	-1.414000	0.02471	2.550000	0.86006	0.462000	0.41574	TCG	.		0.637	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		A	150069172	C	A	150069172	4	1	135	1	0	0	0	0	0	1	0	0	13259	893	31	4	1019	4	REPIN1	7	150069172	Nonsense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	638359	150069172	9069491	60	12031											
DLGAP2	9228	broad.mit.edu	37	chr8	1513950	1513950	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacattaaagccatgggggaCgaggagagcggagagtcaga	14	5	16	6	2	1	3	1	0	0	3	1	7	1	4	1	4	3	0	1	4	3	2	rs371842482		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:1513950C>T	ENST00000421627.2	+	3	1226	c.1092C>T	c.(1090-1092)gaC>gaT	p.D364D	RP11-666I19.2_ENST00000518063.1_RNA	NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	443					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CCATGGGGGACGAGGAGAGCG	0.567																																					p.D364D													.	DLGAP2-22	0			c.C1092T						.	C		2,4336		0,2,2167	47	52	50		1092	-7.2	0.2	8		50	0,8586		0,0,4293	no	coding-synonymous	DLGAP2	NM_004745.3		0,2,6460	TT,TC,CC		0.0,0.0461,0.0155		364/976	1513950	2,12922	2169	4293	6462	SO:0001819	synonymous_variant	9228	exon3			GGGGGACGAGGAG	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"discs, large (Drosophila) homolog-associated protein 2"			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1092C>T	8.37:g.1513950C>T		Somatic	136	0		WXS	Illumina HiSeq	Phase_I	199	6	NM_004745	0	0	0	0	0	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	37	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	C	8.974	0.973749	0.18736	4.61E-4	0.0	ENSG00000198010	ENST00000520901	.	.	.	4.55	-7.15	0.01521	.	.	.	.	.	T	0.62925	0.2468	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67023	-0.5775	4	.	.	.	-8.2505	16.0777	0.80979	0.0:0.2339:0.0:0.7661	.	.	.	.	M	381	.	.	T	+	2	0	DLGAP2	1501357	0.455000	0.25736	0.228000	0.23943	0.986000	0.74619	-0.333000	0.07894	-1.726000	0.01370	-0.236000	0.12185	ACG	.		0.567	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		T	1513950	C	T	1513950	2	4	135	1	0	0	0	0	0	0	0	1	4571	535	19	1		1	DLGAP2	8	1513950	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		1513950	144850072	61	12032											
MTUS1	57509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	17612803	17612803	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggcatgatgtgatataaAggtgcagttaactttatcca	13	13	10	5	0	0	2	0	2	0	0	1	3	1	2	1	2	2	3	1	2	5	5	rs374892928		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:17612803A>G	ENST00000262102.6	-	2	738	c.514T>C	c.(514-516)Ttt>Ctt	p.F172L	MTUS1_ENST00000381862.3_Missense_Mutation_p.F172L|MTUS1_ENST00000519263.1_Missense_Mutation_p.F172L|MTUS1_ENST00000381869.3_Missense_Mutation_p.F172L	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	172					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TGTGATATAAAGGTGCAGTTA	0.438																																					p.F172L		.											.	MTUS1-92	0			c.T514C						.						146	132	136					8																	17612803		1963	4150	6113	SO:0001583	missense	57509	exon2			ATATAAAGGTGCA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.514T>C	8.37:g.17612803A>G	ENSP00000262102:p.Phe172Leu	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	224	34	NM_001001924	0	0	1	1	0	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.316888	0.40996	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.30182	2.43;2.5;2.43;1.54	4.09	2.91	0.33838	.	0.407817	0.21445	N	0.074440	T	0.21921	0.0528	L	0.32530	0.975	0.09310	N	0.999999	B;B;P	0.44139	0.356;0.206;0.827	B;B;B	0.43331	0.104;0.052;0.416	T	0.05886	-1.0858	9	.	.	.	-5.1088	5.1218	0.14863	0.5864:0.2499:0.0:0.1636	.	172;172;172	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	L	172	ENSP00000371293:F172L;ENSP00000262102:F172L;ENSP00000430167:F172L;ENSP00000371286:F172L	.	F	-	1	0	MTUS1	17657083	0.265000	0.24102	0.123000	0.21794	0.013000	0.08279	1.311000	0.33562	0.883000	0.36040	-0.490000	0.04691	TTT	.		0.438	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17612803	A	G	17612803	3	3	135	1	0	0	0	0	1	0	0	0	9990	72	3	3	3673	3	MTUS1	8	17612803	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	16098853	17612803	128751219	62	12033											
MYST3	7994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	41794945	41794945	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatctcaaacgtgggttctaAtcttggcattggcctctcgg	7	13	11	10	2	4	0	1	0	4	0	6	1	4	0	1	4	1	2	1	4	2	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:41794945A>T	ENST00000396930.3	-	17	3724	c.3181T>A	c.(3181-3183)Tta>Ata	p.L1061I	KAT6A_ENST00000265713.2_Missense_Mutation_p.L1061I|KAT6A_ENST00000406337.1_Missense_Mutation_p.L1061I	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1061					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GTGGGTTCTAATCTTGGCATT	0.428																																					p.L1061I		.											.	.	0			c.T3181A						.						120	115	117					8																	41794945		2203	4300	6503	SO:0001583	missense	7994	exon17			GTTCTAATCTTGG	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	13013	protein-coding gene	gene with protein product	"Monocytic leukemia zinc finger protein"	601408	"runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3"	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3181T>A	8.37:g.41794945A>T	ENSP00000380136:p.Leu1061Ile	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	281	58	NM_001099412	0	0	0	0	0	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	13.75	2.330228	0.41297	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	T;T;T	0.66099	-0.19;-0.19;-0.19	5.63	3.27	0.37495	.	0.000000	0.53938	D	0.000041	T	0.73853	0.3640	M	0.69823	2.125	0.42293	D	0.992149	D	0.69078	0.997	D	0.78314	0.991	T	0.72571	-0.4253	10	0.62326	D	0.03	-9.4799	7.9093	0.29780	0.6901:0.0:0.3099:0.0	.	1061	Q92794	KAT6A_HUMAN	I	1061;1061;1061;641	ENSP00000265713:L1061I;ENSP00000385888:L1061I;ENSP00000380136:L1061I	ENSP00000265713:L1061I	L	-	1	2	KAT6A	41914102	0.999000	0.42202	0.996000	0.52242	0.990000	0.78478	3.600000	0.54052	0.436000	0.26393	0.528000	0.53228	TTA	.		0.428	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		T	41794945	A	T	41794945	3	4	135	1	0	0	0	0	1	0	0	0	10129	98	4	5	2841	5	MYST3	8	41794945	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	24182142	41794945	104569077	63	12034											
WWP1	11059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	87423961	87423961	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgcagaattggaatctgaaGctagaagtatattagagcct	14	11	11	5	0	1	4	0	1	1	3	1	5	1	5	1	1	3	3	1	1	8	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:87423961G>C	ENST00000517970.1	+	9	1226	c.919G>C	c.(919-921)Gct>Cct	p.A307P	WWP1_ENST00000265428.4_Missense_Mutation_p.A307P|WWP1_ENST00000349423.2_Missense_Mutation_p.A89P|WWP1_ENST00000341922.2_Missense_Mutation_p.A177P	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	307					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						GGAATCTGAAGCTAGAAGTAT	0.408																																					p.A307P		.											.	WWP1-659	0			c.G919C						.						78	76	77					8																	87423961		2203	4300	6503	SO:0001583	missense	11059	exon9			TCTGAAGCTAGAA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.919G>C	8.37:g.87423961G>C	ENSP00000427793:p.Ala307Pro	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	111	18	NM_007013	0	0	4	5	1	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	37	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	5.203	0.222924	0.09863	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	T;T;T;T	0.46451	0.89;0.89;0.87;0.89	5.69	4.81	0.61882	.	0.669254	0.14402	N	0.321845	T	0.21962	0.0529	N	0.08118	0	0.39335	D	0.965486	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.003	T	0.08513	-1.0718	10	0.30078	T	0.28	.	7.2873	0.26346	0.1504:0.1403:0.7094:0.0	.	89;307	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	P	307;307;177;89	ENSP00000427793:A307P;ENSP00000265428:A307P;ENSP00000340564:A177P;ENSP00000342665:A89P	ENSP00000265428:A307P	A	+	1	0	WWP1	87493077	0.557000	0.26546	0.093000	0.20910	0.015000	0.08874	0.271000	0.18626	1.410000	0.46936	0.650000	0.86243	GCT	.		0.408	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		C	87423961	G	C	87423961	3	2	135	1	0	0	0	0	1	0	0	0	17448	971	34	4	945	4	WWP1	8	87423961	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	45629016	87423961	58940061	64	12035											
EIF3H	8667	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	117661151	117661151	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatcagcaactgtagattcTtccccaaatgattgctgaaa	13	11	6	11	0	2	3	1	2	1	1	3	3	3	3	3	0	3	3	3	0	4	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:117661151T>G	ENST00000276682.4	-	8	1530	c.764A>C	c.(763-765)aAg>aCg	p.K255T	EIF3H_ENST00000521861.1_Missense_Mutation_p.K241T					eukaryotic translation initiation factor 3, subunit H											large_intestine(2)|lung(10)|skin(1)	13	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					CTGTAGATTCTTCCCCAAATG	0.333																																					p.K241T													.	EIF3H-658	0			c.A722C						.						187	166	173					8																	117661151		2203	4300	6503	SO:0001583	missense	8667	exon6			AGATTCTTCCCCA	U54559	CCDS6319.1	8q24.11	2007-07-27	2007-07-27	2007-07-27	ENSG00000147677	ENSG00000147677			3273	protein-coding gene	gene with protein product		603912	"eukaryotic translation initiation factor 3, subunit 3 gamma, 40kDa"	EIF3S3		9341143	Standard	NM_003756		Approved	eIF3-gamma, eIF3-p40, eIF3h	uc003yoa.3	O15372	OTTHUMG00000164919	ENST00000276682.4:c.764A>C	8.37:g.117661151T>G	ENSP00000276682:p.Lys255Thr	Somatic	106	1		WXS	Illumina HiSeq	Phase_I	147	36	NM_003756	0	0	136	219	83		Missense_Mutation	SNP	ENST00000276682.4	37		.	.	.	.	.	.	.	.	.	.	T	26.6	4.753458	0.89753	.	.	ENSG00000147677	ENST00000521861;ENST00000276682;ENST00000518949	T;T	0.52526	0.69;0.66	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.69251	0.3090	M	0.81112	2.525	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.64144	0.922;0.922	T	0.73228	-0.4049	10	0.62326	D	0.03	-27.6801	16.4116	0.83717	0.0:0.0:0.0:1.0	.	255;241	B3KS98;O15372	.;EIF3H_HUMAN	T	241;255;209	ENSP00000429931:K241T;ENSP00000276682:K255T	ENSP00000276682:K255T	K	-	2	0	EIF3H	117730332	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	8.040000	0.89188	2.276000	0.75962	0.528000	0.53228	AAG	.		0.333	EIF3H-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000380913.1	NM_003756		G	117661151	T	G	117661151	3	3	135	1	0	0	0	0	1	0	0	0	5031	1609	56	5	348	5	EIF3H	8	117661151	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	30237190	117661151	28702871	65	12036											
PLIN2	123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	19126158	19126158	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagagcactggtcatggcCacggaggtgatggtcttcac	8	8	15	10	1	3	2	2	1	1	1	3	3	3	3	1	6	1	2	1	6	0	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:19126158C>A	ENST00000276914.2	-	3	359	c.180G>T	c.(178-180)gtG>gtT	p.V60V	PLIN2_ENST00000411567.1_Silent_p.V60V|PLIN2_ENST00000380465.3_Silent_p.V60V|PLIN2_ENST00000380464.3_Silent_p.V60V	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	60					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						TGGTCATGGCCACGGAGGTGA	0.527																																					p.V60V		.											.	PLIN2-92	0			c.G180T						.						160	124	136					9																	19126158		2203	4300	6503	SO:0001819	synonymous_variant	123	exon3			CATGGCCACGGAG	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.180G>T	9.37:g.19126158C>A		Somatic	207	0		WXS	Illumina HiSeq	Phase_I	263	49	NM_001122	0	1	21	53	31	Q9BSC3	Silent	SNP	ENST00000276914.2	37	CCDS6490.1																																																																																			.		0.527	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		A	19126158	C	A	19126158	2	1	135	1	0	0	0	0	0	0	0	1	12116	581	21	4		4	PLIN2	9	19126158	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		19126158	122087273	66	12037											
AGTPBP1	23287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	88233969	88233969	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aagcaacacctggtcgcattCcactgacttcaaagtaaaac	15	8	6	12	1	1	1	1	1	0	0	3	1	2	1	2	1	3	3	2	1	5	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:88233969C>G	ENST00000357081.3	-	17	2408	c.2264G>C	c.(2263-2265)gGa>gCa	p.G755A	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.G593A|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.G767A|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.G715A			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	755					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						TGGTCGCATTCCACTGACTTC	0.328																																					p.G715A		.											.	AGTPBP1-158	0			c.G2144C						.						92	93	92					9																	88233969		2203	4300	6503	SO:0001583	missense	23287	exon17			CGCATTCCACTGA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 1", "tubulinyl-Tyr carboxypeptidase", "carboxypeptidase-tubulin", "tyrosine carboxypeptidase", "soluble carboxypeptidase"	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.2264G>C	9.37:g.88233969C>G	ENSP00000349592:p.Gly755Ala	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	130	27	NM_015239	0	0	3	3	0	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	C	16.55	3.154898	0.57259	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.38	5.38	0.77491	.	0.097920	0.64402	D	0.000001	T	0.55593	0.1930	M	0.67517	2.055	0.80722	D	1	B;D;D;P	0.76494	0.34;0.992;0.999;0.729	B;P;D;B	0.73708	0.257;0.872;0.981;0.439	T	0.54057	-0.8350	10	0.48119	T	0.1	-15.9497	19.1333	0.93415	0.0:1.0:0.0:0.0	.	767;755;593;715	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	A	755;715;767;593	ENSP00000349592:G755A;ENSP00000365251:G715A;ENSP00000365277:G767A;ENSP00000402804:G593A	ENSP00000349592:G755A	G	-	2	0	AGTPBP1	87423789	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.890000	0.69774	2.532000	0.85374	0.650000	0.86243	GGA	.		0.328	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88233969	C	G	88233969	3	3	135	1	0	0	0	0	1	0	0	0	400	855	30	4	1456	4	AGTPBP1	9	88233969	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	69107811	88233969	52979462	67	12038											
ASS1	445	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	133342187	133342187	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acctgatggagtacgcaaagGtatggccgagtctccccacc	10	7	11	13	2	1	1	0	1	1	0	2	3	1	2	5	3	1	3	5	3	3	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:133342187G>C	ENST00000372394.1	+	7	976		c.e7+1		ASS1_ENST00000493984.2_Splice_Site|ASS1_ENST00000372393.3_Splice_Site|ASS1_ENST00000352480.5_Splice_Site			P00966	ASSY_HUMAN	argininosuccinate synthase 1						acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	GTACGCAAAGGTATGGCCGAG	0.612																																					.													.	ASS1-91	0			c.495+1G>C						.						104	84	90					9																	133342187		2203	4300	6503	SO:0001630	splice_region_variant	445	exon7			GCAAAGGTATGGC	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"argininosuccinate synthetase"	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.495+1G>C	9.37:g.133342187G>C		Somatic	171	1		WXS	Illumina HiSeq	Phase_I	226	30	NM_000050	0	0	0	0	0	Q6LDL2|Q86UZ0|Q96GT4	Splice_Site	SNP	ENST00000372394.1	37	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.498082	0.26861	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393;ENST00000422569;ENST00000443588	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8195	0.85742	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ASS1	132332008	1.000000	0.71417	0.996000	0.52242	0.068000	0.16541	8.950000	0.93019	2.187000	0.69744	0.462000	0.41574	.	.		0.612	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	Intron	C	133342187	G	C	133342187	5	2	135	1	0	0	0	0	0	0	1	0	1062	1275	44	4	514	4	ASS1	9	133342187	Splice_Site	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	45108218	133342187	7871244	68	12039											
PHPT1	29085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139744582	139744582	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagattcacgtgtacggctAttccatggtgagccgcagcc	9	9	12	11	3	1	2	1	1	0	1	2	3	2	2	3	2	3	3	3	2	3	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:139744582A>G	ENST00000247665.10	+	2	615	c.278A>G	c.(277-279)tAt>tGt	p.Y93C	MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000492540.1_3'UTR|MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Missense_Mutation_p.Y93C|PHPT1_ENST00000545326.1_Missense_Mutation_p.Y93C	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	93					negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		GTGTACGGCTATTCCATGGTG	0.662																																					p.Y93C		.											.	PHPT1-90	0			c.A278G						.						93	86	88					9																	139744582		2202	4300	6502	SO:0001583	missense	29085	exon2			ACGGCTATTCCAT	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"phosphohistidine phosphatase 14kDa", " sex-regulated protein janus-a"	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.278A>G	9.37:g.139744582A>G	ENSP00000247665:p.Tyr93Cys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	179	30	NM_001135861	0	0	1	7	6	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	.	.	.	.	.	.	.	.	.	.	.	22.3	4.267724	0.80469	.	.	ENSG00000054148	ENST00000371661;ENST00000545326;ENST00000247665	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	T	0.80979	0.4728	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.83346	-0.0005	8	0.46703	T	0.11	-0.3441	13.1692	0.59589	1.0:0.0:0.0:0.0	.	93;93	Q9NRX4-2;Q9NRX4	.;PHP14_HUMAN	C	93	.	ENSP00000247665:Y93C	Y	+	2	0	PHPT1	138864403	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	5.655000	0.67981	1.703000	0.51240	0.374000	0.22700	TAT	.		0.662	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		G	139744582	A	G	139744582	3	3	135	1	0	0	0	0	1	0	0	0	11886	449	16	3	284	3	PHPT1	9	139744582	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	6402395	139744582	1468849	69	12040											
ADARB2	105	broad.mit.edu	37	chr10	1405639	1405640	+	Frame_Shift_Ins	INS	-	-	G																															aactcctggaagagcgtgtcINSggggaaatcggcctggtcgg																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr10:1405639_1405640insG	ENST00000381312.1	-	3	985_986	c.660_661insC	c.(658-663)cccgacfs	p.D221fs	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	221					mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		AAGAGCGTGTCGGGGAAATCGG	0.762																																					p.D221fs													.	ADARB2-153	0			c.661_662insC						.																																			SO:0001589	frameshift_variant	105	exon3			GCGTGTCGGGGAA	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"RED2 homolog (rat)"	602065	"adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)", "adenosine deaminase, RNA-specific, B2"			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.661dupC	10.37:g.1405643_1405643dupG	ENSP00000370713:p.Asp221fs	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_018702	0	0	0	0	0	B2RPJ5|Q5VUT6|Q5VW42	Frame_Shift_Ins	INS	ENST00000381312.1	37	CCDS7058.1																																																																																			.		0.762	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		G	1405640	-	G	1405639	7	5	135	1	0	1	1	0	0	0	0	0	283	884	31	0	1590	0	ADARB2	10	1405639	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10		1405639	134129108	70	12041											
CSGALNACT2	55454	broad.mit.edu	37	chr10	43659419	43659419	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggacaagggagaggtcttGatgtttttctgtgatgttga	8	15	15	3	0	2	4	0	3	2	1	2	6	2	5	0	3	0	2	0	3	1	4	rs79064394		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr10:43659419G>T	ENST00000374466.3	+	5	1421	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	362					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.L362F(5)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GAGAGGTCTTGATGTTTTTCT	0.433																																					p.L362F													.	CSGALNACT2-69	5	Substitution - Missense(5)	endometrium(4)|kidney(1)	c.G1086T						.						223	221	222					10																	43659419		2203	4300	6503	SO:0001583	missense	55454	exon5			GGTCTTGATGTTT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1086G>T	10.37:g.43659419G>T	ENSP00000363590:p.Leu362Phe	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	173	6	NM_018590	0	0	3	3	0	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499782	0.85176	.	.	ENSG00000169826	ENST00000374466	T	0.27256	1.68	6.08	5.17	0.71159	.	0.064535	0.64402	D	0.000004	T	0.57359	0.2048	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63721	-0.6573	10	0.87932	D	0	-11.7375	14.8306	0.70146	0.0683:0.0:0.9317:0.0	.	362	Q8N6G5	CGAT2_HUMAN	F	362	ENSP00000363590:L362F	ENSP00000363590:L362F	L	+	3	2	CSGALNACT2	42979425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.894000	0.99253	0.591000	0.81541	TTG	.		0.433	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43659419	G	T	43659419	3	4	135	1	0	0	0	0	1	0	0	0	3945	1281	45	4	1100	4	CSGALNACT2	10	43659419	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	42253780	43659419	91875328	71	12042											
NOLC1	9221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103917872	103917872	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggccaagagctctgattctGattctgactcaagctccgag	10	10	10	11	1	4	4	1	3	3	1	5	5	5	4	2	1	2	2	2	1	2	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr10:103917872G>A	ENST00000605788.1	+	5	743	c.508G>A	c.(508-510)Gat>Aat	p.D170N	NOLC1_ENST00000405356.1_Missense_Mutation_p.D170N|NOLC1_ENST00000488254.2_Missense_Mutation_p.D171N|NOLC1_ENST00000603742.1_5'UTR	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	170	11 X 12 AA approximate repeats of an acidic serine cluster.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		CTCTGATTCTGATTCTGACTC	0.488																																					p.D170N		.											.	NOLC1-91	0			c.G508A						.						88	90	89					10																	103917872		2203	4300	6503	SO:0001583	missense	9221	exon5			GATTCTGATTCTG	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.508G>A	10.37:g.103917872G>A	ENSP00000474710:p.Asp170Asn	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	193	35	NM_004741	0	0	4	6	2	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948000	0.73787	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.52057	0.68	5.72	5.72	0.89469	.	0.256859	0.33834	N	0.004509	T	0.68796	0.3040	M	0.77313	2.365	0.80722	D	1	D;D;D	0.63046	0.992;0.992;0.986	P;P;P	0.61592	0.891;0.891;0.78	T	0.71341	-0.4622	10	0.66056	D	0.02	-7.6697	18.8652	0.92289	0.0:0.0:1.0:0.0	.	171;170;170	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	N	170	ENSP00000385410:D170N	ENSP00000359024:D170N	D	+	1	0	NOLC1	103907862	1.000000	0.71417	0.959000	0.39883	0.796000	0.44982	6.775000	0.75018	2.709000	0.92574	0.561000	0.74099	GAT	.		0.488	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		A	103917872	G	A	103917872	3	1	135	1	0	0	0	0	1	0	0	0	10555	1290	45	2	526	2	NOLC1	10	103917872	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	60258453	103917872	31616875	72	12043											
CNGA4	1262	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6261868	6261868	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagatgcggctttctacccaGatcatgcactggtgaagaag	11	9	11	10	1	2	4	1	1	1	3	2	4	2	4	1	2	3	2	1	2	3	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:6261868G>C	ENST00000379936.2	+	4	959	c.844G>C	c.(844-846)Gat>Cat	p.D282H	CNGA4_ENST00000533426.1_Splice_Site	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	282					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTTCTACCCAGATCATGCACT	0.552																																					p.D282H													.	CNGA4-91	0			c.G844C						.						100	89	93					11																	6261868		2201	4296	6497	SO:0001583	missense	1262	exon4			TACCCAGATCATG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2152	protein-coding gene	gene with protein product		609472	"cyclic nucleotide gated channel beta 2"	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.844G>C	11.37:g.6261868G>C	ENSP00000369268:p.Asp282His	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	292	49	NM_001037329	0	0	0	0	0		Missense_Mutation	SNP	ENST00000379936.2	37	CCDS31408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.83|14.83	2.653921|2.653921	0.47362|0.47362	.|.	.|.	ENSG00000132259|ENSG00000132259	ENST00000533426|ENST00000379936	.|D	.|0.96716	.|-4.1	5.3|5.3	4.39|4.39	0.52855|0.52855	.|Cyclic nucleotide-binding-like (1);	.|0.138507	.|0.64402	.|D	.|0.000004	.|D	.|0.92084	.|0.7491	N|N	0.25647|0.25647	0.755|0.755	0.40621|0.40621	D|D	0.981768|0.981768	.|B;B	.|0.21147	.|0.044;0.052	.|B;B	.|0.25884	.|0.008;0.064	.|D	.|0.89286	.|0.3615	.|10	.|0.66056	.|D	.|0.02	.|.	9.3632|9.3632	0.38208|0.38208	0.1652:0.0:0.8348:0.0|0.1652:0.0:0.8348:0.0	.|.	.|282;242	.|Q8IV77;Q8IV77-2	.|CNGA4_HUMAN;.	.|H	-1|282	.|ENSP00000369268:D282H	.|ENSP00000369268:D282H	.|D	+|+	.|1	.|0	CNGA4|CNGA4	6218444|6218444	0.664000|0.664000	0.27457|0.27457	0.997000|0.997000	0.53966|0.53966	0.939000|0.939000	0.58152|0.58152	1.232000|1.232000	0.32636|0.32636	1.376000|1.376000	0.46267|0.46267	0.561000|0.561000	0.74099|0.74099	.|GAT	.		0.552	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329		C	6261868	G	C	6261868	3	2	135	1	0	0	0	0	1	0	0	0	3605	942	33	4	858	4	CNGA4	11	6261868	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		6261868	128744648	73	12044											
DNHD1	144132	broad.mit.edu	37	chr11	6561201	6561201	+	Frame_Shift_Del	DEL	C	C	-																															cagctgcgcctgctcaacttCatcctgcatgtaccctacga																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:6561201delC	ENST00000527990.2	+	16	3516	c.3516delC	c.(3514-3516)ttcfs	p.F1172fs	DNHD1_ENST00000254579.6_Frame_Shift_Del_p.F1172fs			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1172					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TGCTCAACTTCATCCTGCATG	0.582																																					p.F1172fs													.	DNHD1-24	0			c.3516delC						.						62	66	65					11																	6561201		692	1591	2283	SO:0001589	frameshift_variant	144132	exon18			CAACTTCATCCTG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.3516delC	11.37:g.6561201delC	ENSP00000436180:p.Phe1172fs	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	220	19	NM_144666	0	0	0	0	0	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Frame_Shift_Del	DEL	ENST00000527990.2	37	CCDS44532.1																																																																																			.		0.582	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		-	6561201	C	-	6561201	7	5	135	1	0	1	0	1	0	0	0	0	4679	825	29	0	3587	0	DNHD1	11	6561201	Frame_Shift_Del	DEL	C	TCGA-HE-A5NK-01A-11D-A26P-10	299333	6561201	128445315	74	12045											
OR2AG2	338755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6789370	6789370	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgtgtagaaaacagagatGatgttgtcttgtttggggct	10	15	13	3	0	1	3	0	1	1	2	1	4	1	3	0	2	1	4	0	2	3	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:6789370G>T	ENST00000338569.2	-	1	916	c.819C>A	c.(817-819)atC>atA	p.I273I		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	273						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AAACAGAGATGATGTTGTCTT	0.512																																					p.I273I		.											.	OR2AG2-71	0			c.C819A						.						151	138	142					11																	6789370		2201	4296	6497	SO:0001819	synonymous_variant	338755	exon1			AGAGATGATGTTG	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"GPCR / Class A : Olfactory receptors"	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.819C>A	11.37:g.6789370G>T		Somatic	332	0		WXS	Illumina HiSeq	Phase_I	456	86	NM_001004490	0	0	0	0	0		Silent	SNP	ENST00000338569.2	37	CCDS31413.1																																																																																			.		0.512	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		T	6789370	G	T	6789370	2	4	135	1	0	0	0	0	0	0	0	1	11011	1280	45	4		4	OR2AG2	11	6789370	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	228169	6789370	128217146	75	12046											
RBM14	10432	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	66384484	66384484	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccaggaactgcgcagccTcttcgagcgccgcggacgcg	7	4	15	15	7	1	0	0	0	1	0	2	4	1	2	3	2	5	1	3	2	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:66384484T>C	ENST00000310137.4	+	1	432	c.293T>C	c.(292-294)cTc>cCc	p.L98P	RBM14_ENST00000409738.4_Missense_Mutation_p.L98P|RBM4_ENST00000503028.2_5'UTR|RBM14-RBM4_ENST00000511114.1_3'UTR|RBM14-RBM4_ENST00000412278.2_Missense_Mutation_p.L98P|RBM14_ENST00000393979.3_Missense_Mutation_p.L98P|RBM14_ENST00000443702.1_Missense_Mutation_p.L98P|RNU4-39P_ENST00000362455.1_RNA|RBM14-RBM4_ENST00000500635.2_Missense_Mutation_p.L98P|RBM4_ENST00000514361.3_Missense_Mutation_p.L98P|RBM14_ENST00000409372.1_Missense_Mutation_p.L98P	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	98	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTGCGCAGCCTCTTCGAGCGC	0.647																																					p.L98P		.											.	RBM14-92	0			c.T293C						.						52	62	59					11																	66384484		2141	4173	6314	SO:0001583	missense	10432	exon1			GCAGCCTCTTCGA	AF080561	CCDS8147.1, CCDS55772.1, CCDS55773.1	11q13.2	2013-02-12			ENSG00000239306	ENSG00000239306		"RNA binding motif (RRM) containing"	14219	protein-coding gene	gene with protein product	"coactivator activator", "SYT interacting protein"	612409				9285794	Standard	NM_006328		Approved	SIP, SYTIP1, COAA, DKFZp779J0927	uc001oit.3	Q96PK6	OTTHUMG00000140380	ENST00000310137.4:c.293T>C	11.37:g.66384484T>C	ENSP00000311747:p.Leu98Pro	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	67	8	NM_001198837	0	0	2	3	1	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	37	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.761857	0.69763	.	.	ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000248643;ENSG00000248643	ENST00000310137;ENST00000393979;ENST00000409372;ENST00000443702;ENST00000409738;ENST00000412278;ENST00000500635	T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.19	4.01	0.46588	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.257070	0.27811	N	0.017747	T	0.58977	0.2160	H	0.94808	3.585	0.80722	D	1	D;D;D;B	0.89917	1.0;0.999;0.995;0.213	D;D;D;B	0.87578	0.998;0.964;0.974;0.398	T	0.68002	-0.5524	10	0.59425	D	0.04	-4.9687	10.4857	0.44719	0.0:0.0:0.1621:0.8379	.	98;98;98;98	B0LM41;Q96PK6-2;Q2PYN1;Q96PK6	.;.;.;RBM14_HUMAN	P	98	ENSP00000311747:L98P;ENSP00000377548:L98P;ENSP00000386518:L98P;ENSP00000414650:L98P;ENSP00000386995:L98P;ENSP00000388552:L98P;ENSP00000421279:L98P	ENSP00000311747:L98P	L	+	2	0	RBM14;RBM14-RBM4	66141060	0.914000	0.31030	1.000000	0.80357	0.966000	0.64601	1.791000	0.38744	1.971000	0.57363	0.459000	0.35465	CTC	.		0.647	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		C	66384484	T	C	66384484	3	2	135	1	0	0	0	0	1	0	0	0	13147	1551	54	3	295	3	RBM14	11	66384484	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	59595114	66384484	68622032	76	12047											
FGF3	2248	broad.mit.edu;bcgsc.ca	37	chr11	69625251	69625251	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtccctgtggtccagcacgCggggcaggaacagggaggac	8	4	18	11	2	0	0	0	0	0	0	2	3	2	3	2	7	2	2	2	7	1	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:69625251C>T	ENST00000334134.2	-	3	632	c.542G>A	c.(541-543)cGc>cAc	p.R181H		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	181					anatomical structure morphogenesis (GO:0009653)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			GTCCAGCACGCGGGGCAGGAA	0.687																																					p.R181H													.	FGF3-847	0			c.G542A						.						22	24	23					11																	69625251		2190	4268	6458	SO:0001583	missense	2248	exon3			AGCACGCGGGGCA		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"INT-2 proto-oncogene protein", "oncogene INT2", "V-INT2 murine mammary tumor virus integration site oncogene homolog", "murine mammary tumor virus integration site 2, mouse"	164950	"fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.542G>A	11.37:g.69625251C>T	ENSP00000334122:p.Arg181His	Somatic	71	1		WXS	Illumina HiSeq	Phase_I	110	6	NM_005247	0	0	0	0	0	Q0VG69	Missense_Mutation	SNP	ENST00000334134.2	37	CCDS8195.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849693	0.91277	.	.	ENSG00000186895	ENST00000334134	T	0.69435	-0.4	4.01	4.01	0.46588	.	0.055897	0.64402	D	0.000002	T	0.73713	0.3622	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.73244	-0.4044	9	.	.	.	.	16.1475	0.81580	0.0:1.0:0.0:0.0	.	181	P11487	FGF3_HUMAN	H	181	ENSP00000334122:R181H	.	R	-	2	0	FGF3	69334432	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.414000	0.66405	1.763000	0.52060	0.462000	0.41574	CGC	C|1.000;T|0.000		0.687	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247		T	69625251	C	T	69625251	3	4	135	1	0	0	0	0	1	0	0	0	5872	768	27	1	181	1	FGF3	11	69625251	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	3240767	69625251	65381265	77	12048											
AQP11	282679	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	77301546	77301546	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaaagcggtcatcacagAggccgtctgctcctttctct	7	11	9	14	2	5	1	3	0	2	1	7	1	6	1	2	2	2	2	2	2	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:77301546A>G	ENST00000313578.3	+	1	867	c.509A>G	c.(508-510)gAg>gGg	p.E170G	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	170					endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			GTCATCACAGAGGCCGTCTGC	0.557																																					p.E170G													.	AQP11-90	0			c.A509G						.						119	115	117					11																	77301546		2200	4292	6492	SO:0001583	missense	282679	exon1			TCACAGAGGCCGT	AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301		"Ion channels / Aquaporins"	19940	protein-coding gene	gene with protein product		609914				16107722	Standard	NM_173039		Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.509A>G	11.37:g.77301546A>G	ENSP00000318770:p.Glu170Gly	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	197	39	NM_173039	0	0	0	1	1		Missense_Mutation	SNP	ENST00000313578.3	37	CCDS8251.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.576863	0.86645	.	.	ENSG00000178301	ENST00000313578	T	0.70399	-0.48	5.54	5.54	0.83059	Aquaporin-like (2);	0.000000	0.85682	D	0.000000	D	0.84737	0.5538	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87033	0.2136	10	0.87932	D	0	-14.4732	15.6787	0.77349	1.0:0.0:0.0:0.0	.	170	Q8NBQ7	AQP11_HUMAN	G	170	ENSP00000318770:E170G	ENSP00000318770:E170G	E	+	2	0	AQP11	76979194	1.000000	0.71417	0.812000	0.32479	0.716000	0.41182	7.467000	0.80930	2.107000	0.64212	0.402000	0.26972	GAG	.		0.557	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039		G	77301546	A	G	77301546	3	3	135	1	0	0	0	0	1	0	0	0	823	304	11	3	511	3	AQP11	11	77301546	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	7676295	77301546	57704970	78	12049											
MAML2	84441	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	95712439	95712440	+	Frame_Shift_Ins	INS	-	-	T																															ttagctgattgggtctgagaINSttcagacccctgaggggacc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:95712439_95712440insT	ENST00000524717.1	-	5	4427_4428	c.3143_3144insA	c.(3142-3144)aatfs	p.N1048fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	1048					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TGGGTCTGAGATTCAGACCCCT	0.5			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.N1048fs		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.3144_3145insA						.																																			SO:0001589	frameshift_variant	84441	exon5			.	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.3144dupA	11.37:g.95712441_95712441dupT	ENSP00000434552:p.Asn1048fs	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	214	49	NM_032427	0	0	0	0	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Ins	INS	ENST00000524717.1	37	CCDS44714.1																																																																																			.		0.5	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95712440	-	T	95712439	7	5	135	1	0	1	1	0	0	0	0	0	9231	330	12	0	330	0	MAML2	11	95712439	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	18410893	95712439	39294077	79	12050											
KIAA1377	57562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	101832493	101832493	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aatttggtgatgaagttaatCagataaccaattctgaaacc	16	12	7	6	0	2	4	1	3	1	1	2	4	2	4	2	1	2	1	2	1	6	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:101832493C>G	ENST00000263468.8	+	6	997	c.727C>G	c.(727-729)Cag>Gag	p.Q243E	KIAA1377_ENST00000537689.1_Missense_Mutation_p.Q44E	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	243										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		TGAAGTTAATCAGATAACCAA	0.313																																					p.Q243E		.											.	KIAA1377-136	0			c.C727G						.						39	42	41					11																	101832493		2199	4295	6494	SO:0001583	missense	57562	exon6			GTTAATCAGATAA	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.727C>G	11.37:g.101832493C>G	ENSP00000263468:p.Gln243Glu	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	73	14	NM_020802	0	0	0	0	0	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444976	0.25987	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07908	3.15;3.15	5.51	5.51	0.81932	.	0.475599	0.20115	N	0.098938	T	0.12860	0.0312	M	0.70595	2.14	0.22684	N	0.998852	B	0.24823	0.112	B	0.26094	0.066	T	0.07597	-1.0764	10	0.48119	T	0.1	0.0806	11.3463	0.49563	0.1257:0.6801:0.1941:0.0	.	243	Q9P2H0	K1377_HUMAN	E	243;44	ENSP00000263468:Q243E;ENSP00000443184:Q44E	ENSP00000263468:Q243E	Q	+	1	0	KIAA1377	101337703	0.999000	0.42202	0.995000	0.50966	0.907000	0.53573	1.559000	0.36320	2.595000	0.87683	0.561000	0.74099	CAG	.		0.313	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		G	101832493	C	G	101832493	3	3	135	1	0	0	0	0	1	0	0	0	8248	827	29	4	749	4	KIAA1377	11	101832493	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	6120054	101832493	33174023	80	12051											
OR8B2	26595	bcgsc.ca	37	chr11	124252684	124252692	+	In_Frame_Del	DEL	GGAGGAGGG	GGAGGAGGG	-																															ggtgctggtgcaggaaagctGgaggagggggagtatgtcac																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	GGAGGAGGG	GGAGGAGGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:124252684_124252692delGGAGGAGGG	ENST00000375013.2	-	1	566_574	c.548_556delCCCTCCTCC	c.(547-558)cccctcctccag>cag	p.PLL183del		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGGAAAGCTGGAGGAGGGGGAGTATGTC	0.488																																					p.183_186del													.	OR8B2-68	0			c.548_556del						.																																			SO:0001651	inframe_deletion	26595	exon1			AAAGCTGGAGGAG	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"GPCR / Class A : Olfactory receptors"	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.548_556delCCCTCCTCC	11.37:g.124252684_124252692delGGAGGAGGG	ENSP00000364152:p.Pro183_Leu185del	Somatic	871	1		WXS	Illumina HiSeq	Phase_1	1060	38	NM_001005468	0	0	0	0	0	Q8NGH2	In_Frame_Del	DEL	ENST00000375013.2	37	CCDS31708.1																																																																																			.		0.488	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468		-	124252692	GGAGGAGGG	-	124252684	7	5	135	1	0	1	0	1	0	0	0	0	11253	1357	47	0	388	0	OR8B2	11	124252684	In_Frame_Del	DEL	GGAGGAGGG	TCGA-HE-A5NK-01A-11D-A26P-10	22420191	124252684	10753832	81	12052											
CACNA1C	775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	2763057	2763057	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttcttcatctacgcggtgatCgggatgcaggtagggaggct	7	11	15	8	3	3	1	1	1	2	0	4	3	3	3	0	5	2	3	0	5	2	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:2763057C>T	ENST00000347598.4	+	35	4275	c.4275C>T	c.(4273-4275)atC>atT	p.I1425I	CACNA1C_ENST00000399617.1_Silent_p.I1377I|CACNA1C_ENST00000344100.3_Silent_p.I1399I|CACNA1C_ENST00000399637.1_Silent_p.I1377I|CACNA1C_ENST00000399597.1_Silent_p.I1377I|CACNA1C_ENST00000399638.1_Silent_p.I1405I|CACNA1C_ENST00000399644.1_Silent_p.I1377I|CACNA1C_ENST00000399641.1_Silent_p.I1377I|CACNA1C_ENST00000399601.1_Silent_p.I1377I|CACNA1C_ENST00000399606.1_Silent_p.I1397I|CACNA1C_ENST00000399603.1_Silent_p.I1377I|CACNA1C_ENST00000399621.1_Silent_p.I1377I|CACNA1C_ENST00000327702.7_Silent_p.I1377I|CACNA1C_ENST00000399595.1_Silent_p.I1366I|CACNA1C_ENST00000399649.1_Silent_p.I1364I|CACNA1C_ENST00000399655.1_Silent_p.I1377I|CACNA1C_ENST00000335762.5_Silent_p.I1402I|CACNA1C_ENST00000399629.1_Silent_p.I1394I|CACNA1C_ENST00000399634.1_Silent_p.I1377I|CACNA1C_ENST00000399591.1_Silent_p.I1366I|CACNA1C_ENST00000406454.3_Silent_p.I1377I|CACNA1C_ENST00000402845.3_Silent_p.I1377I	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1425					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGCGGTGATCGGGATGCAGG	0.627																																					p.I1425I		.											.	CACNA1C-34	0			c.C4275T						.						75	78	77					12																	2763057		2028	4203	6231	SO:0001819	synonymous_variant	775	exon35			GGTGATCGGGATG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.4275C>T	12.37:g.2763057C>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	109	27	NM_199460	0	0	0	0	0	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																			.		0.627	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2763057	C	T	2763057	2	4	135	1	0	0	0	0	0	0	0	1	2546	874	31	1		1	CACNA1C	12	2763057	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		2763057	131088838	82	12053											
A2M	2	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	9242617	9242617	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcacagtgaaattcacatTtcctgaaaaaaaaggccagt	16	9	7	9	0	2	2	2	2	0	0	3	2	3	2	2	1	0	1	2	1	5	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:9242617T>A	ENST00000318602.7	-	21	2906	c.2599A>T	c.(2599-2601)Aat>Tat	p.N867Y		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	867					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	AAATTCACATTTCCTGAAAAA	0.438																																					p.N867Y		.											.	A2M-515	0			c.A2599T						.						119	118	118					12																	9242617		1893	4112	6005	SO:0001583	missense	2	exon21			TCACATTTCCTGA	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2599A>T	12.37:g.9242617T>A	ENSP00000323929:p.Asn867Tyr	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	171	35	NM_000014	0	0	0	0	0	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.24|11.24	1.580426|1.580426	0.28180|0.28180	.|.	.|.	ENSG00000175899|ENSG00000175899	ENST00000543436|ENST00000318602;ENST00000540099	.|T	.|0.17054	.|2.3	5.68|5.68	3.33|3.33	0.38152|0.38152	.|.	.|0.737822	.|0.13068	.|N	.|0.416350	T|T	0.19327|0.19327	0.0464|0.0464	M|M	0.80028|0.80028	2.48|2.48	0.09310|0.09310	N|N	1|1	.|B	.|0.17465	.|0.022	.|B	.|0.15870	.|0.014	T|T	0.41998|0.41998	-0.9477|-0.9477	5|10	.|0.66056	.|D	.|0.02	.|.	0.9957|0.9957	0.01466|0.01466	0.1621:0.1524:0.1695:0.516|0.1621:0.1524:0.1695:0.516	.|.	.|867	.|P01023	.|A2MG_HUMAN	D|Y	114|867;882	.|ENSP00000323929:N867Y	.|ENSP00000323929:N867Y	E|N	-|-	3|1	2|0	A2M|A2M	9133884|9133884	0.000000|0.000000	0.05858|0.05858	0.405000|0.405000	0.26409|0.26409	0.850000|0.850000	0.48378|0.48378	0.257000|0.257000	0.18369|0.18369	0.955000|0.955000	0.37878|0.37878	-0.336000|-0.336000	0.08194|0.08194	GAA|AAT	.		0.438	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9242617	T	A	9242617	3	1	135	1	0	0	0	0	1	0	0	0	4	1841	64	5	1889	5	A2M	12	9242617	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	6479560	9242617	124609278	83	12054											
PTPRB	5787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	71002988	71002988	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggcacaacgcggcccccagGgtgtcactgctatagatgag	9	6	14	12	2	1	2	1	1	0	1	1	2	1	2	2	3	2	2	2	3	3	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:71002988G>A	ENST00000261266.5	-	2	215	c.186C>T	c.(184-186)acC>acT	p.T62T	PTPRB_ENST00000551525.1_Silent_p.T279T|PTPRB_ENST00000550857.1_Silent_p.T62T|PTPRB_ENST00000451516.2_Silent_p.T62T|PTPRB_ENST00000550358.1_Silent_p.T280T|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000538708.1_Silent_p.T62T|PTPRB_ENST00000334414.6_Silent_p.T280T	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	62	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CGGCCCCCAGGGTGTCACTGC	0.498																																					p.T280T		.											.	PTPRB-226	0			c.C840T						.						86	90	88					12																	71002988		1923	4116	6039	SO:0001819	synonymous_variant	5787	exon4			CCCCAGGGTGTCA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.186C>T	12.37:g.71002988G>A		Somatic	275	0		WXS	Illumina HiSeq	Phase_I	372	77	NM_001109754	0	0	0	0	0	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.252789	0.01469	.	.	ENSG00000127329	ENST00000547715	.	.	.	4.75	-4.0	0.04057	.	.	.	.	.	T	0.17023	0.0409	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.21930	-1.0231	4	.	.	.	.	0.6526	0.00829	0.3902:0.1252:0.1784:0.3062	.	.	.	.	S	54	.	.	P	-	1	0	PTPRB	69289255	0.707000	0.27866	0.000000	0.03702	0.051000	0.14879	-0.453000	0.06778	-1.290000	0.02372	-0.194000	0.12790	CCT	.		0.498	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			A	71002988	G	A	71002988	2	1	135	1	0	0	0	0	0	0	0	1	12828	1219	43	2		2	PTPRB	12	71002988	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	61760371	71002988	62848907	84	12055											
HIP1R	9026	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123342922	123342922	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggtgagcagggcccaggagGccttggatgccgtgagcacc	7	6	17	11	1	0	2	0	2	0	0	0	4	0	4	4	5	3	2	4	5	0	1	rs375880257		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:123342922G>A	ENST00000253083.4	+	20	2115	c.1990G>A	c.(1990-1992)Gcc>Acc	p.A664T		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	664					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GGCCCAGGAGGCCTTGGATGC	0.687													G|||	1	0.000199681	8e-04	0	5008	,	,		17393	0		0	False		,,,				2504	0				p.A664T													.	HIP1R-91	0			c.G1990A						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	54	53	54		1990	5.2	0.9	12		54	0,8600		0,0,4300	no	missense	HIP1R	NM_003959.1	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	664/1069	123342922	1,13005	2203	4300	6503	SO:0001583	missense	9026	exon20			CAGGAGGCCTTGG	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.1990G>A	12.37:g.123342922G>A	ENSP00000253083:p.Ala664Thr	Somatic	198	1		WXS	Illumina HiSeq	Phase_I	259	60	NM_003959	0	0	2	5	3	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	G	9.409	1.080136	0.20309	2.27E-4	0.0	ENSG00000130787	ENST00000253083	T	0.19105	2.17	5.24	5.24	0.73138	.	0.069873	0.56097	N	0.000030	T	0.19967	0.0480	L	0.49350	1.555	0.39383	D	0.966281	B	0.20550	0.046	B	0.14023	0.01	T	0.05566	-1.0877	10	0.17832	T	0.49	-27.4445	14.146	0.65351	0.0745:0.0:0.9255:0.0	.	664	O75146	HIP1R_HUMAN	T	664	ENSP00000253083:A664T	ENSP00000253083:A664T	A	+	1	0	HIP1R	121908875	1.000000	0.71417	0.941000	0.38009	0.429000	0.31625	5.185000	0.65076	2.436000	0.82500	0.561000	0.74099	GCC	.		0.687	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		A	123342922	G	A	123342922	3	1	135	1	0	0	0	0	1	0	0	0	7136	1203	42	2	2068	2	HIP1R	12	123342922	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	52339934	123342922	10508973	85	12056											
PGAM5	192111	hgsc.bcm.edu;bcgsc.ca	37	chr12	133294130	133294130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatagagaccaccgataTcatcagccggcacctgccag	11	5	9	16	3	2	1	2	0	0	1	2	3	2	1	6	1	2	1	6	1	2	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:133294130T>C	ENST00000498926.2	+	3	534	c.476T>C	c.(475-477)aTc>aCc	p.I159T	PGAM5_ENST00000543955.1_Missense_Mutation_p.I10T|PGAM5_ENST00000454808.2_Missense_Mutation_p.I10T|PGAM5_ENST00000317555.2_Missense_Mutation_p.I159T|PXMP2_ENST00000545677.1_3'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	159					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		ACCACCGATATCATCAGCCGG	0.632																																					p.I159T		.											.	PGAM5-90	0			c.T476C						.						49	55	53					12																	133294130		2203	4298	6501	SO:0001583	missense	192111	exon3			CCGATATCATCAG	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.476T>C	12.37:g.133294130T>C	ENSP00000438465:p.Ile159Thr	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	43	4	NM_138575	0	0	8	8	0	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	37	CCDS53845.1	.	.	.	.	.	.	.	.	.	.	T	19.44	3.827390	0.71143	.	.	ENSG00000247077	ENST00000317555;ENST00000498926;ENST00000543955;ENST00000454808	T;T	0.73681	1.36;-0.77	5.6	5.6	0.85130	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	D	0.86577	0.5966	M	0.79693	2.465	0.80722	D	1	D;D	0.76494	0.999;0.988	D;D	0.81914	0.995;0.962	D	0.88249	0.2915	10	0.66056	D	0.02	-3.8102	15.8035	0.78473	0.0:0.0:0.0:1.0	.	159;159	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	T	159;159;10;10	ENSP00000321503:I159T;ENSP00000438465:I159T	ENSP00000321503:I159T	I	+	2	0	PGAM5	131804203	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	7.459000	0.80802	2.130000	0.65690	0.482000	0.46254	ATC	.		0.632	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		C	133294130	T	C	133294130	3	2	135	1	0	0	0	0	1	0	0	0	11802	1435	50	3	486	3	PGAM5	12	133294130	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	9951208	133294130	557765	86	12057											
MTRF1	9617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41791352	41791352	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatccaggcccttcccacCacataaaaattcctggtaaa	13	9	5	14	0	0	1	0	1	0	0	3	1	3	1	5	2	0	1	5	2	5	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr13:41791352C>T	ENST00000379480.4	-	10	1337	c.1237G>A	c.(1237-1239)Ggt>Agt	p.G413S	MTRF1_ENST00000379477.1_Missense_Mutation_p.G413S|MTRF1_ENST00000430347.2_Silent_p.V461V	NM_004294.2	NP_004285.2	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	413					regulation of translational termination (GO:0006449)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)			breast(1)|endometrium(4)|large_intestine(3)|lung(6)	14		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		CCCTTCCCACCACATAAAAAT	0.348																																					p.G413S		.											.	MTRF1-90	0			c.G1237A						.						56	61	59					13																	41791352		2203	4300	6503	SO:0001583	missense	9617	exon10			TCCCACCACATAA	AF072934	CCDS9378.1	13q14.1-q14.3	2008-07-18			ENSG00000120662	ENSG00000120662			7469	protein-coding gene	gene with protein product	"mitochontrial peptide chain release factor 1"	604601				9838146, 10773675	Standard	NM_004294		Approved	RF1, MTTRF1, MGC47721	uc001uxy.3	O75570	OTTHUMG00000016790	ENST00000379480.4:c.1237G>A	13.37:g.41791352C>T	ENSP00000368793:p.Gly413Ser	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	181	38	NM_004294	0	0	0	0	0	B4DG01|Q5T6Y5|Q8IUQ6	Missense_Mutation	SNP	ENST00000379480.4	37	CCDS9378.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.505562	0.64410	.	.	ENSG00000120662	ENST00000379480;ENST00000379477	T;T	0.58210	0.35;0.35	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75068	-0.3448	10	0.87932	D	0	-9.2822	16.8351	0.85955	0.0:1.0:0.0:0.0	.	413	O75570	RF1M_HUMAN	S	413	ENSP00000368793:G413S;ENSP00000368790:G413S	ENSP00000368790:G413S	G	-	1	0	MTRF1	40689352	1.000000	0.71417	1.000000	0.80357	0.228000	0.25075	4.053000	0.57427	2.583000	0.87209	0.655000	0.94253	GGT	.		0.348	MTRF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044666.3	NM_004294		T	41791352	C	T	41791352	3	4	135	1	0	0	0	0	1	0	0	0	9984	594	21	2	104	2	MTRF1	13	41791352	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		41791352	73378526	87	12058											
BCL2L2	599	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23776985	23776985	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atagccgcccggatggcgacCccagcctcggccccagacac	8	3	11	19	4	0	1	0	0	0	1	1	3	0	2	7	3	2	0	7	3	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr14:23776985C>A	ENST00000250405.5	+	3	238	c.9C>A	c.(7-9)acC>acA	p.T3T	BCL2L2-PABPN1_ENST00000557008.1_Silent_p.T3T|BCL2L2-PABPN1_ENST00000553781.1_Silent_p.T3T	NM_001199839.1|NM_004050.4	NP_001186768.1|NP_004041	Q92843	B2CL2_HUMAN	BCL2-like 2	3					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|Sertoli cell proliferation (GO:0060011)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|lung(4)|prostate(1)	6	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00654)		GGATGGCGACCCCAGCCTCGG	0.562																																					p.T3T		.											.	.	0			c.C9A						.						53	63	60					14																	23776985		2203	4298	6501	SO:0001819	synonymous_variant	100529063	exon3			GGCGACCCCAGCC	D87461	CCDS9591.1	14q11.2-q12	2014-03-07			ENSG00000129473	ENSG00000129473		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	995	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 51"	601931				8761287	Standard	NM_001199839		Approved	KIAA0271, BCL-W, PPP1R51		Q92843	OTTHUMG00000028738	ENST00000250405.5:c.9C>A	14.37:g.23776985C>A		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_001199864	0	0	1	1	0	A8K0F4|Q2M3U0|Q5U0H4	Silent	SNP	ENST00000250405.5	37	CCDS9591.1																																																																																			.		0.562	BCL2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071763.3	NM_004050		A	23776985	C	A	23776985	2	1	135	1	0	0	0	0	0	0	0	1	1375	610	22	4		4	BCL2L2	14	23776985	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		23776985	83572555	88	12059											
SAV1	60485	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	51132105	51132106	+	Frame_Shift_Del	DEL	CT	CT	-																															aatgactgagaagaaccataCtctctagggacatctgctag																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr14:51132105_51132106delCT	ENST00000324679.4	-	2	689_690	c.326_327delAG	c.(325-327)gagfs	p.E109fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	109					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					AAGAACCATACTCTCTAGGGAC	0.376																																					p.109_109del		.											.	SAV1-658	0			c.326_327del						.																																			SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.326_327delAG	14.37:g.51132109_51132110delCT	ENSP00000324729:p.Glu109fs	Somatic	725	0		WXS	Illumina HiSeq	Phase_I	757	161	NM_021818	0	0	0	0	0	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Frame_Shift_Del	DEL	ENST00000324679.4	37	CCDS9701.1																																																																																			.		0.376	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			-	51132106	CT	-	51132105	7	5	135	1	0	1	0	1	0	0	0	0	13888	564	20	0	840	0	SAV1	14	51132105	Frame_Shift_Del	DEL	CT	TCGA-HE-A5NK-01A-11D-A26P-10	27355120	51132105	56217435	89	12060											
MAP1A	4130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43817788	43817788	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttacagcagaaagacaaaActctggagcacaaggaggtg	16	7	11	7	0	1	2	0	0	1	2	1	4	1	4	0	3	4	2	0	3	5	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr15:43817788A>G	ENST00000300231.5	+	4	4567	c.4117A>G	c.(4117-4119)Act>Gct	p.T1373A	MAP1A_ENST00000382031.1_Missense_Mutation_p.T1611A|MAP1A_ENST00000399453.1_Missense_Mutation_p.T1373A			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1373					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GAAAGACAAAACTCTGGAGCA	0.443																																					p.T1373A		.											.	MAP1A-141	0			c.A4117G						.						99	96	97					15																	43817788		1906	4125	6031	SO:0001583	missense	4130	exon4			GACAAAACTCTGG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4117A>G	15.37:g.43817788A>G	ENSP00000300231:p.Thr1373Ala	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	171	52	NM_002373	0	0	0	1	1	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	A	9.136	1.012745	0.19277	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.02280	4.36;4.36;4.36	4.47	1.97	0.26223	.	.	.	.	.	T	0.02807	0.0084	M	0.63428	1.95	0.09310	N	0.999998	B	0.33549	0.417	B	0.30495	0.116	T	0.41431	-0.9509	9	0.27785	T	0.31	0.3065	5.6758	0.17747	0.7318:0.171:0.0972:0.0	.	1373	P78559	MAP1A_HUMAN	A	1611;1373;1373	ENSP00000371462:T1611A;ENSP00000382380:T1373A;ENSP00000300231:T1373A	ENSP00000300231:T1373A	T	+	1	0	MAP1A	41605080	0.004000	0.15560	0.999000	0.59377	0.716000	0.41182	1.917000	0.39996	0.866000	0.35629	0.460000	0.39030	ACT	.		0.443	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		G	43817788	A	G	43817788	3	3	135	1	0	0	0	0	1	0	0	0	9252	43	2	3	4119	3	MAP1A	15	43817788	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		43817788	58713604	90	12061											
CP110	9738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19548820	19548820	+	Missense_Mutation	SNP	A	A	T																															cataacaagtggaataactgAacaagaaaggcaacatttgc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:19548820A>T	ENST00000381396.5	+	4	2076	c.1829A>T	c.(1828-1830)gAa>gTa	p.E610V	CCP110_ENST00000396212.2_Missense_Mutation_p.E610V|CCP110_ENST00000396208.2_Missense_Mutation_p.E610V	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	610					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						GGAATAACTGAACAAGAAAGG	0.348																																					p.E610V		.											.	CCP110-90	0			c.A1829T						.						67	72	70					16																	19548820		2197	4300	6497	SO:0001583	missense	9738	exon4			TAACTGAACAAGA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1829A>T	16.37:g.19548820A>T	ENSP00000370803:p.Glu610Val	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	235	40	NM_001199022	0	0	0	0	0	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.527464	0.44969	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.16897	2.31;2.31;2.31	5.17	5.17	0.71159	.	0.139138	0.46145	D	0.000310	T	0.16557	0.0398	L	0.58101	1.795	0.30579	N	0.762718	P;P	0.45715	0.865;0.865	B;B	0.42555	0.391;0.391	T	0.30090	-0.9990	10	0.48119	T	0.1	-1.1381	3.1962	0.06634	0.6412:0.1436:0.0771:0.1382	.	610;610	O43303;O43303-2	CP110_HUMAN;.	V	610	ENSP00000379515:E610V;ENSP00000370803:E610V;ENSP00000379511:E610V	ENSP00000370803:E610V	E	+	2	0	CCP110	19456321	1.000000	0.71417	0.981000	0.43875	0.972000	0.66771	2.685000	0.46959	1.933000	0.56026	0.460000	0.39030	GAA	.		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		T	19548820	A	T	19548820	3	4	135	1	0	0	0	0	1	0	0	0	3794	246	9	5	1839	5	CP110	16	19548820	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		19548820	70805933	91	12062	122	2									
CP110	9738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19548822	19548822	+	Missense_Mutation	SNP	C	C	A																															taacaagtggaataactgaaCaagaaaggcaacatttgcca																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:19548822C>A	ENST00000381396.5	+	4	2078	c.1831C>A	c.(1831-1833)Caa>Aaa	p.Q611K	CCP110_ENST00000396212.2_Missense_Mutation_p.Q611K|CCP110_ENST00000396208.2_Missense_Mutation_p.Q611K	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	611					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						AATAACTGAACAAGAAAGGCA	0.348																																					p.Q611K		.											.	CCP110-90	0			c.C1831A						.						66	71	69					16																	19548822		2197	4300	6497	SO:0001583	missense	9738	exon4			ACTGAACAAGAAA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.1831C>A	16.37:g.19548822C>A	ENSP00000370803:p.Gln611Lys	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	234	40	NM_001199022	0	0	0	0	0	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694577	0.48202	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.19105	2.17;2.17;2.17	5.17	5.17	0.71159	.	0.260422	0.33127	N	0.005246	T	0.25005	0.0607	L	0.58101	1.795	0.35963	D	0.834752	P;P	0.41978	0.767;0.767	B;B	0.41510	0.359;0.359	T	0.33904	-0.9850	10	0.72032	D	0.01	-0.143	12.0805	0.53667	0.0:0.9211:0.0:0.0789	.	611;611	O43303;O43303-2	CP110_HUMAN;.	K	611	ENSP00000379515:Q611K;ENSP00000370803:Q611K;ENSP00000379511:Q611K	ENSP00000370803:Q611K	Q	+	1	0	CCP110	19456323	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	3.793000	0.55484	2.385000	0.81259	0.563000	0.77884	CAA	.		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		A	19548822	C	A	19548822	3	1	135	1	0	0	0	0	1	0	0	0	3794	479	17	4	1841	4	CP110	16	19548822	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	2	19548822	70805931	92	12063	122	2									
PRR14	78994	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	30666137	30666137	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgtcccccccaatgaagctGgagttgaagatcgccatctc	9	8	9	15	2	1	3	0	2	1	1	4	4	2	4	5	1	1	2	5	1	3	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:30666137G>A	ENST00000542965.2	+	7	1302	c.846G>A	c.(844-846)ctG>ctA	p.L282L	PRR14_ENST00000300835.4_Silent_p.L282L			Q9BWN1	PRR14_HUMAN	proline rich 14	282	Pro-rich.									breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CAATGAAGCTGGAGTTGAAGA	0.637																																					p.L282L		.											.	PRR14-90	0			c.G846A						.						19	23	21					16																	30666137		2192	4295	6487	SO:0001819	synonymous_variant	78994	exon8			GAAGCTGGAGTTG	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.846G>A	16.37:g.30666137G>A		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	37	6	NM_024031	0	0	9	16	7	Q8WTX2	Silent	SNP	ENST00000542965.2	37	CCDS10687.1																																																																																			.		0.637	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031		A	30666137	G	A	30666137	2	1	135	1	0	0	0	0	0	0	0	1	12615	1335	47	2		2	PRR14	16	30666137	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	11117315	30666137	59688616	93	12064											
ITGAX	3687	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	31374006	31374006	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccccgctaccagcacaccGggaaggctgtcatcttcacc	8	6	8	19	2	3	0	2	0	1	0	3	1	3	1	6	2	2	3	6	2	2	2	rs554674355		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:31374006G>C	ENST00000268296.4	+	12	1412	c.1291G>C	c.(1291-1293)Ggg>Cgg	p.G431R	ITGAX_ENST00000562522.1_Missense_Mutation_p.G431R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	431					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCAGCACACCGGGAAGGCTGT	0.647																																					p.G431R		.											.	ITGAX-229	0			c.G1291C						.						34	33	33					16																	31374006		2197	4300	6497	SO:0001583	missense	3687	exon12			CACACCGGGAAGG	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1291G>C	16.37:g.31374006G>C	ENSP00000268296:p.Gly431Arg	Somatic	371	0		WXS	Illumina HiSeq	Phase_I	523	116	NM_000887	0	0	9	10	1	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	g	18.79	3.698354	0.68386	.	.	ENSG00000140678	ENST00000268296	T	0.54479	0.57	3.76	2.69	0.31865	.	.	.	.	.	T	0.80979	0.4728	H	0.98559	4.265	0.33798	D	0.62635	D	0.89917	1.0	D	0.87578	0.998	D	0.87513	0.2441	9	0.87932	D	0	.	10.1899	0.43019	0.0:0.2038:0.7962:0.0	.	431	P20702	ITAX_HUMAN	R	431	ENSP00000268296:G431R	ENSP00000268296:G431R	G	+	1	0	ITGAX	31281507	0.999000	0.42202	0.997000	0.53966	0.899000	0.52679	3.647000	0.54403	1.829000	0.53265	0.448000	0.29417	GGG	.		0.647	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		C	31374006	G	C	31374006	3	2	135	1	0	0	0	0	1	0	0	0	7910	1116	39	4	1337	4	ITGAX	16	31374006	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	707869	31374006	58980747	94	12065											
ALOX12B	242	ucsc.edu;bcgsc.ca	37	chr17	7990699	7990699	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccacaatggtcagtgagatgGagtcccgtgttcccgacaag	10	8	12	11	2	1	1	1	1	0	1	3	4	3	2	3	2	0	1	3	2	2	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:7990699G>C	ENST00000319144.4	-	1	322	c.62C>G	c.(61-63)tCc>tGc	p.S21C	MIR4314_ENST00000583321.1_RNA	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	21	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						CAGTGAGATGGAGTCCCGTGT	0.577										Multiple Myeloma(8;0.094)																											p.S21C													.	ALOX12B-226	0			c.C62G						.						263	188	213					17																	7990699		2203	4300	6503	SO:0001583	missense	242	exon1			GAGATGGAGTCCC	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"Arachidonate lipoxygenases"	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.62C>G	17.37:g.7990699G>C	ENSP00000315167:p.Ser21Cys	Somatic	329	2		WXS	Illumina HiSeq		389	82	NM_001139	0	0	0	0	0		Missense_Mutation	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	G	6.255	0.415202	0.11870	.	.	ENSG00000179477	ENST00000319144	T	0.77750	-1.12	4.78	-3.77	0.04346	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.472031	0.23382	N	0.048781	T	0.64034	0.2562	L	0.35854	1.095	0.09310	N	0.999999	B	0.15719	0.014	B	0.24394	0.053	T	0.55140	-0.8187	10	0.40728	T	0.16	-16.6531	11.2422	0.48977	0.0:0.4855:0.3194:0.1951	.	21	O75342	LX12B_HUMAN	C	21	ENSP00000315167:S21C	ENSP00000315167:S21C	S	-	2	0	ALOX12B	7931424	0.993000	0.37304	0.042000	0.18584	0.279000	0.26890	0.479000	0.22228	-0.316000	0.08690	-0.314000	0.08810	TCC	.		0.577	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			C	7990699	G	C	7990699	3	2	135	1	0	0	0	0	1	0	0	0	537	1174	41	4	2103	4	ALOX12B	17	7990699	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		7990699	73204511	95	12066											
GHDC	84514	broad.mit.edu;bcgsc.ca	37	chr17	40344519	40344519	+	Frame_Shift_Del	DEL	A	A	-																															catcagtctccaggcccaagAaaacatccagaagttcgaca																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:40344519delA	ENST00000301671.8	-	4	1070	c.629delT	c.(628-630)ttcfs	p.F210fs	GHDC_ENST00000587427.1_Frame_Shift_Del_p.F210fs|GHDC_ENST00000436923.2_Frame_Shift_Del_p.F210fs|GHDC_ENST00000593209.1_Frame_Shift_Del_p.F210fs|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000414034.3_Frame_Shift_Del_p.F210fs|GHDC_ENST00000428494.2_Frame_Shift_Del_p.F171fs			Q8N2G8	GHDC_HUMAN	GH3 domain containing	210						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CAGGCCCAAGAAAACATCCAG	0.652																																					p.F210fs													.	GHDC-90	0			c.629delT						.						82	94	89					17																	40344519		2202	4298	6500	SO:0001589	frameshift_variant	84514	exon5			CCCAAGAAAACAT	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.629delT	17.37:g.40344519delA	ENSP00000301671:p.Phe210fs	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	194	19	NM_001142623	0	0	0	0	0	B4DQS4|E9PDB5|Q9BXM6	Frame_Shift_Del	DEL	ENST00000301671.8	37	CCDS11422.1																																																																																			.		0.652	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		-	40344519	A	-	40344519	7	5	135	1	0	1	0	1	0	0	0	0	6389	246	9	0	1076	0	GHDC	17	40344519	Frame_Shift_Del	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	32353820	40344519	40850691	96	12067											
AOC3	8639	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41004649	41004649	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaatacgtgatgccttttGtgtgtttgaacagaaccagg	11	12	11	7	1	0	3	0	2	0	1	0	4	0	3	2	1	4	1	2	1	4	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:41004649G>A	ENST00000308423.2	+	1	1449	c.1289G>A	c.(1288-1290)tGt>tAt	p.C430Y	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	430					amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	GATGCCTTTTGTGTGTTTGAA	0.592																																					p.C430Y	NSCLC(3;192 220 10664 11501 16477)												.	AOC3-516	0			c.G1289A						.						96	85	89					17																	41004649		2203	4300	6503	SO:0001583	missense	8639	exon1			CCTTTTGTGTGTT	AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"vascular adhesion protein 1"	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.1289G>A	17.37:g.41004649G>A	ENSP00000312326:p.Cys430Tyr	Somatic	397	1		WXS	Illumina HiSeq	Phase_I	489	78	NM_003734	0	0	0	0	0	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	37	CCDS11444.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749416	0.69533	.	.	ENSG00000131471	ENST00000308423	T	0.11604	2.76	4.64	4.64	0.57946	Copper amine oxidase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.45357	0.1338	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60850	-0.7181	10	0.87932	D	0	.	18.0666	0.89392	0.0:0.0:1.0:0.0	.	430	Q16853	AOC3_HUMAN	Y	430	ENSP00000312326:C430Y	ENSP00000312326:C430Y	C	+	2	0	AOC3	38258175	1.000000	0.71417	1.000000	0.80357	0.780000	0.44128	7.595000	0.82710	2.591000	0.87537	0.591000	0.81541	TGT	.		0.592	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734		A	41004649	G	A	41004649	3	1	135	1	0	0	0	0	1	0	0	0	728	1377	48	2	1291	2	AOC3	17	41004649	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	660130	41004649	40190561	97	12068											
MMD	23531	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	53485137	53485138	+	Frame_Shift_Ins	INS	-	-	AG																															agaagcagcaatgaagaaatINSagataaccattctatcacac																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:53485137_53485138insAG	ENST00000262065.3	-	4	609_610	c.313_314insCT	c.(313-315)tatfs	p.Y105fs		NM_012329.2	NP_036461.2	Q15546	PAQRB_HUMAN	monocyte to macrophage differentiation-associated	105					cytolysis (GO:0019835)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						AATGAAGAAATAGATAACCATT	0.386																																					p.Y105fs		.											.	MMD-90	0			c.314_315insCT						.																																			SO:0001589	frameshift_variant	23531	exon4			.	X85750	CCDS11586.1	17q	2008-05-02				ENSG00000108960			7153	protein-coding gene	gene with protein product		604467				7503749, 16044242	Standard	NM_012329		Approved	MMA, PAQR11	uc002iui.3	Q15546		ENST00000262065.3:c.312_313dupCT	17.37:g.53485138_53485139dupAG	ENSP00000262065:p.Tyr105fs	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	115	31	NM_012329	0	0	0	0	0	B2R6X9|D3DTY6|Q8TAN7	Frame_Shift_Ins	INS	ENST00000262065.3	37	CCDS11586.1																																																																																			.		0.386	MMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439214.1			AG	53485138	-	AG	53485137	7	5	135	1	0	1	1	0	0	0	0	0	9668	1406	49	0	418	0	MMD	17	53485137	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	12480488	53485137	27710073	98	12069											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833490	56833490	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacccgaacccgaacccgaGtccgagcccgagcccgaacc	11	1	10	19	6	0	0	0	0	0	0	1	7	1	0	7	0	6	0	7	0	4	0	rs59676153		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:56833490G>A	ENST00000308249.2	+	1	261	c.132G>A	c.(130-132)gaG>gaA	p.E44E		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			ccgaacccgagtccgagcccg	0.706																																					p.E44E		.											.	PPM1E-291	0			c.G132A						.																																			SO:0001819	synonymous_variant	22843	exon1			ACCCGAGTCCGAG	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19322	protein-coding gene	gene with protein product	"partner of PIX 1", "nuclear calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1E (PP2C domain containing)"			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.132G>A	17.37:g.56833490G>A		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	97	9	NM_014906	0	0	0	0	0	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	37	CCDS11613.1																																																																																			.		0.706	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		A	56833490	G	A	56833490	2	1	135	1	0	0	0	0	0	0	0	1	12367	1020	36	2		2	PPM1E	17	56833490	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	3348353	56833490	24361720	99	12070											
CLTC	1213	ucsc.edu	37	chr17	57746160	57746160	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttttattttctgggatcCattgttaactttagccagga	8	18	7	8	0	2	0	0	0	2	0	3	2	3	2	2	2	2	1	2	2	3	8			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:57746160C>T	ENST00000269122.3	+	14	2425	c.2151C>T	c.(2149-2151)tcC>tcT	p.S717S	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Silent_p.S717S	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	717	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TTCTGGGATCCATTGTTAACT	0.328			T	"ALK, TFE3"	"ALCL, renal "																																p.S717S				Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC-835	0			c.C2151T						.						125	119	121					17																	57746160		2203	4300	6503	SO:0001819	synonymous_variant	1213	exon14			GGGATCCATTGTT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2151C>T	17.37:g.57746160C>T		Somatic	39	0		WXS	Illumina HiSeq		28	4	NM_004859	0	0	9	9	0	D3DU00|Q6N0A0|Q86TF2	Silent	SNP	ENST00000269122.3	37	CCDS32696.1																																																																																			.		0.328	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		T	57746160	C	T	57746160	2	4	135	1	0	0	0	0	0	0	0	1	3572	581	21	2		2	CLTC	17	57746160	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	912670	57746160	23449050	100	12071											
KCNH6	81033	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	61616010	61616010	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	atcctgcgcgacgacgtggtCgtggccatcctaggtgggtc	5	9	15	12	5	0	0	0	0	0	0	4	2	2	0	3	4	1	0	3	4	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:61616010C>G	ENST00000583023.1	+	8	1952	c.1941C>G	c.(1939-1941)gtC>gtG	p.V647V	KCNH6_ENST00000314672.5_Silent_p.V647V|KCNH6_ENST00000581784.1_Silent_p.V594V|KCNH6_ENST00000456941.2_Silent_p.V594V	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	647					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	ACGACGTGGTCGTGGCCATCC	0.662																																					p.V647V													.	KCNH6-91	0			c.C1941G						.						46	42	43					17																	61616010		2203	4300	6503	SO:0001819	synonymous_variant	81033	exon8			CGTGGTCGTGGCC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1941C>G	17.37:g.61616010C>G		Somatic	264	2		WXS	Illumina HiSeq	Phase_I	331	67	NM_030779	0	0	0	0	0	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			.		0.662	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		G	61616010	C	G	61616010	2	3	135	1	0	0	0	0	0	0	0	1	8057	871	31	4		4	KCNH6	17	61616010	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	3869850	61616010	19579200	101	12072											
RNF213	57674	broad.mit.edu;bcgsc.ca	37	chr17	78350139	78350141	+	In_Frame_Del	DEL	GAT	GAT	-																															aaattcattggcgaatgcaaGatcctttcacctcctgatat																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:78350139_78350141delGAT	ENST00000582970.1	+	52	13367_13369	c.13224_13226delGAT	c.(13222-13227)aagatc>aac	p.4408_4409KI>N	RNF213_ENST00000336301.6_In_Frame_Del_p.2481_2482KI>N|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_In_Frame_Del_p.4457_4458KI>N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4408					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCGAATGCAAGATCCTTTCACCT	0.433																																					p.4408_4409del													.	RNF213-577	0			c.13224_13226del						.																																			SO:0001651	inframe_deletion	57674	exon52			ATGCAAGATCCTT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"RING-type (C3HC4) zinc fingers"	14539	protein-coding gene	gene with protein product		613768	"chromosome 17 open reading frame 27", "KIAA1618", "moyamoya disease 2", "Moyamoya disease 2"	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13224_13226delGAT	17.37:g.78350139_78350141delGAT	ENSP00000464087:p.Lys4408_Ile4409delinsAsn	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	254	32	NM_001256071	0	0	0	0	0	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	In_Frame_Del	DEL	ENST00000582970.1	37	CCDS58606.1																																																																																			.		0.433	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		-	78350141	GAT	-	78350139	7	5	135	1	0	1	0	1	0	0	0	0	13509	933	33	0	13745	0	RNF213	17	78350139	In_Frame_Del	DEL	GAT	TCGA-HE-A5NK-01A-11D-A26P-10	16734129	78350139	2845071	102	12073											
ZNF236	7776	hgsc.bcm.edu;bcgsc.ca	37	chr18	74680294	74680294	+	Nonstop_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctcacccacgtcttctGatgcgagttggaagtacacc	8	9	10	14	2	3	1	1	1	2	0	3	3	3	2	3	2	2	2	3	2	2	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr18:74680294G>T	ENST00000253159.8	+	31	5735	c.5537G>T	c.(5536-5538)tGa>tTa	p.*1846L	ZNF236_ENST00000320610.9_Nonstop_Mutation_p.*1848L	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	0					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		CACGTCTTCTGATGCGAGTTG	0.542																																					p.X1846L		.											.	ZNF236-94	0			c.G5537T						.						65	76	72					18																	74680294		1938	4135	6073	SO:0001578	stop_lost	7776	exon31			TCTTCTGATGCGA	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"Zinc fingers, C2H2-type"	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.5537G>T	18.37:g.74680294G>T	ENSP00000253159:p.*1846Leuext*8	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	72	4	NM_007345	0	0	0	0	0	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	G	8.724	0.914980	0.17907	.	.	ENSG00000130856	ENST00000253159	.	.	.	4.91	4.04	0.47022	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5206	0.61566	0.0765:0.0:0.9235:0.0	.	.	.	.	L	1846	.	.	X	+	2	2	ZNF236	72809282	1.000000	0.71417	0.888000	0.34837	0.039000	0.13416	5.969000	0.70422	1.207000	0.43291	0.557000	0.71058	TGA	.		0.542	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			T	74680294	G	T	74680294	4	4	135	1	0	0	0	0	0	0	0	0	17821	1285	45	4	5659	4	ZNF236	18	74680294	Nonstop_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		74680294	3396954	103	12074											
DOT1L	84444	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	2210830	2210830	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcacgctcagaccgtgtctCagacggcggcctcctcaccc	6	7	10	18	4	3	2	3	0	1	2	5	2	4	2	4	2	1	2	4	2	0	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:2210830C>T	ENST00000398665.3	+	14	1363	c.1327C>T	c.(1327-1329)Cag>Tag	p.Q443*	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	443					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACCGTGTCTCAGACGGCGGC	0.692																																					p.Q443X		.											.	DOT1L-132	0			c.C1327T						.						26	34	31					19																	2210830		1991	4142	6133	SO:0001587	stop_gained	84444	exon14			GTGTCTCAGACGG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.1327C>T	19.37:g.2210830C>T	ENSP00000381657:p.Gln443*	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	151	35	NM_032482	0	0	0	0	0	O60379|Q96JL1	Nonsense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.878112	0.91664	.	.	ENSG00000104885	ENST00000398665;ENST00000221482	.	.	.	4.84	4.84	0.62591	.	0.625695	0.16263	N	0.222122	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-7.1526	16.9353	0.86202	0.0:1.0:0.0:0.0	.	.	.	.	X	443	.	ENSP00000221482:Q443X	Q	+	1	0	DOT1L	2161830	0.963000	0.33076	0.020000	0.16555	0.076000	0.17211	4.755000	0.62198	2.222000	0.72286	0.561000	0.74099	CAG	.		0.692	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2210830	C	T	2210830	4	4	135	1	0	0	0	0	0	1	0	0	4720	827	29	2	1381	2	DOT1L	19	2210830	Nonsense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		2210830	56918153	104	12075											
TSPAN16	26526	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11408999	11408999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggagcgactaaagagagcaGaggcacgctcttgtttgtaa	12	9	13	7	2	1	2	0	0	1	2	1	5	1	3	0	2	2	5	0	2	3	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:11408999G>A	ENST00000316737.1	+	2	401	c.251G>A	c.(250-252)aGa>aAa	p.R84K	TSPAN16_ENST00000592955.1_Missense_Mutation_p.R84K|CTC-510F12.4_ENST00000586356.1_RNA|TSPAN16_ENST00000590327.1_Missense_Mutation_p.R84K	NM_012466.2	NP_036598.1	Q9UKR8	TSN16_HUMAN	tetraspanin 16	84						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	12						AAAGAGAGCAGAGGCACGCTC	0.522																																					p.R84K													.	TSPAN16-91	0			c.G251A						.						96	73	81					19																	11408999		2203	4300	6503	SO:0001583	missense	26526	exon2			AGAGCAGAGGCAC	BC029908	CCDS12256.1, CCDS62549.1, CCDS62550.1	19p13.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000130167	ENSG00000130167		"Tetraspanins"	30725	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 16"	TM4SF16		10500248	Standard	NM_012466		Approved	TM4-B, TM-8	uc002mqv.1	Q9UKR8	OTTHUMG00000180833	ENST00000316737.1:c.251G>A	19.37:g.11408999G>A	ENSP00000319486:p.Arg84Lys	Somatic	178	1		WXS	Illumina HiSeq	Phase_I	218	44	NM_012466	0	0	0	0	0	K7EN22|K7EPD8|Q8N6J7	Missense_Mutation	SNP	ENST00000316737.1	37	CCDS12256.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021270	0.54576	.	.	ENSG00000130167	ENST00000316737;ENST00000337994	T;T	0.77750	-1.12;-1.12	3.57	3.57	0.40892	.	0.000000	0.37530	N	0.002042	T	0.78130	0.4235	L	0.38692	1.165	0.09310	N	1	D	0.69078	0.997	D	0.79108	0.992	T	0.65467	-0.6161	10	0.09084	T	0.74	-17.1852	10.972	0.47444	0.0:0.0:1.0:0.0	.	84	Q9UKR8	TSN16_HUMAN	K	84	ENSP00000319486:R84K;ENSP00000338759:R84K	ENSP00000319486:R84K	R	+	2	0	TSPAN16	11269999	0.208000	0.23494	0.207000	0.23584	0.052000	0.14988	2.108000	0.41854	2.287000	0.76781	0.462000	0.41574	AGA	.		0.522	TSPAN16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453204.1	NM_012466		A	11408999	G	A	11408999	3	1	135	1	0	0	0	0	1	0	0	0	16673	942	33	2	257	2	TSPAN16	19	11408999	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	9198169	11408999	47719984	105	12076											
ZNF653	115950	broad.mit.edu	37	chr19	11594521	11594521	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgggcttgtgatccgggtgGcttttgagcgtgtggaactt	4	14	17	6	2	0	2	0	2	0	0	1	3	1	3	1	4	2	2	1	4	1	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:11594521G>A	ENST00000293771.5	-	9	1960	c.1824C>T	c.(1822-1824)agC>agT	p.S608S	ELAVL3_ENST00000592218.1_5'Flank|ELAVL3_ENST00000359227.3_5'Flank|CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	608					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						GATCCGGGTGGCTTTTGAGCG	0.617																																					p.S608S	Pancreas(83;980 1446 4542 6441 43352)												.	ZNF653-90	0			c.C1824T						.						232	183	199					19																	11594521		2203	4300	6503	SO:0001819	synonymous_variant	115950	exon9			CGGGTGGCTTTTG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1824C>T	19.37:g.11594521G>A		Somatic	97	1		WXS	Illumina HiSeq	Phase_I	162	7	NM_138783	0	0	8	9	1	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			.		0.617	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		A	11594521	G	A	11594521	2	1	135	1	0	0	0	0	0	0	0	1	18098	1194	42	2		2	ZNF653	19	11594521	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	185522	11594521	47534462	106	12077											
HAPLN4	404037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19371725	19371725	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtgacgttgcggaggaccagGgaggcatccccaggcccgtc	7	5	16	13	3	0	1	0	1	0	0	2	4	1	4	4	5	1	2	4	5	0	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:19371725G>A	ENST00000291481.7	-	3	444	c.381C>T	c.(379-381)tcC>tcT	p.S127S	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	127	Ig-like C2-type.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	GGAGGACCAGGGAGGCATCCC	0.652																																					p.S127S		.											.	HAPLN4-91	0			c.C381T						.						66	61	63					19																	19371725		2203	4300	6503	SO:0001819	synonymous_variant	404037	exon3			GACCAGGGAGGCA	AB107883	CCDS12398.1	19p13.1	2013-01-11						"Immunoglobulin superfamily / V-set domain containing"	31357	protein-coding gene	gene with protein product	"brain link protein 2"					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.381C>T	19.37:g.19371725G>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	50	12	NM_023002	0	0	0	0	0	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	37	CCDS12398.1																																																																																			.		0.652	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002		A	19371725	G	A	19371725	2	1	135	1	0	0	0	0	0	0	0	1	6978	1219	43	2		2	HAPLN4	19	19371725	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	7777204	19371725	39757258	107	12078											
GRAMD1A	57655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35500151	35500151	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggtggagaagggatcagAtagctcctcagagaagggtg	12	7	16	6	0	2	3	2	0	0	3	3	6	3	4	1	4	1	1	1	4	3	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:35500151A>C	ENST00000317991.5	+	2	329	c.137A>C	c.(136-138)gAt>gCt	p.D46A	GRAMD1A_ENST00000504615.2_5'UTR|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.D46A|GRAMD1A_ENST00000424536.2_Missense_Mutation_p.D46A|GRAMD1A_ENST00000598073.1_3'UTR|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.D133A	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	46						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AAGGGATCAGATAGCTCCTCA	0.647																																					p.D46A		.											.	GRAMD1A-90	0			c.A137C						.						38	45	43					19																	35500151		1939	4128	6067	SO:0001583	missense	57655	exon2			GATCAGATAGCTC	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.137A>C	19.37:g.35500151A>C	ENSP00000441032:p.Asp46Ala	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	138	22	NM_020895	0	0	2	5	3	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.579681	0.65992	.	.	ENSG00000089351	ENST00000453966;ENST00000317991;ENST00000411896	T;T	0.25250	1.81;1.83	4.67	4.67	0.58626	.	0.081214	0.49916	D	0.000124	T	0.30665	0.0772	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.60160	0.987;0.978;0.987;0.987	P;P;P;P	0.61477	0.889;0.698;0.841;0.889	T	0.05402	-1.0887	10	0.45353	T	0.12	.	12.1081	0.53823	1.0:0.0:0.0:0.0	.	46;46;46;133	Q96CP6-3;Q96CP6;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.	A	133;46;46	ENSP00000441032:D46A;ENSP00000439267:D46A	ENSP00000441032:D46A	D	+	2	0	GRAMD1A	40191991	1.000000	0.71417	0.569000	0.28460	0.688000	0.40055	4.842000	0.62831	1.965000	0.57142	0.459000	0.35465	GAT	.		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		C	35500151	A	C	35500151	3	2	135	1	0	0	0	0	1	0	0	0	6768	333	12	5	143	5	GRAMD1A	19	35500151	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	16128426	35500151	23628832	108	12079											
DHX34	9704	ucsc.edu;bcgsc.ca	37	chr19	47858386	47858386	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctcctgcgacaaatccagCgggaacccagcctgccccag	9	5	10	17	2	0	0	0	0	0	0	2	2	2	1	6	1	6	1	6	1	2	0	rs371092274		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:47858386C>T	ENST00000328771.4	+	3	1145	c.796C>T	c.(796-798)Cgg>Tgg	p.R266W		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	266	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		ACAAATCCAGCGGGAACCCAG	0.597																																					p.R266W													.	DHX34-231	0			c.C796T						.	C	TRP/ARG	0,4406		0,0,2203	88	76	80		796	4.8	1	19		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	DHX34	NM_014681.5	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	266/1144	47858386	1,13005	2203	4300	6503	SO:0001583	missense	9704	exon3			ATCCAGCGGGAAC	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.796C>T	19.37:g.47858386C>T	ENSP00000331907:p.Arg266Trp	Somatic	194	2		WXS	Illumina HiSeq		281	54	NM_014681	0	0	2	2	0	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867337	0.72065	0.0	1.16E-4	ENSG00000134815	ENST00000328771;ENST00000257252	T	0.07688	3.17	4.76	4.76	0.60689	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.110120	0.36374	N	0.002626	T	0.23014	0.0556	M	0.77820	2.39	0.46061	D	0.99884	D;D	0.67145	0.996;0.996	P;P	0.56788	0.806;0.803	T	0.00849	-1.1541	10	0.87932	D	0	-0.0613	11.7971	0.52106	0.176:0.824:0.0:0.0	.	266;266	Q14147;B4E3G3	DHX34_HUMAN;.	W	266	ENSP00000331907:R266W	ENSP00000257252:R266W	R	+	1	2	DHX34	52550226	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.007000	0.29860	2.213000	0.71641	0.456000	0.33151	CGG	.		0.597	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		T	47858386	C	T	47858386	3	4	135	1	0	0	0	0	1	0	0	0	4518	759	27	1	802	1	DHX34	19	47858386	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	12358235	47858386	11270597	109	12080											
CGB	1082	broad.mit.edu	37	chr19	49526376	49526377	+	Frame_Shift_Ins	INS	-	-	T																															ccgcgcgggcagccagggagINSccggatggactcgaagcgca																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:49526376_49526377insT	ENST00000357383.4	-	3	625_626	c.264_265insA	c.(262-267)cggctcfs	p.L89fs	CTB-60B18.6_ENST00000591656.1_Frame_Shift_Ins_p.L75fs	NM_000737.3	NP_000728.1	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide	89					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|peptide hormone processing (GO:0016486)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			large_intestine(1)	1		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CAGCCAGGGAGCCGGATGGACT	0.693																																					p.L89fs													.	CGB-22	0			c.265_266insA						.																																			SO:0001589	frameshift_variant	1082	exon3			CAGGGAGCCGGAT	J00117	CCDS12749.1	19q13.3	2013-02-25				ENSG00000104827		"Endogenous ligands"	1886	protein-coding gene	gene with protein product		118860				6774259, 6194155	Standard	NM_000737		Approved	CGB3	uc002plv.2	P01233		ENST00000357383.4:c.264_265insA	19.37:g.49526376_49526377insT	ENSP00000349954:p.Leu89fs	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	10	2	NM_000737	0	0	0	0	0	A1A5E0|B9ZVP5|Q13991|Q14000|Q3KPI3|Q3SY41|Q8WTT5|Q8WXL1|Q8WXL2|Q8WXL3|Q8WXL4	Frame_Shift_Ins	INS	ENST00000357383.4	37	CCDS12749.1																																																																																			.		0.693	CGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452164.2	NM_000737		T	49526377	-	T	49526376	7	5	135	1	0	1	1	0	0	0	0	0	3302	971	34	0	236	0	CGB	19	49526376	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	1667990	49526376	9602607	110	12081											
ZNF418	147686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58438722	58438722	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagtgtgaactcgctgaTgctgaacaaggctgccctta	9	10	10	12	1	0	3	0	3	0	0	2	3	1	3	2	1	4	3	2	1	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:58438722T>A	ENST00000396147.1	-	4	1118	c.827A>T	c.(826-828)cAt>cTt	p.H276L	ZNF418_ENST00000599852.1_Missense_Mutation_p.H191L|ZNF418_ENST00000425570.3_Missense_Mutation_p.H297L|ZNF418_ENST00000595830.1_Missense_Mutation_p.H276L|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	276					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		AACTCGCTGATGCTGAACAAG	0.433																																					p.H276L		.											.	ZNF418-90	0			c.A827T						.						90	92	91					19																	58438722		2189	4296	6485	SO:0001583	missense	147686	exon4			CGCTGATGCTGAA	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.827A>T	19.37:g.58438722T>A	ENSP00000379451:p.His276Leu	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	172	34	NM_133460	0	0	0	0	0	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	37	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	11.49	1.655252	0.29425	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	D;D	0.86865	-2.18;-2.18	2.26	1.15	0.20763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.90147	0.6921	H	0.98295	4.195	0.09310	N	0.999995	P	0.38110	0.618	B	0.33254	0.16	D	0.83866	0.0271	9	0.87932	D	0	.	6.5871	0.22626	0.2146:0.0:0.0:0.7854	.	276	Q8TF45	ZN418_HUMAN	L	276;297;242	ENSP00000379451:H276L;ENSP00000407039:H297L	ENSP00000379451:H276L	H	-	2	0	ZNF418	63130534	.	.	0.001000	0.08648	0.109000	0.19521	.	.	0.129000	0.18514	0.240000	0.17902	CAT	.		0.433	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		A	58438722	T	A	58438722	3	1	135	1	0	0	0	0	1	0	0	0	17927	1464	51	5	1207	5	ZNF418	19	58438722	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	8912346	58438722	690261	111	12082											
KIF16B	55614	broad.mit.edu	37	chr20	16359622	16359622	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctcctctccagcctggccaGggcccgctccagcgcctctc	3	8	9	21	2	3	0	0	0	3	0	7	0	4	0	7	2	2	1	7	2	0	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:16359622G>A	ENST00000354981.2	-	19	3182	c.3025C>T	c.(3025-3027)Ctg>Ttg	p.L1009L	KIF16B_ENST00000408042.1_Silent_p.L1009L|KIF16B_ENST00000378003.2_Silent_p.L235L|KIF16B_ENST00000355755.3_Silent_p.L1009L	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1009	Glu-rich.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						AGCCTGGCCAGGGCCCGCTCC	0.557																																					p.L1009L													.	KIF16B-291	0			c.C3025T						.						82	87	85					20																	16359622		2203	4300	6503	SO:0001819	synonymous_variant	55614	exon19			TGGCCAGGGCCCG	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"Kinesins"	15869	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 23"	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3025C>T	20.37:g.16359622G>A		Somatic	97	1		WXS	Illumina HiSeq	Phase_I	132	4	NM_001199865	0	0	3	3	0	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			.		0.557	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16359622	G	A	16359622	2	1	135	1	0	0	0	0	0	0	0	1	8299	991	35	2		2	KIF16B	20	16359622	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		16359622	46665898	112	12083											
CST9L	128821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	23546696	23546696	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagttctccccagcagtagcTccattgagaatacagtcttg	10	12	8	11	0	2	1	0	1	2	1	4	2	3	1	3	0	3	4	3	0	4	6			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:23546696T>G	ENST00000376979.3	-	2	567	c.269A>C	c.(268-270)gAg>gCg	p.E90A		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	90						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					CAGCAGTAGCTCCATTGAGAA	0.468																																					p.E90A		.											.	CST9L-90	0			c.A269C						.						205	177	187					20																	23546696		2203	4300	6503	SO:0001583	missense	128821	exon2			AGTAGCTCCATTG		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.269A>C	20.37:g.23546696T>G	ENSP00000366178:p.Glu90Ala	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	338	67	NM_080610	0	0	0	0	0	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	37	CCDS13157.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.067516	0.36470	.	.	ENSG00000101435	ENST00000376979	T	0.28666	1.6	1.92	1.92	0.25849	Proteinase inhibitor I25, cystatin (2);	0.919888	0.08938	N	0.872000	T	0.44265	0.1285	M	0.75264	2.295	0.09310	N	1	D	0.58970	0.984	P	0.55749	0.783	T	0.23619	-1.0183	10	0.37606	T	0.19	.	5.8418	0.18637	0.0:0.0:0.0:1.0	.	90	Q9H4G1	CST9L_HUMAN	A	90	ENSP00000366178:E90A	ENSP00000366178:E90A	E	-	2	0	CST9L	23494696	0.004000	0.15560	0.108000	0.21378	0.004000	0.04260	0.143000	0.16115	1.118000	0.41863	0.402000	0.26972	GAG	.		0.468	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		G	23546696	T	G	23546696	3	3	135	1	0	0	0	0	1	0	0	0	3986	1551	54	5	182	5	CST9L	20	23546696	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	7187074	23546696	39478824	113	12084											
SLC32A1	140679	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37356957	37356957	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaggcagccgcgccttttTcccggcctgctacagcggcg	5	7	14	15	5	0	0	0	0	0	0	1	1	1	1	4	4	4	2	4	4	2	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:37356957T>C	ENST00000217420.1	+	2	1516	c.1253T>C	c.(1252-1254)tTc>tCc	p.F418S		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	418					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CGCGCCTTTTTCCCGGCCTGC	0.632																																					p.F418S													.	SLC32A1-90	0			c.T1253C						.						31	34	33					20																	37356957		2203	4300	6503	SO:0001583	missense	140679	exon2			CCTTTTTCCCGGC	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"Solute carriers"	11018	protein-coding gene	gene with protein product			"vesicular inhibitory amino acid transporter"	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.1253T>C	20.37:g.37356957T>C	ENSP00000217420:p.Phe418Ser	Somatic	60	1		WXS	Illumina HiSeq	Phase_I	92	25	NM_080552	0	0	0	0	0	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.946656	0.53186	.	.	ENSG00000101438	ENST00000217420	T	0.02140	4.43	4.45	4.45	0.53987	.	0.050284	0.85682	D	0.000000	T	0.04679	0.0127	M	0.72894	2.215	0.80722	D	1	B	0.26195	0.144	B	0.32211	0.142	T	0.31223	-0.9951	10	0.34782	T	0.22	-23.406	11.9404	0.52896	0.0:0.0:0.0:1.0	.	418	Q9H598	VIAAT_HUMAN	S	418	ENSP00000217420:F418S	ENSP00000217420:F418S	F	+	2	0	SLC32A1	36790371	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.944000	0.87722	1.786000	0.52430	0.460000	0.39030	TTC	.		0.632	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		C	37356957	T	C	37356957	3	2	135	1	0	0	0	0	1	0	0	0	14597	1783	62	3	1259	3	SLC32A1	20	37356957	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	13810261	37356957	25668563	114	12085											
DHX35	60625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37653978	37653978	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaagcttcttgtcaagtttCaagtgcccaggaagtctagt	12	12	9	8	0	4	0	2	0	2	0	4	1	4	1	1	1	2	2	1	1	6	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:37653978C>T	ENST00000252011.3	+	18	1810	c.1777C>T	c.(1777-1779)Caa>Taa	p.Q593*	DHX35_ENST00000373325.2_Nonsense_Mutation_p.Q593*|DHX35_ENST00000373323.4_Nonsense_Mutation_p.Q562*	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	593					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TGTCAAGTTTCAAGTGCCCAG	0.443																																					p.Q593X		.											.	DHX35-226	0			c.C1777T						.						176	185	182					20																	37653978		2203	4300	6503	SO:0001587	stop_gained	60625	exon18			AAGTTTCAAGTGC	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1777C>T	20.37:g.37653978C>T	ENSP00000252011:p.Gln593*	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	222	42	NM_021931	0	0	1	2	1	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Nonsense_Mutation	SNP	ENST00000252011.3	37	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	C	38	6.967926	0.97971	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321;ENST00000449559	.	.	.	5.41	4.4	0.53042	.	0.097447	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4304	0.44405	0.3784:0.6216:0.0:0.0	.	.	.	.	X	593;593;562;73;57	.	ENSP00000252011:Q593X	Q	+	1	0	DHX35	37087392	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.037000	0.64170	2.530000	0.85305	0.655000	0.94253	CAA	.		0.443	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		T	37653978	C	T	37653978	4	4	135	1	0	0	0	0	0	1	0	0	4519	827	29	2	1847	2	DHX35	20	37653978	Nonsense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	297021	37653978	25371542	115	12086											
SLC9A8	23315	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	48431566	48431566	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttccccaatacaactcaTgagggtttcaatgtcaccct	11	11	7	12	0	3	1	3	1	0	0	4	1	4	1	3	2	2	2	3	2	4	3	rs536021956		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:48431566T>C	ENST00000361573.2	+	2	90	c.48T>C	c.(46-48)caT>caC	p.H16H	SLC9A8_ENST00000417961.1_Silent_p.H16H|SLC9A8_ENST00000539601.1_5'UTR|SLC9A8_ENST00000541138.1_5'UTR			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	16					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			ATACAACTCATGAGGGTTTCA	0.522																																					p.H16H		.											.	SLC9A8-91	0			c.T48C						.						90	78	82					20																	48431566		2203	4300	6503	SO:0001819	synonymous_variant	23315	exon2			AACTCATGAGGGT	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.48T>C	20.37:g.48431566T>C		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	184	45	NM_001260491	0	0	2	2	0	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			.		0.522	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		C	48431566	T	C	48431566	2	2	135	1	0	0	0	0	0	0	0	1	14752	1461	51	3		3	SLC9A8	20	48431566	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	10777588	48431566	14593954	116	12087											
MYO18B	84700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	26422672	26422672	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcgagggaaaagctgccCagtccttcagcggccctctc	7	8	11	15	2	2	0	1	0	1	0	5	2	3	1	3	2	3	1	3	2	2	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:26422672C>T	ENST00000407587.2	+	43	6904	c.6735C>T	c.(6733-6735)ccC>ccT	p.P2245P	MYO18B_ENST00000536101.1_Silent_p.P2244P|MYO18B_ENST00000335473.7_Silent_p.P2244P			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2244						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AAAAGCTGCCCAGTCCTTCAG	0.607																																					p.P2244P		.											.	MYO18B-142	0			c.C6732T						.						24	25	25					22																	26422672		1910	4104	6014	SO:0001819	synonymous_variant	84700	exon43			GCTGCCCAGTCCT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"Myosins / Myosin superfamily : Class XVIII"	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.6735C>T	22.37:g.26422672C>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	159	30	NM_032608	0	0	0	0	0	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	C	10.77	1.444427	0.25987	.	.	ENSG00000133454	ENST00000543971	T	0.55234	0.53	4.94	-4.84	0.03151	.	0.116110	0.34002	N	0.004359	T	0.50394	0.1613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53315	-0.8456	7	0.72032	D	0.01	.	5.3684	0.16127	0.2432:0.2637:0.4198:0.0733	.	.	.	.	L	194	ENSP00000444262:P194L	ENSP00000444262:P194L	P	+	2	0	MYO18B	24752672	0.013000	0.17824	0.962000	0.40283	0.992000	0.81027	-1.785000	0.01767	-0.418000	0.07450	0.491000	0.48974	CCA	.		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26422672	C	T	26422672	2	4	135	1	0	0	0	0	0	0	0	1	10091	581	21	2		2	MYO18B	22	26422672	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		26422672	24881894	117	12088											
NEFH	4744	bcgsc.ca	37	chr22	29885429	29885429	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccggctgaggccaagtcTccagagaaggccaagtcccc	10	5	11	15	1	2	2	1	1	1	1	4	3	3	2	6	3	0	1	6	3	3	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:29885429T>C	ENST00000310624.6	+	4	1833	c.1800T>C	c.(1798-1800)tcT>tcC	p.S600S		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	600	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGCCAAGTCTCCAGAGAAGG	0.552																																					p.S600S													.	NEFH-90	0			c.T1800C						.						65	62	63					22																	29885429		2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			CAAGTCTCCAGAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1800T>C	22.37:g.29885429T>C		Somatic	221	2		WXS	Illumina HiSeq	Phase_1	293	32	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			.		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		C	29885429	T	C	29885429	2	2	135	1	0	0	0	0	0	0	0	1	10340	1538	54	3		3	NEFH	22	29885429	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	3462757	29885429	21419137	118	12089			1	36		3	3	194	N	T_G_-	3.067843e-07
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	335	34	NM_021076	0	0	1	1	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	135	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	133	29885562	21419004	119	12090			1	36		3	3	194	N	T_G_-	3.067843e-07
NEFH	4744	broad.mit.edu	37	chr22	29885622	29885623	+	In_Frame_Ins	INS	-	-	AGGAAG																															agaggccaagtcccctgagaINSaggccaagtccccagtgaag																								rs267607534|rs267607535		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:29885622_29885623insAGGAAG	ENST00000310624.6	+	4	2026_2027	c.1993_1994insAGGAAG	c.(1993-1995)aag>aAGGAAGag	p.665_666insEE		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	671	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GTCCCCTGAGAAGGCCAAGTCC	0.579																																					p.K665delinsKEE													.	NEFH-90	0			c.1993_1994insAGGAAG						.																																			SO:0001652	inframe_insertion	4744	exon4			CCTGAGAAGGCCA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	Exception_encountered	22.37:g.29885622_29885623insAGGAAG	ENSP00000311997:p.Lys665_Ala666insGluGlu	Somatic	472	0		WXS	Illumina HiSeq	Phase_I	595	9	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																			.		0.579	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		AGGAAG	29885623	-	AGGAAG	29885622	7	5	135	1	0	1	1	0	0	0	0	0	10340	247	9	0	2007	0	NEFH	22	29885622	In_Frame_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	60	29885622	21418944	120	12091			1	36		3	3	194	N	T_G_-	3.067843e-07
BAIAP2L2	80115	hgsc.bcm.edu	37	chr22	38483172	38483172	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggttcatgggtgtcatgggGgacatggaggtcatggaggt	7	10	20	4	0	3	0	3	0	0	0	3	3	3	3	0	8	0	1	0	8	0	1	rs539447143	byFrequency	TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:38483172G>T	ENST00000381669.3	-	11	1362	c.1218C>A	c.(1216-1218)tcC>tcA	p.S406S	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	406					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					gtgtcatgggggacatggagg	0.662													G|||	30	0.00599042	0.0068	0.0014	5008	,	,		13061	0		0.004	False		,,,				2504	0.0164				p.S406S		.											.	BAIAP2L2-91	0			c.C1218A						.						31	37	35					22																	38483172		1925	4122	6047	SO:0001819	synonymous_variant	80115	exon11			CATGGGGGACATG	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1218C>A	22.37:g.38483172G>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	146	17	NM_025045	0	0	17	17	0	B0QYE2|Q96BG7	Silent	SNP	ENST00000381669.3	37	CCDS43018.1																																																																																			.		0.662	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		T	38483172	G	T	38483172	2	4	135	1	0	0	0	0	0	0	0	1	1304	1219	43	4		4	BAIAP2L2	22	38483172	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	8597550	38483172	12821394	121	12092											
GRAP2	9402	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	40367067	40367067	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcctcttccctgccaactaCgtggcacccatgacccgata	8	8	8	17	2	1	1	0	1	1	0	2	2	2	1	5	2	3	1	5	2	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:40367067C>T	ENST00000344138.4	+	8	1235	c.972C>T	c.(970-972)taC>taT	p.Y324Y	GRAP2_ENST00000544756.1_Silent_p.Y252Y|GRAP2_ENST00000399090.2_Silent_p.Y211Y|GRAP2_ENST00000543252.1_Silent_p.Y272Y|GRAP2_ENST00000540310.1_Silent_p.Y258Y|GRAP2_ENST00000407075.3_Silent_p.Y324Y	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	324	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CTGCCAACTACGTGGCACCCA	0.582																																					p.Y324Y													.	GRAP2-227	0			c.C972T						.						77	67	71					22																	40367067		2203	4300	6503	SO:0001819	synonymous_variant	9402	exon8			CAACTACGTGGCA	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"SH2 domain containing"	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.972C>T	22.37:g.40367067C>T		Somatic	104	1		WXS	Illumina HiSeq	Phase_I	112	30	NM_004810	0	0	2	2	0	B7Z8I3|O43726|Q9NRB7	Silent	SNP	ENST00000344138.4	37	CCDS13999.1																																																																																			.		0.582	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		T	40367067	C	T	40367067	2	4	135	1	0	0	0	0	0	0	0	1	6775	547	19	1		1	GRAP2	22	40367067	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	1883895	40367067	10937499	122	12093											
SMC1B	27127	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	45785629	45785630	+	Missense_Mutation	DNP	GC	GC	CT																															cgaggaatgtctcaggttcaGctctttcctccttcagaaat																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:45785629_45785630GC>CT	ENST00000357450.4	-	10	1692_1693	c.1693_1694GC>AG	c.(1693-1695)GCt>AGt	p.A565S	SMC1B_ENST00000404354.3_Missense_Mutation_p.A565S	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	565	Flexible hinge.				meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CTCAGGTTCAGCTCTTTCCTCC	0.386																																					p.A565S													.	SMC1B-229	0			c.G1693A						.																																			SO:0001583	missense	27127	exon10			GTTCAGCTCTTTC	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"Structural maintenance of chromosomes proteins"	11112	protein-coding gene	gene with protein product		608685	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1693_1694delinsCT	22.37:g.45785629_45785630delinsCT	ENSP00000350036:p.Ala565Ser	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	169	36	NM_148674	0	0	0	0	0	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	DNP	ENST00000357450.4	37	CCDS43027.1																																																																																			.		0.386	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		CT	45785630	GC	CT	45785629	3	2	135	1	0	0	0	0	1	0	0	0	14814	971	34	4	2077	4	SMC1B	22	45785629	Missense_Mutation	DNP	GC	TCGA-HE-A5NK-01A-11D-A26P-10	5418562	45785629	5518937	123	12094											
SHANK3	85358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	51159826	51159826	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggaggagcggaagtcacccGaggacaagaagtccatgatc	13	4	15	9	2	1	2	1	1	0	1	3	7	2	6	2	4	1	0	2	4	3	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:51159826G>A	ENST00000414786.2	+	21	3750	c.3523G>A	c.(3523-3525)Gag>Aag	p.E1175K	SHANK3_ENST00000262795.3_Missense_Mutation_p.E1205K|SHANK3_ENST00000445220.2_Missense_Mutation_p.E1191K			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1189					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GAAGTCACCCGAGGACAAGAA	0.662																																					p.E1175K		.											.	SHANK3-69	0			c.G3523A						.						39	48	45					22																	51159826		2100	4200	6300	SO:0001583	missense	85358	exon21			TCACCCGAGGACA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3523G>A	22.37:g.51159826G>A	ENSP00000464552:p.Glu1175Lys	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	213	39	NM_033517	0	0	0	0	0	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		.	.	.	.	.	.	.	.	.	.	G	15.47	2.843265	0.51057	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.26373	1.74;1.74	4.58	4.58	0.56647	.	0.163605	0.51477	D	0.000081	T	0.25827	0.0629	M	0.70275	2.135	0.29353	N	0.865219	D;P;P	0.53462	0.96;0.492;0.921	B;B;B	0.34489	0.184;0.024;0.163	T	0.43556	-0.9384	10	0.56958	D	0.05	.	14.8583	0.70359	0.0:0.0:1.0:0.0	.	1189;1190;1205	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	K	1205;1191	ENSP00000442518:E1205K;ENSP00000446078:E1191K	ENSP00000442518:E1205K	E	+	1	0	SHANK3	49506692	1.000000	0.71417	0.875000	0.34327	0.943000	0.58893	8.323000	0.90002	2.093000	0.63338	0.462000	0.41574	GAG	.		0.662	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		A	51159826	G	A	51159826	3	1	135	1	0	0	0	0	1	0	0	0	14298	1059	37	1	3699	1	SHANK3	22	51159826	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	5374197	51159826	144740	124	12095											
BMP15	9210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	50658965	50658965	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaccttccctgatgtctaaCgcttggaaagagatggatat	13	11	9	8	1	1	2	0	1	1	1	2	5	2	4	2	2	2	1	2	2	4	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chrX:50658965C>T	ENST00000252677.3	+	2	537	c.537C>T	c.(535-537)aaC>aaT	p.N179N		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	179					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					TGATGTCTAACGCTTGGAAAG	0.473																																					p.N179N		.											.	BMP15-132	0			c.C537T						.						116	94	101					X																	50658965		2203	4299	6502	SO:0001819	synonymous_variant	9210	exon2			GTCTAACGCTTGG	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"Bone morphogenetic proteins"	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.537C>T	X.37:g.50658965C>T		Somatic	184	0		WXS	Illumina HiSeq	Phase_I	217	78	NM_005448	0	0	0	0	0	Q17RM6|Q5JST1|Q9UMS1	Silent	SNP	ENST00000252677.3	37	CCDS14334.1																																																																																			.		0.473	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		T	50658965	C	T	50658965	2	4	135	1	0	0	0	0	0	0	0	1	1459	535	19	1		1	BMP15	23	50658965	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		50658965	104611595	125	12096											
ZCCHC5	203430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chrX	77913359	77913359	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctccagaggctcctggggagGtggaagctcaaggaactcta	10	7	14	10	0	2	1	1	0	1	1	4	4	4	4	2	6	2	2	2	6	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chrX:77913359G>A	ENST00000321110.1	-	2	854	c.559C>T	c.(559-561)Cct>Tct	p.P187S		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	187	Pro-rich.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						TCCTGGGGAGGTGGAAGCTCA	0.537																																					p.P187S		.											.	ZCCHC5-131	0			c.C559T						.						41	41	41					X																	77913359		2203	4300	6503	SO:0001583	missense	203430	exon2			GGGGAGGTGGAAG	AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"Zinc fingers, CCHC domain containing"	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.559C>T	X.37:g.77913359G>A	ENSP00000316794:p.Pro187Ser	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	47	18	NM_152694	0	0	0	0	0	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.432832	0.01108	.	.	ENSG00000179300	ENST00000321110	T	0.17691	2.26	3.46	-5.74	0.02391	.	.	.	.	.	T	0.05547	0.0146	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40289	-0.9571	9	0.07175	T	0.84	.	1.35	0.02171	0.2436:0.2501:0.329:0.1772	.	187	Q8N8U3	ZCHC5_HUMAN	S	187	ENSP00000316794:P187S	ENSP00000316794:P187S	P	-	1	0	ZCCHC5	77800015	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.423000	0.01030	-1.795000	0.01255	-3.016000	0.00074	CCT	.		0.537	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		A	77913359	G	A	77913359	3	1	135	1	0	0	0	0	1	0	0	0	17623	1261	44	2	872	2	ZCCHC5	23	77913359	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	27254394	77913359	77357201	126	12097											
SRPX2	27286	broad.mit.edu	37	chrX	99919925	99919925	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggaagatgggagatggagTggaggcgagcctgtatgtgt	10	9	19	3	1	0	2	0	0	0	2	0	7	0	5	1	5	1	1	1	5	2	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chrX:99919925T>G	ENST00000373004.3	+	5	938	c.510T>G	c.(508-510)agT>agG	p.S170R		NM_014467.2	NP_055282.1	O60687	SRPX2_HUMAN	sushi-repeat containing protein, X-linked 2	170	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				angiogenesis (GO:0001525)|cell motility (GO:0048870)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of synapse assembly (GO:0051965)|regulation of phosphorylation (GO:0042325)|single organismal cell-cell adhesion (GO:0016337)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|excitatory synapse (GO:0060076)|extracellular space (GO:0005615)|synaptic membrane (GO:0097060)	hepatocyte growth factor binding (GO:0036458)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)	19						GGAGATGGAGTGGAGGCGAGC	0.517																																					p.S170R													.	SRPX2-132	0			c.T510G						.						58	48	52					X																	99919925		2203	4300	6503	SO:0001583	missense	27286	exon5			ATGGAGTGGAGGC	AF393649	CCDS14471.1	Xq21.33-q23	2011-01-25	2011-01-25		ENSG00000102359	ENSG00000102359			30668	protein-coding gene	gene with protein product		300642	"sushi-repeat-containing protein, X-linked 2"			9864177	Standard	NM_014467		Approved	SRPUL	uc004egb.3	O60687	OTTHUMG00000022003	ENST00000373004.3:c.510T>G	X.37:g.99919925T>G	ENSP00000362095:p.Ser170Arg	Somatic	121	7		WXS	Illumina HiSeq	Phase_I	124	9	NM_014467	0	0	2	2	0	B3KQT3|Q8WW85	Missense_Mutation	SNP	ENST00000373004.3	37	CCDS14471.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.587119	0.66105	.	.	ENSG00000102359	ENST00000373004	T	0.68765	-0.35	5.74	0.76	0.18442	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.83986	0.5373	H	0.94658	3.565	0.58432	D	0.999999	D	0.76494	0.999	D	0.87578	0.998	D	0.84349	0.0531	9	.	.	.	-15.0606	10.4888	0.44739	0.0:0.4289:0.0:0.5711	.	170	O60687	SRPX2_HUMAN	R	170	ENSP00000362095:S170R	.	S	+	3	2	SRPX2	99806581	0.023000	0.18921	0.999000	0.59377	0.990000	0.78478	-0.866000	0.04245	0.004000	0.14682	-0.335000	0.08231	AGT	.		0.517	SRPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057486.1	NM_014467		G	99919925	T	G	99919925	3	3	135	1	0	0	0	0	1	0	0	0	15197	1693	59	5	524	5	SRPX2	23	99919925	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	22006566	99919925	55350635	127	12098											
PRAMEF12	390999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	12837407	12837407	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccatcctgcctgccctgAgccgctgctcccagctcagc	4	7	10	20	2	1	1	1	1	0	0	3	1	3	1	6	0	6	3	6	0	0	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:12837407A>T	ENST00000357726.4	+	3	1144	c.1117A>T	c.(1117-1119)Agc>Tgc	p.S373C		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	373					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTGCCCTGAGCCGCTGCTC	0.627																																					p.S373C		.											.	PRAMEF12-25	0			c.A1117T						.						99	101	100					1																	12837407		2203	4300	6503	SO:0001583	missense	390999	exon3			GCCCTGAGCCGCT		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.1117A>T	1.37:g.12837407A>T	ENSP00000350358:p.Ser373Cys	Somatic	505	0		WXS	Illumina HiSeq	Phase_I	737	215	NM_001080830	0	0	0	0	0		Missense_Mutation	SNP	ENST00000357726.4	37	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	15.97	2.990792	0.54041	.	.	ENSG00000116726	ENST00000357726	T	0.12672	2.66	2.72	1.59	0.23543	.	0.618526	0.16899	N	0.194981	T	0.32102	0.0818	M	0.83384	2.64	0.27627	N	0.948171	D	0.89917	1.0	D	0.85130	0.997	T	0.10451	-1.0629	10	0.56958	D	0.05	.	3.0429	0.06143	0.6004:0.2557:0.1439:0.0	.	373	O95522	PRA12_HUMAN	C	373	ENSP00000350358:S373C	ENSP00000350358:S373C	S	+	1	0	PRAMEF12	12759994	0.357000	0.24938	0.906000	0.35671	0.303000	0.27691	-0.407000	0.07178	0.455000	0.26910	0.164000	0.16699	AGC	.		0.627	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12837407	A	T	12837407	3	4	136	1	0	0	0	0	1	0	0	0	12457	304	11	5	1127	5	PRAMEF12	1	12837407	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		12837407	236413214	1	12099											
SPEN	23013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	16257911	16257911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgaggaaggttcatcaggtGaccagccgccttatctggat	9	11	12	9	1	3	2	2	2	1	0	3	4	3	4	3	4	1	1	3	4	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:16257911G>A	ENST00000375759.3	+	11	5380	c.5176G>A	c.(5176-5178)Gac>Aac	p.D1726N		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1726					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TTCATCAGGTGACCAGCCGCC	0.587																																					p.D1726N		.											.	SPEN-298	0			c.G5176A						.						136	148	144					1																	16257911		2203	4300	6503	SO:0001583	missense	23013	exon11			TCAGGTGACCAGC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"RNA binding motif (RRM) containing"	17575	protein-coding gene	gene with protein product		613484	"SPEN homolog, transcriptional regulator (Drosophila)", "spen homolog, transcriptional regulator (Drosophila)"			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.5176G>A	1.37:g.16257911G>A	ENSP00000364912:p.Asp1726Asn	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	152	16	NM_015001	0	0	5	6	1	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032932	0.54790	.	.	ENSG00000065526	ENST00000375759	T	0.09163	3.01	5.16	4.25	0.50352	.	.	.	.	.	T	0.08891	0.0220	N	0.24115	0.695	0.09310	N	1	B	0.32245	0.361	B	0.30646	0.118	T	0.24548	-1.0157	9	0.40728	T	0.16	-3.0207	13.4332	0.61068	0.0759:0.0:0.9241:0.0	.	1726	Q96T58	MINT_HUMAN	N	1726	ENSP00000364912:D1726N	ENSP00000364912:D1726N	D	+	1	0	SPEN	16130498	0.999000	0.42202	0.001000	0.08648	0.749000	0.42624	6.058000	0.71126	1.152000	0.42452	0.467000	0.42956	GAC	.		0.587	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16257911	G	A	16257911	3	1	136	1	0	0	0	0	1	0	0	0	15070	1290	45	2	5218	2	SPEN	1	16257911	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3420504	16257911	232992710	2	12100											
TAL1	6886	broad.mit.edu	37	chr1	47685614	47685614	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccccaccacagggtcCttgccagtcttggcccgctg	5	7	10	19	1	1	0	0	0	1	0	2	0	2	0	7	2	2	1	7	2	0	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:47685614C>G	ENST00000294339.3	-	4	1350	c.774G>C	c.(772-774)aaG>aaC	p.K258N	TAL1_ENST00000371884.2_Missense_Mutation_p.K258N|TAL1_ENST00000459729.1_5'UTR|TAL1_ENST00000371883.3_Missense_Mutation_p.K260N	NM_003189.2	NP_003180.1	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	258					angiogenesis (GO:0001525)|astrocyte fate commitment (GO:0060018)|basophil differentiation (GO:0030221)|cell fate commitment (GO:0045165)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|hemangioblast cell differentiation (GO:0060217)|hematopoietic stem cell differentiation (GO:0060218)|hemopoiesis (GO:0030097)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|platelet formation (GO:0030220)|positive regulation of cell division (GO:0051781)|positive regulation of chromatin assembly or disassembly (GO:0045799)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell proliferation (GO:0042127)|regulation of mast cell differentiation (GO:0060375)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord association neuron differentiation (GO:0021527)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|E-box binding (GO:0070888)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription factor binding (GO:0001085)|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)			haematopoietic_and_lymphoid_tissue(1)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	15						CCACAGGGTCCTTGCCAGTCT	0.642			T	"TRD@, SIL"	lymphoblastic leukemia/biphasic																																p.K258N				Dom	yes		1	1p32	6886	T-cell acute lymphocytic leukemia 1 (SCL)		L	.	TAL1-1082	0			c.G774C						.						11	11	11					1																	47685614		2201	4287	6488	SO:0001583	missense	6886	exon4			AGGGTCCTTGCCA	M29038	CCDS547.1	1p32	2013-05-21	2001-12-04		ENSG00000162367	ENSG00000162367		"Basic helix-loop-helix proteins"	11556	protein-coding gene	gene with protein product		187040		TCL5		2740341	Standard	NM_001287347		Approved	SCL, bHLHa17	uc009vyq.2	P17542	OTTHUMG00000007847	ENST00000294339.3:c.774G>C	1.37:g.47685614C>G	ENSP00000294339:p.Lys258Asn	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	58	16	NM_003189	0	0	0	0	0	D3DQ24	Missense_Mutation	SNP	ENST00000294339.3	37	CCDS547.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.673282	0.67928	.	.	ENSG00000162367	ENST00000371884;ENST00000371883;ENST00000294339	D;D;D	0.97811	-4.54;-4.55;-4.54	5.01	4.1	0.47936	Helix-loop-helix DNA-binding (1);	0.120919	0.52532	D	0.000063	D	0.94991	0.8379	L	0.27053	0.805	0.41923	D	0.990522	D	0.60160	0.987	P	0.50708	0.648	D	0.93287	0.6665	10	0.51188	T	0.08	.	5.5117	0.16884	0.0:0.6676:0.0:0.3324	.	258	P17542	TAL1_HUMAN	N	258;260;258	ENSP00000360951:K258N;ENSP00000360950:K260N;ENSP00000294339:K258N	ENSP00000294339:K258N	K	-	3	2	TAL1	47458201	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.494000	0.22467	1.344000	0.45657	0.579000	0.79373	AAG	.		0.642	TAL1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021640.1	NM_003189		G	47685614	C	G	47685614	3	3	136	1	0	0	0	0	1	0	0	0	15573	680	24	4	225	4	TAL1	1	47685614	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	31427703	47685614	201565007	3	12101											
ABCA4	24	broad.mit.edu	37	chr1	94486858	94486858	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctaatgacggtgattccAtactcctcggggctcctgtc	6	12	11	12	2	0	2	0	2	0	0	5	2	3	2	3	4	1	2	3	4	2	3	rs61750561		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:94486858A>G	ENST00000370225.3	-	35	5042	c.4956T>C	c.(4954-4956)taT>taC	p.Y1652Y	ABCA4_ENST00000536513.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1652			Y -> D (in STGD1). {ECO:0000269|PubMed:10206579}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CGGTGATTCCATACTCCTCGG	0.547																																					p.Y1652Y													.	ABCA4-162	0			c.T4956C	GRCh37	CM012882	ABCA4	M	rs61750561	.						184	177	180					1																	94486858		2203	4300	6503	SO:0001819	synonymous_variant	24	exon35			GATTCCATACTCC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.4956T>C	1.37:g.94486858A>G		Somatic	172	0		WXS	Illumina HiSeq	Phase_I	214	6	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			.		0.547	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		G	94486858	A	G	94486858	2	3	136	1	0	0	0	0	0	0	0	1	34	224	8	3		3	ABCA4	1	94486858	Silent	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	46801244	94486858	154763763	4	12102											
NBPF15	284565	broad.mit.edu;bcgsc.ca	37	chr1	148594427	148594427	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgatggaagtggaagaGcctgaagtcttacaggactc	11	9	14	7	0	1	3	0	2	1	1	2	6	1	6	1	3	3	1	1	3	4	1	rs587634015	byFrequency	TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:148594427G>C	ENST00000369187.3	+	19	2289	c.1800G>C	c.(1798-1800)gaG>gaC	p.E600D	NBPF15_ENST00000442702.2_Missense_Mutation_p.E600D	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	600	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					AAGTGGAAGAGCCTGAAGTCT	0.458																																					p.E600D													.	.	0			c.G1800C						.																																			SO:0001583	missense	728936	exon16			GGAAGAGCCTGAA	BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"neuroblastoma breakpoint family"	28791	protein-coding gene	gene with protein product		610414, 614005	"neuroblastoma breakpoint family, member 16"	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1800G>C	1.37:g.148594427G>C	ENSP00000358188:p.Glu600Asp	Somatic	485	1		WXS	Illumina HiSeq	Phase_I	550	104	NM_001102663	0	0	27	33	6	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	10.47	1.358251	0.24598	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.15372	2.43;2.43	0.502	0.502	0.16932	DUF1220 (2);	.	.	.	.	T	0.19005	0.0456	M	0.86420	2.815	0.09310	N	1	B	0.29188	0.236	P	0.44860	0.462	T	0.41106	-0.9527	8	0.66056	D	0.02	.	.	.	.	.	600	Q8N660	NBPFF_HUMAN	D	600	ENSP00000416864:E600D;ENSP00000358188:E600D	ENSP00000358188:E600D	E	+	3	2	NBPF15	146861051	0.937000	0.31787	0.003000	0.11579	0.003000	0.03518	0.894000	0.28350	0.557000	0.29117	0.377000	0.23210	GAG	G|1.000;A|0.000		0.458	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638		C	148594427	G	C	148594427	3	2	136	1	0	0	0	0	1	0	0	0	10221	962	34	4	1858	4	NBPF15	1	148594427	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	54107569	148594427	100656194	5	12103											
CADM3	57863	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	159170698	159170698	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caggaggggacgacaagaagGaatatttcatctagaggcgc	14	6	14	7	2	2	2	1	0	1	2	2	6	2	5	0	5	0	0	0	5	5	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:159170698G>T	ENST00000368125.4	+	9	1340	c.1183G>T	c.(1183-1185)Gaa>Taa	p.E395*	CTA-134P22.2_ENST00000609696.1_RNA|CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000497636.1_3'UTR|DARC_ENST00000537147.1_5'Flank|CADM3_ENST00000368124.4_Nonsense_Mutation_p.E429*	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	395					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					CGACAAGAAGGAATATTTCAT	0.617																																					p.E429X		.											.	CADM3-92	0			c.G1285T						.						78	76	77					1																	159170698		2203	4300	6503	SO:0001587	stop_gained	57863	exon10			AAGAAGGAATATT	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17601	protein-coding gene	gene with protein product	"nectin-like 1"	609743	"immunoglobulin superfamily, member 4B"	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.1183G>T	1.37:g.159170698G>T	ENSP00000357107:p.Glu395*	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	239	25	NM_021189	0	0	0	0	0	Q8IZQ9|Q9NVJ5|Q9UJP1	Nonsense_Mutation	SNP	ENST00000368125.4	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	G	38	6.895315	0.97916	.	.	ENSG00000162706	ENST00000368124;ENST00000368125	.	.	.	3.81	3.81	0.43845	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.48571	D	0.999671	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.2211	0.59887	0.0:0.0:1.0:0.0	.	.	.	.	X	429;395	.	ENSP00000357106:E429X	E	+	1	0	CADM3	157437322	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.966000	0.93397	1.965000	0.57142	0.591000	0.81541	GAA	.		0.617	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		T	159170698	G	T	159170698	4	4	136	1	0	0	0	0	0	1	0	0	2574	1175	41	4	1323	4	CADM3	1	159170698	Nonsense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	10576271	159170698	90079923	6	12104											
C1orf129	80133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	170965712	170965712	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcaacaggtggatattactCtaatgaaggagaatttctgg	13	12	11	5	0	2	2	0	1	2	1	2	4	2	3	0	4	3	1	0	4	6	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:170965712C>G	ENST00000367758.3	+	14	1501	c.1402C>G	c.(1402-1404)Cta>Gta	p.L468V	MROH9_ENST00000367759.4_Missense_Mutation_p.L468V	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	468																	GGATATTACTCTAATGAAGGA	0.443																																					p.L468V		.											.	.	0			c.C1402G						.						181	172	175					1																	170965712		1873	4113	5986	SO:0001583	missense	80133	exon14			ATTACTCTAATGA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"maestro heat-like repeat containing"	26287	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 129"	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1402C>G	1.37:g.170965712C>G	ENSP00000356732:p.Leu468Val	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	138	32	NM_025063	0	0	0	0	0	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.85|17.85	3.489337|3.489337	0.64074|0.64074	.|.	.|.	ENSG00000117501|ENSG00000117501	ENST00000367759;ENST00000367758|ENST00000426136	T;T|.	0.67698|.	-0.28;1.49|.	5.75|5.75	5.75|5.75	0.90469|0.90469	Armadillo-like helical (1);|.	0.127327|.	0.36101|.	N|.	0.002798|.	T|T	0.49626|0.49626	0.1568|0.1568	M|M	0.69823|0.69823	2.125|2.125	0.29405|0.29405	N|N	0.86168|0.86168	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.997;0.997|.	T|T	0.49390|0.49390	-0.8945|-0.8945	10|5	0.72032|.	D|.	0.01|.	-13.2876|-13.2876	15.4599|15.4599	0.75346|0.75346	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	468;468|.	F5GWX6;Q5TGP6|.	.;CA129_HUMAN|.	V|C	468|74	ENSP00000356733:L468V;ENSP00000356732:L468V|.	ENSP00000356732:L468V|.	L|S	+|+	1|2	2|0	C1orf129|C1orf129	169232336|169232336	0.790000|0.790000	0.28787|0.28787	0.271000|0.271000	0.24616|0.24616	0.008000|0.008000	0.06430|0.06430	3.549000|3.549000	0.53681|0.53681	2.716000|2.716000	0.92895|0.92895	0.655000|0.655000	0.94253|0.94253	CTA|TCT	.		0.443	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		G	170965712	C	G	170965712	3	3	136	1	0	0	0	0	1	0	0	0	2002	912	32	4	1452	4	C1orf129	1	170965712	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	11795014	170965712	78284909	7	12105											
EPHX1	2052	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	226030105	226030105	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcctgtgggtctggctgccTatattctagagaagttttcc	6	15	10	10	0	2	1	0	0	2	1	4	2	4	1	3	2	1	2	3	2	4	6			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:226030105T>C	ENST00000366837.4	+	7	1166	c.970T>C	c.(970-972)Tat>Cat	p.Y324H	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Missense_Mutation_p.Y324H	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	324					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TCTGGCTGCCTATATTCTAGA	0.582																																					p.Y324H													.	EPHX1-281	0			c.T970C						.						121	130	127					1																	226030105		2203	4300	6503	SO:0001583	missense	2052	exon7			GCTGCCTATATTC	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.970T>C	1.37:g.226030105T>C	ENSP00000355802:p.Tyr324His	Somatic	104	1		WXS	Illumina HiSeq	Phase_I	132	33	NM_001136018	0	0	52	73	21	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	37	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.776408	0.90195	.	.	ENSG00000143819	ENST00000272167;ENST00000366837	T;T	0.08102	3.13;3.13	5.33	5.33	0.75918	Alpha/beta hydrolase fold-1 (1);	0.000000	0.85682	D	0.000000	T	0.41050	0.1142	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.57248	-0.7844	10	0.87932	D	0	-30.0957	15.5961	0.76583	0.0:0.0:0.0:1.0	.	324	P07099	HYEP_HUMAN	H	324	ENSP00000272167:Y324H;ENSP00000355802:Y324H	ENSP00000272167:Y324H	Y	+	1	0	EPHX1	224096728	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	7.914000	0.87478	2.137000	0.66172	0.533000	0.62120	TAT	.		0.582	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		C	226030105	T	C	226030105	3	2	136	1	0	0	0	0	1	0	0	0	5192	1522	53	3	992	3	EPHX1	1	226030105	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	55064393	226030105	23220516	8	12106											
LYST	1130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	235872510	235872510	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcagactctagagcctgccGatggatgaggataaaaagac	14	7	12	8	1	2	4	1	1	1	3	2	7	2	6	2	2	2	0	2	2	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:235872510G>A	ENST00000389794.3	-	44	10198	c.10024C>T	c.(10024-10026)Cgg>Tgg	p.R3342W	LYST_ENST00000389793.2_Missense_Mutation_p.R3342W|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3342	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AGAGCCTGCCGATGGATGAGG	0.483																																					p.R3342W		.											.	LYST-143	0			c.C10024T						.						97	95	96					1																	235872510		2203	4300	6503	SO:0001583	missense	1130	exon44			CCTGCCGATGGAT	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.10024C>T	1.37:g.235872510G>A	ENSP00000374444:p.Arg3342Trp	Somatic	275	0		WXS	Illumina HiSeq	Phase_I	291	82	NM_000081	0	0	1	1	0	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601748	0.87055	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.74209	-0.82;-0.82	5.39	4.47	0.54385	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.91345	0.7270	H	0.98005	4.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94675	0.7860	10	0.87932	D	0	.	15.9845	0.80142	0.0:0.0:0.8645:0.1355	.	3342	Q99698	LYST_HUMAN	W	3342	ENSP00000374444:R3342W;ENSP00000374443:R3342W	ENSP00000374443:R3342W	R	-	1	2	LYST	233939133	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.049000	0.71053	1.391000	0.46566	0.655000	0.94253	CGG	.		0.483	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235872510	G	A	235872510	3	1	136	1	0	0	0	0	1	0	0	0	9153	1057	37	1	1421	1	LYST	1	235872510	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	9842405	235872510	13378111	9	12107											
NCOA1	8648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	24929447	24929447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccccctagggagcacagtGggctttctcctcaagatgac	8	10	10	13	0	2	2	1	1	1	1	4	3	3	3	3	2	1	2	3	2	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:24929447G>A	ENST00000406961.1	+	13	1760	c.1108G>A	c.(1108-1110)Ggg>Agg	p.G370R	NCOA1_ENST00000348332.3_Missense_Mutation_p.G370R|NCOA1_ENST00000405141.1_Missense_Mutation_p.G370R|NCOA1_ENST00000395856.3_Missense_Mutation_p.G370R|NCOA1_ENST00000288599.5_Missense_Mutation_p.G370R|NCOA1_ENST00000407230.1_Missense_Mutation_p.G219R|NCOA1_ENST00000538539.1_Missense_Mutation_p.G370R			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	370	Interaction with STAT3.				androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAGCACAGTGGGCTTTCTCC	0.383			T	PAX3	alveolar rhadomyosarcoma																																p.G370R		.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1-228	0			c.G1108A						.						65	66	66					2																	24929447		2203	4300	6503	SO:0001583	missense	8648	exon11			CACAGTGGGCTTT	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.1108G>A	2.37:g.24929447G>A	ENSP00000385216:p.Gly370Arg	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	70	24	NM_147223	0	0	0	0	0	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	G	7.212	0.595682	0.13875	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02158	4.54;4.54;4.42;4.54;4.54;4.54;4.54	5.02	5.02	0.67125	.	0.298923	0.37483	N	0.002071	T	0.01940	0.0061	L	0.34521	1.04	0.29230	N	0.873364	B;B;B;B	0.31790	0.34;0.28;0.014;0.203	B;B;B;B	0.33392	0.101;0.163;0.049;0.127	T	0.38156	-0.9674	10	0.20046	T	0.44	.	4.5462	0.12081	0.083:0.1533:0.6049:0.1588	.	370;370;370;219	Q15788-3;Q15788;Q15788-2;B5MCN7	.;NCOA1_HUMAN;.;.	R	370;370;219;370;370;370;370	ENSP00000385216:G370R;ENSP00000385097:G370R;ENSP00000385195:G219R;ENSP00000444039:G370R;ENSP00000320940:G370R;ENSP00000288599:G370R;ENSP00000379197:G370R	ENSP00000288599:G370R	G	+	1	0	NCOA1	24782951	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.987000	0.49378	2.485000	0.83878	0.655000	0.94253	GGG	.		0.383	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		A	24929447	G	A	24929447	3	1	136	1	0	0	0	0	1	0	0	0	10254	1348	47	2	1142	2	NCOA1	2	24929447	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		24929447	218269926	10	12108											
LRPPRC	10128	broad.mit.edu;bcgsc.ca	37	chr2	44203320	44203320	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacaagggcactgaatacTgcctctgtaactgggagatc	11	9	11	10	0	2	2	1	1	1	1	3	3	2	2	1	2	3	2	1	2	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:44203320T>A	ENST00000260665.7	-	6	756	c.699A>T	c.(697-699)gcA>gcT	p.A233A	LRPPRC_ENST00000409946.1_Silent_p.A233A|LRPPRC_ENST00000409659.1_Silent_p.A233A	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	233					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CACTGAATACTGCCTCTGTAA	0.403																																					p.A233A													.	LRPPRC-93	0			c.A699T						.						84	82	83					2																	44203320		2203	4300	6503	SO:0001819	synonymous_variant	10128	exon6			GAATACTGCCTCT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.699A>T	2.37:g.44203320T>A		Somatic	98	1		WXS	Illumina HiSeq	Phase_I	60	18	NM_133259	0	0	3	7	4	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			.		0.403	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		A	44203320	T	A	44203320	2	1	136	1	0	0	0	0	0	0	0	1	8990	1567	55	5		5	LRPPRC	2	44203320	Silent	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	19273873	44203320	198996053	11	12109											
TTL	150465	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	113260589	113260589	+	Frame_Shift_Del	DEL	A	A	-																															atgttgataatttccaagacAaaacctgccatttgaccaat																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:113260589delA	ENST00000233336.6	+	5	897	c.706delA	c.(706-708)aaafs	p.K236fs		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	236	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		TTTCCAAGACAAAACCTGCCA	0.388			T	ETV6	ALL																																p.K236fs		.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	.	TTL-658	0			c.706delA						.						126	124	125					2																	113260589		2203	4300	6503	SO:0001589	frameshift_variant	150465	exon5			.		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.706delA	2.37:g.113260589delA	ENSP00000233336:p.Lys236fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	126	31	NM_153712	0	0	0	0	0	Q585T3|Q7Z302|Q8N426	Frame_Shift_Del	DEL	ENST00000233336.6	37	CCDS2096.1																																																																																			.		0.388	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		-	113260589	A	-	113260589	7	5	136	1	0	1	0	1	0	0	0	0	16754	131	5	0	724	0	TTL	2	113260589	Frame_Shift_Del	DEL	A	TCGA-HE-A5NL-01A-11D-A26P-10	69057269	113260589	129938784	12	12110											
GAD1	2571	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	171705820	171705820	+	Frame_Shift_Del	DEL	A	A	-																															cctggggaggtgggctgctcAtgtccaggaagcaccgccat																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:171705820delA	ENST00000358196.3	+	12	1694	c.1144delA	c.(1144-1146)atgfs	p.M382fs		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	382					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						TGGGCTGCTCATGTCCAGGAA	0.537																																					p.M382fs		.											.	GAD1-91	0			c.1144delA						.						76	67	70					2																	171705820		2203	4300	6503	SO:0001589	frameshift_variant	2571	exon12			.		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1144delA	2.37:g.171705820delA	ENSP00000350928:p.Met382fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	138	50	NM_000817	0	0	0	0	0	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Frame_Shift_Del	DEL	ENST00000358196.3	37	CCDS2239.1																																																																																			.		0.537	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			-	171705820	A	-	171705820	7	5	136	1	0	1	0	1	0	0	0	0	6198	217	8	0	1227	0	GAD1	2	171705820	Frame_Shift_Del	DEL	A	TCGA-HE-A5NL-01A-11D-A26P-10	58445231	171705820	71493553	13	12111											
FN1	2335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	216274676	216274676	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggtcacaggtgtgctggtGctggtggtggtgaagtcaaa	7	11	17	6	0	2	1	2	1	0	0	2	1	2	1	0	6	2	2	0	6	2	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:216274676G>T	ENST00000359671.1	-	14	2368	c.2103C>A	c.(2101-2103)agC>agA	p.S701R	FN1_ENST00000443816.1_Missense_Mutation_p.S701R|FN1_ENST00000354785.4_Missense_Mutation_p.S701R|FN1_ENST00000432072.2_Missense_Mutation_p.S701R|FN1_ENST00000356005.4_Missense_Mutation_p.S701R|FN1_ENST00000323926.6_Missense_Mutation_p.S701R|FN1_ENST00000336916.4_Missense_Mutation_p.S701R|FN1_ENST00000346544.3_Missense_Mutation_p.S701R|FN1_ENST00000357009.2_Missense_Mutation_p.S701R|FN1_ENST00000421182.1_Missense_Mutation_p.S701R|FN1_ENST00000345488.5_Missense_Mutation_p.S701R|FN1_ENST00000357867.4_Missense_Mutation_p.S701R|FN1_ENST00000446046.1_Missense_Mutation_p.S701R			P02751	FINC_HUMAN	fibronectin 1	701	Fibronectin type-III 1.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GTGTGCTGGTGCTGGTGGTGG	0.557																																					p.S701R		.											.	FN1-584	0			c.C2103A						.						370	375	373					2																	216274676		2203	4300	6503	SO:0001583	missense	2335	exon14			GCTGGTGCTGGTG		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"Fibronectin type III domain containing", "Endogenous ligands"	3778	protein-coding gene	gene with protein product	"migration-stimulating factor", "cold-insoluble globulin"	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2103C>A	2.37:g.216274676G>T	ENSP00000352696:p.Ser701Arg	Somatic	398	0		WXS	Illumina HiSeq	Phase_I	506	121	NM_212476	0	0	4	4	0	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	G	11.17	1.559369	0.27827	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.47869	0.83;2.19;2.35;0.92;2.42;2.05;2.4;2.07;2.37;2.08;1.58;0.9;1.49	5.65	3.84	0.44239	.	0.360826	0.30464	N	0.009573	T	0.56077	0.1961	L	0.44542	1.39	0.42852	D	0.994085	D;B;B;B;B;P;D;B;B;D	0.89917	1.0;0.353;0.17;0.17;0.106;0.533;0.998;0.17;0.17;0.987	D;P;B;B;B;B;P;B;B;P	0.87578	0.998;0.522;0.079;0.127;0.036;0.326;0.865;0.127;0.127;0.904	T	0.54549	-0.8277	10	0.40728	T	0.16	.	8.8981	0.35476	0.2229:0.0:0.7771:0.0	.	701;701;701;701;701;701;701;701;701;701	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	R	701	ENSP00000394423:S701R;ENSP00000323534:S701R;ENSP00000338200:S701R;ENSP00000350534:S701R;ENSP00000346839:S701R;ENSP00000352696:S701R;ENSP00000265312:S701R;ENSP00000273049:S701R;ENSP00000349509:S701R;ENSP00000410422:S701R;ENSP00000415018:S701R;ENSP00000399538:S701R;ENSP00000348285:S701R	ENSP00000265313:S701R	S	-	3	2	FN1	215982921	1.000000	0.71417	0.896000	0.35187	0.102000	0.19082	1.257000	0.32932	1.531000	0.49152	-0.140000	0.14226	AGC	.		0.557	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216274676	G	T	216274676	3	4	136	1	0	0	0	0	1	0	0	0	5981	1310	46	4	5462	4	FN1	2	216274676	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	44568856	216274676	26924697	14	12112											
PDCD6IP	10015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	33840351	33840351	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtactgccgcgcggcggAggagctcagcaagctgcgcc	7	4	15	15	5	1	0	1	0	0	0	1	2	1	2	3	3	6	4	3	3	2	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr3:33840351A>C	ENST00000307296.3	+	1	508	c.131A>C	c.(130-132)gAg>gCg	p.E44A	RP11-10C24.3_ENST00000604982.1_lincRNA|PDCD6IP_ENST00000457054.2_Missense_Mutation_p.E44A|RP11-10C24.1_ENST00000605513.1_lincRNA			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	44	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CGCGCGGCGGAGGAGCTCAGC	0.692																																					p.E44A		.											.	PDCD6IP-228	0			c.A131C						.						10	11	11					3																	33840351		2139	4155	6294	SO:0001583	missense	10015	exon1			CGGCGGAGGAGCT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.131A>C	3.37:g.33840351A>C	ENSP00000307387:p.Glu44Ala	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	111	28	NM_013374	0	0	7	10	3	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824727	0.50739	.	.	ENSG00000170248	ENST00000307296;ENST00000457054;ENST00000413073	T;T;T	0.16324	2.35;2.35;2.35	5.03	5.03	0.67393	BRO1 domain (3);	0.048074	0.85682	D	0.000000	T	0.09202	0.0227	N	0.13299	0.325	0.80722	D	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.11329	0.006;0.006;0.002	T	0.14364	-1.0475	10	0.08381	T	0.77	-21.2451	11.3154	0.49388	0.8641:0.0:0.0:0.1359	.	44;44;44	C5MQH7;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	A	44	ENSP00000307387:E44A;ENSP00000411825:E44A;ENSP00000406693:E44A	ENSP00000307387:E44A	E	+	2	0	PDCD6IP	33815355	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.731000	0.74785	2.108000	0.64289	0.482000	0.46254	GAG	.		0.692	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			C	33840351	A	C	33840351	3	2	136	1	0	0	0	0	1	0	0	0	11650	304	11	5	133	5	PDCD6IP	3	33840351	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		33840351	164182079	15	12113											
ARHGEF3	50650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56766301	56766301	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgaatgcccctcgcagggagCcacccagcctcacttctcca	8	7	8	18	1	2	1	1	1	1	0	4	2	2	2	6	1	3	1	6	1	1	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr3:56766301C>A	ENST00000296315.3	-	9	1361	c.1193G>T	c.(1192-1194)gGc>gTc	p.G398V	ARHGEF3_ENST00000413728.2_Missense_Mutation_p.G404V|ARHGEF3_ENST00000495373.1_Missense_Mutation_p.G398V|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.G430V|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.G369V|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.G404V	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	398	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		TCGCAGGGAGCCACCCAGCCT	0.552																																					p.G430V		.											.	ARHGEF3-228	0			c.G1289T						.						116	102	106					3																	56766301		2203	4300	6503	SO:0001583	missense	50650	exon12			AGGGAGCCACCCA	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"Rho guanine nucleotide exchange factors"	683	protein-coding gene	gene with protein product	"exchange factor found in platelets and leukemic and neuronal tissues, XPLN", "RhoGEF protein"	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.1193G>T	3.37:g.56766301C>A	ENSP00000296315:p.Gly398Val	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	202	46	NM_001128615	0	0	8	8	0	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120131	0.94385	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373	T;T;T;T;T;T	0.28666	1.88;1.79;1.8;1.8;1.82;1.6	5.83	5.83	0.93111	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.999;1.0;0.999;0.998;0.999	D;D;D;D;D;D;D	0.79108	0.982;0.97;0.982;0.982;0.982;0.97;0.992	T	0.46871	-0.9160	10	0.09590	T	0.72	-7.7666	20.1218	0.97964	0.0:1.0:0.0:0.0	.	404;369;196;398;430;398;404	E9PG37;E7EU49;Q9NR81-4;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;.;ARHG3_HUMAN;.	V	398;430;404;404;369;398	ENSP00000296315:G398V;ENSP00000341071:G430V;ENSP00000410922:G404V;ENSP00000420420:G404V;ENSP00000418826:G369V;ENSP00000417986:G398V	ENSP00000296315:G398V	G	-	2	0	ARHGEF3	56741341	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.763000	0.94921	0.561000	0.74099	GGC	.		0.552	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		A	56766301	C	A	56766301	3	1	136	1	0	0	0	0	1	0	0	0	904	739	26	4	395	4	ARHGEF3	3	56766301	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	22925950	56766301	141256129	16	12114											
MED12L	116931	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	150877786	150877786	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcggggcccccagccctggCccccccggccctggcatgag	4	4	13	20	2	0	1	0	1	0	0	1	1	0	1	7	5	1	1	7	5	0	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr3:150877786C>T	ENST00000474524.1	+	7	1043	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	MED12L_ENST00000309237.4_Silent_p.G335G|MED12L_ENST00000422248.2_Silent_p.G335G|MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	335						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CCAGCCCTGGCCCCCCCGGCC	0.582																																					p.G335G													.	MED12L-576	0			c.C1005T						.						83	94	90					3																	150877786		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon7			CCCTGGCCCCCCC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.1005C>T	3.37:g.150877786C>T		Somatic	50	1		WXS	Illumina HiSeq	Phase_I	109	53	NM_053002	0	0	0	0	0	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			.		0.582	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	150877786	C	T	150877786	2	4	136	1	0	0	0	0	0	0	0	1	9454	726	26	2		2	MED12L	3	150877786	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	94111485	150877786	47144644	17	12115											
SPON2	10417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1164263	1164263	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatgaaggccctggggctCtgtcgcagccgcaccagtgt	6	7	16	12	2	1	1	0	1	1	0	2	2	1	2	3	4	1	3	3	4	1	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:1164263C>A	ENST00000290902.5	-	5	1070	c.738G>T	c.(736-738)caG>caT	p.Q246H	SPON2_ENST00000431380.1_Missense_Mutation_p.Q246H|RP11-20I20.4_ENST00000609548.1_RNA	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	246					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CCCTGGGGCTCTGTCGCAGCC	0.637																																					p.Q246H		.											.	SPON2-90	0			c.G738T						.						104	102	103					4																	1164263		2203	4300	6503	SO:0001583	missense	10417	exon5			GGGGCTCTGTCGC	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.738G>T	4.37:g.1164263C>A	ENSP00000290902:p.Gln246His	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	124	46	NM_012445	0	0	0	0	0	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	37	CCDS3347.1	.	.	.	.	.	.	.	.	.	.	C	4.701	0.130282	0.08981	.	.	ENSG00000159674	ENST00000290902;ENST00000431380	T;T	0.10005	2.92;2.92	4.73	0.866	0.19079	.	0.275166	0.40640	N	0.001054	T	0.10465	0.0256	M	0.62723	1.935	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.20773	-1.0265	10	0.48119	T	0.1	.	5.9277	0.19122	0.0:0.4937:0.254:0.2523	.	246;246	D3DVN9;Q9BUD6	.;SPON2_HUMAN	H	246	ENSP00000290902:Q246H;ENSP00000394832:Q246H	ENSP00000290902:Q246H	Q	-	3	2	SPON2	1154263	0.003000	0.15002	0.455000	0.27031	0.047000	0.14425	-0.195000	0.09546	0.077000	0.16863	0.603000	0.83216	CAG	.		0.637	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			A	1164263	C	A	1164263	3	1	136	1	0	0	0	0	1	0	0	0	15115	912	32	4	265	4	SPON2	4	1164263	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		1164263	189990013	18	12116											
SEL1L3	23231	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	25819805	25819806	+	Frame_Shift_Ins	INS	-	-	T																															gcctggaacaagctggggtgINStttgtctttcagctccttct																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:25819805_25819806insT	ENST00000399878.3	-	9	1640_1641	c.1518_1519insA	c.(1516-1521)aaacacfs	p.H507fs	SEL1L3_ENST00000502949.1_Frame_Shift_Ins_p.H354fs|SEL1L3_ENST00000264868.5_Frame_Shift_Ins_p.H472fs	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	507						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						AAGCTGGGGTGTTTGTCTTTCA	0.55																																					p.H507fs		.											.	.	0			c.1519_1520insA						.																																			SO:0001589	frameshift_variant	23231	exon9			.	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1519dupA	4.37:g.25819808_25819808dupT	ENSP00000382767:p.His507fs	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	198	49	NM_015187	0	0	0	0	0	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Frame_Shift_Ins	INS	ENST00000399878.3	37	CCDS47037.1																																																																																			.		0.55	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25819806	-	T	25819805	7	5	136	1	0	1	1	0	0	0	0	0	14044	1377	48	0	1943	0	SEL1L3	4	25819805	Frame_Shift_Ins	INS	-	TCGA-HE-A5NL-01A-11D-A26P-10	24655542	25819805	165334471	19	12117											
KLB	152831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39435931	39435931	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cattggatcgagccaaaccgGtcggaaaacacgatggatat	14	7	11	9	4	0	0	0	0	0	0	2	5	0	3	2	4	3	0	2	4	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:39435931G>T	ENST00000257408.4	+	2	1024	c.927G>T	c.(925-927)cgG>cgT	p.R309R		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	309	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						AGCCAAACCGGTCGGAAAACA	0.473																																					p.R309R		.											.	KLB-69	0			c.G927T						.						118	101	107					4																	39435931		2203	4300	6503	SO:0001819	synonymous_variant	152831	exon2			AAACCGGTCGGAA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.927G>T	4.37:g.39435931G>T		Somatic	307	0		WXS	Illumina HiSeq	Phase_I	373	119	NM_175737	0	0	0	0	0	Q2M3K8	Silent	SNP	ENST00000257408.4	37	CCDS3451.1																																																																																			.		0.473	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		T	39435931	G	T	39435931	2	4	136	1	0	0	0	0	0	0	0	1	8353	1248	44	4		4	KLB	4	39435931	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	13616126	39435931	151718345	20	12118											
GABRG1	2565	hgsc.bcm.edu;bcgsc.ca	37	chr4	46043272	46043272	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggatggagaccaggagtcatCtgagcacaataataaatgaa	17	7	11	6	0	2	3	1	2	1	1	2	6	2	5	1	3	1	1	1	3	5	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:46043272C>T	ENST00000295452.4	-	9	1299		c.e9-1			NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1						gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	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)|Ketazolam(DB01587)|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)	CAGGAGTCATCTGAGCACAAT	0.388																																					.		.											.	GABRG1-92	0			c.1132-1G>A						.						44	46	45					4																	46043272		2203	4297	6500	SO:0001630	splice_region_variant	2565	exon10			AGTCATCTGAGCA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.1132-1G>A	4.37:g.46043272C>T		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	70	17	NM_173536	0	0	0	0	0	Q5H9T8	Splice_Site	SNP	ENST00000295452.4	37	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.483181	0.26598	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.36548	D	0.871662	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8364	0.40971	0.0:0.9066:0.0:0.0934	.	.	.	.	.	-1	.	.	.	-	.	.	GABRG1	45738029	0.279000	0.24239	0.267000	0.24556	0.006000	0.05464	1.471000	0.35365	2.436000	0.82500	0.585000	0.79938	.	.		0.388	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	Intron	T	46043272	C	T	46043272	5	4	136	1	0	0	0	0	0	0	1	0	6190	927	32	2	270	2	GABRG1	4	46043272	Splice_Site	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	6607341	46043272	145111004	21	12119											
G3BP2	9908	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76570830	76570830	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtttctcgctctcttgcAgctcttgtttttttctcttc	1	22	6	12	1	4	0	0	0	4	0	8	0	4	0	0	1	2	5	0	1	0	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:76570830A>T	ENST00000359707.4	-	12	2018	c.1233T>A	c.(1231-1233)gcT>gcA	p.A411A	G3BP2_ENST00000395719.3_Silent_p.A411A|G3BP2_ENST00000357854.3_Silent_p.A378A	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	411					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GCTCTCTTGCAGCTCTTGTTT	0.453																																					p.A411A													.	G3BP2-153	0			c.T1233A						.						226	187	200					4																	76570830		2203	4300	6503	SO:0001819	synonymous_variant	9908	exon12			TCTTGCAGCTCTT	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"RNA binding motif (RRM) containing"	30291	protein-coding gene	gene with protein product	"Ras-GTPase activating protein SH3 domain-binding protein 2"					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.1233T>A	4.37:g.76570830A>T		Somatic	204	1		WXS	Illumina HiSeq	Phase_I	226	59	NM_012297	0	0	10	14	4	A8K6X1|O60606|O75149|Q9UPA1	Silent	SNP	ENST00000359707.4	37	CCDS3571.1																																																																																			.		0.453	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		T	76570830	A	T	76570830	2	4	136	1	0	0	0	0	0	0	0	1	6161	175	7	5		5	G3BP2	4	76570830	Silent	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	30527558	76570830	114583446	22	12120											
ARHGAP24	83478	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	86916564	86916564	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agagcaagacttttttggggGgaactttgaggaccctgttt	9	13	13	6	0	0	3	0	1	0	2	0	5	0	5	1	4	2	2	1	4	2	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:86916564G>A	ENST00000395184.1	+	9	2223	c.1757G>A	c.(1756-1758)gGg>gAg	p.G586E	ARHGAP24_ENST00000395183.2_Missense_Mutation_p.G491E|ARHGAP24_ENST00000264343.4_Missense_Mutation_p.G493E	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	586					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		TTTTTTGGGGGGAACTTTGAG	0.562																																					p.G586E													.	ARHGAP24-227	0			c.G1757A						.						71	74	73					4																	86916564		2203	4300	6503	SO:0001583	missense	83478	exon9			TTGGGGGGAACTT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1757G>A	4.37:g.86916564G>A	ENSP00000378611:p.Gly586Glu	Somatic	153	1		WXS	Illumina HiSeq	Phase_I	166	55	NM_001025616	0	0	5	16	11	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	37	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135263	0.37728	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.14144	2.88;2.54;2.53;2.53	5.73	4.85	0.62838	.	0.101205	0.64402	D	0.000002	T	0.17662	0.0424	L	0.60455	1.87	0.48830	D	0.999715	B;B;P	0.50066	0.086;0.04;0.931	B;B;B	0.44224	0.035;0.01;0.444	T	0.07252	-1.0782	10	0.10377	T	0.69	.	18.1969	0.89825	0.0:0.1889:0.8111:0.0	.	491;493;586	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	E	586;491;501;493	ENSP00000378611:G586E;ENSP00000378610:G491E;ENSP00000425589:G501E;ENSP00000264343:G493E	ENSP00000264343:G493E	G	+	2	0	ARHGAP24	87135588	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	5.010000	0.64004	2.710000	0.92621	0.491000	0.48974	GGG	.		0.562	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		A	86916564	G	A	86916564	3	1	136	1	0	0	0	0	1	0	0	0	873	1232	43	2	1903	2	ARHGAP24	4	86916564	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	10345734	86916564	104237712	23	12121											
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	126239108	126239108	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaatctgcgttacagcatTgtctctggcaatggactggg	8	12	12	9	1	2	0	0	0	2	0	3	1	2	1	0	3	3	4	0	3	3	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:126239108T>C	ENST00000394329.3	+	1	1555	c.1542T>C	c.(1540-1542)atT>atC	p.I514I		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	514	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GTTACAGCATTGTCTCTGGCA	0.562											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I514I		.											.	FAT4-108	0			c.T1542C						.						63	65	65					4																	126239108		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon1			CAGCATTGTCTCT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1542T>C	4.37:g.126239108T>C		Somatic	150	0	1548	WXS	Illumina HiSeq	Phase_I	147	55	NM_024582	0	0	0	0	0	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.		0.562	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126239108	T	C	126239108	2	2	136	1	0	0	0	0	0	0	0	1	5711	1800	63	3		3	FAT4	4	126239108	Silent	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	39322544	126239108	64915168	24	12122											
HAND2	9464	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	174450317	174450317	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgagccagccatggaagtAggggttctcctcatggctgc	8	9	14	10	0	2	1	1	1	1	0	3	3	2	2	3	4	3	3	3	4	2	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:174450317A>T	ENST00000359562.4	-	1	1063	c.124T>A	c.(124-126)Tac>Aac	p.Y42N	HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000502896.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000503474.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000502941.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2_ENST00000505300.1_5'UTR	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	42					adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		CCATGGAAGTAGGGGTTCTCC	0.726																																					p.Y42N		.											.	HAND2-91	0			c.T124A						.						5	6	6					4																	174450317		1939	3897	5836	SO:0001583	missense	9464	exon1			GGAAGTAGGGGTT	AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.124T>A	4.37:g.174450317A>T	ENSP00000352565:p.Tyr42Asn	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	29	7	NM_021973	0	0	0	0	0	B6ECG9|O95300|O95301|P97833|Q494T1	Missense_Mutation	SNP	ENST00000359562.4	37	CCDS3819.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688940	0.68271	.	.	ENSG00000164107	ENST00000359562;ENST00000393686	D	0.97066	-4.23	3.57	3.57	0.40892	.	0.281047	0.34178	N	0.004194	D	0.96078	0.8722	L	0.38175	1.15	0.58432	D	0.999995	D;D;D	0.63046	0.992;0.992;0.986	P;P;P	0.57204	0.815;0.815;0.701	D	0.94998	0.8140	10	0.39692	T	0.17	-0.0407	12.291	0.54819	1.0:0.0:0.0:0.0	.	42;42;42	B6ECG9;P61296;E9PCP7	.;HAND2_HUMAN;.	N	42	ENSP00000352565:Y42N	ENSP00000352565:Y42N	Y	-	1	0	HAND2	174686892	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.391000	0.66266	1.491000	0.48482	0.379000	0.24179	TAC	.		0.726	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			T	174450317	A	T	174450317	3	4	136	1	0	0	0	0	1	0	0	0	6971	420	15	5	537	5	HAND2	4	174450317	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	48211209	174450317	16703959	25	12123											
WDR17	116966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	177056301	177056301	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actgcaaattcaaacctgacGatcctaatcttttagcaaca	15	11	4	11	1	2	1	1	1	1	0	3	2	3	1	2	0	4	2	2	0	5	4	rs140987021		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:177056301G>A	ENST00000280190.4	+	9	1369	c.1213G>A	c.(1213-1215)Gat>Aat	p.D405N	WDR17_ENST00000507824.2_Missense_Mutation_p.D388N|WDR17_ENST00000393643.2_Missense_Mutation_p.D381N|WDR17_ENST00000508596.1_Missense_Mutation_p.D381N			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	405										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CAAACCTGACGATCCTAATCT	0.353																																					p.D405N		.											.	WDR17-95	0			c.G1213A						.	G	ASN/ASP,ASN/ASP	0,4406		0,0,2203	121	122	122		1213,1141	2.4	1	4	dbSNP_134	122	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	WDR17	NM_170710.4,NM_181265.3	23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	405/1323,381/1284	177056301	1,13005	2203	4300	6503	SO:0001583	missense	116966	exon9			CCTGACGATCCTA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1213G>A	4.37:g.177056301G>A	ENSP00000280190:p.Asp405Asn	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	190	62	NM_170710	0	0	0	0	0	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326502	0.24080	0.0	1.16E-4	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.58652	0.35;3.58;0.32	5.5	2.42	0.29668	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.265065	0.38164	N	0.001790	T	0.30324	0.0761	N	0.13198	0.31	0.48571	D	0.999678	B;B	0.19445	0.036;0.036	B;B	0.18871	0.023;0.023	T	0.15150	-1.0447	10	0.05525	T	0.97	-17.5458	6.7154	0.23300	0.433:0.0:0.567:0.0	.	381;405	E7EQX0;Q8IZU2	.;WDR17_HUMAN	N	381;381;405;388	ENSP00000422763:D381N;ENSP00000377258:D381N;ENSP00000280190:D405N	ENSP00000280190:D405N	D	+	1	0	WDR17	177293295	1.000000	0.71417	0.998000	0.56505	0.740000	0.42216	3.339000	0.52135	0.703000	0.31848	0.650000	0.86243	GAT	G|1.000;A|0.000		0.353	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			A	177056301	G	A	177056301	3	1	136	1	0	0	0	0	1	0	0	0	17310	1058	37	1	1243	1	WDR17	4	177056301	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	2605984	177056301	14097975	26	12124											
CENPK	64105	broad.mit.edu;bcgsc.ca	37	chr5	64824334	64824341	+	Frame_Shift_Del	DEL	CCCAAGGT	CCCAAGGT	-																															aatggtcttctagaaactcgCccaaggtactcaagagtttc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	CCCAAGGT	CCCAAGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:64824334_64824341delCCCAAGGT	ENST00000396679.1	-	9	749_756	c.535_542delACCTTGGG	c.(535-543)accttgggcfs	p.TLG179fs	CENPK_ENST00000242872.3_Frame_Shift_Del_p.TLG179fs|CENPK_ENST00000508421.1_Frame_Shift_Del_p.TLG149fs|CENPK_ENST00000510693.1_Frame_Shift_Del_p.TLG116fs|CENPK_ENST00000514814.1_Frame_Shift_Del_p.TLG179fs|CENPK_ENST00000506282.2_5'UTR	NM_022145.4	NP_071428.2	Q9BS16	CENPK_HUMAN	centromere protein K	179					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)	10		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)		TAGAAACTCGCCCAAGGTACTCAAGAGT	0.264																																					p.179_181del													.	CENPK-90	0			c.535_542del						.																																			SO:0001589	frameshift_variant	64105	exon9			AACTCGCCCAAGG	BC008504	CCDS3984.1	5q12.3	2013-11-05			ENSG00000123219	ENSG00000123219			29479	protein-coding gene	gene with protein product		611502				8950979	Standard	NM_022145		Approved	FKSG14, SOLT, CENP-K	uc003jtu.3	Q9BS16	OTTHUMG00000131227	ENST00000396679.1:c.535_542delACCTTGGG	5.37:g.64824334_64824341delCCCAAGGT	ENSP00000379911:p.Thr179fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	68	8	NM_001267038	0	0	0	0	0	Q9H4L0	Frame_Shift_Del	DEL	ENST00000396679.1	37	CCDS3984.1																																																																																			.		0.264	CENPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253971.2	NM_022145		-	64824341	CCCAAGGT	-	64824334	7	5	136	1	0	1	0	1	0	0	0	0	3241	739	26	0	279	0	CENPK	5	64824334	Frame_Shift_Del	DEL	CCCAAGGT	TCGA-HE-A5NL-01A-11D-A26P-10		64824334	116090926	27	12125											
RGMB	285704	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	98115590	98115591	+	Frame_Shift_Del	DEL	GG	GG	-																															tcacagccacgctggagccaGggaacacaggagaggggacc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:98115590_98115591delGG	ENST00000513185.1	+	2	879_880	c.443_444delGG	c.(442-444)aggfs	p.R148fs	RGMB_ENST00000308234.7_Frame_Shift_Del_p.R189fs|RGMB_ENST00000504776.1_3'UTR			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	148					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		GCTGGAGCCAGGGAACACAGGA	0.51																																					p.189_189del		.											.	.	0			c.566_567del						.																																			SO:0001589	frameshift_variant	285704	exon4			.	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.443_444delGG	5.37:g.98115590_98115591delGG	ENSP00000423256:p.Arg148fs	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	204	65	NM_001012761	0	0	0	0	0	D6R9A0|Q8NC92	Frame_Shift_Del	DEL	ENST00000513185.1	37																																																																																				.		0.51	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		-	98115591	GG	-	98115590	7	5	136	1	0	1	0	1	0	0	0	0	13313	1000	35	0	576	0	RGMB	5	98115590	Frame_Shift_Del	DEL	GG	TCGA-HE-A5NL-01A-11D-A26P-10	33291256	98115590	82799670	28	12126											
ANKHD1	54882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	139876316	139876316	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacaaagataagatagaagaActtaaaaagaacagagaaga	26	4	8	3	0	0	7	0	0	0	7	0	8	0	7	0	0	3	0	0	0	11	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:139876316A>G	ENST00000360839.2	+	15	2611	c.2457A>G	c.(2455-2457)gaA>gaG	p.E819E	ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.E819E|ANKHD1_ENST00000297183.6_Silent_p.E819E|ANKHD1_ENST00000462121.1_3'UTR	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	819						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGATAGAAGAACTTAAAAAGA	0.368																																					p.E819E		.											.	ANKHD1-185	0			c.A2457G						.						69	73	71					5																	139876316		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon15			AGAAGAACTTAAA	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"Ankyrin repeat domain containing"	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.2457A>G	5.37:g.139876316A>G		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	61	29	NM_017747	0	0	5	6	1	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	37	CCDS4225.1																																																																																			.		0.368	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139876316	A	G	139876316	2	3	136	1	0	0	0	0	0	0	0	1	628	40	2	3		3	ANKHD1	5	139876316	Silent	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	41760726	139876316	41038944	29	12127											
FAT2	2196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	150921871	150921871	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtagcaggtgacctgcctGttctgctcagaaatgtcagc	9	11	11	10	0	3	2	2	1	1	1	3	2	3	2	2	1	4	4	2	1	2	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:150921871G>T	ENST00000261800.5	-	9	8829	c.8817C>A	c.(8815-8817)aaC>aaA	p.N2939K		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2939	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGACCTGCCTGTTCTGCTCAG	0.502																																					p.N2939K		.											.	FAT2-96	0			c.C8817A						.						127	121	123					5																	150921871		2203	4300	6503	SO:0001583	missense	2196	exon9			CTGCCTGTTCTGC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.8817C>A	5.37:g.150921871G>T	ENSP00000261800:p.Asn2939Lys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	104	30	NM_001447	0	0	0	0	0	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921781	0.73213	.	.	ENSG00000086570	ENST00000261800	T	0.59906	0.23	6.05	1.26	0.21427	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	T	0.76807	0.4039	M	0.89601	3.045	0.47511	D	0.999445	D	0.89917	1.0	D	0.97110	1.0	T	0.77199	-0.2675	10	0.56958	D	0.05	.	10.6765	0.45789	0.4552:0.0:0.5448:0.0	.	2939	Q9NYQ8	FAT2_HUMAN	K	2939	ENSP00000261800:N2939K	ENSP00000261800:N2939K	N	-	3	2	FAT2	150902064	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	1.206000	0.32321	0.147000	0.19030	0.650000	0.86243	AAC	.		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150921871	G	T	150921871	3	4	136	1	0	0	0	0	1	0	0	0	5709	1368	48	4	4292	4	FAT2	5	150921871	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	11045555	150921871	29993389	30	12128											
KIF4B	285643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	154395501	154395501	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaacttgaaagaaacttccaGaaacaatccagtgtgctcag	17	8	7	9	0	1	3	1	1	0	2	3	3	3	3	2	0	4	1	2	0	5	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:154395501G>A	ENST00000435029.4	+	1	2242	c.2082G>A	c.(2080-2082)caG>caA	p.Q694Q		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	694	Interaction with PRC1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GAAACTTCCAGAAACAATCCA	0.438																																					p.Q694Q		.											.	KIF4B-1	0			c.G2082A						.						103	107	106					5																	154395501		2203	4300	6503	SO:0001819	synonymous_variant	285643	exon1			CTTCCAGAAACAA	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2082G>A	5.37:g.154395501G>A		Somatic	302	0		WXS	Illumina HiSeq	Phase_I	320	79	NM_001099293	0	0	0	0	0		Silent	SNP	ENST00000435029.4	37	CCDS47324.1																																																																																			.		0.438	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			A	154395501	G	A	154395501	2	1	136	1	0	0	0	0	0	0	0	1	8325	933	33	2		2	KIF4B	5	154395501	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3473630	154395501	26519759	31	12129											
CASP8AP2	9994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90577520	90577520	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagtctgataattcaagcaGtaaatcaagttgttcttctt	12	15	8	6	0	5	1	2	1	3	0	5	2	5	2	0	1	1	4	0	1	5	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr6:90577520G>T	ENST00000551025.1	+	0	5948									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AATTCAAGCAGTAAATCAAGT	0.423																																					p.S1504I	Colon(187;1656 2025 17045 31481 39901)	.											.	CASP8AP2-24	0			c.G4511T						.						84	80	82					6																	90577520		1902	4115	6017			9994	exon8			CAAGCAGTAAATC	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577520G>T		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	156	44	NM_001137667	0	0	0	1	1		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.		0.423	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90577520	G	T	90577520	1	4	136	0	1	0	0	0	0	0	0	0	2684	1029	36	4		4	CASP8AP2	6	90577520	RNA	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		90577520	80537547	32	12130											
FBXO30	84085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	146126628	146126628	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agttactttgttttgaatcaCcatgtaaattctgattctgg	10	18	7	6	0	3	2	1	2	2	0	3	2	3	2	1	1	1	3	1	1	4	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr6:146126628C>T	ENST00000237281.4	-	2	1080	c.914G>A	c.(913-915)gGt>gAt	p.G305D		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	305							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G305D(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		TTTTGAATCACCATGTAAATT	0.403																																					p.G305D		.											.	FBXO30-291	1	Substitution - Missense(1)	lung(1)	c.G914A						.						125	119	121					6																	146126628		2203	4300	6503	SO:0001583	missense	84085	exon2			GAATCACCATGTA	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"F-boxes /  "other""	15600	protein-coding gene	gene with protein product		609101	"F-box only protein, helicase, 18"				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.914G>A	6.37:g.146126628C>T	ENSP00000237281:p.Gly305Asp	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	84	16	NM_032145	0	0	1	1	0	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	.	.	.	.	.	.	.	.	.	.	C	0.042	-1.281092	0.01398	.	.	ENSG00000118496	ENST00000237281	T	0.17691	2.26	5.29	0.298	0.15766	.	1.121610	0.06334	N	0.706654	T	0.02767	0.0083	L	0.36672	1.1	0.22127	N	0.999344	B	0.02656	0.0	B	0.01281	0.0	T	0.40905	-0.9538	10	0.08381	T	0.77	-3.4918	2.8503	0.05555	0.1103:0.4508:0.2365:0.2024	.	305	Q8TB52	FBX30_HUMAN	D	305	ENSP00000237281:G305D	ENSP00000237281:G305D	G	-	2	0	FBXO30	146168321	0.000000	0.05858	0.946000	0.38457	0.946000	0.59487	0.028000	0.13644	0.046000	0.15833	0.655000	0.94253	GGT	.		0.403	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2			T	146126628	C	T	146126628	3	4	136	1	0	0	0	0	1	0	0	0	5759	507	18	2	1331	2	FBXO30	6	146126628	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	55549108	146126628	24988439	33	12131											
ABCB4	5244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	87037472	87037472	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcacctccaggctcagccCctgaagcactggcacgtttg	7	9	9	16	1	2	1	2	1	0	0	3	1	3	1	4	2	2	4	4	2	1	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:87037472C>T	ENST00000265723.4	-	25	3271	c.3160G>A	c.(3160-3162)Ggg>Agg	p.G1054R	ABCB4_ENST00000453593.1_Missense_Mutation_p.G1007R|ABCB4_ENST00000358400.3_Missense_Mutation_p.G1007R|ABCB4_ENST00000359206.3_Missense_Mutation_p.G1054R|ABCB4_ENST00000545634.1_Missense_Mutation_p.G1054R	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	1054	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AGGCTCAGCCCCTGAAGCACT	0.498																																					p.G1054R		.											.	ABCB4-96	0			c.G3160A						.						82	80	81					7																	87037472		2203	4300	6503	SO:0001583	missense	5244	exon25			TCAGCCCCTGAAG	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.3160G>A	7.37:g.87037472C>T	ENSP00000265723:p.Gly1054Arg	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	150	30	NM_018849	0	0	3	5	2	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	37	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390489	0.82902	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77;-2.77	5.19	3.18	0.36537	ABC transporter-like (1);	0.158975	0.56097	N	0.000029	D	0.92632	0.7659	L	0.51914	1.62	0.80722	D	1	P;D;P	0.54047	0.947;0.964;0.939	P;D;D	0.68943	0.789;0.961;0.914	D	0.91904	0.5534	10	0.87932	D	0	-4.0274	11.256	0.49054	0.0:0.8415:0.0:0.1585	.	1007;1054;1054	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	R	1054;1007;1054;1007;1054	ENSP00000352135:G1054R;ENSP00000351172:G1007R;ENSP00000265723:G1054R;ENSP00000392983:G1007R;ENSP00000437465:G1054R	ENSP00000265723:G1054R	G	-	1	0	ABCB4	86875408	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.034000	0.57289	0.565000	0.29255	0.655000	0.94253	GGG	.		0.498	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87037472	C	T	87037472	3	4	136	1	0	0	0	0	1	0	0	0	43	623	22	2	716	2	ABCB4	7	87037472	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		87037472	72101191	34	12132											
SLC25A40	55972	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	87466048	87466048	+	Frame_Shift_Del	DEL	A	A	-																															aaagcaagtatttttacctgAaaataatccggaaaatccat																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:87466048delA	ENST00000341119.5	-	11	1247	c.901delT	c.(901-903)tcafs	p.S301fs		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	301					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					TTTTTACCTGAAAATAATCCG	0.264																																					p.S301fs		.											.	SLC25A40-91	0			c.901delT						.						25	27	26					7																	87466048		2182	4244	6426	SO:0001589	frameshift_variant	55972	exon11			.	AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"Solute carriers"	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.901delT	7.37:g.87466048delA	ENSP00000344831:p.Ser301fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	112	21	NM_018843	0	0	0	0	0	A8K483|D6W5P6|Q53GB1|Q9UHR1	Frame_Shift_Del	DEL	ENST00000341119.5	37	CCDS5610.1																																																																																			.		0.264	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843		-	87466048	A	-	87466048	7	5	136	1	0	1	0	1	0	0	0	0	14537	246	9	0	123	0	SLC25A40	7	87466048	Frame_Shift_Del	DEL	A	TCGA-HE-A5NL-01A-11D-A26P-10	428576	87466048	71672615	35	12133											
TECPR1	25851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	97847037	97847037	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagccgtggcccttgggCtcgtgaggctgcacgccggt	3	8	15	15	4	0	1	0	1	0	0	2	1	1	1	4	4	2	3	4	4	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:97847037C>T	ENST00000447648.2	-	25	3650	c.3351G>A	c.(3349-3351)gaG>gaA	p.E1117E	TECPR1_ENST00000379795.3_Silent_p.E1119E			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1117					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGCCCTTGGGCTCGTGAGGCT	0.667																																					p.E1117E		.											.	TECPR1-91	0			c.G3351A						.						12	16	15					7																	97847037		2009	3915	5924	SO:0001819	synonymous_variant	25851	exon25			CTTGGGCTCGTGA		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.3351G>A	7.37:g.97847037C>T		Somatic	15	0		WXS	Illumina HiSeq	Phase_I	68	20	NM_015395	0	0	6	8	2	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			.		0.667	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		T	97847037	C	T	97847037	2	4	136	1	0	0	0	0	0	0	0	1	15775	796	28	2		2	TECPR1	7	97847037	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	10380989	97847037	61291626	36	12134											
MEPCE	56257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100030705	100030705	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctacgccctgggggcaTcctggtcctagagccccaac	7	6	11	17	1	0	1	0	0	0	1	2	1	2	1	6	3	3	2	6	3	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:100030705T>A	ENST00000310512.2	+	2	2223	c.1835T>A	c.(1834-1836)aTc>aAc	p.I612N	RP11-758P17.2_ENST00000492523.1_RNA|MEPCE_ENST00000414441.1_Missense_Mutation_p.I143N|PPP1R35_ENST00000476185.1_5'Flank	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	612	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCTGGGGGCATCCTGGTCCTA	0.577																																					p.I612N		.											.	MEPCE-91	0			c.T1835A						.						72	69	70					7																	100030705		2203	4300	6503	SO:0001583	missense	56257	exon2			GGGGCATCCTGGT	AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"bin3, bicoid-interacting 3, homolog (Drosophila)"	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	ENST00000310512.2:c.1835T>A	7.37:g.100030705T>A	ENSP00000308546:p.Ile612Asn	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	367	83	NM_019606	0	0	35	53	18	B3KP86|D6W5V7|Q9NPD4	Missense_Mutation	SNP	ENST00000310512.2	37	CCDS5693.1	.	.	.	.	.	.	.	.	.	.	T	19.74	3.883852	0.72410	.	.	ENSG00000146834	ENST00000414441;ENST00000425355;ENST00000310512	T;T	0.46819	0.86;0.86	5.37	5.37	0.77165	Bin3-type S-adenosyl-L-methionine binding domain (1);Bicoid-interacting 3 (1);	0.077394	0.52532	D	0.000064	T	0.50837	0.1639	L	0.45352	1.415	0.45066	D	0.998087	D	0.59357	0.985	P	0.58013	0.831	T	0.46470	-0.9189	10	0.29301	T	0.29	-24.0822	8.2283	0.31582	0.0:0.0895:0.0:0.9105	.	612	Q7L2J0	MEPCE_HUMAN	N	143;143;612	ENSP00000400875:I143N;ENSP00000308546:I612N	ENSP00000308546:I612N	I	+	2	0	MEPCE	99868641	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	5.644000	0.67902	2.156000	0.67533	0.379000	0.24179	ATC	.		0.577	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			A	100030705	T	A	100030705	3	1	136	1	0	0	0	0	1	0	0	0	9502	1435	50	5	1841	5	MEPCE	7	100030705	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	2183668	100030705	59107958	37	12135											
ELP3	55140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	28047190	28047190	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cggcaccaggaattattataGaaagatcggctacagattac	15	9	9	8	2	0	3	0	0	0	3	1	4	0	4	1	3	2	2	1	3	7	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:28047190G>C	ENST00000256398.8	+	15	1969	c.1592G>C	c.(1591-1593)aGa>aCa	p.R531T	ELP3_ENST00000542181.1_Missense_Mutation_p.R402T|ELP3_ENST00000524103.1_Missense_Mutation_p.R459T|ELP3_ENST00000521015.1_Missense_Mutation_p.R517T|ELP3_ENST00000380353.4_Missense_Mutation_p.R439T|ELP3_ENST00000537665.1_Missense_Mutation_p.R412T	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	531	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		AATTATTATAGAAAGATCGGC	0.468																																					p.R531T		.											.	ELP3-90	0			c.G1592C						.						127	132	130					8																	28047190		2203	4300	6503	SO:0001583	missense	55140	exon15			ATTATAGAAAGAT		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"Chromatin-modifying enzymes / K-acetyltransferases", "Elongator acetyltransferase complex subunits"	20696	protein-coding gene	gene with protein product		612722	"elongation protein 3 homolog (S. cerevisiae)"			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.1592G>C	8.37:g.28047190G>C	ENSP00000256398:p.Arg531Thr	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	82	28	NM_018091	0	0	7	12	5	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Missense_Mutation	SNP	ENST00000256398.8	37	CCDS6065.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.297498	0.60086	.	.	ENSG00000134014	ENST00000521015;ENST00000256398;ENST00000542181;ENST00000524103;ENST00000537665;ENST00000380353	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	5.13	5.13	0.70059	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.44371	0.1290	H	0.96604	3.85	0.58432	D	0.999995	B;B	0.24576	0.106;0.062	B;B	0.31337	0.128;0.128	T	0.56238	-0.8012	10	0.72032	D	0.01	-17.8026	13.9575	0.64160	0.0:0.0:1.0:0.0	.	412;531	B4DE19;Q9H9T3	.;ELP3_HUMAN	T	517;531;402;459;412;439	ENSP00000428449:R517T;ENSP00000256398:R531T;ENSP00000439242:R402T;ENSP00000429180:R459T;ENSP00000445558:R412T;ENSP00000369711:R439T	ENSP00000256398:R531T	R	+	2	0	ELP3	28103109	1.000000	0.71417	0.978000	0.43139	0.982000	0.71751	4.723000	0.61965	2.669000	0.90835	0.655000	0.94253	AGA	.		0.468	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		C	28047190	G	C	28047190	3	2	136	1	0	0	0	0	1	0	0	0	5094	942	33	4	1650	4	ELP3	8	28047190	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		28047190	118316832	38	12136											
TRIM55	84675	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	67064722	67064722	+	Frame_Shift_Del	DEL	T	T	-																															tagaaaatgttcaaacagagTttccaggagaagatgaaaac																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:67064722delT	ENST00000315962.4	+	8	1469	c.1096delT	c.(1096-1098)tttfs	p.F366fs	TRIM55_ENST00000276573.7_Frame_Shift_Del_p.F366fs|TRIM55_ENST00000353317.5_Frame_Shift_Del_p.F366fs|TRIM55_ENST00000350034.4_Intron	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	366					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			TCAAACAGAGTTTCCAGGAGA	0.498																																					p.F366fs		.											.	TRIM55-230	0			c.1096delT						.						70	70	70					8																	67064722		2203	4300	6503	SO:0001589	frameshift_variant	84675	exon8			.	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	14215	protein-coding gene	gene with protein product		606469	"ring finger protein 29", "tripartite motif-containing 55"	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1096delT	8.37:g.67064722delT	ENSP00000323913:p.Phe366fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	44	17	NM_184086	0	0	0	0	0	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Frame_Shift_Del	DEL	ENST00000315962.4	37	CCDS6184.1																																																																																			.		0.498	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		-	67064722	T	-	67064722	7	5	136	1	0	1	0	1	0	0	0	0	16562	1725	60	0	1126	0	TRIM55	8	67064722	Frame_Shift_Del	DEL	T	TCGA-HE-A5NL-01A-11D-A26P-10	39017532	67064722	79299300	39	12137											
CSMD3	114788	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr8	113516202	113516202	+	Missense_Mutation	SNP	T	T	C																															gtcatagtttggttctatgcTaaaactgaaaaaaaaaagga																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:113516202T>C	ENST00000297405.5	-	30	5144	c.4900A>G	c.(4900-4902)Agc>Ggc	p.S1634G	CSMD3_ENST00000455883.2_Missense_Mutation_p.S1530G|CSMD3_ENST00000343508.3_Missense_Mutation_p.S1594G|CSMD3_ENST00000352409.3_Missense_Mutation_p.S1634G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1634	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGTTCTATGCTAAAACTgaaa	0.308										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S1634G		.											.	CSMD3-1132	0			c.A4900G						.						69	67	68					8																	113516202		2203	4300	6503	SO:0001583	missense	114788	exon30			CTATGCTAAAACT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4900A>G	8.37:g.113516202T>C	ENSP00000297405:p.Ser1634Gly	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	32	10	NM_198123	0	0	0	0	0	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.897390	0.72639	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23	4.96	4.96	0.65561	CUB (5);	0.056809	0.64402	D	0.000002	T	0.31104	0.0786	L	0.55990	1.75	0.33482	D	0.587596	B;B;P	0.49635	0.007;0.008;0.926	B;B;P	0.58454	0.026;0.044;0.839	T	0.33266	-0.9875	10	0.22706	T	0.39	.	14.7774	0.69740	0.0:0.0:0.0:1.0	.	1530;1634;1594	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	G	1594;1634;974;1530;1634	ENSP00000345799:S1594G;ENSP00000297405:S1634G;ENSP00000341558:S974G;ENSP00000412263:S1530G;ENSP00000343124:S1634G	ENSP00000297405:S1634G	S	-	1	0	CSMD3	113585378	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.657000	0.83745	2.069000	0.61940	0.455000	0.32223	AGC	.		0.308	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113516202	T	C	113516202	3	2	136	1	0	0	0	0	1	0	0	0	3952	1522	53	3	6391	3	CSMD3	8	113516202	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	46451480	113516202	32847820	40	12138	123	2									
CSMD3	114788	hgsc.bcm.edu;bcgsc.ca	37	chr8	113516207	113516207	+	Splice_Site	SNP	C	C	G																															agtttggttctatgctaaaaCtgaaaaaaaaaaggaaagaa																								rs76670724		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:113516207C>G	ENST00000297405.5	-	30	5140		c.e30-1		CSMD3_ENST00000455883.2_Splice_Site|CSMD3_ENST00000343508.3_Splice_Site|CSMD3_ENST00000352409.3_Splice_Site	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TATGCTAAAACTgaaaaaaaa	0.318										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											.		.											.	CSMD3-1132	0			c.4584-1G>C						.						61	60	60					8																	113516207		2203	4299	6502	SO:0001630	splice_region_variant	114788	exon30			CTAAAACTGAAAA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.4896-1G>C	8.37:g.113516207C>G		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	25	9	NM_052900	0	0	0	0	0	Q96PZ3	Splice_Site	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736213	0.69189	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.378	0.90441	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD3	113585383	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	7.446000	0.80609	2.560000	0.86352	0.557000	0.71058	.	.		0.318	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Intron	G	113516207	C	G	113516207	5	3	136	1	0	0	0	0	0	0	1	0	3952	579	20	4	6396	4	CSMD3	8	113516207	Splice_Site	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	5	113516207	32847815	41	12139	123	2									
ZNF79	7633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130206739	130206739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccttacaagtgcagtgaaTgtggaagagccttcagccag	12	8	12	9	0	1	2	1	1	0	1	1	3	1	3	3	1	5	1	3	1	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr9:130206739T>C	ENST00000342483.5	+	5	1166	c.760T>C	c.(760-762)Tgt>Cgt	p.C254R	ZNF79_ENST00000543471.1_Missense_Mutation_p.C230R	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	254					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)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						GTGCAGTGAATGTGGAAGAGC	0.532																																					p.C254R		.											.	ZNF79-90	0			c.T760C						.						101	92	95					9																	130206739		2203	4300	6503	SO:0001583	missense	7633	exon5			AGTGAATGTGGAA	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"Zinc fingers, C2H2-type"	13153	protein-coding gene	gene with protein product		194552	"zinc finger protein 79 (pT7)"			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.760T>C	9.37:g.130206739T>C	ENSP00000362446:p.Cys254Arg	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	129	35	NM_007135	0	0	0	0	0	Q5VVW1|Q96NV1	Missense_Mutation	SNP	ENST00000342483.5	37	CCDS6871.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.034463	0.54896	.	.	ENSG00000196152	ENST00000342483;ENST00000543471	D;D	0.85955	-2.05;-2.05	3.53	2.38	0.29361	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92404	0.7589	H	0.98682	4.3	0.80722	D	1	D	0.53745	0.962	P	0.53313	0.723	D	0.90977	0.4824	9	0.87932	D	0	.	6.7985	0.23738	0.0:0.1169:0.0:0.8831	.	254	Q15937	ZNF79_HUMAN	R	254;230	ENSP00000362446:C254R;ENSP00000438418:C230R	ENSP00000362446:C254R	C	+	1	0	ZNF79	129246560	1.000000	0.71417	0.659000	0.29680	0.986000	0.74619	5.308000	0.65768	0.555000	0.29079	0.533000	0.62120	TGT	.		0.532	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135		C	130206739	T	C	130206739	3	2	136	1	0	0	0	0	1	0	0	0	18193	1464	51	3	778	3	ZNF79	9	130206739	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10		130206739	11006692	42	12140											
ACBD5	91452	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr10	27529275	27529275	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcaaactctggatcacctTcacggccgcctcaaacctag	10	7	8	16	3	4	0	3	0	1	0	4	1	4	1	4	3	2	1	4	3	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr10:27529275T>G	ENST00000375888.1	-	1	212	c.148A>C	c.(148-150)Aag>Cag	p.K50Q	ACBD5_ENST00000375897.3_5'UTR|ACBD5_ENST00000375901.1_5'UTR|ACBD5_ENST00000476758.1_5'UTR|ACBD5_ENST00000375905.4_Missense_Mutation_p.K17Q|ACBD5_ENST00000396271.3_Missense_Mutation_p.K52Q|RP11-85G18.6_ENST00000574842.1_lincRNA			Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	50	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.				peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TGGATCACCTTCACGGCCGCC	0.617																																					p.K52Q		.											.	ACBD5-90	0			c.A154C						.						101	91	94					10																	27529275		2203	4300	6503	SO:0001583	missense	91452	exon2			TCACCTTCACGGC	AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897			23338	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 5"			12056414	Standard	NR_024150		Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000375888.1:c.148A>C	10.37:g.27529275T>G	ENSP00000365049:p.Lys50Gln	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	136	39	NM_145698	0	0	2	4	2	B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	Missense_Mutation	SNP	ENST00000375888.1	37		.	.	.	.	.	.	.	.	.	.	T	24.0	4.487454	0.84854	.	.	ENSG00000107897	ENST00000375889;ENST00000396271;ENST00000375905;ENST00000375888;ENST00000426079;ENST00000412279	T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89	4.87	4.87	0.63330	.	0.087964	0.85682	D	0.000000	T	0.42921	0.1224	L	0.45352	1.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	T	0.25082	-1.0142	10	0.46703	T	0.11	-20.8054	14.7721	0.69688	0.0:0.0:0.0:1.0	.	52;50	Q5T8D3-3;B7Z2R7	.;.	Q	47;52;17;50;59;17	ENSP00000379568:K52Q;ENSP00000365070:K17Q;ENSP00000365049:K50Q;ENSP00000401591:K59Q;ENSP00000393398:K17Q	ENSP00000365049:K50Q	K	-	1	0	ACBD5	27569281	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.285000	0.58989	1.945000	0.56424	0.383000	0.25322	AAG	.		0.617	ACBD5-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000047314.1	NM_145698		G	27529275	T	G	27529275	3	3	136	1	0	0	0	0	1	0	0	0	125	1792	62	5	1471	5	ACBD5	10	27529275	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10		27529275	108005472	43	12141											
ATRNL1	26033	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	117075179	117075179	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attggaatgcaccacagtgaGatggttcttgacaccaatct	12	11	9	9	0	2	2	0	2	2	1	2	4	2	3	2	2	1	2	2	2	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr10:117075179G>A	ENST00000355044.3	+	18	3096	c.2970G>A	c.(2968-2970)gaG>gaA	p.E990E	ATRNL1_ENST00000423111.2_Silent_p.E87E|ATRNL1_ENST00000303745.7_De_novo_Start_OutOfFrame	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	990	PSI 5.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ACCACAGTGAGATGGTTCTTG	0.413																																					p.E990E													.	ATRNL1-96	0			c.G2970A						.						128	119	122					10																	117075179		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon18			CAGTGAGATGGTT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2970G>A	10.37:g.117075179G>A		Somatic	136	1		WXS	Illumina HiSeq	Phase_I	152	41	NM_207303	0	0	0	0	0	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	G	6.849	0.525834	0.13066	.	.	ENSG00000107518	ENST00000526373	.	.	.	5.34	1.35	0.21983	.	.	.	.	.	T	0.52125	0.1715	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42548	-0.9445	4	.	.	.	-8.6523	5.6587	0.17656	0.2884:0.1549:0.5567:0.0	.	.	.	.	N	120	.	.	D	+	1	0	ATRNL1	117065169	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	1.591000	0.36665	0.628000	0.30357	-0.391000	0.06502	GAT	.		0.413	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		A	117075179	G	A	117075179	2	1	136	1	0	0	0	0	0	0	0	1	1208	933	33	2		2	ATRNL1	10	117075179	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	89545904	117075179	18459568	44	12142											
MKI67	4288	broad.mit.edu	37	chr10	129905112	129905113	+	Frame_Shift_Del	DEL	TG	TG	-																															ttaccatctcctgttggctcTgtgtgtgtgtgtgtagtctc																								rs145960091		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr10:129905112_129905113delTG	ENST00000368654.3	-	13	5366_5367	c.4991_4992delCA	c.(4990-4992)acafs	p.T1664fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.T1304fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1664	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTGTTGGCTCTGTGTGTGTGTG	0.51																																					p.1664_1664del													.	MKI67-519	0			c.4991_4992del						.																																			SO:0001589	frameshift_variant	4288	exon13			TGGCTCTGTGTGT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4991_4992delCA	10.37:g.129905122_129905123delTG	ENSP00000357643:p.Thr1664fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	184	9	NM_002417	0	0	0	0	0	Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	37	CCDS7659.1																																																																																			.		0.51	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		-	129905113	TG	-	129905112	7	5	136	1	0	1	0	1	0	0	0	0	9623	1567	55	0	4790	0	MKI67	10	129905112	Frame_Shift_Del	DEL	TG	TCGA-HE-A5NL-01A-11D-A26P-10	12829933	129905112	5629635	45	12143											
MUC5B	727897	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	1264092	1264092	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgggcaccacctggacccgCctatcacagaccaccacacc	10	4	7	20	1	1	1	1	0	0	1	1	2	1	2	7	2	0	1	7	2	1	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:1264092C>T	ENST00000529681.1	+	31	6040	c.5982C>T	c.(5980-5982)cgC>cgT	p.R1994R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.R1997R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1994	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCTGGACCCGCCTATCACAGA	0.637																																					p.R1994R		.											.	.	0			c.C5982T						.						118	172	154					11																	1264092		2117	4210	6327	SO:0001819	synonymous_variant	727897	exon31			GACCCGCCTATCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.5982C>T	11.37:g.1264092C>T		Somatic	785	0		WXS	Illumina HiSeq	Phase_I	1304	383	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1264092	C	T	1264092	2	4	136	1	0	0	0	0	0	0	0	1	10004	726	26	2		2	MUC5B	11	1264092	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		1264092	133742424	46	12144											
NAV2	89797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	19890497	19890497	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacatagatgcctgcttgaaTttcctggcagctaagggaat	12	11	10	8	0	0	2	0	1	0	1	1	3	1	3	2	2	4	3	2	2	5	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:19890497T>A	ENST00000396087.3	+	4	564	c.465T>A	c.(463-465)aaT>aaA	p.N155K	NAV2_ENST00000360655.4_Missense_Mutation_p.N91K|NAV2_ENST00000540292.1_Missense_Mutation_p.N86K|NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000527559.2_Missense_Mutation_p.N84K|NAV2_ENST00000349880.4_Missense_Mutation_p.N155K|NAV2_ENST00000396085.1_Missense_Mutation_p.N155K	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	155	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCTGCTTGAATTTCCTGGCAG	0.438																																					p.N155K		.											.	NAV2-96	0			c.T465A						.						70	71	70					11																	19890497		2199	4293	6492	SO:0001583	missense	89797	exon4			CTTGAATTTCCTG	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"pore membrane and/or filament interacting like protein 2", "retinoic acid inducible gene in neuroblastoma 1", "helicase, APC down-regulated 1"	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.465T>A	11.37:g.19890497T>A	ENSP00000379396:p.Asn155Lys	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_145117	0	0	1	2	1	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.133723	0.56828	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.56444	0.46;0.46;0.46;0.46;0.46;0.46	5.87	5.87	0.94306	.	0.090463	0.47852	D	0.000201	T	0.36166	0.0957	N	0.05177	-0.1	0.80722	D	1	B;B	0.20052	0.002;0.041	B;B	0.34722	0.034;0.188	T	0.29610	-1.0006	9	.	.	.	.	13.7906	0.63138	0.0:0.0:0.0:1.0	.	155;91	Q8IVL1-3;Q8IVL1-4	.;.	K	91;155;155;155;84;86	ENSP00000353871:N91K;ENSP00000379394:N155K;ENSP00000309577:N155K;ENSP00000379396:N155K;ENSP00000435395:N84K;ENSP00000443489:N86K	.	N	+	3	2	NAV2	19847073	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.897000	0.39799	2.242000	0.73789	0.533000	0.62120	AAT	.		0.438	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	19890497	T	A	19890497	3	1	136	1	0	0	0	0	1	0	0	0	10209	1490	52	5	558	5	NAV2	11	19890497	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	18626405	19890497	115116019	47	12145											
GAS2	2620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	22759307	22759307	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctagagcttggccggattGcagccaggtaggtcaaacca	10	8	13	10	1	1	1	1	0	0	1	1	2	1	2	3	4	5	4	3	4	3	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:22759307G>A	ENST00000454584.2	+	5	771	c.466G>A	c.(466-468)Gca>Aca	p.A156T	GAS2_ENST00000433790.1_Missense_Mutation_p.A156T|GAS2_ENST00000278187.3_Missense_Mutation_p.A156T	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	156	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						TGGCCGGATTGCAGCCAGGTA	0.458																																					p.A156T		.											.	GAS2-652	0			c.G466A						.						145	122	130					11																	22759307		2203	4300	6503	SO:0001583	missense	2620	exon5			CGGATTGCAGCCA	BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.466G>A	11.37:g.22759307G>A	ENSP00000401145:p.Ala156Thr	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	210	60	NM_177553	0	0	0	0	0	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Missense_Mutation	SNP	ENST00000454584.2	37	CCDS7858.1	.	.	.	.	.	.	.	.	.	.	G	34	5.368653	0.95900	.	.	ENSG00000148935	ENST00000528582;ENST00000454584;ENST00000278187;ENST00000532398;ENST00000433790	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	5.64	5.64	0.86602	Calponin homology domain (3);	0.051266	0.85682	D	0.000000	T	0.70605	0.3243	M	0.82923	2.615	0.52501	D	0.999956	P	0.52316	0.952	P	0.62885	0.908	T	0.74256	-0.3724	10	0.72032	D	0.01	-13.9779	17.5008	0.87731	0.0:0.0:1.0:0.0	.	156	O43903	GAS2_HUMAN	T	156	ENSP00000432584:A156T;ENSP00000401145:A156T;ENSP00000278187:A156T;ENSP00000435946:A156T;ENSP00000396708:A156T	ENSP00000278187:A156T	A	+	1	0	GAS2	22715883	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.950000	0.75977	2.664000	0.90586	0.650000	0.86243	GCA	.		0.458	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553		A	22759307	G	A	22759307	3	1	136	1	0	0	0	0	1	0	0	0	6265	1319	46	2	480	2	GAS2	11	22759307	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	2868810	22759307	112247209	48	12146											
PAMR1	25891	broad.mit.edu;bcgsc.ca	37	chr11	35492269	35492269	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccgctcgttgccacagaCacgcttgatgatctggccat	7	10	11	13	3	1	3	0	2	1	1	2	3	1	3	3	2	1	3	3	2	0	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:35492269C>A	ENST00000378880.2	-	5	1037	c.592G>T	c.(592-594)Gtc>Ttc	p.V198F	PAMR1_ENST00000378878.3_Intron|PAMR1_ENST00000532848.1_Missense_Mutation_p.V158F|PAMR1_ENST00000534803.1_5'UTR|PAMR1_ENST00000278360.3_Missense_Mutation_p.V198F	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	198	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TTGCCACAGACACGCTTGATG	0.517																																					p.V198F													.	PAMR1-70	0			c.G592T						.						138	109	119					11																	35492269		2202	4298	6500	SO:0001583	missense	25891	exon5			CACAGACACGCTT		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.592G>T	11.37:g.35492269C>A	ENSP00000368158:p.Val198Phe	Somatic	195	1		WXS	Illumina HiSeq	Phase_I	264	16	NM_001001991	0	0	0	0	0	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	C	0.044	-1.272703	0.01421	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000532848;ENST00000527605	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.39	-1.35	0.09114	CUB (5);	0.174175	0.53938	N	0.000059	T	0.03011	0.0089	N	0.00116	-2.08	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43556	-0.9384	10	0.87932	D	0	.	8.1749	0.31276	0.6507:0.2318:0.1175:0.0	.	198;198	Q6UXH9;Q6UXH9-2	PAMR1_HUMAN;.	F	198;198;158;158	ENSP00000278360:V198F;ENSP00000368158:V198F;ENSP00000433868:V158F;ENSP00000432591:V158F	ENSP00000278360:V198F	V	-	1	0	PAMR1	35448845	1.000000	0.71417	0.947000	0.38551	0.104000	0.19210	3.458000	0.53014	-0.534000	0.06315	-0.181000	0.13052	GTC	.		0.517	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		A	35492269	C	A	35492269	3	1	136	1	0	0	0	0	1	0	0	0	11439	478	17	4	1653	4	PAMR1	11	35492269	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	12732962	35492269	99514247	49	12147											
SLC43A3	29015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57182446	57182446	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccatgttggtcagcaaggaGttgagagtgccaatgaagag	12	8	15	6	0	1	3	1	2	0	2	1	5	1	4	2	2	2	3	2	2	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:57182446G>C	ENST00000395123.2	-	10	1207	c.903C>G	c.(901-903)aaC>aaG	p.N301K	SLC43A3_ENST00000528098.1_5'Flank|SLC43A3_ENST00000529554.1_Missense_Mutation_p.N301K|SLC43A3_ENST00000352187.1_Missense_Mutation_p.N301K|SLC43A3_ENST00000395124.1_Missense_Mutation_p.N301K|SLC43A3_ENST00000533524.1_Missense_Mutation_p.N314K	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	301					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						TCAGCAAGGAGTTGAGAGTGC	0.582																																					p.N301K		.											.	SLC43A3-90	0			c.C903G						.						129	110	117					11																	57182446		2201	4296	6497	SO:0001583	missense	29015	exon10			CAAGGAGTTGAGA	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.903C>G	11.37:g.57182446G>C	ENSP00000378555:p.Asn301Lys	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	69	21	NM_017611	0	0	4	4	0	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434719	0.62955	.	.	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005	T;T;T;T;T;T	0.58652	0.37;0.37;0.37;0.37;0.37;0.32	5.05	4.13	0.48395	Major facilitator superfamily domain, general substrate transporter (1);	0.094270	0.64402	D	0.000001	T	0.58395	0.2119	M	0.71296	2.17	0.43924	D	0.99657	P;B;B	0.37548	0.599;0.186;0.343	B;B;B	0.44278	0.445;0.158;0.314	T	0.56019	-0.8048	10	0.06625	T	0.88	-17.6813	12.7477	0.57289	0.0:0.1658:0.8342:0.0	.	314;301;301	E7EQD2;Q8NBI5;A8K2X6	.;S43A3_HUMAN;.	K	301;301;301;301;314;301	ENSP00000378555:N301K;ENSP00000378556:N301K;ENSP00000337561:N301K;ENSP00000436254:N301K;ENSP00000434515:N314K;ENSP00000435893:N301K	ENSP00000337561:N301K	N	-	3	2	SLC43A3	56939022	1.000000	0.71417	0.996000	0.52242	0.418000	0.31294	6.596000	0.74113	1.117000	0.41842	0.563000	0.77884	AAC	.		0.582	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		C	57182446	G	C	57182446	3	2	136	1	0	0	0	0	1	0	0	0	14666	1020	36	4	592	4	SLC43A3	11	57182446	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	21690177	57182446	77824070	50	12148											
TUT1	64852	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	62343357	62343370	+	Frame_Shift_Del	DEL	GTAAAGGGATCGGC	GTAAAGGGATCGGC	-																															ctgggtgaagggtgcaagggGtaaagggatcggcgtagcag																								rs149885942|rs371469091		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	GTAAAGGGATCGGC	GTAAAGGGATCGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:62343357_62343370delGTAAAGGGATCGGC	ENST00000476907.1	-	9	2512_2525	c.1821_1834delGCCGATCCCTTTAC	c.(1819-1836)acgccgatccctttacccfs	p.PIPLP608fs	TUT1_ENST00000308436.7_Frame_Shift_Del_p.PIPLP646fs|EEF1G_ENST00000532986.1_5'Flank|EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000329251.4_5'Flank|MIR3654_ENST00000496634.2_Intron			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	608					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GGTGCAAGGGGTAAAGGGATCGGCGTAGCAGAGA	0.636																																					p.645_650del		.											.	TUT1-91	0			c.1935_1948del						.																																			SO:0001589	frameshift_variant	64852	exon9			.	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"RNA binding motif (RRM) containing"	26184	protein-coding gene	gene with protein product	"RNA uridylyltransferase", "U6 TUTase", "TUTase 6"	610641	"RNA binding motif protein 21"	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.1821_1834delGCCGATCCCTTTAC	11.37:g.62343357_62343370delGTAAAGGGATCGGC	ENSP00000419607:p.Pro608fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	130	27	NM_022830	0	0	0	0	0	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Frame_Shift_Del	DEL	ENST00000476907.1	37																																																																																				.		0.636	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		-	62343370	GTAAAGGGATCGGC	-	62343357	7	5	136	1	0	1	0	1	0	0	0	0	16813	1261	44	0	794	0	TUT1	11	62343357	Frame_Shift_Del	DEL	GTAAAGGGATCGGC	TCGA-HE-A5NL-01A-11D-A26P-10	5160911	62343357	72663159	51	12149											
PDE2A	5138	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	72292965	72292965	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtagttgttgatgaaattCatgtcctgcagcatgctcag	9	15	10	7	0	2	2	2	2	0	0	3	2	3	2	1	0	3	6	1	0	2	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:72292965C>T	ENST00000334456.5	-	22	2123	c.1878G>A	c.(1876-1878)atG>atA	p.M626I	PDE2A_ENST00000444035.2_Missense_Mutation_p.M617I|RP11-169D4.2_ENST00000545254.1_RNA|PDE2A_ENST00000376450.3_Missense_Mutation_p.M370I|PDE2A_ENST00000418754.2_Missense_Mutation_p.M511I|PDE2A_ENST00000540345.1_Missense_Mutation_p.M617I|PDE2A_ENST00000544570.1_Missense_Mutation_p.M619I	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	626					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	TGATGAAATTCATGTCCTGCA	0.577																																					p.M626I													.	PDE2A-156	0			c.G1878A						.						78	79	78					11																	72292965		2200	4293	6493	SO:0001583	missense	5138	exon22			GAAATTCATGTCC	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"Phosphodiesterases"	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.1878G>A	11.37:g.72292965C>T	ENSP00000334910:p.Met626Ile	Somatic	88	1		WXS	Illumina HiSeq	Phase_I	112	37	NM_002599	0	0	0	0	0	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Missense_Mutation	SNP	ENST00000334456.5	37	CCDS8216.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.890586	0.72524	.	.	ENSG00000186642	ENST00000334456;ENST00000376450;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345;ENST00000420501;ENST00000441209;ENST00000542223	T;T;T;T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.51	5.51	0.81932	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.058122	0.64402	D	0.000002	T	0.69913	0.3164	L	0.46157	1.445	0.53688	D	0.999977	B;B;B;B;B;B	0.31968	0.162;0.087;0.149;0.349;0.087;0.237	B;B;B;B;B;B	0.33042	0.079;0.051;0.051;0.157;0.051;0.051	T	0.68708	-0.5337	10	0.40728	T	0.16	.	16.1456	0.81563	0.0:1.0:0.0:0.0	.	511;626;617;619;626;370	E9PEF1;O00408;E9PGI1;F6W5Z0;B2R646;Q6ZMR1	.;PDE2A_HUMAN;.;.;.;.	I	626;370;617;695;619;511;617;5;167;57	ENSP00000334910:M626I;ENSP00000365633:M370I;ENSP00000411657:M617I;ENSP00000442256:M619I;ENSP00000410310:M511I;ENSP00000446399:M617I;ENSP00000388997:M5I;ENSP00000392457:M167I;ENSP00000440834:M57I	ENSP00000334910:M626I	M	-	3	0	PDE2A	71970613	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.040000	0.76551	2.605000	0.88082	0.563000	0.77884	ATG	.		0.577	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599		T	72292965	C	T	72292965	3	4	136	1	0	0	0	0	1	0	0	0	11662	826	29	2	987	2	PDE2A	11	72292965	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	9949608	72292965	62713551	52	12150											
MYO7A	4647	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	76891503	76891503	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgagcgccaagaaggccaaGgaggaggccgagcgcaagca	14	1	16	10	3	0	2	0	1	0	1	0	5	0	4	3	4	3	2	3	4	4	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:76891503G>A	ENST00000409709.3	+	22	2942	c.2670G>A	c.(2668-2670)aaG>aaA	p.K890K	MYO7A_ENST00000409893.1_Silent_p.K890K|MYO7A_ENST00000409619.2_Silent_p.K879K|MYO7A_ENST00000458637.2_Silent_p.K890K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	890					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGAAGGCCAAGGAGGAGGCCG	0.612																																					p.K890K													.	MYO7A-138	0			c.G2670A						.						38	46	43					11																	76891503		2114	4210	6324	SO:0001819	synonymous_variant	4647	exon22			GGCCAAGGAGGAG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.2670G>A	11.37:g.76891503G>A		Somatic	56	1		WXS	Illumina HiSeq	Phase_I	112	34	NM_001127179	0	0	2	2	0	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.		0.612	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76891503	G	A	76891503	2	1	136	1	0	0	0	0	0	0	0	1	10107	991	35	2		2	MYO7A	11	76891503	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	4598538	76891503	58115013	53	12151											
KBTBD3	143879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	105925034	105925034	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacttgaagaaatgatgacaActggaagaacatttccacat	18	9	7	7	0	0	5	0	3	0	2	1	6	1	6	1	1	3	0	1	1	6	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:105925034A>T	ENST00000526793.1	-	3	541	c.382T>A	c.(382-384)Ttg>Atg	p.L128M	KBTBD3_ENST00000534815.1_Missense_Mutation_p.L49M|KBTBD3_ENST00000531837.1_Missense_Mutation_p.L128M	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	124										NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		AATGATGACAACTGGAAGAAC	0.308																																					p.L128M		.											.	KBTBD3-91	0			c.T382A						.						82	88	86					11																	105925034		2201	4298	6499	SO:0001583	missense	143879	exon3			ATGACAACTGGAA	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.382T>A	11.37:g.105925034A>T	ENSP00000436262:p.Leu128Met	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	107	34	NM_152433	0	0	1	1	0	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	37	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	A	7.067	0.567452	0.13560	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.72835	-0.69;-0.69;-0.69	5.22	1.55	0.23275	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.271361	0.35936	N	0.002898	T	0.47451	0.1446	N	0.21545	0.675	0.32074	N	0.594092	B;B	0.23377	0.052;0.084	B;B	0.23018	0.043;0.029	T	0.33650	-0.9860	10	0.33940	T	0.23	.	1.1059	0.01693	0.4145:0.1523:0.286:0.1472	.	128;124	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	M	49;128;128	ENSP00000431910:L49M;ENSP00000436262:L128M;ENSP00000432163:L128M	ENSP00000436262:L128M	L	-	1	2	KBTBD3	105430244	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	1.122000	0.31295	0.006000	0.14734	-0.421000	0.06004	TTG	.		0.308	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		T	105925034	A	T	105925034	3	4	136	1	0	0	0	0	1	0	0	0	8015	40	2	5	1460	5	KBTBD3	11	105925034	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	29033531	105925034	29081482	54	12152											
ESAM	90952	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	124623587	124623587	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcaggcaccatcacaggCacagcacccatgcggctcaa	11	4	11	15	1	2	0	2	0	0	0	2	0	2	0	2	4	2	5	2	4	1	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:124623587C>T	ENST00000278927.5	-	7	1257	c.1128G>A	c.(1126-1128)gtG>gtA	p.V376V	ESAM_ENST00000442070.2_Intron|VSIG2_ENST00000326621.5_5'Flank|VSIG2_ENST00000403470.1_5'Flank	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	376					blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		CCATCACAGGCACAGCACCCA	0.577																																					p.V376V		.											.	ESAM-90	0			c.G1128A						.						56	58	57					11																	124623587		2201	4299	6500	SO:0001819	synonymous_variant	90952	exon7			CACAGGCACAGCA	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.1128G>A	11.37:g.124623587C>T		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	84	7	NM_138961	0	0	19	19	0	B4DVN8|Q96T50	Silent	SNP	ENST00000278927.5	37	CCDS8453.1																																																																																			.		0.577	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961		T	124623587	C	T	124623587	2	4	136	1	0	0	0	0	0	0	0	1	5260	697	25	2		2	ESAM	11	124623587	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	18698553	124623587	10382929	55	12153											
NTM	50863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	132180102	132180102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagtcccctcagcagaatTccagtggtacaaggatgaca	13	7	10	11	0	1	2	1	1	0	1	3	3	3	3	3	2	3	3	3	2	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:132180102T>C	ENST00000374786.1	+	5	1237	c.758T>C	c.(757-759)tTc>tCc	p.F253S	NTM_ENST00000427481.2_Missense_Mutation_p.F244S|NTM_ENST00000374791.3_Missense_Mutation_p.F253S|NTM_ENST00000539799.1_Missense_Mutation_p.F253S|NTM_ENST00000474900.1_3'UTR|NTM_ENST00000374784.1_Missense_Mutation_p.F253S|NTM_ENST00000425719.2_Missense_Mutation_p.F253S	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	253	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						TCAGCAGAATTCCAGTGGTAC	0.517																																					p.F253S		.											.	NTM-95	0			c.T758C						.						165	162	163					11																	132180102		2201	4297	6498	SO:0001583	missense	50863	exon5			CAGAATTCCAGTG	AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"Immunoglobulin superfamily / I-set domain containing"	17941	protein-coding gene	gene with protein product	"neurotrimin", "IgLON family member 2"	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.758T>C	11.37:g.132180102T>C	ENSP00000363918:p.Phe253Ser	Somatic	229	0		WXS	Illumina HiSeq	Phase_I	307	91	NM_001144059	0	0	0	0	0	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.9|27.9	4.869133|4.869133	0.91587|0.91587	.|.	.|.	ENSG00000182667|ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784|ENST00000457381	T;T;T;T;T;T|.	0.67523|.	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78886|0.78886	0.4354|0.4354	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.91635|.	0.998;0.999;0.996;0.999;0.997;0.997|.	T|T	0.80251|0.80251	-0.1460|-0.1460	10|5	0.13853|.	T|.	0.58|.	-27.0916|-27.0916	16.6288|16.6288	0.85011|0.85011	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	253;244;253;253;253;253|.	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2|.	.;.;.;NTRI_HUMAN;.;.|.	S|P	253;253;244;253;253;253|5	ENSP00000363923:F253S;ENSP00000437668:F253S;ENSP00000416320:F244S;ENSP00000363918:F253S;ENSP00000396722:F253S;ENSP00000363916:F253S|.	ENSP00000363916:F253S|.	F|S	+|+	2|1	0|0	NTM|NTM	131685312|131685312	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.864000|5.864000	0.69575|0.69575	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	TTC|TCC	.		0.517	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		C	132180102	T	C	132180102	3	2	136	1	0	0	0	0	1	0	0	0	10725	1783	62	3	862	3	NTM	11	132180102	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	7556515	132180102	2826414	56	12154											
TCHP	84260	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	110341898	110341898	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaacttgcaggaaagaagAatccgggagcagcacgggaa	16	4	14	7	2	0	3	0	1	0	2	1	6	1	6	1	3	4	3	1	3	5	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr12:110341898A>T	ENST00000312777.5	+	3	559	c.345A>T	c.(343-345)agA>agT	p.R115S	TCHP_ENST00000405876.4_Missense_Mutation_p.R115S	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						AGGAAAGAAGAATCCGGGAGC	0.577																																					p.R115S													.	TCHP-91	0			c.A345T						.						59	52	55					12																	110341898		2200	4296	6496	SO:0001583	missense	84260	exon3			AAGAAGAATCCGG	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"mitostatin"	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.345A>T	12.37:g.110341898A>T	ENSP00000324404:p.Arg115Ser	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	146	28	NM_001143852	0	0	3	5	2		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.905459	0.33628	.	.	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.42900	1.52;1.52;0.96	5.08	-4.39	0.03611	.	0.427244	0.26723	N	0.022822	T	0.19967	0.0480	L	0.38175	1.15	0.20926	N	0.99982	B	0.17852	0.024	B	0.10450	0.005	T	0.12066	-1.0562	10	0.18276	T	0.48	-3.2278	1.3904	0.02249	0.3888:0.1111:0.3091:0.1911	.	115	Q9BT92	TCHP_HUMAN	S	115	ENSP00000384520:R115S;ENSP00000324404:R115S;ENSP00000441835:R115S	ENSP00000324404:R115S	R	+	3	2	TCHP	108826281	0.872000	0.30054	0.473000	0.27253	0.658000	0.38924	1.003000	0.29809	-0.513000	0.06496	0.456000	0.33151	AGA	.		0.577	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300		T	110341898	A	T	110341898	3	4	136	1	0	0	0	0	1	0	0	0	15734	243	9	5	351	5	TCHP	12	110341898	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		110341898	23509997	57	12155											
EXOSC8	11340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	37583387	37583387	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagttacaagacacaaagAagttaaaaaactgatggatg	20	7	9	5	0	0	3	0	1	0	2	0	4	0	4	0	1	3	3	0	1	7	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr13:37583387A>G	ENST00000389704.3	+	11	1047	c.782A>G	c.(781-783)gAa>gGa	p.E261G		NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	261					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		AGACACAAAGAAGTTAAAAAA	0.338																																					p.E261G		.											.	EXOSC8-91	0			c.A782G						.						57	56	56					13																	37583387		2203	4300	6503	SO:0001583	missense	11340	exon11			ACAAAGAAGTTAA	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"CBP-interacting protein 3", "Opa interacting protein 2"	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.782A>G	13.37:g.37583387A>G	ENSP00000374354:p.Glu261Gly	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	138	29	NM_181503	0	0	5	11	6	O43480|Q5TBA5	Missense_Mutation	SNP	ENST00000389704.3	37	CCDS31958.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862459	0.71949	.	.	ENSG00000120699	ENST00000389704;ENST00000379809;ENST00000481013	T	0.52754	0.65	5.92	5.92	0.95590	Exoribonuclease, phosphorolytic domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.77820	2.39	0.80722	D	1	P;D	0.76494	0.944;0.999	P;D	0.69654	0.56;0.965	T	0.71052	-0.4704	10	0.49607	T	0.09	-29.8227	16.3593	0.83251	1.0:0.0:0.0:0.0	.	233;261	Q5JXM0;Q96B26	.;EXOS8_HUMAN	G	261;233;54	ENSP00000374354:E261G	ENSP00000369137:E233G	E	+	2	0	EXOSC8	36481387	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.372000	0.90127	2.267000	0.75376	0.383000	0.25322	GAA	.		0.338	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503		G	37583387	A	G	37583387	3	3	136	1	0	0	0	0	1	0	0	0	5333	246	9	3	824	3	EXOSC8	13	37583387	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		37583387	77586491	58	12156											
KIAA0564	23078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	42293875	42293875	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagagaccttcagtcggaaAtttctgtattaaaaaaaaat	17	11	8	5	1	2	1	1	0	1	1	3	4	2	3	1	2	0	1	1	2	7	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr13:42293875A>G	ENST00000379310.3	-	26	3036	c.2968T>C	c.(2968-2970)Ttt>Ctt	p.F990L	VWA8_ENST00000281496.6_Missense_Mutation_p.F990L	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	990						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										TCAGTCGGAAATTTCTGTATT	0.294																																					p.F990L		.											.	.	0			c.T2968C						.						68	64	65					13																	42293875		2203	4300	6503	SO:0001583	missense	23078	exon26			TCGGAAATTTCTG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2968T>C	13.37:g.42293875A>G	ENSP00000368612:p.Phe990Leu	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	62	30	NM_015058	0	0	0	0	0	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.023069	0.93462	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.26810	1.71;1.71	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	M	0.87456	2.885	0.80722	D	1	D	0.59357	0.985	P	0.57720	0.826	T	0.61133	-0.7124	10	0.62326	D	0.03	.	15.7306	0.77800	1.0:0.0:0.0:0.0	.	990	A3KMH1	K0564_HUMAN	L	894;990;990	ENSP00000368612:F990L;ENSP00000281496:F990L	ENSP00000251030:F894L	F	-	1	0	KIAA0564	41191875	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.248000	0.95456	2.175000	0.68902	0.477000	0.44152	TTT	.		0.294	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42293875	A	G	42293875	3	3	136	1	0	0	0	0	1	0	0	0	8206	101	4	3	2833	3	KIAA0564	13	42293875	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	4710488	42293875	72876003	59	12157											
TIMM9	26520	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	58878635	58878635	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataccttacctgttttatcTgatcagattctggtatttgt	9	19	6	7	0	3	2	1	1	2	1	3	2	3	2	2	1	2	2	2	1	5	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr14:58878635T>C	ENST00000395159.2	-	4	554	c.29A>G	c.(28-30)cAg>cGg	p.Q10R	TIMM9_ENST00000555593.1_Missense_Mutation_p.Q10R|RP11-517O13.1_ENST00000556734.1_RNA|TIMM9_ENST00000556007.2_Missense_Mutation_p.Q10R|TIMM9_ENST00000216463.4_Intron|TIMM9_ENST00000555061.1_Missense_Mutation_p.Q10R|TIMM9_ENST00000555404.1_Missense_Mutation_p.Q10R	NM_012460.2	NP_036592.1	Q9Y5J7	TIM9_HUMAN	translocase of inner mitochondrial membrane 9 homolog (yeast)	10					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein import into mitochondrial inner membrane (GO:0045039)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)|mitochondrion (GO:0005739)	chaperone binding (GO:0051087)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			kidney(2)|skin(1)	3						CTGTTTTATCTGATCAGATTC	0.353																																					p.Q10R		.											.	TIMM9-90	0			c.A29G						.						113	110	111					14																	58878635		2203	4300	6503	SO:0001583	missense	26520	exon4			TTTATCTGATCAG	AF150100	CCDS9735.1	14q22.3-q24	2008-07-04	2001-11-28		ENSG00000100575	ENSG00000100575			11819	protein-coding gene	gene with protein product		607384	"translocase of inner mitochondrial membrane 9 (yeast) homolog"			10552927, 14726512	Standard	NM_012460		Approved	TIM9A	uc001xds.3	Q9Y5J7	OTTHUMG00000140322	ENST00000395159.2:c.29A>G	14.37:g.58878635T>C	ENSP00000378588:p.Gln10Arg	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	75	35	NM_012460	0	0	0	0	0	B2R584	Missense_Mutation	SNP	ENST00000395159.2	37	CCDS9735.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.480758	0.84747	.	.	ENSG00000100575	ENST00000395159;ENST00000555593;ENST00000556007;ENST00000555061;ENST00000555404;ENST00000555097;ENST00000553450	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.81302	0.4794	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.84141	0.0417	9	0.87932	D	0	-16.1458	14.6598	0.68861	0.0:0.0:0.0:1.0	.	10	Q9Y5J7	TIM9_HUMAN	R	10	ENSP00000378588:Q10R;ENSP00000451006:Q10R;ENSP00000452091:Q10R;ENSP00000450638:Q10R;ENSP00000451198:Q10R;ENSP00000450624:Q10R	ENSP00000216463:Q10R	Q	-	2	0	TIMM9	57948388	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.606000	0.82863	2.130000	0.65690	0.528000	0.53228	CAG	.		0.353	TIMM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276936.2			C	58878635	T	C	58878635	3	2	136	1	0	0	0	0	1	0	0	0	15948	1580	55	3	252	3	TIMM9	14	58878635	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10		58878635	48470905	60	12158											
WDR72	256764	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	53815462	53815462	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtcaggcatgtcctccAcgtcttggaagtttgccgag	7	12	11	11	2	3	0	1	0	2	0	5	2	5	1	3	2	1	2	3	2	1	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr15:53815462A>G	ENST00000396328.1	-	19	3445	c.3206T>C	c.(3205-3207)gTg>gCg	p.V1069A	WDR72_ENST00000360509.5_Missense_Mutation_p.V1069A|WDR72_ENST00000567224.1_5'UTR|WDR72_ENST00000559418.1_Missense_Mutation_p.V1079A|WDR72_ENST00000557913.1_Missense_Mutation_p.V1066A	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	1069										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		CATGTCCTCCACGTCTTGGAA	0.443																																					p.V1069A		.											.	WDR72-92	0			c.T3206C						.						190	181	184					15																	53815462		2194	4293	6487	SO:0001583	missense	256764	exon19			TCCTCCACGTCTT	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"WD repeat domain containing"	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.3206T>C	15.37:g.53815462A>G	ENSP00000379619:p.Val1069Ala	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	70	14	NM_182758	0	0	1	9	8	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	A	0.124	-1.121308	0.01785	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.33216	1.42;1.42	6.17	1.97	0.26223	.	1.192530	0.05923	N	0.633818	T	0.09949	0.0244	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	10	0.10636	T	0.68	.	1.0072	0.01489	0.2223:0.1286:0.3848:0.2643	.	1069	Q3MJ13	WDR72_HUMAN	A	1069	ENSP00000379619:V1069A;ENSP00000353699:V1069A	ENSP00000353699:V1069A	V	-	2	0	WDR72	51602754	0.018000	0.18449	0.000000	0.03702	0.436000	0.31835	0.638000	0.24674	0.137000	0.18759	-0.177000	0.13119	GTG	.		0.443	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		G	53815462	A	G	53815462	3	3	136	1	0	0	0	0	1	0	0	0	17355	159	6	3	110	3	WDR72	15	53815462	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		53815462	48715930	61	12159											
TLN2	83660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	63097959	63097959	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctgagccggaaagccgTgtcagatatgttgacggctt	10	9	12	10	3	1	3	1	2	0	1	1	4	1	4	3	2	3	2	3	2	3	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr15:63097959T>A	ENST00000561311.1	+	50	6868	c.6638T>A	c.(6637-6639)gTg>gAg	p.V2213E	TLN2_ENST00000306829.6_Missense_Mutation_p.V2213E			Q9Y4G6	TLN2_HUMAN	talin 2	2213					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CGGAAAGCCGTGTCAGATATG	0.512																																					p.V2213E		.											.	TLN2-573	0			c.T6638A						.						77	68	71					15																	63097959		2203	4300	6503	SO:0001583	missense	83660	exon48			AAGCCGTGTCAGA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6638T>A	15.37:g.63097959T>A	ENSP00000453508:p.Val2213Glu	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	196	56	NM_015059	0	0	1	5	4	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	32	5.119444	0.94385	.	.	ENSG00000171914	ENST00000306829	T	0.77098	-1.07	5.83	5.83	0.93111	.	0.055071	0.64402	D	0.000001	T	0.79724	0.4495	M	0.62723	1.935	0.80722	D	1	P	0.40398	0.716	B	0.43478	0.421	T	0.82133	-0.0608	10	0.87932	D	0	-21.9765	16.2009	0.82078	0.0:0.0:0.0:1.0	.	2213	Q9Y4G6	TLN2_HUMAN	E	2213	ENSP00000303476:V2213E	ENSP00000303476:V2213E	V	+	2	0	TLN2	60885012	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.997000	0.88414	2.235000	0.73313	0.533000	0.62120	GTG	.		0.512	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63097959	T	A	63097959	3	1	136	1	0	0	0	0	1	0	0	0	15980	1696	59	5	6828	5	TLN2	15	63097959	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	9282497	63097959	39433433	62	12160											
MEGF11	84465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	66190397	66190397	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggatatagctggagttatGaccgcaaccttcttggacca	10	11	10	10	1	1	1	0	1	1	0	1	4	1	4	3	3	2	3	3	3	4	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr15:66190397G>A	ENST00000409699.2	-	23	3182	c.3010C>T	c.(3010-3012)Cat>Tat	p.H1004Y	MEGF11_ENST00000395625.2_Missense_Mutation_p.H929Y|MEGF11_ENST00000360698.4_3'UTR|MEGF11_ENST00000422354.1_Missense_Mutation_p.H1004Y|MEGF11_ENST00000288745.3_Missense_Mutation_p.H929Y|MEGF11_ENST00000478721.1_5'Flank			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	1004					homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						CTGGAGTTATGACCGCAACCT	0.463																																					p.H1004Y		.											.	MEGF11-69	0			c.C3010T						.						124	107	113					15																	66190397		2201	4299	6500	SO:0001583	missense	84465	exon23			AGTTATGACCGCA	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.3010C>T	15.37:g.66190397G>A	ENSP00000386908:p.His1004Tyr	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	139	34	NM_032445	0	0	0	0	0	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.943794	0.00479	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625	D;D;D;D	0.86694	-2.16;-2.05;-2.16;-2.05	5.03	4.11	0.48088	.	0.766593	0.10702	U	0.643968	T	0.77191	0.4094	N	0.22421	0.69	0.18873	N	0.999982	B;B	0.22746	0.015;0.074	B;B	0.24269	0.008;0.052	T	0.56619	-0.7949	10	0.02654	T	1	.	12.3211	0.54985	0.0833:0.0:0.9167:0.0	.	1004;929	A6BM72;A6BM72-2	MEG11_HUMAN;.	Y	1004;929;1004;929	ENSP00000386908:H1004Y;ENSP00000288745:H929Y;ENSP00000414475:H1004Y;ENSP00000378987:H929Y	ENSP00000288745:H929Y	H	-	1	0	MEGF11	63977451	0.017000	0.18338	0.046000	0.18839	0.418000	0.31294	1.820000	0.39032	1.300000	0.44818	0.655000	0.94253	CAT	.		0.463	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		A	66190397	G	A	66190397	3	1	136	1	0	0	0	0	1	0	0	0	9486	1290	45	2	128	2	MEGF11	15	66190397	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3092438	66190397	36340995	63	12161											
DNAH3	55567	bcgsc.ca	37	chr16	20976403	20976403	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcattcagggcctggagccGatctaccaccagcttcagct	8	9	10	14	1	4	0	3	0	1	0	4	2	4	1	4	2	4	2	4	2	1	3	rs143399673		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:20976403G>A	ENST00000261383.3	-	53	8802	c.8803C>T	c.(8803-8805)Cgg>Tgg	p.R2935W	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2935	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GCCTGGAGCCGATCTACCACC	0.532																																					p.R2935W													.	DNAH3-167	0			c.C8803T						.	G	TRP/ARG	1,4401	2.1+/-5.4	0,1,2200	190	180	183		8803	5	0.1	16	dbSNP_134	183	0,8600		0,0,4300	no	missense	DNAH3	NM_017539.1	101	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	2935/4117	20976403	1,13001	2201	4300	6501	SO:0001583	missense	55567	exon53			GGAGCCGATCTAC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"Axonemal dyneins"	2949	protein-coding gene	gene with protein product		603334	"dynein, axonemal, heavy polypeptide 3"			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8803C>T	16.37:g.20976403G>A	ENSP00000261383:p.Arg2935Trp	Somatic	110	3		WXS	Illumina HiSeq	Phase_1	159	74	NM_017539	0	0	0	0	0	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.444776	0.25987	2.27E-4	0.0	ENSG00000158486	ENST00000261383	T	0.74632	-0.86	5.93	4.96	0.65561	Dynein heavy chain, coiled coil stalk (1);	0.153499	0.43260	D	0.000600	D	0.88262	0.6389	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.90761	0.4665	10	0.87932	D	0	.	16.4106	0.83712	0.0:0.0:0.8675:0.1325	.	2935	Q8TD57	DYH3_HUMAN	W	2935	ENSP00000261383:R2935W	ENSP00000261383:R2935W	R	-	1	2	DNAH3	20883904	1.000000	0.71417	0.054000	0.19295	0.001000	0.01503	3.924000	0.56476	1.485000	0.48380	0.655000	0.94253	CGG	G|1.000;A|0.000		0.532	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	20976403	G	A	20976403	3	1	136	1	0	0	0	0	1	0	0	0	4614	1057	37	1	3586	1	DNAH3	16	20976403	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		20976403	69378350	64	12162											
EEF2K	29904	ucsc.edu;bcgsc.ca	37	chr16	22291588	22291588	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacggactgtgatgagggCggtgagtacgacggaatgca	11	7	17	6	4	0	4	0	4	0	0	0	7	0	6	0	4	2	2	0	4	2	1	rs543402357		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:22291588C>T	ENST00000263026.5	+	17	2433	c.1959C>T	c.(1957-1959)ggC>ggT	p.G653G		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	653					insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		GTGATGAGGGCGGTGAGTACG	0.612													C|||	1	0.000199681	0	0.0014	5008	,	,		19850	0		0	False		,,,				2504	0				p.G653G	NSCLC(195;1411 2157 20319 27471 51856)												.	EEF2K-856	0			c.C1959T						.						108	84	92					16																	22291588		2197	4300	6497	SO:0001819	synonymous_variant	29904	exon17			TGAGGGCGGTGAG	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.1959C>T	16.37:g.22291588C>T		Somatic	219	2		WXS	Illumina HiSeq		408	200	NM_013302	0	0	0	3	3	Q8N588	Silent	SNP	ENST00000263026.5	37	CCDS10604.1																																																																																			.		0.612	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		T	22291588	C	T	22291588	2	4	136	1	0	0	0	0	0	0	0	1	4941	755	27	1		1	EEF2K	16	22291588	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	1315185	22291588	68063165	65	12163											
IL21R	50615	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27459983	27459983	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccaagaggctgcagctcacGgagctacaagaaccagcaga	14	3	12	12	1	1	3	1	0	0	3	1	4	1	4	2	2	6	5	2	2	4	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:27459983G>T	ENST00000337929.3	+	9	1469	c.996G>T	c.(994-996)acG>acT	p.T332T	IL21R_ENST00000395754.4_Silent_p.T332T|IL21R_ENST00000564583.1_3'UTR|IL21R_ENST00000395755.1_Silent_p.T332T|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Silent_p.T332T	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	332					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						TGCAGCTCACGGAGCTACAAG	0.662			T	BCL6	NHL																																p.T354T				Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R-660	0			c.G1062T						.						27	29	28					16																	27459983		2196	4297	6493	SO:0001819	synonymous_variant	50615	exon10			GCTCACGGAGCTA	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.996G>T	16.37:g.27459983G>T		Somatic	94	1		WXS	Illumina HiSeq	Phase_I	259	65	NM_181079	0	0	0	0	0	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	37	CCDS10630.1																																																																																			.		0.662	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27459983	G	T	27459983	2	4	136	1	0	0	0	0	0	0	0	1	7692	1103	39	4		4	IL21R	16	27459983	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	5168395	27459983	62894770	66	12164											
POLR2C	5432	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57503976	57503976	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aagtggaaccctactgcaggGgtggcttttgaatacgatcc	10	10	12	9	1	0	1	0	1	0	0	1	3	1	2	2	4	4	2	2	4	5	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:57503976G>A	ENST00000219252.5	+	7	881	c.543G>A	c.(541-543)ggG>ggA	p.G181G	POLR2C_ENST00000564651.1_3'UTR	NM_032940.2	NP_116558.1	P19387	RPB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide C, 33kDa	181					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	10						CTACTGCAGGGGTGGCTTTTG	0.537																																					p.G181G		.											.	POLR2C-90	0			c.G543A						.						67	63	64					16																	57503976		2198	4300	6498	SO:0001819	synonymous_variant	5432	exon7			TGCAGGGGTGGCT		CCDS10782.1	16q13-q21	2013-01-21	2002-08-29		ENSG00000102978	ENSG00000102978		"RNA polymerase subunits"	9189	protein-coding gene	gene with protein product	"RNA polymerase II subunit 3"	180663	"polymerase (RNA) II (DNA directed) polypeptide C (33kD)"			8034326	Standard	NM_032940		Approved	RPB3	uc002elt.1	P19387	OTTHUMG00000133464	ENST00000219252.5:c.543G>A	16.37:g.57503976G>A		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	337	182	NM_032940	0	0	13	47	34	O15161	Silent	SNP	ENST00000219252.5	37	CCDS10782.1																																																																																			.		0.537	POLR2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257340.3	NM_032940		A	57503976	G	A	57503976	2	1	136	1	0	0	0	0	0	0	0	1	12242	1219	43	2		2	POLR2C	16	57503976	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	30043993	57503976	32850777	67	12165											
KLHDC4	54758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	87760467	87760467	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccccgtccctgacggggaCagcttgctccatgtgaaggt	6	8	14	13	2	0	2	0	2	0	0	2	3	2	3	4	4	2	2	4	4	1	1	rs548850415		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:87760467C>T	ENST00000270583.5	-	7	721	c.663G>A	c.(661-663)ctG>ctA	p.L221L	KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Silent_p.L164L|KLHDC4_ENST00000347925.5_Silent_p.L190L	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	221										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		CTGACGGGGACAGCTTGCTCC	0.557																																					p.L221L		.											.	KLHDC4-182	0			c.G663A						.						91	90	90					16																	87760467		2198	4300	6498	SO:0001819	synonymous_variant	54758	exon7			CGGGGACAGCTTG	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.663G>A	16.37:g.87760467C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	269	142	NM_017566	0	0	2	9	7	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Silent	SNP	ENST00000270583.5	37	CCDS10963.1																																																																																			.		0.557	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		T	87760467	C	T	87760467	2	4	136	1	0	0	0	0	0	0	0	1	8379	465	17	2		2	KLHDC4	16	87760467	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	30256491	87760467	2594286	68	12166											
WDR81	124997	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	1630178	1630178	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccagttttagaggccactcCctgtgaggctagctggacca	8	9	12	12	0	0	2	0	1	0	1	1	3	1	3	4	3	1	3	4	3	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:1630178C>G	ENST00000409644.1	+	1	1925	c.1925C>G	c.(1924-1926)cCc>cGc	p.P642R	WDR81_ENST00000309182.5_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000437219.2_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	642					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GAGGCCACTCCCTGTGAGGCT	0.587																																					p.P642R		.											.	WDR81-91	0			c.C1925G						.						7	9	9					17																	1630178		690	1579	2269	SO:0001583	missense	124997	exon1			CCACTCCCTGTGA	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"WD repeat domain containing"	26600	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 166"	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.1925C>G	17.37:g.1630178C>G	ENSP00000386609:p.Pro642Arg	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	99	42	NM_001163809	0	0	4	7	3	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	4.713	0.132661	0.09032	.	.	ENSG00000167716	ENST00000409644	T	0.56275	0.47	5.59	4.62	0.57501	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52646	-0.8548	6	0.33940	T	0.23	.	9.7471	0.40453	0.0:0.8428:0.0:0.1572	.	.	.	.	R	642	ENSP00000386609:P642R	ENSP00000386609:P642R	P	+	2	0	WDR81	1576928	0.940000	0.31905	0.835000	0.33067	0.224000	0.24922	3.300000	0.51834	1.349000	0.45751	0.462000	0.41574	CCC	.		0.587	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		G	1630178	C	G	1630178	3	3	136	1	0	0	0	0	1	0	0	0	17363	623	22	4	1989	4	WDR81	17	1630178	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		1630178	79565032	69	12167											
NUP88	4927	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	5312151	5312152	+	Frame_Shift_Ins	INS	-	-	A																															ctttgccgttttgtccaaatINSagagtctttgggactgctgc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:5312151_5312152insA	ENST00000573584.1	-	5	1267_1268	c.758_759insT	c.(757-759)ctafs	p.L253fs		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	253					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TTTGTCCAAATAGAGTCTTTGG	0.436																																					p.L253fs		.											.	NUP88-204	0			c.759_760insT						.																																			SO:0001589	frameshift_variant	4927	exon5			.	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"nucleoporin 88kD"			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.759dupT	17.37:g.5312152_5312152dupA	ENSP00000458954:p.Leu253fs	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	254	61	NM_002532	0	0	0	0	0	D3DTM2|Q9BWE5	Frame_Shift_Ins	INS	ENST00000573584.1	37	CCDS11070.1																																																																																			.		0.436	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		A	5312152	-	A	5312151	7	5	136	1	0	1	1	0	0	0	0	0	10797	1393	49	0	1518	0	NUP88	17	5312151	Frame_Shift_Ins	INS	-	TCGA-HE-A5NL-01A-11D-A26P-10	3681973	5312151	75883059	70	12168											
C17orf104	284071	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	42744034	42744034	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taactgtcacaatattcagaCaaatgatacagctaagacaa	19	9	5	8	0	2	3	2	1	0	2	2	3	2	3	0	0	3	1	0	0	7	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:42744034C>T	ENST00000409122.2	+	5	897	c.755C>T	c.(754-756)aCa>aTa	p.T252I	C17orf104_ENST00000409464.1_Missense_Mutation_p.T86I|C17orf104_ENST00000359945.3_Missense_Mutation_p.T252I	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	252										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						AATATTCAGACAAATGATACA	0.353																																					p.T252I		.											.	C17orf104-22	0			c.C755T						.						72	63	66					17																	42744034		2203	4300	6503	SO:0001583	missense	284071	exon5			TTCAGACAAATGA		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.755C>T	17.37:g.42744034C>T	ENSP00000386452:p.Thr252Ile	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	190	12	NM_001145080	0	0	0	0	0	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418212	0.25552	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000456912;ENST00000409464	T;T;T;T;T	0.35048	1.33;1.33;1.63;1.63;1.34	5.54	4.58	0.56647	.	0.518815	0.20253	N	0.096034	T	0.24547	0.0595	N	0.14661	0.345	0.24157	N	0.995676	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.14023	0.01;0.006;0.006	T	0.15350	-1.0440	10	0.39692	T	0.17	-10.3947	14.6777	0.68993	0.0:0.9298:0.0:0.0702	.	252;252;86	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	I	252;252;86;86;86	ENSP00000353028:T252I;ENSP00000386452:T252I;ENSP00000399809:T86I;ENSP00000397957:T86I;ENSP00000386586:T86I	ENSP00000353028:T252I	T	+	2	0	C17orf104	40099560	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.331000	0.52075	1.468000	0.48064	0.591000	0.81541	ACA	.		0.353	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		T	42744034	C	T	42744034	3	4	136	1	0	0	0	0	1	0	0	0	1855	478	17	2	773	2	C17orf104	17	42744034	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	37431883	42744034	38451176	71	12169											
SLC35B1	10237	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	47781478	47781478	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccattcccagcagcaaTgtcgaccaaaggttgatgtt	11	10	8	12	1	1	1	1	1	0	0	3	2	2	1	3	1	2	4	3	1	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:47781478T>A	ENST00000240333.6	-	6	760	c.639A>T	c.(637-639)acA>acT	p.T213T	SLC35B1_ENST00000415270.2_Silent_p.T250T			P78383	S35B1_HUMAN	solute carrier family 35, member B1	213					transport (GO:0006810)|UDP-galactose transmembrane transport (GO:0072334)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	UDP-galactose transmembrane transporter activity (GO:0005459)			endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(1)	7						CCAGCAGCAATGTCGACCAAA	0.527																																					p.T213T													.	SLC35B1-90	0			c.A639T						.						220	173	189					17																	47781478		2203	4300	6503	SO:0001819	synonymous_variant	10237	exon6			CAGCAATGTCGAC	D16978	CCDS11552.1, CCDS11552.2	17q21.32	2013-05-22			ENSG00000121073	ENSG00000121073		"Solute carriers"	20798	protein-coding gene	gene with protein product		610790				9010752	Standard	NM_005827		Approved	UGTREL1	uc002iph.1	P78383	OTTHUMG00000161638	ENST00000240333.6:c.639A>T	17.37:g.47781478T>A		Somatic	209	1		WXS	Illumina HiSeq	Phase_I	433	103	NM_005827	0	0	32	39	7	B4DEC4|J3KQV4|Q96EW7	Silent	SNP	ENST00000240333.6	37	CCDS11552.1																																																																																			.		0.527	SLC35B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365564.2	NM_005827		A	47781478	T	A	47781478	2	1	136	1	0	0	0	0	0	0	0	1	14607	1451	51	5		5	SLC35B1	17	47781478	Silent	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	5037444	47781478	33413732	72	12170											
PRKAR1A	5573	broad.mit.edu;bcgsc.ca	37	chr17	66526491	66526491	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccccttgaagtgcgttaaGctggaccgacctagatttga	9	10	12	10	2	0	3	0	2	0	1	0	5	0	4	4	2	2	2	4	2	3	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:66526491G>A	ENST00000589228.1	+	11	1175	c.1047G>A	c.(1045-1047)aaG>aaA	p.K349K	PRKAR1A_ENST00000358598.2_Silent_p.K349K|PRKAR1A_ENST00000586397.1_Silent_p.K349K|PRKAR1A_ENST00000392711.1_Silent_p.K349K|PRKAR1A_ENST00000588188.2_Intron|PRKAR1A_ENST00000536854.2_Silent_p.K349K	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	349					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					AGTGCGTTAAGCTGGACCGAC	0.488			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												p.K349K	Ovarian(167;637 1670 33025 39608 46699 51856)		yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	.	PRKAR1A-1141	0			c.G1047A						.						262	211	228					17																	66526491		2203	4300	6503	SO:0001819	synonymous_variant	5573	exon11	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;	CGTTAAGCTGGAC		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.1047G>A	17.37:g.66526491G>A		Somatic	194	0		WXS	Illumina HiSeq	Phase_I	351	10	NM_212472	0	0	118	122	4	K7ER48|Q567S7	Silent	SNP	ENST00000589228.1	37	CCDS11678.1																																																																																			.		0.488	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			A	66526491	G	A	66526491	2	1	136	1	0	0	0	0	0	0	0	1	12532	962	34	2		2	PRKAR1A	17	66526491	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	18745013	66526491	14668719	73	12171											
CD300A	11314	broad.mit.edu	37	chr17	72473598	72473598	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgctgctcctctccctgcTggcattgttgctgcttctgt	1	15	9	16	1	2	0	0	0	2	0	4	0	3	0	3	1	4	7	3	1	0	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:72473598T>C	ENST00000360141.3	+	4	845	c.557T>C	c.(556-558)cTg>cCg	p.L186P	CD300A_ENST00000310828.5_Missense_Mutation_p.L73P|CD300A_ENST00000577511.1_Missense_Mutation_p.L56P|CD300A_ENST00000392625.3_Missense_Mutation_p.L73P|CD300A_ENST00000361933.3_Intron	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	186					cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						CTCTCCCTGCTGGCATTGTTG	0.532																																					p.L186P													.	CD300A-92	0			c.T557C						.						75	63	67					17																	72473598		2203	4300	6503	SO:0001583	missense	11314	exon4			CCCTGCTGGCATT	BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	19319	protein-coding gene	gene with protein product		606790	"CD300a antigen"			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.557T>C	17.37:g.72473598T>C	ENSP00000353259:p.Leu186Pro	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	169	4	NM_007261	0	0	2	2	0	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Missense_Mutation	SNP	ENST00000360141.3	37	CCDS32720.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.505708	0.44558	.	.	ENSG00000167851	ENST00000360141;ENST00000392625;ENST00000310828	T;T	0.52983	0.64;0.64	3.8	2.69	0.31865	.	0.741961	0.10047	N	0.722712	T	0.58779	0.2146	L	0.47190	1.495	0.09310	N	0.999997	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.98;0.98;0.997	T	0.42155	-0.9468	10	0.87932	D	0	.	6.5794	0.22585	0.0:0.1194:0.0:0.8806	.	73;73;186	Q9UGN4-4;Q9UGN4-2;Q9UGN4	.;.;CLM8_HUMAN	P	186;73;73	ENSP00000353259:L186P;ENSP00000308188:L73P	ENSP00000308188:L73P	L	+	2	0	CD300A	69985193	0.006000	0.16342	0.001000	0.08648	0.251000	0.25915	1.861000	0.39438	0.566000	0.29273	0.374000	0.22700	CTG	.		0.532	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261		C	72473598	T	C	72473598	3	2	136	1	0	0	0	0	1	0	0	0	3002	1580	55	3	571	3	CD300A	17	72473598	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	5947107	72473598	8721612	74	12172											
ZACN	353174	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74076354	74076354	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggctctgggtggactggagGgaccagagcccccaggctcg	7	5	17	12	1	1	1	0	0	1	1	2	4	1	4	3	6	1	2	3	6	0	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:74076354G>T	ENST00000334586.5	+	5	476	c.393G>T	c.(391-393)agG>agT	p.R131S	ZACN_ENST00000392503.2_Intron|EXOC7_ENST00000591724.1_5'Flank	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	131					ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						TGGACTGGAGGGACCAGAGCC	0.662																																					p.R131S													.	ZACN-90	0			c.G393T						.						50	48	48					17																	74076354		2203	4300	6503	SO:0001583	missense	353174	exon5			CTGGAGGGACCAG	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"Ligand-gated ion channels / Zinc activated channels"	29504	protein-coding gene	gene with protein product		610935	"ligand-gated ion channel, zinc activated 1"	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.393G>T	17.37:g.74076354G>T	ENSP00000334854:p.Arg131Ser	Somatic	128	1		WXS	Illumina HiSeq	Phase_I	294	116	NM_180990	0	0	0	0	0	Q2TB29|Q6ZWK3|Q86YW4	Missense_Mutation	SNP	ENST00000334586.5	37	CCDS11740.2	.	.	.	.	.	.	.	.	.	.	G	6.430	0.447387	0.12223	.	.	ENSG00000186919	ENST00000334586	T	0.76839	-1.05	4.57	3.59	0.41128	Neurotransmitter-gated ion-channel ligand-binding (3);	0.656443	0.12755	N	0.441853	T	0.66519	0.2797	L	0.36672	1.1	0.80722	D	1	B	0.33000	0.393	B	0.28916	0.096	T	0.60667	-0.7218	10	0.33940	T	0.23	.	10.1865	0.43000	0.0964:0.0:0.9036:0.0	.	131	Q401N2	ZACN_HUMAN	S	131	ENSP00000334854:R131S	ENSP00000334854:R131S	R	+	3	2	ZACN	71587949	0.923000	0.31300	0.985000	0.45067	0.962000	0.63368	1.248000	0.32827	1.121000	0.41925	0.655000	0.94253	AGG	.		0.662	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990		T	74076354	G	T	74076354	3	4	136	1	0	0	0	0	1	0	0	0	17543	1223	43	4	411	4	ZACN	17	74076354	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	1602756	74076354	7118856	75	12173											
QRICH2	84074	bcgsc.ca	37	chr17	74288508	74288508	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggaccaaaccatgctgaTctgcaccaggttggaccaaa	12	8	10	11	0	1	1	0	1	1	0	1	3	1	3	4	3	3	4	4	3	2	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:74288508T>A	ENST00000262765.5	-	4	1981	c.1802A>T	c.(1801-1803)gAt>gTt	p.D601V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	601	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						ACCATGCTGATCTGCACCAGG	0.537																																					p.D601V													.	QRICH2-94	0			c.A1802T						.						168	134	145					17																	74288508		2203	4300	6503	SO:0001583	missense	84074	exon4			TGCTGATCTGCAC	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1802A>T	17.37:g.74288508T>A	ENSP00000262765:p.Asp601Val	Somatic	272	2		WXS	Illumina HiSeq	Phase_1	512	27	NM_032134	0	0	0	0	0	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	T	8.120	0.780708	0.16120	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.21734	1.99	4.82	-9.63	0.00544	.	.	.	.	.	T	0.06735	0.0172	N	0.16478	0.41	0.09310	N	1	P;B	0.37276	0.589;0.138	B;B	0.33454	0.164;0.033	T	0.14200	-1.0481	9	0.18710	T	0.47	0.7097	1.6345	0.02739	0.4588:0.2138:0.0952:0.2322	.	601;601	B5MD94;Q9H0J4	.;QRIC2_HUMAN	V	601	ENSP00000262765:D601V	ENSP00000262765:D601V	D	-	2	0	QRICH2	71800103	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.623000	0.00059	-2.309000	0.00651	-0.444000	0.05651	GAT	.		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74288508	T	A	74288508	3	1	136	1	0	0	0	0	1	0	0	0	12912	1435	50	5	3253	5	QRICH2	17	74288508	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	212154	74288508	6906702	76	12174											
RNF152	220441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	59483369	59483369	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtctccgggcagcagcgcacGctccttggagatgggcaggg	6	6	17	12	3	1	1	0	0	1	1	3	2	2	1	2	4	2	5	2	4	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr18:59483369G>C	ENST00000312828.3	-	2	1427	c.328C>G	c.(328-330)Cgt>Ggt	p.R110G		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	110					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				AGCAGCGCACGCTCCTTGGAG	0.627																																					p.R110G		.											.	RNF152-226	0			c.C328G						.						68	74	72					18																	59483369		2203	4300	6503	SO:0001583	missense	220441	exon2			GCGCACGCTCCTT	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"RING-type (C3HC4) zinc fingers"	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.328C>G	18.37:g.59483369G>C	ENSP00000316628:p.Arg110Gly	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	78	26	NM_173557	0	0	0	0	0	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	37	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	G	5.884	0.347185	0.11126	.	.	ENSG00000176641	ENST00000312828	D	0.83335	-1.71	4.97	4.97	0.65823	.	0.139197	0.44902	D	0.000405	T	0.69424	0.3109	N	0.17082	0.46	0.45621	D	0.998557	B	0.06786	0.001	B	0.06405	0.002	T	0.63501	-0.6623	10	0.18710	T	0.47	-3.5749	13.096	0.59192	0.0:0.0:0.7221:0.2779	.	110	Q8N8N0	RN152_HUMAN	G	110	ENSP00000316628:R110G	ENSP00000316628:R110G	R	-	1	0	RNF152	57634349	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.456000	0.53000	2.600000	0.87896	0.655000	0.94253	CGT	.		0.627	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557		C	59483369	G	C	59483369	3	2	136	1	0	0	0	0	1	0	0	0	13485	1087	38	4	287	4	RNF152	18	59483369	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		59483369	18593879	77	12175											
BTBD2	55643	broad.mit.edu	37	chr19	2015365	2015365	+	Frame_Shift_Del	DEL	T	T	-																															gcacgtcgcacagcacctcgTtgttgaagaggaaggcgaag																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:2015365delT	ENST00000255608.4	-	1	354	c.338delA	c.(337-339)aacfs	p.N113fs	BTBD2_ENST00000590646.1_Intron	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	113						cytoplasmic mRNA processing body (GO:0000932)				endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCACCTCGTTGTTGAAGAG	0.741																																					p.N113fs													.	BTBD2-92	0			c.338delA						.						19	12	14					19																	2015365		1832	3545	5377	SO:0001589	frameshift_variant	55643	exon1			ACCTCGTTGTTGA	AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"BTB/POZ domain containing"	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.338delA	19.37:g.2015365delT	ENSP00000255608:p.Asn113fs	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_017797	0	0	0	0	0	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Frame_Shift_Del	DEL	ENST00000255608.4	37	CCDS12078.1																																																																																			.		0.741	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2			-	2015365	T	-	2015365	7	5	136	1	0	1	0	1	0	0	0	0	1546	1725	60	0	1275	0	BTBD2	19	2015365	Frame_Shift_Del	DEL	T	TCGA-HE-A5NL-01A-11D-A26P-10		2015365	57113618	78	12176											
ATP13A1	57130	broad.mit.edu;bcgsc.ca	37	chr19	19762514	19762515	+	Frame_Shift_Ins	INS	-	-	TGCAGGA																															cacctttctcggagggaggcINStgcaggatcagcgtgtgggc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:19762514_19762515insTGCAGGA	ENST00000357324.6	-	17	2344_2345	c.2318_2319insTCCTGCA	c.(2317-2319)cagfs	p.Q773fs	ATP13A1_ENST00000496082.1_5'Flank|ATP13A1_ENST00000291503.5_Frame_Shift_Ins_p.Q655fs	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	773						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CGGAGGGAGGCTGCAGGATCAG	0.609																																					p.Q773fs	Esophageal Squamous(142;920 1789 9047 14684 24777)												.	ATP13A1-138	0			c.2319_2320insTCCTGCA						.																																			SO:0001589	frameshift_variant	57130	exon17			GGGAGGCTGCAGG	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.2312_2318dupTCCTGCA	19.37:g.19762515_19762521dupTGCAGGA	ENSP00000349877:p.Gln773fs	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	227	36	NM_020410	0	0	0	0	0	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Frame_Shift_Ins	INS	ENST00000357324.6	37	CCDS32970.2																																																																																			.		0.609	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		TGCAGGA	19762515	-	TGCAGGA	19762514	7	5	136	1	0	1	1	0	0	0	0	0	1124	796	28	0	1335	0	ATP13A1	19	19762514	Frame_Shift_Ins	INS	-	TCGA-HE-A5NL-01A-11D-A26P-10	17747149	19762514	39366469	79	12177											
PSG11	5680	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	43519496	43519496	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atagtaagaggtgactgaagGgaaaattctggggaggtctg	13	9	16	3	0	2	3	0	2	2	1	2	5	2	5	0	5	0	1	0	5	5	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:43519496G>T	ENST00000401740.1	-	4	839	c.736C>A	c.(736-738)Cct>Act	p.P246T	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000320078.7_Missense_Mutation_p.P246T|PSG11_ENST00000306322.7_Missense_Mutation_p.P124T|PSG11_ENST00000403486.1_Missense_Mutation_p.P124T			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	244	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				GTGACTGAAGGGAAAATTCTG	0.468																																					p.P246T		.											.	.	0			c.C736A						.						112	125	120					19																	43519496		2199	4298	6497	SO:0001583	missense	5680	exon4			CTGAAGGGAAAAT	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9516	protein-coding gene	gene with protein product	"pregnancy specific beta-1-glycoprotein 13"	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.736C>A	19.37:g.43519496G>T	ENSP00000384995:p.Pro246Thr	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	102	46	NM_002785	0	0	0	0	0	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	g	7.213	0.595792	0.13875	.	.	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	0.961	-0.805	0.10879	Immunoglobulin-like (1);	.	.	.	.	T	0.80154	0.4571	M	0.84683	2.71	0.09310	N	1	B;B	0.28636	0.085;0.218	B;P	0.45037	0.078;0.467	T	0.75110	-0.3433	9	0.87932	D	0	.	4.7032	0.12837	0.2746:0.0:0.7254:0.0	.	124;246	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	T	246;124;124;246	ENSP00000319140:P246T;ENSP00000385427:P124T;ENSP00000304913:P124T;ENSP00000384995:P246T	ENSP00000304913:P124T	P	-	1	0	PSG11	48211336	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.167000	0.16602	-1.109000	0.02996	-1.109000	0.02080	CCT	.		0.468	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		T	43519496	G	T	43519496	3	4	136	1	0	0	0	0	1	0	0	0	12683	1232	43	4	279	4	PSG11	19	43519496	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	23756982	43519496	15609487	80	12178											
ZNF415	55786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53612760	53612760	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgatggtagaagaaattaTttggggtggtgaaactgagg	12	13	15	1	0	0	5	0	3	0	2	0	5	0	5	0	5	1	1	0	5	5	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:53612760T>A	ENST00000500065.4	-	4	871	c.538A>T	c.(538-540)Ata>Tta	p.I180L	ZNF415_ENST00000243643.4_Missense_Mutation_p.I180L|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.I192L|ZNF415_ENST00000455735.2_Missense_Mutation_p.I228L|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000440291.1_Missense_Mutation_p.I167L|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.I228L	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		GAAGAAATTATTTGGGGTGGT	0.383																																					p.I180L		.											.	ZNF415-91	0			c.A538T						.						103	100	101					19																	53612760		2203	4300	6503	SO:0001583	missense	55786	exon4			AAATTATTTGGGG	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.538A>T	19.37:g.53612760T>A	ENSP00000439435:p.Ile180Leu	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	80	29	NM_018355	0	0	0	0	0	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.538587	0.27475	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15	2.74	-0.82	0.10826	.	.	.	.	.	T	0.07007	0.0178	L	0.31578	0.945	0.09310	N	1	B;B;B;B;B;B	0.29085	0.033;0.041;0.038;0.11;0.033;0.232	B;B;B;B;B;B	0.34138	0.015;0.028;0.017;0.033;0.02;0.176	T	0.39440	-0.9614	9	0.59425	D	0.04	.	6.2583	0.20885	0.0:0.3858:0.0:0.6142	.	180;228;228;180;167;192	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	L	180;180;228;192;228;167	ENSP00000243643:I180L;ENSP00000439435:I180L;ENSP00000396492:I228L;ENSP00000395055:I192L;ENSP00000388787:I228L;ENSP00000414601:I167L	ENSP00000243643:I180L	I	-	1	0	ZNF415	58304572	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-0.921000	0.04008	-0.410000	0.07542	0.260000	0.18958	ATA	.		0.383	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		A	53612760	T	A	53612760	3	1	136	1	0	0	0	0	1	0	0	0	17924	1493	52	5	1133	5	ZNF415	19	53612760	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	10093264	53612760	5516223	81	12179											
SEL1L2	80343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	13868446	13868446	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	actttcttgtaataacttagGgcaacttcacaattctgtag	12	15	6	8	0	3	0	1	0	2	0	3	0	3	0	0	1	2	3	0	1	6	8			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:13868446G>T	ENST00000284951.5	-	8	788	c.714C>A	c.(712-714)gcC>gcA	p.A238A	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Silent_p.A238A			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	238						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						AATAACTTAGGGCAACTTCAC	0.299																																					p.A238A		.											.	SEL1L2-70	0			c.C714A						.						129	123	125					20																	13868446		1817	4072	5889	SO:0001819	synonymous_variant	80343	exon8			ACTTAGGGCAACT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"chromosome 20 open reading frame 50"	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.714C>A	20.37:g.13868446G>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	83	21	NM_001271539	0	0	0	0	0	B4DXX5	Silent	SNP	ENST00000284951.5	37																																																																																				.		0.299	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		T	13868446	G	T	13868446	2	4	136	1	0	0	0	0	0	0	0	1	14043	1219	43	4		4	SEL1L2	20	13868446	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		13868446	49157074	82	12180											
ZNF337	26152	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	25656225	25656225	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaaatggcctttcccccgAgtgtgtccactgatgtctaa	9	13	8	11	1	1	1	0	1	1	0	3	2	3	1	4	1	0	0	4	1	3	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:25656225A>T	ENST00000376436.1	-	4	2238	c.1699T>A	c.(1699-1701)Tcg>Acg	p.S567T	RP4-694B14.5_ENST00000421829.1_RNA|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000439498.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|ZNF337_ENST00000538750.1_Missense_Mutation_p.S535T|RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000414393.1_RNA|ZNF337_ENST00000252979.5_Missense_Mutation_p.S567T			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	567					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(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CTTTCCCCCGAGTGTGTCCAC	0.473																																					p.S567T													.	ZNF337-90	0			c.T1699A						.						92	83	86					20																	25656225		2203	4300	6503	SO:0001583	missense	26152	exon5			CCCCCGAGTGTGT		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"Zinc fingers, C2H2-type", "-"	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.1699T>A	20.37:g.25656225A>T	ENSP00000365619:p.Ser567Thr	Somatic	194	1		WXS	Illumina HiSeq	Phase_I	238	86	NM_015655	0	0	1	6	5	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	37	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	8.160	0.789335	0.16258	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000538750	T;T;T	0.12879	2.64;2.64;2.64	1.29	-2.14	0.07123	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.02403	-0.565	0.22457	N	0.999081	B;B	0.13145	0.007;0.007	B;B	0.04013	0.001;0.001	T	0.41520	-0.9504	9	0.02654	T	1	.	5.6207	0.17455	0.3135:0.0:0.0:0.6864	.	535;567	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	T	567;567;535	ENSP00000365619:S567T;ENSP00000252979:S567T;ENSP00000442181:S535T	ENSP00000252979:S567T	S	-	1	0	ZNF337	25604225	0.892000	0.30473	0.005000	0.12908	0.954000	0.61252	0.661000	0.25023	-0.602000	0.05775	0.248000	0.18094	TCG	.		0.473	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			T	25656225	A	T	25656225	3	4	136	1	0	0	0	0	1	0	0	0	17885	304	11	5	560	5	ZNF337	20	25656225	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	11787779	25656225	37369295	83	12181											
TRPC4AP	26133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33623074	33623074	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcgagtcgccagtttgcaAagccgctcaacaaagccagg	11	8	10	12	3	1	0	1	0	0	0	3	1	1	0	3	1	4	3	3	1	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:33623074A>C	ENST00000252015.2	-	8	992	c.903T>G	c.(901-903)ctT>ctG	p.L301L	TRPC4AP_ENST00000432634.2_Silent_p.L262L|TRPC4AP_ENST00000451813.2_Silent_p.L301L|TRPC4AP_ENST00000539834.1_5'UTR			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	301	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			CCAGTTTGCAAAGCCGCTCAA	0.507																																					p.L301L		.											.	TRPC4AP-91	0			c.T903G						.						87	78	81					20																	33623074		2203	4300	6503	SO:0001819	synonymous_variant	26133	exon8			TTTGCAAAGCCGC	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.903T>G	20.37:g.33623074A>C		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	90	26	NM_199368	0	0	7	15	8	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			.		0.507	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		C	33623074	A	C	33623074	2	2	136	1	0	0	0	0	0	0	0	1	16614	1	1	5		5	TRPC4AP	20	33623074	Silent	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	7966849	33623074	29402446	84	12182			1	37		2	2	26	N	C_A	7.510202e-05
TRPC4AP	26133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33623099	33623099	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctcaacaaagccaggaatgCtgagaagggccgctgccagg	12	4	14	11	1	1	1	1	1	0	1	1	3	1	2	3	3	4	3	3	3	4	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:33623099C>A	ENST00000252015.2	-	8	967	c.878G>T	c.(877-879)aGc>aTc	p.S293I	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.S254I|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.S293I|TRPC4AP_ENST00000539834.1_5'Flank			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	293	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GCCAGGAATGCTGAGAAGGGC	0.498																																					p.S293I		.											.	TRPC4AP-91	0			c.G878T						.						61	57	58					20																	33623099		2203	4300	6503	SO:0001583	missense	26133	exon8			GGAATGCTGAGAA	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.878G>T	20.37:g.33623099C>A	ENSP00000252015:p.Ser293Ile	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	75	20	NM_199368	0	0	0	0	0	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929049	0.52759	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000432634;ENST00000541994	T;T;T	0.27720	1.65;1.65;1.65	5.49	4.45	0.53987	.	0.085031	0.85682	D	0.000000	T	0.13329	0.0323	N	0.14661	0.345	0.80722	D	1	B;P;P	0.38335	0.396;0.475;0.627	B;B;B	0.31614	0.044;0.133;0.133	T	0.03524	-1.1028	10	0.54805	T	0.06	.	3.5606	0.07881	0.0:0.6443:0.0:0.3557	.	254;293;293	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	I	293;293;254;278	ENSP00000252015:S293I;ENSP00000400614:S293I;ENSP00000400497:S254I	ENSP00000252015:S293I	S	-	2	0	TRPC4AP	33086760	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	3.786000	0.55431	2.587000	0.87381	0.557000	0.71058	AGC	.		0.498	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		A	33623099	C	A	33623099	3	1	136	1	0	0	0	0	1	0	0	0	16614	797	28	4	1563	4	TRPC4AP	20	33623099	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	25	33623099	29402421	85	12183			1	37		2	2	26	N	C_A	7.510202e-05
TP53TG5	27296	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44005903	44005903	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcagtgaatgccaacacCttttggccagcttatgcagt	10	11	10	10	0	0	2	0	2	0	0	0	2	0	2	3	1	5	3	3	1	3	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:44005903C>A	ENST00000372726.3	-	3	359	c.203G>T	c.(202-204)aGg>aTg	p.R68M	TP53TG5_ENST00000537995.1_Missense_Mutation_p.R52M|TP53TG5_ENST00000494455.1_5'UTR|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1-DBNDD2_ENST00000475242.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	68					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						ATGCCAACACCTTTTGGCCAG	0.517																																					p.R68M													.	TP53TG5-90	0			c.G203T						.						198	185	189					20																	44005903		2203	4300	6503	SO:0001583	missense	27296	exon3			CAACACCTTTTGG	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 10"	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.203G>T	20.37:g.44005903C>A	ENSP00000361811:p.Arg68Met	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	150	45	NM_014477	0	0	0	0	0		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.757255	0.69648	.	.	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.20598	2.06;2.06	5.52	2.25	0.28309	.	0.633338	0.15520	N	0.258106	T	0.34978	0.0916	L	0.46157	1.445	0.29922	N	0.82262	D	0.89917	1.0	D	0.73380	0.98	T	0.15235	-1.0444	10	0.87932	D	0	-16.0632	8.937	0.35706	0.0:0.6414:0.2788:0.0798	.	68	Q9Y2B4	T53G5_HUMAN	M	68;52	ENSP00000361811:R68M;ENSP00000438374:R52M	ENSP00000361811:R68M	R	-	2	0	TP53TG5	43439317	0.434000	0.25570	0.996000	0.52242	0.996000	0.88848	0.351000	0.20096	0.765000	0.33221	0.655000	0.94253	AGG	.		0.517	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477		A	44005903	C	A	44005903	3	1	136	1	0	0	0	0	1	0	0	0	16424	681	24	4	681	4	TP53TG5	20	44005903	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	10382804	44005903	19019617	86	12184											
PCK1	5105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	56140806	56140806	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtcaatgccgacctcccCtgtgaaatcgagagagagat	13	7	10	11	2	1	3	1	1	0	2	3	7	2	3	4	0	1	0	4	0	3	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:56140806C>A	ENST00000319441.4	+	10	1979	c.1815C>A	c.(1813-1815)ccC>ccA	p.P605P	PCK1_ENST00000543666.1_Silent_p.P288P	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	605					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CCGACCTCCCCTGTGAAATCG	0.463																																					p.P605P		.											.	PCK1-227	0			c.C1815A						.						54	50	51					20																	56140806		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon10			CCTCCCCTGTGAA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1815C>A	20.37:g.56140806C>A		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	151	50	NM_002591	0	0	25	65	40	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			.		0.463	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			A	56140806	C	A	56140806	2	1	136	1	0	0	0	0	0	0	0	1	11607	668	24	4		4	PCK1	20	56140806	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	12134903	56140806	6884714	87	12185											
ZGPAT	84619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	62366740	62366740	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgcaaggtcaggctccTggggccctagaagccggggc	8	5	16	12	1	1	1	1	0	0	1	2	1	2	1	3	6	3	3	3	6	4	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:62366740T>A	ENST00000328969.5	+	6	1408	c.1281T>A	c.(1279-1281)ccT>ccA	p.P427P	LIME1_ENST00000309546.3_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.P407P|ZGPAT_ENST00000448100.2_Silent_p.P407P|ZGPAT_ENST00000355969.6_Silent_p.P407P|RP4-583P15.14_ENST00000467211.1_5'Flank|RP4-583P15.15_ENST00000490623.2_Missense_Mutation_p.L313Q|ZGPAT_ENST00000357119.4_Silent_p.P398P	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	427					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GTCAGGCTCCTGGGGCCCTAG	0.672																																					p.P427P		.											.	ZGPAT-90	0			c.T1281A						.						20	23	22					20																	62366740		2183	4294	6477	SO:0001819	synonymous_variant	84619	exon6			GGCTCCTGGGGCC	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"Zinc fingers, CCCH-type domain containing", "G patch domain containing"	15948	protein-coding gene	gene with protein product			"KIAA1847"	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.1281T>A	20.37:g.62366740T>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	61	20	NM_032527	0	0	20	37	17	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	37	CCDS13534.1																																																																																			.		0.672	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		A	62366740	T	A	62366740	2	1	136	1	0	0	0	0	0	0	0	1	17706	1567	55	5		5	ZGPAT	20	62366740	Silent	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	6225934	62366740	658780	88	12186											
NEFH	4744	bcgsc.ca	37	chr22	29885458	29885458	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaagtccccagtgaaggAagaagcaaagtcaccggctg	13	4	13	11	1	1	2	1	1	0	1	2	3	2	3	4	3	1	2	4	3	5	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr22:29885458A>C	ENST00000310624.6	+	4	1862	c.1829A>C	c.(1828-1830)gAa>gCa	p.E610A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	610	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						ccagtgaaggaagaagcaaag	0.567																																					p.E610A													.	NEFH-90	0			c.A1829C						.						66	64	65					22																	29885458		2203	4300	6503	SO:0001583	missense	4744	exon4			TGAAGGAAGAAGC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1829A>C	22.37:g.29885458A>C	ENSP00000311997:p.Glu610Ala	Somatic	197	0		WXS	Illumina HiSeq	Phase_1	247	10	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	A	6.939	0.543004	0.13250	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	T	0.30448	1.53	4.98	1.5	0.22942	.	0.000000	0.37577	N	0.002038	T	0.29190	0.0726	M	0.69823	2.125	0.30754	N	0.74477	P	0.43392	0.805	P	0.45753	0.492	T	0.20075	-1.0286	10	0.14656	T	0.56	.	3.2852	0.06929	0.4892:0.0:0.239:0.2717	.	610	P12036	NFH_HUMAN	A	610	ENSP00000311997:E610A	ENSP00000311997:E610A	E	+	2	0	NEFH	28215458	0.987000	0.35691	0.168000	0.22838	0.172000	0.22775	3.046000	0.49846	0.238000	0.21222	0.377000	0.23210	GAA	.		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		C	29885458	A	C	29885458	3	2	136	1	0	0	0	0	1	0	0	0	10340	246	9	5	1843	5	NEFH	22	29885458	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		29885458	21419108	89	12187											
LGALS2	3957	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	37966307	37966307	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagaggacatgttgaacccgCcccttacgctcaggtagctc	10	8	10	13	2	1	2	1	1	0	1	2	3	1	3	3	2	3	4	3	2	4	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr22:37966307C>T	ENST00000215886.4	-	4	536	c.362G>A	c.(361-363)gGc>gAc	p.G121D		NM_006498.2	NP_006489.1	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	121	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)|galactoside binding (GO:0016936)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)	11	Melanoma(58;0.0574)					GTTGAACCCGCCCCTTACGCT	0.498																																					p.G121D	GBM(193;1840 2185 13711 20676 24505)	.											.	LGALS2-154	0			c.G362A						.						90	94	93					22																	37966307		2203	4300	6503	SO:0001583	missense	3957	exon4			AACCCGCCCCTTA		CCDS13950.1	22q13.1	2011-08-04	2007-02-01		ENSG00000100079	ENSG00000100079		"Lectins, galactoside-binding"	6562	protein-coding gene	gene with protein product	"galectin 2"	150571				1988031, 15356130	Standard	NM_006498		Approved	HL14	uc003ata.3	P05162	OTTHUMG00000150590	ENST00000215886.4:c.362G>A	22.37:g.37966307C>T	ENSP00000215886:p.Gly121Asp	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	174	10	NM_006498	0	0	18	20	2	Q6FGY4	Missense_Mutation	SNP	ENST00000215886.4	37	CCDS13950.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824838	0.50739	.	.	ENSG00000100079	ENST00000215886	T	0.68181	-0.31	5.65	1.17	0.20885	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.292084	0.42821	D	0.000648	T	0.64983	0.2648	M	0.82056	2.57	0.09310	N	0.999994	B	0.30870	0.298	B	0.30943	0.122	T	0.59958	-0.7356	10	0.62326	D	0.03	0.0582	10.2071	0.43120	0.0:0.7317:0.0:0.2683	.	121	P05162	LEG2_HUMAN	D	121	ENSP00000215886:G121D	ENSP00000215886:G121D	G	-	2	0	LGALS2	36296253	0.010000	0.17322	0.000000	0.03702	0.000000	0.00434	1.026000	0.30103	0.056000	0.16144	-0.291000	0.09656	GGC	.		0.498	LGALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318991.1	NM_006498		T	37966307	C	T	37966307	3	4	136	1	0	0	0	0	1	0	0	0	8763	739	26	2	40	2	LGALS2	22	37966307	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	8080849	37966307	13338259	90	12188											
PNPLA3	80339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	44333050	44333050	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccccggagtcggctgccttgGctgtgaggctggagggagat	5	8	18	10	2	0	2	0	1	0	1	1	5	0	4	3	6	1	3	3	6	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr22:44333050G>A	ENST00000216180.3	+	6	1050	c.877G>A	c.(877-879)Gct>Act	p.A293T	PNPLA3_ENST00000423180.2_Missense_Mutation_p.A289T	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	293					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				GGCTGCCTTGGCTGTGAGGCT	0.617																																					p.A293T		.											.	PNPLA3-90	0			c.G877A						.						105	84	91					22																	44333050		2203	4300	6503	SO:0001583	missense	80339	exon6			GCCTTGGCTGTGA		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"Patatin-like phospholipase domain containing"	18590	protein-coding gene	gene with protein product		609567	"chromosome 22 open reading frame 20", "adiponutrin"	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.877G>A	22.37:g.44333050G>A	ENSP00000216180:p.Ala293Thr	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	133	44	NM_025225	0	0	0	0	0	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	.	.	.	.	.	.	.	.	.	.	G	8.597	0.885868	0.17540	.	.	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.28895	1.59;1.59	3.7	-1.2	0.09554	.	.	.	.	.	T	0.13670	0.0331	N	0.22421	0.69	0.09310	N	1	B	0.30326	0.276	B	0.25614	0.062	T	0.25363	-1.0134	9	0.18276	T	0.48	-0.1582	1.9895	0.03443	0.1065:0.1711:0.3719:0.3504	.	293	Q9NST1	PLPL3_HUMAN	T	293;289	ENSP00000216180:A293T;ENSP00000397987:A289T	ENSP00000216180:A293T	A	+	1	0	PNPLA3	42664383	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.317000	0.08060	-0.232000	0.09811	0.462000	0.41574	GCT	.		0.617	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225		A	44333050	G	A	44333050	3	1	136	1	0	0	0	0	1	0	0	0	12192	1203	42	2	899	2	PNPLA3	22	44333050	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	6366743	44333050	6971516	91	12189											
TLR7	51284	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	12906681	12906681	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtccttgagtggccaacaaaCccgcaagctcacccatactt	11	8	7	15	1	1	1	1	1	0	0	2	1	2	1	4	1	4	2	4	1	4	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chrX:12906681C>A	ENST00000380659.3	+	3	3193	c.3054C>A	c.(3052-3054)aaC>aaA	p.N1018K		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	1018	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	GGCCAACAAACCCGCAAGCTC	0.498																																					p.N1018K													.	TLR7-564	0			c.C3054A						.						132	132	132					X																	12906681		2203	4300	6503	SO:0001583	missense	51284	exon3			AACAAACCCGCAA	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.3054C>A	X.37:g.12906681C>A	ENSP00000370034:p.Asn1018Lys	Somatic	73	1		WXS	Illumina HiSeq	Phase_I	59	38	NM_016562	0	0	4	4	0	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	37	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.709113	0.48517	.	.	ENSG00000196664	ENST00000380659	T	0.02552	4.25	5.72	3.77	0.43336	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.126973	0.49916	D	0.000130	T	0.12305	0.0299	M	0.82630	2.6	0.53005	D	0.999963	D	0.57257	0.979	P	0.62298	0.9	T	0.00128	-1.2018	10	0.87932	D	0	.	7.9627	0.30081	0.0:0.5072:0.0:0.4928	.	1018	Q9NYK1	TLR7_HUMAN	K	1018	ENSP00000370034:N1018K	ENSP00000370034:N1018K	N	+	3	2	TLR7	12816602	0.966000	0.33281	0.997000	0.53966	0.987000	0.75469	0.178000	0.16820	0.448000	0.26722	0.600000	0.82982	AAC	.		0.498	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		A	12906681	C	A	12906681	3	1	136	1	0	0	0	0	1	0	0	0	15988	506	18	4	3060	4	TLR7	23	12906681	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		12906681	142363879	92	12190											
FAM47A	158724	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	34148836	34148836	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccgacgagtcttgggaggCtccgagcggagactggacgt	7	7	17	10	5	1	1	0	0	1	1	3	7	3	3	2	4	1	1	2	4	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chrX:34148836C>T	ENST00000346193.3	-	1	1611	c.1560G>A	c.(1558-1560)gaG>gaA	p.E520E		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	520										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TCTTGGGAGGCTCCGAGCGGA	0.657																																					p.E520E													.	FAM47A-134	0			c.G1560A						.						29	31	30					X																	34148836		2188	4287	6475	SO:0001819	synonymous_variant	158724	exon1			GGGAGGCTCCGAG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1560G>A	X.37:g.34148836C>T		Somatic	23	1		WXS	Illumina HiSeq	Phase_I	79	52	NM_203408	0	0	0	0	0	A8K8I9|Q8TAA0	Silent	SNP	ENST00000346193.3	37	CCDS43926.1																																																																																			.		0.657	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34148836	C	T	34148836	2	4	136	1	0	0	0	0	0	0	0	1	5588	796	28	2		2	FAM47A	23	34148836	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	21242155	34148836	121121724	93	12191											
IL9R	3581	broad.mit.edu	37	chrX	155239822	155239824	+	In_Frame_Del	DEL	CAA	CAA	-																															agcagcagcagcagcagcagCaacaacaacaactactgtgc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chrX:155239822_155239824delCAA	ENST00000244174.5	+	9	1493_1495	c.1314_1316delCAA	c.(1312-1317)agcaac>agc	p.N442del	IL9R_ENST00000540897.1_3'UTR|IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000424344.3_In_Frame_Del_p.N421del	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	442	Poly-Asn.				cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)	p.N439S(1)		NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					gcagcagcagcaacaacaacaAC	0.635																																					p.438_439del													.	IL9R-40	1	Substitution - Missense(1)	kidney(1)	c.1314_1316del						.																																			SO:0001651	inframe_deletion	3581	exon9			CAGCAGCAACAAC	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1314_1316delCAA	X.37:g.155239831_155239833delCAA	ENSP00000244174:p.Asn442del	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	239	8	NM_002186	0	0	0	0	0	B9ZVT0|Q14634|Q8WWU1|Q96TF0	In_Frame_Del	DEL	ENST00000244174.5	37	CCDS14771.4																																																																																			.		0.635	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		-	155239824	CAA	-	155239822	7	5	136	1	0	1	0	1	0	0	0	0	7729	709	25	0	1348	0	IL9R	23	155239822	In_Frame_Del	DEL	CAA	TCGA-HE-A5NL-01A-11D-A26P-10	121090986	155239822	30738	94	12192											
BAI2	576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	32205741	32205741	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgtcccacttctccttgttTtccgcatccaccatgaagct	6	14	5	16	2	1	1	0	1	1	0	6	1	4	1	5	0	1	3	5	0	1	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr1:32205741T>G	ENST00000373658.3	-	13	2369	c.2028A>C	c.(2026-2028)gaA>gaC	p.E676D	BAI2_ENST00000398538.1_Missense_Mutation_p.E664D|BAI2_ENST00000398556.3_Missense_Mutation_p.E624D|BAI2_ENST00000257070.4_Missense_Mutation_p.E676D|BAI2_ENST00000398547.1_Missense_Mutation_p.E609D|BAI2_ENST00000527361.1_Missense_Mutation_p.E676D|BAI2_ENST00000440175.2_Missense_Mutation_p.E318D|BAI2_ENST00000398542.1_Missense_Mutation_p.E609D|BAI2_ENST00000373655.2_Missense_Mutation_p.E676D	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	676					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		TCTCCTTGTTTTCCGCATCCA	0.612																																					p.E676D		.											.	BAI2-526	0			c.A2028C						.						125	110	115					1																	32205741		2203	4300	6503	SO:0001583	missense	576	exon13			CTTGTTTTCCGCA	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"-", "GPCR / Class B : Orphans"	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.2028A>C	1.37:g.32205741T>G	ENSP00000362762:p.Glu676Asp	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	148	50	NM_001703	0	0	2	2	0	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	T	18.09	3.546810	0.65198	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125	T;T;T;T;T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89	4.62	1.63	0.23807	Domain of unknown function DUF3497 (1);	0.192067	0.26106	N	0.026319	T	0.16385	0.0394	L	0.54323	1.7	0.32584	N	0.528032	P;D;B;P;P;P	0.52996	0.804;0.957;0.307;0.815;0.804;0.815	P;P;P;P;P;P	0.53313	0.526;0.723;0.534;0.631;0.526;0.631	T	0.12268	-1.0554	10	0.46703	T	0.11	.	7.784	0.29080	0.0:0.6153:0.0:0.3847	.	676;664;318;609;676;676	O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;BAI2_HUMAN	D	624;609;676;676;609;676;676;318;664;614	ENSP00000381564:E624D;ENSP00000381555:E609D;ENSP00000362762:E676D;ENSP00000362759:E676D;ENSP00000381550:E609D;ENSP00000257070:E676D;ENSP00000435397:E676D;ENSP00000391071:E318D;ENSP00000381548:E664D;ENSP00000410921:E614D	ENSP00000257070:E676D	E	-	3	2	BAI2	31978328	1.000000	0.71417	0.975000	0.42487	0.765000	0.43378	0.796000	0.26986	0.124000	0.18369	-0.474000	0.04947	GAA	.		0.612	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		G	32205741	T	G	32205741	3	3	137	1	0	0	0	0	1	0	0	0	1300	1838	64	5	2813	5	BAI2	1	32205741	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10		32205741	217044880	1	12193											
PMF1	632	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	156209392	156209392	+	5'Flank	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgagggagcctgagtgAggagaccgccagccccagaa	10	4	16	11	1	0	5	0	3	0	2	0	7	0	6	5	2	3	1	5	2	1	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr1:156209392A>C	ENST00000368272.4	+	0	0				PMF1_ENST00000567140.1_Intron|PMF1-BGLAP_ENST00000368276.4_Intron|PMF1_ENST00000368279.3_3'UTR|PMF1_ENST00000565805.1_Intron|PMF1_ENST00000368273.4_Nonstop_Mutation_p.*208C|PMF1-BGLAP_ENST00000320139.5_Intron|PMF1_ENST00000368277.3_Nonstop_Mutation_p.*206C|PMF1-BGLAP_ENST00000490491.1_Intron	NM_199173.4	NP_954642.1	P02818	OSTCN_HUMAN	bone gamma-carboxyglutamate (gla) protein						bone development (GO:0060348)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cell aging (GO:0007569)|cellular response to growth factor stimulus (GO:0071363)|cellular response to vitamin D (GO:0071305)|odontogenesis (GO:0042476)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of osteoclast differentiation (GO:0045670)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to hydroxyisoflavone (GO:0033594)|response to mechanical stimulus (GO:0009612)|response to testosterone (GO:0033574)|response to vitamin D (GO:0033280)|response to vitamin K (GO:0032571)|response to zinc ion (GO:0010043)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|perikaryon (GO:0043204)|rough endoplasmic reticulum (GO:0005791)	calcium ion binding (GO:0005509)|hydroxyapatite binding (GO:0046848)|structural constituent of bone (GO:0008147)|structural molecule activity (GO:0005198)			large_intestine(3)|lung(1)|urinary_tract(1)	5	Hepatocellular(266;0.158)				Gallium nitrate(DB05260)|Menadione(DB00170)|Phylloquinone(DB01022)	AGCCTGAGTGAGGAGACCGCC	0.572																																					p.X208C		.											.	PMF1-44	0			c.A624C						.						81	85	84					1																	156209392		2203	4300	6503	SO:0001631	upstream_gene_variant	11243	exon5			TGAGTGAGGAGAC	X04143	CCDS1134.1	1q22	2014-05-13	2008-08-01		ENSG00000242252	ENSG00000242252			1043	protein-coding gene	gene with protein product	"osteocalcin"	112260				2785029, 2394711	Standard	NM_199173		Approved	OCN	uc001fnt.3	P02818	OTTHUMG00000014819		1.37:g.156209392A>C	Exception_encountered	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	121	42	NM_001199654	0	0	35	80	45	Q5TCK6	Missense_Mutation	SNP	ENST00000368272.4	37	CCDS1134.1	.	.	.	.	.	.	.	.	.	.	a	16.96	3.267332	0.59540	.	.	ENSG00000160783	ENST00000368273;ENST00000368277	.	.	.	5.07	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4393	0.27174	0.9034:0.0:0.0966:0.0	.	.	.	.	C	208;206	.	.	X	+	3	0	PMF1	154476016	0.998000	0.40836	0.883000	0.34634	0.969000	0.65631	2.898000	0.48672	1.073000	0.40885	0.529000	0.55759	TGA	.		0.572	BGLAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040867.2	NM_199173		C	156209392	A	C	156209392	1	2	137	0	1	0	0	0	0	0	0	0	12159	317	11	5		5	PMF1	1	156209392	5'Flank	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	124003651	156209392	93041229	2	12194											
OR2T3	343173	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	248637175	248637175	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgagcttccccttttgccAgtctaggaaaatcctgagtt	9	13	8	11	0	1	2	0	2	1	0	3	3	3	3	4	1	2	2	4	1	3	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr1:248637175A>C	ENST00000359594.2	+	1	549	c.524A>C	c.(523-525)cAg>cCg	p.Q175P		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCCTTTTGCCAGTCTAGGAAA	0.527																																					p.Q175P		.											.	OR2T3-69	0			c.A524C						.						42	39	40					1																	248637175		2162	4256	6418	SO:0001583	missense	343173	exon1			TTTGCCAGTCTAG		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"GPCR / Class A : Olfactory receptors"	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.524A>C	1.37:g.248637175A>C	ENSP00000352604:p.Gln175Pro	Somatic	467	1		WXS	Illumina HiSeq	Phase_I	430	119	NM_001005495	0	0	0	0	0	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	a	10.12	1.262159	0.23051	.	.	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	-2.34	0.06704	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.27629	0.0679	N	0.20807	0.61	0.09310	N	1	B	0.29909	0.261	B	0.40602	0.334	T	0.45396	-0.9264	9	0.66056	D	0.02	.	8.3181	0.32113	0.2131:0.0:0.7869:0.0	.	175	Q8NH03	OR2T3_HUMAN	P	175	ENSP00000352604:Q175P	ENSP00000352604:Q175P	Q	+	2	0	OR2T3	246703798	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.077000	0.11394	-1.019000	0.03358	0.156000	0.16432	CAG	.		0.527	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		C	248637175	A	C	248637175	3	2	137	1	0	0	0	0	1	0	0	0	11049	188	7	5	526	5	OR2T3	1	248637175	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	92427783	248637175	613446	3	12195											
MPHOSPH10	10199	broad.mit.edu	37	chr2	71376396	71376396	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaacagctgctgaaaaaaCagctacagacaagaaacgag	22	3	8	8	1	0	3	0	1	0	2	0	4	0	3	0	0	7	3	0	0	8	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr2:71376396C>T	ENST00000244230.2	+	10	2061	c.1709C>T	c.(1708-1710)aCa>aTa	p.T570I		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	570					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						GCTGAAAAAACAGCTACAGAC	0.333																																					p.T570I													.	MPHOSPH10-93	0			c.C1709T						.						38	35	36					2																	71376396		2201	4299	6500	SO:0001583	missense	10199	exon10			AAAAAACAGCTAC	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1709C>T	2.37:g.71376396C>T	ENSP00000244230:p.Thr570Ile	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	77	7	NM_005791	0	0	64	66	2	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831810	0.91036	.	.	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.12879	2.64;2.64	5.64	5.64	0.86602	.	0.097879	0.64402	D	0.000001	T	0.47078	0.1426	M	0.90870	3.155	0.58432	D	0.999998	D	0.69078	0.997	D	0.70716	0.97	T	0.54437	-0.8294	10	0.62326	D	0.03	.	17.585	0.87979	0.0:1.0:0.0:0.0	.	570	O00566	MPP10_HUMAN	I	570;430	ENSP00000244230:T570I;ENSP00000393034:T430I	ENSP00000244230:T570I	T	+	2	0	MPHOSPH10	71229904	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.007000	0.63984	2.837000	0.97791	0.655000	0.94253	ACA	.		0.333	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		T	71376396	C	T	71376396	3	4	137	1	0	0	0	0	1	0	0	0	9750	478	17	2	1747	2	MPHOSPH10	2	71376396	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		71376396	171822977	4	12196											
WDR54	84058	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74651108	74651108	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgagcctgcccagggacAggtgagtggacttcccctac	8	6	12	15	1	0	1	0	1	0	0	1	4	1	3	5	3	3	0	5	3	1	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr2:74651108A>G	ENST00000348227.4	+	6	621	c.533A>G	c.(532-534)cAg>cGg	p.Q178R	WDR54_ENST00000409791.1_Splice_Site_p.Q126R|WDR54_ENST00000461531.1_3'UTR	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54	178										breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						GCCCAGGGACAGGTGAGTGGA	0.597																																					p.Q178R													.	WDR54-90	0			c.A533G						.						72	67	69					2																	74651108		2203	4300	6503	SO:0001630	splice_region_variant	84058	exon6			AGGGACAGGTGAG	AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"WD repeat domain containing"	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951	ENST00000348227.4:c.534+1A>G	2.37:g.74651108A>G		Somatic	118	3		WXS	Illumina HiSeq	Phase_I	141	26	NM_032118	0	0	1	1	0	D6W5I3|Q53H85|Q86V45	Missense_Mutation	SNP	ENST00000348227.4	37	CCDS1940.1	.	.	.	.	.	.	.	.	.	.	A	8.262	0.811387	0.16537	.	.	ENSG00000005448	ENST00000409791;ENST00000426787;ENST00000348227	T;T	0.50277	0.75;0.75	5.23	4.05	0.47172	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.490280	0.21308	N	0.076697	T	0.28928	0.0718	N	0.22421	0.69	0.37494	D	0.916488	B	0.20671	0.047	B	0.17098	0.017	T	0.12293	-1.0553	10	0.23891	T	0.37	.	5.7368	0.18071	0.7423:0.169:0.0887:0.0	.	178	Q9H977	WDR54_HUMAN	R	126;160;178	ENSP00000387236:Q126R;ENSP00000006526:Q178R	ENSP00000006526:Q178R	Q	+	2	0	WDR54	74504616	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.121000	0.50438	0.795000	0.33922	0.528000	0.53228	CAG	.		0.597	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252213.1	NM_032118	Missense_Mutation	G	74651108	A	G	74651108	5	3	137	1	0	0	0	0	0	0	1	0	17339	202	7	3	551	3	WDR54	2	74651108	Splice_Site	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	3274712	74651108	168548265	5	12197											
INO80D	54891	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	206921631	206921631	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttcttcctctcttttttcggGataaagccaagtacctgcaa	9	15	6	11	1	2	0	0	0	2	0	5	1	3	1	3	1	3	2	3	1	5	7			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr2:206921631G>A	ENST00000403263.1	-	4	659	c.255C>T	c.(253-255)atC>atT	p.I85I		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	85					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						CTTTTTTCGGGATAAAGCCAA	0.408																																					p.I85I													.	INO80D-91	0			c.C255T						.						103	90	94					2																	206921631		1900	4118	6018	SO:0001819	synonymous_variant	54891	exon4			TTTCGGGATAAAG		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"INO80 complex subunits"	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.255C>T	2.37:g.206921631G>A		Somatic	113	1		WXS	Illumina HiSeq	Phase_I	134	61	NM_017759	0	0	0	0	0	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			.		0.408	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		A	206921631	G	A	206921631	2	1	137	1	0	0	0	0	0	0	0	1	7770	1164	41	2		2	INO80D	2	206921631	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	132270523	206921631	36277742	6	12198											
ERBB4	2066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	212248449	212248449	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccacaataggccggatcCgcccattctgtttataaaaa	12	10	7	12	2	1	0	0	0	1	0	2	1	2	1	4	2	1	1	4	2	6	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr2:212248449C>T	ENST00000342788.4	-	28	4128	c.3818G>A	c.(3817-3819)cGg>cAg	p.R1273Q	ERBB4_ENST00000436443.1_Missense_Mutation_p.R1257Q|ERBB4_ENST00000402597.1_Missense_Mutation_p.R1263Q	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1273					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	AGGCCGGATCCGCCCATTCTG	0.532										TSP Lung(8;0.080)																											p.R1273Q		.											.	ERBB4-1461	0			c.G3818A						.						89	91	91					2																	212248449		2203	4300	6503	SO:0001583	missense	2066	exon28			CGGATCCGCCCAT	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3818G>A	2.37:g.212248449C>T	ENSP00000342235:p.Arg1273Gln	Somatic	178	1		WXS	Illumina HiSeq	Phase_I	197	111	NM_005235	0	0	0	0	0	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328293	0.60743	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.75367	-0.92;-0.93;-0.92	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000001	T	0.72518	0.3470	L	0.44542	1.39	0.52501	D	0.999958	P;P;P;P	0.50710	0.938;0.873;0.938;0.897	P;P;P;B	0.44860	0.462;0.462;0.462;0.273	T	0.73151	-0.4073	10	0.42905	T	0.14	.	19.39	0.94576	0.0:1.0:0.0:0.0	.	1247;1263;1257;1273	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	Q	1273;1257;1263	ENSP00000342235:R1273Q;ENSP00000403204:R1257Q;ENSP00000385565:R1263Q	ENSP00000342235:R1273Q	R	-	2	0	ERBB4	211956694	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.584000	0.67490	2.812000	0.96745	0.557000	0.71058	CGG	.		0.532	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212248449	C	T	212248449	3	4	137	1	0	0	0	0	1	0	0	0	5222	652	23	1	112	1	ERBB4	2	212248449	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	5326818	212248449	30950924	7	12199											
CCDC66	285331	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56627039	56627039	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctttcagtgctgtgaaacaAgaactgcaaagaaaatggat	16	9	9	7	0	1	3	1	1	0	2	1	4	1	4	1	1	4	2	1	1	6	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr3:56627039A>C	ENST00000394672.3	+	8	1048	c.978A>C	c.(976-978)caA>caC	p.Q326H	CCDC66_ENST00000436465.2_Missense_Mutation_p.Q326H|CCDC66_ENST00000326595.7_Missense_Mutation_p.Q292H	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	326					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		CTGTGAAACAAGAACTGCAAA	0.333																																					p.Q326H		.											.	CCDC66-135	0			c.A978C						.						100	108	106					3																	56627039		2203	4300	6503	SO:0001583	missense	285331	exon8			GAAACAAGAACTG	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.978A>C	3.37:g.56627039A>C	ENSP00000378167:p.Gln326His	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	69	30	NM_001141947	0	0	0	0	0	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456082	0.63401	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.23950	1.88;1.88;1.88	5.6	0.516	0.17019	.	0.359209	0.26542	N	0.023798	T	0.19005	0.0456	L	0.55103	1.725	0.80722	D	1	B	0.17038	0.02	B	0.19391	0.025	T	0.06661	-1.0814	10	0.38643	T	0.18	-3.3314	2.9391	0.05824	0.4431:0.0:0.258:0.2989	.	326	A2RUB6	CCD66_HUMAN	H	326;292;326	ENSP00000378167:Q326H;ENSP00000326050:Q292H;ENSP00000404320:Q326H	ENSP00000326050:Q292H	Q	+	3	2	CCDC66	56602079	0.989000	0.36119	0.920000	0.36463	0.969000	0.65631	0.062000	0.14389	-0.134000	0.11516	0.533000	0.62120	CAA	.		0.333	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		C	56627039	A	C	56627039	3	2	137	1	0	0	0	0	1	0	0	0	2844	69	3	5	1008	5	CCDC66	3	56627039	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10		56627039	141395391	8	12200											
TRIM42	287015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	140401754	140401754	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgcaacgactgcctcaaGgccttccactcggatgtggc	7	9	11	14	2	1	0	1	0	0	0	3	2	2	1	3	3	3	1	3	3	2	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr3:140401754G>A	ENST00000286349.3	+	2	983	c.792G>A	c.(790-792)aaG>aaA	p.K264K		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	264						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ACTGCCTCAAGGCCTTCCACT	0.617																																					p.K264K		.											.	TRIM42-227	0			c.G792A						.						115	102	106					3																	140401754		2203	4300	6503	SO:0001819	synonymous_variant	287015	exon2			CCTCAAGGCCTTC	AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"Tripartite motif containing / Tripartite motif containing", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing", "RING-type (C3HC4) zinc fingers"	19014	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 40"		"tripartite motif-containing 42"				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.792G>A	3.37:g.140401754G>A		Somatic	277	0		WXS	Illumina HiSeq	Phase_I	248	102	NM_152616	0	0	0	0	0	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	37	CCDS3113.1																																																																																			.		0.617	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140401754	G	A	140401754	2	1	137	1	0	0	0	0	0	0	0	1	16550	991	35	2		2	TRIM42	3	140401754	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	83774715	140401754	57620676	9	12201											
PRKCI	5584	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	170013708	170013708	+	Frame_Shift_Del	DEL	A	A	-																															tatctttctagttattttggAaaaacaaattcgcataccac																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr3:170013708delA	ENST00000295797.4	+	15	1732	c.1427delA	c.(1426-1428)gaafs	p.E476fs		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	GTTATTTTGGAAAAACAAATT	0.289																																					p.E476fs		.											.	PRKCI-1378	0			c.1427delA						.						51	55	54					3																	170013708		2202	4298	6500	SO:0001589	frameshift_variant	5584	exon15			.		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1427delA	3.37:g.170013708delA	ENSP00000295797:p.Glu476fs	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	85	42	NM_002740	0	0	0	0	0	D3DNQ4|Q8WW06	Frame_Shift_Del	DEL	ENST00000295797.4	37	CCDS3212.2																																																																																			.		0.289	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		-	170013708	A	-	170013708	7	5	137	1	0	1	0	1	0	0	0	0	12543	246	9	0	1485	0	PRKCI	3	170013708	Frame_Shift_Del	DEL	A	TCGA-IA-A40U-01A-11D-A25F-10	29611954	170013708	28008722	10	12202											
CDKL2	8999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	76532433	76532433	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgggttgccacataatcaGtataaacctccccaggagct	12	9	8	12	1	1	0	1	0	0	0	3	1	2	1	4	2	3	3	4	2	4	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:76532433G>A	ENST00000429927.2	-	4	1179	c.476C>T	c.(475-477)aCt>aTt	p.T159I	CDKL2_ENST00000307465.4_Missense_Mutation_p.T159I	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	159	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CACATAATCAGTATAAACCTC	0.443																																					p.T159I		.											.	CDKL2-454	0			c.C476T						.						90	86	87					4																	76532433		2203	4300	6503	SO:0001583	missense	8999	exon4			TAATCAGTATAAA	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"Cyclin-dependent kinases"	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.476C>T	4.37:g.76532433G>A	ENSP00000412365:p.Thr159Ile	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	125	41	NM_003948	0	0	2	2	0	B2R695	Missense_Mutation	SNP	ENST00000429927.2	37	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	g	23.8	4.454370	0.84209	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	T;T	0.68025	-0.3;-0.3	4.72	4.72	0.59763	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.81945	0.4930	M	0.78344	2.41	0.50813	D	0.999894	D;D	0.89917	1.0;1.0	D;D	0.81914	0.988;0.995	D	0.84486	0.0608	9	0.87932	D	0	-11.7169	16.9749	0.86310	0.0:0.0:1.0:0.0	.	159;159	B4DH08;Q92772	.;CDKL2_HUMAN	I	159	ENSP00000412365:T159I;ENSP00000306340:T159I	ENSP00000306340:T159I	T	-	2	0	CDKL2	76751457	1.000000	0.71417	0.946000	0.38457	0.908000	0.53690	8.407000	0.90218	2.605000	0.88082	0.639000	0.83563	ACT	.		0.443	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		A	76532433	G	A	76532433	3	1	137	1	0	0	0	0	1	0	0	0	3160	1029	36	2	1037	2	CDKL2	4	76532433	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		76532433	114621843	11	12203											
SYNPO2	171024	hgsc.bcm.edu;bcgsc.ca	37	chr4	119947961	119947961	+	Missense_Mutation	SNP	A	A	C																															agttcccctagctgagaaccAaagaagtggtcccgactgtg																								rs70944826	byFrequency	TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:119947961A>C	ENST00000429713.2	+	3	619	c.437A>C	c.(436-438)cAa>cCa	p.Q146P	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.Q146P|SYNPO2_ENST00000434046.2_Missense_Mutation_p.Q146P	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	146						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GCTGAGAACCAAAGAAGTGGT	0.557																																					p.Q146P		.											.	SYNPO2-92	0			c.A437C						.						43	45	44					4																	119947961		2203	4300	6503	SO:0001583	missense	171024	exon3			AGAACCAAAGAAG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.437A>C	4.37:g.119947961A>C	ENSP00000395143:p.Gln146Pro	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	162	48	NM_001128934	0	0	0	0	0	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	.	.	.	.	.	.	.	.	.	.	A	8.210	0.800113	0.16397	.	.	ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046	T;T;T	0.08896	3.04;3.04;3.04	5.51	2.93	0.34026	.	0.395951	0.21221	N	0.078143	T	0.07999	0.0200	M	0.62723	1.935	0.09310	N	1	B;P;B;B	0.34757	0.165;0.467;0.165;0.165	B;B;B;B	0.28139	0.043;0.086;0.069;0.043	T	0.28459	-1.0043	10	0.59425	D	0.04	-2.8964	4.6069	0.12382	0.561:0.1597:0.2792:0.0	.	146;146;146;146	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.;.;.;SYNP2_HUMAN	P	146	ENSP00000306015:Q146P;ENSP00000395143:Q146P;ENSP00000390965:Q146P	ENSP00000306015:Q146P	Q	+	2	0	SYNPO2	120167409	0.019000	0.18553	0.400000	0.26346	0.322000	0.28314	1.517000	0.35867	0.792000	0.33850	0.455000	0.32223	CAA	.		0.557	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			C	119947961	A	C	119947961	3	2	137	1	0	0	0	0	1	0	0	0	15489	130	5	5	447	5	SYNPO2	4	119947961	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	43415528	119947961	71206315	12	12204	124	2									
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119947965	119947967	+	In_Frame_Del	DEL	AAG	AAG	-																															cccctagctgagaaccaaagAagtggtcccgactgtgcagg																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:119947965_119947967delAAG	ENST00000429713.2	+	3	623_625	c.441_443delAAG	c.(439-444)agaagt>agt	p.R147del	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_In_Frame_Del_p.R147del|SYNPO2_ENST00000434046.2_In_Frame_Del_p.R147del	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	147				Missing (in Ref. 3; AL832031). {ECO:0000305}.		actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGAACCAAAGAAGTGGTCCCGAC	0.552																																					p.147_148del		.											.	SYNPO2-92	0			c.441_443del						.																																			SO:0001651	inframe_deletion	171024	exon3			.	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.441_443delAAG	4.37:g.119947965_119947967delAAG	ENSP00000395143:p.Arg147del	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	165	32	NM_001128934	0	0	0	0	0	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	In_Frame_Del	DEL	ENST00000429713.2	37	CCDS47129.1																																																																																			.		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			-	119947967	AAG	-	119947965	7	5	137	1	0	1	0	1	0	0	0	0	15489	243	9	0	451	0	SYNPO2	4	119947965	In_Frame_Del	DEL	AAG	TCGA-IA-A40U-01A-11D-A25F-10	4	119947965	71206311	13	12205	124	2									
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	126240999	126240999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttttgaaatggtgcagccaGattttgagttgcatgccatc	9	14	10	8	0	0	3	0	2	0	1	1	3	0	3	2	1	4	3	2	1	1	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:126240999G>A	ENST00000394329.3	+	1	3446	c.3433G>A	c.(3433-3435)Gat>Aat	p.D1145N		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1145	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GGTGCAGCCAGATTTTGAGTT	0.453																																					p.D1145N		.											.	FAT4-108	0			c.G3433A						.						160	162	162					4																	126240999		1913	4132	6045	SO:0001583	missense	79633	exon1			CAGCCAGATTTTG	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"Cadherins / Cadherin-related"	23109	protein-coding gene	gene with protein product	"cadherin-related family member 11"	612411	"FAT tumor suppressor homolog 4 (Drosophila)"			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.3433G>A	4.37:g.126240999G>A	ENSP00000377862:p.Asp1145Asn	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	96	30	NM_024582	0	0	0	0	0	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592284	0.28357	.	.	ENSG00000196159	ENST00000394329	T	0.49432	0.78	4.99	4.14	0.48551	Cadherin (4);Cadherin-like (1);	0.223514	0.21270	N	0.077330	T	0.36580	0.0972	L	0.37507	1.11	0.80722	D	1	B	0.11235	0.004	B	0.10450	0.005	T	0.12400	-1.0549	10	0.13108	T	0.6	.	13.9069	0.63841	0.0744:0.0:0.9256:0.0	.	1145	Q6V0I7	FAT4_HUMAN	N	1145	ENSP00000377862:D1145N	ENSP00000377862:D1145N	D	+	1	0	FAT4	126460449	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.076000	0.71267	1.299000	0.44798	0.561000	0.74099	GAT	.		0.453	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126240999	G	A	126240999	3	1	137	1	0	0	0	0	1	0	0	0	5711	942	33	2	3435	2	FAT4	4	126240999	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	6293034	126240999	64913277	14	12206											
ADCY2	108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	7816984	7816984	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtttgttctcaggagccCgagcggcagtacatgcacat	8	11	12	10	2	1	0	1	0	1	0	2	2	1	1	1	2	4	5	1	2	1	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:7816984C>T	ENST00000338316.4	+	23	2978	c.2889C>T	c.(2887-2889)ccC>ccT	p.P963P	ADCY2_ENST00000537121.1_Silent_p.P783P	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	963					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CTCAGGAGCCCGAGCGGCAGT	0.502											OREG0016499	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P963P		.											.	ADCY2-97	0			c.C2889T						.						148	124	132					5																	7816984		2203	4300	6503	SO:0001819	synonymous_variant	108	exon23			GGAGCCCGAGCGG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"Adenylate cyclases"	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2889C>T	5.37:g.7816984C>T		Somatic	234	0	644	WXS	Illumina HiSeq	Phase_I	181	17	NM_020546	0	0	0	0	0	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			.		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7816984	C	T	7816984	2	4	137	1	0	0	0	0	0	0	0	1	294	639	23	1		1	ADCY2	5	7816984	Silent	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		7816984	173098276	15	12207											
NUP155	9631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	37307409	37307409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggaatgcacctttcttggaAggcctgaagtccaactatgt	10	12	10	9	0	1	1	0	1	1	0	2	3	2	3	3	3	2	1	3	3	5	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:37307409A>G	ENST00000231498.3	-	25	3096	c.2893T>C	c.(2893-2895)Ttc>Ctc	p.F965L	NUP155_ENST00000381843.2_Missense_Mutation_p.F906L|NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000513532.1_Missense_Mutation_p.F901L	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	965					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTTTCTTGGAAGGCCTGAAGT	0.358																																					p.F965L		.											.	NUP155-205	0			c.T2893C						.						112	104	106					5																	37307409		2203	4300	6503	SO:0001583	missense	9631	exon25			CTTGGAAGGCCTG	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"nucleoporin 155kD"			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.2893T>C	5.37:g.37307409A>G	ENSP00000231498:p.Phe965Leu	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	165	67	NM_153485	0	0	0	0	0	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	37	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.964993	0.74131	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	T;T;T	0.77750	-1.11;-1.1;-1.12	5.3	5.3	0.74995	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77778	0.4181	L	0.56124	1.755	0.58432	D	0.999999	P;P	0.45827	0.867;0.568	P;P	0.48063	0.565;0.534	T	0.74734	-0.3565	10	0.20046	T	0.44	-2.0962	15.2661	0.73663	1.0:0.0:0.0:0.0	.	901;965	E9PF10;O75694	.;NU155_HUMAN	L	965;906;927;901	ENSP00000231498:F965L;ENSP00000371265:F906L;ENSP00000422019:F901L	ENSP00000231498:F965L	F	-	1	0	NUP155	37343166	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.959000	0.93110	2.016000	0.59253	0.533000	0.62120	TTC	.		0.358	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		G	37307409	A	G	37307409	3	3	137	1	0	0	0	0	1	0	0	0	10782	72	3	3	1326	3	NUP155	5	37307409	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	29490425	37307409	143607851	16	12208											
PAM	5066	hgsc.bcm.edu;broad.mit.edu	37	chr5	102237063	102237063	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatcttttttttaatagtccGatacatacttctgcatgtct	10	19	4	8	1	3	0	0	0	3	0	4	1	4	0	1	0	3	1	1	0	5	8			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:102237063G>A	ENST00000438793.3	+	3	684	c.214G>A	c.(214-216)Gat>Aat	p.D72N	PAM_ENST00000379787.4_5'UTR|PAM_ENST00000348126.2_Missense_Mutation_p.D72N|PAM_ENST00000274392.9_Intron|PAM_ENST00000346918.2_Missense_Mutation_p.D72N|PAM_ENST00000455264.2_Missense_Mutation_p.D72N|PAM_ENST00000304400.7_Missense_Mutation_p.D72N	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	72	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TTAATAGTCCGATACATACTT	0.353																																					p.D72N		.											.	PAM-68	0			c.G214A						.						106	107	107					5																	102237063		2203	4300	6503	SO:0001583	missense	5066	exon3			TAGTCCGATACAT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.214G>A	5.37:g.102237063G>A	ENSP00000396493:p.Asp72Asn	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	63	4	NM_138822	0	0	0	0	0	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	37	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.396904	0.83120	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.39	5.39	0.77823	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.092891	0.64402	D	0.000001	T	0.69205	0.3085	M	0.86651	2.83	0.80722	D	1	D;D;P;D;D	0.76494	0.993;0.997;0.798;0.991;0.999	P;P;B;P;D	0.64237	0.824;0.826;0.236;0.73;0.923	T	0.74494	-0.3647	10	0.66056	D	0.02	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	72;72;72;72;72	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	N	72	ENSP00000396493:D72N;ENSP00000282992:D72N;ENSP00000314638:D72N;ENSP00000306100:D72N;ENSP00000403461:D72N	ENSP00000306100:D72N	D	+	1	0	PAM	102264962	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	6.709000	0.74665	2.668000	0.90789	0.650000	0.86243	GAT	.		0.353	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102237063	G	A	102237063	3	1	137	1	0	0	0	0	1	0	0	0	11438	1058	37	1	224	1	PAM	5	102237063	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	64929654	102237063	78678197	17	12209											
RNF14	9604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	141357939	141357939	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcgtggtcctgtttgcctgGatgcaatttcttaaggaaga	9	13	12	7	1	1	1	0	0	1	1	2	3	2	3	2	3	3	2	2	3	3	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:141357939G>T	ENST00000394520.2	+	5	687	c.378G>T	c.(376-378)tgG>tgT	p.W126C	AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000540015.1_Intron|RNF14_ENST00000502341.1_3'UTR|RNF14_ENST00000394514.2_5'UTR|RNF14_ENST00000394519.1_Missense_Mutation_p.W126C|RNF14_ENST00000347642.3_Missense_Mutation_p.W126C|RNF14_ENST00000394515.3_Intron|RNF14_ENST00000356143.1_Missense_Mutation_p.W126C	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	126	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		TGTTTGCCTGGATGCAATTTC	0.448																																					p.W126C		.											.	RNF14-226	0			c.G378T						.						126	113	117					5																	141357939		2203	4300	6503	SO:0001583	missense	9604	exon5			TGCCTGGATGCAA	AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"RING-type (C3HC4) zinc fingers"	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.378G>T	5.37:g.141357939G>T	ENSP00000378028:p.Trp126Cys	Somatic	306	0		WXS	Illumina HiSeq	Phase_I	248	70	NM_001201365	0	0	6	16	10	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	37	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419220	0.83559	.	.	ENSG00000013561	ENST00000511961;ENST00000506822;ENST00000356143;ENST00000394520;ENST00000347642;ENST00000506938;ENST00000507163;ENST00000394519	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.67	5.67	0.87782	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	T	0.72645	0.3486	M	0.90922	3.16	0.80722	D	1	D	0.59767	0.986	D	0.72338	0.977	T	0.74490	-0.3648	10	0.37606	T	0.19	.	19.8351	0.96655	0.0:0.0:1.0:0.0	.	126	Q9UBS8	RNF14_HUMAN	C	126	ENSP00000423420:W126C;ENSP00000423273:W126C;ENSP00000348462:W126C;ENSP00000378028:W126C;ENSP00000324956:W126C;ENSP00000420837:W126C;ENSP00000422527:W126C;ENSP00000378027:W126C	ENSP00000324956:W126C	W	+	3	0	RNF14	141338123	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.513000	0.98010	2.702000	0.92279	0.558000	0.71614	TGG	.		0.448	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2	NM_004290		T	141357939	G	T	141357939	3	4	137	1	0	0	0	0	1	0	0	0	13475	1183	41	4	388	4	RNF14	5	141357939	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	39120876	141357939	39557321	18	12210											
GEMIN5	25929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	154278113	154278113	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacaactcatcctctcctaCgatggcagccaactctgcag	11	8	7	15	1	3	1	1	0	2	1	5	2	4	1	3	1	5	2	3	1	3	1	rs144363013	byFrequency	TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:154278113C>T	ENST00000285873.7	-	23	3307	c.3232G>A	c.(3232-3234)Gta>Ata	p.V1078I		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	1078					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCTCTCCTACGATGGCAGCC	0.552													C|||	2	0.000399361	8e-04	0	5008	,	,		18001	0		0.001	False		,,,				2504	0				p.V1078I		.											.	GEMIN5-228	0			c.G3232A						.	C	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	95	86	89		3232	2.2	0	5	dbSNP_134	89	6,8594	5.0+/-18.6	0,6,4294	yes	missense	GEMIN5	NM_015465.3	29	0,9,6494	TT,TC,CC		0.0698,0.0681,0.0692	benign	1078/1509	154278113	9,12997	2203	4300	6503	SO:0001583	missense	25929	exon23			CTCCTACGATGGC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.3232G>A	5.37:g.154278113C>T	ENSP00000285873:p.Val1078Ile	Somatic	301	0		WXS	Illumina HiSeq	Phase_I	244	85	NM_015465	0	0	0	2	2	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	C	7.692	0.691317	0.15039	6.81E-4	6.98E-4	ENSG00000082516	ENST00000285873	T	0.69806	-0.43	5.91	2.19	0.27852	.	0.811288	0.11495	N	0.558347	T	0.47097	0.1427	L	0.36672	1.1	0.09310	N	1	P;P	0.36768	0.569;0.569	B;B	0.22152	0.038;0.038	T	0.13098	-1.0522	10	0.20519	T	0.43	-0.487	8.1531	0.31152	0.1114:0.6337:0.0:0.2549	.	1077;1078	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	I	1078	ENSP00000285873:V1078I	ENSP00000285873:V1078I	V	-	1	0	GEMIN5	154258306	0.247000	0.23920	0.000000	0.03702	0.428000	0.31595	0.291000	0.18994	0.135000	0.18707	-0.797000	0.03246	GTA	C|1.000;T|0.000		0.552	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			T	154278113	C	T	154278113	3	4	137	1	0	0	0	0	1	0	0	0	6351	536	19	1	1318	1	GEMIN5	5	154278113	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	12920174	154278113	26637147	19	12211											
TULP1	7287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	35471606	35471606	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgtcaaagaccgtgaagcGgttccccaggaggttggacc	9	8	14	10	2	1	2	1	1	0	1	2	4	2	4	4	4	1	3	4	4	2	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr6:35471606G>C	ENST00000229771.6	-	12	1211	c.1132C>G	c.(1132-1134)Cgc>Ggc	p.R378G	TULP1_ENST00000322263.4_Missense_Mutation_p.R325G	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	378			R -> H (in RP14).		dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						ACCGTGAAGCGGTTCCCCAGG	0.607																																					p.R378G	GBM(55;1027 1091 11115 23439)	.											.	TULP1-92	0			c.C1132G						.						44	39	41					6																	35471606		2203	4300	6503	SO:0001583	missense	7287	exon12			TGAAGCGGTTCCC	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.1132C>G	6.37:g.35471606G>C	ENSP00000229771:p.Arg378Gly	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	44	20	NM_003322	0	0	0	0	0	O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	37	CCDS4807.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398726	0.62177	.	.	ENSG00000112041	ENST00000229771;ENST00000322263	D;D	0.85861	-2.04;-2.04	4.95	4.08	0.47627	Tubby, C-terminal (4);	0.060704	0.64402	D	0.000009	D	0.82976	0.5154	L	0.60455	1.87	0.33292	D	0.563614	D;P	0.56035	0.974;0.913	P;P	0.58577	0.841;0.584	D	0.83863	0.0269	10	0.87932	D	0	-13.8748	7.85	0.29448	0.0803:0.0:0.6548:0.2649	.	325;378	O00294-2;O00294	.;TULP1_HUMAN	G	378;325	ENSP00000229771:R378G;ENSP00000319414:R325G	ENSP00000229771:R378G	R	-	1	0	TULP1	35579584	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.638000	0.67861	1.075000	0.40932	0.491000	0.48974	CGC	.		0.607	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			C	35471606	G	C	35471606	3	2	137	1	0	0	0	0	1	0	0	0	16806	1116	39	4	512	4	TULP1	6	35471606	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		35471606	135643461	20	12212											
COL12A1	1303	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	75884802	75884802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgtctccagccccagacgCatacaaggctgtcacagata	11	6	10	14	2	2	2	1	0	1	2	3	2	2	2	3	2	2	2	3	2	3	2	rs373259425		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr6:75884802C>T	ENST00000322507.8	-	13	2971	c.2662G>A	c.(2662-2664)Gcg>Acg	p.A888T	COL12A1_ENST00000416123.2_Missense_Mutation_p.A888T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.A888T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	888	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						GCCCCAGACGCATACAAGGCT	0.478																																					p.A888T													.	COL12A1-142	0			c.G2662A						.						209	208	208					6																	75884802		1993	4171	6164	SO:0001583	missense	1303	exon13			CAGACGCATACAA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2662G>A	6.37:g.75884802C>T	ENSP00000325146:p.Ala888Thr	Somatic	295	2		WXS	Illumina HiSeq	Phase_I	258	98	NM_004370	0	0	0	0	0	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.450680	0.26074	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.56941	0.43;0.43;0.43	5.94	5.06	0.68205	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.273480	0.31847	N	0.006967	T	0.22322	0.0538	L	0.37630	1.12	0.32335	N	0.560601	B	0.22080	0.064	B	0.23275	0.045	T	0.09250	-1.0683	10	0.23891	T	0.37	.	9.8609	0.41114	0.1406:0.7907:0.0:0.0688	.	888	Q99715	COCA1_HUMAN	T	888	ENSP00000325146:A888T;ENSP00000412864:A888T;ENSP00000421216:A888T	ENSP00000325146:A888T	A	-	1	0	COL12A1	75941522	1.000000	0.71417	0.997000	0.53966	0.907000	0.53573	1.159000	0.31749	1.499000	0.48617	-0.319000	0.08680	GCG	.		0.478	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75884802	C	T	75884802	3	4	137	1	0	0	0	0	1	0	0	0	3675	710	25	2	6745	2	COL12A1	6	75884802	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	40413196	75884802	95230265	21	12213											
CNKSR3	154043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	154732110	154732110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttttgtgggcagaatgtTggtttccaccgagtacccag	8	13	11	9	1	0	1	0	0	0	1	1	2	1	1	3	2	1	4	3	2	2	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr6:154732110T>C	ENST00000607772.1	-	11	1781	c.1237A>G	c.(1237-1239)Aac>Gac	p.N413D	CNKSR3_ENST00000479339.1_Missense_Mutation_p.N333D|CNKSR3_ENST00000433165.2_Missense_Mutation_p.N238D	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	413	DUF1170.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		GGCAGAATGTTGGTTTCCACC	0.502																																					p.N413D		.											.	CNKSR3-26	0			c.A1237G						.						186	176	179					6																	154732110		2203	4300	6503	SO:0001583	missense	154043	exon11			GAATGTTGGTTTC	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.1237A>G	6.37:g.154732110T>C	ENSP00000475915:p.Asn413Asp	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	163	60	NM_173515	0	0	31	51	20	Q5SGD5|Q96N65	Missense_Mutation	SNP	ENST00000607772.1	37	CCDS5246.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.416814	0.42918	.	.	ENSG00000153721	ENST00000367209;ENST00000367213;ENST00000433165;ENST00000479339;ENST00000424998	T;T;T	0.46063	1.48;0.88;0.89	5.82	5.82	0.92795	Connector enhancer of kinase suppressor of ras 2 (1);	0.275495	0.38326	N	0.001731	T	0.26846	0.0657	L	0.59436	1.845	0.20764	N	0.999854	B	0.27625	0.183	B	0.31495	0.131	T	0.17349	-1.0372	10	0.59425	D	0.04	.	12.6716	0.56870	0.0:0.0:0.1375:0.8625	.	413	Q6P9H4	CNKR3_HUMAN	D	188;413;238;333;175	ENSP00000356182:N413D;ENSP00000414185:N238D;ENSP00000418975:N333D	ENSP00000356178:N188D	N	-	1	0	CNKSR3	154773802	0.999000	0.42202	0.966000	0.40874	0.822000	0.46500	3.065000	0.49994	2.222000	0.72286	0.533000	0.62120	AAC	.		0.502	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		C	154732110	T	C	154732110	3	2	137	1	0	0	0	0	1	0	0	0	3614	1812	63	3	442	3	CNKSR3	6	154732110	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10	78847308	154732110	16382957	22	12214											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116397543	116397543	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcatttcaatatgtccataAttatttcaaatggccacggg	13	13	7	8	1	2	0	2	0	0	0	3	0	3	0	2	2	1	1	2	2	5	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr7:116397543A>C	ENST00000318493.6	+	7	2102	c.1915A>C	c.(1915-1917)Att>Ctt	p.I639L	MET_ENST00000436117.2_Missense_Mutation_p.I639L|MET_ENST00000397752.3_Missense_Mutation_p.I639L			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TATGTCCATAATTATTTCAAA	0.323			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.I639L		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	0			c.A1915C						.						88	86	86					7																	116397543		1844	4100	5944	SO:0001583	missense	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCATAATTATTT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1915A>C	7.37:g.116397543A>C	ENSP00000317272:p.Ile639Leu	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	86	40	NM_000245	0	0	6	10	4	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.917098	0.33815	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.58652	0.32;0.32;0.32	5.4	-0.479	0.12089	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.634640	0.17750	N	0.163272	T	0.36991	0.0987	L	0.33485	1.01	0.58432	D	0.999999	B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.10450	0.001;0.002;0.004;0.005;0.004;0.004;0.001;0.004	T	0.07731	-1.0757	10	0.33141	T	0.24	.	2.8283	0.05491	0.6225:0.12:0.1419:0.1157	.	639;639;639;639;611;639;639;639	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;P08581-2;P08581	.;.;.;.;.;.;.;MET_HUMAN	L	639	ENSP00000380860:I639L;ENSP00000317272:I639L;ENSP00000410980:I639L	ENSP00000317272:I639L	I	+	1	0	MET	116184779	0.099000	0.21834	0.845000	0.33349	0.858000	0.48976	0.480000	0.22244	0.057000	0.16193	-0.334000	0.08254	ATT	.		0.323	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116397543	A	C	116397543	3	2	137	1	0	0	0	0	1	0	0	0	9510	101	4	5	1937	5	MET	7	116397543	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10		116397543	42741120	23	12215											
COPG2	26958	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	130337745	130337745	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacatcctcagagatggtaGccatttctttgatggtaagg	10	13	10	8	0	3	2	2	1	1	1	4	3	4	2	2	3	1	2	2	3	2	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr7:130337745G>C	ENST00000445977.2	-	5	376	c.287C>G	c.(286-288)gCt>gGt	p.A96G				Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2	96					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)	structural molecule activity (GO:0005198)			large_intestine(1)	1	Melanoma(18;0.0435)					AGAGATGGTAGCCATTTCTTT	0.318																																					.													.	.	0			.						.						85	79	81					7																	130337745		1852	4093	5945	SO:0001583	missense	26958	.			ATGGTAGCCATTT	AF157833	CCDS75662.1	7q32	2010-06-22			ENSG00000158623	ENSG00000158623			2237	protein-coding gene	gene with protein product	"coat protein, nonclathrin, gamma-2-cop"	604355				10556286, 10995575	Standard	NM_001290033		Approved	2-COP	uc003vqh.1	Q9UBF2	OTTHUMG00000155364	ENST00000445977.2:c.287C>G	7.37:g.130337745G>C	ENSP00000393912:p.Ala96Gly	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	92	22	.	0	0	1	1	0	A6NH74|Q2NLA0|Q54AC3|Q8WVW8	Missense_Mutation	SNP	ENST00000445977.2	37		.	.	.	.	.	.	.	.	.	.	G	28.6	4.934045	0.92458	.	.	ENSG00000158623	ENST00000445977;ENST00000330992	T;T	0.15487	2.42;2.42	5.11	5.11	0.69529	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	T	0.39627	0.1085	M	0.78049	2.395	0.80722	D	1	P	0.45902	0.868	P	0.56216	0.794	T	0.24621	-1.0155	10	0.72032	D	0.01	.	16.3759	0.83392	0.0:0.0:1.0:0.0	.	96	Q9UBF2	COPG2_HUMAN	G	96	ENSP00000393912:A96G;ENSP00000331218:A96G	ENSP00000331218:A96G	A	-	2	0	COPG2	129988285	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.255000	0.89846	2.517000	0.84864	0.585000	0.79938	GCT	.		0.318	COPG2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_012133		C	130337745	G	C	130337745	3	2	137	1	0	0	0	0	1	0	0	0	3738	971	34	4	955	4	COPG2	7	130337745	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	13940202	130337745	28800918	24	12216											
MFHAS1	9258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	8643536	8643536	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacagccacaaacgtcacTggtttctgtgcttttcacca	9	12	6	14	1	3	0	2	0	1	0	4	0	4	0	3	1	3	2	3	1	1	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr8:8643536T>C	ENST00000276282.6	-	3	3741	c.3155A>G	c.(3154-3156)cAg>cGg	p.Q1052R	MFHAS1_ENST00000520091.1_5'UTR	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	1052										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CAAACGTCACTGGTTTCTGTG	0.473																																					p.Q1052R	Melanoma(103;1201 2045 17515 28966)	.											.	MFHAS1-90	0			c.A3155G						.						192	159	170					8																	8643536		2203	4300	6503	SO:0001583	missense	9258	exon3			CGTCACTGGTTTC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.3155A>G	8.37:g.8643536T>C	ENSP00000276282:p.Gln1052Arg	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	135	13	NM_004225	0	0	1	1	0	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.679279	0.68042	.	.	ENSG00000147324	ENST00000276282	T	0.35236	1.32	5.61	5.61	0.85477	.	0.000000	0.42420	D	0.000702	T	0.36580	0.0972	N	0.08118	0	0.31388	N	0.678181	D	0.54601	0.967	P	0.62382	0.901	T	0.47749	-0.9093	10	0.87932	D	0	.	12.4865	0.55877	0.0:0.0:0.0:1.0	.	1052	Q9Y4C4	MFHA1_HUMAN	R	1052	ENSP00000276282:Q1052R	ENSP00000276282:Q1052R	Q	-	2	0	MFHAS1	8680946	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	2.564000	0.45931	2.266000	0.75297	0.533000	0.62120	CAG	.		0.473	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8643536	T	C	8643536	3	2	137	1	0	0	0	0	1	0	0	0	9546	1580	55	3	7	3	MFHAS1	8	8643536	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10		8643536	137720486	25	12217											
C9orf89	84270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	95874554	95874555	+	Missense_Mutation	DNP	TG	TG	GT																															tgtgggactggccctgctccTgtactgctatccgccaggtg																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr9:95874554_95874555TG>GT	ENST00000375464.2	+	5	547_548	c.419_420TG>GT	c.(418-420)cTG>cGT	p.L140R	C9orf89_ENST00000488630.1_3'UTR	NM_032310.3	NP_115686.3	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89	145					negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	CARD domain binding (GO:0050700)			endometrium(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						GCCCTGCTCCTGTACTGCTATC	0.668																																					p.L140R		.											.	C9orf89-90	0			c.G420T						.																																			SO:0001583	missense	84270	exon5			GCTCCTGTACTGC	AK057716	CCDS6702.2	9q22.32	2012-03-16			ENSG00000165233	ENSG00000165233			28148	protein-coding gene	gene with protein product	"Bcl10-interacting protein with CARD"					12477932	Standard	XM_005252273		Approved	MGC11115, bA370F5.1, BinCARD	uc004atd.3	Q96LW7	OTTHUMG00000020243	Exception_encountered	9.37:g.95874554_95874555delinsGT	ENSP00000364613:p.Leu140Arg	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	56	23	NM_032310	0	0	0	0	0	Q5BJH8|Q9BSY2	Missense_Mutation	DNP	ENST00000375464.2	37	CCDS6702.2																																																																																			.		0.668	C9orf89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053128.1	NM_032310		GT	95874555	TG	GT	95874554	3	3	137	1	0	0	0	0	1	0	0	0	2509	1580	55	5	437	5	C9orf89	9	95874554	Missense_Mutation	DNP	TG	TCGA-IA-A40U-01A-11D-A25F-10		95874554	45338877	26	12218											
CCDC3	83643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	13043327	13043327	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccccacgcctggtcgcacaGcatctcgacctcggccgagt	6	6	11	18	5	1	0	0	0	1	0	4	2	1	0	5	2	1	2	5	2	0	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:13043327G>T	ENST00000378825.3	-	1	370	c.244C>A	c.(244-246)Ctg>Atg	p.L82M	CCDC3_ENST00000378839.1_Intron	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	82						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			TGGTCGCACAGCATCTCGACC	0.706																																					p.L82M		.											.	CCDC3-91	0			c.C244A						.						14	16	15					10																	13043327		2194	4293	6487	SO:0001583	missense	83643	exon1			CGCACAGCATCTC	BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.244C>A	10.37:g.13043327G>T	ENSP00000368102:p.Leu82Met	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	70	27	NM_031455	0	0	1	1	0	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029083	0.75504	.	.	ENSG00000151468	ENST00000378825	.	.	.	4.55	3.65	0.41850	.	0.000000	0.64402	D	0.000001	T	0.75788	0.3897	M	0.74258	2.255	0.50813	D	0.999899	D	0.76494	0.999	D	0.71656	0.974	T	0.76623	-0.2891	9	0.54805	T	0.06	-8.5593	11.5639	0.50794	0.0889:0.0:0.9111:0.0	.	82	Q9BQI4	CCDC3_HUMAN	M	82	.	ENSP00000368102:L82M	L	-	1	2	CCDC3	13083333	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.135000	0.71696	0.905000	0.36596	-0.224000	0.12420	CTG	.		0.706	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		T	13043327	G	T	13043327	3	4	137	1	0	0	0	0	1	0	0	0	2810	962	34	4	580	4	CCDC3	10	13043327	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		13043327	122491420	27	12219											
C10orf72	196740	hgsc.bcm.edu;bcgsc.ca	37	chr10	50311832	50311835	+	Intron	DEL	GGGC	GGGC	-																															atggttaagtctgcggtgaaGggcaaagagtgaggtagtat																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	GGGC	GGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:50311832_50311835delGGGC	ENST00000332853.4	-	2	481				VSTM4_ENST00000298454.3_Frame_Shift_Del_p.LP176fs	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						CTGCGGTGAAGGGCAAAGAGTGAG	0.49																																					p.176_177del		.											.	VSTM4-154	0			c.528_531del						.																																			SO:0001627	intron_variant	196740	exon3			.	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.457+3803GCCC>-	10.37:g.50311832_50311835delGGGC		Somatic	201	0		WXS	Illumina HiSeq	Phase_I	130	34	NM_144984	0	0	0	0	0	B4DNI6|Q96MX7	Frame_Shift_Del	DEL	ENST00000332853.4	37	CCDS31198.1																																																																																			.		0.49	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		-	50311835	GGGC	-	50311832	6	5	137	0	1	1	0	1	0	0	0	0	1619	987	35	0		0	C10orf72	10	50311832	Intron	DEL	GGGC	TCGA-IA-A40U-01A-11D-A25F-10	37268505	50311832	85222915	28	12220											
C10orf76	79591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	103789497	103789497	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctcgaatgagtgcgcaCagggtctgcagaaatgagag	12	7	13	9	2	1	3	0	2	1	2	3	5	2	3	1	1	2	2	1	1	2	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:103789497C>T	ENST00000370033.4	-	5	431	c.312G>A	c.(310-312)ctG>ctA	p.L104L	C10orf76_ENST00000311122.5_Silent_p.L104L	NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	104						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		TGAGTGCGCACAGGGTCTGCA	0.473																																					p.L104L		.											.	C10orf76-90	0			c.G312A						.						112	104	107					10																	103789497		1928	4137	6065	SO:0001819	synonymous_variant	79591	exon5			TGCGCACAGGGTC	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.312G>A	10.37:g.103789497C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	46	10	NM_024541	0	0	0	0	0	Q2TB87|Q9H8Z9	Silent	SNP	ENST00000370033.4	37	CCDS41563.1																																																																																			.		0.473	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050007.1	NM_024541		T	103789497	C	T	103789497	2	4	137	1	0	0	0	0	0	0	0	1	1620	465	17	2		2	C10orf76	10	103789497	Silent	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	53477665	103789497	31745250	29	12221											
PSD	5662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104173630	104173630	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcctctgcctcctcctcCtcccctctctgtgtccaagg	2	12	7	20	0	2	0	0	0	2	0	8	0	7	0	8	2	1	0	8	2	1	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:104173630C>A	ENST00000020673.5	-	5	1975	c.1449G>T	c.(1447-1449)gaG>gaT	p.E483D	PSD_ENST00000406432.1_Missense_Mutation_p.E483D|PSD_ENST00000492902.2_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	483	Poly-Glu.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CCTCCTCCTCCTCCCCTCTCT	0.677																																					p.E483D		.											.	PSD-272	0			c.G1449T						.						30	34	33					10																	104173630		2203	4300	6503	SO:0001583	missense	5662	exon6			CTCCTCCTCCCCT	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1449G>T	10.37:g.104173630C>A	ENSP00000020673:p.Glu483Asp	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	147	50	NM_001270965	0	0	0	0	0	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	37	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.379979	0.42207	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.19806	2.12;2.12	4.65	0.0368	0.14193	.	0.480088	0.20167	N	0.097814	T	0.11067	0.0270	N	0.24115	0.695	0.20638	N	0.999877	B	0.16396	0.017	B	0.09377	0.004	T	0.35895	-0.9770	10	0.13853	T	0.58	.	9.4906	0.38958	0.0:0.5847:0.0:0.4153	.	483	A5PKW4	PSD1_HUMAN	D	483;386;483	ENSP00000020673:E483D;ENSP00000384830:E483D	ENSP00000020673:E483D	E	-	3	2	PSD	104163620	0.473000	0.25878	0.998000	0.56505	0.989000	0.77384	-0.538000	0.06120	0.064000	0.16427	0.456000	0.33151	GAG	.		0.677	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			A	104173630	C	A	104173630	3	1	137	1	0	0	0	0	1	0	0	0	12675	680	24	4	1677	4	PSD	10	104173630	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	384133	104173630	31361117	30	12222											
LRDD	79751	ucsc.edu	37	chr11	799396	799396	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcccatgcgtcggatgctgtCctggtacttgcggcggccga	4	9	15	13	5	0	0	0	0	0	0	2	2	1	1	3	4	4	2	3	4	1	2	rs370316550		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:799396C>T	ENST00000531214.1	-	0	0				PIDD_ENST00000411829.2_Missense_Mutation_p.D865N|PIDD_ENST00000347755.5_Missense_Mutation_p.D882N	NM_001191060.1	NP_001177989.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGGATGCTGTCCTGGTACTTG	0.701																																					p.D882N	Colon(93;848 1468 3270 23355 49636)												.	PIDD-205	0			c.G2644A						.						59	62	61					11																	799396		2203	4294	6497	SO:0001631	upstream_gene_variant	55367	exon16			TGCTGTCCTGGTA	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"Solute carriers"	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		11.37:g.799396C>T	Exception_encountered	Somatic	64	0		WXS	Illumina HiSeq		47	4	NM_145886	0	0	13	13	0	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000531214.1	37	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.809838	0.50421	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	D;D	0.93076	-3.16;-3.16	5.04	5.04	0.67666	DEATH-like (1);	0.275088	0.34411	N	0.003990	D	0.87370	0.6160	N	0.24115	0.695	0.34027	D	0.653334	P;B;P	0.38504	0.561;0.302;0.634	B;B;B	0.33620	0.109;0.167;0.167	D	0.92063	0.5658	10	0.66056	D	0.02	.	14.0391	0.64663	0.0:0.8486:0.1514:0.0	.	882;725;865	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	N	865;882	ENSP00000416801:D865N;ENSP00000337797:D882N	ENSP00000337797:D882N	D	-	1	0	PIDD	789396	0.995000	0.38212	0.925000	0.36789	0.081000	0.17604	4.915000	0.63355	2.338000	0.79540	0.448000	0.29417	GAC	.		0.701	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1			T	799396	C	T	799396	1	4	137	0	1	0	0	0	0	0	0	0	8961	855	30	2		2	LRDD	11	799396	5'Flank	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		799396	134207120	31	12223											
PSMA1	5682	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	14536021	14536021	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaatctggaatccaaacactCctgacgcataaaattactaa	18	9	4	10	1	1	1	0	1	1	0	3	2	3	2	2	1	2	1	2	1	7	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:14536021C>A	ENST00000396394.2	-	5	667	c.271G>T	c.(271-273)Gag>Tag	p.E91*	PSMA1_ENST00000418988.2_Nonsense_Mutation_p.E97*|PSMA1_ENST00000396393.1_Nonsense_Mutation_p.E91*|PSMA1_ENST00000530457.1_Nonsense_Mutation_p.E66*|PSMA1_ENST00000419365.2_Nonsense_Mutation_p.E91*|PSMA1_ENST00000555531.1_Nonsense_Mutation_p.E91*	NM_002786.3	NP_002777.1	P25786	PSA1_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 1	91					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	3						TCCAAACACTCCTGACGCATA	0.308																																					p.E97X													.	PSMA1-92	0			c.G289T						.						43	41	42					11																	14536021		2200	4294	6494	SO:0001587	stop_gained	5682	exon6			AACACTCCTGACG	X61969	CCDS7816.1, CCDS31431.1	11p15.1	2005-10-10			ENSG00000129084	ENSG00000129084		"Proteasome (prosome, macropain) subunits"	9530	protein-coding gene	gene with protein product		602854				1398136, 2025653	Standard	NM_148976		Approved	HC2, NU, PROS30, MGC14542, MGC14575, MGC14751, MGC1667, MGC21459, MGC22853, MGC23915	uc001mlk.3	P25786	OTTHUMG00000165825	ENST00000396394.2:c.271G>T	11.37:g.14536021C>A	ENSP00000379676:p.Glu91*	Somatic	100	1		WXS	Illumina HiSeq	Phase_I	113	41	NM_148976	0	0	69	79	10	A8K400|Q53YE8|Q9BRV9	Nonsense_Mutation	SNP	ENST00000396394.2	37	CCDS7816.1	.	.	.	.	.	.	.	.	.	.	C	39	7.563044	0.98361	.	.	ENSG00000129084	ENST00000419365;ENST00000396394;ENST00000396393;ENST00000530457;ENST00000418988	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-21.0217	19.5544	0.95335	0.0:1.0:0.0:0.0	.	.	.	.	X	91;91;91;66;97	.	ENSP00000379675:E91X	E	-	1	0	PSMA1	14492597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.018000	0.76406	2.623000	0.88846	0.591000	0.81541	GAG	.		0.308	PSMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386421.3	NM_002786		A	14536021	C	A	14536021	4	1	137	1	0	0	0	0	0	1	0	0	12695	864	30	4	594	4	PSMA1	11	14536021	Nonsense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	13736625	14536021	120470495	32	12224											
INPPL1	3636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	71944164	71944164	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cacctaccgctatgagcgggGttcccgggacacatatgcct	8	8	11	14	3	0	1	0	1	0	0	1	2	1	2	4	3	3	2	4	3	3	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:71944164G>T	ENST00000298229.2	+	17	2201	c.1997G>T	c.(1996-1998)gGt>gTt	p.G666V	INPPL1_ENST00000541756.1_Missense_Mutation_p.G424V|INPPL1_ENST00000538751.1_Missense_Mutation_p.G424V	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	666					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TATGAGCGGGGTTCCCGGGAC	0.602																																					p.G666V		.											.	INPPL1-660	0			c.G1997T						.						49	48	48					11																	71944164		2200	4293	6493	SO:0001583	missense	3636	exon17			AGCGGGGTTCCCG	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"Sterile alpha motif (SAM) domain containing", "SH2 domain containing"	6080	protein-coding gene	gene with protein product	"51C protein"	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.1997G>T	11.37:g.71944164G>T	ENSP00000298229:p.Gly666Val	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	158	66	NM_001567	0	0	5	10	5	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	37	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	g	18.33	3.599890	0.66332	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751	D;D;D	0.95656	-3.77;-3.77;-3.77	5.66	5.66	0.87406	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.230735	0.44688	D	0.000437	D	0.98457	0.9486	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.98338	1.0537	10	0.27082	T	0.32	.	17.588	0.87988	0.0:0.0:1.0:0.0	.	666	O15357	SHIP2_HUMAN	V	666;424;424	ENSP00000298229:G666V;ENSP00000446360:G424V;ENSP00000444619:G424V	ENSP00000298229:G666V	G	+	2	0	INPPL1	71621812	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.393000	0.97256	2.830000	0.97506	0.655000	0.94253	GGT	.		0.602	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71944164	G	T	71944164	3	4	137	1	0	0	0	0	1	0	0	0	7782	1261	44	4	2063	4	INPPL1	11	71944164	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	57408143	71944164	63062352	33	12225											
MMP27	64066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102563689	102563689	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtactggaaagcagcaTcaacacggatactgattcca	13	10	8	10	1	1	1	1	1	0	0	2	3	2	3	1	2	5	3	1	2	4	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:102563689T>G	ENST00000260229.4	-	9	1368	c.1277A>C	c.(1276-1278)gAt>gCt	p.D426A		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	426					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GAAAGCAGCATCAACACGGAT	0.413																																					p.D426A		.											.	MMP27-229	0			c.A1277C						.						215	201	206					11																	102563689		2203	4299	6502	SO:0001583	missense	64066	exon9			GCAGCATCAACAC	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"matrix metalloprotease 27"		"matrix metalloproteinase 27"			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1277A>C	11.37:g.102563689T>G	ENSP00000260229:p.Asp426Ala	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	157	48	NM_022122	0	0	0	0	0	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756835	0.49362	.	.	ENSG00000137675	ENST00000260229	T	0.20598	2.06	5.67	4.55	0.56014	Hemopexin/matrixin (2);	0.204141	0.33813	N	0.004526	T	0.50497	0.1619	M	0.90483	3.12	0.53688	D	0.999973	D	0.76494	0.999	D	0.67900	0.954	T	0.58578	-0.7612	10	0.72032	D	0.01	.	11.5591	0.50766	0.0:0.0698:0.0:0.9302	.	426	Q9H306	MMP27_HUMAN	A	426	ENSP00000260229:D426A	ENSP00000260229:D426A	D	-	2	0	MMP27	102068899	0.445000	0.25657	0.431000	0.26735	0.430000	0.31655	2.306000	0.43673	0.996000	0.38943	0.529000	0.55759	GAT	.		0.413	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		G	102563689	T	G	102563689	3	3	137	1	0	0	0	0	1	0	0	0	9689	1435	50	5	272	5	MMP27	11	102563689	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10	30619525	102563689	32442827	34	12226											
PAFAH1B2	5049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117038364	117038364	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaacccctgcatgaactgatCatgcagttgttggaggaaac	13	9	10	9	0	1	2	1	2	0	0	1	4	1	4	2	2	5	4	2	2	3	2	rs569223304		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:117038364C>G	ENST00000527958.1	+	6	798	c.639C>G	c.(637-639)atC>atG	p.I213M	PAFAH1B2_ENST00000419197.2_Intron|PAFAH1B2_ENST00000529887.2_Intron|PAFAH1B2_ENST00000530272.1_Intron|PAFAH1B2_ENST00000526888.1_Intron	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	213					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		ATGAACTGATCATGCAGTTGT	0.488			T	IGH@	MLCLS																																p.I213M		.		Dom	yes		11	11q23	5049	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"		L	.	PAFAH1B2-204	0			c.C639G						.						82	68	73					11																	117038364		2201	4296	6497	SO:0001583	missense	5049	exon6			ACTGATCATGCAG	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"PAF-AH1b alpha 2 subunit"	602508	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.639C>G	11.37:g.117038364C>G	ENSP00000435289:p.Ile213Met	Somatic	340	0		WXS	Illumina HiSeq	Phase_I	330	137	NM_002572	0	0	23	27	4	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Missense_Mutation	SNP	ENST00000527958.1	37	CCDS8380.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.458076	0.63401	.	.	ENSG00000168092	ENST00000527958;ENST00000304808	T;T	0.56776	0.62;0.44	5.49	5.49	0.81192	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	0.053461	0.85682	D	0.000000	T	0.64360	0.2591	L	0.54323	1.7	0.80722	D	1	P	0.40931	0.733	P	0.51193	0.662	T	0.65685	-0.6108	10	0.72032	D	0.01	-9.1136	19.3671	0.94468	0.0:1.0:0.0:0.0	.	213	P68402	PA1B2_HUMAN	M	213;159	ENSP00000435289:I213M;ENSP00000304006:I159M	ENSP00000304006:I159M	I	+	3	3	PAFAH1B2	116543574	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.100000	0.50275	2.593000	0.87608	0.563000	0.77884	ATC	.		0.488	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572		G	117038364	C	G	117038364	3	3	137	1	0	0	0	0	1	0	0	0	11411	816	29	4	657	4	PAFAH1B2	11	117038364	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	14474675	117038364	17968152	35	12227											
RECQL	5965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	21623145	21623145	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atatcaggcatcatcgatttTtcttttcttagctcctgtat	8	19	5	9	1	4	0	2	0	2	0	6	1	5	0	1	1	1	3	1	1	3	7			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:21623145T>G	ENST00000444129.2	-	15	2401	c.1933A>C	c.(1933-1935)Aaa>Caa	p.K645Q	RECQL_ENST00000421138.2_Missense_Mutation_p.K645Q|PYROXD1_ENST00000538582.1_3'UTR|PYROXD1_ENST00000240651.9_3'UTR	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	645					DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						TCATCGATTTTTCTTTTCTTA	0.313								Other identified genes with known or suspected DNA repair function																													p.K645Q		.											.	RECQL-228	0			c.A1933C						.						79	81	80					12																	21623145		2202	4297	6499	SO:0001583	missense	5965	exon16			CGATTTTTCTTTT	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"DNA helicase Q1-like"	600537	"RecQ protein-like (DNA helicase Q1-like)"			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.1933A>C	12.37:g.21623145T>G	ENSP00000416739:p.Lys645Gln	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	427	263	NM_032941	0	0	11	54	43	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	37	CCDS31756.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429403	0.62844	.	.	ENSG00000004700	ENST00000444129;ENST00000421138	T;T	0.57907	0.37;0.37	4.56	4.56	0.56223	.	0.597468	0.16648	N	0.205325	T	0.48926	0.1527	L	0.32530	0.975	0.33037	D	0.530956	P	0.52316	0.952	P	0.49140	0.601	T	0.62553	-0.6830	10	0.66056	D	0.02	-7.7317	10.4656	0.44604	0.0:0.0:0.0:1.0	.	645	P46063	RECQ1_HUMAN	Q	645	ENSP00000416739:K645Q;ENSP00000395449:K645Q	ENSP00000395449:K645Q	K	-	1	0	RECQL	21514412	1.000000	0.71417	0.988000	0.46212	0.886000	0.51366	3.310000	0.51911	2.036000	0.60181	0.528000	0.53228	AAA	.		0.313	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		G	21623145	T	G	21623145	3	3	137	1	0	0	0	0	1	0	0	0	13233	1850	64	5	20	5	RECQL	12	21623145	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10		21623145	112228750	36	12228											
HOXC10	3226	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54382989	54382989	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacaccacaggaaattggcTgacagcaaagagcggaagga	18	3	12	8	1	0	2	0	1	0	1	0	5	0	5	1	4	3	2	1	4	4	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:54382989T>C	ENST00000303460.4	+	2	862	c.788T>C	c.(787-789)cTg>cCg	p.L263P	MIR196A2_ENST00000385189.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron|HOXC10_ENST00000511575.1_3'UTR	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	263					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						GGAAATTGGCTGACAGCAAAG	0.428											OREG0021882	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L263P													.	HOXC10-91	0			c.T788C						.						64	62	63					12																	54382989		2203	4300	6503	SO:0001583	missense	3226	exon2			ATTGGCTGACAGC		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"Homeoboxes / ANTP class : HOXL subclass"	5122	protein-coding gene	gene with protein product		605560	"homeo box C10"	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.788T>C	12.37:g.54382989T>C	ENSP00000307321:p.Leu263Pro	Somatic	148	1	999	WXS	Illumina HiSeq	Phase_I	226	47	NM_017409	0	0	48	71	23	O15219|O15220|Q9BVD5	Missense_Mutation	SNP	ENST00000303460.4	37	CCDS8868.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.041980	0.55003	.	.	ENSG00000180818	ENST00000303460	D	0.95724	-3.79	3.97	3.97	0.46021	Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000004	D	0.95233	0.8454	M	0.70842	2.15	0.80722	D	1	P	0.43607	0.812	P	0.46585	0.521	D	0.95488	0.8566	10	0.87932	D	0	.	12.5235	0.56073	0.0:0.0:0.0:1.0	.	263	Q9NYD6	HXC10_HUMAN	P	263	ENSP00000307321:L263P	ENSP00000307321:L263P	L	+	2	0	HOXC10	52669256	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.993000	0.88291	1.743000	0.51761	0.374000	0.22700	CTG	.		0.428	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			C	54382989	T	C	54382989	3	2	137	1	0	0	0	0	1	0	0	0	7330	1580	55	3	794	3	HOXC10	12	54382989	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10	32759844	54382989	79468906	37	12229											
NCKAP1L	3071	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	54905823	54905823	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcagggctccctctacatcaCccttatccgtgaggatgtgc	7	10	10	14	1	2	1	1	1	1	0	4	2	4	2	3	2	2	2	3	2	2	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:54905823C>A	ENST00000293373.6	+	9	954	c.875C>A	c.(874-876)aCc>aAc	p.T292N	NCKAP1L_ENST00000552211.1_3'UTR|NCKAP1L_ENST00000545638.2_Missense_Mutation_p.T242N	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	292					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CTCTACATCACCCTTATCCGT	0.522																																					p.T292N													.	NCKAP1L-93	0			c.C875A						.						144	125	132					12																	54905823		2203	4300	6503	SO:0001583	missense	3071	exon9			ACATCACCCTTAT	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.875C>A	12.37:g.54905823C>A	ENSP00000293373:p.Thr292Asn	Somatic	332	1		WXS	Illumina HiSeq	Phase_I	518	88	NM_005337	0	0	2	2	0	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.724890	0.68959	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.34072	1.38;1.38	5.61	5.61	0.85477	.	0.108403	0.64402	D	0.000011	T	0.50837	0.1639	M	0.65498	2.005	0.37617	D	0.921162	D	0.55385	0.971	P	0.52823	0.71	T	0.54728	-0.8250	10	0.42905	T	0.14	-19.2572	17.1917	0.86881	0.0:1.0:0.0:0.0	.	292	P55160	NCKPL_HUMAN	N	292;242	ENSP00000293373:T292N;ENSP00000445596:T242N	ENSP00000293373:T292N	T	+	2	0	NCKAP1L	53192090	0.976000	0.34144	1.000000	0.80357	0.786000	0.44442	2.377000	0.44300	2.665000	0.90641	0.558000	0.71614	ACC	.		0.522	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		A	54905823	C	A	54905823	3	1	137	1	0	0	0	0	1	0	0	0	10248	507	18	4	909	4	NCKAP1L	12	54905823	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	522834	54905823	78946072	38	12230											
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	59308047	59308047	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaataacgaagactcacaCttctcgaaggctttgaaggt	15	9	8	9	2	2	2	1	1	1	1	3	4	2	2	0	2	1	1	0	2	6	3	rs373824765		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:59308047C>T	ENST00000320743.3	-	2	593	c.307G>A	c.(307-309)Gtg>Atg	p.V103M	LRIG3_ENST00000379141.4_Splice_Site_p.V43M	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	103					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)			AAGACTCACACTTCTCGAAGG	0.323			T	ROS1	NSCLC																																p.V103M		.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3-229	0			c.G307A						.	C	MET/VAL,MET/VAL	0,4406		0,0,2203	97	104	101		127,307	4	1	12		101	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice	LRIG3	NM_001136051.1,NM_153377.3	21,21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	43/1060,103/1120	59308047	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	121227	exon2			CTCACACTTCTCG	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.308+1G>A	12.37:g.59308047C>T		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	88	13	NM_153377	0	0	0	0	0	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.352857	0.41700	0.0	1.16E-4	ENSG00000139263	ENST00000379141;ENST00000320743;ENST00000552267	T;T;T	0.55052	1.74;1.53;0.54	5.86	3.99	0.46301	.	0.234157	0.21955	N	0.066677	T	0.44850	0.1313	M	0.63428	1.95	0.41104	D	0.985693	B;B	0.24823	0.112;0.02	B;B	0.24541	0.054;0.006	T	0.31696	-0.9934	9	.	.	.	.	5.4651	0.16637	0.0:0.5541:0.1389:0.307	.	43;103	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	M	43;103;10	ENSP00000368436:V43M;ENSP00000326759:V103M;ENSP00000449109:V10M	.	V	-	1	0	LRIG3	57594314	0.999000	0.42202	1.000000	0.80357	0.987000	0.75469	0.426000	0.21363	0.753000	0.32945	0.655000	0.94253	GTG	.		0.323	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	Missense_Mutation	T	59308047	C	T	59308047	5	4	137	1	0	0	0	0	0	0	1	0	8971	579	20	2	3124	2	LRIG3	12	59308047	Splice_Site	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	4402224	59308047	74543848	39	12231											
RBM19	9904	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	114400219	114400220	+	Splice_Site	DNP	TC	TC	CT																															cctgaaacgctcctccttcaTctaggacagagggaaaggaa																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:114400219_114400220TC>CT	ENST00000545145.2	-	2	115	c.37_37GA>AG	c.(37-39)GAat>AGaat	p.E13R	RBM19_ENST00000261741.5_Splice_Site_p.E13R|RBM19_ENST00000392561.3_Splice_Site_p.E13R	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	13	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCCTCCTTCATCTAGGACAGAG	0.54																																					.													.	RBM19-95	0			c.37-1G>A						.																																			SO:0001630	splice_region_variant	9904	exon3			CTTCATCTAGGAC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.37_37delinsCT	12.37:g.114400219_114400220delinsCT		Somatic	104	1		WXS	Illumina HiSeq	Phase_I	130	91	NM_001146699	0	0	0	0	0	A8K5X9|Q9BPY6|Q9UFN5	Splice_Site	DNP	ENST00000545145.2	37	CCDS9172.1																																																																																			.		0.54	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	Missense_Mutation	CT	114400220	TC	CT	114400219	5	2	137	1	0	0	0	0	0	0	1	0	13153	1449	50	3	2937	3	RBM19	12	114400219	Splice_Site	DNP	TC	TCGA-IA-A40U-01A-11D-A25F-10	55092172	114400219	19451676	40	12232											
UBC	7316	ucsc.edu;bcgsc.ca	37	chr12	125397655	125397655	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctctgagacggagtacCaggtgcaaggtggactcttt	9	9	12	11	1	2	1	0	1	2	1	2	4	2	3	3	4	2	2	3	4	2	2	rs544863778		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:125397655C>A	ENST00000536769.1	-	1	2239	c.663G>T	c.(661-663)ctG>ctT	p.L221L	UBC_ENST00000339647.5_Silent_p.L221L|UBC_ENST00000536661.1_5'Flank|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Silent_p.L145L|UBC_ENST00000538617.1_Intron			P0CG48	UBC_HUMAN	ubiquitin C	221	Ubiquitin-like 3. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|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 type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		GACGGAGTACCAGGTGCAAGG	0.512																																					p.L221L													.	UBC-46	0			c.G663T						.						221	196	204					12																	125397655		2203	4299	6502	SO:0001819	synonymous_variant	7316	exon2			GAGTACCAGGTGC		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.663G>T	12.37:g.125397655C>A		Somatic	627	2		WXS	Illumina HiSeq		894	224	NM_021009	1	0	1200	1614	413	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			.		0.512	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009		A	125397655	C	A	125397655	2	1	137	1	0	0	0	0	0	0	0	1	16875	581	21	4		4	UBC	12	125397655	Silent	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	10997436	125397655	8454240	41	12233											
C14orf156	81892	ucsc.edu	37	chr14	78174462	78174462	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctttagtctgaagatggcggCctcagcagcgagaggtgctg	8	9	15	9	2	2	3	1	1	1	2	2	4	2	3	1	3	3	2	1	3	2	2	rs552083394		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr14:78174462C>A	ENST00000557342.1	+	1	49	c.8C>A	c.(7-9)gCc>gAc	p.A3D	SLIRP_ENST00000557431.1_Missense_Mutation_p.A3D|SLIRP_ENST00000238688.5_Missense_Mutation_p.A3D|SLIRP_ENST00000557623.1_Missense_Mutation_p.A3D|ALKBH1_ENST00000216489.3_5'Flank	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	3					mitochondrion morphogenesis (GO:0070584)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	acrosomal vesicle (GO:0001669)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|sperm flagellum (GO:0036126)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			kidney(1)|prostate(1)	2						AAGATGGCGGCCTCAGCAGCG	0.567																																					p.A3D													.	SLIRP-90	0			c.C8A						.						58	59	59					14																	78174462		2203	4300	6503	SO:0001583	missense	81892	exon1			TGGCGGCCTCAGC	AF253980	CCDS9866.1, CCDS58331.1, CCDS73668.1	14q24.3	2013-02-12	2011-06-17	2011-06-17	ENSG00000119705	ENSG00000119705		"RNA binding motif (RRM) containing"	20495	protein-coding gene	gene with protein product		610211	"chromosome 14 open reading frame 156"	C14orf156		16762838	Standard	NM_031210		Approved	DC50	uc001xue.5	Q9GZT3		ENST00000557342.1:c.8C>A	14.37:g.78174462C>A	ENSP00000450909:p.Ala3Asp	Somatic	61	1		WXS	Illumina HiSeq		44	2	NM_001267864	0	0	6	6	0	J3KMY7	Missense_Mutation	SNP	ENST00000557342.1	37	CCDS9866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.20|16.20	3.055129|3.055129	0.55325|0.55325	.|.	.|.	ENSG00000119705|ENSG00000119705	ENST00000557342;ENST00000238688;ENST00000557623;ENST00000557431|ENST00000556831	T;T;T;T|.	0.59638|.	0.72;0.68;1.02;0.25|.	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.74419|0.74419	0.3714|0.3714	M|M	0.70595|0.70595	2.14|2.14	0.37545|0.37545	D|D	0.918469|0.918469	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.76356|0.76356	-0.2989|-0.2989	10|5	0.32370|.	T|.	0.25|.	-0.5502|-0.5502	16.6407|16.6407	0.85098|0.85098	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	3|.	Q9GZT3|.	SLIRP_HUMAN|.	D|T	3|1	ENSP00000450909:A3D;ENSP00000238688:A3D;ENSP00000452057:A3D;ENSP00000450849:A3D|.	ENSP00000238688:A3D|.	A|P	+|+	2|1	0|0	SLIRP|SLIRP	77244215|77244215	0.984000|0.984000	0.35163|0.35163	0.959000|0.959000	0.39883|0.39883	0.159000|0.159000	0.22180|0.22180	3.389000|3.389000	0.52516|0.52516	2.732000|2.732000	0.93576|0.93576	0.650000|0.650000	0.86243|0.86243	GCC|CCT	.		0.567	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210		A	78174462	C	A	78174462	3	1	137	1	0	0	0	0	1	0	0	0	1758	739	26	4	10	4	C14orf156	14	78174462	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		78174462	29175078	42	12234											
CLMN	79789	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	95670380	95670380	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caggttcttactgcagaaagGatccttgtaggtgtcagcct	9	12	11	9	0	2	1	1	0	1	1	3	2	3	2	2	3	3	3	2	3	3	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr14:95670380G>A	ENST00000298912.4	-	9	1419	c.1306C>T	c.(1306-1308)Cct>Tct	p.P436S		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	436					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTGCAGAAAGGATCCTTGTAG	0.478																																					p.P436S		.											.	CLMN-90	0			c.C1306T						.						115	110	112					14																	95670380		2203	4300	6503	SO:0001583	missense	79789	exon9			AGAAAGGATCCTT	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1306C>T	14.37:g.95670380G>A	ENSP00000298912:p.Pro436Ser	Somatic	221	0		WXS	Illumina HiSeq	Phase_I	113	68	NM_024734	0	0	0	0	0	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	G	5.446	0.267351	0.10294	.	.	ENSG00000165959	ENST00000298912	D	0.91894	-2.93	5.91	3.07	0.35406	.	0.178386	0.27311	N	0.019959	T	0.81555	0.4847	N	0.08118	0	0.09310	N	0.999997	B	0.16802	0.019	B	0.14023	0.01	T	0.71755	-0.4497	10	0.62326	D	0.03	.	8.3135	0.32086	0.0:0.6159:0.3036:0.0805	.	436	Q96JQ2	CLMN_HUMAN	S	436	ENSP00000298912:P436S	ENSP00000298912:P436S	P	-	1	0	CLMN	94740133	0.051000	0.20477	0.007000	0.13788	0.002000	0.02628	0.554000	0.23407	0.388000	0.25054	-0.839000	0.03059	CCT	.		0.478	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			A	95670380	G	A	95670380	3	1	137	1	0	0	0	0	1	0	0	0	3548	1174	41	2	1722	2	CLMN	14	95670380	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	17495918	95670380	11679160	43	12235											
CHRFAM7A	89832	bcgsc.ca	37	chr15	30665219	30665220	+	Frame_Shift_Del	DEL	AT	AT	-																															cattggggatatagccactgAtatctgcctcctgcatctgc																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	AT	AT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr15:30665219_30665220delAT	ENST00000299847.2	-	6	742_743	c.289_290delAT	c.(289-291)atcfs	p.I97fs	CHRFAM7A_ENST00000397827.3_Frame_Shift_Del_p.I6fs|CHRFAM7A_ENST00000567722.1_5'Flank|CHRFAM7A_ENST00000401522.3_Frame_Shift_Del_p.I6fs	NM_139320.1	NP_647536.1	Q494W8	CRFM7_HUMAN	CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion	97						integral component of membrane (GO:0016021)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(1)|skin(2)	6		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		ATAGCCACTGATATCTGCCTCC	0.5																																					p.97_97del													.	CHRFAM7A-45	0			c.289_290del						.																																			SO:0001589	frameshift_variant	89832	exon6			CCACTGATATCTG	AF029838	CCDS32184.1, CCDS42008.1	15q13.2	2013-04-24	2006-02-01		ENSG00000166664	ENSG00000166664			15781	protein-coding gene	gene with protein product		609756				11829490	Standard	NM_139320		Approved	D-10, CHRNA7-DR1	uc001zdt.1	Q494W8	OTTHUMG00000175645	ENST00000299847.2:c.289_290delAT	15.37:g.30665221_30665222delAT	ENSP00000299847:p.Ile97fs	Somatic	882	1		WXS	Illumina HiSeq	Phase_1	631	230	NM_139320	0	0	0	0	0	A8KAB9	Frame_Shift_Del	DEL	ENST00000299847.2	37	CCDS32184.1																																																																																			.		0.5	CHRFAM7A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430700.1	NM_148911		-	30665220	AT	-	30665219	7	5	137	1	0	1	0	1	0	0	0	0	3381	333	12	0	968	0	CHRFAM7A	15	30665219	Frame_Shift_Del	DEL	AT	TCGA-IA-A40U-01A-11D-A25F-10		30665219	71866173	44	12236											
FAM82A2	55177	bcgsc.ca	37	chr15	41043764	41043764	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctggttctcttccatgtgGcatctggaaagcaggcccca	7	11	10	13	0	3	0	0	0	3	0	5	1	4	1	3	4	1	3	3	4	1	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr15:41043764G>T	ENST00000260385.6	-	3	1451	c.384C>A	c.(382-384)tgC>tgA	p.C128*	RMDN3_ENST00000338376.3_Nonsense_Mutation_p.C128*|RMDN3_ENST00000558560.1_5'UTR			Q96TC7	RMD3_HUMAN	regulator of microtubule dynamics 3	128					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)	integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CTTCCATGTGGCATCTGGAAA	0.562																																					p.C128X													.	.	0			c.C384A						.						80	77	78					15																	41043764		2203	4300	6503	SO:0001587	stop_gained	55177	exon4			CATGTGGCATCTG	AK001441	CCDS10063.1	15q15.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000137824	ENSG00000137824			25550	protein-coding gene	gene with protein product		611873	"family with sequence similarity 82, member A2"	FAM82C, FAM82A2		12975309	Standard	XM_005254531		Approved	FLJ10579, PTPIP51, RMD3	uc001zmp.1	Q96TC7	OTTHUMG00000130066	ENST00000260385.6:c.384C>A	15.37:g.41043764G>T	ENSP00000260385:p.Cys128*	Somatic	66	0		WXS	Illumina HiSeq	Phase_1	47	4	NM_018145	0	0	0	0	0	A9UMZ9|B3KRR3|Q6ZWE9|Q96H23|Q96SD6|Q9H6G1|Q9NVQ6	Nonsense_Mutation	SNP	ENST00000260385.6	37	CCDS10063.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.318354	0.81469	.	.	ENSG00000137824	ENST00000260385;ENST00000338376;ENST00000426872	.	.	.	4.93	-6.67	0.01783	.	0.173950	0.48286	D	0.000187	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-4.3853	0.9165	0.01305	0.3395:0.1799:0.2985:0.1821	.	.	.	.	X	128;128;65	.	ENSP00000260385:C128X	C	-	3	2	FAM82A2	38831056	0.443000	0.25641	0.715000	0.30552	0.868000	0.49771	-0.645000	0.05409	-1.259000	0.02468	0.484000	0.47621	TGC	.		0.562	RMDN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252357.1	NM_018145		T	41043764	G	T	41043764	4	4	137	1	0	0	0	0	0	1	0	0	5650	1195	42	4	1068	4	FAM82A2	15	41043764	Nonsense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	10378545	41043764	61487628	45	12237											
CSPG4	1464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75968209	75968209	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctgaacatgttggcctcaagGaagctcaggaagcctccctt	10	9	10	12	0	2	1	2	1	0	0	3	3	3	3	3	3	3	2	3	3	4	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr15:75968209G>C	ENST00000308508.5	-	10	6743	c.6651C>G	c.(6649-6651)ttC>ttG	p.F2217L	CTD-2026K11.1_ENST00000569467.1_RNA|AC105020.1_ENST00000435356.1_5'Flank	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2217	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGGCCTCAAGGAAGCTCAGGA	0.622																																					p.F2217L		.											.	CSPG4-229	0			c.C6651G						.						80	78	79					15																	75968209		2197	4294	6491	SO:0001583	missense	1464	exon10			CTCAAGGAAGCTC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6651C>G	15.37:g.75968209G>C	ENSP00000312506:p.Phe2217Leu	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	56	21	NM_001897	0	0	6	6	0	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931673	0.34096	.	.	ENSG00000173546	ENST00000308508;ENST00000537176	T	0.18657	2.2	5.33	2.43	0.29744	.	0.080794	0.52532	N	0.000076	T	0.15609	0.0376	L	0.50333	1.59	0.24930	N	0.991921	B	0.10296	0.003	B	0.08055	0.003	T	0.36261	-0.9755	10	0.09843	T	0.71	.	8.3535	0.32316	0.3053:0.0:0.6947:0.0	.	2217	Q6UVK1	CSPG4_HUMAN	L	2217;249	ENSP00000312506:F2217L	ENSP00000312506:F2217L	F	-	3	2	CSPG4	73755264	1.000000	0.71417	0.865000	0.33974	0.938000	0.57974	0.970000	0.29383	0.251000	0.21505	0.561000	0.74099	TTC	.		0.622	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75968209	G	C	75968209	3	2	137	1	0	0	0	0	1	0	0	0	3966	1165	41	4	321	4	CSPG4	15	75968209	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	34924445	75968209	26563183	46	12238											
RHCG	51458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90030138	90030138	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acaggaagttgaagcccacgGcgctgaagccgtagcgctgc	10	5	14	12	4	0	2	0	2	0	0	0	3	0	3	2	2	4	4	2	2	4	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr15:90030138G>A	ENST00000268122.4	-	2	331	c.263C>T	c.(262-264)gCc>gTc	p.A88V	RHCG_ENST00000544600.1_Missense_Mutation_p.A88V	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	88					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					GAAGCCCACGGCGCTGAAGCC	0.622																																					p.A88V		.											.	RHCG-226	0			c.C263T						.						65	56	59					15																	90030138		2200	4299	6499	SO:0001583	missense	51458	exon2			CCCACGGCGCTGA	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.263C>T	15.37:g.90030138G>A	ENSP00000268122:p.Ala88Val	Somatic	379	0		WXS	Illumina HiSeq	Phase_I	357	159	NM_016321	0	0	0	0	0	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	37	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	g	17.75	3.466191	0.63625	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.23552	1.9;1.9	4.76	2.79	0.32731	Ammonium transporter AmtB-like (3);	0.658388	0.16053	N	0.231841	T	0.49592	0.1566	M	0.88310	2.945	0.21386	N	0.99971	P	0.49358	0.923	P	0.53760	0.734	T	0.50021	-0.8876	9	.	.	.	-2.9237	14.3657	0.66805	0.0:0.4295:0.5705:0.0	.	88	Q9UBD6	RHCG_HUMAN	V	88;88;79	ENSP00000438123:A88V;ENSP00000268122:A88V	.	A	-	2	0	RHCG	87831142	0.691000	0.27709	0.099000	0.21106	0.817000	0.46193	2.392000	0.44433	0.397000	0.25310	0.479000	0.44913	GCC	.		0.622	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		A	90030138	G	A	90030138	3	1	137	1	0	0	0	0	1	0	0	0	13358	1203	42	2	1212	2	RHCG	15	90030138	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	14061929	90030138	12501254	47	12239											
STUB1	339123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	732019	732019	+	3'UTR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagcactcaactcttcacaGgacaagtacatggcggacat	14	7	8	12	1	3	0	2	0	1	0	3	2	3	2	0	3	3	2	0	3	3	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr16:732019G>T	ENST00000293882.4	-	0	1779				STUB1_ENST00000566181.2_Splice_Site|STUB1_ENST00000219548.4_Splice_Site|JMJD8_ENST00000454700.1_3'UTR|JMJD8_ENST00000609261.1_3'UTR|LA16c-313D11.9_ENST00000571933.1_RNA|LA16c-313D11.9_ENST00000567091.1_RNA|STUB1_ENST00000565677.1_Splice_Site|STUB1_ENST00000564370.1_Splice_Site|JMJD8_ENST00000412368.2_3'UTR			Q96S16	JMJD8_HUMAN	jumonji domain containing 8							extracellular vesicular exosome (GO:0070062)				breast(1)	1						ACTCTTCACAGGACAAGTACA	0.592																																					.		.											.	STUB1-226	0			c.613-1G>T						.						196	177	184					16																	732019		2201	4300	6501	SO:0001624	3_prime_UTR_variant	10273	exon5			TTCACAGGACAAG		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 20"	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.*775C>A	16.37:g.732019G>T		Somatic	220	0		WXS	Illumina HiSeq	Phase_I	276	156	NM_005861	0	1	100	324	223	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	Splice_Site	SNP	ENST00000293882.4	37		.	.	.	.	.	.	.	.	.	.	G	13.81	2.348521	0.41599	.	.	ENSG00000103266	ENST00000219548	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8172	0.85737	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STUB1	672020	1.000000	0.71417	0.999000	0.59377	0.292000	0.27327	8.863000	0.92288	2.366000	0.80165	0.555000	0.69702	.	.		0.592	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920		T	732019	G	T	732019	1	4	137	0	1	0	0	0	0	0	0	0	15367	1014	35	4		4	STUB1	16	732019	3'UTR	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		732019	89622734	48	12240											
GLG1	2734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	74505165	74505165	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatcaggtccccagagtctAtctggttatctgccacatcc	8	11	7	15	0	4	1	1	0	3	1	6	1	6	1	5	2	1	1	5	2	2	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr16:74505165A>C	ENST00000422840.2	-	15	2134	c.2135T>G	c.(2134-2136)aTa>aGa	p.I712R	GLG1_ENST00000205061.5_Missense_Mutation_p.I712R|GLG1_ENST00000447066.2_Missense_Mutation_p.I701R	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	712					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CCCAGAGTCTATCTGGTTATC	0.458																																					p.I712R		.											.	GLG1-136	0			c.T2135G						.						251	213	226					16																	74505165		2198	4300	6498	SO:0001583	missense	2734	exon15			GAGTCTATCTGGT		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2135T>G	16.37:g.74505165A>C	ENSP00000405984:p.Ile712Arg	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	227	60	NM_001145667	0	0	9	11	2	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.122299	0.37436	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	L	0.49350	1.555	0.80722	D	1	D;D;D	0.65815	0.984;0.995;0.97	D;P;P	0.65684	0.937;0.901;0.905	T	0.62595	-0.6821	9	0.16896	T	0.51	-0.9347	16.8222	0.85835	1.0:0.0:0.0:0.0	.	712;712;701	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	R	712;701;712	.	ENSP00000205061:I712R	I	-	2	0	GLG1	73062666	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.923000	0.70045	2.371000	0.80710	0.533000	0.62120	ATA	.		0.458	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		C	74505165	A	C	74505165	3	2	137	1	0	0	0	0	1	0	0	0	6456	449	16	5	1532	5	GLG1	16	74505165	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	73773146	74505165	15849588	49	12241											
C16orf46	123775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81094972	81094972	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctttgcactccccgtttctGcagaagctgcaaggcagcaa	9	9	10	13	1	1	1	0	0	1	1	2	1	2	1	2	1	5	8	2	1	3	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr16:81094972G>A	ENST00000299578.5	-	4	1217	c.982C>T	c.(982-984)Cag>Tag	p.Q328*	C16orf46_ENST00000378611.4_Nonsense_Mutation_p.Q328*|RP11-303E16.8_ENST00000564536.1_RNA|C16orf46_ENST00000444657.3_5'Flank	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	328						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						CCCCGTTTCTGCAGAAGCTGC	0.552																																					p.Q328X		.											.	C16orf46-90	0			c.C982T						.						103	101	102					16																	81094972		2202	4300	6502	SO:0001587	stop_gained	123775	exon3			GTTTCTGCAGAAG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.982C>T	16.37:g.81094972G>A	ENSP00000299578:p.Gln328*	Somatic	250	0		WXS	Illumina HiSeq	Phase_I	316	83	NM_001100873	0	0	2	2	0	Q96MA7	Nonsense_Mutation	SNP	ENST00000299578.5	37	CCDS10932.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.561321	0.45590	.	.	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	.	.	.	5.23	1.87	0.25490	.	0.466272	0.20153	N	0.098118	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	14.4868	0.67622	0.0:0.414:0.5859:0.0	.	.	.	.	X	328;55;328	.	ENSP00000299578:Q328X	Q	-	1	0	C16orf46	79652473	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	1.093000	0.30939	0.653000	0.30826	0.563000	0.77884	CAG	.		0.552	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337		A	81094972	G	A	81094972	4	1	137	1	0	0	0	0	0	1	0	0	1819	1328	46	2	237	2	C16orf46	16	81094972	Nonsense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	6589807	81094972	9259781	50	12242											
TRPV1	7442	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3480482	3480482	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacggcacaggtctctcaggAtcatctgcaggagacagcag	12	6	12	11	1	4	1	2	0	2	1	5	3	4	2	0	4	3	3	0	4	1	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:3480482A>G	ENST00000571088.1	-	12	1931	c.1718T>C	c.(1717-1719)aTc>aCc	p.I573T	TRPV1_ENST00000425167.2_Missense_Mutation_p.I584T|TRPV1_ENST00000174621.6_Missense_Mutation_p.I571T|SHPK_ENST00000572705.1_Missense_Mutation_p.I573T|RP11-235E17.3_ENST00000573568.1_RNA|TRPV1_ENST00000576351.1_Missense_Mutation_p.I563T|TRPV1_ENST00000399756.4_Missense_Mutation_p.I573T|TRPV1_ENST00000310522.5_Missense_Mutation_p.I513T|TRPV1_ENST00000399759.3_Missense_Mutation_p.I573T	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	573					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	GTCTCTCAGGATCATCTGCAG	0.602																																					p.I573T	Melanoma(38;962 1762 15789)	.											.	TRPV1-23	0			c.T1718C						.						34	34	34					17																	3480482		2044	4170	6214	SO:0001583	missense	7442	exon12			CTCAGGATCATCT	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1718T>C	17.37:g.3480482A>G	ENSP00000461007:p.Ile573Thr	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	257	125	NM_018727	0	0	0	0	0	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749434	0.69533	.	.	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68	5.15	5.15	0.70609	Ion transport (1);	0.045746	0.85682	D	0.000000	D	0.95007	0.8384	M	0.88842	2.985	0.58432	D	0.999999	P;D;D;P	0.63046	0.764;0.975;0.992;0.77	B;P;P;B	0.58660	0.394;0.717;0.843;0.282	D	0.95830	0.8857	10	0.87932	D	0	-0.9535	14.4569	0.67423	1.0:0.0:0.0:0.0	.	573;571;513;584	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	T	573;573;571;584;513	ENSP00000382661:I573T;ENSP00000382659:I573T;ENSP00000174621:I571T;ENSP00000409627:I584T;ENSP00000311692:I513T	ENSP00000174621:I571T	I	-	2	0	TRPV1	3427231	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	6.734000	0.74801	2.072000	0.62099	0.460000	0.39030	ATC	.		0.602	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		G	3480482	A	G	3480482	3	3	137	1	0	0	0	0	1	0	0	0	16628	333	12	3	494	3	TRPV1	17	3480482	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10		3480482	77714728	51	12243											
NCOR1	9611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	15968952	15968952	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgcgtaaagctgatactGacttgggtaacctggagttg	10	12	12	7	1	0	2	0	2	0	0	0	3	0	3	1	2	4	4	1	2	4	6			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:15968952G>T	ENST00000268712.3	-	33	5055	c.4798C>A	c.(4798-4800)Cag>Aag	p.Q1600K	NCOR1_ENST00000395857.3_Missense_Mutation_p.Q184K|NCOR1_ENST00000395851.1_Missense_Mutation_p.Q1616K	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1600	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AGCTGATACTGACTTGGGTAA	0.453																																					p.Q1616K		.											.	NCOR1-229	0			c.C4846A						.						154	137	143					17																	15968952		2203	4300	6503	SO:0001583	missense	9611	exon32			GATACTGACTTGG	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"thyroid hormone- and retinoic acid receptor-associated corepressor 1", "protein phosphatase 1, regulatory subunit 109"	600849	"nuclear receptor co-repressor 1"			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4798C>A	17.37:g.15968952G>T	ENSP00000268712:p.Gln1600Lys	Somatic	222	0		WXS	Illumina HiSeq	Phase_I	279	72	NM_001190440	0	0	5	6	1	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087095	0.76642	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.47528	0.84;0.84;0.84	5.58	5.58	0.84498	.	0.104733	0.64402	D	0.000003	T	0.65964	0.2742	L	0.57536	1.79	0.40995	D	0.984889	D;D;P;P;P	0.59767	0.986;0.962;0.9;0.94;0.856	D;P;B;P;P	0.72338	0.977;0.53;0.366;0.57;0.501	T	0.63611	-0.6598	10	0.39692	T	0.17	-9.3223	18.5647	0.91113	0.0:0.0:1.0:0.0	.	410;1504;1600;1616;120	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1	.;.;NCOR1_HUMAN;.;.	K	1600;1616;1504;184	ENSP00000268712:Q1600K;ENSP00000379192:Q1616K;ENSP00000379198:Q184K	ENSP00000268712:Q1600K	Q	-	1	0	NCOR1	15909677	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.984000	0.76186	2.625000	0.88918	0.557000	0.71058	CAG	.		0.453	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15968952	G	T	15968952	3	4	137	1	0	0	0	0	1	0	0	0	10261	1299	45	4	2580	4	NCOR1	17	15968952	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	12488470	15968952	65226258	52	12244											
KCNJ12	3768	broad.mit.edu;bcgsc.ca	37	chr17	21318895	21318895	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgtggacatccgctggCggtacatgctgctcatcttc	5	12	11	13	2	2	0	1	0	1	0	4	1	3	1	2	3	3	4	2	3	1	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:21318895C>T	ENST00000583088.1	+	3	1136	c.241C>T	c.(241-243)Cgg>Tgg	p.R81W	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R81W	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	81					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.R81G(1)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CATCCGCTGGCGGTACATGCT	0.577										Prostate(3;0.18)																											p.R81W													.	.	1	Substitution - Missense(1)	lung(1)	c.C241T						.						205	126	153					17																	21318895		2203	4300	6503	SO:0001583	missense	100134444	exon3			CGCTGGCGGTACA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6258	protein-coding gene	gene with protein product		602323	"potassium inwardly-rectifying channel, subfamily J, inhibitor 1"	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.241C>T	17.37:g.21318895C>T	ENSP00000463778:p.Arg81Trp	Somatic	300	2		WXS	Illumina HiSeq	Phase_I	373	48	NM_001194958	0	0	0	0	0	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.843005	0.71488	.	.	ENSG00000184185	ENST00000331718	D	0.96011	-3.88	5.33	4.31	0.51392	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98128	0.9382	H	0.95043	3.615	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98223	1.0479	10	0.87932	D	0	.	10.7711	0.46323	0.4271:0.5729:0.0:0.0	.	81	Q14500	IRK12_HUMAN	W	81	ENSP00000328150:R81W	ENSP00000328150:R81W	R	+	1	2	KCNJ12	21259488	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.669000	0.46825	2.506000	0.84524	0.591000	0.81541	CGG	.		0.577	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21318895	C	T	21318895	3	4	137	1	0	0	0	0	1	0	0	0	8067	759	27	1	243	1	KCNJ12	17	21318895	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	5349943	21318895	59876315	53	12245											
LRRC37A	9884	broad.mit.edu	37	chr17	44410017	44410018	+	Frame_Shift_Ins	INS	-	-	T																															gattatacttttctgcctcaINSttgtggtaaggacaataatt																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:44410017_44410018insT	ENST00000320254.5	+	10	4807_4808	c.4804_4805insT	c.(4804-4806)attfs	p.I1602fs	ARL17B_ENST00000575960.1_Intron|LRRC37A_ENST00000393465.3_Frame_Shift_Ins_p.I1602fs|LRRC37A_ENST00000496930.1_Frame_Shift_Ins_p.I640fs|ARL17B_ENST00000434041.2_Intron|ARL17B_ENST00000570618.1_Intron|ARL17B_ENST00000575698.1_Intron	NM_014834.4	NP_055649.4	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A	1602						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|pancreas(6)|prostate(1)|skin(1)	11		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		TTTCTGCCTCATTGTGGTAAGG	0.376																																					p.I1602fs													.	LRRC37A-22	0			c.4804_4805insT						.																																			SO:0001589	frameshift_variant	9884	exon10			TGCCTCATTGTGG	BC040501	CCDS11504.2	17q21.31	2014-04-01			ENSG00000176681	ENSG00000176681			29069	protein-coding gene	gene with protein product						9628581, 15533724	Standard	NM_014834		Approved	KIAA0563	uc031rbr.1	A6NMS7	OTTHUMG00000149841	ENST00000320254.5:c.4806dupT	17.37:g.44410019_44410019dupT	ENSP00000326324:p.Ile1602fs	Somatic	349	2		WXS	Illumina HiSeq	Phase_I	412	111	NM_014834	0	0	0	0	0	Q68DY2|Q8IWC7	Frame_Shift_Ins	INS	ENST00000320254.5	37	CCDS11504.2																																																																																			.		0.376	LRRC37A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313519.3	NM_014834		T	44410018	-	T	44410017	7	5	137	1	0	1	1	0	0	0	0	0	9016	217	8	0	4842	0	LRRC37A	17	44410017	Frame_Shift_Ins	INS	-	TCGA-IA-A40U-01A-11D-A25F-10	23091122	44410017	36785193	54	12246											
DNAH17	8632	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	76449535	76449535	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagatggcctgctcgatGacatccaggtagctgcgggc	7	8	14	12	3	0	2	0	1	0	1	3	4	2	2	3	3	3	3	3	3	1	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:76449535G>T	ENST00000585328.1	-	65	10528	c.10404C>A	c.(10402-10404)gtC>gtA	p.V3468V	DNAH17_ENST00000389840.5_Silent_p.V3459V|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3459	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CCTGCTCGATGACATCCAGGT	0.617																																					p.V3473V		.											.	DNAH17-142	0			c.C10419A						.						112	76	88					17																	76449535		2203	4300	6503	SO:0001819	synonymous_variant	8632	exon65			CTCGATGACATCC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"Axonemal dyneins"	2946	protein-coding gene	gene with protein product		610063	"dynein, axonemal, heavy polypeptide 17", "dynein, axonemal, heavy chain like 1", "dynein, axonemal, heavy like 1"	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.10404C>A	17.37:g.76449535G>T		Somatic	203	0		WXS	Illumina HiSeq	Phase_I	238	118	NM_173628	0	0	0	0	0	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.		0.617	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76449535	G	T	76449535	2	4	137	1	0	0	0	0	0	0	0	1	4612	1277	45	4		4	DNAH17	17	76449535	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	32039518	76449535	4745675	55	12247											
PTPRM	5797	hgsc.bcm.edu;bcgsc.ca	37	chr18	8314790	8314790	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgcagacgatcattccCgagtgaggctgcagacaata	11	9	10	11	2	1	3	1	1	0	2	2	5	2	3	2	1	2	3	2	1	2	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr18:8314790C>T	ENST00000332175.8	+	19	3852	c.2815C>T	c.(2815-2817)Cga>Tga	p.R939*	PTPRM_ENST00000580170.1_Nonsense_Mutation_p.R952*|PTPRM_ENST00000400053.4_Nonsense_Mutation_p.R877*|PTPRM_ENST00000444013.1_Nonsense_Mutation_p.R726*|PTPRM_ENST00000400060.4_Nonsense_Mutation_p.R953*	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	939	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CGATCATTCCCGAGTGAGGCT	0.353																																					p.R952X		.											.	PTPRM-228	0			c.C2854T						.						149	142	145					18																	8314790		2203	4300	6503	SO:0001587	stop_gained	5797	exon21			CATTCCCGAGTGA	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2815C>T	18.37:g.8314790C>T	ENSP00000331418:p.Arg939*	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	72	4	NM_001105244	0	0	0	0	0	A7MBN1|D3DUH8|J3QL11	Nonsense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	50	17.034461	0.99877	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.1802	0.98196	0.0:1.0:0.0:0.0	.	.	.	.	X	939;953;877;726	.	ENSP00000331418:R939X	R	+	1	2	PTPRM	8304790	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.775000	0.55349	2.777000	0.95525	0.655000	0.94253	CGA	.		0.353	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8314790	C	T	8314790	4	4	137	1	0	0	0	0	0	1	0	0	12838	644	23	1	2936	1	PTPRM	18	8314790	Nonsense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		8314790	69762458	56	12248											
MAP4K1	11184	hgsc.bcm.edu;bcgsc.ca	37	chr19	39101749	39101755	+	Frame_Shift_Del	DEL	ATGAAGT	ATGAAGT	-																															tcttagtcagagtgactttgAtgaagttgtggaaggcagcc																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	ATGAAGT	ATGAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr19:39101749_39101755delATGAAGT	ENST00000591517.1	-	11	774_780	c.746_752delACTTCAT	c.(745-753)aacttcatcfs	p.NFI249fs	MAP4K1_ENST00000586296.1_Frame_Shift_Del_p.NFI249fs|MAP4K1_ENST00000396857.2_Frame_Shift_Del_p.NFI249fs|MAP4K1_ENST00000423454.2_Intron|MAP4K1_ENST00000589002.1_Intron|MAP4K1_ENST00000589130.1_Frame_Shift_Del_p.NFI245fs	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGTGACTTTGATGAAGTTGTGGAAGGC	0.575																																					p.249_251del		.											.	MAP4K1-980	0			c.746_752del						.																																			SO:0001589	frameshift_variant	11184	exon11			.	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6863	protein-coding gene	gene with protein product	"hematopoietic progenitor kinase 1"	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.746_752delACTTCAT	19.37:g.39101749_39101755delATGAAGT	ENSP00000465039:p.Asn249fs	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	141	29	NM_007181	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000591517.1	37	CCDS59385.1																																																																																			.		0.575	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		-	39101755	ATGAAGT	-	39101749	7	5	137	1	0	1	0	1	0	0	0	0	9284	333	12	0	1899	0	MAP4K1	19	39101749	Frame_Shift_Del	DEL	ATGAAGT	TCGA-IA-A40U-01A-11D-A25F-10		39101749	20027234	57	12249											
KLK14	43847	broad.mit.edu	37	chr19	51584905	51584905	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgccacggctgggagctccgGgtgcacgtatggccaccaat	7	7	14	13	3	0	0	0	0	0	0	1	1	1	1	4	4	3	4	4	4	2	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr19:51584905G>T	ENST00000156499.2	-	4	362	c.144C>A	c.(142-144)acC>acA	p.T48T	KLK14_ENST00000391802.1_Silent_p.T48T			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	48	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		GGGAGCTCCGGGTGCACGTAT	0.617																																					p.T48T	GBM(117;2161 2172 2448 22911)												.	KLK14-226	0			c.C144A						.						28	30	29					19																	51584905		1959	4087	6046	SO:0001819	synonymous_variant	43847	exon4			GCTCCGGGTGCAC	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"Kallikreins"	6362	protein-coding gene	gene with protein product		606135	"kallikrein 14"			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.144C>A	19.37:g.51584905G>T		Somatic	71	0		WXS	Illumina HiSeq	Phase_I	94	4	NM_022046	0	0	0	0	0	A7UNK5|Q1RMZ2|Q6B089	Silent	SNP	ENST00000156499.2	37	CCDS12823.2																																																																																			.		0.617	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046		T	51584905	G	T	51584905	2	4	137	1	0	0	0	0	0	0	0	1	8423	1219	43	4		4	KLK14	19	51584905	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	12483156	51584905	7544078	58	12250											
MZF1	7593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	59082699	59082699	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctctagcttcaccatgaCaggcccctcatcttctgggg	6	11	9	15	0	5	1	2	1	3	0	6	1	6	1	4	3	1	1	4	3	1	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr19:59082699C>T	ENST00000215057.2	-	2	618	c.58G>A	c.(58-60)Gtc>Atc	p.V20I	AC016629.8_ENST00000593642.1_RNA|MZF1_ENST00000594234.1_Missense_Mutation_p.V20I|MZF1_ENST00000599369.1_Missense_Mutation_p.V20I|MZF1_ENST00000594108.1_Missense_Mutation_p.V20I|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	20					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		TTCACCATGACAGGCCCCTCA	0.627																																					p.V20I		.											.	MZF1-91	0			c.G58A						.						32	37	35					19																	59082699		2200	4300	6500	SO:0001583	missense	7593	exon2			CCATGACAGGCCC	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"-", "Zinc fingers, C2H2-type"	13108	protein-coding gene	gene with protein product		194550	"zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.58G>A	19.37:g.59082699C>T	ENSP00000215057:p.Val20Ile	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	117	39	NM_198055	0	0	3	3	0	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	.	9.755	1.168475	0.21621	.	.	ENSG00000099326	ENST00000215057	T	0.06768	3.26	4.06	-3.61	0.04556	.	0.426572	0.17300	N	0.179278	T	0.02848	0.0085	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.42032	-0.9475	9	.	.	.	-14.6825	5.3908	0.16244	0.0:0.4053:0.1456:0.4491	.	20;20	Q7Z729;P28698	.;MZF1_HUMAN	I	20	ENSP00000215057:V20I	.	V	-	1	0	MZF1	63774511	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.161000	0.10026	-0.559000	0.06110	-0.878000	0.02970	GTC	.		0.627	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		T	59082699	C	T	59082699	3	4	137	1	0	0	0	0	1	0	0	0	10133	478	17	2	2166	2	MZF1	19	59082699	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	7497794	59082699	46284	59	12251											
SALL4	57167	bcgsc.ca	37	chr20	50406632	50406632	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgggagactttgacttgatgCtttcggcttgactattggcc	6	14	12	9	2	0	4	0	3	0	1	1	5	0	4	1	3	1	2	1	3	1	6			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr20:50406632C>T	ENST00000217086.4	-	2	2501	c.2390G>A	c.(2389-2391)aGc>aAc	p.S797N	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	797					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGACTTGATGCTTTCGGCTTG	0.527																																					p.S797N													.	SALL4-92	0			c.G2390A						.						80	78	79					20																	50406632		2203	4300	6503	SO:0001583	missense	57167	exon2			TTGATGCTTTCGG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"Zinc fingers, C2H2-type"	15924	protein-coding gene	gene with protein product		607343	"sal (Drosophila)-like 4", "sal-like 4 (Drosophila)"				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2390G>A	20.37:g.50406632C>T	ENSP00000217086:p.Ser797Asn	Somatic	205	0		WXS	Illumina HiSeq	Phase_1	213	7	NM_020436	0	0	0	0	0	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.064014	0.36373	.	.	ENSG00000101115	ENST00000217086	T	0.10005	2.92	5.67	5.67	0.87782	.	0.000000	0.50627	D	0.000108	T	0.31513	0.0799	M	0.75777	2.31	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.00950	-1.1503	10	0.27785	T	0.31	-29.5056	19.7711	0.96366	0.0:1.0:0.0:0.0	.	797	Q9UJQ4	SALL4_HUMAN	N	797	ENSP00000217086:S797N	ENSP00000217086:S797N	S	-	2	0	SALL4	49840039	0.910000	0.30920	0.792000	0.32020	0.831000	0.47069	1.873000	0.39558	2.654000	0.90174	0.655000	0.94253	AGC	.		0.527	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			T	50406632	C	T	50406632	3	4	137	1	0	0	0	0	1	0	0	0	13845	797	28	2	783	2	SALL4	20	50406632	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		50406632	12618888	60	12252											
TAB1	10454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	39814795	39814795	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gggttgcaggtgacacagctGaacgtggaccacaccacaga	12	5	13	11	1	0	3	0	2	0	1	0	4	0	4	2	3	3	3	2	3	1	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr22:39814795G>A	ENST00000216160.6	+	6	671	c.609G>A	c.(607-609)ctG>ctA	p.L203L	TAB1_ENST00000331454.3_Silent_p.L203L	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	203	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						TGACACAGCTGAACGTGGACC	0.537																																					p.L203L		.											.	TAB1-522	0			c.G609A						.						164	122	136					22																	39814795		2203	4300	6503	SO:0001819	synonymous_variant	10454	exon6			ACAGCTGAACGTG	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"TAK1-binding protein 1", "mitogen-activated protein kinase kinase kinase 7 interacting protein 1"	602615	"mitogen-activated protein kinase kinase kinase 7 interacting protein 1"	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.609G>A	22.37:g.39814795G>A		Somatic	206	0		WXS	Illumina HiSeq	Phase_I	179	68	NM_153497	0	0	5	11	6	Q2PP09|Q8IZW2	Silent	SNP	ENST00000216160.6	37	CCDS13993.1																																																																																			.		0.537	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		A	39814795	G	A	39814795	2	1	137	1	0	0	0	0	0	0	0	1	15527	1277	45	2		2	TAB1	22	39814795	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		39814795	11489771	61	12253											
LRRC8B	23507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90048545	90048545	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgccgtctgttacgagaaAcagctccattggtttgcaaa	11	11	10	9	2	1	1	0	0	1	1	2	3	2	1	2	1	5	4	2	1	3	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr1:90048545A>G	ENST00000330947.2	+	5	696	c.336A>G	c.(334-336)aaA>aaG	p.K112K	LRRC8B_ENST00000358200.4_Silent_p.K112K|RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000439853.1_Silent_p.K112K	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	112					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		GTTACGAGAAACAGCTCCATT	0.512																																					p.K112K		.											.	LRRC8B-92	0			c.A336G						.						158	154	155					1																	90048545		2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			CGAGAAACAGCTC	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"T cell activation leucine repeat rich protein"	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.336A>G	1.37:g.90048545A>G		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	174	61	NM_015350	0	0	0	0	0	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			.		0.512	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350		G	90048545	A	G	90048545	2	3	138	1	0	0	0	0	0	0	0	1	9047	40	2	3		3	LRRC8B	1	90048545	Silent	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10		90048545	159202076	1	12254											
OTX1	5013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	63282730	63282730	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaagaagtcctctccagTgcgggagagctcgggctccg	9	6	14	12	3	1	3	0	0	1	3	5	4	3	3	3	2	2	2	3	2	3	0			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:63282730T>A	ENST00000282549.2	+	5	620	c.344T>A	c.(343-345)gTg>gAg	p.V115E	OTX1_ENST00000366671.3_Missense_Mutation_p.V115E	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	115					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					TCCTCTCCAGTGCGGGAGAGC	0.647																																					p.V115E		.											.	OTX1-70	0			c.T344A						.						37	38	38					2																	63282730		2203	4300	6503	SO:0001583	missense	5013	exon5			CTCCAGTGCGGGA		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"Homeoboxes / PRD class"	8521	protein-coding gene	gene with protein product		600036	"orthodenticle (Drosophila) homolog 1", "orthodenticle homolog 1 (Drosophila)"			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.344T>A	2.37:g.63282730T>A	ENSP00000282549:p.Val115Glu	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	239	86	NM_014562	0	0	0	0	0	A6NHA2|B3KTJ4|Q53TG6	Missense_Mutation	SNP	ENST00000282549.2	37	CCDS1873.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.497563	0.64186	.	.	ENSG00000115507	ENST00000366671;ENST00000282549	D;D	0.90385	-2.66;-2.66	3.69	2.55	0.30701	.	0.158837	0.42053	D	0.000765	T	0.79411	0.4441	N	0.19112	0.55	0.41015	D	0.985031	P	0.45531	0.86	P	0.45232	0.474	T	0.76572	-0.2910	10	0.06757	T	0.87	.	3.9166	0.09225	0.0:0.3229:0.0:0.6771	.	115	P32242	OTX1_HUMAN	E	115	ENSP00000355631:V115E;ENSP00000282549:V115E	ENSP00000282549:V115E	V	+	2	0	OTX1	63136234	0.998000	0.40836	1.000000	0.80357	0.945000	0.59286	3.890000	0.56220	1.676000	0.50930	0.460000	0.39030	GTG	.		0.647	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			A	63282730	T	A	63282730	3	1	138	1	0	0	0	0	1	0	0	0	11346	1696	59	5	354	5	OTX1	2	63282730	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		63282730	179916643	2	12255											
PNO1	56902	bcgsc.ca	37	chr2	68388842	68388842	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagaaaccaaggatgttagtGctctgacaaaagcagctgat	16	8	10	7	0	1	3	0	2	1	1	1	4	1	4	1	1	4	4	1	1	6	1	rs528399980		TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:68388842G>T	ENST00000263657.2	+	3	476	c.385G>T	c.(385-387)Gct>Tct	p.A129S	RP11-474G23.1_ENST00000406334.3_Intron	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	129						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						GGATGTTAGTGCTCTGACAAA	0.338													G|||	1	0.000199681	0	0	5008	,	,		19513	0		0	False		,,,				2504	0.001				p.A129S	NSCLC(83;642 1410 13044 32832 40058)												.	PNO1-68	0			c.G385T						.						106	110	108					2																	68388842		2203	4300	6503	SO:0001583	missense	56902	exon3			GTTAGTGCTCTGA	AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"RNA binding protein"		"KH-type RNA binding protein 1", "KH-type RNA-binding protein 1"	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.385G>T	2.37:g.68388842G>T	ENSP00000263657:p.Ala129Ser	Somatic	63	0		WXS	Illumina HiSeq	Phase_1	52	4	NM_020143	0	0	13	13	0	A8K6Q0|Q53G13|Q8WVB8	Missense_Mutation	SNP	ENST00000263657.2	37	CCDS1885.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023360	0.54683	.	.	ENSG00000115946	ENST00000263657	T	0.41400	1.0	6.02	5.12	0.69794	.	0.100235	0.64402	N	0.000002	T	0.34919	0.0914	L	0.35487	1.065	0.58432	D	0.999999	B	0.12630	0.006	B	0.13407	0.009	T	0.06110	-1.0845	10	0.30078	T	0.28	1.5014	16.5765	0.84681	0.0:0.0:0.8687:0.1313	.	129	Q9NRX1	PNO1_HUMAN	S	129	ENSP00000263657:A129S	ENSP00000263657:A129S	A	+	1	0	PNO1	68242346	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.568000	0.60857	1.511000	0.48818	0.650000	0.86243	GCT	.		0.338	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143		T	68388842	G	T	68388842	3	4	138	1	0	0	0	0	1	0	0	0	12187	1319	46	4	395	4	PNO1	2	68388842	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	5106112	68388842	174810531	3	12256											
KCNJ3	3760	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	155555531	155555531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggacctcaagtggcgcTggaacctcttcatcttcatt	7	13	10	11	1	5	0	3	0	2	0	5	2	5	2	2	4	1	1	2	4	2	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:155555531T>C	ENST00000295101.2	+	1	721	c.244T>C	c.(244-246)Tgg>Cgg	p.W82R	AC061961.2_ENST00000443901.1_RNA|KCNJ3_ENST00000544049.1_Missense_Mutation_p.W82R	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	82					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	CAAGTGGCGCTGGAACCTCTT	0.592																																					p.W82R		.											.	KCNJ3-92	0			c.T244C						.						147	139	142					2																	155555531		2203	4300	6503	SO:0001583	missense	3760	exon1			TGGCGCTGGAACC	U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.244T>C	2.37:g.155555531T>C	ENSP00000295101:p.Trp82Arg	Somatic	352	0		WXS	Illumina HiSeq	Phase_I	467	30	NM_001260509	0	0	1	1	0	B4DEW7|Q8TBI0	Missense_Mutation	SNP	ENST00000295101.2	37	CCDS2200.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.585481	0.66105	.	.	ENSG00000162989	ENST00000295101;ENST00000544049	D;D	0.94184	-3.37;-3.37	5.16	5.16	0.70880	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.063086	0.64402	D	0.000001	D	0.95717	0.8607	M	0.73430	2.235	0.80722	D	1	D;D	0.54207	0.965;0.965	P;P	0.60886	0.88;0.879	D	0.96140	0.9099	10	0.87932	D	0	.	13.8034	0.63216	0.0:0.0:0.0:1.0	.	82;82	B4DEW7;P48549	.;IRK3_HUMAN	R	82	ENSP00000295101:W82R;ENSP00000438410:W82R	ENSP00000295101:W82R	W	+	1	0	KCNJ3	155263777	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.981000	0.88123	1.946000	0.56461	0.454000	0.30748	TGG	.		0.592	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		C	155555531	T	C	155555531	3	2	138	1	0	0	0	0	1	0	0	0	8073	1580	55	3	246	3	KCNJ3	2	155555531	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10	87166689	155555531	87643842	4	12257											
TTN	7273	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	179615958	179615958	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgagcttatttcagaagaCgtatctaaaagagataattt	15	14	7	5	1	2	4	1	1	1	3	2	5	2	4	0	0	1	2	0	0	6	7	rs145004106	byFrequency	TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:179615958C>T	ENST00000591111.1	-	45	10585				TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000360870.5_Silent_p.T3723T|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCAGAAGACGTATCTAAAA	0.358													C|||	2	0.000399361	8e-04	0	5008	,	,		20087	0.001		0	False		,,,				2504	0				p.T3723T		.											.	TTN-636	0			c.G11169A						.	C	,,,,	1,4403	2.1+/-5.4	0,1,2201	61	60	60		,,11169,,	-1.5	0	2	dbSNP_134	60	1,8593	1.2+/-3.3	0,1,4296	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,2,6497	TT,TC,CC		0.0116,0.0227,0.0154	,,,,	,,3723/5605,,	179615958	2,12996	2202	4297	6499	SO:0001627	intron_variant	7273	exon46			AGAAGACGTATCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+1892G>A	2.37:g.179615958C>T		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	121	36	NM_133379	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|1.000;T|0.000		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179615958	C	T	179615958	1	4	138	0	1	0	0	0	0	0	0	0	16768	523	19	1		1	TTN	2	179615958	Intron	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10	24060427	179615958	63583415	5	12258											
SLC11A1	6556	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219249037	219249037	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgagcattgctttcctggaCccaggaaacatcgagtcaga	12	9	10	10	1	1	2	1	1	0	1	3	5	2	4	2	2	3	2	2	2	1	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:219249037C>A	ENST00000233202.6	+	3	562	c.222C>A	c.(220-222)gaC>gaA	p.D74E	SLC11A1_ENST00000473367.1_Intron|SLC11A1_ENST00000539932.1_5'UTR	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	74	Pro/Ser-rich.				activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTTCCTGGACCCAGGAAACA	0.592																																					p.D74E													.	SLC11A1-93	0			c.C222A						.						116	112	113					2																	219249037		2203	4300	6503	SO:0001583	missense	6556	exon3			CCTGGACCCAGGA	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"Solute carriers"	10907	protein-coding gene	gene with protein product	"natural resistance-associated macrophage protein 1"	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.222C>A	2.37:g.219249037C>A	ENSP00000233202:p.Asp74Glu	Somatic	123	1		WXS	Illumina HiSeq	Phase_I	103	32	NM_000578	0	0	2	2	0	C0H5Y3	Missense_Mutation	SNP	ENST00000233202.6	37	CCDS2415.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.050694	0.75960	.	.	ENSG00000018280	ENST00000233202	T	0.56103	0.48	5.06	0.964	0.19655	.	0.000000	0.85682	D	0.000000	T	0.78710	0.4326	H	0.97214	3.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.80641	-0.1292	10	0.87932	D	0	-45.4925	9.4926	0.38969	0.0:0.6108:0.0:0.3892	.	74;74;74	Q9HBK0;B4DQ73;P49279	.;.;NRAM1_HUMAN	E	74	ENSP00000233202:D74E	ENSP00000233202:D74E	D	+	3	2	SLC11A1	218957281	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.564000	0.23563	0.306000	0.22856	0.561000	0.74099	GAC	.		0.592	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578		A	219249037	C	A	219249037	3	1	138	1	0	0	0	0	1	0	0	0	14412	506	18	4	232	4	SLC11A1	2	219249037	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10	39633079	219249037	23950336	6	12259											
CRBN	51185	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	3209472	3209472	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatttgcactttagcttgcTggattctaaaataaagagaa	15	13	8	5	0	1	1	0	0	1	1	1	4	1	2	0	1	3	3	0	1	7	7			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:3209472T>G	ENST00000231948.4	-	5	555	c.533A>C	c.(532-534)cAg>cCg	p.Q178P	CRBN_ENST00000432408.2_Missense_Mutation_p.Q177P	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	178	Lon.				negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)			endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	TTTAGCTTGCTGGATTCTAAA	0.333																																					p.Q178P		.											.	CRBN-91	0			c.A533C						.						90	89	89					3																	3209472		2203	4300	6503	SO:0001583	missense	51185	exon5			GCTTGCTGGATTC	BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"mental retardation, non-syndromic, autosomal recessive, 2A"	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.533A>C	3.37:g.3209472T>G	ENSP00000231948:p.Gln178Pro	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	52	19	NM_016302	0	0	0	0	0	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Missense_Mutation	SNP	ENST00000231948.4	37	CCDS2562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.59|13.59	2.282820|2.282820	0.40394|0.40394	.|.	.|.	ENSG00000113851|ENSG00000113851	ENST00000231948;ENST00000432408;ENST00000546075|ENST00000424814;ENST00000450014	T;T|.	0.40225|.	1.04;1.04|.	5.1|5.1	5.1|5.1	0.69264|0.69264	Peptidase S16, lon N-terminal (2);PUA-like domain (1);|.	0.056186|.	0.64402|.	D|.	0.000001|.	T|T	0.38931|0.38931	0.1059|0.1059	N|N	0.08118|0.08118	0|0	0.54753|0.54753	D|D	0.999981|0.999981	B;B;B|.	0.06786|.	0.001;0.0;0.001|.	B;B;B|.	0.08055|.	0.003;0.002;0.003|.	T|T	0.31779|0.31779	-0.9931|-0.9931	10|5	0.29301|.	T|.	0.29|.	-13.9919|-13.9919	15.19|15.19	0.73035|0.73035	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	115;177;178|.	F5H3U1;Q96SW2-2;Q96SW2|.	.;.;CRBN_HUMAN|.	P|R	178;177;115|174	ENSP00000231948:Q178P;ENSP00000412499:Q177P|.	ENSP00000231948:Q178P|.	Q|S	-|-	2|1	0|0	CRBN|CRBN	3184472|3184472	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.567000|3.567000	0.53813|0.53813	2.045000|2.045000	0.60652|0.60652	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.		0.333	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302		G	3209472	T	G	3209472	3	3	138	1	0	0	0	0	1	0	0	0	3857	1580	55	5	823	5	CRBN	3	3209472	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		3209472	194812958	7	12260											
ACVR2B	93	broad.mit.edu	37	chr3	38519723	38519723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcctttccctcatcgtcctGctggccttttggatgtaccg	3	14	10	14	2	1	0	1	0	0	0	4	1	3	1	5	3	2	2	5	3	1	4			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:38519723G>A	ENST00000352511.4	+	4	934	c.462G>A	c.(460-462)ctG>ctA	p.L154L		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	154					activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		TCATCGTCCTGCTGGCCTTTT	0.642																																					p.L154L													.	ACVR2B-942	0			c.G462A						.						70	70	70					3																	38519723		2203	4300	6503	SO:0001819	synonymous_variant	93	exon4			CGTCCTGCTGGCC	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.462G>A	3.37:g.38519723G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	142	4	NM_001106	0	0	1	1	0	Q4VAV0	Silent	SNP	ENST00000352511.4	37	CCDS2679.1																																																																																			.		0.642	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		A	38519723	G	A	38519723	2	1	138	1	0	0	0	0	0	0	0	1	224	1306	46	2		2	ACVR2B	3	38519723	Silent	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	35310251	38519723	159502707	8	12261											
KLHDC8B	200942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49212303	49212303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccatggctgaaggcagcGtctttagcctgggtggcctg	5	9	16	11	2	1	1	0	1	1	0	1	1	1	1	3	4	2	2	3	4	2	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:49212303G>A	ENST00000332780.2	+	4	879	c.670G>A	c.(670-672)Gtc>Atc	p.V224I	KLHDC8B_ENST00000476495.2_3'UTR|C3orf84_ENST00000443990.1_5'Flank	NM_173546.2	NP_775817.1	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	224						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGAAGGCAGCGTCTTTAGCCT	0.592																																					p.V224I		.											.	KLHDC8B-90	0			c.G670A						.						50	51	51					3																	49212303		2203	4300	6503	SO:0001583	missense	200942	exon4			GGCAGCGTCTTTA		CCDS2791.1	3p21.31	2008-02-05			ENSG00000185909	ENSG00000185909			28557	protein-coding gene	gene with protein product		613169					Standard	NM_173546		Approved	MGC35097	uc003cwh.3	Q8IXV7	OTTHUMG00000156814	ENST00000332780.2:c.670G>A	3.37:g.49212303G>A	ENSP00000327468:p.Val224Ile	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	58	31	NM_173546	0	0	9	17	8		Missense_Mutation	SNP	ENST00000332780.2	37	CCDS2791.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.459584	0.26248	.	.	ENSG00000185909	ENST00000332780	T	0.71222	-0.55	5.97	2.98	0.34508	Kelch-type beta propeller (1);	0.187468	0.46145	N	0.000320	T	0.44498	0.1296	N	0.12182	0.205	0.32968	D	0.521921	B;B	0.25272	0.103;0.122	B;B	0.16289	0.009;0.015	T	0.44590	-0.9318	10	0.14252	T	0.57	-25.1154	6.9162	0.24361	0.1603:0.0:0.608:0.2317	.	178;224	B4DFM2;Q8IXV7	.;KLD8B_HUMAN	I	224	ENSP00000327468:V224I	ENSP00000327468:V224I	V	+	1	0	KLHDC8B	49187307	0.897000	0.30589	0.786000	0.31890	0.987000	0.75469	1.471000	0.35365	0.874000	0.35823	0.655000	0.94253	GTC	.		0.592	KLHDC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345974.1	NM_173546		A	49212303	G	A	49212303	3	1	138	1	0	0	0	0	1	0	0	0	8384	1145	40	1	680	1	KLHDC8B	3	49212303	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	10692580	49212303	148810127	9	12262											
EPHA6	285220	broad.mit.edu	37	chr3	96533514	96533514	+	Frame_Shift_Del	DEL	A	A	-																															gaggagctccccggcgccgcAggcagcgtcctcctccgaag																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:96533514delA	ENST00000389672.5	+	1	85	c.47delA	c.(46-48)cagfs	p.Q16fs	EPHA6_ENST00000470610.2_Frame_Shift_Del_p.Q16fs|EPHA6_ENST00000542517.1_5'Flank	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	0						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						CCGGCGCCGCAGGCAGCGTCC	0.711																																					p.Q16fs													.	EPHA6-1561	0			c.47delA						.						17	21	20					3																	96533514		2057	4183	6240	SO:0001589	frameshift_variant	285220	exon1			CGCCGCAGGCAGC	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.47delA	3.37:g.96533514delA	ENSP00000374323:p.Gln16fs	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	6	3	NM_001080448	0	0	0	0	0	D6RAL5	Frame_Shift_Del	DEL	ENST00000389672.5	37	CCDS46876.1																																																																																			.		0.711	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		-	96533514	A	-	96533514	7	5	138	1	0	1	0	1	0	0	0	0	5184	188	7	0	49	0	EPHA6	3	96533514	Frame_Shift_Del	DEL	A	TCGA-IA-A40X-01A-11D-A25F-10	47321211	96533514	101488916	10	12263											
CHRD	8646	bcgsc.ca	37	chr3	184106751	184106751	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggctcggggaaggagagtcGatgctgttcccgctgcacgg	6	8	17	10	4	0	1	0	0	0	1	3	4	1	2	1	5	2	5	1	5	1	1	rs200027250		TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:184106751G>A	ENST00000204604.1	+	22	3026	c.2780G>A	c.(2779-2781)cGa>cAa	p.R927Q	CHRD_ENST00000545352.1_Missense_Mutation_p.R469Q|CHRD_ENST00000348986.3_Missense_Mutation_p.R887Q|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.R927Q	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	927	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AAGGAGAGTCGATGCTGTTCC	0.622													G|||	1	0.000199681	8e-04	0	5008	,	,		16920	0		0	False		,,,				2504	0				p.R927Q													.	CHRD-93	0			c.G2780A						.						93	78	83					3																	184106751		2203	4300	6503	SO:0001583	missense	8646	exon22			AGAGTCGATGCTG	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.2780G>A	3.37:g.184106751G>A	ENSP00000204604:p.Arg927Gln	Somatic	80	0		WXS	Illumina HiSeq	Phase_1	86	4	NM_003741	0	0	25	25	0	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	16.82	3.229186	0.58777	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	4.93	3.09	0.35607	von Willebrand factor, type C (1);	0.295775	0.28109	N	0.016569	T	0.45518	0.1346	N	0.11064	0.09	0.18873	N	0.999989	P;D;P;D	0.67145	0.944;0.996;0.954;0.993	B;P;B;P	0.51385	0.201;0.668;0.262;0.57	T	0.30534	-0.9975	10	0.21540	T	0.41	-3.6881	6.6856	0.23144	0.098:0.18:0.722:0.0	.	469;887;927;927	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	Q	927;927;887;469	ENSP00000204604:R927Q;ENSP00000408972:R927Q;ENSP00000334036:R887Q;ENSP00000442948:R469Q	ENSP00000204604:R927Q	R	+	2	0	CHRD	185589445	0.823000	0.29233	0.936000	0.37596	0.526000	0.34562	2.487000	0.45268	0.456000	0.26937	0.655000	0.94253	CGA	G|0.999;A|0.000		0.622	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		A	184106751	G	A	184106751	3	1	138	1	0	0	0	0	1	0	0	0	3378	1058	37	1	2866	1	CHRD	3	184106751	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	87573237	184106751	13915679	11	12264											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811102	140811102	+	Silent	SNP	C	C	T																															tgctgctgctgctgctgctgCtgctgctgctgctgctgctg																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr4:140811102C>T	ENST00000509479.2	-	2	2344	c.1488G>A	c.(1486-1488)caG>caA	p.Q496Q	MAML3_ENST00000398940.1_Silent_p.Q35Q|MAML3_ENST00000327122.5_Silent_p.Q340Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.542																																					p.Q496Q		.											.	MAML3-455	0			c.G1488A						.						13	19	17					4																	140811102		2124	4242	6366	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1488G>A	4.37:g.140811102C>T		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	92	12	NM_018717	0	4	3216	3314	94		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811102	C	T	140811102	2	4	138	1	0	0	0	0	0	0	0	1	9232	796	28	2		2	MAML3	4	140811102	Silent	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		140811102	50343174	12	12265	125	2									
MAML3	55534	hgsc.bcm.edu	37	chr4	140811104	140811104	+	Missense_Mutation	SNP	G	G	T																															ctgctgctgctgctgctgctGctgctgctgctgctgctgtt																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr4:140811104G>T	ENST00000509479.2	-	2	2342	c.1486C>A	c.(1486-1488)Cag>Aag	p.Q496K	MAML3_ENST00000398940.1_Missense_Mutation_p.Q35K|MAML3_ENST00000327122.5_Missense_Mutation_p.Q340K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgctgctgctgctgctgctgc	0.542																																					p.Q496K		.											.	MAML3-455	0			c.C1486A						.						13	18	17					4																	140811104		2145	4254	6399	SO:0001583	missense	55534	exon2			GCTGCTGCTGCTG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1486C>A	4.37:g.140811104G>T	ENSP00000421180:p.Gln496Lys	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	93	10	NM_018717	10	2	2727	2741	2		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	g	6.502	0.460780	0.12342	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.64260	0.89;-0.09	4.53	4.53	0.55603	.	0.116387	0.37577	N	0.002035	T	0.39937	0.1097	N	0.08118	0	0.32507	N	0.538137	B	0.22276	0.067	B	0.19391	0.025	T	0.35025	-0.9805	10	0.06494	T	0.89	.	17.2683	0.87093	0.0:0.0:1.0:0.0	.	496	Q96JK9	MAML3_HUMAN	K	496;340;35	ENSP00000421180:Q496K;ENSP00000313316:Q340K	ENSP00000313316:Q340K	Q	-	1	0	MAML3	141030554	0.998000	0.40836	0.988000	0.46212	0.665000	0.39181	0.180000	0.16860	2.038000	0.60285	0.455000	0.32223	CAG	.		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811104	G	T	140811104	3	4	138	1	0	0	0	0	1	0	0	0	9232	1328	46	4	1938	4	MAML3	4	140811104	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	2	140811104	50343172	13	12266	125	2									
SLC6A19	340024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1219218	1219218	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagtggcccaaggaggtgctCacaggtacgtgtgcagtcgg	9	7	16	9	2	1	0	1	0	0	0	2	1	1	1	1	5	3	3	1	5	3	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr5:1219218C>T	ENST00000304460.10	+	9	1430	c.1374C>T	c.(1372-1374)ctC>ctT	p.L458L		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	458					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AGGAGGTGCTCACAGGTACGT	0.642																																					p.L458L		.											.	SLC6A19-90	0			c.C1374T						.						117	100	106					5																	1219218		2201	4298	6499	SO:0001819	synonymous_variant	340024	exon9			GGTGCTCACAGGT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1374C>T	5.37:g.1219218C>T		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	106	41	NM_001003841	0	0	0	0	0	A8K446	Silent	SNP	ENST00000304460.10	37	CCDS34130.1																																																																																			.		0.642	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		T	1219218	C	T	1219218	2	4	138	1	0	0	0	0	0	0	0	1	14714	813	29	2		2	SLC6A19	5	1219218	Silent	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		1219218	179696042	14	12267											
LYRM4	57128	hgsc.bcm.edu	37	chr6	5260906	5260906	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgtaggcgctgaaacgctTgctctctctcagcatcgccc	7	11	9	14	3	2	1	1	1	2	0	5	1	2	1	1	1	3	5	1	1	2	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr6:5260906T>A	ENST00000330636.4	-	1	266	c.61A>T	c.(61-63)Aag>Tag	p.K21*	LYRM4_ENST00000464010.1_Nonsense_Mutation_p.K21*|LYRM4_ENST00000468929.1_Nonsense_Mutation_p.K21*|LYRM4_ENST00000500576.2_Nonsense_Mutation_p.K21*|LYRM4_ENST00000480566.1_Nonsense_Mutation_p.K21*|FARS2_ENST00000324331.6_5'Flank|FARS2_ENST00000274680.4_5'Flank	NM_020408.4	NP_065141.3	Q9HD34	LYRM4_HUMAN	LYR motif containing 4	21					small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)				endometrium(1)	1	Ovarian(93;0.11)	all_hematologic(90;0.0901)				CTGAAACGCTTGCTCTCTCTC	0.627																																					p.K21X	NSCLC(130;1006 2426 17608 36797)	.											.	LYRM4-90	0			c.A61T						.						25	24	24					6																	5260906		2161	4232	6393	SO:0001587	stop_gained	57128	exon1			AACGCTTGCTCTC	AF258559	CCDS4493.1, CCDS54961.1	6p25.1	2008-02-05	2006-09-19	2006-09-19	ENSG00000214113	ENSG00000214113		"LYR motif containing"	21365	protein-coding gene	gene with protein product		613311	"chromosome 6 open reading frame 149"	C6orf149			Standard	XM_005249239		Approved	CGI-203, ISD11	uc021ykw.1	Q9HD34	OTTHUMG00000014173	ENST00000330636.4:c.61A>T	6.37:g.5260906T>A	ENSP00000418787:p.Lys21*	Somatic	6	0		WXS	Illumina HiSeq	Phase_I	13	9	NM_020408	0	0	12	27	15	A8K543|Q5XKP1	Nonsense_Mutation	SNP	ENST00000330636.4	37	CCDS4493.1	.	.	.	.	.	.	.	.	.	.	T	40	8.023762	0.98616	.	.	ENSG00000214113	ENST00000468929;ENST00000330636;ENST00000464010;ENST00000480566;ENST00000500576	.	.	.	5.04	1.08	0.20341	.	0.185374	0.32753	U	0.005684	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-6.0522	1.2294	0.01940	0.1825:0.1031:0.1903:0.5241	.	.	.	.	X	21	.	ENSP00000418787:K21X	K	-	1	0	LYRM4	5205905	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.725000	0.25970	1.898000	0.54952	0.533000	0.62120	AAG	.		0.627	LYRM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353461.3	NM_020408		A	5260906	T	A	5260906	4	1	138	1	0	0	0	0	0	1	0	0	9146	1821	63	5	504	5	LYRM4	6	5260906	Nonsense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		5260906	165854161	15	12268											
ABCF1	23	broad.mit.edu	37	chr6	30550906	30550906	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgaaaatgacttctccGtgtcccaggcggagatgtcc	9	9	11	12	2	1	3	0	2	1	1	4	4	3	3	3	2	1	1	3	2	2	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr6:30550906G>A	ENST00000326195.8	+	10	968	c.856G>A	c.(856-858)Gtg>Atg	p.V286M	ABCF1_ENST00000396515.4_Intron|ABCF1_ENST00000376545.3_Missense_Mutation_p.V248M|MIR877_ENST00000401282.1_RNA	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	286					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						TGACTTCTCCGTGTCCCAGGC	0.498																																					p.V286M													.	ABCF1-92	0			c.G856A						.						89	93	92					6																	30550906		1509	2708	4217	SO:0001583	missense	23	exon10			TTCTCCGTGTCCC	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"ATP binding cassette transporters / subfamily F"	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.856G>A	6.37:g.30550906G>A	ENSP00000313603:p.Val286Met	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	125	3	NM_001025091	0	0	22	22	0	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	37	CCDS34380.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.738855	0.69304	.	.	ENSG00000204574	ENST00000326195;ENST00000376545;ENST00000455943;ENST00000441867	T;T;T	0.55930	0.52;0.83;0.49	5.41	5.41	0.78517	.	0.280189	0.34002	N	0.004351	T	0.43942	0.1270	L	0.41573	1.285	0.80722	D	1	P;P;P	0.52692	0.905;0.955;0.955	P;P;P	0.51079	0.557;0.658;0.658	T	0.16453	-1.0402	10	0.22109	T	0.4	-26.4394	17.9672	0.89102	0.0:0.0:1.0:0.0	.	248;286;286	Q2L6I2;Q8NE71;A2BF75	.;ABCF1_HUMAN;.	M	286;248;287;287	ENSP00000313603:V286M;ENSP00000365728:V248M;ENSP00000405512:V287M	ENSP00000313603:V286M	V	+	1	0	ABCF1	30658885	1.000000	0.71417	0.997000	0.53966	0.953000	0.61014	5.478000	0.66806	2.553000	0.86117	0.313000	0.20887	GTG	.		0.498	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			A	30550906	G	A	30550906	3	1	138	1	0	0	0	0	1	0	0	0	65	1145	40	1	894	1	ABCF1	6	30550906	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	25290000	30550906	140564161	16	12269											
TNRC18	84629	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5396874	5396874	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgcttgccaactgctcctGgtcgctggccatcttcttct	3	15	8	15	1	3	0	0	0	3	0	5	0	4	0	3	2	4	3	3	2	1	4			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr7:5396874G>A	ENST00000430969.1	-	16	5215	c.4867C>T	c.(4867-4869)Cag>Tag	p.Q1623*	TNRC18_ENST00000399537.4_Nonsense_Mutation_p.Q1623*	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1623							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		AACTGCTCCTGGTCGCTGGCC	0.507																																					p.Q1623X													.	TNRC18-46	0			c.C4867T						.						46	47	46					7																	5396874		2005	4189	6194	SO:0001587	stop_gained	84629	exon16			GCTCCTGGTCGCT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4867C>T	7.37:g.5396874G>A	ENSP00000395538:p.Gln1623*	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	112	48	NM_001080495	0	0	9	15	6	A8MX41|Q96JH1|Q96K91	Nonsense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	g	35	5.528361	0.96446	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	.	.	.	5.25	5.25	0.73442	.	0.000000	0.37348	N	0.002123	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	18.8572	0.92257	0.0:0.0:1.0:0.0	.	.	.	.	X	1623;1623;678;113	.	ENSP00000382452:Q1623X	Q	-	1	0	TNRC18	5363400	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.932000	0.87634	2.456000	0.83038	0.561000	0.74099	CAG	.		0.507	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5396874	G	A	5396874	4	1	138	1	0	0	0	0	0	1	0	0	16371	1357	47	2	4099	2	TNRC18	7	5396874	Nonsense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		5396874	153741789	17	12270											
C7orf31	136895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	25182389	25182389	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggagcgaaggttttaggaggTtttgggtagaatactggctt	9	13	16	3	1	0	1	0	0	0	1	0	4	0	3	0	6	2	4	0	6	5	7			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr7:25182389T>G	ENST00000409280.1	-	8	1037	c.729A>C	c.(727-729)aaA>aaC	p.K243N	C7orf31_ENST00000283905.3_Missense_Mutation_p.K243N			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	243										autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						TTTTAGGAGGTTTTGGGTAGA	0.378																																					p.K243N		.											.	C7orf31-90	0			c.A729C						.						91	98	95					7																	25182389		2203	4300	6503	SO:0001583	missense	136895	exon8			AGGAGGTTTTGGG	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.729A>C	7.37:g.25182389T>G	ENSP00000386604:p.Lys243Asn	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	89	38	NM_138811	0	0	0	1	1	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131855	0.56828	.	.	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.08720	3.06;3.06	5.51	3.06	0.35304	.	0.133847	0.47093	D	0.000247	T	0.21267	0.0512	M	0.65975	2.015	0.30063	N	0.810728	D	0.76494	0.999	D	0.74674	0.984	T	0.03597	-1.1021	10	0.40728	T	0.16	-1.5455	7.6462	0.28321	0.0:0.3231:0.0:0.6769	.	243	Q8N865	CG031_HUMAN	N	243	ENSP00000386604:K243N;ENSP00000283905:K243N	ENSP00000283905:K243N	K	-	3	2	C7orf31	25148914	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	0.178000	0.16820	0.357000	0.24183	0.397000	0.26171	AAA	.		0.378	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811		G	25182389	T	G	25182389	3	3	138	1	0	0	0	0	1	0	0	0	2393	1722	60	5	1055	5	C7orf31	7	25182389	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10	19785515	25182389	133956274	18	12271											
NOM1	64434	hgsc.bcm.edu	37	chr7	156742605	156742605	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcgtgcacgcgacttcggaAggcgaggctcccgggggttg	5	8	17	11	6	0	0	0	0	0	0	3	3	1	1	1	5	1	3	1	5	1	3	rs149616380	byFrequency	TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr7:156742605A>G	ENST00000275820.3	+	1	189	c.174A>G	c.(172-174)gaA>gaG	p.E58E		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	58	Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		CGACTTCGGAAGGCGAGGCTC	0.706													.|||	55	0.0109824	0.0401	0.0029	5008	,	,		10993	0		0	False		,,,				2504	0				p.E58E		.											.	NOM1-90	0			c.A174G						.	G		110,3692		1,108,1792	8	10	9		174	2.3	0	7	dbSNP_134	9	0,7382		0,0,3691	no	coding-synonymous	NOM1	NM_138400.1		1,108,5483	GG,GA,AA		0.0,2.8932,0.9835		58/861	156742605	110,11074	1901	3691	5592	SO:0001819	synonymous_variant	64434	exon1			TTCGGAAGGCGAG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 113"	611269	"chromosome 7 open reading frame 3"	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.174A>G	7.37:g.156742605A>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_138400	0	0	2	2	0	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			A|0.993;G|0.007		0.706	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		G	156742605	A	G	156742605	2	3	138	1	0	0	0	0	0	0	0	1	10556	69	3	3		3	NOM1	7	156742605	Silent	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10	131560216	156742605	2396058	19	12272											
KIAA1539	80256	ucsc.edu;bcgsc.ca	37	chr9	35106598	35106598	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acaggggaggcactggggggGctcagcaggcctggcccctt	6	5	18	12	0	1	0	1	0	0	0	1	1	1	1	3	8	1	3	3	8	0	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr9:35106598G>T	ENST00000378561.1	-	4	4051	c.996C>A	c.(994-996)agC>agA	p.S332R	FAM214B_ENST00000378554.2_Missense_Mutation_p.S332R|FAM214B_ENST00000603301.1_Missense_Mutation_p.S332R|FAM214B_ENST00000378557.1_Missense_Mutation_p.S332R|FAM214B_ENST00000488109.2_Missense_Mutation_p.S332R|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000378566.1_Missense_Mutation_p.S27R|FAM214B_ENST00000322813.5_Missense_Mutation_p.S332R|FAM214B_ENST00000605244.1_Missense_Mutation_p.S332R			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	332						nucleus (GO:0005634)											CACTGGGGGGGCTCAGCAGGC	0.622																																					p.S332R													.	.	0			c.C996A						.						11	13	13					9																	35106598		2179	4273	6452	SO:0001583	missense	80256	exon5			GGGGGGGCTCAGC	AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"KIAA1539"	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.996C>A	9.37:g.35106598G>T	ENSP00000367823:p.Ser332Arg	Somatic	45	0		WXS	Illumina HiSeq		37	4	NM_025182	0	0	9	9	0	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Missense_Mutation	SNP	ENST00000378561.1	37	CCDS6578.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.442584	0.43326	.	.	ENSG00000005238	ENST00000378566;ENST00000322813;ENST00000378561;ENST00000378557;ENST00000378554	.	.	.	5.38	4.47	0.54385	.	0.226724	0.42821	D	0.000655	T	0.38612	0.1047	N	0.14661	0.345	0.45129	D	0.998147	B	0.25169	0.119	B	0.29440	0.102	T	0.16660	-1.0395	9	0.11485	T	0.65	-21.9657	13.3283	0.60473	0.0781:0.0:0.9219:0.0	.	332	Q7L5A3	K1539_HUMAN	R	27;332;332;332;332	.	ENSP00000319897:S332R	S	-	3	2	KIAA1539	35096598	0.008000	0.16893	0.996000	0.52242	0.978000	0.69477	0.174000	0.16743	2.813000	0.96785	0.655000	0.94253	AGC	.		0.622	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182		T	35106598	G	T	35106598	3	4	138	1	0	0	0	0	1	0	0	0	8263	1194	42	4	640	4	KIAA1539	9	35106598	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		35106598	106106833	20	12273											
C9orf153	389766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	88844472	88844472	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgaacattgaggaagggtgGcttctctattgtcctcagct	8	13	11	9	0	2	2	1	2	1	0	4	3	3	3	1	3	2	2	1	3	3	4			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr9:88844472G>A	ENST00000376001.3	-	2	127	c.47C>T	c.(46-48)gCc>gTc	p.A16V	C9orf153_ENST00000339137.3_Missense_Mutation_p.A16V|C9orf153_ENST00000469914.1_5'UTR	NM_001276366.1	NP_001263295.1	Q5TBE3	CI153_HUMAN	chromosome 9 open reading frame 153	16										breast(1)|lung(1)	2						AGGAAGGGTGGCTTCTCTATT	0.393																																					p.A16V		.											.	C9orf153-90	0			c.C47T						.						173	130	144					9																	88844472		2203	4300	6503	SO:0001583	missense	389766	exon3			AGGGTGGCTTCTC		CCDS35055.1, CCDS35055.2	9q22.1	2012-04-03			ENSG00000187753	ENSG00000187753			31456	protein-coding gene	gene with protein product							Standard	NM_001276366		Approved	bA507D14.1	uc031teh.1	Q5TBE3	OTTHUMG00000020134	ENST00000376001.3:c.47C>T	9.37:g.88844472G>A	ENSP00000365169:p.Ala16Val	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	103	37	NM_001276368	0	0	0	0	0	Q5TBE4	Missense_Mutation	SNP	ENST00000376001.3	37	CCDS35055.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166595	0.38217	.	.	ENSG00000187753	ENST00000339137;ENST00000376001	T;T	0.43294	0.95;0.95	3.33	-2.4	0.06583	.	1.675050	0.04061	N	0.306344	T	0.22704	0.0548	N	0.24115	0.695	0.09310	N	1	P;P	0.42584	0.784;0.642	B;B	0.33690	0.168;0.089	T	0.15093	-1.0449	10	0.52906	T	0.07	.	2.4955	0.04621	0.1061:0.1403:0.2414:0.5123	.	16;16	Q5TBE3;Q5TBE3-2	CI153_HUMAN;.	V	16	ENSP00000344865:A16V;ENSP00000365169:A16V	ENSP00000344865:A16V	A	-	2	0	C9orf153	88034292	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.853000	0.04303	-0.543000	0.06240	0.655000	0.94253	GCC	.		0.393	C9orf153-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052913.1	NM_001010907		A	88844472	G	A	88844472	3	1	138	1	0	0	0	0	1	0	0	0	2470	1203	42	2	270	2	C9orf153	9	88844472	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	53737874	88844472	52368959	21	12274											
CTNNA3	29119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	67726425	67726425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctcagctttaacttgactgCagattttcagttggtgggag	8	15	11	7	0	2	2	2	1	1	1	3	3	2	3	0	2	3	3	0	2	1	6			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr10:67726425C>T	ENST00000433211.2	-	17	2519	c.2345G>A	c.(2344-2346)tGc>tAc	p.C782Y	CTNNA3_ENST00000373735.1_5'UTR|CTNNA3_ENST00000373744.4_Missense_Mutation_p.C782Y	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						AACTTGACTGCAGATTTTCAG	0.438																																					p.C782Y		.											.	CTNNA3-234	0			c.G2345A						.						114	109	111					10																	67726425		2203	4300	6503	SO:0001583	missense	29119	exon17			TGACTGCAGATTT	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.2345G>A	10.37:g.67726425C>T	ENSP00000389714:p.Cys782Tyr	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	131	53	NM_013266	0	0	0	0	0		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771295	0.69992	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000373735	T;T;T	0.37915	1.17;1.17;1.17	5.41	3.56	0.40772	.	0.000000	0.64402	D	0.000004	T	0.39911	0.1096	M	0.75447	2.3	0.80722	D	1	P	0.37500	0.597	B	0.38562	0.276	T	0.36383	-0.9750	10	0.72032	D	0.01	-1.9994	10.42	0.44344	0.0:0.8383:0.0:0.1617	.	782	Q9UI47	CTNA3_HUMAN	Y	782;782;121	ENSP00000389714:C782Y;ENSP00000362849:C782Y;ENSP00000362840:C121Y	ENSP00000362840:C121Y	C	-	2	0	CTNNA3	67396431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	0.771000	0.33359	0.650000	0.86243	TGC	.		0.438	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	67726425	C	T	67726425	3	4	138	1	0	0	0	0	1	0	0	0	4020	710	25	2	350	2	CTNNA3	10	67726425	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		67726425	67808322	22	12275											
NUP98	4928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	3744474	3744474	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaagacgtttcttcactgcTtccttccagcccatttcgca	9	13	5	14	2	2	1	1	0	1	1	5	1	4	1	3	0	2	3	3	0	2	5			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr11:3744474T>A	ENST00000324932.7	-	16	2479	c.2059A>T	c.(2059-2061)Agc>Tgc	p.S687C	NUP98_ENST00000397004.4_Missense_Mutation_p.S687C|NUP98_ENST00000355260.3_Missense_Mutation_p.S687C|NUP98_ENST00000397007.4_Missense_Mutation_p.S704C|NUP98_ENST00000359171.4_Missense_Mutation_p.S687C	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	704					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TCTTCACTGCTTCCTTCCAGC	0.433			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.S704C		.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98-703	0			c.A2110T						.						181	154	163					11																	3744474		2201	4298	6499	SO:0001583	missense	4928	exon16			CACTGCTTCCTTC	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.2059A>T	11.37:g.3744474T>A	ENSP00000316032:p.Ser687Cys	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	251	93	NM_005387	0	0	2	2	0	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.985170	0.74474	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.	.	.	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.77046	0.4073	M	0.70275	2.135	0.53005	D	0.999969	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.85130	0.98;0.951;0.997;0.997	T	0.79546	-0.1759	9	0.62326	D	0.03	.	13.3986	0.60870	0.0:0.0:0.0:1.0	.	704;687;687;687	P52948-3;P52948-4;P52948-2;P52948-5	.;.;.;.	C	687;687;687;687;704	.	ENSP00000316032:S687C	S	-	1	0	NUP98	3701050	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.800000	0.62524	1.773000	0.52216	0.477000	0.44152	AGC	.		0.433	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		A	3744474	T	A	3744474	3	1	138	1	0	0	0	0	1	0	0	0	10799	1609	56	5	3436	5	NUP98	11	3744474	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		3744474	131262042	23	12276											
MTMR2	8898	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	95568462	95568462	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttacagtcctttatacaaCagtttggacaggagtgacac	12	12	8	9	0	1	1	0	1	1	0	2	3	2	3	1	2	3	1	1	2	4	5			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr11:95568462C>T	ENST00000346299.5	-	15	2264	c.1924G>A	c.(1924-1926)Gtt>Att	p.V642I	MTMR2_ENST00000393223.3_Missense_Mutation_p.V570I|MTMR2_ENST00000409459.1_Missense_Mutation_p.V570I|MTMR2_ENST00000352297.7_Missense_Mutation_p.V570I	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	642					cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTTTATACAACAGTTTGGACA	0.438																																					p.V642I													.	MTMR2-91	0			c.G1924A						.						103	91	95					11																	95568462		2201	4297	6498	SO:0001583	missense	8898	exon15			ATACAACAGTTTG	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1924G>A	11.37:g.95568462C>T	ENSP00000345752:p.Val642Ile	Somatic	124	1		WXS	Illumina HiSeq	Phase_I	158	56	NM_016156	0	0	17	37	20	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	37	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159321	0.57368	.	.	ENSG00000087053	ENST00000346299;ENST00000393223;ENST00000409459;ENST00000352297	D;D;D;D	0.95756	-3.55;-3.8;-3.8;-3.8	6.17	6.17	0.99709	.	0.050299	0.85682	D	0.000000	D	0.89626	0.6769	N	0.08118	0	0.52501	D	0.99995	B	0.27229	0.172	B	0.22386	0.039	D	0.85343	0.1097	10	0.17369	T	0.5	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	642	Q13614	MTMR2_HUMAN	I	642;570;570;570	ENSP00000345752:V642I;ENSP00000376915:V570I;ENSP00000386882:V570I;ENSP00000343737:V570I	ENSP00000345752:V642I	V	-	1	0	MTMR2	95208110	1.000000	0.71417	0.221000	0.23827	0.035000	0.12851	4.526000	0.60566	2.941000	0.99782	0.655000	0.94253	GTT	.		0.438	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		T	95568462	C	T	95568462	3	4	138	1	0	0	0	0	1	0	0	0	9969	478	17	2	11	2	MTMR2	11	95568462	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10	91823988	95568462	39438054	24	12277											
EFCAB4B	84766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	3765545	3765545	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttctgctccagctcttGactgcgggcttgaaacctct	6	13	9	13	1	3	2	0	2	3	0	4	2	4	2	2	1	4	4	2	1	1	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr12:3765545G>T	ENST00000252322.1	-	9	1258	c.790C>A	c.(790-792)Caa>Aaa	p.Q264K	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.Q264K|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.Q264K	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		264					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TCCAGCTCTTGACTGCGGGCT	0.517																																					p.Q264K		.											.	EFCAB4B-92	0			c.C790A						.						117	98	105					12																	3765545		2203	4300	6503	SO:0001583	missense	84766	exon9			GCTCTTGACTGCG																												ENST00000252322.1:c.790C>A	12.37:g.3765545G>T	ENSP00000252322:p.Gln264Lys	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	109	37	NM_001144958	0	0	0	0	0	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	g	8.882	0.951842	0.18431	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.21031	2.03;2.62;2.62	4.87	4.87	0.63330	.	0.650048	0.16394	N	0.216346	T	0.15003	0.0362	L	0.31294	0.92	0.27366	N	0.955823	B;B;B	0.22346	0.068;0.037;0.022	B;B;B	0.15484	0.006;0.013;0.006	T	0.10154	-1.0642	10	0.23302	T	0.38	-9.002	11.0361	0.47802	0.0:0.0:0.8142:0.1858	.	264;264;264	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	K	264	ENSP00000409382:Q264K;ENSP00000412496:Q264K;ENSP00000252322:Q264K	ENSP00000252322:Q264K	Q	-	1	0	EFCAB4B	3635806	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.957000	0.56730	2.385000	0.81259	0.556000	0.70494	CAA	.		0.517	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			T	3765545	G	T	3765545	3	4	138	1	0	0	0	0	1	0	0	0	4948	1299	45	4	1645	4	EFCAB4B	12	3765545	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		3765545	130086350	25	12278											
GPR133	283383	hgsc.bcm.edu	37	chr12	131476916	131476917	+	Frame_Shift_Ins	INS	-	-	AC																															gtaagtccctctcggagcagINSacagccttgaatctcaccaa																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr12:131476916_131476917insAC	ENST00000261654.5	+	8	1504_1505	c.945_946insAC	c.(946-948)acafs	p.T316fs	GPR133_ENST00000535015.1_Frame_Shift_Ins_p.T348fs|RP11-76C10.5_ENST00000542980.1_lincRNA	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	316					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(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		TCTCGGAGCAGACAGCCTTGAA	0.5																																					p.Q315fs		.											.	GPR133-191	0			c.945_946insAC						.																																			SO:0001589	frameshift_variant	283383	exon8			.	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"-", "GPCR / Class B : Orphans"	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.946_947dupAC	12.37:g.131476917_131476918dupAC	ENSP00000261654:p.Thr316fs	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	91	28	NM_198827	0	0	0	0	0	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Frame_Shift_Ins	INS	ENST00000261654.5	37	CCDS9272.1																																																																																			.		0.5	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		AC	131476917	-	AC	131476916	7	5	138	1	0	1	1	0	0	0	0	0	6663	933	33	0	975	0	GPR133	12	131476916	Frame_Shift_Ins	INS	-	TCGA-IA-A40X-01A-11D-A25F-10	127711371	131476916	2374979	26	12279											
HECTD1	25831	broad.mit.edu	37	chr14	31604103	31604103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcattgagactgcagtcatCaacatgggtatacaaagaag	15	10	9	7	0	3	2	3	1	0	2	3	3	3	2	0	1	3	2	0	1	5	4			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr14:31604103C>T	ENST00000399332.1	-	22	4041	c.3553G>A	c.(3553-3555)Gat>Aat	p.D1185N	HECTD1_ENST00000553700.1_Missense_Mutation_p.D1185N	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1185					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CTGCAGTCATCAACATGGGTA	0.388																																					p.D1185N													.	HECTD1-570	0			c.G3553A						.						72	65	67					14																	31604103		1855	4088	5943	SO:0001583	missense	25831	exon22			AGTCATCAACATG	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.3553G>A	14.37:g.31604103C>T	ENSP00000382269:p.Asp1185Asn	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	119	5	NM_015382	0	0	2	2	0	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.697335	0.88830	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.17054	2.3;2.3;2.3	5.91	5.91	0.95273	Galactose-binding domain-like (1);Sad1/UNC-like, C-terminal (1);	0.000000	0.85682	U	0.000000	T	0.30103	0.0754	N	0.17800	0.525	0.80722	D	1	P;D	0.69078	0.743;0.997	P;D	0.79108	0.758;0.992	T	0.02639	-1.1130	10	0.38643	T	0.18	-13.5834	20.2983	0.98569	0.0:1.0:0.0:0.0	.	1185;1185	D3DS86;Q9ULT8	.;HECD1_HUMAN	N	1185;1187;1185;659	ENSP00000450697:D1185N;ENSP00000382269:D1185N;ENSP00000451860:D659N	ENSP00000261312:D1187N	D	-	1	0	HECTD1	30673854	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.800000	0.85949	2.802000	0.96397	0.655000	0.94253	GAT	.		0.388	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31604103	C	T	31604103	3	4	138	1	0	0	0	0	1	0	0	0	7060	826	29	2	4367	2	HECTD1	14	31604103	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		31604103	75745437	27	12280											
IL21R	50615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27445763	27445763	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccccagcacgctcaccCttacctggtaagtagccggg	8	7	9	17	2	1	0	1	0	0	0	2	0	2	0	6	2	3	4	6	2	3	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr16:27445763C>G	ENST00000337929.3	+	3	618	c.145C>G	c.(145-147)Ctt>Gtt	p.L49V	IL21R_ENST00000395755.1_Missense_Mutation_p.L49V|IL21R_ENST00000564089.1_Missense_Mutation_p.L49V|IL21R_ENST00000395754.4_Missense_Mutation_p.L49V	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	49	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CACGCTCACCCTTACCTGGTA	0.612			T	BCL6	NHL																																p.L71V		.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R-660	0			c.C211G						.						92	67	75					16																	27445763		2197	4300	6497	SO:0001583	missense	50615	exon4			CTCACCCTTACCT	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.145C>G	16.37:g.27445763C>G	ENSP00000338010:p.Leu49Val	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	89	42	NM_181079	0	0	0	0	0	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	c	3.641	-0.073506	0.07184	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	D;D;D	0.97994	-4.65;-4.65;-4.65	4.39	0.877	0.19145	Fibronectin, type III (1);	55.521400	0.00166	N	0.000000	D	0.96272	0.8784	M	0.67953	2.075	0.80722	D	1	B	0.21225	0.053	B	0.17722	0.019	D	0.85799	0.1372	10	0.34782	T	0.22	-22.7421	6.3283	0.21257	0.3777:0.4383:0.184:0.0	.	49	Q9HBE5	IL21R_HUMAN	V	49	ENSP00000338010:L49V;ENSP00000379104:L49V;ENSP00000379103:L49V	ENSP00000338010:L49V	L	+	1	0	IL21R	27353264	0.011000	0.17503	0.032000	0.17829	0.011000	0.07611	0.263000	0.18478	0.530000	0.28619	0.555000	0.69702	CTT	.		0.612	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		G	27445763	C	G	27445763	3	3	138	1	0	0	0	0	1	0	0	0	7692	681	24	4	151	4	IL21R	16	27445763	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		27445763	62908990	28	12281											
IL21R	50615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27459874	27459874	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgggtgggtgcaccctTcactggctccagcctggagc	7	8	14	12	0	1	0	1	0	0	0	2	2	2	1	3	4	3	2	3	4	1	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr16:27459874T>C	ENST00000337929.3	+	9	1360	c.887T>C	c.(886-888)tTc>tCc	p.F296S	IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395755.1_Missense_Mutation_p.F296S|IL21R_ENST00000564089.1_Missense_Mutation_p.F296S|IL21R_ENST00000395754.4_Missense_Mutation_p.F296S|IL21R_ENST00000564583.1_3'UTR	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	296					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						GGTGCACCCTTCACTGGCTCC	0.547			T	BCL6	NHL																																p.F318S		.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R-660	0			c.T953C						.						16	19	18					16																	27459874		2177	4255	6432	SO:0001583	missense	50615	exon10			CACCCTTCACTGG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"Interleukins and interleukin receptors", "CD molecules"	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.887T>C	16.37:g.27459874T>C	ENSP00000338010:p.Phe296Ser	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	172	62	NM_181079	0	0	1	1	0	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.495777	0.26774	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.37411	1.2;1.2;1.2	5.24	2.9	0.33743	.	0.718376	0.13350	N	0.394470	T	0.26810	0.0656	M	0.64997	1.995	0.09310	N	1	P	0.41265	0.744	B	0.38327	0.271	T	0.17776	-1.0358	10	0.06365	T	0.9	-23.6851	4.7668	0.13135	0.1986:0.0:0.1808:0.6206	.	296	Q9HBE5	IL21R_HUMAN	S	296	ENSP00000338010:F296S;ENSP00000379104:F296S;ENSP00000379103:F296S	ENSP00000338010:F296S	F	+	2	0	IL21R	27367375	0.006000	0.16342	0.739000	0.30968	0.006000	0.05464	1.501000	0.35693	1.980000	0.57719	0.459000	0.35465	TTC	.		0.547	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		C	27459874	T	C	27459874	3	2	138	1	0	0	0	0	1	0	0	0	7692	1783	62	3	917	3	IL21R	16	27459874	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10	14111	27459874	62894879	29	12282											
TRIM37	4591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	57134407	57134407	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgaaccatctctacacgaTattcatatctaaaattgaaa	16	12	5	8	1	3	2	1	2	2	0	4	3	3	2	1	1	2	0	1	1	7	6			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr17:57134407T>C	ENST00000262294.7	-	13	1287	c.1028A>G	c.(1027-1029)tAt>tGt	p.Y343C	TRIM37_ENST00000393066.3_Missense_Mutation_p.Y343C|RN7SL716P_ENST00000580539.1_RNA|TRIM37_ENST00000393065.2_Missense_Mutation_p.Y309C|TRIM37_ENST00000376149.3_Missense_Mutation_p.Y221C	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	343	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CTCTACACGATATTCATATCT	0.318									Mulibrey Nanism																												p.Y343C		.											.	TRIM37-660	0			c.A1028G						.						63	61	62					17																	57134407		2203	4300	6503	SO:0001583	missense	4591	exon13	Familial Cancer Database	Perheentupa syndrome	ACACGATATTCAT	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1028A>G	17.37:g.57134407T>C	ENSP00000262294:p.Tyr343Cys	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	36	21	NM_015294	0	0	0	0	0	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.164224	0.78339	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	5.43	5.43	0.79202	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.81635	0.4864	M	0.86420	2.815	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.943	D;D;P	0.87578	0.998;0.998;0.896	D	0.84579	0.0660	10	0.56958	D	0.05	-9.1299	15.4842	0.75551	0.0:0.0:0.0:1.0	.	309;221;343	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	C	343;343;221;309	ENSP00000376785:Y343C;ENSP00000262294:Y343C;ENSP00000365319:Y221C;ENSP00000376784:Y309C	ENSP00000262294:Y343C	Y	-	2	0	TRIM37	54489189	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.036000	0.88901	2.048000	0.60808	0.482000	0.46254	TAT	.		0.318	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		C	57134407	T	C	57134407	3	2	138	1	0	0	0	0	1	0	0	0	16544	1406	49	3	1922	3	TRIM37	17	57134407	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		57134407	24060803	30	12283											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	117	0		WXS	Illumina HiSeq		118	2	NM_031203	0	0	1	1	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	138	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		8527467	50601516	31	12284											
ZNF536	9745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	30936011	30936011	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcggctgccaaggctgcggaGatggaccccgtgaacagcta	9	5	15	12	3	0	2	0	1	0	1	0	4	0	3	3	4	4	3	3	4	3	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr19:30936011G>C	ENST00000355537.3	+	2	1689	c.1542G>C	c.(1540-1542)gaG>gaC	p.E514D		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	514					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					AGGCTGCGGAGATGGACCCCG	0.632																																					p.E514D		.											.	ZNF536-144	0			c.G1542C						.						38	43	42					19																	30936011		2202	4299	6501	SO:0001583	missense	9745	exon2			TGCGGAGATGGAC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"Zinc fingers, C2H2-type"	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1542G>C	19.37:g.30936011G>C	ENSP00000347730:p.Glu514Asp	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	44	21	NM_014717	0	0	0	0	0	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833785	0.50951	.	.	ENSG00000198597	ENST00000355537	T	0.16743	2.32	5.53	2.25	0.28309	.	0.000000	0.85682	D	0.000000	T	0.33962	0.0881	M	0.64404	1.975	0.41871	D	0.99027	D;D	0.69078	0.997;0.997	D;D	0.72625	0.978;0.978	T	0.02020	-1.1228	10	0.51188	T	0.08	-39.7837	9.9979	0.41911	0.2217:0.0:0.7783:0.0	.	514;514	A7E228;O15090	.;ZN536_HUMAN	D	514	ENSP00000347730:E514D	ENSP00000347730:E514D	E	+	3	2	ZNF536	35627851	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	1.738000	0.38207	0.276000	0.22118	0.655000	0.94253	GAG	.		0.632	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		C	30936011	G	C	30936011	3	2	138	1	0	0	0	0	1	0	0	0	18006	933	33	4	1544	4	ZNF536	19	30936011	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	22408544	30936011	28192972	32	12285											
CEACAM8	1088	broad.mit.edu	37	chr19	43098028	43098028	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagctgagcagtggtgggcGggttccagaaggtgaaaagt	10	8	18	5	1	0	4	0	3	0	1	1	4	1	4	1	4	2	3	1	4	3	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr19:43098028G>A	ENST00000244336.5	-	2	190	c.89C>T	c.(88-90)cCg>cTg	p.P30L	LIPE-AS1_ENST00000594688.1_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	30					immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				AGTGGTGGGCGGGTTCCAGAA	0.507																																					p.P30L													.	CEACAM8-91	0			c.C89T						.						109	101	104					19																	43098028		2203	4300	6503	SO:0001583	missense	1088	exon2			GTGGGCGGGTTCC	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.89C>T	19.37:g.43098028G>A	ENSP00000244336:p.Pro30Leu	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	109	4	NM_001816	0	0	0	0	0	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	g	4.232	0.042039	0.08196	.	.	ENSG00000124469	ENST00000244336	T	0.16897	2.31	1.63	0.565	0.17309	.	.	.	.	.	T	0.08626	0.0214	N	0.20445	0.575	0.09310	N	1	B	0.21147	0.052	B	0.23852	0.049	T	0.42327	-0.9458	9	0.14252	T	0.57	.	3.9174	0.09228	0.2332:0.0:0.7668:0.0	.	30	P31997	CEAM8_HUMAN	L	30	ENSP00000244336:P30L	ENSP00000244336:P30L	P	-	2	0	CEACAM8	47789868	0.002000	0.14202	0.021000	0.16686	0.463000	0.32649	-0.315000	0.08081	0.242000	0.21303	0.313000	0.20887	CCG	.		0.507	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			A	43098028	G	A	43098028	3	1	138	1	0	0	0	0	1	0	0	0	3204	1116	39	1	976	1	CEACAM8	19	43098028	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	12162017	43098028	16030955	33	12286											
KCNN4	3783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44278354	44278354	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccctcacctctcggccaCggacagcacccaggcggtgg	7	5	11	18	3	3	0	2	0	1	0	4	1	3	1	4	5	1	1	4	5	0	0			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr19:44278354C>T	ENST00000262888.3	-	3	1068	c.673G>A	c.(673-675)Gtg>Atg	p.V225M		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	225					calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	CTCTCGGCCACGGACAGCACC	0.677											OREG0025535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V225M		.											.	KCNN4-92	0			c.G673A						.						17	19	18					19																	44278354		2196	4295	6491	SO:0001583	missense	3783	exon3			CGGCCACGGACAG	AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6293	protein-coding gene	gene with protein product		602754				9380751, 9407042, 16382103	Standard	NM_002250		Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.673G>A	19.37:g.44278354C>T	ENSP00000262888:p.Val225Met	Somatic	41	0	922	WXS	Illumina HiSeq	Phase_I	89	48	NM_002250	0	0	0	0	0	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	37	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.961648	0.74016	.	.	ENSG00000104783	ENST00000262888;ENST00000407385	T	0.24538	1.85	4.31	4.31	0.51392	Ion transport 2 (1);	0.149552	0.43416	D	0.000563	T	0.41834	0.1176	L	0.42245	1.32	0.40618	D	0.981731	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.961	T	0.36529	-0.9744	10	0.56958	D	0.05	-28.677	14.7241	0.69329	0.0:1.0:0.0:0.0	.	119;225	D1MQ10;O15554	.;KCNN4_HUMAN	M	225;93	ENSP00000262888:V225M	ENSP00000262888:V225M	V	-	1	0	KCNN4	48970194	0.982000	0.34865	0.985000	0.45067	0.977000	0.68977	2.272000	0.43373	2.104000	0.64026	0.478000	0.44815	GTG	.		0.677	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250		T	44278354	C	T	44278354	3	4	138	1	0	0	0	0	1	0	0	0	8102	536	19	1	634	1	KCNN4	19	44278354	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10	1180326	44278354	14850629	34	12287											
C20orf185	359710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	31660577	31660577	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttaatatcaatttttccaAttcagttctggagatcgtag	11	17	6	7	1	4	1	2	0	2	1	6	2	5	1	1	1	0	2	1	1	5	7			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr20:31660577A>G	ENST00000375494.3	+	14	1379	c.1379A>G	c.(1378-1380)aAt>aGt	p.N460S		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	460					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										AATTTTTCCAATTCAGTTCTG	0.473																																					p.N460S		.											.	.	0			c.A1379G						.						156	143	148					20																	31660577		2203	4300	6503	SO:0001583	missense	359710	exon14			TTTCCAATTCAGT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"BPI fold containing"	16178	protein-coding gene	gene with protein product		615717	"chromosome 20 open reading frame 185"	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1379A>G	20.37:g.31660577A>G	ENSP00000364643:p.Asn460Ser	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	163	62	NM_182658	0	0	0	0	0	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	A	1.299	-0.605319	0.03717	.	.	ENSG00000186190	ENST00000375494	T	0.09255	3.0	4.64	-3.29	0.05017	.	0.321650	0.26258	N	0.025402	T	0.07638	0.0192	L	0.53561	1.675	0.24245	N	0.995343	B	0.02656	0.0	B	0.08055	0.003	T	0.41413	-0.9510	10	0.15499	T	0.54	0.023	6.6155	0.22774	0.4895:0.4045:0.106:0.0	.	460	P59826	BPIB3_HUMAN	S	460	ENSP00000364643:N460S	ENSP00000364643:N460S	N	+	2	0	BPIFB3	31124238	0.983000	0.35010	0.689000	0.30133	0.014000	0.08584	-0.057000	0.11768	-0.887000	0.03961	-1.064000	0.02280	AAT	.		0.473	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		G	31660577	A	G	31660577	3	3	138	1	0	0	0	0	1	0	0	0	2103	101	4	3	1433	3	C20orf185	20	31660577	Missense_Mutation	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10		31660577	31364943	35	12288											
FAM83C	128876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33874582	33874582	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttagccgtttctcatccccaGacccagctccagccgtgcga	7	9	8	17	3	1	1	1	0	1	1	4	2	3	1	6	0	4	2	6	0	1	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr20:33874582G>C	ENST00000374408.3	-	4	2096	c.2000C>G	c.(1999-2001)tCt>tGt	p.S667C	EIF6_ENST00000374436.3_5'Flank|FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000374443.3_5'Flank|EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374450.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	667										central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			CTCATCCCCAGACCCAGCTCC	0.617																																					p.S667C		.											.	FAM83C-92	0			c.C2000G						.						54	48	50					20																	33874582		2203	4300	6503	SO:0001583	missense	128876	exon4			TCCCCAGACCCAG	AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 128"	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.2000C>G	20.37:g.33874582G>C	ENSP00000363529:p.Ser667Cys	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	236	101	NM_178468	0	0	0	0	0	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	37	CCDS13251.1	.	.	.	.	.	.	.	.	.	.	G	9.533	1.111448	0.20714	.	.	ENSG00000125998	ENST00000374408	T	0.11385	2.78	4.93	3.99	0.46301	.	1.069840	0.07374	N	0.886296	T	0.15392	0.0371	L	0.59436	1.845	0.09310	N	1	P	0.50369	0.934	B	0.43916	0.436	T	0.23691	-1.0181	10	0.87932	D	0	-20.9594	6.8394	0.23955	0.0917:0.0:0.7235:0.1848	.	667	Q9BQN1	FA83C_HUMAN	C	667	ENSP00000363529:S667C	ENSP00000363529:S667C	S	-	2	0	FAM83C	33337996	0.485000	0.25972	0.025000	0.17156	0.218000	0.24690	2.726000	0.47302	1.235000	0.43724	0.462000	0.41574	TCT	.		0.617	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3			C	33874582	G	C	33874582	3	2	138	1	0	0	0	0	1	0	0	0	5654	942	33	4	247	4	FAM83C	20	33874582	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	2214005	33874582	29150938	36	12289											
TMPRSS3	64699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43802332	43802332	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctggatggtccatgacttgGggaggtacaagctgaaatga	11	9	14	7	0	0	3	0	3	0	0	1	5	1	5	2	5	2	2	2	5	3	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr21:43802332G>C	ENST00000291532.3	-	9	1749	c.794C>G	c.(793-795)cCc>cGc	p.P265R	TMPRSS3_ENST00000398397.3_Missense_Mutation_p.P265R|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.P263R|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.P265R|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.P349R	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	265	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						CCATGACTTGGGGAGGTACAA	0.493																																					p.P265R		.											.	TMPRSS3-155	0			c.C794G						.						68	51	57					21																	43802332		2203	4300	6503	SO:0001583	missense	64699	exon9			GACTTGGGGAGGT	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"Serine peptidases / Transmembrane"	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.794C>G	21.37:g.43802332G>C	ENSP00000291532:p.Pro265Arg	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	70	27	NM_001256317	0	0	0	0	0	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.853752	0.71719	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4	4.8	4.8	0.61643	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000001	D	0.92984	0.7767	L	0.58428	1.81	0.53688	D	0.999975	D;D;P;D	0.76494	0.998;0.999;0.949;0.999	D;D;P;D	0.74348	0.977;0.983;0.803;0.982	D	0.92525	0.6028	9	.	.	.	.	17.8827	0.88845	0.0:0.0:1.0:0.0	.	265;265;265;263	P57727-3;P57727-5;P57727;B7WPR2	.;.;TMPS3_HUMAN;.	R	265;265;263;349;265	ENSP00000291532:P265R;ENSP00000411013:P265R;ENSP00000381442:P263R;ENSP00000369762:P349R;ENSP00000381434:P265R	.	P	-	2	0	TMPRSS3	42675401	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	7.925000	0.87563	2.213000	0.71641	0.655000	0.94253	CCC	.		0.493	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			C	43802332	G	C	43802332	3	2	138	1	0	0	0	0	1	0	0	0	16280	1232	43	4	673	4	TMPRSS3	21	43802332	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		43802332	4327563	37	12290											
MMP11	4320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24125618	24125618	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctatgcctacttcctgcgcGgccgcctctactggaagttt	5	12	10	14	3	1	0	0	0	1	0	2	1	2	1	4	2	4	2	4	2	4	5			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr22:24125618G>T	ENST00000215743.3	+	8	1406	c.1354G>T	c.(1354-1356)Ggc>Tgc	p.G452C	AP000349.1_ENST00000598975.1_Silent_p.A176A	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	452					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	CTTCCTGCGCGGCCGCCTCTA	0.622																																					p.G452C		.											.	MMP11-291	0			c.G1354T						.						102	82	89					22																	24125618		2203	4300	6503	SO:0001583	missense	4320	exon8			CTGCGCGGCCGCC		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"matrix metalloproteinase 11 (stromelysin 3)"	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1354G>T	22.37:g.24125618G>T	ENSP00000215743:p.Gly452Cys	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	166	21	NM_005940	0	0	44	52	8	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383170	0.82792	.	.	ENSG00000099953	ENST00000215743	T	0.10382	2.88	4.73	4.73	0.59995	Hemopexin/matrixin (2);	0.049339	0.85682	D	0.000000	T	0.45915	0.1366	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61549	-0.7040	10	0.87932	D	0	.	17.3138	0.87217	0.0:0.0:1.0:0.0	.	452	P24347	MMP11_HUMAN	C	452	ENSP00000215743:G452C	ENSP00000215743:G452C	G	+	1	0	MMP11	22455618	1.000000	0.71417	0.971000	0.41717	0.995000	0.86356	7.028000	0.76470	2.649000	0.89929	0.650000	0.86243	GGC	.		0.622	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		T	24125618	G	T	24125618	3	4	138	1	0	0	0	0	1	0	0	0	9675	1116	39	4	1384	4	MMP11	22	24125618	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		24125618	27178948	38	12291											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	115	18	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	138	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	5759944	29885562	21419004	39	12292											
VCX	26609	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	7811790	7811790	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaccactgagtcaggagagCgaggtggaagaaccactgag	14	4	15	8	1	1	4	1	2	0	2	1	8	1	5	2	3	3	0	2	3	3	0	rs200229312		TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:7811790C>T	ENST00000381059.3	+	3	573	c.354C>T	c.(352-354)agC>agT	p.S118S	VCX_ENST00000341408.4_Silent_p.S118S	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	118	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.S118S(1)		NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GTCAGGAGAGCGAGGTGGAAG	0.637																																					p.S118S		.											.	VCX-22	1	Substitution - coding silent(1)	endometrium(1)	c.C354T						.						54	67	62					X																	7811790		2129	4090	6219	SO:0001819	synonymous_variant	26609	exon3			GGAGAGCGAGGTG	AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"variable charge, X chromosome"			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.354C>T	X.37:g.7811790C>T		Somatic	269	0		WXS	Illumina HiSeq	Phase_I	308	103	NM_013452	0	0	3	3	0	A0JNS5|Q4V774|Q9P0H3	Silent	SNP	ENST00000381059.3	37	CCDS14128.1																																																																																			.		0.637	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452		T	7811790	C	T	7811790	2	4	138	1	0	0	0	0	0	0	0	1	17175	767	27	1		1	VCX	23	7811790	Silent	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		7811790	147458770	40	12293											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382384	24382385	+	IGR	DNP	GC	GC	AT																															ctgctgctattgctgctgctGctgctgctgctgctgctgct																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:24382384_24382385GC>AT								AC004552.1 (15361 upstream) : PDK3 (100952 downstream)																							tgctgctgctgctgctgctgct	0.579																																					.		.											.	.	0			c.C1508T						.																																			SO:0001628	intergenic_variant	100130302	exon1			CTGCTGCTGCTGC																													X.37:g.24382384_24382385delinsAT		Somatic	244	0		WXS	Illumina HiSeq	Phase_I	324	25	NM_001136234	0	0	0	0	0		Missense_Mutation	DNP		37																																																																																				.	0	0.579									AT	24382385	GC	AT	24382384	1	1	138	0	1	0	0	0	0	0	0	0	5592	1319	46	2		2	FAM48B1	23	24382384	IGR	DNP	GC	TCGA-IA-A40X-01A-11D-A25F-10	16570594	24382384	130888176	41	12294											
GAB3	139716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	153908429	153908429	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcatgggggctggtgAtgctgaattgaagtccaggg	7	10	17	7	0	0	3	0	3	0	0	1	3	1	3	1	4	3	4	1	4	2	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:153908429A>G	ENST00000369575.3	-	9	1655	c.1624T>C	c.(1624-1626)Tca>Cca	p.S542P	GAB3_ENST00000496390.1_5'UTR|GAB3_ENST00000424127.2_Missense_Mutation_p.S543P	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	542					macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GGGGCTGGTGATGCTGAATTG	0.488																																					p.S543P		.											.	GAB3-227	0			c.T1627C						.						205	201	202					X																	153908429		2203	4300	6503	SO:0001583	missense	139716	exon9			CTGGTGATGCTGA	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"Pleckstrin homology (PH) domain containing"	17515	protein-coding gene	gene with protein product	"DOS/Gab family member 3", "Gab3 scaffolding protein"	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.1624T>C	X.37:g.153908429A>G	ENSP00000358588:p.Ser542Pro	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	149	57	NM_001081573	0	0	0	0	0	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	37	CCDS14760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.60|17.60	3.430652|3.430652	0.62844|0.62844	.|.	.|.	ENSG00000160219|ENSG00000160219	ENST00000454973|ENST00000369575;ENST00000424127	.|T;T	.|0.28895	.|1.59;1.91	5.36|5.36	4.2|4.2	0.49525|0.49525	.|.	.|0.063412	.|0.64402	.|D	.|0.000004	T|T	0.54775|0.54775	0.1879|0.1879	M|M	0.84219|0.84219	2.685|2.685	0.52099|0.52099	D|D	0.999946|0.999946	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.83275	.|0.996;0.996	T|T	0.55829|0.55829	-0.8079|-0.8079	5|10	.|0.72032	.|D	.|0.01	-5.3879|-5.3879	8.3095|8.3095	0.32062|0.32062	0.9048:0.0:0.0952:0.0|0.9048:0.0:0.0952:0.0	.|.	.|543;542	.|E9PB44;Q8WWW8	.|.;GAB3_HUMAN	T|P	23|542;543	.|ENSP00000358588:S542P;ENSP00000399588:S543P	.|ENSP00000358588:S542P	I|S	-|-	2|1	0|0	GAB3|GAB3	153561623|153561623	0.998000|0.998000	0.40836|0.40836	0.338000|0.338000	0.25549|0.25549	0.747000|0.747000	0.42532|0.42532	3.865000|3.865000	0.56033|0.56033	0.695000|0.695000	0.31675|0.31675	0.412000|0.412000	0.27726|0.27726	ATC|TCA	.		0.488	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		G	153908429	A	G	153908429	3	3	138	1	0	0	0	0	1	0	0	0	6169	333	12	3	144	3	GAB3	23	153908429	Missense_Mutation	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10	129526045	153908429	1362131	42	12295											
TAS1R2	80834	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19181215	19181215	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgctggcgctcctctgacGtcatgttctggttgggctgc	2	12	15	12	3	3	1	1	1	2	0	4	1	4	1	1	4	1	5	1	4	0	2	rs79635934	byFrequency	TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:19181215G>A	ENST00000375371.3	-	3	770	c.749C>T	c.(748-750)aCg>aTg	p.T250M	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	250					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CTCCTCTGACGTCATGTTCTG	0.657													G|||	2	0.000399361	8e-04	0	5008	,	,		20261	0		0	False		,,,				2504	0.001				p.T250M													.	TAS1R2-93	0			c.C749T						.						57	51	53					1																	19181215		2203	4300	6503	SO:0001583	missense	80834	exon3			TCTGACGTCATGT		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.749C>T	1.37:g.19181215G>A	ENSP00000364520:p.Thr250Met	Somatic	61	1		WXS	Illumina HiSeq	Phase_I	50	9	NM_152232	0	0	0	0	0	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	4.948	0.176107	0.09443	.	.	ENSG00000179002	ENST00000375371	D	0.83335	-1.71	4.99	0.249	0.15531	Extracellular ligand-binding receptor (1);	0.889934	0.09444	N	0.801346	T	0.70894	0.3276	L	0.40543	1.245	0.09310	N	1	B	0.27679	0.185	B	0.29176	0.099	T	0.56950	-0.7894	10	0.32370	T	0.25	.	0.6727	0.00861	0.2718:0.2522:0.3128:0.1632	.	250	Q8TE23	TS1R2_HUMAN	M	250	ENSP00000364520:T250M	ENSP00000364520:T250M	T	-	2	0	TAS1R2	19053802	0.005000	0.15991	0.001000	0.08648	0.002000	0.02628	0.849000	0.27723	0.185000	0.20105	-0.254000	0.11334	ACG	G|0.999;A|0.000		0.657	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19181215	G	A	19181215	3	1	139	1	0	0	0	0	1	0	0	0	15595	1145	40	1	1786	1	TAS1R2	1	19181215	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		19181215	230069406	1	12296											
VCAM1	7412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	101198018	101198018	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcagcccttcctccatcCtggaggaaggcagttctgtg	6	11	12	12	0	2	0	1	0	1	0	5	2	5	2	4	4	1	2	4	4	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:101198018C>G	ENST00000294728.2	+	7	1671	c.1570C>G	c.(1570-1572)Ctg>Gtg	p.L524V	VCAM1_ENST00000347652.2_Missense_Mutation_p.L432V|VCAM1_ENST00000370115.1_Missense_Mutation_p.L325V|VCAM1_ENST00000370119.4_Missense_Mutation_p.L462V	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	524	Ig-like C2-type 6.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TTCCTCCATCCTGGAGGAAGG	0.537																																					p.L524V		.											.	VCAM1-90	0			c.C1570G						.						66	70	69					1																	101198018		2203	4300	6503	SO:0001583	missense	7412	exon7			TCCATCCTGGAGG	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1570C>G	1.37:g.101198018C>G	ENSP00000294728:p.Leu524Val	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	27	9	NM_001078	0	0	210	441	231	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	C	2.960	-0.214840	0.06101	.	.	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728;ENST00000370115	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.57	-3.82	0.04281	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.317042	0.32884	N	0.005531	T	0.00524	0.0017	N	0.01048	-1.04	0.09310	N	1	B;B;B	0.19706	0.001;0.038;0.0	B;B;B	0.23150	0.007;0.044;0.008	T	0.33675	-0.9859	10	0.02654	T	1	-0.0111	4.6967	0.12808	0.1001:0.1771:0.5014:0.2214	.	462;432;524	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	V	462;432;524;325	ENSP00000359137:L462V;ENSP00000304611:L432V;ENSP00000294728:L524V;ENSP00000359133:L325V	ENSP00000294728:L524V	L	+	1	2	VCAM1	100970606	0.000000	0.05858	0.002000	0.10522	0.771000	0.43674	-1.681000	0.01937	-0.367000	0.08052	-0.140000	0.14226	CTG	.		0.537	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		G	101198018	C	G	101198018	3	3	139	1	0	0	0	0	1	0	0	0	17170	680	24	4	1596	4	VCAM1	1	101198018	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	82016803	101198018	148052603	2	12297											
CLCC1	23155	broad.mit.edu	37	chr1	109477463	109477464	+	Frame_Shift_Ins	INS	-	-	T																															tgtcttggccagagacaggcINSttggccgactggctgctttc																								rs371820348		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:109477463_109477464insT	ENST00000369971.2	-	11	1613_1614	c.1484_1485insA	c.(1483-1485)aagfs	p.K495fs	AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000415331.1_Frame_Shift_Ins_p.K445fs|CLCC1_ENST00000369970.3_Frame_Shift_Ins_p.K445fs|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000302500.4_Frame_Shift_Ins_p.K374fs|CLCC1_ENST00000356970.2_Frame_Shift_Ins_p.K495fs|CLCC1_ENST00000369968.2_Frame_Shift_Ins_p.K310fs|CLCC1_ENST00000348264.2_Frame_Shift_Ins_p.K310fs|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000369969.2_Frame_Shift_Ins_p.K374fs	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	495						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		CAGAGACAGGCTTGGCCGACTG	0.55																																					p.K495fs													.	CLCC1-91	0			c.1485_1486insA						.																																			SO:0001589	frameshift_variant	23155	exon11			GACAGGCTTGGCC	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"Mid1-related chloride channel (yeast)"					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.1485dupA	1.37:g.109477465_109477465dupT	ENSP00000358988:p.Lys495fs	Somatic	311	0		WXS	Illumina HiSeq	Phase_I	212	11	NM_001048210	0	0	0	0	0	O94861|Q8WYP8|Q8WYP9|Q9BU25	Frame_Shift_Ins	INS	ENST00000369971.2	37	CCDS41362.1																																																																																			.		0.55	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127		T	109477464	-	T	109477463	7	5	139	1	0	1	1	0	0	0	0	0	3466	796	28	0	174	0	CLCC1	1	109477463	Frame_Shift_Ins	INS	-	TCGA-IA-A40Y-01A-11D-A25F-10	8279445	109477463	139773158	3	12298											
GON4L	54856	ucsc.edu	37	chr1	155726782	155726782	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tggaccccgatctcttttttCctcttgttctttgaggctgt	3	19	8	11	1	3	1	0	1	3	0	5	3	4	2	3	2	0	2	3	2	0	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:155726782C>T	ENST00000368331.1	-	27	5532	c.5484G>A	c.(5482-5484)agG>agA	p.R1828R	GON4L_ENST00000437809.1_Silent_p.R1828R|GON4L_ENST00000271883.5_Silent_p.R1828R	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1828					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCTCTTTTTTCCTCTTGTTCT	0.438																																					p.R1828R													.	GON4L-93	0			c.G5484A						.						120	114	116					1																	155726782		1859	4096	5955	SO:0001819	synonymous_variant	54856	exon27			TTTTTTCCTCTTG	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5484G>A	1.37:g.155726782C>T		Somatic	107	0		WXS	Illumina HiSeq		206	3	NM_001037533	0	0	9	10	1	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Silent	SNP	ENST00000368331.1	37																																																																																				.		0.438	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		T	155726782	C	T	155726782	2	4	139	1	0	0	0	0	0	0	0	1	6592	854	30	2		2	GON4L	1	155726782	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	46249319	155726782	93523839	4	12299											
TTC24	164118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156552861	156552861	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggggcagcggtgggagcaggGccggagctttggcagcctgg	5	5	22	9	2	0	0	0	0	0	0	0	2	0	2	2	8	4	4	2	8	0	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:156552861G>C	ENST00000368237.3	+	3	938	c.938G>C	c.(937-939)gGc>gCc	p.G313A	TTC24_ENST00000368236.3_Missense_Mutation_p.G313A|TTC24_ENST00000478081.1_Intron			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	313										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGGGAGCAGGGCCGGAGCTTT	0.657																																					p.G313A		.											.	TTC24-46	0			c.G938C						.						33	39	37					1																	156552861		2031	4169	6200	SO:0001583	missense	164118	exon4			AGCAGGGCCGGAG		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"Tetratricopeptide (TTC) repeat domain containing"	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.938G>C	1.37:g.156552861G>C	ENSP00000357220:p.Gly313Ala	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	183	38	NM_001105669	0	0	0	0	0	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.276|7.276	0.608179|0.608179	0.14002|0.14002	.|.	.|.	ENSG00000187862|ENSG00000187862	ENST00000340086;ENST00000413282|ENST00000368236;ENST00000368237	.|T;T	.|0.70869	.|-0.52;-0.52	4.72|4.72	4.72|4.72	0.59763|0.59763	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|0.000000	.|0.48767	.|D	.|0.000175	T|T	0.56761|0.56761	0.2007|0.2007	L|L	0.33245|0.33245	0.995|0.995	0.37041|0.37041	D|D	0.897135|0.897135	.|D	.|0.62365	.|0.991	.|P	.|0.60541	.|0.876	T|T	0.59402|0.59402	-0.7461|-0.7461	5|10	.|0.02654	.|T	.|1	-14.4059|-14.4059	13.0458|13.0458	0.58925|0.58925	0.0:0.163:0.8369:0.0|0.0:0.163:0.8369:0.0	.|.	.|313	.|A2A3L6	.|TTC24_HUMAN	P|A	86;78|313	.|ENSP00000357219:G313A;ENSP00000357220:G313A	.|ENSP00000357219:G313A	A|G	+|+	1|2	0|0	TTC24|TTC24	154819485|154819485	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.445000|4.445000	0.60007|0.60007	2.474000|2.474000	0.83562|0.83562	0.455000|0.455000	0.32223|0.32223	GCC|GGC	.		0.657	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		C	156552861	G	C	156552861	3	2	139	1	0	0	0	0	1	0	0	0	16725	1203	42	4	948	4	TTC24	1	156552861	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	826079	156552861	92697760	5	12300											
SPTA1	6708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158596772	158596772	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctatcttggaagaaatctctTtgttctgactttcctcctgc	7	17	6	11	0	3	2	0	1	3	1	6	3	5	3	2	1	1	1	2	1	3	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:158596772T>C	ENST00000368147.4	-	41	5870	c.5690A>G	c.(5689-5691)aAa>aGa	p.K1897R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1897					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGAAATCTCTTTGTTCTGACT	0.413																																					p.K1897R		.											.	SPTA1-142	0			c.A5690G						.						127	125	126					1																	158596772		1849	4090	5939	SO:0001583	missense	6708	exon41			ATCTCTTTGTTCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"EF-hand domain containing"	11272	protein-coding gene	gene with protein product	"elliptocytosis 2"	182860	"spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5690A>G	1.37:g.158596772T>C	ENSP00000357129:p.Lys1897Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	127	19	NM_003126	0	0	0	0	0	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827369	0.32329	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53640	0.61;0.61	4.87	3.73	0.42828	.	.	.	.	.	T	0.15435	0.0372	N	0.21448	0.665	0.29575	N	0.849575	B	0.02656	0.0	B	0.12837	0.008	T	0.14643	-1.0465	9	0.46703	T	0.11	.	8.4299	0.32750	0.3124:0.0:0.0:0.6876	.	1897	P02549	SPTA1_HUMAN	R	1897;1894	ENSP00000357130:K1897R;ENSP00000357129:K1894R	ENSP00000357129:K1894R	K	-	2	0	SPTA1	156863396	0.976000	0.34144	0.910000	0.35882	0.968000	0.65278	0.874000	0.28065	0.864000	0.35578	0.460000	0.39030	AAA	.		0.413	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158596772	T	C	158596772	3	2	139	1	0	0	0	0	1	0	0	0	15148	1841	64	3	1617	3	SPTA1	1	158596772	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	2043911	158596772	90653849	6	12301											
OLFML2B	25903	broad.mit.edu;bcgsc.ca	37	chr1	161989778	161989778	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcgcagggattgagggcCgatgggggtgctacacaggc	7	6	17	11	2	0	1	0	1	0	0	1	3	0	2	2	5	2	2	2	5	1	2	rs138821383		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:161989778C>G	ENST00000294794.3	-	2	792	c.369G>C	c.(367-369)tcG>tcC	p.S123S	OLFML2B_ENST00000367940.2_Silent_p.S123S	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	123					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			GATTGAGGGCCGATGGGGGTG	0.592																																					p.S123S													.	OLFML2B-69	0			c.G369C						.						69	68	68					1																	161989778		2203	4300	6503	SO:0001819	synonymous_variant	25903	exon2			GAGGGCCGATGGG	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.369G>C	1.37:g.161989778C>G		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	190	8	NM_015441	0	0	4	4	0	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Silent	SNP	ENST00000294794.3	37	CCDS1236.1																																																																																			C|0.999;T|0.000		0.592	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		G	161989778	C	G	161989778	2	3	139	1	0	0	0	0	0	0	0	1	10884	639	23	4		4	OLFML2B	1	161989778	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	3393006	161989778	87260843	7	12302											
HHIPL2	79802	broad.mit.edu;bcgsc.ca	37	chr1	222715413	222715413	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcctgtcccccgtccccagtGaatatgtacatatagccatc	9	10	7	15	1	0	1	0	1	0	0	3	1	2	1	6	0	2	1	6	0	5	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:222715413G>A	ENST00000343410.6	-	3	1117	c.1059C>T	c.(1057-1059)ttC>ttT	p.F353F		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	353					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)	p.F353F(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		CGTCCCCAGTGAATATGTACA	0.507																																					p.F353F													.	HHIPL2-69	1	Substitution - coding silent(1)	stomach(1)	c.C1059T						.						69	66	67					1																	222715413		2203	4300	6503	SO:0001819	synonymous_variant	79802	exon3			CCCAGTGAATATG	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"KIAA1822-like"	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1059C>T	1.37:g.222715413G>A		Somatic	165	0		WXS	Illumina HiSeq	Phase_I	207	10	NM_024746	0	0	2	2	0	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			.		0.507	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		A	222715413	G	A	222715413	2	1	139	1	0	0	0	0	0	0	0	1	7115	1281	45	2		2	HHIPL2	1	222715413	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	60725635	222715413	26535208	8	12303											
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	237993878	237993878	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgattacttcgacacagtgCcacatggctttgaaacccac	12	10	7	12	1	0	2	0	2	0	0	1	3	0	2	2	1	3	1	2	1	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:237993878C>T	ENST00000366574.2	+	103	15021	c.14704C>T	c.(14704-14706)Cca>Tca	p.P4902S	RYR2_ENST00000360064.6_Missense_Mutation_p.P4908S|RYR2_ENST00000542537.1_Missense_Mutation_p.P4886S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4902			P -> L (in CPVT1). {ECO:0000269|PubMed:14571276}.		BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CGACACAGTGCCACATGGCTT	0.433																																					p.P4902S		.											.	RYR2-158	0			c.C14704T						.						213	200	204					1																	237993878		1968	4170	6138	SO:0001583	missense	6262	exon103			ACAGTGCCACATG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.14704C>T	1.37:g.237993878C>T	ENSP00000355533:p.Pro4902Ser	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	212	74	NM_001035	0	0	0	0	0	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	34	5.362728	0.95877	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96774	-4.12;-4.08;-4.11	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000007	D	0.97539	0.9194	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98376	1.0556	10	0.87932	D	0	-8.5845	19.143	0.93452	0.0:1.0:0.0:0.0	.	4902	Q92736	RYR2_HUMAN	S	4902;4908;4886	ENSP00000355533:P4902S;ENSP00000353174:P4908S;ENSP00000443798:P4886S	ENSP00000353174:P4908S	P	+	1	0	RYR2	236060501	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.773000	0.85462	2.509000	0.84616	0.561000	0.74099	CCA	.		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237993878	C	T	237993878	3	4	139	1	0	0	0	0	1	0	0	0	13801	739	26	2	15114	2	RYR2	1	237993878	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	15278465	237993878	11256743	9	12304											
CHRM3	1131	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	240072456	240072456	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtgacaaaaaaaagaggCgcaagcagcagtaccagcag	18	3	12	8	1	0	2	0	1	0	1	0	2	0	2	1	1	4	5	1	1	6	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:240072456C>T	ENST00000255380.4	+	5	2484	c.1705C>T	c.(1705-1707)Cgc>Tgc	p.R569C		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	569					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AAAAAAGAGGCGCAAGCAGCA	0.498																																					p.R569C		.											.	CHRM3-95	0			c.C1705T						.						49	49	49					1																	240072456		2203	4300	6503	SO:0001583	missense	1131	exon5			AAGAGGCGCAAGC	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1952	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 3"	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.1705C>T	1.37:g.240072456C>T	ENSP00000255380:p.Arg569Cys	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	210	18	NM_000740	0	0	0	0	0	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593426	0.66219	.	.	ENSG00000133019	ENST00000255380	T	0.38887	1.11	5.58	5.58	0.84498	.	0.120714	0.51477	D	0.000092	T	0.58637	0.2136	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	P	0.57324	0.818	T	0.60459	-0.7259	10	0.72032	D	0.01	-16.0194	19.5758	0.95444	0.0:1.0:0.0:0.0	.	569	P20309	ACM3_HUMAN	C	569	ENSP00000255380:R569C	ENSP00000255380:R569C	R	+	1	0	CHRM3	238139079	0.996000	0.38824	0.992000	0.48379	0.986000	0.74619	3.339000	0.52135	2.632000	0.89209	0.655000	0.94253	CGC	.		0.498	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		T	240072456	C	T	240072456	3	4	139	1	0	0	0	0	1	0	0	0	3384	768	27	1	1707	1	CHRM3	1	240072456	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	2078578	240072456	9178165	10	12305											
OR2L3	391192	broad.mit.edu	37	chr1	248224862	248224862	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcatctatagcctgaggaaCaaggaggtgatgggggccct	11	8	14	8	0	2	2	1	2	1	0	2	4	2	4	2	5	2	0	2	5	4	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:248224862C>A	ENST00000359959.3	+	1	879	c.879C>A	c.(877-879)aaC>aaA	p.N293K	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			GCCTGAGGAACAAGGAGGTGA	0.498																																					p.N293K													.	OR2L3-68	0			c.C879A						.						57	58	58					1																	248224862		2203	4300	6503	SO:0001583	missense	391192	exon1			GAGGAACAAGGAG	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.879C>A	1.37:g.248224862C>A	ENSP00000353044:p.Asn293Lys	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	178	5	NM_001004687	0	0	0	0	0	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.724007	0.30593	.	.	ENSG00000198128	ENST00000359959	T	0.50001	0.76	2.01	2.01	0.26516	.	.	.	.	.	T	0.71230	0.3315	H	0.96889	3.9	0.26668	N	0.971781	D	0.54601	0.967	P	0.53224	0.721	T	0.67534	-0.5646	9	0.87932	D	0	.	11.9452	0.52924	0.0:1.0:0.0:0.0	.	293	Q8NG85	OR2L3_HUMAN	K	293	ENSP00000353044:N293K	ENSP00000353044:N293K	N	+	3	2	OR2L3	246291485	0.000000	0.05858	0.983000	0.44433	0.575000	0.36095	-1.063000	0.03465	1.119000	0.41883	0.456000	0.33151	AAC	.		0.498	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		A	248224862	C	A	248224862	3	1	139	1	0	0	0	0	1	0	0	0	11034	477	17	4	881	4	OR2L3	1	248224862	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	8152406	248224862	1025759	11	12306											
RAD51AP2	729475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	17699184	17699184	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcatttctaattccatgtaTatcgtgtatagaggtgctgg	9	16	9	7	1	2	1	1	0	1	1	4	1	3	1	1	2	1	3	1	2	5	7			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:17699184T>G	ENST00000399080.2	-	1	522	c.499A>C	c.(499-501)Ata>Cta	p.I167L		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	167										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ATTCCATGTATATCGTGTATA	0.423																																					p.I167L		.											.	RAD51AP2-23	0			c.A499C						.						64	62	63					2																	17699184		1913	4131	6044	SO:0001583	missense	729475	exon1			CATGTATATCGTG	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.499A>C	2.37:g.17699184T>G	ENSP00000382030:p.Ile167Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	125	27	NM_001099218	0	0	0	0	0		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.291283	0.23564	.	.	ENSG00000214842	ENST00000399080	T	0.30182	1.54	3.6	-4.94	0.03057	.	.	.	.	.	T	0.18509	0.0444	N	0.19112	0.55	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.21690	-1.0238	9	0.48119	T	0.1	.	12.4465	0.55653	0.0:0.7287:0.0:0.2713	.	167	Q09MP3	R51A2_HUMAN	L	167	ENSP00000382030:I167L	ENSP00000382030:I167L	I	-	1	0	RAD51AP2	17562665	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.991000	0.00657	-1.048000	0.03238	-0.290000	0.09829	ATA	.		0.423	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		G	17699184	T	G	17699184	3	3	139	1	0	0	0	0	1	0	0	0	13019	1406	49	5	2992	5	RAD51AP2	2	17699184	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10		17699184	225500189	12	12307											
DNMT3A	1788	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	25458669	25458669	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctttatggagtttgacctcGtagtaatggtcctcactttg	7	16	10	8	1	1	1	1	1	0	0	3	2	2	2	2	2	0	4	2	2	3	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:25458669G>A	ENST00000264709.3	-	22	2841	c.2504C>T	c.(2503-2505)aCg>aTg	p.T835M	DNMT3A_ENST00000380746.4_Missense_Mutation_p.T646M|DNMT3A_ENST00000321117.5_Missense_Mutation_p.T835M|DNMT3A_ENST00000402667.1_Missense_Mutation_p.T612M|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	835	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTTGACCTCGTAGTAATGGT	0.438			"Mis, F, N, S"		AML																																p.T835M				Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A-1924	0			c.C2504T						.						171	155	160					2																	25458669		2203	4300	6503	SO:0001583	missense	1788	exon22			GACCTCGTAGTAA		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2504C>T	2.37:g.25458669G>A	ENSP00000264709:p.Thr835Met	Somatic	146	1		WXS	Illumina HiSeq	Phase_I	271	88	NM_175629	0	0	27	46	19	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	37	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.953779	0.92660	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97089	-4.24;-4.24;-4.24;-4.24	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.98617	0.9537	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.991;0.997	D	0.99453	1.0941	10	0.72032	D	0.01	-6.841	18.1492	0.89669	0.0:0.0:1.0:0.0	.	835;646	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	M	646;835;835;612	ENSP00000370122:T646M;ENSP00000324375:T835M;ENSP00000264709:T835M;ENSP00000384237:T612M	ENSP00000264709:T835M	T	-	2	0	DNMT3A	25312173	1.000000	0.71417	0.993000	0.49108	0.988000	0.76386	9.697000	0.98697	2.717000	0.92951	0.650000	0.86243	ACG	.		0.438	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		A	25458669	G	A	25458669	3	1	139	1	0	0	0	0	1	0	0	0	4687	1145	40	1	242	1	DNMT3A	2	25458669	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	7759485	25458669	217740704	13	12308											
C2orf70	339778	broad.mit.edu	37	chr2	26785532	26785532	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgagttcaatgccgcctacGtgccccctggactcatgccc	6	8	9	18	3	2	0	2	0	0	0	2	2	2	1	6	1	4	1	6	1	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:26785532G>T	ENST00000329615.3	+	1	83	c.52G>T	c.(52-54)Gtg>Ttg	p.V18L	C2orf70_ENST00000409392.1_5'UTR	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	18						nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						TGCCGCCTACGTGCCCCCTGG	0.701																																					p.V18L													.	C2orf70-69	0			c.G52T						.						17	25	23					2																	26785532		2041	4159	6200	SO:0001583	missense	339778	exon1			GCCTACGTGCCCC		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"hypothetical protein LOC339778"						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.52G>T	2.37:g.26785532G>T	ENSP00000332875:p.Val18Leu	Somatic	144	1		WXS	Illumina HiSeq	Phase_I	165	6	NM_001105519	0	0	13	13	0		Missense_Mutation	SNP	ENST00000329615.3	37	CCDS42661.1	.	.	.	.	.	.	.	.	.	.	g	23.4	4.409415	0.83340	.	.	ENSG00000173557	ENST00000329615	T	0.32515	1.45	5.27	5.27	0.74061	.	0.000000	0.47455	D	0.000235	T	0.40979	0.1139	M	0.68317	2.08	0.80722	D	1	D	0.53312	0.959	P	0.51895	0.683	T	0.21415	-1.0246	10	0.41790	T	0.15	-16.9952	9.9347	0.41543	0.0921:0.0:0.9079:0.0	.	18	A6NJV1	CB070_HUMAN	L	18	ENSP00000332875:V18L	ENSP00000332875:V18L	V	+	1	0	C2orf70	26639036	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.156000	0.50708	2.462000	0.83206	0.558000	0.71614	GTG	.		0.701	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519		T	26785532	G	T	26785532	3	4	139	1	0	0	0	0	1	0	0	0	2196	1145	40	4	54	4	C2orf70	2	26785532	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	1326863	26785532	216413841	14	12309											
CEBPZ	10153	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	37430124	37430124	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atacaaataggctggaatcaTttaagtttcttttctttttt	11	20	5	5	0	3	0	1	0	2	0	3	1	3	1	0	2	1	2	0	2	5	10			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:37430124T>A	ENST00000234170.5	-	14	3057	c.2912A>T	c.(2911-2913)aAt>aTt	p.N971I	AC007390.5_ENST00000397064.2_Intron|AC007390.5_ENST00000406711.1_Intron|AC007390.5_ENST00000392061.2_Intron|AC007390.5_ENST00000402297.1_3'UTR	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	971					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				GCTGGAATCATTTAAGTTTCT	0.264																																					p.N971I		.											.	CEBPZ-91	0			c.A2912T						.						54	58	57					2																	37430124		2200	4294	6494	SO:0001583	missense	10153	exon14			GAATCATTTAAGT	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.2912A>T	2.37:g.37430124T>A	ENSP00000234170:p.Asn971Ile	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	216	75	NM_005760	0	0	64	122	58	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	T	6.448	0.450836	0.12223	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.14144	2.53	5.53	-1.96	0.07525	.	0.448282	0.25529	N	0.030057	T	0.11367	0.0277	L	0.44542	1.39	0.09310	N	1	B	0.26744	0.158	B	0.26517	0.07	T	0.16897	-1.0387	10	0.72032	D	0.01	.	11.4206	0.49978	0.0:0.2571:0.0:0.7429	.	971	Q03701	CEBPZ_HUMAN	I	971	ENSP00000234170:N971I	ENSP00000234170:N971I	N	-	2	0	CEBPZ	37283628	0.000000	0.05858	0.014000	0.15608	0.199000	0.23934	-0.102000	0.10956	-0.622000	0.05626	-0.400000	0.06385	AAT	.		0.264	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37430124	T	A	37430124	3	1	139	1	0	0	0	0	1	0	0	0	3210	1493	52	5	264	5	CEBPZ	2	37430124	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	10644592	37430124	205769249	15	12310											
PREPL	9581	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	44566372	44566372	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtaaaggaccccatgtattcGcttctggataagtactggtg	10	12	11	8	1	1	0	0	0	1	0	2	2	1	2	2	3	1	4	2	3	5	6	rs145356495		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:44566372G>A	ENST00000409936.1	-	7	1320	c.883C>T	c.(883-885)Cga>Tga	p.R295*	PREPL_ENST00000378520.3_Nonsense_Mutation_p.R295*|PREPL_ENST00000378511.3_Nonsense_Mutation_p.R295*|PREPL_ENST00000409411.1_Nonsense_Mutation_p.R206*|PREPL_ENST00000260648.6_Nonsense_Mutation_p.R295*|PREPL_ENST00000409957.1_Nonsense_Mutation_p.R206*|PREPL_ENST00000541738.1_Nonsense_Mutation_p.R206*|PREPL_ENST00000409272.1_Nonsense_Mutation_p.R295*|PREPL_ENST00000410081.1_Nonsense_Mutation_p.R295*	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	295						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CCATGTATTCGCTTCTGGATA	0.413																																					p.R295X		.											.	PREPL-91	0			c.C883T						.	G	stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	113	109	110		883,883,883,883,616,616,883	3.4	1	2	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,	295/666,295/662,295/728,295/728,206/639,206/639,295/728	44566372	1,13005	2203	4300	6503	SO:0001587	stop_gained	9581	exon7			GTATTCGCTTCTG	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.883C>T	2.37:g.44566372G>A	ENSP00000386543:p.Arg295*	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	182	14	NM_001171603	0	0	21	21	0	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Nonsense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	G	36	5.741979	0.96873	0.0	1.16E-4	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	.	.	.	5.46	3.39	0.38822	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.5424	14.6218	0.68592	0.0:0.0:0.6226:0.3774	.	.	.	.	X	206;206;206;295;295;295;295;295;295	.	ENSP00000260648:R295X	R	-	1	2	PREPL	44419876	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.377000	0.34317	1.221000	0.43506	0.650000	0.86243	CGA	G|1.000;A|0.000		0.413	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		A	44566372	G	A	44566372	4	1	139	1	0	0	0	0	0	1	0	0	12504	1095	38	1	1336	1	PREPL	2	44566372	Nonsense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	7136248	44566372	198633001	16	12311											
PREPL	9581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	44566451	44566451	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagtagtcttgttcataatAtttatggtgaggaaacgact	13	14	10	4	1	2	1	1	1	1	0	2	4	2	2	0	2	1	2	0	2	6	7			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:44566451A>G	ENST00000409936.1	-	7	1241	c.804T>C	c.(802-804)aaT>aaC	p.N268N	PREPL_ENST00000378520.3_Silent_p.N268N|PREPL_ENST00000378511.3_Silent_p.N268N|PREPL_ENST00000409411.1_Silent_p.N179N|PREPL_ENST00000260648.6_Silent_p.N268N|PREPL_ENST00000409957.1_Silent_p.N179N|PREPL_ENST00000541738.1_Silent_p.N179N|PREPL_ENST00000409272.1_Silent_p.N268N|PREPL_ENST00000410081.1_Silent_p.N268N	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	268						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TGTTCATAATATTTATGGTGA	0.413																																					p.N268N		.											.	PREPL-91	0			c.T804C						.						84	79	81					2																	44566451		2203	4300	6503	SO:0001819	synonymous_variant	9581	exon7			CATAATATTTATG	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.804T>C	2.37:g.44566451A>G		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	142	16	NM_001171603	0	0	13	13	0	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Silent	SNP	ENST00000409936.1	37	CCDS33190.1																																																																																			.		0.413	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		G	44566451	A	G	44566451	2	3	139	1	0	0	0	0	0	0	0	1	12504	446	16	3		3	PREPL	2	44566451	Silent	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	79	44566451	198632922	17	12312											
CCDC88A	55704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	55561724	55561724	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttttcttgaaagatgcttTcaggagctccaaacccttct	9	15	7	10	0	3	2	1	1	2	1	4	3	4	3	2	1	3	3	2	1	2	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:55561724T>G	ENST00000436346.1	-	15	3074	c.2233A>C	c.(2233-2235)Aaa>Caa	p.K745Q	AC012358.8_ENST00000599475.1_RNA|AC012358.8_ENST00000608103.1_RNA|CCDC88A_ENST00000336838.6_Missense_Mutation_p.K745Q|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000599352.1_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.K745Q|CCDC88A_ENST00000413716.2_Missense_Mutation_p.K745Q|AC012358.8_ENST00000594078.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	745					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						AAAGATGCTTTCAGGAGCTCC	0.363																																					p.K745Q		.											.	CCDC88A-94	0			c.A2233C						.						91	93	92					2																	55561724		2202	4299	6501	SO:0001583	missense	55704	exon15			ATGCTTTCAGGAG	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"Galpha-interacting vesicle-associated protein", "Akt-phosphorylation enhancer", "girdin", "girders of actin filaments"	609736	"KIAA1212"	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.2233A>C	2.37:g.55561724T>G	ENSP00000410608:p.Lys745Gln	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	74	14	NM_018084	0	0	2	2	0	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	T	14.75	2.628283	0.46944	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.17213	2.29;2.51;2.48;2.3	4.86	4.86	0.63082	.	0.126339	0.34725	U	0.003726	T	0.17238	0.0414	L	0.46885	1.475	0.80722	D	1	B;P;B;B;B	0.44478	0.061;0.836;0.018;0.009;0.031	B;B;B;B;B	0.40101	0.145;0.319;0.092;0.028;0.028	T	0.03130	-1.1069	10	0.29301	T	0.29	-11.7377	14.7941	0.69865	0.0:0.0:0.0:1.0	.	745;745;745;745;745	B7ZM78;Q3V6T2-2;Q3V6T2;Q3V6T2-3;Q3V6T2-4	.;.;GRDN_HUMAN;.;.	Q	745	ENSP00000338728:K745Q;ENSP00000263630:K745Q;ENSP00000410608:K745Q;ENSP00000404431:K745Q	ENSP00000263630:K745Q	K	-	1	0	CCDC88A	55415228	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.647000	0.67923	1.956000	0.56807	0.374000	0.22700	AAA	.		0.363	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		G	55561724	T	G	55561724	3	3	139	1	0	0	0	0	1	0	0	0	2869	1792	62	5	3454	5	CCDC88A	2	55561724	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	10995273	55561724	187637649	18	12313											
MBD5	55777	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	149247732	149247732	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaactatgatgagttttaagGagagactagagaacactgtg	15	10	12	4	0	0	4	0	2	0	2	0	8	0	5	0	1	2	1	0	1	5	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:149247732G>A	ENST00000407073.1	+	12	4829	c.3832G>A	c.(3832-3834)Gag>Aag	p.E1278K	MBD5_ENST00000404807.1_Missense_Mutation_p.E1511K	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1278					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		GAGTTTTAAGGAGAGACTAGA	0.413																																					p.E1278K		.											.	MBD5-95	0			c.G3832A						.						61	62	61					2																	149247732		2203	4300	6503	SO:0001583	missense	55777	exon12			TTTAAGGAGAGAC	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.3832G>A	2.37:g.149247732G>A	ENSP00000386049:p.Glu1278Lys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	64	6	NM_018328	0	0	6	7	1	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493136	0.84962	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.63913	0.15;-0.07	5.89	5.89	0.94794	.	0.093845	0.46442	D	0.000287	T	0.68366	0.2993	N	0.24115	0.695	0.58432	D	0.999999	B;D	0.64830	0.302;0.994	B;P	0.61397	0.182;0.888	T	0.71421	-0.4598	10	0.87932	D	0	-2.9361	20.2363	0.98357	0.0:0.0:1.0:0.0	.	1511;1278	E9PHH0;Q9P267	.;MBD5_HUMAN	K	1278;1511	ENSP00000386049:E1278K;ENSP00000384672:E1511K	ENSP00000384672:E1511K	E	+	1	0	MBD5	148964202	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.039000	0.93777	2.789000	0.95967	0.655000	0.94253	GAG	.		0.413	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			A	149247732	G	A	149247732	3	1	139	1	0	0	0	0	1	0	0	0	9372	1175	41	2	3858	2	MBD5	2	149247732	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	93686008	149247732	93951641	19	12314											
C2orf77	129881	hgsc.bcm.edu;bcgsc.ca	37	chr2	170506849	170506849	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aattgtttaccacaatggctCgatattctgcaattgttttt	10	18	6	7	1	1	0	0	0	1	0	2	1	1	0	1	1	2	4	1	1	5	8			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:170506849C>T	ENST00000447353.1	-	7	1247	c.1142G>A	c.(1141-1143)cGa>cAa	p.R381Q		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	381																	CACAATGGCTCGATATTCTGC	0.338																																					p.R381Q		.											.	.	0			c.G1142A						.						86	76	79					2																	170506849		1811	4068	5879	SO:0001583	missense	129881	exon7			ATGGCTCGATATT	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"hypothetical LOC129881"		"chromosome 2 open reading frame 77"	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.1142G>A	2.37:g.170506849C>T	ENSP00000391504:p.Arg381Gln	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	64	4	NM_001085447	0	0	0	0	0	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543115	0.86022	.	.	ENSG00000154479	ENST00000447353	T	0.15256	2.44	5.42	5.42	0.78866	.	.	.	.	.	T	0.41096	0.1144	M	0.71581	2.175	0.45946	D	0.998779	D	0.89917	1.0	D	0.87578	0.998	T	0.06267	-1.0836	9	0.30854	T	0.27	.	16.2096	0.82148	0.0:1.0:0.0:0.0	.	381	Q0VFZ6	CB077_HUMAN	Q	381	ENSP00000391504:R381Q	ENSP00000391504:R381Q	R	-	2	0	C2orf77	170215095	1.000000	0.71417	0.986000	0.45419	0.965000	0.64279	4.503000	0.60407	2.565000	0.86533	0.558000	0.71614	CGA	.		0.338	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		T	170506849	C	T	170506849	3	4	139	1	0	0	0	0	1	0	0	0	2200	884	31	1	528	1	C2orf77	2	170506849	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	21259117	170506849	72692524	20	12315											
TTN	7273	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179469564	179469564	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcaagaggggcatcccatgtCaagtagcaagattcagcttt	12	10	10	9	0	3	2	3	0	0	2	4	2	4	2	1	2	2	4	1	2	4	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:179469564C>G	ENST00000591111.1	-	231	49553	c.49329G>C	c.(49327-49329)ttG>ttC	p.L16443F	TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L9144F|TTN_ENST00000460472.2_Missense_Mutation_p.L9019F|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L15516F|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L18084F|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L9211F|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16443	Fibronectin type-III 19. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATCCCATGTCAAGTAGCAAG	0.433																																					p.L18084F													.	TTN-636	0			c.G54252C						.						131	119	123					2																	179469564		1901	4143	6044	SO:0001583	missense	7273	exon281			CCATGTCAAGTAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.49329G>C	2.37:g.179469564C>G	ENSP00000465570:p.Leu16443Phe	Somatic	236	1		WXS	Illumina HiSeq	Phase_I	237	42	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	8.786	0.929337	0.18131	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	5.74	2.93	0.34026	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.81484	0.4832	M	0.93808	3.46	0.42388	D	0.992518	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.81760	-0.0785	9	0.87932	D	0	.	8.5796	0.33621	0.0:0.6169:0.0:0.3831	.	9019;9144;9211;16443	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	15516;9019;9211;9144;9019	ENSP00000343764:L15516F;ENSP00000434586:L9019F;ENSP00000340554:L9211F;ENSP00000352154:L9144F	ENSP00000340554:L9211F	L	-	3	2	TTN	179177809	0.812000	0.29077	0.999000	0.59377	0.928000	0.56348	-0.105000	0.10907	0.421000	0.25980	0.563000	0.77884	TTG	.		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179469564	C	G	179469564	3	3	139	1	0	0	0	0	1	0	0	0	16768	825	29	4	53769	4	TTN	2	179469564	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	8962715	179469564	63729809	21	12316											
SF3B1	23451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	198265617	198265617	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caatcctggatataatttctGctgcacctactttgtttgcc	8	16	6	11	0	1	0	0	0	1	0	2	1	2	1	3	1	4	3	3	1	4	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:198265617G>A	ENST00000335508.6	-	18	2631	c.2540C>T	c.(2539-2541)gCa>gTa	p.A847V	SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	847					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TATAATTTCTGCTGCACCTAC	0.358			Mis		myelodysplastic syndrome																																p.A847V		.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.C2540T						.						99	97	98					2																	198265617		2203	4300	6503	SO:0001583	missense	23451	exon18			ATTTCTGCTGCAC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2540C>T	2.37:g.198265617G>A	ENSP00000335321:p.Ala847Val	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	78	11	NM_012433	0	0	109	140	31	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833082	0.71258	.	.	ENSG00000115524	ENST00000335508	T	0.65549	-0.16	5.77	5.77	0.91146	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59622	0.2207	L	0.41961	1.31	0.80722	D	1	B	0.14438	0.01	B	0.18561	0.022	T	0.52917	-0.8511	10	0.48119	T	0.1	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	847	O75533	SF3B1_HUMAN	V	847	ENSP00000335321:A847V	ENSP00000335321:A847V	A	-	2	0	SF3B1	197973862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.737000	0.98831	2.885000	0.99019	0.655000	0.94253	GCA	.		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198265617	G	A	198265617	3	1	139	1	0	0	0	0	1	0	0	0	14181	1319	46	2	1406	2	SF3B1	2	198265617	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	18796053	198265617	44933756	22	12317											
PLEKHM3	389072	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	208725904	208725904	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagatgaaccccttctggCtacaaagactgcagctgtac	12	8	8	13	0	1	3	0	1	1	2	1	3	1	3	2	1	5	4	2	1	4	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:208725904C>G	ENST00000427836.2	-	7	2522	c.2033G>C	c.(2032-2034)aGc>aCc	p.S678T	PLEKHM3_ENST00000389247.4_Missense_Mutation_p.S678T	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	678					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCCCTTCTGGCTACAAAGACT	0.418																																					p.S678T		.											.	PLEKHM3-23	0			c.G2033C						.						148	142	144					2																	208725904		1924	4136	6060	SO:0001583	missense	389072	exon7			TTCTGGCTACAAA	AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"Pleckstrin homology (PH) domain containing"	34006	protein-coding gene	gene with protein product	"differentiation associated protein"		"pleckstrin homology domain containing, family M, member 1-like"	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.2033G>C	2.37:g.208725904C>G	ENSP00000417003:p.Ser678Thr	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	133	7	NM_001080475	0	0	0	0	0	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	37	CCDS42808.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.28|15.28	2.787482|2.787482	0.49997|0.49997	.|.	.|.	ENSG00000178385|ENSG00000178385	ENST00000427836;ENST00000389247|ENST00000447645	D;D|.	0.83163|.	-1.68;-1.69|.	5.06|5.06	5.06|5.06	0.68205|0.68205	Protein kinase C-like, phorbol ester/diacylglycerol binding (1);|.	0.045109|.	0.85682|.	D|.	0.000000|.	T|.	0.55321|.	0.1913|.	N|N	0.21194|0.21194	0.64|0.64	0.52501|0.52501	D|D	0.999957|0.999957	P|.	0.39060|.	0.657|.	P|.	0.46585|.	0.521|.	T|.	0.48875|.	-0.8996|.	10|.	0.09084|.	T|.	0.74|.	.|.	18.9822|18.9822	0.92758|0.92758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	678|.	Q6ZWE6|.	PKHM3_HUMAN|.	T|Y	678|429	ENSP00000417003:S678T;ENSP00000373899:S678T|.	ENSP00000373899:S678T|.	S|X	-|-	2|3	0|2	PLEKHM3|PLEKHM3	208434149|208434149	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.870000|5.870000	0.69620|0.69620	2.763000|2.763000	0.94921|0.94921	0.655000|0.655000	0.94253|0.94253	AGC|TAG	.		0.418	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475		G	208725904	C	G	208725904	3	3	139	1	0	0	0	0	1	0	0	0	12108	797	28	4	260	4	PLEKHM3	2	208725904	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	10460287	208725904	34473469	23	12318											
DGKD	8527	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	234368474	234368474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtggacggagaggcctgggtCcagccgccagggtacattcg	7	6	17	11	3	0	1	0	0	0	1	2	3	1	2	4	5	2	1	4	5	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:234368474C>T	ENST00000264057.2	+	23	2778	c.2766C>T	c.(2764-2766)gtC>gtT	p.V922V	DGKD_ENST00000409813.3_Silent_p.V878V	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	922					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	AGGCCTGGGTCCAGCCGCCAG	0.602																																					p.V922V		.											.	DGKD-676	0			c.C2766T						.						76	66	69					2																	234368474		2203	4300	6503	SO:0001819	synonymous_variant	8527	exon23			CTGGGTCCAGCCG	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2766C>T	2.37:g.234368474C>T		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	134	8	NM_152879	0	0	0	1	1	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	37	CCDS2504.1																																																																																			.		0.602	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234368474	C	T	234368474	2	4	139	1	0	0	0	0	0	0	0	1	4478	842	30	2		2	DGKD	2	234368474	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	25642570	234368474	8830899	24	12319											
FANCD2	2177	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	10089633	10089633	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtgttcatccattctgtcGctggctcagagtttgcttca	6	16	9	10	1	4	1	3	0	1	1	6	1	5	1	1	1	1	5	1	1	0	4	rs564577177		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:10089633G>A	ENST00000419585.1	+	16	1472	c.1311G>A	c.(1309-1311)tcG>tcA	p.S437S	FANCD2_ENST00000383806.1_Silent_p.S437S|FANCD2_ENST00000287647.3_Silent_p.S437S|FANCD2_ENST00000383807.1_Silent_p.S437S			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	437					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCATTCTGTCGCTGGCTCAGA	0.408			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S437S		.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2-229	0			c.G1311A						.						171	174	173					3																	10089633		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCTGTCGCTGGCT	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"Fanconi anemia, complementation groups"	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1311G>A	3.37:g.10089633G>A		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	107	8	NM_001018115	0	0	1	1	0	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			.		0.408	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			A	10089633	G	A	10089633	2	1	139	1	0	0	0	0	0	0	0	1	5684	1074	38	1		1	FANCD2	3	10089633	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		10089633	187932797	25	12320											
SCN11A	11280	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	38962716	38962716	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaccagcttcttcacagagCgtagcaaggcccccacgatg	10	7	10	14	2	2	2	1	1	1	1	2	3	2	2	3	1	3	3	3	1	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:38962716C>T	ENST00000302328.3	-	6	941	c.743G>A	c.(742-744)cGc>cAc	p.R248H	SCN11A_ENST00000450244.1_Missense_Mutation_p.R248H|SCN11A_ENST00000444237.2_Missense_Mutation_p.R248H|SCN11A_ENST00000456224.3_Missense_Mutation_p.R248H	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	248					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTCACAGAGCGTAGCAAGGC	0.542																																					p.R248H		.											.	SCN11A-99	0			c.G743A						.						115	111	112					3																	38962716		2203	4300	6503	SO:0001583	missense	11280	exon6			ACAGAGCGTAGCA	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10583	protein-coding gene	gene with protein product		604385	"sodium channel, voltage-gated, type XI, alpha polypeptide", "sodium channel, voltage-gated, type XII, alpha"	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.743G>A	3.37:g.38962716C>T	ENSP00000307599:p.Arg248His	Somatic	149	1		WXS	Illumina HiSeq	Phase_I	138	106	NM_014139	0	0	0	0	0	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.085095	0.36758	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08	4.67	3.79	0.43588	Ion transport (1);	0.217778	0.42964	D	0.000631	D	0.94729	0.8299	N	0.25332	0.735	0.32489	N	0.540524	B	0.26081	0.141	B	0.22880	0.042	D	0.92393	0.5923	10	0.16896	T	0.51	.	7.3286	0.26569	0.0:0.7983:0.0:0.2017	.	248	Q9UI33	SCNBA_HUMAN	H	248	ENSP00000307599:R248H;ENSP00000400945:R248H;ENSP00000416757:R248H;ENSP00000408028:R248H	ENSP00000307599:R248H	R	-	2	0	SCN11A	38937720	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.635000	0.61332	0.966000	0.38159	0.585000	0.79938	CGC	.		0.542	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38962716	C	T	38962716	3	4	139	1	0	0	0	0	1	0	0	0	13945	768	27	1	4716	1	SCN11A	3	38962716	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	28873083	38962716	159059714	26	12321											
ZBTB38	253461	broad.mit.edu	37	chr3	141162716	141162716	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttgccattactgcaacaaaGtatttgcattggctgagtac	11	13	8	9	0	0	1	0	1	0	0	0	1	0	1	1	1	6	5	1	1	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:141162716G>A	ENST00000514251.1	+	4	1765	c.1486G>A	c.(1486-1488)Gta>Ata	p.V496I	ZBTB38_ENST00000321464.5_Missense_Mutation_p.V497I|ZBTB38_ENST00000441582.2_Missense_Mutation_p.V496I					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						CTGCAACAAAGTATTTGCATT	0.418																																					p.V496I													.	ZBTB38-25	0			c.G1486A						.						99	92	94					3																	141162716		1929	4124	6053	SO:0001583	missense	253461	exon8			AACAAAGTATTTG	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1486G>A	3.37:g.141162716G>A	ENSP00000426387:p.Val496Ile	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	94	3	NM_001080412	0	0	4	4	0		Missense_Mutation	SNP	ENST00000514251.1	37	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.791622	0.90367	.	.	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000001	T	0.64907	0.2641	N	0.21240	0.645	0.49213	D	0.999765	D;D	0.71674	0.998;0.998	D;D	0.81914	0.994;0.995	T	0.62714	-0.6796	9	.	.	.	-22.0045	19.1701	0.93574	0.0:0.0:1.0:0.0	.	497;496	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	I	496;496;496;497	ENSP00000424254:V496I;ENSP00000426387:V496I;ENSP00000406955:V496I;ENSP00000372635:V497I	.	V	+	1	0	ZBTB38	142645406	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.476000	0.97823	2.543000	0.85770	0.650000	0.86243	GTA	.		0.418	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			A	141162716	G	A	141162716	3	1	139	1	0	0	0	0	1	0	0	0	17571	1029	36	2	1488	2	ZBTB38	3	141162716	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	102200000	141162716	56859714	27	12322											
AADACL2	344752	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	151475280	151475280	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcatgaacatattgaggaTggaattcatggagctttatc	12	14	10	5	0	2	2	2	2	0	0	3	5	2	5	0	3	2	2	0	3	4	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:151475280T>C	ENST00000356517.3	+	5	1213	c.1104T>C	c.(1102-1104)gaT>gaC	p.D368D	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	368						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			ATATTGAGGATGGAATTCATG	0.338																																					p.D368D		.											.	AADACL2-90	0			c.T1104C						.						97	95	96					3																	151475280		2203	4299	6502	SO:0001819	synonymous_variant	344752	exon5			TGAGGATGGAATT	BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.1104T>C	3.37:g.151475280T>C		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	191	15	NM_207365	0	0	0	0	0	Q5HYJ4	Silent	SNP	ENST00000356517.3	37	CCDS3161.2																																																																																			.		0.338	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342288.3	NM_207365		C	151475280	T	C	151475280	2	2	139	1	0	0	0	0	0	0	0	1	11	1461	51	3		3	AADACL2	3	151475280	Silent	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	10312564	151475280	46547150	28	12323											
SI	6476	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	164767590	164767590	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaattttaccaggagtaaacGgtggataattcaatttgttt	14	15	8	4	1	1	0	1	0	0	0	1	2	1	2	1	3	2	2	1	3	6	7			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:164767590G>A	ENST00000264382.3	-	14	1648	c.1586C>T	c.(1585-1587)cCg>cTg	p.P529L		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	529	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AGGAGTAAACGGTGGATAATT	0.279										HNSCC(35;0.089)																											p.P529L		.											.	SI-104	0			c.C1586T						.						90	100	97					3																	164767590		2203	4289	6492	SO:0001583	missense	6476	exon14			GTAAACGGTGGAT	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"Oligosaccharide alpha-1,6-glucosidase"	609845	"sucrase-isomaltase"			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1586C>T	3.37:g.164767590G>A	ENSP00000264382:p.Pro529Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	131	9	NM_001041	0	0	0	0	0	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.778691	0.70107	.	.	ENSG00000090402	ENST00000264382	D	0.91686	-2.89	5.58	5.58	0.84498	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97188	0.9081	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.97952	1.0332	10	0.87932	D	0	.	18.5615	0.91101	0.0:0.0:1.0:0.0	.	529	P14410	SUIS_HUMAN	L	529	ENSP00000264382:P529L	ENSP00000264382:P529L	P	-	2	0	SI	166250284	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	9.114000	0.94329	2.622000	0.88805	0.585000	0.79938	CCG	.		0.279	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164767590	G	A	164767590	3	1	139	1	0	0	0	0	1	0	0	0	14329	1116	39	1	4037	1	SI	3	164767590	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	13292310	164767590	33254840	29	12324											
KLB	152831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39439409	39439409	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggtctctcctggatggctttGaatggcaggatgcttacacc	7	12	12	10	0	1	1	0	1	1	0	3	3	2	3	2	5	2	3	2	5	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:39439409G>C	ENST00000257408.4	+	3	1496	c.1399G>C	c.(1399-1401)Gaa>Caa	p.E467Q		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	467	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						GGATGGCTTTGAATGGCAGGA	0.428																																					p.E467Q		.											.	KLB-69	0			c.G1399C						.						189	178	182					4																	39439409		2203	4300	6503	SO:0001583	missense	152831	exon3			GGCTTTGAATGGC	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1399G>C	4.37:g.39439409G>C	ENSP00000257408:p.Glu467Gln	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	112	15	NM_175737	0	0	0	0	0	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956339	0.92726	.	.	ENSG00000134962	ENST00000257408	T	0.41065	1.01	6.03	5.19	0.71726	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.095361	0.64402	D	0.000001	T	0.77239	0.4101	H	0.98446	4.235	0.51767	D	0.999938	D;D	0.76494	0.999;0.999	D;D	0.66716	0.946;0.946	D	0.86716	0.1939	10	0.87932	D	0	-28.1831	15.0523	0.71885	0.0674:0.0:0.9326:0.0	.	467;467	B7ZL50;Q86Z14	.;KLOTB_HUMAN	Q	467	ENSP00000257408:E467Q	ENSP00000257408:E467Q	E	+	1	0	KLB	39115804	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	1.562000	0.49601	0.655000	0.94253	GAA	.		0.428	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		C	39439409	G	C	39439409	3	2	139	1	0	0	0	0	1	0	0	0	8353	1291	45	4	1409	4	KLB	4	39439409	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		39439409	151714867	30	12325											
FIP1L1	81608	broad.mit.edu	37	chr4	54244014	54244014	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggggcggccatgtcggcCggcgaggtcgagcgcctagt	4	6	18	13	7	0	0	0	0	0	0	3	2	0	0	3	6	1	0	3	6	1	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:54244014C>T	ENST00000337488.6	+	1	203	c.9C>T	c.(7-9)gcC>gcT	p.A3A	FIP1L1_ENST00000358575.5_Silent_p.A3A|FIP1L1_ENST00000306932.6_Silent_p.A3A|FIP1L1_ENST00000507922.1_Silent_p.A3A|FIP1L1_ENST00000507166.1_Silent_p.A3A	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	3	Necessary for stimulating PAPOLA activity.|Sufficient for interaction with PAPOLA.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CCATGTCGGCCGGCGAGGTCG	0.672			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.A3A				Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1-1083	0			c.C9T						.						39	55	50					4																	54244014		2191	4292	6483	SO:0001819	synonymous_variant	81608	exon1			GTCGGCCGGCGAG	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"FIP1 like 1 (S. cerevisiae)", "FIP1L1 cleavage and polyadenylation specific factor subunit"			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.9C>T	4.37:g.54244014C>T		Somatic	44	1		WXS	Illumina HiSeq	Phase_I	22	9	NM_030917	0	0	3	7	4	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Silent	SNP	ENST00000337488.6	37	CCDS3491.1																																																																																			.		0.672	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		T	54244014	C	T	54244014	2	4	139	1	0	0	0	0	0	0	0	1	5915	639	23	1		1	FIP1L1	4	54244014	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	14804605	54244014	136910262	31	12326											
POLR2B	5431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57889646	57889646	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caccaatagacgctataccaAgagagactgtagcacttttc	14	9	7	11	1	0	3	0	0	0	3	1	4	0	3	2	0	2	3	2	0	6	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:57889646A>T	ENST00000381227.1	+	20	3079	c.2666A>T	c.(2665-2667)aAg>aTg	p.K889M	POLR2B_ENST00000431623.2_Missense_Mutation_p.K814M|POLR2B_ENST00000441246.2_Missense_Mutation_p.K882M|POLR2B_ENST00000314595.5_Missense_Mutation_p.K889M			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	889					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					CGCTATACCAAGAGAGACTGT	0.413																																					p.K889M		.											.	POLR2B-92	0			c.A2666T						.						108	104	105					4																	57889646		2203	4300	6503	SO:0001583	missense	5431	exon19			ATACCAAGAGAGA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"RNA polymerase subunits"	9188	protein-coding gene	gene with protein product		180661	"polymerase (RNA) II (DNA directed) polypeptide B (140kD)"			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2666A>T	4.37:g.57889646A>T	ENSP00000370625:p.Lys889Met	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	92	7	NM_000938	0	0	28	30	2	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	37	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834179	0.91036	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	6.04	6.04	0.98038	RNA polymerase Rpb2, OB-fold (1);DNA-directed RNA polymerase, subunit 2, domain 6 (1);	0.000000	0.85682	D	0.000000	D	0.88066	0.6337	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90731	0.4642	10	0.87932	D	0	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	814;889	C9J4M6;P30876	.;RPB2_HUMAN	M	889;814;882;889	ENSP00000370625:K889M;ENSP00000391096:K814M;ENSP00000391452:K882M;ENSP00000312735:K889M	ENSP00000312735:K889M	K	+	2	0	POLR2B	57584403	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.317000	0.78254	0.460000	0.39030	AAG	.		0.413	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		T	57889646	A	T	57889646	3	4	139	1	0	0	0	0	1	0	0	0	12241	72	3	5	2740	5	POLR2B	4	57889646	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	3645632	57889646	133264630	32	12327											
SMARCAD1	56916	broad.mit.edu	37	chr4	95174021	95174021	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtagtggtgaagaagtgatgGaggatggctataaaggtaaa	15	9	16	1	0	0	3	0	2	0	1	0	5	0	5	0	5	0	3	0	5	8	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:95174021G>A	ENST00000354268.4	+	9	1217	c.1144G>A	c.(1144-1146)Gag>Aag	p.E382K	SMARCAD1_ENST00000509418.1_5'Flank|SMARCAD1_ENST00000457823.2_Missense_Mutation_p.E382K			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	382					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AGAAGTGATGGAGGATGGCTA	0.378																																					p.E382K													.	SMARCAD1-229	0			c.G1144A						.						97	94	95					4																	95174021		2203	4300	6503	SO:0001583	missense	56916	exon9			GTGATGGAGGATG	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.1144G>A	4.37:g.95174021G>A	ENSP00000346217:p.Glu382Lys	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	61	4	NM_001128429	0	0	4	4	0	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759725	0.49468	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268	D;D;D	0.88277	-2.36;-2.36;-2.35	5.58	5.58	0.84498	.	0.000000	0.50627	D	0.000119	D	0.85936	0.5813	L	0.54323	1.7	0.80722	D	1	P;B	0.41910	0.764;0.157	B;B	0.32762	0.152;0.077	D	0.86276	0.1664	10	0.42905	T	0.14	-9.6286	19.5837	0.95482	0.0:0.0:1.0:0.0	.	382;382	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	K	382	ENSP00000351947:E382K;ENSP00000415576:E382K;ENSP00000346217:E382K	ENSP00000346217:E382K	E	+	1	0	SMARCAD1	95393044	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.116000	0.77119	2.630000	0.89119	0.655000	0.94253	GAG	.		0.378	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		A	95174021	G	A	95174021	3	1	139	1	0	0	0	0	1	0	0	0	14804	1175	41	2	1174	2	SMARCAD1	4	95174021	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	37284375	95174021	95980255	33	12328											
GUCY1B3	2983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	156724870	156724870	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccacctggccttggacaTgatggaaattgctggccagg	8	9	13	11	0	0	1	0	1	0	0	0	3	0	3	4	5	2	1	4	5	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:156724870T>G	ENST00000264424.8	+	11	1590	c.1508T>G	c.(1507-1509)aTg>aGg	p.M503R	GUCY1B3_ENST00000507146.1_Missense_Mutation_p.M478R|GUCY1B3_ENST00000513437.1_Missense_Mutation_p.M435R|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.M483R|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.M525R|GUCY1B3_ENST00000505154.1_Missense_Mutation_p.M435R|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.M470R	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	503	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		GCCTTGGACATGATGGAAATT	0.423																																					p.M503R		.											.	.	0			c.T1508G						.						76	79	78					4																	156724870		1960	4160	6120	SO:0001583	missense	2983	exon11			TGGACATGATGGA	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1508T>G	4.37:g.156724870T>G	ENSP00000264424:p.Met503Arg	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	39	4	NM_000857	0	0	16	21	5	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	37	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327658	0.81690	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.61	5.61	0.85477	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.93848	0.8032	H	0.96576	3.845	0.80722	D	1	P;P;D;P;P	0.58970	0.94;0.941;0.984;0.875;0.867	P;P;D;P;P	0.65010	0.735;0.86;0.931;0.517;0.735	D	0.95757	0.8797	10	0.87932	D	0	.	16.1025	0.81194	0.0:0.0:0.0:1.0	.	483;525;478;470;503	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	R	435;525;483;478;503;470;435	ENSP00000427226:M435R;ENSP00000426786:M525R;ENSP00000426319:M483R;ENSP00000422313:M478R;ENSP00000264424:M503R;ENSP00000420842:M470R;ENSP00000425065:M435R	ENSP00000264424:M503R	M	+	2	0	GUCY1B3	156944320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.990000	0.88215	2.254000	0.74563	0.533000	0.62120	ATG	.		0.423	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			G	156724870	T	G	156724870	3	3	139	1	0	0	0	0	1	0	0	0	6916	1464	51	5	1550	5	GUCY1B3	4	156724870	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	61550849	156724870	34429406	34	12329											
SDHA	6389	ucsc.edu;bcgsc.ca	37	chr5	235358	235358	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcatttcagagacagccatGatcttcgctggcgtggacgt	8	10	13	10	3	2	2	1	1	1	1	3	4	2	3	1	3	1	2	1	3	0	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:235358G>A	ENST00000264932.6	+	9	1279	c.1164G>A	c.(1162-1164)atG>atA	p.M388I	SDHA_ENST00000504309.1_Missense_Mutation_p.M388I|SDHA_ENST00000510361.1_Missense_Mutation_p.M340I	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	388					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	AGACAGCCATGATCTTCGCTG	0.602									Familial Paragangliomas																												p.M388I													.	SDHA-226	0			c.G1164A						.						68	61	63					5																	235358		2203	4300	6503	SO:0001583	missense	6389	exon9	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	AGCCATGATCTTC	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1164G>A	5.37:g.235358G>A	ENSP00000264932:p.Met388Ile	Somatic	444	4		WXS	Illumina HiSeq		569	92	NM_004168	0	0	78	89	11	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	N	18.72	3.683429	0.68157	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.68331	-0.32;-0.32;-0.32	5.12	5.12	0.69794	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.60353	0.2262	L	0.35542	1.07	0.80722	D	1	P;B;B;B;B	0.37276	0.589;0.005;0.121;0.024;0.024	B;B;B;B;B	0.39299	0.296;0.01;0.097;0.017;0.017	T	0.64605	-0.6368	10	0.56958	D	0.05	.	16.4201	0.83755	0.0:0.0:1.0:0.0	.	340;388;388;388;394	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	I	388;243;388;340	ENSP00000264932:M388I;ENSP00000426514:M388I;ENSP00000427703:M340I	ENSP00000264932:M388I	M	+	3	0	SDHA	288358	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	8.994000	0.93529	2.541000	0.85698	0.557000	0.71058	ATG	.		0.602	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		A	235358	G	A	235358	3	1	139	1	0	0	0	0	1	0	0	0	13995	1290	45	2	1198	2	SDHA	5	235358	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		235358	180679902	35	12330											
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	13771076	13771076	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcaatatcataggaagtgagGaagtgttcagacactagaga	16	9	11	5	0	3	3	3	1	0	2	3	6	3	5	0	2	0	1	0	2	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:13771076G>T	ENST00000265104.4	-	56	9491	c.9387C>A	c.(9385-9387)ttC>ttA	p.F3129L	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3129	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGGAAGTGAGGAAGTGTTCAG	0.388									Kartagener syndrome																												p.F3129L		.											.	DNAH5-182	0			c.C9387A						.						63	60	61					5																	13771076		2203	4300	6503	SO:0001583	missense	1767	exon56	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTGAGGAAGTGT	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"Axonemal dyneins"	2950	protein-coding gene	gene with protein product	"dynein heavy chain 5"	603335	"dynein, axonemal, heavy polypeptide 5"			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9387C>A	5.37:g.13771076G>T	ENSP00000265104:p.Phe3129Leu	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	104	7	NM_001369	0	0	0	0	0	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521574	0.44866	.	.	ENSG00000039139	ENST00000265104	T	0.54071	0.59	5.71	2.58	0.30949	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.67268	0.2875	M	0.89601	3.045	0.80722	D	1	B	0.31989	0.35	P	0.46585	0.521	T	0.68792	-0.5315	10	0.72032	D	0.01	.	7.8099	0.29226	0.1782:0.0:0.6883:0.1335	.	3129	Q8TE73	DYH5_HUMAN	L	3129	ENSP00000265104:F3129L	ENSP00000265104:F3129L	F	-	3	2	DNAH5	13824076	1.000000	0.71417	1.000000	0.80357	0.201000	0.24016	2.368000	0.44222	0.759000	0.33084	-0.152000	0.13540	TTC	.		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13771076	G	T	13771076	3	4	139	1	0	0	0	0	1	0	0	0	4615	1165	41	4	4583	4	DNAH5	5	13771076	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	13535718	13771076	167144184	36	12331											
NNT	23530	broad.mit.edu	37	chr5	43677873	43677873	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caataccccattgctgatttGgtaaagatgctcactgagca	12	11	8	10	0	1	3	1	2	0	1	1	3	1	3	2	1	4	4	2	1	4	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:43677873G>T	ENST00000264663.5	+	19	3062	c.2841G>T	c.(2839-2841)ttG>ttT	p.L947F	NNT_ENST00000512996.2_Missense_Mutation_p.L816F|NNT_ENST00000344920.4_Missense_Mutation_p.L947F	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	947					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TTGCTGATTTGGTAAAGATGC	0.403																																					p.L947F													.	NNT-92	0			c.G2841T						.						158	153	155					5																	43677873		2203	4300	6503	SO:0001583	missense	23530	exon19			TGATTTGGTAAAG	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.2841G>T	5.37:g.43677873G>T	ENSP00000264663:p.Leu947Phe	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	110	4	NM_182977	0	0	31	31	0	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	37	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.620944	0.66787	.	.	ENSG00000112992	ENST00000542759;ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.90955	-2.76;-2.76;-2.76	5.19	4.32	0.51571	.	0.196995	0.43579	D	0.000550	D	0.90810	0.7114	M	0.65320	2	0.54753	D	0.999983	P	0.45634	0.863	P	0.49332	0.607	D	0.90075	0.4166	10	0.51188	T	0.08	-2.1643	10.6804	0.45811	0.2048:0.0:0.7952:0.0	.	947	Q13423	NNTM_HUMAN	F	462;947;947;816	ENSP00000264663:L947F;ENSP00000343873:L947F;ENSP00000426343:L816F	ENSP00000264663:L947F	L	+	3	2	NNT	43713630	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.031000	0.49728	1.311000	0.45024	0.558000	0.71614	TTG	.		0.403	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		T	43677873	G	T	43677873	3	4	139	1	0	0	0	0	1	0	0	0	10536	1339	47	4	2911	4	NNT	5	43677873	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	29906797	43677873	137237387	37	12332											
DDX4	54514	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	55110902	55110902	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atatgttcatcgaattgggcGtactggtcgttgtgggaata	9	14	13	5	3	1	0	1	0	0	0	3	2	1	1	0	3	1	3	0	3	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:55110902G>A	ENST00000505374.1	+	20	1981	c.1889G>A	c.(1888-1890)cGt>cAt	p.R630H	DDX4_ENST00000511853.1_Missense_Mutation_p.R481H|DDX4_ENST00000354991.5_Missense_Mutation_p.R596H|DDX4_ENST00000514278.2_Missense_Mutation_p.R610H|DDX4_ENST00000353507.5_Missense_Mutation_p.R596H	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	630	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				CGAATTGGGCGTACTGGTCGT	0.393																																					p.R630H		.											.	DDX4-227	0			c.G1889A						.						183	179	180					5																	55110902		2203	4300	6503	SO:0001583	missense	54514	exon20			TTGGGCGTACTGG	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1889G>A	5.37:g.55110902G>A	ENSP00000424838:p.Arg630His	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	287	16	NM_024415	0	0	0	0	0	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	37	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106807	0.56291	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000354991;ENST00000511853	D;D;D;D;D	0.99143	-5.48;-5.48;-5.48;-5.48;-5.48	5.69	3.83	0.44106	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99576	0.9847	H	0.99042	4.41	0.47737	D	0.999505	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97744	1.0210	10	0.87932	D	0	-18.9385	12.9225	0.58241	0.0:0.1242:0.7465:0.1293	.	610;481;596;630	D6RDK4;E9PCD8;Q9NQI0-2;Q9NQI0	.;.;.;DDX4_HUMAN	H	596;610;630;596;481	ENSP00000334167:R596H;ENSP00000425359:R610H;ENSP00000424838:R630H;ENSP00000347087:R596H;ENSP00000423123:R481H	ENSP00000334167:R596H	R	+	2	0	DDX4	55146659	1.000000	0.71417	0.997000	0.53966	0.125000	0.20455	7.630000	0.83225	1.390000	0.46547	-0.305000	0.09177	CGT	.		0.393	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		A	55110902	G	A	55110902	3	1	139	1	0	0	0	0	1	0	0	0	4366	1145	40	1	2004	1	DDX4	5	55110902	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	11433029	55110902	125804358	38	12333											
RASA1	5921	bcgsc.ca	37	chr5	86645138	86645138	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcgatttaaaatatgtccaAcgccaaacaatcagtttatg	16	11	6	8	2	1	0	1	0	0	0	2	1	2	0	2	0	3	1	2	0	7	5	rs560064316		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:86645138A>T	ENST00000274376.6	+	8	1774	c.1210A>T	c.(1210-1212)Acg>Tcg	p.T404S	RASA1_ENST00000506290.1_Missense_Mutation_p.T238S|RASA1_ENST00000512763.1_Missense_Mutation_p.T237S|RASA1_ENST00000456692.2_Missense_Mutation_p.T227S	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	404	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AATATGTCCAACGCCAAACAA	0.348																																					p.T404S													.	RASA1-661	0			c.A1210T						.						75	79	78					5																	86645138		2201	4298	6499	SO:0001583	missense	5921	exon8			TGTCCAACGCCAA		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1210A>T	5.37:g.86645138A>T	ENSP00000274376:p.Thr404Ser	Somatic	103	2		WXS	Illumina HiSeq	Phase_1	89	32	NM_002890	0	0	4	7	3	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.894664	0.72639	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	5.78	5.78	0.91487	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	N	0.16656	0.425	0.58432	D	0.999999	P;B;P;B;P	0.39094	0.488;0.196;0.488;0.305;0.659	B;B;B;B;B	0.43889	0.357;0.254;0.357;0.298;0.435	D	0.83771	0.0220	10	0.32370	T	0.25	.	16.1143	0.81295	1.0:0.0:0.0:0.0	.	238;237;238;227;404	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	S	404;437;227;237;238	ENSP00000274376:T404S;ENSP00000411221:T227S;ENSP00000422008:T237S;ENSP00000420905:T238S	ENSP00000274376:T404S	T	+	1	0	RASA1	86680894	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.294000	0.78760	2.198000	0.70561	0.477000	0.44152	ACG	.		0.348	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		T	86645138	A	T	86645138	3	4	139	1	0	0	0	0	1	0	0	0	13092	43	2	5	1252	5	RASA1	5	86645138	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	31534236	86645138	94270122	39	12334											
SLCO6A1	133482	broad.mit.edu	37	chr5	101811427	101811427	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcagaagtagtattctcaggGactttaactagtggtgctcc	10	12	11	8	0	1	1	1	0	1	1	3	2	2	2	1	2	2	4	1	2	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:101811427G>A	ENST00000506729.1	-	4	1044	c.873C>T	c.(871-873)gtC>gtT	p.V291V	SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379810.1_Silent_p.V229V|SLCO6A1_ENST00000389019.3_Silent_p.V229V|SLCO6A1_ENST00000513675.1_Silent_p.V229V|SLCO6A1_ENST00000379807.3_Silent_p.V291V			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TATTCTCAGGGACTTTAACTA	0.333																																					p.V291V													.	SLCO6A1-96	0			c.C873T						.						114	109	111					5																	101811427		2203	4300	6503	SO:0001819	synonymous_variant	133482	exon4			CTCAGGGACTTTA	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"Solute carriers"	23613	protein-coding gene	gene with protein product	"cancer/testis antigen 48"	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.873C>T	5.37:g.101811427G>A		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	84	4	NM_173488	0	0	0	0	0	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																			.		0.333	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101811427	G	A	101811427	2	1	139	1	0	0	0	0	0	0	0	1	14764	1161	41	2		2	SLCO6A1	5	101811427	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	15166289	101811427	79103833	40	12335											
PCDHGA1	56114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140711698	140711698	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccacgacttggacagcaatGagaatgcacaaatcacttac	15	7	7	12	1	1	1	1	1	0	1	1	4	1	2	1	1	3	2	1	1	4	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:140711698G>A	ENST00000517417.1	+	1	1447	c.1447G>A	c.(1447-1449)Gag>Aag	p.E483K	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.E483K	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	483	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACAGCAATGAGAATGCACA	0.537																																					p.E483K		.											.	PCDHGA1-137	0			c.G1447A						.						113	121	119					5																	140711698		2203	4300	6503	SO:0001583	missense	56114	exon1			AGCAATGAGAATG	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.1447G>A	5.37:g.140711698G>A	ENSP00000431083:p.Glu483Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	75	15	NM_018912	0	0	0	0	0	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	G	6.770	0.511030	0.12883	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.51574	4.68;0.7	3.82	2.91	0.33838	Cadherin (4);Cadherin-like (1);	0.321295	0.22123	N	0.064320	T	0.43523	0.1251	L	0.52266	1.64	0.09310	N	0.999999	B;B	0.14805	0.011;0.009	B;B	0.24701	0.049;0.055	T	0.42430	-0.9452	10	0.46703	T	0.11	.	12.8583	0.57899	0.0:0.3118:0.6881:0.0	.	483;483	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	K	483	ENSP00000431083:E483K;ENSP00000367345:E483K	ENSP00000367345:E483K	E	+	1	0	PCDHGA1	140691882	0.000000	0.05858	0.121000	0.21740	0.494000	0.33585	0.184000	0.16939	0.905000	0.36596	0.557000	0.71058	GAG	.		0.537	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140711698	G	A	140711698	3	1	139	1	0	0	0	0	1	0	0	0	11576	1291	45	2	1449	2	PCDHGA1	5	140711698	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	38900271	140711698	40203562	41	12336											
CLINT1	9685	broad.mit.edu	37	chr5	157285975	157285975	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgcaccttccacatgttcaAcatcgtgccccgcgcgggac	7	7	10	17	5	1	0	1	0	0	0	3	1	2	1	4	1	2	2	4	1	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:157285975A>T	ENST00000411809.2	-	1	208	c.4T>A	c.(4-6)Ttg>Atg	p.L2M	CLINT1_ENST00000296951.5_De_novo_Start_InFrame|CLINT1_ENST00000523908.1_Missense_Mutation_p.L2M|CLINT1_ENST00000523094.1_De_novo_Start_OutOfFrame|CLINT1_ENST00000530742.1_Intron	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	2					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CACATGTTCAACATCGTGCCC	0.701																																					p.L2M	Colon(22;427 587 2170 6147 14291)												.	CLINT1-48	0			c.T4A						.						34	41	39					5																	157285975		2024	4177	6201	SO:0001583	missense	9685	exon1			TGTTCAACATCGT	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.4T>A	5.37:g.157285975A>T	ENSP00000388340:p.Leu2Met	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	87	3	NM_014666	0	0	25	27	2	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Missense_Mutation	SNP	ENST00000411809.2	37	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.694344	0.48202	.	.	ENSG00000113282	ENST00000411809;ENST00000523908	T;T	0.48836	0.8;0.8	5.11	3.95	0.45737	ENTH/VHS (1);	.	.	.	.	T	0.37237	0.0996	L	0.43152	1.355	0.80722	D	1	B;B	0.25105	0.118;0.118	B;B	0.25884	0.064;0.064	T	0.21245	-1.0251	9	0.54805	T	0.06	.	6.1994	0.20567	0.7953:0.0:0.2047:0.0	.	2;2	B7Z6F8;Q14677	.;EPN4_HUMAN	M	2	ENSP00000388340:L2M;ENSP00000429824:L2M	ENSP00000388340:L2M	L	-	1	2	CLINT1	157218553	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.819000	0.39022	0.789000	0.33779	0.533000	0.62120	TTG	.		0.701	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666		T	157285975	A	T	157285975	3	4	139	1	0	0	0	0	1	0	0	0	3537	40	2	5	1921	5	CLINT1	5	157285975	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	16574277	157285975	23629285	42	12337											
FLT4	2324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	180050943	180050943	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggcctgtaccttattctTtccctccacaaactcggtcc	6	13	6	16	1	1	0	0	0	1	0	5	0	4	0	5	2	2	2	5	2	3	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:180050943T>A	ENST00000261937.6	-	11	1618	c.1540A>T	c.(1540-1542)Aag>Tag	p.K514*	FLT4_ENST00000502649.1_Nonsense_Mutation_p.K514*|FLT4_ENST00000393347.3_Nonsense_Mutation_p.K514*|FLT4_ENST00000424276.2_5'UTR	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	514	Ig-like C2-type 5.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACCTTATTCTTTCCCTCCACA	0.602																																					p.K514X	Colon(97;1075 1466 27033 27547 35871)	.											.	FLT4-1490	0			c.A1540T						.						95	82	87					5																	180050943		2203	4300	6503	SO:0001587	stop_gained	2324	exon11			TATTCTTTCCCTC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.1540A>T	5.37:g.180050943T>A	ENSP00000261937:p.Lys514*	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	197	21	NM_182925	0	0	0	0	0	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Nonsense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	T	39	7.440611	0.98286	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.8621	0.46833	0.0:0.0:0.2833:0.7166	.	.	.	.	X	514;514;514;324	.	ENSP00000261937:K514X	K	-	1	0	FLT4	179983549	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	3.078000	0.50096	1.906000	0.55180	0.459000	0.35465	AAG	.		0.602	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180050943	T	A	180050943	4	1	139	1	0	0	0	0	0	1	0	0	5963	1850	64	5	2639	5	FLT4	5	180050943	Nonsense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	22764968	180050943	864317	43	12338											
HIST1H2AE	3012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	26217223	26217223	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtctggacgtggaaagcaAggcggcaaagctcgggcaaa	13	5	15	8	3	1	0	0	0	1	0	2	2	1	2	0	5	2	4	0	5	4	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:26217223A>T	ENST00000303910.2	+	1	59	c.21A>T	c.(19-21)caA>caT	p.Q7H	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	7						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	10		all_hematologic(11;0.196)				GTGGAAAGCAAGGCGGCAAAG	0.502																																					p.Q7H		.											.	HIST1H2AE-92	0			c.A21T						.						62	55	57					6																	26217223		2203	4300	6503	SO:0001583	missense	3012	exon1			AAAGCAAGGCGGC	M60752	CCDS4595.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000168274	ENSG00000277075		"Histones / Replication-dependent"	4724	protein-coding gene	gene with protein product		602786	"H2A histone family, member A", "histone 1, H2ae"	H2AFA		9119399, 1916825, 12408966	Standard	NM_021052		Approved	H2A/a, H2A.1	uc003nha.1	P04908	OTTHUMG00000014440	ENST00000303910.2:c.21A>T	6.37:g.26217223A>T	ENSP00000303373:p.Gln7His	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	131	68	NM_021052	0	0	3	4	1	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	37	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.551016	0.27739	.	.	ENSG00000168274	ENST00000303910	T	0.42900	0.96	4.08	-4.32	0.03688	.	0.000000	0.32640	U	0.005837	T	0.14830	0.0358	N	0.17474	0.49	0.34285	D	0.682566	.	.	.	.	.	.	T	0.14811	-1.0459	8	0.66056	D	0.02	.	10.9427	0.47283	0.6741:0.0:0.3259:0.0	.	.	.	.	H	7	ENSP00000303373:Q7H	ENSP00000303373:Q7H	Q	+	3	2	HIST1H2AE	26325202	0.014000	0.17966	0.774000	0.31636	0.857000	0.48899	-1.328000	0.02680	-1.206000	0.02641	0.533000	0.62120	CAA	.		0.502	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		T	26217223	A	T	26217223	3	4	139	1	0	0	0	0	1	0	0	0	7153	69	3	5	23	5	HIST1H2AE	6	26217223	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10		26217223	144897844	44	12339											
PKHD1	5314	broad.mit.edu;bcgsc.ca	37	chr6	51889790	51889790	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caggtctgctggtcaatataGactgacgtggtgttctgtcc	7	13	12	9	1	3	2	1	1	2	1	4	2	4	2	1	3	1	2	1	3	3	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:51889790G>A	ENST00000371117.3	-	32	5093	c.4818C>T	c.(4816-4818)gtC>gtT	p.V1606V	PKHD1_ENST00000340994.4_Silent_p.V1606V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1606	IPT/TIG 11.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGTCAATATAGACTGACGTGG	0.507																																					p.V1606V													.	PKHD1-603	0			c.C4818T						.						148	133	138					6																	51889790		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon32			AATATAGACTGAC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.4818C>T	6.37:g.51889790G>A		Somatic	209	0		WXS	Illumina HiSeq	Phase_I	209	9	NM_170724	0	0	0	0	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			.		0.507	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51889790	G	A	51889790	2	1	139	1	0	0	0	0	0	0	0	1	11997	929	33	2		2	PKHD1	6	51889790	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	25672567	51889790	119225277	45	12340											
KIAA1009	22832	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	84911470	84911470	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaccattagcaagcatgcCagttttttcttcttcctaaa	10	17	4	10	0	2	0	0	0	2	0	3	0	3	0	3	0	4	3	3	0	5	9			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:84911470C>T	ENST00000403245.3	-	8	817	c.703G>A	c.(703-705)Ggc>Agc	p.G235S	KIAA1009_ENST00000257766.4_Missense_Mutation_p.G159S	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		GCAAGCATGCCAGTTTTTTCT	0.264																																					p.G235S													.	KIAA1009-91	0			c.G703A						.						14	15	15					6																	84911470		2167	4247	6414	SO:0001583	missense	22832	exon8			GCATGCCAGTTTT																												ENST00000403245.3:c.703G>A	6.37:g.84911470C>T	ENSP00000385215:p.Gly235Ser	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	90	46	NM_014895	0	0	4	6	2		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	C	21.2	4.111524	0.77210	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.13538	2.58;2.58	5.26	4.38	0.52667	.	0.088446	0.49305	D	0.000147	T	0.20495	0.0493	M	0.78637	2.42	0.34708	D	0.72746	D;D	0.69078	0.994;0.997	P;P	0.60682	0.83;0.878	T	0.06180	-1.0841	10	0.40728	T	0.16	-2.3175	11.4271	0.50018	0.1804:0.8196:0.0:0.0	.	235;235	Q5TB80;C9JFM9	QN1_HUMAN;.	S	159;235	ENSP00000257766:G159S;ENSP00000385215:G235S	ENSP00000257766:G159S	G	-	1	0	KIAA1009	84968189	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	1.971000	0.40530	1.304000	0.44892	0.563000	0.77884	GGC	.		0.264	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			T	84911470	C	T	84911470	3	4	139	1	0	0	0	0	1	0	0	0	8224	594	21	2	3588	2	KIAA1009	6	84911470	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	33021680	84911470	86203597	46	12341											
PM20D2	135293	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	89859124	89859124	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttatctaccagatatggcTgaacatgagtgagtaatcaa	14	11	9	7	0	2	4	1	3	1	1	2	4	2	4	1	1	2	3	1	1	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:89859124T>A	ENST00000275072.4	+	2	701	c.606T>A	c.(604-606)gcT>gcA	p.A202A		NM_001010853.1	NP_001010853.1	Q8IYS1	P20D2_HUMAN	peptidase M20 domain containing 2	202						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|skin(1)	12		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		CAGATATGGCTGAACATGAGT	0.373																																					p.A202A		.											.	PM20D2-68	0			c.T606A						.						135	136	135					6																	89859124		2203	4300	6503	SO:0001819	synonymous_variant	135293	exon2			TATGGCTGAACAT	BC035036	CCDS34499.1	6q15	2014-07-14	2007-11-14	2007-11-14	ENSG00000146281	ENSG00000146281			21408	protein-coding gene	gene with protein product	"&#946;-alanyl-lysine dipeptidase"	615913	"aminoacylase 1-like 2"	ACY1L2		24891507	Standard	NM_001010853		Approved	bA63L7.3	uc003pmz.4	Q8IYS1	OTTHUMG00000015193	ENST00000275072.4:c.606T>A	6.37:g.89859124T>A		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	79	6	NM_001010853	0	0	0	0	0	B4DYJ2|Q5T7J9|Q6MZV2|Q86XD9	Silent	SNP	ENST00000275072.4	37	CCDS34499.1																																																																																			.		0.373	PM20D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041477.1	NM_001010853		A	89859124	T	A	89859124	2	1	139	1	0	0	0	0	0	0	0	1	12155	1567	55	5		5	PM20D2	6	89859124	Silent	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	4947654	89859124	81255943	47	12342											
HDDC2	51020	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	125619919	125619919	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctggtgctatgtccccaaCgatgcattctgccatatcat	8	13	8	12	1	2	0	1	0	1	0	3	1	3	0	3	1	5	3	3	1	3	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:125619919C>T	ENST00000398153.2	-	3	292	c.250G>A	c.(250-252)Gtt>Att	p.V84I	HDDC2_ENST00000368377.4_Intron|HDDC2_ENST00000608295.1_Missense_Mutation_p.V84I|HDDC2_ENST00000608284.1_Missense_Mutation_p.V84I	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	84	HD.					extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(4)	6			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		ATGTCCCCAACGATGCATTCT	0.413																																					p.V84I		.											.	HDDC2-90	0			c.G250A						.						190	168	175					6																	125619919		1925	4164	6089	SO:0001583	missense	51020	exon3			CCCCAACGATGCA	AF151888	CCDS43503.1	6q13-q24.3	2008-02-05	2005-08-22	2005-08-22	ENSG00000111906	ENSG00000111906			21078	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 74"	C6orf74		10810093	Standard	NM_016063		Approved	CGI-130, dJ167O5.2	uc003qaa.1	Q7Z4H3	OTTHUMG00000015506	ENST00000398153.2:c.250G>A	6.37:g.125619919C>T	ENSP00000381220:p.Val84Ile	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	185	85	NM_016063	0	0	44	51	7	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Missense_Mutation	SNP	ENST00000398153.2	37	CCDS43503.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039411	0.93630	.	.	ENSG00000111906	ENST00000398153	T	0.43688	0.94	5.62	4.76	0.60689	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.000000	0.64402	U	0.000001	T	0.35770	0.0943	L	0.48877	1.53	0.80722	D	1	D	0.60575	0.988	P	0.51895	0.683	T	0.28004	-1.0057	10	0.59425	D	0.04	.	13.6517	0.62314	0.0:0.9242:0.0:0.0758	.	84	Q7Z4H3	HDDC2_HUMAN	I	84	ENSP00000381220:V84I	ENSP00000381220:V84I	V	-	1	0	HDDC2	125661618	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.426000	0.80270	1.527000	0.49086	0.655000	0.94253	GTT	.		0.413	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063		T	125619919	C	T	125619919	3	4	139	1	0	0	0	0	1	0	0	0	7037	536	19	1	380	1	HDDC2	6	125619919	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	35760795	125619919	45495148	48	12343											
SNX10	29887	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	26404687	26404687	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acaactgccagaacttccatCtaaaaacctgtttttcaaca	15	11	3	12	0	2	1	1	0	1	1	3	1	3	1	3	0	5	1	3	0	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:26404687C>G	ENST00000338523.4	+	5	420	c.233C>G	c.(232-234)tCt>tGt	p.S78C	SNX10_ENST00000396376.1_Missense_Mutation_p.S78C|SNX10_ENST00000446848.2_Missense_Mutation_p.S104C|SNX10_ENST00000409367.1_Missense_Mutation_p.S38C|SNX10_ENST00000409838.1_5'UTR	NM_001199835.1|NM_013322.2	NP_001186764.1|NP_037454.2	Q9Y5X0	SNX10_HUMAN	sorting nexin 10	78	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.|Required for the interaction with ATP6V1D.				cilium assembly (GO:0042384)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|osteoclast differentiation (GO:0030316)|protein localization to centrosome (GO:0071539)|protein localization to cilium (GO:0061512)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extrinsic component of endosome membrane (GO:0031313)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|ATPase binding (GO:0051117)			endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	6						GAACTTCCATCTAAAAACCTG	0.408											OREG0017908	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S78C		.											.	SNX10-226	0			c.C233G						.						58	61	60					7																	26404687		2203	4300	6503	SO:0001583	missense	29887	exon5			TTCCATCTAAAAA	AF121860	CCDS5399.1, CCDS56470.1	7p15.2	2008-05-22			ENSG00000086300	ENSG00000086300		"Sorting nexins"	14974	protein-coding gene	gene with protein product		614780				17012226	Standard	NM_013322		Approved		uc010kuu.3	Q9Y5X0	OTTHUMG00000023650	ENST00000338523.4:c.233C>G	7.37:g.26404687C>G	ENSP00000343709:p.Ser78Cys	Somatic	81	0	786	WXS	Illumina HiSeq	Phase_I	109	6	NM_001199835	0	0	33	34	1	E9PFH5|Q8IYT5	Missense_Mutation	SNP	ENST00000338523.4	37	CCDS5399.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333040	0.81801	.	.	ENSG00000086300	ENST00000416246;ENST00000338523;ENST00000446848;ENST00000396376;ENST00000409367	T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18	6.17	6.17	0.99709	Phox homologous domain (5);	0.052852	0.85682	D	0.000000	T	0.61540	0.2355	M	0.68952	2.095	0.47659	D	0.999481	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.917	T	0.57711	-0.7764	10	0.56958	D	0.05	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	104;78	B4DJM0;Q9Y5X0	.;SNX10_HUMAN	C	104;78;104;78;38	ENSP00000408164:S104C;ENSP00000343709:S78C;ENSP00000395474:S104C;ENSP00000379661:S78C;ENSP00000387274:S38C	ENSP00000343709:S78C	S	+	2	0	SNX10	26371212	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.525000	0.73795	2.941000	0.99782	0.655000	0.94253	TCT	.		0.408	SNX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214120.1			G	26404687	C	G	26404687	3	3	139	1	0	0	0	0	1	0	0	0	14913	913	32	4	247	4	SNX10	7	26404687	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		26404687	132733976	49	12344											
CCDC129	223075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	31609394	31609394	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctttgtatgaacaagggatGgttcaaatgactgtgaaaga	14	12	11	4	0	2	4	1	3	1	1	2	5	2	5	0	2	1	2	0	2	5	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:31609394G>T	ENST00000407970.3	+	5	317	c.279G>T	c.(277-279)atG>atT	p.M93I	CCDC129_ENST00000319386.3_Missense_Mutation_p.M93I|CCDC129_ENST00000451887.2_Missense_Mutation_p.M119I|CCDC129_ENST00000482748.1_3'UTR|CCDC129_ENST00000409210.1_Start_Codon_SNP_p.M1I	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	93										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AACAAGGGATGGTTCAAATGA	0.373																																					p.M119I		.											.	.	0			c.G357T						.						119	101	107					7																	31609394		2203	4300	6503	SO:0001583	missense	223075	exon5			AGGGATGGTTCAA	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.279G>T	7.37:g.31609394G>T	ENSP00000384416:p.Met93Ile	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	147	24	NM_001257968	0	0	0	0	0	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116871	0.37339	.	.	ENSG00000180347	ENST00000409717;ENST00000456011;ENST00000319386;ENST00000407970;ENST00000454513;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T;T;T;T	0.39997	1.05;1.07;2.39;2.66;1.06;2.63;2.3	5.49	0.437	0.16555	.	0.576671	0.16859	N	0.196589	T	0.20373	0.0490	N	0.21448	0.665	0.20563	N	0.999888	B;B;B;B	0.20887	0.049;0.049;0.049;0.049	B;B;B;B	0.17433	0.008;0.018;0.018;0.018	T	0.18777	-1.0326	10	0.12766	T	0.61	-0.3883	3.0709	0.06230	0.1436:0.2578:0.4642:0.1344	.	119;103;93;93	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	I	93;93;93;93;93;119;103;1	ENSP00000387220:M93I;ENSP00000390544:M93I;ENSP00000313062:M93I;ENSP00000384416:M93I;ENSP00000413233:M93I;ENSP00000395835:M119I;ENSP00000387214:M1I	ENSP00000313062:M93I	M	+	3	0	CCDC129	31575919	0.999000	0.42202	0.971000	0.41717	0.937000	0.57800	0.316000	0.19469	-0.088000	0.12506	0.655000	0.94253	ATG	.		0.373	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31609394	G	T	31609394	3	4	139	1	0	0	0	0	1	0	0	0	2770	1348	47	4	293	4	CCDC129	7	31609394	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	5204707	31609394	127529269	50	12345											
CFTR	1080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	117267708	117267708	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaattcacacgtgaagaaaGatgacatctggccctcaggg	14	7	11	9	1	3	5	2	2	1	3	3	5	3	5	1	2	0	0	1	2	3	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:117267708G>T	ENST00000003084.6	+	22	3733	c.3601G>T	c.(3601-3603)Gat>Tat	p.D1201Y	AC000111.6_ENST00000456270.1_RNA|CFTR_ENST00000454343.1_Missense_Mutation_p.D1140Y	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1201					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	CGTGAAGAAAGATGACATCTG	0.413									Cystic Fibrosis																												p.D1201Y		.											.	CFTR-518	0			c.G3601T						.						86	78	81					7																	117267708		2203	4300	6503	SO:0001583	missense	1080	exon22	Familial Cancer Database	CF	AAGAAAGATGACA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators", "ATP binding cassette transporters / subfamily C"	1884	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family C, member 7"	602421	"cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.3601G>T	7.37:g.117267708G>T	ENSP00000003084:p.Asp1201Tyr	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	103	24	NM_000492	0	0	0	0	0	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.99|13.99	2.402264|2.402264	0.42613|0.42613	.|.	.|.	ENSG00000001626|ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809|ENST00000468795	D;D;D|D	0.93366|0.93366	-3.15;-2.96;-3.21|-3.21	5.86|5.86	2.07|2.07	0.26955|0.26955	.|.	0.549977|.	0.20348|.	N|.	0.094112|.	D|D	0.91140|0.91140	0.7210|0.7210	L|L	0.45581|0.45581	1.43|1.43	0.34472|0.34472	D|D	0.702874|0.702874	P|.	0.47409|.	0.895|.	B|.	0.43536|.	0.423|.	D|D	0.89511|0.89511	0.3771|0.3771	10|7	0.72032|0.66056	D|D	0.01|0.02	-3.7623|-3.7623	5.6055|5.6055	0.17377|0.17377	0.261:0.0:0.6124:0.1266|0.261:0.0:0.6124:0.1266	.|.	1201|.	P13569|.	CFTR_HUMAN|.	Y|N	1201;1140;1171|142	ENSP00000003084:D1201Y;ENSP00000403677:D1140Y;ENSP00000389119:D1171Y|ENSP00000419254:K142N	ENSP00000003084:D1201Y|ENSP00000419254:K142N	D|K	+|+	1|3	0|2	CFTR|CFTR	117054944|117054944	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.591000|0.591000	0.36615|0.36615	2.668000|2.668000	0.46816|0.46816	0.177000|0.177000	0.19895|0.19895	-0.142000|-0.142000	0.14014|0.14014	GAT|AAG	.		0.413	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117267708	G	T	117267708	3	4	139	1	0	0	0	0	1	0	0	0	3300	942	33	4	3687	4	CFTR	7	117267708	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	85658314	117267708	41870955	51	12346											
RNF133	168433	broad.mit.edu	37	chr7	122338189	122338189	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatgtcattaggcttatagcGttcaaagcaaattacgcagc	13	12	8	8	2	2	0	2	0	0	0	2	0	2	0	0	1	4	4	0	1	7	6	rs137950690		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:122338189G>A	ENST00000340112.2	-	1	1021	c.784C>T	c.(784-786)Cgc>Tgc	p.R262C	CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000449022.2_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	262					protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						GGCTTATAGCGTTCAAAGCAA	0.403																																					p.R262C	Colon(198;1778 2057 7449 19869 45985)												.	RNF133-227	0			c.C784T						.	G	,,,CYS/ARG	0,4406		0,0,2203	159	148	152		,,,784	2.6	0.3	7	dbSNP_134	152	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,intron,missense	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,benign	,,,262/377	122338189	2,13004	2203	4300	6503	SO:0001583	missense	168433	exon1			TATAGCGTTCAAA	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"RING-type (C3HC4) zinc fingers"	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.784C>T	7.37:g.122338189G>A	ENSP00000344489:p.Arg262Cys	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	191	7	NM_139175	0	0	0	0	0	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	.	.	.	.	.	.	.	.	.	.	G	0.871	-0.731875	0.03135	0.0	2.33E-4	ENSG00000188050	ENST00000340112	T	0.43294	0.95	5.53	2.62	0.31277	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.713262	0.12945	U	0.426283	T	0.26011	0.0634	N	0.21282	0.65	0.09310	N	0.999999	B	0.23891	0.093	B	0.20767	0.031	T	0.20306	-1.0279	10	0.62326	D	0.03	.	4.5179	0.11945	0.091:0.4253:0.36:0.1236	.	262	Q8WVZ7	RN133_HUMAN	C	262	ENSP00000344489:R262C	ENSP00000344489:R262C	R	-	1	0	RNF133	122125425	0.051000	0.20477	0.293000	0.24932	0.004000	0.04260	0.822000	0.27352	0.672000	0.31204	-0.424000	0.05967	CGC	G|1.000;A|0.000		0.403	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		A	122338189	G	A	122338189	3	1	139	1	0	0	0	0	1	0	0	0	13471	1145	40	1	350	1	RNF133	7	122338189	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	5070481	122338189	36800474	52	12347											
CCNE2	9134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	95906316	95906316	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggggattccgtctggctggGctggggctgctgcttagctt	2	12	18	9	1	1	0	0	0	1	0	2	1	2	1	1	6	3	6	1	6	1	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr8:95906316G>A	ENST00000520509.1	-	3	298	c.46C>T	c.(46-48)Ccc>Tcc	p.P16S	NDUFAF6_ENST00000396113.1_5'Flank|CCNE2_ENST00000523476.1_5'Flank|CCNE2_ENST00000308108.4_Missense_Mutation_p.P16S|CCNE2_ENST00000396133.3_Missense_Mutation_p.P16S			O96020	CCNE2_HUMAN	cyclin E2	16					cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					GTCTGGCTGGGCTGGGGCTGC	0.443																																					p.P16S		.											.	CCNE2-414	0			c.C46T						.						141	161	154					8																	95906316		2203	4300	6503	SO:0001583	missense	9134	exon3			GGCTGGGCTGGGG	AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305			1590	protein-coding gene	gene with protein product		603775				9840927, 9840943	Standard	NM_057749		Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.46C>T	8.37:g.95906316G>A	ENSP00000429089:p.Pro16Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	89	19	NM_057749	0	0	2	2	0	O95439	Missense_Mutation	SNP	ENST00000520509.1	37	CCDS6264.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.072843	0.36566	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000396133	T;T;T	0.30981	1.94;1.94;1.51	5.29	2.11	0.27256	.	0.268590	0.33980	N	0.004370	T	0.24470	0.0593	L	0.50333	1.59	0.30643	N	0.7563	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.24977	-1.0145	10	0.13853	T	0.58	.	11.6218	0.51121	0.0:0.1897:0.6789:0.1315	.	16;16	Q8WUE3;O96020	.;CCNE2_HUMAN	S	16	ENSP00000429089:P16S;ENSP00000309181:P16S;ENSP00000379437:P16S	ENSP00000309181:P16S	P	-	1	0	CCNE2	95975492	0.949000	0.32298	1.000000	0.80357	0.956000	0.61745	0.420000	0.21263	0.601000	0.29879	0.561000	0.74099	CCC	.		0.443	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379808.1	NM_057749, NM_004702		A	95906316	G	A	95906316	3	1	139	1	0	0	0	0	1	0	0	0	2927	1203	42	2	1208	2	CCNE2	8	95906316	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		95906316	50457706	53	12348											
DPYS	1807	broad.mit.edu	37	chr8	105478888	105478888	+	Frame_Shift_Del	DEL	G	G	-																															cgcggcggggcgggtaccttGgtgccctggtggaagtcgtc																										TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr8:105478888delG	ENST00000351513.2	-	1	393	c.261delC	c.(259-261)accfs	p.T87fs		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	87					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			cgggTACCTTGGTGCCCTGGT	0.736																																					p.T87fs													.	DPYS-229	0			c.261delC						.						16	9	11					8																	105478888		1505	2849	4354	SO:0001589	frameshift_variant	1807	exon1			TACCTTGGTGCCC	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.261delC	8.37:g.105478888delG	ENSP00000276651:p.Thr87fs	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001385	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000351513.2	37	CCDS6302.1																																																																																			.		0.736	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		-	105478888	G	-	105478888	7	5	139	1	0	1	0	1	0	0	0	0	4757	1335	47	0	1334	0	DPYS	8	105478888	Frame_Shift_Del	DEL	G	TCGA-IA-A40Y-01A-11D-A25F-10	9572572	105478888	40885134	54	12349											
PARP10	84875	broad.mit.edu;bcgsc.ca	37	chr8	145059064	145059064	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcccctcctgttcctgcaacCccacaggcctcaggcttacc	6	8	7	20	0	1	0	1	0	0	0	3	0	3	0	8	2	3	3	8	2	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr8:145059064C>G	ENST00000313028.7	-	5	1200	c.1106G>C	c.(1105-1107)gGg>gCg	p.G369A	PARP10_ENST00000533665.1_5'Flank|PARP10_ENST00000525773.1_Missense_Mutation_p.G381A|PARP10_ENST00000524918.1_Missense_Mutation_p.G369A	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	369					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTCCTGCAACCCCACAGGCCT	0.647																																					p.G369A													.	PARP10-526	0			c.G1106C						.						73	81	78					8																	145059064		2203	4300	6503	SO:0001583	missense	84875	exon5			TGCAACCCCACAG	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"Poly (ADP-ribose) polymerases"	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.1106G>C	8.37:g.145059064C>G	ENSP00000325618:p.Gly369Ala	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	102	20	NM_032789	0	0	29	39	10	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627392	0.28978	.	.	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773;ENST00000313059	T;T;T;T	0.75938	2.51;2.48;2.47;-0.98	3.68	-1.16	0.09678	.	1.065050	0.07452	U	0.899186	T	0.57301	0.2044	L	0.39898	1.24	0.09310	N	1	P;P;P	0.52842	0.884;0.956;0.884	B;B;B	0.38985	0.14;0.287;0.14	T	0.48514	-0.9029	10	0.08837	T	0.75	.	7.4919	0.27466	0.0:0.4833:0.0:0.5167	.	381;369;369	E9PNI7;E9PK67;Q53GL7	.;.;PAR10_HUMAN	A	369;75;369;381;284	ENSP00000431620:G369A;ENSP00000325618:G369A;ENSP00000434776:G381A;ENSP00000314320:G284A	ENSP00000325618:G369A	G	-	2	0	PARP10	145131052	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.791000	0.04599	-0.164000	0.10927	-0.269000	0.10298	GGG	.		0.647	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789		G	145059064	C	G	145059064	3	3	139	1	0	0	0	0	1	0	0	0	11481	623	22	4	1999	4	PARP10	8	145059064	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	39580176	145059064	1304958	55	12350											
IFT74	80173	hgsc.bcm.edu;bcgsc.ca	37	chr9	26962063	26962075	+	Frame_Shift_Del	DEL	GAAATATTCGAGT	GAAATATTCGAGT	-																															tgggatacgacccctatcagGaaatattcgagtggcaactg																								rs200556379|rs542289534		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	GAAATATTCGAGT	GAAATATTCGAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:26962063_26962075delGAAATATTCGAGT	ENST00000443698.1	+	2	269_281	c.98_110delGAAATATTCGAGT	c.(97-111)ggaaatattcgagtgfs	p.GNIRV33fs	IFT74_ENST00000380062.5_Frame_Shift_Del_p.GNIRV33fs|IFT74_ENST00000433700.1_Frame_Shift_Del_p.GNIRV33fs|IFT74_ENST00000429045.2_Frame_Shift_Del_p.GNIRV33fs	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	33	Basic region.				cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		CCCCTATCAGGAAATATTCGAGTGGCAACTGCA	0.493																																					p.33_37del		.											.	IFT74-515	0			c.98_110del						.																																			SO:0001589	frameshift_variant	80173	exon2			.	AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872		"Intraflagellar transport homologs"	21424	protein-coding gene	gene with protein product	"capillary morphogenesis protein 1"	608040	"coiled-coil domain containing 2", "intraflagellar transport 74 homolog (Chlamydomonas)"	CCDC2		11683410	Standard	NM_001099223		Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.98_110delGAAATATTCGAGT	9.37:g.26962063_26962075delGAAATATTCGAGT	ENSP00000404122:p.Gly33fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	27	10	NM_001099222	0	0	0	0	0	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Frame_Shift_Del	DEL	ENST00000443698.1	37	CCDS43793.1																																																																																			.		0.493	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103		-	26962075	GAAATATTCGAGT	-	26962063	7	5	139	1	0	1	0	1	0	0	0	0	7584	1174	41	0	100	0	IFT74	9	26962063	Frame_Shift_Del	DEL	GAAATATTCGAGT	TCGA-IA-A40Y-01A-11D-A25F-10		26962063	114251368	56	12351											
ALAD	210	broad.mit.edu;bcgsc.ca	37	chr9	116153879	116153879	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaccaagggcctcagcatCtcttccagccgcttcacacc	8	8	6	19	1	3	0	2	0	1	0	6	0	5	0	6	1	2	2	6	1	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:116153879C>T	ENST00000409155.3	-	4	385	c.189G>A	c.(187-189)gaG>gaA	p.E63E	ALAD_ENST00000482001.1_5'UTR|ALAD_ENST00000277315.5_Silent_p.E46E	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	63					cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	GCCTCAGCATCTCTTCCAGCC	0.577																																					p.E63E													.	ALAD-90	0			c.G189A						.						82	75	77					9																	116153879		2203	4300	6503	SO:0001819	synonymous_variant	210	exon4			CAGCATCTCTTCC	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"porphobilinogen synthase"	125270	"aminolevulinate, delta-, dehydratase"			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.189G>A	9.37:g.116153879C>T		Somatic	189	0		WXS	Illumina HiSeq	Phase_I	116	5	NM_000031	0	0	4	4	0	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Silent	SNP	ENST00000409155.3	37	CCDS6794.2																																																																																			.		0.577	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		T	116153879	C	T	116153879	2	4	139	1	0	0	0	0	0	0	0	1	483	912	32	2		2	ALAD	9	116153879	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	89191816	116153879	25059552	57	12352											
PHF19	26147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	123620475	123620475	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cactgctgtccgaggggcagCgtccatccagctcagctgcc	6	7	12	16	2	1	0	1	0	0	0	4	1	4	0	4	2	5	4	4	2	0	0	rs144405933		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:123620475C>T	ENST00000373896.3	-	15	1742	c.1490G>A	c.(1489-1491)cGc>cAc	p.R497H	PHF19_ENST00000419155.1_Missense_Mutation_p.R288H|PHF19_ENST00000487555.1_5'UTR	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	497					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CGAGGGGCAGCGTCCATCCAG	0.597																																					p.R497H		.											.	PHF19-136	0			c.G1490A						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	79	71	74		1490	3	0.6	9	dbSNP_134	74	0,8600		0,0,4300	no	missense	PHF19	NM_015651.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	497/581	123620475	1,13005	2203	4300	6503	SO:0001583	missense	26147	exon15			GGGCAGCGTCCAT	BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"Tudor domain containing", "Zinc fingers, PHD-type"	24566	protein-coding gene	gene with protein product	"polycomb-like 3", "tudor domain containing 19B"	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.1490G>A	9.37:g.123620475C>T	ENSP00000363003:p.Arg497His	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	45	21	NM_015651	0	0	1	5	4	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Missense_Mutation	SNP	ENST00000373896.3	37	CCDS35116.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059942	0.76074	2.27E-4	0.0	ENSG00000119403	ENST00000544082;ENST00000373896;ENST00000419155	T;T	0.49432	1.79;0.78	4.97	3.03	0.35002	.	0.659654	0.15009	N	0.285669	T	0.39627	0.1085	N	0.24115	0.695	0.36632	D	0.876372	D	0.67145	0.996	P	0.49502	0.613	T	0.36841	-0.9731	10	0.45353	T	0.12	-8.0699	9.2722	0.37679	0.0:0.8127:0.0:0.1873	.	497	Q5T6S3	PHF19_HUMAN	H	497;497;288	ENSP00000363003:R497H;ENSP00000407433:R288H	ENSP00000363003:R497H	R	-	2	0	PHF19	122660296	0.728000	0.28080	0.574000	0.28523	0.897000	0.52465	0.193000	0.17116	0.449000	0.26747	-0.367000	0.07326	CGC	C|1.000;T|0.000		0.597	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308		T	123620475	C	T	123620475	3	4	139	1	0	0	0	0	1	0	0	0	11855	768	27	1	256	1	PHF19	9	123620475	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	7466596	123620475	17592956	58	12353											
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16955917	16955917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gattctccactcgcagatccGgccatgaggatttgggttcg	7	11	12	11	3	1	2	0	1	1	1	5	4	2	3	3	3	0	2	3	3	0	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:16955917G>A	ENST00000377833.4	-	48	7491	c.7426C>T	c.(7426-7428)Cgg>Tgg	p.R2476W		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2476	CUB 18. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCGCAGATCCGGCCATGAGGA	0.532																																					p.R2476W		.											.	CUBN-166	0			c.C7426T						.						113	107	109					10																	16955917		2203	4300	6503	SO:0001583	missense	8029	exon48			AGATCCGGCCATG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.7426C>T	10.37:g.16955917G>A	ENSP00000367064:p.Arg2476Trp	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	42	14	NM_001081	0	0	0	1	1	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165155	0.38217	.	.	ENSG00000107611	ENST00000377833	T	0.28895	1.59	5.42	2.44	0.29823	CUB (5);	0.173875	0.27686	N	0.018262	T	0.32585	0.0834	M	0.76838	2.35	0.80722	D	1	B	0.20988	0.05	B	0.18561	0.022	T	0.11060	-1.0603	10	0.59425	D	0.04	.	8.2013	0.31426	0.0727:0.0:0.5311:0.3961	.	2476	O60494	CUBN_HUMAN	W	2476	ENSP00000367064:R2476W	ENSP00000367064:R2476W	R	-	1	2	CUBN	16995923	1.000000	0.71417	0.175000	0.22980	0.703000	0.40648	1.663000	0.37429	0.219000	0.20840	0.591000	0.81541	CGG	.		0.532	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16955917	G	A	16955917	3	1	139	1	0	0	0	0	1	0	0	0	4057	1115	39	1	3525	1	CUBN	10	16955917	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		16955917	118578830	59	12354											
BMI1	648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	22618246	22618246	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggagaactggaaagtgaCtctgggagtgacaaggccaa	13	6	15	7	0	1	3	0	2	1	1	1	6	1	5	1	4	1	1	1	4	4	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:22618246C>G	ENST00000376663.3	+	10	1261	c.756C>G	c.(754-756)gaC>gaG	p.D252E	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.D395E	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	252	Pro/Ser-rich.				chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						TGGAAAGTGACTCTGGGAGTG	0.493																																					p.D395E		.											.	.	0			c.C1185G						.						92	86	88					10																	22618246		2203	4300	6503	SO:0001583	missense	0	exon14			AAGTGACTCTGGG	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	1066	protein-coding gene	gene with protein product		164831	"polycomb group ring finger 4", "B lymphoma Mo-MLV insertion region 1 homolog (mouse)"	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.756C>G	10.37:g.22618246C>G	ENSP00000365851:p.Asp252Glu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	65	22	NM_001204062	0	0	38	51	13	Q16030|Q5T8Z3|Q96F37	Missense_Mutation	SNP	ENST00000376663.3	37	CCDS7138.1	.	.	.	.	.	.	.	.	.	.	C	2.210	-0.380859	0.05000	.	.	ENSG00000168283	ENST00000376691;ENST00000376663;ENST00000443519	T;T	0.46063	1.61;0.88	5.58	5.58	0.84498	.	0.045306	0.85682	D	0.000000	T	0.28532	0.0706	N	0.20328	0.56	0.49483	D	0.99979	B;B	0.26547	0.152;0.091	B;B	0.23275	0.03;0.045	T	0.11542	-1.0583	10	0.06891	T	0.86	-6.5673	19.1861	0.93644	0.0:1.0:0.0:0.0	.	252;252	Q5U0M5;P35226	.;BMI1_HUMAN	E	164;252;157	ENSP00000365851:D252E;ENSP00000390768:D157E	ENSP00000365851:D252E	D	+	3	2	BMI1	22658252	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.602000	0.61098	2.638000	0.89438	0.650000	0.86243	GAC	.		0.493	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180		G	22618246	C	G	22618246	3	3	139	1	0	0	0	0	1	0	0	0	1456	564	20	4	790	4	BMI1	10	22618246	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	5662329	22618246	112916501	60	12355											
ABCC2	1244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101578919	101578919	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtagttctggggaatggaaCaattgtagagaaaggatcct	13	11	13	4	0	1	1	0	0	1	1	2	5	2	4	1	4	1	3	1	4	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:101578919C>A	ENST00000370449.4	+	19	2626	c.2513C>A	c.(2512-2514)aCa>aAa	p.T838K		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	838	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	GGGAATGGAACAATTGTAGAG	0.403																																					p.T838K		.											.	ABCC2-91	0			c.C2513A						.						111	111	111					10																	101578919		2203	4300	6503	SO:0001583	missense	1244	exon19			ATGGAACAATTGT	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"ATP binding cassette transporters / subfamily C"	53	protein-coding gene	gene with protein product		601107	"canalicular multispecific organic anion transporter 1"	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.2513C>A	10.37:g.101578919C>A	ENSP00000359478:p.Thr838Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	105	21	NM_000392	0	0	0	0	0	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.655317	0.00779	.	.	ENSG00000023839	ENST00000370449	T	0.75050	-0.9	5.6	2.69	0.31865	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.560580	0.20863	N	0.084313	T	0.43033	0.1229	N	0.04355	-0.22	0.09310	N	0.999999	B	0.11235	0.004	B	0.10450	0.005	T	0.25847	-1.0120	10	0.07813	T	0.8	-14.5155	3.6997	0.08378	0.1227:0.5036:0.2384:0.1353	.	838	Q92887	MRP2_HUMAN	K	838	ENSP00000359478:T838K	ENSP00000359478:T838K	T	+	2	0	ABCC2	101568909	0.000000	0.05858	0.950000	0.38849	0.198000	0.23893	-0.155000	0.10115	0.699000	0.31761	0.561000	0.74099	ACA	.		0.403	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101578919	C	A	101578919	3	1	139	1	0	0	0	0	1	0	0	0	53	478	17	4	2587	4	ABCC2	10	101578919	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	78960673	101578919	33955828	61	12356											
TRIM8	81603	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104404529	104404529	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagcggcctcgtacgctGcccagagtgcaaccaggcct	8	5	13	15	3	0	1	0	0	0	1	1	2	0	2	4	3	5	3	4	3	2	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:104404529G>C	ENST00000302424.7	+	1	277	c.155G>C	c.(154-156)tGc>tCc	p.C52S	RP11-47A8.5_ENST00000607967.1_lincRNA	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	52					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTCGTACGCTGCCCAGAGTGC	0.612																																					p.C52S													.	TRIM8-227	0			c.G155C						.						33	37	35					10																	104404529		2202	4300	6502	SO:0001583	missense	81603	exon1			TACGCTGCCCAGA	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.155G>C	10.37:g.104404529G>C	ENSP00000302120:p.Cys52Ser	Somatic	162	2		WXS	Illumina HiSeq	Phase_I	122	15	NM_030912	0	0	58	61	3	A6NI31|Q9C028	Missense_Mutation	SNP	ENST00000302424.7	37	CCDS31274.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154435	0.78114	.	.	ENSG00000171206	ENST00000302424;ENST00000369896	T	0.54479	0.57	3.53	3.53	0.40419	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.84714	0.5533	H	0.99619	4.66	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92169	0.5742	10	0.87932	D	0	.	16.3843	0.83500	0.0:0.0:1.0:0.0	.	52	Q9BZR9	TRIM8_HUMAN	S	52	ENSP00000302120:C52S	ENSP00000302120:C52S	C	+	2	0	TRIM8	104394519	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.361000	0.97122	2.277000	0.76020	0.561000	0.74099	TGC	.		0.612	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		C	104404529	G	C	104404529	3	2	139	1	0	0	0	0	1	0	0	0	16581	1319	46	4	157	4	TRIM8	10	104404529	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	2825610	104404529	31130218	62	12357											
OR6A2	8590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6816105	6816105	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gacagcatacagtacagagaCcaacttgttggtgtcaaaag	15	8	10	8	0	1	1	1	0	0	1	1	3	1	1	1	1	4	3	1	1	5	4	rs369095527		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:6816105C>A	ENST00000332601.3	-	1	1023	c.835G>T	c.(835-837)Gtc>Ttc	p.V279F		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	279					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGTACAGAGACCAACTTGTTG	0.468																																					p.V279F		.											.	OR6A2-94	0			c.G835T						.	C	PHE/VAL	0,4402		0,0,2201	139	130	133		835	4.1	0.9	11		133	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR6A2	NM_003696.2	50	0,1,6496	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	279/328	6816105	1,12993	2201	4296	6497	SO:0001583	missense	8590	exon1			CAGAGACCAACTT	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"GPCR / Class A : Olfactory receptors"	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.835G>T	11.37:g.6816105C>A	ENSP00000330384:p.Val279Phe	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	152	18	NM_003696	0	0	0	0	0	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	37	CCDS7772.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.845132	0.32606	0.0	1.16E-4	ENSG00000184933	ENST00000332601	T	0.38722	1.12	5.04	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000122	T	0.51719	0.1691	L	0.42632	1.34	0.33539	D	0.594625	D	0.89917	1.0	D	0.97110	1.0	T	0.63959	-0.6519	10	0.87932	D	0	.	7.3142	0.26491	0.0:0.7407:0.1697:0.0896	.	279	O95222	OR6A2_HUMAN	F	279	ENSP00000330384:V279F	ENSP00000330384:V279F	V	-	1	0	OR6A2	6772681	0.000000	0.05858	0.883000	0.34634	0.059000	0.15707	-0.095000	0.11077	1.508000	0.48769	0.655000	0.94253	GTC	.		0.468	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		A	6816105	C	A	6816105	3	1	139	1	0	0	0	0	1	0	0	0	11212	507	18	4	152	4	OR6A2	11	6816105	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		6816105	128190411	63	12358											
IGSF22	283284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	18738381	18738381	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagcgtgtgcgtcagaccAtcttcggacaccgtgatttc	8	12	10	11	4	2	2	1	1	1	1	4	3	2	3	2	1	2	0	2	1	1	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:18738381A>G	ENST00000513874.1	-	10	1279	c.1140T>C	c.(1138-1140)gaT>gaC	p.D380D	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	380										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						GCGTCAGACCATCTTCGGACA	0.522																																					p.D380D		.											.	IGSF22-140	0			c.T1140C						.						242	237	238					11																	18738381		2077	4197	6274	SO:0001819	synonymous_variant	283284	exon10			CAGACCATCTTCG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1140T>C	11.37:g.18738381A>G		Somatic	443	0		WXS	Illumina HiSeq	Phase_I	370	109	NM_173588	0	0	0	0	0	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																			.		0.522	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		G	18738381	A	G	18738381	2	3	139	1	0	0	0	0	0	0	0	1	7621	214	8	3		3	IGSF22	11	18738381	Silent	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	11922276	18738381	116268135	64	12359											
OR4S1	256148	broad.mit.edu;bcgsc.ca	37	chr11	48328626	48328626	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cctttgctgaaccctttgatCtatacactaaggaacaacga	13	11	6	11	1	1	2	0	2	1	0	1	4	1	3	2	1	5	1	2	1	6	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:48328626C>G	ENST00000319988.1	+	1	852	c.852C>G	c.(850-852)atC>atG	p.I284M		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						ACCCTTTGATCTATACACTAA	0.458																																					p.I284M													.	OR4S1-69	0			c.C852G						.						116	103	108					11																	48328626		2201	4298	6499	SO:0001583	missense	256148	exon1			TTTGATCTATACA	AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"GPCR / Class A : Olfactory receptors"	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.852C>G	11.37:g.48328626C>G	ENSP00000321447:p.Ile284Met	Somatic	254	0		WXS	Illumina HiSeq	Phase_I	170	8	NM_001004725	0	0	0	0	0	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.826742	0.32329	.	.	ENSG00000176555	ENST00000319988	T	0.57273	0.41	5.02	-0.74	0.11115	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.72415	0.3457	M	0.91612	3.225	0.29229	N	0.87339	D	0.89917	1.0	D	0.91635	0.999	T	0.63633	-0.6593	9	0.87932	D	0	.	5.8325	0.18588	0.1251:0.5577:0.0:0.3173	.	284	Q8NGB4	OR4S1_HUMAN	M	284	ENSP00000321447:I284M	ENSP00000321447:I284M	I	+	3	3	OR4S1	48285202	0.001000	0.12720	0.255000	0.24374	0.385000	0.30292	-1.467000	0.02352	-0.015000	0.14150	0.655000	0.94253	ATC	.		0.458	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		G	48328626	C	G	48328626	3	3	139	1	0	0	0	0	1	0	0	0	11108	903	32	4	854	4	OR4S1	11	48328626	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	29590245	48328626	86677890	65	12360											
OR4D9	390199	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	59282746	59282746	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctctctctgtgatggcgtttGaccgctatatagccatctcc	6	14	8	13	2	3	2	0	2	3	0	5	2	3	2	3	1	1	2	3	1	3	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:59282746G>C	ENST00000329328.3	+	1	361	c.361G>C	c.(361-363)Gac>Cac	p.D121H		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						GATGGCGTTTGACCGCTATAT	0.522																																					p.D121H		.											.	OR4D9-68	0			c.G361C						.						83	80	81					11																	59282746		2201	4295	6496	SO:0001583	missense	390199	exon1			GCGTTTGACCGCT	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"GPCR / Class A : Olfactory receptors"	15178	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily D, member 9 pseudogene"				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.361G>C	11.37:g.59282746G>C	ENSP00000328563:p.Asp121His	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	72	6	NM_001004711	0	0	0	0	0	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617776	0.46736	.	.	ENSG00000172742	ENST00000329328	T	0.55234	0.53	4.16	4.16	0.48862	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	U	0.000643	T	0.80053	0.4553	H	0.95437	3.67	0.40769	D	0.983072	D	0.89917	1.0	D	0.81914	0.995	D	0.87427	0.2386	10	0.87932	D	0	-6.8922	15.3691	0.74548	0.0:0.0:1.0:0.0	.	121	Q8NGE8	OR4D9_HUMAN	H	121	ENSP00000328563:D121H	ENSP00000328563:D121H	D	+	1	0	OR4D9	59039322	1.000000	0.71417	0.849000	0.33467	0.015000	0.08874	9.723000	0.98772	2.002000	0.58637	0.563000	0.77884	GAC	.		0.522	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		C	59282746	G	C	59282746	3	2	139	1	0	0	0	0	1	0	0	0	11085	1290	45	4	363	4	OR4D9	11	59282746	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	10954120	59282746	75723770	66	12361											
SLCO2B1	11309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	74875111	74875111	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcgcttcggcctctccaGccagacgtcggggctgctgg	5	7	15	14	4	1	1	0	0	1	1	4	2	1	1	3	4	3	3	3	4	1	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:74875111G>T	ENST00000289575.5	+	3	646	c.251G>T	c.(250-252)aGc>aTc	p.S84I	SLCO2B1_ENST00000454962.2_Intron|SLCO2B1_ENST00000532236.1_Intron|SLCO2B1_ENST00000531756.1_Intron|SLCO2B1_ENST00000341411.4_5'UTR|SLCO2B1_ENST00000526660.1_Intron|SLCO2B1_ENST00000525650.1_Intron|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.S62I	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	84					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	GGCCTCTCCAGCCAGACGTCG	0.637																																					p.S84I		.											.	SLCO2B1-154	0			c.G251T						.						26	22	23					11																	74875111		2200	4293	6493	SO:0001583	missense	11309	exon3			TCTCCAGCCAGAC	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.251G>T	11.37:g.74875111G>T	ENSP00000289575:p.Ser84Ile	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	99	9	NM_007256	0	0	1	2	1	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	37	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547002	0.86022	.	.	ENSG00000137491	ENST00000531713;ENST00000289575;ENST00000527180;ENST00000534186;ENST00000428359	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	4.82	4.82	0.62117	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.80303	0.4598	H	0.95328	3.655	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.86661	0.1904	10	0.87932	D	0	.	15.3904	0.74739	0.0:0.0:1.0:0.0	.	84	O94956	SO2B1_HUMAN	I	62;84;62;62;62	ENSP00000432889:S62I;ENSP00000289575:S84I;ENSP00000436513:S62I;ENSP00000433872:S62I;ENSP00000388912:S62I	ENSP00000289575:S84I	S	+	2	0	SLCO2B1	74552759	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.180000	0.94867	2.240000	0.73641	0.591000	0.81541	AGC	.		0.637	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		T	74875111	G	T	74875111	3	4	139	1	0	0	0	0	1	0	0	0	14759	971	34	4	261	4	SLCO2B1	11	74875111	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	15592365	74875111	60131405	67	12362											
ODZ4	26011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	78413254	78413254	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagccaaagcggtggctgaCtccagggttgcgtggatggc	8	7	16	10	2	0	1	0	1	0	0	1	2	1	2	2	5	3	2	2	5	1	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:78413254C>A	ENST00000278550.7	-	28	4866	c.4404G>T	c.(4402-4404)gaG>gaT	p.E1468D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1468					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CGGTGGCTGACTCCAGGGTTG	0.567																																					p.E1468D		.											.	.	0			c.G4404T						.						59	60	60					11																	78413254		2071	4210	6281	SO:0001583	missense	26011	exon28			GGCTGACTCCAGG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"odz, odd Oz/ten-m homolog 4 (Drosophila)"	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.4404G>T	11.37:g.78413254C>A	ENSP00000278550:p.Glu1468Asp	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	58	30	NM_001098816	0	0	0	0	0	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.428265	0.62844	.	.	ENSG00000149256	ENST00000278550	D	0.90004	-2.6	5.53	5.53	0.82687	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.89636	0.6772	L	0.35593	1.075	0.50467	D	0.999876	D	0.64830	0.994	D	0.70716	0.97	D	0.87315	0.2314	9	.	.	.	.	10.0702	0.42328	0.0:0.8536:0.0:0.1464	.	1468	Q6N022	TEN4_HUMAN	D	1468	ENSP00000278550:E1468D	.	E	-	3	2	ODZ4	78090902	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.803000	0.27083	2.882000	0.98803	0.655000	0.94253	GAG	.		0.567	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78413254	C	A	78413254	3	1	139	1	0	0	0	0	1	0	0	0	10863	564	20	4	3933	4	ODZ4	11	78413254	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	3538143	78413254	56593262	68	12363											
A2M	2	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	9251341	9251341	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agactttgtgatgggctgaaGctcaaatccacctgtgaaat	12	11	10	8	0	1	4	1	3	0	1	2	4	2	4	2	1	1	2	2	1	3	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:9251341G>C	ENST00000318602.7	-	15	2020	c.1713C>G	c.(1711-1713)agC>agG	p.S571R		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	571					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	ATGGGCTGAAGCTCAAATCCA	0.527																																					p.S571R		.											.	A2M-515	0			c.C1713G						.						45	46	46					12																	9251341		2203	4300	6503	SO:0001583	missense	2	exon15			GCTGAAGCTCAAA	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1713C>G	12.37:g.9251341G>C	ENSP00000323929:p.Ser571Arg	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	88	15	NM_000014	0	0	0	0	0	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720504	0.30503	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.62232	0.04	5.55	3.61	0.41365	Alpha-2-macroglobulin, N-terminal 2 (1);	0.741044	0.13685	N	0.369887	T	0.55924	0.1951	L	0.60455	1.87	0.33904	D	0.638822	B	0.24092	0.097	B	0.30316	0.114	T	0.61574	-0.7035	10	0.36615	T	0.2	.	5.8923	0.18919	0.0783:0.135:0.6479:0.1387	.	571	P01023	A2MG_HUMAN	R	571;586	ENSP00000323929:S571R	ENSP00000323929:S571R	S	-	3	2	A2M	9142608	0.512000	0.26186	0.998000	0.56505	0.376000	0.30014	0.897000	0.28390	1.484000	0.48361	0.655000	0.94253	AGC	.		0.527	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		C	9251341	G	C	9251341	3	2	139	1	0	0	0	0	1	0	0	0	4	962	34	4	2799	4	A2M	12	9251341	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		9251341	124600554	69	12364											
ABCD2	225	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	39973352	39973352	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttacttatgataaaacataCgagccatgcccattctttgc	12	13	5	11	1	1	1	0	1	1	0	1	2	1	1	2	0	6	0	2	0	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:39973352C>T	ENST00000308666.3	-	8	1997	c.1862G>A	c.(1861-1863)cGt>cAt	p.R621H		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	621	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)	p.R621L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						ATAAAACATACGAGCCATGCC	0.358																																					p.R621H		.											.	ABCD2-95	1	Substitution - Missense(1)	lung(1)	c.G1862A						.						141	136	138					12																	39973352		2203	4300	6503	SO:0001583	missense	225	exon8			AACATACGAGCCA	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1862G>A	12.37:g.39973352C>T	ENSP00000310688:p.Arg621His	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	72	13	NM_005164	0	0	0	0	0	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.589233	0.86851	.	.	ENSG00000173208	ENST00000308666	D	0.99893	-7.57	5.08	5.08	0.68730	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.069130	0.56097	D	0.000022	D	0.99932	0.9969	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.95891	0.8907	9	.	.	.	-16.2697	18.5246	0.90967	0.0:1.0:0.0:0.0	.	621	Q9UBJ2	ABCD2_HUMAN	H	621	ENSP00000310688:R621H	.	R	-	2	0	ABCD2	38259619	1.000000	0.71417	0.983000	0.44433	0.666000	0.39218	7.520000	0.81821	2.381000	0.81170	0.579000	0.79373	CGT	.		0.358	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		T	39973352	C	T	39973352	3	4	139	1	0	0	0	0	1	0	0	0	61	536	19	1	372	1	ABCD2	12	39973352	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	30722011	39973352	93878543	70	12365											
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	49431988	49431988	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagctcaggatcagtatatgCcagcaggtcaaactcgtctc	11	9	9	12	1	4	0	3	0	1	0	6	1	4	1	1	2	4	3	1	2	3	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:49431988C>G	ENST00000301067.7	-	34	9150	c.9151G>C	c.(9151-9153)Gca>Cca	p.A3051P	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3051					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TCAGTATATGCCAGCAGGTCA	0.517																																					p.A3051P		.											.	MLL2-612	0			c.G9151C						.						97	95	95					12																	49431988		2015	4202	6217	SO:0001583	missense	8085	exon34			TATATGCCAGCAG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7133	protein-coding gene	gene with protein product		602113	"trinucleotide repeat containing 21", "myeloid/lymphoid or mixed-lineage leukemia 2"	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.9151G>C	12.37:g.49431988C>G	ENSP00000301067:p.Ala3051Pro	Somatic	235	0		WXS	Illumina HiSeq	Phase_I	256	59	NM_003482	0	0	1	2	1	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.202944	0.38905	.	.	ENSG00000167548	ENST00000301067	D	0.94457	-3.43	5.11	5.11	0.69529	.	0.000000	0.38272	N	0.001746	D	0.96284	0.8788	L	0.49126	1.545	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.96801	0.9589	10	0.87932	D	0	.	17.698	0.88286	0.0:1.0:0.0:0.0	.	3051	O14686	MLL2_HUMAN	P	3051	ENSP00000301067:A3051P	ENSP00000301067:A3051P	A	-	1	0	MLL2	47718255	1.000000	0.71417	0.972000	0.41901	0.971000	0.66376	7.707000	0.84623	2.549000	0.85964	0.655000	0.94253	GCA	.		0.517	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49431988	C	G	49431988	3	3	139	1	0	0	0	0	1	0	0	0	9646	739	26	4	7546	4	MLL2	12	49431988	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	9458636	49431988	84419907	71	12366											
SHMT2	6472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57625677	57625677	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acgaccggatcatggggctgGacctgcccgatgggggccag	7	5	17	12	3	1	0	1	0	0	0	1	4	1	2	4	6	1	1	4	6	0	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:57625677G>C	ENST00000328923.3	+	4	945	c.493G>C	c.(493-495)Gac>Cac	p.D165H	SHMT2_ENST00000393827.4_Missense_Mutation_p.W59C|SHMT2_ENST00000449049.3_Missense_Mutation_p.D144H|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.D144H|SHMT2_ENST00000557487.1_Missense_Mutation_p.D165H|SHMT2_ENST00000414700.3_Missense_Mutation_p.D144H	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	165					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CATGGGGCTGGACCTGCCCGA	0.587																																					p.D165H	Esophageal Squamous(150;1369 2416 49071 49364)	.											.	SHMT2-91	0			c.G493C						.						30	27	28					12																	57625677		2203	4300	6503	SO:0001583	missense	6472	exon4			GGGCTGGACCTGC	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.493G>C	12.37:g.57625677G>C	ENSP00000333667:p.Asp165His	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	75	15	NM_005412	0	0	85	118	33	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	37	CCDS8934.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.546641|4.546641	0.86022|0.86022	.|.	.|.	ENSG00000182199|ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000555634;ENST00000556689;ENST00000414700;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737|ENST00000393827	T;T;T;T;T;T;T;T;T;T;T;T;T|T	0.50001|0.31510	1.39;0.76;0.76;0.76;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39|1.49	4.53|4.53	4.53|4.53	0.55603|0.55603	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.57110|0.57110	0.2031|0.2031	M|M	0.89163|0.89163	3.01|3.01	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|D	0.71674|0.67145	0.998;0.993;0.997|0.996	D;D;P|P	0.66497|0.57371	0.944;0.925;0.815|0.819	T|T	0.68228|0.68228	-0.5464|-0.5464	10|9	0.87932|0.87932	D|D	0|0	-5.8122|-5.8122	16.58|16.58	0.84712|0.84712	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	174;165;165|59	B4DWA7;Q8N1A5;P34897|B4DLV4	.;.;GLYM_HUMAN|.	H|C	165;165;4;165;144;144;144;144;144;144;144;144;144|59	ENSP00000333667:D165H;ENSP00000452315:D165H;ENSP00000450930:D4H;ENSP00000452035:D165H;ENSP00000406881:D144H;ENSP00000452161:D144H;ENSP00000450893:D144H;ENSP00000452045:D144H;ENSP00000452419:D144H;ENSP00000451968:D144H;ENSP00000452404:D144H;ENSP00000413770:D144H;ENSP00000451495:D144H|ENSP00000377413:W59C	ENSP00000333667:D165H|ENSP00000377413:W59C	D|W	+|+	1|3	0|0	SHMT2|SHMT2	55911944|55911944	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.657000|9.657000	0.98554|0.98554	2.517000|2.517000	0.84864|0.84864	0.561000|0.561000	0.74099|0.74099	GAC|TGG	.		0.587	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		C	57625677	G	C	57625677	3	2	139	1	0	0	0	0	1	0	0	0	14318	1174	41	4	507	4	SHMT2	12	57625677	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	8193689	57625677	76226218	72	12367											
CYP27B1	1594	bcgsc.ca	37	chr12	58160674	58160674	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cccccccttgcagaaaagttCggccagaaagctgggcgtag	10	6	12	13	2	0	2	0	0	0	2	1	2	0	2	4	2	2	4	4	2	4	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:58160674C>G	ENST00000228606.4	-	1	360	c.151G>C	c.(151-153)Gaa>Caa	p.E51Q	CYP27B1_ENST00000546496.1_5'Flank	NM_000785.3	NP_000776.1	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B, polypeptide 1	51					bone mineralization (GO:0030282)|calcitriol biosynthetic process from calciol (GO:0036378)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|decidualization (GO:0046697)|G1 to G0 transition (GO:0070314)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of bone mineralization (GO:0030500)|response to estrogen (GO:0043627)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	calcidiol 1-monooxygenase activity (GO:0004498)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|urinary_tract(1)	15	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Alfacalcidol(DB01436)|Calcidiol(DB00146)|Corticotropin(DB01285)|Ergocalciferol(DB00153)	CAGAAAAGTTCGGCCAGAAAG	0.632																																					p.E51Q													.	CYP27B1-514	0			c.G151C						.						65	73	70					12																	58160674		2203	4300	6503	SO:0001583	missense	1594	exon1			AAAGTTCGGCCAG	AB006987	CCDS8954.1	12q14.1	2013-11-13	2003-01-14		ENSG00000111012	ENSG00000111012		"Cytochrome P450s"	2606	protein-coding gene	gene with protein product	"VDDR I", "1alpha(OH)ase", "25-Hydroxyvitamin D3 1alpha-hydroxylase"	609506	"cytochrome P450, subfamily XXVIIB (25-hydroxyvitamin D-1-alpha-hydroxylase), polypeptide 1"	VDD1, PDDR		9295274, 9344864	Standard	NM_000785		Approved	CYP1, P450c1	uc001spz.1	O15528	OTTHUMG00000170457	ENST00000228606.4:c.151G>C	12.37:g.58160674C>G	ENSP00000228606:p.Glu51Gln	Somatic	164	0		WXS	Illumina HiSeq	Phase_1	203	9	NM_000785	0	0	0	0	0	B2RC61|Q548T3	Missense_Mutation	SNP	ENST00000228606.4	37	CCDS8954.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.516287	0.85495	.	.	ENSG00000111012	ENST00000228606	T	0.68479	-0.33	5.26	5.26	0.73747	.	0.059156	0.64402	D	0.000003	T	0.54127	0.1839	N	0.12920	0.275	0.49299	D	0.999778	B	0.30634	0.288	B	0.39094	0.29	T	0.48603	-0.9021	10	0.08837	T	0.75	.	17.7796	0.88519	0.0:1.0:0.0:0.0	.	51	O15528	CP27B_HUMAN	Q	51	ENSP00000228606:E51Q	ENSP00000228606:E51Q	E	-	1	0	CYP27B1	56446941	1.000000	0.71417	0.963000	0.40424	0.870000	0.49936	6.357000	0.73051	2.729000	0.93468	0.655000	0.94253	GAA	.		0.632	CYP27B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409248.1	NM_000785		G	58160674	C	G	58160674	3	3	139	1	0	0	0	0	1	0	0	0	4165	893	31	4	1411	4	CYP27B1	12	58160674	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	534997	58160674	75691221	73	12368											
TCP11L2	255394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	106717360	106717360	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	attatgagtctcagaccgcaCcttcaacgccagttggtgga	10	10	10	11	2	2	2	2	1	1	1	3	3	2	3	3	2	1	2	3	2	2	3	rs138241328		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:106717360C>G	ENST00000299045.3	+	6	882	c.708C>G	c.(706-708)caC>caG	p.H236Q	TCP11L2_ENST00000547153.1_Missense_Mutation_p.H236Q|TCP11L2_ENST00000552690.1_3'UTR|TCP11L2_ENST00000546625.1_Missense_Mutation_p.H236Q	NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	236										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						TCAGACCGCACCTTCAACGCC	0.343																																					p.H236Q		.											.	TCP11L2-93	0			c.C708G						.						55	60	58					12																	106717360		2203	4300	6503	SO:0001583	missense	255394	exon6			ACCGCACCTTCAA	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.708C>G	12.37:g.106717360C>G	ENSP00000299045:p.His236Gln	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	153	22	NM_152772	0	0	2	2	0	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	37	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024466	0.54683	.	.	ENSG00000166046	ENST00000547153;ENST00000299045;ENST00000546625	T;T;T	0.10960	2.82;2.82;2.82	5.76	2.51	0.30379	.	0.573213	0.19030	N	0.124583	T	0.07908	0.0198	N	0.25380	0.74	0.27925	N	0.938083	P;B;B	0.34815	0.47;0.13;0.138	B;B;B	0.39465	0.3;0.039;0.022	T	0.27020	-1.0086	10	0.25751	T	0.34	-14.6909	5.8057	0.18438	0.0:0.5201:0.1733:0.3066	.	236;236;236	Q8N4U5;G3V1Y9;G3V1Z2	T11L2_HUMAN;.;.	Q	236	ENSP00000448952:H236Q;ENSP00000299045:H236Q;ENSP00000449123:H236Q	ENSP00000299045:H236Q	H	+	3	2	TCP11L2	105241490	0.044000	0.20184	0.935000	0.37517	0.949000	0.60115	-0.293000	0.08320	0.588000	0.29660	0.655000	0.94253	CAC	C|1.000;T|0.000		0.343	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772		G	106717360	C	G	106717360	3	3	139	1	0	0	0	0	1	0	0	0	15747	506	18	4	726	4	TCP11L2	12	106717360	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	48556686	106717360	27134535	74	12369											
C12orf34	84915	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	110207030	110207030	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcaagggctatgagacGgtggccgtgccccggctact	6	7	16	12	3	0	1	0	1	0	1	0	2	0	1	3	5	2	3	3	5	3	2	rs138993259		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:110207030G>A	ENST00000538780.1	+	3	2012	c.1296G>A	c.(1294-1296)acG>acA	p.T432T	FAM222A_ENST00000358906.3_Silent_p.T432T|FAM222A-AS1_ENST00000541723.1_RNA|FAM222A-AS1_ENST00000541460.1_RNA	NM_032829.2	NP_116218.2	Q5U5X8	F222A_HUMAN	family with sequence similarity 222, member A	432																	GCTATGAGACGGTGGCCGTGC	0.627																																					p.T432T		.											.	.	0			c.G1296A						.	G		0,4396		0,0,2198	22	18	19		1296	-6.8	0.9	12	dbSNP_134	19	1,8569		0,1,4284	no	coding-synonymous	C12orf34	NM_032829.2		0,1,6482	AA,AG,GG		0.0117,0.0,0.0077		432/453	110207030	1,12965	2198	4285	6483	SO:0001819	synonymous_variant	84915	exon3			TGAGACGGTGGCC	AK027627	CCDS9133.1	12q24.11	2012-04-27	2012-04-27	2012-04-27	ENSG00000139438	ENSG00000139438			25915	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 34"	C12orf34		12477932	Standard	NM_032829		Approved	FLJ14721	uc001tpd.2	Q5U5X8	OTTHUMG00000169260	ENST00000538780.1:c.1296G>A	12.37:g.110207030G>A		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	209	18	NM_032829	0	0	0	0	0	Q8NCD5|Q96SP6	Silent	SNP	ENST00000538780.1	37	CCDS9133.1																																																																																			G|1.000;A|0.000		0.627	FAM222A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403175.1	NM_032829		A	110207030	G	A	110207030	2	1	139	1	0	0	0	0	0	0	0	1	1685	1103	39	1		1	C12orf34	12	110207030	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	3489670	110207030	23644865	75	12370											
TRPV4	59341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	110234478	110234478	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgccgtgtgtcctcatccGtcacctcccgccggatgatg	4	10	12	15	4	2	1	2	1	0	0	5	2	5	2	6	2	1	0	6	2	0	0	rs374197231		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:110234478G>A	ENST00000418703.2	-	6	1278	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	TRPV4_ENST00000544971.1_Intron|TRPV4_ENST00000261740.2_Missense_Mutation_p.T395M|TRPV4_ENST00000541794.1_Missense_Mutation_p.T348M|TRPV4_ENST00000537083.1_Intron|TRPV4_ENST00000392719.2_Missense_Mutation_p.T348M|TRPV4_ENST00000536838.1_Missense_Mutation_p.T361M|TRPV4_ENST00000346520.2_Intron	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	395					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						GTCCTCATCCGTCACCTCCCG	0.627																																					p.T395M		.											.	TRPV4-94	0			c.C1184T						.	G	MET/THR,MET/THR,,MET/THR,	0,4406		0,0,2203	102	85	91		1043,1082,,1184,	3.2	0.9	12		91	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,missense,intron	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	81,81,,81,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,probably-damaging,	348/825,361/838,,395/872,	110234478	1,13005	2203	4300	6503	SO:0001583	missense	59341	exon7			TCATCCGTCACCT	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18083	protein-coding gene	gene with protein product	"osmosensitive transient receptor potential channel 4"	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.1184C>T	12.37:g.110234478G>A	ENSP00000406191:p.Thr395Met	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	113	18	NM_021625	0	0	5	5	0	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	37	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037326	0.35989	0.0	1.16E-4	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000541794;ENST00000536838	D;D;D;D;D	0.89552	-2.53;-2.53;-2.31;-2.31;-2.53	5.16	3.22	0.36961	.	0.149468	0.64402	D	0.000018	T	0.81631	0.4863	L	0.31476	0.935	0.80722	D	1	D;B;B	0.54772	0.968;0.184;0.32	P;B;B	0.45276	0.475;0.103;0.103	T	0.78386	-0.2224	10	0.38643	T	0.18	-9.8296	6.9524	0.24552	0.0814:0.0:0.6258:0.2927	.	395;348;361	Q9HBA0;Q9HBA0-4;Q9HBA0-5	TRPV4_HUMAN;.;.	M	395;395;348;348;361	ENSP00000406191:T395M;ENSP00000261740:T395M;ENSP00000376480:T348M;ENSP00000442167:T348M;ENSP00000444336:T361M	ENSP00000261740:T395M	T	-	2	0	TRPV4	108718861	0.916000	0.31088	0.919000	0.36401	0.863000	0.49368	1.418000	0.34782	1.181000	0.42912	-0.251000	0.11542	ACG	.		0.627	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625		A	110234478	G	A	110234478	3	1	139	1	0	0	0	0	1	0	0	0	16631	1145	40	1	1471	1	TRPV4	12	110234478	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	27448	110234478	23617417	76	12371											
EP400	57634	broad.mit.edu	37	chr12	132522575	132522575	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcaaagctgaggagtttgtGgtgctttctcaggaaccttc	8	13	12	8	0	2	1	2	1	1	0	4	3	2	3	1	3	3	3	1	3	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:132522575G>A	ENST00000333577.4	+	33	6358	c.6249G>A	c.(6247-6249)gtG>gtA	p.V2083V	EP400_ENST00000332482.4_Silent_p.V2010V|EP400_ENST00000330386.6_Silent_p.V1966V|EP400_ENST00000389561.2_Silent_p.V2047V|EP400_ENST00000389562.2_Silent_p.V2046V			Q96L91	EP400_HUMAN	E1A binding protein p400	2083					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		AGGAGTTTGTGGTGCTTTCTC	0.458																																					p.V2047V													.	EP400-520	0			c.G6141A						.						201	183	189					12																	132522575		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon32			GTTTGTGGTGCTT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.6249G>A	12.37:g.132522575G>A		Somatic	317	1		WXS	Illumina HiSeq	Phase_I	382	8	NM_015409	0	0	13	14	1	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.		0.458	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132522575	G	A	132522575	2	1	139	1	0	0	0	0	0	0	0	1	5162	1335	47	2		2	EP400	12	132522575	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	22288097	132522575	1329320	77	12372											
RCBTB1	55213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	50134123	50134123	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccaccacttgcttgatcaaGagattggtacagacctggac	11	10	9	11	0	1	3	1	1	0	2	2	5	2	4	3	2	2	2	3	2	2	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr13:50134123G>C	ENST00000378302.2	-	5	635	c.375C>G	c.(373-375)ctC>ctG	p.L125L	RCBTB1_ENST00000546015.1_Silent_p.L125L|RCBTB1_ENST00000258646.3_Silent_p.L125L	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	125					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GCTTGATCAAGAGATTGGTAC	0.483																																					p.L125L		.											.	RCBTB1-91	0			c.C375G						.						210	203	206					13																	50134123		2203	4300	6503	SO:0001819	synonymous_variant	55213	exon5			GATCAAGAGATTG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"BTB/POZ domain containing"	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.375C>G	13.37:g.50134123G>C		Somatic	224	0		WXS	Illumina HiSeq	Phase_I	217	47	NM_018191	0	0	2	3	1	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	37	CCDS9418.1																																																																																			.		0.483	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191		C	50134123	G	C	50134123	2	2	139	1	0	0	0	0	0	0	0	1	13203	929	33	4		4	RCBTB1	13	50134123	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		50134123	65035755	78	12373											
NALCN	259232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	101881861	101881861	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaaactcccaagctttttTccaggaccaaatatcttgta	13	12	4	12	0	1	0	0	0	1	0	3	1	3	1	4	1	2	2	4	1	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr13:101881861T>C	ENST00000251127.6	-	13	1590	c.1509A>G	c.(1507-1509)ggA>ggG	p.G503G	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Silent_p.G503G	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	503					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CAAGCTTTTTTCCAGGACCAA	0.398																																					p.G503G		.											.	NALCN-167	0			c.A1509G						.						104	112	110					13																	101881861		2203	4300	6503	SO:0001819	synonymous_variant	259232	exon13			CTTTTTTCCAGGA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1509A>G	13.37:g.101881861T>C		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	18	7	NM_052867	0	0	0	0	0	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			.		0.398	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		C	101881861	T	C	101881861	2	2	139	1	0	0	0	0	0	0	0	1	10173	1770	62	3		3	NALCN	13	101881861	Silent	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	51747738	101881861	13288017	79	12374											
HECTD1	25831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	31582629	31582629	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaaattaagaatatcactaCtttgaagagtagaaatggcc	17	12	7	5	0	1	4	1	1	0	3	1	4	1	4	1	1	1	1	1	1	9	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:31582629C>T	ENST00000399332.1	-	33	6406	c.5918G>A	c.(5917-5919)aGt>aAt	p.S1973N	HECTD1_ENST00000553700.1_Missense_Mutation_p.S1973N	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1973					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AATATCACTACTTTGAAGAGT	0.388																																					p.S1973N		.											.	HECTD1-570	0			c.G5918A						.						167	164	165					14																	31582629		1831	4088	5919	SO:0001583	missense	25831	exon33			TCACTACTTTGAA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"Ankyrin repeat domain containing"	20157	protein-coding gene	gene with protein product			"HECT domain containing 1"			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.5918G>A	14.37:g.31582629C>T	ENSP00000382269:p.Ser1973Asn	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	52	10	NM_015382	0	0	4	12	8	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.089|1.089	-0.664515|-0.664515	0.03428|0.03428	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957|ENST00000554882	T;T;T|.	0.43294|.	0.95;0.95;1.2|.	5.94|5.94	2.88|2.88	0.33553|0.33553	.|.	0.115316|.	0.56097|.	U|.	0.000027|.	T|T	0.46112|0.46112	0.1376|0.1376	L|L	0.40543|0.40543	1.245|1.245	0.38847|0.38847	D|D	0.956199|0.956199	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.30679|0.30679	-0.9970|-0.9970	10|5	0.18276|.	T|.	0.48|.	-2.8194|-2.8194	6.637|6.637	0.22889|0.22889	0.0:0.4212:0.0:0.5788|0.0:0.4212:0.0:0.5788	.|.	1973;1973|.	D3DS86;Q9ULT8|.	.;HECD1_HUMAN|.	N|I	1973;1975;1973;1400|339	ENSP00000450697:S1973N;ENSP00000382269:S1973N;ENSP00000451860:S1400N|.	ENSP00000261312:S1975N|.	S|V	-|-	2|1	0|0	HECTD1|HECTD1	30652380|30652380	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.020000|0.020000	0.10135|0.10135	2.462000|2.462000	0.45049|0.45049	0.363000|0.363000	0.24346|0.24346	-0.145000|-0.145000	0.13849|0.13849	AGT|GTA	.		0.388	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31582629	C	T	31582629	3	4	139	1	0	0	0	0	1	0	0	0	7060	565	20	2	1958	2	HECTD1	14	31582629	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		31582629	75766911	80	12375											
HEATR5A	25938	broad.mit.edu;bcgsc.ca	37	chr14	31763220	31763220	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagtttttccatgatacAggatgctaaagagtaaatgt	13	13	9	6	0	0	2	0	1	0	1	1	3	1	3	1	1	3	4	1	1	5	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:31763220A>G	ENST00000389961.3	-	34	5691	c.5692T>C	c.(5692-5694)Tgt>Cgt	p.C1898R	HEATR5A_ENST00000439727.1_Missense_Mutation_p.C1611R|HEATR5A_ENST00000543095.2_Missense_Mutation_p.C1904R|RP11-596D21.1_ENST00000551799.1_RNA|HEATR5A_ENST00000439348.1_Missense_Mutation_p.C1823R			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1898										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TCCATGATACAGGATGCTAAA	0.398																																					p.C1904R													.	HEATR5A-23	0			c.T5710C						.						119	103	108					14																	31763220		1848	4109	5957	SO:0001583	missense	25938	exon35			TGATACAGGATGC	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 125"	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.5692T>C	14.37:g.31763220A>G	ENSP00000374611:p.Cys1898Arg	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	101	5	NM_015473	0	0	1	2	1	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		.	.	.	.	.	.	.	.	.	.	A	0.006	-2.045063	0.00398	.	.	ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095	T;T;T;T	0.67865	-0.07;-0.29;-0.07;-0.07	5.22	1.47	0.22746	.	0.352635	0.30227	N	0.010105	T	0.20129	0.0484	N	0.00237	-1.79	0.19575	N	0.999969	B	0.02656	0.0	B	0.01281	0.0	T	0.40683	-0.9550	10	0.02654	T	1	.	4.434	0.11542	0.6479:0.0:0.2188:0.1333	.	1823	Q86XA9-2	.	R	1898;1823;1611;1904	ENSP00000374611:C1898R;ENSP00000405407:C1823R;ENSP00000408681:C1611R;ENSP00000437968:C1904R	ENSP00000374611:C1898R	C	-	1	0	HEATR5A	30832971	0.000000	0.05858	0.277000	0.24703	0.168000	0.22595	0.567000	0.23608	0.317000	0.23160	-0.509000	0.04479	TGT	.		0.398	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		G	31763220	A	G	31763220	3	3	139	1	0	0	0	0	1	0	0	0	7052	188	7	3	438	3	HEATR5A	14	31763220	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	180591	31763220	75586320	81	12376											
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64519117	64519117	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactcaaagatcacagcaatTagaatttaagttggaagaaa	20	9	7	5	0	2	3	2	0	0	3	2	4	2	4	0	1	2	2	0	1	8	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:64519117T>G	ENST00000344113.4	+	48	8698	c.8486T>G	c.(8485-8487)tTa>tGa	p.L2829*	SYNE2_ENST00000554584.1_Nonsense_Mutation_p.L2862*|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.L2829*|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2829					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCACAGCAATTAGAATTTAAG	0.343																																					p.L2829X		.											.	SYNE2-164	0			c.T8486G						.						43	41	42					14																	64519117		1811	4086	5897	SO:0001587	stop_gained	23224	exon48			AGCAATTAGAATT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8486T>G	14.37:g.64519117T>G	ENSP00000341781:p.Leu2829*	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	45	6	NM_182914	0	0	0	0	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	50	16.272729	0.99859	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	5.27	5.27	0.74061	.	0.000000	0.38720	N	0.001585	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7819	0.63087	0.0:0.0:0.0:1.0	.	.	.	.	X	2829;2829;2862;2862	.	ENSP00000261678:L2862X	L	+	2	0	SYNE2	63588870	0.992000	0.36948	0.998000	0.56505	0.933000	0.57130	5.172000	0.65003	2.004000	0.58718	0.260000	0.18958	TTA	.		0.343	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64519117	T	G	64519117	4	3	139	1	0	0	0	0	0	1	0	0	15478	1764	61	5	8672	5	SYNE2	14	64519117	Nonsense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	32755897	64519117	42830423	82	12377											
CKB	1152	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	103988811	103988811	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgcagcttcagtgcgttgTggctgttggagaagggcatg	7	10	17	7	2	1	1	1	0	0	1	1	2	1	1	0	3	3	6	0	3	1	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:103988811T>G	ENST00000348956.2	-	2	377	c.20A>C	c.(19-21)cAc>cCc	p.H7P	RP11-600F24.7_ENST00000568177.1_RNA	NM_001823.4	NP_001814.2	P12277	KCRB_HUMAN	creatine kinase, brain	7					cellular chloride ion homeostasis (GO:0030644)|cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(2)|prostate(1)	3		Melanoma(154;0.155)	Epithelial(46;0.14)		Creatine(DB00148)	CAGTGCGTTGTGGCTGTTGGA	0.706																																					p.H7P	Esophageal Squamous(186;2492 2823 49929 50127)	.											.	CKB-115	0			c.A20C						.						49	43	45					14																	103988811		2201	4300	6501	SO:0001583	missense	1152	exon2			GCGTTGTGGCTGT		CCDS9981.1	14q32.32	2012-10-02			ENSG00000166165	ENSG00000166165	2.7.3.2		1991	protein-coding gene	gene with protein product		123280		CKBB			Standard	NM_001823		Approved		uc001ynf.2	P12277	OTTHUMG00000171786	ENST00000348956.2:c.20A>C	14.37:g.103988811T>G	ENSP00000299198:p.His7Pro	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	22	9	NM_001823	0	0	0	29	29	A8K236|B2R5R4|Q2LE07|Q6FG40|Q9UC66	Missense_Mutation	SNP	ENST00000348956.2	37	CCDS9981.1	.	.	.	.	.	.	.	.	.	.	T	14.98	2.696367	0.48202	.	.	ENSG00000166165	ENST00000348956;ENST00000428256;ENST00000553878	T;T	0.38240	1.82;1.15	4.17	4.17	0.49024	ATP:guanido phosphotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	M	0.82193	2.58	0.80722	D	1	P	0.48503	0.911	P	0.55112	0.769	T	0.64896	-0.6299	10	0.87932	D	0	.	13.5095	0.61504	0.0:0.0:0.0:1.0	.	7	P12277	KCRB_HUMAN	P	7	ENSP00000299198:H7P;ENSP00000451904:H7P	ENSP00000299198:H7P	H	-	2	0	CKB	103058564	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	6.860000	0.75473	1.783000	0.52377	0.246000	0.17985	CAC	.		0.706	CKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415111.1			G	103988811	T	G	103988811	3	3	139	1	0	0	0	0	1	0	0	0	3452	1696	59	5	1153	5	CKB	14	103988811	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	39469694	103988811	3360729	83	12378											
SOLH	6650	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	598994	598994	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggccgtggtctctgcagaAcaatgtgagcttcgtggatg	8	11	14	8	2	1	2	0	1	1	1	3	3	1	3	1	3	3	2	1	3	2	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr16:598994A>G	ENST00000219611.2	+	5	1814	c.1451A>G	c.(1450-1452)aAc>aGc	p.N484S	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	484					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCTCTGCAGAACAATGTGAGC	0.662																																					p.N484S		.											.	SOLH-523	0			c.A1451G						.						112	92	99					16																	598994		2198	4297	6495	SO:0001630	splice_region_variant	6650	exon5			TGCAGAACAATGT	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.1450-1A>G	16.37:g.598994A>G		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	65	4	NM_005632	0	0	2	2	0	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	a	10.23	1.292148	0.23564	.	.	ENSG00000103326	ENST00000219611	T	0.40756	1.02	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (1);	0.090831	0.64402	D	0.000001	T	0.49372	0.1553	L	0.27053	0.805	0.58432	D	0.999994	D	0.71674	0.998	D	0.77004	0.989	T	0.43147	-0.9409	10	0.30854	T	0.27	.	13.6292	0.62186	1.0:0.0:0.0:0.0	.	484	O75808	CAN15_HUMAN	S	484	ENSP00000219611:N484S	ENSP00000219611:N484S	N	+	2	0	SOLH	538995	1.000000	0.71417	0.967000	0.41034	0.345000	0.29048	6.977000	0.76141	1.903000	0.55091	0.454000	0.30748	AAC	.		0.662	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	Missense_Mutation	G	598994	A	G	598994	5	3	139	1	0	0	0	0	0	0	1	0	14957	57	2	3	1457	3	SOLH	16	598994	Splice_Site	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10		598994	89755759	84	12379											
TMEM219	124446	broad.mit.edu	37	chr16	29982731	29982731	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtacccctccctaggaGgagctggctctgtgtggctc	4	10	12	15	0	1	0	0	0	1	0	3	2	2	2	4	4	2	4	4	4	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr16:29982731G>A	ENST00000566848.1	+	4	1055	c.588G>A	c.(586-588)gaG>gaA	p.E196E	TAOK2_ENST00000308893.4_5'Flank|TAOK2_ENST00000543033.1_5'Flank|TMEM219_ENST00000561899.2_Silent_p.E196E|TMEM219_ENST00000279396.6_Silent_p.E196E|TAOK2_ENST00000279394.3_5'Flank|TMEM219_ENST00000414689.2_Silent_p.E196E			Q86XT9	TM219_HUMAN	transmembrane protein 219	196					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(1)|prostate(2)	4						CTCCCTAGGAGGAGCTGGCTC	0.582																																					p.E196E													.	TMEM219-90	0			c.G588A						.						114	118	117					16																	29982731		2037	4174	6211	SO:0001819	synonymous_variant	124446	exon5			CTAGGAGGAGCTG		CCDS42145.1	16p11.2	2008-08-08			ENSG00000149932	ENSG00000149932			25201	protein-coding gene	gene with protein product							Standard	NM_194280		Approved		uc010bzk.1	Q86XT9		ENST00000566848.1:c.588G>A	16.37:g.29982731G>A		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	160	4	NM_001083613	0	0	1	1	0	D5FK14|Q8WVV8	Silent	SNP	ENST00000566848.1	37	CCDS42145.1																																																																																			.		0.582	TMEM219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435307.1	NM_001083613		A	29982731	G	A	29982731	2	1	139	1	0	0	0	0	0	0	0	1	16174	991	35	2		2	TMEM219	16	29982731	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	29383737	29982731	60372022	85	12380											
DNAH2	146754	broad.mit.edu;bcgsc.ca	37	chr17	7689597	7689597	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaagactgcctcatggcgCattctacaggcctccctgtc	7	9	10	15	1	2	1	1	0	1	1	4	1	3	1	3	3	2	2	3	3	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:7689597C>T	ENST00000572933.1	+	40	7745	c.6285C>T	c.(6283-6285)cgC>cgT	p.R2095R	DNAH2_ENST00000389173.2_Silent_p.R2095R			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2095	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CCTCATGGCGCATTCTACAGG	0.582																																					p.R2095R													.	DNAH2-102	0			c.C6285T						.						63	59	61					17																	7689597		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon39			ATGGCGCATTCTA	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.6285C>T	17.37:g.7689597C>T		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	87	6	NM_020877	0	0	0	0	0	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			.		0.582	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7689597	C	T	7689597	2	4	139	1	0	0	0	0	0	0	0	1	4613	697	25	2		2	DNAH2	17	7689597	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		7689597	73505613	86	12381											
MYH8	4626	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	10300168	10300168	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggctgcacaggctgcattAgacctttccacatcaagcat	11	9	9	12	0	1	1	1	0	0	1	2	1	2	1	2	2	3	5	2	2	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:10300168A>T	ENST00000403437.2	-	31	4408	c.4314T>A	c.(4312-4314)tcT>tcA	p.S1438S	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1438					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						AGGCTGCATTAGACCTTTCCA	0.463									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.S1438S		.											.	MYH8-101	0			c.T4314A						.						110	100	103					17																	10300168		2203	4300	6503	SO:0001819	synonymous_variant	4626	exon31	Familial Cancer Database	Carney Complex Variant	TGCATTAGACCTT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"Myosins / Myosin superfamily : Class II"	7578	protein-coding gene	gene with protein product		160741	"myosin, heavy polypeptide 8, skeletal muscle, perinatal"			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.4314T>A	17.37:g.10300168A>T		Somatic	177	0		WXS	Illumina HiSeq	Phase_I	230	19	NM_002472	0	0	0	0	0	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			.		0.463	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10300168	A	T	10300168	2	4	139	1	0	0	0	0	0	0	0	1	10066	407	15	5		5	MYH8	17	10300168	Silent	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	2610571	10300168	70895042	87	12382											
TMEM132E	124842	broad.mit.edu;bcgsc.ca	37	chr17	32956104	32956104	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcaccagccagtcagtcaagCggaggatcatgtggcacatt	11	8	11	11	1	4	0	4	0	0	0	4	2	4	2	2	3	2	1	2	3	1	1	rs371393529		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:32956104C>G	ENST00000321639.5	+	5	1277	c.949C>G	c.(949-951)Cgg>Ggg	p.R317G		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	317						integral component of membrane (GO:0016021)		p.R317W(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		GTCAGTCAAGCGGAGGATCAT	0.612																																					p.R317G													.	TMEM132E-68	1	Substitution - Missense(1)	cervix(1)	c.C949G						.						100	93	95					17																	32956104		2203	4300	6503	SO:0001583	missense	124842	exon5			GTCAAGCGGAGGA	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.949C>G	17.37:g.32956104C>G	ENSP00000316532:p.Arg317Gly	Somatic	298	0		WXS	Illumina HiSeq	Phase_I	304	10	NM_207313	0	0	2	2	0	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	c	9.345	1.063991	0.20067	.	.	ENSG00000181291	ENST00000321639	T	0.18960	2.18	4.51	3.53	0.40419	.	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	L	0.39397	1.21	0.49130	D	0.999751	D	0.89917	1.0	D	0.85130	0.997	T	0.03514	-1.1029	10	0.15499	T	0.54	-29.8251	11.4588	0.50197	0.3265:0.6735:0.0:0.0	.	317	Q6IEE7	T132E_HUMAN	G	317	ENSP00000316532:R317G	ENSP00000316532:R317G	R	+	1	2	TMEM132E	29980217	0.995000	0.38212	0.984000	0.44739	0.044000	0.14063	1.296000	0.33389	1.236000	0.43740	0.447000	0.29281	CGG	.		0.612	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		G	32956104	C	G	32956104	3	3	139	1	0	0	0	0	1	0	0	0	16080	759	27	4	967	4	TMEM132E	17	32956104	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	22655936	32956104	48239106	88	12383											
CLTC	1213	broad.mit.edu;bcgsc.ca	37	chr17	57728648	57728648	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtcttctttcctccagaaGcacaaaatgattttcctgtt	10	16	5	10	0	2	2	0	1	2	1	5	2	5	2	3	0	1	2	3	0	3	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:57728648G>T	ENST00000269122.3	+	5	1040	c.766G>T	c.(766-768)Gca>Tca	p.A256S	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Missense_Mutation_p.A256S	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	256	Globular terminal domain.|WD40-like repeat 5.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCCTCCAGAAGCACAAAATGA	0.353			T	"ALK, TFE3"	"ALCL, renal "																																p.A256S				Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC-835	0			c.G766T						.						146	149	148					17																	57728648		2203	4300	6503	SO:0001583	missense	1213	exon5			CCAGAAGCACAAA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.766G>T	17.37:g.57728648G>T	ENSP00000269122:p.Ala256Ser	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	195	8	NM_004859	0	0	24	25	1	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	35	5.556566	0.96514	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.24350	1.86;1.86	5.62	5.62	0.85841	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.000000	0.85682	D	0.000000	T	0.63640	0.2528	M	0.93283	3.4	0.80722	D	1	D;P	0.58268	0.982;0.857	D;P	0.72338	0.977;0.876	T	0.68992	-0.5263	10	0.44086	T	0.13	.	20.0333	0.97547	0.0:0.0:1.0:0.0	.	256;256	Q00610;Q00610-2	CLH1_HUMAN;.	S	256	ENSP00000269122:A256S;ENSP00000376763:A256S	ENSP00000269122:A256S	A	+	1	0	CLTC	55083430	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.810000	0.96702	0.585000	0.79938	GCA	.		0.353	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		T	57728648	G	T	57728648	3	4	139	1	0	0	0	0	1	0	0	0	3572	971	34	4	784	4	CLTC	17	57728648	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	24772544	57728648	23466562	89	12384											
BPTF	2186	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	65960510	65960510	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggggttgaagagggtgctccGttccttacaggtgagacccc	7	9	15	10	1	0	3	0	2	0	2	2	4	2	3	4	4	2	3	4	4	2	3	rs368469411		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:65960510G>T	ENST00000321892.4	+	27	8883	c.8822G>T	c.(8821-8823)cGt>cTt	p.R2941L	BPTF_ENST00000424123.3_Missense_Mutation_p.R2659L|BPTF_ENST00000335221.5_Missense_Mutation_p.R2798L|BPTF_ENST00000306378.6_Missense_Mutation_p.R2815L			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2941					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AGGGTGCTCCGTTCCTTACAG	0.458																																					p.R2815L		.											.	BPTF-94	0			c.G8444T						.						83	74	77					17																	65960510		2203	4300	6503	SO:0001583	missense	2186	exon25			TGCTCCGTTCCTT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"Zinc fingers, PHD-type"	3581	protein-coding gene	gene with protein product		601819	"fetal Alzheimer antigen"	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8822G>T	17.37:g.65960510G>T	ENSP00000315454:p.Arg2941Leu	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	153	14	NM_182641	0	0	1	1	0	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	37		.	.	.	.	.	.	.	.	.	.	G	16.21	3.057919	0.55325	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892;ENST00000342579	T;T;T	0.30448	1.53;1.53;1.53	5.65	5.65	0.86999	.	.	.	.	.	T	0.52435	0.1734	L	0.49455	1.56	0.80722	D	1	P;P;D;D	0.76494	0.587;0.872;0.999;0.999	B;P;D;D	0.80764	0.187;0.773;0.994;0.994	T	0.45190	-0.9278	9	0.49607	T	0.09	-6.4917	19.7202	0.96139	0.0:0.0:1.0:0.0	.	146;619;2815;2798	E9PE19;B4DJV8;Q12830-2;Q12830-4	.;.;.;.	L	2815;2798;2941;146	ENSP00000307208:R2815L;ENSP00000334351:R2798L;ENSP00000315454:R2941L	ENSP00000307208:R2815L	R	+	2	0	BPTF	63390972	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.807000	0.99171	2.660000	0.90430	0.555000	0.69702	CGT	.		0.458	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65960510	G	T	65960510	3	4	139	1	0	0	0	0	1	0	0	0	1498	1145	40	4	8928	4	BPTF	17	65960510	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	8231862	65960510	15234700	90	12385											
CBX4	8535	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	77807886	77807886	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttcgtcctgggcctcggctgGaggcttctccgccgtcgtgg	1	11	15	14	5	1	0	0	0	1	0	6	1	2	1	4	5	0	2	4	5	0	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:77807886G>C	ENST00000269397.4	-	5	1732	c.1555C>G	c.(1555-1557)Cca>Gca	p.P519A		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	519	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GCCTCGGCTGGAGGCTTCTCC	0.672																																					p.P519A		.											.	CBX4-228	0			c.C1555G						.						36	45	42					17																	77807886		2201	4296	6497	SO:0001583	missense	8535	exon5			CGGCTGGAGGCTT	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1555C>G	17.37:g.77807886G>C	ENSP00000269397:p.Pro519Ala	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	77	7	NM_003655	0	0	8	10	2	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	37	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	g	8.387	0.838920	0.16891	.	.	ENSG00000141582	ENST00000269397;ENST00000343048	.	.	.	3.16	3.16	0.36331	.	3.167460	0.02836	N	0.127360	T	0.20251	0.0487	N	0.11560	0.145	0.19575	N	0.999969	B	0.20261	0.043	B	0.17433	0.018	T	0.25152	-1.0140	9	0.12103	T	0.63	-14.3825	5.4008	0.16295	0.1115:0.0:0.6877:0.2008	.	519	O00257	CBX4_HUMAN	A	519;249	.	ENSP00000269397:P519A	P	-	1	0	CBX4	75422481	0.931000	0.31567	0.470000	0.27216	0.496000	0.33645	2.539000	0.45718	1.796000	0.52611	0.299000	0.19835	CCA	.		0.672	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		C	77807886	G	C	77807886	3	2	139	1	0	0	0	0	1	0	0	0	2726	1174	41	4	131	4	CBX4	17	77807886	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	11847376	77807886	3387324	91	12386											
AZI1	22994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79165083	79165083	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctcaatctccttgtcccggCctttccggatttcttccctc	3	15	6	17	2	3	0	1	0	2	0	8	1	6	1	5	2	0	1	5	2	1	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:79165083C>A	ENST00000269392.4	-	22	2931	c.2684G>T	c.(2683-2685)gGc>gTc	p.G895V	AZI1_ENST00000575907.1_Missense_Mutation_p.G859V|AZI1_ENST00000450824.2_Missense_Mutation_p.G892V|AZI1_ENST00000374782.3_Missense_Mutation_p.G856V	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		895					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CTTGTCCCGGCCTTTCCGGAT	0.667																																					p.G892V		.											.	AZI1-136	0			c.G2675T						.						84	79	81					17																	79165083		2203	4300	6503	SO:0001583	missense	22994	exon22			TCCCGGCCTTTCC																												ENST00000269392.4:c.2684G>T	17.37:g.79165083C>A	ENSP00000269392:p.Gly895Val	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	169	32	NM_014984	0	0	33	35	2	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		.	.	.	.	.	.	.	.	.	.	C	13.17	2.157738	0.38119	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.14266	2.52;2.55;2.52	4.37	0.923	0.19413	.	0.413716	0.23832	N	0.044131	T	0.06690	0.0171	L	0.29908	0.895	0.54753	D	0.999988	B;B;P;P	0.37122	0.218;0.135;0.583;0.583	B;B;B;B	0.32090	0.081;0.055;0.14;0.14	T	0.35992	-0.9766	10	0.41790	T	0.15	-20.1739	1.6764	0.02823	0.1712:0.4525:0.148:0.2282	.	892;895;856;892	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	V	892;856;895	ENSP00000393583:G892V;ENSP00000363914:G856V;ENSP00000269392:G895V	ENSP00000269392:G895V	G	-	2	0	AZI1	76779678	0.999000	0.42202	0.994000	0.49952	0.993000	0.82548	0.828000	0.27435	0.474000	0.27392	0.491000	0.48974	GGC	.		0.667	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			A	79165083	C	A	79165083	3	1	139	1	0	0	0	0	1	0	0	0	1241	739	26	4	587	4	AZI1	17	79165083	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	1357197	79165083	2030127	92	12387											
SERPINB3	6317	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	61322975	61322975	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aggaaagggtgattacaatgGaactcttcattagttgaagt	14	12	11	4	0	2	2	1	2	1	0	2	4	2	4	0	3	2	1	0	3	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr18:61322975G>C	ENST00000283752.5	-	8	1232	c.1089C>G	c.(1087-1089)ttC>ttG	p.F363L	SERPINB3_ENST00000332821.8_Missense_Mutation_p.F311L|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	363					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GATTACAATGGAACTCTTCAT	0.458																																					p.F363L													.	SERPINB3-228	0			c.C1089G						.						171	168	169					18																	61322975		2203	4300	6503	SO:0001583	missense	6317	exon8			ACAATGGAACTCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1089C>G	18.37:g.61322975G>C	ENSP00000283752:p.Phe363Leu	Somatic	281	2		WXS	Illumina HiSeq	Phase_I	186	72	NM_006919	0	0	0	0	0	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.657623	0.47467	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.87571	-2.27;-2.27	2.96	-2.58	0.06228	Serpin domain (3);Protease inhibitor I4, serpin, conserved site (1);	0.163773	0.28940	N	0.013642	D	0.82962	0.5151	M	0.74546	2.27	0.20403	N	0.999908	B;B	0.24651	0.02;0.108	B;B	0.28638	0.044;0.092	T	0.73372	-0.4003	10	0.62326	D	0.03	.	6.4823	0.22069	0.5376:0.1327:0.3296:0.0	.	311;363	P29508-2;P29508	.;SPB3_HUMAN	L	363;311	ENSP00000283752:F363L;ENSP00000329498:F311L	ENSP00000283752:F363L	F	-	3	2	SERPINB3	59473955	0.000000	0.05858	0.001000	0.08648	0.956000	0.61745	0.135000	0.15952	-0.655000	0.05387	0.449000	0.29647	TTC	.		0.458	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		C	61322975	G	C	61322975	3	2	139	1	0	0	0	0	1	0	0	0	14134	1165	41	4	87	4	SERPINB3	18	61322975	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		61322975	16754273	93	12388											
PGLYRP2	114770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15587343	15587343	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacgcagaagctgtgtgtctGgtcttggcagctggcacttt	6	12	13	10	1	2	1	0	0	2	1	2	1	2	1	0	3	2	5	0	3	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr19:15587343G>T	ENST00000340880.4	-	2	618	c.138C>A	c.(136-138)acC>acA	p.T46T	PGLYRP2_ENST00000292609.4_Silent_p.T46T	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	46			T -> A (in dbSNP:rs3813135). {ECO:0000269|PubMed:12975309}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CTGTGTGTCTGGTCTTGGCAG	0.587																																					p.T46T		.											.	PGLYRP2-93	0			c.C138A						.						50	47	48					19																	15587343		2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			GTGTCTGGTCTTG	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"peptidoglycan recognition protein L precursor", "peptidoglycan recognition protein-like", "N-acetylmuramoyl-L-alanine amidase"	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.138C>A	19.37:g.15587343G>T		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	123	19	NM_052890	0	0	0	0	0	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			.		0.587	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		T	15587343	G	T	15587343	2	4	139	1	0	0	0	0	0	0	0	1	11820	1335	47	4		4	PGLYRP2	19	15587343	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		15587343	43541640	94	12389											
GRAMD1A	57655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35512474	35512474	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcgctcattgagaagaactCgtggagcggcattgaagact	11	9	13	8	3	1	4	1	2	0	3	3	6	1	5	0	2	2	2	0	2	3	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr19:35512474C>T	ENST00000317991.5	+	14	1736	c.1544C>T	c.(1543-1545)tCg>tTg	p.S515L	GRAMD1A_ENST00000504615.2_Missense_Mutation_p.S281L|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.S602L|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.S508L|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	515						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GAGAAGAACTCGTGGAGCGGC	0.582																																					p.S515L		.											.	GRAMD1A-90	0			c.C1544T						.						70	73	72					19																	35512474		1948	4122	6070	SO:0001583	missense	57655	exon14			AGAACTCGTGGAG	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.1544C>T	19.37:g.35512474C>T	ENSP00000441032:p.Ser515Leu	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	95	24	NM_020895	0	1	74	102	27	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.182600	0.57800	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.22336	1.96;1.96;1.96	4.33	4.33	0.51752	.	0.086126	0.48767	D	0.000164	T	0.29458	0.0734	L	0.60455	1.87	0.42985	D	0.994471	D;P;D;D	0.62365	0.971;0.83;0.991;0.968	B;B;P;P	0.48873	0.439;0.086;0.539;0.593	T	0.07635	-1.0762	10	0.51188	T	0.08	.	14.3583	0.66752	0.0:1.0:0.0:0.0	.	515;515;281;508	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2	.;GRM1A_HUMAN;.;.	L	601;281;515;508	ENSP00000423728:S281L;ENSP00000441032:S515L;ENSP00000439267:S508L	ENSP00000441032:S515L	S	+	2	0	GRAMD1A	40204314	0.806000	0.28996	0.955000	0.39395	0.977000	0.68977	2.268000	0.43338	2.255000	0.74692	0.491000	0.48974	TCG	.		0.582	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		T	35512474	C	T	35512474	3	4	139	1	0	0	0	0	1	0	0	0	6768	893	31	1	1598	1	GRAMD1A	19	35512474	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	19925131	35512474	23616509	95	12390											
ZNF585B	92285	broad.mit.edu;bcgsc.ca	37	chr19	37680577	37680577	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcacctgggcagctgtgaCgtggcctctcaccctgcagt	6	9	11	15	1	2	1	2	1	1	0	3	1	2	1	3	2	2	3	3	2	0	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr19:37680577C>T	ENST00000532828.2	-	4	529	c.278G>A	c.(277-279)cGt>cAt	p.R93H	ZNF585B_ENST00000312908.5_5'Flank|ZNF585B_ENST00000586320.1_Missense_Mutation_p.R78H|ZNF585B_ENST00000527838.1_Missense_Mutation_p.R93H|ZNF585B_ENST00000531805.1_Missense_Mutation_p.R38H|CTC-454I21.3_ENST00000585860.2_Missense_Mutation_p.R93H	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	93	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GCAGCTGTGACGTGGCCTCTC	0.498																																					p.R93H	Melanoma(93;882 1454 18863 28917 48427)												.	ZNF585B-91	0			c.G278A						.						159	125	136					19																	37680577		2203	4300	6503	SO:0001583	missense	92285	exon4			CTGTGACGTGGCC	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"Zinc fingers, C2H2-type", "-"	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.278G>A	19.37:g.37680577C>T	ENSP00000433773:p.Arg93His	Somatic	270	0		WXS	Illumina HiSeq	Phase_I	186	8	NM_152279	0	0	0	0	0	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050057	0.19827	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000527838	T;T;T	0.09163	3.03;3.01;6.62	2.55	-1.74	0.08056	Krueppel-associated box (1);	1.911660	0.03152	N	0.168174	T	0.10937	0.0267	L	0.48218	1.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	10	0.33940	T	0.23	.	6.7578	0.23524	0.0:0.6143:0.0:0.3857	.	93	Q52M93	Z585B_HUMAN	H	38;93;93	ENSP00000436774:R38H;ENSP00000433773:R93H;ENSP00000435268:R93H	ENSP00000435268:R93H	R	-	2	0	ZNF585B	42372417	0.000000	0.05858	0.000000	0.03702	0.268000	0.26511	-0.529000	0.06186	-0.421000	0.07416	0.305000	0.20034	CGT	.		0.498	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		T	37680577	C	T	37680577	3	4	139	1	0	0	0	0	1	0	0	0	18050	536	19	1	2039	1	ZNF585B	19	37680577	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	2168103	37680577	21448406	96	12391											
AHCY	191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	32873337	32873337	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggttggtgaaggagttaCtcatcacgaagctggggtgg	8	10	16	7	1	2	1	2	1	0	0	2	3	2	2	1	6	2	3	1	6	3	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr20:32873337C>T	ENST00000217426.2	-	9	1153	c.1076G>A	c.(1075-1077)aGt>aAt	p.S359N	CTD-3216D2.5_ENST00000609218.1_RNA|AHCY_ENST00000538132.1_Missense_Mutation_p.S331N	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	359					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GAAGGAGTTACTCATCACGAA	0.587																																					p.S359N		.											.	AHCY-91	0			c.G1076A						.						91	78	82					20																	32873337		2203	4300	6503	SO:0001583	missense	191	exon9			GAGTTACTCATCA	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.1076G>A	20.37:g.32873337C>T	ENSP00000217426:p.Ser359Asn	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	140	27	NM_000687	0	0	163	182	19	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Missense_Mutation	SNP	ENST00000217426.2	37	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040615	0.93630	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	T;T	0.79033	-1.23;-1.23	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.88952	0.6577	H	0.96777	3.88	0.80722	D	1	P	0.48589	0.912	P	0.48524	0.58	D	0.92976	0.6402	10	0.87932	D	0	.	18.522	0.90956	0.0:1.0:0.0:0.0	.	359	P23526	SAHH_HUMAN	N	359;331	ENSP00000217426:S359N;ENSP00000442820:S331N	ENSP00000217426:S359N	S	-	2	0	AHCY	32336998	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.701000	0.84566	2.457000	0.83068	0.650000	0.86243	AGT	.		0.587	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		T	32873337	C	T	32873337	3	4	139	1	0	0	0	0	1	0	0	0	409	565	20	2	230	2	AHCY	20	32873337	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		32873337	30152183	97	12392											
SFRS6	6431	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	42089596	42089596	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgctacctgttccacccTcaaaggcccgttctgtgtcc	5	10	8	18	3	2	0	1	0	1	0	4	0	4	0	6	1	1	3	6	1	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr20:42089596T>G	ENST00000244020.3	+	6	1034	c.928T>G	c.(928-930)Tca>Gca	p.S310A		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	310	Arg/Ser-rich (RS domain).				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						TGTTCCACCCTCAAAGGCCCG	0.502																																					p.S310A													.	SRSF6-289	0			c.T928G						.						83	82	83					20																	42089596		2203	4300	6503	SO:0001583	missense	6431	exon6			CCACCCTCAAAGG	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.928T>G	20.37:g.42089596T>G	ENSP00000244020:p.Ser310Ala	Somatic	90	1		WXS	Illumina HiSeq	Phase_I	97	14	NM_006275	0	0	442	541	98	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	37	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.674496	0.29693	.	.	ENSG00000124193	ENST00000244020	T	0.38722	1.12	5.64	4.47	0.54385	.	0.467630	0.22589	N	0.058110	T	0.22589	0.0545	N	0.08118	0	0.39375	D	0.966157	B	0.15141	0.012	B	0.06405	0.002	T	0.08764	-1.0706	10	0.25751	T	0.34	.	11.8146	0.52202	0.0:0.0:0.1463:0.8537	.	310	Q13247	SRSF6_HUMAN	A	310	ENSP00000244020:S310A	ENSP00000244020:S310A	S	+	1	0	SRSF6	41523010	.	.	1.000000	0.80357	0.919000	0.55068	.	.	2.265000	0.75225	0.482000	0.46254	TCA	.		0.502	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		G	42089596	T	G	42089596	3	3	139	1	0	0	0	0	1	0	0	0	14213	1551	54	5	950	5	SFRS6	20	42089596	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	9216259	42089596	20935924	98	12393											
ZBP1	81030	broad.mit.edu;bcgsc.ca	37	chr20	56195329	56195329	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtactgtaccttctctgcccGggtcagcaggagcctgggcc	5	9	13	14	1	2	0	1	0	1	0	3	1	2	1	4	3	5	3	4	3	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr20:56195329G>A	ENST00000371173.3	-	1	200	c.23C>T	c.(22-24)cCg>cTg	p.P8L	ZBP1_ENST00000538947.1_5'UTR|ZBP1_ENST00000395822.3_Missense_Mutation_p.P8L|ZBP1_ENST00000340462.4_Missense_Mutation_p.P8L|ZBP1_ENST00000541799.1_Missense_Mutation_p.P8L|ZBP1_ENST00000343535.4_Missense_Mutation_p.P8L	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	8					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TTCTCTGCCCGGGTCAGCAGG	0.587																																					p.P8L													.	ZBP1-228	0			c.C23T						.						35	31	32					20																	56195329		2200	4298	6498	SO:0001583	missense	81030	exon1			CTGCCCGGGTCAG	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"DNA-dependent activator of IRFs"	606750	"chromosome 20 open reading frame 183"	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.23C>T	20.37:g.56195329G>A	ENSP00000360215:p.Pro8Leu	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	240	8	NM_001160419	0	0	0	0	0	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	G	1.396	-0.579487	0.03854	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.17370	3.34;2.28;3.35;3.27;2.96	3.23	-2.64	0.06114	Winged helix-turn-helix transcription repressor DNA-binding (1);	1.393840	0.04956	N	0.461273	T	0.08044	0.0201	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.24426	0.103;0.006;0.02;0.006	B;B;B;B	0.21360	0.034;0.002;0.003;0.002	T	0.33420	-0.9869	10	0.02654	T	1	-0.6611	8.1512	0.31141	0.7008:0.0:0.2992:0.0	.	8;8;8;8	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	L	8	ENSP00000360215:P8L;ENSP00000379167:P8L;ENSP00000344954:P8L;ENSP00000340584:P8L;ENSP00000440552:P8L	ENSP00000344954:P8L	P	-	2	0	ZBP1	55628735	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.330000	0.07925	-0.567000	0.06046	-1.141000	0.01876	CCG	.		0.587	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		A	56195329	G	A	56195329	3	1	139	1	0	0	0	0	1	0	0	0	17553	1116	39	1	1375	1	ZBP1	20	56195329	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	14105733	56195329	6830191	99	12394											
SMTN	6525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	31484747	31484747	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctgccatccgccgtgtacgGgctcaggagattgagggtat	7	9	15	10	3	1	2	1	1	0	1	2	3	2	2	3	3	2	4	3	3	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr22:31484747G>C	ENST00000347557.2	+	5	575	c.357G>C	c.(355-357)cgG>cgC	p.R119R	SMTN_ENST00000358743.1_Silent_p.R119R|SMTN_ENST00000333137.7_Silent_p.R119R	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	119					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						GCCGTGTACGGGCTCAGGAGA	0.632											OREG0026472	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R175R		.											.	SMTN-154	0			c.G525C						.						75	63	67					22																	31484747		2202	4300	6502	SO:0001819	synonymous_variant	6525	exon4			TGTACGGGCTCAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.357G>C	22.37:g.31484747G>C		Somatic	141	0	825	WXS	Illumina HiSeq	Phase_I	94	26	NM_001207018	0	0	4	7	3	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	37	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	G	5.557	0.287703	0.10513	.	.	ENSG00000183963	ENST00000438223	.	.	.	4.79	1.3	0.21679	.	.	.	.	.	T	0.43055	0.1230	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26744	-1.0094	4	.	.	.	-19.7875	1.9964	0.03457	0.2418:0.1338:0.4874:0.137	.	.	.	.	R	174	.	.	G	+	1	0	SMTN	29814747	1.000000	0.71417	0.975000	0.42487	0.527000	0.34593	0.687000	0.25407	0.543000	0.28864	0.655000	0.94253	GGC	.		0.632	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		C	31484747	G	C	31484747	2	2	139	1	0	0	0	0	0	0	0	1	14846	1219	43	4		4	SMTN	22	31484747	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		31484747	19819819	100	12395											
RAC2	5880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37627391	37627391	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggtgcccaccaggatgaTgggtgtgctggggcagtggt	5	10	18	8	0	0	1	0	1	0	0	0	2	0	2	2	6	2	2	2	6	0	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr22:37627391T>A	ENST00000249071.6	-	5	449	c.328A>T	c.(328-330)Atc>Ttc	p.I110F	RAC2_ENST00000405484.1_Missense_Mutation_p.I103F|RAC2_ENST00000406508.1_Missense_Mutation_p.I66F	NM_002872.3	NP_002863.1	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	110					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell projection assembly (GO:0030031)|G-protein coupled receptor signaling pathway (GO:0007186)|lymphocyte aggregation (GO:0071593)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|regulation of cell-substrate adhesion (GO:0010810)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of neutrophil migration (GO:1902622)|regulation of respiratory burst (GO:0060263)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	12					Dextromethorphan(DB00514)	ACCAGGATGATGGGTGTGCTG	0.632																																					p.I110F		.											.	RAC2-723	0			c.A328T						.						91	78	83					22																	37627391		2203	4300	6503	SO:0001583	missense	5880	exon5			GGATGATGGGTGT	M64595	CCDS13945.1	22q13.1	2014-09-17			ENSG00000128340	ENSG00000128340		"Endogenous ligands"	9802	protein-coding gene	gene with protein product		602049				2674130	Standard	NM_002872		Approved	EN-7	uc003arc.3	P15153	OTTHUMG00000150540	ENST00000249071.6:c.328A>T	22.37:g.37627391T>A	ENSP00000249071:p.Ile110Phe	Somatic	273	0		WXS	Illumina HiSeq	Phase_I	225	83	NM_002872	0	0	13	34	21	Q9UDJ4	Missense_Mutation	SNP	ENST00000249071.6	37	CCDS13945.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992414	0.74703	.	.	ENSG00000128340	ENST00000249071;ENST00000406508;ENST00000405484;ENST00000441619	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	4.98	4.98	0.66077	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	L	0.47190	1.495	0.80722	D	1	B	0.22746	0.074	B	0.36030	0.216	T	0.63554	-0.6611	10	0.22109	T	0.4	.	14.9666	0.71198	0.0:0.0:0.0:1.0	.	110	P15153	RAC2_HUMAN	F	110;66;103;110	ENSP00000249071:I110F;ENSP00000385270:I66F;ENSP00000385590:I103F;ENSP00000403778:I110F	ENSP00000249071:I110F	I	-	1	0	RAC2	35957337	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.003000	0.58678	0.459000	0.35465	ATC	.		0.632	RAC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318812.1			A	37627391	T	A	37627391	3	1	139	1	0	0	0	0	1	0	0	0	13007	1464	51	5	258	5	RAC2	22	37627391	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	6142644	37627391	13677175	101	12396											
SEPT6	23157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	118797595	118797595	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctccccttcgaatttggtgTtgaacagggtgtccatgagg	7	12	13	9	1	0	2	0	2	0	0	3	3	2	2	3	3	1	2	3	3	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chrX:118797595T>A	ENST00000343984.5	-	3	455	c.191A>T	c.(190-192)aAc>aTc	p.N64I	SEPT6_ENST00000394610.1_Missense_Mutation_p.N64I|SEPT6_ENST00000354228.4_Missense_Mutation_p.N64I|SEPT6_ENST00000394617.2_Missense_Mutation_p.N94I|SEPT6_ENST00000394616.4_Missense_Mutation_p.N6I|SEPT6_ENST00000489216.1_Missense_Mutation_p.N64I|SEPT6_ENST00000360156.7_Missense_Mutation_p.N64I|SEPT6_ENST00000354416.3_Missense_Mutation_p.N64I	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	64	Septin-type G.				cytokinesis (GO:0000910)|viral process (GO:0016032)	axon terminus (GO:0043679)|kinetochore (GO:0000776)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(3)	17						GAATTTGGTGTTGAACAGGGT	0.502			T	MLL	AML																																p.N64I		.		Dom	yes		X	Xq24	23157	septin 6		L	.	SEPT6-969	0			c.A191T						.						213	198	203					X																	118797595		2203	4300	6503	SO:0001583	missense	23157	exon3			TTGGTGTTGAACA	D50918	CCDS14583.1, CCDS14584.1, CCDS14585.1	Xq24	2013-01-21			ENSG00000125354	ENSG00000125354		"Septins"	15848	protein-coding gene	gene with protein product		300683				8590280, 10744683	Standard	NM_015129		Approved	KIAA0128, SEP2, SEPT2, MGC16619, MGC20339	uc004erv.3	Q14141	OTTHUMG00000022280	ENST00000343984.5:c.191A>T	X.37:g.118797595T>A	ENSP00000341524:p.Asn64Ile	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	87	9	NM_145802	0	0	2	4	2	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Missense_Mutation	SNP	ENST00000343984.5	37	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	t	21.9	4.214865	0.79352	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394616;ENST00000394617;ENST00000520510	T;T;T;T;T;T;D;T	0.81739	1.28;1.28;1.28;1.28;1.28;1.28;-1.53;1.28	4.47	4.47	0.54385	.	0.081767	0.85682	D	0.000000	D	0.91415	0.7291	H	0.94925	3.6	0.80722	D	1	D;P;D;D	0.60575	0.973;0.922;0.961;0.988	P;P;P;D	0.67548	0.894;0.908;0.864;0.952	D	0.93282	0.6661	10	0.72032	D	0.01	.	12.648	0.56746	0.0:0.0:0.0:1.0	.	94;6;64;64	F5H1J5;B4E049;Q14141;Q548C9	.;.;SEPT6_HUMAN;.	I	64;64;64;64;64;64;6;94;64	ENSP00000353278:N64I;ENSP00000346169:N64I;ENSP00000418715:N64I;ENSP00000346397:N64I;ENSP00000378108:N64I;ENSP00000341524:N64I;ENSP00000378114:N6I;ENSP00000378115:N94I	ENSP00000341524:N64I	N	-	2	0	SEPT6	118681623	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.649000	0.83500	1.736000	0.51660	0.483000	0.47432	AAC	.		0.502	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802		A	118797595	T	A	118797595	3	1	139	1	0	0	0	0	1	0	0	0	14100	1725	60	5	1167	5	SEPT6	23	118797595	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10		118797595	36472965	102	12397											
FATE1	89885	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	150889896	150889896	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgccaaagcccagaatgctGagagaatcaggccatgggga	13	5	13	10	0	1	3	1	1	0	2	1	5	1	4	3	3	3	1	3	3	3	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chrX:150889896G>A	ENST00000370350.3	+	3	349	c.264G>A	c.(262-264)ctG>ctA	p.L88L		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	88						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGAATGCTGAGAGAATCAG	0.542																																					p.L88L													.	FATE1-131	0			c.G264A						.						94	79	84					X																	150889896		2203	4300	6503	SO:0001819	synonymous_variant	89885	exon3			AATGCTGAGAGAA	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.264G>A	X.37:g.150889896G>A		Somatic	391	1		WXS	Illumina HiSeq	Phase_I	270	39	NM_033085	0	0	0	0	0		Silent	SNP	ENST00000370350.3	37	CCDS14700.1																																																																																			.		0.542	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085		A	150889896	G	A	150889896	2	1	139	1	0	0	0	0	0	0	0	1	5712	1277	45	2		2	FATE1	23	150889896	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	32092301	150889896	4380664	103	12398											
RSC1A1	6248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15987648	15987648	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcagtggagacagaaaaaTtaacaggtacttcatctgac	16	10	8	7	0	3	3	2	1	1	2	3	4	3	3	0	2	2	1	0	2	5	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:15987648T>C	ENST00000345034.1	+	1	1285	c.1285T>C	c.(1285-1287)Tta>Cta	p.L429L	DDI2_ENST00000480945.1_3'UTR	NM_006511.1	NP_006502.1	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1, member 1	429					intestinal absorption (GO:0050892)|negative regulation of transport (GO:0051051)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	brush border (GO:0005903)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel inhibitor activity (GO:0008200)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)	11		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GACAGAAAAATTAACAGGTAC	0.433																																					p.L429L		.											.	RSC1A1-91	0			c.T1285C						.						51	51	51					1																	15987648		2203	4300	6503	SO:0001819	synonymous_variant	6248	exon1			GAAAAATTAACAG	BN000122, X82877	CCDS161.1	1p36.1	1998-08-25			ENSG00000215695	ENSG00000215695			10458	protein-coding gene	gene with protein product		601966					Standard	NM_006511		Approved	RS1	uc010obn.2	Q92681	OTTHUMG00000067830	ENST00000345034.1:c.1285T>C	1.37:g.15987648T>C		Somatic	87	1		WXS	Illumina HiSeq	Phase_I	74	34	NM_006511	0	0	1	3	2	B2RBP5	Silent	SNP	ENST00000345034.1	37	CCDS161.1																																																																																			.		0.433	RSC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145500.1	NM_006511		C	15987648	T	C	15987648	2	2	140	1	0	0	0	0	0	0	0	1	13730	1490	52	3		3	RSC1A1	1	15987648	Silent	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		15987648	233262973	1	12399											
NCDN	23154	hgsc.bcm.edu	37	chr1	36026434	36026444	+	Frame_Shift_Del	DEL	GATTTCCAGAA	GATTTCCAGAA	-																															tgttgcggggcctcagtgagGatttccagaaagctgaggat																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	GATTTCCAGAA	GATTTCCAGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:36026434_36026444delGATTTCCAGAA	ENST00000373243.2	+	3	1065_1075	c.682_692delGATTTCCAGAA	c.(682-693)gatttccagaaafs	p.DFQK228fs	NCDN_ENST00000356090.4_Frame_Shift_Del_p.DFQK228fs|NCDN_ENST00000459931.1_3'UTR|NCDN_ENST00000373253.3_Frame_Shift_Del_p.DFQK211fs	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	228					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCTCAGTGAGGATTTCCAGAAAGCTGAGGAT	0.654																																					p.228_231del		.											.	NCDN-155	0			c.682_692del						.																																			SO:0001589	frameshift_variant	23154	exon3			.	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.682_692delGATTTCCAGAA	1.37:g.36026434_36026444delGATTTCCAGAA	ENSP00000362340:p.Asp228fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	60	20	NM_014284	0	0	0	0	0	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Frame_Shift_Del	DEL	ENST00000373243.2	37	CCDS392.1																																																																																			.		0.654	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		-	36026444	GATTTCCAGAA	-	36026434	7	5	140	1	0	1	0	1	0	0	0	0	10240	1174	41	0	692	0	NCDN	1	36026434	Frame_Shift_Del	DEL	GATTTCCAGAA	TCGA-IZ-8195-01A-31D-2396-08	20038786	36026434	213224187	2	12400											
PGM1	5236	hgsc.bcm.edu;broad.mit.edu	37	chr1	64117371	64117371	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggaggtggaagctgagggcGcaaacaaaatgatgaaggac	16	4	16	5	1	0	3	0	3	0	0	0	6	0	6	0	5	2	2	0	5	5	0	rs201303497		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:64117371G>A	ENST00000371084.3	+	9	1525	c.1312G>A	c.(1312-1314)Gca>Aca	p.A438T	PGM1_ENST00000540265.1_Missense_Mutation_p.A241T|PGM1_ENST00000483707.1_3'UTR|PGM1_ENST00000371083.4_Missense_Mutation_p.A456T	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	438					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						AGCTGAGGGCGCAAACAAAAT	0.512													G|||	1	0.000199681	8e-04	0	5008	,	,		17958	0		0	False		,,,				2504	0				p.A456T		.											.	PGM1-228	0			c.G1366A						.						136	130	132					1																	64117371		2203	4300	6503	SO:0001583	missense	5236	exon9			GAGGGCGCAAACA	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1312G>A	1.37:g.64117371G>A	ENSP00000360125:p.Ala438Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	42	3	NM_001172818	0	0	139	139	0	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	27.4	4.830886	0.91036	.	.	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	T;T;T	0.49139	0.79;0.79;0.79	5.69	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.64768	0.2628	M	0.92555	3.32	0.47037	D	0.999295	D;P	0.76494	0.999;0.94	P;B	0.57776	0.827;0.306	T	0.75422	-0.3323	10	0.56958	D	0.05	-42.0023	15.1823	0.72968	0.0679:0.0:0.9321:0.0	.	456;438	P36871-2;P36871	.;PGM1_HUMAN	T	414;438;241;456	ENSP00000360125:A438T;ENSP00000443449:A241T;ENSP00000360124:A456T	ENSP00000360124:A456T	A	+	1	0	PGM1	63889959	1.000000	0.71417	0.265000	0.24526	0.910000	0.53928	9.813000	0.99286	1.540000	0.49301	0.655000	0.94253	GCA	G|0.999;A|0.000		0.512	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633		A	64117371	G	A	64117371	3	1	140	1	0	0	0	0	1	0	0	0	11823	1087	38	1	1650	1	PGM1	1	64117371	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	28090937	64117371	185133250	3	12401											
AMY1A	276	hgsc.bcm.edu	37	chr1	104203011	104203011	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggttggggtttcatgcCttctgacagagcgcttgtct	7	13	13	8	1	3	3	1	1	2	2	3	3	3	3	1	3	2	3	1	3	1	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:104203011C>T	ENST00000370083.4	+	7	1128	c.908C>T	c.(907-909)cCt>cTt	p.P303L		NM_001008221.1|NM_004038.3	NP_001008222.1|NP_004029.2	P04745	AMY1_HUMAN	amylase, alpha 1A (salivary)	303					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)						all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)		GGTTTCATGCCTTCTGACAGA	0.423																																					p.P303L	Pancreas(131;743 2392 43382 44986)	.											.	.	0			c.C908T						.						13	14	13					1																	104203011		1525	3443	4968	SO:0001583	missense	276	exon7			TCATGCCTTCTGA		CCDS30782.1	1p21	2012-10-02	2007-05-03		ENSG00000237763	ENSG00000237763	3.2.1.1		474	protein-coding gene	gene with protein product		104700	"amylase, alpha 1A; salivary"	AMY1			Standard	XM_005270755		Approved		uc001duv.3	P04745	OTTHUMG00000011020	ENST00000370083.4:c.908C>T	1.37:g.104203011C>T	ENSP00000359100:p.Pro303Leu	Somatic	667	1		WXS	Illumina HiSeq	Phase_I	547	106	NM_001008221	0	0	0	0	0	A6NJS5|A8K8H6|Q13763|Q5T083	Missense_Mutation	SNP	ENST00000370083.4	37	CCDS30782.1	.	.	.	.	.	.	.	.	.	.	c	16.08	3.022827	0.54683	.	.	ENSG00000237763	ENST00000370083	D	0.98012	-4.66	2.38	2.38	0.29361	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.177118	0.51477	D	0.000100	D	0.97461	0.9169	.	.	.	0.80722	D	1	D	0.54772	0.968	P	0.56648	0.803	D	0.97391	0.9989	9	0.87932	D	0	.	12.3897	0.55352	0.0:1.0:0.0:0.0	.	303	P04745	AMY1_HUMAN	L	303	ENSP00000359100:P303L	ENSP00000359100:P303L	P	+	2	0	AMY1A	104004534	1.000000	0.71417	0.993000	0.49108	0.426000	0.31534	5.529000	0.67135	1.150000	0.42419	0.184000	0.17185	CCT	.		0.423	AMY1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030304.2	NM_001008221		T	104203011	C	T	104203011	3	4	140	1	0	0	0	0	1	0	0	0	591	681	24	2	930	2	AMY1A	1	104203011	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	40085640	104203011	145047610	4	12402											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109792762	109792762	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgccgccgctgctgctgctgTtgctgctgctgctgccgccg	0	10	14	17	5	0	0	0	0	0	0	0	0	0	0	4	0	8	9	4	0	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:109792762T>C	ENST00000271332.3	+	1	122	c.61T>C	c.(61-63)Ttg>Ctg	p.L21L		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	21					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		gctgctgctgttgctgctgct	0.746																																					p.L21L	NSCLC(158;1285 2011 34800 34852 42084)	.											.	CELSR2-526	0			c.T61C						.						9	11	11					1																	109792762		1973	3925	5898	SO:0001819	synonymous_variant	1952	exon1			CTGCTGTTGCTGC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.61T>C	1.37:g.109792762T>C		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001408	0	0	0	12	12	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			.		0.746	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		C	109792762	T	C	109792762	2	2	140	1	0	0	0	0	0	0	0	1	3228	1722	60	3		3	CELSR2	1	109792762	Silent	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	5589751	109792762	139457859	5	12403											
CAPZA1	829	hgsc.bcm.edu	37	chr1	113202331	113202331	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgttttaataggaatggtcGttggagatcagagtggaagt	11	13	15	2	1	1	2	1	0	0	2	2	5	1	4	0	4	0	2	0	4	4	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:113202331G>A	ENST00000263168.3	+	7	1187	c.515G>A	c.(514-516)cGt>cAt	p.R172H	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	172					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGAATGGTCGTTGGAGATCA	0.438																																					p.R172H		.											.	CAPZA1-514	0			c.G515A						.						95	88	91					1																	113202331		2203	4300	6503	SO:0001583	missense	829	exon7			ATGGTCGTTGGAG	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.515G>A	1.37:g.113202331G>A	ENSP00000263168:p.Arg172His	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	37	3	NM_006135	0	0	0	0	0	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	37	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	G	36	5.611435	0.96637	.	.	ENSG00000116489	ENST00000263168	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.73908	0.3647	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.72600	-0.4244	9	0.48119	T	0.1	-28.1951	19.3394	0.94335	0.0:0.0:1.0:0.0	.	172	P52907	CAZA1_HUMAN	H	172	.	ENSP00000263168:R172H	R	+	2	0	CAPZA1	113003854	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.776000	0.99001	2.739000	0.93911	0.655000	0.94253	CGT	.		0.438	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		A	113202331	G	A	113202331	3	1	140	1	0	0	0	0	1	0	0	0	2646	1145	40	1	541	1	CAPZA1	1	113202331	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	3409569	113202331	136048290	6	12404											
KIAA1614	57710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	180885553	180885553	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acagggagtgagtccctgctCtgcttcccaagagtggtcat	8	10	12	11	0	2	2	1	1	1	1	4	3	4	3	2	2	2	2	2	2	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:180885553C>T	ENST00000367588.4	+	2	369	c.314C>T	c.(313-315)tCt>tTt	p.S105F		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	105										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						AGTCCCTGCTCTGCTTCCCAA	0.587																																					p.S105F		.											.	KIAA1614-26	0			c.C314T						.						80	89	86					1																	180885553		2038	4181	6219	SO:0001583	missense	57710	exon2			CCTGCTCTGCTTC	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.314C>T	1.37:g.180885553C>T	ENSP00000356560:p.Ser105Phe	Somatic	162	0		WXS	Illumina HiSeq	Phase_I	108	44	NM_020950	0	0	1	3	2	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050241	0.19827	.	.	ENSG00000135835	ENST00000367588	T	0.05580	3.42	4.87	1.69	0.24217	.	1.482150	0.04336	N	0.353230	T	0.03695	0.0105	N	0.08118	0	0.29690	N	0.841037	B	0.23735	0.09	B	0.20955	0.032	T	0.40905	-0.9538	9	0.37606	T	0.19	-0.5476	3.0596	0.06195	0.2088:0.5355:0.0:0.2557	.	105	Q5VZ46	K1614_HUMAN	F	105	ENSP00000356560:S105F	ENSP00000356560:S105F	S	+	2	0	KIAA1614	179152176	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.043000	0.13971	0.143000	0.18926	0.655000	0.94253	TCT	.		0.587	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		T	180885553	C	T	180885553	3	4	140	1	0	0	0	0	1	0	0	0	8269	913	32	2	320	2	KIAA1614	1	180885553	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	67683222	180885553	68365068	7	12405											
C1orf25	81627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	185094118	185094118	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcatgaattgaaaactgacTttgaggcgtacactctgatt	12	13	9	7	1	1	5	0	5	1	0	1	5	1	5	0	1	3	2	0	1	4	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:185094118T>A	ENST00000367506.5	-	12	1985	c.1717A>T	c.(1717-1719)Agt>Tgt	p.S573C	TRMT1L_ENST00000367504.3_3'UTR	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	573	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.				adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						GAAAACTGACTTTGAGGCGTA	0.358																																					p.S573C		.											.	TRMT1L-92	0			c.A1717T						.						143	134	137					1																	185094118		2203	4300	6503	SO:0001583	missense	81627	exon12			ACTGACTTTGAGG	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.1717A>T	1.37:g.185094118T>A	ENSP00000356476:p.Ser573Cys	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	112	42	NM_030934	0	0	12	17	5	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Missense_Mutation	SNP	ENST00000367506.5	37	CCDS1366.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.575763	0.65878	.	.	ENSG00000121486	ENST00000367506;ENST00000458395	.	.	.	4.79	4.79	0.61399	.	0.178960	0.64402	D	0.000016	T	0.44829	0.1312	N	0.08118	0	0.80722	D	1	D	0.56287	0.975	P	0.53689	0.732	T	0.49818	-0.8899	9	0.38643	T	0.18	-18.1595	14.6174	0.68558	0.0:0.0:0.0:1.0	.	573	Q7Z2T5	TRM1L_HUMAN	C	573;197	.	ENSP00000356476:S573C	S	-	1	0	TRMT1L	183360741	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.348000	0.73009	1.935000	0.56089	0.477000	0.44152	AGT	.		0.358	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		A	185094118	T	A	185094118	3	1	140	1	0	0	0	0	1	0	0	0	2040	1609	56	5	500	5	C1orf25	1	185094118	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	4208565	185094118	64156503	8	12406											
CABC1	56997	hgsc.bcm.edu	37	chr1	227169815	227169815	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctctgcaaggtgcgtggtgCggcactcaagctgggccaga	7	7	16	11	2	2	1	1	0	1	1	2	1	2	1	1	4	4	4	1	4	2	0	rs368872986		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:227169815C>T	ENST00000366779.1	+	11	3589	c.818C>T	c.(817-819)gCg>gTg	p.A273V	ADCK3_ENST00000458507.2_5'UTR|ADCK3_ENST00000366777.3_Missense_Mutation_p.A273V|ADCK3_ENST00000366778.1_Missense_Mutation_p.A221V|ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000433743.2_5'UTR			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	273					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						GTGCGTGGTGCGGCACTCAAG	0.682																																					p.A273V		.											.	ADCK3-361	0			c.C818T						.	C	VAL/ALA	0,4400		0,0,2200	25	23	24		818	5.1	0.9	1		24	1,8591		0,1,4295	no	missense	ADCK3	NM_020247.4	64	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	273/648	227169815	1,12991	2200	4296	6496	SO:0001583	missense	56997	exon6			GTGGTGCGGCACT	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"coenzyme Q8 homolog (yeast)"	606980	"chaperone-ABC1 (activity of bc1 complex, S.pombe)-like", "chaperone, ABC1 activity of bc1 complex like (S. pombe)", "chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.818C>T	1.37:g.227169815C>T	ENSP00000355741:p.Ala273Val	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_020247	0	0	26	26	0	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Missense_Mutation	SNP	ENST00000366779.1	37	CCDS1557.1	.	.	.	.	.	.	.	.	.	.	C	33	5.203948	0.95033	0.0	1.16E-4	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000366775;ENST00000405743	T;T;T;T;T	0.76316	-0.88;-0.86;-0.88;-1.01;-1.0	5.1	5.1	0.69264	.	0.052474	0.85682	D	0.000000	D	0.89480	0.6727	M	0.89968	3.075	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	D	0.91390	0.5134	10	0.59425	D	0.04	-27.9144	18.4947	0.90861	0.0:1.0:0.0:0.0	.	273	Q8NI60	ADCK3_HUMAN	V	273;221;273;198;118;224	ENSP00000355741:A273V;ENSP00000355740:A221V;ENSP00000355739:A273V;ENSP00000355738:A198V;ENSP00000355737:A118V	ENSP00000355737:A118V	A	+	2	0	ADCK3	225236438	1.000000	0.71417	0.941000	0.38009	0.495000	0.33615	7.705000	0.84606	2.378000	0.81104	0.491000	0.48974	GCG	.		0.682	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247		T	227169815	C	T	227169815	3	4	140	1	0	0	0	0	1	0	0	0	2533	768	27	1	836	1	CABC1	1	227169815	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	42075697	227169815	22080806	9	12407											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228539078	228539078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagttccagacactgagtgAgcctcgcagcggcctgctag	9	7	12	13	2	0	3	0	2	0	1	2	3	1	3	3	1	3	3	3	1	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:228539078A>G	ENST00000422127.1	+	78	18520	c.18476A>G	c.(18475-18477)gAg>gGg	p.E6159G	OBSCN_ENST00000366707.4_Missense_Mutation_p.E3793G|OBSCN_ENST00000570156.2_Missense_Mutation_p.E7116G|OBSCN_ENST00000284548.11_Missense_Mutation_p.E6159G|OBSCN_ENST00000366709.4_Missense_Mutation_p.E3278G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6159	Ig-like 53.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACACTGAGTGAGCCTCGCAGC	0.652																																					p.E7116G		.											.	OBSCN-403	0			c.A21347G						.						30	37	35					1																	228539078		2092	4188	6280	SO:0001583	missense	84033	exon89			TGAGTGAGCCTCG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18476A>G	1.37:g.228539078A>G	ENSP00000409493:p.Glu6159Gly	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	9	2	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.86|19.86	3.904910|3.904910	0.72868|0.72868	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709|ENST00000441106	T;T;T;T|.	0.69306|.	-0.39;-0.39;-0.39;-0.39|.	5.34|5.34	5.34|5.34	0.76211|0.76211	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.227351|.	0.34628|.	N|.	0.003818|.	T|.	0.59432|.	0.2193|.	L|L	0.39147|0.39147	1.195|1.195	0.53005|0.53005	D|D	0.999969|0.999969	D;D|.	0.56968|.	0.978;0.973|.	P;P|.	0.51974|.	0.686;0.559|.	T|.	0.56463|.	-0.7975|.	10|.	0.54805|.	T|.	0.06|.	.|.	15.305|15.305	0.73985|0.73985	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	6159;6159|.	Q5VST9;Q5VST9-3|.	OBSCN_HUMAN;.|.	G|W	6159;6159;3793;3278|775	ENSP00000284548:E6159G;ENSP00000409493:E6159G;ENSP00000355668:E3793G;ENSP00000355670:E3278G|.	ENSP00000284548:E6159G|.	E|X	+|+	2|3	0|0	OBSCN|OBSCN	226605701|226605701	1.000000|1.000000	0.71417|0.71417	0.912000|0.912000	0.35992|0.35992	0.006000|0.006000	0.05464|0.05464	8.760000|8.760000	0.91671|0.91671	2.040000|2.040000	0.60383|0.60383	0.402000|0.402000	0.26972|0.26972	GAG|TGA	.		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228539078	A	G	228539078	3	3	140	1	0	0	0	0	1	0	0	0	10838	304	11	3	18782	3	OBSCN	1	228539078	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	1369263	228539078	20711543	10	12408											
C1orf150	148823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247737622	247737622	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatgcccttcttaggactTctgttagtaggccttgttcc	7	16	8	10	0	2	0	0	0	2	0	3	1	3	1	3	2	1	3	3	2	5	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:247737622T>C	ENST00000366488.4	+	5	450	c.346T>C	c.(346-348)Tct>Cct	p.S116P	GCSAML_ENST00000527541.1_Missense_Mutation_p.S84P|GCSAML_ENST00000536561.1_Missense_Mutation_p.S96P|GCSAML_ENST00000366491.2_Missense_Mutation_p.S96P|RP11-978I15.10_ENST00000446347.1_RNA|GCSAML_ENST00000527084.1_Missense_Mutation_p.S84P|RP11-978I15.10_ENST00000435333.1_RNA|GCSAML_ENST00000463359.1_Missense_Mutation_p.S84P|GCSAML_ENST00000366489.1_Missense_Mutation_p.S96P	NM_001281836.1|NM_001281837.1|NM_001281853.1|NM_145278.3	NP_001268765.1|NP_001268766.1|NP_001268782.1|NP_660321.1	Q5JQS6	GSAML_HUMAN	germinal center-associated, signaling and motility-like	116																	TCTTAGGACTTCTGTTAGTAG	0.433																																					p.S116P		.											.	.	0			c.T346C						.						154	129	137					1																	247737622		2203	4300	6503	SO:0001583	missense	148823	exon5			AGGACTTCTGTTA	AK126682	CCDS1635.1, CCDS60470.1, CCDS73058.1	1q44	2012-08-23	2012-08-23	2012-08-23	ENSG00000169224	ENSG00000169224			29583	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 150"	C1orf150			Standard	NM_001281834		Approved	FLJ44728	uc001idf.3	Q5JQS6	OTTHUMG00000040648	ENST00000366488.4:c.346T>C	1.37:g.247737622T>C	ENSP00000355444:p.Ser116Pro	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	89	36	NM_145278	0	0	0	0	0	B2R4Y5|B3KX46|Q5JQT3	Missense_Mutation	SNP	ENST00000366488.4	37	CCDS1635.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.350166	0.24512	.	.	ENSG00000169224	ENST00000527084;ENST00000527541;ENST00000366491;ENST00000366489;ENST00000463359;ENST00000366488;ENST00000536561	.	.	.	3.91	2.73	0.32206	.	1.484660	0.04639	N	0.405118	T	0.28830	0.0715	L	0.34521	1.04	0.09310	N	1	P	0.47677	0.899	P	0.45099	0.469	T	0.12091	-1.0561	9	0.02654	T	1	-1.0246	7.2357	0.26067	0.0:0.0:0.2272:0.7728	.	116	Q5JQS6	CA150_HUMAN	P	84;84;96;96;84;116;96	.	ENSP00000355444:S116P	S	+	1	0	C1orf150	245804245	0.001000	0.12720	0.001000	0.08648	0.338000	0.28826	0.818000	0.27295	0.638000	0.30545	0.482000	0.46254	TCT	.		0.433	GCSAML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097745.4	NM_145278		C	247737622	T	C	247737622	3	2	140	1	0	0	0	0	1	0	0	0	2010	1783	62	3	364	3	C1orf150	1	247737622	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	19198544	247737622	1512999	11	12409											
OR2M2	391194	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	248344277	248344277	+	Frame_Shift_Del	DEL	A	A	-																															gctaaattcttctttctaatAtccatctttttctatgatgt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:248344277delA	ENST00000359682.2	+	1	990	c.990delA	c.(988-990)atafs	p.I330fs		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	330						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCTTTCTAATATCCATCTTTT	0.318																																					p.I330fs		.											.	OR2M2-72	0			c.990delA						.						164	175	171					1																	248344277		2203	4300	6503	SO:0001589	frameshift_variant	391194	exon1			.	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"GPCR / Class A : Olfactory receptors"	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.990delA	1.37:g.248344277delA	ENSP00000352710:p.Ile330fs	Somatic	201	0		WXS	Illumina HiSeq	Phase_I	166	49	NM_001004688	0	0	0	0	0	A3KFT4	Frame_Shift_Del	DEL	ENST00000359682.2	37	CCDS31106.1																																																																																			.		0.318	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		-	248344277	A	-	248344277	7	5	140	1	0	1	0	1	0	0	0	0	11036	439	16	0	992	0	OR2M2	1	248344277	Frame_Shift_Del	DEL	A	TCGA-IZ-8195-01A-31D-2396-08	606655	248344277	906344	12	12410											
ASAP2	8853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	9528579	9528579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatcttgcagaatgagactTacggagccctcctgagtggc	9	9	12	11	1	1	3	0	2	1	2	2	5	2	4	2	2	3	2	2	2	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:9528579T>C	ENST00000281419.3	+	22	2627	c.2287T>C	c.(2287-2289)Tac>Cac	p.Y763H	ASAP2_ENST00000315273.4_Missense_Mutation_p.Y763H|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	763					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						GAATGAGACTTACGGAGCCCT	0.597																																					p.Y763H		.											.	ASAP2-90	0			c.T2287C						.						45	50	48					2																	9528579		2203	4300	6503	SO:0001583	missense	8853	exon22			GAGACTTACGGAG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2287T>C	2.37:g.9528579T>C	ENSP00000281419:p.Tyr763His	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	49	22	NM_001135191	0	0	0	0	0	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	37	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806023	0.70682	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.57436	0.41;0.4	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.66137	0.2759	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.915	T	0.61724	-0.7004	10	0.23891	T	0.37	.	15.7424	0.77910	0.0:0.0:0.0:1.0	.	763;763	O43150-2;O43150	.;ASAP2_HUMAN	H	763	ENSP00000281419:Y763H;ENSP00000316404:Y763H	ENSP00000281419:Y763H	Y	+	1	0	ASAP2	9446030	1.000000	0.71417	0.081000	0.20488	0.971000	0.66376	7.614000	0.82996	2.118000	0.64928	0.459000	0.35465	TAC	.		0.597	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9528579	T	C	9528579	3	2	140	1	0	0	0	0	1	0	0	0	1012	1754	61	3	2373	3	ASAP2	2	9528579	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		9528579	233670794	13	12411											
SLC4A1AP	22950	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27888159	27888159	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatgggttgcacctggggaAtgggtaagaaattaaaattg	14	10	14	3	0	0	2	0	0	0	2	0	3	0	3	1	4	1	3	1	4	5	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:27888159A>G	ENST00000326019.6	+	2	1300	c.1018A>G	c.(1018-1020)Atg>Gtg	p.M340V	SUPT7L_ENST00000337768.5_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000405491.1_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	340						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					CACCTGGGGAATGGGTAAGAA	0.388																																					p.M340V		.											.	SLC4A1AP-90	0			c.A1018G						.						133	138	136					2																	27888159		2203	4300	6503	SO:0001583	missense	22950	exon2			TGGGGAATGGGTA		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"lung cancer oncogene 3"	602655	"solute carrier family 4 (anion exchanger), member 1, adapter protein"			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.1018A>G	2.37:g.27888159A>G	ENSP00000323837:p.Met340Val	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	120	56	NM_018158	0	0	0	0	0	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Missense_Mutation	SNP	ENST00000326019.6	37	CCDS33166.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135945	0.77662	.	.	ENSG00000163798	ENST00000326019	T	0.51574	0.7	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.58921	0.2156	M	0.84948	2.725	0.80722	D	1	P	0.42010	0.768	B	0.43386	0.418	T	0.67821	-0.5571	10	0.72032	D	0.01	-17.2495	15.2303	0.73383	1.0:0.0:0.0:0.0	.	340	Q9BWU0	NADAP_HUMAN	V	340	ENSP00000323837:M340V	ENSP00000323837:M340V	M	+	1	0	SLC4A1AP	27741663	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.617000	0.74210	1.995000	0.58328	0.379000	0.24179	ATG	.		0.388	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158		G	27888159	A	G	27888159	3	3	140	1	0	0	0	0	1	0	0	0	14685	101	4	3	1024	3	SLC4A1AP	2	27888159	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	18359580	27888159	215311214	14	12412											
GPR75	10936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	54080607	54080607	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggagataacatgtaggcAgagtttgtttcatgatggga	11	14	13	3	0	1	3	1	1	0	2	1	5	1	4	0	3	1	4	0	3	2	5			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:54080607A>G	ENST00000394705.2	-	2	1557	c.1287T>C	c.(1285-1287)tcT>tcC	p.S429S	GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	429					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of neuron death (GO:1901214)	integral component of plasma membrane (GO:0005887)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			ACATGTAGGCAGAGTTTGTTT	0.448																																					p.S429S		.											.	GPR75-92	0			c.T1287C						.						122	122	122					2																	54080607		2203	4300	6503	SO:0001819	synonymous_variant	10936	exon2			GTAGGCAGAGTTT	AF101472	CCDS1849.1	2p16	2012-08-21			ENSG00000119737	ENSG00000119737		"GPCR / Class A : Orphans"	4526	protein-coding gene	gene with protein product		606704				10381362	Standard	NM_006794		Approved	WI-31133	uc002rxo.3	O95800	OTTHUMG00000129280	ENST00000394705.2:c.1287T>C	2.37:g.54080607A>G		Somatic	303	0		WXS	Illumina HiSeq	Phase_I	190	49	NM_006794	0	0	0	0	0	B2RC02|Q6NWR2	Silent	SNP	ENST00000394705.2	37	CCDS1849.1																																																																																			.		0.448	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2			G	54080607	A	G	54080607	2	3	140	1	0	0	0	0	0	0	0	1	6728	175	7	3		3	GPR75	2	54080607	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	26192448	54080607	189118766	15	12413											
USP39	10713	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	85875075	85875075	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacaggcaaatggtatgaatTacaagacctccaggtgactg	14	8	11	8	0	0	3	0	2	0	1	1	4	1	3	2	3	1	2	2	3	5	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:85875075T>G	ENST00000323701.6	+	12	1596	c.1586T>G	c.(1585-1587)tTa>tGa	p.L529*	USP39_ENST00000409766.3_Missense_Mutation_p.Y484D|USP39_ENST00000450066.2_Nonsense_Mutation_p.L426*|USP39_ENST00000459775.1_3'UTR|USP39_ENST00000409025.1_Intron|USP39_ENST00000409470.1_Nonsense_Mutation_p.L529*	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	529	USP.				cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						TGGTATGAATTACAAGACCTC	0.478																																					p.L529X		.											.	USP39-658	0			c.T1586G						.						98	91	93					2																	85875075		2203	4300	6503	SO:0001587	stop_gained	10713	exon12			ATGAATTACAAGA	AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"Ubiquitin-specific peptidases"	20071	protein-coding gene	gene with protein product	"snRNP assembly defective 1 homolog (S.cerevisiae)", "small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"	611594	"ubiquitin specific protease 39"			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.1586T>G	2.37:g.85875075T>G	ENSP00000312981:p.Leu529*	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	102	44	NM_001256725	0	0	18	19	1	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Nonsense_Mutation	SNP	ENST00000323701.6	37	CCDS33234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	37|37	6.533352|6.533352	0.97641|0.97641	.|.	.|.	ENSG00000168883|ENSG00000168883	ENST00000450066;ENST00000409268;ENST00000409470;ENST00000323701|ENST00000409766	.|T	.|0.19105	.|2.17	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.065227|.	0.56097|.	D|.	0.000040|.	.|T	.|0.21145	.|0.0509	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|B	.|0.21905	.|0.062	.|B	.|0.21360	.|0.034	.|T	.|0.16129	.|-1.0413	.|7	0.14252|0.87932	T|D	0.57|0	-7.4979|-7.4979	14.3391|14.3391	0.66614|0.66614	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|484	.|G5E9H0	.|.	X|D	426;466;529;529|484	.|ENSP00000386803:Y484D	ENSP00000312981:L529X|ENSP00000386803:Y484D	L|Y	+|+	2|1	0|0	USP39|USP39	85728586|85728586	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.995000|0.995000	0.86356|0.86356	7.252000|7.252000	0.78309|0.78309	2.265000|2.265000	0.75225|0.75225	0.533000|0.533000	0.62120|0.62120	TTA|TAC	.		0.478	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590		G	85875075	T	G	85875075	4	3	140	1	0	0	0	0	0	1	0	0	17103	1764	61	5	1632	5	USP39	2	85875075	Nonsense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	31794468	85875075	157324298	16	12414											
MBD5	55777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	149248040	149248040	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattgatacattatagaccAaggacgttcaatgttggcga	14	11	10	6	2	1	2	1	1	0	1	1	5	1	3	1	2	1	2	1	2	6	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:149248040A>C	ENST00000407073.1	+	12	5137	c.4140A>C	c.(4138-4140)ccA>ccC	p.P1380P	MBD5_ENST00000404807.1_Silent_p.P1613P	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1380					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		ATTATAGACCAAGGACGTTCA	0.453																																					p.P1380P		.											.	MBD5-95	0			c.A4140C						.						77	78	78					2																	149248040		2203	4300	6503	SO:0001819	synonymous_variant	55777	exon12			TAGACCAAGGACG	AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.4140A>C	2.37:g.149248040A>C		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	109	51	NM_018328	0	0	2	7	5	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Silent	SNP	ENST00000407073.1	37	CCDS33302.1																																																																																			.		0.453	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			C	149248040	A	C	149248040	2	2	140	1	0	0	0	0	0	0	0	1	9372	117	5	5		5	MBD5	2	149248040	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	63372965	149248040	93951333	17	12415											
PAX3	5077	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	223066673	223066673	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaggcttactttgtccataCtgcccatattggtagcctgt	8	14	8	11	0	0	0	0	0	0	0	1	0	1	0	3	2	4	2	3	2	5	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:223066673C>T	ENST00000350526.4	-	8	1546	c.1410G>A	c.(1408-1410)caG>caA	p.Q470Q	PAX3_ENST00000409551.3_Silent_p.Q469Q|PAX3_ENST00000392070.2_Silent_p.Q470Q|PAX3_ENST00000336840.6_Intron|PAX3_ENST00000392069.2_Silent_p.Q470Q|PAX3_ENST00000344493.4_Intron|PAX3_ENST00000464706.1_5'Flank	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	470					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTTGTCCATACTGCCCATATT	0.468			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.Q470Q		.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3-1821	0			c.G1410A						.						99	93	95					2																	223066673		2203	4300	6503	SO:0001819	synonymous_variant	5077	exon8			TCCATACTGCCCA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1410G>A	2.37:g.223066673C>T		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	82	8	NM_181457	0	0	0	0	0	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	37	CCDS42826.1																																																																																			.		0.468	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223066673	C	T	223066673	2	4	140	1	0	0	0	0	0	0	0	1	11506	564	20	2		2	PAX3	2	223066673	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	73818633	223066673	20132700	18	12416											
DOCK10	55619	hgsc.bcm.edu	37	chr2	225630473	225630473	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agatgagatggagaccgtggGtagggccggagttgctttgc	8	9	18	6	2	0	3	0	1	0	3	0	6	0	4	2	4	2	3	2	4	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:225630473G>C	ENST00000258390.7	-	56	6593	c.6526C>G	c.(6526-6528)Ccc>Gcc	p.P2176A	DOCK10_ENST00000409592.3_Missense_Mutation_p.P2170A	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2176					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GAGACCGTGGGTAGGGCCGGA	0.512																																					p.P2176A		.											.	DOCK10-92	0			c.C6526G						.						143	143	143					2																	225630473		1919	4127	6046	SO:0001583	missense	55619	exon56			CCGTGGGTAGGGC	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"Pleckstrin homology (PH) domain containing"	23479	protein-coding gene	gene with protein product	"zizimin3"	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.6526C>G	2.37:g.225630473G>C	ENSP00000258390:p.Pro2176Ala	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_014689	0	0	2	2	0	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	G	4.364	0.067136	0.08388	.	.	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.18338	2.22;2.23	5.12	4.24	0.50183	.	1.033560	0.07661	N	0.933647	T	0.11196	0.0273	N	0.08118	0	0.09310	N	1	B;B	0.16603	0.018;0.003	B;B	0.14023	0.01;0.007	T	0.31971	-0.9924	10	0.37606	T	0.19	.	12.029	0.53388	0.0809:0.0:0.9191:0.0	.	2176;2170	Q96BY6;B3FL70	DOC10_HUMAN;.	A	2170;2176	ENSP00000386694:P2170A;ENSP00000258390:P2176A	ENSP00000258390:P2176A	P	-	1	0	DOCK10	225338717	0.970000	0.33590	0.027000	0.17364	0.009000	0.06853	3.388000	0.52509	1.162000	0.42619	0.561000	0.74099	CCC	.		0.512	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225630473	G	C	225630473	3	2	140	1	0	0	0	0	1	0	0	0	4696	1261	44	4	38	4	DOCK10	2	225630473	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	2563800	225630473	17568900	19	12417											
MYD88	30	hgsc.bcm.edu	37	chr3	38180515	38180515	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgctggagctgggacccagCattggtgaggacgtcccctt	6	9	14	12	1	0	1	0	1	0	0	1	4	1	4	3	4	3	3	3	4	0	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr3:38180515C>T	ENST00000333167.8	-	0	0				MYD88_ENST00000495303.1_Silent_p.S121S|ACAA1_ENST00000544624.1_5'Flank|MYD88_ENST00000424893.1_Silent_p.S121S|MYD88_ENST00000417037.2_Silent_p.S121S|MYD88_ENST00000396334.3_Silent_p.S121S|ACAA1_ENST00000450296.1_5'Flank|ACAA1_ENST00000301810.7_5'Flank|ACAA1_ENST00000444607.2_5'Flank|MYD88_ENST00000443433.2_Silent_p.S121S	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		TGGGACCCAGCATTGGTGAGG	0.662																																					p.S121S		.											.	MYD88-901	0			c.C363T						.						27	30	29					3																	38180515		2203	4300	6503	SO:0001631	upstream_gene_variant	4615	exon1			ACCCAGCATTGGT	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		3.37:g.38180515C>T	Exception_encountered	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_002468	0	0	0	0	0	G5E935|Q96CA6	Silent	SNP	ENST00000333167.8	37	CCDS2673.1																																																																																			.		0.662	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		T	38180515	C	T	38180515	1	4	140	0	1	0	0	0	0	0	0	0	10048	709	25	2		2	MYD88	3	38180515	5'Flank	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		38180515	159841915	20	12418											
CELSR3	1951	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48690562	48690562	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcacctggtccagaaggAgatgggaagcacggcccgag	11	4	15	11	2	1	2	1	0	0	2	2	5	2	3	3	4	1	1	3	4	2	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr3:48690562A>C	ENST00000164024.4	-	10	5787	c.5507T>G	c.(5506-5508)cTc>cGc	p.L1836R	CELSR3_ENST00000544264.1_Missense_Mutation_p.L1836R	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1836	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTCCAGAAGGAGATGGGAAGC	0.622																																					p.L1836R		.											.	CELSR3-523	0			c.T5507G						.						69	59	62					3																	48690562		2203	4300	6503	SO:0001583	missense	1951	exon10			AGAAGGAGATGGG	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3230	protein-coding gene	gene with protein product	"flamingo homolog 1 (Drosophila)"	604264	"cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5507T>G	3.37:g.48690562A>C	ENSP00000164024:p.Leu1836Arg	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	65	28	NM_001407	0	0	0	0	0	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.699442	0.88830	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	D;D	0.81821	-1.54;-1.54	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.88584	0.6476	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.988;1.0	D	0.88600	0.3149	9	0.45353	T	0.12	.	15.3149	0.74065	1.0:0.0:0.0:0.0	.	1836;1906	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	R	1836	ENSP00000164024:L1836R;ENSP00000445694:L1836R	ENSP00000164024:L1836R	L	-	2	0	CELSR3	48665566	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.549000	0.90672	2.026000	0.59711	0.460000	0.39030	CTC	.		0.622	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		C	48690562	A	C	48690562	3	2	140	1	0	0	0	0	1	0	0	0	3229	304	11	5	4535	5	CELSR3	3	48690562	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	10510047	48690562	149331868	21	12419											
COL6A6	131873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	130292932	130292932	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgtcagcctcaacagagTgcgaataggagcggcccagt	11	7	13	10	2	2	2	2	1	0	1	2	4	2	3	2	2	4	0	2	2	3	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr3:130292932T>A	ENST00000358511.6	+	7	3141	c.3110T>A	c.(3109-3111)gTg>gAg	p.V1037E	COL6A6_ENST00000453409.2_Missense_Mutation_p.V1037E	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1037	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						CTCAACAGAGTGCGAATAGGA	0.418																																					p.V1037E		.											.	COL6A6-76	0			c.T3110A						.						67	62	64					3																	130292932		1868	4100	5968	SO:0001583	missense	131873	exon7			ACAGAGTGCGAAT	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.3110T>A	3.37:g.130292932T>A	ENSP00000351310:p.Val1037Glu	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	41	20	NM_001102608	0	0	0	0	0	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.993314	0.54041	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.85171	-1.95;-1.95	5.15	3.99	0.46301	von Willebrand factor, type A (3);	0.000000	0.52532	D	0.000074	D	0.92596	0.7648	M	0.92784	3.345	0.38839	D	0.956029	D	0.58268	0.982	P	0.62740	0.906	D	0.93390	0.6751	10	0.66056	D	0.02	.	10.6799	0.45809	0.0:0.0762:0.0:0.9238	.	1037	A6NMZ7	CO6A6_HUMAN	E	1037	ENSP00000351310:V1037E;ENSP00000399236:V1037E	ENSP00000351310:V1037E	V	+	2	0	COL6A6	131775622	0.928000	0.31464	0.677000	0.29947	0.260000	0.26232	3.286000	0.51724	0.919000	0.36945	0.459000	0.35465	GTG	.		0.418	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130292932	T	A	130292932	3	1	140	1	0	0	0	0	1	0	0	0	3709	1696	59	5	3136	5	COL6A6	3	130292932	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	81602370	130292932	67729498	22	12420											
ASTE1	28990	hgsc.bcm.edu	37	chr3	130743293	130743300	+	Frame_Shift_Del	DEL	TTCTCGAT	TTCTCGAT	-																															cagagaagttccttaacattTtctcgatccttttttgggag																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	TTCTCGAT	TTCTCGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr3:130743293_130743300delTTCTCGAT	ENST00000264992.3	-	3	1292_1299	c.851_858delATCGAGAA	c.(850-858)gatcgagaafs	p.DRE284fs	NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000356918.4_5'Flank|ASTE1_ENST00000514044.1_Frame_Shift_Del_p.DRE284fs|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000429253.2_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	284					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.R285*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						CCTTAACATTTTCTCGATCCTTTTTTGG	0.447																																					p.284_286del		.											.	ASTE1-90	1	Substitution - Nonsense(1)	large_intestine(1)	c.851_858del						.																																			SO:0001589	frameshift_variant	28990	exon3			.	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.851_858delATCGAGAA	3.37:g.130743293_130743300delTTCTCGAT	ENSP00000264992:p.Asp284fs	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	66	20	NM_014065	0	0	0	0	0	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Frame_Shift_Del	DEL	ENST00000264992.3	37	CCDS3068.1																																																																																			.		0.447	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		-	130743300	TTCTCGAT	-	130743293	7	5	140	1	0	1	0	1	0	0	0	0	1063	1838	64	0	1197	0	ASTE1	3	130743293	Frame_Shift_Del	DEL	TTCTCGAT	TCGA-IZ-8195-01A-31D-2396-08	450361	130743293	67279137	23	12421											
LRPAP1	4043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	3519768	3519768	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgggcactcaccagcctcAgtgctgtagccctggtggct	5	8	14	14	1	2	0	2	0	0	0	2	0	2	0	3	4	3	4	3	4	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:3519768A>G	ENST00000500728.2	-	5	890	c.744T>C	c.(742-744)acT>acC	p.T248T	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	248	LDL receptor binding. {ECO:0000255}.				extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CACCAGCCTCAGTGCTGTAGC	0.657																																					p.T248T		.											.	LRPAP1-92	0			c.T744C						.						40	37	38					4																	3519768		2203	4300	6503	SO:0001819	synonymous_variant	4043	exon5			AGCCTCAGTGCTG		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.744T>C	4.37:g.3519768A>G		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	41	13	NM_002337	0	0	0	0	0	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			.		0.657	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			G	3519768	A	G	3519768	2	3	140	1	0	0	0	0	0	0	0	1	8989	175	7	3		3	LRPAP1	4	3519768	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		3519768	187634508	24	12422											
TBC1D19	55296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr4	26737100	26737100	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatcccttttcatggatttTcaatgtatggtaagttgggc	8	18	9	6	0	2	0	2	0	0	0	3	1	3	1	1	3	0	3	1	3	4	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:26737100T>A	ENST00000264866.4	+	16	1386	c.1108T>A	c.(1108-1110)Tca>Aca	p.S370T	TBC1D19_ENST00000511789.1_Missense_Mutation_p.S305T	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	370	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TCATGGATTTTCAATGTATGG	0.264																																					p.S370T		.											.	TBC1D19-153	0			c.T1108A						.						40	36	38					4																	26737100		2186	4257	6443	SO:0001583	missense	55296	exon16			GGATTTTCAATGT	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.1108T>A	4.37:g.26737100T>A	ENSP00000264866:p.Ser370Thr	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	22	7	NM_018317	0	0	0	0	0	B9A6M0|Q9NUX1	Missense_Mutation	SNP	ENST00000264866.4	37	CCDS3439.1	.	.	.	.	.	.	.	.	.	.	T	7.982	0.751339	0.15778	.	.	ENSG00000109680	ENST00000264866;ENST00000511789	T;T	0.12361	2.69;2.69	5.7	5.7	0.88788	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	L	0.31065	0.9	0.80722	D	1	B;D;D	0.53885	0.013;0.963;0.963	B;D;D	0.69824	0.02;0.966;0.966	T	0.01879	-1.1255	10	0.02654	T	1	-10.0854	15.9517	0.79843	0.0:0.0:0.0:1.0	.	305;370;370	B9A6M0;A8K0R6;Q8N5T2	.;.;TBC19_HUMAN	T	370;305	ENSP00000264866:S370T;ENSP00000425569:S305T	ENSP00000264866:S370T	S	+	1	0	TBC1D19	26346198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.742000	0.74843	2.172000	0.68678	0.519000	0.50382	TCA	.		0.264	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		A	26737100	T	A	26737100	3	1	140	1	0	0	0	0	1	0	0	0	15639	1783	62	5	1170	5	TBC1D19	4	26737100	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	23217332	26737100	164417176	25	12423											
AFF1	4299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	88029381	88029381	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtcagaaagcaccagtGactcagacagttcctcagac	14	6	9	12	0	3	5	3	1	0	4	4	5	4	5	2	0	1	2	2	0	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:88029381G>T	ENST00000307808.6	+	10	1846	c.1426G>T	c.(1426-1428)Gac>Tac	p.D476Y	AFF1_ENST00000395146.4_Missense_Mutation_p.D483Y|AFF1_ENST00000544085.1_Missense_Mutation_p.D114Y	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	476					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		AAGCACCAGTGACTCAGACAG	0.512																																					p.D483Y		.											.	AFF1-289	0			c.G1447T						.						114	104	108					4																	88029381		2203	4300	6503	SO:0001583	missense	4299	exon11			ACCAGTGACTCAG	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1426G>T	4.37:g.88029381G>T	ENSP00000305689:p.Asp476Tyr	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	64	24	NM_001166693	0	0	4	7	3	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	37	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164359	0.78339	.	.	ENSG00000172493	ENST00000395146;ENST00000307808;ENST00000511722;ENST00000544085;ENST00000514970	T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22	5.5	5.5	0.81552	.	0.131246	0.52532	D	0.000065	T	0.80319	0.4601	L	0.59436	1.845	0.54753	D	0.999987	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.977;0.977;0.977	T	0.80761	-0.1238	10	0.66056	D	0.02	-14.424	19.7664	0.96346	0.0:0.0:1.0:0.0	.	483;476;476	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	Y	483;476;114;114;167	ENSP00000378578:D483Y;ENSP00000305689:D476Y;ENSP00000424766:D114Y;ENSP00000440843:D114Y;ENSP00000424881:D167Y	ENSP00000305689:D476Y	D	+	1	0	AFF1	88248405	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.723000	0.91458	2.735000	0.93741	0.655000	0.94253	GAC	.		0.512	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	88029381	G	T	88029381	3	4	140	1	0	0	0	0	1	0	0	0	356	1290	45	4	1506	4	AFF1	4	88029381	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	61292281	88029381	103124895	26	12424											
SEC24B	10427	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	110415933	110415933	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccaacacttcagcctggttAtcagaatgctacagcaccac	12	9	6	14	0	2	1	2	0	0	1	3	1	3	1	3	1	5	3	3	1	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:110415933A>G	ENST00000265175.5	+	6	1464	c.1409A>G	c.(1408-1410)tAt>tGt	p.Y470C	SEC24B_ENST00000399100.2_Missense_Mutation_p.Y435C|SEC24B_ENST00000504968.2_Missense_Mutation_p.Y501C	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	470					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|aorta morphogenesis (GO:0035909)|auditory receptor cell stereocilium organization (GO:0060088)|cellular protein metabolic process (GO:0044267)|cochlear nucleus development (GO:0021747)|COPII vesicle coating (GO:0048208)|coronary artery morphogenesis (GO:0060982)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|lung lobe morphogenesis (GO:0060463)|membrane organization (GO:0061024)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|pulmonary artery morphogenesis (GO:0061156)|regulation of cargo loading into COPII-coated vesicle (GO:1901301)|regulation of establishment of planar polarity involved in neural tube closure (GO:0090178)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|membrane (GO:0016020)	transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CAGCCTGGTTATCAGAATGCT	0.473																																					p.Y470C		.											.	SEC24B-137	0			c.A1409G						.						116	117	117					4																	110415933		2080	4262	6342	SO:0001583	missense	10427	exon6			CTGGTTATCAGAA	AJ131245	CCDS43260.1, CCDS47124.1, CCDS75179.1	4q25	2013-10-21	2013-10-21		ENSG00000138802	ENSG00000138802			10704	protein-coding gene	gene with protein product		607184	"SEC24 (S. cerevisiae) related gene family, member B", "SEC24 family, member B (S. cerevisiae)"			10075675, 10329445	Standard	XM_005262688		Approved		uc003hzk.3	O95487	OTTHUMG00000161372	ENST00000265175.5:c.1409A>G	4.37:g.110415933A>G	ENSP00000265175:p.Tyr470Cys	Somatic	188	0		WXS	Illumina HiSeq	Phase_I	144	59	NM_006323	0	0	2	5	3	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	37	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.754236	0.69648	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.23754	1.89;1.89;1.89	5.47	5.47	0.80525	.	.	.	.	.	T	0.48943	0.1528	M	0.65975	2.015	0.54753	D	0.999987	D;P;D;D;D	0.89917	0.997;0.951;1.0;0.998;1.0	D;P;D;D;D	0.81914	0.926;0.759;0.995;0.947;0.995	T	0.50849	-0.8779	9	0.72032	D	0.01	2.3658	13.7816	0.63085	1.0:0.0:0.0:0.0	.	385;69;501;435;470	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	C	501;435;470	ENSP00000428564:Y501C;ENSP00000382051:Y435C;ENSP00000265175:Y470C	ENSP00000265175:Y470C	Y	+	2	0	SEC24B	110635382	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.401000	0.73256	2.064000	0.61679	0.533000	0.62120	TAT	.		0.473	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			G	110415933	A	G	110415933	3	3	140	1	0	0	0	0	1	0	0	0	14027	449	16	3	1431	3	SEC24B	4	110415933	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	22386552	110415933	80738343	27	12425											
SPATA5	166378	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	123848831	123848831	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccagaattcccttattcAtcttggactcaacactatga	12	14	4	11	0	3	2	2	1	1	1	5	3	5	3	2	1	1	0	2	1	4	6	rs201699296		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:123848831A>G	ENST00000274008.4	+	2	275	c.206A>G	c.(205-207)cAt>cGt	p.H69R	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	69					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						TCCCTTATTCATCTTGGACTC	0.338													A|||	1	0.000199681	0	0.0014	5008	,	,		18755	0		0	False		,,,				2504	0				p.H69R		.											.	SPATA5-90	0			c.A206G						.						116	116	116					4																	123848831		2203	4300	6503	SO:0001583	missense	166378	exon2			TTATTCATCTTGG	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"ATPases / AAA-type"	18119	protein-coding gene	gene with protein product	"ATPase family gene 2 homolog (S. cerevisiae)"	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.206A>G	4.37:g.123848831A>G	ENSP00000274008:p.His69Arg	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	116	53	NM_145207	0	0	0	0	0	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Missense_Mutation	SNP	ENST00000274008.4	37	CCDS3730.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	14.82	2.648636	0.47258	.	.	ENSG00000145375	ENST00000274008	T	0.80480	-1.38	4.38	4.38	0.52667	Aspartate decarboxylase-like fold (1);	0.066103	0.64402	D	0.000008	T	0.64994	0.2649	N	0.11427	0.14	0.38412	D	0.945945	B;B	0.23249	0.049;0.082	B;B	0.25140	0.016;0.058	T	0.65084	-0.6254	10	0.38643	T	0.18	-13.2842	12.66	0.56809	1.0:0.0:0.0:0.0	.	69;69	Q8NB90;Q8NB90-3	SPAT5_HUMAN;.	R	69	ENSP00000274008:H69R	ENSP00000274008:H69R	H	+	2	0	SPATA5	124068281	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.210000	0.77924	1.992000	0.58205	0.533000	0.62120	CAT	A|0.999;G|0.000		0.338	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207		G	123848831	A	G	123848831	3	3	140	1	0	0	0	0	1	0	0	0	15043	217	8	3	212	3	SPATA5	4	123848831	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	13432898	123848831	67305445	28	12426											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811108	140811108	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgctgctgctgctgttgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:140811108C>T	ENST00000509479.2	-	2	2338	c.1482G>A	c.(1480-1482)caG>caA	p.Q494Q	MAML3_ENST00000398940.1_Silent_p.Q33Q|MAML3_ENST00000327122.5_Silent_p.Q338Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.537																																					p.Q494Q		.											.	MAML3-455	0			c.G1482A						.						14	19	17					4																	140811108		2165	4272	6437	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1482G>A	4.37:g.140811108C>T		Somatic	71	1		WXS	Illumina HiSeq	Phase_I	63	4	NM_018717	0	0	488	488	0		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.		0.537	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811108	C	T	140811108	2	4	140	1	0	0	0	0	0	0	0	1	9232	796	28	2		2	MAML3	4	140811108	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	16962277	140811108	50343168	29	12427											
TRIM2	23321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	154215496	154215496	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctcttcagttcatctctgaAatcattcatcagttaaccaa	12	14	4	11	0	7	1	5	1	2	0	8	1	7	1	1	0	1	3	1	0	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:154215496A>T	ENST00000437508.2	+	5	765	c.564A>T	c.(562-564)gaA>gaT	p.E188D	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Missense_Mutation_p.E215D	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	188					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TCATCTCTGAAATCATTCATC	0.413																																					p.E215D		.											.	TRIM2-650	0			c.A645T						.						108	103	104					4																	154215496		2203	4300	6503	SO:0001583	missense	23321	exon5			CTCTGAAATCATT	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.564A>T	4.37:g.154215496A>T	ENSP00000415812:p.Glu188Asp	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	83	33	NM_015271	0	0	8	15	7	D3DP09|O60272|Q9BSI9|Q9UFZ1	Missense_Mutation	SNP	ENST00000437508.2	37	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.411858	0.42817	.	.	ENSG00000109654	ENST00000437508;ENST00000338700;ENST00000433687	T;T;T	0.71222	-0.54;-0.55;-0.23	6.17	5.0	0.66597	B-box, C-terminal (1);	0.041315	0.85682	D	0.000000	T	0.57829	0.2080	L	0.34521	1.04	0.54753	D	0.999982	B;B	0.12013	0.005;0.005	B;B	0.10450	0.005;0.005	T	0.50693	-0.8798	10	0.17369	T	0.5	-3.329	12.1877	0.54250	0.9342:0.0:0.0658:0.0	.	215;188	D3DP09;Q9C040	.;TRIM2_HUMAN	D	188;215;102	ENSP00000415812:E188D;ENSP00000339659:E215D;ENSP00000400375:E102D	ENSP00000339659:E215D	E	+	3	2	TRIM2	154434946	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.959000	0.56744	1.166000	0.42689	0.533000	0.62120	GAA	.		0.413	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			T	154215496	A	T	154215496	3	4	140	1	0	0	0	0	1	0	0	0	16527	11	1	5	663	5	TRIM2	4	154215496	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	13404388	154215496	36938780	30	12428											
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	155225827	155225827	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaacaaacttaccaattaTgtgatattcaacagctctgt	16	12	4	9	0	2	1	1	1	1	0	2	1	2	1	1	0	5	1	1	0	7	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:155225827T>C	ENST00000357232.4	-	17	4233	c.4234A>G	c.(4234-4236)Ata>Gta	p.I1412V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1412	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TTACCAATTATGTGATATTCA	0.418																																					p.I1412V		.											.	DCHS2-94	0			c.A4234G						.						59	58	59					4																	155225827		2203	4300	6503	SO:0001583	missense	54798	exon17			CAATTATGTGATA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"Cadherins / Cadherin-related"	23111	protein-coding gene	gene with protein product	"cadherin-related family member 7"	612486	"cadherin-like 27", "dachsous 2 (Drosophila)"	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4234A>G	4.37:g.155225827T>C	ENSP00000349768:p.Ile1412Val	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	48	23	NM_017639	0	0	0	0	0	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	7.389	0.630312	0.14257	.	.	ENSG00000197410	ENST00000357232	T	0.58797	0.31	5.09	3.91	0.45181	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	M	0.74258	2.255	0.80722	D	1	D	0.57899	0.981	P	0.58077	0.832	T	0.70784	-0.4778	10	0.56958	D	0.05	.	10.979	0.47483	0.0:0.074:0.0:0.926	.	1412	Q6V1P9	PCD23_HUMAN	V	1412	ENSP00000349768:I1412V	ENSP00000349768:I1412V	I	-	1	0	DCHS2	155445277	0.984000	0.35163	0.546000	0.28166	0.036000	0.12997	2.011000	0.40922	0.883000	0.36040	0.460000	0.39030	ATA	.		0.418	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155225827	T	C	155225827	3	2	140	1	0	0	0	0	1	0	0	0	4294	1464	51	3	4552	3	DCHS2	4	155225827	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	1010331	155225827	35928449	31	12429											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187539116	187539116	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtctctcttttcatggtcaAgttcctttaaagttgtaatc	8	19	6	8	0	4	0	2	0	2	0	7	0	5	0	1	1	0	3	1	1	4	7			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:187539116A>G	ENST00000441802.2	-	10	8833	c.8624T>C	c.(8623-8625)cTt>cCt	p.L2875P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2875	Cadherin 26. {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						TTCATGGTCAAGTTCCTTTAA	0.418										HNSCC(5;0.00058)																											p.L2875P	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.T8624C						.						175	154	161					4																	187539116		1930	4152	6082	SO:0001583	missense	2195	exon10			TGGTCAAGTTCCT	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.8624T>C	4.37:g.187539116A>G	ENSP00000406229:p.Leu2875Pro	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	67	26	NM_005245	0	0	20	36	16		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.557734	0.65425	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.75154	-0.91	4.86	4.86	0.63082	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.90256	0.6953	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93285	0.6663	10	0.87932	D	0	.	14.9179	0.70812	1.0:0.0:0.0:0.0	.	2875	Q14517	FAT1_HUMAN	P	2875;2877	ENSP00000406229:L2875P	ENSP00000260147:L2877P	L	-	2	0	FAT1	187776110	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	9.139000	0.94554	2.167000	0.68274	0.528000	0.53228	CTT	.		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187539116	A	G	187539116	3	3	140	1	0	0	0	0	1	0	0	0	5708	72	3	3	5214	3	FAT1	4	187539116	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	32313289	187539116	3615160	32	12430											
SLC6A19	340024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	1219640	1219640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctcatctgcctggggacaTtcctcattggcttcatcttc	5	14	8	14	0	5	0	3	0	2	0	7	1	6	1	3	3	1	1	3	3	0	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:1219640T>C	ENST00000304460.10	+	10	1455	c.1399T>C	c.(1399-1401)Ttc>Ctc	p.F467L		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	467					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CCTGGGGACATTCCTCATTGG	0.627																																					p.F467L		.											.	SLC6A19-90	0			c.T1399C						.						140	118	125					5																	1219640		2203	4300	6503	SO:0001583	missense	340024	exon10			GGGACATTCCTCA	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1399T>C	5.37:g.1219640T>C	ENSP00000305302:p.Phe467Leu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	51	20	NM_001003841	0	0	0	0	0	A8K446	Missense_Mutation	SNP	ENST00000304460.10	37	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	T	8.371	0.835267	0.16820	.	.	ENSG00000174358	ENST00000304460	T	0.76316	-1.01	4.83	4.83	0.62350	.	0.341281	0.33691	N	0.004644	T	0.79311	0.4424	M	0.83603	2.65	0.09310	N	1	B	0.12630	0.006	B	0.17722	0.019	T	0.70128	-0.4957	10	0.41790	T	0.15	.	14.3784	0.66895	0.0:0.0:0.0:1.0	.	467	Q695T7	S6A19_HUMAN	L	467	ENSP00000305302:F467L	ENSP00000305302:F467L	F	+	1	0	SLC6A19	1272640	0.950000	0.32346	0.052000	0.19188	0.038000	0.13279	3.934000	0.56553	1.801000	0.52704	0.391000	0.25812	TTC	.		0.627	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		C	1219640	T	C	1219640	3	2	140	1	0	0	0	0	1	0	0	0	14714	1493	52	3	1437	3	SLC6A19	5	1219640	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		1219640	179695620	33	12431											
TRIO	7204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	14497016	14497016	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcttggcacacagcactcCgtttaaggaaaaaatctgag	14	9	8	10	1	2	1	0	1	2	0	3	2	3	2	1	2	1	3	1	2	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:14497016C>A	ENST00000344204.4	+	50	7933	c.7909C>A	c.(7909-7911)Cgt>Agt	p.R2637S	TRIO_ENST00000537187.1_Missense_Mutation_p.R2461S|TRIO_ENST00000344135.5_Missense_Mutation_p.R136S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2637					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CACAGCACTCCGTTTAAGGAA	0.448																																					p.R2637S		.											.	TRIO-562	0			c.C7909A						.						121	112	115					5																	14497016		2203	4300	6503	SO:0001583	missense	7204	exon50			GCACTCCGTTTAA	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.7909C>A	5.37:g.14497016C>A	ENSP00000339299:p.Arg2637Ser	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	80	35	NM_007118	0	0	4	9	5	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915239	0.92178	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000344135	T;T;T	0.71341	-0.56;-0.36;-0.53	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.82282	0.5003	M	0.65498	2.005	0.36519	D	0.87004	D	0.89917	1.0	D	0.79784	0.993	D	0.84372	0.0544	10	0.37606	T	0.19	.	16.8938	0.86094	0.0:1.0:0.0:0.0	.	2637	O75962	TRIO_HUMAN	S	2637;2461;2324;136	ENSP00000339299:R2637S;ENSP00000446348:R2461S;ENSP00000339291:R136S	ENSP00000339291:R136S	R	+	1	0	TRIO	14550016	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.596000	0.67570	2.414000	0.81942	0.655000	0.94253	CGT	.		0.448	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14497016	C	A	14497016	3	1	140	1	0	0	0	0	1	0	0	0	16585	652	23	4	8107	4	TRIO	5	14497016	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	13277376	14497016	166418244	34	12432											
POLK	51426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	74892358	74892358	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgagaatttggaaatatcaGagaattcagatgactgtcag	16	11	10	4	0	3	4	3	2	0	3	3	7	3	5	0	1	0	0	0	1	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:74892358G>C	ENST00000241436.4	+	13	2012	c.1840G>C	c.(1840-1842)Gag>Cag	p.E614Q	POLK_ENST00000380481.3_Missense_Mutation_p.E524Q|CTC-366B18.2_ENST00000511329.1_RNA|POLK_ENST00000508526.1_Missense_Mutation_p.E416Q|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000352007.5_Missense_Mutation_p.E416Q|POLK_ENST00000504026.1_Intron	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	614					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		GGAAATATCAGAGAATTCAGA	0.368								DNA polymerases (catalytic subunits)																													p.E614Q		.											.	POLK-229	0			c.G1840C						.						106	108	107					5																	74892358		2203	4300	6503	SO:0001583	missense	51426	exon13			ATATCAGAGAATT	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1840G>C	5.37:g.74892358G>C	ENSP00000241436:p.Glu614Gln	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	171	76	NM_016218	0	0	4	7	3	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	37	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.027552	0.54683	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000508526;ENST00000380481	T;T;T;T	0.58358	1.15;0.34;0.34;1.13	5.15	4.28	0.50868	.	0.893154	0.09986	N	0.730347	T	0.50480	0.1618	M	0.65498	2.005	0.22888	N	0.998601	B;B	0.28419	0.211;0.098	B;B	0.23275	0.045;0.021	T	0.43909	-0.9362	10	0.48119	T	0.1	-2.8619	9.5091	0.39065	0.0815:0.1534:0.7651:0.0	.	416;614	Q9UBT6-3;Q9UBT6	.;POLK_HUMAN	Q	614;416;416;524	ENSP00000241436:E614Q;ENSP00000342256:E416Q;ENSP00000426853:E416Q;ENSP00000369848:E524Q	ENSP00000241436:E614Q	E	+	1	0	POLK	74928114	0.025000	0.19082	0.097000	0.21041	0.978000	0.69477	0.423000	0.21313	1.148000	0.42385	0.655000	0.94253	GAG	.		0.368	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		C	74892358	G	C	74892358	3	2	140	1	0	0	0	0	1	0	0	0	12230	943	33	4	1886	4	POLK	5	74892358	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	60395342	74892358	106022902	35	12433											
BHMT	635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	78426847	78426847	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatggctggggagtgaccAaaggaacagccgagctgatg	12	5	16	8	1	0	3	0	2	0	1	0	6	0	5	2	4	3	2	2	4	2	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:78426847A>G	ENST00000274353.5	+	8	1236	c.1129A>G	c.(1129-1131)Aaa>Gaa	p.K377E	BHMT_ENST00000524080.1_Missense_Mutation_p.K224E|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	377					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)	GGGAGTGACCAAAGGAACAGC	0.493																																					p.K377E		.											.	BHMT-91	0			c.A1129G						.						113	126	121					5																	78426847		2203	4300	6503	SO:0001583	missense	635	exon8			GTGACCAAAGGAA	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.1129A>G	5.37:g.78426847A>G	ENSP00000274353:p.Lys377Glu	Somatic	247	1		WXS	Illumina HiSeq	Phase_I	164	53	NM_001713	0	0	0	2	2	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	37	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	A	18.22	3.574689	0.65878	.	.	ENSG00000145692	ENST00000274353;ENST00000524080	T;T	0.33865	1.42;1.39	5.55	4.38	0.52667	.	0.086125	0.85682	D	0.000000	T	0.28532	0.0706	M	0.70595	2.14	0.58432	D	0.999998	P;B	0.36599	0.56;0.182	B;B	0.24006	0.05;0.029	T	0.21621	-1.0240	10	0.02654	T	1	-19.2971	12.7653	0.57388	0.8628:0.1372:0.0:0.0	.	224;377	E5RJH0;Q93088	.;BHMT1_HUMAN	E	377;224	ENSP00000274353:K377E;ENSP00000428240:K224E	ENSP00000274353:K377E	K	+	1	0	BHMT	78462603	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.446000	0.80609	0.929000	0.37192	0.533000	0.62120	AAA	.		0.493	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		G	78426847	A	G	78426847	3	3	140	1	0	0	0	0	1	0	0	0	1426	131	5	3	1159	3	BHMT	5	78426847	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	3534489	78426847	102488413	36	12434											
MSH3	4437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	80040402	80040402	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttgggagacggaagttaaaGaagtgggtgacccagccact	12	8	14	7	1	0	3	0	1	0	2	0	5	0	4	2	3	1	1	2	3	4	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:80040402G>A	ENST00000265081.6	+	12	1811	c.1731G>A	c.(1729-1731)aaG>aaA	p.K577K	MSH3_ENST00000512258.1_3'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	577					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		GGAAGTTAAAGAAGTGGGTGA	0.338								Mismatch excision repair (MMR)																													p.K577K	Melanoma(88;1010 1399 13793 26548 36275)	.											.	MSH3-661	0			c.G1731A						.						22	25	24					5																	80040402		2200	4295	6495	SO:0001819	synonymous_variant	4437	exon12			GTTAAAGAAGTGG	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1731G>A	5.37:g.80040402G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	52	20	NM_002439	0	0	0	0	0	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			.		0.338	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		A	80040402	G	A	80040402	2	1	140	1	0	0	0	0	0	0	0	1	9896	933	33	2		2	MSH3	5	80040402	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	1613555	80040402	100874858	37	12435											
DMXL1	1657	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	118500212	118500213	+	Frame_Shift_Ins	INS	-	-	AGTCATTT																															tttcttcaggcctgtctacaINSagtcattttgcttgggcatt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:118500212_118500213insAGTCATTT	ENST00000311085.8	+	20	4793_4794	c.4713_4714insAGTCATTT	c.(4714-4716)agtfs	p.-1572fs	DMXL1_ENST00000539542.1_Frame_Shift_Ins_p.-1572fs	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1											breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GCCTGTCTACAAGTCATTTTGC	0.342																																					p.T1571fs		.											.	DMXL1-92	0			c.4713_4714insAGTCATTT						.																																			SO:0001589	frameshift_variant	1657	exon20			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.4714_4721dupAGTCATTT	5.37:g.118500213_118500220dupAGTCATTT	ENSP00000309690:p.Ser1572fs	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	62	20	NM_005509	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000311085.8	37	CCDS4125.1																																																																																			.		0.342	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		AGTCATTT	118500213	-	AGTCATTT	118500212	7	5	140	1	0	1	1	0	0	0	0	0	4605	117	5	0	4791	0	DMXL1	5	118500212	Frame_Shift_Ins	INS	-	TCGA-IZ-8195-01A-31D-2396-08	38459810	118500212	62415048	38	12436											
SOX30	11063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	157075894	157075894	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtccttactgaagggagtAtctggtatgcctacatgaca	10	12	10	9	0	1	2	0	2	1	0	2	3	2	3	2	2	3	2	2	2	5	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:157075894A>T	ENST00000265007.6	-	2	1319	c.978T>A	c.(976-978)gaT>gaA	p.D326E	SOX30_ENST00000311371.5_Missense_Mutation_p.D326E|SOX30_ENST00000519442.1_Missense_Mutation_p.D21E	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	326					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGAAGGGAGTATCTGGTATGC	0.428																																					p.D326E	Esophageal Squamous(31;525 799 19355 21125 41744)	.											.	SOX30-91	0			c.T978A						.						126	111	116					5																	157075894		2203	4300	6503	SO:0001583	missense	11063	exon2			GGGAGTATCTGGT	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"SRY (sex determining region Y)-boxes"	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.978T>A	5.37:g.157075894A>T	ENSP00000265007:p.Asp326Glu	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	106	41	NM_178424	0	0	0	0	0	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588194	0.66105	.	.	ENSG00000039600	ENST00000311371;ENST00000265007;ENST00000519442	D;D;D	0.97976	-4.64;-4.3;-4.57	5.72	-2.31	0.06765	High mobility group, superfamily (1);	0.152930	0.45867	D	0.000328	D	0.95793	0.8631	N	0.08118	0	0.30089	N	0.808462	D;D;D	0.76494	0.999;0.99;0.983	D;D;P	0.78314	0.991;0.933;0.858	D	0.92745	0.6211	10	0.66056	D	0.02	.	14.1885	0.65623	0.5913:0.0:0.4087:0.0	.	21;326;326	B4DXW7;O94993-2;O94993	.;.;SOX30_HUMAN	E	326;326;21	ENSP00000309343:D326E;ENSP00000265007:D326E;ENSP00000427984:D21E	ENSP00000265007:D326E	D	-	3	2	SOX30	157008472	0.992000	0.36948	0.971000	0.41717	0.971000	0.66376	0.280000	0.18790	-0.732000	0.04856	-1.477000	0.00996	GAT	.		0.428	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		T	157075894	A	T	157075894	3	4	140	1	0	0	0	0	1	0	0	0	14984	446	16	5	1299	5	SOX30	5	157075894	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	38575682	157075894	23839366	39	12437											
NHP2	55651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	177580732	177580732	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcgatggggttctggttGaccagcagctcctggtaggt	5	11	16	9	2	1	1	0	1	1	0	2	2	2	1	2	5	3	5	2	5	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:177580732G>T	ENST00000274606.3	-	1	236	c.87C>A	c.(85-87)gtC>gtA	p.V29V	NHP2_ENST00000314397.4_Silent_p.V29V	NM_017838.3	NP_060308.1	Q9NX24	NHP2_HUMAN	NHP2 ribonucleoprotein	29					rRNA pseudouridine synthesis (GO:0031118)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|kidney(1)|ovary(2)	4						GGTTCTGGTTGACCAGCAGCT	0.662																																					p.V29V		.											.	NHP2-90	0			c.C87A						.						22	26	25					5																	177580732		2202	4299	6501	SO:0001819	synonymous_variant	55651	exon1			CTGGTTGACCAGC	AF161404	CCDS4432.1, CCDS34308.1	5q35.3	2014-09-17	2012-12-10	2008-10-13	ENSG00000145912	ENSG00000145912			14377	protein-coding gene	gene with protein product		606470	"nucleolar protein family A, member 2 (H/ACA small nucleolar RNPs)", "NHP2 ribonucleoprotein homolog (yeast)"	NOLA2		11074001	Standard	NM_017838		Approved	FLJ20479	uc003mir.2	Q9NX24	OTTHUMG00000130886	ENST00000274606.3:c.87C>A	5.37:g.177580732G>T		Somatic	70	1		WXS	Illumina HiSeq	Phase_I	39	20	NM_017838	0	0	70	128	58	A6NKY8|Q9P095	Silent	SNP	ENST00000274606.3	37	CCDS4432.1																																																																																			.		0.662	NHP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253471.1	NM_017838		T	177580732	G	T	177580732	2	4	140	1	0	0	0	0	0	0	0	1	10435	1277	45	4		4	NHP2	5	177580732	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	20504838	177580732	3334528	40	12438											
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179193185	179193185	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcccaggaggggcctcaGagctgtcctctgcccaccag	7	5	14	15	0	2	1	1	0	1	1	3	2	3	2	5	4	2	1	5	4	0	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:179193185G>T	ENST00000292599.3	+	2	1437	c.1174G>T	c.(1174-1176)Gag>Tag	p.E392*	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGGGCCTCAGAGCTGTCCTC	0.657																																					p.E392X		.											.	MAML1-848	0			c.G1174T						.						42	46	45					5																	179193185		2203	4300	6503	SO:0001587	stop_gained	9794	exon2			GCCTCAGAGCTGT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1174G>T	5.37:g.179193185G>T	ENSP00000292599:p.Glu392*	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	104	28	NM_014757	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	G	39	7.386389	0.98252	.	.	ENSG00000161021	ENST00000292599;ENST00000376951	.	.	.	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-25.6288	18.0213	0.89255	0.0:0.0:1.0:0.0	.	.	.	.	X	392;429	.	ENSP00000292599:E392X	E	+	1	0	MAML1	179125791	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.169000	0.94788	2.250000	0.74265	0.305000	0.20034	GAG	.		0.657	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		T	179193185	G	T	179193185	4	4	140	1	0	0	0	0	0	1	0	0	9230	943	33	4	1180	4	MAML1	5	179193185	Nonsense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	1612453	179193185	1722075	41	12439											
TBC1D9B	23061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179320371	179320371	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaacatggagaagaagagcTcctggtcgcgggtgtccaca	11	6	15	9	2	0	3	0	0	0	3	3	5	2	4	2	4	2	1	2	4	3	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:179320371T>A	ENST00000356834.3	-	5	711	c.674A>T	c.(673-675)gAg>gTg	p.E225V	TBC1D9B_ENST00000355235.3_Missense_Mutation_p.E225V	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	225						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGAAGAGCTCCTGGTCGCG	0.607																																					p.E225V		.											.	TBC1D9B-154	0			c.A674T						.						86	76	79					5																	179320371		2203	4300	6503	SO:0001583	missense	23061	exon5			AAGAGCTCCTGGT	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.674A>T	5.37:g.179320371T>A	ENSP00000349291:p.Glu225Val	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	69	24	NM_198868	0	0	20	40	20	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	37	CCDS43408.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.196607	0.79015	.	.	ENSG00000197226	ENST00000356834;ENST00000355235	T;T	0.11712	2.75;2.84	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.26304	0.0642	L	0.58810	1.83	0.80722	D	1	D;D;P	0.69078	0.997;0.995;0.79	P;P;B	0.62649	0.87;0.905;0.441	T	0.01087	-1.1456	10	0.59425	D	0.04	-27.504	14.075	0.64885	0.0:0.0:0.0:1.0	.	225;225;225	A1L3A9;Q66K14-2;Q66K14	.;.;TBC9B_HUMAN	V	225	ENSP00000349291:E225V;ENSP00000347375:E225V	ENSP00000347375:E225V	E	-	2	0	TBC1D9B	179252977	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	7.791000	0.85805	1.929000	0.55896	0.260000	0.18958	GAG	.		0.607	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		A	179320371	T	A	179320371	3	1	140	1	0	0	0	0	1	0	0	0	15660	1551	54	5	3150	5	TBC1D9B	5	179320371	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	127186	179320371	1594889	42	12440											
TBC1D7	51256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	13307966	13307966	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagattcaagtattgttcAaacgcttttggctaaagatt	12	15	7	7	1	2	2	2	0	0	2	3	2	3	2	1	1	1	4	1	1	5	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:13307966A>C	ENST00000379300.3	-	6	774	c.531T>G	c.(529-531)ttT>ttG	p.F177L	TBC1D7_ENST00000343141.4_Missense_Mutation_p.F131L|TBC1D7_ENST00000607532.1_5'UTR|TBC1D7_ENST00000607658.1_Missense_Mutation_p.F150L|TBC1D7_ENST00000379307.2_Missense_Mutation_p.F150L|TBC1D7_ENST00000356436.4_Missense_Mutation_p.F177L	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	177	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			AGTATTGTTCAAACGCTTTTG	0.398																																					p.F177L		.											.	TBC1D7-91	0			c.T531G						.						74	70	71					6																	13307966		2203	4300	6503	SO:0001583	missense	51256	exon6			TTGTTCAAACGCT	AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.531T>G	6.37:g.13307966A>C	ENSP00000368602:p.Phe177Leu	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	85	26	NM_001143965	0	0	0	0	0	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Missense_Mutation	SNP	ENST00000379300.3	37	CCDS4523.1	.	.	.	.	.	.	.	.	.	.	A	6.453	0.451648	0.12223	.	.	ENSG00000145979	ENST00000334971;ENST00000356436;ENST00000379300;ENST00000379307;ENST00000343141;ENST00000452989;ENST00000450347;ENST00000422136;ENST00000446018;ENST00000420456	T;T;T;T;T;T;T;T;T	0.26660	2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;1.72	6.17	1.03	0.20045	Rab-GAP/TBC domain (3);	0.105355	0.64402	D	0.000003	T	0.02970	0.0088	N	0.11154	0.105	0.48236	D	0.999617	B;B;B;B	0.09022	0.0;0.0;0.0;0.002	B;B;B;B	0.08055	0.0;0.003;0.001;0.002	T	0.35450	-0.9788	10	0.08837	T	0.75	-16.1625	5.7639	0.18215	0.5313:0.2616:0.2071:0.0	.	131;150;150;177	Q2TU37;Q5SZL5;Q9P0N9-2;Q9P0N9	.;.;.;TBCD7_HUMAN	L	118;177;177;150;131;150;150;177;150;150	ENSP00000348813:F177L;ENSP00000368602:F177L;ENSP00000368609:F150L;ENSP00000343100:F131L;ENSP00000414292:F150L;ENSP00000404680:F150L;ENSP00000394425:F177L;ENSP00000417005:F150L;ENSP00000412102:F150L	ENSP00000334212:F118L	F	-	3	2	TBC1D7	13415945	0.997000	0.39634	1.000000	0.80357	0.901000	0.52897	0.600000	0.24104	0.165000	0.19558	0.533000	0.62120	TTT	.		0.398	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495		C	13307966	A	C	13307966	3	2	140	1	0	0	0	0	1	0	0	0	15656	127	5	5	362	5	TBC1D7	6	13307966	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		13307966	157807101	43	12441											
ZNF292	23036	broad.mit.edu	37	chr6	87928395	87928395	+	Frame_Shift_Del	DEL	A	A	-																															ctcaagagactggggtgtggAaaaacccggtactgtgcact																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:87928395delA	ENST00000369577.3	+	4	527	c.484delA	c.(484-486)aaafs	p.K162fs	ZNF292_ENST00000369578.2_3'UTR|ZNF292_ENST00000339907.4_Frame_Shift_Del_p.K162fs	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	162						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TGGGGTGTGGAAAAACCCGGT	0.368																																					p.K162fs													.	ZNF292-72	0			c.484delA						.						42	41	42					6																	87928395		1826	4076	5902	SO:0001589	frameshift_variant	23036	exon4			GTGTGGAAAAACC	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.484delA	6.37:g.87928395delA	ENSP00000358590:p.Lys162fs	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	14	7	NM_015021	0	0	0	0	0	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Frame_Shift_Del	DEL	ENST00000369577.3	37	CCDS47457.1																																																																																			.		0.368	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		-	87928395	A	-	87928395	7	5	140	1	0	1	0	1	0	0	0	0	17858	247	9	0	498	0	ZNF292	6	87928395	Frame_Shift_Del	DEL	A	TCGA-IZ-8195-01A-31D-2396-08	74620429	87928395	83186672	44	12442											
AIM1	202	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	106968989	106968991	+	In_Frame_Del	DEL	TCT	TCT	-																															ttgaacaaagaacagtcaaaTcttctgcccgacaactcctt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:106968989_106968991delTCT	ENST00000369066.3	+	2	3169_3171	c.2682_2684delTCT	c.(2680-2685)aatctt>aat	p.L896del		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AACAGTCAAATCTTCTGCCCGAC	0.463																																					p.894_895del		.											.	AIM1-139	0			c.2682_2684del						.																																			SO:0001651	inframe_deletion	202	exon2			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2682_2684delTCT	6.37:g.106968992_106968994delTCT	ENSP00000358062:p.Leu896del	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	148	55	NM_001624	0	0	0	0	0	Q6P2P0|Q9BTM3	In_Frame_Del	DEL	ENST00000369066.3	37	CCDS34506.1																																																																																			.		0.463	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106968991	TCT	-	106968989	7	5	140	1	0	1	0	1	0	0	0	0	430	1432	50	0	2688	0	AIM1	6	106968989	In_Frame_Del	DEL	TCT	TCGA-IZ-8195-01A-31D-2396-08	19040594	106968989	64146078	45	12443											
AHI1	54806	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	135644423	135644423	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgcgatggatggttagttCatctgatcgattcgctgtgt	6	15	12	8	4	2	1	1	1	1	0	5	4	3	2	1	2	0	3	1	2	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:135644423C>A	ENST00000367800.4	-	23	3421	c.3205G>T	c.(3205-3207)Gaa>Taa	p.E1069*	AHI1_ENST00000457866.2_Nonsense_Mutation_p.E1069*|AHI1_ENST00000417892.2_Nonsense_Mutation_p.E423*	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1069	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		ATGGTTAGTTCATCTGATCGA	0.438																																					p.E1069X		.											.	AHI1-227	0			c.G3205T						.						99	91	93					6																	135644423		1940	4132	6072	SO:0001587	stop_gained	54806	exon24			TTAGTTCATCTGA	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3205G>T	6.37:g.135644423C>A	ENSP00000356774:p.Glu1069*	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	27	13	NM_017651	0	0	2	2	0	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Nonsense_Mutation	SNP	ENST00000367800.4	37	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.418512|7.418512	0.98272|0.98272	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602|ENST00000367799	.|.	.|.	.|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.72606	.|0.3481	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68503	.|-0.5391	.|4	0.52906|.	T|.	0.07|.	-28.0524|-28.0524	20.6208|20.6208	0.99490|0.99490	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	1069;1069;423;1069|568	.|.	ENSP00000265602:E1069X|.	E|M	-|-	1|3	0|0	AHI1|AHI1	135686116|135686116	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.487000|7.487000	0.81328|0.81328	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	GAA|ATG	.		0.438	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		A	135644423	C	A	135644423	4	1	140	1	0	0	0	0	0	1	0	0	413	835	29	4	405	4	AHI1	6	135644423	Nonsense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	28675434	135644423	35470644	46	12444											
REPS1	85021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	139251190	139251190	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttgcttggaggagcttcaGcaggagagcctgaataacct	11	9	12	9	0	1	2	1	1	0	1	1	5	1	4	2	3	5	3	2	3	2	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:139251190G>C	ENST00000450536.2	-	9	1755	c.1181C>G	c.(1180-1182)gCt>gGt	p.A394G	REPS1_ENST00000367663.4_Missense_Mutation_p.A394G|REPS1_ENST00000415951.2_Missense_Mutation_p.A394G|REPS1_ENST00000258062.5_Missense_Mutation_p.A394G|REPS1_ENST00000409812.2_Missense_Mutation_p.A394G			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	394					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		AGGAGCTTCAGCAGGAGAGCC	0.418																																					p.A394G		.											.	REPS1-522	0			c.C1181G						.						146	123	131					6																	139251190		2203	4300	6503	SO:0001583	missense	85021	exon9			GCTTCAGCAGGAG		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1181C>G	6.37:g.139251190G>C	ENSP00000392065:p.Ala394Gly	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	107	49	NM_001128617	0	0	9	20	11	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	37		.	.	.	.	.	.	.	.	.	.	G	14.17	2.454329	0.43634	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.34667	1.37;1.35;1.37;1.37;1.37;1.36	5.72	5.72	0.89469	.	0.168464	0.53938	D	0.000060	T	0.17534	0.0421	L	0.36672	1.1	0.46749	D	0.999188	B;B;P;B;B	0.38504	0.005;0.007;0.634;0.002;0.361	B;B;B;B;B	0.33620	0.009;0.006;0.167;0.002;0.081	T	0.02691	-1.1123	10	0.24483	T	0.36	-10.4052	18.069	0.89399	0.0:0.0:1.0:0.0	.	394;342;394;394;394	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	G	394;394;380;394;394;394;342	ENSP00000392065:A394G;ENSP00000356635:A394G;ENSP00000434251:A380G;ENSP00000386699:A394G;ENSP00000258062:A394G;ENSP00000397941:A394G	ENSP00000258062:A394G	A	-	2	0	REPS1	139292883	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	7.353000	0.79414	2.700000	0.92200	0.563000	0.77884	GCT	.		0.418	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			C	139251190	G	C	139251190	3	2	140	1	0	0	0	0	1	0	0	0	13260	971	34	4	1257	4	REPS1	6	139251190	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	3606767	139251190	31863877	47	12445											
UST	10090	hgsc.bcm.edu	37	chr6	149068615	149068615	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcgcggatccctggcccCatggggcccctatggggggc	3	5	18	15	3	0	0	0	0	0	0	1	1	1	1	5	8	0	0	5	8	1	1	rs559911654		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:149068615C>T	ENST00000367463.4	+	1	152	c.49C>T	c.(49-51)Cat>Tat	p.H17Y		NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	17					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		TCCCTGGCCCCATGGGGCCCC	0.706													C|||	1	0.000199681	0	0	5008	,	,		9452	0.001		0	False		,,,				2504	0				p.H17Y		.											.	UST-92	0			c.C49T						.						5	7	7					6																	149068615		2063	4069	6132	SO:0001583	missense	10090	exon1			TGGCCCCATGGGG	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"Sulfotransferases, membrane-bound"	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.49C>T	6.37:g.149068615C>T	ENSP00000356433:p.His17Tyr	Somatic	7	2		WXS	Illumina HiSeq	Phase_I	7	5	NM_005715	0	0	0	1	1	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	37	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	c	4.610	0.113276	0.08831	.	.	ENSG00000111962	ENST00000367463	T	0.47177	0.85	3.58	2.71	0.32032	.	0.732533	0.12547	N	0.459427	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24657	-1.0154	10	0.87932	D	0	-3.7085	5.6822	0.17782	0.0:0.75:0.0:0.2499	.	17	Q9Y2C2	UST_HUMAN	Y	17	ENSP00000356433:H17Y	ENSP00000356433:H17Y	H	+	1	0	UST	149110308	1.000000	0.71417	0.941000	0.38009	0.005000	0.04900	3.877000	0.56123	0.694000	0.31654	-0.157000	0.13467	CAT	.		0.706	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		T	149068615	C	T	149068615	3	4	140	1	0	0	0	0	1	0	0	0	17126	594	21	2	51	2	UST	6	149068615	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	9817425	149068615	22046452	48	12446											
HOXA3	3200	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	27147884	27147884	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcccctgccgccgtgtagcGcttctgtgggggtggcgggg	1	8	19	13	5	1	0	0	0	1	0	1	0	1	0	4	5	2	2	4	5	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr7:27147884G>A	ENST00000396352.4	-	3	1181	c.982C>T	c.(982-984)Cgc>Tgc	p.R328C	HOXA3_ENST00000521401.1_5'Flank|HOXA3_ENST00000317201.2_Missense_Mutation_p.R328C|HOXA-AS2_ENST00000518088.1_RNA	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	328					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						GCCGTGTAGCGCTTCTGTGGG	0.726																																					p.R328C	Esophageal Squamous(136;1368 1743 5685 7935 50360)	.											.	HOXA3-153	0			c.C982T						.						6	8	7					7																	27147884		2050	4012	6062	SO:0001583	missense	3200	exon3			TGTAGCGCTTCTG		CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.982C>T	7.37:g.27147884G>A	ENSP00000379640:p.Arg328Cys	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_030661	0	0	2	5	3	A4D181	Missense_Mutation	SNP	ENST00000396352.4	37	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.104964	0.37145	.	.	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000396350	D;D	0.86769	-2.17;-2.17	5.68	4.8	0.61643	.	0.046305	0.85682	D	0.000000	D	0.89842	0.6832	M	0.79123	2.44	0.80722	D	1	D	0.62365	0.991	P	0.50231	0.635	D	0.90827	0.4713	10	0.87932	D	0	.	13.1397	0.59428	0.0:0.0:0.5656:0.4344	.	328	O43365	HXA3_HUMAN	C	328;328;170	ENSP00000379640:R328C;ENSP00000324884:R328C	ENSP00000324884:R328C	R	-	1	0	HOXA3	27114409	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	3.812000	0.55628	1.395000	0.46643	0.655000	0.94253	CGC	.		0.726	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			A	27147884	G	A	27147884	3	1	140	1	0	0	0	0	1	0	0	0	7314	1087	38	1	353	1	HOXA3	7	27147884	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		27147884	131990779	49	12447											
ABCA13	154664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48411809	48411809	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgatccatttcctggcCtggttcctggagaacatggc	7	11	11	12	0	0	2	0	1	0	1	3	3	3	2	5	4	1	1	5	4	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr7:48411809C>A	ENST00000435803.1	+	33	10872	c.10848C>A	c.(10846-10848)gcC>gcA	p.A3616A		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3616					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATTTCCTGGCCTGGTTCCTGG	0.463																																					p.A3616A		.											.	ABCA13-521	0			c.C10848A						.						178	170	173					7																	48411809		2026	4187	6213	SO:0001819	synonymous_variant	154664	exon33			CCTGGCCTGGTTC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.10848C>A	7.37:g.48411809C>A		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	84	32	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.		0.463	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48411809	C	A	48411809	2	1	140	1	0	0	0	0	0	0	0	1	31	668	24	4		4	ABCA13	7	48411809	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	21263925	48411809	110726854	50	12448											
TMEM139	135932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	142983611	142983611	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agttggaccaaccaccccccTacagcactgttgtgataccc	10	8	7	16	0	0	1	0	1	0	0	0	2	0	2	6	1	4	3	6	1	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr7:142983611T>C	ENST00000359333.3	+	3	853	c.340T>C	c.(340-342)Tac>Cac	p.Y114H	TMEM139_ENST00000409102.1_Missense_Mutation_p.Y114H|CASP2_ENST00000392925.2_5'Flank|TMEM139_ENST00000471161.1_3'UTR|AC073342.12_ENST00000446192.1_RNA|TMEM139_ENST00000409244.1_Missense_Mutation_p.Y114H|TMEM139_ENST00000409541.1_Missense_Mutation_p.Y114H|TMEM139_ENST00000410004.1_Missense_Mutation_p.Y114H|CASP2_ENST00000310447.5_5'Flank|AC073342.12_ENST00000427392.1_RNA	NM_001242775.2|NM_001282876.1|NM_001282877.1	NP_001229704.1|NP_001269805.1|NP_001269806.1	Q8IV31	TM139_HUMAN	transmembrane protein 139	114						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|ovary(1)|prostate(1)	7	Melanoma(164;0.059)					ACCACCCCCCTACAGCACTGT	0.577																																					p.Y114H		.											.	TMEM139-90	0			c.T340C						.						72	77	75					7																	142983611		2203	4300	6503	SO:0001583	missense	135932	exon4			CCCCCCTACAGCA	AK075067	CCDS5878.1	7q34	2006-03-17			ENSG00000178826	ENSG00000178826			22058	protein-coding gene	gene with protein product							Standard	NM_153345		Approved	FLJ90586	uc003wck.4	Q8IV31	OTTHUMG00000152652	ENST00000359333.3:c.340T>C	7.37:g.142983611T>C	ENSP00000352284:p.Tyr114His	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	148	46	NM_001242773	0	0	34	73	39	B2RCL5|D3DXD4|Q6ZME2|Q8NC22|Q96AU8	Missense_Mutation	SNP	ENST00000359333.3	37	CCDS5878.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.391665	0.62066	.	.	ENSG00000178826	ENST00000409102;ENST00000359333;ENST00000409244;ENST00000409541;ENST00000410004	.	.	.	5.1	5.1	0.69264	.	0.000000	0.56097	D	0.000028	T	0.72423	0.3458	M	0.65498	2.005	0.36979	D	0.894208	D	0.89917	1.0	D	0.91635	0.999	T	0.79264	-0.1875	9	0.87932	D	0	-14.1344	11.6253	0.51142	0.0:0.0:0.0:1.0	.	114	Q8IV31	TM139_HUMAN	H	114	.	ENSP00000352284:Y114H	Y	+	1	0	TMEM139	142693733	0.999000	0.42202	0.998000	0.56505	0.511000	0.34104	3.868000	0.56055	2.076000	0.62316	0.456000	0.33151	TAC	.		0.577	TMEM139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327145.1	NM_153345		C	142983611	T	C	142983611	3	2	140	1	0	0	0	0	1	0	0	0	16086	1522	53	3	346	3	TMEM139	7	142983611	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	94571802	142983611	16155052	51	12449											
CA8	767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	61192348	61192348	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagaggcggacatccaacagCgaggggtcatacctagcctc	11	5	13	12	2	1	1	1	0	0	1	3	4	2	2	3	4	4	0	3	4	3	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:61192348C>T	ENST00000317995.4	-	2	456	c.192G>A	c.(190-192)tcG>tcA	p.S64S		NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	64					one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	CATCCAACAGCGAGGGGTCAT	0.473																																					p.S64S		.											.	CA8-90	0			c.G192A						.						92	86	88					8																	61192348		2203	4300	6503	SO:0001819	synonymous_variant	767	exon2			CAACAGCGAGGGG	L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"Carbonic anhydrases"	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.192G>A	8.37:g.61192348C>T		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	103	66	NM_004056	0	0	0	0	0	A8K0A5|B3KQZ7|Q32MY2	Silent	SNP	ENST00000317995.4	37	CCDS6174.1																																																																																			.		0.473	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383445.1			T	61192348	C	T	61192348	2	4	140	1	0	0	0	0	0	0	0	1	2529	755	27	1		1	CA8	8	61192348	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		61192348	85171674	52	12450											
ZC3H3	23144	hgsc.bcm.edu	37	chr8	144550696	144550696	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccggatgatggccaggctgCgctgcactgcccggctgcag	5	6	16	14	3	0	1	0	1	0	0	0	2	0	2	3	4	4	5	3	4	0	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:144550696C>T	ENST00000262577.5	-	7	1992	c.1961G>A	c.(1960-1962)cGc>cAc	p.R654H		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	654					mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			GGCCAGGCTGCGCTGCACTGC	0.677																																					p.R654H		.											.	ZC3H3-91	0			c.G1961A						.						24	30	28					8																	144550696		2191	4297	6488	SO:0001583	missense	23144	exon7			AGGCTGCGCTGCA	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"Zinc fingers, CCCH-type domain containing"	28972	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 3"	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.1961G>A	8.37:g.144550696C>T	ENSP00000262577:p.Arg654His	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	28	2	NM_015117	0	0	15	15	0	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864699	0.91511	.	.	ENSG00000014164	ENST00000262577	T	0.04049	3.72	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000001	T	0.21267	0.0512	M	0.68952	2.095	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.00382	-1.1775	10	0.72032	D	0.01	-20.1301	18.3055	0.90179	0.0:1.0:0.0:0.0	.	654	Q8IXZ2	ZC3H3_HUMAN	H	654	ENSP00000262577:R654H	ENSP00000262577:R654H	R	-	2	0	ZC3H3	144621839	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	7.212000	0.77941	2.348000	0.79779	0.561000	0.74099	CGC	.		0.677	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117		T	144550696	C	T	144550696	3	4	140	1	0	0	0	0	1	0	0	0	17601	768	27	1	909	1	ZC3H3	8	144550696	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	83358348	144550696	1813326	53	12451											
MAPK15	225689	hgsc.bcm.edu	37	chr8	144802400	144802400	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccttctgctgccccagAcctcctggctctcggctcag	5	9	8	19	1	3	1	1	0	2	1	5	1	4	1	6	2	2	3	6	2	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:144802400A>G	ENST00000338033.4	+	8	841	c.722A>G	c.(721-723)gAc>gGc	p.D241G	RP11-429J17.5_ENST00000527908.1_RNA|MAPK15_ENST00000395107.4_Splice_Site_p.D258G|MAPK15_ENST00000395108.2_Intron	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCTGCCCCAGACCTCCTGGCT	0.682																																					p.D241G		.											.	MAPK15-1378	0			c.A722G						.						25	24	24					8																	144802400		2195	4292	6487	SO:0001630	splice_region_variant	225689	exon8			CCCCAGACCTCCT	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"Mitogen-activated protein kinase cascade / Kinases"	24667	protein-coding gene	gene with protein product	"extracellular signal regulated kinase 8"					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.722-1A>G	8.37:g.144802400A>G		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_139021	0	0	0	0	0	Q2TCF9|Q8N362	Missense_Mutation	SNP	ENST00000338033.4	37	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	a	18.12	3.553270	0.65425	.	.	ENSG00000181085	ENST00000338033;ENST00000395107	T;T	0.67698	-0.28;-0.28	3.64	3.64	0.41730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053347	0.64402	D	0.000001	T	0.76730	0.4028	M	0.63428	1.95	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.78455	-0.2197	10	0.87932	D	0	.	10.1299	0.42672	1.0:0.0:0.0:0.0	.	241	Q8TD08	MK15_HUMAN	G	241;258	ENSP00000337691:D241G;ENSP00000378539:D258G	ENSP00000337691:D241G	D	+	2	0	MAPK15	144874388	0.998000	0.40836	0.996000	0.52242	0.669000	0.39330	1.934000	0.40163	1.521000	0.48983	0.397000	0.26171	GAC	.		0.682	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	Missense_Mutation	G	144802400	A	G	144802400	5	3	140	1	0	0	0	0	0	0	1	0	9302	289	10	3	752	3	MAPK15	8	144802400	Splice_Site	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	251704	144802400	1561622	54	12452											
GPT	2875	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	145732311	145732312	+	Frame_Shift_Ins	INS	-	-	A																															ggatgaccattctgccccccINSttggagaaactgcggctgct																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:145732311_145732312insA	ENST00000528431.1	+	12	1576_1577	c.1419_1420insA	c.(1420-1422)ttgfs	p.L474fs	MFSD3_ENST00000301327.4_5'Flank|GPT_ENST00000394955.2_Frame_Shift_Ins_p.L474fs			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	474					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)		L-Alanine(DB00160)|Phenelzine(DB00780)	TTCTGCCCCCCTTGGAGAAACT	0.629																																					p.P473fs		.											.	GPT-91	0			c.1419_1420insA						.																																			SO:0001589	frameshift_variant	2875	exon11			.		CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	Exception_encountered	8.37:g.145732311_145732312insA	ENSP00000433586:p.Leu474fs	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	109	36	NM_005309	0	0	0	0	0	B0YJ18|D3DWM7|P78398|Q93076	Frame_Shift_Ins	INS	ENST00000528431.1	37	CCDS6430.1																																																																																			.		0.629	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1			A	145732312	-	A	145732311	7	5	140	1	0	1	1	0	0	0	0	0	6758	668	24	0	1461	0	GPT	8	145732311	Frame_Shift_Ins	INS	-	TCGA-IZ-8195-01A-31D-2396-08	929911	145732311	631711	55	12453											
FBXO10	26267	hgsc.bcm.edu	37	chr9	37537315	37537315	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgagttcagcactaggCagctgggcagctgaatggat	10	8	15	8	0	1	2	1	2	0	0	1	3	1	3	0	3	3	7	0	3	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:37537315C>A	ENST00000432825.2	-	3	1259	c.1211G>T	c.(1210-1212)tGc>tTc	p.C404F	FBXO10_ENST00000541829.1_Intron|FBXO10_ENST00000543968.1_5'Flank|RP11-613M10.8_ENST00000544475.1_5'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	404					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		CAGCACTAGGCAGCTGGGCAG	0.592																																					p.C404F		.											.	FBXO10-637	0			c.G1211T						.						20	23	22					9																	37537315		2001	4173	6174	SO:0001583	missense	26267	exon3			ACTAGGCAGCTGG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"F-boxes /  "other""	13589	protein-coding gene	gene with protein product		609092	"F-box only protein 10"			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1211G>T	9.37:g.37537315C>A	ENSP00000403802:p.Cys404Phe	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	26	2	NM_012166	0	0	0	0	0	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.876989	0.33162	.	.	ENSG00000147912	ENST00000432825	T	0.43294	0.95	5.46	3.59	0.41128	Carbohydrate-binding/sugar hydrolysis domain (1);	0.267734	0.36134	N	0.002765	T	0.21103	0.0508	N	0.14661	0.345	0.80722	D	1	B	0.26775	0.159	B	0.20955	0.032	T	0.10154	-1.0642	10	0.52906	T	0.07	-29.5035	4.512	0.11915	0.1905:0.6273:0.0:0.1822	.	404	Q9UK96	FBX10_HUMAN	F	404	ENSP00000403802:C404F	ENSP00000276960:C404F	C	-	2	0	FBXO10	37527315	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	1.381000	0.34362	2.543000	0.85770	0.655000	0.94253	TGC	.		0.592	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			A	37537315	C	A	37537315	3	1	140	1	0	0	0	0	1	0	0	0	5745	710	25	4	1695	4	FBXO10	9	37537315	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		37537315	103676116	56	12454											
CBWD3	220869	hgsc.bcm.edu	37	chr9	70490003	70490003	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgtcgtctcaatgggaacCaattcaggacaatcctcctc	10	10	8	13	2	2	0	2	0	1	0	7	2	4	2	3	2	2	0	3	2	4	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:70490003C>A	ENST00000382405.3	-	1	243	c.66G>T	c.(64-66)ttG>ttT	p.L22F	CBWD5_ENST00000429800.2_Missense_Mutation_p.L22F|CBWD5_ENST00000377392.5_5'Flank|CBWD5_ENST00000377395.4_Missense_Mutation_p.L22F|CBWD5_ENST00000377384.1_Missense_Mutation_p.L22F|CBWD5_ENST00000430059.2_Missense_Mutation_p.L22F			Q5RIA9	CBWD5_HUMAN	COBW domain containing 5	22							ATP binding (GO:0005524)								all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CAATGGGAACCAATTCAGGAC	0.537																																					p.L22F		.											.	CBWD5-22	0			c.G66T						.						5	4	4					9																	70490003		1428	2636	4064	SO:0001583	missense	220869	exon1			GGGAACCAATTCA	BC067803, BC082271	CCDS75841.1, CCDS75843.1, CCDS75844.1	9q13	2005-08-23			ENSG00000147996	ENSG00000147996			24584	protein-coding gene	gene with protein product	"dopamine responsive protein"						Standard	XM_005272748		Approved		uc004ack.3	Q5RIA9	OTTHUMG00000013336	ENST00000382405.3:c.66G>T	9.37:g.70490003C>A	ENSP00000371842:p.Leu22Phe	Somatic	528	0		WXS	Illumina HiSeq	Phase_I	380	46	NM_001024916	0	0	32	33	1	Q8N7U8	Missense_Mutation	SNP	ENST00000382405.3	37		.	.	.	.	.	.	.	.	.	.	.	17.81	3.480990	0.63849	.	.	ENSG00000147996	ENST00000382405;ENST00000377395;ENST00000430059;ENST00000429800;ENST00000377384	T;T;T;T;T	0.53206	2.83;2.76;2.82;2.79;0.63	3.14	3.14	0.36123	.	0.000000	0.64402	D	0.000001	T	0.63331	0.2502	M	0.75884	2.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65166	-0.6234	10	0.62326	D	0.03	-15.2117	7.7474	0.28877	0.2503:0.7497:0.0:0.0	.	22;22;22	B4DNG9;Q5RIA9-3;Q5RIA9	.;.;CBWD5_HUMAN	F	22	ENSP00000371842:L22F;ENSP00000366612:L22F;ENSP00000397999:L22F;ENSP00000405076:L22F;ENSP00000366601:L22F	ENSP00000366601:L22F	L	-	3	2	CBWD5	69729823	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.362000	0.52314	1.738000	0.51689	0.393000	0.25936	TTG	.		0.537	CBWD5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000037131.2			A	70490003	C	A	70490003	3	1	140	1	0	0	0	0	1	0	0	0	2720	593	21	4	1181	4	CBWD3	9	70490003	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	32952688	70490003	70723428	57	12455											
C9orf5	23731	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	111853340	111853340	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttcctatttcaggccttcGtctgcccagagtaggtgaag	7	12	11	11	2	2	2	1	1	1	1	4	2	3	2	3	2	1	2	3	2	3	5			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:111853340G>A	ENST00000374586.3	-	5	1043	c.1012C>T	c.(1012-1014)Cga>Tga	p.R338*		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	338						integral component of membrane (GO:0016021)											TCAGGCCTTCGTCTGCCCAGA	0.502																																					p.R338X		.											.	.	0			c.C1012T						.						102	105	104					9																	111853340		1918	4124	6042	SO:0001587	stop_gained	23731	exon5			GCCTTCGTCTGCC	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 5"	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.1012C>T	9.37:g.111853340G>A	ENSP00000363714:p.Arg338*	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	85	15	NM_032012	0	0	25	25	0	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Nonsense_Mutation	SNP	ENST00000374586.3	37	CCDS43858.1	.	.	.	.	.	.	.	.	.	.	G	36	5.709073	0.96821	.	.	ENSG00000106771	ENST00000374587;ENST00000374586;ENST00000223608	.	.	.	5.68	3.78	0.43462	.	0.612323	0.16965	N	0.192324	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.7849	16.3662	0.83325	0.0:0.2216:0.7784:0.0	.	.	.	.	X	338	.	ENSP00000223608:R338X	R	-	1	2	C9orf5	110893161	1.000000	0.71417	0.646000	0.29493	0.959000	0.62525	3.441000	0.52893	0.708000	0.31955	0.563000	0.77884	CGA	.		0.502	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		A	111853340	G	A	111853340	4	1	140	1	0	0	0	0	0	1	0	0	2492	1153	40	1	1683	1	C9orf5	9	111853340	Nonsense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	41363337	111853340	29360091	58	12456											
C9orf171	389799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	135447853	135447853	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaccgggaagagtgtgccGtgcgccaggggaccctgcgg	6	4	17	14	4	0	1	0	0	0	1	0	3	0	3	5	4	3	0	5	4	1	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:135447853G>A	ENST00000343036.2	+	7	967	c.919G>A	c.(919-921)Gtg>Atg	p.V307M	C9orf171_ENST00000393216.2_Missense_Mutation_p.V271M	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	307										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						AGAGTGTGCCGTGCGCCAGGG	0.602																																					p.V307M		.											.	C9orf171-157	0			c.G919A						.						54	52	53					9																	135447853		2203	4300	6503	SO:0001583	missense	389799	exon7			TGTGCCGTGCGCC	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.919G>A	9.37:g.135447853G>A	ENSP00000343290:p.Val307Met	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	62	32	NM_207417	0	0	0	0	0	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.648988	0.67358	.	.	ENSG00000188523	ENST00000343036;ENST00000393216	T;T	0.24350	1.87;1.86	5.53	4.62	0.57501	.	0.411149	0.21865	N	0.067979	T	0.34193	0.0889	L	0.36672	1.1	0.21897	N	0.999488	D;D	0.76494	0.995;0.999	P;P	0.60117	0.578;0.869	T	0.07195	-1.0785	10	0.56958	D	0.05	.	10.6586	0.45690	0.0906:0.0:0.9094:0.0	.	271;307	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	M	307;271	ENSP00000343290:V307M;ENSP00000376909:V271M	ENSP00000343290:V307M	V	+	1	0	C9orf171	134437674	0.997000	0.39634	0.952000	0.39060	0.875000	0.50365	3.331000	0.52075	2.617000	0.88574	0.542000	0.68232	GTG	.		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		A	135447853	G	A	135447853	3	1	140	1	0	0	0	0	1	0	0	0	2476	1145	40	1	945	1	C9orf171	9	135447853	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	23594513	135447853	5765578	59	12457											
SNAPC4	6621	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139273027	139273027	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggtacaggaacagggagaagCccctgggctgtgagcaccca	11	4	15	11	0	0	2	0	1	0	1	0	4	0	3	3	4	4	3	3	4	3	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:139273027C>G	ENST00000298532.2	-	21	3620	c.3252G>C	c.(3250-3252)ggG>ggC	p.G1084G		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CAGGGAGAAGCCCCTGGGCTG	0.687																																					p.G1084G													.	SNAPC4-90	0			c.G3252C						.						6	7	7					9																	139273027		2086	4149	6235	SO:0001819	synonymous_variant	6621	exon21			GAGAAGCCCCTGG	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"small nuclear RNA activating complex, polypeptide 4, 190kD"			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.3252G>C	9.37:g.139273027C>G		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	16	4	NM_003086	0	0	1	2	1		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			.		0.687	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		G	139273027	C	G	139273027	2	3	140	1	0	0	0	0	0	0	0	1	14869	726	26	4		4	SNAPC4	9	139273027	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	3825174	139273027	1940404	60	12458											
GTPBP4	23560	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	1061760	1061760	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaaagcgggaagactctgCtcccccgtcctctgtggccc	8	7	11	15	2	2	2	0	0	2	2	4	3	4	3	4	2	2	1	4	2	3	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:1061760C>A	ENST00000360803.4	+	16	1758	c.1676C>A	c.(1675-1677)gCt>gAt	p.A559D	GTPBP4_ENST00000538293.1_Missense_Mutation_p.A443D|GTPBP4_ENST00000545048.1_Missense_Mutation_p.A512D	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	559					GTP catabolic process (GO:0006184)|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 collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		GAAGACTCTGCTCCCCCGTCC	0.552																																					p.A559D		.											.	GTPBP4-92	0			c.C1676A						.						137	124	128					10																	1061760		2203	4300	6503	SO:0001583	missense	23560	exon16			ACTCTGCTCCCCC	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"G protein-binding protein CRFG", " GTP-binding protein"					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.1676C>A	10.37:g.1061760C>A	ENSP00000354040:p.Ala559Asp	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	166	55	NM_012341	0	0	6	13	7	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Missense_Mutation	SNP	ENST00000360803.4	37	CCDS31132.1	.	.	.	.	.	.	.	.	.	.	C	4.232	0.041906	0.08196	.	.	ENSG00000107937	ENST00000360803;ENST00000538293;ENST00000545048	T;T;T	0.32753	1.44;1.45;1.44	5.67	2.86	0.33363	.	0.344788	0.32868	N	0.005550	T	0.13628	0.0330	N	0.14661	0.345	0.34292	D	0.683401	B	0.10296	0.003	B	0.17098	0.017	T	0.20638	-1.0269	10	0.12103	T	0.63	-11.4058	4.131	0.10149	0.2318:0.1869:0.0:0.5813	.	559	Q9BZE4	NOG1_HUMAN	D	559;443;512	ENSP00000354040:A559D;ENSP00000444277:A443D;ENSP00000445473:A512D	ENSP00000354040:A559D	A	+	2	0	GTPBP4	1051760	0.537000	0.26386	0.749000	0.31150	0.005000	0.04900	0.845000	0.27668	0.256000	0.21614	-0.218000	0.12543	GCT	.		0.552	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341		A	1061760	C	A	1061760	3	1	140	1	0	0	0	0	1	0	0	0	6903	797	28	4	1738	4	GTPBP4	10	1061760	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		1061760	134472987	61	12459											
KLF6	1316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	3822362	3822362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcggaagtgcctggttaactCatcacttcttgcaaaacgcc	10	11	8	12	2	3	0	2	0	1	0	4	1	3	1	2	2	4	2	2	2	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:3822362C>T	ENST00000497571.1	-	3	996	c.736G>A	c.(736-738)Gag>Aag	p.E246K	KLF6_ENST00000542957.1_Intron|KLF6_ENST00000173785.4_5'UTR	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	246					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		CTGGTTAACTCATCACTTCTT	0.542																																					p.E246K		.											.	KLF6-1134	0			c.G736A						.						222	168	186					10																	3822362		2203	4300	6503	SO:0001583	missense	1316	exon3			TTAACTCATCACT	U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	2235	protein-coding gene	gene with protein product	"GC-rich binding factor"	602053	"core promoter element binding protein"	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.736G>A	10.37:g.3822362C>T	ENSP00000419923:p.Glu246Lys	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	77	23	NM_001300	0	0	43	90	47	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Missense_Mutation	SNP	ENST00000497571.1	37	CCDS7060.1	.	.	.	.	.	.	.	.	.	.	C	36	5.975022	0.97162	.	.	ENSG00000067082	ENST00000497571	T	0.51071	0.72	5.67	5.67	0.87782	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.053414	0.85682	D	0.000000	T	0.56156	0.1966	N	0.17379	0.485	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.995;0.998	T	0.62234	-0.6897	10	0.87932	D	0	.	18.7705	0.91890	0.0:1.0:0.0:0.0	.	204;246	D3GC14;Q99612	.;KLF6_HUMAN	K	246	ENSP00000419923:E246K	ENSP00000419923:E246K	E	-	1	0	KLF6	3812362	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.702000	0.84576	2.677000	0.91161	0.561000	0.74099	GAG	.		0.542	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			T	3822362	C	T	3822362	3	4	140	1	0	0	0	0	1	0	0	0	8371	835	29	2	123	2	KLF6	10	3822362	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	2760602	3822362	131712385	62	12460											
KIN	509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	7829859	7829859	+	5'Flank	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccttggacttgatcctgttgGcgatagccttgggagtaaga	8	12	13	8	1	0	2	0	1	0	1	1	5	1	4	3	3	1	2	3	3	2	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:7829859G>C	ENST00000356708.7	+	0	0				KIN_ENST00000535925.1_Missense_Mutation_p.A13G|KIN_ENST00000379562.4_Missense_Mutation_p.A13G|ATP5C1_ENST00000335698.4_5'Flank|ATP5C1_ENST00000541227.1_5'Flank|KIN_ENST00000543003.1_5'UTR	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1						ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						GATCCTGTTGGCGATAGCCTT	0.612																																					p.A13G	Melanoma(143;1012 1820 16249 30920 33158)	.											.	KIN-230	0			c.C38G						.						108	107	108					10																	7829859		2203	4300	6503	SO:0001631	upstream_gene_variant	22944	exon1			CTGTTGGCGATAG	D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639		10.37:g.7829859G>C	Exception_encountered	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	145	67	NM_012311	0	0	1	1	0	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Missense_Mutation	SNP	ENST00000356708.7	37	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942900	0.73672	.	.	ENSG00000151657	ENST00000535925;ENST00000379562	.	.	.	5.97	5.97	0.96955	.	0.224004	0.45606	D	0.000341	T	0.48714	0.1515	L	0.41236	1.265	0.80722	D	1	P;P	0.40970	0.734;0.734	B;B	0.28991	0.097;0.097	T	0.53387	-0.8446	9	0.52906	T	0.07	-11.2701	20.4301	0.99081	0.0:0.0:1.0:0.0	.	13;13	B4DX32;O60870	.;KIN17_HUMAN	G	13	.	ENSP00000368881:A13G	A	-	2	0	KIN	7869865	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.909000	0.48758	2.834000	0.97654	0.557000	0.71058	GCC	.		0.612	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		C	7829859	G	C	7829859	1	2	140	0	1	0	0	0	0	0	0	0	8336	1203	42	4		4	KIN	10	7829859	5'Flank	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	4007497	7829859	127704888	63	12461											
MGEA5	10724	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	103563517	103563517	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacatcttttctcactccAttcatgtttgatttgtacca	9	18	3	11	0	3	1	2	1	2	0	5	1	4	1	2	0	2	2	2	0	2	7			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:103563517A>G	ENST00000361464.3	-	7	1406	c.1011T>C	c.(1009-1011)aaT>aaC	p.N337N	MGEA5_ENST00000439817.1_Silent_p.N337N|MGEA5_ENST00000370094.3_Silent_p.N337N|MGEA5_ENST00000357797.5_Silent_p.N337N	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	337					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		TTCTCACTCCATTCATGTTTG	0.438																																					p.N337N		.											.	MGEA5-93	0			c.T1011C						.						113	107	109					10																	103563517		2203	4300	6503	SO:0001819	synonymous_variant	10724	exon7			CACTCCATTCATG	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"nuclear cytoplasmic O-GlcNAcase and acetyltransferase"	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.1011T>C	10.37:g.103563517A>G		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	116	9	NM_001142434	0	0	9	9	0	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Silent	SNP	ENST00000361464.3	37	CCDS7520.1																																																																																			.		0.438	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		G	103563517	A	G	103563517	2	3	140	1	0	0	0	0	0	0	0	1	9580	214	8	3		3	MGEA5	10	103563517	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	95733658	103563517	31971230	64	12462											
NPS	594857	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr10	129347639	129347639	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgggaagtccaaaatgattAggtaaaaggctacgtttttc	13	13	10	5	1	0	1	0	1	0	0	2	2	1	2	1	3	1	3	1	3	7	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:129347639A>G	ENST00000398023.1	+	1	27	c.7A>G	c.(7-9)Agc>Ggc	p.S3G		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	3					neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						CAAAATGATTAGGTAAAAGGC	0.348																																					p.S3G		.											.	NPS-22	0			c.A7G						.						120	114	116					10																	129347639		1824	4084	5908	SO:0001630	splice_region_variant	594857	exon1			ATGATTAGGTAAA	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"Endogenous ligands"	33940	protein-coding gene	gene with protein product	"prepro-neuropeptide S"	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.8+1A>G	10.37:g.129347639A>G		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	37	4	NM_001030013	0	0	0	0	0		Missense_Mutation	SNP	ENST00000398023.1	37	CCDS41577.1	.	.	.	.	.	.	.	.	.	.	A	1.347	-0.592491	0.03799	.	.	ENSG00000214285	ENST00000398023	T	0.33216	1.42	5.72	0.828	0.18841	.	0.509696	0.13562	N	0.378760	T	0.14056	0.0340	.	.	.	0.21861	N	0.999501	B	0.14805	0.011	B	0.14578	0.011	T	0.34875	-0.9811	9	0.08599	T	0.76	2.0E-4	9.0261	0.36230	0.7136:0.0:0.2864:0.0	.	3	P0C0P6	NPS_HUMAN	G	3	ENSP00000381105:S3G	ENSP00000381105:S3G	S	+	1	0	NPS	129237629	0.925000	0.31364	0.777000	0.31699	0.054000	0.15201	1.856000	0.39389	-0.032000	0.13758	-0.899000	0.02877	AGC	.		0.348	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013	Missense_Mutation	G	129347639	A	G	129347639	5	3	140	1	0	0	0	0	0	0	1	0	10625	434	15	3	9	3	NPS	10	129347639	Splice_Site	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	25784122	129347639	6187108	65	12463											
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6662595	6662595	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtgcccacgccgctgccctCttgggcagagatgaagtaca	8	8	12	13	2	1	2	0	1	1	1	1	3	1	2	3	1	3	3	3	1	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:6662595C>G	ENST00000299441.3	-	2	661	c.250G>C	c.(250-252)Gag>Cag	p.E84Q		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	84	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCGCTGCCCTCTTGGGCAGAG	0.627																																					p.E84Q		.											.	DCHS1-73	0			c.G250C						.						35	35	35					11																	6662595		2201	4296	6497	SO:0001583	missense	8642	exon2			TGCCCTCTTGGGC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.250G>C	11.37:g.6662595C>G	ENSP00000299441:p.Glu84Gln	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	49	20	NM_003737	0	0	2	4	2	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772553	0.69992	.	.	ENSG00000166341	ENST00000299441	T	0.38401	1.14	5.41	5.41	0.78517	Cadherin (3);Cadherin-like (1);	0.000000	0.47093	D	0.000243	T	0.50103	0.1596	L	0.33245	0.995	0.54753	D	0.999986	D	0.69078	0.997	D	0.75020	0.985	T	0.42344	-0.9457	10	0.40728	T	0.16	.	18.1884	0.89799	0.0:1.0:0.0:0.0	.	84	Q96JQ0	PCD16_HUMAN	Q	84	ENSP00000299441:E84Q	ENSP00000299441:E84Q	E	-	1	0	DCHS1	6619171	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.783000	0.85696	2.536000	0.85505	0.643000	0.83706	GAG	.		0.627	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		G	6662595	C	G	6662595	3	3	140	1	0	0	0	0	1	0	0	0	4293	922	32	4	9726	4	DCHS1	11	6662595	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		6662595	128343921	66	12464											
OR5F1	338674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55761615	55761615	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaatgacaagctgctgaCatggcttgtgttgaccatga	12	10	11	8	0	0	5	0	4	0	1	0	5	0	5	1	1	2	4	1	1	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:55761615C>T	ENST00000278409.1	-	1	486	c.487G>A	c.(487-489)Gtc>Atc	p.V163I		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	163					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					AAGCTGCTGACATGGCTTGTG	0.483																																					p.V163I		.											.	OR5F1-70	0			c.G487A						.						73	69	71					11																	55761615		2201	4296	6497	SO:0001583	missense	338674	exon1			TGCTGACATGGCT	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.487G>A	11.37:g.55761615C>T	ENSP00000278409:p.Val163Ile	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	108	48	NM_003697	0	0	0	0	0	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	C	1.364	-0.588052	0.03799	.	.	ENSG00000149133	ENST00000278409	T	0.00099	8.73	2.8	-5.6	0.02497	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.02111	-0.68	0.09310	N	1	B	0.14012	0.009	B	0.15870	0.014	T	0.02975	-1.1087	9	0.33141	T	0.24	.	7.0422	0.25027	0.1404:0.1464:0.0:0.7132	.	163	O95221	OR5F1_HUMAN	I	163	ENSP00000278409:V163I	ENSP00000278409:V163I	V	-	1	0	OR5F1	55518191	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-2.797000	0.00763	-0.940000	0.03705	0.297000	0.19635	GTC	.		0.483	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		T	55761615	C	T	55761615	3	4	140	1	0	0	0	0	1	0	0	0	11184	478	17	2	460	2	OR5F1	11	55761615	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	49099020	55761615	79244901	67	12465			1	38		2	2	22	N	C_A	7.190426e-05
OR5F1	338674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55761636	55761636	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggcttgtgttgaccatgaAgttcagcaaccctgcagcaa	11	10	10	10	0	1	2	1	2	0	0	1	2	1	2	2	1	4	6	2	1	3	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:55761636A>C	ENST00000278409.1	-	1	465	c.466T>G	c.(466-468)Ttc>Gtc	p.F156V		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	156					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					TTGACCATGAAGTTCAGCAAC	0.507																																					p.F156V		.											.	OR5F1-70	0			c.T466G						.						56	55	55					11																	55761636		2201	4296	6497	SO:0001583	missense	338674	exon1			CCATGAAGTTCAG	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.466T>G	11.37:g.55761636A>C	ENSP00000278409:p.Phe156Val	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	95	31	NM_003697	0	0	0	0	0	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	A	4.403	0.074536	0.08485	.	.	ENSG00000149133	ENST00000278409	T	0.36157	1.27	2.96	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.15089	0.0364	N	0.02286	-0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19095	-1.0316	9	0.87932	D	0	.	7.3055	0.26445	0.7399:0.0:0.0:0.2601	.	156	O95221	OR5F1_HUMAN	V	156	ENSP00000278409:F156V	ENSP00000278409:F156V	F	-	1	0	OR5F1	55518212	0.000000	0.05858	0.976000	0.42696	0.068000	0.16541	-0.848000	0.04326	1.136000	0.42199	0.155000	0.16302	TTC	.		0.507	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		C	55761636	A	C	55761636	3	2	140	1	0	0	0	0	1	0	0	0	11184	72	3	5	481	5	OR5F1	11	55761636	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	21	55761636	79244880	68	12466			1	38		2	2	22	N	C_A	7.190426e-05
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751585	76751585	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcggccacgagggcatccTggcccttcggcgtgcagctt	5	7	14	15	4	0	0	0	0	0	0	2	1	1	0	3	4	3	3	3	4	0	2	rs11292199		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:76751585T>G	ENST00000354301.5	+	4	1076	c.988T>G	c.(988-990)Tgg>Ggg	p.W330G	B3GNT6_ENST00000421061.1_Splice_Site|B3GNT6_ENST00000533140.1_Silent_p.P330P	NM_138706.3	NP_619651.3	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						GAGGGCATCCTGGCCCTTCGG	0.697																																					.		.											.	.	0			c.988+1T>G						.						6	5	6					11																	76751585		1175	2610	3785	SO:0001630	splice_region_variant	192134	exon3			GCATCCTGGCCCT	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000354301.5:c.988-1T>G	11.37:g.76751585T>G		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_138706	0	0	0	0	0	Q4TTN0	Splice_Site	SNP	ENST00000354301.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	7.627|7.627	0.677983|0.677983	0.14841|0.14841	.|.	.|.	ENSG00000198488|ENSG00000198488	ENST00000354301;ENST00000421061|ENST00000354301	.|T	.|0.27104	.|1.69	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34308	.|0.0893	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.12142	.|-1.0559	.|4	.|0.54805	.|T	.|0.06	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|G	-1|330	.|ENSP00000346256:W330G	.|ENSP00000346256:W330G	.|W	+|+	.|1	.|0	B3GNT6|B3GNT6	76429233|76429233	0.988000|0.988000	0.35896|0.35896	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	0.000000|0.000000	0.12993|0.12993	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	.|TGG	.		0.697	B3GNT6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138706	Missense_Mutation	G	76751585	T	G	76751585	5	3	140	1	0	0	0	0	0	0	1	0	1262	1567	55	5	992	5	B3GNT6	11	76751585	Splice_Site	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	20989949	76751585	58254931	69	12467											
MYO7A	4647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	76903188	76903188	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagggcgcccaggagcgcaaCgccccctggaggctcttctt	6	6	13	16	3	2	0	0	0	2	0	2	2	2	2	3	4	2	2	3	4	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:76903188C>T	ENST00000409709.3	+	31	4289	c.4017C>T	c.(4015-4017)aaC>aaT	p.N1339N	MYO7A_ENST00000409619.2_Silent_p.N1328N|MYO7A_ENST00000458637.2_Silent_p.N1339N	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1339	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGGAGCGCAACGCCCCCTGGA	0.662											OREG0021258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N1339N		.											.	MYO7A-138	0			c.C4017T						.						59	69	66					11																	76903188		2114	4216	6330	SO:0001819	synonymous_variant	4647	exon31			GCGCAACGCCCCC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"A-kinase anchor proteins", "Myosins / Myosin superfamily : Class VII"	7606	protein-coding gene	gene with protein product		276903	"myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.4017C>T	11.37:g.76903188C>T		Somatic	106	0	1171	WXS	Illumina HiSeq	Phase_I	77	35	NM_000260	0	0	0	0	0	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.		0.662	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76903188	C	T	76903188	2	4	140	1	0	0	0	0	0	0	0	1	10107	535	19	1		1	MYO7A	11	76903188	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	151603	76903188	58103328	70	12468											
PRDM10	56980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	129817185	129817185	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcctccagtctgcctagaggGgtctgcagagttgccaaagg	8	8	14	11	0	2	2	0	0	2	2	3	2	3	2	4	3	3	2	4	3	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:129817185G>A	ENST00000360871.3	-	5	606	c.375C>T	c.(373-375)acC>acT	p.T125T	PRDM10_ENST00000358825.5_Silent_p.T125T|PRDM10_ENST00000528746.1_Silent_p.T99T|PRDM10_ENST00000423662.2_Silent_p.T39T|PRDM10_ENST00000526082.1_Silent_p.T39T|PRDM10_ENST00000304538.6_Silent_p.T39T	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TGCCTAGAGGGGTCTGCAGAG	0.547																																					p.T125T		.											.	PRDM10-91	0			c.C375T						.						202	123	150					11																	129817185		2201	4297	6498	SO:0001819	synonymous_variant	56980	exon5			TAGAGGGGTCTGC	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"Zinc fingers, C2H2-type"	13995	protein-coding gene	gene with protein product	"PRDM zinc finger transcription factor", "PR-domain family member 7", "tristanin"					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.375C>T	11.37:g.129817185G>A		Somatic	93	1		WXS	Illumina HiSeq	Phase_I	79	28	NM_020228	0	0	2	2	0	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			.		0.547	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129817185	G	A	129817185	2	1	140	1	0	0	0	0	0	0	0	1	12480	1219	43	2		2	PRDM10	11	129817185	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	52913997	129817185	5189331	71	12469											
LRP1	4035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57573720	57573720	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagcagccccatggccttGtcgtccaccctctgcgtggg	4	9	13	15	2	1	0	0	0	1	0	3	1	2	1	5	3	3	1	5	3	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr12:57573720G>A	ENST00000243077.3	+	30	5588	c.5122G>A	c.(5122-5124)Gtc>Atc	p.V1708I		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1708					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCATGGCCTTGTCGTCCACCC	0.622																																					p.V1708I		.											.	LRP1-596	0			c.G5122A						.						80	84	82					12																	57573720		2203	4300	6503	SO:0001583	missense	4035	exon30			GGCCTTGTCGTCC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"CD molecules", "Low density lipoprotein receptors"	6692	protein-coding gene	gene with protein product		107770	"alpha-2-macroglobulin receptor"	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5122G>A	12.37:g.57573720G>A	ENSP00000243077:p.Val1708Ile	Somatic	200	0		WXS	Illumina HiSeq	Phase_I	127	54	NM_002332	0	0	9	17	8	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135943	0.77662	.	.	ENSG00000123384	ENST00000243077	D	0.91792	-2.91	5.01	5.01	0.66863	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000008	D	0.94814	0.8325	L	0.58669	1.825	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	D	0.94336	0.7566	10	0.46703	T	0.11	.	17.2551	0.87053	0.0:0.0:1.0:0.0	.	1708	Q07954	LRP1_HUMAN	I	1708	ENSP00000243077:V1708I	ENSP00000243077:V1708I	V	+	1	0	LRP1	55859987	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	9.622000	0.98378	2.606000	0.88127	0.655000	0.94253	GTC	.		0.622	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57573720	G	A	57573720	3	1	140	1	0	0	0	0	1	0	0	0	8976	1377	48	2	5240	2	LRP1	12	57573720	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		57573720	76278175	72	12470											
C12orf51	283450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112668608	112668608	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccacatgcccactgatgaaGggacgcacaggatcagtcct	11	6	11	13	1	1	2	1	2	0	0	2	4	2	4	3	2	1	1	3	2	1	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr12:112668608G>A	ENST00000430131.2	-	39	6098	c.4953C>T	c.(4951-4953)ccC>ccT	p.P1651P	HECTD4_ENST00000550722.1_Silent_p.P1927P|HECTD4_ENST00000377560.5_Silent_p.P1901P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1651					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CACTGATGAAGGGACGCACAG	0.498																																					p.P1939P		.											.	.	0			c.C5817T						.						84	76	79					12																	112668608		2068	4230	6298	SO:0001819	synonymous_variant	283450	exon40			GATGAAGGGACGC	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 51"	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.4953C>T	12.37:g.112668608G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	15	5	NM_001109662	0	0	1	4	3	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				.		0.498	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112668608	G	A	112668608	2	1	140	1	0	0	0	0	0	0	0	1	1700	987	35	2		2	C12orf51	12	112668608	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	55094888	112668608	21183287	73	12471											
ZMYM5	9205	hgsc.bcm.edu	37	chr13	20398977	20398977	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctgtattatcttttggAaagttaaaatttcttacttg	10	19	5	7	0	2	0	0	0	2	0	3	1	3	1	1	1	1	2	1	1	6	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:20398977A>G	ENST00000337963.4	-	8	1914	c.1650T>C	c.(1648-1650)ttT>ttC	p.F550F		NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	550						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		tatcttttggaaagttaaaat	0.378																																					p.F550F		.											.	ZMYM5-90	0			c.T1650C						.						23	21	22					13																	20398977		1568	3582	5150	SO:0001819	synonymous_variant	9205	exon8			TTTTGGAAAGTTA	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.1650T>C	13.37:g.20398977A>G		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	14	2	NM_001142684	0	0	5	5	0	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Silent	SNP	ENST00000337963.4	37																																																																																				.		0.378	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		G	20398977	A	G	20398977	2	3	140	1	0	0	0	0	0	0	0	1	17735	243	9	3		3	ZMYM5	13	20398977	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		20398977	94770901	74	12472											
MTMR6	9107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	25823587	25823587	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgaatgtaacaattccttgGtgaggatgccatctgtttgc	9	14	10	8	0	1	2	0	2	1	0	2	3	2	3	2	2	3	2	2	2	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:25823587G>C	ENST00000381801.5	-	14	2410	c.1649C>G	c.(1648-1650)aCc>aGc	p.T550S	AL590787.1_ENST00000408397.1_RNA|MTMR6_ENST00000540661.1_Intron	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	550					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		CAATTCCTTGGTGAGGATGCC	0.353																																					p.T550S		.											.	MTMR6-94	0			c.C1649G						.						145	137	139					13																	25823587		2203	4300	6503	SO:0001583	missense	9107	exon14			TCCTTGGTGAGGA	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.1649C>G	13.37:g.25823587G>C	ENSP00000371221:p.Thr550Ser	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	58	24	NM_004685	0	0	6	14	8	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	37	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252375	0.22880	.	.	ENSG00000139505	ENST00000381801;ENST00000319298	D	0.94092	-3.35	5.65	4.76	0.60689	.	0.280543	0.39210	N	0.001422	D	0.82701	0.5094	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74551	-0.3628	10	0.15066	T	0.55	.	6.229	0.20724	0.0787:0.1336:0.6502:0.1375	.	550	Q9Y217	MTMR6_HUMAN	S	550;118	ENSP00000371221:T550S	ENSP00000317987:T118S	T	-	2	0	MTMR6	24721587	0.998000	0.40836	0.987000	0.45799	0.992000	0.81027	0.947000	0.29082	2.833000	0.97629	0.655000	0.94253	ACC	.		0.353	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		C	25823587	G	C	25823587	3	2	140	1	0	0	0	0	1	0	0	0	9972	1261	44	4	220	4	MTMR6	13	25823587	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	5424610	25823587	89346291	75	12473											
C13orf23	80209	hgsc.bcm.edu	37	chr13	39588610	39588610	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgacttgctggggtggaaAatgctatatggaagggggaa	11	10	17	3	0	0	1	0	1	0	0	0	4	0	4	0	6	2	3	0	6	6	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:39588610A>C	ENST00000352251.3	-	11	1612	c.779T>G	c.(778-780)tTt>tGt	p.F260C	PROSER1_ENST00000350125.3_Missense_Mutation_p.F238C|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	260	Pro-rich.																TGGGGTGGAAAATGCTATATG	0.378																																					p.F260C		.											.	.	0			c.T779G						.						57	54	55					13																	39588610		2203	4300	6503	SO:0001583	missense	80209	exon11			GTGGAAAATGCTA	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 23"	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.779T>G	13.37:g.39588610A>C	ENSP00000332034:p.Phe260Cys	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_025138	0	0	0	0	0	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	A	17.32	3.359517	0.61403	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.34472	1.37;1.36	5.09	5.09	0.68999	.	.	.	.	.	T	0.52435	0.1734	L	0.59436	1.845	0.38844	D	0.956135	D;D	0.69078	0.997;0.997	D;D	0.63192	0.912;0.912	T	0.55049	-0.8201	8	.	.	.	-18.4404	14.0355	0.64642	1.0:0.0:0.0:0.0	.	238;260	A6NJ97;Q86XN7	.;PRSR1_HUMAN	C	260;238	ENSP00000332034:F260C;ENSP00000339123:F238C	.	F	-	2	0	PROSER1	38486610	1.000000	0.71417	0.263000	0.24496	0.887000	0.51463	6.071000	0.71229	1.912000	0.55364	0.528000	0.53228	TTT	.		0.378	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		C	39588610	A	C	39588610	3	2	140	1	0	0	0	0	1	0	0	0	1725	14	1	5	2067	5	C13orf23	13	39588610	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	13765023	39588610	75581268	76	12474											
IPO5	3843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	98652854	98652854	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggacttggtggaaagctcGttctgccgatgatcaaggaa	10	9	14	8	3	2	1	1	1	1	0	3	5	2	4	1	4	2	2	1	4	3	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:98652854G>A	ENST00000490680.1	+	10	1128	c.1063G>A	c.(1063-1065)Gtt>Att	p.V355I	IPO5_ENST00000261574.5_Missense_Mutation_p.V373I|IPO5_ENST00000539640.1_Missense_Mutation_p.V230I			O00410	IPO5_HUMAN	importin 5	355	Ran-GTP binding. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						TGGAAAGCTCGTTCTGCCGAT	0.418																																					p.V373I		.											.	IPO5-228	0			c.G1117A						.						138	119	125					13																	98652854		2203	4300	6503	SO:0001583	missense	3843	exon13			AAGCTCGTTCTGC	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.1063G>A	13.37:g.98652854G>A	ENSP00000418393:p.Val355Ile	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	67	33	NM_002271	0	0	11	20	9	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	37		.	.	.	.	.	.	.	.	.	.	G	14.28	2.486959	0.44249	.	.	ENSG00000065150	ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.99	5.99	0.97316	Armadillo-like helical (1);Armadillo-type fold (1);	0.052583	0.85682	D	0.000000	T	0.10465	0.0256	N	0.05280	-0.08	0.58432	D	0.999996	B;B;B	0.17852	0.024;0.013;0.023	B;B;B	0.23716	0.021;0.013;0.048	T	0.21177	-1.0253	10	0.07644	T	0.81	-0.6551	20.4756	0.99175	0.0:0.0:1.0:0.0	.	230;355;373	B4E0R6;O00410;O00410-3	.;IPO5_HUMAN;.	I	373;355;355;230	ENSP00000261574:V373I;ENSP00000350219:V355I;ENSP00000418393:V355I;ENSP00000445126:V230I	ENSP00000261574:V373I	V	+	1	0	IPO5	97450855	1.000000	0.71417	0.795000	0.32087	0.974000	0.67602	6.319000	0.72871	2.847000	0.97988	0.655000	0.94253	GTT	.		0.418	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		A	98652854	G	A	98652854	3	1	140	1	0	0	0	0	1	0	0	0	7817	1145	40	1	1159	1	IPO5	13	98652854	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	59064244	98652854	16517024	77	12475											
FARP1	10160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99037979	99037979	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattgcccgtcggctagagAtgtatggaatccggttgcac	9	10	13	9	3	0	2	0	0	0	2	2	4	1	3	2	3	2	4	2	3	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:99037979A>C	ENST00000319562.6	+	8	935	c.670A>C	c.(670-672)Atg>Ctg	p.M224L	FARP1_ENST00000595437.1_Missense_Mutation_p.M224L|FARP1_ENST00000376586.2_Missense_Mutation_p.M224L	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	224	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TCGGCTAGAGATGTATGGAAT	0.488																																					p.M224L		.											.	FARP1-290	0			c.A670C						.						102	98	99					13																	99037979		2203	4300	6503	SO:0001583	missense	10160	exon8			CTAGAGATGTATG	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.670A>C	13.37:g.99037979A>C	ENSP00000322926:p.Met224Leu	Somatic	183	0		WXS	Illumina HiSeq	Phase_I	110	39	NM_005766	0	0	34	68	34	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.839552	0.51057	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	D;D	0.82619	-1.63;-1.63	5.85	4.63	0.57726	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.075237	0.85682	D	0.000000	D	0.88555	0.6468	M	0.63428	1.95	0.58432	D	0.999996	B;D	0.60575	0.019;0.988	B;D	0.77557	0.026;0.99	D	0.86464	0.1781	10	0.32370	T	0.25	.	12.9994	0.58666	0.8652:0.1348:0.0:0.0	.	224;224	Q9Y4F1;C9JME2	FARP1_HUMAN;.	L	224	ENSP00000365771:M224L;ENSP00000322926:M224L	ENSP00000322926:M224L	M	+	1	0	FARP1	97835980	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.144000	0.71762	0.994000	0.38892	0.533000	0.62120	ATG	.		0.488	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		C	99037979	A	C	99037979	3	2	140	1	0	0	0	0	1	0	0	0	5695	333	12	5	919	5	FARP1	13	99037979	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	385125	99037979	16131899	78	12476											
MYO16	23026	hgsc.bcm.edu	37	chr13	109793009	109793009	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcatcgccgcccctgctccaCcgcgcgccggaggacgaggc	5	3	14	19	7	0	0	0	0	0	0	2	3	1	2	6	3	1	2	6	3	0	0	rs141423536	byFrequency	TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:109793009C>T	ENST00000357550.2	+	31	4424	c.4383C>T	c.(4381-4383)caC>caT	p.H1461H	MYO16_ENST00000356711.2_Silent_p.H1461H	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCCTGCTCCACCGCGCGCCGG	0.761													C|||	89	0.0177716	0.0023	0.0317	5008	,	,		6208	0		0.0527	False		,,,				2504	0.0112				p.H1483H		.											.	MYO16-142	0			c.C4449T						.						1	2	2					13																	109793009		1243	2621	3864	SO:0001819	synonymous_variant	23026	exon32			GCTCCACCGCGCG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"Myosins / Myosin superfamily : Class XVI", "Ankyrin repeat domain containing"	29822	protein-coding gene	gene with protein product	"neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3", "protein phosphatase 1, regulatory subunit 107"	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4383C>T	13.37:g.109793009C>T		Somatic	1	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_001198950	0	0	0	0	0		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			C|0.974;T|0.026		0.761	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109793009	C	T	109793009	2	4	140	1	0	0	0	0	0	0	0	1	10089	506	18	2		2	MYO16	13	109793009	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	10755030	109793009	5376869	79	12477											
C14orf73	91828	hgsc.bcm.edu	37	chr14	103569068	103569068	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacgcccgcggctgcgagcaGctctatatcctgctggactg	6	8	13	14	4	1	0	0	0	1	0	2	3	2	1	2	2	4	4	2	2	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr14:103569068G>C	ENST00000380069.3	+	2	1084	c.1008G>C	c.(1006-1008)caG>caC	p.Q336H		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	336					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						GCTGCGAGCAGCTCTATATCC	0.711																																					p.Q336H		.											.	EXOC3L4-23	0			c.G1008C						.						3	5	4					14																	103569068		1976	3896	5872	SO:0001583	missense	91828	exon2			CGAGCAGCTCTAT	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 73"	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.1008G>C	14.37:g.103569068G>C	ENSP00000369409:p.Gln336His	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	4	2	NM_001077594	0	0	0	0	0	Q14CR2	Missense_Mutation	SNP	ENST00000380069.3	37	CCDS32163.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.766182	0.49574	.	.	ENSG00000205436	ENST00000380069	T	0.06449	3.3	4.09	3.1	0.35709	.	0.178569	0.34853	N	0.003631	T	0.16514	0.0397	M	0.65975	2.015	0.35903	D	0.830539	D	0.89917	1.0	D	0.79108	0.992	T	0.05257	-1.0896	10	0.72032	D	0.01	-32.8675	3.7055	0.08398	0.1324:0.0:0.6206:0.247	.	336	Q17RC7	EX3L4_HUMAN	H	336	ENSP00000369409:Q336H	ENSP00000369409:Q336H	Q	+	3	2	EXOC3L4	102638821	0.999000	0.42202	1.000000	0.80357	0.611000	0.37282	0.218000	0.17622	2.124000	0.65301	0.491000	0.48974	CAG	.		0.711	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093		C	103569068	G	C	103569068	3	2	140	1	0	0	0	0	1	0	0	0	1783	962	34	4	1014	4	C14orf73	14	103569068	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		103569068	3780472	80	12478											
RYR3	6263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	33961646	33961646	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatttccatgaggaccttcTccttcactgtggtaagctgc	7	14	9	11	0	2	2	1	2	1	0	4	3	3	3	3	2	2	2	3	2	1	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:33961646T>C	ENST00000389232.4	+	37	5781	c.5711T>C	c.(5710-5712)cTc>cCc	p.L1904P	RYR3_ENST00000415757.3_Missense_Mutation_p.L1904P	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1904	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GAGGACCTTCTCCTTCACTGT	0.463																																					p.L1904P		.											.	RYR3-520	0			c.T5711C						.						86	83	84					15																	33961646		1868	4102	5970	SO:0001583	missense	6263	exon37			ACCTTCTCCTTCA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.5711T>C	15.37:g.33961646T>C	ENSP00000373884:p.Leu1904Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	53	21	NM_001243996	0	0	0	0	0	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.851326	0.51270	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.71341	-0.54;-0.56	5.65	4.53	0.55603	.	0.156082	0.44097	D	0.000496	T	0.69771	0.3148	M	0.61703	1.905	0.54753	D	0.999987	P;P	0.44195	0.787;0.828	B;B	0.43413	0.419;0.296	T	0.72821	-0.4177	10	0.87932	D	0	.	11.6133	0.51074	0.0:0.0688:0.0:0.9312	.	1904;1904	Q15413-2;Q15413	.;RYR3_HUMAN	P	1904	ENSP00000373884:L1904P;ENSP00000399610:L1904P	ENSP00000354735:L1904P	L	+	2	0	RYR3	31748938	1.000000	0.71417	0.639000	0.29394	0.964000	0.63967	3.815000	0.55651	1.158000	0.42547	0.533000	0.62120	CTC	.		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	33961646	T	C	33961646	3	2	140	1	0	0	0	0	1	0	0	0	13802	1551	54	3	5857	3	RYR3	15	33961646	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		33961646	68569746	81	12479											
ACTC1	70	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	35085735	35085735	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctgggcttcatcacctacGtaggagtccttctgacccat	7	12	8	14	1	4	1	2	1	2	0	5	2	5	2	3	2	1	2	3	2	2	4	rs149432225		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:35085735G>A	ENST00000290378.4	-	3	820	c.165C>T	c.(163-165)taC>taT	p.Y55Y	ACTC1_ENST00000557860.1_5'Flank|RP11-814P5.1_ENST00000503496.1_RNA	NM_005159.4	NP_005150.1	P68032	ACTC_HUMAN	actin, alpha, cardiac muscle 1	55					actin filament-based movement (GO:0030048)|actin-myosin filament sliding (GO:0033275)|actomyosin structure organization (GO:0031032)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|heart contraction (GO:0060047)|muscle filament sliding (GO:0030049)|negative regulation of apoptotic process (GO:0043066)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|skeletal muscle thin filament assembly (GO:0030240)	actin filament (GO:0005884)|actomyosin, actin portion (GO:0042643)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|I band (GO:0031674)|membrane (GO:0016020)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|myosin binding (GO:0017022)			central_nervous_system(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	31		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		CATCACCTACGTAGGAGTCCT	0.473																																					p.Y55Y		.											.	ACTC1-92	0			c.C165T						.	G		3,4399	6.2+/-15.9	0,3,2198	64	53	57		165	-10.9	0.4	15	dbSNP_134	57	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ACTC1	NM_005159.4		0,4,6495	AA,AG,GG		0.0116,0.0682,0.0308		55/378	35085735	4,12994	2201	4298	6499	SO:0001819	synonymous_variant	70	exon3			ACCTACGTAGGAG	BC009978	CCDS10041.1	15q14	2014-09-17	2006-08-24	2006-08-24	ENSG00000159251	ENSG00000159251			143	protein-coding gene	gene with protein product		102540	"actin, alpha, cardiac muscle"	ACTC		1639426	Standard	NM_005159		Approved	CMD1R	uc001ziu.1	P68032	OTTHUMG00000129675	ENST00000290378.4:c.165C>T	15.37:g.35085735G>A		Somatic	94	1		WXS	Illumina HiSeq	Phase_I	74	34	NM_005159	0	0	0	0	0	P04270	Silent	SNP	ENST00000290378.4	37	CCDS10041.1																																																																																			G|1.000;A|0.000		0.473	ACTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251876.3	NM_005159		A	35085735	G	A	35085735	2	1	140	1	0	0	0	0	0	0	0	1	195	1140	40	1		1	ACTC1	15	35085735	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	1124089	35085735	67445657	82	12480											
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	39885784	39885784	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggctcagggatactcgggccTttctgtgaaagttgtaaact	9	12	12	8	1	2	1	1	1	1	0	3	2	2	2	1	3	2	3	1	3	4	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:39885784T>C	ENST00000260356.5	+	19	3347	c.3182T>C	c.(3181-3183)cTt>cCt	p.L1061P	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1061	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TACTCGGGCCTTTCTGTGAAA	0.582																																					p.L1061P		.											.	THBS1-653	0			c.T3182C						.						107	105	106					15																	39885784		2200	4297	6497	SO:0001583	missense	7057	exon19			CGGGCCTTTCTGT		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"thrombospondin-1p180"	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.3182T>C	15.37:g.39885784T>C	ENSP00000260356:p.Leu1061Pro	Somatic	257	0		WXS	Illumina HiSeq	Phase_I	179	67	NM_003246	0	0	9	11	2	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.514534	0.85389	.	.	ENSG00000137801	ENST00000260356	D	0.95853	-3.83	5.77	5.77	0.91146	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.32357	N	0.006219	D	0.97049	0.9036	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.989;1.0	D	0.97737	1.0206	10	0.87932	D	0	-8.1512	16.0747	0.80960	0.0:0.0:0.0:1.0	.	976;1061	B4E3J7;P07996	.;TSP1_HUMAN	P	1061	ENSP00000260356:L1061P	ENSP00000260356:L1061P	L	+	2	0	THBS1	37673076	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.036000	0.88901	2.190000	0.69967	0.533000	0.62120	CTT	.		0.582	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		C	39885784	T	C	39885784	3	2	140	1	0	0	0	0	1	0	0	0	15885	1609	56	3	3252	3	THBS1	15	39885784	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	4800049	39885784	62645608	83	12481											
CGNL1	84952	hgsc.bcm.edu	37	chr15	57808995	57808995	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaatgtcgaggtcttggcGagcaggagcaacacttcaga	12	7	13	9	2	2	2	1	0	1	2	3	5	2	3	0	3	3	2	0	3	2	2	rs76645518		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:57808995G>T	ENST00000281282.5	+	9	2499	c.2421G>T	c.(2419-2421)gcG>gcT	p.A807A		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	807						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		AGGTCTTGGCGAGCAGGAGCA	0.512																																					p.A807A		.											.	CGNL1-100	0			c.G2421T						.						50	48	49					15																	57808995		2192	4292	6484	SO:0001819	synonymous_variant	84952	exon10			CTTGGCGAGCAGG	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.2421G>T	15.37:g.57808995G>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	32	3	NM_001252335	0	0	1	1	0	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Silent	SNP	ENST00000281282.5	37	CCDS10161.1																																																																																			G|0.999;A|0.001		0.512	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		T	57808995	G	T	57808995	2	4	140	1	0	0	0	0	0	0	0	1	3310	1045	37	4		4	CGNL1	15	57808995	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	17923211	57808995	44722397	84	12482											
HMG20A	10363	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	77759508	77759508	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcgagacagcaatgcaccCaaatccccccttacaggata	13	7	6	15	1	0	1	0	0	0	1	2	3	1	2	4	1	3	2	4	1	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:77759508C>A	ENST00000381714.3	+	5	737	c.309C>A	c.(307-309)ccC>ccA	p.P103P	HMG20A_ENST00000336216.4_Silent_p.P103P	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	103					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						GCAATGCACCCAAATCCCCCC	0.428																																					p.P103P		.											.	HMG20A-228	0			c.C309A						.						92	88	90					15																	77759508		2196	4294	6490	SO:0001819	synonymous_variant	10363	exon5			TGCACCCAAATCC	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.309C>A	15.37:g.77759508C>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	75	28	NM_018200	0	0	11	20	9	A6NHY3|D3DW78|Q53G31|Q9NSF6	Silent	SNP	ENST00000381714.3	37	CCDS10295.1																																																																																			.		0.428	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		A	77759508	C	A	77759508	2	1	140	1	0	0	0	0	0	0	0	1	7242	581	21	4		4	HMG20A	15	77759508	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	19950513	77759508	24771884	85	12483											
C15orf42	90381	broad.mit.edu	37	chr15	90118913	90118913	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgccctgcgcctcctcacCtatctgagttgccgattcgg	4	10	10	17	4	2	1	1	1	1	0	4	2	3	1	6	1	2	1	6	1	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:90118913C>A	ENST00000268138.7	+	1	201	c.96C>A	c.(94-96)acC>acA	p.T32T	TICRR_ENST00000560985.1_Silent_p.T32T|RP11-429B14.1_ENST00000559041.1_RNA			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	32					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										GCCTCCTCACCTATCTGAGTT	0.687																																					p.T32T													.	.	0			c.C96A						.						6	7	6					15																	90118913		1706	3871	5577	SO:0001819	synonymous_variant	90381	exon1			CCTCACCTATCTG	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.96C>A	15.37:g.90118913C>A		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	13	4	NM_152259	0	0	0	0	0	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			.		0.687	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90118913	C	A	90118913	2	1	140	1	0	0	0	0	0	0	0	1	1800	668	24	4		4	C15orf42	15	90118913	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	12359405	90118913	12412479	86	12484											
MLST8	64223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	2258565	2258565	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggggagtcctcccgcggCtggatgtggggctgcgcctt	2	8	17	14	4	0	0	0	0	0	0	2	2	2	2	4	6	1	2	4	6	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:2258565C>T	ENST00000569417.1	+	8	1167	c.813C>T	c.(811-813)ggC>ggT	p.G271G	MLST8_ENST00000382450.4_Silent_p.G270G|MLST8_ENST00000397124.1_Silent_p.G271G|MLST8_ENST00000564088.1_Silent_p.G271G|MLST8_ENST00000301725.7_3'UTR|MLST8_ENST00000301724.10_Silent_p.G271G|MLST8_ENST00000565250.1_Silent_p.G271G	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	271					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				large_intestine(3)|lung(2)|skin(1)	6						CCTCCCGCGGCTGGATGTGGG	0.677																																					p.G271G		.											.	MLST8-392	0			c.C813T						.						61	74	70					16																	2258565		2030	4167	6197	SO:0001819	synonymous_variant	64223	exon8			CCGCGGCTGGATG		CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"WD repeat domain containing"	24825	protein-coding gene	gene with protein product	"G protein beta subunit like"	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.813C>T	16.37:g.2258565C>T		Somatic	276	0		WXS	Illumina HiSeq	Phase_I	198	45	NM_001199174	0	0	104	158	54	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Silent	SNP	ENST00000569417.1	37	CCDS10462.2																																																																																			.		0.677	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372		T	2258565	C	T	2258565	2	4	140	1	0	0	0	0	0	0	0	1	9659	784	28	2		2	MLST8	16	2258565	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		2258565	88096188	87	12485											
PPP4C	5531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30094761	30094761	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatccggggcaaccatgagaGtcgccagatcacgcaggtct	10	6	13	12	3	2	2	1	1	1	2	4	4	3	2	3	3	1	2	3	3	1	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:30094761G>A	ENST00000279387.7	+	6	518	c.350G>A	c.(349-351)aGt>aAt	p.S117N	PPP4C_ENST00000561610.1_Missense_Mutation_p.S117N	NM_002720.1	NP_002711.1	P60510	PP4C_HUMAN	protein phosphatase 4, catalytic subunit	117					dephosphorylation (GO:0016311)|NIK/NF-kappaB signaling (GO:0038061)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase 4 complex (GO:0030289)	metal ion binding (GO:0046872)|NF-kappaB-inducing kinase activity (GO:0004704)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(2)|pancreas(1)|skin(1)|urinary_tract(1)	9						AACCATGAGAGTCGCCAGATC	0.592																																					p.S117N		.											.	PPP4C-226	0			c.G350A						.						101	92	95					16																	30094761		2197	4300	6497	SO:0001583	missense	5531	exon6			ATGAGAGTCGCCA		CCDS10669.1	16p11.2	2010-03-17	2010-03-05		ENSG00000149923	ENSG00000149923	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9319	protein-coding gene	gene with protein product	"protein phosphatase X, catalytic subunit"	602035	"protein phosphatase 4 (formerly X), catalytic subunit"			9177794	Standard	NM_002720		Approved	PP4, PPX	uc002dwf.3	P60510	OTTHUMG00000132113	ENST00000279387.7:c.350G>A	16.37:g.30094761G>A	ENSP00000279387:p.Ser117Asn	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	165	102	NM_002720	0	0	25	65	40	P33172	Missense_Mutation	SNP	ENST00000279387.7	37	CCDS10669.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.690325	0.88735	.	.	ENSG00000149923	ENST00000279387	D	0.85861	-2.04	5.83	5.83	0.93111	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.136138	0.64402	D	0.000003	D	0.94751	0.8306	H	0.97315	3.98	0.80722	D	1	P	0.44380	0.834	P	0.55785	0.784	D	0.95816	0.8845	10	0.87932	D	0	1.9966	18.8865	0.92379	0.0:0.0:1.0:0.0	.	117	P60510	PP4C_HUMAN	N	117	ENSP00000279387:S117N	ENSP00000279387:S117N	S	+	2	0	PPP4C	30002262	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	2.862000	0.48388	2.761000	0.94854	0.650000	0.86243	AGT	.		0.592	PPP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255155.2	NM_002720		A	30094761	G	A	30094761	3	1	140	1	0	0	0	0	1	0	0	0	12431	1029	36	2	368	2	PPP4C	16	30094761	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	27836196	30094761	60259992	88	12486											
ITFG1	81533	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	47189669	47189669	+	Frame_Shift_Del	DEL	T	T	-																															aaccggtgggcttcttgtcgTttttctctatcatctgcttt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:47189669delT	ENST00000320640.6	-	18	2028	c.1800delA	c.(1798-1800)aaafs	p.K600fs	RP11-329J18.2_ENST00000565694.1_RNA|RP11-329J18.2_ENST00000564705.1_RNA|ITFG1_ENST00000568047.1_5'UTR|ITFG1_ENST00000544001.2_3'UTR	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	600						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				CTTCTTGTCGTTTTTCTCTAT	0.328																																					p.K600fs		.											.	ITFG1-91	0			c.1800delA						.						158	171	167					16																	47189669		2202	4300	6502	SO:0001589	frameshift_variant	81533	exon18			.	AF503339	CCDS10728.1	16q12.1	2008-02-05			ENSG00000129636	ENSG00000129636			30697	protein-coding gene	gene with protein product	"T cell immunomodulatory protein"	611803				12598909	Standard	NM_030790		Approved	CDA08, TIP	uc002eet.3	Q8TB96	OTTHUMG00000133103	ENST00000320640.6:c.1800delA	16.37:g.47189669delT	ENSP00000319918:p.Lys600fs	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	239	77	NM_030790	0	0	0	0	0	Q96SR4|Q9BRE2|Q9H2V9	Frame_Shift_Del	DEL	ENST00000320640.6	37	CCDS10728.1																																																																																			.		0.328	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790		-	47189669	T	-	47189669	7	5	140	1	0	1	0	1	0	0	0	0	7890	1722	60	0	42	0	ITFG1	16	47189669	Frame_Shift_Del	DEL	T	TCGA-IZ-8195-01A-31D-2396-08	17094908	47189669	43165084	89	12487											
MARVELD3	91862	broad.mit.edu;bcgsc.ca	37	chr16	71663293	71663293	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccccttcggagagatatcTgccctcgacccccaggcctg	7	7	9	18	2	1	1	0	0	1	1	3	4	1	2	6	2	1	0	6	2	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:71663293T>A	ENST00000268485.3	+	2	535	c.491T>A	c.(490-492)cTg>cAg	p.L164Q	MARVELD3_ENST00000565261.1_Missense_Mutation_p.C110S|MARVELD3_ENST00000567501.1_5'UTR|MARVELD3_ENST00000299952.4_Missense_Mutation_p.L164Q|RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000567566.1_Missense_Mutation_p.L164Q	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	164	Pro-rich.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GAGAGATATCTGCCCTCGACC	0.502																																					p.L164Q													.	MARVELD3-91	0			c.T491A						.						97	90	92					16																	71663293		2198	4300	6498	SO:0001583	missense	91862	exon2			GATATCTGCCCTC	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.491T>A	16.37:g.71663293T>A	ENSP00000268485:p.Leu164Gln	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	118	5	NM_001017967	0	0	9	9	0	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	.	.	.	.	.	.	.	.	.	.	T	9.698	1.153699	0.21371	.	.	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.49139	0.79;0.84	5.57	3.3	0.37823	.	0.821835	0.11320	N	0.576170	T	0.48857	0.1523	L	0.34521	1.04	0.09310	N	0.999993	D;D;D	0.71674	0.958;0.958;0.998	P;P;P	0.62560	0.66;0.66;0.904	T	0.28776	-1.0033	10	0.18276	T	0.48	-13.3398	6.9002	0.24279	0.0:0.1987:0.0:0.8013	.	164;164;187	Q96A59-2;Q96A59;Q9BSH2	.;MALD3_HUMAN;.	Q	164	ENSP00000268485:L164Q;ENSP00000299952:L164Q	ENSP00000268485:L164Q	L	+	2	0	MARVELD3	70220794	0.001000	0.12720	0.001000	0.08648	0.051000	0.14879	0.598000	0.24074	0.958000	0.37956	0.459000	0.35465	CTG	.		0.502	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858		A	71663293	T	A	71663293	3	1	140	1	0	0	0	0	1	0	0	0	9344	1580	55	5	497	5	MARVELD3	16	71663293	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	24473624	71663293	18691460	90	12488											
ABR	29	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	916353	916353	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccggctcaccccgttcaTctcaatcacgtccgtgtgcc	5	10	7	19	4	4	0	4	0	1	0	7	0	6	0	6	1	1	2	6	1	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:916353T>C	ENST00000302538.5	-	17	1989	c.1843A>G	c.(1843-1845)Atg>Gtg	p.M615V	ABR_ENST00000574437.1_Missense_Mutation_p.M569V|ABR_ENST00000291107.2_Missense_Mutation_p.M578V|ABR_ENST00000572441.1_Missense_Mutation_p.M66V|ABR_ENST00000543210.2_Missense_Mutation_p.M66V|ABR_ENST00000536794.2_Missense_Mutation_p.M397V|ABR_ENST00000544583.2_Missense_Mutation_p.M569V	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	615					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		ACCCCGTTCATCTCAATCACG	0.632																																					p.M615V	Esophageal Squamous(197;2016 2115 4129 29033 46447)	.											.	ABR-91	0			c.A1843G						.						232	177	196					17																	916353		2203	4300	6503	SO:0001583	missense	29	exon17			CGTTCATCTCAAT	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	81	protein-coding gene	gene with protein product		600365	"active BCR-related gene"			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.1843A>G	17.37:g.916353T>C	ENSP00000303909:p.Met615Val	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	129	39	NM_021962	0	0	1	1	0	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	37	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152234	0.57259	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000543210	T;T;T;T;T	0.19532	2.17;2.18;2.14;3.39;3.13	5.77	5.77	0.91146	C2 calcium/lipid-binding domain, CaLB (1);	0.046264	0.85682	D	0.000000	T	0.39733	0.1089	M	0.65975	2.015	0.41941	D	0.990616	B;B;P;B	0.43578	0.128;0.452;0.811;0.129	B;P;P;B	0.60789	0.101;0.455;0.879;0.045	T	0.15037	-1.0451	10	0.16896	T	0.51	.	12.5258	0.56085	0.0:0.0:0.0:1.0	.	397;66;578;615	B7Z683;F5H3S2;Q12979-2;Q12979	.;.;.;ABR_HUMAN	V	615;569;578;397;66	ENSP00000303909:M615V;ENSP00000442048:M569V;ENSP00000291107:M578V;ENSP00000437429:M397V;ENSP00000445198:M66V	ENSP00000291107:M578V	M	-	1	0	ABR	863103	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.919000	0.56439	2.220000	0.72140	0.529000	0.55759	ATG	.		0.632	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			C	916353	T	C	916353	3	2	140	1	0	0	0	0	1	0	0	0	99	1435	50	3	764	3	ABR	17	916353	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		916353	80278857	91	12489											
CTNS	1497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	3550808	3550808	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agctcgaccaacgtcagcctCaccctgcggtaagttcctgg	8	8	10	15	3	2	0	2	0	0	0	4	1	3	0	4	2	4	3	4	2	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:3550808C>T	ENST00000046640.3	+	4	725	c.132C>T	c.(130-132)ctC>ctT	p.L44L	CTNS_ENST00000441220.2_Intron|CTNS_ENST00000381870.3_Silent_p.L44L|CTNS_ENST00000414524.2_Intron|CTNS_ENST00000399306.2_Silent_p.L44L|CTNS_ENST00000488623.1_3'UTR	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	44					adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	ACGTCAGCCTCACCCTGCGGT	0.602																																					p.L44L		.											.	CTNS-90	0			c.C132T						.						135	100	112					17																	3550808		2203	4300	6503	SO:0001819	synonymous_variant	1497	exon4			CAGCCTCACCCTG	AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"cystinosis, nephropathic"			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.132C>T	17.37:g.3550808C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	94	13	NM_001031681	0	0	0	0	0	D3DTJ5|Q8IZ01|Q9UNK6	Silent	SNP	ENST00000046640.3	37	CCDS11031.1																																																																																			.		0.602	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937		T	3550808	C	T	3550808	2	4	140	1	0	0	0	0	0	0	0	1	4027	813	29	2		2	CTNS	17	3550808	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	2634455	3550808	77644402	92	12490											
GPR179	440435	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	36486249	36486249	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgggatttagggaagAtcttgggcctgtcttcgtcc	5	13	15	8	1	2	1	0	0	2	1	4	3	3	3	2	4	0	1	2	4	2	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:36486249A>C	ENST00000342292.4	-	11	3223	c.3203T>G	c.(3202-3204)aTc>aGc	p.I1068S	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1068					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TTTAGGGAAGATCTTGGGCCT	0.562																																					p.I1068S		.											.	GPR179-93	0			c.T3203G						.						70	76	74					17																	36486249		2078	4209	6287	SO:0001583	missense	440435	exon11			GGGAAGATCTTGG		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3203T>G	17.37:g.36486249A>C	ENSP00000345060:p.Ile1068Ser	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	113	28	NM_001004334	0	0	0	0	0		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	A	0.624	-0.819832	0.02776	.	.	ENSG00000188888	ENST00000342292	T	0.52295	0.67	5.14	2.9	0.33743	.	0.633204	0.14796	N	0.297947	T	0.28200	0.0696	N	0.24115	0.695	0.18873	N	0.999981	B	0.15473	0.013	B	0.14023	0.01	T	0.17592	-1.0364	10	0.25106	T	0.35	-0.9541	3.9932	0.09546	0.6254:0.1793:0.1953:0.0	.	1068	Q6PRD1	GP179_HUMAN	S	1068	ENSP00000345060:I1068S	ENSP00000345060:I1068S	I	-	2	0	GPR179	33739775	0.000000	0.05858	0.494000	0.27515	0.138000	0.21146	-0.354000	0.07681	0.427000	0.26145	0.379000	0.24179	ATC	.		0.562	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			C	36486249	A	C	36486249	3	2	140	1	0	0	0	0	1	0	0	0	6694	333	12	5	3904	5	GPR179	17	36486249	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	32935441	36486249	44708961	93	12491											
FOXK2	3607	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	80543893	80543893	+	Frame_Shift_Del	DEL	C	C	-																															tgaccacctcgacctcccagCcacccgtcgtgcagacggtt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:80543893delC	ENST00000335255.5	+	7	1567	c.1393delC	c.(1393-1395)ccafs	p.P466fs	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	466					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			GACCTCCCAGCCACCCGTCGT	0.632																																					p.P465fs		.											.	FOXK2-226	0			c.1393delC						.						69	56	60					17																	80543893		2200	4294	6494	SO:0001589	frameshift_variant	3607	exon7			.	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1393delC	17.37:g.80543893delC	ENSP00000335677:p.Pro466fs	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	70	22	NM_004514	0	0	0	0	0	A6NEP5|Q13622|Q13623|Q13624	Frame_Shift_Del	DEL	ENST00000335255.5	37	CCDS11813.1																																																																																			.		0.632	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		-	80543893	C	-	80543893	7	5	140	1	0	1	0	1	0	0	0	0	6034	739	26	0	1419	0	FOXK2	17	80543893	Frame_Shift_Del	DEL	C	TCGA-IZ-8195-01A-31D-2396-08	44057644	80543893	651317	94	12492											
IL29	282618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	39787490	39787490	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggagttgcagctctcctgtcTtccccgggaattgggacctg	5	11	13	12	1	2	0	0	0	2	0	4	3	3	3	4	3	2	3	4	3	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:39787490T>G	ENST00000333625.2	+	2	314	c.217T>G	c.(217-219)Ttc>Gtc	p.F73V		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	73					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										CTCTCCTGTCTTCCCCGGGAA	0.572																																					p.F73V		.											.	.	0			c.T217G						.						91	86	88					19																	39787490		2203	4300	6503	SO:0001583	missense	282618	exon2			CCTGTCTTCCCCG	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"Interferons"	18363	protein-coding gene	gene with protein product		607403	"interleukin 29", "interleukin 29 (interferon, lambda 1)"	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.217T>G	19.37:g.39787490T>G	ENSP00000329991:p.Phe73Val	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	55	23	NM_172140	0	0	0	0	0	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	37	CCDS12531.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470360	0.63625	.	.	ENSG00000182393	ENST00000333625	T	0.35421	1.31	3.69	3.69	0.42338	.	0.094954	0.46758	D	0.000269	T	0.59770	0.2218	M	0.84846	2.72	0.25011	N	0.991407	D	0.71674	0.998	D	0.71870	0.975	T	0.54098	-0.8344	10	0.66056	D	0.02	-28.5284	10.3642	0.44012	0.0:0.0:0.0:1.0	.	73	Q8IU54	IL29_HUMAN	V	73	ENSP00000329991:F73V	ENSP00000329991:F73V	F	+	1	0	IL29	44479330	0.956000	0.32656	0.939000	0.37840	0.068000	0.16541	1.113000	0.31184	1.553000	0.49476	0.374000	0.22700	TTC	.		0.572	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140		G	39787490	T	G	39787490	3	3	140	1	0	0	0	0	1	0	0	0	7706	1609	56	5	223	5	IL29	19	39787490	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		39787490	19341493	95	12493											
PRR19	284338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	42814766	42814766	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgcctcagccttcatcaccCctgttgccccgaacctctgt	5	11	6	19	1	4	0	3	0	1	0	4	1	4	0	7	0	4	1	7	0	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:42814766C>T	ENST00000499536.2	+	2	1756	c.945C>T	c.(943-945)ccC>ccT	p.P315P	PRR19_ENST00000598490.1_3'UTR|TMEM145_ENST00000598766.1_5'Flank|TMEM145_ENST00000301204.3_5'Flank|PRR19_ENST00000341747.3_Silent_p.P315P			A6NJB7	PRR19_HUMAN	proline rich 19	315	Pro-rich.									NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	10		Prostate(69;0.00682)				CTTCATCACCCCTGTTGCCCC	0.652																																					p.P315P		.											.	PRR19-68	0			c.C945T						.						71	82	78					19																	42814766		2203	4300	6503	SO:0001819	synonymous_variant	284338	exon3			ATCACCCCTGTTG	AK124116	CCDS33036.1	19q13.2	2007-12-17				ENSG00000188368			33728	protein-coding gene	gene with protein product							Standard	NM_199285		Approved	MGC70924	uc002oti.3	A6NJB7		ENST00000499536.2:c.945C>T	19.37:g.42814766C>T		Somatic	300	0		WXS	Illumina HiSeq	Phase_I	218	83	NM_199285	0	0	0	0	0	A8K663|B3KW48|Q6P584	Silent	SNP	ENST00000499536.2	37	CCDS33036.1																																																																																			.		0.652	PRR19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463735.1	NM_199285		T	42814766	C	T	42814766	2	4	140	1	0	0	0	0	0	0	0	1	12620	610	22	2		2	PRR19	19	42814766	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	3027276	42814766	16314217	96	12494											
RSPH6A	81492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46317875	46317875	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctcgggctcaggcacctggGcactgtagtgtgggaagccc	6	7	16	12	1	1	0	1	0	0	0	2	1	1	1	2	4	1	5	2	4	2	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:46317875G>C	ENST00000221538.3	-	1	702	c.560C>G	c.(559-561)gCc>gGc	p.A187G	RSPH6A_ENST00000597055.1_Missense_Mutation_p.A187G|SYMPK_ENST00000598155.1_5'Flank	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	187						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						AGGCACCTGGGCACTGTAGTG	0.612																																					p.A187G		.											.	RSPH6A-91	0			c.C560G						.						41	42	42					19																	46317875		2203	4300	6503	SO:0001583	missense	81492	exon1			ACCTGGGCACTGT	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.560C>G	19.37:g.46317875G>C	ENSP00000221538:p.Ala187Gly	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	67	24	NM_030785	0	0	0	0	0	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	G	7.970	0.748802	0.15710	.	.	ENSG00000104941	ENST00000221538	T	0.14022	2.54	4.76	-7.87	0.01183	.	1.573020	0.03646	N	0.240221	T	0.05273	0.0140	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35822	-0.9773	10	0.12766	T	0.61	-6.7105	6.8603	0.24064	0.3005:0.342:0.3575:0.0	.	187	Q9H0K4	RSH6A_HUMAN	G	187	ENSP00000221538:A187G	ENSP00000221538:A187G	A	-	2	0	RSPH6A	51009715	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.503000	0.06383	-1.022000	0.03346	-0.274000	0.10170	GCC	.		0.612	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			C	46317875	G	C	46317875	3	2	140	1	0	0	0	0	1	0	0	0	13739	1203	42	4	1617	4	RSPH6A	19	46317875	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	3503109	46317875	12811108	97	12495											
MYPOP	339344	hgsc.bcm.edu	37	chr19	46394100	46394100	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatctccaccttgggggcCggtgggggcaggacaggcct	5	7	18	11	1	1	1	0	1	1	0	2	2	1	2	4	7	0	1	4	7	0	1	rs142323830	byFrequency	TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:46394100C>T	ENST00000322217.5	-	3	1067	c.981G>A	c.(979-981)ccG>ccA	p.P327P		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	327	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						CCTTGGGGGCCGGTGGGGGCA	0.697													T|||	49	0.00978435	0.003	0.0159	5008	,	,		4018	0		0.0278	False		,,,				2504	0.0061				p.P327P		.											.	MYPOP-90	0			c.G981A						.	T		20,3674		0,20,1827	3	3	3		981	-5.3	0	19	dbSNP_134	3	242,7102		1,240,3431	no	coding-synonymous	MYPOP	NM_001012643.2		1,260,5258	TT,TC,CC		3.2952,0.5414,2.3736		327/400	46394100	262,10776	1847	3672	5519	SO:0001819	synonymous_variant	339344	exon3			GGGGGCCGGTGGG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"p42 Myb-related transcription factor, partner of profilin"					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.981G>A	19.37:g.46394100C>T		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	7	6	NM_001012643	0	0	2	3	1		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			C|0.989;T|0.011		0.697	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643		T	46394100	C	T	46394100	2	4	140	1	0	0	0	0	0	0	0	1	10124	639	23	1		1	MYPOP	19	46394100	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	76225	46394100	12734883	98	12496											
PEG3	5178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	57325186	57325186	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgttcgatgtagcctgagcActccccaaaggcatttgcag	10	9	10	12	2	0	1	0	1	0	0	2	2	1	1	3	1	3	5	3	1	2	3	rs530969342		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:57325186A>G	ENST00000326441.9	-	10	4987	c.4624T>C	c.(4624-4626)Tgc>Cgc	p.C1542R	PEG3_ENST00000598410.1_Missense_Mutation_p.C1418R|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.C1542R|PEG3_ENST00000593695.1_Missense_Mutation_p.C1416R|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000391708.3_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1542					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TAGCCTGAGCACTCCCCAAAG	0.488													A|||	0	0	0	0	5008	,	,		21323	0		0	False		,,,				2504	0				p.C1542R		.											.	PEG3-164	0			c.T4624C						.						158	137	144					19																	57325186		2203	4300	6503	SO:0001583	missense	5178	exon9			CTGAGCACTCCCC	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"Zinc fingers, C2H2-type", "-", "-", "-"	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.4624T>C	19.37:g.57325186A>G	ENSP00000326581:p.Cys1542Arg	Somatic	186	0		WXS	Illumina HiSeq	Phase_I	114	35	NM_001146184	0	0	0	0	0	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417219	0.25552	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.03330	3.97;3.97	3.95	-1.91	0.07641	.	0.139082	0.33712	N	0.004636	T	0.01800	0.0057	N	0.19112	0.55	.	.	.	B;B;B	0.29432	0.159;0.244;0.244	B;B;B	0.29176	0.031;0.047;0.099	T	0.41324	-0.9515	9	0.23302	T	0.38	-3.4232	0.998	0.01471	0.2243:0.3544:0.1312:0.2901	.	1418;1542;1477	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	R	1542	ENSP00000326581:C1542R;ENSP00000403051:C1542R	ENSP00000326581:C1542R	C	-	1	0	ZIM2	62016998	0.001000	0.12720	0.008000	0.14137	0.951000	0.60555	0.315000	0.19451	-0.525000	0.06391	0.482000	0.46254	TGC	.		0.488	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			G	57325186	A	G	57325186	3	3	140	1	0	0	0	0	1	0	0	0	11746	159	6	3	146	3	PEG3	19	57325186	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	10931086	57325186	1803797	99	12497											
ZNF814	730051	broad.mit.edu	37	chr19	58384658	58384660	+	In_Frame_Del	DEL	CTT	CTT	-																															tggtgtacaaggaggtgagaCttcttcttaaataattttcc																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:58384658_58384660delCTT	ENST00000435989.2	-	3	2332_2334	c.2098_2100delAAG	c.(2098-2100)aagdel	p.K700del	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	700					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						GGAGGTGAGACTTCTTCTTAAAT	0.384																																					p.700_700del													.	.	0			c.2098_2100del						.																																			SO:0001651	inframe_deletion	730051	exon3			GTGAGACTTCTTC		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.2098_2100delAAG	19.37:g.58384664_58384666delCTT	ENSP00000410545:p.Lys700del	Somatic	12	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_001144989	0	0	0	0	0	A6NF35	In_Frame_Del	DEL	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.384	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		-	58384660	CTT	-	58384658	7	5	140	1	0	1	0	1	0	0	0	0	18208	564	20	0	471	0	ZNF814	19	58384658	In_Frame_Del	DEL	CTT	TCGA-IZ-8195-01A-31D-2396-08	1059472	58384658	744325	100	12498											
SAMHD1	25939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	35532631	35532631	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagcactggcaacctcttTtggaagagattcatagtcct	10	14	8	9	0	2	1	1	0	1	1	3	3	3	2	2	2	2	2	2	2	4	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr20:35532631T>C	ENST00000262878.4	-	13	1631	c.1432A>G	c.(1432-1434)Aaa>Gaa	p.K478E		NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	478					dATP catabolic process (GO:0046061)|defense response to virus (GO:0051607)|dGTP catabolic process (GO:0006203)|immune response (GO:0006955)|innate immune response (GO:0045087)|protein homotetramerization (GO:0051289)|regulation of innate immune response (GO:0045088)	intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dGTP binding (GO:0032567)|dGTPase activity (GO:0008832)|nucleic acid binding (GO:0003676)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	20		Myeloproliferative disorder(115;0.00878)				GCAACCTCTTTTGGAAGAGAT	0.388																																					p.K478E		.											.	SAMHD1-90	0			c.A1432G						.						167	160	163					20																	35532631		2203	4300	6503	SO:0001583	missense	25939	exon13			CCTCTTTTGGAAG	AF228421	CCDS13288.1	20q11.23	2014-09-17			ENSG00000101347	ENSG00000101347		"Sterile alpha motif (SAM) domain containing"	15925	protein-coding gene	gene with protein product	"HD domain containing 1", "monocyte protein 5", "Aicardi-Goutieres syndrome 5"	606754				11064105, 11230166	Standard	NM_015474		Approved	SBBI88, Mg11, HDDC1, MOP-5, AGS5	uc002xgh.2	Q9Y3Z3	OTTHUMG00000032402	ENST00000262878.4:c.1432A>G	20.37:g.35532631T>C	ENSP00000262878:p.Lys478Glu	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	210	124	NM_015474	0	0	6	7	1	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	37	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	T	3.335	-0.135924	0.06711	.	.	ENSG00000101347	ENST00000262878	D	0.95035	-3.59	5.58	-1.17	0.09648	.	0.908554	0.09627	N	0.776782	T	0.81880	0.4916	N	0.05012	-0.13	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.70040	-0.4981	10	0.12103	T	0.63	-4.9058	2.7471	0.05270	0.1081:0.3573:0.2665:0.2681	.	478	Q9Y3Z3	SAMH1_HUMAN	E	478	ENSP00000262878:K478E	ENSP00000262878:K478E	K	-	1	0	SAMHD1	34966045	0.001000	0.12720	0.005000	0.12908	0.362000	0.29581	-0.100000	0.10990	-0.173000	0.10761	0.460000	0.39030	AAA	.		0.388	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		C	35532631	T	C	35532631	3	2	140	1	0	0	0	0	1	0	0	0	13860	1850	64	3	464	3	SAMHD1	20	35532631	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		35532631	27492889	101	12499											
FITM2	128486	hgsc.bcm.edu	37	chr20	42939740	42939740	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtagcgccgcacggccgcccGcaccagcgttccccgcaaca	7	3	11	20	7	0	0	0	0	0	0	1	0	1	0	6	1	3	5	6	1	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr20:42939740G>A	ENST00000396825.3	-	1	69	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W		NM_001080472.1	NP_001073941.1	Q8N6M3	FITM2_HUMAN	fat storage-inducing transmembrane protein 2	17					cellular triglyceride homeostasis (GO:0035356)|cytoskeleton organization (GO:0007010)|lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of cell morphogenesis (GO:0022604)|regulation of triglyceride biosynthetic process (GO:0010866)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)				endometrium(2)|lung(2)|skin(2)	6						ACGGCCGCCCGCACCAGCGTT	0.692											OREG0025965	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R17W		.											.	FITM2-24	0			c.C49T						.						44	41	42					20																	42939740		2197	4298	6495	SO:0001583	missense	128486	exon1			CCGCCCGCACCAG	BC029662	CCDS33473.1	20q13.12	2009-04-29	2009-04-29	2009-04-29	ENSG00000197296	ENSG00000197296			16135	protein-coding gene	gene with protein product	"fat inducing transcript 2"	612029	"chromosome 20 open reading frame 142"	C20orf142		18160536	Standard	NM_001080472		Approved	dJ881L22.2, FIT2	uc002xlr.1	Q8N6M3	OTTHUMG00000032522	ENST00000396825.3:c.49C>T	20.37:g.42939740G>A	ENSP00000380037:p.Arg17Trp	Somatic	40	0	912	WXS	Illumina HiSeq	Phase_I	39	2	NM_001080472	0	0	0	0	0	A1L492|B9EGQ4|Q5TE59|Q9H3Y1	Missense_Mutation	SNP	ENST00000396825.3	37	CCDS33473.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987782	0.74589	.	.	ENSG00000197296	ENST00000396825	.	.	.	5.21	4.17	0.49024	.	0.606331	0.16941	N	0.193271	T	0.46737	0.1408	N	0.24115	0.695	0.32924	D	0.516204	D	0.76494	0.999	P	0.57620	0.824	T	0.58098	-0.7696	9	0.66056	D	0.02	.	8.8643	0.35276	0.0:0.1241:0.3961:0.4799	.	17	Q8N6M3	FITM2_HUMAN	W	17	.	ENSP00000380037:R17W	R	-	1	2	FITM2	42373154	0.867000	0.29959	0.999000	0.59377	0.698000	0.40448	1.213000	0.32407	0.962000	0.38057	0.484000	0.47621	CGG	G|1.000;A|0.000		0.692	FITM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079342.2	XM_371399		A	42939740	G	A	42939740	3	1	140	1	0	0	0	0	1	0	0	0	5918	1086	38	1	747	1	FITM2	20	42939740	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	7407109	42939740	20085780	102	12500											
SFRS15	57466	hgsc.bcm.edu	37	chr21	33057763	33057763	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggaatggatactggtggAgttataggaggtgggggtcc	9	9	20	3	0	0	0	0	0	0	0	1	5	1	5	1	9	1	1	1	9	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr21:33057763A>G	ENST00000286835.7	-	18	2626	c.2244T>C	c.(2242-2244)acT>acC	p.T748T	SCAF4_ENST00000399804.1_Silent_p.T748T|SCAF4_ENST00000434667.3_Silent_p.T733T	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	748						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						ATACTGGTGGAGTTATAGGAG	0.433																																					p.T748T		.											.	SCAF4-90	0			c.T2244C						.						92	94	93					21																	33057763		2203	4300	6503	SO:0001819	synonymous_variant	57466	exon18			TGGTGGAGTTATA	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"RNA binding motif (RRM) containing"	19304	protein-coding gene	gene with protein product			"splicing factor, arginine/serine-rich 15"	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.2244T>C	21.37:g.33057763A>G		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	96	5	NM_020706	0	0	10	10	0	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																			.		0.433	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889		G	33057763	A	G	33057763	2	3	140	1	0	0	0	0	0	0	0	1	14203	291	11	3		3	SFRS15	21	33057763	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		33057763	15072132	103	12501											
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40080409	40080409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagccagaaaggcccagaaaAgggcactggcactggaaccc	14	2	12	13	0	0	2	0	0	0	2	0	3	0	3	3	4	2	2	3	4	4	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr22:40080409A>G	ENST00000402142.3	+	36	5933	c.5933A>G	c.(5932-5934)aAg>aGg	p.K1978R	CACNA1I_ENST00000400164.3_Missense_Mutation_p.K1943R|CACNA1I_ENST00000404898.1_Missense_Mutation_p.K1943R|CACNA1I_ENST00000336649.4_Missense_Mutation_p.K1984R|CACNA1I_ENST00000407673.1_Missense_Mutation_p.K1943R|CACNA1I_ENST00000401624.1_Missense_Mutation_p.K1978R	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1978					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GGCCCAGAAAAGGGCACTGGC	0.642																																					p.K1978R		.											.	CACNA1I-135	0			c.A5933G						.						41	46	44					22																	40080409		2027	4190	6217	SO:0001583	missense	8911	exon36			CAGAAAAGGGCAC	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.5933A>G	22.37:g.40080409A>G	ENSP00000385019:p.Lys1978Arg	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	36	2	NM_021096	0	0	0	0	0	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	6.096	0.385972	0.11524	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.96967	-4.17;-4.13;-4.16;-4.12;-4.19;-4.1	5.05	2.86	0.33363	.	2.583880	0.02234	U	0.065144	D	0.91523	0.7323	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.20459	0.045;0.0;0.0;0.0	B;B;B;B	0.18561	0.022;0.001;0.001;0.0	T	0.81258	-0.1014	10	0.19147	T	0.46	.	2.9533	0.05868	0.6285:0.1545:0.0779:0.139	.	1943;1978;1943;1978	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	R	1978;1943;1978;1943;1984;1943	ENSP00000385019:K1978R;ENSP00000384093:K1943R;ENSP00000383887:K1978R;ENSP00000385680:K1943R;ENSP00000337829:K1984R;ENSP00000383028:K1943R	ENSP00000337829:K1984R	K	+	2	0	CACNA1I	38410355	0.997000	0.39634	0.308000	0.25141	0.069000	0.16628	1.737000	0.38197	0.255000	0.21593	0.459000	0.35465	AAG	.		0.642	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		G	40080409	A	G	40080409	3	3	140	1	0	0	0	0	1	0	0	0	2552	72	3	3	6075	3	CACNA1I	22	40080409	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		40080409	11224157	104	12502											
CXorf59	286464	hgsc.bcm.edu	37	chrX	36103603	36103603	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacctgtagataaccatgaaAaaagggtaattcaactccat	17	10	6	8	0	1	2	1	1	0	1	2	2	2	2	3	1	3	2	3	1	8	5			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chrX:36103603A>G	ENST00000313548.4	+	5	775	c.589A>G	c.(589-591)Aaa>Gaa	p.K197E		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	197						integral component of membrane (GO:0016021)											TAACCATGAAAAAAGGGTAAT	0.368																																					p.K197E		.											.	.	0			c.A589G						.						77	71	73					X																	36103603		2202	4300	6502	SO:0001583	missense	286464	exon5			CATGAAAAAAGGG	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"chromosome X open reading frame 59"	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.589A>G	X.37:g.36103603A>G	ENSP00000324767:p.Lys197Glu	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	39	2	NM_173695	0	0	0	0	0		Missense_Mutation	SNP	ENST00000313548.4	37	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.721792	0.00092	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	0.158	0.158	0.14942	.	0.426104	0.20758	N	0.086213	T	0.16685	0.0401	N	0.14661	0.345	0.09310	N	1	P	0.34587	0.458	B	0.39152	0.292	T	0.31861	-0.9928	8	0.02654	T	1	.	.	.	.	.	197	Q8N9S7	CX059_HUMAN	E	197	.	ENSP00000324767:K197E	K	+	1	0	CXorf59	36013524	0.994000	0.37717	0.097000	0.21041	0.017000	0.09413	0.241000	0.18065	0.160000	0.19432	0.158000	0.16466	AAA	.		0.368	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		G	36103603	A	G	36103603	3	3	140	1	0	0	0	0	1	0	0	0	4121	15	1	3	603	3	CXorf59	23	36103603	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		36103603	119166957	105	12503											
ZFY	7544	broad.mit.edu	37	chrY	2843189	2843189	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccactggagtgaccatcgatGcagaatcagaaatggatcct	13	8	10	10	1	1	3	1	1	0	2	3	6	2	5	3	2	1	1	3	2	2	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chrY:2843189G>C	ENST00000155093.3	+	4	1009	c.688G>C	c.(688-690)Gca>Cca	p.A230P	ZFY_ENST00000449237.1_Missense_Mutation_p.A204P|ZFY-AS1_ENST00000417305.1_RNA|ZFY_ENST00000431102.1_Missense_Mutation_p.A39P|ZFY_ENST00000383052.1_Missense_Mutation_p.A230P	NM_003411.3	NP_003402.2	P08048	ZFY_HUMAN	zinc finger protein, Y-linked	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|kidney(3)|large_intestine(1)|lung(3)	8						GACCATCGATGCAGAATCAGA	0.398																																					p.A230P													.	.	0			c.G688C						.						103	103	103					Y																	2843189		614	1956	2570	SO:0001583	missense	7544	exon4			ATCGATGCAGAAT	L10393	CCDS14774.1, CCDS48200.1, CCDS48201.1	Yp11.3	2013-01-08			ENSG00000067646	ENSG00000067646		"Zinc fingers, C2H2-type"	12870	protein-coding gene	gene with protein product		490000				2497060	Standard	NM_001145275		Approved	ZNF911	uc004fqj.3	P08048	OTTHUMG00000036159	ENST00000155093.3:c.688G>C	Y.37:g.2843189G>C	ENSP00000155093:p.Ala230Pro	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	11	2	NM_003411	0	0	0	0	0	B4DVF7|Q14021|Q15558|Q1RME9|Q24JR0|Q96TF3	Missense_Mutation	SNP	ENST00000155093.3	37	CCDS14774.1																																																																																			.		0.398	ZFY-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088063.1	NM_003411		C	2843189	G	C	2843189	3	2	140	1	0	0	0	0	1	0	0	0	17694	1319	46	4	698	4	ZFY	24	2843189	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		2843189	56530377	106	12504											
DDI2	84301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15956839	15956839	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacttaccccgaatagatttCagtagtatagctgtgcctgg	10	12	10	9	1	1	1	1	0	0	1	1	3	1	1	3	1	3	3	3	1	6	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:15956839C>T	ENST00000480945.1	+	3	459	c.288C>T	c.(286-288)ttC>ttT	p.F96F		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	96							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAATAGATTTCAGTAGTATAG	0.463																																					p.F96F		.											.	DDI2-44	0			c.C288T						.						87	90	89					1																	15956839		2203	4300	6503	SO:0001819	synonymous_variant	84301	exon3			AGATTTCAGTAGT		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.288C>T	1.37:g.15956839C>T		Somatic	168	0		WXS	Illumina HiSeq	Phase_I	133	66	NM_032341	0	0	0	2	2	A8KAE1|Q7RTZ0|Q9BRT1	Silent	SNP	ENST00000480945.1	37	CCDS30607.1																																																																																			.		0.463	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		T	15956839	C	T	15956839	2	4	141	1	0	0	0	0	0	0	0	1	4335	825	29	2		2	DDI2	1	15956839	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		15956839	233293782	1	12505											
PLA2G5	5322	hgsc.bcm.edu	37	chr1	20416294	20416294	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acggacaggtgctgttgggcGcatgaccactgctatgggcg	7	8	16	10	3	0	1	0	1	0	0	0	2	0	2	1	4	2	4	1	4	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:20416294G>A	ENST00000375108.3	+	4	466	c.198G>A	c.(196-198)gcG>gcA	p.A66A	PLA2G5_ENST00000486277.1_3'UTR	NM_000929.2	NP_000920.1	P39877	PA2G5_HUMAN	phospholipase A2, group V	66					arachidonic acid secretion (GO:0050482)|glycerophospholipid biosynthetic process (GO:0046474)|leukotriene biosynthetic process (GO:0019370)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|heparin binding (GO:0008201)			NS(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		GCTGTTGGGCGCATGACCACT	0.567																																					p.A66A		.											.	PLA2G5-515	0			c.G198A						.						92	75	81					1																	20416294		2203	4300	6503	SO:0001819	synonymous_variant	5322	exon4			TTGGGCGCATGAC	U03090	CCDS202.1	1p36-p34	2008-09-19			ENSG00000127472	ENSG00000127472	3.1.1.4		9038	protein-coding gene	gene with protein product		601192				8838795, 8300559	Standard	NM_000929		Approved		uc001bcy.3	P39877	OTTHUMG00000002698	ENST00000375108.3:c.198G>A	1.37:g.20416294G>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	59	3	NM_000929	0	0	0	0	0	Q8N435	Silent	SNP	ENST00000375108.3	37	CCDS202.1																																																																																			.		0.567	PLA2G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007668.1	NM_000929		A	20416294	G	A	20416294	2	1	141	1	0	0	0	0	0	0	0	1	12033	1074	38	1		1	PLA2G5	1	20416294	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	4459455	20416294	228834327	2	12506											
MSH4	4438	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	76269502	76269502	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caagctcatcttctgcacgaGatactaattatcctcaaaca	14	11	4	12	1	4	1	2	0	2	1	5	2	5	1	1	0	4	2	1	0	5	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:76269502G>A	ENST00000263187.3	+	2	435	c.331G>A	c.(331-333)Gat>Aat	p.D111N		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	111					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						TTCTGCACGAGATACTAATTA	0.363								Mismatch excision repair (MMR)																													p.D111N		.											.	MSH4-660	0			c.G331A						.						97	101	100					1																	76269502		2203	4300	6503	SO:0001583	missense	4438	exon2			GCACGAGATACTA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.331G>A	1.37:g.76269502G>A	ENSP00000263187:p.Asp111Asn	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	110	52	NM_002440	0	0	0	0	0	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326532	0.24080	.	.	ENSG00000057468	ENST00000263187	D	0.87256	-2.23	4.73	3.81	0.43845	.	0.591556	0.15780	N	0.245000	T	0.61776	0.2374	N	0.24115	0.695	0.09310	N	1	B	0.19817	0.039	B	0.11329	0.006	T	0.55392	-0.8148	10	0.49607	T	0.09	-16.9831	6.3049	0.21133	0.16:0.0:0.6929:0.147	.	111	O15457	MSH4_HUMAN	N	111	ENSP00000263187:D111N	ENSP00000263187:D111N	D	+	1	0	MSH4	76042090	0.920000	0.31207	0.889000	0.34880	0.806000	0.45545	3.225000	0.51246	0.984000	0.38629	-0.266000	0.10368	GAT	.		0.363	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		A	76269502	G	A	76269502	3	1	141	1	0	0	0	0	1	0	0	0	9897	942	33	2	337	2	MSH4	1	76269502	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	55853208	76269502	172981119	3	12507											
LRRC8C	84230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	90180228	90180228	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacattcgatttatcccccCtgaaattggagttctacaaa	12	13	6	10	1	1	2	0	2	1	0	3	4	2	3	3	1	1	1	3	1	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:90180228C>A	ENST00000370454.4	+	3	2354	c.2099C>A	c.(2098-2100)cCt>cAt	p.P700H	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	700					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		TTTATCCCCCCTGAAATTGGA	0.383																																					p.P700H		.											.	LRRC8C-97	0			c.C2099A						.						68	63	65					1																	90180228		2203	4299	6502	SO:0001583	missense	84230	exon3			TCCCCCCTGAAAT		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"hypothetical protein AD158"	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.2099C>A	1.37:g.90180228C>A	ENSP00000359483:p.Pro700His	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	77	29	NM_032270	0	0	1	1	0	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849986	0.32699	.	.	ENSG00000171488	ENST00000370454	T	0.25414	1.8	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	M	0.78049	2.395	0.80722	D	1	B	0.25351	0.124	B	0.24269	0.052	T	0.02789	-1.1110	10	0.35671	T	0.21	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	700	Q8TDW0	LRC8C_HUMAN	H	700	ENSP00000359483:P700H	ENSP00000359483:P700H	P	+	2	0	LRRC8C	89952816	1.000000	0.71417	0.801000	0.32222	0.989000	0.77384	6.050000	0.71063	2.941000	0.99782	0.655000	0.94253	CCT	.		0.383	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		A	90180228	C	A	90180228	3	1	141	1	0	0	0	0	1	0	0	0	9048	681	24	4	2105	4	LRRC8C	1	90180228	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	13910726	90180228	159070393	4	12508											
RBM15	64783	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110882978	110882978	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcttggccgcctgcccccTccacctccgccaccattgcc	3	8	7	23	2	1	0	0	0	1	0	3	0	3	0	10	1	2	1	10	1	0	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:110882978T>C	ENST00000369784.3	+	1	1851	c.951T>C	c.(949-951)ccT>ccC	p.P317P	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Silent_p.P317P|RBM15_ENST00000487146.2_Silent_p.P317P	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	317					negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GCCTGCCCCCTCCACCTCCGC	0.607			T	MKL1	acute megakaryocytic leukemia																																p.P317P		.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15-661	0			c.T951C						.						46	52	50					1																	110882978		2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			GCCCCCTCCACCT	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"RNA binding motif (RRM) containing"	14959	protein-coding gene	gene with protein product	"one twenty-two"	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.951T>C	1.37:g.110882978T>C		Somatic	214	1		WXS	Illumina HiSeq	Phase_I	112	53	NM_022768	0	0	5	5	0	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	37	CCDS822.1																																																																																			.		0.607	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		C	110882978	T	C	110882978	2	2	141	1	0	0	0	0	0	0	0	1	13148	1538	54	3		3	RBM15	1	110882978	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	20702750	110882978	138367643	5	12509											
ANKRD35	148741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145561688	145561688	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccctgatcatgctgaccAgctgcctgctggtcagaagg	7	9	13	12	0	2	3	2	2	0	1	2	3	2	3	3	3	4	3	3	3	1	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:145561688A>G	ENST00000355594.4	+	10	1463	c.1376A>G	c.(1375-1377)cAg>cGg	p.Q459R		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	459										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CATGCTGACCAGCTGCCTGCT	0.592																																					p.Q459R	Melanoma(9;127 754 22988 51047)	.											.	ANKRD35-95	0			c.A1376G						.						55	63	60					1																	145561688		2203	4300	6503	SO:0001583	missense	148741	exon10			CTGACCAGCTGCC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1376A>G	1.37:g.145561688A>G	ENSP00000347802:p.Gln459Arg	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	113	48	NM_144698	0	0	0	0	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	a	0.294	-0.978340	0.02197	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.67698	-0.28	5.54	0.0734	0.14390	.	0.859396	0.09865	N	0.745663	T	0.33760	0.0874	M	0.63428	1.95	0.09310	N	1	B	0.26935	0.164	B	0.22601	0.04	T	0.16158	-1.0412	10	0.27785	T	0.31	-2.3373	2.517	0.04670	0.4852:0.2931:0.0804:0.1412	.	459	Q8N283	ANR35_HUMAN	R	368;459	ENSP00000347802:Q459R	ENSP00000347802:Q459R	Q	+	2	0	ANKRD35	144273045	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	1.054000	0.30455	0.044000	0.15775	-0.253000	0.11424	CAG	.		0.592	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		G	145561688	A	G	145561688	3	3	141	1	0	0	0	0	1	0	0	0	664	188	7	3	1414	3	ANKRD35	1	145561688	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	34678710	145561688	103688933	6	12510											
ATP8B2	57198	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	154314963	154314968	+	In_Frame_Del	DEL	GTTTGA	GTTTGA	-																															tggctgtatgtaggtgatgtGtttgacgtcctgggacacaa																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	GTTTGA	GTTTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:154314963_154314968delGTTTGA	ENST00000368489.3	+	14	1350_1355	c.1350_1355delGTTTGA	c.(1348-1356)gtgtttgac>gtc	p.FD451del		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	437					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TAGGTGATGTGTTTGACGTCCTGGGA	0.49																																					p.450_452del		.											.	ATP8B2-92	0			c.1350_1355del						.																																			SO:0001651	inframe_deletion	57198	exon14			.	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1350_1355delGTTTGA	1.37:g.154314963_154314968delGTTTGA	ENSP00000357475:p.Phe451_Asp452del	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	67	13	NM_020452	0	0	0	0	0	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	In_Frame_Del	DEL	ENST00000368489.3	37	CCDS1066.1																																																																																			.		0.49	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		-	154314968	GTTTGA	-	154314963	7	5	141	1	0	1	0	1	0	0	0	0	1196	1364	48	0	1534	0	ATP8B2	1	154314963	In_Frame_Del	DEL	GTTTGA	TCGA-IZ-8196-01A-11D-2396-08	8753275	154314963	94935658	7	12511	126	3									
ATP8B2	57198	bcgsc.ca	37	chr1	154314970	154314970	+	Missense_Mutation	SNP	G	G	C																															atgtaggtgatgtgtttgacGtcctgggacacaaagctgaa																								rs201587979		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:154314970G>C	ENST00000368489.3	+	14	1357	c.1357G>C	c.(1357-1359)Gtc>Ctc	p.V453L		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	439					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGTGTTTGACGTCCTGGGACA	0.488																																					p.V453L													.	ATP8B2-92	0			c.G1357C						.						218	191	200					1																	154314970		2203	4300	6503	SO:0001583	missense	57198	exon14			TTTGACGTCCTGG	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1357G>C	1.37:g.154314970G>C	ENSP00000357475:p.Val453Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_1	65	14	NM_020452	0	0	7	7	0	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	37	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	G	9.215	1.031832	0.19590	.	.	ENSG00000143515	ENST00000368489	T	0.62639	0.01	5.49	4.55	0.56014	.	0.196433	0.33382	N	0.004963	T	0.19485	0.0468	N	0.03294	-0.36	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07462	-1.0771	10	0.22109	T	0.4	.	12.1628	0.54113	0.0:0.1722:0.8278:0.0	.	453	P98198-3	.	L	453	ENSP00000357475:V453L	ENSP00000357475:V453L	V	+	1	0	ATP8B2	152581594	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.253000	0.43205	1.267000	0.44247	0.561000	0.74099	GTC	G|0.999;A|0.001		0.488	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		C	154314970	G	C	154314970	3	2	141	1	0	0	0	0	1	0	0	0	1196	1145	40	4	1541	4	ATP8B2	1	154314970	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	7	154314970	94935651	8	12512	126	3									
ATP8B2	57198	bcgsc.ca	37	chr1	154314972	154314972	+	Silent	SNP	C	C	T																															gtaggtgatgtgtttgacgtCctgggacacaaagctgaatt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:154314972C>T	ENST00000368489.3	+	14	1359	c.1359C>T	c.(1357-1359)gtC>gtT	p.V453V		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	439					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGTTTGACGTCCTGGGACACA	0.483																																					p.V453V													.	ATP8B2-92	0			c.C1359T						.						217	190	199					1																	154314972		2203	4300	6503	SO:0001819	synonymous_variant	57198	exon14			TGACGTCCTGGGA	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1359C>T	1.37:g.154314972C>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_1	65	15	NM_020452	0	0	7	7	0	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			.		0.483	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		T	154314972	C	T	154314972	2	4	141	1	0	0	0	0	0	0	0	1	1196	842	30	2		2	ATP8B2	1	154314972	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	2	154314972	94935649	9	12513	126	3									
MAEL	84944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	166974561	166974561	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatctaccaacaaaaatttCtcaaggagccctctaagact	15	9	6	11	0	3	1	1	0	3	1	4	3	3	3	2	2	3	0	2	2	6	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:166974561C>A	ENST00000367872.4	+	8	1016	c.772C>A	c.(772-774)Ctc>Atc	p.L258I	MAEL_ENST00000491055.1_3'UTR|RNA5SP65_ENST00000363166.1_RNA|MAEL_ENST00000367870.2_Missense_Mutation_p.L227I	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	258					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						ACAAAAATTTCTCAAGGAGCC	0.398																																					p.L258I		.											.	MAEL-91	0			c.C772A						.						73	78	76					1																	166974561		2203	4300	6503	SO:0001583	missense	84944	exon8			AAATTTCTCAAGG	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.772C>A	1.37:g.166974561C>A	ENSP00000356846:p.Leu258Ile	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	62	28	NM_032858	0	0	2	2	0	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	37	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825645	0.32237	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.47869	0.85;0.83;0.85	5.66	4.75	0.60458	.	0.324591	0.26193	N	0.025795	T	0.13927	0.0337	N	0.08118	0	0.23765	N	0.996906	B;B	0.32071	0.301;0.355	B;B	0.38225	0.209;0.268	T	0.05920	-1.0856	10	0.42905	T	0.14	.	7.8331	0.29355	0.0:0.7505:0.1634:0.086	.	227;258	E9JVC3;Q96JY0	.;MAEL_HUMAN	I	258;227;227	ENSP00000356846:L258I;ENSP00000356844:L227I;ENSP00000402143:L227I	ENSP00000356844:L227I	L	+	1	0	MAEL	165241185	0.611000	0.26992	0.982000	0.44146	0.989000	0.77384	1.344000	0.33941	1.389000	0.46526	0.591000	0.81541	CTC	.		0.398	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		A	166974561	C	A	166974561	3	1	141	1	0	0	0	0	1	0	0	0	9179	913	32	4	802	4	MAEL	1	166974561	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	12659589	166974561	82276060	10	12514											
CNTN2	6900	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	205028742	205028742	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tttgcacccagcatcaaggcCcggttcccagcagagaccta	10	7	9	15	1	1	1	1	0	0	1	2	2	2	1	4	2	3	4	4	2	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:205028742C>A	ENST00000331830.4	+	7	1013	c.729C>A	c.(727-729)gcC>gcA	p.A243A	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	243	Ig-like C2-type 3.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GCATCAAGGCCCGGTTCCCAG	0.582																																					p.A243A	Melanoma(183;2548 2817 37099 41192)	.											.	CNTN2-91	0			c.C729A						.						90	91	91					1																	205028742		2203	4300	6503	SO:0001819	synonymous_variant	6900	exon7			CAAGGCCCGGTTC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.729C>A	1.37:g.205028742C>A		Somatic	287	0		WXS	Illumina HiSeq	Phase_I	155	53	NM_005076	0	0	0	0	0	P78432|Q5T054	Silent	SNP	ENST00000331830.4	37	CCDS1449.1																																																																																			.		0.582	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		A	205028742	C	A	205028742	2	1	141	1	0	0	0	0	0	0	0	1	3647	610	22	4		4	CNTN2	1	205028742	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	38054181	205028742	44221879	11	12515											
AHCTF1	25909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247070995	247070995	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaaacacagatggcgccCttgtctcattacactttctc	9	12	7	13	1	2	1	1	0	2	1	4	2	2	2	1	2	2	0	1	2	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:247070995C>T	ENST00000391829.2	-	5	745	c.622G>A	c.(622-624)Ggg>Agg	p.G208R	AHCTF1_ENST00000326225.3_Missense_Mutation_p.G217R|AHCTF1_ENST00000366508.1_Missense_Mutation_p.G243R			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	208	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			AGATGGCGCCCTTGTCTCATT	0.383																																					p.G217R	Colon(145;197 1800 4745 15099 26333)	.											.	AHCTF1-97	0			c.G649A						.						135	127	130					1																	247070995		2203	4300	6503	SO:0001583	missense	25909	exon5			GGCGCCCTTGTCT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"ELYS transcription factor like protein TMBS62"	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.622G>A	1.37:g.247070995C>T	ENSP00000375705:p.Gly208Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	124	58	NM_015446	0	0	7	9	2	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		.	.	.	.	.	.	.	.	.	.	C	22.0	4.223797	0.79576	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.20738	2.05;2.05;2.05	5.76	5.76	0.90799	.	0.051494	0.85682	D	0.000000	T	0.26195	0.0639	N	0.19112	0.55	0.58432	D	0.999999	D;D	0.59767	0.986;0.981	P;P	0.56474	0.799;0.706	T	0.00761	-1.1577	10	0.37606	T	0.19	-24.8597	15.7857	0.78300	0.0:0.8645:0.1355:0.0	.	243;208	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	R	243;217;208	ENSP00000355464:G243R;ENSP00000355465:G217R;ENSP00000375705:G208R	ENSP00000355465:G217R	G	-	1	0	AHCTF1	245137618	1.000000	0.71417	0.982000	0.44146	0.994000	0.84299	5.686000	0.68211	2.880000	0.98712	0.650000	0.86243	GGG	.		0.383	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247070995	C	T	247070995	3	4	141	1	0	0	0	0	1	0	0	0	408	681	24	2	6306	2	AHCTF1	1	247070995	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	42042253	247070995	2179626	12	12516											
OR2L8	391190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	248112473	248112473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagtttcttcttcttggCattaggaggtgcagaagcac	9	13	11	8	0	4	2	1	0	3	2	4	3	4	3	0	3	2	4	0	3	2	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:248112473C>T	ENST00000357191.3	+	1	314	c.314C>T	c.(313-315)gCa>gTa	p.A105V	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TTCTTCTTGGCATTAGGAGGT	0.433																																					p.A105V		.											.	OR2L8-70	0			c.C314T						.						335	270	292					1																	248112473		2203	4300	6503	SO:0001583	missense	391190	exon1			TCTTGGCATTAGG	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"GPCR / Class A : Olfactory receptors"	15014	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily L, member 8"				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.314C>T	1.37:g.248112473C>T	ENSP00000349719:p.Ala105Val	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	393	140	NM_001001963	0	0	0	0	0	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	8.579	0.881879	0.17467	.	.	ENSG00000196936	ENST00000357191	T	0.00349	7.99	1.64	1.64	0.23874	GPCR, rhodopsin-like superfamily (1);	0.542717	0.13750	U	0.365321	T	0.00178	0.0005	N	0.20483	0.58	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.41805	-0.9488	10	0.87932	D	0	.	3.6931	0.08354	0.0:0.5144:0.0:0.4856	.	105	Q8NGY9	OR2L8_HUMAN	V	105	ENSP00000349719:A105V	ENSP00000349719:A105V	A	+	2	0	OR2L8	246179096	0.000000	0.05858	0.699000	0.30290	0.027000	0.11550	-0.195000	0.09546	0.905000	0.36596	0.479000	0.44913	GCA	.		0.433	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			T	248112473	C	T	248112473	3	4	141	1	0	0	0	0	1	0	0	0	11035	710	25	2	316	2	OR2L8	1	248112473	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	1041478	248112473	1138148	13	12517											
MBOAT2	129642	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	9002791	9002791	+	Frame_Shift_Del	DEL	A	A	-																															tcctgggtataccccgtgccAaatggcagagagaatgaacg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:9002791delA	ENST00000305997.3	-	11	1312	c.1114delT	c.(1114-1116)tggfs	p.W372fs	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	372					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ACCCCGTGCCAAATGGCAGAG	0.408																																					p.W372fs	Ovarian(194;1699 3813 22401)	.											.	MBOAT2-90	0			c.1114delT						.						96	91	93					2																	9002791		2203	4300	6503	SO:0001589	frameshift_variant	129642	exon11			.	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"O-acyltransferase (membrane bound) domain containing 2"	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.1114delT	2.37:g.9002791delA	ENSP00000302177:p.Trp372fs	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	86	39	NM_138799	0	0	0	0	0	A9EDR2|Q8NCE7|Q96KY4	Frame_Shift_Del	DEL	ENST00000305997.3	37	CCDS1660.1																																																																																			.		0.408	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		-	9002791	A	-	9002791	7	5	141	1	0	1	0	1	0	0	0	0	9382	130	5	0	460	0	MBOAT2	2	9002791	Frame_Shift_Del	DEL	A	TCGA-IZ-8196-01A-11D-2396-08		9002791	234196582	14	12518											
TAF1B	9014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	10051000	10051000	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtagctatcattgtggTggtattgaaactgctctttc	8	16	10	7	0	2	1	1	1	1	0	3	1	2	1	0	2	4	5	0	2	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:10051000T>C	ENST00000263663.5	+	10	1279	c.1091T>C	c.(1090-1092)gTg>gCg	p.V364A	TAF1B_ENST00000396242.3_Missense_Mutation_p.V109A	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	364	C-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATCATTGTGGTGGTATTGAAA	0.358																																					p.V364A		.											.	TAF1B-92	0			c.T1091C						.						195	157	170					2																	10051000		2203	4300	6503	SO:0001583	missense	9014	exon10			TTGTGGTGGTATT	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.1091T>C	2.37:g.10051000T>C	ENSP00000263663:p.Val364Ala	Somatic	53	1		WXS	Illumina HiSeq	Phase_I	76	32	NM_005680	0	0	2	4	2	B4DI42|F8WD72|Q15574|Q8WVC3	Missense_Mutation	SNP	ENST00000263663.5	37	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.730164	0.30684	.	.	ENSG00000115750	ENST00000263663;ENST00000396242	T;T	0.04194	3.68;3.68	5.8	5.8	0.92144	.	0.235349	0.42821	D	0.000656	T	0.07188	0.0182	L	0.46885	1.475	0.24866	N	0.992313	B;P	0.46142	0.051;0.873	B;B	0.40782	0.02;0.34	T	0.25502	-1.0130	9	.	.	.	-9.4571	16.1464	0.81575	0.0:0.0:0.0:1.0	.	364;364	Q53T94;Q53T94-2	TAF1B_HUMAN;.	A	364;109	ENSP00000263663:V364A;ENSP00000379542:V109A	.	V	+	2	0	TAF1B	9968451	0.975000	0.34042	0.043000	0.18650	0.218000	0.24690	3.000000	0.49481	2.220000	0.72140	0.383000	0.25322	GTG	.		0.358	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		C	10051000	T	C	10051000	3	2	141	1	0	0	0	0	1	0	0	0	15552	1696	59	3	1129	3	TAF1B	2	10051000	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	1048209	10051000	233148373	15	12519											
LPIN1	23175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	11960558	11960558	+	Missense_Mutation	SNP	G	G	C																															atgtgtattcatacaagcaaGtaggagtgtctttgaataga																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:11960558G>C	ENST00000256720.2	+	19	2524	c.2431G>C	c.(2431-2433)Gta>Cta	p.V811L	LPIN1_ENST00000449576.2_Missense_Mutation_p.V896L|LPIN1_ENST00000396097.1_Missense_Mutation_p.V541L|LPIN1_ENST00000425416.2_Missense_Mutation_p.V817L|LPIN1_ENST00000404113.2_Missense_Mutation_p.V312L|LPIN1_ENST00000396099.1_Missense_Mutation_p.V853L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	811	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ATACAAGCAAGTAGGAGTGTC	0.348																																					p.V896L		.											.	LPIN1-156	0			c.G2686C						.						117	110	112					2																	11960558		2203	4300	6503	SO:0001583	missense	23175	exon21			AAGCAAGTAGGAG	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2431G>C	2.37:g.11960558G>C	ENSP00000256720:p.Val811Leu	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	74	28	NM_001261428	0	0	6	6	0	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	35	5.510636	0.96386	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113	T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	6.02	6.02	0.97574	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.055717	0.64402	D	0.000001	D	0.90007	0.6880	M	0.87682	2.9	0.80722	D	1	D;D;D	0.64830	0.994;0.988;0.975	D;P;P	0.68039	0.955;0.907;0.883	D	0.90458	0.4444	10	0.87932	D	0	-24.1549	20.5407	0.99260	0.0:0.0:1.0:0.0	.	312;896;811	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	L	896;853;817;811;541;312	ENSP00000397908:V896L;ENSP00000379406:V853L;ENSP00000401522:V817L;ENSP00000256720:V811L;ENSP00000379404:V541L;ENSP00000386120:V312L	ENSP00000256720:V811L	V	+	1	0	LPIN1	11878009	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.357000	0.97099	2.865000	0.98341	0.655000	0.94253	GTA	.		0.348	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		C	11960558	G	C	11960558	3	2	141	1	0	0	0	0	1	0	0	0	8943	1029	36	4	2501	4	LPIN1	2	11960558	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	1909558	11960558	231238815	16	12520	127	2									
LPIN1	23175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	11960560	11960560	+	Silent	SNP	A	A	G																															gtgtattcatacaagcaagtAggagtgtctttgaatagaat																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:11960560A>G	ENST00000256720.2	+	19	2526	c.2433A>G	c.(2431-2433)gtA>gtG	p.V811V	LPIN1_ENST00000449576.2_Silent_p.V896V|LPIN1_ENST00000396097.1_Silent_p.V541V|LPIN1_ENST00000425416.2_Silent_p.V817V|LPIN1_ENST00000404113.2_Silent_p.V312V|LPIN1_ENST00000396099.1_Silent_p.V853V	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	811	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ACAAGCAAGTAGGAGTGTCTT	0.348																																					p.V896V		.											.	LPIN1-156	0			c.A2688G						.						118	111	113					2																	11960560		2203	4300	6503	SO:0001819	synonymous_variant	23175	exon21			GCAAGTAGGAGTG	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2433A>G	2.37:g.11960560A>G		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	75	29	NM_001261428	0	0	7	7	0	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			.		0.348	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		G	11960560	A	G	11960560	2	3	141	1	0	0	0	0	0	0	0	1	8943	407	15	3		3	LPIN1	2	11960560	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	2	11960560	231238813	17	12521	127	2									
KIF3C	3797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	26178417	26178417	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcgtctcaccttcttgAgtttcttggttttgacctcc	4	17	8	12	1	3	2	1	2	3	0	5	2	4	2	3	1	2	3	3	1	0	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:26178417A>C	ENST00000264712.3	-	3	2342	c.1763T>G	c.(1762-1764)cTc>cGc	p.L588R	KIF3C_ENST00000405914.1_Missense_Mutation_p.L588R	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	588					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACCTTCTTGAGTTTCTTGGT	0.587																																					p.L588R		.											.	KIF3C-94	0			c.T1763G						.						229	186	200					2																	26178417		2203	4300	6503	SO:0001583	missense	3797	exon3			TTCTTGAGTTTCT		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"Kinesins"	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.1763T>G	2.37:g.26178417A>C	ENSP00000264712:p.Leu588Arg	Somatic	299	0		WXS	Illumina HiSeq	Phase_I	155	62	NM_002254	0	0	0	0	0	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	37	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.593287	0.66219	.	.	ENSG00000084731	ENST00000264712;ENST00000542511;ENST00000405914	T;T	0.78481	-1.18;-1.18	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.81669	0.4871	M	0.92026	3.265	0.80722	D	1	B;B	0.30686	0.095;0.29	B;B	0.28638	0.037;0.092	D	0.83422	0.0033	10	0.72032	D	0.01	.	13.0867	0.59144	1.0:0.0:0.0:0.0	.	588;588	B7ZM25;O14782	.;KIF3C_HUMAN	R	588;394;588	ENSP00000264712:L588R;ENSP00000385030:L588R	ENSP00000264712:L588R	L	-	2	0	KIF3C	26031921	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.119000	0.94362	1.998000	0.58463	0.459000	0.35465	CTC	.		0.587	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			C	26178417	A	C	26178417	3	2	141	1	0	0	0	0	1	0	0	0	8323	304	11	5	642	5	KIF3C	2	26178417	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	14217857	26178417	217020956	18	12522											
RBKS	64080	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	28004505	28004506	+	Frame_Shift_Ins	INS	-	-	T																															aacagagtaagcggaaggtcINSttttttgtaagggtaagatg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:28004505_28004506insT	ENST00000302188.3	-	8	1697_1698	c.945_946insA	c.(943-948)aaagacfs	p.D316fs	AC110084.1_ENST00000601759.1_Intron	NM_022128.1	NP_071411.1	Q9H477	RBSK_HUMAN	ribokinase	316					D-ribose catabolic process (GO:0019303)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ribokinase activity (GO:0004747)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(172;0.155)					AGCGGAAGGTCTTTTTTGTAAG	0.421																																					p.D316fs		.											.	RBKS-92	0			c.946_947insA						.																																			SO:0001589	frameshift_variant	64080	exon8			.	BC017425	CCDS1762.1	2p23.3	2008-02-05			ENSG00000171174	ENSG00000171174	2.7.1.15		30325	protein-coding gene	gene with protein product		611132				8382990	Standard	NM_022128		Approved	DKFZp686G13268, RBSK	uc002rlo.1	Q9H477	OTTHUMG00000097833	ENST00000302188.3:c.946dupA	2.37:g.28004511_28004511dupT	ENSP00000306817:p.Asp316fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	134	42	NM_022128	0	0	0	0	0	A9UK04|B4DV96	Frame_Shift_Ins	INS	ENST00000302188.3	37	CCDS1762.1																																																																																			.		0.421	RBKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215118.1	NM_022128		T	28004506	-	T	28004505	7	5	141	1	0	1	1	0	0	0	0	0	13140	913	32	0	26	0	RBKS	2	28004505	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	1826088	28004505	215194868	19	12523											
PLEKHH2	130271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	43953471	43953471	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaggttgacagatcttgtGattcagatgaagattatgaa	15	12	11	3	0	2	8	1	4	1	4	2	8	2	8	0	1	0	1	0	1	4	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:43953471G>T	ENST00000282406.4	+	17	2712	c.2602G>T	c.(2602-2604)Gat>Tat	p.D868Y		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	868	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CAGATCTTGTGATTCAGATGA	0.388																																					p.D868Y		.											.	PLEKHH2-92	0			c.G2602T						.						108	102	104					2																	43953471		2203	4300	6503	SO:0001583	missense	130271	exon17			TCTTGTGATTCAG	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"Pleckstrin homology (PH) domain containing"	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2602G>T	2.37:g.43953471G>T	ENSP00000282406:p.Asp868Tyr	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	74	27	NM_172069	0	0	27	61	34	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667945	0.88348	.	.	ENSG00000152527	ENST00000282406	T	0.77750	-1.12	5.57	5.57	0.84162	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.049073	0.85682	D	0.000000	D	0.88887	0.6559	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	D	0.89680	0.3890	10	0.87932	D	0	-23.2912	19.5645	0.95388	0.0:0.0:1.0:0.0	.	868;305	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	Y	868	ENSP00000282406:D868Y	ENSP00000282406:D868Y	D	+	1	0	PLEKHH2	43806975	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.386000	0.97228	2.599000	0.87857	0.650000	0.86243	GAT	.		0.388	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		T	43953471	G	T	43953471	3	4	141	1	0	0	0	0	1	0	0	0	12103	1290	45	4	2664	4	PLEKHH2	2	43953471	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	15948966	43953471	199245902	20	12524											
RAB1A	5861	hgsc.bcm.edu	37	chr2	65318133	65318133	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttacctgatctgtcacatcaTacacaactatgatgccatgg	12	12	6	11	0	3	2	2	2	1	0	3	2	3	2	2	1	4	0	2	1	4	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:65318133T>C	ENST00000409784.3	-	4	462	c.272A>G	c.(271-273)tAt>tGt	p.Y91C	RAB1A_ENST00000409892.1_Intron|RAB1A_ENST00000494188.1_Intron|RAB1A_ENST00000260638.8_Intron|RAB1A_ENST00000398529.3_Intron|RAB1A_ENST00000409751.1_Missense_Mutation_p.Y59C|RAB1A_ENST00000356214.7_Intron	NM_004161.4	NP_004152.1	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family	91					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cargo loading into COPII-coated vesicle (GO:0090110)|cell migration (GO:0016477)|defense response to bacterium (GO:0042742)|endocytosis (GO:0006897)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|growth hormone secretion (GO:0030252)|GTP catabolic process (GO:0006184)|interleukin-8 secretion (GO:0072606)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|positive regulation of glycoprotein metabolic process (GO:1903020)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle transport along microtubule (GO:0047496)|vesicle-mediated transport (GO:0016192)|virion assembly (GO:0019068)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|melanosome (GO:0042470)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|lung(3)|prostate(1)	6						TGTCACATCATACACAACTAT	0.393																																					p.Y91C		.											.	RAB1A-227	0			c.A272G						.						99	94	95					2																	65318133		1908	4132	6040	SO:0001583	missense	5861	exon4			ACATCATACACAA	M28209	CCDS46305.1, CCDS46306.1	2p14	2008-02-05		2002-03-17	ENSG00000138069	ENSG00000138069		"RAB, member RAS oncogene"	9758	protein-coding gene	gene with protein product	"Rab GTPase YPT1 homolog (yeast)"	179508		RAB1		2501306	Standard	NM_004161		Approved	YPT1	uc002sdm.3	P62820	OTTHUMG00000152725	ENST00000409784.3:c.272A>G	2.37:g.65318133T>C	ENSP00000387286:p.Tyr91Cys	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_004161	0	0	196	196	0	P11476|Q6FIE7|Q96N61|Q9Y3T2	Missense_Mutation	SNP	ENST00000409784.3	37	CCDS46306.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.498528	0.85069	.	.	ENSG00000138069	ENST00000409784;ENST00000409751	D;D	0.84070	-1.8;-1.8	5.38	5.38	0.77491	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92564	0.7638	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94061	0.7326	10	0.87932	D	0	.	15.6846	0.77400	0.0:0.0:0.0:1.0	.	91	P62820	RAB1A_HUMAN	C	91;59	ENSP00000387286:Y91C;ENSP00000386672:Y59C	ENSP00000386672:Y59C	Y	-	2	0	RAB1A	65171637	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.161000	0.67846	0.454000	0.30748	TAT	.		0.393	RAB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327572.1	NM_004161		C	65318133	T	C	65318133	3	2	141	1	0	0	0	0	1	0	0	0	12937	1406	49	3	357	3	RAB1A	2	65318133	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	21364662	65318133	177881240	21	12525											
DNAH6	1768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	84777109	84777109	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaccatctcactgacaagctAaaacgaacaccttcagcaga	17	6	5	13	1	2	2	2	1	1	1	3	3	2	2	2	0	5	2	2	0	5	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:84777109A>T	ENST00000237449.6	+	8	1421	c.1413A>T	c.(1411-1413)ctA>ctT	p.L471L	DNAH6_ENST00000398278.2_Silent_p.L471L|DNAH6_ENST00000389394.3_Silent_p.L471L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	471	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						CTGACAAGCTAAAACGAACAC	0.358																																					p.L471L		.											.	DNAH6-69	0			c.A1413T						.						94	83	87					2																	84777109		2203	4300	6503	SO:0001819	synonymous_variant	1768	exon9			CAAGCTAAAACGA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"Axonemal dyneins"	2951	protein-coding gene	gene with protein product		603336	"dynein, axonemal, heavy polypeptide 6", "dynein heavy chain-like 1"	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1413A>T	2.37:g.84777109A>T		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	66	25	NM_001370	0	0	0	0	0	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			.		0.358	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84777109	A	T	84777109	2	4	141	1	0	0	0	0	0	0	0	1	4616	349	13	5		5	DNAH6	2	84777109	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	19458976	84777109	158422264	22	12526											
POTEF	728378	hgsc.bcm.edu	37	chr2	130872496	130872496	+	Frame_Shift_Del	DEL	T	T	-																															gcaccatataagagcagtgcTttggccattaatttatcttc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:130872496delT	ENST00000409914.2	-	5	1167	c.768delA	c.(766-768)aaafs	p.K256fs	POTEF_ENST00000361163.4_Frame_Shift_Del_p.K266fs|POTEF_ENST00000360967.5_Frame_Shift_Del_p.K256fs|POTEF_ENST00000357462.5_Frame_Shift_Del_p.K256fs	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	256					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						AGAGCAGTGCTTTGGCCATTA	0.338																																					p.K256fs		.											.	POTEF-27	0			c.768delA						.						3	3	3					2																	130872496		1247	2882	4129	SO:0001589	frameshift_variant	728378	exon5			.	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33905	protein-coding gene	gene with protein product			"ANKRD26-like family C, member 1B"	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.768delA	2.37:g.130872496delT	ENSP00000386786:p.Lys256fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	114	18	NM_001099771	0	0	0	0	0	A6NC34	Frame_Shift_Del	DEL	ENST00000409914.2	37	CCDS46409.1																																																																																			.		0.338	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		-	130872496	T	-	130872496	7	5	141	1	0	1	0	1	0	0	0	0	12291	1606	56	0	2511	0	POTEF	2	130872496	Frame_Shift_Del	DEL	T	TCGA-IZ-8196-01A-11D-2396-08	46095387	130872496	112326877	23	12527											
POTEE	445582	hgsc.bcm.edu	37	chr2	131981572	131981572	+	Frame_Shift_Del	DEL	A	A	-																															atgaagataaattaatggccAaagcactgctcttatatggt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:131981572delA	ENST00000356920.5	+	3	860	c.766delA	c.(766-768)aaafs	p.K256fs	POTEE_ENST00000358087.5_Frame_Shift_Del_p.K266fs|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	256					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											ATTAATGGCCAAAGCACTGCT	0.338																																					p.K256fs		.											.	.	0			c.766delA						.						1	1	1					2																	131981572		992	2313	3305	SO:0001589	frameshift_variant	445582	exon3			.	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"POTE ankyrin domain containing", "Ankyrin repeat domain containing"	33895	protein-coding gene	gene with protein product	"cancer/testis antigen family 104, member 2"	608914	"ANKRD26-like family C, member 1A"	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.766delA	2.37:g.131981572delA	ENSP00000439189:p.Lys256fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	131	29	NM_001083538	0	0	0	0	0	Q6S8J4|Q6S8J5|Q6S8J8	Frame_Shift_Del	DEL	ENST00000356920.5	37	CCDS46414.1																																																																																			.		0.338	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		-	131981572	A	-	131981572	7	5	141	1	0	1	0	1	0	0	0	0	12290	131	5	0	776	0	POTEE	2	131981572	Frame_Shift_Del	DEL	A	TCGA-IZ-8196-01A-11D-2396-08	1109076	131981572	111217801	24	12528											
MCM6	4175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	136620201	136620202	+	Missense_Mutation	DNP	CT	CT	AG																															gaaattggctcttagctgtaCttgggtcaccaacaatgcaa																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:136620201_136620202CT>AG	ENST00000264156.2	-	8	1255_1256	c.1195_1196AG>CT	c.(1195-1197)AGt>CTt	p.S399L	MCM6_ENST00000492091.1_5'UTR	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	399	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(15)|prostate(2)|skin(1)	29				BRCA - Breast invasive adenocarcinoma(221;0.166)		CTTAGCTGTACTTGGGTCACCA	0.485																																					p.S399L	Ovarian(196;141 2104 8848 24991 25939)	.											.	MCM6	0			c.A1195C						.																																			SO:0001583	missense	4175	exon8			CTGTACTTGGGTC		CCDS2179.1	2q14-q21	2008-02-05	2007-04-04		ENSG00000076003	ENSG00000076003			6949	protein-coding gene	gene with protein product	"MIS5 homolog (S.pombe)"	601806	"minichromosome maintenance deficient (mis5, S. pombe) 6", "MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae)", "minichromosome maintenance deficient 6 homolog (S. cerevisiae)"				Standard	NM_005915		Approved	Mis5	uc002tuw.4	Q14566	OTTHUMG00000131739	ENST00000264156.2:c.1195_1196delinsAG	2.37:g.136620201_136620202delinsAG	ENSP00000264156:p.Ser399Leu	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	179	78		0	0	0	0	0	B2R6H2|Q13504|Q99859	Missense_Mutation	DNP	ENST00000264156.2	37	CCDS2179.1																																																																																			.		0.485	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		AG	136620202	CT	AG	136620201	3	1	141	1	0	0	0	0	1	0	0	0	9416	565	20	4	1309	4	MCM6	2	136620201	Missense_Mutation	DNP	CT	TCGA-IZ-8196-01A-11D-2396-08	4638629	136620201	106579172	25	12529											
HOXD8	3234	broad.mit.edu;bcgsc.ca	37	chr2	176995325	176995341	+	Frame_Shift_Del	DEL	GCCCTCCGGGACTGGGT	GCCCTCCGGGACTGGGT	-																															cacccgcacccgtccccgccGccctccgggactgggtgcgg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	GCCCTCCGGGACTGGGT	GCCCTCCGGGACTGGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:176995325_176995341delGCCCTCCGGGACTGGGT	ENST00000313173.4	+	1	858_874	c.231_247delGCCCTCCGGGACTGGGT	c.(229-249)ccgccctccgggactgggtgcfs	p.PSGTGC78fs	HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000429017.1_Intron|HOXD8_ENST00000544999.1_Frame_Shift_Del_p.PSGTGC78fs|HOXD8_ENST00000548663.1_Intron|HOXD8_ENST00000450510.2_Frame_Shift_Del_p.PSGTGC78fs	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8	78					anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		CGTCCCCGCCGCCCTCCGGGACTGGGTGCGGCGGTAG	0.788																																					p.77_83del													.	HOXD8-90	0			c.231_247del						.																																			SO:0001589	frameshift_variant	3234	exon1			CCCGCCGCCCTCC		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"Homeoboxes / ANTP class : HOXL subclass"	5139	protein-coding gene	gene with protein product		142985	"homeo box D8"	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.231_247delGCCCTCCGGGACTGGGT	2.37:g.176995325_176995341delGCCCTCCGGGACTGGGT	ENSP00000315949:p.Pro78fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	14	6	NM_001199746	0	0	0	0	0	F8WBG7|Q5BL00|Q8IXZ1	Frame_Shift_Del	DEL	ENST00000313173.4	37	CCDS2268.1																																																																																			.		0.788	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1			-	176995341	GCCCTCCGGGACTGGGT	-	176995325	7	5	141	1	0	1	0	1	0	0	0	0	7346	1074	38	0	233	0	HOXD8	2	176995325	Frame_Shift_Del	DEL	GCCCTCCGGGACTGGGT	TCGA-IZ-8196-01A-11D-2396-08	40375124	176995325	66204048	26	12530											
ATG9A	79065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220090289	220090289	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggcaaccacaaagaggAactgcctggggagttgggaa	14	5	15	7	0	0	2	0	1	0	1	0	5	0	5	2	5	3	2	2	5	5	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:220090289A>C	ENST00000409618.1	-	6	657	c.218T>G	c.(217-219)tTc>tGc	p.F73C	ATG9A_ENST00000488833.1_5'Flank|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000396761.2_Missense_Mutation_p.F73C|ATG9A_ENST00000409422.1_Missense_Mutation_p.F12C|ATG9A_ENST00000361242.4_Missense_Mutation_p.F73C			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	73					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CACAAAGAGGAACTGCCTGGG	0.532																																					p.F73C		.											.	ATG9A-91	0			c.T218G						.						71	74	73					2																	220090289		2019	4190	6209	SO:0001583	missense	79065	exon6			AAGAGGAACTGCC	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.218T>G	2.37:g.220090289A>C	ENSP00000386710:p.Phe73Cys	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	59	22	NM_001077198	0	0	0	0	0	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	37	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.360020	0.61403	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422;ENST00000436856;ENST00000457841;ENST00000428226;ENST00000432520;ENST00000439812;ENST00000443140;ENST00000434939	T;T;T;T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.05	5.05	0.67936	.	0.057192	0.64402	D	0.000001	T	0.73513	0.3596	M	0.78916	2.43	0.58432	D	0.999995	D	0.58620	0.983	B	0.43783	0.431	T	0.79808	-0.1647	10	0.72032	D	0.01	.	15.2471	0.73513	1.0:0.0:0.0:0.0	.	73	Q7Z3C6	ATG9A_HUMAN	C	73;73;73;12;73;73;73;73;73;73;73	ENSP00000379983:F73C;ENSP00000386710:F73C;ENSP00000355173:F73C;ENSP00000386535:F12C;ENSP00000401530:F73C;ENSP00000404750:F73C;ENSP00000409164:F73C;ENSP00000406785:F73C;ENSP00000413569:F73C;ENSP00000416435:F73C;ENSP00000394345:F73C	ENSP00000355173:F73C	F	-	2	0	ATG9A	219798533	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.040000	0.93783	2.251000	0.74343	0.482000	0.46254	TTC	.		0.532	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		C	220090289	A	C	220090289	3	2	141	1	0	0	0	0	1	0	0	0	1103	246	9	5	2345	5	ATG9A	2	220090289	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	43094964	220090289	23109084	27	12531											
SPHKAP	80309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	228860230	228860230	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggaagagcaggtacctcatGgatcgctcactgagctggag	10	7	15	9	1	2	2	2	1	0	1	3	5	2	5	1	4	3	4	1	4	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:228860230G>C	ENST00000392056.3	-	8	4675	c.4629C>G	c.(4627-4629)tcC>tcG	p.S1543S	SPHKAP_ENST00000344657.5_Silent_p.S1543S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1543						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GGTACCTCATGGATCGCTCAC	0.483																																					p.S1543S		.											.	SPHKAP-167	0			c.C4629G						.						226	197	207					2																	228860230		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon8			CCTCATGGATCGC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"A-kinase anchor proteins"	30619	protein-coding gene	gene with protein product	"sphingosine kinase type 1-interacting protein"	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4629C>G	2.37:g.228860230G>C		Somatic	298	1		WXS	Illumina HiSeq	Phase_I	283	107	NM_030623	0	0	0	0	0	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																			.		0.483	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		C	228860230	G	C	228860230	2	2	141	1	0	0	0	0	0	0	0	1	15080	1335	47	4		4	SPHKAP	2	228860230	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	8769941	228860230	14339143	28	12532											
CAMK1	8536	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9802445	9802445	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatagaagggagggtaacCgcagagcctgggcagggaga	12	4	18	7	1	1	3	1	0	0	3	1	5	1	4	2	4	2	3	2	4	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:9802445C>T	ENST00000256460.3	-	8	817	c.640G>A	c.(640-642)Ggt>Agt	p.G214S	OGG1_ENST00000449570.2_Intron|OGG1_ENST00000302008.8_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	214	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.G214S(1)		endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		GGAGGGTAACCGCAGAGCCTG	0.552																																					p.G214S		.											.	CAMK1-335	1	Substitution - Missense(1)	endometrium(1)	c.G640A						.						82	77	78					3																	9802445		2203	4300	6503	SO:0001583	missense	8536	exon8			GGTAACCGCAGAG	L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.640G>A	3.37:g.9802445C>T	ENSP00000256460:p.Gly214Ser	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	46	22	NM_003656	0	0	2	3	1	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	37	CCDS2582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.258485|5.258485	0.95368|0.95368	.|.	.|.	ENSG00000134072|ENSG00000134072	ENST00000256460|ENST00000421120	T|.	0.58210|.	0.35|.	5.13|5.13	5.13|5.13	0.70059|0.70059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82962|0.82962	0.5151|0.5151	M|M	0.87269|0.87269	2.87|2.87	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.80764|.	0.994|.	D|D	0.85554|0.85554	0.1223|0.1223	10|5	0.87932|.	D|.	0|.	-14.0937|-14.0937	17.3689|17.3689	0.87371|0.87371	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	214|.	Q14012|.	KCC1A_HUMAN|.	S|Q	214|60	ENSP00000256460:G214S|.	ENSP00000256460:G214S|.	G|R	-|-	1|2	0|0	CAMK1|CAMK1	9777445|9777445	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.793000|0.793000	0.44817|0.44817	7.648000|7.648000	0.83479|0.83479	2.384000|2.384000	0.81235|0.81235	0.655000|0.655000	0.94253|0.94253	GGT|CGG	.		0.552	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		T	9802445	C	T	9802445	3	4	141	1	0	0	0	0	1	0	0	0	2602	652	23	1	492	1	CAMK1	3	9802445	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		9802445	188219985	29	12533											
C3orf71	646450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48956091	48956091	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatctcgacgggagacgcTggtaggcgaatagtggctcc	10	7	14	10	4	1	1	0	0	1	1	3	4	2	1	1	4	1	3	1	4	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:48956091T>A	ENST00000408959.2	-	1	727	c.492A>T	c.(490-492)ccA>ccT	p.P164P	ARIH2_ENST00000356401.4_5'Flank|ARIH2_ENST00000449376.1_5'Flank	NM_001123040.1	NP_001116512.1	Q8N7S6	ARI2O_HUMAN	ariadne homolog 2 opposite strand	164						integral component of membrane (GO:0016021)											CGGGAGACGCTGGTAGGCGAA	0.587																																					p.P164P		.											.	.	0			c.A492T						.						47	49	49					3																	48956091		1568	3582	5150	SO:0001819	synonymous_variant	646450	exon1			AGACGCTGGTAGG	DA461567	CCDS43088.1	3p21.31	2012-10-08	2012-10-08	2012-10-08	ENSG00000221883	ENSG00000221883			34425	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 71"	C3orf71			Standard	NM_001123040		Approved		uc010hkk.1	Q8N7S6	OTTHUMG00000156672	ENST00000408959.2:c.492A>T	3.37:g.48956091T>A		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	58	34	NM_001123040	0	0	0	0	0		Silent	SNP	ENST00000408959.2	37	CCDS43088.1																																																																																			.		0.587	ARIH2OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345247.1	NM_001123040		A	48956091	T	A	48956091	2	1	141	1	0	0	0	0	0	0	0	1	2249	1567	55	5		5	C3orf71	3	48956091	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	39153646	48956091	149066339	30	12534											
ARHGEF3	50650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	56789065	56789065	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgacgcacacatcgaaggTctcactccacagcttgctat	11	10	7	13	2	1	1	1	1	1	0	4	2	2	1	1	1	2	3	1	1	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:56789065T>A	ENST00000296315.3	-	3	487	c.319A>T	c.(319-321)Acc>Tcc	p.T107S	ARHGEF3_ENST00000497267.1_Missense_Mutation_p.T78S|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.T113S|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.T139S|ARHGEF3_ENST00000495373.1_Missense_Mutation_p.T107S|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.T113S|ARHGEF3_ENST00000498517.1_5'UTR	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	107					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		ACATCGAAGGTCTCACTCCAC	0.587																																					p.T139S		.											.	ARHGEF3-228	0			c.A415T						.						165	147	153					3																	56789065		2203	4300	6503	SO:0001583	missense	50650	exon6			CGAAGGTCTCACT	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"Rho guanine nucleotide exchange factors"	683	protein-coding gene	gene with protein product	"exchange factor found in platelets and leukemic and neuronal tissues, XPLN", "RhoGEF protein"	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.319A>T	3.37:g.56789065T>A	ENSP00000296315:p.Thr107Ser	Somatic	267	1		WXS	Illumina HiSeq	Phase_I	184	87	NM_001128615	0	0	5	7	2	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	T	35	5.460720	0.96240	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373;ENST00000468727;ENST00000473779	T;T;T;T;T;T;T;T	0.67345	1.6;1.6;1.6;1.6;1.6;1.6;-0.26;-0.26	5.32	5.32	0.75619	Dbl homology (DH) domain (1);	0.000000	0.85682	D	0.000000	T	0.79476	0.4452	M	0.74881	2.28	0.54753	D	0.999988	D;P;P;D;D;D	0.58268	0.969;0.938;0.882;0.982;0.982;0.982	P;P;P;P;P;P	0.60682	0.798;0.628;0.55;0.878;0.855;0.878	T	0.81760	-0.0785	10	0.59425	D	0.04	-11.4376	15.6104	0.76713	0.0:0.0:0.0:1.0	.	113;78;107;139;107;113	E9PG37;E7EU49;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;ARHG3_HUMAN;.	S	107;139;113;113;78;107;108;125	ENSP00000296315:T107S;ENSP00000341071:T139S;ENSP00000410922:T113S;ENSP00000420420:T113S;ENSP00000418826:T78S;ENSP00000417986:T107S;ENSP00000417087:T108S;ENSP00000420402:T125S	ENSP00000296315:T107S	T	-	1	0	ARHGEF3	56764105	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.991000	0.88244	2.156000	0.67533	0.533000	0.62120	ACC	.		0.587	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		A	56789065	T	A	56789065	3	1	141	1	0	0	0	0	1	0	0	0	904	1667	58	5	1293	5	ARHGEF3	3	56789065	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	7832974	56789065	141233365	31	12535											
RNF13	11342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	149678575	149678575	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gctaactaaaaccaaaaaaaCctgtccagtgtgcaagcaaa	19	6	6	10	0	0	0	0	0	0	0	1	0	1	0	3	0	5	3	3	0	8	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:149678575C>G	ENST00000344229.3	+	11	1532	c.830C>G	c.(829-831)aCc>aGc	p.T277S	RNF13_ENST00000361785.6_Missense_Mutation_p.T158S|RNF13_ENST00000392894.3_Missense_Mutation_p.T277S	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	277					protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACCAAAAAAACCTGTCCAGTG	0.398																																					p.T277S		.											.	RNF13-227	0			c.C830G						.						67	66	66					3																	149678575		2203	4300	6503	SO:0001583	missense	11342	exon11			AAAAAACCTGTCC	AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"RING-type (C3HC4) zinc fingers"	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.830C>G	3.37:g.149678575C>G	ENSP00000341361:p.Thr277Ser	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	69	24	NM_007282	0	0	46	92	46	A6NC87|B3KR12|Q05D66|Q6IBJ9	Missense_Mutation	SNP	ENST00000344229.3	37	CCDS3146.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.38|17.38	3.374025|3.374025	0.61735|0.61735	.|.	.|.	ENSG00000082996|ENSG00000082996	ENST00000468289|ENST00000392894;ENST00000344229;ENST00000491086;ENST00000543506;ENST00000361785;ENST00000482083	.|T;T;T;T;T	.|0.41065	.|1.01;1.01;1.01;1.01;1.01	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.46852|0.46852	0.1414|0.1414	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|B;P	.|0.38565	.|0.213;0.637	.|B;P	.|0.46452	.|0.193;0.517	T|T	0.19745|0.19745	-1.0296|-1.0296	5|10	.|0.41790	.|T	.|0.15	-20.7775|-20.7775	20.6397|20.6397	0.99537|0.99537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|158;277	.|B3KR12;O43567	.|.;RNF13_HUMAN	K|S	78|277;277;158;277;158;158	.|ENSP00000376628:T277S;ENSP00000341361:T277S;ENSP00000420667:T158S;ENSP00000355268:T158S;ENSP00000418863:T158S	.|ENSP00000341361:T277S	N|T	+|+	3|2	2|0	RNF13|RNF13	151161265|151161265	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.487000|7.487000	0.81328|0.81328	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.		0.398	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384		G	149678575	C	G	149678575	3	3	141	1	0	0	0	0	1	0	0	0	13469	507	18	4	864	4	RNF13	3	149678575	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	92889510	149678575	48343855	32	12536											
PSMD2	5708	hgsc.bcm.edu	37	chr3	184019770	184019770	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatgcagagcatgaggcttgCgacctgcttatggaaattga	12	10	12	7	1	0	3	0	2	0	1	0	5	0	4	1	2	4	4	1	2	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:184019770C>T	ENST00000310118.4	+	5	1173	c.615C>T	c.(613-615)tgC>tgT	p.C205C	PSMD2_ENST00000435761.1_Silent_p.C46C|PSMD2_ENST00000439383.1_Silent_p.C75C|EIF2B5_ENST00000444495.1_Intron	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	205					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	ATGAGGCTTGCGACCTGCTTA	0.507																																					p.C205C	Colon(24;313 636 6917 9932 15554)	.											.	PSMD2-90	0			c.C615T						.						115	106	109					3																	184019770		2203	4300	6503	SO:0001819	synonymous_variant	5708	exon5			GGCTTGCGACCTG	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"Proteasome (prosome, macropain) subunits"	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.615C>T	3.37:g.184019770C>T		Somatic	150	1		WXS	Illumina HiSeq	Phase_I	165	9	NM_002808	0	1	80	82	1	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Silent	SNP	ENST00000310118.4	37	CCDS3258.1																																																																																			.		0.507	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		T	184019770	C	T	184019770	2	4	141	1	0	0	0	0	0	0	0	1	12727	776	27	1		1	PSMD2	3	184019770	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	34341195	184019770	14002660	33	12537											
GABRA2	2555	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	46312218	46312218	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatttcagaggacatgaatgAgcatccattgggaaatcctc	14	10	9	8	0	1	3	1	2	0	1	4	5	3	5	2	2	1	1	2	2	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr4:46312218A>T	ENST00000510861.1	-	6	704	c.531T>A	c.(529-531)gcT>gcA	p.A177A	GABRA2_ENST00000381620.4_Silent_p.A177A|GABRA2_ENST00000515082.1_Silent_p.A177A|GABRA2_ENST00000507069.1_Silent_p.A177A|GABRA2_ENST00000356504.1_Silent_p.A177A|GABRA2_ENST00000514090.1_Silent_p.A177A|GABRA2_ENST00000540012.1_Silent_p.A122A			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	177					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|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)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	GACATGAATGAGCATCCATTG	0.388																																					p.A177A		.											.	GABRA2-94	0			c.T531A						.						135	130	132					4																	46312218		2203	4300	6503	SO:0001819	synonymous_variant	2555	exon6			TGAATGAGCATCC		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.531T>A	4.37:g.46312218A>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	125	52	NM_000807	0	0	0	0	0	A8K0U7|B7Z1H8|Q59G14	Silent	SNP	ENST00000510861.1	37	CCDS3471.1																																																																																			.		0.388	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			T	46312218	A	T	46312218	2	4	141	1	0	0	0	0	0	0	0	1	6180	291	11	5		5	GABRA2	4	46312218	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		46312218	144842058	34	12538											
CLOCK	9575	hgsc.bcm.edu	37	chr4	56322462	56322462	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggttcttcaacagtgcaCatttcctacaaataaataat	14	14	5	8	0	2	0	1	0	1	0	3	0	3	0	1	1	3	2	1	1	6	7			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr4:56322462C>G	ENST00000309964.4	-	11	1048	c.798G>C	c.(796-798)atG>atC	p.M266I	CLOCK_ENST00000381322.1_Missense_Mutation_p.M266I|CLOCK_ENST00000513440.1_Missense_Mutation_p.M266I	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	266	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			CAACAGTGCACATTTCCTACa	0.294																																					p.M266I		.											.	CLOCK-515	0			c.G798C						.						28	29	29					4																	56322462		2196	4288	6484	SO:0001583	missense	9575	exon12			AGTGCACATTTCC	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.798G>C	4.37:g.56322462C>G	ENSP00000308741:p.Met266Ile	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	25	2	NM_004898	0	0	0	0	0	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.724925	0.89298	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.04015	3.73;3.73;3.73	5.5	5.5	0.81552	PAS (1);	0.069843	0.85682	D	0.000000	T	0.10937	0.0267	M	0.68952	2.095	0.80722	D	1	B	0.21520	0.057	B	0.27715	0.082	T	0.03566	-1.1024	10	0.72032	D	0.01	.	19.3891	0.94573	0.0:1.0:0.0:0.0	.	266	O15516	CLOCK_HUMAN	I	266	ENSP00000308741:M266I;ENSP00000370723:M266I;ENSP00000426983:M266I	ENSP00000308741:M266I	M	-	3	0	CLOCK	56017219	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.818000	0.86416	2.579000	0.87056	0.591000	0.81541	ATG	.		0.294	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		G	56322462	C	G	56322462	3	3	141	1	0	0	0	0	1	0	0	0	3555	478	17	4	1790	4	CLOCK	4	56322462	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	10010244	56322462	134831814	35	12539											
HERC5	51191	hgsc.bcm.edu	37	chr4	89408218	89408218	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttattgtcatttccatttttAggacgcttcagaaaatgtac	11	17	6	7	1	2	1	2	0	0	1	3	2	3	2	1	1	1	2	1	1	5	8			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr4:89408218A>G	ENST00000264350.3	+	15	2004		c.e15-1		HERC5_ENST00000508159.1_Splice_Site	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5						cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		TTCCATTTTTAGGACGCTTCA	0.343																																					.	Esophageal Squamous(39;887 1012 34045 50514)	.											.	HERC5-664	0			c.1852-2A>G						.						74	73	73					4																	89408218		2203	4298	6501	SO:0001630	splice_region_variant	51191	exon15			ATTTTTAGGACGC	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"hect domain and RLD 5"			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1852-1A>G	4.37:g.89408218A>G		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_016323	0	0	0	0	0	B2RTQ1|Q69G20	Splice_Site	SNP	ENST00000264350.3	37	CCDS3630.1	.	.	.	.	.	.	.	.	.	.	A	12.50	1.955460	0.34471	.	.	ENSG00000138646	ENST00000264350;ENST00000508159	.	.	.	4.09	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6988	0.51558	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HERC5	89627241	1.000000	0.71417	1.000000	0.80357	0.496000	0.33645	4.111000	0.57838	2.084000	0.62774	0.482000	0.46254	.	.		0.343	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	Intron	G	89408218	A	G	89408218	5	3	141	1	0	0	0	0	0	0	1	0	7082	434	15	3	1908	3	HERC5	4	89408218	Splice_Site	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	33085756	89408218	101746058	36	12540											
GALNTL6	442117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	173269759	173269759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaggttggacttcactcctgCggaccatacacagtataatt	12	11	8	10	1	1	0	1	0	0	0	2	2	2	2	2	3	2	2	2	3	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr4:173269759C>T	ENST00000506823.1	+	5	1129	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	GALNTL6_ENST00000508122.1_Missense_Mutation_p.R141W|GALNTL6_ENST00000457021.1_3'UTR	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	158	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TTCACTCCTGCGGACCATACA	0.428																																					p.R158W		.											.	GALNTL6-137	0			c.C472T						.						141	132	135					4																	173269759		2203	4300	6503	SO:0001583	missense	442117	exon5			CTCCTGCGGACCA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"Glycosyltransferase family 2 domain containing"	33844	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase-like 6"	615138	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.472C>T	4.37:g.173269759C>T	ENSP00000423313:p.Arg158Trp	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	171	88	NM_001034845	0	0	0	0	0	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	37	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.376971	0.61735	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.63913	-0.07;-0.07	5.38	1.32	0.21799	Glycosyl transferase, family 2 (1);	0.730958	0.11188	N	0.590274	D	0.88228	0.6380	H	0.99425	4.56	0.48341	D	0.999638	D	0.89917	1.0	D	0.97110	1.0	D	0.89622	0.3849	10	0.87932	D	0	.	14.8011	0.69916	0.6209:0.3791:0.0:0.0	.	158	Q49A17	GLTL6_HUMAN	W	158;158;141	ENSP00000423313:R158W;ENSP00000423827:R141W	ENSP00000385382:R158W	R	+	1	2	GALNTL6	173506334	0.987000	0.35691	1.000000	0.80357	0.979000	0.70002	0.342000	0.19926	0.212000	0.20703	-0.470000	0.05040	CGG	.		0.428	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		T	173269759	C	T	173269759	3	4	141	1	0	0	0	0	1	0	0	0	6245	759	27	1	486	1	GALNTL6	4	173269759	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	83861541	173269759	17884517	37	12541											
SLC9A3	6550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	476140	476140	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcccccagcgcacctttcTccttgatggtgaaattctgc	6	11	10	14	1	2	2	0	2	2	0	3	2	2	2	4	2	2	1	4	2	1	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:476140T>A	ENST00000264938.3	-	14	2144	c.2135A>T	c.(2134-2136)gAg>gTg	p.E712V	CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.5_ENST00000342584.3_5'Flank|CTD-2228K2.7_ENST00000606288.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.E703V|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000606319.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	712					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CGCACCTTTCTCCTTGATGGT	0.642																																					p.E712V		.											.	SLC9A3-90	0			c.A2135T						.						24	26	25					5																	476140		2203	4300	6503	SO:0001583	missense	6550	exon14			CCTTTCTCCTTGA		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2135A>T	5.37:g.476140T>A	ENSP00000264938:p.Glu712Val	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	24	9	NM_004174	0	0	20	20	0	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	37	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	T	9.100	1.003901	0.19199	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.72942	-0.7;-0.7	3.93	3.93	0.45458	.	11.221700	0.00508	N	0.000168	T	0.70360	0.3215	M	0.64997	1.995	0.30953	N	0.724513	B;P	0.35433	0.222;0.501	B;B	0.35470	0.059;0.203	T	0.57470	-0.7806	10	0.25106	T	0.35	.	9.4489	0.38714	0.0:0.0:0.0:1.0	.	703;712	E9PF67;P48764	.;SL9A3_HUMAN	V	712;703	ENSP00000264938:E712V;ENSP00000422983:E703V	ENSP00000264938:E712V	E	-	2	0	SLC9A3	529140	0.009000	0.17119	0.998000	0.56505	0.230000	0.25150	0.875000	0.28079	1.565000	0.49641	0.155000	0.16302	GAG	.		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		A	476140	T	A	476140	3	1	141	1	0	0	0	0	1	0	0	0	14745	1551	54	5	385	5	SLC9A3	5	476140	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08		476140	180439120	38	12542											
ADAMTS16	170690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	5235155	5235155	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atggagggaagttctgtgagGgctccactcgcactctgaag	9	9	14	9	1	2	2	0	2	2	0	4	4	3	4	1	3	0	3	1	3	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:5235155G>C	ENST00000274181.7	+	13	2017	c.1879G>C	c.(1879-1881)Ggc>Cgc	p.G627R	ADAMTS16_ENST00000513709.1_3'UTR	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	627	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GTTCTGTGAGGGCTCCACTCG	0.443																																					p.G627R		.											.	ADAMTS16-275	0			c.G1879C						.						66	69	68					5																	5235155		1926	4118	6044	SO:0001583	missense	170690	exon13			TGTGAGGGCTCCA	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1879G>C	5.37:g.5235155G>C	ENSP00000274181:p.Gly627Arg	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	81	34	NM_139056	0	0	15	22	7	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.337693	0.60963	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.09163	3.01	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.54886	0.1886	H	0.99565	4.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.76984	-0.2756	10	0.72032	D	0.01	.	17.2614	0.87071	0.0:0.0:1.0:0.0	.	627;627	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	R	627	ENSP00000274181:G627R	ENSP00000274181:G627R	G	+	1	0	ADAMTS16	5288155	1.000000	0.71417	0.963000	0.40424	0.056000	0.15407	9.323000	0.96364	2.446000	0.82766	0.655000	0.94253	GGC	.		0.443	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		C	5235155	G	C	5235155	3	2	141	1	0	0	0	0	1	0	0	0	261	1232	43	4	1929	4	ADAMTS16	5	5235155	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	4759015	5235155	175680105	39	12543											
RNASEN	29102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	31526783	31526783	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagggccttgcgctgacggaGgcatgggtggggggaagggt	6	6	23	6	2	0	1	0	1	0	0	0	4	0	3	1	8	1	2	1	8	1	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:31526783G>T	ENST00000511367.2	-	4	501	c.257C>A	c.(256-258)cCt>cAt	p.P86H	DROSHA_ENST00000344624.3_Missense_Mutation_p.P86H|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000513349.1_Missense_Mutation_p.P86H|DROSHA_ENST00000442743.1_Missense_Mutation_p.P86H	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	86	Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						CGCTGACGGAGGCATGGGTGG	0.592																																					p.P86H		.											.	DROSHA-227	0			c.C257A						.						29	33	32					5																	31526783		1994	4160	6154	SO:0001583	missense	29102	exon4			GACGGAGGCATGG	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"drosha, ribonuclease type III", "drosha, double-stranded RNA-specific endoribonuclease"	608828	"ribonuclease type III, nuclear"	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.257C>A	5.37:g.31526783G>T	ENSP00000425979:p.Pro86His	Somatic	47	1		WXS	Illumina HiSeq	Phase_I	46	22	NM_013235	0	0	4	17	13	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.502885	0.64298	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	T;T;T;T;T	0.48522	1.29;1.29;0.81;0.81;0.88	5.41	5.41	0.78517	.	0.192038	0.44902	D	0.000411	T	0.45816	0.1361	N	0.19112	0.55	0.39763	D	0.972056	P;D;D	0.63046	0.878;0.992;0.992	P;P;P	0.51355	0.575;0.667;0.667	T	0.38824	-0.9643	10	0.30078	T	0.28	-6.4282	19.2155	0.93776	0.0:0.0:1.0:0.0	.	86;86;86	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	H	86;86;86;86;79;79;86	ENSP00000425979:P86H;ENSP00000339845:P86H;ENSP00000409335:P86H;ENSP00000424161:P86H;ENSP00000430921:P86H	ENSP00000265075:P79H	P	-	2	0	DROSHA	31562540	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	6.322000	0.72886	2.535000	0.85469	0.655000	0.94253	CCT	.		0.592	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		T	31526783	G	T	31526783	3	4	141	1	0	0	0	0	1	0	0	0	13449	1000	35	4	3995	4	RNASEN	5	31526783	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	26291628	31526783	149388477	40	12544											
IL7R	3575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	35876145	35876145	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagattcatagggtggatGacattcaagctagagatgaa	14	9	12	6	0	2	4	2	2	0	2	2	6	2	5	1	2	1	1	1	2	4	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:35876145G>T	ENST00000303115.3	+	8	1066	c.937G>T	c.(937-939)Gac>Tac	p.D313Y	IL7R_ENST00000343305.4_3'UTR	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	313					B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			TAGGGTGGATGACATTCAAGC	0.438			"Mis, O"		"ALL, ETP ALL"		Severe combined immune deficiency																														p.D313Y		.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R-157	0			c.G937T						.						89	84	85					5																	35876145		2203	4300	6503	SO:0001583	missense	3575	exon8			GTGGATGACATTC	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.937G>T	5.37:g.35876145G>T	ENSP00000306157:p.Asp313Tyr	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	87	37	NM_002185	0	0	3	3	0	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199424	0.79015	.	.	ENSG00000168685	ENST00000303115;ENST00000505875	T;T	0.35421	1.9;1.31	6.06	6.06	0.98353	.	0.458345	0.25467	N	0.030468	T	0.30854	0.0778	N	0.14661	0.345	0.80722	D	1	D	0.56521	0.976	P	0.46975	0.533	T	0.09885	-1.0654	10	0.72032	D	0.01	-1.5157	16.1283	0.81408	0.0:0.0:1.0:0.0	.	313	P16871	IL7RA_HUMAN	Y	313;79	ENSP00000306157:D313Y;ENSP00000420923:D79Y	ENSP00000306157:D313Y	D	+	1	0	IL7R	35911902	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	3.729000	0.54999	2.871000	0.98454	0.655000	0.94253	GAC	.		0.438	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2			T	35876145	G	T	35876145	3	4	141	1	0	0	0	0	1	0	0	0	7726	1290	45	4	967	4	IL7R	5	35876145	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	4349362	35876145	145039115	41	12545											
TBCA	6902	hgsc.bcm.edu;broad.mit.edu	37	chr5	76987260	76987260	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcaggcttctaacttcaCtgaatccagtactaaacgtg	11	13	7	10	1	3	1	2	1	1	0	4	1	4	1	1	1	3	3	1	1	5	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:76987260C>A	ENST00000380377.4	-	4	413	c.310G>T	c.(310-312)Gtg>Ttg	p.V104L	TBCA_ENST00000517881.1_5'UTR|TBCA_ENST00000306388.6_3'UTR|TBCA_ENST00000517679.1_Missense_Mutation_p.V115L|TBCA_ENST00000518338.2_Missense_Mutation_p.V127L|TBCA_ENST00000520361.1_Missense_Mutation_p.V75L|TBCA_ENST00000522370.1_Missense_Mutation_p.V80L	NM_004607.2	NP_004598.1	O75347	TBCA_HUMAN	tubulin folding cofactor A	104					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_lung(232;0.000511)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.02e-49)|Epithelial(54;1.05e-44)|all cancers(79;4.08e-40)		TCTAACTTCACTGAATCCAGT	0.333																																					p.V104L		.											.	TBCA-91	0			c.G310T						.						55	53	54					5																	76987260		2202	4292	6494	SO:0001583	missense	6902	exon4			ACTTCACTGAATC	AF038952	CCDS4040.1, CCDS75263.1	5q14.1	2008-02-05	2006-11-21		ENSG00000171530	ENSG00000171530			11579	protein-coding gene	gene with protein product		610058	"tubulin-specific chaperone a"			9653160, 8706133	Standard	XM_005248586		Approved		uc003kfh.1	O75347	OTTHUMG00000102173	ENST00000380377.4:c.310G>T	5.37:g.76987260C>A	ENSP00000369736:p.Val104Leu	Somatic	10	1		WXS	Illumina HiSeq	Phase_I	38	13	NM_004607	0	0	109	215	106	B4DT30	Missense_Mutation	SNP	ENST00000380377.4	37	CCDS4040.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.671277	0.47781	.	.	ENSG00000171530	ENST00000380377;ENST00000517679;ENST00000520361;ENST00000522370	.	.	.	5.76	4.9	0.64082	.	0.056024	0.64402	D	0.000001	T	0.62913	0.2467	M	0.77820	2.39	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.62553	-0.6830	9	0.54805	T	0.06	.	12.0348	0.53418	0.0:0.8608:0.0:0.1392	.	104	O75347	TBCA_HUMAN	L	104;115;75;80	.	ENSP00000369736:V104L	V	-	1	0	TBCA	77023016	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.282000	0.51693	1.442000	0.47568	-0.143000	0.13931	GTG	.		0.333	TBCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220021.3	NM_004607		A	76987260	C	A	76987260	3	1	141	1	0	0	0	0	1	0	0	0	15661	565	20	4	20	4	TBCA	5	76987260	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	41111115	76987260	103928000	42	12546											
PPIC	5480	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	122359696	122359696	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctctatggagtgcaccacTgtctggtgagagaaaagtag	12	9	13	7	0	2	2	0	1	2	1	2	4	2	3	1	2	2	3	1	2	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:122359696T>A	ENST00000306442.4	-	5	628	c.513A>T	c.(511-513)acA>acT	p.T171T	RN7SL689P_ENST00000577215.1_RNA	NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	171	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	AGTGCACCACTGTCTGGTGAG	0.478																																					p.T171T	Ovarian(99;690 1502 20765 45543 49568)	.											.	PPIC-91	0			c.A513T						.						203	187	192					5																	122359696		2203	4300	6503	SO:0001819	synonymous_variant	5480	exon5			CACCACTGTCTGG	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.513A>T	5.37:g.122359696T>A		Somatic	177	0		WXS	Illumina HiSeq	Phase_I	188	76	NM_000943	0	0	0	0	0	A4LBB5	Silent	SNP	ENST00000306442.4	37	CCDS4133.1																																																																																			.		0.478	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943		A	122359696	T	A	122359696	2	1	141	1	0	0	0	0	0	0	0	1	12349	1567	55	5		5	PPIC	5	122359696	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	45372436	122359696	58555564	43	12547											
PCDHA8	56140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140223201	140223201	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgctctggtgaggggccaccGaagacggacctcatggcctt	7	8	14	12	2	2	2	1	1	1	1	2	4	2	3	4	5	1	1	4	5	1	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:140223201G>A	ENST00000531613.1	+	1	2295	c.2295G>A	c.(2293-2295)ccG>ccA	p.P765P	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000378123.3_Silent_p.P765P|PCDHA4_ENST00000530339.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	765					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGGGCCACCGAAGACGGACC	0.592																																					p.P765P		.											.	PCDHA8-92	0			c.G2295A						.						59	60	60					5																	140223201		2196	4262	6458	SO:0001819	synonymous_variant	56140	exon1			GCCACCGAAGACG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"Cadherins / Protocadherins : Clustered"	8674	other	complex locus constituent	"KIAA0345-like 6"	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.2295G>A	5.37:g.140223201G>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	40	32	NM_031856	0	0	0	0	0	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																			.		0.592	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140223201	G	A	140223201	2	1	141	1	0	0	0	0	0	0	0	1	11556	1045	37	1		1	PCDHA8	5	140223201	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	17863505	140223201	40692059	44	12548											
PCDHGA12	26025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140811805	140811805	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcacttattccctggctgaGaacaccatccaaggggcaag	12	8	9	12	0	1	1	1	1	0	1	3	2	3	1	3	3	1	2	3	3	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:140811805G>A	ENST00000252085.3	+	1	1621	c.1479G>A	c.(1477-1479)gaG>gaA	p.E493E	PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	493	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTGGCTGAGAACACCATCC	0.557																																					p.E493E		.											.	PCDHGA12-27	0			c.G1479A						.						75	81	79					5																	140811805		2203	4300	6503	SO:0001819	synonymous_variant	26025	exon1			GGCTGAGAACACC	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"Cadherins / Protocadherins : Clustered"	8699	other	protocadherin	"fibroblast cadherin FIB3"	603059	"cadherin 21"	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1479G>A	5.37:g.140811805G>A		Somatic	161	0		WXS	Illumina HiSeq	Phase_I	87	36	NM_032094	0	0	0	0	0	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																			.		0.557	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140811805	G	A	140811805	2	1	141	1	0	0	0	0	0	0	0	1	11579	933	33	2		2	PCDHGA12	5	140811805	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	588604	140811805	40103455	45	12549											
LARP1	23367	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	154183178	154183178	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctctctaccaaccactgTcccagagtcaccaaactacc	11	7	4	19	1	2	1	1	0	1	1	4	1	3	1	6	0	4	1	6	0	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:154183178T>A	ENST00000336314.4	+	13	2105	c.2081T>A	c.(2080-2082)gTc>gAc	p.V694D		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	771					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCAACCACTGTCCCAGAGTCA	0.582																																					p.V694D		.											.	LARP1-94	0			c.T2081A						.						153	132	139					5																	154183178		2203	4300	6503	SO:0001583	missense	23367	exon13			CCACTGTCCCAGA	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"La ribonucleoprotein domain containing"	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.2081T>A	5.37:g.154183178T>A	ENSP00000336721:p.Val694Asp	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	64	29	NM_015315	0	0	49	85	36	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.11|18.11	3.551818|3.551818	0.65311|0.65311	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000518677|ENST00000336314;ENST00000518297;ENST00000524248	.|T;T;T	.|0.38240	.|1.67;1.15;1.22	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.59459|0.59459	0.2195|0.2195	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.997;0.998	.|D;D	.|0.74348	.|0.92;0.983	T|T	0.60551|0.60551	-0.7241|-0.7241	5|10	.|0.48119	.|T	.|0.1	-16.9963|-16.9963	15.9212|15.9212	0.79575|0.79575	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|771;694	.|Q6PKG0;Q6PKG0-3	.|LARP1_HUMAN;.	T|D	85|694;771;566	.|ENSP00000336721:V694D;ENSP00000428589:V771D;ENSP00000429904:V566D	.|ENSP00000336721:V694D	S|V	+|+	1|2	0|0	LARP1|LARP1	154163371|154163371	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.186000|0.186000	0.23388|0.23388	7.633000|7.633000	0.83260|0.83260	2.155000|2.155000	0.67459|0.67459	0.460000|0.460000	0.39030|0.39030	TCC|GTC	.		0.582	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		A	154183178	T	A	154183178	3	1	141	1	0	0	0	0	1	0	0	0	8649	1667	58	5	2131	5	LARP1	5	154183178	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	13371373	154183178	26732082	46	12550											
PANK3	79646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	167995656	167995656	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtaaaagatacctactgtgcGaaaatctttttcaaacttgt	14	14	6	7	1	2	1	1	0	1	1	2	2	2	1	1	0	4	1	1	0	7	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:167995656G>A	ENST00000239231.6	-	2	692	c.376C>T	c.(376-378)Cgc>Tgc	p.R126C	PANK3_ENST00000520504.1_5'Flank	NM_024594.3	NP_078870.1	Q9H999	PANK3_HUMAN	pantothenate kinase 3	126					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.R126C(1)		NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		CCTACTGTGCGAAAATCTTTT	0.373																																					p.R126C		.											.	PANK3-91	1	Substitution - Missense(1)	cervix(1)	c.C376T						.						80	77	78					5																	167995656		2203	4300	6503	SO:0001583	missense	79646	exon2			CTGTGCGAAAATC	AK022961	CCDS4368.1	5q35.1	2008-02-05			ENSG00000120137	ENSG00000120137			19365	protein-coding gene	gene with protein product		606161				11479594	Standard	NM_024594		Approved	FLJ12899	uc003lzz.2	Q9H999	OTTHUMG00000130410	ENST00000239231.6:c.376C>T	5.37:g.167995656G>A	ENSP00000239231:p.Arg126Cys	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	102	36	NM_024594	0	0	0	0	0	D3DQL1|Q53FJ9|Q7RTX4	Missense_Mutation	SNP	ENST00000239231.6	37	CCDS4368.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021887	0.75275	.	.	ENSG00000120137	ENST00000239231;ENST00000522176	D;D	0.99582	-6.22;-6.22	5.81	5.81	0.92471	.	0.045054	0.85682	D	0.000000	D	0.99387	0.9784	M	0.72118	2.19	0.80722	D	1	D	0.61697	0.99	P	0.54856	0.762	D	0.99429	1.0935	10	0.54805	T	0.06	-7.4746	19.0666	0.93114	0.0:0.0:1.0:0.0	.	126	Q9H999	PANK3_HUMAN	C	126;111	ENSP00000239231:R126C;ENSP00000428631:R111C	ENSP00000239231:R126C	R	-	1	0	PANK3	167928234	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.446000	0.66600	2.736000	0.93811	0.655000	0.94253	CGC	.		0.373	PANK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252793.2	NM_024594		A	167995656	G	A	167995656	3	1	141	1	0	0	0	0	1	0	0	0	11444	1058	37	1	760	1	PANK3	5	167995656	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	13812478	167995656	12919604	47	12551											
DHX16	8449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30640454	30640454	+	Silent	SNP	G	G	T																															aagtcccgggccggcccactGagatccaaggtatcagtgtc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:30640454G>T	ENST00000376442.3	-	1	360	c.165C>A	c.(163-165)ctC>ctA	p.L55L		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	55					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CCGGCCCACTGAGATCCAAGG	0.652																																					p.L55L		.											.	DHX16-228	0			c.C165A						.						51	54	53					6																	30640454		1508	2709	4217	SO:0001819	synonymous_variant	8449	exon1			CCCACTGAGATCC	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.165C>A	6.37:g.30640454G>T		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	66	24	NM_003587	0	0	10	10	0	O60322|Q5JP45|Q969X7|Q96QC1	Silent	SNP	ENST00000376442.3	37	CCDS4685.1																																																																																			.		0.652	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		T	30640454	G	T	30640454	2	4	141	1	0	0	0	0	0	0	0	1	4513	1277	45	4		4	DHX16	6	30640454	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		30640454	140474613	48	12552	128	2									
DHX16	8449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30640464	30640464	+	Missense_Mutation	SNP	G	G	T																															ccggcccactgagatccaagGtatcagtgtctcgtaggcgc																								rs375439029		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:30640464G>T	ENST00000376442.3	-	1	350	c.155C>A	c.(154-156)aCc>aAc	p.T52N		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	52					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						GAGATCCAAGGTATCAGTGTC	0.647																																					p.T52N		.											.	DHX16-228	0			c.C155A						.						52	55	54					6																	30640464		1509	2709	4218	SO:0001583	missense	8449	exon1			TCCAAGGTATCAG	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.155C>A	6.37:g.30640464G>T	ENSP00000365625:p.Thr52Asn	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	70	23	NM_003587	0	0	13	13	0	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	37	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604490	0.46423	.	.	ENSG00000204560	ENST00000376442	T	0.02709	4.19	4.61	4.61	0.57282	.	0.054721	0.64402	D	0.000001	T	0.01661	0.0053	L	0.52364	1.645	0.80722	D	1	P	0.41673	0.759	B	0.37267	0.245	T	0.63844	-0.6545	10	0.17832	T	0.49	.	16.3585	0.83245	0.0:0.0:1.0:0.0	.	52	O60231	DHX16_HUMAN	N	52	ENSP00000365625:T52N	ENSP00000365625:T52N	T	-	2	0	DHX16	30748443	1.000000	0.71417	0.876000	0.34364	0.601000	0.36947	7.517000	0.81783	2.395000	0.81488	0.400000	0.26472	ACC	.		0.647	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		T	30640464	G	T	30640464	3	4	141	1	0	0	0	0	1	0	0	0	4513	1261	44	4	3050	4	DHX16	6	30640464	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	10	30640464	140474603	49	12553	128	2									
TNF	7124	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31545047	31545049	+	In_Frame_Del	DEL	CCC	CCC	-																															ctcttcaagggccaaggctgCccctccacccatgtgctcct																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:31545047_31545049delCCC	ENST00000449264.2	+	4	610_612	c.435_437delCCC	c.(433-438)tgcccc>tgc	p.P146del		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	146					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	GCCAAGGCTGCCCCTCCACCCAT	0.611									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.145_146del		.											.	TNF-1085	0			c.435_437del						.																																			SO:0001651	inframe_deletion	7124	exon4	Familial Cancer Database	incl.: Familial Head and Neck Cancer	.	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.435_437delCCC	6.37:g.31545047_31545049delCCC	ENSP00000398698:p.Pro146del	Somatic	259	0		WXS	Illumina HiSeq	Phase_I	119	42	NM_000594	0	0	0	0	0	O43647|Q9P1Q2|Q9UIV3	In_Frame_Del	DEL	ENST00000449264.2	37	CCDS4702.1																																																																																			.		0.611	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			-	31545049	CCC	-	31545047	7	5	141	1	0	1	0	1	0	0	0	0	16303	747	26	0	449	0	TNF	6	31545047	In_Frame_Del	DEL	CCC	TCGA-IZ-8196-01A-11D-2396-08	904583	31545047	139570020	50	12554											
DAXX	1616	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	33287821	33287822	+	Frame_Shift_Ins	INS	-	-	A																															tcctcttcgtcctcctcttcINSatcatcctcctgaccctcct																								rs145347312		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:33287821_33287822insA	ENST00000374542.5	-	5	1635_1636	c.1431_1432insT	c.(1429-1434)gatgaafs	p.E478fs	ZBTB22_ENST00000431845.2_5'Flank|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000414083.2_Frame_Shift_Ins_p.E403fs|DAXX_ENST00000266000.6_Frame_Shift_Ins_p.E478fs|ZBTB22_ENST00000418724.1_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	478	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						tcctcctcttcatcatcctcct	0.505			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.E490_E491delinsX		.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX-731	0			c.1468_1469insT						.																																			SO:0001589	frameshift_variant	1616	exon5			.	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"death-associated protein 6"			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1432dupT	6.37:g.33287822_33287822dupA	ENSP00000363668:p.Glu478fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	22	10	NM_001141970	0	0	0	0	0	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Nonsense_Mutation	INS	ENST00000374542.5	37	CCDS4776.1																																																																																			.		0.505	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			A	33287822	-	A	33287821	7	5	141	1	0	1	1	0	0	0	0	0	4249	835	29	0	806	0	DAXX	6	33287821	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	1742774	33287821	137827246	51	12555											
MDN1	23195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90426453	90426453	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgtcaacccattcaaatgtgCcatggctatggccactggcc	9	10	9	13	0	2	0	2	0	0	0	2	0	2	0	4	3	2	1	4	3	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:90426453C>T	ENST00000369393.3	-	44	6774	c.6659G>A	c.(6658-6660)gGc>gAc	p.G2220D	MDN1_ENST00000428876.1_Missense_Mutation_p.G2220D			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2220					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTCAAATGTGCCATGGCTATG	0.473																																					p.G2220D		.											.	MDN1-100	0			c.G6659A						.						114	95	101					6																	90426453		2203	4300	6503	SO:0001583	missense	23195	exon44			AATGTGCCATGGC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6659G>A	6.37:g.90426453C>T	ENSP00000358400:p.Gly2220Asp	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	94	38	NM_014611	0	0	2	4	2	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.900696	0.72754	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.58210	0.35;0.35	5.35	5.35	0.76521	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	T	0.75428	0.3848	M	0.91768	3.24	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.77640	-0.2512	10	0.42905	T	0.14	.	19.4391	0.94811	0.0:1.0:0.0:0.0	.	2220	Q9NU22	MDN1_HUMAN	D	2220	ENSP00000358400:G2220D;ENSP00000413970:G2220D	ENSP00000358400:G2220D	G	-	2	0	MDN1	90483174	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.600000	0.82769	2.660000	0.90430	0.557000	0.71058	GGC	.		0.473	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90426453	C	T	90426453	3	4	141	1	0	0	0	0	1	0	0	0	9440	739	26	2	10367	2	MDN1	6	90426453	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	57138632	90426453	80688614	52	12556											
SIM1	6492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	100895187	100895187	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatacagtgtggcctggaggAgcgactgttgtgcacgatgg	8	9	17	7	2	0	0	0	0	0	0	0	5	0	2	1	4	3	2	1	4	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:100895187A>T	ENST00000369208.3	-	9	1737	c.955T>A	c.(955-957)Tcc>Acc	p.S319T	SIM1_ENST00000262901.4_Missense_Mutation_p.S319T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	319	PAC.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GGCCTGGAGGAGCGACTGTTG	0.597																																					p.S319T		.											.	SIM1-94	0			c.T955A						.						165	123	137					6																	100895187		2203	4300	6503	SO:0001583	missense	6492	exon8			TGGAGGAGCGACT	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.955T>A	6.37:g.100895187A>T	ENSP00000358210:p.Ser319Thr	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	59	22	NM_005068	0	0	8	17	9	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.772481	0.90108	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.16457	2.34;2.34	6.17	6.17	0.99709	PAS fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.39085	1.19	0.58432	D	0.999999	D	0.76494	0.999	D	0.73380	0.98	T	0.01273	-1.1399	10	0.49607	T	0.09	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	319	P81133	SIM1_HUMAN	T	319	ENSP00000358210:S319T;ENSP00000262901:S319T	ENSP00000262901:S319T	S	-	1	0	SIM1	101001908	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.296000	0.78790	2.371000	0.80710	0.533000	0.62120	TCC	.		0.597	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		T	100895187	A	T	100895187	3	4	141	1	0	0	0	0	1	0	0	0	14355	304	11	5	1361	5	SIM1	6	100895187	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	10468734	100895187	70219880	53	12557											
REV3L	5980	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	111695488	111695488	+	Frame_Shift_Del	DEL	T	T	-																															gattggaaaggtcaaatataTttttttgaattaacgttgat																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:111695488delT	ENST00000358835.3	-	14	4524	c.4070delA	c.(4069-4071)aatfs	p.N1357fs	REV3L_ENST00000368805.1_Frame_Shift_Del_p.N1357fs|REV3L_ENST00000368802.3_Frame_Shift_Del_p.N1357fs|REV3L_ENST00000435970.1_Frame_Shift_Del_p.N1279fs			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1357					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		GTCAAATATATTTTTTTGAAT	0.308								DNA polymerases (catalytic subunits)																													p.N1357fs		.											.	REV3L-294	0			c.4070delA						.						63	69	67					6																	111695488		2201	4296	6497	SO:0001589	frameshift_variant	5980	exon13			.	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"DNA polymerases"	9968	protein-coding gene	gene with protein product	"polymerase, DNA, zeta"	602776	"REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta", "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.4070delA	6.37:g.111695488delT	ENSP00000351697:p.Asn1357fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	134	52	NM_002912	0	0	0	0	0	O43214|Q5TC33	Frame_Shift_Del	DEL	ENST00000358835.3	37	CCDS5091.2																																																																																			.		0.308	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		-	111695488	T	-	111695488	7	5	141	1	0	1	0	1	0	0	0	0	13272	1493	52	0	5402	0	REV3L	6	111695488	Frame_Shift_Del	DEL	T	TCGA-IZ-8196-01A-11D-2396-08	10800301	111695488	59419579	54	12558											
AHR	196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	17362177	17362177	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggccaggataactgtagAgcagcaaatttcagagaagg	15	6	14	6	0	1	2	1	0	0	2	1	5	1	4	1	4	3	3	1	4	4	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:17362177A>T	ENST00000242057.4	+	3	949	c.306A>T	c.(304-306)agA>agT	p.R102S		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	102					apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	ATAACTGTAGAGCAGCAAATT	0.333																																					p.R102S		.											.	AHR-227	0			c.A306T						.						67	68	68					7																	17362177		2203	4299	6502	SO:0001583	missense	196	exon3			CTGTAGAGCAGCA	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.306A>T	7.37:g.17362177A>T	ENSP00000242057:p.Arg102Ser	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	102	47	NM_001621	0	0	91	177	86	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	2.672	-0.277392	0.05679	.	.	ENSG00000106546	ENST00000242057	T	0.05199	3.48	0.235	-0.47	0.12131	.	0.875214	0.10272	N	0.694599	T	0.07503	0.0189	M	0.69823	2.125	0.09310	N	1	B	0.29162	0.235	B	0.30401	0.115	T	0.42015	-0.9476	9	0.22706	T	0.39	.	.	.	.	.	102	P35869	AHR_HUMAN	S	102	ENSP00000242057:R102S	ENSP00000242057:R102S	R	+	3	2	AHR	17328702	0.648000	0.27313	0.005000	0.12908	0.666000	0.39218	-0.535000	0.06142	-0.797000	0.04450	-0.818000	0.03119	AGA	.		0.333	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		T	17362177	A	T	17362177	3	4	141	1	0	0	0	0	1	0	0	0	416	301	11	5	316	5	AHR	7	17362177	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		17362177	141776486	55	12559											
TWISTNB	221830	ucsc.edu	37	chr7	19738032	19738032	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttttcttttcttttttttCtttttatggtcactttggta	3	28	5	5	0	4	0	1	0	3	0	4	0	4	0	0	2	0	2	0	2	2	13			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:19738032C>T	ENST00000222567.5	-	4	994	c.924G>A	c.(922-924)aaG>aaA	p.K308K		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	308	Lys-rich.				transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						TCTTTTTTTTCTTTTTATGGT	0.378																																					p.K308K													.	TWISTNB-91	0			c.G924A						.						113	126	122					7																	19738032		2200	4298	6498	SO:0001819	synonymous_variant	221830	exon4			TTTTTTCTTTTTA	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.924G>A	7.37:g.19738032C>T		Somatic	125	0		WXS	Illumina HiSeq		419	5	NM_001002926	0	0	16	16	0	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																			.		0.378	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			T	19738032	C	T	19738032	2	4	141	1	0	0	0	0	0	0	0	1	16817	912	32	2		2	TWISTNB	7	19738032	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	2375855	19738032	139400631	56	12560											
CHN2	1124	ucsc.edu;bcgsc.ca	37	chr7	29519827	29519827	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaactgctggccgtagcctTcggggtgaaggtgggtgtca	7	9	17	8	2	1	2	1	1	0	1	2	2	1	2	2	5	3	2	2	5	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:29519827T>C	ENST00000222792.6	+	7	1106				CHN2_ENST00000435288.2_Intron|CHN2_ENST00000409041.4_Missense_Mutation_p.F34S|CHN2_ENST00000546235.1_Intron|CHN2_ENST00000439711.2_Missense_Mutation_p.F34S|CHN2_ENST00000539389.1_Intron|CHN2_ENST00000495789.2_Intron|CHN2_ENST00000539406.1_Intron|CHN2_ENST00000421775.2_Missense_Mutation_p.F34S|CHN2_ENST00000424025.2_Missense_Mutation_p.F34S	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2						positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						GCCGTAGCCTTCGGGGTGAAG	0.537																																					p.F34S	Ovarian(1;44 48 13232 18918 31480)												.	CHN2-229	0			c.T101C						.						119	128	125					7																	29519827		1327	2309	3636	SO:0001627	intron_variant	1124	exon1			TAGCCTTCGGGGT	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"Rho GTPase activating proteins", "SH2 domain containing"	1944	protein-coding gene	gene with protein product	"beta chimerin", "chimaerin 2"	602857	"chimerin (chimaerin) 2"			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.577-68T>C	7.37:g.29519827T>C		Somatic	38	0		WXS	Illumina HiSeq		46	26	NM_001039936	0	0	0	0	0	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	37	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.428851	0.25726	.	.	ENSG00000106069	ENST00000409041;ENST00000424025;ENST00000439711;ENST00000421775	T;T;T;T	0.74737	-0.36;0.05;-0.87;0.26	5.64	3.21	0.36854	.	.	.	.	.	T	0.59459	0.2195	N	0.22421	0.69	0.22424	N	0.99911	P;B;B;B;B;B;B;B	0.34909	0.475;0.072;0.0;0.013;0.017;0.021;0.003;0.135	B;B;B;B;B;B;B;B	0.26202	0.067;0.029;0.0;0.006;0.022;0.007;0.001;0.058	T	0.49652	-0.8917	9	0.87932	D	0	.	12.6683	0.56853	0.0:0.0:0.2607:0.7393	.	34;34;34;34;34;34;34;34	B3VCF1;B3VCF2;B3VCF5;B3VCF4;B3VCF7;B3VCF3;B3VCF6;E9PGE0	.;.;.;.;.;.;.;.	S	34	ENSP00000386849:F34S;ENSP00000406337:F34S;ENSP00000387425:F34S;ENSP00000394284:F34S	ENSP00000386849:F34S	F	+	2	0	CHN2	29486352	1.000000	0.71417	0.308000	0.25141	0.080000	0.17528	4.766000	0.62279	0.475000	0.27415	-0.299000	0.09455	TTC	.		0.537	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067		C	29519827	T	C	29519827	1	2	141	0	1	0	0	0	0	0	0	0	3369	1783	62	3		3	CHN2	7	29519827	Intron	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	9781795	29519827	129618836	57	12561											
PDE1C	5137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	31877507	31877507	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctggctgctgcagagcagtCttcattgctttgatttgttg	5	17	11	8	0	3	2	1	1	2	1	3	2	3	2	0	1	4	6	0	1	0	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:31877507C>T	ENST00000396191.1	-	10	1514	c.1059G>A	c.(1057-1059)aaG>aaA	p.K353K	PDE1C_ENST00000396182.2_Silent_p.K353K|PDE1C_ENST00000396184.3_Silent_p.K353K|PDE1C_ENST00000396193.1_Silent_p.K413K|PDE1C_ENST00000321453.7_Silent_p.K353K	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	353	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GCAGAGCAGTCTTCATTGCTT	0.433																																					p.K413K		.											.	PDE1C-94	0			c.G1239A						.						194	187	189					7																	31877507		2203	4300	6503	SO:0001819	synonymous_variant	5137	exon11			AGCAGTCTTCATT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1059G>A	7.37:g.31877507C>T		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	416	169	NM_001191058	0	0	0	0	0	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	37	CCDS55099.1																																																																																			.		0.433	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			T	31877507	C	T	31877507	2	4	141	1	0	0	0	0	0	0	0	1	11661	912	32	2		2	PDE1C	7	31877507	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	2357680	31877507	127261156	58	12562											
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	82579067	82579067	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggatttgggtggggaaggagCcagctgtactgtggaatctg	8	10	18	5	0	1	0	0	0	1	0	1	4	1	4	1	6	3	2	1	6	3	2	rs370030206		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:82579067C>A	ENST00000333891.9	-	6	11174	c.10837G>T	c.(10837-10839)Gct>Tct	p.A3613S	PCLO_ENST00000437081.1_Missense_Mutation_p.A333S|PCLO_ENST00000423517.2_Missense_Mutation_p.A3613S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GGGGAAGGAGCCAGCTGTACT	0.483																																					p.A3613S		.											.	PCLO-29	0			c.G10837T						.	C	SER/ALA,SER/ALA	1,4111		0,1,2055	106	107	106		10837,10837	5.6	1	7		106	1,8435		0,1,4217	no	missense,missense	PCLO	NM_033026.5,NM_014510.2	99,99	0,2,6272	AA,AC,CC		0.0119,0.0243,0.0159	benign,benign	3613/5143,3613/4936	82579067	2,12546	2056	4218	6274	SO:0001583	missense	27445	exon6			AAGGAGCCAGCTG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"aczonin"	604918	"piccolo (presynaptic cytomatrix protein)"			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.10837G>T	7.37:g.82579067C>A	ENSP00000334319:p.Ala3613Ser	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	234	127	NM_014510	0	0	8	15	7		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536177	0.27475	2.43E-4	1.19E-4	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.15603	2.41;2.41	5.61	5.61	0.85477	.	.	.	.	.	T	0.19327	0.0464	L	0.33485	1.01	0.30557	N	0.764896	B;B;B	0.28419	0.008;0.211;0.211	B;B;B	0.29716	0.004;0.106;0.106	T	0.09443	-1.0674	9	0.87932	D	0	.	19.6465	0.95778	0.0:1.0:0.0:0.0	.	3544;3613;3613	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	S	3544;3613;3613;333	ENSP00000334319:A3613S;ENSP00000388393:A3613S	ENSP00000334319:A3613S	A	-	1	0	PCLO	82417003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.155000	0.58131	2.642000	0.89623	0.650000	0.86243	GCT	.		0.483	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82579067	C	A	82579067	3	1	141	1	0	0	0	0	1	0	0	0	11609	739	26	4	4688	4	PCLO	7	82579067	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	50701560	82579067	76559596	59	12563											
MET	4233	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	116422117	116422117	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatatcttgcaagcaaaaagTttgtccacagagacttggct	14	11	8	8	0	1	1	0	0	1	1	2	2	2	1	1	1	2	4	1	1	5	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:116422117T>A	ENST00000318493.6	+	18	3839	c.3652T>A	c.(3652-3654)Ttt>Att	p.F1218I	MET_ENST00000539704.1_Missense_Mutation_p.F70I|MET_ENST00000397752.3_Missense_Mutation_p.F1200I			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.F1218V(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AAGCAAAAAGTTTGTCCACAG	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.F1218I		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	1	Substitution - Missense(1)	kidney(1)	c.T3652A						.						57	55	56					7																	116422117		1836	4092	5928	SO:0001583	missense	4233	exon18	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AAAAAGTTTGTCC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3652T>A	7.37:g.116422117T>A	ENSP00000317272:p.Phe1218Ile	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	75	31	NM_001127500	1	0	296	546	249	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.735740	0.89482	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.25414	1.8;1.8;1.8	5.87	5.87	0.94306	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37128	0.0992	N	0.16862	0.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.35201	-0.9798	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1218;1200	P08581-2;P08581	.;MET_HUMAN	I	1200;1218;70	ENSP00000380860:F1200I;ENSP00000317272:F1218I;ENSP00000445020:F70I	ENSP00000317272:F1218I	F	+	1	0	MET	116209353	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.972000	0.88022	2.371000	0.80710	0.533000	0.62120	TTT	.		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116422117	T	A	116422117	3	1	141	1	0	0	0	0	1	0	0	0	9510	1725	60	5	3718	5	MET	7	116422117	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	33843050	116422117	42716546	60	12564											
CTTNBP2	83992	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	117431390	117431391	+	Frame_Shift_Ins	INS	-	-	C																															cacagcctgcaggtgccacaINSgttaaatctatggatggttt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:117431390_117431391insC	ENST00000160373.3	-	4	1950_1951	c.1859_1860insG	c.(1858-1860)actfs	p.T620fs	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	620					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CAGGTGCCACAGTTAAATCTAT	0.559																																					p.T620fs		.											.	CTTNBP2-94	0			c.1860_1861insG						.																																			SO:0001589	frameshift_variant	83992	exon4			.		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1859_1860insG	7.37:g.117431390_117431391insC	ENSP00000160373:p.Thr620fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	103	55	NM_033427	0	0	0	0	0	O43389|Q7LG11|Q9C0A5	Frame_Shift_Ins	INS	ENST00000160373.3	37	CCDS5774.1																																																																																			.		0.559	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		C	117431391	-	C	117431390	7	5	141	1	0	1	1	0	0	0	0	0	4051	175	7	0	3211	0	CTTNBP2	7	117431390	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	1009273	117431390	41707273	61	12565	129	2									
CTTNBP2	83992	hgsc.bcm.edu;bcgsc.ca	37	chr7	117431391	117431391	+	Frame_Shift_Del	DEL	G	G	-																															cacagcctgcaggtgccacaGttaaatctatggatggtttt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:117431391delG	ENST00000160373.3	-	4	1950	c.1859delC	c.(1858-1860)actfs	p.T620fs	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	620					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AGGTGCCACAGTTAAATCTAT	0.562																																					p.T620fs		.											.	CTTNBP2-94	0			c.1859delC						.						65	62	63					7																	117431391		2203	4300	6503	SO:0001589	frameshift_variant	83992	exon4			.		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"Ankyrin repeat domain containing"	15679	protein-coding gene	gene with protein product		609772	"cortactin binding protein 2"	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1859delC	7.37:g.117431391delG	ENSP00000160373:p.Thr620fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	105	29	NM_033427	0	0	0	0	0	O43389|Q7LG11|Q9C0A5	Frame_Shift_Del	DEL	ENST00000160373.3	37	CCDS5774.1																																																																																			.		0.562	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		-	117431391	G	-	117431391	7	5	141	1	0	1	0	1	0	0	0	0	4051	1029	36	0	3212	0	CTTNBP2	7	117431391	Frame_Shift_Del	DEL	G	TCGA-IZ-8196-01A-11D-2396-08	1	117431391	41707272	62	12566	129	2									
CHRNB3	1142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	42565553	42565553	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatgaaaagaatcagctgatGacaaccaatgtgtggctcaa	16	8	10	7	0	2	4	2	3	0	1	2	5	2	4	1	1	2	2	1	1	6	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:42565553G>A	ENST00000289957.2	+	3	353	c.225G>A	c.(223-225)atG>atA	p.M75I	RP11-412B14.1_ENST00000527318.1_RNA	NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	75					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	ATCAGCTGATGACAACCAATG	0.313																																					p.M75I		.											.	CHRNB3-91	0			c.G225A						.						72	73	72					8																	42565553		2203	4300	6503	SO:0001583	missense	1142	exon3			GCTGATGACAACC	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.225G>A	8.37:g.42565553G>A	ENSP00000289957:p.Met75Ile	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	37	21	NM_000749	0	0	0	0	0	Q15827	Missense_Mutation	SNP	ENST00000289957.2	37	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	19.35	3.810373	0.70797	.	.	ENSG00000147432	ENST00000534391;ENST00000289957	T	0.78816	-1.21	6.03	6.03	0.97812	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.76702	0.4024	L	0.33624	1.015	0.80722	D	1	P	0.36712	0.566	B	0.43990	0.438	T	0.77763	-0.2466	10	0.87932	D	0	.	18.1139	0.89545	0.0:0.0:1.0:0.0	.	75	Q05901	ACHB3_HUMAN	I	1;75	ENSP00000289957:M75I	ENSP00000289957:M75I	M	+	3	0	CHRNB3	42684710	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.752000	0.91632	2.876000	0.98609	0.644000	0.83932	ATG	.		0.313	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			A	42565553	G	A	42565553	3	1	141	1	0	0	0	0	1	0	0	0	3398	1290	45	2	235	2	CHRNB3	8	42565553	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		42565553	103798469	63	12567											
RBM12B	389677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	94747484	94747484	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagagtatttttgtgaaacAtgtccgggcctatctctctc	8	15	9	9	1	2	2	0	2	2	1	5	3	3	2	2	1	1	1	2	1	3	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:94747484A>G	ENST00000399300.2	-	3	1368	c.1155T>C	c.(1153-1155)caT>caC	p.H385H	RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Silent_p.H385H	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	385							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TTTGTGAAACATGTCCGGGCC	0.368																																					p.H385H		.											.	RBM12B-90	0			c.T1155C						.						124	121	122					8																	94747484		1836	4085	5921	SO:0001819	synonymous_variant	389677	exon3			TGAAACATGTCCG		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1155T>C	8.37:g.94747484A>G		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	236	96	NM_203390	0	0	5	8	3	A8MYB5	Silent	SNP	ENST00000399300.2	37	CCDS43755.1																																																																																			.		0.368	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		G	94747484	A	G	94747484	2	3	141	1	0	0	0	0	0	0	0	1	13146	214	8	3		3	RBM12B	8	94747484	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	52181931	94747484	51616538	64	12568											
VPS13B	157680	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	100514063	100514063	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactataaagctctttgctcCagatcctgaaaataaaggca	15	11	6	9	0	1	2	0	1	1	1	3	2	3	2	2	1	3	3	2	1	8	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:100514063C>T	ENST00000358544.2	+	26	4130	c.4019C>T	c.(4018-4020)cCa>cTa	p.P1340L	VPS13B_ENST00000395996.1_Missense_Mutation_p.P1340L|VPS13B_ENST00000357162.2_Missense_Mutation_p.P1340L	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1340					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTCTTTGCTCCAGATCCTGAA	0.483																																					p.P1340L	Colon(161;2205 2542 7338 31318)	.											.	VPS13B-301	0			c.C4019T						.						132	135	134					8																	100514063		2203	4300	6503	SO:0001583	missense	157680	exon26			TTGCTCCAGATCC	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"Cohen syndrome 1"	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.4019C>T	8.37:g.100514063C>T	ENSP00000351346:p.Pro1340Leu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	140	54	NM_152564	0	0	2	4	2	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507355	0.44558	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.45276	0.9;0.9;0.9	5.22	5.22	0.72569	.	0.215869	0.38548	N	0.001641	T	0.32315	0.0825	L	0.34521	1.04	0.53688	D	0.999974	B;B;B;B	0.09022	0.001;0.002;0.001;0.001	B;B;B;B	0.10450	0.005;0.004;0.004;0.002	T	0.06807	-1.0806	10	0.31617	T	0.26	.	12.4938	0.55916	0.0:0.9229:0.0:0.0771	.	1339;1340;1340;1340	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	L	1340	ENSP00000349685:P1340L;ENSP00000351346:P1340L;ENSP00000379318:P1340L	ENSP00000349685:P1340L	P	+	2	0	VPS13B	100583239	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.508000	0.67006	2.589000	0.87451	0.557000	0.71058	CCA	.		0.483	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100514063	C	T	100514063	3	4	141	1	0	0	0	0	1	0	0	0	17223	594	21	2	4240	2	VPS13B	8	100514063	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	5766579	100514063	45849959	65	12569											
DGAT1	8694	ucsc.edu	37	chr8	145540219	145540219	+	Nonstop_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccctcaggtgcagctcAggcctctgccgctggggcct	4	7	14	16	1	3	0	2	0	1	0	3	0	3	0	4	5	3	3	4	5	0	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:145540219A>T	ENST00000332324.4	-	17	1738	c.1465T>A	c.(1465-1467)Tga>Aga	p.*489R	DGAT1_ENST00000527438.1_5'UTR|GS1-393G12.12_ENST00000525023.1_RNA	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	0					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			GGTGCAGCTCAGGCCTCTGCC	0.632																																					p.X489R													.	.	0			c.T1465A						.						45	37	39					8																	145540219		2190	4290	6480	SO:0001578	stop_lost	8694	exon17			CAGCTCAGGCCTC	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"diacylglycerol O-acyltransferase homolog 1 (mouse)"			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.1465T>A	8.37:g.145540219A>T		Somatic	24	0		WXS	Illumina HiSeq		6	1	NM_012079	0	0	14	14	0	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	37	CCDS6420.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.549930	0.27652	.	.	ENSG00000185000	ENST00000332324	.	.	.	3.37	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.464	0.32944	1.0:0.0:0.0:0.0	.	.	.	.	R	489	.	.	X	-	1	0	DGAT1	145511027	0.544000	0.26441	0.972000	0.41901	0.034000	0.12701	0.494000	0.22467	1.800000	0.52685	0.459000	0.35465	TGA	.		0.632	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079		T	145540219	A	T	145540219	4	4	141	1	0	0	0	0	0	0	0	0	4468	201	7	5	5	5	DGAT1	8	145540219	Nonstop_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	45026156	145540219	823803	66	12570											
C10orf18	54906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	5788364	5788364	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccagtgatatgtcagagcTctgtgtacggcacccttgaa	10	10	11	10	1	2	3	1	2	1	1	2	3	2	3	2	1	3	3	2	1	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:5788364T>C	ENST00000328090.5	+	15	3605	c.2980T>C	c.(2980-2982)Tct>Cct	p.S994P	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	994																	ATGTCAGAGCTCTGTGTACGG	0.483																																					p.S994P		.											.	.	0			c.T2980C						.						102	100	100					10																	5788364		2007	4170	6177	SO:0001583	missense	54906	exon15			CAGAGCTCTGTGT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 18"	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.2980T>C	10.37:g.5788364T>C	ENSP00000328426:p.Ser994Pro	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	113	55	NM_017782	0	0	9	20	11	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	T	5.833	0.337978	0.11013	.	.	ENSG00000108021	ENST00000328090	D	0.97811	-4.55	5.37	2.97	0.34412	.	0.115838	0.39407	N	0.001362	D	0.94601	0.8260	L	0.43701	1.375	0.09310	N	1	B	0.34161	0.439	B	0.37422	0.249	D	0.88914	0.3361	10	0.48119	T	0.1	.	4.643	0.12558	0.1675:0.0913:0.0:0.7412	.	994	Q5VWN6	F208B_HUMAN	P	994	ENSP00000328426:S994P	ENSP00000328426:S994P	S	+	1	0	C10orf18	5828370	0.079000	0.21365	0.210000	0.23637	0.008000	0.06430	0.877000	0.28106	0.304000	0.22809	0.460000	0.39030	TCT	.		0.483	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		C	5788364	T	C	5788364	3	2	141	1	0	0	0	0	1	0	0	0	1600	1551	54	3	3026	3	C10orf18	10	5788364	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08		5788364	129746383	67	12571											
C1QL3	389941	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	16556595	16556595	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcctccatgggctttccCgccatctaatttgatataga	8	15	7	11	1	1	2	0	1	1	1	4	2	4	2	4	1	0	2	4	1	3	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:16556595C>T	ENST00000298943.3	-	2	1639	c.700G>A	c.(700-702)Ggg>Agg	p.G234R		NM_001010908.1	NP_001010908.1	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	234	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				regulation of synapse organization (GO:0050807)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)		p.G234W(1)		breast(1)|endometrium(3)|kidney(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TGGGCTTTCCCGCCATCTAAT	0.393																																					p.G234R		.											.	C1QL3-91	1	Substitution - Missense(1)	lung(1)	c.G700A						.						148	137	141					10																	16556595		2203	4300	6503	SO:0001583	missense	389941	exon2			CTTTCCCGCCATC		CCDS31156.1	10p13	2012-03-26			ENSG00000165985	ENSG00000165985			19359	protein-coding gene	gene with protein product		615227				21378161	Standard	NM_001010908		Approved	K100, C1ql, C1QTNF13, CTRP13	uc001ioj.1	Q5VWW1	OTTHUMG00000017738	ENST00000298943.3:c.700G>A	10.37:g.16556595C>T	ENSP00000298943:p.Gly234Arg	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	118	47	NM_001010908	0	0	4	13	9	A0PJY4|A0PJY5	Missense_Mutation	SNP	ENST00000298943.3	37	CCDS31156.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486586	0.84854	.	.	ENSG00000165985	ENST00000298943;ENST00000448557	T	0.25749	1.78	5.71	5.71	0.89125	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.85682	D	0.000000	T	0.52322	0.1727	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.44907	-0.9297	10	0.48119	T	0.1	.	19.8415	0.96690	0.0:1.0:0.0:0.0	.	234	Q5VWW1	C1QL3_HUMAN	R	234;211	ENSP00000298943:G234R	ENSP00000298943:G234R	G	-	1	0	C1QL3	16596601	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.818000	0.86416	2.700000	0.92200	0.655000	0.94253	GGG	.		0.393	C1QL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047003.1	XM_372305		T	16556595	C	T	16556595	3	4	141	1	0	0	0	0	1	0	0	0	1966	652	23	1	71	1	C1QL3	10	16556595	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	10768231	16556595	118978152	68	12572											
ITGB1	3688	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	33201013	33201013	+	Frame_Shift_Del	DEL	G	G	-																															tcactgttaacttcatctgtGctgcattcacaatgtctacc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:33201013delG	ENST00000396033.2	-	12	1644	c.1509delC	c.(1507-1509)agcfs	p.S503fs	ITGB1_ENST00000374956.4_Frame_Shift_Del_p.S503fs|ITGB1_ENST00000423113.1_Frame_Shift_Del_p.S503fs|ITGB1_ENST00000302278.3_Frame_Shift_Del_p.S503fs	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	503	Cysteine-rich tandem repeats.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	CTTCATCTGTGCTGCATTCAC	0.413																																					p.S503fs		.											.	ITGB1-1084	0			c.1509delC						.						143	120	128					10																	33201013		2203	4300	6503	SO:0001589	frameshift_variant	3688	exon12			.	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1509delC	10.37:g.33201013delG	ENSP00000379350:p.Ser503fs	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	95	41	NM_002211	0	0	0	0	0	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Frame_Shift_Del	DEL	ENST00000396033.2	37	CCDS7174.1																																																																																			.		0.413	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		-	33201013	G	-	33201013	7	5	141	1	0	1	0	1	0	0	0	0	7911	1310	46	0	1145	0	ITGB1	10	33201013	Frame_Shift_Del	DEL	G	TCGA-IZ-8196-01A-11D-2396-08	16644418	33201013	102333734	69	12573											
RUFY2	55680	broad.mit.edu;ucsc.edu	37	chr10	70152941	70152941	+	Missense_Mutation	SNP	T	T	A																															ataattcttttggtctaataTggcagcaatttgaacattcc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:70152941T>A	ENST00000602465.1	-	7	704	c.604A>T	c.(604-606)Ata>Tta	p.I202L	RUFY2_ENST00000388768.2_Missense_Mutation_p.I237L|RUFY2_ENST00000399200.2_Missense_Mutation_p.I168L|RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000454950.2_Missense_Mutation_p.I144L			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	251	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						TGGTCTAATATGGCAGCAATT	0.264																																					p.I237L													.	RUFY2-91	0			c.A709T						.						53	54	53					10																	70152941		1792	4056	5848	SO:0001583	missense	55680	exon7			CTAATATGGCAGC	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"Zinc fingers, FYVE domain containing"	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.604A>T	10.37:g.70152941T>A	ENSP00000473462:p.Ile202Leu	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	16	3	NM_017987	0	0	1	1	0	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Missense_Mutation	SNP	ENST00000602465.1	37		.	.	.	.	.	.	.	.	.	.	T	13.22	2.171217	0.38315	.	.	ENSG00000204130	ENST00000388768;ENST00000399200;ENST00000454950	T;T;T	0.51325	0.71;1.91;1.56	5.17	4.04	0.47022	.	0.512339	0.22301	N	0.061872	T	0.38295	0.1035	L	0.43923	1.385	0.58432	D	0.999997	B;B;B;B	0.24963	0.006;0.004;0.004;0.115	B;B;B;B	0.24974	0.007;0.009;0.009;0.057	T	0.12400	-1.0549	10	0.25751	T	0.34	.	10.6902	0.45867	0.0:0.0746:0.0:0.9254	.	144;202;168;237	B4DFR0;Q8WXA3-2;Q8WXA3-4;Q8WXA3-3	.;.;.;.	L	237;168;144	ENSP00000373420:I237L;ENSP00000382151:I168L;ENSP00000404986:I144L	ENSP00000373420:I237L	I	-	1	0	RUFY2	69822947	1.000000	0.71417	0.974000	0.42286	0.914000	0.54420	6.053000	0.71089	0.988000	0.38734	0.482000	0.46254	ATA	.		0.264	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		A	70152941	T	A	70152941	3	1	141	1	0	0	0	0	1	0	0	0	13771	1464	51	5	1377	5	RUFY2	10	70152941	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	36951928	70152941	65381806	70	12574	130	2									
RUFY2	55680	broad.mit.edu;ucsc.edu	37	chr10	70152944	70152944	+	Missense_Mutation	SNP	C	C	T																															attcttttggtctaatatggCagcaatttgaacattcctaa																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:70152944C>T	ENST00000602465.1	-	7	701	c.601G>A	c.(601-603)Gcc>Acc	p.A201T	RUFY2_ENST00000388768.2_Missense_Mutation_p.A236T|RUFY2_ENST00000399200.2_Missense_Mutation_p.A167T|RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000454950.2_Missense_Mutation_p.A143T			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	250	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						TCTAATATGGCAGCAATTTGA	0.264																																					p.A236T													.	RUFY2-91	0			c.G706A						.						55	55	55					10																	70152944		1792	4057	5849	SO:0001583	missense	55680	exon7			ATATGGCAGCAAT	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"Zinc fingers, FYVE domain containing"	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.601G>A	10.37:g.70152944C>T	ENSP00000473462:p.Ala201Thr	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	16	3	NM_017987	0	0	3	3	0	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Missense_Mutation	SNP	ENST00000602465.1	37		.	.	.	.	.	.	.	.	.	.	C	16.07	3.019397	0.54576	.	.	ENSG00000204130	ENST00000388768;ENST00000399200;ENST00000454950	T;T;T	0.54279	0.58;1.81;1.42	5.17	5.17	0.71159	.	0.353403	0.32459	N	0.006069	T	0.50360	0.1611	L	0.55481	1.735	0.58432	D	0.999999	B;B;B;P	0.38827	0.131;0.206;0.419;0.649	B;B;B;B	0.36666	0.039;0.059;0.168;0.23	T	0.49303	-0.8954	10	0.31617	T	0.26	.	18.8515	0.92232	0.0:1.0:0.0:0.0	.	143;201;167;236	B4DFR0;Q8WXA3-2;Q8WXA3-4;Q8WXA3-3	.;.;.;.	T	236;167;143	ENSP00000373420:A236T;ENSP00000382151:A167T;ENSP00000404986:A143T	ENSP00000373420:A236T	A	-	1	0	RUFY2	69822950	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.829000	0.62737	2.671000	0.90904	0.591000	0.81541	GCC	.		0.264	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		T	70152944	C	T	70152944	3	4	141	1	0	0	0	0	1	0	0	0	13771	710	25	2	1380	2	RUFY2	10	70152944	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	3	70152944	65381803	71	12575	130	2									
NOLC1	9221	hgsc.bcm.edu	37	chr10	103917063	103917063	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggaggaggaggaagttcaAgggcctccagcaaagaaggc	14	3	17	7	0	1	1	1	0	0	1	2	6	2	5	2	6	1	2	2	6	4	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:103917063A>G	ENST00000605788.1	+	3	529	c.294A>G	c.(292-294)caA>caG	p.Q98Q	NOLC1_ENST00000405356.1_Silent_p.Q98Q|NOLC1_ENST00000488254.2_Silent_p.Q99Q|NOLC1_ENST00000603742.1_Intron	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	98	11 X 12 AA approximate repeats of an acidic serine cluster.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		AGGAAGTTCAAGGGCCTCCAG	0.512																																					p.Q98Q		.											.	NOLC1-91	0			c.A294G						.						76	72	74					10																	103917063		2203	4300	6503	SO:0001819	synonymous_variant	9221	exon3			AGTTCAAGGGCCT	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.294A>G	10.37:g.103917063A>G		Somatic	60	1		WXS	Illumina HiSeq	Phase_I	57	3	NM_004741	0	0	31	31	0	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			.		0.512	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		G	103917063	A	G	103917063	2	3	141	1	0	0	0	0	0	0	0	1	10555	69	3	3		3	NOLC1	10	103917063	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	33764119	103917063	31617684	72	12576											
LRDD	55367	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	803185	803185	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctactcacccagagaggctGggaggctctgcagccggttg	7	7	15	12	1	2	1	1	0	1	1	2	3	2	2	2	4	3	5	2	4	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:803185G>T	ENST00000347755.5	-	3	839	c.698C>A	c.(697-699)cCa>cAa	p.P233Q	PIDD_ENST00000534649.1_5'Flank|PIDD_ENST00000411829.2_Missense_Mutation_p.P233Q	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					CAGAGAGGCTGGGAGGCTCTG	0.657																																					p.P233Q		.											.	PIDD-205	0			c.C698A						.						17	22	20					11																	803185		2195	4277	6472	SO:0001583	missense	55367	exon3			GAGGCTGGGAGGC																												ENST00000347755.5:c.698C>A	11.37:g.803185G>T	ENSP00000337797:p.Pro233Gln	Somatic	96	2		WXS	Illumina HiSeq	Phase_I	50	25	NM_145887	0	0	4	5	1		Missense_Mutation	SNP	ENST00000347755.5	37	CCDS7716.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.400654	0.83120	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.26518	1.73;1.73	4.55	4.55	0.56014	.	0.151531	0.45126	D	0.000399	T	0.66208	0.2766	H	0.96777	3.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;1.0	T	0.80084	-0.1530	10	0.87932	D	0	.	17.4818	0.87674	0.0:0.0:1.0:0.0	.	233;87;233	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	Q	233	ENSP00000416801:P233Q;ENSP00000337797:P233Q	ENSP00000337797:P233Q	P	-	2	0	PIDD	793185	1.000000	0.71417	0.936000	0.37596	0.623000	0.37688	5.191000	0.65110	2.369000	0.80426	0.555000	0.69702	CCA	.		0.657	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1			T	803185	G	T	803185	3	4	141	1	0	0	0	0	1	0	0	0	8961	1348	47	4	2090	4	LRDD	11	803185	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		803185	134203331	73	12577											
MUC2	4583	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1097183	1097183	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggtgtgtcggccacaggTgcaggtgaacaggcaggcgg	8	6	18	9	2	0	1	0	1	0	0	1	1	0	1	1	7	2	2	1	7	1	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:1097183T>G	ENST00000441003.2	+	35	6626	c.6599T>G	c.(6598-6600)gTg>gGg	p.V2200G	MUC2_ENST00000361558.6_Splice_Site_p.V338G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4562					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CGGCCACAGGTGCAGGTGAAC	0.627																																					p.V2196G													.	MUC2-90	0			c.T6587G						.						53	68	63					11																	1097183		2181	4273	6454	SO:0001630	splice_region_variant	4583	exon36			CACAGGTGCAGGT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6598-1T>G	11.37:g.1097183T>G		Somatic	140	1		WXS	Illumina HiSeq	Phase_I	51	21	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	t	14.27	2.484198	0.44147	.	.	ENSG00000198788	ENST00000441003;ENST00000361558	T;T	0.69561	-0.41;-0.41	3.72	3.72	0.42706	.	.	.	.	.	T	0.80884	0.4709	M	0.81239	2.535	0.53005	D	0.999963	D	0.89917	1.0	D	0.75484	0.986	D	0.83792	0.0231	9	0.87932	D	0	.	12.583	0.56401	0.0:0.0:0.0:1.0	.	2200	E7EUV1	.	G	2200;338	ENSP00000415183:V2200G;ENSP00000354885:V338G	ENSP00000354885:V338G	V	+	2	0	MUC2	1087183	1.000000	0.71417	0.986000	0.45419	0.327000	0.28475	4.611000	0.61162	1.555000	0.49500	0.459000	0.35465	GTG	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Missense_Mutation	G	1097183	T	G	1097183	5	3	141	1	0	0	0	0	0	0	1	0	10000	1710	59	5	6729	5	MUC2	11	1097183	Splice_Site	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	293998	1097183	133909333	74	12578											
TPP1	1200	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	6638089	6638089	+	Splice_Site	DEL	A	A	-																															catggaaatactgctccaggAactatggagggagtcagagc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:6638089delA	ENST00000299427.6	-	7	749	c.689delT	c.(688-690)ttc>tc	p.F230fs	RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000534644.1_5'Flank|TPP1_ENST00000533371.1_5'UTR	NM_000391.3	NP_000382.3	P49638	TTPA_HUMAN	tripeptidyl peptidase I	0	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)	Vitamin E(DB00163)	CTGCTCCAGGAACTATGGAGG	0.567																																					p.F230fs		.											.	TPP1-90	0			c.689delT						.						84	82	83					11																	6638089		2201	4296	6497	SO:0001630	splice_region_variant	1200	exon7			.	AF017456	CCDS7770.1	11p15.4	2014-09-17	2004-12-09	2004-12-10	ENSG00000166340	ENSG00000166340			2073	protein-coding gene	gene with protein product	"TPP I"	607998	"ceroid-lipofuscinosis, neuronal 2, late infantile (Jansky-Bielschowsky disease)", "spinocerebellar ataxia, autosomal recessive 7"	CLN2, SCAR7		9653647, 23418007	Standard	NM_000391		Approved		uc001mel.1	O14773	OTTHUMG00000133404	ENST00000299427.6:c.688-1T>-	11.37:g.6638089delA		Somatic	171	0		WXS	Illumina HiSeq	Phase_I	103	54	NM_000391	0	0	0	0	0	Q71V64	Frame_Shift_Del	DEL	ENST00000299427.6	37	CCDS7770.1																																																																																			.		0.567	TPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257261.2		Frame_Shift_Del	-	6638089	A	-	6638089	8	5	141	1	0	1	0	1	0	0	1	0	16444	260	9	0	1030	0	TPP1	11	6638089	Splice_Site	DEL	A	TCGA-IZ-8196-01A-11D-2396-08	5540906	6638089	128368427	75	12579											
API5	8539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	43342441	43342441	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcctcgagtggcagataTactaacgcaacttttgcaga	11	12	8	10	2	1	2	0	0	1	2	3	3	2	2	1	1	4	3	1	1	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:43342441T>C	ENST00000531273.1	+	3	441	c.302T>C	c.(301-303)aTa>aCa	p.I101T	API5_ENST00000378852.3_Missense_Mutation_p.I101T|API5_ENST00000455725.2_Missense_Mutation_p.I90T|API5_ENST00000420461.2_Missense_Mutation_p.I47T|API5_ENST00000534695.1_Intron|API5_ENST00000534600.1_Missense_Mutation_p.I101T			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	101	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						GTGGCAGATATACTAACGCAA	0.343																																					p.I101T	Pancreas(1;98 122 5625 20895 49453)	.											.	API5-136	0			c.T302C						.						83	85	84					11																	43342441		2203	4300	6503	SO:0001583	missense	8539	exon3			CAGATATACTAAC	U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.302T>C	11.37:g.43342441T>C	ENSP00000431391:p.Ile101Thr	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	93	42	NM_006595	0	0	20	34	14	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Missense_Mutation	SNP	ENST00000531273.1	37	CCDS44572.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.975544	0.74360	.	.	ENSG00000166181	ENST00000455725;ENST00000531273;ENST00000420461;ENST00000378852;ENST00000534600	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	6.13	6.13	0.99165	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.36220	0.0959	L	0.45422	1.42	0.58432	D	0.999999	P;P;D;P	0.61697	0.951;0.92;0.99;0.952	P;P;P;P	0.61722	0.675;0.551;0.893;0.6	T	0.01570	-1.1322	10	0.34782	T	0.22	-2.8866	16.4795	0.84153	0.0:0.0:0.0:1.0	.	47;101;90;101	B4DGR0;Q9BZZ5;B4E283;Q9BZZ5-2	.;API5_HUMAN;.;.	T	90;101;47;101;101	ENSP00000399341:I90T;ENSP00000431391:I101T;ENSP00000402540:I47T;ENSP00000368129:I101T;ENSP00000434462:I101T	ENSP00000368129:I101T	I	+	2	0	API5	43299017	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.981000	0.88123	2.367000	0.80283	0.529000	0.55759	ATA	.		0.343	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		C	43342441	T	C	43342441	3	2	141	1	0	0	0	0	1	0	0	0	773	1406	49	3	312	3	API5	11	43342441	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	36704352	43342441	91664075	76	12580											
OR8I2	120586	hgsc.bcm.edu;broad.mit.edu	37	chr11	55861616	55861616	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtggcatctgtattctataCgattgtcattcccatgctga	8	15	9	9	1	3	1	1	1	2	0	4	2	4	1	1	2	2	3	1	2	3	6	rs140206966	byFrequency	TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:55861616C>T	ENST00000302124.2	+	1	864	c.833C>T	c.(832-834)aCg>aTg	p.T278M		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T278M(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GTATTCTATACGATTGTCATT	0.408																																					p.T278M		.											.	OR8I2-113	1	Substitution - Missense(1)	endometrium(1)	c.C833T						.						62	61	62					11																	55861616		2201	4296	6497	SO:0001583	missense	120586	exon1			TCTATACGATTGT	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"GPCR / Class A : Olfactory receptors"	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.833C>T	11.37:g.55861616C>T	ENSP00000303864:p.Thr278Met	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	96	8	NM_001003750	0	0	0	0	0	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.876897	0.33162	.	.	ENSG00000172154	ENST00000302124	T	0.00262	8.4	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	U	0.000856	T	0.00608	0.0020	M	0.83118	2.625	0.32279	N	0.567785	D	0.89917	1.0	D	0.70935	0.971	T	0.50988	-0.8762	10	0.87932	D	0	-16.3432	15.8041	0.78481	0.0:1.0:0.0:0.0	.	278	Q8N0Y5	OR8I2_HUMAN	M	278	ENSP00000303864:T278M	ENSP00000303864:T278M	T	+	2	0	OR8I2	55618192	0.000000	0.05858	0.985000	0.45067	0.054000	0.15201	0.638000	0.24674	2.120000	0.65058	0.447000	0.29281	ACG	C|0.999;A|0.001		0.408	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		T	55861616	C	T	55861616	3	4	141	1	0	0	0	0	1	0	0	0	11266	536	19	1	835	1	OR8I2	11	55861616	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	12519175	55861616	79144900	77	12581											
HNRNPUL2	221092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62488862	62488862	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactaaaaggtctcggctttTggggtccatctctggctcct	7	13	10	11	1	2	0	0	0	2	0	6	0	4	0	2	5	1	2	2	5	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:62488862T>C	ENST00000301785.5	-	9	1708	c.1516A>G	c.(1516-1518)Aaa>Gaa	p.K506E	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.K506E	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	506						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCTCGGCTTTTGGGGTCCATC	0.428																																					p.K506E		.											.	HNRNPUL2-22	0			c.A1516G						.						153	158	157					11																	62488862		1846	4094	5940	SO:0001583	missense	221092	exon9			GGCTTTTGGGGTC		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1516A>G	11.37:g.62488862T>C	ENSP00000301785:p.Lys506Glu	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	214	87	NM_001079559	0	0	91	154	63	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	37	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.709456	0.68730	.	.	ENSG00000214753	ENST00000301785	T	0.40756	1.02	5.99	5.99	0.97316	Zeta toxin domain (1);	0.158288	0.64402	D	0.000020	T	0.40719	0.1128	N	0.25286	0.73	0.35130	D	0.767875	P	0.51791	0.948	P	0.51866	0.682	T	0.49934	-0.8886	10	0.30854	T	0.27	-16.7044	14.4463	0.67352	0.0:0.0:0.0:1.0	.	506	Q1KMD3	HNRL2_HUMAN	E	506	ENSP00000301785:K506E	ENSP00000301785:K506E	K	-	1	0	HNRNPUL2	62245438	0.897000	0.30589	1.000000	0.80357	0.995000	0.86356	1.144000	0.31565	2.291000	0.77112	0.533000	0.62120	AAA	.		0.428	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		C	62488862	T	C	62488862	3	2	141	1	0	0	0	0	1	0	0	0	7296	1821	63	3	751	3	HNRNPUL2	11	62488862	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	6627246	62488862	72517654	78	12582											
PCF11	51585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	82877727	82877727	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttccaagtctgccaaaagAtggaaatctggttgggaaga	14	9	12	6	0	2	2	0	0	2	2	3	4	3	4	2	3	1	2	2	3	5	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:82877727A>G	ENST00000298281.4	+	5	2240	c.1788A>G	c.(1786-1788)agA>agG	p.R596R		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	596					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CTGCCAAAAGATGGAAATCTG	0.343																																					p.R596R		.											.	PCF11-23	0			c.A1788G						.						74	75	75					11																	82877727		1755	3854	5609	SO:0001819	synonymous_variant	51585	exon5			CAAAAGATGGAAA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)", "PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.1788A>G	11.37:g.82877727A>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	135	65	NM_015885	0	0	21	34	13	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			.		0.343	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877727	A	G	82877727	2	3	141	1	0	0	0	0	0	0	0	1	11599	330	12	3		3	PCF11	11	82877727	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	20388865	82877727	52128789	79	12583											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825424	95825424	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctgctgctgttgctgctGttgctgttgggtgtagtgta	2	17	15	7	0	0	0	0	0	0	0	0	0	0	0	0	1	6	11	0	1	2	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:95825424G>T	ENST00000524717.1	-	2	3055	c.1771C>A	c.(1771-1773)Cag>Aag	p.Q591K		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	591					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				tgttgctgctgttgctgTTGG	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q591K		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	0			c.C1771A						.						53	58	56					11																	95825424		2172	4257	6429	SO:0001583	missense	84441	exon2			GCTGCTGTTGCTG	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1771C>A	11.37:g.95825424G>T	ENSP00000434552:p.Gln591Lys	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	10	4	NM_032427	0	0	31	31	0	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	.	.	.	.	.	.	.	.	.	.	G	6.985	0.551899	0.13374	.	.	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.75154	-0.91;-0.91	4.16	4.16	0.48862	.	0.641420	0.14538	N	0.313463	T	0.65719	0.2718	L	0.48642	1.525	0.36744	D	0.882387	B	0.23316	0.083	B	0.18871	0.023	T	0.62695	-0.6800	10	0.09084	T	0.74	-0.3554	14.8068	0.69962	0.0:0.0:1.0:0.0	.	591	Q8IZL2	MAML2_HUMAN	K	591	ENSP00000434552:Q591K;ENSP00000412394:Q591K	ENSP00000412394:Q591K	Q	-	1	0	MAML2	95465072	1.000000	0.71417	0.944000	0.38274	0.017000	0.09413	3.476000	0.53143	2.151000	0.67156	0.555000	0.69702	CAG	.		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825424	G	T	95825424	3	4	141	1	0	0	0	0	1	0	0	0	9231	1386	48	4	1715	4	MAML2	11	95825424	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	12947697	95825424	39181092	80	12584											
NCAM1	4684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113078684	113078684	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atctgcattgctgagaacaaGgctggcgagcaggatgcgac	11	7	14	9	2	1	1	0	1	1	1	1	5	1	2	0	3	5	4	0	3	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:113078684G>C	ENST00000533760.1	+	7	1121	c.522G>C	c.(520-522)aaG>aaC	p.K174N	NCAM1_ENST00000316851.7_Missense_Mutation_p.K282N|NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.K291N	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	292	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CTGAGAACAAGGCTGGCGAGC	0.532																																					p.K292N		.											.	NCAM1-23	0			c.G876C						.						61	61	61					11																	113078684		2078	4216	6294	SO:0001583	missense	4684	exon8			GAACAAGGCTGGC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.522G>C	11.37:g.113078684G>C	ENSP00000473281:p.Lys174Asn	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	20	6	NM_001242608	0	0	0	0	0	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	G	18.41	3.617792	0.66787	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.68181	-0.31;-0.31	5.57	3.47	0.39725	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.041493	0.85682	D	0.000000	T	0.78400	0.4277	.	.	.	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.997;0.995;0.994;0.983	D;D;D;D;D	0.71870	0.963;0.917;0.975;0.952;0.925	T	0.79697	-0.1695	9	0.87932	D	0	-16.9107	8.6894	0.34258	0.2821:0.0:0.7179:0.0	.	292;292;292;292;292	P13591-5;P13591-1;P13591;P13591-3;P13591-6	.;.;NCAM1_HUMAN;.;.	N	174;291;282	ENSP00000384055:K291N;ENSP00000318472:K282N	ENSP00000318472:K282N	K	+	3	2	NCAM1	112583894	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	3.113000	0.50376	1.347000	0.45714	0.655000	0.94253	AAG	.		0.532	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		C	113078684	G	C	113078684	3	2	141	1	0	0	0	0	1	0	0	0	10228	991	35	4	903	4	NCAM1	11	113078684	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	17253260	113078684	21927832	81	12585											
C3AR1	719	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	8211578	8211578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggagtttctgggtcagtaaGcaatgacaggactccaaaaa	14	8	12	7	0	2	1	1	1	1	0	3	3	3	3	1	3	1	3	1	3	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:8211578G>A	ENST00000307637.4	-	2	1407	c.1204C>T	c.(1204-1206)Ctt>Ttt	p.L402F		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	402					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		GGGTCAGTAAGCAATGACAGG	0.483																																					p.L402F		.											.	C3AR1-227	0			c.C1204T						.						73	68	70					12																	8211578		2203	4300	6503	SO:0001583	missense	719	exon2			CAGTAAGCAATGA	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.1204C>T	12.37:g.8211578G>A	ENSP00000302079:p.Leu402Phe	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	67	8	NM_004054	0	0	16	16	0	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	37	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.321727	0.01320	.	.	ENSG00000171860	ENST00000307637	T	0.37235	1.21	5.26	0.103	0.14526	GPCR, rhodopsin-like superfamily (1);	1.231120	0.05729	N	0.599303	T	0.12518	0.0304	N	0.01800	-0.715	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23332	-1.0191	10	0.15499	T	0.54	.	3.1161	0.06375	0.4472:0.0:0.2539:0.2989	.	402	Q16581	C3AR_HUMAN	F	402	ENSP00000302079:L402F	ENSP00000302079:L402F	L	-	1	0	C3AR1	8102845	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.859000	0.04277	0.118000	0.18165	-0.238000	0.12139	CTT	.		0.483	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			A	8211578	G	A	8211578	3	1	141	1	0	0	0	0	1	0	0	0	2211	971	34	2	248	2	C3AR1	12	8211578	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		8211578	125640317	82	12586											
KLRC1	3821	hgsc.bcm.edu	37	chr12	10602537	10602537	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagttcttgtattcagggAagaattgttgtgcctctgta	8	16	11	6	0	3	2	1	1	2	1	3	3	3	3	1	1	1	4	1	1	4	7			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:10602537A>G	ENST00000359151.3	-	4	494	c.313T>C	c.(313-315)Tcc>Ccc	p.S105P	KLRC1_ENST00000544822.1_Missense_Mutation_p.S105P|KLRC1_ENST00000536188.1_Missense_Mutation_p.S105P|KLRC1_ENST00000347831.5_Intron|KLRC1_ENST00000408006.3_Intron	NM_002259.4	NP_002250	P26715	NKG2A_HUMAN	killer cell lectin-like receptor subfamily C, member 1	105					cell surface receptor signaling pathway (GO:0007166)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16						GTATTCAGGGAAGAATTGTTG	0.224																																					p.S105P		.											.	KLRC1-514	0			c.T313C						.						14	15	15					12																	10602537		2104	4159	6263	SO:0001583	missense	3821	exon4			TCAGGGAAGAATT	U54782	CCDS8625.1, CCDS8626.1	12p13	2010-06-30			ENSG00000134545	ENSG00000134545		"Killer cell lectin-like receptors", "CD molecules"	6374	protein-coding gene	gene with protein product	"NKG2-1/B activating NK receptor"	161555		NKG2		9598306	Standard	NM_002259		Approved	NKG2-A, NKG2-B, CD159a	uc001qyl.3	P26715		ENST00000359151.3:c.313T>C	12.37:g.10602537A>G	ENSP00000352064:p.Ser105Pro	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_002259	0	0	1	1	0		Missense_Mutation	SNP	ENST00000359151.3	37	CCDS8625.1	.	.	.	.	.	.	.	.	.	.	A	8.768	0.925219	0.18056	.	.	ENSG00000134545	ENST00000536188;ENST00000359151;ENST00000544822	T;T;T	0.09630	2.96;2.96;2.96	2.63	2.63	0.31362	C-type lectin fold (1);	0.831025	0.10137	N	0.711294	T	0.33323	0.0859	M	0.91090	3.175	0.09310	N	1	D	0.63046	0.992	D	0.63381	0.914	T	0.14811	-1.0459	10	0.27082	T	0.32	.	7.1333	0.25515	1.0:0.0:0.0:0.0	.	105	P26715	NKG2A_HUMAN	P	105	ENSP00000441432:S105P;ENSP00000352064:S105P;ENSP00000438038:S105P	ENSP00000352064:S105P	S	-	1	0	KLRC1	10493804	0.002000	0.14202	0.009000	0.14445	0.043000	0.13939	1.323000	0.33701	1.461000	0.47929	0.383000	0.25322	TCC	.		0.224	KLRC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400115.1	NM_002259		G	10602537	A	G	10602537	3	3	141	1	0	0	0	0	1	0	0	0	8436	246	9	3	404	3	KLRC1	12	10602537	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	2390959	10602537	123249358	83	12587											
ESPL1	9700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53687232	53687232	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggggctgcacctatagccTatggcttgcctgtctctctg	4	14	11	12	0	2	0	0	0	2	0	3	0	2	0	3	3	3	3	3	3	3	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:53687232T>C	ENST00000257934.4	+	31	6428	c.6337T>C	c.(6337-6339)Tat>Cat	p.Y2113H	PFDN5_ENST00000551018.1_5'Flank|PFDN5_ENST00000351500.3_5'Flank|ESPL1_ENST00000552462.1_Missense_Mutation_p.Y2113H|PFDN5_ENST00000334478.4_5'Flank|PFDN5_ENST00000550846.1_5'Flank	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	2113					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						ACCTATAGCCTATGGCTTGCC	0.527																																					p.Y2113H	Colon(53;1069 1201 2587 5382)	.											.	ESPL1-228	0			c.T6337C						.						64	65	65					12																	53687232		2203	4300	6503	SO:0001583	missense	9700	exon31			ATAGCCTATGGCT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"separin", "separase", "separin, cysteine protease"	604143	"extra spindle poles like 1 (S. cerevisiae)"			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.6337T>C	12.37:g.53687232T>C	ENSP00000257934:p.Tyr2113His	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	97	45	NM_012291	0	0	1	2	1		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234561	0.79800	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.56444	0.46;0.46	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.76702	0.4024	M	0.90198	3.095	0.53688	D	0.999976	D	0.89917	1.0	D	0.87578	0.998	T	0.82204	-0.0573	10	0.87932	D	0	.	13.8969	0.63778	0.0:0.0:0.0:1.0	.	2113	Q14674	ESPL1_HUMAN	H	2113;1788;2113	ENSP00000257934:Y2113H;ENSP00000449831:Y2113H	ENSP00000257934:Y2113H	Y	+	1	0	ESPL1	51973499	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.612000	0.82975	2.178000	0.69098	0.460000	0.39030	TAT	.		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		C	53687232	T	C	53687232	3	2	141	1	0	0	0	0	1	0	0	0	5266	1522	53	3	6455	3	ESPL1	12	53687232	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	43084695	53687232	80164663	84	12588											
DUSP6	1848	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	89743102	89743107	+	In_Frame_Del	DEL	CTGGAA	CTGGAA	-																															ggtaaaatacagctgctgtgCtggaaccctgttgtcacatg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	CTGGAA	CTGGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:89743102_89743107delCTGGAA	ENST00000279488.7	-	3	2301_2306	c.1070_1075delTTCCAG	c.(1069-1077)gttccagca>gca	p.VP357del	DUSP6_ENST00000547140.1_5'Flank|DUSP6_ENST00000547291.1_In_Frame_Del_p.VP232del|DUSP6_ENST00000308385.6_In_Frame_Del_p.VP211del	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	357	Tyrosine-protein phosphatase.				cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						AGCTGCTGTGCTGGAACCCTGTTGTC	0.5																																					p.357_359del	Colon(132;3456 5224)	.											.	DUSP6-846	0			c.1070_1075del						.																																			SO:0001651	inframe_deletion	1848	exon3			.	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.1070_1075delTTCCAG	12.37:g.89743102_89743107delCTGGAA	ENSP00000279488:p.Val357_Pro358del	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	129	41	NM_001946	0	0	0	0	0	O75109|Q53Y75|Q9BSH6	In_Frame_Del	DEL	ENST00000279488.7	37	CCDS9033.1																																																																																			.		0.5	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		-	89743107	CTGGAA	-	89743102	7	5	141	1	0	1	0	1	0	0	0	0	4840	797	28	0	74	0	DUSP6	12	89743102	In_Frame_Del	DEL	CTGGAA	TCGA-IZ-8196-01A-11D-2396-08	36055870	89743102	44108793	85	12589											
ALDH2	217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	112227694	112227694	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgacggagacttcttcagcTacacacgccatgaacctgtg	10	10	9	12	2	2	3	1	2	1	1	2	4	2	3	2	1	3	1	2	1	2	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:112227694T>C	ENST00000261733.2	+	5	569	c.508T>C	c.(508-510)Tac>Cac	p.Y170H	RP11-162P23.2_ENST00000546840.2_Silent_p.A166A|ALDH2_ENST00000416293.3_Missense_Mutation_p.Y123H	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	170					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	CTTCTTCAGCTACACACGCCA	0.527			T	HMGA2	leiomyoma																																p.Y170H		.		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	.	ALDH2-228	0			c.T508C						.						100	87	91					12																	112227694		2203	4300	6503	SO:0001583	missense	217	exon5			TTCAGCTACACAC	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.508T>C	12.37:g.112227694T>C	ENSP00000261733:p.Tyr170His	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	61	21	NM_000690	0	0	152	262	110	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	37	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.792458	0.90453	.	.	ENSG00000257767;ENSG00000111275;ENSG00000111275;ENSG00000111275;ENSG00000111275	ENST00000546840;ENST00000416293;ENST00000261733;ENST00000553044;ENST00000552234	T;T	0.77620	-1.11;-1.11	5.17	5.17	0.71159	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.172373	0.53938	D	0.000059	D	0.89612	0.6765	M	0.88105	2.93	0.53688	D	0.999979	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.987;0.997;0.998	D	0.91609	0.5301	10	0.72032	D	0.01	.	15.3139	0.74059	0.0:0.0:0.0:1.0	.	123;170;170	E7EUE5;F8VXI5;P05091	.;.;ALDH2_HUMAN	H	151;123;170;170;30	ENSP00000403349:Y123H;ENSP00000261733:Y170H	ENSP00000261733:Y170H	Y	+	1	0	ALDH2;RP11-162P23.2	110712077	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.655000	0.83696	2.071000	0.62044	0.460000	0.39030	TAC	.		0.527	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690		C	112227694	T	C	112227694	3	2	141	1	0	0	0	0	1	0	0	0	496	1522	53	3	526	3	ALDH2	12	112227694	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	22484592	112227694	21624201	86	12590											
HNF1A	6927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	121437158	121437158	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaccgacaccaccaaccTgagcgccctggccagcctca	10	4	7	20	2	2	1	2	1	0	0	2	2	2	1	7	1	3	0	7	1	1	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:121437158T>C	ENST00000257555.6	+	8	1815	c.1589T>C	c.(1588-1590)cTg>cCg	p.L530P	HNF1A_ENST00000544413.1_Missense_Mutation_p.L530P|HNF1A_ENST00000541395.1_Missense_Mutation_p.L530P|RP11-216P16.2_ENST00000606238.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	530					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACCACCAACCTGAGCGCCCTG	0.687									Hepatic Adenoma, Familial Clustering of																												p.L530P		.											.	HNF1A-1745	0			c.T1589C						.						83	85	84					12																	121437158		2203	4300	6503	SO:0001583	missense	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCAACCTGAGCGC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"Homeoboxes / HNF class"	11621	protein-coding gene	gene with protein product		142410	"transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1589T>C	12.37:g.121437158T>C	ENSP00000257555:p.Leu530Pro	Somatic	399	0		WXS	Illumina HiSeq	Phase_I	116	54	NM_000545	0	0	12	19	7	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760491	0.89932	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000544413	D;D;D	0.98617	-5.03;-5.03;-5.03	5.52	5.52	0.82312	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.000000	0.48286	D	0.000189	D	0.98658	0.9550	L	0.52573	1.65	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.993;0.996	D	0.99890	1.1133	10	0.72032	D	0.01	-15.5351	14.8565	0.70341	0.0:0.0:0.0:1.0	.	530;530	F5H0K0;P20823	.;HNF1A_HUMAN	P	530;422;530;351;530;530	ENSP00000257555:L530P;ENSP00000443112:L530P;ENSP00000438804:L530P	ENSP00000257555:L530P	L	+	2	0	HNF1A	119921541	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.616000	0.83018	2.104000	0.64026	0.528000	0.53228	CTG	.		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		C	121437158	T	C	121437158	3	2	141	1	0	0	0	0	1	0	0	0	7272	1580	55	3	1619	3	HNF1A	12	121437158	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	9209464	121437158	12414737	87	12591											
BRCA2	675	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	32907353	32907353	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctttgaagaatgcaggtttaAtatccactttgaaaaagaaa	17	12	7	5	0	0	4	0	2	0	2	1	4	1	4	1	1	1	2	1	1	7	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr13:32907353A>C	ENST00000380152.3	+	10	1971	c.1738A>C	c.(1738-1740)Ata>Cta	p.I580L	BRCA2_ENST00000544455.1_Missense_Mutation_p.I580L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	580					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGCAGGTTTAATATCCACTTT	0.338			"D, Mis, N, F, S"		"breast, ovarian, pancreatic"	"breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.I580L	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"L, E"	.	BRCA2-3153	0			c.A1738C						.						44	49	47					13																	32907353		2203	4300	6503	SO:0001583	missense	675	exon10	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GGTTTAATATCCA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"Fanconi anemia, complementation groups"	1101	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 2"	600185	"Fanconi anemia, complementation group D1"	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1738A>C	13.37:g.32907353A>C	ENSP00000369497:p.Ile580Leu	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	93	49	NM_000059	0	0	0	0	0	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.677622	0.47886	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00776	5.71;5.71	5.5	4.32	0.51571	.	0.150989	0.47093	D	0.000244	T	0.00906	0.0030	M	0.70275	2.135	0.25438	N	0.988123	P;B	0.39748	0.686;0.402	B;B	0.32211	0.088;0.142	T	0.45190	-0.9278	10	0.15952	T	0.53	.	5.4332	0.16464	0.7537:0.0:0.0834:0.1629	.	580;580	P51587;A1YBP1	BRCA2_HUMAN;.	L	580;580;578	ENSP00000369497:I580L;ENSP00000439902:I580L	ENSP00000369497:I580L	I	+	1	0	BRCA2	31805353	0.997000	0.39634	0.995000	0.50966	0.698000	0.40448	0.972000	0.29409	1.016000	0.39470	0.528000	0.53228	ATA	.		0.338	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		C	32907353	A	C	32907353	3	2	141	1	0	0	0	0	1	0	0	0	1502	101	4	5	1772	5	BRCA2	13	32907353	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		32907353	82262525	88	12592											
ESD	2098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	47354151	47354151	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtacagggttgcaaattggAgcaaatgctgacacagactt	14	9	11	7	0	0	2	0	1	0	1	0	3	0	3	0	2	4	5	0	2	3	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr13:47354151A>G	ENST00000378720.3	-	8	701	c.519T>C	c.(517-519)gcT>gcC	p.A173A	ESD_ENST00000495654.1_5'UTR|ESD_ENST00000378697.1_Silent_p.A144A	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	173					formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	TGCAAATTGGAGCAAATGCTG	0.333																																					p.A173A		.											.	ESD-91	0			c.T519C						.						91	91	91					13																	47354151		2203	4299	6502	SO:0001819	synonymous_variant	2098	exon8			AATTGGAGCAAAT	M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"S-formylglutathione hydrolase"	133280	"esterase D/formylglutathione hydrolase"				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.519T>C	13.37:g.47354151A>G		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	101	42	NM_001984	0	0	86	181	95	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Silent	SNP	ENST00000378720.3	37	CCDS9404.1	.	.	.	.	.	.	.	.	.	.	A	9.962	1.223120	0.22457	.	.	ENSG00000139684	ENST00000412582	.	.	.	6.16	3.7	0.42460	.	.	.	.	.	T	0.57140	0.2033	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50717	-0.8795	4	.	.	.	-8.9614	7.2303	0.26038	0.6488:0.2815:0.0697:0.0	.	.	.	.	P	121	.	.	L	-	2	0	ESD	46252152	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.509000	0.35780	0.536000	0.28733	-0.299000	0.09455	CTC	.		0.333	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1			G	47354151	A	G	47354151	2	3	141	1	0	0	0	0	0	0	0	1	5263	291	11	3		3	ESD	13	47354151	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	14446798	47354151	67815727	89	12593											
OR11G2	390439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	20666034	20666034	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaccagacgtctctgtacCaatcttgtggtcaattgctg	9	13	9	10	1	3	2	1	1	2	1	4	2	3	2	2	1	2	2	2	1	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:20666034C>T	ENST00000357366.3	+	1	540	c.540C>T	c.(538-540)acC>acT	p.T180T		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	180						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GTCTCTGTACCAATCTTGTGG	0.448																																					p.T180T		.											.	OR11G2-70	0			c.C540T						.						111	94	100					14																	20666034		2203	4300	6503	SO:0001819	synonymous_variant	390439	exon1			CTGTACCAATCTT		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.540C>T	14.37:g.20666034C>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	112	39	NM_001005503	0	0	0	0	0	Q6IF09|Q96R33	Silent	SNP	ENST00000357366.3	37	CCDS32032.1																																																																																			.		0.448	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			T	20666034	C	T	20666034	2	4	141	1	0	0	0	0	0	0	0	1	10951	581	21	2		2	OR11G2	14	20666034	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		20666034	86683506	90	12594											
SLC22A17	51310	hgsc.bcm.edu	37	chr14	23816377	23816377	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcggcagcttgggaggagaAgagcccaaggacagagaaag	14	2	18	7	1	0	3	0	0	0	3	0	7	0	5	1	5	2	2	1	5	3	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:23816377A>G	ENST00000206544.8	-	8	1597	c.1261T>C	c.(1261-1263)Ttc>Ctc	p.F421L	SLC22A17_ENST00000397260.3_Missense_Mutation_p.F292L|SLC22A17_ENST00000354772.3_Missense_Mutation_p.F403L|SLC22A17_ENST00000397267.1_Missense_Mutation_p.F421L|SLC22A17_ENST00000474057.1_5'UTR	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	421					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGGGAGGAGAAGAGCCCAAGG	0.612																																					p.F421L		.											.	SLC22A17-226	0			c.T1261C						.						81	59	66					14																	23816377		2203	4300	6503	SO:0001583	missense	51310	exon8			AGGAGAAGAGCCC	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"Solute carriers"	23095	protein-coding gene	gene with protein product	"neutrophil gelatinase-associated lipocalin receptor"	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1261T>C	14.37:g.23816377A>G	ENSP00000206544:p.Phe421Leu	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_020372	0	0	40	40	0	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Missense_Mutation	SNP	ENST00000206544.8	37	CCDS9593.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.086485	0.36855	.	.	ENSG00000092096	ENST00000354772;ENST00000397260;ENST00000206544;ENST00000397267	T;T;T;T	0.59364	0.27;0.27;0.27;0.27	5.36	5.36	0.76844	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.39145	0.1067	N	0.21324	0.655	0.53688	D	0.999976	B;P	0.36909	0.114;0.573	B;B	0.36534	0.057;0.227	T	0.36939	-0.9727	10	0.02654	T	1	-21.8141	13.1705	0.59595	1.0:0.0:0.0:0.0	.	403;421	Q8WUG5-2;Q8WUG5	.;S22AH_HUMAN	L	403;292;421;421	ENSP00000346824:F403L;ENSP00000380430:F292L;ENSP00000206544:F421L;ENSP00000380437:F421L	ENSP00000206544:F421L	F	-	1	0	SLC22A17	22886217	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.295000	0.43576	2.163000	0.67991	0.460000	0.39030	TTC	.		0.612	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372		G	23816377	A	G	23816377	3	3	141	1	0	0	0	0	1	0	0	0	14480	72	3	3	363	3	SLC22A17	14	23816377	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	3150343	23816377	83533163	91	12595											
C14orf37	145407	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	58563683	58563683	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcttcatcctcttcatcCtcatcttcttgtccctctag	4	19	2	16	0	9	0	3	0	6	0	12	0	12	0	3	0	0	0	3	0	1	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:58563683C>G	ENST00000267485.7	-	5	2042	c.1848G>C	c.(1846-1848)gaG>gaC	p.E616D		NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	616	Glu-rich.					integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						cctcttcatcctcatcttctt	0.398																																					p.E616D		.											.	C14orf37-90	0			c.G1848C						.						195	145	162					14																	58563683		2203	4300	6503	SO:0001583	missense	145407	exon5			TTCATCCTCATCT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1848G>C	14.37:g.58563683C>G	ENSP00000267485:p.Glu616Asp	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	55	27	NM_001001872	0	0	0	2	2	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.093373	0.36952	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.11063	2.81	4.97	-3.62	0.04543	Armadillo-like helical (1);	0.466239	0.19773	N	0.106394	T	0.07143	0.0181	L	0.38531	1.155	0.30330	N	0.786721	B;B;B	0.24576	0.106;0.106;0.106	B;B;B	0.26770	0.073;0.073;0.073	T	0.12016	-1.0564	10	0.87932	D	0	-0.7422	5.8628	0.18759	0.0:0.3161:0.242:0.4419	.	654;616;616	B4DMS4;A8K990;Q86TY3	.;.;CN037_HUMAN	D	616;654	ENSP00000267485:E616D	ENSP00000267485:E616D	E	-	3	2	C14orf37	57633436	0.186000	0.23225	0.976000	0.42696	0.636000	0.38137	-1.104000	0.03326	-0.558000	0.06118	0.561000	0.74099	GAG	.		0.398	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		G	58563683	C	G	58563683	3	3	141	1	0	0	0	0	1	0	0	0	1775	680	24	4	492	4	C14orf37	14	58563683	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	34747306	58563683	48785857	92	12596											
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	64596614	64596614	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactccaggaggtttacaaaTtagaggtatgcctgagcaga	13	10	11	7	0	0	3	0	1	0	2	1	4	1	4	2	3	4	3	2	3	5	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:64596614T>A	ENST00000344113.4	+	75	14346	c.14134T>A	c.(14134-14136)Tta>Ata	p.L4712I	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000357395.3_Missense_Mutation_p.L1097I|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1097I|SYNE2_ENST00000554584.1_Missense_Mutation_p.L4629I|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1346I|SYNE2_ENST00000358025.3_Missense_Mutation_p.L4712I	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4712					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GGTTTACAAATTAGAGGTATG	0.458																																					p.L4712I		.											.	SYNE2-164	0			c.T14134A						.						113	112	112					14																	64596614		2203	4300	6503	SO:0001583	missense	23224	exon75			TACAAATTAGAGG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.14134T>A	14.37:g.64596614T>A	ENSP00000341781:p.Leu4712Ile	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	59	29	NM_182914	0	0	0	0	0	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.481904	0.26598	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.71934	1.34;1.34;1.34;-0.61;1.34;1.34	5.23	1.55	0.23275	.	0.000000	0.40144	N	0.001175	T	0.76300	0.3968	M	0.72894	2.215	0.80722	D	1	D;D;D	0.69078	0.997;0.987;0.995	D;P;D	0.67231	0.95;0.841;0.926	T	0.70197	-0.4938	10	0.27785	T	0.31	.	5.4414	0.16511	0.0:0.2145:0.1349:0.6506	.	1097;4712;4712	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	I	4712;1097;4712;4629;4629;1346;1097	ENSP00000350719:L4712I;ENSP00000349969:L1097I;ENSP00000341781:L4712I;ENSP00000452570:L4629I;ENSP00000450831:L1346I;ENSP00000378249:L1097I	ENSP00000261678:L4629I	L	+	1	2	SYNE2	63666367	1.000000	0.71417	0.996000	0.52242	0.717000	0.41224	0.934000	0.28910	0.084000	0.17077	-0.274000	0.10170	TTA	.		0.458	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64596614	T	A	64596614	3	1	141	1	0	0	0	0	1	0	0	0	15478	1490	52	5	14428	5	SYNE2	14	64596614	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	6032931	64596614	42752926	93	12597											
TTC8	123016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	89307438	89307438	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaggcccagcacgcagagTggaaggccaggcactatgga	11	4	14	12	1	1	1	1	0	0	1	1	3	1	3	2	5	1	3	2	5	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:89307438T>A	ENST00000345383.5	+	4	441	c.357T>A	c.(355-357)agT>agA	p.S119R	TTC8_ENST00000358622.5_5'Flank|Y_RNA_ENST00000384612.1_RNA|TTC8_ENST00000346301.4_Missense_Mutation_p.S119R|TTC8_ENST00000380656.2_Missense_Mutation_p.S129R|TTC8_ENST00000536576.1_5'UTR|TTC8_ENST00000338104.6_Missense_Mutation_p.S119R|TTC8_ENST00000354441.6_Intron	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	129					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						GCACGCAGAGTGGAAGGCCAG	0.498																																					p.S129R		.											.	TTC8-90	0			c.T387A						.						67	75	72					14																	89307438		2203	4300	6503	SO:0001583	missense	123016	exon5			GCAGAGTGGAAGG	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"Tetratricopeptide (TTC) repeat domain containing"	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.357T>A	14.37:g.89307438T>A	ENSP00000339486:p.Ser119Arg	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	127	52	NM_144596	0	0	3	7	4	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	37	CCDS9885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	17.54|17.54|17.54	3.414274|3.414274|3.414274	0.62511|0.62511|0.62511	.|.|.	.|.|.	ENSG00000165533|ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000346301;ENST00000338104;ENST00000380656;ENST00000556651|ENST00000554686|ENST00000343648	T;T;T;T|.|.	0.80738|.|.	-1.3;-1.39;-1.41;-1.3|.|.	5.46|5.46|5.46	1.8|1.8|1.8	0.24995|0.24995|0.24995	.|.|.	0.153416|.|.	0.56097|.|.	D|.|.	0.000029|.|.	T|T|T	0.68613|0.68613|0.68613	0.3020|0.3020|0.3020	M|M|M	0.76574|0.76574|0.76574	2.34|2.34|2.34	0.80722|0.80722|0.80722	D|D|D	1|1|1	P;D;B;D;B|.|.	0.54601|.|.	0.808;0.967;0.012;0.967;0.012|.|.	B;P;B;P;B|.|.	0.51918|.|.	0.368;0.595;0.054;0.684;0.054|.|.	T|T|T	0.64045|0.64045|0.64045	-0.6499|-0.6499|-0.6499	10|5|5	0.66056|.|.	D|.|.	0.02|.|.	-16.3432|-16.3432|-16.3432	9.1746|9.1746|9.1746	0.37105|0.37105|0.37105	0.0:0.2088:0.0:0.7912|0.0:0.2088:0.0:0.7912|0.0:0.2088:0.0:0.7912	.|.|.	129;119;129;119;129|.|.	Q8TAM2;G3V2Z9;Q8TAM2-3;G3V324;Q8TAM2-4|.|.	TTC8_HUMAN;.;.;.;.|.|.	R|E|R	119;119;119;129;119|109|171	ENSP00000339486:S119R;ENSP00000298324:S119R;ENSP00000337653:S119R;ENSP00000370031:S129R|.|.	ENSP00000337653:S119R|.|.	S|V|W	+|+|+	3|2|1	2|0|0	TTC8|TTC8|TTC8	88377191|88377191|88377191	0.719000|0.719000|0.719000	0.27986|0.27986|0.27986	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	-0.225000|-0.225000|-0.225000	0.09151|0.09151|0.09151	0.065000|0.065000|0.065000	0.16485|0.16485|0.16485	0.460000|0.460000|0.460000	0.39030|0.39030|0.39030	AGT|GTG|TGG	.		0.498	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		A	89307438	T	A	89307438	3	1	141	1	0	0	0	0	1	0	0	0	16747	1693	59	5	405	5	TTC8	14	89307438	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	24710824	89307438	18042102	94	12598											
CDC42BPB	9578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	103438368	103438368	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgccgggacaccttctgcTtctgggcacggagctctgcc	4	9	13	15	2	3	0	0	0	3	0	3	2	3	2	3	3	4	4	3	3	0	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:103438368T>A	ENST00000361246.2	-	13	2060	c.1772A>T	c.(1771-1773)aAg>aTg	p.K591M		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CACCTTCTGCTTCTGGGCACG	0.617																																					p.K591M		.											.	CDC42BPB-581	0			c.A1772T						.						112	95	100					14																	103438368		2203	4300	6503	SO:0001583	missense	9578	exon13			TTCTGCTTCTGGG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"CDC42-binding protein kinase beta (DMPK-like)"			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1772A>T	14.37:g.103438368T>A	ENSP00000355237:p.Lys591Met	Somatic	293	0		WXS	Illumina HiSeq	Phase_I	132	60	NM_006035	0	0	64	125	61		Missense_Mutation	SNP	ENST00000361246.2	37	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560047	0.86335	.	.	ENSG00000198752	ENST00000361246	D	0.82619	-1.63	5.31	4.15	0.48705	.	0.045881	0.85682	D	0.000000	D	0.90456	0.7011	M	0.84948	2.725	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.90167	0.4232	10	0.56958	D	0.05	.	10.9197	0.47156	0.0:0.0743:0.0:0.9257	.	591	Q9Y5S2	MRCKB_HUMAN	M	591	ENSP00000355237:K591M	ENSP00000355237:K591M	K	-	2	0	CDC42BPB	102508121	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.228000	0.72288	0.860000	0.35481	0.460000	0.39030	AAG	.		0.617	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		A	103438368	T	A	103438368	3	1	141	1	0	0	0	0	1	0	0	0	3079	1609	56	5	3463	5	CDC42BPB	14	103438368	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	14130930	103438368	3911172	95	12599											
KIAA0284	283638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	105353612	105353612	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcctcagagaggcagcaTcacccacttggcccgacgga	10	5	11	15	2	2	1	2	0	0	1	3	4	3	2	3	3	1	2	3	3	0	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:105353612T>G	ENST00000414716.3	+	12	3264	c.3036T>G	c.(3034-3036)caT>caG	p.H1012Q	CEP170B_ENST00000418279.1_Missense_Mutation_p.H942Q|CEP170B_ENST00000453495.1_Missense_Mutation_p.H1013Q|CEP170B_ENST00000556508.1_Missense_Mutation_p.H942Q	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1012						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGAGGCAGCATCACCCACTTG	0.687																																					p.H1012Q		.											.	.	0			c.T3036G						.						11	15	14					14																	105353612		2073	4183	6256	SO:0001583	missense	283638	exon12			GCAGCATCACCCA	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.3036T>G	14.37:g.105353612T>G	ENSP00000404151:p.His1012Gln	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	35	14	NM_001112726	0	0	5	23	18	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	37	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	T	4.535	0.099232	0.08681	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	3.85	-6.94	0.01633	.	1.152450	0.06494	N	0.735156	T	0.24736	0.0600	N	0.22421	0.69	0.09310	N	1	B;B;B	0.23735	0.002;0.09;0.01	B;B;B	0.16722	0.008;0.016;0.014	T	0.31971	-0.9924	10	0.59425	D	0.04	-0.1639	8.1321	0.31033	0.0:0.3657:0.4378:0.1965	.	1012;1012;942	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	Q	942;1012;1013;942	ENSP00000451249:H942Q;ENSP00000404151:H1012Q;ENSP00000407238:H1013Q;ENSP00000415006:H942Q	ENSP00000404151:H1012Q	H	+	3	2	KIAA0284	104424657	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-3.141000	0.00586	-1.631000	0.01543	-0.537000	0.04273	CAT	.		0.687	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		G	105353612	T	G	105353612	3	3	141	1	0	0	0	0	1	0	0	0	8187	1432	50	5	3078	5	KIAA0284	14	105353612	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	1915244	105353612	1995928	96	12600											
CATSPER2	117155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43928412	43928412	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttaccagggaattcgggAggtccctaaagaaaaagaca	15	7	11	8	1	0	2	0	0	0	2	2	4	1	4	2	3	1	1	2	3	6	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:43928412A>G	ENST00000321596.5	-	8	1047	c.848T>C	c.(847-849)cTc>cCc	p.L283P	CATSPER2_ENST00000355438.2_Missense_Mutation_p.L283P|CATSPER2_ENST00000354127.4_Missense_Mutation_p.L283P|CATSPER2_ENST00000381761.1_Missense_Mutation_p.L289P|CATSPER2_ENST00000396879.1_Missense_Mutation_p.L283P|RNU6-610P_ENST00000384264.1_RNA|STRC_ENST00000541030.1_Intron			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	283					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GGAATTCGGGAGGTCCCTAAA	0.413																																					p.L283P		.											.	CATSPER2-91	0			c.T848C						.						53	54	53					15																	43928412		2199	4296	6495	SO:0001583	missense	117155	exon8			TTCGGGAGGTCCC	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.848T>C	15.37:g.43928412A>G	ENSP00000321463:p.Leu283Pro	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	73	28	NM_054020	0	0	0	0	0	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	A	5.296	0.239992	0.10023	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01;-5.01	4.81	4.81	0.61882	Ion transport (1);	0.856615	0.09979	N	0.731205	D	0.97885	0.9305	M	0.82823	2.61	0.33841	D	0.631417	B;B	0.29481	0.206;0.245	B;B	0.35727	0.133;0.209	D	0.99974	1.2121	10	0.87932	D	0	.	10.6643	0.45721	1.0:0.0:0.0:0.0	.	289;283	F8W9H2;Q96P56	.;CTSR2_HUMAN	P	283;283;289;283;283;283	ENSP00000380088:L283P;ENSP00000371180:L289P;ENSP00000321463:L283P;ENSP00000339137:L283P;ENSP00000347613:L283P	ENSP00000299989:L283P	L	-	2	0	CATSPER2	41715704	0.211000	0.23529	0.127000	0.21898	0.013000	0.08279	3.770000	0.55310	2.013000	0.59113	0.533000	0.62120	CTC	.		0.413	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		G	43928412	A	G	43928412	3	3	141	1	0	0	0	0	1	0	0	0	2694	304	11	3	768	3	CATSPER2	15	43928412	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		43928412	58602980	97	12601											
NEO1	4756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	73590713	73590713	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttcgaaatacccccagcaCtgacaccatgccagcctctt	10	8	6	17	2	1	1	0	1	1	0	2	2	1	1	5	0	4	2	5	0	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:73590713C>T	ENST00000339362.5	+	28	4373	c.3926C>T	c.(3925-3927)aCt>aTt	p.T1309I	NEO1_ENST00000560262.1_Missense_Mutation_p.T1256I|NEO1_ENST00000261908.6_Missense_Mutation_p.T1309I|NEO1_ENST00000558964.1_Missense_Mutation_p.T1298I			Q92859	NEO1_HUMAN	neogenin 1	1309					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						ACCCCCAGCACTGACACCATG	0.483																																					p.T1309I		.											.	NEO1-116	0			c.C3926T						.						81	76	78					15																	73590713		2198	4297	6495	SO:0001583	missense	4756	exon27			CCAGCACTGACAC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.3926C>T	15.37:g.73590713C>T	ENSP00000341198:p.Thr1309Ile	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	70	36	NM_002499	0	0	26	56	30	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.924141	0.73213	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T	0.42900	0.96	5.28	5.28	0.74379	Neogenin, C-terminal (1);	0.294982	0.37857	N	0.001913	T	0.32704	0.0838	N	0.14661	0.345	0.41912	D	0.990476	B;B;B;P	0.37594	0.408;0.408;0.372;0.601	B;B;B;B	0.42959	0.304;0.324;0.295;0.403	T	0.16247	-1.0409	10	0.36615	T	0.2	-15.6613	14.1931	0.65652	0.0:0.8505:0.1495:0.0	.	1256;1298;1020;1309	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	I	1256;1020;1309	ENSP00000261908:T1309I	ENSP00000261908:T1309I	T	+	2	0	NEO1	71377766	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.492000	0.66893	2.479000	0.83701	0.655000	0.94253	ACT	.		0.483	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		T	73590713	C	T	73590713	3	4	141	1	0	0	0	0	1	0	0	0	10362	565	20	2	4032	2	NEO1	15	73590713	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	29662301	73590713	28940679	98	12602											
IREB2	3658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	78755356	78755356	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaagatgttatgaacattTtagactggaaaaccaaacaa	19	9	8	5	0	0	3	0	1	0	2	0	5	0	5	1	2	3	1	1	2	8	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:78755356T>A	ENST00000258886.8	+	3	348	c.199T>A	c.(199-201)Tta>Ata	p.L67I	IREB2_ENST00000560440.1_Missense_Mutation_p.L67I	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	67					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)		TATGAACATTTTAGACTGGAA	0.378																																					p.L67I	NSCLC(200;764 2208 35157 49871 50830)	.											.	IREB2-90	0			c.T199A						.						214	201	205					15																	78755356		2196	4293	6489	SO:0001583	missense	3658	exon3			AACATTTTAGACT	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	ENST00000258886.8:c.199T>A	15.37:g.78755356T>A	ENSP00000258886:p.Leu67Ile	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	183	75	NM_004136	0	0	5	8	3	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018887	0.75275	.	.	ENSG00000136381	ENST00000258886	T	0.44881	0.91	5.87	3.57	0.40892	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);	0.000000	0.85682	D	0.000000	T	0.53254	0.1785	L	0.52573	1.65	0.51482	D	0.999929	D;P	0.69078	0.997;0.577	D;P	0.91635	0.999;0.774	T	0.42616	-0.9441	10	0.23891	T	0.37	.	10.2319	0.43260	0.0:0.1334:0.0:0.8666	.	67;67	P48200;Q8WVK6	IREB2_HUMAN;.	I	67	ENSP00000258886:L67I	ENSP00000258886:L67I	L	+	1	2	IREB2	76542411	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.725000	0.25970	0.574000	0.29417	0.533000	0.62120	TTA	.		0.378	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		A	78755356	T	A	78755356	3	1	141	1	0	0	0	0	1	0	0	0	7847	1838	64	5	209	5	IREB2	15	78755356	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	5164643	78755356	23776036	99	12603											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81166242	81166242	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgggagctgctgggaggcagGacttcctcttcaaggccatg	7	9	15	10	0	2	0	1	0	1	0	3	3	3	3	2	5	2	3	2	5	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:81166242G>C	ENST00000394685.3	+	3	441	c.22G>C	c.(22-24)Gac>Cac	p.D8H	KIAA1199_ENST00000220244.3_Missense_Mutation_p.D8H|KIAA1199_ENST00000356249.5_Missense_Mutation_p.D8H			Q8WUJ3	CEMIP_HUMAN		8					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.D8N(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TGGGAGGCAGGACTTCCTCTT	0.577																																					p.D8H		.											.	KIAA1199-93	1	Substitution - Missense(1)	kidney(1)	c.G22C						.						70	54	60					15																	81166242		2202	4298	6500	SO:0001583	missense	57214	exon2			AGGCAGGACTTCC																												ENST00000394685.3:c.22G>C	15.37:g.81166242G>C	ENSP00000378177:p.Asp8His	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	8	2	NM_018689	0	0	0	0	0	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	G	8.342	0.828847	0.16749	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	T;T;T	0.66460	-0.21;-0.21;-0.21	4.92	-2.97	0.05530	.	6.948940	0.00166	N	0.000000	T	0.48537	0.1505	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17806	-1.0357	10	0.14656	T	0.56	-8.0685	5.165	0.15081	0.3585:0.2796:0.3619:0.0	.	8	Q8WUJ3	K1199_HUMAN	H	8	ENSP00000220244:D8H;ENSP00000378177:D8H;ENSP00000348583:D8H	ENSP00000220244:D8H	D	+	1	0	KIAA1199	78953297	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.356000	0.02609	-0.329000	0.08527	-0.165000	0.13383	GAC	.		0.577	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			C	81166242	G	C	81166242	3	2	141	1	0	0	0	0	1	0	0	0	8234	1174	41	4	24	4	KIAA1199	15	81166242	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	2410886	81166242	21365150	100	12604											
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84592741	84592741	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgatatggtccaccgtccTccagccatgagccaggcctg	7	9	11	14	1	0	2	0	2	0	0	3	2	3	2	7	2	2	0	7	2	1	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:84592741T>C	ENST00000286744.5	+	17	2297	c.2073T>C	c.(2071-2073)ccT>ccC	p.P691P	ADAMTSL3_ENST00000567476.1_Silent_p.P691P	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	691						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TCCACCGTCCTCCAGCCATGA	0.542																																					p.P691P		.											.	ADAMTSL3-1153	0			c.T2073C						.						114	82	93					15																	84592741		2203	4300	6503	SO:0001819	synonymous_variant	57188	exon17			CCGTCCTCCAGCC	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2073T>C	15.37:g.84592741T>C		Somatic	60	1		WXS	Illumina HiSeq	Phase_I	59	4	NM_207517	0	0	17	17	0	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			.		0.542	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		C	84592741	T	C	84592741	2	2	141	1	0	0	0	0	0	0	0	1	276	1538	54	3		3	ADAMTSL3	15	84592741	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	3426499	84592741	17938651	101	12605											
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23366804	23366804	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attcggagctgagccctgcaActaccggtgagagccacccc	9	6	11	15	2	0	2	0	2	0	1	1	4	0	3	5	2	6	2	5	2	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:23366804A>G	ENST00000343070.2	+	4	946	c.770A>G	c.(769-771)aAc>aGc	p.N257S	SCNN1B_ENST00000568923.1_Missense_Mutation_p.N230S|SCNN1B_ENST00000307331.5_Missense_Mutation_p.N302S|SCNN1B_ENST00000568085.1_Missense_Mutation_p.N257S	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	257					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	GAGCCCTGCAACTACCGGTGA	0.617																																					p.N257S		.											.	SCNN1B-157	0			c.A770G						.						54	50	51					16																	23366804		2197	4300	6497	SO:0001583	missense	6338	exon4			CCTGCAACTACCG	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.770A>G	16.37:g.23366804A>G	ENSP00000345751:p.Asn257Ser	Somatic	135	1		WXS	Illumina HiSeq	Phase_I	56	3	NM_000336	0	0	0	0	0	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	37	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	A	3.670	-0.067779	0.07228	.	.	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.62105	0.05;0.05	5.15	-3.89	0.04193	.	0.496689	0.22488	N	0.059415	T	0.32224	0.0822	N	0.11789	0.175	0.20563	N	0.999889	B	0.06786	0.001	B	0.10450	0.005	T	0.27640	-1.0068	10	0.12103	T	0.63	-23.0248	7.6249	0.28206	0.603:0.1229:0.2741:0.0	.	257	P51168	SCNNB_HUMAN	S	257;302	ENSP00000345751:N257S;ENSP00000302874:N302S	ENSP00000302874:N302S	N	+	2	0	SCNN1B	23274305	0.021000	0.18746	0.394000	0.26270	0.652000	0.38707	-0.173000	0.09854	-0.587000	0.05890	-0.366000	0.07423	AAC	.		0.617	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			G	23366804	A	G	23366804	3	3	141	1	0	0	0	0	1	0	0	0	13960	43	2	3	780	3	SCNN1B	16	23366804	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		23366804	66987949	102	12606											
HS3ST4	9951	hgsc.bcm.edu	37	chr16	26147416	26147416	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccagaagacagcagtgccccGaggtgcttaggcaagagcaa	13	4	13	11	1	0	3	0	0	0	3	0	4	0	3	3	2	4	4	3	2	4	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:26147416G>A	ENST00000331351.5	+	2	1610	c.1218G>A	c.(1216-1218)ccG>ccA	p.P406P	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	406					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		GCAGTGCCCCGAGGTGCTTAG	0.463																																					p.P406P		.											.	HS3ST4-67	0			c.G1218A						.						52	48	49					16																	26147416		1568	3582	5150	SO:0001819	synonymous_variant	9951	exon2			TGCCCCGAGGTGC	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.1218G>A	16.37:g.26147416G>A		Somatic	29	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_006040	0	0	0	0	0	Q5QI42|Q8NDC2	Silent	SNP	ENST00000331351.5	37	CCDS53995.1																																																																																			.		0.463	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		A	26147416	G	A	26147416	2	1	141	1	0	0	0	0	0	0	0	1	7388	1045	37	1		1	HS3ST4	16	26147416	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	2780612	26147416	64207337	103	12607											
SEPHS2	22928	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30456715	30456715	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgatgcccagggctggaaAggtggggctggggcccgctc	5	5	18	13	2	0	0	0	0	0	0	1	2	0	1	3	7	1	3	3	7	1	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:30456715A>G	ENST00000478753.2	-	1	787	c.334T>C	c.(334-336)Ttt>Ctt	p.F112L	SEPHS2_ENST00000500504.2_Missense_Mutation_p.F112L|SEPHS2_ENST00000542752.1_Missense_Mutation_p.F55L			Q99611	SPS2_HUMAN	selenophosphate synthetase 2	112					selenocysteine biosynthetic process (GO:0016260)		ATP binding (GO:0005524)|selenide, water dikinase activity (GO:0004756)			breast(3)|cervix(1)|kidney(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	10						AGGGCTGGAAAGGTGGGGCTG	0.711																																					.	Esophageal Squamous(81;1142 1261 11202 24614 35697)												.	SEPHS2-138	0			.						.						11	13	12					16																	30456715		1861	4083	5944	SO:0001583	missense	22928	.			CTGGAAAGGTGGG	BC002381		16p11.2	2013-02-15			ENSG00000179918	ENSG00000179918			19686	protein-coding gene	gene with protein product		606218				10608886	Standard	NM_012248		Approved	SPS2, SPS2b	uc021tgl.1	Q99611	OTTHUMG00000176988	ENST00000478753.2:c.334T>C	16.37:g.30456715A>G	ENSP00000418669:p.Phe112Leu	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	34	19	.	0	0	15	30	15	Q9BUQ2	Missense_Mutation	SNP	ENST00000478753.2	37		.	.	.	.	.	.	.	.	.	.	A	1.894	-0.454758	0.04540	.	.	ENSG00000179918	ENST00000478753;ENST00000542752;ENST00000418751;ENST00000500504	T;T;T	0.40476	1.03;1.06;1.04	5.4	-0.181	0.13291	PurM, N-terminal-like (1);	1.421770	0.04168	N	0.324249	T	0.19927	0.0479	N	0.08118	0	0.09310	N	0.999996	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.15752	-1.0426	10	0.08381	T	0.77	0.0554	5.092	0.14713	0.5253:0.1521:0.3225:0.0	.	112;55	Q99611;F5H8F9	SPS2_HUMAN;.	L	112;55;63;112	ENSP00000418669:F112L;ENSP00000443601:F55L;ENSP00000426234:F112L	ENSP00000390233:F63L	F	-	1	0	SEPHS2	30364216	0.000000	0.05858	0.000000	0.03702	0.148000	0.21650	-0.584000	0.05800	0.073000	0.16731	-0.408000	0.06270	TTT	.		0.711	SEPHS2-001	KNOWN	basic|seleno	protein_coding	protein_coding	OTTHUMT00000109640.11	NM_012248		G	30456715	A	G	30456715	3	3	141	1	0	0	0	0	1	0	0	0	14087	72	3	3	1016	3	SEPHS2	16	30456715	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	4309299	30456715	59898038	104	12608											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	30733503	30733503	+	Frame_Shift_Del	DEL	C	C	-																															acaacgtccagtggctaatgCagggggaagcaaacctctca																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:30733503delC	ENST00000262518.4	+	22	3987	c.3602delC	c.(3601-3603)gcafs	p.A1201fs	SRCAP_ENST00000395059.2_Frame_Shift_Del_p.A1201fs|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.A1105fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1201	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GTGGCTAATGCAGGGGGAAGC	0.577																																					p.A1201fs		.											.	SRCAP-94	0			c.3602delC						.						128	106	113					16																	30733503		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon22			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3602delC	16.37:g.30733503delC	ENSP00000262518:p.Ala1201fs	Somatic	238	0		WXS	Illumina HiSeq	Phase_I	97	33	NM_006662	0	0	0	0	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.577	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30733503	C	-	30733503	7	5	141	1	0	1	0	1	0	0	0	0	15167	710	25	0	3680	0	SRCAP	16	30733503	Frame_Shift_Del	DEL	C	TCGA-IZ-8196-01A-11D-2396-08	276788	30733503	59621250	105	12609	131	3									
SRCAP	10847	hgsc.bcm.edu;bcgsc.ca	37	chr16	30733505	30733505	+	Missense_Mutation	SNP	G	G	A																															aacgtccagtggctaatgcaGggggaagcaaacctctcacc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:30733505G>A	ENST00000262518.4	+	22	3989	c.3604G>A	c.(3604-3606)Ggg>Agg	p.G1202R	SRCAP_ENST00000395059.2_Missense_Mutation_p.G1202R|SRCAP_ENST00000344771.4_Missense_Mutation_p.G1106R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1202	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GGCTAATGCAGGGGGAAGCAA	0.572																																					p.G1202R		.											.	SRCAP-94	0			c.G3604A						.						129	107	114					16																	30733505		2197	4300	6497	SO:0001583	missense	10847	exon22			AATGCAGGGGGAA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3604G>A	16.37:g.30733505G>A	ENSP00000262518:p.Gly1202Arg	Somatic	245	0		WXS	Illumina HiSeq	Phase_I	102	38	NM_006662	0	0	7	7	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973443	0.53614	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.90900	-2.71;-2.68;-2.75	4.68	4.68	0.58851	.	0.000000	0.49305	D	0.000153	D	0.85961	0.5819	N	0.14661	0.345	0.20821	N	0.999846	P;D;P	0.53462	0.859;0.96;0.933	P;P;P	0.51229	0.572;0.663;0.462	T	0.78420	-0.2211	10	0.31617	T	0.26	-8.9406	12.9347	0.58307	0.0:0.1644:0.8356:0.0	.	1106;1202;1202	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	R	1202;1202;1106	ENSP00000262518:G1202R;ENSP00000378499:G1202R;ENSP00000343042:G1106R	ENSP00000262518:G1202R	G	+	1	0	SRCAP	30641006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.941000	0.49011	2.414000	0.81942	0.462000	0.41574	GGG	.		0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30733505	G	A	30733505	3	1	141	1	0	0	0	0	1	0	0	0	15167	1000	35	2	3682	2	SRCAP	16	30733505	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	2	30733505	59621248	106	12610	131	3									
SRCAP	10847	hgsc.bcm.edu	37	chr16	30733507	30733507	+	Frame_Shift_Del	DEL	G	G	-																															cgtccagtggctaatgcaggGggaagcaaacctctcacctt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:30733507delG	ENST00000262518.4	+	22	3991	c.3606delG	c.(3604-3606)gggfs	p.G1203fs	SRCAP_ENST00000395059.2_Frame_Shift_Del_p.G1203fs|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.G1107fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1203	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CTAATGCAGGGGGAAGCAAAC	0.572																																					p.G1202fs		.											.	SRCAP-94	0			c.3606delG						.						129	107	114					16																	30733507		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon22			.	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3606delG	16.37:g.30733507delG	ENSP00000262518:p.Gly1203fs	Somatic	245	0		WXS	Illumina HiSeq	Phase_I	102	27	NM_006662	0	0	0	0	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30733507	G	-	30733507	7	5	141	1	0	1	0	1	0	0	0	0	15167	1219	43	0	3684	0	SRCAP	16	30733507	Frame_Shift_Del	DEL	G	TCGA-IZ-8196-01A-11D-2396-08	2	30733507	59621246	107	12611	131	3									
CDH8	1006	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	61851550	61851550	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcgccgtgtctttaaagggCcccctgccactgaagcgtgg	6	9	13	13	3	1	1	0	1	1	0	2	1	1	1	4	2	2	0	4	2	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:61851550C>T	ENST00000577390.1	-	7	2064	c.1110G>A	c.(1108-1110)ggG>ggA	p.G370G	CDH8_ENST00000584337.1_Silent_p.G370G|CDH8_ENST00000577730.1_Silent_p.G370G|CDH8_ENST00000299345.6_Silent_p.G370G	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	370	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CTTTAAAGGGCCCCCTGCCAC	0.468																																					p.G370G		.											.	CDH8-161	0			c.G1110A						.						86	68	74					16																	61851550		2203	4300	6503	SO:0001819	synonymous_variant	1006	exon7			AAAGGGCCCCCTG	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1110G>A	16.37:g.61851550C>T		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	90	44	NM_001796	0	0	0	0	0	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																			.		0.468	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61851550	C	T	61851550	2	4	141	1	0	0	0	0	0	0	0	1	3122	726	26	2		2	CDH8	16	61851550	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	31118043	61851550	28503203	108	12612											
NAE1	8883	hgsc.bcm.edu	37	chr16	66857505	66857505	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggcagcttcagctcggttcTttttaaaaacaaagcattta	12	14	7	8	1	2	0	1	0	1	0	3	0	2	0	0	2	4	5	0	2	5	7			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:66857505T>C	ENST00000290810.3	-	5	347		c.e5-2		NAE1_ENST00000564040.2_Splice_Site|NAE1_ENST00000379463.2_Splice_Site|NAE1_ENST00000359087.4_Splice_Site|NAE1_ENST00000394074.2_Splice_Site			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1						mitotic DNA replication checkpoint (GO:0033314)|neuron apoptotic process (GO:0051402)|protein neddylation (GO:0045116)|regulation of apoptotic process (GO:0042981)|regulation of neuron apoptotic process (GO:0043523)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|protein heterodimerization activity (GO:0046982)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	AGCTCGGTTCTTTTTAAAAAC	0.328																																					.		.											.	NAE1-69	0			c.250-2A>G						.						54	53	53					16																	66857505		2199	4298	6497	SO:0001630	splice_region_variant	8883	exon6			CGGTTCTTTTTAA	U50939	CCDS10820.1, CCDS42171.1, CCDS42172.1, CCDS67050.1	16q22	2013-09-26	2007-12-11	2007-12-11	ENSG00000159593	ENSG00000159593		"Ubiquitin-like modifier activating enzymes"	621	protein-coding gene	gene with protein product		603385	"amyloid beta precursor protein binding protein 1, 59kDa"	APPBP1		8626687, 12740388	Standard	XM_005256215		Approved	ula-1	uc002eqf.3	Q13564	OTTHUMG00000137513	ENST00000290810.3:c.250-2A>G	16.37:g.66857505T>C		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_003905	0	0	0	0	0	A6NCK0|A6NFN4|A8MU28|B2R700|B3KUP9	Splice_Site	SNP	ENST00000290810.3	37	CCDS10820.1	.	.	.	.	.	.	.	.	.	.	T	16.97	3.269067	0.59540	.	.	ENSG00000159593	ENST00000359087;ENST00000290810;ENST00000379463	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2991	0.73933	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NAE1	65415006	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.688000	0.74557	2.075000	0.62263	0.383000	0.25322	.	.		0.328	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	NM_003905	Intron	C	66857505	T	C	66857505	5	2	141	1	0	0	0	0	0	0	1	0	10164	1623	56	3	1420	3	NAE1	16	66857505	Splice_Site	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	5005955	66857505	23497248	109	12613											
CDT1	81620	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	88872437	88872437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcgtcccacagaggctgacGgagcagccccccagctcacg	8	4	11	18	3	1	2	1	1	0	1	3	3	2	3	4	2	3	3	4	2	0	0	rs368718178		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:88872437G>A	ENST00000301019.4	+	6	1460	c.841G>A	c.(841-843)Gga>Aga	p.G281R		NM_030928.3	NP_112190.2			chromatin licensing and DNA replication factor 1											central_nervous_system(1)|endometrium(2)|kidney(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(80;0.0476)		AGAGGCTGACGGAGCAGCCCC	0.672																																					p.G281R	Melanoma(159;511 3380 30971)	.											.	CDT1-227	0			c.G841A						.	G	ARG/GLY	1,4361		0,1,2180	15	17	16		841	-3.5	0	16		16	0,8566		0,0,4283	no	missense	CDT1	NM_030928.3	125	0,1,6463	AA,AG,GG		0.0,0.0229,0.0077	possibly-damaging	281/547	88872437	1,12927	2181	4283	6464	SO:0001583	missense	81620	exon6			GCTGACGGAGCAG	AF070552	CCDS32510.1	16q24.3	2014-08-12			ENSG00000167513	ENSG00000167513			24576	protein-coding gene	gene with protein product		605525				11896191, 11555648	Standard	NM_030928		Approved	DUP, RIS2	uc002flu.3	Q9H211	OTTHUMG00000173467	ENST00000301019.4:c.841G>A	16.37:g.88872437G>A	ENSP00000301019:p.Gly281Arg	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	12	5	NM_030928	0	0	0	0	0		Missense_Mutation	SNP	ENST00000301019.4	37	CCDS32510.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.253471	0.39797	2.29E-4	0.0	ENSG00000167513	ENST00000301019	T	0.23552	1.9	4.83	-3.49	0.04724	.	1.014200	0.07884	N	0.970068	T	0.13030	0.0316	L	0.35487	1.065	0.30312	N	0.788448	P	0.51351	0.944	B	0.38458	0.274	T	0.37033	-0.9723	10	0.20046	T	0.44	.	4.4942	0.11828	0.0996:0.2944:0.5056:0.1004	.	281	Q9H211	CDT1_HUMAN	R	281	ENSP00000301019:G281R	ENSP00000301019:G281R	G	+	1	0	CDT1	87399938	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	0.790000	0.26900	-0.552000	0.06167	0.462000	0.41574	GGA	.		0.672	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928		A	88872437	G	A	88872437	3	1	141	1	0	0	0	0	1	0	0	0	3186	1117	39	1	863	1	CDT1	16	88872437	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	22014932	88872437	1482316	110	12614											
DLG4	1742	bcgsc.ca	37	chr17	7100206	7100206	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccaggcccgtggagcccCggtggatcacaattcgcctc	7	6	12	16	3	1	0	1	0	0	0	3	2	1	2	5	4	2	0	5	4	1	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:7100206C>T	ENST00000399506.2	-	9	1144	c.953G>A	c.(952-954)cGg>cAg	p.R318Q	DLG4_ENST00000399510.2_Missense_Mutation_p.R361Q|DLG4_ENST00000302955.6_Missense_Mutation_p.R315Q			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	318	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	CGTGGAGCCCCGGTGGATCAC	0.642																																					p.R361Q													.	DLG4-24	0			c.G1082A						.						35	44	41					17																	7100206		2118	4260	6378	SO:0001583	missense	1742	exon11			GAGCCCCGGTGGA	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.953G>A	17.37:g.7100206C>T	ENSP00000382425:p.Arg318Gln	Somatic	72	0		WXS	Illumina HiSeq	Phase_1	41	4	NM_001365	0	0	4	4	0	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	37		.	.	.	.	.	.	.	.	.	.	C	29.4	4.999950	0.93227	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.55930	0.49;0.49;0.49	5.28	5.28	0.74379	PDZ/DHR/GLGF (3);	.	.	.	.	T	0.72342	0.3448	M	0.88570	2.965	0.58432	D	0.999997	P;P;D;D	0.76494	0.955;0.904;0.999;0.998	P;P;D;D	0.70716	0.802;0.758;0.955;0.97	T	0.72988	-0.4124	9	0.30078	T	0.28	.	9.9464	0.41611	0.0:0.9084:0.0:0.0916	.	358;318;315;361	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	Q	318;315;361;361;258;361	ENSP00000382425:R318Q;ENSP00000307471:R315Q;ENSP00000382428:R361Q	ENSP00000293813:R361Q	R	-	2	0	DLG4	7040930	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.127000	0.50484	2.455000	0.83008	0.655000	0.94253	CGG	.		0.642	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		T	7100206	C	T	7100206	3	4	141	1	0	0	0	0	1	0	0	0	4568	652	23	1	1269	1	DLG4	17	7100206	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		7100206	74095004	111	12615											
MAP2K4	6416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	12016635	12016635	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtggacagcttgtggactcTattgccaagacaagagatgc	12	9	12	8	0	1	2	0	0	1	2	1	5	1	4	1	2	3	1	1	2	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:12016635T>C	ENST00000353533.5	+	7	834	c.771T>C	c.(769-771)tcT>tcC	p.S257S	MAP2K4_ENST00000415385.3_Silent_p.S268S|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	257	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TTGTGGACTCTATTGCCAAGA	0.453			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.S257S		.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4-3134	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.T771C						.						105	101	102					17																	12016635		2203	4300	6503	SO:0001819	synonymous_variant	6416	exon7			GGACTCTATTGCC	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.771T>C	17.37:g.12016635T>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	159	104	NM_003010	0	0	14	42	28	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Silent	SNP	ENST00000353533.5	37	CCDS11162.1																																																																																			.		0.453	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			C	12016635	T	C	12016635	2	2	141	1	0	0	0	0	0	0	0	1	9264	1509	53	3		3	MAP2K4	17	12016635	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	4916429	12016635	69178575	112	12616											
NAGLU	4669	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	40695935	40695935	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtgaggccgaggccgatttCtacgagcagaacagccgcta	11	6	13	11	4	1	2	0	1	1	1	1	5	1	2	3	2	4	2	3	2	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:40695935C>T	ENST00000225927.2	+	6	2012	c.1911C>T	c.(1909-1911)ttC>ttT	p.F637F	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	637					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	AGGCCGATTTCTACGAGCAGA	0.627																																					p.F637F		.											.	NAGLU-90	0			c.C1911T						.						25	21	22					17																	40695935		2202	4295	6497	SO:0001819	synonymous_variant	4669	exon6			CGATTTCTACGAG		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"Sanfilippo disease IIIB"	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.1911C>T	17.37:g.40695935C>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	21	10	NM_000263	0	0	12	12	0		Silent	SNP	ENST00000225927.2	37	CCDS11427.1																																																																																			.		0.627	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		T	40695935	C	T	40695935	2	4	141	1	0	0	0	0	0	0	0	1	10168	912	32	2		2	NAGLU	17	40695935	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	28679300	40695935	40499275	113	12617											
LSM12	124801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42117589	42117589	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attgcataggcctggctcagCttctcctccttctctgtccg	4	14	8	15	1	3	0	1	0	2	0	7	0	5	0	4	2	2	3	4	2	1	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:42117589C>T	ENST00000591247.1	-	4	616	c.294G>A	c.(292-294)aaG>aaA	p.K98K	LSM12_ENST00000585388.1_Silent_p.K98K|LSM12_ENST00000293406.3_Silent_p.K98K	NM_152344.3	NP_689557.1	Q3MHD2	LSM12_HUMAN	LSM12 homolog (S. cerevisiae)	98										NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	6		Breast(137;0.0313)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CCTGGCTCAGCTTCTCCTCCT	0.517																																					p.K98K		.											.	LSM12-90	0			c.G294A						.						99	72	81					17																	42117589		2203	4300	6503	SO:0001819	synonymous_variant	124801	exon4			GCTCAGCTTCTCC	BC044587	CCDS11475.1	17q21.31	2007-08-21				ENSG00000161654			26407	protein-coding gene	gene with protein product		611793				15225602	Standard	NM_152344		Approved	FLJ30656	uc002iev.3	Q3MHD2		ENST00000591247.1:c.294G>A	17.37:g.42117589C>T		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	67	42	NM_152344	0	0	14	33	19	Q86YB1|Q96NL5	Silent	SNP	ENST00000591247.1	37	CCDS11475.1																																																																																			.		0.517	LSM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457672.1	NM_152344		T	42117589	C	T	42117589	2	4	141	1	0	0	0	0	0	0	0	1	9078	796	28	2		2	LSM12	17	42117589	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	1421654	42117589	39077621	114	12618											
HEATR6	63897	hgsc.bcm.edu	37	chr17	58156270	58156270	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaccgacaacttgcacagcAgccatcttttctacgggcgg	10	8	10	13	3	2	0	0	0	2	0	2	2	2	0	2	2	6	2	2	2	3	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:58156270A>G	ENST00000184956.6	-	1	22	c.6T>C	c.(4-6)gcT>gcC	p.A2A	HEATR6_ENST00000585976.1_Silent_p.A2A|HEATR6_ENST00000585712.1_5'UTR|CTD-2319I12.2_ENST00000589740.1_lincRNA	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	2							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			CTTGCACAGCAGCCATCTTTT	0.622																																					p.A2A		.											.	HEATR6-227	0			c.T6C						.						11	10	10					17																	58156270		2183	4273	6456	SO:0001819	synonymous_variant	63897	exon1			CACAGCAGCCATC	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"amplified in breast cancer 1"					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.6T>C	17.37:g.58156270A>G		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	24	2	NM_022070	0	0	1	1	0	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Silent	SNP	ENST00000184956.6	37	CCDS11623.1																																																																																			.		0.622	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		G	58156270	A	G	58156270	2	3	141	1	0	0	0	0	0	0	0	1	7054	175	7	3		3	HEATR6	17	58156270	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	16038681	58156270	23038940	115	12619											
ERN1	2081	hgsc.bcm.edu	37	chr17	62133043	62133043	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactggctttacctccatcgTcttgttccagggaggggctg	6	12	12	11	1	1	0	0	0	1	0	4	1	3	1	3	4	2	3	3	4	2	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:62133043T>C	ENST00000433197.3	-	13	1759	c.1664A>G	c.(1663-1665)gAc>gGc	p.D555G		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						ACCTCCATCGTCTTGTTCCAG	0.562																																					p.D555G		.											.	ERN1-784	0			c.A1664G						.						26	28	27					17																	62133043		2048	4218	6266	SO:0001583	missense	2081	exon13			CCATCGTCTTGTT	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1664A>G	17.37:g.62133043T>C	ENSP00000401445:p.Asp555Gly	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	50	3	NM_001433	0	0	0	0	0		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.650204	0.29336	.	.	ENSG00000178607	ENST00000433197	T	0.60797	0.16	5.01	5.01	0.66863	.	0.062618	0.64402	D	0.000008	T	0.35624	0.0938	N	0.08118	0	0.47511	D	0.999447	B	0.29037	0.231	B	0.19946	0.027	T	0.25257	-1.0137	10	0.36615	T	0.2	-24.8143	13.317	0.60413	0.0:0.0:0.0:1.0	.	555	O75460	ERN1_HUMAN	G	555	ENSP00000401445:D555G	ENSP00000401445:D555G	D	-	2	0	ERN1	59486775	1.000000	0.71417	0.377000	0.26055	0.153000	0.21895	5.452000	0.66638	1.880000	0.54463	0.334000	0.21626	GAC	.		0.562	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		C	62133043	T	C	62133043	3	2	141	1	0	0	0	0	1	0	0	0	5250	1667	58	3	1309	3	ERN1	17	62133043	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	3976773	62133043	19062167	116	12620											
AMH	268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	2249551	2249551	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctcccccctgcgggtggtgGgggctctaagcgcctatgag	4	8	16	13	2	1	1	0	1	1	0	2	1	2	1	4	4	2	2	4	4	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:2249551G>T	ENST00000221496.4	+	1	242	c.220G>T	c.(220-222)Ggg>Tgg	p.G74W	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	74					aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGGGTGGTGGGGGCTCTAAG	0.692									Persistant Mullerian Duct Syndrome (type I and II)																												p.G74W		.											.	AMH-130	0			c.G220T						.						8	11	10					19																	2249551		2163	4282	6445	SO:0001583	missense	268	exon1	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	GTGGTGGGGGCTC	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"Endogenous ligands"	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.220G>T	19.37:g.2249551G>T	ENSP00000221496:p.Gly74Trp	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	11	6	NM_000479	0	0	0	0	0	O75246|Q6GTN3	Missense_Mutation	SNP	ENST00000221496.4	37	CCDS12085.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527815	0.27299	.	.	ENSG00000104899	ENST00000221496	D	0.94687	-3.49	3.75	3.75	0.43078	.	0.168909	0.38548	U	0.001642	D	0.95010	0.8385	L	0.34521	1.04	0.44555	D	0.997518	D	0.89917	1.0	D	0.91635	0.999	D	0.95614	0.8675	10	0.87932	D	0	-23.8931	14.1364	0.65291	0.0:0.0:1.0:0.0	.	74	P03971	MIS_HUMAN	W	74	ENSP00000221496:G74W	ENSP00000221496:G74W	G	+	1	0	AMH	2200551	1.000000	0.71417	0.103000	0.21229	0.001000	0.01503	5.367000	0.66127	1.657000	0.50732	0.462000	0.41574	GGG	.		0.692	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479		T	2249551	G	T	2249551	3	4	141	1	0	0	0	0	1	0	0	0	572	1232	43	4	222	4	AMH	19	2249551	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		2249551	56879432	117	12621											
CLEC4M	10332	hgsc.bcm.edu	37	chr19	7832420	7832420	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacttcctacagctgcagActtccaggagtaaccgcttc	11	9	8	13	1	0	2	0	0	0	2	3	3	2	3	3	1	5	4	3	1	3	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:7832420A>T	ENST00000327325.5	+	6	1073	c.955A>T	c.(955-957)Act>Tct	p.T319S	CLEC4M_ENST00000595496.1_Missense_Mutation_p.T183S|CLEC4M_ENST00000596363.1_Intron|CLEC4M_ENST00000394122.2_Missense_Mutation_p.T307S|CLEC4M_ENST00000334806.5_Missense_Mutation_p.T268S|CLEC4M_ENST00000357361.2_Intron|CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000359059.5_Missense_Mutation_p.T252S|CLEC4M_ENST00000596707.1_Missense_Mutation_p.T252S|CLEC4M_ENST00000248228.4_Missense_Mutation_p.T297S	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	319	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						ACAGCTGCAGACTTCCAGGAG	0.552																																					p.T319S		.											.	CLEC4M-91	0			c.A955T						.						102	89	94					19																	7832420		2203	4300	6503	SO:0001583	missense	10332	exon6			CTGCAGACTTCCA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"C-type lectin domain containing", "CD molecules"	13523	protein-coding gene	gene with protein product		605872	"CD299 antigen"	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.955A>T	19.37:g.7832420A>T	ENSP00000316228:p.Thr319Ser	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	90	6	NM_014257	0	0	0	0	0	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	37	CCDS12187.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.947181	0.00475	.	.	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000334806;ENST00000359059	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	2.42	-4.84	0.03151	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.08044	0.0201	N	0.25426	0.745	0.09310	N	0.999998	B;B;B;B;B;B	0.09022	0.002;0.0;0.001;0.0;0.001;0.001	B;B;B;B;B;B	0.13407	0.007;0.0;0.004;0.007;0.002;0.009	T	0.38735	-0.9647	9	0.13108	T	0.6	.	3.4919	0.07641	0.3644:0.0:0.3242:0.3114	.	268;252;319;307;296;183	B4E2Z5;Q9H2X3-5;Q9H2X3;E7ENS9;Q9H2X3-8;Q9H2X3-7	.;.;CLC4M_HUMAN;.;.;.	S	319;307;297;268;252	ENSP00000316228:T319S;ENSP00000377680:T307S;ENSP00000248228:T297S;ENSP00000335228:T268S;ENSP00000351954:T252S	ENSP00000248228:T297S	T	+	1	0	CLEC4M	7738420	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.311000	0.08124	-2.225000	0.00724	-2.665000	0.00146	ACT	.		0.552	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257		T	7832420	A	T	7832420	3	4	141	1	0	0	0	0	1	0	0	0	3524	275	10	5	998	5	CLEC4M	19	7832420	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	5582869	7832420	51296563	118	12622											
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8645860	8645860	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgagcaccagggggcagtAggcgaccttgttcacatcct	8	10	12	11	1	1	1	1	1	0	0	2	2	2	1	3	3	1	4	3	3	1	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:8645860A>G	ENST00000597188.1	-	26	3499	c.3229T>C	c.(3229-3231)Tac>Cac	p.Y1077H	AC130469.2_ENST00000597256.1_RNA|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.Y1077H|ADAMTS10_ENST00000595838.1_Missense_Mutation_p.Y564H	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	1077	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						AGGGGGCAGTAGGCGACCTTG	0.617											OREG0025220	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y1077H		.											.	ADAMTS10-229	0			c.T3229C						.						51	42	45					19																	8645860		2203	4300	6503	SO:0001583	missense	81794	exon26			GGCAGTAGGCGAC	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.3229T>C	19.37:g.8645860A>G	ENSP00000471851:p.Tyr1077His	Somatic	68	0	650	WXS	Illumina HiSeq	Phase_I	23	2	NM_030957	0	0	1	1	0	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	37	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.904566	0.92035	.	.	ENSG00000142303	ENST00000270328	T	0.48836	0.8	5.47	5.47	0.80525	PLAC (2);	0.000000	0.64402	U	0.000001	T	0.61640	0.2363	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.64769	-0.6329	10	0.87932	D	0	.	14.7435	0.69474	1.0:0.0:0.0:0.0	.	1077;564	Q9H324;E9PCI6	ATS10_HUMAN;.	H	1077	ENSP00000270328:Y1077H	ENSP00000270328:Y1077H	Y	-	1	0	ADAMTS10	8551860	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.849000	0.92178	2.075000	0.62263	0.448000	0.29417	TAC	.		0.617	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		G	8645860	A	G	8645860	3	3	141	1	0	0	0	0	1	0	0	0	256	420	15	3	86	3	ADAMTS10	19	8645860	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	813440	8645860	50483123	119	12623											
CD97	976	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	14518917	14518918	+	Frame_Shift_Ins	INS	-	-	A																															ctccaggccctcagggcatcINSagagtccggcatatgaaggc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:14518917_14518918insA	ENST00000242786.5	+	20	2572_2573	c.2492_2493insA	c.(2491-2496)tcagagfs	p.E832fs	DDX39A_ENST00000592927.1_5'Flank|CD97_ENST00000357355.3_Frame_Shift_Ins_p.E783fs|CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000358600.3_Frame_Shift_Ins_p.E739fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	832					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTCAGGGCATCAGAGTCCGGCA	0.663																																					p.S831fs		.											.	CD97-570	0			c.2492_2493insA						.																																			SO:0001589	frameshift_variant	976	exon20			.		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"CD molecules", "-", "GPCR / Class B : Orphans"	1711	protein-coding gene	gene with protein product	"leukocyte antigen CD97", "seven-span transmembrane protein", "seven-transmembrane, heterodimeric receptor associated with inflammation", "seven transmembrane helix receptor"	601211	"CD97 antigen"			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.2493dupA	19.37:g.14518918_14518918dupA	ENSP00000242786:p.Glu832fs	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	47	18	NM_078481	0	0	0	0	0	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Ins	INS	ENST00000242786.5	37	CCDS32929.1																																																																																			.		0.663	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		A	14518918	-	A	14518917	7	5	141	1	0	1	1	0	0	0	0	0	3055	838	29	0	2570	0	CD97	19	14518917	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	5873057	14518917	44610066	120	12624											
DHX34	9704	hgsc.bcm.edu	37	chr19	47856881	47856881	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tccactcaggtgccccagtaCctgctggctgctggcttcag	5	10	11	15	0	2	0	2	0	0	0	3	0	3	0	4	3	4	5	4	3	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:47856881C>G	ENST00000328771.4	+	2	943	c.594C>G	c.(592-594)taC>taG	p.Y198*		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	198	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		TGCCCCAGTACCTGCTGGCTG	0.637																																					p.Y198X		.											.	DHX34-231	0			c.C594G						.						22	25	24					19																	47856881		2203	4300	6503	SO:0001587	stop_gained	9704	exon2			CCAGTACCTGCTG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"DEAH-boxes"	16719	protein-coding gene	gene with protein product		615475	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.594C>G	19.37:g.47856881C>G	ENSP00000331907:p.Tyr198*	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	31	2	NM_014681	0	0	8	8	0	B4DMY8	Nonsense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	.	.	.	.	.	.	.	.	.	.	C	40	8.010007	0.98607	.	.	ENSG00000134815	ENST00000328771;ENST00000257252	.	.	.	5.26	5.26	0.73747	.	0.000000	0.49305	D	0.000157	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.6164	17.6312	0.88108	0.0:1.0:0.0:0.0	.	.	.	.	X	198	.	ENSP00000257252:Y198X	Y	+	3	2	DHX34	52548721	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.207000	0.32333	2.461000	0.83175	0.555000	0.69702	TAC	.		0.637	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		G	47856881	C	G	47856881	4	3	141	1	0	0	0	0	0	1	0	0	4518	518	18	4	596	4	DHX34	19	47856881	Nonsense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	33337964	47856881	11272102	121	12625											
SNPH	9751	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	1286555	1286555	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggctttgccgctcccagCggcgccagggccagcccatc	4	6	12	19	3	0	0	0	0	0	0	2	0	1	0	6	3	3	2	6	3	0	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr20:1286555C>T	ENST00000381873.3	+	6	1578	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W	SNPH_ENST00000381867.1_Missense_Mutation_p.R492W	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	448					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CCGCTCCCAGCGGCGCCAGGG	0.672																																					p.R448W		.											.	SNPH-92	0			c.C1342T						.						16	10	12					20																	1286555		2131	4210	6341	SO:0001583	missense	9751	exon6			TCCCAGCGGCGCC		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.1342C>T	20.37:g.1286555C>T	ENSP00000371297:p.Arg448Trp	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	13	7	NM_014723	0	0	1	2	1	Q8IYI3	Missense_Mutation	SNP	ENST00000381873.3	37	CCDS13012.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.712880	0.48517	.	.	ENSG00000101298	ENST00000381873;ENST00000381867	.	.	.	4.24	1.16	0.20824	.	0.431073	0.21513	N	0.073349	T	0.59729	0.2215	M	0.62723	1.935	0.31113	N	0.709748	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.61088	-0.7133	9	0.87932	D	0	-28.0671	7.7271	0.28765	0.5262:0.3946:0.0:0.0791	.	492;448	O15079-2;O15079	.;SNPH_HUMAN	W	448;492	.	ENSP00000371291:R492W	R	+	1	2	SNPH	1234555	0.992000	0.36948	0.981000	0.43875	0.898000	0.52572	0.375000	0.20518	0.083000	0.17047	-0.268000	0.10319	CGG	.		0.672	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723		T	1286555	C	T	1286555	3	4	141	1	0	0	0	0	1	0	0	0	14882	759	27	1	1356	1	SNPH	20	1286555	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		1286555	61738965	122	12626											
LSM14B	149986	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	60705292	60705292	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagatgtagtccagccggcaGctgtgcaagctcaagggcag	10	7	14	10	1	1	1	1	0	0	1	2	1	2	1	2	2	4	6	2	2	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr20:60705292G>A	ENST00000279068.6	+	5	773	c.613G>A	c.(613-615)Gct>Act	p.A205T	LSM14B_ENST00000253001.4_Intron	NM_144703.2	NP_653304.2	Q9BX40	LS14B_HUMAN	LSM14B, SCD6 homolog B (S. cerevisiae)	205					multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)	ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|lung(4)	8	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CCAGCCGGCAGCTGTGCAAGC	0.567																																					p.A205T		.											.	LSM14B-22	0			c.G613A						.						29	30	30					20																	60705292		2046	4199	6245	SO:0001583	missense	149986	exon5			CCGGCAGCTGTGC	AF172328	CCDS46626.1	20q13.33	2010-01-27	2006-12-21	2006-01-24	ENSG00000149657	ENSG00000149657			15887	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 40", "family with sequence similarity 61, member B", "LSM14 homolog B (SCD6, S. cerevisiae)"	C20orf40, FAM61B			Standard	NM_144703		Approved	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B	uc010gjy.1	Q9BX40	OTTHUMG00000032901	ENST00000279068.6:c.613G>A	20.37:g.60705292G>A	ENSP00000279068:p.Ala205Thr	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	12	5	NM_144703	0	0	17	27	10	Q6PFW8|Q96LH8	Missense_Mutation	SNP	ENST00000279068.6	37	CCDS46626.1	.	.	.	.	.	.	.	.	.	.	G	5.458	0.269581	0.10349	.	.	ENSG00000149657	ENST00000279068;ENST00000444156;ENST00000400318;ENST00000370906;ENST00000361670	T;T;T	0.45668	0.94;0.94;0.89	5.59	-1.32	0.09201	.	.	.	.	.	T	0.23846	0.0577	L	0.38531	1.155	0.54753	D	0.999981	B;B;B;B	0.22346	0.003;0.068;0.001;0.002	B;B;B;B	0.15484	0.002;0.013;0.002;0.002	T	0.10543	-1.0625	9	0.16896	T	0.51	.	4.4602	0.11663	0.1547:0.3504:0.4009:0.094	.	125;161;205;231	E9PG81;C9J454;Q9BX40;Q5TBQ0	.;.;LS14B_HUMAN;.	T	205;161;231;161;125	ENSP00000279068:A205T;ENSP00000383172:A231T;ENSP00000355209:A125T	ENSP00000279068:A205T	A	+	1	0	LSM14B	60138687	0.769000	0.28531	0.908000	0.35775	0.211000	0.24417	0.566000	0.23593	0.278000	0.22164	-0.324000	0.08512	GCT	.		0.567	LSM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079996.4	NM_144703		A	60705292	G	A	60705292	3	1	141	1	0	0	0	0	1	0	0	0	9080	971	34	2	631	2	LSM14B	20	60705292	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	59418737	60705292	2320228	123	12627											
CABLES2	81928	hgsc.bcm.edu	37	chr20	60982024	60982024	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcacctgcgtggggctgagCaggccctggggcgcgggggt	3	5	22	11	3	0	1	0	1	0	0	0	1	0	1	2	8	2	3	2	8	0	0	rs146975578	byFrequency	TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr20:60982024C>T	ENST00000279101.5	-	1	317	c.309G>A	c.(307-309)ctG>ctA	p.L103L		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	103	Pro-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGGGGCTGAGCAGGCCCTggg	0.816													C|||	637	0.127196	0.2095	0.17	5008	,	,		6090	0.001		0.2018	False		,,,				2504	0.0389				p.L103L		.											.	CABLES2-91	0			c.G309A						.	C		368,2140		30,308,916	3	3	3		309	0.7	1	20	dbSNP_134	3	899,4587		90,719,1934	no	coding-synonymous	CABLES2	NM_031215.2		120,1027,2850	TT,TC,CC		16.3872,14.673,15.8494		103/479	60982024	1267,6727	1254	2743	3997	SO:0001819	synonymous_variant	81928	exon1			GCTGAGCAGGCCC	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 150"	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.309G>A	20.37:g.60982024C>T		Somatic	6	1		WXS	Illumina HiSeq	Phase_I	3	3	NM_031215	0	0	0	0	0	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	37	CCDS33503.1																																																																																			C|0.860;T|0.140		0.816	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265		T	60982024	C	T	60982024	2	4	141	1	0	0	0	0	0	0	0	1	2536	697	25	2		2	CABLES2	20	60982024	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	276732	60982024	2043496	124	12628											
DOPEY2	9980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	37626086	37626086	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagattatcccaacggcaaGtgcatcccagctaacccttg	11	8	8	14	1	0	1	0	0	0	1	2	1	2	1	3	1	4	4	3	1	4	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr21:37626086G>A	ENST00000399151.3	+	23	5223	c.5138G>A	c.(5137-5139)aGt>aAt	p.S1713N		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1713					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CCAACGGCAAGTGCATCCCAG	0.468																																					p.S1713N		.											.	DOPEY2-91	0			c.G5138A						.						139	136	137					21																	37626086		2203	4300	6503	SO:0001583	missense	9980	exon23			CGGCAAGTGCATC	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"chromosome 21 open reading frame 5"	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.5138G>A	21.37:g.37626086G>A	ENSP00000382104:p.Ser1713Asn	Somatic	220	1		WXS	Illumina HiSeq	Phase_I	177	75	NM_005128	0	0	7	7	0	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.982780	0.34942	.	.	ENSG00000142197	ENST00000399151	T	0.13778	2.56	5.5	1.28	0.21552	.	0.040315	0.85682	N	0.000000	T	0.12518	0.0304	L	0.50919	1.6	0.30386	N	0.781515	B;B	0.27192	0.171;0.107	B;B	0.24848	0.056;0.025	T	0.10177	-1.0641	10	0.31617	T	0.26	-7.5998	11.6148	0.51083	0.0646:0.3448:0.5907:0.0	.	1713;1713	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	N	1713	ENSP00000382104:S1713N	ENSP00000382104:S1713N	S	+	2	0	DOPEY2	36547956	1.000000	0.71417	0.001000	0.08648	0.018000	0.09664	6.006000	0.70724	0.231000	0.21079	0.655000	0.94253	AGT	.		0.468	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		A	37626086	G	A	37626086	3	1	141	1	0	0	0	0	1	0	0	0	4719	1029	36	2	5224	2	DOPEY2	21	37626086	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		37626086	10503809	125	12629											
BRWD1	54014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	40641908	40641908	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtcctgcagataacataaTtctggaatcaaagggatgtg	14	11	10	6	0	2	1	1	0	1	1	3	3	3	3	1	2	2	1	1	2	4	3	rs540249994		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr21:40641908T>A	ENST00000333229.2	-	15	1774	c.1447A>T	c.(1447-1449)Att>Ttt	p.I483F	BRWD1_ENST00000380800.3_Missense_Mutation_p.I483F|BRWD1_ENST00000342449.3_Missense_Mutation_p.I483F	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	483					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				GATAACATAATTCTGGAATCA	0.333																																					p.I483F	Melanoma(170;988 1986 4794 16843 39731)	.											.	BRWD1-94	0			c.A1447T						.						105	99	101					21																	40641908		2203	4300	6503	SO:0001583	missense	54014	exon15			ACATAATTCTGGA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"WD repeat domain containing"	12760	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 107", "WD repeat domain 9"	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.1447A>T	21.37:g.40641908T>A	ENSP00000330753:p.Ile483Phe	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	48	26	NM_018963	0	0	4	8	4	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.681151|4.681151	0.88542|0.88542	.|.	.|.	ENSG00000185658|ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800|ENST00000455867	T;T;T|.	0.59224|.	0.28;0.28;0.28|.	5.57|5.57	5.57|5.57	0.84162|0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.080378|.	0.53938|.	D|.	0.000059|.	T|T	0.45337|0.45337	0.1337|0.1337	L|L	0.27944|0.27944	0.81|0.81	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;0.999;1.0|.	D;D;D|.	0.91635|.	0.996;0.999;0.99|.	T|T	0.38200|0.38200	-0.9672|-0.9672	10|5	0.87932|.	D|.	0|.	-10.9067|-10.9067	10.1398|10.1398	0.42728|0.42728	0.0:0.0743:0.0:0.9257|0.0:0.0743:0.0:0.9257	.|.	194;483;483|.	Q5R2U6;Q9NSI6-2;Q9NSI6|.	.;.;BRWD1_HUMAN|.	F|I	483|194	ENSP00000330753:I483F;ENSP00000344333:I483F;ENSP00000370178:I483F|.	ENSP00000330753:I483F|.	I|N	-|-	1|2	0|0	BRWD1|BRWD1	39563778|39563778	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	3.879000|3.879000	0.56138|0.56138	2.130000|2.130000	0.65690|0.65690	0.455000|0.455000	0.32223|0.32223	ATT|AAT	.		0.333	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		A	40641908	T	A	40641908	3	1	141	1	0	0	0	0	1	0	0	0	1528	1493	52	5	5866	5	BRWD1	21	40641908	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	3015822	40641908	7487987	126	12630											
PDE9A	5152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	44152003	44152003	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgaaagtggacaggtagAgcccaggcccagagagcccc	12	5	13	11	0	0	3	0	1	0	2	0	5	0	4	4	3	2	1	4	3	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr21:44152003A>G	ENST00000291539.6	+	5	446	c.386A>G	c.(385-387)gAg>gGg	p.E129G	PDE9A_ENST00000398234.3_Intron|PDE9A_ENST00000539837.1_Intron|PDE9A_ENST00000470987.1_Intron|PDE9A_ENST00000398229.3_Intron|PDE9A_ENST00000398225.3_Missense_Mutation_p.E88G|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000398236.3_Intron|PDE9A_ENST00000328862.6_Missense_Mutation_p.E103G|PDE9A_ENST00000398224.3_Intron|PDE9A_ENST00000335440.6_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000335512.4_Intron|PDE9A_ENST00000398232.3_Missense_Mutation_p.E62G|PDE9A_ENST00000380328.2_Intron|AP001627.1_ENST00000437426.1_RNA	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	129					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	GGACAGGTAGAGCCCAGGCCC	0.652																																					p.E129G		.											.	PDE9A-92	0			c.A386G						.						56	59	58					21																	44152003		2203	4300	6503	SO:0001583	missense	5152	exon5			AGGTAGAGCCCAG	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"Phosphodiesterases"	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.386A>G	21.37:g.44152003A>G	ENSP00000291539:p.Glu129Gly	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	50	26	NM_002606	0	0	9	11	2	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	A	5.981	0.364909	0.11296	.	.	ENSG00000160191	ENST00000291539;ENST00000398232;ENST00000328862;ENST00000398225	T;T;T;T	0.69435	-0.37;-0.4;-0.39;-0.38	2.62	-5.23	0.02798	.	2.493450	0.01301	N	0.010305	T	0.41026	0.1141	N	0.08118	0	0.09310	N	1	B;B;B;B	0.19706	0.038;0.003;0.003;0.002	B;B;B;B	0.19391	0.025;0.001;0.001;0.0	T	0.17930	-1.0353	10	0.49607	T	0.09	.	0.789	0.01054	0.4523:0.1816:0.1307:0.2354	.	62;103;88;129	O76083-13;O76083-15;O76083-14;O76083	.;.;.;PDE9A_HUMAN	G	129;62;103;88	ENSP00000291539:E129G;ENSP00000381287:E62G;ENSP00000328699:E103G;ENSP00000381281:E88G	ENSP00000291539:E129G	E	+	2	0	PDE9A	43025072	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.271000	0.18626	-2.215000	0.00733	0.383000	0.25322	GAG	.		0.652	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			G	44152003	A	G	44152003	3	3	141	1	0	0	0	0	1	0	0	0	11681	304	11	3	484	3	PDE9A	21	44152003	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	3510095	44152003	3977892	127	12631											
COL6A1	1291	hgsc.bcm.edu	37	chr21	47421874	47421874	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accccggtgccggtcccacaGttcgagccagggcagtcgta	7	6	13	15	4	0	0	0	0	0	0	3	1	1	0	5	3	2	3	5	3	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr21:47421874G>A	ENST00000361866.3	+	31	2070		c.e31-1		COL6A1_ENST00000498614.1_Splice_Site	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		CGGTCCCACAGTTCGAGCCAG	0.662																																					.		.											.	COL6A1-91	0			c.1957-1G>A						.						32	31	31					21																	47421874		2203	4300	6503	SO:0001630	splice_region_variant	1291	exon31			CCCACAGTTCGAG	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"Collagens"	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1957-1G>A	21.37:g.47421874G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	30	2	NM_001848	0	0	0	0	0	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Splice_Site	SNP	ENST00000361866.3	37	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	9.648	1.140692	0.21205	.	.	ENSG00000142156	ENST00000361866	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9973	0.86371	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL6A1	46246302	1.000000	0.71417	0.966000	0.40874	0.032000	0.12392	5.447000	0.66606	2.020000	0.59435	0.462000	0.41574	.	.		0.662	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	Intron	A	47421874	G	A	47421874	5	1	141	1	0	0	0	0	0	0	1	0	3705	1043	36	2	2078	2	COL6A1	21	47421874	Splice_Site	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	3269871	47421874	708021	128	12632											
CYTSA	23384	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24734414	24734414	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gagcccaagtcctatgaaaaCccctcctgcagcagctgtgt	10	8	9	14	0	0	1	0	1	0	0	2	2	2	1	5	0	5	3	5	0	4	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr22:24734414C>T	ENST00000314328.9	+	10	2906	c.2621C>T	c.(2620-2622)aCc>aTc	p.T874I	SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.T874I|SPECC1L_ENST00000541492.1_Missense_Mutation_p.T874I|SPECC1L_ENST00000437398.1_Missense_Mutation_p.T874I	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	874					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						CCTATGAAAACCCCTCCTGCA	0.498																																					p.T874I		.											.	SPECC1L-92	0			c.C2621T						.						162	158	160					22																	24734414		2203	4300	6503	SO:0001583	missense	23384	exon9			TGAAAACCCCTCC	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"cytokinesis and spindle organization A", "cytospin A"	614140	"SPECC1-like"			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.2621C>T	22.37:g.24734414C>T	ENSP00000325785:p.Thr874Ile	Somatic	242	0		WXS	Illumina HiSeq	Phase_I	216	89	NM_001145468	0	0	28	51	23	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	c	29.1	4.976045	0.92982	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000314328;ENST00000541492	T;T;T	0.53640	0.61;0.61;0.61	5.69	5.69	0.88448	.	0.050156	0.85682	D	0.000000	T	0.69124	0.3076	M	0.68593	2.085	0.80722	D	1	D;P	0.89917	1.0;0.906	D;P	0.91635	0.999;0.521	T	0.69614	-0.5098	10	0.72032	D	0.01	-23.2113	19.1962	0.93690	0.0:1.0:0.0:0.0	.	874;874	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	I	902;874;874;874	ENSP00000393363:T874I;ENSP00000325785:T874I;ENSP00000439633:T874I	ENSP00000325785:T874I	T	+	2	0	SPECC1L	23064414	1.000000	0.71417	0.982000	0.44146	0.996000	0.88848	5.103000	0.64578	2.865000	0.98341	0.655000	0.94253	ACC	.		0.498	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		T	24734414	C	T	24734414	3	4	141	1	0	0	0	0	1	0	0	0	4215	507	18	2	2651	2	CYTSA	22	24734414	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		24734414	26570152	129	12633											
GGT1	2678	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	25023938	25023938	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcacctgccaatttcaTccagccaggtatggggtgga	8	9	10	14	0	2	0	2	0	0	0	3	1	3	1	6	4	2	1	6	4	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr22:25023938T>C	ENST00000400382.1	+	13	2083	c.1328T>C	c.(1327-1329)aTc>aCc	p.I443T	GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000403838.1_Missense_Mutation_p.I99T|GGT1_ENST00000248923.4_Missense_Mutation_p.I443T|GGT1_ENST00000401885.1_Missense_Mutation_p.I99T|GGT1_ENST00000406383.2_Missense_Mutation_p.I443T|GGT1_ENST00000404920.1_Missense_Mutation_p.I99T|GGT1_ENST00000404223.1_Missense_Mutation_p.I99T|GGT1_ENST00000400380.1_Missense_Mutation_p.I443T|GGT1_ENST00000400383.1_Missense_Mutation_p.I443T|GGT1_ENST00000404532.1_Missense_Mutation_p.I99T			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	443					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GCCAATTTCATCCAGCCAGGT	0.617																																					p.I443T		.											.	GGT1-90	0			c.T1328C						.						42	50	47					22																	25023938		2202	4297	6499	SO:0001583	missense	2678	exon13			ATTTCATCCAGCC	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"CD molecules", "Gamma-glutamyltransferases"	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1328T>C	22.37:g.25023938T>C	ENSP00000383232:p.Ile443Thr	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	99	48	NM_013430	0	0	0	0	0	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	13.53	2.265969	0.40095	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.42086	0.1187	H	0.98256	4.185	0.46901	D	0.999246	D	0.89917	1.0	D	0.79784	0.993	T	0.61232	-0.7104	10	0.87932	D	0	-34.9439	11.6793	0.51448	0.0:0.0:0.0:1.0	.	443	P19440	GGT1_HUMAN	T	443;443;443;443;443;443;99;99;99;99;99	ENSP00000248923:I443T;ENSP00000393537:I443T;ENSP00000383232:I443T;ENSP00000383233:I443T;ENSP00000383231:I443T;ENSP00000385975:I443T;ENSP00000384381:I99T;ENSP00000385445:I99T;ENSP00000384820:I99T;ENSP00000385016:I99T;ENSP00000385001:I99T	ENSP00000248923:I443T	I	+	2	0	GGT1	23353938	1.000000	0.71417	0.952000	0.39060	0.028000	0.11728	7.217000	0.77982	1.593000	0.50029	0.373000	0.22412	ATC	.		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		C	25023938	T	C	25023938	3	2	141	1	0	0	0	0	1	0	0	0	6381	1435	50	3	1362	3	GGT1	22	25023938	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	289524	25023938	26280628	130	12634											
CHKB	1120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	51018475	51018475	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcctcgtgagtataatcataAacccactcacaaaaatggtt	15	11	5	10	1	2	1	2	1	0	0	4	1	3	1	2	1	1	2	2	1	6	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr22:51018475A>C	ENST00000406938.2	-	8	1072	c.855T>G	c.(853-855)gtT>gtG	p.V285V	CPT1B_ENST00000395650.2_5'Flank|CPT1B_ENST00000434492.2_5'Flank|CHKB-CPT1B_ENST00000453634.1_5'Flank|CPT1B_ENST00000360719.2_5'Flank|CHKB-CPT1B_ENST00000452668.1_5'Flank|CHKB-AS1_ENST00000380711.3_RNA|CPT1B_ENST00000457250.1_5'Flank|CPT1B_ENST00000440709.1_5'Flank|CPT1B_ENST00000312108.7_5'Flank|CHKB_ENST00000463053.1_5'Flank|CPT1B_ENST00000405237.3_5'Flank	NM_005198.4	NP_005189.2	Q9Y259	CHKB_HUMAN	choline kinase beta	285					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline kinase activity (GO:0004103)|ethanolamine kinase activity (GO:0004305)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|ovary(3)|skin(1)|urinary_tract(1)	15		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;4.04e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.79e-74)|Epithelial(4;6.17e-70)|GBM - Glioblastoma multiforme(4;5.68e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.205)	Choline(DB00122)	TATAATCATAAACCCACTCAC	0.522																																					p.V285V		.											.	CHKB-90	0			c.T855G						.						88	94	92					22																	51018475		2203	4300	6503	SO:0001819	synonymous_variant	1120	exon8			ATCATAAACCCAC	AB029886	CCDS14099.1	22q13.33	2011-02-16	2004-04-19	2004-04-19	ENSG00000100288	ENSG00000100288			1938	protein-coding gene	gene with protein product		612395	"choline kinase-like"	CHKL		9224698, 15003397	Standard	NM_005198		Approved	CHETK	uc003bmv.3	Q9Y259	OTTHUMG00000150275	ENST00000406938.2:c.855T>G	22.37:g.51018475A>C		Somatic	125	0		WXS	Illumina HiSeq	Phase_I	134	54	NM_005198	0	0	14	20	6	A0PJM6|Q13388	Silent	SNP	ENST00000406938.2	37	CCDS14099.1																																																																																			.		0.522	CHKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317267.3	NM_005198		C	51018475	A	C	51018475	2	2	141	1	0	0	0	0	0	0	0	1	3354	1	1	5		5	CHKB	22	51018475	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	25994537	51018475	286091	131	12635											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53563131	53563131	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgctgaaggtgaggtcatAgcctagtgtggagacatcat	11	10	14	6	0	2	3	2	2	0	1	2	4	2	3	1	3	2	1	1	3	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chrX:53563131A>G	ENST00000342160.3	-	79	12965	c.12508T>C	c.(12508-12510)Tat>Cat	p.Y4170H	HUWE1_ENST00000262854.6_Missense_Mutation_p.Y4170H			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4170	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GTGAGGTCATAGCCTAGTGTG	0.428																																					p.Y4170H		.											.	HUWE1-280	0			c.T12508C						.						187	126	147					X																	53563131		2203	4300	6503	SO:0001583	missense	10075	exon80			GGTCATAGCCTAG	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"HECT, UBA and WWE domain containing 1"			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12508T>C	X.37:g.53563131A>G	ENSP00000340648:p.Tyr4170His	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_031407	0	0	58	58	0	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.03|11.03	1.517867|1.517867	0.27211|0.27211	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052;ENST00000426907|ENST00000342160;ENST00000262854	.|T;T	.|0.57595	.|0.39;0.39	5.57|5.57	4.39|4.39	0.52855|0.52855	.|HECT (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.65069|0.65069	0.2656|0.2656	M|M	0.75777|0.75777	2.31|2.31	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.47604	.|0.735;0.898	.|P;P	.|0.56648	.|0.646;0.803	T|T	0.64028|0.64028	-0.6503|-0.6503	5|10	.|0.44086	.|T	.|0.13	.|.	10.3659|10.3659	0.44024|0.44024	0.8507:0.0:0.0:0.1493|0.8507:0.0:0.0:0.1493	.|.	.|4170;4154	.|Q7Z6Z7;Q7Z6Z7-2	.|HUWE1_HUMAN;.	P|H	3203;992|4170	.|ENSP00000340648:Y4170H;ENSP00000262854:Y4170H	.|ENSP00000262854:Y4170H	L|Y	-|-	2|1	0|0	HUWE1|HUWE1	53579856|53579856	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.465000|0.465000	0.32709|0.32709	8.644000|8.644000	0.91044|0.91044	0.816000|0.816000	0.34421|0.34421	-0.415000|-0.415000	0.06103|0.06103	CTA|TAT	.		0.428	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		G	53563131	A	G	53563131	3	3	141	1	0	0	0	0	1	0	0	0	7482	420	15	3	636	3	HUWE1	23	53563131	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		53563131	101707429	132	12636											
PLCH2	9651	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	2418423	2418423	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccagaaaacaagagtaagggGctgctgggcattgatggtga	13	7	15	6	0	0	4	0	2	0	2	0	4	0	4	1	4	2	4	1	4	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:2418423G>A	ENST00000419816.2	+	6	1168	c.894G>A	c.(892-894)ggG>ggA	p.G298G	PLCH2_ENST00000449969.1_Silent_p.G271G|PLCH2_ENST00000378486.3_Silent_p.G298G|PLCH2_ENST00000288766.5_Intron|PLCH2_ENST00000378488.3_Silent_p.G298G			O75038	PLCH2_HUMAN	phospholipase C, eta 2	298					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		AGAGTAAGGGGCTGCTGGGCA	0.632																																					p.G298G		.											.	PLCH2-229	0			c.G894A						.						55	59	57					1																	2418423		2096	4214	6310	SO:0001819	synonymous_variant	9651	exon6			TAAGGGGCTGCTG	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"EF-hand domain containing"	29037	protein-coding gene	gene with protein product		612836	"phospholipase C-like 4"	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.894G>A	1.37:g.2418423G>A		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	45	10	NM_014638	0	0	0	0	0	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37																																																																																				.		0.632	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2418423	G	A	2418423	2	1	142	1	0	0	0	0	0	0	0	1	12064	1190	42	2		2	PLCH2	1	2418423	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		2418423	246832198	1	12637											
PER3	8863	broad.mit.edu	37	chr1	7854051	7854051	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatgtgctccggtgaaaccTtttttctgcaggatccggta	8	13	11	9	2	1	1	0	1	1	0	3	3	3	2	3	3	3	3	3	3	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:7854051T>C	ENST00000361923.2	+	5	799	c.624T>C	c.(622-624)ccT>ccC	p.P208P	PER3_ENST00000377541.1_Silent_p.P208P|PER3_ENST00000377532.3_Silent_p.P209P	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	208					circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CGGTGAAACCTTTTTTCTGCA	0.443																																					p.P208P													.	PER3-93	0			c.T624C						.						147	143	144					1																	7854051		2203	4300	6503	SO:0001819	synonymous_variant	8863	exon5			GAAACCTTTTTTC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"period (Drosophila) homolog 3", "period homolog 3 (Drosophila)"			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.624T>C	1.37:g.7854051T>C		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	80	4	NM_016831	0	0	0	0	0	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			.		0.443	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		C	7854051	T	C	7854051	2	2	142	1	0	0	0	0	0	0	0	1	11757	1596	56	3		3	PER3	1	7854051	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	5435628	7854051	241396570	2	12638											
CASZ1	54897	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10713663	10713663	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acggcacccaggaggctgggGgtgcccacaggcagggaggt	8	3	19	11	1	0	0	0	0	0	0	0	2	0	2	2	8	1	3	2	8	0	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:10713663G>A	ENST00000377022.3	-	11	2768	c.2451C>T	c.(2449-2451)acC>acT	p.T817T	CASZ1_ENST00000344008.5_Silent_p.T817T|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	817					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGAGGCTGGGGGTGCCCACAG	0.716																																					p.T817T													.	CASZ1-113	0			c.C2451T						.						13	18	16					1																	10713663		2187	4276	6463	SO:0001819	synonymous_variant	54897	exon11			GCTGGGGGTGCCC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2451C>T	1.37:g.10713663G>A		Somatic	84	1		WXS	Illumina HiSeq	Phase_I	103	40	NM_001079843	0	0	1	4	3	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			.		0.716	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10713663	G	A	10713663	2	1	142	1	0	0	0	0	0	0	0	1	2691	1219	43	2		2	CASZ1	1	10713663	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	2859612	10713663	238536958	3	12639											
CASZ1	54897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10714628	10714628	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcacgtcagacgtgctcgtGtacaccttgttacagcccac	9	10	8	14	3	2	1	2	0	0	1	3	1	2	1	2	0	4	3	2	0	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:10714628G>A	ENST00000377022.3	-	10	2003	c.1686C>T	c.(1684-1686)taC>taT	p.Y562Y	CASZ1_ENST00000344008.5_Silent_p.Y562Y|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	562					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		ACGTGCTCGTGTACACCTTGT	0.597																																					p.Y562Y		.											.	CASZ1-113	0			c.C1686T						.						210	193	199					1																	10714628		2203	4300	6503	SO:0001819	synonymous_variant	54897	exon10			GCTCGTGTACACC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.1686C>T	1.37:g.10714628G>A		Somatic	158	0		WXS	Illumina HiSeq	Phase_I	165	52	NM_001079843	0	0	2	2	0	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			.		0.597	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10714628	G	A	10714628	2	1	142	1	0	0	0	0	0	0	0	1	2691	1372	48	2		2	CASZ1	1	10714628	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	965	10714628	238535993	4	12640											
KDM1A	23028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	23380289	23380289	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gataatccaaagattcagctGacatttgaggctactctcca	13	11	7	10	0	2	3	1	2	1	1	4	4	3	3	2	1	2	2	2	1	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:23380289G>A	ENST00000356634.3	+	4	836	c.687G>A	c.(685-687)ctG>ctA	p.L229L	KDM1A_ENST00000400181.4_Silent_p.L249L|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000542151.1_Silent_p.L249L	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	229	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						AGATTCAGCTGACATTTGAGG	0.323																																					p.L249L		.											.	KDM1A-206	0			c.G747A						.						92	84	87					1																	23380289		2203	4300	6503	SO:0001819	synonymous_variant	23028	exon5			TCAGCTGACATTT	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"Chromatin-modifying enzymes / K-demethylases"	29079	protein-coding gene	gene with protein product		609132	"amine oxidase (flavin containing) domain 2", "lysine (K)-specific demethylase 1"	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.687G>A	1.37:g.23380289G>A		Somatic	314	1		WXS	Illumina HiSeq	Phase_I	133	47	NM_001009999	0	0	3	6	3	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			.		0.323	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23380289	G	A	23380289	2	1	142	1	0	0	0	0	0	0	0	1	8143	1277	45	2		2	KDM1A	1	23380289	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	12665661	23380289	225870332	5	12641											
WDR65	149465	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	43675436	43675439	+	Frame_Shift_Del	DEL	TTGA	TTGA	-																															ccttcgagagatatcggcgtTtgatgtcacctacaccgcca																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	TTGA	TTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:43675436_43675439delTTGA	ENST00000372492.4	+	11	2102_2105	c.1778_1781delTTGA	c.(1777-1782)tttgatfs	p.FD593fs	WDR65_ENST00000528956.1_Frame_Shift_Del_p.FD593fs	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		593										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ATATCGGCGTTTGATGTCACCTAC	0.574																																					p.593_594del		.											.	WDR65-91	0			c.1778_1781del						.																																			SO:0001589	frameshift_variant	149465	exon11			.																												ENST00000372492.4:c.1778_1781delTTGA	1.37:g.43675436_43675439delTTGA	ENSP00000361570:p.Phe593fs	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	67	19	NM_152498	0	0	0	0	0	A6NKQ3|Q17RI9|Q5TAI0	Frame_Shift_Del	DEL	ENST00000372492.4	37																																																																																				.		0.574	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			-	43675439	TTGA	-	43675436	7	5	142	1	0	1	0	1	0	0	0	0	17349	1841	64	0	1816	0	WDR65	1	43675436	Frame_Shift_Del	DEL	TTGA	TCGA-IZ-A6M8-01A-11D-A31X-10	20295147	43675436	205575185	6	12642											
TESK2	10420	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	45812448	45812448	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcatcatagtccagcccgaAattctgtggatgggtatgga	11	10	12	8	1	2	0	1	0	1	0	3	3	3	2	2	3	2	2	2	3	3	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:45812448A>T	ENST00000372086.3	-	9	1196	c.796T>A	c.(796-798)Ttc>Atc	p.F266I	TESK2_ENST00000538496.1_Missense_Mutation_p.F183I|TESK2_ENST00000341771.6_Intron|TESK2_ENST00000372084.1_Intron|TESK2_ENST00000486676.1_5'UTR	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					TCCAGCCCGAAATTCTGTGGA	0.502																																					p.F266I		.											.	TESK2-624	0			c.T796A						.						79	82	81					1																	45812448		1949	4153	6102	SO:0001583	missense	10420	exon9			GCCCGAAATTCTG	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.796T>A	1.37:g.45812448A>T	ENSP00000361158:p.Phe266Ile	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	116	47	NM_007170	0	0	0	0	0	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	37	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	A	34	5.297190	0.95574	.	.	ENSG00000070759	ENST00000372086;ENST00000372083;ENST00000538496	D;D	0.81579	-1.51;-1.51	6.08	6.08	0.98989	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.86573	0.5965	L	0.42581	1.335	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87288	0.2297	10	0.62326	D	0.03	-8.8357	16.6438	0.85155	1.0:0.0:0.0:0.0	.	266	Q96S53	TESK2_HUMAN	I	266;250;183	ENSP00000361158:F266I;ENSP00000441746:F183I	ENSP00000361155:F250I	F	-	1	0	TESK2	45585035	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.317000	0.96327	2.333000	0.79357	0.533000	0.62120	TTC	.		0.502	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		T	45812448	A	T	45812448	3	4	142	1	0	0	0	0	1	0	0	0	15800	14	1	5	931	5	TESK2	1	45812448	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	2137012	45812448	203438173	7	12643											
IPP	3652	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	46206860	46206860	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catggcaggcaatttgctcaGagaactgaaaaattccaatg	15	9	9	8	0	1	2	1	1	0	1	2	3	2	2	1	2	2	3	1	2	5	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:46206860G>A	ENST00000396478.3	-	3	539	c.437C>T	c.(436-438)tCt>tTt	p.S146F		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	146						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					AATTTGCTCAGAGAACTGAAA	0.413																																					p.S146F													.	IPP-91	0			c.C437T						.						85	84	84					1																	46206860		2203	4300	6503	SO:0001583	missense	3652	exon3			TGCTCAGAGAACT	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.437C>T	1.37:g.46206860G>A	ENSP00000379739:p.Ser146Phe	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	126	39	NM_001145349	0	0	1	2	1	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.838259	0.51057	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.71461	-0.57;-0.57	5.19	4.21	0.49690	BTB/Kelch-associated (2);	0.352326	0.31949	N	0.006810	T	0.72875	0.3515	M	0.64997	1.995	0.40491	D	0.980549	P;P	0.44877	0.544;0.845	P;P	0.46110	0.467;0.504	T	0.78966	-0.1995	10	0.87932	D	0	.	15.4999	0.75691	0.0:0.1387:0.8613:0.0	.	146;146	Q9Y573;A2A6V3	IPP_HUMAN;.	F	146	ENSP00000353024:S146F;ENSP00000379739:S146F	ENSP00000353024:S146F	S	-	2	0	IPP	45979447	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.054000	0.64275	2.586000	0.87340	0.655000	0.94253	TCT	.		0.413	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		A	46206860	G	A	46206860	3	1	142	1	0	0	0	0	1	0	0	0	7821	942	33	2	1447	2	IPP	1	46206860	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	394412	46206860	203043761	8	12644											
ELTD1	64123	hgsc.bcm.edu;bcgsc.ca	37	chr1	79470814	79470814	+	Frame_Shift_Del	DEL	C	C	-																															tgcaatagcaggcttcaattCcattgcgtatttcacatttt																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:79470814delC	ENST00000370742.3	-	2	176	c.113delG	c.(112-114)ggafs	p.G38fs		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	38	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.G38E(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		GGCTTCAATTCCATTGCGTAT	0.348																																					p.G38fs		.											.	ELTD1-24	1	Substitution - Missense(1)	endometrium(1)	c.113delG						.						140	127	131					1																	79470814		1864	4103	5967	SO:0001589	frameshift_variant	64123	exon2			.	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.113delG	1.37:g.79470814delC	ENSP00000359778:p.Gly38fs	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	82	20	NM_022159	0	0	0	0	0	B1AR71|Q5KU34	Frame_Shift_Del	DEL	ENST00000370742.3	37	CCDS41352.1																																																																																			.		0.348	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		-	79470814	C	-	79470814	7	5	142	1	0	1	0	1	0	0	0	0	5097	855	30	0	2015	0	ELTD1	1	79470814	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M8-01A-11D-A31X-10	33263954	79470814	169779807	9	12645											
MCOLN3	55283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	85506767	85506767	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atatgtgtcatccattcggtCcatatatccttttaggaaaa	12	15	6	8	1	1	0	1	0	0	0	5	1	4	1	3	2	0	0	3	2	6	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:85506767C>G	ENST00000370589.2	-	3	374	c.322G>C	c.(322-324)Gac>Cac	p.D108H	MCOLN3_ENST00000370587.1_Missense_Mutation_p.D108H|MCOLN3_ENST00000341115.4_Intron|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	108					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TCCATTCGGTCCATATATCCT	0.378																																					p.D108H		.											.	MCOLN3-91	0			c.G322C						.						235	209	217					1																	85506767		2203	4300	6503	SO:0001583	missense	55283	exon3			TTCGGTCCATATA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.322G>C	1.37:g.85506767C>G	ENSP00000359621:p.Asp108His	Somatic	213	0		WXS	Illumina HiSeq	Phase_I	125	44	NM_018298	0	0	0	0	0	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	37	CCDS701.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.712652	0.68730	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370587	T;T	0.62364	0.03;0.03	5.76	5.76	0.90799	.	0.048278	0.85682	D	0.000000	T	0.77239	0.4101	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.69824	0.966;0.965	T	0.77608	-0.2524	10	0.56958	D	0.05	-2.0809	19.9857	0.97347	0.0:1.0:0.0:0.0	.	108;108	B1ANB7;Q8TDD5	.;MCLN3_HUMAN	H	108	ENSP00000359621:D108H;ENSP00000359619:D108H	ENSP00000304843:D108H	D	-	1	0	MCOLN3	85279355	1.000000	0.71417	0.506000	0.27664	0.660000	0.38997	5.767000	0.68850	2.706000	0.92434	0.655000	0.94253	GAC	.		0.378	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		G	85506767	C	G	85506767	3	3	142	1	0	0	0	0	1	0	0	0	9422	855	30	4	1383	4	MCOLN3	1	85506767	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	6035953	85506767	163743854	10	12646											
TRIM45	80263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	117660955	117660955	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttctgcagctgcagggaaTtttccttctgggcccgtatg	5	13	11	12	1	2	0	0	0	2	0	3	1	3	1	3	2	3	4	3	2	2	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:117660955T>G	ENST00000256649.4	-	2	1449	c.923A>C	c.(922-924)aAt>aCt	p.N308T	TRIM45_ENST00000369464.3_Missense_Mutation_p.N308T|TRIM45_ENST00000369461.3_Missense_Mutation_p.N251T	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	308					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		CTGCAGGGAATTTTCCTTCTG	0.567																																					p.N308T		.											.	TRIM45-226	0			c.A923C						.						76	74	74					1																	117660955		2203	4300	6503	SO:0001583	missense	80263	exon2			AGGGAATTTTCCT		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19018	protein-coding gene	gene with protein product		609318	"tripartite motif-containing 45"			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.923A>C	1.37:g.117660955T>G	ENSP00000256649:p.Asn308Thr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	99	33	NM_001145635	0	0	1	1	0	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.352209	0.24512	.	.	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;D;D	0.85629	-2.01;-2.01;-2.01	5.11	3.96	0.45880	.	0.242716	0.47852	N	0.000216	T	0.66557	0.2801	L	0.35723	1.085	0.44254	D	0.997108	B;B	0.16802	0.019;0.011	B;B	0.15870	0.014;0.006	T	0.63594	-0.6602	10	0.37606	T	0.19	-26.5032	11.6751	0.51425	0.0:0.0:0.1477:0.8522	.	308;308	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	T	308;308;251	ENSP00000256649:N308T;ENSP00000358476:N308T;ENSP00000358473:N251T	ENSP00000256649:N308T	N	-	2	0	TRIM45	117462478	1.000000	0.71417	0.823000	0.32752	0.520000	0.34377	2.680000	0.46918	0.932000	0.37266	0.533000	0.62120	AAT	.		0.567	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188		G	117660955	T	G	117660955	3	3	142	1	0	0	0	0	1	0	0	0	16553	1493	52	5	839	5	TRIM45	1	117660955	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	32154188	117660955	131589666	11	12647											
CHD1L	9557	hgsc.bcm.edu	37	chr1	146747129	146747130	+	Frame_Shift_Ins	INS	-	-	A																															ctcatcgcattggccaaaacINSaagtaagtgatttttttctg																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:146747129_146747130insA	ENST00000369258.4	+	13	1403_1404	c.1383_1384insA	c.(1384-1386)aagfs	p.K462fs	CHD1L_ENST00000369259.3_Frame_Shift_Ins_p.K258fs|CHD1L_ENST00000431239.1_Frame_Shift_Ins_p.K368fs|CHD1L_ENST00000361293.5_Frame_Shift_Ins_p.K181fs|CHD1L_ENST00000467213.1_3'UTR	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	462	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					TTGGCCAAAACAAGTAAGTGAT	0.45																																					p.N461fs		.											.	CHD1L-231	0			c.1383_1384insA						.																																			SO:0001589	frameshift_variant	9557	exon13			.	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1385dupA	1.37:g.146747131_146747131dupA	ENSP00000358262:p.Lys462fs	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	86	15	NM_004284	0	0	0	0	0	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Frame_Shift_Ins	INS	ENST00000369258.4	37	CCDS927.1																																																																																			.		0.45	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		A	146747130	-	A	146747129	7	5	142	1	0	1	1	0	0	0	0	0	3330	477	17	0	1433	0	CHD1L	1	146747129	Frame_Shift_Ins	INS	-	TCGA-IZ-A6M8-01A-11D-A31X-10	29086174	146747129	102503492	12	12648											
SETDB1	9869	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	150900339	150900347	+	In_Frame_Del	DEL	AGATGGATT	AGATGGATT	-																															catcgatgaggaactggagaAgatggattgtgtacagcaac																								rs201917860|rs200122173		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	AGATGGATT	AGATGGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:150900339_150900347delAGATGGATT	ENST00000271640.5	+	2	339_347	c.149_157delAGATGGATT	c.(148-159)aagatggattgt>agt	p.50_53KMDC>S	SETDB1_ENST00000368962.2_In_Frame_Del_p.50_53KMDC>S|SETDB1_ENST00000368969.4_In_Frame_Del_p.50_53KMDC>S|SETDB1_ENST00000368963.1_In_Frame_Del_p.50_53KMDC>S|SETDB1_ENST00000459773.1_3'UTR	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	50					bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GAACTGGAGAAGATGGATTGTGTACAGCA	0.474																																					p.50_53del		.											.	SETDB1-228	0			c.149_157del						.																																			SO:0001651	inframe_deletion	9869	exon2			.	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.149_157delAGATGGATT	1.37:g.150900339_150900347delAGATGGATT	ENSP00000271640:p.Lys50_Cys53delinsSer	Somatic	261	0		WXS	Illumina HiSeq	Phase_I	219	59	NM_012432	0	0	0	0	0	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	In_Frame_Del	DEL	ENST00000271640.5	37	CCDS44217.1																																																																																			.		0.474	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			-	150900347	AGATGGATT	-	150900339	7	5	142	1	0	1	0	1	0	0	0	0	14170	72	3	0	151	0	SETDB1	1	150900339	In_Frame_Del	DEL	AGATGGATT	TCGA-IZ-A6M8-01A-11D-A31X-10	4153210	150900339	98350282	13	12649											
ABL2	27	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	179076969	179076969	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtagctcctgcaggctgaGttccagtttgctcacagcct	6	12	10	13	0	1	1	1	1	0	0	3	1	3	1	3	1	4	7	3	1	1	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:179076969G>T	ENST00000502732.1	-	12	3636	c.3433C>A	c.(3433-3435)Ctc>Atc	p.L1145I	ABL2_ENST00000344730.3_Missense_Mutation_p.L1027I|ABL2_ENST00000408940.3_Missense_Mutation_p.L1109I|ABL2_ENST00000367623.4_Missense_Mutation_p.L1124I|ABL2_ENST00000511413.1_Missense_Mutation_p.L1042I|ABL2_ENST00000507173.1_Missense_Mutation_p.L1021I|ABL2_ENST00000504405.1_Missense_Mutation_p.L1006I|ABL2_ENST00000512653.1_Missense_Mutation_p.L1130I	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	1145	F-actin-binding. {ECO:0000250}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TGCAGGCTGAGTTCCAGTTTG	0.507			T	ETV6	AML																																p.L1145I				Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2-1081	0			c.C3433A						.						71	72	71					1																	179076969		2203	4300	6503	SO:0001583	missense	27	exon12			GGCTGAGTTCCAG	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.3433C>A	1.37:g.179076969G>T	ENSP00000427562:p.Leu1145Ile	Somatic	118	1		WXS	Illumina HiSeq	Phase_I	126	39	NM_007314	0	0	2	6	4	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	37	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.854385	0.32791	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413	T;T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.65	4.72	0.59763	F-actin binding (2);	0.142456	0.32068	N	0.006637	T	0.42877	0.1222	L	0.43152	1.355	0.37518	D	0.917409	D;B;B;D;D;D;D;B	0.76494	0.999;0.003;0.001;0.99;0.999;0.999;0.999;0.005	D;B;B;D;D;D;D;B	0.83275	0.993;0.004;0.004;0.979;0.996;0.993;0.996;0.006	T	0.38090	-0.9677	10	0.20046	T	0.44	.	10.5331	0.44988	0.0:0.1448:0.7048:0.1504	.	1124;1021;1042;1006;1145;1130;1109;1027	P42684-6;P42684-7;P42684-5;P42684-4;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;ABL2_HUMAN;.;.;.	I	1145;1109;1027;1130;1006;1124;1021;1042	ENSP00000427562:L1145I;ENSP00000386152:L1109I;ENSP00000339209:L1027I;ENSP00000423578:L1130I;ENSP00000426831:L1006I;ENSP00000356595:L1124I;ENSP00000423413:L1021I;ENSP00000424697:L1042I	ENSP00000339209:L1027I	L	-	1	0	ABL2	177343592	0.997000	0.39634	0.993000	0.49108	0.835000	0.47333	2.092000	0.41700	1.326000	0.45319	0.655000	0.94253	CTC	.		0.507	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		T	179076969	G	T	179076969	3	4	142	1	0	0	0	0	1	0	0	0	93	1029	36	4	119	4	ABL2	1	179076969	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	28176630	179076969	70173652	14	12650											
ZNF281	23528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	200378264	200378264	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtaatacgtcacggtggtgCtgggctggttgctgctggac	6	11	16	8	2	1	0	1	0	0	0	1	1	1	1	0	5	4	6	0	5	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:200378264C>T	ENST00000294740.3	-	2	694	c.570G>A	c.(568-570)caG>caA	p.Q190Q	ZNF281_ENST00000367353.1_Silent_p.Q190Q|ZNF281_ENST00000367352.3_Silent_p.Q154Q	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	190					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						CACGGTGGTGCTGGGCTGGTT	0.562																																					p.Q190Q		.											.	ZNF281-154	0			c.G570A						.						101	97	98					1																	200378264		2203	4300	6503	SO:0001819	synonymous_variant	23528	exon2			GTGGTGCTGGGCT	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"Zinc fingers, C2H2-type"	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.570G>A	1.37:g.200378264C>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	87	35	NM_012482	0	0	0	0	0	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	37	CCDS1402.1																																																																																			.		0.562	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		T	200378264	C	T	200378264	2	4	142	1	0	0	0	0	0	0	0	1	17850	796	28	2		2	ZNF281	1	200378264	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	21301295	200378264	48872357	15	12651											
LBR	3930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	225600280	225600280	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaaatgactgtacacgtaAtgaaactctacgccctggaa	16	8	8	9	2	1	3	0	2	1	1	1	4	1	4	1	1	3	2	1	1	7	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:225600280A>C	ENST00000338179.2	-	8	1085	c.960T>G	c.(958-960)caT>caG	p.H320Q	AC092811.1_ENST00000366845.2_5'Flank|LBR_ENST00000272163.4_Missense_Mutation_p.H320Q	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	320					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TGTACACGTAATGAAACTCTA	0.413																																					p.H320Q		.											.	LBR-228	0			c.T960G						.						79	80	80					1																	225600280		2203	4300	6503	SO:0001583	missense	3930	exon8			CACGTAATGAAAC	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.960T>G	1.37:g.225600280A>C	ENSP00000339883:p.His320Gln	Somatic	540	1		WXS	Illumina HiSeq	Phase_I	407	97	NM_194442	0	0	1	2	1	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	37	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	A	10.74	1.434732	0.25813	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.97811	-4.55;-4.55	6.07	-0.357	0.12579	.	1.680490	0.02408	N	0.081343	D	0.92440	0.7600	N	0.04203	-0.255	0.09310	N	1	B	0.23128	0.08	B	0.18263	0.021	D	0.86742	0.1955	10	0.29301	T	0.29	3.4658	9.9056	0.41375	0.6743:0.0:0.3257:0.0	.	320	Q14739	LBR_HUMAN	Q	320	ENSP00000272163:H320Q;ENSP00000339883:H320Q	ENSP00000272163:H320Q	H	-	3	2	LBR	223666903	0.080000	0.21391	0.000000	0.03702	0.029000	0.11900	0.526000	0.22971	-0.299000	0.08909	0.533000	0.62120	CAT	.		0.413	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		C	225600280	A	C	225600280	3	2	142	1	0	0	0	0	1	0	0	0	8673	98	4	5	915	5	LBR	1	225600280	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	25222016	225600280	23650341	16	12652											
C2orf84	653140	ucsc.edu;bcgsc.ca	37	chr2	24413283	24413283	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcttttcttcacagtcCtgaaaagctcatctatgcag	9	15	6	11	0	5	1	2	1	3	0	6	1	6	1	1	0	3	3	1	0	3	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:24413283C>T	ENST00000295150.3	+	6	490	c.404C>T	c.(403-405)cCt>cTt	p.P135L	RP11-507M3.1_ENST00000584973.1_3'UTR	NM_001040710.1	NP_001035800.1	Q86W67	F228A_HUMAN	family with sequence similarity 228, member A	135																	CTTCACAGTCCTGAAAAGCTC	0.403																																					p.P135L													.	.	0			c.C404T						.						27	27	27					2																	24413283		1863	4086	5949	SO:0001583	missense	653140	exon6			ACAGTCCTGAAAA		CCDS42659.1	2p23.3	2012-07-04	2012-07-04	2012-07-04	ENSG00000186453	ENSG00000186453			34418	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 84"	C2orf84			Standard	NM_001040710		Approved	FLJ30851	uc002rfc.3	Q86W67	OTTHUMG00000151903	ENST00000295150.3:c.404C>T	2.37:g.24413283C>T	ENSP00000295150:p.Pro135Leu	Somatic	290	3		WXS	Illumina HiSeq		234	62	NM_001040710	0	0	0	0	0		Missense_Mutation	SNP	ENST00000295150.3	37	CCDS42659.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.859698	0.51376	.	.	ENSG00000186453	ENST00000295150;ENST00000415196	T;T	0.49432	0.79;0.78	3.64	2.77	0.32553	.	0.665350	0.13290	N	0.399077	T	0.31167	0.0788	N	0.19112	0.55	0.19300	N	0.99998	B	0.22683	0.073	B	0.25884	0.064	T	0.20638	-1.0269	10	0.46703	T	0.11	1.0E-4	7.0592	0.25115	0.0:0.8788:0.0:0.1212	.	135	Q86W67	CB084_HUMAN	L	135;36	ENSP00000295150:P135L;ENSP00000416595:P36L	ENSP00000295150:P135L	P	+	2	0	C2orf84	24266787	0.562000	0.26586	0.120000	0.21714	0.061000	0.15899	0.376000	0.20535	1.121000	0.41925	0.650000	0.86243	CCT	.		0.403	FAM228A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324342.1	NM_001040710		T	24413283	C	T	24413283	3	4	142	1	0	0	0	0	1	0	0	0	2205	681	24	2	422	2	C2orf84	2	24413283	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		24413283	218786090	17	12653											
SULT6B1	391365	hgsc.bcm.edu;bcgsc.ca	37	chr2	37414574	37414575	+	Frame_Shift_Ins	INS	-	-	T																															ttttttagaaacagcatataINSttaattcactgacaatgtgg																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:37414574_37414575insT	ENST00000535679.1	-	2	234_235	c.235_236insA	c.(235-237)atafs	p.I79fs	SULT6B1_ENST00000407963.1_Frame_Shift_Ins_p.I41fs|SULT6B1_ENST00000379149.2_Frame_Shift_Ins_p.I79fs|SULT6B1_ENST00000260637.3_Frame_Shift_Ins_p.I41fs			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	79						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				AACAGCATATATTAATTCACTG	0.327																																					p.I41fs		.											.	SULT6B1-91	0			c.122_123insA						.																																			SO:0001589	frameshift_variant	391365	exon2			.	AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"Sulfotransferases, cytosolic"	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.236dupA	2.37:g.37414576_37414576dupT	ENSP00000444081:p.Ile79fs	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	104	30	NM_001032377	0	0	0	0	0	B2RTS7	Frame_Shift_Ins	INS	ENST00000535679.1	37																																																																																				.		0.327	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		T	37414575	-	T	37414574	7	5	142	1	0	1	1	0	0	0	0	0	15416	449	16	0	699	0	SULT6B1	2	37414574	Frame_Shift_Ins	INS	-	TCGA-IZ-A6M8-01A-11D-A31X-10	13001291	37414574	205784799	18	12654											
SOS1	6654	bcgsc.ca	37	chr2	39284009	39284009	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttataacctaggacctccTgcaaaattaaaagaaaagca	18	10	5	8	0	0	1	0	0	0	1	1	2	1	2	3	1	3	2	3	1	9	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:39284009T>C	ENST00000426016.1	-	5	432		c.e5-2		SOS1_ENST00000395038.2_Splice_Site|SOS1_ENST00000402219.2_Splice_Site|SOS1_ENST00000428721.2_Splice_Site			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)						apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TAGGACCTCCTGCAAAATTAA	0.299									Noonan syndrome																												.													.	SOS1-851	0			c.346-2A>G						.						101	117	111					2																	39284009		2198	4295	6493	SO:0001630	splice_region_variant	6654	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	ACCTCCTGCAAAA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.346-2A>G	2.37:g.39284009T>C		Somatic	117	4		WXS	Illumina HiSeq	Phase_1	43	21	NM_005633	0	0	0	0	0	A8K2G3|B4DXG2	Splice_Site	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.361515	0.82353	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721;ENST00000451331	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7191	0.77694	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SOS1	39137513	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	7.904000	0.87408	2.118000	0.64928	0.377000	0.23210	.	.		0.299	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	Intron	C	39284009	T	C	39284009	5	2	142	1	0	0	0	0	0	0	1	0	14968	1594	55	3	3737	3	SOS1	2	39284009	Splice_Site	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	1869435	39284009	203915364	19	12655											
GMCL1	64395	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	70096993	70096993	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctcgaaggagcatagcatTtaggtaggatgagatttccc	11	10	12	8	1	0	1	0	1	0	1	2	5	1	3	2	3	2	3	2	3	4	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:70096993T>G	ENST00000282570.3	+	12	1612	c.1361T>G	c.(1360-1362)tTt>tGt	p.F454C		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	454					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						AGCATAGCATTTAGGTAGGAT	0.398																																					p.F454C		.											.	GMCL1-93	0			c.T1361G						.						138	118	125					2																	70096993		2203	4300	6503	SO:0001583	missense	64395	exon12			TAGCATTTAGGTA	AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.1361T>G	2.37:g.70096993T>G	ENSP00000282570:p.Phe454Cys	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	56	20	NM_178439	0	0	0	0	0	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	37	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723230	0.48728	.	.	ENSG00000087338	ENST00000282570	T	0.56103	0.48	5.22	5.22	0.72569	.	0.108148	0.64402	D	0.000004	T	0.63534	0.2519	L	0.44542	1.39	0.46113	D	0.99887	D	0.76494	0.999	D	0.70227	0.968	T	0.64478	-0.6398	10	0.51188	T	0.08	-38.9046	13.3387	0.60533	0.0:0.0:0.0:1.0	.	454	Q96IK5	GMCL1_HUMAN	C	454	ENSP00000282570:F454C	ENSP00000282570:F454C	F	+	2	0	GMCL1	69950497	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.799000	0.55529	2.090000	0.63153	0.533000	0.62120	TTT	.		0.398	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70096993	T	G	70096993	3	3	142	1	0	0	0	0	1	0	0	0	6505	1841	64	5	1407	5	GMCL1	2	70096993	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	30812984	70096993	173102380	20	12656											
PCDP1	200373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	120362785	120362785	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagggcactgaaatttcaaaAacgagacagatgaaggaggc	17	5	12	7	1	1	4	1	2	0	2	1	6	1	5	0	3	1	1	0	3	4	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:120362785A>C	ENST00000413369.3	+	11	1140	c.1053A>C	c.(1051-1053)aaA>aaC	p.K351N	PCDP1_ENST00000597189.1_3'UTR|PCDP1_ENST00000602047.1_Missense_Mutation_p.K65N	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					AAATTTCAAAAACGAGACAGA	0.383																																					p.K351N		.											.	.	0			c.A1053C						.						67	70	69					2																	120362785		2203	4300	6503	SO:0001583	missense	0	exon11			TTCAAAAACGAGA																												ENST00000413369.3:c.1053A>C	2.37:g.120362785A>C	ENSP00000393222:p.Lys351Asn	Somatic	419	0		WXS	Illumina HiSeq	Phase_I	280	80	NM_001271049	0	0	2	4	2		Missense_Mutation	SNP	ENST00000413369.3	37	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535164	0.45176	.	.	ENSG00000163075	ENST00000295220;ENST00000413369	T	0.19938	2.11	5.22	2.87	0.33458	.	0.239906	0.36338	N	0.002660	T	0.12433	0.0302	L	0.34521	1.04	0.80722	D	1	P;B	0.35011	0.48;0.291	B;B	0.27715	0.082;0.082	T	0.13872	-1.0493	10	0.27082	T	0.32	-25.951	8.4885	0.33086	0.8403:0.0:0.1597:0.0	.	195;351	Q4G0U5-3;Q4G0U5	.;PCDP1_HUMAN	N	65;351	ENSP00000393222:K351N	ENSP00000295220:K65N	K	+	3	2	AC069154.2	120079255	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.660000	0.37397	0.460000	0.27045	0.533000	0.62120	AAA	.		0.383	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			C	120362785	A	C	120362785	3	2	142	1	0	0	0	0	1	0	0	0	11598	11	1	5	205	5	PCDP1	2	120362785	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	50265792	120362785	122836588	21	12657											
MKI67IP	84365	bcgsc.ca	37	chr2	122494414	122494414	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattggcccagccgggccagAaaaagtcgccatgccaaaag	13	4	12	12	2	0	1	0	0	0	1	1	2	0	1	5	2	2	0	5	2	4	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:122494414A>G	ENST00000285814.4	-	1	85	c.13T>C	c.(13-15)Tct>Cct	p.S5P		NM_032390.4	NP_115766.3	Q9BYG3	MK67I_HUMAN		5					negative regulation of phosphatase activity (GO:0010923)|protein complex assembly (GO:0006461)|rRNA metabolic process (GO:0016072)|rRNA transcription (GO:0009303)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12						GCCGGGCCAGAAAAAGTCGCC	0.627																																					p.S5P													.	MKI67IP-90	0			c.T13C						.						28	28	28					2																	122494414		2203	4300	6503	SO:0001583	missense	84365	exon1			GGCCAGAAAAAGT																												ENST00000285814.4:c.13T>C	2.37:g.122494414A>G	ENSP00000285814:p.Ser5Pro	Somatic	146	3		WXS	Illumina HiSeq	Phase_1	156	53	NM_032390	0	0	4	9	5	A8K788|Q8TB66|Q96ED4	Missense_Mutation	SNP	ENST00000285814.4	37	CCDS2135.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.324189	0.24080	.	.	ENSG00000155438	ENST00000285814;ENST00000409201;ENST00000451734	T;T	0.35973	2.19;1.28	3.13	-6.26	0.02033	.	2.322460	0.01768	N	0.030964	T	0.24509	0.0594	L	0.33485	1.01	0.09310	N	1	B;P	0.49961	0.013;0.93	B;B	0.41571	0.01;0.36	T	0.40869	-0.9540	10	0.49607	T	0.09	6.4386	3.9147	0.09217	0.2927:0.5044:0.0971:0.1058	.	5;5	B4DSM4;Q9BYG3	.;MK67I_HUMAN	P	5	ENSP00000285814:S5P;ENSP00000398116:S5P	ENSP00000285814:S5P	S	-	1	0	MKI67IP	122210884	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.354000	0.02614	-2.375000	0.00598	-0.489000	0.04712	TCT	.		0.627	MKI67IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254239.2			G	122494414	A	G	122494414	3	3	142	1	0	0	0	0	1	0	0	0	9624	246	9	3	896	3	MKI67IP	2	122494414	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	2131629	122494414	120704959	22	12658											
SCN1A	6323	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	166908235	166908235	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaataattcttacttgaatCttgaatatatgacttccagt	14	16	4	7	0	2	3	0	3	2	0	3	3	3	3	1	0	1	0	1	0	7	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:166908235C>A	ENST00000303395.4	-	6	957	c.958G>T	c.(958-960)Gat>Tat	p.D320Y	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.D320Y|SCN1A_ENST00000423058.2_Missense_Mutation_p.D320Y|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.D320Y			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	320					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTACTTGAATCTTGAATATAT	0.299																																					p.D320Y													.	SCN1A-147	0			c.G958T						.						39	40	40					2																	166908235		2201	4295	6496	SO:0001583	missense	6323	exon6			TTGAATCTTGAAT	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10585	protein-coding gene	gene with protein product		182389	"febrile convulsions 3"	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.958G>T	2.37:g.166908235C>A	ENSP00000303540:p.Asp320Tyr	Somatic	199	1		WXS	Illumina HiSeq	Phase_I	105	38	NM_001165964	0	0	0	0	0	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860340	0.71834	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96554	-4.05;-4.05;-4.01;-3.98	5.41	5.41	0.78517	Ion transport (1);	0.161043	0.43919	D	0.000516	D	0.97845	0.9292	M	0.67953	2.075	0.54753	D	0.999989	P;D;D	0.89917	0.841;0.998;1.0	P;D;D	0.87578	0.552;0.974;0.998	D	0.98223	1.0479	10	0.62326	D	0.03	.	19.5538	0.95333	0.0:1.0:0.0:0.0	.	320;320;320	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	Y	320	ENSP00000407030:D320Y;ENSP00000303540:D320Y;ENSP00000364554:D320Y;ENSP00000386312:D320Y	ENSP00000303540:D320Y	D	-	1	0	SCN1A	166616481	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.926000	0.48892	2.688000	0.91661	0.655000	0.94253	GAT	.		0.299	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		A	166908235	C	A	166908235	3	1	142	1	0	0	0	0	1	0	0	0	13946	913	32	4	5155	4	SCN1A	2	166908235	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	44413821	166908235	76291138	23	12659											
IHH	3549	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219920296	219920296	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctggcaaatgtggcccggAagcgggctgccggctccgtg	5	6	18	12	4	0	0	0	0	0	0	1	1	1	1	3	6	2	4	3	6	2	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:219920296A>G	ENST00000295731.6	-	3	868	c.869T>C	c.(868-870)tTc>tCc	p.F290S		NM_002181.3	NP_002172.2	Q14623	IHH_HUMAN	indian hedgehog	290					bone resorption (GO:0045453)|camera-type eye photoreceptor cell fate commitment (GO:0060220)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|chondrocyte proliferation (GO:0035988)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint development (GO:0072498)|epithelial cell morphogenesis (GO:0003382)|epithelial cell-cell adhesion (GO:0090136)|head morphogenesis (GO:0060323)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intein-mediated protein splicing (GO:0016539)|maternal process involved in female pregnancy (GO:0060135)|multicellular organism growth (GO:0035264)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of eye pigmentation (GO:0048074)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell differentiation in thymus (GO:0033085)|neuron development (GO:0048666)|osteoblast differentiation (GO:0001649)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of growth (GO:0040008)|response to estradiol (GO:0032355)|retinal pigment epithelium development (GO:0003406)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|somite development (GO:0061053)|vitelline membrane formation (GO:0030704)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|patched binding (GO:0005113)|peptidase activity (GO:0008233)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGTGGCCCGGAAGCGGGCTGC	0.667																																					p.F290S													.	IHH-710	0			c.T869C						.						24	28	26					2																	219920296		2202	4299	6501	SO:0001583	missense	3549	exon3			GCCCGGAAGCGGG	L38517	CCDS33380.1	2q33-q35	2013-02-15	2013-02-15		ENSG00000163501	ENSG00000163501			5956	protein-coding gene	gene with protein product		600726	"Indian hedgehog (Drosophila) homolog", "Indian hedgehog homolog (Drosophila)"			7590746, 14770182	Standard	NM_002181		Approved	HHG2, BDA1	uc002vjo.2	Q14623	OTTHUMG00000154631	ENST00000295731.6:c.869T>C	2.37:g.219920296A>G	ENSP00000295731:p.Phe290Ser	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	60	17	NM_002181	0	0	2	3	1	B9EGM5|O43322|Q8N4B9	Missense_Mutation	SNP	ENST00000295731.6	37	CCDS33380.1	.	.	.	.	.	.	.	.	.	.	A	17.61	3.431635	0.62844	.	.	ENSG00000163501	ENST00000295731	D	0.98792	-5.14	5.16	5.16	0.70880	Hedgehog/intein hint, N-terminal (1);Peptidase C46, hedgehog protein, hint region (1);	0.051418	0.85682	D	0.000000	D	0.97626	0.9222	L	0.57536	1.79	0.45662	D	0.998585	P	0.49185	0.92	P	0.47744	0.556	D	0.97010	0.9735	10	0.20519	T	0.43	-0.671	13.8287	0.63366	1.0:0.0:0.0:0.0	.	290	Q14623	IHH_HUMAN	S	290	ENSP00000295731:F290S	ENSP00000295731:F290S	F	-	2	0	IHH	219628540	0.991000	0.36638	0.999000	0.59377	0.936000	0.57629	1.540000	0.36115	1.929000	0.55896	0.459000	0.35465	TTC	.		0.667	IHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336408.2	NM_002181		G	219920296	A	G	219920296	3	3	142	1	0	0	0	0	1	0	0	0	7628	246	9	3	370	3	IHH	2	219920296	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	53012061	219920296	23279077	24	12660											
PER2	8864	broad.mit.edu	37	chr2	239186362	239186362	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actcacctctggcgggcatcCggtggctccaccagcatccc	6	7	10	18	2	2	0	1	0	1	0	5	0	5	0	5	4	1	3	5	4	0	0	rs561050117		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:239186362C>T	ENST00000254657.3	-	2	495	c.216G>A	c.(214-216)ccG>ccA	p.P72P	PER2_ENST00000254658.3_Silent_p.P72P|PER2_ENST00000440245.1_Silent_p.P72P|PER2_ENST00000355768.2_Silent_p.P72P	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	72					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		GGCGGGCATCCGGTGGCTCCA	0.577													C|||	1	0.000199681	0	0	5008	,	,		16985	0		0	False		,,,				2504	0.001				p.P72P													.	PER2-154	0			c.G216A						.						47	48	48					2																	239186362		2203	4300	6503	SO:0001819	synonymous_variant	8864	exon2			GGCATCCGGTGGC	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"period (Drosophila) homolog 2", "period homolog 2 (Drosophila)"			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.216G>A	2.37:g.239186362C>T		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	27	4	NM_022817	0	0	0	0	0	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			.		0.577	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		T	239186362	C	T	239186362	2	4	142	1	0	0	0	0	0	0	0	1	11756	639	23	1		1	PER2	2	239186362	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	19266066	239186362	4013011	25	12661											
PTPN23	25930	hgsc.bcm.edu;bcgsc.ca	37	chr3	47452317	47452317	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctggggtcctggggcagcCgccaccccccctacacaccc	5	4	11	21	1	0	0	0	0	0	0	1	0	1	0	8	4	2	1	8	4	1	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:47452317C>G	ENST00000265562.4	+	20	3106	c.3029C>G	c.(3028-3030)cCg>cGg	p.P1010R	PTPN23_ENST00000431726.1_Missense_Mutation_p.P884R	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1010	His.|Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGGGGCAGCCGCCACCCCCC	0.687																																					p.P1010R		.											.	PTPN23-227	0			c.C3029G						.						15	20	18					3																	47452317		2139	4247	6386	SO:0001583	missense	25930	exon20			GGCAGCCGCCACC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.3029C>G	3.37:g.47452317C>G	ENSP00000265562:p.Pro1010Arg	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	130	35	NM_015466	0	0	3	7	4	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923200	0.33908	.	.	ENSG00000076201	ENST00000265562	T	0.02763	4.17	4.29	3.18	0.36537	.	0.362779	0.25154	N	0.032736	T	0.02342	0.0072	N	0.19112	0.55	0.41800	D	0.989917	P;P	0.37824	0.609;0.609	B;B	0.39738	0.308;0.308	T	0.62310	-0.6881	10	0.37606	T	0.19	-4.7843	6.2976	0.21095	0.0:0.6978:0.0:0.3022	.	884;1010	B4DST5;Q9H3S7	.;PTN23_HUMAN	R	1010	ENSP00000265562:P1010R	ENSP00000265562:P1010R	P	+	2	0	PTPN23	47427321	0.000000	0.05858	0.892000	0.35008	0.632000	0.37999	0.244000	0.18124	0.976000	0.38417	0.557000	0.71058	CCG	.		0.687	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		G	47452317	C	G	47452317	3	3	142	1	0	0	0	0	1	0	0	0	12820	652	23	4	3107	4	PTPN23	3	47452317	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		47452317	150570113	26	12662											
RNF123	63891	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49737921	49737921	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggactacgaggtacaagAttgcctcaagcagttgatga	13	8	11	9	1	1	3	1	2	0	1	1	5	1	4	2	2	4	3	2	2	4	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:49737921A>G	ENST00000327697.6	+	14	1271	c.1127A>G	c.(1126-1128)gAt>gGt	p.D376G	RNF123_ENST00000432042.1_Missense_Mutation_p.D230G	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	376					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GAGGTACAAGATTGCCTCAAG	0.572																																					p.D376G													.	RNF123-584	0			c.A1127G						.						103	93	97					3																	49737921		2203	4300	6503	SO:0001583	missense	63891	exon14			TACAAGATTGCCT	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"RING-type (C3HC4) zinc fingers"	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.1127A>G	3.37:g.49737921A>G	ENSP00000328287:p.Asp376Gly	Somatic	104	1		WXS	Illumina HiSeq	Phase_I	105	40	NM_022064	0	0	1	4	3	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.064583	0.55432	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75589	-0.66;-0.95	5.15	5.15	0.70609	.	0.285942	0.32935	N	0.005472	T	0.55784	0.1942	N	0.08118	0	0.80722	D	1	B;P	0.34522	0.255;0.455	B;B	0.32465	0.031;0.146	T	0.61637	-0.7022	10	0.48119	T	0.1	-16.8059	14.1621	0.65452	1.0:0.0:0.0:0.0	.	230;376	C9J266;Q5XPI4	.;RN123_HUMAN	G	376;376;230	ENSP00000328287:D376G;ENSP00000392443:D230G	ENSP00000328287:D376G	D	+	2	0	RNF123	49712925	1.000000	0.71417	0.996000	0.52242	0.936000	0.57629	6.802000	0.75175	1.953000	0.56701	0.533000	0.62120	GAT	.		0.572	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		G	49737921	A	G	49737921	3	3	142	1	0	0	0	0	1	0	0	0	13465	333	12	3	1177	3	RNF123	3	49737921	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	2285604	49737921	148284509	27	12663											
IL17RD	54756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	57136553	57136553	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaagagcgtcgcgaatgcCgatatgactaccagtggcac	11	7	13	10	4	0	3	0	2	0	1	1	5	0	3	2	1	3	1	2	1	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:57136553C>T	ENST00000296318.7	-	10	1021	c.933G>A	c.(931-933)tcG>tcA	p.S311S	IL17RD_ENST00000463523.1_Silent_p.S167S|IL17RD_ENST00000320057.5_Silent_p.S167S|IL17RD_ENST00000427856.2_Silent_p.S287S	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	311					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TCGCGAATGCCGATATGACTA	0.547																																					p.S311S		.											.	IL17RD-500	0			c.G933A						.						70	69	69					3																	57136553		2203	4300	6503	SO:0001819	synonymous_variant	54756	exon10			GAATGCCGATATG	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.933G>A	3.37:g.57136553C>T		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	138	37	NM_017563	0	0	0	0	0	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	37	CCDS2880.2																																																																																			.		0.547	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		T	57136553	C	T	57136553	2	4	142	1	0	0	0	0	0	0	0	1	7663	639	23	1		1	IL17RD	3	57136553	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	7398632	57136553	140885877	28	12664											
HSPBAP1	79663	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122471457	122471457	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagttcaatccatgagtttAtactgacagtgacaggatca	13	11	8	9	0	2	3	2	3	0	0	3	4	3	4	2	1	1	2	2	1	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:122471457A>G	ENST00000306103.2	-	6	949	c.806T>C	c.(805-807)aTa>aCa	p.I269T	snoU13_ENST00000459192.1_RNA|HSPBAP1_ENST00000383659.1_3'UTR|HSPBAP1_ENST00000465044.1_5'Flank	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	269	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		CCATGAGTTTATACTGACAGT	0.348																																					p.I269T													.	HSPBAP1-227	0			c.T806C						.						94	87	89					3																	122471457		2203	4300	6503	SO:0001583	missense	79663	exon6			GAGTTTATACTGA	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"HSPB (heat shock 27kD) associated protein 1"			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.806T>C	3.37:g.122471457A>G	ENSP00000302562:p.Ile269Thr	Somatic	293	1		WXS	Illumina HiSeq	Phase_I	169	46	NM_024610	0	0	5	6	1	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.359468	0.82353	.	.	ENSG00000169087	ENST00000306103	T	0.13196	2.61	5.3	5.3	0.74995	Cupin, JmjC-type (1);Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.153054	0.56097	D	0.000021	T	0.31358	0.0794	M	0.74467	2.265	0.80722	D	1	D	0.56035	0.974	P	0.55303	0.773	T	0.04708	-1.0932	10	0.66056	D	0.02	.	14.5845	0.68315	1.0:0.0:0.0:0.0	.	269	Q96EW2	HBAP1_HUMAN	T	269	ENSP00000302562:I269T	ENSP00000302562:I269T	I	-	2	0	HSPBAP1	123954147	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.442000	0.90317	2.232000	0.73038	0.528000	0.53228	ATA	.		0.348	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610		G	122471457	A	G	122471457	3	3	142	1	0	0	0	0	1	0	0	0	7446	449	16	3	672	3	HSPBAP1	3	122471457	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	65334904	122471457	75550973	29	12665											
DNAJC13	23317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132207851	132207851	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacacataccaaacaggctTtcaagtcagaagaggtaagc	17	6	8	10	0	2	2	2	0	0	2	2	2	2	2	1	2	3	2	1	2	5	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:132207851T>C	ENST00000260818.6	+	31	3702	c.3454T>C	c.(3454-3456)Ttc>Ctc	p.F1152L		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1152					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CAAACAGGCTTTCAAGTCAGA	0.333																																					p.F1152L		.											.	DNAJC13-272	0			c.T3454C						.						64	65	64					3																	132207851		2203	4300	6503	SO:0001583	missense	23317	exon31			CAGGCTTTCAAGT	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"Heat shock proteins / DNAJ (HSP40)"	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.3454T>C	3.37:g.132207851T>C	ENSP00000260818:p.Phe1152Leu	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_015268	0	0	0	0	0	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.653771	0.88056	.	.	ENSG00000138246	ENST00000260818	T	0.18174	2.23	5.57	5.57	0.84162	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.16171	0.0389	L	0.47716	1.5	0.80722	D	1	P	0.52463	0.953	B	0.39217	0.294	T	0.04708	-1.0932	10	0.25106	T	0.35	.	15.7007	0.77538	0.0:0.0:0.0:1.0	.	1152	O75165	DJC13_HUMAN	L	1152	ENSP00000260818:F1152L	ENSP00000260818:F1152L	F	+	1	0	DNAJC13	133690541	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.807000	0.75201	2.236000	0.73375	0.528000	0.53228	TTC	.		0.333	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132207851	T	C	132207851	3	2	142	1	0	0	0	0	1	0	0	0	4643	1841	64	3	3572	3	DNAJC13	3	132207851	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	9736394	132207851	65814579	30	12666											
WHSC1	7468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1977074	1977074	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtctgggcaatgaaaaaacgGtctgccggtgtggagcctcc	9	8	14	10	2	2	1	0	1	2	0	3	2	3	2	3	4	3	1	3	4	4	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:1977074G>C	ENST00000382895.3	+	22	3999	c.3568G>C	c.(3568-3570)Gtc>Ctc	p.V1190L	WHSC1_ENST00000508803.1_Missense_Mutation_p.V1190L|SCARNA22_ENST00000503991.1_RNA|WHSC1_ENST00000382888.3_Missense_Mutation_p.V538L|WHSC1_ENST00000382891.5_Missense_Mutation_p.V1190L|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382892.2_Missense_Mutation_p.V1190L	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	1190	Post-SET. {ECO:0000255|PROSITE- ProRule:PRU00155}.				anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		TGAAAAAACGGTCTGCCGGTG	0.532			T	IGH@	MM																																p.V1190L		.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1-664	0			c.G3568C						.						101	93	96					4																	1977074		2203	4300	6503	SO:0001583	missense	7468	exon20			AAAACGGTCTGCC	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"Zinc fingers, PHD-type"	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.3568G>C	4.37:g.1977074G>C	ENSP00000372351:p.Val1190Leu	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	111	24	NM_133335	0	0	1	3	2	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.627438	0.46944	.	.	ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D;D;D;D;D	0.97066	-3.61;-3.61;-3.61;-3.61;-4.23	4.91	4.91	0.64330	Post-SET domain (2);	0.000000	0.49916	D	0.000140	D	0.93523	0.7933	L	0.42008	1.315	0.80722	D	1	B;B	0.30361	0.009;0.277	B;B	0.21151	0.012;0.033	D	0.91080	0.4899	10	0.30854	T	0.27	.	12.0537	0.53522	0.0793:0.0:0.9207:0.0	.	538;1190	A2A2T2;O96028	.;NSD2_HUMAN	L	1190;1190;1190;1190;538	ENSP00000423972:V1190L;ENSP00000372347:V1190L;ENSP00000372348:V1190L;ENSP00000372351:V1190L;ENSP00000372344:V538L	ENSP00000372344:V538L	V	+	1	0	WHSC1	1946872	1.000000	0.71417	0.974000	0.42286	0.874000	0.50279	5.102000	0.64572	2.719000	0.93026	0.655000	0.94253	GTC	.		0.532	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		C	1977074	G	C	1977074	3	2	142	1	0	0	0	0	1	0	0	0	17395	1261	44	4	3718	4	WHSC1	4	1977074	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		1977074	189177202	31	12667											
WDR19	57728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	39205336	39205336	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaccgaacctctgctgctgaAagcatggtaagaattctaat	13	10	9	9	1	2	2	0	1	2	1	2	4	2	2	2	1	4	4	2	1	5	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:39205336A>C	ENST00000399820.3	+	7	751	c.597A>C	c.(595-597)gaA>gaC	p.E199D	WDR19_ENST00000288634.7_Missense_Mutation_p.E39D|WDR19_ENST00000506503.1_Missense_Mutation_p.E199D	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	199					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						CTGCTGCTGAAAGCATGGTAA	0.353																																					p.E199D		.											.	WDR19-67	0			c.A597C						.						92	83	86					4																	39205336		1872	4111	5983	SO:0001583	missense	57728	exon7			TGCTGAAAGCATG	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"WD repeat domain containing", "Intraflagellar transport homologs"	18340	protein-coding gene	gene with protein product	"intraflagellar transport 144 homolog (Chlamydomonas)"	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.597A>C	4.37:g.39205336A>C	ENSP00000382717:p.Glu199Asp	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	66	21	NM_025132	0	0	0	0	0	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.488399	0.44249	.	.	ENSG00000157796	ENST00000399820;ENST00000509560;ENST00000512112;ENST00000288634;ENST00000506503;ENST00000399836	T;T;T;T	0.66099	3.42;2.2;-0.19;3.42	5.64	1.62	0.23740	WD40 repeat-like-containing domain (1);	0.134922	0.64402	D	0.000003	T	0.51941	0.1704	M	0.64080	1.96	0.38720	D	0.953425	B;B	0.19445	0.002;0.036	B;B	0.20767	0.007;0.031	T	0.38714	-0.9648	10	0.23891	T	0.37	-17.3314	6.2227	0.20691	0.6749:0.1242:0.2008:0.0	.	199;199	Q8NEZ3;D6R9P6	WDR19_HUMAN;.	D	199;140;39;39;199;198	ENSP00000382717:E199D;ENSP00000426918:E140D;ENSP00000288634:E39D;ENSP00000423491:E199D	ENSP00000288634:E39D	E	+	3	2	WDR19	38881731	1.000000	0.71417	0.974000	0.42286	0.955000	0.61496	0.886000	0.28241	0.111000	0.17947	0.455000	0.32223	GAA	.		0.353	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			C	39205336	A	C	39205336	3	2	142	1	0	0	0	0	1	0	0	0	17312	11	1	5	623	5	WDR19	4	39205336	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	37228262	39205336	151948940	32	12668											
EXOC1	55763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	56737307	56737307	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcatataaaggcccttcAggaaggagatcttgcttctt	11	12	10	8	0	4	1	2	0	2	1	4	3	4	2	1	4	1	1	1	4	4	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:56737307A>C	ENST00000381295.2	+	7	1220	c.872A>C	c.(871-873)cAg>cCg	p.Q291P	EXOC1_ENST00000349598.6_Missense_Mutation_p.Q291P|EXOC1_ENST00000346134.7_Missense_Mutation_p.Q291P	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	291					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					AAGGCCCTTCAGGAAGGAGAT	0.453																																					p.Q291P		.											.	EXOC1-950	0			c.A872C						.						95	83	87					4																	56737307		2203	4300	6503	SO:0001583	missense	55763	exon7			CCCTTCAGGAAGG	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.872A>C	4.37:g.56737307A>C	ENSP00000370695:p.Gln291Pro	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	53	18	NM_018261	0	0	0	0	0	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.604708	0.46423	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.97	4.77	0.60923	.	0.224009	0.46758	D	0.000269	T	0.57489	0.2057	L	0.53249	1.67	0.54753	D	0.999985	P;P	0.47191	0.891;0.626	P;P	0.46885	0.466;0.53	T	0.54200	-0.8329	9	0.30854	T	0.27	.	12.5014	0.55957	0.8746:0.0:0.0:0.1254	.	291;291	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	P	291	.	ENSP00000326514:Q291P	Q	+	2	0	EXOC1	56432064	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	5.837000	0.69381	1.053000	0.40415	-0.480000	0.04831	CAG	.		0.453	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56737307	A	C	56737307	3	2	142	1	0	0	0	0	1	0	0	0	5314	188	7	5	894	5	EXOC1	4	56737307	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	17531971	56737307	134416969	33	12669											
DSPP	1834	bcgsc.ca	37	chr4	88536142	88536142	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcagtgacagcagtgatagTagtgacagcagcaacagcag	15	5	13	8	0	0	3	0	3	0	0	0	3	0	3	0	0	6	6	0	0	3	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:88536142T>C	ENST00000282478.7	+	4	2361	c.2328T>C	c.(2326-2328)agT>agC	p.S776S	DSPP_ENST00000399271.1_Silent_p.S776S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	776	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgatagtagtgacagca	0.507																																					p.S776S													.	DSPP-90	0			c.T2328C						.						85	96	92					4																	88536142		1664	2989	4653	SO:0001819	synonymous_variant	1834	exon5			TGATAGTAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2328T>C	4.37:g.88536142T>C		Somatic	342	7		WXS	Illumina HiSeq	Phase_1	312	27	NM_014208	0	0	0	0	0	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.507	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88536142	T	C	88536142	2	2	142	1	0	0	0	0	0	0	0	1	4793	1635	57	3		3	DSPP	4	88536142	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	31798835	88536142	102618134	34	12670											
SMARCA5	8467	broad.mit.edu	37	chr4	144445524	144445524	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attttcatcttaacagttacCgacaccgtagaacagagcaa	15	10	6	10	2	2	2	1	0	1	2	2	3	2	2	2	0	4	3	2	0	5	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:144445524C>T	ENST00000283131.3	+	4	886	c.424C>T	c.(424-426)Cga>Tga	p.R142*		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	142					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					TAACAGTTACCGACACCGTAG	0.383																																					p.R142X													.	SMARCA5-227	0			c.C424T						.						88	87	87					4																	144445524		2203	4300	6503	SO:0001587	stop_gained	8467	exon4			AGTTACCGACACC	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.424C>T	4.37:g.144445524C>T	ENSP00000283131:p.Arg142*	Somatic	506	1		WXS	Illumina HiSeq	Phase_I	294	4	NM_003601	0	0	0	0	0		Nonsense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	C	40	8.410910	0.98799	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	.	.	.	5.75	3.81	0.43845	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.783	16.3196	0.82941	0.2523:0.7477:0.0:0.0	.	.	.	.	X	142;85;85	.	ENSP00000283131:R142X	R	+	1	2	SMARCA5	144664974	0.991000	0.36638	1.000000	0.80357	0.749000	0.42624	2.926000	0.48892	1.395000	0.46643	0.591000	0.81541	CGA	.		0.383	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			T	144445524	C	T	144445524	4	4	142	1	0	0	0	0	0	1	0	0	14803	644	23	1	438	1	SMARCA5	4	144445524	Nonsense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	55909382	144445524	46708752	35	12671											
DDX60L	91351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	169315621	169315621	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaaatttacctaccctaaTaagcccttttacaaagagta	17	11	4	9	0	0	2	0	0	0	2	0	2	0	2	3	0	4	1	3	0	9	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:169315621T>A	ENST00000511577.1	-	28	4052	c.3805A>T	c.(3805-3807)Att>Ttt	p.I1269F	DDX60L_ENST00000505890.1_Missense_Mutation_p.I1270F|DDX60L_ENST00000260184.7_Missense_Mutation_p.I1269F			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1269	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CCTACCCTAATAAGCCCTTTT	0.323																																					p.I1269F		.											.	DDX60L-69	0			c.A3805T						.						67	62	63					4																	169315621		1803	4068	5871	SO:0001583	missense	91351	exon28			CCCTAATAAGCCC	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3805A>T	4.37:g.169315621T>A	ENSP00000422423:p.Ile1269Phe	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	46	12	NM_001012967	0	0	0	0	0	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.62|13.62	2.293047|2.293047	0.40594|0.40594	.|.	.|.	ENSG00000181381|ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890|ENST00000514580	T;T;T|.	0.59224|.	0.28;0.28;0.28|.	3.16|3.16	1.95|1.95	0.26073|0.26073	Helicase, C-terminal (3);|.	0.000000|.	0.36591|.	U|.	0.002501|.	T|T	0.60183|0.60183	0.2249|0.2249	M|M	0.87682|0.87682	2.9|2.9	0.09310|0.09310	N|N	0.999999|0.999999	D;D|.	0.71674|.	0.994;0.998|.	D;D|.	0.65773|.	0.922;0.938|.	T|T	0.52961|0.52961	-0.8505|-0.8505	10|5	0.66056|.	D|.	0.02|.	.|.	7.0872|7.0872	0.25264|0.25264	0.0:0.118:0.0:0.882|0.0:0.118:0.0:0.882	.|.	1270;1269|.	D6R906;Q5H9U9|.	.;DDX6L_HUMAN|.	F|F	1269;1269;1270|156	ENSP00000260184:I1269F;ENSP00000422423:I1269F;ENSP00000422202:I1270F|.	ENSP00000260184:I1269F|.	I|Y	-|-	1|2	0|0	DDX60L|DDX60L	169552196|169552196	0.721000|0.721000	0.28007|0.28007	0.002000|0.002000	0.10522|0.10522	0.093000|0.093000	0.18481|0.18481	1.244000|1.244000	0.32778|0.32778	0.248000|0.248000	0.21435|0.21435	0.383000|0.383000	0.25322|0.25322	ATT|TAT	.		0.323	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169315621	T	A	169315621	3	1	142	1	0	0	0	0	1	0	0	0	4385	1406	49	5	1359	5	DDX60L	4	169315621	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	24870097	169315621	21838655	36	12672											
SSBP2	23635	ucsc.edu	37	chr5	80724477	80724477	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttggagtgcccggttgattaCtcaggctcatattattggga	8	14	12	7	1	2	1	2	1	0	0	2	3	2	3	1	4	2	2	1	4	3	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr5:80724477C>T	ENST00000320672.4	-	16	1193	c.983G>A	c.(982-984)aGt>aAt	p.S328N	SSBP2_ENST00000509053.1_Intron|SSBP2_ENST00000505980.1_Missense_Mutation_p.S308N|SSBP2_ENST00000510060.1_5'UTR|SSBP2_ENST00000514493.1_Missense_Mutation_p.S298N|SSBP2_ENST00000515395.1_Missense_Mutation_p.S306N	NM_001256732.1|NM_001256733.1|NM_012446.3	NP_001243661.1|NP_001243662.1|NP_036578.2	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2	328					regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)		SSBP2/JAK2(4)	central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		CGGTTGATTACTCAGGCTCAT	0.368																																					p.S336N													.	SSBP2-223	0			c.G1007A						.						78	79	79					5																	80724477		2203	4299	6502	SO:0001583	missense	23635	exon16			TGATTACTCAGGC	AF077048	CCDS4056.1, CCDS58960.1, CCDS58961.1, CCDS58962.1, CCDS58963.1, CCDS75268.1	5q14.1	2012-05-25	2001-11-28		ENSG00000145687	ENSG00000145687			15831	protein-coding gene	gene with protein product		607389	"single-stranded DNA-binding protein 2"			11230166, 11042152	Standard	NM_001256732		Approved	HSPC116	uc003khp.4	P81877	OTTHUMG00000119039	ENST00000320672.4:c.983G>A	5.37:g.80724477C>T	ENSP00000322977:p.Ser328Asn	Somatic	56	0		WXS	Illumina HiSeq		31	4	NM_001256732	0	0	12	12	0	B2R5W1|B7Z1J2|B7Z2L9|B7Z665|D6RH18|E9PB74|E9PDA8|Q8N2Q2|Q9BWW6|Q9Y4T7	Missense_Mutation	SNP	ENST00000320672.4	37	CCDS4056.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795107	0.50208	.	.	ENSG00000145687	ENST00000320672;ENST00000514493;ENST00000380182;ENST00000504985;ENST00000512923;ENST00000505980;ENST00000515395	.	.	.	5.65	5.65	0.86999	.	0.076218	0.85682	D	0.000000	T	0.39091	0.1065	N	0.05574	-0.02	0.42256	D	0.991994	B;B;B;B;B	0.20164	0.009;0.005;0.003;0.017;0.042	B;B;B;B;B	0.22880	0.032;0.042;0.014;0.018;0.026	T	0.33059	-0.9883	9	0.08179	T	0.78	-14.1851	20.096	0.97843	0.0:1.0:0.0:0.0	.	306;308;281;306;328	E9PB74;B7Z1J2;A6ND70;B7Z665;P81877	.;.;.;.;SSBP2_HUMAN	N	328;298;281;242;231;308;306	.	ENSP00000322977:S328N	S	-	2	0	SSBP2	80760233	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.017000	0.49615	2.819000	0.97034	0.650000	0.86243	AGT	.		0.368	SSBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239249.1	NM_012446		T	80724477	C	T	80724477	3	4	142	1	0	0	0	0	1	0	0	0	15212	565	20	2	110	2	SSBP2	5	80724477	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		80724477	100190783	37	12673											
DMXL1	1657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	118479556	118479556	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatatgttggtgaagtcttTaacatcgtcagtcaacaatc	14	13	7	7	1	3	1	2	1	1	0	5	1	3	1	0	1	2	1	0	1	6	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr5:118479556T>C	ENST00000311085.8	+	14	2477	c.2397T>C	c.(2395-2397)ttT>ttC	p.F799F	DMXL1_ENST00000539542.1_Silent_p.F799F	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	799										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GTGAAGTCTTTAACATCGTCA	0.299																																					p.F799F		.											.	DMXL1-92	0			c.T2397C						.						110	116	114					5																	118479556		2201	4299	6500	SO:0001819	synonymous_variant	1657	exon14			AGTCTTTAACATC	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2397T>C	5.37:g.118479556T>C		Somatic	601	1		WXS	Illumina HiSeq	Phase_I	303	97	NM_005509	0	0	0	0	0		Silent	SNP	ENST00000311085.8	37	CCDS4125.1																																																																																			.		0.299	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		C	118479556	T	C	118479556	2	2	142	1	0	0	0	0	0	0	0	1	4605	1751	61	3		3	DMXL1	5	118479556	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	37755079	118479556	62435704	38	12674											
MEGF10	84466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	126705695	126705695	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agggaccaactgctccagtgGtaagtttccacctgctgttg	8	11	11	11	0	0	0	0	0	0	0	2	1	2	1	4	2	3	5	4	2	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr5:126705695G>T	ENST00000274473.6	+	6	679		c.e6+1		MEGF10_ENST00000508365.1_Splice_Site|MEGF10_ENST00000503335.2_Splice_Site|MEGF10_ENST00000418761.2_Splice_Site	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10						homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TGCTCCAGTGGTAAGTTTCCA	0.537																																					.		.											.	MEGF10-94	0			c.412+1G>T						.						176	140	152					5																	126705695		2203	4300	6503	SO:0001630	splice_region_variant	84466	exon5			CCAGTGGTAAGTT	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.412+1G>T	5.37:g.126705695G>T		Somatic	33	0		WXS	Illumina HiSeq	Phase_I	42	13	NM_001256545	0	0	0	0	0	Q68DE5|Q8WUL3	Splice_Site	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749510	0.89753	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1131	0.93326	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MEGF10	126733594	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.844000	0.99494	2.506000	0.84524	0.558000	0.71614	.	.		0.537	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	Intron	T	126705695	G	T	126705695	5	4	142	1	0	0	0	0	0	0	1	0	9485	1275	44	4	427	4	MEGF10	5	126705695	Splice_Site	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	8226139	126705695	54209565	39	12675											
HFE	3077	broad.mit.edu;bcgsc.ca	37	chr6	26091332	26091332	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aaaatcacaaccacagcaagGgtatgtggagagggggcctc	14	5	13	9	0	1	1	1	0	0	1	2	2	1	1	2	4	2	2	2	4	5	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr6:26091332G>C	ENST00000357618.5	+	2	462	c.340G>C	c.(340-342)Gag>Cag	p.E114Q	HFE_ENST00000488199.1_Intron|HFE_ENST00000470149.1_Splice_Site_p.E114Q|HFE_ENST00000336625.8_Splice_Site_p.V114L|HFE_ENST00000309234.6_Splice_Site_p.E114Q|HFE_ENST00000349999.4_Intron|HFE_ENST00000397022.3_Splice_Site_p.E91Q|HFE_ENST00000353147.5_Intron|HFE_ENST00000317896.7_Splice_Site_p.V114L|HFE_ENST00000461397.1_Splice_Site_p.E114Q|HFE_ENST00000352392.4_Intron	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	114	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCACAGCAAGGGTATGTGGAG	0.488									Hemochromatosis																												p.E114Q													.	HFE-90	0			c.G340C						.						104	106	105					6																	26091332		2203	4300	6503	SO:0001630	splice_region_variant	3077	exon2	Familial Cancer Database		AGCAAGGGTATGT		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"Immunoglobulin superfamily / C1-set domain containing"	4886	protein-coding gene	gene with protein product	"high Fe"	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.340+1G>C	6.37:g.26091332G>C		Somatic	73	1		WXS	Illumina HiSeq	Phase_I	69	24	NM_139006	0	0	1	1	0	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.68|13.68	2.309910|2.309910	0.40895|0.40895	.|.	.|.	ENSG00000010704|ENSG00000010704	ENST00000397022;ENST00000535098;ENST00000539147;ENST00000357618;ENST00000470149;ENST00000461397;ENST00000309234|ENST00000317896;ENST00000336625	D;D;D;D;D|T;T	0.89617|0.02737	-2.54;-2.54;-2.54;-2.54;-2.54|4.57;4.18	4.98|4.98	4.1|4.1	0.47936|0.47936	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	0.860579|.	0.09959|.	N|.	0.733694|.	T|T	0.02047|0.02047	0.0064|0.0064	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	B;B;B;B|B;B	0.19817|0.27559	0.039;0.031;0.006;0.011|0.181;0.115	B;B;B;B|B;B	0.17979|0.30943	0.02;0.007;0.011;0.013|0.051;0.122	T|T	0.29027|0.29027	-1.0025|-1.0025	10|9	0.87932|0.54805	D|T	0|0.06	.|.	9.3734|9.3734	0.38268|0.38268	0.0977:0.0:0.9023:0.0|0.0977:0.0:0.9023:0.0	.|.	114;114;91;114|114;114	Q6B0J5;Q30201-3;Q30201-5;Q30201|Q30201-7;Q30201-10	.;.;.;HFE_HUMAN|.;.	Q|L	91;114;9;114;114;114;114|114	ENSP00000380217:E91Q;ENSP00000417404:E114Q;ENSP00000419725:E114Q;ENSP00000420802:E114Q;ENSP00000311698:E114Q|ENSP00000313776:V114L;ENSP00000337819:V114L	ENSP00000311698:E114Q|ENSP00000313776:V114L	E|V	+|+	1|1	0|0	HFE|HFE	26199311|26199311	0.978000|0.978000	0.34361|0.34361	0.984000|0.984000	0.44739|0.44739	0.976000|0.976000	0.68499|0.68499	0.989000|0.989000	0.29629|0.29629	1.308000|1.308000	0.44962|0.44962	0.655000|0.655000	0.94253|0.94253	GAG|GTG	.		0.488	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1		Missense_Mutation	C	26091332	G	C	26091332	5	2	142	1	0	0	0	0	0	0	1	0	7102	1246	43	4	346	4	HFE	6	26091332	Splice_Site	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		26091332	145023735	40	12676											
ORC3L	23595	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	88362905	88362905	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttaagtcttattgtgaaaAccaccttggcagcacagcta	12	13	7	9	0	1	1	0	1	1	0	1	1	1	1	2	1	3	3	2	1	5	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr6:88362905A>T	ENST00000392844.3	+	14	1502	c.1454A>T	c.(1453-1455)aAc>aTc	p.N485I	ORC3_ENST00000257789.4_Missense_Mutation_p.N485I|ORC3_ENST00000417380.2_3'UTR|ORC3_ENST00000546266.1_Missense_Mutation_p.N342I	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	485					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						TATTGTGAAAACCACCTTGGC	0.418																																					p.N485I													.	ORC3-206	0			c.A1454T						.						102	101	101					6																	88362905		2203	4300	6503	SO:0001583	missense	23595	exon14			GTGAAAACCACCT	AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"origin recognition complex, subunit 3 (yeast homolog)-like", "origin recognition complex, subunit 3-like (yeast)", "origin recognition complex, subunit 3 honolog (yeast)"	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.1454A>T	6.37:g.88362905A>T	ENSP00000376586:p.Asn485Ile	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	79	23	NM_181837	0	0	6	11	5	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Missense_Mutation	SNP	ENST00000392844.3	37	CCDS43486.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.081722	0.55861	.	.	ENSG00000135336	ENST00000392844;ENST00000257789;ENST00000546266	T;T;T	0.12147	3.07;3.07;2.71	5.71	5.71	0.89125	.	0.141687	0.64402	D	0.000009	T	0.03390	0.0098	N	0.14661	0.345	0.24464	N	0.994423	B;B;B;B;B	0.31290	0.009;0.318;0.009;0.004;0.029	B;B;B;B;B	0.28849	0.014;0.095;0.005;0.005;0.088	T	0.30851	-0.9964	10	0.36615	T	0.2	-12.2882	13.939	0.64043	1.0:0.0:0.0:0.0	.	485;485;423;485;485	B7ZAI3;B7Z8A5;B4E014;Q9UBD5;Q9UBD5-2	.;.;.;ORC3_HUMAN;.	I	485;485;342	ENSP00000376586:N485I;ENSP00000257789:N485I;ENSP00000444695:N342I	ENSP00000257789:N485I	N	+	2	0	ORC3	88419624	1.000000	0.71417	0.995000	0.50966	0.903000	0.53119	4.074000	0.57577	2.171000	0.68590	0.533000	0.62120	AAC	.		0.418	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2			T	88362905	A	T	88362905	3	4	142	1	0	0	0	0	1	0	0	0	11289	43	2	5	1508	5	ORC3L	6	88362905	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	62271573	88362905	82752162	41	12677											
PLEKHG1	57480	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	151161158	151161158	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctatagtaatggagagttagCagatttctgtctcccaccag	11	12	9	9	0	2	2	0	0	2	2	3	3	2	2	2	1	1	3	2	1	4	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr6:151161158C>T	ENST00000358517.2	+	16	3495	c.3284C>T	c.(3283-3285)gCa>gTa	p.A1095V	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.A1095V			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1095							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)		GGAGAGTTAGCAGATTTCTGT	0.488																																					p.A1095V													.	PLEKHG1-92	0			c.C3284T						.						63	63	63					6																	151161158		2203	4300	6503	SO:0001583	missense	57480	exon17			AGTTAGCAGATTT	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.3284C>T	6.37:g.151161158C>T	ENSP00000351318:p.Ala1095Val	Somatic	117	1		WXS	Illumina HiSeq	Phase_I	152	49	NM_001029884	0	0	0	0	0	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803848	0.50315	.	.	ENSG00000120278	ENST00000367328;ENST00000358517	T;T	0.67345	-0.26;-0.26	5.81	4.91	0.64330	.	0.092382	0.85682	N	0.000000	T	0.44393	0.1291	L	0.41236	1.265	0.45541	D	0.998498	B;B	0.20052	0.041;0.041	B;B	0.17722	0.019;0.019	T	0.48570	-0.9024	10	0.52906	T	0.07	.	14.0507	0.64734	0.0:0.925:0.0:0.075	.	902;1095	Q5EBL9;Q9ULL1	.;PKHG1_HUMAN	V	1095	ENSP00000356297:A1095V;ENSP00000351318:A1095V	ENSP00000351318:A1095V	A	+	2	0	PLEKHG1	151202851	0.925000	0.31364	0.994000	0.49952	0.938000	0.57974	1.969000	0.40510	1.392000	0.46585	0.655000	0.94253	GCA	.		0.488	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			T	151161158	C	T	151161158	3	4	142	1	0	0	0	0	1	0	0	0	12094	710	25	2	3342	2	PLEKHG1	6	151161158	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	62798253	151161158	19953909	42	12678											
HEATR2	54919	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	769345	769345	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatcgggcccctgatgcAgaccatctcccaccagcact	8	8	8	17	1	2	3	0	2	2	1	4	3	2	3	5	1	2	2	5	1	0	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr7:769345A>C	ENST00000297440.6	+	2	661	c.641A>C	c.(640-642)cAg>cCg	p.Q214P	PRKAR1B_ENST00000403562.1_5'Flank|PRKAR1B_ENST00000488474.1_5'Flank|HEATR2_ENST00000438961.1_3'UTR|PRKAR1B_ENST00000537384.1_5'Flank|HEATR2_ENST00000313147.5_Missense_Mutation_p.Q214P	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	214						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		CCCCTGATGCAGACCATCTCC	0.622																																					p.Q214P													.	HEATR2-69	0			c.A641C						.						79	63	69					7																	769345		2203	4300	6503	SO:0001583	missense	54919	exon2			TGATGCAGACCAT	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.641A>C	7.37:g.769345A>C	ENSP00000297440:p.Gln214Pro	Somatic	70	1		WXS	Illumina HiSeq	Phase_I	98	23	NM_017802	0	0	4	4	0	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	37	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.146749	0.57151	.	.	ENSG00000164818	ENST00000297440;ENST00000313147	T;T	0.18502	2.21;2.21	5.06	5.06	0.68205	Armadillo-like helical (1);Armadillo-type fold (1);	0.285236	0.28114	N	0.016547	T	0.18045	0.0433	L	0.45137	1.4	0.52501	D	0.99995	D	0.57899	0.981	B	0.44044	0.439	T	0.02774	-1.1112	10	0.27082	T	0.32	-19.4779	14.8182	0.70050	1.0:0.0:0.0:0.0	.	214	Q86Y56	HEAT2_HUMAN	P	214	ENSP00000297440:Q214P;ENSP00000321451:Q214P	ENSP00000297440:Q214P	Q	+	2	0	HEATR2	735871	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.233000	0.65337	1.904000	0.55121	0.460000	0.39030	CAG	.		0.622	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802		C	769345	A	C	769345	3	2	142	1	0	0	0	0	1	0	0	0	7049	188	7	5	647	5	HEATR2	7	769345	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10		769345	158369318	43	12679											
SDK1	221935	broad.mit.edu;bcgsc.ca	37	chr7	4056809	4056809	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccttcgtggcgcaggtaccgCctggctggccttcccggaga	4	8	14	15	4	0	1	0	0	0	1	2	2	1	1	5	5	1	3	5	5	1	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr7:4056809C>T	ENST00000404826.2	+	17	2566	c.2427C>T	c.(2425-2427)cgC>cgT	p.R809R	SDK1_ENST00000389531.3_Silent_p.R809R	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	809	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCAGGTACCGCCTGGCTGGCC	0.567																																					p.R809R													.	SDK1-138	0			c.C2427T						.						54	47	49					7																	4056809		2203	4300	6503	SO:0001819	synonymous_variant	221935	exon17			GTACCGCCTGGCT	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	19307	protein-coding gene	gene with protein product		607216	"sidekick homolog 1 (chicken)", "sidekick homolog 1, cell adhesion molecule (chicken)"			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.2427C>T	7.37:g.4056809C>T		Somatic	97	2		WXS	Illumina HiSeq	Phase_I	114	62	NM_152744	0	0	0	0	0	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			.		0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4056809	C	T	4056809	2	4	142	1	0	0	0	0	0	0	0	1	14000	726	26	2		2	SDK1	7	4056809	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	3287464	4056809	155081854	44	12680											
CDK13	8621	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	40134339	40134339	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgaatatagccatggtccTattgcagtcctggcaaacag	11	12	9	9	0	0	1	0	1	0	0	2	1	2	1	3	2	3	2	3	2	5	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr7:40134339T>C	ENST00000181839.4	+	14	4904	c.4299T>C	c.(4297-4299)ccT>ccC	p.P1433P	CDK13_ENST00000340829.5_Silent_p.P1373P	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	1433					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						GCCATGGTCCTATTGCAGTCC	0.463																																					p.P1433P													.	CDK13-548	0			c.T4299C						.						125	110	115					7																	40134339		2203	4300	6503	SO:0001819	synonymous_variant	8621	exon14			TGGTCCTATTGCA	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.4299T>C	7.37:g.40134339T>C		Somatic	107	2		WXS	Illumina HiSeq	Phase_I	147	35	NM_003718	0	0	1	2	1	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Silent	SNP	ENST00000181839.4	37	CCDS5461.1																																																																																			.		0.463	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		C	40134339	T	C	40134339	2	2	142	1	0	0	0	0	0	0	0	1	3135	1509	53	3		3	CDK13	7	40134339	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	36077530	40134339	119004324	45	12681											
PIK3CG	5294	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	106508582	106508582	+	Frame_Shift_Del	DEL	C	C	-																															gcggaggtggccagccgcgaCcccaagctctacgccatgca																								rs377396894		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr7:106508582delC	ENST00000359195.3	+	2	886	c.576delC	c.(574-576)gacfs	p.D192fs	PIK3CG_ENST00000440650.2_Frame_Shift_Del_p.D192fs|PIK3CG_ENST00000496166.1_Frame_Shift_Del_p.D192fs	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	192					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CCAGCCGCGACCCCAAGCTCT	0.617																																					p.D192fs		.											.	PIK3CG-1316	0			c.576delC						.						70	74	73					7																	106508582		2203	4300	6503	SO:0001589	frameshift_variant	5294	exon2			.		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"phosphoinositide-3-kinase, catalytic, gamma polypeptide"				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.576delC	7.37:g.106508582delC	ENSP00000352121:p.Asp192fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	82	22	NM_002649	0	0	0	0	0	A4D0Q6|Q8IV23|Q9BZC8	Frame_Shift_Del	DEL	ENST00000359195.3	37	CCDS5739.1																																																																																			.		0.617	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			-	106508582	C	-	106508582	7	5	142	1	0	1	0	1	0	0	0	0	11942	506	18	0	578	0	PIK3CG	7	106508582	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M8-01A-11D-A31X-10	66374243	106508582	52630081	46	12682											
ENTPD4	9583	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	23294705	23294705	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggatttcatctttaatGtctaggggtaggcaggggtc	7	14	14	6	0	3	0	1	0	2	0	4	1	3	1	0	6	1	3	0	6	3	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr8:23294705G>A	ENST00000358689.4	-	10	1351	c.1116C>T	c.(1114-1116)gaC>gaT	p.D372D	ENTPD4_ENST00000417069.2_Silent_p.D364D|ENTPD4_ENST00000521321.1_5'Flank|ENTPD4_ENST00000356206.6_Silent_p.D364D	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	372					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		CATCTTTAATGTCTAGGGGTA	0.458																																					p.D372D													.	ENTPD4-92	0			c.C1116T						.						128	102	111					8																	23294705		2203	4300	6503	SO:0001819	synonymous_variant	9583	exon10			TTTAATGTCTAGG	AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"lysosomal apyrase-like 1"	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.1116C>T	8.37:g.23294705G>A		Somatic	155	1		WXS	Illumina HiSeq	Phase_I	140	37	NM_004901	0	0	2	4	2	D3DSS3|O15092	Silent	SNP	ENST00000358689.4	37	CCDS6041.1																																																																																			.		0.458	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901		A	23294705	G	A	23294705	2	1	142	1	0	0	0	0	0	0	0	1	5154	1368	48	2		2	ENTPD4	8	23294705	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		23294705	123069317	47	12683											
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	37729061	37729061	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	attgtccagggatgtgccagGaggcgggcttggactcccat	7	9	15	10	1	0	0	0	0	0	0	2	3	2	3	3	5	1	1	3	5	0	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr8:37729061G>C	ENST00000330843.4	-	4	3271	c.3259C>G	c.(3259-3261)Cct>Gct	p.P1087A	RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000287263.4_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	1087					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)			GATGTGCCAGGAGGCGGGCTT	0.552											OREG0018713	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1087A		.											.	RAB11FIP1-92	0			c.C3259G						.						190	202	198					8																	37729061		2203	4300	6503	SO:0001583	missense	80223	exon4			TGCCAGGAGGCGG	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.3259C>G	8.37:g.37729061G>C	ENSP00000331342:p.Pro1087Ala	Somatic	45	0	872	WXS	Illumina HiSeq	Phase_I	69	30	NM_001002814	0	0	0	0	0	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.368051	0.24771	.	.	ENSG00000156675	ENST00000330843	T	0.11712	2.75	5.24	0.717	0.18196	.	0.271342	0.26499	N	0.024035	T	0.05823	0.0152	L	0.36672	1.1	0.09310	N	0.999994	P;B	0.37101	0.582;0.057	B;B	0.33392	0.163;0.02	T	0.32481	-0.9905	10	0.19590	T	0.45	-8.4888	3.2151	0.06696	0.4377:0.2192:0.3431:0.0	.	416;1087	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	A	1087	ENSP00000331342:P1087A	ENSP00000331342:P1087A	P	-	1	0	RAB11FIP1	37848219	0.746000	0.28272	0.013000	0.15412	0.003000	0.03518	1.420000	0.34804	0.206000	0.20587	-0.136000	0.14681	CCT	.		0.552	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		C	37729061	G	C	37729061	3	2	142	1	0	0	0	0	1	0	0	0	12925	1174	41	4	604	4	RAB11FIP1	8	37729061	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	14434356	37729061	108634961	48	12684											
EFCAB1	79645	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	49647695	49647695	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtgtccgtcagcttctgcaGtttcttgcggttcatgtctg	3	16	12	10	2	5	0	2	0	3	0	6	0	6	0	1	2	3	4	1	2	0	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr8:49647695G>A	ENST00000262103.3	-	1	96	c.16C>T	c.(16-18)Ctg>Ttg	p.L6L	EFCAB1_ENST00000433756.1_Silent_p.L6L|EFCAB1_ENST00000523092.1_Silent_p.L6L|EFCAB1_ENST00000521002.1_5'UTR	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	6							calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				AGCTTCTGCAGTTTCTTGCGG	0.627																																					p.L6L													.	EFCAB1-90	0			c.C16T						.						171	157	162					8																	49647695		2203	4300	6503	SO:0001819	synonymous_variant	79645	exon1			TCTGCAGTTTCTT		CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.16C>T	8.37:g.49647695G>A		Somatic	70	1		WXS	Illumina HiSeq	Phase_I	60	22	NM_024593	0	0	0	0	0	B4DSB4|E7EVN7	Silent	SNP	ENST00000262103.3	37	CCDS6145.1																																																																																			.		0.627	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		A	49647695	G	A	49647695	2	1	142	1	0	0	0	0	0	0	0	1	4944	1020	36	2		2	EFCAB1	8	49647695	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	11918634	49647695	96716327	49	12685											
RUNX1T1	862	ucsc.edu;bcgsc.ca	37	chr8	93088202	93088202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgttccttaccttgacaatAttcaaagttcccttttttcc	8	18	3	12	0	1	1	1	1	0	0	4	1	4	1	4	0	1	2	4	0	4	9			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr8:93088202A>G	ENST00000523629.1	-	2	533	c.79T>C	c.(79-81)Tat>Cat	p.Y27H	RUNX1T1_ENST00000265814.3_Missense_Mutation_p.Y27H|RUNX1T1_ENST00000520724.1_Intron|RUNX1T1_ENST00000518844.1_5'UTR|RUNX1T1_ENST00000522163.1_5'UTR|RUNX1T1_ENST00000436581.2_Intron|RUNX1T1_ENST00000360348.2_Intron	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	27					fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CCTTGACAATATTCAAAGTTC	0.323																																					p.Y27H													.	RUNX1T1-1196	0			c.T79C						.						148	143	145					8																	93088202		2203	4300	6503	SO:0001583	missense	862	exon2			GACAATATTCAAA	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"Zinc fingers, MYND-type"	1535	protein-coding gene	gene with protein product		133435	"core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.79T>C	8.37:g.93088202A>G	ENSP00000428543:p.Tyr27His	Somatic	66	1		WXS	Illumina HiSeq		43	12	NM_001198628	0	0	0	0	0	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.192939	0.38707	.	.	ENSG00000079102	ENST00000523629;ENST00000265814;ENST00000518992;ENST00000519847;ENST00000522467;ENST00000517919;ENST00000520583;ENST00000523168;ENST00000521375;ENST00000520974;ENST00000518954;ENST00000520428;ENST00000518449	T;T;T	0.48201	1.46;1.46;0.82	5.48	5.48	0.80851	.	.	.	.	.	T	0.36524	0.0970	L	0.29908	0.895	0.33916	D	0.640263	B	0.30664	0.289	B	0.26094	0.066	T	0.50101	-0.8867	9	0.35671	T	0.21	33.7713	14.4227	0.67196	1.0:0.0:0.0:0.0	.	27	Q06455	MTG8_HUMAN	H	27	ENSP00000428543:Y27H;ENSP00000265814:Y27H;ENSP00000431094:Y27H	ENSP00000265814:Y27H	Y	-	1	0	RUNX1T1	93157378	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.070000	0.57548	2.210000	0.71456	0.460000	0.39030	TAT	.		0.323	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		G	93088202	A	G	93088202	3	3	142	1	0	0	0	0	1	0	0	0	13779	449	16	3	1790	3	RUNX1T1	8	93088202	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	43440507	93088202	53275820	50	12686											
GRINA	2907	broad.mit.edu	37	chr8	145065567	145065567	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtcagccagggtacccccAtggccccagcccctaccccc	6	4	9	22	1	1	0	1	0	0	0	1	0	1	0	9	3	4	1	9	3	2	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr8:145065567A>C	ENST00000313269.5	+	2	454	c.176A>C	c.(175-177)cAt>cCt	p.H59P	GRINA_ENST00000395068.4_Missense_Mutation_p.H59P	NM_000837.1	NP_000828.1	Q7Z429	LFG1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	59	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	9	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGGTACCCCCATGGCCCCAGC	0.701																																					p.H59P													.	GRINA-90	0			c.A176C						.						5	6	6					8																	145065567		2054	4104	6158	SO:0001583	missense	2907	exon2			ACCCCCATGGCCC	NM_001009184	CCDS34961.1	8q24.3	2010-03-18	2008-04-01						4589	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 3"	138251		NMDARA1		1719427, 8406459	Standard	XM_005250899		Approved	HNRGW, TMBIM3, LFG1	uc003zao.1	Q7Z429		ENST00000313269.5:c.176A>C	8.37:g.145065567A>C	ENSP00000314380:p.His59Pro	Somatic	154	6		WXS	Illumina HiSeq	Phase_I	155	14	NM_001009184	0	0	36	36	0	B3KXM7|O43836|Q8IVW7	Missense_Mutation	SNP	ENST00000313269.5	37	CCDS34961.1	.	.	.	.	.	.	.	.	.	.	A	9.808	1.182408	0.21870	.	.	ENSG00000178719	ENST00000313269;ENST00000529301;ENST00000395068;ENST00000530898;ENST00000537637	T;T;T	0.23552	1.92;1.9;1.92	4.86	4.86	0.63082	.	0.419238	0.23836	N	0.044091	T	0.12347	0.0300	N	0.03608	-0.345	0.27083	N	0.963048	B	0.02656	0.0	B	0.01281	0.0	T	0.13899	-1.0492	10	0.34782	T	0.22	-2.4157	12.7237	0.57156	1.0:0.0:0.0:0.0	.	59	Q7Z429	GRINA_HUMAN	P	59;59;59;59;40	ENSP00000314380:H59P;ENSP00000432706:H59P;ENSP00000378507:H59P	ENSP00000314380:H59P	H	+	2	0	GRINA	145137555	0.998000	0.40836	0.947000	0.38551	0.731000	0.41821	3.380000	0.52448	1.961000	0.56991	0.462000	0.41574	CAT	.		0.701	GRINA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384048.1	NM_001009184		C	145065567	A	C	145065567	3	2	142	1	0	0	0	0	1	0	0	0	6806	217	8	5	178	5	GRINA	8	145065567	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	51977365	145065567	1298455	51	12687											
DOCK8	81704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	441958	441958	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggatgaacaggagtttgtCtacaaagagcctgcaattac	13	11	10	7	0	1	2	0	1	1	1	1	4	1	4	1	2	5	2	1	2	5	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:441958C>T	ENST00000453981.1	+	42	5551	c.5439C>T	c.(5437-5439)gtC>gtT	p.V1813V	DOCK8_ENST00000469391.1_Silent_p.V1713V|DOCK8_ENST00000382329.1_Silent_p.V1280V|DOCK8_ENST00000432829.2_Silent_p.V1745V			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1813	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AGGAGTTTGTCTACAAAGAGC	0.403																																					p.V1813V		.											.	DOCK8-517	0			c.C5439T						.						111	106	108					9																	441958		2203	4300	6503	SO:0001819	synonymous_variant	81704	exon42			GTTTGTCTACAAA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.5439C>T	9.37:g.441958C>T		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	83	35	NM_203447	0	0	4	4	0	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			.		0.403	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	441958	C	T	441958	2	4	142	1	0	0	0	0	0	0	0	1	4704	900	32	2		2	DOCK8	9	441958	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		441958	140771473	52	12688											
TAF1L	138474	ucsc.edu;bcgsc.ca	37	chr9	32632528	32632528	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcttggcatttttcagggaaAggcgacgaaggtctgcatct	9	11	13	8	2	3	0	1	0	2	0	3	3	3	1	0	4	1	3	0	4	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:32632528A>G	ENST00000242310.4	-	1	3139	c.3050T>C	c.(3049-3051)cTt>cCt	p.L1017P	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1017					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTTCAGGGAAAGGCGACGAAG	0.453																																					p.L1017P													.	TAF1L-870	0			c.T3050C						.						258	244	248					9																	32632528		2203	4298	6501	SO:0001583	missense	138474	exon1			AGGGAAAGGCGAC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3050T>C	9.37:g.32632528A>G	ENSP00000418379:p.Leu1017Pro	Somatic	256	2		WXS	Illumina HiSeq		287	90	NM_153809	0	0	0	0	0	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456647	0.63401	.	.	ENSG00000122728	ENST00000242310	T	0.16457	2.34	0.479	0.479	0.16796	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.117031	0.64402	D	0.000013	T	0.42877	0.1222	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.34675	-0.9819	10	0.87932	D	0	.	5.1959	0.15236	0.9999:0.0:1.0E-4:0.0	.	1017	Q8IZX4	TAF1L_HUMAN	P	1017	ENSP00000418379:L1017P	ENSP00000418379:L1017P	L	-	2	0	TAF1L	32622528	1.000000	0.71417	0.965000	0.40720	0.794000	0.44872	5.776000	0.68924	0.426000	0.26116	0.164000	0.16699	CTT	.		0.453	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32632528	A	G	32632528	3	3	142	1	0	0	0	0	1	0	0	0	15555	72	3	3	2434	3	TAF1L	9	32632528	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	32190570	32632528	108580903	53	12689											
SHB	6461	broad.mit.edu	37	chr9	37956019	37956019	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccgcgaaggtgagggggAtgactgccgcttctcgttgc	5	9	16	11	4	1	2	0	2	1	0	3	4	2	3	2	3	2	2	2	3	1	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:37956019A>G	ENST00000377707.3	-	4	1652	c.1087T>C	c.(1087-1089)Tcc>Ccc	p.S363P	RP11-613M10.9_ENST00000540557.1_3'UTR	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	363	Mediates interaction with LAT, PTK2/FAK1, JAK1 and JAK3.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		GGTGAGGGGGATGACTGCCGC	0.602																																					p.S363P													.	SHB-92	0			c.T1087C						.						39	33	35					9																	37956019		1990	4146	6136	SO:0001583	missense	6461	exon4			AGGGGGATGACTG		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"SH2 domain containing"	10838	protein-coding gene	gene with protein product		600314	"SHB adaptor protein (a Src homology 2 protein)", "SHB (Src homology 2 domain containing) adaptor protein B"			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.1087T>C	9.37:g.37956019A>G	ENSP00000366936:p.Ser363Pro	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	86	4	NM_003028	0	0	69	69	0	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Missense_Mutation	SNP	ENST00000377707.3	37	CCDS43806.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.827960	0.50845	.	.	ENSG00000107338	ENST00000377707	T	0.36520	1.25	5.68	5.68	0.88126	.	0.117982	0.39341	N	0.001400	T	0.33760	0.0874	N	0.12182	0.205	0.80722	D	1	D	0.61697	0.99	P	0.53649	0.731	T	0.24297	-1.0164	10	0.52906	T	0.07	-16.6295	13.8702	0.63615	1.0:0.0:0.0:0.0	.	363	Q15464	SHB_HUMAN	P	363	ENSP00000366936:S363P	ENSP00000366936:S363P	S	-	1	0	SHB	37946019	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	6.114000	0.71560	2.161000	0.67846	0.460000	0.39030	TCC	.		0.602	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1			G	37956019	A	G	37956019	3	3	142	1	0	0	0	0	1	0	0	0	14300	333	12	3	454	3	SHB	9	37956019	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	5323491	37956019	103257412	54	12690											
PRKACG	5568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	71628289	71628289	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atctggatgggctggtcggcGtagaagggtgggaagcccac	8	7	18	8	2	1	1	0	0	1	1	2	3	1	3	1	6	1	2	1	6	3	1	rs140133619		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:71628289G>A	ENST00000377276.2	-	1	750	c.720C>T	c.(718-720)taC>taT	p.Y240Y		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	240	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.Y240Y(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GCTGGTCGGCGTAGAAGGGTG	0.602																																					p.Y240Y	Esophageal Squamous(110;2236 2623 32146)	.											.	PRKACG-1061	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C720T						.						70	68	68					9																	71628289		2203	4300	6503	SO:0001819	synonymous_variant	5568	exon1			GTCGGCGTAGAAG	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.720C>T	9.37:g.71628289G>A		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	91	28	NM_002732	0	0	0	0	0	O60850|Q5VZ02|Q86YI1	Silent	SNP	ENST00000377276.2	37	CCDS6625.1																																																																																			G|1.000;C|0.000		0.602	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			A	71628289	G	A	71628289	2	1	142	1	0	0	0	0	0	0	0	1	12528	1140	40	1		1	PRKACG	9	71628289	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	33672270	71628289	69585142	55	12691											
GDA	9615	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	74838062	74838062	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtgaagcccatagtgacAccacgtttttccctctcctg	9	11	8	13	1	1	3	0	2	1	1	3	3	2	3	4	0	1	1	4	0	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:74838062A>G	ENST00000358399.3	+	7	726	c.633A>G	c.(631-633)acA>acG	p.T211T	GDA_ENST00000545168.1_Silent_p.T137T|GDA_ENST00000238018.4_Silent_p.T211T|GDA_ENST00000376986.1_Intron|GDA_ENST00000477618.1_3'UTR|GDA_ENST00000376989.3_Intron	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	211					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		CCATAGTGACACCACGTTTTT	0.388																																					p.T211T													.	GDA-230	0			c.A633G						.						187	173	177					9																	74838062		2203	4300	6503	SO:0001819	synonymous_variant	9615	exon7			AGTGACACCACGT	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.633A>G	9.37:g.74838062A>G		Somatic	146	1		WXS	Illumina HiSeq	Phase_I	88	19	NM_004293	0	0	7	16	9	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Silent	SNP	ENST00000358399.3	37	CCDS6641.1																																																																																			.		0.388	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1			G	74838062	A	G	74838062	2	3	142	1	0	0	0	0	0	0	0	1	6326	146	6	3		3	GDA	9	74838062	Silent	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	3209773	74838062	66375369	56	12692											
ZNF462	58499	ucsc.edu;bcgsc.ca	37	chr9	109688639	109688639	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcaccaagtttccaatactGctctgctgaatacccaaact	13	11	4	13	0	2	1	1	1	1	0	3	1	3	1	3	0	5	3	3	0	6	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:109688639G>A	ENST00000277225.5	+	3	2735	c.2446G>A	c.(2446-2448)Gct>Act	p.A816T	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Missense_Mutation_p.A816T			Q96JM2	ZN462_HUMAN	zinc finger protein 462	816					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TTCCAATACTGCTCTGCTGAA	0.433																																					p.A816T													.	ZNF462-95	0			c.G2446A						.						81	79	80					9																	109688639		2203	4300	6503	SO:0001583	missense	58499	exon3			AATACTGCTCTGC	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.2446G>A	9.37:g.109688639G>A	ENSP00000277225:p.Ala816Thr	Somatic	126	2		WXS	Illumina HiSeq		117	30	NM_021224	0	0	0	0	0	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.310351	0.23821	.	.	ENSG00000148143	ENST00000277225;ENST00000457913	T;T	0.05996	3.36;3.81	5.87	3.01	0.34805	.	0.369247	0.28016	N	0.016934	T	0.03827	0.0108	N	0.19112	0.55	0.80722	D	1	B;B	0.20052	0.041;0.037	B;B	0.21360	0.016;0.034	T	0.48080	-0.9066	9	.	.	.	.	6.0149	0.19596	0.1469:0.0:0.4517:0.4014	.	816;816	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	T	816	ENSP00000277225:A816T;ENSP00000414570:A816T	.	A	+	1	0	ZNF462	108728460	0.183000	0.23186	0.395000	0.26283	0.986000	0.74619	0.537000	0.23144	0.377000	0.24735	0.650000	0.86243	GCT	.		0.433	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		A	109688639	G	A	109688639	3	1	142	1	0	0	0	0	1	0	0	0	17958	1319	46	2	2452	2	ZNF462	9	109688639	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	34850577	109688639	31524792	57	12693											
DNM1	1759	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130982346	130982346	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtgatgtgctggagaacaaGctgctccccctgcgcagagg	8	7	14	12	2	0	3	0	1	0	2	1	4	1	3	2	2	5	4	2	2	2	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:130982346G>A	ENST00000372923.3	+	5	761	c.669G>A	c.(667-669)aaG>aaA	p.K223K	DNM1_ENST00000486160.1_Silent_p.K223K|DNM1_ENST00000393594.3_Silent_p.K223K|DNM1_ENST00000341179.7_Silent_p.K223K|DNM1_ENST00000475805.1_Silent_p.K223K	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	223	Dynamin-type G.				endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						TGGAGAACAAGCTGCTCCCCC	0.647																																					.	GBM(113;146 1575 2722 28670 29921)												.	DNM1-228	0			.						.						95	77	83					9																	130982346		2203	4300	6503	SO:0001819	synonymous_variant	1759	.			GAACAAGCTGCTC	L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"Pleckstrin homology (PH) domain containing"	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.669G>A	9.37:g.130982346G>A		Somatic	154	0		WXS	Illumina HiSeq	Phase_I	153	46	.	0	0	0	4	4	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Silent	SNP	ENST00000372923.3	37	CCDS6895.1																																																																																			.		0.647	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408		A	130982346	G	A	130982346	2	1	142	1	0	0	0	0	0	0	0	1	4681	962	34	2		2	DNM1	9	130982346	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	21293707	130982346	10231085	58	12694											
URM1	81605	broad.mit.edu	37	chr9	131151640	131151640	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctgcccttgctgcttcaGtgggaaagcgttgggcctct	4	11	12	14	1	2	0	1	0	1	0	2	1	2	1	4	2	4	3	4	2	1	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:131151640G>T	ENST00000452446.1	+	4	351	c.289G>T	c.(289-291)Gtg>Ttg	p.V97L	URM1_ENST00000372850.1_3'UTR|URM1_ENST00000483206.1_3'UTR|URM1_ENST00000372853.4_Intron|RP11-339B21.11_ENST00000609303.1_lincRNA	NM_001135947.2	NP_001129419.1			ubiquitin related modifier 1											cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	5						TGCTGCTTCAGTGGGAAAGCG	0.617																																					p.V97L													.	URM1-90	0			c.G289T						.						51	48	49					9																	131151640		1327	2309	3636	SO:0001583	missense	81605	exon4			GCTTCAGTGGGAA	AK097029	CCDS6900.1, CCDS48035.1, CCDS59148.1	9q34.13	2010-06-24	2010-06-24	2006-11-28	ENSG00000167118	ENSG00000167118			28378	protein-coding gene	gene with protein product		612693	"chromosome 9 open reading frame 74", "ubiquitin related modifier 1 homolog (S. cerevisiae)"	C9orf74		16046629, 16864801	Standard	NM_030914		Approved	MGC2668	uc011may.2	Q9BTM9	OTTHUMG00000020742	ENST00000452446.1:c.289G>T	9.37:g.131151640G>T	ENSP00000412922:p.Val97Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	95	4	NM_001135947	0	0	0	0	0		Missense_Mutation	SNP	ENST00000452446.1	37	CCDS48035.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932635	0.34096	.	.	ENSG00000167118	ENST00000452446	.	.	.	3.84	0.924	0.19418	.	.	.	.	.	T	0.23451	0.0567	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.22626	-1.0211	6	.	.	.	.	6.151	0.20313	0.107:0.3997:0.4933:0.0	.	97	Q9BTM9-2	.	L	97	.	.	V	+	1	0	URM1	130191461	0.029000	0.19370	0.002000	0.10522	0.123000	0.20343	0.709000	0.25734	0.202000	0.20498	-0.947000	0.02670	GTG	.		0.617	URM1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_030914		T	131151640	G	T	131151640	3	4	142	1	0	0	0	0	1	0	0	0	17060	1029	36	4	303	4	URM1	9	131151640	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	169294	131151640	10061791	59	12695											
MAMDC4	158056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139748712	139748712	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caccactgccagaacaaggtCtgcgtggagccccagcagct	10	5	11	15	1	1	1	0	0	1	1	1	2	1	2	4	2	6	2	4	2	2	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:139748712C>T	ENST00000317446.2	+	7	770	c.720C>T	c.(718-720)gtC>gtT	p.V240V	MAMDC4_ENST00000445819.1_Silent_p.V240V|MAMDC4_ENST00000485732.1_3'UTR	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		AGAACAAGGTCTGCGTGGAGC	0.667																																					p.V240V		.											.	MAMDC4-156	0			c.C720T						.						25	27	26					9																	139748712		2193	4296	6489	SO:0001819	synonymous_variant	158056	exon7			CAAGGTCTGCGTG	AL834531	CCDS7010.1	9q34.3	2013-10-21			ENSG00000177943	ENSG00000177943			24083	protein-coding gene	gene with protein product	"apical early endosomal glycoprotein precursor", "endotubin"					7829488	Standard	NM_206920		Approved	AEGP, DKFZp434M1411	uc004cjs.3	Q6UXC1	OTTHUMG00000020951	ENST00000317446.2:c.720C>T	9.37:g.139748712C>T		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	130	38	NM_206920	0	0	0	0	0		Silent	SNP	ENST00000317446.2	37	CCDS7010.1																																																																																			.		0.667	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920		T	139748712	C	T	139748712	2	4	142	1	0	0	0	0	0	0	0	1	9229	900	32	2		2	MAMDC4	9	139748712	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	8597072	139748712	1464719	60	12696											
C10orf47	254427	broad.mit.edu;bcgsc.ca	37	chr10	11911626	11911626	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccaggagggagctgcgcGccccctccccgccggtggag	4	3	15	19	4	0	0	0	0	0	0	1	3	1	3	7	4	2	1	7	4	0	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr10:11911626G>C	ENST00000277570.5	+	4	683	c.529G>C	c.(529-531)Gcc>Ccc	p.A177P	PROSER2-AS1_ENST00000445498.1_RNA|PROSER2-AS1_ENST00000453242.1_RNA|PROSER2_ENST00000379200.1_5'Flank	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	177	Pro-rich.																GGAGCTGCGCGCCCCCTCCCC	0.692																																					p.A177P													.	.	0			c.G529C						.						11	13	12					10																	11911626		2186	4290	6476	SO:0001583	missense	254427	exon4			CTGCGCGCCCCCT	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 47", "proline and serine-rich protein 2"	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.529G>C	10.37:g.11911626G>C	ENSP00000277570:p.Ala177Pro	Somatic	149	15		WXS	Illumina HiSeq	Phase_I	145	56	NM_153256	0	0	4	8	4	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Missense_Mutation	SNP	ENST00000277570.5	37	CCDS7085.1	.	.	.	.	.	.	.	.	.	.	G	3.538	-0.094234	0.07053	.	.	ENSG00000148426	ENST00000379208;ENST00000277570;ENST00000379202	T	0.08008	3.14	4.4	-8.8	0.00817	.	0.716974	0.13006	N	0.421269	T	0.03305	0.0096	N	0.19112	0.55	0.09310	N	0.999999	B	0.09022	0.002	B	0.08055	0.003	T	0.34925	-0.9809	10	0.87932	D	0	3.0E-4	0.8901	0.01252	0.1745:0.2477:0.1899:0.3878	.	177	Q86WR7	CJ047_HUMAN	P	177	ENSP00000277570:A177P	ENSP00000277570:A177P	A	+	1	0	C10orf47	11951632	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.577000	0.05847	-2.779000	0.00361	0.305000	0.20034	GCC	.		0.692	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256		C	11911626	G	C	11911626	3	2	142	1	0	0	0	0	1	0	0	0	1609	1087	38	4	539	4	C10orf47	10	11911626	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		11911626	123623121	61	12697											
GPAM	57678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	113913352	113913352	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atattctagaagtttttgtcGgttgcattgaggtagaaaag	12	15	11	3	1	1	3	0	1	1	2	2	3	1	3	0	2	1	4	0	2	6	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr10:113913352G>A	ENST00000348367.4	-	22	2640	c.2443C>T	c.(2443-2445)Cga>Tga	p.R815*	GPAM_ENST00000423155.1_Nonsense_Mutation_p.R815*			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	815					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		AGTTTTTGTCGGTTGCATTGA	0.383																																					p.R815X	Ovarian(161;1017 2606 18293 52943)	.											.	GPAM-92	0			c.C2443T						.						126	131	129					10																	113913352		2203	4300	6503	SO:0001587	stop_gained	57678	exon22			TTTGTCGGTTGCA	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.2443C>T	10.37:g.113913352G>A	ENSP00000265276:p.Arg815*	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	91	30	NM_001244949	0	0	0	0	0	Q5VW51|Q86TA3	Nonsense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	G	40	8.137750	0.98672	.	.	ENSG00000119927	ENST00000348367;ENST00000423155	.	.	.	5.59	4.63	0.57726	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.7284	11.4195	0.49974	0.0:0.0:0.7192:0.2808	.	.	.	.	X	815	.	ENSP00000265276:R815X	R	-	1	2	GPAM	113903342	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.487000	0.45268	2.640000	0.89533	0.655000	0.94253	CGA	.		0.383	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		A	113913352	G	A	113913352	4	1	142	1	0	0	0	0	0	1	0	0	6608	1124	39	1	47	1	GPAM	10	113913352	Nonsense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	102001726	113913352	21621395	62	12698											
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	6652589	6652589	+	Frame_Shift_Del	DEL	T	T	-																															tctccccctcatctggatccTtcgcctgcagagtcgtcacc																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr11:6652589delT	ENST00000299441.3	-	8	4136	c.3725delA	c.(3724-3726)aagfs	p.K1242fs	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1242	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCTGGATCCTTCGCCTGCAG	0.552																																					p.K1242fs		.											.	DCHS1-73	0			c.3725delA						.						206	169	181					11																	6652589		2201	4296	6497	SO:0001589	frameshift_variant	8642	exon8			.	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"Cadherins / Cadherin-related"	13681	protein-coding gene	gene with protein product	"cadherin-related family member 6"	603057	"protocadherin 16", "dachsous 1 (Drosophila)"	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3725delA	11.37:g.6652589delT	ENSP00000299441:p.Lys1242fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	77	21	NM_003737	0	0	0	0	0	O15098	Frame_Shift_Del	DEL	ENST00000299441.3	37	CCDS7771.1																																																																																			.		0.552	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		-	6652589	T	-	6652589	7	5	142	1	0	1	0	1	0	0	0	0	4293	1609	56	0	6227	0	DCHS1	11	6652589	Frame_Shift_Del	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		6652589	128353927	63	12699											
IGSF22	283284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	18731076	18731076	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgcctgagatggggatCtttgtgcacttggaccactc	7	11	13	10	0	1	1	0	1	1	1	2	4	1	3	2	4	2	1	2	4	0	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr11:18731076C>A	ENST00000513874.1	-	18	2995	c.2856G>T	c.(2854-2856)aaG>aaT	p.K952N	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	851										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						AGATGGGGATCTTTGTGCACT	0.577																																					p.K952N		.											.	IGSF22-140	0			c.G2856T						.						100	105	104					11																	18731076		1974	4152	6126	SO:0001583	missense	283284	exon18			GGGGATCTTTGTG	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2856G>T	11.37:g.18731076C>A	ENSP00000421191:p.Lys952Asn	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	102	34	NM_173588	0	0	0	0	0	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.345544	0.41498	.	.	ENSG00000179057	ENST00000513874	T	0.56776	0.44	4.39	2.46	0.29980	.	.	.	.	.	T	0.47948	0.1473	N	0.12182	0.205	0.09310	N	0.999997	D	0.69078	0.997	D	0.80764	0.994	T	0.34104	-0.9842	9	0.18276	T	0.48	.	7.069	0.25167	0.0:0.7288:0.1744:0.0969	.	952	D6RGV7	.	N	952	ENSP00000421191:K952N	ENSP00000322422:K851N	K	-	3	2	IGSF22	18687652	0.000000	0.05858	0.578000	0.28575	0.994000	0.84299	-0.453000	0.06778	0.464000	0.27142	0.655000	0.94253	AAG	.		0.577	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18731076	C	A	18731076	3	1	142	1	0	0	0	0	1	0	0	0	7621	912	32	4	1148	4	IGSF22	11	18731076	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	12078487	18731076	116275440	64	12700											
GRIN2B	2904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	13768093	13768093	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccattgctgcgtgacaccaTgacactgatgcctgtctcta	8	11	8	14	1	1	3	0	3	1	0	2	3	1	3	3	0	3	1	3	0	1	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:13768093T>C	ENST00000609686.1	-	7	1818	c.1609A>G	c.(1609-1611)Atg>Gtg	p.M537V		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	537					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGTGACACCATGACACTGATG	0.517																																					p.M537V		.											.	GRIN2B-231	0			c.A1609G						.						195	151	166					12																	13768093		2203	4300	6503	SO:0001583	missense	2904	exon7			ACACCATGACACT		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.1609A>G	12.37:g.13768093T>C	ENSP00000477455:p.Met537Val	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	82	21	NM_000834	0	0	0	0	0	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.266041	0.80358	.	.	ENSG00000150086	ENST00000279593	T	0.22134	1.97	6.17	6.17	0.99709	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	L	0.53780	1.695	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	T	0.21655	-1.0239	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	537	Q13224	NMDE2_HUMAN	V	537	ENSP00000279593:M537V	ENSP00000279593:M537V	M	-	1	0	GRIN2B	13659360	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.035000	0.88872	2.371000	0.80710	0.533000	0.62120	ATG	.		0.517	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			C	13768093	T	C	13768093	3	2	142	1	0	0	0	0	1	0	0	0	6801	1464	51	3	2873	3	GRIN2B	12	13768093	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		13768093	120083802	65	12701											
AMHR2	269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53825014	53825014	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttgggatgcagacccagaAgcacggctgacagctgagtg	10	7	15	9	1	0	4	0	2	0	2	0	5	0	5	1	2	3	5	1	2	1	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:53825014A>T	ENST00000257863.4	+	11	1559	c.1479A>T	c.(1477-1479)gaA>gaT	p.E493D	AMHR2_ENST00000550311.1_3'UTR|AMHR2_ENST00000379791.3_Missense_Mutation_p.E398D	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	493	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	CAGACCCAGAAGCACGGCTGA	0.607																																					p.E493D		.											.	AMHR2-628	0			c.A1479T						.						88	84	86					12																	53825014		2203	4300	6503	SO:0001583	missense	269	exon11			CCCAGAAGCACGG	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1479A>T	12.37:g.53825014A>T	ENSP00000257863:p.Glu493Asp	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	68	22	NM_020547	0	0	0	0	0	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	37	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.844229	0.71488	.	.	ENSG00000135409	ENST00000257863;ENST00000379791	T;D	0.93659	-0.22;-3.26	4.86	3.72	0.42706	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38959	N	0.001503	D	0.92512	0.7622	N	0.25094	0.71	0.29470	N	0.857082	D	0.76494	0.999	D	0.80764	0.994	D	0.87493	0.2428	10	0.62326	D	0.03	.	8.3026	0.32023	0.9085:0.0:0.0915:0.0	.	493	Q16671	AMHR2_HUMAN	D	493;398	ENSP00000257863:E493D;ENSP00000369117:E398D	ENSP00000257863:E493D	E	+	3	2	AMHR2	52111281	0.998000	0.40836	0.998000	0.56505	0.971000	0.66376	0.443000	0.21644	0.998000	0.38996	0.460000	0.39030	GAA	.		0.607	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		T	53825014	A	T	53825014	3	4	142	1	0	0	0	0	1	0	0	0	573	69	3	5	1521	5	AMHR2	12	53825014	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	40056921	53825014	80026881	66	12702											
TARBP2	8620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53899840	53899840	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacccagccggccactgtgTgtcatggctctgcaaccacc	7	7	9	18	1	2	0	1	0	1	0	2	0	2	0	6	2	3	2	6	2	1	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:53899840T>C	ENST00000267017.3	-	0	592				TARBP2_ENST00000552857.1_3'UTR|TARBP2_ENST00000266987.2_Missense_Mutation_p.C337R|TARBP2_ENST00000456234.2_Missense_Mutation_p.C316R|TARBP2_ENST00000394357.2_Missense_Mutation_p.C316R	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						GGCCACTGTGTGTCATGGCTC	0.632																																					p.C337R		.											.	TARBP2-226	0			c.T1009C						.						48	44	46					12																	53899840		2203	4300	6503	SO:0001628	intergenic_variant	6895	exon9			ACTGTGTGTCATG	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		12.37:g.53899840T>C		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	71	20	NM_134323	0	0	19	43	24	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	37	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.437352	0.83885	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000394357	D;D;D	0.82255	-1.59;-1.59;-1.59	5.15	5.15	0.70609	Double-stranded RNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.91047	0.7183	M	0.83223	2.63	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	D	0.92199	0.5766	10	0.66056	D	0.02	-6.1074	14.2562	0.66053	0.0:0.0:0.0:1.0	.	337	Q15633	TRBP2_HUMAN	R	337;316;316	ENSP00000266987:C337R;ENSP00000416077:C316R;ENSP00000377885:C316R	ENSP00000266987:C337R	C	+	1	0	TARBP2	52186107	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.900000	0.63252	2.075000	0.62263	0.402000	0.26972	TGT	.		0.632	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		C	53899840	T	C	53899840	1	2	142	0	1	0	0	0	0	0	0	0	15588	1696	59	3		3	TARBP2	12	53899840	IGR	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	74826	53899840	79952055	67	12703											
FAM119B	25895	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	58166555	58166555	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tctgagtcggaatcggtgttCccgcgggaggtcgggctctt	4	11	16	10	5	2	1	0	1	2	0	6	3	3	3	1	5	0	2	1	5	1	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:58166555C>T	ENST00000300209.8	+	1	173	c.48C>T	c.(46-48)ttC>ttT	p.F16F	METTL1_ENST00000257848.7_5'Flank|METTL1_ENST00000548681.1_5'Flank|METTL21B_ENST00000548256.1_Intron|RP11-571M6.15_ENST00000471530.1_5'Flank|METTL1_ENST00000324871.7_5'UTR|AC025165.1_ENST00000582738.1_RNA|METTL21B_ENST00000552307.1_3'UTR|METTL21B_ENST00000333012.5_Silent_p.F16F|METTL21B_ENST00000551420.1_Intron	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	16						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						AATCGGTGTTCCCGCGGGAGG	0.647																																					p.F16F													.	METTL21B-514	0			c.C48T						.						37	36	36					12																	58166555		2202	4300	6502	SO:0001819	synonymous_variant	25895	exon1			GGTGTTCCCGCGG	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.48C>T	12.37:g.58166555C>T		Somatic	128	3		WXS	Illumina HiSeq	Phase_I	106	41	NM_015433	0	0	3	5	2	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																			.		0.647	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		T	58166555	C	T	58166555	2	4	142	1	0	0	0	0	0	0	0	1	5430	854	30	2		2	FAM119B	12	58166555	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	4266715	58166555	75685340	68	12704											
MON2	23041	bcgsc.ca	37	chr12	62931886	62931886	+	Frame_Shift_Del	DEL	G	G	-																															aattttacagcatcttgtgtGgattctgggattaaagccta																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:62931886delG	ENST00000393632.2	+	17	2520	c.2129delG	c.(2128-2130)tggfs	p.W710fs	MON2_ENST00000546600.1_Frame_Shift_Del_p.W710fs|MON2_ENST00000552115.1_Frame_Shift_Del_p.W710fs|MON2_ENST00000393630.3_Frame_Shift_Del_p.W710fs|MON2_ENST00000552738.1_Frame_Shift_Del_p.W687fs|MON2_ENST00000393629.2_Frame_Shift_Del_p.W710fs|MON2_ENST00000280379.6_Frame_Shift_Del_p.W710fs	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	710					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CATCTTGTGTGGATTCTGGGA	0.353																																					p.W710X													.	MON2-514	0			c.2129delG						.						43	49	47					12																	62931886		2202	4300	6502	SO:0001589	frameshift_variant	23041	exon17			TTGTGTGGATTCT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.2129delG	12.37:g.62931886delG	ENSP00000377252:p.Trp710fs	Somatic	161	1		WXS	Illumina HiSeq	Phase_1	89	24	NM_015026	0	0	0	0	0	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Nonsense_Mutation	DEL	ENST00000393632.2	37	CCDS31849.1																																																																																			.		0.353	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		-	62931886	G	-	62931886	7	5	142	1	0	1	0	1	0	0	0	0	9725	1357	47	0	2195	0	MON2	12	62931886	Frame_Shift_Del	DEL	G	TCGA-IZ-A6M8-01A-11D-A31X-10	4765331	62931886	70920009	69	12705											
ATP2B1	490	broad.mit.edu	37	chr12	90029004	90029004	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaccttcaccttcttccTccccaacagaaacttctcca	9	13	1	18	0	4	1	2	0	2	1	7	1	6	1	6	0	2	0	6	0	2	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:90029004T>C	ENST00000428670.3	-	4	887	c.431A>G	c.(430-432)gAg>gGg	p.E144G	ATP2B1_ENST00000348959.3_Missense_Mutation_p.E144G|ATP2B1_ENST00000359142.3_Missense_Mutation_p.E144G|ATP2B1_ENST00000261173.2_Missense_Mutation_p.E144G			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	144					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						ACCTTCTTCCTCCCCAACAGA	0.383																																					p.E144G													.	ATP2B1-516	0			c.A431G						.						81	70	74					12																	90029004		2203	4300	6503	SO:0001583	missense	490	exon3			TCTTCCTCCCCAA	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.431A>G	12.37:g.90029004T>C	ENSP00000392043:p.Glu144Gly	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	33	3	NM_001001323	0	0	0	0	0	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	37	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.860274	0.51482	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670	D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.85965	0.5820	L	0.54323	1.7	0.51012	D	0.999905	B;B	0.12013	0.001;0.005	B;B	0.25506	0.003;0.061	T	0.80513	-0.1349	9	.	.	.	-19.9952	11.6181	0.51102	0.1327:0.0:0.0:0.8673	.	144;144	P20020-3;P20020-2	.;.	G	144	ENSP00000261173:E144G;ENSP00000343599:E144G;ENSP00000352054:E144G;ENSP00000392043:E144G	.	E	-	2	0	ATP2B1	88553135	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.227000	0.58612	2.367000	0.80283	0.528000	0.53228	GAG	.		0.383	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		C	90029004	T	C	90029004	3	2	142	1	0	0	0	0	1	0	0	0	1140	1551	54	3	3461	3	ATP2B1	12	90029004	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	27097118	90029004	43822891	70	12706											
SBNO1	55206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	123815855	123815855	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctgctatcgtccttccttttCctacaccggcaccatcacct	6	13	4	18	2	1	0	1	0	0	0	5	0	4	0	6	1	2	2	6	1	2	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:123815855C>G	ENST00000602398.1	-	8	1104	c.977G>C	c.(976-978)gGa>gCa	p.G326A	SBNO1_ENST00000602750.1_Missense_Mutation_p.G325A|SBNO1_ENST00000267176.4_Missense_Mutation_p.G325A|SBNO1_ENST00000420886.2_Missense_Mutation_p.G326A			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	326					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CCTTCCTTTTCCTACACCGGC	0.408																																					p.G326A		.											.	SBNO1-292	0			c.G977C						.						152	138	143					12																	123815855		2203	4300	6503	SO:0001583	missense	55206	exon7			CCTTTTCCTACAC	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.977G>C	12.37:g.123815855C>G	ENSP00000473665:p.Gly326Ala	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	94	33	NM_001167856	0	0	1	1	0	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	C	32	5.164386	0.94727	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.99940	-8.38;-8.38	5.83	5.83	0.93111	Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.99955	0.9981	H	0.96015	3.755	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.91635	0.999;0.993;0.998	D	0.96352	0.9259	10	0.87932	D	0	-27.8907	20.1218	0.97964	0.0:1.0:0.0:0.0	.	326;325;324	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	A	326;325;325	ENSP00000387361:G326A;ENSP00000267176:G325A	ENSP00000267176:G325A	G	-	2	0	SBNO1	122381808	1.000000	0.71417	0.958000	0.39756	0.998000	0.95712	7.794000	0.85869	2.763000	0.94921	0.561000	0.74099	GGA	.		0.408	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		G	123815855	C	G	123815855	3	3	142	1	0	0	0	0	1	0	0	0	13894	855	30	4	3304	4	SBNO1	12	123815855	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	33786851	123815855	10036040	71	12707											
ZMYM5	9205	bcgsc.ca	37	chr13	20413049	20413049	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaattctgcttacgaagtaaGgccactggtgataaagaatc	15	10	9	7	1	1	2	0	1	1	1	2	3	1	2	1	2	2	2	1	2	7	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr13:20413049G>T	ENST00000337963.4	-	5	927	c.663C>A	c.(661-663)gcC>gcA	p.A221A	RP11-61K9.2_ENST00000422148.2_RNA|ZMYM5_ENST00000382907.4_Intron|ZMYM5_ENST00000382905.4_Silent_p.A221A	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	221						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TACGAAGTAAGGCCACTGGTG	0.403																																					p.A221A													.	ZMYM5-90	0			c.C663A						.						159	162	161					13																	20413049		2203	4300	6503	SO:0001819	synonymous_variant	9205	exon5			AAGTAAGGCCACT	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.663C>A	13.37:g.20413049G>T		Somatic	220	5		WXS	Illumina HiSeq	Phase_1	169	68	NM_001039650	0	0	0	1	1	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Silent	SNP	ENST00000337963.4	37																																																																																				.		0.403	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		T	20413049	G	T	20413049	2	4	142	1	0	0	0	0	0	0	0	1	17735	987	35	4		4	ZMYM5	13	20413049	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		20413049	94756829	72	12708											
NBEA	26960	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	35731352	35731352	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgtatcatgcaataaaatAtgaatggggaggctggagag	14	11	13	3	0	1	2	1	1	0	1	1	4	1	3	0	4	1	3	0	4	6	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr13:35731352A>G	ENST00000400445.3	+	21	3323	c.2789A>G	c.(2788-2790)tAt>tGt	p.Y930C	NBEA_ENST00000540320.1_Missense_Mutation_p.Y930C|NBEA_ENST00000379939.2_Missense_Mutation_p.Y930C|NBEA_ENST00000310336.4_Missense_Mutation_p.Y930C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	930					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GCAATAAAATATGAATGGGGA	0.383																																					p.Y930C													.	NBEA-144	0			c.A2789G						.						71	73	72					13																	35731352		1826	4083	5909	SO:0001583	missense	26960	exon21			TAAAATATGAATG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2789A>G	13.37:g.35731352A>G	ENSP00000383295:p.Tyr930Cys	Somatic	94	1		WXS	Illumina HiSeq	Phase_I	65	16	NM_015678	0	0	0	0	0	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.414824	0.83449	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.37	5.37	0.77165	.	0.069707	0.64402	D	0.000014	T	0.75280	0.3828	M	0.67953	2.075	0.80722	D	1	D	0.63046	0.992	P	0.54499	0.754	T	0.77827	-0.2443	10	0.54805	T	0.06	.	15.6702	0.77267	1.0:0.0:0.0:0.0	.	930	Q5T321	.	C	930	ENSP00000440951:Y930C;ENSP00000383295:Y930C;ENSP00000369271:Y930C;ENSP00000308534:Y930C	ENSP00000308534:Y930C	Y	+	2	0	NBEA	34629352	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	9.287000	0.95975	2.171000	0.68590	0.528000	0.53228	TAT	.		0.383	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35731352	A	G	35731352	3	3	142	1	0	0	0	0	1	0	0	0	10212	449	16	3	2871	3	NBEA	13	35731352	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	15318303	35731352	79438526	73	12709											
SERPINE3	647174	broad.mit.edu	37	chr13	51922450	51922450	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgccccgtgacaaagacAcccccctgagccacatcgag	10	5	9	17	2	0	3	0	2	0	1	1	4	0	3	6	0	3	1	6	0	1	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr13:51922450A>C	ENST00000521255.1	+	4	862	c.802A>C	c.(802-804)Acc>Ccc	p.T268P	SERPINE3_ENST00000400389.4_Missense_Mutation_p.T268P|MIR5693_ENST00000577722.1_RNA|SERPINE3_ENST00000524365.1_Missense_Mutation_p.T268P	NM_001101320.1	NP_001094790.1	A8MV23	SERP3_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	268					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(2)	2						TGACAAAGACACCCCCCTGAG	0.612																																					p.T268P													.	SERPINE3-24	0			c.A802C						.						61	80	74					13																	51922450		2118	4246	6364	SO:0001583	missense	647174	exon4			AAAGACACCCCCC	AX772926	CCDS53870.1	13q14.3	2014-02-18			ENSG00000253309	ENSG00000253309		"Serine (or cysteine) peptidase inhibitors"	24774	protein-coding gene	gene with protein product						24172014	Standard	NM_001101320		Approved		uc001vfh.2	A8MV23	OTTHUMG00000016943	ENST00000521255.1:c.802A>C	13.37:g.51922450A>C	ENSP00000428316:p.Thr268Pro	Somatic	74	13		WXS	Illumina HiSeq	Phase_I	89	20	NM_001101320	0	0	0	0	0	B1V8P3	Missense_Mutation	SNP	ENST00000521255.1	37	CCDS53870.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.134471	0.37630	.	.	ENSG00000253309	ENST00000524365;ENST00000521255;ENST00000400389	D;D;D	0.84516	-1.86;-1.86;-1.86	5.19	-5.14	0.02875	Serpin domain (3);	0.090377	0.42964	U	0.000633	D	0.89767	0.6810	M	0.85197	2.74	0.09310	N	1	B;D	0.63046	0.18;0.992	B;D	0.63793	0.067;0.918	D	0.85624	0.1266	10	0.59425	D	0.04	.	12.8081	0.57626	0.492:0.0:0.508:0.0	.	268;268	A8MV23-2;A8MV23	.;SERP3_HUMAN	P	268	ENSP00000430755:T268P;ENSP00000428316:T268P;ENSP00000441468:T268P	ENSP00000441468:T268P	T	+	1	0	SERPINE3	50820451	0.393000	0.25237	0.000000	0.03702	0.099000	0.18886	2.777000	0.47717	-1.107000	0.03004	-0.242000	0.12053	ACC	.		0.612	SERPINE3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045021.2	NM_001101320		C	51922450	A	C	51922450	3	2	142	1	0	0	0	0	1	0	0	0	14145	159	6	5	816	5	SERPINE3	13	51922450	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	16191098	51922450	63247428	74	12710											
TPP2	7174	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	103271166	103271166	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctggccctgtatatgactGcttggtatggcatgatggcg	6	13	13	9	1	0	2	0	2	0	0	1	2	1	2	2	4	1	4	2	4	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr13:103271166G>T	ENST00000376065.4	+	5	626	c.590G>T	c.(589-591)tGc>tTc	p.C197F	TPP2_ENST00000376052.3_Missense_Mutation_p.C197F	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	197	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTATATGACTGCTTGGTATGG	0.358																																					p.C197F													.	TPP2-92	0			c.G590T						.						174	167	169					13																	103271166		2203	4300	6503	SO:0001583	missense	7174	exon5			ATGACTGCTTGGT	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.590G>T	13.37:g.103271166G>T	ENSP00000365233:p.Cys197Phe	Somatic	117	2		WXS	Illumina HiSeq	Phase_I	74	30	NM_003291	0	0	0	0	0	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	37	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592962	0.86953	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.69	5.69	0.88448	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.000000	0.85682	D	0.000000	D	0.84120	0.5402	M	0.83483	2.645	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85728	0.1329	9	0.87932	D	0	.	19.8131	0.96556	0.0:0.0:1.0:0.0	.	197	P29144	TPP2_HUMAN	F	197	.	ENSP00000365220:C197F	C	+	2	0	TPP2	102069167	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.476000	0.97823	2.682000	0.91365	0.585000	0.79938	TGC	.		0.358	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			T	103271166	G	T	103271166	3	4	142	1	0	0	0	0	1	0	0	0	16445	1319	46	4	608	4	TPP2	13	103271166	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	51348716	103271166	11898712	75	12711											
ABHD13	84945	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	108882148	108882149	+	Missense_Mutation	DNP	GG	GG	TT																															tttctttttggccgttccttGggtggagcagtggctattca																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr13:108882148_108882149GG>TT	ENST00000375898.3	+	2	883_884	c.582_583GG>TT	c.(580-585)ttGGgt>ttTTgt	p.194_195LG>FC		NM_032859.2	NP_116248.2	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	194						integral component of membrane (GO:0016021)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					GCCGTTCCTTGGGTGGAGCAGT	0.406																																					p.LG194FC	Pancreas(22;506 789 38166 45896 51596)	.											.	ABHD13-93	0			c.G583T						.																																			SO:0001583	missense	84945	exon2			TCCTTGGGTGGAG	AK027812	CCDS32007.1	13q33.2	2007-04-03	2006-03-10	2006-03-10	ENSG00000139826	ENSG00000139826		"Abhydrolase domain containing"	20293	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 6"	C13orf6			Standard	NM_032859		Approved	bA153I24.2, FLJ14906, BEM46L1	uc001vqq.3	Q7L211	OTTHUMG00000017330	Exception_encountered	13.37:g.108882148_108882149delinsTT	ENSP00000365063:p.L194_G195delinsFC	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	89	25	NM_032859	0	0	0	0	0	B3KWE7|Q8NBW1|Q96JX9	Missense_Mutation	DNP	ENST00000375898.3	37	CCDS32007.1																																																																																			.		0.406	ABHD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045743.1	NM_032859		TT	108882149	GG	TT	108882148	3	4	142	1	0	0	0	0	1	0	0	0	78	1339	47	4	584	4	ABHD13	13	108882148	Missense_Mutation	DNP	GG	TCGA-IZ-A6M8-01A-11D-A31X-10	5610982	108882148	6287730	76	12712											
TTC5	91875	broad.mit.edu;ucsc.edu	37	chr14	20774052	20774052	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctacggccccacctgcaaTttctgcaagatcggcttgac	9	10	8	14	2	2	2	0	1	2	1	3	2	2	2	3	2	3	3	3	2	3	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr14:20774052T>C	ENST00000258821.3	-	1	101	c.45A>G	c.(43-45)aaA>aaG	p.K15K	CTD-2292M16.7_ENST00000553419.1_RNA	NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	15					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		CCACCTGCAATTTCTGCAAGA	0.502											OREG0022552	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K15K													.	TTC5-91	0			c.A45G						.						135	118	124					14																	20774052		2203	4300	6503	SO:0001819	synonymous_variant	91875	exon1			CTGCAATTTCTGC	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"Tetratricopeptide (TTC) repeat domain containing"	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.45A>G	14.37:g.20774052T>C		Somatic	74	1	743	WXS	Illumina HiSeq	Phase_I	73	10	NM_138376	0	0	0	0	0	A8MQ18|Q96HF9	Silent	SNP	ENST00000258821.3	37	CCDS9546.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.117697	0.56505	.	.	ENSG00000136319	ENST00000423949	.	.	.	4.95	3.72	0.42706	.	.	.	.	.	T	0.57489	0.2057	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54636	-0.8264	4	.	.	.	.	8.3016	0.32017	0.0:0.0:0.2007:0.7993	.	.	.	.	V	15	.	.	I	-	1	0	TTC5	19843892	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.381000	0.34362	2.201000	0.70794	0.533000	0.62120	ATT	.		0.502	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376		C	20774052	T	C	20774052	2	2	142	1	0	0	0	0	0	0	0	1	16744	1490	52	3		3	TTC5	14	20774052	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		20774052	86575488	77	12713											
SNX6	58533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	35062293	35062293	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcagatttagcagatgcatCcttaactcggttatgatact	12	14	7	8	1	1	3	1	1	0	2	3	3	2	3	1	1	4	3	1	1	4	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr14:35062293C>A	ENST00000362031.4	-	8	742	c.712G>T	c.(712-714)Gat>Tat	p.D238Y	SNX6_ENST00000355110.5_Missense_Mutation_p.D114Y|SNX6_ENST00000396534.3_Missense_Mutation_p.D110Y|SNX6_ENST00000396526.3_Missense_Mutation_p.D110Y	NM_152233.2	NP_689419.2	Q9UNH7	SNX6_HUMAN	sorting nexin 6	226					intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|intracellular (GO:0005622)|nucleus (GO:0005634)	phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			endometrium(4)|lung(1)|ovary(1)	6	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		GCAGATGCATCCTTAACTCGG	0.299																																					p.D238Y		.											.	SNX6-226	0			c.G712T						.						75	74	74					14																	35062293		2202	4298	6500	SO:0001583	missense	58533	exon8			ATGCATCCTTAAC	AF121856	CCDS9648.1, CCDS41942.1	14q13	2010-08-05			ENSG00000129515	ENSG00000129515		"Sorting nexins"	14970	protein-coding gene	gene with protein product		606098				11279102	Standard	XM_006720224		Approved		uc001wsf.1	Q9UNH7	OTTHUMG00000140213	ENST00000362031.4:c.712G>T	14.37:g.35062293C>A	ENSP00000355217:p.Asp238Tyr	Somatic	269	0		WXS	Illumina HiSeq	Phase_I	127	31	NM_152233	0	0	4	9	5	C0H5W9|Q9Y449	Missense_Mutation	SNP	ENST00000362031.4	37	CCDS41942.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345615	0.82022	.	.	ENSG00000129515	ENST00000396526;ENST00000396534;ENST00000362031;ENST00000355110;ENST00000557265	T;T;T;T;T	0.54071	1.5;1.5;1.5;1.5;0.59	4.69	4.69	0.59074	Vps5 C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75317	0.3833	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.80360	-0.1415	10	0.87932	D	0	-17.283	17.6053	0.88036	0.0:1.0:0.0:0.0	.	114;226	B4DJS7;Q9UNH7	.;SNX6_HUMAN	Y	110;110;238;114;201	ENSP00000379779:D110Y;ENSP00000379785:D110Y;ENSP00000355217:D238Y;ENSP00000347230:D114Y;ENSP00000452577:D201Y	ENSP00000347230:D114Y	D	-	1	0	SNX6	34132044	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.993000	0.76245	2.340000	0.79590	0.561000	0.74099	GAT	.		0.299	SNX6-002	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276642.3			A	35062293	C	A	35062293	3	1	142	1	0	0	0	0	1	0	0	0	14938	855	30	4	572	4	SNX6	14	35062293	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	14288241	35062293	72287247	78	12714											
LTBP2	4053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	75019017	75019017	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ataggcaggtggcagaacttCccggtggagttggcggggca	8	7	18	8	2	0	1	0	0	0	1	1	2	1	2	1	8	1	4	1	8	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr14:75019017C>G	ENST00000261978.4	-	6	1658	c.1272G>C	c.(1270-1272)ggG>ggC	p.G424G	LTBP2_ENST00000556690.1_Silent_p.G424G|LTBP2_ENST00000557425.1_Intron|CTD-2207P18.1_ENST00000554552.1_lincRNA	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	424	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GGCAGAACTTCCCGGTGGAGT	0.652																																					p.G424G		.											.	LTBP2-92	0			c.G1272C						.						39	41	40					14																	75019017		2203	4300	6503	SO:0001819	synonymous_variant	4053	exon6			GAACTTCCCGGTG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"Latent transforming growth factor, beta binding proteins"	6715	protein-coding gene	gene with protein product		602091	"chromosome 14 open reading frame 141"	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1272G>C	14.37:g.75019017C>G		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	83	26	NM_000428	0	0	0	0	0	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																			.		0.652	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		G	75019017	C	G	75019017	2	3	142	1	0	0	0	0	0	0	0	1	9099	842	30	4		4	LTBP2	14	75019017	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	39956724	75019017	32330523	79	12715											
C14orf4	64207	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	77492877	77492877	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccgtggggtactcaatgAacagcttcaattcgtagtcc	10	10	10	11	2	2	1	2	1	0	0	4	1	3	1	2	2	4	3	2	2	5	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr14:77492877A>G	ENST00000238647.3	-	1	2157	c.1259T>C	c.(1258-1260)tTc>tCc	p.F420S		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	420					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						GTACTCAATGAACAGCTTCAA	0.592																																					p.F420S													.	IRF2BPL-90	0			c.T1259C						.						46	39	42					14																	77492877		2203	4300	6503	SO:0001583	missense	64207	exon1			TCAATGAACAGCT	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.1259T>C	14.37:g.77492877A>G	ENSP00000238647:p.Phe420Ser	Somatic	93	1		WXS	Illumina HiSeq	Phase_I	100	31	NM_024496	1	0	9	13	3	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	37	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.924484	0.92319	.	.	ENSG00000119669	ENST00000238647	T	0.17691	2.26	3.92	3.92	0.45320	.	0.000000	0.64402	U	0.000002	T	0.30916	0.0780	L	0.52573	1.65	0.53005	D	0.99996	D	0.71674	0.998	P	0.61874	0.895	T	0.03840	-1.0999	10	0.72032	D	0.01	0.109	11.7465	0.51823	1.0:0.0:0.0:0.0	.	420	Q9H1B7	I2BPL_HUMAN	S	420	ENSP00000238647:F420S	ENSP00000238647:F420S	F	-	2	0	IRF2BPL	76562630	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.290000	0.89925	1.638000	0.50547	0.379000	0.24179	TTC	.		0.592	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		G	77492877	A	G	77492877	3	3	142	1	0	0	0	0	1	0	0	0	1777	246	9	3	1135	3	C14orf4	14	77492877	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	2473860	77492877	29856663	80	12716											
TJP1	7082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	30019082	30019082	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacataacctcattctcatTgtttttactccttgcttaga	9	17	5	10	0	2	1	2	0	1	1	4	2	3	2	2	1	3	2	2	1	3	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr15:30019082T>G	ENST00000346128.6	-	17	2688	c.2214A>C	c.(2212-2214)acA>acC	p.T738T	TJP1_ENST00000400011.2_Silent_p.T742T|RP11-680F8.4_ENST00000560740.1_RNA|TJP1_ENST00000545208.2_Silent_p.T738T|TJP1_ENST00000356107.6_Silent_p.T738T	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	738	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TCATTCTCATTGTTTTTACTC	0.363																																					p.T738T	Melanoma(77;681 1843 6309 6570)	.											.	TJP1-95	0			c.A2214C						.						161	147	151					15																	30019082		1861	4096	5957	SO:0001819	synonymous_variant	7082	exon17			TCTCATTGTTTTT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"zona occludens 1", "tight junction protein ZO-1"	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.2214A>C	15.37:g.30019082T>G		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	110	26	NM_175610	0	0	0	0	0	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																			.		0.363	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		G	30019082	T	G	30019082	2	3	142	1	0	0	0	0	0	0	0	1	15961	1799	63	5		5	TJP1	15	30019082	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		30019082	72512310	81	12717											
TP53BP1	7158	ucsc.edu;bcgsc.ca	37	chr15	43748739	43748739	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcaacggaacactctcCatattttcttctttgagttc	9	15	7	10	1	3	1	0	1	3	0	5	2	3	2	1	2	3	2	1	2	3	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr15:43748739C>T	ENST00000263801.3	-	12	2304	c.2052G>A	c.(2050-2052)atG>atA	p.M684I	TP53BP1_ENST00000382044.4_Missense_Mutation_p.M689I|TP53BP1_ENST00000450115.2_Missense_Mutation_p.M689I|TP53BP1_ENST00000382039.3_Missense_Mutation_p.M689I|TP53BP1_ENST00000605155.1_5'Flank	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	684					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GAACACTCTCCATATTTTCTT	0.453								Other conserved DNA damage response genes																													p.M689I													.	TP53BP1-294	0			c.G2067A						.						103	107	106					15																	43748739		2201	4298	6499	SO:0001583	missense	7158	exon12			ACTCTCCATATTT	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2052G>A	15.37:g.43748739C>T	ENSP00000263801:p.Met684Ile	Somatic	130	2		WXS	Illumina HiSeq		93	30	NM_001141980	0	0	0	0	0	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	4.757	0.140854	0.09083	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	4.94	4.02	0.46733	.	0.617223	0.16860	N	0.196566	T	0.34890	0.0913	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.17077	-1.0381	10	0.35671	T	0.21	-1.1578	8.3535	0.32316	0.0:0.7608:0.1558:0.0834	.	689;684;689;689	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	I	684;689;689;689;689	ENSP00000263801:M684I;ENSP00000371475:M689I;ENSP00000371470:M689I;ENSP00000393497:M689I;ENSP00000388028:M689I	ENSP00000263801:M684I	M	-	3	0	TP53BP1	41536031	0.024000	0.19004	0.838000	0.33150	0.330000	0.28571	1.028000	0.30128	1.203000	0.43233	0.563000	0.77884	ATG	.		0.453	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			T	43748739	C	T	43748739	3	4	142	1	0	0	0	0	1	0	0	0	16416	594	21	2	3934	2	TP53BP1	15	43748739	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	13729657	43748739	58782653	82	12718											
HMG20A	10363	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	77750833	77750833	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagtaatgatctggctacCactgggtaagcagctgcttt	10	11	12	8	0	1	2	0	1	1	1	1	3	1	2	1	2	4	6	1	2	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr15:77750833C>G	ENST00000381714.3	+	3	512	c.84C>G	c.(82-84)acC>acG	p.T28T	HMG20A_ENST00000336216.4_Silent_p.T28T	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	28					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						ATCTGGCTACCACTGGGTAAG	0.453																																					p.T28T		.											.	HMG20A-228	0			c.C84G						.						92	88	89					15																	77750833		2196	4294	6490	SO:0001819	synonymous_variant	10363	exon3			GGCTACCACTGGG	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.84C>G	15.37:g.77750833C>G		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	45	15	NM_018200	0	0	0	0	0	A6NHY3|D3DW78|Q53G31|Q9NSF6	Silent	SNP	ENST00000381714.3	37	CCDS10295.1																																																																																			.		0.453	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		G	77750833	C	G	77750833	2	3	142	1	0	0	0	0	0	0	0	1	7242	581	21	4		4	HMG20A	15	77750833	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	34002094	77750833	24780559	83	12719											
IREB2	3658	broad.mit.edu	37	chr15	78758793	78758793	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcgcagattgagaatacAcccatcctgtgtccttttca	9	14	6	12	1	2	2	1	1	1	2	5	3	4	2	3	0	1	1	3	0	2	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr15:78758793A>T	ENST00000258886.8	+	5	740	c.591A>T	c.(589-591)acA>acT	p.T197T	IREB2_ENST00000560440.1_Silent_p.T197T|IREB2_ENST00000559427.1_3'UTR	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	197					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)		TTGAGAATACACCCATCCTGT	0.413																																					p.T197T	NSCLC(200;764 2208 35157 49871 50830)												.	IREB2-90	0			c.A591T						.						129	125	126					15																	78758793		2196	4293	6489	SO:0001819	synonymous_variant	3658	exon5			GAATACACCCATC	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	ENST00000258886.8:c.591A>T	15.37:g.78758793A>T		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	91	4	NM_004136	0	0	0	0	0	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Silent	SNP	ENST00000258886.8	37	CCDS10302.1																																																																																			.		0.413	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		T	78758793	A	T	78758793	2	4	142	1	0	0	0	0	0	0	0	1	7847	146	6	5		5	IREB2	15	78758793	Silent	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	1007960	78758793	23772599	84	12720											
MEFV	4210	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	3304171	3304171	+	Frame_Shift_Del	DEL	T	T	-																															aatttaccggtgaccgaatgTtctggatttccagggccttc																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr16:3304171delT	ENST00000219596.1	-	2	936	c.897delA	c.(895-897)gaafs	p.E299fs	MEFV_ENST00000536379.1_Intron|MEFV_ENST00000541159.1_Intron|MEFV_ENST00000339854.4_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	299					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						tgacCGAATGTTCTGGATTTC	0.562																																					p.E299fs		.											.	MEFV-228	0			c.897delA						.						53	56	55					16																	3304171		2197	4300	6497	SO:0001589	frameshift_variant	4210	exon2			.	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.897delA	16.37:g.3304171delT	ENSP00000219596:p.Glu299fs	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	62	14	NM_000243	0	0	0	0	0	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Frame_Shift_Del	DEL	ENST00000219596.1	37	CCDS10498.1																																																																																			.		0.562	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		-	3304171	T	-	3304171	7	5	142	1	0	1	0	1	0	0	0	0	9484	1722	60	0	1484	0	MEFV	16	3304171	Frame_Shift_Del	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		3304171	87050582	85	12721											
APOB48R	55911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	28509637	28509637	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaggcatgatgggacccCggtgccagccaggagaaggc	9	5	16	11	1	1	3	0	2	1	1	1	5	1	4	4	5	2	1	4	5	1	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr16:28509637C>G	ENST00000431282.1	+	4	3174	c.3164C>G	c.(3163-3165)cCg>cGg	p.P1055R	APOBR_ENST00000564831.1_Missense_Mutation_p.P1064R|CLN3_ENST00000569430.1_5'Flank|CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Intron			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	1055					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GATGGGACCCCGGTGCCAGCC	0.672																																					p.P1064R		.											.	APOBR-90	0			c.C3191G						.						16	21	19					16																	28509637		1941	4148	6089	SO:0001583	missense	55911	exon3			GGACCCCGGTGCC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.3164C>G	16.37:g.28509637C>G	ENSP00000416094:p.Pro1055Arg	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	93	10	NM_018690	0	0	43	43	0	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	C	13.49	2.251925	0.39797	.	.	ENSG00000184730	ENST00000431282	T	0.61742	0.08	4.84	4.84	0.62591	.	.	.	.	.	T	0.62962	0.2471	L	0.34521	1.04	0.34997	D	0.755616	D;D	0.71674	0.998;0.998	D;D	0.64687	0.928;0.928	T	0.69026	-0.5254	8	.	.	.	-4.4525	13.4548	0.61193	0.0:1.0:0.0:0.0	.	1055;1055	Q0VD83;Q9NS13	APOBR_HUMAN;.	R	1055	ENSP00000416094:P1055R	.	P	+	2	0	APOBR	28417138	0.950000	0.32346	0.996000	0.52242	0.736000	0.42039	2.535000	0.45685	2.236000	0.73375	0.457000	0.33378	CCG	.		0.672	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		G	28509637	C	G	28509637	3	3	142	1	0	0	0	0	1	0	0	0	786	652	23	4	3178	4	APOB48R	16	28509637	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	25205466	28509637	61845116	86	12722											
SF3B3	23450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	70605581	70605581	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctccatatcttagaatgtGattgatggagacctctgtga	10	15	9	7	0	3	5	0	3	3	2	4	6	3	5	2	1	0	0	2	1	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr16:70605581G>A	ENST00000302516.5	+	26	3730	c.3519G>A	c.(3517-3519)gtG>gtA	p.V1173V		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	1173					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CTTAGAATGTGATTGATGGAG	0.428																																					p.V1173V		.											.	SF3B3-91	0			c.G3519A						.						51	48	49					16																	70605581		2198	4300	6498	SO:0001819	synonymous_variant	23450	exon26			GAATGTGATTGAT	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.3519G>A	16.37:g.70605581G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	93	24	NM_012426	0	0	0	0	0	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	37	CCDS10894.1																																																																																			.		0.428	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		A	70605581	G	A	70605581	2	1	142	1	0	0	0	0	0	0	0	1	14184	1277	45	2		2	SF3B3	16	70605581	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	42095944	70605581	19749172	87	12723											
TRPV3	162514	broad.mit.edu	37	chr17	3438998	3438998	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcgatggcgatgttcagcGccgtctgccctgcggagcgg	4	8	16	13	6	2	0	1	0	1	0	3	3	2	1	2	3	4	2	2	3	0	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:3438998G>T	ENST00000576742.1	-	7	974	c.653C>A	c.(652-654)gCg>gAg	p.A218E	TRPV3_ENST00000301365.4_Missense_Mutation_p.A218E|TRPV3_ENST00000572519.1_Missense_Mutation_p.A218E	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	218					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GATGTTCAGCGCCGTCTGCCC	0.736																																					p.A218E													.	TRPV3-94	0			c.C653A						.						8	9	9					17																	3438998		2163	4231	6394	SO:0001583	missense	162514	exon7			TTCAGCGCCGTCT	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.653C>A	17.37:g.3438998G>T	ENSP00000461518:p.Ala218Glu	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	26	4	NM_001258205	0	0	0	0	0	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	G	36	5.688246	0.96784	.	.	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	T	0.71341	-0.56	5.03	5.03	0.67393	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	D	0.89491	0.6730	H	0.96111	3.77	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;0.999;0.997;0.999;1.0;1.0;0.997	D;D;D;D;D;D;P	0.91635	0.979;0.993;0.933;0.993;0.999;0.999;0.89	D	0.92506	0.6012	10	0.87932	D	0	-11.7793	18.2979	0.90153	0.0:0.0:1.0:0.0	.	202;202;218;202;218;218;218	E7EV24;B7ZKP9;Q2M3L1;B7ZKP6;Q8NET8-3;Q8NET8;Q8NET8-2	.;.;.;.;.;TRPV3_HUMAN;.	E	218;218;202	ENSP00000301365:A218E	ENSP00000301365:A218E	A	-	2	0	TRPV3	3385748	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.422000	0.97458	2.741000	0.93983	0.555000	0.69702	GCG	.		0.736	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		T	3438998	G	T	3438998	3	4	142	1	0	0	0	0	1	0	0	0	16630	1087	38	4	1767	4	TRPV3	17	3438998	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		3438998	77756212	88	12724											
C17orf39	79018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17962263	17962263	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagagctgaagaatggagacTacgtcttcatgaggtggaag	14	8	14	5	1	2	5	1	2	1	3	2	7	2	6	0	3	2	1	0	3	5	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:17962263T>A	ENST00000268719.4	+	4	861	c.688T>A	c.(688-690)Tac>Aac	p.Y230N		NM_024052.4	NP_076957.3	Q8IVV7	GID4_HUMAN	GID complex subunit 4	230																	GAATGGAGACTACGTCTTCAT	0.458																																					p.Y230N		.											.	.	0			c.T688A						.						75	68	71					17																	17962263		2203	4300	6503	SO:0001583	missense	79018	exon4			GGAGACTACGTCT	AK127580	CCDS11190.1	17p11.2	2013-07-31	2013-07-31	2012-07-20	ENSG00000141034	ENSG00000141034			28453	protein-coding gene	gene with protein product	"vacuolar import and degradation 24"		"chromosome 17 open reading frame 39", "GID complex subunit 4, VID24 homolog (S. cerevisiae)"	C17orf39		11997338	Standard	NM_024052		Approved	VID24	uc002gsg.1	Q8IVV7	OTTHUMG00000059398	ENST00000268719.4:c.688T>A	17.37:g.17962263T>A	ENSP00000268719:p.Tyr230Asn	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	125	33	NM_024052	0	0	6	10	4	Q8TEB5|Q9BW50	Missense_Mutation	SNP	ENST00000268719.4	37	CCDS11190.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995621	0.54147	.	.	ENSG00000141034	ENST00000268719	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	L	0.48642	1.525	0.80722	D	1	B	0.24317	0.101	B	0.20184	0.028	T	0.51387	-0.8712	9	0.23302	T	0.38	-15.1166	16.1549	0.81657	0.0:0.0:0.0:1.0	.	230	Q8IVV7	CQ039_HUMAN	N	230	.	ENSP00000268719:Y230N	Y	+	1	0	C17orf39	17902988	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.797000	0.85911	2.209000	0.71365	0.533000	0.62120	TAC	.		0.458	GID4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132071.2	NM_024052		A	17962263	T	A	17962263	3	1	142	1	0	0	0	0	1	0	0	0	1860	1522	53	5	702	5	C17orf39	17	17962263	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	14523265	17962263	63232947	89	12725											
CORO6	84940	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27948314	27948314	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atggccaggaatttggggttGacggcacagaaggagctgtc	10	8	16	7	1	0	2	0	1	0	1	1	4	0	4	1	6	1	3	1	6	2	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:27948314G>A	ENST00000445145.2	-	1	127	c.126C>T	c.(124-126)gtC>gtT	p.V42V	CORO6_ENST00000580212.1_Silent_p.V42V|CORO6_ENST00000345068.5_Silent_p.V42V|RP11-68I3.10_ENST00000582367.1_RNA|RP11-68I3.2_ENST00000581474.1_RNA|CORO6_ENST00000577909.1_Intron|CORO6_ENST00000584969.1_Silent_p.V42V|CORO6_ENST00000388767.3_Silent_p.V42V			Q6QEF8	CORO6_HUMAN	coronin 6	42					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)	actin filament binding (GO:0051015)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(2)	14						ATTTGGGGTTGACGGCACAGA	0.592																																					p.V42V													.	CORO6-90	0			c.C126T						.						75	80	78					17																	27948314		2187	4295	6482	SO:0001819	synonymous_variant	84940	exon1			GGGGTTGACGGCA	AF193039	CCDS11252.2	17q11.2	2013-01-10			ENSG00000167549	ENSG00000167549		"Coronins", "WD repeat domain containing"	21356	protein-coding gene	gene with protein product							Standard	NM_032854		Approved	FLJ14871	uc002hel.2	Q6QEF8	OTTHUMG00000132732	ENST00000445145.2:c.126C>T	17.37:g.27948314G>A		Somatic	83	1		WXS	Illumina HiSeq	Phase_I	119	48	NM_032854	0	0	0	0	0	B3KU26|Q71MF3|Q8WYH7|Q96K02	Silent	SNP	ENST00000445145.2	37																																																																																				.		0.592	CORO6-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000447831.1	NM_032854		A	27948314	G	A	27948314	2	1	142	1	0	0	0	0	0	0	0	1	3764	1277	45	2		2	CORO6	17	27948314	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	9986051	27948314	53246896	90	12726											
TOP2A	7153	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	38562843	38562844	+	Frame_Shift_Ins	INS	-	-	T																															ttcattacaaacctttgtaaINStatttgactttccatttttt																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:38562843_38562844insT	ENST00000423485.1	-	15	1993_1994	c.1835_1836insA	c.(1834-1836)tatfs	p.Y612fs		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	612					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	AACCTTTGTAATATTTGACTTT	0.317																																					p.Y612_Y613delinsX		.											.	TOP2A-655	0			c.1836_1837insA						.																																			SO:0001589	frameshift_variant	7153	exon15			.		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"topoisomerase (DNA) II alpha (170kD)"	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.1836dupA	17.37:g.38562844_38562844dupT	ENSP00000411532:p.Tyr612fs	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	70	31	NM_001067	0	0	0	0	0	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Nonsense_Mutation	INS	ENST00000423485.1	37	CCDS45672.1																																																																																			.		0.317	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			T	38562844	-	T	38562843	7	5	142	1	0	1	1	0	0	0	0	0	16398	108	4	0	2843	0	TOP2A	17	38562843	Frame_Shift_Ins	INS	-	TCGA-IZ-A6M8-01A-11D-A31X-10	10614529	38562843	42632367	91	12727											
KRTAP3-2	83897	bcgsc.ca	37	chr17	39155883	39155883	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gttgagggtctccaggcccgGagttggctggcaggagttga	6	9	18	8	1	1	2	0	2	1	0	2	4	1	4	2	6	0	5	2	6	0	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:39155883G>C	ENST00000391587.1	-	1	255	c.223C>G	c.(223-225)Ccg>Gcg	p.P75A		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	75						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				TCCAGGCCCGGAGTTGGCTGG	0.622																																					p.P75A													.	.	0			c.C223G						.						61	79	73					17																	39155883		2201	4296	6497	SO:0001583	missense	83897	exon1			GGCCCGGAGTTGG	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"Keratin associated proteins"	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.223C>G	17.37:g.39155883G>C	ENSP00000375429:p.Pro75Ala	Somatic	107	3		WXS	Illumina HiSeq	Phase_1	153	90	NM_031959	0	0	0	0	0		Missense_Mutation	SNP	ENST00000391587.1	37	CCDS32644.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.718303	0.30503	.	.	ENSG00000212900	ENST00000391587	T	0.34472	1.36	5.76	5.76	0.90799	.	0.000000	0.56097	D	0.000025	T	0.47154	0.1430	.	.	.	0.38317	D	0.943408	P	0.45348	0.856	P	0.48454	0.578	T	0.53222	-0.8469	9	0.72032	D	0.01	.	15.5326	0.75977	0.0:0.0:1.0:0.0	.	75	Q9BYR7	KRA32_HUMAN	A	75	ENSP00000375429:P75A	ENSP00000375429:P75A	P	-	1	0	KRTAP3-2	36409409	1.000000	0.71417	0.922000	0.36590	0.095000	0.18619	4.486000	0.60286	2.732000	0.93576	0.558000	0.71614	CCG	.		0.622	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1			C	39155883	G	C	39155883	3	2	142	1	0	0	0	0	1	0	0	0	8567	1174	41	4	77	4	KRTAP3-2	17	39155883	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	593040	39155883	42039327	92	12728											
TEX14	56155	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	56676917	56676918	+	Frame_Shift_Del	DEL	GA	GA	-																															cataaatggagcagggcaagGagcatcttgattctgagtct																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:56676917_56676918delGA	ENST00000240361.8	-	14	1891_1892	c.1806_1807delTC	c.(1804-1809)gctcctfs	p.P603fs	TEX14_ENST00000349033.5_Frame_Shift_Del_p.P597fs|TEX14_ENST00000389934.3_Frame_Shift_Del_p.P597fs			Q8IWB6	TEX14_HUMAN	testis expressed 14	603					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCAGGGCAAGGAGCATCTTGAT	0.53																																					p.602_603del		.											.	TEX14-810	0			c.1806_1807del						.																																			SO:0001589	frameshift_variant	56155	exon14			.	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1806_1807delTC	17.37:g.56676917_56676918delGA	ENSP00000240361:p.Pro603fs	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	81	35	NM_001201457	0	0	0	0	0	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Frame_Shift_Del	DEL	ENST00000240361.8	37	CCDS56042.1																																																																																			.		0.53	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			-	56676918	GA	-	56676917	7	5	142	1	0	1	0	1	0	0	0	0	15810	1174	41	0	2766	0	TEX14	17	56676917	Frame_Shift_Del	DEL	GA	TCGA-IZ-A6M8-01A-11D-A31X-10	17521034	56676917	24518293	93	12729											
ACOX1	51	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73953542	73953542	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgaaaaattcacttacgcCcaccaggccaccatttaatg	13	9	6	13	1	1	1	1	1	0	0	1	1	1	1	4	1	1	1	4	1	4	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:73953542C>G	ENST00000301608.4	-	4	596	c.536G>C	c.(535-537)gGg>gCg	p.G179A	ACOX1_ENST00000293217.5_Missense_Mutation_p.G179A|ACOX1_ENST00000591857.1_5'UTR|ACOX1_ENST00000537812.1_Missense_Mutation_p.G141A	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	179					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	TCACTTACGCCCACCAGGCCA	0.443																																					p.G179A													.	ACOX1-91	0			c.G536C						.						112	106	108					17																	73953542		2203	4300	6503	SO:0001583	missense	51	exon4			TTACGCCCACCAG	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"acyl-Coenzyme A oxidase 1, palmitoyl"			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.536G>C	17.37:g.73953542C>G	ENSP00000301608:p.Gly179Ala	Somatic	148	2		WXS	Illumina HiSeq	Phase_I	149	73	NM_007292	0	0	0	0	0	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.012128	0.54468	.	.	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.69685	-0.42;-0.42;-0.42	5.64	5.64	0.86602	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.096704	0.64402	D	0.000001	T	0.69593	0.3128	L	0.60845	1.875	0.80722	D	1	P;P;B;B	0.35481	0.504;0.504;0.329;0.446	B;B;B;B	0.40285	0.117;0.232;0.325;0.107	T	0.67260	-0.5715	10	0.37606	T	0.19	-20.1018	19.7014	0.96054	0.0:1.0:0.0:0.0	.	111;141;179;179	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	A	179;179;141;179;111	ENSP00000301608:G179A;ENSP00000293217:G179A;ENSP00000441257:G141A	ENSP00000293217:G179A	G	-	2	0	ACOX1	71465137	1.000000	0.71417	0.988000	0.46212	0.923000	0.55619	7.480000	0.81109	2.657000	0.90304	0.637000	0.83480	GGG	.		0.443	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1			G	73953542	C	G	73953542	3	3	142	1	0	0	0	0	1	0	0	0	158	623	22	4	1490	4	ACOX1	17	73953542	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	17276625	73953542	7241668	94	12730											
FASN	2194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80047603	80047603	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acactcctcccaggacaagcCtatggcagagccagcctcag	11	5	9	16	0	1	1	1	0	0	1	3	2	3	2	5	2	3	1	5	2	2	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:80047603C>G	ENST00000306749.2	-	12	2089		c.e12-1			NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase						acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CAGGACAAGCCTATGGCAGAG	0.652																																					.	Colon(59;314 1043 11189 28578 32273)	.											.	FASN-90	0			c.1871-1G>C						.						16	15	16					17																	80047603		2171	4272	6443	SO:0001630	splice_region_variant	2194	exon13			ACAAGCCTATGGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.1871-1G>C	17.37:g.80047603C>G		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	92	15	NM_004104	0	0	0	0	0	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Splice_Site	SNP	ENST00000306749.2	37	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865470	0.51588	.	.	ENSG00000169710	ENST00000306749	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9623	0.86275	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FASN	77640892	1.000000	0.71417	0.168000	0.22838	0.067000	0.16453	5.505000	0.66981	1.997000	0.58415	0.561000	0.74099	.	.		0.652	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	Intron	G	80047603	C	G	80047603	5	3	142	1	0	0	0	0	0	0	1	0	5702	695	24	4	5793	4	FASN	17	80047603	Splice_Site	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	6094061	80047603	1147607	95	12731											
ANKRD29	147463	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	21214112	21214112	+	Splice_Site	DEL	T	T	-																															ccaacagggcggtgcccccgTcctatggacatgcaaagtat																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr18:21214112delT	ENST00000592179.1	-	5	486	c.332delA	c.(331-333)gac>gc	p.D111fs	ANKRD29_ENST00000284207.7_Splice_Site_p.D111fs|ANKRD29_ENST00000322980.9_Splice_Site_p.D111fs	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	111										breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GGTGCCCCCGTCCTATGGACA	0.498																																					p.D111fs		.											.	ANKRD29-156	0			c.332delA						.						74	59	64					18																	21214112		2203	4300	6503	SO:0001630	splice_region_variant	147463	exon5			.	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"Ankyrin repeat domain containing"	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.331-1A>-	18.37:g.21214112delT		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_173505	0	0	0	0	0	B2R972|Q6ZWE8|Q96LU9	Frame_Shift_Del	DEL	ENST00000592179.1	37	CCDS11879.1																																																																																			.		0.498	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505	Frame_Shift_Del	-	21214112	T	-	21214112	8	5	142	1	0	1	0	1	0	0	1	0	657	1681	58	0	597	0	ANKRD29	18	21214112	Splice_Site	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		21214112	56863136	96	12732	132	2									
ANKRD29	147463	bcgsc.ca	37	chr18	21214114	21214114	+	Splice_Site	SNP	C	C	T																															aacagggcggtgcccccgtcCtatggacatgcaaagtataa																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr18:21214114C>T	ENST00000592179.1	-	5	485		c.e5-1		ANKRD29_ENST00000284207.7_Splice_Site|ANKRD29_ENST00000322980.9_Splice_Site	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29											breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGCCCCCGTCCTATGGACATG	0.502																																					.													.	ANKRD29-156	0			c.331-1G>A						.						72	58	63					18																	21214114		2203	4300	6503	SO:0001630	splice_region_variant	147463	exon6			CCCGTCCTATGGA	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"Ankyrin repeat domain containing"	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.331-1G>A	18.37:g.21214114C>T		Somatic	53	1		WXS	Illumina HiSeq	Phase_1	56	18	NM_173505	0	0	0	0	0	B2R972|Q6ZWE8|Q96LU9	Splice_Site	SNP	ENST00000592179.1	37	CCDS11879.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298068	0.40694	.	.	ENSG00000154065	ENST00000322980;ENST00000284207	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8957	0.92423	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKRD29	19468112	1.000000	0.71417	0.986000	0.45419	0.061000	0.15899	6.746000	0.74866	2.832000	0.97577	0.655000	0.94253	.	.		0.502	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505	Intron	T	21214114	C	T	21214114	5	4	142	1	0	0	0	0	0	0	1	0	657	695	24	2	599	2	ANKRD29	18	21214114	Splice_Site	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	2	21214114	56863134	97	12733	132	2									
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9057871	9057871	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctagtctcagagaaggcagGatttgatgtgaaaacagtgg	13	9	13	6	0	1	3	1	2	1	1	2	5	1	4	1	3	1	1	1	3	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:9057871G>A	ENST00000397910.4	-	3	29778	c.29575C>T	c.(29575-29577)Cct>Tct	p.P9859S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9861	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGAAGGCAGGATTTGATGTG	0.478																																					p.P9859S		.											.	MUC16-566	0			c.C29575T						.						147	138	141					19																	9057871		1987	4169	6156	SO:0001583	missense	94025	exon3			AGGCAGGATTTGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29575C>T	19.37:g.9057871G>A	ENSP00000381008:p.Pro9859Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	123	36	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.787	-0.044427	0.07452	.	.	ENSG00000181143	ENST00000397910	T	0.26223	1.75	2.62	0.396	0.16309	.	.	.	.	.	T	0.23330	0.0564	N	0.14661	0.345	.	.	.	D	0.54207	0.965	P	0.59703	0.862	T	0.26503	-1.0101	8	0.87932	D	0	.	3.8274	0.08859	0.1494:0.2545:0.5961:0.0	.	9859	B5ME49	.	S	9859	ENSP00000381008:P9859S	ENSP00000381008:P9859S	P	-	1	0	MUC16	8918871	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.124000	0.03260	0.181000	0.19994	-1.109000	0.02080	CCT	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9057871	G	A	9057871	3	1	142	1	0	0	0	0	1	0	0	0	9998	1174	41	2	14276	2	MUC16	19	9057871	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		9057871	50071112	98	12734											
CARM1	10498	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11019856	11019856	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctaccagcgcgccatcctGcaaaaccacaccgacttcaa	13	5	5	18	3	1	0	1	0	0	0	2	1	2	0	6	0	4	1	6	0	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:11019856G>A	ENST00000327064.4	+	4	721	c.531G>A	c.(529-531)ctG>ctA	p.L177L	CARM1_ENST00000344150.4_Silent_p.L177L	NM_199141.1	NP_954592.1	Q86X55	CARM1_HUMAN	coactivator-associated arginine methyltransferase 1	177	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cellular lipid metabolic process (GO:0044255)|endochondral bone morphogenesis (GO:0060350)|histone H3-R17 methylation (GO:0034971)|histone H3-R2 methylation (GO:0034970)|histone methylation (GO:0016571)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of protein binding (GO:0032091)|pathogenesis (GO:0009405)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-R17 specific) (GO:0035642)|histone-arginine N-methyltransferase activity (GO:0008469)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|lysine-acetylated histone binding (GO:0070577)|protein methyltransferase activity (GO:0008276)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	13						GCGCCATCCTGCAAAACCACA	0.517																																					p.L177L													.	CARM1-90	0			c.G531A						.						102	77	86					19																	11019856		2203	4300	6503	SO:0001819	synonymous_variant	10498	exon4			CATCCTGCAAAAC	AF055027	CCDS12250.1	19p13.2	2010-10-11			ENSG00000142453	ENSG00000142453		"Protein arginine methyltransferases"	23393	protein-coding gene	gene with protein product		603934				10381882, 11724789	Standard	NM_199141		Approved	PRMT4	uc002mpz.3	Q86X55		ENST00000327064.4:c.531G>A	19.37:g.11019856G>A		Somatic	73	1		WXS	Illumina HiSeq	Phase_I	60	20	NM_199141	0	0	5	13	8	A6NN38	Silent	SNP	ENST00000327064.4	37	CCDS12250.1																																																																																			.		0.517	CARM1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452625.1	XM_032719		A	11019856	G	A	11019856	2	1	142	1	0	0	0	0	0	0	0	1	2661	1306	46	2		2	CARM1	19	11019856	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	1961985	11019856	48109127	99	12735											
FCGBP	8857	broad.mit.edu	37	chr19	40366441	40366444	+	Frame_Shift_Del	DEL	CGCA	CGCA	-																															acgccgccggcacgcgcaggCgcacgaagctgtccccatcg																								rs145808007	byFrequency	TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	CGCA	CGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:40366441_40366444delCGCA	ENST00000221347.6	-	30	13797_13800	c.13790_13793delTGCG	c.(13789-13794)gtgcgcfs	p.VR4597fs		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4597	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CACGCGCAGGCGCACGAAGCTGTC	0.672																																					p.4597_4598del													.	FCGBP-98	0			c.13790_13793del						.																																			SO:0001589	frameshift_variant	8857	exon30			CGCAGGCGCACGA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13790_13793delTGCG	19.37:g.40366441_40366444delCGCA	ENSP00000221347:p.Val4597fs	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	98	8	NM_003890	0	0	0	0	0	O95784	Frame_Shift_Del	DEL	ENST00000221347.6	37	CCDS12546.1																																																																																			.		0.672	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		-	40366444	CGCA	-	40366441	7	5	142	1	0	1	0	1	0	0	0	0	5797	768	27	0	2452	0	FCGBP	19	40366441	Frame_Shift_Del	DEL	CGCA	TCGA-IZ-A6M8-01A-11D-A31X-10	29346585	40366441	18762542	100	12736											
ZNF45	7596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44419046	44419046	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcatgagccctttggttaAtttgaagatgagagctccag	10	12	11	8	0	0	4	0	3	0	2	1	5	1	4	2	1	3	3	2	1	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:44419046A>C	ENST00000269973.5	-	10	1632	c.542T>G	c.(541-543)aTt>aGt	p.I181S	RP11-15A1.2_ENST00000586247.1_RNA|ZNF45_ENST00000589703.1_Missense_Mutation_p.I181S	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	181					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						CCTTTGGTTAATTTGAAGATG	0.443																																					p.I181S		.											.	ZNF45-91	0			c.T542G						.						126	128	127					19																	44419046		2203	4300	6503	SO:0001583	missense	7596	exon10			TGGTTAATTTGAA	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"Zinc fingers, C2H2-type", "-"	13111	protein-coding gene	gene with protein product		194554	"zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)", "zinc finger protein 13"	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.542T>G	19.37:g.44419046A>C	ENSP00000269973:p.Ile181Ser	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	74	25	NM_003425	0	0	0	1	1	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	.	.	.	.	.	.	.	.	.	.	A	6.279	0.419509	0.11928	.	.	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.15139	2.45	3.91	-3.04	0.05412	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	2.004110	0.02863	N	0.130523	T	0.07279	0.0184	N	0.13299	0.325	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18178	-1.0345	10	0.08179	T	0.78	0.9799	0.481	0.00547	0.3318:0.133:0.2741:0.2611	.	181	Q02386	ZNF45_HUMAN	S	181	ENSP00000269973:I181S	ENSP00000269973:I181S	I	-	2	0	ZNF45	49110886	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-5.448000	0.00121	-0.856000	0.04120	0.260000	0.18958	ATT	.		0.443	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425		C	44419046	A	C	44419046	3	2	142	1	0	0	0	0	1	0	0	0	17953	101	4	5	1510	5	ZNF45	19	44419046	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	4052605	44419046	14709937	101	12737											
ZNF534	147658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52941044	52941044	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacttaaaaatcaacatggaTtaactcttcagttacatctg	15	13	4	9	0	4	0	2	0	2	0	4	1	4	1	0	1	3	1	0	1	6	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:52941044T>A	ENST00000332323.6	+	4	431	c.370T>A	c.(370-372)Tta>Ata	p.L124I	ZNF534_ENST00000433050.1_Missense_Mutation_p.L111I|ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Intron	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	124					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)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						TCAACATGGATTAACTCTTCA	0.353																																					p.L124I		.											.	ZNF534-68	0			c.T370A						.						71	60	63					19																	52941044		1568	3582	5150	SO:0001583	missense	147658	exon4			CATGGATTAACTC	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"Zinc fingers, C2H2-type", "-"	26337	protein-coding gene	gene with protein product			"KRAB domain only 3"	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.370T>A	19.37:g.52941044T>A	ENSP00000327538:p.Leu124Ile	Somatic	455	0		WXS	Illumina HiSeq	Phase_I	257	82	NM_001143939	0	0	0	0	0	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	37	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	T	9.193	1.026520	0.19512	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.07444	3.19;3.23	1.69	1.69	0.24217	.	.	.	.	.	T	0.11750	0.0286	M	0.62723	1.935	0.09310	N	1	P;P	0.44344	0.833;0.524	P;B	0.45276	0.475;0.095	T	0.14309	-1.0477	9	0.45353	T	0.12	.	6.6481	0.22947	0.0:0.0:0.0:1.0	.	111;124	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	I	124;111;123	ENSP00000327538:L124I;ENSP00000391358:L111I	ENSP00000327538:L124I	L	+	1	2	ZNF534	57632856	0.001000	0.12720	0.012000	0.15200	0.302000	0.27658	-0.032000	0.12266	0.751000	0.32900	0.172000	0.16884	TTA	.		0.353	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		A	52941044	T	A	52941044	3	1	142	1	0	0	0	0	1	0	0	0	18005	1490	52	5	384	5	ZNF534	19	52941044	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	8521998	52941044	6187939	102	12738											
CRNKL1	51340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	20033152	20033152	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcgcttgagccgtgacggaGgcggcaccgtttccatggtg	5	9	15	12	5	0	2	0	2	0	0	2	3	1	3	3	4	1	3	3	4	0	2	rs140622884		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr20:20033152G>A	ENST00000377340.2	-	2	349	c.318C>T	c.(316-318)gcC>gcT	p.A106A	C20orf26_ENST00000377309.2_5'Flank|C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000245957.5_5'Flank|CRNKL1_ENST00000377327.4_Silent_p.A94A|CRNKL1_ENST00000536226.1_5'Flank|C20orf26_ENST00000389656.3_5'Flank	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	106					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CCGTGACGGAGGCGGCACCGT	0.607																																					p.A106A		.											.	CRNKL1-137	0			c.C318T						.	G		1,4405	2.1+/-5.4	0,1,2202	74	70	71		318	-9	0	20	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous	CRNKL1	NM_016652.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		106/849	20033152	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51340	exon2			GACGGAGGCGGCA	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.318C>T	20.37:g.20033152G>A		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	131	38	NM_016652	0	0	0	0	0	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Silent	SNP	ENST00000377340.2	37	CCDS33446.1																																																																																			G|1.000;A|0.000		0.607	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			A	20033152	G	A	20033152	2	1	142	1	0	0	0	0	0	0	0	1	3897	987	35	2		2	CRNKL1	20	20033152	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		20033152	42992368	103	12739											
TM9SF4	9777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	30730877	30730877	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgtaccgtgtcgtccgcttCgaggtgattccccagagcat	7	10	11	13	5	0	2	0	1	0	1	4	3	2	2	4	1	2	3	4	1	1	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr20:30730877C>T	ENST00000398022.2	+	6	856	c.621C>T	c.(619-621)ttC>ttT	p.F207F	TM9SF4_ENST00000217315.5_Silent_p.F190F	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	207						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TCGTCCGCTTCGAGGTGATTC	0.597																																					p.F207F		.											.	TM9SF4-514	0			c.C621T						.						151	107	122					20																	30730877		2203	4300	6503	SO:0001819	synonymous_variant	9777	exon6			CCGCTTCGAGGTG	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.621C>T	20.37:g.30730877C>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	69	17	NM_014742	0	0	8	8	0	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	37	CCDS13196.2																																																																																			.		0.597	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30730877	C	T	30730877	2	4	142	1	0	0	0	0	0	0	0	1	16012	883	31	1		1	TM9SF4	20	30730877	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	10697725	30730877	32294643	104	12740											
CDH4	1002	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	60427908	60427908	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgacaaccgccctgagttCatcaaccaggtctacaacgg	13	7	8	13	2	3	2	2	2	1	0	3	2	3	2	3	2	4	1	3	2	5	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr20:60427908C>A	ENST00000360469.5	+	6	919	c.831C>A	c.(829-831)ttC>ttA	p.F277L	CDH4_ENST00000543233.1_Missense_Mutation_p.F203L	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	277	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GCCCTGAGTTCATCAACCAGG	0.582																																					p.F277L													.	CDH4-282	0			c.C831A						.						219	174	189					20																	60427908		2203	4300	6503	SO:0001583	missense	1002	exon6			TGAGTTCATCAAC	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"Cadherins / Major cadherins"	1763	protein-coding gene	gene with protein product	"R-Cadherin"	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.831C>A	20.37:g.60427908C>A	ENSP00000353656:p.Phe277Leu	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	100	34	NM_001794	0	0	0	0	0	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789775	0.50102	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.78707	-1.2;-1.2	4.76	3.7	0.42460	Cadherin (3);Cadherin-like (1);	0.110955	0.64402	D	0.000008	T	0.80204	0.4580	M	0.92880	3.355	0.58432	D	0.999995	B	0.25609	0.13	B	0.17433	0.018	T	0.80190	-0.1485	9	.	.	.	.	11.0665	0.47979	0.0:0.8229:0.0:0.1771	.	277	P55283	CADH4_HUMAN	L	277;185;203	ENSP00000353656:F277L;ENSP00000443301:F203L	.	F	+	3	2	CDH4	59861303	0.662000	0.27439	0.994000	0.49952	0.873000	0.50193	1.182000	0.32029	2.202000	0.70862	0.561000	0.74099	TTC	.		0.582	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		A	60427908	C	A	60427908	3	1	142	1	0	0	0	0	1	0	0	0	3118	825	29	4	853	4	CDH4	20	60427908	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	29697031	60427908	2597612	105	12741											
PRODH	5625	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18909899	18909899	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcagccctggatgcgatgcCcaactttgcgacactttcct	7	11	8	15	2	1	0	1	0	0	0	2	3	2	1	3	1	5	0	3	1	1	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr22:18909899C>A	ENST00000357068.6	-	7	1133	c.868G>T	c.(868-870)Ggc>Tgc	p.G290C	PRODH_ENST00000420436.1_Missense_Mutation_p.G182C|PRODH_ENST00000334029.2_Missense_Mutation_p.G182C	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	290					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	GATGCGATGCCCAACTTTGCG	0.562																																					p.G290C													.	PRODH-289	0			c.G868T						.						92	78	83					22																	18909899		2203	4300	6503	SO:0001583	missense	5625	exon8			CGATGCCCAACTT	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"proline dehydrogenase (proline oxidase )"			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.868G>T	22.37:g.18909899C>A	ENSP00000349577:p.Gly290Cys	Somatic	125	2		WXS	Illumina HiSeq	Phase_I	148	52	NM_016335	0	0	0	8	8	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Missense_Mutation	SNP	ENST00000357068.6	37	CCDS13754.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	21.2|21.2	4.109058|4.109058	0.77096|0.77096	.|.	.|.	ENSG00000100033|ENSG00000100033	ENST00000357068;ENST00000399694;ENST00000450579|ENST00000438924	T;T|.	0.64803|.	-0.12;0.61|.	4.63|4.63	4.63|4.63	0.57726|0.57726	Proline dehydrogenase (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.80210|0.80210	0.4581|0.4581	M|M	0.88105|0.88105	2.93|2.93	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.83981|0.83981	0.0332|0.0332	10|6	0.87932|.	D|.	0|.	-23.324|-23.324	15.5145|15.5145	0.75812|0.75812	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	206;290;182|.	O43272-1;O43272;E7EQL6|.	.;PROD_HUMAN;.|.	C|V	290;83;131|150	ENSP00000349577:G290C;ENSP00000396806:G131C|.	ENSP00000334726:G182C|.	G|G	-|-	1|2	0|0	PRODH|PRODH	17289899|17289899	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.860000|0.860000	0.49131|0.49131	6.925000|6.925000	0.75829|0.75829	2.316000|2.316000	0.78162|0.78162	0.638000|0.638000	0.83543|0.83543	GGC|GGG	.		0.562	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335		A	18909899	C	A	18909899	3	1	142	1	0	0	0	0	1	0	0	0	12577	623	22	4	966	4	PRODH	22	18909899	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		18909899	32394667	106	12742											
KDM6A	7403	hgsc.bcm.edu;bcgsc.ca	37	chrX	44918293	44918293	+	Frame_Shift_Del	DEL	T	T	-																															gttcaggatgcctttatatcTtacaggcagtctattgataa																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chrX:44918293delT	ENST00000377967.4	+	11	959	c.918delT	c.(916-918)tctfs	p.S306fs	KDM6A_ENST00000543216.1_Frame_Shift_Del_p.S306fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.S306fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.S306fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	306	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						CCTTTATATCTTACAGGCAGT	0.318			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.S306fs	Colon(129;1273 1667 15230 27352 52914)	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A-2748	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.918delT						.						88	79	82					X																	44918293		2203	4300	6503	SO:0001589	frameshift_variant	7403	exon11			.	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"Chromatin-modifying enzymes / K-demethylases", "Tetratricopeptide (TTC) repeat domain containing"	12637	protein-coding gene	gene with protein product		300128	"ubiquitously transcribed tetratricopeptide repeat, X chromosome"	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.918delT	X.37:g.44918293delT	ENSP00000367203:p.Ser306fs	Somatic	295	0		WXS	Illumina HiSeq	Phase_I	163	50	NM_021140	0	0	0	0	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																			.		0.318	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44918293	T	-	44918293	7	5	142	1	0	1	0	1	0	0	0	0	8158	1596	56	0	960	0	KDM6A	23	44918293	Frame_Shift_Del	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		44918293	110352267	107	12743											
ATP7A	538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	77268391	77268391	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcagtttttcggaggctggTacttctacattcaggcttat	7	16	10	8	1	2	0	1	0	1	0	3	1	2	1	0	4	3	5	0	4	3	7			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chrX:77268391T>A	ENST00000341514.6	+	10	2343	c.2188T>A	c.(2188-2190)Tac>Aac	p.Y730N	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	730					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CGGAGGCTGGTACTTCTACAT	0.343																																					p.Y730N		.											.	ATP7A-130	0			c.T2188A						.						139	122	127					X																	77268391		2203	4296	6499	SO:0001583	missense	538	exon10			GGCTGGTACTTCT	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2188T>A	X.37:g.77268391T>A	ENSP00000345728:p.Tyr730Asn	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	38	22	NM_000052	0	0	0	0	0	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	37	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.309564	0.60414	.	.	ENSG00000165240	ENST00000341514	T	0.75938	-0.98	5.64	-1.38	0.09027	.	0.505078	0.21943	N	0.066860	T	0.73345	0.3575	L	0.51422	1.61	0.80722	D	1	P	0.38729	0.644	P	0.48654	0.585	T	0.71629	-0.4535	10	0.59425	D	0.04	-15.6701	11.7399	0.51786	0.0:0.5586:0.0:0.4414	.	730	Q04656	ATP7A_HUMAN	N	730	ENSP00000345728:Y730N	ENSP00000345728:Y730N	Y	+	1	0	ATP7A	77155047	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	0.785000	0.26830	-0.249000	0.09569	0.381000	0.24937	TAC	.		0.343	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		A	77268391	T	A	77268391	3	1	142	1	0	0	0	0	1	0	0	0	1191	1638	57	5	2222	5	ATP7A	23	77268391	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	32350098	77268391	78002169	108	12744											
CLSTN1	22883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	9809529	9809529	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtctccttaccacagagccgGtggagggacttctctgagta	8	10	12	11	1	2	2	0	1	2	1	4	4	2	4	3	3	2	1	3	3	2	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:9809529G>A	ENST00000377298.4	-	7	1767	c.975C>T	c.(973-975)caC>caT	p.H325H	CLSTN1_ENST00000361311.4_Silent_p.H315H|CLSTN1_ENST00000377288.3_Silent_p.H325H	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	325					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CACAGAGCCGGTGGAGGGACT	0.557																																					p.H325H		.											.	CLSTN1-523	0			c.C975T						.						100	102	101					1																	9809529		2203	4300	6503	SO:0001819	synonymous_variant	22883	exon7			GAGCCGGTGGAGG	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.975C>T	1.37:g.9809529G>A		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	74	32	NM_001009566	0	0	0	0	0	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Silent	SNP	ENST00000377298.4	37	CCDS30580.1																																																																																			.		0.557	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			A	9809529	G	A	9809529	2	1	143	1	0	0	0	0	0	0	0	1	3567	1252	44	2		2	CLSTN1	1	9809529	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		9809529	239441092	1	12745											
CSDE1	7812	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	115277116	115277116	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtttctttttcaacagcaTaatgttgcgagcacttacag	10	16	7	8	1	2	0	1	0	1	0	2	1	2	0	0	0	5	4	0	0	3	7	rs200868850		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:115277116T>A	ENST00000358528.4	-	7	955	c.529A>T	c.(529-531)Atg>Ttg	p.M177L	CSDE1_ENST00000438362.2_Missense_Mutation_p.M223L|CSDE1_ENST00000261443.5_Missense_Mutation_p.M146L|CSDE1_ENST00000530886.1_Missense_Mutation_p.M47L|CSDE1_ENST00000369530.1_Missense_Mutation_p.M192L|CSDE1_ENST00000534699.1_Missense_Mutation_p.M177L|CSDE1_ENST00000339438.6_Missense_Mutation_p.M146L	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	177	CSD 2; truncated.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCAACAGCATAATGTTGCGA	0.388																																					p.M223L		.											.	CSDE1-227	0			c.A667T						.						80	80	80					1																	115277116		2203	4300	6503	SO:0001583	missense	7812	exon8			ACAGCATAATGTT		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"upstream of NRAS"	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.529A>T	1.37:g.115277116T>A	ENSP00000351329:p.Met177Leu	Somatic	389	0		WXS	Illumina HiSeq	Phase_I	295	34	NM_001242891	0	1	3	4	0	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.752407	0.49362	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699;ENST00000529046	.	.	.	5.82	4.67	0.58626	Nucleic acid-binding, OB-fold-like (1);	0.141721	0.64402	D	0.000006	T	0.42337	0.1198	L	0.29908	0.895	0.36744	D	0.882387	B;B;B	0.29805	0.04;0.0;0.257	B;B;P	0.44623	0.008;0.0;0.455	T	0.48198	-0.9056	9	0.42905	T	0.14	-0.4958	13.0463	0.58928	0.0:0.0:0.1344:0.8656	.	192;177;223	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	L	146;223;177;146;47;192;177;47	.	ENSP00000261443:M146L	M	-	1	0	CSDE1	115078639	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.781000	0.55394	0.999000	0.39023	0.460000	0.39030	ATG	.		0.388	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		A	115277116	T	A	115277116	3	1	143	1	0	0	0	0	1	0	0	0	3935	1406	49	5	1923	5	CSDE1	1	115277116	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	105467587	115277116	133973505	2	12746											
POLR3C	10623	broad.mit.edu	37	chr1	145608259	145608259	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgccagtcgcacaaatgtGtttgatacttcagcatagtc	10	13	8	10	1	2	1	1	1	1	0	4	1	2	1	1	0	3	3	1	0	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:145608259G>T	ENST00000334163.3	-	4	598	c.438C>A	c.(436-438)aaC>aaA	p.N146K	POLR3C_ENST00000369294.1_Missense_Mutation_p.N146K|RNF115_ENST00000369291.5_5'Flank|POLR3C_ENST00000471254.1_5'UTR	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	146					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			GCACAAATGTGTTTGATACTT	0.517																																					p.N146K													.	POLR3C-91	0			c.C438A						.						186	166	173					1																	145608259		2203	4300	6503	SO:0001583	missense	10623	exon4			AAATGTGTTTGAT	AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"RNA polymerase subunits"	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.438C>A	1.37:g.145608259G>T	ENSP00000334564:p.Asn146Lys	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	89	4	NM_006468	0	0	4	4	0	O15317|Q9Y3R6	Missense_Mutation	SNP	ENST00000334163.3	37	CCDS921.1	.	.	.	.	.	.	.	.	.	.	G	5.188	0.220179	0.09863	.	.	ENSG00000186141	ENST00000334163;ENST00000369294	T;T	0.39229	1.09;1.09	5.41	3.53	0.40419	RNA polymerase III Rpc82, C -terminal (1);	0.652107	0.17151	N	0.185056	T	0.09468	0.0233	N	0.20986	0.625	0.40998	D	0.984907	B;B;B	0.11235	0.003;0.002;0.004	B;B;B	0.12156	0.002;0.002;0.007	T	0.16424	-1.0403	10	0.06236	T	0.91	-13.0953	9.1782	0.37125	0.1803:0.0:0.8197:0.0	.	146;146;146	E9PHH9;Q9BUI4;Q53F76	.;RPC3_HUMAN;.	K	146	ENSP00000334564:N146K;ENSP00000358300:N146K	ENSP00000334564:N146K	N	-	3	2	POLR3C	144319616	0.975000	0.34042	0.976000	0.42696	0.395000	0.30598	1.682000	0.37628	0.640000	0.30582	0.655000	0.94253	AAC	.		0.517	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468		T	145608259	G	T	145608259	3	4	143	1	0	0	0	0	1	0	0	0	12256	1368	48	4	1214	4	POLR3C	1	145608259	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	30331143	145608259	103642362	3	12747											
ACP6	51205	broad.mit.edu	37	chr1	147142085	147142085	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcagctcggccagggccAcccgccgctggtgcaggcag	5	4	15	17	3	0	0	0	0	0	0	1	0	0	0	5	4	3	5	5	4	0	0	rs201678741		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:147142085A>C	ENST00000369238.6	-	1	533	c.86T>G	c.(85-87)gTg>gGg	p.V29G	ACP6_ENST00000392988.2_Missense_Mutation_p.V29G	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	29					dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					GGCCAGGGCCACCCGCCGCTG	0.657																																					p.V29G													.	ACP6-94	0			c.T86G						.						12	10	11					1																	147142085		2053	4027	6080	SO:0001583	missense	51205	exon1			AGGGCCACCCGCC	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.86T>G	1.37:g.147142085A>C	ENSP00000358241:p.Val29Gly	Somatic	82	22		WXS	Illumina HiSeq	Phase_I	58	24	NM_016361	0	0	4	4	0	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Missense_Mutation	SNP	ENST00000369238.6	37	CCDS928.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.149393	0.37923	.	.	ENSG00000162836	ENST00000369238;ENST00000392988	T;T	0.48522	2.65;0.81	5.28	-5.16	0.02857	.	0.609019	0.16327	N	0.219309	T	0.09555	0.0235	L	0.34521	1.04	0.43385	D	0.99549	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.22730	-1.0208	10	0.19147	T	0.46	.	1.0577	0.01593	0.2021:0.3491:0.2212:0.2275	.	29;29	Q9NPH0-2;Q9NPH0	.;PPA6_HUMAN	G	29	ENSP00000358241:V29G;ENSP00000376714:V29G	ENSP00000358241:V29G	V	-	2	0	ACP6	145608709	0.001000	0.12720	0.927000	0.36925	0.947000	0.59692	-0.635000	0.05471	-0.919000	0.03803	-0.460000	0.05396	GTG	.		0.657	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361		C	147142085	A	C	147142085	3	2	143	1	0	0	0	0	1	0	0	0	165	159	6	5	1240	5	ACP6	1	147142085	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	1533826	147142085	102108536	4	12748											
RPRD2	23248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150443766	150443766	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgaaagctacccccgagAgctctccaattctgtatcta	12	10	7	12	1	3	3	0	1	3	2	4	4	3	3	3	0	3	3	3	0	5	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:150443766A>C	ENST00000369068.4	+	11	2346	c.2342A>C	c.(2341-2343)gAg>gCg	p.E781A	RPRD2_ENST00000539519.1_Missense_Mutation_p.E755A|RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.E755A	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	781	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TACCCCCGAGAGCTCTCCAAT	0.498																																					p.E781A		.											.	RPRD2-23	0			c.A2342C						.						84	79	81					1																	150443766		1895	4111	6006	SO:0001583	missense	23248	exon11			CCCGAGAGCTCTC	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"KIAA0460"	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.2342A>C	1.37:g.150443766A>C	ENSP00000358064:p.Glu781Ala	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	109	43	NM_015203	0	0	0	0	0	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.534839	0.64972	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.53206	0.63;0.63;0.63	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000001	T	0.22781	0.0550	N	0.24115	0.695	0.32162	N	0.582853	B;P;P	0.46784	0.319;0.816;0.884	B;B;B	0.40477	0.048;0.177;0.33	T	0.14035	-1.0487	10	0.59425	D	0.04	-7.9453	15.2872	0.73835	1.0:0.0:0.0:0.0	.	755;781;755	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	A	755;755;781	ENSP00000383785:E755A;ENSP00000445482:E755A;ENSP00000358064:E781A	ENSP00000358064:E781A	E	+	2	0	RPRD2	148710390	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.543000	0.73874	2.194000	0.70268	0.529000	0.55759	GAG	.		0.498	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150443766	A	C	150443766	3	2	143	1	0	0	0	0	1	0	0	0	13649	304	11	5	2384	5	RPRD2	1	150443766	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	3301681	150443766	98806855	5	12749											
RPTN	126638	broad.mit.edu	37	chr1	152128054	152128054	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgaccatagtgggaactTtggccttgtccgtctggctg	5	13	13	10	1	2	1	0	1	2	0	3	2	3	2	3	3	1	1	3	3	2	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:152128054T>C	ENST00000316073.3	-	3	1585	c.1521A>G	c.(1519-1521)caA>caG	p.Q507Q		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	507	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.Q507Q(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGTGGGAACTTTGGCCTTGTC	0.498																																					p.Q507Q													.	RPTN-68	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A1521G						.						824	714	748					1																	152128054		1568	3582	5150	SO:0001819	synonymous_variant	126638	exon3			GGAACTTTGGCCT	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"EF-hand domain containing"	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1521A>G	1.37:g.152128054T>C		Somatic	141	2		WXS	Illumina HiSeq	Phase_I	113	4	NM_001122965	0	0	0	0	0	B7ZBZ3	Silent	SNP	ENST00000316073.3	37	CCDS41397.1																																																																																			.		0.498	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		C	152128054	T	C	152128054	2	2	143	1	0	0	0	0	0	0	0	1	13696	1838	64	3		3	RPTN	1	152128054	Silent	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	1684288	152128054	97122567	6	12750											
KIAA1614	57710	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	180885446	180885457	+	In_Frame_Del	DEL	TCCCAGGGTATG	TCCCAGGGTATG	-																															agcctgatggccccccagccTcccagggtatggggagtaca																								rs377550267		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	TCCCAGGGTATG	TCCCAGGGTATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:180885446_180885457delTCCCAGGGTATG	ENST00000367588.4	+	2	262_273	c.207_218delTCCCAGGGTATG	c.(205-219)cctcccagggtatgg>ccg	p.PRVW70del		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	70										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CCCCCCAGCCTCCCAGGGTATGGGGAGTACAG	0.599																																					p.69_73del		.											.	KIAA1614-26	0			c.207_218del						.																																			SO:0001651	inframe_deletion	57710	exon2			.	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.207_218delTCCCAGGGTATG	1.37:g.180885446_180885457delTCCCAGGGTATG	ENSP00000356560:p.Pro70_Trp73del	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	53	17	NM_020950	0	0	0	0	0	Q5VZ45|Q9HCF8	In_Frame_Del	DEL	ENST00000367588.4	37	CCDS41442.1																																																																																			.		0.599	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		-	180885457	TCCCAGGGTATG	-	180885446	7	5	143	1	0	1	0	1	0	0	0	0	8269	1538	54	0	213	0	KIAA1614	1	180885446	In_Frame_Del	DEL	TCCCAGGGTATG	TCGA-IZ-A6M9-01A-11D-A31X-10	28757392	180885446	68365175	7	12751											
KDM5B	10765	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	202701002	202701002	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgagaagggggagtgcaaAtatgaggttctgttgtccca	10	11	15	5	0	1	2	0	2	1	1	2	4	2	3	1	3	1	4	1	3	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:202701002A>C	ENST00000367265.3	-	24	5139	c.3975T>G	c.(3973-3975)taT>taG	p.Y1325*	KDM5B_ENST00000367264.2_Nonsense_Mutation_p.Y1361*	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1325					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GGGAGTGCAAATATGAGGTTC	0.408																																					p.Y1325X		.											.	KDM5B-273	0			c.T3975G						.						111	106	108					1																	202701002		2203	4300	6503	SO:0001587	stop_gained	10765	exon24			GTGCAAATATGAG	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	18039	protein-coding gene	gene with protein product	"cancer/testis antigen 31", "protein phosphatase 1, regulatory subunit 98"	605393	"Jumonji, AT rich interactive domain 1B (RBP2-like)", "jumonji, AT rich interactive domain 1B"	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3975T>G	1.37:g.202701002A>C	ENSP00000356234:p.Tyr1325*	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	70	21	NM_006618	0	0	4	4	0	O95811|Q15752|Q9Y3Q5	Nonsense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	A	47	13.303743	0.99733	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	.	.	.	5.78	3.41	0.39046	.	0.229878	0.47093	D	0.000247	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4004	7.269	0.26246	0.7476:0.1297:0.1226:0.0	.	.	.	.	X	1325;1167;1361;1167	.	ENSP00000235790:Y1167X	Y	-	3	2	KDM5B	200967625	0.999000	0.42202	0.375000	0.26029	0.998000	0.95712	1.112000	0.31172	1.096000	0.41439	0.533000	0.62120	TAT	.		0.408	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		C	202701002	A	C	202701002	4	2	143	1	0	0	0	0	0	1	0	0	8155	108	4	5	675	5	KDM5B	1	202701002	Nonsense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	21815556	202701002	46549619	8	12752											
PLXNA2	5362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	208234136	208234136	+	Missense_Mutation	SNP	A	A	T																															gacccaggttcacgccatggAtggtcactcgcgtccctcct																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:208234136A>T	ENST00000367033.3	-	13	3390	c.2633T>A	c.(2632-2634)aTc>aAc	p.I878N		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	878	IPT/TIG 1.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CACGCCATGGATGGTCACTCG	0.582																																					p.I878N		.											.	PLXNA2-92	0			c.T2633A						.						64	59	60					1																	208234136		2203	4300	6503	SO:0001583	missense	5362	exon13			CCATGGATGGTCA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2633T>A	1.37:g.208234136A>T	ENSP00000356000:p.Ile878Asn	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	89	39	NM_025179	0	0	0	0	0	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751914	0.89753	.	.	ENSG00000076356	ENST00000367033	T	0.70869	-0.52	4.75	4.75	0.60458	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.87744	0.6254	H	0.94847	3.59	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.91215	0.5002	10	0.87932	D	0	.	14.2819	0.66219	1.0:0.0:0.0:0.0	.	878	O75051	PLXA2_HUMAN	N	878	ENSP00000356000:I878N	ENSP00000356000:I878N	I	-	2	0	PLXNA2	206300759	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.956000	0.93066	1.787000	0.52448	0.533000	0.62120	ATC	.		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208234136	A	T	208234136	3	4	143	1	0	0	0	0	1	0	0	0	12146	333	12	5	3131	5	PLXNA2	1	208234136	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	5533134	208234136	41016485	9	12753	133	2									
PLXNA2	5362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	208234142	208234142	+	Missense_Mutation	SNP	A	A	G																															ggttcacgccatggatggtcActcgcgtccctccttccggc																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:208234142A>G	ENST00000367033.3	-	13	3384	c.2627T>C	c.(2626-2628)gTg>gCg	p.V876A		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	876	IPT/TIG 1.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		ATGGATGGTCACTCGCGTCCC	0.587																																					p.V876A		.											.	PLXNA2-92	0			c.T2627C						.						62	57	59					1																	208234142		2203	4300	6503	SO:0001583	missense	5362	exon13			ATGGTCACTCGCG	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"Plexins"	9100	protein-coding gene	gene with protein product	"plexin 2", "plexin-A2", "semaphorin receptor OCT", "transmembrane protein OCT"	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2627T>C	1.37:g.208234142A>G	ENSP00000356000:p.Val876Ala	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	84	38	NM_025179	0	0	0	0	0	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.008254	0.93346	.	.	ENSG00000076356	ENST00000367033	T	0.66815	-0.23	4.75	4.75	0.60458	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81917	0.4924	M	0.91920	3.255	0.80722	D	1	D	0.54397	0.966	P	0.55824	0.785	D	0.86680	0.1916	10	0.87932	D	0	.	14.2819	0.66219	1.0:0.0:0.0:0.0	.	876	O75051	PLXA2_HUMAN	A	876	ENSP00000356000:V876A	ENSP00000356000:V876A	V	-	2	0	PLXNA2	206300765	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.956000	0.93066	1.787000	0.52448	0.533000	0.62120	GTG	.		0.587	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		G	208234142	A	G	208234142	3	3	143	1	0	0	0	0	1	0	0	0	12146	159	6	3	3137	3	PLXNA2	1	208234142	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	6	208234142	41016479	10	12754	133	2									
PTPN14	5784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214557537	214557537	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttaagcatgtgggccgtgCtgtagttatggctgccctgc	5	13	13	10	1	1	0	0	0	1	0	1	0	1	0	2	2	4	5	2	2	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:214557537C>T	ENST00000366956.5	-	13	1855	c.1661G>A	c.(1660-1662)aGc>aAc	p.S554N	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	554					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GTGGGCCGTGCTGTAGTTATG	0.632																																					p.S554N	Colon(92;557 1424 24372 34121 40073)	.											.	PTPN14-290	0			c.G1661A						.						67	69	68					1																	214557537		2203	4300	6503	SO:0001583	missense	5784	exon13			GCCGTGCTGTAGT	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1661G>A	1.37:g.214557537C>T	ENSP00000355923:p.Ser554Asn	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	50	20	NM_005401	0	0	0	0	0	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	5.545	0.285458	0.10513	.	.	ENSG00000152104	ENST00000366956	T	0.67523	-0.27	5.51	-1.94	0.07571	.	0.544215	0.22141	N	0.064056	T	0.36635	0.0974	N	0.11560	0.145	0.28282	N	0.923954	B	0.02656	0.0	B	0.01281	0.0	T	0.21759	-1.0236	10	0.14252	T	0.57	.	6.8274	0.23891	0.113:0.4191:0.0:0.468	.	554	Q15678	PTN14_HUMAN	N	554	ENSP00000355923:S554N	ENSP00000355923:S554N	S	-	2	0	PTPN14	212624160	0.001000	0.12720	0.056000	0.19401	0.764000	0.43329	-0.747000	0.04823	-0.259000	0.09432	0.650000	0.86243	AGC	.		0.632	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214557537	C	T	214557537	3	4	143	1	0	0	0	0	1	0	0	0	12813	797	28	2	1930	2	PTPN14	1	214557537	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	6323395	214557537	34693084	11	12755											
DNAJC5G	285126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27500675	27500675	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatcacctgggtaggaaacTggccttgcggtatcatcccg	8	10	12	11	2	2	0	2	0	0	0	3	1	3	1	3	4	2	3	3	4	4	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:27500675T>A	ENST00000296097.3	+	4	585	c.167T>A	c.(166-168)cTg>cAg	p.L56Q	DNAJC5G_ENST00000404433.1_Missense_Mutation_p.L40Q|DNAJC5G_ENST00000402462.1_Missense_Mutation_p.L56Q|SLC30A3_ENST00000447008.2_5'Flank|DNAJC5G_ENST00000406962.1_Intron	NM_173650.1	NP_775921.1	Q8N7S2	DNJ5G_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 gamma	56	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					membrane (GO:0016020)				cervix(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTAGGAAACTGGCCTTGCGG	0.488																																					p.L56Q		.											.	DNAJC5G-226	0			c.T167A						.						107	102	104					2																	27500675		2203	4300	6503	SO:0001583	missense	285126	exon4			GGAAACTGGCCTT	AF368277	CCDS1744.1	2p23	2011-09-02			ENSG00000163793	ENSG00000163793		"Heat shock proteins / DNAJ (HSP40)"	24844	protein-coding gene	gene with protein product		613946					Standard	NM_173650		Approved	FLJ40417, CSP-gamma	uc002rjl.1	Q8N7S2	OTTHUMG00000097079	ENST00000296097.3:c.167T>A	2.37:g.27500675T>A	ENSP00000296097:p.Leu56Gln	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	79	21	NM_173650	0	0	0	0	0	B4DY29|Q53SY5|Q8IYQ4|Q96RJ8	Missense_Mutation	SNP	ENST00000296097.3	37	CCDS1744.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.492169	0.64074	.	.	ENSG00000163793	ENST00000296097;ENST00000402462;ENST00000404433	T;T;T	0.46819	0.86;0.86;0.86	5.09	5.09	0.68999	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.40554	N	0.001066	T	0.65780	0.2724	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69247	-0.5195	10	0.72032	D	0.01	.	12.8356	0.57771	0.0:0.0:0.0:1.0	.	56	Q8N7S2	DNJ5G_HUMAN	Q	56;56;40	ENSP00000296097:L56Q;ENSP00000384305:L56Q;ENSP00000385829:L40Q	ENSP00000296097:L56Q	L	+	2	0	DNAJC5G	27354179	1.000000	0.71417	1.000000	0.80357	0.243000	0.25628	7.834000	0.86773	1.926000	0.55796	0.455000	0.32223	CTG	.		0.488	DNAJC5G-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214200.1	NM_173650		A	27500675	T	A	27500675	3	1	143	1	0	0	0	0	1	0	0	0	4663	1580	55	5	173	5	DNAJC5G	2	27500675	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		27500675	215698698	12	12756											
GPR39	2863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	133403162	133403162	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcagagaatggttttCaggagcatgaagtttgaatg	11	12	13	5	0	1	3	1	2	0	1	1	5	1	4	0	2	3	5	0	2	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:133403162C>A	ENST00000329321.3	+	2	1814	c.1345C>A	c.(1345-1347)Cag>Aag	p.Q449K	LYPD1_ENST00000397463.2_3'UTR|GPR39_ENST00000470071.1_3'UTR	NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	449					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAATGGTTTTCAGGAGCATGA	0.532																																					p.Q449K		.											.	GPR39-226	0			c.C1345A						.						54	58	57					2																	133403162		2203	4300	6503	SO:0001583	missense	2863	exon2			GGTTTTCAGGAGC	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"GPCR / Class A : Orphans"	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.1345C>A	2.37:g.133403162C>A	ENSP00000327417:p.Gln449Lys	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	64	30	NM_001508	0	0	0	1	1	B2RC12|B6V9G4|Q08AS2|Q53R01	Missense_Mutation	SNP	ENST00000329321.3	37	CCDS2170.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.834578	0.00579	.	.	ENSG00000183840	ENST00000329321	T	0.65178	-0.14	5.15	3.18	0.36537	.	3.248910	0.01165	N	0.006739	T	0.56992	0.2023	L	0.57536	1.79	0.37755	D	0.926099	B	0.02656	0.0	B	0.01281	0.0	T	0.51741	-0.8667	10	0.16896	T	0.51	.	4.3592	0.11194	0.4322:0.446:0.0:0.1219	.	449	O43194	GPR39_HUMAN	K	449	ENSP00000327417:Q449K	ENSP00000327417:Q449K	Q	+	1	0	GPR39	133119632	0.326000	0.24669	0.628000	0.29241	0.050000	0.14768	0.714000	0.25808	1.393000	0.46605	-0.188000	0.12872	CAG	.		0.532	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			A	133403162	C	A	133403162	3	1	143	1	0	0	0	0	1	0	0	0	6713	827	29	4	1351	4	GPR39	2	133403162	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	105902487	133403162	109796211	13	12757											
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152382499	152382499	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acatgcttggtcacttccttGacgtgaacagtgtcccgggt	7	12	11	11	2	1	2	1	2	0	0	3	2	3	2	2	2	2	1	2	2	1	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:152382499G>A	ENST00000172853.10	-	122	17178	c.17031C>T	c.(17029-17031)gtC>gtT	p.V5677V	NEB_ENST00000397345.3_Silent_p.V7378V|NEB_ENST00000409198.1_Silent_p.V5677V|NEB_ENST00000604864.1_Silent_p.V7378V|NEB_ENST00000603639.1_Silent_p.V7378V|NEB_ENST00000427231.2_Silent_p.V7378V			P20929	NEBU_HUMAN	nebulin	5677					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.V5677V(1)|p.V7378V(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCACTTCCTTGACGTGAACAG	0.483																																					p.V7413V		.											.	NEB-145	2	Substitution - coding silent(2)	lung(2)	c.C22239T						.						300	294	296					2																	152382499		2038	4201	6239	SO:0001819	synonymous_variant	4703	exon151			TTCCTTGACGTGA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"nemaline myopathy type 2"	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.17031C>T	2.37:g.152382499G>A		Somatic	126	0		WXS	Illumina HiSeq	Phase_I	102	25	NM_001271208	0	0	0	0	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	10.46	1.355381	0.24512	.	.	ENSG00000183091	ENST00000434685	.	.	.	6.07	5.2	0.72013	.	.	.	.	.	T	0.63885	0.2549	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62756	-0.6787	4	.	.	.	.	12.0778	0.53653	0.0656:0.1214:0.813:0.0	.	.	.	.	L	1	.	.	S	-	2	0	NEB	152090745	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.792000	0.62467	1.582000	0.49881	0.655000	0.94253	TCA	.		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152382499	G	A	152382499	2	1	143	1	0	0	0	0	0	0	0	1	10328	1277	45	2		2	NEB	2	152382499	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	18979337	152382499	90816874	14	12758											
AGPS	8540	broad.mit.edu;bcgsc.ca	37	chr2	178301756	178301756	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggaaggaatgtttgagcGaattcctgatatagttttat	12	14	11	4	1	0	2	0	2	0	0	1	5	1	4	1	2	1	2	1	2	6	6			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:178301756G>T	ENST00000264167.4	+	5	757	c.611G>T	c.(610-612)cGa>cTa	p.R204L	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	204	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)	p.R204Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			ATGTTTGAGCGAATTCCTGAT	0.303																																					p.R204L													.	AGPS-92	1	Substitution - Missense(1)	large_intestine(1)	c.G611T						.						125	132	130					2																	178301756		2203	4300	6503	SO:0001583	missense	8540	exon5			TTGAGCGAATTCC	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.611G>T	2.37:g.178301756G>T	ENSP00000264167:p.Arg204Leu	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	115	5	NM_003659	0	0	1	1	0	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	37	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541251	0.85917	.	.	ENSG00000018510	ENST00000264167;ENST00000536686	D	0.81739	-1.53	5.52	4.64	0.57946	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (2);	0.000000	0.85682	D	0.000000	D	0.89760	0.6808	M	0.83852	2.665	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.91173	0.4970	10	0.87932	D	0	.	14.2952	0.66308	0.0719:0.0:0.9281:0.0	.	204	O00116	ADAS_HUMAN	L	204;74	ENSP00000264167:R204L	ENSP00000264167:R204L	R	+	2	0	AGPS	178010002	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.468000	0.90393	1.315000	0.45114	0.655000	0.94253	CGA	.		0.303	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			T	178301756	G	T	178301756	3	4	143	1	0	0	0	0	1	0	0	0	394	1058	37	4	629	4	AGPS	2	178301756	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	25919257	178301756	64897617	15	12759											
COL3A1	1281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	189867767	189867767	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctcctggagttgcaggaccCcctggaggttctggacctgc	5	9	13	14	0	1	0	0	0	1	0	2	4	2	4	5	5	2	3	5	5	0	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:189867767C>T	ENST00000304636.3	+	36	2702	c.2532C>T	c.(2530-2532)ccC>ccT	p.P844P	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	844	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TTGCAGGACCCCCTGGAGGTT	0.493																																					p.P844P		.											.	COL3A1-581	0			c.C2532T						.						51	61	58					2																	189867767		2068	4020	6088	SO:0001819	synonymous_variant	1281	exon36			AGGACCCCCTGGA	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"Collagens"	2201	protein-coding gene	gene with protein product		120180	"Ehlers-Danlos syndrome type IV, autosomal dominant"	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2532C>T	2.37:g.189867767C>T		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	79	26	NM_000090	0	0	0	0	0	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																			.		0.493	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189867767	C	T	189867767	2	4	143	1	0	0	0	0	0	0	0	1	3694	610	22	2		2	COL3A1	2	189867767	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	11566011	189867767	53331606	16	12760											
NBEAL1	65065	ucsc.edu;bcgsc.ca	37	chr2	204045155	204045155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tattcctgctacctggcaagCtcttatggataatccatatg	10	14	7	10	0	1	0	0	0	1	0	3	1	3	1	3	2	3	3	3	2	6	6			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:204045155C>T	ENST00000449802.1	+	42	6761	c.6428C>T	c.(6427-6429)gCt>gTt	p.A2143V		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2143	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.									NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						ACCTGGCAAGCTCTTATGGAT	0.328																																					p.A2143V													.	NBEAL1-92	0			c.C6428T						.						121	114	116					2																	204045155		1833	4088	5921	SO:0001583	missense	65065	exon42			GGCAAGCTCTTAT	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"WD repeat domain containing"	20681	protein-coding gene	gene with protein product		609816	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6428C>T	2.37:g.204045155C>T	ENSP00000399903:p.Ala2143Val	Somatic	107	2		WXS	Illumina HiSeq		62	27	NM_001114132	0	0	0	0	0	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	C	34	5.404068	0.96051	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.80033	-1.33;-1.33	5.85	5.85	0.93711	BEACH domain (4);	0.266934	0.43260	D	0.000585	D	0.86426	0.5930	M	0.72479	2.2	0.58432	D	0.999998	P;P	0.52692	0.907;0.955	P;P	0.51974	0.686;0.673	D	0.86616	0.1876	10	0.56958	D	0.05	.	19.7681	0.96350	0.0:1.0:0.0:0.0	.	2143;2132	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	V	2143;2143;158	ENSP00000399903:A2143V;ENSP00000388466:A158V	ENSP00000344985:A2143V	A	+	2	0	NBEAL1	203753400	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	7.624000	0.83124	2.768000	0.95171	0.655000	0.94253	GCT	.		0.328	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204045155	C	T	204045155	3	4	143	1	0	0	0	0	1	0	0	0	10213	797	28	2	6590	2	NBEAL1	2	204045155	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	14177388	204045155	39154218	17	12761											
PRKAR2A	5576	broad.mit.edu	37	chr3	48884918	48884918	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggcctcgcgcaggcgggTgaagtactccactgcgaatt	7	7	15	12	5	0	1	0	1	0	0	2	2	1	1	2	3	2	2	2	3	3	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:48884918T>G	ENST00000265563.8	-	1	361	c.112A>C	c.(112-114)Acc>Ccc	p.T38P	PRKAR2A-AS1_ENST00000435419.1_RNA|PRKAR2A-AS1_ENST00000431705.1_RNA|PRKAR2A-AS1_ENST00000416209.2_RNA|PRKAR2A_ENST00000296446.8_Missense_Mutation_p.T38P|PRKAR2A_ENST00000454963.1_Missense_Mutation_p.T38P|PRKAR2A-AS1_ENST00000412171.2_RNA	NM_004157.2	NP_004148.1	P13861	KAP2_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, alpha	38	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)		SLC26A6/PRKAR2A(2)	breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)		CGCAGGCGGGTGAAGTACTCC	0.731																																					p.T38P													.	PRKAR2A-1108	0			c.A112C						.																																			SO:0001583	missense	5576	exon1			GGCGGGTGAAGTA		CCDS2778.1	3p21.3-p21.2	2009-07-10			ENSG00000114302	ENSG00000114302	2.7.11.1		9391	protein-coding gene	gene with protein product		176910		PRKAR2		9676433	Standard	NM_004157		Approved		uc003cux.1	P13861	OTTHUMG00000133540	ENST00000265563.8:c.112A>C	3.37:g.48884918T>G	ENSP00000265563:p.Thr38Pro	Somatic	99	16		WXS	Illumina HiSeq	Phase_I	84	22	NM_004157	0	0	0	0	0	Q16823|Q9BUB1	Missense_Mutation	SNP	ENST00000265563.8	37	CCDS2778.1	.	.	.	.	.	.	.	.	.	.	T	17.06	3.292833	0.60086	.	.	ENSG00000114302	ENST00000265563;ENST00000454963;ENST00000296446;ENST00000419216	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	3.86	3.86	0.44501	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (3);	0.000000	0.56097	D	0.000034	D	0.87325	0.6149	M	0.88031	2.925	0.80722	D	1	D;D	0.61080	0.989;0.989	D;D	0.71656	0.974;0.974	D	0.86994	0.2112	10	0.45353	T	0.12	-0.0721	8.6605	0.34091	0.0:0.0973:0.0:0.9027	.	38;38	Q9BUB1;P13861	.;KAP2_HUMAN	P	38	ENSP00000265563:T38P;ENSP00000394041:T38P;ENSP00000296446:T38P;ENSP00000411432:T38P	ENSP00000265563:T38P	T	-	1	0	PRKAR2A	48859922	1.000000	0.71417	1.000000	0.80357	0.292000	0.27327	3.137000	0.50562	1.521000	0.48983	0.377000	0.23210	ACC	.		0.731	PRKAR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257518.1			G	48884918	T	G	48884918	3	3	143	1	0	0	0	0	1	0	0	0	12534	1696	59	5	1146	5	PRKAR2A	3	48884918	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		48884918	149137512	18	12762											
GLT8D1	55830	bcgsc.ca	37	chr3	52731772	52731772	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtattgttgagagtaacaatGtagaaaatcacattggagcg	15	11	11	4	1	1	2	1	1	0	2	1	4	1	3	0	1	2	4	0	1	6	6	rs370367748		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:52731772G>T	ENST00000407584.3	-	5	1144	c.294C>A	c.(292-294)taC>taA	p.Y98*	GLT8D1_ENST00000266014.5_Nonsense_Mutation_p.Y98*|GLT8D1_ENST00000394783.3_Nonsense_Mutation_p.Y98*|GLT8D1_ENST00000478968.2_Nonsense_Mutation_p.Y98*|GLT8D1_ENST00000463827.1_5'Flank|GLT8D1_ENST00000491606.1_Nonsense_Mutation_p.Y98*	NM_001010983.1|NM_001278280.1	NP_001010983.1|NP_001265209.1	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	98						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)	8				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GAGTAACAATGTAGAAAATCA	0.483																																					p.Y98X													.	GLT8D1-90	0			c.C294A						.						139	128	132					3																	52731772		2203	4300	6503	SO:0001587	stop_gained	55830	exon4			AACAATGTAGAAA	AY358579	CCDS2862.1	3p21.1	2013-02-22			ENSG00000016864	ENSG00000016864		"Glycosyltransferase family 8 domain containing"	24870	protein-coding gene	gene with protein product						12975309	Standard	NM_152932		Approved	AD-017, FLJ14611	uc003dfi.4	Q68CQ7	OTTHUMG00000158759	ENST00000407584.3:c.294C>A	3.37:g.52731772G>T	ENSP00000385730:p.Tyr98*	Somatic	90	2		WXS	Illumina HiSeq	Phase_1	62	51	NM_152932	0	0	1	4	3	Q7Z4D1|Q8N2J6|Q9P0I5	Nonsense_Mutation	SNP	ENST00000407584.3	37	CCDS2862.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388865	0.82902	.	.	ENSG00000016864	ENST00000478968;ENST00000394783;ENST00000407584;ENST00000266014;ENST00000491606;ENST00000479553;ENST00000489119	.	.	.	5.89	5.89	0.94794	.	0.173276	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-11.4738	9.9543	0.41657	0.1851:0.0:0.8149:0.0	.	.	.	.	X	98	.	ENSP00000266014:Y98X	Y	-	3	2	GLT8D1	52706812	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.845000	0.48254	2.793000	0.96121	0.655000	0.94253	TAC	.		0.483	GLT8D1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352065.3	NM_152932		T	52731772	G	T	52731772	4	4	143	1	0	0	0	0	0	1	0	0	6489	1372	48	4	849	4	GLT8D1	3	52731772	Nonsense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	3846854	52731772	145290658	19	12763											
MAGI1	9223	broad.mit.edu	37	chr3	66023695	66023695	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgacggccttgaaggtgaCggcctccttgcagctgtcga	6	10	13	12	3	1	3	0	3	1	0	3	4	2	3	3	3	2	2	3	3	1	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:66023695C>T	ENST00000497477.2	-	1	288	c.289G>A	c.(289-291)Gtc>Atc	p.V97I	MAGI1_ENST00000483466.1_Missense_Mutation_p.V97I|MAGI1_ENST00000402939.2_Missense_Mutation_p.V97I|MAGI1_ENST00000330909.8_Missense_Mutation_p.V97I			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	97	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		TTGAAGGTGACGGCCTCCTTG	0.652																																					p.V97I													.	MAGI1-661	0			c.G289A						.						65	76	72					3																	66023695		2197	4295	6492	SO:0001583	missense	9223	exon1			AGGTGACGGCCTC	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.289G>A	3.37:g.66023695C>T	ENSP00000424369:p.Val97Ile	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	166	5	NM_001033057	0	0	0	0	0	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	9.397	1.077120	0.20227	.	.	ENSG00000151276	ENST00000402939;ENST00000330909;ENST00000483466;ENST00000497477	T;T;T;T	0.21932	2.54;2.12;2.12;1.98	5.77	5.77	0.91146	PDZ/DHR/GLGF (3);Guanylate kinase (1);	0.144117	0.46145	D	0.000305	T	0.09423	0.0232	N	0.16478	0.41	0.33586	D	0.600553	B;B;B;B;B	0.32526	0.066;0.015;0.015;0.374;0.042	B;B;B;B;B	0.20955	0.006;0.006;0.006;0.028;0.032	T	0.10177	-1.0641	10	0.02654	T	1	-14.5033	10.9889	0.47539	0.0:0.887:0.0:0.113	.	97;97;97;97;97	Q96QZ7;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	MAGI1_HUMAN;.;.;.;.	I	97	ENSP00000385450:V97I;ENSP00000331157:V97I;ENSP00000420323:V97I;ENSP00000424369:V97I	ENSP00000331157:V97I	V	-	1	0	MAGI1	65998735	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.773000	0.47686	2.724000	0.93272	0.655000	0.94253	GTC	.		0.652	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	66023695	C	T	66023695	3	4	143	1	0	0	0	0	1	0	0	0	9215	536	19	1	4425	1	MAGI1	3	66023695	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	13291923	66023695	131998735	20	12764											
LRIG1	26018	broad.mit.edu	37	chr3	66433543	66433543	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggtcccatccttcctgcagCctgctgcgggcaggacgctc	4	9	12	16	2	0	0	0	0	0	0	4	1	3	1	4	3	4	4	4	3	0	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:66433543C>T	ENST00000273261.3	-	15	2878	c.2354G>A	c.(2353-2355)gGc>gAc	p.G785D	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Missense_Mutation_p.G762D	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	785					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		CTTCCTGCAGCCTGCTGCGGG	0.607																																					p.G785D													.	LRIG1-230	0			c.G2354A						.						134	128	130					3																	66433543		2203	4300	6503	SO:0001583	missense	26018	exon15			CTGCAGCCTGCTG	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"Immunoglobulin superfamily / I-set domain containing"	17360	protein-coding gene	gene with protein product	"ortholog of mouse integral membrane glycoprotein LIG-1", "leucine-rich repeat protein LRIG1"	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2354G>A	3.37:g.66433543C>T	ENSP00000273261:p.Gly785Asp	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	79	3	NM_015541	0	0	1	1	0	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.689783	0.29962	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.67345	-0.23;-0.26	5.88	5.88	0.94601	.	0.102414	0.64402	D	0.000002	T	0.62405	0.2425	L	0.50333	1.59	0.40098	D	0.976331	B;B;B	0.19445	0.036;0.004;0.021	B;B;B	0.25405	0.032;0.025;0.06	T	0.57608	-0.7782	10	0.33141	T	0.24	.	14.3978	0.67022	0.0:0.9299:0.0:0.0701	.	762;785;785	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	D	785;762;688	ENSP00000273261:G785D;ENSP00000373208:G762D	ENSP00000273261:G785D	G	-	2	0	LRIG1	66516233	0.997000	0.39634	0.995000	0.50966	0.199000	0.23934	1.418000	0.34782	2.782000	0.95742	0.655000	0.94253	GGC	.		0.607	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		T	66433543	C	T	66433543	3	4	143	1	0	0	0	0	1	0	0	0	8969	739	26	2	947	2	LRIG1	3	66433543	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	409848	66433543	131588887	21	12765											
FBXO40	51725	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121345735	121345735	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccacctttagaatcagacCacgaggaagatacgtctcct	12	9	7	13	2	2	3	1	0	1	3	4	5	3	4	4	1	1	0	4	1	4	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:121345735C>T	ENST00000338040.4	+	4	2522	c.2108C>T	c.(2107-2109)cCa>cTa	p.P703L		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	703					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		AGAATCAGACCACGAGGAAGA	0.478																																					p.P703L													.	FBXO40-273	0			c.C2108T						.						77	77	77					3																	121345735		2203	4300	6503	SO:0001583	missense	51725	exon4			TCAGACCACGAGG	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.2108C>T	3.37:g.121345735C>T	ENSP00000337510:p.Pro703Leu	Somatic	90	1		WXS	Illumina HiSeq	Phase_I	57	48	NM_016298	0	0	0	0	0	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.468980	0.26335	.	.	ENSG00000163833	ENST00000338040	T	0.30448	1.53	6.17	4.36	0.52297	.	0.734910	0.13029	N	0.419516	T	0.27663	0.0680	L	0.44542	1.39	0.25676	N	0.985842	B	0.06786	0.001	B	0.08055	0.003	T	0.20907	-1.0261	10	0.66056	D	0.02	0.0962	9.7888	0.40692	0.1392:0.7879:0.0:0.0728	.	703	Q9UH90	FBX40_HUMAN	L	703	ENSP00000337510:P703L	ENSP00000337510:P703L	P	+	2	0	FBXO40	122828425	0.002000	0.14202	0.072000	0.20136	0.410000	0.31052	0.687000	0.25407	0.907000	0.36646	0.655000	0.94253	CCA	.		0.478	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		T	121345735	C	T	121345735	3	4	143	1	0	0	0	0	1	0	0	0	5768	594	21	2	2118	2	FBXO40	3	121345735	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	54912192	121345735	76676695	22	12766											
FAIM	55179	broad.mit.edu	37	chr3	138341182	138341182	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgggaaaagtctcaagaaGtatatggaggacagatcaaa	19	7	11	4	0	2	2	2	0	1	2	3	5	2	5	0	3	0	1	0	3	8	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:138341182G>T	ENST00000393035.2	+	3	373	c.264G>T	c.(262-264)aaG>aaT	p.K88N	FAIM_ENST00000393034.2_Missense_Mutation_p.K88N|FAIM_ENST00000464668.1_Missense_Mutation_p.K88N|FAIM_ENST00000338446.4_Missense_Mutation_p.K122N|FAIM_ENST00000360570.3_Missense_Mutation_p.K110N	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule	88					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						GTCTCAAGAAGTATATGGAGG	0.378																																					p.K122N													.	FAIM-227	0			c.G366T						.						111	112	112					3																	138341182		2203	4300	6503	SO:0001583	missense	55179	exon4			CAAGAAGTATATG	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.264G>T	3.37:g.138341182G>T	ENSP00000376755:p.Lys88Asn	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	104	4	NM_001033030	0	0	65	65	0	Q6IAN2	Missense_Mutation	SNP	ENST00000393035.2	37	CCDS3103.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663788	0.67700	.	.	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28	5.82	1.5	0.22942	.	0.045770	0.85682	N	0.000000	T	0.56978	0.2022	M	0.85945	2.785	0.80722	D	1	D;D;D;P	0.59767	0.986;0.985;0.985;0.934	D;P;D;P	0.64237	0.911;0.897;0.923;0.82	T	0.59579	-0.7428	10	0.52906	T	0.07	-9.3449	10.4652	0.44602	0.3213:0.0:0.6787:0.0	.	88;110;122;88	Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2	FAIM1_HUMAN;.;.;.	N	122;110;88;88;88;88	ENSP00000342805:K122N;ENSP00000353775:K110N;ENSP00000376755:K88N;ENSP00000376754:K88N;ENSP00000417642:K88N;ENSP00000420543:K88N	ENSP00000342805:K122N	K	+	3	2	FAIM	139823872	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	1.529000	0.35996	0.370000	0.24538	0.650000	0.86243	AAG	.		0.378	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032		T	138341182	G	T	138341182	3	4	143	1	0	0	0	0	1	0	0	0	5391	1020	36	4	424	4	FAIM	3	138341182	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	16995447	138341182	59681248	23	12767											
SCHIP1	100505385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	159606614	159606614	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgtatcttcagctgccAcacatgcctcatataagtga	10	13	6	12	0	3	1	2	1	1	0	3	1	3	1	3	0	3	2	3	0	3	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:159606614A>T	ENST00000460298.1	+	6	1321	c.1080A>T	c.(1078-1080)ccA>ccT	p.P360P	IQCJ-SCHIP1_ENST00000476809.1_Silent_p.P449P|IQCJ-SCHIP1_ENST00000337808.6_Silent_p.P400P|SCHIP1_ENST00000482804.1_Silent_p.P173P|SCHIP1_ENST00000445224.2_Silent_p.P157P|IQCJ-SCHIP1_ENST00000412423.2_Silent_p.P387P|IQCJ-SCHIP1_ENST00000527095.1_Silent_p.P168P|IQCJ-SCHIP1_ENST00000485419.1_Silent_p.P476P					IQCJ-SCHIP1 readthrough											central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						TTCAGCTGCCACACATGCCTC	0.433																																					p.P476P		.											.	.	0			c.A1428T						.						138	130	132					3																	159606614		2203	4300	6503	SO:0001819	synonymous_variant	100505385	exon9			GCTGCCACACATG		CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588			38842	other	readthrough							Standard	NM_001197113		Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000460298.1:c.1080A>T	3.37:g.159606614A>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	81	63	NM_001197113	0	0	0	0	0		Silent	SNP	ENST00000460298.1	37																																																																																				.		0.433	IQCJ-SCHIP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000352558.2	NM_001197113		T	159606614	A	T	159606614	2	4	143	1	0	0	0	0	0	0	0	1	13936	146	6	5		5	SCHIP1	3	159606614	Silent	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	21265432	159606614	38415816	24	12768											
FGFRL1	53834	broad.mit.edu;bcgsc.ca	37	chr4	1018104	1018104	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacgttcccacagagcggAcccgttccaagcccgtgctc	7	6	10	18	4	0	1	0	0	0	1	3	2	2	2	5	1	3	3	5	1	1	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:1018104A>C	ENST00000398484.2	+	7	1304	c.724A>C	c.(724-726)Acc>Ccc	p.T242P	FGFRL1_ENST00000510644.1_Missense_Mutation_p.T242P|FGFRL1_ENST00000264748.6_Missense_Mutation_p.T242P|FGFRL1_ENST00000504138.1_Missense_Mutation_p.T242P			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	242					diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CACAGAGCGGACCCGTTCCAA	0.706																																					p.T242P													.	FGFRL1-90	0			c.A724C						.						39	37	38					4																	1018104		2199	4275	6474	SO:0001583	missense	53834	exon6			GAGCGGACCCGTT		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"Immunoglobulin superfamily / I-set domain containing"	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.724A>C	4.37:g.1018104A>C	ENSP00000381498:p.Thr242Pro	Somatic	55	1		WXS	Illumina HiSeq	Phase_I	42	27	NM_001004356	0	0	0	0	0	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Missense_Mutation	SNP	ENST00000398484.2	37	CCDS3344.1	.	.	.	.	.	.	.	.	.	.	a	19.31	3.802814	0.70682	.	.	ENSG00000127418	ENST00000398484;ENST00000542622;ENST00000510644;ENST00000504138;ENST00000264748	T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61	5.24	4.03	0.46877	.	0.049213	0.85682	N	0.000000	T	0.79730	0.4496	M	0.64260	1.97	0.80722	D	1	D	0.71674	0.998	D	0.67103	0.949	T	0.79990	-0.1570	10	0.66056	D	0.02	-28.2282	11.4565	0.50185	0.8487:0.1513:0.0:0.0	.	242	Q8N441	FGRL1_HUMAN	P	242;212;242;242;242	ENSP00000381498:T242P;ENSP00000425025:T242P;ENSP00000423091:T242P;ENSP00000264748:T242P	ENSP00000264748:T242P	T	+	1	0	FGFRL1	1008104	0.997000	0.39634	0.913000	0.36048	0.638000	0.38207	3.318000	0.51975	0.810000	0.34279	0.463000	0.42550	ACC	.		0.706	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923		C	1018104	A	C	1018104	3	2	143	1	0	0	0	0	1	0	0	0	5888	275	10	5	742	5	FGFRL1	4	1018104	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10		1018104	190136172	25	12769											
FAM193A	8603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	2632748	2632748	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagatgaaggtccgcctgcTccggcagctgtcggctgcgg	5	7	17	12	4	0	2	0	1	0	1	3	3	2	2	3	5	3	4	3	5	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:2632748T>A	ENST00000324666.5	+	3	368	c.17T>A	c.(16-18)cTc>cAc	p.L6H	FAM193A_ENST00000545951.1_Missense_Mutation_p.L6H|FAM193A_ENST00000505311.1_Missense_Mutation_p.L6H|FAM193A_ENST00000382839.3_Missense_Mutation_p.L6H|FAM193A_ENST00000502458.1_Missense_Mutation_p.L6H	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	6										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GTCCGCCTGCTCCGGCAGCTG	0.632																																					p.L6H		.											.	FAM193A-93	0			c.T17A						.						42	45	44					4																	2632748		2202	4300	6502	SO:0001583	missense	8603	exon3			GCCTGCTCCGGCA	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 8"	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.17T>A	4.37:g.2632748T>A	ENSP00000324587:p.Leu6His	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	60	18	NM_003704	0	0	0	0	0	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.881897	0.91740	.	.	ENSG00000125386	ENST00000509050;ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458	T;T;T;T	0.53640	0.63;1.02;0.61;0.67	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.65460	0.2693	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.996;0.999	T	0.68534	-0.5383	10	0.87932	D	0	-27.2496	14.8927	0.70620	0.0:0.0:0.0:1.0	.	6;6;6;6;6	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	H	6	ENSP00000372290:L6H;ENSP00000324587:L6H;ENSP00000443617:L6H;ENSP00000427505:L6H	ENSP00000324587:L6H	L	+	2	0	FAM193A	2602546	1.000000	0.71417	0.996000	0.52242	0.879000	0.50718	7.680000	0.84062	2.108000	0.64289	0.533000	0.62120	CTC	.		0.632	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		A	2632748	T	A	2632748	3	1	143	1	0	0	0	0	1	0	0	0	5540	1551	54	5	19	5	FAM193A	4	2632748	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	1614644	2632748	188521528	26	12770											
LNX1	84708	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	54343069	54343069	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagtactatcgaggatgaTgttcttttcaataatgccac	11	15	8	7	1	2	2	1	2	1	0	3	4	2	3	1	1	2	2	1	1	4	7	rs151307935		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:54343069T>C	ENST00000263925.7	-	9	2057	c.1743A>G	c.(1741-1743)acA>acG	p.T581T	LNX1_ENST00000306888.2_Silent_p.T485T|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	581	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TCGAGGATGATGTTCTTTTCA	0.512																																					p.T581T		.											.	LNX1-229	0			c.A1743G						.						180	180	180					4																	54343069		2203	4300	6503	SO:0001819	synonymous_variant	84708	exon9			GGATGATGTTCTT	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1743A>G	4.37:g.54343069T>C		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	46	21	NM_001126328	0	0	1	3	2	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Silent	SNP	ENST00000263925.7	37	CCDS47057.1																																																																																			T|1.000;G|0.000		0.512	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			C	54343069	T	C	54343069	2	2	143	1	0	0	0	0	0	0	0	1	8888	1451	51	3		3	LNX1	4	54343069	Silent	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	51710321	54343069	136811207	27	12771											
CEP135	9662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	56876035	56876035	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaggaaaacagaagactgcAagatgacctggctacaatgg	17	6	11	7	0	0	4	0	1	0	3	0	5	0	5	1	3	3	2	1	3	7	2	rs148279836		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:56876035A>G	ENST00000257287.4	+	19	2595	c.2471A>G	c.(2470-2472)cAa>cGa	p.Q824R		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	824					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AGAAGACTGCAAGATGACCTG	0.388																																					p.Q824R		.											.	CEP135-94	0			c.A2471G						.	A	ARG/GLN	1,4405	2.1+/-5.4	0,1,2202	83	82	82		2471	5.5	1	4	dbSNP_134	82	0,8600		0,0,4300	no	missense	CEP135	NM_025009.3	43	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	824/1141	56876035	1,13005	2203	4300	6503	SO:0001583	missense	9662	exon19			GACTGCAAGATGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2471A>G	4.37:g.56876035A>G	ENSP00000257287:p.Gln824Arg	Somatic	251	0		WXS	Illumina HiSeq	Phase_I	144	45	NM_025009	0	0	0	0	0	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.375961	0.82682	2.27E-4	0.0	ENSG00000174799	ENST00000257287	T	0.09911	2.93	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.30854	0.0778	M	0.66939	2.045	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.01508	-1.1337	10	0.28530	T	0.3	.	15.8895	0.79286	1.0:0.0:0.0:0.0	.	824	Q66GS9	CP135_HUMAN	R	824	ENSP00000257287:Q824R	ENSP00000257287:Q824R	Q	+	2	0	CEP135	56570792	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	8.565000	0.90730	2.207000	0.71202	0.533000	0.62120	CAA	A|1.000;G|0.000		0.388	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		G	56876035	A	G	56876035	3	3	143	1	0	0	0	0	1	0	0	0	3253	130	5	3	2541	3	CEP135	4	56876035	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	2532966	56876035	134278241	28	12772											
CEP135	9662	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	56885619	56885619	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacctcgaatcattgttggCtacaaacagagataaagaat	18	9	7	7	1	1	2	1	0	0	2	2	4	1	2	1	1	3	2	1	1	7	4	rs370534878		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:56885619C>T	ENST00000257287.4	+	23	3237	c.3113C>T	c.(3112-3114)gCt>gTt	p.A1038V		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	1038					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TCATTGTTGGCTACAAACAGA	0.363																																					p.A1038V													.	CEP135-94	0			c.C3113T						.						82	77	79					4																	56885619		2203	4300	6503	SO:0001583	missense	9662	exon23			TGTTGGCTACAAA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.3113C>T	4.37:g.56885619C>T	ENSP00000257287:p.Ala1038Val	Somatic	232	1		WXS	Illumina HiSeq	Phase_I	139	53	NM_025009	0	0	1	2	1	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995763	0.35226	.	.	ENSG00000174799	ENST00000257287	T	0.14022	2.54	4.96	4.12	0.48240	.	0.118380	0.56097	D	0.000024	T	0.17152	0.0412	L	0.43757	1.38	0.34364	D	0.69129	P	0.34864	0.473	B	0.42653	0.394	T	0.21655	-1.0239	10	0.29301	T	0.29	.	13.6448	0.62275	0.0:0.9246:0.0:0.0754	.	1038	Q66GS9	CP135_HUMAN	V	1038	ENSP00000257287:A1038V	ENSP00000257287:A1038V	A	+	2	0	CEP135	56580376	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.087000	0.57671	1.235000	0.43724	0.650000	0.86243	GCT	.		0.363	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56885619	C	T	56885619	3	4	143	1	0	0	0	0	1	0	0	0	3253	797	28	2	3199	2	CEP135	4	56885619	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	9584	56885619	134268657	29	12773											
LRRC14B	389257	broad.mit.edu;bcgsc.ca	37	chr5	194906	194906	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggccttcttggcagactgtgCccacgctgcccacctggagg	5	8	13	15	1	1	1	0	0	1	1	1	2	1	2	4	4	2	2	4	4	0	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr5:194906C>T	ENST00000328278.3	+	2	1011	c.983C>T	c.(982-984)gCc>gTc	p.A328V	CTD-2083E4.7_ENST00000563761.1_RNA	NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	328										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						GCAGACTGTGCCCACGCTGCC	0.647																																					p.A328V													.	LRRC14B-69	0			c.C983T						.						34	40	38					5																	194906		2151	4252	6403	SO:0001583	missense	389257	exon2			ACTGTGCCCACGC		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.983C>T	5.37:g.194906C>T	ENSP00000327675:p.Ala328Val	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	69	5	NM_001080478	0	0	0	0	0		Missense_Mutation	SNP	ENST00000328278.3	37	CCDS47184.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.469465	0.01044	.	.	ENSG00000185028	ENST00000328278	T	0.08193	3.12	5.82	-3.37	0.04898	.	1.007700	0.07960	N	0.982296	T	0.04907	0.0132	N	0.20986	0.625	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47275	-0.9130	10	0.15952	T	0.53	.	7.6661	0.28432	0.1368:0.1683:0.0:0.6948	.	328	A6NHZ5	LR14B_HUMAN	V	328	ENSP00000327675:A328V	ENSP00000327675:A328V	A	+	2	0	LRRC14B	247906	0.013000	0.17824	0.001000	0.08648	0.145000	0.21501	0.399000	0.20916	-0.483000	0.06772	-0.367000	0.07326	GCC	.		0.647	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478		T	194906	C	T	194906	3	4	143	1	0	0	0	0	1	0	0	0	8994	739	26	2	989	2	LRRC14B	5	194906	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		194906	180720354	30	12774											
PECI	10455	bcgsc.ca	37	chr6	4133832	4133832	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcacttcgtttcctggatccTttttcaagagtttcacttga	7	18	6	10	1	3	2	3	1	0	1	6	3	5	3	2	1	0	2	2	1	1	6			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:4133832T>C	ENST00000380118.3	-	2	200	c.164A>G	c.(163-165)aAg>aGg	p.K55R	ECI2_ENST00000361538.2_Missense_Mutation_p.K25R|RP3-400B16.1_ENST00000427049.2_lincRNA|RP3-400B16.4_ENST00000527831.1_RNA|ECI2_ENST00000380125.2_Missense_Mutation_p.K25R|ECI2_ENST00000465828.1_Missense_Mutation_p.K25R|ECI2_ENST00000413766.2_5'UTR			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	55	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.				fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						TCCTGGATCCTTTTTCAAGAG	0.398																																					p.K55R													.	ECI2-90	0			c.A164G						.						217	201	206					6																	4133832		2203	4300	6503	SO:0001583	missense	10455	exon2			GGATCCTTTTTCA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"acyl-Coenzyme A binding domain containing 2", " Hepatocellular carcinoma-associated antigen 88"	608024	"peroxisomal D3,D2-enoyl-CoA isomerase"	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.164A>G	6.37:g.4133832T>C	ENSP00000369461:p.Lys55Arg	Somatic	164	1		WXS	Illumina HiSeq	Phase_1	129	5	NM_206836	0	0	5	5	0	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	37	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.191753	0.78902	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000361538;ENST00000465828;ENST00000495548	T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83	5.98	5.98	0.97165	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP (4);	21.516500	0.00166	N	0.000000	T	0.31796	0.0808	M	0.78223	2.4	0.80722	D	1	B	0.20988	0.05	B	0.35899	0.213	T	0.34850	-0.9812	10	0.54805	T	0.06	.	14.4143	0.67139	0.0:0.0:0.0:1.0	.	55	O75521	ECI2_HUMAN	R	55;25;25;25;102	ENSP00000369461:K55R;ENSP00000369468:K25R;ENSP00000354737:K25R;ENSP00000420309:K25R;ENSP00000417459:K102R	ENSP00000354737:K25R	K	-	2	0	ECI2	4078831	0.659000	0.27411	0.999000	0.59377	0.997000	0.91878	3.003000	0.49505	2.289000	0.77006	0.533000	0.62120	AAG	.		0.398	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117		C	4133832	T	C	4133832	3	2	143	1	0	0	0	0	1	0	0	0	11742	1609	56	3	1056	3	PECI	6	4133832	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		4133832	166981235	31	12775											
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	38825504	38825504	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccatgtgcatcagagagatAtttttgatgacttggtaagg	11	14	11	5	0	1	4	1	2	0	2	2	5	2	4	1	2	1	2	1	2	2	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:38825504A>G	ENST00000359357.3	+	40	5547	c.5293A>G	c.(5293-5295)Att>Gtt	p.I1765V	DNAH8_ENST00000449981.2_Missense_Mutation_p.I1982V|DNAH8_ENST00000441566.1_Missense_Mutation_p.I1765V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1765					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TCAGAGAGATATTTTTGATGA	0.308																																					p.I1982V		.											.	DNAH8-615	0			c.A5944G						.						110	106	107					6																	38825504		2203	4300	6503	SO:0001583	missense	1769	exon42			AGAGATATTTTTG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.5293A>G	6.37:g.38825504A>G	ENSP00000352312:p.Ile1765Val	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	111	53	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	21.7	4.181365	0.78677	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.20332	2.09;2.09;2.08	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.21590	0.0520	L	0.46670	1.46	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.06862	-1.0803	10	0.02654	T	1	.	16.0707	0.80928	1.0:0.0:0.0:0.0	.	1765	Q96JB1	DYH8_HUMAN	V	1970;1970;1765;1765	ENSP00000333363:I1970V;ENSP00000352312:I1765V;ENSP00000402294:I1765V	ENSP00000333363:I1970V	I	+	1	0	DNAH8	38933482	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.271000	0.95698	2.194000	0.70268	0.533000	0.62120	ATT	.		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38825504	A	G	38825504	3	3	143	1	0	0	0	0	1	0	0	0	4618	449	16	3	5443	3	DNAH8	6	38825504	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	34691672	38825504	132289563	32	12776											
FBXO5	26271	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	153293427	153293427	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcagagaattcattgtgtcGactataagtagaacctttct	12	14	7	8	1	3	2	2	0	1	2	4	4	3	2	1	0	1	1	1	0	5	6			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:153293427G>A	ENST00000229758.3	-	4	1130	c.1072C>T	c.(1072-1074)Cga>Tga	p.R358*	FBXO5_ENST00000367241.3_Nonsense_Mutation_p.R312*|FBXO5_ENST00000477822.1_5'UTR	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	358					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		TCATTGTGTCGACTATAAGTA	0.333																																					p.R358X	NSCLC(121;372 1757 17721 17977 29669)												.	FBXO5-658	0			c.C1072T						.						100	97	98					6																	153293427		2203	4300	6503	SO:0001587	stop_gained	26271	exon4			TGTGTCGACTATA	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"F-boxes /  "other""	13584	protein-coding gene	gene with protein product		606013	"F-box only protein 5"			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.1072C>T	6.37:g.153293427G>A	ENSP00000229758:p.Arg358*	Somatic	135	2		WXS	Illumina HiSeq	Phase_I	86	32	NM_012177	0	0	1	1	0	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Nonsense_Mutation	SNP	ENST00000229758.3	37	CCDS5242.1	.	.	.	.	.	.	.	.	.	.	G	37	6.362282	0.97507	.	.	ENSG00000112029	ENST00000229758;ENST00000367241	.	.	.	5.75	5.75	0.90469	.	0.614218	0.15057	N	0.282948	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7102	13.8697	0.63610	0.0:0.0:0.7458:0.2542	.	.	.	.	X	358;312	.	ENSP00000229758:R358X	R	-	1	2	FBXO5	153335120	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.898000	0.48672	2.696000	0.92011	0.655000	0.94253	CGA	.		0.333	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1			A	153293427	G	A	153293427	4	1	143	1	0	0	0	0	0	1	0	0	5777	1066	37	1	279	1	FBXO5	6	153293427	Nonsense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	114467923	153293427	17821640	33	12777											
EZR	7430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	159188095	159188095	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcatctcgggcctgggacaGctcgctgctcagcgtctgta	5	10	12	14	3	4	0	2	0	2	0	6	1	4	1	1	2	3	4	1	2	1	1	rs367907031		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:159188095G>C	ENST00000367075.3	-	14	1780	c.1612C>G	c.(1612-1614)Ctg>Gtg	p.L538V	EZR_ENST00000337147.7_Missense_Mutation_p.L538V|EZR_ENST00000392177.4_Missense_Mutation_p.L506V|MIR3918_ENST00000581555.1_RNA	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin	538	Interaction with SCYL3.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of endothelial barrier (GO:0061028)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|filopodium assembly (GO:0046847)|leukocyte cell-cell adhesion (GO:0007159)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|receptor internalization (GO:0031623)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|astrocyte projection (GO:0097449)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell tip (GO:0051286)|ciliary basal body (GO:0036064)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|microspike (GO:0044393)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|Schwann cell microvillus (GO:0097454)|T-tubule (GO:0030315)|uropod (GO:0001931)|vesicle (GO:0031982)	actin filament binding (GO:0051015)|cell adhesion molecule binding (GO:0050839)|poly(A) RNA binding (GO:0044822)		EZR/ROS1(4)	breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	15		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		GCCTGGGACAGCTCGCTGCTC	0.562			T	ROS1	NSCLC																																p.L538V		.		Dom	yes		6	6q25.3	7430	ezrin		E	.	EZR-70	0			c.C1612G						.						180	157	165					6																	159188095		2203	4300	6503	SO:0001583	missense	7430	exon13			GGGACAGCTCGCT	AF187552	CCDS5258.1	6q25.3	2010-12-10	2007-11-29	2007-11-29	ENSG00000092820	ENSG00000092820		"A-kinase anchor proteins"	12691	protein-coding gene	gene with protein product	"cytovillin 2"	123900	"villin 2 (ezrin)"	VIL2			Standard	NM_003379		Approved		uc003qrt.4	P15311	OTTHUMG00000015917	ENST00000367075.3:c.1612C>G	6.37:g.159188095G>C	ENSP00000356042:p.Leu538Val	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	95	32	NM_003379	0	0	203	377	174	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Missense_Mutation	SNP	ENST00000367075.3	37	CCDS5258.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.747324	0.69533	.	.	ENSG00000092820	ENST00000337147;ENST00000367075;ENST00000392177	D;D;D	0.88586	-2.4;-2.4;-2.4	5.37	0.447	0.16608	Moesin (1);Ezrin/radixin/moesin, C-terminal (1);	0.067471	0.64402	D	0.000011	D	0.92074	0.7488	M	0.87617	2.895	0.58432	D	0.999996	D;D	0.71674	0.998;0.989	D;D	0.75484	0.986;0.976	D	0.91442	0.5174	10	0.87932	D	0	.	9.9553	0.41663	0.3142:0.0:0.6858:0.0	.	506;538	E7EQR4;P15311	.;EZRI_HUMAN	V	538;538;506	ENSP00000338934:L538V;ENSP00000356042:L538V;ENSP00000376016:L506V	ENSP00000338934:L538V	L	-	1	2	EZR	159108083	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	3.249000	0.51437	0.007000	0.14760	0.561000	0.74099	CTG	.		0.562	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379		C	159188095	G	C	159188095	3	2	143	1	0	0	0	0	1	0	0	0	5348	962	34	4	152	4	EZR	6	159188095	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	5894668	159188095	11926972	34	12778											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		.											.	TBP-91	0			c.G180A						.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	6.37:g.170871004G>A		Somatic	47	0		WXS	Illumina HiSeq	Phase_I	41	5	NM_003194	0	0	3	3	0	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	143	1	0	0	0	0	0	0	0	1	15676	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	11682909	170871004	244063	35	12779											
DNAH11	8701	broad.mit.edu	37	chr7	21788203	21788203	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcttcctttcctcaggtgtcGcatcagccggatcttacgaa	7	12	9	13	3	3	0	2	0	1	0	6	2	5	1	3	2	2	2	3	2	2	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:21788203G>A	ENST00000409508.3	+	52	8547	c.8516G>A	c.(8515-8517)cGc>cAc	p.R2839H	DNAH11_ENST00000328843.6_Missense_Mutation_p.R2846H	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2846	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						CTCAGGTGTCGCATCAGCCGG	0.493									Kartagener syndrome																												.													.	DNAH11-146	0			.						.						50	50	50					7																	21788203		1924	4134	6058	SO:0001583	missense	8701	.	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGTGTCGCATCAG	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"Axonemal dyneins"	2942	protein-coding gene	gene with protein product	"dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like"	603339	"dynein, axonemal, heavy polypeptide 11"			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.8516G>A	7.37:g.21788203G>A	ENSP00000475939:p.Arg2839His	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	69	3	.	0	0	0	0	0	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	16.53	3.147816	0.57151	.	.	ENSG00000105877	ENST00000328843	T	0.48836	0.8	5.7	5.7	0.88788	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.64402	D	0.000016	T	0.69314	0.3097	.	.	.	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.71056	-0.4703	9	0.56958	D	0.05	.	15.0327	0.71720	0.0699:0.0:0.9301:0.0	.	2846	Q96DT5	DYH11_HUMAN	H	2846	ENSP00000330671:R2846H	ENSP00000330671:R2846H	R	+	2	0	DNAH11	21754728	1.000000	0.71417	0.863000	0.33907	0.063000	0.16089	6.315000	0.72853	2.705000	0.92388	0.650000	0.86243	CGC	.		0.493	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777		A	21788203	G	A	21788203	3	1	143	1	0	0	0	0	1	0	0	0	4610	1087	38	1	8744	1	DNAH11	7	21788203	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		21788203	137350460	36	12780											
ZNF273	10793	broad.mit.edu;bcgsc.ca	37	chr7	64389208	64389214	+	Frame_Shift_Del	DEL	TTACTAA	TTACTAA	-																															ctttaactggtcctcaactcTtactaaacataagagaattc																								rs555033749		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	TTACTAA	TTACTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:64389208_64389214delTTACTAA	ENST00000476120.1	+	4	1573_1579	c.1502_1508delTTACTAA	c.(1501-1509)cttactaaafs	p.LTK501fs	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Frame_Shift_Del_p.LTK436fs	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	501					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(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TCCTCAACTCTTACTAAACATAAGAGA	0.386																																					p.501_503del	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)												.	ZNF273-90	0			c.1502_1508del						.																																			SO:0001589	frameshift_variant	10793	exon4			CAACTCTTACTAA	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1502_1508delTTACTAA	7.37:g.64389208_64389214delTTACTAA	ENSP00000418719:p.Leu501fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	70	9	NM_021148	0	0	0	0	0	B3KQZ5|Q6P3V4	Frame_Shift_Del	DEL	ENST00000476120.1	37	CCDS5528.2																																																																																			.		0.386	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			-	64389214	TTACTAA	-	64389208	7	5	143	1	0	1	0	1	0	0	0	0	17840	1609	56	0	1516	0	ZNF273	7	64389208	Frame_Shift_Del	DEL	TTACTAA	TCGA-IZ-A6M9-01A-11D-A31X-10	42601005	64389208	94749455	37	12781	134	2									
ZNF273	10793	bcgsc.ca	37	chr7	64389216	64389216	+	Missense_Mutation	SNP	C	C	T																															ggtcctcaactcttactaaaCataagagaattcatactgga																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:64389216C>T	ENST00000476120.1	+	4	1581	c.1510C>T	c.(1510-1512)Cat>Tat	p.H504Y	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.H439Y	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	504					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(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TCTTACTAAACATAAGAGAAT	0.383																																					p.H504Y	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)												.	ZNF273-90	0			c.C1510T						.						48	50	49					7																	64389216		2203	4297	6500	SO:0001583	missense	10793	exon4			ACTAAACATAAGA	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"Zinc fingers, C2H2-type", "-"	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1510C>T	7.37:g.64389216C>T	ENSP00000418719:p.His504Tyr	Somatic	79	0		WXS	Illumina HiSeq	Phase_1	69	10	NM_021148	0	0	5	5	0	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	19.11	3.764673	0.69878	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	D;D	0.86769	-2.17;-2.17	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94301	0.8169	H	0.95328	3.655	0.26486	N	0.975022	D	0.89917	1.0	D	0.87578	0.998	D	0.85433	0.1150	9	0.72032	D	0.01	.	7.3527	0.26700	0.0:1.0:0.0:0.0	.	504	Q14593	ZN273_HUMAN	Y	504;439	ENSP00000418719:H504Y;ENSP00000324518:H439Y	ENSP00000324518:H439Y	H	+	1	0	ZNF273	64026651	0.997000	0.39634	0.806000	0.32338	0.805000	0.45488	5.366000	0.66122	0.202000	0.20498	0.205000	0.17691	CAT	.		0.383	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			T	64389216	C	T	64389216	3	4	143	1	0	0	0	0	1	0	0	0	17840	478	17	2	1524	2	ZNF273	7	64389216	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	8	64389216	94749447	38	12782	134	2									
AUTS2	26053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	70255844	70255844	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacaagacccctccgacAgcagcgctgagcgcacctcc	10	4	8	19	3	1	2	1	1	0	1	3	3	3	2	5	0	4	3	5	0	2	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:70255844A>G	ENST00000342771.4	+	19	3963	c.3642A>G	c.(3640-3642)acA>acG	p.T1214T	AUTS2_ENST00000406775.2_Silent_p.T1190T	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1214										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCCCTCCGACAGCAGCGCTGA	0.672																																					p.T1214T		.											.	AUTS2-92	0			c.A3642G						.						41	45	43					7																	70255844		2203	4299	6502	SO:0001819	synonymous_variant	26053	exon19			TCCGACAGCAGCG	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3642A>G	7.37:g.70255844A>G		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	106	30	NM_015570	0	0	0	0	0	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1																																																																																			.		0.672	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			G	70255844	A	G	70255844	2	3	143	1	0	0	0	0	0	0	0	1	1226	175	7	3		3	AUTS2	7	70255844	Silent	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	5866628	70255844	88882819	39	12783											
GTF2IRD2	84163	broad.mit.edu	37	chr7	74211898	74211898	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccggatgaattatacaacaGatggacttcagttccgcacc	12	10	8	11	2	1	2	1	1	0	1	3	4	3	4	3	2	2	2	3	2	4	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:74211898G>C	ENST00000405086.2	-	16	2142	c.1953C>G	c.(1951-1953)atC>atG	p.I651M	GTF2IRD2_ENST00000451013.2_Missense_Mutation_p.I198M	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	651					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						ttatacaacagatggacttca	0.532																																					p.I651M	NSCLC(40;560 1096 7501 40315 49546)												.	GTF2IRD2-23	0			c.C1953G						.						4	5	5					7																	74211898		1559	3279	4838	SO:0001583	missense	84163	exon16			ACAACAGATGGAC	BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"transcription factor GTF2IRD2"	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1953C>G	7.37:g.74211898G>C	ENSP00000385491:p.Ile651Met	Somatic	365	0		WXS	Illumina HiSeq	Phase_I	434	85	NM_173537	0	1	13	16	2	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Missense_Mutation	SNP	ENST00000405086.2	37	CCDS5576.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.616433	0.00828	.	.	ENSG00000196275	ENST00000405086;ENST00000451013	T;T	0.28255	1.62;1.62	1.74	-2.06	0.07298	Ribonuclease H-like (1);	.	.	.	.	T	0.20861	0.0502	L	0.35542	1.07	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.22800	-1.0206	9	0.33940	T	0.23	-2.7586	9.9695	0.41745	0.0:0.2899:0.7101:0.0	.	651	Q86UP8	GTD2A_HUMAN	M	651;198	ENSP00000385491:I651M;ENSP00000406723:I198M	ENSP00000385491:I651M	I	-	3	3	GTF2IRD2	73849834	0.000000	0.05858	0.005000	0.12908	0.021000	0.10359	-3.493000	0.00452	-0.542000	0.06249	-0.580000	0.04137	ATC	.		0.532	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537		C	74211898	G	C	74211898	3	2	143	1	0	0	0	0	1	0	0	0	6890	932	33	4	900	4	GTF2IRD2	7	74211898	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	3956054	74211898	84926765	40	12784											
NUP205	23165	broad.mit.edu	37	chr7	135307641	135307641	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccctcatggaagtggtctgtCgagatgcttgtgatggtcat	7	13	13	8	1	3	2	2	1	1	1	4	4	3	3	1	3	1	1	1	3	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:135307641C>T	ENST00000285968.6	+	31	4473	c.4447C>T	c.(4447-4449)Cga>Tga	p.R1483*		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1483					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.R1483*(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						AGTGGTCTGTCGAGATGCTTG	0.383																																					p.R1483X													.	NUP205-207	1	Substitution - Nonsense(1)	lung(1)	c.C4447T						.						98	95	96					7																	135307641		2203	4300	6503	SO:0001587	stop_gained	23165	exon31			GTCTGTCGAGATG	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.4447C>T	7.37:g.135307641C>T	ENSP00000285968:p.Arg1483*	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	152	6	NM_015135	0	0	4	4	0	A6H8X3|Q86YC1	Nonsense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	C	44	10.870996	0.99481	.	.	ENSG00000155561	ENST00000285968	.	.	.	4.83	3.93	0.45458	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-33.0615	14.5921	0.68373	0.1474:0.8526:0.0:0.0	.	.	.	.	X	1483	.	ENSP00000285968:R1483X	R	+	1	2	NUP205	134958181	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.263000	0.43293	1.129000	0.42072	-0.293000	0.09583	CGA	.		0.383	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			T	135307641	C	T	135307641	4	4	143	1	0	0	0	0	0	1	0	0	10785	876	31	1	4569	1	NUP205	7	135307641	Nonsense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	61095743	135307641	23831022	41	12785											
RP1L1	94137	broad.mit.edu	37	chr8	10470455	10470455	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcatcccaccctgcagggccGgggtccccacaccccaggct	6	4	11	20	1	0	0	0	0	0	0	2	0	2	0	7	4	1	3	7	4	0	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:10470455G>A	ENST00000382483.3	-	4	1376	c.1153C>T	c.(1153-1155)Cgg>Tgg	p.R385W		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	385					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTGCAGGGCCGGGGTCCCCAC	0.657																																					p.R385W													.	RP1L1-139	0			c.C1153T						.						43	49	47					8																	10470455		1876	4098	5974	SO:0001583	missense	94137	exon4			AGGGCCGGGGTCC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1153C>T	8.37:g.10470455G>A	ENSP00000371923:p.Arg385Trp	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	43	3	NM_178857	0	0	0	0	0	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.762894	0.49574	.	.	ENSG00000183638	ENST00000382483	T	0.04275	3.66	4.78	-0.522	0.11928	.	0.688275	0.11554	U	0.552455	T	0.07413	0.0187	N	0.22421	0.69	0.09310	N	1	D	0.89917	1.0	P	0.61328	0.887	T	0.35847	-0.9772	10	0.62326	D	0.03	-5.29	5.6606	0.17667	0.0:0.1827:0.5552:0.2621	.	385	A6NKC6	.	W	385	ENSP00000371923:R385W	ENSP00000371923:R385W	R	-	1	2	RP1L1	10507865	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.052000	0.14163	0.116000	0.18110	-0.479000	0.04858	CGG	.		0.657	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10470455	G	A	10470455	3	1	143	1	0	0	0	0	1	0	0	0	13565	1115	39	1	6053	1	RP1L1	8	10470455	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		10470455	135893567	42	12786											
MTFR1	9650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	66617127	66617127	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcagagctcagattgccaaAattgtgacccagcaggagca	13	7	10	11	0	2	3	2	1	0	2	2	4	2	4	2	1	4	3	2	1	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:66617127A>C	ENST00000262146.4	+	5	606	c.480A>C	c.(478-480)aaA>aaC	p.K160N	MTFR1_ENST00000517944.1_3'UTR|MTFR1_ENST00000458689.2_Missense_Mutation_p.K127N	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	160					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			AGATTGCCAAAATTGTGACCC	0.458																																					p.K160N		.											.	MTFR1-91	0			c.A480C						.						27	28	27					8																	66617127		2203	4300	6503	SO:0001583	missense	9650	exon5			TGCCAAAATTGTG		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"likely ortholog of chicken chondrocyte protein with a poly proline region"					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.480A>C	8.37:g.66617127A>C	ENSP00000262146:p.Lys160Asn	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	127	51	NM_014637	0	0	0	0	0	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Missense_Mutation	SNP	ENST00000262146.4	37	CCDS6182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.72|19.72	3.879273|3.879273	0.72294|0.72294	.|.	.|.	ENSG00000066855|ENSG00000066855	ENST00000518609;ENST00000262146;ENST00000458689|ENST00000518800	T;T|T	0.50813|0.49432	0.73;0.73|0.78	5.24|5.24	1.59|1.59	0.23543|0.23543	.|.	0.095465|0.095465	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.59932|0.59932	0.2230|0.2230	M|M	0.84683|0.84683	2.71|2.71	0.44789|0.44789	D|D	0.997793|0.997793	P;D;D;D|.	0.76494|.	0.947;0.992;0.998;0.999|.	P;D;D;D|.	0.74674|.	0.905;0.954;0.94;0.984|.	T|T	0.56044|0.56044	-0.8044|-0.8044	10|8	0.42905|0.41790	T|T	0.14|0.15	-28.337|-28.337	7.9704|7.9704	0.30124|0.30124	0.6814:0.0:0.3186:0.0|0.6814:0.0:0.3186:0.0	.|.	160;144;127;160|.	B4E3G8;E5RJS5;E7EP84;Q15390|.	.;.;.;MTFR1_HUMAN|.	N|T	144;160;127|118	ENSP00000262146:K160N;ENSP00000391502:K127N|ENSP00000430621:K118T	ENSP00000262146:K160N|ENSP00000430621:K118T	K|K	+|+	3|2	2|0	MTFR1|MTFR1	66779681|66779681	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.987000|0.987000	0.75469|0.75469	1.601000|1.601000	0.36773|0.36773	0.035000|0.035000	0.15519|0.15519	0.460000|0.460000	0.39030|0.39030	AAA|AAA	.		0.458	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637		C	66617127	A	C	66617127	3	2	143	1	0	0	0	0	1	0	0	0	9950	11	1	5	494	5	MTFR1	8	66617127	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	56146672	66617127	79746895	43	12787											
SULF1	23213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	70488224	70488224	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtccctgcaagtcatgaaCaaaacgagaaagattatgga	16	7	11	7	1	1	3	1	1	0	2	2	5	2	4	1	2	3	1	1	2	6	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:70488224C>G	ENST00000260128.4	+	6	909	c.192C>G	c.(190-192)aaC>aaG	p.N64K	SULF1_ENST00000419716.3_Missense_Mutation_p.N64K|SULF1_ENST00000458141.2_Missense_Mutation_p.N64K|SULF1_ENST00000402687.4_Missense_Mutation_p.N64K	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	64					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AAGTCATGAACAAAACGAGAA	0.522																																					p.N64K		.											.	SULF1-518	0			c.C192G						.						80	67	71					8																	70488224		2203	4300	6503	SO:0001583	missense	23213	exon6			CATGAACAAAACG	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.192C>G	8.37:g.70488224C>G	ENSP00000260128:p.Asn64Lys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	89	33	NM_001128205	0	0	0	0	0	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648999	0.29336	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000529134;ENST00000402687;ENST00000419716;ENST00000528783;ENST00000525999	D;D;D;D;D;T;D	0.96265	-3.96;-3.96;-3.23;-3.96;-3.96;0.86;-3.96	5.23	2.96	0.34315	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.93861	0.8036	M	0.67397	2.05	0.53688	D	0.999974	B	0.06786	0.001	B	0.10450	0.005	D	0.89996	0.4111	10	0.22109	T	0.4	.	10.5049	0.44828	0.0:0.7019:0.0:0.2981	.	64	Q8IWU6	SULF1_HUMAN	K	64	ENSP00000403040:N64K;ENSP00000260128:N64K;ENSP00000432178:N64K;ENSP00000385704:N64K;ENSP00000390315:N64K;ENSP00000436949:N64K;ENSP00000431753:N64K	ENSP00000260128:N64K	N	+	3	2	SULF1	70650778	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.135000	0.31454	1.123000	0.41961	0.650000	0.86243	AAC	.		0.522	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		G	70488224	C	G	70488224	3	3	143	1	0	0	0	0	1	0	0	0	15402	477	17	4	198	4	SULF1	8	70488224	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	3871097	70488224	75875798	44	12788											
DPYS	1807	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	105393497	105393499	+	In_Frame_Del	DEL	CTT	CTT	-																															tctggatttcagtgtggcgaCttctcccttatagggtgcac																								rs148864394	byFrequency	TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:105393497_105393499delCTT	ENST00000351513.2	-	9	1619_1621	c.1487_1489delAAG	c.(1486-1491)gaagtc>gtc	p.E496del	DPYS_ENST00000521601.1_5'UTR	NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	496					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AGTGTGGCGACTTCTCCCTTATA	0.483																																					p.496_497del		.											.	DPYS-229	0			c.1487_1489del						.																																			SO:0001651	inframe_deletion	1807	exon9			.	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.1487_1489delAAG	8.37:g.105393497_105393499delCTT	ENSP00000276651:p.Glu496del	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	55	26	NM_001385	0	0	0	0	0		In_Frame_Del	DEL	ENST00000351513.2	37	CCDS6302.1																																																																																			.		0.483	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		-	105393499	CTT	-	105393497	7	5	143	1	0	1	0	1	0	0	0	0	4757	565	20	0	74	0	DPYS	8	105393497	In_Frame_Del	DEL	CTT	TCGA-IZ-A6M9-01A-11D-A31X-10	34905273	105393497	40970525	45	12789											
CSMD3	114788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	114326898	114326898	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaaaacaatttgtattctAtttcgttcttctgctattat	11	20	4	6	1	3	1	0	1	3	0	4	1	3	1	0	0	2	3	0	0	7	9			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:114326898A>C	ENST00000297405.5	-	2	547	c.303T>G	c.(301-303)aaT>aaG	p.N101K	CSMD3_ENST00000455883.2_Missense_Mutation_p.N101K|CSMD3_ENST00000343508.3_Missense_Mutation_p.N61K|CSMD3_ENST00000352409.3_Missense_Mutation_p.N101K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	101	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N101N(1)|p.N61N(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTTGTATTCTATTTCGTTCTT	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N101K		.											.	CSMD3-1132	2	Substitution - coding silent(2)	lung(2)	c.T303G						.						171	162	165					8																	114326898		2203	4300	6503	SO:0001583	missense	114788	exon2			TATTCTATTTCGT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.303T>G	8.37:g.114326898A>C	ENSP00000297405:p.Asn101Lys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	131	52	NM_052900	0	0	0	0	0	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.621352	0.46736	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.72	3.38	0.38709	CUB (5);	0.077066	0.47455	D	0.000223	T	0.24699	0.0599	L	0.28740	0.885	0.28547	N	0.911799	P;P;D;P;B	0.69078	0.827;0.93;0.997;0.77;0.395	B;P;P;B;B	0.61132	0.275;0.526;0.884;0.253;0.341	T	0.09796	-1.0658	10	0.09338	T	0.73	.	4.6113	0.12404	0.5913:0.0:0.4087:0.0	.	101;101;101;101;61	Q7Z407-3;Q7Z407-4;Q7Z407-5;Q7Z407;Q7Z407-2	.;.;.;CSMD3_HUMAN;.	K	61;101;101;101	ENSP00000345799:N61K;ENSP00000297405:N101K;ENSP00000412263:N101K;ENSP00000343124:N101K	ENSP00000297405:N101K	N	-	3	2	CSMD3	114396074	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.778000	0.55371	0.998000	0.38996	0.455000	0.32223	AAT	.		0.353	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	114326898	A	C	114326898	3	2	143	1	0	0	0	0	1	0	0	0	3952	446	16	5	11100	5	CSMD3	8	114326898	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	8933401	114326898	32037124	46	12790											
SIGMAR1	10280	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	34637563	34637563	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagcgtactgccgcgccaaCtgcgctatctcttcgcgctg	5	9	10	17	6	1	0	0	0	1	0	3	0	1	0	3	0	5	3	3	0	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:34637563C>G	ENST00000277010.4	-	1	205	c.132G>C	c.(130-132)caG>caC	p.Q44H	SIGMAR1_ENST00000477726.1_Missense_Mutation_p.Q44H|SIGMAR1_ENST00000461426.1_5'UTR|SIGMAR1_ENST00000378892.1_5'UTR	NM_001282208.1|NM_005866.2	NP_001269137.1|NP_005857.1	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1	44					cell death (GO:0008219)|lipid transport (GO:0006869)|nervous system development (GO:0007399)|regulation of neuron apoptotic process (GO:0043523)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|nuclear envelope (GO:0005635)	drug binding (GO:0008144)|opioid receptor activity (GO:0004985)			large_intestine(1)|lung(1)	2					Amitriptyline(DB00321)|Dextromethorphan(DB00514)|Nortriptyline(DB00540)|Pentazocine(DB00652)|Remoxipride(DB00409)	GCCGCGCCAACTGCGCTATCT	0.701																																					p.Q44H		.											.	SIGMAR1-90	0			c.G132C						.						15	18	17					9																	34637563		2195	4292	6487	SO:0001583	missense	10280	exon1			CGCCAACTGCGCT	BC004899	CCDS6562.1, CCDS6563.1	9p13.3	2008-12-18	2008-12-18	2008-12-18	ENSG00000147955	ENSG00000147955			8157	protein-coding gene	gene with protein product		601978	"opioid receptor, sigma 1"	OPRS1		8954936, 9453537	Standard	NM_005866		Approved	SR-BP1	uc003zvb.3	Q99720	OTTHUMG00000019829	ENST00000277010.4:c.132G>C	9.37:g.34637563C>G	ENSP00000277010:p.Gln44His	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	33	7	NM_005866	0	0	4	4	0	D3DRM7|O00673|O00725|Q0Z9W6|Q153Z1|Q2TSD1|Q53GN2|Q7Z653|Q8N7H3|Q9NYX0	Missense_Mutation	SNP	ENST00000277010.4	37	CCDS6562.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.641021	0.47153	.	.	ENSG00000147955	ENST00000277010;ENST00000477726	T;T	0.64618	-0.11;-0.11	4.7	3.8	0.43715	.	0.332724	0.31519	N	0.007517	T	0.63757	0.2538	L	0.52011	1.625	0.29794	N	0.832985	D;D;P	0.59357	0.958;0.985;0.879	P;P;P	0.52598	0.574;0.703;0.559	T	0.63897	-0.6533	10	0.56958	D	0.05	-7.6325	9.982	0.41819	0.3691:0.6309:0.0:0.0	.	44;44;44	B4DR71;A2A3U5;Q99720	.;.;SGMR1_HUMAN	H	44	ENSP00000277010:Q44H;ENSP00000420022:Q44H	ENSP00000277010:Q44H	Q	-	3	2	SIGMAR1	34627563	0.996000	0.38824	1.000000	0.80357	0.969000	0.65631	1.763000	0.38461	1.194000	0.43101	0.561000	0.74099	CAG	.		0.701	SIGMAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052204.1	NM_005866		G	34637563	C	G	34637563	3	3	143	1	0	0	0	0	1	0	0	0	14348	564	20	4	555	4	SIGMAR1	9	34637563	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		34637563	106575868	47	12791											
TMOD1	7111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	100286582	100286582	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aaaatgagctggatgagctgGaccctgatgtgagtaggtgc	11	9	15	6	0	0	4	0	4	0	0	0	6	0	6	1	3	3	3	1	3	3	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:100286582G>A	ENST00000259365.4	+	2	325	c.112G>A	c.(112-114)Gac>Aac	p.D38N	TMOD1_ENST00000395211.2_Missense_Mutation_p.D38N	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	38					adult locomotory behavior (GO:0008344)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)	cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|membrane (GO:0016020)|myofibril (GO:0030016)		p.D38N(1)		breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(2)|urinary_tract(1)	11		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		GGATGAGCTGGACCCTGATGT	0.512																																					p.D38N		.											.	TMOD1-90	1	Substitution - Missense(1)	kidney(1)	c.G112A						.						138	112	121					9																	100286582		2203	4300	6503	SO:0001583	missense	7111	exon2			GAGCTGGACCCTG		CCDS6726.1	9q22	2008-07-21		2003-03-21	ENSG00000136842	ENSG00000136842			11871	protein-coding gene	gene with protein product		190930		D9S57E, TMOD		1370827, 8661028	Standard	NM_003275		Approved	ETMOD	uc004axl.2	P28289	OTTHUMG00000020325	ENST00000259365.4:c.112G>A	9.37:g.100286582G>A	ENSP00000259365:p.Asp38Asn	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	77	30	NM_001166116	0	0	0	0	0	B2RB77|Q5T7W3|Q9BUF1	Missense_Mutation	SNP	ENST00000259365.4	37	CCDS6726.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821210	0.90873	.	.	ENSG00000136842	ENST00000395211;ENST00000259365	T;T	0.54279	0.58;0.58	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.76814	0.4040	M	0.87097	2.86	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.81468	-0.0919	10	0.87932	D	0	-31.3023	17.3565	0.87337	0.0:0.0:1.0:0.0	.	38	P28289	TMOD1_HUMAN	N	38	ENSP00000378637:D38N;ENSP00000259365:D38N	ENSP00000259365:D38N	D	+	1	0	TMOD1	99326403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.283000	0.78640	2.534000	0.85438	0.585000	0.79938	GAC	.		0.512	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053320.2	NM_003275		A	100286582	G	A	100286582	3	1	143	1	0	0	0	0	1	0	0	0	16265	1174	41	2	114	2	TMOD1	9	100286582	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	65649019	100286582	40926849	48	12792											
CTNNAL1	8727	broad.mit.edu	37	chr9	111775718	111775718	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggcgggtccgggagaggcgGccatggccctcggtctatcc	4	6	17	14	5	1	1	0	0	1	1	4	2	3	1	4	7	0	0	4	7	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:111775718G>T	ENST00000325551.4	-	1	91	c.5C>A	c.(4-6)gCc>gAc	p.A2D	CTNNAL1_ENST00000325580.6_Missense_Mutation_p.A2D|CTNNAL1_ENST00000374593.4_Missense_Mutation_p.A2D|CTNNAL1_ENST00000374595.4_Missense_Mutation_p.A2D	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	2					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		GGGAGAGGCGGCCATGGCCCT	0.746																																					p.A2D													.	CTNNAL1-228	0			c.C5A						.						3	4	4					9																	111775718		1652	3413	5065	SO:0001583	missense	8727	exon1			GAGGCGGCCATGG	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.5C>A	9.37:g.111775718G>T	ENSP00000320434:p.Ala2Asp	Somatic	47	2		WXS	Illumina HiSeq	Phase_I	55	7	NM_003798	0	0	0	0	0	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	37	CCDS6775.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439682	0.43326	.	.	ENSG00000119326	ENST00000374595;ENST00000325551;ENST00000325580;ENST00000374593	T;T;T;T	0.68765	1.53;1.64;1.52;-0.35	3.82	3.82	0.43975	.	0.000000	0.40144	N	0.001171	T	0.45677	0.1354	N	0.08118	0	0.37305	D	0.908868	B;B;B	0.23058	0.048;0.079;0.048	B;B;B	0.21546	0.015;0.035;0.015	T	0.54682	-0.8257	10	0.87932	D	0	-4.838	11.0862	0.48089	0.0:0.0:1.0:0.0	.	2;2;2	B2RBI4;Q9UBT7-2;Q9UBT7	.;.;CTNL1_HUMAN	D	2	ENSP00000363723:A2D;ENSP00000320434:A2D;ENSP00000323351:A2D;ENSP00000363721:A2D	ENSP00000320434:A2D	A	-	2	0	CTNNAL1	110815539	1.000000	0.71417	0.994000	0.49952	0.107000	0.19398	1.855000	0.39378	1.942000	0.56320	0.561000	0.74099	GCC	.		0.746	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		T	111775718	G	T	111775718	3	4	143	1	0	0	0	0	1	0	0	0	4021	1203	42	4	2275	4	CTNNAL1	9	111775718	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	11489136	111775718	29437713	49	12793											
PKN3	29941	broad.mit.edu	37	chr9	131469297	131469297	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cacaggaccgcaaggcactgGctgaggtcaggccccagccc	9	3	13	16	1	1	1	1	1	0	0	1	2	1	2	4	5	1	3	4	5	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:131469297G>A	ENST00000291906.4	+	5	1039	c.646G>A	c.(646-648)Gct>Act	p.A216T	RN7SL560P_ENST00000577943.1_RNA	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	216					epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CAAGGCACTGGCTGAGGTCAG	0.612																																					p.A216T													.	PKN3-521	0			c.G646A						.						82	80	80					9																	131469297		2203	4300	6503	SO:0001583	missense	29941	exon5			GCACTGGCTGAGG	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.646G>A	9.37:g.131469297G>A	ENSP00000291906:p.Ala216Thr	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	58	3	NM_013355	0	0	0	0	0	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.905684	0.52333	.	.	ENSG00000160447	ENST00000291906	T	0.20069	2.1	5.05	4.11	0.48088	.	.	.	.	.	T	0.31451	0.0797	M	0.66939	2.045	0.54753	D	0.99998	P;P	0.44380	0.834;0.645	P;B	0.48189	0.57;0.371	T	0.04855	-1.0922	9	0.48119	T	0.1	.	12.6655	0.56840	0.0:0.0:0.835:0.165	.	216;216	Q05BU1;Q6P5Z2	.;PKN3_HUMAN	T	216	ENSP00000291906:A216T	ENSP00000291906:A216T	A	+	1	0	PKN3	130509118	1.000000	0.71417	0.096000	0.21009	0.046000	0.14306	4.414000	0.59802	2.345000	0.79718	0.555000	0.69702	GCT	.		0.612	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131469297	G	A	131469297	3	1	143	1	0	0	0	0	1	0	0	0	12007	1203	42	2	664	2	PKN3	9	131469297	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	19693579	131469297	9744134	50	12794											
PRDM12	59335	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	133556745	133556745	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgctcgcacatgcgcatcCacacgctggacaagcccttc	8	7	9	17	4	0	0	0	0	0	0	3	1	1	1	2	1	3	4	2	1	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:133556745C>T	ENST00000253008.2	+	5	853	c.793C>T	c.(793-795)Cac>Tac	p.H265Y		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	265					neurogenesis (GO:0022008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		CATGCGCATCCACACGCTGGA	0.711																																					p.H265Y		.											.	PRDM12-90	0			c.C793T						.						11	13	12					9																	133556745		2188	4269	6457	SO:0001583	missense	59335	exon5			CGCATCCACACGC	AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"Zinc fingers, C2H2-type"	13997	protein-coding gene	gene with protein product	"PR-domain containing protein 12", "PR-domain zinc finger protein 12"					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.793C>T	9.37:g.133556745C>T	ENSP00000253008:p.His265Tyr	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	73	29	NM_021619	0	0	0	0	0	A3KFK9	Missense_Mutation	SNP	ENST00000253008.2	37	CCDS6934.1	.	.	.	.	.	.	.	.	.	.	C	35	5.424499	0.96111	.	.	ENSG00000130711	ENST00000253008	T	0.67523	-0.27	4.31	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.84120	0.5402	M	0.89353	3.025	0.54753	D	0.999986	D	0.76494	0.999	D	0.87578	0.998	D	0.88039	0.2780	10	0.87932	D	0	-38.3997	15.763	0.78101	0.0:1.0:0.0:0.0	.	265	Q9H4Q4	PRD12_HUMAN	Y	265	ENSP00000253008:H265Y	ENSP00000253008:H265Y	H	+	1	0	PRDM12	132546566	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.432000	0.80349	1.954000	0.56735	0.561000	0.74099	CAC	.		0.711	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1	NM_021619		T	133556745	C	T	133556745	3	4	143	1	0	0	0	0	1	0	0	0	12482	594	21	2	811	2	PRDM12	9	133556745	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	2087448	133556745	7656686	51	12795											
GDI2	2665	hgsc.bcm.edu;bcgsc.ca	37	chr10	5855180	5855180	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagccctggcgcccaccgtCaggccggtgcccagcacgat	6	5	12	18	4	2	0	2	0	0	0	2	1	2	0	5	3	3	1	5	3	0	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr10:5855180C>A	ENST00000380191.4	-	1	332	c.42G>T	c.(40-42)ctG>ctT	p.L14L	RP11-318E3.9_ENST00000608273.1_lincRNA|GDI2_ENST00000380132.4_5'UTR|GDI2_ENST00000380181.3_Silent_p.L14L	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	14					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						CGCCCACCGTCAGGCCGGTGC	0.751																																					p.L14L		.											.	GDI2-90	0			c.G42T						.						8	9	9					10																	5855180		2144	4238	6382	SO:0001819	synonymous_variant	2665	exon1			CACCGTCAGGCCG	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.42G>T	10.37:g.5855180C>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	50	24	NM_001115156	0	0	0	0	0	O43928|Q5SX88|Q9UQM6	Silent	SNP	ENST00000380191.4	37	CCDS7071.1																																																																																			.		0.751	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		A	5855180	C	A	5855180	2	1	143	1	0	0	0	0	0	0	0	1	6341	813	29	4		4	GDI2	10	5855180	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		5855180	129679567	52	12796											
ZNF33B	7582	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	43088707	43088707	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgagagagggttgacttaTggctaaagaatttcccacat	12	12	11	6	0	0	4	0	2	0	2	1	5	1	4	1	2	0	3	1	2	4	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr10:43088707T>C	ENST00000359467.3	-	5	1805	c.1691A>G	c.(1690-1692)cAt>cGt	p.H564R	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	564					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)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						GGTTGACTTATGGCTAAAGAA	0.413																																					p.H564R	Melanoma(137;1247 1767 16772 25727 43810)												.	ZNF33B-90	0			c.A1691G						.						120	120	120					10																	43088707		2203	4300	6503	SO:0001583	missense	7582	exon5			GACTTATGGCTAA	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1691A>G	10.37:g.43088707T>C	ENSP00000352444:p.His564Arg	Somatic	117	1		WXS	Illumina HiSeq	Phase_I	75	37	NM_006955	0	0	4	6	2	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.326415	0.24080	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.17691	2.26	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37219	N	0.002197	T	0.05868	0.0153	N	0.01529	-0.815	0.27560	N	0.950226	P	0.40834	0.73	B	0.40782	0.34	T	0.27938	-1.0059	10	0.19590	T	0.45	.	9.0257	0.36227	0.0:0.0:0.0:1.0	.	564	Q06732	ZN33B_HUMAN	R	564;530	ENSP00000352444:H564R	ENSP00000352444:H564R	H	-	2	0	ZNF33B	42408713	0.000000	0.05858	1.000000	0.80357	0.980000	0.70556	-0.095000	0.11077	1.449000	0.47699	0.341000	0.21757	CAT	.		0.413	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		C	43088707	T	C	43088707	3	2	143	1	0	0	0	0	1	0	0	0	17887	1464	51	3	649	3	ZNF33B	10	43088707	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	37233527	43088707	92446040	53	12797											
COL17A1	1308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105795252	105795252	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgcagcaaggagaggagcTcctcataggaggttcccggc	9	6	14	12	2	1	1	1	0	0	1	4	4	3	3	2	5	2	4	2	5	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr10:105795252T>G	ENST00000353479.5	-	49	3778	c.3488A>C	c.(3487-3489)gAg>gCg	p.E1163A	COL17A1_ENST00000369733.3_Missense_Mutation_p.E1118A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1163	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GGAGAGGAGCTCCTCATAGGA	0.627																																					p.E1163A		.											.	COL17A1-95	0			c.A3488C						.						29	33	32					10																	105795252		2203	4300	6503	SO:0001583	missense	1308	exon49			AGGAGCTCCTCAT	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"Collagens"	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.3488A>C	10.37:g.105795252T>G	ENSP00000340937:p.Glu1163Ala	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	105	16	NM_000494	0	0	10	10	0	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.290516	0.23478	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.91740	-2.9;-2.8	4.83	3.68	0.42216	.	0.150217	0.30329	N	0.009864	D	0.84633	0.5515	L	0.34521	1.04	0.80722	D	1	B	0.30406	0.278	B	0.30179	0.112	T	0.76542	-0.2921	10	0.10902	T	0.67	-20.9225	9.6783	0.40054	0.1549:0.0:0.0:0.8451	.	1163	Q9UMD9	COHA1_HUMAN	A	1163;1118	ENSP00000340937:E1163A;ENSP00000358748:E1118A	ENSP00000340937:E1163A	E	-	2	0	COL17A1	105785242	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.356000	0.44116	0.845000	0.35118	-0.695000	0.03696	GAG	.		0.627	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		G	105795252	T	G	105795252	3	3	143	1	0	0	0	0	1	0	0	0	3680	1551	54	5	1037	5	COL17A1	10	105795252	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	62706545	105795252	29739495	54	12798											
MUC2	4583	broad.mit.edu	37	chr11	1092630	1092630	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagccctccaaccaccacTcccagccctccaacaaccac	11	3	2	25	0	0	0	0	0	0	0	3	0	3	0	9	0	5	0	9	0	3	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:1092630T>C	ENST00000441003.2	+	30	4476	c.4449T>C	c.(4447-4449)acT>acC	p.T1483T	MUC2_ENST00000359061.5_Silent_p.T1484T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4218	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caaccaccactcccaGCCCTC	0.632																																					p.T1483T													.	MUC2-90	0			c.T4449C						.						242	368	324					11																	1092630		1607	3000	4607	SO:0001819	synonymous_variant	4583	exon30			CACCACTCCCAGC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4449T>C	11.37:g.1092630T>C		Somatic	157	17		WXS	Illumina HiSeq	Phase_I	134	29	NM_002457	0	0	0	0	0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1092630	T	C	1092630	2	2	143	1	0	0	0	0	0	0	0	1	10000	1538	54	3		3	MUC2	11	1092630	Silent	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		1092630	133913886	55	12799											
SMPD1	6609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	6412728	6412728	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acctctttgaggatgacatgGtggaggtgtggagacgctca	9	10	15	7	1	2	3	1	2	1	1	2	6	2	5	1	5	0	1	1	5	0	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:6412728G>A	ENST00000342245.4	+	2	601	c.433G>A	c.(433-435)Gtg>Atg	p.V145M	SMPD1_ENST00000356761.2_Missense_Mutation_p.V145M|SMPD1_ENST00000533196.1_Intron|SMPD1_ENST00000299397.3_Missense_Mutation_p.V145M|SMPD1_ENST00000527275.1_Missense_Mutation_p.V144M	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	143	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.				cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	GGATGACATGGTGGAGGTGTG	0.582																																					p.V145M		.											.	SMPD1-90	0			c.G433A						.						76	63	68					11																	6412728		2201	4296	6497	SO:0001583	missense	6609	exon2			GACATGGTGGAGG	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.433G>A	11.37:g.6412728G>A	ENSP00000340409:p.Val145Met	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	52	19	NM_000543	0	0	10	15	5	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	37	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553731	0.65425	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.97731	-4.51;-4.51;-4.51;-4.51	5.11	5.11	0.69529	Saposin-like (2);Saposin B (2);	0.178891	0.37857	N	0.001919	D	0.96892	0.8985	L	0.54323	1.7	0.42449	D	0.99274	P;P;P	0.46706	0.818;0.883;0.579	B;P;P	0.51516	0.366;0.672;0.472	D	0.96137	0.9097	10	0.49607	T	0.09	-7.0221	9.6331	0.39791	0.0956:0.0:0.9044:0.0	.	144;145;143	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	M	145;145;145;144	ENSP00000299397:V145M;ENSP00000349203:V145M;ENSP00000340409:V145M;ENSP00000435350:V144M	ENSP00000299397:V145M	V	+	1	0	SMPD1	6369304	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.869000	0.48444	2.382000	0.81193	0.650000	0.86243	GTG	.		0.582	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		A	6412728	G	A	6412728	3	1	143	1	0	0	0	0	1	0	0	0	14836	1261	44	2	439	2	SMPD1	11	6412728	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	5320098	6412728	128593788	56	12800											
PEX16	9409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	45936221	45936221	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggactgctcatggttgccagGgctgtggtcaccatctagca	7	10	13	11	0	3	0	2	0	1	0	3	1	3	1	2	4	3	4	2	4	1	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:45936221G>A	ENST00000378750.5	-	6	718	c.475C>T	c.(475-477)Cct>Tct	p.P159S	PEX16_ENST00000532681.1_Missense_Mutation_p.P64S|PEX16_ENST00000241041.3_Missense_Mutation_p.P159S|PEX16_ENST00000532554.1_5'UTR			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	159					ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)	p.P159T(1)		large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		TGGTTGCCAGGGCTGTGGTCA	0.582																																					p.P159S		.											.	PEX16-93	1	Substitution - Missense(1)	large_intestine(1)	c.C475T						.						154	129	137					11																	45936221		2203	4299	6502	SO:0001583	missense	9409	exon6			TGCCAGGGCTGTG	AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.475C>T	11.37:g.45936221G>A	ENSP00000368024:p.Pro159Ser	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	59	21	NM_004813	0	0	63	115	52	Q9BWB9	Missense_Mutation	SNP	ENST00000378750.5	37	CCDS31472.1	.	.	.	.	.	.	.	.	.	.	G	0.052	-1.248308	0.01469	.	.	ENSG00000121680	ENST00000241041;ENST00000378750;ENST00000532681;ENST00000533151;ENST00000525192	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	6.04	-5.2	0.02823	.	1.274680	0.04746	N	0.423709	T	0.05868	0.0153	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.28744	-1.0034	10	0.06236	T	0.91	2.692	1.5964	0.02665	0.2746:0.3442:0.2067:0.1744	.	159;159	Q9Y5Y5;Q9Y5Y5-2	PEX16_HUMAN;.	S	159;159;64;55;64	ENSP00000241041:P159S;ENSP00000368024:P159S;ENSP00000434654:P64S;ENSP00000433045:P55S;ENSP00000431309:P64S	ENSP00000241041:P159S	P	-	1	0	PEX16	45892797	0.000000	0.05858	0.001000	0.08648	0.474000	0.32979	-1.251000	0.02882	-0.602000	0.05775	0.561000	0.74099	CCT	.		0.582	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174		A	45936221	G	A	45936221	3	1	143	1	0	0	0	0	1	0	0	0	11769	1232	43	2	652	2	PEX16	11	45936221	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	39523493	45936221	89070295	57	12801											
OR5J2	282775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	55944703	55944703	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgttgctgttaaccttctccGgagtcattgccatggccacc	6	13	9	13	1	2	0	1	0	1	0	3	1	2	1	5	2	3	3	5	2	1	4	rs143728764	byFrequency	TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:55944703G>A	ENST00000312298.1	+	1	610	c.610G>A	c.(610-612)Gga>Aga	p.G204R		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					AACCTTCTCCGGAGTCATTGC	0.468													.|||	2	0.000399361	0	0	5008	,	,		23855	0		0.002	False		,,,				2504	0				p.G204R		.											.	OR5J2-115	0			c.G610A						.	A	ARG/GLY	1,4401	2.1+/-5.4	0,1,2200	168	129	142		610	1.6	0	11	dbSNP_134	142	2,8590	3.0+/-9.4	0,2,4294	yes	missense	OR5J2	NM_001005492.1	125	0,3,6494	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging	204/313	55944703	3,12991	2201	4296	6497	SO:0001583	missense	282775	exon1			TTCTCCGGAGTCA	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"GPCR / Class A : Olfactory receptors"	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.610G>A	11.37:g.55944703G>A	ENSP00000310788:p.Gly204Arg	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	66	8	NM_001005492	0	0	0	0	0	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	37	CCDS31522.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	g	9.690	1.151524	0.21371	2.27E-4	2.33E-4	ENSG00000174957	ENST00000312298	T	0.38401	1.14	4.55	1.59	0.23543	GPCR, rhodopsin-like superfamily (1);	0.240868	0.29059	N	0.013277	T	0.47710	0.1460	M	0.90977	3.165	0.09310	N	1	P	0.45569	0.861	P	0.45037	0.467	T	0.48811	-0.9002	10	0.72032	D	0.01	.	7.9468	0.29991	0.334:0.0:0.666:0.0	.	204	Q8NH18	OR5J2_HUMAN	R	204	ENSP00000310788:G204R	ENSP00000310788:G204R	G	+	1	0	OR5J2	55701279	0.000000	0.05858	0.034000	0.17996	0.001000	0.01503	0.042000	0.13949	0.497000	0.27926	-0.185000	0.12909	GGA	G|1.000;A|0.000		0.468	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		A	55944703	G	A	55944703	3	1	143	1	0	0	0	0	1	0	0	0	11191	1117	39	1	612	1	OR5J2	11	55944703	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	10008482	55944703	79061813	58	12802											
C11orf57	55216	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	111953315	111953315	+	Frame_Shift_Del	DEL	C	C	-																															aagcagaaaaaaaggtcacaCaaaaaacagaagaaaagcaa																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:111953315delC	ENST00000280352.9	+	6	1134	c.498delC	c.(496-498)cacfs	p.H166fs	C11orf57_ENST00000420986.2_Frame_Shift_Del_p.H166fs|C11orf57_ENST00000393047.3_Frame_Shift_Del_p.H167fs|TIMM8B_ENST00000507614.1_5'Flank|C11orf57_ENST00000532163.1_Frame_Shift_Del_p.H138fs	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	166	Lys-rich.									autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AAAGGTCACACAAAAAACAGA	0.413																																					p.H167fs		.											.	C11orf57-155	0			c.501delC						.						99	105	103					11																	111953315		2201	4297	6498	SO:0001589	frameshift_variant	55216	exon6			.	BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.498delC	11.37:g.111953315delC	ENSP00000339076:p.His166fs	Somatic	256	0		WXS	Illumina HiSeq	Phase_I	209	79	NM_001082969	0	0	0	0	0	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Frame_Shift_Del	DEL	ENST00000280352.9	37	CCDS41715.1																																																																																			.		0.413	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		-	111953315	C	-	111953315	7	5	143	1	0	1	0	1	0	0	0	0	1654	477	17	0	519	0	C11orf57	11	111953315	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M9-01A-11D-A31X-10	56008612	111953315	23053201	59	12803											
VPS11	55823	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	118952015	118952015	+	Frame_Shift_Del	DEL	C	C	-																															cgagatctccatgatcaattCcagcatcaggtggggatgag																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:118952015delC	ENST00000300793.6	+	16	2691	c.2649delC	c.(2647-2649)ttcfs	p.F883fs	VPS11_ENST00000527798.1_3'UTR	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11 homolog (S. cerevisiae)	884					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		ATGATCAATTCCAGCATCAGG	0.532																																					.		.											.	VPS11-25	0			.						.						50	52	51					11																	118952015		1948	4151	6099	SO:0001589	frameshift_variant	55823	.			.	AB027508	CCDS73404.1	11q23	2008-02-05	2006-12-19			ENSG00000160695		"RING-type (C3HC4) zinc fingers"	14583	protein-coding gene	gene with protein product		608549	"vacuolar protein sorting 11 (yeast homolog)"				Standard	NM_021729		Approved	RNF108, PEP5	uc010ryx.2	Q9H270		ENST00000300793.6:c.2649delC	11.37:g.118952015delC	ENSP00000475301:p.Phe883fs	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	55	25	.	0	0	0	0	0	Q8WY89|Q96EP8|Q9H6D9|Q9HCS6	Targeted_Region	DEL	ENST00000300793.6	37																																																																																				.		0.532	VPS11-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021729		-	118952015	C	-	118952015	7	5	143	1	0	1	0	1	0	0	0	0	17221	854	30	0	2709	0	VPS11	11	118952015	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M9-01A-11D-A31X-10	6998700	118952015	16054501	60	12804											
ITPR2	3709	broad.mit.edu	37	chr12	26714818	26714818	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctgcaccatatttgaatgGctcttcatgaaaagagtatt	12	14	7	8	0	3	3	1	2	2	1	3	3	3	3	1	1	1	3	1	1	5	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr12:26714818G>T	ENST00000381340.3	-	35	5114	c.4698C>A	c.(4696-4698)agC>agA	p.S1566R		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1566					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TATTTGAATGGCTCTTCATGA	0.433																																					p.S1566R													.	ITPR2-542	0			c.C4698A						.						58	58	58					12																	26714818		1879	4118	5997	SO:0001583	missense	3709	exon35			TGAATGGCTCTTC	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"Ion channels / Inositol triphosphate receptors"	6181	protein-coding gene	gene with protein product	"cilia and flagella associated protein 48"	600144	"inositol 1,4,5-triphosphate receptor, type 2"			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4698C>A	12.37:g.26714818G>T	ENSP00000370744:p.Ser1566Arg	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	106	3	NM_002223	0	0	0	0	0	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.667994	0.47677	.	.	ENSG00000123104	ENST00000381340	T	0.68331	-0.32	4.59	0.0451	0.14228	.	0.401114	0.31233	N	0.008004	T	0.52451	0.1735	L	0.46819	1.47	0.80722	D	1	B	0.28933	0.228	B	0.29267	0.1	T	0.44498	-0.9324	10	0.72032	D	0.01	.	4.8656	0.13607	0.416:0.0:0.4445:0.1395	.	1566	Q14571	ITPR2_HUMAN	R	1566	ENSP00000370744:S1566R	ENSP00000370744:S1566R	S	-	3	2	ITPR2	26606085	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	1.059000	0.30517	0.105000	0.17753	0.655000	0.94253	AGC	.		0.433	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26714818	G	T	26714818	3	4	143	1	0	0	0	0	1	0	0	0	7942	1194	42	4	3499	4	ITPR2	12	26714818	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		26714818	107137077	61	12805											
DNAJC22	79962	bcgsc.ca	37	chr12	49745201	49745201	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacaacctggaccagacagaGgaggcacagaggcacttcct	13	4	11	13	0	0	3	0	0	0	3	1	5	1	5	3	4	1	2	3	4	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr12:49745201G>T	ENST00000549441.2	+	4	2146	c.942G>T	c.(940-942)gaG>gaT	p.E314D	DNAJC22_ENST00000395069.3_Missense_Mutation_p.E314D			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	314	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						ACCAGACAGAGGAGGCACAGA	0.547																																					p.E314D													.	DNAJC22-159	0			c.G942T						.						59	59	59					12																	49745201		2203	4300	6503	SO:0001583	missense	79962	exon3			GACAGAGGAGGCA	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.942G>T	12.37:g.49745201G>T	ENSP00000446830:p.Glu314Asp	Somatic	132	0		WXS	Illumina HiSeq	Phase_1	120	5	NM_024902	0	0	16	16	0	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	37	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.564963	0.65651	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.33438	1.41;1.41	5.5	3.53	0.40419	Heat shock protein DnaJ, N-terminal (5);	0.154813	0.56097	D	0.000021	T	0.18882	0.0453	N	0.20357	0.565	0.47511	D	0.999446	P	0.36354	0.549	B	0.40038	0.317	T	0.05517	-1.0880	10	0.37606	T	0.19	-7.4243	4.2702	0.10783	0.1957:0.0:0.6268:0.1776	.	314	Q8N4W6	DJC22_HUMAN	D	314	ENSP00000446830:E314D;ENSP00000378508:E314D	ENSP00000378508:E314D	E	+	3	2	DNAJC22	48031468	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	0.731000	0.26058	0.748000	0.32831	0.555000	0.69702	GAG	.		0.547	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		T	49745201	G	T	49745201	3	4	143	1	0	0	0	0	1	0	0	0	4652	991	35	4	948	4	DNAJC22	12	49745201	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	23030383	49745201	84106694	62	12806											
R3HDM2	22864	broad.mit.edu	37	chr12	57663626	57663626	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aatagttggaagtggggaggGgctgacccgtggaagccatg	10	7	18	6	1	0	1	0	1	0	0	0	4	0	4	2	6	1	2	2	6	4	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr12:57663626G>T	ENST00000347140.3	-	15	1844	c.1454C>A	c.(1453-1455)cCc>cAc	p.P485H	R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000403821.2_Missense_Mutation_p.P519H|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Missense_Mutation_p.P499H|R3HDM2_ENST00000358907.2_Missense_Mutation_p.P485H|R3HDM2_ENST00000413953.2_Missense_Mutation_p.P212H|R3HDM2_ENST00000441731.2_Missense_Mutation_p.P180H			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	485	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						AGTGGGGAGGGGCTGACCCGT	0.572																																					p.P485H													.	R3HDM2-92	0			c.C1454A						.						120	106	111					12																	57663626		2203	4300	6503	SO:0001583	missense	22864	exon13			GGGAGGGGCTGAC	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1454C>A	12.37:g.57663626G>T	ENSP00000317903:p.Pro485His	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	81	5	NM_014925	0	0	0	0	0	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.3|25.3	4.627176|4.627176	0.87560|0.87560	.|.	.|.	ENSG00000179912|ENSG00000179912	ENST00000413953;ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821|ENST00000466401	T;T;T;T;T;T;T;T|.	0.41400|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.058617|0.058617	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.69305|0.69305	0.3096|0.3096	L|L	0.42245|0.42245	1.32|1.32	0.54753|0.54753	D|D	0.999983|0.999983	D;D;D;D;D|.	0.76494|.	0.999;0.997;0.997;0.997;0.999|.	D;P;P;P;D|.	0.65874|.	0.939;0.817;0.817;0.817;0.939|.	T|T	0.70360|0.70360	-0.4893|-0.4893	10|7	0.87932|0.66056	D|D	0|0.02	-11.5485|-11.5485	18.0786|18.0786	0.89436|0.89436	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	212;519;499;485;212|.	B4DDZ2;B5MCG9;B5MCU0;Q9Y2K5;E9PAL1|.	.;.;.;R3HD2_HUMAN;.|.	H|T	212;212;485;499;485;180;250;519|83	ENSP00000409146:P212H;ENSP00000377400:P212H;ENSP00000317903:P485H;ENSP00000385839:P499H;ENSP00000351784:P485H;ENSP00000408536:P180H;ENSP00000394676:P250H;ENSP00000385169:P519H|.	ENSP00000317903:P485H|ENSP00000449326:P83T	P|P	-|-	2|1	0|0	R3HDM2|R3HDM2	55949893|55949893	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.841000|8.841000	0.92131|0.92131	2.890000|2.890000	0.99128|0.99128	0.650000|0.650000	0.86243|0.86243	CCC|CCC	.		0.572	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		T	57663626	G	T	57663626	3	4	143	1	0	0	0	0	1	0	0	0	12920	1232	43	4	1516	4	R3HDM2	12	57663626	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	7918425	57663626	76188269	63	12807											
ARL6IP4	23457	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	123465766	123465770	+	5'UTR	DEL	AGAGC	AGAGC	-																															gtcggaaaagagaaagaagaAgagcaggaaagacacctcga																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	AGAGC	AGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr12:123465766_123465770delAGAGC	ENST00000542678.1	-	0	426_430				ARL6IP4_ENST00000412505.2_Frame_Shift_Del_p.KS27fs|RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000453766.2_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000315580.5_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000357866.4_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000426960.2_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000454885.2_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000439686.2_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000392435.2_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000543566.1_Frame_Shift_Del_p.KS150fs			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9						peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		AGAAAGAAGAAGAGCAGGAAAGACA	0.683																																					p.150_151del	Ovarian(49;786 1333 9175 38236)	.											.	ARL6IP4-90	0			c.449_453del						.																																			SO:0001623	5_prime_UTR_variant	51329	exon2			.	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"ATP binding cassette transporters / subfamily B"	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.-2413GCTCT>-	12.37:g.123465766_123465770delAGAGC		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	144	31	NM_018694	0	0	0	0	0	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	37	CCDS9241.1																																																																																			.		0.683	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		-	123465770	AGAGC	-	123465766	6	5	143	0	1	1	0	1	0	0	0	0	944	72	3	0		0	ARL6IP4	12	123465766	5'UTR	DEL	AGAGC	TCGA-IZ-A6M9-01A-11D-A31X-10	65802140	123465766	10386129	64	12808											
NUFIP1	26747	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	45563329	45563329	+	Frame_Shift_Del	DEL	G	G	-																															ccgggaagaatctgggcgtcGaaggggggcggagccccggg																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:45563329delG	ENST00000379161.4	-	1	289	c.243delC	c.(241-243)ttcfs	p.F81fs	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000361121.2_5'Flank|GPALPP1_ENST00000379151.4_5'Flank	NM_012345.2	NP_036477.2	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein interacting protein 1	81	Pro-rich.				box C/D snoRNP assembly (GO:0000492)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA processing (GO:0006396)	cytosolic ribosome (GO:0022626)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|pre-snoRNP complex (GO:0070761)|presynaptic active zone (GO:0048786)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(4)|skin(3)	18		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		TCTGGGCGTCGAAGGGGGGCG	0.657																																					p.F81fs		.											.	NUFIP1-90	0			c.243delC						.						14	17	16					13																	45563329		2189	4285	6474	SO:0001589	frameshift_variant	26747	exon1			.	AF159548	CCDS9393.1	13q14	2008-02-05			ENSG00000083635	ENSG00000083635			8057	protein-coding gene	gene with protein product		604354				10556305, 10894927	Standard	NM_012345		Approved	NUFIP	uc001uzp.2	Q9UHK0	OTTHUMG00000016842	ENST00000379161.4:c.243delC	13.37:g.45563329delG	ENSP00000368459:p.Phe81fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	113	22	NM_012345	0	0	0	0	0	Q8WVM5|Q96SG1	Frame_Shift_Del	DEL	ENST00000379161.4	37	CCDS9393.1																																																																																			.		0.657	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345		-	45563329	G	-	45563329	7	5	143	1	0	1	0	1	0	0	0	0	10774	1049	37	0	1284	0	NUFIP1	13	45563329	Frame_Shift_Del	DEL	G	TCGA-IZ-A6M9-01A-11D-A31X-10		45563329	69606549	65	12809											
DACH1	1602	broad.mit.edu	37	chr13	72440446	72440446	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctgctgctgctactactGctgctgctgctgctgctgct	2	14	11	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	11	0	0	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:72440446G>A	ENST00000359684.2	-	1	461	c.462C>T	c.(460-462)agC>agT	p.S154S	DACH1_ENST00000313174.7_Silent_p.S154S|DACH1_ENST00000354591.4_Silent_p.S154S|DACH1_ENST00000305425.4_Silent_p.S154S			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	154	Poly-Ser.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		tgctactactgctgctgctgc	0.662																																					p.S154S													.	DACH1-135	0			c.C462T						.						3	4	4					13																	72440446		1701	3505	5206	SO:0001819	synonymous_variant	1602	exon1			ACTACTGCTGCTG	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"dachshund homolog (Drosophila)", "dachshund homolog 1 (Drosophila)"	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.462C>T	13.37:g.72440446G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	17	3	NM_080759	0	0	0	0	0	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Silent	SNP	ENST00000359684.2	37																																																																																				.		0.662	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		A	72440446	G	A	72440446	2	1	143	1	0	0	0	0	0	0	0	1	4226	1310	46	2		2	DACH1	13	72440446	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	26877117	72440446	42729432	66	12810											
LMO7	4008	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr13	76395479	76395497	+	Frame_Shift_Del	DEL	AAAGAAGATTCTACCACTT	AAAGAAGATTCTACCACTT	-																															cttatccttcagaaattcccAaagaagattctaccactttt																								rs200351536|rs532984694|rs149099643	byFrequency	TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	AAAGAAGATTCTACCACTT	AAAGAAGATTCTACCACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:76395479_76395497delAAAGAAGATTCTACCACTT	ENST00000321797.8	+	12	2396_2414	c.1675_1693delAAAGAAGATTCTACCACTT	c.(1675-1695)aaagaagattctaccacttttfs	p.KEDSTTF559fs	LMO7_ENST00000341547.4_Frame_Shift_Del_p.KEDSTTF510fs|LMO7_ENST00000526202.1_Frame_Shift_Del_p.KEDSTTF409fs|LMO7_ENST00000357063.3_Frame_Shift_Del_p.KEDSTTF844fs|LMO7_ENST00000465261.2_Frame_Shift_Del_p.KEDSTTF559fs|LMO7_ENST00000377534.3_Frame_Shift_Del_p.KEDSTTF844fs			Q8WWI1	LMO7_HUMAN	LIM domain 7	844					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AGAAATTCCCAAAGAAGATTCTACCACTTTTGCAAAAAG	0.457																																					p.559_565del		.											.	LMO7-586	0			c.1675_1693del						.																																			SO:0001589	frameshift_variant	4008	exon11			.	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"F-box only protein 20"	604362	"LIM domain only 7"	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.1675_1693delAAAGAAGATTCTACCACTT	13.37:g.76395479_76395497delAAAGAAGATTCTACCACTT	ENSP00000317802:p.Lys559fs	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	104	28	NM_015842	0	0	0	0	0	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Frame_Shift_Del	DEL	ENST00000321797.8	37																																																																																				.		0.457	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		-	76395497	AAAGAAGATTCTACCACTT	-	76395479	7	5	143	1	0	1	0	1	0	0	0	0	8878	131	5	0	2588	0	LMO7	13	76395479	Frame_Shift_Del	DEL	AAAGAAGATTCTACCACTT	TCGA-IZ-A6M9-01A-11D-A31X-10	3955033	76395479	38774399	67	12811											
TMTC4	84899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	101287091	101287091	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggacacacagacagagcacTtctgaaaagctgttcctcac	13	7	9	12	0	2	3	1	1	1	2	3	4	3	4	1	1	2	3	1	1	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:101287091T>G	ENST00000376234.3	-	11	1606	c.1417A>C	c.(1417-1419)Agt>Cgt	p.S473R	TMTC4_ENST00000342624.5_Missense_Mutation_p.S492R|TMTC4_ENST00000328767.5_Missense_Mutation_p.S362R|TMTC4_ENST00000462211.1_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	473						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GACAGAGCACTTCTGAAAAGC	0.493																																					p.S492R		.											.	TMTC4-155	0			c.A1474C						.						135	140	139					13																	101287091		2203	4300	6503	SO:0001583	missense	84899	exon12			GAGCACTTCTGAA		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"Tetratricopeptide (TTC) repeat domain containing"	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1417A>C	13.37:g.101287091T>G	ENSP00000365408:p.Ser473Arg	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	62	21	NM_032813	0	0	1	1	0	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.428259	0.83667	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.52526	0.66;0.66;0.66	5.55	5.55	0.83447	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.75406	0.3845	M	0.91663	3.23	0.80722	D	1	D;D;D;P	0.89917	1.0;0.999;1.0;0.737	D;D;D;P	0.97110	0.997;0.994;1.0;0.565	T	0.81901	-0.0720	10	0.87932	D	0	.	15.7439	0.77922	0.0:0.0:0.0:1.0	.	362;473;473;492	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	R	473;492;362	ENSP00000365408:S473R;ENSP00000343871:S492R;ENSP00000365409:S362R	ENSP00000365409:S362R	S	-	1	0	TMTC4	100085092	1.000000	0.71417	0.954000	0.39281	0.652000	0.38707	7.590000	0.82653	2.134000	0.65973	0.456000	0.33151	AGT	.		0.493	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		G	101287091	T	G	101287091	3	3	143	1	0	0	0	0	1	0	0	0	16295	1609	56	5	840	5	TMTC4	13	101287091	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	24891612	101287091	13882787	68	12812											
FBXO34	55030	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55817793	55817793	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagctagctgttcaaaaaacTgcacaaactcacctgcaatt	15	10	5	11	0	2	0	2	0	0	0	2	0	2	0	1	0	6	5	1	0	7	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr14:55817793T>A	ENST00000313833.4	+	2	930	c.685T>A	c.(685-687)Tgc>Agc	p.C229S	FBXO34_ENST00000440021.1_Missense_Mutation_p.C229S	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	229										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						TTCAAAAAACTGCACAAACTC	0.512																																					p.C229S													.	FBXO34-228	0			c.T685A						.						83	76	79					14																	55817793		2203	4300	6503	SO:0001583	missense	55030	exon2			AAAAACTGCACAA	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.685T>A	14.37:g.55817793T>A	ENSP00000313159:p.Cys229Ser	Somatic	79	1		WXS	Illumina HiSeq	Phase_I	74	29	NM_017943	0	0	1	1	0	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	T	6.831	0.522583	0.13066	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.46819	0.86;0.86	5.08	5.08	0.68730	.	0.167805	0.40818	N	0.001006	T	0.45836	0.1362	M	0.63428	1.95	0.47511	D	0.999442	B	0.12630	0.006	B	0.17722	0.019	T	0.37430	-0.9706	10	0.21014	T	0.42	-14.1611	15.0107	0.71547	0.0:0.0:0.0:1.0	.	229	Q9NWN3	FBX34_HUMAN	S	229	ENSP00000313159:C229S;ENSP00000394117:C229S	ENSP00000313159:C229S	C	+	1	0	FBXO34	54887546	1.000000	0.71417	0.967000	0.41034	0.171000	0.22731	4.380000	0.59581	2.136000	0.66102	0.528000	0.53228	TGC	.		0.512	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			A	55817793	T	A	55817793	3	1	143	1	0	0	0	0	1	0	0	0	5763	1580	55	5	687	5	FBXO34	14	55817793	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		55817793	51531747	69	12813											
ACOT4	122970	broad.mit.edu	37	chr14	74060593	74060593	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagaagccgtatgctacatGcttcaacatccccaggttct	11	10	8	12	1	2	1	1	0	1	1	3	2	3	1	3	1	5	4	3	1	5	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr14:74060593G>T	ENST00000326303.4	+	2	899	c.645G>T	c.(643-645)atG>atT	p.M215I		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	215					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		TATGCTACATGCTTCAACATC	0.423																																					p.M215I													.	ACOT4-90	0			c.G645T						.						150	147	148					14																	74060593		2203	4300	6503	SO:0001583	missense	122970	exon2			CTACATGCTTCAA	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"Acyl CoA thioesterases"	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.645G>T	14.37:g.74060593G>T	ENSP00000323071:p.Met215Ile	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	66	3	NM_152331	0	0	1	1	0	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.254564	0.59212	.	.	ENSG00000177465	ENST00000326303	T	0.28069	1.63	5.39	4.47	0.54385	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.301034	0.37437	N	0.002098	T	0.37705	0.1013	M	0.65975	2.015	0.47183	D	0.999347	P	0.41313	0.745	B	0.42555	0.391	T	0.34551	-0.9824	10	0.72032	D	0.01	-12.828	13.8627	0.63571	0.0:0.153:0.847:0.0	.	215	Q8N9L9	ACOT4_HUMAN	I	215	ENSP00000323071:M215I	ENSP00000323071:M215I	M	+	3	0	ACOT4	73130346	0.997000	0.39634	0.990000	0.47175	0.742000	0.42306	2.664000	0.46783	1.215000	0.43411	0.561000	0.74099	ATG	.		0.423	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331		T	74060593	G	T	74060593	3	4	143	1	0	0	0	0	1	0	0	0	153	1319	46	4	651	4	ACOT4	14	74060593	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	18242800	74060593	33288947	70	12814											
KIAA1409	57578	broad.mit.edu	37	chr14	94088804	94088804	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgcggtagcccactgaCgctgaagcaaaaacgagacc	12	5	10	14	3	0	3	0	2	0	1	1	4	1	3	3	1	4	3	3	1	4	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr14:94088804C>T	ENST00000393151.2	+	30	5225	c.5225C>T	c.(5224-5226)aCg>aTg	p.T1742M	UNC79_ENST00000555664.1_Missense_Mutation_p.T1742M|UNC79_ENST00000256339.4_Missense_Mutation_p.T1565M|UNC79_ENST00000553484.1_Missense_Mutation_p.T1764M			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1742					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGCCCACTGACGCTGAAGCAA	0.582																																					p.T1565M													.	.	0			c.C4694T						.						67	71	70					14																	94088804		2203	4300	6503	SO:0001583	missense	57578	exon30			CACTGACGCTGAA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.5225C>T	14.37:g.94088804C>T	ENSP00000376858:p.Thr1742Met	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	85	4	NM_020818	0	0	0	0	0	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	C	15.99	2.995180	0.54147	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.27104	1.75;1.69;1.76;1.75	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.43100	0.1232	L	0.32530	0.975	0.52501	D	0.999953	D	0.89917	1.0	D	0.87578	0.998	T	0.39683	-0.9602	10	0.87932	D	0	-15.2232	18.72	0.91689	0.0:1.0:0.0:0.0	.	1764	C9JQL1	.	M	1565;1742;1764;1742;1764	ENSP00000256339:T1565M;ENSP00000450868:T1742M;ENSP00000451360:T1764M;ENSP00000376858:T1742M	ENSP00000256339:T1565M	T	+	2	0	KIAA1409	93158557	1.000000	0.71417	0.553000	0.28255	0.624000	0.37722	7.294000	0.78760	2.433000	0.82419	0.305000	0.20034	ACG	.		0.582	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94088804	C	T	94088804	3	4	143	1	0	0	0	0	1	0	0	0	8251	536	19	1	4800	1	KIAA1409	14	94088804	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	20028211	94088804	13260736	71	12815											
SPTBN5	51332	broad.mit.edu	37	chr15	42143073	42143073	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtgctgcccagggctcGccaccagctctcagcctgct	5	8	11	17	1	1	0	1	0	1	0	3	0	1	0	4	1	6	5	4	1	0	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr15:42143073G>A	ENST00000320955.6	-	66	11127	c.10900C>T	c.(10900-10902)Cga>Tga	p.R3634*	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3634	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCCAGGGCTCGCCACCAGCTC	0.647																																					p.R3599X													.	SPTBN5-91	0			c.C10795T						.						19	24	22					15																	42143073		2149	4252	6401	SO:0001587	stop_gained	51332	exon66			GGGCTCGCCACCA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"beta V spectrin"	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.10900C>T	15.37:g.42143073G>A	ENSP00000317790:p.Arg3634*	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	48	3	NM_016642	0	1	25	26	0		Nonsense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	52	18.710897	0.99909	.	.	ENSG00000137877	ENST00000320955	.	.	.	3.79	1.91	0.25777	.	1.938660	0.03085	N	0.158980	.	.	.	.	.	.	0.44055	A	0.996793	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1913	0.25826	0.0981:0.1862:0.7158:0.0	.	.	.	.	X	3634	.	ENSP00000317790:R3634X	R	-	1	2	SPTBN5	39930365	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	0.503000	0.22610	0.582000	0.29556	-0.119000	0.15052	CGA	.		0.647	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42143073	G	A	42143073	4	1	143	1	0	0	0	0	0	1	0	0	15154	1095	38	1	136	1	SPTBN5	15	42143073	Nonsense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		42143073	60388319	72	12816											
MEGF11	84465	broad.mit.edu	37	chr15	66250030	66250030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagaccagcctggctggCaggtacaagctccagttact	10	7	11	13	0	0	1	0	0	0	1	1	2	1	1	4	3	4	5	4	3	3	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr15:66250030C>T	ENST00000409699.2	-	10	1314	c.1142G>A	c.(1141-1143)tGc>tAc	p.C381Y	MEGF11_ENST00000288745.3_Missense_Mutation_p.C306Y|MEGF11_ENST00000422354.1_Missense_Mutation_p.C381Y|MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000395625.2_Missense_Mutation_p.C306Y|MEGF11_ENST00000360698.4_Missense_Mutation_p.C381Y			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	381					homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						GCCTGGCTGGCAGGTACAAGC	0.587																																					p.C381Y													.	MEGF11-69	0			c.G1142A						.						49	44	45					15																	66250030		2201	4298	6499	SO:0001583	missense	84465	exon10			GGCTGGCAGGTAC	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.1142G>A	15.37:g.66250030C>T	ENSP00000386908:p.Cys381Tyr	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	95	4	NM_032445	0	0	0	0	0	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356687	0.82243	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625;ENST00000360698;ENST00000455812	D;D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4;-3.4	4.87	4.87	0.63330	EGF-like, laminin (3);EGF-like region, conserved site (2);	0.000000	0.46442	U	0.000299	D	0.98582	0.9526	H	0.99894	4.905	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.992;1.0	D	0.99544	1.0964	10	0.87932	D	0	.	17.3629	0.87356	0.0:1.0:0.0:0.0	.	381;306	A6BM72;A6BM72-2	MEG11_HUMAN;.	Y	381;306;381;306;381;85	ENSP00000386908:C381Y;ENSP00000288745:C306Y;ENSP00000414475:C381Y;ENSP00000378987:C306Y;ENSP00000353919:C381Y;ENSP00000401400:C85Y	ENSP00000288745:C306Y	C	-	2	0	MEGF11	64037084	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.684000	0.84104	2.420000	0.82092	0.561000	0.74099	TGC	.		0.587	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		T	66250030	C	T	66250030	3	4	143	1	0	0	0	0	1	0	0	0	9486	710	25	2	2048	2	MEGF11	15	66250030	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	24106957	66250030	36281362	73	12817											
WDR90	197335	broad.mit.edu	37	chr16	707223	707223	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgtcctccgagtggcaggTtgggccccctgcagccactc	5	8	12	16	1	0	0	0	0	0	0	3	1	2	0	5	3	2	3	5	3	0	1	rs78538490		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:707223T>G	ENST00000293879.4	+	20	2473		c.e20+2		LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Splice_Site			Q96KV7	WDR90_HUMAN	WD repeat domain 90											endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GAGTGGCAGGTTGGGCCCCCT	0.692																																					.													.	WDR90-92	0			c.2473+2T>G						.						4	5	5					16																	707223		1769	3825	5594	SO:0001630	splice_region_variant	197335	exon20			GGCAGGTTGGGCC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2473+2T>G	16.37:g.707223T>G		Somatic	77	6		WXS	Illumina HiSeq	Phase_I	92	8	NM_145294	0	0	2	2	0	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Splice_Site	SNP	ENST00000293879.4	37	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637594	0.47049	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	.	.	.	4.41	4.41	0.53225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.127	0.59360	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR90	647224	0.999000	0.42202	0.986000	0.45419	0.177000	0.22998	3.227000	0.51262	1.761000	0.52028	0.402000	0.26972	.	.		0.692	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	Intron	G	707223	T	G	707223	5	3	143	1	0	0	0	0	0	0	1	0	17370	1739	60	5	2553	5	WDR90	16	707223	Splice_Site	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		707223	89647530	74	12818											
APOB48R	55911	hgsc.bcm.edu	37	chr16	28507452	28507452	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcaggaggggaggaggccGggacagcctcaggaggggac	9	2	20	10	1	2	0	2	0	0	0	2	6	2	6	3	9	1	0	3	9	0	0	rs370148393		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:28507452G>T	ENST00000431282.1	+	3	1073	c.1063G>T	c.(1063-1065)Ggg>Tgg	p.G355W	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000564831.1_Missense_Mutation_p.G364W|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000328423.5_Missense_Mutation_p.G355W			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	355	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GGAGGAGGCCGGGACAGCCTC	0.672																																					p.G364W		.											.	APOBR-90	0			c.G1090T						.						14	17	16					16																	28507452		1944	4097	6041	SO:0001583	missense	55911	exon2			GAGGCCGGGACAG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1063G>T	16.37:g.28507452G>T	ENSP00000416094:p.Gly355Trp	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	29	6	NM_018690	0	0	0	0	0	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	G	11.71	1.718826	0.30503	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.60548	0.18;0.18	3.86	-2.49	0.06403	.	.	.	.	.	T	0.33059	0.0850	N	0.19112	0.55	0.09310	N	1	B	0.33777	0.425	B	0.27715	0.082	T	0.13980	-1.0489	9	0.72032	D	0.01	.	3.7884	0.08710	0.5999:0.0:0.2159:0.1841	.	355	Q9NS13	.	W	355	ENSP00000327669:G355W;ENSP00000416094:G355W	ENSP00000327669:G355W	G	+	1	0	APOBR	28414953	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.825000	0.04433	-0.783000	0.04534	-0.487000	0.04747	GGG	.		0.672	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		T	28507452	G	T	28507452	3	4	143	1	0	0	0	0	1	0	0	0	786	1116	39	4	1073	4	APOB48R	16	28507452	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	27800229	28507452	61847301	75	12819											
ZNF689	115509	broad.mit.edu	37	chr16	30616114	30616114	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcgagaggaggaggagaagCgccgctcgcagtccgggcac	9	2	19	11	5	0	2	0	0	0	2	2	6	1	4	2	5	1	3	2	5	1	0	rs374687630		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:30616114C>T	ENST00000287461.3	-	3	1311	c.974G>A	c.(973-975)cGc>cAc	p.R325H	RP11-146F11.5_ENST00000563540.1_RNA|ZNF689_ENST00000566673.1_5'UTR	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	325					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GGAGGAGAAGCGCCGCTCGCA	0.697																																					p.R325H													.	ZNF689-68	0			c.G974A						.	C	HIS/ARG	1,4393	2.1+/-5.4	0,1,2196	37	31	33		974	5.2	1	16		33	0,8600		0,0,4300	no	missense	ZNF689	NM_138447.1	29	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	probably-damaging	325/501	30616114	1,12993	2197	4300	6497	SO:0001583	missense	115509	exon3			GAGAAGCGCCGCT	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"Zinc fingers, C2H2-type", "-"	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.974G>A	16.37:g.30616114C>T	ENSP00000287461:p.Arg325His	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	45	3	NM_138447	0	0	0	0	0	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	37	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	c	18.99	3.740643	0.69304	2.28E-4	0.0	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.53640	0.61	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000133	T	0.61286	0.2335	L	0.43757	1.38	0.34736	D	0.730231	D	0.89917	1.0	D	0.71414	0.973	T	0.69691	-0.5077	10	0.72032	D	0.01	-21.8329	16.5866	0.84728	0.0:1.0:0.0:0.0	.	325	Q96CS4	ZN689_HUMAN	H	325	ENSP00000287461:R325H	ENSP00000287461:R325H	R	-	2	0	ZNF689	30523615	0.001000	0.12720	0.977000	0.42913	0.544000	0.35116	1.554000	0.36266	2.868000	0.98415	0.555000	0.69702	CGC	.		0.697	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		T	30616114	C	T	30616114	3	4	143	1	0	0	0	0	1	0	0	0	18126	768	27	1	532	1	ZNF689	16	30616114	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	2108662	30616114	59738639	76	12820											
CNOT1	23019	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	58592566	58592570	+	Frame_Shift_Del	DEL	CAAGA	CAAGA	-																															actaagagatgtcattccagCaagagggtcaatctaaagaa																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	CAAGA	CAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:58592566_58592570delCAAGA	ENST00000317147.5	-	18	2471_2475	c.2139_2143delTCTTG	c.(2137-2145)cctcttgctfs	p.LA714fs	CNOT1_ENST00000569732.1_5'Flank|SNORA50_ENST00000384225.2_RNA|CNOT1_ENST00000569240.1_Frame_Shift_Del_p.LA714fs|CNOT1_ENST00000441024.2_Frame_Shift_Del_p.LA714fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	714					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GTCATTCCAGCAAGAGGGTCAATCT	0.4																																					p.713_715del		.											.	CNOT1-95	0			c.2139_2143del						.																																			SO:0001589	frameshift_variant	23019	exon18			.	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.2139_2143delTCTTG	16.37:g.58592566_58592570delCAAGA	ENSP00000320949:p.Leu714fs	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	97	46	NM_206999	0	0	0	0	0	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Del	DEL	ENST00000317147.5	37	CCDS10799.1																																																																																			.		0.4	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		-	58592570	CAAGA	-	58592566	7	5	143	1	0	1	0	1	0	0	0	0	3623	710	25	0	5337	0	CNOT1	16	58592566	Frame_Shift_Del	DEL	CAAGA	TCGA-IZ-A6M9-01A-11D-A31X-10	27976452	58592566	31762187	77	12821											
EDC4	23644	broad.mit.edu;bcgsc.ca	37	chr16	67913803	67913803	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtagcagcagcagcagcagCagtagcagcagctcccttac	11	5	12	13	0	0	0	0	0	0	0	1	0	1	0	1	1	10	11	1	1	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:67913803C>T	ENST00000358933.5	+	16	2111	c.1872C>T	c.(1870-1872)agC>agT	p.S624S	CTC-479C5.10_ENST00000572067.1_lincRNA|AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	624	Ser-rich.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		gcagcagcagcagtagcagca	0.602																																					p.S624S													.	EDC4-92	0			c.C1872T						.						36	33	34					16																	67913803		2193	4282	6475	SO:0001819	synonymous_variant	23644	exon16			CAGCAGCAGTAGC	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.1872C>T	16.37:g.67913803C>T		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	47	5	NM_014329	0	0	1	1	0	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	37	CCDS10849.1																																																																																			.		0.602	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		T	67913803	C	T	67913803	2	4	143	1	0	0	0	0	0	0	0	1	4919	709	25	2		2	EDC4	16	67913803	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	9321237	67913803	22440950	78	12822											
PDPR	55066	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	70163023	70163023	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcaagtgctgcctcccaaaAtggtgagcaggtttttgcat	9	11	12	9	0	0	1	0	1	0	0	1	1	1	1	2	3	4	5	2	3	3	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:70163023A>T	ENST00000288050.4	+	6	1562	c.605A>T	c.(604-606)aAt>aTt	p.N202I	PDPR_ENST00000568530.1_Missense_Mutation_p.N202I|PDPR_ENST00000398122.3_Missense_Mutation_p.N102I	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	202					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GCCTCCCAAAATGGTGAGCAG	0.512																																					p.N202I		.											.	PDPR-135	0			c.A605T						.						111	104	106					16																	70163023		1953	4159	6112	SO:0001583	missense	55066	exon6			CCCAAAATGGTGA		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.605A>T	16.37:g.70163023A>T	ENSP00000288050:p.Asn202Ile	Somatic	379	0		WXS	Illumina HiSeq	Phase_I	473	124	NM_017990	0	0	1	2	1	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	37	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196035	0.38806	.	.	ENSG00000090857	ENST00000288050;ENST00000398122	D;D	0.82167	-1.58;-1.58	4.5	3.4	0.38934	FAD dependent oxidoreductase (1);	0.236187	0.40385	N	0.001112	T	0.77765	0.4179	L	0.55213	1.73	0.80722	D	1	B	0.23806	0.091	B	0.28784	0.094	T	0.69224	-0.5201	10	0.31617	T	0.26	.	9.0915	0.36614	0.9111:0.0:0.0889:0.0	.	202	Q8NCN5	PDPR_HUMAN	I	202;102	ENSP00000288050:N202I;ENSP00000381190:N102I	ENSP00000288050:N202I	N	+	2	0	PDPR	68720524	1.000000	0.71417	0.967000	0.41034	0.965000	0.64279	5.368000	0.66133	0.581000	0.29539	0.455000	0.32223	AAT	.		0.512	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		T	70163023	A	T	70163023	3	4	143	1	0	0	0	0	1	0	0	0	11715	101	4	5	619	5	PDPR	16	70163023	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	2249220	70163023	20191730	79	12823											
KARS	3735	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr16	75678300	75678300	+	Intron	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcgcagggaccccctaacAagccttacagcagcttgcgt	9	8	10	14	2	0	0	0	0	0	0	0	1	0	1	3	1	7	3	3	1	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:75678300A>T	ENST00000302445.3	-	2	102				KARS_ENST00000319410.5_Silent_p.L9L|KARS_ENST00000568378.1_Silent_p.L9L	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase						cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	ACCCCCTAACAAGCCTTACAG	0.552																																					p.L9L		.											.	KARS-92	0			c.T27A						.						50	47	48					16																	75678300		1568	3582	5150	SO:0001627	intron_variant	3735	exon2			CCTAACAAGCCTT	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"Aminoacyl tRNA synthetases / Class II"	6215	protein-coding gene	gene with protein product	"lysine tRNA ligase"	601421	"deafness, autosomal recessive 89"	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.63-2679T>A	16.37:g.75678300A>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	96	54	NM_001130089	0	0	1	1	0	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Silent	SNP	ENST00000302445.3	37	CCDS10923.1																																																																																			.		0.552	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548		T	75678300	A	T	75678300	1	4	143	0	1	0	0	0	0	0	0	0	8001	117	5	5		5	KARS	16	75678300	Intron	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	5515277	75678300	14676453	80	12824											
ANKRD11	29123	broad.mit.edu	37	chr16	89345819	89345819	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgctgggcctgggcgtcGtcgtcctcggagccgcgggc	2	7	19	13	6	0	0	0	0	0	0	4	2	1	2	3	5	2	1	3	5	0	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:89345819G>A	ENST00000301030.4	-	9	7591	c.7131C>T	c.(7129-7131)gaC>gaT	p.D2377D	ANKRD11_ENST00000378330.2_Silent_p.D2377D	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2377					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.D2377D(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CCTGGGCGTCGTCGTCCTCGG	0.716																																					p.D2377D													.	ANKRD11-139	1	Substitution - coding silent(1)	large_intestine(1)	c.C7131T						.						2	2	2					16																	89345819		1332	2736	4068	SO:0001819	synonymous_variant	29123	exon9			GGCGTCGTCGTCC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"Ankyrin repeat domain containing"	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.7131C>T	16.37:g.89345819G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	31	3	NM_001256183	0	0	6	6	0	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																			.		0.716	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89345819	G	A	89345819	2	1	143	1	0	0	0	0	0	0	0	1	639	1136	40	1		1	ANKRD11	16	89345819	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	13667519	89345819	1008934	81	12825											
TSR1	55720	broad.mit.edu	37	chr17	2237906	2237906	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctattgacattcagagtctGccctcgaacatagcctgaaa	12	10	7	12	1	2	3	1	2	1	1	3	4	2	3	3	0	3	0	3	0	4	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:2237906G>T	ENST00000301364.5	-	5	1920	c.841C>A	c.(841-843)Cag>Aag	p.Q281K	TSR1_ENST00000576112.2_Missense_Mutation_p.Q265K|SGSM2_ENST00000426855.2_5'Flank|SGSM2_ENST00000268989.3_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	281					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						TTCAGAGTCTGCCCTCGAACA	0.458																																					p.Q281K													.	TSR1-91	0			c.C841A						.						126	125	125					17																	2237906		2203	4300	6503	SO:0001583	missense	55720	exon5			GAGTCTGCCCTCG	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"TSR1, 20S rRNA accumulation, homolog (yeast)"			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.841C>A	17.37:g.2237906G>T	ENSP00000301364:p.Gln281Lys	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	142	4	NM_018128	0	0	0	0	0	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.026899	0.35797	.	.	ENSG00000167721	ENST00000301364	T	0.40225	1.04	5.4	4.4	0.53042	AARP2CN (2);	0.317953	0.36374	N	0.002639	T	0.27731	0.0682	L	0.27053	0.805	0.38853	D	0.956327	B	0.13594	0.008	B	0.19666	0.026	T	0.11299	-1.0593	10	0.05525	T	0.97	-1.3011	14.1036	0.65072	0.0:0.0:0.8438:0.1562	.	281	Q2NL82	TSR1_HUMAN	K	281	ENSP00000301364:Q281K	ENSP00000301364:Q281K	Q	-	1	0	TSR1	2184656	0.996000	0.38824	0.778000	0.31720	0.919000	0.55068	4.100000	0.57762	1.207000	0.43291	0.655000	0.94253	CAG	.		0.458	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		T	2237906	G	T	2237906	3	4	143	1	0	0	0	0	1	0	0	0	16697	1328	46	4	1617	4	TSR1	17	2237906	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		2237906	78957304	82	12826											
BCL6B	255877	broad.mit.edu	37	chr17	6927003	6927003	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtcgctatgggttcccccGccgccccggagggagcgctg	3	7	16	15	5	0	0	0	0	0	0	2	2	1	2	5	3	1	3	5	3	1	2	rs578215266		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:6927003G>T	ENST00000293805.5	+	2	105	c.13G>T	c.(13-15)Gcc>Tcc	p.A5S	BCL6B_ENST00000572216.1_3'UTR	NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	5					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						GGGTTCCCCCGCCGCCCCGGA	0.647																																					p.A5S													.	BCL6B-227	0			c.G13T						.						17	19	19					17																	6927003		1982	4123	6105	SO:0001583	missense	255877	exon2			TCCCCCGCCGCCC	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1002	protein-coding gene	gene with protein product		608992	"zinc finger protein 62", "B-cell CLL/lymphoma 6, member B (zinc finger protein)"	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.13G>T	17.37:g.6927003G>T	ENSP00000293805:p.Ala5Ser	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_181844	0	0	0	0	0	Q6PCB4	Missense_Mutation	SNP	ENST00000293805.5	37	CCDS42248.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.016817	0.93404	.	.	ENSG00000161940	ENST00000293805	T	0.07567	3.18	5.78	3.81	0.43845	.	0.802457	0.11693	N	0.538677	T	0.09862	0.0242	L	0.46157	1.445	0.09310	N	1	B	0.23591	0.088	B	0.25506	0.061	T	0.25745	-1.0123	10	0.87932	D	0	.	8.4482	0.32856	0.1756:0.0:0.8244:0.0	.	5	Q8N143	BCL6B_HUMAN	S	5	ENSP00000293805:A5S	ENSP00000293805:A5S	A	+	1	0	BCL6B	6867727	0.119000	0.22226	0.002000	0.10522	0.548000	0.35241	2.746000	0.47467	0.803000	0.34113	0.655000	0.94253	GCC	.		0.647	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844		T	6927003	G	T	6927003	3	4	143	1	0	0	0	0	1	0	0	0	1378	1087	38	4	15	4	BCL6B	17	6927003	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	4689097	6927003	74268207	83	12827											
PHF23	79142	broad.mit.edu	37	chr17	7139965	7139965	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccttctcttggatgactttGctttcttaacaaaagtctgg	8	16	7	10	0	3	1	0	1	3	0	4	2	3	2	1	2	2	1	1	2	3	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:7139965G>T	ENST00000320316.3	-	4	507	c.281C>A	c.(280-282)gCa>gAa	p.A94E	DVL2_ENST00000005340.5_5'Flank|PHF23_ENST00000571362.1_Intron|PHF23_ENST00000454255.2_Missense_Mutation_p.A90E|PHF23_ENST00000576955.1_5'UTR|DVL2_ENST00000575458.1_5'Flank|PHF23_ENST00000570753.1_5'UTR	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	94							zinc ion binding (GO:0008270)			breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						GGATGACTTTGCTTTCTTAAC	0.587																																					p.A94E													.	PHF23-90	0			c.C281A						.						100	110	106					17																	7139965		1945	4139	6084	SO:0001583	missense	79142	exon4			GACTTTGCTTTCT	AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"Zinc fingers, PHD-type"	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.281C>A	17.37:g.7139965G>T	ENSP00000322579:p.Ala94Glu	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	66	3	NM_024297	0	0	6	6	0	A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Missense_Mutation	SNP	ENST00000320316.3	37	CCDS42250.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225605	0.79576	.	.	ENSG00000040633	ENST00000320316;ENST00000454255;ENST00000043410	T;T	0.35789	1.29;1.34	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.51041	0.1651	L	0.39898	1.24	0.58432	D	0.999998	D	0.89917	1.0	D	0.80764	0.994	T	0.52170	-0.8611	10	0.66056	D	0.02	-11.0369	15.399	0.74823	0.0:0.0:1.0:0.0	.	94	Q9BUL5	PHF23_HUMAN	E	94;90;94	ENSP00000322579:A94E;ENSP00000414607:A90E	ENSP00000043410:A94E	A	-	2	0	PHF23	7080689	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.954000	0.87848	2.488000	0.83962	0.557000	0.71058	GCA	.		0.587	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440047.1	NM_024297		T	7139965	G	T	7139965	3	4	143	1	0	0	0	0	1	0	0	0	11861	1319	46	4	938	4	PHF23	17	7139965	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	212962	7139965	74055245	84	12828											
MYH4	4622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10358389	10358389	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagcaggccagctttgaaGaaaaccttatgaaagaacaa	17	6	8	10	0	0	4	0	2	0	2	0	4	0	4	3	1	4	2	3	1	7	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:10358389G>T	ENST00000255381.2	-	21	2414	c.2304C>A	c.(2302-2304)ttC>ttA	p.F768L	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	768	Actin-binding. {ECO:0000250}.|Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CAGCTTTGAAGAAAACCTTAT	0.403																																					p.F768L		.											.	MYH4-102	0			c.C2304A						.						169	108	129					17																	10358389		2203	4300	6503	SO:0001583	missense	4622	exon21			TTTGAAGAAAACC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.2304C>A	17.37:g.10358389G>T	ENSP00000255381:p.Phe768Leu	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	115	31	NM_017533	0	0	0	0	0		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962237	0.74016	.	.	ENSG00000141048	ENST00000255381	D	0.94280	-3.39	5.04	5.04	0.67666	Myosin head, motor domain (2);	0.000000	0.39475	U	0.001344	D	0.97340	0.9130	H	0.96691	3.865	0.58432	D	0.999998	P	0.40794	0.729	P	0.51229	0.663	D	0.98383	1.0559	10	0.62326	D	0.03	.	18.7298	0.91731	0.0:0.0:1.0:0.0	.	768	Q9Y623	MYH4_HUMAN	L	768	ENSP00000255381:F768L	ENSP00000255381:F768L	F	-	3	2	MYH4	10299114	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	3.989000	0.56958	2.497000	0.84241	0.313000	0.20887	TTC	.		0.403	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10358389	G	T	10358389	3	4	143	1	0	0	0	0	1	0	0	0	10062	933	33	4	3595	4	MYH4	17	10358389	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	3218424	10358389	70836821	85	12829											
C17orf48	56985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10608594	10608594	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgaattctataacttcagTagagagtatttaacacactc	15	13	5	8	0	2	2	1	1	1	1	3	3	2	2	0	0	2	2	0	0	6	8			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:10608594T>G	ENST00000379774.4	+	2	442	c.351T>G	c.(349-351)agT>agG	p.S117R	ADPRM_ENST00000609540.1_Missense_Mutation_p.S117R	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	117							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										ATAACTTCAGTAGAGAGTATT	0.358																																					p.S117R		.											.	.	0			c.T351G						.						83	78	80					17																	10608594		2203	4300	6503	SO:0001583	missense	56985	exon2			CTTCAGTAGAGAG	BC070155	CCDS11159.2	17p13.1	2012-07-20	2012-07-20	2012-07-20	ENSG00000170222	ENSG00000170222	3.6.1.13, 3.6.1.16, 3.6.1.53		30925	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 48"	C17orf48		18352857	Standard	XM_005256738		Approved	MDS006	uc002gmt.3	Q3LIE5	OTTHUMG00000130366	ENST00000379774.4:c.351T>G	17.37:g.10608594T>G	ENSP00000369099:p.Ser117Arg	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	149	81	NM_020233	0	0	2	6	4	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	37	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	T	13.35	2.211314	0.39102	.	.	ENSG00000170222	ENST00000379774	D	0.84800	-1.9	5.64	-3.05	0.05396	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.80919	0.4716	M	0.65498	2.005	0.80722	D	1	B	0.22080	0.064	B	0.27380	0.079	T	0.67264	-0.5714	10	0.21014	T	0.42	-25.0558	14.2725	0.66159	0.0:0.7691:0.1179:0.113	.	117	Q3LIE5	ADPRM_HUMAN	R	117	ENSP00000369099:S117R	ENSP00000369099:S117R	S	+	3	2	C17orf48	10549319	0.999000	0.42202	0.983000	0.44433	0.902000	0.53008	0.629000	0.24538	-0.424000	0.07382	-0.299000	0.09455	AGT	.		0.358	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		G	10608594	T	G	10608594	3	3	143	1	0	0	0	0	1	0	0	0	1864	1635	57	5	353	5	C17orf48	17	10608594	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	250205	10608594	70586616	86	12830											
CCDC144A	9720	ucsc.edu;bcgsc.ca	37	chr17	16612498	16612498	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaaatatcatccatccatActatcatccatactctgggt	14	12	3	12	0	3	0	2	0	1	0	6	0	6	0	3	1	2	0	3	1	6	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:16612498A>G	ENST00000360524.8	+	5	1203	c.1127A>G	c.(1126-1128)tAc>tGc	p.Y376C	CCDC144A_ENST00000340621.5_Missense_Mutation_p.Y375C|CCDC144A_ENST00000399273.1_Missense_Mutation_p.Y376C|CCDC144A_ENST00000456009.1_Intron|RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.Y376C|CCDC144A_ENST00000443444.2_Missense_Mutation_p.Y376C|RN7SL620P_ENST00000580704.1_RNA	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	376																	ATCCATCCATACTATCATCCA	0.378																																					p.Y376C													.	.	0			c.A1127G						.						107	100	102					17																	16612498		1830	4077	5907	SO:0001583	missense	9720	exon5			ATCCATACTATCA	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	ENST00000360524.8:c.1127A>G	17.37:g.16612498A>G	ENSP00000353717:p.Tyr376Cys	Somatic	783	4		WXS	Illumina HiSeq		869	213	NM_014695	0	0	0	0	0	O60311|Q6ZU57	Missense_Mutation	SNP	ENST00000360524.8	37	CCDS45621.1	.	.	.	.	.	.	.	.	.	.	.	9.422	1.083342	0.20309	.	.	ENSG00000170160	ENST00000340621;ENST00000399273;ENST00000443444;ENST00000448331;ENST00000360524;ENST00000360495	T;T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07;2.07	1.26	-2.52	0.06346	.	.	.	.	.	T	0.12390	0.0301	N	0.14661	0.345	0.09310	N	1	D	0.62365	0.991	P	0.49477	0.612	T	0.08534	-1.0717	8	.	.	.	.	2.6285	0.04937	0.4796:0.3278:0.0:0.1927	.	376	A2RUR9	C144A_HUMAN	C	375;376;376;376;376;376	ENSP00000344740:Y375C;ENSP00000382215:Y376C;ENSP00000439262:Y376C;ENSP00000440655:Y376C;ENSP00000353717:Y376C;ENSP00000353685:Y376C	.	Y	+	2	0	CCDC144A	16553223	0.024000	0.19004	0.000000	0.03702	0.076000	0.17211	0.184000	0.16939	-1.073000	0.03137	0.147000	0.16070	TAC	.		0.378	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			G	16612498	A	G	16612498	3	3	143	1	0	0	0	0	1	0	0	0	2783	391	14	3	1145	3	CCDC144A	17	16612498	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	6003904	16612498	64582712	87	12831											
SUPT6H	6830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	27014486	27014486	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaaagggacccacctcctGaaggtaggattggagtgaat	12	7	14	8	1	0	2	0	2	0	0	1	6	1	6	3	5	0	1	3	5	4	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:27014486G>T	ENST00000314616.6	+	23	3286	c.3003G>T	c.(3001-3003)ctG>ctT	p.L1001L	SUPT6H_ENST00000347486.4_Silent_p.L1001L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1001	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CCCACCTCCTGAAGGTAGGAT	0.458																																					p.L1001L		.											.	SUPT6H-93	0			c.G3003T						.						46	41	43					17																	27014486		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon23			CCTCCTGAAGGTA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3003G>T	17.37:g.27014486G>T		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	44	10	NM_003170	0	0	0	0	0	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																			.		0.458	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27014486	G	T	27014486	2	4	143	1	0	0	0	0	0	0	0	1	15432	1277	45	4		4	SUPT6H	17	27014486	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	10401988	27014486	54180724	88	12832											
CACNB1	782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37341119	37341119	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggggcacatgctctgtcTggggggggaagcagggaggg	7	5	23	6	0	2	0	0	0	2	0	2	2	2	2	0	9	2	3	0	9	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:37341119T>A	ENST00000394303.3	-	8	856		c.e8-2		CACNB1_ENST00000344140.5_Splice_Site|CACNB1_ENST00000394310.3_Splice_Site|CACNB1_ENST00000582877.1_5'Flank	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit						axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGCTCTGTCTGGGGGGGGAA	0.627																																					.	Esophageal Squamous(5;100 366 38393 41452 45827)	.											.	CACNB1-154	0			c.649-2A>T						.						33	30	31					17																	37341119		2203	4300	6503	SO:0001630	splice_region_variant	782	exon9			TCTGTCTGGGGGG		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.649-2A>T	17.37:g.37341119T>A		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	83	50	NM_000723	0	0	0	0	0	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Splice_Site	SNP	ENST00000394303.3	37	CCDS42311.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618558	0.66787	.	.	ENSG00000067191	ENST00000539338;ENST00000394303;ENST00000344140;ENST00000394310;ENST00000536613	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1992	0.65690	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CACNB1	34594645	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.867000	0.87062	1.992000	0.58205	0.454000	0.30748	.	.		0.627	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3		Intron	A	37341119	T	A	37341119	5	1	143	1	0	0	0	0	0	0	1	0	2558	1594	55	5	1282	5	CACNB1	17	37341119	Splice_Site	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	10326633	37341119	43854091	89	12833											
ERBB2	2064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37883597	37883597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggagccctctgaagaggaggCccccaggtctccactggcac	8	5	13	15	0	2	2	0	1	2	1	3	4	2	4	4	5	1	1	4	5	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:37883597C>T	ENST00000269571.5	+	26	3368	c.3209C>T	c.(3208-3210)gCc>gTc	p.A1070V	MIEN1_ENST00000474210.1_5'Flank|ERBB2_ENST00000584450.1_Intron|ERBB2_ENST00000541774.1_Missense_Mutation_p.A1055V|ERBB2_ENST00000445658.2_Missense_Mutation_p.A794V|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000406381.2_Missense_Mutation_p.A1040V|ERBB2_ENST00000540147.1_Missense_Mutation_p.A1040V|ERBB2_ENST00000584601.1_Missense_Mutation_p.A1040V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	1070					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GAAGAGGAGGCCCCCAGGTCT	0.617		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.A1070V		.		Dom	yes		17	17q21.1	2064	"v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"		E	.	ERBB2-9959	0			c.C3209T						.						35	39	38					17																	37883597		2203	4300	6503	SO:0001583	missense	2064	exon26			AGGAGGCCCCCAG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"CD molecules"	3430	protein-coding gene	gene with protein product	"neuro/glioblastoma derived oncogene homolog"	164870	"v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.3209C>T	17.37:g.37883597C>T	ENSP00000269571:p.Ala1070Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	74	21	NM_004448	0	0	99	134	35	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978099	0.34942	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.75704	-0.95;-0.95;-0.93;-0.96;-0.95	5.41	5.41	0.78517	.	.	.	.	.	T	0.63260	0.2496	L	0.29908	0.895	0.58432	D	0.99999	B;B;B	0.19817	0.017;0.019;0.039	B;B;B	0.18561	0.01;0.022;0.01	T	0.57854	-0.7739	9	0.17369	T	0.5	.	15.9084	0.79447	0.0:1.0:0.0:0.0	.	794;1055;1070	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	1040;1055;794;1070;1040	ENSP00000385185:A1040V;ENSP00000446466:A1055V;ENSP00000404047:A794V;ENSP00000269571:A1070V;ENSP00000443562:A1040V	ENSP00000269571:A1070V	A	+	2	0	ERBB2	35137123	0.667000	0.27484	0.997000	0.53966	0.976000	0.68499	2.804000	0.47931	2.515000	0.84797	0.561000	0.74099	GCC	.		0.617	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37883597	C	T	37883597	3	4	143	1	0	0	0	0	1	0	0	0	5219	739	26	2	3311	2	ERBB2	17	37883597	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	542478	37883597	43311613	90	12834											
C17orf77	146723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72588562	72588562	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgtatgttgcaaggtgtGcccaaacttttgtgcatgtg	8	14	12	7	0	0	0	0	0	0	0	0	0	0	0	1	1	4	4	1	1	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:72588562G>T	ENST00000392620.1	+	3	739	c.377G>T	c.(376-378)tGc>tTc	p.C126F	CD300LD_ENST00000375352.1_5'Flank|C17orf77_ENST00000328023.2_Missense_Mutation_p.C126F	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	126	Cys-rich.					extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						TGCAAGGTGTGCCCAAACTTT	0.458																																					p.C126F		.											.	C17orf77-90	0			c.G377T						.						151	143	145					17																	72588562		2203	4300	6503	SO:0001583	missense	146723	exon3			AGGTGTGCCCAAA		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.377G>T	17.37:g.72588562G>T	ENSP00000376396:p.Cys126Phe	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	65	18	NM_152460	0	0	0	0	0		Missense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	.	.	.	.	.	.	.	.	.	.	G	2.196	-0.384056	0.04966	.	.	ENSG00000182352	ENST00000392620;ENST00000328023	T;T	0.55760	0.5;0.5	2.64	1.62	0.23740	.	.	.	.	.	T	0.39436	0.1078	N	0.08118	0	0.09310	N	1	D	0.59767	0.986	P	0.53861	0.736	T	0.18650	-1.0330	8	.	.	.	.	7.2654	0.26227	0.0:0.2771:0.7229:0.0	.	126	Q96MU5	CQ077_HUMAN	F	126	ENSP00000376396:C126F;ENSP00000329353:C126F	.	C	+	2	0	C17orf77	70100157	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.150000	0.16263	0.651000	0.30788	0.609000	0.83330	TGC	.		0.458	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460		T	72588562	G	T	72588562	3	4	143	1	0	0	0	0	1	0	0	0	1887	1319	46	4	379	4	C17orf77	17	72588562	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	34704965	72588562	8606648	91	12835											
ZNF407	55628	broad.mit.edu	37	chr18	72775888	72775888	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagccatggcctctcaggagCgggcacaggtggccttcaag	8	6	14	13	1	2	0	2	0	1	0	3	1	2	1	3	5	2	1	3	5	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr18:72775888C>T	ENST00000299687.5	+	8	6211	c.6211C>T	c.(6211-6213)Cgg>Tgg	p.R2071W		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2071					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTCTCAGGAGCGGGCACAGGT	0.662																																					p.R2071W													.	ZNF407-92	0			c.C6211T						.						38	46	43					18																	72775888		2106	4222	6328	SO:0001583	missense	55628	exon8			CAGGAGCGGGCAC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6211C>T	18.37:g.72775888C>T	ENSP00000299687:p.Arg2071Trp	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	42	3	NM_017757	0	0	0	0	0	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122778	0.37436	.	.	ENSG00000215421	ENST00000299687	T	0.15372	2.43	4.42	2.43	0.29744	.	.	.	.	.	T	0.34019	0.0883	M	0.67953	2.075	0.80722	D	1	D	0.71674	0.998	P	0.61592	0.891	T	0.16600	-1.0397	9	0.87932	D	0	.	11.8945	0.52650	0.4417:0.5583:0.0:0.0	.	2071	Q9C0G0	ZN407_HUMAN	W	2071	ENSP00000299687:R2071W	ENSP00000299687:R2071W	R	+	1	2	ZNF407	70904876	0.715000	0.27946	0.648000	0.29521	0.838000	0.47535	1.314000	0.33597	0.866000	0.35629	-0.448000	0.05591	CGG	.		0.662	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		T	72775888	C	T	72775888	3	4	143	1	0	0	0	0	1	0	0	0	17919	759	27	1	6371	1	ZNF407	18	72775888	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		72775888	5301360	92	12836											
TMPRSS9	360200	broad.mit.edu	37	chr19	2410353	2410353	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactcactgacaggatggtGtgcgctggctacctggacgg	7	9	14	11	2	2	1	2	1	0	0	2	3	2	3	1	5	2	2	1	5	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr19:2410353G>A	ENST00000332578.3	+	8	1113	c.1113G>A	c.(1111-1113)gtG>gtA	p.V371V		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	371	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAGGATGGTGTGCGCTGGCT	0.577																																					p.V371V													.	TMPRSS9-91	0			c.G1113A						.						90	76	81					19																	2410353		2203	4300	6503	SO:0001819	synonymous_variant	360200	exon8			GATGGTGTGCGCT	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"Serine peptidases / Transmembrane"	30079	protein-coding gene	gene with protein product	"polyserase 1"	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1113G>A	19.37:g.2410353G>A		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	72	3	NM_182973	0	0	0	0	0	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			.		0.577	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		A	2410353	G	A	2410353	2	1	143	1	0	0	0	0	0	0	0	1	16285	1364	48	2		2	TMPRSS9	19	2410353	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		2410353	56718630	93	12837											
XAB2	56949	broad.mit.edu	37	chr19	7684501	7684501	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcaggctcccaaacactgCggctggcacgctctgctgct	6	9	10	16	2	2	0	1	0	1	0	3	0	3	0	1	3	4	6	1	3	1	1	rs538580383		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr19:7684501C>T	ENST00000358368.4	-	19	2576	c.2539G>A	c.(2539-2541)Gca>Aca	p.A847T	XAB2_ENST00000534844.1_Missense_Mutation_p.A844T	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	847					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CCAAACACTGCGGCTGGCACG	0.647								Direct reversal of damage;Nucleotide excision repair (NER)					c|||	1	0.000199681	0	0.0014	5008	,	,		8461	0		0	False		,,,				2504	0				p.A847T													.	XAB2-272	0			c.G2539A						.						25	24	24					19																	7684501		2201	4297	6498	SO:0001583	missense	56949	exon19			ACACTGCGGCTGG	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"SYF1 homolog, RNA splicing factor (S. cerevisiae)", "SYF1 pre-mRNA-splicing factor"	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.2539G>A	19.37:g.7684501C>T	ENSP00000351137:p.Ala847Thr	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	61	3	NM_020196	0	1	173	174	0	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	37	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	c	12.83	2.055385	0.36277	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.23552	1.9;1.9	4.94	3.67	0.42095	.	0.076238	0.50627	U	0.000101	T	0.14056	0.0340	L	0.41415	1.275	0.24814	N	0.992626	P	0.45827	0.867	B	0.27796	0.083	T	0.29701	-1.0003	10	0.48119	T	0.1	-17.4672	8.1134	0.30928	0.1619:0.7401:0.0:0.098	.	847	Q9HCS7	SYF1_HUMAN	T	847;844	ENSP00000351137:A847T;ENSP00000438225:A844T	ENSP00000351137:A847T	A	-	1	0	XAB2	7590501	0.953000	0.32496	0.089000	0.20774	0.506000	0.33950	2.124000	0.42006	2.315000	0.78130	0.479000	0.44913	GCA	.		0.647	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		T	7684501	C	T	7684501	3	4	143	1	0	0	0	0	1	0	0	0	17451	768	27	1	32	1	XAB2	19	7684501	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	5274148	7684501	51444482	94	12838											
MARCH2	51257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8503277	8503277	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggctgccccacaggtctcCttccgctaccactgccagct	6	8	9	18	1	1	0	0	0	1	0	3	0	2	0	6	2	4	3	6	2	1	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr19:8503277C>T	ENST00000602117.1	+	5	1043	c.588C>T	c.(586-588)tcC>tcT	p.S196S	MARCH2_ENST00000601283.1_Intron|MARCH2_ENST00000215555.2_Silent_p.S196S|MARCH2_ENST00000381035.4_Silent_p.S126S|MARCH2_ENST00000393944.1_Silent_p.S196S			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	196					endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						CACAGGTCTCCTTCCGCTACC	0.637																																					p.S196S		.											.	MARCH2-70	0			c.C588T						.						54	54	54					19																	8503277		2203	4300	6503	SO:0001819	synonymous_variant	51257	exon5			GGTCTCCTTCCGC	AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	28038	protein-coding gene	gene with protein product		613332	"membrane-associated ring finger (C3HC4) 2"			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.588C>T	19.37:g.8503277C>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	62	22	NM_001005415	0	0	1	5	4	A6NP10|Q5H785|Q8N5A3|Q96B78	Silent	SNP	ENST00000602117.1	37	CCDS12202.1																																																																																			.		0.637	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2	NM_016496		T	8503277	C	T	8503277	2	4	143	1	0	0	0	0	0	0	0	1	9326	668	24	2		2	MARCH2	19	8503277	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	818776	8503277	50625706	95	12839											
FBL	2091	broad.mit.edu	37	chr19	40331279	40331279	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcttcctcctcctccaccGccgccgccgcctccacctcc	2	8	4	27	4	1	0	0	0	1	0	7	0	7	0	13	0	0	0	13	0	0	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr19:40331279G>A	ENST00000221801.3	-	2	272	c.159C>T	c.(157-159)ggC>ggT	p.G53G	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	53	DMA/Gly-rich.				histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		ctcctccaccgccgccgccgc	0.657																																					p.G53G													.	FBL-91	0			c.C159T						.						18	21	20					19																	40331279		2201	4299	6500	SO:0001819	synonymous_variant	2091	exon2			TCCACCGCCGCCG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.159C>T	19.37:g.40331279G>A		Somatic	107	1		WXS	Illumina HiSeq	Phase_I	80	3	NM_001436	0	0	0	0	0	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	37	CCDS12545.1																																																																																			.		0.657	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		A	40331279	G	A	40331279	2	1	143	1	0	0	0	0	0	0	0	1	5715	1074	38	1		1	FBL	19	40331279	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	31828002	40331279	18797704	96	12840											
EPB41L1	2036	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	34765954	34765956	+	In_Frame_Del	DEL	CTT	CTT	-																															aaggactacttcggcctgacCttctgtgatgctgacagcca																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr20:34765954_34765956delCTT	ENST00000338074.2	+	4	584_586	c.423_425delCTT	c.(421-426)accttc>acc	p.F142del	EPB41L1_ENST00000373946.3_In_Frame_Del_p.F111del|EPB41L1_ENST00000202028.5_In_Frame_Del_p.F80del|EPB41L1_ENST00000441639.1_In_Frame_Del_p.F80del|EPB41L1_ENST00000373941.1_In_Frame_Del_p.F142del|EPB41L1_ENST00000373950.2_Intron	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	142	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					TCGGCCTGACCTTCTGTGATGCT	0.576																																					p.141_142del		.											.	EPB41L1-93	0			c.423_425del						.																																			SO:0001651	inframe_deletion	2036	exon5			.	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.423_425delCTT	20.37:g.34765954_34765956delCTT	ENSP00000337168:p.Phe142del	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	50	20	NM_001258329	0	0	0	0	0	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	In_Frame_Del	DEL	ENST00000338074.2	37	CCDS13271.1																																																																																			.		0.576	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		-	34765956	CTT	-	34765954	7	5	143	1	0	1	0	1	0	0	0	0	5165	668	24	0	433	0	EPB41L1	20	34765954	In_Frame_Del	DEL	CTT	TCGA-IZ-A6M9-01A-11D-A31X-10		34765954	28259566	97	12841											
ZNF335	63925	bcgsc.ca	37	chr20	44592465	44592465	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atccgggcaggagggggctgCgttctctgcatctgactggc	5	9	16	11	2	2	1	0	1	2	0	4	2	3	2	1	5	2	4	1	5	0	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr20:44592465C>T	ENST00000322927.2	-	8	1367	c.1267G>A	c.(1267-1269)Gca>Aca	p.A423T	ZNF335_ENST00000426788.1_Missense_Mutation_p.A268T	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	423					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GAGGGGGCTGCGTTCTCTGCA	0.637																																					p.A423T													.	ZNF335-94	0			c.G1267A						.						80	78	79					20																	44592465		2203	4300	6503	SO:0001583	missense	63925	exon8			GGGCTGCGTTCTC	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1267G>A	20.37:g.44592465C>T	ENSP00000325326:p.Ala423Thr	Somatic	88	0		WXS	Illumina HiSeq	Phase_1	75	5	NM_022095	0	0	1	1	0	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	37	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.051468	0.36181	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.08102	3.24;3.13	4.81	1.61	0.23674	.	0.186864	0.45606	N	0.000356	T	0.03608	0.0103	N	0.12182	0.205	0.26398	N	0.976472	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43163	-0.9408	10	0.17369	T	0.5	-4.5635	5.2985	0.15766	0.0:0.4872:0.0:0.5128	.	268;423	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	T	423;200;268	ENSP00000325326:A423T;ENSP00000397098:A268T	ENSP00000243961:A200T	A	-	1	0	ZNF335	44025872	0.210000	0.23517	0.028000	0.17463	0.687000	0.40016	0.545000	0.23268	0.633000	0.30452	0.555000	0.69702	GCA	.		0.637	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		T	44592465	C	T	44592465	3	4	143	1	0	0	0	0	1	0	0	0	17884	768	27	1	2845	1	ZNF335	20	44592465	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	9826511	44592465	18433055	98	12842											
SYCP2	10388	bcgsc.ca	37	chr20	58475248	58475248	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtttttgatatattttgaaGgtttagcaaattcctttggg	9	20	9	3	0	0	2	0	2	0	0	1	2	1	2	1	2	1	3	1	2	5	10			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr20:58475248G>T	ENST00000357552.3	-	18	1574	c.1349C>A	c.(1348-1350)cCt>cAt	p.P450H	SYCP2_ENST00000371001.2_Missense_Mutation_p.P450H			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	450					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ATATTTTGAAGGTTTAGCAAA	0.363																																					p.P450H													.	SYCP2-525	0			c.C1349A						.						136	123	127					20																	58475248		2202	4299	6501	SO:0001583	missense	10388	exon17			TTTGAAGGTTTAG	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1349C>A	20.37:g.58475248G>T	ENSP00000350162:p.Pro450His	Somatic	109	0		WXS	Illumina HiSeq	Phase_1	88	5	NM_014258	0	0	0	0	0	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.525062	0.27299	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.18502	2.46;2.46;2.21	5.37	2.19	0.27852	.	0.750306	0.11861	N	0.522405	T	0.28896	0.0717	M	0.62723	1.935	0.09310	N	1	D;P	0.58620	0.983;0.895	P;P	0.59825	0.864;0.606	T	0.08638	-1.0712	10	0.52906	T	0.07	-2.3323	4.4928	0.11822	0.0912:0.1516:0.6019:0.1552	.	450;450	A2A341;Q9BX26	.;SYCP2_HUMAN	H	450	ENSP00000360040:P450H;ENSP00000350162:P450H;ENSP00000402456:P450H	ENSP00000350162:P450H	P	-	2	0	SYCP2	57908643	0.019000	0.18553	0.057000	0.19452	0.155000	0.21991	1.388000	0.34442	1.258000	0.44101	0.650000	0.86243	CCT	.		0.363	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		T	58475248	G	T	58475248	3	4	143	1	0	0	0	0	1	0	0	0	15464	1000	35	4	3355	4	SYCP2	20	58475248	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	13882783	58475248	4550272	99	12843											
CLTCL1	8218	broad.mit.edu	37	chr22	19213138	19213138	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctccaccgataaggagcCaaagaaattgacaagccact	16	6	7	12	1	0	2	0	1	0	1	2	4	2	3	5	1	2	0	5	1	4	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr22:19213138C>A	ENST00000263200.10	-	13	2038	c.1966G>T	c.(1966-1968)Ggc>Tgc	p.G656C	CLTCL1_ENST00000353891.5_Missense_Mutation_p.G656C|CLTCL1_ENST00000427926.1_Missense_Mutation_p.G656C	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	656	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GATAAGGAGCCAAAGAAATTG	0.473			T	?	ALCL																																p.G656C				Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1-230	0			c.G1966T						.																																			SO:0001583	missense	8218	exon13			AGGAGCCAAAGAA		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"clathrin, heavy polypeptide-like 1"	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.1966G>T	22.37:g.19213138C>A	ENSP00000445677:p.Gly656Cys	Somatic	47	12		WXS	Illumina HiSeq	Phase_I	55	9	NM_001835	0	0	0	0	0	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.027241	0.75390	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.53857	0.6;0.6;0.6	4.0	4.0	0.46444	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.78755	0.4333	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85440	0.1154	10	0.87932	D	0	-20.3922	16.6486	0.85183	0.0:1.0:0.0:0.0	.	656;656	P53675-2;P53675	.;CLH2_HUMAN	C	656	ENSP00000439662:G656C;ENSP00000445677:G656C;ENSP00000441158:G656C	ENSP00000445677:G656C	G	-	1	0	CLTCL1	17593138	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	5.229000	0.65316	2.220000	0.72140	0.655000	0.94253	GGC	.		0.473	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19213138	C	A	19213138	3	1	143	1	0	0	0	0	1	0	0	0	3573	594	21	4	3036	4	CLTCL1	22	19213138	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		19213138	32091428	100	12844											
MORC2	22880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	31345772	31345772	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccgtactgcccaatctgagTagactcaggtgttcgcttgg	7	11	11	12	2	2	2	1	1	1	1	3	2	2	2	2	2	2	4	2	2	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr22:31345772T>G	ENST00000397641.3	-	5	691	c.283A>C	c.(283-285)Act>Cct	p.T95P	MORC2_ENST00000215862.4_Missense_Mutation_p.T33P			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	95						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CCAATCTGAGTAGACTCAGGT	0.463																																					p.T33P		.											.	MORC2-92	0			c.A97C						.						139	127	131					22																	31345772		2203	4300	6503	SO:0001583	missense	22880	exon6			TCTGAGTAGACTC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.283A>C	22.37:g.31345772T>G	ENSP00000380763:p.Thr95Pro	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	59	23	NM_014941	0	0	1	1	0	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	37		.	.	.	.	.	.	.	.	.	.	T	26.9	4.777606	0.90195	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	D;D	0.95205	-3.64;-3.64	5.62	5.62	0.85841	ATPase-like, ATP-binding domain (4);	0.050861	0.85682	D	0.000000	D	0.94968	0.8372	L	0.35341	1.055	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	D	0.94117	0.7376	10	0.30854	T	0.27	.	15.8169	0.78608	0.0:0.0:0.0:1.0	.	95	Q9Y6X9	MORC2_HUMAN	P	95;33	ENSP00000380763:T95P;ENSP00000215862:T33P	ENSP00000215862:T33P	T	-	1	0	MORC2	29675772	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.698000	0.84413	2.151000	0.67156	0.482000	0.46254	ACT	.		0.463	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		G	31345772	T	G	31345772	3	3	143	1	0	0	0	0	1	0	0	0	9727	1638	57	5	2903	5	MORC2	22	31345772	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	12132634	31345772	19958794	101	12845											
RRP7A	27341	broad.mit.edu;bcgsc.ca	37	chr22	42910736	42910736	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgaacgtgtccacttccacCctcagggcctcagggtcggg	7	8	12	14	2	2	1	2	1	0	0	5	1	4	1	4	3	1	0	4	3	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr22:42910736C>T	ENST00000323013.6	-	5	525	c.510G>A	c.(508-510)agG>agA	p.R170R	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	170							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						CCACTTCCACCCTCAGGGCCT	0.637																																					p.R170R													.	RRP7A-91	0			c.G510A						.						35	36	36					22																	42910736		2202	4297	6499	SO:0001819	synonymous_variant	27341	exon5			TTCCACCCTCAGG	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.510G>A	22.37:g.42910736C>T		Somatic	191	0		WXS	Illumina HiSeq	Phase_I	141	14	NM_015703	1	0	86	89	2	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Silent	SNP	ENST00000323013.6	37	CCDS14036.1																																																																																			.		0.637	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703		T	42910736	C	T	42910736	2	4	143	1	0	0	0	0	0	0	0	1	13721	622	22	2		2	RRP7A	22	42910736	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	11564964	42910736	8393830	102	12846											
MAGED2	10916	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	54841947	54841947	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtgccagcactggtgcCagtaccagtaccaataacag	12	6	11	12	0	0	0	0	0	0	0	0	0	0	0	4	2	6	4	4	2	4	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:54841947C>T	ENST00000375068.1	+	12	1886	c.1653C>T	c.(1651-1653)gcC>gcT	p.A551A	MAGED2_ENST00000375053.2_Silent_p.A551A|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375058.1_Silent_p.A551A|MAGED2_ENST00000218439.4_Silent_p.A551A|MAGED2_ENST00000375062.4_Silent_p.A466A|MAGED2_ENST00000396224.1_Silent_p.A551A|MAGED2_ENST00000347546.4_Silent_p.A533A|MAGED2_ENST00000375060.1_Silent_p.A466A			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	551						membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						gcactggtgccagtaccagta	0.602																																					p.A551A		.											.	MAGED2-195	0			c.C1653T						.						35	28	30					X																	54841947		2197	4291	6488	SO:0001819	synonymous_variant	10916	exon12			TGGTGCCAGTACC	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated protein", "breast cancer associated gene 1", "melanoma-associated antigen D2", "hepatocellular carcinoma-associated protein HCA10"	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.1653C>T	X.37:g.54841947C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	47	4	NM_201222	0	0	359	386	27	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	37	CCDS14362.1																																																																																			.		0.602	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		T	54841947	C	T	54841947	2	4	143	1	0	0	0	0	0	0	0	1	9209	581	21	2		2	MAGED2	23	54841947	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		54841947	100428613	103	12847											
TCEAL4	79921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	102841929	102841929	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggagagccagggagtgAaacaagggctgcaggaaagc	15	3	17	6	0	0	3	0	2	0	1	0	6	0	5	1	4	4	2	1	4	4	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:102841929A>T	ENST00000472745.1	+	3	878	c.326A>T	c.(325-327)gAa>gTa	p.E109V	TCEAL4_ENST00000472484.1_Missense_Mutation_p.E109V|TCEAL4_ENST00000372629.4_Missense_Mutation_p.E252V|TCEAL4_ENST00000494801.1_Missense_Mutation_p.E109V|TCEAL4_ENST00000415568.2_Missense_Mutation_p.E109V|TCEAL4_ENST00000468024.1_Missense_Mutation_p.E109V			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	109	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						CCAGGGAGTGAAACAAGGGCT	0.507																																					p.E109V		.											.	TCEAL4-130	0			c.A326T						.						67	67	67					X																	102841929		2203	4300	6503	SO:0001583	missense	79921	exon3			GGAGTGAAACAAG	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.326A>T	X.37:g.102841929A>T	ENSP00000424314:p.Glu109Val	Somatic	153	1		WXS	Illumina HiSeq	Phase_I	126	104	NM_001006935	0	0	10	150	140	Q8WY12|Q9H2H1|Q9H775	Missense_Mutation	SNP	ENST00000472745.1	37	CCDS14510.2	.	.	.	.	.	.	.	.	.	.	A	10.28	1.307826	0.23821	.	.	ENSG00000133142	ENST00000372629;ENST00000468024;ENST00000472484;ENST00000415568;ENST00000414064;ENST00000472745;ENST00000494801;ENST00000469586	T;T;T;T;T;T;T	0.35973	1.32;1.28;1.28;1.28;1.28;1.28;1.44	3.99	1.55	0.23275	.	0.216564	0.23312	N	0.049559	T	0.38214	0.1032	M	0.63843	1.955	0.09310	N	1	P	0.38250	0.624	P	0.45577	0.486	T	0.25187	-1.0139	10	0.56958	D	0.05	.	5.2758	0.15649	0.7556:0.0:0.2444:0.0	.	109	Q96EI5	TCAL4_HUMAN	V	252;109;109;109;80;109;109;109	ENSP00000361712:E252V;ENSP00000421857:E109V;ENSP00000421156:E109V;ENSP00000415564:E109V;ENSP00000424314:E109V;ENSP00000427494:E109V;ENSP00000427053:E109V	ENSP00000361712:E252V	E	+	2	0	TCEAL4	102728585	0.003000	0.15002	0.001000	0.08648	0.387000	0.30353	1.156000	0.31712	0.221000	0.20879	-0.681000	0.03757	GAA	.		0.507	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		T	102841929	A	T	102841929	3	4	143	1	0	0	0	0	1	0	0	0	15705	246	9	5	328	5	TCEAL4	23	102841929	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	47999982	102841929	52428631	104	12848											
DOCK11	139818	ucsc.edu;bcgsc.ca	37	chrX	117786022	117786022	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attatcaataattttgcaaaTagtgacagacctatgaaggt	16	13	7	5	0	1	3	1	2	0	1	1	3	1	3	1	1	1	1	1	1	7	6			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:117786022T>C	ENST00000276202.7	+	42	4740	c.4677T>C	c.(4675-4677)aaT>aaC	p.N1559N	DOCK11_ENST00000276204.6_Silent_p.N1559N	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1559					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						ATTTTGCAAATAGTGACAGAC	0.348																																					p.N1559N													.	DOCK11-93	0			c.T4677C						.						71	70	70					X																	117786022		2203	4295	6498	SO:0001819	synonymous_variant	139818	exon42			TGCAAATAGTGAC	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.4677T>C	X.37:g.117786022T>C		Somatic	219	2		WXS	Illumina HiSeq		148	111	NM_144658	0	0	0	0	0	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			.		0.348	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		C	117786022	T	C	117786022	2	2	143	1	0	0	0	0	0	0	0	1	4697	1403	49	3		3	DOCK11	23	117786022	Silent	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	14944093	117786022	37484538	105	12849											
SLC25A5	292	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	118603720	118603720	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggagcagggagttctgtccTtctggcgcggtaacctggcc	6	9	15	11	2	2	0	0	0	2	0	3	2	3	2	3	5	2	3	3	5	1	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:118603720T>G	ENST00000317881.8	+	2	324	c.208T>G	c.(208-210)Ttc>Gtc	p.F70V	SLC25A5-AS1_ENST00000446986.1_RNA|SLC25A5_ENST00000460013.1_3'UTR	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	70					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	AGTTCTGTCCTTCTGGCGCGG	0.498																																					p.F70V		.											.	SLC25A5-131	0			c.T208G						.						166	157	160					X																	118603720		2203	4300	6503	SO:0001583	missense	292	exon2			CTGTCCTTCTGGC	BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"Solute carriers"	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.208T>G	X.37:g.118603720T>G	ENSP00000360671:p.Phe70Val	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	63	45	NM_001152	0	0	14	109	95	B2RCV1|O43350	Missense_Mutation	SNP	ENST00000317881.8	37	CCDS14578.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.010876	0.75046	.	.	ENSG00000005022	ENST00000317881	T	0.80214	-1.35	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.90290	0.6963	M	0.90198	3.095	0.58432	D	0.999999	D	0.63880	0.993	D	0.69824	0.966	D	0.91908	0.5537	10	0.87932	D	0	.	12.1849	0.54231	0.0:0.0:0.0:1.0	.	70	P05141	ADT2_HUMAN	V	70	ENSP00000360671:F70V	ENSP00000360671:F70V	F	+	1	0	SLC25A5	118487748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.575000	0.82447	1.622000	0.50330	0.430000	0.28490	TTC	.		0.498	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152		G	118603720	T	G	118603720	3	3	143	1	0	0	0	0	1	0	0	0	14544	1609	56	5	214	5	SLC25A5	23	118603720	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	817698	118603720	36666840	106	12850											
SFN	2810	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27189915	27189915	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattgagcagaaaagcaacgAggagggctcggaggagaagg	15	4	17	5	2	0	3	0	1	0	2	1	7	0	5	0	5	3	3	0	5	5	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:27189915A>G	ENST00000339276.4	+	1	283	c.212A>G	c.(211-213)gAg>gGg	p.E71G		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		AAAAGCAACGAGGAGGGCTCG	0.627																																					p.E71G		.											.	SFN-658	0			c.A212G						.						69	74	72					1																	27189915		2203	4300	6503	SO:0001583	missense	2810	exon1			GCAACGAGGAGGG	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"14-3-3 sigma"	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.212A>G	1.37:g.27189915A>G	ENSP00000340989:p.Glu71Gly	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	116	46	NM_006142	0	0	10	15	5	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.535187	0.27475	.	.	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.39787	1.06	5.96	5.96	0.96718	14-3-3 domain (4);	0.106868	0.41396	D	0.000892	T	0.16938	0.0407	N	0.00873	-1.125	0.27459	N	0.9532	B	0.02656	0.0	B	0.04013	0.001	T	0.13818	-1.0495	10	0.54805	T	0.06	-27.1227	12.0125	0.53295	0.8558:0.1442:0.0:0.0	.	71	P31947	1433S_HUMAN	G	71	ENSP00000340989:E71G	ENSP00000340989:E71G	E	+	2	0	SFN	27062502	1.000000	0.71417	0.994000	0.49952	0.719000	0.41307	4.148000	0.58085	2.270000	0.75569	0.533000	0.62120	GAG	.		0.627	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142		G	27189915	A	G	27189915	3	3	144	1	0	0	0	0	1	0	0	0	14191	304	11	3	214	3	SFN	1	27189915	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		27189915	222060706	1	12851											
GPR3	2827	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	27720330	27720350	+	In_Frame_Del	DEL	GCCTGGCTCTCAGCTGGCTCA	GCCTGGCTCTCAGCTGGCTCA	-																															ggggtgcaggcagccctctgGcctggctctcagctggctca																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	GCCTGGCTCTCAGCTGGCTCA	GCCTGGCTCTCAGCTGGCTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:27720330_27720350delGCCTGGCTCTCAGCTGGCTCA	ENST00000374024.3	+	2	127_147	c.28_48delGCCTGGCTCTCAGCTGGCTCA	c.(28-48)gcctggctctcagctggctcadel	p.AWLSAGS10del		NM_005281.3	NP_005272.1	P46089	GPR3_HUMAN	G protein-coupled receptor 3	10					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|regulation of meiosis (GO:0040020)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(3)|ovary(1)|skin(1)	8		Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.81e-26)|Colorectal(126;1.24e-08)|KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;4.45e-06)|Lung(427;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|LUSC - Lung squamous cell carcinoma(448;0.008)|READ - Rectum adenocarcinoma(331;0.0419)		CAGCCCTCTGGCCTGGCTCTCAGCTGGCTCAGGCAACGTGA	0.633																																					p.10_16del		.											.	GPR3-91	0			c.28_48del						.																																			SO:0001651	inframe_deletion	2827	exon2			.	BC032702	CCDS303.1	1p36.1-p35	2012-08-21			ENSG00000181773	ENSG00000181773		"GPCR / Class A : Orphans"	4484	protein-coding gene	gene with protein product		600241				7851889	Standard	NM_005281		Approved	ACCA	uc001bod.4	P46089	OTTHUMG00000003397	ENST00000374024.3:c.28_48delGCCTGGCTCTCAGCTGGCTCA	1.37:g.27720330_27720350delGCCTGGCTCTCAGCTGGCTCA	ENSP00000363136:p.Ala10_Ser16del	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	184	32	NM_005281	0	0	0	0	0	A8K570	In_Frame_Del	DEL	ENST00000374024.3	37	CCDS303.1																																																																																			.		0.633	GPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009522.1	NM_005281		-	27720350	GCCTGGCTCTCAGCTGGCTCA	-	27720330	7	5	144	1	0	1	0	1	0	0	0	0	6706	1203	42	0	30	0	GPR3	1	27720330	In_Frame_Del	DEL	GCCTGGCTCTCAGCTGGCTCA	TCGA-J7-6720-01A-11D-2136-08	530415	27720330	221530291	2	12852											
PIAS3	10401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145578967	145578967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagagaggttctgccaggagCcaaatgtgattataccatac	13	9	10	9	0	1	2	0	1	1	1	1	4	1	3	3	2	4	1	3	2	4	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:145578967C>T	ENST00000393045.2	+	4	635	c.545C>T	c.(544-546)gCc>gTc	p.A182V	PIAS3_ENST00000369298.1_Missense_Mutation_p.A147V|PIAS3_ENST00000369299.3_Missense_Mutation_p.A173V	NM_006099.3	NP_006090.2	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	182	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				positive regulation of gene expression (GO:0010628)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)|synapse (GO:0045202)	enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)	28	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTGCCAGGAGCCAAATGTGAT	0.527																																					p.A182V		.											.	PIAS3-658	0			c.C545T						.						109	97	101					1																	145578967		2203	4300	6503	SO:0001583	missense	10401	exon4			CAGGAGCCAAATG	AB021868	CCDS72866.1	1q21	2011-10-11			ENSG00000131788	ENSG00000131788		"Zinc fingers, MIZ-type"	16861	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 5"	605987				10319586	Standard	NM_006099		Approved	FLJ14651, ZMIZ5	uc001eoc.1	Q9Y6X2	OTTHUMG00000013750	ENST00000393045.2:c.545C>T	1.37:g.145578967C>T	ENSP00000376765:p.Ala182Val	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	131	48	NM_006099	0	0	3	4	1	Q9UFI3	Missense_Mutation	SNP	ENST00000393045.2	37	CCDS920.2	.	.	.	.	.	.	.	.	.	.	C	14.25	2.478871	0.44044	.	.	ENSG00000131788	ENST00000393046;ENST00000369299;ENST00000393045;ENST00000369298	T;T;T;T	0.44881	0.93;0.91;1.54;1.51	4.33	4.33	0.51752	PINIT domain (1);	0.000000	0.49916	D	0.000123	T	0.13841	0.0335	N	0.17474	0.49	0.38130	D	0.938123	B;P	0.47841	0.024;0.901	B;B	0.41088	0.061;0.347	T	0.03240	-1.1057	10	0.13108	T	0.6	-12.7129	14.3972	0.67020	0.0:1.0:0.0:0.0	.	173;182	F8WA94;Q9Y6X2	.;PIAS3_HUMAN	V	173;173;182;147	ENSP00000376766:A173V;ENSP00000358305:A173V;ENSP00000376765:A182V;ENSP00000358304:A147V	ENSP00000358304:A147V	A	+	2	0	PIAS3	144290324	0.999000	0.42202	1.000000	0.80357	0.582000	0.36321	1.616000	0.36933	2.230000	0.72887	0.655000	0.94253	GCC	.		0.527	PIAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038533.4	NM_006099		T	145578967	C	T	145578967	3	4	144	1	0	0	0	0	1	0	0	0	11903	739	26	2	559	2	PIAS3	1	145578967	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	117858637	145578967	103671654	3	12853											
C1orf182	128229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156309583	156309583	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tagtcatcctaacagaaaagGtgtgtgttggaggccctgct	10	11	12	8	0	1	1	1	0	0	1	2	2	2	2	2	3	2	2	2	3	4	3	rs113369857		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:156309583G>C	ENST00000368255.3	+	2	394		c.e2+1		TSACC_ENST00000368252.1_Splice_Site|TSACC_ENST00000470342.1_Splice_Site|TSACC_ENST00000466306.1_Splice_Site|CCT3_ENST00000295688.3_5'Flank|CCT3_ENST00000368259.2_5'Flank|CCT3_ENST00000472765.2_5'Flank|CCT3_ENST00000368256.3_5'Flank|CCT3_ENST00000368261.3_5'Flank|TSACC_ENST00000368253.2_Splice_Site|TSACC_ENST00000481479.1_Splice_Site|TSACC_ENST00000368251.1_Splice_Site|TSACC_ENST00000368254.1_Splice_Site	NM_144627.3	NP_653228.1	Q96A04	TSACC_HUMAN	TSSK6 activating co-chaperone							cytoplasm (GO:0005737)	chaperone binding (GO:0051087)										AACAGAAAAGGTGTGTGTTGG	0.483																																					.		.											.	.	0			c.34+1G>C						.						147	127	134					1																	156309583		2203	4300	6503	SO:0001630	splice_region_variant	128229	exon2			GAAAAGGTGTGTG	AY048672	CCDS1141.1	1q22	2012-08-16	2012-08-16	2012-08-16	ENSG00000163467	ENSG00000163467			30636	protein-coding gene	gene with protein product	"SSTK-interacting protein"		"chromosome 1 open reading frame 182"	C1orf182		20829357	Standard	NM_144627		Approved	SSTK-IP, SIP	uc001foo.3	Q96A04	OTTHUMG00000024060	ENST00000368255.3:c.34+1G>C	1.37:g.156309583G>C		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	59	17	NM_144627	0	0	0	0	0	D3DVB9	Splice_Site	SNP	ENST00000368255.3	37	CCDS1141.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.792835	0.50102	.	.	ENSG00000163467	ENST00000368255;ENST00000368254;ENST00000368253;ENST00000368252;ENST00000368251	.	.	.	2.76	2.76	0.32466	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1866	0.37174	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf182	154576207	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	2.090000	0.41682	1.852000	0.53769	0.467000	0.42956	.	.		0.483	TSACC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060594.1	NM_144627	Intron	C	156309583	G	C	156309583	5	2	144	1	0	0	0	0	0	0	1	0	2024	1275	44	4	37	4	C1orf182	1	156309583	Splice_Site	SNP	G	TCGA-J7-6720-01A-11D-2136-08	10730616	156309583	92941038	4	12854											
HSPA6	3310	hgsc.bcm.edu	37	chr1	161495275	161495275	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgcgccaagcgcacccTgtcctccagcacccaggcca	8	4	10	19	3	0	1	0	1	0	0	2	1	2	1	6	1	3	2	6	1	1	0	rs200790521		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:161495275T>C	ENST00000309758.4	+	1	1240	c.827T>C	c.(826-828)cTg>cCg	p.L276P	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	276					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AAGCGCACCCTGTCCTCCAGC	0.622																																					p.L276P		.											.	HSPA6-226	0			c.T827C						.						25	27	26					1																	161495275		2201	4300	6501	SO:0001583	missense	3310	exon1			GCACCCTGTCCTC		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"Heat shock proteins / HSP70"	5239	protein-coding gene	gene with protein product		140555	"heat shock 70kD protein 6 (HSP70B')"			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.827T>C	1.37:g.161495275T>C	ENSP00000310219:p.Leu276Pro	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	52	4	NM_002155	0	0	8	10	2	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	16.96	3.266320	0.59540	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.02177	4.41	3.12	3.12	0.35913	.	0.000000	0.30920	U	0.008619	T	0.21145	0.0509	H	0.99996	5.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.47100	-0.9143	10	0.87932	D	0	.	9.3095	0.37895	0.0:0.0:0.0:1.0	.	276	P17066	HSP76_HUMAN	P	276;252	ENSP00000310219:L276P	ENSP00000310219:L276P	L	+	2	0	HSPA6	159761899	1.000000	0.71417	0.918000	0.36340	0.903000	0.53119	4.067000	0.57527	1.264000	0.44198	0.443000	0.29094	CTG	.		0.622	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155		C	161495275	T	C	161495275	3	2	144	1	0	0	0	0	1	0	0	0	7436	1580	55	3	829	3	HSPA6	1	161495275	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08	5185692	161495275	87755346	5	12855											
LBR	3930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	225598057	225598057	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	taactaaaatcatggccaagGatggaacagcgcggtcctgt	13	8	11	9	2	1	0	1	0	0	0	2	2	2	2	2	4	3	0	2	4	5	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:225598057G>C	ENST00000338179.2	-	10	1375	c.1250C>G	c.(1249-1251)tCc>tGc	p.S417C	AC092811.1_ENST00000366845.2_5'Flank|LBR_ENST00000272163.4_Missense_Mutation_p.S417C	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	417					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		CATGGCCAAGGATGGAACAGC	0.423																																					p.S417C		.											.	LBR-228	0			c.C1250G						.						129	126	127					1																	225598057		2203	4300	6503	SO:0001583	missense	3930	exon10			GCCAAGGATGGAA	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"Tudor domain containing"	6518	protein-coding gene	gene with protein product	"tudor domain containing 18"	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.1250C>G	1.37:g.225598057G>C	ENSP00000339883:p.Ser417Cys	Somatic	159	1		WXS	Illumina HiSeq	Phase_I	161	57	NM_194442	0	0	8	12	4	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	37	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970100	0.92855	.	.	ENSG00000143815	ENST00000272163;ENST00000338179;ENST00000424022	D;D;D	0.98280	-4.84;-4.84;-4.84	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.99390	0.9785	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98628	1.0670	10	0.87932	D	0	-31.0258	20.5827	0.99408	0.0:0.0:1.0:0.0	.	417	Q14739	LBR_HUMAN	C	417;417;48	ENSP00000272163:S417C;ENSP00000339883:S417C;ENSP00000397817:S48C	ENSP00000272163:S417C	S	-	2	0	LBR	223664680	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	9.737000	0.98831	2.941000	0.99782	0.655000	0.94253	TCC	.		0.423	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		C	225598057	G	C	225598057	3	2	144	1	0	0	0	0	1	0	0	0	8673	1174	41	4	617	4	LBR	1	225598057	Missense_Mutation	SNP	G	TCGA-J7-6720-01A-11D-2136-08	64102782	225598057	23652564	6	12856											
ANKRD36B	0	hgsc.bcm.edu	37	chr2	98156684	98156684	+	IGR	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcaaggctggtcgtctctGagaagacactgaaaagcaaa	14	8	10	9	1	2	3	1	2	1	2	4	4	2	3	0	2	1	2	0	2	5	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:98156684G>C								AC159540.1 (65635 upstream) : ANKRD36B (7343 downstream)																							GGTCGTCTCTGAGAAGACACT	0.313																																					p.Q632E		.											.	.	0			c.C1894G						.						67	53	58					2																	98156684		1550	2478	4028	SO:0001628	intergenic_variant	57730	exon29			GTCTCTGAGAAGA																													2.37:g.98156684G>C		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	32	2	NM_025190	0	0	0	0	0		Missense_Mutation	SNP		37																																																																																				.	0	0.313									C	98156684	G	C	98156684	1	2	144	0	1	0	0	0	0	0	0	0	666	1299	45	4		4	ANKRD36B	2	98156684	IGR	SNP	G	TCGA-J7-6720-01A-11D-2136-08		98156684	145042689	7	12857											
CALCRL	10203	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	188245425	188245425	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatggatcaaagtcctgaaAgtaatcagggcagagctgca	14	8	12	7	0	2	3	2	2	0	1	3	4	3	4	1	2	2	4	1	2	3	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:188245425A>G	ENST00000409998.1	-	7	1055	c.274T>C	c.(274-276)Ttt>Ctt	p.F92L	CALCRL_ENST00000410068.1_Missense_Mutation_p.F92L|AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000392370.3_Missense_Mutation_p.F92L			Q16602	CALRL_HUMAN	calcitonin receptor-like	92					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			AAGTCCTGAAAGTAATCAGGG	0.418																																					p.F92L		.											.	CALCRL-523	0			c.T274C						.						68	66	67					2																	188245425		2203	4300	6503	SO:0001583	missense	10203	exon5			CCTGAAAGTAATC	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"GPCR / Class B : Calcitonin receptors"	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.274T>C	2.37:g.188245425A>G	ENSP00000386972:p.Phe92Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	67	34	NM_001271751	0	0	2	3	1	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	31	5.083990	0.94100	.	.	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.64803	-0.12;-0.12;-0.12	5.29	5.29	0.74685	GPCR, family 2, extracellular hormone receptor domain (3);	0.000000	0.64402	D	0.000002	T	0.54886	0.1886	L	0.42008	1.315	0.80722	D	1	P	0.46220	0.874	B	0.42495	0.389	T	0.53041	-0.8494	10	0.25751	T	0.34	.	13.2254	0.59912	1.0:0.0:0.0:0.0	.	92	Q16602	CALRL_HUMAN	L	92	ENSP00000376177:F92L;ENSP00000386972:F92L;ENSP00000387190:F92L	ENSP00000376177:F92L	F	-	1	0	CALCRL	187953670	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.861000	0.75478	2.221000	0.72209	0.455000	0.32223	TTT	.		0.418	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		G	188245425	A	G	188245425	3	3	144	1	0	0	0	0	1	0	0	0	2586	72	3	3	1151	3	CALCRL	2	188245425	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	90088741	188245425	54953948	8	12858											
WDR12	55759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	203762106	203762106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttccaaggaccagatcCgagaagtcttatcataagaa	14	10	7	10	1	2	3	1	0	1	3	5	5	5	4	4	1	0	0	4	1	5	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:203762106C>T	ENST00000261015.4	-	5	1120	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	WDR12_ENST00000477723.1_5'Flank	NM_018256.3	NP_060726.3			WD repeat domain 12											endometrium(3)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)	13						GGACCAGATCCGAGAAGTCTT	0.383																																					p.R124Q		.											.	WDR12-90	0			c.G371A						.						105	97	100					2																	203762106		2203	4300	6503	SO:0001583	missense	55759	exon5			CAGATCCGAGAAG	AF242546	CCDS2356.1	2q33.1	2013-01-09			ENSG00000138442	ENSG00000138442		"WD repeat domain containing"	14098	protein-coding gene	gene with protein product						16043514, 17353269	Standard	NM_018256		Approved	YTM1, FLJ10881	uc002uzl.3	Q9GZL7	OTTHUMG00000132855	ENST00000261015.4:c.371G>A	2.37:g.203762106C>T	ENSP00000261015:p.Arg124Gln	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	107	26	NM_018256	0	0	5	7	2		Missense_Mutation	SNP	ENST00000261015.4	37	CCDS2356.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695498	0.48202	.	.	ENSG00000138442	ENST00000261015	T	0.67865	-0.29	5.33	4.45	0.53987	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.056455	0.64402	N	0.000001	T	0.70570	0.3239	M	0.87827	2.91	0.53688	D	0.999978	B;B	0.21753	0.06;0.06	B;B	0.13407	0.009;0.009	T	0.71034	-0.4709	10	0.56958	D	0.05	-7.5369	13.8674	0.63596	0.0:0.9263:0.0:0.0737	.	124;124	Q53T99;Q9GZL7	.;WDR12_HUMAN	Q	124	ENSP00000261015:R124Q	ENSP00000261015:R124Q	R	-	2	0	WDR12	203470351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.869000	0.63028	1.229000	0.43630	-0.218000	0.12543	CGG	.		0.383	WDR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256329.4	NM_018256		T	203762106	C	T	203762106	3	4	144	1	0	0	0	0	1	0	0	0	17307	652	23	1	936	1	WDR12	2	203762106	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	15516681	203762106	39437267	9	12859											
COL4A3	1285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	228145271	228145271	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggacttccaggtctccctgGaactccaggaaatgaagggc	10	8	12	11	0	1	1	0	1	1	0	4	4	3	4	3	5	1	0	3	5	3	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:228145271G>T	ENST00000396578.3	+	30	2501	c.2339G>T	c.(2338-2340)gGa>gTa	p.G780V	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	780	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		GGTCTCCCTGGAACTCCAGGA	0.498																																					p.G780V		.											.	COL4A3-132	0			c.G2339T	GRCh37	CM034405	COL4A3	M		.						102	104	103					2																	228145271		1895	4117	6012	SO:0001583	missense	1285	exon30			TCCCTGGAACTCC		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.2339G>T	2.37:g.228145271G>T	ENSP00000379823:p.Gly780Val	Somatic	175	0		WXS	Illumina HiSeq	Phase_I	198	66	NM_000091	0	0	2	3	1	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249670	0.59212	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.99353	-5.77	5.49	5.49	0.81192	.	0.000000	0.56097	D	0.000033	D	0.99542	0.9836	M	0.93016	3.37	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.98235	1.0485	10	0.87932	D	0	.	16.2931	0.82759	0.0:0.0:1.0:0.0	.	780;780;780;780	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	V	780	ENSP00000379823:G780V	ENSP00000323334:G780V	G	+	2	0	COL4A3	227853515	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.405000	0.66351	2.596000	0.87737	0.557000	0.71058	GGA	.		0.498	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228145271	G	T	228145271	3	4	144	1	0	0	0	0	1	0	0	0	3697	1174	41	4	2457	4	COL4A3	2	228145271	Missense_Mutation	SNP	G	TCGA-J7-6720-01A-11D-2136-08	24383165	228145271	15054102	10	12860											
FBXO36	130888	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr2	230875429	230875429	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctgtgcatgtctgataaActgtgggaacagatagtcca	12	10	11	8	0	1	2	0	1	1	1	2	3	2	3	1	1	4	2	1	1	4	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:230875429A>G	ENST00000283946.3	+	4	414	c.396A>G	c.(394-396)aaA>aaG	p.K132K	FBXO36_ENST00000409992.1_Silent_p.K112K|FBXO36_ENST00000373652.3_Silent_p.K101K	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	132	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		TGTCTGATAAACTGTGGGAAC	0.532																																					p.K132K		.											.	FBXO36-227	0			c.A396G						.						63	56	58					2																	230875429		2203	4300	6503	SO:0001819	synonymous_variant	130888	exon4			TGATAAACTGTGG	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.396A>G	2.37:g.230875429A>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	64	17	NM_174899	0	0	6	7	1	B3KVQ6|Q53TE6|Q8WWD4	Silent	SNP	ENST00000283946.3	37	CCDS2472.1																																																																																			.		0.532	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		G	230875429	A	G	230875429	2	3	144	1	0	0	0	0	0	0	0	1	5764	40	2	3		3	FBXO36	2	230875429	Silent	SNP	A	TCGA-J7-6720-01A-11D-2136-08	2730158	230875429	12323944	11	12861											
ACY1	95	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	52020519	52020519	+	Splice_Site	DEL	G	G	-																															gcaggctttgccctggatgaGggtgagcaggttggcaagcc																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:52020519delG	ENST00000404366.2	+	7	671	c.525delG	c.(523-525)gag>ga	p.E175fs	ACY1_ENST00000476854.1_Splice_Site_p.E175fs|ABHD14A-ACY1_ENST00000463937.1_Splice_Site_p.E276fs|ACY1_ENST00000494103.1_Intron|ACY1_ENST00000458031.2_Splice_Site_p.E265fs|ACY1_ENST00000476351.1_Splice_Site_p.E140fs	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	175					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CCCTGGATGAGGGTGAGCAGG	0.612																																					p.E175fs		.											.	ACY1-154	0			c.525delG						.						60	60	60					3																	52020519		2203	4300	6503	SO:0001630	splice_region_variant	95	exon7			.	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.526+1G>-	3.37:g.52020519delG		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	85	37	NM_001198897	0	0	0	0	0	C9J6I6|C9J9D8|C9JWD4	Frame_Shift_Del	DEL	ENST00000404366.2	37	CCDS2844.1																																																																																			.		0.612	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666	Frame_Shift_Del	-	52020519	G	-	52020519	8	5	144	1	0	1	0	1	0	0	1	0	226	1014	35	0	547	0	ACY1	3	52020519	Splice_Site	DEL	G	TCGA-J7-6720-01A-11D-2136-08		52020519	146001911	12	12862											
TWF2	11344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52269098	52269098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccagcccgtgccttggcaAagaattccttcagctcttcc	8	10	8	15	1	2	1	1	0	1	1	4	1	4	1	5	1	4	2	5	1	2	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:52269098A>G	ENST00000305533.5	-	2	293	c.50T>C	c.(49-51)tTt>tCt	p.F17S	TLR9_ENST00000597542.1_5'UTR|TWF2_ENST00000499914.2_Missense_Mutation_p.F17S	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	17	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TGCCTTGGCAAAGAATTCCTT	0.572																																					p.F17S		.											.	TWF2-757	0			c.T50C						.						112	98	103					3																	52269098		2203	4300	6503	SO:0001583	missense	11344	exon2			TTGGCAAAGAATT	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"protein tyrosine kinase 9-like (A6-related protein)", "PTK9L protein tyrosine kinase 9-like (A6-related protein)", "twinfilin, actin-binding protein, homolog 2 (Drosophila)"	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.50T>C	3.37:g.52269098A>G	ENSP00000303908:p.Phe17Ser	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	103	33	NM_007284	0	0	22	28	6	Q9Y3F5	Missense_Mutation	SNP	ENST00000305533.5	37	CCDS2849.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727062	0.89390	.	.	ENSG00000247596	ENST00000305533;ENST00000499914	T;T	0.46063	0.88;0.88	4.58	4.58	0.56647	Actin-binding, cofilin/tropomyosin type (2);	.	.	.	.	T	0.71863	0.3390	M	0.93375	3.41	0.48288	D	0.999623	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80141	-0.1506	9	0.87932	D	0	.	13.2613	0.60106	1.0:0.0:0.0:0.0	.	17;17	D6RG15;Q6IBS0	.;TWF2_HUMAN	S	17	ENSP00000303908:F17S;ENSP00000426464:F17S	ENSP00000303908:F17S	F	-	2	0	TWF2	52244138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.871000	0.92346	1.927000	0.55829	0.459000	0.35465	TTT	.		0.572	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2			G	52269098	A	G	52269098	3	3	144	1	0	0	0	0	1	0	0	0	16815	14	1	3	1031	3	TWF2	3	52269098	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	248579	52269098	145753332	13	12863											
FNDC3B	64778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	172025192	172025192	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgtaaagggatcctgctcCgagcctgttagcttcaccac	8	10	9	14	2	1	0	1	0	0	0	4	2	4	1	5	1	3	4	5	1	3	3	rs145255541		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:172025192C>G	ENST00000336824.4	+	10	1200	c.1101C>G	c.(1099-1101)tcC>tcG	p.S367S	FNDC3B_ENST00000416957.1_Silent_p.S367S|FNDC3B_ENST00000415807.2_Silent_p.S367S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	367	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GATCCTGCTCCGAGCCTGTTA	0.502																																					p.S367S		.											.	FNDC3B-155	0			c.C1101G						.						154	129	138					3																	172025192		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon10			CTGCTCCGAGCCT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"Fibronectin type III domain containing"	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1101C>G	3.37:g.172025192C>G		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	131	39	NM_001135095	0	0	3	5	2	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			C|1.000;T|0.000		0.502	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		G	172025192	C	G	172025192	2	3	144	1	0	0	0	0	0	0	0	1	5989	639	23	4		4	FNDC3B	3	172025192	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08	119756094	172025192	25997238	14	12864											
PPP2R2C	5522	hgsc.bcm.edu	37	chr4	6325301	6325301	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgcggaagaagttgttgtAggccccggtcatgatgacgc	9	9	14	9	3	1	3	1	2	0	1	1	4	1	4	2	3	1	3	2	3	3	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:6325301A>G	ENST00000382599.4	-	9	1288	c.1072T>C	c.(1072-1074)Tac>Cac	p.Y358H	PPP2R2C_ENST00000515571.1_Missense_Mutation_p.Y341H|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.Y351H|PPP2R2C_ENST00000507294.1_Missense_Mutation_p.Y351H|PPP2R2C_ENST00000335585.5_Missense_Mutation_p.Y358H			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	358					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						AAGTTGTTGTAGGCCCCGGTC	0.612																																					p.Y358H		.											.	PPP2R2C-1084	0			c.T1072C						.						49	43	45					4																	6325301		2201	4300	6501	SO:0001583	missense	5522	exon9			TGTTGTAGGCCCC	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9306	protein-coding gene	gene with protein product	"PP2A subunit B isoform gamma"	605997	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.1072T>C	4.37:g.6325301A>G	ENSP00000372042:p.Tyr358His	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	40	2	NM_181876	0	0	0	0	0	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	37		.	.	.	.	.	.	.	.	.	.	A	20.8	4.055114	0.75960	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	4.31	4.31	0.51392	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61350	0.2340	M	0.91038	3.17	0.80722	D	1	D;D;D;D	0.69078	0.997;0.997;0.997;0.968	D;D;D;D	0.70935	0.971;0.971;0.971;0.96	T	0.71328	-0.4626	10	0.87932	D	0	-55.5355	12.7994	0.57578	1.0:0.0:0.0:0.0	.	351;358;341;358	B7Z3Y1;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;2ABG_HUMAN;.;.	H	358;351;341;358;351	ENSP00000335083:Y358H;ENSP00000423649:Y351H;ENSP00000422374:Y341H;ENSP00000372042:Y358H;ENSP00000425247:Y351H	ENSP00000335083:Y358H	Y	-	1	0	PPP2R2C	6376202	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.018000	0.88722	1.803000	0.52742	0.454000	0.30748	TAC	.		0.612	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		G	6325301	A	G	6325301	3	3	144	1	0	0	0	0	1	0	0	0	12415	420	15	3	275	3	PPP2R2C	4	6325301	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		6325301	184828975	15	12865											
TBC1D14	57533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	7026865	7026865	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgttcgaggacatcctgaCcaagatggacttcattcaca	11	10	9	11	1	2	2	2	1	0	1	4	5	3	4	2	2	0	2	2	2	1	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:7026865C>A	ENST00000409757.4	+	13	2016	c.1892C>A	c.(1891-1893)aCc>aAc	p.T631N	TBC1D14_ENST00000451522.2_Missense_Mutation_p.T351N|TBC1D14_ENST00000446947.2_Missense_Mutation_p.T278N|TBC1D14_ENST00000448507.1_Missense_Mutation_p.T631N|TBC1D14_ENST00000410031.1_Missense_Mutation_p.T403N	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	631					negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						GACATCCTGACCAAGATGGAC	0.612																																					p.T631N		.											.	TBC1D14-92	0			c.C1892A						.						145	117	127					4																	7026865		2203	4300	6503	SO:0001583	missense	57533	exon13			TCCTGACCAAGAT	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.1892C>A	4.37:g.7026865C>A	ENSP00000386921:p.Thr631Asn	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	168	45	NM_001113361	0	0	10	21	11	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	C	14.93	2.681226	0.47886	.	.	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000446947	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.15	5.15	0.70609	Rab-GAP/TBC domain (2);	0.162937	0.53938	D	0.000045	T	0.19287	0.0463	N	0.08118	0	0.58432	D	0.999994	B;B;B	0.34372	0.451;0.02;0.187	B;B;B	0.43838	0.242;0.104;0.433	T	0.25082	-1.0142	10	0.66056	D	0.02	-12.687	17.6366	0.88124	0.0:1.0:0.0:0.0	.	278;351;631	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	N	631;631;403;351;278	ENSP00000404041:T631N;ENSP00000386921:T631N;ENSP00000386343:T403N;ENSP00000388886:T351N;ENSP00000405875:T278N	ENSP00000386921:T631N	T	+	2	0	TBC1D14	7077766	0.256000	0.24012	1.000000	0.80357	0.994000	0.84299	1.090000	0.30902	2.409000	0.81822	0.561000	0.74099	ACC	.		0.612	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		A	7026865	C	A	7026865	3	1	144	1	0	0	0	0	1	0	0	0	15635	507	18	4	1945	4	TBC1D14	4	7026865	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	701564	7026865	184127411	16	12866											
CEP135	9662	hgsc.bcm.edu	37	chr4	56832006	56832006	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgcttgagactgctgataAagagcttggggaagcaaagg	13	8	15	5	0	0	3	0	2	0	2	0	5	0	4	0	3	4	4	0	3	4	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:56832006A>G	ENST00000257287.4	+	8	1149	c.1025A>G	c.(1024-1026)aAa>aGa	p.K342R		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	342					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					ACTGCTGATAAAGAGCTTGGG	0.373																																					p.K342R		.											.	CEP135-94	0			c.A1025G						.						93	93	93					4																	56832006		2203	4300	6503	SO:0001583	missense	9662	exon8			CTGATAAAGAGCT	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"KIAA0635", "centrosomal protein 4"	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1025A>G	4.37:g.56832006A>G	ENSP00000257287:p.Lys342Arg	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	38	2	NM_025009	0	0	1	1	0	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	12.94	2.089853	0.36855	.	.	ENSG00000174799	ENST00000257287	T	0.41065	1.01	5.67	4.45	0.53987	.	0.451804	0.27486	N	0.019155	T	0.36908	0.0984	M	0.67953	2.075	0.25303	N	0.989268	B	0.11235	0.004	B	0.13407	0.009	T	0.30238	-0.9985	10	0.16896	T	0.51	.	7.8125	0.29239	0.7915:0.138:0.0705:0.0	.	342	Q66GS9	CP135_HUMAN	R	342	ENSP00000257287:K342R	ENSP00000257287:K342R	K	+	2	0	CEP135	56526763	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	2.985000	0.49362	0.948000	0.37687	0.377000	0.23210	AAA	.		0.373	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		G	56832006	A	G	56832006	3	3	144	1	0	0	0	0	1	0	0	0	3253	14	1	3	1051	3	CEP135	4	56832006	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	49805141	56832006	134322270	17	12867											
PDLIM5	10611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	95496927	95496927	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcaccatcgtctgccttcaCcccagcccatgcgaccacct	8	8	5	20	2	3	0	2	0	1	0	4	1	3	0	7	0	3	0	7	0	0	1	rs200734812		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:95496927C>G	ENST00000317968.4	+	5	588	c.452C>G	c.(451-453)aCc>aGc	p.T151S	PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.T29S|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000508216.1_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	151					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		TCTGCCTTCACCCCAGCCCAT	0.542																																					p.T151S		.											.	PDLIM5-117	0			c.C452G						.						332	281	299					4																	95496927		2203	4300	6503	SO:0001583	missense	10611	exon5			CCTTCACCCCAGC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.452C>G	4.37:g.95496927C>G	ENSP00000321746:p.Thr151Ser	Somatic	346	0		WXS	Illumina HiSeq	Phase_I	408	111	NM_006457	0	0	8	14	6	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981800	0.53827	.	.	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.58940	0.72;0.3	5.25	5.25	0.73442	.	0.106561	0.64402	D	0.000004	T	0.72566	0.3476	M	0.65975	2.015	0.80722	D	1	D	0.69078	0.997	D	0.70716	0.97	T	0.66337	-0.5949	10	0.13470	T	0.59	.	19.2104	0.93751	0.0:1.0:0.0:0.0	.	151	Q96HC4	PDLI5_HUMAN	S	151;29	ENSP00000321746:T151S;ENSP00000442187:T29S	ENSP00000321746:T151S	T	+	2	0	PDLIM5	95715950	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.993000	0.63895	2.590000	0.87494	0.655000	0.94253	ACC	C|0.999;T|0.001		0.542	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			G	95496927	C	G	95496927	3	3	144	1	0	0	0	0	1	0	0	0	11709	507	18	4	466	4	PDLIM5	4	95496927	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	38664921	95496927	95657349	18	12868											
SH3RF1	57630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	170028338	170028338	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgccagaaagcaacttcaAcaaaccctttttttctttct	11	13	5	12	1	3	1	1	0	2	1	3	1	3	1	2	1	4	1	2	1	4	5			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:170028338A>G	ENST00000284637.9	-	11	2499	c.2158T>C	c.(2158-2160)Ttg>Ctg	p.L720L		NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	720					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		AGCAACTTCAACAAACCCTTT	0.468																																					p.L720L		.											.	SH3RF1-567	0			c.T2158C						.						26	30	29					4																	170028338		2196	4289	6485	SO:0001819	synonymous_variant	57630	exon11			ACTTCAACAAACC	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"RING-type (C3HC4) zinc fingers"	17650	protein-coding gene	gene with protein product	"plenty of SH3 domains"		"SH3 multiple domains 2"	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.2158T>C	4.37:g.170028338A>G		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	77	23	NM_020870	0	0	2	5	3	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Silent	SNP	ENST00000284637.9	37	CCDS34099.1																																																																																			.		0.468	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		G	170028338	A	G	170028338	2	3	144	1	0	0	0	0	0	0	0	1	14290	40	2	3		3	SH3RF1	4	170028338	Silent	SNP	A	TCGA-J7-6720-01A-11D-2136-08	74531411	170028338	21125938	19	12869											
MYO10	4651	hgsc.bcm.edu	37	chr5	16877717	16877717	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcagggacttgttctcaCctgaccatagtctgtccgga	7	11	11	12	1	2	1	1	1	2	0	4	3	3	3	3	2	1	3	3	2	1	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:16877717C>G	ENST00000513610.1	-	2	575		c.e2+1		MYO10_ENST00000507288.1_Splice_Site	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X						ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CTTGTTCTCACCTGACCATAG	0.527																																					.		.											.	MYO10-3	0			c.120+1G>C						.						98	100	99					5																	16877717		2024	4184	6208	SO:0001630	splice_region_variant	4651	exon3			TTCTCACCTGACC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"Myosins / Myosin superfamily : Class X", "Pleckstrin homology (PH) domain containing"	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.120+1G>C	5.37:g.16877717C>G		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	35	2	NM_012334	0	0	0	0	0	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Splice_Site	SNP	ENST00000513610.1	37	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.073138	0.55646	.	.	ENSG00000145555	ENST00000513610;ENST00000513882;ENST00000507288	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0413	0.80683	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYO10	16930717	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	5.214000	0.65236	2.379000	0.81126	0.561000	0.74099	.	.		0.527	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	Intron	G	16877717	C	G	16877717	5	3	144	1	0	0	0	0	0	0	1	0	10087	521	18	4	6215	4	MYO10	5	16877717	Splice_Site	SNP	C	TCGA-J7-6720-01A-11D-2136-08		16877717	164037543	20	12870											
GIN1	54826	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	102444326	102444335	+	Frame_Shift_Del	DEL	AGTGTAGTTG	AGTGTAGTTG	-																															tgccacttctctcacttggcAgtgtagttgaatgatattca																								rs371302288		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	AGTGTAGTTG	AGTGTAGTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:102444326_102444335delAGTGTAGTTG	ENST00000399004.2	-	2	171_180	c.77_86delCAACTACACT	c.(76-87)tcaactacactgfs	p.STTL26fs	GIN1_ENST00000508629.1_Frame_Shift_Del_p.STTL26fs	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	26					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		CTCACTTGGCAGTGTAGTTGAATGATATTC	0.343																																					p.26_29del		.											.	GIN1-92	0			c.77_86del						.																																			SO:0001589	frameshift_variant	54826	exon2			.	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"gypsy integrase 1", "Ty3/Gypsy integrase 1"		"zinc finger, H2C2 domain containing"	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.77_86delCAACTACACT	5.37:g.102444326_102444335delAGTGTAGTTG	ENSP00000381970:p.Ser26fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	71	16	NM_017676	0	0	0	0	0	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Frame_Shift_Del	DEL	ENST00000399004.2	37	CCDS43349.1																																																																																			.		0.343	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		-	102444335	AGTGTAGTTG	-	102444326	7	5	144	1	0	1	0	1	0	0	0	0	6406	188	7	0	1510	0	GIN1	5	102444326	Frame_Shift_Del	DEL	AGTGTAGTTG	TCGA-J7-6720-01A-11D-2136-08	85566609	102444326	78470934	21	12871											
LOX	4015	hgsc.bcm.edu	37	chr5	121413456	121413456	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgttggctgcaccagggacGgcggcgcccgggtcccggcg	3	4	19	15	7	0	0	0	0	0	0	1	1	1	1	3	6	1	3	3	6	0	1	rs2278226	byFrequency	TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:121413456G>C	ENST00000231004.4	-	1	524	c.225C>G	c.(223-225)gcC>gcG	p.A75A	LOX_ENST00000513319.1_5'Flank	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	75					blood vessel development (GO:0001568)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|wound healing (GO:0042060)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)			endometrium(1)|lung(6)|prostate(1)	8		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		CACCAGGGACGGCGGCGCCCG	0.721													G|||	46	0.0091853	8e-04	0.0101	5008	,	,		11081	0.0367		0	False		,,,				2504	0.001				p.A75A		.											.	LOX-650	0			c.C225G						.						3	4	4					5																	121413456		1880	3759	5639	SO:0001819	synonymous_variant	4015	exon1			AGGGACGGCGGCG		CCDS4129.1	5q23.3-q31.2	2008-02-05			ENSG00000113083	ENSG00000113083	1.4.3.13		6664	protein-coding gene	gene with protein product		153455				1685472	Standard	NM_002317		Approved		uc003ksu.3	P28300	OTTHUMG00000128914	ENST00000231004.4:c.225C>G	5.37:g.121413456G>C		Somatic	4	2		WXS	Illumina HiSeq	Phase_I	12	4	NM_002317	0	0	0	0	0	B2R5Q3|Q5FWF0	Silent	SNP	ENST00000231004.4	37	CCDS4129.1																																																																																			G|0.017;C|0.983		0.721	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			C	121413456	G	C	121413456	2	2	144	1	0	0	0	0	0	0	0	1	8923	1103	39	4		4	LOX	5	121413456	Silent	SNP	G	TCGA-J7-6720-01A-11D-2136-08	18969130	121413456	59501804	22	12872											
HINT1	3094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	130500845	130500845	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcggatgatcttcccaaaGatcgtgtcgccaccaggccg	8	9	11	13	4	1	2	0	1	1	1	4	3	2	3	4	2	1	0	4	2	1	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:130500845G>T	ENST00000304043.5	-	1	333	c.54C>A	c.(52-54)atC>atA	p.I18I	HINT1_ENST00000508488.1_Silent_p.I18I|HINT1_ENST00000506207.1_Intron|HINT1_ENST00000513012.1_Silent_p.I18I|HINT1_ENST00000506908.1_Silent_p.I18I	NM_005340.6	NP_005331.1	P49773	HINT1_HUMAN	histidine triad nucleotide binding protein 1	18	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|purine ribonucleotide catabolic process (GO:0009154)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|protein kinase C binding (GO:0005080)			endometrium(1)|large_intestine(1)|lung(3)	5		all_cancers(142;0.0452)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Adenosine monophosphate(DB00131)	TCTTCCCAAAGATCGTGTCGC	0.587																																					p.I18I		.											.	HINT1-90	0			c.C54A						.						83	74	77					5																	130500845		2203	4300	6503	SO:0001819	synonymous_variant	3094	exon1			CCCAAAGATCGTG	BC007090	CCDS4147.1	5q31.2	2010-03-30	2001-11-28	2002-03-08	ENSG00000169567	ENSG00000169567			4912	protein-coding gene	gene with protein product		601314	"histidine triad nucleotide-binding protein"	PRKCNH1, HINT		8812426	Standard	NM_005340		Approved	PKCI-1	uc003kve.4	P49773	OTTHUMG00000128995	ENST00000304043.5:c.54C>A	5.37:g.130500845G>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	107	40	NM_005340	1	0	297	538	240	Q9H5W8	Silent	SNP	ENST00000304043.5	37	CCDS4147.1																																																																																			.		0.587	HINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250984.1	NM_005340		T	130500845	G	T	130500845	2	4	144	1	0	0	0	0	0	0	0	1	7132	932	33	4		4	HINT1	5	130500845	Silent	SNP	G	TCGA-J7-6720-01A-11D-2136-08	9087389	130500845	50414415	23	12873											
TBC1D9B	23061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	179326225	179326225	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgaaggtggtgatatcttcCtcactgtcgaagatggacag	11	10	12	8	2	2	2	1	1	1	1	4	5	3	3	1	3	0	0	1	3	3	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:179326225C>T	ENST00000356834.3	-	3	349	c.312G>A	c.(310-312)gaG>gaA	p.E104E	TBC1D9B_ENST00000355235.3_Silent_p.E104E	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	104						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGATATCTTCCTCACTGTCGA	0.478																																					p.E104E		.											.	TBC1D9B-154	0			c.G312A						.						186	155	166					5																	179326225		2203	4300	6503	SO:0001819	synonymous_variant	23061	exon3			ATCTTCCTCACTG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"EF-hand domain containing"	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.312G>A	5.37:g.179326225C>T		Somatic	45	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_198868	0	0	10	17	7	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			.		0.478	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		T	179326225	C	T	179326225	2	4	144	1	0	0	0	0	0	0	0	1	15660	680	24	2		2	TBC1D9B	5	179326225	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08	48825380	179326225	1589035	24	12874											
CDKAL1	54901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	20846322	20846322	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggtgtctcaatgcttgtAcctactgcaaaactaaacac	14	10	6	11	0	1	0	1	0	1	0	2	0	1	0	1	1	6	3	1	1	7	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:20846322A>G	ENST00000378610.1	+	7	665	c.655A>G	c.(655-657)Acc>Gcc	p.T219A	CDKAL1_ENST00000378624.4_Missense_Mutation_p.T149A|CDKAL1_ENST00000274695.4_Missense_Mutation_p.T219A			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	219					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			CAATGCTTGTACCTACTGCAA	0.343																																					p.T219A		.											.	CDKAL1-92	0			c.A655G						.						75	75	75					6																	20846322		2203	4300	6503	SO:0001583	missense	54901	exon9			GCTTGTACCTACT	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.655A>G	6.37:g.20846322A>G	ENSP00000367873:p.Thr219Ala	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	69	23	NM_017774	0	0	1	5	4	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	37	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.612488	0.87258	.	.	ENSG00000145996	ENST00000274695;ENST00000378624;ENST00000378610	T;T;T	0.24151	1.87;1.87;1.87	5.81	5.81	0.92471	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Methylthiotransferase, conserved site (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	M	0.66378	2.025	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.951	T	0.42378	-0.9455	10	0.87932	D	0	.	16.1616	0.81721	1.0:0.0:0.0:0.0	.	149;219	Q5VV42-2;Q5VV42	.;CDKAL_HUMAN	A	219;149;219	ENSP00000274695:T219A;ENSP00000367889:T149A;ENSP00000367873:T219A	ENSP00000274695:T219A	T	+	1	0	CDKAL1	20954301	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.971000	0.76105	2.218000	0.71995	0.377000	0.23210	ACC	.		0.343	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		G	20846322	A	G	20846322	3	3	144	1	0	0	0	0	1	0	0	0	3158	391	14	3	681	3	CDKAL1	6	20846322	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		20846322	150268745	25	12875											
TJAP1	93643	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	43472653	43472653	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccggagtctctactgctcaAttcagcccagtcaggcagcg	8	8	11	14	2	4	0	3	0	1	0	5	1	4	1	2	2	4	2	2	2	2	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:43472653A>G	ENST00000372445.5	+	11	1110	c.734A>G	c.(733-735)aAt>aGt	p.N245S	TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000372452.1_Missense_Mutation_p.N235S|TJAP1_ENST00000372449.1_Missense_Mutation_p.N245S|TJAP1_ENST00000259751.1_Missense_Mutation_p.N235S|TJAP1_ENST00000438588.2_Missense_Mutation_p.N245S|TJAP1_ENST00000372444.2_Missense_Mutation_p.N235S|TJAP1_ENST00000436109.2_Missense_Mutation_p.N235S	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	245					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CTACTGCTCAATTCAGCCCAG	0.637																																					p.N245S		.											.	TJAP1-90	0			c.A734G						.						88	89	88					6																	43472653		2203	4300	6503	SO:0001583	missense	93643	exon11			TGCTCAATTCAGC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.734A>G	6.37:g.43472653A>G	ENSP00000361522:p.Asn245Ser	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	182	20	NM_001146016	0	0	12	12	0	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	37	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681816	0.68042	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04;2.04;2.04	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.21022	0.0506	L	0.31664	0.95	0.58432	D	0.999999	D;D	0.89917	0.998;1.0	D;D	0.83275	0.987;0.996	T	0.05037	-1.0910	10	0.20046	T	0.44	-53.1615	14.9298	0.70906	1.0:0.0:0.0:0.0	.	245;235	Q5JTD0;Q5JTD0-2	TJAP1_HUMAN;.	S	235;245;235;235;235;235;245;245	ENSP00000361521:N235S;ENSP00000361522:N245S;ENSP00000407080:N235S;ENSP00000259751:N235S;ENSP00000361530:N235S;ENSP00000361527:N245S;ENSP00000408769:N245S	ENSP00000259751:N235S	N	+	2	0	TJAP1	43580631	1.000000	0.71417	0.995000	0.50966	0.806000	0.45545	8.900000	0.92551	1.912000	0.55364	0.459000	0.35465	AAT	.		0.637	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		G	43472653	A	G	43472653	3	3	144	1	0	0	0	0	1	0	0	0	15960	101	4	3	764	3	TJAP1	6	43472653	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	22626331	43472653	127642414	26	12876											
ZDHHC14	79683	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	158093775	158093785	+	Frame_Shift_Del	DEL	TTCAGAGCACC	TTCAGAGCACC	-																															gtgcgaccaagaccagtgcaTtcagagcaccaaattcgttt																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	TTCAGAGCACC	TTCAGAGCACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:158093775_158093785delTTCAGAGCACC	ENST00000359775.5	+	9	1977_1987	c.1088_1098delTTCAGAGCACC	c.(1087-1098)attcagagcaccfs	p.IQST363fs	ZDHHC14_ENST00000341375.8_3'UTR|ZDHHC14_ENST00000414563.2_Intron			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	363					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		GACCAGTGCATTCAGAGCACCAAATTCGTTT	0.664																																					p.363_366del		.											.	ZDHHC14-227	0			c.1088_1098del						.																																			SO:0001589	frameshift_variant	79683	exon9			.	AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"Zinc fingers, DHHC-type"	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.1088_1098delTTCAGAGCACC	6.37:g.158093775_158093785delTTCAGAGCACC	ENSP00000352821:p.Ile363fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	71	11	NM_024630	0	0	0	0	0	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Frame_Shift_Del	DEL	ENST00000359775.5	37	CCDS5252.1																																																																																			.		0.664	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746		-	158093785	TTCAGAGCACC	-	158093775	7	5	144	1	0	1	0	1	0	0	0	0	17636	1493	52	0	1122	0	ZDHHC14	6	158093775	Frame_Shift_Del	DEL	TTCAGAGCACC	TCGA-J7-6720-01A-11D-2136-08	114621122	158093775	13021292	27	12877											
THBS2	7058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	169642014	169642014	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgacatgcggacccaggCgcagcgtctctgtgttctca	6	10	13	12	3	2	1	1	1	2	0	4	2	2	2	1	3	2	2	1	3	0	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:169642014C>G	ENST00000366787.3	-	6	983	c.734G>C	c.(733-735)cGc>cCc	p.R245P	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	245					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGGACCCAGGCGCAGCGTCTC	0.647																																					p.R245P	Esophageal Squamous(91;219 1934 18562 44706)	.											.	THBS2-95	0			c.G734C						.						50	45	47					6																	169642014		2202	4300	6502	SO:0001583	missense	7058	exon6			CCCAGGCGCAGCG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.734G>C	6.37:g.169642014C>G	ENSP00000355751:p.Arg245Pro	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	91	34	NM_003247	0	0	11	13	2	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	6.539	0.467797	0.12402	.	.	ENSG00000186340	ENST00000366787	T	0.80994	-1.44	4.75	0.174	0.15040	.	0.371764	0.19184	U	0.120604	T	0.47525	0.1450	N	0.22421	0.69	0.22412	N	0.999129	B	0.26845	0.161	B	0.25506	0.061	T	0.44922	-0.9296	10	0.46703	T	0.11	-42.5921	9.6944	0.40147	0.0:0.2486:0.0:0.7513	.	245	P35442	TSP2_HUMAN	P	245	ENSP00000355751:R245P	ENSP00000355751:R245P	R	-	2	0	THBS2	169383939	0.998000	0.40836	0.177000	0.23020	0.004000	0.04260	0.342000	0.19926	0.182000	0.20032	-0.658000	0.03865	CGC	.		0.647	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		G	169642014	C	G	169642014	3	3	144	1	0	0	0	0	1	0	0	0	15886	768	27	4	2856	4	THBS2	6	169642014	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	11548239	169642014	1473053	28	12878											
PURB	5814	broad.mit.edu	37	chr7	44924131	44924131	+	Frame_Shift_Del	DEL	A	A	-																															catctcatccgcataccggcAaaaggcgcctccgaacttgc																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr7:44924131delA	ENST00000395699.2	-	1	829	c.817delT	c.(817-819)tgcfs	p.C273fs	MIR4657_ENST00000578157.1_RNA|RP4-673M15.1_ENST00000608450.1_RNA	NM_033224.3	NP_150093.1	Q96QR8	PURB_HUMAN	purine-rich element binding protein B	273					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of myeloid cell differentiation (GO:0045637)|transcription, DNA-templated (GO:0006351)	DNA replication factor A complex (GO:0005662)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(3)|prostate(1)|skin(1)	7						GCATACCGGCAAAAGGCGCCT	0.582																																					p.C273fs													.	PURB-90	0			c.817delT						.						95	104	101					7																	44924131		2203	4300	6503	SO:0001589	frameshift_variant	5814	exon1			ACCGGCAAAAGGC		CCDS5499.1	7p13	2008-07-18			ENSG00000146676	ENSG00000146676			9702	protein-coding gene	gene with protein product		608887				1448097	Standard	NM_033224		Approved	PURBETA	uc003tme.3	Q96QR8	OTTHUMG00000023578	ENST00000395699.2:c.817delT	7.37:g.44924131delA	ENSP00000379051:p.Cys273fs	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	419	7	NM_033224	0	0	0	0	0	A4D2L7	Frame_Shift_Del	DEL	ENST00000395699.2	37	CCDS5499.1																																																																																			.		0.582	PURB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251332.2	NM_033224		-	44924131	A	-	44924131	7	5	144	1	0	1	0	1	0	0	0	0	12860	130	5	0	125	0	PURB	7	44924131	Frame_Shift_Del	DEL	A	TCGA-J7-6720-01A-11D-2136-08		44924131	114214532	29	12879											
ZNF679	168417	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	63726979	63726979	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aattcatactggagagaaacCctacacatgtgaagaatgtg	16	9	9	7	0	1	3	1	1	0	2	1	5	1	4	1	1	3	0	1	1	6	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr7:63726979C>G	ENST00000421025.1	+	5	1237	c.968C>G	c.(967-969)cCc>cGc	p.P323R	ZNF679_ENST00000255746.4_Missense_Mutation_p.P323R	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	323					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						GGAGAGAAACCCTACACATGT	0.398																																					p.P323R													.	ZNF679-1	0			c.C968G						.						26	27	27					7																	63726979		692	1591	2283	SO:0001583	missense	168417	exon5			AGAAACCCTACAC	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"Zinc fingers, C2H2-type", "-"	28650	protein-coding gene	gene with protein product	"hypothetical protein MGC42415"					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.968C>G	7.37:g.63726979C>G	ENSP00000416809:p.Pro323Arg	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	97	33	NM_153363	0	0	40	40	0		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576050	0.28092	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.17213	2.29;2.29	0.81	0.81	0.18732	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28962	0.0719	L	0.46819	1.47	0.37644	D	0.922144	D	0.89917	1.0	D	0.97110	1.0	T	0.11641	-1.0579	9	0.72032	D	0.01	.	6.9761	0.24677	0.0:1.0:0.0:0.0	.	323	Q8IYX0	ZN679_HUMAN	R	323	ENSP00000416809:P323R;ENSP00000255746:P323R	ENSP00000255746:P323R	P	+	2	0	ZNF679	63364414	0.775000	0.28604	0.437000	0.26809	0.440000	0.31957	3.755000	0.55197	0.181000	0.19994	0.184000	0.17185	CCC	.		0.398	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		G	63726979	C	G	63726979	3	3	144	1	0	0	0	0	1	0	0	0	18118	623	22	4	982	4	ZNF679	7	63726979	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	18802848	63726979	95411684	30	12880											
KCTD7	154881	hgsc.bcm.edu	37	chr7	66094155	66094155	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggagccggccacgccgacggCcacgcaggcggggcacgcgc	6	0	18	17	8	0	0	0	0	0	0	0	2	0	1	4	6	1	2	4	6	0	0			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr7:66094155C>G	ENST00000275532.3	+	1	288	c.104C>G	c.(103-105)gCc>gGc	p.A35G	KCTD7_ENST00000443322.1_Missense_Mutation_p.A35G	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	35					cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						ACGCCGACGGCCACGCAGGCG	0.761																																					p.A35G		.											.	KCTD7-92	0			c.C104G						.						11	12	11					7																	66094155		2154	4203	6357	SO:0001583	missense	154881	exon1			CGACGGCCACGCA	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"potassium channel tetramerisation domain containing 7"			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.104C>G	7.37:g.66094155C>G	ENSP00000275532:p.Ala35Gly	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_001167961	0	0	0	0	0	A4D2M4|Q8IVR0	Missense_Mutation	SNP	ENST00000275532.3	37	CCDS5534.1	.	.	.	.	.	.	.	.	.	.	N	25.8	4.676338	0.88445	.	.	ENSG00000243335	ENST00000275532;ENST00000443322;ENST00000449064	T;T	0.65178	-0.14;-0.14	3.93	3.93	0.45458	.	.	.	.	.	T	0.47619	0.1455	N	0.19112	0.55	0.80722	D	1	B	0.25105	0.118	B	0.24006	0.05	T	0.44711	-0.9310	9	0.33940	T	0.23	.	15.2139	0.73247	0.0:1.0:0.0:0.0	.	35	Q96MP8	KCTD7_HUMAN	G	35	ENSP00000275532:A35G;ENSP00000411624:A35G	ENSP00000275532:A35G	A	+	2	0	KCTD7	65731590	1.000000	0.71417	1.000000	0.80357	0.499000	0.33736	5.266000	0.65525	2.056000	0.61249	0.154000	0.16183	GCC	.		0.761	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033		G	66094155	C	G	66094155	3	3	144	1	0	0	0	0	1	0	0	0	8135	739	26	4	106	4	KCTD7	7	66094155	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	2367176	66094155	93044508	31	12881											
RELN	5649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	103292216	103292216	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	accaggagcgcccatggttgGtagaaaattccaagctgaca	13	7	11	10	1	0	2	0	1	0	1	1	3	1	3	3	3	2	3	3	3	4	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr7:103292216G>C	ENST00000428762.1	-	15	1943	c.1784C>G	c.(1783-1785)aCc>aGc	p.T595S	RELN_ENST00000424685.2_Missense_Mutation_p.T595S|RELN_ENST00000343529.5_Missense_Mutation_p.T595S	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	595					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCCATGGTTGGTAGAAAATTC	0.463																																					p.T595S	NSCLC(146;835 1944 15585 22231 52158)	.											.	RELN-574	0			c.C1784G						.						64	52	56					7																	103292216		2203	4300	6503	SO:0001583	missense	5649	exon15			TGGTTGGTAGAAA		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.1784C>G	7.37:g.103292216G>C	ENSP00000392423:p.Thr595Ser	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	90	43	NM_173054	0	0	0	2	2	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.770518	0.90108	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.25085	1.82;1.82;1.82	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.47801	0.1465	L	0.46157	1.445	0.58432	D	0.999998	D;D	0.76494	0.999;0.982	D;D	0.77557	0.99;0.952	T	0.34279	-0.9835	10	0.66056	D	0.02	.	20.0693	0.97712	0.0:0.0:1.0:0.0	.	595;595	P78509-2;P78509	.;RELN_HUMAN	S	595	ENSP00000392423:T595S;ENSP00000345694:T595S;ENSP00000388446:T595S	ENSP00000345694:T595S	T	-	2	0	RELN	103079452	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.476000	0.97823	2.758000	0.94735	0.563000	0.77884	ACC	.		0.463	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103292216	G	C	103292216	3	2	144	1	0	0	0	0	1	0	0	0	13252	1261	44	4	8802	4	RELN	7	103292216	Missense_Mutation	SNP	G	TCGA-J7-6720-01A-11D-2136-08	37198061	103292216	55846447	32	12882											
JPH1	56704	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	75227665	75227665	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttgagcacgaaaccgccGcgggtgccggccgggctgtc	7	5	16	13	6	0	1	0	1	0	0	1	2	0	1	4	3	3	3	4	3	2	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:75227665G>A	ENST00000342232.4	-	2	610	c.570C>T	c.(568-570)cgC>cgT	p.R190R		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	190					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			CGAAACCGCCGCGGGTGCCGG	0.682																																					p.R190R		.											.	JPH1-91	0			c.C570T						.						14	18	16					8																	75227665		2161	4223	6384	SO:0001819	synonymous_variant	56704	exon2			ACCGCCGCGGGTG	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.570C>T	8.37:g.75227665G>A		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	73	24	NM_020647	0	0	0	0	0	B2RTZ0	Silent	SNP	ENST00000342232.4	37	CCDS6217.1																																																																																			.		0.682	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			A	75227665	G	A	75227665	2	1	144	1	0	0	0	0	0	0	0	1	7981	1074	38	1		1	JPH1	8	75227665	Silent	SNP	G	TCGA-J7-6720-01A-11D-2136-08		75227665	71136357	33	12883											
FAM135B	51059	broad.mit.edu;bcgsc.ca	37	chr8	139180285	139180285	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggacagctggctgtgcgTctgtatcctggggagcacat	7	9	15	10	1	1	0	0	0	1	0	2	2	2	2	1	4	3	4	1	4	1	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:139180285T>C	ENST00000395297.1	-	12	1281	c.1111A>G	c.(1111-1113)Acg>Gcg	p.T371A		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	371										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGGCTGTGCGTCTGTATCCTG	0.587										HNSCC(54;0.14)																											p.T371A													.	FAM135B-31	0			c.A1111G						.						84	91	89					8																	139180285		2108	4234	6342	SO:0001583	missense	51059	exon12			TGTGCGTCTGTAT	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1111A>G	8.37:g.139180285T>C	ENSP00000378710:p.Thr371Ala	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	161	7	NM_015912	0	0	0	0	0	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	T	12.75	2.032813	0.35893	.	.	ENSG00000147724	ENST00000395297	D	0.88201	-2.35	5.66	3.16	0.36331	.	0.611892	0.17190	N	0.183555	D	0.85852	0.5793	M	0.63428	1.95	0.27501	N	0.951993	B	0.19817	0.039	B	0.16722	0.016	T	0.75422	-0.3323	10	0.38643	T	0.18	-6.9288	10.1146	0.42583	0.2674:0.0:0.0:0.7326	.	371	Q49AJ0	F135B_HUMAN	A	371	ENSP00000378710:T371A	ENSP00000276737:T371A	T	-	1	0	FAM135B	139249467	0.993000	0.37304	0.963000	0.40424	0.275000	0.26752	2.562000	0.45914	0.433000	0.26313	0.533000	0.62120	ACG	.		0.587	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139180285	T	C	139180285	3	2	144	1	0	0	0	0	1	0	0	0	5465	1667	58	3	3145	3	FAM135B	8	139180285	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08	63952620	139180285	7183737	34	12884											
CYP11B1	1584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	143956729	143956729	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagacccacagggtagagcCtggaggtgggggcatccata	11	5	15	10	0	0	2	0	0	0	2	1	3	1	3	3	5	1	2	3	5	2	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:143956729C>G	ENST00000292427.4	-	7	1154		c.e7-1		CYP11B1_ENST00000517471.1_Splice_Site|CYP11B1_ENST00000377675.3_Splice_Site	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1						aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	AGGGTAGAGCCTGGAGGTGGG	0.602									Familial Hyperaldosteronism type I																												.		.											.	CYP11B1-94	0			c.1122-1G>C						.						39	43	41					8																	143956729		2203	4300	6503	SO:0001630	splice_region_variant	1584	exon8	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TAGAGCCTGGAGG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"Cytochrome P450s"	2591	protein-coding gene	gene with protein product	"steroid 11-beta-monooxygenase"	610613	"cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.1122-1G>C	8.37:g.143956729C>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	40	16	NM_001026213	0	0	0	0	0	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Splice_Site	SNP	ENST00000292427.4	37	CCDS6392.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.78|13.78	2.338412|2.338412	0.41398|0.41398	.|.	.|.	ENSG00000160882|ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675|ENST00000519285	.|D	.|0.97480	.|-4.4	3.12|3.12	3.12|3.12	0.35913|0.35913	.|.	.|.	.|.	.|.	.|.	.|D	.|0.96836	.|0.8967	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.95728	.|0.8772	.|5	.|.	.|.	.|.	.|.	12.4777|12.4777	0.55823|0.55823	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|T	-1|52	.|ENSP00000430144:R52T	.|.	.|R	-|-	.|2	.|0	CYP11B1|CYP11B1	143953731|143953731	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.194000|0.194000	0.23727|0.23727	4.120000|4.120000	0.57897|0.57897	2.055000|2.055000	0.61198|0.61198	0.555000|0.555000	0.69702|0.69702	.|AGG	.		0.602	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		Intron	G	143956729	C	G	143956729	5	3	144	1	0	0	0	0	0	0	1	0	4151	695	24	4	402	4	CYP11B1	8	143956729	Splice_Site	SNP	C	TCGA-J7-6720-01A-11D-2136-08	4776444	143956729	2407293	35	12885											
COL13A1	1305	hgsc.bcm.edu	37	chr10	71582134	71582134	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccttgtacagaaatggaagCtccactcaaggaggcgccgg	11	7	12	11	2	1	1	1	0	0	1	3	3	3	3	3	4	2	2	3	4	4	2	rs200528707	byFrequency	TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr10:71582134C>T	ENST00000398978.3	+	2	796	c.304C>T	c.(304-306)Ctc>Ttc	p.L102F	COL13A1_ENST00000398966.3_Missense_Mutation_p.L102F|COL13A1_ENST00000520133.1_Missense_Mutation_p.L102F|COL13A1_ENST00000517713.1_Missense_Mutation_p.L102F|COL13A1_ENST00000520267.1_Missense_Mutation_p.L102F|COL13A1_ENST00000398972.3_Missense_Mutation_p.L102F|COL13A1_ENST00000354547.3_Missense_Mutation_p.L102F|COL13A1_ENST00000356340.3_Missense_Mutation_p.L102F|COL13A1_ENST00000398973.3_Missense_Mutation_p.L102F|COL13A1_ENST00000398969.3_Missense_Mutation_p.L102F|COL13A1_ENST00000398971.3_Missense_Mutation_p.L102F|COL13A1_ENST00000522165.1_Missense_Mutation_p.L102F|COL13A1_ENST00000398968.3_Missense_Mutation_p.L102F|COL13A1_ENST00000398964.3_Missense_Mutation_p.L102F|COL13A1_ENST00000398974.3_Missense_Mutation_p.L102F|COL13A1_ENST00000357811.3_Missense_Mutation_p.L102F	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						GAAATGGAAGCTCCACTCAAG	0.572													C|||	20	0.00399361	0	0	5008	,	,		17666	0.0169		0	False		,,,				2504	0.0031				p.L102F		.											.	COL13A1-91	0			c.C304T						.						27	29	28					10																	71582134		1905	4130	6035	SO:0001583	missense	1305	exon2			TGGAAGCTCCACT	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.304C>T	10.37:g.71582134C>T	ENSP00000381949:p.Leu102Phe	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	26	13	NM_080802	0	0	0	0	0		Missense_Mutation	SNP	ENST00000398978.3	37	CCDS44419.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	C	11.24	1.578987	0.28180	.	.	ENSG00000197467	ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000398964;ENST00000398969;ENST00000356340;ENST00000398972;ENST00000398973;ENST00000398978;ENST00000354547;ENST00000357811;ENST00000520267;ENST00000517713;ENST00000522165;ENST00000520133	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.92595	-2.83;-2.86;-2.91;-2.94;-2.99;-2.85;-3.07;-2.86;-2.98;-2.99;-2.93;-2.94;-2.78;-2.84;-2.92;-2.79	5.56	4.65	0.58169	.	0.192295	0.25938	N	0.027325	T	0.72811	0.3507	N	0.02158	-0.66	0.24671	N	0.993418	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.21606	0.004;0.058;0.002;0.001;0.001;0.001;0.001;0.001;0.001;0.003;0.002;0.002;0.016;0.002;0.002;0.002;0.001;0.002	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.20184	0.005;0.028;0.011;0.005;0.005;0.005;0.005;0.005;0.005;0.005;0.011;0.011;0.011;0.011;0.011;0.011;0.005;0.011	T	0.67665	-0.5612	10	0.40728	T	0.16	-2.2423	9.5332	0.39207	0.0:0.9015:0.0:0.0985	.	102;102;102;102;102;102;102;102;102;102;102;102;102;102;102;102;102;102	Q5TAT6;Q5TAT6-5;Q5TAT6-6;E9PEG9;E7ES55;E7ES51;E7ES47;E7ES46;E7ES49;E7EWL8;Q5TAT6-3;Q5TAT6-4;E7EX21;Q5TAT6-7;Q5TAT6-8;Q5TAT6-2;E7ES56;G5E987	CODA1_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	F	102	ENSP00000381946:L102F;ENSP00000381943:L102F;ENSP00000381940:L102F;ENSP00000381938:L102F;ENSP00000381936:L102F;ENSP00000381941:L102F;ENSP00000348695:L102F;ENSP00000381944:L102F;ENSP00000381945:L102F;ENSP00000381949:L102F;ENSP00000346553:L102F;ENSP00000350463:L102F;ENSP00000428057:L102F;ENSP00000430061:L102F;ENSP00000428342:L102F;ENSP00000430173:L102F	ENSP00000346553:L102F	L	+	1	0	COL13A1	71252140	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	0.275000	0.18698	1.327000	0.45338	0.561000	0.74099	CTC	C|0.999;T|0.001		0.572	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		T	71582134	C	T	71582134	3	4	144	1	0	0	0	0	1	0	0	0	3676	797	28	2	310	2	COL13A1	10	71582134	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		71582134	63952613	36	12886											
SFRP5	6425	hgsc.bcm.edu	37	chr10	99531063	99531063	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcggcggcggcgctaccTggaggcgcggtggcgggcag	4	3	22	12	8	0	0	0	0	0	0	0	1	0	1	1	9	1	2	1	9	1	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr10:99531063T>C	ENST00000266066.3	-	1	646	c.528A>G	c.(526-528)ccA>ccG	p.P176P		NM_003015.3	NP_003006.2	Q5T4F7	SFRP5_HUMAN	secreted frizzled-related protein 5	176					anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell differentiation (GO:0030154)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|establishment or maintenance of cell polarity (GO:0007163)|gonad development (GO:0008406)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis (GO:2000057)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|post-anal tail morphogenesis (GO:0036342)|signal transduction (GO:0007165)|vasculature development (GO:0001944)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			large_intestine(1)|lung(4)	5		Colorectal(252;0.234)		Epithelial(162;4.98e-10)|all cancers(201;3.58e-08)		CGGCGCTACCTGGAGGCGCGG	0.721																																					p.P176P		.											.	SFRP5-658	0			c.A528G						.						6	6	6					10																	99531063		1857	3775	5632	SO:0001630	splice_region_variant	6425	exon1			GCTACCTGGAGGC	AF017988	CCDS7472.1	10q24	2008-07-10			ENSG00000120057	ENSG00000120057		"Secreted frizzled-related proteins"	10779	protein-coding gene	gene with protein product	"secreted apoptosis related protein 3"	604158				9391078	Standard	NM_003015		Approved	SARP3	uc001kor.4	Q5T4F7	OTTHUMG00000018866	ENST00000266066.3:c.529+1A>G	10.37:g.99531063T>C		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	20	2	NM_003015	0	0	0	0	0	O14780|Q86TH7	Silent	SNP	ENST00000266066.3	37	CCDS7472.1																																																																																			.		0.721	SFRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049742.1	NM_003015	Silent	C	99531063	T	C	99531063	5	2	144	1	0	0	0	0	0	0	1	0	14196	1594	55	3	437	3	SFRP5	10	99531063	Splice_Site	SNP	T	TCGA-J7-6720-01A-11D-2136-08	27948929	99531063	36003684	37	12887											
ING4	51147	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	6761549	6761549	+	Frame_Shift_Del	DEL	C	C	-																															catcagaggggtggacactgCcaaaggtcactgagggcatc																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr12:6761549delC	ENST00000396807.4	-	6	574	c.536delG	c.(535-537)ggcfs	p.G179fs	ING4_ENST00000486287.1_Intron|ING4_ENST00000446105.2_Frame_Shift_Del_p.G175fs|ING4_ENST00000444704.2_Frame_Shift_Del_p.G155fs|ING4_ENST00000341550.4_Frame_Shift_Del_p.G178fs|ING4_ENST00000412586.2_Frame_Shift_Del_p.G176fs|ING4_ENST00000423703.2_Intron	NM_001127582.1|NM_001127585.1|NM_001127586.1|NM_016162.3	NP_001121054.1|NP_001121057.1|NP_001121058.1|NP_057246.2	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4	179					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|protein acetylation (GO:0006473)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(3)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	10						GTGGACACTGCCAAAGGTCAC	0.512																																					p.G179fs		.											.	ING4-515	0			c.536delG						.						186	161	169					12																	6761549		2203	4300	6503	SO:0001589	frameshift_variant	51147	exon6			.	AF063594	CCDS8555.1, CCDS44812.1, CCDS44813.1, CCDS44814.1, CCDS44815.1, CCDS44816.1	12p13.32	2013-01-28			ENSG00000111653	ENSG00000111653		"Zinc fingers, PHD-type"	19423	protein-coding gene	gene with protein product		608524				12750254	Standard	NM_001127582		Approved	p29ING4, my036	uc001qpw.4	Q9UNL4	OTTHUMG00000141274	ENST00000396807.4:c.536delG	12.37:g.6761549delC	ENSP00000380024:p.Gly179fs	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	169	49	NM_001127582	0	0	0	0	0	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Frame_Shift_Del	DEL	ENST00000396807.4	37	CCDS44813.1																																																																																			.		0.512	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287		-	6761549	C	-	6761549	7	5	144	1	0	1	0	1	0	0	0	0	7759	739	26	0	225	0	ING4	12	6761549	Frame_Shift_Del	DEL	C	TCGA-J7-6720-01A-11D-2136-08		6761549	127090346	38	12888											
FGD4	121512	bcgsc.ca	37	chr12	32777967	32777968	+	In_Frame_Ins	INS	-	-	TTTTTT																															tgaaaccttcagaaatgcaaINSttgcaaaggataatgacatt																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr12:32777967_32777968insTTTTTT	ENST00000427716.2	+	13	2024_2025	c.1600_1601insTTTTTT	c.(1600-1602)att>aTTTTTTtt	p.534_535insFF	FGD4_ENST00000531134.1_In_Frame_Ins_p.619_620insFF|FGD4_ENST00000266482.3_In_Frame_Ins_p.286_287insFF|FGD4_ENST00000525053.1_In_Frame_Ins_p.646_647insFF|FGD4_ENST00000534526.2_In_Frame_Ins_p.671_672insFF|FGD4_ENST00000546442.1_In_Frame_Ins_p.441_442insFF	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	534					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					CAGAAATGCAATTGCAAAGGAT	0.347																																					p.I534delinsIFF													.	FGD4-229	0			c.1600_1601insTTTTTT						.																																			SO:0001652	inframe_insertion	121512	exon13			AATGCAATTGCAA	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"Zinc fingers, FYVE domain containing", "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	19125	protein-coding gene	gene with protein product		611104	"FGD1 family, member 4"			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	Exception_encountered	12.37:g.32777967_32777968insTTTTTT	ENSP00000394487:p.Ile534_Ala535insPhePhe	Somatic	189	0		WXS	Illumina HiSeq	Phase_1	177	17	NM_139241	0	0	0	0	0	Q6ULS2|Q8TCP6	In_Frame_Ins	INS	ENST00000427716.2	37	CCDS8727.1																																																																																			.		0.347	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		TTTTTT	32777968	-	TTTTTT	32777967	7	5	144	1	0	1	1	0	0	0	0	0	5854	101	4	0	1642	0	FGD4	12	32777967	In_Frame_Ins	INS	-	TCGA-J7-6720-01A-11D-2136-08	26016418	32777967	101073928	39	12889											
TCTN2	79867	bcgsc.ca	37	chr12	124171453	124171453	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtgtttggaggagacgtcaAtcctccttttgatcagctct	7	14	10	10	2	3	2	2	1	1	1	5	4	5	3	2	2	1	2	2	2	1	3	rs139927033		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr12:124171453A>G	ENST00000303372.5	+	6	763	c.635A>G	c.(634-636)aAt>aGt	p.N212S	TCTN2_ENST00000426174.2_Missense_Mutation_p.N211S	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	212					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		GGAGACGTCAATCCTCCTTTT	0.532																																					p.N212S													.	TCTN2-91	0			c.A635G						.	A	SER/ASN,SER/ASN	0,4406		0,0,2203	280	232	248		632,635	-2.3	0	12	dbSNP_134	248	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	TCTN2	NM_001143850.1,NM_024809.3	46,46	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	benign,benign	211/697,212/698	124171453	4,13002	2203	4300	6503	SO:0001583	missense	79867	exon6			ACGTCAATCCTCC	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"Tectonic proteins"	25774	protein-coding gene	gene with protein product	"Meckel syndrome, type 8"	613846	"chromosome 12 open reading frame 38"	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.635A>G	12.37:g.124171453A>G	ENSP00000304941:p.Asn212Ser	Somatic	241	0		WXS	Illumina HiSeq	Phase_1	278	7	NM_024809	0	0	18	20	2	A8K7Y8|B3KPW5|Q9H966	Missense_Mutation	SNP	ENST00000303372.5	37	CCDS9253.1	.	.	.	.	.	.	.	.	.	.	A	0.775	-0.764322	0.02996	0.0	4.65E-4	ENSG00000168778	ENST00000426174;ENST00000303372	D;D	0.82167	-1.58;-1.58	5.65	-2.33	0.06724	Domain of unknown function DUF1619 (1);	0.399950	0.26126	N	0.026184	T	0.62998	0.2474	N	0.21194	0.64	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.006	T	0.52260	-0.8599	10	0.02654	T	1	-39.997	9.4511	0.38727	0.3983:0.1153:0.4864:0.0	.	211;212	A8K7Y8;Q96GX1	.;TECT2_HUMAN	S	211;212	ENSP00000395171:N211S;ENSP00000304941:N212S	ENSP00000304941:N212S	N	+	2	0	TCTN2	122737406	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	0.134000	0.15932	-0.787000	0.04510	-1.446000	0.01064	AAT	A|1.000;G|0.000		0.532	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		G	124171453	A	G	124171453	3	3	144	1	0	0	0	0	1	0	0	0	15755	101	4	3	657	3	TCTN2	12	124171453	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	91393486	124171453	9680442	40	12890											
DGKH	160851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	42742631	42742632	+	Missense_Mutation	DNP	GG	GG	AT																															ttcttgtttgtggaggcgatGgaagtgtaggttgggttttg																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr13:42742631_42742632GG>AT	ENST00000337343.4	+	10	1195_1196	c.1174_1175GG>AT	c.(1174-1176)GGa>ATa	p.G392I	DGKH_ENST00000261491.5_Missense_Mutation_p.G392I|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000540693.1_Missense_Mutation_p.G392I|DGKH_ENST00000536612.1_Missense_Mutation_p.G256I|DGKH_ENST00000538674.1_Missense_Mutation_p.G147I|DGKH_ENST00000379274.2_Missense_Mutation_p.G256I	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	392	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TGGAGGCGATGGAAGTGTAGGT	0.322																																					p.G392I		.											.	DGKH	0			c.G1175T						.																																			SO:0001583	missense	160851	exon11			GCGATGGAAGTGT	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	Exception_encountered	13.37:g.42742631_42742632delinsAT	ENSP00000337572:p.Gly392Ile	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	69	19		0	0	0	0	0	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	DNP	ENST00000337343.4	37	CCDS9381.1																																																																																			.		0.322	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		AT	42742632	GG	AT	42742631	3	1	144	1	0	0	0	0	1	0	0	0	4481	1349	47	2	1212	2	DGKH	13	42742631	Missense_Mutation	DNP	GG	TCGA-J7-6720-01A-11D-2136-08		42742631	72427247	41	12891											
RPGRIP1	57096	hgsc.bcm.edu	37	chr14	21769356	21769356	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caagtgggacacagacagctCcacacagccggtgcaccggt	11	4	12	14	2	0	1	0	0	0	1	1	2	1	2	3	3	3	2	3	3	1	0	rs144585562	byFrequency	TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:21769356C>G	ENST00000400017.2	+	3	450	c.450C>G	c.(448-450)ctC>ctG	p.L150L	RPGRIP1_ENST00000206660.6_Silent_p.L150L|RPGRIP1_ENST00000556336.1_Silent_p.L150L|RPGRIP1_ENST00000557771.1_Silent_p.L150L	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	150					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		ACAGACAGCTCCACACAGCCG	0.642													c|||	38	0.00758786	0	0	5008	,	,		14975	0.0367		0	False		,,,				2504	0.001				p.L150L		.											.	RPGRIP1-140	0			c.C450G						.	C		1,4023		0,1,2011	14	19	17		450	-4.9	0	14	dbSNP_134	17	0,8274		0,0,4137	no	coding-synonymous	RPGRIP1	NM_020366.3		0,1,6148	GG,GC,CC		0.0,0.0249,0.0081		150/1287	21769356	1,12297	2012	4137	6149	SO:0001819	synonymous_variant	57096	exon3			ACAGCTCCACACA	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.450C>G	14.37:g.21769356C>G		Somatic	10	2		WXS	Illumina HiSeq	Phase_I	12	8	NM_020366	0	0	0	0	0	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																			C|0.993;G|0.007		0.642	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		G	21769356	C	G	21769356	2	3	144	1	0	0	0	0	0	0	0	1	13581	842	30	4		4	RPGRIP1	14	21769356	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08		21769356	85580184	42	12892											
HAUS4	54930	hgsc.bcm.edu;bcgsc.ca	37	chr14	23415759	23415759	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagaccttgctgaactccTggagggcccaccgcttgttc	6	10	12	13	1	0	2	0	1	0	1	2	3	1	3	4	3	2	4	4	3	2	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:23415759T>A	ENST00000206474.7	-	10	1319	c.1067A>T	c.(1066-1068)cAg>cTg	p.Q356L	RP11-298I3.5_ENST00000555074.1_Silent_p.P185P|HAUS4_ENST00000397409.4_Missense_Mutation_p.Q230L|HAUS4_ENST00000490506.1_Missense_Mutation_p.Q232L|HAUS4_ENST00000555986.1_Missense_Mutation_p.Q311L|HAUS4_ENST00000554446.1_5'UTR|RP11-298I3.1_ENST00000548819.1_RNA|HAUS4_ENST00000342454.8_Missense_Mutation_p.Q311L|HAUS4_ENST00000555367.1_Missense_Mutation_p.Q311L|RP11-298I3.1_ENST00000548322.1_RNA|HAUS4_ENST00000347758.2_Missense_Mutation_p.Q230L|HAUS4_ENST00000541587.1_Missense_Mutation_p.Q356L			Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4	356					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|cervix(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)	14						GCTGAACTCCTGGAGGGCCCA	0.562																																					p.Q356L		.											.	HAUS4-91	0			c.A1067T						.						71	64	66					14																	23415759		2203	4300	6503	SO:0001583	missense	54930	exon10			AACTCCTGGAGGG	AK000431	CCDS9580.1, CCDS53886.1	14q11.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000092036	ENSG00000092036		"HAUS augmin-like complex subunits"	20163	protein-coding gene	gene with protein product		613431	"chromosome 14 open reading frame 94"	C14orf94		19427217	Standard	NM_017815		Approved	FLJ20424	uc001wht.3	Q9H6D7	OTTHUMG00000028710	ENST00000206474.7:c.1067A>T	14.37:g.23415759T>A	ENSP00000206474:p.Gln356Leu	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	89	5	NM_001166269	0	0	83	83	0	B7WP17|D3DS34|Q86T15|Q86T16|Q86U43|Q9NX59	Missense_Mutation	SNP	ENST00000206474.7	37	CCDS9580.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.185415	0.38609	.	.	ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000259132	ENST00000206474;ENST00000490506;ENST00000541587;ENST00000342454;ENST00000347758;ENST00000397409;ENST00000555367;ENST00000555986;ENST00000555074	.	.	.	5.8	3.46	0.39613	.	0.358284	0.32328	N	0.006245	T	0.33904	0.0879	L	0.50333	1.59	0.30627	N	0.757909	B;P;B	0.42518	0.0;0.782;0.001	B;B;B	0.40256	0.003;0.324;0.004	T	0.40136	-0.9579	9	0.52906	T	0.07	-10.115	5.9375	0.19173	0.1466:0.0786:0.0:0.7748	.	311;230;356	Q9H6D7-4;Q9H6D7-2;Q9H6D7	.;.;HAUS4_HUMAN	L	356;232;356;311;230;230;311;311;133	.	ENSP00000206474:Q356L	Q	-	2	0	RP11-298I3.5;HAUS4	22485599	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	0.712000	0.25779	1.014000	0.39417	-0.409000	0.06214	CAG	.		0.562	HAUS4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071680.3			A	23415759	T	A	23415759	3	1	144	1	0	0	0	0	1	0	0	0	6989	1580	55	5	28	5	HAUS4	14	23415759	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08	1646403	23415759	83933781	43	12893											
ACIN1	22985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23549776	23549776	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccatcatctcctctggtttTactctaggtatctcttcccc	5	17	4	15	0	5	0	1	0	4	0	9	0	7	0	4	2	1	2	4	2	3	5			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:23549776T>C	ENST00000262710.1	-	6	1269	c.942A>G	c.(940-942)gtA>gtG	p.V314V	ACIN1_ENST00000555053.1_Silent_p.V314V|ACIN1_ENST00000457657.1_Silent_p.V274V|ACIN1_ENST00000605057.1_Silent_p.V256V|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	314	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CCTCTGGTTTTACTCTAGGTA	0.453																																					p.V314V		.											.	ACIN1-156	0			c.A942G						.						246	213	224					14																	23549776		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			TGGTTTTACTCTA	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 152"	604562	"apoptotic chromatin condensation inducer in the nucleus"	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.942A>G	14.37:g.23549776T>C		Somatic	160	0		WXS	Illumina HiSeq	Phase_I	182	54	NM_001164814	0	0	10	10	0	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	37	CCDS9587.1																																																																																			.		0.453	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23549776	T	C	23549776	2	2	144	1	0	0	0	0	0	0	0	1	142	1741	61	3		3	ACIN1	14	23549776	Silent	SNP	T	TCGA-J7-6720-01A-11D-2136-08	134017	23549776	83799764	44	12894											
ADCY4	196883	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	24793367	24793367	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaggccagacagtgcaggCagccagtgcagcatcttggg	10	5	14	12	0	1	1	0	0	1	1	1	1	1	1	3	3	4	4	3	3	0	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:24793367C>A	ENST00000310677.4	-	17	2060	c.1947G>T	c.(1945-1947)ctG>ctT	p.L649L	ADCY4_ENST00000554068.2_Silent_p.L649L|ADCY4_ENST00000418030.2_Silent_p.L649L|ADCY4_ENST00000396747.3_Silent_p.L342L	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	649					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		ACAGTGCAGGCAGCCAGTGCA	0.612																																					p.L649L		.											.	ADCY4-93	0			c.G1947T						.						64	63	63					14																	24793367		2203	4300	6503	SO:0001819	synonymous_variant	196883	exon17			TGCAGGCAGCCAG	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"Adenylate cyclases"	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.1947G>T	14.37:g.24793367C>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	80	6	NM_001198592	0	0	0	0	0	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	37	CCDS9627.1																																																																																			.		0.612	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			A	24793367	C	A	24793367	2	1	144	1	0	0	0	0	0	0	0	1	296	697	25	4		4	ADCY4	14	24793367	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08	1243591	24793367	82556173	45	12895											
JKAMP	51528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	59965574	59965574	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaagtatttatgctgcactTtacttcttcccaattttaac	12	17	3	9	0	1	0	0	0	1	0	2	0	2	0	1	0	4	3	1	0	7	9			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:59965574T>C	ENST00000261247.9	+	5	735	c.588T>C	c.(586-588)ctT>ctC	p.L196L	JKAMP_ENST00000554271.1_Silent_p.L210L|JKAMP_ENST00000425728.2_Silent_p.L190L|JKAMP_ENST00000356057.5_Silent_p.L204L|RP11-701B16.2_ENST00000554253.1_RNA	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	211					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						ATGCTGCACTTTACTTCTTCC	0.373																																					p.L196L		.											.	JKAMP-67	0			c.T588C						.						125	113	117					14																	59965574		1831	4097	5928	SO:0001819	synonymous_variant	51528	exon5			TGCACTTTACTTC	AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"Jun N-terminal kinase 1-associated membrane protein"	611176	"chromosome 14 open reading frame 100"	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.588T>C	14.37:g.59965574T>C		Somatic	19	0		WXS	Illumina HiSeq	Phase_I	31	12	NM_016475	0	0	29	59	30	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Silent	SNP	ENST00000261247.9	37	CCDS45116.1																																																																																			.		0.373	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625		C	59965574	T	C	59965574	2	2	144	1	0	0	0	0	0	0	0	1	7970	1828	64	3		3	JKAMP	14	59965574	Silent	SNP	T	TCGA-J7-6720-01A-11D-2136-08	35172207	59965574	47383966	46	12896											
C15orf44	81556	bcgsc.ca	37	chr15	65871974	65871974	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaaaccaaaggctagagcGgcctttcgcaaacggttcag	13	6	12	10	3	1	1	1	0	0	1	2	2	1	2	2	4	3	3	2	4	4	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr15:65871974G>T	ENST00000395644.4	-	12	1664	c.1329C>A	c.(1327-1329)gcC>gcA	p.A443A	VWA9_ENST00000442903.3_Silent_p.A407A|VWA9_ENST00000420799.2_Silent_p.A386A|VWA9_ENST00000569491.1_Silent_p.A393A|VWA9_ENST00000431261.2_Silent_p.A364A|VWA9_ENST00000313182.2_Silent_p.A443A|VWA9_ENST00000567744.1_Silent_p.A479A			Q96SY0	VWA9_HUMAN	von Willebrand factor A domain containing 9	443																	AGGCTAGAGCGGCCTTTCGCA	0.502																																					p.A425A													.	.	0			c.C1275A						.						53	47	49					15																	65871974		2201	4299	6500	SO:0001819	synonymous_variant	81556	exon12			TAGAGCGGCCTTT	AL136662	CCDS55969.1, CCDS45283.1	15q22.31	2012-09-27	2012-09-27	2012-09-27	ENSG00000138614	ENSG00000138614			25372	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 44"	C15orf44		11230166	Standard	NM_001136043		Approved	DKFZP564O1664	uc010uja.2	Q96SY0	OTTHUMG00000133159	ENST00000395644.4:c.1329C>A	15.37:g.65871974G>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_1	59	5	NM_001207058	0	0	27	28	1	B4DDI6|B4DVD5|Q49AH8|Q96HX5|Q9H0S5	Silent	SNP	ENST00000395644.4	37																																																																																				.		0.502	VWA9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420604.3	NM_030800		T	65871974	G	T	65871974	2	4	144	1	0	0	0	0	0	0	0	1	1802	1103	39	4		4	C15orf44	15	65871974	Silent	SNP	G	TCGA-J7-6720-01A-11D-2136-08		65871974	36659418	47	12897											
KIAA1199	57214	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	81221510	81221511	+	Frame_Shift_Del	DEL	AG	AG	-																															agcggaaggaccctccctatAggccagtaggtttgcaacca																								rs201251202		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr15:81221510_81221511delAG	ENST00000394685.3	+	21	3026_3027	c.2607_2608delAG	c.(2605-2610)ataggcfs	p.IG869fs	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Frame_Shift_Del_p.IG869fs|KIAA1199_ENST00000356249.5_Frame_Shift_Del_p.IG869fs			Q8WUJ3	CEMIP_HUMAN		869					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CCCTCCCTATAGGCCAGTAGGT	0.51																																					p.869_870del		.											.	KIAA1199-93	0			c.2607_2608del						.																																			SO:0001589	frameshift_variant	57214	exon20			.																												ENST00000394685.3:c.2607_2608delAG	15.37:g.81221510_81221511delAG	ENSP00000378177:p.Ile869fs	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	141	54	NM_018689	0	0	0	0	0	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Frame_Shift_Del	DEL	ENST00000394685.3	37	CCDS10315.1																																																																																			.		0.51	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			-	81221511	AG	-	81221510	7	5	144	1	0	1	0	1	0	0	0	0	8234	410	15	0	2681	0	KIAA1199	15	81221510	Frame_Shift_Del	DEL	AG	TCGA-J7-6720-01A-11D-2136-08	15349536	81221510	21309882	48	12898											
NLRC3	197358	bcgsc.ca	37	chr16	3594282	3594282	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgttgaccttcagtgcaCgggccaccgcacacgctccg	6	8	11	16	4	1	1	1	1	0	0	2	1	2	1	4	1	1	4	4	1	0	2	rs371668578		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr16:3594282C>T	ENST00000301749.7	-	0	3224				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|LA16c-390H2.4_ENST00000573820.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTTCAGTGCACGGGCCACCGC	0.572																																					p.R940H													.	NLRC3-96	0			c.G2819A						.	C	HIS/ARG	1,4171		0,1,2085	72	78	76		2820	2.2	0	16		76	3,8447		0,3,4222	no	missense	NLRC3	NM_178844.2	29	0,4,6307	TT,TC,CC		0.0355,0.024,0.0317	possibly-damaging	940/1066	3594282	4,12618	2086	4225	6311			197358	exon17			AGTGCACGGGCCA	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3594282C>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_1	77	6	NM_178844	0	0	2	2	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	9.068	0.996164	0.19043	2.4E-4	3.55E-4	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.53206	0.63;0.63;0.63	5.28	2.24	0.28232	.	0.730148	0.13751	N	0.365282	T	0.28101	0.0693	N	0.16602	0.42	0.09310	N	1	B	0.20887	0.049	B	0.10450	0.005	T	0.16364	-1.0405	10	0.45353	T	0.12	.	5.9625	0.19307	0.0:0.677:0.1533:0.1697	.	986	C9JLH9	.	H	940;911;986	ENSP00000301749:R940H;ENSP00000352039:R911H;ENSP00000414415:R986H	ENSP00000301749:R940H	R	-	2	0	NLRC3	3534283	0.000000	0.05858	0.008000	0.14137	0.346000	0.29079	-0.547000	0.06055	0.351000	0.24027	-0.208000	0.12717	CGT	.		0.572	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3594282	C	T	3594282	1	4	144	0	1	0	0	0	0	0	0	0	10494	536	19	1		1	NLRC3	16	3594282	RNA	SNP	C	TCGA-J7-6720-01A-11D-2136-08		3594282	86760471	49	12899											
SBK1	388228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	28330355	28330355	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtttgtgaacaagagcaaaaCcaagctgaagaacttcctac	16	8	8	9	0	0	4	0	2	0	2	1	4	1	4	2	0	6	3	2	0	8	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr16:28330355C>T	ENST00000341901.4	+	3	1055	c.266C>T	c.(265-267)aCc>aTc	p.T89I		NM_001024401.2	NP_001019572.1	Q52WX2	SBK1_HUMAN	SH3 domain binding kinase 1	89	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(3)|ovary(1)	5						AAGAGCAAAACCAAGCTGAAG	0.532																																					p.T89I		.											.	SBK1-311	0			c.C266T						.						170	156	161					16																	28330355		2197	4300	6497	SO:0001583	missense	388228	exon3			GCAAAACCAAGCT		CCDS32416.1	16p11.2	2013-09-27	2013-09-27			ENSG00000188322			17699	protein-coding gene	gene with protein product			"SH3-binding domain kinase 1"				Standard	XM_005255315		Approved	Sbk	uc002dpd.3	Q52WX2		ENST00000341901.4:c.266C>T	16.37:g.28330355C>T	ENSP00000343248:p.Thr89Ile	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	250	85	NM_001024401	0	0	0	2	2		Missense_Mutation	SNP	ENST00000341901.4	37	CCDS32416.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.991381	0.74703	.	.	ENSG00000188322	ENST00000341901	T	0.65549	-0.16	4.98	4.03	0.46877	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.62732	0.2452	L	0.33339	1.005	0.54753	D	0.999985	D	0.52996	0.957	P	0.57324	0.818	T	0.59958	-0.7356	10	0.35671	T	0.21	-23.5445	11.1208	0.48289	0.0:0.9084:0.0:0.0916	.	89	Q52WX2	SBK1_HUMAN	I	89	ENSP00000343248:T89I	ENSP00000343248:T89I	T	+	2	0	SBK1	28237856	1.000000	0.71417	0.989000	0.46669	0.901000	0.52897	7.769000	0.85360	1.089000	0.41292	-0.141000	0.14075	ACC	.		0.532	SBK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387677.1	XM_370948		T	28330355	C	T	28330355	3	4	144	1	0	0	0	0	1	0	0	0	13892	507	18	2	272	2	SBK1	16	28330355	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	24736073	28330355	62024398	50	12900											
GLG1	2734	broad.mit.edu	37	chr16	74640708	74640708	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgccgggccggaggcccAcccgccgggaaaggcggctg	5	1	17	18	6	0	0	0	0	0	0	0	2	0	2	7	6	0	1	7	6	1	0			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr16:74640708A>C	ENST00000422840.2	-	1	284	c.285T>G	c.(283-285)ggT>ggG	p.G95G	GLG1_ENST00000205061.5_Silent_p.G95G|GLG1_ENST00000447066.2_Silent_p.G95G	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	95					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CCGGAGGCCCACCCGCCGGGA	0.706																																					p.G95G													.	GLG1-136	0			c.T285G						.						4	6	6					16																	74640708		1890	3823	5713	SO:0001819	synonymous_variant	2734	exon1			AGGCCCACCCGCC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.285T>G	16.37:g.74640708A>C		Somatic	16	3		WXS	Illumina HiSeq	Phase_I	28	10	NM_001145667	0	0	1	1	0	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	37	CCDS45527.1																																																																																			.		0.706	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		C	74640708	A	C	74640708	2	2	144	1	0	0	0	0	0	0	0	1	6456	146	6	5		5	GLG1	16	74640708	Silent	SNP	A	TCGA-J7-6720-01A-11D-2136-08	46310353	74640708	15714045	51	12901											
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgggcggcaccacctgaTacgggtgctcacagctccac	7	7	12	15	2	2	1	1	1	1	0	3	1	3	1	3	3	3	3	3	3	1	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr17:39197304T>C	ENST00000306271.4	-	1	409	c.346A>G	c.(346-348)Atc>Gtc	p.I116V		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	116						keratin filament (GO:0045095)		p.I116V(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CACCACCTGATACGGGTGCTC	0.662																																					p.I116V		.											.	.	1	Substitution - Missense(1)	NS(1)	c.A346G						.						22	27	25					17																	39197304		2019	4148	6167	SO:0001583	missense	81851	exon1			ACCTGATACGGGT	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"Keratin associated proteins"	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.346A>G	17.37:g.39197304T>C	ENSP00000305975:p.Ile116Val	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	79	6	NM_030967	0	0	0	0	0	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	T	8.173	0.792133	0.16258	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.29655	1.56	4.28	-1.23	0.09465	.	.	.	.	.	T	0.12135	0.0295	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34079	-0.9843	9	0.20046	T	0.44	.	9.4726	0.38851	0.0:0.573:0.0:0.427	.	116	Q07627	KRA11_HUMAN	V	116;106	ENSP00000305975:I116V	ENSP00000305975:I116V	I	-	1	0	KRTAP1-1	36450830	0.132000	0.22450	0.024000	0.17045	0.516000	0.34256	0.017000	0.13399	-0.199000	0.10317	0.529000	0.55759	ATC	.		0.662	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		C	39197304	T	C	39197304	3	2	144	1	0	0	0	0	1	0	0	0	8523	1406	49	3	191	3	KRTAP1-1	17	39197304	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08		39197304	41997906	52	12902											
FASN	2194	hgsc.bcm.edu	37	chr17	80041950	80041950	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gatgagcagcgtctccccggGgcgcacccgcccacgcacca	7	3	12	19	5	1	1	0	1	1	0	2	2	1	1	5	2	2	3	5	2	0	0	rs45557233	byFrequency	TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr17:80041950G>A	ENST00000306749.2	-	29	5217	c.4999C>T	c.(4999-5001)Ccc>Tcc	p.P1667S	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1667	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GTCTCCCCGGGGCGCACCCGC	0.726													.|||	142	0.0283546	0	0	5008	,	,		14181	0.1319		0	False		,,,				2504	0.0092				p.P1667S	Colon(59;314 1043 11189 28578 32273)	.											.	FASN-90	0			c.C4999T						.	G	SER/PRO	8,4182		0,8,2087	9	12	11		4999	2.4	0	17	dbSNP_127	11	0,8266		0,0,4133	yes	missense	FASN	NM_004104.4	74	0,8,6220	AA,AG,GG		0.0,0.1909,0.0642	benign	1667/2512	80041950	8,12448	2095	4133	6228	SO:0001583	missense	2194	exon29			CCCCGGGGCGCAC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"Short chain dehydrogenase/reductase superfamily / Atypical members"	3594	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 27X, member 1"	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.4999C>T	17.37:g.80041950G>A	ENSP00000304592:p.Pro1667Ser	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	8	6	NM_004104	0	0	1	3	2	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	65	0.02976190476190476	0	0.0	0	0.0	65	0.11363636363636363	0	0.0	G	1.339	-0.594657	0.03771	0.001909	0.0	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.32023	1.47	4.57	2.39	0.29439	GroES-like (1);Polyketide synthase, enoylreductase (1);NAD(P)-binding domain (1);	1.149520	0.06390	N	0.716872	T	0.00524	0.0017	L	0.48986	1.54	0.09310	N	1	B	0.23185	0.081	B	0.24701	0.055	T	0.16541	-1.0399	10	0.27082	T	0.32	-1.4574	5.5522	0.17097	0.112:0.0:0.4323:0.4557	rs45557233	1667	P49327	FAS_HUMAN	S	1667;632	ENSP00000304592:P1667S	ENSP00000304592:P1667S	P	-	1	0	FASN	77635239	0.586000	0.26782	0.003000	0.11579	0.003000	0.03518	3.926000	0.56491	0.903000	0.36546	0.491000	0.48974	CCC	G|0.970;A|0.030		0.726	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80041950	G	A	80041950	3	1	144	1	0	0	0	0	1	0	0	0	5702	1232	43	2	2596	2	FASN	17	80041950	Missense_Mutation	SNP	G	TCGA-J7-6720-01A-11D-2136-08	40844646	80041950	1153260	53	12903											
PSG2	5670	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	43585217	43585217	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attatttgaccgtctactacAtatgatgtaatgtaatggta	13	16	7	5	1	1	2	0	2	1	0	1	2	1	2	1	1	2	3	1	1	7	8			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr19:43585217A>T	ENST00000406487.1	-	2	344	c.246T>A	c.(244-246)taT>taA	p.Y82*	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	82	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CGTCTACTACATATGATGTAA	0.438																																					p.Y82X		.											.	PSG2-90	0			c.T246A						.						170	174	173					19																	43585217		2203	4298	6501	SO:0001587	stop_gained	5670	exon2			TACTACATATGAT		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9519	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta-1-glycoprotein 7", "carcinoembryonic antigen SG8"	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.246T>A	19.37:g.43585217A>T	ENSP00000385706:p.Tyr82*	Somatic	456	0		WXS	Illumina HiSeq	Phase_I	513	141	NM_031246	0	0	2	2	0	Q8TCD9|Q9UEA4|Q9UQ78	Nonsense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	.	.	.	.	.	.	.	.	.	.	N	10.75	1.438722	0.25900	.	.	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	.	.	.	0.569	-0.723	0.11181	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	82	.	ENSP00000332984:Y82X	Y	-	3	2	PSG2	48277057	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.017000	0.12590	-0.394000	0.07727	0.155000	0.16302	TAT	.		0.438	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		T	43585217	A	T	43585217	4	4	144	1	0	0	0	0	0	1	0	0	12684	224	8	5	777	5	PSG2	19	43585217	Nonsense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		43585217	15543766	54	12904											
PTGIR	5739	hgsc.bcm.edu	37	chr19	47126848	47126848	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttctgctggcggtacatgCggcagaggctgagggtgacc	6	8	17	10	2	1	3	0	2	1	1	1	3	1	3	1	5	3	5	1	5	1	2	rs2229131	byFrequency	TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr19:47126848C>T	ENST00000291294.2	-	2	768	c.635G>A	c.(634-636)cGc>cAc	p.R212H	PTGIR_ENST00000598865.1_5'UTR|PTGIR_ENST00000596260.1_Missense_Mutation_p.R212H|PTGIR_ENST00000594275.1_Intron|PTGIR_ENST00000597185.1_Intron	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	212					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	GCGGTACATGCGGCAGAGGCT	0.701													C|||	37	0.00738818	0	0	5008	,	,		14423	0.0367		0	False		,,,				2504	0				p.R212H		.											.	PTGIR-522	0			c.G635A						.						11	12	12					19																	47126848		2113	4132	6245	SO:0001583	missense	5739	exon2			TACATGCGGCAGA		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"GPCR / Class A : Prostanoid receptors"	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.635G>A	19.37:g.47126848C>T	ENSP00000291294:p.Arg212His	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	7	4	NM_000960	0	0	0	0	0		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.734063	0.48939	.	.	ENSG00000160013	ENST00000291294	T	0.43688	0.94	4.75	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	0.148074	0.46145	N	0.000314	T	0.30417	0.0764	L	0.33710	1.025	0.35614	D	0.808912	B	0.24533	0.105	B	0.21546	0.035	T	0.32295	-0.9912	10	0.39692	T	0.17	-13.5	9.867	0.41150	0.0:0.898:0.0:0.102	rs2229131	212	P43119	PI2R_HUMAN	H	212	ENSP00000291294:R212H	ENSP00000291294:R212H	R	-	2	0	PTGIR	51818688	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.343000	0.44001	1.184000	0.42957	0.563000	0.77884	CGC	C|1.000;|0.000		0.701	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1			T	47126848	C	T	47126848	3	4	144	1	0	0	0	0	1	0	0	0	12781	768	27	1	533	1	PTGIR	19	47126848	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	3541631	47126848	12002135	55	12905											
ZNF347	84671	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	53643573	53643575	+	In_Frame_Del	DEL	TGA	TGA	-																															tctctccactatgaattctgTgatggcttgcaaggtttgaa																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr19:53643573_53643575delTGA	ENST00000334197.7	-	5	2574_2576	c.2506_2508delTCA	c.(2506-2508)tcadel	p.S836del	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_In_Frame_Del_p.S837del|ZNF347_ENST00000452676.2_In_Frame_Del_p.S837del	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	836					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		ATGAATTCTGTGATGGCTTGCAA	0.394																																					p.837_837del	Melanoma(64;205 1597 17324 45721)	.											.	ZNF347-90	0			c.2509_2511del						.																																			SO:0001651	inframe_deletion	84671	exon5			.	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2506_2508delTCA	19.37:g.53643573_53643575delTGA	ENSP00000334146:p.Ser836del	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	170	46	NM_001172675	0	0	0	0	0	B3KU77|B9EG59|G5E9N4|Q8TCN1	In_Frame_Del	DEL	ENST00000334197.7	37	CCDS33097.1																																																																																			.		0.394	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		-	53643575	TGA	-	53643573	7	5	144	1	0	1	0	1	0	0	0	0	17893	1683	59	0	15	0	ZNF347	19	53643573	In_Frame_Del	DEL	TGA	TCGA-J7-6720-01A-11D-2136-08	6516725	53643573	5485410	56	12906											
TGM6	343641	broad.mit.edu;bcgsc.ca	37	chr20	2384361	2384361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggcacgaggatgagagcCgggagcgtgtatactcaaac	11	7	15	8	3	1	1	1	1	0	1	1	5	1	3	1	3	4	2	1	3	3	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr20:2384361C>T	ENST00000202625.2	+	9	1289	c.1228C>T	c.(1228-1230)Cgg>Tgg	p.R410W	TGM6_ENST00000381423.1_Missense_Mutation_p.R410W	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	410					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	GGATGAGAGCCGGGAGCGTGT	0.582																																					p.R410W													.	TGM6-94	0			c.C1228T						.						117	102	107					20																	2384361		2203	4300	6503	SO:0001583	missense	343641	exon9			GAGAGCCGGGAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"Transglutaminases"	16255	protein-coding gene	gene with protein product	"spinocerebellar ataxia 35"	613900	"transglutaminase 3-like"	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1228C>T	20.37:g.2384361C>T	ENSP00000202625:p.Arg410Trp	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	124	6	NM_198994	0	0	0	0	0	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	37	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.707089	0.48412	.	.	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.74526	-0.85;-0.85	4.84	2.82	0.32997	.	0.503753	0.20705	N	0.087198	T	0.76905	0.4053	L	0.49126	1.545	0.25334	N	0.989007	D;D	0.71674	0.998;0.997	P;P	0.56916	0.809;0.628	T	0.67933	-0.5542	10	0.66056	D	0.02	-13.0667	10.1216	0.42623	0.3642:0.6358:0.0:0.0	.	410;410	O95932-2;O95932	.;TGM3L_HUMAN	W	410	ENSP00000202625:R410W;ENSP00000370831:R410W	ENSP00000202625:R410W	R	+	1	2	TGM6	2332361	0.001000	0.12720	0.983000	0.44433	0.361000	0.29550	0.639000	0.24690	0.711000	0.32018	0.549000	0.68633	CGG	.		0.582	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		T	2384361	C	T	2384361	3	4	144	1	0	0	0	0	1	0	0	0	15866	643	23	1	1262	1	TGM6	20	2384361	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		2384361	60641159	57	12907											
COL6A2	1292	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47542788	47542788	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacatgtgttccctgtcacaGggaggccgaggcgactttgg	8	9	14	10	2	1	0	1	0	0	0	2	3	2	1	2	4	1	1	2	4	1	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr21:47542788G>A	ENST00000300527.4	+	21	1712		c.e21-1		COL6A2_ENST00000397763.1_Splice_Site|COL6A2_ENST00000409416.1_Splice_Site|COL6A2_ENST00000357838.4_Splice_Site|COL6A2_ENST00000310645.5_Splice_Site	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CCCTGTCACAGGGAGGCCGAG	0.547																																					.		.											.	COL6A2-515	0			c.1609-1G>A						.						86	75	79					21																	47542788		2203	4298	6501	SO:0001630	splice_region_variant	1292	exon21			GTCACAGGGAGGC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"Collagens"	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.1609-1G>A	21.37:g.47542788G>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	93	31	NM_058175	0	0	0	1	1	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Splice_Site	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073193	0.36566	.	.	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	.	.	.	3.54	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9711	0.80019	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL6A2	46367216	1.000000	0.71417	0.991000	0.47740	0.337000	0.28794	7.524000	0.81866	1.909000	0.55274	0.491000	0.48974	.	.		0.547	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		Intron	A	47542788	G	A	47542788	5	1	144	1	0	0	0	0	0	0	1	0	3706	1014	35	2	1686	2	COL6A2	21	47542788	Splice_Site	SNP	G	TCGA-J7-6720-01A-11D-2136-08		47542788	587107	58	12908											
PCNT	5116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	47809247	47809247	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctttctcatgagcccagaAagtgtgcgggagtgtgagca	10	9	14	8	1	1	3	1	2	1	1	2	4	1	4	1	1	4	2	1	1	1	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr21:47809247A>T	ENST00000359568.5	+	19	3848	c.3741A>T	c.(3739-3741)gaA>gaT	p.E1247D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1247					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TGAGCCCAGAAAGTGTGCGGG	0.587																																					p.E1247D		.											.	PCNT-141	0			c.A3741T						.						95	94	94					21																	47809247		2203	4300	6503	SO:0001583	missense	5116	exon19			CCCAGAAAGTGTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"kendrin", "Seckel syndrome 4"	605925	"pericentrin 2 (kendrin)"	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.3741A>T	21.37:g.47809247A>T	ENSP00000352572:p.Glu1247Asp	Somatic	208	0		WXS	Illumina HiSeq	Phase_I	197	71	NM_006031	0	0	1	1	0	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.761428	0.49468	.	.	ENSG00000160299	ENST00000359568	T	0.02032	4.49	5.44	-10.3	0.00346	.	.	.	.	.	T	0.07279	0.0184	M	0.70275	2.135	0.09310	N	1	B;D	0.76494	0.193;0.999	B;D	0.78314	0.08;0.991	T	0.02269	-1.1185	9	0.66056	D	0.02	.	8.9466	0.35762	0.6619:0.2264:0.1118:0.0	.	1129;1247	O95613-2;O95613	.;PCNT_HUMAN	D	1247	ENSP00000352572:E1247D	ENSP00000352572:E1247D	E	+	3	2	PCNT	46633675	0.000000	0.05858	0.000000	0.03702	0.169000	0.22640	-1.857000	0.01660	-1.903000	0.01093	-0.456000	0.05471	GAA	.		0.587	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47809247	A	T	47809247	3	4	144	1	0	0	0	0	1	0	0	0	11616	11	1	5	3815	5	PCNT	21	47809247	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	266459	47809247	320648	59	12909											
OSBP2	23762	hgsc.bcm.edu	37	chr22	31137192	31137192	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccgtggaaccatcaaccTgtccaccgcgcacattgaca	10	7	9	15	3	1	1	1	1	0	0	2	2	2	2	5	1	3	1	5	1	2	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr22:31137192T>A	ENST00000332585.6	+	2	793	c.689T>A	c.(688-690)cTg>cAg	p.L230Q	OSBP2_ENST00000403222.3_Missense_Mutation_p.L65Q|OSBP2_ENST00000382310.3_Missense_Mutation_p.L230Q|OSBP2_ENST00000407373.1_Missense_Mutation_p.L57Q|OSBP2_ENST00000446658.2_Missense_Mutation_p.L230Q	NM_001282739.1|NM_001282740.1|NM_001282741.1|NM_001282742.1|NM_030758.3	NP_001269668.1|NP_001269669.1|NP_001269670.1|NP_001269671.1|NP_110385.1	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2	230	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				lipid transport (GO:0006869)	membrane (GO:0016020)	cholesterol binding (GO:0015485)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						ACCATCAACCTGTCCACCGCG	0.567																																					p.L230Q		.											.	OSBP2-114	0			c.T689A						.						51	53	53					22																	31137192		2028	4163	6191	SO:0001583	missense	23762	exon2			TCAACCTGTCCAC		CCDS43002.1, CCDS63448.1, CCDS63449.1, CCDS63450.1, CCDS63451.1	22q12.2	2013-01-10			ENSG00000184792	ENSG00000184792		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8504	protein-coding gene	gene with protein product		606729		OSBPL1		10591208, 11278871, 11802775	Standard	NM_001282738		Approved	KIAA1664, ORP-4, ORP4	uc003aiy.1	Q969R2	OTTHUMG00000151153	ENST00000332585.6:c.689T>A	22.37:g.31137192T>A	ENSP00000332576:p.Leu230Gln	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_030758	0	0	0	0	0	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Missense_Mutation	SNP	ENST00000332585.6	37	CCDS43002.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.662468	0.88251	.	.	ENSG00000184792	ENST00000438716;ENST00000403222;ENST00000407373;ENST00000332585;ENST00000382310;ENST00000446658	T;T;D;D;D	0.84146	-0.42;-0.41;-1.81;-1.81;-1.81	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000005	D	0.95943	0.8679	H	0.99516	4.605	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;1.0	D;D;D;D;D	0.81914	0.989;0.98;0.98;0.995;0.995	D	0.97875	1.0288	10	0.87932	D	0	-22.7415	15.0591	0.71939	0.0:0.0:0.0:1.0	.	230;65;57;230;230	B4DFA8;B4DKE4;Q6ZN50;Q0VF99;Q969R2	.;.;.;.;OSBP2_HUMAN	Q	65;65;57;230;230;230	ENSP00000384213:L65Q;ENSP00000385237:L57Q;ENSP00000332576:L230Q;ENSP00000371747:L230Q;ENSP00000392080:L230Q	ENSP00000332576:L230Q	L	+	2	0	OSBP2	29467192	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.040000	0.89188	2.040000	0.60383	0.379000	0.24179	CTG	.		0.567	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758		A	31137192	T	A	31137192	3	1	144	1	0	0	0	0	1	0	0	0	11300	1580	55	5	695	5	OSBP2	22	31137192	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08		31137192	20167374	60	12910											
TTLL12	23170	broad.mit.edu;bcgsc.ca	37	chr22	43579135	43579149	+	In_Frame_Del	DEL	CACTTCCCCAGCGTC	CACTTCCCCAGCGTC	-																															tccacttgcatgatcccaaaCacttccccagcgtcgaaaac																								rs146360108|rs571455195		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	CACTTCCCCAGCGTC	CACTTCCCCAGCGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr22:43579135_43579149delCACTTCCCCAGCGTC	ENST00000216129.6	-	2	247_261	c.184_198delGACGCTGGGGAAGTG	c.(184-198)gacgctggggaagtgdel	p.DAGEV62del		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	62					cellular protein modification process (GO:0006464)			p.D62D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				TGATCCCAAACACTTCCCCAGCGTCGAAAACCTGG	0.637																																					p.62_66del													.	TTLL12-90	1	Substitution - coding silent(1)	large_intestine(1)	c.184_198del						.																																			SO:0001651	inframe_deletion	23170	exon2			CCCAAACACTTCC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"Tubulin tyrosine ligase-like family"	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.184_198delGACGCTGGGGAAGTG	22.37:g.43579135_43579149delCACTTCCCCAGCGTC	ENSP00000216129:p.Asp62_Val66del	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	204	16	NM_015140	0	0	0	0	0	Q20WK5|Q9UGU3	In_Frame_Del	DEL	ENST00000216129.6	37	CCDS14047.1																																																																																			.		0.637	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140		-	43579149	CACTTCCCCAGCGTC	-	43579135	7	5	144	1	0	1	0	1	0	0	0	0	16758	465	17	0	1788	0	TTLL12	22	43579135	In_Frame_Del	DEL	CACTTCCCCAGCGTC	TCGA-J7-6720-01A-11D-2136-08	12441943	43579135	7725431	61	12911											
PRDM16	63976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	3334451	3334451	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcagccatgaaggcggaCtcgggcagctccctgcagcc	7	7	13	14	2	0	1	0	1	0	0	2	2	1	2	3	3	5	4	3	3	1	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:3334451C>T	ENST00000270722.5	+	11	2800	c.2751C>T	c.(2749-2751)gaC>gaT	p.D917D	PRDM16_ENST00000378398.3_Silent_p.D917D|PRDM16_ENST00000378391.2_Silent_p.D917D|PRDM16_ENST00000511072.1_Silent_p.D918D|PRDM16_ENST00000514189.1_Silent_p.D917D|PRDM16_ENST00000441472.2_Silent_p.D916D|PRDM16_ENST00000442529.2_Silent_p.D916D|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	917	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		TGAAGGCGGACTCGGGCAGCT	0.602			T	EVI1	"MDS, AML"																																p.D917D		.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16-660	0			c.C2751T						.						97	108	104					1																	3334451		2039	4191	6230	SO:0001819	synonymous_variant	63976	exon11			GGCGGACTCGGGC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.2751C>T	1.37:g.3334451C>T		Somatic	178	0		WXS	Illumina HiSeq	Phase_I	311	80	NM_022114	0	0	0	0	0	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			.		0.602	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		T	3334451	C	T	3334451	2	4	145	1	0	0	0	0	0	0	0	1	12486	564	20	2		2	PRDM16	1	3334451	Silent	SNP	C	TCGA-J7-8537-01A-11D-2396-08		3334451	245916170	1	12912											
PRAMEF16	654348	hgsc.bcm.edu	37	chr1	13497726	13497726	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaatcttgagccccttggAgctctgctagagaaagttgc	10	10	10	11	0	2	2	0	1	2	1	2	4	2	3	3	1	4	3	3	1	3	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:13497726A>C	ENST00000376121.3	+	3	1053	c.1023A>C	c.(1021-1023)ggA>ggC	p.G341G		NM_001045480.1	NP_001038945.1	Q5VWM1	PRA16_HUMAN	PRAME family member 16	341					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)							Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGCCCCTTGGAGCTCTGCTAG	0.527																																					p.G341G		.											.	.	0			c.A1023C						.						75	55	62					1																	13497726		1972	3482	5454	SO:0001819	synonymous_variant	654348	exon3			CCTTGGAGCTCTG			1p36.21	2013-01-17			ENSG00000204488			"-"	25767	protein-coding gene	gene with protein product							Standard	NM_001045480		Approved	OTTHUMG00000002933	uc001aux.3	Q5VWM1	OTTHUMG00000002933	ENST00000376121.3:c.1023A>C	1.37:g.13497726A>C		Somatic	48	1		WXS	Illumina HiSeq	Phase_I	48	4	NM_001045480	0	0	0	0	0		Silent	SNP	ENST00000376121.3	37	CCDS41259.1																																																																																			.		0.527	PRAMEF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008178.1	NM_001045480		C	13497726	A	C	13497726	2	2	145	1	0	0	0	0	0	0	0	1	12460	291	11	5		5	PRAMEF16	1	13497726	Silent	SNP	A	TCGA-J7-8537-01A-11D-2396-08	10163275	13497726	235752895	2	12913											
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19176018	19176018	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtggtccaggagagtgaaGttgaccttccagatctcctc	8	11	12	10	0	1	4	0	2	1	2	5	5	3	4	4	3	0	1	4	3	1	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:19176018G>T	ENST00000375371.3	-	4	1305	c.1284C>A	c.(1282-1284)aaC>aaA	p.N428K	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	428					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GGAGAGTGAAGTTGACCTTCC	0.552																																					p.N428K		.											.	TAS1R2-93	0			c.C1284A						.						64	59	61					1																	19176018		2203	4300	6503	SO:0001583	missense	80834	exon4			AGTGAAGTTGACC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	14905	protein-coding gene	gene with protein product		606226	"G protein-coupled receptor 71"	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1284C>A	1.37:g.19176018G>T	ENSP00000364520:p.Asn428Lys	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	121	30	NM_152232	0	0	0	0	0	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.127587	0.56721	.	.	ENSG00000179002	ENST00000375371	D	0.86497	-2.13	5.16	2.1	0.27182	Extracellular ligand-binding receptor (1);	0.344112	0.24479	N	0.038174	D	0.87908	0.6296	L	0.48935	1.535	0.28764	N	0.900721	D	0.71674	0.998	D	0.66979	0.948	T	0.79815	-0.1644	10	0.52906	T	0.07	.	5.3671	0.16119	0.194:0.1632:0.6428:0.0	.	428	Q8TE23	TS1R2_HUMAN	K	428	ENSP00000364520:N428K	ENSP00000364520:N428K	N	-	3	2	TAS1R2	19048605	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	0.985000	0.29578	0.518000	0.28383	0.561000	0.74099	AAC	.		0.552	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19176018	G	T	19176018	3	4	145	1	0	0	0	0	1	0	0	0	15595	1020	36	4	1247	4	TAS1R2	1	19176018	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	5678292	19176018	230074603	3	12914											
ALDH4A1	8659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19201049	19201049	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccggcagcattcctcagcAcctttgtggcctcctgcacg	5	10	10	16	2	1	0	1	0	0	0	3	0	3	0	5	2	4	4	5	2	0	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:19201049A>G	ENST00000375341.3	-	14	1744	c.1487T>C	c.(1486-1488)gTg>gCg	p.V496A	ALDH4A1_ENST00000290597.5_Missense_Mutation_p.V496A|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.V445A|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.V436A	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	496					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ATTCCTCAGCACCTTTGTGGC	0.617																																					p.V496A		.											.	ALDH4A1-226	0			c.T1487C						.						183	149	160					1																	19201049		2203	4300	6503	SO:0001583	missense	8659	exon14			CTCAGCACCTTTG	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"Aldehyde dehydrogenases"	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.1487T>C	1.37:g.19201049A>G	ENSP00000364490:p.Val496Ala	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	290	67	NM_003748	0	0	3	102	99	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	.	.	.	.	.	.	.	.	.	.	A	0.577	-0.838870	0.02692	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309	T;T;T;T	0.74632	-0.86;-0.86;1.68;-0.86	5.36	4.24	0.50183	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.644592	0.17853	N	0.159761	T	0.42471	0.1204	N	0.02697	-0.525	0.23113	N	0.998271	B	0.02656	0.0	B	0.06405	0.002	T	0.33574	-0.9863	10	0.07644	T	0.81	-25.7928	5.0242	0.14376	0.7201:0.1868:0.0931:0.0	.	496	P30038	AL4A1_HUMAN	A	496;496;445;436	ENSP00000290597:V496A;ENSP00000364490:V496A;ENSP00000446071:V445A;ENSP00000442988:V436A	ENSP00000290597:V496A	V	-	2	0	ALDH4A1	19073636	0.387000	0.25188	0.907000	0.35723	0.356000	0.29392	3.436000	0.52856	2.025000	0.59659	0.459000	0.35465	GTG	.		0.617	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			G	19201049	A	G	19201049	3	3	145	1	0	0	0	0	1	0	0	0	501	159	6	3	212	3	ALDH4A1	1	19201049	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	25031	19201049	230049572	4	12915											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27106580	27106580	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaacaccttggttacacTcgccaacatctcggggcagt	11	8	10	12	2	1	0	0	0	1	0	3	1	1	1	2	4	3	2	2	4	4	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:27106580T>C	ENST00000324856.7	+	20	6562	c.6191T>C	c.(6190-6192)cTc>cCc	p.L2064P	ARID1A_ENST00000374152.2_Missense_Mutation_p.L1681P|ARID1A_ENST00000457599.2_Missense_Mutation_p.L1847P|ARID1A_ENST00000540690.1_Missense_Mutation_p.L392P	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2064					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TTGGTTACACTCGCCAACATC	0.557			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.L2064P		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.T6191C						.						136	137	137					1																	27106580		2203	4300	6503	SO:0001583	missense	8289	exon20			TTACACTCGCCAA	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.6191T>C	1.37:g.27106580T>C	ENSP00000320485:p.Leu2064Pro	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	238	58	NM_006015	0	0	10	17	7	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793741	0.70452	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.71698	0.88;0.88;0.88;-0.59	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.84447	0.5474	M	0.81239	2.535	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	D	0.86848	0.2021	10	0.87932	D	0	-10.1896	15.3414	0.74300	0.0:0.0:0.0:1.0	.	1681;2064;1847	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	P	2064;1847;1681;392	ENSP00000320485:L2064P;ENSP00000387636:L1847P;ENSP00000363267:L1681P;ENSP00000442437:L392P	ENSP00000320485:L2064P	L	+	2	0	ARID1A	26979167	1.000000	0.71417	0.585000	0.28666	0.975000	0.68041	7.676000	0.84012	2.273000	0.75805	0.482000	0.46254	CTC	.		0.557	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27106580	T	C	27106580	3	2	145	1	0	0	0	0	1	0	0	0	913	1551	54	3	6269	3	ARID1A	1	27106580	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	7905531	27106580	222144041	5	12916											
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36642065	36642065	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgccagccccctgacgccGtgcagcgtcacccgaagcgt	6	5	11	19	6	1	1	1	1	0	0	2	2	2	1	6	0	4	1	6	0	1	0	rs139644057	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:36642065G>A	ENST00000373151.2	+	7	1332	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	MAP7D1_ENST00000474796.1_3'UTR|MAP7D1_ENST00000373150.4_Silent_p.P340P|MAP7D1_ENST00000373148.4_5'Flank|MAP7D1_ENST00000316156.4_Silent_p.P335P	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	372					microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CCCTGACGCCGTGCAGCGTCA	0.801													G|||	234	0.0467252	0.0053	0.0533	5008	,	,		5421	0.1736		0.007	False		,,,				2504	0.0082				p.P372P		.											.	MAP7D1-138	0			c.G1116A						.	G		20,2340		0,20,1160	2	2	2		1116	-1.3	0.7	1	dbSNP_134	2	9,4939		0,9,2465	no	coding-synonymous	MAP7D1	NM_018067.3		0,29,3625	AA,AG,GG		0.1819,0.8475,0.3968		372/842	36642065	29,7279	1180	2474	3654	SO:0001819	synonymous_variant	55700	exon7			GACGCCGTGCAGC	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"proline arginine rich coiled coil 1", "arginine/proline rich coiled-coil 1"	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.1116G>A	1.37:g.36642065G>A		Somatic	3	1		WXS	Illumina HiSeq	Phase_I	9	5	NM_018067	0	0	1	2	1	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.952;A|0.048		0.801	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		A	36642065	G	A	36642065	2	1	145	1	0	0	0	0	0	0	0	1	9292	1132	40	1		1	MAP7D1	1	36642065	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	9535485	36642065	212608556	6	12917											
HIVEP3	59269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	42047804	42047804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggcaagtgtctggctgcGctggggccattggaactcct	5	10	15	11	1	1	0	0	0	1	0	2	1	2	1	2	5	2	3	2	5	2	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:42047804G>A	ENST00000372583.1	-	4	3550	c.2665C>T	c.(2665-2667)Cgc>Tgc	p.R889C	HIVEP3_ENST00000429157.2_Missense_Mutation_p.R889C|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R889C|HIVEP3_ENST00000247584.5_Missense_Mutation_p.R889C|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	889	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R889C(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GTCTGGCTGCGCTGGGGCCAT	0.597																																					p.R889C		.											.	HIVEP3-157	1	Substitution - Missense(1)	large_intestine(1)	c.C2665T						.						54	63	60					1																	42047804		2203	4300	6503	SO:0001583	missense	59269	exon4			GGCTGCGCTGGGG	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.2665C>T	1.37:g.42047804G>A	ENSP00000361664:p.Arg889Cys	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	299	70	NM_024503	0	0	1	1	0	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679130	0.68042	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	4.95	4.95	0.65309	.	0.000000	0.53938	D	0.000060	T	0.73466	0.3590	M	0.76727	2.345	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.76107	-0.3080	10	0.87932	D	0	2.8066	11.1037	0.48190	0.0:0.0:0.6936:0.3063	.	889;889	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	C	889	ENSP00000361665:R889C;ENSP00000361664:R889C;ENSP00000247584:R889C;ENSP00000410828:R889C	ENSP00000247584:R889C	R	-	1	0	HIVEP3	41820391	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.841000	0.69409	2.562000	0.86427	0.462000	0.41574	CGC	.		0.597	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	42047804	G	A	42047804	3	1	145	1	0	0	0	0	1	0	0	0	7209	1087	38	1	4579	1	HIVEP3	1	42047804	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	5405739	42047804	207202817	7	12918											
YBX1	4904	hgsc.bcm.edu	37	chr1	43166460	43166460	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttcattgcaggggccctcCtcgccaaagacagcctagag	9	7	11	14	2	1	2	1	0	0	2	3	2	2	2	4	2	2	2	4	2	2	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:43166460C>T	ENST00000321358.7	+	7	888	c.749C>T	c.(748-750)cCt>cTt	p.P250L		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	250					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGGGGCCCTCCTCGCCAAAGA	0.498																																					p.P250L		.											.	YBX1-95	0			c.C749T						.						28	25	26					1																	43166460		2203	4300	6503	SO:0001583	missense	4904	exon7			GCCCTCCTCGCCA	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.749C>T	1.37:g.43166460C>T	ENSP00000361626:p.Pro250Leu	Somatic	30	1		WXS	Illumina HiSeq	Phase_I	82	6	NM_004559	0	0	2	2	0	P16990|P16991|Q14972|Q15325|Q5FVF0	Missense_Mutation	SNP	ENST00000321358.7	37	CCDS470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.49|17.49	3.403460|3.403460	0.62288|0.62288	.|.	.|.	ENSG00000065978|ENSG00000065978	ENST00000318612;ENST00000436427|ENST00000321358	.|T	.|0.36340	.|1.26	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|0.148105	.|0.64402	.|D	.|0.000006	T|T	0.41050|0.41050	0.1142|0.1142	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	.|B	.|0.29862	.|0.259	.|B	.|0.30179	.|0.112	T|T	0.36817|0.36817	-0.9732|-0.9732	6|10	0.30078|0.56958	T|D	0.28|0.05	-2.6639|-2.6639	16.6288|16.6288	0.85011|0.85011	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|250	.|P67809	.|YBOX1_HUMAN	F|L	241;300|250	.|ENSP00000361626:P250L	ENSP00000361621:L241F|ENSP00000361626:P250L	L|P	+|+	1|2	0|0	YBX1|YBX1	42939047|42939047	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.152000|7.152000	0.77419|0.77419	2.501000|2.501000	0.84356|0.84356	0.552000|0.552000	0.68991|0.68991	CTC|CCT	.		0.498	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559		T	43166460	C	T	43166460	3	4	145	1	0	0	0	0	1	0	0	0	17502	681	24	2	775	2	YBX1	1	43166460	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	1118656	43166460	206084161	8	12919											
IPP	3652	broad.mit.edu	37	chr1	46184897	46184898	+	Frame_Shift_Del	DEL	AC	AC	-																															aaagcatagatagccccataAcacacacacactcctaagcc																								rs144663569		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:46184897_46184898delAC	ENST00000396478.3	-	6	1265_1266	c.1163_1164delGT	c.(1162-1164)tgtfs	p.C388fs		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	388						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TAGCCCCATAACACACACACAC	0.347																																					p.388_388del													.	IPP-91	0			c.1163_1164del						.																																			SO:0001589	frameshift_variant	3652	exon6			CCCATAACACACA	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1163_1164delGT	1.37:g.46184907_46184908delAC	ENSP00000379739:p.Cys388fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	118	7	NM_001145349	0	0	0	0	0	A2A6V4|D3DQ11|Q8N5C3	Frame_Shift_Del	DEL	ENST00000396478.3	37	CCDS30702.1																																																																																			.		0.347	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		-	46184898	AC	-	46184897	7	5	145	1	0	1	0	1	0	0	0	0	7821	41	2	0	708	0	IPP	1	46184897	Frame_Shift_Del	DEL	AC	TCGA-J7-8537-01A-11D-2396-08	3018437	46184897	203065724	9	12920											
FNBP1L	54874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94009756	94009756	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaacttaacagagaactacaGaaagaatcagaccaaaagta	22	5	7	7	0	1	4	1	0	0	4	1	6	1	4	1	0	4	1	1	0	9	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:94009756G>A	ENST00000271234.7	+	12	1408	c.1257G>A	c.(1255-1257)caG>caA	p.Q419Q	FNBP1L_ENST00000370256.4_Silent_p.Q414Q|FNBP1L_ENST00000260506.8_Silent_p.Q361Q|FNBP1L_ENST00000370253.2_Silent_p.Q361Q|FNBP1L_ENST00000604705.1_Silent_p.Q419Q	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	419	Interaction with CDC42.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		GAGAACTACAGAAAGAATCAG	0.373																																					p.Q419Q		.											.	FNBP1L-227	0			c.G1257A						.						71	67	68					1																	94009756		1827	4080	5907	SO:0001819	synonymous_variant	54874	exon12			ACTACAGAAAGAA		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.1257G>A	1.37:g.94009756G>A		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	59	17	NM_001164473	0	0	20	39	19	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Silent	SNP	ENST00000271234.7	37	CCDS53343.1																																																																																			.		0.373	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		A	94009756	G	A	94009756	2	1	145	1	0	0	0	0	0	0	0	1	5985	933	33	2		2	FNBP1L	1	94009756	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	47824859	94009756	155240865	10	12921											
KCNC4	3749	bcgsc.ca	37	chr1	110754159	110754159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtctcctcctaccgcgggcGcaagtcggggaacaagcctc	7	7	12	15	4	1	0	0	0	1	0	5	1	2	1	4	3	3	1	4	3	4	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:110754159G>A	ENST00000369787.3	+	1	65	c.38G>A	c.(37-39)cGc>cAc	p.R13H	KCNC4_ENST00000413138.3_Missense_Mutation_p.R13H|KCNC4_ENST00000438661.2_Missense_Mutation_p.R13H|KCNC4-AS1_ENST00000455967.1_RNA	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	13	Inactivation gate.				potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		TACCGCGGGCGCAAGTCGGGG	0.637																																					p.R13H													.	KCNC4-154	0			c.G38A						.						42	44	43					1																	110754159		2202	4300	6502	SO:0001583	missense	3749	exon1			GCGGGCGCAAGTC	BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6236	protein-coding gene	gene with protein product		176265	"chromosome 1 open reading frame 30"	C1orf30		1920536, 1740329, 16382104	Standard	NM_004978		Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000369787.3:c.38G>A	1.37:g.110754159G>A	ENSP00000358802:p.Arg13His	Somatic	45	0		WXS	Illumina HiSeq	Phase_1	108	5	NM_001039574	0	0	7	7	0	Q3MIM4|Q5TBI6	Missense_Mutation	SNP	ENST00000369787.3	37	CCDS821.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.441799	0.83993	.	.	ENSG00000116396	ENST00000369787;ENST00000413138;ENST00000438661	D;D;D	0.97710	-4.5;-4.49;-4.5	3.53	3.53	0.40419	Potassium channel, voltage dependent, Kv3, inactivation domain (1);	.	.	.	.	D	0.95661	0.8589	N	0.08118	0	0.58432	D	0.999995	D;D;D	0.76494	0.988;0.986;0.999	P;B;D	0.80764	0.611;0.36;0.994	D	0.97118	0.9809	9	0.62326	D	0.03	.	14.8461	0.70261	0.0:0.0:1.0:0.0	.	13;13;13	Q03721;Q03721-3;Q03721-2	KCNC4_HUMAN;.;.	H	13	ENSP00000358802:R13H;ENSP00000388029:R13H;ENSP00000393655:R13H	ENSP00000358802:R13H	R	+	2	0	KCNC4	110555682	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.313000	0.78978	1.812000	0.52913	0.462000	0.41574	CGC	.		0.637	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		A	110754159	G	A	110754159	3	1	145	1	0	0	0	0	1	0	0	0	8038	1087	38	1	40	1	KCNC4	1	110754159	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	16744403	110754159	138496462	11	12922											
FLG	2312	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	152277075	152277075	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgaatggtgtcctgaccCtcttgggacgctgagtgcct	6	10	12	13	2	1	2	0	2	1	0	2	4	2	3	4	2	1	1	4	2	1	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:152277075C>A	ENST00000368799.1	-	3	10322	c.10287G>T	c.(10285-10287)gaG>gaT	p.E3429D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3429	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCTGACCCTCTTGGGACG	0.612									Ichthyosis																												p.E3429D		.											.	FLG-106	0			c.G10287T						.						245	252	250					1																	152277075		2203	4299	6502	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCCTCTTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"EF-hand domain containing"	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10287G>T	1.37:g.152277075C>A	ENSP00000357789:p.Glu3429Asp	Somatic	584	1		WXS	Illumina HiSeq	Phase_I	1349	247	NM_002016	0	0	2	2	0	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.296547	0.40594	.	.	ENSG00000143631	ENST00000368799	T	0.01705	4.68	4.17	-5.64	0.02466	.	.	.	.	.	T	0.00754	0.0025	L	0.41824	1.3	0.09310	N	1	P	0.44478	0.836	P	0.54499	0.754	T	0.31943	-0.9925	9	0.20046	T	0.44	.	0.6472	0.00820	0.3782:0.2562:0.1242:0.2414	.	3429	P20930	FILA_HUMAN	D	3429	ENSP00000357789:E3429D	ENSP00000357789:E3429D	E	-	3	2	FLG	150543699	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-6.083000	0.00082	-1.572000	0.01661	0.454000	0.30748	GAG	.		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152277075	C	A	152277075	3	1	145	1	0	0	0	0	1	0	0	0	5941	680	24	4	1902	4	FLG	1	152277075	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	41522916	152277075	96973546	12	12923											
CEP350	9857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	180047678	180047678	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattccagaagaattaggcAgccctgctgttgaatatgta	12	11	9	9	0	0	3	0	1	0	2	1	3	1	3	3	1	2	4	3	1	6	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:180047678A>T	ENST00000367607.3	+	29	6266	c.5848A>T	c.(5848-5850)Agc>Tgc	p.S1950C		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1950					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AGAATTAGGCAGCCCTGCTGT	0.433																																					p.S1950C		.											.	CEP350-26	0			c.A5848T						.						65	63	63					1																	180047678		2203	4300	6503	SO:0001583	missense	9857	exon29			TTAGGCAGCCCTG	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.5848A>T	1.37:g.180047678A>T	ENSP00000356579:p.Ser1950Cys	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	55	10	NM_014810	0	0	2	2	0	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.0|21.0	4.087658|4.087658	0.76642|0.76642	.|.	.|.	ENSG00000135837|ENSG00000135837	ENST00000429851|ENST00000367607	.|T	.|0.57907	.|0.37	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	.|0.000000	.|0.53938	.|D	.|0.000045	T|T	0.70254|0.70254	0.3203|0.3203	M|M	0.71581|0.71581	2.175|2.175	0.49299|0.49299	D|D	0.999774|0.999774	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.79784	.|0.993;0.988	T|T	0.71573|0.71573	-0.4552|-0.4552	5|9	.|.	.|.	.|.	.|.	14.1282|14.1282	0.65235|0.65235	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1950;1950	.|E7EU22;Q5VT06	.|.;CE350_HUMAN	L|C	124|1950	.|ENSP00000356579:S1950C	.|.	Q|S	+|+	2|1	0|0	CEP350|CEP350	178314301|178314301	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.777000|0.777000	0.43975|0.43975	4.336000|4.336000	0.59304|0.59304	2.140000|2.140000	0.66376|0.66376	0.482000|0.482000	0.46254|0.46254	CAG|AGC	.		0.433	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180047678	A	T	180047678	3	4	145	1	0	0	0	0	1	0	0	0	3260	188	7	5	5958	5	CEP350	1	180047678	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	27770603	180047678	69202943	13	12924											
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	237617770	237617770	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgtaagcctaagtctgcagGatctcattggctacttccac	9	11	8	13	1	2	0	1	0	2	0	4	1	3	1	3	2	3	3	3	2	3	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:237617770G>T	ENST00000366574.2	+	15	1689	c.1372G>T	c.(1372-1374)Gat>Tat	p.D458Y	RYR2_ENST00000542537.1_Missense_Mutation_p.D442Y|RYR2_ENST00000360064.6_Missense_Mutation_p.D456Y	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	458					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AAGTCTGCAGGATCTCATTGG	0.463																																					p.D458Y		.											.	RYR2-158	0			c.G1372T						.						84	82	82					1																	237617770		1919	4125	6044	SO:0001583	missense	6262	exon15			CTGCAGGATCTCA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"Ion channels / Ryanodine receptors", "EF-hand domain containing"	10484	protein-coding gene	gene with protein product		180902	"arrhythmogenic right ventricular dysplasia 2"	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1372G>T	1.37:g.237617770G>T	ENSP00000355533:p.Asp458Tyr	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	104	22	NM_001035	0	0	0	0	0	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403612	0.62288	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91180	-2.8;-2.8;-2.8	5.8	5.8	0.92144	Intracellular calcium-release channel (1);	0.000000	0.64402	U	0.000006	D	0.96131	0.8739	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.96166	0.9119	10	0.87932	D	0	.	20.0679	0.97707	0.0:0.0:1.0:0.0	.	458	Q92736	RYR2_HUMAN	Y	458;456;442	ENSP00000355533:D458Y;ENSP00000353174:D456Y;ENSP00000443798:D442Y	ENSP00000353174:D456Y	D	+	1	0	RYR2	235684393	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	9.804000	0.99143	2.747000	0.94245	0.551000	0.68910	GAT	.		0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237617770	G	T	237617770	3	4	145	1	0	0	0	0	1	0	0	0	13801	1174	41	4	1430	4	RYR2	1	237617770	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	57570092	237617770	11632851	14	12925											
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224864	248224864	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catctatagcctgaggaacaAggaggtgatgggggccctga	11	7	15	8	0	1	3	0	3	1	0	1	5	1	5	2	5	2	0	2	5	4	2	rs543066146		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:248224864A>G	ENST00000359959.3	+	1	881	c.881A>G	c.(880-882)aAg>aGg	p.K294R	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CTGAGGAACAAGGAGGTGATG	0.502													a|||	1	0.000199681	0	0	5008	,	,		18589	0.001		0	False		,,,				2504	0				p.K294R		.											.	OR2L3-68	0			c.A881G						.						56	57	57					1																	248224864		2203	4300	6503	SO:0001583	missense	391192	exon1			GGAACAAGGAGGT	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"GPCR / Class A : Olfactory receptors"	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.881A>G	1.37:g.248224864A>G	ENSP00000353044:p.Lys294Arg	Somatic	121	2		WXS	Illumina HiSeq	Phase_I	251	16	NM_001004687	0	0	0	0	0	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	A	9.463	1.093601	0.20471	.	.	ENSG00000198128	ENST00000359959	T	0.41065	1.01	2.01	-0.867	0.10655	.	.	.	.	.	T	0.36054	0.0953	M	0.63169	1.94	0.23762	N	0.996914	B	0.21821	0.061	B	0.23852	0.049	T	0.32348	-0.9910	9	0.37606	T	0.19	.	6.329	0.21259	0.7597:0.0:0.2403:0.0	.	294	Q8NG85	OR2L3_HUMAN	R	294	ENSP00000353044:K294R	ENSP00000353044:K294R	K	+	2	0	OR2L3	246291487	0.000000	0.05858	0.908000	0.35775	0.606000	0.37113	0.414000	0.21164	-0.373000	0.07979	-0.475000	0.04921	AAG	.		0.502	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		G	248224864	A	G	248224864	3	3	145	1	0	0	0	0	1	0	0	0	11034	72	3	3	883	3	OR2L3	1	248224864	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	10607094	248224864	1025757	15	12926											
GEN1	348654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	17962008	17962008	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaattccaagttaaattcggGgatttcccctgatcctacat	11	13	7	10	1	0	1	0	1	0	0	4	3	3	2	4	2	1	1	4	2	5	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:17962008G>A	ENST00000381254.2	+	14	1743	c.1529G>A	c.(1528-1530)gGg>gAg	p.G510E	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Missense_Mutation_p.G510E	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	510					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)					TTAAATTCGGGGATTTCCCCT	0.373								Homologous recombination																													p.G510E		.											.	GEN1-359	0			c.G1529A						.						82	80	80					2																	17962008		2203	4300	6503	SO:0001583	missense	348654	exon14			ATTCGGGGATTTC	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.1529G>A	2.37:g.17962008G>A	ENSP00000370653:p.Gly510Glu	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	98	15	NM_182625	0	0	0	0	0	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	37	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.178672	0.00308	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000528873;ENST00000536097	T;T;T	0.38560	1.96;1.96;1.13	5.46	1.86	0.25419	.	0.276329	0.30742	N	0.008968	T	0.11196	0.0273	N	0.01048	-1.04	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.36939	-0.9727	10	0.02654	T	1	-9.6119	7.6912	0.28569	0.7505:0.0:0.2495:0.0	.	510	Q17RS7	GEN_HUMAN	E	510;510;281;147	ENSP00000318977:G510E;ENSP00000370653:G510E;ENSP00000431542:G281E	ENSP00000318977:G510E	G	+	2	0	GEN1	17825489	0.204000	0.23447	0.429000	0.26710	0.003000	0.03518	1.257000	0.32932	0.473000	0.27368	-0.469000	0.05056	GGG	.		0.373	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		A	17962008	G	A	17962008	3	1	145	1	0	0	0	0	1	0	0	0	6355	1232	43	2	1579	2	GEN1	2	17962008	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08		17962008	225237365	16	12927											
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	21238283	21238283	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaaactgtggagccataaGctgtagcagatgagtccatt	12	10	12	7	0	0	2	0	1	0	1	1	4	1	4	2	2	4	3	2	2	3	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:21238283G>A	ENST00000233242.1	-	22	3594	c.3467C>T	c.(3466-3468)gCt>gTt	p.A1156V		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1156					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAGCCATAAGCTGTAGCAGA	0.507																																					p.A1156V		.											.	APOB-175	0			c.C3467T						.						140	121	128					2																	21238283		2203	4300	6503	SO:0001583	missense	338	exon22			CCATAAGCTGTAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3467C>T	2.37:g.21238283G>A	ENSP00000233242:p.Ala1156Val	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	201	35	NM_000384	0	0	0	0	0	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830038	0.50845	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00686	5.85	5.49	5.49	0.81192	.	0.100022	0.44483	D	0.000457	T	0.01870	0.0059	M	0.67953	2.075	0.80722	D	1	D	0.58620	0.983	P	0.53313	0.723	T	0.63216	-0.6687	10	0.06099	T	0.92	.	13.2457	0.60022	0.0756:0.0:0.9244:0.0	.	1156	P04114	APOB_HUMAN	V	1156	ENSP00000233242:A1156V	ENSP00000233242:A1156V	A	-	2	0	APOB	21091788	0.822000	0.29219	0.991000	0.47740	0.903000	0.53119	1.269000	0.33074	2.767000	0.95098	0.655000	0.94253	GCT	.		0.507	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21238283	G	A	21238283	3	1	145	1	0	0	0	0	1	0	0	0	785	971	34	2	10256	2	APOB	2	21238283	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	3276275	21238283	221961090	17	12928											
RNF103	7844	hgsc.bcm.edu	37	chr2	86832538	86832538	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acccagcctcttctcctgcaAtatctacaagagaggaaact	13	9	6	13	0	3	1	0	0	3	1	4	3	3	2	3	1	4	1	3	1	5	3	rs373749370		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:86832538A>C	ENST00000237455.4	-	4	1454	c.486T>G	c.(484-486)taT>taG	p.Y162*	CHMP3_ENST00000439940.2_Intron|RNF103-CHMP3_ENST00000604011.1_Intron|AC015971.2_ENST00000426549.1_RNA|RNF103_ENST00000477307.1_5'UTR|AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000439077.1_RNA	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	162					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						TTCTCCTGCAATATCTACAAG	0.408																																					p.Y162X		.											.	RNF103-226	0			c.T486G						.						69	67	68					2																	86832538		2203	4300	6503	SO:0001587	stop_gained	7844	exon4			CCTGCAATATCTA	D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.486T>G	2.37:g.86832538A>C	ENSP00000237455:p.Tyr162*	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	111	8	NM_005667	0	0	0	0	0	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Nonsense_Mutation	SNP	ENST00000237455.4	37	CCDS33237.1	.	.	.	.	.	.	.	.	.	.	A	44	11.057122	0.99509	.	.	ENSG00000239305	ENST00000237455	.	.	.	5.64	2.81	0.32909	.	0.059364	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5564	10.5449	0.45054	0.2165:0.0:0.7835:0.0	.	.	.	.	X	162	.	ENSP00000237455:Y162X	Y	-	3	2	RNF103	86686049	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	1.451000	0.35145	0.714000	0.32081	-0.468000	0.05107	TAT	.		0.408	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		C	86832538	A	C	86832538	4	2	145	1	0	0	0	0	0	1	0	0	13455	108	4	5	1575	5	RNF103	2	86832538	Nonsense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	65594255	86832538	156366835	18	12929											
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141607702	141607702	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagtttctaacccagttccGttaataaaagctcgtttaat	13	14	5	9	2	1	0	0	0	1	0	3	0	2	0	2	0	2	5	2	0	5	7	rs368565366		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:141607702G>A	ENST00000389484.3	-	29	5879	c.4908C>T	c.(4906-4908)aaC>aaT	p.N1636N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1636					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACCCAGTTCCGTTAATAAAAG	0.318										TSP Lung(27;0.18)																											p.N1636N	Colon(99;50 2074 2507 20106)	.											.	LRP1B-311	0			c.C4908T						.	A		1,4405	4.2+/-10.8	0,1,2202	162	169	167		4908	0.2	1	2		167	0,8600		0,0,4300	no	coding-synonymous	LRP1B	NM_018557.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1636/4600	141607702	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon29			AGTTCCGTTAATA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4908C>T	2.37:g.141607702G>A		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	123	25	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			.		0.318	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141607702	G	A	141607702	2	1	145	1	0	0	0	0	0	0	0	1	8980	1136	40	1		1	LRP1B	2	141607702	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	54775164	141607702	101591671	19	12930											
ORC2L	4999	bcgsc.ca	37	chr2	201791481	201791490	+	Splice_Site	DEL	TGAAACTTAC	TGAAACTTAC	-																															gtttttccctttaacattttTgaaacttactgatttcacac																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TGAAACTTAC	TGAAACTTAC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:201791481_201791490delTGAAACTTAC	ENST00000234296.2	-	12	1300		c.e12+1		RN7SL694P_ENST00000584245.1_RNA	NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2						DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						TTAACATTTTTGAAACTTACTGATTTCACA	0.367																																					.													.	ORC2-209	0			.						.																																			SO:0001630	splice_region_variant	4999	.			CATTTTTGAAACT		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1050+1GTAAGTTTCA>-	2.37:g.201791481_201791490delTGAAACTTAC		Somatic	124	0		WXS	Illumina HiSeq	Phase_1	132	6	.	0	0	0	0	0	Q13204|Q53TX5	Splice_Site	DEL	ENST00000234296.2	37	CCDS2334.1																																																																																			.		0.367	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190	Intron	-	201791490	TGAAACTTAC	-	201791481	8	5	145	1	0	1	0	1	0	0	1	0	11288	1827	63	0		0	ORC2L	2	201791481	Splice_Site	DEL	TGAAACTTAC	TCGA-J7-8537-01A-11D-2396-08	60183779	201791481	41407892	20	12931											
IGSF10	285313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151161388	151161388	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgagacaactgtttggtTtgcaagaatccaggtaactg	11	13	10	7	0	1	2	0	1	1	2	2	3	2	2	1	2	3	4	1	2	4	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr3:151161388T>A	ENST00000282466.3	-	5	5346	c.5347A>T	c.(5347-5349)Aac>Tac	p.N1783Y	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1783	Ig-like C2-type 4.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTGTTTGGTTTGCAAGAATC	0.498																																					p.N1783Y		.											.	IGSF10-102	0			c.A5347T						.						125	112	116					3																	151161388		2203	4300	6503	SO:0001583	missense	285313	exon5			TTTGGTTTGCAAG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5347A>T	3.37:g.151161388T>A	ENSP00000282466:p.Asn1783Tyr	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	170	45	NM_178822	0	0	0	0	0	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.546893	0.65198	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.80909	-1.43	5.25	5.25	0.73442	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000074	D	0.89522	0.6739	M	0.85099	2.735	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.90304	0.4332	9	.	.	.	.	11.1386	0.48390	0.0:0.0747:0.0:0.9253	.	1783	Q6WRI0	IGS10_HUMAN	Y	1783;410	ENSP00000282466:N1783Y	.	N	-	1	0	IGSF10	152644078	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.209000	0.58493	1.989000	0.58080	0.477000	0.44152	AAC	.		0.498	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151161388	T	A	151161388	3	1	145	1	0	0	0	0	1	0	0	0	7618	1841	64	5	2580	5	IGSF10	3	151161388	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08		151161388	46861042	21	12932											
GOLIM4	27333	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	167742778	167742778	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actttgtttttgctcttcatTttcatctggcaaattttctt	6	23	4	8	0	5	0	2	0	3	0	5	0	5	0	0	1	1	3	0	1	1	9			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr3:167742778T>C	ENST00000470487.1	-	13	2418	c.1729A>G	c.(1729-1731)Aat>Gat	p.N577D	GOLIM4_ENST00000309027.4_Missense_Mutation_p.N549D	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	577	Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TGCTCTTCATTTTCATCTGGC	0.408																																					p.N577D		.											.	GOLIM4-291	0			c.A1729G						.						220	192	202					3																	167742778		2203	4300	6503	SO:0001583	missense	27333	exon13			CTTCATTTTCATC	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"golgi phosphoprotein 4"	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1729A>G	3.37:g.167742778T>C	ENSP00000417354:p.Asn577Asp	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	194	36	NM_014498	0	0	52	88	36		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.649660	0.67358	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	6.0	6.0	0.97389	.	0.224151	0.53938	D	0.000046	T	0.55577	0.1929	M	0.69823	2.125	0.35647	D	0.811481	P;P	0.40875	0.731;0.731	B;B	0.36845	0.234;0.234	T	0.63937	-0.6524	9	0.15499	T	0.54	-6.4985	16.56	0.84537	0.0:0.0:0.0:1.0	.	549;577	F8W785;O00461	.;GOLI4_HUMAN	D	577;549	.	ENSP00000309893:N549D	N	-	1	0	GOLIM4	169225472	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.450000	0.60041	2.313000	0.78055	0.454000	0.30748	AAT	.		0.408	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			C	167742778	T	C	167742778	3	2	145	1	0	0	0	0	1	0	0	0	6586	1841	64	3	377	3	GOLIM4	3	167742778	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	16581390	167742778	30279652	22	12933											
BST1	683	hgsc.bcm.edu	37	chr4	15704874	15704874	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcgcgcgcgcggtggcgcgGggagggcaccagcgcacact	5	2	20	14	8	0	0	0	0	0	0	0	1	0	1	1	6	1	2	1	6	0	0	rs2302468	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr4:15704874G>C	ENST00000265016.4	+	1	302	c.107G>C	c.(106-108)gGg>gCg	p.G36A	BST1_ENST00000382346.3_Missense_Mutation_p.G36A	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	36				G -> A (in Ref. 1; BAA04885). {ECO:0000305}.	humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						cggtggcgcggggAGGGCACC	0.736													G|||	381	0.0760783	0.0212	0.0389	5008	,	,		9714	0.2103		0.008	False		,,,				2504	0.1084				p.G36A		.											.	BST1-90	0			c.G107C						.	G	ALA/GLY	23,3787		0,23,1882	3	4	4		107	3.4	1	4	dbSNP_100	4	19,7693		0,19,3837	no	missense	BST1	NM_004334.2	60	0,42,5719	CC,CG,GG		0.2464,0.6037,0.3645	possibly-damaging	36/319	15704874	42,11480	1905	3856	5761	SO:0001583	missense	683	exon1			GGCGCGGGGAGGG	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"CD molecules"	1118	protein-coding gene	gene with protein product	"NAD(+) nucleosidase", "ADP-ribosyl cyclase 2"	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.107G>C	4.37:g.15704874G>C	ENSP00000265016:p.Gly36Ala	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	10	6	NM_004334	0	0	0	0	0	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	141	0.06456043956043957	13	0.026422764227642278	10	0.027624309392265192	112	0.1958041958041958	6	0.0079155672823219	G	14.40	2.524166	0.44866	0.006037	0.002464	ENSG00000109743	ENST00000265016;ENST00000382346	T;T	0.17370	2.28;2.28	3.39	3.39	0.38822	.	0.510528	0.20699	N	0.087320	T	0.00039	0.0001	M	0.63843	1.955	0.36618	P	0.12441999999999998	D	0.76494	0.999	D	0.80764	0.994	T	0.04005	-1.0985	9	0.62326	D	0.03	-9.3919	10.4016	0.44233	0.0:0.0:1.0:0.0	rs2302468	36	Q10588	BST1_HUMAN	A	36	ENSP00000265016:G36A;ENSP00000371783:G36A	ENSP00000265016:G36A	G	+	2	0	BST1	15313972	0.859000	0.29813	0.955000	0.39395	0.020000	0.10135	2.992000	0.49417	1.879000	0.54435	0.462000	0.41574	GGG	G|0.084;C|0.916		0.736	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334		C	15704874	G	C	15704874	3	2	145	1	0	0	0	0	1	0	0	0	1536	1232	43	4	109	4	BST1	4	15704874	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08		15704874	175449402	23	12934											
CENPE	1062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	104117119	104117119	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatgaattgccctgggtatAactcccaaatgatcttctga	11	13	7	10	0	3	3	1	3	2	0	4	3	4	3	2	1	2	1	2	1	4	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr4:104117119A>C	ENST00000265148.3	-	4	404	c.315T>G	c.(313-315)gtT>gtG	p.V105V	CENPE_ENST00000380026.3_Silent_p.V105V	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	105	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CCCTGGGTATAACTCCCAAAT	0.358																																					p.V105V		.											.	CENPE-277	0			c.T315G						.						106	101	103					4																	104117119		2202	4300	6502	SO:0001819	synonymous_variant	1062	exon4			GGGTATAACTCCC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"Kinesins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1856	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 61"	117143	"centromere protein E (312kD)"			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.315T>G	4.37:g.104117119A>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	49	10	NM_001813	0	0	0	0	0	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			.		0.358	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104117119	A	C	104117119	2	2	145	1	0	0	0	0	0	0	0	1	3236	349	13	5		5	CENPE	4	104117119	Silent	SNP	A	TCGA-J7-8537-01A-11D-2396-08	88412245	104117119	87037157	24	12935											
MAML3	55534	broad.mit.edu	37	chr4	140810639	140810641	+	In_Frame_Del	DEL	GCT	GCT	-																															ctggagctgtggaggtggcgGctgctgctgctgctgctgct																								rs372496848		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr4:140810639_140810641delGCT	ENST00000509479.2	-	2	2805_2807	c.1949_1951delAGC	c.(1948-1953)cagccg>ccg	p.Q650del	MAML3_ENST00000327122.5_In_Frame_Del_p.Q494del|MAML3_ENST00000398940.1_In_Frame_Del_p.Q178del	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					GGAGGTGGCGgctgctgctgctg	0.586																																					p.646_647del													.	MAML3-455	0			c.1937_1939del						.																																			SO:0001651	inframe_deletion	55534	exon3			GTGGCGGCTGCTG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1949_1951delAGC	4.37:g.140810648_140810650delGCT	ENSP00000421180:p.Gln650del	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	173	11	NM_018717	0	0	0	0	0		In_Frame_Del	DEL	ENST00000509479.2	37	CCDS54805.1																																																																																			.		0.586	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			-	140810641	GCT	-	140810639	7	5	145	1	0	1	0	1	0	0	0	0	9232	1203	42	0	1481	0	MAML3	4	140810639	In_Frame_Del	DEL	GCT	TCGA-J7-8537-01A-11D-2396-08	36693520	140810639	50343637	25	12936											
FAT1	2195	broad.mit.edu	37	chr4	187539365	187539365	+	Frame_Shift_Del	DEL	G	G	-																															cttggatactaacatctacaGaagccaccatctcatggtca																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr4:187539365delG	ENST00000441802.2	-	10	8584	c.8375delC	c.(8374-8376)tctfs	p.S2792fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2792	Cadherin 25. {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						AACATCTACAGAAGCCACCAT	0.443										HNSCC(5;0.00058)																											p.S2792fs	Colon(197;1040 2055 4143 4984 49344)												.	FAT1-34	0			c.8375delC						.						197	193	194					4																	187539365		1966	4163	6129	SO:0001589	frameshift_variant	2195	exon10			TCTACAGAAGCCA	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.8375delC	4.37:g.187539365delG	ENSP00000406229:p.Ser2792fs	Somatic	314	0		WXS	Illumina HiSeq	Phase_I	371	9	NM_005245	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187539365	G	-	187539365	7	5	145	1	0	1	0	1	0	0	0	0	5708	942	33	0	5463	0	FAT1	4	187539365	Frame_Shift_Del	DEL	G	TCGA-J7-8537-01A-11D-2396-08	46728726	187539365	3614911	26	12937											
TPPP	11076	hgsc.bcm.edu	37	chr5	678087	678087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccgattccagcgacagcCtcttggctgcccggtccttc	4	10	9	18	3	1	0	0	0	1	0	5	2	4	0	6	2	3	1	6	2	0	3	rs570878136	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:678087C>T	ENST00000360578.5	-	2	210	c.89G>A	c.(88-90)aGg>aAg	p.R30K	CTD-2589H19.6_ENST00000607068.1_RNA	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	30	Mediates interaction with LIMK1.				microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.R30K(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CAGCGACAGCCTCTTGGCTGC	0.677													C|||	15	0.00299521	0.0061	0	5008	,	,		16462	0.0069		0	False		,,,				2504	0				p.R30K		.											.	TPPP-90	1	Substitution - Missense(1)	prostate(1)	c.G89A						.						14	17	16					5																	678087		2199	4295	6494	SO:0001583	missense	11076	exon2			GACAGCCTCTTGG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"brain specific protein p25 alpha"	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.89G>A	5.37:g.678087C>T	ENSP00000353785:p.Arg30Lys	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	73	5	NM_007030	0	0	3	3	0		Missense_Mutation	SNP	ENST00000360578.5	37	CCDS3856.1	.	.	.	.	.	.	.	.	.	.	c	14.67	2.605282	0.46423	.	.	ENSG00000171368	ENST00000360578	T	0.45276	0.9	5.23	5.23	0.72850	.	0.149935	0.44902	D	0.000407	T	0.29588	0.0738	L	0.29908	0.895	0.44635	D	0.997618	B	0.15141	0.012	B	0.13407	0.009	T	0.11867	-1.0570	10	0.05436	T	0.98	-54.1656	16.5545	0.84482	0.0:1.0:0.0:0.0	.	30	O94811	TPPP_HUMAN	K	30	ENSP00000353785:R30K	ENSP00000353785:R30K	R	-	2	0	TPPP	731087	1.000000	0.71417	0.998000	0.56505	0.405000	0.30901	4.081000	0.57627	2.437000	0.82529	0.491000	0.48974	AGG	.		0.677	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030		T	678087	C	T	678087	3	4	145	1	0	0	0	0	1	0	0	0	16446	681	24	2	582	2	TPPP	5	678087	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		678087	180237173	27	12938											
IL6ST	3572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	55247844	55247844	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacaggaagttggtcccactCtaagacagcttcgtttttcc	10	12	8	11	1	1	1	0	0	1	1	4	2	3	2	2	2	2	3	2	2	3	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:55247844C>G	ENST00000381298.2	-	13	1924	c.1612G>C	c.(1612-1614)Gag>Cag	p.E538Q	IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.E538Q|IL6ST_ENST00000502326.3_Missense_Mutation_p.E538Q|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381294.3_Missense_Mutation_p.E477Q|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000381293.2_Intron	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	538	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TGGTCCCACTCTAAGACAGCT	0.348			O		hepatocellular ca																																p.E538Q		.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST-290	0			c.G1612C						.						75	64	68					5																	55247844		2203	4300	6503	SO:0001583	missense	3572	exon13			CCCACTCTAAGAC	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6021	protein-coding gene	gene with protein product	"gp130, oncostatin M receptor"	600694	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1612G>C	5.37:g.55247844C>G	ENSP00000370698:p.Glu538Gln	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	64	6	NM_002184	0	0	25	44	19	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.897415	0.33535	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.57273	0.41;0.41;0.41	5.83	5.83	0.93111	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.455228	0.26089	N	0.026407	T	0.22085	0.0532	N	0.01352	-0.895	0.80722	D	1	B;B;B	0.18610	0.008;0.029;0.008	B;B;B	0.21151	0.011;0.033;0.011	T	0.29181	-1.0020	10	0.13853	T	0.58	.	9.4221	0.38557	0.0:0.7741:0.1461:0.0799	.	538;477;538	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	Q	538;538;477	ENSP00000370698:E538Q;ENSP00000338799:E538Q;ENSP00000370694:E477Q	ENSP00000338799:E538Q	E	-	1	0	IL6ST	55283601	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.907000	0.28531	2.770000	0.95276	0.655000	0.94253	GAG	.		0.348	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		G	55247844	C	G	55247844	3	3	145	1	0	0	0	0	1	0	0	0	7724	922	32	4	1164	4	IL6ST	5	55247844	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	54569757	55247844	125667416	28	12939											
PCDHGA1	56114	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	140712677	140712677	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaccattttctcaggtaaActtttgtgatgaatgtatca	12	15	8	6	0	2	2	2	2	1	0	3	3	2	3	1	2	2	2	1	2	5	6			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:140712677A>G	ENST00000517417.1	+	1	2421				PCDHGA1_ENST00000378105.3_Missense_Mutation_p.N809S	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCAGGTAAACTTTTGTGAT	0.388																																					p.N809S		.											.	PCDHGA1-137	0			c.A2426G						.						50	53	52					5																	140712677		2203	4300	6503	SO:0001627	intron_variant	56114	exon1			AGGTAAACTTTTG	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"Cadherins / Protocadherins : Clustered"	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2421+5A>G	5.37:g.140712677A>G		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	173	34	NM_031993	0	0	4	4	0	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	.	2.192	-0.385092	0.04966	.	.	ENSG00000204956	ENST00000378105	T	0.47869	0.83	4.15	0.129	0.14739	.	0.924660	0.08888	U	0.879068	T	0.21427	0.0516	N	0.08118	0	0.09310	N	0.999996	B	0.13145	0.007	B	0.09377	0.004	T	0.20174	-1.0283	9	.	.	.	.	2.5439	0.04732	0.462:0.0:0.194:0.344	.	809	Q9Y5H4-2	.	S	809	ENSP00000367345:N809S	.	N	+	2	0	PCDHGA1	140692861	0.001000	0.12720	0.351000	0.25721	0.671000	0.39405	-0.689000	0.05144	-0.058000	0.13177	-0.468000	0.05107	AAC	.		0.388	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140712677	A	G	140712677	1	3	145	0	1	0	0	0	0	0	0	0	11576	43	2	3		3	PCDHGA1	5	140712677	Intron	SNP	A	TCGA-J7-8537-01A-11D-2396-08	85464833	140712677	40202583	29	12940											
CSF1R	1436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	149433707	149433707	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcagcaggtcaggtgctcActagagctctcctcctccag	7	9	10	15	1	3	1	2	0	1	1	7	1	5	1	3	2	3	4	3	2	1	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:149433707A>T	ENST00000286301.3	-	22	3135	c.2844T>A	c.(2842-2844)agT>agA	p.S948R		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	948					cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	TCAGGTGCTCACTAGAGCTCT	0.602																																					p.S948R		.											.	CSF1R-2640	0			c.T2844A						.						38	35	36					5																	149433707		2203	4300	6503	SO:0001583	missense	1436	exon22			GTGCTCACTAGAG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.2844T>A	5.37:g.149433707A>T	ENSP00000286301:p.Ser948Arg	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	67	14	NM_005211	0	0	71	71	0	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	A	9.983	1.228611	0.22542	.	.	ENSG00000182578	ENST00000286301	T	0.30182	1.54	5.25	-4.77	0.03219	.	0.092077	0.47852	D	0.000212	T	0.23133	0.0559	L	0.50333	1.59	0.54753	D	0.999989	D	0.54397	0.966	B	0.44315	0.446	T	0.11792	-1.0573	10	0.51188	T	0.08	.	7.9653	0.30095	0.2777:0.0:0.6023:0.12	.	948	P07333	CSF1R_HUMAN	R	948	ENSP00000286301:S948R	ENSP00000286301:S948R	S	-	3	2	CSF1R	149413900	0.078000	0.21339	0.618000	0.29105	0.009000	0.06853	-0.609000	0.05635	-0.866000	0.04068	-0.490000	0.04691	AGT	.		0.602	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		T	149433707	A	T	149433707	3	4	145	1	0	0	0	0	1	0	0	0	3938	156	6	5	78	5	CSF1R	5	149433707	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	8721030	149433707	31481553	30	12941											
ZNF184	7738	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	27420221	27420223	+	In_Frame_Del	DEL	TGG	TGG	-																															ttgagtaaggtgtgtgctccTggtgaaggttttatcacatt																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:27420221_27420223delTGG	ENST00000211936.6	-	6	1399_1401	c.1115_1117delCCA	c.(1114-1119)accagg>agg	p.T372del	ZNF184_ENST00000377419.1_In_Frame_Del_p.T372del	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TGTGTGCTCCTGGTGAAGGTTTT	0.379																																					p.372_373del		.											.	ZNF184-91	0			c.1115_1117del						.																																			SO:0001651	inframe_deletion	7738	exon6			.	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1115_1117delCCA	6.37:g.27420221_27420223delTGG	ENSP00000211936:p.Thr372del	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	103	20	NM_007149	0	0	0	0	0	B2R715|O60792|Q8TBA9	In_Frame_Del	DEL	ENST00000211936.6	37	CCDS4624.1																																																																																			.		0.379	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		-	27420223	TGG	-	27420221	7	5	145	1	0	1	0	1	0	0	0	0	17783	1579	55	0	1142	0	ZNF184	6	27420221	In_Frame_Del	DEL	TGG	TCGA-J7-8537-01A-11D-2396-08		27420221	143694846	31	12942											
HLA-G	3135	ucsc.edu	37	chr6	29797253	29797253	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gactatgaggccaccctgagGtgctgggccctgggcttcta	6	9	14	12	0	1	2	0	2	1	0	1	3	1	2	3	4	1	2	3	4	2	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:29797253G>A	ENST00000360323.6	+	4	702	c.678G>A	c.(676-678)agG>agA	p.R226R	HLA-G_ENST00000376818.3_Silent_p.R134R|HLA-G_ENST00000376828.2_Silent_p.R231R|HLA-G_ENST00000428701.1_Silent_p.R226R|HLA-G_ENST00000376815.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	226	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)	p.R226S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CCACCCTGAGGTGCTGGGCCC	0.592																																					p.R226R													.	HLA-G-517	1	Substitution - Missense(1)	lung(1)	c.G678A						.						92	96	94					6																	29797253		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			CCTGAGGTGCTGG		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.678G>A	6.37:g.29797253G>A		Somatic	229	0		WXS	Illumina HiSeq		542	2	NM_002127	1	2	7214	7221	4		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			.		0.592	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		A	29797253	G	A	29797253	2	1	145	1	0	0	0	0	0	0	0	1	7233	1252	44	2		2	HLA-G	6	29797253	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	2377032	29797253	141317814	32	12943											
VARS	7407	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	31762754	31762754	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgggccccccaggcctgctgGccacagcagctgggccacag	6	4	14	17	0	0	0	0	0	0	0	0	0	0	0	6	4	3	3	6	4	0	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:31762754G>T	ENST00000375663.3	-	2	681	c.241C>A	c.(241-243)Cca>Aca	p.P81T	LSM2_ENST00000491421.1_5'Flank|VARS_ENST00000444930.2_Intron	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	81					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	AGGCCTGCTGGCCACAGCAGC	0.711																																					p.P81T		.											.	VARS-93	0			c.C241A						.						13	19	16					6																	31762754		1478	2637	4115	SO:0001583	missense	7407	exon2			CTGCTGGCCACAG	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	12651	protein-coding gene	gene with protein product	"valine tRNA ligase 1, cytoplasmic"	192150	"valyl-tRNA synthetase 2"	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.241C>A	6.37:g.31762754G>T	ENSP00000364815:p.Pro81Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	86	15	NM_006295	0	0	14	21	7	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505254	0.44558	.	.	ENSG00000204394	ENST00000375663;ENST00000440048	T;T	0.06849	3.25;3.25	5.24	5.24	0.73138	Glutathione S-transferase, N-terminal (1);	0.142308	0.47455	D	0.000231	T	0.04003	0.0112	N	0.24115	0.695	0.80722	D	1	P	0.44139	0.827	P	0.45276	0.475	T	0.29366	-1.0014	10	0.87932	D	0	-2.2071	9.8609	0.41114	0.0931:0.0:0.9069:0.0	.	81	P26640	SYVC_HUMAN	T	81	ENSP00000364815:P81T;ENSP00000413925:P81T	ENSP00000364815:P81T	P	-	1	0	VARS	31870733	1.000000	0.71417	0.999000	0.59377	0.392000	0.30506	2.707000	0.47143	2.461000	0.83175	0.462000	0.41574	CCA	.		0.711	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		T	31762754	G	T	31762754	3	4	145	1	0	0	0	0	1	0	0	0	17156	1203	42	4	3669	4	VARS	6	31762754	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	1965501	31762754	139352313	33	12944											
AARS2	57505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	44272835	44272835	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtagttgtacttggggctgTcgtcagttgggggcactcct	5	13	15	8	1	1	0	1	0	0	0	3	0	2	0	1	4	1	6	1	4	2	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:44272835T>A	ENST00000244571.4	-	11	1537	c.1535A>T	c.(1534-1536)gAc>gTc	p.D512V	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTTGGGGCTGTCGTCAGTTGG	0.607											OREG0017473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D512V		.											.	AARS2-91	0			c.A1535T						.						128	121	123					6																	44272835		2203	4300	6503	SO:0001583	missense	57505	exon11			GGGCTGTCGTCAG	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	21022	protein-coding gene	gene with protein product	"alanine tRNA ligase 2, mitochondrial"	612035	"alanyl-tRNA synthetase like", "alanyl-tRNA synthetase 2, mitochondrial (putative)"	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.1535A>T	6.37:g.44272835T>A	ENSP00000244571:p.Asp512Val	Somatic	179	0	922	WXS	Illumina HiSeq	Phase_I	370	34	NM_020745	0	0	14	17	3		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.385639	0.42308	.	.	ENSG00000124608	ENST00000244571	T	0.72725	-0.68	5.01	3.83	0.44106	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.096640	0.64402	D	0.000001	T	0.77478	0.4136	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79962	-0.1582	10	0.87932	D	0	-17.649	12.7414	0.57255	0.0:0.0715:0.0:0.9285	.	512	Q5JTZ9	SYAM_HUMAN	V	512	ENSP00000244571:D512V	ENSP00000244571:D512V	D	-	2	0	AARS2	44380813	1.000000	0.71417	0.925000	0.36789	0.052000	0.14988	5.622000	0.67750	0.272000	0.22027	-1.186000	0.01703	GAC	.		0.607	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		A	44272835	T	A	44272835	3	1	145	1	0	0	0	0	1	0	0	0	20	1667	58	5	1470	5	AARS2	6	44272835	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	12510081	44272835	126842232	34	12945											
FOXK1	221937	broad.mit.edu	37	chr7	4802068	4802068	+	Frame_Shift_Del	DEL	C	C	-																															ggagtgatcgcagctgccggCccccaggggccaggcaccgg																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr7:4802068delC	ENST00000328914.4	+	9	2175	c.2175delC	c.(2173-2175)ggcfs	p.G725fs	FOXK1_ENST00000446823.1_Frame_Shift_Del_p.G562fs	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CAGCTGCCGGCCCCCAGGGGC	0.706																																					p.G725fs													.	FOXK1-516	0			c.2175delC						.						6	8	8					7																	4802068		2034	3968	6002	SO:0001589	frameshift_variant	221937	exon9			TGCCGGCCCCCAG	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.2175delC	7.37:g.4802068delC	ENSP00000328720:p.Gly725fs	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_001037165	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000328914.4	37	CCDS34591.1																																																																																			.		0.706	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			-	4802068	C	-	4802068	7	5	145	1	0	1	0	1	0	0	0	0	6033	726	26	0	2209	0	FOXK1	7	4802068	Frame_Shift_Del	DEL	C	TCGA-J7-8537-01A-11D-2396-08		4802068	154336595	35	12946											
PUS7	54517	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	105099624	105099624	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaaacttaccagaagcaaAaactggtggtgtcttccctt	13	11	8	9	0	1	1	0	0	1	1	2	1	2	1	2	2	4	2	2	2	6	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr7:105099624A>G	ENST00000356362.2	-	15	2054	c.1840T>C	c.(1840-1842)Ttt>Ctt	p.F614L	PUS7_ENST00000469408.1_Missense_Mutation_p.F614L	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	614					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						CCAGAAGCAAAAACTGGTGGT	0.353																																					p.F614L	Colon(138;2387 3051 17860)	.											.	PUS7-90	0			c.T1840C						.						136	115	122					7																	105099624		2203	4300	6503	SO:0001583	missense	54517	exon15			AAGCAAAAACTGG	AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"pseudouridylate synthase 7 homolog (S. cerevisiae)"			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.1840T>C	7.37:g.105099624A>G	ENSP00000348722:p.Phe614Leu	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	85	16	NM_019042	0	0	0	0	0	Q75MG4|Q9NX19	Missense_Mutation	SNP	ENST00000356362.2	37	CCDS34725.1	.	.	.	.	.	.	.	.	.	.	A	10.52	1.372308	0.24857	.	.	ENSG00000091127	ENST00000356362;ENST00000544995;ENST00000469408	T;T	0.40756	1.02;1.02	5.28	5.28	0.74379	Pseudouridine synthase, catalytic domain (1);	0.171422	0.52532	N	0.000075	T	0.17831	0.0428	N	0.03608	-0.345	0.40339	D	0.979018	B;B	0.11235	0.004;0.004	B;B	0.14023	0.01;0.005	T	0.14699	-1.0463	10	0.10377	T	0.69	-1.6592	8.8965	0.35467	0.9072:0.0:0.0928:0.0	.	614;614	B3KY42;Q96PZ0	.;PUS7_HUMAN	L	614	ENSP00000348722:F614L;ENSP00000417402:F614L	ENSP00000348722:F614L	F	-	1	0	PUS7	104886860	1.000000	0.71417	0.993000	0.49108	0.860000	0.49131	5.995000	0.70631	1.995000	0.58328	0.460000	0.39030	TTT	.		0.353	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		G	105099624	A	G	105099624	3	3	145	1	0	0	0	0	1	0	0	0	12865	14	1	3	153	3	PUS7	7	105099624	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	100297556	105099624	54039039	36	12947											
RINT1	60561	hgsc.bcm.edu	37	chr7	105177143	105177143	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accttaaatctttaaagaaaCttgataaactcatagaacag	19	11	4	7	0	2	3	1	1	1	2	2	3	2	3	1	0	3	0	1	0	9	6			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr7:105177143C>A	ENST00000257700.2	+	3	451	c.220C>A	c.(220-222)Ctt>Att	p.L74I		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	74					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TTTAAAGAAACTTGATAAACT	0.323																																					p.L74I		.											.	RINT1-517	0			c.C220A						.						91	91	91					7																	105177143		2203	4300	6503	SO:0001583	missense	60561	exon3			AAGAAACTTGATA	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.220C>A	7.37:g.105177143C>A	ENSP00000257700:p.Leu74Ile	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	85	5	NM_021930	0	0	10	10	0	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	37	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804297	0.70682	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.25579	1.79	5.2	5.2	0.72013	.	0.130682	0.50627	D	0.000108	T	0.24699	0.0599	L	0.53249	1.67	0.38375	D	0.944982	B	0.26975	0.165	B	0.19391	0.025	T	0.07539	-1.0767	10	0.26408	T	0.33	-14.7993	13.9955	0.64397	0.0:0.8482:0.1518:0.0	.	74	Q6NUQ1	RINT1_HUMAN	I	74;43	ENSP00000257700:L74I	ENSP00000257700:L74I	L	+	1	0	RINT1	104964379	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.435000	0.52849	2.412000	0.81896	0.491000	0.48974	CTT	.		0.323	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		A	105177143	C	A	105177143	3	1	145	1	0	0	0	0	1	0	0	0	13408	565	20	4	230	4	RINT1	7	105177143	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	77519	105177143	53961520	37	12948											
C8orf79	57604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	12879058	12879058	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccagccttccagacactcTagtttagactttgatcacca	10	12	6	13	0	2	3	1	1	1	2	4	3	4	3	4	0	1	1	4	0	2	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr8:12879058T>C	ENST00000524591.2	+	5	1359	c.870T>C	c.(868-870)tcT>tcC	p.S290S	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	290							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						CCAGACACTCTAGTTTAGACT	0.423																																					p.S290S		.											.	KIAA1456-90	0			c.T870C						.						79	77	78					8																	12879058		1869	4097	5966	SO:0001819	synonymous_variant	57604	exon5			ACACTCTAGTTTA	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"chromosome 8 open reading frame 79"	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.870T>C	8.37:g.12879058T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	110	26	NM_020844	0	0	0	0	0	Q96AW6	Silent	SNP	ENST00000524591.2	37	CCDS47808.1																																																																																			.		0.423	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677		C	12879058	T	C	12879058	2	2	145	1	0	0	0	0	0	0	0	1	2444	1509	53	3		3	C8orf79	8	12879058	Silent	SNP	T	TCGA-J7-8537-01A-11D-2396-08		12879058	133484964	38	12949											
ST8SIA6	338596	hgsc.bcm.edu;broad.mit.edu	37	chr10	17495608	17495608	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggctccggagcgtcctcagCgctgcgggggtgccgtgggt	2	7	20	12	5	1	0	1	0	0	0	3	1	3	1	3	5	4	2	3	5	0	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr10:17495608C>T	ENST00000377602.4	-	2	224	c.150G>A	c.(148-150)gcG>gcA	p.A50A		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	50					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						GCGTCCTCAGCGCTGCGGGGG	0.706																																					p.A50A		.											.	ST8SIA6-91	0			c.G150A						.						8	10	9					10																	17495608		2170	4271	6441	SO:0001819	synonymous_variant	338596	exon2			CCTCAGCGCTGCG		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"Sialyltransferases"	23317	protein-coding gene	gene with protein product	"ST8Sia VI"	610139	"sialyltransferase 8F (alpha-2, 8-sialyltransferase)"	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.150G>A	10.37:g.17495608C>T		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	25	9	NM_001004470	0	0	0	0	0	B0YJ97|B9EH72|Q5VZH4	Silent	SNP	ENST00000377602.4	37	CCDS31158.1																																																																																			.		0.706	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		T	17495608	C	T	17495608	2	4	145	1	0	0	0	0	0	0	0	1	15268	755	27	1		1	ST8SIA6	10	17495608	Silent	SNP	C	TCGA-J7-8537-01A-11D-2396-08		17495608	118039139	39	12950											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124361509	124361509	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgcccggtttggccagggTtcaggacccattgtcctgga	7	10	13	11	1	1	0	1	0	0	0	2	2	2	2	4	5	1	2	4	5	1	3	rs547823770	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr10:124361509T>C	ENST00000338354.3	+	29	3646	c.3540T>C	c.(3538-3540)ggT>ggC	p.G1180G	DMBT1_ENST00000368956.2_Silent_p.G681G|DMBT1_ENST00000344338.3_Silent_p.G1170G|DMBT1_ENST00000368955.3_Silent_p.G1170G|DMBT1_ENST00000368909.3_Silent_p.G1180G|DMBT1_ENST00000330163.4_Silent_p.G681G|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1180	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TTGGCCAGGGTTCAGGACCCA	0.587													C|||	130	0.0259585	0.0378	0.0086	5008	,	,		10270	0.0635		0.001	False		,,,				2504	0.0092				p.G1180G	Ovarian(182;93 2026 18125 22222 38972)	.											.	DMBT1-494	0			c.T3540C						.						10	15	14					10																	124361509		507	2121	2628	SO:0001819	synonymous_variant	1755	exon29			CCAGGGTTCAGGA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.3540T>C	10.37:g.124361509T>C		Somatic	29	1		WXS	Illumina HiSeq	Phase_I	35	9	NM_007329	0	0	0	0	0	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				.		0.587	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		C	124361509	T	C	124361509	2	2	145	1	0	0	0	0	0	0	0	1	4588	1712	60	3		3	DMBT1	10	124361509	Silent	SNP	T	TCGA-J7-8537-01A-11D-2396-08	106865901	124361509	11173238	40	12951											
MKI67	4288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	129910454	129910454	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaacatatcatctgtaaaaTatcatgttgacttcggctga	13	13	8	7	1	3	2	2	2	1	0	4	3	3	3	0	2	1	3	0	2	5	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr10:129910454T>G	ENST00000368654.3	-	9	2287	c.1912A>C	c.(1912-1914)Att>Ctt	p.I638L	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.I278L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	638					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				ATCTGTAAAATATCATGTTGA	0.398																																					p.I638L		.											.	MKI67-519	0			c.A1912C						.						96	89	91					10																	129910454		2203	4300	6503	SO:0001583	missense	4288	exon9			GTAAAATATCATG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1912A>C	10.37:g.129910454T>G	ENSP00000357643:p.Ile638Leu	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	175	39	NM_002417	0	0	4	6	2	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.815996	0.50527	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01369	5.0;4.97	4.47	2.03	0.26663	.	0.382408	0.22081	N	0.064888	T	0.01765	0.0056	M	0.63428	1.95	0.09310	N	1	B;B;B	0.32573	0.376;0.376;0.259	B;B;B	0.36418	0.224;0.224;0.112	T	0.42137	-0.9469	10	0.35671	T	0.21	.	0.8729	0.01218	0.167:0.161:0.1731:0.4989	.	637;278;638	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	638;278;637;213	ENSP00000357643:I638L;ENSP00000357642:I278L	ENSP00000357641:I213L	I	-	1	0	MKI67	129800444	0.000000	0.05858	0.002000	0.10522	0.491000	0.33493	-0.129000	0.10515	0.725000	0.32318	0.533000	0.62120	ATT	.		0.398	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129910454	T	G	129910454	3	3	145	1	0	0	0	0	1	0	0	0	9623	1406	49	5	7886	5	MKI67	10	129910454	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	5548945	129910454	5624293	41	12952											
TSG101	7251	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	18541141	18541142	+	Frame_Shift_Del	DEL	TG	TG	-																															ttcacgtacagttaggtctcTgtatttgtactgaaaagcaa																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr11:18541141_18541142delTG	ENST00000251968.3	-	2	466_467	c.51_52delCA	c.(49-54)tacagafs	p.YR17fs	TSG101_ENST00000536719.1_Frame_Shift_Del_p.YR17fs|TSG101_ENST00000357193.3_Intron	NM_006292.3	NP_006283.1	Q99816	TS101_HUMAN	tumor susceptibility 101	17	UEV. {ECO:0000255|PROSITE- ProRule:PRU00652}.				cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	22						GTTAGGTCTCTGTATTTGTACT	0.307																																					p.17_18del	GBM(99;1348 1396 8611 26475 50572)	.											.	TSG101-90	0			c.51_52del						.																																			SO:0001589	frameshift_variant	7251	exon2			.	U82130	CCDS7842.1	11p15	2013-08-22	2013-08-22		ENSG00000074319	ENSG00000074319			15971	protein-coding gene	gene with protein product		601387	"tumor susceptibility gene 10", "tumor susceptibility gene 101"	TSG10		9019400, 9241264	Standard	NM_006292		Approved	VPS23	uc001mor.3	Q99816	OTTHUMG00000167725	ENST00000251968.3:c.51_52delCA	11.37:g.18541141_18541142delTG	ENSP00000251968:p.Tyr17fs	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	136	24	NM_006292	0	0	0	0	0	Q9BUM5	Frame_Shift_Del	DEL	ENST00000251968.3	37	CCDS7842.1																																																																																			.		0.307	TSG101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395906.1	NM_006292		-	18541142	TG	-	18541141	7	5	145	1	0	1	0	1	0	0	0	0	16649	1588	55	0	1156	0	TSG101	11	18541141	Frame_Shift_Del	DEL	TG	TCGA-J7-8537-01A-11D-2396-08		18541141	116465375	42	12953											
INCENP	3619	hgsc.bcm.edu	37	chr11	61914245	61914245	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagcagcgggagcaggagcGgcgggagcaggagcggcgcg	9	0	23	9	6	0	1	0	0	0	1	0	5	0	5	0	6	6	3	0	6	0	0	rs570082372	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr11:61914245G>A	ENST00000394818.3	+	15	2277	c.2075G>A	c.(2074-2076)cGg>cAg	p.R692Q	INCENP_ENST00000278849.4_Missense_Mutation_p.R688Q	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	692					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						gagcaggagcggcgggagcag	0.721													G|||	6	0.00119808	8e-04	0.0014	5008	,	,		11645	0.003		0	False		,,,				2504	0.001				p.R692Q		.											.	INCENP-227	0			c.G2075A						.						5	6	6					11																	61914245		1771	3489	5260	SO:0001583	missense	3619	exon15			AGGAGCGGCGGGA	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"inner centromere protein antigens (135kD, 155kD)"			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.2075G>A	11.37:g.61914245G>A	ENSP00000378295:p.Arg692Gln	Somatic	4	1		WXS	Illumina HiSeq	Phase_I	6	3	NM_001040694	0	0	1	1	0	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	G	8.011	0.757448	0.15846	.	.	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.15487	2.42;2.43	2.39	2.39	0.29439	.	0.179764	0.25894	N	0.027616	T	0.31231	0.0790	M	0.63843	1.955	0.32643	N	0.520424	D;D;D	0.64830	0.99;0.994;0.99	D;D;D	0.72982	0.953;0.979;0.953	T	0.26950	-1.0088	10	0.25106	T	0.35	.	8.5503	0.33447	0.0:0.0:1.0:0.0	.	688;688;692	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	Q	692;688	ENSP00000378295:R692Q;ENSP00000278849:R688Q	ENSP00000278849:R688Q	R	+	2	0	INCENP	61670821	1.000000	0.71417	0.995000	0.50966	0.588000	0.36517	1.743000	0.38258	1.695000	0.51148	0.064000	0.15345	CGG	.		0.721	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61914245	G	A	61914245	3	1	145	1	0	0	0	0	1	0	0	0	7754	1116	39	1	2129	1	INCENP	11	61914245	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	43373104	61914245	73092271	43	12954											
PUS7L	83448	hgsc.bcm.edu	37	chr12	44149019	44149019	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aagaaacacaaagaactaaaCctgattctataatctgtatc	19	10	4	8	0	2	3	0	1	2	2	3	3	2	3	1	0	3	1	1	0	9	5	rs148928799		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr12:44149019C>A	ENST00000416848.2	-	2	518	c.30G>T	c.(28-30)agG>agT	p.R10S	PUS7L_ENST00000431332.3_Intron|PUS7L_ENST00000553166.1_Missense_Mutation_p.R10S|PUS7L_ENST00000551923.1_Missense_Mutation_p.R10S|PUS7L_ENST00000344862.5_Missense_Mutation_p.R10S	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	10					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		AAGAACTAAACCTGATTCTAT	0.338																																					p.R10S		.											.	PUS7L-91	0			c.G30T						.						30	32	31					12																	44149019		2196	4283	6479	SO:0001583	missense	83448	exon2			ACTAAACCTGATT	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.30G>T	12.37:g.44149019C>A	ENSP00000415899:p.Arg10Ser	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	61	4	NM_001098614	0	0	0	0	0	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	.	.	.	.	.	.	.	.	.	.	C	8.447	0.852287	0.17106	.	.	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000553166;ENST00000549868	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.03	-1.34	0.09143	Pseudouridine synthase, catalytic domain (1);	0.482336	0.21493	N	0.073657	T	0.15739	0.0379	M	0.63428	1.95	0.09310	N	0.999995	B	0.23128	0.08	B	0.22601	0.04	T	0.17653	-1.0362	10	0.42905	T	0.14	-4.2765	1.7427	0.02955	0.1104:0.3295:0.217:0.343	.	10	Q9H0K6	PUS7L_HUMAN	S	10	ENSP00000415899:R10S;ENSP00000343081:R10S;ENSP00000447706:R10S;ENSP00000446865:R10S;ENSP00000449502:R10S	ENSP00000343081:R10S	R	-	3	2	PUS7L	42435286	0.005000	0.15991	0.063000	0.19743	0.732000	0.41865	-0.177000	0.09796	-0.362000	0.08113	0.561000	0.74099	AGG	C|1.000;T|0.000		0.338	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		A	44149019	C	A	44149019	3	1	145	1	0	0	0	0	1	0	0	0	12866	506	18	4	2107	4	PUS7L	12	44149019	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		44149019	89702876	44	12955											
ANAPC5	51433	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	121766167	121766168	+	Missense_Mutation	DNP	TC	TC	CA																															ttttctgtgcgatgctgataTcgatgagctctgacaggctg																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr12:121766167_121766168TC>CA	ENST00000261819.3	-	10	1376_1377	c.1255_1256GA>TG	c.(1255-1257)GAt>TGt	p.D419C	ANAPC5_ENST00000535482.1_Missense_Mutation_p.D85C|ANAPC5_ENST00000344395.4_Missense_Mutation_p.D307C|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000541887.1_Missense_Mutation_p.D406C|ANAPC5_ENST00000441917.2_Missense_Mutation_p.D307C	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	419					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GATGCTGATATCGATGAGCTCT	0.545																																					p.D419C		.											.	ANAPC5	0			c.G1255T						.																																			SO:0001583	missense	51433	exon10			TGATATCGATGAG	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.1255_1256delinsCA	12.37:g.121766167_121766168delinsCA	ENSP00000261819:p.Asp419Cys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	121	18		0	0	0	0	0	E9PFB2|Q8N4H7|Q9BQD4	Missense_Mutation	DNP	ENST00000261819.3	37	CCDS9220.1																																																																																			.		0.545	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			CA	121766168	TC	CA	121766167	3	2	145	1	0	0	0	0	1	0	0	0	605	1435	50	3	1043	3	ANAPC5	12	121766167	Missense_Mutation	DNP	TC	TCGA-J7-8537-01A-11D-2396-08	77617148	121766167	12085728	45	12956											
LATS2	26524	broad.mit.edu	37	chr13	21562482	21562483	+	In_Frame_Ins	INS	-	-	GGGGCG																															cgtccaagccctccgcagccINSggggcgggggcgggggcggg																								rs56252009|rs550642106	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr13:21562482_21562483insGGGGCG	ENST00000382592.4	-	4	1841_1842	c.1436_1437insCGCCCC	c.(1435-1437)ccg>ccCGCCCCg	p.479_479P>PAP	LATS2_ENST00000472754.1_5'Flank|LATS2_ENST00000542899.1_In_Frame_Ins_p.479_479P>PAP	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2									p.P473_A480delPAPAPAPA(2)|p.P479_A480insGR(1)		breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CCTCCGCAgccggggcgggggc	0.787														1274	0.254393	0.1566	0.3429	5008	,	,		6446	0.2133		0.338	False		,,,				2504	0.2802				p.P479delinsPAP													.	LATS2-1404	3	Deletion - In frame(2)|Insertion - In frame(1)	breast(2)|pancreas(1)	c.1437_1438insCGCCCC						.			22,194		10,2,96						-10.2	0		dbSNP_119	2	119,543		56,7,268	no	coding	LATS2	NM_014572.2		66,9,364	A1A1,A1R,RR		17.9758,10.1852,16.0592				141,737				SO:0001652	inframe_insertion	26524	exon4			CGCAGCCGGGGCG	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"LATS (large tumor suppressor, Drosophila) homolog 2", "LATS, large tumor suppressor, homolog 2 (Drosophila)"			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.1431_1436dupCGCCCC	13.37:g.21562483_21562488dupGGGGCG	ENSP00000372035:p.AlaPro479dup	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	15	4	NM_014572	0	0	0	0	0		In_Frame_Ins	INS	ENST00000382592.4	37	CCDS9294.1																																																																																			.		0.787	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			GGGGCG	21562483	-	GGGGCG	21562482	7	5	145	1	0	1	1	0	0	0	0	0	8668	639	23	0	1849	0	LATS2	13	21562482	In_Frame_Ins	INS	-	TCGA-J7-8537-01A-11D-2396-08		21562482	93607396	46	12957											
MCF2L	23263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	113741757	113741757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctccctcctacagctacaAgcagtccttaaacgtaagtg	12	9	7	13	1	0	0	0	0	0	0	3	0	3	0	3	0	6	4	3	0	6	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr13:113741757A>G	ENST00000375608.3	+	23	2730	c.2672A>G	c.(2671-2673)aAg>aGg	p.K891R	MCF2L_ENST00000375601.3_Missense_Mutation_p.K865R|MCF2L_ENST00000423482.2_Missense_Mutation_p.K859R|MCF2L_ENST00000442652.2_Missense_Mutation_p.K891R|MCF2L_ENST00000434480.2_Missense_Mutation_p.K867R|MCF2L_ENST00000421756.1_Missense_Mutation_p.K865R|MCF2L_ENST00000375604.2_Missense_Mutation_p.K918R|MCF2L_ENST00000375597.4_Missense_Mutation_p.K859R|MCF2L_ENST00000535094.2_Missense_Mutation_p.K861R|MCF2L_ENST00000397030.1_Missense_Mutation_p.K894R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	891	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				TACAGCTACAAGCAGTCCTTA	0.592																																					p.K861R		.											.	MCF2L-228	0			c.A2582G						.						45	39	41					13																	113741757		2202	4299	6501	SO:0001583	missense	23263	exon22			GCTACAAGCAGTC	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.2672A>G	13.37:g.113741757A>G	ENSP00000364758:p.Lys891Arg	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	56	12	NM_001112732	0	0	0	0	0	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.93|19.93	3.918654|3.918654	0.73098|0.73098	.|.	.|.	ENSG00000126217|ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749|ENST00000413354;ENST00000261963	T;T;T;T;T;T;T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0|.	5.08|5.08	5.08|5.08	0.68730|0.68730	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84678|0.84678	0.5525|0.5525	M|M	0.92367|0.92367	3.3|3.3	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.999;1.0|.	D;D;D;D;D|.	0.91635|.	0.998;0.998;0.998;0.996;0.999|.	D|D	0.88684|0.88684	0.3204|0.3204	10|5	0.87932|.	D|.	0|.	.|.	14.8626|14.8626	0.70392|0.70392	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	859;861;918;859;891|.	E9PDN8;O15068-9;G5E9A1;O15068-4;O15068|.	.;.;.;.;MCF2L_HUMAN|.	R|G	891;891;918;894;861;865;865;867;859;859;702|91;32	ENSP00000364758:K891R;ENSP00000401422:K891R;ENSP00000364754:K918R;ENSP00000380225:K894R;ENSP00000440374:K861R;ENSP00000397285:K865R;ENSP00000364751:K865R;ENSP00000407722:K867R;ENSP00000405639:K859R;ENSP00000364747:K859R|.	ENSP00000364747:K859R|.	K|S	+|+	2|1	0|0	MCF2L|MCF2L	112789758|112789758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.524000|0.524000	0.34500|0.34500	9.084000|9.084000	0.94076|0.94076	1.902000|1.902000	0.55061|0.55061	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.		0.592	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			G	113741757	A	G	113741757	3	3	145	1	0	0	0	0	1	0	0	0	9404	72	3	3	2934	3	MCF2L	13	113741757	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	92179275	113741757	1428121	47	12958											
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35269498	35269498	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctcttcttcaacaatttTtttcaattcttccctctttt	6	23	0	12	0	7	0	2	0	5	0	9	0	8	0	1	0	1	0	1	0	3	9			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr14:35269498T>A	ENST00000382422.2	-	8	1387	c.1060A>T	c.(1060-1062)Aaa>Taa	p.K354*	BAZ1A_ENST00000358716.4_Nonsense_Mutation_p.K354*|BAZ1A_ENST00000360310.1_Nonsense_Mutation_p.K354*|AL355885.1_ENST00000581314.1_RNA			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	354					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		tcaacaatttttttcaattct	0.299																																					p.K354X		.											.	BAZ1A-291	0			c.A1060T						.						29	27	28					14																	35269498		2174	4241	6415	SO:0001587	stop_gained	11177	exon9			CAATTTTTTTCAA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"Zinc fingers, PHD-type"	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.1060A>T	14.37:g.35269498T>A	ENSP00000371859:p.Lys354*	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	29	3	NM_182648	0	0	21	21	0	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Nonsense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	T	42	9.525045	0.99195	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	.	.	.	4.96	4.96	0.65561	.	0.419939	0.27986	N	0.017055	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5831	0.50902	0.0:0.0:0.0:1.0	.	.	.	.	X	354;354;354;38	.	ENSP00000351555:K354X	K	-	1	0	BAZ1A	34339249	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.925000	0.56484	2.168000	0.68352	0.482000	0.46254	AAA	.		0.299	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			A	35269498	T	A	35269498	4	1	145	1	0	0	0	0	0	1	0	0	1330	1850	64	5	3686	5	BAZ1A	14	35269498	Nonsense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08		35269498	72080042	48	12959											
HSPA2	3306	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	65009419	65009419	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcaaactttaccaaggtggtCctggcggcggcagcggcggc	7	6	16	12	4	0	0	0	0	0	0	1	0	1	0	2	7	3	2	2	7	3	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr14:65009419C>A	ENST00000394709.1	+	2	1928	c.1852C>A	c.(1852-1854)Cct>Act	p.P618T	HSPA2_ENST00000247207.6_Missense_Mutation_p.P618T|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	618					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CCAAGGTGGTCCTggcggcgg	0.552																																					p.P618T	Pancreas(136;1211 1835 24894 31984 38227)	.											.	HSPA2-226	0			c.C1852A						.						48	50	50					14																	65009419		2203	4300	6503	SO:0001583	missense	3306	exon1			GGTGGTCCTGGCG	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"Heat shock proteins / HSP70"	5235	protein-coding gene	gene with protein product		140560	"heat shock 70kD protein 2"				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.1852C>A	14.37:g.65009419C>A	ENSP00000378199:p.Pro618Thr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	106	30	NM_021979	0	0	6	6	0	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	3.079	-0.189353	0.06299	.	.	ENSG00000126803	ENST00000394709;ENST00000247207;ENST00000545222	T;T	0.13538	2.58;2.58	5.43	2.55	0.30701	.	1.329050	0.05831	U	0.617584	T	0.08447	0.0210	N	0.11201	0.11	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40365	-0.9567	10	0.29301	T	0.29	0.1445	7.9468	0.29991	0.0:0.6354:0.2799:0.0847	.	618	P54652	HSP72_HUMAN	T	618;618;392	ENSP00000378199:P618T;ENSP00000247207:P618T	ENSP00000247207:P618T	P	+	1	0	HSPA2	64079172	1.000000	0.71417	0.954000	0.39281	0.732000	0.41865	2.213000	0.42844	0.254000	0.21573	-0.230000	0.12252	CCT	.		0.552	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65009419	C	A	65009419	3	1	145	1	0	0	0	0	1	0	0	0	7432	855	30	4	1854	4	HSPA2	14	65009419	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	29739921	65009419	42340121	49	12960											
EIF2AK4	440275	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40324962	40324962	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgtgtattcacaggtggAtctacccaaagaaacaatat	14	12	8	7	0	2	1	1	0	1	1	2	2	2	2	1	2	2	1	1	2	6	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr15:40324962A>G	ENST00000263791.5	+	37	4776	c.4733A>G	c.(4732-4734)gAt>gGt	p.D1578G	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.D1550G	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1578					cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TCACAGGTGGATCTACCCAAA	0.388																																					p.D1578G		.											.	EIF2AK4-757	0			c.A4733G						.						110	106	107					15																	40324962		1929	4132	6061	SO:0001583	missense	440275	exon37			AGGTGGATCTACC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.4733A>G	15.37:g.40324962A>G	ENSP00000263791:p.Asp1578Gly	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	78	16	NM_001013703	0	0	0	0	0	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.042322	0.75732	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.61742	0.08;0.08	5.89	5.89	0.94794	Serine/threonine-protein kinase GCN2, anticodon binding domain (1);	0.000000	0.85682	D	0.000000	T	0.65238	0.2672	N	0.24115	0.695	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.69577	-0.5108	10	0.72032	D	0.01	-24.8288	15.9741	0.80044	1.0:0.0:0.0:0.0	.	1550;1578	Q9P2K8-2;Q9P2K8	.;E2AK4_HUMAN	G	1578;1550	ENSP00000263791:D1578G;ENSP00000372174:D1550G	ENSP00000263791:D1578G	D	+	2	0	EIF2AK4	38112254	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	5.973000	0.70456	2.246000	0.74042	0.533000	0.62120	GAT	.		0.388	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40324962	A	G	40324962	3	3	145	1	0	0	0	0	1	0	0	0	5010	333	12	3	4879	3	EIF2AK4	15	40324962	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08		40324962	62206430	50	12961											
TMC7	79905	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	19051691	19051691	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacgctggccaattttatCaccccaatgatctttgccaa	11	12	5	13	1	3	1	2	1	1	0	3	1	3	1	4	1	1	1	4	1	4	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr16:19051691C>A	ENST00000304381.5	+	9	1390	c.1260C>A	c.(1258-1260)atC>atA	p.I420I	TMC7_ENST00000421369.3_Silent_p.I310I|TMC7_ENST00000569532.1_Silent_p.I420I	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	420					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						CCAATTTTATCACCCCAATGA	0.418																																					p.I420I		.											.	TMC7-93	0			c.C1260A						.						142	121	128					16																	19051691		2197	4300	6497	SO:0001819	synonymous_variant	79905	exon9			TTTTATCACCCCA	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1260C>A	16.37:g.19051691C>A		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	184	37	NM_024847	0	0	3	5	2	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	37	CCDS10573.1																																																																																			.		0.418	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		A	19051691	C	A	19051691	2	1	145	1	0	0	0	0	0	0	0	1	16022	816	29	4		4	TMC7	16	19051691	Silent	SNP	C	TCGA-J7-8537-01A-11D-2396-08		19051691	71303062	51	12962											
NETO2	81831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	47117430	47117430	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcgggaggcggtggaggagCgccgcatcttctggtagttg	6	8	19	8	4	2	0	0	0	2	0	2	3	2	3	1	6	2	3	1	6	1	3	rs372424394		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr16:47117430C>T	ENST00000562435.1	-	9	1664	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	NETO2_ENST00000303155.5_Missense_Mutation_p.R420H	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	427					regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)				breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				GGTGGAGGAGCGCCGCATCTT	0.537										HNSCC(25;0.065)			C|||	1	0.000199681	0	0.0014	5008	,	,		16407	0		0	False		,,,				2504	0				p.R427H		.											.	NETO2-90	0			c.G1280A						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	92	85	87		1280,1259	3.8	1	16		87	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NETO2	NM_018092.4,NM_001201477.1	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	427/526,420/519	47117430	1,13005	2203	4300	6503	SO:0001583	missense	81831	exon9			GAGGAGCGCCGCA	AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.1280G>A	16.37:g.47117430C>T	ENSP00000455169:p.Arg427His	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	372	78	NM_018092	0	0	15	29	14	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Missense_Mutation	SNP	ENST00000562435.1	37	CCDS10727.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.539890	0.65085	0.0	1.16E-4	ENSG00000171208	ENST00000303155	.	.	.	5.78	3.83	0.44106	.	0.048904	0.85682	N	0.000000	T	0.48677	0.1513	L	0.52126	1.63	0.53005	D	0.999961	P;B;B	0.37914	0.611;0.244;0.357	B;B;B	0.32022	0.139;0.033;0.072	T	0.51268	-0.8727	9	0.66056	D	0.02	.	12.2767	0.54739	0.0:0.8634:0.0:0.1366	.	284;427;103	B7Z4I7;Q8NC67;Q8NC67-2	.;NETO2_HUMAN;.	H	427	.	ENSP00000306726:R427H	R	-	2	0	NETO2	45674931	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	4.088000	0.57678	0.801000	0.34066	0.655000	0.94253	CGC	.		0.537	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092		T	47117430	C	T	47117430	3	4	145	1	0	0	0	0	1	0	0	0	10366	768	27	1	301	1	NETO2	16	47117430	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	28065739	47117430	43237323	52	12963											
EIF4A1	1973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7478578	7478578	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgagaattggctcagcaggTaagagtggcttctattccct	9	12	11	9	1	2	2	1	0	1	2	4	3	3	2	1	3	1	4	1	3	3	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:7478578T>G	ENST00000293831.8	+	4	361		c.e4+2		SNORD10_ENST00000459579.1_RNA|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000380512.5_Missense_Mutation_p.V100G|SNORA48_ENST00000386847.1_RNA|EIF4A1_ENST00000582746.1_Splice_Site|SNORA67_ENST00000384423.1_RNA|EIF4A1_ENST00000577269.1_Splice_Site	NM_001416.3	NP_001407.1	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A1						cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			NS(1)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	22						GCTCAGCAGGTAAGAGTGGCT	0.488																																					.	Melanoma(120;278 1668 15796 27423 46368)	.											.	EIF4A1-227	0			c.345+2T>G						.						73	70	71					17																	7478578		2203	4300	6503	SO:0001630	splice_region_variant	1973	exon4			AGCAGGTAAGAGT	D13748	CCDS11113.1, CCDS58511.1	17p13	2012-02-23	2010-02-10		ENSG00000161960	ENSG00000161960		"DEAD-boxes"	3282	protein-coding gene	gene with protein product		602641	"eukaryotic translation initiation factor 4A, isoform 1"	EIF4A		8493113, 9790779	Standard	NM_001416		Approved	DDX2A, EIF-4A		P60842	OTTHUMG00000108149	ENST00000293831.8:c.345+2T>G	17.37:g.7478578T>G		Somatic	134	0		WXS	Illumina HiSeq	Phase_I	190	41	NM_001204510	0	0	1	1	0	B2R6L8|D3DTP9|J3QLC4|P04765|Q5U018|Q61516	Splice_Site	SNP	ENST00000293831.8	37	CCDS11113.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.031827|4.031827	0.75504|0.75504	.|.	.|.	ENSG00000161960|ENSG00000161960	ENST00000293831|ENST00000380512	.|T	.|0.17213	.|2.29	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|.	.|.	.|.	.|.	.|T	.|0.29749	.|0.0743	.|.	.|.	.|.	0.48511|0.48511	D|D	0.999669|0.999669	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.01195	.|-1.1422	.|5	.|.	.|.	.|.	.|.	13.4334|13.4334	0.61068|0.61068	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	.|G	-1|100	.|ENSP00000369881:V100G	.|.	.|V	+|+	.|2	.|0	EIF4A1|EIF4A1	7419302|7419302	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.957000|0.957000	0.61999|0.61999	7.698000|7.698000	0.84413|0.84413	2.077000|2.077000	0.62373|0.62373	0.459000|0.459000	0.35465|0.35465	.|GTA	.		0.488	EIF4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226952.6	NM_001416	Intron	G	7478578	T	G	7478578	5	3	145	1	0	0	0	0	0	0	1	0	5037	1652	57	5	361	5	EIF4A1	17	7478578	Splice_Site	SNP	T	TCGA-J7-8537-01A-11D-2396-08		7478578	73716632	53	12964											
MED24	9862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38187790	38187790	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgaccaggggagctcataCttgcagcgctggtcagcttt	7	10	14	10	1	2	1	2	1	0	0	2	2	2	2	1	4	5	4	1	4	1	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:38187790C>G	ENST00000394128.2	-	11	1149		c.e11+1		MED24_ENST00000501516.3_Splice_Site|MED24_ENST00000394126.1_Splice_Site|MED24_ENST00000394127.2_Splice_Site|MED24_ENST00000356271.3_Splice_Site|MED24_ENST00000479829.1_5'Flank	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24						androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GGAGCTCATACTTGCAGCGCT	0.557																																					.		.											.	MED24-187	0			c.1028+1G>C						.						84	82	82					17																	38187790		2203	4300	6503	SO:0001630	splice_region_variant	9862	exon11			CTCATACTTGCAG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"thyroid hormone receptor associated protein 4", "cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1067+1G>C	17.37:g.38187790C>G		Somatic	156	0		WXS	Illumina HiSeq	Phase_I	356	55	NM_001079518	0	0	0	7	7	A8K4S5|B3KMR9|Q14143|Q9NNY5	Splice_Site	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948640	0.73787	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4676	0.87638	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MED24	35441316	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	3.743000	0.55104	2.533000	0.85409	0.561000	0.74099	.	.		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	Intron	G	38187790	C	G	38187790	5	3	145	1	0	0	0	0	0	0	1	0	9467	579	20	4	1965	4	MED24	17	38187790	Splice_Site	SNP	C	TCGA-J7-8537-01A-11D-2396-08	30709212	38187790	43007420	54	12965											
MPP3	4356	broad.mit.edu	37	chr17	41888202	41888203	+	Frame_Shift_Del	DEL	TT	TT	-																															tccacatccaccaaacaaacTttgtttttggccataacagc																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:41888202_41888203delTT	ENST00000398389.4	-	18	1595_1596	c.1430_1431delAA	c.(1429-1431)aaafs	p.K477fs	MPP3_ENST00000398393.1_Frame_Shift_Del_p.K502fs	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	477	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		CCAAACAAACTTTGTTTTTGGC	0.45																																					p.477_477del													.	MPP3-91	0			c.1430_1431del						.																																			SO:0001589	frameshift_variant	4356	exon18			ACAAACTTTGTTT		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"MAGUK p55 subfamily member 3", "discs, large (Drosophila) homolog 3", "membrane protein palmitoylated 3"	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.1430_1431delAA	17.37:g.41888202_41888203delTT	ENSP00000381425:p.Lys477fs	Somatic	260	0		WXS	Illumina HiSeq	Phase_I	505	8	NM_001932	0	0	0	0	0	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Frame_Shift_Del	DEL	ENST00000398389.4	37	CCDS42344.1																																																																																			.		0.45	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932		-	41888203	TT	-	41888202	7	5	145	1	0	1	0	1	0	0	0	0	9760	1606	56	0	338	0	MPP3	17	41888202	Frame_Shift_Del	DEL	TT	TCGA-J7-8537-01A-11D-2396-08	3700412	41888202	39307008	55	12966											
NPEPPS	9520	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	45669357	45669357	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatctgaggttgatgagatAtttgatgctatatcatatag	12	15	9	5	0	2	4	1	4	1	1	2	5	2	4	1	1	1	2	1	1	5	7			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:45669357A>T	ENST00000322157.4	+	11	1533	c.1296A>T	c.(1294-1296)atA>atT	p.I432I	NPEPPS_ENST00000530173.1_Silent_p.I428I|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Silent_p.I352I	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	432					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						TTGATGAGATATTTGATGCTA	0.383																																					p.I432I		.											.	NPEPPS-90	0			c.A1296T						.						123	78	93					17																	45669357		2021	4151	6172	SO:0001819	synonymous_variant	9520	exon11			TGAGATATTTGAT	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1296A>T	17.37:g.45669357A>T		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	133	17	NM_006310	0	0	54	123	69	B7Z463|Q6P145|Q9NP16|Q9UEM2	Silent	SNP	ENST00000322157.4	37	CCDS45721.1																																																																																			.		0.383	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		T	45669357	A	T	45669357	2	4	145	1	0	0	0	0	0	0	0	1	10601	439	16	5		5	NPEPPS	17	45669357	Silent	SNP	A	TCGA-J7-8537-01A-11D-2396-08	3781155	45669357	35525853	56	12967											
CCDC45	90799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62532827	62532827	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaacaaaggagacgccaccaGgatgaactggactccatgga	15	4	12	10	1	0	2	0	1	0	1	1	7	1	5	3	4	2	0	3	4	3	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:62532827G>C	ENST00000556440.2	+	18	2688	c.2178G>C	c.(2176-2178)caG>caC	p.Q726H	CEP95_ENST00000553412.1_Missense_Mutation_p.Q562H	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	726						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						GACGCCACCAGGATGAACTGG	0.458																																					p.Q726H		.											.	CEP95-23	0			c.G2178C						.						78	82	81					17																	62532827		2022	4184	6206	SO:0001583	missense	90799	exon18			CCACCAGGATGAA	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2178G>C	17.37:g.62532827G>C	ENSP00000450461:p.Gln726His	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	155	47	NM_138363	0	0	7	17	10	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	37	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146995	0.57151	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.37411	1.25;1.2	5.48	3.5	0.40072	.	0.125921	0.53938	D	0.000047	T	0.51839	0.1698	L	0.59436	1.845	0.35792	D	0.822454	D	0.89917	1.0	D	0.73380	0.98	T	0.61964	-0.6954	10	0.72032	D	0.01	-13.7497	9.6268	0.39754	0.275:0.0:0.725:0.0	.	726	Q96GE4	CEP95_HUMAN	H	661;726;562	ENSP00000450461:Q726H;ENSP00000450906:Q562H	ENSP00000438458:Q661H	Q	+	3	2	CEP95	59963289	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	0.926000	0.28804	0.805000	0.34159	0.650000	0.86243	CAG	.		0.458	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		C	62532827	G	C	62532827	3	2	145	1	0	0	0	0	1	0	0	0	2822	991	35	4	2248	4	CCDC45	17	62532827	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	16863470	62532827	18662383	57	12968											
LINGO3	645191	hgsc.bcm.edu	37	chr19	2290499	2290499	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcggcgcggcagaggaagCggacgtcttcgcccgcggtg	5	5	17	14	8	1	1	0	0	1	1	3	3	1	3	2	5	1	1	2	5	1	1	rs7258841	byFrequency	TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr19:2290499C>T	ENST00000585527.1	-	1	1524	c.1277G>A	c.(1276-1278)cGc>cAc	p.R426H	LINGO3_ENST00000404279.1_Missense_Mutation_p.R426H			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	426	Ig-like C2-type.		R -> H (in dbSNP:rs7258841).			integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						GCAGAGGAAGCGGACGTCTTC	0.756													C|||	1440	0.28754	0.4017	0.2536	5008	,	,		9136	0.3363		0.1292	False		,,,				2504	0.2699				p.R426H		.											.	.	0			c.G1277A						.						1	2	2					19																	2290499		1143	2693	3836	SO:0001583	missense	645191	exon2			AGGAAGCGGACGT	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"Immunoglobulin superfamily / I-set domain containing"	21206	protein-coding gene	gene with protein product		609792	"leucine rich repeat neuronal 6B"	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.1277G>A	19.37:g.2290499C>T	ENSP00000467753:p.Arg426His	Somatic	1	1		WXS	Illumina HiSeq	Phase_I	7	7	NM_001101391	0	0	0	0	0		Missense_Mutation	SNP	ENST00000585527.1	37	CCDS45905.1	581	0.266025641025641	199	0.40447154471544716	83	0.2292817679558011	203	0.3548951048951049	96	0.1266490765171504	c	8.925	0.961929	0.18583	.	.	ENSG00000220008	ENST00000404279	T	0.68624	-0.34	4.12	2.99	0.34606	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.12527	0.23	0.37498	P	0.08333100000000004	B	0.12013	0.005	B	0.12156	0.007	T	0.28744	-1.0034	8	0.10902	T	0.67	.	10.7018	0.45931	0.0:0.5797:0.4203:0.0	rs7258841	426	P0C6S8	LIGO3_HUMAN	H	426	ENSP00000384979:R426H	ENSP00000384979:R426H	R	-	2	0	LINGO3	2241499	0.985000	0.35326	1.000000	0.80357	0.779000	0.44077	0.931000	0.28871	1.852000	0.53769	0.462000	0.41574	CGC	C|0.734;T|0.266		0.756	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391		T	2290499	C	T	2290499	3	4	145	1	0	0	0	0	1	0	0	0	8839	768	27	1	505	1	LINGO3	19	2290499	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		2290499	56838484	58	12969											
ZNF682	91120	hgsc.bcm.edu	37	chr19	20117835	20117835	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatgttttctctatttagaTttgatgatttactaaagact	11	21	5	4	0	1	4	0	2	1	2	2	4	1	4	0	0	1	1	0	0	6	10			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr19:20117835T>C	ENST00000397165.2	-	4	636	c.476A>G	c.(475-477)aAt>aGt	p.N159S	ZNF682_ENST00000597972.1_Missense_Mutation_p.N165S|ZNF682_ENST00000358523.5_Missense_Mutation_p.N127S|ZNF682_ENST00000397162.1_Missense_Mutation_p.N127S|ZNF682_ENST00000595736.1_Missense_Mutation_p.N83S|ZNF682_ENST00000596019.1_Intron	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	159					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TCTATTTAGATTTGATGATTT	0.294																																					p.N159S		.											.	ZNF682-92	0			c.A476G						.						67	62	64					19																	20117835		1813	4079	5892	SO:0001583	missense	91120	exon4			TTTAGATTTGATG	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"Zinc fingers, C2H2-type", "-"	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.476A>G	19.37:g.20117835T>C	ENSP00000380351:p.Asn159Ser	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	42	3	NM_033196	0	0	0	0	0	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	.	.	.	.	.	.	.	.	.	.	T	2.164	-0.391440	0.04932	.	.	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.35973	1.28;1.28;1.28	1.23	-2.47	0.06442	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21962	0.0529	L	0.33245	0.995	0.09310	N	1	B	0.12630	0.006	B	0.18871	0.023	T	0.20571	-1.0271	9	0.39692	T	0.17	.	3.5569	0.07867	0.0:0.2275:0.2188:0.5538	.	159	O95780	ZN682_HUMAN	S	159;127;127	ENSP00000380351:N159S;ENSP00000380348:N127S;ENSP00000351324:N127S	ENSP00000351324:N127S	N	-	2	0	ZNF682	19978835	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.780000	0.04654	-0.909000	0.03852	-0.483000	0.04790	AAT	.		0.294	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196		C	20117835	T	C	20117835	3	2	145	1	0	0	0	0	1	0	0	0	18121	1493	52	3	1024	3	ZNF682	19	20117835	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	17827336	20117835	39011148	59	12970											
ZNF419	79744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	58005060	58005060	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgcagcgactgtgggaaaTtttttacccaatgctcaagc	11	11	10	9	1	1	0	1	0	0	0	1	2	1	1	1	1	5	2	1	1	4	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr19:58005060T>G	ENST00000221735.7	+	5	1321	c.1135T>G	c.(1135-1137)Ttt>Gtt	p.F379V	ZNF419_ENST00000442920.2_Missense_Mutation_p.F366V|ZNF419_ENST00000415379.2_Missense_Mutation_p.F333V|ZNF419_ENST00000426954.2_Missense_Mutation_p.F367V|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000354197.4_Missense_Mutation_p.F367V|ZNF419_ENST00000424930.2_Missense_Mutation_p.F380V|ZNF419_ENST00000347466.6_Missense_Mutation_p.F347V			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	379					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CTGTGGGAAATTTTTTACCCA	0.408																																					p.F380V		.											.	ZNF419-90	0			c.T1138G						.						81	85	84					19																	58005060		2200	4297	6497	SO:0001583	missense	79744	exon5			GGGAAATTTTTTA	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.1135T>G	19.37:g.58005060T>G	ENSP00000221735:p.Phe379Val	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	227	42	NM_001098491	0	0	6	6	0	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.405079	0.25378	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.16743	3.25;3.25;3.25;3.25;3.25;2.32;3.25	2.26	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14614	0.0353	N	0.02539	-0.55	0.23454	N	0.997643	D;D;D;D;B;D;B	0.69078	0.985;0.991;0.997;0.991;0.292;0.996;0.292	D;D;D;D;B;D;B	0.79108	0.966;0.982;0.992;0.988;0.071;0.986;0.071	T	0.25222	-1.0138	9	0.38643	T	0.18	.	7.3178	0.26511	0.0:0.0:0.2246:0.7754	.	333;333;366;367;380;347;379	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	V	354;380;367;367;366;380;347;333;379	ENSP00000388864:F380V;ENSP00000390916:F367V;ENSP00000346136:F367V;ENSP00000414709:F366V;ENSP00000299860:F347V;ENSP00000392129:F333V;ENSP00000221735:F379V	ENSP00000221735:F379V	F	+	1	0	ZNF419	62696872	0.000000	0.05858	0.044000	0.18714	0.111000	0.19643	-1.253000	0.02877	0.101000	0.17610	0.260000	0.18958	TTT	.		0.408	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		G	58005060	T	G	58005060	3	3	145	1	0	0	0	0	1	0	0	0	17928	1493	52	5	1156	5	ZNF419	19	58005060	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	37887225	58005060	1123923	60	12971											
C20orf7	79133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	13775537	13775537	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcgttttagctgatgaagaAttccttcccttcaaagaaaa	14	12	7	8	1	1	4	1	2	0	2	3	4	3	4	2	0	2	2	2	0	6	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr20:13775537A>T	ENST00000378106.5	+	5	548	c.429A>T	c.(427-429)gaA>gaT	p.E143D	NDUFAF5_ENST00000475968.1_Intron|NDUFAF5_ENST00000463598.1_Intron	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	143					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)										CTGATGAAGAATTCCTTCCCT	0.318																																					p.E143D		.											.	.	0			c.A429T						.						105	105	105					20																	13775537		2203	4300	6503	SO:0001583	missense	79133	exon5			TGAAGAATTCCTT		CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"Mitochondrial respiratory chain complex assembly factors"	15899	protein-coding gene	gene with protein product		612360	"chromosome 20 open reading frame 7"	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.429A>T	20.37:g.13775537A>T	ENSP00000367346:p.Glu143Asp	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	48	6	NM_024120	0	0	10	19	9	A8K166|Q6GPH3|Q9H6F4	Missense_Mutation	SNP	ENST00000378106.5	37	CCDS13118.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.282700	0.80692	.	.	ENSG00000101247	ENST00000378106;ENST00000536501	D	0.85484	-1.99	5.93	2.37	0.29283	Methyltransferase type 11 (1);	0.000000	0.85682	D	0.000000	D	0.88362	0.6416	L	0.49513	1.565	0.80722	D	1	D;D	0.89917	1.0;0.985	D;D	0.81914	0.995;0.951	D	0.86347	0.1708	10	0.72032	D	0.01	-15.2415	9.9234	0.41478	0.7238:0.0:0.2762:0.0	.	143;143	Q5TEU4;B3KR61	CT007_HUMAN;.	D	143	ENSP00000367346:E143D	ENSP00000437325:E143D	E	+	3	2	C20orf7	13723537	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.111000	0.41883	0.126000	0.18424	-0.408000	0.06270	GAA	.		0.318	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375		T	13775537	A	T	13775537	3	4	145	1	0	0	0	0	1	0	0	0	2121	98	4	5	467	5	C20orf7	20	13775537	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08		13775537	49249983	61	12972											
FAM83D	81610	hgsc.bcm.edu	37	chr20	37555364	37555364	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggactcgttcggctcctcGcacgactgctcttcgggcac	5	9	12	15	5	1	0	0	0	1	0	6	3	2	1	1	3	1	5	1	3	0	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr20:37555364G>A	ENST00000217429.4	+	1	410	c.369G>A	c.(367-369)tcG>tcA	p.S123S		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	93					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				TCGGCTCCTCGCACGACTGCT	0.721																																					p.S123S		.											.	FAM83D-93	0			c.G369A						.						3	4	4					20																	37555364		1771	3831	5602	SO:0001819	synonymous_variant	81610	exon1			CTCCTCGCACGAC	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.369G>A	20.37:g.37555364G>A		Somatic	6	1		WXS	Illumina HiSeq	Phase_I	10	5	NM_030919	0	0	4	7	3	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Silent	SNP	ENST00000217429.4	37	CCDS42872.1																																																																																			.		0.721	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			A	37555364	G	A	37555364	2	1	145	1	0	0	0	0	0	0	0	1	5655	1074	38	1		1	FAM83D	20	37555364	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	23779827	37555364	25470156	62	12973											
GART	2618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	34904710	34904710	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctttgcaacaatcacccCttttccagctgcaagaccac	10	10	5	16	0	2	1	1	0	1	1	3	1	3	1	4	0	4	4	4	0	3	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr21:34904710C>T	ENST00000381831.3	-	5	732	c.469G>A	c.(469-471)Ggg>Agg	p.G157R	GART_ENST00000381839.3_Missense_Mutation_p.G157R|GART_ENST00000381815.4_Missense_Mutation_p.G157R|GART_ENST00000361093.5_Missense_Mutation_p.G157R|GART_ENST00000497313.1_5'UTR	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	157	ATP-grasp.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	ACAATCACCCCTTTTCCAGCT	0.428																																					p.G157R		.											.	GART-91	0			c.G469A						.						213	227	222					21																	34904710		2203	4300	6503	SO:0001583	missense	2618	exon5			TCACCCCTTTTCC	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.469G>A	21.37:g.34904710C>T	ENSP00000371253:p.Gly157Arg	Somatic	402	0		WXS	Illumina HiSeq	Phase_I	627	130	NM_001136005	0	0	49	84	35	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	37	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	C	35	5.450836	0.96205	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000361093;ENST00000430874;ENST00000426819	T;T;T;T;T;T	0.67698	0.46;0.46;0.46;0.38;-0.15;-0.28	6.07	6.07	0.98685	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain (1);	0.000000	0.85682	D	0.000000	D	0.87787	0.6265	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.89842	0.4003	10	0.87932	D	0	-20.8496	20.6593	0.99626	0.0:1.0:0.0:0.0	.	157	P22102	PUR2_HUMAN	R	157	ENSP00000371236:G157R;ENSP00000371253:G157R;ENSP00000371261:G157R;ENSP00000354388:G157R;ENSP00000413040:G157R;ENSP00000398631:G157R	ENSP00000354388:G157R	G	-	1	0	GART	33826580	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.487000	0.81328	2.885000	0.99019	0.655000	0.94253	GGG	.		0.428	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		T	34904710	C	T	34904710	3	4	145	1	0	0	0	0	1	0	0	0	6263	681	24	2	2639	2	GART	21	34904710	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		34904710	13225185	63	12974											
ADORA2A	135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24837246	24837246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtctcaacggccacccgcCaggagtgtgggccaacggca	8	4	13	16	4	1	0	1	0	1	0	2	1	1	1	5	4	2	1	5	4	2	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr22:24837246C>T	ENST00000337539.7	+	3	1487	c.1028C>T	c.(1027-1029)cCa>cTa	p.P343L	ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	343					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	GGCCACCCGCCAGGAGTGTGG	0.662																																					p.P343L		.											.	ADORA2A-90	0			c.C1028T						.						25	22	23					22																	24837246		2202	4299	6501	SO:0001583	missense	135	exon3			ACCCGCCAGGAGT	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.1028C>T	22.37:g.24837246C>T	ENSP00000336630:p.Pro343Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	71	17	NM_000675	0	0	14	14	0	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	37	CCDS13826.1	.	.	.	.	.	.	.	.	.	.	C	1.893	-0.454933	0.04540	.	.	ENSG00000128271	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596	T;T	0.62941	0.01;-0.01	4.95	0.288	0.15719	.	0.374401	0.24291	N	0.039802	T	0.37972	0.1023	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08722	-1.0708	10	0.26408	T	0.33	-1.5144	3.3452	0.07132	0.1839:0.3375:0.0:0.4785	.	343	P29274	AA2AR_HUMAN	L	343	ENSP00000414802:P343L;ENSP00000336630:P343L	ENSP00000336630:P343L	P	+	2	0	ADORA2A	23167246	0.000000	0.05858	0.000000	0.03702	0.511000	0.34104	0.577000	0.23758	0.177000	0.19895	0.462000	0.41574	CCA	.		0.662	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24837246	C	T	24837246	3	4	145	1	0	0	0	0	1	0	0	0	327	594	21	2	1034	2	ADORA2A	22	24837246	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		24837246	26467320	64	12975											
GRPR	2925	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	16168549	16168550	+	Frame_Shift_Ins	INS	-	-	C																															cattccagaggccgtgttttINSctgacctccatcccttccat																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:16168549_16168550insC	ENST00000380289.2	+	2	933_934	c.535_536insC	c.(535-537)tctfs	p.S179fs	RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000435789.1_RNA|RP11-431J24.2_ENST00000454712.2_RNA	NM_005314.2	NP_005305.1	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	179					cell proliferation (GO:0008283)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)|G-protein coupled peptide receptor activity (GO:0008528)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(3)|stomach(1)|upper_aerodigestive_tract(3)	25	Hepatocellular(33;0.183)					GGCCGTGTTTTCTGACCTCCAT	0.505																																					p.S179fs		.											.	GRPR-565	0			c.535_536insC						.																																			SO:0001589	frameshift_variant	2925	exon2			.		CCDS14174.1	Xp22.2	2014-02-21			ENSG00000126010	ENSG00000126010		"GPCR / Class A : Bombesin receptors"	4609	protein-coding gene	gene with protein product	"bombesin receptor 2"	305670					Standard	NM_005314		Approved	BB2	uc004cxj.3	P30550	OTTHUMG00000021189	ENST00000380289.2:c.536dupC	X.37:g.16168550_16168550dupC	ENSP00000369643:p.Ser179fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	376	68	NM_005314	0	0	0	0	0	B2R910	Frame_Shift_Ins	INS	ENST00000380289.2	37	CCDS14174.1																																																																																			.		0.505	GRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055901.1	NM_005314		C	16168550	-	C	16168549	7	5	145	1	0	1	1	0	0	0	0	0	6829	1783	62	0	541	0	GRPR	23	16168549	Frame_Shift_Ins	INS	-	TCGA-J7-8537-01A-11D-2396-08		16168549	139102011	65	12976											
CNKSR2	22866	broad.mit.edu	37	chrX	21627678	21627680	+	In_Frame_Del	DEL	GAG	GAG	-																															aacccccagaggtggaggaaGaggaggaggaggaggaggag																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:21627678_21627680delGAG	ENST00000379510.3	+	20	2671_2673	c.2635_2637delGAG	c.(2635-2637)gagdel	p.E886del	CNKSR2_ENST00000425654.2_In_Frame_Del_p.E856del|CNKSR2_ENST00000543067.1_In_Frame_Del_p.E837del|CNKSR2_ENST00000279451.4_In_Frame_Del_p.E886del	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	886	Poly-Glu.				regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						ggtggaggaagaggaggaggagg	0.517																																					p.879_879del													.	CNKSR2-625	0			c.2635_2637del						.																																			SO:0001651	inframe_deletion	22866	exon20			GAGGAAGAGGAGG	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.2635_2637delGAG	X.37:g.21627687_21627689delGAG	ENSP00000368824:p.Glu886del	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	140	9	NM_014927	0	0	0	0	0	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	In_Frame_Del	DEL	ENST00000379510.3	37	CCDS14198.1																																																																																			.		0.517	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927		-	21627680	GAG	-	21627678	7	5	145	1	0	1	0	1	0	0	0	0	3613	943	33	0	2713	0	CNKSR2	23	21627678	In_Frame_Del	DEL	GAG	TCGA-J7-8537-01A-11D-2396-08	5459129	21627678	133642882	66	12977											
RP2	6102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	46713306	46713306	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagatgcagggctaagtatCttcaacaatacatggagtaa	17	9	9	6	0	2	1	1	0	1	1	2	2	2	2	0	2	3	4	0	2	7	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:46713306C>G	ENST00000218340.3	+	2	659	c.498C>G	c.(496-498)atC>atG	p.I166M		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	166	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						GGCTAAGTATCTTCAACAATA	0.403																																					p.I166M		.											.	RP2-130	0			c.C498G						.						111	97	101					X																	46713306		2203	4300	6503	SO:0001583	missense	6102	exon2			AAGTATCTTCAAC	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.498C>G	X.37:g.46713306C>G	ENSP00000218340:p.Ile166Met	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	229	34	NM_006915	0	0	1	9	8	Q86XJ7|Q9NU67	Missense_Mutation	SNP	ENST00000218340.3	37	CCDS14270.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637203	0.47049	.	.	ENSG00000102218	ENST00000218340	D	0.86627	-2.15	5.64	3.89	0.44902	Tubulin binding cofactor C (1);C-CAP/cofactor C-like domain (1);	0.093345	0.64402	D	0.000001	D	0.89646	0.6775	M	0.65975	2.015	0.48632	D	0.999683	P	0.52316	0.952	P	0.57324	0.818	D	0.87427	0.2386	10	0.48119	T	0.1	-23.7323	9.0313	0.36260	0.0:0.7697:0.0:0.2303	.	166	O75695	XRP2_HUMAN	M	166	ENSP00000218340:I166M	ENSP00000218340:I166M	I	+	3	3	RP2	46598250	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.459000	0.35234	0.558000	0.29135	-0.191000	0.12829	ATC	.		0.403	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		G	46713306	C	G	46713306	3	3	145	1	0	0	0	0	1	0	0	0	13566	903	32	4	504	4	RP2	23	46713306	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	25085628	46713306	108557254	67	12978											
SLITRK2	84631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	144904238	144904238	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctaggtaacaacgggttaCaggagatccgaacgggggca	13	5	14	9	3	0	1	0	0	0	1	1	3	1	1	2	5	4	3	2	5	5	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:144904238C>T	ENST00000370490.1	+	1	4550	c.295C>T	c.(295-297)Cag>Tag	p.Q99*	SLITRK2_ENST00000434188.2_Nonsense_Mutation_p.Q99*|SLITRK2_ENST00000447897.2_Nonsense_Mutation_p.Q99*|SLITRK2_ENST00000428560.2_Nonsense_Mutation_p.Q99*|SLITRK2_ENST00000413937.2_Nonsense_Mutation_p.Q99*			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	99					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CAACGGGTTACAGGAGATCCG	0.458																																					p.Q99X		.											.	SLITRK2-136	0			c.C295T						.						77	69	72					X																	144904238		2203	4300	6503	SO:0001587	stop_gained	84631	exon5			GGGTTACAGGAGA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"slit-like 1 (Drosophila)"	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.295C>T	X.37:g.144904238C>T	ENSP00000359521:p.Gln99*	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	243	48	NM_001144005	0	0	0	0	0	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Nonsense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	C	59	34.326611	0.99982	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	.	.	.	4.88	4.01	0.46588	.	0.066024	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-7.1777	12.0035	0.53246	0.0:0.8284:0.1716:0.0	.	.	.	.	X	99	.	ENSP00000334374:Q99X	Q	+	1	0	SLITRK2	144711930	1.000000	0.71417	0.996000	0.52242	0.494000	0.33585	7.818000	0.86416	0.832000	0.34804	-0.218000	0.12543	CAG	.		0.458	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144904238	C	T	144904238	4	4	145	1	0	0	0	0	0	1	0	0	14775	479	17	2	297	2	SLITRK2	23	144904238	Nonsense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	98190932	144904238	10366322	68	12979											
RPS6KA1	6195	ucsc.edu	37	chr1	26873742	26873742	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtatgctatgaaggtgctGaagaaggcaacgctgaaagg	13	8	14	6	1	0	4	0	3	0	1	0	4	0	4	0	3	3	5	0	3	7	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:26873742G>A	ENST00000374168.2	+	4	442	c.288G>A	c.(286-288)ctG>ctA	p.L96L	RPS6KA1_ENST00000374166.4_Silent_p.L96L|RPS6KA1_ENST00000374162.2_Silent_p.L4L|RPS6KA1_ENST00000526792.1_Silent_p.L4L|RPS6KA1_ENST00000530003.1_Silent_p.L80L|RPS6KA1_ENST00000531382.1_Silent_p.L105L	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	96	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		TGAAGGTGCTGAAGAAGGCAA	0.597																																					p.L105L													.	RPS6KA1-510	0			c.G315A						.						70	62	65					1																	26873742		2203	4300	6503	SO:0001819	synonymous_variant	6195	exon3			GGTGCTGAAGAAG	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"ribosomal protein S6 kinase, 90kD, polypeptide 1"			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.288G>A	1.37:g.26873742G>A		Somatic	76	0		WXS	Illumina HiSeq		61	3	NM_001006665	1	0	15	23	7	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Silent	SNP	ENST00000374168.2	37	CCDS284.1																																																																																			.		0.597	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953		A	26873742	G	A	26873742	2	1	146	1	0	0	0	0	0	0	0	1	13682	1277	45	2		2	RPS6KA1	1	26873742	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10		26873742	222376879	1	12980											
TRIM62	55223	broad.mit.edu	37	chr1	33625315	33625315	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagtgaggccaccccagcCaggaaggtgtgccggtcggt	8	5	16	12	2	0	1	0	1	0	0	1	3	0	2	5	5	2	0	5	5	1	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:33625315C>T	ENST00000291416.5	-	3	968	c.735G>A	c.(733-735)ctG>ctA	p.L245L	TRIM62_ENST00000485148.1_5'UTR|TRIM62_ENST00000543586.1_Silent_p.L124L	NM_018207.2	NP_060677.2	Q9BVG3	TRI62_HUMAN	tripartite motif containing 62	245					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)				CCACCCCAGCCAGGAAGGTGT	0.682																																					p.L245L													.	TRIM62-226	0			c.G735A						.						32	34	33					1																	33625315		2203	4300	6503	SO:0001819	synonymous_variant	55223	exon3			CCCAGCCAGGAAG	BC007999	CCDS376.1	1p35.1	2013-10-11	2011-01-25		ENSG00000116525	ENSG00000116525		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	25574	protein-coding gene	gene with protein product	"ductal epithelium-associated RING Chromosome 1"		"tripartite motif-containing 62"			19536326	Standard	NM_018207		Approved	FLJ10759, DEAR1	uc001bxb.3	Q9BVG3	OTTHUMG00000004132	ENST00000291416.5:c.735G>A	1.37:g.33625315C>T		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	18	3	NM_018207	0	0	0	0	0	B3KVH5|B4DTE4|D3DPR1|Q9NVG0	Silent	SNP	ENST00000291416.5	37	CCDS376.1																																																																																			.		0.682	TRIM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011890.1	NM_018207		T	33625315	C	T	33625315	2	4	146	1	0	0	0	0	0	0	0	1	16570	581	21	2		2	TRIM62	1	33625315	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	6751573	33625315	215625306	2	12981											
FHL3	2275	broad.mit.edu	37	chr1	38463363	38463363	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acccttgtcccacctacgatGgggcgcttgcagctgctgca	6	9	11	15	2	0	0	0	0	0	0	1	1	1	0	3	2	5	5	3	2	1	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:38463363G>T	ENST00000373016.3	-	5	849	c.681C>A	c.(679-681)ccC>ccA	p.P227P	FHL3_ENST00000485803.1_5'UTR	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN	four and a half LIM domains 3	227	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|muscle organ development (GO:0007517)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)|Z disc (GO:0030018)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CACCTACGATGGGGCGCTTGC	0.592																																					p.P227P													.	FHL3-90	0			c.C681A						.						90	84	86					1																	38463363		2203	4300	6503	SO:0001819	synonymous_variant	2275	exon5			TACGATGGGGCGC	BC011697	CCDS30678.1	1p34.3	2008-02-05			ENSG00000183386	ENSG00000183386			3704	protein-coding gene	gene with protein product		602790				8753811, 10226657	Standard	NM_004468		Approved	SLIM2	uc001cck.3	Q13643	OTTHUMG00000004434	ENST00000373016.3:c.681C>A	1.37:g.38463363G>T		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	60	4	NM_004468	0	0	3	3	0	D3DPT6|Q6I9T0|Q9BVA2	Silent	SNP	ENST00000373016.3	37	CCDS30678.1																																																																																			.		0.592	FHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012958.1	NM_004468		T	38463363	G	T	38463363	2	4	146	1	0	0	0	0	0	0	0	1	5899	1335	47	4		4	FHL3	1	38463363	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	4838048	38463363	210787258	3	12982											
LPAR3	23566	broad.mit.edu	37	chr1	85331710	85331710	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcccaacacacaaaacaaTcacaagctttgttcctgtcc	13	9	4	15	1	1	0	1	0	0	0	4	0	4	0	3	0	3	2	3	0	5	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:85331710T>G	ENST00000440886.1	-	1	132	c.94A>C	c.(94-96)Att>Ctt	p.I32L	LPAR3_ENST00000370611.3_Missense_Mutation_p.I32L|LPAR3_ENST00000491034.1_5'UTR			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	32					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						CACAAAACAATCACAAGCTTT	0.383																																					p.I32L													.	LPAR3-502	0			c.A94C						.						114	122	119					1																	85331710		2203	4300	6503	SO:0001583	missense	23566	exon2			AAACAATCACAAG	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	14298	protein-coding gene	gene with protein product		605106	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.94A>C	1.37:g.85331710T>G	ENSP00000395389:p.Ile32Leu	Somatic	364	1		WXS	Illumina HiSeq	Phase_I	317	7	NM_012152	0	0	0	0	0	A0AVA3	Missense_Mutation	SNP	ENST00000440886.1	37	CCDS700.1	.	.	.	.	.	.	.	.	.	.	T	2.940	-0.219154	0.06101	.	.	ENSG00000171517	ENST00000440886;ENST00000370611	T;T	0.35236	1.32;1.32	5.58	5.58	0.84498	.	0.864598	0.08979	U	0.866129	T	0.09905	0.0243	N	0.21142	0.635	0.34287	D	0.682867	B	0.02656	0.0	B	0.04013	0.001	T	0.09729	-1.0661	10	0.07990	T	0.79	.	10.4572	0.44557	0.0:0.082:0.0:0.918	.	32	Q9UBY5	LPAR3_HUMAN	L	32	ENSP00000395389:I32L;ENSP00000359643:I32L	ENSP00000359643:I32L	I	-	1	0	LPAR3	85104298	0.867000	0.29959	0.964000	0.40570	0.801000	0.45260	2.523000	0.45580	2.118000	0.64928	0.383000	0.25322	ATT	.		0.383	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152		G	85331710	T	G	85331710	3	3	146	1	0	0	0	0	1	0	0	0	8931	1435	50	5	975	5	LPAR3	1	85331710	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	46868347	85331710	163918911	4	12983											
CTTNBP2NL	55917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	112999075	112999075	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagagagttttccagcagaaAgaacccatgggagcaacata	16	6	10	9	0	0	3	0	0	0	3	1	5	1	4	2	1	4	3	2	1	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:112999075A>G	ENST00000271277.6	+	6	1186	c.961A>G	c.(961-963)Aga>Gga	p.R321G		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	321					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCAGCAGAAAGAACCCATGG	0.483																																					p.R321G		.											.	CTTNBP2NL-92	0			c.A961G						.						136	140	138					1																	112999075		2203	4300	6503	SO:0001583	missense	55917	exon6			GCAGAAAGAACCC	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.961A>G	1.37:g.112999075A>G	ENSP00000271277:p.Arg321Gly	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	118	20	NM_018704	0	0	2	3	1	B3KMS5|Q96B40	Missense_Mutation	SNP	ENST00000271277.6	37	CCDS845.1	.	.	.	.	.	.	.	.	.	.	A	2.835	-0.241767	0.05906	.	.	ENSG00000143079	ENST00000271277	T	0.22945	1.93	5.88	4.73	0.59995	.	0.247257	0.38778	N	0.001578	T	0.08714	0.0216	L	0.44542	1.39	0.09310	N	1	B	0.17038	0.02	B	0.14023	0.01	T	0.22208	-1.0223	10	0.22109	T	0.4	-12.5708	12.215	0.54402	0.8572:0.1428:0.0:0.0	.	321	Q9P2B4	CT2NL_HUMAN	G	321	ENSP00000271277:R321G	ENSP00000271277:R321G	R	+	1	2	CTTNBP2NL	112800598	0.600000	0.26899	0.921000	0.36526	0.055000	0.15305	1.467000	0.35321	1.017000	0.39495	0.533000	0.62120	AGA	.		0.483	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		G	112999075	A	G	112999075	3	3	146	1	0	0	0	0	1	0	0	0	4052	64	3	3	975	3	CTTNBP2NL	1	112999075	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	27667365	112999075	136251546	5	12984											
ANKRD35	148741	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	145561841	145561841	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgagaaaaggatgctgcccGgggggctttgtcaagaccgg	9	6	17	9	3	1	2	1	0	0	2	1	4	1	3	2	5	2	2	2	5	3	1	rs201815402		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:145561841G>A	ENST00000355594.4	+	10	1616	c.1529G>A	c.(1528-1530)cGg>cAg	p.R510Q		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	510										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GATGCTGCCCGGGGGGCTTTG	0.632																																					p.R510Q	Melanoma(9;127 754 22988 51047)	.											.	ANKRD35-95	0			c.G1529A						.						87	104	98					1																	145561841		2201	4300	6501	SO:0001583	missense	148741	exon10			CTGCCCGGGGGGC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1529G>A	1.37:g.145561841G>A	ENSP00000347802:p.Arg510Gln	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	96	11	NM_144698	0	0	0	0	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	g	13.79	2.341545	0.41498	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.67865	-0.29	5.23	4.31	0.51392	.	0.342769	0.20873	N	0.084127	T	0.46756	0.1409	M	0.70595	2.14	0.80722	D	1	B	0.32324	0.364	B	0.24006	0.05	T	0.51364	-0.8715	10	0.34782	T	0.22	-6.7716	11.0303	0.47769	0.0:0.0:0.8146:0.1853	.	510	Q8N283	ANR35_HUMAN	Q	419;510	ENSP00000347802:R510Q	ENSP00000347802:R510Q	R	+	2	0	ANKRD35	144273198	0.749000	0.28305	0.965000	0.40720	0.652000	0.38707	1.901000	0.39838	1.405000	0.46838	0.651000	0.88453	CGG	G|0.999;T|0.000		0.632	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145561841	G	A	145561841	3	1	146	1	0	0	0	0	1	0	0	0	664	1116	39	1	1567	1	ANKRD35	1	145561841	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	32562766	145561841	103688780	6	12985											
PEAR1	375033	broad.mit.edu	37	chr1	156879832	156879832	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggttgtgccagtcgctGtgactgtgaccactctgatg	8	11	13	9	1	1	4	0	3	1	1	2	4	1	4	2	1	1	2	2	1	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:156879832G>A	ENST00000338302.3	+	14	1835	c.1610G>A	c.(1609-1611)tGt>tAt	p.C537Y	PEAR1_ENST00000292357.7_Missense_Mutation_p.C537Y			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	537					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCCAGTCGCTGTGACTGTGAC	0.627																																					p.C537Y													.	PEAR1-71	0			c.G1610A						.						139	119	126					1																	156879832		2203	4300	6503	SO:0001583	missense	375033	exon13			GTCGCTGTGACTG	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"multiple EGF-like-domains 12"	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1610G>A	1.37:g.156879832G>A	ENSP00000344465:p.Cys537Tyr	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	22	3	NM_001080471	0	0	4	5	1	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.073667	0.76415	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	T;T	0.72835	-0.69;-0.69	4.71	4.71	0.59529	EGF-like, laminin (1);	0.000000	0.53938	D	0.000048	D	0.87410	0.6170	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90879	0.4752	10	0.72032	D	0.01	.	15.1995	0.73122	0.0:0.0:1.0:0.0	.	537	Q5VY43	PEAR1_HUMAN	Y	537	ENSP00000344465:C537Y;ENSP00000292357:C537Y	ENSP00000292357:C537Y	C	+	2	0	PEAR1	155146456	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.844000	0.92147	2.447000	0.82792	0.561000	0.74099	TGT	.		0.627	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		A	156879832	G	A	156879832	3	1	146	1	0	0	0	0	1	0	0	0	11738	1377	48	2	1656	2	PEAR1	1	156879832	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	11317991	156879832	92370789	7	12986											
DDR2	4921	broad.mit.edu	37	chr1	162688920	162688920	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctatcttgagttctgcaaaaGctcaggttaatccaggtaac	12	12	8	9	0	3	1	1	1	2	0	4	1	4	1	1	2	3	5	1	2	5	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:162688920G>C	ENST00000367922.3	+	4	505	c.67G>C	c.(67-69)Gct>Cct	p.A23P	DDR2_ENST00000367921.3_Missense_Mutation_p.A23P	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	23					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	TTCTGCAAAAGCTCAGGTTAA	0.453																																					p.A23P	NSCLC(161;314 2006 8283 19651 23192)												.	DDR2-1464	0			c.G67C						.						176	152	160					1																	162688920		2203	4300	6503	SO:0001583	missense	4921	exon4			GCAAAAGCTCAGG	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.67G>C	1.37:g.162688920G>C	ENSP00000356899:p.Ala23Pro	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	61	3	NM_001014796	0	0	0	0	0	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	37	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.115339	0.37339	.	.	ENSG00000162733	ENST00000446985;ENST00000415555;ENST00000542391;ENST00000367922;ENST00000367921	D;D;D;D	0.97976	-4.37;-4.64;-1.84;-1.84	4.25	4.25	0.50352	.	0.636214	0.14742	N	0.301137	D	0.91379	0.7280	N	0.21448	0.665	0.34326	D	0.687194	B	0.06786	0.001	B	0.13407	0.009	D	0.87367	0.2348	9	0.41790	T	0.15	.	12.3368	0.55071	0.0:0.0:1.0:0.0	.	23	Q16832	DDR2_HUMAN	P	23	ENSP00000400309:A23P;ENSP00000391310:A23P;ENSP00000356899:A23P;ENSP00000356898:A23P	ENSP00000356898:A23P	A	+	1	0	DDR2	160955544	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.311000	0.59147	2.364000	0.80123	0.467000	0.42956	GCT	.		0.453	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		C	162688920	G	C	162688920	3	2	146	1	0	0	0	0	1	0	0	0	4343	971	34	4	69	4	DDR2	1	162688920	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	5809088	162688920	86561701	8	12987											
ILDR2	387597	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	166890003	166890003	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gttgctgtggtagggcaggtCgcggccgcggtaggacgggc	4	7	21	9	5	0	0	0	0	0	0	1	1	0	1	1	7	1	5	1	7	2	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:166890003C>T	ENST00000271417.3	-	9	1880	c.1825G>A	c.(1825-1827)Gac>Aac	p.D609N	ILDR2_ENST00000529071.1_Missense_Mutation_p.D590N|ILDR2_ENST00000469934.2_Intron|ILDR2_ENST00000526687.1_Missense_Mutation_p.D501N|ILDR2_ENST00000525740.1_Missense_Mutation_p.D482N|ILDR2_ENST00000528703.1_Missense_Mutation_p.D550N|ILDR2_ENST00000529387.1_Intron	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	609					cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						TAGGGCAGGTCGCGGCCGCGG	0.687																																					p.D609N		.											.	ILDR2-91	0			c.G1825A						.						6	9	8					1																	166890003		2076	4108	6184	SO:0001583	missense	387597	exon9			GCAGGTCGCGGCC	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"LISCH-like"		"chromosome 1 open reading frame 32"	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.1825G>A	1.37:g.166890003C>T	ENSP00000271417:p.Asp609Asn	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	31	7	NM_199351	0	0	0	0	0		Missense_Mutation	SNP	ENST00000271417.3	37	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069172	0.76301	.	.	ENSG00000143195	ENST00000271417;ENST00000525740;ENST00000529071;ENST00000526687;ENST00000528703	T;T;T;T;T	0.77750	0.5;-1.12;0.5;-1.12;-0.12	4.76	4.76	0.60689	.	3.853080	0.00892	N	0.002254	T	0.64638	0.2616	L	0.56769	1.78	0.35061	D	0.761595	P	0.49358	0.923	B	0.36030	0.216	T	0.57464	-0.7807	9	0.62326	D	0.03	.	12.8493	0.57848	0.1631:0.8369:0.0:0.0	.	609	Q71H61	ILDR2_HUMAN	N	609;482;590;501;550	ENSP00000271417:D609N;ENSP00000436120:D482N;ENSP00000436882:D590N;ENSP00000434273:D501N;ENSP00000432750:D550N	ENSP00000271417:D609N	D	-	1	0	ILDR2	165156627	1.000000	0.71417	0.997000	0.53966	0.735000	0.41995	4.789000	0.62446	2.171000	0.68590	0.561000	0.74099	GAC	.		0.687	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351		T	166890003	C	T	166890003	3	4	146	1	0	0	0	0	1	0	0	0	7731	884	31	1	102	1	ILDR2	1	166890003	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	4201083	166890003	82360618	9	12988											
TPR	7175	hgsc.bcm.edu;broad.mit.edu	37	chr1	186316562	186316562	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttagctgactcacaagatcAtccacatcttctttgttgct	9	15	5	12	0	4	2	2	1	2	1	5	2	5	2	1	0	2	3	1	0	2	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:186316562A>G	ENST00000367478.4	-	22	3101	c.2805T>C	c.(2803-2805)gaT>gaC	p.D935D		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	935					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TCACAAGATCATCCACATCTT	0.368			T	NTRK1	papillary thyroid																																p.D935D		.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR-228	0			c.T2805C						.						213	200	204					1																	186316562		1964	4159	6123	SO:0001819	synonymous_variant	7175	exon22			AAGATCATCCACA	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"translocated promoter region (to activated MET oncogene)"			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2805T>C	1.37:g.186316562A>G		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	70	4	NM_003292	0	0	3	4	1	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																			.		0.368	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		G	186316562	A	G	186316562	2	3	146	1	0	0	0	0	0	0	0	1	16449	214	8	3		3	TPR	1	186316562	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	19426559	186316562	62934059	10	12989											
ASPM	259266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	197072290	197072290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcactttcataccacgatAagctgactgtaaagttacta	13	13	5	10	1	2	1	2	1	1	0	3	2	2	1	1	0	3	3	1	0	6	6			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:197072290A>G	ENST00000367409.4	-	18	6347	c.6091T>C	c.(6091-6093)Tat>Cat	p.Y2031H	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2031	IQ 14. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						ATACCACGATAAGCTGACTGT	0.328																																					p.Y2031H		.											.	ASPM-615	0			c.T6091C						.						94	99	97					1																	197072290		2203	4298	6501	SO:0001583	missense	259266	exon18			CACGATAAGCTGA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.6091T>C	1.37:g.197072290A>G	ENSP00000356379:p.Tyr2031His	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	100	17	NM_018136	0	0	1	1	0	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	a	19.52	3.842459	0.71488	.	.	ENSG00000066279	ENST00000367409	T	0.27557	1.66	5.6	4.46	0.54185	.	0.174809	0.40302	N	0.001123	T	0.59959	0.2232	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.63541	-0.6614	10	0.41790	T	0.15	.	11.3347	0.49496	0.8639:0.0:0.0:0.1361	.	2031	Q8IZT6	ASPM_HUMAN	H	2031	ENSP00000356379:Y2031H	ENSP00000356379:Y2031H	Y	-	1	0	ASPM	195338913	1.000000	0.71417	0.632000	0.29296	0.972000	0.66771	7.212000	0.77941	0.930000	0.37217	0.524000	0.50904	TAT	.		0.328	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197072290	A	G	197072290	3	3	146	1	0	0	0	0	1	0	0	0	1057	362	13	3	4386	3	ASPM	1	197072290	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	10755728	197072290	52178331	11	12990											
CR1L	1379	broad.mit.edu	37	chr1	207890832	207890832	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttttgtccaaatcctccaGctatccttaatgggagacac	10	13	6	12	0	1	1	0	0	1	1	5	2	5	1	4	1	1	1	4	1	3	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:207890832G>T	ENST00000508064.2	+	11	1498	c.1438G>T	c.(1438-1440)Gct>Tct	p.A480S		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	480	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						AAATCCTCCAGCTATCCTTAA	0.413																																					p.A480S													.	CR1L-46	0			c.G1438T						.						94	87	89					1																	207890832		1819	4074	5893	SO:0001583	missense	1379	exon11			CCTCCAGCTATCC	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"Complement system"	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1438G>T	1.37:g.207890832G>T	ENSP00000421736:p.Ala480Ser	Somatic	275	0		WXS	Illumina HiSeq	Phase_I	200	6	NM_175710	0	0	5	5	0	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	.	.	.	.	.	.	.	.	.	.	.	1.011	-0.687807	0.03328	.	.	ENSG00000197721	ENST00000508064	T	0.62941	-0.01	2.9	-5.8	0.02347	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.33294	0.0858	N	0.16862	0.45	0.09310	N	1	B	0.21071	0.051	B	0.28305	0.088	T	0.33777	-0.9855	9	0.10636	T	0.68	.	0.2712	0.00232	0.3235:0.2626:0.1505:0.2635	.	480	Q2VPA4	CR1L_HUMAN	S	480	ENSP00000421736:A480S	ENSP00000421736:A480S	A	+	1	0	CR1L	205957455	0.000000	0.05858	0.000000	0.03702	0.336000	0.28762	-0.640000	0.05440	-2.312000	0.00648	0.305000	0.20034	GCT	.		0.413	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		T	207890832	G	T	207890832	3	4	146	1	0	0	0	0	1	0	0	0	3847	971	34	4	1480	4	CR1L	1	207890832	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	10818542	207890832	41359789	12	12991											
IFT172	26160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27702392	27702392	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttacctggctaggtcccacaTacgtcaactcaaacttgttc	10	12	6	13	1	2	0	2	0	0	0	4	0	3	0	2	2	4	2	2	2	5	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:27702392T>A	ENST00000260570.3	-	10	1092	c.989A>T	c.(988-990)tAt>tTt	p.Y330F	IFT172_ENST00000359466.6_Missense_Mutation_p.Y330F|IFT172_ENST00000416524.2_Missense_Mutation_p.Y309F	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	330					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					AGGTCCCACATACGTCAACTC	0.507																																					p.Y330F		.											.	IFT172-154	0			c.A989T						.						164	142	150					2																	27702392		2203	4300	6503	SO:0001583	missense	26160	exon10			CCCACATACGTCA	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.989A>T	2.37:g.27702392T>A	ENSP00000260570:p.Tyr330Phe	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	97	12	NM_015662	0	0	4	4	0	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	37	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.547345	0.65311	.	.	ENSG00000138002	ENST00000260570;ENST00000359466;ENST00000416524	T;T;T	0.23147	1.92;1.92;1.92	5.64	5.64	0.86602	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.30230	0.0758	M	0.64404	1.975	0.80722	D	1	B;P;B;B	0.35821	0.394;0.523;0.394;0.322	B;B;B;B	0.38378	0.228;0.272;0.144;0.2	T	0.04320	-1.0960	10	0.25106	T	0.35	-9.0488	14.6686	0.68926	0.0:0.0:0.0:1.0	.	330;330;330;330	A5PKZ0;Q9UG01-2;E7EP25;Q9UG01	.;.;.;IF172_HUMAN	F	330;330;309	ENSP00000260570:Y330F;ENSP00000352443:Y330F;ENSP00000407408:Y309F	ENSP00000260570:Y330F	Y	-	2	0	IFT172	27555896	1.000000	0.71417	0.988000	0.46212	0.937000	0.57800	7.558000	0.82253	2.138000	0.66242	0.533000	0.62120	TAT	.		0.507	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		A	27702392	T	A	27702392	3	1	146	1	0	0	0	0	1	0	0	0	7578	1406	49	5	4416	5	IFT172	2	27702392	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		27702392	215496981	13	12992											
TCF7L1	83439	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	85361150	85361150	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctccgcaggcggagaggcgCccgcagcccgtccgggacac	6	2	15	18	6	0	1	0	0	0	1	2	3	2	2	5	4	1	2	5	4	0	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:85361150C>G	ENST00000282111.3	+	2	536	c.261C>G	c.(259-261)cgC>cgG	p.R87R		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	87					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CGGAGAGGCGCCCGCAGCCCG	0.697																																					p.R87R		.											.	TCF7L1-585	0			c.C261G						.						19	25	23					2																	85361150		2200	4299	6499	SO:0001819	synonymous_variant	83439	exon2			GAGGCGCCCGCAG	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.261C>G	2.37:g.85361150C>G		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	117	19	NM_031283	0	0	0	0	0	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000282111.3	37	CCDS1971.1																																																																																			.		0.697	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		G	85361150	C	G	85361150	2	3	146	1	0	0	0	0	0	0	0	1	15729	726	26	4		4	TCF7L1	2	85361150	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	57658758	85361150	157838223	14	12993											
RNF103	7844	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	86832185	86832185	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggcatattatatatgccaAtatctgtcatataactcttg	13	16	5	7	0	3	0	1	0	2	0	3	0	3	0	1	1	2	1	1	1	8	8			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:86832185A>G	ENST00000237455.4	-	4	1807	c.839T>C	c.(838-840)aTt>aCt	p.I280T	AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000426549.1_RNA|AC015971.2_ENST00000439077.1_RNA|RNF103_ENST00000477307.1_5'UTR|CHMP3_ENST00000439940.2_Intron|RNF103-CHMP3_ENST00000604011.1_Intron	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	280					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						ATATATGCCAATATCTGTCAT	0.353																																					p.I280T		.											.	RNF103-226	0			c.T839C						.						45	48	47					2																	86832185		2203	4300	6503	SO:0001583	missense	7844	exon4			ATGCCAATATCTG	D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.839T>C	2.37:g.86832185A>G	ENSP00000237455:p.Ile280Thr	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	133	8	NM_005667	0	0	6	6	0	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Missense_Mutation	SNP	ENST00000237455.4	37	CCDS33237.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790231	0.31685	.	.	ENSG00000239305	ENST00000237455	T	0.48522	0.81	5.1	5.1	0.69264	.	0.052243	0.85682	D	0.000000	T	0.43033	0.1229	L	0.51422	1.61	0.53688	D	0.999973	B	0.20052	0.041	B	0.16289	0.015	T	0.28073	-1.0055	10	0.30078	T	0.28	-13.0155	14.881	0.70534	1.0:0.0:0.0:0.0	.	280	O00237	RN103_HUMAN	T	280	ENSP00000237455:I280T	ENSP00000237455:I280T	I	-	2	0	RNF103	86685696	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.953000	0.93041	1.937000	0.56155	0.377000	0.23210	ATT	.		0.353	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		G	86832185	A	G	86832185	3	3	146	1	0	0	0	0	1	0	0	0	13455	101	4	3	1222	3	RNF103	2	86832185	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	1471035	86832185	156367188	15	12994											
MALL	7851	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	110873286	110873286	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctcgggcaggaagaaggcGaaagggatggtgaggaacag	14	3	19	5	2	0	2	0	1	0	1	1	6	0	5	0	6	2	2	0	6	4	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:110873286G>A	ENST00000272462.2	-	1	857	c.84C>T	c.(82-84)ttC>ttT	p.F28F	MALL_ENST00000427178.1_Silent_p.F28F	NM_005434.4	NP_005425.1	Q13021	MALL_HUMAN	mal, T-cell differentiation protein-like	28	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cholesterol homeostasis (GO:0042632)	clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	9				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)		GGAAGAAGGCGAAAGGGATGG	0.726																																					p.F28F		.											.	MALL-92	0			c.C84T						.						21	22	21					2																	110873286		2184	4286	6470	SO:0001819	synonymous_variant	7851	exon1			GAAGGCGAAAGGG	U17077	CCDS2085.1	2q13	2008-02-05			ENSG00000144063	ENSG00000144063			6818	protein-coding gene	gene with protein product		602022				9326933	Standard	NM_005434		Approved	BENE	uc002tfk.3	Q13021	OTTHUMG00000131196	ENST00000272462.2:c.84C>T	2.37:g.110873286G>A		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	178	22	NM_005434	0	0	3	3	0	B3KWR6|Q9BTU0	Silent	SNP	ENST00000272462.2	37	CCDS2085.1																																																																																			.		0.726	MALL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253921.1	NM_005434		A	110873286	G	A	110873286	2	1	146	1	0	0	0	0	0	0	0	1	9226	1049	37	1		1	MALL	2	110873286	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	24041101	110873286	132326087	16	12995											
SLC20A1	6574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	113418053	113418053	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaccaatatggcttctacTctatggtggtgttggtatct	9	15	9	8	0	3	0	0	0	3	0	3	0	3	0	1	4	2	3	1	4	6	6			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:113418053T>C	ENST00000272542.3	+	9	2236	c.1697T>C	c.(1696-1698)cTc>cCc	p.L566P		NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	566					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						TGGCTTCTACTCTATGGTGGT	0.458																																					p.L566P		.											.	SLC20A1-92	0			c.T1697C						.						180	174	176					2																	113418053		2203	4300	6503	SO:0001583	missense	6574	exon9			TTCTACTCTATGG		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"Solute carriers"	10946	protein-coding gene	gene with protein product	"gibbon ape leukemia virus receptor 1"	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.1697T>C	2.37:g.113418053T>C	ENSP00000272542:p.Leu566Pro	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	176	29	NM_005415	0	0	12	18	6	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	37	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.570460	0.86542	.	.	ENSG00000144136	ENST00000272542	D	0.91996	-2.95	5.81	5.81	0.92471	.	0.062816	0.64402	D	0.000004	D	0.95191	0.8441	M	0.68593	2.085	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.992	D	0.95405	0.8493	10	0.66056	D	0.02	-33.1091	14.1127	0.65132	0.0:0.0:0.0:1.0	.	566;566	A7LNJ1;Q8WUM9	.;S20A1_HUMAN	P	566	ENSP00000272542:L566P	ENSP00000272542:L566P	L	+	2	0	SLC20A1	113134524	1.000000	0.71417	0.926000	0.36857	0.997000	0.91878	8.040000	0.89188	2.226000	0.72624	0.482000	0.46254	CTC	.		0.458	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		C	113418053	T	C	113418053	3	2	146	1	0	0	0	0	1	0	0	0	14470	1551	54	3	1727	3	SLC20A1	2	113418053	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	2544767	113418053	129781320	17	12996											
INHBB	3625	hgsc.bcm.edu	37	chr2	121106693	121106693	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatggcctcgcctcctcccGggtccgcctatacttcttca	5	11	8	17	3	2	1	1	0	1	1	6	1	5	1	6	2	1	0	6	2	2	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:121106693G>A	ENST00000295228.3	+	2	513	c.467G>A	c.(466-468)cGg>cAg	p.R156Q		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	156					activin receptor signaling pathway (GO:0032924)|cell differentiation (GO:0030154)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|cellular response to starvation (GO:0009267)|defense response (GO:0006952)|fat cell differentiation (GO:0045444)|growth (GO:0040007)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of hepatocyte growth factor biosynthetic process (GO:0048178)|negative regulation of insulin secretion (GO:0046676)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|response to mechanical stimulus (GO:0009612)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|host cell surface receptor binding (GO:0046789)|protein homodimerization activity (GO:0042803)	p.R156Q(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(4)|pancreas(2)|skin(2)	15		Prostate(154;0.122)				GCCTCCTCCCGGGTCCGCCTA	0.557																																					p.R156Q		.											.	INHBB-93	1	Substitution - Missense(1)	large_intestine(1)	c.G467A						.						53	58	56					2																	121106693		2203	4300	6503	SO:0001583	missense	3625	exon2			CCTCCCGGGTCCG		CCDS2132.1	2q14.2	2014-01-30	2007-07-30		ENSG00000163083	ENSG00000163083		"Endogenous ligands"	6067	protein-coding gene	gene with protein product		147390	"inhibin, beta B (activin AB beta polypeptide)"			3345731	Standard	NM_002193		Approved		uc002tmn.2	P09529	OTTHUMG00000131437	ENST00000295228.3:c.467G>A	2.37:g.121106693G>A	ENSP00000295228:p.Arg156Gln	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	96	5	NM_002193	0	0	3	3	0	Q53T31|Q8N1D3	Missense_Mutation	SNP	ENST00000295228.3	37	CCDS2132.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.497539	0.26861	.	.	ENSG00000163083	ENST00000295228	T	0.66995	-0.24	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.555848	0.17053	N	0.188863	T	0.53850	0.1822	L	0.31664	0.95	0.33909	D	0.639429	B	0.24823	0.112	B	0.26094	0.066	T	0.59316	-0.7477	10	0.30854	T	0.27	-3.725	11.2497	0.49017	0.0848:0.0:0.9151:0.0	.	156	P09529	INHBB_HUMAN	Q	156	ENSP00000295228:R156Q	ENSP00000295228:R156Q	R	+	2	0	INHBB	120823163	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.966000	0.70395	2.804000	0.96469	0.655000	0.94253	CGG	.		0.557	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1			A	121106693	G	A	121106693	3	1	146	1	0	0	0	0	1	0	0	0	7763	1116	39	1	473	1	INHBB	2	121106693	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	7688640	121106693	122092680	18	12997											
ANKRD44	91526	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	197878244	197878244	+	Frame_Shift_Del	DEL	G	G	-																															acaagacctacctgaggcatGaagtggggttcttttggtta																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:197878244delG	ENST00000328737.2	-	18	1916	c.1840delC	c.(1840-1842)catfs	p.H614fs	ANKRD44_ENST00000337207.5_Frame_Shift_Del_p.H614fs|ANKRD44_ENST00000282272.8_Frame_Shift_Del_p.H631fs|ANKRD44_ENST00000450567.1_Frame_Shift_Del_p.H614fs			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	639										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CCTGAGGCATGAAGTGGGGTT	0.443																																					p.H639fs		.											.	ANKRD44-230	0			c.1915delC						.						168	160	163					2																	197878244		2203	4300	6503	SO:0001589	frameshift_variant	91526	exon18			.	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	25259	protein-coding gene	gene with protein product	"protein phosphatase 6 ankyrin repeat subunit B"						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1840delC	2.37:g.197878244delG	ENSP00000331516:p.His614fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	134	31	NM_001195144	0	0	0	0	0	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Frame_Shift_Del	DEL	ENST00000328737.2	37																																																																																				.		0.443	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		-	197878244	G	-	197878244	7	5	146	1	0	1	0	1	0	0	0	0	672	1290	45	0	955	0	ANKRD44	2	197878244	Frame_Shift_Del	DEL	G	TCGA-KV-A6GD-01A-11D-A31X-10	76771551	197878244	45321129	19	12998											
EEF1B2	1933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	207027278	207027278	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgggatgatgagacagatAtggcgaaattagaggagtgc	13	9	15	4	1	0	4	0	2	0	3	0	8	0	6	0	3	1	0	0	3	3	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:207027278A>T	ENST00000392222.2	+	5	838	c.463A>T	c.(463-465)Atg>Ttg	p.M155L	EEF1B2_ENST00000392221.1_Missense_Mutation_p.M155L|NDUFS1_ENST00000233190.6_5'Flank|SNORD51_ENST00000384320.2_RNA|EEF1B2_ENST00000236957.5_Missense_Mutation_p.M155L|SNORA41_ENST00000384675.1_RNA	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	155					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)			breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						TGAGACAGATATGGCGAAATT	0.388																																					p.M155L		.											.	EEF1B2-227	0			c.A463T						.						125	132	129					2																	207027278		2203	4300	6503	SO:0001583	missense	1933	exon6			ACAGATATGGCGA	X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.463A>T	2.37:g.207027278A>T	ENSP00000376056:p.Met155Leu	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	209	28	NM_021121	1	0	640	769	128	A8K795|Q6IBH9	Missense_Mutation	SNP	ENST00000392222.2	37	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.990128	0.54041	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222	.	.	.	5.24	5.24	0.73138	Translation elongation factor EF1B/ribosomal protein S6 (1);Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange (3);	0.071117	0.85682	D	0.000000	T	0.54902	0.1887	L	0.39245	1.2	0.80722	D	1	B	0.02656	0.0	B	0.20384	0.029	T	0.50651	-0.8803	9	0.33940	T	0.23	-16.9302	15.1403	0.72607	1.0:0.0:0.0:0.0	.	155	P24534	EF1B_HUMAN	L	155	.	ENSP00000236957:M155L	M	+	1	0	EEF1B2	206735523	1.000000	0.71417	0.994000	0.49952	0.958000	0.62258	9.237000	0.95368	1.984000	0.57885	0.533000	0.62120	ATG	.		0.388	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663		T	207027278	A	T	207027278	3	4	146	1	0	0	0	0	1	0	0	0	4936	449	16	5	481	5	EEF1B2	2	207027278	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	9149034	207027278	36172095	20	12999											
COL4A3	1285	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	228131751	228131751	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acagtgcccttatatcccagGgcctcccggtctcccaggat	7	9	9	16	1	1	0	0	0	1	0	4	1	3	1	5	3	1	0	5	3	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:228131751G>T	ENST00000396578.3	+	23	1613	c.1451G>T	c.(1450-1452)gGg>gTg	p.G484V	AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000433324.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	484	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		TATATCCCAGGGCCTCCCGGT	0.468																																					p.G484V													.	COL4A3-132	0			c.G1451T						.						66	66	66					2																	228131751		1865	4098	5963	SO:0001583	missense	1285	exon23			TCCCAGGGCCTCC		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"Collagens"	2204	protein-coding gene	gene with protein product	"tumstatin"	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.1451G>T	2.37:g.228131751G>T	ENSP00000379823:p.Gly484Val	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	74	14	NM_000091	0	0	0	1	1	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971284	0.34754	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.99353	-5.77	5.36	5.36	0.76844	.	0.000000	0.56097	D	0.000028	D	0.99579	0.9848	H	0.95365	3.66	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97996	1.0357	10	0.72032	D	0.01	.	14.5754	0.68243	0.0:0.0:1.0:0.0	.	484;484;484;484	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	V	484	ENSP00000379823:G484V	ENSP00000323334:G484V	G	+	2	0	COL4A3	227839995	1.000000	0.71417	0.778000	0.31720	0.010000	0.07245	4.981000	0.63819	2.515000	0.84797	0.655000	0.94253	GGG	.		0.468	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228131751	G	T	228131751	3	4	146	1	0	0	0	0	1	0	0	0	3697	1232	43	4	1541	4	COL4A3	2	228131751	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	21104473	228131751	15067622	21	13000											
RAB17	64284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	238494741	238494741	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccaggagaaccagcttgaaCacacggggctggctgggggc	9	4	16	12	1	0	2	0	1	0	1	0	3	0	2	2	6	3	3	2	6	2	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:238494741C>A	ENST00000264601.3	-	2	686	c.57G>T	c.(55-57)gtG>gtT	p.V19V	RAB17_ENST00000409576.1_Intron|RAB17_ENST00000416106.1_5'UTR|RAB17_ENST00000409822.1_Intron|RAB17_ENST00000538644.1_5'UTR	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	19			V -> A (in dbSNP:rs3751112). {ECO:0000269|Ref.3}.		cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		CCAGCTTGAACACACGGGGCT	0.597																																					p.V19V	Colon(56;987 1029 6466 13943 27336)	.											.	RAB17-227	0			c.G57T						.						57	57	57					2																	238494741		2203	4300	6503	SO:0001819	synonymous_variant	64284	exon2			CTTGAACACACGG	AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839		"RAB, member RAS oncogene"	16523	protein-coding gene	gene with protein product		602206				9624171	Standard	NM_022449		Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.57G>T	2.37:g.238494741C>A		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	120	18	NM_022449	0	0	24	37	13	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Silent	SNP	ENST00000264601.3	37	CCDS2520.1	.	.	.	.	.	.	.	.	.	.	C	6.279	0.419620	0.11928	.	.	ENSG00000124839	ENST00000430445	.	.	.	4.69	-3.2	0.05156	.	.	.	.	.	T	0.49029	0.1533	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.40515	-0.9559	4	.	.	.	-6.0609	5.8207	0.18526	0.0869:0.4881:0.2678:0.1572	.	.	.	.	F	1	.	.	C	-	2	0	RAB17	238159480	0.001000	0.12720	0.004000	0.12327	0.070000	0.16714	-0.140000	0.10342	-0.948000	0.03668	-1.094000	0.02160	TGT	.		0.597	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2			A	238494741	C	A	238494741	2	1	146	1	0	0	0	0	0	0	0	1	12934	465	17	4		4	RAB17	2	238494741	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	10362990	238494741	4704632	22	13001											
HDLBP	3069	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	242173343	242173343	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atcttgggatggtatttgggGtctacagtgacactcagctt	8	14	12	7	0	3	1	1	1	2	0	3	2	3	2	0	4	2	2	0	4	2	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:242173343G>A	ENST00000391975.1	-	24	3407	c.3180C>T	c.(3178-3180)gaC>gaT	p.D1060D	HDLBP_ENST00000391976.2_Silent_p.D1060D|HDLBP_ENST00000427183.2_Silent_p.D1027D|HDLBP_ENST00000310931.4_Silent_p.D1060D	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1060	KH 13. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		GGTATTTGGGGTCTACAGTGA	0.468																																					p.D1060D													.	HDLBP-290	0			c.C3180T						.						159	146	151					2																	242173343		2203	4300	6503	SO:0001819	synonymous_variant	3069	exon24			TTTGGGGTCTACA		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3180C>T	2.37:g.242173343G>A		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	90	5	NM_005336	0	0	90	123	33	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	37	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	9.945	1.218600	0.22373	.	.	ENSG00000115677	ENST00000373292	.	.	.	5.56	-0.0544	0.13813	.	.	.	.	.	T	0.59797	0.2220	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56685	-0.7938	4	.	.	.	-47.1969	12.584	0.56406	0.4388:0.0:0.5612:0.0	.	.	.	.	S	869	.	.	P	-	1	0	HDLBP	241822016	0.997000	0.39634	0.995000	0.50966	0.986000	0.74619	0.367000	0.20382	0.046000	0.15833	0.563000	0.77884	CCC	.		0.468	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		A	242173343	G	A	242173343	2	1	146	1	0	0	0	0	0	0	0	1	7046	1252	44	2		2	HDLBP	2	242173343	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	3678602	242173343	1026030	23	13002											
SLC6A6	6533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	14508107	14508107	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgctgccgggcgcgggcgcAggcatcaagttctatctgta	7	8	14	12	5	3	0	1	0	2	0	3	0	3	0	1	3	1	5	1	3	3	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr3:14508107A>G	ENST00000454876.2	+	7	1145	c.816A>G	c.(814-816)gcA>gcG	p.A272A	SLC6A6_ENST00000360861.3_Silent_p.A272A			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	272				A -> R (in Ref. 1; CAA79481). {ECO:0000305}.	amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						GCGCGGGCGCAGGCATCAAGT	0.632																																					p.A272A		.											.	SLC6A6-91	0			c.A816G						.						80	70	73					3																	14508107		2203	4300	6503	SO:0001819	synonymous_variant	6533	exon7			GGGCGCAGGCATC		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"Solute carriers"	11052	protein-coding gene	gene with protein product	"taurine transporter"	186854	"solute carrier family 6 (neurotransmitter transporter, taurine), member 6"			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.816A>G	3.37:g.14508107A>G		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	64	9	NM_003043	0	0	4	4	0	B2RNU7|Q9BRI2|Q9BXB0	Silent	SNP	ENST00000454876.2	37	CCDS33705.1																																																																																			.		0.632	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		G	14508107	A	G	14508107	2	3	146	1	0	0	0	0	0	0	0	1	14720	175	7	3		3	SLC6A6	3	14508107	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		14508107	183514323	24	13003											
TMEM115	11070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50396218	50396218	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagctccaaggccccccAgaggggctccagcaaacgcc	10	2	12	17	1	0	1	0	0	0	1	2	2	2	1	6	3	4	4	6	3	2	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr3:50396218A>G	ENST00000266025.3	-	1	823	c.277T>C	c.(277-279)Tgg>Cgg	p.W93R	XXcos-LUCA11.5_ENST00000606589.1_Intron	NM_007024.4	NP_008955.1	Q12893	TM115_HUMAN	transmembrane protein 115	93					negative regulation of cell proliferation (GO:0008285)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)|prostate(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AAGGCCCCCCAGAGGGGCTCC	0.622																																					p.W93R		.											.	TMEM115-278	0			c.T277C						.						55	68	64					3																	50396218		2203	4300	6503	SO:0001583	missense	11070	exon1			CCCCCCAGAGGGG	BC011948	CCDS2828.1	3p21.31	2008-11-04			ENSG00000126062	ENSG00000126062			30055	protein-coding gene	gene with protein product	"placental protein 6"	607069				11085536	Standard	NM_007024		Approved	PL6	uc003dan.1	Q12893	OTTHUMG00000044212	ENST00000266025.3:c.277T>C	3.37:g.50396218A>G	ENSP00000266025:p.Trp93Arg	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	86	12	NM_007024	0	0	94	122	28	A2IDB7|O14568|Q6IAY4|Q9UIX3	Missense_Mutation	SNP	ENST00000266025.3	37	CCDS2828.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.371161	0.82573	.	.	ENSG00000126062	ENST00000266025	T	0.11712	2.75	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.46555	-0.9183	10	0.87932	D	0	.	14.4388	0.67301	1.0:0.0:0.0:0.0	.	93	Q12893	TM115_HUMAN	R	93	ENSP00000266025:W93R	ENSP00000266025:W93R	W	-	1	0	TMEM115	50371222	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.943000	0.92975	2.110000	0.64415	0.460000	0.39030	TGG	.		0.622	TMEM115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102784.3	NM_007024		G	50396218	A	G	50396218	3	3	146	1	0	0	0	0	1	0	0	0	16061	188	7	3	786	3	TMEM115	3	50396218	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	35888111	50396218	147626212	25	13004											
P2RY1	5028	hgsc.bcm.edu;broad.mit.edu	37	chr3	152554007	152554007	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgtttctgacatgcatcAgtgcccaccggtacagcggt	7	12	10	12	2	3	1	1	1	2	0	3	1	3	1	2	2	4	3	2	2	1	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr3:152554007A>G	ENST00000305097.3	+	1	1272	c.436A>G	c.(436-438)Agt>Ggt	p.S146G		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	146					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			GACATGCATCAGTGCCCACCG	0.507																																					p.S146G		.											.	P2RY1-500	0			c.A436G						.						91	79	83					3																	152554007		2203	4300	6503	SO:0001583	missense	5028	exon1			TGCATCAGTGCCC	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.436A>G	3.37:g.152554007A>G	ENSP00000304767:p.Ser146Gly	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	90	5	NM_002563	0	0	0	0	0		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164790	0.78339	.	.	ENSG00000169860	ENST00000305097	T	0.80994	-1.44	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.90844	0.7124	M	0.92122	3.275	0.58432	D	0.999999	D	0.63046	0.992	P	0.60012	0.867	D	0.92885	0.6326	10	0.72032	D	0.01	.	15.2728	0.73717	1.0:0.0:0.0:0.0	.	146	P47900	P2RY1_HUMAN	G	146	ENSP00000304767:S146G	ENSP00000304767:S146G	S	+	1	0	P2RY1	154036697	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	9.210000	0.95106	2.186000	0.69663	0.533000	0.62120	AGT	.		0.507	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		G	152554007	A	G	152554007	3	3	146	1	0	0	0	0	1	0	0	0	11372	188	7	3	438	3	P2RY1	3	152554007	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	102157789	152554007	45468423	26	13005											
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1807653	1807653	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggcccggggcatggagtacTtggcctcccagaaggtgggc	6	7	17	11	1	0	1	0	0	0	1	1	2	1	2	3	7	1	2	3	7	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr4:1807653T>A	ENST00000260795.2	+	12	1924	c.1822T>A	c.(1822-1824)Ttg>Atg	p.L608M	FGFR3_ENST00000440486.2_Missense_Mutation_p.L608M|FGFR3_ENST00000340107.4_Missense_Mutation_p.L610M|FGFR3_ENST00000481110.2_Missense_Mutation_p.L609M|FGFR3_ENST00000352904.1_Missense_Mutation_p.L496M|FGFR3_ENST00000412135.2_Missense_Mutation_p.L496M			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	608	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CATGGAGTACTTGGCCTCCCA	0.662		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.L610M		.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3-9542	0			c.T1828A						.						39	47	44					4																	1807653		2203	4299	6502	SO:0001583	missense	2261	exon13	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GAGTACTTGGCCT	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3690	protein-coding gene	gene with protein product		134934	"achondroplasia, thanatophoric dwarfism"	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1822T>A	4.37:g.1807653T>A	ENSP00000260795:p.Leu608Met	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	55	17	NM_001163213	0	0	0	0	0	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	c	11.98	1.799537	0.31869	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04;-3.04	4.18	1.33	0.21861	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.95586	0.8565	M	0.86805	2.84	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.998;0.991	D	0.94568	0.7768	10	0.87932	D	0	.	10.2771	0.43517	0.0:0.681:0.0:0.319	.	610;496;608;609	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	M	609;610;608;496;608;496	ENSP00000420533:L609M;ENSP00000339824:L610M;ENSP00000414914:L608M;ENSP00000412903:L496M;ENSP00000260795:L608M;ENSP00000231803:L496M	ENSP00000260795:L608M	L	+	1	2	FGFR3	1777451	0.995000	0.38212	0.995000	0.50966	0.390000	0.30446	0.568000	0.23623	0.311000	0.23014	-1.193000	0.01689	TTG	.		0.662	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		A	1807653	T	A	1807653	3	1	146	1	0	0	0	0	1	0	0	0	5886	1606	56	5	2023	5	FGFR3	4	1807653	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		1807653	189346623	27	13006											
SLC4A4	8671	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	72413388	72413388	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaagagtcactggaacccTtgtgtttattctgactggtc	10	13	9	9	0	2	2	1	1	1	1	3	3	2	3	1	2	1	1	1	2	3	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr4:72413388T>C	ENST00000264485.5	+	20	2762	c.2645T>C	c.(2644-2646)cTt>cCt	p.L882P	SLC4A4_ENST00000340595.3_Missense_Mutation_p.L838P|SLC4A4_ENST00000425175.1_Missense_Mutation_p.L882P|SLC4A4_ENST00000351898.6_Intron	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	882					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	ACTGGAACCCTTGTGTTTATT	0.373																																					p.L882P		.											.	SLC4A4-95	0			c.T2645C						.						217	212	214					4																	72413388		2203	4300	6503	SO:0001583	missense	8671	exon20			GAACCCTTGTGTT	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"Solute carriers"	11030	protein-coding gene	gene with protein product		603345	"solute carrier family 4, sodium bicarbonate cotransporter, member 4"	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2645T>C	4.37:g.72413388T>C	ENSP00000264485:p.Leu882Pro	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	82	7	NM_001098484	0	0	1	1	0	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277920	0.80692	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000340595	D;D;D	0.82167	-1.58;-1.58;-1.58	5.81	5.81	0.92471	Bicarbonate transporter, C-terminal (1);	0.329506	0.33980	N	0.004364	D	0.87661	0.6233	M	0.80183	2.485	0.80722	D	1	P;P;B	0.40230	0.708;0.481;0.242	P;B;B	0.46208	0.507;0.419;0.427	D	0.89124	0.3505	10	0.87932	D	0	.	16.167	0.81768	0.0:0.0:0.0:1.0	.	882;838;882	A5JJ20;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	P	882;882;838	ENSP00000264485:L882P;ENSP00000393557:L882P;ENSP00000344272:L838P	ENSP00000264485:L882P	L	+	2	0	SLC4A4	72632252	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.184000	0.72008	2.210000	0.71456	0.533000	0.62120	CTT	.		0.373	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		C	72413388	T	C	72413388	3	2	146	1	0	0	0	0	1	0	0	0	14688	1609	56	3	2840	3	SLC4A4	4	72413388	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	70605735	72413388	118740888	28	13007											
NKD2	85409	broad.mit.edu	37	chr5	1038447	1038449	+	In_Frame_Del	DEL	CAC	CAC	-																															agcaccaccaccaccacgagCaccaccaccaccaccaccac																								rs3840989		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:1038447_1038449delCAC	ENST00000296849.5	+	10	1544_1546	c.1315_1317delCAC	c.(1315-1317)cacdel	p.H447del	NKD2_ENST00000382730.2_In_Frame_Del_p.P86del|NKD2_ENST00000274150.4_3'UTR	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	447	His-rich.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccaccacgagcaccaccaccacc	0.69																																					p.439_439del													.	NKD2-226	0			c.1315_1317del						.																																			SO:0001651	inframe_deletion	85409	exon10			CACGAGCACCACC	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"EF-hand domain containing"	17046	protein-coding gene	gene with protein product	"naked cuticle-2", "Dvl-binding protein NKD2"	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1315_1317delCAC	5.37:g.1038456_1038458delCAC	ENSP00000296849:p.His447del	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	16	5	NM_033120	0	0	0	0	0	Q96EK8|Q9BSN0	In_Frame_Del	DEL	ENST00000296849.5	37	CCDS3859.1																																																																																			.		0.69	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		-	1038449	CAC	-	1038447	7	5	146	1	0	1	0	1	0	0	0	0	10468	710	25	0	1353	0	NKD2	5	1038447	In_Frame_Del	DEL	CAC	TCGA-KV-A6GD-01A-11D-A31X-10		1038447	179876813	29	13008											
TRIO	7204	broad.mit.edu	37	chr5	14358383	14358385	+	In_Frame_Del	DEL	CAG	CAG	-																															acctcatcaagcgctttggcCagcagcagcagaccaccctg																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:14358383_14358385delCAG	ENST00000344204.4	+	12	2167_2169	c.2143_2145delCAG	c.(2143-2145)cagdel	p.Q718del	TRIO_ENST00000537187.1_In_Frame_Del_p.Q718del|TRIO_ENST00000509967.2_In_Frame_Del_p.Q669del	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	718	Poly-Gln.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GCGCTTTGGCCAGCAGCAGCAGA	0.631																																					p.715_715del													.	TRIO-562	0			c.2143_2145del						.																																			SO:0001651	inframe_deletion	7204	exon12			TTTGGCCAGCAGC	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing"	12303	protein-coding gene	gene with protein product		601893	"triple functional domain (PTPRF interacting)"			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.2143_2145delCAG	5.37:g.14358392_14358394delCAG	ENSP00000339299:p.Gln718del	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	233	7	NM_007118	0	0	0	0	0	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	In_Frame_Del	DEL	ENST00000344204.4	37	CCDS3883.1																																																																																			.		0.631	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		-	14358385	CAG	-	14358383	7	5	146	1	0	1	0	1	0	0	0	0	16585	595	21	0	2189	0	TRIO	5	14358383	In_Frame_Del	DEL	CAG	TCGA-KV-A6GD-01A-11D-A31X-10	13319936	14358383	166556877	30	13009											
ISL1	3670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	50680410	50680410	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctatgtgttggttgcggcAatcagattcacgatcagtat	9	13	10	9	2	3	1	3	0	0	1	3	2	3	1	1	2	1	4	1	2	3	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:50680410A>G	ENST00000230658.7	+	2	649	c.64A>G	c.(64-66)Aat>Gat	p.N22D	ISL1_ENST00000511384.1_Missense_Mutation_p.N22D|CTD-2314G24.2_ENST00000559112.2_RNA	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	22	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				atrial septum morphogenesis (GO:0060413)|axon regeneration (GO:0031103)|cardiac cell fate determination (GO:0060913)|cardiac muscle cell myoblast differentiation (GO:0060379)|cardiac right ventricle morphogenesis (GO:0003215)|cellular response to glucocorticoid stimulus (GO:0071385)|endocardial cushion morphogenesis (GO:0003203)|innervation (GO:0060384)|mesenchymal cell differentiation (GO:0048762)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of protein homodimerization activity (GO:0090074)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate specification (GO:0048665)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|pancreas development (GO:0031016)|peripheral nervous system neuron axonogenesis (GO:0048936)|pharyngeal system development (GO:0060037)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage colony-stimulating factor production (GO:1901258)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|retinal ganglion cell axon guidance (GO:0031290)|secondary heart field specification (GO:0003139)|sensory system development (GO:0048880)|spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron differentiation (GO:0021522)|trigeminal nerve development (GO:0021559)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(11)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		Lung NSC(810;0.000845)|Breast(144;0.0411)				TGGTTGCGGCAATCAGATTCA	0.393																																					p.N22D		.											.	ISL1-515	0			c.A64G						.						141	131	134					5																	50680410		1856	4100	5956	SO:0001583	missense	3670	exon2			TGCGGCAATCAGA	BC031213	CCDS43314.1	5q11.2	2012-03-09	2007-07-13		ENSG00000016082	ENSG00000016082		"Homeoboxes / LIM class"	6132	protein-coding gene	gene with protein product		600366	"ISL1 transcription factor, LIM/homeodomain, (islet-1)"			7912209	Standard	NM_002202		Approved	Isl-1, ISLET1	uc003jor.3	P61371	OTTHUMG00000162281	ENST00000230658.7:c.64A>G	5.37:g.50680410A>G	ENSP00000230658:p.Asn22Asp	Somatic	189	0		WXS	Illumina HiSeq	Phase_I	173	47	NM_002202	0	0	0	0	0	P20663|P47894	Missense_Mutation	SNP	ENST00000230658.7	37	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.682347	0.47991	.	.	ENSG00000016082	ENST00000230658;ENST00000503187;ENST00000511384	D;D	0.87029	-2.2;-2.2	6.16	6.16	0.99307	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	T	0.79040	0.4379	N	0.13098	0.295	0.58432	D	0.999993	P	0.36183	0.542	B	0.36030	0.216	T	0.78427	-0.2208	10	0.31617	T	0.26	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	22	P61371	ISL1_HUMAN	D	22	ENSP00000230658:N22D;ENSP00000422676:N22D	ENSP00000230658:N22D	N	+	1	0	ISL1	50716167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.543000	0.82106	2.367000	0.80283	0.528000	0.53228	AAT	.		0.393	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202		G	50680410	A	G	50680410	3	3	146	1	0	0	0	0	1	0	0	0	7877	130	5	3	70	3	ISL1	5	50680410	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	36322027	50680410	130234850	31	13010											
SEC24A	10802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	134060676	134060676	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttttattcctaagggatgaGagtccaatgaaagcaaactt	14	12	8	7	0	0	2	0	2	0	1	2	4	2	3	2	1	2	1	2	1	5	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:134060676G>C	ENST00000398844.2	+	23	3462	c.3174G>C	c.(3172-3174)gaG>gaC	p.E1058D		NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	1058					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TAAGGGATGAGAGTCCAATGA	0.323																																					p.E1058D		.											.	SEC24A-68	0			c.G3174C						.						60	56	57					5																	134060676		1806	4068	5874	SO:0001583	missense	10802	exon23			GGATGAGAGTCCA	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.3174G>C	5.37:g.134060676G>C	ENSP00000381823:p.Glu1058Asp	Somatic	409	0		WXS	Illumina HiSeq	Phase_I	404	43	NM_021982	0	0	0	0	0	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	37	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	G	7.791	0.711484	0.15239	.	.	ENSG00000113615	ENST00000398844	T	0.28666	1.6	5.68	5.68	0.88126	.	0.045285	0.85682	D	0.000000	T	0.11623	0.0283	N	0.04260	-0.245	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29731	-1.0002	10	0.10902	T	0.67	-12.469	5.5239	0.16947	0.1812:0.1697:0.6491:0.0	.	822;1058	B4E205;O95486	.;SC24A_HUMAN	D	1058	ENSP00000381823:E1058D	ENSP00000381823:E1058D	E	+	3	2	SEC24A	134088575	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.734000	0.26101	2.691000	0.91804	0.650000	0.86243	GAG	.		0.323	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			C	134060676	G	C	134060676	3	2	146	1	0	0	0	0	1	0	0	0	14026	933	33	4	3264	4	SEC24A	5	134060676	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	83380266	134060676	46854584	32	13011											
HNRNPA0	10949	broad.mit.edu	37	chr5	137088931	137088931	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagctactgcctccaccGccgccgccgccgccgctctt	3	6	8	24	6	1	0	0	0	1	0	2	0	2	0	10	0	3	2	10	0	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:137088931G>A	ENST00000314940.4	-	1	1108	c.825C>T	c.(823-825)ggC>ggT	p.G275G		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	275	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)	p.G275G(1)		large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			Tgcctccaccgccgccgccgc	0.632																																					p.G275G													.	HNRNPA0-68	1	Substitution - coding silent(1)	large_intestine(1)	c.C825T						.						9	13	11					5																	137088931		1925	3891	5816	SO:0001819	synonymous_variant	10949	exon1			TCCACCGCCGCCG	U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"RNA binding motif (RRM) containing"	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.825C>T	5.37:g.137088931G>A		Somatic	74	1		WXS	Illumina HiSeq	Phase_I	87	7	NM_006805	0	0	94	95	1	Q6IB18	Silent	SNP	ENST00000314940.4	37	CCDS4193.1																																																																																			.		0.632	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805		A	137088931	G	A	137088931	2	1	146	1	0	0	0	0	0	0	0	1	7277	1074	38	1		1	HNRNPA0	5	137088931	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	3028255	137088931	43826329	33	13012											
C5orf41	153222	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	172518246	172518246	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaactaaatgcagtcctgAagaagatgaggaggacgagg	15	5	14	7	1	0	4	0	2	0	2	1	7	1	6	2	3	2	1	2	3	5	1	rs374100928		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:172518246A>T	ENST00000296953.2	+	4	1383	c.1064A>T	c.(1063-1065)gAa>gTa	p.E355V	CREBRF_ENST00000520420.1_Missense_Mutation_p.E355V|CREBRF_ENST00000540014.1_Missense_Mutation_p.E355V|CREBRF_ENST00000522692.1_Missense_Mutation_p.E355V	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	355	Glu-rich.				negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCAGTCCtgaagaagatgag	0.443																																					p.E355V		.											.	.	0			c.A1064T						.						63	50	54					5																	172518246		2203	4300	6503	SO:0001583	missense	153222	exon4			GTCCTGAAGAAGA	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.1064A>T	5.37:g.172518246A>T	ENSP00000296953:p.Glu355Val	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	169	32	NM_153607	0	0	4	5	1	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	37	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.323089	0.60634	.	.	ENSG00000164463	ENST00000522692;ENST00000296953;ENST00000540014;ENST00000520420;ENST00000538538;ENST00000393776	T;T;T;T	0.70749	-0.51;2.19;2.19;-0.51	5.52	5.52	0.82312	.	0.433677	0.23268	N	0.050045	T	0.75525	0.3861	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.991;0.996	T	0.78703	-0.2101	10	0.66056	D	0.02	.	15.3153	0.74069	1.0:0.0:0.0:0.0	.	355;355	Q8IUR6;Q8IUR6-2	CE041_HUMAN;.	V	355	ENSP00000431107:E355V;ENSP00000296953:E355V;ENSP00000440075:E355V;ENSP00000428290:E355V	ENSP00000296953:E355V	E	+	2	0	C5orf41	172450852	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.297000	0.72757	2.103000	0.63969	0.533000	0.62120	GAA	.		0.443	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		T	172518246	A	T	172518246	3	4	146	1	0	0	0	0	1	0	0	0	2306	246	9	5	1074	5	C5orf41	5	172518246	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	35429315	172518246	8397014	34	13013											
AGXT2L2	85007	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	177649897	177649897	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggggaatgatctgcccTcccacactgggcagagactc	9	6	13	13	0	1	2	0	1	1	1	3	4	2	3	2	3	1	2	2	3	1	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:177649897T>C	ENST00000308158.5	-	7	891	c.657A>G	c.(655-657)ggA>ggG	p.G219G	PHYKPL_ENST00000481811.1_Intron	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase	219						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	TGATCTGCCCTCCCACACTGG	0.582																																					p.G219G													.	AGXT2L2-91	0			c.A657G						.						94	80	85					5																	177649897		2203	4300	6503	SO:0001819	synonymous_variant	85007	exon7			CTGCCCTCCCACA	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.657A>G	5.37:g.177649897T>C		Somatic	97	1		WXS	Illumina HiSeq	Phase_I	76	8	NM_153373	0	0	15	21	6	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Silent	SNP	ENST00000308158.5	37	CCDS4434.1																																																																																			.		0.582	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		C	177649897	T	C	177649897	2	2	146	1	0	0	0	0	0	0	0	1	407	1538	54	3		3	AGXT2L2	5	177649897	Silent	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	5131651	177649897	3265363	35	13014											
TBC1D7	51256	broad.mit.edu;ucsc.edu	37	chr6	13307840	13307840	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacctacttgcctctgtaaActggattcaggcaaacatcc	12	10	7	12	0	2	1	1	0	1	1	3	2	3	2	3	2	4	2	3	2	4	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr6:13307840A>T	ENST00000379300.3	-	6	900	c.657T>A	c.(655-657)agT>agA	p.S219R	TBC1D7_ENST00000607658.1_Missense_Mutation_p.S192R|TBC1D7_ENST00000356436.4_Missense_Mutation_p.S219R|TBC1D7_ENST00000607532.1_5'UTR|TBC1D7_ENST00000343141.4_Missense_Mutation_p.S173R|TBC1D7_ENST00000379307.2_Missense_Mutation_p.S192R	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	219	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			GCCTCTGTAAACTGGATTCAG	0.478																																					p.S219R													.	TBC1D7-91	0			c.T657A						.						116	114	115					6																	13307840		2203	4300	6503	SO:0001583	missense	51256	exon6			CTGTAAACTGGAT	AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.657T>A	6.37:g.13307840A>T	ENSP00000368602:p.Ser219Arg	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	48	3	NM_001143965	0	0	0	1	1	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Missense_Mutation	SNP	ENST00000379300.3	37	CCDS4523.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.464789	0.84425	.	.	ENSG00000145979	ENST00000334971;ENST00000356436;ENST00000379300;ENST00000379307;ENST00000343141;ENST00000452989;ENST00000450347;ENST00000422136;ENST00000446018;ENST00000420456	T;T;T;T;T;T;T;T;T	0.42900	1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94;0.96	6.17	2.41	0.29592	Rab-GAP/TBC domain (3);	0.474423	0.28504	N	0.015120	T	0.47507	0.1449	M	0.81682	2.555	0.54753	D	0.999986	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.966;0.999;0.992;0.999	T	0.45977	-0.9224	10	0.26408	T	0.33	-0.0635	8.4637	0.32942	0.7018:0.0:0.2982:0.0	.	173;192;192;219	Q2TU37;Q5SZL5;Q9P0N9-2;Q9P0N9	.;.;.;TBCD7_HUMAN	R	160;219;219;192;173;192;192;219;192;192	ENSP00000348813:S219R;ENSP00000368602:S219R;ENSP00000368609:S192R;ENSP00000343100:S173R;ENSP00000414292:S192R;ENSP00000404680:S192R;ENSP00000394425:S219R;ENSP00000417005:S192R;ENSP00000412102:S192R	ENSP00000334212:S160R	S	-	3	2	TBC1D7	13415819	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	1.781000	0.38644	0.177000	0.19895	0.533000	0.62120	AGT	.		0.478	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495		T	13307840	A	T	13307840	3	4	146	1	0	0	0	0	1	0	0	0	15656	40	2	5	236	5	TBC1D7	6	13307840	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		13307840	157807227	36	13015											
SESN1	27244	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	109309823	109309823	+	Frame_Shift_Del	DEL	T	T	-																															ttcaggagtgcaaacaacagTtttgatataaactttaaagc																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr6:109309823delT	ENST00000356644.7	-	9	1409	c.1315delA	c.(1315-1317)actfs	p.T439fs	SESN1_ENST00000302071.2_Frame_Shift_Del_p.T373fs|SESN1_ENST00000436639.2_Frame_Shift_Del_p.T498fs	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	439					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		CAAACAACAGTTTTGATATAA	0.343																																					p.T498fs		.											.	SESN1-227	0			c.1492delA						.						83	75	77					6																	109309823		2203	4300	6503	SO:0001589	frameshift_variant	27244	exon9			.	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.1315delA	6.37:g.109309823delT	ENSP00000349061:p.Thr439fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	56	13	NM_014454	0	0	0	0	0	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Frame_Shift_Del	DEL	ENST00000356644.7	37	CCDS56445.1																																																																																			.		0.343	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454		-	109309823	T	-	109309823	7	5	146	1	0	1	0	1	0	0	0	0	14156	1725	60	0	171	0	SESN1	6	109309823	Frame_Shift_Del	DEL	T	TCGA-KV-A6GD-01A-11D-A31X-10	96001983	109309823	61805244	37	13016											
HIVEP2	3097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	143090738	143090738	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtaagcttgccggttccaGgcctatgcatagcagccaga	10	9	11	11	1	0	1	0	0	0	1	1	1	1	1	4	2	5	5	4	2	3	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr6:143090738G>T	ENST00000367604.1	-	4	5777	c.5138C>A	c.(5137-5139)cCt>cAt	p.P1713H	HIVEP2_ENST00000367603.2_Missense_Mutation_p.P1713H|HIVEP2_ENST00000012134.2_Missense_Mutation_p.P1713H			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1713					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GCCGGTTCCAGGCCTATGCAT	0.433																																					p.P1713H	Esophageal Squamous(107;843 1510 13293 16805 42198)	.											.	HIVEP2-95	0			c.C5138A						.						118	109	112					6																	143090738		1861	4116	5977	SO:0001583	missense	3097	exon5			GTTCCAGGCCTAT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5138C>A	6.37:g.143090738G>T	ENSP00000356576:p.Pro1713His	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	93	17	NM_006734	0	0	1	1	0	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231189	0.58777	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02863	4.13;4.13;4.13	5.95	4.11	0.48088	.	0.192613	0.56097	D	0.000024	T	0.04907	0.0132	M	0.72894	2.215	0.47407	D	0.999417	D	0.67145	0.996	P	0.58013	0.831	T	0.10019	-1.0648	10	0.87932	D	0	-17.5678	8.3283	0.32171	0.135:0.1282:0.7368:0.0	.	1713	P31629	ZEP2_HUMAN	H	1713	ENSP00000356576:P1713H;ENSP00000356575:P1713H;ENSP00000012134:P1713H	ENSP00000012134:P1713H	P	-	2	0	HIVEP2	143132431	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	6.728000	0.74769	1.514000	0.48869	0.655000	0.94253	CCT	.		0.433	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			T	143090738	G	T	143090738	3	4	146	1	0	0	0	0	1	0	0	0	7208	1000	35	4	2226	4	HIVEP2	6	143090738	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	33780915	143090738	28024329	38	13017											
EIF2AK1	27102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	6084205	6084205	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcttacctcgtggctgaaTcacatgaacatgttctatcc	9	12	8	12	2	2	2	1	2	1	0	4	2	3	2	2	2	2	3	2	2	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr7:6084205T>G	ENST00000199389.6	-	7	864	c.718A>C	c.(718-720)Att>Ctt	p.I240L	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.I116L|EIF2AK1_ENST00000495565.1_5'UTR	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	240	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CGTGGCTGAATCACATGAACA	0.468																																					p.I240L		.											.	EIF2AK1-408	0			c.A718C						.						99	79	86					7																	6084205		2203	4300	6503	SO:0001583	missense	27102	exon7			GCTGAATCACATG	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.718A>C	7.37:g.6084205T>G	ENSP00000199389:p.Ile240Leu	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	41	6	NM_001134335	0	0	0	0	0	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	37	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	.	1.012	-0.687440	0.03328	.	.	ENSG00000086232	ENST00000199389;ENST00000536084	T;T	0.14144	2.53;2.53	5.2	2.36	0.29203	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.526065	0.21443	N	0.074457	T	0.06826	0.0174	N	0.17723	0.515	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.006;0.002;0.002	T	0.42932	-0.9422	10	0.11485	T	0.65	-0.4159	5.4401	0.16504	0.0:0.4964:0.2696:0.234	.	116;240;240	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	L	240;116	ENSP00000199389:I240L;ENSP00000445784:I116L	ENSP00000199389:I240L	I	-	1	0	EIF2AK1	6050731	0.000000	0.05858	0.062000	0.19696	0.277000	0.26821	-0.787000	0.04618	0.180000	0.19960	-0.248000	0.11899	ATT	.		0.468	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		G	6084205	T	G	6084205	3	3	146	1	0	0	0	0	1	0	0	0	5007	1435	50	5	1210	5	EIF2AK1	7	6084205	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		6084205	153054458	39	13018											
CLCN1	1180	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	143049049	143049049	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaggaggatgaggatgaactGatcctttgaccccctcccac	10	8	11	12	0	0	4	0	4	0	0	2	8	2	7	4	3	1	0	4	3	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr7:143049049G>A	ENST00000343257.2	+	23	3045	c.2958G>A	c.(2956-2958)ctG>ctA	p.L986L		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	986					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					AGGATGAACTGATCCTTTGAC	0.617																																					p.L986L		.											.	CLCN1-156	0			c.G2958A						.						85	83	84					7																	143049049		2203	4300	6503	SO:0001819	synonymous_variant	1180	exon23			TGAACTGATCCTT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"Ion channels / Chloride channels : Voltage-sensitive"	2019	protein-coding gene	gene with protein product	"Thomsen disease, autosomal dominant"	118425	"chloride channel 1, skeletal muscle"			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2958G>A	7.37:g.143049049G>A		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	105	23	NM_000083	0	0	0	0	0	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																			.		0.617	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		A	143049049	G	A	143049049	2	1	146	1	0	0	0	0	0	0	0	1	3468	1277	45	2		2	CLCN1	7	143049049	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	136964844	143049049	16089614	40	13019											
ANK1	286	ucsc.edu	37	chr8	41566447	41566447	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagactacgggccaccTccacctggttctgcttggca	7	8	11	15	1	1	1	0	0	1	1	2	1	2	1	4	3	3	5	4	3	1	3	rs372122833		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr8:41566447T>C	ENST00000347528.4	-	17	1930	c.1847A>G	c.(1846-1848)gAg>gGg	p.E616G	ANK1_ENST00000396942.1_Missense_Mutation_p.E616G|ANK1_ENST00000289734.7_Missense_Mutation_p.E616G|ANK1_ENST00000379758.2_Missense_Mutation_p.E616G|ANK1_ENST00000265709.8_Missense_Mutation_p.E649G|ANK1_ENST00000352337.4_Missense_Mutation_p.E616G|ANK1_ENST00000396945.1_Missense_Mutation_p.E616G	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	616	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			ACGGGCCACCTCCACCTGGTT	0.607																																					p.E649G													.	ANK1-716	0			c.A1946G						.						80	71	74					8																	41566447		2203	4300	6503	SO:0001583	missense	286	exon17			GCCACCTCCACCT	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.1847A>G	8.37:g.41566447T>C	ENSP00000339620:p.Glu616Gly	Somatic	31	0		WXS	Illumina HiSeq		42	4	NM_001142446	0	0	0	0	0	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.194486	0.78902	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	5.51	5.51	0.81932	Ankyrin repeat-containing domain (3);	0.102848	0.64402	D	0.000003	T	0.64057	0.2564	L	0.45470	1.425	0.80722	D	1	P;P;B;B;P	0.40107	0.703;0.664;0.027;0.354;0.703	B;B;B;B;B	0.40410	0.328;0.188;0.023;0.048;0.328	T	0.69011	-0.5258	10	0.87932	D	0	.	15.6125	0.76737	0.0:0.0:0.0:1.0	.	649;616;616;616;616	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	G	616;616;616;616;616;616;649;616	ENSP00000339620:E616G;ENSP00000289734:E616G;ENSP00000369082:E616G;ENSP00000380149:E616G;ENSP00000380147:E616G;ENSP00000309131:E616G;ENSP00000265709:E649G	ENSP00000265709:E649G	E	-	2	0	ANK1	41685604	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	6.276000	0.72601	2.091000	0.63221	0.459000	0.35465	GAG	.		0.607	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		C	41566447	T	C	41566447	3	2	146	1	0	0	0	0	1	0	0	0	620	1551	54	3	4256	3	ANK1	8	41566447	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		41566447	104797575	41	13020											
UBR5	51366	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	103287958	103287958	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccaggttctgctccaacaTcttccatgaataccctgccg	9	11	6	15	1	2	1	0	1	2	0	5	1	5	1	5	1	4	2	5	1	3	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr8:103287958T>C	ENST00000520539.1	-	46	7214	c.6608A>G	c.(6607-6609)gAt>gGt	p.D2203G	UBR5_ENST00000521922.1_Missense_Mutation_p.D2197G|UBR5_ENST00000220959.4_Missense_Mutation_p.D2203G|UBR5_ENST00000518205.1_5'Flank	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2203					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TGCTCCAACATCTTCCATGAA	0.418																																					p.D2203G	Ovarian(131;96 1741 5634 7352 27489)												.	UBR5-761	0			c.A6608G						.						97	83	88					8																	103287958		2203	4300	6503	SO:0001583	missense	51366	exon46			CCAACATCTTCCA	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"Ubiquitin protein ligase E3 component n-recognins"	16806	protein-coding gene	gene with protein product		608413	"E3 ubiquitin protein ligase, HECT domain containing, 1"	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.6608A>G	8.37:g.103287958T>C	ENSP00000429084:p.Asp2203Gly	Somatic	118	1		WXS	Illumina HiSeq	Phase_I	117	13	NM_015902	0	0	3	6	3	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.749637	0.89753	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922;ENST00000521566	T;T;T	0.54071	0.59;0.6;0.6	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.69278	0.3093	M	0.67397	2.05	0.58432	D	0.999999	D;D	0.65815	0.995;0.972	D;P	0.64687	0.928;0.871	T	0.73285	-0.4031	10	0.87932	D	0	.	15.3625	0.74492	0.0:0.0:0.0:1.0	.	2197;2203	E7EMW7;O95071	.;UBR5_HUMAN	G	2203;2203;2197;28	ENSP00000429084:D2203G;ENSP00000220959:D2203G;ENSP00000427819:D2197G	ENSP00000220959:D2203G	D	-	2	0	UBR5	103357134	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.698000	0.84413	2.046000	0.60703	0.528000	0.53228	GAT	.		0.418	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		C	103287958	T	C	103287958	3	2	146	1	0	0	0	0	1	0	0	0	16938	1435	50	3	1847	3	UBR5	8	103287958	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	61721511	103287958	43076064	42	13021											
SNTB1	6641	broad.mit.edu	37	chr8	121706046	121706046	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgacggggggtctgaggtgCtgccccctaaccgaggggat	7	7	17	10	2	1	2	0	2	1	0	1	4	1	3	3	6	3	1	3	6	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr8:121706046C>T	ENST00000395601.3	-	3	1088	c.674G>A	c.(673-675)aGc>aAc	p.S225N	SNTB1_ENST00000519177.1_5'UTR|SNTB1_ENST00000517992.1_Missense_Mutation_p.S225N	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	225	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GTCTGAGGTGCTGCCCCCTAA	0.572																																					p.S225N													.	SNTB1-228	0			c.G674A						.						96	93	94					8																	121706046		2203	4300	6503	SO:0001583	missense	6641	exon2			GAGGTGCTGCCCC	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.674G>A	8.37:g.121706046C>T	ENSP00000378965:p.Ser225Asn	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	92	4	NM_021021	0	0	5	5	0	A8K9E0|O14912|Q4KMG8	Missense_Mutation	SNP	ENST00000395601.3	37	CCDS6334.1	.	.	.	.	.	.	.	.	.	.	C	7.745	0.702140	0.15172	.	.	ENSG00000172164	ENST00000395601;ENST00000517992	T;T	0.54479	0.57;0.57	5.96	4.09	0.47781	Pleckstrin homology domain (2);	0.980591	0.08401	N	0.951494	T	0.40791	0.1131	N	0.24115	0.695	0.09310	N	1	B;B	0.23806	0.015;0.091	B;B	0.15870	0.011;0.014	T	0.25047	-1.0143	10	0.39692	T	0.17	.	11.9555	0.52978	0.0998:0.5015:0.3986:0.0	.	225;225	Q13884;Q13884-2	SNTB1_HUMAN;.	N	225	ENSP00000378965:S225N;ENSP00000431124:S225N	ENSP00000378965:S225N	S	-	2	0	SNTB1	121775227	0.125000	0.22332	0.041000	0.18516	0.069000	0.16628	2.938000	0.48987	1.476000	0.48215	0.655000	0.94253	AGC	.		0.572	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		T	121706046	C	T	121706046	3	4	146	1	0	0	0	0	1	0	0	0	14904	797	28	2	966	2	SNTB1	8	121706046	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	18418088	121706046	24657976	43	13022											
TRPM3	80036	broad.mit.edu;bcgsc.ca	37	chr9	73151135	73151136	+	Frame_Shift_Ins	INS	-	-	T																															ttgttggacagggttctctcINStgagttatcaccctcctggg																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr9:73151135_73151136insT	ENST00000377110.3	-	25	5100_5101	c.4857_4858insA	c.(4855-4860)tcagagfs	p.E1620fs	TRPM3_ENST00000423814.3_Frame_Shift_Ins_p.E1647fs|TRPM3_ENST00000377106.1_Frame_Shift_Ins_p.E1492fs|TRPM3_ENST00000358082.3_Frame_Shift_Ins_p.E1482fs|TRPM3_ENST00000357533.2_Frame_Shift_Ins_p.E1624fs|TRPM3_ENST00000396280.5_Frame_Shift_Ins_p.E1469fs|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000377105.1_Frame_Shift_Ins_p.E1479fs|TRPM3_ENST00000396292.4_Frame_Shift_Ins_p.E1492fs|TRPM3_ENST00000408909.2_Frame_Shift_Ins_p.E1479fs|TRPM3_ENST00000360823.2_Frame_Shift_Ins_p.E1482fs|TRPM3_ENST00000396285.1_Frame_Shift_Ins_p.E1479fs			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1645					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						AGGGTTCTCTCTGAGTTATCAC	0.55																																					p.E1620fs													.	TRPM3-521	0			c.4858_4859insA						.																																			SO:0001589	frameshift_variant	80036	exon25			TTCTCTCTGAGTT	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"Voltage-gated ion channels / Transient receptor potential cation channels"	17992	protein-coding gene	gene with protein product	"melastatin 2"	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4858dupA	9.37:g.73151136_73151136dupT	ENSP00000366314:p.Glu1620fs	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	129	15	NM_001007471	0	0	0	0	0	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Frame_Shift_Ins	INS	ENST00000377110.3	37	CCDS43835.1																																																																																			.		0.55	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		T	73151136	-	T	73151135	7	5	146	1	0	1	1	0	0	0	0	0	16620	922	32	0	269	0	TRPM3	9	73151135	Frame_Shift_Ins	INS	-	TCGA-KV-A6GD-01A-11D-A31X-10		73151135	68062296	44	13023											
CTSL1	1514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	90344596	90344596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcagttgcaactgtggggCccatttctgttgctattgat	7	14	12	8	0	1	1	0	1	1	0	1	1	1	1	1	3	3	5	1	3	2	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr9:90344596C>T	ENST00000343150.5	+	6	1620	c.730C>T	c.(730-732)Ccc>Tcc	p.P244S	CTSL_ENST00000340342.6_Missense_Mutation_p.P244S|CTSL_ENST00000495822.1_3'UTR			P07711	CATL1_HUMAN	cathepsin L	244					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										AACTGTGGGGCCCATTTCTGT	0.428																																					p.P244S		.											.	CTSL1-93	0			c.C730T						.						153	147	149					9																	90344596		2203	4300	6503	SO:0001583	missense	1514	exon6			GTGGGGCCCATTT	X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.730C>T	9.37:g.90344596C>T	ENSP00000345344:p.Pro244Ser	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	81	16	NM_145918	0	1	759	886	126	Q6IAV1|Q96QJ0	Missense_Mutation	SNP	ENST00000343150.5	37	CCDS6675.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562005	0.65538	.	.	ENSG00000135047	ENST00000343150;ENST00000340342	T;T	0.58652	0.32;0.32	4.19	4.19	0.49359	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.86167	0.5868	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92638	0.6122	10	0.87932	D	0	.	16.7092	0.85380	0.0:1.0:0.0:0.0	.	244	P07711	CATL1_HUMAN	S	244	ENSP00000345344:P244S;ENSP00000365061:P244S	ENSP00000365061:P244S	P	+	1	0	CTSL1	89534416	1.000000	0.71417	0.118000	0.21660	0.300000	0.27592	6.804000	0.75186	2.134000	0.65973	0.655000	0.94253	CCC	.		0.428	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		T	90344596	C	T	90344596	3	4	146	1	0	0	0	0	1	0	0	0	4044	739	26	2	748	2	CTSL1	9	90344596	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	17193461	90344596	50868835	45	13024											
CSGALNACT2	55454	broad.mit.edu	37	chr10	43659419	43659419	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggacaagggagaggtcttGatgtttttctgtgatgttga	8	15	15	3	0	2	4	0	3	2	1	2	6	2	5	0	3	0	2	0	3	1	4	rs79064394		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr10:43659419G>T	ENST00000374466.3	+	5	1421	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	362					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.L362F(5)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GAGAGGTCTTGATGTTTTTCT	0.433																																					p.L362F													.	CSGALNACT2-69	5	Substitution - Missense(5)	endometrium(4)|kidney(1)	c.G1086T						.						223	221	222					10																	43659419		2203	4300	6503	SO:0001583	missense	55454	exon5			GGTCTTGATGTTT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1086G>T	10.37:g.43659419G>T	ENSP00000363590:p.Leu362Phe	Somatic	177	1		WXS	Illumina HiSeq	Phase_I	132	4	NM_018590	0	0	9	9	0	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499782	0.85176	.	.	ENSG00000169826	ENST00000374466	T	0.27256	1.68	6.08	5.17	0.71159	.	0.064535	0.64402	D	0.000004	T	0.57359	0.2048	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63721	-0.6573	10	0.87932	D	0	-11.7375	14.8306	0.70146	0.0683:0.0:0.9317:0.0	.	362	Q8N6G5	CGAT2_HUMAN	F	362	ENSP00000363590:L362F	ENSP00000363590:L362F	L	+	3	2	CSGALNACT2	42979425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.894000	0.99253	0.591000	0.81541	TTG	.		0.433	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43659419	G	T	43659419	3	4	146	1	0	0	0	0	1	0	0	0	3945	1281	45	4	1100	4	CSGALNACT2	10	43659419	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10		43659419	91875328	46	13025											
IFIT5	24138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	91177012	91177012	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttggagttagaatgtcAttttacatggaatttactta	11	18	8	4	0	2	1	1	0	1	1	2	3	2	3	0	2	2	2	0	2	6	7			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr10:91177012A>G	ENST00000371795.4	+	2	269	c.56A>G	c.(55-57)cAt>cGt	p.H19R	IFIT5_ENST00000416601.1_Missense_Mutation_p.H19R|LIPA_ENST00000371837.1_5'Flank	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	19					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						TTAGAATGTCATTTTACATGG	0.318																																					p.H19R		.											.	IFIT5-90	0			c.A56G						.						69	71	70					10																	91177012		2203	4300	6503	SO:0001583	missense	24138	exon2			AATGTCATTTTAC	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.56A>G	10.37:g.91177012A>G	ENSP00000360860:p.His19Arg	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	125	16	NM_012420	0	0	3	3	0	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Missense_Mutation	SNP	ENST00000371795.4	37	CCDS7403.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.890598	0.72524	.	.	ENSG00000152778	ENST00000371795;ENST00000416601	T;T	0.60797	0.16;0.16	6.16	6.16	0.99307	.	0.045911	0.85682	D	0.000000	T	0.77253	0.4103	M	0.80847	2.515	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	T	0.80284	-0.1447	10	0.87932	D	0	-13.583	15.9872	0.80168	1.0:0.0:0.0:0.0	.	19;19	Q13325;B4DDV1	IFIT5_HUMAN;.	R	19	ENSP00000360860:H19R;ENSP00000414042:H19R	ENSP00000360860:H19R	H	+	2	0	IFIT5	91166992	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.666000	0.68059	2.367000	0.80283	0.528000	0.53228	CAT	.		0.318	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		G	91177012	A	G	91177012	3	3	146	1	0	0	0	0	1	0	0	0	7546	217	8	3	62	3	IFIT5	10	91177012	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	47517593	91177012	44357735	47	13026											
XPNPEP1	7511	broad.mit.edu	37	chr10	111642221	111642221	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tctcgctcacagcatagctgGccttgtcactgacccacacc	8	9	7	17	1	3	1	2	1	1	0	4	1	3	1	3	1	2	3	3	1	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr10:111642221G>A	ENST00000502935.1	-	10	1129	c.1010C>T	c.(1009-1011)gCc>gTc	p.A337V	XPNPEP1_ENST00000430337.1_5'Flank|XPNPEP1_ENST00000369683.1_Missense_Mutation_p.A223V|XPNPEP1_ENST00000322238.8_Missense_Mutation_p.A337V|XPNPEP1_ENST00000369680.4_Missense_Mutation_p.A294V					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble											endometrium(2)|kidney(9)|large_intestine(4)|lung(9)|ovary(3)|pancreas(2)|skin(1)|urinary_tract(1)	31		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)		AGCATAGCTGGCCTTGTCACT	0.567																																					p.A337V													.	XPNPEP1-94	0			c.C1010T						.						129	106	114					10																	111642221		2203	4300	6503	SO:0001583	missense	7511	exon10			TAGCTGGCCTTGT		CCDS7560.1, CCDS7560.2, CCDS53576.1	10q25.3	2006-01-16	2002-07-17		ENSG00000108039	ENSG00000108039	3.4.11.9		12822	protein-coding gene	gene with protein product		602443	"X-prolyl aminopeptidase (aminopeptidase P)-like"	XPNPEP, XPNPEPL1, XPNPEPL			Standard	NM_020383		Approved		uc001kyp.2	Q9NQW7	OTTHUMG00000019029	ENST00000502935.1:c.1010C>T	10.37:g.111642221G>A	ENSP00000421566:p.Ala337Val	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	62	3	NM_001167604	0	0	25	25	0		Missense_Mutation	SNP	ENST00000502935.1	37	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520589	0.85495	.	.	ENSG00000108039	ENST00000502935;ENST00000369683;ENST00000322238;ENST00000369680;ENST00000403138	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	L	0.37561	1.115	0.80722	D	1	B;D;P	0.55605	0.296;0.972;0.898	B;B;B	0.40982	0.017;0.345;0.144	T	0.27872	-1.0061	9	0.15952	T	0.53	-17.9818	18.2859	0.90114	0.0:0.0:1.0:0.0	.	337;337;294	B4E2P4;G5E9Y2;Q9NQW7	.;.;XPP1_HUMAN	V	337;223;337;294;294	.	ENSP00000324011:A337V	A	-	2	0	XPNPEP1	111632211	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.864000	0.92294	2.757000	0.94681	0.655000	0.94253	GCC	.		0.567	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2			A	111642221	G	A	111642221	3	1	146	1	0	0	0	0	1	0	0	0	17475	1203	42	2	1038	2	XPNPEP1	10	111642221	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	20465209	111642221	23892526	48	13027											
OR52B2	255725	broad.mit.edu	37	chr11	6191110	6191110	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaagcttcgggtgatgacGgccagagcaatcctccccac	10	6	11	14	2	0	4	0	2	0	2	3	4	2	4	4	2	2	2	4	2	2	1	rs369907116		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:6191110G>A	ENST00000530810.1	-	1	528	c.447C>T	c.(445-447)gcC>gcT	p.A149A	RP11-290F24.3_ENST00000529961.1_RNA	NM_001004052.1	NP_001004052.1	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B, member 2	149						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(15)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGTGATGACGGCCAGAGCAA	0.517																																					p.A149A	NSCLC(5;186 261 1778 7098 14207)												.	.	0			c.C447T						.	G		0,4304		0,0,2152	60	61	61		447	4.3	1	11		61	1,8527		0,1,4263	no	coding-synonymous	OR52B2	NM_001004052.1		0,1,6415	AA,AG,GG		0.0117,0.0,0.0078		149/324	6191110	1,12831	2152	4264	6416	SO:0001819	synonymous_variant	255725	exon1			GATGACGGCCAGA	AB065763	CCDS53598.1	11p15.4	2012-08-09				ENSG00000255307		"GPCR / Class A : Olfactory receptors"	15207	protein-coding gene	gene with protein product							Standard	NM_001004052		Approved		uc010qzy.2	Q96RD2		ENST00000530810.1:c.447C>T	11.37:g.6191110G>A		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	55	4	NM_001004052	0	0	0	0	0	Q8NGM7	Silent	SNP	ENST00000530810.1	37	CCDS53598.1																																																																																			.		0.517	OR52B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385977.1	NM_001004052		A	6191110	G	A	6191110	2	1	146	1	0	0	0	0	0	0	0	1	11137	1103	39	1		1	OR52B2	11	6191110	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10		6191110	128815406	49	13028											
USH1C	10083	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	17542471	17542471	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcagtgatggttttaggcaAgagtagctgttcctttgagc	9	13	13	6	0	0	3	0	2	0	1	1	3	1	3	1	2	3	6	1	2	3	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:17542471A>C	ENST00000318024.4	-	14	1264	c.1156T>G	c.(1156-1158)Ttg>Gtg	p.L386V	USH1C_ENST00000005226.7_Missense_Mutation_p.L386V|USH1C_ENST00000527720.1_Missense_Mutation_p.L355V|USH1C_ENST00000527020.1_Missense_Mutation_p.L367V	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	386					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						GTTTTAGGCAAGAGTAGCTGT	0.488																																					p.L386V		.											.	USH1C-91	0			c.T1156G						.						457	438	444					11																	17542471		2200	4293	6493	SO:0001583	missense	10083	exon14			TAGGCAAGAGTAG	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"harmonin"	605242	"deafness, autosomal recessive 18"	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1156T>G	11.37:g.17542471A>C	ENSP00000317018:p.Leu386Val	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	87	9	NM_005709	0	0	60	118	58	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	A	9.184	1.024225	0.19433	.	.	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226	T;T;T;T	0.63913	1.77;1.77;2.01;-0.07	5.7	-8.8	0.00817	.	0.781295	0.12318	N	0.479554	T	0.26159	0.0638	N	0.08118	0	0.09310	N	1	B;B;B	0.14438	0.01;0.006;0.0	B;B;B	0.15870	0.014;0.006;0.001	T	0.28554	-1.0040	10	0.11485	T	0.65	.	3.9214	0.09245	0.2554:0.0946:0.4467:0.2034	.	367;386;386	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	V	386;355;367;386	ENSP00000317018:L386V;ENSP00000432944:L355V;ENSP00000436934:L367V;ENSP00000005226:L386V	ENSP00000005226:L386V	L	-	1	2	USH1C	17499047	0.000000	0.05858	0.002000	0.10522	0.642000	0.38348	-1.114000	0.03293	-1.238000	0.02535	-1.039000	0.02377	TTG	.		0.488	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		C	17542471	A	C	17542471	3	2	146	1	0	0	0	0	1	0	0	0	17067	69	3	5	1677	5	USH1C	11	17542471	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	11351361	17542471	117464045	50	13029											
OR5M3	219482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	56237348	56237348	+	Missense_Mutation	SNP	A	A	T																															aagagatgataattacagtcAgggaatatgtgaagttaatg																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:56237348A>T	ENST00000312240.2	-	1	666	c.626T>A	c.(625-627)cTg>cAg	p.L209Q		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	209						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					AATTACAGTCAGGGAATATGT	0.438																																					p.L209Q		.											.	OR5M3-70	0			c.T626A						.						111	109	110					11																	56237348		2201	4296	6497	SO:0001583	missense	219482	exon1			ACAGTCAGGGAAT	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.626T>A	11.37:g.56237348A>T	ENSP00000312208:p.Leu209Gln	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	173	20	NM_001004742	0	0	0	0	0	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	A	7.810	0.715500	0.15306	.	.	ENSG00000174937	ENST00000312240	T	0.49432	0.78	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33854	N	0.004500	T	0.71753	0.3377	H	0.97240	3.965	0.09310	N	1	B	0.19445	0.036	B	0.40038	0.317	T	0.68884	-0.5291	10	0.72032	D	0.01	-8.3442	12.8019	0.57591	1.0:0.0:0.0:0.0	.	209	Q8NGP4	OR5M3_HUMAN	Q	209	ENSP00000312208:L209Q	ENSP00000312208:L209Q	L	-	2	0	OR5M3	55993924	0.207000	0.23482	0.002000	0.10522	0.005000	0.04900	4.573000	0.60893	1.897000	0.54924	0.448000	0.29417	CTG	.		0.438	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		T	56237348	A	T	56237348	3	4	146	1	0	0	0	0	1	0	0	0	11201	188	7	5	299	5	OR5M3	11	56237348	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	38694877	56237348	78769168	51	13030	135	2									
OR5M3	219482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	56237358	56237358	+	Missense_Mutation	SNP	T	T	A																															aattacagtcagggaatatgTgaagttaatgccggcaagta																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:56237358T>A	ENST00000312240.2	-	1	656	c.616A>T	c.(616-618)Aca>Tca	p.T206S		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					AGGGAATATGTGAAGTTAATG	0.428																																					p.T206S		.											.	OR5M3-70	0			c.A616T						.						120	118	119					11																	56237358		2201	4296	6497	SO:0001583	missense	219482	exon1			AATATGTGAAGTT	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"GPCR / Class A : Olfactory receptors"	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.616A>T	11.37:g.56237358T>A	ENSP00000312208:p.Thr206Ser	Somatic	205	0		WXS	Illumina HiSeq	Phase_I	172	20	NM_001004742	0	0	0	0	0	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	T	3.617	-0.078287	0.07184	.	.	ENSG00000174937	ENST00000312240	T	0.37058	1.22	5.08	-0.403	0.12400	GPCR, rhodopsin-like superfamily (1);	0.993240	0.08161	N	0.988433	T	0.16981	0.0408	N	0.11255	0.115	0.09310	N	1	B	0.14012	0.009	B	0.23150	0.044	T	0.31194	-0.9952	10	0.22706	T	0.39	-3.9091	3.5764	0.07936	0.2773:0.1679:0.0:0.5548	.	206	Q8NGP4	OR5M3_HUMAN	S	206	ENSP00000312208:T206S	ENSP00000312208:T206S	T	-	1	0	OR5M3	55993934	0.000000	0.05858	0.552000	0.28243	0.327000	0.28475	-0.845000	0.04340	0.248000	0.21435	0.448000	0.29417	ACA	.		0.428	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		A	56237358	T	A	56237358	3	1	146	1	0	0	0	0	1	0	0	0	11201	1696	59	5	309	5	OR5M3	11	56237358	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	10	56237358	78769158	52	13031	135	2									
SSRP1	6749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57100282	57100282	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatgcagatggcatctccCgtggcctggattacatccgc	9	9	11	12	2	1	2	0	0	1	2	3	3	2	3	3	3	2	2	3	3	2	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:57100282C>A	ENST00000278412.2	-	6	851	c.585G>T	c.(583-585)acG>acT	p.T195T		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	195					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						TGGCATCTCCCGTGGCCTGGA	0.562																																					p.T195T	Colon(89;1000 1340 6884 23013 41819)	.											.	SSRP1-228	0			c.G585T						.						65	63	64					11																	57100282		2201	4296	6497	SO:0001819	synonymous_variant	6749	exon6			ATCTCCCGTGGCC	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"facilitates chromatin remodeling 80 kDa subunit"	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.585G>T	11.37:g.57100282C>A		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	72	15	NM_003146	0	0	32	44	12	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			.		0.562	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		A	57100282	C	A	57100282	2	1	146	1	0	0	0	0	0	0	0	1	15226	639	23	4		4	SSRP1	11	57100282	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	862924	57100282	77906234	53	13032											
SYVN1	84447	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	64900251	64900251	+	Splice_Site	DEL	T	T	-																															gatgttggggctgcgttccaTctgaggcagagcacagaaga																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:64900251delT	ENST00000377190.3	-	5	473	c.379delA	c.(379-381)atg>tg	p.M127fs	SYVN1_ENST00000526060.1_Splice_Site_p.M127fs|SYVN1_ENST00000294256.8_Splice_Site_p.M127fs|SYVN1_ENST00000307289.6_Intron|SYVN1_ENST00000526121.1_5'Flank	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	127					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CTGCGTTCCATCTGAGGCAGA	0.612																																					p.M127fs		.											.	SYVN1-91	0			c.379delA						.						97	97	97					11																	64900251		2201	4297	6498	SO:0001630	splice_region_variant	84447	exon5			.	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"RING-type (C3HC4) zinc fingers"	20738	protein-coding gene	gene with protein product	"HMG-coA reductase degradation 1 homolog (S. cerevisiae)"	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.379-1A>-	11.37:g.64900251delT		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	49	11	NM_172230	0	0	0	0	0	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Frame_Shift_Del	DEL	ENST00000377190.3	37	CCDS31605.1																																																																																			.		0.612	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	Frame_Shift_Del	-	64900251	T	-	64900251	8	5	146	1	0	1	0	1	0	0	1	0	15519	1449	50	0	1522	0	SYVN1	11	64900251	Splice_Site	DEL	T	TCGA-KV-A6GD-01A-11D-A31X-10	7799969	64900251	70106265	54	13033											
FRMD8	83786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65168213	65168213	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcatgtcctgctgggcctgCgcttccaggagctgtcgtgg	4	10	15	12	2	0	0	0	0	0	0	3	1	2	1	3	3	4	4	3	3	0	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:65168213C>T	ENST00000317568.5	+	9	1109	c.946C>T	c.(946-948)Cgc>Tgc	p.R316C	FRMD8_ENST00000355991.5_Missense_Mutation_p.R260C|FRMD8_ENST00000416776.2_Missense_Mutation_p.R282C	NM_031904.3	NP_114110.1	Q9BZ67	FRMD8_HUMAN	FERM domain containing 8	316	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|urinary_tract(1)	17						GCTGGGCCTGCGCTTCCAGGA	0.657																																					p.R316C		.											.	FRMD8-227	0			c.C946T						.						48	38	41					11																	65168213		2201	4296	6497	SO:0001583	missense	83786	exon9			GGCCTGCGCTTCC	AK074850	CCDS8102.1, CCDS73320.1	11q13.1	2007-08-14			ENSG00000126391	ENSG00000126391			25462	protein-coding gene	gene with protein product						12477932	Standard	NM_031904		Approved	FLJ90369, FKSG44	uc001odu.4	Q9BZ67	OTTHUMG00000166275	ENST00000317568.5:c.946C>T	11.37:g.65168213C>T	ENSP00000319726:p.Arg316Cys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	82	13	NM_031904	0	0	4	5	1	B4E2P1|Q86V56|Q8NCB5	Missense_Mutation	SNP	ENST00000317568.5	37	CCDS8102.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.609302	0.46527	.	.	ENSG00000126391	ENST00000317568;ENST00000355991;ENST00000416776	D;T;D	0.84223	-1.81;-1.22;-1.82	4.49	3.56	0.40772	FERM domain (1);	0.572355	0.18795	N	0.130960	D	0.84813	0.5555	.	.	.	0.48452	D	0.999659	B;B;D	0.71674	0.041;0.175;0.998	B;B;P	0.48654	0.01;0.028;0.585	D	0.83999	0.0342	9	0.56958	D	0.05	-14.6802	9.9641	0.41715	0.3682:0.6317:0.0:0.0	.	282;260;316	B4E2P1;Q9BZ67-2;Q9BZ67	.;.;FRMD8_HUMAN	C	316;260;282	ENSP00000319726:R316C;ENSP00000348270:R260C;ENSP00000392111:R282C	ENSP00000319726:R316C	R	+	1	0	FRMD8	64924789	0.940000	0.31905	1.000000	0.80357	0.991000	0.79684	1.023000	0.30065	0.998000	0.38996	0.549000	0.68633	CGC	.		0.657	FRMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388833.1	NM_031904		T	65168213	C	T	65168213	3	4	146	1	0	0	0	0	1	0	0	0	6075	768	27	1	976	1	FRMD8	11	65168213	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	267962	65168213	69838303	55	13034											
MUS81	80198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65631192	65631192	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaccaatcctagagacccaGgtgaagggccgtggacaggc	12	4	14	11	1	0	3	0	1	0	2	1	5	1	4	4	4	0	0	4	4	3	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:65631192G>A	ENST00000308110.4	+	9	1310	c.961G>A	c.(961-963)Gca>Aca	p.A321T	MUS81_ENST00000533035.1_Splice_Site_p.A246T|EFEMP2_ENST00000532648.1_5'Flank|CFL1_ENST00000534769.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	321	ERCC4.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		TAGAGACCCAGGTGAAGGGCC	0.637								Homologous recombination																													p.A321T		.											.	MUS81-227	0			c.G961A						.						59	64	63					11																	65631192		2201	4296	6497	SO:0001630	splice_region_variant	80198	exon9			GACCCAGGTGAAG		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"	606591	"MUS81 endonuclease homolog (yeast)", "MUS81 endonuclease homolog (S. cerevisiae)"			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.961+1G>A	11.37:g.65631192G>A		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	110	21	NM_025128	0	0	2	4	2	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	37	CCDS8115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.03|11.03	1.519664|1.519664	0.27211|0.27211	.|.	.|.	ENSG00000172732|ENSG00000172732	ENST00000533035;ENST00000308110;ENST00000437855|ENST00000529374	T;T|.	0.22945|.	1.93;1.93|.	5.14|5.14	3.2|3.2	0.36748|0.36748	DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);ERCC4 domain (2);|.	0.343384|.	0.32430|.	N|.	0.006119|.	T|T	0.43656|0.43656	0.1257|0.1257	L|L	0.35288|0.35288	1.05|1.05	0.36284|0.36284	D|D	0.855981|0.855981	B|.	0.29805|.	0.257|.	B|.	0.31442|.	0.13|.	T|T	0.46317|0.46317	-0.9200|-0.9200	10|5	0.13470|.	T|.	0.59|.	-1.6633|-1.6633	6.6325|6.6325	0.22865|0.22865	0.0927:0.0:0.7303:0.177|0.0927:0.0:0.7303:0.177	.|.	321|.	Q96NY9|.	MUS81_HUMAN|.	T|N	246;321;321|245	ENSP00000432287:A246T;ENSP00000307853:A321T|.	ENSP00000307853:A321T|.	A|S	+|+	1|2	0|0	MUS81|MUS81	65387768|65387768	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.034000|0.034000	0.12701|0.12701	3.588000|3.588000	0.53964|0.53964	1.370000|1.370000	0.46153|0.46153	0.563000|0.563000	0.77884|0.77884	GCA|AGC	.		0.637	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	Missense_Mutation	A	65631192	G	A	65631192	5	1	146	1	0	0	0	0	0	0	1	0	10013	1014	35	2	995	2	MUS81	11	65631192	Splice_Site	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	462979	65631192	69375324	56	13035											
TCIRG1	10312	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	67811752	67811752	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgcacaagtgcctcattgccGaggcctggtgctctgtgcga	6	9	13	13	3	2	0	1	0	1	0	2	2	2	0	3	2	4	2	3	2	1	1	rs372690969		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:67811752G>A	ENST00000265686.3	+	9	1069	c.961G>A	c.(961-963)Gag>Aag	p.E321K	TCIRG1_ENST00000532635.1_Missense_Mutation_p.E105K	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	321					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						CCTCATTGCCGAGGCCTGGTG	0.697																																					p.E321K													.	TCIRG1-227	0			c.G961A						.	G	LYS/GLU,LYS/GLU	0,4388		0,0,2194	31	28	29		961,313	4.5	1	11		29	1,8581		0,1,4290	no	missense,missense	TCIRG1	NM_006019.3,NM_006053.3	56,56	0,1,6484	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging,probably-damaging	321/831,105/615	67811752	1,12969	2194	4291	6485	SO:0001583	missense	10312	exon9			ATTGCCGAGGCCT	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"ATPases / V-type"	11647	protein-coding gene	gene with protein product	"T-cell immune response cDNA 7"	604592	"T-cell, immune regulator 1", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.961G>A	11.37:g.67811752G>A	ENSP00000265686:p.Glu321Lys	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	55	7	NM_006019	0	0	33	34	1	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.2|23.2	4.390688|4.390688	0.82902|0.82902	0.0|0.0	1.17E-4|1.17E-4	ENSG00000110719|ENSG00000110719	ENST00000265686;ENST00000532635|ENST00000529364	D;D|.	0.87650|.	-2.28;-2.28|.	5.44|5.44	4.53|4.53	0.55603|0.55603	.|.	0.103326|.	0.64402|.	D|.	0.000004|.	T|T	0.75788|0.75788	0.3897|0.3897	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.71414|.	0.973|.	T|T	0.77765|0.77765	-0.2465|-0.2465	10|5	0.87932|.	D|.	0|.	-18.098|-18.098	12.3719|12.3719	0.55260|0.55260	0.0826:0.0:0.9174:0.0|0.0826:0.0:0.9174:0.0	.|.	321|.	Q13488|.	VPP3_HUMAN|.	K|Q	321;105|154	ENSP00000265686:E321K;ENSP00000434407:E105K|.	ENSP00000265686:E321K|.	E|R	+|+	1|2	0|0	TCIRG1|TCIRG1	67568328|67568328	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.202000|0.202000	0.24057|0.24057	7.852000|7.852000	0.86927|0.86927	2.554000|2.554000	0.86153|0.86153	0.462000|0.462000	0.41574|0.41574	GAG|CGA	.		0.697	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019		A	67811752	G	A	67811752	3	1	146	1	0	0	0	0	1	0	0	0	15735	1059	37	1	991	1	TCIRG1	11	67811752	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	2180560	67811752	67194764	57	13036											
INPPL1	3636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	71948603	71948603	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccccaggcccctcaccAgccagcactttcctggggga	6	6	10	19	0	1	0	1	0	0	0	2	1	2	1	7	3	3	1	7	3	0	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:71948603A>G	ENST00000298229.2	+	26	3519	c.3315A>G	c.(3313-3315)ccA>ccG	p.P1105P	PHOX2A_ENST00000544057.1_5'Flank|INPPL1_ENST00000538751.1_Silent_p.P863P|INPPL1_ENST00000541756.1_Silent_p.P863P	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1105	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						GCCCCTCACCAGCCAGCACTT	0.692																																					p.P1105P		.											.	INPPL1-660	0			c.A3315G						.						19	21	20					11																	71948603		2108	4155	6263	SO:0001819	synonymous_variant	3636	exon26			CTCACCAGCCAGC	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"Sterile alpha motif (SAM) domain containing", "SH2 domain containing"	6080	protein-coding gene	gene with protein product	"51C protein"	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.3315A>G	11.37:g.71948603A>G		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	72	17	NM_001567	0	0	40	56	16	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	37	CCDS8213.1																																																																																			.		0.692	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		G	71948603	A	G	71948603	2	3	146	1	0	0	0	0	0	0	0	1	7782	175	7	3		3	INPPL1	11	71948603	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	4136851	71948603	63057913	58	13037											
ARAP1	116985	broad.mit.edu;ucsc.edu	37	chr11	72423580	72423580	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagactggccacgcgcaCggcccgtgggactcggctcg	6	4	15	16	6	0	1	0	0	0	1	2	2	0	2	2	4	1	3	2	4	0	0	rs558010391		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:72423580C>G	ENST00000393609.3	-	6	983	c.781G>C	c.(781-783)Gtg>Ctg	p.V261L	ARAP1_ENST00000393605.3_Missense_Mutation_p.V21L|ARAP1_ENST00000359373.5_Missense_Mutation_p.V261L|ARAP1_ENST00000334211.8_Missense_Mutation_p.V16L|ARAP1_ENST00000426523.1_Missense_Mutation_p.V16L|ARAP1_ENST00000455638.2_Missense_Mutation_p.V261L|ARAP1_ENST00000429686.1_Missense_Mutation_p.V16L	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	261					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GCCACGCGCACGGCCCGTGGG	0.667													C|||	1	0.000199681	8e-04	0	5008	,	,		12493	0		0	False		,,,				2504	0				p.V261L	Ovarian(102;1198 1520 13195 17913 37529)												.	ARAP1-91	0			c.G781C						.						146	121	130					11																	72423580		2200	4293	6493	SO:0001583	missense	116985	exon6			CGCGCACGGCCCG	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16925	protein-coding gene	gene with protein product		606646	"centaurin, delta 2"	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.781G>C	11.37:g.72423580C>G	ENSP00000377233:p.Val261Leu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	54	3	NM_001040118	0	0	18	26	8	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.223925	0.79576	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.08458	3.2;3.2;3.18;3.23;3.2;3.24;3.09	4.34	4.34	0.51931	.	0.240731	0.28322	N	0.015777	T	0.16599	0.0399	L	0.29908	0.895	0.30306	N	0.789	P;P;D;P;D	0.53312	0.931;0.931;0.959;0.931;0.959	P;P;D;D;D	0.68621	0.872;0.872;0.959;0.911;0.94	T	0.00773	-1.1572	10	0.62326	D	0.03	.	12.2025	0.54335	0.0:1.0:0.0:0.0	.	16;16;261;261;21	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	L	261;261;21;16;261;16;16;50	ENSP00000352332:V261L;ENSP00000390461:V261L;ENSP00000377230:V21L;ENSP00000335506:V16L;ENSP00000377233:V261L;ENSP00000392264:V16L;ENSP00000403127:V16L	ENSP00000335506:V16L	V	-	1	0	ARAP1	72101228	0.982000	0.34865	0.998000	0.56505	0.906000	0.53458	3.800000	0.55537	2.250000	0.74265	0.561000	0.74099	GTG	.		0.667	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		G	72423580	C	G	72423580	3	3	146	1	0	0	0	0	1	0	0	0	838	536	19	4	3691	4	ARAP1	11	72423580	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	474977	72423580	62582936	59	13038											
C2CD3	26005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	73796809	73796809	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaactcagggcagaaagaaCaggccacagggtgggttcgg	13	4	16	8	1	1	3	1	0	0	3	2	3	1	3	1	5	2	2	1	5	3	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:73796809C>G	ENST00000334126.7	-	21	3990	c.3764G>C	c.(3763-3765)tGt>tCt	p.C1255S	C2CD3_ENST00000313663.7_Missense_Mutation_p.C1255S			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1255	C2 1.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GCAGAAAGAACAGGCCACAGG	0.547																																					p.C1255S		.											.	C2CD3-75	0			c.G3764C						.						86	75	79					11																	73796809		2200	4293	6493	SO:0001583	missense	26005	exon21			AAAGAACAGGCCA	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3764G>C	11.37:g.73796809C>G	ENSP00000334379:p.Cys1255Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	132	19	NM_015531	0	0	2	4	2	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	C	20.1	3.935426	0.73442	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.37411	1.2;1.2;1.2	5.8	4.88	0.63580	.	0.169348	0.50627	D	0.000102	T	0.27241	0.0668	L	0.29908	0.895	0.42377	D	0.992478	P	0.47910	0.902	B	0.40066	0.318	T	0.03008	-1.1083	10	0.37606	T	0.19	-9.4621	13.9561	0.64150	0.0:0.9267:0.0:0.0733	.	1255	Q4AC94-1	.	S	1255;1255;1255;63	ENSP00000334379:C1255S;ENSP00000323339:C1255S;ENSP00000388750:C63S	ENSP00000323339:C1255S	C	-	2	0	C2CD3	73474457	0.998000	0.40836	1.000000	0.80357	0.951000	0.60555	3.590000	0.53979	2.742000	0.94016	0.655000	0.94253	TGT	.		0.547	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		G	73796809	C	G	73796809	3	3	146	1	0	0	0	0	1	0	0	0	2160	478	17	4	2171	4	C2CD3	11	73796809	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	1373229	73796809	61209707	60	13039											
C11orf30	56946	broad.mit.edu	37	chr11	76183839	76183839	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacagttgcagtaacagctGtggtgtcctctacaccatct	10	12	8	11	0	2	0	0	0	2	0	3	0	3	0	2	1	5	4	2	1	3	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:76183839G>T	ENST00000529032.1	+	7	1063	c.1063G>T	c.(1063-1065)Gtg>Ttg	p.V355L	C11orf30_ENST00000343878.3_Missense_Mutation_p.V355L|C11orf30_ENST00000525038.1_Missense_Mutation_p.V370L|C11orf30_ENST00000533248.1_Missense_Mutation_p.V369L|C11orf30_ENST00000525919.1_Missense_Mutation_p.V356L|C11orf30_ENST00000524767.1_Missense_Mutation_p.V370L|C11orf30_ENST00000524490.1_Missense_Mutation_p.V356L|C11orf30_ENST00000334736.3_Missense_Mutation_p.V355L			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	355	Interaction with BRCA2.|Ser-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						AGTAACAGCTGTGGTGTCCTC	0.433																																					p.V355L													.	C11orf30-232	0			c.G1063T						.						150	122	132					11																	76183839		2200	4292	6492	SO:0001583	missense	56946	exon8			ACAGCTGTGGTGT	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.1063G>T	11.37:g.76183839G>T	ENSP00000432327:p.Val355Leu	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	106	3	NM_020193	0	0	1	1	0	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	37	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.490244	0.84962	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.67581	0.2908	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D;D;D	0.67145	0.994;0.994;0.994;0.996;0.996;0.994;0.994;0.994	D;D;D;D;D;D;D;D	0.76071	0.97;0.97;0.97;0.987;0.987;0.97;0.97;0.97	T	0.60047	-0.7339	9	0.26408	T	0.33	-5.3729	20.8794	0.99867	0.0:0.0:1.0:0.0	.	369;370;370;355;305;356;356;355	B7ZKT8;B7ZKU2;B7ZKU0;Q7Z589-2;F5H2F0;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;.;.;EMSY_HUMAN	L	356;355;355;305;370;369;356;370;355	.	ENSP00000334130:V355L	V	+	1	0	C11orf30	75861487	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GTG	.		0.433	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		T	76183839	G	T	76183839	3	4	146	1	0	0	0	0	1	0	0	0	1640	1377	48	4	1089	4	C11orf30	11	76183839	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	2387030	76183839	58822677	61	13040											
MAML2	84441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr11	95825407	95825407	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgctgctgttgctgctgttg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs61901862		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q596Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.532			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q596Q		.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2-850	1	Substitution - coding silent(1)	kidney(1)	c.G1788A						.						28	35	33					11																	95825407		2119	4148	6267	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1788G>A	11.37:g.95825407C>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	95	11	NM_032427	1	0	223	230	6	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			C|0.250;T|0.750		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825407	C	T	95825407	2	4	146	1	0	0	0	0	0	0	0	1	9231	796	28	2		2	MAML2	11	95825407	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	19641568	95825407	39181109	62	13041											
YAP1	10413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	102100555	102100555	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagatggaatgaacatagaaGgagaggagctgatgccaagt	16	6	15	4	0	0	5	0	2	0	3	0	9	0	7	1	3	3	1	1	3	5	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:102100555G>T	ENST00000282441.5	+	9	1787	c.1399G>T	c.(1399-1401)Gga>Tga	p.G467*	YAP1_ENST00000524575.1_Nonsense_Mutation_p.G289*|YAP1_ENST00000526343.1_Nonsense_Mutation_p.G413*|YAP1_ENST00000531439.1_Nonsense_Mutation_p.G451*|RP11-864G5.3_ENST00000526310.1_RNA|YAP1_ENST00000345877.2_Nonsense_Mutation_p.G417*|YAP1_ENST00000537274.1_Nonsense_Mutation_p.G455*|YAP1_ENST00000528834.1_3'UTR	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	467	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		GAACATAGAAGGAGAGGAGCT	0.483																																					p.G467X	Colon(50;247 1103 7861 28956)	.											.	YAP1-659	0			c.G1399T						.						131	123	126					11																	102100555		2203	4299	6502	SO:0001587	stop_gained	10413	exon9			ATAGAAGGAGAGG		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"Yes-associated protein 1, 65kDa"			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1399G>T	11.37:g.102100555G>T	ENSP00000282441:p.Gly467*	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	94	15	NM_001130145	0	0	4	6	2	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Nonsense_Mutation	SNP	ENST00000282441.5	37	CCDS44716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.303129|8.303129	0.98750|0.98750	.|.	.|.	ENSG00000137693|ENSG00000137693	ENST00000526343;ENST00000282441;ENST00000537274;ENST00000345877;ENST00000445250;ENST00000531439;ENST00000524575|ENST00000529029	.|.	.|.	.|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.77638	.|0.4160	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73658	.|-0.3913	.|4	0.87932|.	D|.	0|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	413;467;455;417;384;451;289|220	.|.	ENSP00000282441:G467X|.	G|K	+|+	1|3	0|2	YAP1|YAP1	101605765|101605765	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.981000|0.981000	0.71138|0.71138	9.441000|9.441000	0.97557|0.97557	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGA|AAG	.		0.483	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		T	102100555	G	T	102100555	4	4	146	1	0	0	0	0	0	1	0	0	17499	1001	35	4	1445	4	YAP1	11	102100555	Nonsense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	6275148	102100555	32905961	63	13042											
ARHGAP32	9743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	128933815	128933815	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctaaggtcagttcgtcAggggcccgagcagtgtacct	8	9	12	12	2	3	0	2	0	1	0	4	1	3	0	3	3	2	3	3	3	2	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:128933815A>G	ENST00000310343.9	-	8	824	c.825T>C	c.(823-825)ccT>ccC	p.P275P	ARHGAP32_ENST00000524655.1_Silent_p.P201P	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	275	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TCAGTTCGTCAGGGGCCCGAG	0.433																																					p.P275P		.											.	ARHGAP32-231	0			c.T825C						.						162	158	160					11																	128933815		1566	3579	5145	SO:0001819	synonymous_variant	9743	exon8			TTCGTCAGGGGCC	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"Rho GTPase activating proteins"	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.825T>C	11.37:g.128933815A>G		Somatic	158	0		WXS	Illumina HiSeq	Phase_I	139	24	NM_001142685	0	0	0	0	0	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			.		0.433	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		G	128933815	A	G	128933815	2	3	146	1	0	0	0	0	0	0	0	1	881	175	7	3		3	ARHGAP32	11	128933815	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	26833260	128933815	6072701	64	13043											
CLSTN3	9746	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7302198	7302198	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtgggggatgacctggaTcccgagcgggaaagcctgct	7	7	17	10	2	0	1	0	1	0	0	1	5	1	4	3	5	3	1	3	5	1	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr12:7302198T>C	ENST00000266546.6	+	14	2604	c.2154T>C	c.(2152-2154)gaT>gaC	p.D718D	CLSTN3_ENST00000537408.1_Silent_p.D730D	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	718					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						ATGACCTGGATCCCGAGCGGG	0.572																																					p.D718D		.											.	CLSTN3-153	0			c.T2154C						.						86	78	80					12																	7302198		2203	4300	6503	SO:0001819	synonymous_variant	9746	exon14			CCTGGATCCCGAG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.2154T>C	12.37:g.7302198T>C		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	67	21	NM_014718	0	0	27	61	34	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	37	CCDS8575.1																																																																																			.		0.572	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		C	7302198	T	C	7302198	2	2	146	1	0	0	0	0	0	0	0	1	3569	1432	50	3		3	CLSTN3	12	7302198	Silent	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		7302198	126549697	65	13044											
MON2	23041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	62954577	62954577	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagcttgaagatttgaatcTatggtgggctgcgtggaata	10	13	14	4	1	1	4	0	3	1	1	1	5	1	5	0	3	2	2	0	3	5	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr12:62954577T>A	ENST00000393632.2	+	26	4107	c.3716T>A	c.(3715-3717)cTa>cAa	p.L1239Q	MON2_ENST00000552738.1_Missense_Mutation_p.L1216Q|MON2_ENST00000393630.3_Missense_Mutation_p.L1240Q|MON2_ENST00000546600.1_Missense_Mutation_p.L1239Q|MON2_ENST00000393629.2_Missense_Mutation_p.L1239Q|MON2_ENST00000280379.6_Missense_Mutation_p.L1240Q	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1239					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GATTTGAATCTATGGTGGGCT	0.393																																					p.L1239Q		.											.	MON2-514	0			c.T3716A						.						92	90	91					12																	62954577		2203	4300	6503	SO:0001583	missense	23041	exon26			TGAATCTATGGTG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.3716T>A	12.37:g.62954577T>A	ENSP00000377252:p.Leu1239Gln	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	99	22	NM_015026	0	0	2	4	2	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.100011	0.76983	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000001	T	0.79857	0.4518	L	0.52759	1.655	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.979;1.0;1.0	D;P;P;D;D	0.83275	0.99;0.861;0.793;0.994;0.996	T	0.79308	-0.1857	9	.	.	.	-5.6366	15.0609	0.71951	0.0:0.0:0.0:1.0	.	1239;1216;1239;114;1239	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	Q	1239;1240;1240;1239;1216;1239	ENSP00000377252:L1239Q;ENSP00000377250:L1240Q;ENSP00000280379:L1240Q;ENSP00000447407:L1239Q;ENSP00000449215:L1216Q;ENSP00000377249:L1239Q	.	L	+	2	0	MON2	61240844	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.787000	0.85759	2.031000	0.59945	0.377000	0.23210	CTA	.		0.393	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		A	62954577	T	A	62954577	3	1	146	1	0	0	0	0	1	0	0	0	9725	1522	53	5	3818	5	MON2	12	62954577	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	55652379	62954577	70897318	66	13045											
MRPS31	10240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	41323388	41323388	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtggctaactgcttagcaaAttccacatcccaaagtgaag	13	10	8	10	0	0	1	0	1	0	0	2	1	2	1	2	1	3	3	2	1	5	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr13:41323388A>T	ENST00000323563.6	-	6	880	c.844T>A	c.(844-846)Ttt>Att	p.F282I	MRPS31_ENST00000498078.1_5'UTR	NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	282						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		TGCTTAGCAAATTCCACATCC	0.368																																					p.F282I		.											.	MRPS31-226	0			c.T844A						.						103	90	94					13																	41323388		2203	4300	6503	SO:0001583	missense	10240	exon6			TAGCAAATTCCAC	Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738		"Mitochondrial ribosomal proteins / small subunits"	16632	protein-coding gene	gene with protein product		611992				11279123, 8567980	Standard	NM_005830		Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.844T>A	13.37:g.41323388A>T	ENSP00000315397:p.Phe282Ile	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	88	8	NM_005830	0	0	8	19	11	B2RCS3|Q5VYC8|Q8WTV8	Missense_Mutation	SNP	ENST00000323563.6	37	CCDS9372.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196191	0.58126	.	.	ENSG00000102738	ENST00000323563	T	0.30182	1.54	5.17	5.17	0.71159	.	0.105571	0.64402	D	0.000003	T	0.50973	0.1647	M	0.80982	2.52	0.40731	D	0.982746	D	0.71674	0.998	D	0.65233	0.933	T	0.54255	-0.8321	10	0.37606	T	0.19	.	8.5691	0.33558	0.912:0.0:0.088:0.0	.	282	Q92665	RT31_HUMAN	I	282	ENSP00000315397:F282I	ENSP00000315397:F282I	F	-	1	0	MRPS31	40221388	1.000000	0.71417	0.995000	0.50966	0.613000	0.37349	2.868000	0.48436	1.947000	0.56498	0.524000	0.50904	TTT	.		0.368	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044640.2			T	41323388	A	T	41323388	3	4	146	1	0	0	0	0	1	0	0	0	9866	101	4	5	351	5	MRPS31	13	41323388	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		41323388	73846490	67	13046											
COL4A2	1284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	111117912	111117912	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacctggaccaccaggctTcctgggccctcctggccccg	4	8	10	19	1	0	0	0	0	0	0	2	1	2	1	8	4	1	1	8	4	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr13:111117912T>A	ENST00000360467.5	+	25	2243	c.1937T>A	c.(1936-1938)tTc>tAc	p.F646Y	COL4A2-AS2_ENST00000458403.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	646	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CCACCAGGCTTCCTGGGCCCT	0.597																																					p.F646Y		.											.	COL4A2-95	0			c.T1937A						.						29	34	32					13																	111117912		1873	4094	5967	SO:0001583	missense	1284	exon25			CAGGCTTCCTGGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"Collagens"	2203	protein-coding gene	gene with protein product	"canstatin", "collagen type IV alpha 2"	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1937T>A	13.37:g.111117912T>A	ENSP00000353654:p.Phe646Tyr	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	124	14	NM_001846	0	0	49	60	11	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.456320	0.01071	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93247	-3.19	4.82	3.55	0.40652	.	0.654622	0.13725	N	0.367070	D	0.84942	0.5584	N	0.17674	0.51	0.09310	N	0.999999	B	0.23650	0.089	B	0.17098	0.017	T	0.72966	-0.4131	10	0.29301	T	0.29	.	5.8702	0.18799	0.1497:0.0841:0.0:0.7662	.	646	P08572	CO4A2_HUMAN	Y	646	ENSP00000353654:F646Y	ENSP00000257309:F646Y	F	+	2	0	COL4A2	109915913	0.000000	0.05858	0.103000	0.21229	0.102000	0.19082	0.319000	0.19522	1.802000	0.52723	0.379000	0.24179	TTC	.		0.597	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		A	111117912	T	A	111117912	3	1	146	1	0	0	0	0	1	0	0	0	3696	1783	62	5	2031	5	COL4A2	13	111117912	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	69794524	111117912	4051966	68	13047											
GTF2A1	2957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	81659105	81659105	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtataacttgagtcttatTtcctgtaaataagatttgct	12	17	7	5	0	1	2	0	1	1	1	2	2	2	2	1	1	2	3	1	1	6	8			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr14:81659105T>A	ENST00000553612.1	-	7	1094	c.691A>T	c.(691-693)Aat>Tat	p.N231Y	GTF2A1_ENST00000434192.2_Missense_Mutation_p.N192Y	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	231					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		TGAGTCTTATTTCCTGTAAAT	0.502																																					p.N231Y		.											.	GTF2A1-153	0			c.A691T						.						174	172	173					14																	81659105		2203	4300	6503	SO:0001583	missense	2957	exon7			TCTTATTTCCTGT	X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"General transcription factors"	4646	protein-coding gene	gene with protein product		600520	"glucose regulated protein, 58kD pseudogene"			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.691A>T	14.37:g.81659105T>A	ENSP00000452454:p.Asn231Tyr	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	77	9	NM_015859	0	0	3	3	0	Q3KNQ9	Missense_Mutation	SNP	ENST00000553612.1	37	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.444489	0.83993	.	.	ENSG00000165417	ENST00000553612;ENST00000344860;ENST00000434192	T;T	0.44083	0.93;0.93	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.62588	0.2440	M	0.68952	2.095	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	T	0.64723	-0.6340	10	0.52906	T	0.07	-21.9526	15.3673	0.74531	0.0:0.0:0.0:1.0	.	231	P52655	TF2AA_HUMAN	Y	231;192;192	ENSP00000452454:N231Y;ENSP00000409492:N192Y	ENSP00000298173:N231Y	N	-	1	0	GTF2A1	80728858	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.643000	0.83403	2.084000	0.62774	0.533000	0.62120	AAT	.		0.502	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859		A	81659105	T	A	81659105	3	1	146	1	0	0	0	0	1	0	0	0	6873	1841	64	5	451	5	GTF2A1	14	81659105	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		81659105	25690435	69	13048											
SETD3	84193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	99929881	99929881	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgcacatactcttcccaCtcttttcctgggccaggcgc	6	12	7	16	1	3	0	0	0	3	0	5	0	5	0	3	2	2	1	3	2	1	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr14:99929881C>T	ENST00000331768.5	-	3	297	c.138G>A	c.(136-138)gaG>gaA	p.E46E	SETD3_ENST00000329331.3_Silent_p.E46E|SETD3_ENST00000453938.1_5'UTR|SETD3_ENST00000436070.2_Silent_p.E46E	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	46					histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				ACTCTTCCCACTCTTTTCCTG	0.413																																					p.E46E		.											.	SETD3-514	0			c.G138A						.						84	71	76					14																	99929881		2203	4300	6503	SO:0001819	synonymous_variant	84193	exon3			TTCCCACTCTTTT	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.138G>A	14.37:g.99929881C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	63	11	NM_032233	0	0	11	14	3	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Silent	SNP	ENST00000331768.5	37	CCDS9951.1																																																																																			.		0.413	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		T	99929881	C	T	99929881	2	4	146	1	0	0	0	0	0	0	0	1	14164	564	20	2		2	SETD3	14	99929881	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	18270776	99929881	7419659	70	13049											
MTMR15	22909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	31197838	31197838	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattcagaggcaaaatctcaTagttctgcagatgatgcttc	12	12	9	8	0	3	3	2	1	2	2	5	4	3	3	0	1	2	4	0	1	3	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:31197838T>G	ENST00000362065.4	+	2	1263	c.972T>G	c.(970-972)caT>caG	p.H324Q	FAN1_ENST00000565466.1_Missense_Mutation_p.H324Q|FAN1_ENST00000561594.1_Missense_Mutation_p.H324Q|FAN1_ENST00000561607.1_Missense_Mutation_p.H324Q	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	324					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						CAAAATCTCATAGTTCTGCAG	0.418								Direct reversal of damage																													p.H324Q		.											.	FAN1-90	0			c.T972G						.						71	67	68					15																	31197838		2202	4300	6502	SO:0001583	missense	22909	exon2			ATCTCATAGTTCT		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"KIAA1018", "myotubularin related protein 15"	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.972T>G	15.37:g.31197838T>G	ENSP00000354497:p.His324Gln	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	86	16	NM_001146095	0	0	1	1	0	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	T	3.821	-0.037772	0.07497	.	.	ENSG00000198690	ENST00000362065	T	0.40756	1.02	5.46	-9.68	0.00528	.	2.519990	0.00901	N	0.002356	T	0.18299	0.0439	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17228	-1.0376	10	0.12766	T	0.61	0.1551	2.0377	0.03543	0.2596:0.2533:0.3519:0.1352	.	324;324	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	Q	324	ENSP00000354497:H324Q	ENSP00000354497:H324Q	H	+	3	2	FAN1	28985130	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-3.615000	0.00414	-2.231000	0.00718	-0.291000	0.09656	CAT	.		0.418	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		G	31197838	T	G	31197838	3	3	146	1	0	0	0	0	1	0	0	0	9968	1403	49	5	974	5	MTMR15	15	31197838	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		31197838	71333554	71	13050											
DMXL2	23312	broad.mit.edu	37	chr15	51828388	51828388	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtaactgggaatgagagtTggaagccaagccacattaga	15	7	12	7	0	0	2	0	1	0	2	0	5	0	4	2	2	3	2	2	2	5	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:51828388T>G	ENST00000251076.5	-	12	2576	c.2289A>C	c.(2287-2289)ccA>ccC	p.P763P	DMXL2_ENST00000449909.3_Silent_p.P763P|DMXL2_ENST00000543779.2_Silent_p.P763P	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	763						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GAATGAGAGTTGGAAGCCAAG	0.358																																					p.P763P													.	DMXL2-99	0			c.A2289C						.						96	84	88					15																	51828388		2194	4292	6486	SO:0001819	synonymous_variant	23312	exon12			GAGAGTTGGAAGC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2289A>C	15.37:g.51828388T>G		Somatic	109	3		WXS	Illumina HiSeq	Phase_I	92	5	NM_001174117	0	0	1	1	0	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			.		0.358	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		G	51828388	T	G	51828388	2	3	146	1	0	0	0	0	0	0	0	1	4606	1799	63	5		5	DMXL2	15	51828388	Silent	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	20630550	51828388	50703004	72	13051											
ONECUT1	3175	broad.mit.edu	37	chr15	53081865	53081867	+	In_Frame_Del	DEL	GGT	GGT	-																															caggctgtgctcaggggcccGgtggtggtggtggtaatctc																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	GGT	GGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:53081865_53081867delGGT	ENST00000305901.5	-	1	342_344	c.215_217delACC	c.(214-219)caccgg>cgg	p.H72del	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	72	Poly-His.				B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		TCAGGGGCCCGGTGGTGGTGGTG	0.719																																					p.72_73del													.	ONECUT1-68	0			c.215_217del						.																																			SO:0001651	inframe_deletion	3175	exon1			GGGCCCGGTGGTG	U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"Homeoboxes / CUT class"	8138	protein-coding gene	gene with protein product		604164	"one cut domain, family member 1"	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.215_217delACC	15.37:g.53081874_53081876delGGT	ENSP00000302630:p.His72del	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_004498	0	0	0	0	0	B2RTV4|Q99744|Q9UMR6	In_Frame_Del	DEL	ENST00000305901.5	37	CCDS10150.1																																																																																			.		0.719	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2			-	53081867	GGT	-	53081865	7	5	146	1	0	1	0	1	0	0	0	0	10894	1115	39	0	1188	0	ONECUT1	15	53081865	In_Frame_Del	DEL	GGT	TCGA-KV-A6GD-01A-11D-A31X-10	1253477	53081865	49449527	73	13052											
SIN3A	25942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75705130	75705130	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gactttggcaggtgggggctGaggagctggctgggcaggag	6	7	22	6	0	0	1	0	1	0	0	0	4	0	3	0	8	1	5	0	8	0	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:75705130G>A	ENST00000394947.3	-	5	1044	c.730C>T	c.(730-732)Cag>Tag	p.Q244*	SIN3A_ENST00000394949.4_Nonsense_Mutation_p.Q244*|SIN3A_ENST00000360439.4_Nonsense_Mutation_p.Q244*	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GGTGggggctgaggagctggc	0.552																																					p.Q244X		.											.	SIN3A-230	0			c.C730T						.						81	75	77					15																	75705130		2197	4294	6491	SO:0001587	stop_gained	25942	exon5			GGGGCTGAGGAGC	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.730C>T	15.37:g.75705130G>A	ENSP00000378402:p.Gln244*	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	89	12	NM_001145358	0	0	3	3	0		Nonsense_Mutation	SNP	ENST00000394947.3	37	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	37	6.213995	0.97380	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	.	.	.	6.04	5.12	0.69794	.	0.098566	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-11.3013	14.2887	0.66263	0.0708:0.0:0.9292:0.0	.	.	.	.	X	244	.	ENSP00000353622:Q244X	Q	-	1	0	SIN3A	73492183	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.867000	0.99620	1.557000	0.49525	0.561000	0.74099	CAG	.		0.552	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75705130	G	A	75705130	4	1	146	1	0	0	0	0	0	1	0	0	14357	1299	45	2	3159	2	SIN3A	15	75705130	Nonsense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	22623265	75705130	26826262	74	13053											
RASGRF1	5923	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	79350728	79350728	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcctcgatctgctgccgaAgctgcttggccacggtcttc	5	11	10	15	3	2	0	0	0	2	0	5	2	3	0	3	2	4	3	3	2	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:79350728A>T	ENST00000419573.3	-	3	753	c.479T>A	c.(478-480)cTt>cAt	p.L160H	RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Missense_Mutation_p.L160H	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	160					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CTGCTGCCGAAGCTGCTTGGC	0.602																																					p.L160H		.											.	RASGRF1-662	0			c.T479A						.						124	101	109					15																	79350728		2196	4293	6489	SO:0001583	missense	5923	exon3			TGCCGAAGCTGCT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.479T>A	15.37:g.79350728A>T	ENSP00000405963:p.Leu160His	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	44	4	NM_001145648	0	0	0	0	0	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982389	0.74474	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.46819	0.86	4.59	4.59	0.56863	.	0.000000	0.64402	D	0.000005	T	0.62258	0.2413	L	0.55481	1.735	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.85130	0.954;0.984;0.993;0.997	T	0.65492	-0.6155	10	0.87932	D	0	.	11.9588	0.52997	1.0:0.0:0.0:0.0	.	160;160;160;160	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	H	160	ENSP00000405963:L160H	ENSP00000378224:L160H	L	-	2	0	RASGRF1	77137783	1.000000	0.71417	0.997000	0.53966	0.677000	0.39632	8.730000	0.91510	1.917000	0.55516	0.443000	0.29094	CTT	.		0.602	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79350728	A	T	79350728	3	4	146	1	0	0	0	0	1	0	0	0	13104	72	3	5	3446	5	RASGRF1	15	79350728	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	3645598	79350728	23180664	75	13054											
GRIN2A	2903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	9858489	9858489	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttattgaggttatccttcTgccggttggccacaaatgtt	8	15	10	8	1	1	1	0	1	1	0	2	1	2	1	3	3	1	4	3	3	3	6			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr16:9858489T>C	ENST00000396573.2	-	14	3221	c.2912A>G	c.(2911-2913)cAg>cGg	p.Q971R	GRIN2A_ENST00000535259.1_Missense_Mutation_p.Q814R|GRIN2A_ENST00000404927.2_Missense_Mutation_p.Q971R|GRIN2A_ENST00000330684.3_Missense_Mutation_p.Q971R|GRIN2A_ENST00000396575.2_Missense_Mutation_p.Q971R|GRIN2A_ENST00000562109.1_Missense_Mutation_p.Q971R	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	971					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTTATCCTTCTGCCGGTTGGC	0.468																																					p.Q971R		.											.	GRIN2A-349	0			c.A2912G						.						151	131	137					16																	9858489		2197	4300	6497	SO:0001583	missense	2903	exon14			TCCTTCTGCCGGT		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2912A>G	16.37:g.9858489T>C	ENSP00000379818:p.Gln971Arg	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	84	27	NM_000833	0	0	0	0	0	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	T	5.637	0.302152	0.10678	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.11712	2.75;2.75;2.76;2.75;2.75	5.33	5.33	0.75918	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.088776	0.85682	D	0.000000	T	0.08714	0.0216	L	0.27053	0.805	0.23293	N	0.997962	B;B;B	0.24317	0.034;0.101;0.005	B;B;B	0.29440	0.062;0.102;0.008	T	0.32428	-0.9907	9	.	.	.	.	10.6354	0.45563	0.0:0.0:0.1607:0.8393	.	814;971;971	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	R	971;971;814;971;971	ENSP00000379818:Q971R;ENSP00000385872:Q971R;ENSP00000441572:Q814R;ENSP00000332549:Q971R;ENSP00000379820:Q971R	.	Q	-	2	0	GRIN2A	9765990	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.691000	0.61738	2.016000	0.59253	0.533000	0.62120	CAG	.		0.468	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			C	9858489	T	C	9858489	3	2	146	1	0	0	0	0	1	0	0	0	6800	1580	55	3	1486	3	GRIN2A	16	9858489	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		9858489	80496264	76	13055											
ITGAX	3687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31373395	31373395	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctggaatccttttctcccaGgatggccccgttctgggggc	4	11	12	14	1	2	0	0	0	2	0	4	2	3	2	5	5	0	1	5	5	1	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr16:31373395G>A	ENST00000268296.4	+	11	1207		c.e11-1		ITGAX_ENST00000562522.1_Splice_Site	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)						blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TTTTCTCCCAGGATGGCCCCG	0.592																																					.		.											.	ITGAX-229	0			c.1087-1G>A						.						82	87	86					16																	31373395		2197	4300	6497	SO:0001630	splice_region_variant	3687	exon11			CTCCCAGGATGGC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1087-1G>A	16.37:g.31373395G>A		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	74	10	NM_000887	0	0	0	0	0	Q8IVA6	Splice_Site	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	g	13.52	2.262216	0.39995	.	.	ENSG00000140678	ENST00000268296	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4899	0.67645	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGAX	31280896	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	5.608000	0.67654	2.217000	0.71921	0.580000	0.79431	.	.		0.592	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	Intron	A	31373395	G	A	31373395	5	1	146	1	0	0	0	0	0	0	1	0	7910	1014	35	2	1128	2	ITGAX	16	31373395	Splice_Site	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	21514906	31373395	58981358	77	13056											
ITGAX	3687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31383064	31383064	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagccgagtccgagtcctcGggctgaaggcacactgtgaa	9	7	14	11	3	0	3	0	3	0	0	3	5	2	3	3	2	1	2	3	2	2	0	rs368436373		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr16:31383064G>A	ENST00000268296.4	+	17	2240	c.2119G>A	c.(2119-2121)Ggg>Agg	p.G707R	ITGAX_ENST00000562522.1_Missense_Mutation_p.G707R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	707					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCGAGTCCTCGGGCTGAAGGC	0.652																																					p.G707R		.											.	ITGAX-229	0			c.G2119A						.	G	ARG/GLY	0,4394		0,0,2197	60	54	56		2119	4.4	0	16		56	2,8598	2.2+/-6.3	0,2,4298	no	missense	ITGAX	NM_000887.3	125	0,2,6495	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	707/1164	31383064	2,12992	2197	4300	6497	SO:0001583	missense	3687	exon17			GTCCTCGGGCTGA	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"CD molecules", "Complement system", "Integrins"	6152	protein-coding gene	gene with protein product		151510	"integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2119G>A	16.37:g.31383064G>A	ENSP00000268296:p.Gly707Arg	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	54	5	NM_000887	0	1	33	34	0	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.741680	0.49151	0.0	2.33E-4	ENSG00000140678	ENST00000268296	T	0.44881	0.91	5.4	4.43	0.53597	Integrin alpha-2 (1);	.	.	.	.	T	0.51398	0.1672	L	0.55834	1.745	0.09310	N	1	D	0.59767	0.986	P	0.56514	0.8	T	0.38436	-0.9661	9	0.49607	T	0.09	.	10.5956	0.45336	0.0933:0.0:0.9067:0.0	.	707	P20702	ITAX_HUMAN	R	707	ENSP00000268296:G707R	ENSP00000268296:G707R	G	+	1	0	ITGAX	31290565	0.076000	0.21285	0.028000	0.17463	0.033000	0.12548	2.282000	0.43461	2.662000	0.90505	0.655000	0.94253	GGG	.		0.652	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31383064	G	A	31383064	3	1	146	1	0	0	0	0	1	0	0	0	7910	1116	39	1	2185	1	ITGAX	16	31383064	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	9669	31383064	58971689	78	13057											
KIAA0664	23277	bcgsc.ca	37	chr17	2601710	2601710	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgccacgtaggccgccaCgtcccccccgaagtccttgt	5	6	12	18	5	0	0	0	0	0	0	2	1	2	0	7	2	0	1	7	2	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:2601710C>T	ENST00000570628.2	-	10	1432	c.1327G>A	c.(1327-1329)Gtg>Atg	p.V443M	CLUH_ENST00000435359.1_Missense_Mutation_p.V443M|CLUH_ENST00000538975.1_Missense_Mutation_p.V443M			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	443					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											TAGGCCGCCACGTCCCCCCCG	0.627																																					p.V443M													.	.	0			c.G1327A						.						45	52	50					17																	2601710		2123	4211	6334	SO:0001583	missense	23277	exon10			CCGCCACGTCCCC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"KIAA0664"	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.1327G>A	17.37:g.2601710C>T	ENSP00000458986:p.Val443Met	Somatic	106	0		WXS	Illumina HiSeq	Phase_1	108	5	NM_015229	0	0	26	26	0	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.904464	0.52333	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	T;T	0.80393	-1.37;-1.37	5.41	5.41	0.78517	.	0.289374	0.39210	N	0.001425	T	0.76018	0.3929	N	0.14661	0.345	0.35837	D	0.825776	D;D	0.61697	0.99;0.981	P;P	0.56648	0.803;0.803	T	0.80061	-0.1540	10	0.38643	T	0.18	.	11.6201	0.51113	0.0:0.9191:0.0:0.0809	.	443;443	O75153;C9J6D7	K0664_HUMAN;.	M	443	ENSP00000388872:V443M;ENSP00000439628:V443M	ENSP00000320468:V443M	V	-	1	0	KIAA0664	2548460	0.996000	0.38824	0.998000	0.56505	0.297000	0.27493	2.506000	0.45433	2.532000	0.85374	0.655000	0.94253	GTG	.		0.627	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		T	2601710	C	T	2601710	3	4	146	1	0	0	0	0	1	0	0	0	8210	536	19	1	2670	1	KIAA0664	17	2601710	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10		2601710	78593500	79	13058											
MFAP4	4239	broad.mit.edu	37	chr17	19288499	19288499	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggggagatggagaagtcagCgtacttggcataggccgtgt	9	8	17	7	3	1	2	1	0	0	2	1	4	1	2	1	5	2	2	1	5	3	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:19288499C>T	ENST00000299610.4	-	5	517	c.433G>A	c.(433-435)Gct>Act	p.A145T	MFAP4_ENST00000395592.2_Missense_Mutation_p.A169T|MFAP4_ENST00000574313.2_5'Flank|MFAP4_ENST00000497081.2_Missense_Mutation_p.A170T	NM_002404.2	NP_002395.1	P55083	MFAP4_HUMAN	microfibrillar-associated protein 4	145	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|cellular response to UV-B (GO:0071493)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|regulation of collagen metabolic process (GO:0010712)|UV protection (GO:0009650)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)				large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	10	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GAGAAGTCAGCGTACTTGGCA	0.577																																					p.A169T													.	MFAP4-514	0			c.G505A						.						184	131	149					17																	19288499		2203	4300	6503	SO:0001583	missense	4239	exon5			AGTCAGCGTACTT	L38486	CCDS11208.1, CCDS56023.1	17p11.2	2013-02-06			ENSG00000166482	ENSG00000166482		"Fibrinogen C domain containing"	7035	protein-coding gene	gene with protein product	"microfibril-associated glycoprotein 4"	600596				7633408	Standard	NM_001198695		Approved		uc002gvs.3	P55083	OTTHUMG00000059585	ENST00000299610.4:c.433G>A	17.37:g.19288499C>T	ENSP00000299610:p.Ala145Thr	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	109	5	NM_001198695	0	0	106	106	0	A8KAJ1|A8MVM2|B4E317|Q6P680	Missense_Mutation	SNP	ENST00000299610.4	37	CCDS11208.1	.	.	.	.	.	.	.	.	.	.	c	7.070	0.568193	0.13560	.	.	ENSG00000166482	ENST00000395592;ENST00000299610	T;T	0.20881	2.04;2.04	5.0	-0.0266	0.13930	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.423620	0.04430	N	0.369121	T	0.10680	0.0261	N	0.05608	-0.01	0.09310	N	1	B;B	0.16396	0.001;0.017	B;B	0.12837	0.003;0.008	T	0.29181	-1.0020	10	0.26408	T	0.33	.	5.4949	0.16797	0.0:0.5367:0.1482:0.3151	.	145;169	P55083;A8MVM2	MFAP4_HUMAN;.	T	169;145	ENSP00000378957:A169T;ENSP00000299610:A145T	ENSP00000299610:A145T	A	-	1	0	MFAP4	19229092	0.000000	0.05858	0.003000	0.11579	0.115000	0.19883	-0.283000	0.08433	0.158000	0.19367	0.550000	0.68814	GCT	.		0.577	MFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132493.2	NM_002404		T	19288499	C	T	19288499	3	4	146	1	0	0	0	0	1	0	0	0	9542	768	27	1	342	1	MFAP4	17	19288499	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	16686789	19288499	61906711	80	13059											
PSMD11	5717	broad.mit.edu	37	chr17	30771555	30771555	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtaagatggcggcggcggCggtggtggagttccagagag	7	6	21	7	5	0	2	0	0	0	2	1	4	1	3	1	8	0	2	1	8	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:30771555C>T	ENST00000261712.3	+	1	277	c.14C>T	c.(13-15)gCg>gTg	p.A5V	PSMD11_ENST00000457654.2_Missense_Mutation_p.A5V	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	5					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome assembly (GO:0043248)|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)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			gcggcggcggcggtggtggAG	0.701																																					p.A5V	Ovarian(130;1038 1716 9294 11987 19279)												.	PSMD11-91	0			c.C14T						.						18	18	18					17																	30771555		2186	4270	6456	SO:0001583	missense	5717	exon1			CGGCGGCGGTGGT	AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"Proteasome (prosome, macropain) subunits"	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.14C>T	17.37:g.30771555C>T	ENSP00000261712:p.Ala5Val	Somatic	120	1		WXS	Illumina HiSeq	Phase_I	152	6	NM_002815	0	0	12	12	0	A8K3I7|E1P663|O00495|Q53FT5	Missense_Mutation	SNP	ENST00000261712.3	37	CCDS11272.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999150	0.74818	.	.	ENSG00000108671	ENST00000261712	.	.	.	5.25	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.24928	0.0605	N	0.08118	0	0.53688	D	0.999975	P;B	0.37038	0.579;0.212	B;B	0.33392	0.163;0.049	T	0.08086	-1.0739	9	0.27785	T	0.31	-19.5166	11.4424	0.50105	0.0:0.9133:0.0:0.0867	.	5;5	B4DTS5;O00231	.;PSD11_HUMAN	V	5	.	ENSP00000261712:A5V	A	+	2	0	PSMD11	27795668	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.945000	0.75947	1.455000	0.47813	0.558000	0.71614	GCG	.		0.701	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2	NM_002815		T	30771555	C	T	30771555	3	4	146	1	0	0	0	0	1	0	0	0	12723	768	27	1	16	1	PSMD11	17	30771555	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	11483056	30771555	50423655	81	13060											
COL1A1	1277	broad.mit.edu;bcgsc.ca	37	chr17	48277127	48277128	+	Missense_Mutation	DNP	GC	GC	AT																															gccgcacctgagccgtcgggGcagacgggacagcactcgcc																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:48277127_48277128GC>AT	ENST00000225964.5	-	2	402_403	c.284_285GC>AT	c.(283-285)tGC>tAT	p.C95Y		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	95	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	AGCCGTCGGGGCAGACGGGACA	0.728			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.C95Y				Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1-986	0			c.G284A						.																																			SO:0001583	missense	1277	exon2			TCGGGGCAGACGG	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"Collagens"	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.284_285delinsAT	17.37:g.48277127_48277128delinsAT	ENSP00000225964:p.Cys95Tyr	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	60	6	NM_000088	0	0	0	0	0	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Missense_Mutation	DNP	ENST00000225964.5	37	CCDS11561.1																																																																																			.		0.728	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			AT	48277128	GC	AT	48277127	3	1	146	1	0	0	0	0	1	0	0	0	3683	1195	42	2	4309	2	COL1A1	17	48277127	Missense_Mutation	DNP	GC	TCGA-KV-A6GD-01A-11D-A31X-10	17505572	48277127	32918083	82	13061											
SFRS1	6426	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	56083837	56083837	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaaactccacccgcagacgGtacccatcgtaatcatagcc	12	6	8	15	3	1	1	1	0	0	1	3	2	2	2	4	2	3	3	4	2	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:56083837G>T	ENST00000258962.4	-	2	454	c.246C>A	c.(244-246)taC>taA	p.Y82*	SRSF1_ENST00000582730.2_Nonsense_Mutation_p.Y82*|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000584773.1_Nonsense_Mutation_p.Y82*|SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000581497.1_5'Flank	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	82	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Y82*(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CCCGCAGACGGTACCCATCGT	0.637																																					p.Y82X		.											.	SRSF1-290	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C246A						.						30	28	29					17																	56083837		2203	4298	6501	SO:0001587	stop_gained	6426	exon2			CAGACGGTACCCA		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10780	protein-coding gene	gene with protein product	"splicing factor 2", "pre-mRNA-splicing factor SF2, P33 subunit", "alternate splicing factor", "SR splicing factor 1"	600812	"splicing factor, arginine/serine-rich 1"	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.246C>A	17.37:g.56083837G>T	ENSP00000258962:p.Tyr82*	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	206	20	NM_006924	0	0	22	24	2	B2R6Z7|D3DTZ3|Q13809	Nonsense_Mutation	SNP	ENST00000258962.4	37	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149607	0.78001	.	.	ENSG00000136450	ENST00000258962	.	.	.	5.96	-2.82	0.05787	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	13.3631	0.60667	0.5712:0.0:0.4287:0.0	.	.	.	.	X	82	.	ENSP00000258962:Y82X	Y	-	3	2	SRSF1	53438836	1.000000	0.71417	0.931000	0.37212	0.911000	0.54048	0.912000	0.28597	-0.291000	0.09012	-0.794000	0.03295	TAC	.		0.637	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		T	56083837	G	T	56083837	4	4	146	1	0	0	0	0	0	1	0	0	14197	1256	44	4	566	4	SFRS1	17	56083837	Nonsense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	7806710	56083837	25111373	83	13062											
NETO1	81832	hgsc.bcm.edu;bcgsc.ca	37	chr18	70450990	70450990	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccacatgcggatcaccccaAgacccgtgcgtagcatgaca	11	5	9	16	3	1	2	1	1	0	1	1	3	1	3	4	1	3	2	4	1	2	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr18:70450990A>T	ENST00000327305.6	-	7	1448	c.791T>A	c.(790-792)cTt>cAt	p.L264H	NETO1_ENST00000583169.1_Missense_Mutation_p.L264H|NETO1_ENST00000299430.2_Missense_Mutation_p.L263H	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	264	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GATCACCCCAAGACCCGTGCG	0.478																																					p.L264H		.											.	NETO1-94	0			c.T791A						.						193	165	174					18																	70450990		2203	4300	6503	SO:0001583	missense	81832	exon7			ACCCCAAGACCCG	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.791T>A	18.37:g.70450990A>T	ENSP00000313088:p.Leu264His	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	88	7	NM_001201465	0	0	0	0	0	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.261669	0.80358	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.18174	2.23;2.23	5.27	5.27	0.74061	CUB (5);	0.000000	0.53938	D	0.000058	T	0.36082	0.0954	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;0.994	D;D	0.87578	0.998;0.957	T	0.08146	-1.0736	10	0.72032	D	0.01	-10.3986	15.5016	0.75703	1.0:0.0:0.0:0.0	.	263;264	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	H	264;263	ENSP00000313088:L264H;ENSP00000299430:L263H	ENSP00000299430:L263H	L	-	2	0	NETO1	68601970	1.000000	0.71417	0.058000	0.19502	0.790000	0.44656	9.287000	0.95975	2.102000	0.63906	0.528000	0.53228	CTT	.		0.478	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		T	70450990	A	T	70450990	3	4	146	1	0	0	0	0	1	0	0	0	10365	72	3	5	826	5	NETO1	18	70450990	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		70450990	7626258	84	13063											
DOT1L	84444	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	2226194	2226194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgccaggtggtggcttggCgggaaggaagcccgcgcccg	5	7	18	11	4	0	0	0	0	0	0	0	2	0	2	3	6	2	1	3	6	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:2226194C>T	ENST00000398665.3	+	27	3710	c.3674C>T	c.(3673-3675)gCg>gTg	p.A1225V		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1225					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGGCTTGGCGGGAAGGAAG	0.677																																					p.A1225V		.											.	DOT1L-132	0			c.C3674T						.						12	16	15					19																	2226194		1920	4101	6021	SO:0001583	missense	84444	exon27			GCTTGGCGGGAAG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.3674C>T	19.37:g.2226194C>T	ENSP00000381657:p.Ala1225Val	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	68	12	NM_032482	0	0	0	0	0	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.379238	0.24944	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000457590	T;T	0.30182	1.95;1.54	4.54	-0.654	0.11443	.	1.117080	0.06764	N	0.782394	T	0.21103	0.0508	L	0.31294	0.92	0.09310	N	1	B;B	0.16396	0.002;0.017	B;B	0.09377	0.001;0.004	T	0.32719	-0.9896	10	0.87932	D	0	-8.2664	5.1085	0.14796	0.0:0.5858:0.1604:0.2538	.	1225;1225	Q8TEK3;Q8TEK3-2	DOT1L_HUMAN;.	V	1225;1225;105	ENSP00000381657:A1225V;ENSP00000407411:A105V	ENSP00000221482:A1225V	A	+	2	0	DOT1L	2177194	0.000000	0.05858	0.000000	0.03702	0.225000	0.24961	0.096000	0.15147	-0.246000	0.09611	0.491000	0.48974	GCG	.		0.677	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2226194	C	T	2226194	3	4	146	1	0	0	0	0	1	0	0	0	4720	768	27	1	3780	1	DOT1L	19	2226194	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10		2226194	56902789	85	13064											
SF4	57794	broad.mit.edu	37	chr19	19416711	19416711	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgtcctcgtcaggggacTggaagacactcgggcggtgc	6	7	15	13	4	1	1	1	0	0	1	5	3	2	3	2	5	1	0	2	5	1	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:19416711T>C	ENST00000247001.5	-	4	832	c.485A>G	c.(484-486)cAg>cGg	p.Q162R	SUGP1_ENST00000585763.1_5'UTR|SUGP1_ENST00000334782.5_Missense_Mutation_p.Q162R	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	162					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						GTCAGGGGACTGGAAGACACT	0.662																																					p.Q162R													.	SUGP1-91	0			c.A485G						.						54	53	53					19																	19416711		2203	4300	6503	SO:0001583	missense	57794	exon4			GGGGACTGGAAGA	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"G patch domain containing"	18643	protein-coding gene	gene with protein product		607992	"splicing factor 4"	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.485A>G	19.37:g.19416711T>C	ENSP00000247001:p.Gln162Arg	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	47	3	NM_172231	0	0	7	7	0	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	T	14.98	2.697947	0.48307	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	T	0.23348	1.91	4.44	4.44	0.53790	.	0.216607	0.44097	D	0.000485	T	0.22781	0.0550	L	0.59436	1.845	0.33038	D	0.531103	P	0.36199	0.543	B	0.31946	0.138	T	0.29488	-1.0010	10	0.17832	T	0.49	.	12.5289	0.56102	0.0:0.0:0.0:1.0	.	162	Q8IWZ8	SUGP1_HUMAN	R	162	ENSP00000247001:Q162R	ENSP00000247001:Q162R	Q	-	2	0	SUGP1	19277711	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	3.078000	0.50096	1.650000	0.50662	0.460000	0.39030	CAG	.		0.662	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		C	19416711	T	C	19416711	3	2	146	1	0	0	0	0	1	0	0	0	14187	1580	55	3	1496	3	SF4	19	19416711	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	17190517	19416711	39712272	86	13065											
PDCD2L	84306	broad.mit.edu	37	chr19	34895341	34895341	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtcgcccggcggccatggcGgccgttctgaagccggtgct	3	7	17	14	6	1	1	0	1	1	0	2	1	1	1	4	6	2	2	4	6	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:34895341G>T	ENST00000246535.3	+	1	53	c.6G>T	c.(4-6)gcG>gcT	p.A2A	PDCD2L_ENST00000587065.2_5'Flank|RP11-618P17.4_ENST00000606020.1_Intron	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	2					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CGGCCATGGCGGCCGTTCTGA	0.662																																					p.A2A													.	PDCD2L-91	0			c.G6T						.						3	4	4					19																	34895341		1697	3332	5029	SO:0001819	synonymous_variant	84306	exon1			CATGGCGGCCGTT	BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.6G>T	19.37:g.34895341G>T		Somatic	80	1		WXS	Illumina HiSeq	Phase_I	73	3	NM_032346	0	0	0	0	0		Silent	SNP	ENST00000246535.3	37	CCDS12438.1																																																																																			.		0.662	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346		T	34895341	G	T	34895341	2	4	146	1	0	0	0	0	0	0	0	1	11646	1103	39	4		4	PDCD2L	19	34895341	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	15478630	34895341	24233642	87	13066											
RYR1	6261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	38948847	38948847	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	accgagggctacaccccctaCcctggggccggcgagggctg	6	4	15	16	3	0	0	0	0	0	0	0	2	0	0	5	5	2	2	5	5	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:38948847C>G	ENST00000359596.3	+	18	2082	c.2082C>G	c.(2080-2082)taC>taG	p.Y694*	RYR1_ENST00000355481.4_Nonsense_Mutation_p.Y694*|RYR1_ENST00000360985.3_Nonsense_Mutation_p.Y694*			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	694	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACACCCCCTACCCTGGGGCCG	0.637																																					p.Y694X		.											.	RYR1-100	0			c.C2082G						.						52	51	51					19																	38948847		2203	4300	6503	SO:0001587	stop_gained	6261	exon18			CCCCTACCCTGGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2082C>G	19.37:g.38948847C>G	ENSP00000352608:p.Tyr694*	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	46	8	NM_001042723	0	0	0	0	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Nonsense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	41	8.988435	0.99027	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	.	.	.	5.02	5.02	0.67125	.	0.000000	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9369	0.58320	0.0:0.9196:0.0:0.0804	.	.	.	.	X	694	.	ENSP00000347667:Y694X	Y	+	3	2	RYR1	43640687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.109000	0.41863	2.623000	0.88846	0.549000	0.68633	TAC	.		0.637	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38948847	C	G	38948847	4	3	146	1	0	0	0	0	0	1	0	0	13800	518	18	4	2152	4	RYR1	19	38948847	Nonsense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	4053506	38948847	20180136	88	13067											
PSG5	5673	hgsc.bcm.edu;broad.mit.edu	37	chr19	43679366	43679366	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggatgctgggatccacttaCcagagacttcgactgtcatg	10	10	11	10	1	1	1	1	0	0	1	3	5	2	3	2	2	2	1	2	2	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:43679366C>T	ENST00000366175.3	-	4	1095		c.e4+1		PSG5_ENST00000342951.6_Splice_Site|PSG5_ENST00000407356.1_Splice_Site|PSG5_ENST00000599812.1_Splice_Site|PSG5_ENST00000407568.1_Intron|PSG5_ENST00000404580.1_Missense_Mutation_p.G322D			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5						female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GATCCACTTACCAGAGACTTC	0.463																																					.		.											.	PSG5-93	0			c.964+1G>A						.						125	148	140					19																	43679366		2202	4292	6494	SO:0001630	splice_region_variant	5673	exon5			CACTTACCAGAGA		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9522	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta 1 glycoprotein"	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.964+1G>A	19.37:g.43679366C>T		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	114	12	NM_002781	0	0	0	0	0	Q15239|Q96QJ1|Q9UQ75	Splice_Site	SNP	ENST00000366175.3	37	CCDS12617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|c	5.814|5.814	0.334421|0.334421	0.11013|0.11013	.|.	.|.	ENSG00000204941|ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951|ENST00000404580	.|T	.|0.01252	.|5.1	1.25|1.25	1.25|1.25	0.21368|0.21368	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00967	.|0.0032	.|.	.|.	.|.	0.23661|0.23661	N|N	0.99718|0.99718	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.49634	.|-0.8919	.|6	.|0.15499	.|T	.|0.54	.|.	5.8107|5.8107	0.18465|0.18465	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|D	-1|322	.|ENSP00000385250:G322D	.|ENSP00000385250:G322D	.|G	-|-	.|2	.|0	PSG5|PSG5	48371206|48371206	0.321000|0.321000	0.24625|0.24625	0.181000|0.181000	0.23098|0.23098	0.040000|0.040000	0.13550|0.13550	0.696000|0.696000	0.25541|0.25541	0.644000|0.644000	0.30656|0.30656	0.184000|0.184000	0.17185|0.17185	.|GGT	.		0.463	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	Intron	T	43679366	C	T	43679366	5	4	146	1	0	0	0	0	0	0	1	0	12687	521	18	2	50	2	PSG5	19	43679366	Splice_Site	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	4730519	43679366	15449617	89	13068											
NLRP8	126205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56487643	56487643	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgtgtgaggccctgaagaaCcctgactgtacattacagat	11	10	10	10	0	0	5	0	3	0	2	0	5	0	5	2	1	3	1	2	1	4	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:56487643C>T	ENST00000291971.3	+	8	2921	c.2850C>T	c.(2848-2850)aaC>aaT	p.N950N	NLRP8_ENST00000590542.1_Silent_p.N931N	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	950					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCCTGAAGAACCCTGACTGTA	0.453																																					p.N950N		.											.	NLRP8-361	0			c.C2850T						.						139	135	136					19																	56487643		2203	4300	6503	SO:0001819	synonymous_variant	126205	exon8			GAAGAACCCTGAC	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2850C>T	19.37:g.56487643C>T		Somatic	188	0		WXS	Illumina HiSeq	Phase_I	151	22	NM_176811	0	0	0	0	0	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			.		0.453	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		T	56487643	C	T	56487643	2	4	146	1	0	0	0	0	0	0	0	1	10509	506	18	2		2	NLRP8	19	56487643	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	12808277	56487643	2641340	90	13069											
ACTR5	79913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37383625	37383625	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacaaatggcggtgtcctgaTtattatgagaataatgtcca	13	12	9	7	1	0	2	0	2	0	1	2	3	2	2	2	2	0	0	2	2	5	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr20:37383625T>C	ENST00000243903.4	+	4	838	c.801T>C	c.(799-801)gaT>gaC	p.D267D		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	267					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				GGTGTCCTGATTATTATGAGA	0.418																																					p.D267D		.											.	ACTR5-90	0			c.T801C						.						67	71	70					20																	37383625		2203	4300	6503	SO:0001819	synonymous_variant	79913	exon4			TCCTGATTATTAT	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"INO80 complex subunits"	14671	protein-coding gene	gene with protein product	"INO80 complex subunit M"		"ARP5 (actin-related protein 5, yeast) homolog"			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.801T>C	20.37:g.37383625T>C		Somatic	245	0		WXS	Illumina HiSeq	Phase_I	256	56	NM_024855	0	0	0	0	0	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	37	CCDS13308.1																																																																																			.		0.418	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		C	37383625	T	C	37383625	2	2	146	1	0	0	0	0	0	0	0	1	215	1490	52	3		3	ACTR5	20	37383625	Silent	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		37383625	25641895	91	13070											
PREX1	57580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	47361658	47361658	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aaatccttatgaacttccagGatgtcttcgatgttcgagaa	12	13	8	8	2	1	2	0	1	1	1	5	5	3	3	2	1	1	1	2	1	4	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr20:47361658G>A	ENST00000371941.3	-	3	340	c.318C>T	c.(316-318)atC>atT	p.I106I	PREX1_ENST00000396220.1_Silent_p.I106I	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	106	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GAACTTCCAGGATGTCTTCGA	0.473																																					p.I106I		.											.	PREX1-231	0			c.C318T						.						159	163	162					20																	47361658		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon3			TTCCAGGATGTCT	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.318C>T	20.37:g.47361658G>A		Somatic	130	0		WXS	Illumina HiSeq	Phase_I	79	22	NM_020820	0	0	4	4	0	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			.		0.473	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47361658	G	A	47361658	2	1	146	1	0	0	0	0	0	0	0	1	12505	1164	41	2		2	PREX1	20	47361658	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	9978033	47361658	15663862	92	13071											
GNAS	2778	broad.mit.edu	37	chr20	57429158	57429158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccctctgggtcccaggcGccatcggcagcccatcccaa	6	6	9	20	2	1	0	0	0	1	0	5	0	4	0	6	3	1	1	6	3	1	0	rs542409237		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr20:57429158G>A	ENST00000371100.4	+	1	1390	c.838G>A	c.(838-840)Gcc>Acc	p.A280T	GNAS_ENST00000371102.4_Missense_Mutation_p.A280T|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000306120.3_Silent_p.A216A|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371099.2_Missense_Mutation_p.A280T	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0			R -> G (in PHP1A). {ECO:0000269|PubMed:11926205}.|R -> K (in PHP1A). {ECO:0000269|PubMed:11788646}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GGTCCCAGGCGCCATCGGCAG	0.682			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)			G|||	1	0.000199681	0	0	5008	,	,		14006	0.001		0	False		,,,				2504	0				p.A280T	Colon(117;935 1597 6045 8307 46442)			Dom	yes		20	20q13.2	2778	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	yes	E	.	GNAS-4767	0			c.G838A						.						13	15	15					20																	57429158		1827	4020	5847	SO:0001583	missense	2778	exon1			CCAGGCGCCATCG	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"secretogranin VI"	139320	"guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.838G>A	20.37:g.57429158G>A	ENSP00000360141:p.Ala280Thr	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	120	4	NM_080425	0	0	0	0	0	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	37	CCDS46622.1	.	.	.	.	.	.	.	.	.	.	G	7.769	0.707084	0.15239	.	.	ENSG00000087460	ENST00000371099;ENST00000371100;ENST00000371102	D;D	0.90261	-2.64;-2.63	4.03	1.02	0.19986	.	12.416800	0.00751	N	0.001065	D	0.83275	0.5219	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.68618	-0.5361	10	0.27785	T	0.31	.	6.1229	0.20164	0.3301:0.0:0.6699:0.0	.	280	Q5JWF2	GNAS1_HUMAN	T	280	ENSP00000360141:A280T;ENSP00000360143:A280T	ENSP00000360140:A280T	A	+	1	0	GNAS	56862553	0.001000	0.12720	0.001000	0.08648	0.197000	0.23852	0.342000	0.19926	0.272000	0.22027	-0.254000	0.11334	GCC	.		0.682	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516		A	57429158	G	A	57429158	3	1	146	1	0	0	0	0	1	0	0	0	6530	1087	38	1	1582	1	GNAS	20	57429158	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	10067500	57429158	5596362	93	13072											
SLC25A1	6576	broad.mit.edu	37	chr22	19165669	19165669	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccccggtaccgcggcgggTgcgagcgctcgtccagctgc	3	6	16	16	7	0	0	0	0	0	0	2	1	1	0	4	3	6	3	4	3	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr22:19165669T>G	ENST00000215882.5	-	2	335	c.179A>C	c.(178-180)cAc>cCc	p.H60P	SLC25A1_ENST00000461267.1_5'UTR|SLC25A1_ENST00000451283.1_5'UTR|CLTCL1_ENST00000442042.2_5'Flank	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	60					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		CCGCGGCGGGTGCGAGCGCTC	0.746																																					p.H67P													.	SLC25A1-90	0			c.A200C						.						7	8	7					22																	19165669		2051	4085	6136	SO:0001583	missense	6576	exon1			GGCGGGTGCGAGC	U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"Solute carriers"	10979	protein-coding gene	gene with protein product		190315	"solute carrier family 20 (mitochondrial citrate transporter), member 3"	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.179A>C	22.37:g.19165669T>G	ENSP00000215882:p.His60Pro	Somatic	47	3		WXS	Illumina HiSeq	Phase_I	101	19	NM_001256534	0	0	29	30	1	A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	37	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.874271	0.51695	.	.	ENSG00000100075	ENST00000215882	T	0.78364	-1.17	4.77	3.7	0.42460	Mitochondrial carrier domain (2);	0.321554	0.31233	N	0.008017	T	0.55497	0.1924	N	0.04655	-0.195	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43556	-0.9384	10	0.29301	T	0.29	-14.0182	11.3684	0.49686	0.0:0.0:0.1523:0.8477	.	60	P53007	TXTP_HUMAN	P	60	ENSP00000215882:H60P	ENSP00000215882:H60P	H	-	2	0	SLC25A1	17545669	1.000000	0.71417	0.407000	0.26434	0.997000	0.91878	5.920000	0.70017	0.638000	0.30545	0.448000	0.29417	CAC	.		0.746	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984		G	19165669	T	G	19165669	3	3	146	1	0	0	0	0	1	0	0	0	14503	1696	59	5	788	5	SLC25A1	22	19165669	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		19165669	32138897	94	13073											
GSTT1	2952	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	24384206	24384206	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcagggctgggacagcAggtccaggtacagctccagg	8	4	17	12	2	0	0	0	0	0	0	2	1	2	1	2	6	3	5	2	6	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr22:24384206A>T	ENST00000248935.5	-	1	78	c.26T>A	c.(25-27)cTg>cAg	p.L9Q	GSTT1_ENST00000439996.2_5'UTR	NM_000853.2	NP_000844.2	P30711	GSTT1_HUMAN		9	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)	6					Carboplatin(DB00958)|Cisplatin(DB00515)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)	CTGGGACAGCAGGTCCAGGTA	0.592									Myelodysplasia and Acute Myeloid Leukemia (AML), Familial																												p.L9Q		.											.	GSTT1-91	0			c.T26A						.						77	72	74					22																	24384206		1700	3601	5301	SO:0001583	missense	2952	exon1	Familial Cancer Database	incl.: Familial Myelodysplastic syndrome (late-onset), Familial AML, Familial Monocytic Leukemia, Familial Monosomy 7 and AML	GACAGCAGGTCCA																												ENST00000248935.5:c.26T>A	22.37:g.24384206A>T	ENSP00000248935:p.Leu9Gln	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	84	22	NM_000853	0	0	0	0	0	O00226|Q5TZY2|Q6IC69|Q969K8|Q96IY3	Missense_Mutation	SNP	ENST00000248935.5	37	CCDS13822.1	.	.	.	.	.	.	.	.	.	.	.	28.3	4.911220	0.92178	.	.	ENSG00000184674	ENST00000248935;ENST00000382792;ENST00000452369;ENST00000417870;ENST00000447865	T;T;T	0.64085	-0.08;-0.08;-0.08	5.31	5.31	0.75309	Glutathione S-transferase, N-terminal (1);Thioredoxin-like fold (2);	0.000000	0.64402	U	0.000006	T	0.77922	0.4203	M	0.80508	2.5	0.80722	D	1	D	0.63046	0.992	D	0.63957	0.92	T	0.81464	-0.0921	10	0.87932	D	0	-11.7318	13.568	0.61830	1.0:0.0:0.0:0.0	.	9	P30711	GSTT1_HUMAN	Q	9	ENSP00000248935:L9Q;ENSP00000406003:L9Q;ENSP00000397362:L9Q	ENSP00000248935:L9Q	L	-	2	0	GSTT1	22714206	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	8.005000	0.88553	2.163000	0.67991	0.451000	0.29950	CTG	.		0.592	GSTT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320184.2			T	24384206	A	T	24384206	3	4	146	1	0	0	0	0	1	0	0	0	6866	188	7	5	716	5	GSTT1	22	24384206	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	5218537	24384206	26920360	95	13074											
CCDC117	150275	broad.mit.edu;bcgsc.ca	37	chr22	29176936	29176936	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttttttctttttttcagTtgtccagtaagaaagaaaag	12	19	6	4	0	2	2	1	0	1	2	3	2	3	2	1	0	0	2	1	0	4	9			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr22:29176936T>A	ENST00000249064.4	+	3	416	c.240T>A	c.(238-240)gaT>gaA	p.D80E	CCDC117_ENST00000421503.2_Intron|CCDC117_ENST00000443309.2_5'UTR|CCDC117_ENST00000448492.2_Splice_Site_p.R62R	NM_001284263.1|NM_001284265.1|NM_173510.2	NP_001271192.1|NP_001271194.1|NP_775781.1	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117	80										breast(1)|kidney(1)|large_intestine(4)|upper_aerodigestive_tract(1)	7						TTTTTTTCAGTTGTCCAGTAA	0.338																																					p.D80E													.	CCDC117-91	0			c.T240A						.						47	44	45					22																	29176936		2203	4300	6503	SO:0001630	splice_region_variant	150275	exon3			TTTCAGTTGTCCA	AK091133	CCDS13846.1, CCDS63435.1, CCDS63436.1	22q12.1	2006-06-27			ENSG00000159873	ENSG00000159873			26599	protein-coding gene	gene with protein product						12477932	Standard	NM_001284263		Approved	FLJ33814	uc003aeb.3	Q8IWD4	OTTHUMG00000151091	ENST00000249064.4:c.240-1T>A	22.37:g.29176936T>A		Somatic	149	1		WXS	Illumina HiSeq	Phase_I	102	10	NM_173510	0	0	0	0	0	A8K0F1|B7Z2V1|B7Z860|Q6ICA7|Q8N278	Missense_Mutation	SNP	ENST00000249064.4	37	CCDS13846.1	.	.	.	.	.	.	.	.	.	.	T	10.25	1.299486	0.23650	.	.	ENSG00000159873	ENST00000249064	T	0.17528	2.27	5.37	1.95	0.26073	.	0.365309	0.26757	N	0.022642	T	0.06735	0.0172	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.34601	-0.9822	9	.	.	.	.	2.228	0.03989	0.1453:0.0882:0.321:0.4454	.	80	Q8IWD4	CC117_HUMAN	E	80	ENSP00000249064:D80E	.	D	+	3	2	CCDC117	27506936	0.993000	0.37304	0.924000	0.36721	0.943000	0.58893	0.209000	0.17435	0.017000	0.15025	0.459000	0.35465	GAT	.		0.338	CCDC117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321258.1	NM_173510	Missense_Mutation	A	29176936	T	A	29176936	5	1	146	1	0	0	0	0	0	0	1	0	2760	1739	60	5	250	5	CCDC117	22	29176936	Splice_Site	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	4792730	29176936	22127630	96	13075											
RP2	6102	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	46696623	46696623	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggccaaagcagtacagctggGatcagcgcgagaaggtaatg	13	5	15	8	2	1	1	1	0	0	1	1	3	1	2	1	3	4	4	1	3	4	2	rs377324837		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chrX:46696623G>T	ENST00000218340.3	+	1	249	c.88G>T	c.(88-90)Gat>Tat	p.D30Y		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	30	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						GTACAGCTGGGATCAGCGCGA	0.657																																					p.D30Y													.	RP2-130	0			c.G88T						.						67	44	52					X																	46696623		2133	4095	6228	SO:0001583	missense	6102	exon1			AGCTGGGATCAGC	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.88G>T	X.37:g.46696623G>T	ENSP00000218340:p.Asp30Tyr	Somatic	231	1		WXS	Illumina HiSeq	Phase_I	202	55	NM_006915	0	0	0	0	0	Q86XJ7|Q9NU67	Missense_Mutation	SNP	ENST00000218340.3	37	CCDS14270.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.801424	0.70682	.	.	ENSG00000102218	ENST00000218340	D	0.90955	-2.76	3.85	3.85	0.44370	C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93413	0.7899	M	0.78049	2.395	0.58432	D	0.999998	D	0.63046	0.992	P	0.60068	0.868	D	0.93614	0.6941	10	0.72032	D	0.01	-5.5346	10.3577	0.43974	0.0:0.0:1.0:0.0	.	30	O75695	XRP2_HUMAN	Y	30	ENSP00000218340:D30Y	ENSP00000218340:D30Y	D	+	1	0	RP2	46581567	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.164000	0.58190	1.903000	0.55091	0.462000	0.41574	GAT	.		0.657	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		T	46696623	G	T	46696623	3	4	146	1	0	0	0	0	1	0	0	0	13566	1174	41	4	90	4	RP2	23	46696623	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10		46696623	108573937	97	13076											
CASZ1	54897	broad.mit.edu	37	chr1	10714185	10714185	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtagaacttcttgaagccGtccttggcgtaggcatcgtc	7	13	11	10	3	1	2	0	1	1	1	4	2	2	2	2	2	2	3	2	2	4	6	rs377121758		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:10714185G>T	ENST00000377022.3	-	11	2246	c.1929C>A	c.(1927-1929)gaC>gaA	p.D643E	CASZ1_ENST00000344008.5_Missense_Mutation_p.D643E|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	643					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TCTTGAAGCCGTCCTTGGCGT	0.562																																					p.D643E													.	CASZ1-113	0			c.C1929A						.						136	126	130					1																	10714185		2203	4300	6503	SO:0001583	missense	54897	exon11			GAAGCCGTCCTTG	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.1929C>A	1.37:g.10714185G>T	ENSP00000366221:p.Asp643Glu	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	96	4	NM_001079843	0	0	3	3	0	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.882411	0.72294	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.84	-1.82	0.07857	.	0.136617	0.64402	D	0.000004	T	0.60444	0.2269	L	0.39397	1.21	0.43018	D	0.994564	P;P;D	0.76494	0.916;0.951;0.999	P;P;D	0.85130	0.72;0.72;0.997	T	0.56032	-0.8046	9	0.18710	T	0.47	-36.0167	12.0394	0.53444	0.5645:0.0:0.4355:0.0	.	667;643;643	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	E	643	.	ENSP00000339445:D643E	D	-	3	2	CASZ1	10636772	0.542000	0.26426	0.982000	0.44146	0.998000	0.95712	-0.024000	0.12435	-0.435000	0.07264	0.561000	0.74099	GAC	.		0.562	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		T	10714185	G	T	10714185	3	4	147	1	0	0	0	0	1	0	0	0	2691	1136	40	4	3398	4	CASZ1	1	10714185	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		10714185	238536436	1	13077											
CTTNBP2NL	55917	broad.mit.edu	37	chr1	112999438	112999438	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcgtttattggggtcatcaGctagcagccctggctaccag	8	10	12	11	1	2	0	2	0	0	0	2	0	2	0	2	3	5	4	2	3	3	5			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:112999438G>T	ENST00000271277.6	+	6	1549	c.1324G>T	c.(1324-1326)Gct>Tct	p.A442S		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	442					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGGGTCATCAGCTAGCAGCCC	0.542																																					p.A442S													.	CTTNBP2NL-92	0			c.G1324T						.						229	234	232					1																	112999438		2203	4300	6503	SO:0001583	missense	55917	exon6			TCATCAGCTAGCA	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1324G>T	1.37:g.112999438G>T	ENSP00000271277:p.Ala442Ser	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	67	3	NM_018704	0	0	0	0	0	B3KMS5|Q96B40	Missense_Mutation	SNP	ENST00000271277.6	37	CCDS845.1	.	.	.	.	.	.	.	.	.	.	G	7.655	0.683704	0.14907	.	.	ENSG00000143079	ENST00000271277	T	0.22134	1.97	5.56	5.56	0.83823	.	0.227351	0.47852	D	0.000204	T	0.08447	0.0210	L	0.35414	1.06	0.46499	D	0.999075	B	0.20052	0.041	B	0.19666	0.026	T	0.11227	-1.0596	10	0.09338	T	0.73	-9.3431	19.1035	0.93283	0.0:0.0:1.0:0.0	.	442	Q9P2B4	CT2NL_HUMAN	S	442	ENSP00000271277:A442S	ENSP00000271277:A442S	A	+	1	0	CTTNBP2NL	112800961	0.987000	0.35691	0.752000	0.31206	0.804000	0.45430	6.778000	0.75043	2.609000	0.88269	0.462000	0.41574	GCT	.		0.542	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		T	112999438	G	T	112999438	3	4	147	1	0	0	0	0	1	0	0	0	4052	971	34	4	1338	4	CTTNBP2NL	1	112999438	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	102285253	112999438	136251183	2	13078											
C1orf92	149499	broad.mit.edu	37	chr1	156897772	156897772	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgacgcctcctgctggaaaaAgggacacaggagcgctcgcg	10	4	14	13	5	0	0	0	0	0	0	2	4	1	3	2	3	2	2	2	3	2	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:156897772A>G	ENST00000337428.7	+	9	1126	c.972A>G	c.(970-972)aaA>aaG	p.K324K	LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	324										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TGCTGGAAAAAGGGACACAGG	0.677											OREG0013892	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K324K													.	LRRC71-91	0			c.A972G						.						25	37	33					1																	156897772		1978	4130	6108	SO:0001819	synonymous_variant	149499	exon9			GGAAAAAGGGACA	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 92"	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.972A>G	1.37:g.156897772A>G		Somatic	313	3	1782	WXS	Illumina HiSeq	Phase_I	329	5	NM_144702	0	0	0	0	0	Q96M24	Silent	SNP	ENST00000337428.7	37	CCDS44249.1																																																																																			.		0.677	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702		G	156897772	A	G	156897772	2	3	147	1	0	0	0	0	0	0	0	1	2075	69	3	3		3	C1orf92	1	156897772	Silent	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	43898334	156897772	92352849	3	13079											
C1orf112	55732	bcgsc.ca	37	chr1	169771829	169771829	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagaggactgtcaagccaaaAtttggaaatccagaccactc	15	7	8	11	0	1	2	1	0	0	2	3	4	2	4	3	2	1	0	3	2	4	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:169771829A>T	ENST00000286031.6	+	4	834	c.134A>T	c.(133-135)aAt>aTt	p.N45I	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000413811.2_Missense_Mutation_p.N16I|C1orf112_ENST00000359326.4_Missense_Mutation_p.N45I|C1orf112_ENST00000456684.1_Missense_Mutation_p.N103I	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	45										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TCAAGCCAAAATTTGGAAATC	0.328																																					p.N45I													.	C1orf112-90	0			c.A134T						.						68	72	71					1																	169771829		2203	4297	6500	SO:0001583	missense	55732	exon4			GCCAAAATTTGGA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.134A>T	1.37:g.169771829A>T	ENSP00000286031:p.Asn45Ile	Somatic	258	5		WXS	Illumina HiSeq	Phase_1	235	73	NM_018186	0	0	0	0	0	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.700017	0.88924	.	.	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000456684;ENST00000286031	T;T;T	0.69561	0.57;-0.41;0.57	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.78635	0.4314	M	0.77616	2.38	0.53688	D	0.999975	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.82143	-0.0603	10	0.87932	D	0	-23.1688	15.1562	0.72743	1.0:0.0:0.0:0.0	.	16;45;103	B4E0A9;Q9NSG2;B4DRP7	.;CA112_HUMAN;.	I	16;45;103;45	ENSP00000352276:N45I;ENSP00000415583:N103I;ENSP00000286031:N45I	ENSP00000286031:N45I	N	+	2	0	C1orf112	168038453	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.430000	0.73391	2.251000	0.74343	0.528000	0.53228	AAT	.		0.328	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		T	169771829	A	T	169771829	3	4	147	1	0	0	0	0	1	0	0	0	1991	101	4	5	140	5	C1orf112	1	169771829	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	12874057	169771829	79478792	4	13080											
HMCN1	83872	broad.mit.edu	37	chr1	186023105	186023105	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcaaagaaagaatacaaTctgcaagtttacagtaagtt	18	10	7	6	0	1	2	0	0	1	2	1	2	1	2	0	0	4	5	0	0	8	5			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:186023105T>G	ENST00000271588.4	+	44	7078	c.6849T>G	c.(6847-6849)aaT>aaG	p.N2283K	HMCN1_ENST00000367492.2_Missense_Mutation_p.N2283K	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2283	Ig-like C2-type 20.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAGAATACAATCTGCAAGTTT	0.363																																					p.N2283K													.	HMCN1-113	0			c.T6849G						.						102	102	102					1																	186023105		2203	4300	6503	SO:0001583	missense	83872	exon44			ATACAATCTGCAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"Fibulins", "Immunoglobulin superfamily / I-set domain containing"	19194	protein-coding gene	gene with protein product	"fibulin 6"	608548	"age-related macular degeneration 1 (senile macular degeneration)"	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.6849T>G	1.37:g.186023105T>G	ENSP00000271588:p.Asn2283Lys	Somatic	42	1		WXS	Illumina HiSeq	Phase_I	45	12	NM_031935	0	0	0	0	0	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	T	0.116	-1.131462	0.01756	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.65916	-0.18;-0.18	4.93	1.27	0.21489	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.656047	0.17688	N	0.165378	T	0.39733	0.1089	L	0.33339	1.005	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.27806	-1.0063	10	0.05525	T	0.97	.	5.3345	0.15949	0.0:0.2528:0.1406:0.6066	.	2283	Q96RW7	HMCN1_HUMAN	K	2283	ENSP00000271588:N2283K;ENSP00000356462:N2283K	ENSP00000271588:N2283K	N	+	3	2	HMCN1	184289728	0.012000	0.17670	0.020000	0.16555	0.527000	0.34593	0.684000	0.25364	0.024000	0.15214	0.338000	0.21704	AAT	.		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186023105	T	G	186023105	3	3	147	1	0	0	0	0	1	0	0	0	7241	1432	50	5	7023	5	HMCN1	1	186023105	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	16251276	186023105	63227516	5	13081											
PIK3C2B	5287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204413511	204413511	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcatctgagagtgagccaAtccactgcacagccatacga	13	6	9	13	1	1	2	0	2	1	1	2	4	2	2	3	0	5	2	3	0	2	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:204413511A>G	ENST00000367187.3	-	18	3276	c.2720T>C	c.(2719-2721)aTt>aCt	p.I907T	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.I879T	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	907	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GAGTGAGCCAATCCACTGCAC	0.582																																					p.I907T		.											.	PIK3C2B-1310	0			c.T2720C						.						83	68	73					1																	204413511		2203	4300	6503	SO:0001583	missense	5287	exon18			GAGCCAATCCACT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"phosphoinositide-3-kinase, class 2, beta polypeptide"			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.2720T>C	1.37:g.204413511A>G	ENSP00000356155:p.Ile907Thr	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	43	23	NM_002646	0	0	0	1	1	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.730234	0.89390	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.67345	-0.26;-0.26	5.98	5.98	0.97165	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.045667	0.85682	D	0.000000	D	0.82559	0.5063	M	0.85197	2.74	0.51482	D	0.999921	D;D	0.61697	0.98;0.99	P;P	0.62885	0.908;0.903	D	0.85512	0.1198	10	0.87932	D	0	.	16.1192	0.81329	1.0:0.0:0.0:0.0	.	879;907	F5GWN5;O00750	.;P3C2B_HUMAN	T	907;879	ENSP00000356155:I907T;ENSP00000400561:I879T	ENSP00000356155:I907T	I	-	2	0	PIK3C2B	202680134	1.000000	0.71417	0.999000	0.59377	0.902000	0.53008	9.339000	0.96797	2.288000	0.76882	0.482000	0.46254	ATT	.		0.582	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		G	204413511	A	G	204413511	3	3	147	1	0	0	0	0	1	0	0	0	11936	101	4	3	2252	3	PIK3C2B	1	204413511	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	18390406	204413511	44837110	6	13082											
HLX	3142	broad.mit.edu	37	chr1	221057861	221057861	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggagtggtgggagcagcGgcggcggcggcaatagtttc	6	7	20	8	4	0	0	0	0	0	0	1	2	0	2	0	7	2	3	0	7	2	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:221057861G>A	ENST00000366903.6	+	4	2783	c.1282G>A	c.(1282-1284)Ggc>Agc	p.G428S	HLX_ENST00000549319.1_Missense_Mutation_p.G214S	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	428	Ser-rich.				cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G431delG(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		tgggagcagcggcggcggcgg	0.642																																					p.G428S													.	HLX-70	1	Deletion - In frame(1)	large_intestine(1)	c.G1282A						.						25	24	25					1																	221057861		2203	4300	6503	SO:0001583	missense	3142	exon4			AGCAGCGGCGGCG	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"Homeoboxes / ANTP class : NKL subclass"	4978	protein-coding gene	gene with protein product		142995	"H2.0 (Drosophila)-like homeo box 1", "H2.0-like homeobox 1 (Drosophila)", "H2.0-like homeobox 1"	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1282G>A	1.37:g.221057861G>A	ENSP00000355870:p.Gly428Ser	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	96	3	NM_021958	0	0	1	1	0	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.198731	0.38806	.	.	ENSG00000136630	ENST00000366903;ENST00000549319	D;D	0.91996	-2.65;-2.95	2.86	-0.687	0.11320	.	0.951617	0.08586	N	0.923819	T	0.78483	0.4290	N	0.14661	0.345	0.23320	N	0.997912	B	0.10296	0.003	B	0.06405	0.002	T	0.65689	-0.6107	10	0.02654	T	1	.	3.3157	0.07032	0.4133:0.2112:0.3755:0.0	.	428	Q14774	HLX_HUMAN	S	428;214	ENSP00000355870:G428S;ENSP00000449882:G214S	ENSP00000355870:G428S	G	+	1	0	HLX	219124484	0.977000	0.34250	0.038000	0.18304	0.016000	0.09150	1.135000	0.31454	0.081000	0.16988	-0.291000	0.09656	GGC	.		0.642	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958		A	221057861	G	A	221057861	3	1	147	1	0	0	0	0	1	0	0	0	7237	1116	39	1	1296	1	HLX	1	221057861	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	16644350	221057861	28192760	7	13083											
TLR5	7100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223286235	223286235	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaggagcctctcagtggTgttgaggacctgggggacct	7	8	16	10	0	1	1	1	1	1	0	2	4	1	4	3	5	2	2	3	5	0	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:223286235T>A	ENST00000540964.1	-	4	600	c.139A>T	c.(139-141)Acc>Tcc	p.T47S	TLR5_ENST00000342210.6_Missense_Mutation_p.T47S			O60602	TLR5_HUMAN	toll-like receptor 5	47					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		CTCTCAGTGGTGTTGAGGACC	0.547																																					p.T47S		.											.	TLR5-525	0			c.A139T						.						62	63	62					1																	223286235		2203	4300	6503	SO:0001583	missense	7100	exon6			CAGTGGTGTTGAG		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.139A>T	1.37:g.223286235T>A	ENSP00000440643:p.Thr47Ser	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	168	70	NM_003268	0	0	0	0	0	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480409	0.26598	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	D;D;D	0.82526	-1.62;-1.62;-1.62	4.75	3.6	0.41247	.	0.354369	0.30510	N	0.009461	T	0.70430	0.3223	L	0.48362	1.52	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.50516	-0.8819	10	0.09084	T	0.74	.	3.4825	0.07607	0.0:0.2019:0.2085:0.5896	.	47	O60602	TLR5_HUMAN	S	47	ENSP00000440643:T47S;ENSP00000355846:T47S;ENSP00000340089:T47S	ENSP00000340089:T47S	T	-	1	0	TLR5	221352858	0.318000	0.24598	0.004000	0.12327	0.995000	0.86356	0.650000	0.24858	0.751000	0.32900	0.533000	0.62120	ACC	.		0.547	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223286235	T	A	223286235	3	1	147	1	0	0	0	0	1	0	0	0	15986	1696	59	5	2441	5	TLR5	1	223286235	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	2228374	223286235	25964386	8	13084											
SIPA1L2	57568	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	232539257	232539257	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ataagggcagctcttgggccCcttccaggtcctgcccatgc	6	9	11	15	0	1	0	0	0	1	0	3	0	3	0	5	3	3	2	5	3	1	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:232539257C>T	ENST00000366630.1	-	20	5235	c.4877G>A	c.(4876-4878)gGg>gAg	p.G1626E	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.G682E|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.G1626E			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1626					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CTCTTGGGCCCCTTCCAGGTC	0.562																																					p.G1626E													.	SIPA1L2-95	0			c.G4877A						.						64	71	69					1																	232539257		1959	4156	6115	SO:0001583	missense	57568	exon19			TGGGCCCCTTCCA	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4877G>A	1.37:g.232539257C>T	ENSP00000355589:p.Gly1626Glu	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	61	26	NM_020808	0	0	0	1	1	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	5.973	0.363555	0.11296	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.29397	1.57;1.57;1.57	5.04	3.16	0.36331	.	0.545601	0.19376	N	0.115763	T	0.15046	0.0363	N	0.16478	0.41	0.33489	D	0.588516	B;B	0.20052	0.002;0.041	B;B	0.17722	0.019;0.011	T	0.20571	-1.0271	10	0.14656	T	0.56	-10.7471	5.5271	0.16964	0.0:0.6269:0.1476:0.2255	.	1626;682	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	E	1626;1626;682	ENSP00000355589:G1626E;ENSP00000262861:G1626E;ENSP00000309102:G682E	ENSP00000262861:G1626E	G	-	2	0	SIPA1L2	230605880	0.978000	0.34361	0.987000	0.45799	0.992000	0.81027	2.333000	0.43912	0.723000	0.32274	0.644000	0.83932	GGG	.		0.562	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232539257	C	T	232539257	3	4	147	1	0	0	0	0	1	0	0	0	14362	623	22	2	303	2	SIPA1L2	1	232539257	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	9253022	232539257	16711364	9	13085											
SLC30A3	7781	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27480036	27480036	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtaccttgaagtagatgaGgatggaggcagccagtaccc	11	8	14	8	0	0	3	0	2	0	1	0	5	0	5	3	4	3	4	3	4	4	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr2:27480036G>C	ENST00000233535.4	-	5	1115	c.763C>G	c.(763-765)Ctc>Gtc	p.L255V	SLC30A3_ENST00000447008.2_Missense_Mutation_p.L250V	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	255					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGTAGATGAGGATGGAGGCA	0.612																																					p.L255V													.	SLC30A3-90	0			c.C763G						.						79	76	77					2																	27480036		2203	4300	6503	SO:0001583	missense	7781	exon5			AGATGAGGATGGA	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"Solute carriers"	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.763C>G	2.37:g.27480036G>C	ENSP00000233535:p.Leu255Val	Somatic	147	2		WXS	Illumina HiSeq	Phase_I	171	43	NM_003459	0	0	0	0	0	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	37	CCDS1743.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.353230	0.24512	.	.	ENSG00000115194	ENST00000233535;ENST00000447008;ENST00000445870;ENST00000432351	T;T;T	0.66460	-0.21;-0.21;-0.21	4.88	4.88	0.63580	.	0.122293	0.53938	D	0.000044	T	0.40595	0.1123	N	0.01668	-0.77	0.37697	D	0.924059	B;B	0.15930	0.012;0.015	B;B	0.31101	0.076;0.124	T	0.44360	-0.9333	10	0.22706	T	0.39	-24.7171	11.753	0.51859	0.0:0.1782:0.8218:0.0	.	250;255	F5H3B7;Q99726	.;ZNT3_HUMAN	V	255;250;192;206	ENSP00000233535:L255V;ENSP00000415226:L250V;ENSP00000414320:L206V	ENSP00000233535:L255V	L	-	1	0	SLC30A3	27333540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.584000	0.46102	2.429000	0.82318	0.555000	0.69702	CTC	.		0.612	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			C	27480036	G	C	27480036	3	2	147	1	0	0	0	0	1	0	0	0	14588	1000	35	4	419	4	SLC30A3	2	27480036	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		27480036	215719337	10	13086											
FBXO11	80204	broad.mit.edu;bcgsc.ca	37	chr2	48132850	48132850	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccggttggcggctcggaCggagttcatttgccgggctg	3	11	16	11	5	2	0	1	0	1	0	4	2	2	2	2	6	1	4	2	6	0	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr2:48132850C>G	ENST00000403359.3	-	1	82	c.10G>C	c.(10-12)Gtc>Ctc	p.V4L	AC079807.2_ENST00000417692.1_RNA|FBXO11_ENST00000316377.4_5'Flank|AC079807.2_ENST00000432064.1_RNA|FBXO11_ENST00000378314.3_5'Flank|AC079807.2_ENST00000439870.1_RNA	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	4					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCGGCTCGGACGGAGTTCATT	0.721			"Mis, F, D"		DLBCL																																p.V4L				Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11-659	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.G10C						.						3	3	3					2																	48132850		748	1783	2531	SO:0001583	missense	80204	exon1			CTCGGACGGAGTT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.10G>C	2.37:g.48132850C>G	ENSP00000384823:p.Val4Leu	Somatic	57	1		WXS	Illumina HiSeq	Phase_I	60	17	NM_001190274	0	0	0	0	0	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	37	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109165	0.56398	.	.	ENSG00000138081	ENST00000403359	T	0.55234	0.53	2.44	2.44	0.29823	.	.	.	.	.	T	0.37945	0.1022	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.43702	-0.9375	7	0.87932	D	0	-16.2404	10.0511	0.42216	0.0:1.0:0.0:0.0	.	.	.	.	L	4	ENSP00000384823:V4L	ENSP00000384823:V4L	V	-	1	0	FBXO11	47986354	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.264000	0.58859	1.345000	0.45676	0.491000	0.48974	GTC	.		0.721	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		G	48132850	C	G	48132850	3	3	147	1	0	0	0	0	1	0	0	0	5746	536	19	4	2955	4	FBXO11	2	48132850	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	20652814	48132850	195066523	11	13087											
CSRNP3	80034	broad.mit.edu	37	chr2	166535409	166535409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagtgctcacagtagttctAtgggccctgtcgctcactcc	7	12	9	13	1	3	0	2	0	1	0	5	0	4	0	2	1	1	4	2	1	3	4	rs144629858		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr2:166535409A>G	ENST00000342316.4	+	5	1176	c.904A>G	c.(904-906)Atg>Gtg	p.M302V	CSRNP3_ENST00000409420.1_Missense_Mutation_p.M334V|CSRNP3_ENST00000314499.7_Missense_Mutation_p.M302V	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	302					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						CAGTAGTTCTATGGGCCCTGT	0.493																																					p.M302V													.	CSRNP3-157	0			c.A904G						.	A	VAL/MET,VAL/MET	0,4406		0,0,2203	69	68	69		904,904	5.8	1	2	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CSRNP3	NM_001172173.1,NM_024969.3	21,21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	302/586,302/586	166535409	1,13005	2203	4300	6503	SO:0001583	missense	80034	exon7			AGTTCTATGGGCC	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30729	protein-coding gene	gene with protein product	"TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73"		"family with sequence similarity 130, member A2"	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.904A>G	2.37:g.166535409A>G	ENSP00000344042:p.Met302Val	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	172	5	NM_001172173	0	0	0	0	0	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	37	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	A	9.199	1.028096	0.19512	0.0	1.16E-4	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000342316;ENST00000409420	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.77	5.77	0.91146	.	0.255061	0.46758	D	0.000261	T	0.28234	0.0697	L	0.27053	0.805	0.39036	D	0.960042	B	0.17268	0.021	B	0.16722	0.016	T	0.16217	-1.0410	10	0.12103	T	0.63	-17.1574	11.3019	0.49311	0.8478:0.1521:0.0:0.0	.	302	Q8WYN3	CSRN3_HUMAN	V	302;309;302;302;334	ENSP00000412081:M302V;ENSP00000318258:M302V;ENSP00000344042:M302V;ENSP00000387195:M334V	ENSP00000318258:M302V	M	+	1	0	CSRNP3	166243655	0.974000	0.33945	1.000000	0.80357	0.997000	0.91878	1.752000	0.38349	2.195000	0.70347	0.528000	0.53228	ATG	A|1.000;G|0.000		0.493	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		G	166535409	A	G	166535409	3	3	147	1	0	0	0	0	1	0	0	0	3971	449	16	3	918	3	CSRNP3	2	166535409	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	118402559	166535409	76663964	12	13088											
AGPS	8540	broad.mit.edu	37	chr2	178257705	178257705	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgagtgcaaagcgcggagagCcgcgtcggcggccacggcag	8	3	18	12	7	0	2	0	1	0	1	1	3	0	2	2	4	3	2	2	4	1	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr2:178257705C>T	ENST00000264167.4	+	1	334	c.188C>T	c.(187-189)gCc>gTc	p.A63V	AGPS_ENST00000409888.1_Missense_Mutation_p.A63V|AC074286.1_ENST00000397057.2_RNA|NFE2L2_ENST00000464747.1_5'Flank	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	63					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			GCGCGGAGAGCCGCGTCGGCG	0.701																																					p.A63V													.	AGPS-92	0			c.C188T						.						2	3	3					2																	178257705		1427	2821	4248	SO:0001583	missense	8540	exon1			GGAGAGCCGCGTC	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.188C>T	2.37:g.178257705C>T	ENSP00000264167:p.Ala63Val	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	136	4	NM_003659	0	0	0	0	0	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	37	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273488	0.80580	.	.	ENSG00000018510	ENST00000264167;ENST00000409888	D	0.97850	-4.57	4.57	4.57	0.56435	.	0.581401	0.16956	N	0.192694	D	0.97179	0.9078	L	0.29908	0.895	0.30660	N	0.75453	D	0.63880	0.993	D	0.65443	0.935	D	0.94907	0.8061	10	0.36615	T	0.2	.	14.3917	0.66983	0.0:1.0:0.0:0.0	.	63	O00116	ADAS_HUMAN	V	63	ENSP00000264167:A63V	ENSP00000264167:A63V	A	+	2	0	AGPS	177965951	0.832000	0.29368	0.997000	0.53966	0.997000	0.91878	2.006000	0.40874	2.358000	0.79984	0.655000	0.94253	GCC	.		0.701	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			T	178257705	C	T	178257705	3	4	147	1	0	0	0	0	1	0	0	0	394	739	26	2	190	2	AGPS	2	178257705	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	11722296	178257705	64941668	13	13089											
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	179424419	179424419	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagtcatttctgttggcatTttcaatggtcagtgatgtac	9	16	10	6	0	4	2	3	1	1	1	4	2	4	2	0	2	1	3	0	2	2	5			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr2:179424419T>A	ENST00000591111.1	-	276	81741	c.81517A>T	c.(81517-81519)Aat>Tat	p.N27173Y	TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N19941Y|TTN_ENST00000589042.1_Missense_Mutation_p.N28814Y|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N26246Y|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N19874Y|TTN_ENST00000460472.2_Missense_Mutation_p.N19749Y|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27173	Ig-like 129.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGTTGGCATTTTCAATGGTC	0.423																																					p.N28814Y		.											.	TTN-636	0			c.A86440T						.						167	157	160					2																	179424419		2006	4191	6197	SO:0001583	missense	7273	exon326			TGGCATTTTCAAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.81517A>T	2.37:g.179424419T>A	ENSP00000465570:p.Asn27173Tyr	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	163	44	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	11.56	1.673934	0.29693	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51941	0.1704	M	0.70595	2.14	0.39978	D	0.974889	P;P;P;P	0.49253	0.921;0.921;0.921;0.921	B;B;B;B	0.42163	0.378;0.378;0.378;0.378	T	0.62742	-0.6790	9	0.87932	D	0	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	19749;19874;19941;27173	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	26246;19749;19941;19874;19746	ENSP00000343764:N26246Y;ENSP00000434586:N19749Y;ENSP00000340554:N19941Y;ENSP00000352154:N19874Y	ENSP00000340554:N19941Y	N	-	1	0	TTN	179132665	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.039000	0.57325	2.326000	0.78906	0.533000	0.62120	AAT	.		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179424419	T	A	179424419	3	1	147	1	0	0	0	0	1	0	0	0	16768	1841	64	5	21687	5	TTN	2	179424419	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	1166714	179424419	63774954	14	13090											
EDEM1	9695	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	5229984	5229984	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccactgccgcggccgtgggcCcgaccgcggggacccgtgag	4	3	17	17	7	0	1	0	1	0	0	0	3	0	2	6	4	1	0	6	4	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:5229984C>G	ENST00000256497.4	+	1	627	c.494C>G	c.(493-495)cCc>cGc	p.P165R	AC026202.1_ENST00000600805.1_5'Flank|AC026202.3_ENST00000439325.1_RNA|EDEM1_ENST00000445686.1_5'Flank	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	165					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		GGCCGTGGGCCCGACCGCGGG	0.736																																					p.P165R		.											.	EDEM1-137	0			c.C494G						.						8	10	10					3																	5229984		2079	4182	6261	SO:0001583	missense	9695	exon1			GTGGGCCCGACCG	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.494C>G	3.37:g.5229984C>G	ENSP00000256497:p.Pro165Arg	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	54	32	NM_014674	0	0	0	0	0	A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	37	CCDS33686.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679794	0.47886	.	.	ENSG00000134109	ENST00000256497	T	0.81415	-1.49	4.81	4.81	0.61882	.	0.109188	0.64402	D	0.000005	T	0.69097	0.3073	N	0.25957	0.775	0.80722	D	1	B	0.32653	0.379	B	0.34180	0.177	T	0.66685	-0.5861	10	0.05959	T	0.93	-8.2011	17.4653	0.87631	0.0:1.0:0.0:0.0	.	165	Q92611	EDEM1_HUMAN	R	165	ENSP00000256497:P165R	ENSP00000256497:P165R	P	+	2	0	EDEM1	5204984	1.000000	0.71417	0.691000	0.30163	0.932000	0.56968	5.419000	0.66435	2.199000	0.70637	0.491000	0.48974	CCC	.		0.736	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		G	5229984	C	G	5229984	3	3	147	1	0	0	0	0	1	0	0	0	4922	623	22	4	496	4	EDEM1	3	5229984	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10		5229984	192792446	15	13091											
ACY1	95	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52022828	52022828	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgctgccactgacaacCgctatatccgcgcggtgagc	7	8	11	15	4	0	2	0	2	0	0	1	2	1	2	4	1	5	2	4	1	3	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:52022828C>A	ENST00000404366.2	+	14	1194	c.1048C>A	c.(1048-1050)Cgc>Agc	p.R350S	ACY1_ENST00000476854.1_Missense_Mutation_p.R285S|ACY1_ENST00000494103.1_Missense_Mutation_p.R278S|ABHD14A-ACY1_ENST00000463937.1_Missense_Mutation_p.R451S|ACY1_ENST00000476351.1_Missense_Mutation_p.R315S|ACY1_ENST00000458031.2_Missense_Mutation_p.R440S	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	350					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CACTGACAACCGCTATATCCG	0.567																																					p.R350S		.											.	ACY1-154	0			c.C1048A						.						160	172	168					3																	52022828		2203	4300	6503	SO:0001583	missense	95	exon14			GACAACCGCTATA	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.1048C>A	3.37:g.52022828C>A	ENSP00000384296:p.Arg350Ser	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	138	65	NM_001198895	0	0	284	876	592	C9J6I6|C9J9D8|C9JWD4	Missense_Mutation	SNP	ENST00000404366.2	37	CCDS2844.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.709106	0.68615	.	.	ENSG00000114786;ENSG00000114786;ENSG00000114786;ENSG00000243989;ENSG00000243989;ENSG00000243989;ENSG00000243989	ENST00000458031;ENST00000463937;ENST00000232907;ENST00000476854;ENST00000476351;ENST00000494103;ENST00000404366	T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.75766	0.3894	M	0.91872	3.25	0.80722	D	1	D;D	0.76494	0.991;0.999	D;D	0.68039	0.955;0.951	T	0.80522	-0.1345	10	0.62326	D	0.03	-13.0341	19.4166	0.94703	0.0:1.0:0.0:0.0	.	440;350	B4DNW0;Q03154	.;ACY1_HUMAN	S	440;451;350;285;315;278;350	ENSP00000390557:R440S;ENSP00000420487:R451S;ENSP00000419262:R285S;ENSP00000417056:R315S;ENSP00000417618:R278S;ENSP00000384296:R350S	ENSP00000384296:R350S	R	+	1	0	ACY1;RP11-155D18.11	51997868	1.000000	0.71417	1.000000	0.80357	0.175000	0.22909	6.896000	0.75665	2.679000	0.91253	0.655000	0.94253	CGC	.		0.567	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666		A	52022828	C	A	52022828	3	1	147	1	0	0	0	0	1	0	0	0	226	652	23	4	1098	4	ACY1	3	52022828	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	46792844	52022828	145999602	16	13092											
NT5DC2	64943	broad.mit.edu	37	chr3	52558884	52558884	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcacctgcctcgactccGcgtcctgataggtctgggga	6	8	12	15	3	1	1	0	1	1	0	4	3	3	2	5	3	2	1	5	3	1	1	rs201813711	byFrequency	TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:52558884G>A	ENST00000307076.4	-	13	1650	c.1250C>T	c.(1249-1251)gCg>gTg	p.A417V	NT5DC2_ENST00000422318.2_Missense_Mutation_p.A454V|NT5DC2_ENST00000459839.1_Missense_Mutation_p.A429V|NT5DC2_ENST00000307092.4_Missense_Mutation_p.A358V	NM_022908.2	NP_075059.1	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2	417							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)|prostate(1)|stomach(1)	6				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		CCTCGACTCCGCGTCCTGATA	0.667													G|||	3	0.000599042	0	0	5008	,	,		14820	0.003		0	False		,,,				2504	0				p.A454V													.	NT5DC2-514	0			c.C1361T						.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	50	51	51		1361,1250	3	0.2	3		51	1,8597	1.2+/-3.3	0,1,4298	yes	missense,missense	NT5DC2	NM_001134231.1,NM_022908.2	64,64	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	454/558,417/521	52558884	1,13003	2203	4299	6502	SO:0001583	missense	64943	exon13			GACTCCGCGTCCT	AF131781	CCDS2858.1, CCDS46843.1	3p21.1	2006-02-03			ENSG00000168268	ENSG00000168268			25717	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_022908		Approved	FLJ12442	uc003den.3	Q9H857	OTTHUMG00000158626	ENST00000307076.4:c.1250C>T	3.37:g.52558884G>A	ENSP00000302468:p.Ala417Val	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	82	4	NM_001134231	0	0	43	43	0	C9JTZ6|E9PAL9|O95888|Q96C80|Q9H9Z8	Missense_Mutation	SNP	ENST00000307076.4	37	CCDS2858.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	11.24	1.579578	0.28180	0.0	1.16E-4	ENSG00000168268	ENST00000307092;ENST00000463947;ENST00000307076;ENST00000422318;ENST00000459839	T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9	5.04	3.05	0.35203	HAD-like domain (1);	0.304028	0.35936	N	0.002898	T	0.20007	0.0481	L	0.52364	1.645	0.21064	N	0.999799	B;B;P	0.36048	0.334;0.212;0.534	B;B;B	0.31547	0.085;0.041;0.132	T	0.12268	-1.0554	10	0.42905	T	0.14	-19.2435	8.8026	0.34918	0.1554:0.0:0.6959:0.1487	.	429;417;454	C9JTZ6;Q9H857;E9PAL9	.;NT5D2_HUMAN;.	V	358;131;417;454;429	ENSP00000306017:A358V;ENSP00000418780:A131V;ENSP00000302468:A417V;ENSP00000406933:A454V;ENSP00000419547:A429V	ENSP00000302468:A417V	A	-	2	0	NT5DC2	52533924	0.988000	0.35896	0.246000	0.24233	0.417000	0.31264	5.316000	0.65815	1.131000	0.42111	0.491000	0.48974	GCG	G|0.999;A|0.001		0.667	NT5DC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000351509.1	NM_022908		A	52558884	G	A	52558884	3	1	147	1	0	0	0	0	1	0	0	0	10717	1087	38	1	320	1	NT5DC2	3	52558884	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	536056	52558884	145463546	17	13093											
MCM2	4171	broad.mit.edu	37	chr3	127323557	127323557	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcagagggaggcagcagagCgggccatgcggcagcgtgac	9	3	19	10	3	1	3	1	1	0	2	1	4	1	4	1	4	4	3	1	4	0	0	rs201721106		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:127323557C>T	ENST00000265056.7	+	3	587	c.343C>T	c.(343-345)Cgg>Tgg	p.R115W		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	115	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						GGCAGCAGAGCGGGCCATGCG	0.692													C|||	1	0.000199681	0	0	5008	,	,		16493	0		0.001	False		,,,				2504	0				p.R115W													.	MCM2-230	0			c.C343T						.	C	TRP/ARG	0,4406		0,0,2203	21	25	24		343	3.4	1	3	dbSNP_134	24	1,8597	1.2+/-3.3	0,1,4298	no	missense	MCM2	NM_004526.2	101	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	115/905	127323557	1,13003	2203	4299	6502	SO:0001583	missense	4171	exon3			GCAGAGCGGGCCA	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"mitotin"	116945	"minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)", "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.343C>T	3.37:g.127323557C>T	ENSP00000265056:p.Arg115Trp	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	103	4	NM_004526	0	0	0	0	0	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	37	CCDS3043.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.51	3.639211	0.67244	0.0	1.16E-4	ENSG00000073111	ENST00000265056;ENST00000480910	T;T	0.25749	1.78;1.78	5.29	3.38	0.38709	.	0.176748	0.50627	D	0.000109	T	0.44603	0.1301	M	0.76170	2.325	0.44352	D	0.997248	D	0.76494	0.999	P	0.56788	0.806	T	0.53027	-0.8496	10	0.72032	D	0.01	-32.7362	14.2509	0.66019	0.3832:0.6168:0.0:0.0	.	115	P49736	MCM2_HUMAN	W	115;106	ENSP00000265056:R115W;ENSP00000419802:R106W	ENSP00000265056:R115W	R	+	1	2	MCM2	128806247	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	2.910000	0.48766	1.182000	0.42928	0.591000	0.81541	CGG	C|0.999;T|0.000		0.692	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			T	127323557	C	T	127323557	3	4	147	1	0	0	0	0	1	0	0	0	9411	759	27	1	353	1	MCM2	3	127323557	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	74764673	127323557	70698873	18	13094											
PLXND1	23129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	129281631	129281631	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccccattcccacccaccAaggtcgacgtcctctgcacg	7	7	7	20	3	1	0	0	0	1	0	4	1	3	0	6	1	2	1	6	1	1	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:129281631A>G	ENST00000324093.4	-	27	5002	c.4824T>C	c.(4822-4824)ctT>ctC	p.L1608L	PLXND1_ENST00000393239.1_Splice_Site_p.L1608L	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1608					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CCCACCCACCAAGGTCGACGT	0.627																																					p.L1608L	Ovarian(97;366 1484 3738 22084 39045)	.											.	PLXND1-90	0			c.T4824C						.						64	56	58					3																	129281631		2203	4300	6503	SO:0001630	splice_region_variant	23129	exon27			CCCACCAAGGTCG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"Plexins"	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.4825+1T>C	3.37:g.129281631A>G		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	50	25	NM_015103	0	0	0	0	0	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			.		0.627	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	Silent	G	129281631	A	G	129281631	5	3	147	1	0	0	0	0	0	0	1	0	12153	144	5	3	993	3	PLXND1	3	129281631	Splice_Site	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	1958074	129281631	68740799	19	13095											
TNIK	23043	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	170846580	170846580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctgaaggactccgaccttgGgggcaggttggggtcagata	8	8	17	8	1	1	2	1	1	0	1	2	4	2	3	2	6	0	3	2	6	2	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:170846580G>A	ENST00000436636.2	-	16	2040	c.1696C>T	c.(1696-1698)Cca>Tca	p.P566S	TNIK_ENST00000369326.5_Missense_Mutation_p.P537S|TNIK_ENST00000475336.1_Intron|TNIK_ENST00000460047.1_Intron|TNIK_ENST00000284483.8_Missense_Mutation_p.P566S|TNIK_ENST00000470834.1_Missense_Mutation_p.P537S|TNIK_ENST00000357327.5_Missense_Mutation_p.P537S|TNIK_ENST00000538048.1_Intron|TNIK_ENST00000341852.6_Intron|TNIK_ENST00000488470.1_Intron	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	566	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			TCCGACCTTGGGGGCAGGTTG	0.557																																					p.P566S													.	TNIK-550	0			c.C1696T						.						53	57	56					3																	170846580		1961	4156	6117	SO:0001583	missense	23043	exon16			ACCTTGGGGGCAG	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.1696C>T	3.37:g.170846580G>A	ENSP00000399511:p.Pro566Ser	Somatic	57	2		WXS	Illumina HiSeq	Phase_I	108	45	NM_015028	0	0	0	2	2	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.993752	0.54041	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000284483;ENST00000357327;ENST00000470834	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	5.11	5.11	0.69529	.	0.055369	0.64402	D	0.000001	T	0.35624	0.0938	N	0.17723	0.515	0.80722	D	1	B;B;B;B	0.32128	0.178;0.357;0.033;0.243	B;B;B;B	0.36959	0.237;0.237;0.084;0.119	T	0.10800	-1.0614	10	0.06625	T	0.88	.	18.7271	0.91718	0.0:0.0:1.0:0.0	.	537;566;537;566	Q9UKE5-6;Q9UKE5-4;Q9UKE5-2;Q9UKE5	.;.;.;TNIK_HUMAN	S	566;537;566;537;537	ENSP00000399511:P566S;ENSP00000358332:P537S;ENSP00000284483:P566S;ENSP00000349880:P537S;ENSP00000419990:P537S	ENSP00000284483:P566S	P	-	1	0	TNIK	172329274	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.298000	0.78815	2.652000	0.90054	0.561000	0.74099	CCA	.		0.557	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796		A	170846580	G	A	170846580	3	1	147	1	0	0	0	0	1	0	0	0	16345	1232	43	2	2458	2	TNIK	3	170846580	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	41564949	170846580	27175850	20	13096											
SEL1L3	23231	broad.mit.edu	37	chr4	25760681	25760681	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcgattagcagggccaggtTaaaaaatccctaaaaacaag	17	7	8	9	1	0	0	0	0	0	0	2	1	1	0	2	2	2	2	2	2	8	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr4:25760681T>A	ENST00000399878.3	-	21	3087	c.2965A>T	c.(2965-2967)Aac>Tac	p.N989Y	SEL1L3_ENST00000264868.5_Missense_Mutation_p.N954Y|SEL1L3_ENST00000502949.1_Missense_Mutation_p.N836Y	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	989						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						AGGGCCAGGTTAAAAAATCCC	0.373																																					p.N989Y													.	.	0			c.A2965T						.						112	109	110					4																	25760681		1847	4089	5936	SO:0001583	missense	23231	exon21			CCAGGTTAAAAAA	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"KIAA0746 protein"					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.2965A>T	4.37:g.25760681T>A	ENSP00000382767:p.Asn989Tyr	Somatic	101	5		WXS	Illumina HiSeq	Phase_I	108	13	NM_015187	0	0	2	2	0	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.1|22.1	4.238808|4.238808	0.79800|0.79800	.|.	.|.	ENSG00000091490|ENSG00000091490	ENST00000510448|ENST00000399878;ENST00000264868;ENST00000502949;ENST00000507618	.|T;T;T;T	.|0.57752	.|0.38;0.38;0.38;0.38	5.71|5.71	5.71|5.71	0.89125|0.89125	.|Tetratricopeptide-like helical (1);	.|0.099166	.|0.64402	.|D	.|0.000001	T|T	0.71392|0.71392	0.3334|0.3334	M|M	0.68952|0.68952	2.095|2.095	0.45216|0.45216	D|D	0.998226|0.998226	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.83275	.|0.995;0.996	T|T	0.74636|0.74636	-0.3599|-0.3599	5|10	.|0.87932	.|D	.|0	-28.0464|-28.0464	15.9869|15.9869	0.80160|0.80160	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|396;989	.|B4DTH5;Q68CR1	.|.;SE1L3_HUMAN	F|Y	15|989;954;836;80	.|ENSP00000382767:N989Y;ENSP00000264868:N954Y;ENSP00000425438:N836Y;ENSP00000426050:N80Y	.|ENSP00000264868:N954Y	L|N	-|-	3|1	2|0	SEL1L3|SEL1L3	25369779|25369779	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.480000|5.480000	0.66820|0.66820	2.171000|2.171000	0.68590|0.68590	0.533000|0.533000	0.62120|0.62120	TTA|AAC	.		0.373	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25760681	T	A	25760681	3	1	147	1	0	0	0	0	1	0	0	0	14044	1754	61	5	449	5	SEL1L3	4	25760681	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		25760681	165393595	21	13097											
SLC30A5	64924	bcgsc.ca	37	chr5	68413165	68413165	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgactgctctgctttagtcAtgggactttttgctgccctg	4	17	10	10	0	2	1	1	1	1	0	2	2	2	2	1	1	4	3	1	1	1	5	rs377546157		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr5:68413165A>G	ENST00000396591.3	+	11	1991	c.1381A>G	c.(1381-1383)Atg>Gtg	p.M461V	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	461					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TGCTTTAGTCATGGGACTTTT	0.453																																					p.M461V													.	SLC30A5-226	0			c.A1381G						.						198	185	189					5																	68413165		2203	4300	6503	SO:0001583	missense	64924	exon11			TTAGTCATGGGAC	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1381A>G	5.37:g.68413165A>G	ENSP00000379836:p.Met461Val	Somatic	112	4		WXS	Illumina HiSeq	Phase_1	134	62	NM_022902	0	0	3	5	2	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	37	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	A	13.39	2.224205	0.39300	.	.	ENSG00000145740	ENST00000396591;ENST00000438236	T	0.59224	0.28	5.44	5.44	0.79542	.	0.136502	0.64402	D	0.000002	T	0.41696	0.1170	N	0.13299	0.325	0.80722	D	1	B;B;B	0.14012	0.001;0.005;0.009	B;B;B	0.20384	0.029;0.012;0.029	T	0.25676	-1.0125	10	0.23302	T	0.38	.	15.3146	0.74065	1.0:0.0:0.0:0.0	.	290;290;461	Q9H9X0;Q8TAD4-2;Q8TAD4	.;.;ZNT5_HUMAN	V	461;74	ENSP00000379836:M461V	ENSP00000379836:M461V	M	+	1	0	SLC30A5	68448921	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	5.332000	0.65911	2.287000	0.76781	0.482000	0.46254	ATG	.		0.453	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			G	68413165	A	G	68413165	3	3	147	1	0	0	0	0	1	0	0	0	14590	217	8	3	1511	3	SLC30A5	5	68413165	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10		68413165	112502095	22	13098											
GPR150	285601	broad.mit.edu	37	chr5	94957233	94957233	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgagggcggcttgcgcccAccccctccgcgccccagacc	5	3	12	21	5	0	1	0	0	0	1	1	3	1	1	7	2	1	1	7	2	0	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr5:94957233A>C	ENST00000380007.2	+	1	1452	c.1254A>C	c.(1252-1254)ccA>ccC	p.P418P		NM_199243.1	NP_954713.1	Q8NGU9	GP150_HUMAN	G protein-coupled receptor 150	418	Poly-Pro.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(2)	2		all_cancers(142;0.000462)|all_epithelial(76;2.44e-06)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)		all cancers(79;1.82e-16)		GCTTGCGCCCACCCCCTCCGC	0.682																																					p.P418P													.	GPR150-90	0			c.A1254C						.						9	10	10					5																	94957233		2123	4114	6237	SO:0001819	synonymous_variant	285601	exon1			GCGCCCACCCCCT	BC030197	CCDS4074.1	5q15	2012-08-21			ENSG00000178015	ENSG00000178015		"GPCR / Class A : Orphans"	23628	protein-coding gene	gene with protein product						12679517	Standard	NM_199243		Approved	PGR11	uc003kle.1	Q8NGU9	OTTHUMG00000121170	ENST00000380007.2:c.1254A>C	5.37:g.94957233A>C		Somatic	56	2		WXS	Illumina HiSeq	Phase_I	64	6	NM_199243	0	0	1	1	0		Silent	SNP	ENST00000380007.2	37	CCDS4074.1																																																																																			.		0.682	GPR150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241657.2			C	94957233	A	C	94957233	2	2	147	1	0	0	0	0	0	0	0	1	6676	146	6	5		5	GPR150	5	94957233	Silent	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	26544068	94957233	85958027	23	13099											
KCNN2	3781	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	113740442	113740442	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttaataagataaacttcaAtacacgttttgttatgaaga	17	14	5	5	1	1	3	1	1	0	2	1	3	1	3	0	0	2	2	0	0	8	8			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr5:113740442A>G	ENST00000512097.3	+	4	1908	c.890A>G	c.(889-891)aAt>aGt	p.N297S	KCNN2_ENST00000264773.3_Missense_Mutation_p.N297S|KCNN2_ENST00000507750.1_Intron			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	297					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	ATAAACTTCAATACACGTTTT	0.373																																					p.N297S													.	KCNN2-92	0			c.A890G						.						128	126	127					5																	113740442		2202	4300	6502	SO:0001583	missense	3781	exon3			ACTTCAATACACG	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.890A>G	5.37:g.113740442A>G	ENSP00000427120:p.Asn297Ser	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	65	18	NM_021614	0	0	0	0	0	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Missense_Mutation	SNP	ENST00000512097.3	37	CCDS4114.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974549	0.74246	.	.	ENSG00000080709	ENST00000512097;ENST00000264773	D;D	0.98701	-5.08;-5.08	5.33	5.33	0.75918	.	0.089556	0.85682	D	0.000000	D	0.98679	0.9557	M	0.86805	2.84	0.80722	D	1	P	0.44877	0.845	P	0.48770	0.589	D	0.99525	1.0959	10	0.87932	D	0	-4.5111	14.9498	0.71064	1.0:0.0:0.0:0.0	.	297	Q9H2S1	KCNN2_HUMAN	S	297	ENSP00000427120:N297S;ENSP00000264773:N297S	ENSP00000264773:N297S	N	+	2	0	KCNN2	113768341	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.224000	0.95209	2.016000	0.59253	0.402000	0.26972	AAT	.		0.373	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		G	113740442	A	G	113740442	3	3	147	1	0	0	0	0	1	0	0	0	8100	101	4	3	900	3	KCNN2	5	113740442	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	18783209	113740442	67174818	24	13100											
F13A1	2162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	6222265	6222266	+	Splice_Site	INS	-	-	CACA																															ccattgtcaatcaaactcacINScacactgaatccttggtgag																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:6222265_6222266insCACA	ENST00000264870.3	-	8	1377_1378		c.e8+1			NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide						blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	ATCAAACTCACCACACTGAATC	0.376																																					.		.											.	F13A1-519	0			c.1112+1->TGTG						.																																			SO:0001630	splice_region_variant	2162	exon9			.	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1112+1->TGTG	6.37:g.6222266_6222269dupCACA		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	56	22	NM_000129	0	0	0	0	0	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Splice_Site	INS	ENST00000264870.3	37	CCDS4496.1																																																																																			.		0.376	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	Intron	CACA	6222266	-	CACA	6222265	8	5	147	1	0	1	1	0	0	0	1	0	5353	521	18	0	1117	0	F13A1	6	6222265	Splice_Site	INS	-	TCGA-KV-A6GE-01A-11D-A31X-10		6222265	164892802	25	13101											
HIST1H1E	3008	broad.mit.edu	37	chr6	26157244	26157244	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaccgccaagcccaaggcagCcaagccaaagaaggcggcag	14	0	13	14	2	0	1	0	0	0	1	0	2	0	1	5	3	3	2	5	3	5	0	rs537217446		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:26157244C>T	ENST00000304218.3	+	1	686	c.626C>T	c.(625-627)gCc>gTc	p.A209V	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	209					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						CCCAAGGCAGCCAAGCCAAAG	0.542													C|||	1	0.000199681	8e-04	0	5008	,	,		15493	0		0	False		,,,				2504	0				p.A209V													.	HIST1H1E-154	0			c.C626T						.						31	33	32					6																	26157244		2202	4291	6493	SO:0001583	missense	3008	exon1			AGGCAGCCAAGCC	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"Histones / Replication-dependent"	4718	protein-coding gene	gene with protein product		142220	"H1 histone family, member 4", "histone 1, H1e"	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.626C>T	6.37:g.26157244C>T	ENSP00000307705:p.Ala209Val	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	156	6	NM_005321	0	0	0	0	0	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	12.89	2.073411	0.36566	.	.	ENSG00000168298	ENST00000304218	T	0.25579	1.79	5.51	4.64	0.57946	.	0.141424	0.45867	D	0.000340	T	0.33760	0.0874	L	0.58810	1.83	0.49798	D	0.999827	D	0.57571	0.98	D	0.70227	0.968	T	0.06075	-1.0847	10	0.36615	T	0.2	-4.4289	13.8813	0.63684	0.0:0.9262:0.0:0.0738	.	209	P10412	H14_HUMAN	V	209	ENSP00000307705:A209V	ENSP00000307705:A209V	A	+	2	0	HIST1H1E	26265223	0.958000	0.32768	1.000000	0.80357	0.999000	0.98932	3.856000	0.55964	1.452000	0.47756	0.655000	0.94253	GCC	.		0.542	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26157244	C	T	26157244	3	4	147	1	0	0	0	0	1	0	0	0	7147	739	26	2	628	2	HIST1H1E	6	26157244	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	19934979	26157244	144957823	26	13102											
MDGA1	266727	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	37622225	37622225	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaccactgcagctgggggagGggatcaccgcctgtcagcag	8	5	16	12	1	2	0	2	0	0	0	2	3	2	2	3	4	3	3	3	4	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:37622225G>T	ENST00000434837.3	-	6	1985	c.807C>A	c.(805-807)ccC>ccA	p.P269P	MDGA1_ENST00000505425.1_Silent_p.P269P|MDGA1_ENST00000297153.7_Silent_p.P269P	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	269	Ig-like 3.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						GCTGGGGGAGGGGATCACCGC	0.642																																					p.P269P		.											.	MDGA1-91	0			c.C807A						.						45	48	47					6																	37622225		2076	4205	6281	SO:0001819	synonymous_variant	266727	exon6			GGGGAGGGGATCA	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.807C>A	6.37:g.37622225G>T		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	79	34	NM_153487	0	0	0	0	0	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	37	CCDS47417.1																																																																																			.		0.642	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37622225	G	T	37622225	2	4	147	1	0	0	0	0	0	0	0	1	9431	1219	43	4		4	MDGA1	6	37622225	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	11464981	37622225	133492842	27	13103											
FILIP1	27145	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	76023889	76023889	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagattttagttttaaaagTttcttactttcttcaattag	11	21	4	5	0	4	1	2	0	2	1	4	1	4	1	0	0	1	2	0	0	6	9	rs540413529		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:76023889T>A	ENST00000237172.7	-	5	1989	c.1659A>T	c.(1657-1659)aaA>aaT	p.K553N	FILIP1_ENST00000393004.2_Missense_Mutation_p.K553N|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Missense_Mutation_p.K454N	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	553										breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GTTTTAAAAGTTTCTTACTTT	0.299																																					p.K553N													.	FILIP1-94	0			c.A1659T						.						53	55	55					6																	76023889		2202	4296	6498	SO:0001583	missense	27145	exon5			TAAAAGTTTCTTA	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.1659A>T	6.37:g.76023889T>A	ENSP00000237172:p.Lys553Asn	Somatic	133	2		WXS	Illumina HiSeq	Phase_I	121	41	NM_015687	0	0	0	0	0	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.365070	0.41902	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.20881	2.04;2.04;2.07	5.95	3.25	0.37280	.	0.000000	0.85682	D	0.000000	T	0.31327	0.0793	M	0.79258	2.445	0.50039	D	0.99984	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.986;0.994	T	0.07731	-1.0757	10	0.52906	T	0.07	-33.9484	9.0168	0.36175	0.0:0.6368:0.0:0.3632	.	553;553;553	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	N	553;553;454	ENSP00000376728:K553N;ENSP00000237172:K553N;ENSP00000359037:K454N	ENSP00000237172:K553N	K	-	3	2	FILIP1	76080609	0.998000	0.40836	1.000000	0.80357	0.983000	0.72400	0.593000	0.23999	0.437000	0.26423	-0.132000	0.14878	AAA	.		0.299	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76023889	T	A	76023889	3	1	147	1	0	0	0	0	1	0	0	0	5913	1722	60	5	1990	5	FILIP1	6	76023889	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	38401664	76023889	95091178	28	13104											
USP45	85015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	99894085	99894085	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccggatccactactggaTctgaacagcccagtctgctt	10	9	8	14	1	2	1	0	1	2	0	3	3	3	3	3	2	4	1	3	2	2	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:99894085T>C	ENST00000327681.6	-	14	2095	c.1563A>G	c.(1561-1563)agA>agG	p.R521R	USP45_ENST00000369233.2_Silent_p.R473R|USP45_ENST00000392738.2_Silent_p.R201R|USP45_ENST00000500704.2_Silent_p.R521R|USP45_ENST00000539675.1_Intron	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	521	USP.		R -> T (in dbSNP:rs41288947). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CACTACTGGATCTGAACAGCC	0.483																																					p.R521R		.											.	USP45-637	0			c.A1563G						.						83	69	74					6																	99894085		2203	4300	6503	SO:0001819	synonymous_variant	85015	exon14			ACTGGATCTGAAC	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.1563A>G	6.37:g.99894085T>C		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	60	23	NM_001080481	0	0	0	0	0	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Silent	SNP	ENST00000327681.6	37	CCDS34501.1																																																																																			.		0.483	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		C	99894085	T	C	99894085	2	2	147	1	0	0	0	0	0	0	0	1	17109	1432	50	3		3	USP45	6	99894085	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	23870196	99894085	71220982	29	13105											
ENPP1	5167	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	132211511	132211511	+	Frame_Shift_Del	DEL	G	G	-																															atgactcctcatgggttgaaGaattgttaatgttacacaga																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:132211511delG	ENST00000360971.2	+	25	2658	c.2638delG	c.(2638-2640)gaafs	p.E880fs		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	880	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	ATGGGTTGAAGAATTGTTAAT	0.388																																					p.E880fs	Colon(104;336 1535 5856 11019 33782)	.											.	ENPP1-95	0			c.2638delG						.						132	123	126					6																	132211511		2203	4300	6503	SO:0001589	frameshift_variant	5167	exon25			.	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2638delG	6.37:g.132211511delG	ENSP00000354238:p.Glu880fs	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	167	46	NM_006208	0	0	0	0	0	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Frame_Shift_Del	DEL	ENST00000360971.2	37	CCDS5150.2																																																																																			.		0.388	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			-	132211511	G	-	132211511	7	5	147	1	0	1	0	1	0	0	0	0	5142	943	33	0	2736	0	ENPP1	6	132211511	Frame_Shift_Del	DEL	G	TCGA-KV-A6GE-01A-11D-A31X-10	32317426	132211511	38903556	30	13106	136	2									
ENPP1	5167	bcgsc.ca	37	chr6	132211512	132211512	+	Missense_Mutation	SNP	A	A	T																															tgactcctcatgggttgaagAattgttaatgttacacagag																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:132211512A>T	ENST00000360971.2	+	25	2659	c.2639A>T	c.(2638-2640)gAa>gTa	p.E880V		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	880	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	TGGGTTGAAGAATTGTTAATG	0.393																																					p.E880V	Colon(104;336 1535 5856 11019 33782)												.	ENPP1-95	0			c.A2639T						.						132	123	126					6																	132211512		2203	4300	6503	SO:0001583	missense	5167	exon25			TTGAAGAATTGTT	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2639A>T	6.37:g.132211512A>T	ENSP00000354238:p.Glu880Val	Somatic	168	1		WXS	Illumina HiSeq	Phase_1	168	46	NM_006208	0	0	4	4	0	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	37	CCDS5150.2	.	.	.	.	.	.	.	.	.	.	A	20.5	4.005981	0.74932	.	.	ENSG00000197594	ENST00000360971	T	0.69926	-0.44	5.73	5.73	0.89815	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.231734	0.43260	D	0.000599	T	0.80788	0.4690	M	0.87381	2.88	0.50632	D	0.999888	D	0.63880	0.993	D	0.72075	0.976	D	0.83861	0.0268	10	0.56958	D	0.05	-9.8218	15.671	0.77274	1.0:0.0:0.0:0.0	.	880	P22413	ENPP1_HUMAN	V	880	ENSP00000354238:E880V	ENSP00000354238:E880V	E	+	2	0	ENPP1	132253205	1.000000	0.71417	0.927000	0.36925	0.638000	0.38207	7.323000	0.79105	2.184000	0.69523	0.477000	0.44152	GAA	.		0.393	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			T	132211512	A	T	132211512	3	4	147	1	0	0	0	0	1	0	0	0	5142	246	9	5	2737	5	ENPP1	6	132211512	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	1	132211512	38903555	31	13107	136	2									
COPS6	10980	ucsc.edu;bcgsc.ca	37	chr7	99686962	99686962	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggagtgtttccgtcgcTctccatccccttgtcattct	4	15	8	14	2	3	0	1	0	2	0	7	1	5	1	4	1	0	2	4	1	0	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr7:99686962T>C	ENST00000303904.3	+	2	163	c.126T>C	c.(124-126)gcT>gcC	p.A42A	COPS6_ENST00000418625.1_Silent_p.A41A	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	42	MPN.				cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TTTCCGTCGCTCTCCATCCCC	0.607																																					p.A42A													.	COPS6-658	0			c.T126C						.						152	139	143					7																	99686962		2203	4300	6503	SO:0001819	synonymous_variant	10980	exon2			CGTCGCTCTCCAT	BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"COP9 subunit 6 (MOV34 homolog, 34 kD)"	614729	"COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.126T>C	7.37:g.99686962T>C		Somatic	70	2		WXS	Illumina HiSeq		76	33	NM_006833	0	0	111	203	92	A4D2A3|O15387	Silent	SNP	ENST00000303904.3	37	CCDS5682.1																																																																																			.		0.607	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833		C	99686962	T	C	99686962	2	2	147	1	0	0	0	0	0	0	0	1	3743	1538	54	3		3	COPS6	7	99686962	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		99686962	59451701	32	13108											
FLNC	2318	broad.mit.edu	37	chr7	128483884	128483885	+	Frame_Shift_Ins	INS	-	-	G																															acagtgacttatggcggggaINSccctgtccccaagagcccct																								rs200474685		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr7:128483884_128483885insG	ENST00000325888.8	+	19	3107_3108	c.2846_2847insG	c.(2845-2850)gaccctfs	p.D949fs	FLNC_ENST00000346177.6_Frame_Shift_Ins_p.D949fs	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	949					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TATGGCGGGGACCCTGTCCCCA	0.535																																					p.D949fs													.	FLNC-141	0			c.2846_2847insG						.																																			SO:0001589	frameshift_variant	2318	exon19			GCGGGGACCCTGT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	Exception_encountered	7.37:g.128483884_128483885insG	ENSP00000327145:p.Asp949fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	206	6	NM_001127487	0	0	0	0	0	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Frame_Shift_Ins	INS	ENST00000325888.8	37	CCDS43644.1																																																																																			.		0.535	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			G	128483885	-	G	128483884	7	5	147	1	0	1	1	0	0	0	0	0	5954	275	10	0	2920	0	FLNC	7	128483884	Frame_Shift_Ins	INS	-	TCGA-KV-A6GE-01A-11D-A31X-10	28796922	128483884	30654779	33	13109											
ZNF425	155054	broad.mit.edu	37	chr7	148800800	148800800	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacactcatcacaagaaaaAggcctctccccactgtgaag	14	6	6	15	0	3	2	2	1	1	1	4	2	3	2	4	1	0	0	4	1	4	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr7:148800800A>G	ENST00000378061.2	-	4	2295	c.2163T>C	c.(2161-2163)ccT>ccC	p.P721P		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	721					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CACAAGAAAAAGGCCTCTCCC	0.567																																					p.P721P													.	ZNF425-136	0			c.T2163C						.						77	68	71					7																	148800800		2203	4300	6503	SO:0001819	synonymous_variant	155054	exon4			AGAAAAAGGCCTC	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.2163T>C	7.37:g.148800800A>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	101	3	NM_001001661	0	0	1	1	0	B3KPM1|Q08AG3	Silent	SNP	ENST00000378061.2	37	CCDS34773.1																																																																																			.		0.567	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		G	148800800	A	G	148800800	2	3	147	1	0	0	0	0	0	0	0	1	17931	59	3	3		3	ZNF425	7	148800800	Silent	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	20316916	148800800	10337863	34	13110											
TGS1	96764	broad.mit.edu;bcgsc.ca	37	chr8	56686242	56686242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattgaggagcgggaggattGtaagatactgtgcctttgct	9	12	14	6	1	0	2	0	1	0	1	0	5	0	5	1	3	4	2	1	3	2	5	rs140849025		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr8:56686242G>A	ENST00000260129.5	+	1	542	c.65G>A	c.(64-66)tGt>tAt	p.C22Y	TMEM68_ENST00000521229.1_5'Flank|TMEM68_ENST00000519784.1_5'Flank|TMEM68_ENST00000334667.2_5'Flank|TMEM68_ENST00000434581.2_5'Flank|TMEM68_ENST00000522576.1_5'Flank|TMEM68_ENST00000523073.1_5'Flank	NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	22					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CGGGAGGATTGTAAGATACTG	0.488																																					p.C22Y	Esophageal Squamous(34;275 823 4842 34837 48447)												.	TGS1-227	0			c.G65A						.						138	138	138					8																	56686242		2203	4300	6503	SO:0001583	missense	96764	exon1			AGGATTGTAAGAT	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"nuclear receptor coactivator 6 interacting protein", "trimethylguanosine synthase homolog (S. cerevisiae)"	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.65G>A	8.37:g.56686242G>A	ENSP00000260129:p.Cys22Tyr	Somatic	67	2		WXS	Illumina HiSeq	Phase_I	47	38	NM_024831	0	0	0	0	0	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-4.651060	0.00000	.	.	ENSG00000137574	ENST00000260129	T	0.16743	2.32	4.83	-9.65	0.00537	.	2.328040	0.01178	N	0.007037	T	0.04003	0.0112	N	0.01267	-0.92	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33828	-0.9853	10	0.02654	T	1	11.8686	4.4565	0.11645	0.0822:0.3072:0.4524:0.1581	.	22	Q96RS0	TGS1_HUMAN	Y	22	ENSP00000260129:C22Y	ENSP00000260129:C22Y	C	+	2	0	TGS1	56848796	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.180000	0.00279	-7.058000	0.00002	-3.382000	0.00040	TGT	G|1.000;T|0.000		0.488	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		A	56686242	G	A	56686242	3	1	147	1	0	0	0	0	1	0	0	0	15869	1377	48	2	67	2	TGS1	8	56686242	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		56686242	89677780	35	13111											
PRDM14	63978	broad.mit.edu	37	chr8	70981965	70981965	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaagtcttcctccacggtgGccaggctgtttctgtagtgt	5	13	13	10	1	2	0	0	0	2	0	4	1	4	1	3	4	0	3	3	4	2	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr8:70981965G>T	ENST00000276594.2	-	2	332	c.131C>A	c.(130-132)gCc>gAc	p.A44D		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	44					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			CTCCACGGTGGCCAGGCTGTT	0.657																																					p.A44D	NSCLC(129;99 1813 5906 40656 46114)												.	PRDM14-93	0			c.C131A						.						15	16	16					8																	70981965		2196	4295	6491	SO:0001583	missense	63978	exon2			ACGGTGGCCAGGC	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.131C>A	8.37:g.70981965G>T	ENSP00000276594:p.Ala44Asp	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	63	5	NM_024504	0	0	0	0	0	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	37	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524450	0.44969	.	.	ENSG00000147596	ENST00000276594;ENST00000426346	T	0.12255	2.7	5.48	2.68	0.31781	.	0.713478	0.12923	N	0.428054	T	0.09905	0.0243	L	0.27053	0.805	0.09310	N	1	B	0.30482	0.281	B	0.24701	0.055	T	0.23048	-1.0199	10	0.66056	D	0.02	0.2737	9.427	0.38586	0.076:0.2701:0.6538:0.0	.	44	Q9GZV8	PRD14_HUMAN	D	44	ENSP00000276594:A44D	ENSP00000276594:A44D	A	-	2	0	PRDM14	71144519	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.601000	0.24119	0.261000	0.21753	0.655000	0.94253	GCC	.		0.657	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			T	70981965	G	T	70981965	3	4	147	1	0	0	0	0	1	0	0	0	12484	1203	42	4	1612	4	PRDM14	8	70981965	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	14295723	70981965	75382057	36	13112											
STOML2	30968	broad.mit.edu	37	chr9	35101777	35101777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tttgagctagctgggtgacgGcatactcagggtcctccaca	8	10	12	11	1	1	2	1	2	0	0	3	2	3	2	2	3	3	3	2	3	2	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr9:35101777G>A	ENST00000356493.5	-	5	436	c.374C>T	c.(373-375)gCc>gTc	p.A125V	STOML2_ENST00000452248.2_Missense_Mutation_p.A125V|STOML2_ENST00000487490.1_Intron	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	125					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CTGGGTGACGGCATACTCAGG	0.507																																					p.A125V													.	STOML2-90	0			c.C374T						.						148	147	147					9																	35101777		2203	4300	6503	SO:0001583	missense	30968	exon5			GTGACGGCATACT	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.374C>T	9.37:g.35101777G>A	ENSP00000348886:p.Ala125Val	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	107	4	NM_013442	0	0	79	79	0	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	ENST00000356493.5	37	CCDS6577.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226127	0.95173	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.94046	-3.34;-3.34	5.17	5.17	0.71159	.	0.098302	0.64402	D	0.000002	D	0.98381	0.9462	H	0.99130	4.44	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.87578	0.995;0.998	D	0.99593	1.0976	10	0.87932	D	0	-1.6791	18.4617	0.90741	0.0:0.0:1.0:0.0	.	125;125	B4E1K7;Q9UJZ1	.;STML2_HUMAN	V	125	ENSP00000348886:A125V;ENSP00000395743:A125V	ENSP00000348886:A125V	A	-	2	0	STOML2	35091777	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.657000	0.98554	2.691000	0.91804	0.655000	0.94253	GCC	.		0.507	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442		A	35101777	G	A	35101777	3	1	147	1	0	0	0	0	1	0	0	0	15346	1203	42	2	720	2	STOML2	9	35101777	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		35101777	106111654	37	13113											
CREB3	57704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35736272	35736272	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtacctgctatgtactccTctgacacaagggggagcctg	8	11	11	11	0	1	1	0	1	1	0	2	2	2	2	3	2	4	3	3	2	4	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr9:35736272T>C	ENST00000378103.3	-	0	3611				CREB3_ENST00000486056.1_3'UTR|CREB3_ENST00000353704.2_Missense_Mutation_p.S249P|GBA2_ENST00000467252.1_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TATGTACTCCTCTGACACAAG	0.552											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S249P		.											.	CREB3-90	0			c.T745C						.						220	207	211					9																	35736272		2203	4300	6503	SO:0001628	intergenic_variant	10488	exon8			TACTCCTCTGACA	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		9.37:g.35736272T>C		Somatic	75	0	857	WXS	Illumina HiSeq	Phase_I	55	23	NM_006368	0	0	21	48	27	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	37	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018246	0.75275	.	.	ENSG00000107175	ENST00000353704	T	0.67865	-0.29	5.68	4.56	0.56223	.	0.238919	0.43260	D	0.000597	T	0.74068	0.3668	L	0.56769	1.78	0.42787	D	0.993883	D;D	0.76494	0.999;0.996	D;D	0.66196	0.942;0.919	T	0.71394	-0.4606	10	0.26408	T	0.33	.	10.8203	0.46601	0.0:0.0743:0.0:0.9257	.	273;249	O43889;O43889-2	CREB3_HUMAN;.	P	249	ENSP00000342136:S249P	ENSP00000342136:S249P	S	+	1	0	CREB3	35726272	0.999000	0.42202	0.698000	0.30274	0.980000	0.70556	3.862000	0.56009	2.182000	0.69389	0.533000	0.62120	TCT	.		0.552	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		C	35736272	T	C	35736272	1	2	147	0	1	0	0	0	0	0	0	0	3861	1551	54	3		3	CREB3	9	35736272	IGR	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	634495	35736272	105477159	38	13114											
MAP3K8	1326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	30748425	30748425	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggaacttcctgagaacaTtgctggtagggacaccctgc	9	9	12	11	0	0	1	0	1	0	1	1	4	1	3	2	3	4	3	2	3	3	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr10:30748425T>G	ENST00000263056.1	+	8	1964	c.1268T>G	c.(1267-1269)aTt>aGt	p.I423S	MAP3K8_ENST00000375321.1_Missense_Mutation_p.I423S|MAP3K8_ENST00000542547.1_Missense_Mutation_p.I423S	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	423			Missing (in oncogenic form).		cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				CCTGAGAACATTGCTGGTAGG	0.527																																					p.I423S		.											.	MAP3K8-981	0			c.T1268G						.						70	62	65					10																	30748425		2203	4300	6503	SO:0001583	missense	1326	exon7			AGAACATTGCTGG	D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.1268T>G	10.37:g.30748425T>G	ENSP00000263056:p.Ile423Ser	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	42	17	NM_001244134	0	0	0	0	0	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Missense_Mutation	SNP	ENST00000263056.1	37	CCDS7166.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.944339	0.53079	.	.	ENSG00000107968	ENST00000375328;ENST00000263056;ENST00000542547;ENST00000375321	T;T;T	0.70749	-0.51;-0.51;-0.51	4.91	4.91	0.64330	Protein kinase-like domain (1);	0.048008	0.85682	D	0.000000	T	0.52517	0.1739	N	0.24115	0.695	0.80722	D	1	P	0.35575	0.51	B	0.32211	0.142	T	0.52638	-0.8549	10	0.08599	T	0.76	.	14.5659	0.68176	0.0:0.0:0.0:1.0	.	423	P41279	M3K8_HUMAN	S	423	ENSP00000263056:I423S;ENSP00000443610:I423S;ENSP00000364470:I423S	ENSP00000263056:I423S	I	+	2	0	MAP3K8	30788431	1.000000	0.71417	0.979000	0.43373	0.850000	0.48378	5.323000	0.65858	1.850000	0.53721	0.519000	0.50382	ATT	.		0.527	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204		G	30748425	T	G	30748425	3	3	147	1	0	0	0	0	1	0	0	0	9281	1493	52	5	1290	5	MAP3K8	10	30748425	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		30748425	104786322	39	13115											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6592937	6592937	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggctacaggtcctacatgcGgagtgggacccaatagctgg	9	7	15	10	1	0	0	0	0	0	0	1	2	1	2	2	5	4	2	2	5	4	3	rs544585664		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr11:6592937G>T	ENST00000527990.2	+	41	13983	c.13983G>T	c.(13981-13983)gcG>gcT	p.A4661A	DNHD1_ENST00000254579.6_Silent_p.A4661A			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4661					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TCCTACATGCGGAGTGGGACC	0.627																																					p.A4661A		.											.	DNHD1-24	0			c.G13983T						.						36	46	43					11																	6592937		2097	4219	6316	SO:0001819	synonymous_variant	144132	exon43			ACATGCGGAGTGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 47", "dynein heavy chain domain 1-like", "coiled-coil domain containing 35"	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.13983G>T	11.37:g.6592937G>T		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_144666	0	0	9	9	0	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			.		0.627	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6592937	G	T	6592937	2	4	147	1	0	0	0	0	0	0	0	1	4679	1103	39	4		4	DNHD1	11	6592937	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		6592937	128413579	40	13116											
PACS1	55690	broad.mit.edu;bcgsc.ca	37	chr11	66008916	66008916	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagccctaatagcccataTggggacgtgattggcctcca	10	8	12	11	1	0	1	0	1	0	0	1	3	1	3	4	4	2	0	4	4	3	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr11:66008916T>A	ENST00000320580.4	+	22	2481	c.2448T>A	c.(2446-2448)taT>taA	p.Y816*	PACS1_ENST00000524815.1_5'UTR|PACS1_ENST00000529757.1_Nonsense_Mutation_p.Y352*	NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	816					protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)		RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						ATAGCCCATATGGGGACGTGA	0.612																																					p.Y816X													.	PACS1-74	0			c.T2448A						.						35	29	31					11																	66008916		2200	4295	6495	SO:0001587	stop_gained	55690	exon22			CCCATATGGGGAC	AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115			30032	protein-coding gene	gene with protein product		607492				12855553, 14608369	Standard	NM_018026		Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.2448T>A	11.37:g.66008916T>A	ENSP00000316454:p.Tyr816*	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	46	17	NM_018026	0	0	5	6	1	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	Nonsense_Mutation	SNP	ENST00000320580.4	37	CCDS8129.1	.	.	.	.	.	.	.	.	.	.	T	34	5.312003	0.95655	.	.	ENSG00000175115	ENST00000320580;ENST00000529757	.	.	.	5.42	-2.15	0.07102	.	0.188559	0.46442	D	0.000283	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.3124	11.7077	0.51607	0.0:0.6645:0.0:0.3355	.	.	.	.	X	816;352	.	ENSP00000316454:Y816X	Y	+	3	2	PACS1	65765492	0.032000	0.19561	0.784000	0.31847	0.413000	0.31143	-0.715000	0.04997	-0.559000	0.06110	-0.290000	0.09829	TAT	.		0.612	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391690.2	NM_018026		A	66008916	T	A	66008916	4	1	147	1	0	0	0	0	0	1	0	0	11398	1471	51	5	2534	5	PACS1	11	66008916	Nonsense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	59415979	66008916	68997600	41	13117											
CLCF1	23529	broad.mit.edu;bcgsc.ca	37	chr11	67135057	67135057	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcactgcagggaggtgccaGagcaccgtgcacaggcacgc	9	3	16	13	2	0	1	0	0	0	1	0	2	0	2	2	4	4	5	2	4	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr11:67135057G>T	ENST00000312438.7	-	2	254	c.57C>A	c.(55-57)ctC>ctA	p.L19L	AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000533438.1_Silent_p.L9L|CLCF1_ENST00000528474.1_Silent_p.L9L	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	19					B cell differentiation (GO:0030183)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)	CNTFR-CLCF1 complex (GO:0097059)|CRLF-CLCF1 complex (GO:0097058)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	ciliary neurotrophic factor receptor binding (GO:0005127)|cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			endometrium(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			GGAGGTGCCAGAGCACCGTGC	0.662																																					p.L19L													.	CLCF1-90	0			c.C57A						.						96	77	83					11																	67135057		2200	4295	6495	SO:0001819	synonymous_variant	23529	exon2			GTGCCAGAGCACC	BC012939	CCDS31617.1, CCDS53666.1	11q13.3	2014-01-28	2006-07-03		ENSG00000175505	ENSG00000175505			17412	protein-coding gene	gene with protein product	"B-cell stimulating factor 3", "cold-induced sweating syndrome 2", "novel neurotrophin-1"	607672	"CRLF1 associated cytokine-like factor 1"			10500198, 10448081, 16782820	Standard	NM_001166212		Approved	NNT1, BSF3, CLC, NR6, CISS2, BSF-3, NNT-1	uc010rpp.2	Q9UBD9	OTTHUMG00000167669	ENST00000312438.7:c.57C>A	11.37:g.67135057G>T		Somatic	41	1		WXS	Illumina HiSeq	Phase_I	46	15	NM_013246	0	0	5	20	15	B4DNT4|Q6NZA4	Silent	SNP	ENST00000312438.7	37	CCDS31617.1																																																																																			.		0.662	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246		T	67135057	G	T	67135057	2	4	147	1	0	0	0	0	0	0	0	1	3467	929	33	4		4	CLCF1	11	67135057	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	1126141	67135057	67871459	42	13118											
DSCAML1	57453	broad.mit.edu	37	chr11	117389379	117389380	+	Frame_Shift_Ins	INS	-	-	G																															tcgagggcccaggtgaccgtINSggggggcggggcgcccttgg																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr11:117389379_117389380insG	ENST00000321322.6	-	7	1492_1493	c.1491_1492insC	c.(1489-1494)cccacgfs	p.T498fs	DSCAML1_ENST00000527706.1_Frame_Shift_Ins_p.T228fs	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	438	Ig-like C2-type 5.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CAGGTGACCGTGGGGGGCGGGG	0.658																																					p.T498fs													.	DSCAML1-159	0			c.1492_1493insC						.																																			SO:0001589	frameshift_variant	57453	exon7			TGACCGTGGGGGG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1492dupC	11.37:g.117389385_117389385dupG	ENSP00000315465:p.Thr498fs	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	32	8	NM_020693	0	0	0	0	0	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Frame_Shift_Ins	INS	ENST00000321322.6	37	CCDS8384.1																																																																																			.		0.658	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		G	117389380	-	G	117389379	7	5	147	1	0	1	1	0	0	0	0	0	4780	1696	59	0	4957	0	DSCAML1	11	117389379	Frame_Shift_Ins	INS	-	TCGA-KV-A6GE-01A-11D-A31X-10	50254322	117389379	17617137	43	13119											
CD163L1	283316	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7528456	7528456	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatctcccacagaaagagaTatggcatctccacagtttaa	14	10	7	10	0	2	3	0	1	2	2	4	4	2	3	2	1	0	2	2	1	3	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:7528456T>A	ENST00000313599.3	-	10	2583	c.2526A>T	c.(2524-2526)atA>atT	p.I842I	CD163L1_ENST00000396630.1_Silent_p.I842I|CD163L1_ENST00000416109.2_Silent_p.I852I|CD163L1_ENST00000544331.1_5'UTR			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	842	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CAGAAAGAGATATGGCATCTC	0.458																																					p.I842I													.	CD163L1-100	0			c.A2526T						.						112	106	108					12																	7528456		2203	4300	6503	SO:0001819	synonymous_variant	283316	exon10			AAGAGATATGGCA	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.2526A>T	12.37:g.7528456T>A		Somatic	96	1		WXS	Illumina HiSeq	Phase_I	132	66	NM_174941	0	0	0	0	0	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			.		0.458	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7528456	T	A	7528456	2	1	147	1	0	0	0	0	0	0	0	1	2974	1396	49	5		5	CD163L1	12	7528456	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		7528456	126323439	44	13120											
TAS2R30	259293	bcgsc.ca	37	chr12	11285978	11285978	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccgcaaaactgaaagaaaaAtctgctttagcttcttgttt	13	13	7	8	1	2	2	0	1	2	1	2	2	2	2	1	0	3	4	1	0	6	5			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:11285978A>G	ENST00000539585.1	-	1	1265	c.866T>C	c.(865-867)aTt>aCt	p.I289T	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	289					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						TGAAAGAAAAATCTGCTTTAG	0.428																																					p.I289T													.	.	0			c.T866C						.						147	148	148					12																	11285978		1983	4196	6179	SO:0001583	missense	259293	exon1			AGAAAAATCTGCT	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19112	protein-coding gene	gene with protein product		613963	"taste receptor, type 2, member 47"	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.866T>C	12.37:g.11285978A>G	ENSP00000444736:p.Ile289Thr	Somatic	218	3		WXS	Illumina HiSeq	Phase_1	315	25	NM_001097643	0	0	0	0	0	Q645X7	Missense_Mutation	SNP	ENST00000539585.1	37	CCDS53750.1	.	.	.	.	.	.	.	.	.	.	-	0.008	-1.869761	0.00542	.	.	ENSG00000256188	ENST00000539585	T	0.35048	1.33	2.8	-4.06	0.03986	.	.	.	.	.	T	0.07728	0.0194	N	0.00972	-1.085	0.09310	N	1	B	0.10296	0.003	B	0.14023	0.01	T	0.28839	-1.0031	9	0.02654	T	1	.	2.665	0.05041	0.2603:0.0:0.3629:0.3768	.	289	P59541	T2R30_HUMAN	T	289	ENSP00000444736:I289T	ENSP00000444736:I289T	I	-	2	0	TAS2R30	11177245	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.224000	0.09164	-0.744000	0.04778	-1.351000	0.01236	ATT	.		0.428	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643		G	11285978	A	G	11285978	3	3	147	1	0	0	0	0	1	0	0	0	15605	101	4	3	97	3	TAS2R30	12	11285978	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	3757522	11285978	122565917	45	13121											
ABCC9	10060	ucsc.edu;bcgsc.ca	37	chr12	22089587	22089587	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attatatgaagaaatgttgtTaccacaaaatgaaaggctca	18	11	7	5	0	1	3	1	2	0	1	1	3	1	3	1	1	1	3	1	1	8	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:22089587T>C	ENST00000261201.4	-	1	21	c.22A>G	c.(22-24)Aac>Gac	p.N8D	ABCC9_ENST00000345162.2_Missense_Mutation_p.N8D|ABCC9_ENST00000326684.4_Missense_Mutation_p.N8D|ABCC9_ENST00000538350.1_Missense_Mutation_p.N8D|ABCC9_ENST00000261200.4_Missense_Mutation_p.N8D	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	8					defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	GAAATGTTGTTACCACAAAAT	0.343																																					p.N8D													.	ABCC9-96	0			c.A22G						.						93	94	94					12																	22089587		2203	4300	6503	SO:0001583	missense	10060	exon1			TGTTGTTACCACA	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"ATP binding cassette transporters / subfamily C"	60	protein-coding gene	gene with protein product	"sulfonylurea receptor 2"	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.22A>G	12.37:g.22089587T>C	ENSP00000261201:p.Asn8Asp	Somatic	220	2		WXS	Illumina HiSeq		309	76	NM_005691	0	0	0	0	0	O60707	Missense_Mutation	SNP	ENST00000261201.4	37	CCDS8694.1	.	.	.	.	.	.	.	.	.	.	T	13.01	2.110455	0.37242	.	.	ENSG00000069431	ENST00000261200;ENST00000261201;ENST00000345162;ENST00000326684;ENST00000538350	D;D;D;D;D	0.96745	-2.96;-2.98;-2.97;-4.09;-4.11	5.32	1.71	0.24356	.	0.221661	0.52532	N	0.000061	D	0.91981	0.7460	L	0.47716	1.5	0.34815	D	0.738083	B;B;B;B	0.33549	0.002;0.001;0.0;0.417	B;B;B;B	0.28011	0.008;0.005;0.002;0.085	D	0.88614	0.3158	10	0.34782	T	0.22	-7.4686	9.0179	0.36182	0.0:0.2105:0.0:0.7895	.	8;8;8;8	G3V1N6;Q8N4N7;O60706;O60706-2	.;.;ABCC9_HUMAN;.	D	8	ENSP00000261200:N8D;ENSP00000261201:N8D;ENSP00000261202:N8D;ENSP00000317518:N8D;ENSP00000442604:N8D	ENSP00000261200:N8D	N	-	1	0	ABCC9	21980854	0.990000	0.36364	0.632000	0.29296	0.919000	0.55068	2.126000	0.42026	0.139000	0.18822	0.523000	0.50628	AAC	.		0.343	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		C	22089587	T	C	22089587	3	2	147	1	0	0	0	0	1	0	0	0	59	1754	61	3	4921	3	ABCC9	12	22089587	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	10803609	22089587	111762308	46	13122											
DDX11	1663	bcgsc.ca	37	chr12	31237539	31237539	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcaggccaggaggaagcAgcgagaagaacgcctgcagc	13	1	17	10	2	0	2	0	0	0	2	0	6	0	5	2	4	6	3	2	4	3	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:31237539A>G	ENST00000407793.2	+	4	667	c.416A>G	c.(415-417)cAg>cGg	p.Q139R	DDX11_ENST00000228264.6_Missense_Mutation_p.Q113R|DDX11_ENST00000545668.1_Missense_Mutation_p.Q139R|DDX11_ENST00000251758.5_Missense_Mutation_p.Q139R|DDX11_ENST00000542838.1_Missense_Mutation_p.Q139R|DDX11_ENST00000350437.4_Missense_Mutation_p.Q139R	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	139	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AGGAGGAAGCAGCGAGAAGAA	0.582										Multiple Myeloma(12;0.14)																											p.Q139R													.	DDX11-229	0			c.A416G						.						23	25	24					12																	31237539		2199	4289	6488	SO:0001583	missense	1663	exon4			GGAAGCAGCGAGA	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.416A>G	12.37:g.31237539A>G	ENSP00000384703:p.Gln139Arg	Somatic	321	8		WXS	Illumina HiSeq	Phase_1	436	201	NM_030653	0	0	4	4	0	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	A	6.614	0.481678	0.12581	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000251758;ENST00000228264;ENST00000415475;ENST00000545668;ENST00000350437;ENST00000535317	T;T;T;T;T;T;T;T	0.02606	4.23;4.23;4.23;4.23;4.23;4.23;4.23;4.23	4.06	1.62	0.23740	Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.191160	0.44902	N	0.000406	T	0.01320	0.0043	N	0.04260	-0.245	0.24037	N	0.996095	B;B;B;B	0.16802	0.019;0.019;0.01;0.01	B;B;B;B	0.16289	0.01;0.01;0.015;0.015	T	0.48502	-0.9030	10	0.24483	T	0.36	.	5.3691	0.16131	0.7235:0.1777:0.0987:0.0	.	139;139;139;139	B4DZY1;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	R	139;139;139;113;113;139;139;175	ENSP00000443426:Q139R;ENSP00000384703:Q139R;ENSP00000251758:Q139R;ENSP00000228264:Q113R;ENSP00000406457:Q113R;ENSP00000440402:Q139R;ENSP00000309965:Q139R;ENSP00000440171:Q175R	ENSP00000228264:Q113R	Q	+	2	0	DDX11	31128806	1.000000	0.71417	0.914000	0.36105	0.007000	0.05969	3.416000	0.52707	0.226000	0.20979	-0.710000	0.03640	CAG	.		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		G	31237539	A	G	31237539	3	3	147	1	0	0	0	0	1	0	0	0	4349	188	7	3	426	3	DDX11	12	31237539	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	9147952	31237539	102614356	47	13123											
KRT5	3852	broad.mit.edu	37	chr12	52913574	52913574	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagggtcttgatctgctcGcgctcctcggtcctcaccct	3	13	10	15	3	3	2	1	2	2	0	7	2	5	2	3	2	1	2	3	2	0	2	rs200658792		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:52913574G>T	ENST00000252242.4	-	1	897	c.507C>A	c.(505-507)cgC>cgA	p.R169R		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	169	Coil 1A.|Rod.		R -> P (in DM-EBS; dbSNP:rs60720877). {ECO:0000269|PubMed:16786515}.		cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGATCTGCTCGCGCTCCTCGG	0.502																																					p.R169R													.	KRT5-90	0			c.C507A						.						183	175	178					12																	52913574		2203	4300	6503	SO:0001819	synonymous_variant	3852	exon1			CTGCTCGCGCTCC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.507C>A	12.37:g.52913574G>T		Somatic	159	2		WXS	Illumina HiSeq	Phase_I	179	4	NM_000424	0	0	0	0	0	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1																																																																																			G|0.999;A|0.000		0.502	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			T	52913574	G	T	52913574	2	4	147	1	0	0	0	0	0	0	0	1	8500	1074	38	4		4	KRT5	12	52913574	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	21676035	52913574	80938321	48	13124											
METAP2	10988	broad.mit.edu	37	chr12	95867964	95867964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcgggcaacatggcgggTgtggaggaggtagcggcctc	6	7	18	10	3	1	0	0	0	1	0	3	2	1	2	1	7	2	2	1	7	2	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:95867964T>G	ENST00000323666.5	+	1	238	c.9T>G	c.(7-9)ggT>ggG	p.G3G	METAP2_ENST00000261220.9_Silent_p.G3G|METAP2_ENST00000550777.1_Silent_p.G3G|METAP2_ENST00000546753.1_Silent_p.G3G|METAP2_ENST00000551840.1_Silent_p.G3G	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						ACATGGCGGGTGTGGAGGAGG	0.652																																					p.G3G													.	METAP2-90	0			c.T9G						.						34	42	39					12																	95867964		2203	4297	6500	SO:0001819	synonymous_variant	10988	exon1			GGCGGGTGTGGAG	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.9T>G	12.37:g.95867964T>G		Somatic	107	24		WXS	Illumina HiSeq	Phase_I	126	43	NM_006838	0	0	4	4	0		Silent	SNP	ENST00000323666.5	37	CCDS9052.1																																																																																			.		0.652	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		G	95867964	T	G	95867964	2	3	147	1	0	0	0	0	0	0	0	1	9512	1683	59	5		5	METAP2	12	95867964	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	42954390	95867964	37983931	49	13125											
VSIG10	54621	hgsc.bcm.edu	37	chr12	118506351	118506351	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctcctcctcctcCtcttcctcttctgaatccac	3	15	1	22	0	3	1	0	1	3	0	12	1	12	1	9	0	0	0	9	0	1	2	rs373328738		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:118506351C>T	ENST00000359236.5	-	8	1674	c.1398G>A	c.(1396-1398)gaG>gaA	p.E466E		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	466	Glu-rich.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						cctcctcctcctcttcctctt	0.458																																					p.E466E		.											.	.	0			c.G1398A						.						96	91	92					12																	118506351		2045	4191	6236	SO:0001819	synonymous_variant	54621	exon8			CTCCTCCTCTTCC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1398G>A	12.37:g.118506351C>T		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	132	8	NM_019086	0	0	1	1	0	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			.		0.458	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		T	118506351	C	T	118506351	2	4	147	1	0	0	0	0	0	0	0	1	17256	680	24	2		2	VSIG10	12	118506351	Silent	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	22638387	118506351	15345544	50	13126											
PARP4	143	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	25021252	25021252	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagggcctcgggcacatctgGattgagttgctgccatttga	7	11	13	10	1	1	2	0	2	1	0	2	3	1	3	2	3	2	3	2	3	0	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr13:25021252G>C	ENST00000381989.3	-	26	3292	c.3187C>G	c.(3187-3189)Cca>Gca	p.P1063A		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1063					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GGCACATCTGGATTGAGTTGC	0.488																																					p.P1063A													.	PARP4-94	0			c.C3187G						.						66	61	63					13																	25021252		2203	4300	6503	SO:0001583	missense	143	exon26			CATCTGGATTGAG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"Poly (ADP-ribose) polymerases"	271	protein-coding gene	gene with protein product	"von Willebrand factor A domain containing 5C"	607519	"ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3187C>G	13.37:g.25021252G>C	ENSP00000371419:p.Pro1063Ala	Somatic	208	2		WXS	Illumina HiSeq	Phase_I	193	55	NM_006437	0	0	0	0	0	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.637295	0.00114	.	.	ENSG00000102699	ENST00000381989	T	0.02032	4.49	4.71	-9.42	0.00610	.	1.340860	0.04661	N	0.408863	T	0.01558	0.0050	L	0.38175	1.15	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.46803	-0.9165	10	0.08179	T	0.78	1.0731	4.7321	0.12970	0.163:0.2649:0.4575:0.1146	.	1063	Q9UKK3	PARP4_HUMAN	A	1063	ENSP00000371419:P1063A	ENSP00000371419:P1063A	P	-	1	0	PARP4	23919252	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.667000	0.01961	-2.376000	0.00598	-1.768000	0.00664	CCA	.		0.488	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		C	25021252	G	C	25021252	3	2	147	1	0	0	0	0	1	0	0	0	11489	1174	41	4	2023	4	PARP4	13	25021252	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		25021252	90148626	51	13127											
PRMT5	10419	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23397402	23397402	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatggagaaagctttcccAcaattagcgtattccagtct	11	12	7	11	1	1	1	0	0	1	1	4	2	4	1	3	1	2	2	3	1	4	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr14:23397402A>G	ENST00000324366.8	-	3	471	c.248T>C	c.(247-249)gTg>gCg	p.V83A	RP11-298I3.1_ENST00000548819.1_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000553641.1_5'UTR|PRMT5_ENST00000397440.4_Missense_Mutation_p.V66A|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000216350.8_Intron|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000553897.1_Intron|PRMT5_ENST00000397441.2_Missense_Mutation_p.V66A|PRMT5_ENST00000538452.1_5'UTR	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	83	TIM barrel. {ECO:0000269|PubMed:23071334}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		AAGCTTTCCCACAATTAGCGT	0.433																																					p.V83A		.											.	PRMT5-91	0			c.T248C						.						92	82	85					14																	23397402		2203	4300	6503	SO:0001583	missense	10419	exon3			TTTCCCACAATTA	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.248T>C	14.37:g.23397402A>G	ENSP00000319169:p.Val83Ala	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	85	33	NM_006109	0	0	2	8	6	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	37	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564340	0.86335	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000553550;ENST00000554867;ENST00000556616;ENST00000554910;ENST00000421938	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.80534	0.4641	M	0.84683	2.71	0.80722	D	1	D;D;D	0.71674	0.963;0.991;0.998	D;P;D	0.68765	0.959;0.73;0.96	D	0.83988	0.0336	9	0.87932	D	0	-13.1665	14.9141	0.70781	1.0:0.0:0.0:0.0	.	66;83;66	A8MTP3;O14744;A8MZ91	.;ANM5_HUMAN;.	A	83;66;66;83;83;45;41;93	.	ENSP00000319169:V83A	V	-	2	0	PRMT5	22467242	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.199000	0.89731	2.176000	0.68965	0.455000	0.32223	GTG	.		0.433	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			G	23397402	A	G	23397402	3	3	147	1	0	0	0	0	1	0	0	0	12568	159	6	3	1725	3	PRMT5	14	23397402	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10		23397402	83952138	52	13128											
DIO2	1734	broad.mit.edu	37	chr14	80669247	80669247	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcactggggcggcaaggAgaaacgctccagaagctgct	10	5	15	11	3	0	2	0	0	0	2	2	3	1	2	1	5	3	5	1	5	3	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr14:80669247A>T	ENST00000557010.1	-	4	992	c.607T>A	c.(607-609)Tcc>Acc	p.S203T	DIO2_ENST00000422005.3_3'UTR|DIO2_ENST00000557125.1_3'UTR|DIO2_ENST00000555750.1_Missense_Mutation_p.S239T|DIO2_ENST00000438257.4_Missense_Mutation_p.S203T	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	203					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		GGCGGCAAGGAGAAACGCTCC	0.557											OREG0022848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	DIO2-22	0			.						.						71	75	74					14																	80669247		2047	4193	6240	SO:0001583	missense	1734	.			GCAAGGAGAAACG	AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1.97.1.10		2884	protein-coding gene	gene with protein product	"thyroxine deiodinase, type II", "deiodonase-2", "deiodinase-2"	601413				8755651, 10343107	Standard	NM_001007023		Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.607T>A	14.37:g.80669247A>T	ENSP00000451419:p.Ser203Thr	Somatic	62	0	1200	WXS	Illumina HiSeq	Phase_I	74	3	.	0	0	0	0	0	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	Missense_Mutation	SNP	ENST00000557010.1	37	CCDS45146.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.132860	0.77662	.	.	ENSG00000211448	ENST00000438257;ENST00000557010;ENST00000555750	T;T;T	0.31247	1.51;1.51;1.5	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000002	T	0.55321	0.1913	M	0.73598	2.24	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.67103	0.915;0.949;0.945	T	0.57171	-0.7857	10	0.51188	T	0.08	.	16.0828	0.81017	1.0:0.0:0.0:0.0	.	239;203;239	Q92813-2;Q92813;G3V315	.;IOD2_HUMAN;.	T	203;203;239	ENSP00000405854:S203T;ENSP00000451419:S203T;ENSP00000450980:S239T	ENSP00000405854:S203T	S	-	1	0	DIO2	79739000	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.369000	0.79578	2.199000	0.70637	0.528000	0.53228	TCC	.		0.557	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000413428.2			T	80669247	A	T	80669247	3	4	147	1	0	0	0	0	1	0	0	0	4536	304	11	5	218	5	DIO2	14	80669247	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	57271845	80669247	26680293	53	13129											
C14orf102	55051	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	90756895	90756895	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaggcctccaccagctggaaCtgaagatcatggctggaaag	13	6	12	10	0	1	2	1	1	0	1	2	4	2	4	3	4	2	2	3	4	4	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr14:90756895C>A	ENST00000354366.3	-	10	2131	c.1899G>T	c.(1897-1899)caG>caT	p.Q633H	NRDE2_ENST00000357904.3_Missense_Mutation_p.Q402H	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	633																	CCAGCTGGAACTGAAGATCAT	0.458																																					p.Q633H													.	.	0			c.G1899T						.						79	81	81					14																	90756895		2203	4300	6503	SO:0001583	missense	55051	exon10			CTGGAACTGAAGA	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 102"	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.1899G>T	14.37:g.90756895C>A	ENSP00000346335:p.Gln633His	Somatic	118	1		WXS	Illumina HiSeq	Phase_I	108	44	NM_017970	0	0	0	1	1	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	37	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329880	0.24167	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.33438	1.41;1.41	5.9	4.91	0.64330	.	0.316430	0.34700	N	0.003759	T	0.32615	0.0835	M	0.71581	2.175	0.53688	D	0.999972	B	0.27823	0.19	B	0.31495	0.131	T	0.12760	-1.0535	10	0.40728	T	0.16	-15.6305	8.4865	0.33074	0.0:0.7126:0.1565:0.1309	.	633	Q9H7Z3	CN102_HUMAN	H	633;402	ENSP00000346335:Q633H;ENSP00000350579:Q402H	ENSP00000346335:Q633H	Q	-	3	2	C14orf102	89826648	0.863000	0.29885	0.933000	0.37362	0.148000	0.21650	0.219000	0.17641	2.788000	0.95919	0.650000	0.86243	CAG	.		0.458	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		A	90756895	C	A	90756895	3	1	147	1	0	0	0	0	1	0	0	0	1739	564	20	4	1615	4	C14orf102	14	90756895	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	10087648	90756895	16592645	54	13130											
BAHD1	22893	broad.mit.edu;bcgsc.ca	37	chr15	40751319	40751319	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctaaaactgagccaggagcGggagctacccctgcggctgc	9	5	13	14	2	0	1	0	1	0	0	0	3	0	3	4	3	7	2	4	3	3	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr15:40751319G>A	ENST00000416165.1	+	2	727	c.656G>A	c.(655-657)cGg>cAg	p.R219Q	BAHD1_ENST00000561234.1_Missense_Mutation_p.R219Q|BAHD1_ENST00000560846.1_Missense_Mutation_p.R219Q	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	219					heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		AGCCAGGAGCGGGAGCTACCC	0.647																																					p.R219Q													.	BAHD1-90	0			c.G656A						.						27	32	30					15																	40751319		2203	4300	6503	SO:0001583	missense	22893	exon2			AGGAGCGGGAGCT	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.656G>A	15.37:g.40751319G>A	ENSP00000396976:p.Arg219Gln	Somatic	46	1		WXS	Illumina HiSeq	Phase_I	49	25	NM_014952	0	0	0	1	1	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	37	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078117	0.76528	.	.	ENSG00000140320	ENST00000416165	T	0.22743	1.94	5.0	5.0	0.66597	.	0.171717	0.38005	N	0.001842	T	0.16938	0.0407	N	0.14661	0.345	0.37906	D	0.931219	D;D;D	0.56746	0.977;0.961;0.977	P;B;P	0.49140	0.601;0.397;0.601	T	0.02109	-1.1212	10	0.59425	D	0.04	-19.1008	9.8207	0.40880	0.1236:0.0:0.8764:0.0	.	219;219;219	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	Q	219	ENSP00000396976:R219Q	ENSP00000396976:R219Q	R	+	2	0	BAHD1	38538611	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.090000	0.50191	2.750000	0.94351	0.655000	0.94253	CGG	.		0.647	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40751319	G	A	40751319	3	1	147	1	0	0	0	0	1	0	0	0	1298	1116	39	1	658	1	BAHD1	15	40751319	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		40751319	61780073	55	13131											
TP53BP1	7158	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43749148	43749148	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaactggagacatgggttccGtatcctcaatctgtgtgttt	8	14	11	8	1	2	1	1	0	1	1	4	3	4	1	2	2	1	3	2	2	3	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr15:43749148G>A	ENST00000263801.3	-	12	1895	c.1643C>T	c.(1642-1644)aCg>aTg	p.T548M	TP53BP1_ENST00000382044.4_Missense_Mutation_p.T553M|TP53BP1_ENST00000450115.2_Missense_Mutation_p.T553M|TP53BP1_ENST00000382039.3_Missense_Mutation_p.T553M|TP53BP1_ENST00000605155.1_5'Flank	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	548					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CATGGGTTCCGTATCCTCAAT	0.408								Other conserved DNA damage response genes																													p.T553M													.	TP53BP1-294	0			c.C1658T						.						146	130	135					15																	43749148		2201	4298	6499	SO:0001583	missense	7158	exon12			GGTTCCGTATCCT	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.1643C>T	15.37:g.43749148G>A	ENSP00000263801:p.Thr548Met	Somatic	76	1		WXS	Illumina HiSeq	Phase_I	74	26	NM_001141980	0	0	0	0	0	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.865405	0.32977	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17	5.04	3.17	0.36434	.	0.402681	0.25610	N	0.029482	T	0.35941	0.0949	L	0.59436	1.845	0.26495	N	0.97487	D;D;D;D	0.76494	0.995;0.999;0.999;0.999	P;P;D;D	0.67382	0.762;0.894;0.951;0.951	T	0.07986	-1.0744	10	0.48119	T	0.1	-2.4294	8.306	0.32042	0.2433:0.0:0.7567:0.0	.	553;548;553;553	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	M	548;553;553;553;553	ENSP00000263801:T548M;ENSP00000371475:T553M;ENSP00000371470:T553M;ENSP00000393497:T553M;ENSP00000388028:T553M	ENSP00000263801:T548M	T	-	2	0	TP53BP1	41536440	0.941000	0.31946	0.984000	0.44739	0.741000	0.42261	1.664000	0.37439	0.634000	0.30469	-0.244000	0.11960	ACG	.		0.408	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43749148	G	A	43749148	3	1	147	1	0	0	0	0	1	0	0	0	16416	1145	40	1	4343	1	TP53BP1	15	43749148	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	2997829	43749148	58782244	56	13132											
VPS13C	54832	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	62211580	62211580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgactggcattgggattccGtacattatacaatcgccgtc	10	12	9	10	3	0	1	0	1	0	0	3	2	1	2	2	2	2	2	2	2	4	5			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr15:62211580G>A	ENST00000261517.5	-	58	7619	c.7546C>T	c.(7546-7548)Cgg>Tgg	p.R2516W	VPS13C_ENST00000395896.4_Missense_Mutation_p.R2516W|VPS13C_ENST00000395898.3_Missense_Mutation_p.R2473W|VPS13C_ENST00000249837.3_Missense_Mutation_p.R2473W	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TTGGGATTCCGTACATTATAC	0.423																																					p.R2516W													.	VPS13C-92	0			c.C7546T						.						147	144	145					15																	62211580		2203	4299	6502	SO:0001583	missense	54832	exon58			GATTCCGTACATT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.7546C>T	15.37:g.62211580G>A	ENSP00000261517:p.Arg2516Trp	Somatic	118	2		WXS	Illumina HiSeq	Phase_I	107	35	NM_020821	0	0	0	0	0		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369251	0.24771	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.50548	0.74;0.74;0.91	5.35	2.37	0.29283	.	0.191981	0.43579	N	0.000554	T	0.36441	0.0967	L	0.54323	1.7	0.34837	D	0.740249	B;B;B;B	0.29909	0.136;0.261;0.261;0.17	B;B;B;B	0.23419	0.031;0.031;0.046;0.014	T	0.40040	-0.9584	10	0.56958	D	0.05	.	5.3262	0.15908	0.1657:0.0:0.4056:0.4287	.	2473;2516;2473;2516	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	W	2473;2516;2516;2516	ENSP00000249837:R2473W;ENSP00000261517:R2516W;ENSP00000379233:R2516W	ENSP00000249837:R2473W	R	-	1	2	VPS13C	59998872	0.752000	0.28338	0.148000	0.22405	0.563000	0.35712	1.599000	0.36751	0.290000	0.22444	-0.181000	0.13052	CGG	.		0.423	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62211580	G	A	62211580	3	1	147	1	0	0	0	0	1	0	0	0	17224	1144	40	1	3855	1	VPS13C	15	62211580	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	18462432	62211580	40319812	57	13133											
VPS13C	54832	broad.mit.edu	37	chr15	62219326	62219326	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctctcttttctctgagaaaAgggcaagcgagcactttcag	10	11	9	11	1	3	1	1	1	2	1	5	3	3	1	1	1	2	2	1	1	3	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr15:62219326A>G	ENST00000261517.5	-	52	6553	c.6480T>C	c.(6478-6480)ccT>ccC	p.P2160P	VPS13C_ENST00000395896.4_Silent_p.P2160P|VPS13C_ENST00000395898.3_Silent_p.P2117P|VPS13C_ENST00000249837.3_Silent_p.P2117P	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CTCTGAGAAAAGGGCAAGCGA	0.423																																					p.P2160P													.	VPS13C-92	0			c.T6480C						.						120	118	119					15																	62219326		2203	4300	6503	SO:0001819	synonymous_variant	54832	exon52			GAGAAAAGGGCAA	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6480T>C	15.37:g.62219326A>G		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	120	4	NM_020821	0	0	0	0	0		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			.		0.423	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		G	62219326	A	G	62219326	2	3	147	1	0	0	0	0	0	0	0	1	17224	59	3	3		3	VPS13C	15	62219326	Silent	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	7746	62219326	40312066	58	13134											
PARP6	56965	broad.mit.edu	37	chr15	72552951	72552951	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggagatggaacggttcatGaggcgcccaacccgaagctc	11	5	13	12	3	1	2	1	1	0	1	2	5	1	3	2	4	3	2	2	4	3	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr15:72552951G>T	ENST00000569795.1	-	10	1311	c.624C>A	c.(622-624)ctC>ctA	p.L208L	PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000287196.9_Silent_p.L208L|PARP6_ENST00000260376.7_Silent_p.L208L			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	208							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						AACGGTTCATGAGGCGCCCAA	0.557																																					p.L208L													.	PARP6-522	0			c.C624A						.						376	370	372					15																	72552951		1920	4129	6049	SO:0001819	synonymous_variant	56965	exon9			GTTCATGAGGCGC	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.624C>A	15.37:g.72552951G>T		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	66	4	NM_020214	0	0	9	9	0	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Silent	SNP	ENST00000569795.1	37	CCDS10241.2																																																																																			.		0.557	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		T	72552951	G	T	72552951	2	4	147	1	0	0	0	0	0	0	0	1	11490	1277	45	4		4	PARP6	15	72552951	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	10333625	72552951	29978441	59	13135											
NPTN	27020	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	73884465	73884465	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ataatgacctcttcactggtGacaatccttggctctgtaat	10	14	7	10	0	3	2	1	2	2	0	4	2	4	2	2	2	0	2	2	2	3	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr15:73884465G>A	ENST00000345330.4	-	3	650	c.453C>T	c.(451-453)gtC>gtT	p.V151V	NPTN_ENST00000563691.1_Silent_p.V151V|NPTN_ENST00000351217.6_Silent_p.V35V|NPTN_ENST00000564551.1_Intron|NPTN_ENST00000545878.1_Silent_p.V151V|NPTN_ENST00000287226.8_Silent_p.V151V|NPTN_ENST00000562924.1_Silent_p.V35V|NPTN_ENST00000542234.1_Intron	NM_001161363.1|NM_012428.3	NP_001154835.1|NP_036560.1	Q9Y639	NPTN_HUMAN	neuroplastin	151	Ig-like 2.|Narpin; mediates binding with FGFR1 and has antidepressant-like activity. {ECO:0000250}.				homophilic cell adhesion (GO:0007156)|long-term synaptic potentiation (GO:0060291)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)	cell adhesion molecule binding (GO:0050839)|type 1 fibroblast growth factor receptor binding (GO:0005105)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	13						CTTCACTGGTGACAATCCTTG	0.532																																					p.V151V	Pancreas(101;1519 1568 9459 19537 41286)|Esophageal Squamous(143;1278 1787 35254 36835 44843)												.	NPTN-90	0			c.C453T						.						156	117	130					15																	73884465		2198	4297	6495	SO:0001819	synonymous_variant	27020	exon3			ACTGGTGACAATC	AF035287	CCDS10249.1, CCDS10250.1, CCDS58379.1, CCDS58380.1	15q24.1	2013-01-29	2006-02-22	2006-02-22	ENSG00000156642	ENSG00000156642		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17867	protein-coding gene	gene with protein product		612820	"stromal cell derived factor receptor 1"	SDFR1		8619474, 9110174	Standard	NM_012428		Approved	SDR1, GP55, GP65, np65, np55	uc002avs.3	Q9Y639	OTTHUMG00000137586	ENST00000345330.4:c.453C>T	15.37:g.73884465G>A		Somatic	61	1		WXS	Illumina HiSeq	Phase_I	59	21	NM_001161363	0	0	0	0	0	B2RAL7|B7Z4D3|B7ZLL2|Q17R52|Q59EJ9|Q6NVX7|Q9Y640	Silent	SNP	ENST00000345330.4	37	CCDS10249.1																																																																																			.		0.532	NPTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268980.1	NM_012428		A	73884465	G	A	73884465	2	1	147	1	0	0	0	0	0	0	0	1	10627	1277	45	2		2	NPTN	15	73884465	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	1331514	73884465	28646927	60	13136											
PRSS27	83886	broad.mit.edu	37	chr16	2762757	2762757	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctcaccccagctgatcAcccccgcctgcagccacgac	8	4	7	22	2	2	1	2	1	0	0	2	2	2	1	7	0	4	2	7	0	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr16:2762757A>C	ENST00000302641.3	-	6	791	c.737T>G	c.(736-738)gTg>gGg	p.V246G	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	246	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						CCAGCTGATCACCCCCGCCTG	0.667																																					p.V246G													.	PRSS27-91	0			c.T737G						.						27	24	25					16																	2762757		2178	4284	6462	SO:0001583	missense	83886	exon6			CTGATCACCCCCG	AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"Serine peptidases / Serine peptidases"	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.737T>G	16.37:g.2762757A>C	ENSP00000306390:p.Val246Gly	Somatic	69	24		WXS	Illumina HiSeq	Phase_I	97	30	NM_031948	0	0	4	4	0		Missense_Mutation	SNP	ENST00000302641.3	37	CCDS10476.1	.	.	.	.	.	.	.	.	.	.	.	16.11	3.030268	0.54790	.	.	ENSG00000172382	ENST00000302641;ENST00000543965	D	0.85861	-2.04	5.21	5.21	0.72293	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.48286	D	0.000182	D	0.94670	0.8281	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.987;0.992	D	0.96007	0.8998	10	0.87932	D	0	.	13.0312	0.58842	1.0:0.0:0.0:0.0	.	246;210	Q9BQR3;B3KP25	PRS27_HUMAN;.	G	246;210	ENSP00000306390:V246G	ENSP00000306390:V246G	V	-	2	0	PRSS27	2702758	0.956000	0.32656	0.212000	0.23672	0.512000	0.34134	8.849000	0.92178	1.969000	0.57287	0.459000	0.35465	GTG	.		0.667	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948		C	2762757	A	C	2762757	3	2	147	1	0	0	0	0	1	0	0	0	12650	159	6	5	139	5	PRSS27	16	2762757	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10		2762757	87591996	61	13137											
ELMO3	79767	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67236173	67236173	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgtgtgagctgctccGtgttggggagccctgtgagt	3	12	17	9	1	0	2	0	2	0	0	1	3	1	3	2	2	4	5	2	2	0	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr16:67236173G>C	ENST00000360833.1	+	12	1412	c.1355G>C	c.(1354-1356)cGt>cCt	p.R452P	ELMO3_ENST00000477898.1_Missense_Mutation_p.R303P|ELMO3_ENST00000393997.2_Missense_Mutation_p.R469P|MIR328_ENST00000385213.1_RNA			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	416	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		GAGCTGCTCCGTGTTGGGGAG	0.642																																					p.R469P													.	ELMO3-90	0			c.G1406C						.						72	80	77					16																	67236173		2198	4300	6498	SO:0001583	missense	79767	exon13			TGCTCCGTGTTGG		CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"Engulfment and cell motility proteins"	17289	protein-coding gene	gene with protein product		606422	"engulfment and cell motility 3 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.1355G>C	16.37:g.67236173G>C	ENSP00000354077:p.Arg452Pro	Somatic	90	1		WXS	Illumina HiSeq	Phase_I	105	54	NM_024712	0	0	10	57	47	B4DV86|Q9H8A5	Missense_Mutation	SNP	ENST00000360833.1	37		.	.	.	.	.	.	.	.	.	.	G	11.93	1.785844	0.31593	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.33438	1.41;1.41	5.62	-8.47	0.00939	Engulfment/cell motility, ELMO (2);	0.430306	0.28977	N	0.013534	T	0.38612	0.1047	M	0.66939	2.045	0.48185	D	0.999606	P;P;P	0.47604	0.752;0.898;0.898	P;P;P	0.52598	0.703;0.697;0.697	T	0.62909	-0.6754	10	0.87932	D	0	0.0214	17.3874	0.87420	0.3634:0.0:0.6366:0.0	.	416;452;469	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	P	452;469	ENSP00000354077:R452P;ENSP00000377566:R469P	ENSP00000354077:R452P	R	+	2	0	ELMO3	65793674	0.006000	0.16342	0.002000	0.10522	0.156000	0.22039	0.112000	0.15479	-1.379000	0.02118	-1.029000	0.02412	CGT	.		0.642	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712		C	67236173	G	C	67236173	3	2	147	1	0	0	0	0	1	0	0	0	5080	1145	40	4	1456	4	ELMO3	16	67236173	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	64473416	67236173	23118580	62	13138											
PRMT7	54496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr16	68386313	68386313	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgtggttgtggagttcaggGtaggccacccaggggatgtt	6	11	17	7	0	1	0	1	0	0	0	1	2	1	2	2	6	0	4	2	6	1	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr16:68386313G>A	ENST00000339507.5	+	15	2405		c.e15+1		PRMT7_ENST00000441236.1_Splice_Site|PRMT7_ENST00000449359.3_Splice_Site|PRMT7_ENST00000348497.4_Splice_Site			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7						cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		GGAGTTCAGGGTAGGCCACCC	0.622																																					.		.											.	PRMT7-90	0			c.1425+1G>A						.						40	38	39					16																	68386313		2198	4300	6498	SO:0001630	splice_region_variant	54496	exon13			TTCAGGGTAGGCC	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"Protein arginine methyltransferases"	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1575+1G>A	16.37:g.68386313G>A		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	22	9	NM_001184824	0	0	0	1	1	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Splice_Site	SNP	ENST00000339507.5	37	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.947713	0.73787	.	.	ENSG00000132600	ENST00000449359;ENST00000441236;ENST00000348497;ENST00000339507	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9994	0.80280	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRMT7	66943814	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	9.352000	0.97076	2.392000	0.81423	0.655000	0.94253	.	.		0.622	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	Intron	A	68386313	G	A	68386313	5	1	147	1	0	0	0	0	0	0	1	0	12570	1275	44	2	1626	2	PRMT7	16	68386313	Splice_Site	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	1150140	68386313	21968440	63	13139											
DHX38	9785	bcgsc.ca	37	chr16	72132887	72132887	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctccctcctacaaatataacGagtgggccgatgacagaaga	14	7	9	11	2	0	3	0	1	0	2	2	5	2	3	3	1	2	0	3	1	5	3	rs557237564		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr16:72132887G>A	ENST00000268482.3	+	6	1335	c.826G>A	c.(826-828)Gag>Aag	p.E276K	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	276					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CAAATATAACGAGTGGGCCGA	0.592																																					p.E276K	Melanoma(97;711 1442 7855 13832 28836)												.	DHX38-227	0			c.G826A						.						57	56	56					16																	72132887		2198	4300	6498	SO:0001583	missense	9785	exon6			TATAACGAGTGGG	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.826G>A	16.37:g.72132887G>A	ENSP00000268482:p.Glu276Lys	Somatic	77	2		WXS	Illumina HiSeq	Phase_1	116	56	NM_014003	0	0	0	1	1	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.080529	0.36662	.	.	ENSG00000140829	ENST00000268482	T	0.02916	4.11	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.02929	0.0087	L	0.27053	0.805	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.50101	-0.8867	10	0.09843	T	0.71	.	18.3634	0.90383	0.0:0.0:1.0:0.0	.	276	Q92620	PRP16_HUMAN	K	276	ENSP00000268482:E276K	ENSP00000268482:E276K	E	+	1	0	DHX38	70690388	1.000000	0.71417	0.390000	0.26220	0.533000	0.34776	9.262000	0.95591	2.419000	0.82065	0.563000	0.77884	GAG	.		0.592	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72132887	G	A	72132887	3	1	147	1	0	0	0	0	1	0	0	0	4522	1059	37	1	844	1	DHX38	16	72132887	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	3746574	72132887	18221866	64	13140											
MYH4	4622	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	10369879	10369879	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctccagcttcggtcttggCtgtcaccttccccccttccc	3	12	7	19	1	2	0	1	0	1	0	6	0	5	0	6	2	2	3	6	2	0	4	rs148833814		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr17:10369879C>T	ENST00000255381.2	-	3	294	c.184G>A	c.(184-186)Gcc>Acc	p.A62T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	62					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TCGGTCTTGGCTGTCACCTTC	0.463																																					p.A62T													.	MYH4-102	0			c.G184A						.	C	THR/ALA	0,4406		0,0,2203	201	188	192		184	4.5	0.3	17	dbSNP_134	192	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYH4	NM_017533.2	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	62/1940	10369879	1,13005	2203	4300	6503	SO:0001583	missense	4622	exon3			TCTTGGCTGTCAC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"Myosins / Myosin superfamily : Class II"	7574	protein-coding gene	gene with protein product		160742	"myosin, heavy polypeptide 4, skeletal muscle"			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.184G>A	17.37:g.10369879C>T	ENSP00000255381:p.Ala62Thr	Somatic	108	1		WXS	Illumina HiSeq	Phase_I	119	56	NM_017533	0	0	0	0	0		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324097	0.60634	0.0	1.16E-4	ENSG00000141048	ENST00000255381	T	0.80304	-1.36	4.53	4.53	0.55603	Myosin, N-terminal, SH3-like (1);	0.261790	0.19148	U	0.121502	T	0.76069	0.3936	L	0.41492	1.28	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.73544	-0.3949	10	0.66056	D	0.02	.	17.8023	0.88591	0.0:1.0:0.0:0.0	.	62	Q9Y623	MYH4_HUMAN	T	62	ENSP00000255381:A62T	ENSP00000255381:A62T	A	-	1	0	MYH4	10310604	0.240000	0.23847	0.284000	0.24805	0.914000	0.54420	4.544000	0.60691	2.498000	0.84270	0.650000	0.86243	GCC	C|1.000;T|0.000		0.463	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10369879	C	T	10369879	3	4	147	1	0	0	0	0	1	0	0	0	10062	797	28	2	5787	2	MYH4	17	10369879	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10		10369879	70825331	65	13141											
BLMH	642	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	28614937	28614937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgggctgtgtccacaaaaGcactcaagaagaaataacag	16	7	9	9	0	2	2	1	0	1	2	3	2	3	2	1	1	2	2	1	1	6	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr17:28614937G>A	ENST00000261714.6	-	4	524	c.350C>T	c.(349-351)gCt>gTt	p.A117V	BLMH_ENST00000394819.3_Missense_Mutation_p.A30V|BLMH_ENST00000582669.1_5'Flank|RNU6-1267P_ENST00000410747.1_RNA	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	117					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	GTCCACAAAAGCACTCAAGAA	0.388																																					p.A117V	Pancreas(127;628 1772 12912 33293 36203)	.											.	BLMH-91	0			c.C350T						.						88	85	86					17																	28614937		2203	4300	6503	SO:0001583	missense	642	exon4			ACAAAAGCACTCA	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.350C>T	17.37:g.28614937G>A	ENSP00000261714:p.Ala117Val	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	76	17	NM_000386	0	0	8	13	5	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769945	0.69992	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.44881	0.91;0.91	5.95	5.95	0.96441	.	0.197192	0.52532	D	0.000067	T	0.45637	0.1352	M	0.63208	1.945	0.51233	D	0.999918	B;B	0.23540	0.087;0.036	B;B	0.25759	0.063;0.039	T	0.31530	-0.9940	10	0.49607	T	0.09	-8.7167	17.5491	0.87871	0.0:0.0:1.0:0.0	.	30;117	E7EMN3;Q13867	.;BLMH_HUMAN	V	117;30	ENSP00000261714:A117V;ENSP00000378296:A30V	ENSP00000261714:A117V	A	-	2	0	BLMH	25639063	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.945000	0.63568	2.824000	0.97209	0.655000	0.94253	GCT	.		0.388	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386		A	28614937	G	A	28614937	3	1	147	1	0	0	0	0	1	0	0	0	1447	971	34	2	1053	2	BLMH	17	28614937	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	18245058	28614937	52580273	66	13142											
CACNB1	782	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37343149	37343149	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aacctcacagccctccttcaCcagccgcccgatccaccagt	9	6	5	21	2	2	0	2	0	0	0	4	1	4	0	8	0	3	0	8	0	1	1	rs201083692	byFrequency	TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr17:37343149C>G	ENST00000394303.3	-	5	655	c.448G>C	c.(448-450)Gtg>Ctg	p.V150L	CACNB1_ENST00000582877.1_5'UTR|CACNB1_ENST00000394310.3_Missense_Mutation_p.V150L|CACNB1_ENST00000344140.5_Missense_Mutation_p.V150L	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	150	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CCCTCCTTCACCAGCCGCCCG	0.572																																					p.V150L	Esophageal Squamous(5;100 366 38393 41452 45827)												.	CACNB1-154	0			c.G448C						.						62	58	59					17																	37343149		2203	4300	6503	SO:0001583	missense	782	exon5			CCTTCACCAGCCG		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.448G>C	17.37:g.37343149C>G	ENSP00000377840:p.Val150Leu	Somatic	108	3		WXS	Illumina HiSeq	Phase_I	115	54	NM_199248	0	0	0	0	0	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Missense_Mutation	SNP	ENST00000394303.3	37	CCDS42311.1	.	.	.	.	.	.	.	.	.	.	C	31	5.061866	0.93846	.	.	ENSG00000067191	ENST00000539338;ENST00000394303;ENST00000344140;ENST00000394310;ENST00000536613	D;D;D	0.83335	-1.71;-1.71;-1.71	5.06	5.06	0.68205	Src homology-3 domain (3);	0.000000	0.85682	D	0.000000	D	0.92166	0.7516	M	0.86420	2.815	0.80722	D	1	P;D;D;P;D	0.64830	0.902;0.984;0.988;0.902;0.994	D;D;D;P;D	0.78314	0.927;0.926;0.991;0.893;0.97	D	0.93547	0.6883	10	0.87932	D	0	-16.2167	17.1868	0.86868	0.0:1.0:0.0:0.0	.	103;150;150;150;150	F5H6X1;Q6TME4;Q02641-2;Q02641-3;Q02641	.;.;.;.;CACB1_HUMAN	L	100;150;150;150;103	ENSP00000377840:V150L;ENSP00000345461:V150L;ENSP00000377847:V150L	ENSP00000345461:V150L	V	-	1	0	CACNB1	34596675	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.711000	0.84669	2.362000	0.80069	0.313000	0.20887	GTG	C|0.999;T|0.001		0.572	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			G	37343149	C	G	37343149	3	3	147	1	0	0	0	0	1	0	0	0	2558	507	18	4	1652	4	CACNB1	17	37343149	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	8728212	37343149	43852061	67	13143											
SLC25A39	51629	broad.mit.edu;bcgsc.ca	37	chr17	42399919	42399919	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggattggagagaggagggCactggggaaaggcagggggc	10	4	23	4	0	0	1	0	0	0	1	0	6	0	5	0	9	0	2	0	9	1	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr17:42399919C>T	ENST00000377095.5	-	5	311	c.192G>A	c.(190-192)ttG>ttA	p.L64L	SLC25A39_ENST00000225308.8_Intron|SLC25A39_ENST00000590194.1_Intron|SLC25A39_ENST00000586016.1_Intron|SLC25A39_ENST00000537904.2_Intron	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	64					heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GAGAGGAGGGCACTGGGGAAA	0.587																																					p.L64L													.	SLC25A39-91	0			c.G192A						.						64	54	58					17																	42399919		2203	4300	6503	SO:0001630	splice_region_variant	51629	exon5			GGAGGGCACTGGG	BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"Solute carriers"	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.191-1G>A	17.37:g.42399919C>T		Somatic	92	2		WXS	Illumina HiSeq	Phase_I	116	64	NM_001143780	0	0	1	1	0	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Silent	SNP	ENST00000377095.5	37	CCDS45700.1																																																																																			.		0.587	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016	Silent	T	42399919	C	T	42399919	5	4	147	1	0	0	0	0	0	0	1	0	14535	724	25	2	919	2	SLC25A39	17	42399919	Splice_Site	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	5056770	42399919	38795291	68	13144											
NACA2	342538	ucsc.edu	37	chr17	59668318	59668318	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacatagccttccgtgccCtcttttcactccgactctgt	5	14	7	15	2	3	0	1	0	2	0	5	2	5	1	4	1	2	0	4	1	1	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr17:59668318C>T	ENST00000521764.1	-	1	245	c.224G>A	c.(223-225)aGg>aAg	p.R75K		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	75	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					CTTCCGTGCCCTCTTTTCACT	0.458																																					p.R75K													.	NACA2-91	0			c.G224A						.						246	229	234					17																	59668318		2203	4300	6503	SO:0001583	missense	342538	exon1			CGTGCCCTCTTTT	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"alpha-NAC protein"	609274	"nascent-polypeptide-associated complex alpha polypeptide-like"	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.224G>A	17.37:g.59668318C>T	ENSP00000427802:p.Arg75Lys	Somatic	121	0		WXS	Illumina HiSeq		189	1	NM_199290	0	0	0	1015	1015	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976583	0.34848	.	.	ENSG00000253506	ENST00000521764	T	0.17528	2.27	0.753	-0.748	0.11087	Nascent polypeptide-associated complex NAC (2);	0.072360	0.50627	N	0.000118	T	0.01489	0.0048	N	0.00010	-3.04	0.23577	N	0.997375	B	0.02656	0.0	B	0.01281	0.0	T	0.46076	-0.9217	9	.	.	.	.	4.0866	0.09950	0.0:0.257:0.0:0.743	.	75	Q9H009	NACA2_HUMAN	K	75	ENSP00000427802:R75K	.	R	-	2	0	NACA2	57023100	1.000000	0.71417	0.973000	0.42090	0.773000	0.43773	3.300000	0.51834	-0.188000	0.10499	-0.624000	0.04008	AGG	.		0.458	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		T	59668318	C	T	59668318	3	4	147	1	0	0	0	0	1	0	0	0	10159	681	24	2	427	2	NACA2	17	59668318	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	17268399	59668318	21526892	69	13145											
AFG3L2	10939	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	12367020	12367020	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagtgatttctctcccggAtctcttgagcagcaagtaaa	11	11	8	11	1	2	2	0	2	2	0	5	3	3	3	2	1	2	3	2	1	4	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr18:12367020A>G	ENST00000269143.3	-	5	727	c.496T>C	c.(496-498)Tcc>Ccc	p.S166P		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	166					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	TCTCTCCCGGATCTCTTGAGC	0.448																																					p.S166P													.	AFG3L2-90	0			c.T496C						.						114	108	110					18																	12367020		2203	4300	6503	SO:0001583	missense	10939	exon5			TCCCGGATCTCTT	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.496T>C	18.37:g.12367020A>G	ENSP00000269143:p.Ser166Pro	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	123	42	NM_006796	0	0	16	28	12	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	37	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.248845	0.39797	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	T	0.78364	-1.17	5.72	5.72	0.89469	Peptidase M41, FtsH extracellular (1);Peptidase M41, FtsH (1);	0.163104	0.56097	D	0.000030	T	0.58337	0.2115	N	0.05441	-0.05	0.46167	D	0.998904	B	0.06786	0.001	B	0.12837	0.008	T	0.55522	-0.8128	10	0.29301	T	0.29	-0.123	10.65	0.45642	0.9197:0.0:0.0803:0.0	.	166	Q9Y4W6	AFG32_HUMAN	P	166;181	ENSP00000269143:S166P	ENSP00000269143:S166P	S	-	1	0	AFG3L2	12357020	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.808000	0.47963	2.182000	0.69389	0.533000	0.62120	TCC	.		0.448	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		G	12367020	A	G	12367020	3	3	147	1	0	0	0	0	1	0	0	0	360	333	12	3	1949	3	AFG3L2	18	12367020	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10		12367020	65710228	70	13146											
MUC16	94025	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9088827	9088827	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagtgaatttagagaccatTacagtagcagagagagaagt	17	8	12	4	0	0	4	0	1	0	3	0	8	0	4	1	0	2	2	1	0	6	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:9088827T>C	ENST00000397910.4	-	1	3191	c.2988A>G	c.(2986-2988)gtA>gtG	p.V996V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	996	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TAGAGACCATTACAGTAGCAG	0.468																																					p.V996V													.	MUC16-566	0			c.A2988G						.						257	242	247					19																	9088827		1979	4156	6135	SO:0001819	synonymous_variant	94025	exon1			GACCATTACAGTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.2988A>G	19.37:g.9088827T>C		Somatic	117	1		WXS	Illumina HiSeq	Phase_I	96	35	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			.		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9088827	T	C	9088827	2	2	147	1	0	0	0	0	0	0	0	1	9998	1741	61	3		3	MUC16	19	9088827	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		9088827	50040156	71	13147											
NKPD1	284353	broad.mit.edu	37	chr19	45655438	45655438	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcggatgagacccatgcGccggcggatggagtggtcca	7	6	17	11	4	0	1	0	1	0	1	2	5	1	4	3	6	1	1	3	6	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:45655438G>T	ENST00000438936.2	-	3	1802	c.1591C>A	c.(1591-1593)Cgc>Agc	p.R531S	NKPD1_ENST00000317951.4_Missense_Mutation_p.R753S|AC005757.7_ENST00000589594.1_lincRNA|NKPD1_ENST00000429338.1_Intron|NKPD1_ENST00000589776.1_Missense_Mutation_p.R531S			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1	531						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		AGACCCATGCGCCGGCGGATG	0.716																																					p.R753S													.	NKPD1-68	0			c.C2257A						.						6	9	8					19																	45655438		1926	4080	6006	SO:0001583	missense	284353	exon4			CCATGCGCCGGCG	AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521	ENST00000438936.2:c.1591C>A	19.37:g.45655438G>T	ENSP00000401739:p.Arg531Ser	Somatic	57	2		WXS	Illumina HiSeq	Phase_I	40	4	NM_198478	0	0	0	0	0	B7ZLG6|D6RH15|Q8N2A2	Missense_Mutation	SNP	ENST00000438936.2	37		.	.	.	.	.	.	.	.	.	.	G	16.14	3.037590	0.54896	.	.	ENSG00000179846	ENST00000317951;ENST00000438936	T;T	0.44083	0.93;0.95	5.43	4.39	0.52855	.	.	.	.	.	T	0.39784	0.1091	L	0.46157	1.445	0.80722	D	1	P	0.52842	0.956	P	0.51866	0.682	T	0.33007	-0.9885	9	0.07644	T	0.81	-10.5324	8.5125	0.33226	0.1757:0.0:0.8243:0.0	.	531	Q17RQ9	NKPD1_HUMAN	S	753;531	ENSP00000321976:R753S;ENSP00000401739:R531S	ENSP00000321976:R753S	R	-	1	0	NKPD1	50347278	0.989000	0.36119	1.000000	0.80357	0.986000	0.74619	1.381000	0.34362	1.292000	0.44672	0.561000	0.74099	CGC	.		0.716	NKPD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000360950.2	NM_198478		T	45655438	G	T	45655438	3	4	147	1	0	0	0	0	1	0	0	0	10472	1087	38	4	245	4	NKPD1	19	45655438	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	36566611	45655438	13473545	72	13148											
ZNF677	342926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	53740610	53740610	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttattacatttgtaaggtTtttctccagtgtgaattctc	9	20	6	6	0	2	1	0	1	2	0	4	1	2	1	1	1	1	2	1	1	4	8			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:53740610T>C	ENST00000598513.1	-	5	1520	c.1370A>G	c.(1369-1371)aAa>aGa	p.K457R	ZNF677_ENST00000333952.4_Missense_Mutation_p.K457R	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	457					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)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		TTTGTAAGGTTTTTCTCCAGT	0.378																																					p.K457R		.											.	ZNF677-91	0			c.A1370G						.						54	52	53					19																	53740610		2203	4300	6503	SO:0001583	missense	342926	exon5			TAAGGTTTTTCTC	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"Zinc fingers, C2H2-type", "-"	28730	protein-coding gene	gene with protein product	"hypothetical protein MGC48625"					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1370A>G	19.37:g.53740610T>C	ENSP00000469391:p.Lys457Arg	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	80	23	NM_182609	0	0	0	0	0		Missense_Mutation	SNP	ENST00000598513.1	37	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.227295	0.58668	.	.	ENSG00000197928	ENST00000333952	T	0.24908	1.83	2.21	1.14	0.20703	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37393	N	0.002104	T	0.26085	0.0636	N	0.13272	0.32	0.25071	N	0.990998	D	0.67145	0.996	D	0.69142	0.962	T	0.05194	-1.0900	10	0.72032	D	0.01	.	6.5871	0.22626	0.0:0.0:0.2456:0.7543	.	457	Q86XU0	ZN677_HUMAN	R	457	ENSP00000334394:K457R	ENSP00000334394:K457R	K	-	2	0	ZNF677	58432422	0.880000	0.30214	0.998000	0.56505	0.997000	0.91878	0.417000	0.21214	0.277000	0.22141	0.533000	0.62120	AAA	.		0.378	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		C	53740610	T	C	53740610	3	2	147	1	0	0	0	0	1	0	0	0	18116	1841	64	3	388	3	ZNF677	19	53740610	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	8085172	53740610	5388373	73	13149											
LILRA5	353514	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54822787	54822787	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgtggctgggggtcacAgggcccacagggaacagggc	8	4	17	12	0	1	0	1	0	0	0	1	1	1	1	2	6	1	1	2	6	1	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:54822787A>C	ENST00000301219.3	-	5	728	c.609T>G	c.(607-609)ccT>ccG	p.P203P	AC008984.2_ENST00000507363.1_RNA|LILRA5_ENST00000432233.3_Silent_p.P203P|LILRA5_ENST00000346508.3_Silent_p.P191P|LILRA5_ENST00000446712.3_Silent_p.P191P	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	203	Ig-like C2-type 2.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGGGGTCACAGGGCCCACAG	0.592																																					p.P203P													.	LILRA5-91	0			c.T609G						.						54	56	55					19																	54822787		2203	4300	6503	SO:0001819	synonymous_variant	353514	exon5			GGTCACAGGGCCC	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.609T>G	19.37:g.54822787A>C		Somatic	99	1		WXS	Illumina HiSeq	Phase_I	102	36	NM_181879	0	0	2	2	0	A6NHI3	Silent	SNP	ENST00000301219.3	37	CCDS12888.1																																																																																			.		0.592	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		C	54822787	A	C	54822787	2	2	147	1	0	0	0	0	0	0	0	1	8810	175	7	5		5	LILRA5	19	54822787	Silent	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	1082177	54822787	4306196	74	13150											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		.											.	.	0			c.C968A						.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	115	8	NM_001144989	0	0	1	1	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	147	1	0	0	0	0	1	0	0	0	18208	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	3563003	58385790	743193	75	13151	137	3									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		.											.	.	0			c.G965A						.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	107	8	NM_001144989	0	0	1	1	0	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	147	1	0	0	0	0	1	0	0	0	18208	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	3	58385793	743190	76	13152	137	3									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385798	58385799	+	Missense_Mutation	DNP	CC	CC	TT																															ccacattcataaggtcttttCccagtgtgaactctctgatg																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:58385798_58385799CC>TT	ENST00000435989.2	-	3	1193_1194	c.959_960GG>AA	c.(958-960)gGG>gAA	p.G320E	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	320					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G320E(1)|p.G320G(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AAGGTCTTTTCCCAGTGTGAAC	0.356																																					p.G320E		.											.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	central_nervous_system(2)	c.G959A						.																																			SO:0001583	missense	730051	exon3			CTTTTCCCAGTGT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.959_960delinsTT	19.37:g.58385798_58385799delinsTT	ENSP00000410545:p.Gly320Glu	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	99	7	NM_001144989	0	0	0	0	0	A6NF35	Missense_Mutation	DNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.356	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		TT	58385799	CC	TT	58385798	3	4	147	1	0	0	0	0	1	0	0	0	18208	842	30	2	1611	2	ZNF814	19	58385798	Missense_Mutation	DNP	CC	TCGA-KV-A6GE-01A-11D-A31X-10	5	58385798	743185	77	13153	137	3									
ZNF814	730051	bcgsc.ca	37	chr19	58385873	58385873	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacattctccacattcatgTtttttttcagtgtgaactct	8	18	4	11	0	4	1	2	1	2	0	5	1	4	1	2	0	1	1	2	0	1	6	rs397978905	byFrequency	TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:58385873T>C	ENST00000435989.2	-	3	1119	c.885A>G	c.(883-885)aaA>aaG	p.K295K	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	295					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CACATTCATGTTTTTTTTCAG	0.358																																					p.K295K													.	.	0			c.A885G						.						17	13	14					19																	58385873		687	1561	2248	SO:0001819	synonymous_variant	730051	exon3			TTCATGTTTTTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.885A>G	19.37:g.58385873T>C		Somatic	47	3		WXS	Illumina HiSeq	Phase_1	33	8	NM_001144989	0	0	0	0	0	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		C	58385873	T	C	58385873	2	2	147	1	0	0	0	0	0	0	0	1	18208	1722	60	3		3	ZNF814	19	58385873	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	75	58385873	743110	78	13154											
AHCY	191	broad.mit.edu	37	chr20	32873357	32873357	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcatcacgaagctggggtgGcccatggcacaacccaggtt	9	7	12	13	1	2	0	2	0	0	0	2	1	2	0	2	5	2	3	2	5	2	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr20:32873357G>T	ENST00000217426.2	-	9	1133	c.1056C>A	c.(1054-1056)ggC>ggA	p.G352G	CTD-3216D2.5_ENST00000609218.1_RNA|AHCY_ENST00000538132.1_Silent_p.G324G	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	352					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						AGCTGGGGTGGCCCATGGCAC	0.607																																					p.G352G													.	AHCY-91	0			c.C1056A						.						81	69	73					20																	32873357		2203	4300	6503	SO:0001819	synonymous_variant	191	exon9			GGGGTGGCCCATG	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.1056C>A	20.37:g.32873357G>T		Somatic	89	2		WXS	Illumina HiSeq	Phase_I	85	7	NM_000687	0	0	105	117	12	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Silent	SNP	ENST00000217426.2	37	CCDS13233.1																																																																																			.		0.607	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		T	32873357	G	T	32873357	2	4	147	1	0	0	0	0	0	0	0	1	409	1190	42	4		4	AHCY	20	32873357	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		32873357	30152163	79	13155											
C20orf132	140699	broad.mit.edu;bcgsc.ca	37	chr20	35772168	35772168	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcatttagcggcagagctGtggagctccaggaattctcg	10	9	13	9	2	1	1	0	0	1	1	3	3	2	3	1	3	4	4	1	3	3	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr20:35772168G>A	ENST00000400441.3	-	11	1286	c.1287C>T	c.(1285-1287)caC>caT	p.H429H	MROH8_ENST00000217333.8_Silent_p.H309H|MROH8_ENST00000441008.2_Silent_p.H415H			Q9H579	MROH8_HUMAN	maestro heat-like repeat family member 8	314																	CGGCAGAGCTGTGGAGCTCCA	0.383																																					.													.	.	0			.						.						64	59	61					20																	35772168		1841	4088	5929	SO:0001819	synonymous_variant	140699	.			AGAGCTGTGGAGC	AL136172		20q11.22	2012-12-19	2012-12-19	2012-12-19	ENSG00000101353	ENSG00000101353		"maestro heat-like repeat containing"	16125	protein-coding gene	gene with protein product	"hypothetical protein LOC140699"		"chromosome 20 open reading frame 131", "chromosome 20 open reading frame 132"	C20orf131, C20orf132		11780052, 15635413	Standard	NM_152503		Approved	dJ621N11.4, dJ621N11.3	uc010zvu.2	Q9H579	OTTHUMG00000032407	ENST00000400441.3:c.1287C>T	20.37:g.35772168G>A		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	173	8	.	0	0	2	2	0	Q5JYQ6	Silent	SNP	ENST00000400441.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.008|0.008	-1.910082|-1.910082	0.00508|0.00508	.|.	.|.	ENSG00000101353|ENSG00000101353	ENST00000417458;ENST00000421643|ENST00000343811;ENST00000400440	.|.	.|.	.|.	5.19|5.19	-0.111|-0.111	0.13576|0.13576	.|.	.|.	.|.	.|.	.|.	.|T	.|0.31575	.|0.0801	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.29305	.|-1.0016	.|4	.|.	.|.	.|.	-0.5771|-0.5771	7.5762|7.5762	0.27937|0.27937	0.4617:0.0:0.5383:0.0|0.4617:0.0:0.5383:0.0	.|.	.|.	.|.	.|.	X|I	108;431|456;460	.|.	.|.	Q|T	-|-	1|2	0|0	C20orf132|C20orf132	35205582|35205582	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.368000|0.368000	0.20399|0.20399	-0.051000|-0.051000	0.13334|0.13334	-0.768000|-0.768000	0.03414|0.03414	CAG|ACA	.		0.383	MROH8-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152503		A	35772168	G	A	35772168	2	1	147	1	0	0	0	0	0	0	0	1	2092	1368	48	2		2	C20orf132	20	35772168	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	2898811	35772168	27253352	80	13156											
TRAPPC10	7109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45502876	45502876	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctaccggaagactgcggagtGgcttaccaagcacaagacgt	12	6	12	11	3	0	2	0	0	0	2	0	4	0	4	2	3	4	2	2	3	5	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr21:45502876G>A	ENST00000291574.4	+	14	2106	c.1931G>A	c.(1930-1932)tGg>tAg	p.W644*		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	644					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACTGCGGAGTGGCTTACCAAG	0.512																																					p.W644X		.											.	TRAPPC10-92	0			c.G1931A						.						162	150	154					21																	45502876		2203	4300	6503	SO:0001587	stop_gained	7109	exon14			CGGAGTGGCTTAC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"Trafficking protein particle complex"	11868	protein-coding gene	gene with protein product	"trafficking protein particle complex subunit 130", "TRAPP 130 kDa subunit"	602103	"transmembrane protein 1"	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1931G>A	21.37:g.45502876G>A	ENSP00000291574:p.Trp644*	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	67	32	NM_003274	0	0	0	1	1	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Nonsense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	G	38	7.254018	0.98168	.	.	ENSG00000160218	ENST00000291574	.	.	.	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	19.1791	0.93615	0.0:0.0:1.0:0.0	.	.	.	.	X	644	.	ENSP00000291574:W644X	W	+	2	0	TRAPPC10	44327304	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	5.397000	0.66302	2.622000	0.88805	0.655000	0.94253	TGG	.		0.512	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		A	45502876	G	A	45502876	4	1	147	1	0	0	0	0	0	1	0	0	16490	1357	47	2	1985	2	TRAPPC10	21	45502876	Nonsense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		45502876	2627019	81	13157											
CELSR1	9620	broad.mit.edu	37	chr22	46763676	46763676	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaagctcagtgcatcgcGgttcacagccagcagcccca	10	6	11	14	2	2	1	2	1	0	0	3	1	2	1	3	1	5	4	3	1	1	1	rs367719288		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr22:46763676G>T	ENST00000262738.3	-	28	8028	c.8029C>A	c.(8029-8031)Cgc>Agc	p.R2677S		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2677					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGTGCATCGCGGTTCACAGCC	0.657											OREG0026655	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R2677S													.	CELSR1-525	0			c.C8029A						.						41	36	38					22																	46763676		2198	4298	6496	SO:0001583	missense	9620	exon28			CATCGCGGTTCAC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	1850	protein-coding gene	gene with protein product	"flamingo homolog 2 (Drosophila)"	604523	"cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8029C>A	22.37:g.46763676G>T	ENSP00000262738:p.Arg2677Ser	Somatic	126	1	941	WXS	Illumina HiSeq	Phase_I	116	6	NM_014246	0	0	6	6	0	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	g	0.561	-0.845056	0.02671	.	.	ENSG00000075275	ENST00000262738	T	0.36520	1.25	4.94	-4.58	0.03410	GPCR, family 2-like (1);	0.067050	0.64402	N	0.000020	T	0.06371	0.0164	N	0.00332	-1.63	0.80722	D	1	B	0.11235	0.004	B	0.12156	0.007	T	0.33828	-0.9853	10	0.09084	T	0.74	.	6.9268	0.24419	0.0:0.3515:0.2591:0.3894	.	2677	Q9NYQ6	CELR1_HUMAN	S	2677	ENSP00000262738:R2677S	ENSP00000262738:R2677S	R	-	1	0	CELSR1	45142340	0.862000	0.29867	0.221000	0.23827	0.298000	0.27526	0.959000	0.29240	-1.070000	0.03149	-0.546000	0.04227	CGC	.		0.657	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46763676	G	T	46763676	3	4	147	1	0	0	0	0	1	0	0	0	3227	1116	39	4	1047	4	CELSR1	22	46763676	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		46763676	4540890	82	13158											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19482811	19482811	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctaactcggtctgtgaaccaGgtaaccacacggctttgatg	10	10	10	11	2	1	2	0	2	1	0	2	2	1	2	2	3	3	2	2	3	3	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:19482811G>A	ENST00000375254.3	-	42	6053	c.6026C>T	c.(6025-6027)cCt>cTt	p.P2009L	UBR4_ENST00000375267.2_Missense_Mutation_p.P2009L|UBR4_ENST00000375217.2_Missense_Mutation_p.P2009L|UBR4_ENST00000375226.2_Missense_Mutation_p.P2009L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2009					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CTGTGAACCAGGTAACCACAC	0.438																																					p.P2009L		.											.	UBR4-612	0			c.C6026T						.						139	122	128					1																	19482811		2203	4300	6503	SO:0001583	missense	23352	exon42			GAACCAGGTAACC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6026C>T	1.37:g.19482811G>A	ENSP00000364403:p.Pro2009Leu	Somatic	474	1		WXS	Illumina HiSeq	Phase_I	418	155	NM_020765	0	0	6	9	3	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	34	5.380190	0.95945	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;2.69	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.63402	0.2508	M	0.87827	2.91	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.68800	-0.5313	10	0.87932	D	0	.	19.3843	0.94550	0.0:0.0:1.0:0.0	.	2009	Q5T4S7	UBR4_HUMAN	L	2009;2009;2009;2009;719;1225	ENSP00000364403:P2009L;ENSP00000364416:P2009L;ENSP00000364365:P2009L;ENSP00000364374:P2009L;ENSP00000404897:P719L	ENSP00000364365:P2009L	P	-	2	0	UBR4	19355398	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.969000	0.93411	2.814000	0.96858	0.591000	0.81541	CCT	.		0.438	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19482811	G	A	19482811	3	1	148	1	0	0	0	0	1	0	0	0	16937	1000	35	2	9785	2	UBR4	1	19482811	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		19482811	229767810	1	13159											
ADPRHL2	54936	broad.mit.edu	37	chr1	36557328	36557328	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgatgtctttgagcctgccCgggcccagtttaacgggaaa	8	9	13	11	3	1	1	0	1	1	0	1	3	1	2	3	2	3	1	3	2	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:36557328C>T	ENST00000373178.4	+	3	448	c.418C>T	c.(418-420)Cgg>Tgg	p.R140W		NM_017825.2	NP_060295.1	Q9NX46	ARHL2_HUMAN	ADP-ribosylhydrolase like 2	140						mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(ADP-ribose) glycohydrolase activity (GO:0004649)			cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|pancreas(1)	8		Myeloproliferative disorder(586;0.0393)				TGAGCCTGCCCGGGCCCAGTT	0.562																																					p.R140W													.	ADPRHL2-91	0			c.C418T						.						78	82	81					1																	36557328		2203	4300	6503	SO:0001583	missense	54936	exon3			CCTGCCCGGGCCC	AJ427295	CCDS402.1	1p34.3	2008-02-05			ENSG00000116863	ENSG00000116863			21304	protein-coding gene	gene with protein product		610624				12070318, 16278211	Standard	NM_017825		Approved	ARH3, FLJ20446	uc001bzt.3	Q9NX46	OTTHUMG00000007628	ENST00000373178.4:c.418C>T	1.37:g.36557328C>T	ENSP00000362273:p.Arg140Trp	Somatic	111	1		WXS	Illumina HiSeq	Phase_I	104	5	NM_017825	0	0	20	20	0	Q53G94|Q6IAB8|Q9BY47	Missense_Mutation	SNP	ENST00000373178.4	37	CCDS402.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703805	0.68501	.	.	ENSG00000116863	ENST00000373178;ENST00000540867	T	0.31247	1.5	5.35	3.38	0.38709	.	0.105277	0.64402	D	0.000009	T	0.52306	0.1726	M	0.71296	2.17	0.33910	D	0.639556	D	0.89917	1.0	D	0.75484	0.986	T	0.65158	-0.6236	10	0.46703	T	0.11	-17.9963	13.2367	0.59972	0.5987:0.4013:0.0:0.0	.	140	Q9NX46	ARHL2_HUMAN	W	140;60	ENSP00000362273:R140W	ENSP00000362273:R140W	R	+	1	2	ADPRHL2	36329915	0.841000	0.29509	0.996000	0.52242	0.970000	0.65996	1.654000	0.37334	0.544000	0.28883	0.563000	0.77884	CGG	.		0.562	ADPRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020199.1	NM_017825		T	36557328	C	T	36557328	3	4	148	1	0	0	0	0	1	0	0	0	333	643	23	1	428	1	ADPRHL2	1	36557328	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	17074517	36557328	212693293	2	13160											
STK40	83931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36820910	36820910	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtagtgctgcaggttgatgAggtcagcggtcttatcgctg	6	12	15	8	3	2	2	1	2	1	0	3	2	2	2	0	3	3	5	0	3	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:36820910A>T	ENST00000373129.3	-	6	873	c.467T>A	c.(466-468)cTc>cAc	p.L156H	STK40_ENST00000359297.2_Missense_Mutation_p.L156H|STK40_ENST00000482458.1_5'UTR|STK40_ENST00000373130.3_Missense_Mutation_p.L161H|STK40_ENST00000373132.3_Missense_Mutation_p.L156H	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CAGGTTGATGAGGTCAGCGGT	0.557																																					p.L156H		.											.	STK40-83	0			c.T467A						.						278	239	252					1																	36820910		2203	4300	6503	SO:0001583	missense	83931	exon6			TTGATGAGGTCAG	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.467T>A	1.37:g.36820910A>T	ENSP00000362221:p.Leu156His	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	187	66	NM_032017	0	0	6	7	1	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.006207	0.93287	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.69175	-0.38;1.96;1.96;-0.38	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064019	0.64402	D	0.000004	D	0.87200	0.6118	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.958;0.975	D	0.90870	0.4745	10	0.87932	D	0	-15.2233	15.5237	0.75885	1.0:0.0:0.0:0.0	.	156;161;156	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	H	156;156;161;156	ENSP00000362221:L156H;ENSP00000352245:L156H;ENSP00000362222:L161H;ENSP00000362224:L156H	ENSP00000352245:L156H	L	-	2	0	STK40	36593497	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	8.857000	0.92250	2.263000	0.75096	0.379000	0.24179	CTC	.		0.557	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		T	36820910	A	T	36820910	3	4	148	1	0	0	0	0	1	0	0	0	15339	304	11	5	868	5	STK40	1	36820910	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	263582	36820910	212429711	3	13161											
KIAA0754	643314	broad.mit.edu	37	chr1	39880152	39880152	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggattaaattcagatgaggtAattgtccattttgattctgg	11	16	10	4	0	2	3	1	2	1	1	3	4	3	4	1	3	0	1	1	3	3	7			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:39880152A>T	ENST00000530275.1	+	1	4002	c.3807A>T	c.(3805-3807)gtA>gtT	p.V1269V	MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000564288.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1269										central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGATGAGGTAATTGTCCATT	0.443																																					p.V1405V													.	.	0			c.A4215T						.						78	80	79					1																	39880152		1941	4140	6081	SO:0001819	synonymous_variant	643314	exon1			TGAGGTAATTGTC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3807A>T	1.37:g.39880152A>T		Somatic	67	2		WXS	Illumina HiSeq	Phase_I	89	22	NM_015038	0	0	0	0	0	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				.		0.443	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39880152	A	T	39880152	2	4	148	1	0	0	0	0	0	0	0	1	8213	349	13	5		5	KIAA0754	1	39880152	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	3059242	39880152	209370469	4	13162											
HSPB11	51668	broad.mit.edu;bcgsc.ca	37	chr1	54395757	54395757	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaatccttacatgtttgtGgaaacaaataatgaattcct	14	15	5	7	0	1	1	1	1	0	0	3	2	3	2	2	1	2	1	2	1	6	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:54395757G>A	ENST00000194214.5	-	3	549	c.160C>T	c.(160-162)Cac>Tac	p.H54Y	HSPB11_ENST00000489675.1_5'Flank|HSPB11_ENST00000371378.2_Missense_Mutation_p.H54Y|HSPB11_ENST00000371377.3_Missense_Mutation_p.H54Y|HSPB11_ENST00000371376.1_Missense_Mutation_p.H54Y	NM_016126.2	NP_057210.2	Q9Y547	IFT25_HUMAN	heat shock protein family B (small), member 11	54					cell adhesion (GO:0007155)|heart development (GO:0007507)|left/right axis specification (GO:0070986)|lung development (GO:0030324)|protein transport (GO:0015031)|response to stress (GO:0006950)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle B (GO:0030992)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	9						ACATGTTTGTGGAAACAAATA	0.318																																					p.H54Y													.	HSPB11-90	0			c.C160T						.						91	86	88					1																	54395757		1801	4066	5867	SO:0001583	missense	51668	exon3			GTTTGTGGAAACA	AF100747	CCDS41341.1	1p32	2014-02-21	2008-06-24	2008-06-24	ENSG00000081870	ENSG00000081870		"Intraflagellar transport homologs", "Heat shock proteins / HSPB"	25019	protein-coding gene	gene with protein product	"intraflagellar transport 25 homolog (Chlamydomonas)"		"chromosome 1 open reading frame 41"	C1orf41		11042152, 19253336	Standard	NM_016126		Approved	HSPCO34, PP25, IFT25	uc001cwh.3	Q9Y547	OTTHUMG00000008408	ENST00000194214.5:c.160C>T	1.37:g.54395757G>A	ENSP00000194214:p.His54Tyr	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	132	5	NM_016126	0	0	10	10	0	A6NG57|D3DQ45|Q9Y684	Missense_Mutation	SNP	ENST00000194214.5	37	CCDS41341.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723851	0.68959	.	.	ENSG00000081870	ENST00000194214;ENST00000371378;ENST00000371377;ENST00000371376	D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78	5.96	5.96	0.96718	Coagulation factor 5/8 C-terminal type domain (1);Galactose-binding domain-like (1);	0.284349	0.38959	N	0.001502	D	0.98286	0.9432	L	0.51422	1.61	0.37457	D	0.915078	P;P	0.52463	0.953;0.871	D;P	0.63793	0.918;0.538	D	0.99932	1.1332	10	0.59425	D	0.04	-15.3098	15.9014	0.79380	0.0:0.0:1.0:0.0	.	54;54	A6NIR2;Q9Y547	.;HSB11_HUMAN	Y	54	ENSP00000194214:H54Y;ENSP00000360429:H54Y;ENSP00000360428:H54Y;ENSP00000360427:H54Y	ENSP00000194214:H54Y	H	-	1	0	HSPB11	54168345	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	3.202000	0.51067	2.833000	0.97629	0.591000	0.81541	CAC	.		0.318	HSPB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023114.1	NM_016126		A	54395757	G	A	54395757	3	1	148	1	0	0	0	0	1	0	0	0	7440	1348	47	2	290	2	HSPB11	1	54395757	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	14515605	54395757	194854864	5	13163											
CELSR2	1952	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	109807154	109807154	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagcatcaacgtggagcaaGgctgtagcctgcctgaccct	10	7	12	12	1	1	2	1	1	0	1	1	3	1	3	3	2	5	4	3	2	3	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:109807154G>A	ENST00000271332.3	+	11	5429	c.5368G>A	c.(5368-5370)Ggc>Agc	p.G1790S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1790	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CGTGGAGCAAGGCTGTAGCCT	0.587																																					p.G1790S	NSCLC(158;1285 2011 34800 34852 42084)	.											.	CELSR2-526	0			c.G5368A						.						190	170	177					1																	109807154		2203	4300	6503	SO:0001583	missense	1952	exon11			GAGCAAGGCTGTA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans"	3231	protein-coding gene	gene with protein product		604265	"cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.5368G>A	1.37:g.109807154G>A	ENSP00000271332:p.Gly1790Ser	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	126	50	NM_001408	0	0	6	10	4	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643501	0.87859	.	.	ENSG00000143126	ENST00000271332	D	0.87179	-2.22	4.79	4.79	0.61399	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	D	0.93190	0.7831	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93620	0.6947	9	0.62326	D	0.03	.	18.0161	0.89241	0.0:0.0:1.0:0.0	.	1790	Q9HCU4	CELR2_HUMAN	S	1790	ENSP00000271332:G1790S	ENSP00000271332:G1790S	G	+	1	0	CELSR2	109608677	1.000000	0.71417	0.996000	0.52242	0.712000	0.41017	9.202000	0.95026	2.504000	0.84457	0.561000	0.74099	GGC	.		0.587	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109807154	G	A	109807154	3	1	148	1	0	0	0	0	1	0	0	0	3228	1000	35	2	5410	2	CELSR2	1	109807154	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	55411397	109807154	139443467	6	13164											
ADAMTSL4	54507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	150531493	150531493	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtggtctgccttgggaGtggggcagccctcgggccag	3	9	17	12	1	2	0	0	0	2	0	3	1	2	1	3	5	2	1	3	5	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:150531493G>T	ENST00000369038.2	+	14	2816	c.2615G>T	c.(2614-2616)aGt>aTt	p.S872I	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.S895I|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.S872I			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	872	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			TGCCTTGGGAGTGGGGCAGCC	0.692																																					p.S872I		.											.	ADAMTSL4-92	0			c.G2615T						.						15	19	18					1																	150531493		2201	4296	6497	SO:0001583	missense	54507	exon16			TTGGGAGTGGGGC	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"thrombospondin repeat containing 1"	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2615G>T	1.37:g.150531493G>T	ENSP00000358034:p.Ser872Ile	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	29	19	NM_019032	0	0	2	5	3	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525215	0.64747	.	.	ENSG00000143382	ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038	T;T;T	0.60797	0.16;0.16;0.16	5.63	5.63	0.86233	.	.	.	.	.	T	0.66973	0.2844	L	0.53617	1.68	0.46564	D	0.999104	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.74674	0.981;0.984;0.973	T	0.68315	-0.5441	9	0.62326	D	0.03	.	17.1708	0.86830	0.0:0.0:1.0:0.0	.	833;895;872	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	I	872;410;895;872	ENSP00000271643:S872I;ENSP00000358035:S895I;ENSP00000358034:S872I	ENSP00000271643:S872I	S	+	2	0	ADAMTSL4	148798117	0.765000	0.28485	0.987000	0.45799	0.293000	0.27360	2.637000	0.46553	2.655000	0.90218	0.462000	0.41574	AGT	.		0.692	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		T	150531493	G	T	150531493	3	4	148	1	0	0	0	0	1	0	0	0	277	1029	36	4	2744	4	ADAMTSL4	1	150531493	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	40724339	150531493	98719128	7	13165											
TCHHL1	126637	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152059687	152059687	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcttctctccatgggtcCactctgttatttccaactgc	5	16	7	13	0	2	0	0	0	2	0	6	0	5	0	3	2	2	2	3	2	2	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:152059687C>T	ENST00000368806.1	-	3	535	c.471G>A	c.(469-471)gtG>gtA	p.V157V		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	157							calcium ion binding (GO:0005509)			breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TCCATGGGTCCACTCTGTTAT	0.453																																					p.V157V													.	TCHHL1-92	0			c.G471A						.						131	118	122					1																	152059687		2203	4300	6503	SO:0001819	synonymous_variant	126637	exon3			TGGGTCCACTCTG		CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"S100 calcium binding proteins"	31796	protein-coding gene	gene with protein product			"S100 calcium binding protein A17"	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.471G>A	1.37:g.152059687C>T		Somatic	180	1		WXS	Illumina HiSeq	Phase_I	175	54	NM_001008536	0	0	0	0	0	B2RPK8|Q5VTJ9	Silent	SNP	ENST00000368806.1	37	CCDS30857.1																																																																																			.		0.453	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		T	152059687	C	T	152059687	2	4	148	1	0	0	0	0	0	0	0	1	15733	581	21	2		2	TCHHL1	1	152059687	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	1528194	152059687	97190934	8	13166											
KCNN3	3782	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154744543	154744543	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gggcagatggtcatgagcgtCttcatgacaaagcgggtgtt	9	10	15	7	2	3	3	2	2	1	1	3	3	3	3	0	3	2	2	0	3	1	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:154744543C>T	ENST00000271915.4	-	3	1671	c.1356G>A	c.(1354-1356)aaG>aaA	p.K452K	KCNN3_ENST00000361147.4_Silent_p.K147K|KCNN3_ENST00000358505.2_Silent_p.K139K	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	457					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	TCATGAGCGTCTTCATGACAA	0.562																																					p.K452K													.	KCNN3-91	0			c.G1356A						.						141	105	117					1																	154744543		2203	4300	6503	SO:0001819	synonymous_variant	3782	exon3			GAGCGTCTTCATG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.1356G>A	1.37:g.154744543C>T		Somatic	167	1		WXS	Illumina HiSeq	Phase_I	122	50	NM_001204087	0	0	0	0	0	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.		0.562	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154744543	C	T	154744543	2	4	148	1	0	0	0	0	0	0	0	1	8101	912	32	2		2	KCNN3	1	154744543	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	2684856	154744543	94506078	9	13167											
ROBLD3	28956	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	156027791	156027791	+	Frame_Shift_Del	DEL	G	G	-																															gggccgtgtagccatcacccGagtggccaaccttctgctgt																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:156027791delG	ENST00000368305.4	+	3	392	c.254delG	c.(253-255)cgafs	p.R85fs	LAMTOR2_ENST00000368302.3_Frame_Shift_Del_p.R85fs|LAMTOR2_ENST00000368304.5_Intron	NM_014017.3	NP_054736.1	Q9Y2Q5	LTOR2_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	85					activation of MAPKK activity (GO:0000186)|cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|Ragulator complex (GO:0071986)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7						GCCATCACCCGAGTGGCCAAC	0.577																																					p.R85fs		.											.	LAMTOR2-523	0			c.254delG						.						205	152	170					1																	156027791		2203	4300	6503	SO:0001589	frameshift_variant	28956	exon3			.	BC024190	CCDS1128.1, CCDS44243.1	1q22	2014-09-17	2011-02-15	2011-02-15	ENSG00000116586	ENSG00000116586			29796	protein-coding gene	gene with protein product	"mitogen activated protein binding protein interacting protein", "MAPKSP1 adaptor protein", "endosomal adaptor protein"	610389	"roadblock domain containing 3"	ROBLD3		11042152	Standard	NM_014017		Approved	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2	uc001fnb.3	Q9Y2Q5	OTTHUMG00000017462	ENST00000368305.4:c.254delG	1.37:g.156027791delG	ENSP00000357288:p.Arg85fs	Somatic	311	0		WXS	Illumina HiSeq	Phase_I	315	118	NM_014017	0	0	0	0	0	Q5VY97|Q5VY98|Q5VY99	Frame_Shift_Del	DEL	ENST00000368305.4	37	CCDS1128.1																																																																																			.		0.577	LAMTOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046197.1	NM_014017		-	156027791	G	-	156027791	7	5	148	1	0	1	0	1	0	0	0	0	13544	1058	37	0	264	0	ROBLD3	1	156027791	Frame_Shift_Del	DEL	G	TCGA-MH-A55W-01A-11D-A26P-10	1283248	156027791	93222830	10	13168											
ELK4	2005	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	205588957	205588957	+	Intron	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgagaaatggggtaactttCacatgacagtcacacataac	16	9	8	8	0	2	2	2	2	0	1	2	3	2	2	0	2	2	1	0	2	3	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:205588957C>G	ENST00000357992.4	-	3	1420				ELK4_ENST00000289703.4_Nonstop_Mutation_p.*406S|ELK4_ENST00000468523.1_5'Flank	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)						cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			GGGTAACTTTCACATGACAGT	0.289			T	SLC45A3	prostate																																p.X406S		.		Dom	yes		1	1q32	2005	"ELK4, ETS-domain protein (SRF accessory protein 1)"		E	.	ELK4-658	0			c.G1217C						.						48	48	48					1																	205588957		2203	4300	6503	SO:0001627	intron_variant	2005	exon3			AACTTTCACATGA	M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.1080+136G>C	1.37:g.205588957C>G		Somatic	58	0		WXS	Illumina HiSeq	Phase_I	75	27	NM_021795	0	0	1	1	0	P28323|Q6GSJ2	Missense_Mutation	SNP	ENST00000357992.4	37	CCDS1456.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744796	0.30865	.	.	ENSG00000158711	ENST00000289703	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5541	0.61749	0.0:1.0:0.0:0.0	.	.	.	.	S	406	.	.	X	-	2	2	ELK4	203855580	0.000000	0.05858	0.860000	0.33809	0.233000	0.25261	0.118000	0.15605	2.344000	0.79699	0.655000	0.94253	TGA	.		0.289	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795		G	205588957	C	G	205588957	1	3	148	0	1	0	0	0	0	0	0	0	5074	837	29	4		4	ELK4	1	205588957	Intron	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	49561166	205588957	43661664	11	13169											
OR13G1	441933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	247836182	247836183	+	Missense_Mutation	DNP	CG	CG	AA																															agaaggaaaacatacatgggCgtatgcaaggtgttgttata																								rs200763482	byFrequency	TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:247836182_247836183CG>AA	ENST00000359688.2	-	1	182_183	c.161_162CG>TT	c.(160-162)aCG>aTT	p.T54I	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	54						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T54M(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CATACATGGGCGTATGCAAGGT	0.421																																					p.T54I		.											.	OR13G1-69	1	Substitution - Missense(1)	endometrium(1)	c.C161T						.																																			SO:0001583	missense	441933	exon1			ATGGGCGTATGCA	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"GPCR / Class A : Olfactory receptors"	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.161_162delinsAA	1.37:g.247836182_247836183delinsAA	ENSP00000352717:p.Thr54Ile	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	155	51	NM_001005487	0	0	0	0	0	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	DNP	ENST00000359688.2	37	CCDS31094.1																																																																																			G|0.999;A|0.000		0.421	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		AA	247836183	CG	AA	247836182	3	1	148	1	0	0	0	0	1	0	0	0	10968	755	27	4	765	4	OR13G1	1	247836182	Missense_Mutation	DNP	CG	TCGA-MH-A55W-01A-11D-A26P-10	42247225	247836182	1414439	12	13170											
GEN1	348654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	17962535	17962535	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttacaaaattatcatatcctCaggataatctacaaccagat	17	12	3	9	0	3	1	2	0	1	1	4	2	4	2	2	1	3	0	2	1	8	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:17962535C>G	ENST00000381254.2	+	14	2270	c.2056C>G	c.(2056-2058)Cag>Gag	p.Q686E	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Missense_Mutation_p.Q686E	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	686					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)					ATCATATCCTCAGGATAATCT	0.348								Homologous recombination																													p.Q686E		.											.	GEN1-359	0			c.C2056G						.						75	82	79					2																	17962535		2203	4300	6503	SO:0001583	missense	348654	exon14			TATCCTCAGGATA	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.2056C>G	2.37:g.17962535C>G	ENSP00000370653:p.Gln686Glu	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	108	54	NM_182625	0	0	1	1	0	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	37	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	C	2.631	-0.286254	0.05605	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000536097	T;T	0.24723	1.84;1.84	5.41	2.48	0.30137	.	0.967756	0.08453	N	0.943658	T	0.25494	0.0620	M	0.62723	1.935	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.31888	-0.9927	10	0.59425	D	0.04	0.3588	4.3539	0.11169	0.1364:0.6005:0.1325:0.1307	.	686	Q17RS7	GEN_HUMAN	E	686;686;323	ENSP00000318977:Q686E;ENSP00000370653:Q686E	ENSP00000318977:Q686E	Q	+	1	0	GEN1	17826016	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.195000	0.17155	0.717000	0.32145	0.655000	0.94253	CAG	.		0.348	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		G	17962535	C	G	17962535	3	3	148	1	0	0	0	0	1	0	0	0	6355	827	29	4	2106	4	GEN1	2	17962535	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		17962535	225236838	13	13171											
ITSN2	50618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	24469667	24469667	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattaacccacttccataccAggatgaaaggcaggtgtggc	13	8	10	10	0	0	1	0	1	0	0	1	2	1	2	3	4	2	1	3	4	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:24469667A>G	ENST00000355123.4	-	28	3827	c.3384T>C	c.(3382-3384)ccT>ccC	p.P1128P	ITSN2_ENST00000361999.3_Splice_Site_p.P1101P|ITSN2_ENST00000406921.3_Splice_Site_p.P1128P	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1128	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCCATACCAGGATGAAAGG	0.383																																					p.P1128P		.											.	ITSN2-539	0			c.T3384C						.						87	87	87					2																	24469667		2203	4300	6503	SO:0001630	splice_region_variant	50618	exon28			CATACCAGGATGA	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"Rho guanine nucleotide exchange factors", "EF-hand domain containing"	6184	protein-coding gene	gene with protein product	"SH3 domain protein 1B", "SH3P18-like WASP associated protein"	604464	"SH3 domain protein 1B"	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3385+1T>C	2.37:g.24469667A>G		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	71	35	NM_147152	0	0	0	0	0	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	A	11.59	1.683791	0.29872	.	.	ENSG00000198399	ENST00000416160	.	.	.	5.59	-2.45	0.06481	.	.	.	.	.	T	0.43122	0.1233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35624	-0.9781	4	.	.	.	.	4.57	0.12205	0.3227:0.0:0.2426:0.4346	.	.	.	.	P	56	.	.	L	-	2	0	ITSN2	24323171	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	1.158000	0.31737	-0.097000	0.12307	0.383000	0.25322	CTG	.		0.383	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	Silent	G	24469667	A	G	24469667	5	3	148	1	0	0	0	0	0	0	1	0	7948	202	7	3	1812	3	ITSN2	2	24469667	Splice_Site	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	6507132	24469667	218729706	14	13172											
ADCY3	109	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	25051028	25051029	+	Splice_Site	DNP	GA	GA	AC																															gtgtagtactggagacagctGagctggaggccaggacggcg																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:25051028_25051029GA>AC	ENST00000260600.5	-	13	3025_3026	c.2174_2175TC>GT	c.(2173-2175)cTC>cGT	p.L725R	ADCY3_ENST00000450524.1_5'UTR|ADCY3_ENST00000405392.1_Intron|RP11-443B20.1_ENST00000606114.1_RNA	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	725					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GGAGACAGCTGAGCTGGAGGCC	0.604											OREG0014498	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L725R													.	ADCY3-94	0			c.T2174G						.																																			SO:0001630	splice_region_variant	109	exon13			CAGCTGAGCTGGA	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"Adenylate cyclases"	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.2174_2175delinsAC	2.37:g.25051028_25051029delinsAC		Somatic	92	1	776	WXS	Illumina HiSeq	Phase_I	142	82	NM_004036	0	0	0	0	0	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	DNP	ENST00000260600.5	37	CCDS1715.1																																																																																			.		0.604	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		Missense_Mutation	AC	25051029	GA	AC	25051028	5	1	148	1	0	0	0	0	0	0	1	0	295	1277	45	2	1295	2	ADCY3	2	25051028	Splice_Site	DNP	GA	TCGA-MH-A55W-01A-11D-A26P-10	581361	25051028	218148345	15	13173											
SLC5A6	8884	hgsc.bcm.edu;bcgsc.ca	37	chr2	27428892	27428892	+	Splice_Site	DEL	A	A	-																															caccacggcttactgcacttAccagagctgtatagacggta																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:27428892delA	ENST00000310574.3	-	6	1053		c.e6+1		SLC5A6_ENST00000408041.1_Splice_Site|SLC5A6_ENST00000461319.1_5'Flank	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6						biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	TACTGCACTTACCAGAGCTGT	0.502																																					.		.											.	SLC5A6-92	0			c.579+2T>-						.						87	75	79					2																	27428892		2203	4300	6503	SO:0001630	splice_region_variant	8884	exon7			.	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.579+1T>-	2.37:g.27428892delA		Somatic	453	0		WXS	Illumina HiSeq	Phase_I	512	109	NM_021095	0	0	0	0	0	B2RB85|D6W549|Q969Y5	Splice_Site	DEL	ENST00000310574.3	37	CCDS1740.1																																																																																			.		0.502	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095	Intron	-	27428892	A	-	27428892	8	5	148	1	0	1	0	1	0	0	1	0	14701	405	14	0	1374	0	SLC5A6	2	27428892	Splice_Site	DEL	A	TCGA-MH-A55W-01A-11D-A26P-10	2377864	27428892	215770481	16	13174											
NRBP1	29959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27660178	27660178	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtcctcatatgtgccacAggaagccatcagcagtgcca	12	7	10	12	0	2	1	2	0	0	1	3	2	3	2	4	1	4	1	4	1	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:27660178A>T	ENST00000233557.3	+	11	1686	c.854A>T	c.(853-855)cAg>cTg	p.Q285L	NRBP1_ENST00000379863.3_Missense_Mutation_p.Q293L|NRBP1_ENST00000379852.3_Missense_Mutation_p.Q285L			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	285	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					TATGTGCCACAGGAAGCCATC	0.463																																					p.Q285L		.											.	NRBP1-334	0			c.A854T						.						78	72	74					2																	27660178		2203	4300	6503	SO:0001583	missense	29959	exon10			TGCCACAGGAAGC	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.854A>T	2.37:g.27660178A>T	ENSP00000233557:p.Gln285Leu	Somatic	381	2		WXS	Illumina HiSeq	Phase_I	415	233	NM_013392	0	0	19	57	38	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	37	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	A	16.36	3.100500	0.56183	.	.	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863	T;T;T	0.32272	1.46;1.46;1.46	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.28928	0.0718	L	0.28014	0.82	0.80722	D	1	B;B;B	0.32862	0.387;0.049;0.06	B;B;B	0.40256	0.324;0.039;0.021	T	0.08513	-1.0718	10	0.40728	T	0.16	-13.0877	14.6481	0.68774	1.0:0.0:0.0:0.0	.	265;293;285	B4DW31;F8W6G1;Q9UHY1	.;.;NRBP_HUMAN	L	285;265;285;293	ENSP00000233557:Q285L;ENSP00000369181:Q285L;ENSP00000369192:Q293L	ENSP00000233557:Q285L	Q	+	2	0	NRBP1	27513682	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.394000	0.79862	2.138000	0.66242	0.533000	0.62120	CAG	.		0.463	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		T	27660178	A	T	27660178	3	4	148	1	0	0	0	0	1	0	0	0	10668	188	7	5	888	5	NRBP1	2	27660178	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	231286	27660178	215539195	17	13175											
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	109380179	109380179	+	Frame_Shift_Del	DEL	A	A	-																															cccctcctgcagcttacagtAacagtgaaagccttttaggt																								rs201854838		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:109380179delA	ENST00000283195.6	+	20	3310	c.3184delA	c.(3184-3186)aacfs	p.N1062fs		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1062					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AGCTTACAGTAACAGTGAAAG	0.443																																					p.N1062fs		.											.	RANBP2-675	0			c.3184delA						.						74	77	76					2																	109380179		2203	4300	6503	SO:0001589	frameshift_variant	5903	exon20			.	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.3184delA	2.37:g.109380179delA	ENSP00000283195:p.Asn1062fs	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	110	53	NM_006267	0	0	0	0	0	Q13074|Q15280|Q53TE2|Q59FH7	Frame_Shift_Del	DEL	ENST00000283195.6	37	CCDS2079.1																																																																																			.		0.443	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		-	109380179	A	-	109380179	7	5	148	1	0	1	0	1	0	0	0	0	13060	362	13	0	3262	0	RANBP2	2	109380179	Frame_Shift_Del	DEL	A	TCGA-MH-A55W-01A-11D-A26P-10	81720001	109380179	133819194	18	13176											
NPHP1	4867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	110922202	110922202	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttccacagtctccatcctAtttcgcatcagaactattag	10	14	4	13	1	3	1	1	0	2	1	7	1	5	1	3	0	1	1	3	0	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:110922202A>T	ENST00000393272.3	-	8	931	c.834T>A	c.(832-834)aaT>aaA	p.N278K	NPHP1_ENST00000445609.2_Intron|NPHP1_ENST00000417665.1_Intron|NPHP1_ENST00000355301.4_Intron|NPHP1_ENST00000316534.4_Missense_Mutation_p.N278K	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	278					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						TCTCCATCCTATTTCGCATCA	0.463																																					p.N278K		.											.	NPHP1-92	0			c.T834A						.						185	182	183					2																	110922202		2203	4300	6503	SO:0001583	missense	4867	exon8			CATCCTATTTCGC	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.834T>A	2.37:g.110922202A>T	ENSP00000376953:p.Asn278Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	130	38	NM_207181	0	0	0	2	2	O14837	Missense_Mutation	SNP	ENST00000393272.3	37	CCDS46385.1	.	.	.	.	.	.	.	.	.	.	A	11.00	1.510348	0.27036	.	.	ENSG00000144061	ENST00000316534;ENST00000393272	T;T	0.60171	0.21;0.21	4.36	-3.69	0.04450	.	1.449030	0.04895	U	0.450299	T	0.35038	0.0918	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.09335	-1.0679	10	0.23302	T	0.38	-2.1995	1.7177	0.02905	0.4617:0.1409:0.2537:0.1437	.	278;278	O15259;O15259-4	NPHP1_HUMAN;.	K	278	ENSP00000313169:N278K;ENSP00000376953:N278K	ENSP00000313169:N278K	N	-	3	2	NPHP1	110279491	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.481000	0.06552	-0.376000	0.07943	-1.092000	0.02172	AAT	.		0.463	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		T	110922202	A	T	110922202	3	4	148	1	0	0	0	0	1	0	0	0	10605	446	16	5	1419	5	NPHP1	2	110922202	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	1542023	110922202	132277171	19	13177											
CLASP1	23332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	122161975	122161975	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggtcagcaaacatccgaGtgaagatctcacacaacctt	14	7	9	11	1	2	2	2	1	1	1	4	4	3	2	2	1	3	1	2	1	3	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:122161975G>C	ENST00000263710.4	-	26	3094	c.2705C>G	c.(2704-2706)aCt>aGt	p.T902S	CLASP1_ENST00000397587.3_Missense_Mutation_p.T882S|CLASP1_ENST00000409078.3_Missense_Mutation_p.T874S|CLASP1_ENST00000545861.1_Missense_Mutation_p.T649S|CLASP1_ENST00000541859.1_Missense_Mutation_p.T635S|CLASP1_ENST00000541377.1_Missense_Mutation_p.T880S|CLASP1_ENST00000455322.2_Missense_Mutation_p.T874S	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	902					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					AAACATCCGAGTGAAGATCTC	0.408																																					p.T902S		.											.	CLASP1-91	0			c.C2705G						.						102	99	100					2																	122161975		1978	4156	6134	SO:0001583	missense	23332	exon26			ATCCGAGTGAAGA	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"multiple asters 1"	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2705C>G	2.37:g.122161975G>C	ENSP00000263710:p.Thr902Ser	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	160	44	NM_015282	0	0	5	8	3	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	G	29.9	5.041443	0.93685	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.37	5.37	0.77165	Armadillo-like helical (1);Armadillo-type fold (1);	0.045519	0.85682	D	0.000000	T	0.76615	0.4012	L	0.55481	1.735	0.58432	D	0.999999	D;D;P;P	0.76494	0.999;0.999;0.865;0.74	D;D;P;P	0.79108	0.992;0.968;0.604;0.617	T	0.77496	-0.2566	10	0.59425	D	0.04	-15.1313	19.1123	0.93321	0.0:0.0:1.0:0.0	.	874;882;880;902	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	S	902;874;882;880;635;874;649	ENSP00000263710:T902S;ENSP00000389372:T874S;ENSP00000380717:T882S;ENSP00000441625:T880S;ENSP00000441770:T635S;ENSP00000386442:T874S;ENSP00000438620:T649S	ENSP00000263710:T902S	T	-	2	0	CLASP1	121878445	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.496000	0.97967	2.518000	0.84900	0.563000	0.77884	ACT	.		0.408	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		C	122161975	G	C	122161975	3	2	148	1	0	0	0	0	1	0	0	0	3460	1029	36	4	1967	4	CLASP1	2	122161975	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	11239773	122161975	121037398	20	13178											
KIF1A	547	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	241725900	241725900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggttcaggaggtcacggaCgcgctcacagtaaatctcca	10	7	13	11	3	4	0	3	0	1	0	5	2	4	2	1	5	0	3	1	5	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:241725900C>T	ENST00000320389.7	-	6	618	c.460G>A	c.(460-462)Gtc>Atc	p.V154I	KIF1A_ENST00000498729.2_Missense_Mutation_p.V154I	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	154	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		AGGTCACGGACGCGCTCACAG	0.652																																					p.V154I		.											.	KIF1A-91	0			c.G460A						.						112	117	115					2																	241725900		2085	4227	6312	SO:0001583	missense	547	exon6			CACGGACGCGCTC	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"Kinesins", "Pleckstrin homology (PH) domain containing"	888	protein-coding gene	gene with protein product		601255	"axonal transport of synaptic vesicles", "chromosome 2 open reading frame 20", "spastic paraplegia 30 (autosomal recessive)"	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.460G>A	2.37:g.241725900C>T	ENSP00000322791:p.Val154Ile	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	238	22	NM_001244008	0	0	0	0	0	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.399825	0.83120	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.74315	-0.83;-0.83;-0.83	4.55	4.55	0.56014	Kinesin, motor domain (4);	0.000000	0.64402	U	0.000001	T	0.80681	0.4669	L	0.35414	1.06	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.983;0.996	D	0.83722	0.0193	10	0.87932	D	0	.	17.3339	0.87274	0.0:1.0:0.0:0.0	.	154;154;154	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	I	154	ENSP00000322791:V154I;ENSP00000438388:V154I;ENSP00000384231:V154I	ENSP00000322791:V154I	V	-	1	0	KIF1A	241374573	1.000000	0.71417	0.911000	0.35937	0.436000	0.31835	5.859000	0.69539	2.087000	0.62958	0.643000	0.83706	GTC	.		0.652	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		T	241725900	C	T	241725900	3	4	148	1	0	0	0	0	1	0	0	0	8304	536	19	1	4780	1	KIF1A	2	241725900	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	119563925	241725900	1473473	21	13179											
FYCO1	79443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	46009857	46009857	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccttctctgctgctcctagCtccaggccctgcaggcatgt	4	12	9	16	0	1	0	0	0	1	0	5	0	4	0	4	2	4	5	4	2	1	2	rs372875711		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:46009857C>A	ENST00000296137.2	-	8	1174	c.969G>T	c.(967-969)gaG>gaT	p.E323D	FYCO1_ENST00000535325.1_Missense_Mutation_p.E323D	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	323					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CTGCTCCTAGCTCCAGGCCCT	0.627																																					p.E323D		.											.	FYCO1-91	0			c.G969T						.						71	64	66					3																	46009857		2203	4300	6503	SO:0001583	missense	79443	exon8			TCCTAGCTCCAGG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"Zinc fingers, FYVE domain containing"	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.969G>T	3.37:g.46009857C>A	ENSP00000296137:p.Glu323Asp	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	47	11	NM_024513	0	0	5	9	4	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822936	0.71028	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.28454	1.61;1.69	5.66	5.66	0.87406	.	0.237259	0.43260	D	0.000588	T	0.42539	0.1207	M	0.67953	2.075	0.34032	D	0.653899	D;P	0.63880	0.993;0.932	P;B	0.56127	0.792;0.362	T	0.54390	-0.8301	10	0.28530	T	0.3	-23.5428	8.7704	0.34728	0.0:0.8728:0.0:0.1272	.	323;323	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	D	323	ENSP00000296137:E323D;ENSP00000441178:E323D	ENSP00000296137:E323D	E	-	3	2	FYCO1	45984861	0.931000	0.31567	0.984000	0.44739	0.507000	0.33981	1.633000	0.37113	2.671000	0.90904	0.655000	0.94253	GAG	.		0.627	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		A	46009857	C	A	46009857	3	1	148	1	0	0	0	0	1	0	0	0	6144	796	28	4	3511	4	FYCO1	3	46009857	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		46009857	152012573	22	13180											
RBM5	10181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50155814	50155814	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccaaaggcagcgcataTggtttgtcgggcgccgattc	8	8	15	10	4	0	0	0	0	0	0	2	2	0	1	2	4	2	3	2	4	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:50155814T>A	ENST00000347869.3	+	25	2548	c.2373T>A	c.(2371-2373)taT>taA	p.Y791*	RP11-493K19.3_ENST00000437204.1_RNA|RP11-493K19.3_ENST00000425674.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	791	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCAGCGCATATGGTTTGTCGG	0.557																																					p.Y791X		.											.	RBM5-278	0			c.T2373A						.						93	81	85					3																	50155814		2203	4300	6503	SO:0001587	stop_gained	10181	exon25			CGCATATGGTTTG	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"G patch domain containing", "RNA binding motif (RRM) containing"	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.2373T>A	3.37:g.50155814T>A	ENSP00000343054:p.Tyr791*	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	150	63	NM_005778	0	0	28	43	15	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Nonsense_Mutation	SNP	ENST00000347869.3	37	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	T	35	5.436728	0.96168	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	.	.	.	5.56	0.508	0.16972	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.522	10.6385	0.45579	0.0:0.4157:0.0:0.5843	.	.	.	.	X	791;790;481	.	ENSP00000343054:Y791X	Y	+	3	2	RBM5	50130818	0.435000	0.25577	0.988000	0.46212	0.413000	0.31143	-0.355000	0.07671	0.075000	0.16796	0.528000	0.53228	TAT	.		0.557	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		A	50155814	T	A	50155814	4	1	148	1	0	0	0	0	0	1	0	0	13175	1471	51	5	2467	5	RBM5	3	50155814	Nonsense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	4145957	50155814	147866616	23	13181											
KIAA1524	57650	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	108288411	108288411	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctgagtgagcatatggCgcagctgagtcactgaacag	11	9	12	9	1	3	4	2	4	1	0	3	4	3	4	0	1	3	3	0	1	2	1	rs375108755		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:108288411C>T	ENST00000295746.8	-	9	1014	c.938G>A	c.(937-939)cGc>cAc	p.R313H	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_Missense_Mutation_p.R154H	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	313					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAGCATATGGCGCAGCTGAGT	0.418																																					p.R313H													.	KIAA1524-92	0			c.G938A						.	C	HIS/ARG	0,4406		0,0,2203	59	56	57		938	5.8	1	3		57	1,8597	1.2+/-3.3	0,1,4298	no	missense	KIAA1524	NM_020890.2	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	313/906	108288411	1,13003	2203	4299	6502	SO:0001583	missense	57650	exon9			ATATGGCGCAGCT	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.938G>A	3.37:g.108288411C>T	ENSP00000295746:p.Arg313His	Somatic	195	2		WXS	Illumina HiSeq	Phase_I	276	111	NM_020890	0	0	0	0	0	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	37	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255797	0.95336	0.0	1.16E-4	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.14391	2.51;2.65	5.85	5.85	0.93711	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.38719	0.1051	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04103	-1.0977	10	0.87932	D	0	-5.9074	18.3439	0.90314	0.0:1.0:0.0:0.0	.	313	Q8TCG1	CIP2A_HUMAN	H	154;313	ENSP00000419487:R154H;ENSP00000295746:R313H	ENSP00000295746:R313H	R	-	2	0	KIAA1524	109771101	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.424000	0.73366	2.773000	0.95371	0.655000	0.94253	CGC	.		0.418	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		T	108288411	C	T	108288411	3	4	148	1	0	0	0	0	1	0	0	0	8260	768	27	1	1831	1	KIAA1524	3	108288411	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	58132597	108288411	89734019	24	13182											
WDR52	55779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113120585	113120585	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctattgtctcaaaatcccatAtcttgtaaaatgaaaagaaa	18	12	4	7	0	2	2	1	1	2	1	4	2	3	2	1	0	0	1	1	0	9	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:113120585A>C	ENST00000295868.2	-	10	1334	c.1172T>G	c.(1171-1173)aTa>aGa	p.I391R	WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA|WDR52_ENST00000393845.2_Splice_Site_p.I391R	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						AAAATCCCATATCTTGTAAAA	0.308																																					p.I391R		.											.	WDR52-90	0			c.T1172G						.						60	60	60					3																	113120585		2203	4298	6501	SO:0001630	splice_region_variant	55779	exon10			TCCCATATCTTGT																												ENST00000295868.2:c.1171-1T>G	3.37:g.113120585A>C		Somatic	38	0		WXS	Illumina HiSeq	Phase_I	81	36	NM_001164496	0	0	0	0	0		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.838251	0.71373	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.70631	-0.5;3.01	5.63	5.63	0.86233	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.79446	0.4447	L	0.59436	1.845	0.80722	D	1	D	0.69078	0.997	P	0.59012	0.85	T	0.81839	-0.0748	9	0.87932	D	0	.	15.8341	0.78787	1.0:0.0:0.0:0.0	.	391	Q96MT7	WDR52_HUMAN	R	391	ENSP00000377428:I391R;ENSP00000295868:I391R	ENSP00000295868:I391R	I	-	2	0	WDR52	114603275	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.300000	0.59079	2.144000	0.66660	0.533000	0.62120	ATA	.		0.308	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		Missense_Mutation	C	113120585	A	C	113120585	5	2	148	1	0	0	0	0	0	0	1	0	17337	463	16	5	4511	5	WDR52	3	113120585	Splice_Site	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	4832174	113120585	84901845	25	13183											
KALRN	8997	broad.mit.edu	37	chr3	124209630	124209630	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgctgatccggaaggggCgggagcggcacttgttcctc	6	8	16	11	4	0	1	0	1	0	0	4	3	2	3	2	5	1	3	2	5	1	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:124209630C>T	ENST00000240874.3	+	30	4637	c.4480C>T	c.(4480-4482)Cgg>Tgg	p.R1494W	KALRN_ENST00000360013.3_Missense_Mutation_p.R1494W|KALRN_ENST00000460856.1_Missense_Mutation_p.R1485W	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1494	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CCGGAAGGGGCGGGAGCGGCA	0.488																																					p.R1494W													.	KALRN-738	0			c.C4480T						.						74	82	79					3																	124209630		2203	4300	6503	SO:0001583	missense	8997	exon30			AAGGGGCGGGAGC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	4814	protein-coding gene	gene with protein product	"serine/threonine kinase with Dbl and pleckstrin homology domains"	604605	"huntingtin-associated protein interacting protein (duo)"	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4480C>T	3.37:g.124209630C>T	ENSP00000240874:p.Arg1494Trp	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	80	5	NM_003947	0	0	0	0	0	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.974277	0.74246	.	.	ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013	T;T;T	0.12147	2.71;2.71;2.71	5.28	5.28	0.74379	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.64402	D	0.000001	T	0.47838	0.1467	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.987;1.0	T	0.56739	-0.7929	10	0.87932	D	0	.	19.1106	0.93315	0.0:1.0:0.0:0.0	.	1485;1494;1494	C9IZQ6;O60229;O60229-2	.;KALRN_HUMAN;.	W	1485;1494;1494	ENSP00000418611:R1485W;ENSP00000240874:R1494W;ENSP00000353109:R1494W	ENSP00000240874:R1494W	R	+	1	2	KALRN	125692320	0.996000	0.38824	1.000000	0.80357	0.993000	0.82548	3.539000	0.53604	2.763000	0.94921	0.650000	0.86243	CGG	.		0.488	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124209630	C	T	124209630	3	4	148	1	0	0	0	0	1	0	0	0	7996	759	27	1	4598	1	KALRN	3	124209630	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	11089045	124209630	73812800	26	13184											
IFT122	55764	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	129214436	129214436	+	Frame_Shift_Del	DEL	T	T	-																															tgtacaccgacctctgcatgTttgagtatgccaaggtaacc																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:129214436delT	ENST00000348417.2	+	18	2271	c.2194delT	c.(2194-2196)tttfs	p.F732fs	IFT122_ENST00000349441.2_Frame_Shift_Del_p.F621fs|IFT122_ENST00000347300.2_Frame_Shift_Del_p.F673fs|IFT122_ENST00000507564.1_Frame_Shift_Del_p.F724fs|IFT122_ENST00000440957.2_Frame_Shift_Del_p.F523fs|IFT122_ENST00000504021.1_Frame_Shift_Del_p.F608fs|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000296266.3_Frame_Shift_Del_p.F783fs|IFT122_ENST00000431818.2_Frame_Shift_Del_p.F582fs	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	732					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						CCTCTGCATGTTTGAGTATGC	0.537																																					p.F783fs		.											.	IFT122-92	0			c.2347delT						.						118	106	110					3																	129214436		2203	4300	6503	SO:0001589	frameshift_variant	55764	exon19			.	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.2194delT	3.37:g.129214436delT	ENSP00000324005:p.Phe732fs	Somatic	294	0		WXS	Illumina HiSeq	Phase_I	251	114	NM_052985	0	0	0	0	0	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Frame_Shift_Del	DEL	ENST00000348417.2	37	CCDS3061.1																																																																																			.		0.537	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		-	129214436	T	-	129214436	7	5	148	1	0	1	0	1	0	0	0	0	7576	1725	60	0	2421	0	IFT122	3	129214436	Frame_Shift_Del	DEL	T	TCGA-MH-A55W-01A-11D-A26P-10	5004806	129214436	68807994	27	13185											
CCRL1	51554	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	132319273	132319273	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagaaccagtcaacagattAttattatgaggaaaatgaaa	20	9	7	5	0	1	4	1	2	0	2	1	5	1	5	1	1	2	0	1	1	8	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:132319273A>C	ENST00000249887.2	+	2	128	c.32A>C	c.(31-33)tAt>tCt	p.Y11S	ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000355458.3_Intron|ACAD11_ENST00000545291.1_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	11					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										TCAACAGATTATTATTATGAG	0.343																																					p.Y11S													.	CCRL1-658	0			c.A32C						.						26	27	27					3																	132319273		2200	4297	6497	SO:0001583	missense	51554	exon1			CAGATTATTATTA	AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"GPCR / Class A : Chemokine receptors : Atypical"	1611	protein-coding gene	gene with protein product		606065	"chemokine (C-C motif) receptor-like 1"	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.32A>C	3.37:g.132319273A>C	ENSP00000249887:p.Tyr11Ser	Somatic	196	1		WXS	Illumina HiSeq	Phase_I	231	84	NM_178445	0	0	0	1	1	B2R9U7	Missense_Mutation	SNP	ENST00000249887.2	37	CCDS3075.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.190302	0.38707	.	.	ENSG00000129048	ENST00000249887;ENST00000424114	T	0.35048	1.33	5.22	5.22	0.72569	.	0.306400	0.31949	N	0.006803	T	0.26085	0.0636	L	0.43152	1.355	0.48511	D	0.999662	P	0.39480	0.675	B	0.33121	0.158	T	0.05257	-1.0896	10	0.21540	T	0.41	.	10.5061	0.44834	0.8378:0.1622:0.0:0.0	.	11	Q9NPB9	CCRL1_HUMAN	S	11	ENSP00000249887:Y11S	ENSP00000249887:Y11S	Y	+	2	0	CCRL1	133801963	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	5.519000	0.67074	1.970000	0.57323	0.482000	0.46254	TAT	.		0.343	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557		C	132319273	A	C	132319273	3	2	148	1	0	0	0	0	1	0	0	0	2955	449	16	5	34	5	CCRL1	3	132319273	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	3104837	132319273	65703157	28	13186											
MYNN	55892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	169496621	169496621	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaagaggtggtcactaaatGcaaaataaagatggaagatt	18	8	12	3	0	1	3	1	0	0	3	1	5	1	5	0	4	1	1	0	4	8	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:169496621G>A	ENST00000349841.5	+	3	995	c.332G>A	c.(331-333)tGc>tAc	p.C111Y	MYNN_ENST00000392733.1_Missense_Mutation_p.C111Y|MYNN_ENST00000356716.4_Missense_Mutation_p.C111Y|MYNN_ENST00000544106.1_Missense_Mutation_p.C111Y|RP11-362K14.5_ENST00000602342.1_RNA	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	111					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			GTCACTAAATGCAAAATAAAG	0.348																																					p.C111Y		.											.	MYNN-91	0			c.G332A						.						92	98	96					3																	169496621		2203	4300	6503	SO:0001583	missense	55892	exon4			CTAAATGCAAAAT	AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.332G>A	3.37:g.169496621G>A	ENSP00000326240:p.Cys111Tyr	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	81	32	NM_001185118	0	0	0	2	2	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Missense_Mutation	SNP	ENST00000349841.5	37	CCDS3207.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.352343	0.61293	.	.	ENSG00000085274	ENST00000356716;ENST00000349841;ENST00000392733;ENST00000544106	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.54	5.54	0.83059	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.93530	0.7935	H	0.98802	4.335	0.49915	D	0.999837	D;D	0.76494	0.999;0.998	D;D	0.81914	0.995;0.992	D	0.95900	0.8914	10	0.87932	D	0	.	19.4966	0.95075	0.0:0.0:1.0:0.0	.	111;111	Q9NPC7-2;Q9NPC7	.;MYNN_HUMAN	Y	111	ENSP00000349150:C111Y;ENSP00000326240:C111Y;ENSP00000376492:C111Y;ENSP00000440637:C111Y	ENSP00000326240:C111Y	C	+	2	0	MYNN	170979315	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.825000	0.69286	2.616000	0.88540	0.650000	0.86243	TGC	.		0.348	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657		A	169496621	G	A	169496621	3	1	148	1	0	0	0	0	1	0	0	0	10086	1319	46	2	338	2	MYNN	3	169496621	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	37177348	169496621	28525809	29	13187											
ATP11B	23200	broad.mit.edu	37	chr3	182607235	182607235	+	Frame_Shift_Del	DEL	T	T	-																															gcctcttaagtattaaaacaTttctttattggaccatcctg																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:182607235delT	ENST00000323116.5	+	25	3141	c.2881delT	c.(2881-2883)tttfs	p.F961fs		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	961					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TATTAAAACATTTCTTTATTG	0.328																																					p.F961fs													.	ATP11B-93	0			c.2881delT						.						78	79	79					3																	182607235		2201	4299	6500	SO:0001589	frameshift_variant	23200	exon25			AAAACATTTCTTT	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"ATPases / P-type"	13553	protein-coding gene	gene with protein product		605869	"ATPase, Class VI, type 11B"			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2881delT	3.37:g.182607235delT	ENSP00000321195:p.Phe961fs	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	17	9	NM_014616	0	0	0	0	0	Q96FN1|Q9UKK7	Frame_Shift_Del	DEL	ENST00000323116.5	37	CCDS33896.1																																																																																			.		0.328	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616		-	182607235	T	-	182607235	7	5	148	1	0	1	0	1	0	0	0	0	1121	1493	52	0	2979	0	ATP11B	3	182607235	Frame_Shift_Del	DEL	T	TCGA-MH-A55W-01A-11D-A26P-10	13110614	182607235	15415195	30	13188											
KNG1	3827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186435425	186435425	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaattgactgcaatgacaagGatttatttaaagctgtggat	15	13	9	4	0	0	2	0	2	0	0	0	4	0	4	0	2	2	2	0	2	6	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:186435425G>T	ENST00000265023.4	+	1	306	c.94G>T	c.(94-96)Gat>Tat	p.D32Y	RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000447445.1_Missense_Mutation_p.D32Y|KNG1_ENST00000287611.2_Missense_Mutation_p.D32Y	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	32	Cystatin kininogen-type 1. {ECO:0000255|PROSITE-ProRule:PRU00979}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		CAATGACAAGGATTTATTTAA	0.393																																					p.D32Y		.											.	KNG1-92	0			c.G94T						.						119	121	121					3																	186435425		2203	4299	6502	SO:0001583	missense	3827	exon1			GACAAGGATTTAT		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.94G>T	3.37:g.186435425G>T	ENSP00000265023:p.Asp32Tyr	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	157	37	NM_000893	0	0	0	0	0	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192786	0.38707	.	.	ENSG00000113889	ENST00000287611;ENST00000265023;ENST00000447445;ENST00000432028	T;T;T	0.29655	1.56;1.56;1.56	5.2	4.31	0.51392	Proteinase inhibitor I25, cystatin (2);	0.603229	0.15391	N	0.264803	T	0.51805	0.1696	M	0.71581	2.175	0.22017	N	0.999412	D;D	0.89917	0.994;1.0	D;D	0.72075	0.976;0.975	T	0.39014	-0.9634	10	0.51188	T	0.08	-6.5792	10.4191	0.44340	0.0929:0.0:0.9071:0.0	.	32;32	P01042;P01042-2	KNG1_HUMAN;.	Y	32;32;32;20	ENSP00000287611:D32Y;ENSP00000265023:D32Y;ENSP00000396025:D32Y	ENSP00000265023:D32Y	D	+	1	0	KNG1	187918119	0.221000	0.23642	0.035000	0.18076	0.403000	0.30841	2.124000	0.42006	1.302000	0.44855	0.455000	0.32223	GAT	.		0.393	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		T	186435425	G	T	186435425	3	4	148	1	0	0	0	0	1	0	0	0	8448	1174	41	4	96	4	KNG1	3	186435425	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	3828190	186435425	11587005	31	13189											
CPZ	8532	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	8607801	8607801	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctacctagcccagtacctGtgctctgagtacctgcttgg	7	12	9	13	0	2	1	0	1	2	0	2	1	2	1	4	1	6	4	4	1	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:8607801G>C	ENST00000360986.4	+	5	969	c.795G>C	c.(793-795)ctG>ctC	p.L265L	CPZ_ENST00000382480.2_Silent_p.L128L|CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000315782.6_Silent_p.L254L	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	265					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCCAGTACCTGTGCTCTGAGT	0.607																																					p.L265L													.	CPZ-93	0			c.G795C						.						147	112	124					4																	8607801		2203	4300	6503	SO:0001819	synonymous_variant	8532	exon5			GTACCTGTGCTCT	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"metallocarboxypeptidase Z"	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.795G>C	4.37:g.8607801G>C		Somatic	175	1		WXS	Illumina HiSeq	Phase_I	206	71	NM_001014447	0	0	0	0	0	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			.		0.607	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		C	8607801	G	C	8607801	2	2	148	1	0	0	0	0	0	0	0	1	3845	1364	48	4		4	CPZ	4	8607801	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		8607801	182546475	32	13190											
TBC1D19	55296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	26585819	26585819	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggctagggcaggggaaatgTtgcaggaggagtcggacctc	9	6	19	7	1	0	0	0	0	0	0	2	4	0	4	1	7	1	4	1	7	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:26585819T>C	ENST00000264866.4	+	1	282	c.4T>C	c.(4-6)Ttg>Ctg	p.L2L	TBC1D19_ENST00000511789.1_Silent_p.L2L	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	2							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				AGGGGAAATGTTGCAGGAGGA	0.627																																					p.L2L		.											.	TBC1D19-153	0			c.T4C						.						44	45	45					4																	26585819		2203	4298	6501	SO:0001819	synonymous_variant	55296	exon1			GAAATGTTGCAGG	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.4T>C	4.37:g.26585819T>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	70	29	NM_018317	0	0	1	2	1	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	37	CCDS3439.1																																																																																			.		0.627	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		C	26585819	T	C	26585819	2	2	148	1	0	0	0	0	0	0	0	1	15639	1722	60	3		3	TBC1D19	4	26585819	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	17978018	26585819	164568457	33	13191											
N4BP2	55728	ucsc.edu	37	chr4	40122111	40122111	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgttggtgactggccagttGataagactattggtcagagg	9	13	14	5	0	1	4	1	2	0	2	1	4	1	4	1	4	0	2	1	4	2	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:40122111G>A	ENST00000261435.6	+	9	2796	c.2380G>A	c.(2380-2382)Gat>Aat	p.D794N		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	794					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						CTGGCCAGTTGATAAGACTAT	0.363																																					p.D794N													.	N4BP2-602	0			c.G2380A						.						49	50	50					4																	40122111		2203	4299	6502	SO:0001583	missense	55728	exon9			CCAGTTGATAAGA	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2380G>A	4.37:g.40122111G>A	ENSP00000261435:p.Asp794Asn	Somatic	26	0		WXS	Illumina HiSeq		45	4	NM_018177	0	0	0	0	0	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.067078	0.76301	.	.	ENSG00000078177	ENST00000261435;ENST00000381804	T	0.20881	2.04	5.64	5.64	0.86602	.	0.119478	0.53938	D	0.000057	T	0.31949	0.0813	L	0.56769	1.78	0.39414	D	0.966804	P;P	0.46142	0.873;0.799	P;B	0.47346	0.544;0.343	T	0.06075	-1.0847	10	0.72032	D	0.01	-15.067	16.7169	0.85399	0.0:0.1289:0.8711:0.0	.	794;794	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	N	794;714	ENSP00000261435:D794N	ENSP00000261435:D794N	D	+	1	0	N4BP2	39798506	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.227000	0.58612	2.681000	0.91329	0.561000	0.74099	GAT	.		0.363	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		A	40122111	G	A	40122111	3	1	148	1	0	0	0	0	1	0	0	0	10135	1290	45	2	2406	2	N4BP2	4	40122111	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	13536292	40122111	151032165	34	13192											
GRSF1	2926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	71702003	71702003	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catactcagggggtggtggaAggtcttccaggtaagtagtt	9	11	15	6	0	2	0	1	0	1	0	3	1	3	1	1	6	1	3	1	6	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:71702003A>G	ENST00000254799.6	-	2	503	c.386T>C	c.(385-387)cTt>cCt	p.L129P	GRSF1_ENST00000439371.1_5'UTR|GRSF1_ENST00000545193.1_Missense_Mutation_p.L11P|GRSF1_ENST00000502323.1_5'UTR|GRSF1_ENST00000508091.1_5'UTR	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	129	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			GGGTGGTGGAAGGTCTTCCAG	0.413																																					p.L129P		.											.	.	0			c.T386C						.						82	84	83					4																	71702003		1848	4089	5937	SO:0001583	missense	2926	exon2			GGTGGAAGGTCTT	BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.386T>C	4.37:g.71702003A>G	ENSP00000254799:p.Leu129Pro	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	154	46	NM_002092	0	0	15	30	15	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Missense_Mutation	SNP	ENST00000254799.6	37	CCDS47069.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.72|14.72	2.619082|2.619082	0.46736|0.46736	.|.	.|.	ENSG00000132463|ENSG00000132463	ENST00000514161|ENST00000254799;ENST00000540657;ENST00000499044;ENST00000545193	.|T;T;T	.|0.21734	.|2.05;2.03;1.99	4.51|4.51	4.51|4.51	0.55191|0.55191	.|RNA recognition motif domain (1);	.|0.718315	.|0.12425	.|N	.|0.470117	T|T	0.15998|0.15998	0.0385|0.0385	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P;P	.|0.47350	.|0.79;0.894	.|B;P	.|0.45037	.|0.202;0.467	T|T	0.02917|0.02917	-1.1094|-1.1094	5|10	.|0.45353	.|T	.|0.12	-2.599|-2.599	5.3313|5.3313	0.15934|0.15934	0.6438:0.1816:0.0:0.1746|0.6438:0.1816:0.0:0.1746	.|.	.|42;129	.|B7Z5F9;Q12849	.|.;GRSF1_HUMAN	L|P	66|129;61;102;11	.|ENSP00000254799:L129P;ENSP00000427354:L102P;ENSP00000443380:L11P	.|ENSP00000254799:L129P	F|L	-|-	1|2	0|0	GRSF1|GRSF1	71920867|71920867	0.827000|0.827000	0.29292|0.29292	0.959000|0.959000	0.39883|0.39883	0.674000|0.674000	0.39518|0.39518	3.964000|3.964000	0.56780|0.56780	1.881000|1.881000	0.54492|0.54492	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.		0.413	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		G	71702003	A	G	71702003	3	3	148	1	0	0	0	0	1	0	0	0	6830	72	3	3	1088	3	GRSF1	4	71702003	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	31579892	71702003	119452273	35	13193											
TBC1D9	23158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	141600812	141600812	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taaaagcaaaggtggttaatGctgaggtacatccaaccctg	14	9	10	8	0	0	1	0	1	0	0	1	1	1	1	2	3	4	4	2	3	6	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:141600812G>A	ENST00000442267.2	-	4	620	c.546C>T	c.(544-546)agC>agT	p.S182S		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	182	GRAM 1.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GGTGGTTAATGCTGAGGTACA	0.448																																					p.S182S		.											.	TBC1D9-23	0			c.C546T						.						69	67	67					4																	141600812		1837	4092	5929	SO:0001819	synonymous_variant	23158	exon4			GTTAATGCTGAGG	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"EF-hand domain containing"	21710	protein-coding gene	gene with protein product			"TBC1 domain family, member 9"			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.546C>T	4.37:g.141600812G>A		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	82	30	NM_015130	0	0	1	3	2	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			.		0.448	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141600812	G	A	141600812	2	1	148	1	0	0	0	0	0	0	0	1	15659	1310	46	2		2	TBC1D9	4	141600812	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	69898809	141600812	49553464	36	13194											
EGFLAM	133584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	38418272	38418272	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaccgaggctttcaaggCtgtgtgcagtcgctcgctgt	8	10	12	11	3	1	0	1	0	0	0	3	1	1	0	1	2	2	5	1	2	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:38418272C>A	ENST00000354891.3	+	12	1945	c.1599C>A	c.(1597-1599)ggC>ggA	p.G533G	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000322350.5_Silent_p.G533G|EGFLAM_ENST00000336740.6_Silent_p.G299G	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	533	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GCTTTCAAGGCTGTGTGCAGT	0.542																																					p.G533G	Colon(62;485 1295 3347 17454)	.											.	EGFLAM-187	0			c.C1599A						.						96	100	98					5																	38418272		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon12			TCAAGGCTGTGTG	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"Fibronectin type III domain containing"	26810	protein-coding gene	gene with protein product	"pikachurin", "agrin-like"					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1599C>A	5.37:g.38418272C>A		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	120	35	NM_001205301	0	0	0	0	0	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	37	CCDS56363.1																																																																																			.		0.542	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		A	38418272	C	A	38418272	2	1	148	1	0	0	0	0	0	0	0	1	4977	784	28	4		4	EGFLAM	5	38418272	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		38418272	142496988	37	13195											
DAB2	1601	broad.mit.edu	37	chr5	39383200	39383200	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcaggattaggggtgggAaagaagttgagattggcaga	13	8	18	2	0	1	3	1	1	0	3	1	7	1	6	0	6	0	2	0	6	3	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:39383200A>G	ENST00000320816.6	-	10	1328	c.861T>C	c.(859-861)ttT>ttC	p.F287F	DAB2_ENST00000509337.1_Silent_p.F266F|DAB2_ENST00000339788.6_Intron|DAB2_ENST00000545653.1_Silent_p.F266F|DAB2_ENST00000512525.1_5'Flank	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	287	Required for localization to clathrin- coated pits. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TAGGGGTGGGAAAGAAGTTGA	0.473																																					p.F287F													.	DAB2-227	0			c.T861C						.						143	150	148					5																	39383200		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon10			GGTGGGAAAGAAG	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)", "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.861T>C	5.37:g.39383200A>G		Somatic	182	0		WXS	Illumina HiSeq	Phase_I	183	6	NM_001343	0	0	27	28	1	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	37	CCDS34149.1																																																																																			.		0.473	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		G	39383200	A	G	39383200	2	3	148	1	0	0	0	0	0	0	0	1	4224	243	9	3		3	DAB2	5	39383200	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	964928	39383200	141532060	38	13196											
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	89979468	89979468	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatagactctgatcctgaTggtgatctcgccttcacctc	9	12	7	13	1	3	4	1	3	2	1	6	4	4	4	3	1	1	0	3	1	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:89979468T>C	ENST00000405460.2	+	28	5826	c.5730T>C	c.(5728-5730)gaT>gaC	p.D1910D		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1910	Calx-beta 13. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTGATCCTGATGGTGATCTCG	0.418																																					p.D1910D		.											.	GPR98-103	0			c.T5730C						.						69	70	70					5																	89979468		1951	4141	6092	SO:0001819	synonymous_variant	84059	exon28			TCCTGATGGTGAT	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"-", "GPCR / Class B : Orphans"	17416	protein-coding gene	gene with protein product		602851	"monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5730T>C	5.37:g.89979468T>C		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	108	38	NM_032119	0	0	0	0	0	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			.		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89979468	T	C	89979468	2	2	148	1	0	0	0	0	0	0	0	1	6742	1461	51	3		3	GPR98	5	89979468	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	50596268	89979468	90935792	39	13197											
STK10	6793	hgsc.bcm.edu	37	chr5	171471934	171471934	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaacttggcggccttgctTggggtggaggggtttgggca	6	10	19	6	1	0	1	0	0	0	1	0	2	0	2	1	8	2	3	1	8	2	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:171471934T>G	ENST00000176763.5	-	19	3202	c.2859A>C	c.(2857-2859)ccA>ccC	p.P953P		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	953					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGGCCTTGCTTGGGGTGGAGG	0.607																																					p.P953P		.											.	STK10-1022	0			c.A2859C						.						83	77	79					5																	171471934		2203	4300	6503	SO:0001819	synonymous_variant	6793	exon19			CTTGCTTGGGGTG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.2859A>C	5.37:g.171471934T>G		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	98	5	NM_005990	0	0	8	8	0	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																			.		0.607	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		G	171471934	T	G	171471934	2	3	148	1	0	0	0	0	0	0	0	1	15318	1799	63	5		5	STK10	5	171471934	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	81492466	171471934	9443326	40	13198											
NSD1	64324	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	176709581	176709584	+	Splice_Site	DEL	AAGT	AAGT	-																															ctatatgctcaccctagacaAagtaagtaatgggaaatgct																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:176709581_176709584delAAGT	ENST00000439151.2	+	19	6053_6054	c.6008_6009delAAGT	c.(6007-6009)aaa>a	p.K2003fs	NSD1_ENST00000354179.4_Splice_Site_p.K1734fs|NSD1_ENST00000361032.4_Splice_Site_p.K1900fs|NSD1_ENST00000347982.4_Splice_Site_p.K1734fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2003	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		ACCCTAGACAAAGTAAGTAATGGG	0.397			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.2003_2003del		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.6008_6009del						.																																			SO:0001630	splice_region_variant	64324	exon19	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	.	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6009+1AAGT>-	5.37:g.176709585_176709588delAAGT		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	83	24	NM_022455	0	0	0	0	0	Q96PD8|Q96RN7	Frame_Shift_Del	DEL	ENST00000439151.2	37	CCDS4412.1																																																																																			.		0.397	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	Frame_Shift_Del	-	176709584	AAGT	-	176709581	8	5	148	1	0	1	0	1	0	0	1	0	10695	28	1	0	6078	0	NSD1	5	176709581	Splice_Site	DEL	AAGT	TCGA-MH-A55W-01A-11D-A26P-10	5237647	176709581	4205679	41	13199											
TNXB	7148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32038155	32038155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccacagctccccaaggCggggtggggcccctgggctg	5	5	15	16	1	1	0	1	0	0	0	2	0	2	0	5	6	1	2	5	6	1	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:32038155C>T	ENST00000375244.3	-	14	5228	c.5027G>A	c.(5026-5028)cGc>cAc	p.R1676H	TNXB_ENST00000375247.2_Missense_Mutation_p.R1676H			P22105	TENX_HUMAN	tenascin XB	1758	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CTCCCCAAGGCGGGGTGGGGC	0.597																																					p.R1676H		.											.	TNXB-90	0			c.G5027A						.						14	16	15					6																	32038155		1903	4094	5997	SO:0001583	missense	7148	exon14			CCAAGGCGGGGTG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5027G>A	6.37:g.32038155C>T	ENSP00000364393:p.Arg1676His	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	82	27	NM_019105	0	0	1	1	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	11.28	1.593489	0.28357	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.04603	3.59;3.59	4.34	0.318	0.15867	.	0.470849	0.16112	N	0.229047	T	0.03263	0.0095	M	0.88241	2.94	0.23773	N	0.996888	B	0.26775	0.159	B	0.23716	0.048	T	0.22173	-1.0224	10	0.49607	T	0.09	.	8.1222	0.30978	0.0:0.6178:0.0:0.3822	.	1676	P22105-3	.	H	1676	ENSP00000364393:R1676H;ENSP00000364396:R1676H	ENSP00000364393:R1676H	R	-	2	0	TNXB	32146133	0.991000	0.36638	0.989000	0.46669	0.365000	0.29674	0.675000	0.25232	0.160000	0.19432	-0.302000	0.09304	CGC	.		0.597	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32038155	C	T	32038155	3	4	148	1	0	0	0	0	1	0	0	0	16378	768	27	1	9810	1	TNXB	6	32038155	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		32038155	139076912	42	13200											
KCNK5	8645	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	39159405	39159412	+	Frame_Shift_Del	DEL	TTGTGGAC	TTGTGGAC	-																															gccgccgcttcttaatggctTtgtggacttccacaaacatg																								rs13208158	byFrequency	TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TTGTGGAC	TTGTGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:39159405_39159412delTTGTGGAC	ENST00000359534.3	-	5	1092_1099	c.754_761delGTCCACAA	c.(754-762)gtccacaaafs	p.VHK252fs		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	252					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						CTTAATGGCTTTGTGGACTTCCACAAAC	0.591																																					p.252_254del		.											.	KCNK5-227	0			c.754_761del						.																																			SO:0001589	frameshift_variant	8645	exon5			.	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.754_761delGTCCACAA	6.37:g.39159405_39159412delTTGTGGAC	ENSP00000352527:p.Val252fs	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	95	20	NM_003740	0	0	0	0	0	B2RAQ6|B5TJL2|Q5VV76	Frame_Shift_Del	DEL	ENST00000359534.3	37	CCDS4841.1																																																																																			.		0.591	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740		-	39159412	TTGTGGAC	-	39159405	7	5	148	1	0	1	0	1	0	0	0	0	8090	1841	64	0	742	0	KCNK5	6	39159405	Frame_Shift_Del	DEL	TTGTGGAC	TCGA-MH-A55W-01A-11D-A26P-10	7121250	39159405	131955662	43	13201											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	51768400	51768400	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctgaacatcttacctctaTaacattggtgggactgcaga	12	11	9	9	0	2	2	0	1	2	1	2	3	2	3	1	2	5	2	1	2	4	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:51768400T>G	ENST00000371117.3	-	43	7266	c.6991A>C	c.(6991-6993)Ata>Cta	p.I2331L	PKHD1_ENST00000340994.4_Missense_Mutation_p.I2331L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2331			I -> K (in ARPKD). {ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12506140}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTTACCTCTATAACATTGGTG	0.478																																					p.I2331L		.											.	PKHD1-603	0			c.A6991C						.						173	163	167					6																	51768400		2203	4300	6503	SO:0001583	missense	5314	exon43			CCTCTATAACATT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.6991A>C	6.37:g.51768400T>G	ENSP00000360158:p.Ile2331Leu	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	118	41	NM_170724	0	0	0	0	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	7.897	0.733493	0.15574	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.82803	-1.65;-1.65	5.87	-2.49	0.06403	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.766468	0.11605	N	0.547353	T	0.44074	0.1276	N	0.12182	0.205	0.09310	N	1	B;B;B	0.15141	0.012;0.006;0.012	B;B;B	0.17722	0.008;0.007;0.019	T	0.39440	-0.9614	10	0.44086	T	0.13	.	6.1429	0.20269	0.0:0.2716:0.2385:0.4899	.	2331;2331;2331	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	L	2331	ENSP00000360158:I2331L;ENSP00000341097:I2331L	ENSP00000341097:I2331L	I	-	1	0	PKHD1	51876359	0.002000	0.14202	0.004000	0.12327	0.326000	0.28443	-0.160000	0.10041	-0.465000	0.06953	0.528000	0.53228	ATA	.		0.478	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51768400	T	G	51768400	3	3	148	1	0	0	0	0	1	0	0	0	11997	1406	49	5	5372	5	PKHD1	6	51768400	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	12608995	51768400	119346667	44	13202											
GCM1	8521	hgsc.bcm.edu;bcgsc.ca	37	chr6	52993368	52993369	+	In_Frame_Ins	INS	-	-	AAA																															gctggtcagaggaaaaggatINSaattggaataacagttgtca																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:52993368_52993369insAAA	ENST00000259803.7	-	6	1157_1158	c.946_947insTTT	c.(946-948)tat>tTTTat	p.315_316insF	RP11-506E9.3_ENST00000566420.1_RNA	NM_003643.3	NP_003634.2	Q9NP62	GCM1_HUMAN	glial cells missing homolog 1 (Drosophila)	315					anatomical structure morphogenesis (GO:0009653)|astrocyte fate commitment (GO:0060018)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell differentiation involved in embryonic placenta development (GO:0060706)|positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|skin(1)	24	Lung NSC(77;0.0755)					AGGAAAAGGATAATTGGAATAA	0.48																																					p.Y316delinsFY		.											.	GCM1-90	0			c.947_948insTTT						.																																			SO:0001652	inframe_insertion	8521	exon6			.	D88613	CCDS4950.1	6p21-p12	2008-08-29	2001-11-28	2002-09-27	ENSG00000137270	ENSG00000137270			4197	protein-coding gene	gene with protein product		603715	"glial cells missing (Drosophila) homolog a"	GCMA		8962155	Standard	NM_003643		Approved	hGCMa	uc003pbp.3	Q9NP62	OTTHUMG00000014871	ENST00000259803.7:c.946_947insTTT	6.37:g.52993368_52993369insAAA	ENSP00000259803:p.Asn315_Tyr316insPhe	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	112	22	NM_003643	0	0	0	0	0	Q4VAQ7|Q5T0X0|Q99468|Q9P1X3	In_Frame_Ins	INS	ENST00000259803.7	37	CCDS4950.1																																																																																			.		0.48	GCM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040953.1			AAA	52993369	-	AAA	52993368	7	5	148	1	0	1	1	0	0	0	0	0	6317	1406	49	0	367	0	GCM1	6	52993368	In_Frame_Ins	INS	-	TCGA-MH-A55W-01A-11D-A26P-10	1224968	52993368	118121699	45	13203											
MDN1	23195	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90459294	90459294	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataaagtcctgggggattttGggtggcaaaaagcataaacc	14	9	12	6	0	0	0	0	0	0	0	1	1	1	1	2	4	2	2	2	4	6	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:90459294G>A	ENST00000369393.3	-	25	3698	c.3583C>T	c.(3583-3585)Caa>Taa	p.Q1195*	MDN1_ENST00000428876.1_Nonsense_Mutation_p.Q1195*			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1195					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GGGGGATTTTGGGTGGCAAAA	0.413																																					p.Q1195X													.	MDN1-100	0			c.C3583T						.						157	170	166					6																	90459294		2203	4300	6503	SO:0001587	stop_gained	23195	exon25			GATTTTGGGTGGC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.3583C>T	6.37:g.90459294G>A	ENSP00000358400:p.Gln1195*	Somatic	138	1		WXS	Illumina HiSeq	Phase_I	138	70	NM_014611	0	0	0	0	0	O15019|Q5T794	Nonsense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	41	9.048239	0.99048	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.1649	0.98147	0.0:0.0:1.0:0.0	.	.	.	.	X	1195;1195;1122	.	ENSP00000358400:Q1195X	Q	-	1	0	MDN1	90516015	1.000000	0.71417	0.939000	0.37840	0.819000	0.46315	9.378000	0.97191	2.753000	0.94483	0.655000	0.94253	CAA	.		0.413	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90459294	G	A	90459294	4	1	148	1	0	0	0	0	0	1	0	0	9440	1357	47	2	13519	2	MDN1	6	90459294	Nonsense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	37465926	90459294	80655773	46	13204											
AKAP12	9590	hgsc.bcm.edu;bcgsc.ca	37	chr6	151671659	151671659	+	Frame_Shift_Del	DEL	C	C	-																															aaagcaatgggaggagaccaCcagaaagctgatgaggccgg																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:151671659delC	ENST00000253332.1	+	3	2322	c.2133delC	c.(2131-2133)cacfs	p.H711fs	AKAP12_ENST00000359755.5_Frame_Shift_Del_p.H606fs|AKAP12_ENST00000354675.6_Frame_Shift_Del_p.H613fs|AKAP12_ENST00000402676.2_Frame_Shift_Del_p.H711fs			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	711					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)		GAGGAGACCACCAGAAAGCTG	0.532																																					p.H711fs	Melanoma(141;1616 1805 10049 24534 51979)	.											.	AKAP12-293	0			c.2133delC						.						96	106	103					6																	151671659		2203	4300	6503	SO:0001589	frameshift_variant	9590	exon4			.	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.2133delC	6.37:g.151671659delC	ENSP00000253332:p.His711fs	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	142	50	NM_005100	0	0	0	0	0	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Frame_Shift_Del	DEL	ENST00000253332.1	37	CCDS5229.1																																																																																			.		0.532	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			-	151671659	C	-	151671659	7	5	148	1	0	1	0	1	0	0	0	0	448	506	18	0	2172	0	AKAP12	6	151671659	Frame_Shift_Del	DEL	C	TCGA-MH-A55W-01A-11D-A26P-10	61212365	151671659	19443408	47	13205											
ZBTB2	57621	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	151686673	151686676	+	Frame_Shift_Del	DEL	TTTC	TTTC	-																															cattcagtctagtaagacggTttcttgttcctttttgatgg																								rs143773461		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TTTC	TTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:151686673_151686676delTTTC	ENST00000325144.4	-	3	1665_1668	c.1525_1528delGAAA	c.(1525-1530)gaaaccfs	p.ET509fs		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E509K(2)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		AGTAAGACGGTTTCTTGTTCCTTT	0.446																																					p.509_510del		.											.	ZBTB2-91	2	Substitution - Missense(2)	lung(1)|skin(1)	c.1525_1528del						.																																			SO:0001589	frameshift_variant	57621	exon3			.	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.1525_1528delGAAA	6.37:g.151686673_151686676delTTTC	ENSP00000323183:p.Glu509fs	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	127	39	NM_020861	0	0	0	0	0	A8K7C7|Q5SZ81|Q9P245	Frame_Shift_Del	DEL	ENST00000325144.4	37	CCDS5231.1																																																																																			.		0.446	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		-	151686676	TTTC	-	151686673	7	5	148	1	0	1	0	1	0	0	0	0	17560	1725	60	0	20	0	ZBTB2	6	151686673	Frame_Shift_Del	DEL	TTTC	TCGA-MH-A55W-01A-11D-A26P-10	15014	151686673	19428394	48	13206											
BBS9	27241	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	33380559	33380559	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acttgaacgtttctgtcgtgGtttctcctaactttgattca	7	18	7	9	2	3	2	1	2	2	0	5	2	3	2	1	1	2	2	1	1	2	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:33380559G>C	ENST00000242067.6	+	11	1770	c.1249G>C	c.(1249-1251)Gtt>Ctt	p.V417L	BBS9_ENST00000354265.4_Missense_Mutation_p.V417L|BBS9_ENST00000396127.2_Missense_Mutation_p.V417L|BBS9_ENST00000355070.2_Missense_Mutation_p.V417L|BBS9_ENST00000350941.3_Missense_Mutation_p.V417L	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	417					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			TTCTGTCGTGGTTTCTCCTAA	0.338									Bardet-Biedl syndrome																												p.V417L		.											.	BBS9-230	0			c.G1249C						.						187	175	179					7																	33380559		2203	4300	6503	SO:0001583	missense	27241	exon11	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GTCGTGGTTTCTC		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"parathyroid hormone responsive B1 gene"	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1249G>C	7.37:g.33380559G>C	ENSP00000242067:p.Val417Leu	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	94	34	NM_014451	0	0	4	9	5	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	37	CCDS43566.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.515586	0.44763	.	.	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000396125;ENST00000537775	D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.84727	0.5536	M	0.62723	1.935	0.80722	D	1	P;P;B;P	0.34864	0.473;0.473;0.245;0.473	B;B;B;B	0.42112	0.133;0.376;0.169;0.376	T	0.82524	-0.0414	10	0.31617	T	0.26	-21.4487	12.2466	0.54574	0.0859:0.0:0.9141:0.0	.	417;417;417;417	Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;PTHB1_HUMAN	L	417;417;417;417;417;417;417;295	ENSP00000242067:V417L;ENSP00000313122:V417L;ENSP00000379433:V417L;ENSP00000347182:V417L;ENSP00000346214:V417L	ENSP00000242067:V417L	V	+	1	0	BBS9	33347084	0.998000	0.40836	0.341000	0.25589	0.957000	0.61999	3.026000	0.49689	2.433000	0.82419	0.650000	0.86243	GTT	.		0.338	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			C	33380559	G	C	33380559	3	2	148	1	0	0	0	0	1	0	0	0	1343	1261	44	4	1287	4	BBS9	7	33380559	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		33380559	125758104	49	13207											
GBAS	2631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	56046042	56046042	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaattttcttttgtttcaGttcacaatgttaaaccggaa	11	18	6	6	1	3	1	2	1	1	0	3	2	3	2	1	1	1	3	1	1	5	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:56046042G>C	ENST00000322090.3	+	3	261		c.e3-1		GBAS_ENST00000446778.1_Intron|GBAS_ENST00000487370.1_Splice_Site	NM_001483.2	NP_001474.1	O75323	NIPS2_HUMAN	glioblastoma amplified sequence						ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TTTTGTTTCAGTTCACAATGT	0.323																																					.		.											.	GBAS-514	0			c.233-1G>C						.						178	160	166					7																	56046042		2203	4300	6503	SO:0001630	splice_region_variant	2631	exon3			GTTTCAGTTCACA	AF029786	CCDS5521.1, CCDS56488.1	7p12	2014-03-11			ENSG00000146729	ENSG00000146729			4179	protein-coding gene	gene with protein product		603004				9615231, 9661659, 20888800	Standard	NM_001483		Approved	NIPSNAP2	uc003tre.2	O75323	OTTHUMG00000022932	ENST00000322090.3:c.233-1G>C	7.37:g.56046042G>C		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	213	89	NM_001483	0	0	0	0	0	C9IYJ3|O43801|Q53X96	Splice_Site	SNP	ENST00000322090.3	37	CCDS5521.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279038	0.80692	.	.	ENSG00000146729	ENST00000322090	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0588	0.93078	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GBAS	56013536	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.510000	0.98004	2.744000	0.94065	0.655000	0.94253	.	.		0.323	GBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251524.1	NM_001483	Intron	C	56046042	G	C	56046042	5	2	148	1	0	0	0	0	0	0	1	0	6289	1043	36	4	242	4	GBAS	7	56046042	Splice_Site	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	22665483	56046042	103092621	50	13208											
TAF6	6878	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	99711723	99711723	+	Frame_Shift_Del	DEL	T	T	-																															tgacctcatccgttagcagcTggcaggtctcctcctgaatc																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:99711723delT	ENST00000344095.4	-	2	635	c.110delA	c.(109-111)cagfs	p.Q37fs	TAF6_ENST00000497233.1_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000437822.2_Frame_Shift_Del_p.Q74fs|TAF6_ENST00000418432.2_5'UTR|TAF6_ENST00000452041.1_Frame_Shift_Del_p.Q37fs|TAF6_ENST00000472509.1_Frame_Shift_Del_p.Q94fs|TAF6_ENST00000453269.2_Frame_Shift_Del_p.Q37fs	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	37					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGTTAGCAGCTGGCAGGTCTC	0.582																																					p.Q74fs		.											.	TAF6-91	0			c.221delA						.						140	126	130					7																	99711723		2203	4300	6503	SO:0001589	frameshift_variant	6878	exon2			.		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD", "transcription initiation factor TFIID 70 kD subunit"	602955	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.110delA	7.37:g.99711723delT	ENSP00000344537:p.Gln37fs	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	421	177	NM_001190415	0	0	0	0	0	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Frame_Shift_Del	DEL	ENST00000344095.4	37	CCDS5686.1																																																																																			.		0.582	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		-	99711723	T	-	99711723	7	5	148	1	0	1	0	1	0	0	0	0	15562	1580	55	0	1979	0	TAF6	7	99711723	Frame_Shift_Del	DEL	T	TCGA-MH-A55W-01A-11D-A26P-10	43665681	99711723	59426940	51	13209											
SLC13A4	26266	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	135370357	135370357	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacacgaggatgcatgccagCagggtgacagcccacggtgg	10	4	16	11	2	0	1	0	1	0	0	0	4	0	2	2	4	4	2	2	4	0	0	rs375873088	byFrequency	TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:135370357C>A	ENST00000354042.4	-	14	2207	c.1518G>T	c.(1516-1518)ctG>ctT	p.L506L	C7orf73_ENST00000422968.1_Intron|SLC13A4_ENST00000491630.1_5'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	506					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						TGCATGCCAGCAGGGTGACAG	0.552																																					p.L506L													.	SLC13A4-90	0			c.G1518T						.						200	174	183					7																	135370357		2203	4300	6503	SO:0001819	synonymous_variant	26266	exon14			TGCCAGCAGGGTG	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1518G>T	7.37:g.135370357C>A		Somatic	157	1		WXS	Illumina HiSeq	Phase_I	243	88	NM_012450	0	0	0	0	0	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	37	CCDS5840.1																																																																																			.		0.552	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		A	135370357	C	A	135370357	2	1	148	1	0	0	0	0	0	0	0	1	14426	697	25	4		4	SLC13A4	7	135370357	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	35658634	135370357	23768306	52	13210											
MLL3	58508	broad.mit.edu	37	chr7	151921114	151921114	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatacctatcacattgtctAcattgcagaataagatcttc	14	13	4	10	0	3	2	1	0	2	2	4	2	3	2	1	0	3	1	1	0	6	7			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:151921114A>T	ENST00000262189.6	-	20	3527	c.3309T>A	c.(3307-3309)tgT>tgA	p.C1103*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.C1103*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1103					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.C1103*(10)									CACATTGTCTACATTGCAGAA	0.338																																					p.C1103X													.	MLL3-1398	10	Substitution - Nonsense(10)	kidney(6)|endometrium(4)	c.T3309A						.						56	51	52					7																	151921114		2203	4300	6503	SO:0001587	stop_gained	58508	exon20			TTGTCTACATTGC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3309T>A	7.37:g.151921114A>T	ENSP00000262189:p.Cys1103*	Somatic	239	1		WXS	Illumina HiSeq	Phase_I	450	9	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	41	8.814636	0.98964	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.39	-2.79	0.05841	.	0.000000	0.50627	D	0.000105	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2367	0.59972	0.4373:0.0:0.5627:0.0	rs4024337	.	.	.	X	1103	.	ENSP00000262189:C1103X	C	-	3	2	MLL3	151552047	0.735000	0.28153	0.983000	0.44433	0.992000	0.81027	-0.154000	0.10130	-0.431000	0.07307	0.528000	0.53228	TGT	.		0.338	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151921114	A	T	151921114	4	4	148	1	0	0	0	0	0	1	0	0	9647	389	14	5	11586	5	MLL3	7	151921114	Nonsense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	16550757	151921114	7217549	53	13211											
ANK1	286	broad.mit.edu;bcgsc.ca	37	chr8	41582026	41582026	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggagcaactgggccacgTtgaggttctcgtagtgagcc	8	9	15	9	2	1	3	0	3	1	0	2	4	1	4	2	3	3	4	2	3	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr8:41582026T>G	ENST00000347528.4	-	7	742	c.659A>C	c.(658-660)aAc>aCc	p.N220T	ANK1_ENST00000265709.8_Missense_Mutation_p.N253T|ANK1_ENST00000379758.2_Missense_Mutation_p.N220T|ANK1_ENST00000396942.1_Missense_Mutation_p.N220T|ANK1_ENST00000289734.7_Missense_Mutation_p.N220T|ANK1_ENST00000352337.4_Missense_Mutation_p.N220T|ANK1_ENST00000396945.1_Missense_Mutation_p.N220T	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	220	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CTGGGCCACGTTGAGGTTCTC	0.572																																					p.N253T													.	ANK1-716	0			c.A758C						.						37	34	35					8																	41582026		2203	4300	6503	SO:0001583	missense	286	exon7			GCCACGTTGAGGT	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"Ankyrin repeat domain containing"	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.659A>C	8.37:g.41582026T>G	ENSP00000339620:p.Asn220Thr	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	42	7	NM_001142446	0	0	0	0	0	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.989986	0.74589	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.52	3.08	0.35506	Ankyrin repeat-containing domain (3);	0.145630	0.64402	D	0.000018	T	0.53965	0.1829	N	0.25094	0.71	0.80722	D	1	P;P;P;P;P	0.44690	0.586;0.841;0.699;0.651;0.538	P;P;B;P;P	0.49561	0.615;0.615;0.358;0.582;0.492	T	0.53620	-0.8413	10	0.72032	D	0.01	.	8.5499	0.33444	0.0:0.257:0.0:0.743	.	253;220;220;220;220	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	T	220;220;220;220;220;220;253;220	ENSP00000339620:N220T;ENSP00000289734:N220T;ENSP00000369082:N220T;ENSP00000380149:N220T;ENSP00000380147:N220T;ENSP00000309131:N220T;ENSP00000265709:N253T	ENSP00000265709:N253T	N	-	2	0	ANK1	41701183	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	2.870000	0.48451	0.361000	0.24292	-0.417000	0.06048	AAC	.		0.572	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		G	41582026	T	G	41582026	3	3	148	1	0	0	0	0	1	0	0	0	620	1725	60	5	5484	5	ANK1	8	41582026	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10		41582026	104781996	54	13212											
TRPM6	140803	broad.mit.edu	37	chr9	77448994	77448994	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagatttttctcaaggaatGagaggaatgggatttcaagg	13	11	12	5	0	2	2	2	1	1	2	3	6	2	5	1	4	0	0	1	4	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr9:77448994G>A	ENST00000360774.1	-	6	826	c.589C>T	c.(589-591)Cat>Tat	p.H197Y	TRPM6_ENST00000449912.2_Missense_Mutation_p.H192Y|TRPM6_ENST00000451710.3_Missense_Mutation_p.H197Y|TRPM6_ENST00000376871.3_Missense_Mutation_p.H197Y|TRPM6_ENST00000376864.4_Missense_Mutation_p.H197Y|TRPM6_ENST00000359047.2_Missense_Mutation_p.H197Y|TRPM6_ENST00000483186.1_5'Flank|TRPM6_ENST00000376872.3_Missense_Mutation_p.H197Y|TRPM6_ENST00000361255.3_Missense_Mutation_p.H192Y	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	197					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CTCAAGGAATGAGAGGAATGG	0.408																																					p.H197Y													.	TRPM6-335	0			c.C589T						.						134	124	127					9																	77448994		2203	4300	6503	SO:0001583	missense	140803	exon6			AGGAATGAGAGGA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.589C>T	9.37:g.77448994G>A	ENSP00000354006:p.His197Tyr	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	175	5	NM_017662	0	0	0	0	0	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592060	0.28357	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09;4.09;4.09;4.09	5.84	4.9	0.64082	.	0.532611	0.23708	N	0.045358	T	0.03136	0.0092	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;P	0.35600	0.037;0.037;0.011;0.027;0.323;0.511	B;B;B;B;B;B	0.36464	0.058;0.01;0.006;0.015;0.162;0.225	T	0.39078	-0.9631	10	0.72032	D	0.01	.	14.2191	0.65812	0.0:0.0:0.8037:0.1963	.	197;197;197;197;197;192	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	Y	197;197;197;197;192;192;196;197;197	ENSP00000354006:H197Y;ENSP00000407341:H197Y;ENSP00000366068:H197Y;ENSP00000366067:H197Y;ENSP00000396672:H192Y;ENSP00000354962:H192Y;ENSP00000366060:H197Y;ENSP00000351942:H197Y	ENSP00000351942:H197Y	H	-	1	0	TRPM6	76638814	0.546000	0.26457	0.283000	0.24790	0.960000	0.62799	3.317000	0.51968	1.325000	0.45301	0.491000	0.48974	CAT	.		0.408	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77448994	G	A	77448994	3	1	148	1	0	0	0	0	1	0	0	0	16623	1290	45	2	5615	2	TRPM6	9	77448994	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		77448994	63764437	55	13213											
GOLGA2	2801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131021446	131021446	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctcaccaactccctcacCtgggtttcctgcaactcttg	6	11	6	18	0	3	0	2	0	1	0	5	0	5	0	5	1	3	2	5	1	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr9:131021446C>T	ENST00000421699.2	-	19	2028	c.2016G>A	c.(2014-2016)caG>caA	p.Q672Q	AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Splice_Site_p.Q660Q	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	672					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						ACTCCCTCACCTGGGTTTCCT	0.632																																					p.Q672Q		.											.	GOLGA2-91	0			c.G2016A						.						42	46	45					9																	131021446		2203	4300	6503	SO:0001630	splice_region_variant	2801	exon19			CCTCACCTGGGTT	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.2016+1G>A	9.37:g.131021446C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	61	22	NM_004486	0	0	0	1	1	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	37	CCDS6896.2																																																																																			.		0.632	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	Silent	T	131021446	C	T	131021446	5	4	148	1	0	0	0	0	0	0	1	0	6572	695	24	2	1024	2	GOLGA2	9	131021446	Splice_Site	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	53572452	131021446	10191985	56	13214											
C9orf78	51759	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	132593305	132593305	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgttcctcatgttccacGatccctttcctcttctttag	4	19	4	14	1	4	0	1	0	3	0	8	1	8	0	4	0	0	2	4	0	1	7			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr9:132593305G>T	ENST00000372447.3	-	6	440	c.387C>A	c.(385-387)atC>atA	p.I129I	C9orf78_ENST00000461762.1_5'UTR	NM_016520.2	NP_057604.1	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78	129						cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)	13		Ovarian(14;0.00556)				CATGTTCCACGATCCCTTTCC	0.478																																					p.I129I													.	C9orf78-90	0			c.C387A						.						180	159	166					9																	132593305		2203	4300	6503	SO:0001819	synonymous_variant	51759	exon6			TTCCACGATCCCT	BC017570	CCDS6931.1	9q34.2	2012-03-16			ENSG00000136819	ENSG00000136819			24932	protein-coding gene	gene with protein product	"Hepatocellular carcinoma-associated antigen 59"					11042152, 12097419	Standard	NM_016520		Approved	HSPC220, HCA59	uc004byp.3	Q9NZ63	OTTHUMG00000020796	ENST00000372447.3:c.387C>A	9.37:g.132593305G>T		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	123	45	NM_016520	0	0	13	30	17	B3KPX8|Q8WVU6|Q9NT39	Silent	SNP	ENST00000372447.3	37	CCDS6931.1																																																																																			.		0.478	C9orf78-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054625.1	NM_016520		T	132593305	G	T	132593305	2	4	148	1	0	0	0	0	0	0	0	1	2502	1048	37	4		4	C9orf78	9	132593305	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	1571859	132593305	8620126	57	13215											
PRKCQ	5588	broad.mit.edu	37	chr10	6557067	6557067	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggacccgcagtcaaagtTggacaagccaatccgaagaa	15	4	11	11	2	1	1	1	0	0	1	2	4	2	3	3	2	1	3	3	2	5	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:6557067T>G	ENST00000263125.5	-	2	130	c.31A>C	c.(31-33)Aac>Cac	p.N11H	PRKCQ_ENST00000397176.2_Missense_Mutation_p.N11H|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	11	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CAGTCAAAGTTGGACAAGCCA	0.488																																					p.N11H	Ovarian(50;572 1126 10530 25349 30594)												.	PRKCQ-1380	0			c.A31C						.						54	56	55					10																	6557067		2203	4300	6503	SO:0001583	missense	5588	exon2			CAAAGTTGGACAA	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.31A>C	10.37:g.6557067T>G	ENSP00000263125:p.Asn11His	Somatic	95	3		WXS	Illumina HiSeq	Phase_I	106	9	NM_006257	0	0	2	2	0	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	37	CCDS7079.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742344	0.49151	.	.	ENSG00000065675	ENST00000263125;ENST00000397176	T;T	0.68331	-0.32;-0.26	5.2	3.99	0.46301	C2 calcium/lipid-binding domain, CaLB (1);	0.240987	0.44097	D	0.000499	T	0.52025	0.1709	N	0.22421	0.69	0.80722	D	1	B;B	0.09022	0.0;0.002	B;B	0.11329	0.006;0.003	T	0.52668	-0.8545	10	0.49607	T	0.09	.	12.6635	0.56828	0.0:0.0:0.1369:0.8631	.	11;11	Q04759-2;Q04759	.;KPCT_HUMAN	H	11	ENSP00000263125:N11H;ENSP00000380361:N11H	ENSP00000263125:N11H	N	-	1	0	PRKCQ	6597073	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.294000	0.59043	2.090000	0.63153	0.460000	0.39030	AAC	.		0.488	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		G	6557067	T	G	6557067	3	3	148	1	0	0	0	0	1	0	0	0	12544	1812	63	5	2157	5	PRKCQ	10	6557067	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10		6557067	128977680	58	13216											
PCDH15	65217	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	55600213	55600213	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tccaatggactccactacgaCcttggcaccaggaatttgtt	10	11	8	12	1	0	0	0	0	0	0	2	3	2	2	4	3	1	2	4	3	3	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:55600213C>A	ENST00000320301.6	-	29	4244	c.3850G>T	c.(3850-3852)Gtc>Ttc	p.V1284F	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.V1284F|PCDH15_ENST00000409834.1_Missense_Mutation_p.V895F|PCDH15_ENST00000414778.1_Missense_Mutation_p.V1289F|PCDH15_ENST00000395438.1_Missense_Mutation_p.V1284F|PCDH15_ENST00000395433.1_Missense_Mutation_p.V1262F|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Missense_Mutation_p.V1291F|PCDH15_ENST00000437009.1_Missense_Mutation_p.V1213F|PCDH15_ENST00000395445.1_Missense_Mutation_p.V1291F|PCDH15_ENST00000395432.2_Missense_Mutation_p.V1247F|PCDH15_ENST00000395430.1_Missense_Mutation_p.V1284F|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373957.3_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1284					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TCCACTACGACCTTGGCACCA	0.448										HNSCC(58;0.16)																											p.V1289F													.	PCDH15-193	0			c.G3865T						.						100	90	93					10																	55600213		2203	4300	6503	SO:0001583	missense	65217	exon30			CTACGACCTTGGC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"Cadherins / Cadherin-related"	14674	protein-coding gene	gene with protein product	"cadherin-related family member 15"	605514	"deafness, autosomal recessive 23", "protocadherin 15"	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3850G>T	10.37:g.55600213C>A	ENSP00000322604:p.Val1284Phe	Somatic	180	1		WXS	Illumina HiSeq	Phase_I	109	44	NM_001142763	0	0	0	0	0	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.130044	0.77549	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.65732	0.07;0.11;-0.01;0.01;0.02;-0.12;-0.14;-0.09;-0.14;-0.16;-0.17	5.43	5.43	0.79202	.	.	.	.	.	T	0.73321	0.3572	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;0.999;0.999;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.998;0.999;0.999;0.999;0.999;0.999;0.998;0.998;0.999;0.999;0.998;0.999;0.999	T	0.75431	-0.3320	9	0.87932	D	0	.	19.1946	0.93682	0.0:1.0:0.0:0.0	.	1262;1284;1284;1289;1213;1247;1284;1284;1291;1291;1284;1289;1284	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	F	1291;1289;1284;1284;895;1291;1247;1284;1262;1284;1284;1289;1213	ENSP00000363076:V1291F;ENSP00000410304:V1289F;ENSP00000378826:V1284F;ENSP00000386693:V895F;ENSP00000378832:V1291F;ENSP00000378820:V1247F;ENSP00000354950:V1284F;ENSP00000378821:V1262F;ENSP00000322604:V1284F;ENSP00000378818:V1284F;ENSP00000412628:V1213F	ENSP00000322604:V1284F	V	-	1	0	PCDH15	55270219	1.000000	0.71417	0.995000	0.50966	0.949000	0.60115	4.762000	0.62250	2.703000	0.92315	0.579000	0.79373	GTC	.		0.448	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55600213	C	A	55600213	3	1	148	1	0	0	0	0	1	0	0	0	11537	507	18	4	3656	4	PCDH15	10	55600213	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	49043146	55600213	79934534	59	13217											
NRG3	10718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	83635808	83635808	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctcctaccttcacgatTctactccctcctggaccctg	5	12	4	20	1	2	0	1	0	1	0	6	2	6	1	7	1	2	0	7	1	2	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:83635808T>C	ENST00000404547.1	+	1	712	c.712T>C	c.(712-714)Tct>Cct	p.S238P	NRG3_ENST00000372141.2_Missense_Mutation_p.S238P|NRG3_ENST00000404576.2_5'Flank|NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000556918.1_5'Flank			P56975	NRG3_HUMAN	neuregulin 3	238	Ser/Thr-rich.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		CCTTCACGATTCTACTCCCTC	0.602																																					p.S238P		.											.	NRG3-522	0			c.T712C						.						100	74	83					10																	83635808		2203	4300	6503	SO:0001583	missense	10718	exon1			CACGATTCTACTC	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.712T>C	10.37:g.83635808T>C	ENSP00000384796:p.Ser238Pro	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	150	62	NM_001165972	0	0	0	0	0	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.288753	0.59976	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.32515	1.45;1.46	4.14	4.14	0.48551	.	0.174325	0.27831	N	0.017667	T	0.35913	0.0948	L	0.36672	1.1	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.54759	0.76;0.76	T	0.13282	-1.0515	10	0.59425	D	0.04	-18.5043	11.474	0.50286	0.0:0.0:0.0:1.0	.	238;238	B9EGV5;P56975-4	.;.	P	238	ENSP00000361214:S238P;ENSP00000384796:S238P	ENSP00000361214:S238P	S	+	1	0	NRG3	83625788	0.998000	0.40836	0.059000	0.19551	0.993000	0.82548	5.633000	0.67825	1.879000	0.54435	0.529000	0.55759	TCT	.		0.602	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		C	83635808	T	C	83635808	3	2	148	1	0	0	0	0	1	0	0	0	10675	1783	62	3	714	3	NRG3	10	83635808	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	28035595	83635808	51898939	60	13218											
KIF11	3832	bcgsc.ca	37	chr10	94373230	94373230	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcaatccctgttgactttgGgaagggtcattactgccctt	8	14	9	10	0	2	1	2	1	0	0	3	2	3	2	2	2	2	1	2	2	3	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:94373230G>A	ENST00000260731.3	+	8	976	c.886G>A	c.(886-888)Gga>Aga	p.G296R		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	296	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GTTGACTTTGGGAAGGGTCAT	0.438																																					p.G296R	Colon(47;212 1003 2764 4062 8431)												.	KIF11-227	0			c.G886A						.						96	96	96					10																	94373230		2203	4300	6503	SO:0001583	missense	3832	exon8			ACTTTGGGAAGGG	X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"Kinesins"	6388	protein-coding gene	gene with protein product		148760	"kinesin-like 1"	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.886G>A	10.37:g.94373230G>A	ENSP00000260731:p.Gly296Arg	Somatic	61	0		WXS	Illumina HiSeq	Phase_1	66	4	NM_004523	0	0	0	0	0	A0AV49|B2RMV3|Q15716|Q5VWX0	Missense_Mutation	SNP	ENST00000260731.3	37	CCDS7422.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984191	0.93044	.	.	ENSG00000138160	ENST00000260731	D	0.88201	-2.35	5.58	5.58	0.84498	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.96090	0.8726	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96656	0.9485	10	0.87932	D	0	.	19.579	0.95458	0.0:0.0:1.0:0.0	.	296	P52732	KIF11_HUMAN	R	296	ENSP00000260731:G296R	ENSP00000260731:G296R	G	+	1	0	KIF11	94363210	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.732000	0.98816	2.617000	0.88574	0.591000	0.81541	GGA	.		0.438	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		A	94373230	G	A	94373230	3	1	148	1	0	0	0	0	1	0	0	0	8293	1233	43	2	916	2	KIF11	10	94373230	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	10737422	94373230	41161517	61	13219											
CYP2C8	1558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	96818110	96818110	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acctgctccattttgatcagGaagcaatcgataaagtcccg	12	10	8	11	2	1	1	1	1	0	0	4	3	3	2	3	1	2	2	3	1	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:96818110G>C	ENST00000371270.3	-	5	895	c.801C>G	c.(799-801)ttC>ttG	p.F267L	CYP2C8_ENST00000539050.1_Missense_Mutation_p.F181L|CYP2C8_ENST00000535898.1_Missense_Mutation_p.F165L	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	267					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	TTTTGATCAGGAAGCAATCGA	0.353																																					p.F267L		.											.	CYP2C8-90	0			c.C801G						.						163	145	151					10																	96818110		2203	4300	6503	SO:0001583	missense	1558	exon5			GATCAGGAAGCAA	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"Cytochrome P450s"	2622	protein-coding gene	gene with protein product		601129	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.801C>G	10.37:g.96818110G>C	ENSP00000360317:p.Phe267Leu	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	121	48	NM_000770	0	0	0	0	0	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557052	0.27827	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.06687	3.27;3.27;3.27	4.17	-0.451	0.12214	.	0.000000	0.85682	U	0.000000	T	0.07638	0.0192	L	0.29908	0.895	0.29573	N	0.849721	P;P;P;P	0.50617	0.922;0.937;0.779;0.937	P;P;P;P	0.50109	0.459;0.594;0.631;0.49	T	0.16424	-1.0403	10	0.49607	T	0.09	.	4.5328	0.12013	0.2874:0.0:0.5591:0.1535	.	181;165;235;267	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	L	267;234;165;181	ENSP00000360317:F267L;ENSP00000445062:F165L;ENSP00000442343:F181L	ENSP00000360317:F267L	F	-	3	2	CYP2C8	96808100	0.998000	0.40836	0.741000	0.31004	0.173000	0.22820	0.270000	0.18607	0.011000	0.14865	0.305000	0.20034	TTC	.		0.353	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		C	96818110	G	C	96818110	3	2	148	1	0	0	0	0	1	0	0	0	4173	1165	41	4	691	4	CYP2C8	10	96818110	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	2444880	96818110	38716637	62	13220											
SORBS1	10580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	97096528	97096528	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcctgcccccctctctgctTtcctctcatattgtccactc	3	14	4	20	1	2	0	1	0	2	0	7	0	4	0	6	0	2	1	6	0	1	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:97096528T>G	ENST00000361941.3	-	28	3415	c.3389A>C	c.(3388-3390)aAa>aCa	p.K1130T	SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371247.2_Missense_Mutation_p.K1130T|SORBS1_ENST00000371227.4_Missense_Mutation_p.K1084T|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000277982.5_Missense_Mutation_p.K989T|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371246.2_Missense_Mutation_p.K989T|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000371245.3_Intron	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		CCTCTCTGCTTTCCTCTCATA	0.552																																					p.K1130T		.											.	SORBS1-155	0			c.A3389C						.						74	71	72					10																	97096528		2203	4300	6503	SO:0001583	missense	10580	exon28			TCTGCTTTCCTCT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.3389A>C	10.37:g.97096528T>G	ENSP00000355136:p.Lys1130Thr	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	116	50	NM_001034954	0	0	0	0	0		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813778	0.32053	.	.	ENSG00000095637	ENST00000371247;ENST00000371227;ENST00000371246;ENST00000361941;ENST00000277982	T;T;T;T;T	0.08984	3.09;3.03;3.38;3.09;3.38	5.58	3.22	0.36961	.	0.488362	0.17388	N	0.176042	T	0.04815	0.0130	N	0.19112	0.55	0.80722	D	1	B;B;B	0.30281	0.275;0.079;0.275	B;B;B	0.27076	0.076;0.035;0.076	T	0.46331	-0.9199	10	0.15499	T	0.54	-0.5924	7.5752	0.27931	0.0:0.1794:0.0:0.8206	.	1084;1130;989	Q9BX66-11;Q9BX66;Q9BX66-2	.;SRBS1_HUMAN;.	T	1130;1084;989;1130;989	ENSP00000360293:K1130T;ENSP00000360271:K1084T;ENSP00000360292:K989T;ENSP00000355136:K1130T;ENSP00000277982:K989T	ENSP00000277982:K989T	K	-	2	0	SORBS1	97086518	0.873000	0.30073	0.996000	0.52242	0.854000	0.48673	0.144000	0.16135	0.406000	0.25560	0.459000	0.35465	AAA	.		0.552	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			G	97096528	T	G	97096528	3	3	148	1	0	0	0	0	1	0	0	0	14959	1841	64	5	569	5	SORBS1	10	97096528	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	278418	97096528	38438219	63	13221											
GPR123	84435	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	134912186	134912187	+	Frame_Shift_Del	DEL	TT	TT	-																															ggccggcacacgctcctgaaTttctgcttccacgcggccct																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:134912186_134912187delTT	ENST00000392607.3	+	4	610_611	c.174_175delTT	c.(172-177)aatttcfs	p.F59fs	GPR123_ENST00000607359.1_Frame_Shift_Del_p.F779fs	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	59					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CGCTCCTGAATTTCTGCTTCCA	0.658																																					p.58_59del		.											.	GPR123-90	0			c.174_175del						.																																			SO:0001589	frameshift_variant	84435	exon4			.	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.174_175delTT	10.37:g.134912186_134912187delTT	ENSP00000376384:p.Phe59fs	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	55	18	NM_001083909	0	0	0	0	0	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Frame_Shift_Del	DEL	ENST00000392607.3	37	CCDS41580.1																																																																																			.		0.658	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			-	134912187	TT	-	134912186	7	5	148	1	0	1	0	1	0	0	0	0	6657	1490	52	0	184	0	GPR123	10	134912186	Frame_Shift_Del	DEL	TT	TCGA-MH-A55W-01A-11D-A26P-10	37815658	134912186	622561	64	13222											
MARK2	2011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	63671476	63671476	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcctaaccatgccagggtcCcgggcctccacggcttctgc	6	7	11	17	2	1	0	0	0	1	0	3	0	3	0	6	3	4	1	6	3	1	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:63671476C>G	ENST00000509502.2	+	15	1894	c.1431C>G	c.(1429-1431)tcC>tcG	p.S477S	MARK2_ENST00000350490.7_Intron|MARK2_ENST00000315032.8_Silent_p.S511S|MARK2_ENST00000413835.2_Intron|MARK2_ENST00000402010.2_Silent_p.S511S|MARK2_ENST00000425897.2_Intron|MARK2_ENST00000408948.3_Intron|MARK2_ENST00000361128.5_Intron|MARK2_ENST00000513765.2_Silent_p.S478S|MARK2_ENST00000377810.3_Intron|MARK2_ENST00000377809.4_Silent_p.S511S|MARK2_ENST00000502399.3_Silent_p.S510S|MARK2_ENST00000508192.1_Intron	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2											autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						TGCCAGGGTCCCGGGCCTCCA	0.652																																					p.S511S		.											.	MARK2-766	0			c.C1533G						.						39	41	40					11																	63671476		1818	4074	5892	SO:0001819	synonymous_variant	2011	exon15			AGGGTCCCGGGCC	BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"ELKL motif kinase 1", "serine/threonine kinase", "protein-serine/threonine kinase", "Ser/Thr protein kinase PAR-1B"	600526	"ELKL motif kinase"	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.1431C>G	11.37:g.63671476C>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	38	13	NM_001039469	0	0	1	3	2		Silent	SNP	ENST00000509502.2	37	CCDS41665.1																																																																																			.		0.652	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		G	63671476	C	G	63671476	2	3	148	1	0	0	0	0	0	0	0	1	9338	610	22	4		4	MARK2	11	63671476	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		63671476	71335040	65	13223											
DPF2	5977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65107956	65107956	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcctttcttggactcaCagaccggagtagcccagagc	8	8	11	14	1	2	2	1	0	1	2	2	4	2	4	4	2	3	1	4	2	1	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:65107956C>G	ENST00000528416.1	+	2	266	c.133C>G	c.(133-135)Cag>Gag	p.Q45E	DPF2_ENST00000415073.2_Missense_Mutation_p.Q45E|DPF2_ENST00000252268.4_Missense_Mutation_p.Q45E|DPF2_ENST00000532264.1_Intron	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	45					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						CTTGGACTCACAGACCGGAGT	0.562																																					p.Q45E		.											.	DPF2-91	0			c.C133G						.						102	103	103					11																	65107956		2201	4297	6498	SO:0001583	missense	5977	exon2			GACTCACAGACCG	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"Zinc fingers, PHD-type"	9964	protein-coding gene	gene with protein product		601671	"requiem, apoptosis response zinc finger gene"	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.133C>G	11.37:g.65107956C>G	ENSP00000436901:p.Gln45Glu	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	137	53	NM_006268	0	0	9	13	4	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	37	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118519	0.94385	.	.	ENSG00000133884	ENST00000528416;ENST00000415073;ENST00000252268	D;D;D	0.92647	-3.06;-3.06;-3.08	5.52	5.52	0.82312	.	0.000000	0.35870	N	0.002937	D	0.96269	0.8783	M	0.83953	2.67	0.80722	D	1	D;D;D	0.76494	0.963;0.999;0.963	D;D;D	0.91635	0.973;0.999;0.973	D	0.96656	0.9485	10	0.87932	D	0	-25.3906	16.9414	0.86219	0.0:1.0:0.0:0.0	.	45;45;45	B4DT58;E9PN04;Q92785	.;.;REQU_HUMAN	E	45	ENSP00000436901:Q45E;ENSP00000399714:Q45E;ENSP00000252268:Q45E	ENSP00000252268:Q45E	Q	+	1	0	DPF2	64864532	1.000000	0.71417	0.968000	0.41197	0.994000	0.84299	7.818000	0.86416	2.588000	0.87417	0.655000	0.94253	CAG	.		0.562	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		G	65107956	C	G	65107956	3	3	148	1	0	0	0	0	1	0	0	0	4728	479	17	4	139	4	DPF2	11	65107956	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	1436480	65107956	69898560	66	13224											
ADRBK1	156	bcgsc.ca	37	chr11	67048958	67048958	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaagtgcctggacaaaaagCgcatcaagatgaagcagggg	15	5	14	7	1	1	3	1	2	0	1	1	4	1	4	1	3	3	2	1	3	5	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:67048958C>T	ENST00000308595.5	+	9	966	c.676C>T	c.(676-678)Cgc>Tgc	p.R226C	ADRBK1_ENST00000526285.1_Missense_Mutation_p.R226C	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	GGACAAAAAGCGCATCAAGAT	0.657																																					p.R226C													.	ADRBK1-521	0			c.C676T						.						76	69	71					11																	67048958		2200	4295	6495	SO:0001583	missense	156	exon9			AAAAAGCGCATCA	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"Pleckstrin homology (PH) domain containing"	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.676C>T	11.37:g.67048958C>T	ENSP00000312262:p.Arg226Cys	Somatic	45	0		WXS	Illumina HiSeq	Phase_1	62	4	NM_001619	0	0	13	13	0	B0ZBE1|Q13837|Q6GTT3	Missense_Mutation	SNP	ENST00000308595.5	37	CCDS8156.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.716682	0.48622	.	.	ENSG00000173020	ENST00000308595;ENST00000526285	T;T	0.66815	-0.23;-0.23	5.0	4.08	0.47627	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000007	T	0.79667	0.4485	M	0.70108	2.13	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.81805	-0.0764	10	0.87932	D	0	-13.2398	12.8248	0.57714	0.2975:0.7025:0.0:0.0	.	226;226	P25098;E9PRV7	ARBK1_HUMAN;.	C	226	ENSP00000312262:R226C;ENSP00000434126:R226C	ENSP00000312262:R226C	R	+	1	0	ADRBK1	66805534	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	2.696000	0.47052	1.225000	0.43566	-0.282000	0.10007	CGC	.		0.657	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		T	67048958	C	T	67048958	3	4	148	1	0	0	0	0	1	0	0	0	343	768	27	1	710	1	ADRBK1	11	67048958	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	1941002	67048958	67957558	67	13225											
FAT3	120114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	92599961	92599961	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcggcagcggccctggaatcTtgggcatctcgggccgtgct	4	8	16	13	4	2	0	0	0	2	0	3	1	2	1	2	5	2	3	2	5	1	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:92599961T>A	ENST00000298047.6	+	21	11730	c.11713T>A	c.(11713-11715)Ttg>Atg	p.L3905M	FAT3_ENST00000525166.1_Missense_Mutation_p.L3755M|FAT3_ENST00000533797.1_Missense_Mutation_p.L240M|FAT3_ENST00000409404.2_Missense_Mutation_p.L3905M			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3905	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CCCTGGAATCTTGGGCATCTC	0.592										TCGA Ovarian(4;0.039)																											p.L3905M		.											.	FAT3-73	0			c.T11713A						.						29	34	32					11																	92599961		2046	4196	6242	SO:0001583	missense	120114	exon21			GGAATCTTGGGCA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"Cadherins / Cadherin-related"	23112	protein-coding gene	gene with protein product	"cadherin-related family member 10"	612483	"FAT tumor suppressor homolog 3 (Drosophila)"			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11713T>A	11.37:g.92599961T>A	ENSP00000298047:p.Leu3905Met	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	102	43	NM_001008781	0	0	0	0	0	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	T	14.78	2.638068	0.47153	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	5.77	-6.79	0.01715	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.65688	0.2715	L	0.35414	1.06	0.80722	D	1	P;P	0.39601	0.68;0.645	B;B	0.43194	0.249;0.411	T	0.61367	-0.7077	9	0.49607	T	0.09	.	24.6348	0.99991	0.0:0.8789:0.0:0.1211	.	3905;3905	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	M	3905;3905;3755;240	ENSP00000298047:L3905M;ENSP00000387040:L3905M;ENSP00000432586:L3755M;ENSP00000436399:L240M	ENSP00000298047:L3905M	L	+	1	2	FAT3	92239609	0.086000	0.21541	0.260000	0.24451	0.815000	0.46073	-0.484000	0.06528	-1.317000	0.02292	-0.379000	0.06801	TTG	.		0.592	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92599961	T	A	92599961	3	1	148	1	0	0	0	0	1	0	0	0	5710	1606	56	5	11795	5	FAT3	11	92599961	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	25551003	92599961	42406555	68	13226											
ALKBH8	91801	ucsc.edu	37	chr11	107423870	107423870	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctttatctacattgttgtTctcatagtggaactcataac	11	17	5	8	0	4	0	2	0	3	0	5	1	4	1	0	1	3	2	0	1	5	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:107423870T>C	ENST00000428149.2	-	5	710	c.559A>G	c.(559-561)Aac>Gac	p.N187D	ALKBH8_ENST00000530933.1_5'Flank|ALKBH8_ENST00000429370.1_Missense_Mutation_p.N187D|ALKBH8_ENST00000389568.3_Missense_Mutation_p.N187D|ALKBH8_ENST00000417449.2_Missense_Mutation_p.N190D	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	187					cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		ACATTGTTGTTCTCATAGTGG	0.294																																					p.N187D													.	ALKBH8-68	0			c.A559G						.						143	131	135					11																	107423870		2200	4294	6494	SO:0001583	missense	91801	exon5			TGTTGTTCTCATA	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"Alkylation repair homologs", "RNA binding motif (RRM) containing"	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.559A>G	11.37:g.107423870T>C	ENSP00000415885:p.Asn187Asp	Somatic	15	0		WXS	Illumina HiSeq		38	4	NM_138775	0	0	1	1	0	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	37	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	T	20.3	3.961973	0.74016	.	.	ENSG00000137760	ENST00000428149;ENST00000429370;ENST00000389568;ENST00000417449	T;T;T;T	0.30448	2.81;1.53;2.81;2.81	5.52	4.4	0.53042	.	0.097141	0.64402	D	0.000002	T	0.42154	0.1190	M	0.67953	2.075	0.36045	D	0.84038	P	0.45283	0.855	P	0.51582	0.674	T	0.50866	-0.8777	10	0.37606	T	0.19	-14.8904	10.7841	0.46395	0.0:0.0748:0.0:0.9252	.	187	Q96BT7	ALKB8_HUMAN	D	187;187;187;190	ENSP00000415885:N187D;ENSP00000391225:N187D;ENSP00000374219:N187D;ENSP00000397673:N190D	ENSP00000260318:N187D	N	-	1	0	ALKBH8	106929080	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.671000	0.68095	0.922000	0.37019	-0.376000	0.06991	AAC	.		0.294	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		C	107423870	T	C	107423870	3	2	148	1	0	0	0	0	1	0	0	0	533	1783	62	3	1467	3	ALKBH8	11	107423870	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	14823909	107423870	27582646	69	13227											
C2CD2L	9854	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	118984691	118984704	+	Splice_Site	DEL	TTTCCAAGGTAACA	TTTCCAAGGTAACA	-																															cactctcatcatctctggtgTttccaaggtaacagggctct																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TTTCCAAGGTAACA	TTTCCAAGGTAACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:118984691_118984704delTTTCCAAGGTAACA	ENST00000528586.1	+	8	930_937	c.860_867delTTTCCAAGGTAACA	c.(859-867)gtttccaag>g	p.VSK287fs	C2CD2L_ENST00000336702.3_Splice_Site_p.VSK540fs			O14523	C2C2L_HUMAN	C2CD2-like	539						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)	13						ATCTCTGGTGTTTCCAAGGTAACAGGGCTCTGGG	0.598																																					p.540_542del		.											.	C2CD2L-68	0			c.1619_1626del						.																																			SO:0001630	splice_region_variant	9854	exon12			.	AK025223	CCDS8413.1	11q23.3	2008-04-22	2008-04-22	2008-04-22		ENSG00000172375			29000	protein-coding gene	gene with protein product			"transmembrane protein 24"	TMEM24		15289880	Standard	XM_005271738		Approved	KIAA0285	uc001pvn.3	O14523		ENST00000528586.1:c.867+1TTTCCAAGGTAACA>-	11.37:g.118984691_118984704delTTTCCAAGGTAACA		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	126	30	NM_014807	0	0	0	0	0	Q86UT7|Q86V04|Q8N522|Q8TBN4|Q96G10	Frame_Shift_Del	DEL	ENST00000528586.1	37																																																																																				.		0.598	C2CD2L-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000388199.2	NM_014807	Frame_Shift_Del	-	118984704	TTTCCAAGGTAACA	-	118984691	8	5	148	1	0	1	0	1	0	0	1	0	2159	1725	60	0	1665	0	C2CD2L	11	118984691	Splice_Site	DEL	TTTCCAAGGTAACA	TCGA-MH-A55W-01A-11D-A26P-10	11560821	118984691	16021825	70	13228											
CCDC15	80071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	124847425	124847425	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggataaatacaggaataagaGgagagttgcccattaaggtc	16	8	12	5	0	0	2	0	0	0	2	1	5	0	4	1	4	2	1	1	4	6	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:124847425G>C	ENST00000344762.5	+	6	941	c.682G>C	c.(682-684)Gga>Cga	p.G228R	CCDC15_ENST00000529051.1_Missense_Mutation_p.G228R	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	228						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		AGGAATAAGAGGAGAGTTGCC	0.378																																					p.G228R		.											.	CCDC15-69	0			c.G682C						.						67	65	66					11																	124847425		1828	4076	5904	SO:0001583	missense	80071	exon6			ATAAGAGGAGAGT	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.682G>C	11.37:g.124847425G>C	ENSP00000341684:p.Gly228Arg	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	57	19	NM_025004	0	0	0	0	0	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	.	.	.	.	.	.	.	.	.	.	G	2.444	-0.327892	0.05314	.	.	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.31510	1.49;1.57	3.57	0.63	0.17693	.	.	.	.	.	T	0.20455	0.0492	L	0.31926	0.97	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.22591	-1.0212	9	0.46703	T	0.11	-1.5802	5.3366	0.15961	0.3864:0.0:0.6136:0.0	.	228	Q0P6D6	CCD15_HUMAN	R	228	ENSP00000435403:G228R;ENSP00000341684:G228R	ENSP00000341684:G228R	G	+	1	0	CCDC15	124352635	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	0.169000	0.16641	0.314000	0.23086	-0.363000	0.07495	GGA	.		0.378	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004		C	124847425	G	C	124847425	3	2	148	1	0	0	0	0	1	0	0	0	2790	1001	35	4	700	4	CCDC15	11	124847425	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	5862734	124847425	10159091	71	13229											
STT3A	3703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	125478106	125478106	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaagttgaatccacaacaaTttgaagttcttttccggagc	12	12	8	9	1	1	2	0	2	1	0	3	3	3	3	2	1	2	3	2	1	5	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:125478106T>G	ENST00000529196.1	+	10	1089	c.883T>G	c.(883-885)Ttt>Gtt	p.F295V	STT3A_ENST00000531491.1_Missense_Mutation_p.F203V|STT3A_ENST00000392708.4_Missense_Mutation_p.F295V			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	295					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TCCACAACAATTTGAAGTTCT	0.507																																					p.F295V		.											.	STT3A-90	0			c.T883G						.						145	136	139					11																	125478106		2201	4299	6500	SO:0001583	missense	3703	exon9			CAACAATTTGAAG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.883T>G	11.37:g.125478106T>G	ENSP00000436962:p.Phe295Val	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	96	43	NM_152713	0	0	6	21	15	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	37	CCDS8458.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	34|34	5.361297|5.361297	0.95877|0.95877	.|.	.|.	ENSG00000134910|ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491|ENST00000526726	.|.	.|.	.|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84561|0.84561	0.5499|0.5499	M|M	0.91818|0.91818	3.245|3.245	0.80722|0.80722	D|D	1|1	P;P;D|.	0.53151|.	0.923;0.925;0.958|.	P;P;P|.	0.59012|.	0.622;0.85;0.85|.	D|D	0.88159|0.88159	0.2856|0.2856	9|5	0.66056|.	D|.	0.02|.	-19.0074|-19.0074	15.5287|15.5287	0.75932|0.75932	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	203;203;295|.	B4DJ24;E9PNQ1;P46977|.	.;.;STT3A_HUMAN|.	V|K	295;295;203|52	.|.	ENSP00000376472:F295V|.	F|N	+|+	1|3	0|2	STT3A|STT3A	124983316|124983316	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.990000|0.990000	0.78478|0.78478	8.040000|8.040000	0.89188|0.89188	2.148000|2.148000	0.66965|0.66965	0.533000|0.533000	0.62120|0.62120	TTT|AAT	.		0.507	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		G	125478106	T	G	125478106	3	3	148	1	0	0	0	0	1	0	0	0	15365	1493	52	5	913	5	STT3A	11	125478106	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	630681	125478106	9528410	72	13230											
IQSEC3	440073	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	275007	275007	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaagttcgtggaggacctGaaggagtccattgctgaggt	10	9	15	7	1	0	3	0	2	0	1	2	6	1	6	2	4	1	2	2	4	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:275007G>A	ENST00000538872.1	+	11	3040	c.2922G>A	c.(2920-2922)ctG>ctA	p.L974L	IQSEC3_ENST00000382841.2_Silent_p.L671L|RP11-598F7.6_ENST00000537295.1_lincRNA|RP11-598F7.5_ENST00000540136.1_RNA|IQSEC3_ENST00000326261.4_Silent_p.L974L			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	974	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		TGGAGGACCTGAAGGAGTCCA	0.602																																					p.L974L		.											.	IQSEC3-560	0			c.G2922A						.						80	76	77					12																	275007		2203	4300	6503	SO:0001819	synonymous_variant	440073	exon11			GGACCTGAAGGAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2922G>A	12.37:g.275007G>A		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	195	100	NM_001170738	0	0	0	0	0	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																			.		0.602	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		A	275007	G	A	275007	2	1	148	1	0	0	0	0	0	0	0	1	7840	1277	45	2		2	IQSEC3	12	275007	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		275007	133576888	73	13231											
CD163L1	283316	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7527336	7527336	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggctgtccccatccactagGcggagccgtttgtcctctta	5	11	10	15	3	1	0	0	0	1	0	4	1	4	1	5	3	1	2	5	3	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:7527336G>T	ENST00000313599.3	-	13	3168	c.3111C>A	c.(3109-3111)cgC>cgA	p.R1037R	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Silent_p.R1047R|CD163L1_ENST00000396630.1_Silent_p.R1037R			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1037	SRCR 10. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CATCCACTAGGCGGAGCCGTT	0.522											OREG0021653	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1037R													.	CD163L1-100	0			c.C3111A						.						32	30	31					12																	7527336		2203	4300	6503	SO:0001819	synonymous_variant	283316	exon13			CACTAGGCGGAGC	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"CD163 antigen-like 1"			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3111C>A	12.37:g.7527336G>T		Somatic	142	1	642	WXS	Illumina HiSeq	Phase_I	183	53	NM_174941	0	0	0	0	0	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			.		0.522	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		T	7527336	G	T	7527336	2	4	148	1	0	0	0	0	0	0	0	1	2974	1190	42	4		4	CD163L1	12	7527336	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	7252329	7527336	126324559	74	13232											
SFRS2IP	9169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	46342224	46342224	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagttaatcactaaccttaTacagcttttagaattttcat	15	16	3	7	0	2	1	2	0	0	1	2	1	2	1	1	0	3	2	1	0	7	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:46342224T>C	ENST00000369367.3	-	5	627	c.394A>G	c.(394-396)Ata>Gta	p.I132V	SCAF11_ENST00000419565.2_Missense_Mutation_p.I132V	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	132					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						ACTAACCTTATACAGCTTTTA	0.308																																					p.I132V		.											.	SCAF11-93	0			c.A394G						.						116	104	108					12																	46342224		1804	4076	5880	SO:0001583	missense	9169	exon5			ACCTTATACAGCT	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"RING-type (C3HC4) zinc fingers"	10784	protein-coding gene	gene with protein product		603668	"splicing factor, arginine/serine-rich 2, interacting protein", "serine/arginine-rich splicing factor 2, interacting protein"	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.394A>G	12.37:g.46342224T>C	ENSP00000358374:p.Ile132Val	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	25	13	NM_004719	0	0	0	0	0	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	0.096	-1.159474	0.01686	.	.	ENSG00000139218	ENST00000369367;ENST00000419565;ENST00000547018	T;T;T	0.40756	1.02;1.02;1.02	5.76	2.03	0.26663	.	2.058940	0.02882	U	0.132917	T	0.21103	0.0508	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21895	-1.0232	10	0.10377	T	0.69	.	7.6398	0.28288	0.0:0.2476:0.0:0.7524	.	132	Q99590	SCAFB_HUMAN	V	132;132;72	ENSP00000358374:I132V;ENSP00000413036:I132V;ENSP00000446746:I72V	ENSP00000358374:I132V	I	-	1	0	SCAF11	44628491	0.005000	0.15991	0.024000	0.17045	0.748000	0.42578	-0.080000	0.11339	0.095000	0.17434	0.460000	0.39030	ATA	.		0.308	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		C	46342224	T	C	46342224	3	2	148	1	0	0	0	0	1	0	0	0	14209	1406	49	3	4041	3	SFRS2IP	12	46342224	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	38814888	46342224	87509671	75	13233											
MTERFD3	80298	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	107371368	107371368	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttaatggtgccacagggttAaataatggccttactttttt	10	17	8	6	0	0	0	0	0	0	0	0	0	0	0	2	3	2	1	2	3	5	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:107371368A>C	ENST00000552029.1	-	2	3193	c.1125T>G	c.(1123-1125)ttT>ttG	p.F375L	MTERFD3_ENST00000392830.2_Missense_Mutation_p.F375L|C12orf23_ENST00000551237.1_Intron|MTERFD3_ENST00000240050.4_Missense_Mutation_p.F375L			Q49AM1	MTEF2_HUMAN		375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						CCACAGGGTTAAATAATGGCC	0.353																																					p.F375L		.											.	MTERFD3-68	0			c.T1125G						.						114	112	113					12																	107371368		2202	4300	6502	SO:0001583	missense	80298	exon3			AGGGTTAAATAAT																												ENST00000552029.1:c.1125T>G	12.37:g.107371368A>C	ENSP00000447651:p.Phe375Leu	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	124	68	NM_001033050	0	0	6	8	2	Q53HM2|Q9H4L6|Q9H7Y9	Missense_Mutation	SNP	ENST00000552029.1	37	CCDS9111.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167376	0.78339	.	.	ENSG00000120832	ENST00000392830;ENST00000240050;ENST00000552029	T;T;T	0.26373	1.74;1.74;1.74	5.95	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.33614	0.0869	M	0.63843	1.955	0.58432	D	0.999997	P	0.48503	0.911	P	0.49387	0.609	T	0.11867	-1.0570	10	0.87932	D	0	7.5321	8.7341	0.34516	0.859:0.0:0.141:0.0	.	375	Q49AM1	MTER3_HUMAN	L	375	ENSP00000376575:F375L;ENSP00000240050:F375L;ENSP00000447651:F375L	ENSP00000240050:F375L	F	-	3	2	MTERFD3	105895498	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.017000	0.64047	2.272000	0.75746	0.460000	0.39030	TTT	.		0.353	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			C	107371368	A	C	107371368	3	2	148	1	0	0	0	0	1	0	0	0	9946	359	13	5	36	5	MTERFD3	12	107371368	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	61029144	107371368	26480527	76	13234											
DIABLO	56616	bcgsc.ca	37	chr12	122710521	122710521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcagcggtacctgaagaatGaagttacgctgcgcgacagc	11	6	13	11	5	0	3	0	2	0	1	0	4	0	3	1	1	5	4	1	1	5	2	rs373013757		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:122710521G>A	ENST00000443649.3	-	2	858	c.41C>T	c.(40-42)tCa>tTa	p.S14L	DIABLO_ENST00000353548.6_Missense_Mutation_p.S14L|RP11-512M8.5_ENST00000535844.1_Intron|DIABLO_ENST00000464942.2_5'UTR|DIABLO_ENST00000413918.1_Missense_Mutation_p.S14L|DIABLO_ENST00000475784.1_5'Flank|DIABLO_ENST00000267169.6_5'UTR	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	14					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)				breast(1)|endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	7	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		CCTGAAGAATGAAGTTACGCT	0.682													g|||	1	0.000199681	8e-04	0	5008	,	,		11936	0		0	False		,,,				2504	0				p.S14L													.	DIABLO-659	0			c.C41T						.		LEU/SER,LEU/SER	1,4399		0,1,2199	19	17	18		41,41	1.8	0	12		18	0,8578		0,0,4289	no	missense,missense	DIABLO	NM_138929.3,NM_019887.4	145,145	0,1,6488	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	14/196,14/240	122710521	1,12977	2200	4289	6489	SO:0001583	missense	56616	exon2			AAGAATGAAGTTA	AF262240	CCDS9228.1, CCDS9229.1, CCDS73541.1	12q24.31	2011-08-02	2011-03-11		ENSG00000184047	ENSG00000184047			21528	protein-coding gene	gene with protein product	"second mitochondria-derived activator of caspase"	605219				12749848, 17237824, 21722859	Standard	NM_019887		Approved	SMAC, DIABLO-S, FLJ25049, FLJ10537, DFNA64	uc010tab.2	Q9NR28	OTTHUMG00000157014	ENST00000443649.3:c.41C>T	12.37:g.122710521G>A	ENSP00000398495:p.Ser14Leu	Somatic	33	0		WXS	Illumina HiSeq	Phase_1	52	4	NM_138929	0	0	1	1	0	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Missense_Mutation	SNP	ENST00000443649.3	37	CCDS9228.1	.	.	.	.	.	.	.	.	.	.	g	8.145	0.786089	0.16189	2.27E-4	0.0	ENSG00000184047	ENST00000413918;ENST00000443649;ENST00000353548	T;T;T	0.74947	-0.89;-0.89;-0.89	4.66	1.81	0.25067	.	0.737030	0.13496	N	0.383642	T	0.61578	0.2358	L	0.44542	1.39	0.09310	N	1	B;B	0.34103	0.437;0.053	B;B	0.27608	0.074;0.081	T	0.53301	-0.8458	10	0.87932	D	0	2.2226	7.2325	0.26051	0.2852:0.0:0.7148:0.0	.	14;14	Q6W3F3;Q9NR28	.;DBLOH_HUMAN	L	14	ENSP00000411638:S14L;ENSP00000398495:S14L;ENSP00000320343:S14L	ENSP00000339963:S14L	S	-	2	0	DIABLO	121276474	0.024000	0.19004	0.000000	0.03702	0.001000	0.01503	0.692000	0.25482	0.201000	0.20466	-0.342000	0.07992	TCA	.		0.682	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887		A	122710521	G	A	122710521	3	1	148	1	0	0	0	0	1	0	0	0	4528	1294	45	2	702	2	DIABLO	12	122710521	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	15339153	122710521	11141374	77	13235											
MMP17	4326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	132334421	132334421	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgtctccgacttcagcctcCcgcctggcggcatcgacgct	4	8	10	19	6	2	0	1	0	1	0	5	2	3	0	5	2	1	2	5	2	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:132334421C>T	ENST00000360564.1	+	9	1381	c.1279C>T	c.(1279-1281)Ccg>Tcg	p.P427S	MMP17_ENST00000535291.1_Missense_Mutation_p.P343S|MMP17_ENST00000535004.1_Intron	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	427					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	CTTCAGCCTCCCGCCTGGCGG	0.587																																					p.P427S		.											.	MMP17-226	0			c.C1279T						.						105	109	108					12																	132334421		2203	4300	6503	SO:0001583	missense	4326	exon9			AGCCTCCCGCCTG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"matrix metalloproteinase 17 (membrane-inserted)"			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1279C>T	12.37:g.132334421C>T	ENSP00000353767:p.Pro427Ser	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	270	85	NM_016155	0	0	0	0	0	Q14850	Missense_Mutation	SNP	ENST00000360564.1	37	CCDS31927.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629492	0.87660	.	.	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000534865;ENST00000542648	T;T;T;T	0.04603	3.59;3.59;3.59;3.59	4.48	4.48	0.54585	Hemopexin/matrixin (2);	0.064020	0.64402	D	0.000006	T	0.23492	0.0568	M	0.83483	2.645	0.80722	D	1	D	0.65815	0.995	D	0.68039	0.955	T	0.04509	-1.0946	10	0.72032	D	0.01	.	17.1756	0.86841	0.0:1.0:0.0:0.0	.	427	Q9ULZ9	MMP17_HUMAN	S	427;343;268;57	ENSP00000353767:P427S;ENSP00000441106:P343S;ENSP00000442104:P268S;ENSP00000439542:P57S	ENSP00000353767:P427S	P	+	1	0	MMP17	130900374	1.000000	0.71417	0.995000	0.50966	0.701000	0.40568	7.727000	0.84838	2.054000	0.61138	0.471000	0.43371	CCG	.		0.587	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		T	132334421	C	T	132334421	3	4	148	1	0	0	0	0	1	0	0	0	9681	623	22	2	1313	2	MMP17	12	132334421	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	9623900	132334421	1517474	78	13236											
SUCLA2	8803	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	48571053	48571053	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggaacggagacaccagcttCttgcaataattccatactca	13	9	8	11	1	2	1	1	0	1	1	3	3	3	2	2	2	4	2	2	2	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr13:48571053C>G	ENST00000378654.3	-	2	252	c.196G>C	c.(196-198)Gaa>Caa	p.E66Q	SUCLA2_ENST00000497202.1_5'UTR|SUCLA2_ENST00000534875.1_Missense_Mutation_p.E8Q|SUCLA2_ENST00000544100.1_5'UTR|SUCLA2_ENST00000543413.1_Missense_Mutation_p.E8Q	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	66	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	ACACCAGCTTCTTGCAATAAT	0.393																																					p.E66Q													.	SUCLA2-226	0			c.G196C						.						126	114	118					13																	48571053		2203	4300	6503	SO:0001583	missense	8803	exon2			CAGCTTCTTGCAA	AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.196G>C	13.37:g.48571053C>G	ENSP00000367923:p.Glu66Gln	Somatic	115	1		WXS	Illumina HiSeq	Phase_I	187	55	NM_003850	0	0	6	10	4	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Missense_Mutation	SNP	ENST00000378654.3	37	CCDS9406.1	.	.	.	.	.	.	.	.	.	.	c	13.38	2.219646	0.39201	.	.	ENSG00000136143	ENST00000378654;ENST00000378645;ENST00000534875;ENST00000543413	T;T;T	0.71817	-0.6;-0.6;-0.6	5.63	5.63	0.86233	ATP-grasp fold (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.109463	0.64402	D	0.000002	T	0.56819	0.2011	N	0.17872	0.535	0.80722	D	1	B;B	0.22276	0.067;0.031	B;B	0.29267	0.1;0.1	T	0.52719	-0.8538	10	0.27785	T	0.31	-27.7135	12.0435	0.53466	0.0:0.9215:0.0:0.0785	.	66;66	E5KS55;Q9P2R7	.;SUCB1_HUMAN	Q	66;44;8;8	ENSP00000367923:E66Q;ENSP00000438182:E8Q;ENSP00000441056:E8Q	ENSP00000367912:E44Q	E	-	1	0	SUCLA2	47469054	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.665000	0.68052	2.656000	0.90262	0.591000	0.81541	GAA	.		0.393	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1			G	48571053	C	G	48571053	3	3	148	1	0	0	0	0	1	0	0	0	15395	922	32	4	1235	4	SUCLA2	13	48571053	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		48571053	66598825	79	13237											
STK24	8428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99127511	99127511	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtcctcttacctttaatGtctctgtggattttcttctc	5	20	6	10	0	4	0	0	0	4	0	7	2	5	1	2	1	1	0	2	1	2	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr13:99127511G>T	ENST00000376547.3	-	4	613	c.468C>A	c.(466-468)gaC>gaA	p.D156E	STK24_ENST00000397517.2_Missense_Mutation_p.D144E|STK24_ENST00000539966.1_Missense_Mutation_p.D125E	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TACCTTTAATGTCTCTGTGGA	0.443																																					p.D156E		.											.	STK24-979	0			c.C468A						.						108	99	102					13																	99127511		2203	4300	6503	SO:0001583	missense	8428	exon4			TTTAATGTCTCTG	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"STE20-like kinase 3", "sterile 20-like kinase 3"	604984	"serine/threonine kinase 24 (Ste20, yeast homolog)"			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.468C>A	13.37:g.99127511G>T	ENSP00000365730:p.Asp156Glu	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	123	25	NM_003576	0	0	0	0	0	O14840|Q5JV92	Missense_Mutation	SNP	ENST00000376547.3	37	CCDS9488.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.3|20.3	3.964958|3.964958	0.74131|0.74131	.|.	.|.	ENSG00000102572|ENSG00000102572	ENST00000397517;ENST00000376547;ENST00000539966;ENST00000376533;ENST00000543110|ENST00000444574	D;D;D|.	0.92911|.	-3.13;-3.13;-3.13|.	4.93|4.93	-3.84|-3.84	0.04256|0.04256	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.64402|.	U|.	0.000020|.	D|D	0.84361|0.84361	0.5455|0.5455	H|H	0.97340|0.97340	3.985|3.985	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	D|D	0.85372|0.85372	0.1114|0.1114	10|5	0.87932|.	D|.	0|.	.|.	11.1814|11.1814	0.48631|0.48631	0.5388:0.0:0.4612:0.0|0.5388:0.0:0.4612:0.0	.|.	125;144;156|.	B4DR80;Q5U0E6;Q9Y6E0|.	.;.;STK24_HUMAN|.	E|N	144;156;125;132;144|62	ENSP00000380651:D144E;ENSP00000365730:D156E;ENSP00000442539:D125E|.	ENSP00000365716:D132E|.	D|H	-|-	3|1	2|0	STK24|STK24	97925512|97925512	0.972000|0.972000	0.33761|0.33761	0.957000|0.957000	0.39632|0.39632	0.955000|0.955000	0.61496|0.61496	0.333000|0.333000	0.19768|0.19768	-0.885000|-0.885000	0.03971|0.03971	-0.390000|-0.390000	0.06520|0.06520	GAC|CAT	.		0.443	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576		T	99127511	G	T	99127511	3	4	148	1	0	0	0	0	1	0	0	0	15325	1368	48	4	895	4	STK24	13	99127511	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	50556458	99127511	16042367	80	13238											
CIDEB	27141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24775587	24775587	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataggcctcttacccttgtaGggctccagctctgaccagac	8	10	9	14	0	2	2	0	1	2	1	3	2	3	2	4	2	2	3	4	2	3	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:24775587G>C	ENST00000336557.5	-	6	1631	c.329C>G	c.(328-330)cCt>cGt	p.P110R	CIDEB_ENST00000258807.5_Missense_Mutation_p.P110R|CIDEB_ENST00000554411.1_Missense_Mutation_p.P110R|NOP9_ENST00000267425.3_3'UTR|LTB4R2_ENST00000528054.1_5'Flank			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	110	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TACCCTTGTAGGGCTCCAGCT	0.562																																					p.P110R		.											.	CIDEB-90	0			c.C329G						.						140	111	121					14																	24775587		2203	4300	6503	SO:0001583	missense	27141	exon5			CTTGTAGGGCTCC	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.329C>G	14.37:g.24775587G>C	ENSP00000337731:p.Pro110Arg	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	150	51	NM_014430	0	0	4	6	2	D3DS73|Q546V8|Q9NNW9	Missense_Mutation	SNP	ENST00000336557.5	37	CCDS32056.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.541298	0.45280	.	.	ENSG00000136305	ENST00000554411;ENST00000336557;ENST00000258807;ENST00000541830	T;T;T	0.48522	0.81;0.81;0.81	4.43	4.43	0.53597	Caspase-activated nuclease CIDE-N (2);	0.163888	0.56097	D	0.000036	T	0.67468	0.2896	M	0.87827	2.91	0.80722	D	1	P	0.37038	0.579	P	0.53224	0.721	T	0.72371	-0.4314	10	0.72032	D	0.01	-12.5195	11.7635	0.51918	0.0:0.0:0.8233:0.1767	.	110	Q9UHD4	CIDEB_HUMAN	R	110	ENSP00000451089:P110R;ENSP00000337731:P110R;ENSP00000258807:P110R	ENSP00000258807:P110R	P	-	2	0	CIDEB	23845427	0.995000	0.38212	0.513000	0.27749	0.217000	0.24651	2.732000	0.47352	2.307000	0.77673	0.561000	0.74099	CCT	.		0.562	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			C	24775587	G	C	24775587	3	2	148	1	0	0	0	0	1	0	0	0	3432	1000	35	4	342	4	CIDEB	14	24775587	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		24775587	82573953	81	13239											
ACTR10	55860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	58680398	58680398	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttggggagcactacccctagGaggaaaagctcttcacaagt	12	8	11	10	0	2	0	1	0	1	0	2	3	2	3	2	4	3	2	2	4	5	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:58680398G>C	ENST00000254286.4	+	6	580	c.500G>C	c.(499-501)gGa>gCa	p.G167A		NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	167					microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						CTACCCCTAGGAGGAAAAGCT	0.363																																					p.G167A		.											.	ACTR10-90	0			c.G500C						.						68	66	67					14																	58680398		2203	4300	6503	SO:0001583	missense	55860	exon6			CCCTAGGAGGAAA	AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966			17372	protein-coding gene	gene with protein product						12857853	Standard	NM_018477		Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.500G>C	14.37:g.58680398G>C	ENSP00000254286:p.Gly167Ala	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	27	16	NM_018477	0	0	10	20	10	Q9H9Y5|Q9NWY2	Missense_Mutation	SNP	ENST00000254286.4	37	CCDS32090.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201439	0.58234	.	.	ENSG00000131966	ENST00000543474;ENST00000254286	D	0.94497	-3.44	5.8	5.8	0.92144	.	0.101891	0.64402	D	0.000002	D	0.88066	0.6337	N	0.13003	0.285	0.80722	D	1	B	0.27166	0.17	B	0.30716	0.119	D	0.83755	0.0211	10	0.02654	T	1	-16.7897	17.2104	0.86929	0.0:0.0:1.0:0.0	.	167	Q9NZ32	ARP10_HUMAN	A	167	ENSP00000254286:G167A	ENSP00000254286:G167A	G	+	2	0	ACTR10	57750151	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.523000	0.81856	2.748000	0.94277	0.655000	0.94253	GGA	.		0.363	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411405.1			C	58680398	G	C	58680398	3	2	148	1	0	0	0	0	1	0	0	0	208	1174	41	4	522	4	ACTR10	14	58680398	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	33904811	58680398	48669142	82	13240											
SPTLC2	9517	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	78036838	78036838	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcctctagttcttcatgCttgtccaggtttcctgtgtg	4	17	9	11	0	3	0	1	0	2	0	6	0	6	0	3	1	2	4	3	1	1	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:78036838C>A	ENST00000216484.2	-	5	838	c.645G>T	c.(643-645)aaG>aaT	p.K215N		NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	215					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	GTTCTTCATGCTTGTCCAGGT	0.368																																					p.K215N		.											.	SPTLC2-92	0			c.G645T						.						128	115	119					14																	78036838		2203	4300	6503	SO:0001583	missense	9517	exon5			TTCATGCTTGTCC	AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.645G>T	14.37:g.78036838C>A	ENSP00000216484:p.Lys215Asn	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	75	34	NM_004863	0	0	0	0	0	Q16685	Missense_Mutation	SNP	ENST00000216484.2	37	CCDS9865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.04|12.04	1.817411|1.817411	0.32145|0.32145	.|.	.|.	ENSG00000100596|ENSG00000100596	ENST00000554901|ENST00000216484	.|D	.|0.90444	.|-2.67	5.49|5.49	1.55|1.55	0.23275|0.23275	.|Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.169622	.|0.56097	.|D	.|0.000039	D|D	0.82559|0.82559	0.5063|0.5063	L|L	0.27053|0.27053	0.805|0.805	0.54753|0.54753	D|D	0.999983|0.999983	.|B	.|0.17038	.|0.02	.|B	.|0.20577	.|0.03	T|T	0.71119|0.71119	-0.4685|-0.4685	5|10	.|0.34782	.|T	.|0.22	-25.2504|-25.2504	10.0683|10.0683	0.42317|0.42317	0.0:0.4966:0.0:0.5034|0.0:0.4966:0.0:0.5034	.|.	.|215	.|O15270	.|SPTC2_HUMAN	S|N	152|215	.|ENSP00000216484:K215N	.|ENSP00000216484:K215N	A|K	-|-	1|3	0|2	SPTLC2|SPTLC2	77106591|77106591	0.942000|0.942000	0.31987|0.31987	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	0.022000|0.022000	0.13511|0.13511	0.071000|0.071000	0.16664|0.16664	-0.137000|-0.137000	0.14449|0.14449	GCA|AAG	.		0.368	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863		A	78036838	C	A	78036838	3	1	148	1	0	0	0	0	1	0	0	0	15156	796	28	4	1075	4	SPTLC2	14	78036838	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	19356440	78036838	29312702	83	13241											
C14orf159	80017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	91681816	91681816	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtactcatgtgctgtccaCagtcagtacctgaggaaagc	10	10	10	11	0	2	1	2	1	0	0	3	2	3	2	2	1	4	3	2	1	3	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:91681816C>T	ENST00000523771.1	+	13	2220	c.1617C>T	c.(1615-1617)caC>caT	p.H539H	C14orf159_ENST00000522322.1_Silent_p.H539H|C14orf159_ENST00000520328.1_Silent_p.H487H|C14orf159_ENST00000521077.2_Silent_p.H504H|C14orf159_ENST00000428926.2_Silent_p.H539H|C14orf159_ENST00000256324.10_Silent_p.H544H|C14orf159_ENST00000523816.1_Silent_p.H539H|C14orf159_ENST00000412671.2_Silent_p.H544H|C14orf159_ENST00000518868.1_Silent_p.H544H|C14orf159_ENST00000525393.2_Silent_p.H415H			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	539						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		GTGCTGTCCACAGTCAGTACC	0.552																																					p.H544H		.											.	C14orf159-92	0			c.C1632T						.						117	103	108					14																	91681816		2203	4300	6503	SO:0001819	synonymous_variant	80017	exon13			TGTCCACAGTCAG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1617C>T	14.37:g.91681816C>T		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	95	39	NM_001102368	0	0	18	42	24	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	C	3.836	-0.034789	0.07543	.	.	ENSG00000133943	ENST00000522816	.	.	.	5.34	-3.48	0.04739	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.34900	-0.9810	4	.	.	.	.	7.4016	0.26967	0.0:0.1871:0.1388:0.6741	.	.	.	.	I	140	.	.	T	+	2	0	C14orf159	90751569	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.541000	0.06099	-0.508000	0.06540	-0.175000	0.13238	ACA	.		0.552	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		T	91681816	C	T	91681816	2	4	148	1	0	0	0	0	0	0	0	1	1759	477	17	2		2	C14orf159	14	91681816	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	13644978	91681816	15667724	84	13242											
MARK3	4140	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	103969341	103969341	+	Frame_Shift_Del	DEL	G	G	-																															ggacatgatgcgggaaatccGcaaagtgttggacgccaata																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:103969341delG	ENST00000429436.2	+	18	2549	c.2039delG	c.(2038-2040)cgcfs	p.R680fs	MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000416682.2_Frame_Shift_Del_p.R679fs|MARK3_ENST00000440884.3_Frame_Shift_Del_p.R586fs|MARK3_ENST00000553942.1_Frame_Shift_Del_p.R671fs|MARK3_ENST00000303622.9_Frame_Shift_Del_p.R656fs|MARK3_ENST00000335102.5_Frame_Shift_Del_p.R703fs|MARK3_ENST00000216288.7_Frame_Shift_Del_p.R640fs	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	680						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.I639_K641del(2)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			CGGGAAATCCGCAAAGTGTTG	0.532																																					p.R680fs		.											.	MARK3-360	2	Deletion - In frame(2)	central_nervous_system(2)	c.2039delG						.						69	71	71					14																	103969341		2055	4220	6275	SO:0001589	frameshift_variant	4140	exon18			.	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.2039delG	14.37:g.103969341delG	ENSP00000411397:p.Arg680fs	Somatic	303	0		WXS	Illumina HiSeq	Phase_I	203	69	NM_001128918	0	0	0	0	0	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Frame_Shift_Del	DEL	ENST00000429436.2	37	CCDS45165.1																																																																																			.		0.532	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		-	103969341	G	-	103969341	7	5	148	1	0	1	0	1	0	0	0	0	9339	1087	38	0	2109	0	MARK3	14	103969341	Frame_Shift_Del	DEL	G	TCGA-MH-A55W-01A-11D-A26P-10	12287525	103969341	3380199	85	13243											
AHNAK2	113146	broad.mit.edu	37	chr14	105406110	105406110	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgactttagctgctgcttcAccccctgttgctgccggtgc	3	14	10	14	1	1	1	1	1	0	0	1	1	1	1	3	1	6	5	3	1	1	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:105406110A>C	ENST00000333244.5	-	7	15797	c.15678T>G	c.(15676-15678)ggT>ggG	p.G5226G	AHNAK2_ENST00000557457.1_Silent_p.G224G	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5226						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTGCTGCTTCACCCCCTGTTG	0.572																																					p.G5226G													.	AHNAK2-47	0			c.T15678G						.						250	268	262					14																	105406110		2031	4186	6217	SO:0001819	synonymous_variant	113146	exon7			TGCTTCACCCCCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.15678T>G	14.37:g.105406110A>C		Somatic	91	9		WXS	Illumina HiSeq	Phase_I	95	23	NM_138420	0	0	32	32	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.		0.572	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105406110	A	C	105406110	2	2	148	1	0	0	0	0	0	0	0	1	415	146	6	5		5	AHNAK2	14	105406110	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	1436769	105406110	1943430	86	13244											
MGA	23269	bcgsc.ca	37	chr15	42057124	42057124	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	actccacacacctctgccaaCcttgtgatgactccgcaagg	10	8	7	16	1	1	2	0	2	1	0	3	2	3	2	5	1	2	1	5	1	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:42057124C>T	ENST00000570161.1	+	22	7785	c.7785C>T	c.(7783-7785)aaC>aaT	p.N2595N	MGA_ENST00000389936.4_Silent_p.N2556N|MGA_ENST00000545763.1_Silent_p.N2386N|MGA_ENST00000219905.7_Silent_p.N2595N|MGA_ENST00000566586.1_Silent_p.N2386N			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCTCTGCCAACCTTGTGATGA	0.453																																					p.N2595N													.	MGA-522	0			c.C7785T						.						108	110	110					15																	42057124		2018	4179	6197	SO:0001819	synonymous_variant	23269	exon23			TGCCAACCTTGTG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"MAX dimerization proteins", "T-boxes"	14010	protein-coding gene	gene with protein product			"MAX gene associated"				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7785C>T	15.37:g.42057124C>T		Somatic	157	0		WXS	Illumina HiSeq	Phase_1	135	5	NM_001164273	0	0	0	0	0	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			.		0.453	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42057124	C	T	42057124	2	4	148	1	0	0	0	0	0	0	0	1	9565	506	18	2		2	MGA	15	42057124	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		42057124	60474268	87	13245											
ELL3	80237	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	44066413	44066413	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcctcgccgaactcttttAatctctgctcccagctctat	6	15	5	15	2	3	0	0	0	3	0	7	1	5	0	3	0	3	3	3	0	3	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:44066413A>C	ENST00000319359.3	-	9	1646	c.1005T>G	c.(1003-1005)atT>atG	p.I335M	RP11-296A16.1_ENST00000417761.2_3'UTR|ELL3_ENST00000497465.1_5'UTR|SERF2_ENST00000381359.1_5'Flank	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	335					DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)			cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		GAACTCTTTTAATCTCTGCTC	0.512																																					p.I335M													.	ELL3-91	0			c.T1005G						.						97	91	93					15																	44066413		2198	4298	6496	SO:0001583	missense	80237	exon9			TCTTTTAATCTCT	AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.1005T>G	15.37:g.44066413A>C	ENSP00000320346:p.Ile335Met	Somatic	160	1		WXS	Illumina HiSeq	Phase_I	144	58	NM_025165	0	0	0	1	1	B3KQ66|B3KX08|Q6I9Z7|Q9H634	Missense_Mutation	SNP	ENST00000319359.3	37	CCDS10102.1	.	.	.	.	.	.	.	.	.	.	A	9.435	1.086448	0.20390	.	.	ENSG00000128886	ENST00000319359	T	0.21543	2.0	5.92	0.357	0.16079	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.091491	0.48286	D	0.000192	T	0.08088	0.0202	N	0.04132	-0.27	0.43994	D	0.996697	B;B;P	0.35050	0.334;0.334;0.482	B;B;B	0.35655	0.15;0.15;0.207	T	0.26326	-1.0106	10	0.34782	T	0.22	-19.7297	6.1561	0.20338	0.2417:0.3845:0.3738:0.0	.	335;335;289	B3KX08;Q9HB65;B3KQ66	.;ELL3_HUMAN;.	M	335	ENSP00000320346:I335M	ENSP00000320346:I335M	I	-	3	3	ELL3	41853705	0.993000	0.37304	1.000000	0.80357	0.829000	0.46940	0.127000	0.15790	0.374000	0.24650	-0.479000	0.04858	ATT	.		0.512	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165		C	44066413	A	C	44066413	3	2	148	1	0	0	0	0	1	0	0	0	5077	358	13	5	200	5	ELL3	15	44066413	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	2009289	44066413	58464979	88	13246											
FAM63B	54629	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	59139573	59139573	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgggaaagcctacacaacgtAgatggtgatggaaatttctg	13	10	12	6	1	1	2	0	1	1	1	1	4	1	4	1	3	3	1	1	3	5	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:59139573A>T	ENST00000559228.1	+	7	1528	c.1446A>T	c.(1444-1446)gtA>gtT	p.V482V	FAM63B_ENST00000450403.2_Silent_p.V482V			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	482										central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						TACACAACGTAGATGGTGATG	0.388																																					p.V482V		.											.	FAM63B-90	0			c.A1446T						.						143	132	135					15																	59139573		1828	4082	5910	SO:0001819	synonymous_variant	54629	exon7			CAACGTAGATGGT	AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.1446A>T	15.37:g.59139573A>T		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	48	17	NM_001040450	0	0	3	4	1	B2RTT8|Q9ULQ6	Silent	SNP	ENST00000559228.1	37	CCDS42046.1																																																																																			.		0.388	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092		T	59139573	A	T	59139573	2	4	148	1	0	0	0	0	0	0	0	1	5616	407	15	5		5	FAM63B	15	59139573	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	15073160	59139573	43391819	89	13247											
DAPK2	23604	broad.mit.edu;ucsc.edu	37	chr15	64200745	64200745	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggtgctgctcctcctccgtgGgtggagggctttcctcctgg	1	12	15	13	1	0	0	0	0	0	0	5	1	5	1	5	5	2	3	5	5	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:64200745G>A	ENST00000457488.1	-	12	1117	c.1087C>T	c.(1087-1089)Cca>Tca	p.P363S	DAPK2_ENST00000261891.3_Missense_Mutation_p.P363S	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	363					anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CTCCTCCGTGGGTGGAGGGCT	0.602																																					p.P363S													.	DAPK2-333	0			c.C1087T						.						54	39	44					15																	64200745		2202	4299	6501	SO:0001583	missense	23604	exon12			TCCGTGGGTGGAG	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.1087C>T	15.37:g.64200745G>A	ENSP00000408277:p.Pro363Ser	Somatic	60	1		WXS	Illumina HiSeq	Phase_I	48	10	NM_014326	0	0	0	0	0	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	37	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.788395	0.31685	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.66638	-0.22;-0.22	5.26	4.34	0.51931	.	0.242826	0.26048	N	0.026647	T	0.52306	0.1726	L	0.36672	1.1	0.38280	D	0.942401	B	0.19331	0.035	B	0.15052	0.012	T	0.48387	-0.9040	10	0.13853	T	0.58	.	11.0466	0.47863	0.087:0.0:0.913:0.0	.	363	Q9UIK4	DAPK2_HUMAN	S	363	ENSP00000261891:P363S;ENSP00000408277:P363S	ENSP00000261891:P363S	P	-	1	0	DAPK2	61987798	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.491000	0.35583	1.217000	0.43442	0.655000	0.94253	CCA	.		0.602	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		A	64200745	G	A	64200745	3	1	148	1	0	0	0	0	1	0	0	0	4242	1232	43	2	29	2	DAPK2	15	64200745	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	5061172	64200745	38330647	90	13248											
ACAN	176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	89400337	89400337	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggaatagaggatgtcagTgaacttccttcaggagaagg	12	10	13	6	0	3	3	2	1	1	2	4	6	4	5	1	4	1	0	1	4	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:89400337T>A	ENST00000561243.1	+	11	4521	c.4521T>A	c.(4519-4521)agT>agA	p.S1507R	ACAN_ENST00000352105.7_Missense_Mutation_p.S1507R|ACAN_ENST00000439576.2_Missense_Mutation_p.S1507R|ACAN_ENST00000559004.1_Missense_Mutation_p.S1507R			P16112	PGCA_HUMAN	aggrecan	1508	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGATGTCAGTGAACTTCCTT	0.493																																					p.S1507R		.											.	ACAN-25	0			c.T4521A						.						69	70	70					15																	89400337		1870	4099	5969	SO:0001583	missense	176	exon12			TGTCAGTGAACTT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.4521T>A	15.37:g.89400337T>A	ENSP00000453342:p.Ser1507Arg	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	50	13	NM_001135	0	0	0	0	0	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.503317	0.44558	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.97016	-4.21;-4.21	3.27	0.774	0.18521	.	.	.	.	.	D	0.97309	0.9120	M	0.79926	2.475	0.09310	N	1	D;D	0.76494	0.999;0.998	D;D	0.72982	0.979;0.953	D	0.91248	0.5027	9	0.56958	D	0.05	.	6.8295	0.23902	0.0:0.3522:0.0:0.6478	.	1507;1507	E7ENV9;E7EX88	.;.	R	1507;1507;1393	ENSP00000387356:S1507R;ENSP00000341615:S1507R	ENSP00000268134:S1393R	S	+	3	2	ACAN	87201341	0.000000	0.05858	0.002000	0.10522	0.944000	0.59088	-0.304000	0.08199	0.050000	0.15949	0.260000	0.18958	AGT	.		0.493	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89400337	T	A	89400337	3	1	148	1	0	0	0	0	1	0	0	0	117	1693	59	5	4563	5	ACAN	15	89400337	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	25199592	89400337	13131055	91	13249											
RBBP6	5930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	24581079	24581079	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgataaaaccaaacggaagaAtgatggatctgctgtgtcca	15	9	10	7	1	1	3	0	2	1	1	2	5	2	5	2	2	3	1	2	2	5	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr16:24581079A>T	ENST00000319715.4	+	17	3500	c.3068A>T	c.(3067-3069)aAt>aTt	p.N1023I	RBBP6_ENST00000348022.2_Missense_Mutation_p.N989I|RBBP6_ENST00000381039.3_Intron	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1023	Interaction with RB1. {ECO:0000250}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		AAACGGAAGAATGATGGATCT	0.383																																					p.N1023I		.											.	RBBP6-230	0			c.A3068T						.						89	93	92					16																	24581079		2197	4300	6497	SO:0001583	missense	5930	exon17			GGAAGAATGATGG		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3068A>T	16.37:g.24581079A>T	ENSP00000317872:p.Asn1023Ile	Somatic	37	0		WXS	Illumina HiSeq	Phase_I	80	28	NM_006910	0	0	0	1	1	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.597918	0.46318	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.14516	2.5;2.5	5.66	1.57	0.23409	.	0.405156	0.23413	N	0.048451	T	0.06280	0.0162	N	0.19112	0.55	0.23724	N	0.997013	B;B	0.22983	0.078;0.047	B;B	0.21151	0.033;0.014	T	0.31971	-0.9924	10	0.28530	T	0.3	-9.0723	1.0512	0.01580	0.2899:0.3403:0.1901:0.1797	.	989;1023	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	I	1023;989	ENSP00000317872:N1023I;ENSP00000316291:N989I	ENSP00000317872:N1023I	N	+	2	0	RBBP6	24488580	0.343000	0.24818	0.990000	0.47175	0.994000	0.84299	0.309000	0.19332	-0.006000	0.14370	0.533000	0.62120	AAT	.		0.383	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24581079	A	T	24581079	3	4	148	1	0	0	0	0	1	0	0	0	13135	101	4	5	3188	5	RBBP6	16	24581079	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10		24581079	65773674	92	13250											
CHST6	4166	bcgsc.ca	37	chr16	75513372	75513372	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacggcccactggaagaggtCggacaggttgcggcgccaag	9	4	16	12	4	0	1	0	0	0	1	1	3	0	3	2	6	1	1	2	6	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr16:75513372C>T	ENST00000332272.4	-	3	534	c.355G>A	c.(355-357)Gac>Aac	p.D119N	CHST6_ENST00000390664.2_Missense_Mutation_p.D119N|RP11-77K12.4_ENST00000530512.3_RNA	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	119					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGGAAGAGGTCGGACAGGTTG	0.657																																					p.D119N													.	CHST6-90	0			c.G355A						.						48	43	45					16																	75513372		2198	4298	6496	SO:0001583	missense	4166	exon3			AGAGGTCGGACAG	AF280086	CCDS10918.1	16q22	2008-02-05			ENSG00000183196	ENSG00000183196		"Sulfotransferases, membrane-bound"	6938	protein-coding gene	gene with protein product		605294		MCDC1		8644739, 11017086	Standard	NM_021615		Approved		uc002fef.3	Q9GZX3	OTTHUMG00000137612	ENST00000332272.4:c.355G>A	16.37:g.75513372C>T	ENSP00000328983:p.Asp119Asn	Somatic	32	1		WXS	Illumina HiSeq	Phase_1	95	61	NM_021615	0	0	0	0	0	D3DUK3	Missense_Mutation	SNP	ENST00000332272.4	37	CCDS10918.1	.	.	.	.	.	.	.	.	.	.	C	10.50	1.368045	0.24771	.	.	ENSG00000183196	ENST00000332272;ENST00000390664	D;D	0.96491	-4.03;-4.03	4.56	4.56	0.56223	Sulfotransferase domain (1);	0.298026	0.35378	N	0.003256	D	0.91835	0.7416	N	0.25380	0.74	0.35691	D	0.814828	B	0.15719	0.014	B	0.16289	0.015	D	0.90235	0.4282	10	0.15499	T	0.54	.	14.8296	0.70137	0.0:1.0:0.0:0.0	.	119	Q9GZX3	CHST6_HUMAN	N	119	ENSP00000328983:D119N;ENSP00000375079:D119N	ENSP00000328983:D119N	D	-	1	0	CHST6	74070873	0.877000	0.30153	0.985000	0.45067	0.943000	0.58893	1.700000	0.37815	2.078000	0.62432	0.591000	0.81541	GAC	.		0.657	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615		T	75513372	C	T	75513372	3	4	148	1	0	0	0	0	1	0	0	0	3414	884	31	1	836	1	CHST6	16	75513372	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	50932293	75513372	14841381	93	13251											
ARHGEF15	22899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	8215790	8215790	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctcagaatggctctgccTcagctcctggcactgtgcgg	5	10	13	13	1	3	1	2	0	1	1	4	1	4	1	2	4	3	4	2	4	1	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:8215790T>G	ENST00000361926.3	+	2	543	c.433T>G	c.(433-435)Tca>Gca	p.S145A	ARHGEF15_ENST00000421050.1_Missense_Mutation_p.S145A	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	145					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						TGGCTCTGCCTCAGCTCCTGG	0.672																																					p.S145A		.											.	ARHGEF15-230	0			c.T433G						.						54	54	54					17																	8215790		2203	4300	6503	SO:0001583	missense	22899	exon2			TCTGCCTCAGCTC	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.433T>G	17.37:g.8215790T>G	ENSP00000355026:p.Ser145Ala	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	74	35	NM_025014	0	0	1	1	0	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	37	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.574696	0.28092	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	T;T	0.74632	-0.86;-0.86	5.12	4.03	0.46877	.	1.787260	0.03046	N	0.153884	T	0.79569	0.4468	L	0.29908	0.895	0.24301	N	0.99513	D;D;P	0.58268	0.982;0.982;0.884	D;D;B	0.67548	0.952;0.952;0.262	T	0.62053	-0.6935	10	0.45353	T	0.12	-10.5299	7.7269	0.28765	0.0:0.0947:0.0:0.9053	.	145;145;46	D3DTR7;O94989;B4DTR5	.;ARHGF_HUMAN;.	A	145;46;145	ENSP00000355026:S145A;ENSP00000412505:S145A	ENSP00000355026:S145A	S	+	1	0	ARHGEF15	8156515	0.954000	0.32549	0.913000	0.36048	0.921000	0.55340	1.645000	0.37238	0.969000	0.38237	0.454000	0.30748	TCA	.		0.672	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		G	8215790	T	G	8215790	3	3	148	1	0	0	0	0	1	0	0	0	898	1551	54	5	435	5	ARHGEF15	17	8215790	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10		8215790	72979420	94	13252											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	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|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y	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	265	268					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	175	11		WXS	Illumina HiSeq		402	33	NM_145301	0	0	3	20	17	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		T	15457087	C	T	15457087	3	4	148	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	7241297	15457087	65738123	95	13253											
FBXO47	494188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	37099134	37099134	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttccacttagcattaggAgacgtgcattattctctaga	10	15	8	8	1	1	2	0	0	1	2	3	3	2	2	1	1	2	3	1	1	4	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:37099134A>G	ENST00000378079.2	-	9	1179	c.980T>C	c.(979-981)cTc>cCc	p.L327P		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	327										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						TAGCATTAGGAGACGTGCATT	0.403																																					p.L327P		.											.	FBXO47-90	0			c.T980C						.						98	91	93					17																	37099134		2203	4300	6503	SO:0001583	missense	494188	exon9			ATTAGGAGACGTG		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.980T>C	17.37:g.37099134A>G	ENSP00000367319:p.Leu327Pro	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	101	34	NM_001008777	0	0	0	0	0	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	37	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.378341	0.61735	.	.	ENSG00000204952	ENST00000378079	T	0.61158	0.13	5.9	4.8	0.61643	.	0.254055	0.40385	N	0.001113	T	0.71626	0.3362	M	0.66939	2.045	0.58432	D	0.999995	D	0.76494	0.999	D	0.67231	0.95	T	0.73902	-0.3836	10	0.87932	D	0	-13.2646	12.1337	0.53957	0.8566:0.1434:0.0:0.0	.	327	Q5MNV8	FBX47_HUMAN	P	327	ENSP00000367319:L327P	ENSP00000367319:L327P	L	-	2	0	FBXO47	34352660	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.161000	0.77505	1.013000	0.39391	0.482000	0.46254	CTC	.		0.403	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		G	37099134	A	G	37099134	3	3	148	1	0	0	0	0	1	0	0	0	5775	304	11	3	390	3	FBXO47	17	37099134	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	21642047	37099134	44096076	96	13254											
COPZ2	51226	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	46103806	46103806	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacagccttcatttcaataaCgaccatttaatttgttcctt	11	16	3	11	1	2	0	2	0	0	0	3	1	3	0	3	0	2	1	3	0	3	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:46103806C>G	ENST00000006101.4	-	10	614	c.615G>C	c.(613-615)tcG>tcC	p.S205S	COPZ2_ENST00000584666.1_5'UTR	NM_016429.2	NP_057513.1	Q9P299	COPZ2_HUMAN	coatomer protein complex, subunit zeta 2	207					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)				lung(3)|upper_aerodigestive_tract(1)	4						ATTTCAATAACGACCATTTAA	0.507											OREG0024510	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.													.	.	0			.						.						71	79	77					17																	46103806		1868	4095	5963	SO:0001819	synonymous_variant	51226	.			CAATAACGACCAT	AB037938	CCDS74092.1	17q21.2	2008-07-18				ENSG00000005243			19356	protein-coding gene	gene with protein product	"nonclathrin coat protein zeta-COP", "zeta2-COP", "zeta-2 coat protein"	615526				11056392	Standard	NM_016429		Approved	MGC23008	uc002imy.3	Q9P299		ENST00000006101.4:c.615G>C	17.37:g.46103806C>G		Somatic	36	0	936	WXS	Illumina HiSeq	Phase_I	60	16	.	0	0	12	20	8		Silent	SNP	ENST00000006101.4	37																																																																																				.		0.507	COPZ2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016429		G	46103806	C	G	46103806	2	3	148	1	0	0	0	0	0	0	0	1	3748	523	19	4		4	COPZ2	17	46103806	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	9004672	46103806	35091404	97	13255											
AMZ2	51321	hgsc.bcm.edu;bcgsc.ca	37	chr17	66246341	66246341	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgttagatgcaaataataCggcactccgaacagacacta	15	10	7	9	2	0	2	0	0	0	2	1	3	1	2	1	1	3	3	1	1	6	5	rs532820909		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:66246341C>T	ENST00000359904.3	+	2	1145	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000577985.1_Missense_Mutation_p.R5W|RP11-147L13.2_ENST00000577698.1_RNA|AMZ2_ENST00000359783.4_Missense_Mutation_p.R5W|AMZ2_ENST00000392720.2_Missense_Mutation_p.R5W|AMZ2_ENST00000577273.1_Missense_Mutation_p.R5W|AMZ2_ENST00000580753.1_Missense_Mutation_p.R5W|AMZ2_ENST00000577866.1_Missense_Mutation_p.R5W	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	5							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			GCAAATAATACGGCACTCCGA	0.343													C|||	1	0.000199681	0	0	5008	,	,		20400	0		0	False		,,,				2504	0.001				p.R5W		.											.	AMZ2-22	0			c.C13T						.						75	79	78					17																	66246341		2203	4300	6503	SO:0001583	missense	51321	exon2			ATAATACGGCACT	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.13C>T	17.37:g.66246341C>T	ENSP00000352976:p.Arg5Trp	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	59	5	NM_001033574	0	0	0	0	0	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Missense_Mutation	SNP	ENST00000359904.3	37	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	C	0.090	-1.168251	0.01660	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.19938	2.11;2.11;2.11	3.71	1.58	0.23477	.	0.721746	0.11673	N	0.540610	T	0.21718	0.0523	L	0.57536	1.79	0.09310	N	1	D;D	0.61697	0.978;0.99	B;B	0.43623	0.425;0.425	T	0.14090	-1.0485	10	0.87932	D	0	-32.5953	7.065	0.25147	0.1861:0.451:0.3629:0.0	.	5;5	A6NLD9;Q86W34	.;AMZ2_HUMAN	W	5	ENSP00000352976:R5W;ENSP00000352831:R5W;ENSP00000376481:R5W	ENSP00000352831:R5W	R	+	1	2	AMZ2	63757936	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.302000	0.19192	0.320000	0.23234	0.456000	0.33151	CGG	.		0.343	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		T	66246341	C	T	66246341	3	4	148	1	0	0	0	0	1	0	0	0	597	527	19	1	15	1	AMZ2	17	66246341	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	20142535	66246341	14948869	98	13256											
C17orf70	80233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79518169	79518169	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcaggcatcggggtccacAgggatcacgggggaaggctg	9	5	18	9	2	1	0	1	0	0	0	3	2	2	2	1	7	1	3	1	7	1	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:79518169A>G	ENST00000327787.8	-	3	397	c.351T>C	c.(349-351)ccT>ccC	p.P117P	C17orf70_ENST00000425898.2_5'Flank|C17orf70_ENST00000537152.1_5'UTR			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	117					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			CGGGGTCCACAGGGATCACGG	0.647																																					p.P117P		.											.	C17orf70-92	0			c.T351C						.						6	8	7					17																	79518169		1251	2219	3470	SO:0001819	synonymous_variant	80233	exon3			GTCCACAGGGATC	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 100kDa"	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.351T>C	17.37:g.79518169A>G		Somatic	446	1		WXS	Illumina HiSeq	Phase_I	559	133	NM_025161	0	0	15	19	4	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Silent	SNP	ENST00000327787.8	37	CCDS32765.2																																																																																			.		0.647	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		G	79518169	A	G	79518169	2	3	148	1	0	0	0	0	0	0	0	1	1882	175	7	3		3	C17orf70	17	79518169	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	13271828	79518169	1677041	99	13257											
DLGAP1	9229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	3508641	3508641	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gttgggcactgcccactgcgGttcggatttttcctagaact	6	13	11	11	2	0	1	0	0	0	1	2	2	1	2	2	3	3	3	2	3	2	5	rs538990113		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr18:3508641G>A	ENST00000315677.3	-	11	3093	c.2498C>T	c.(2497-2499)aCc>aTc	p.T833I	DLGAP1_ENST00000539435.1_Missense_Mutation_p.T541I|DLGAP1_ENST00000400150.3_Missense_Mutation_p.T549I|DLGAP1_ENST00000400147.2_Missense_Mutation_p.T531I|DLGAP1_ENST00000400155.1_Missense_Mutation_p.T539I|DLGAP1_ENST00000400149.3_Missense_Mutation_p.T523I|DLGAP1_ENST00000581699.1_Missense_Mutation_p.T539I|DLGAP1_ENST00000400145.2_Missense_Mutation_p.T531I|DLGAP1_ENST00000581527.1_Missense_Mutation_p.T833I|DLGAP1_ENST00000515196.2_Missense_Mutation_p.T833I|DLGAP1_ENST00000584874.1_Missense_Mutation_p.T833I|DLGAP1_ENST00000534970.1_Missense_Mutation_p.T517I	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	833					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				GCCCACTGCGGTTCGGATTTT	0.413																																					p.T833I		.											.	DLGAP1-229	0			c.C2498T						.						64	58	60					18																	3508641		2203	4300	6503	SO:0001583	missense	9229	exon11			ACTGCGGTTCGGA	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"discs, large (Drosophila) homolog-associated protein 1"			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.2498C>T	18.37:g.3508641G>A	ENSP00000316377:p.Thr833Ile	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	70	24	NM_001242761	0	0	1	1	0	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	37	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008210	0.75046	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	T;T;T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.66	4.74	0.60224	.	0.160479	0.56097	D	0.000030	T	0.24812	0.0602	L	0.48362	1.52	0.44908	D	0.997921	D;P;P;P;P;D;P;P	0.54397	0.966;0.939;0.758;0.662;0.758;0.958;0.758;0.714	P;P;P;B;P;B;P;B	0.47705	0.522;0.522;0.555;0.398;0.555;0.387;0.555;0.419	T	0.00885	-1.1527	10	0.87932	D	0	-22.5862	11.1457	0.48430	0.0:0.1378:0.7192:0.1429	.	833;517;529;539;541;531;833;531	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;O14490-3;O14490;O14490-2	.;.;.;.;.;.;DLGP1_HUMAN;.	I	833;531;549;523;539;517;541;531;833	ENSP00000316377:T833I;ENSP00000383011:T531I;ENSP00000383014:T549I;ENSP00000383013:T523I;ENSP00000383019:T539I;ENSP00000437817:T517I;ENSP00000446312:T541I;ENSP00000383010:T531I;ENSP00000445973:T833I	ENSP00000316377:T833I	T	-	2	0	DLGAP1	3498641	1.000000	0.71417	0.969000	0.41365	0.997000	0.91878	4.878000	0.63093	2.656000	0.90262	0.655000	0.94253	ACC	.		0.413	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			A	3508641	G	A	3508641	3	1	148	1	0	0	0	0	1	0	0	0	4570	1261	44	2	447	2	DLGAP1	18	3508641	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		3508641	74568607	100	13258											
RALBP1	10928	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	9524704	9524704	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtctaacatggccacgatgcCcacgctgccagagacccagg	10	5	11	15	2	1	1	0	0	1	1	1	3	1	1	4	2	3	1	4	2	1	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr18:9524704C>G	ENST00000019317.4	+	5	1389	c.1166C>G	c.(1165-1167)cCc>cGc	p.P389R	RALBP1_ENST00000383432.3_Missense_Mutation_p.P389R			Q15311	RBP1_HUMAN	ralA binding protein 1	389					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	GCCACGATGCCCACGCTGCCA	0.537																																					p.P389R													.	RALBP1-522	0			c.C1166G						.						51	44	46					18																	9524704		2203	4300	6503	SO:0001583	missense	10928	exon5			CGATGCCCACGCT	L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.1166C>G	18.37:g.9524704C>G	ENSP00000019317:p.Pro389Arg	Somatic	130	1		WXS	Illumina HiSeq	Phase_I	124	48	NM_006788	0	0	13	26	13	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.900504	0.92035	.	.	ENSG00000017797	ENST00000019317;ENST00000383432	T;T	0.11169	2.8;2.8	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.33059	0.0850	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.00899	-1.1522	10	0.66056	D	0.02	-11.5257	19.7818	0.96418	0.0:1.0:0.0:0.0	.	389	Q15311	RBP1_HUMAN	R	389	ENSP00000019317:P389R;ENSP00000372924:P389R	ENSP00000019317:P389R	P	+	2	0	RALBP1	9514704	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.629000	0.83207	2.736000	0.93811	0.655000	0.94253	CCC	.		0.537	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		G	9524704	C	G	9524704	3	3	148	1	0	0	0	0	1	0	0	0	13044	623	22	4	1180	4	RALBP1	18	9524704	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	6016063	9524704	68552544	101	13259											
DSG4	147409	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	28966661	28966661	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgcttaaggtgaaggaatTtgacattgaaaatggcacta	14	13	10	4	0	0	3	0	3	0	0	0	4	0	4	0	3	1	2	0	3	6	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr18:28966661T>A	ENST00000308128.4	+	3	230	c.95T>A	c.(94-96)tTt>tAt	p.F32Y	RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.F32Y|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	32					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GTGAAGGAATTTGACATTGAA	0.393																																					p.F32Y													.	DSG4-177	0			c.T95A						.						83	81	82					18																	28966661		2203	4300	6503	SO:0001583	missense	147409	exon3			AGGAATTTGACAT	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"Cadherins / Major cadherins"	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.95T>A	18.37:g.28966661T>A	ENSP00000311859:p.Phe32Tyr	Somatic	131	2		WXS	Illumina HiSeq	Phase_I	160	65	NM_001134453	0	0	0	0	0	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	T	4.207	0.037227	0.08148	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.58940	0.36;0.3	5.32	4.07	0.47477	.	0.332353	0.16946	N	0.193117	T	0.21962	0.0529	N	0.01576	-0.805	0.20821	N	0.999849	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.31779	-0.9931	10	0.02654	T	1	.	6.1963	0.20552	0.137:0.0:0.218:0.645	.	32;32	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	Y	32	ENSP00000311859:F32Y;ENSP00000352785:F32Y	ENSP00000311859:F32Y	F	+	2	0	DSG4	27220659	0.997000	0.39634	0.997000	0.53966	0.919000	0.55068	1.382000	0.34374	2.137000	0.66172	0.528000	0.53228	TTT	.		0.393	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		A	28966661	T	A	28966661	3	1	148	1	0	0	0	0	1	0	0	0	4790	1841	64	5	105	5	DSG4	18	28966661	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	19441957	28966661	49110587	102	13260											
DSG2	1829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	29116286	29116286	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgcagagtatgtgaatgtTactgcagaggacctggatgg	11	10	15	5	0	0	3	0	1	0	2	0	6	0	5	1	3	3	4	1	3	3	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr18:29116286T>C	ENST00000261590.8	+	11	1754	c.1545T>C	c.(1543-1545)gtT>gtC	p.V515V		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	515			V -> I (in dbSNP:rs2230235).		apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			ATGTGAATGTTACTGCAGAGG	0.483																																					p.V515V		.											.	DSG2-563	0			c.T1545C						.						94	89	90					18																	29116286		1963	4174	6137	SO:0001819	synonymous_variant	1829	exon11			GAATGTTACTGCA	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"Cadherins / Major cadherins"	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.1545T>C	18.37:g.29116286T>C		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	109	35	NM_001943	0	0	18	29	11	Q4KKU6	Silent	SNP	ENST00000261590.8	37	CCDS42423.1																																																																																			.		0.483	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		C	29116286	T	C	29116286	2	2	148	1	0	0	0	0	0	0	0	1	4788	1741	61	3		3	DSG2	18	29116286	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	149625	29116286	48960962	103	13261											
UBXN6	80700	ucsc.edu	37	chr19	4453972	4453972	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggggccccaggcccgggActgcttctgctccagccggg	3	7	16	15	2	1	0	0	0	1	0	2	1	2	1	5	5	3	2	5	5	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr19:4453972A>G	ENST00000301281.6	-	2	326	c.202T>C	c.(202-204)Tcc>Ccc	p.S68P	UBXN6_ENST00000394765.3_Missense_Mutation_p.S15P|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	68						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						CAGGCCCGGGACTGCTTCTGC	0.692																																					p.S68P													.	UBXN6-90	0			c.T202C						.						71	82	78					19																	4453972		2203	4300	6503	SO:0001583	missense	80700	exon2			CCCGGGACTGCTT	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"UBX domain containing"	14928	protein-coding gene	gene with protein product		611946	"UBX domain-containing 1", "UBX domain containing 1"	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.202T>C	19.37:g.4453972A>G	ENSP00000301281:p.Ser68Pro	Somatic	13	0		WXS	Illumina HiSeq		12	4	NM_025241	0	0	39	73	34	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	.	.	.	.	.	.	.	.	.	.	A	8.094	0.775072	0.16051	.	.	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.45668	1.94;0.89	4.24	3.2	0.36748	.	0.377447	0.27048	N	0.021186	T	0.08846	0.0219	N	0.00237	-1.79	0.22292	N	0.999225	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.33059	-0.9883	10	0.07325	T	0.83	-14.2173	5.506	0.16854	0.1175:0.2038:0.6787:0.0	.	15;68	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	P	68;15	ENSP00000301281:S68P;ENSP00000378246:S15P	ENSP00000301281:S68P	S	-	1	0	UBXN6	4404972	1.000000	0.71417	0.667000	0.29798	0.762000	0.43233	2.474000	0.45154	0.747000	0.32809	-0.415000	0.06103	TCC	.		0.692	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241		G	4453972	A	G	4453972	3	3	148	1	0	0	0	0	1	0	0	0	16950	275	10	3	1163	3	UBXN6	19	4453972	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10		4453972	54675011	104	13262											
LRRC8E	80131	broad.mit.edu	37	chr19	7964010	7964010	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggaaggcaggggagggTgagaaggagaaagtgctggc	11	3	22	5	1	0	2	0	1	0	2	0	6	0	4	1	8	1	2	1	8	3	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr19:7964010T>G	ENST00000306708.6	+	3	704	c.603T>G	c.(601-603)ggT>ggG	p.G201G	AC010336.1_ENST00000539278.1_3'UTR	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	201					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						CAGGGGAGGGTGAGAAGGAGA	0.642																																					p.G201G													.	LRRC8E-92	0			c.T603G						.						42	48	46					19																	7964010		2203	4300	6503	SO:0001819	synonymous_variant	80131	exon4			GGAGGGTGAGAAG		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.603T>G	19.37:g.7964010T>G		Somatic	81	16		WXS	Illumina HiSeq	Phase_I	93	28	NM_001268284	0	0	1	1	0	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	37	CCDS12189.1																																																																																			.		0.642	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		G	7964010	T	G	7964010	2	3	148	1	0	0	0	0	0	0	0	1	9050	1683	59	5		5	LRRC8E	19	7964010	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	3510038	7964010	51164973	105	13263											
ZNF799	90576	ucsc.edu;bcgsc.ca	37	chr19	12502160	12502160	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttcatgacttttcagtGaactaggacaatcaaagcct	12	14	6	9	0	4	2	3	2	1	0	4	3	4	3	1	1	2	0	1	1	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr19:12502160G>T	ENST00000430385.3	-	4	1252	c.1052C>A	c.(1051-1053)tCa>tAa	p.S351*	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Nonsense_Mutation_p.S319*	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	351					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(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						ACTTTTCAGTGAACTAGGACA	0.413																																					p.S351X													.	ZNF799-74	0			c.C1052A						.						161	157	158					19																	12502160		2203	4300	6503	SO:0001587	stop_gained	90576	exon4			TTCAGTGAACTAG	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"Zinc fingers, C2H2-type", "-"	28071	protein-coding gene	gene with protein product			"zinc finger protein 842"	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1052C>A	19.37:g.12502160G>T	ENSP00000411084:p.Ser351*	Somatic	80	2		WXS	Illumina HiSeq		91	35	NM_001080821	0	0	1	4	3		Nonsense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	G	38	7.279860	0.98182	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	.	.	.	1.31	-1.62	0.08372	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.5092	0.04652	0.1876:0.0:0.3077:0.5047	.	.	.	.	X	319;351	.	ENSP00000415278:S319X	S	-	2	0	ZNF799	12363160	0.000000	0.05858	0.001000	0.08648	0.117000	0.20001	-0.475000	0.06599	-0.373000	0.07979	0.430000	0.28490	TCA	.		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		T	12502160	G	T	12502160	4	4	148	1	0	0	0	0	0	1	0	0	18198	1294	45	4	883	4	ZNF799	19	12502160	Nonsense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	4538150	12502160	46626823	106	13264											
RDH13	112724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	55570627	55570627	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccttgctggggcaagcccCaccggtgacatagtccctga	7	7	13	14	1	0	2	0	2	0	0	1	2	1	2	5	4	2	2	5	4	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr19:55570627C>A	ENST00000415061.3	-	2	225	c.82G>T	c.(82-84)Ggg>Tgg	p.G28W	RDH13_ENST00000396247.3_5'UTR	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	28					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	GGGCAAGCCCCACCGGTGACA	0.632																																					p.G28W		.											.	RDH13-92	0			c.G82T						.						28	27	27					19																	55570627		1567	3580	5147	SO:0001583	missense	112724	exon2			AAGCCCCACCGGT		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19978	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 3"		"retinol dehydrogenase 13 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.82G>T	19.37:g.55570627C>A	ENSP00000391121:p.Gly28Trp	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	87	37	NM_001145971	0	0	7	12	5	Q6UX79|Q96G88	Missense_Mutation	SNP	ENST00000415061.3	37	CCDS54320.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.395156	0.83011	.	.	ENSG00000160439	ENST00000415061;ENST00000291892	D;D	0.83673	-1.75;-1.63	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.88930	0.6571	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89139	0.3515	10	0.59425	D	0.04	.	14.7528	0.69540	0.0:1.0:0.0:0.0	.	28	Q8NBN7	RDH13_HUMAN	W	28	ENSP00000391121:G28W;ENSP00000291892:G28W	ENSP00000291892:G28W	G	-	1	0	RDH13	60262439	0.988000	0.35896	0.311000	0.25182	0.164000	0.22412	3.974000	0.56852	2.635000	0.89317	0.650000	0.86243	GGG	.		0.632	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412		A	55570627	C	A	55570627	3	1	148	1	0	0	0	0	1	0	0	0	13224	594	21	4	937	4	RDH13	19	55570627	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	43068467	55570627	3558356	107	13265											
SLC32A1	140679	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	37353586	37353607	+	Frame_Shift_Del	DEL	GGGCGCTGAAGCGCCCGTCGAG	GGGCGCTGAAGCGCCCGTCGAG	-																															ggagagccctgcggggacgaGggcgctgaagcgcccgtcga																								rs148951877		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	GGGCGCTGAAGCGCCCGTCGAG	GGGCGCTGAAGCGCCCGTCGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr20:37353586_37353607delGGGCGCTGAAGCGCCCGTCGAG	ENST00000217420.1	+	1	482_503	c.219_240delGGGCGCTGAAGCGCCCGTCGAG	c.(217-240)gagggcgctgaagcgcccgtcgagfs	p.EGAEAPVE73fs		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	73					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	GCGGGGACGAGGGCGCTGAAGCGCCCGTCGAGGGAGACATCC	0.671																																					p.73_80del		.											.	SLC32A1-90	0			c.219_240del						.																																			SO:0001589	frameshift_variant	140679	exon1			.	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"Solute carriers"	11018	protein-coding gene	gene with protein product			"vesicular inhibitory amino acid transporter"	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.219_240delGGGCGCTGAAGCGCCCGTCGAG	20.37:g.37353586_37353607delGGGCGCTGAAGCGCCCGTCGAG	ENSP00000217420:p.Glu73fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	111	42	NM_080552	0	0	0	0	0	Q8N489	Frame_Shift_Del	DEL	ENST00000217420.1	37	CCDS13307.1																																																																																			.		0.671	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		-	37353607	GGGCGCTGAAGCGCCCGTCGAG	-	37353586	7	5	148	1	0	1	0	1	0	0	0	0	14597	991	35	0	221	0	SLC32A1	20	37353586	Frame_Shift_Del	DEL	GGGCGCTGAAGCGCCCGTCGAG	TCGA-MH-A55W-01A-11D-A26P-10		37353586	25671934	108	13266											
NCOA3	8202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	46254225	46254225	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttaggaccgcttttacttcaGgcaagtataaagattttaac	13	14	7	7	1	1	1	1	0	0	1	1	2	1	2	1	2	2	3	1	2	7	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr20:46254225G>A	ENST00000371998.3	+	5	548	c.357G>A	c.(355-357)caG>caA	p.Q119Q	NCOA3_ENST00000341724.6_Splice_Site_p.Q119Q|NCOA3_ENST00000372004.3_Splice_Site_p.Q119Q|NCOA3_ENST00000371997.3_Splice_Site_p.Q119Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	119	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TTTTACTTCAGGCAAGTATAA	0.343																																					p.Q119Q		.											.	NCOA3-229	0			c.G357A						.						76	71	73					20																	46254225		2203	4300	6503	SO:0001630	splice_region_variant	8202	exon5			ACTTCAGGCAAGT	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7670	protein-coding gene	gene with protein product	"receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1"	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.357+1G>A	20.37:g.46254225G>A		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	42	15	NM_181659	0	0	0	0	0	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			.		0.343	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	Silent	A	46254225	G	A	46254225	5	1	148	1	0	0	0	0	0	0	1	0	10256	1014	35	2	367	2	NCOA3	20	46254225	Splice_Site	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	8900639	46254225	16771295	109	13267											
ADNP	23394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	49509272	49509272	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggatacatttgtaggtgAgctttttctcaactggatga	11	15	10	5	0	1	2	1	2	1	0	2	4	1	4	0	3	3	2	0	3	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr20:49509272A>G	ENST00000396029.3	-	5	2546	c.1979T>C	c.(1978-1980)cTc>cCc	p.L660P	ADNP_ENST00000371602.4_Missense_Mutation_p.L660P|ADNP_ENST00000396032.3_Missense_Mutation_p.L660P|ADNP_ENST00000349014.3_Missense_Mutation_p.L660P	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	660					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						TTTGTAGGTGAGCTTTTTCTC	0.458																																					p.L660P		.											.	ADNP-92	0			c.T1979C						.						168	159	162					20																	49509272		2203	4300	6503	SO:0001583	missense	23394	exon5			TAGGTGAGCTTTT	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1979T>C	20.37:g.49509272A>G	ENSP00000379346:p.Leu660Pro	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	233	102	NM_015339	0	0	7	17	10	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	37	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.907002	0.33628	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.45276	0.1334	N	0.17082	0.46	0.80722	D	1	B	0.25486	0.127	B	0.25140	0.058	T	0.40720	-0.9548	9	0.54805	T	0.06	-14.7154	16.4177	0.83748	1.0:0.0:0.0:0.0	.	660	Q9H2P0	ADNP_HUMAN	P	660	.	ENSP00000342905:L660P	L	-	2	0	ADNP	48942679	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.941000	0.92964	2.267000	0.75376	0.528000	0.53228	CTC	.		0.458	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		G	49509272	A	G	49509272	3	3	148	1	0	0	0	0	1	0	0	0	323	304	11	3	1333	3	ADNP	20	49509272	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	3255047	49509272	13516248	110	13268											
LIPI	149998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	15561570	15561570	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagccagactgttttcttttGtgtgttgaaattaacattaa	12	17	7	5	0	1	2	0	1	1	1	1	2	1	2	1	0	2	2	1	0	4	7	rs569460311		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr21:15561570G>A	ENST00000536861.1	-	2	216	c.217C>T	c.(217-219)Caa>Taa	p.Q73*	LIPI_ENST00000344577.2_Nonsense_Mutation_p.Q94*			Q6XZB0	LIPI_HUMAN	lipase, member I	73					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		GTTTTCTTTTGTGTGTTGAAA	0.378																																					p.Q94X		.											.	LIPI-70	0			c.C280T						.						140	125	130					21																	15561570		2203	4300	6503	SO:0001587	stop_gained	149998	exon2			TCTTTTGTGTGTT	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.217C>T	21.37:g.15561570G>A	ENSP00000440381:p.Gln73*	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	155	46	NM_198996	0	0	0	0	0	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Nonsense_Mutation	SNP	ENST00000536861.1	37		.	.	.	.	.	.	.	.	.	.	G	25.4	4.631384	0.87660	.	.	ENSG00000188992	ENST00000344577;ENST00000536861	.	.	.	5.3	-2.36	0.06663	.	1.079770	0.06983	N	0.820308	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	1.3793	0.02227	0.1755:0.2196:0.1309:0.474	.	.	.	.	X	94;73	.	ENSP00000343331:Q94X	Q	-	1	0	LIPI	14483441	0.000000	0.05858	0.001000	0.08648	0.986000	0.74619	0.242000	0.18087	-0.342000	0.08363	-0.152000	0.13540	CAA	.		0.378	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		A	15561570	G	A	15561570	4	1	148	1	0	0	0	0	0	1	0	0	8848	1386	48	2	1201	2	LIPI	21	15561570	Nonsense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		15561570	32568325	111	13269											
HLCS	3141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	38309141	38309141	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gtctctgagagcactgtcctCcagcaggtggtagagaatat	10	10	12	9	0	1	2	0	1	1	2	4	4	3	2	2	2	2	3	2	2	3	2	rs148324626		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr21:38309141C>G	ENST00000399120.1	-	5	1834	c.604G>C	c.(604-606)Gag>Cag	p.E202Q	HLCS_ENST00000336648.4_Missense_Mutation_p.E202Q	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	202					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GCACTGTCCTCCAGCAGGTGG	0.582																																					p.E202Q		.											.	HLCS-157	0			c.G604C						.	C	GLN/GLU,GLN/GLU,GLN/GLU	1,4405	2.1+/-5.4	0,1,2202	70	73	72		604,604,604	3	0	21	dbSNP_134	72	0,8600		0,0,4300	no	missense,missense,missense	HLCS	NM_000411.6,NM_001242784.1,NM_001242785.1	29,29,29	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	benign,benign,benign	202/727,202/727,202/727	38309141	1,13005	2203	4300	6503	SO:0001583	missense	3141	exon5			TGTCCTCCAGCAG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.604G>C	21.37:g.38309141C>G	ENSP00000382071:p.Glu202Gln	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	154	54	NM_000411	0	0	3	3	0	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	37	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	C	9.293	1.051089	0.19827	2.27E-4	0.0	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98164	-4.76;-4.76	5.91	2.99	0.34606	.	0.383875	0.32258	N	0.006346	D	0.94745	0.8304	L	0.35723	1.085	0.09310	N	1	B;B	0.13145	0.007;0.003	B;B	0.09377	0.004;0.004	D	0.84732	0.0746	10	0.15952	T	0.53	.	10.2355	0.43280	0.0:0.6608:0.2659:0.0733	.	202;202	B2RAH1;P50747	.;BPL1_HUMAN	Q	202	ENSP00000382071:E202Q;ENSP00000338387:E202Q	ENSP00000338387:E202Q	E	-	1	0	HLCS	37231011	0.279000	0.24239	0.001000	0.08648	0.283000	0.27025	1.771000	0.38542	0.335000	0.23614	0.655000	0.94253	GAG	C|1.000;G|0.000		0.582	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			G	38309141	C	G	38309141	3	3	148	1	0	0	0	0	1	0	0	0	7234	864	30	4	1608	4	HLCS	21	38309141	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	22747571	38309141	9820754	112	13270											
C21orf29	54084	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45949793	45949793	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgctgggacacagccttggGgtggcgtctgagcccggcag	5	7	17	12	2	1	1	0	1	1	0	1	2	1	2	2	5	3	2	2	5	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr21:45949793G>A	ENST00000323084.4	-	5	743	c.678C>T	c.(676-678)acC>acT	p.T226T	TSPEAR_ENST00000397916.1_Silent_p.T158T	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	226	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						ACAGCCTTGGGGTGGCGTCTG	0.662																																					p.T226T		.											.	TSPEAR-244	0			c.C678T						.						35	39	37					21																	45949793		2203	4300	6503	SO:0001819	synonymous_variant	54084	exon5			CCTTGGGGTGGCG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"chromosome 21 open reading frame 29", "deafness, autosomal recessive 98"	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.678C>T	21.37:g.45949793G>A		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	28	12	NM_144991	0	0	0	0	0		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			.		0.662	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45949793	G	A	45949793	2	1	148	1	0	0	0	0	0	0	0	1	2130	1219	43	2		2	C21orf29	21	45949793	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	7640652	45949793	2180102	113	13271											
IL17RA	23765	hgsc.bcm.edu	37	chr22	17566096	17566096	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgcgactcctggaccacCgggcgctggtctgctcccag	4	7	12	18	3	1	0	0	0	1	0	3	2	3	1	5	3	2	2	5	3	0	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:17566096C>A	ENST00000319363.6	+	1	248	c.115C>A	c.(115-117)Cgg>Agg	p.R39R	IL17RA_ENST00000477874.1_3'UTR	NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	39					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		CCTGGACCACCGGGCGCTGGT	0.766																																					p.R39R		.											.	IL17RA-92	0			c.C115A						.						2	2	2					22																	17566096		1628	3503	5131	SO:0001819	synonymous_variant	23765	exon1			GACCACCGGGCGC	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"Interleukins and interleukin receptors", "CD molecules"	5985	protein-coding gene	gene with protein product		605461	"interleukin 17 receptor"	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.115C>A	22.37:g.17566096C>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	8	8	NM_014339	0	0	0	1	1	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	37	CCDS13739.1																																																																																			.		0.766	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		A	17566096	C	A	17566096	2	1	148	1	0	0	0	0	0	0	0	1	7660	643	23	4		4	IL17RA	22	17566096	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		17566096	33738470	114	13272											
HIC2	23119	ucsc.edu	37	chr22	21800382	21800382	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acccctgcaaggaggaggagGagaacggcaaggatgcaagt	14	3	16	8	1	0	1	0	0	0	1	0	6	0	5	2	6	3	3	2	6	4	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:21800382G>A	ENST00000443632.2	+	2	1570	c.1198G>A	c.(1198-1200)Gag>Aag	p.E400K	HIC2_ENST00000407598.2_Missense_Mutation_p.E400K|HIC2_ENST00000407464.2_Missense_Mutation_p.E400K			Q96JB3	HIC2_HUMAN	hypermethylated in cancer 2	400					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)				GGAGGAGGAGGAGAACGGCAA	0.672																																					p.E400K	NSCLC(23;437 858 2282 27947 40366)												.	HIC2-703	0			c.G1198A						.						24	23	23					22																	21800382		2192	4281	6473	SO:0001583	missense	23119	exon3			GAGGAGGAGAACG	AB028943	CCDS13789.1	22q11.21	2013-01-09			ENSG00000169635	ENSG00000169635		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18595	protein-coding gene	gene with protein product		607712				11554746	Standard	NM_015094		Approved	KIAA1020, HRG22, ZBTB30, ZNF907	uc002zur.4	Q96JB3	OTTHUMG00000150781	ENST00000443632.2:c.1198G>A	22.37:g.21800382G>A	ENSP00000387757:p.Glu400Lys	Somatic	10	0		WXS	Illumina HiSeq		21	4	NM_015094	0	0	0	0	0	Q504T6|Q96KR3|Q9NSM9|Q9UPX9	Missense_Mutation	SNP	ENST00000443632.2	37	CCDS13789.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.790874	0.50102	.	.	ENSG00000169635	ENST00000407464;ENST00000407598;ENST00000443632	T;T;T	0.11821	2.74;2.74;2.74	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.14960	0.0361	M	0.65498	2.005	0.49130	D	0.999756	B	0.34200	0.441	B	0.32465	0.146	T	0.03818	-1.1001	10	0.02654	T	1	.	16.225	0.82285	0.0:0.0:1.0:0.0	.	400	Q96JB3	HIC2_HUMAN	K	400	ENSP00000385319:E400K;ENSP00000384889:E400K;ENSP00000387757:E400K	ENSP00000385319:E400K	E	+	1	0	HIC2	20130382	1.000000	0.71417	0.990000	0.47175	0.380000	0.30137	6.248000	0.72418	2.694000	0.91930	0.655000	0.94253	GAG	.		0.672	HIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320061.2			A	21800382	G	A	21800382	3	1	148	1	0	0	0	0	1	0	0	0	7123	1175	41	2	1204	2	HIC2	22	21800382	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	4234286	21800382	29504184	115	13273											
CSNK1E	1454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	38690131	38690131	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctgtgaggctgggatcCgggagacctcttgccgccca	6	8	13	14	2	2	2	1	1	1	1	3	4	3	3	5	3	1	1	5	3	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:38690131C>T	ENST00000396832.1	-	9	1462	c.1202G>A	c.(1201-1203)cGg>cAg	p.R401Q	CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000400206.2_Missense_Mutation_p.R401Q|CSNK1E_ENST00000403904.1_Missense_Mutation_p.R401Q|CSNK1E_ENST00000359867.3_Missense_Mutation_p.R401Q	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	401					cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GGCTGGGATCCGGGAGACCTC	0.662																																					p.R401Q	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	.											.	CSNK1E-1193	0			c.G1202A						.						26	27	27					22																	38690131		2201	4300	6501	SO:0001583	missense	1454	exon9			GGGATCCGGGAGA		CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923			2453	protein-coding gene	gene with protein product		600863				7797465, 10535959	Standard	NM_001894		Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000396832.1:c.1202G>A	22.37:g.38690131C>T	ENSP00000380044:p.Arg401Gln	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	53	14	NM_001894	0	0	8	10	2		Missense_Mutation	SNP	ENST00000396832.1	37	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.600758|4.600758	0.87055|0.87055	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000366216|ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904	.|T;T;T;T	.|0.57436	.|0.4;0.4;0.4;0.4	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.055638	.|0.64402	.|D	.|0.000001	T|T	0.59211|0.59211	0.2177|0.2177	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	T|T	0.65175|0.65175	-0.6232|-0.6232	5|10	.|0.56958	.|D	.|0.05	.|.	20.063|20.063	0.97692|0.97692	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|401	.|P49674	.|KC1E_HUMAN	R|Q	104|401	.|ENSP00000352929:R401Q;ENSP00000380044:R401Q;ENSP00000383067:R401Q;ENSP00000384074:R401Q	.|ENSP00000352929:R401Q	G|R	-|-	1|2	0|0	CSNK1E|CSNK1E	37020077|37020077	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.254000|0.254000	0.26022|0.26022	7.482000|7.482000	0.81143|0.81143	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.		0.662	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		T	38690131	C	T	38690131	3	4	148	1	0	0	0	0	1	0	0	0	3959	652	23	1	56	1	CSNK1E	22	38690131	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	16889749	38690131	12614435	116	13274											
SHANK3	85358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	51160300	51160300	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcccagcagtgagccacccCctgcccctgagtctgcagcc	7	5	10	19	0	1	2	0	2	1	0	1	2	1	2	7	0	6	2	7	0	0	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:51160300C>G	ENST00000414786.2	+	21	4224	c.3997C>G	c.(3997-3999)Cct>Gct	p.P1333A	SHANK3_ENST00000262795.3_Missense_Mutation_p.P1363A|SHANK3_ENST00000445220.2_Missense_Mutation_p.P1349A			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1347	Pro-rich.		V -> G. {ECO:0000269|PubMed:20385823}.		adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		TGAGCCACCCCCTGCCCCTGA	0.711																																					p.P1333A		.											.	SHANK3-69	0			c.C3997G						.						8	10	9					22																	51160300		1900	4008	5908	SO:0001583	missense	85358	exon21			CCACCCCCTGCCC	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3997C>G	22.37:g.51160300C>G	ENSP00000464552:p.Pro1333Ala	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	36	10	NM_033517	0	0	0	0	0	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		.	.	.	.	.	.	.	.	.	.	C	15.71	2.913103	0.52439	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.18960	2.18;2.18	5.11	5.11	0.69529	.	0.073236	0.56097	D	0.000028	T	0.28167	0.0695	M	0.78456	2.415	0.28658	N	0.906287	B;B;B	0.28512	0.176;0.096;0.214	B;B;B	0.25884	0.064;0.036;0.052	T	0.13683	-1.0500	10	0.34782	T	0.22	.	16.0382	0.80645	0.0:1.0:0.0:0.0	.	1347;1348;1363	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	A	1363;1349	ENSP00000442518:P1363A;ENSP00000446078:P1349A	ENSP00000442518:P1363A	P	+	1	0	SHANK3	49507166	0.230000	0.23740	0.974000	0.42286	0.986000	0.74619	1.882000	0.39648	2.381000	0.81170	0.462000	0.41574	CCT	.		0.711	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		G	51160300	C	G	51160300	3	3	148	1	0	0	0	0	1	0	0	0	14298	623	22	4	4173	4	SHANK3	22	51160300	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	12470169	51160300	144266	117	13275											
WWC3	55841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	10066562	10066562	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagtttgtctttgatgataAaacaagacttgtagaccgag	15	12	9	5	1	1	4	0	2	1	2	1	5	1	4	1	0	1	2	1	0	5	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chrX:10066562A>C	ENST00000380861.4	+	8	1065	c.674A>C	c.(673-675)aAa>aCa	p.K225T	WWC3_ENST00000454666.1_Missense_Mutation_p.K225T	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	225					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TTTGATGATAAAACAAGACTT	0.353																																					p.K225T		.											.	WWC3-134	0			c.A674C						.						78	73	75					X																	10066562		2203	4300	6503	SO:0001583	missense	55841	exon8			ATGATAAAACAAG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"WW, C2 and coiled-coil domain containing"	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.674A>C	X.37:g.10066562A>C	ENSP00000370242:p.Lys225Thr	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	38	27	NM_015691	0	0	0	6	6	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155337	0.57259	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000398613	T;T	0.05199	3.48;3.48	5.49	5.49	0.81192	.	0.217302	0.48286	D	0.000185	T	0.07954	0.0199	L	0.51422	1.61	0.39975	D	0.974846	P	0.39424	0.673	B	0.37144	0.242	T	0.38845	-0.9642	10	0.19590	T	0.45	-27.9526	14.6222	0.68594	1.0:0.0:0.0:0.0	.	225	Q9ULE0	WWC3_HUMAN	T	225	ENSP00000370242:K225T;ENSP00000399584:K225T	ENSP00000370242:K225T	K	+	2	0	WWC3	10026562	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.309000	0.51903	1.834000	0.53371	0.339000	0.21740	AAA	.		0.353	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		C	10066562	A	C	10066562	3	2	148	1	0	0	0	0	1	0	0	0	17446	14	1	5	700	5	WWC3	23	10066562	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10		10066562	145203998	118	13276											
SSX5	6758	broad.mit.edu	37	chrX	48054486	48054486	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtagagctttaatgctgctgGctggctctcttcccaccttc	5	14	9	13	0	1	1	0	0	1	1	4	1	2	1	2	2	3	6	2	2	2	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chrX:48054486G>T	ENST00000376923.1	-	2	69				SSX5_ENST00000347757.1_Intron|SSX5_ENST00000311798.1_Missense_Mutation_p.A50D			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						AATGCTGCTGGCTGGCTCTCT	0.522																																					p.A50D													.	SSX5-90	0			c.C149A						.						68	59	62					X																	48054486		2203	4299	6502	SO:0001627	intron_variant	6758	exon3			CTGCTGGCTGGCT	BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.70-196C>A	X.37:g.48054486G>T		Somatic	236	1		WXS	Illumina HiSeq	Phase_I	260	6	NM_021015	0	0	0	0	0	Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	SNP	ENST00000376923.1	37	CCDS14289.1	.	.	.	.	.	.	.	.	.	.	N	7.535	0.659410	0.14645	.	.	ENSG00000165583	ENST00000311798	T	0.10288	2.89	1.18	0.234	0.15390	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.09310	N	1	B	0.23540	0.087	B	0.20384	0.029	T	0.45411	-0.9263	8	0.15066	T	0.55	.	3.1437	0.06464	0.3293:0.0:0.6707:0.0	.	50	O60225-2	.	D	50	ENSP00000312415:A50D	ENSP00000312415:A50D	A	-	2	0	SSX5	47939430	0.000000	0.05858	0.001000	0.08648	0.150000	0.21749	-0.180000	0.09754	0.017000	0.15025	0.171000	0.16805	GCC	.		0.522	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015		T	48054486	G	T	48054486	1	4	148	0	1	0	0	0	0	0	0	0	15240	1203	42	4		4	SSX5	23	48054486	Intron	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	37987924	48054486	107216074	119	13277											
RLIM	51132	broad.mit.edu	37	chrX	73811995	73811995	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtatttaagattctacgaatGggaattctgatggtactgac	12	14	10	5	1	2	3	0	2	2	1	2	5	2	4	0	2	2	2	0	2	6	7			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chrX:73811995G>T	ENST00000332687.6	-	4	1373	c.1155C>A	c.(1153-1155)ccC>ccA	p.P385P	RLIM_ENST00000349225.2_Silent_p.P385P	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	385					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTCTACGAATGGGAATTCTGA	0.413																																					p.P385P	Esophageal Squamous(169;1899 1923 14997 18818 32118)												.	RLIM-228	0			c.C1155A						.						109	98	102					X																	73811995		2203	4300	6503	SO:0001819	synonymous_variant	51132	exon5			ACGAATGGGAATT	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1155C>A	X.37:g.73811995G>T		Somatic	104	0		WXS	Illumina HiSeq	Phase_I	79	4	NM_183353	0	0	1	1	0	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Silent	SNP	ENST00000332687.6	37	CCDS14427.1																																																																																			.		0.413	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		T	73811995	G	T	73811995	2	4	148	1	0	0	0	0	0	0	0	1	13422	1335	47	4		4	RLIM	23	73811995	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	25757509	73811995	81458565	120	13278											
XIAP	331	bcgsc.ca	37	chrX	123020210	123020210	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgcttctttgttttgggccGgaatcttaatattcgaagtg	7	18	10	6	2	2	0	0	0	2	0	3	2	2	1	1	2	1	2	1	2	4	8	rs368511826		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chrX:123020210G>T	ENST00000371199.3	+	2	997	c.698G>T	c.(697-699)cGg>cTg	p.R233L	XIAP_ENST00000468691.1_Intron|XIAP_ENST00000434753.3_Missense_Mutation_p.R233L|XIAP_ENST00000355640.3_Missense_Mutation_p.R233L	NM_001167.3	NP_001158.2	P98170	XIAP_HUMAN	X-linked inhibitor of apoptosis	233					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|copper ion homeostasis (GO:0055070)|inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of protein ubiquitination (GO:0031398)|protein ubiquitination (GO:0016567)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R233Q(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)	25						GTTTTGGGCCGGAATCTTAAT	0.403									X-linked Lymphoproliferative syndrome																												p.R233L													.	XIAP-1084	1	Substitution - Missense(1)	endometrium(1)	c.G698T						.						110	102	104					X																	123020210		2203	4300	6503	SO:0001583	missense	331	exon2	Familial Cancer Database	XLP, Duncan syndrome, Familial Fatal Epstein-Barr Infection, incl. XLP2	TGGGCCGGAATCT	U45880	CCDS14606.1	Xq25	2014-09-17	2008-03-04	2008-03-04	ENSG00000101966	ENSG00000101966		"Baculoviral IAP repeat containing"	592	protein-coding gene	gene with protein product		300079	"baculoviral IAP repeat-containing 4"	API3, BIRC4		8552191, 8654366	Standard	NM_001167		Approved	hILP	uc010nqu.3	P98170	OTTHUMG00000022336	ENST00000371199.3:c.698G>T	X.37:g.123020210G>T	ENSP00000360242:p.Arg233Leu	Somatic	46	2		WXS	Illumina HiSeq	Phase_1	41	23	NM_001204401	0	0	0	0	0	D3DTF2|Q9NQ14	Missense_Mutation	SNP	ENST00000371199.3	37	CCDS14606.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.853544	0.51270	.	.	ENSG00000101966	ENST00000434753;ENST00000371199;ENST00000355640	T;T;T	0.70986	-0.53;-0.53;-0.53	5.81	5.81	0.92471	Baculoviral inhibition of apoptosis protein repeat (1);	0.000000	0.64402	D	0.000003	T	0.80523	0.4639	M	0.66939	2.045	0.45354	D	0.998347	D	0.71674	0.998	D	0.63597	0.916	T	0.80448	-0.1378	9	.	.	.	-30.5957	13.2865	0.60245	0.0768:0.0:0.9232:0.0	.	233	P98170	XIAP_HUMAN	L	233	ENSP00000395230:R233L;ENSP00000360242:R233L;ENSP00000347858:R233L	.	R	+	2	0	XIAP	122847891	1.000000	0.71417	0.997000	0.53966	0.604000	0.37047	3.016000	0.49607	2.461000	0.83175	0.508000	0.49915	CGG	.		0.403	XIAP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058165.5	NM_001167		T	123020210	G	T	123020210	3	4	148	1	0	0	0	0	1	0	0	0	17461	1116	39	4	700	4	XIAP	23	123020210	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	49208215	123020210	32250350	121	13279											
PNCK	139728	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	152938463	152938463	+	Splice_Site	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacgcgcgcgcacactcaCgagccgagcctctcgcggat	8	4	11	18	8	2	0	1	0	1	0	3	3	2	1	2	1	2	1	2	1	0	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chrX:152938463C>G	ENST00000370150.1	-	2	247		c.e2+1		PNCK_ENST00000370142.1_Splice_Site|PNCK_ENST00000340888.3_Splice_Site|PNCK_ENST00000475172.1_Splice_Site|PNCK_ENST00000370145.4_Splice_Site|PNCK_ENST00000447676.2_Splice_Site|PNCK_ENST00000393831.2_Splice_Site			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase							cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					cgcacactcacGAGCCGAGCC	0.592																																					.													.	PNCK-207	0			c.119+1G>C						.						47	32	37					X																	152938463		2201	4288	6489	SO:0001630	splice_region_variant	139728	exon3			CACTCACGAGCCG	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.68+1G>C	X.37:g.152938463C>G		Somatic	112	6		WXS	Illumina HiSeq	Phase_I	91	66	NM_001135740	0	0	0	0	0	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Splice_Site	SNP	ENST00000370150.1	37																																																																																				.		0.592	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452	Intron	G	152938463	C	G	152938463	5	3	148	1	0	0	0	0	0	0	1	0	12171	550	19	4	1002	4	PNCK	23	152938463	Splice_Site	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	29918253	152938463	2332097	122	13280											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19504023	19504023	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	atcaaagatgagaaggaggcGagccaagataagcggcacga	17	3	14	7	3	1	3	1	1	0	3	1	7	1	4	1	3	2	1	1	3	4	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:19504023G>C	ENST00000375254.3	-	19	2596	c.2569C>G	c.(2569-2571)Cgc>Ggc	p.R857G	UBR4_ENST00000375217.2_Missense_Mutation_p.R857G|UBR4_ENST00000375226.2_Missense_Mutation_p.R857G|UBR4_ENST00000375267.2_Missense_Mutation_p.R857G	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	857					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AGAAGGAGGCGAGCCAAGATA	0.498																																					p.R857G		.											.	UBR4-612	0			c.C2569G						.						133	126	128					1																	19504023		2203	4300	6503	SO:0001583	missense	23352	exon19			GGAGGCGAGCCAA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.2569C>G	1.37:g.19504023G>C	ENSP00000364403:p.Arg857Gly	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	256	130	NM_020765	0	0	0	0	0	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909893	0.92107	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.60728	0.2291	L	0.50333	1.59	0.80722	D	1	D	0.60160	0.987	D	0.67725	0.953	T	0.61043	-0.7142	10	0.87932	D	0	.	19.4792	0.95002	0.0:0.0:1.0:0.0	.	857	Q5T4S7	UBR4_HUMAN	G	857;857;857;857;73	ENSP00000364403:R857G;ENSP00000364416:R857G;ENSP00000364365:R857G;ENSP00000364374:R857G	ENSP00000364365:R857G	R	-	1	0	UBR4	19376610	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.238000	0.95380	2.713000	0.92767	0.655000	0.94253	CGC	.		0.498	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19504023	G	C	19504023	3	2	149	1	0	0	0	0	1	0	0	0	16937	1058	37	4	13334	4	UBR4	1	19504023	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		19504023	229746598	1	13281											
GJB5	2709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	35223633	35223633	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcatcacccccacggtacCacctcttcctgcaaacaaga	11	7	6	17	1	3	1	2	0	1	1	4	1	4	1	5	2	3	2	5	2	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:35223633C>T	ENST00000338513.1	+	2	875	c.702C>T	c.(700-702)acC>acT	p.T234T	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	234					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				CCCACGGTACCACCTCTTCCT	0.572																																					p.T234T		.											.	GJB5-91	0			c.C702T						.						156	129	138					1																	35223633		2203	4300	6503	SO:0001819	synonymous_variant	2709	exon2			CGGTACCACCTCT	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"Ion channels / Gap junction proteins (connexins)"	4287	protein-coding gene	gene with protein product	"connexin 31.1"	604493	"gap junction protein, beta 5 (connexin 31.1)", "gap junction protein, beta 5"			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.702C>T	1.37:g.35223633C>T		Somatic	415	0		WXS	Illumina HiSeq	Phase_I	332	145	NM_005268	0	0	0	0	0	Q9UPA3	Silent	SNP	ENST00000338513.1	37	CCDS382.1																																																																																			.		0.572	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268		T	35223633	C	T	35223633	2	4	149	1	0	0	0	0	0	0	0	1	6431	581	21	2		2	GJB5	1	35223633	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	15719610	35223633	214026988	2	13282											
GNL2	29889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	38040324	38040324	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagtcctcagcattctccCaagaatcaatcttgtatgtt	12	13	6	10	0	4	1	2	0	2	1	6	2	5	1	2	0	1	3	2	0	5	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:38040324C>G	ENST00000373062.3	-	11	1342	c.1244G>C	c.(1243-1245)tGg>tCg	p.W415S		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	415					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				AGCATTCTCCCAAGAATCAAT	0.418																																					p.W415S		.											.	GNL2-91	0			c.G1244C						.						92	85	88					1																	38040324		2203	4300	6503	SO:0001583	missense	29889	exon11			TTCTCCCAAGAAT	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.1244G>C	1.37:g.38040324C>G	ENSP00000362153:p.Trp415Ser	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	92	46	NM_013285	0	0	12	15	3	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.	.	.	.	.	.	.	.	.	.	C	33	5.223863	0.95139	.	.	ENSG00000134697	ENST00000373062	T	0.12774	2.65	5.87	5.87	0.94306	GTP-binding protein, orthogonal bundle domain (1);	0.000000	0.85682	D	0.000000	T	0.45438	0.1342	M	0.86420	2.815	0.80722	D	1	D	0.63046	0.992	D	0.66497	0.944	T	0.44143	-0.9347	10	0.72032	D	0.01	-11.3487	20.5827	0.99408	0.0:1.0:0.0:0.0	.	415	Q13823	NOG2_HUMAN	S	415	ENSP00000362153:W415S	ENSP00000362153:W415S	W	-	2	0	GNL2	37812911	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.786000	0.85741	2.941000	0.99782	0.655000	0.94253	TGG	.		0.418	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		G	38040324	C	G	38040324	3	3	149	1	0	0	0	0	1	0	0	0	6556	595	21	4	975	4	GNL2	1	38040324	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	2816691	38040324	211210297	3	13283											
ATP1A1	476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	116941337	116941337	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggggattgctggctcagAtgtgtccaagcaagctgctg	8	11	14	8	0	1	1	1	0	0	1	2	2	2	2	1	3	4	5	1	3	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:116941337A>G	ENST00000295598.5	+	16	2471	c.2219A>G	c.(2218-2220)gAt>gGt	p.D740G	ATP1A1_ENST00000369496.4_Missense_Mutation_p.D709G|ATP1A1_ENST00000537345.1_Missense_Mutation_p.D740G	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	740					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GCTGGCTCAGATGTGTCCAAG	0.493																																					p.D740G		.											.	ATP1A1-91	0			c.A2219G						.						201	191	194					1																	116941337		2203	4300	6503	SO:0001583	missense	476	exon16			GCTCAGATGTGTC	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2219A>G	1.37:g.116941337A>G	ENSP00000295598:p.Asp740Gly	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	152	60	NM_000701	0	0	140	288	148	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.803837	0.90623	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000369496	D;D;D	0.83419	-1.72;-1.72;-1.72	5.23	5.23	0.72850	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.92622	0.7656	H	0.94847	3.59	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.97110	1.0;0.999	D	0.94580	0.7778	10	0.87932	D	0	.	15.2911	0.73868	1.0:0.0:0.0:0.0	.	740;740	F5H3A1;P05023	.;AT1A1_HUMAN	G	740;740;709	ENSP00000295598:D740G;ENSP00000445306:D740G;ENSP00000358508:D709G	ENSP00000295598:D740G	D	+	2	0	ATP1A1	116742860	1.000000	0.71417	0.550000	0.28217	0.991000	0.79684	9.139000	0.94554	2.195000	0.70347	0.533000	0.62120	GAT	.		0.493	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		G	116941337	A	G	116941337	3	3	149	1	0	0	0	0	1	0	0	0	1129	333	12	3	2297	3	ATP1A1	1	116941337	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	78901013	116941337	132309284	4	13284											
LCE2A	353139	hgsc.bcm.edu	37	chr1	152671534	152671534	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagctctgggggctgctgcGgctccagctctgggggctgc	2	8	17	14	1	2	0	0	0	2	0	3	0	3	0	2	5	5	6	2	5	0	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:152671534G>A	ENST00000368779.1	+	2	208	c.157G>A	c.(157-159)Ggc>Agc	p.G53S		NM_178428.3	NP_848515.1	Q5TA79	LCE2A_HUMAN	late cornified envelope 2A	53	Cys-rich.				keratinization (GO:0031424)			p.C51_G64delCCGSSSGGCCSSGG(2)		breast(1)|large_intestine(1)|liver(2)|lung(4)	8	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGCTGCTGCGGCTCCAGCTC	0.692																																					p.G53S		.											.	LCE2A-68	2	Deletion - In frame(2)	liver(2)	c.G157A						.						48	61	56					1																	152671534		2203	4299	6502	SO:0001583	missense	353139	exon2			TGCTGCGGCTCCA		CCDS1021.1	1q21.3	2008-02-05			ENSG00000187173	ENSG00000187173		"Late cornified envelopes"	29469	protein-coding gene	gene with protein product		612609				11698679	Standard	NM_178428		Approved	LEP9	uc001faj.3	Q5TA79	OTTHUMG00000012392	ENST00000368779.1:c.157G>A	1.37:g.152671534G>A	ENSP00000357768:p.Gly53Ser	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	40	6	NM_178428	0	0	0	0	0	A4QMZ9	Missense_Mutation	SNP	ENST00000368779.1	37	CCDS1021.1	.	.	.	.	.	.	.	.	.	.	-	6.374	0.437046	0.12104	.	.	ENSG00000187173	ENST00000368779	T	0.03717	3.83	3.72	2.79	0.32731	.	.	.	.	.	T	0.01222	0.0040	L	0.51853	1.615	0.09310	N	1	P	0.39964	0.697	B	0.29353	0.101	T	0.47394	-0.9121	9	0.87932	D	0	.	6.8388	0.23951	0.1374:0.0:0.8626:0.0	.	53	Q5TA79	LCE2A_HUMAN	S	53	ENSP00000357768:G53S	ENSP00000357768:G53S	G	+	1	0	LCE2A	150938158	0.982000	0.34865	0.111000	0.21465	0.270000	0.26580	0.561000	0.23515	0.525000	0.28522	0.580000	0.79431	GGC	.		0.692	LCE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034512.1	NM_178428		A	152671534	G	A	152671534	3	1	149	1	0	0	0	0	1	0	0	0	8686	1116	39	1	159	1	LCE2A	1	152671534	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	35730197	152671534	96579087	5	13285											
OR6Y1	391112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	158517180	158517180	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggagaatgccttttggCggccctgagcagaagggatc	9	8	16	8	1	0	3	0	1	0	2	1	5	0	4	2	5	2	1	2	5	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:158517180C>T	ENST00000302617.3	-	1	715	c.716G>A	c.(715-717)cGc>cAc	p.R239H		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					TGCCTTTTGGCGGCCCTGAGC	0.522																																					p.R239H		.											.	OR6Y1-69	0			c.G716A						.						137	136	137					1																	158517180		2202	4300	6502	SO:0001583	missense	391112	exon1			TTTTGGCGGCCCT	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"GPCR / Class A : Olfactory receptors"	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.716G>A	1.37:g.158517180C>T	ENSP00000304807:p.Arg239His	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	173	81	NM_001005189	0	0	0	0	0	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487953	0.64074	.	.	ENSG00000197532	ENST00000302617	T	0.00333	8.07	5.34	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000631	T	0.00524	0.0017	M	0.90759	3.145	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.30297	-0.9983	10	0.87932	D	0	.	13.4384	0.61096	0.0:0.9214:0.0:0.0786	.	239	Q8NGX8	OR6Y1_HUMAN	H	239	ENSP00000304807:R239H	ENSP00000304807:R239H	R	-	2	0	OR6Y1	156783804	0.003000	0.15002	0.951000	0.38953	0.889000	0.51656	1.500000	0.35682	2.763000	0.94921	0.655000	0.94253	CGC	.		0.522	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		T	158517180	C	T	158517180	3	4	149	1	0	0	0	0	1	0	0	0	11239	768	27	1	263	1	OR6Y1	1	158517180	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	5845646	158517180	90733441	6	13286											
BAT2L2	23215	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	171506567	171506567	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatcctcatgctgagcctcAacaagcaactactcccaaag	13	8	5	15	0	2	1	2	1	0	0	4	1	4	1	3	0	6	2	3	0	6	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:171506567A>G	ENST00000338920.4	+	15	2690	c.2453A>G	c.(2452-2454)cAa>cGa	p.Q818R	PRRC2C_ENST00000367742.3_Missense_Mutation_p.Q820R|PRRC2C_ENST00000392078.3_Missense_Mutation_p.Q820R|PRRC2C_ENST00000426496.2_Missense_Mutation_p.Q818R	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	818					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GCTGAGCCTCAACAAGCAACT	0.403																																					p.Q818R													.	.	0			c.A2453G						.						53	43	47					1																	171506567		2203	4299	6502	SO:0001583	missense	23215	exon15			AGCCTCAACAAGC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"BAT2 domain containing 1", "HLA-B associated transcript 2-like 2"	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.2453A>G	1.37:g.171506567A>G	ENSP00000343629:p.Gln818Arg	Somatic	147	1		WXS	Illumina HiSeq	Phase_I	146	58	NM_015172	0	0	0	0	0	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	A	10.98	1.503319	0.26949	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	T;T;T;T	0.07021	3.23;3.23;3.23;3.23	5.42	3.01	0.34805	.	0.156139	0.29631	N	0.011615	T	0.02494	0.0076	L	0.32530	0.975	0.35787	D	0.822122	P	0.42409	0.779	B	0.38500	0.275	T	0.52983	-0.8502	10	0.21014	T	0.42	.	12.7484	0.57293	0.6068:0.3932:0.0:0.0	.	818	Q9Y520-4	.	R	820;819;818;820;818;575;577	ENSP00000375928:Q820R;ENSP00000410219:Q818R;ENSP00000356716:Q820R;ENSP00000343629:Q818R	ENSP00000343629:Q818R	Q	+	2	0	PRRC2C	169773191	0.998000	0.40836	0.985000	0.45067	0.912000	0.54170	1.913000	0.39956	0.336000	0.23639	-0.320000	0.08662	CAA	.		0.403	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171506567	A	G	171506567	3	3	149	1	0	0	0	0	1	0	0	0	1322	130	5	3	2507	3	BAT2L2	1	171506567	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	12989387	171506567	77744054	7	13287											
FAM129A	116496	ucsc.edu	37	chr1	184767284	184767284	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tttcaacgtgaatcatattgGtatgatctgcaaagatgaac	14	13	8	6	1	3	4	2	3	1	1	3	4	3	4	0	1	3	2	0	1	6	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:184767284G>A	ENST00000367511.3	-	13	1788	c.1595C>T	c.(1594-1596)aCc>aTc	p.T532I	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	532					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						AATCATATTGGTATGATCTGC	0.408																																					p.T532I													.	FAM129A-94	0			c.C1595T						.						101	93	96					1																	184767284		2203	4300	6503	SO:0001583	missense	116496	exon13			ATATTGGTATGAT	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.1595C>T	1.37:g.184767284G>A	ENSP00000356481:p.Thr532Ile	Somatic	29	0		WXS	Illumina HiSeq		41	4	NM_052966	0	0	0	0	0	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035316	0.54896	.	.	ENSG00000135842	ENST00000367511	T	0.11604	2.76	5.37	5.37	0.77165	.	0.232950	0.42821	D	0.000646	T	0.26991	0.0661	L	0.60455	1.87	0.42181	D	0.991681	P;D	0.71674	0.815;0.998	P;D	0.66351	0.49;0.943	T	0.00406	-1.1759	10	0.59425	D	0.04	-14.0264	13.185	0.59675	0.0:0.0:0.8412:0.1588	.	63;532	Q5TEY9;Q9BZQ8	.;NIBAN_HUMAN	I	532	ENSP00000356481:T532I	ENSP00000356481:T532I	T	-	2	0	FAM129A	183033907	1.000000	0.71417	0.872000	0.34217	0.960000	0.62799	6.237000	0.72345	2.512000	0.84698	0.655000	0.94253	ACC	.		0.408	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			A	184767284	G	A	184767284	3	1	149	1	0	0	0	0	1	0	0	0	5452	1261	44	2	1199	2	FAM129A	1	184767284	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	13260717	184767284	64483337	8	13288											
TMEM206	55248	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	212548558	212548558	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttggactttctggatgaaagGatctttccattcaaagacca	12	13	8	8	0	3	2	1	1	2	1	4	5	4	5	2	3	0	0	2	3	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:212548558G>A	ENST00000261455.4	-	7	1005	c.868C>T	c.(868-870)Cct>Tct	p.P290S	TMEM206_ENST00000535273.1_Missense_Mutation_p.P351S	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	290						cell surface (GO:0009986)|integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	17				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		TGGATGAAAGGATCTTTCCAT	0.318																																					p.P351S													.	TMEM206-153	0			c.C1051T						.						79	77	78					1																	212548558		2203	4300	6503	SO:0001583	missense	55248	exon8			TGAAAGGATCTTT	AK024066	CCDS1504.1, CCDS55687.1	1q32.3	2008-02-05	2008-01-17	2008-01-17	ENSG00000065600	ENSG00000065600			25593	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 75"	C1orf75		12477932	Standard	NM_018252		Approved	FLJ10874	uc010pte.2	Q9H813	OTTHUMG00000036751	ENST00000261455.4:c.868C>T	1.37:g.212548558G>A	ENSP00000261455:p.Pro290Ser	Somatic	139	1		WXS	Illumina HiSeq	Phase_I	190	68	NM_001198862	0	0	2	3	1	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	37	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.751203	0.89753	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.72953	0.3525	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.946	T	0.73855	-0.3851	9	0.87932	D	0	-7.061	20.5827	0.99408	0.0:0.0:1.0:0.0	.	351;290	B7Z4D6;Q9H813	.;TM206_HUMAN	S	290;351	.	ENSP00000261455:P290S	P	-	1	0	TMEM206	210615181	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.190000	0.65104	2.941000	0.99782	0.655000	0.94253	CCT	.		0.318	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		A	212548558	G	A	212548558	3	1	149	1	0	0	0	0	1	0	0	0	16163	1174	41	2	192	2	TMEM206	1	212548558	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	27781274	212548558	36702063	9	13289											
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	228469852	228469852	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgcaccaagtgatgccgggGaggtggtcttctctgtgcgg	5	10	16	10	2	2	1	0	1	2	0	3	2	2	2	2	5	3	1	2	5	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:228469852G>T	ENST00000422127.1	+	31	8460	c.8416G>T	c.(8416-8418)Gag>Tag	p.E2806*	OBSCN_ENST00000570156.2_Nonsense_Mutation_p.E3235*|OBSCN_ENST00000359599.6_Nonsense_Mutation_p.E1653*|OBSCN_ENST00000284548.11_Nonsense_Mutation_p.E2806*|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2806	Ig-like 27.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGATGCCGGGGAGGTGGTCTT	0.647																																					p.E3235X		.											.	OBSCN-403	0			c.G9703T						.						32	38	36					1																	228469852		1989	4156	6145	SO:0001587	stop_gained	84033	exon36			GCCGGGGAGGTGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"Rho guanine nucleotide exchange factors", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.8416G>T	1.37:g.228469852G>T	ENSP00000409493:p.Glu2806*	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	232	108	NM_001271223	0	0	1	1	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.448476	0.63178	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	.	.	.	4.21	4.21	0.49690	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	16.9495	0.86240	0.0:0.0:1.0:0.0	.	.	.	.	X	2806;2806;1653;505;212	.	ENSP00000284548:E2806X	E	+	1	0	OBSCN	226536475	1.000000	0.71417	0.992000	0.48379	0.321000	0.28281	9.350000	0.97070	2.063000	0.61619	0.462000	0.41574	GAG	.		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228469852	G	T	228469852	4	4	149	1	0	0	0	0	0	1	0	0	10838	1175	41	4	8534	4	OBSCN	1	228469852	Nonsense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	15921294	228469852	20780769	10	13290											
LYST	1130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	235884164	235884164	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccatattccagaagattaggGaggttatttgtgagtatatt	12	15	10	4	0	0	3	0	1	0	2	1	4	1	4	2	2	0	2	2	2	6	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:235884164G>A	ENST00000389794.3	-	40	9531	c.9357C>T	c.(9355-9357)ctC>ctT	p.L3119L	LYST_ENST00000389793.2_Silent_p.L3119L|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3119					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GAAGATTAGGGAGGTTATTTG	0.328																																					p.L3119L		.											.	LYST-143	0			c.C9357T						.						121	119	120					1																	235884164		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon40			ATTAGGGAGGTTA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"WD repeat domain containing"	1968	protein-coding gene	gene with protein product		606897	"Chediak-Higashi syndrome 1"	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.9357C>T	1.37:g.235884164G>A		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	71	28	NM_000081	0	0	0	0	0	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.		0.328	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235884164	G	A	235884164	2	1	149	1	0	0	0	0	0	0	0	1	9153	1161	41	2		2	LYST	1	235884164	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	7414312	235884164	13366457	11	13291											
FAM110C	642273	hgsc.bcm.edu;broad.mit.edu	37	chr2	45688	45688	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgcggtgaagttctccctcCccagggcctccaccacctcg	5	7	9	20	3	1	1	0	1	1	0	5	1	3	1	8	2	0	1	8	2	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:45688C>T	ENST00000327669.4	-	1	697	c.698G>A	c.(697-699)gGg>gAg	p.G233E	FAM110C_ENST00000460464.1_5'Flank	NM_001077710.2	NP_001071178.2	Q1W6H9	F110C_HUMAN	family with sequence similarity 110, member C	233					positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell projection assembly (GO:0060491)	cell cortex (GO:0005938)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|kidney(1)|lung(2)	4	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00221)		all cancers(51;0.000815)|Epithelial(75;0.00379)|OV - Ovarian serous cystadenocarcinoma(76;0.0127)|GBM - Glioblastoma multiforme(21;0.232)		GTTCTCCCTCCCCAGGGCCTC	0.682																																					p.G233E		.											.	FAM110C-68	0			c.G698A						.						12	15	14					2																	45688		2074	4200	6274	SO:0001583	missense	642273	exon1			TCCCTCCCCAGGG	DQ431183	CCDS42645.1	2p25.3	2011-12-01			ENSG00000184731	ENSG00000184731			33340	protein-coding gene	gene with protein product		611395				17499476, 19698782	Standard	NM_001077710		Approved		uc010yim.2	Q1W6H9	OTTHUMG00000151321	ENST00000327669.4:c.698G>A	2.37:g.45688C>T	ENSP00000328347:p.Gly233Glu	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	18	10	NM_001077710	0	0	0	0	0		Missense_Mutation	SNP	ENST00000327669.4	37	CCDS42645.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.618544	0.66787	.	.	ENSG00000184731	ENST00000327669	T	0.50548	0.74	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.67011	0.2848	M	0.70595	2.14	0.42278	D	0.992084	D	0.71674	0.998	D	0.74674	0.984	T	0.71879	-0.4459	10	0.72032	D	0.01	-10.2308	15.3421	0.74306	0.0:1.0:0.0:0.0	.	233	Q1W6H9	F110C_HUMAN	E	233	ENSP00000328347:G233E	ENSP00000328347:G233E	G	-	2	0	FAM110C	35688	0.991000	0.36638	0.057000	0.19452	0.348000	0.29142	3.654000	0.54453	2.277000	0.76020	0.561000	0.74099	GGG	.		0.682	FAM110C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322220.1	NM_001077710		T	45688	C	T	45688	3	4	149	1	0	0	0	0	1	0	0	0	5414	623	22	2	275	2	FAM110C	2	45688	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		45688	243153685	12	13292											
SMC6	79677	ucsc.edu	37	chr2	17881597	17881597	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctttttgttgctccatatGttcctcaaccattttcattt	6	22	3	10	0	3	0	2	0	1	0	5	0	5	0	3	0	2	3	3	0	2	9			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:17881597G>A	ENST00000448223.2	-	21	2541	c.2272C>T	c.(2272-2274)Cat>Tat	p.H758Y	SMC6_ENST00000351948.4_Missense_Mutation_p.H758Y|SMC6_ENST00000402989.1_Missense_Mutation_p.H758Y|SMC6_ENST00000381272.4_Missense_Mutation_p.H784Y	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	758					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGCTCCATATGTTCCTCAACC	0.264																																					p.H758Y													.	SMC6-292	0			c.C2272T						.						159	148	152					2																	17881597		2202	4300	6502	SO:0001583	missense	79677	exon21			CCATATGTTCCTC	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2272C>T	2.37:g.17881597G>A	ENSP00000404092:p.His758Tyr	Somatic	40	0		WXS	Illumina HiSeq		42	4	NM_001142286	0	0	2	2	0	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.514803	0.27123	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.18	2.74	0.32292	RecF/RecN/SMC (1);	0.479711	0.22822	N	0.055207	T	0.14227	0.0344	N	0.08118	0	0.20307	N	0.999914	B;B	0.18166	0.026;0.001	B;B	0.14578	0.011;0.002	T	0.16928	-1.0386	10	0.51188	T	0.08	.	6.2662	0.20928	0.0:0.1374:0.4642:0.3984	.	784;758	Q96SB8-2;Q96SB8	.;SMC6_HUMAN	Y	758;758;784;758	ENSP00000404092:H758Y;ENSP00000323439:H758Y;ENSP00000370672:H784Y;ENSP00000384539:H758Y	ENSP00000323439:H758Y	H	-	1	0	SMC6	17745078	1.000000	0.71417	0.998000	0.56505	0.854000	0.48673	0.719000	0.25881	0.384000	0.24942	-0.484000	0.04775	CAT	.		0.264	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17881597	G	A	17881597	3	1	149	1	0	0	0	0	1	0	0	0	14819	1377	48	2	1035	2	SMC6	2	17881597	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	17835909	17881597	225317776	13	13293											
DNMT3A	1788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	25469542	25469542	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggaagccccccagggccCattcaatcatgggcttgttc	7	9	11	14	0	2	0	2	0	0	0	3	1	2	1	4	3	1	3	4	3	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:25469542C>T	ENST00000264709.3	-	10	1563	c.1226G>A	c.(1225-1227)tGg>tAg	p.W409*	DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.W186*|DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.W409*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.W220*	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	409					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCCAGGGCCCATTCAATCAT	0.647			"Mis, F, N, S"		AML																																p.W409X		.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A-1924	0			c.G1226A						.						61	61	61					2																	25469542		2203	4298	6501	SO:0001587	stop_gained	1788	exon10			AGGGCCCATTCAA		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1226G>A	2.37:g.25469542C>T	ENSP00000264709:p.Trp409*	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	112	48	NM_175629	0	0	0	0	0	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	ENST00000264709.3	37	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	37	6.406269	0.97542	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.0978	15.5438	0.76077	0.0:1.0:0.0:0.0	.	.	.	.	X	220;409;409;186	.	ENSP00000264709:W409X	W	-	2	0	DNMT3A	25323046	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.528000	0.81941	2.535000	0.85469	0.655000	0.94253	TGG	.		0.647	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25469542	C	T	25469542	4	4	149	1	0	0	0	0	0	1	0	0	4687	595	21	2	1568	2	DNMT3A	2	25469542	Nonsense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	7587945	25469542	217729831	14	13294											
C2orf16	84226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27801772	27801772	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagatattttgcagcctgAagagacctatatagacccta	14	10	8	9	0	0	4	0	1	0	3	0	6	0	4	3	0	2	1	3	0	6	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:27801772A>T	ENST00000408964.2	+	1	2384	c.2333A>T	c.(2332-2334)gAa>gTa	p.E778V	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	778						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TTGCAGCCTGAAGAGACCTAT	0.403																																					p.E778V		.											.	C2orf16-67	0			c.A2333T						.						170	168	168					2																	27801772		1824	4081	5905	SO:0001583	missense	84226	exon1			AGCCTGAAGAGAC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"P-S-E-R-S-H-H-S repeats containing"						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2333A>T	2.37:g.27801772A>T	ENSP00000386190:p.Glu778Val	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	39	16	NM_032266	0	0	0	0	0	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.022880	0.35701	.	.	ENSG00000221843	ENST00000408964	T	0.06768	3.26	5.39	-2.51	0.06365	.	.	.	.	.	T	0.05868	0.0153	N	0.24115	0.695	0.09310	N	1	P	0.46512	0.879	P	0.45449	0.481	T	0.28681	-1.0036	9	0.66056	D	0.02	.	2.4234	0.04454	0.285:0.1502:0.4258:0.139	.	778	Q68DN1	CB016_HUMAN	V	778	ENSP00000386190:E778V	ENSP00000386190:E778V	E	+	2	0	C2orf16	27655276	0.056000	0.20664	0.033000	0.17914	0.105000	0.19272	0.158000	0.16422	-0.136000	0.11475	0.459000	0.35465	GAA	.		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27801772	A	T	27801772	3	4	149	1	0	0	0	0	1	0	0	0	2163	246	9	5	2335	5	C2orf16	2	27801772	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	2332230	27801772	215397601	15	13295											
GEMIN6	79833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	39008788	39008788	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagaagctgatgcatttgttCacgtctggagactgcaaagc	11	10	12	8	1	2	3	1	1	1	2	2	5	2	3	0	1	4	4	0	1	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:39008788C>T	ENST00000281950.3	+	3	374	c.258C>T	c.(256-258)ttC>ttT	p.F86F	GEMIN6_ENST00000409566.1_3'UTR|GEMIN6_ENST00000409011.1_3'UTR	NM_024775.9	NP_079051.9	Q8WXD5	GEMI6_HUMAN	gem (nuclear organelle) associated protein 6	86					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				kidney(1)|large_intestine(3)|pancreas(1)	5		all_hematologic(82;0.21)				TGCATTTGTTCACGTCTGGAG	0.478																																					p.F86F		.											.	GEMIN6-226	0			c.C258T						.						102	88	92					2																	39008788		2203	4300	6503	SO:0001819	synonymous_variant	79833	exon3			TTTGTTCACGTCT	AF453443	CCDS1799.1	2p22.1	2014-05-14			ENSG00000152147	ENSG00000152147			20044	protein-coding gene	gene with protein product		607006				11748230	Standard	NM_024775		Approved	FLJ23459	uc002rrc.3	Q8WXD5	OTTHUMG00000128588	ENST00000281950.3:c.258C>T	2.37:g.39008788C>T		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	127	43	NM_024775	0	0	12	21	9	B2RDP8|Q53SI5|Q8WVB4|Q9H5G6	Silent	SNP	ENST00000281950.3	37	CCDS1799.1																																																																																			.		0.478	GEMIN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250441.3			T	39008788	C	T	39008788	2	4	149	1	0	0	0	0	0	0	0	1	6352	825	29	2		2	GEMIN6	2	39008788	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	11207016	39008788	204190585	16	13296											
TSPYL6	388951	broad.mit.edu	37	chr2	54482521	54482521	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gacagctgtgggtggtggcgGaaagcagtgacccagaagcc	10	5	17	9	1	0	2	0	1	0	1	0	4	0	3	2	4	3	2	2	4	2	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:54482521G>A	ENST00000317802.7	-	1	888	c.768C>T	c.(766-768)ttC>ttT	p.F256F	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	256					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						GGTGGTGGCGGAAAGCAGTGA	0.517																																					p.F256F													.	TSPYL6-90	0			c.C768T						.						72	73	73					2																	54482521		2142	4280	6422	SO:0001819	synonymous_variant	388951	exon1			GTGGCGGAAAGCA	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.768C>T	2.37:g.54482521G>A		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	129	5	NM_001003937	0	0	0	0	0	Q6NUJ3	Silent	SNP	ENST00000317802.7	37	CCDS42682.1																																																																																			.		0.517	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		A	54482521	G	A	54482521	2	1	149	1	0	0	0	0	0	0	0	1	16696	1165	41	2		2	TSPYL6	2	54482521	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	15473733	54482521	188716852	17	13297											
ZNF638	27332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	71607375	71607375	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaggtgaagaaaaagacTttagagtcaaagaaagtatc	21	7	10	3	0	1	6	1	1	0	5	2	6	1	6	0	1	0	1	0	1	8	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:71607375T>C	ENST00000409544.1	+	9	2919	c.2289T>C	c.(2287-2289)acT>acC	p.T763T	ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000377802.2_Silent_p.T763T|RNU6-105P_ENST00000363909.1_RNA|ZNF638_ENST00000355812.3_Silent_p.T763T|ZNF638_ENST00000264447.4_Silent_p.T763T	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	763					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AGAAAAAGACTTTAGAGTCAA	0.249																																					p.T763T		.											.	ZNF638-94	0			c.T2289C						.						33	33	33					2																	71607375		2189	4242	6431	SO:0001819	synonymous_variant	27332	exon9			AAAGACTTTAGAG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"RNA binding motif (RRM) containing"	17894	protein-coding gene	gene with protein product		614349	"zinc finger, matrin-like"	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.2289T>C	2.37:g.71607375T>C		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	118	49	NM_014497	0	0	0	1	1	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																			.		0.249	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		C	71607375	T	C	71607375	2	2	149	1	0	0	0	0	0	0	0	1	18087	1596	56	3		3	ZNF638	2	71607375	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	17124854	71607375	171591998	18	13298											
FER1L5	90342	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	97359251	97359251	+	RNA	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacccctccagggcccttcAttcgggtggtcttcctgaac	5	11	9	16	1	2	1	1	1	1	0	5	1	4	1	5	3	2	0	5	3	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:97359251A>T	ENST00000457909.1	+	0	1760							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						AGGGCCCTTCATTCGGGTGGT	0.612																																					p.I1128F		.											.	FER1L5-23	0			c.A3382T						.						58	69	66					2																	97359251		692	1591	2283			90342	exon31			CCCTTCATTCGGG	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		2.37:g.97359251A>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	85	34	NM_001113382	0	0	0	0	0	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	37		.	.	.	.	.	.	.	.	.	.	A	9.661	1.144037	0.21205	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	5.31	-0.268	0.12934	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.57651	0.2068	M	0.62723	1.935	.	.	.	P	0.50369	0.934	P	0.52856	0.711	T	0.66508	-0.5906	7	0.66056	D	0.02	-3.7442	9.6818	0.40074	0.4125:0.0:0.5875:0.0	.	1128	A0AVI2	FR1L5_HUMAN	F	1128;1086	.	ENSP00000444148:I1128F	I	+	1	0	FER1L5	96722978	0.149000	0.22717	0.255000	0.24374	0.514000	0.34195	1.218000	0.32467	-0.049000	0.13379	0.459000	0.35465	ATT	.		0.612	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		T	97359251	A	T	97359251	1	4	149	0	1	0	0	0	0	0	0	0	5833	217	8	5		5	FER1L5	2	97359251	RNA	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	25751876	97359251	145840122	19	13299											
ST6GAL2	84620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	107459932	107459932	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcacccgcctcctctggaCctgtgcagccggaaaagccc	7	7	9	18	2	2	0	1	0	1	0	3	2	3	2	6	2	3	1	6	2	2	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:107459932C>G	ENST00000409382.3	-	2	1112	c.502G>C	c.(502-504)Gtc>Ctc	p.V168L	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.V168L|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.V168L	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	168					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CTCCTCTGGACCTGTGCAGCC	0.662																																					p.V168L		.											.	ST6GAL2-191	0			c.G502C						.						78	90	86					2																	107459932		2203	4300	6503	SO:0001583	missense	84620	exon2			TCTGGACCTGTGC	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"sialyltransferase 2 (monosialoganglioside sialyltransferase)"	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.502G>C	2.37:g.107459932C>G	ENSP00000386942:p.Val168Leu	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	165	63	NM_032528	0	0	0	0	0	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	C	1.093	-0.663505	0.03428	.	.	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.30714	2.53;2.53;1.52	2.52	1.61	0.23674	.	2.704170	0.01639	N	0.023935	T	0.17109	0.0411	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17501	-1.0367	10	0.19147	T	0.46	.	6.3831	0.21546	0.0:0.6285:0.0:0.3715	.	168;168	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	L	168	ENSP00000355273:V168L;ENSP00000386942:V168L;ENSP00000387332:V168L	ENSP00000355273:V168L	V	-	1	0	ST6GAL2	106826364	0.000000	0.05858	0.000000	0.03702	0.186000	0.23388	0.013000	0.13310	0.339000	0.23719	0.561000	0.74099	GTC	.		0.662	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		G	107459932	C	G	107459932	3	3	149	1	0	0	0	0	1	0	0	0	15254	507	18	4	1194	4	ST6GAL2	2	107459932	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	10100681	107459932	135739441	20	13300											
RANBP2	5903	ucsc.edu;bcgsc.ca	37	chr2	109381778	109381778	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cttcagagacaagcaaggctCcaaagagcggatttgaggga	14	6	13	8	1	1	3	1	1	0	2	2	6	2	5	1	3	2	2	1	3	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:109381778C>G	ENST00000283195.6	+	20	4909	c.4783C>G	c.(4783-4785)Cca>Gca	p.P1595A		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1595					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AAGCAAGGCTCCAAAGAGCGG	0.448																																					p.P1595A													.	RANBP2-675	0			c.C4783G						.						122	124	123					2																	109381778		2203	4300	6503	SO:0001583	missense	5903	exon20			AAGGCTCCAAAGA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.4783C>G	2.37:g.109381778C>G	ENSP00000283195:p.Pro1595Ala	Somatic	387	2		WXS	Illumina HiSeq		441	193	NM_006267	0	0	0	0	0	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	c	10.31	1.314111	0.23908	.	.	ENSG00000153201	ENST00000283195	T	0.28069	1.63	4.78	0.353	0.16058	.	.	.	.	.	T	0.16557	0.0398	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.31308	-0.9948	9	0.16896	T	0.51	0.078	4.6119	0.12406	0.2692:0.5227:0.1308:0.0773	.	1595	P49792	RBP2_HUMAN	A	1595	ENSP00000283195:P1595A	ENSP00000283195:P1595A	P	+	1	0	RANBP2	108748210	0.000000	0.05858	0.990000	0.47175	0.914000	0.54420	-1.871000	0.01640	0.124000	0.18369	0.655000	0.94253	CCA	.		0.448	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109381778	C	G	109381778	3	3	149	1	0	0	0	0	1	0	0	0	13060	855	30	4	4861	4	RANBP2	2	109381778	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	1921846	109381778	133817595	21	13301											
TNFAIP6	7130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	152235994	152235994	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcaaggaaaaaatacaagtActacttctactggaaataaa	20	9	6	6	0	2	0	1	0	1	0	2	2	2	2	0	2	4	1	0	2	12	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:152235994A>T	ENST00000243347.3	+	6	856	c.781A>T	c.(781-783)Act>Tct	p.T261S		NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	261					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	AAATACAAGTACTACTTCTAC	0.333																																					p.T261S		.											.	TNFAIP6-90	0			c.A781T						.						84	90	88					2																	152235994		2203	4300	6503	SO:0001583	missense	7130	exon6			ACAAGTACTACTT		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.781A>T	2.37:g.152235994A>T	ENSP00000243347:p.Thr261Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	83	39	NM_007115	0	0	0	3	3	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	CCDS2193.1	.	.	.	.	.	.	.	.	.	.	A	8.550	0.875364	0.17395	.	.	ENSG00000123610	ENST00000243347	T	0.18174	2.23	5.56	1.83	0.25207	.	0.332619	0.29185	N	0.012896	T	0.07773	0.0195	N	0.17082	0.46	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.33497	-0.9866	10	0.21540	T	0.41	.	3.4438	0.07473	0.6522:0.0:0.1812:0.1666	.	261	P98066	TSG6_HUMAN	S	261	ENSP00000243347:T261S	ENSP00000243347:T261S	T	+	1	0	TNFAIP6	151944240	0.044000	0.20184	0.250000	0.24296	0.441000	0.31987	1.210000	0.32370	0.063000	0.16370	0.533000	0.62120	ACT	.		0.333	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115		T	152235994	A	T	152235994	3	4	149	1	0	0	0	0	1	0	0	0	16307	391	14	5	803	5	TNFAIP6	2	152235994	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	42854216	152235994	90963379	22	13302											
SLC4A10	57282	bcgsc.ca	37	chr2	162821643	162821643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctggttggatgatttgatgcCcgagagtaagaaaaagaaac	15	9	12	5	1	0	5	0	2	0	3	0	7	0	6	1	2	2	2	1	2	4	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:162821643C>T	ENST00000446997.1	+	23	3212	c.3119C>T	c.(3118-3120)cCc>cTc	p.P1040L	SLC4A10_ENST00000375514.5_Missense_Mutation_p.P1021L|SLC4A10_ENST00000421911.1_Missense_Mutation_p.P1040L|SLC4A10_ENST00000415876.2_Missense_Mutation_p.P1010L|SLC4A10_ENST00000272716.5_Missense_Mutation_p.P1010L	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	1040					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	GATTTGATGCCCGAGAGTAAG	0.348																																					p.P1040L													.	SLC4A10-229	0			c.C3119T						.						81	75	77					2																	162821643		1812	4083	5895	SO:0001583	missense	57282	exon23			TGATGCCCGAGAG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.3119C>T	2.37:g.162821643C>T	ENSP00000393066:p.Pro1040Leu	Somatic	35	0		WXS	Illumina HiSeq	Phase_1	48	4	NM_001178015	0	0	0	0	0	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation	SNP	ENST00000446997.1	37	CCDS54411.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973232	0.92919	.	.	ENSG00000144290	ENST00000375514;ENST00000415876;ENST00000272716;ENST00000449513;ENST00000446997;ENST00000421911;ENST00000415711	T;T;T;T;D	0.82893	-1.43;-1.43;-1.44;-1.44;-1.66	5.93	5.04	0.67666	.	0.054718	0.85682	D	0.000000	D	0.91205	0.7229	M	0.93550	3.43	0.80722	D	1	P;P;D	0.57571	0.552;0.552;0.98	B;B;P	0.52957	0.331;0.331;0.714	D	0.93475	0.6822	10	0.87932	D	0	.	16.4058	0.83669	0.1326:0.8674:0.0:0.0	.	1021;1010;1040	F8W675;Q6U841-2;Q6U841	.;.;S4A10_HUMAN	L	1021;1010;1010;1009;1040;1040;1039	ENSP00000364664:P1021L;ENSP00000395797:P1010L;ENSP00000272716:P1010L;ENSP00000393066:P1040L;ENSP00000404486:P1040L	ENSP00000272716:P1010L	P	+	2	0	SLC4A10	162529889	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	1.460000	0.47911	0.655000	0.94253	CCC	.		0.348	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		T	162821643	C	T	162821643	3	4	149	1	0	0	0	0	1	0	0	0	14683	623	22	2	3294	2	SLC4A10	2	162821643	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	10585649	162821643	80377730	23	13303											
SMARCAL1	50485	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	217285132	217285132	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacaggccggccttccatcaGctccatccctttcatttgtc	6	12	7	16	1	2	0	2	0	0	0	6	1	5	0	5	2	1	1	5	2	0	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:217285132G>A	ENST00000357276.4	+	5	1303	c.973G>A	c.(973-975)Gct>Act	p.A325T	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.A325T	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	325					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CCTTCCATCAGCTCCATCCCT	0.562									Schimke Immuno-Osseous Dysplasia																												p.A325T		.											.	SMARCAL1-293	0			c.G973A						.						121	100	108					2																	217285132		2203	4300	6503	SO:0001583	missense	50485	exon5	Familial Cancer Database	SIOD	CCATCAGCTCCAT	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"HepA-related protein", "ATP-driven annealing helicase"	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.973G>A	2.37:g.217285132G>A	ENSP00000349823:p.Ala325Thr	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	249	93	NM_014140	0	0	1	2	1	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590173	0.46214	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128;ENST00000412913	D;D;T;D;T	0.86097	-2.04;-2.04;1.45;-2.07;0.63	4.85	4.85	0.62838	.	0.704849	0.14015	N	0.347188	T	0.80711	0.4675	L	0.59436	1.845	0.09310	N	1	P	0.37612	0.602	B	0.31290	0.127	T	0.71968	-0.4432	10	0.28530	T	0.3	-12.6293	13.2969	0.60303	0.0:0.1601:0.8399:0.0	.	325	Q9NZC9	SMAL1_HUMAN	T	325;325;224;189;45	ENSP00000349823:A325T;ENSP00000350940:A325T;ENSP00000392997:A224T;ENSP00000375974:A189T;ENSP00000390248:A45T	ENSP00000349823:A325T	A	+	1	0	SMARCAL1	216993377	0.682000	0.27624	0.373000	0.26003	0.202000	0.24057	4.009000	0.57110	2.531000	0.85337	0.561000	0.74099	GCT	.		0.562	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			A	217285132	G	A	217285132	3	1	149	1	0	0	0	0	1	0	0	0	14805	971	34	2	983	2	SMARCAL1	2	217285132	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	54463489	217285132	25914241	24	13304											
IGFBP5	3488	ucsc.edu;bcgsc.ca	37	chr2	217541549	217541549	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tccatgcctggcagcttcatCccgtacttgtccacgcacca	7	10	7	17	2	1	0	1	0	0	0	4	0	4	0	5	1	3	4	5	1	1	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:217541549C>G	ENST00000233813.4	-	4	1493	c.744G>C	c.(742-744)ggG>ggC	p.G248G		NM_000599.3	NP_000590.1	P24593	IBP5_HUMAN	insulin-like growth factor binding protein 5	248	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cellular protein metabolic process (GO:0044267)|cellular response to cAMP (GO:0071320)|cellular response to organic cyclic compound (GO:0071407)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hair follicle morphogenesis (GO:0031069)|intracellular signal transduction (GO:0035556)|mammary gland involution (GO:0060056)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|striated muscle cell differentiation (GO:0051146)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|insulin-like growth factor binding protein complex (GO:0016942)	insulin-like growth factor I binding (GO:0031994)			endometrium(1)|large_intestine(3)|lung(1)	5		Renal(323;0.0822)		Epithelial(149;2.1e-06)|all cancers(144;0.000165)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCAGCTTCATCCCGTACTTGT	0.612																																					p.G248G													.	IGFBP5-522	0			c.G744C						.						207	166	180					2																	217541549		2203	4300	6503	SO:0001819	synonymous_variant	3488	exon4			CTTCATCCCGTAC		CCDS2405.1	2q35	2014-09-16			ENSG00000115461	ENSG00000115461			5474	protein-coding gene	gene with protein product		146734				7511611	Standard	NM_000599		Approved		uc002vgj.4	P24593	OTTHUMG00000133058	ENST00000233813.4:c.744G>C	2.37:g.217541549C>G		Somatic	317	3		WXS	Illumina HiSeq		329	128	NM_000599	0	0	0	1	1	Q5U0A3	Silent	SNP	ENST00000233813.4	37	CCDS2405.1																																																																																			.		0.612	IGFBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256674.2	NM_000599		G	217541549	C	G	217541549	2	3	149	1	0	0	0	0	0	0	0	1	7603	842	30	4		4	IGFBP5	2	217541549	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	256417	217541549	25657824	25	13305											
KCNJ13	3769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233633228	233633228	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggagcagagtagccagAggacttgatggtgtaatgga	11	9	16	5	0	0	3	0	1	0	2	0	6	0	6	1	4	3	4	1	4	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:233633228A>T	ENST00000233826.3	-	3	895	c.756T>A	c.(754-756)ccT>ccA	p.P252P	KCNJ13_ENST00000410029.1_Silent_p.P252P|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000452341.2_Intron|AC064852.4_ENST00000427571.1_RNA	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	252					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		GAGTAGCCAGAGGACTTGATG	0.443																																					p.P252P		.											.	KCNJ13-90	0			c.T756A						.						129	118	122					2																	233633228		2203	4300	6503	SO:0001819	synonymous_variant	3769	exon3			AGCCAGAGGACTT	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.756T>A	2.37:g.233633228A>T		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	200	87	NM_002242	0	0	0	0	0	A0PGH1|O76023|Q53SA1|Q8N3Y4	Silent	SNP	ENST00000233826.3	37	CCDS2498.1																																																																																			.		0.443	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242		T	233633228	A	T	233633228	2	4	149	1	0	0	0	0	0	0	0	1	8068	291	11	5		5	KCNJ13	2	233633228	Silent	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	16091679	233633228	9566145	26	13306											
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233659498	233659498	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcccctgtcgcagattccTtcagatacagcctctcctct	7	11	6	17	1	3	2	1	0	2	2	6	2	4	2	5	0	3	1	5	0	1	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:233659498T>A	ENST00000409547.1	+	15	1634	c.1323T>A	c.(1321-1323)ccT>ccA	p.P441P	GIGYF2_ENST00000409451.3_Silent_p.P462P|GIGYF2_ENST00000409480.1_Silent_p.P463P|GIGYF2_ENST00000409196.3_Silent_p.P435P|GIGYF2_ENST00000373566.3_Silent_p.P463P|GIGYF2_ENST00000373563.4_Silent_p.P441P|GIGYF2_ENST00000452341.2_Silent_p.P272P	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	441	Pro-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CGCAGATTCCTTCAGATACAG	0.478																																					p.P462P		.											.	GIGYF2-28	0			c.T1386A						.						292	293	293					2																	233659498		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon15			GATTCCTTCAGAT	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1323T>A	2.37:g.233659498T>A		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	92	44	NM_001103147	0	0	0	0	0	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	37	CCDS33401.1																																																																																			.		0.478	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233659498	T	A	233659498	2	1	149	1	0	0	0	0	0	0	0	1	6398	1596	56	5		5	GIGYF2	2	233659498	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	26270	233659498	9539875	27	13307											
KIAA1407	57577	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	113697143	113697143	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgaagaaaatgtacacaAaattttcttacttcttcctg	13	17	4	7	0	2	2	0	1	2	1	3	2	3	2	1	0	2	1	1	0	7	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr3:113697143A>C	ENST00000295878.3	-	16	2642	c.2496T>G	c.(2494-2496)ttT>ttG	p.F832L		NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	832										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						AATGTACACAAAATTTTCTTA	0.393																																					p.F832L		.											.	KIAA1407-92	0			c.T2496G						.						73	74	74					3																	113697143		2203	4300	6503	SO:0001583	missense	57577	exon16			TACACAAAATTTT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2496T>G	3.37:g.113697143A>C	ENSP00000295878:p.Phe832Leu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	63	27	NM_020817	0	0	3	3	0	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	A	7.654	0.683498	0.14907	.	.	ENSG00000163617	ENST00000295878	T	0.28666	1.6	4.46	-2.16	0.07080	.	0.462954	0.22456	N	0.059825	T	0.05135	0.0137	N	0.00413	-1.525	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38415	-0.9662	10	0.05620	T	0.96	.	5.5621	0.17150	0.256:0.3712:0.3728:0.0	.	832	Q8NCU4	K1407_HUMAN	L	832	ENSP00000295878:F832L	ENSP00000295878:F832L	F	-	3	2	KIAA1407	115179833	0.000000	0.05858	0.000000	0.03702	0.745000	0.42441	-1.005000	0.03674	-0.297000	0.08934	0.528000	0.53228	TTT	.		0.393	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113697143	A	C	113697143	3	2	149	1	0	0	0	0	1	0	0	0	8250	11	1	5	322	5	KIAA1407	3	113697143	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		113697143	84325287	28	13308											
ABCC5	10057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	183669307	183669307	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaacttcatagggcttcgaaGgatccttcggaaaagctcgt	12	10	10	9	3	1	0	1	0	0	0	5	3	2	2	1	3	2	2	1	3	5	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr3:183669307G>C	ENST00000334444.6	-	20	3106	c.2866C>G	c.(2866-2868)Ctt>Gtt	p.L956V	ABCC5_ENST00000265586.6_Missense_Mutation_p.L956V	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	956	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GGGCTTCGAAGGATCCTTCGG	0.542																																					p.L956V		.											.	ABCC5-137	0			c.C2866G						.						74	79	77					3																	183669307		2004	4191	6195	SO:0001583	missense	10057	exon20			TTCGAAGGATCCT	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"ATP binding cassette transporters / subfamily C"	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.2866C>G	3.37:g.183669307G>C	ENSP00000333926:p.Leu956Val	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	71	41	NM_005688	0	0	2	3	1	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299975	0.81136	.	.	ENSG00000114770	ENST00000334444;ENST00000265586	D;D	0.91843	-2.92;-2.92	6.11	5.23	0.72850	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.92616	0.7654	M	0.74647	2.275	0.58432	D	0.999996	P;P	0.43024	0.771;0.798	P;B	0.44422	0.449;0.387	D	0.92434	0.5956	10	0.49607	T	0.09	-14.3754	15.2019	0.73147	0.067:0.0:0.933:0.0	.	956;956	Q86UX3;O15440	.;MRP5_HUMAN	V	956	ENSP00000333926:L956V;ENSP00000265586:L956V	ENSP00000265586:L956V	L	-	1	0	ABCC5	185152001	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	6.461000	0.73522	1.590000	0.49995	0.655000	0.94253	CTT	.		0.542	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		C	183669307	G	C	183669307	3	2	149	1	0	0	0	0	1	0	0	0	56	1000	35	4	1491	4	ABCC5	3	183669307	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	69972164	183669307	14353123	29	13309											
KIAA0226	9711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	197408102	197408102	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaatgagcaggtccttggaGaagttgctgacgtagtactt	10	13	12	6	1	0	3	0	2	0	1	1	4	1	3	1	2	3	5	1	2	4	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr3:197408102G>A	ENST00000296343.5	-	16	2327	c.2328C>T	c.(2326-2328)ttC>ttT	p.F776F	KIAA0226_ENST00000273582.5_Silent_p.F731F|KIAA0226_ENST00000389665.5_Silent_p.F801F	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	776					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GGTCCTTGGAGAAGTTGCTGA	0.522																																					p.F776F	Esophageal Squamous(3;167 355 3763 15924)	.											.	KIAA0226-22	0			c.C2328T						.						154	149	151					3																	197408102		2046	4228	6274	SO:0001819	synonymous_variant	9711	exon16			CTTGGAGAAGTTG	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.2328C>T	3.37:g.197408102G>A		Somatic	177	0		WXS	Illumina HiSeq	Phase_I	154	72	NM_014687	0	0	0	0	0	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.648|8.648	0.897483|0.897483	0.17686|0.17686	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	4.55|4.55	3.66|3.66	0.41972|0.41972	.|.	.|.	.|.	.|.	.|.	T|T	0.63046|0.63046	0.2478|0.2478	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.61667|0.61667	-0.7016|-0.7016	4|4	.|.	.|.	.|.	.|.	12.4295|12.4295	0.55565|0.55565	0.0825:0.0:0.9175:0.0|0.0825:0.0:0.9175:0.0	.|.	.|.	.|.	.|.	F|F	738|560	.|.	.|.	L|S	-|-	1|2	0|0	KIAA0226|KIAA0226	198892499|198892499	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	2.466000|2.466000	0.45084|0.45084	1.244000|1.244000	0.43870|0.43870	0.555000|0.555000	0.69702|0.69702	CTC|TCT	.		0.522	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197408102	G	A	197408102	2	1	149	1	0	0	0	0	0	0	0	1	8183	933	33	2		2	KIAA0226	3	197408102	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	13738795	197408102	614328	30	13310											
GAK	2580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	882734	882734	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggaagccgccatacggcTggtcgtactccgccagcgcc	7	5	12	17	5	0	0	0	0	0	0	2	1	1	1	6	3	4	2	6	3	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:882734T>A	ENST00000314167.4	-	11	1216	c.1106A>T	c.(1105-1107)cAg>cTg	p.Q369L	GAK_ENST00000511163.1_Missense_Mutation_p.Q290L	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	369					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GCCATACGGCTGGTCGTACTC	0.662																																					p.Q369L		.											.	GAK-568	0			c.A1106T						.						45	40	42					4																	882734		2200	4293	6493	SO:0001583	missense	2580	exon11			TACGGCTGGTCGT	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"Heat shock proteins / DNAJ (HSP40)"	4113	protein-coding gene	gene with protein product	"auxilin-2"	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1106A>T	4.37:g.882734T>A	ENSP00000314499:p.Gln369Leu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	63	29	NM_005255	0	0	6	12	6	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185496	0.57909	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	T;T	0.79352	-0.8;-1.26	4.55	4.55	0.56014	.	0.739757	0.13112	N	0.412872	T	0.80544	0.4643	M	0.76002	2.32	0.58432	D	0.999999	D;P;P;P	0.54772	0.968;0.883;0.944;0.937	P;P;B;B	0.48654	0.585;0.48;0.4;0.256	T	0.79271	-0.1872	10	0.45353	T	0.12	-33.1852	10.2933	0.43610	0.0:0.0:0.0:1.0	.	290;290;369;265	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	L	369;290	ENSP00000314499:Q369L;ENSP00000421361:Q290L	ENSP00000314499:Q369L	Q	-	2	0	GAK	872734	1.000000	0.71417	0.993000	0.49108	0.052000	0.14988	6.860000	0.75473	1.679000	0.50963	0.459000	0.35465	CAG	.		0.662	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		A	882734	T	A	882734	3	1	149	1	0	0	0	0	1	0	0	0	6215	1580	55	5	2901	5	GAK	4	882734	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		882734	190271542	31	13311											
ADD1	118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	2916729	2916729	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaccgtgagctggaggagtAccgcagggaggtggagagga	11	4	20	6	2	0	3	0	1	0	2	0	8	0	7	2	6	2	3	2	6	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:2916729A>G	ENST00000398129.1	+	12	1744	c.1724A>G	c.(1723-1725)tAc>tGc	p.Y575C	ADD1_ENST00000398125.1_Missense_Mutation_p.Y606C|ADD1_ENST00000355842.3_Missense_Mutation_p.Y606C|ADD1_ENST00000398123.2_Missense_Mutation_p.Y606C|ADD1_ENST00000513328.2_Missense_Mutation_p.Y575C|ADD1_ENST00000264758.7_Missense_Mutation_p.Y606C|ADD1_ENST00000446856.1_Missense_Mutation_p.Y575C|ADD1_ENST00000503455.2_Missense_Mutation_p.Y606C			P35611	ADDA_HUMAN	adducin 1 (alpha)	575					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTGGAGGAGTACCGCAGGGAG	0.587																																					p.Y606C	Esophageal Squamous(71;505 1201 20414 34538 37449)	.											.	ADD1-92	0			c.A1817G						.						100	95	96					4																	2916729		2203	4300	6503	SO:0001583	missense	118	exon13			AGGAGTACCGCAG	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1724A>G	4.37:g.2916729A>G	ENSP00000381197:p.Tyr575Cys	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	196	89	NM_176801	0	0	62	103	41	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	37	CCDS43205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.3|26.3	4.720674|4.720674	0.89205|0.89205	.|.	.|.	ENSG00000087274|ENSG00000087274	ENST00000514940;ENST00000541843|ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129	.|T;T;T;T;T;T;T;T	.|0.31247	.|1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.56775|0.56775	0.2008|0.2008	M|M	0.73430|0.73430	2.235|2.235	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|0.993;1.0;1.0;0.997;1.0	.|D;D;D;P;D	.|0.87578	.|0.928;0.977;0.998;0.863;0.992	T|T	0.61816|0.61816	-0.6985|-0.6985	5|10	.|0.87932	.|D	.|0	-15.9835|-15.9835	15.4885|15.4885	0.75587|0.75587	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|606;575;606;575;606	.|Q86XM2;P35611;P35611-3;P35611-2;A2A3N8	.|.;ADDA_HUMAN;.;.;.	A|C	312;21|606;575;606;575;606;606;606;575	.|ENSP00000264758:Y606C;ENSP00000399828:Y575C;ENSP00000381193:Y606C;ENSP00000421907:Y575C;ENSP00000423024:Y606C;ENSP00000348100:Y606C;ENSP00000381191:Y606C;ENSP00000381197:Y575C	.|ENSP00000264758:Y606C	T|Y	+|+	1|2	0|0	ADD1|ADD1	2886527|2886527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	8.766000|8.766000	0.91728|0.91728	2.060000|2.060000	0.61445|0.61445	0.460000|0.460000	0.39030|0.39030	ACC|TAC	.		0.587	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		G	2916729	A	G	2916729	3	3	149	1	0	0	0	0	1	0	0	0	304	391	14	3	1863	3	ADD1	4	2916729	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	2033995	2916729	188237547	32	13312											
SLC10A4	201780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48487158	48487158	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtggctgactacattgtgaAggtaaggccccctcttccct	7	11	11	12	0	1	2	0	2	1	0	2	2	2	2	3	4	1	2	3	4	3	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:48487158A>C	ENST00000273861.4	+	2	1019	c.800A>C	c.(799-801)aAg>aCg	p.K267T		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	267						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						TACATTGTGAAGGTAAGGCCC	0.522																																					p.K267T		.											.	SLC10A4-90	0			c.A800C						.						73	72	72					4																	48487158		2203	4300	6503	SO:0001630	splice_region_variant	201780	exon2			TTGTGAAGGTAAG	BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"Solute carriers"	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.801+1A>C	4.37:g.48487158A>C		Somatic	157	0		WXS	Illumina HiSeq	Phase_I	198	71	NM_152679	0	0	0	0	0	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	37	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.242171	0.79912	.	.	ENSG00000145248	ENST00000273861	T	0.10763	2.84	5.03	5.03	0.67393	.	0.044192	0.85682	D	0.000000	T	0.19967	0.0480	L	0.56340	1.77	0.80722	D	1	P	0.51537	0.946	P	0.51550	0.673	T	0.00480	-1.1714	10	0.44086	T	0.13	-29.9309	15.2283	0.73367	1.0:0.0:0.0:0.0	.	267	Q96EP9	NTCP4_HUMAN	T	267	ENSP00000273861:K267T	ENSP00000273861:K267T	K	+	2	0	SLC10A4	48181915	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	8.506000	0.90518	2.237000	0.73441	0.460000	0.39030	AAG	.		0.522	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679	Missense_Mutation	C	48487158	A	C	48487158	5	2	149	1	0	0	0	0	0	0	1	0	14408	86	3	5	806	5	SLC10A4	4	48487158	Splice_Site	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	45570429	48487158	142667118	33	13313											
KIAA1211	57482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57182735	57182735	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctcgcccccaggccccgagGaaaggaagggacagaagagg	12	1	15	13	2	0	2	0	0	0	2	1	6	0	5	5	5	0	0	5	5	3	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:57182735G>A	ENST00000504228.1	+	6	3172	c.3067G>A	c.(3067-3069)Gaa>Aaa	p.E1023K	KIAA1211_ENST00000541073.1_Missense_Mutation_p.E1016K|KIAA1211_ENST00000264229.6_Missense_Mutation_p.E1023K			Q6ZU35	K1211_HUMAN	KIAA1211	1023										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AGGCCCCGAGGAAAGGAAGGG	0.647																																					p.E1023K		.											.	KIAA1211-70	0			c.G3067A						.						16	19	18					4																	57182735		1988	4152	6140	SO:0001583	missense	57482	exon8			CCCGAGGAAAGGA	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.3067G>A	4.37:g.57182735G>A	ENSP00000423366:p.Glu1023Lys	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	66	18	NM_020722	0	0	0	0	0	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437122	0.43224	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073	T;T;T	0.78003	-1.14;-1.14;-1.14	5.24	3.44	0.39384	.	.	.	.	.	T	0.67970	0.2950	L	0.44542	1.39	0.09310	N	1	B;B;B	0.28350	0.208;0.084;0.084	B;B;B	0.21917	0.022;0.037;0.037	T	0.58301	-0.7660	9	0.44086	T	0.13	-11.2684	8.9225	0.35621	0.2382:0.0:0.7618:0.0	.	1016;1016;1023	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	K	1023;1023;1016	ENSP00000264229:E1023K;ENSP00000423366:E1023K;ENSP00000444006:E1016K	ENSP00000264229:E1023K	E	+	1	0	KIAA1211	56877492	0.169000	0.23002	0.190000	0.23270	0.164000	0.22412	2.380000	0.44327	1.140000	0.42260	0.561000	0.74099	GAA	.		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57182735	G	A	57182735	3	1	149	1	0	0	0	0	1	0	0	0	8236	1175	41	2	3085	2	KIAA1211	4	57182735	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	8695577	57182735	133971541	34	13314											
BTC	685	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	75695357	75695357	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccaccacacagtgaaggAtcactagaccttcaaattca	14	8	6	13	0	3	2	3	1	0	1	3	3	3	3	3	1	1	0	3	1	3	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:75695357A>C	ENST00000395743.3	-	2	434	c.74T>G	c.(73-75)aTc>aGc	p.I25S		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	25					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			ACAGTGAAGGATCACTAGACC	0.403																																					p.I25S													.	BTC-523	0			c.T74G						.						81	78	79					4																	75695357		2203	4300	6503	SO:0001583	missense	685	exon2			TGAAGGATCACTA	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.74T>G	4.37:g.75695357A>C	ENSP00000379092:p.Ile25Ser	Somatic	134	1		WXS	Illumina HiSeq	Phase_I	156	57	NM_001729	0	0	0	0	0	Q96F48	Missense_Mutation	SNP	ENST00000395743.3	37	CCDS3566.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.68|15.68	2.903687|2.903687	0.52333|0.52333	.|.	.|.	ENSG00000174808|ENSG00000174808	ENST00000395743|ENST00000512743	T|.	0.12672|.	2.66|.	4.03|4.03	4.03|4.03	0.46877|0.46877	.|.	0.209768|.	0.41823|.	D|.	0.000807|.	T|T	0.46964|0.46964	0.1420|0.1420	L|L	0.47716|0.47716	1.5|1.5	0.29910|0.29910	N|N	0.823672|0.823672	P|.	0.47677|.	0.899|.	P|.	0.48227|.	0.571|.	T|T	0.45352|0.45352	-0.9267|-0.9267	10|5	0.66056|.	D|.	0.02|.	-17.9524|-17.9524	9.6494|9.6494	0.39888|0.39888	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	25|.	P35070|.	BTC_HUMAN|.	S|A	25|4	ENSP00000379092:I25S|.	ENSP00000379092:I25S|.	I|S	-|-	2|1	0|0	BTC|BTC	75914381|75914381	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.841000|0.841000	0.47740|0.47740	2.227000|2.227000	0.42972|0.42972	2.055000|2.055000	0.61198|0.61198	0.482000|0.482000	0.46254|0.46254	ATC|TCC	.		0.403	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1			C	75695357	A	C	75695357	3	2	149	1	0	0	0	0	1	0	0	0	1552	333	12	5	478	5	BTC	4	75695357	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	18512622	75695357	115458919	35	13315											
C4orf17	84103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100434294	100434294	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgagggcaaaggcagccataTtatggctagaaatgtaagct	14	8	12	7	1	0	1	0	0	0	1	0	2	0	1	1	3	2	5	1	3	6	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:100434294T>C	ENST00000326581.4	+	2	418	c.56T>C	c.(55-57)aTt>aCt	p.I19T	C4orf17_ENST00000514652.1_Missense_Mutation_p.I19T	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	19										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GGCAGCCATATTATGGCTAGA	0.468																																					p.I19T		.											.	C4orf17-90	0			c.T56C						.						102	86	92					4																	100434294		2203	4300	6503	SO:0001583	missense	84103	exon2			GCCATATTATGGC	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.56T>C	4.37:g.100434294T>C	ENSP00000322582:p.Ile19Thr	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	151	65	NM_032149	0	0	0	0	0	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242808	0.22796	.	.	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.18338	2.22;2.22	4.76	-9.53	0.00575	.	1.807420	0.02601	N	0.101018	T	0.15089	0.0364	L	0.57536	1.79	0.09310	N	1	B	0.24426	0.103	B	0.25140	0.058	T	0.39354	-0.9618	10	0.66056	D	0.02	1.4304	5.5029	0.16838	0.1118:0.1614:0.5637:0.1631	.	19	Q53FE4	CD017_HUMAN	T	19	ENSP00000322582:I19T;ENSP00000427663:I19T	ENSP00000322582:I19T	I	+	2	0	C4orf17	100653317	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.503000	0.06383	-1.204000	0.02648	-0.256000	0.11100	ATT	.		0.468	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149		C	100434294	T	C	100434294	3	2	149	1	0	0	0	0	1	0	0	0	2258	1493	52	3	58	3	C4orf17	4	100434294	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	24738937	100434294	90719982	36	13316											
TBCK	93627	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	107163709	107163709	+	Frame_Shift_Del	DEL	C	C	-																															gaccttgtccaaagctttcaCcatcctcaaagagaaaactg																								rs371959745		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:107163709delC	ENST00000273980.5	-	13	1535	c.1088delG	c.(1087-1089)ggtfs	p.G363fs	TBCK_ENST00000432496.2_Frame_Shift_Del_p.G363fs|TBCK_ENST00000394706.3_Frame_Shift_Del_p.G324fs|TBCK_ENST00000394708.2_Frame_Shift_Del_p.G363fs|TBCK_ENST00000361687.4_Frame_Shift_Del_p.G300fs					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						AAAGCTTTCACCATCCTCAAA	0.313																																					p.G363fs		.											.	TBCK-336	0			c.1088delG						.						67	65	66					4																	107163709		2203	4300	6503	SO:0001589	frameshift_variant	93627	exon12			.		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1088delG	4.37:g.107163709delC	ENSP00000273980:p.Gly363fs	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	28	17	NM_001163436	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000273980.5	37	CCDS54788.1																																																																																			.		0.313	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		-	107163709	C	-	107163709	7	5	149	1	0	1	0	1	0	0	0	0	15668	507	18	0	1653	0	TBCK	4	107163709	Frame_Shift_Del	DEL	C	TCGA-MH-A55Z-01A-11D-A26P-10	6729415	107163709	83990567	37	13317											
NDST3	9348	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	118975229	118975229	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagttgactgtggcgaccTccaacacctaccatatcaac	13	8	7	13	1	1	2	1	1	0	1	2	3	2	2	4	1	3	1	4	1	5	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:118975229T>G	ENST00000296499.5	+	2	567	c.164T>G	c.(163-165)cTc>cGc	p.L55R	NDST3_ENST00000433996.2_Missense_Mutation_p.L55R	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	55	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						TGTGGCGACCTCCAACACCTA	0.443																																					p.L55R													.	NDST3-153	0			c.T164G						.						115	113	114					4																	118975229		2203	4300	6503	SO:0001583	missense	9348	exon2			GCGACCTCCAACA	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"Sulfotransferases, membrane-bound"	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.164T>G	4.37:g.118975229T>G	ENSP00000296499:p.Leu55Arg	Somatic	173	1		WXS	Illumina HiSeq	Phase_I	173	52	NM_004784	0	0	0	0	0	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	T	12.23	1.875654	0.33162	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.44881	1.24;0.91	5.53	5.53	0.82687	.	0.404758	0.24922	N	0.034522	T	0.29491	0.0735	N	0.26042	0.785	0.31434	N	0.672752	B;B;P	0.49559	0.001;0.091;0.925	B;B;P	0.44990	0.002;0.148;0.466	T	0.17806	-1.0357	10	0.15499	T	0.54	.	7.5856	0.27991	0.0:0.0731:0.1414:0.7856	.	55;55;55	B4DI67;O95803;O95803-2	.;NDST3_HUMAN;.	R	55	ENSP00000296499:L55R;ENSP00000396625:L55R	ENSP00000296499:L55R	L	+	2	0	NDST3	119194677	0.051000	0.20477	0.954000	0.39281	0.344000	0.29017	1.922000	0.40045	2.083000	0.62718	0.528000	0.53228	CTC	.		0.443	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		G	118975229	T	G	118975229	3	3	149	1	0	0	0	0	1	0	0	0	10283	1551	54	5	166	5	NDST3	4	118975229	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	11811520	118975229	72179047	38	13318											
SH3D19	152503	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	152096316	152096316	+	Missense_Mutation	SNP	T	T	A																															tctcagtcccagagtcccacTctccagaagctctgttagca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:152096316T>A	ENST00000409252.2	-	6	907	c.200A>T	c.(199-201)gAg>gTg	p.E67V	SH3D19_ENST00000455740.1_Missense_Mutation_p.E67V|SH3D19_ENST00000304527.4_Missense_Mutation_p.E67V|SH3D19_ENST00000427414.2_Missense_Mutation_p.E67V|SH3D19_ENST00000409598.4_Missense_Mutation_p.E67V|SH3D19_ENST00000424281.1_Missense_Mutation_p.E67V|SH3D19_ENST00000604030.1_5'Flank|SH3D19_ENST00000514152.1_Missense_Mutation_p.E67V			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	67					cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				AGAGTCCCACTCTCCAGAAGC	0.517																																					p.E67V		.											.	SH3D19-92	0			c.A200T						.						85	85	85					4																	152096316		2203	4300	6503	SO:0001583	missense	152503	exon1			TCCCACTCTCCAG	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"EEN binding protein"	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.200A>T	4.37:g.152096316T>A	ENSP00000386848:p.Glu67Val	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	76	34	NM_001128924	0	0	0	0	0	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	37	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134175	0.77662	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.06449	3.3;3.3;3.3;3.3;3.3;3.3;3.3	6.07	3.59	0.41128	.	2.410060	0.02778	U	0.120587	T	0.23451	0.0567	M	0.62723	1.935	0.38335	D	0.943906	D;D;D	0.63046	0.969;0.982;0.992	P;P;P	0.61397	0.625;0.849;0.888	T	0.00024	-1.2325	10	0.87932	D	0	-8.5478	10.825	0.46627	0.0:0.1277:0.0:0.8723	.	67;67;67	Q5HYK7;Q5HYK7-2;Q5HYK7-3	SH319_HUMAN;.;.	V	67	ENSP00000387030:E67V;ENSP00000302913:E67V;ENSP00000416708:E67V;ENSP00000404542:E67V;ENSP00000415694:E67V;ENSP00000386848:E67V;ENSP00000423449:E67V	ENSP00000302913:E67V	E	-	2	0	SH3D19	152315766	0.997000	0.39634	0.976000	0.42696	0.954000	0.61252	2.976000	0.49289	0.514000	0.28300	0.533000	0.62120	GAG	.		0.517	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		A	152096316	T	A	152096316	3	1	149	1	0	0	0	0	1	0	0	0	14281	1551	54	5	2232	5	SH3D19	4	152096316	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	33121087	152096316	39057960	39	13319	138	3									
SH3D19	152503	hgsc.bcm.edu;bcgsc.ca	37	chr4	152096322	152096322	+	Missense_Mutation	SNP	G	G	A																															tcccagagtcccactctccaGaagctctgttagcagctggt																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:152096322G>A	ENST00000409252.2	-	6	901	c.194C>T	c.(193-195)tCt>tTt	p.S65F	SH3D19_ENST00000455740.1_Missense_Mutation_p.S65F|SH3D19_ENST00000304527.4_Missense_Mutation_p.S65F|SH3D19_ENST00000427414.2_Missense_Mutation_p.S65F|SH3D19_ENST00000409598.4_Missense_Mutation_p.S65F|SH3D19_ENST00000424281.1_Missense_Mutation_p.S65F|SH3D19_ENST00000604030.1_5'Flank|SH3D19_ENST00000514152.1_Missense_Mutation_p.S65F			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	65					cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				CCACTCTCCAGAAGCTCTGTT	0.527																																					p.S65F		.											.	SH3D19-92	0			c.C194T						.						85	85	85					4																	152096322		2203	4300	6503	SO:0001583	missense	152503	exon1			TCTCCAGAAGCTC	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"EEN binding protein"	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.194C>T	4.37:g.152096322G>A	ENSP00000386848:p.Ser65Phe	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	83	40	NM_001128924	0	0	0	0	0	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	37	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	G	19.49	3.838322	0.71373	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.06068	3.35;3.35;3.35;3.35;3.35;3.35;3.35	6.07	4.34	0.51931	.	0.591075	0.16731	N	0.201834	T	0.21674	0.0522	M	0.64997	1.995	0.35608	D	0.808417	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.08534	-1.0717	10	0.87932	D	0	-5.1533	12.0719	0.53622	0.0648:0.1217:0.8135:0.0	.	65;65;65	Q5HYK7;Q5HYK7-2;Q5HYK7-3	SH319_HUMAN;.;.	F	65	ENSP00000387030:S65F;ENSP00000302913:S65F;ENSP00000416708:S65F;ENSP00000404542:S65F;ENSP00000415694:S65F;ENSP00000386848:S65F;ENSP00000423449:S65F	ENSP00000302913:S65F	S	-	2	0	SH3D19	152315772	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	5.083000	0.64456	0.883000	0.36040	0.655000	0.94253	TCT	.		0.527	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		A	152096322	G	A	152096322	3	1	149	1	0	0	0	0	1	0	0	0	14281	942	33	2	2238	2	SH3D19	4	152096322	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	6	152096322	39057954	40	13320	138	3									
SH3D19	152503	hgsc.bcm.edu;bcgsc.ca	37	chr4	152096326	152096326	+	Frame_Shift_Del	DEL	C	C	-																															agagtcccactctccagaagCtctgttagcagctggtttgg																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:152096326delC	ENST00000409252.2	-	6	897	c.190delG	c.(190-192)gctfs	p.A64fs	SH3D19_ENST00000455740.1_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000304527.4_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000427414.2_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000409598.4_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000424281.1_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000604030.1_5'Flank|SH3D19_ENST00000514152.1_Frame_Shift_Del_p.A64fs			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	64					cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				TCTCCAGAAGCTCTGTTAGCA	0.532																																					p.A64fs		.											.	SH3D19-92	0			c.190delG						.						86	86	86					4																	152096326		2203	4300	6503	SO:0001589	frameshift_variant	152503	exon1			.	BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686			30418	protein-coding gene	gene with protein product	"EEN binding protein"	608674				12477932	Standard	NM_001009555		Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.190delG	4.37:g.152096326delC	ENSP00000386848:p.Ala64fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	81	39	NM_001128924	0	0	0	0	0	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Frame_Shift_Del	DEL	ENST00000409252.2	37	CCDS34077.2																																																																																			.		0.532	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		-	152096326	C	-	152096326	7	5	149	1	0	1	0	1	0	0	0	0	14281	797	28	0	2242	0	SH3D19	4	152096326	Frame_Shift_Del	DEL	C	TCGA-MH-A55Z-01A-11D-A26P-10	4	152096326	39057950	41	13321	138	3									
FSTL5	56884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	162307106	162307106	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtggttccttgagactcttTatcatcttgaccttcccaga	8	15	7	11	0	3	3	1	2	2	2	5	4	5	3	3	1	0	1	3	1	1	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:162307106T>A	ENST00000306100.5	-	16	2773	c.2337A>T	c.(2335-2337)atA>atT	p.I779I	FSTL5_ENST00000536695.1_Silent_p.I778I|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000427802.2_Silent_p.I769I|FSTL5_ENST00000379164.4_Silent_p.I778I	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	779						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TGAGACTCTTTATCATCTTGA	0.458																																					p.I779I		.											.	FSTL5-158	0			c.A2337T						.						179	163	168					4																	162307106		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon16			ACTCTTTATCATC	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"EF-hand domain containing", "Immunoglobulin superfamily / I-set domain containing"	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.2337A>T	4.37:g.162307106T>A		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	153	74	NM_020116	0	0	0	0	0	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			.		0.458	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		A	162307106	T	A	162307106	2	1	149	1	0	0	0	0	0	0	0	1	6099	1744	61	5		5	FSTL5	4	162307106	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	10210780	162307106	28847170	42	13322											
WDR17	116966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	177089815	177089815	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagtgtccccttttgttacGttaacaggaatttggcagct	9	14	10	8	1	0	0	0	0	0	0	1	2	1	1	2	2	3	4	2	2	4	5	rs371828424		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:177089815G>C	ENST00000280190.4	+	25	3256	c.3100G>C	c.(3100-3102)Gtt>Ctt	p.V1034L	WDR17_ENST00000393643.2_Missense_Mutation_p.V1010L|WDR17_ENST00000507824.2_Intron|WDR17_ENST00000508596.1_Intron			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1034										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CTTTTGTTACGTTAACAGGAA	0.338																																					p.V1034L		.											.	WDR17-95	0			c.G3100C						.						134	127	129					4																	177089815		2203	4300	6503	SO:0001583	missense	116966	exon25			TGTTACGTTAACA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3100G>C	4.37:g.177089815G>C	ENSP00000280190:p.Val1034Leu	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	77	30	NM_170710	0	0	0	0	0	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	g	1.369	-0.586595	0.03827	.	.	ENSG00000150627	ENST00000393643;ENST00000280190;ENST00000507824	T;T	0.54866	0.61;0.55	5.1	-2.02	0.07388	.	0.528184	0.15689	N	0.249514	T	0.20292	0.0488	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27773	-1.0064	10	0.02654	T	1	0.4761	4.7601	0.13104	0.4883:0.0:0.3534:0.1582	.	1034	Q8IZU2	WDR17_HUMAN	L	1010;1034;1010	ENSP00000377258:V1010L;ENSP00000280190:V1034L	ENSP00000280190:V1034L	V	+	1	0	WDR17	177326809	0.081000	0.21417	0.000000	0.03702	0.003000	0.03518	-0.019000	0.12546	-0.243000	0.09653	-1.290000	0.01357	GTT	.		0.338	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			C	177089815	G	C	177089815	3	2	149	1	0	0	0	0	1	0	0	0	17310	1145	40	4	3194	4	WDR17	4	177089815	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	14782709	177089815	14064461	43	13323											
CCDC110	256309	ucsc.edu;bcgsc.ca	37	chr4	186382296	186382296	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacttttgttcaatatttcActgatttccgactgtacctt	9	19	4	9	1	2	1	2	1	0	0	3	2	3	1	2	0	2	2	2	0	4	9			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:186382296A>G	ENST00000307588.3	-	5	330	c.255T>C	c.(253-255)agT>agC	p.S85S	CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000393540.3_Intron|CCDC110_ENST00000510617.1_Silent_p.S85S	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	85						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TCAATATTTCACTGATTTCCG	0.284																																					p.S85S													.	CCDC110-90	0			c.T255C						.						101	100	101					4																	186382296		2203	4297	6500	SO:0001819	synonymous_variant	256309	exon5			TATTTCACTGATT	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.255T>C	4.37:g.186382296A>G		Somatic	43	0		WXS	Illumina HiSeq		40	4	NM_152775	0	0	0	0	0	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	37	CCDS3843.1																																																																																			.		0.284	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		G	186382296	A	G	186382296	2	3	149	1	0	0	0	0	0	0	0	1	2753	156	6	3		3	CCDC110	4	186382296	Silent	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	9292481	186382296	4771980	44	13324											
TNPO1	3842	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	72183032	72183032	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaatcaggcattttggtttTaggagcaattgctgaaggta	12	13	12	4	0	1	2	1	1	0	1	1	3	1	3	0	4	2	5	0	4	5	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:72183032T>G	ENST00000337273.5	+	12	1712	c.1286T>G	c.(1285-1287)tTa>tGa	p.L429*	TNPO1_ENST00000523768.1_Nonsense_Mutation_p.L379*|TNPO1_ENST00000454282.1_Nonsense_Mutation_p.L379*|TNPO1_ENST00000506351.2_Nonsense_Mutation_p.L421*	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	429					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		ATTTTGGTTTTAGGAGCAATT	0.358																																					p.L429X		.											.	TNPO1-228	0			c.T1286G						.						99	97	98					5																	72183032		2203	4300	6503	SO:0001587	stop_gained	3842	exon12			TGGTTTTAGGAGC	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"Importins"	6401	protein-coding gene	gene with protein product	"importin 2"	602901	"karyopherin (importin) beta 2"	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.1286T>G	5.37:g.72183032T>G	ENSP00000336712:p.Leu429*	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	72	10	NM_002270	0	0	0	0	0	B4DVC6|Q92957|Q92975	Nonsense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.770905	0.90108	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.9103	15.3454	0.74334	0.0:0.0:0.0:1.0	.	.	.	.	X	429;379;379;421	.	ENSP00000336712:L429X	L	+	2	0	TNPO1	72218788	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.651000	0.83577	2.099000	0.63709	0.528000	0.53228	TTA	.		0.358	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		G	72183032	T	G	72183032	4	3	149	1	0	0	0	0	0	1	0	0	16367	1764	61	5	1332	5	TNPO1	5	72183032	Nonsense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		72183032	108732228	45	13325											
BRD8	10902	ucsc.edu;bcgsc.ca	37	chr5	137507060	137507060	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtactcactttggtgtctCagtggtctctaaaagctccg	7	15	9	10	1	3	0	2	0	2	0	6	0	4	0	1	2	2	2	1	2	3	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:137507060C>T	ENST00000254900.5	-	4	597	c.226G>A	c.(226-228)Gag>Aag	p.E76K	BRD8_ENST00000411594.2_Missense_Mutation_p.E76K|BRD8_ENST00000455658.2_Missense_Mutation_p.E35K|BRD8_ENST00000230901.5_Missense_Mutation_p.E76K|BRD8_ENST00000402931.1_Missense_Mutation_p.E76K	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	76					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTTGGTGTCTCAGTGGTCTCT	0.368																																					p.E76K													.	BRD8-91	0			c.G226A						.						121	122	122					5																	137507060		2203	4300	6503	SO:0001583	missense	10902	exon4			GTGTCTCAGTGGT	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.226G>A	5.37:g.137507060C>T	ENSP00000254900:p.Glu76Lys	Somatic	37	0		WXS	Illumina HiSeq		38	4	NM_001164326	0	0	0	0	0	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Missense_Mutation	SNP	ENST00000254900.5	37	CCDS4198.1	.	.	.	.	.	.	.	.	.	.	C	34	5.410624	0.96072	.	.	ENSG00000112983	ENST00000254900;ENST00000454473;ENST00000418329;ENST00000230901;ENST00000402931;ENST00000411594;ENST00000455658;ENST00000430331	T;T;T;T;T;T;T	0.48201	1.29;0.84;0.84;0.98;1.05;0.82;1.08	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D;D	0.69078	0.99;0.997;0.993;0.996;0.996;0.997	D;D;D;D;D;D	0.76071	0.979;0.98;0.956;0.987;0.987;0.985	T	0.62553	-0.6830	10	0.72032	D	0.01	-12.8674	18.5411	0.91029	0.0:1.0:0.0:0.0	.	35;60;76;76;76;76	F8W820;B4DN43;A8K1N6;Q9H0E9-4;Q9H0E9-2;Q9H0E9	.;.;.;.;.;BRD8_HUMAN	K	76;71;71;76;76;76;35;120	ENSP00000254900:E76K;ENSP00000398067:E71K;ENSP00000398873:E71K;ENSP00000230901:E76K;ENSP00000384845:E76K;ENSP00000394330:E76K;ENSP00000408396:E35K	ENSP00000230901:E76K	E	-	1	0	BRD8	137534959	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.719000	0.84751	2.697000	0.92050	0.563000	0.77884	GAG	.		0.368	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		T	137507060	C	T	137507060	3	4	149	1	0	0	0	0	1	0	0	0	1509	835	29	2	3864	2	BRD8	5	137507060	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	65324028	137507060	43408200	46	13326											
SLC23A1	9963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	138718252	138718252	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtacaacatgtcaaacttagGctctgtgggtagcggggtcg	9	10	14	8	2	2	0	1	0	1	0	3	0	2	0	0	4	4	3	0	4	5	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:138718252G>A	ENST00000348729.3	-	2	125	c.79C>T	c.(79-81)Cct>Tct	p.P27S	SLC23A1_ENST00000503919.1_5'UTR|SLC23A1_ENST00000353963.3_Missense_Mutation_p.P27S	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	27					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	TCAAACTTAGGCTCTGTGGGT	0.582																																					p.P27S		.											.	SLC23A1-90	0			c.C79T						.						134	111	118					5																	138718252		2203	4300	6503	SO:0001583	missense	9963	exon2			ACTTAGGCTCTGT	AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"Solute carriers"	10974	protein-coding gene	gene with protein product		603790	"solute carrier family 23 (nucleobase transporters), member 2"	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.79C>T	5.37:g.138718252G>A	ENSP00000302701:p.Pro27Ser	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	170	76	NM_005847	0	0	1	1	0	O95191|Q8WWB6|Q9UGH4|Q9UI39	Missense_Mutation	SNP	ENST00000348729.3	37	CCDS4212.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.410755	0.25465	.	.	ENSG00000170482	ENST00000353963;ENST00000348729;ENST00000339881;ENST00000453898;ENST00000508270	T;T	0.17370	2.28;2.29	4.68	2.9	0.33743	.	0.428794	0.24659	N	0.036652	T	0.08670	0.0215	N	0.08118	0	0.31262	N	0.692759	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.06552	-1.0820	10	0.87932	D	0	-27.6722	8.6703	0.34145	0.1818:0.0:0.8182:0.0	.	27;27	Q9UHI7;Q9UHI7-2	S23A1_HUMAN;.	S	27;27;27;27;101	ENSP00000302851:P27S;ENSP00000302701:P27S	ENSP00000343584:P27S	P	-	1	0	SLC23A1	138746151	0.993000	0.37304	0.987000	0.45799	0.446000	0.32137	1.322000	0.33689	0.600000	0.29862	0.456000	0.33151	CCT	.		0.582	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		A	138718252	G	A	138718252	3	1	149	1	0	0	0	0	1	0	0	0	14494	1203	42	2	1781	2	SLC23A1	5	138718252	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	1211192	138718252	42197008	47	13327											
FAT2	2196	hgsc.bcm.edu	37	chr5	150911353	150911353	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccgagactgtgacggtGcccagcgtggacagcggtat	9	6	14	12	4	0	2	0	1	0	1	0	4	0	3	3	3	3	1	3	3	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:150911353G>A	ENST00000261800.5	-	13	9618	c.9606C>T	c.(9604-9606)ggC>ggT	p.G3202G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3202	Cadherin 28. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGTGACGGTGCCCAGCGTGG	0.672																																					p.G3202G		.											.	FAT2-96	0			c.C9606T						.						101	89	93					5																	150911353		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon13			GACGGTGCCCAGC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"Cadherins / Cadherin-related"	3596	protein-coding gene	gene with protein product	"cadherin-related family member 9"	604269	"FAT tumor suppressor (Drosophila) homolog 2", "FAT tumor suppressor homolog 2 (Drosophila)"			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9606C>T	5.37:g.150911353G>A		Somatic	9	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_001447	0	0	0	0	0	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	5.409	0.260626	0.10239	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.34	3.55	0.40652	.	.	.	.	.	T	0.55673	0.1935	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49133	-0.8971	4	.	.	.	.	6.8949	0.24251	0.1533:0.1441:0.7025:0.0	.	.	.	.	Y	61	.	.	H	-	1	0	FAT2	150891546	1.000000	0.71417	1.000000	0.80357	0.436000	0.31835	2.210000	0.42816	0.630000	0.30394	0.557000	0.71058	CAC	.		0.672	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150911353	G	A	150911353	2	1	149	1	0	0	0	0	0	0	0	1	5709	1306	46	2		2	FAT2	5	150911353	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	12193101	150911353	30003907	48	13328											
LCP2	3937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	169680134	169680134	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcttacctcttcctccgCgggggatgggggccgaggtt	3	11	14	13	3	2	0	0	0	2	0	5	2	4	1	4	5	1	1	4	5	1	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:169680134C>T	ENST00000046794.5	-	18	1849	c.1234G>A	c.(1234-1236)Gcg>Acg	p.A412T	LCP2_ENST00000521416.1_Missense_Mutation_p.A207T	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	412					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TCTTCCTCCGCGGGGGATGGG	0.458																																					p.A412T		.											.	LCP2-23	0			c.G1234A						.						36	34	35					5																	169680134		1815	4077	5892	SO:0001583	missense	3937	exon18			CCTCCGCGGGGGA		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"SH2 domain containing"	6529	protein-coding gene	gene with protein product	"76 kDa tyrosine phosphoprotein", "SH2 domain-containing leukocyte protein of 76kD"	601603	"lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.1234G>A	5.37:g.169680134C>T	ENSP00000046794:p.Ala412Thr	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	43	12	NM_005565	0	0	0	0	0	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293873	0.23564	.	.	ENSG00000043462	ENST00000046794;ENST00000521416	D;D	0.92805	-3.11;-3.11	5.74	3.01	0.34805	.	0.541975	0.19974	N	0.101934	T	0.75481	0.3855	N	0.02539	-0.55	0.09310	N	1	B;B	0.18610	0.029;0.001	B;B	0.08055	0.003;0.001	T	0.62835	-0.6770	9	.	.	.	-3.3438	5.838	0.18617	0.154:0.685:0.0:0.1611	.	207;412	E7ESF6;Q13094	.;LCP2_HUMAN	T	412;207	ENSP00000046794:A412T;ENSP00000428871:A207T	.	A	-	1	0	LCP2	169612712	0.001000	0.12720	0.002000	0.10522	0.112000	0.19704	0.873000	0.28052	0.445000	0.26639	0.563000	0.77884	GCG	.		0.458	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		T	169680134	C	T	169680134	3	4	149	1	0	0	0	0	1	0	0	0	8713	768	27	1	383	1	LCP2	5	169680134	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	18768781	169680134	11235126	49	13329											
ADAMTS2	9509	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	178553061	178553061	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctttgggcttcgagagggcGgcacagaagccacggtgtac	8	7	16	10	3	0	2	0	0	0	2	1	3	0	2	1	4	2	4	1	4	2	3	rs370747086		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:178553061G>T	ENST00000251582.7	-	18	2789	c.2688C>A	c.(2686-2688)gcC>gcA	p.A896A		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	896	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TCGAGAGGGCGGCACAGAAGC	0.637																																					p.A896A													.	ADAMTS2-228	0			c.C2688A						.						84	84	84					5																	178553061		2203	4300	6503	SO:0001819	synonymous_variant	9509	exon18			GAGGGCGGCACAG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"ADAM metallopeptidases with thrombospondin type 1 motif"	218	protein-coding gene	gene with protein product	"procollagen I N-proteinase", "procollagen N-endopeptidase"	604539	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2688C>A	5.37:g.178553061G>T		Somatic	65	1		WXS	Illumina HiSeq	Phase_I	86	27	NM_014244	0	0	0	0	0		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.		0.637	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178553061	G	T	178553061	2	4	149	1	0	0	0	0	0	0	0	1	265	1103	39	4		4	ADAMTS2	5	178553061	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	8872927	178553061	2362199	50	13330											
CANX	821	hgsc.bcm.edu;bcgsc.ca	37	chr5	179136997	179136997	+	Frame_Shift_Del	DEL	C	C	-																															cgggtatctatgaagaaaaaCatgctaagaggccagatgca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:179136997delC	ENST00000247461.4	+	7	852	c.652delC	c.(652-654)catfs	p.H218fs	CANX_ENST00000415618.2_Frame_Shift_Del_p.H253fs|CANX_ENST00000452673.2_Frame_Shift_Del_p.H218fs|CANX_ENST00000503126.1_3'UTR|CANX_ENST00000512607.2_Frame_Shift_Del_p.H110fs|CANX_ENST00000504734.1_Frame_Shift_Del_p.H218fs	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	218					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	TGAAGAAAAACATGCTAAGAG	0.373																																					p.H218fs		.											.	CANX-90	0			c.652delC						.						132	135	134					5																	179136997		2203	4300	6503	SO:0001589	frameshift_variant	821	exon7			.	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"major histocompatibility complex class I antigen-binding protein p88"	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910	ENST00000247461.4:c.652delC	5.37:g.179136997delC	ENSP00000247461:p.His218fs	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	59	19	NM_001746	0	0	0	0	0	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Frame_Shift_Del	DEL	ENST00000247461.4	37	CCDS4447.1																																																																																			.		0.373	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		-	179136997	C	-	179136997	7	5	149	1	0	1	0	1	0	0	0	0	2624	478	17	0	674	0	CANX	5	179136997	Frame_Shift_Del	DEL	C	TCGA-MH-A55Z-01A-11D-A26P-10	583936	179136997	1778263	51	13331											
ZSCAN12	9753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	28359289	28359289	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctctgatgttcagtatggtCagagttctcagtcaggctta	8	15	10	8	0	5	2	4	1	2	1	7	2	5	2	0	2	0	4	0	2	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr6:28359289C>G	ENST00000361028.1	-	4	923	c.778G>C	c.(778-780)Gac>Cac	p.D260H	ZSCAN12_ENST00000396827.3_Missense_Mutation_p.D260H			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	260					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(2)|endometrium(3)|urinary_tract(1)	6						TCAGTATGGTCAGAGTTCTCA	0.433																																					p.D260H		.											.	.	0			c.G778C						.						219	181	192					6																	28359289		692	1591	2283	SO:0001583	missense	9753	exon4			TATGGTCAGAGTT	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"-", "Zinc fingers, C2H2-type"	13172	protein-coding gene	gene with protein product		603978	"zinc finger protein 305", "zinc finger protein 96"	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.778G>C	6.37:g.28359289C>G	ENSP00000354305:p.Asp260His	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	141	51	NM_001163391	0	0	0	0	0	O43724	Missense_Mutation	SNP	ENST00000361028.1	37		.	.	.	.	.	.	.	.	.	.	C	3.906	-0.021133	0.07634	.	.	ENSG00000158691	ENST00000361028;ENST00000396827	T;T	0.27557	1.66;1.66	3.93	-0.342	0.12635	.	0.768215	0.10643	N	0.650758	T	0.02342	0.0072	N	0.02539	-0.55	0.09310	N	1	P;B	0.47302	0.893;0.38	B;B	0.34301	0.179;0.054	T	0.24548	-1.0157	10	0.22706	T	0.39	.	4.3597	0.11196	0.1506:0.4779:0.0:0.3715	.	260;260	A8K187;O43309	.;ZSC12_HUMAN	H	260	ENSP00000354305:D260H;ENSP00000380039:D260H	ENSP00000354305:D260H	D	-	1	0	ZSCAN12	28467268	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-1.601000	0.02081	0.004000	0.14682	0.650000	0.86243	GAC	.		0.433	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724		G	28359289	C	G	28359289	3	3	149	1	0	0	0	0	1	0	0	0	18260	826	29	4	1061	4	ZSCAN12	6	28359289	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		28359289	142755778	52	13332											
HSD17B8	7923	broad.mit.edu	37	chr6	33172821	33172821	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggagcaaggaggggccgccCcgagggaaccatgctgcctt	8	4	17	12	2	0	0	0	0	0	0	0	4	0	3	5	5	4	2	5	5	2	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr6:33172821C>T	ENST00000374662.3	+	2	222	c.195C>T	c.(193-195)ccC>ccT	p.P65P	MIR219-1_ENST00000362166.1_RNA|HSD17B8_ENST00000469186.1_3'UTR	NM_014234.4	NP_055049.1	Q92506	DHB8_HUMAN	hydroxysteroid (17-beta) dehydrogenase 8	65					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|fatty acid biosynthetic process (GO:0006633)	mitochondrial envelope (GO:0005740)|mitochondrial matrix (GO:0005759)|plasma membrane (GO:0005886)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	9						AGGGGCCGCCCCGAGGGAACC	0.706																																					p.P65P													.	HSD17B8-153	0			c.C195T						.						9	11	10					6																	33172821		1498	2702	4200	SO:0001819	synonymous_variant	7923	exon2			GCCGCCCCGAGGG	D82061	CCDS4769.1	6p21.3	2011-09-14	2002-02-19	2002-02-22	ENSG00000204228	ENSG00000204228	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	3554	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 30C, member 1"	601417	"FabG (beta-ketoacyl-[acyl-carrier-protein] reductase, E coli) like (E. coli)"	FABGL		8812499, 19027726	Standard	NM_014234		Approved	HKE6, D6S2245E, RING2, KE6, H2-KE6, SDR30C1	uc003odi.2	Q92506	OTTHUMG00000031117	ENST00000374662.3:c.195C>T	6.37:g.33172821C>T		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	18	4	NM_014234	0	0	22	22	0	A6NLX7|Q5STP7|Q9UIQ1	Silent	SNP	ENST00000374662.3	37	CCDS4769.1																																																																																			.		0.706	HSD17B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076196.1	NM_014234		T	33172821	C	T	33172821	2	4	149	1	0	0	0	0	0	0	0	1	7410	610	22	2		2	HSD17B8	6	33172821	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	4813532	33172821	137942246	53	13333											
TAAR9	134860	broad.mit.edu;bcgsc.ca	37	chr6	132859693	132859693	+	RNA	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtcactgtgatgcccttcAgcacagtgaggtctgtggag	8	10	14	9	0	3	2	2	2	1	0	3	4	3	3	1	2	2	1	1	2	0	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr6:132859693A>C	ENST00000434551.1	+	0	265					NM_175057.3	NP_778227.3	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9 (gene/pseudogene)						G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)					Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		GATGCCCTTCAGCACAGTGAG	0.453																																					.	Colon(10;433 445 15992 45047 47213)												.	.	0			.						.						203	198	200					6																	132859693		2178	4286	6464			134860	.			CCCTTCAGCACAG	AF380189	CCDS75520.1	6q23.2	2013-10-02	2010-03-12	2005-02-24	ENSG00000237110	ENSG00000237110		"GPCR / Class A : Trace amine associated receptors"	20977	protein-coding gene	gene with protein product		608282	"trace amine receptor 3", "trace amine associated receptor 9"	TRAR3		15718104	Standard	NM_175057		Approved	TA3, TAR3	uc011eci.2	Q96RI9	OTTHUMG00000015578		6.37:g.132859693A>C		Somatic	206	3		WXS	Illumina HiSeq	Phase_I	248	7	.	0	0	0	0	0		Missense_Mutation	SNP	ENST00000434551.1	37																																																																																				.		0.453	TAAR9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000042254.2	NM_175057		C	132859693	A	C	132859693	1	2	149	0	1	0	0	0	0	0	0	0	15526	188	7	5		5	TAAR9	6	132859693	RNA	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	99686872	132859693	38255374	54	13334											
C6orf211	79624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	151790234	151790234	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggaatatttcagtacgatGgtcccctttgacttgattta	10	16	8	7	1	1	2	1	2	0	0	2	4	2	3	2	2	1	1	2	2	4	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr6:151790234G>A	ENST00000367294.3	+	5	1574	c.1315G>A	c.(1315-1317)Ggt>Agt	p.G439S	C6orf211_ENST00000545879.1_Missense_Mutation_p.G320S	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	439										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		TCAGTACGATGGTCCCCTTTG	0.507																																					p.G439S		.											.	C6orf211-90	0			c.G1315A						.						21	22	22					6																	151790234		1959	4161	6120	SO:0001583	missense	79624	exon5			TACGATGGTCCCC	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.1315G>A	6.37:g.151790234G>A	ENSP00000356263:p.Gly439Ser	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	64	24	NM_024573	0	0	8	25	17	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730830	0.30684	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.13089	3.04;2.62	6.16	5.3	0.74995	.	0.212744	0.47852	D	0.000212	T	0.05181	0.0138	L	0.45352	1.415	0.41042	D	0.985231	B	0.22983	0.078	B	0.20184	0.028	T	0.18777	-1.0326	10	0.15499	T	0.54	.	13.6292	0.62186	0.0707:0.0:0.9293:0.0	.	439	Q9H993	CF211_HUMAN	S	439;320	ENSP00000356263:G439S;ENSP00000444121:G320S	ENSP00000356263:G439S	G	+	1	0	C6orf211	151831927	0.998000	0.40836	0.986000	0.45419	0.154000	0.21943	2.502000	0.45398	1.626000	0.50381	0.650000	0.86243	GGT	.		0.507	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		A	151790234	G	A	151790234	3	1	149	1	0	0	0	0	1	0	0	0	2360	1348	47	2	1333	2	C6orf211	6	151790234	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	18930541	151790234	19324833	55	13335											
EIF2AK1	27102	broad.mit.edu;bcgsc.ca	37	chr7	6078295	6078296	+	Frame_Shift_Ins	INS	-	-	A																															gatgtgcagcatcaggtggtINSactgtgcctaggagaggaca																								rs150001751		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:6078295_6078296insA	ENST00000199389.6	-	10	1272_1273	c.1126_1127insT	c.(1126-1128)tacfs	p.Y376fs	EIF2AK1_ENST00000495565.1_5'Flank|EIF2AK1_ENST00000536084.1_Frame_Shift_Ins_p.Y252fs	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	376	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CATCAGGTGGTACTGTGCCTAG	0.505																																					p.Y376fs													.	EIF2AK1-408	0			c.1127_1128insT						.																																			SO:0001589	frameshift_variant	27102	exon10			AGGTGGTACTGTG	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1127dupT	7.37:g.6078296_6078296dupA	ENSP00000199389:p.Tyr376fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	137	20	NM_014413	0	0	0	0	0	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Frame_Shift_Ins	INS	ENST00000199389.6	37	CCDS5345.1																																																																																			.		0.505	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		A	6078296	-	A	6078295	7	5	149	1	0	1	1	0	0	0	0	0	5007	1638	57	0	789	0	EIF2AK1	7	6078295	Frame_Shift_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10		6078295	153060368	56	13336	139	3									
EIF2AK1	27102	hgsc.bcm.edu;bcgsc.ca	37	chr7	6078297	6078297	+	Missense_Mutation	SNP	C	C	G																															atgtgcagcatcaggtggtaCtgtgcctaggagaggacaca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:6078297C>G	ENST00000199389.6	-	10	1271	c.1125G>C	c.(1123-1125)caG>caC	p.Q375H	EIF2AK1_ENST00000495565.1_5'Flank|EIF2AK1_ENST00000536084.1_Missense_Mutation_p.Q251H	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	375	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		TCAGGTGGTACTGTGCCTAGG	0.507																																					p.Q375H		.											.	EIF2AK1-408	0			c.G1125C						.						108	94	99					7																	6078297		2203	4300	6503	SO:0001583	missense	27102	exon10			GTGGTACTGTGCC	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1125G>C	7.37:g.6078297C>G	ENSP00000199389:p.Gln375His	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	134	21	NM_014413	0	0	0	0	0	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	37	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	.	9.811	1.183288	0.21870	.	.	ENSG00000086232	ENST00000199389;ENST00000536084;ENST00000426957	T;T	0.65549	-0.16;-0.16	5.57	2.56	0.30785	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.521490	0.21777	N	0.069272	T	0.53334	0.1790	M	0.64630	1.985	0.31933	N	0.61189	B;B;B	0.20368	0.044;0.007;0.005	B;B;B	0.22386	0.039;0.009;0.01	T	0.56062	-0.8041	10	0.37606	T	0.19	-7.4865	5.5568	0.17121	0.1395:0.6391:0.0:0.2214	.	251;374;375	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	H	375;251;2	ENSP00000199389:Q375H;ENSP00000445784:Q251H	ENSP00000199389:Q375H	Q	-	3	2	EIF2AK1	6044823	1.000000	0.71417	0.996000	0.52242	0.286000	0.27126	0.647000	0.24812	1.341000	0.45600	0.650000	0.86243	CAG	.		0.507	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		G	6078297	C	G	6078297	3	3	149	1	0	0	0	0	1	0	0	0	5007	564	20	4	791	4	EIF2AK1	7	6078297	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	2	6078297	153060366	57	13337	139	3									
EIF2AK1	27102	broad.mit.edu;bcgsc.ca	37	chr7	6078298	6078299	+	Frame_Shift_Ins	INS	-	-	A																															gtgcagcatcaggtggtactINSgtgcctaggagaggacacag																								rs372398524		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:6078298_6078299insA	ENST00000199389.6	-	10	1269_1270	c.1123_1124insT	c.(1123-1125)cagfs	p.Q375fs	EIF2AK1_ENST00000495565.1_5'Flank|EIF2AK1_ENST00000536084.1_Frame_Shift_Ins_p.Q251fs	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	375	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CAGGTGGTACTGTGCCTAGGAG	0.51																																					p.Q375fs													.	EIF2AK1-408	0			c.1124_1125insT						.																																			SO:0001589	frameshift_variant	27102	exon10			TGGTACTGTGCCT	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"heme regulated initiation factor 2 alpha kinase"	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1123_1124insT	7.37:g.6078298_6078299insA	ENSP00000199389:p.Gln375fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	134	20	NM_014413	0	0	0	0	0	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Frame_Shift_Ins	INS	ENST00000199389.6	37	CCDS5345.1																																																																																			.		0.51	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		A	6078299	-	A	6078298	7	5	149	1	0	1	1	0	0	0	0	0	5007	1580	55	0	792	0	EIF2AK1	7	6078298	Frame_Shift_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10	1	6078298	153060365	58	13338	139	3									
NFE2L3	9603	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	26224635	26224636	+	Frame_Shift_Del	DEL	CT	CT	-																															atcaagtctaattcctctcaCtctgtgtgtgatgaaggtgc																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:26224635_26224636delCT	ENST00000056233.3	+	4	1576_1577	c.1317_1318delCT	c.(1315-1320)cactctfs	p.S440fs		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	440					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						ATTCCTCTCACTCTGTGTGTGA	0.421																																					p.439_440del		.											.	NFE2L3-94	0			c.1317_1318del						.																																			SO:0001589	frameshift_variant	9603	exon4			.	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1317_1318delCT	7.37:g.26224637_26224638delCT	ENSP00000056233:p.Ser440fs	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	172	42	NM_004289	0	0	0	0	0	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Frame_Shift_Del	DEL	ENST00000056233.3	37	CCDS5396.1																																																																																			.		0.421	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			-	26224636	CT	-	26224635	7	5	149	1	0	1	0	1	0	0	0	0	10395	564	20	0	1331	0	NFE2L3	7	26224635	Frame_Shift_Del	DEL	CT	TCGA-MH-A55Z-01A-11D-A26P-10	20146337	26224635	132914028	59	13339											
SKAP2	8935	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	26729973	26729973	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttcactggagcactgtcctCttcttcttctgtaaataaac	9	16	5	11	0	5	0	1	0	4	0	6	1	6	1	1	1	2	2	1	1	4	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:26729973C>G	ENST00000345317.2	-	10	1118	c.805G>C	c.(805-807)Gag>Cag	p.E269Q	SKAP2_ENST00000489977.1_5'UTR|SKAP2_ENST00000539623.1_Missense_Mutation_p.E97Q	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	269					B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						GCACTGTCCTCTTCTTCTTCT	0.388																																					p.E269Q													.	SKAP2-91	0			c.G805C						.						231	179	197					7																	26729973		2203	4300	6503	SO:0001583	missense	8935	exon10			TGTCCTCTTCTTC		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.805G>C	7.37:g.26729973C>G	ENSP00000005587:p.Glu269Gln	Somatic	81	1		WXS	Illumina HiSeq	Phase_I	206	45	NM_003930	0	0	0	0	0	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Missense_Mutation	SNP	ENST00000345317.2	37	CCDS5400.1	.	.	.	.	.	.	.	.	.	.	C	6.838	0.523906	0.13066	.	.	ENSG00000005020	ENST00000345317;ENST00000539623;ENST00000535331	T;T	0.33654	1.87;1.4	6.17	6.17	0.99709	Src homology-3 domain (1);	0.266780	0.38111	N	0.001812	T	0.30198	0.0757	L	0.34521	1.04	0.47308	D	0.999385	P;P	0.38922	0.651;0.514	B;B	0.35240	0.198;0.151	T	0.02226	-1.1192	10	0.32370	T	0.25	-4.5212	17.7962	0.88572	0.0:1.0:0.0:0.0	.	254;269	B7Z5N4;O75563	.;SKAP2_HUMAN	Q	269;97;254	ENSP00000005587:E269Q;ENSP00000443593:E97Q	ENSP00000005587:E269Q	E	-	1	0	SKAP2	26696498	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	2.839000	0.48207	2.941000	0.99782	0.655000	0.94253	GAG	.		0.388	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			G	26729973	C	G	26729973	3	3	149	1	0	0	0	0	1	0	0	0	14388	922	32	4	286	4	SKAP2	7	26729973	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	505338	26729973	132408690	60	13340											
PLEKHA8	84725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	30094389	30094389	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcatgacaataacttgacTcagtctggatcagactcaag	15	10	7	9	0	5	3	4	2	1	1	5	4	5	4	0	1	1	0	0	1	4	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:30094389T>C	ENST00000449726.1	+	8	1211	c.861T>C	c.(859-861)acT>acC	p.T287T	PLEKHA8_ENST00000396259.1_Silent_p.T287T|PLEKHA8_ENST00000396257.2_Silent_p.T287T|PLEKHA8_ENST00000258679.7_Silent_p.T287T	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	287				T -> S (in Ref. 1; AAK55424). {ECO:0000305}.	ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						ATAACTTGACTCAGTCTGGAT	0.383																																					p.T287T		.											.	PLEKHA8-357	0			c.T861C						.						149	143	145					7																	30094389		2203	4300	6503	SO:0001819	synonymous_variant	84725	exon8			CTTGACTCAGTCT	BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"Pleckstrin homology (PH) domain containing"	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.861T>C	7.37:g.30094389T>C		Somatic	143	0		WXS	Illumina HiSeq	Phase_I	353	139	NM_001197027	0	0	0	0	0	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Silent	SNP	ENST00000449726.1	37	CCDS56473.1																																																																																			.		0.383	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		C	30094389	T	C	30094389	2	2	149	1	0	0	0	0	0	0	0	1	12088	1538	54	3		3	PLEKHA8	7	30094389	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	3364416	30094389	129044274	61	13341											
POLM	27434	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44114102	44114102	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	catcggaccgcaggactgggGtgctcaggtcctggtggtgc	5	8	17	11	2	1	0	1	0	0	0	3	2	2	2	2	7	2	2	2	7	0	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:44114102G>A	ENST00000242248.5	-	7	964	c.863C>T	c.(862-864)aCc>aTc	p.T288I	POLM_ENST00000492971.1_5'UTR|POLM_ENST00000335195.6_Silent_p.H285H|POLM_ENST00000395831.3_Silent_p.H242H	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	288					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						CAGGACTGGGGTGCTCAGGTC	0.697								DNA polymerases (catalytic subunits)																													p.T288I		.											.	POLM-229	0			c.C863T						.						21	19	20					7																	44114102		2201	4299	6500	SO:0001583	missense	27434	exon7			ACTGGGGTGCTCA	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"DNA polymerases"	9185	protein-coding gene	gene with protein product	"Pol iota"	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.863C>T	7.37:g.44114102G>A	ENSP00000242248:p.Thr288Ile	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	130	40	NM_013284	0	0	22	28	6	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	37	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122221	0.37436	.	.	ENSG00000122678	ENST00000242248	T	0.44083	0.93	5.38	1.23	0.21249	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (1);	.	.	.	.	T	0.42471	0.1204	M	0.68317	2.08	0.80722	D	1	P	0.40211	0.707	B	0.42959	0.403	T	0.33803	-0.9854	9	0.56958	D	0.05	-0.2386	8.6696	0.34143	0.0841:0.4398:0.4761:0.0	.	288	Q9NP87	DPOLM_HUMAN	I	288	ENSP00000242248:T288I	ENSP00000242248:T288I	T	-	2	0	POLM	44080627	0.013000	0.17824	0.506000	0.27664	0.637000	0.38172	0.038000	0.13862	0.231000	0.21079	0.555000	0.69702	ACC	.		0.697	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		A	44114102	G	A	44114102	3	1	149	1	0	0	0	0	1	0	0	0	12232	1261	44	2	641	2	POLM	7	44114102	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	14019713	44114102	115024561	62	13342											
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44735721	44735721	+	Missense_Mutation	SNP	G	G	T																															gcactggctggactctccctGgcctggtgagtgaagaaaca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:44735721G>T	ENST00000222673.5	+	13	1808	c.1766G>T	c.(1765-1767)tGg>tTg	p.W589L	OGDH_ENST00000543843.1_Missense_Mutation_p.W540L|OGDH_ENST00000444676.1_Missense_Mutation_p.W604L|OGDH_ENST00000439616.2_Missense_Mutation_p.W439L|OGDH_ENST00000447398.1_Missense_Mutation_p.W600L|OGDH_ENST00000449767.1_Missense_Mutation_p.W585L	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	589					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	GACTCTCCCTGGCCTGGTGAG	0.438																																					p.W589L		.											.	OGDH-228	0			c.G1766T						.						71	67	68					7																	44735721		2203	4300	6503	SO:0001583	missense	4967	exon13			CTCCCTGGCCTGG	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.1766G>T	7.37:g.44735721G>T	ENSP00000222673:p.Trp589Leu	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	155	35	NM_002541	0	0	0	0	0	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713754	0.89112	.	.	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.06608	3.33;3.28;3.29;3.29;3.29;3.3	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.36303	0.0962	M	0.94021	3.485	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	T	0.51132	-0.8744	10	0.87932	D	0	-15.9477	17.8672	0.88799	0.0:0.0:1.0:0.0	.	384;439;585;600;491;589	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218	.;.;.;.;.;ODO1_HUMAN	L	439;585;600;604;589;540	ENSP00000398576:W439L;ENSP00000392878:W585L;ENSP00000388183:W600L;ENSP00000414662:W604L;ENSP00000222673:W589L;ENSP00000443821:W540L	ENSP00000222673:W589L	W	+	2	0	OGDH	44702246	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.657000	0.98554	2.556000	0.86216	0.655000	0.94253	TGG	.		0.438	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			T	44735721	G	T	44735721	3	4	149	1	0	0	0	0	1	0	0	0	10865	1357	47	4	1985	4	OGDH	7	44735721	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	621619	44735721	114402942	63	13343	140	2									
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	44735723	44735723	+	Missense_Mutation	SNP	C	C	A																															actggctggactctccctggCctggtgagtgaagaaacagt																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:44735723C>A	ENST00000222673.5	+	13	1810	c.1768C>A	c.(1768-1770)Cct>Act	p.P590T	OGDH_ENST00000543843.1_Missense_Mutation_p.P541T|OGDH_ENST00000444676.1_Missense_Mutation_p.P605T|OGDH_ENST00000439616.2_Missense_Mutation_p.P440T|OGDH_ENST00000447398.1_Missense_Mutation_p.P601T|OGDH_ENST00000449767.1_Missense_Mutation_p.P586T	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	590					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CTCTCCCTGGCCTGGTGAGTG	0.438																																					p.P590T		.											.	OGDH-228	0			c.C1768A						.						69	65	67					7																	44735723		2203	4300	6503	SO:0001583	missense	4967	exon13			CCCTGGCCTGGTG	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.1768C>A	7.37:g.44735723C>A	ENSP00000222673:p.Pro590Thr	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	153	34	NM_002541	0	0	0	0	0	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.050408	0.36181	.	.	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.05199	3.49;3.48;3.48;3.48;3.48;3.49	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.06554	0.0168	L	0.31294	0.92	0.80722	D	1	B;B;B;B;B;B	0.17268	0.007;0.007;0.01;0.01;0.001;0.021	B;B;B;B;B;B	0.16289	0.004;0.004;0.015;0.015;0.002;0.009	T	0.40194	-0.9576	10	0.19590	T	0.45	-15.3111	17.8673	0.88799	0.0:1.0:0.0:0.0	.	385;440;586;601;492;590	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218	.;.;.;.;.;ODO1_HUMAN	T	440;586;601;605;590;541	ENSP00000398576:P440T;ENSP00000392878:P586T;ENSP00000388183:P601T;ENSP00000414662:P605T;ENSP00000222673:P590T;ENSP00000443821:P541T	ENSP00000222673:P590T	P	+	1	0	OGDH	44702248	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.651000	0.83577	2.556000	0.86216	0.655000	0.94253	CCT	.		0.438	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			A	44735723	C	A	44735723	3	1	149	1	0	0	0	0	1	0	0	0	10865	739	26	4	1987	4	OGDH	7	44735723	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	2	44735723	114402940	64	13344	140	2									
GRB10	2887	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	50660660	50660660	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgcggtcataaggccaCtcggatgcagtggtgcttga	8	10	13	10	2	2	1	1	1	1	0	3	2	2	2	1	4	3	2	1	4	1	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:50660660C>T	ENST00000401949.1	-	19	2243	c.1774G>A	c.(1774-1776)Gtg>Atg	p.V592M	GRB10_ENST00000406641.1_Missense_Mutation_p.V534M|GRB10_ENST00000439599.1_Missense_Mutation_p.V586M|GRB10_ENST00000402578.1_Missense_Mutation_p.V534M|GRB10_ENST00000407526.1_Missense_Mutation_p.V534M|GRB10_ENST00000398810.2_Missense_Mutation_p.V534M|GRB10_ENST00000398812.2_Missense_Mutation_p.V592M|GRB10_ENST00000357271.5_Missense_Mutation_p.V546M|GRB10_ENST00000335866.3_Missense_Mutation_p.V534M|GRB10_ENST00000403097.1_Missense_Mutation_p.V586M|GRB10_ENST00000402497.1_Missense_Mutation_p.V534M			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	592					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					CATAAGGCCACTCGGATGCAG	0.512									Russell-Silver syndrome																												p.V592M													.	GRB10-1272	0			c.G1774A						.						146	146	146					7																	50660660		2080	4226	6306	SO:0001583	missense	2887	exon16	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	AGGCCACTCGGAT		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1774G>A	7.37:g.50660660C>T	ENSP00000385770:p.Val592Met	Somatic	187	1		WXS	Illumina HiSeq	Phase_I	307	73	NM_005311	0	0	33	42	9	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Missense_Mutation	SNP	ENST00000401949.1	37	CCDS43582.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.589636	0.86851	.	.	ENSG00000106070	ENST00000398812;ENST00000439599;ENST00000335866;ENST00000398810;ENST00000402578;ENST00000403097;ENST00000406641;ENST00000357271;ENST00000407526;ENST00000401949;ENST00000398791;ENST00000402497	D;D;D;D;D;D;D;D;D;D;D	0.85702	-1.93;-1.92;-2.02;-2.02;-2.02;-1.92;-2.02;-1.73;-2.02;-1.93;-2.02	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.89287	0.6672	L	0.57536	1.79	0.80722	D	1	D;D;P	0.54964	0.969;0.969;0.869	P;P;B	0.54815	0.761;0.761;0.361	D	0.89034	0.3444	10	0.52906	T	0.07	-32.1431	19.7417	0.96234	0.0:1.0:0.0:0.0	.	586;546;592	Q13322-4;Q13322-2;Q13322	.;.;GRB10_HUMAN	M	592;586;534;534;534;586;534;546;534;592;124;534	ENSP00000381793:V592M;ENSP00000406716:V586M;ENSP00000338543:V534M;ENSP00000381790:V534M;ENSP00000385189:V534M;ENSP00000385544:V586M;ENSP00000385366:V534M;ENSP00000349818:V546M;ENSP00000385046:V534M;ENSP00000385770:V592M;ENSP00000385748:V534M	ENSP00000338543:V534M	V	-	1	0	GRB10	50628154	1.000000	0.71417	0.975000	0.42487	0.994000	0.84299	7.818000	0.86416	2.661000	0.90470	0.655000	0.94253	GTG	.		0.512	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			T	50660660	C	T	50660660	3	4	149	1	0	0	0	0	1	0	0	0	6777	565	20	2	14	2	GRB10	7	50660660	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	5924937	50660660	108478003	65	13345											
CSPP1	10565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	68107797	68107797	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaaaccaggcactttcaCttggcagggcctgtcgactg	9	9	12	11	1	1	0	1	0	0	0	2	2	1	1	2	4	1	2	2	4	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr8:68107797C>T	ENST00000262215.3	-	0	7225				ARFGEF1_ENST00000520381.1_Intron|ARFGEF1_ENST00000517955.1_5'Flank|CSPP1_ENST00000262210.5_Missense_Mutation_p.T1212I|CSPP1_ENST00000412460.1_Missense_Mutation_p.T867I	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)						endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GGCACTTTCACTTGGCAGGGC	0.493																																					p.T1212I		.											.	CSPP1-138	0			c.C3635T						.						50	51	51					8																	68107797		1953	4158	6111	SO:0001628	intergenic_variant	79848	exon29			CTTTCACTTGGCA	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626		8.37:g.68107797C>T		Somatic	222	0		WXS	Illumina HiSeq	Phase_I	263	84	NM_024790	0	0	5	12	7	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	6.942	0.543635	0.13250	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.32272	1.46;1.48;1.48	5.51	-0.424	0.12321	.	0.554792	0.18305	N	0.145291	T	0.21550	0.0519	L	0.44542	1.39	0.09310	N	1	B;P;P	0.41569	0.256;0.755;0.755	B;B;B	0.35470	0.176;0.203;0.203	T	0.10177	-1.0641	10	0.66056	D	0.02	-1.672	10.1481	0.42776	0.2208:0.5604:0.2188:0.0	.	867;1212;1247	Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5	.;.;CSPP1_HUMAN	I	1212;1247;867;867	ENSP00000262210:T1212I;ENSP00000415782:T867I;ENSP00000430092:T867I	ENSP00000262210:T1212I	T	+	2	0	CSPP1	68270351	0.000000	0.05858	0.008000	0.14137	0.141000	0.21300	0.200000	0.17257	-0.223000	0.09943	-0.181000	0.13052	ACT	.		0.493	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		T	68107797	C	T	68107797	1	4	149	0	1	0	0	0	0	0	0	0	3968	565	20	2		2	CSPP1	8	68107797	IGR	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		68107797	78256225	66	13346											
DCAF13	25879	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	104444950	104444950	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaagctttcatttttacaGcagcaaatgaagattataag	15	13	8	5	0	1	2	1	1	0	1	1	3	1	3	0	1	4	3	0	1	6	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr8:104444950G>T	ENST00000297579.5	+	7	1499	c.1222G>T	c.(1222-1224)Gca>Tca	p.A408S	DCAF13_ENST00000521999.1_3'UTR	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	256					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						CATTTTTACAGCAGCAAATGA	0.308																																					p.A408S													.	DCAF13-135	0			c.G1222T						.						80	87	85					8																	104444950		2203	4297	6500	SO:0001583	missense	25879	exon7			TTTACAGCAGCAA	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.1222G>T	8.37:g.104444950G>T	ENSP00000297579:p.Ala408Ser	Somatic	18	1		WXS	Illumina HiSeq	Phase_I	17	5	NM_015420	0	0	5	5	0	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895183	0.52121	.	.	ENSG00000164934	ENST00000297579	T	0.01397	4.94	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.236141	0.41938	D	0.000800	T	0.02380	0.0073	L	0.43152	1.355	0.80722	D	1	B	0.34241	0.444	B	0.32677	0.15	T	0.62120	-0.6921	10	0.46703	T	0.11	-21.6615	19.6374	0.95740	0.0:0.0:1.0:0.0	.	256	Q9NV06	DCA13_HUMAN	S	408	ENSP00000297579:A408S	ENSP00000297579:A408S	A	+	1	0	DCAF13	104514126	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.624000	0.61254	2.711000	0.92665	0.563000	0.77884	GCA	.		0.308	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		T	104444950	G	T	104444950	3	4	149	1	0	0	0	0	1	0	0	0	4272	971	34	4	1248	4	DCAF13	8	104444950	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	36337153	104444950	41919072	67	13347											
PKHD1L1	93035	broad.mit.edu	37	chr8	110453596	110453596	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tattcaggattaccaacaatGggaaagattcaggtatcagc	15	10	9	7	0	3	1	3	0	0	1	3	3	3	3	1	3	3	1	1	3	6	5			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr8:110453596G>A	ENST00000378402.5	+	34	4296	c.4192G>A	c.(4192-4194)Ggg>Agg	p.G1398R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1398	IPT/TIG 7.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TACCAACAATGGGAAAGATTC	0.289										HNSCC(38;0.096)																											p.G1398R													.	PKHD1L1-145	0			c.G4192A						.						39	39	39					8																	110453596		1809	4056	5865	SO:0001583	missense	93035	exon34			AACAATGGGAAAG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.4192G>A	8.37:g.110453596G>A	ENSP00000367655:p.Gly1398Arg	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	130	5	NM_177531	0	0	0	0	0	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735401	0.69189	.	.	ENSG00000205038	ENST00000378402	D	0.90261	-2.64	5.48	5.48	0.80851	Cupredoxin (1);Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);	0.000000	0.64402	D	0.000002	D	0.95268	0.8465	M	0.78049	2.395	0.38053	D	0.935856	D	0.89917	1.0	D	0.91635	0.999	D	0.96317	0.9233	10	0.87932	D	0	.	17.2099	0.86928	0.0:0.0:1.0:0.0	.	1398	Q86WI1	PKHL1_HUMAN	R	1398	ENSP00000367655:G1398R	ENSP00000367655:G1398R	G	+	1	0	PKHD1L1	110522772	1.000000	0.71417	0.348000	0.25681	0.725000	0.41563	5.168000	0.64978	2.730000	0.93505	0.650000	0.86243	GGG	.		0.289	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110453596	G	A	110453596	3	1	149	1	0	0	0	0	1	0	0	0	11998	1348	47	2	4326	2	PKHD1L1	8	110453596	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	6008646	110453596	35910426	68	13348											
PUF60	22827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144902839	144902839	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagcatttctattgaccgaTtgcaaaggtgagagaggatc	12	11	12	6	1	1	4	0	3	1	1	2	7	1	5	1	2	2	2	1	2	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr8:144902839T>C	ENST00000526683.1	-	5	900	c.345A>G	c.(343-345)caA>caG	p.Q115Q	PUF60_ENST00000524570.1_5'UTR|PUF60_ENST00000456095.2_Silent_p.Q86Q|PUF60_ENST00000313352.7_Intron|PUF60_ENST00000453551.2_Silent_p.Q72Q|PUF60_ENST00000527197.1_Intron|PUF60_ENST00000349157.6_Intron	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	115	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TATTGACCGATTGCAAAGGTG	0.562																																					p.Q115Q		.											.	.	0			c.A345G						.						199	208	205					8																	144902839		2085	4208	6293	SO:0001819	synonymous_variant	22827	exon5			GACCGATTGCAAA	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.345A>G	8.37:g.144902839T>C		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	62	26	NM_078480	0	0	0	0	0	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Silent	SNP	ENST00000526683.1	37	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	T	9.393	1.076050	0.20227	.	.	ENSG00000179950	ENST00000527744	.	.	.	5.28	4.14	0.48551	.	.	.	.	.	T	0.59972	0.2233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55927	-0.8063	4	.	.	.	.	9.9314	0.41525	0.0:0.0798:0.0:0.9202	.	.	.	.	S	113	.	.	N	-	2	0	PUF60	144974827	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.482000	0.60257	0.868000	0.35678	0.533000	0.62120	AAT	.		0.562	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		C	144902839	T	C	144902839	2	2	149	1	0	0	0	0	0	0	0	1	12856	1490	52	3		3	PUF60	8	144902839	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	34449243	144902839	1461183	69	13349											
VLDLR	7436	hgsc.bcm.edu;bcgsc.ca	37	chr9	2643309	2643310	+	In_Frame_Ins	INS	-	-	GCA																															tggcgcccatgagttccagtINSgcagcacctcctcctgcatc																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:2643309_2643310insGCA	ENST00000382100.3	+	5	954_955	c.598_599insGCA	c.(598-600)tgc>tGCAgc	p.201_202insS	RP11-125B21.2_ENST00000599229.1_RNA|VLDLR_ENST00000382099.2_In_Frame_Ins_p.201_202insS	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	201	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TGAGTTCCAGTGCAGCACCTCC	0.589																																					p.C200delinsCS		.											.	VLDLR-516	0			c.598_599insGCA						.																																			SO:0001652	inframe_insertion	7436	exon5			.		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"Low density lipoprotein receptors"	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.602_604dupGCA	9.37:g.2643313_2643315dupGCA	ENSP00000371532:p.Ser203_Ser204dup	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	141	52	NM_003383	0	0	0	0	0	B2RMZ7|D3DRH6|Q5VVF6	In_Frame_Ins	INS	ENST00000382100.3	37	CCDS6446.1																																																																																			.		0.589	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		GCA	2643310	-	GCA	2643309	7	5	149	1	0	1	1	0	0	0	0	0	17207	1696	59	0	616	0	VLDLR	9	2643309	In_Frame_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10		2643309	138570122	70	13350											
STOML2	30968	ucsc.edu;bcgsc.ca	37	chr9	35102144	35102144	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgacaatttccttgagactCtgcacatatcggatccggtc	10	12	8	11	2	1	2	0	2	1	1	5	4	3	3	2	2	1	1	2	2	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:35102144C>G	ENST00000356493.5	-	3	293	c.231G>C	c.(229-231)caG>caC	p.Q77H	STOML2_ENST00000452248.2_Missense_Mutation_p.Q77H|STOML2_ENST00000487490.1_5'UTR	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	77					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CCTTGAGACTCTGCACATATC	0.532																																					p.Q77H													.	STOML2-90	0			c.G231C						.						102	93	96					9																	35102144		2203	4300	6503	SO:0001583	missense	30968	exon3			GAGACTCTGCACA	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.231G>C	9.37:g.35102144C>G	ENSP00000348886:p.Gln77His	Somatic	196	2		WXS	Illumina HiSeq		199	80	NM_013442	0	0	23	44	21	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	ENST00000356493.5	37	CCDS6577.1	.	.	.	.	.	.	.	.	.	.	C	5.880	0.346502	0.11126	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.94457	-3.43;-3.43	5.56	4.66	0.58398	.	0.051019	0.85682	D	0.000000	D	0.89375	0.6697	N	0.21240	0.645	0.58432	D	0.999999	B;B	0.27700	0.002;0.186	B;B	0.37833	0.01;0.259	T	0.83332	-0.0012	10	0.06625	T	0.88	-15.0706	11.5082	0.50479	0.0:0.8569:0.0:0.1431	.	77;77	B4E1K7;Q9UJZ1	.;STML2_HUMAN	H	77	ENSP00000348886:Q77H;ENSP00000395743:Q77H	ENSP00000348886:Q77H	Q	-	3	2	STOML2	35092144	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.331000	0.43894	1.580000	0.49851	0.655000	0.94253	CAG	.		0.532	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442		G	35102144	C	G	35102144	3	3	149	1	0	0	0	0	1	0	0	0	15346	912	32	4	871	4	STOML2	9	35102144	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	32458835	35102144	106111287	71	13351											
ALDH1B1	219	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	38397069	38397069	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagggccaacaacaccaggTatggcctggctgcggctgtg	9	6	15	11	1	0	1	0	0	0	1	0	1	0	1	3	5	3	3	3	5	3	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:38397069T>C	ENST00000377698.3	+	2	1477	c.1324T>C	c.(1324-1326)Tat>Cat	p.Y442H		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	442					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		CAACACCAGGTATGGCCTGGC	0.552																																					p.Y442H													.	ALDH1B1-227	0			c.T1324C						.						69	66	67					9																	38397069		2203	4300	6503	SO:0001583	missense	219	exon2			ACCAGGTATGGCC	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"Aldehyde dehydrogenases"	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.1324T>C	9.37:g.38397069T>C	ENSP00000366927:p.Tyr442His	Somatic	133	2		WXS	Illumina HiSeq	Phase_I	139	51	NM_000692	0	0	8	20	12	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	37	CCDS6615.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294921	0.60086	.	.	ENSG00000137124	ENST00000377698;ENST00000540055	D	0.81659	-1.52	5.7	5.7	0.88788	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.64402	D	0.000018	D	0.92485	0.7614	H	0.95816	3.725	0.54753	D	0.999985	D	0.89917	1.0	D	0.83275	0.996	D	0.94386	0.7609	10	0.87932	D	0	.	13.9161	0.63899	0.0:0.0:0.0:1.0	.	442	P30837	AL1B1_HUMAN	H	442;143	ENSP00000366927:Y442H	ENSP00000366927:Y442H	Y	+	1	0	ALDH1B1	38387069	1.000000	0.71417	0.927000	0.36925	0.539000	0.34962	7.743000	0.85020	2.169000	0.68431	0.533000	0.62120	TAT	.		0.552	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			C	38397069	T	C	38397069	3	2	149	1	0	0	0	0	1	0	0	0	493	1638	57	3	1326	3	ALDH1B1	9	38397069	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	3294925	38397069	102816362	72	13352											
ZNF462	58499	broad.mit.edu	37	chr9	109689599	109689599	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcttgtccactaccagaaaAgacacccagaaataaaggtt	16	8	7	10	0	0	3	0	0	0	3	1	3	1	3	3	1	2	2	3	1	6	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:109689599A>G	ENST00000277225.5	+	3	3695	c.3406A>G	c.(3406-3408)Aga>Gga	p.R1136G	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Missense_Mutation_p.R1136G			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1136					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CTACCAGAAAAGACACCCAGA	0.537																																					p.R1136G													.	ZNF462-95	0			c.A3406G						.						92	96	95					9																	109689599		2203	4300	6503	SO:0001583	missense	58499	exon3			CAGAAAAGACACC	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"Zinc fingers, C2H2-type"	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3406A>G	9.37:g.109689599A>G	ENSP00000277225:p.Arg1136Gly	Somatic	36	0		WXS	Illumina HiSeq	Phase_I	18	3	NM_021224	0	0	0	0	0	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	A	15.28	2.786838	0.49997	.	.	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686	T;T;T	0.12147	2.71;3.1;3.6	5.37	5.37	0.77165	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.33323	0.0859	L	0.54323	1.7	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.77557	0.99;0.987	T	0.03403	-1.1040	10	0.72032	D	0.01	.	15.3692	0.74548	1.0:0.0:0.0:0.0	.	1136;1136	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	G	1136;1136;19	ENSP00000277225:R1136G;ENSP00000414570:R1136G;ENSP00000363818:R19G	ENSP00000277225:R1136G	R	+	1	2	ZNF462	108729420	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.785000	0.62418	2.033000	0.60031	0.459000	0.35465	AGA	.		0.537	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		G	109689599	A	G	109689599	3	3	149	1	0	0	0	0	1	0	0	0	17958	64	3	3	3412	3	ZNF462	9	109689599	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	71292530	109689599	31523832	73	13353											
C9orf50	375759	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	132377793	132377793	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgctcccagtagcggagcgTtgtgtcctgcagggtctcgt	4	10	15	12	4	1	0	0	0	1	0	4	1	3	1	2	2	3	4	2	2	1	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:132377793T>C	ENST00000372478.4	-	4	1051	c.850A>G	c.(850-852)Acg>Gcg	p.T284A	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	284										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				TAGCGGAGCGTTGTGTCCTGC	0.642																																					p.T284A													.	C9orf50-91	0			c.A850G						.						65	56	59					9																	132377793		2203	4300	6503	SO:0001583	missense	375759	exon4			GGAGCGTTGTGTC	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.850A>G	9.37:g.132377793T>C	ENSP00000361556:p.Thr284Ala	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	61	19	NM_199350	0	0	0	2	2	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-2.889554	0.00060	.	.	ENSG00000179058	ENST00000372478	T	0.10099	2.91	3.17	0.155	0.14906	.	0.496540	0.15341	N	0.267481	T	0.02380	0.0073	N	0.01168	-0.975	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.44711	-0.9310	10	0.02654	T	1	-2.9125	5.3025	0.15785	0.0:0.4706:0.407:0.1224	.	284	Q5SZB4	CI050_HUMAN	A	284	ENSP00000361556:T284A	ENSP00000361556:T284A	T	-	1	0	C9orf50	131417614	0.003000	0.15002	0.001000	0.08648	0.108000	0.19459	0.323000	0.19593	0.038000	0.15604	-1.709000	0.00716	ACG	.		0.642	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350		C	132377793	T	C	132377793	3	2	149	1	0	0	0	0	1	0	0	0	2493	1725	60	3	461	3	C9orf50	9	132377793	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	22688194	132377793	8835638	74	13354											
TPRN	286262	hgsc.bcm.edu	37	chr9	140094091	140094091	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcggggaggccgggcccAggtctccctttggcagctcc	3	7	16	15	2	1	0	0	0	1	0	4	1	2	1	4	7	1	3	4	7	0	1	rs60910563	byFrequency	TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:140094091A>G	ENST00000409012.4	-	1	1159	c.1073T>C	c.(1072-1074)cTg>cCg	p.L358P	TPRN_ENST00000541945.1_Intron|TPRN_ENST00000321773.2_Missense_Mutation_p.L297P	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	358					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						GGCCGGGCCCAGGTCTCCCTT	0.672													A|||	94	0.01877	0.0696	0.0029	5008	,	,		12735	0		0	False		,,,				2504	0				p.L358P		.											.	TPRN-90	0			c.T1073C						.	A	PRO/LEU	133,3959		1,131,1914	5	5	5		1073	-2.5	0	9	dbSNP_129	5	0,8162		0,0,4081	yes	missense	TPRN	NM_001128228.2	98	1,131,5995	GG,GA,AA		0.0,3.2502,1.0854	probably-damaging	358/712	140094091	133,12121	2046	4081	6127	SO:0001583	missense	286262	exon1			GGGCCCAGGTCTC	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"chromosome 9 open reading frame 75", "deafness, autosomal recessive 79"	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1073T>C	9.37:g.140094091A>G	ENSP00000387100:p.Leu358Pro	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_001128228	0	0	14	21	7	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Missense_Mutation	SNP	ENST00000409012.4	37	CCDS56594.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	A	0.935	-0.711322	0.03230	0.032502	0.0	ENSG00000176058	ENST00000333046;ENST00000409012;ENST00000321773	.	.	.	3.47	-2.46	0.06461	.	1.261530	0.05899	N	0.629706	T	0.01189	0.0039	N	0.14661	0.345	0.09310	N	0.999999	B	0.24483	0.104	B	0.17433	0.018	T	0.17440	-1.0369	9	0.56958	D	0.05	.	0.3333	0.00322	0.3035:0.2092:0.282:0.2053	rs60910563	358	Q4KMQ1	TPRN_HUMAN	P	156;358;297	.	ENSP00000313704:L297P	L	-	2	0	TPRN	139213912	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-0.236000	0.09003	-0.352000	0.08237	0.374000	0.22700	CTG	A|0.984;G|0.016		0.672	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691		G	140094091	A	G	140094091	3	3	149	1	0	0	0	0	1	0	0	0	16454	188	7	3	1158	3	TPRN	9	140094091	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	7716298	140094091	1119340	75	13355											
ZNF438	220929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	31134006	31134006	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcttccagtggtggaggaGgtcctctttccgtcccagca	5	11	13	12	1	1	0	0	0	1	0	5	2	5	2	4	4	2	2	4	4	0	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:31134006G>A	ENST00000361310.3	-	7	2700	c.2371C>T	c.(2371-2373)Ctc>Ttc	p.L791F	ZNF438_ENST00000452305.1_Missense_Mutation_p.L781F|ZNF438_ENST00000444692.2_Missense_Mutation_p.L781F|ZNF438_ENST00000436087.2_Missense_Mutation_p.L791F|ZNF438_ENST00000331737.6_Missense_Mutation_p.L781F|ZNF438_ENST00000442986.1_Missense_Mutation_p.L791F|ZNF438_ENST00000375311.1_Missense_Mutation_p.L355F|ZNF438_ENST00000538351.2_Missense_Mutation_p.L742F|ZNF438_ENST00000413025.1_Missense_Mutation_p.L791F			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	791					negative regulation of transcription, DNA-templated (GO:0045892)|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(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				TGGTGGAGGAGGTCCTCTTTC	0.537																																					p.L791F		.											.	ZNF438-154	0			c.C2371T						.						188	181	184					10																	31134006		2203	4300	6503	SO:0001583	missense	220929	exon8			GGAGGAGGTCCTC	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"Zinc fingers, C2H2-type"	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.2371C>T	10.37:g.31134006G>A	ENSP00000354663:p.Leu791Phe	Somatic	152	0		WXS	Illumina HiSeq	Phase_I	143	53	NM_182755	0	0	8	12	4	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	37	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766477	0.90020	.	.	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351;ENST00000430896;ENST00000375311	T;T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.29	5.5	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.115961	0.64402	D	0.000014	T	0.37293	0.0998	M	0.68593	2.085	0.36439	D	0.865386	D;D	0.89917	1.0;1.0	D;D	0.77557	0.976;0.99	T	0.44498	-0.9324	10	0.87932	D	0	-20.022	11.0268	0.47748	0.0708:0.1293:0.7998:0.0	.	791;781	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	F	781;791;791;791;791;781;781;742;510;355	ENSP00000333571:L781F;ENSP00000354663:L791F;ENSP00000406934:L791F;ENSP00000412363:L791F;ENSP00000387546:L791F;ENSP00000413060:L781F;ENSP00000410898:L781F;ENSP00000445461:L742F;ENSP00000364460:L355F	ENSP00000333571:L781F	L	-	1	0	ZNF438	31174012	1.000000	0.71417	0.008000	0.14137	0.846000	0.48090	3.398000	0.52579	0.770000	0.33336	0.655000	0.94253	CTC	.		0.537	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		A	31134006	G	A	31134006	3	1	149	1	0	0	0	0	1	0	0	0	17942	1000	35	2	119	2	ZNF438	10	31134006	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		31134006	104400741	76	13356											
ZNF33B	7582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	43088357	43088357	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgctttctctcatgtaaaaTaagtcctgacttcacacaga	12	13	6	10	0	3	2	2	1	1	1	5	2	4	2	1	0	1	2	1	0	3	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:43088357T>C	ENST00000359467.3	-	5	2155	c.2041A>G	c.(2041-2043)Att>Gtt	p.I681V	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	681					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)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						TCATGTAAAATAAGTCCTGAC	0.403																																					p.I681V	Melanoma(137;1247 1767 16772 25727 43810)	.											.	ZNF33B-90	0			c.A2041G						.						123	121	122					10																	43088357		2203	4300	6503	SO:0001583	missense	7582	exon5			GTAAAATAAGTCC	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.2041A>G	10.37:g.43088357T>C	ENSP00000352444:p.Ile681Val	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	76	32	NM_006955	0	0	1	1	0	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	T	4.006	-0.001564	0.07819	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.35605	1.3	2.54	0.118	0.14667	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.852537	0.09554	N	0.786508	T	0.12902	0.0313	N	0.02842	-0.48	0.19300	N	0.999972	B	0.09022	0.002	B	0.09377	0.004	T	0.23404	-1.0189	10	0.30854	T	0.27	.	2.2255	0.03983	0.2309:0.2698:0.0:0.4993	.	681	Q06732	ZN33B_HUMAN	V	681;647	ENSP00000352444:I681V	ENSP00000352444:I681V	I	-	1	0	ZNF33B	42408363	0.000000	0.05858	0.917000	0.36280	0.797000	0.45037	-1.573000	0.02134	0.016000	0.14998	0.336000	0.21669	ATT	.		0.403	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		C	43088357	T	C	43088357	3	2	149	1	0	0	0	0	1	0	0	0	17887	1406	49	3	299	3	ZNF33B	10	43088357	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	11954351	43088357	92446390	77	13357											
RRP12	23223	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	99116859	99116859	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggccctgggcctcagggtcGacgatcctttctgcggtttt	3	12	14	12	3	2	0	1	0	1	0	4	2	3	0	3	4	1	1	3	4	0	3	rs371319861		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:99116859G>A	ENST00000370992.4	-	34	3997	c.3886C>T	c.(3886-3888)Cga>Tga	p.R1296*	RRP12_ENST00000315563.6_Nonsense_Mutation_p.R1196*|RRP12_ENST00000536831.1_Nonsense_Mutation_p.R1014*|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000414986.1_Nonsense_Mutation_p.R1235*	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1296						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CCTCAGGGTCGACGATCCTTT	0.622																																					p.R1296X													.	RRP12-92	0			c.C3886T						.	A	stop/ARG,stop/ARG	0,4406		0,0,2203	86	82	83		3703,3886	1.2	0	10		83	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	RRP12	NM_001145114.1,NM_015179.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1235/1237,1296/1298	99116859	1,13005	2203	4300	6503	SO:0001587	stop_gained	23223	exon34			AGGGTCGACGATC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3886C>T	10.37:g.99116859G>A	ENSP00000360031:p.Arg1296*	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	59	28	NM_015179	0	0	17	36	19	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Nonsense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	g	37	6.020086	0.97205	0.0	1.16E-4	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	.	.	.	5.4	1.22	0.21188	.	0.218072	0.37955	N	0.001863	.	.	.	.	.	.	0.22947	N	0.998522	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.913	5.2587	0.15561	0.0662:0.1203:0.4412:0.3724	.	.	.	.	X	1296;1196;1235;1014	.	ENSP00000324315:R1196X	R	-	1	2	RRP12	99106849	0.005000	0.15991	0.003000	0.11579	0.391000	0.30476	0.593000	0.23999	0.243000	0.21327	-0.215000	0.12644	CGA	.		0.622	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99116859	G	A	99116859	4	1	149	1	0	0	0	0	0	1	0	0	13718	1066	37	1	11	1	RRP12	10	99116859	Nonsense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	56028502	99116859	36417888	78	13358											
AFAP1L2	84632	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	116100456	116100456	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcctggtcaagaatcttgagGaagtcatccaactctgtcag	11	11	9	10	0	5	2	3	1	2	1	7	3	7	3	2	2	1	0	2	2	4	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:116100456G>A	ENST00000304129.4	-	2	80	c.51C>T	c.(49-51)ttC>ttT	p.F17F	AFAP1L2_ENST00000369271.3_Silent_p.F17F|AFAP1L2_ENST00000545353.1_Silent_p.F17F			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	17					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		GAATCTTGAGGAAGTCATCCA	0.537																																					p.F17F		.											.	AFAP1L2-136	0			c.C51T						.						87	85	86					10																	116100456		2203	4300	6503	SO:0001819	synonymous_variant	84632	exon2			CTTGAGGAAGTCA	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"Pleckstrin homology (PH) domain containing"	25901	protein-coding gene	gene with protein product		612420	"KIAA1914"	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.51C>T	10.37:g.116100456G>A		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	95	33	NM_032550	0	0	0	0	0	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			.		0.537	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		A	116100456	G	A	116100456	2	1	149	1	0	0	0	0	0	0	0	1	355	1165	41	2		2	AFAP1L2	10	116100456	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	16983597	116100456	19434291	79	13359											
MKI67	4288	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	129902143	129902143	+	Frame_Shift_Del	DEL	G	G	-																															gttcctcttctactgggtttGgtttcttctttgcacgttgc																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:129902143delG	ENST00000368654.3	-	13	8336	c.7961delC	c.(7960-7962)ccafs	p.P2654fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.P2294fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2654	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TACTGGGTTTGGTTTCTTCTT	0.522																																					p.P2654fs		.											.	MKI67-519	0			c.7961delC						.						171	175	174					10																	129902143		2203	4300	6503	SO:0001589	frameshift_variant	4288	exon13			.	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 105"	176741	"antigen identified by monoclonal antibody Ki-67"			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.7961delC	10.37:g.129902143delG	ENSP00000357643:p.Pro2654fs	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	118	50	NM_002417	0	0	0	0	0	Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	37	CCDS7659.1																																																																																			.		0.522	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		-	129902143	G	-	129902143	7	5	149	1	0	1	0	1	0	0	0	0	9623	1348	47	0	1821	0	MKI67	10	129902143	Frame_Shift_Del	DEL	G	TCGA-MH-A55Z-01A-11D-A26P-10	13801687	129902143	5632604	80	13360											
OR51G2	81282	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	4936503	4936503	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagtgcaaggggtggcagaTagccacaaagcggtcaaagg	14	5	15	7	1	1	1	1	0	0	1	1	1	1	1	1	5	3	2	1	5	5	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:4936503T>C	ENST00000322013.3	-	1	419	c.391A>G	c.(391-393)Atc>Gtc	p.I131V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	131						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)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGGTGGCAGATAGCCACAAAG	0.493																																					p.I131V		.											.	OR51G2-70	0			c.A391G						.						81	80	80					11																	4936503		2201	4298	6499	SO:0001583	missense	81282	exon1			GGCAGATAGCCAC	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"GPCR / Class A : Olfactory receptors"	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.391A>G	11.37:g.4936503T>C	ENSP00000322593:p.Ile131Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	56	23	NM_001005238	0	0	0	0	0	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.145321	0.57044	.	.	ENSG00000176893	ENST00000322013	T	0.50813	0.73	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000099	T	0.55097	0.1899	M	0.86573	2.825	0.44719	D	0.997717	B	0.29301	0.241	B	0.25987	0.065	T	0.60835	-0.7184	10	0.66056	D	0.02	.	14.7227	0.69320	0.0:0.0:0.0:1.0	.	131	Q8NGK0	O51G2_HUMAN	V	131	ENSP00000322593:I131V	ENSP00000322593:I131V	I	-	1	0	OR51G2	4893079	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	7.646000	0.83445	2.343000	0.79666	0.533000	0.62120	ATC	.		0.493	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		C	4936503	T	C	4936503	3	2	149	1	0	0	0	0	1	0	0	0	11125	1406	49	3	557	3	OR51G2	11	4936503	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		4936503	130070013	81	13361											
BDNF	627	hgsc.bcm.edu;bcgsc.ca	37	chr11	27680049	27680056	+	Frame_Shift_Del	DEL	CATGGGGG	CATGGGGG	-																															cctcggatgtttgcttctttCatgggggcagccttcatgca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	CATGGGGG	CATGGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:27680049_27680056delCATGGGGG	ENST00000525528.1	-	1	1149_1156	c.56_63delCCCCCATG	c.(55-63)gcccccatgfs	p.APM19fs	BDNF_ENST00000395980.2_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000395986.2_Frame_Shift_Del_p.APM34fs|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000356660.4_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000438929.1_Frame_Shift_Del_p.APM101fs|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000533131.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000439476.2_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000395978.3_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000395981.3_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395983.3_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000533246.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000418212.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000530861.1_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000532997.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000525950.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000314915.6_Frame_Shift_Del_p.APM27fs|BDNF_ENST00000420794.1_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000530313.1_RNA|BDNF-AS_ENST00000530686.1_RNA	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	19					axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						TTGCTTCTTTCATGGGGGCAGCCTTCAT	0.514																																					p.101_103del		.											.	BDNF-514	0			c.302_309del						.																																			SO:0001589	frameshift_variant	627	exon3			.	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"Endogenous ligands"	1033	protein-coding gene	gene with protein product	"neurotrophin"	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.56_63delCCCCCATG	11.37:g.27680049_27680056delCATGGGGG	ENSP00000437138:p.Ala19fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	91	27	NM_001143810	0	0	0	0	0	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Frame_Shift_Del	DEL	ENST00000525528.1	37	CCDS7866.1																																																																																			.		0.514	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735		-	27680056	CATGGGGG	-	27680049	7	5	149	1	0	1	0	1	0	0	0	0	1395	826	29	0	684	0	BDNF	11	27680049	Frame_Shift_Del	DEL	CATGGGGG	TCGA-MH-A55Z-01A-11D-A26P-10	22743546	27680049	107326467	82	13362											
SYT13	57586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	45277229	45277229	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acccctaccattctgagggaGgatgaacagctcctctgtga	10	9	10	12	0	2	3	0	3	2	0	3	5	3	5	4	2	3	1	4	2	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:45277229G>C	ENST00000020926.3	-	2	508	c.397C>G	c.(397-399)Ctc>Gtc	p.L133V	CTD-2560E9.5_ENST00000534342.1_RNA|CTD-2560E9.5_ENST00000531663.1_RNA	NM_001247987.1|NM_020826.2	NP_001234916.1|NP_065877.1	Q7L8C5	SYT13_HUMAN	synaptotagmin XIII	133					vesicle-mediated transport (GO:0016192)	integral component of plasma membrane (GO:0005887)|transport vesicle (GO:0030133)				breast(1)|large_intestine(3)|lung(16)|ovary(1)|skin(2)	23						TTCTGAGGGAGGATGAACAGC	0.592																																					p.L133V		.											.	SYT13-91	0			c.C397G						.						53	47	49					11																	45277229		2203	4299	6502	SO:0001583	missense	57586	exon2			GAGGGAGGATGAA	AB037848	CCDS31470.1	11p12-p11	2013-01-21			ENSG00000019505	ENSG00000019505		"Synaptotagmins"	14962	protein-coding gene	gene with protein product		607716				11171101	Standard	NM_020826		Approved	KIAA1427	uc001myq.2	Q7L8C5	OTTHUMG00000166504	ENST00000020926.3:c.397C>G	11.37:g.45277229G>C	ENSP00000020926:p.Leu133Val	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	39	17	NM_020826	0	0	0	0	0	A8K4P4|D3DQP1|Q9BQS3|Q9H041|Q9P2C0	Missense_Mutation	SNP	ENST00000020926.3	37	CCDS31470.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.810428	0.50421	.	.	ENSG00000019505	ENST00000020926	T	0.08370	3.1	5.39	5.39	0.77823	.	0.077197	0.52532	D	0.000067	T	0.06917	0.0176	N	0.24115	0.695	0.33493	D	0.588914	B	0.23650	0.089	B	0.21917	0.037	T	0.17501	-1.0367	10	0.30078	T	0.28	.	13.5218	0.61572	0.0:0.0:0.8444:0.1556	.	133	Q7L8C5	SYT13_HUMAN	V	133	ENSP00000020926:L133V	ENSP00000020926:L133V	L	-	1	0	SYT13	45233805	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	3.496000	0.53288	2.679000	0.91253	0.561000	0.74099	CTC	.		0.592	SYT13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390110.1	NM_020826		C	45277229	G	C	45277229	3	2	149	1	0	0	0	0	1	0	0	0	15501	1000	35	4	903	4	SYT13	11	45277229	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	17597180	45277229	89729287	83	13363											
LTBP3	4054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65319017	65319017	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatctgggttctcatactcActgagtccgtggtcacccct	6	12	8	15	1	4	1	3	1	2	0	6	1	5	1	4	2	1	1	4	2	1	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:65319017A>T	ENST00000301873.5	-	9	1817		c.e9+1		LTBP3_ENST00000322147.4_Splice_Site|LTBP3_ENST00000532932.1_5'Flank|LTBP3_ENST00000536982.1_Splice_Site	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3						bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						TCTCATACTCACTGAGTCCGT	0.592																																					.		.											.	LTBP3-91	0			c.1197+2T>A						.						68	58	62					11																	65319017		2201	4297	6498	SO:0001630	splice_region_variant	4054	exon10			ATACTCACTGAGT	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1548+1T>A	11.37:g.65319017A>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	107	35	NM_001164266	0	0	0	0	0	O15107|Q96HB9|Q9H7K2|Q9UFN4	Splice_Site	SNP	ENST00000301873.5	37	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.029156	0.75504	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000526927;ENST00000536982;ENST00000530866	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0038	0.47622	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LTBP3	65075593	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.837000	0.62796	1.861000	0.53984	0.329000	0.21502	.	.		0.592	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070	Intron	T	65319017	A	T	65319017	5	4	149	1	0	0	0	0	0	0	1	0	9100	173	6	5	2441	5	LTBP3	11	65319017	Splice_Site	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	20041788	65319017	69687499	84	13364											
SIPA1	6494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	65412463	65412463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggcatcctgtactgccGggcgggccagggctcggagg	4	6	20	11	3	0	0	0	0	0	0	2	1	1	1	3	7	2	3	3	7	1	1	rs146916012		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:65412463G>A	ENST00000394224.3	+	5	1318	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	SIPA1_ENST00000394227.3_Missense_Mutation_p.R341Q|SIPA1_ENST00000534313.1_Missense_Mutation_p.R341Q|SIPA1_ENST00000527525.1_Missense_Mutation_p.R341Q	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	341	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						CTGTACTGCCGGGCGGGCCAG	0.622																																					p.R341Q		.											.	SIPA1-90	0			c.G1022A						.	G	GLN/ARG,GLN/ARG	0,4402		0,0,2201	86	88	87		1022,1022	4.8	1	11	dbSNP_134	87	2,8592	2.2+/-6.3	0,2,4295	yes	missense,missense	SIPA1	NM_006747.3,NM_153253.29	43,43	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	341/1043,341/1043	65412463	2,12994	2201	4297	6498	SO:0001583	missense	6494	exon5			ACTGCCGGGCGGG	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.1022G>A	11.37:g.65412463G>A	ENSP00000377771:p.Arg341Gln	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	187	88	NM_006747	0	0	1	1	0	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.872939	0.91664	0.0	2.33E-4	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3	4.78	4.78	0.61160	Rap/ran-GAP (1);	0.123367	0.30667	U	0.009135	D	0.94499	0.8229	L	0.41027	1.25	0.47994	D	0.999563	D;D	0.89917	1.0;1.0	D;D	0.69824	0.966;0.926	D	0.94259	0.7500	10	0.45353	T	0.12	-21.0415	15.6687	0.77255	0.0:0.0:1.0:0.0	.	341;341	F6RY50;Q96FS4	.;SIPA1_HUMAN	Q	341	ENSP00000436269:R341Q;ENSP00000433686:R341Q;ENSP00000377771:R341Q;ENSP00000377774:R341Q	ENSP00000377771:R341Q	R	+	2	0	SIPA1	65169039	0.996000	0.38824	0.989000	0.46669	0.990000	0.78478	1.561000	0.36342	2.368000	0.80403	0.561000	0.74099	CGG	G|1.000;A|0.000		0.622	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		A	65412463	G	A	65412463	3	1	149	1	0	0	0	0	1	0	0	0	14360	1116	39	1	1036	1	SIPA1	11	65412463	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	93446	65412463	69594053	85	13365											
EXPH5	23086	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	108380539	108380539	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagtgacctctttacattttCtaagaaagctaactgttgtt	12	16	6	7	0	2	2	0	1	2	1	2	2	2	2	1	0	3	3	1	0	5	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:108380539C>T	ENST00000265843.4	-	6	5805	c.5695G>A	c.(5695-5697)Gaa>Aaa	p.E1899K	EXPH5_ENST00000443411.1_Missense_Mutation_p.E1711K|EXPH5_ENST00000525344.1_Missense_Mutation_p.E1892K|EXPH5_ENST00000428840.1_Missense_Mutation_p.E1823K	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1899					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TTTACATTTTCTAAGAAAGCT	0.413																																					p.E1899K													.	EXPH5-95	0			c.G5695A						.						74	78	77					11																	108380539		2201	4298	6499	SO:0001583	missense	23086	exon6			CATTTTCTAAGAA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"synaptotagmin-like homologue lacking C2 domains b"	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5695G>A	11.37:g.108380539C>T	ENSP00000265843:p.Glu1899Lys	Somatic	136	1		WXS	Illumina HiSeq	Phase_I	125	42	NM_015065	0	0	0	1	1	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933160	0.92458	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000003	T	0.74535	0.3729	M	0.71581	2.175	0.44852	D	0.99786	D	0.89917	1.0	D	0.85130	0.997	T	0.74200	-0.3742	10	0.87932	D	0	-20.3741	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1899	Q8NEV8	EXPH5_HUMAN	K	1899;1823;1711;1892;729	ENSP00000265843:E1899K;ENSP00000391966:E1823K;ENSP00000411390:E1711K;ENSP00000432546:E1892K	ENSP00000265843:E1899K	E	-	1	0	EXPH5	107885749	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	3.765000	0.55272	2.941000	0.99782	0.655000	0.94253	GAA	.		0.413	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108380539	C	T	108380539	3	4	149	1	0	0	0	0	1	0	0	0	5335	922	32	2	278	2	EXPH5	11	108380539	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	42968076	108380539	26625977	86	13366											
CHEK1	1111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	125497532	125497532	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgtgaatagagtaactgaAgaagcagtcgcagtgaagat	15	8	13	5	1	0	6	0	3	0	3	1	6	0	6	0	0	2	4	0	0	6	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:125497532A>C	ENST00000534070.1	+	3	351	c.96A>C	c.(94-96)gaA>gaC	p.E32D	CHEK1_ENST00000438015.1_Missense_Mutation_p.E32D|CHEK1_ENST00000532449.1_Intron|CHEK1_ENST00000278916.3_Missense_Mutation_p.E32D|CHEK1_ENST00000428830.2_Missense_Mutation_p.E32D|CHEK1_ENST00000524737.1_Missense_Mutation_p.E32D|CHEK1_ENST00000544373.1_Missense_Mutation_p.E32D|CHEK1_ENST00000427383.2_Intron	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	32	Interaction with CLSPN. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		GAGTAACTGAAGAAGCAGTCG	0.328								Other conserved DNA damage response genes																													p.E32D		.											.	CHEK1-1509	0			c.A96C						.						50	54	52					11																	125497532		2201	4299	6500	SO:0001583	missense	1111	exon3			AACTGAAGAAGCA	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.96A>C	11.37:g.125497532A>C	ENSP00000435371:p.Glu32Asp	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	71	34	NM_001244846	0	0	0	0	0	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Missense_Mutation	SNP	ENST00000534070.1	37	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.289544	0.23478	.	.	ENSG00000149554	ENST00000438015;ENST00000525396;ENST00000428830;ENST00000544373;ENST00000527013;ENST00000526937;ENST00000534685;ENST00000533778;ENST00000534070;ENST00000524737;ENST00000278916	T;T;T;T;T;T;T;T;T;T;T	0.41400	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.0;1.9;1.9;1.9	5.21	4.09	0.47781	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.23171	0.0560	N	0.05383	-0.06	0.53688	D	0.999972	B;B;B	0.19200	0.027;0.034;0.034	B;B;B	0.25405	0.036;0.06;0.06	T	0.04537	-1.0944	10	0.37606	T	0.19	.	8.9327	0.35680	0.8441:0.0:0.1559:0.0	.	32;32;32	F5H7S4;B5BTY6;O14757	.;.;CHK1_HUMAN	D	32	ENSP00000388648:E32D;ENSP00000434141:E32D;ENSP00000412504:E32D;ENSP00000442317:E32D;ENSP00000431525:E32D;ENSP00000431815:E32D;ENSP00000432470:E32D;ENSP00000433103:E32D;ENSP00000435371:E32D;ENSP00000432890:E32D;ENSP00000278916:E32D	ENSP00000278916:E32D	E	+	3	2	CHEK1	125002742	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.843000	0.27640	0.957000	0.37930	0.477000	0.44152	GAA	.		0.328	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		C	125497532	A	C	125497532	3	2	149	1	0	0	0	0	1	0	0	0	3340	69	3	5	102	5	CHEK1	11	125497532	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	17116993	125497532	9508984	87	13367											
NFRKB	4798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	129747271	129747271	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgggacgcaccacataGtcagttcttctggaatataa	11	11	10	9	1	3	0	1	0	2	0	3	2	3	2	1	2	1	3	1	2	4	5			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:129747271G>A	ENST00000446488.3	-	15	1624	c.1521C>T	c.(1519-1521)gaC>gaT	p.D507D	NFRKB_ENST00000524746.1_Silent_p.D507D|NFRKB_ENST00000524794.1_Silent_p.D532D|NFRKB_ENST00000304521.5_Silent_p.D507D	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	507					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		GCACCACATAGTCAGTTCTTC	0.507																																					p.D532D		.											.	NFRKB-93	0			c.C1596T						.						161	149	153					11																	129747271		2201	4297	6498	SO:0001819	synonymous_variant	4798	exon14			CACATAGTCAGTT		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"INO80 complex subunits"	7802	protein-coding gene	gene with protein product	"nuclear factor related to kappa B binding protein", "DNA-binding protein R kappa B", "INO80 complex subunit G"	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1521C>T	11.37:g.129747271G>A		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	74	27	NM_006165	0	0	0	0	0	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			.		0.507	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		A	129747271	G	A	129747271	2	1	149	1	0	0	0	0	0	0	0	1	10410	1020	36	2		2	NFRKB	11	129747271	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	4249739	129747271	5259245	88	13368											
C12orf57	113246	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7053729	7053729	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	taacgcctgcaacgacatggGtaagatgctgcaattcgtgc	11	9	11	10	3	0	1	0	0	0	1	1	2	0	1	1	1	6	4	1	1	4	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:7053729G>T	ENST00000229281.5	+	2	242	c.143G>T	c.(142-144)gGt>gTt	p.G48V	C12orf57_ENST00000544681.1_Missense_Mutation_p.G48V|RNU7-1_ENST00000458811.1_RNA|C12orf57_ENST00000542222.1_3'UTR|U47924.31_ENST00000607421.1_RNA|PTPN6_ENST00000447931.2_5'Flank|C12orf57_ENST00000537087.1_Splice_Site|PTPN6_ENST00000399448.1_5'Flank|C12orf57_ENST00000540506.2_Missense_Mutation_p.G13V	NM_138425.2	NP_612434.1	Q99622	C10_HUMAN	chromosome 12 open reading frame 57	48						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)	2						AACGACATGGGTAAGATGCTG	0.627											OREG0021642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G48V		.											.	C12orf57-90	0			c.G143T						.						90	66	74					12																	7053729		2203	4300	6503	SO:0001583	missense	113246	exon2			ACATGGGTAAGAT	U47924	CCDS8571.1	12p13.31	2012-05-30			ENSG00000111678	ENSG00000111678			29521	protein-coding gene	gene with protein product		615140				9445485	Standard	NM_138425		Approved	GRCC10, C10	uc009zfj.2	Q99622	OTTHUMG00000169017	ENST00000229281.5:c.143G>T	12.37:g.7053729G>T	ENSP00000229281:p.Gly48Val	Somatic	95	0	638	WXS	Illumina HiSeq	Phase_I	203	118	NM_138425	0	0	93	301	208	B2R4Q6	Missense_Mutation	SNP	ENST00000229281.5	37	CCDS8571.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.552280|4.552280	0.86127|0.86127	.|.	.|.	ENSG00000111678|ENSG00000111678	ENST00000537087|ENST00000545581;ENST00000229281	.|T;T	.|0.75938	.|-0.98;-0.98	3.74|3.74	3.74|3.74	0.42951|0.42951	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.74412	.|0.3713	L|L	0.31664|0.31664	0.95|0.95	0.80722|0.80722	D|D	1|1	.|D;B	.|0.76494	.|0.999;0.106	.|D;B	.|0.74023	.|0.982;0.013	.|T	.|0.67673	.|-0.5610	.|10	.|0.06625	.|T	.|0.88	.|-25.1478	14.5671|14.5671	0.68185|0.68185	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|48;48	.|F5GXW5;Q99622	.|.;C10_HUMAN	.|V	-1|48	.|ENSP00000440602:G48V;ENSP00000229281:G48V	.|ENSP00000229281:G48V	.|G	+|+	.|2	.|0	C12orf57|C12orf57	6923990|6923990	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.007000|9.007000	0.93597|0.93597	2.373000|2.373000	0.80994|0.80994	0.561000|0.561000	0.74099|0.74099	.|GGT	.		0.627	C12orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401959.1	NM_138425		T	7053729	G	T	7053729	3	4	149	1	0	0	0	0	1	0	0	0	1705	1261	44	4	149	4	C12orf57	12	7053729	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		7053729	126798166	89	13369											
TAS2R43	259289	hgsc.bcm.edu	37	chr12	11244149	11244149	+	Frame_Shift_Del	DEL	G	G	-																															aggagatcacagtttgcaaaGcttttatgtggaccttggtg																								rs73064964	byFrequency	TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:11244149delG	ENST00000531678.1	-	1	763	c.680delC	c.(679-681)gctfs	p.A227fs	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	227					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		AGTTTGCAAAGCTTTTATGTG	0.393																																					p.A227fs		.											.	TAS2R43-1	0			c.680delC						.						137	119	125					12																	11244149		2179	4249	6428	SO:0001589	frameshift_variant	259289	exon1			.	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.680delC	12.37:g.11244149delG	ENSP00000431719:p.Ala227fs	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	32	17	NM_176884	0	0	0	0	0	P59546|Q645X4	Frame_Shift_Del	DEL	ENST00000531678.1	37	CCDS53749.1																																																																																			.		0.393	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884		-	11244149	G	-	11244149	7	5	149	1	0	1	0	1	0	0	0	0	15613	971	34	0	253	0	TAS2R43	12	11244149	Frame_Shift_Del	DEL	G	TCGA-MH-A55Z-01A-11D-A26P-10	4190420	11244149	122607746	90	13370											
PLEKHA5	54477	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr12	19500042	19500042	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccttgctctgttatagcAggggcccagttcatctgcct	5	13	10	13	0	3	0	1	0	2	0	4	0	4	0	3	2	3	5	3	2	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:19500042A>G	ENST00000299275.6	+	18	2406				PLEKHA5_ENST00000317589.4_Missense_Mutation_p.R839G|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.R942G|PLEKHA5_ENST00000538714.1_Intron|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.R758G|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.R765G|PLEKHA5_ENST00000355397.3_Intron	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5						reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					CTGTTATAGCAGGGGCCCAGT	0.498																																					p.R942G	Pancreas(196;329 2193 11246 14234 19524)	.											.	PLEKHA5-227	0			c.A2824G						.						91	80	83					12																	19500042		692	1591	2283	SO:0001627	intron_variant	54477	exon24			TATAGCAGGGGCC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2400+1220A>G	12.37:g.19500042A>G		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	172	47	NM_001256470	0	0	0	0	0	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.391185	0.62066	.	.	ENSG00000052126	ENST00000317589;ENST00000542828;ENST00000429027;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92	5.66	4.53	0.55603	.	0.154367	0.42420	D	0.000712	T	0.11196	0.0273	.	.	.	0.80722	D	1	B;B;B;B;B	0.27625	0.08;0.183;0.115;0.115;0.115	B;B;B;B;B	0.33690	0.12;0.168;0.081;0.081;0.031	T	0.06534	-1.0821	9	0.72032	D	0.01	-15.471	7.1521	0.25616	0.7782:0.1481:0.0737:0.0	.	839;758;765;937;942	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3	.;.;.;.;.	G	839;938;942;765;758;731	ENSP00000325155:R839G;ENSP00000404296:R942G;ENSP00000400411:R765G;ENSP00000439837:R758G;ENSP00000440371:R731G	ENSP00000325155:R839G	R	+	1	2	PLEKHA5	19391309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.764000	0.62264	2.137000	0.66172	0.528000	0.53228	AGG	.		0.498	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19500042	A	G	19500042	1	3	149	0	1	0	0	0	0	0	0	0	12085	179	7	3		3	PLEKHA5	12	19500042	Intron	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	8255893	19500042	114351853	91	13371											
KIF21A	55605	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	39709737	39709737	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggaaagaaagtacctgTgtacctccgagagagaggag	14	5	15	7	1	0	3	0	0	0	3	1	7	1	5	3	3	2	3	3	3	4	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:39709737T>C	ENST00000361418.5	-	30	3959	c.3944A>G	c.(3943-3945)cAc>cGc	p.H1315R	KIF21A_ENST00000395670.3_Missense_Mutation_p.H1315R|KIF21A_ENST00000361961.3_Missense_Mutation_p.H1302R|KIF21A_ENST00000541463.2_Intron|KIF21A_ENST00000544797.2_Intron|KIF21A_ENST00000547745.1_Intron			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1315					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				AAAGTACCTGTGTACCTCCGA	0.393																																					p.H1315R													.	KIF21A-97	0			c.A3944G						.						129	130	130					12																	39709737		2203	4300	6503	SO:0001583	missense	55605	exon30			TACCTGTGTACCT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"Kinesins", "WD repeat domain containing"	19349	protein-coding gene	gene with protein product		608283	"fibrosis of the extraocular muscles, congenital, 1"	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3944A>G	12.37:g.39709737T>C	ENSP00000354878:p.His1315Arg	Somatic	308	3		WXS	Illumina HiSeq	Phase_I	544	307	NM_001173464	0	0	0	0	0	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.099|9.099	1.003773|1.003773	0.19199|0.19199	.|.	.|.	ENSG00000139116|ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000361418|ENST00000552961	T;T;T|.	0.69306|.	-0.39;-0.34;-0.31|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.000000|.	0.56097|.	D|.	0.000032|.	T|T	0.69895|0.69895	0.3162|0.3162	L|L	0.57536|0.57536	1.79|1.79	0.43841|0.43841	D|D	0.99642|0.99642	B;B;B|.	0.22983|.	0.025;0.078;0.05|.	B;B;B|.	0.23275|.	0.045;0.04;0.037|.	T|T	0.68777|0.68777	-0.5319|-0.5319	10|5	0.14656|.	T|.	0.56|.	.|.	15.2397|15.2397	0.73458|0.73458	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1315;1302;1272|.	Q7Z4S6;Q7Z4S6-2;Q7Z4S6-3|.	KI21A_HUMAN;.;.|.	R|A	1302;1315;1272;1315|620	ENSP00000354851:H1302R;ENSP00000379029:H1315R;ENSP00000354878:H1315R|.	ENSP00000344501:H1272R|.	H|T	-|-	2|1	0|0	KIF21A|KIF21A	37996004|37996004	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.490000|5.490000	0.66881|0.66881	2.001000|2.001000	0.58596|0.58596	0.482000|0.482000	0.46254|0.46254	CAC|ACA	.		0.393	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		C	39709737	T	C	39709737	3	2	149	1	0	0	0	0	1	0	0	0	8309	1696	59	3	1116	3	KIF21A	12	39709737	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	20209695	39709737	94142158	92	13372											
SPRYD4	283377	broad.mit.edu;bcgsc.ca	37	chr12	56862411	56862411	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcacgttctttgcgcttgtgCcgctggggagccaaacgatt	6	11	13	11	4	1	0	0	0	1	0	1	2	1	1	2	2	4	4	2	2	1	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:56862411C>T	ENST00000338146.5	+	1	111	c.36C>T	c.(34-36)tgC>tgT	p.C12C	MIP_ENST00000555551.1_Intron	NM_207344.3	NP_997227	Q8WW59	SPRY4_HUMAN	SPRY domain containing 4	12	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)	7						TGCGCTTGTGCCGCTGGGGAG	0.567																																					p.C12C													.	SPRYD4-68	0			c.C36T						.						136	125	129					12																	56862411		2203	4300	6503	SO:0001819	synonymous_variant	283377	exon1			CTTGTGCCGCTGG	AL832247	CCDS8920.1	12q13.3	2006-03-09				ENSG00000176422			27468	protein-coding gene	gene with protein product							Standard	NM_207344		Approved	DKFZp686N0877	uc001sli.4	Q8WW59		ENST00000338146.5:c.36C>T	12.37:g.56862411C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	110	5	NM_207344	0	0	6	6	0	A8K7A5	Silent	SNP	ENST00000338146.5	37	CCDS8920.1																																																																																			.		0.567	SPRYD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_207344		T	56862411	C	T	56862411	2	4	149	1	0	0	0	0	0	0	0	1	15142	747	26	2		2	SPRYD4	12	56862411	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	17152674	56862411	76989484	93	13373											
SLC5A8	160728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	101588897	101588897	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagtagaatgtgcagacCacccccgttgccactaccgc	9	7	10	15	2	0	2	0	0	0	2	0	2	0	2	5	0	4	4	5	0	3	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:101588897C>T	ENST00000536262.2	-	4	1071	c.513G>A	c.(511-513)gtG>gtA	p.V171V		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						ATGTGCAGACCACCCCCGTTG	0.403																																					p.V171V	GBM(60;420 1056 13605 22380 47675)	.											.	SLC5A8-90	0			c.G513A						.						99	86	90					12																	101588897		2203	4300	6503	SO:0001819	synonymous_variant	160728	exon4			GCAGACCACCCCC	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"Solute carriers"	19119	protein-coding gene	gene with protein product		608044	"solute carrier family 5 (iodide transporter), member 8"			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.513G>A	12.37:g.101588897C>T		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	108	61	NM_145913	0	0	0	0	0		Silent	SNP	ENST00000536262.2	37	CCDS9080.1																																																																																			.		0.403	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		T	101588897	C	T	101588897	2	4	149	1	0	0	0	0	0	0	0	1	14703	581	21	2		2	SLC5A8	12	101588897	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	44726486	101588897	32262998	94	13374											
BTBD11	121551	hgsc.bcm.edu	37	chr12	107713245	107713245	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtcctggggcctggccgcGcactgtacggcggctgcgct	2	8	16	15	5	0	0	0	0	0	0	1	0	1	0	3	5	2	4	3	5	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:107713245G>A	ENST00000280758.5	+	1	1056	c.528G>A	c.(526-528)gcG>gcA	p.A176A	BTBD11_ENST00000490090.2_Silent_p.A176A|BTBD11_ENST00000420571.2_Silent_p.A176A	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	176						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GCCTGGCCGCGCACTGTACGG	0.697																																					p.A176A		.											.	BTBD11-93	0			c.G528A						.						11	10	10					12																	107713245		2095	4067	6162	SO:0001819	synonymous_variant	121551	exon1			GGCCGCGCACTGT	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.528G>A	12.37:g.107713245G>A		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	10	7	NM_001018072	0	0	0	0	0	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			.		0.697	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	107713245	G	A	107713245	2	1	149	1	0	0	0	0	0	0	0	1	1542	1074	38	1		1	BTBD11	12	107713245	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	6124348	107713245	26138650	95	13375											
PHF11	51131	bcgsc.ca	37	chr13	50098263	50098272	+	Frame_Shift_Del	DEL	CAGGACTTCT	CAGGACTTCT	-																															tcttaagaaatgcaaggaagCaggacttcttaattacttac																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	CAGGACTTCT	CAGGACTTCT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr13:50098263_50098272delCAGGACTTCT	ENST00000378319.3	+	8	721_730	c.680_689delCAGGACTTCT	c.(679-690)gcaggacttcttfs	p.AGLL227fs	PHF11_ENST00000357596.3_Frame_Shift_Del_p.AGLL188fs|PHF11_ENST00000488958.1_Frame_Shift_Del_p.AGLL188fs	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	227					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		TGCAAGGAAGCAGGACTTCTTAATTACTTA	0.329																																					p.227_230del													.	PHF11-90	0			c.680_689del						.																																			SO:0001589	frameshift_variant	51131	exon8			AGGAAGCAGGACT	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"Zinc fingers, PHD-type"	17024	protein-coding gene	gene with protein product	"IgE responsiveness (atopic)"	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.680_689delCAGGACTTCT	13.37:g.50098263_50098272delCAGGACTTCT	ENSP00000367570:p.Ala227fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_1	60	6	NM_001040443	0	0	0	0	0	Q5W0A4|Q5W0A6|Q9Y5A2	Frame_Shift_Del	DEL	ENST00000378319.3	37	CCDS31975.1																																																																																			.		0.329	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119		-	50098272	CAGGACTTCT	-	50098263	7	5	149	1	0	1	0	1	0	0	0	0	11848	710	25	0	710	0	PHF11	13	50098263	Frame_Shift_Del	DEL	CAGGACTTCT	TCGA-MH-A55Z-01A-11D-A26P-10		50098263	65071615	96	13376											
GPC6	10082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	94197565	94197565	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatacatgctgcaccacagaAatggaagacaagttaagcca	17	7	8	9	0	0	2	0	0	0	2	0	3	0	3	2	1	4	3	2	1	6	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr13:94197565A>T	ENST00000377047.4	+	2	825	c.210A>T	c.(208-210)gaA>gaT	p.E70D		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	70					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GCACCACAGAAATGGAAGACA	0.408																																					p.E70D		.											.	GPC6-90	0			c.A210T						.						154	142	146					13																	94197565		2203	4300	6503	SO:0001583	missense	10082	exon2			CACAGAAATGGAA	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.210A>T	13.37:g.94197565A>T	ENSP00000366246:p.Glu70Asp	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	95	42	NM_005708	0	0	0	0	0	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598483	0.46318	.	.	ENSG00000183098	ENST00000377047	T	0.52983	0.64	5.0	3.82	0.43975	.	0.074354	0.51477	D	0.000081	T	0.43919	0.1269	L	0.51853	1.615	0.31140	N	0.706753	B;B	0.21452	0.031;0.056	B;B	0.30646	0.118;0.101	T	0.50110	-0.8866	10	0.46703	T	0.11	.	10.667	0.45736	0.9242:0.0:0.0758:0.0	.	70;70	B4E2M1;Q9Y625	.;GPC6_HUMAN	D	70	ENSP00000366246:E70D	ENSP00000366246:E70D	E	+	3	2	GPC6	92995566	0.997000	0.39634	1.000000	0.80357	0.999000	0.98932	0.672000	0.25187	0.867000	0.35654	0.524000	0.50904	GAA	.		0.408	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		T	94197565	A	T	94197565	3	4	149	1	0	0	0	0	1	0	0	0	6622	11	1	5	216	5	GPC6	13	94197565	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	44099302	94197565	20972313	97	13377											
LRFN5	145581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	42360768	42360768	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacaaggtcaccaaggttagCaatgtttattcccaaactaa	15	10	6	10	0	1	0	1	0	0	0	2	0	2	0	2	2	2	3	2	2	7	5			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr14:42360768C>T	ENST00000298119.4	+	4	2890	c.1701C>T	c.(1699-1701)agC>agT	p.S567S	LRFN5_ENST00000554120.1_Intron|LRFN5_ENST00000554171.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	567						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CCAAGGTTAGCAATGTTTATT	0.458										HNSCC(30;0.082)																											p.S567S		.											.	LRFN5-97	0			c.C1701T						.						103	99	100					14																	42360768		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon4			GGTTAGCAATGTT	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	20360	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 8"	612811	"chromosome 14 open reading frame 146"	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1701C>T	14.37:g.42360768C>T		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	113	43	NM_152447	0	0	1	1	0	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	37	CCDS9678.1																																																																																			.		0.458	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		T	42360768	C	T	42360768	2	4	149	1	0	0	0	0	0	0	0	1	8966	709	25	2		2	LRFN5	14	42360768	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		42360768	64988772	98	13378											
NEK9	91754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	75558059	75558059	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gattaaaccttccattcctcGgtctgcttccattgttcctc	6	16	5	14	1	1	0	0	0	1	0	7	1	5	0	5	1	2	2	5	1	2	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr14:75558059G>A	ENST00000238616.5	-	19	2514	c.2356C>T	c.(2356-2358)Cga>Tga	p.R786*		NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	786	Interaction with NEK6.|Pro/Ser/Thr-rich.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		TCCATTCCTCGGTCTGCTTCC	0.567																																					p.R786X		.											.	NEK9-359	0			c.C2356T						.						116	104	108					14																	75558059		2203	4300	6503	SO:0001587	stop_gained	91754	exon19			TTCCTCGGTCTGC	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.2356C>T	14.37:g.75558059G>A	ENSP00000238616:p.Arg786*	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	70	32	NM_033116	0	0	1	1	0	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Nonsense_Mutation	SNP	ENST00000238616.5	37	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	G	41	9.014481	0.99037	.	.	ENSG00000119638	ENST00000238616	.	.	.	5.66	5.66	0.87406	.	0.295996	0.31673	N	0.007256	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.752	0.96271	0.0:0.0:1.0:0.0	.	.	.	.	X	786	.	ENSP00000238616:R786X	R	-	1	2	NEK9	74627812	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.628000	0.61282	2.668000	0.90789	0.462000	0.41574	CGA	.		0.567	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		A	75558059	G	A	75558059	4	1	149	1	0	0	0	0	0	1	0	0	10357	1124	39	1	599	1	NEK9	14	75558059	Nonsense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	33197291	75558059	31791481	99	13379											
MTMR10	54893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	31251264	31251264	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cttctcccaacaaaagaatgGgaaaagatctttagatcttg	15	11	7	8	0	3	3	0	0	3	3	4	4	3	4	1	1	1	0	1	1	7	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr15:31251264G>C	ENST00000435680.1	-	8	916	c.819C>G	c.(817-819)tcC>tcG	p.S273S	RNU6-466P_ENST00000391224.1_RNA|MTMR10_ENST00000425768.1_3'UTR|MTMR10_ENST00000563714.1_Silent_p.S191S|MTMR10_ENST00000314404.8_Silent_p.S25S	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	273	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		CAAAAGAATGGGAAAAGATCT	0.383																																					p.S273S		.											.	MTMR10-91	0			c.C819G						.						67	63	64					15																	31251264		1866	4106	5972	SO:0001819	synonymous_variant	54893	exon8			AGAATGGGAAAAG	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.819C>G	15.37:g.31251264G>C		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	85	38	NM_017762	0	0	0	2	2	Q6P4Q6	Silent	SNP	ENST00000435680.1	37	CCDS45204.1																																																																																			.		0.383	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		C	31251264	G	C	31251264	2	2	149	1	0	0	0	0	0	0	0	1	9964	1219	43	4		4	MTMR10	15	31251264	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		31251264	71280128	100	13380											
COPS2	9318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	49421727	49421727	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcttaattaattttataaGcacttgtgttctgatgtttc	10	19	7	5	0	1	1	0	1	1	0	2	1	1	1	0	1	1	4	0	1	4	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr15:49421727G>A	ENST00000388901.5	-	11	1148	c.1075C>T	c.(1075-1077)Ctt>Ttt	p.L359F	COPS2_ENST00000542928.1_Missense_Mutation_p.L295F|COPS2_ENST00000299259.6_Missense_Mutation_p.L366F	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	359	PCI.				cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		AATTTTATAAGCACTTGTGTT	0.229																																					p.L366F	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	.											.	COPS2-227	0			c.C1096T						.						24	25	24					15																	49421727		2132	4209	6341	SO:0001583	missense	9318	exon11			TTATAAGCACTTG	AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.1075C>T	15.37:g.49421727G>A	ENSP00000373553:p.Leu359Phe	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	85	35	NM_001143887	0	0	14	23	9	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Missense_Mutation	SNP	ENST00000388901.5	37	CCDS32235.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868385	0.91587	.	.	ENSG00000166200	ENST00000299259;ENST00000388901;ENST00000542928	T;T;T	0.44083	0.93;0.93;0.93	5.05	5.05	0.67936	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	H	0.96208	3.785	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.995;0.998	D	0.84887	0.0834	10	0.72032	D	0.01	-18.1449	18.7719	0.91896	0.0:0.0:1.0:0.0	.	295;367;359	B4DIH5;Q59EL2;P61201	.;.;CSN2_HUMAN	F	366;359;295	ENSP00000299259:L366F;ENSP00000373553:L359F;ENSP00000443664:L295F	ENSP00000299259:L366F	L	-	1	0	COPS2	47209019	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.747000	0.98863	2.498000	0.84270	0.655000	0.94253	CTT	.		0.229	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236		A	49421727	G	A	49421727	3	1	149	1	0	0	0	0	1	0	0	0	3739	971	34	2	268	2	COPS2	15	49421727	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	18170463	49421727	53109665	101	13381											
AP4E1	23431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	51294808	51294808	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagatcctcctgttctacTcttcctgactatttactgta	7	18	4	12	0	3	2	1	1	2	1	6	2	6	2	3	0	2	2	3	0	4	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr15:51294808T>G	ENST00000261842.5	+	21	3469	c.3363T>G	c.(3361-3363)acT>acG	p.T1121T	AP4E1_ENST00000561397.1_3'UTR|AP4E1_ENST00000560508.1_Silent_p.T1046T	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	1121					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		CCTGTTCTACTCTTCCTGACT	0.463																																					p.T1121T		.											.	AP4E1-90	0			c.T3363G						.						275	213	234					15																	51294808		2196	4294	6490	SO:0001819	synonymous_variant	23431	exon21			TTCTACTCTTCCT	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.3363T>G	15.37:g.51294808T>G		Somatic	169	0		WXS	Illumina HiSeq	Phase_I	128	69	NM_007347	0	0	0	0	0	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Silent	SNP	ENST00000261842.5	37	CCDS32240.1																																																																																			.		0.463	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51294808	T	G	51294808	2	3	149	1	0	0	0	0	0	0	0	1	752	1538	54	5		5	AP4E1	15	51294808	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	1873081	51294808	51236584	102	13382											
ADCY9	115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4164714	4164714	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacccccagacacaaactcaGgtacaaaggtaagtgcatga	16	5	8	12	0	1	2	1	1	0	1	1	2	1	2	2	2	3	3	2	2	4	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr16:4164714G>A	ENST00000294016.3	-	2	1268	c.730C>T	c.(730-732)Ctg>Ttg	p.L244L		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	244					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CACAAACTCAGGTACAAAGGT	0.552																																					p.L244L		.											.	ADCY9-139	0			c.C730T						.						58	46	50					16																	4164714		2196	4299	6495	SO:0001819	synonymous_variant	115	exon2			AACTCAGGTACAA	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"Adenylate cyclases"	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.730C>T	16.37:g.4164714G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	154	55	NM_001116	0	0	0	0	0	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			.		0.552	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4164714	G	A	4164714	2	1	149	1	0	0	0	0	0	0	0	1	301	991	35	2		2	ADCY9	16	4164714	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		4164714	86190039	103	13383											
MAP2K4	6416	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	11998978	11998978	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggagtagtgattgcccataCattgttcagttttatggtgc	8	15	11	7	1	1	1	1	1	0	0	1	2	1	2	1	2	3	3	1	2	3	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:11998978C>T	ENST00000353533.5	+	4	543	c.480C>T	c.(478-480)taC>taT	p.Y160Y	MAP2K4_ENST00000581941.1_3'UTR|MAP2K4_ENST00000415385.3_Silent_p.Y171Y	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		ATTGCCCATACATTGTTCAGT	0.373			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.Y160Y				Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4-3134	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.C480T						.						184	173	177					17																	11998978		2203	4300	6503	SO:0001819	synonymous_variant	6416	exon4			CCCATACATTGTT	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.480C>T	17.37:g.11998978C>T		Somatic	114	1		WXS	Illumina HiSeq	Phase_I	219	62	NM_003010	0	0	0	0	0	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Silent	SNP	ENST00000353533.5	37	CCDS11162.1																																																																																			.		0.373	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			T	11998978	C	T	11998978	2	4	149	1	0	0	0	0	0	0	0	1	9264	489	17	2		2	MAP2K4	17	11998978	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		11998978	69196232	104	13384											
MPRIP	23164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	17075111	17075111	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctccagaggcagcaccagcGggagctagagaaacttcgag	12	5	13	11	2	1	2	0	0	1	2	3	5	1	3	2	2	4	3	2	2	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:17075111G>A	ENST00000341712.4	+	16	2243	c.2243G>A	c.(2242-2244)cGg>cAg	p.R748Q	MPRIP_ENST00000395811.5_Missense_Mutation_p.R748Q|RNU6-767P_ENST00000384132.1_RNA|MPRIP_ENST00000444976.1_Missense_Mutation_p.R710Q|MPRIP_ENST00000395804.3_Missense_Mutation_p.R748Q|RP11-45M22.3_ENST00000584203.1_RNA			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	748	Interaction with RHOA.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CAGCACCAGCGGGAGCTAGAG	0.572																																					p.R748Q		.											.	MPRIP-90	0			c.G2243A						.						71	85	80					17																	17075111		2203	4300	6503	SO:0001583	missense	23164	exon16			ACCAGCGGGAGCT	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"Pleckstrin homology (PH) domain containing"	30321	protein-coding gene	gene with protein product	"Rho interacting protein 3"	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.2243G>A	17.37:g.17075111G>A	ENSP00000342379:p.Arg748Gln	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	288	176	NM_015134	0	0	13	38	25	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.7|29.7	5.027583|5.027583	0.93518|0.93518	.|.	.|.	ENSG00000133030|ENSG00000133030	ENST00000414263|ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	.|T;T;T;T	.|0.25579	.|1.79;2.12;2.13;2.13	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.126948	.|0.50627	.|D	.|0.000103	T|T	0.44307|0.44307	0.1287|0.1287	L|L	0.37850|0.37850	1.14|1.14	0.44373|0.44373	D|D	0.99727|0.99727	.|D;P;D	.|0.89917	.|1.0;0.777;1.0	.|D;B;D	.|0.79108	.|0.992;0.346;0.992	T|T	0.12941|0.12941	-1.0528|-1.0528	5|10	.|0.46703	.|T	.|0.11	-16.1602|-16.1602	20.032|20.032	0.97543|0.97543	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1112;748;748	.|Q9Y6X7;Q6WCQ1-2;Q6WCQ1	.|.;.;MPRIP_HUMAN	R|Q	814|710;748;748;748	.|ENSP00000400189:R710Q;ENSP00000379156:R748Q;ENSP00000379149:R748Q;ENSP00000342379:R748Q	.|ENSP00000342379:R748Q	G|R	+|+	1|2	0|0	MPRIP|MPRIP	17015836|17015836	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	9.387000|9.387000	0.97232|0.97232	2.743000|2.743000	0.94032|0.94032	0.655000|0.655000	0.94253|0.94253	GGG|CGG	.		0.572	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17075111	G	A	17075111	3	1	149	1	0	0	0	0	1	0	0	0	9768	1116	39	1	2305	1	MPRIP	17	17075111	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	5076133	17075111	64120099	105	13385											
PCGF2	7703	broad.mit.edu	37	chr17	36891628	36891628	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgggggaggtagggtgggTggctggaggcccatgggaac	7	6	23	5	0	0	0	0	0	0	0	0	3	0	3	1	9	1	2	1	9	2	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:36891628T>G	ENST00000580830.1	-	12	1584	c.883A>C	c.(883-885)Acc>Ccc	p.T295P	PCGF2_ENST00000581345.1_Missense_Mutation_p.T295P|PCGF2_ENST00000578109.1_3'UTR|PCGF2_ENST00000585100.1_3'UTR|PCGF2_ENST00000360797.2_Missense_Mutation_p.T295P|PCGF2_ENST00000579882.1_3'UTR			P35227	PCGF2_HUMAN	polycomb group ring finger 2	295	Pro/Ser-rich.				anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					GTAGGGTGGGTGGCTGGAGGC	0.682											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T295P													.	PCGF2-658	0			c.A883C						.						16	12	13					17																	36891628		2187	4280	6467	SO:0001583	missense	7703	exon11			GGTGGGTGGCTGG	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.883A>C	17.37:g.36891628T>G	ENSP00000461961:p.Thr295Pro	Somatic	38	2	866	WXS	Illumina HiSeq	Phase_I	93	7	NM_007144	0	0	162	163	1	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	37	CCDS32638.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.344960	0.24426	.	.	ENSG00000056661	ENST00000360797	T	0.31247	1.5	4.92	-0.193	0.13244	.	0.651897	0.15163	N	0.277024	T	0.13628	0.0330	N	0.04508	-0.205	0.26765	N	0.969921	B	0.02656	0.0	B	0.01281	0.0	T	0.23583	-1.0184	10	0.23891	T	0.37	-6.6811	12.5227	0.56069	0.0:0.0:0.6437:0.3563	.	295	P35227	PCGF2_HUMAN	P	295	ENSP00000354033:T295P	ENSP00000354033:T295P	T	-	1	0	PCGF2	34145154	0.004000	0.15560	0.536000	0.28039	0.978000	0.69477	-0.673000	0.05239	-0.232000	0.09811	0.459000	0.35465	ACC	.		0.682	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		G	36891628	T	G	36891628	3	3	149	1	0	0	0	0	1	0	0	0	11601	1696	59	5	155	5	PCGF2	17	36891628	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	19816517	36891628	44303582	106	13386											
PSMC3IP	29893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40729246	40729246	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcacctgatccgcaaaataGatcttctgcttgccgtacat	10	12	6	13	2	3	2	1	1	2	1	4	2	4	2	3	0	3	3	3	0	4	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:40729246G>C	ENST00000393795.3	-	3	318	c.210C>G	c.(208-210)atC>atG	p.I70M	PSMC3IP_ENST00000590760.1_De_novo_Start_OutOfFrame|PSMC3IP_ENST00000587209.1_Missense_Mutation_p.I7M|PSMC3IP_ENST00000253789.5_Missense_Mutation_p.I70M	NM_001256015.1|NM_001256016.1|NM_016556.3	NP_001242944.1|NP_001242945.1|NP_057640.1	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein	70					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)|regulation of RNA biosynthetic process (GO:2001141)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(2)	7		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCGCAAAATAGATCTTCTGCT	0.532																																					p.I70M		.											.	PSMC3IP-92	0			c.C210G						.						163	113	130					17																	40729246		2203	4300	6503	SO:0001583	missense	29893	exon3			AAAATAGATCTTC	AB030304, NM_013290, BC008792	CCDS11431.1, CCDS45688.1, CCDS59289.1	17q21.2	2012-04-10				ENSG00000131470		"Proteasome (prosome, macropain) subunits"	17928	protein-coding gene	gene with protein product	"TBP-1 interacting protein"	608665				7490091, 10806355, 11739747	Standard	NM_016556		Approved	TBPIP, GT198, HUMGT198A	uc002iai.3	Q9P2W1		ENST00000393795.3:c.210C>G	17.37:g.40729246G>C	ENSP00000377384:p.Ile70Met	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	173	66	NM_016556	0	0	3	8	5	C5ILB7|Q14458|Q8WXG2|Q96HA2	Missense_Mutation	SNP	ENST00000393795.3	37	CCDS45688.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.105854	0.77096	.	.	ENSG00000131470	ENST00000393795;ENST00000253789	T;T	0.60797	0.16;0.16	5.8	-1.78	0.07957	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.051811	0.85682	D	0.000000	T	0.71753	0.3377	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.71738	-0.4502	10	0.72032	D	0.01	-11.3368	11.3412	0.49533	0.0598:0.0:0.3656:0.5746	.	70;70	Q9P2W1-2;Q9P2W1	.;HOP2_HUMAN	M	70	ENSP00000377384:I70M;ENSP00000253789:I70M	ENSP00000253789:I70M	I	-	3	3	PSMC3IP	37982772	0.947000	0.32204	0.954000	0.39281	0.978000	0.69477	-0.022000	0.12480	-0.533000	0.06323	0.655000	0.94253	ATC	.		0.532	PSMC3IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450427.1	NM_013290		C	40729246	G	C	40729246	3	2	149	1	0	0	0	0	1	0	0	0	12717	932	33	4	467	4	PSMC3IP	17	40729246	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	3837618	40729246	40465964	107	13387											
NPEPPS	9520	broad.mit.edu	37	chr17	45682709	45682709	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctatcccaggctcgagctgGaatcattagcactgtagagg	10	9	11	11	1	1	1	1	0	0	1	3	3	2	2	2	3	2	4	2	3	4	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:45682709G>A	ENST00000322157.4	+	17	2123	c.1886G>A	c.(1885-1887)gGa>gAa	p.G629E	NPEPPS_ENST00000530173.1_Missense_Mutation_p.G625E|NPEPPS_ENST00000544660.1_Missense_Mutation_p.G549E|RP11-580I16.2_ENST00000582389.1_RNA|RP11-580I16.2_ENST00000582066.1_RNA	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	629					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						GCTCGAGCTGGAATCATTAGC	0.403																																					p.G629E													.	NPEPPS-90	0			c.G1886A						.						65	57	59					17																	45682709		1841	4087	5928	SO:0001583	missense	9520	exon17			GAGCTGGAATCAT	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"puromycin-sensitive aminopeptidase", "metalloproteinase MP100"	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1886G>A	17.37:g.45682709G>A	ENSP00000320324:p.Gly629Glu	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	130	6	NM_006310	0	0	0	0	0	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.044695	0.93685	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000544660	T;T;T	0.10860	2.83;2.83;2.83	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	M	0.86864	2.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.997	T	0.32798	-0.9893	10	0.72032	D	0.01	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	625;312;629	E9PLK3;B7Z1H4;P55786	.;.;PSA_HUMAN	E	625;629;549	ENSP00000433287:G625E;ENSP00000320324:G629E;ENSP00000442461:G549E	ENSP00000320324:G629E	G	+	2	0	NPEPPS	43037708	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	GGA	.		0.403	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		A	45682709	G	A	45682709	3	1	149	1	0	0	0	0	1	0	0	0	10601	1174	41	2	1952	2	NPEPPS	17	45682709	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	4953463	45682709	35512501	108	13388											
SLC35B1	10237	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	47780367	47780367	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacacaaccgtcataaagaTgaagctctagagaaagataa	20	7	7	7	1	2	4	1	1	1	3	2	5	2	4	1	0	3	1	1	0	8	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:47780367T>G	ENST00000240333.6	-	8	890	c.769A>C	c.(769-771)Atc>Ctc	p.I257L	SLC35B1_ENST00000415270.2_Missense_Mutation_p.I294L			P78383	S35B1_HUMAN	solute carrier family 35, member B1	257					transport (GO:0006810)|UDP-galactose transmembrane transport (GO:0072334)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	UDP-galactose transmembrane transporter activity (GO:0005459)			endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(1)	7						GTCATAAAGATGAAGCTCTAG	0.468																																					p.I257L													.	SLC35B1-90	0			c.A769C						.						119	120	120					17																	47780367		2203	4300	6503	SO:0001583	missense	10237	exon8			TAAAGATGAAGCT	D16978	CCDS11552.1, CCDS11552.2	17q21.32	2013-05-22			ENSG00000121073	ENSG00000121073		"Solute carriers"	20798	protein-coding gene	gene with protein product		610790				9010752	Standard	NM_005827		Approved	UGTREL1	uc002iph.1	P78383	OTTHUMG00000161638	ENST00000240333.6:c.769A>C	17.37:g.47780367T>G	ENSP00000240333:p.Ile257Leu	Somatic	165	1		WXS	Illumina HiSeq	Phase_I	201	72	NM_005827	0	0	1	1	0	B4DEC4|J3KQV4|Q96EW7	Missense_Mutation	SNP	ENST00000240333.6	37	CCDS11552.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.828281	0.90955	.	.	ENSG00000121073	ENST00000240333;ENST00000415270;ENST00000504260;ENST00000502406;ENST00000503334	T;T;T	0.39056	1.1;1.1;1.1	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.67458	0.2895	M	0.88570	2.965	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.63381	0.914;0.914	T	0.74604	-0.3610	10	0.62326	D	0.03	0.0724	14.8245	0.70101	0.0:0.0:0.0:1.0	.	190;257	D3DTX1;P78383	.;S35B1_HUMAN	L	257;294;133;133;190	ENSP00000240333:I257L;ENSP00000409548:I294L;ENSP00000423323:I190L	ENSP00000240333:I257L	I	-	1	0	SLC35B1	45135366	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.645000	0.83430	2.153000	0.67306	0.533000	0.62120	ATC	.		0.468	SLC35B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365564.2	NM_005827		G	47780367	T	G	47780367	3	3	149	1	0	0	0	0	1	0	0	0	14607	1464	51	5	207	5	SLC35B1	17	47780367	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	2097658	47780367	33414843	109	13389											
TRIM25	7706	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	54969126	54969126	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccagaaagccgggtacaaagCctcagtaaagtccaccctga	14	5	9	13	1	1	2	1	1	0	1	2	2	2	2	5	1	3	2	5	1	5	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:54969126C>G	ENST00000316881.4	-	9	1877	c.1828G>C	c.(1828-1830)Gct>Cct	p.A610P	MIR3614_ENST00000581261.1_RNA|TRIM25_ENST00000573108.1_5'Flank|RP11-670E13.5_ENST00000574826.1_RNA|TRIM25_ENST00000537230.1_Missense_Mutation_p.A610P	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	610	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					GGGTACAAAGCCTCAGTAAAG	0.547																																					p.A610P		.											.	TRIM25-289	0			c.G1828C						.						58	50	53					17																	54969126		2203	4300	6503	SO:0001583	missense	7706	exon9			ACAAAGCCTCAGT	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	12932	protein-coding gene	gene with protein product		600453	"zinc finger protein 147 (estrogen-responsive finger protein)", "tripartite motif-containing 25"	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1828G>C	17.37:g.54969126C>G	ENSP00000323889:p.Ala610Pro	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	194	116	NM_005082	0	0	0	1	1		Missense_Mutation	SNP	ENST00000316881.4	37	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967214	0.53507	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.56103	0.48;0.48	4.87	4.87	0.63330	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122762	0.36374	N	0.002631	T	0.44787	0.1310	N	0.02345	-0.59	0.58432	D	0.999993	D	0.89917	1.0	D	0.83275	0.996	T	0.43798	-0.9369	10	0.02654	T	1	.	18.0042	0.89205	0.0:1.0:0.0:0.0	.	610	Q14258	TRI25_HUMAN	P	610	ENSP00000323889:A610P;ENSP00000445961:A610P	ENSP00000323889:A610P	A	-	1	0	TRIM25	52324125	0.999000	0.42202	0.446000	0.26920	0.105000	0.19272	3.797000	0.55514	2.251000	0.74343	0.561000	0.74099	GCT	.		0.547	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		G	54969126	C	G	54969126	3	3	149	1	0	0	0	0	1	0	0	0	16532	739	26	4	68	4	TRIM25	17	54969126	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	7188759	54969126	26226084	110	13390											
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	21508090	21508090	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgtgttcgtaatcagattTaacatttctacgcctgcttt	8	18	6	9	2	3	1	1	0	2	1	4	1	3	1	1	0	3	3	1	0	3	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr18:21508090T>C	ENST00000313654.9	+	63	8422	c.8181T>C	c.(8179-8181)ttT>ttC	p.F2727F	LAMA3_ENST00000399516.3_Silent_p.F2671F|LAMA3_ENST00000269217.6_Silent_p.F1118F|LAMA3_ENST00000587184.1_Silent_p.F1062F|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2727	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TAATCAGATTTAACATTTCTA	0.408																																					p.F2727F		.											.	LAMA3-100	0			c.T8181C						.						114	97	103					18																	21508090		2203	4300	6503	SO:0001819	synonymous_variant	3909	exon63			CAGATTTAACATT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8181T>C	18.37:g.21508090T>C		Somatic	117	0		WXS	Illumina HiSeq	Phase_I	137	50	NM_198129	0	0	0	0	0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			.		0.408	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		C	21508090	T	C	21508090	2	2	149	1	0	0	0	0	0	0	0	1	8628	1751	61	3		3	LAMA3	18	21508090	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		21508090	56569158	111	13391											
ZNF407	55628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	72345617	72345618	+	Missense_Mutation	DNP	GC	GC	AT																															tcaccagtatagttatttatGcaaagtgtgtaagtattaca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr18:72345617_72345618GC>AT	ENST00000299687.5	+	1	2642_2643	c.2642_2643GC>AT	c.(2641-2643)tGC>tAT	p.C881Y	ZNF407_ENST00000309902.6_Missense_Mutation_p.C881Y|ZNF407_ENST00000577538.1_Missense_Mutation_p.C881Y|ZNF407_ENST00000582337.1_Missense_Mutation_p.C881Y	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	881					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		AGTTATTTATGCAAAGTGTGTA	0.401																																					p.C881Y		.											.	ZNF407-92	0			c.C2643T						.																																			SO:0001583	missense	55628	exon1			TTTATGCAAAGTG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"Zinc fingers, C2H2-type"	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		Exception_encountered	18.37:g.72345617_72345618delinsAT	ENSP00000299687:p.Cys881Tyr	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	132	38	NM_001146190	0	0	0	0	0	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	DNP	ENST00000299687.5	37	CCDS45885.1																																																																																			.		0.401	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		AT	72345618	GC	AT	72345617	3	1	149	1	0	0	0	0	1	0	0	0	17919	1319	46	2	2644	2	ZNF407	18	72345617	Missense_Mutation	DNP	GC	TCGA-MH-A55Z-01A-11D-A26P-10	50837527	72345617	5731631	112	13392											
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	11134305	11134305	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgaggcccagttgcccgaaAaggtgatggagttttgaggg	9	9	16	7	2	0	2	0	2	0	0	1	5	0	3	2	4	1	2	2	4	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr19:11134305A>G	ENST00000429416.3	+	21	3252	c.2971A>G	c.(2971-2973)Aag>Gag	p.K991E	SMARCA4_ENST00000444061.3_Missense_Mutation_p.K991E|SMARCA4_ENST00000590574.1_Missense_Mutation_p.K991E|SMARCA4_ENST00000413806.3_Missense_Mutation_p.K991E|SMARCA4_ENST00000358026.2_Missense_Mutation_p.K991E|SMARCA4_ENST00000450717.3_Missense_Mutation_p.K991E|SMARCA4_ENST00000589677.1_Missense_Mutation_p.K991E|SMARCA4_ENST00000541122.2_Missense_Mutation_p.K991E|SMARCA4_ENST00000344626.4_Missense_Mutation_p.K991E	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	991					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GTTGCCCGAAAAGGTGATGGA	0.607			"F, N, Mis"		NSCLC																																p.K991E		.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	.	SMARCA4-1523	1	Unknown(1)	lung(1)	c.A2971G						.						37	34	35					19																	11134305		2202	4299	6501	SO:0001583	missense	6597	exon20			CCCGAAAAGGTGA	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"SNF2-like 4", "global transcription activator homologous sequence", "sucrose nonfermenting-like 4", "mitotic growth and transcription activator", "BRM/SWI2-related gene 1", "homeotic gene regulator", "nuclear protein GRB1", "brahma protein-like 1", "ATP-dependent helicase SMARCA4"	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2971A>G	19.37:g.11134305A>G	ENSP00000395654:p.Lys991Glu	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	86	32	NM_003072	0	0	0	0	0	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.303884	0.81136	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46;-3.46;-3.46;-3.46	4.9	4.9	0.64082	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98601	0.9532	H	0.99705	4.715	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.996;0.996;0.996;0.992;0.981;0.999;0.996;0.996	D	0.99004	1.0812	10	0.87932	D	0	-39.7655	13.6333	0.62208	1.0:0.0:0.0:0.0	.	991;991;991;991;991;211;991;991	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	E	991;991;1055;991;991;991;991;991	ENSP00000395654:K991E;ENSP00000350720:K991E;ENSP00000343896:K991E;ENSP00000445036:K991E;ENSP00000392837:K991E;ENSP00000397783:K991E;ENSP00000414727:K991E	ENSP00000343896:K991E	K	+	1	0	SMARCA4	10995305	1.000000	0.71417	0.964000	0.40570	0.535000	0.34838	8.855000	0.92236	2.055000	0.61198	0.533000	0.62120	AAG	.		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11134305	A	G	11134305	3	3	149	1	0	0	0	0	1	0	0	0	14802	15	1	3	3045	3	SMARCA4	19	11134305	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		11134305	47994678	113	13393											
CYP2A13	1553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	41599643	41599643	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaccaccctgcgctacggtTtcctgctgctcatgaagcac	7	9	9	16	2	1	1	1	1	0	0	2	1	2	1	3	1	5	6	3	1	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr19:41599643T>G	ENST00000330436.3	+	6	940	c.940T>G	c.(940-942)Ttc>Gtc	p.F314V		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	314					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	GCGCTACGGTTTCCTGCTGCT	0.567																																					p.F314V		.											.	CYP2A13-93	0			c.T940G						.						89	77	81					19																	41599643		2203	4300	6503	SO:0001583	missense	1553	exon6			TACGGTTTCCTGC	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"Cytochrome P450s"	2608	protein-coding gene	gene with protein product		608055	"cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.940T>G	19.37:g.41599643T>G	ENSP00000332679:p.Phe314Val	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	113	43	NM_000766	0	0	0	0	0	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	12.81	2.049285	0.36181	.	.	ENSG00000197838	ENST00000330436	T	0.70045	-0.45	4.58	4.58	0.56647	.	0.157726	0.43919	D	0.000512	T	0.63698	0.2533	N	0.17082	0.46	0.29694	N	0.840704	P	0.51537	0.946	P	0.61003	0.882	T	0.62310	-0.6881	10	0.66056	D	0.02	.	8.6585	0.34077	0.1706:0.0:0.0:0.8293	.	314	Q16696	CP2AD_HUMAN	V	314	ENSP00000332679:F314V	ENSP00000332679:F314V	F	+	1	0	CYP2A13	46291483	0.124000	0.22315	0.995000	0.50966	0.015000	0.08874	0.497000	0.22514	1.945000	0.56424	0.397000	0.26171	TTC	.		0.567	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		G	41599643	T	G	41599643	3	3	149	1	0	0	0	0	1	0	0	0	4167	1841	64	5	962	5	CYP2A13	19	41599643	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	30465338	41599643	17529340	114	13394											
C20orf117	140710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	35438421	35438421	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaattgtcggcctcctcCtttcgtagctgccgctcctg	4	14	9	14	3	0	1	0	1	0	0	5	1	3	1	5	1	2	3	5	1	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr20:35438421C>G	ENST00000357779.3	-	7	2159	c.1833G>C	c.(1831-1833)aaG>aaC	p.K611N	SOGA1_ENST00000456801.2_Missense_Mutation_p.K452N|SOGA1_ENST00000279034.6_Missense_Mutation_p.K611N|SOGA1_ENST00000237536.4_Missense_Mutation_p.K849N			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	611					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						CGGCCTCCTCCTTTCGTAGCT	0.602																																					p.K849N		.											.	.	0			c.G2547C						.						30	32	31					20																	35438421		1994	4177	6171	SO:0001583	missense	140710	exon7			CTCCTCCTTTCGT	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"suppressor of glucose by autophagy", "suppressor of glucose from autophagy"		"chromosome 20 open reading frame 117", "KIAA0889"	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1833G>C	20.37:g.35438421C>G	ENSP00000350424:p.Lys611Asn	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	69	26	NM_080627	0	0	0	0	0	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	C	19.13	3.768785	0.69878	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.15	0.757	0.18427	.	0.174867	0.47852	D	0.000216	T	0.30417	0.0764	L	0.36672	1.1	0.34718	D	0.728409	P	0.51351	0.944	B	0.44163	0.443	T	0.38564	-0.9655	10	0.31617	T	0.26	-53.0208	8.3632	0.32372	0.0:0.5833:0.0:0.4167	.	611	O94964-4	.	N	849;611;452;611	ENSP00000237536:K849N;ENSP00000279034:K611N;ENSP00000413886:K452N;ENSP00000350424:K611N	ENSP00000237536:K849N	K	-	3	2	KIAA0889	34871835	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	0.612000	0.24283	0.319000	0.23209	0.561000	0.74099	AAG	.		0.602	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		G	35438421	C	G	35438421	3	3	149	1	0	0	0	0	1	0	0	0	2089	680	24	4	2536	4	C20orf117	20	35438421	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		35438421	27587099	115	13395											
NPEPL1	79716	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	57282247	57282247	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggggccttcagagccgcAatcaagcaggtgagtgggcc	8	6	16	11	1	2	2	2	1	0	1	2	2	2	2	3	4	2	2	3	4	2	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr20:57282247A>C	ENST00000356091.6	+	7	1179	c.891A>C	c.(889-891)gcA>gcC	p.A297A	NPEPL1_ENST00000525817.1_Silent_p.A249A|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Silent_p.A269A	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	297						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TCAGAGCCGCAATCAAGCAGG	0.687																																					p.A297A		.											.	.	0			c.A891C						.						11	17	15					20																	57282247		1969	4059	6028	SO:0001819	synonymous_variant	79716	exon7			AGCCGCAATCAAG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.891A>C	20.37:g.57282247A>C		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	20	9	NM_024663	0	0	0	0	0	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			.		0.687	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		C	57282247	A	C	57282247	2	2	149	1	0	0	0	0	0	0	0	1	10600	117	5	5		5	NPEPL1	20	57282247	Silent	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	21843826	57282247	5743273	116	13396											
RRP1B	23076	broad.mit.edu	37	chr21	45107950	45107950	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aacagccacaccacgctgccCcagcgcaggaggctgcagaa	12	2	11	16	2	0	1	0	0	0	1	0	2	0	2	4	2	5	4	4	2	2	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr21:45107950C>G	ENST00000340648.4	+	13	1812	c.1695C>G	c.(1693-1695)ccC>ccG	p.P565P		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	565					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		CCACGCTGCCCCAGCGCAGGA	0.632																																					p.P565P													.	RRP1B-91	0			c.C1695G						.						12	14	13					21																	45107950		2190	4292	6482	SO:0001819	synonymous_variant	23076	exon13			GCTGCCCCAGCGC	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 136"	610654	"KIAA0179", "ribosomal RNA processing 1 homolog B (S. cerevisiae)"	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.1695C>G	21.37:g.45107950C>G		Somatic	17	0		WXS	Illumina HiSeq	Phase_I	31	15	NM_015056	0	0	0	0	0	Q8TBZ4	Silent	SNP	ENST00000340648.4	37	CCDS33577.1																																																																																			.		0.632	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056		G	45107950	C	G	45107950	2	3	149	1	0	0	0	0	0	0	0	1	13720	610	22	4		4	RRP1B	21	45107950	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		45107950	3021945	117	13397											
KRTAP10-11	386678	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	46066418	46066418	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgctccagcgcttactccGactcctggcaggtggacgac	6	9	11	15	3	1	0	0	0	1	0	4	3	4	1	3	3	3	3	3	3	1	1	rs371095766		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr21:46066418G>A	ENST00000334670.8	+	1	88	c.43G>A	c.(43-45)Gac>Aac	p.D15N	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	15						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CGCTTACTCCGACTCCTGGCA	0.677																																					p.D15N													.	KRTAP10-11-91	0			c.G43A						.	G	ASN/ASP,	0,4400		0,0,2200	61	67	65		43,	3.7	0.2	21		65	2,8586	2.2+/-6.3	0,2,4292	no	missense,intron	TSPEAR,KRTAP10-11	NM_198692.2,NM_144991.2	23,	0,2,6492	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,	15/299,	46066418	2,12986	2200	4294	6494	SO:0001583	missense	386678	exon1			TACTCCGACTCCT	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"Keratin associated proteins"	20528	protein-coding gene	gene with protein product			"keratin associated protein 10-11"	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.43G>A	21.37:g.46066418G>A	ENSP00000334197:p.Asp15Asn	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	93	35	NM_198692	0	0	0	0	0	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	g	5.038	0.192708	0.09599	0.0	2.33E-4	ENSG00000243489	ENST00000334670	T	0.02812	4.15	3.71	3.71	0.42584	.	.	.	.	.	T	0.03011	0.0089	L	0.53617	1.68	0.09310	N	1	D	0.53462	0.96	B	0.31390	0.129	T	0.48670	-0.9015	9	0.25106	T	0.35	.	12.9535	0.58413	0.0:0.0:1.0:0.0	.	15	P60412	KR10B_HUMAN	N	15	ENSP00000334197:D15N	ENSP00000334197:D15N	D	+	1	0	KRTAP10-11	44890846	0.000000	0.05858	0.176000	0.23000	0.039000	0.13416	0.005000	0.13129	1.614000	0.50241	0.462000	0.41574	GAC	.		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		A	46066418	G	A	46066418	3	1	149	1	0	0	0	0	1	0	0	0	8528	1058	37	1	45	1	KRTAP10-11	21	46066418	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	958468	46066418	2063477	118	13398											
BID	637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	18226632	18226632	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcagtctgcagctcatcgtAgccctcccactggggagcca	8	8	10	15	1	3	0	2	0	1	0	5	1	4	1	3	2	4	3	3	2	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr22:18226632A>G	ENST00000399774.3	-	3	329	c.160T>C	c.(160-162)Tac>Cac	p.Y54H	BID_ENST00000399767.1_5'UTR|BID_ENST00000551952.1_Missense_Mutation_p.Y54H|BID_ENST00000473439.1_5'UTR|BID_ENST00000342111.5_Missense_Mutation_p.Y54H|BID_ENST00000399765.1_Intron|BID_ENST00000317361.7_Missense_Mutation_p.Y100H	NM_001196.3|NM_001244569.1	NP_001187.1|NP_001231498.1	P55957	BID_HUMAN	BH3 interacting domain death agonist	54					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|brain development (GO:0007420)|establishment of protein localization to membrane (GO:0090150)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|intrinsic apoptotic signaling pathway (GO:0097193)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of cell proliferation (GO:0042127)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|release of cytochrome c from mitochondria (GO:0001836)|response to estradiol (GO:0032355)|signal transduction in response to DNA damage (GO:0042770)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial membrane (GO:0032592)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	death receptor binding (GO:0005123)			large_intestine(2)|ovary(1)	3		all_epithelial(15;0.198)		Lung(27;0.0419)		AGCTCATCGTAGCCCTCCCAC	0.632																																					p.Y100H		.											.	BID-1083	0			c.T298C						.						49	50	50					22																	18226632		2203	4300	6503	SO:0001583	missense	637	exon3			CATCGTAGCCCTC	AF042083	CCDS13747.1, CCDS13748.1, CCDS13749.1	22q11.2	2014-03-07			ENSG00000015475	ENSG00000015475		"Endogenous ligands"	1050	protein-coding gene	gene with protein product		601997				8918887, 9721221	Standard	NM_001244567		Approved		uc002znc.2	P55957	OTTHUMG00000150087	ENST00000399774.3:c.160T>C	22.37:g.18226632A>G	ENSP00000382674:p.Tyr54His	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	58	16	NM_197966	0	0	16	17	1	Q549M7|Q71T04|Q7Z4M9|Q8IY86	Missense_Mutation	SNP	ENST00000399774.3	37	CCDS13748.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.641884	0.47153	.	.	ENSG00000015475	ENST00000317361;ENST00000399774;ENST00000342111;ENST00000551952	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.08	-10.2	0.00374	.	2.388480	0.01610	N	0.022462	T	0.11623	0.0283	L	0.29908	0.895	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.10450	0.002;0.005	T	0.13818	-1.0495	10	0.14656	T	0.56	.	7.3234	0.26540	0.4392:0.3405:0.2203:0.0	.	54;100	P55957;P55957-2	BID_HUMAN;.	H	100;54;54;54	ENSP00000318822:Y100H;ENSP00000382674:Y54H;ENSP00000344594:Y54H;ENSP00000449236:Y54H	ENSP00000318822:Y100H	Y	-	1	0	BID	16606632	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.197000	0.01240	-1.410000	0.02035	-0.429000	0.05907	TAC	.		0.632	BID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316178.1	NM_197966		G	18226632	A	G	18226632	3	3	149	1	0	0	0	0	1	0	0	0	1431	420	15	3	443	3	BID	22	18226632	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		18226632	33077934	119	13399											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	160	41	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	149	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	11658930	29885562	21419004	120	13400			1	39		3	3	77	N	T_G_-	4.21061e-08
NEFH	4744	broad.mit.edu	37	chr22	29885622	29885623	+	In_Frame_Ins	INS	-	-	AGGAAG																															agaggccaagtcccctgagaINSaggccaagtccccagtgaag																								rs267607534|rs267607535		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr22:29885622_29885623insAGGAAG	ENST00000310624.6	+	4	2026_2027	c.1993_1994insAGGAAG	c.(1993-1995)aag>aAGGAAGag	p.665_666insEE		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	671	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GTCCCCTGAGAAGGCCAAGTCC	0.579																																					p.K665delinsKEE													.	NEFH-90	0			c.1993_1994insAGGAAG						.																																			SO:0001652	inframe_insertion	4744	exon4			CCTGAGAAGGCCA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	Exception_encountered	22.37:g.29885622_29885623insAGGAAG	ENSP00000311997:p.Lys665_Ala666insGluGlu	Somatic	342	0		WXS	Illumina HiSeq	Phase_I	294	8	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																			.		0.579	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		AGGAAG	29885623	-	AGGAAG	29885622	7	5	149	1	0	1	1	0	0	0	0	0	10340	247	9	0	2007	0	NEFH	22	29885622	In_Frame_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10	60	29885622	21418944	121	13401			1	39		3	3	77	N	T_G_-	4.21061e-08
NEFH	4744	hgsc.bcm.edu	37	chr22	29885638	29885638	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagaaggccaagtccccagTgaaggcagaagcaaagtccc	14	4	12	11	0	0	3	0	2	0	2	2	4	2	3	4	2	1	2	4	2	5	0	rs267607535|rs190692435		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr22:29885638T>A	ENST00000310624.6	+	4	2042	c.2009T>A	c.(2008-2010)gTg>gAg	p.V670E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	676	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGTCCCCAGTGAAGGCAGAA	0.562																																					p.V670E		.											.	NEFH-90	0			c.T2009A						.						93	100	98					22																	29885638		2203	4299	6502	SO:0001583	missense	4744	exon4			CCCCAGTGAAGGC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2009T>A	22.37:g.29885638T>A	ENSP00000311997:p.Val670Glu	Somatic	385	0		WXS	Illumina HiSeq	Phase_I	332	18	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.746577	0.00086	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.82344	-1.6	4.7	1.26	0.21427	.	1.045180	0.07584	N	0.920821	T	0.75162	0.3812	N	0.24115	0.695	0.09310	N	1	B	0.31640	0.333	B	0.41202	0.35	T	0.64050	-0.6498	10	0.45353	T	0.12	.	3.8398	0.08909	0.1553:0.2981:0.0:0.5465	.	676	P12036	NFH_HUMAN	E	670	ENSP00000311997:V670E	ENSP00000311997:V670E	V	+	2	0	NEFH	28215638	0.968000	0.33430	0.005000	0.12908	0.183000	0.23260	0.000000	0.12993	-0.045000	0.13468	0.402000	0.26972	GTG	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885638	T	A	29885638	3	1	149	1	0	0	0	0	1	0	0	0	10340	1696	59	5	2023	5	NEFH	22	29885638	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	16	29885638	21418928	122	13402			1	39		3	3	77	N	T_G_-	4.21061e-08
SFRS17A	8227	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	1719998	1719998	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcctgtcgtgtggtcccCgaggatggctctccagagaa	7	9	13	12	2	1	1	0	0	1	1	5	4	3	2	4	3	1	2	4	3	1	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chrX:1719998C>T	ENST00000313871.3	+	5	1795	c.1599C>T	c.(1597-1599)ccC>ccT	p.P533P		NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	533					B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						GTGTGGTCCCCGAGGATGGCT	0.657													c|||	1	0.000199681	0	0	5008	,	,		14923	0.001		0	False		,,,				2504	0				p.P533P		.											.	AKAP17A-40	0			c.C1599T						.						57	56	56					X																	1719998		2203	4296	6499	SO:0001819	synonymous_variant	8227	exon5			GGTCCCCGAGGAT	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"Pseudoautosomal regions / PAR1", "A-kinase anchor proteins"	18783	protein-coding gene	gene with protein product		312095, 465000	"chromosome X and Y open reading frame 3", "splicing factor, arginine/serine-rich 17A"	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.1599C>T	X.37:g.1719998C>T		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	96	7	NM_005088	0	0	11	12	1	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Silent	SNP	ENST00000313871.3	37	CCDS14116.1																																																																																			.		0.657	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		T	1719998	C	T	1719998	2	4	149	1	0	0	0	0	0	0	0	1	14205	639	23	1		1	SFRS17A	23	1719998	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		1719998	153550562	123	13403											
LPAR4	2846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	78010716	78010716	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcaagatctctggaactgCattccttaccaacatctatg	11	12	6	12	0	2	1	0	0	2	1	4	2	3	2	2	1	5	2	2	1	5	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chrX:78010716C>A	ENST00000435339.3	+	2	736	c.350C>A	c.(349-351)gCa>gAa	p.A117E		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	117					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						TCTGGAACTGCATTCCTTACC	0.423																																					p.A117E		.											.	LPAR4-133	0			c.C350A						.						190	152	165					X																	78010716		2203	4299	6502	SO:0001583	missense	2846	exon2			GAACTGCATTCCT	U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.350C>A	X.37:g.78010716C>A	ENSP00000408205:p.Ala117Glu	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	110	92	NM_005296	0	0	0	0	0	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	37	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.002367	0.54254	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.38077	1.16;1.16	4.21	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.59293	0.2183	M	0.80183	2.485	0.50171	D	0.999859	D	0.63880	0.993	D	0.63877	0.919	T	0.66771	-0.5839	10	0.72032	D	0.01	.	14.3969	0.67018	0.0:1.0:0.0:0.0	.	117	Q99677	LPAR4_HUMAN	E	117	ENSP00000408205:A117E;ENSP00000362398:A117E	ENSP00000362398:A117E	A	+	2	0	LPAR4	77897372	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.452000	0.60054	1.943000	0.56356	0.422000	0.28245	GCA	.		0.423	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		A	78010716	C	A	78010716	3	1	149	1	0	0	0	0	1	0	0	0	8932	710	25	4	352	4	LPAR4	23	78010716	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	76290718	78010716	77259844	124	13404											
MECR	51102	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	29557328	29557328	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgcggagtaggaggaggCggcaggtccgtgacagccag	9	4	20	8	3	0	1	0	1	0	0	1	5	1	5	2	7	2	2	2	7	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:29557328C>T	ENST00000263702.6	-	1	116	c.91G>A	c.(91-93)Gcc>Acc	p.A31T	MECR_ENST00000489248.1_5'UTR|MECR_ENST00000373791.3_5'UTR			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	31					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		TAGGAGGAGGCGGCAGGTCCG	0.701																																					p.A31T		.											.	MECR-91	0			c.G91A						.						9	12	11					1																	29557328		2186	4279	6465	SO:0001583	missense	51102	exon1			AGGAGGCGGCAGG		CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"nuclear receptor binding factor 1", "mitochondrial 2-enoyl thioester reductase"	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.91G>A	1.37:g.29557328C>T	ENSP00000263702:p.Ala31Thr	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	30	20	NM_016011	0	0	1	6	5	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	ENST00000263702.6	37	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106638	0.37145	.	.	ENSG00000116353	ENST00000263702	T	0.03496	3.91	4.92	-0.97	0.10306	.	1.626230	0.03313	N	0.190804	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.44817	-0.9303	9	.	.	.	.	4.5591	0.12151	0.5172:0.3021:0.0:0.1807	.	31	Q9BV79	MECR_HUMAN	T	31	ENSP00000263702:A31T	.	A	-	1	0	MECR	29429915	0.000000	0.05858	0.002000	0.10522	0.434000	0.31775	-1.074000	0.03427	-0.262000	0.09392	-0.140000	0.14226	GCC	.		0.701	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	NM_016011		T	29557328	C	T	29557328	3	4	150	1	0	0	0	0	1	0	0	0	9449	768	27	1	1070	1	MECR	1	29557328	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		29557328	219693293	1	13405											
EIF2C3	192669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36475164	36475164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaggcaacagcaagatctgCaccagatagacaagaggaaa	19	3	10	9	0	1	4	0	0	1	4	1	5	1	5	1	2	3	3	1	2	6	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:36475164C>T	ENST00000373191.4	+	9	1467	c.1118C>T	c.(1117-1119)gCa>gTa	p.A373V	AGO3_ENST00000246314.6_Missense_Mutation_p.A139V|RP4-665N4.8_ENST00000479395.2_RNA|RP4-665N4.8_ENST00000466576.2_RNA	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	373					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										GCAAGATCTGCACCAGATAGA	0.378																																					p.A373V		.											.	.	0			c.C1118T						.						105	98	100					1																	36475164		2203	4300	6503	SO:0001583	missense	192669	exon9			GATCTGCACCAGA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.1118C>T	1.37:g.36475164C>T	ENSP00000362287:p.Ala373Val	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	254	99	NM_024852	0	0	0	1	1	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	37	CCDS399.1	.	.	.	.	.	.	.	.	.	.	C	36	5.888335	0.97068	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.10960	2.82;2.82	6.17	6.17	0.99709	Argonaute/Dicer protein, PAZ (1);	0.000000	0.85682	D	0.000000	T	0.45135	0.1327	M	0.93283	3.4	0.80722	D	1	D	0.71674	0.998	P	0.62491	0.903	T	0.55023	-0.8205	10	0.87932	D	0	-12.0124	20.8794	0.99867	0.0:1.0:0.0:0.0	.	373	Q9H9G7	AGO3_HUMAN	V	373;139	ENSP00000362287:A373V;ENSP00000246314:A139V	ENSP00000246314:A139V	A	+	2	0	EIF2C3	36247751	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GCA	.		0.378	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		T	36475164	C	T	36475164	3	4	150	1	0	0	0	0	1	0	0	0	5018	710	25	2	1152	2	EIF2C3	1	36475164	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	6917836	36475164	212775457	2	13406											
INTS3	65123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153740253	153740253	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggacatgaaggcctgccagGaggacgatgtgcggctcctg	8	7	16	10	2	0	1	0	1	0	0	1	5	1	4	3	5	2	1	3	5	1	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:153740253G>T	ENST00000318967.2	+	21	2762	c.2194G>T	c.(2194-2196)Gag>Tag	p.E732*	INTS3_ENST00000435409.2_Nonsense_Mutation_p.E732*|INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Nonsense_Mutation_p.E526*|INTS3_ENST00000456435.1_Nonsense_Mutation_p.E526*	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	733					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGCCTGCCAGGAGGACGATGT	0.612																																					p.E732X		.											.	INTS3-93	0			c.G2194T						.						113	94	100					1																	153740253		2203	4300	6503	SO:0001587	stop_gained	65123	exon21			TGCCAGGAGGACG	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2194G>T	1.37:g.153740253G>T	ENSP00000318641:p.Glu732*	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	95	33	NM_023015	0	0	5	8	3	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Nonsense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	42	9.404468	0.99161	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	15.6279	0.76878	0.0:0.0:1.0:0.0	.	.	.	.	X	732;526;732;526	.	ENSP00000318641:E732X	E	+	1	0	INTS3	152006877	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	9.055000	0.93873	2.768000	0.95171	0.561000	0.74099	GAG	.		0.612	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		T	153740253	G	T	153740253	4	4	150	1	0	0	0	0	0	1	0	0	7800	1175	41	4	2276	4	INTS3	1	153740253	Nonsense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	117265089	153740253	95510368	3	13407											
CFH	3075	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	196654324	196654324	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaacccggggaaatacagcAaaatgcacaagtactggctg	15	5	11	10	1	0	0	0	0	0	0	0	1	0	1	1	3	5	5	1	3	7	2	rs1061147	byFrequency	TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:196654324A>G	ENST00000359637.2	+	6	791	c.729A>G	c.(727-729)gcA>gcG	p.A243A	CFH_ENST00000367429.4_Silent_p.A307A|CFH_ENST00000439155.2_Silent_p.A307A			P08603	CFAH_HUMAN	complement factor H	307	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						GAAATACAGCAAAATGCACAA	0.393																																					p.A307A		.											.	CFH-566	0			c.A921G	GRCh37	CM057396	CFH	M	rs1061147	.						119	108	112					1																	196654324		2203	4300	6503	SO:0001819	synonymous_variant	3075	exon7			TACAGCAAAATGC	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"Complement system"	4883	protein-coding gene	gene with protein product	"beta-1H", "H factor 2 (complement)", "age-related maculopathy susceptibility 1"	134370	"H factor 1 (complement)"	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000359637.2:c.729A>G	1.37:g.196654324A>G		Somatic	292	0		WXS	Illumina HiSeq	Phase_I	239	84	NM_001014975	0	0	1	1	0	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000359637.2	37																																																																																				A|0.353;C|0.647		0.393	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		G	196654324	A	G	196654324	2	3	150	1	0	0	0	0	0	0	0	1	3289	117	5	3		3	CFH	1	196654324	Silent	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	42914071	196654324	52596297	4	13408											
PTPRC	5788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	198678922	198678922	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aataaccacaagtttactaaCgcaagtaaaattattaaaac	21	10	3	7	1	0	0	0	0	0	0	0	0	0	0	1	0	4	3	1	0	11	7	rs200643724		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:198678922C>T	ENST00000367376.2	+	11	1305	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	PTPRC_ENST00000348564.6_Silent_p.N219N|PTPRC_ENST00000442510.2_Silent_p.N380N|PTPRC_ENST00000352140.3_Silent_p.N330N|PTPRC_ENST00000594404.1_Silent_p.N217N	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	378					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						AGTTTACTAACGCAAGTAAAA	0.269																																					p.N380N		.											.	PTPRC-295	0			c.C1140T						.	C	,	0,4398		0,0,2199	74	89	84		1134,651	-9	0	1		84	2,8534	2.2+/-6.3	0,2,4266	no	coding-synonymous,coding-synonymous	PTPRC	NM_002838.3,NM_080921.2	,	0,2,6465	TT,TC,CC		0.0234,0.0,0.0155	,	378/1305,217/1144	198678922	2,12932	2199	4268	6467	SO:0001819	synonymous_variant	5788	exon11			TACTAACGCAAGT	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1134C>T	1.37:g.198678922C>T		Somatic	222	0		WXS	Illumina HiSeq	Phase_I	149	40	NM_002838	0	0	0	0	0	A8K7W6|Q16614|Q9H0Y6	Silent	SNP	ENST00000367376.2	37																																																																																				C|0.999;T|0.001		0.269	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198678922	C	T	198678922	2	4	150	1	0	0	0	0	0	0	0	1	12829	535	19	1		1	PTPRC	1	198678922	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	2024598	198678922	50571699	5	13409											
GPR37L1	9283	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	202097357	202097357	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtctacgccttctgcaccctCccagagaacgtctgcaacat	9	9	7	16	2	3	1	0	0	3	1	4	2	4	1	3	0	5	2	3	0	3	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:202097357C>T	ENST00000367282.5	+	2	1225	c.1119C>T	c.(1117-1119)ctC>ctT	p.L373L		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	373					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						TCTGCACCCTCCCAGAGAACG	0.622																																					p.L373L		.											.	GPR37L1-91	0			c.C1119T						.						157	139	145					1																	202097357		2203	4300	6503	SO:0001819	synonymous_variant	9283	exon2			CACCCTCCCAGAG	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"GPCR / Class A : Orphans"	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1119C>T	1.37:g.202097357C>T		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	108	8	NM_004767	0	0	0	0	0	B2R7M9|Q5SXP7|Q86VP7	Silent	SNP	ENST00000367282.5	37	CCDS1420.1																																																																																			.		0.622	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		T	202097357	C	T	202097357	2	4	150	1	0	0	0	0	0	0	0	1	6712	842	30	2		2	GPR37L1	1	202097357	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	3418435	202097357	47153264	6	13410											
RCOR3	55758	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	211449723	211449723	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctatttgaacaagcctttaGttttcatggaaagagctttc	11	15	7	8	0	1	2	1	1	0	1	2	3	1	3	2	1	3	2	2	1	5	7			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:211449723G>C	ENST00000367005.4	+	4	446	c.305G>C	c.(304-306)aGt>aCt	p.S102T	RCOR3_ENST00000452621.2_Missense_Mutation_p.S160T|RCOR3_ENST00000419091.2_Missense_Mutation_p.S160T|RCOR3_ENST00000367006.4_Missense_Mutation_p.S160T	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	102	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CAAGCCTTTAGTTTTCATGGA	0.363																																					p.S160T		.											.	RCOR3-91	0			c.G479C						.						164	162	163					1																	211449723		2203	4300	6503	SO:0001583	missense	55758	exon5			CCTTTAGTTTTCA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.305G>C	1.37:g.211449723G>C	ENSP00000355972:p.Ser102Thr	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	104	9	NM_001136223	0	0	1	1	0	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	37	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435982	0.83885	.	.	ENSG00000117625	ENST00000533469;ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.02	5.02	0.67125	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	L	0.35542	1.07	0.80722	D	1	D;B;B;B	0.56035	0.974;0.065;0.364;0.389	D;B;B;B	0.70487	0.969;0.066;0.341;0.198	T	0.21177	-1.0253	9	.	.	.	-4.1499	18.6937	0.91593	0.0:0.0:1.0:0.0	.	160;102;160;160	Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.;RCOR3_HUMAN;.;.	T	102;160;160;160;102	ENSP00000436838:S102T;ENSP00000355973:S160T;ENSP00000398558:S160T;ENSP00000413929:S160T;ENSP00000355972:S102T	.	S	+	2	0	RCOR3	209516346	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.639000	0.98448	2.495000	0.84180	0.484000	0.47621	AGT	.		0.363	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		C	211449723	G	C	211449723	3	2	150	1	0	0	0	0	1	0	0	0	13216	1029	36	4	497	4	RCOR3	1	211449723	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	9352366	211449723	37800898	7	13411											
CENPF	1063	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214815375	214815375	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggaaagtgagaaggagaagGagtgcctgcagcatgaatta	16	6	15	4	0	0	3	0	2	0	2	0	7	0	5	1	3	3	2	1	3	5	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:214815375G>T	ENST00000366955.3	+	12	3862	c.3694G>T	c.(3694-3696)Gag>Tag	p.E1232*		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E1232*(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAAGGAGAAGGAGTGCCTGCA	0.373																																					p.E1232X	Colon(80;575 1284 11000 14801 43496)												.	CENPF-567	1	Substitution - Nonsense(1)	lung(1)	c.G3694T						.						42	46	45					1																	214815375		2203	4298	6501	SO:0001587	stop_gained	1063	exon12			GAGAAGGAGTGCC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3694G>T	1.37:g.214815375G>T	ENSP00000355922:p.Glu1232*	Somatic	187	1		WXS	Illumina HiSeq	Phase_I	118	33	NM_016343	0	0	0	0	0	Q13171|Q13246|Q5VVM7	Nonsense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	42	9.517275	0.99193	.	.	ENSG00000117724	ENST00000366955	.	.	.	5.17	2.19	0.27852	.	1.270870	0.05898	N	0.629477	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	6.3943	0.21603	0.1645:0.1498:0.6857:0.0	.	.	.	.	X	1232	.	ENSP00000355922:E1232X	E	+	1	0	CENPF	212881998	0.848000	0.29623	0.000000	0.03702	0.898000	0.52572	0.913000	0.28611	0.168000	0.19655	0.511000	0.50034	GAG	.		0.373	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214815375	G	T	214815375	4	4	150	1	0	0	0	0	0	1	0	0	3237	1175	41	4	3736	4	CENPF	1	214815375	Nonsense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	3365652	214815375	34435246	8	13412											
CAPN2	824	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	223959597	223959597	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcgattttgataattttgttCggtgtttggttcggctggaa	6	19	12	4	3	0	1	0	1	0	0	3	3	0	2	0	4	0	4	0	4	2	8			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:223959597C>G	ENST00000295006.5	+	19	2299	c.1990C>G	c.(1990-1992)Cgg>Ggg	p.R664G	CAPN2_ENST00000474026.1_3'UTR|CAPN2_ENST00000433674.2_Missense_Mutation_p.R586G	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	664	Domain IV.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		TAATTTTGTTCGGTGTTTGGT	0.443																																					p.R664G													.	CAPN2-523	0			c.C1990G						.						239	216	224					1																	223959597		2203	4300	6503	SO:0001583	missense	824	exon19			TTTGTTCGGTGTT	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"EF-hand domain containing"	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1990C>G	1.37:g.223959597C>G	ENSP00000295006:p.Arg664Gly	Somatic	215	1		WXS	Illumina HiSeq	Phase_I	215	62	NM_001748	0	0	104	220	116	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.284324	0.40394	.	.	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.30981	1.51;1.51	5.63	4.72	0.59763	EF-hand-like domain (1);	0.323633	0.33712	N	0.004621	T	0.21387	0.0515	L	0.27053	0.805	0.51767	D	0.999932	B;B;B	0.29955	0.058;0.151;0.263	B;B;B	0.31016	0.074;0.123;0.114	T	0.05733	-1.0867	10	0.35671	T	0.21	.	9.67	0.40006	0.1402:0.7874:0.0:0.0724	.	586;247;664	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	G	586;664;693	ENSP00000413158:R586G;ENSP00000295006:R664G	ENSP00000295006:R664G	R	+	1	2	CAPN2	222026220	0.061000	0.20836	0.881000	0.34555	0.995000	0.86356	0.282000	0.18829	1.377000	0.46286	0.561000	0.74099	CGG	.		0.443	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		G	223959597	C	G	223959597	3	3	150	1	0	0	0	0	1	0	0	0	2633	875	31	4	2071	4	CAPN2	1	223959597	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	9144222	223959597	25291024	9	13413											
SNAP47	116841	hgsc.bcm.edu;bcgsc.ca	37	chr1	227946738	227946738	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgcttggtggccctttagCtccaagctttggaagacacc	7	11	10	13	0	0	1	0	0	0	1	1	2	1	2	4	3	3	3	4	3	3	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:227946738C>A	ENST00000366759.4	+	3	1089	c.675C>A	c.(673-675)agC>agA	p.S225R	SNAP47_ENST00000366760.1_5'UTR|SNAP47_ENST00000315781.5_Missense_Mutation_p.S225R	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	225					long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GGCCCTTTAGCTCCAAGCTTT	0.433																																					p.S225R		.											.	SNAP47-91	0			c.C675A						.						86	94	91					1																	227946738		2203	4300	6503	SO:0001583	missense	116841	exon3			CTTTAGCTCCAAG	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 142"	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.675C>A	1.37:g.227946738C>A	ENSP00000355721:p.Ser225Arg	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_053052	0	0	26	26	0	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.74|10.74	1.434984|1.434984	0.25813|0.25813	.|.	.|.	ENSG00000143740|ENSG00000143740	ENST00000418653;ENST00000426344|ENST00000366759;ENST00000315781	.|T;T	.|0.17054	.|2.3;2.3	4.95|4.95	0.434|0.434	0.16539|0.16539	.|.	.|0.129162	.|0.64402	.|D	.|0.000001	T|T	0.31231|0.31231	0.0790|0.0790	M|M	0.78637|0.78637	2.42|2.42	0.30113|0.30113	N|N	0.8064|0.8064	.|D;D	.|0.67145	.|0.989;0.996	.|P;P	.|0.61201	.|0.885;0.885	T|T	0.20638|0.20638	-1.0269|-1.0269	5|10	.|0.26408	.|T	.|0.33	-7.4349|-7.4349	8.0504|8.0504	0.30575|0.30575	0.0:0.4696:0.0:0.5304|0.0:0.4696:0.0:0.5304	.|.	.|225;225	.|Q5SQN1;Q5SQN1-2	.|SNP47_HUMAN;.	I|R	38;217|225	.|ENSP00000355721:S225R;ENSP00000314157:S225R	.|ENSP00000314157:S225R	L|S	+|+	1|3	0|2	SNAP47|SNAP47	226013361|226013361	0.994000|0.994000	0.37717|0.37717	0.678000|0.678000	0.29963|0.29963	0.565000|0.565000	0.35776|0.35776	0.206000|0.206000	0.17375|0.17375	-0.047000|-0.047000	0.13423|0.13423	0.561000|0.561000	0.74099|0.74099	CTC|AGC	.		0.433	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052		A	227946738	C	A	227946738	3	1	150	1	0	0	0	0	1	0	0	0	14864	796	28	4	685	4	SNAP47	1	227946738	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	3987141	227946738	21303883	10	13414											
SDCCAG8	10806	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	243419490	243419490	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgcatggcgaagtccccGgagaactctaccctggagga	9	6	14	12	3	1	1	0	0	1	1	2	5	2	3	3	4	3	1	3	4	3	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:243419490G>A	ENST00000366541.3	+	1	133	c.15G>A	c.(13-15)ccG>ccA	p.P5P	SDCCAG8_ENST00000391846.1_Silent_p.P5P|SDCCAG8_ENST00000343783.6_5'UTR|CEP170_ENST00000366544.1_5'Flank|SDCCAG8_ENST00000355875.4_Silent_p.P5P|CEP170_ENST00000366542.1_5'Flank|CEP170_ENST00000366543.1_5'Flank	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	5					establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		CGAAGTCCCCGGAGAACTCTA	0.617																																					p.P5P		.											.	SDCCAG8-90	0			c.G15A						.						78	79	78					1																	243419490		2203	4300	6503	SO:0001819	synonymous_variant	10806	exon1			GTCCCCGGAGAAC	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.15G>A	1.37:g.243419490G>A		Somatic	146	0		WXS	Illumina HiSeq	Phase_I	123	7	NM_006642	0	0	1	1	0	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	37	CCDS31075.1																																																																																			.		0.617	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		A	243419490	G	A	243419490	2	1	150	1	0	0	0	0	0	0	0	1	13991	1103	39	1		1	SDCCAG8	1	243419490	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	15472752	243419490	5831131	11	13415											
MOGS	7841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74688599	74688599	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccgagcctggtgaggaccctCcagatgcccatagtggtgga	8	7	14	12	1	0	2	0	1	0	1	1	5	1	4	5	4	2	0	5	4	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:74688599C>T	ENST00000233616.4	-	4	2479	c.2317G>A	c.(2317-2319)Gag>Aag	p.E773K	MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.E667K|MOGS_ENST00000462443.1_5'Flank	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	773					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						TGAGGACCCTCCAGATGCCCA	0.592																																					p.E773K		.											.	MOGS-90	0			c.G2317A						.						80	88	85					2																	74688599		2075	4200	6275	SO:0001583	missense	7841	exon4			GACCCTCCAGATG	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"glucosidase I", "processing A-glucosidase I"	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.2317G>A	2.37:g.74688599C>T	ENSP00000233616:p.Glu773Lys	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	197	56	NM_006302	0	0	48	70	22	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	C	7.668	0.686371	0.14973	.	.	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.48522	0.81;0.81	4.48	0.633	0.17712	Six-hairpin glycosidase-like (1);	0.109437	0.64402	N	0.000010	T	0.35508	0.0934	L	0.55103	1.725	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.14008	-1.0488	10	0.11794	T	0.64	-2.6164	8.6268	0.33895	0.0:0.6721:0.0:0.3279	.	773	Q13724	MOGS_HUMAN	K	773;667	ENSP00000233616:E773K;ENSP00000388201:E667K	ENSP00000233616:E773K	E	-	1	0	MOGS	74542107	0.580000	0.26733	0.793000	0.32043	0.621000	0.37620	1.175000	0.31944	0.004000	0.14682	-0.244000	0.11960	GAG	.		0.592	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		T	74688599	C	T	74688599	3	4	150	1	0	0	0	0	1	0	0	0	9722	864	30	2	200	2	MOGS	2	74688599	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		74688599	168510774	12	13416											
ACMSD	130013	hgsc.bcm.edu;broad.mit.edu	37	chr2	135621133	135621133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaaagagctgggctttcccGgggtccaaattggcacccac	9	8	12	12	1	0	2	0	1	0	1	2	2	2	2	3	4	1	3	3	4	2	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:135621133G>A	ENST00000356140.5	+	5	554	c.418G>A	c.(418-420)Ggg>Agg	p.G140R	ACMSD_ENST00000283054.4_Missense_Mutation_p.G82R|AC016725.4_ENST00000392929.2_RNA|ACMSD_ENST00000392928.1_Missense_Mutation_p.G82R	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	140					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		GGGCTTTCCCGGGGTCCAAAT	0.632																																					p.G140R		.											.	ACMSD-91	0			c.G418A						.						71	58	62					2																	135621133		2203	4300	6503	SO:0001583	missense	130013	exon5			TTTCCCGGGGTCC	AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.418G>A	2.37:g.135621133G>A	ENSP00000348459:p.Gly140Arg	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	98	6	NM_138326	0	0	94	99	5	Q3B7X3|Q53SR5|Q96KY2	Missense_Mutation	SNP	ENST00000356140.5	37	CCDS2173.2	.	.	.	.	.	.	.	.	.	.	G	28.8	4.950082	0.92660	.	.	ENSG00000153086	ENST00000356140;ENST00000283054;ENST00000392928	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.90518	0.7029	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93490	0.6835	9	0.87932	D	0	-10.2027	19.6085	0.95589	0.0:0.0:1.0:0.0	.	82;140	Q53SR5;Q8TDX5	.;ACMSD_HUMAN	R	140;82;82	.	ENSP00000283054:G82R	G	+	1	0	ACMSD	135337603	1.000000	0.71417	0.959000	0.39883	0.755000	0.42902	9.463000	0.97652	2.618000	0.88619	0.561000	0.74099	GGG	.		0.632	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			A	135621133	G	A	135621133	3	1	150	1	0	0	0	0	1	0	0	0	144	1116	39	1	436	1	ACMSD	2	135621133	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	60932534	135621133	107578240	13	13417											
SSFA2	6744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	182774650	182774650	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aaagtacggagggagaagctCctcatgttccagccacttac	12	8	10	11	1	1	1	1	0	0	1	3	3	3	2	3	2	4	3	3	2	4	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:182774650C>G	ENST00000431877.2	+	9	1617	c.1438C>G	c.(1438-1440)Cct>Gct	p.P480A	SSFA2_ENST00000320370.7_Missense_Mutation_p.P480A|SSFA2_ENST00000428267.2_Missense_Mutation_p.P327A|SSFA2_ENST00000409001.1_Missense_Mutation_p.P480A|SSFA2_ENST00000409136.1_5'Flank	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	480						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			GGGAGAAGCTCCTCATGTTCC	0.368																																					p.P480A		.											.	SSFA2-153	0			c.C1438G						.						71	62	65					2																	182774650		2203	4300	6503	SO:0001583	missense	6744	exon9			GAAGCTCCTCATG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.1438C>G	2.37:g.182774650C>G	ENSP00000388731:p.Pro480Ala	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	92	39	NM_001130445	0	0	0	1	1	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304280	0.81136	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267	T;T;T;T	0.15372	2.66;2.43;2.66;2.66	5.98	5.98	0.97165	.	0.175872	0.50627	D	0.000116	T	0.44138	0.1279	M	0.73598	2.24	0.58432	D	0.999993	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.997;0.997;0.997	T	0.04946	-1.0916	10	0.33141	T	0.24	-18.1989	18.6367	0.91380	0.0:1.0:0.0:0.0	.	327;480;480;480	E7END2;E9PHV5;P28290;P28290-3	.;.;SSFA2_HUMAN;.	A	480;480;480;327	ENSP00000388731:P480A;ENSP00000314669:P480A;ENSP00000387319:P480A;ENSP00000409867:P327A	ENSP00000314669:P480A	P	+	1	0	SSFA2	182482895	0.994000	0.37717	1.000000	0.80357	0.889000	0.51656	3.435000	0.52849	2.847000	0.97988	0.591000	0.81541	CCT	.		0.368	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		G	182774650	C	G	182774650	3	3	150	1	0	0	0	0	1	0	0	0	15215	855	30	4	1472	4	SSFA2	2	182774650	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	47153517	182774650	60424723	14	13418											
NCKAP1	10787	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	183792879	183792879	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	taagacggtcttcaatgcttCctttgtgaattgtaaacaaa	13	14	7	7	1	2	2	1	1	1	1	3	2	3	2	1	1	2	2	1	1	6	6			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:183792879C>T	ENST00000361354.4	-	29	3518	c.3146G>A	c.(3145-3147)gGa>gAa	p.G1049E	NCKAP1_ENST00000478449.1_5'UTR|NCKAP1_ENST00000360982.2_Missense_Mutation_p.G1055E	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	1049					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TTCAATGCTTCCTTTGTGAAT	0.358																																					p.G1055E													.	NCKAP1-92	0			c.G3164A						.						122	116	118					2																	183792879		2203	4300	6503	SO:0001583	missense	10787	exon30			ATGCTTCCTTTGT	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.3146G>A	2.37:g.183792879C>T	ENSP00000355348:p.Gly1049Glu	Somatic	48	1		WXS	Illumina HiSeq	Phase_I	48	14	NM_205842	0	0	37	77	40	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	37	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511992	0.64522	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.27557	1.66;1.66	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	L	0.29908	0.895	0.80722	D	1	B;B	0.20261	0.043;0.035	B;B	0.22152	0.038;0.023	T	0.09618	-1.0666	10	0.06099	T	0.92	-19.0359	19.8353	0.96655	0.0:1.0:0.0:0.0	.	1049;1055	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	E	1049;1055	ENSP00000355348:G1049E;ENSP00000354251:G1055E	ENSP00000354251:G1055E	G	-	2	0	NCKAP1	183501124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.768000	0.85345	2.698000	0.92095	0.586000	0.80456	GGA	.		0.358	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		T	183792879	C	T	183792879	3	4	150	1	0	0	0	0	1	0	0	0	10247	855	30	2	252	2	NCKAP1	2	183792879	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	1018229	183792879	59406494	15	13419											
KCNH8	131096	broad.mit.edu;bcgsc.ca	37	chr3	19554559	19554559	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggaggaagaggaggcagtctCcctctctcccatctgcacaa	10	7	11	13	0	3	1	0	0	3	1	6	4	4	4	2	4	1	2	2	4	2	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:19554559C>T	ENST00000328405.2	+	13	2443	c.2177C>T	c.(2176-2178)tCc>tTc	p.S726F		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	726					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						gaggCAGTCTCCCTCTCTCCC	0.532																																					p.S726F	NSCLC(124;1625 1765 8018 24930 42026)												.	KCNH8-524	0			c.C2177T						.						67	55	59					3																	19554559		2203	4300	6503	SO:0001583	missense	131096	exon13			CAGTCTCCCTCTC	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.2177C>T	3.37:g.19554559C>T	ENSP00000328813:p.Ser726Phe	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	265	13	NM_144633	0	0	0	0	0	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.441905	0.43326	.	.	ENSG00000183960	ENST00000328405	D	0.98792	-5.14	5.44	5.44	0.79542	.	0.000000	0.31709	U	0.007193	D	0.97495	0.9180	L	0.47716	1.5	0.80722	D	1	P	0.37158	0.585	B	0.42188	0.379	D	0.97417	1.0006	9	.	.	.	.	17.4503	0.87590	0.0:1.0:0.0:0.0	.	726	Q96L42	KCNH8_HUMAN	F	726	ENSP00000328813:S726F	.	S	+	2	0	KCNH8	19529563	0.164000	0.22935	0.087000	0.20705	0.252000	0.25951	1.912000	0.39946	2.559000	0.86315	0.585000	0.79938	TCC	.		0.532	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19554559	C	T	19554559	3	4	150	1	0	0	0	0	1	0	0	0	8059	855	30	2	2227	2	KCNH8	3	19554559	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		19554559	178467871	16	13420											
TRANK1	9881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	36874430	36874430	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctaaacacttggcttcacaaCgccgcagaggcctgtgaaaa	13	7	9	12	2	1	2	1	1	0	1	1	2	1	2	2	2	2	2	2	2	5	3	rs370553712		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:36874430C>T	ENST00000429976.2	-	21	6759	c.6512G>A	c.(6511-6513)cGt>cAt	p.R2171H	TRANK1_ENST00000428977.2_Missense_Mutation_p.R1621H|TRANK1_ENST00000301807.6_Missense_Mutation_p.R1621H	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2171							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GGCTTCACAACGCCGCAGAGG	0.438																																					p.R2171H		.											.	TRANK1-24	0			c.G6512A						.	C	HIS/ARG	0,3780		0,0,1890	32	32	32		6512	5.2	0.9	3		32	1,8203		0,1,4101	no	missense	TRANK1	NM_014831.2	29	0,1,5991	TT,TC,CC		0.0122,0.0,0.0083	probably-damaging	2171/2926	36874430	1,11983	1890	4102	5992	SO:0001583	missense	9881	exon21			TCACAACGCCGCA	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	29011	protein-coding gene	gene with protein product	"lupus brain antigen 1", "KIAA0342"					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.6512G>A	3.37:g.36874430C>T	ENSP00000416168:p.Arg2171His	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	22	10	NM_014831	0	0	0	0	0	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812080	0.50527	0.0	1.22E-4	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34667	1.35;1.76;1.35	5.16	5.16	0.70880	.	0.000000	0.48767	D	0.000162	T	0.40743	0.1129	L	0.34521	1.04	0.22156	N	0.999323	D	0.76494	0.999	P	0.57324	0.818	T	0.28459	-1.0043	10	0.72032	D	0.01	.	9.7288	0.40348	0.0:0.8452:0.0:0.1548	.	2171	O15050	TRNK1_HUMAN	H	1621;2171;1621	ENSP00000416826:R1621H;ENSP00000416168:R2171H;ENSP00000301807:R1621H	ENSP00000301807:R1621H	R	-	2	0	TRANK1	36849434	0.977000	0.34250	0.855000	0.33649	0.731000	0.41821	3.068000	0.50018	2.562000	0.86427	0.555000	0.69702	CGT	.		0.438	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		T	36874430	C	T	36874430	3	4	150	1	0	0	0	0	1	0	0	0	16487	536	19	1	2277	1	TRANK1	3	36874430	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	17319871	36874430	161148000	17	13421											
KLHDC8B	200942	ucsc.edu;bcgsc.ca	37	chr3	49212587	49212587	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggccacattgtggccattGggggccttggtaagtctcta	6	11	15	9	0	1	0	0	0	1	0	2	0	1	0	3	6	0	1	3	6	2	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:49212587G>A	ENST00000332780.2	+	5	1068	c.859G>A	c.(859-861)Ggg>Agg	p.G287R	C3orf84_ENST00000443990.1_5'Flank	NM_173546.2	NP_775817.1	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	287						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGTGGCCATTGGGGGCCTTGG	0.602																																					p.G287R													.	KLHDC8B-90	0			c.G859A						.						31	33	33					3																	49212587		2203	4300	6503	SO:0001583	missense	200942	exon5			GCCATTGGGGGCC		CCDS2791.1	3p21.31	2008-02-05			ENSG00000185909	ENSG00000185909			28557	protein-coding gene	gene with protein product		613169					Standard	NM_173546		Approved	MGC35097	uc003cwh.3	Q8IXV7	OTTHUMG00000156814	ENST00000332780.2:c.859G>A	3.37:g.49212587G>A	ENSP00000327468:p.Gly287Arg	Somatic	41	0		WXS	Illumina HiSeq		27	4	NM_173546	0	0	0	0	0		Missense_Mutation	SNP	ENST00000332780.2	37	CCDS2791.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.859659	0.91433	.	.	ENSG00000185909	ENST00000332780;ENST00000538729	D	0.84370	-1.84	5.84	5.84	0.93424	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.95909	0.8668	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97368	0.9974	10	0.87932	D	0	-9.6158	17.2994	0.87178	0.0:0.0:1.0:0.0	.	287	Q8IXV7	KLD8B_HUMAN	R	287;38	ENSP00000327468:G287R	ENSP00000327468:G287R	G	+	1	0	KLHDC8B	49187591	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	8.455000	0.90355	2.769000	0.95229	0.563000	0.77884	GGG	.		0.602	KLHDC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345974.1	NM_173546		A	49212587	G	A	49212587	3	1	150	1	0	0	0	0	1	0	0	0	8384	1348	47	2	873	2	KLHDC8B	3	49212587	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	12338157	49212587	148809843	18	13422											
BAP1	8314	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	52439271	52439271	+	Frame_Shift_Del	DEL	G	G	-																															tgttgggagggctgtgggatGgggcttgtgcgcatgaacca																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:52439271delG	ENST00000460680.1	-	11	1442	c.971delC	c.(970-972)ccafs	p.P324fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.P306fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P324fs*11(1)|p.A323fs*71(1)|p.P324fs*7(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GCTGTGGGATGGGGCTTGTGC	0.592			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.P324fs	GBM(101;493 1458 7992 21037 25532)	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1-1032	3	Deletion - Frameshift(3)	eye(1)|kidney(1)|pleura(1)	c.971delC						.						115	120	118					3																	52439271		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon11			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.971delC	3.37:g.52439271delG	ENSP00000417132:p.Pro324fs	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	81	60	NM_004656	0	0	0	0	0	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	37	CCDS2853.1																																																																																			.		0.592	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52439271	G	-	52439271	7	5	150	1	0	1	0	1	0	0	0	0	1312	1348	47	0	1246	0	BAP1	3	52439271	Frame_Shift_Del	DEL	G	TCGA-MH-A560-01A-11D-A26P-10	3226684	52439271	145583159	19	13423	141	2									
BAP1	8314	hgsc.bcm.edu;bcgsc.ca	37	chr3	52439275	52439275	+	Missense_Mutation	SNP	C	C	A																															gggagggctgtgggatggggCttgtgcgcatgaaccagccg																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:52439275C>A	ENST00000460680.1	-	11	1438	c.967G>T	c.(967-969)Gcc>Tcc	p.A323S	BAP1_ENST00000296288.5_Missense_Mutation_p.A305S	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P324fs*7(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TGGGATGGGGCTTGTGCGCAT	0.592			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.A323S	GBM(101;493 1458 7992 21037 25532)	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1-1032	1	Deletion - Frameshift(1)	pleura(1)	c.G967T						.						113	118	116					3																	52439275		2203	4300	6503	SO:0001583	missense	8314	exon11			ATGGGGCTTGTGC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.967G>T	3.37:g.52439275C>A	ENSP00000417132:p.Ala323Ser	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	84	65	NM_004656	0	0	0	0	0	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.375375	0.24857	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.55588	0.51;0.51	5.7	4.82	0.62117	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.290995	0.39341	N	0.001388	T	0.41789	0.1174	L	0.44542	1.39	0.21782	N	0.999546	B	0.09022	0.002	B	0.14023	0.01	T	0.24512	-1.0158	10	0.24483	T	0.36	-12.9423	9.1237	0.36801	0.0:0.8178:0.0:0.1822	.	323	Q92560	BAP1_HUMAN	S	323;305	ENSP00000417132:A323S;ENSP00000296288:A305S	ENSP00000296288:A305S	A	-	1	0	BAP1	52414315	0.962000	0.33011	0.955000	0.39395	0.115000	0.19883	0.927000	0.28818	1.398000	0.46701	0.655000	0.94253	GCC	.		0.592	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52439275	C	A	52439275	3	1	150	1	0	0	0	0	1	0	0	0	1312	797	28	4	1250	4	BAP1	3	52439275	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	4	52439275	145583155	20	13424	141	2									
COL8A1	1295	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	99514774	99514774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggggggcaacgtgtgggttGctctattcaagaacaacgag	11	8	15	7	2	2	1	1	0	1	1	2	2	2	1	0	4	4	3	0	4	5	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:99514774G>A	ENST00000261037.3	+	5	2409	c.2029G>A	c.(2029-2031)Gct>Act	p.A677T	COL8A1_ENST00000273342.4_Missense_Mutation_p.A677T	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	677	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						CGTGTGGGTTGCTCTATTCAA	0.547																																					p.A677T													.	COL8A1-90	0			c.G2029A						.						94	87	89					3																	99514774		2203	4300	6503	SO:0001583	missense	1295	exon5			TGGGTTGCTCTAT	AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"Collagens"	2215	protein-coding gene	gene with protein product		120251	"chromosome 3 open reading frame 7"	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.2029G>A	3.37:g.99514774G>A	ENSP00000261037:p.Ala677Thr	Somatic	122	1		WXS	Illumina HiSeq	Phase_I	116	82	NM_001850	0	0	4	4	0	D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	ENST00000261037.3	37	CCDS2934.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835784	0.71373	.	.	ENSG00000144810	ENST00000261037;ENST00000273342	T;T	0.75260	-0.92;-0.92	6.08	6.08	0.98989	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.051256	0.85682	D	0.000000	D	0.85423	0.5693	M	0.71581	2.175	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.67548	0.952;0.952	D	0.85567	0.1231	10	0.66056	D	0.02	.	18.1659	0.89727	0.0:0.0:1.0:0.0	.	678;677	E7EPK9;P27658	.;CO8A1_HUMAN	T	677	ENSP00000261037:A677T;ENSP00000273342:A677T	ENSP00000261037:A677T	A	+	1	0	COL8A1	100997464	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	GCT	.		0.547	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850		A	99514774	G	A	99514774	3	1	150	1	0	0	0	0	1	0	0	0	3711	1319	46	2	2035	2	COL8A1	3	99514774	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	47075499	99514774	98507656	21	13425											
XRN1	54464	broad.mit.edu;bcgsc.ca	37	chr3	142030528	142030528	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttcaaagaagctgatgagCtctcccgtggacttactttg	10	12	9	10	1	2	3	1	2	1	1	3	4	2	4	1	1	3	2	1	1	3	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:142030528C>T	ENST00000264951.4	-	42	5063	c.4946G>A	c.(4945-4947)aGc>aAc	p.S1649N	XRN1_ENST00000392981.2_Missense_Mutation_p.S1637N	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1649					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AGCTGATGAGCTCTCCCGTGG	0.448																																					p.S1649N													.	XRN1-93	0			c.G4946A						.						152	153	153					3																	142030528		2203	4300	6503	SO:0001583	missense	54464	exon42			GATGAGCTCTCCC	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.4946G>A	3.37:g.142030528C>T	ENSP00000264951:p.Ser1649Asn	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	101	8	NM_019001	0	0	0	0	0	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	C	5.401	0.259143	0.10239	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.31247	1.5;1.5	5.75	0.665	0.17896	.	1.065370	0.07165	N	0.851388	T	0.19406	0.0466	N	0.24115	0.695	0.09310	N	1	B;B	0.27416	0.178;0.112	B;B	0.18263	0.021;0.009	T	0.24048	-1.0171	10	0.49607	T	0.09	-0.0078	6.6837	0.23134	0.0:0.4384:0.3549:0.2066	.	1637;1649	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	N	1649;1637	ENSP00000264951:S1649N;ENSP00000376707:S1637N	ENSP00000264951:S1649N	S	-	2	0	XRN1	143513218	0.000000	0.05858	0.001000	0.08648	0.218000	0.24690	0.337000	0.19841	-0.162000	0.10964	-0.345000	0.07892	AGC	.		0.448	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142030528	C	T	142030528	3	4	150	1	0	0	0	0	1	0	0	0	17492	797	28	2	178	2	XRN1	3	142030528	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	42515754	142030528	55991902	22	13426											
CLDN11	5010	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	170141043	170141043	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgactgttcttccctgcatcCggatgggccaggagcccggt	5	10	13	13	2	1	1	0	1	1	0	3	3	3	3	4	4	2	2	4	4	0	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:170141043C>T	ENST00000064724.3	+	2	521	c.319C>T	c.(319-321)Cgg>Tgg	p.R107W	CLDN11_ENST00000486975.1_Missense_Mutation_p.R107W|CLDN11_ENST00000451576.1_Missense_Mutation_p.R107W|CLDN11_ENST00000489485.1_3'UTR	NM_005602.5	NP_005593.2	O75508	CLD11_HUMAN	claudin 11	107					axon ensheathment (GO:0008366)|calcium-independent cell-cell adhesion (GO:0016338)|spermatogenesis (GO:0007283)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|liver(2)|lung(3)|ovary(2)	12	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TCCCTGCATCCGGATGGGCCA	0.607																																					p.R107W		.											.	CLDN11-90	0			c.C319T						.						111	105	107					3																	170141043		2203	4300	6503	SO:0001583	missense	5010	exon2			TGCATCCGGATGG	AF068863	CCDS3213.1	3q26.2-q26.3	2008-08-01	2008-08-01		ENSG00000013297	ENSG00000013297		"Claudins"	8514	protein-coding gene	gene with protein product		601326	"oligodendrocyte transmembrane protein"	OTM		8661061, 8797478	Standard	NM_005602		Approved	OSP	uc003fgx.3	O75508	OTTHUMG00000158940	ENST00000064724.3:c.319C>T	3.37:g.170141043C>T	ENSP00000064724:p.Arg107Trp	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	174	15	NM_005602	0	0	1	1	0	B2R7C1|D3DNQ5|Q5U0P3	Missense_Mutation	SNP	ENST00000064724.3	37	CCDS3213.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128510	0.77549	.	.	ENSG00000013297	ENST00000064724;ENST00000486975;ENST00000451576	D;D;D	0.89681	-2.55;-2.55;-2.55	5.81	4.91	0.64330	.	0.175301	0.50627	D	0.000106	D	0.94265	0.8158	M	0.79123	2.44	0.47621	D	0.999477	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.949	D	0.94887	0.8044	10	0.87932	D	0	.	15.8994	0.79362	0.1364:0.8636:0.0:0.0	.	107;107	B4DFI2;O75508	.;CLD11_HUMAN	W	107	ENSP00000064724:R107W;ENSP00000417434:R107W;ENSP00000410185:R107W	ENSP00000064724:R107W	R	+	1	2	CLDN11	171623737	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	2.422000	0.44696	1.391000	0.46566	0.557000	0.71058	CGG	.		0.607	CLDN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352403.1	NM_005602		T	170141043	C	T	170141043	3	4	150	1	0	0	0	0	1	0	0	0	3479	643	23	1	325	1	CLDN11	3	170141043	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	28110515	170141043	27881387	23	13427											
MFN1	55669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	179082985	179082985	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caataatcgttgggatgcctCtgcatcagagccagaatata	13	10	9	9	1	2	2	1	0	1	2	3	3	2	3	2	1	3	2	2	1	5	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:179082985C>G	ENST00000471841.1	+	7	851	c.725C>G	c.(724-726)tCt>tGt	p.S242C	MFN1_ENST00000280653.7_Missense_Mutation_p.S242C|MFN1_ENST00000263969.5_Missense_Mutation_p.S242C	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	242	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			TGGGATGCCTCTGCATCAGAG	0.328																																					p.S242C		.											.	MFN1-155	0			c.C725G						.						50	54	53					3																	179082985		2203	4300	6503	SO:0001583	missense	55669	exon7			ATGCCTCTGCATC	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.725C>G	3.37:g.179082985C>G	ENSP00000420617:p.Ser242Cys	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	86	66	NM_033540	0	0	0	0	0	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	37	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927490	0.73327	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000263969;ENST00000489329;ENST00000474903	D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.66;-3.66	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.98128	0.9382	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;P;P	0.87578	0.998;0.907;0.907	D	0.98003	1.0361	10	0.48119	T	0.1	-19.0836	19.7394	0.96219	0.0:1.0:0.0:0.0	.	242;270;242	Q8IWA4-3;Q4AEJ4;Q8IWA4	.;.;MFN1_HUMAN	C	242;242;242;242;95;105	ENSP00000420617:S242C;ENSP00000280653:S242C;ENSP00000263969:S242C;ENSP00000420148:S95C;ENSP00000419926:S105C	ENSP00000263969:S242C	S	+	2	0	MFN1	180565679	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.739000	0.68622	2.649000	0.89929	0.563000	0.77884	TCT	.		0.328	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		G	179082985	C	G	179082985	3	3	150	1	0	0	0	0	1	0	0	0	9548	913	32	4	747	4	MFN1	3	179082985	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	8941942	179082985	18939445	24	13428											
DSPP	1834	hgsc.bcm.edu	37	chr4	88536475	88536475	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatagcagtgacagcaacgaAagcagcaatagcagtgacag	17	4	12	8	1	0	2	0	2	0	0	0	4	0	2	0	0	6	5	0	0	5	2	rs576476534	byFrequency	TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr4:88536475A>C	ENST00000282478.7	+	4	2694	c.2661A>C	c.(2659-2661)gaA>gaC	p.E887D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.E887D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	887	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcaacgaaagcagcaata	0.488													a|||	3	0.000599042	8e-04	0	5008	,	,		31731	0.001		0.001	False		,,,				2504	0				p.E887D		.											.	DSPP-90	0			c.A2661C						.						76	91	86					4																	88536475		1633	2927	4560	SO:0001583	missense	1834	exon5			CAACGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2661A>C	4.37:g.88536475A>C	ENSP00000282478:p.Glu887Asp	Somatic	321	0		WXS	Illumina HiSeq	Phase_I	356	45	NM_014208	0	0	0	0	0	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	0.030	-1.340968	0.01277	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87650	-2.28;-2.28	0.951	0.0257	0.14146	.	.	.	.	.	T	0.59404	0.2191	N	0.00621	-1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52852	-0.8520	9	0.44086	T	0.13	.	1.9373	0.03340	0.3085:0.4592:0.0:0.2323	.	887	Q9NZW4	DSPP_HUMAN	D	887	ENSP00000382213:E887D;ENSP00000282478:E887D	ENSP00000282478:E887D	E	+	3	2	DSPP	88755499	0.000000	0.05858	0.916000	0.36221	0.001000	0.01503	-1.876000	0.01633	-0.574000	0.05990	-3.628000	0.00027	GAA	.		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88536475	A	C	88536475	3	2	150	1	0	0	0	0	1	0	0	0	4793	11	1	5	2675	5	DSPP	4	88536475	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10		88536475	102617801	25	13429											
FGG	2266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	155526043	155526043	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttccgcagggtgctctggTctgacctgtttggctccccc	2	13	12	14	1	2	1	0	1	2	0	4	1	4	1	4	3	1	5	4	3	0	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr4:155526043T>C	ENST00000336098.3	-	9	1343	c.1305A>G	c.(1303-1305)agA>agG	p.R435R	FGG_ENST00000407946.1_Silent_p.R443R|FGG_ENST00000404648.3_Intron|FGG_ENST00000405164.1_Intron	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	435	Platelet aggregation and Staphylococcus clumping.			R -> Y (in Ref. 15; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	GGTGCTCTGGTCTGACCTGTT	0.433																																					p.R435R		.											.	FGG-90	0			c.A1305G						.						198	188	192					4																	155526043		2203	4300	6503	SO:0001819	synonymous_variant	2266	exon9			CTCTGGTCTGACC		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"Fibrinogen C domain containing", "Endogenous ligands"	3694	protein-coding gene	gene with protein product		134850	"fibrinogen, gamma polypeptide"				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.1305A>G	4.37:g.155526043T>C		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	93	37	NM_021870	0	0	0	0	0	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Silent	SNP	ENST00000336098.3	37	CCDS3788.1																																																																																			.		0.433	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870		C	155526043	T	C	155526043	2	2	150	1	0	0	0	0	0	0	0	1	5889	1664	58	3		3	FGG	4	155526043	Silent	SNP	T	TCGA-MH-A560-01A-11D-A26P-10	66989568	155526043	35628233	26	13430											
CDH18	1016	broad.mit.edu;bcgsc.ca	37	chr5	19612631	19612631	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctccaacttgcccagcCatgtctttggcttgaatgac	8	11	8	14	0	1	2	0	2	1	0	2	2	2	2	4	1	4	1	4	1	2	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr5:19612631C>T	ENST00000507958.1	-	8	1713	c.723G>A	c.(721-723)atG>atA	p.M241I	CDH18_ENST00000274170.4_Missense_Mutation_p.M241I|CDH18_ENST00000502796.1_Missense_Mutation_p.M241I|CDH18_ENST00000506372.1_Missense_Mutation_p.M241I|CDH18_ENST00000382275.1_Missense_Mutation_p.M241I|CDH18_ENST00000511273.1_Missense_Mutation_p.M241I			Q13634	CAD18_HUMAN	cadherin 18, type 2	241	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.M241I(2)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTTGCCCAGCCATGTCTTTGG	0.418																																					p.M241I													.	CDH18-159	2	Substitution - Missense(2)	lung(2)	c.G723A						.						143	132	136					5																	19612631		2203	4300	6503	SO:0001583	missense	1016	exon6			CCCAGCCATGTCT	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"Cadherins / Major cadherins"	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.723G>A	5.37:g.19612631C>T	ENSP00000425093:p.Met241Ile	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	209	7	NM_001167667	0	0	0	0	0	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	33	5.199495	0.94997	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.95	5.95	0.96441	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.69405	0.3107	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.89917	0.99;1.0	D;D	0.91635	0.972;0.999	T	0.66610	-0.5880	9	.	.	.	.	18.9386	0.92597	0.0:1.0:0.0:0.0	.	241;241	B4DHG6;Q13634	.;CAD18_HUMAN	I	241;241;241;241;241;241;187;241	ENSP00000371710:M241I;ENSP00000425093:M241I;ENSP00000274170:M241I;ENSP00000424931:M241I;ENSP00000422138:M241I;ENSP00000427383:M187I;ENSP00000425854:M241I	.	M	-	3	0	CDH18	19648388	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.672000	0.83956	2.817000	0.96982	0.563000	0.77884	ATG	.		0.418	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19612631	C	T	19612631	3	4	150	1	0	0	0	0	1	0	0	0	3109	594	21	2	1681	2	CDH18	5	19612631	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		19612631	161302629	27	13431											
AMACR	23600	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	34004755	34004755	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttataatgcccagtgcacacAtaaggccaccaccagcaaag	15	6	7	13	0	0	0	0	0	0	0	0	0	0	0	4	1	3	2	4	1	4	3	rs147265006		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr5:34004755A>G	ENST00000335606.6	-	3	564	c.476T>C	c.(475-477)aTg>aCg	p.M159T	RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000514195.1_Intron|AMACR_ENST00000382085.3_Missense_Mutation_p.M159T|AMACR_ENST00000502637.1_Missense_Mutation_p.M159T|AMACR_ENST00000426255.2_Missense_Mutation_p.M159T|AMACR_ENST00000382068.3_Intron|AMACR_ENST00000441713.2_Intron|AMACR_ENST00000512079.1_Missense_Mutation_p.M159T|AMACR_ENST00000382072.2_Intron	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	159					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)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						CAGTGCACACATAAGGCCACC	0.463																																					p.M159T													.	AMACR-90	0			c.T476C						.						127	112	117					5																	34004755		2203	4300	6503	SO:0001583	missense	23600	exon3			GCACACATAAGGC	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.476T>C	5.37:g.34004755A>G	ENSP00000334424:p.Met159Thr	Somatic	519	2		WXS	Illumina HiSeq	Phase_I	398	148	NM_014324	0	0	7	13	6	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	3.429	-0.116430	0.06881	.	.	ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637	T;T;T	0.54071	0.59;0.59;0.59	5.92	3.25	0.37280	CoA-transferase family III domain (2);	0.285879	0.49305	D	0.000146	T	0.36552	0.0971	N	0.20845	0.615	0.80722	D	1	B;B;B;B	0.22146	0.016;0.065;0.044;0.044	B;B;B;B	0.25405	0.06;0.02;0.034;0.034	T	0.15838	-1.0423	10	0.37606	T	0.19	-16.8025	11.0712	0.48004	0.855:0.0:0.145:0.0	.	159;159;159;159	B3KMU8;F8W9N1;D6RB81;Q9UHK6	.;.;.;AMACR_HUMAN	T	159	ENSP00000334424:M159T;ENSP00000371517:M159T;ENSP00000424351:M159T	ENSP00000334424:M159T	M	-	2	0	AMACR	34040512	0.734000	0.28142	1.000000	0.80357	0.008000	0.06430	3.781000	0.55394	1.074000	0.40909	-0.250000	0.11733	ATG	A|0.999;G|0.000		0.463	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		G	34004755	A	G	34004755	3	3	150	1	0	0	0	0	1	0	0	0	562	217	8	3	1014	3	AMACR	5	34004755	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	14392124	34004755	146910505	28	13432											
PPWD1	23398	broad.mit.edu;bcgsc.ca	37	chr5	64867921	64867921	+	Frame_Shift_Del	DEL	C	C	-																															cctcctcatgaatataaattCcccaaaaatgtgaactggga																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr5:64867921delC	ENST00000261308.5	+	5	849	c.777delC	c.(775-777)ttcfs	p.F259fs	PPWD1_ENST00000538977.1_Frame_Shift_Del_p.F103fs|PPWD1_ENST00000535264.1_Frame_Shift_Del_p.F229fs	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	259					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		AATATAAATTCCCCAAAAATG	0.393																																					p.F259fs													.	PPWD1-91	0			c.777delC						.						65	70	68					5																	64867921		2203	4300	6503	SO:0001589	frameshift_variant	23398	exon5			TAAATTCCCCAAA	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"WD repeat domain containing"	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.777delC	5.37:g.64867921delC	ENSP00000261308:p.Phe259fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	35	9	NM_015342	0	0	0	0	0	B4DWR9|Q15002|Q7KZ89	Frame_Shift_Del	DEL	ENST00000261308.5	37	CCDS3985.1																																																																																			.		0.393	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342		-	64867921	C	-	64867921	7	5	150	1	0	1	0	1	0	0	0	0	12443	854	30	0	795	0	PPWD1	5	64867921	Frame_Shift_Del	DEL	C	TCGA-MH-A560-01A-11D-A26P-10	30863166	64867921	116047339	29	13433											
TNXB	7148	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32052212	32052212	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcttggcttcagccaccagCggaccatgcctcttcttgcc	6	11	8	16	1	4	0	1	0	3	0	4	1	4	1	5	2	4	1	5	2	0	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr6:32052212C>T	ENST00000375244.3	-	8	3624	c.3423G>A	c.(3421-3423)ccG>ccA	p.P1141P	TNXB_ENST00000375247.2_Silent_p.P1141P			P22105	TENX_HUMAN	tenascin XB	1228					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CAGCCACCAGCGGACCATGCC	0.557																																					p.P1141P													.	TNXB-90	0			c.G3423A						.						68	74	72					6																	32052212		1364	2608	3972	SO:0001819	synonymous_variant	7148	exon8			CACCAGCGGACCA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.3423G>A	6.37:g.32052212C>T		Somatic	174	1		WXS	Illumina HiSeq	Phase_I	150	53	NM_019105	0	0	0	0	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				.		0.557	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32052212	C	T	32052212	2	4	150	1	0	0	0	0	0	0	0	1	16378	755	27	1		1	TNXB	6	32052212	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		32052212	139062855	30	13434											
THSD7A	221981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	11675888	11675888	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctttttcttaataagctcGcgggcttctggatcctttac	6	17	7	11	2	3	0	0	0	3	0	5	1	4	1	1	2	2	2	1	2	3	7	rs375820480		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:11675888G>A	ENST00000423059.4	-	2	1142	c.891C>T	c.(889-891)cgC>cgT	p.R297R	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	297					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TAATAAGCTCGCGGGCTTCTG	0.463										HNSCC(18;0.044)																											p.R297R		.											.	THSD7A-71	0			c.C891T						.	G		0,3716		0,0,1858	137	131	133		891	-11.2	0.6	7		133	1,8219		0,1,4109	no	coding-synonymous	THSD7A	NM_015204.2		0,1,5967	AA,AG,GG		0.0122,0.0,0.0084		297/1658	11675888	1,11935	1858	4110	5968	SO:0001819	synonymous_variant	221981	exon2			AAGCTCGCGGGCT		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.891C>T	7.37:g.11675888G>A		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	46	21	NM_015204	0	0	0	0	0		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			.		0.463	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		A	11675888	G	A	11675888	2	1	150	1	0	0	0	0	0	0	0	1	15911	1074	38	1		1	THSD7A	7	11675888	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		11675888	147462775	31	13435											
ZAN	7455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	100352929	100352929	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcctagctgtgggcccCtctgtcgggagggctgtgtc	3	9	16	13	1	1	0	0	0	1	0	3	1	1	1	4	4	1	2	4	4	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:100352929C>G	ENST00000348028.3	+	0	3370				ZAN_ENST00000546292.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CTGTGGGCCCCTCTGTCGGGA	0.557																																					.													.	ZAN-142	0			.						.						121	127	125					7																	100352929		1929	4130	6059			7455	.			GGGCCCCTCTGTC	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"zonadhesin"			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100352929C>G		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	112	41	.	0	0	0	0	0	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	c	5.830	0.337470	0.11013	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	D;D;D	0.90324	-2.65;-2.65;-2.65	5.13	-0.258	0.12975	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	1.663920	0.03653	N	0.241360	T	0.81470	0.4829	N	0.10645	0.015	0.09310	N	0.999999	B;B	0.18461	0.023;0.028	B;B	0.18263	0.012;0.021	T	0.67518	-0.5650	10	0.30078	T	0.28	.	10.313	0.43721	0.0:0.3794:0.5402:0.0803	.	1069;1069	F5H0T8;Q9Y493	.;ZAN_HUMAN	V	1069	ENSP00000445943:L1069V;ENSP00000445091:L1069V;ENSP00000444427:L1069V	ENSP00000423579:L1069V	L	+	1	0	ZAN	100190865	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.012000	0.12699	-0.157000	0.11059	0.651000	0.88453	CTC	.		0.557	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		G	100352929	C	G	100352929	1	3	150	0	1	0	0	0	0	0	0	0	17546	681	24	4		4	ZAN	7	100352929	RNA	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	88677041	100352929	58785734	32	13436											
IMMP2L	83943	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	111161447	111161447	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccacaggcaccgccacaaaGaagcctttacaaaaggcctt	14	5	8	14	1	0	1	0	0	0	1	0	1	0	1	5	2	2	1	5	2	5	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:111161447G>A	ENST00000405709.2	-	2	499	c.57C>T	c.(55-57)ttC>ttT	p.F19F	IMMP2L_ENST00000331762.3_Silent_p.F19F|IMMP2L_ENST00000447215.1_Silent_p.F19F|IMMP2L_ENST00000452895.1_Silent_p.F19F|IMMP2L_ENST00000437687.1_Silent_p.F19F|IMMP2L_ENST00000415362.1_Silent_p.F19F	NM_032549.3	NP_115938.1	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	19					ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|protein processing involved in protein targeting to mitochondrion (GO:0006627)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial inner membrane peptidase complex (GO:0042720)	peptidase activity (GO:0008233)|serine-type peptidase activity (GO:0008236)			endometrium(3)|large_intestine(6)|lung(5)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		CCGCCACAAAGAAGCCTTTAC	0.433																																					p.F19F		.											.	IMMP2L-93	0			c.C57T						.						107	106	106					7																	111161447		2203	4300	6503	SO:0001819	synonymous_variant	83943	exon2			CACAAAGAAGCCT	AF359563	CCDS5753.1	7q31	2014-01-06	2005-08-17		ENSG00000184903	ENSG00000184903			14598	protein-coding gene	gene with protein product		605977	"IMP2 inner mitochondrial membrane protease-like (S. cerevisiae)", "IMMP2L intronic transcript 1 (non-protein coding)"	IMMP2L-IT1		11254443	Standard	NM_032549		Approved	IMP2	uc010ljr.2	Q96T52	OTTHUMG00000155023	ENST00000405709.2:c.57C>T	7.37:g.111161447G>A		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	58	17	NM_032549	0	0	8	14	6	Q75MF1|Q75MN9|Q75MP0|Q75MS5|Q75MS8|Q96HJ2	Silent	SNP	ENST00000405709.2	37	CCDS5753.1																																																																																			.		0.433	IMMP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338109.4	NM_032549		A	111161447	G	A	111161447	2	1	150	1	0	0	0	0	0	0	0	1	7738	933	33	2		2	IMMP2L	7	111161447	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	10808518	111161447	47977216	33	13437											
KIAA1147	57189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	141365048	141365048	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccacgttcacgtagaagaaAggtttggactcaggaatggt	12	9	13	7	2	2	2	2	0	0	2	2	4	2	4	1	4	0	3	1	4	4	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:141365048A>T	ENST00000536163.1	-	6	890	c.891T>A	c.(889-891)ccT>ccA	p.P297P	RP5-894A10.6_ENST00000602609.1_RNA|KIAA1147_ENST00000482493.1_Silent_p.P193P	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	297										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					CGTAGAAGAAAGGTTTGGACT	0.597																																					p.P297P		.											.	KIAA1147-69	0			c.T891A						.						82	89	87					7																	141365048		2145	4228	6373	SO:0001819	synonymous_variant	57189	exon6			GAAGAAAGGTTTG	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.891T>A	7.37:g.141365048A>T		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	190	65	NM_001080392	0	0	4	7	3	Q9ULS3	Silent	SNP	ENST00000536163.1	37	CCDS47726.1																																																																																			.		0.597	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			T	141365048	A	T	141365048	2	4	150	1	0	0	0	0	0	0	0	1	8231	59	3	5		5	KIAA1147	7	141365048	Silent	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	30203601	141365048	17773615	34	13438											
CUL1	8454	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	148496376	148496376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttgcataggcggccatcGtgagaatcatgaagatgagg	11	10	14	6	2	1	4	1	3	0	2	2	5	1	4	1	3	1	2	1	3	3	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:148496376G>A	ENST00000325222.4	+	21	2425	c.2146G>A	c.(2146-2148)Gtg>Atg	p.V716M	CUL1_ENST00000409469.1_Missense_Mutation_p.V716M|CUL1_ENST00000602748.1_Missense_Mutation_p.V716M	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	716					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GGCGGCCATCGTGAGAATCAT	0.478																																					p.V716M		.											.	CUL1-226	0			c.G2146A						.						139	106	117					7																	148496376		2203	4300	6503	SO:0001583	missense	8454	exon21			GCCATCGTGAGAA	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.2146G>A	7.37:g.148496376G>A	ENSP00000326804:p.Val716Met	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	114	42	NM_003592	0	0	0	0	0	D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	37	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	.	28.3	4.905971	0.92107	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000433865	D;D	0.89270	-2.49;-2.49	5.3	5.3	0.74995	Cullin protein, neddylation domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.96417	0.8831	H	0.96633	3.855	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.65233	0.933;0.64	D	0.97776	1.0229	10	0.87932	D	0	-16.3531	18.9531	0.92647	0.0:0.0:1.0:0.0	.	643;716	E7EWR0;Q13616	.;CUL1_HUMAN	M	716;716;643	ENSP00000387160:V716M;ENSP00000326804:V716M	ENSP00000326804:V716M	V	+	1	0	CUL1	148127309	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.472000	0.97709	2.467000	0.83353	0.557000	0.71058	GTG	.		0.478	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		A	148496376	G	A	148496376	3	1	150	1	0	0	0	0	1	0	0	0	4060	1145	40	1	2224	1	CUL1	7	148496376	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	7131328	148496376	10642287	35	13439											
DEFA6	1671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	6783427	6783427	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcaaagtcctggtcatttGccccacgctgctcctgggca	6	9	11	15	2	1	0	1	0	0	0	3	0	3	0	4	3	2	4	4	3	1	1	rs371286175		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:6783427G>A	ENST00000297436.2	-	1	171	c.131C>T	c.(130-132)gCa>gTa	p.A44V	GS1-24F4.3_ENST00000526235.1_RNA	NM_001926.3	NP_001917.1	Q01524	DEF6_HUMAN	defensin, alpha 6, Paneth cell-specific	44					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)				lung(4)	4			STAD - Stomach adenocarcinoma(24;0.0322)	COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		CTGGTCATTTGCCCCACGCTG	0.557																																					p.A44V		.											.	DEFA6-90	0			c.C131T						.	G	VAL/ALA	0,4406		0,0,2203	70	58	62		131	-3.3	0	8		62	1,8599		0,1,4299	no	missense	DEFA6	NM_001926.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	44/101	6783427	1,13005	2203	4300	6503	SO:0001583	missense	1671	exon1			TCATTTGCCCCAC	M98331	CCDS5960.1	8p23.1	2007-02-20			ENSG00000164822	ENSG00000164822		"Defensins, alpha"	2765	protein-coding gene	gene with protein product		600471				8417977	Standard	NM_001926		Approved	HD-6, DEF6	uc003wqt.3	Q01524	OTTHUMG00000149984	ENST00000297436.2:c.131C>T	8.37:g.6783427G>A	ENSP00000297436:p.Ala44Val	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	65	25	NM_001926	0	0	0	0	0	Q6EZF9	Missense_Mutation	SNP	ENST00000297436.2	37	CCDS5960.1	.	.	.	.	.	.	.	.	.	.	.	2.180	-0.387804	0.04932	0.0	1.16E-4	ENSG00000164822	ENST00000297436	T	0.32023	1.47	1.85	-3.35	0.04928	Defensin propeptide (1);	2.198720	0.02497	N	0.090070	T	0.24624	0.0597	L	0.39245	1.2	0.09310	N	1	B	0.30763	0.294	B	0.29942	0.109	T	0.12293	-1.0553	10	0.44086	T	0.13	.	5.9699	0.19346	0.0:0.1529:0.3749:0.4722	.	44	Q01524	DEF6_HUMAN	V	44	ENSP00000297436:A44V	ENSP00000297436:A44V	A	-	2	0	DEFA6	6770837	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.753000	0.04792	-1.668000	0.01471	-1.471000	0.01009	GCA	.		0.557	DEFA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206739.1	NM_001926		A	6783427	G	A	6783427	3	1	150	1	0	0	0	0	1	0	0	0	4399	1319	46	2	179	2	DEFA6	8	6783427	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		6783427	139580595	36	13440											
MFHAS1	9258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	8655002	8655002	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgactcagcaactcccCtgtaggaggagagagaaaaa	14	5	13	9	0	1	3	1	1	0	2	2	6	2	4	2	3	2	3	2	3	4	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:8655002C>A	ENST00000276282.6	-	2	3585		c.e2-1		MFHAS1_ENST00000520091.1_Splice_Site	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1											endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		AGCAACTCCCCTGTAGGAGGA	0.547																																					.	Melanoma(103;1201 2045 17515 28966)	.											.	MFHAS1-90	0			c.2999-1G>T						.						78	66	70					8																	8655002		2203	4300	6503	SO:0001630	splice_region_variant	9258	exon3			ACTCCCCTGTAGG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"leucine rich repeat containing 65", "malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2999-1G>T	8.37:g.8655002C>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	116	47	NM_004225	0	0	0	0	0	Q96CI0	Splice_Site	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752676	0.89753	.	.	ENSG00000147324	ENST00000276282	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.882	0.92358	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MFHAS1	8692412	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.251000	0.78297	2.703000	0.92315	0.551000	0.68910	.	.		0.547	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	Intron	A	8655002	C	A	8655002	5	1	150	1	0	0	0	0	0	0	1	0	9546	695	24	4	168	4	MFHAS1	8	8655002	Splice_Site	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	1871575	8655002	137709020	37	13441											
PNMA2	10687	broad.mit.edu	37	chr8	26365721	26365721	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccgtggcctgttccaacCagacctcaaaggactcttcc	8	10	7	16	1	3	1	1	0	2	1	6	2	5	2	6	2	1	1	6	2	2	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:26365721C>T	ENST00000522362.2	-	3	1445	c.551G>A	c.(550-552)tGg>tAg	p.W184*	PNMA2_ENST00000522764.1_5'Flank	NM_007257.5	NP_009188.1	Q9UL42	PNMA2_HUMAN	paraneoplastic Ma antigen 2	184					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)	11		all_cancers(63;0.109)|Ovarian(32;2.61e-05)|all_epithelial(46;0.105)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0196)|Epithelial(17;3.13e-11)|Colorectal(74;0.123)		ctgttccaaccagacctcaaa	0.587																																					p.W184X													.	PNMA2-90	0			c.G551A						.						70	71	71					8																	26365721		2203	4300	6503	SO:0001587	stop_gained	10687	exon3			TCCAACCAGACCT		CCDS34868.1	8p21.1	2012-02-09	2012-02-09		ENSG00000240694	ENSG00000240694		"Paraneoplastic Ma antigens"	9159	protein-coding gene	gene with protein product		603970	"paraneoplastic antigen MA2"			10362822	Standard	NM_007257		Approved	MA2, RGAG2	uc003xez.2	Q9UL42	OTTHUMG00000163816	ENST00000522362.2:c.551G>A	8.37:g.26365721C>T	ENSP00000429344:p.Trp184*	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	91	3	NM_007257	0	0	2	2	0	B3KNY9|O94959|O95145|Q49A18|Q9UL43	Nonsense_Mutation	SNP	ENST00000522362.2	37	CCDS34868.1	.	.	.	.	.	.	.	.	.	.	C	42	9.576920	0.99210	.	.	ENSG00000240694	ENST00000522362	.	.	.	4.22	4.22	0.49857	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.614	12.388	0.55343	0.0:1.0:0.0:0.0	.	.	.	.	X	184	.	ENSP00000429344:W184X	W	-	2	0	PNMA2	26421638	1.000000	0.71417	1.000000	0.80357	0.634000	0.38068	2.873000	0.48475	2.640000	0.89533	0.655000	0.94253	TGG	.		0.587	PNMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375709.2	NM_007257		T	26365721	C	T	26365721	4	4	150	1	0	0	0	0	0	1	0	0	12180	595	21	2	547	2	PNMA2	8	26365721	Nonsense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	17710719	26365721	119998301	38	13442											
ADAM9	8754	ucsc.edu	37	chr8	38871523	38871523	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgtggtttatacttacaaCaaggaagggactttaatcac	13	14	8	6	0	1	0	1	0	0	0	1	2	1	2	0	3	3	1	0	3	7	7			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:38871523C>T	ENST00000487273.2	+	4	372	c.294C>T	c.(292-294)aaC>aaT	p.N98N	ADAM9_ENST00000466936.1_Silent_p.N98N|ADAM9_ENST00000481513.1_Silent_p.N98N	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	98				Missing (in Ref. 2; no nucleotide entry). {ECO:0000305}.	activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			ATACTTACAACAAGGAAGGGA	0.308																																					p.N98N													.	ADAM9-227	0			c.C294T						.						135	140	139					8																	38871523		2203	4300	6503	SO:0001819	synonymous_variant	8754	exon4			TTACAACAAGGAA	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.294C>T	8.37:g.38871523C>T		Somatic	45	0		WXS	Illumina HiSeq		34	4	NM_003816	0	0	2	2	0	B7ZLN7|Q10718|Q8NFM6	Silent	SNP	ENST00000487273.2	37	CCDS6112.1																																																																																			.		0.308	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			T	38871523	C	T	38871523	2	4	150	1	0	0	0	0	0	0	0	1	253	477	17	2		2	ADAM9	8	38871523	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	12505802	38871523	107492499	39	13443											
ZC3H3	23144	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	144522452	144522452	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctgacccccctgggcagtgGggaggtgcagccacggcagc	6	4	17	14	1	0	1	0	1	0	0	0	2	0	2	4	5	3	4	4	5	0	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:144522452G>T	ENST00000262577.5	-	11	2605	c.2574C>A	c.(2572-2574)ccC>ccA	p.P858P		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	858					mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			CTGGGCAGTGGGGAGGTGCAG	0.682																																					p.P858P													.	ZC3H3-91	0			c.C2574A						.						15	18	17					8																	144522452		2192	4293	6485	SO:0001819	synonymous_variant	23144	exon11			GCAGTGGGGAGGT	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"Zinc fingers, CCCH-type domain containing"	28972	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 3"	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2574C>A	8.37:g.144522452G>T		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	29	15	NM_015117	0	0	8	12	4	Q14163|Q8N4E2|Q9BUS4	Silent	SNP	ENST00000262577.5	37	CCDS6402.1																																																																																			.		0.682	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117		T	144522452	G	T	144522452	2	4	150	1	0	0	0	0	0	0	0	1	17601	1219	43	4		4	ZC3H3	8	144522452	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	105650929	144522452	1841570	40	13444											
SETX	23064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	135163729	135163729	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgcctgaacatgagaaggtAactctttttctaataaaaat	15	13	6	7	1	2	2	0	2	2	1	3	3	2	2	1	1	2	1	1	1	7	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr9:135163729A>G	ENST00000224140.5	-	17	6400	c.6218T>C	c.(6217-6219)tTa>tCa	p.L2073S	SETX_ENST00000372169.2_Missense_Mutation_p.L2073S|SETX_ENST00000393220.1_Missense_Mutation_p.L2073S	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2073					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		ATGAGAAGGTAACTCTTTTTC	0.358																																					p.L2073S		.											.	SETX-93	0			c.T6218C						.						33	32	32					9																	135163729		2203	4300	6503	SO:0001583	missense	23064	exon17			GAAGGTAACTCTT	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"amyotrophic lateral sclerosis 4", "spinocerebellar ataxia, recessive, non-Friedreich type 1"	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.6218T>C	9.37:g.135163729A>G	ENSP00000224140:p.Leu2073Ser	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	63	25	NM_015046	0	0	0	0	0	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.108442	0.37242	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90900	-2.18;-2.75;-2.26;-1.87	5.5	5.5	0.81552	.	0.381500	0.24779	N	0.035673	D	0.89406	0.6706	L	0.31476	0.935	0.39629	D	0.970154	B;D;D	0.76494	0.203;0.999;0.998	B;D;P	0.68483	0.075;0.958;0.876	D	0.85262	0.1051	10	0.09338	T	0.73	.	8.5286	0.33319	0.9131:0.0:0.0869:0.0	.	2073;2073;2073	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	S	2073;315;2073;2073	ENSP00000224140:L2073S;ENSP00000409143:L315S;ENSP00000361242:L2073S;ENSP00000376913:L2073S	ENSP00000224140:L2073S	L	-	2	0	SETX	134153550	0.972000	0.33761	0.996000	0.52242	0.786000	0.44442	2.256000	0.43231	2.221000	0.72209	0.528000	0.53228	TTA	.		0.358	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135163729	A	G	135163729	3	3	150	1	0	0	0	0	1	0	0	0	14173	372	13	3	1855	3	SETX	9	135163729	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10		135163729	6049702	41	13445											
TAF3	83860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	8007636	8007636	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaaggagaagaaggagaaGgaaagagagaaagagaagag	23	0	18	0	0	0	8	0	0	0	8	0	14	0	9	0	3	0	0	0	3	7	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:8007636G>C	ENST00000344293.5	+	3	2369	c.2163G>C	c.(2161-2163)aaG>aaC	p.K721N		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	721	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						agaaggagaaggaaagagaga	0.383																																					p.K721N		.											.	TAF3-69	0			c.G2163C						.						18	18	18					10																	8007636		1856	4075	5931	SO:0001583	missense	83860	exon3			GGAGAAGGAAAGA	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"Zinc fingers, PHD-type"	17303	protein-coding gene	gene with protein product		606576	"TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.2163G>C	10.37:g.8007636G>C	ENSP00000340271:p.Lys721Asn	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	82	21	NM_031923	0	0	3	5	2	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735163	0.30774	.	.	ENSG00000165632	ENST00000344293	T	0.08634	3.07	5.68	4.59	0.56863	.	0.459877	0.21158	N	0.079203	T	0.13798	0.0334	M	0.81802	2.56	0.49299	D	0.999772	P	0.46706	0.883	B	0.40375	0.327	T	0.02301	-1.1180	10	0.36615	T	0.2	-14.6137	13.0132	0.58743	0.1321:0.0:0.8679:0.0	.	721	Q5VWG9	TAF3_HUMAN	N	721	ENSP00000340271:K721N	ENSP00000340271:K721N	K	+	3	2	TAF3	8047642	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	2.385000	0.44371	2.689000	0.91719	0.655000	0.94253	AAG	.		0.383	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		C	8007636	G	C	8007636	3	2	150	1	0	0	0	0	1	0	0	0	15557	991	35	4	2173	4	TAF3	10	8007636	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		8007636	127527111	42	13446											
DHTKD1	55526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	12139749	12139749	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcggactcatgacgcaggaGgaggtgtctgaaataaaatc	13	7	14	7	2	2	2	1	2	1	0	3	5	2	5	0	5	0	1	0	5	3	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:12139749G>C	ENST00000263035.4	+	8	1487	c.1425G>C	c.(1423-1425)gaG>gaC	p.E475D	DHTKD1_ENST00000465617.1_3'UTR	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	475					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TGACGCAGGAGGAGGTGTCTG	0.488																																					p.E475D		.											.	DHTKD1-515	0			c.G1425C						.						67	62	64					10																	12139749		2203	4300	6503	SO:0001583	missense	55526	exon8			GCAGGAGGAGGTG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.1425G>C	10.37:g.12139749G>C	ENSP00000263035:p.Glu475Asp	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	125	53	NM_018706	0	0	3	6	3	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.11|12.11	1.839538|1.839538	0.32513|0.32513	.|.	.|.	ENSG00000181192|ENSG00000181192	ENST00000263035|ENST00000448829	T|.	0.16196|.	2.36|.	5.35|5.35	1.27|1.27	0.21489|0.21489	Dehydrogenase, E1 component (1);|.	0.112246|.	0.64402|.	D|.	0.000014|.	T|T	0.35770|0.35770	0.0943|0.0943	N|N	0.25144|0.25144	0.715|0.715	0.41129|0.41129	D|D	0.985874|0.985874	B|.	0.14012|.	0.009|.	B|.	0.17979|.	0.02|.	T|T	0.07046|0.07046	-1.0793|-1.0793	10|5	0.24483|.	T|.	0.36|.	-13.3397|-13.3397	4.01|4.01	0.09618|0.09618	0.3596:0.0:0.3864:0.254|0.3596:0.0:0.3864:0.254	.|.	475|.	Q96HY7|.	DHTK1_HUMAN|.	D|R	475|27	ENSP00000263035:E475D|.	ENSP00000263035:E475D|.	E|G	+|+	3|1	2|0	DHTKD1|DHTKD1	12179755|12179755	0.982000|0.982000	0.34865|0.34865	1.000000|1.000000	0.80357|0.80357	0.863000|0.863000	0.49368|0.49368	0.093000|0.093000	0.15086|0.15086	0.264000|0.264000	0.21851|0.21851	0.462000|0.462000	0.41574|0.41574	GAG|GGA	.		0.488	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		C	12139749	G	C	12139749	3	2	150	1	0	0	0	0	1	0	0	0	4511	991	35	4	1455	4	DHTKD1	10	12139749	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	4132113	12139749	123394998	43	13447											
CSGALNACT2	55454	broad.mit.edu	37	chr10	43659419	43659419	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggacaagggagaggtcttGatgtttttctgtgatgttga	8	15	15	3	0	2	4	0	3	2	1	2	6	2	5	0	3	0	2	0	3	1	4	rs79064394		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:43659419G>T	ENST00000374466.3	+	5	1421	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	362					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.L362F(5)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GAGAGGTCTTGATGTTTTTCT	0.433																																					p.L362F													.	CSGALNACT2-69	5	Substitution - Missense(5)	endometrium(4)|kidney(1)	c.G1086T						.						223	221	222					10																	43659419		2203	4300	6503	SO:0001583	missense	55454	exon5			GGTCTTGATGTTT	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"Beta 4-glycosyltransferases"	24292	protein-coding gene	gene with protein product	"chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1086G>T	10.37:g.43659419G>T	ENSP00000363590:p.Leu362Phe	Somatic	142	2		WXS	Illumina HiSeq	Phase_I	154	5	NM_018590	0	0	1	1	0	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499782	0.85176	.	.	ENSG00000169826	ENST00000374466	T	0.27256	1.68	6.08	5.17	0.71159	.	0.064535	0.64402	D	0.000004	T	0.57359	0.2048	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63721	-0.6573	10	0.87932	D	0	-11.7375	14.8306	0.70146	0.0683:0.0:0.9317:0.0	.	362	Q8N6G5	CGAT2_HUMAN	F	362	ENSP00000363590:L362F	ENSP00000363590:L362F	L	+	3	2	CSGALNACT2	42979425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.894000	0.99253	0.591000	0.81541	TTG	.		0.433	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43659419	G	T	43659419	3	4	150	1	0	0	0	0	1	0	0	0	3945	1281	45	4	1100	4	CSGALNACT2	10	43659419	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	31519670	43659419	91875328	44	13448											
NCOA4	8031	broad.mit.edu	37	chr10	51579175	51579175	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaccagagtggcagctccAgtaatagagaaccccttttg	13	8	10	10	0	0	3	0	0	0	3	1	4	1	3	4	1	2	3	4	1	4	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:51579175A>C	ENST00000443446.1	+	2	263	c.34A>C	c.(34-36)Agt>Cgt	p.S12R	NCOA4_ENST00000430396.2_Intron|NCOA4_ENST00000374082.1_Missense_Mutation_p.S12R|NCOA4_ENST00000452682.1_Missense_Mutation_p.S28R|NCOA4_ENST00000438493.1_Missense_Mutation_p.S28R|NCOA4_ENST00000374087.4_Missense_Mutation_p.S12R|NCOA4_ENST00000498586.1_Intron|NCOA4_ENST00000344348.6_Missense_Mutation_p.S12R|NCOA4_ENST00000414907.2_Intron	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	12					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						TGGCAGCTCCAGTAATAGAGA	0.408			T	RET	papillary thyroid																																p.S28R				Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4-1042	0			c.A82C						.						48	55	53					10																	51579175		2203	4300	6503	SO:0001583	missense	8031	exon3			AGCTCCAGTAATA	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.34A>C	10.37:g.51579175A>C	ENSP00000390713:p.Ser12Arg	Somatic	67	3		WXS	Illumina HiSeq	Phase_I	64	7	NM_001145261	0	0	6	6	0	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	37	CCDS7237.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.921905	0.73213	.	.	ENSG00000138293	ENST00000438493;ENST00000452682;ENST00000374087;ENST00000330923;ENST00000344348;ENST00000374082;ENST00000443446	T;T;T;T;T;T	0.21191	2.36;2.34;2.34;2.34;2.02;2.34	5.79	5.79	0.91817	.	0.460516	0.24321	N	0.039555	T	0.23806	0.0576	L	0.32530	0.975	0.80722	D	1	P;D;P	0.53619	0.931;0.961;0.808	P;P;P	0.49752	0.621;0.621;0.467	T	0.01262	-1.1402	10	0.66056	D	0.02	-18.2451	11.0233	0.47730	0.8279:0.0:0.0:0.1721	.	28;28;12	B4E260;E9PAV7;Q13772	.;.;NCOA4_HUMAN	R	28;28;12;12;12;12;12	ENSP00000405146:S28R;ENSP00000395465:S28R;ENSP00000363200:S12R;ENSP00000344552:S12R;ENSP00000363195:S12R;ENSP00000390713:S12R	ENSP00000332421:S12R	S	+	1	0	NCOA4	51249181	0.809000	0.29036	0.998000	0.56505	0.989000	0.77384	0.888000	0.28268	2.212000	0.71576	0.533000	0.62120	AGT	.		0.408	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		C	51579175	A	C	51579175	3	2	150	1	0	0	0	0	1	0	0	0	10257	188	7	5	88	5	NCOA4	10	51579175	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	7919756	51579175	83955572	45	13449											
DNA2	1763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	70182074	70182074	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtcagcataaaattccagttCcagcttcacatctttaaagt	13	13	5	10	0	3	0	2	0	1	0	5	0	5	0	2	0	2	3	2	0	4	6	rs369018277		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:70182074C>T	ENST00000358410.3	-	17	2655	c.2605G>A	c.(2605-2607)Gaa>Aaa	p.E869K	DNA2_ENST00000399180.2_Missense_Mutation_p.E955K|DNA2_ENST00000399179.2_Intron	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	869	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						AATTCCAGTTCCAGCTTCACA	0.393																																					p.E869K		.											.	.	0			c.G2605A						.	C	LYS/GLU	0,3782		0,0,1891	90	87	88		2605	3	1	10		88	1,8241		0,1,4120	no	missense	DNA2	NM_001080449.2	56	0,1,6011	TT,TC,CC		0.0121,0.0,0.0083	possibly-damaging	869/1061	70182074	1,12023	1891	4121	6012	SO:0001583	missense	1763	exon17			CCAGTTCCAGCTT	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"DNA2 DNA replication helicase 2-like (yeast)", "DNA replication helicase 2 homolog (yeast)"	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.2605G>A	10.37:g.70182074C>T	ENSP00000351185:p.Glu869Lys	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	167	58	NM_001080449	0	0	0	0	0	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.14|16.14	3.040039|3.040039	0.55003|0.55003	0.0|0.0	1.21E-4|1.21E-4	ENSG00000138346|ENSG00000138346	ENST00000399180;ENST00000358410|ENST00000440722	D;D|.	0.91464|.	-2.85;-2.83|.	4.93|4.93	3.02|3.02	0.34903|0.34903	.|.	1.268580|.	0.05029|.	N|.	0.474288|.	T|T	0.58779|0.58779	0.2146|0.2146	L|L	0.49350|0.49350	1.555|1.555	0.80722|0.80722	D|D	1|1	P|.	0.49358|.	0.923|.	P|.	0.46796|.	0.527|.	T|T	0.54931|0.54931	-0.8219|-0.8219	10|5	0.11182|.	T|.	0.66|.	.|.	10.956|10.956	0.47358|0.47358	0.0:0.845:0.0:0.155|0.0:0.845:0.0:0.155	.|.	869|.	P51530|.	DNA2L_HUMAN|.	K|E	955;869|190	ENSP00000382133:E955K;ENSP00000351185:E869K|.	ENSP00000351185:E869K|.	E|G	-|-	1|2	0|0	DNA2|DNA2	69852080|69852080	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.905000|0.905000	0.53344|0.53344	2.929000|2.929000	0.48916|0.48916	1.035000|1.035000	0.39972|0.39972	0.655000|0.655000	0.94253|0.94253	GAA|GGA	.		0.393	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			T	70182074	C	T	70182074	3	4	150	1	0	0	0	0	1	0	0	0	4607	864	30	2	597	2	DNA2	10	70182074	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	18602899	70182074	65352673	46	13450											
HELLS	3070	bcgsc.ca	37	chr10	96305697	96305697	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgccagcggaacggcccGcgggcagcggcggtgagtga	7	3	19	12	6	0	2	0	2	0	0	0	3	0	3	2	5	4	2	2	5	1	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:96305697G>A	ENST00000348459.5	+	1	124	c.19G>A	c.(19-21)Gcg>Acg	p.A7T	HELLS_ENST00000394045.1_Missense_Mutation_p.A7T|HELLS_ENST00000394036.1_Missense_Mutation_p.A7T|HELLS_ENST00000394044.1_Missense_Mutation_p.A7T|HELLS_ENST00000371332.4_Missense_Mutation_p.A7T|HELLS_ENST00000239026.6_Missense_Mutation_p.A7T	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		GGAACGGCCCGCGGGCAGCGG	0.692																																					p.A7T													.	HELLS-92	0			c.G19A						.						12	13	13					10																	96305697		2121	4139	6260	SO:0001583	missense	3070	exon1			CGGCCCGCGGGCA	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6", "proliferation-associated SNF2-like protein"	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.19G>A	10.37:g.96305697G>A	ENSP00000239027:p.Ala7Thr	Somatic	152	4		WXS	Illumina HiSeq	Phase_1	67	36	NM_018063	0	0	0	0	0		Missense_Mutation	SNP	ENST00000348459.5	37	CCDS7434.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.777463	0.31411	.	.	ENSG00000119969	ENST00000348459;ENST00000394045;ENST00000394044;ENST00000394036;ENST00000371332;ENST00000239026	D;D;D;D	0.96200	-2.52;-2.2;-3.94;-2.7	4.41	3.43	0.39272	.	0.221844	0.36591	N	0.002517	D	0.89598	0.6761	L	0.29908	0.895	0.22866	N	0.998634	B;P;P;B	0.44946	0.382;0.82;0.846;0.382	B;B;B;B	0.36608	0.039;0.202;0.229;0.058	D	0.85080	0.0945	10	0.72032	D	0.01	-13.4778	9.7376	0.40397	0.0:0.211:0.789:0.0	.	7;7;7;7	Q6I7N8;Q9NRZ9-6;Q9NRZ9-5;Q9NRZ9	.;.;.;HELLS_HUMAN	T	7	ENSP00000239027:A7T;ENSP00000377609:A7T;ENSP00000377608:A7T;ENSP00000360383:A7T	ENSP00000239026:A7T	A	+	1	0	HELLS	96295687	0.218000	0.23608	0.996000	0.52242	0.025000	0.11179	1.648000	0.37271	2.450000	0.82876	0.591000	0.81541	GCG	.		0.692	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063		A	96305697	G	A	96305697	3	1	150	1	0	0	0	0	1	0	0	0	7067	1087	38	1	21	1	HELLS	10	96305697	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	26123623	96305697	39229050	47	13451											
HPSE2	60495	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	100481443	100481443	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agggcgatgacattcttcctCggccgcccaatattagggcc	8	9	11	13	3	1	1	0	1	1	0	3	2	2	1	4	3	0	0	4	3	3	4	rs200916817		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:100481443C>T	ENST00000370552.3	-	5	986	c.927G>A	c.(925-927)ccG>ccA	p.P309P	HPSE2_ENST00000370546.1_Silent_p.P309P|HPSE2_ENST00000404542.1_Silent_p.P197P|HPSE2_ENST00000370549.1_Silent_p.P251P	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	309					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CATTCTTCCTCGGCCGCCCAA	0.438																																					p.P309P		.											.	HPSE2-91	0			c.G927A						.						55	54	54					10																	100481443		2203	4300	6503	SO:0001819	synonymous_variant	60495	exon5			CTTCCTCGGCCGC	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"urofacial syndrome", "heparanase 2"	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.927G>A	10.37:g.100481443C>T		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	64	7	NM_001166246	0	0	0	0	0	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Silent	SNP	ENST00000370552.3	37	CCDS7477.1																																																																																			C|0.999;T|0.001		0.438	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100481443	C	T	100481443	2	4	150	1	0	0	0	0	0	0	0	1	7366	871	31	1		1	HPSE2	10	100481443	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	4175746	100481443	35053304	48	13452											
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	104123472	104123472	+	Frame_Shift_Del	DEL	A	A	-																															tcttcctactcctagctgacAaaaagtttgcccggaagcca																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:104123472delA	ENST00000369983.3	+	17	2280	c.2020delA	c.(2020-2022)aaafs	p.K675fs		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	675					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTAGCTGACAAAAAGTTTGC	0.423																																					p.K675fs		.											.	GBF1-91	0			c.2023delA						.						113	119	117					10																	104123472		2203	4300	6503	SO:0001589	frameshift_variant	8729	exon17			.	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2020delA	10.37:g.104123472delA	ENSP00000359000:p.Lys675fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	69	19	NM_001199378	0	0	0	0	0	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Frame_Shift_Del	DEL	ENST00000369983.3	37	CCDS7533.1																																																																																			.		0.423	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			-	104123472	A	-	104123472	7	5	150	1	0	1	0	1	0	0	0	0	6291	131	5	0	2082	0	GBF1	10	104123472	Frame_Shift_Del	DEL	A	TCGA-MH-A560-01A-11D-A26P-10	3642029	104123472	31411275	49	13453											
ACADSB	36	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	124800167	124800167	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacaaaaggccacctatttGcctcagctcactacagaaaa	16	7	6	12	0	2	1	2	0	0	1	2	2	2	1	3	1	4	1	3	1	7	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:124800167G>A	ENST00000358776.4	+	4	503	c.489G>A	c.(487-489)ttG>ttA	p.L163L	ACADSB_ENST00000496730.2_3'UTR|ACADSB_ENST00000368869.4_Silent_p.L61L	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	163					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	CCACCTATTTGCCTCAGCTCA	0.353																																					p.L163L													.	ACADSB-92	0			c.G489A						.						93	92	92					10																	124800167		2203	4300	6503	SO:0001819	synonymous_variant	36	exon4			CTATTTGCCTCAG	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"acyl-Coenzyme A dehydrogenase, short/branched chain"			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.489G>A	10.37:g.124800167G>A		Somatic	104	1		WXS	Illumina HiSeq	Phase_I	79	20	NM_001609	0	0	3	6	3	B4DQ51|Q5SQN6|Q96CX7	Silent	SNP	ENST00000358776.4	37	CCDS7634.1	.	.	.	.	.	.	.	.	.	.	G	1.569	-0.534723	0.04082	.	.	ENSG00000196177	ENST00000411816	.	.	.	5.41	1.02	0.19986	.	.	.	.	.	T	0.51092	0.1654	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	.	5.0983	0.14745	0.0737:0.1255:0.5425:0.2584	.	.	.	.	Y	169	.	.	C	+	2	0	ACADSB	124790157	0.743000	0.28239	0.081000	0.20488	0.482000	0.33219	1.056000	0.30480	-0.077000	0.12752	-0.345000	0.07892	TGC	.		0.353	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609		A	124800167	G	A	124800167	2	1	150	1	0	0	0	0	0	0	0	1	115	1310	46	2		2	ACADSB	10	124800167	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	20676695	124800167	10734580	50	13454											
FRG2B	441581	broad.mit.edu	37	chr10	135439107	135439107	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cactccttttctggacagttCcctgcaaagaaagcatgtga	11	11	8	11	0	1	2	0	1	1	1	3	3	3	3	2	1	2	3	2	1	2	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:135439107C>T	ENST00000425520.1	-	4	385	c.333G>A	c.(331-333)ggG>ggA	p.G111G	FRG2B_ENST00000443774.1_Splice_Site_p.G112G	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	111						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CTGGACAGTTCCCTGCAAAGA	0.512																																					p.G111G													.	.	0			c.G333A						.						15	19	18					10																	135439107		1984	4077	6061	SO:0001630	splice_region_variant	441581	exon4			ACAGTTCCCTGCA	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.332-1G>A	10.37:g.135439107C>T		Somatic	135	0		WXS	Illumina HiSeq	Phase_I	109	3	NM_001080998	0	0	0	0	0	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			.		0.512	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	Silent	T	135439107	C	T	135439107	5	4	150	1	0	0	0	0	0	0	1	0	6066	869	30	2	506	2	FRG2B	10	135439107	Splice_Site	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	10638940	135439107	95640	51	13455											
CARNS1	57571	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	67186592	67186592	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agccgccggggctgctgcggGgaggggatgccagcctaggg	5	4	21	11	3	0	0	0	0	0	0	0	2	0	2	4	7	5	2	4	7	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr11:67186592G>C	ENST00000307823.3	+	4	813	c.361G>C	c.(361-363)Gga>Cga	p.G121R	CARNS1_ENST00000531040.1_Missense_Mutation_p.G244R|CARNS1_ENST00000423745.2_Missense_Mutation_p.G121R|CARNS1_ENST00000445895.2_Missense_Mutation_p.G244R	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	121					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						GCTGCTGCGGGGAGGGGATGC	0.652																																					p.G244R		.											.	CARNS1-46	0			c.G730C						.						5	7	6					11																	67186592		1871	3990	5861	SO:0001583	missense	57571	exon5			CTGCGGGGAGGGG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.361G>C	11.37:g.67186592G>C	ENSP00000308268:p.Gly121Arg	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	37	20	NM_001166222	0	0	0	0	0	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	G	9.966	1.224062	0.22457	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000539452;ENST00000423745;ENST00000445895	T;T;T;T	0.32753	1.44;1.47;1.47;1.47	4.38	2.5	0.30297	.	.	.	.	.	T	0.31765	0.0807	N	0.19112	0.55	0.09310	N	1	D;P;D	0.62365	0.982;0.94;0.991	P;P;P	0.60068	0.868;0.605;0.868	T	0.09552	-1.0669	9	0.41790	T	0.15	.	7.4523	0.27246	0.2888:0.0:0.7112:0.0	.	244;121;260	F5H427;A5YM72;A5YM72-3	.;CRNS1_HUMAN;.	R	244;121;244;260;121;244	ENSP00000431670:G244R;ENSP00000308268:G121R;ENSP00000401519:G121R;ENSP00000389009:G244R	ENSP00000308268:G121R	G	+	1	0	CARNS1	66943168	0.111000	0.22076	0.569000	0.28460	0.012000	0.07955	2.541000	0.45735	0.487000	0.27698	0.561000	0.74099	GGA	.		0.652	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		C	67186592	G	C	67186592	3	2	150	1	0	0	0	0	1	0	0	0	2662	1233	43	4	744	4	CARNS1	11	67186592	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		67186592	67819924	52	13456											
DYNC2H1	79659	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	103006543	103006543	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcggcattccaaatcagtttAagggagtgggtgaggcagga	11	9	15	6	1	1	1	1	1	0	0	3	3	2	3	1	5	0	3	1	5	2	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr11:103006543A>G	ENST00000375735.2	+	17	2584	c.2440A>G	c.(2440-2442)Aag>Gag	p.K814E	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.K814E	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	814	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AAATCAGTTTAAGGGAGTGGG	0.373																																					p.K814E													.	DYNC2H1-68	0			c.A2440G						.						66	62	63					11																	103006543		1812	4068	5880	SO:0001583	missense	79659	exon17			CAGTTTAAGGGAG	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"Cytoplasmic dyneins"	2962	protein-coding gene	gene with protein product		603297	"dynein, cytoplasmic, heavy polypeptide 2"	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2440A>G	11.37:g.103006543A>G	ENSP00000364887:p.Lys814Glu	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	52	26	NM_001377	0	0	0	0	0	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.479055	0.63849	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.27720	1.65;1.65	5.3	5.3	0.74995	.	.	.	.	.	T	0.29190	0.0726	L	0.51422	1.61	0.42561	D	0.993144	B;B	0.17038	0.02;0.015	B;B	0.24701	0.04;0.055	T	0.10019	-1.0648	9	0.10111	T	0.7	.	15.2748	0.73734	1.0:0.0:0.0:0.0	.	814;814	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	E	814	ENSP00000364887:K814E;ENSP00000381167:K814E	ENSP00000364887:K814E	K	+	1	0	DYNC2H1	102511753	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.018000	0.76406	2.006000	0.58801	0.460000	0.39030	AAG	.		0.373	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103006543	A	G	103006543	3	3	150	1	0	0	0	0	1	0	0	0	4857	363	13	3	2506	3	DYNC2H1	11	103006543	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	35819951	103006543	31999973	53	13457											
C11orf53	341032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	111156468	111156468	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccttgccacccagcacgAgttgcctctcccagcttgag	7	9	9	16	1	1	2	0	2	1	0	2	3	1	2	5	0	4	3	5	0	0	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr11:111156468A>C	ENST00000280325.4	+	4	547	c.400A>C	c.(400-402)Agt>Cgt	p.S134R		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	134										endometrium(1)|large_intestine(2)|lung(3)|skin(2)	8		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)		ACCCAGCACGAGTTGCCTCTC	0.632																																					p.S134R		.											.	C11orf53-226	0			c.A400C						.						76	69	71					11																	111156468		2201	4297	6498	SO:0001583	missense	341032	exon4			AGCACGAGTTGCC	BC039669	CCDS31674.1	11q23.1	2012-05-31			ENSG00000150750	ENSG00000150750			30527	protein-coding gene	gene with protein product						12477932	Standard	NM_198498		Approved	MGC50104	uc001plc.3	Q8IXP5	OTTHUMG00000166656	ENST00000280325.4:c.400A>C	11.37:g.111156468A>C	ENSP00000280325:p.Ser134Arg	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	50	16	NM_198498	0	0	0	0	0		Missense_Mutation	SNP	ENST00000280325.4	37	CCDS31674.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908387	0.52333	.	.	ENSG00000150750	ENST00000280325	.	.	.	4.8	0.97	0.19692	.	0.382752	0.29198	N	0.012842	T	0.39009	0.1062	L	0.55481	1.735	0.09310	N	0.999997	P	0.43701	0.815	P	0.45681	0.49	T	0.21415	-1.0246	9	0.42905	T	0.14	-1.3318	7.5852	0.27989	0.7125:0.0:0.2875:0.0	.	134	Q8IXP5	CK053_HUMAN	R	134	.	ENSP00000280325:S134R	S	+	1	0	C11orf53	110661678	0.055000	0.20627	0.041000	0.18516	0.940000	0.58332	1.282000	0.33226	-0.088000	0.12506	0.459000	0.35465	AGT	.		0.632	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390989.1	NM_198498		C	111156468	A	C	111156468	3	2	150	1	0	0	0	0	1	0	0	0	1652	304	11	5	410	5	C11orf53	11	111156468	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	8149925	111156468	23850048	54	13458											
FOXRED1	55572	broad.mit.edu	37	chr11	126146393	126146393	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaggattaggtagcaactAcctaggtggtcgtagcccca	11	8	13	9	1	0	0	0	0	0	0	1	2	0	2	3	5	4	3	3	5	7	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr11:126146393A>G	ENST00000263578.5	+	9	1150	c.1076A>G	c.(1075-1077)tAc>tGc	p.Y359C	FOXRED1_ENST00000532125.1_Missense_Mutation_p.Y345C|FOXRED1_ENST00000442061.2_Missense_Mutation_p.Y189C|FOXRED1_ENST00000534011.1_3'UTR	NM_017547.3	NP_060017.1	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing 1	359						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		GGTAGCAACTACCTAGGTGGT	0.542																																					p.Y359C													.	FOXRED1-90	0			c.A1076G						.						96	92	94					11																	126146393		2201	4298	6499	SO:0001583	missense	55572	exon9			GCAACTACCTAGG		CCDS8471.1	11q24.2	2006-02-03			ENSG00000110074	ENSG00000110074			26927	protein-coding gene	gene with protein product		613622				10497265	Standard	NM_017547		Approved	H17	uc001qdi.3	Q96CU9	OTTHUMG00000165827	ENST00000263578.5:c.1076A>G	11.37:g.126146393A>G	ENSP00000263578:p.Tyr359Cys	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	205	5	NM_017547	0	0	44	47	3	B3KN84|B4DHU2|Q71MG0|Q9BU39|Q9UKY9	Missense_Mutation	SNP	ENST00000263578.5	37	CCDS8471.1	.	.	.	.	.	.	.	.	.	.	a	26.7	4.764863	0.90020	.	.	ENSG00000110074	ENST00000263578;ENST00000442061;ENST00000532125	D;D;D	0.83075	-1.68;-1.68;-1.68	5.63	5.63	0.86233	FAD dependent oxidoreductase (1);	0.106801	0.64402	D	0.000003	D	0.92714	0.7684	M	0.91038	3.17	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.996	D;D;D	0.72075	0.923;0.976;0.969	D	0.94089	0.7351	9	.	.	.	-9.8756	15.9066	0.79436	1.0:0.0:0.0:0.0	.	345;226;359	Q96CU9-3;B4DI59;Q96CU9	.;.;FXRD1_HUMAN	C	359;189;345	ENSP00000263578:Y359C;ENSP00000404371:Y189C;ENSP00000434178:Y345C	.	Y	+	2	0	FOXRED1	125651603	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	6.418000	0.73341	2.161000	0.67846	0.468000	0.43344	TAC	.		0.542	FOXRED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386434.1	NM_017547		G	126146393	A	G	126146393	3	3	150	1	0	0	0	0	1	0	0	0	6052	391	14	3	1110	3	FOXRED1	11	126146393	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	14989925	126146393	8860123	55	13459											
SLC6A13	6540	broad.mit.edu	37	chr12	347126	347126	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacaggagaggtggcattctCagaggtaccattcagggagc	11	7	15	8	0	2	2	2	0	1	2	3	5	2	3	1	5	2	2	1	5	1	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr12:347126C>T	ENST00000343164.4	-	5	581	c.529G>A	c.(529-531)Gag>Aag	p.E177K	SLC6A13_ENST00000445055.2_Missense_Mutation_p.E85K	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	177					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GTGGCATTCTCAGAGGTACCA	0.532																																					p.E177K													.	SLC6A13-90	0			c.G529A						.						163	138	146					12																	347126		2203	4300	6503	SO:0001583	missense	6540	exon5			CATTCTCAGAGGT	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"Solute carriers"	11046	protein-coding gene	gene with protein product	"GABA transporter 2"	615097	"solute carrier family 6 (neurotransmitter transporter, GABA), member 13"				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.529G>A	12.37:g.347126C>T	ENSP00000339260:p.Glu177Lys	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	220	6	NM_016615	0	0	65	66	1	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	8.909	0.958247	0.18507	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164;ENST00000546319	T;T;T	0.74106	-0.81;-0.81;-0.81	5.23	5.23	0.72850	.	0.158145	0.56097	D	0.000033	T	0.65811	0.2727	L	0.37897	1.145	0.46096	D	0.998866	B;B;B	0.18013	0.018;0.025;0.025	B;B;B	0.29524	0.021;0.103;0.014	T	0.59669	-0.7411	10	0.06494	T	0.89	.	17.3393	0.87291	0.0:1.0:0.0:0.0	.	85;156;177	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	K	85;156;177;85	ENSP00000407104:E85K;ENSP00000339260:E177K;ENSP00000444606:E85K	ENSP00000318097:E156K	E	-	1	0	SLC6A13	217387	0.997000	0.39634	0.994000	0.49952	0.059000	0.15707	3.474000	0.53129	2.596000	0.87737	0.561000	0.74099	GAG	.		0.532	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		T	347126	C	T	347126	3	4	150	1	0	0	0	0	1	0	0	0	14708	835	29	2	1323	2	SLC6A13	12	347126	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		347126	133504769	56	13460											
TPI1	7167	broad.mit.edu;bcgsc.ca	37	chr12	6976718	6976718	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacactgaccttcagcgcctCggctccagcgccatggcgcc	6	6	11	18	4	1	1	1	1	0	0	3	2	2	1	5	2	2	1	5	2	0	1	rs375712848		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr12:6976718C>T	ENST00000229270.4	+	1	436	c.99C>T	c.(97-99)ctC>ctT	p.L33L	TPI1_ENST00000396705.5_5'UTR|TPI1_ENST00000488464.2_5'Flank|TPI1_ENST00000535434.1_5'Flank	NM_001159287.1	NP_001152759.1	P60174	TPIS_HUMAN	triosephosphate isomerase 1	33					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glyceraldehyde-3-phosphate metabolic process (GO:0019682)|glycolytic process (GO:0006096)|multicellular organismal development (GO:0007275)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	triose-phosphate isomerase activity (GO:0004807)			endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|skin(2)	19						TTCAGCGCCTCGGCTCCAGCG	0.642																																					p.L33L													.	TPI1-226	0			c.C99T						.	C	,	1,4387		0,1,2193	12	16	14		,99	-0.5	0	12		14	0,8590		0,0,4295	no	utr-5,coding-synonymous	TPI1	NM_000365.5,NM_001159287.1	,	0,1,6488	TT,TC,CC		0.0,0.0228,0.0077	,	,33/287	6976718	1,12977	2194	4295	6489	SO:0001819	synonymous_variant	7167	exon1			GCGCCTCGGCTCC		CCDS8566.1, CCDS53740.1, CCDS58206.1	12p13.31	2012-10-02			ENSG00000111669	ENSG00000111669	5.3.1.1		12009	protein-coding gene	gene with protein product		190450					Standard	NM_000365		Approved		uc001qrk.4	P60174	OTTHUMG00000133767	ENST00000229270.4:c.99C>T	12.37:g.6976718C>T		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	69	6	NM_001159287	0	0	91	96	5	B7Z5D8|D3DUS9|P00938|Q6FHP9|Q6IS07|Q8WWD0|Q96AG5	Silent	SNP	ENST00000229270.4	37	CCDS53740.1																																																																																			.		0.642	TPI1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258252.1	NM_000365		T	6976718	C	T	6976718	2	4	150	1	0	0	0	0	0	0	0	1	16436	871	31	1		1	TPI1	12	6976718	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	6629592	6976718	126875177	57	13461											
C14orf39	317761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	60921717	60921717	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacttttggcttctcatattAcctgatctgatgagatttct	9	18	6	8	0	3	3	1	3	3	1	4	4	3	3	1	1	2	1	1	1	3	6			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr14:60921717A>T	ENST00000321731.3	-	16	1663		c.e16+1			NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39						multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TTCTCATATTACCTGATCTGA	0.313																																					.		.											.	C14orf39-94	0			c.1503+2T>A						.						36	39	38					14																	60921717		2198	4285	6483	SO:0001630	splice_region_variant	317761	exon17			CATATTACCTGAT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1503+1T>A	14.37:g.60921717A>T		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_174978	0	0	0	0	0	Q08AQ4	Splice_Site	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.563953	0.65651	.	.	ENSG00000179008	ENST00000321731	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5881	0.61944	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C14orf39	59991470	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.199000	0.65152	2.234000	0.73211	0.459000	0.35465	.	.		0.313	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	Intron	T	60921717	A	T	60921717	5	4	150	1	0	0	0	0	0	0	1	0	1776	405	14	5	270	5	C14orf39	14	60921717	Splice_Site	SNP	A	TCGA-MH-A560-01A-11D-A26P-10		60921717	46427823	58	13462											
ATAD5	79915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	29162089	29162089	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttcttgcacaggttcacccTattccgcccaaaaagacagg	11	9	8	13	1	2	1	1	0	1	1	3	1	3	1	3	2	1	3	3	2	3	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:29162089T>A	ENST00000321990.4	+	2	1368	c.990T>A	c.(988-990)ccT>ccA	p.P330P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	330					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AGGTTCACCCTATTCCGCCCA	0.378																																					p.P330P		.											.	ATAD5-93	0			c.T990A						.						49	51	50					17																	29162089		2139	4265	6404	SO:0001819	synonymous_variant	79915	exon2			TCACCCTATTCCG		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"ATPases / AAA-type"	25752	protein-coding gene	gene with protein product	"enhanced level of genomic instability 1 homolog (S. cerevisiae)"	609534	"chromosome 17 open reading frame 41"	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.990T>A	17.37:g.29162089T>A		Somatic	189	0		WXS	Illumina HiSeq	Phase_I	167	75	NM_024857	0	0	0	0	0	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			.		0.378	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		A	29162089	T	A	29162089	2	1	150	1	0	0	0	0	0	0	0	1	1077	1509	53	5		5	ATAD5	17	29162089	Silent	SNP	T	TCGA-MH-A560-01A-11D-A26P-10		29162089	52033121	59	13463											
ORMDL3	94103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	38078866	38078866	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcagcttggggataagcacGctcatcagggacacggtgtt	9	8	15	9	2	2	0	2	0	0	0	2	2	2	2	0	5	2	5	0	5	1	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:38078866G>C	ENST00000394169.1	-	6	1893	c.399C>G	c.(397-399)agC>agG	p.S133R	ORMDL3_ENST00000584220.1_Missense_Mutation_p.S117R|ORMDL3_ENST00000579695.1_Missense_Mutation_p.S133R|ORMDL3_ENST00000304046.2_Missense_Mutation_p.S133R			Q8N138	ORML3_HUMAN	ORMDL sphingolipid biosynthesis regulator 3	133					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|SPOTS complex (GO:0035339)				endometrium(3)|kidney(1)|lung(1)	5	Colorectal(19;0.000442)		Lung(15;0.0234)			GGATAAGCACGCTCATCAGGG	0.557																																					p.S133R		.											.	ORMDL3-68	0			c.C399G						.						149	142	144					17																	38078866		2203	4300	6503	SO:0001583	missense	94103	exon4			AAGCACGCTCATC		CCDS11355.1	17q12	2014-06-16	2014-06-16		ENSG00000172057	ENSG00000172057			16038	protein-coding gene	gene with protein product		610075	"ORM1 (S. cerevisiae)-like 3", "ORM1-like 3 (S. cerevisiae)"			23066021	Standard	NM_139280		Approved		uc002htj.2	Q8N138	OTTHUMG00000133249	ENST00000394169.1:c.399C>G	17.37:g.38078866G>C	ENSP00000377724:p.Ser133Arg	Somatic	159	0		WXS	Illumina HiSeq	Phase_I	141	29	NM_139280	0	0	47	83	36	B3KS83|Q6UY83	Missense_Mutation	SNP	ENST00000394169.1	37	CCDS11355.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582713	0.65992	.	.	ENSG00000172057	ENST00000304046;ENST00000394169	.	.	.	5.39	-5.34	0.02705	.	0.110120	0.64402	D	0.000008	T	0.59432	0.2193	M	0.65975	2.015	0.34860	D	0.74254	P	0.37573	0.6	P	0.47744	0.556	T	0.65915	-0.6052	9	0.51188	T	0.08	-14.1116	13.4255	0.61022	0.658:0.0:0.342:0.0	.	133	Q8N138	ORML3_HUMAN	R	133	.	ENSP00000304858:S133R	S	-	3	2	ORMDL3	35332392	0.062000	0.20869	0.906000	0.35671	0.939000	0.58152	-0.588000	0.05774	-1.031000	0.03308	-0.345000	0.07892	AGC	.		0.557	ORMDL3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257003.1	NM_139280		C	38078866	G	C	38078866	3	2	150	1	0	0	0	0	1	0	0	0	11297	1078	38	4	66	4	ORMDL3	17	38078866	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	8916777	38078866	43116344	60	13464											
CCDC46	201134	ucsc.edu	37	chr17	63923752	63923752	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttgccataaaaactcctttGattgtttctcacgaagagat	12	14	7	8	1	1	2	1	1	1	1	3	4	2	2	2	0	2	2	2	0	4	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:63923752G>A	ENST00000392769.2	-	19	2146	c.1928C>T	c.(1927-1929)tCa>tTa	p.S643L	CEP112_ENST00000535342.2_Missense_Mutation_p.S643L|CEP112_ENST00000537949.1_Missense_Mutation_p.S601L|CEP112_ENST00000541355.1_Missense_Mutation_p.S278L	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	643					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						AAACTCCTTTGATTGTTTCTC	0.303																																					p.S643L													.	CEP112-90	0			c.C1928T						.						102	97	98					17																	63923752		2203	4300	6503	SO:0001583	missense	201134	exon19			TCCTTTGATTGTT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"coiled-coil domain containing 46"	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1928C>T	17.37:g.63923752G>A	ENSP00000376522:p.Ser643Leu	Somatic	23	0		WXS	Illumina HiSeq		34	4	NM_001199165	0	0	5	5	0	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	37	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.834098	0.50951	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000541355;ENST00000537949	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	4.93	4.93	0.64822	.	0.227463	0.36932	N	0.002336	T	0.52917	0.1764	L	0.51422	1.61	0.32590	N	0.527272	D;D;D	0.54964	0.969;0.969;0.969	P;P;P	0.53313	0.723;0.654;0.723	T	0.58440	-0.7636	10	0.22109	T	0.4	-6.2893	15.4349	0.75137	0.0:0.0:1.0:0.0	.	601;601;643	F5GYE8;A2RRR7;Q8N8E3	.;.;CE112_HUMAN	L	643;643;278;601	ENSP00000442784:S643L;ENSP00000376522:S643L;ENSP00000443711:S278L;ENSP00000440775:S601L	ENSP00000376522:S643L	S	-	2	0	CEP112	61354214	0.984000	0.35163	0.409000	0.26459	0.986000	0.74619	4.019000	0.57181	2.446000	0.82766	0.650000	0.86243	TCA	.		0.303	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036		A	63923752	G	A	63923752	3	1	150	1	0	0	0	0	1	0	0	0	2823	1294	45	2	1141	2	CCDC46	17	63923752	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	25844886	63923752	17271458	61	13465											
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65110487	65110487	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtgttcgaatcttattaaTttcaggtccggaattatttg	9	18	9	5	2	2	0	1	0	1	0	4	2	3	1	1	3	0	1	1	3	5	6			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:65110487T>G	ENST00000358691.5	-	28	4037	c.3871A>C	c.(3871-3873)Att>Ctt	p.I1291L	HELZ_ENST00000580168.1_Missense_Mutation_p.I1292L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1291						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					ATCTTATTAATTTCAGGTCCG	0.348																																					p.I1291L		.											.	HELZ-92	0			c.A3871C						.						152	136	141					17																	65110487		1802	4071	5873	SO:0001583	missense	9931	exon28			TATTAATTTCAGG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.3871A>C	17.37:g.65110487T>G	ENSP00000351524:p.Ile1291Leu	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	47	31	NM_014877	0	0	0	3	3	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022328	0.35701	.	.	ENSG00000198265	ENST00000358691	D	0.82344	-1.6	5.65	4.56	0.56223	.	0.541833	0.21875	N	0.067829	T	0.64283	0.2584	N	0.14661	0.345	0.28505	N	0.913814	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50625	-0.8806	10	0.10111	T	0.7	-10.9431	7.073	0.25189	0.0:0.078:0.1469:0.7752	.	1292;1291	B7ZLW2;P42694	.;HELZ_HUMAN	L	1291	ENSP00000351524:I1291L	ENSP00000351524:I1291L	I	-	1	0	HELZ	62540949	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.522000	0.45572	2.154000	0.67381	0.445000	0.29226	ATT	.		0.348	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65110487	T	G	65110487	3	3	150	1	0	0	0	0	1	0	0	0	7070	1493	52	5	1981	5	HELZ	17	65110487	Missense_Mutation	SNP	T	TCGA-MH-A560-01A-11D-A26P-10	1186735	65110487	16084723	62	13466											
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	21511115	21511115	+	Frame_Shift_Del	DEL	G	G	-																															atttttaaatctccacagacGtatatggatggtttactgca																								rs546328935		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr18:21511115delG	ENST00000313654.9	+	65	8767	c.8526delG	c.(8524-8526)acgfs	p.T2842fs	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Frame_Shift_Del_p.T1233fs|LAMA3_ENST00000587184.1_Frame_Shift_Del_p.T1177fs|LAMA3_ENST00000399516.3_Frame_Shift_Del_p.T2786fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2842	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CTCCACAGACGTATATGGATG	0.428																																					p.T2842fs		.											.	LAMA3-100	0			c.8526delG						.						110	110	110					18																	21511115		2203	4300	6503	SO:0001589	frameshift_variant	3909	exon65			.	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8526delG	18.37:g.21511115delG	ENSP00000324532:p.Thr2842fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	49	13	NM_198129	0	0	0	0	0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	37	CCDS42419.1																																																																																			.		0.428	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21511115	G	-	21511115	7	5	150	1	0	1	0	1	0	0	0	0	8628	1132	40	0	8959	0	LAMA3	18	21511115	Frame_Shift_Del	DEL	G	TCGA-MH-A560-01A-11D-A26P-10		21511115	56566133	63	13467	142	2									
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	21511118	21511118	+	Frame_Shift_Del	DEL	T	T	-																															tttaaatctccacagacgtaTatggatggtttactgcatta																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr18:21511118delT	ENST00000313654.9	+	65	8770	c.8529delT	c.(8527-8529)tatfs	p.Y2843fs	LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Frame_Shift_Del_p.Y1234fs|LAMA3_ENST00000587184.1_Frame_Shift_Del_p.Y1178fs|LAMA3_ENST00000399516.3_Frame_Shift_Del_p.Y2787fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2843	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					CACAGACGTATATGGATGGTT	0.428																																					p.Y2843X		.											.	LAMA3-100	0			c.8529delT						.						112	111	111					18																	21511118		2203	4300	6503	SO:0001589	frameshift_variant	3909	exon65			.	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8529delT	18.37:g.21511118delT	ENSP00000324532:p.Tyr2843fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	57	13	NM_198129	0	0	0	0	0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Nonsense_Mutation	DEL	ENST00000313654.9	37	CCDS42419.1																																																																																			.		0.428	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21511118	T	-	21511118	7	5	150	1	0	1	0	1	0	0	0	0	8628	1413	49	0	8962	0	LAMA3	18	21511118	Frame_Shift_Del	DEL	T	TCGA-MH-A560-01A-11D-A26P-10	3	21511118	56566130	64	13468	142	2									
DSC3	1825	bcgsc.ca	37	chr18	28598133	28598133	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaatggtaaaattgactctCcaattggcagtgttaattaa	16	13	7	5	0	1	1	0	1	1	0	2	1	1	1	1	2	0	3	1	2	7	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr18:28598133C>T	ENST00000360428.4	-	9	1247	c.1167G>A	c.(1165-1167)tgG>tgA	p.W389*	DSC3_ENST00000434452.1_Nonsense_Mutation_p.W389*	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	389	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			AATTGACTCTCCAATTGGCAG	0.323																																					p.W389X													.	DSC3-94	0			c.G1167A						.						100	97	98					18																	28598133		2202	4294	6496	SO:0001587	stop_gained	1825	exon9			GACTCTCCAATTG	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"Cadherins / Major cadherins"	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.1167G>A	18.37:g.28598133C>T	ENSP00000353608:p.Trp389*	Somatic	58	0		WXS	Illumina HiSeq	Phase_1	54	4	NM_024423	0	0	0	0	0	A6NN35|Q14200|Q9HAZ9	Nonsense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	C	38	6.731705	0.97796	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	.	.	.	5.36	5.36	0.76844	.	0.784395	0.10265	N	0.695489	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6188	0.76790	0.0:0.8623:0.1377:0.0	.	.	.	.	X	389	.	ENSP00000353608:W389X	W	-	3	0	DSC3	26852131	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.982000	0.56909	2.805000	0.96524	0.579000	0.79373	TGG	.		0.323	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		T	28598133	C	T	28598133	4	4	150	1	0	0	0	0	0	1	0	0	4778	856	30	2	1586	2	DSC3	18	28598133	Nonsense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	7087015	28598133	49479115	65	13469											
CREB3L3	84699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	4171149	4171149	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtccaccagcaagtcaGcccagacaggcacctgtgtc	10	6	10	15	0	1	1	1	0	0	1	3	1	2	1	4	1	3	3	4	1	1	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:4171149G>T	ENST00000078445.2	+	8	1099	c.952G>T	c.(952-954)Gcc>Tcc	p.A318S	CREB3L3_ENST00000602147.1_Missense_Mutation_p.S282I|CREB3L3_ENST00000602257.1_Missense_Mutation_p.A316S|CREB3L3_ENST00000252587.3_Intron|CREB3L3_ENST00000595923.1_Missense_Mutation_p.A317S	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	318					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCAAGTCAGCCCAGACAGG	0.607																																					p.A318S		.											.	CREB3L3-92	0			c.G952T						.						75	70	72					19																	4171149		2203	4300	6503	SO:0001583	missense	84699	exon8			AAGTCAGCCCAGA		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"basic leucine zipper proteins"	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.952G>T	19.37:g.4171149G>T	ENSP00000078445:p.Ala318Ser	Somatic	147	0		WXS	Illumina HiSeq	Phase_I	115	42	NM_032607	0	0	0	0	0	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	37	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462217	0.26248	.	.	ENSG00000060566	ENST00000078445;ENST00000381943	D	0.84800	-1.9	4.58	4.58	0.56647	.	0.130552	0.51477	D	0.000098	D	0.87172	0.6111	M	0.67569	2.06	0.52099	D	0.999947	D;P;P	0.62365	0.991;0.712;0.589	P;B;B	0.57204	0.815;0.396;0.223	D	0.84697	0.0726	10	0.26408	T	0.33	-0.2402	8.6838	0.34225	0.1062:0.0:0.8938:0.0	.	316;317;318	B7ZL69;Q68CJ9-2;Q68CJ9	.;.;CR3L3_HUMAN	S	318;276	ENSP00000078445:A318S	ENSP00000078445:A318S	A	+	1	0	CREB3L3	4122149	0.995000	0.38212	0.954000	0.39281	0.235000	0.25334	4.071000	0.57556	2.093000	0.63338	0.561000	0.74099	GCC	.		0.607	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4171149	G	T	4171149	3	4	150	1	0	0	0	0	1	0	0	0	3864	971	34	4	982	4	CREB3L3	19	4171149	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		4171149	54957834	66	13470											
OR7G3	390883	broad.mit.edu	37	chr19	9237432	9237432	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagatgtcgaccaaggacagGatagagaggaggaagtacat	16	5	14	6	1	0	2	0	0	0	2	1	8	0	6	1	4	1	1	1	4	4	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:9237432G>C	ENST00000305444.2	-	1	194	c.195C>G	c.(193-195)atC>atG	p.I65M		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						CCAAGGACAGGATAGAGAGGA	0.547																																					p.I65M													.	OR7G3-69	0			c.C195G						.						130	103	112					19																	9237432		2203	4300	6503	SO:0001583	missense	390883	exon1			GGACAGGATAGAG		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"GPCR / Class A : Olfactory receptors"	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.195C>G	19.37:g.9237432G>C	ENSP00000302867:p.Ile65Met	Somatic	257	0		WXS	Illumina HiSeq	Phase_I	233	4	NM_001001958	0	0	0	0	0	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	37	CCDS32899.1	.	.	.	.	.	.	.	.	.	.	G	5.991	0.366728	0.11352	.	.	ENSG00000170920	ENST00000305444	T	0.02974	4.09	4.02	-5.34	0.02705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45126	U	0.000383	T	0.01523	0.0049	N	0.12569	0.235	0.09310	N	1	B	0.27732	0.187	B	0.28385	0.089	T	0.39440	-0.9614	10	0.87932	D	0	.	7.1572	0.25645	0.4886:0.116:0.3955:0.0	.	65	Q8NG95	OR7G3_HUMAN	M	65	ENSP00000302867:I65M	ENSP00000302867:I65M	I	-	3	3	OR7G3	9098432	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.199000	0.09491	-1.049000	0.03234	0.558000	0.71614	ATC	.		0.547	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1			C	9237432	G	C	9237432	3	2	150	1	0	0	0	0	1	0	0	0	11250	1164	41	4	746	4	OR7G3	19	9237432	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	5066283	9237432	49891551	67	13471											
ZNF227	7770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44739325	44739325	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaattacccttaggagagAaaccccatccatgtggtgag	14	8	10	9	0	0	3	0	1	0	2	1	5	1	4	4	2	2	0	4	2	4	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:44739325A>T	ENST00000313040.7	+	6	947	c.742A>T	c.(742-744)Aaa>Taa	p.K248*	ZNF227_ENST00000589005.1_Nonsense_Mutation_p.K197*|ZNF227_ENST00000391961.2_Nonsense_Mutation_p.K197*	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	248					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)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CTTAGGAGAGAAACCCCATCC	0.428																																					p.K248X		.											.	ZNF227-91	0			c.A742T						.						50	52	51					19																	44739325		2203	4300	6503	SO:0001587	stop_gained	7770	exon6			GGAGAGAAACCCC	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.742A>T	19.37:g.44739325A>T	ENSP00000321049:p.Lys248*	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	73	29	NM_182490	0	0	1	1	0	B3KRU7|B7Z5P9	Nonsense_Mutation	SNP	ENST00000313040.7	37	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	37	6.426321	0.97559	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980	.	.	.	4.04	1.86	0.25419	.	.	.	.	.	.	.	.	.	.	.	0.23150	N	0.99822	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.6647	0.23035	0.7832:0.0:0.2168:0.0	.	.	.	.	X	248;205;197;227	.	ENSP00000321049:K248X	K	+	1	0	ZNF227	49431165	0.006000	0.16342	0.000000	0.03702	0.751000	0.42716	2.219000	0.42899	0.218000	0.20820	0.460000	0.39030	AAA	.		0.428	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44739325	A	T	44739325	4	4	150	1	0	0	0	0	0	1	0	0	17813	247	9	5	756	5	ZNF227	19	44739325	Nonsense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	35501893	44739325	14389658	68	13472											
C5AR1	728	broad.mit.edu	37	chr19	47823729	47823729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgctccggacgtggagccGcagggccacgcggtccacca	6	4	14	17	5	0	0	0	0	0	0	2	2	2	2	6	4	2	2	6	4	0	0	rs201394213		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:47823729G>A	ENST00000355085.3	+	2	717	c.695G>A	c.(694-696)cGc>cAc	p.R232H		NM_001736.3	NP_001727.1	P21730	C5AR1_HUMAN	complement component 5a receptor 1	232					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|cell proliferation in hindbrain (GO:0021534)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)|complement component C5a signaling pathway (GO:0038178)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of neuron apoptotic process (GO:0043524)|neutrophil chemotaxis (GO:0030593)|organ regeneration (GO:0031100)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)|complement component C5a receptor activity (GO:0004878)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)	20		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)		ACGTGGAGCCGCAGGGCCACG	0.597																																					.													.	C5AR1-93	0			.						.	G	HIS/ARG	0,4406		0,0,2203	91	88	89		695	4.8	1	19		89	1,8599	1.2+/-3.3	0,1,4299	no	missense	C5AR1	NM_001736.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	232/351	47823729	1,13005	2203	4300	6503	SO:0001583	missense	728	.			GGAGCCGCAGGGC		CCDS33063.1	19q13.3-q13.4	2012-08-10	2006-02-09	2006-02-09		ENSG00000197405		"CD molecules", "Complement system", "GPCR / Class A : Complement component receptors"	1338	protein-coding gene	gene with protein product		113995	"complement component 5 receptor 1 (C5a ligand)"	C5R1		1612600	Standard	NM_001736		Approved	C5A, C5AR, CD88	uc002pgj.1	P21730		ENST00000355085.3:c.695G>A	19.37:g.47823729G>A	ENSP00000347197:p.Arg232His	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	146	4	.	0	0	4	4	0		Missense_Mutation	SNP	ENST00000355085.3	37	CCDS33063.1	.	.	.	.	.	.	.	.	.	.	g	28.0	4.881187	0.91740	0.0	1.16E-4	ENSG00000197405	ENST00000355085	T	0.38560	1.13	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.459330	0.21120	U	0.079828	T	0.57359	0.2048	M	0.81179	2.53	0.52099	D	0.999945	D	0.61080	0.989	P	0.52066	0.689	T	0.63470	-0.6630	10	0.51188	T	0.08	.	14.8986	0.70661	0.0:0.0:1.0:0.0	.	232	P21730	C5AR_HUMAN	H	232	ENSP00000347197:R232H	ENSP00000347197:R232H	R	+	2	0	C5AR1	52515569	0.000000	0.05858	0.976000	0.42696	0.893000	0.52053	0.899000	0.28417	2.221000	0.72209	0.472000	0.43445	CGC	.		0.597	C5AR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466925.1	NM_001736		A	47823729	G	A	47823729	3	1	150	1	0	0	0	0	1	0	0	0	2287	1087	38	1	700	1	C5AR1	19	47823729	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	3084404	47823729	11305254	69	13473											
SIGLEC5	8778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52131213	52131213	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggtattggagatgggggTggcgttcagggcaggggagc	6	7	21	7	2	1	1	1	0	0	1	1	3	1	2	1	8	1	3	1	8	1	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:52131213T>A	ENST00000534261.2	-	6	1270	c.871A>T	c.(871-873)Acc>Tcc	p.T291S	SIGLEC5_ENST00000429354.3_Missense_Mutation_p.T291S|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.T291S|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.T291S|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.T291S			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	291	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		GAGATGGGGGTGGCGTTCAGG	0.647																																					p.T291S		.											.	SIGLEC5-92	0			c.A871T						.						64	71	69					19																	52131213		2203	4300	6503	SO:0001583	missense	8778	exon5			TGGGGGTGGCGTT	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"Sialic acid binding Ig-like lectins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.871A>T	19.37:g.52131213T>A	ENSP00000473238:p.Thr291Ser	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	93	37	NM_003830	0	0	0	0	0		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	T	3.867	-0.028769	0.07589	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.13420	2.59;2.59	3.76	-6.36	0.01969	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.943120	0.02702	N	0.111846	T	0.04952	0.0133	N	0.11560	0.145	0.09310	N	1	B	0.32829	0.386	B	0.35931	0.214	T	0.26883	-1.0090	10	0.02654	T	1	.	1.2256	0.01932	0.4652:0.1053:0.2382:0.1914	.	291	O15389	SIGL5_HUMAN	S	291	ENSP00000222107:T291S;ENSP00000415200:T291S	ENSP00000222107:T291S	T	-	1	0	SIGLEC5	56823025	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.639000	0.02011	-1.347000	0.02208	0.383000	0.25322	ACC	.		0.647	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		A	52131213	T	A	52131213	3	1	150	1	0	0	0	0	1	0	0	0	14343	1696	59	5	804	5	SIGLEC5	19	52131213	Missense_Mutation	SNP	T	TCGA-MH-A560-01A-11D-A26P-10	4307484	52131213	6997770	70	13474											
TGIF2	60436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	35219589	35219589	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggagtctcccaagcccCtggtgacccctggtagcaca	8	7	11	15	0	1	1	0	1	1	0	2	2	1	2	5	3	3	3	5	3	2	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr20:35219589C>A	ENST00000373874.2	+	3	668	c.469C>A	c.(469-471)Ctg>Atg	p.L157M	TGIF2-C20orf24_ENST00000558530.1_Intron|TGIF2_ENST00000373872.4_Missense_Mutation_p.L157M|RP5-977B1.11_ENST00000561134.1_RNA	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	157	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				TCCCAAGCCCCTGGTGACCCC	0.632																																					p.L157M		.											.	TGIF2-92	0			c.C469A						.						36	42	40					20																	35219589		2203	4300	6503	SO:0001583	missense	60436	exon3			AAGCCCCTGGTGA	AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"Homeoboxes / TALE class"	15764	protein-coding gene	gene with protein product		607294	"TGFB-induced factor 2 (TALE family homeobox)"			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.469C>A	20.37:g.35219589C>A	ENSP00000362981:p.Leu157Met	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	53	30	NM_021809	0	0	1	2	1	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	37	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390012	0.42410	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	T;T	0.65732	-0.17;-0.17	5.57	2.49	0.30216	.	3.072470	0.00622	N	0.000451	T	0.50718	0.1632	N	0.14661	0.345	0.80722	D	1	P	0.47106	0.89	P	0.44990	0.466	T	0.35822	-0.9773	10	0.46703	T	0.11	-14.2668	5.1002	0.14754	0.1452:0.6315:0.0:0.2233	.	157	Q9GZN2	TGIF2_HUMAN	M	157	ENSP00000362981:L157M;ENSP00000362979:L157M	ENSP00000362979:L157M	L	+	1	2	TGIF2	34653003	0.043000	0.20138	0.816000	0.32577	0.586000	0.36452	0.322000	0.19576	0.262000	0.21774	0.561000	0.74099	CTG	.		0.632	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809		A	35219589	C	A	35219589	3	1	150	1	0	0	0	0	1	0	0	0	15858	680	24	4	475	4	TGIF2	20	35219589	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		35219589	27805931	71	13475											
HNF4A	3172	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	43052875	43052876	+	Frame_Shift_Ins	INS	-	-	C																															ccaagattgacaacctgttgINScaggagatgctgctgggagg																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr20:43052875_43052876insC	ENST00000316099.4	+	8	1199_1200	c.1110_1111insC	c.(1111-1113)cagfs	p.Q371fs	HNF4A_ENST00000457232.1_Frame_Shift_Ins_p.Q349fs|HNF4A_ENST00000443598.2_Frame_Shift_Ins_p.Q371fs|HNF4A_ENST00000609795.1_Frame_Shift_Ins_p.Q349fs|HNF4A_ENST00000415691.2_Frame_Shift_Ins_p.Q371fs|HNF4A_ENST00000316673.4_Frame_Shift_Ins_p.Q349fs|AL132772.1_ENST00000581483.1_RNA	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	371					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			ACAACCTGTTGCAGGAGATGCT	0.609																																					p.L370fs	Colon(79;2 1269 8820 14841 52347)	.											.	HNF4A-227	0			c.1110_1111insC						.																																			SO:0001589	frameshift_variant	3172	exon8			.	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"Nuclear hormone receptors"	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.1111dupC	20.37:g.43052876_43052876dupC	ENSP00000312987:p.Gln371fs	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	148	50	NM_178849	0	0	0	0	0	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Frame_Shift_Ins	INS	ENST00000316099.4	37	CCDS13330.1																																																																																			.		0.609	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			C	43052876	-	C	43052875	7	5	150	1	0	1	1	0	0	0	0	0	7274	1310	46	0	1193	0	HNF4A	20	43052875	Frame_Shift_Ins	INS	-	TCGA-MH-A560-01A-11D-A26P-10	7833286	43052875	19972645	72	13476											
SUSD2	56241	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24583996	24583996	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caacaggtacctggcgggttCcaccatctacttccactgtg	8	10	9	14	1	1	0	0	0	1	0	3	0	3	0	4	3	3	2	4	3	3	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:24583996C>A	ENST00000358321.3	+	13	2495	c.2234C>A	c.(2233-2235)tCc>tAc	p.S745Y		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	745	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						CTGGCGGGTTCCACCATCTAC	0.642																																					p.S745Y		.											.	SUSD2-91	0			c.C2234A						.						80	82	81					22																	24583996		2203	4300	6503	SO:0001583	missense	56241	exon13			CGGGTTCCACCAT	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.2234C>A	22.37:g.24583996C>A	ENSP00000351075:p.Ser745Tyr	Somatic	472	0		WXS	Illumina HiSeq	Phase_I	357	138	NM_019601	0	0	2	3	1	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	37	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366350	0.61513	.	.	ENSG00000099994	ENST00000358321	T	0.68181	-0.31	4.75	4.75	0.60458	Complement control module (2);Sushi/SCR/CCP (3);	0.119454	0.64402	D	0.000016	D	0.83403	0.5247	M	0.89414	3.03	0.41536	D	0.988484	D	0.76494	0.999	D	0.77004	0.989	D	0.86729	0.1947	10	0.72032	D	0.01	-53.0137	13.6888	0.62533	0.0:1.0:0.0:0.0	.	745	Q9UGT4	SUSD2_HUMAN	Y	745	ENSP00000351075:S745Y	ENSP00000351075:S745Y	S	+	2	0	SUSD2	22913996	0.999000	0.42202	0.998000	0.56505	0.451000	0.32288	4.155000	0.58131	2.383000	0.81215	0.505000	0.49811	TCC	.		0.642	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24583996	C	A	24583996	3	1	150	1	0	0	0	0	1	0	0	0	15440	855	30	4	2284	4	SUSD2	22	24583996	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		24583996	26720570	73	13477											
RFPL1	5988	broad.mit.edu	37	chr22	29837996	29837996	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgctgaggagccactgcActtgttttttgctcctccaa	6	14	8	13	0	1	1	0	1	1	0	3	2	3	2	3	1	4	4	3	1	1	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:29837996A>G	ENST00000354373.2	+	2	1048	c.839A>G	c.(838-840)cAc>cGc	p.H280R	RFPL1S_ENST00000539579.1_RNA|RFPL1S_ENST00000461286.3_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	280	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						GAGCCACTGCACTTGTTTTTT	0.463																																					p.H280R													.	RFPL1-90	0			c.A839G						.						104	89	94					22																	29837996		2203	4300	6503	SO:0001583	missense	5988	exon2			CACTGCACTTGTT	AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"RING-type (C3HC4) zinc fingers"	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.839A>G	22.37:g.29837996A>G	ENSP00000346342:p.His280Arg	Somatic	201	2		WXS	Illumina HiSeq	Phase_I	195	5	NM_021026	0	0	0	0	0	Q6IC06|Q9UJ97	Missense_Mutation	SNP	ENST00000354373.2	37	CCDS13857.2	.	.	.	.	.	.	.	.	.	.	G	3.480	-0.106045	0.06924	.	.	ENSG00000128250	ENST00000354373	T	0.67865	-0.29	1.42	0.296	0.15757	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.23133	0.0559	N	0.00387	-1.565	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33574	-0.9863	9	0.02654	T	1	.	4.6941	0.12795	0.6416:0.0:0.3584:0.0	.	280	O75677	RFPL1_HUMAN	R	280	ENSP00000346342:H280R	ENSP00000346342:H280R	H	+	2	0	RFPL1	28167996	0.000000	0.05858	0.003000	0.11579	0.009000	0.06853	-1.609000	0.02066	-0.124000	0.11724	-1.063000	0.02288	CAC	.		0.463	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026		G	29837996	A	G	29837996	3	3	150	1	0	0	0	0	1	0	0	0	13285	159	6	3	845	3	RFPL1	22	29837996	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	5254000	29837996	21466570	74	13478											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	146	49	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	150	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	47566	29885562	21419004	75	13479											
NEFH	4744	broad.mit.edu	37	chr22	29885622	29885623	+	In_Frame_Ins	INS	-	-	AGGAAG																															agaggccaagtcccctgagaINSaggccaagtccccagtgaag																								rs267607534|rs267607535		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:29885622_29885623insAGGAAG	ENST00000310624.6	+	4	2026_2027	c.1993_1994insAGGAAG	c.(1993-1995)aag>aAGGAAGag	p.665_666insEE		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	671	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GTCCCCTGAGAAGGCCAAGTCC	0.579																																					p.K665delinsKEE													.	NEFH-90	0			c.1993_1994insAGGAAG						.																																			SO:0001652	inframe_insertion	4744	exon4			CCTGAGAAGGCCA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	Exception_encountered	22.37:g.29885622_29885623insAGGAAG	ENSP00000311997:p.Lys665_Ala666insGluGlu	Somatic	394	0		WXS	Illumina HiSeq	Phase_I	280	0	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																			.		0.579	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		AGGAAG	29885623	-	AGGAAG	29885622	7	5	150	1	0	1	1	0	0	0	0	0	10340	247	9	0	2007	0	NEFH	22	29885622	In_Frame_Ins	INS	-	TCGA-MH-A560-01A-11D-A26P-10	60	29885622	21418944	76	13480											
CACNG2	10369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	37098581	37098581	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggcagcgaaagcaccaacgGtggttaaaagcatttgaaca	16	6	11	8	2	0	1	0	1	0	0	0	2	0	1	1	3	5	4	1	3	5	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:37098581G>T	ENST00000300105.6	-	1	1022	c.41C>A	c.(40-42)aCc>aAc	p.T14N	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	14					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						AGCACCAACGGTGGTTAAAAG	0.488																																					p.T14N		.											.	CACNG2-90	0			c.C41A						.						154	142	146					22																	37098581		2203	4300	6503	SO:0001583	missense	10369	exon1			CCAACGGTGGTTA	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.41C>A	22.37:g.37098581G>T	ENSP00000300105:p.Thr14Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	149	56	NM_006078	0	0	0	0	0	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	37	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	g	19.64	3.865847	0.71949	.	.	ENSG00000166862	ENST00000300105	D	0.89681	-2.55	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.94971	0.8373	M	0.84948	2.725	0.80722	D	1	D	0.62365	0.991	D	0.76071	0.987	D	0.95765	0.8804	10	0.72032	D	0.01	-20.8031	17.8661	0.88795	0.0:0.0:1.0:0.0	.	14	Q9Y698	CCG2_HUMAN	N	14	ENSP00000300105:T14N	ENSP00000300105:T14N	T	-	2	0	CACNG2	35428527	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.265000	0.95647	2.192000	0.70111	0.546000	0.68486	ACC	.		0.488	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			T	37098581	G	T	37098581	3	4	150	1	0	0	0	0	1	0	0	0	2563	1261	44	4	946	4	CACNG2	22	37098581	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	7212959	37098581	14205985	77	13481											
FAM47A	158724	hgsc.bcm.edu;broad.mit.edu	37	chrX	34148936	34148936	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagtggagactggacctcCgacgtgtcttgggatgttcc	6	10	15	10	3	1	1	0	0	1	1	3	6	3	3	3	3	0	1	3	3	0	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chrX:34148936C>T	ENST00000346193.3	-	1	1511	c.1460G>A	c.(1459-1461)cGg>cAg	p.R487Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	487								p.R487Q(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						ACTGGACCTCCGACGTGTCTT	0.642																																					p.R487Q		.											.	FAM47A-134	1	Substitution - Missense(1)	large_intestine(1)	c.G1460A						.						47	54	51					X																	34148936		2192	4286	6478	SO:0001583	missense	158724	exon1			GACCTCCGACGTG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"similar to hypothetical protein FLJ35782"					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1460G>A	X.37:g.34148936C>T	ENSP00000345029:p.Arg487Gln	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	70	4	NM_203408	0	0	0	0	0	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	c	9.489	1.100058	0.20552	.	.	ENSG00000185448	ENST00000346193	T	0.16196	2.36	0.446	0.446	0.16602	.	.	.	.	.	T	0.10380	0.0254	N	0.24115	0.695	0.09310	N	1	D	0.62365	0.991	P	0.44811	0.461	T	0.23762	-1.0179	8	0.13470	T	0.59	.	.	.	.	.	487	Q5JRC9	FA47A_HUMAN	Q	487	ENSP00000345029:R487Q	ENSP00000345029:R487Q	R	-	2	0	FAM47A	34058857	0.022000	0.18835	0.006000	0.13384	0.016000	0.09150	0.010000	0.13242	0.435000	0.26365	0.183000	0.17082	CGG	.		0.642	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34148936	C	T	34148936	3	4	150	1	0	0	0	0	1	0	0	0	5588	652	23	1	919	1	FAM47A	23	34148936	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		34148936	121121624	78	13482											
TMEM164	84187	bcgsc.ca	37	chrX	109352336	109352336	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcacatgttgaatggagctCttctggcattgctgtttcct	6	16	10	9	0	2	1	0	1	2	0	3	2	3	2	1	2	3	6	1	2	1	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chrX:109352336C>G	ENST00000372073.1	+	4	805	c.469C>G	c.(469-471)Ctt>Gtt	p.L157V	TMEM164_ENST00000372068.2_Missense_Mutation_p.L157V|TMEM164_ENST00000288381.4_Intron|TMEM164_ENST00000372072.3_Missense_Mutation_p.L8V			Q5U3C3	TM164_HUMAN	transmembrane protein 164	157						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|skin(1)	14						GAATGGAGCTCTTCTGGCATT	0.453																																					p.L157V													.	TMEM164-193	0			c.C469G						.						231	186	201					X																	109352336		2203	4300	6503	SO:0001583	missense	84187	exon4			GGAGCTCTTCTGG	AK094127	CCDS14550.2, CCDS55475.1	Xq22.3	2008-02-05			ENSG00000157600	ENSG00000157600			26217	protein-coding gene	gene with protein product						12477932	Standard	NM_032227		Approved	FLJ22679, RP13-360B22.2	uc004eom.3	Q5U3C3	OTTHUMG00000022192	ENST00000372073.1:c.469C>G	X.37:g.109352336C>G	ENSP00000361143:p.Leu157Val	Somatic	78	1		WXS	Illumina HiSeq	Phase_1	57	4	NM_032227	0	0	0	0	0	B3KSQ8|F5H2P2	Missense_Mutation	SNP	ENST00000372073.1	37	CCDS14550.2	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371759	0.61624	.	.	ENSG00000157600	ENST00000372072;ENST00000372073;ENST00000372068	T;T;T	0.48522	0.81;0.81;0.81	5.92	5.92	0.95590	.	0.058058	0.64402	D	0.000003	T	0.54334	0.1852	L	0.52266	1.64	0.53005	D	0.999965	D	0.55800	0.973	P	0.53593	0.73	T	0.49163	-0.8968	10	0.32370	T	0.25	-5.3101	14.484	0.67603	0.0:1.0:0.0:0.0	.	157	Q5U3C3	TM164_HUMAN	V	8;157;157	ENSP00000384075:L8V;ENSP00000361143:L157V;ENSP00000361138:L157V	ENSP00000361138:L157V	L	+	1	0	TMEM164	109238992	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.616000	0.61197	2.498000	0.84270	0.600000	0.82982	CTT	.		0.453	TMEM164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057898.1	NM_032227		G	109352336	C	G	109352336	3	3	150	1	0	0	0	0	1	0	0	0	16111	913	32	4	479	4	TMEM164	23	109352336	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	75203400	109352336	45918224	79	13483											
NOL9	79707	broad.mit.edu	37	chr1	6610594	6610594	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagatgtcttgggcaggctGgccttggctgatggtaaaac	9	10	15	7	0	1	2	0	1	1	1	1	3	1	2	1	5	1	4	1	5	3	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:6610594G>A	ENST00000377705.5	-	2	510	c.478C>T	c.(478-480)Cag>Tag	p.Q160*		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	160					maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGCAGGCTGGCCTTGGCTG	0.473																																					p.Q160X													.	NOL9-515	0			c.C478T						.						118	118	118					1																	6610594		2203	4300	6503	SO:0001587	stop_gained	79707	exon2			CAGGCTGGCCTTG	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"polynucleotide 5'-kinase"					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.478C>T	1.37:g.6610594G>A	ENSP00000366934:p.Gln160*	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_024654	0	0	1	1	0	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Nonsense_Mutation	SNP	ENST00000377705.5	37	CCDS80.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389690	0.82902	.	.	ENSG00000162408	ENST00000377705	.	.	.	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-21.4105	16.6621	0.85243	0.0:0.0:1.0:0.0	.	.	.	.	X	160	.	ENSP00000366934:Q160X	Q	-	1	0	NOL9	6533181	1.000000	0.71417	1.000000	0.80357	0.082000	0.17680	7.800000	0.85949	2.788000	0.95919	0.650000	0.86243	CAG	.		0.473	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654		A	6610594	G	A	6610594	4	1	151	1	0	0	0	0	0	1	0	0	10554	1357	47	2	1674	2	NOL9	1	6610594	Nonsense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		6610594	242640027	1	13484											
RBP7	116362	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	10068242	10068242	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcatgcagagtttggttatCtgggacaatgacaggctcac	10	12	11	8	0	3	2	2	1	1	1	3	3	3	3	0	3	1	4	0	3	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:10068242C>G	ENST00000294435.7	+	3	307	c.264C>G	c.(262-264)atC>atG	p.I88M		NM_052960.2	NP_443192.1	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular	88						cytoplasm (GO:0005737)	retinal binding (GO:0016918)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(1)	2		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GTTTGGTTATCTGGGACAATG	0.468																																					p.I88M		.											.	RBP7-90	0			c.C264G						.						112	104	107					1																	10068242		2203	4300	6503	SO:0001583	missense	116362	exon3			GGTTATCTGGGAC	AF399927	CCDS109.1	1p36.22	2013-03-01			ENSG00000162444	ENSG00000162444		"Fatty acid binding protein family"	30316	protein-coding gene	gene with protein product		608604				12177003	Standard	NM_052960		Approved	CRBPIV	uc001aqq.3	Q96R05	OTTHUMG00000001798	ENST00000294435.7:c.264C>G	1.37:g.10068242C>G	ENSP00000294435:p.Ile88Met	Somatic	194	0		WXS	Illumina HiSeq	Phase_I	148	15	NM_052960	0	0	0	0	0	B2R517|Q5SWJ4	Missense_Mutation	SNP	ENST00000294435.7	37	CCDS109.1	.	.	.	.	.	.	.	.	.	.	C	6.871	0.529995	0.13127	.	.	ENSG00000162444	ENST00000315901;ENST00000294435	T	0.07688	3.17	4.07	0.988	0.19796	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.599344	0.15592	N	0.254321	T	0.07143	0.0181	N	0.19112	0.55	0.09310	N	0.99999	B	0.23650	0.089	B	0.37601	0.254	T	0.37526	-0.9702	10	0.87932	D	0	.	6.2468	0.20823	0.1332:0.6539:0.1302:0.0827	.	88	Q96R05	RET7_HUMAN	M	135;88	ENSP00000294435:I88M	ENSP00000294435:I88M	I	+	3	3	RBP7	9990829	0.000000	0.05858	0.746000	0.31095	0.291000	0.27294	-1.010000	0.03656	0.945000	0.37605	0.644000	0.83932	ATC	.		0.468	RBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005027.2	NM_052960		G	10068242	C	G	10068242	3	3	151	1	0	0	0	0	1	0	0	0	13192	903	32	4	274	4	RBP7	1	10068242	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	3457648	10068242	239182379	2	13485											
PRDM2	7799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	14108836	14108836	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacagcaaccaccgcagaCggacagcggatgcggagatt	13	4	13	11	4	0	2	0	0	0	2	0	5	0	4	2	3	5	3	2	3	2	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:14108836C>T	ENST00000235372.7	+	8	5402	c.4546C>T	c.(4546-4548)Cgg>Tgg	p.R1516W	PRDM2_ENST00000343137.4_Missense_Mutation_p.R1315W|PRDM2_ENST00000413440.1_Missense_Mutation_p.R1315W|PRDM2_ENST00000311066.5_Missense_Mutation_p.R1516W|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1516					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		CCACCGCAGACGGACAGCGGA	0.512																																					p.R1516W		.											.	PRDM2-116	0			c.C4546T						.						72	82	79					1																	14108836		2203	4300	6503	SO:0001583	missense	7799	exon8			CGCAGACGGACAG	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"Chromatin-modifying enzymes / K-methyltransferases"	9347	protein-coding gene	gene with protein product	"retinoblastoma protein-binding zinc finger protein", "retinoblastoma protein-interacting zinc finger protein", "MTE-binding protein", "zinc-finger DNA-binding protein", "GATA-3 binding protein G3B"	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4546C>T	1.37:g.14108836C>T	ENSP00000235372:p.Arg1516Trp	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	107	39	NM_015866	0	0	3	7	4	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127315	0.56721	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.02032	4.6;4.49;4.49;4.49	5.98	4.06	0.47325	.	0.060868	0.64402	D	0.000003	T	0.09598	0.0236	M	0.69823	2.125	0.49051	D	0.999741	D;B;B	0.89917	1.0;0.14;0.445	D;B;B	0.73708	0.981;0.015;0.034	T	0.00638	-1.1632	10	0.87932	D	0	.	8.67	0.34145	0.1498:0.7733:0.0:0.0769	.	1374;1516;1516	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	W	1516;1516;1516;1315;1315	ENSP00000235372:R1516W;ENSP00000312352:R1516W;ENSP00000411103:R1315W;ENSP00000341621:R1315W	ENSP00000235372:R1516W	R	+	1	2	PRDM2	13981423	0.364000	0.24997	0.793000	0.32043	0.983000	0.72400	0.980000	0.29513	0.815000	0.34398	0.591000	0.81541	CGG	.		0.512	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14108836	C	T	14108836	3	4	151	1	0	0	0	0	1	0	0	0	12487	527	19	1	4572	1	PRDM2	1	14108836	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	4040594	14108836	235141785	3	13486											
PLEKHM2	23207	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	16054269	16054269	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgagtagcgctgaggatTctggggtggatgagggacag	8	9	19	5	1	2	3	0	3	2	0	2	6	2	6	0	5	1	2	0	5	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:16054269T>G	ENST00000375799.3	+	9	1929	c.1702T>G	c.(1702-1704)Tct>Gct	p.S568A	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Missense_Mutation_p.S548A	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	568					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CGCTGAGGATTCTGGGGTGGA	0.622																																					p.S568A													.	PLEKHM2-23	0			c.T1702G						.						13	15	14					1																	16054269		2067	4198	6265	SO:0001583	missense	23207	exon9			GAGGATTCTGGGG	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"Pleckstrin homology (PH) domain containing"	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.1702T>G	1.37:g.16054269T>G	ENSP00000364956:p.Ser568Ala	Somatic	276	2		WXS	Illumina HiSeq	Phase_I	191	53	NM_015164	0	0	22	44	22	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	37	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	T	19.73	3.882074	0.72294	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.59502	0.33;0.26	5.55	5.55	0.83447	.	0.139273	0.51477	D	0.000089	T	0.48333	0.1494	L	0.29908	0.895	0.39619	D	0.970004	P	0.45396	0.857	B	0.41332	0.354	T	0.52689	-0.8542	10	0.41790	T	0.15	-13.0585	15.6894	0.77439	0.0:0.0:0.0:1.0	.	568	Q8IWE5	PKHM2_HUMAN	A	568;548	ENSP00000364956:S568A;ENSP00000364950:S548A	ENSP00000364950:S548A	S	+	1	0	PLEKHM2	15926856	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	5.910000	0.69931	2.106000	0.64143	0.533000	0.62120	TCT	.		0.622	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		G	16054269	T	G	16054269	3	3	151	1	0	0	0	0	1	0	0	0	12107	1783	62	5	1736	5	PLEKHM2	1	16054269	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	1945433	16054269	233196352	4	13487											
E2F2	1870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	23848337	23848337	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccaggcactcacacccactgGatgttgttcttggccttctt	6	13	8	14	0	3	0	1	0	2	0	3	1	3	1	3	3	0	3	3	3	0	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:23848337G>C	ENST00000361729.2	-	3	996	c.570C>G	c.(568-570)atC>atG	p.I190M	E2F2_ENST00000487237.1_5'Flank	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	190					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		ACACCCACTGGATGTTGTTCT	0.612																																					p.I190M		.											.	E2F2-417	0			c.C570G						.						123	104	110					1																	23848337		2203	4300	6503	SO:0001583	missense	1870	exon3			CCACTGGATGTTG	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.570C>G	1.37:g.23848337G>C	ENSP00000355249:p.Ile190Met	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	118	45	NM_004091	0	0	0	0	0	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	37	CCDS236.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.382364	0.61845	.	.	ENSG00000007968	ENST00000361729	T	0.15256	2.44	5.35	4.42	0.53409	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.058637	0.64402	D	0.000003	T	0.48840	0.1522	M	0.93241	3.395	0.58432	D	0.999998	D	0.56968	0.978	D	0.65323	0.934	T	0.60865	-0.7178	10	0.87932	D	0	-24.1713	11.9214	0.52793	0.0:0.0:0.6839:0.3161	.	190	Q14209	E2F2_HUMAN	M	190	ENSP00000355249:I190M	ENSP00000355249:I190M	I	-	3	3	E2F2	23720924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.406000	0.44557	1.212000	0.43366	0.591000	0.81541	ATC	.		0.612	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091		C	23848337	G	C	23848337	3	2	151	1	0	0	0	0	1	0	0	0	4878	1164	41	4	763	4	E2F2	1	23848337	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	7794068	23848337	225402284	5	13488											
CD52	1043	hgsc.bcm.edu;bcgsc.ca	37	chr1	26646661	26646661	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccacttctcctcctacaGatacaaactggactctcagg	11	10	5	15	0	2	1	1	0	2	1	6	2	4	2	3	2	3	0	3	2	3	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:26646661G>T	ENST00000374213.2	+	2	115		c.e2-1		UBXN11_ENST00000374217.2_5'Flank|UBXN11_ENST00000374222.1_5'Flank	NM_001803.2	NP_001794.2	P31358	CD52_HUMAN	CD52 molecule						positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory burst (GO:0045730)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				large_intestine(1)	1		all_cancers(24;5.02e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	TCCTCCTACAGATACAAACTG	0.488																																					.		.											.	CD52-90	0			c.55-1G>T						.						108	108	108					1																	26646661		2203	4300	6503	SO:0001630	splice_region_variant	1043	exon2			CCTACAGATACAA		CCDS30647.1	1p36	2008-02-05	2006-03-28	2005-02-07	ENSG00000169442	ENSG00000169442		"CD molecules"	1804	protein-coding gene	gene with protein product		114280	"CD52 antigen (CAMPATH-1 antigen)"	CDW52		1711975	Standard	NM_001803		Approved		uc001bmc.3	P31358	OTTHUMG00000003491	ENST00000374213.2:c.55-1G>T	1.37:g.26646661G>T		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	42	6	NM_001803	0	0	0	0	0	Q5T138|Q9BW46	Splice_Site	SNP	ENST00000374213.2	37	CCDS30647.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299548	0.40694	.	.	ENSG00000169442	ENST00000374213	.	.	.	3.6	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.042	0.47835	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD52	26519248	0.969000	0.33509	0.935000	0.37517	0.213000	0.24496	3.220000	0.51207	2.312000	0.78011	0.655000	0.94253	.	.		0.488	CD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009704.1	NM_001803	Intron	T	26646661	G	T	26646661	5	4	151	1	0	0	0	0	0	0	1	0	3028	956	33	4	60	4	CD52	1	26646661	Splice_Site	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	2798324	26646661	222603960	6	13489											
COL8A2	1296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36564106	36564106	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaggcccctggtcacctcgAatgccaggcactcctggggg	6	7	13	15	1	1	0	1	0	0	0	3	1	2	0	5	5	1	1	5	5	2	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:36564106A>G	ENST00000397799.1	-	4	1400	c.1176T>C	c.(1174-1176)atT>atC	p.I392I	COL8A2_ENST00000303143.4_Silent_p.I392I|COL8A2_ENST00000481785.1_Silent_p.I327I			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	392	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGTCACCTCGAATGCCAGGCA	0.692																																					p.I392I		.											.	COL8A2-90	0			c.T1176C						.						9	10	10					1																	36564106		2188	4274	6462	SO:0001819	synonymous_variant	1296	exon2			ACCTCGAATGCCA	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"Collagens"	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.1176T>C	1.37:g.36564106A>G		Somatic	187	0		WXS	Illumina HiSeq	Phase_I	108	32	NM_005202	0	0	1	2	1	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	37	CCDS403.1																																																																																			.		0.692	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		G	36564106	A	G	36564106	2	3	151	1	0	0	0	0	0	0	0	1	3712	242	9	3		3	COL8A2	1	36564106	Silent	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	9917445	36564106	212686515	7	13490											
CDC20	991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	43826814	43826814	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcatggtgtccctggcaGtccaatgtcctggcaacagg	8	9	13	11	0	0	0	0	0	0	0	3	0	3	0	3	4	2	4	3	4	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:43826814G>C	ENST00000372462.1	+	8	1304	c.1101G>C	c.(1099-1101)caG>caC	p.Q367H	ELOVL1_ENST00000470769.1_5'Flank|CDC20_ENST00000310955.6_Missense_Mutation_p.Q367H|RP1-92O14.3_ENST00000424948.1_RNA			Q12834	CDC20_HUMAN	cell division cycle 20	367					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTCCCTGGCAGTCCAATGTCC	0.572																																					p.Q367H	Esophageal Squamous(137;1154 1759 10362 10401 46925)	.											.	CDC20-227	0			c.G1101C						.						85	76	79					1																	43826814		2203	4300	6503	SO:0001583	missense	991	exon9			CTGGCAGTCCAAT	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"WD repeat domain containing"	1723	protein-coding gene	gene with protein product		603618	"CDC20 (cell division cycle 20, S. cerevisiae, homolog)", "CDC20 cell division cycle 20 homolog (S. cerevisiae)", "cell division cycle 20 homolog (S. cerevisiae)"			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.1101G>C	1.37:g.43826814G>C	ENSP00000361540:p.Gln367His	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	82	32	NM_001255	0	0	1	1	0	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Missense_Mutation	SNP	ENST00000372462.1	37	CCDS484.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886198	0.51908	.	.	ENSG00000117399	ENST00000437896;ENST00000310955;ENST00000372462	T;T	0.29397	1.57;1.57	5.73	0.649	0.17806	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.27098	0.0664	L	0.33668	1.02	0.58432	D	0.999997	P	0.38992	0.653	P	0.45099	0.469	T	0.04481	-1.0948	10	0.62326	D	0.03	-17.7133	9.4478	0.38708	0.4049:0.0:0.5951:0.0	.	367	Q12834	CDC20_HUMAN	H	343;367;367	ENSP00000308450:Q367H;ENSP00000361540:Q367H	ENSP00000308450:Q367H	Q	+	3	2	CDC20	43599401	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.104000	0.50306	0.090000	0.17273	-0.291000	0.09656	CAG	.		0.572	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255		C	43826814	G	C	43826814	3	2	151	1	0	0	0	0	1	0	0	0	3065	1020	36	4	1131	4	CDC20	1	43826814	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	7262708	43826814	205423807	8	13491											
GPBP1L1	60313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	46124748	46124748	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccaagcaggaacaaaatcAtgctgcgccatttaggtcca	14	7	9	11	1	1	0	1	0	0	0	2	1	2	1	3	2	5	2	3	2	5	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:46124748A>G	ENST00000290795.3	-	3	1233	c.12T>C	c.(10-12)caT>caC	p.H4H	GPBP1L1_ENST00000355105.3_Silent_p.H4H			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	4					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					GAACAAAATCATGCTGCGCCA	0.428																																					p.H4H		.											.	GPBP1L1-91	0			c.T12C						.						146	137	140					1																	46124748		2203	4300	6503	SO:0001819	synonymous_variant	60313	exon4			AAAATCATGCTGC		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.12T>C	1.37:g.46124748A>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	89	13	NM_021639	0	0	64	74	10	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	37	CCDS528.1																																																																																			.		0.428	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		G	46124748	A	G	46124748	2	3	151	1	0	0	0	0	0	0	0	1	6616	214	8	3		3	GPBP1L1	1	46124748	Silent	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	2297934	46124748	203125873	9	13492											
AGBL4	84871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	48999847	48999847	+	Nonstop_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcccaggactccgtgtctttAaaaaggggttgaagggtctt	9	12	12	8	1	2	1	0	1	2	0	4	2	4	2	2	4	0	1	2	4	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:48999847A>G	ENST00000371839.1	-	14	1626	c.1510T>C	c.(1510-1512)Taa>Caa	p.*504Q	AGBL4_ENST00000334103.7_Nonstop_Mutation_p.*228Q	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	0					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		CCGTGTCTTTAAAAAGGGGTT	0.507																																					p.X504Q		.											.	AGBL4-137	0			c.T1510C						.						168	152	157					1																	48999847		692	1591	2283	SO:0001578	stop_lost	84871	exon14			GTCTTTAAAAAGG	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 6"					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.1510T>C	1.37:g.48999847A>G	ENSP00000360905:p.*504Gluext*27	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	156	20	NM_032785	0	0	0	0	0	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.181371|4.181371	0.78677|0.78677	.|.	.|.	ENSG00000186094|ENSG00000186094	ENST00000411952|ENST00000371839;ENST00000334103	.|.	.|.	.|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999988|0.999988	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	11.9|11.9	0.52678|0.52678	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	.|Q	-1|504;228	.|.	.|.	.|X	-|-	.|1	.|0	AGBL4|AGBL4	48772434|48772434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.851000|0.851000	0.48451|0.48451	3.026000|3.026000	0.49689|0.49689	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	.|TAA	.		0.507	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		G	48999847	A	G	48999847	4	3	151	1	0	0	0	0	0	0	0	0	377	375	13	3	5	3	AGBL4	1	48999847	Nonstop_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	2875099	48999847	200250774	10	13493											
NFIA	4774	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	61824902	61824902	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacaggccaagggcgctcccCaggaagtggcagtcagtcaa	11	5	13	12	1	2	0	2	0	0	0	3	1	3	1	3	4	1	2	3	4	4	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:61824902C>A	ENST00000403491.3	+	6	1386	c.902C>A	c.(901-903)cCa>cAa	p.P301Q	NFIA_ENST00000485903.2_Missense_Mutation_p.P301Q|NFIA_ENST00000371191.1_Missense_Mutation_p.P324Q|NFIA_ENST00000371187.3_Missense_Mutation_p.P301Q|NFIA_ENST00000371189.4_Missense_Mutation_p.P346Q|NFIA_ENST00000407417.3_Missense_Mutation_p.P293Q|NFIA_ENST00000371185.2_Missense_Mutation_p.P279Q|NFIA_ENST00000479364.1_3'UTR|NFIA_ENST00000371184.2_Intron	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	301					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						GGGCGCTCCCCAGGAAGTGGC	0.527																																					p.P346Q													.	NFIA-92	0			c.C1037A						.						99	97	98					1																	61824902		2203	4300	6503	SO:0001583	missense	4774	exon7			GCTCCCCAGGAAG	U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.902C>A	1.37:g.61824902C>A	ENSP00000384523:p.Pro301Gln	Somatic	272	1		WXS	Illumina HiSeq	Phase_I	271	87	NM_001145512	0	0	2	2	0	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Missense_Mutation	SNP	ENST00000403491.3	37	CCDS44156.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563486	0.86335	.	.	ENSG00000162599	ENST00000371191;ENST00000407417;ENST00000371189;ENST00000403491;ENST00000485903;ENST00000371185;ENST00000371187	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	6.17	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.79964	0.4537	M	0.80422	2.495	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.85130	0.997;0.997;0.997;0.994	T	0.82226	-0.0562	10	0.54805	T	0.06	.	15.327	0.74172	0.0:0.9337:0.0:0.0663	.	346;324;301;301	F8W8W3;B1AKN8;Q12857;Q12857-2	.;.;NFIA_HUMAN;.	Q	324;293;346;301;301;279;301	ENSP00000360233:P324Q;ENSP00000384680:P293Q;ENSP00000360231:P346Q;ENSP00000384523:P301Q;ENSP00000419785:P301Q;ENSP00000360227:P279Q;ENSP00000360229:P301Q	ENSP00000360227:P279Q	P	+	2	0	NFIA	61597490	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	7.173000	0.77612	1.620000	0.50308	0.655000	0.94253	CCA	.		0.527	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595		A	61824902	C	A	61824902	3	1	151	1	0	0	0	0	1	0	0	0	10396	594	21	4	1070	4	NFIA	1	61824902	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	12825055	61824902	187425719	11	13494											
FNBP1L	54874	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	93965136	93965136	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacagaactatgcgaaacaaTtgaggtaagttaattttttt	16	14	7	4	1	0	2	0	1	0	1	0	3	0	2	0	1	4	2	0	1	7	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:93965136T>A	ENST00000271234.7	+	2	287	c.136T>A	c.(136-138)Ttg>Atg	p.L46M	FNBP1L_ENST00000370253.2_Missense_Mutation_p.L46M|FNBP1L_ENST00000604705.1_Missense_Mutation_p.L46M|FNBP1L_ENST00000260506.8_Missense_Mutation_p.L46M|FNBP1L_ENST00000370256.4_Missense_Mutation_p.L46M	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	46	F-BAR domain. {ECO:0000250}.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		TGCGAAACAATTGAGGTAAGT	0.308																																					p.L46M		.											.	FNBP1L-227	0			c.T136A						.						46	44	45					1																	93965136		1815	4062	5877	SO:0001583	missense	54874	exon2			AAACAATTGAGGT		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.136T>A	1.37:g.93965136T>A	ENSP00000271234:p.Leu46Met	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	97	44	NM_001164473	0	0	0	0	0	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Missense_Mutation	SNP	ENST00000271234.7	37	CCDS53343.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.568848	0.65765	.	.	ENSG00000137942	ENST00000370256;ENST00000271234;ENST00000260506;ENST00000370253	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.55	2.05	0.26809	.	0.000000	0.85682	D	0.000000	T	0.69223	0.3087	M	0.84326	2.69	0.80722	D	1	D;P	0.54207	0.965;0.938	P;P	0.61328	0.887;0.855	T	0.69847	-0.5034	10	0.54805	T	0.06	-7.6767	6.8376	0.23945	0.0:0.465:0.0:0.535	.	46;46	Q5T0N5-4;Q5T0N5-3	.;.	M	46	ENSP00000359278:L46M;ENSP00000271234:L46M;ENSP00000260506:L46M;ENSP00000359275:L46M	ENSP00000260506:L46M	L	+	1	2	FNBP1L	93737724	0.711000	0.27906	0.997000	0.53966	0.913000	0.54294	0.165000	0.16564	0.401000	0.25424	-0.605000	0.04089	TTG	.		0.308	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		A	93965136	T	A	93965136	3	1	151	1	0	0	0	0	1	0	0	0	5985	1490	52	5	142	5	FNBP1L	1	93965136	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	32140234	93965136	155285485	12	13495											
ABCA4	24	hgsc.bcm.edu;bcgsc.ca	37	chr1	94522320	94522320	+	Frame_Shift_Del	DEL	A	A	-																															gcatgatggtggcagtggagAaagccaacaagaacaggaag																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:94522320delA	ENST00000370225.3	-	15	2305	c.2219delT	c.(2218-2220)ttcfs	p.F740fs	ABCA4_ENST00000535735.1_Intron	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	740					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGCAGTGGAGAAAGCCAACAA	0.517																																					p.F740fs		.											.	ABCA4-162	0			c.2219delT						.						111	98	102					1																	94522320		2203	4300	6503	SO:0001589	frameshift_variant	24	exon15			.	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.2219delT	1.37:g.94522320delA	ENSP00000359245:p.Phe740fs	Somatic	322	0		WXS	Illumina HiSeq	Phase_I	231	60	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Frame_Shift_Del	DEL	ENST00000370225.3	37	CCDS747.1																																																																																			.		0.517	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		-	94522320	A	-	94522320	7	5	151	1	0	1	0	1	0	0	0	0	34	246	9	0	4746	0	ABCA4	1	94522320	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	557184	94522320	154728301	13	13496											
AQP10	89872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154296801	154296801	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcctgtggtggcccctctgGtgggggccaccgttggcaca	3	9	16	13	1	1	0	0	0	1	0	1	0	1	0	5	6	1	2	5	6	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:154296801G>T	ENST00000324978.3	+	6	791	c.751G>T	c.(751-753)Gtg>Ttg	p.V251L	ATP8B2_ENST00000368487.3_5'Flank|AQP10_ENST00000484864.1_3'UTR	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	251					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGCCCCTCTGGTGGGGGCCAC	0.602											OREG0013832	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V251L		.											.	AQP10-90	0			c.G751T						.						32	35	34					1																	154296801		2201	4290	6491	SO:0001583	missense	89872	exon6			CCTCTGGTGGGGG	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"Ion channels / Aquaporins"	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.751G>T	1.37:g.154296801G>T	ENSP00000318355:p.Val251Leu	Somatic	41	0	1762	WXS	Illumina HiSeq	Phase_I	33	16	NM_080429	0	0	0	0	0	Q5VYD3|Q5VYD4|Q8NG70	Missense_Mutation	SNP	ENST00000324978.3	37	CCDS1065.1	.	.	.	.	.	.	.	.	.	.	G	5.726	0.318459	0.10845	.	.	ENSG00000143595	ENST00000324978	D	0.88124	-2.34	4.46	4.46	0.54185	Aquaporin-like (2);	0.142496	0.45126	D	0.000385	T	0.65688	0.2715	L	0.28608	0.87	0.80722	D	1	B	0.32939	0.391	B	0.34722	0.188	T	0.67345	-0.5694	10	0.02654	T	1	.	12.9205	0.58230	0.0:0.1648:0.8352:0.0	.	251	Q96PS8	AQP10_HUMAN	L	251	ENSP00000318355:V251L	ENSP00000318355:V251L	V	+	1	0	AQP10	152563425	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	1.571000	0.36450	2.510000	0.84645	0.555000	0.69702	GTG	.		0.602	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429		T	154296801	G	T	154296801	3	4	151	1	0	0	0	0	1	0	0	0	822	1261	44	4	773	4	AQP10	1	154296801	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	59774481	154296801	94953820	14	13497											
CENPL	91687	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	173772297	173772298	+	Frame_Shift_Ins	INS	-	-	T																															ttttgcatcctctggatgtaINSttgcgaaagaaatgtccaga																								rs139873333	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:173772297_173772298insT	ENST00000345664.6	-	4	979_980	c.766_767insA	c.(766-768)atafs	p.I256fs	CENPL_ENST00000367710.3_Frame_Shift_Ins_p.I256fs|CENPL_ENST00000356198.2_Frame_Shift_Ins_p.I302fs	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	256					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						CTCTGGATGTATTGCGAAAGAA	0.45																																					p.I302fs		.											.	CENPL-90	0			c.905_906insA						.																																			SO:0001589	frameshift_variant	91687	exon6			.	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"chromosome 1 open reading frame 155"	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.767dupA	1.37:g.173772299_173772299dupT	ENSP00000323543:p.Ile256fs	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	74	18	NM_001127181	0	0	0	0	0	Q5TEL5|Q96ND4	Frame_Shift_Ins	INS	ENST00000345664.6	37	CCDS30938.1																																																																																			.		0.45	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		T	173772298	-	T	173772297	7	5	151	1	0	1	1	0	0	0	0	0	3242	449	16	0	275	0	CENPL	1	173772297	Frame_Shift_Ins	INS	-	TCGA-MH-A561-01A-11D-A26P-10	19475496	173772297	75478324	15	13498	143	2									
CENPL	91687	hgsc.bcm.edu;bcgsc.ca	37	chr1	173772300	173772300	+	Missense_Mutation	SNP	G	G	T																															ttgcatcctctggatgtattGcgaaagaaatgtccagactt																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:173772300G>T	ENST00000345664.6	-	4	977	c.764C>A	c.(763-765)gCa>gAa	p.A255E	CENPL_ENST00000367710.3_Missense_Mutation_p.A255E|CENPL_ENST00000356198.2_Missense_Mutation_p.A301E	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	255					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						TGGATGTATTGCGAAAGAAAT	0.458																																					p.A301E		.											.	CENPL-90	0			c.C902A						.						95	97	96					1																	173772300		2203	4300	6503	SO:0001583	missense	91687	exon6			TGTATTGCGAAAG	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"chromosome 1 open reading frame 155"	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.764C>A	1.37:g.173772300G>T	ENSP00000323543:p.Ala255Glu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	75	19	NM_001127181	0	0	2	2	0	Q5TEL5|Q96ND4	Missense_Mutation	SNP	ENST00000345664.6	37	CCDS30938.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640619	0.67244	.	.	ENSG00000120334	ENST00000356198;ENST00000345664;ENST00000367710	T;T;T	0.41758	1.58;0.99;0.99	5.24	5.24	0.73138	.	0.172946	0.50627	D	0.000109	T	0.47691	0.1459	L	0.43152	1.355	0.39487	D	0.967975	D;P	0.69078	0.997;0.896	D;P	0.63283	0.913;0.602	T	0.50882	-0.8775	10	0.72032	D	0.01	-5.8243	17.633	0.88114	0.0:0.0:1.0:0.0	.	301;255	Q8N0S6-2;Q8N0S6	.;CENPL_HUMAN	E	301;255;255	ENSP00000348527:A301E;ENSP00000323543:A255E;ENSP00000356683:A255E	ENSP00000323543:A255E	A	-	2	0	CENPL	172038923	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.635000	0.67841	2.456000	0.83038	0.655000	0.94253	GCA	.		0.458	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		T	173772300	G	T	173772300	3	4	151	1	0	0	0	0	1	0	0	0	3242	1319	46	4	278	4	CENPL	1	173772300	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	3	173772300	75478321	16	13499	143	2									
RFWD2	64326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	175996826	175996826	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggtagaccacagcttcacTaagggcaaaggacaataaaa	17	7	9	8	0	1	1	1	0	0	1	1	2	1	2	1	3	1	3	1	3	6	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:175996826T>C	ENST00000367669.3	-	15	2127		c.e15-2		RFWD2_ENST00000308769.8_Splice_Site	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						ACAGCTTCACTAAGGGCAAAG	0.388																																					.	Ovarian(134;1413 1765 5706 35534 51541)	.											.	RFWD2-659	0			c.1613-2A>G						.						63	54	57					1																	175996826		2203	4300	6503	SO:0001630	splice_region_variant	64326	exon16			CTTCACTAAGGGC	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.1613-2A>G	1.37:g.175996826T>C		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	78	31	NM_022457	0	0	0	0	0	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Splice_Site	SNP	ENST00000367669.3	37	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586435	0.86851	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6701	0.77267	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RFWD2	174263449	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	7.563000	0.82314	2.174000	0.68829	0.528000	0.53228	.	.		0.388	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457	Intron	C	175996826	T	C	175996826	5	2	151	1	0	0	0	0	0	0	1	0	13292	1536	53	3	608	3	RFWD2	1	175996826	Splice_Site	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	2224526	175996826	73253795	17	13500											
CEP350	9857	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	179959644	179959645	+	Frame_Shift_Del	DEL	GA	GA	-																															atggtgtttaaactttagctGagacacattgaaaataaatt																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:179959644_179959645delGA	ENST00000367607.3	+	4	541_542	c.123_124delGA	c.(121-126)ctgagafs	p.R42fs		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	42					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AACTTTAGCTGAGACACATTGA	0.337																																					p.41_42del		.											.	CEP350-26	0			c.123_124del						.																																			SO:0001589	frameshift_variant	9857	exon4			.	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"centrosome associated protein 350"					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.123_124delGA	1.37:g.179959646_179959647delGA	ENSP00000356579:p.Arg42fs	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	66	14	NM_014810	0	0	0	0	0	O75068|Q8TDK3|Q8WY20	Frame_Shift_Del	DEL	ENST00000367607.3	37	CCDS1336.1																																																																																			.		0.337	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		-	179959645	GA	-	179959644	7	5	151	1	0	1	0	1	0	0	0	0	3260	1277	45	0	133	0	CEP350	1	179959644	Frame_Shift_Del	DEL	GA	TCGA-MH-A561-01A-11D-A26P-10	3962818	179959644	69290977	18	13501											
MR1	3140	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	181003148	181003148	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggaaagagaaggactatggGggaactgatggcgttcctgt	11	8	16	6	2	0	2	0	1	0	1	1	6	1	5	1	5	1	1	1	5	4	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:181003148G>T	ENST00000367580.5	+	1	10	c.5G>T	c.(4-6)gGg>gTg	p.G2V	MR1_ENST00000367579.3_Missense_Mutation_p.G2V|MR1_ENST00000438435.2_3'UTR|MR1_ENST00000282990.6_Missense_Mutation_p.G2V|MR1_ENST00000434571.2_Missense_Mutation_p.G2V	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	2					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	AGGACTATGGGGGAACTGATG	0.483																																					p.G2V	Colon(174;1412 1962 45296 46549 47110)												.	MR1-91	0			c.G5T						.						119	103	108					1																	181003148		2203	4300	6503	SO:0001583	missense	3140	exon2			CTATGGGGGAACT	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"Immunoglobulin superfamily / C1-set domain containing"	4975	protein-coding gene	gene with protein product		600764	"major histocompatibility complex, class I-like sequence"	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.5G>T	1.37:g.181003148G>T	ENSP00000356552:p.Gly2Val	Somatic	183	1		WXS	Illumina HiSeq	Phase_I	157	48	NM_001195035	0	0	0	1	1	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	37	CCDS1342.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053763	0.36277	.	.	ENSG00000153029	ENST00000434571;ENST00000367580;ENST00000282990;ENST00000367579	T;T;T;T	0.01126	5.89;5.88;5.69;5.3	3.89	-7.77	0.01227	.	3.121780	0.01415	N	0.014161	T	0.00875	0.0029	N	0.24115	0.695	0.24595	N	0.993809	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.002;0.001;0.002	T	0.46275	-0.9203	9	0.87932	D	0	.	0.3097	0.00286	0.3905:0.1981:0.1499:0.2615	.	2;2;2;2;2	B4E3B1;Q95460-3;Q95460-2;Q95460;Q95460-4	.;.;.;HMR1_HUMAN;.	V	2	ENSP00000388504:G2V;ENSP00000356552:G2V;ENSP00000282990:G2V;ENSP00000356551:G2V	ENSP00000282990:G2V	G	+	2	0	MR1	179269771	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.543000	0.06084	-2.077000	0.00874	-0.857000	0.03018	GGG	.		0.483	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531		T	181003148	G	T	181003148	3	4	151	1	0	0	0	0	1	0	0	0	9777	1232	43	4	7	4	MR1	1	181003148	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	1043504	181003148	68247473	19	13502											
CACNA1S	779	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201043744	201043744	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gccaggaagacattgagcagGatgtctgagcgggtttagct	10	9	15	7	1	1	3	0	2	1	1	1	5	1	5	1	3	3	3	1	3	2	3	rs561722889		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:201043744G>C	ENST00000362061.3	-	14	2179	c.1953C>G	c.(1951-1953)atC>atG	p.I651M	CACNA1S_ENST00000367338.3_Missense_Mutation_p.I651M	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	651					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CATTGAGCAGGATGTCTGAGC	0.587																																					p.I651M													.	CACNA1S-94	0			c.C1953G						.						63	51	55					1																	201043744		2203	4300	6503	SO:0001583	missense	779	exon14			GAGCAGGATGTCT	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1953C>G	1.37:g.201043744G>C	ENSP00000355192:p.Ile651Met	Somatic	170	1		WXS	Illumina HiSeq	Phase_I	145	50	NM_000069	0	0	0	0	0	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083422	0.55861	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98666	-5.06;-5.06	3.99	3.05	0.35203	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98963	0.9647	M	0.84585	2.705	0.43787	D	0.996323	D	0.76494	0.999	D	0.78314	0.991	D	0.99482	1.0948	10	0.87932	D	0	.	11.1337	0.48362	0.0:0.0:0.6643:0.3357	.	651	Q13698	CAC1S_HUMAN	M	651	ENSP00000355192:I651M;ENSP00000356307:I651M	ENSP00000355192:I651M	I	-	3	3	CACNA1S	199310367	1.000000	0.71417	0.997000	0.53966	0.912000	0.54170	4.778000	0.62368	0.773000	0.33404	0.478000	0.44815	ATC	.		0.587	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		C	201043744	G	C	201043744	3	2	151	1	0	0	0	0	1	0	0	0	2553	1164	41	4	3792	4	CACNA1S	1	201043744	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	20040596	201043744	48206877	20	13503											
ETNK2	55224	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	204101322	204101322	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtggctggtcactttggcAtctccaaggctgacgcttga	6	11	14	10	1	2	2	1	2	1	0	3	2	2	2	1	5	0	4	1	5	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:204101322A>T	ENST00000367202.4	-	8	1301	c.1151T>A	c.(1150-1152)aTg>aAg	p.M384K	ETNK2_ENST00000367201.3_3'UTR|RP11-74C13.4_ENST00000565388.1_RNA|ETNK2_ENST00000367199.2_Missense_Mutation_p.M315K|ETNK2_ENST00000367197.1_Missense_Mutation_p.M66K|ETNK2_ENST00000367198.2_Missense_Mutation_p.M206K	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	384					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TCACTTTGGCATCTCCAAGGC	0.557																																					p.M384K		.											.	ETNK2-493	0			c.T1151A						.						80	77	78					1																	204101322		1564	3580	5144	SO:0001583	missense	55224	exon8			TTTGGCATCTCCA	AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.1151T>A	1.37:g.204101322A>T	ENSP00000356170:p.Met384Lys	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	101	34	NM_018208	0	0	13	13	0	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	37	CCDS1442.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.99|18.99	3.740600|3.740600	0.69304|0.69304	.|.	.|.	ENSG00000143845|ENSG00000143845	ENST00000422072|ENST00000367202;ENST00000367199;ENST00000455266;ENST00000367198;ENST00000367197	.|T;T;T;T	.|0.64260	.|0.34;-0.02;-0.02;-0.09	5.0|5.0	3.82|3.82	0.43975|0.43975	.|.	.|.	.|.	.|.	.|.	T|T	0.62780|0.62780	0.2456|0.2456	L|L	0.58669|0.58669	1.825|1.825	0.38499|0.38499	D|D	0.948185|0.948185	.|P;P	.|0.46859	.|0.877;0.885	.|P;B	.|0.50754	.|0.649;0.446	T|T	0.62305|0.62305	-0.6882|-0.6882	5|9	.|0.28530	.|T	.|0.3	.|.	8.0791|8.0791	0.30733|0.30733	0.7042:0.0:0.0:0.2958|0.7042:0.0:0.0:0.2958	.|.	.|343;384	.|Q9NVF9-3;Q9NVF9	.|.;EKI2_HUMAN	S|K	147|384;315;250;206;66	.|ENSP00000356170:M384K;ENSP00000356167:M315K;ENSP00000356166:M206K;ENSP00000356165:M66K	.|ENSP00000356165:M66K	C|M	-|-	1|2	0|0	ETNK2|ETNK2	202367945|202367945	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	6.504000|6.504000	0.73704|0.73704	1.880000|1.880000	0.54463|0.54463	0.533000|0.533000	0.62120|0.62120	TGC|ATG	.		0.557	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		T	204101322	A	T	204101322	3	4	151	1	0	0	0	0	1	0	0	0	5287	217	8	5	13	5	ETNK2	1	204101322	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	3057578	204101322	45149299	21	13504			1	40		2	2	15	N	C_A	6.376445e-05
ETNK2	55224	ucsc.edu;bcgsc.ca	37	chr1	204101336	204101336	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggcatctccaaggctgaCgcttgaggcttcaccttgaa	8	12	10	11	1	2	3	1	3	1	0	3	3	2	3	2	3	0	4	2	3	2	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:204101336C>T	ENST00000367202.4	-	8	1287	c.1137G>A	c.(1135-1137)gcG>gcA	p.A379A	ETNK2_ENST00000367201.3_3'UTR|RP11-74C13.4_ENST00000565388.1_RNA|ETNK2_ENST00000367199.2_Silent_p.A310A|ETNK2_ENST00000367197.1_Silent_p.A61A|ETNK2_ENST00000367198.2_Silent_p.A201A	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	379					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			CCAAGGCTGACGCTTGAGGCT	0.562																																					p.A379A													.	ETNK2-493	0			c.G1137A						.						84	80	81					1																	204101336		1563	3580	5143	SO:0001819	synonymous_variant	55224	exon8			GGCTGACGCTTGA	AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.1137G>A	1.37:g.204101336C>T		Somatic	182	1		WXS	Illumina HiSeq		123	45	NM_018208	0	0	20	20	0	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Silent	SNP	ENST00000367202.4	37	CCDS1442.2	.	.	.	.	.	.	.	.	.	.	C	3.487	-0.104679	0.06967	.	.	ENSG00000143845	ENST00000422072	.	.	.	5.11	3.06	0.35304	.	.	.	.	.	T	0.62768	0.2455	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60984	-0.7154	4	.	.	.	.	12.2946	0.54838	0.0:0.6725:0.3275:0.0	.	.	.	.	H	142	.	.	R	-	2	0	ETNK2	202367959	0.991000	0.36638	0.728000	0.30774	0.219000	0.24729	0.564000	0.23563	1.113000	0.41760	0.655000	0.94253	CGT	.		0.562	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		T	204101336	C	T	204101336	2	4	151	1	0	0	0	0	0	0	0	1	5287	523	19	1		1	ETNK2	1	204101336	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	14	204101336	45149285	22	13505			1	40		2	2	15	N	C_A	6.376445e-05
C1orf107	27042	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	210006562	210006562	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgaccctgagggaaaaGaagatggggaagagccaccg	13	4	15	9	1	0	5	0	2	0	3	0	7	0	7	3	3	2	1	3	3	4	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:210006562G>T	ENST00000491415.2	+	4	478	c.421G>T	c.(421-423)Gaa>Taa	p.E141*		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	141	Glu-rich.				multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						TGAGGGAAAAGAAGATGGGGA	0.398																																					p.E141X		.											.	DIEXF-91	0			c.G421T						.						59	56	57					1																	210006562		2203	4300	6503	SO:0001587	stop_gained	27042	exon4			GGAAAAGAAGATG	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.421G>T	1.37:g.210006562G>T	ENSP00000419005:p.Glu141*	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	51	17	NM_014388	0	0	4	4	0	O75992|Q4VY00|Q63HL9	Nonsense_Mutation	SNP	ENST00000491415.2	37	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.380543	0.82792	.	.	ENSG00000117597	ENST00000491415	.	.	.	0.225	0.225	0.15325	.	1.807870	0.04544	U	0.388703	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	.	.	.	.	.	.	.	X	141	.	ENSP00000419005:E141X	E	+	1	0	DIEXF	208073185	0.949000	0.32298	0.212000	0.23672	0.934000	0.57294	0.364000	0.20325	0.300000	0.22699	0.305000	0.20034	GAA	.		0.398	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		T	210006562	G	T	210006562	4	4	151	1	0	0	0	0	0	1	0	0	1987	943	33	4	435	4	C1orf107	1	210006562	Nonsense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	5905226	210006562	39244059	23	13506											
CENPF	1063	broad.mit.edu	37	chr1	214816102	214816102	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggaggaggggctcgttcCatccctgtcatcctcttgtg	4	13	12	12	1	2	0	1	0	1	0	6	2	5	2	3	4	0	2	3	4	0	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:214816102C>T	ENST00000366955.3	+	12	4589	c.4421C>T	c.(4420-4422)cCa>cTa	p.P1474L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1570	2 X 96 AA approximate tandem repeats.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GGGCTCGTTCCATCCCTGTCA	0.473																																					p.P1474L	Colon(80;575 1284 11000 14801 43496)												.	CENPF-567	0			c.C4421T						.						69	68	68					1																	214816102		2203	4300	6503	SO:0001583	missense	1063	exon12			TCGTTCCATCCCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.4421C>T	1.37:g.214816102C>T	ENSP00000355922:p.Pro1474Leu	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	74	3	NM_016343	0	0	0	0	0	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	C	0.283	-0.985033	0.02180	.	.	ENSG00000117724	ENST00000366955	T	0.37915	1.17	4.32	-2.65	0.06095	.	1.289640	0.06172	N	0.677842	T	0.10294	0.0252	N	0.01048	-1.04	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.18745	-1.0327	10	0.25751	T	0.34	.	2.3529	0.04288	0.1187:0.3561:0.1342:0.3911	.	1474	P49454	CENPF_HUMAN	L	1474	ENSP00000355922:P1474L	ENSP00000355922:P1474L	P	+	2	0	CENPF	212882725	0.372000	0.25064	0.000000	0.03702	0.001000	0.01503	1.395000	0.34520	-0.107000	0.12088	-0.150000	0.13652	CCA	.		0.473	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214816102	C	T	214816102	3	4	151	1	0	0	0	0	1	0	0	0	3237	594	21	2	4463	2	CENPF	1	214816102	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	4809540	214816102	34434519	24	13507											
CENPF	1063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214820696	214820696	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcttacaagaatctagagAatgagcttgaattgacaaaa	17	11	8	5	0	2	5	0	3	2	2	2	6	2	5	0	0	2	2	0	0	8	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:214820696A>T	ENST00000366955.3	+	13	7951	c.7783A>T	c.(7783-7785)Aat>Tat	p.N2595Y		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2691	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAATCTAGAGAATGAGCTTGA	0.378																																					p.N2595Y	Colon(80;575 1284 11000 14801 43496)	.											.	CENPF-567	0			c.A7783T						.						37	37	37					1																	214820696		2203	4300	6503	SO:0001583	missense	1063	exon13			CTAGAGAATGAGC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7783A>T	1.37:g.214820696A>T	ENSP00000355922:p.Asn2595Tyr	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	55	24	NM_016343	0	0	0	0	0	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.839067	0.32513	.	.	ENSG00000117724	ENST00000366955	T	0.03301	3.98	5.61	3.16	0.36331	.	0.728326	0.11309	N	0.577293	T	0.03608	0.0103	N	0.19112	0.55	0.25270	N	0.989526	P	0.51653	0.947	P	0.44732	0.459	T	0.45963	-0.9225	10	0.59425	D	0.04	.	7.1052	0.25360	0.777:0.1469:0.0761:0.0	.	2691	P49454	CENPF_HUMAN	Y	2595	ENSP00000355922:N2595Y	ENSP00000355922:N2595Y	N	+	1	0	CENPF	212887319	1.000000	0.71417	0.126000	0.21872	0.167000	0.22549	1.705000	0.37867	0.427000	0.26145	0.496000	0.49642	AAT	.		0.378	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214820696	A	T	214820696	3	4	151	1	0	0	0	0	1	0	0	0	3237	246	9	5	7829	5	CENPF	1	214820696	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	4594	214820696	34429925	25	13508											
GREB1	9687	bcgsc.ca	37	chr2	11767087	11767100	+	Splice_Site	DEL	GACAGAGGGATGTC	GACAGAGGGATGTC	-																															atcctggggaatttggtgcaGacagagggatgtcccggaag																								rs538826695|rs201880234		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GACAGAGGGATGTC	GACAGAGGGATGTC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:11767087_11767100delGACAGAGGGATGTC	ENST00000381486.2	+	25	4606_4619	c.4306_4319delGACAGAGGGATGTC	c.(4306-4320)gacagagggatgtcc>c	p.DRGMS1436fs	GREB1_ENST00000396123.1_Splice_Site_p.DRGMS434fs|GREB1_ENST00000234142.5_Splice_Site_p.DRGMS1436fs	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1436						integral component of membrane (GO:0016021)		p.G1438E(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		ATTTGGTGCAGACAGAGGGATGTCCCGGAAGCCG	0.519																																					p.1436_1440del	Ovarian(39;850 945 2785 23371 33093)												.	GREB1-91	1	Substitution - Missense(1)	lung(1)	c.4307_4319del						.																																			SO:0001630	splice_region_variant	9687	exon25			GGTGCAGACAGAG		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"gene regulated by estrogen in breast cancer"	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.4307-1GACAGAGGGATGTC>-	2.37:g.11767087_11767100delGACAGAGGGATGTC		Somatic	159	0		WXS	Illumina HiSeq	Phase_1	140	5	NM_014668	0	0	0	0	0	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Frame_Shift_Del	DEL	ENST00000381486.2	37	CCDS42655.1																																																																																			.		0.519	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	Frame_Shift_Del	-	11767100	GACAGAGGGATGTC	-	11767087	8	5	151	1	0	1	0	1	0	0	1	0	6781	956	33	0	4508	0	GREB1	2	11767087	Splice_Site	DEL	GACAGAGGGATGTC	TCGA-MH-A561-01A-11D-A26P-10		11767087	231432286	26	13509											
FBXO11	80204	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	48040950	48040950	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagaattataaactagaattCcaccattctgtcctccccag	13	11	4	13	0	1	2	0	0	1	2	4	2	4	2	5	0	1	0	5	0	6	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:48040950C>T	ENST00000403359.3	-	17	2135	c.2063G>A	c.(2062-2064)gGa>gAa	p.G688E	FBXO11_ENST00000402508.1_Missense_Mutation_p.G604E|FBXO11_ENST00000316377.4_Missense_Mutation_p.G604E|FBXO11_ENST00000434523.2_Missense_Mutation_p.G112E	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	688					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AACTAGAATTCCACCATTCTG	0.388			"Mis, F, D"		DLBCL																																p.G688E		.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11-659	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2063A						.						118	116	117					2																	48040950		2202	4300	6502	SO:0001583	missense	80204	exon17			AGAATTCCACCAT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"Ubiquitin protein ligase E3 component n-recognins", "F-boxes /  "other""	13590	protein-coding gene	gene with protein product	"ubiquitin protein ligase E3 component n-recognin 6"	607871	"F-box only protein 11"			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.2063G>A	2.37:g.48040950C>T	ENSP00000384823:p.Gly688Glu	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	44	5	NM_001190274	0	0	22	22	0	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	37	CCDS54357.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.136371|5.136371	0.94517|0.94517	.|.	.|.	ENSG00000138081|ENSG00000138081	ENST00000402508;ENST00000403359;ENST00000316377;ENST00000434523|ENST00000493962	D;D;D;D|.	0.90133|.	-2.62;-2.62;-2.62;-2.62|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Pectin lyase fold/virulence factor (2);Carbohydrate-binding/sugar hydrolysis domain (1);F-box domain, Skp2-like (1);Pectin lyase fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.86789|.	0.6017|.	M|M	0.92880|0.92880	3.355|3.355	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.998;1.0|.	D|.	0.89459|.	0.3735|.	10|.	0.66056|.	D|.	0.02|.	-12.1201|-12.1201	19.5994|19.5994	0.95554|0.95554	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	112;688|.	B3KUR1;Q86XK2|.	.;FBX11_HUMAN|.	E|X	604;688;604;112|479	ENSP00000385398:G604E;ENSP00000384823:G688E;ENSP00000323822:G604E;ENSP00000397359:G112E|.	ENSP00000323822:G604E|.	G|W	-|-	2|3	0|0	FBXO11|FBXO11	47894454|47894454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.776000|7.776000	0.85560|0.85560	2.699000|2.699000	0.92147|0.92147	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.		0.388	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		T	48040950	C	T	48040950	3	4	151	1	0	0	0	0	1	0	0	0	5746	855	30	2	834	2	FBXO11	2	48040950	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	36273863	48040950	195158423	27	13510											
AAK1	22848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	69757189	69757189	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgagaattatcaggaattgtGaagtttccatcacaaattgc	14	12	8	7	1	2	2	2	1	0	1	3	4	3	3	1	1	1	1	1	1	5	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:69757189G>A	ENST00000409085.4	-	8	1198	c.822C>T	c.(820-822)ttC>ttT	p.F274F	AAK1_ENST00000409068.1_Silent_p.F274F|AAK1_ENST00000406297.3_Silent_p.F274F|AAK1_ENST00000470281.1_5'Flank	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						CAGGAATTGTGAAGTTTCCAT	0.313																																					p.F274F		.											.	AAK1-333	0			c.C822T						.						58	54	55					2																	69757189		1830	4085	5915	SO:0001819	synonymous_variant	22848	exon8			AATTGTGAAGTTT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.822C>T	2.37:g.69757189G>A		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	125	44	NM_014911	0	0	2	3	1	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			.		0.313	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		A	69757189	G	A	69757189	2	1	151	1	0	0	0	0	0	0	0	1	16	1281	45	2		2	AAK1	2	69757189	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	21716239	69757189	173442184	28	13511											
RTKN	6242	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	74668862	74668862	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcgctgaagaggctgagtcGgaagcggccgcgtttgaact	8	8	16	9	5	0	4	0	3	0	1	2	5	0	5	1	3	2	3	1	3	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:74668862G>T	ENST00000272430.5	-	1	164	c.82C>A	c.(82-84)Cga>Aga	p.R28R	RTKN_ENST00000484453.1_5'UTR|RTKN_ENST00000233330.6_5'Flank|RTKN_ENST00000305557.5_5'Flank	NM_001015055.1	NP_001015055.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						AGGCTGAGTCGGAAGCGGCCG	0.697																																					p.R28R		.											.	RTKN-91	0			c.C82A						.						28	33	31					2																	74668862		2202	4300	6502	SO:0001819	synonymous_variant	6242	exon1			TGAGTCGGAAGCG	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000272430.5:c.82C>A	2.37:g.74668862G>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	38	12	NM_001015055	0	0	27	56	29		Silent	SNP	ENST00000272430.5	37	CCDS33226.1																																																																																			.		0.697	RTKN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328234.1	NM_001015055		T	74668862	G	T	74668862	2	4	151	1	0	0	0	0	0	0	0	1	13754	1124	39	4		4	RTKN	2	74668862	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	4911673	74668862	168530511	29	13512											
AUP1	165545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74755401	74755401	+	5'Flank	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatacaccgtgaaagggacGaaaagtgaccacagcagttc	15	6	11	9	2	0	3	0	3	0	0	1	5	0	4	2	1	2	2	2	1	4	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:74755401G>T	ENST00000404568.3	-	0	0				AUP1_ENST00000377526.3_Missense_Mutation_p.F215L|HTRA2_ENST00000352222.3_5'Flank|HTRA2_ENST00000258080.3_5'Flank|DQX1_ENST00000393951.2_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TGAAAGGGACGAAAAGTGACC	0.537																																					p.F215L		.											.	AUP1-90	0			c.C645A						.						74	80	78					2																	74755401		2044	4193	6237	SO:0001631	upstream_gene_variant	550	exon6			AGGGACGAAAAGT	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		2.37:g.74755401G>T	Exception_encountered	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	60	24	NM_181575	0	0	123	145	22	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701042	0.68501	.	.	ENSG00000115307	ENST00000377526;ENST00000258081;ENST00000412627	D	0.92495	-3.05	5.1	3.01	0.34805	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	M	0.66506	2.035	0.54753	D	0.999982	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.984;0.992;0.997	D	0.91236	0.5018	10	0.33940	T	0.23	-15.5435	8.4169	0.32676	0.226:0.0:0.774:0.0	.	272;281;215	E7EU18;Q9Y679;Q9Y679-2	.;AUP1_HUMAN;.	L	215;279;217	ENSP00000366748:F215L	ENSP00000258081:F279L	F	-	3	2	AUP1	74608909	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.450000	0.35134	0.528000	0.28580	0.462000	0.41574	TTC	.		0.537	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74755401	G	T	74755401	1	4	151	0	1	0	0	0	0	0	0	0	1221	1049	37	4		4	AUP1	2	74755401	5'Flank	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	86539	74755401	168443972	30	13513											
ANKRD57	65124	ucsc.edu;bcgsc.ca	37	chr2	110373074	110373074	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccggtgaacatcgacgcCaggacgagcgggggttacac	9	5	15	12	5	0	1	0	1	0	0	1	4	0	2	2	4	4	1	2	4	2	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:110373074C>T	ENST00000356454.3	+	1	1164	c.1008C>T	c.(1006-1008)gcC>gcT	p.A336A	SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000415095.1_5'Flank|SEPT10_ENST00000437928.1_5'Flank|SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000397712.2_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	336																	ACATCGACGCCAGGACGAGCG	0.642																																					p.A336A													.	.	0			c.C1008T						.						36	40	39					2																	110373074		2202	4299	6501	SO:0001819	synonymous_variant	65124	exon1			CGACGCCAGGACG	AK023346	CCDS33270.1	2q13	2013-01-10	2012-01-12	2012-01-12	ENSG00000198142	ENSG00000198142		"Ankyrin repeat domain containing"	26149	protein-coding gene	gene with protein product			"ankyrin repeat domain 57"	C2orf26, ANKRD57		22234889	Standard	NM_023016		Approved	FLJ21870	uc002tfb.3	Q53LP3	OTTHUMG00000153219	ENST00000356454.3:c.1008C>T	2.37:g.110373074C>T		Somatic	354	2		WXS	Illumina HiSeq		293	128	NM_023016	0	0	1	2	1	Q8NE15|Q9H6U1	Silent	SNP	ENST00000356454.3	37	CCDS33270.1																																																																																			.		0.642	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016		T	110373074	C	T	110373074	2	4	151	1	0	0	0	0	0	0	0	1	683	581	21	2		2	ANKRD57	2	110373074	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	35617673	110373074	132826299	31	13514											
LCT	3938	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	136555630	136555630	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcctgcagccaagctccTgtcacggatccgcgtcttca	7	8	11	15	3	3	0	2	0	1	0	5	2	5	1	4	2	3	2	4	2	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:136555630T>G	ENST00000264162.2	-	13	4955	c.4945A>C	c.(4945-4947)Agg>Cgg	p.R1649R		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1649	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GCCAAGCTCCTGTCACGGATC	0.582											OREG0014998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1649R													.	LCT-101	0			c.A4945C						.						113	103	106					2																	136555630		2203	4300	6503	SO:0001819	synonymous_variant	3938	exon13			AGCTCCTGTCACG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4945A>C	2.37:g.136555630T>G		Somatic	99	1	1626	WXS	Illumina HiSeq	Phase_I	77	11	NM_002299	0	0	0	0	0	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			.		0.582	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		G	136555630	T	G	136555630	2	3	151	1	0	0	0	0	0	0	0	1	8714	1579	55	5		5	LCT	2	136555630	Silent	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	26182556	136555630	106643743	32	13515											
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170136009	170136009	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtttccactagatagatttTattattaacccagtccacag	12	14	6	9	0	0	2	0	0	0	2	2	2	2	2	3	1	1	1	3	1	5	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:170136009T>A	ENST00000263816.3	-	12	1723	c.1438A>T	c.(1438-1440)Aaa>Taa	p.K480*	LRP2_ENST00000443831.1_Nonsense_Mutation_p.K480*	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	480					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AGATAGATTTTATTATTAACC	0.393																																					p.K480X		.											.	LRP2-175	0			c.A1438T						.						98	105	103					2																	170136009		2203	4300	6503	SO:0001587	stop_gained	4036	exon12			AGATTTTATTATT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"Low density lipoprotein receptors"	6694	protein-coding gene	gene with protein product	"megalin"	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.1438A>T	2.37:g.170136009T>A	ENSP00000263816:p.Lys480*	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	81	26	NM_004525	0	0	0	0	0	O00711|Q16215	Nonsense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	39	7.557577	0.98358	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7574	0.78046	0.0:0.0:0.0:1.0	.	.	.	.	X	480	.	.	K	-	1	0	LRP2	169844255	1.000000	0.71417	0.998000	0.56505	0.410000	0.31052	7.971000	0.88012	2.136000	0.66102	0.528000	0.53228	AAA	.		0.393	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170136009	T	A	170136009	4	1	151	1	0	0	0	0	0	1	0	0	8981	1763	61	5	12801	5	LRP2	2	170136009	Nonsense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	33580379	170136009	73063364	33	13516											
GAD1	2571	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	171700591	171700591	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaccagtgtttgtcctcatGgaacaaataacacttaagaa	15	10	7	9	0	1	1	1	0	0	1	2	2	2	2	2	1	2	2	2	1	5	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:171700591G>T	ENST00000358196.3	+	7	1225	c.675G>T	c.(673-675)atG>atT	p.M225I	GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	225					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						TTGTCCTCATGGAACAAATAA	0.368																																					p.M225I		.											.	GAD1-91	0			c.G675T						.						210	215	213					2																	171700591		2203	4300	6503	SO:0001583	missense	2571	exon7			CCTCATGGAACAA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"glutamate decarboxylase 1 (brain, 67kD)"	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.675G>T	2.37:g.171700591G>T	ENSP00000350928:p.Met225Ile	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	119	40	NM_000817	0	0	0	0	0	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500461	0.85176	.	.	ENSG00000128683	ENST00000358196	T	0.36520	1.25	6.17	6.17	0.99709	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.37865	0.1019	L	0.33624	1.015	0.80722	D	1	B	0.30021	0.265	B	0.35312	0.2	T	0.15350	-1.0440	10	0.72032	D	0.01	-26.7667	20.8794	0.99867	0.0:0.0:1.0:0.0	.	225	Q99259	DCE1_HUMAN	I	225	ENSP00000350928:M225I	ENSP00000350928:M225I	M	+	3	0	GAD1	171408837	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.394000	0.97261	2.941000	0.99782	0.655000	0.94253	ATG	.		0.368	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171700591	G	T	171700591	3	4	151	1	0	0	0	0	1	0	0	0	6198	1348	47	4	738	4	GAD1	2	171700591	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	1564582	171700591	71498782	34	13517											
MAP1D	254042	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	172930452	172930452	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtttgtacctctgtaaacAacgtgctctgtcatggtatt	8	16	8	9	1	3	0	1	0	2	0	3	0	3	0	1	1	4	5	1	1	5	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:172930452A>G	ENST00000315796.4	+	4	856	c.469A>G	c.(469-471)Aac>Gac	p.N157D	METAP1D_ENST00000488581.1_Intron	NM_199227.1	NP_954697.1	Q6UB28	MAP12_HUMAN	methionyl aminopeptidase type 1D (mitochondrial)	157					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|protein initiator methionine removal (GO:0070084)	mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235)			NS(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	8						CTCTGTAAACAACGTGCTCTG	0.383																																					p.N157D													.	METAP1D-90	0			c.A469G						.						144	115	125					2																	172930452		2203	4300	6503	SO:0001583	missense	254042	exon4			GTAAACAACGTGC	AY374142, BC029123	CCDS2246.1	2q31.1	2010-09-21			ENSG00000172878	ENSG00000172878			32583	protein-coding gene	gene with protein product	"methionine aminopeptidase 1D"	610267				14532271, 16568094	Standard	NM_199227		Approved	MAP1D, Metap1l	uc002uhk.3	Q6UB28	OTTHUMG00000132283	ENST00000315796.4:c.469A>G	2.37:g.172930452A>G	ENSP00000315152:p.Asn157Asp	Somatic	167	2		WXS	Illumina HiSeq	Phase_I	172	57	NM_199227	0	0	2	3	1	Q1WNX3	Missense_Mutation	SNP	ENST00000315796.4	37	CCDS2246.1	.	.	.	.	.	.	.	.	.	.	A	15.77	2.930691	0.52866	.	.	ENSG00000172878	ENST00000315796	T	0.76060	-0.99	6.16	5.01	0.66863	Peptidase M24, structural domain (3);	0.000000	0.85682	D	0.000000	T	0.71239	0.3316	N	0.25789	0.76	0.58432	D	0.999999	P	0.43701	0.815	P	0.50109	0.631	T	0.73714	-0.3896	10	0.72032	D	0.01	-8.6915	12.3265	0.55013	0.9346:0.0:0.0654:0.0	.	157	Q6UB28	AMP1D_HUMAN	D	157	ENSP00000315152:N157D	ENSP00000315152:N157D	N	+	1	0	METAP1D	172638698	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	8.675000	0.91195	1.153000	0.42468	-0.263000	0.10527	AAC	.		0.383	METAP1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255378.2	NM_199227		G	172930452	A	G	172930452	3	3	151	1	0	0	0	0	1	0	0	0	9254	130	5	3	483	3	MAP1D	2	172930452	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	1229861	172930452	70268921	35	13518											
SSFA2	6744	broad.mit.edu	37	chr2	182763639	182763639	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgaaagtgatgctcaaattGaaaactggtatgtagctgtt	14	13	10	4	0	1	3	1	3	0	0	1	3	1	3	0	1	3	5	0	1	6	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:182763639G>A	ENST00000431877.2	+	5	576	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	SSFA2_ENST00000409001.1_Missense_Mutation_p.E133K|SSFA2_ENST00000428267.2_5'UTR|SSFA2_ENST00000320370.7_Missense_Mutation_p.E133K	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	133						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			TGCTCAAATTGAAAACTGGTA	0.284																																					p.E133K													.	SSFA2-153	0			c.G397A						.						149	158	155					2																	182763639		2203	4300	6503	SO:0001583	missense	6744	exon5			CAAATTGAAAACT	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.397G>A	2.37:g.182763639G>A	ENSP00000388731:p.Glu133Lys	Somatic	59	3		WXS	Illumina HiSeq	Phase_I	50	3	NM_001130445	0	0	0	0	0	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	G	17.12	3.308712	0.60305	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001	T;T;T	0.14516	2.73;2.5;2.73	5.85	5.85	0.93711	.	0.709072	0.13892	N	0.355534	T	0.18718	0.0449	M	0.63428	1.95	0.80722	D	1	B;B;B	0.22800	0.075;0.075;0.075	B;B;B	0.26864	0.074;0.074;0.074	T	0.01844	-1.1262	10	0.34782	T	0.22	-8.7439	13.0329	0.58854	0.0774:0.0:0.9226:0.0	.	133;133;133	E9PHV5;P28290;P28290-3	.;SSFA2_HUMAN;.	K	133	ENSP00000388731:E133K;ENSP00000314669:E133K;ENSP00000387319:E133K	ENSP00000314669:E133K	E	+	1	0	SSFA2	182471884	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.131000	0.64751	2.773000	0.95371	0.655000	0.94253	GAA	.		0.284	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		A	182763639	G	A	182763639	3	1	151	1	0	0	0	0	1	0	0	0	15215	1291	45	2	415	2	SSFA2	2	182763639	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	9833187	182763639	60435734	36	13519											
MSTN	2660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190927181	190927181	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctattcttgaagatttagTgttttgtctccaagtacatg	9	19	7	6	0	3	2	0	1	3	1	4	2	3	2	1	0	1	2	1	0	5	9			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:190927181T>C	ENST00000260950.4	-	1	274	c.142A>G	c.(142-144)Act>Gct	p.T48A	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	48					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			GAAGATTTAGTGTTTTGTCTC	0.378																																					p.T48A		.											.	MSTN-650	0			c.A142G						.						198	194	195					2																	190927181		2203	4300	6503	SO:0001583	missense	2660	exon1			ATTTAGTGTTTTG	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.142A>G	2.37:g.190927181T>C	ENSP00000260950:p.Thr48Ala	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	49	22	NM_005259	0	0	0	0	0	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	37	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307916	0.40895	.	.	ENSG00000138379	ENST00000260950	T	0.64085	-0.08	5.64	5.64	0.86602	Transforming growth factor-beta, N-terminal (1);	0.217803	0.48286	D	0.000186	T	0.51753	0.1693	L	0.29908	0.895	0.43195	D	0.995031	B	0.09022	0.002	B	0.15870	0.014	T	0.43877	-0.9364	10	0.30854	T	0.27	-11.9215	16.0238	0.80522	0.0:0.0:0.0:1.0	.	48	O14793	GDF8_HUMAN	A	48	ENSP00000260950:T48A	ENSP00000260950:T48A	T	-	1	0	MSTN	190635426	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.928000	0.70088	2.367000	0.80283	0.528000	0.53228	ACT	.		0.378	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		C	190927181	T	C	190927181	3	2	151	1	0	0	0	0	1	0	0	0	9918	1696	59	3	997	3	MSTN	2	190927181	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	8163542	190927181	52272192	37	13520											
C2orf69	205327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	200789854	200789854	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actggagtctagaaaatgttGctaccattttagcccaccgg	11	11	9	10	1	1	1	0	0	1	1	1	2	1	2	3	2	3	2	3	2	5	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:200789854G>T	ENST00000319974.5	+	2	586	c.403G>T	c.(403-405)Gct>Tct	p.A135S	C2orf69_ENST00000491721.1_Intron	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	135						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						AGAAAATGTTGCTACCATTTT	0.353																																					p.A135S		.											.	C2orf69-23	0			c.G403T						.						51	48	48					2																	200789854		1819	4077	5896	SO:0001583	missense	205327	exon2			AATGTTGCTACCA		CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"hypothetical protein FLJ38973"					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.403G>T	2.37:g.200789854G>T	ENSP00000312770:p.Ala135Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	92	31	NM_153689	0	0	0	2	2	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	37	CCDS46482.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667963	0.88348	.	.	ENSG00000178074	ENST00000319974	.	.	.	6.03	6.03	0.97812	.	0.049006	0.85682	D	0.000000	D	0.82600	0.5072	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82600	-0.0377	9	0.62326	D	0.03	-10.3396	19.5548	0.95338	0.0:0.0:1.0:0.0	.	135	Q8N8R5	CB069_HUMAN	S	135	.	ENSP00000312770:A135S	A	+	1	0	C2orf69	200498099	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.827000	0.99397	2.854000	0.98071	0.655000	0.94253	GCT	.		0.353	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689		T	200789854	G	T	200789854	3	4	151	1	0	0	0	0	1	0	0	0	2194	1319	46	4	409	4	C2orf69	2	200789854	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	9862673	200789854	42409519	38	13521											
DGKD	8527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	234368926	234368926	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttccctgcacccggagatGctgtccgaggaggaggccac	7	7	14	13	2	0	1	0	0	0	1	2	5	2	3	4	4	2	3	4	4	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:234368926G>T	ENST00000264057.2	+	24	2928	c.2916G>T	c.(2914-2916)atG>atT	p.M972I	DGKD_ENST00000409813.3_Missense_Mutation_p.M928I	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	972					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	ACCCGGAGATGCTGTCCGAGG	0.617																																					p.M972I		.											.	DGKD-676	0			c.G2916T						.						87	79	81					2																	234368926		2203	4300	6503	SO:0001583	missense	8527	exon24			GGAGATGCTGTCC	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing"	2851	protein-coding gene	gene with protein product	"diglyceride kinase"	601826	"diacylglycerol kinase, delta (130kD)"			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2916G>T	2.37:g.234368926G>T	ENSP00000264057:p.Met972Ile	Somatic	544	1		WXS	Illumina HiSeq	Phase_I	376	143	NM_152879	0	0	0	2	2	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	7.872	0.728341	0.15507	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.78364	-0.99;-1.17	4.93	3.12	0.35913	.	0.425083	0.24007	N	0.042416	T	0.41419	0.1158	N	0.00652	-1.29	0.20403	N	0.999909	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33214	-0.9877	10	0.21014	T	0.42	.	4.9917	0.14218	0.132:0.4809:0.3087:0.0784	.	928;972	Q16760-2;Q16760	.;DGKD_HUMAN	I	972;928	ENSP00000264057:M972I;ENSP00000386455:M928I	ENSP00000264057:M972I	M	+	3	0	DGKD	234033665	1.000000	0.71417	0.994000	0.49952	0.551000	0.35334	1.017000	0.29989	0.790000	0.33803	0.563000	0.77884	ATG	.		0.617	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234368926	G	T	234368926	3	4	151	1	0	0	0	0	1	0	0	0	4478	1319	46	4	3034	4	DGKD	2	234368926	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	33579072	234368926	8830447	39	13522											
SCLY	51540	hgsc.bcm.edu	37	chr2	239006933	239006933	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgcagcaccaccagggcCgaggtggacctcgtcgtgca	7	4	15	15	4	0	0	0	0	0	0	2	2	0	1	5	4	2	3	5	4	0	0	rs78475597	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:239006933C>T	ENST00000555827.1	+	12	1339	c.1275C>T	c.(1273-1275)gcC>gcT	p.A425A	ESPNL_ENST00000343063.3_5'Flank|SCLY_ENST00000254663.6_Silent_p.A433A|SCLY_ENST00000429612.2_Silent_p.A219A|ESPNL_ENST00000409169.1_5'Flank|SCLY_ENST00000422984.2_Silent_p.A331A			Q96I15	SCLY_HUMAN	selenocysteine lyase	425					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CCACCAGGGCCGAGGTGGACC	0.716													C|||	26	0.00519169	0	0.0288	5008	,	,		15051	0.006		0	False		,,,				2504	0				p.A433A	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	.											.	SCLY-92	0			c.C1299T						.	C		1,4401		0,1,2200	28	27	27		1299	-9.5	0	2	dbSNP_131	27	1,8591		0,1,4295	no	coding-synonymous	SCLY	NM_016510.5		0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154		433/454	239006933	2,12992	2201	4296	6497	SO:0001819	synonymous_variant	51540	exon12			CAGGGCCGAGGTG	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"putative selenocysteine lyase"	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.1275C>T	2.37:g.239006933C>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_016510	0	0	5	16	11	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37																																																																																				C|0.996;T|0.004		0.716	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510		T	239006933	C	T	239006933	2	4	151	1	0	0	0	0	0	0	0	1	13939	639	23	1		1	SCLY	2	239006933	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	4638007	239006933	4192440	40	13523											
SATB1	6304	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	18390936	18390936	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacagagtctggatggccTcttcgtcagggtacaggccc	8	8	13	12	1	3	2	1	0	2	2	4	3	3	3	2	4	1	1	2	4	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:18390936T>C	ENST00000338745.6	-	11	3752	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G	SATB1_ENST00000417717.2_Missense_Mutation_p.E705G|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.E673G	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	673					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CTGGATGGCCTCTTCGTCAGG	0.517																																					p.E705G		.											.	SATB1-228	0			c.A2114G						.						141	140	140					3																	18390936		2203	4300	6503	SO:0001583	missense	6304	exon12			ATGGCCTCTTCGT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.2018A>G	3.37:g.18390936T>C	ENSP00000341024:p.Glu673Gly	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	175	73	NM_001195470	0	0	13	18	5	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	37	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.370587	0.61624	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	D;D;D	0.96745	-4.11;-4.11;-4.11	5.27	5.27	0.74061	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.049242	0.85682	N	0.000000	D	0.96642	0.8904	L	0.32530	0.975	0.80722	D	1	B;D	0.89917	0.013;1.0	B;D	0.97110	0.004;1.0	D	0.97662	1.0161	10	0.87932	D	0	-15.8047	15.186	0.73002	0.0:0.0:0.0:1.0	.	705;673	Q01826-2;Q01826	.;SATB1_HUMAN	G	673;673;705	ENSP00000341024:E673G;ENSP00000399708:E673G;ENSP00000399518:E705G	ENSP00000341024:E673G	E	-	2	0	SATB1	18365940	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.911000	0.87458	1.993000	0.58246	0.460000	0.39030	GAG	.		0.517	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18390936	T	C	18390936	3	2	151	1	0	0	0	0	1	0	0	0	13885	1551	54	3	277	3	SATB1	3	18390936	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10		18390936	179631494	41	13524											
EPM2AIP1	9852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	37033483	37033483	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgttgcccctactgaaacCaagaacgcttccatttcttt	9	14	6	12	1	1	2	0	1	1	1	2	2	2	2	4	0	4	3	4	0	4	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:37033483C>A	ENST00000322716.5	-	1	1312	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F	MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000458205.2_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	362					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						CTACTGAAACCAAGAACGCTT	0.413																																					p.L362F		.											.	.	0			c.G1086T						.						190	192	191					3																	37033483		1871	4110	5981	SO:0001583	missense	9852	exon1			TGAAACCAAGAAC	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1086G>T	3.37:g.37033483C>A	ENSP00000406027:p.Leu362Phe	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	62	10	NM_014805	0	0	1	2	1	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	37	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275856	0.59649	.	.	ENSG00000178567	ENST00000322716	T	0.31247	1.5	4.71	4.71	0.59529	.	.	.	.	.	T	0.41834	0.1176	L	0.27053	0.805	0.47698	D	0.999499	D	0.76494	0.999	D	0.74674	0.984	T	0.29549	-1.0008	9	0.49607	T	0.09	-10.3057	15.1824	0.72968	0.0:1.0:0.0:0.0	.	362	Q7L775	EPMIP_HUMAN	F	362	ENSP00000406027:L362F	ENSP00000406027:L362F	L	-	3	2	EPM2AIP1	37008487	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	2.648000	0.46647	2.424000	0.82194	0.591000	0.81541	TTG	.		0.413	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		A	37033483	C	A	37033483	3	1	151	1	0	0	0	0	1	0	0	0	5197	593	21	4	741	4	EPM2AIP1	3	37033483	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	18642547	37033483	160988947	42	13525											
SCN10A	6336	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	38740016	38740018	+	In_Frame_Del	DEL	ACT	ACT	-																															aagagcgttggggagaagtaActttgaagtgacttaagaat																								rs200063383	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	ACT	ACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740016_38740018delACT	ENST00000449082.2	-	27	4692_4694	c.4693_4695delAGT	c.(4693-4695)agtdel	p.S1565del		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1565					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGGAGAAGTAACTTTGAAGTGAC	0.478																																					p.1565_1565del		.											.	SCN10A-99	0			c.4693_4695del						.																																			SO:0001651	inframe_deletion	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4693_4695delAGT	3.37:g.38740016_38740018delACT	ENSP00000390600:p.Ser1565del	Somatic	164	0		WXS	Illumina HiSeq	Phase_I	118	18	NM_006514	0	0	0	0	0	A6NDQ1	In_Frame_Del	DEL	ENST00000449082.2	37	CCDS33736.1																																																																																			.		0.478	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38740018	ACT	-	38740016	7	5	151	1	0	1	0	1	0	0	0	0	13944	40	2	0	1179	0	SCN10A	3	38740016	In_Frame_Del	DEL	ACT	TCGA-MH-A561-01A-11D-A26P-10	1706533	38740016	159282414	43	13526	144	2									
SCN10A	6336	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	38740022	38740022	+	Frame_Shift_Del	DEL	A	A	-																															gttggggagaagtaactttgAagtgacttaagaattgcaga																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740022delA	ENST00000449082.2	-	27	4688	c.4689delT	c.(4687-4689)cttfs	p.L1563fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1563					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGTAACTTTGAAGTGACTTAA	0.478																																					p.L1563fs		.											.	SCN10A-99	0			c.4689delT						.						58	59	59					3																	38740022		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4689delT	3.37:g.38740022delA	ENSP00000390600:p.Leu1563fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	107	18	NM_006514	0	0	0	0	0	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	37	CCDS33736.1																																																																																			.		0.478	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38740022	A	-	38740022	7	5	151	1	0	1	0	1	0	0	0	0	13944	233	9	0	1185	0	SCN10A	3	38740022	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	6	38740022	159282408	44	13527	144	2									
LIMD1	8994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	45637412	45637412	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccaaatcttacctttccagTtctgccccgtcatcctcgcc	6	12	4	19	2	3	0	1	0	2	0	6	0	5	0	7	0	2	1	7	0	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:45637412T>G	ENST00000273317.4	+	1	1062	c.1041T>G	c.(1039-1041)agT>agG	p.S347R	LIMD1_ENST00000440097.1_Missense_Mutation_p.S347R|LIMD1_ENST00000465039.1_Intron	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	347					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		ACCTTTCCAGTTCTGCCCCGT	0.622																																					p.S347R		.											.	LIMD1-279	0			c.T1041G						.						78	78	78					3																	45637412		2203	4300	6503	SO:0001583	missense	8994	exon1			TTCCAGTTCTGCC	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.1041T>G	3.37:g.45637412T>G	ENSP00000273317:p.Ser347Arg	Somatic	251	0		WXS	Illumina HiSeq	Phase_I	231	79	NM_014240	0	0	0	2	2	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	37	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	T	9.543	1.113931	0.20795	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.58506	0.33;0.53	4.73	1.1	0.20463	.	1.824180	0.02460	N	0.086523	T	0.44953	0.1318	L	0.29908	0.895	0.09310	N	1	B	0.15141	0.012	B	0.09377	0.004	T	0.14420	-1.0473	10	0.22706	T	0.39	.	6.3277	0.21253	0.0:0.4757:0.0:0.5243	.	347	Q9UGP4	LIMD1_HUMAN	R	347	ENSP00000394537:S347R;ENSP00000273317:S347R	ENSP00000273317:S347R	S	+	3	2	LIMD1	45612416	0.001000	0.12720	0.006000	0.13384	0.180000	0.23129	-0.032000	0.12266	0.203000	0.20529	0.533000	0.62120	AGT	.		0.622	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		G	45637412	T	G	45637412	3	3	151	1	0	0	0	0	1	0	0	0	8820	1722	60	5	1043	5	LIMD1	3	45637412	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	6897390	45637412	152385018	45	13528											
ATRIP	84126	ucsc.edu	37	chr3	48488465	48488465	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctcgcgtcacaggccctgagCcaatgtccggccgcggctcg	5	6	13	17	6	1	1	1	1	0	0	4	1	2	1	4	3	1	1	4	3	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:48488465C>T	ENST00000320211.3	+	1	329	c.216C>T	c.(214-216)agC>agT	p.S72S	ATRIP_ENST00000412052.1_5'Flank|ATRIP_ENST00000357105.6_Intron|RP11-24C3.2_ENST00000438872.1_RNA|RP11-24C3.2_ENST00000435578.1_RNA|ATRIP_ENST00000346691.4_Silent_p.S72S	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	72					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGGCCCTGAGCCAATGTCCGG	0.677								Other conserved DNA damage response genes																													p.S72S													.	ATRIP-23	0			c.C216T						.						18	20	20					3																	48488465		2180	4262	6442	SO:0001819	synonymous_variant	84126	exon1			CCTGAGCCAATGT	AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.216C>T	3.37:g.48488465C>T		Somatic	84	0		WXS	Illumina HiSeq		45	4	NM_130384	0	0	3	3	0	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Silent	SNP	ENST00000320211.3	37	CCDS2768.1																																																																																			.		0.677	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384		T	48488465	C	T	48488465	2	4	151	1	0	0	0	0	0	0	0	1	1206	738	26	2		2	ATRIP	3	48488465	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	2851053	48488465	149533965	46	13529											
GMPPB	29925	broad.mit.edu	37	chr3	49760823	49760823	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaagagtctgtgcctcAccctctgctcctgtgccttc	4	11	10	16	0	3	1	1	0	2	1	5	1	4	1	5	1	3	1	5	1	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:49760823A>C	ENST00000480687.1	-	3	327		c.e3+1		AMIGO3_ENST00000535833.1_Splice_Site|GMPPB_ENST00000308388.6_Splice_Site|GMPPB_ENST00000308375.6_Splice_Site			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TCTGTGCCTCACCCTCTGCTC	0.607																																					.													.	GMPPB-90	0			c.210+2T>G						.						124	116	119					3																	49760823		2203	4300	6503	SO:0001630	splice_region_variant	29925	exon3			TGCCTCACCCTCT	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.210+1T>G	3.37:g.49760823A>C		Somatic	126	7		WXS	Illumina HiSeq	Phase_I	88	11	NM_021971	0	0	0	0	0	A8K6N5|Q9H7U3	Splice_Site	SNP	ENST00000480687.1	37	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.743778	0.69418	.	.	ENSG00000173540	ENST00000480687;ENST00000308375;ENST00000308388	.	.	.	4.32	4.32	0.51571	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7476	0.57289	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GMPPB	49735827	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.493000	0.90474	1.949000	0.56562	0.374000	0.22700	.	.		0.607	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334	Intron	C	49760823	A	C	49760823	5	2	151	1	0	0	0	0	0	0	1	0	6515	173	6	5	979	5	GMPPB	3	49760823	Splice_Site	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	1272358	49760823	148261607	47	13530											
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52416419	52416419	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgtgaagaaggtcctgcTcaaggcgggcctacagaacc	11	7	13	10	1	1	4	1	2	0	2	2	4	2	4	3	3	3	1	3	3	5	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:52416419T>C	ENST00000420323.2	+	50	8150	c.7889T>C	c.(7888-7890)cTc>cCc	p.L2630P		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2630	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AAGGTCCTGCTCAAGGCGGGC	0.582																																					p.L2630P		.											.	DNAH1-67	0			c.T7889C						.						169	177	175					3																	52416419		2125	4239	6364	SO:0001583	missense	25981	exon50			TCCTGCTCAAGGC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.7889T>C	3.37:g.52416419T>C	ENSP00000401514:p.Leu2630Pro	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	143	57	NM_015512	0	0	0	1	1	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529987	0.64860	.	.	ENSG00000114841	ENST00000420323	T	0.54279	0.58	4.49	4.49	0.54785	.	0.155058	0.30126	N	0.010343	T	0.76898	0.4052	M	0.93507	3.425	0.80722	D	1	D	0.61697	0.99	D	0.67725	0.953	T	0.80817	-0.1213	10	0.35671	T	0.21	.	13.9669	0.64213	0.0:0.0:0.0:1.0	.	2630	C9JXH6	.	P	2630	ENSP00000401514:L2630P	ENSP00000401514:L2630P	L	+	2	0	DNAH1	52391459	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	5.444000	0.66587	1.883000	0.54544	0.379000	0.24179	CTC	.		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52416419	T	C	52416419	3	2	151	1	0	0	0	0	1	0	0	0	4608	1551	54	3	8083	3	DNAH1	3	52416419	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	2655596	52416419	145606011	48	13531											
IGSF10	285313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	151166796	151166796	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccatgttagcttcatttcCagactgatctgtcatattca	10	15	6	10	0	4	2	3	1	1	1	5	3	5	2	2	0	1	2	2	0	2	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:151166796C>T	ENST00000282466.3	-	4	972	c.973G>A	c.(973-975)Gga>Aga	p.G325R		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	325					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCTTCATTTCCAGACTGATCT	0.433																																					p.G325R		.											.	IGSF10-102	0			c.G973A						.						108	109	109					3																	151166796		2203	4300	6503	SO:0001583	missense	285313	exon4			CATTTCCAGACTG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"Immunoglobulin superfamily / I-set domain containing"	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.973G>A	3.37:g.151166796C>T	ENSP00000282466:p.Gly325Arg	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	117	46	NM_178822	0	0	0	0	0	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243180	0.39697	.	.	ENSG00000152580	ENST00000282466	T	0.75260	-0.92	5.37	4.5	0.54988	.	0.000000	0.47093	D	0.000256	T	0.67915	0.2944	M	0.64997	1.995	0.38362	D	0.944634	B	0.34200	0.441	B	0.26094	0.066	T	0.72513	-0.4270	10	0.87932	D	0	.	10.7221	0.46046	0.0:0.7971:0.1309:0.072	.	325	Q6WRI0	IGS10_HUMAN	R	325	ENSP00000282466:G325R	ENSP00000282466:G325R	G	-	1	0	IGSF10	152649486	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.805000	0.38883	1.270000	0.44297	0.650000	0.86243	GGA	.		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151166796	C	T	151166796	3	4	151	1	0	0	0	0	1	0	0	0	7618	603	21	2	6958	2	IGSF10	3	151166796	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	98750377	151166796	46855634	49	13532											
BOD1L	259282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	13601745	13601745	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggccctcacagtcttccaccGagctcgtagagatgatgcca	9	8	10	14	2	2	2	1	1	1	1	4	4	3	2	4	1	2	2	4	1	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:13601745G>A	ENST00000040738.5	-	10	6914	c.6779C>T	c.(6778-6780)tCg>tTg	p.S2260L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2260						nucleus (GO:0005634)	DNA binding (GO:0003677)										GTCTTCCACCGAGCTCGTAGA	0.542																																					p.S2260L		.											.	.	0			c.C6779T						.						79	69	72					4																	13601745		2203	4300	6503	SO:0001583	missense	259282	exon10			TCCACCGAGCTCG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.6779C>T	4.37:g.13601745G>A	ENSP00000040738:p.Ser2260Leu	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	149	16	NM_148894	0	0	1	1	0	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194306	0.78902	.	.	ENSG00000038219	ENST00000040738	T	0.12255	2.7	5.46	5.46	0.80206	.	0.000000	0.45126	D	0.000387	T	0.23727	0.0574	M	0.64997	1.995	0.30881	N	0.731467	D	0.63046	0.992	P	0.51055	0.657	T	0.15350	-1.0440	10	0.72032	D	0.01	-3.6924	11.8817	0.52579	0.0832:0.0:0.9168:0.0	.	2260	Q8NFC6	BOD1L_HUMAN	L	2260	ENSP00000040738:S2260L	ENSP00000040738:S2260L	S	-	2	0	BOD1L	13210843	0.993000	0.37304	0.944000	0.38274	0.889000	0.51656	2.414000	0.44627	2.573000	0.86826	0.650000	0.86243	TCG	.		0.542	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13601745	G	A	13601745	3	1	151	1	0	0	0	0	1	0	0	0	1484	1059	37	1	2444	1	BOD1L	4	13601745	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		13601745	177552531	50	13533											
RUFY3	22902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	71588406	71588406	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtgtccatggatggagaatGgctctgcctgcgagagctgg	8	9	16	8	1	1	2	0	0	1	2	2	5	2	3	2	4	3	2	2	4	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:71588406G>T	ENST00000226328.4	+	1	679	c.116G>T	c.(115-117)tGg>tTg	p.W39L	RUFY3_ENST00000381006.3_Missense_Mutation_p.W39L|RUFY3_ENST00000536664.1_Missense_Mutation_p.W5L|RUFY3_ENST00000417478.2_Intron	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	39					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			GATGGAGAATGGCTCTGCCTG	0.532																																					p.W39L		.											.	RUFY3-90	0			c.G116T						.						204	166	179					4																	71588406		2203	4300	6503	SO:0001583	missense	22902	exon1			GAGAATGGCTCTG	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.116G>T	4.37:g.71588406G>T	ENSP00000226328:p.Trp39Leu	Somatic	284	1		WXS	Illumina HiSeq	Phase_I	247	93	NM_001037442	0	0	1	1	0	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797286	0.70567	.	.	ENSG00000018189	ENST00000381006;ENST00000226328;ENST00000536664	T;T;T	0.35973	1.81;1.28;2.13	5.51	5.51	0.81932	.	0.200815	0.47852	D	0.000210	T	0.57227	0.2039	L	0.52011	1.625	0.58432	D	0.999999	B;D;D	0.67145	0.001;0.996;0.967	B;D;P	0.78314	0.002;0.991;0.901	T	0.58301	-0.7660	10	0.87932	D	0	0.0099	19.4131	0.94683	0.0:0.0:1.0:0.0	.	5;39;39	B4DKC2;Q7L099-3;Q7L099	.;.;RUFY3_HUMAN	L	39;39;5	ENSP00000370394:W39L;ENSP00000226328:W39L;ENSP00000443652:W5L	ENSP00000226328:W39L	W	+	2	0	RUFY3	71807270	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.590000	0.87494	0.555000	0.69702	TGG	.		0.532	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		T	71588406	G	T	71588406	3	4	151	1	0	0	0	0	1	0	0	0	13772	1357	47	4	480	4	RUFY3	4	71588406	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	57986661	71588406	119565870	51	13534											
GRID2	2895	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	94138031	94138031	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatcttcaacattgtgtgAtccaaaggatccatttgctc	12	14	6	9	0	2	1	1	1	1	0	5	2	4	2	2	1	2	1	2	1	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:94138031A>G	ENST00000282020.4	+	6	1190	c.932A>G	c.(931-933)gAt>gGt	p.D311G	GRID2_ENST00000510992.1_Missense_Mutation_p.D216G|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	311					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		ACATTGTGTGATCCAAAGGAT	0.413																																					p.D311G													.	GRID2-159	0			c.A932G						.						145	145	145					4																	94138031		2203	4300	6503	SO:0001583	missense	2895	exon6			TGTGTGATCCAAA	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.932A>G	4.37:g.94138031A>G	ENSP00000282020:p.Asp311Gly	Somatic	90	1		WXS	Illumina HiSeq	Phase_I	83	25	NM_001510	0	0	0	0	0	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.329783	0.81690	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	D;D	0.82433	-1.61;-1.61	4.76	4.76	0.60689	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.87277	0.6137	L	0.46157	1.445	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.77004	0.989;0.989	D	0.86678	0.1915	10	0.40728	T	0.16	.	13.7424	0.62855	1.0:0.0:0.0:0.0	.	216;311	E9PH24;O43424	.;GRID2_HUMAN	G	311;216	ENSP00000282020:D311G;ENSP00000421257:D216G	ENSP00000282020:D311G	D	+	2	0	GRID2	94357054	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.754000	0.91642	1.909000	0.55274	0.482000	0.46254	GAT	.		0.413	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			G	94138031	A	G	94138031	3	3	151	1	0	0	0	0	1	0	0	0	6793	333	12	3	954	3	GRID2	4	94138031	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	22549625	94138031	97016245	52	13535											
NFKB1	4790	broad.mit.edu;bcgsc.ca	37	chr4	103501735	103501735	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaaattgtaagaatggacagGacagctggatgtgtgactgg	14	9	14	4	0	0	2	0	1	0	1	0	5	0	5	0	4	1	2	0	4	4	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:103501735G>T	ENST00000505458.1	+	9	1048	c.771G>T	c.(769-771)agG>agT	p.R257S	NFKB1_ENST00000600343.1_Missense_Mutation_p.R77S|NFKB1_ENST00000510638.1_3'UTR|NFKB1_ENST00000226574.4_Missense_Mutation_p.R258S|NFKB1_ENST00000394820.4_Missense_Mutation_p.R257S			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	257	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	GAATGGACAGGACAGCTGGAT	0.413																																					p.R258S													.	NFKB1-912	0			c.G774T						.						126	126	126					4																	103501735		2203	4300	6503	SO:0001583	missense	4790	exon9			GGACAGGACAGCT	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"Ankyrin repeat domain containing"	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.771G>T	4.37:g.103501735G>T	ENSP00000424790:p.Arg257Ser	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	122	7	NM_003998	0	0	32	32	0	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.913709	0.72983	.	.	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458;ENST00000508584	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.5	2.79	0.32731	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.34279	0.0892	L	0.42581	1.335	0.46823	D	0.999212	D;D;D	0.71674	0.989;0.998;0.989	P;P;P	0.62089	0.868;0.82;0.898	T	0.06698	-1.0812	10	0.87932	D	0	.	6.915	0.24355	0.2731:0.1171:0.6098:0.0	.	77;257;258	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	S	258;257;257;51	ENSP00000226574:R258S;ENSP00000378297:R257S;ENSP00000424790:R257S;ENSP00000424815:R51S	ENSP00000226574:R258S	R	+	3	2	NFKB1	103720773	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.650000	0.24858	0.677000	0.31305	0.650000	0.86243	AGG	.		0.413	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			T	103501735	G	T	103501735	3	4	151	1	0	0	0	0	1	0	0	0	10401	1165	41	4	804	4	NFKB1	4	103501735	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	9363704	103501735	87652541	53	13536											
KIAA1109	84162	broad.mit.edu	37	chr4	123185457	123185457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctcagatttcaacactGtcttgtctagtgaccaaaat	12	12	6	11	0	4	2	2	1	2	1	4	2	4	2	2	0	2	0	2	0	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:123185457G>A	ENST00000264501.4	+	45	7565	c.7192G>A	c.(7192-7194)Gtc>Atc	p.V2398I	KIAA1109_ENST00000388738.3_Missense_Mutation_p.V2398I|KIAA1109_ENST00000455637.1_Missense_Mutation_p.V2398I			Q2LD37	K1109_HUMAN	KIAA1109	2398					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTTCAACACTGTCTTGTCTAG	0.403																																					p.V2398I													.	KIAA1109-80	0			c.G7192A						.						101	100	101					4																	123185457		1929	4142	6071	SO:0001583	missense	84162	exon43			AACACTGTCTTGT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.7192G>A	4.37:g.123185457G>A	ENSP00000264501:p.Val2398Ile	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	107	5	NM_015312	0	0	0	0	0	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.158765|4.158765	0.78226|0.78226	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.25414	.|2.43;2.43;1.8	5.92|5.92	5.08|5.08	0.68730|0.68730	.|.	.|0.127540	.|0.30126	.|N	.|0.010349	T|T	0.17323|0.17323	0.0416|0.0416	N|N	0.19112|0.19112	0.55|0.55	0.40902|0.40902	D|D	0.984167|0.984167	.|B;B;B	.|0.15141	.|0.001;0.003;0.012	.|B;B;B	.|0.11329	.|0.004;0.006;0.004	T|T	0.06499|0.06499	-1.0823|-1.0823	5|10	.|0.14656	.|T	.|0.56	.|.	15.1126|15.1126	0.72372|0.72372	0.0674:0.0:0.9326:0.0|0.0674:0.0:0.9326:0.0	.|.	.|2398;2397;2398	.|Q2LD37-6;Q2LD37-2;Q2LD37	.|.;.;K1109_HUMAN	Y|I	355|2398	.|ENSP00000264501:V2398I;ENSP00000373390:V2398I;ENSP00000389925:V2398I	.|ENSP00000264501:V2398I	C|V	+|+	2|1	0|0	KIAA1109|KIAA1109	123404907|123404907	1.000000|1.000000	0.71417|0.71417	0.928000|0.928000	0.36995|0.36995	0.998000|0.998000	0.95712|0.95712	7.792000|7.792000	0.85828|0.85828	1.525000|1.525000	0.49052|0.49052	0.650000|0.650000	0.86243|0.86243	TGT|GTC	.		0.403	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123185457	G	A	123185457	3	1	151	1	0	0	0	0	1	0	0	0	8229	1377	48	2	7362	2	KIAA1109	4	123185457	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	19683722	123185457	67968819	54	13537											
FBXW7	55294	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	153250883	153250883	+	Frame_Shift_Del	DEL	G	G	-																															atcagaaccactaactattcGgttaccacaaaactgtaagc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:153250883delG	ENST00000281708.4	-	8	2406	c.1177delC	c.(1177-1179)cgafs	p.R393fs	FBXW7_ENST00000296555.5_Frame_Shift_Del_p.R275fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.R313fs|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.R393fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.R393fs|FBXW7_ENST00000393956.3_Frame_Shift_Del_p.R217fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	393					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R393*(7)|p.R313*(1)|p.R154*(1)|p.?(1)|p.R275*(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CTAACTATTCGGTTACCACAA	0.343			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.R393fs		.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7-6296	11	Substitution - Nonsense(10)|Unknown(1)	endometrium(5)|large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.1177delC						.						118	107	111					4																	153250883		2203	4300	6503	SO:0001589	frameshift_variant	55294	exon8			.	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1177delC	4.37:g.153250883delG	ENSP00000281708:p.Arg393fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	98	35	NM_033632	0	0	0	0	0	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																			.		0.343	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			-	153250883	G	-	153250883	7	5	151	1	0	1	0	1	0	0	0	0	5788	1124	39	0	966	0	FBXW7	4	153250883	Frame_Shift_Del	DEL	G	TCGA-MH-A561-01A-11D-A26P-10	30065426	153250883	37903393	55	13538											
CENPK	64105	broad.mit.edu	37	chr5	64847424	64847424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttctgccattgactgagttCagcggttaaacattttactt	9	17	7	8	1	2	2	1	2	1	0	2	2	2	2	1	1	4	2	1	1	3	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr5:64847424C>T	ENST00000396679.1	-	5	422	c.208G>A	c.(208-210)Gaa>Aaa	p.E70K	CENPK_ENST00000508421.1_Missense_Mutation_p.E40K|CENPK_ENST00000514814.1_Missense_Mutation_p.E70K|CENPK_ENST00000506282.2_Intron|CENPK_ENST00000510693.1_Missense_Mutation_p.E40K|CENPK_ENST00000242872.3_Missense_Mutation_p.E70K|CENPK_ENST00000510354.1_Missense_Mutation_p.E70K	NM_022145.4	NP_071428.2	Q9BS16	CENPK_HUMAN	centromere protein K	70					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)	10		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)		TGACTGAGTTCAGCGGTTAAA	0.259																																					p.E70K													.	CENPK-90	0			c.G208A						.						69	69	69					5																	64847424		2201	4295	6496	SO:0001583	missense	64105	exon5			TGAGTTCAGCGGT	BC008504	CCDS3984.1	5q12.3	2013-11-05			ENSG00000123219	ENSG00000123219			29479	protein-coding gene	gene with protein product		611502				8950979	Standard	NM_022145		Approved	FKSG14, SOLT, CENP-K	uc003jtu.3	Q9BS16	OTTHUMG00000131227	ENST00000396679.1:c.208G>A	5.37:g.64847424C>T	ENSP00000379911:p.Glu70Lys	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	123	5	NM_001267038	0	0	0	0	0	Q9H4L0	Missense_Mutation	SNP	ENST00000396679.1	37	CCDS3984.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.854522	0.91355	.	.	ENSG00000123219	ENST00000514814;ENST00000396679;ENST00000242872;ENST00000508421;ENST00000510693;ENST00000515497;ENST00000502997;ENST00000510354	.	.	.	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.78666	0.4319	M	0.70275	2.135	0.53005	D	0.999966	D	0.89917	1.0	D	0.87578	0.998	T	0.79339	-0.1844	9	0.72032	D	0.01	-22.078	16.1014	0.81175	0.0:1.0:0.0:0.0	.	70	Q9BS16	CENPK_HUMAN	K	70;70;70;40;40;72;70;70	.	ENSP00000242872:E70K	E	-	1	0	CENPK	64883180	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	3.891000	0.56227	2.878000	0.98634	0.650000	0.86243	GAA	.		0.259	CENPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253971.2	NM_022145		T	64847424	C	T	64847424	3	4	151	1	0	0	0	0	1	0	0	0	3241	835	29	2	629	2	CENPK	5	64847424	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		64847424	116067836	56	13539											
TAF7	6879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140699374	140699374	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaaaagtttttttatcaaTggttttcaagctttccataa	13	18	5	5	0	2	0	2	0	0	0	3	0	3	0	1	1	1	4	1	1	7	9			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr5:140699374T>C	ENST00000313368.5	-	1	956	c.238A>G	c.(238-240)Att>Gtt	p.I80V		NM_005642.2	NP_005633.2	Q15545	TAF7_HUMAN	TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55kDa	80					DNA-templated transcription, initiation (GO:0006352)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of histone acetylation (GO:0035067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermine transport (GO:0000296)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	histone acetyltransferase binding (GO:0035035)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|vitamin D receptor binding (GO:0042809)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTTATCAATGGTTTTCAAG	0.443																																					p.I80V		.											.	TAF7-90	0			c.A238G						.						120	113	116					5																	140699374		2203	4300	6503	SO:0001583	missense	6879	exon1			TATCAATGGTTTT	AF349038	CCDS4259.1	5q31	2008-02-05	2002-08-29	2001-12-07	ENSG00000178913	ENSG00000178913			11541	protein-coding gene	gene with protein product		600573	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, F, 55kD"	TAF2F		7824954	Standard	NM_005642		Approved	TAFII55	uc003ljg.3	Q15545	OTTHUMG00000129628	ENST00000313368.5:c.238A>G	5.37:g.140699374T>C	ENSP00000312709:p.Ile80Val	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	90	29	NM_005642	0	0	37	73	36	B2RBV9|Q13036	Missense_Mutation	SNP	ENST00000313368.5	37	CCDS4259.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307342	0.23821	.	.	ENSG00000178913	ENST00000313368	T	0.23348	1.91	5.08	3.93	0.45458	TAFII55 protein, conserved region (1);	0.259807	0.37809	N	0.001931	T	0.13586	0.0329	N	0.17312	0.475	0.41194	D	0.986322	B	0.09022	0.002	B	0.12837	0.008	T	0.10567	-1.0624	10	0.19590	T	0.45	-6.4089	7.5444	0.27757	0.0:0.0947:0.0:0.9053	.	80	Q15545	TAF7_HUMAN	V	80	ENSP00000312709:I80V	ENSP00000312709:I80V	I	-	1	0	TAF7	140679558	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.373000	0.59537	1.092000	0.41356	0.533000	0.62120	ATT	.		0.443	TAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251823.2	NM_005642		C	140699374	T	C	140699374	3	2	151	1	0	0	0	0	1	0	0	0	15564	1464	51	3	815	3	TAF7	5	140699374	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	75851950	140699374	40215886	57	13540											
TFAP2A	7020	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	10398689	10398689	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctttgtcactgcttttggcGttgttgtccgtgtggctgtt	1	20	12	8	2	2	0	1	0	1	0	3	0	3	0	1	2	1	5	1	2	0	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:10398689G>C	ENST00000482890.1	-	8	1627	c.1275C>G	c.(1273-1275)aaC>aaG	p.N425K	TFAP2A_ENST00000379613.3_Missense_Mutation_p.N427K|TFAP2A_ENST00000379604.2_Missense_Mutation_p.N425K|TFAP2A_ENST00000319516.4_Missense_Mutation_p.N421K|TFAP2A_ENST00000379608.3_Missense_Mutation_p.N419K|TFAP2A_ENST00000497266.1_5'Flank			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	425					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				TGCTTTTGGCGTTGTTGTCCG	0.637																																					p.N425K		.											.	TFAP2A-91	0			c.C1275G						.						303	314	310					6																	10398689		2203	4300	6503	SO:0001583	missense	7020	exon7			TTTGGCGTTGTTG	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1275C>G	6.37:g.10398689G>C	ENSP00000418541:p.Asn425Lys	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	146	46	NM_003220	0	0	0	0	0	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	37	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	G	5.052	0.195211	0.09599	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17	5.41	5.41	0.78517	.	0.166295	0.64402	D	0.000003	T	0.82139	0.4972	N	0.02539	-0.55	0.34515	D	0.707504	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.74665	-0.3589	10	0.08381	T	0.77	-4.3896	19.197	0.93693	0.0:0.0:1.0:0.0	.	421;425;419	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	K	427;425;421;419;425	ENSP00000368933:N427K;ENSP00000368924:N425K;ENSP00000316516:N421K;ENSP00000368928:N419K;ENSP00000418541:N425K	ENSP00000316516:N421K	N	-	3	2	TFAP2A	10506675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.556000	0.53734	2.532000	0.85374	0.655000	0.94253	AAC	.		0.637	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220		C	10398689	G	C	10398689	3	2	151	1	0	0	0	0	1	0	0	0	15819	1136	40	4	42	4	TFAP2A	6	10398689	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		10398689	160716378	58	13541											
KIF13A	63971	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	17817447	17817447	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgtttctccaggacctgaaCcacattttgaactgggtcta	9	14	8	10	0	2	2	0	2	2	0	3	3	2	3	3	2	2	1	3	2	3	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:17817447C>T	ENST00000259711.6	-	17	1909	c.1804G>A	c.(1804-1806)Gtt>Att	p.V602I	KIF13A_ENST00000378826.2_Missense_Mutation_p.V602I|KIF13A_ENST00000378816.5_Missense_Mutation_p.V602I|KIF13A_ENST00000503342.1_5'Flank|KIF13A_ENST00000378843.2_Missense_Mutation_p.V602I|KIF13A_ENST00000378814.5_Missense_Mutation_p.V602I	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	602					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AGGACCTGAACCACATTTTGA	0.532																																					p.V602I		.											.	KIF13A-137	0			c.G1804A						.						74	79	78					6																	17817447		2040	4210	6250	SO:0001583	missense	63971	exon17			CCTGAACCACATT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"Kinesins"	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1804G>A	6.37:g.17817447C>T	ENSP00000259711:p.Val602Ile	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	131	41	NM_001105567	0	0	0	1	1	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074673	0.76415	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58	5.92	5.92	0.95590	.	0.060329	0.64402	D	0.000003	T	0.43787	0.1263	L	0.27053	0.805	0.58432	D	0.99999	B;B;P;B;P	0.37731	0.112;0.094;0.48;0.112;0.607	B;B;B;B;B	0.34722	0.034;0.108;0.188;0.034;0.187	T	0.52064	-0.8625	10	0.08599	T	0.76	.	20.3248	0.98698	0.0:1.0:0.0:0.0	.	573;602;602;602;602	E7ER65;Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;.;KI13A_HUMAN;.	I	602	ENSP00000368091:V602I;ENSP00000259711:V602I;ENSP00000368103:V602I;ENSP00000368120:V602I;ENSP00000368093:V602I	ENSP00000259711:V602I	V	-	1	0	KIF13A	17925426	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.432000	0.80349	2.818000	0.97014	0.655000	0.94253	GTT	.		0.532	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			T	17817447	C	T	17817447	3	4	151	1	0	0	0	0	1	0	0	0	8295	507	18	2	3730	2	KIF13A	6	17817447	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	7418758	17817447	153297620	59	13542											
UHRF1BP1	54887	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	34825520	34825520	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttccttgtcctaatctctaCattcagttaaatggtctgac	9	16	6	10	0	3	1	1	1	2	0	6	1	5	1	2	1	1	2	2	1	4	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:34825520C>T	ENST00000192788.5	+	13	1764	c.1593C>T	c.(1591-1593)taC>taT	p.Y531Y	UHRF1BP1_ENST00000452449.2_Silent_p.Y531Y	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	531							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						CTAATCTCTACATTCAGTTAA	0.398																																					p.Y531Y		.											.	UHRF1BP1-93	0			c.C1593T						.						158	148	151					6																	34825520		1859	4088	5947	SO:0001819	synonymous_variant	54887	exon13			TCTCTACATTCAG	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 107"	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1593C>T	6.37:g.34825520C>T		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	144	9	NM_017754	0	0	0	0	0	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																			.		0.398	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		T	34825520	C	T	34825520	2	4	151	1	0	0	0	0	0	0	0	1	17001	489	17	2		2	UHRF1BP1	6	34825520	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	17008073	34825520	136289547	60	13543											
PRIM2	5558	broad.mit.edu;bcgsc.ca	37	chr6	57467120	57467120	+	3'UTR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaacatccgtcacagctttgGaaaggaaggcaagaggacag	15	5	13	8	1	1	1	1	0	0	1	2	5	2	4	1	4	2	2	1	4	4	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:57467120G>T	ENST00000389488.2	+	0	1148				PRIM2_ENST00000607273.1_3'UTR			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)						DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CACAGCTTTGGAAAGGAAGGC	0.418																																					.													.	PRIM2-227	0			.						.						122	113	116					6																	57467120		1980	4180	6160	SO:0001624	3_prime_UTR_variant	5558	.			GCTTTGGAAAGGA		CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143			9370	protein-coding gene	gene with protein product		176636	"primase, polypeptide 2A (58kD)", "primase, polypeptide 2A, 58kDa"	PRIM2A		8530050, 20675616	Standard	NM_001282487		Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.*1145G>T	6.37:g.57467120G>T		Somatic	299	0		WXS	Illumina HiSeq	Phase_I	293	10	.	0	0	7	7	0	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	Missense_Mutation	SNP	ENST00000389488.2	37																																																																																				.		0.418	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000043468.3	NM_000947		T	57467120	G	T	57467120	1	4	151	0	1	0	0	0	0	0	0	0	12520	1174	41	4		4	PRIM2	6	57467120	3'UTR	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	22641600	57467120	113647947	61	13544											
COL12A1	1303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	75861881	75861881	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctttgtacggcaagttTgccacagcttgcaacaagct	9	11	8	13	1	0	0	0	0	0	0	1	0	1	0	3	1	6	6	3	1	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:75861881T>C	ENST00000322507.8	-	19	4110	c.3801A>G	c.(3799-3801)gcA>gcG	p.A1267A	COL12A1_ENST00000345356.6_Silent_p.A103A|COL12A1_ENST00000416123.2_Silent_p.A1267A|COL12A1_ENST00000483888.2_Silent_p.A1267A	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1267	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACGGCAAGTTTGCCACAGCTT	0.473																																					p.A1267A		.											.	COL12A1-142	0			c.A3801G						.						102	99	100					6																	75861881		1976	4162	6138	SO:0001819	synonymous_variant	1303	exon19			CAAGTTTGCCACA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3801A>G	6.37:g.75861881T>C		Somatic	211	0		WXS	Illumina HiSeq	Phase_I	199	74	NM_004370	0	0	1	2	1	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	T	4.645	0.119852	0.08881	.	.	ENSG00000111799	ENST00000419671	.	.	.	5.94	-10.2	0.00374	.	.	.	.	.	T	0.24851	0.0603	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48570	-0.9024	4	.	.	.	.	5.2576	0.15555	0.078:0.3395:0.3536:0.2289	.	.	.	.	E	9	.	.	K	-	1	0	COL12A1	75918601	0.080000	0.21391	0.440000	0.26846	0.478000	0.33099	-0.719000	0.04974	-1.241000	0.02526	-1.293000	0.01348	AAA	.		0.473	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75861881	T	C	75861881	2	2	151	1	0	0	0	0	0	0	0	1	3675	1799	63	3		3	COL12A1	6	75861881	Silent	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	18394761	75861881	95253186	62	13545											
TMEM30A	55754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	75977367	75977367	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacacagacctcaaatgacTtttccagtgtgaagttaatg	15	11	7	8	0	1	3	1	2	0	1	2	3	2	3	2	0	1	1	2	0	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:75977367T>A	ENST00000230461.6	-	2	664	c.335A>T	c.(334-336)aAg>aTg	p.K112M	TMEM30A_ENST00000370050.5_De_novo_Start_InFrame|TMEM30A_ENST00000475111.2_Intron	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	112					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCAAATGACTTTTCCAGTGT	0.363																																					p.K112M		.											.	TMEM30A-90	0			c.A335T						.						130	135	133					6																	75977367		2203	4300	6503	SO:0001583	missense	55754	exon2			AATGACTTTTCCA	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"chromosome 6 open reading frame 67"	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.335A>T	6.37:g.75977367T>A	ENSP00000230461:p.Lys112Met	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_018247	0	0	0	0	0	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082970	0.76642	.	.	ENSG00000112697	ENST00000230461;ENST00000545449	.	.	.	5.28	5.28	0.74379	.	0.326351	0.37761	N	0.001944	T	0.77890	0.4198	M	0.84326	2.69	0.80722	D	1	B	0.27264	0.173	P	0.47251	0.542	T	0.80511	-0.1350	9	0.66056	D	0.02	.	14.8721	0.70465	0.0:0.0:0.0:1.0	.	112	Q9NV96	CC50A_HUMAN	M	112;96	.	ENSP00000230461:K112M	K	-	2	0	TMEM30A	76034087	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	7.596000	0.82721	1.997000	0.58415	0.454000	0.30748	AAG	.		0.363	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		A	75977367	T	A	75977367	3	1	151	1	0	0	0	0	1	0	0	0	16185	1609	56	5	774	5	TMEM30A	6	75977367	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	115486	75977367	95137700	63	13546											
MAP3K7	6885	hgsc.bcm.edu;bcgsc.ca	37	chr6	91226399	91226400	+	Splice_Site	DEL	GC	GC	-																															cagttctgcaactagttcttGcctacaaacaaataccacat																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:91226399_91226400delGC	ENST00000369329.3	-	17	1802_1803	c.1641_1642delGC	c.(1639-1644)aagcaa>aaaa	p.Q548fs	MAP3K7_ENST00000369327.3_Splice_Site_p.A482fs|MAP3K7_ENST00000369320.1_Splice_Site_p.Q202fs|MAP3K7_ENST00000479630.1_5'UTR|MAP3K7_ENST00000369332.3_Splice_Site_p.Q521fs|MAP3K7_ENST00000369325.3_Splice_Site_p.A509fs	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	548					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		ACTAGTTCTTGCCTACAAACAA	0.351																																					p.547_548del		.											.	MAP3K7-980	0			c.1641_1642del						.																																			SO:0001630	splice_region_variant	6885	exon17			.	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1641-1GC>-	6.37:g.91226399_91226400delGC		Somatic	76	0		WXS	Illumina HiSeq	Phase_I	66	20	NM_145331	0	0	0	0	0	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Frame_Shift_Del	DEL	ENST00000369329.3	37	CCDS5028.1																																																																																			.		0.351	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331	Frame_Shift_Del	-	91226400	GC	-	91226399	8	5	151	1	0	1	0	1	0	0	1	0	9280	1333	46	0	182	0	MAP3K7	6	91226399	Splice_Site	DEL	GC	TCGA-MH-A561-01A-11D-A26P-10	15249032	91226399	79888668	64	13547	145	2									
MAP3K7	6885	bcgsc.ca	37	chr6	91226401	91226401	+	Splice_Site	SNP	C	C	T																															gttctgcaactagttcttgcCtacaaacaaataccacataa																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:91226401C>T	ENST00000369329.3	-	17	1802		c.e17-1		MAP3K7_ENST00000369327.3_Splice_Site|MAP3K7_ENST00000369320.1_Splice_Site|MAP3K7_ENST00000479630.1_Splice_Site|MAP3K7_ENST00000369332.3_Splice_Site|MAP3K7_ENST00000369325.3_Splice_Site	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		TAGTTCTTGCCTACAAACAAA	0.348																																					.													.	MAP3K7-980	0			c.1641-1G>A						.						108	100	103					6																	91226401		2203	4300	6503	SO:0001630	splice_region_variant	6885	exon18			TCTTGCCTACAAA	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1641-1G>A	6.37:g.91226401C>T		Somatic	73	0		WXS	Illumina HiSeq	Phase_1	66	20	NM_145331	0	0	0	0	0	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Splice_Site	SNP	ENST00000369329.3	37	CCDS5028.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939262	0.73557	.	.	ENSG00000135341	ENST00000369332;ENST00000369329;ENST00000369325;ENST00000369327;ENST00000369320;ENST00000450832	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5538	0.95333	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAP3K7	91283122	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.688000	0.91661	0.655000	0.94253	.	.		0.348	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331	Intron	T	91226401	C	T	91226401	5	4	151	1	0	0	0	0	0	0	1	0	9280	695	24	2	184	2	MAP3K7	6	91226401	Splice_Site	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	2	91226401	79888666	65	13548	145	2									
GRIK2	2898	hgsc.bcm.edu;bcgsc.ca	37	chr6	102513771	102513771	+	Intron	DEL	T	T	-																															catcaccatcttcatcatcaTtatcatcatgttcttaataa																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:102513771delT	ENST00000421544.1	+	16	3052				GRIK2_ENST00000413795.1_Intron|GRIK2_ENST00000369138.1_Frame_Shift_Del_p.L888fs|GRIK2_ENST00000369134.4_Intron|GRIK2_ENST00000369137.3_Intron	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2						behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ttcatcatcattatcatcatG	0.363																																					p.L888fs		.											.	GRIK2-157	0			c.2662delT						.						287	228	246					6																	102513771		692	1590	2282	SO:0001627	intron_variant	2898	exon16			.		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2563-2451T>-	6.37:g.102513771delT		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	80	37	NM_001166247	0	0	0	0	0	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Frame_Shift_Del	DEL	ENST00000421544.1	37	CCDS5048.1																																																																																			.		0.363	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			-	102513771	T	-	102513771	6	5	151	0	1	1	0	1	0	0	0	0	6795	1490	52	0		0	GRIK2	6	102513771	Intron	DEL	T	TCGA-MH-A561-01A-11D-A26P-10	11287370	102513771	68601296	66	13549											
HDAC2	3066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr6	114264645	114264645	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgagaattcttcatcacaAgctatccgcttgtctgatgc	9	14	7	11	1	5	2	2	2	3	1	6	3	6	2	1	0	2	2	1	0	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:114264645A>C	ENST00000519065.1	-	12	1624	c.1248T>G	c.(1246-1248)gcT>gcG	p.A416A	HDAC2_ENST00000368632.2_Silent_p.A386A|HDAC2_ENST00000519108.1_Silent_p.A386A|HDAC2_ENST00000398283.2_Silent_p.A510A			Q92769	HDAC2_HUMAN	histone deacetylase 2	416					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	CTTCATCACAAGCTATCCGCT	0.363																																					p.A416A		.											.	HDAC2-660	0			c.T1248G						.						126	110	115					6																	114264645		1841	4082	5923	SO:0001819	synonymous_variant	3066	exon12			ATCACAAGCTATC	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.1248T>G	6.37:g.114264645A>C		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_001527	0	0	54	89	35	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Silent	SNP	ENST00000519065.1	37	CCDS43493.2																																																																																			.		0.363	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			C	114264645	A	C	114264645	2	2	151	1	0	0	0	0	0	0	0	1	7028	59	3	5		5	HDAC2	6	114264645	Silent	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	11750874	114264645	56850422	67	13550											
ELMO1	9844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	37053037	37053037	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagtcgttgcaggtctcaCtagctggaggaaagagatgg	11	8	16	6	1	1	1	1	0	1	1	3	5	1	4	0	5	2	3	0	5	3	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:37053037C>T	ENST00000310758.4	-	16	1951	c.1304G>A	c.(1303-1305)aGt>aAt	p.S435N	ELMO1-AS1_ENST00000419535.1_RNA|ELMO1_ENST00000448602.1_Missense_Mutation_p.S435N|ELMO1_ENST00000341056.3_Missense_Mutation_p.S137N|ELMO1_ENST00000442504.1_Missense_Mutation_p.S435N	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	435	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GCAGGTCTCACTAGCTGGAGG	0.458																																					p.S435N		.											.	ELMO1-96	0			c.G1304A						.						79	75	76					7																	37053037		2203	4300	6503	SO:0001583	missense	9844	exon16			GTCTCACTAGCTG	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1304G>A	7.37:g.37053037C>T	ENSP00000312185:p.Ser435Asn	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	88	31	NM_014800	0	0	0	0	0	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	37	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.774299	0.49786	.	.	ENSG00000155849	ENST00000341056;ENST00000310758;ENST00000361912;ENST00000442504;ENST00000448602	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	6.06	6.06	0.98353	Engulfment/cell motility, ELMO (2);	0.147484	0.64402	D	0.000020	T	0.21841	0.0526	N	0.12527	0.23	0.48571	D	0.999678	B	0.06786	0.001	B	0.12156	0.007	T	0.07366	-1.0776	10	0.22109	T	0.4	.	20.2348	0.98355	0.0:1.0:0.0:0.0	.	435	Q92556	ELMO1_HUMAN	N	137;435;339;435;435	ENSP00000342142:S137N;ENSP00000312185:S435N;ENSP00000406952:S435N;ENSP00000394458:S435N	ENSP00000312185:S435N	S	-	2	0	ELMO1	37019562	1.000000	0.71417	0.988000	0.46212	0.765000	0.43378	4.885000	0.63142	2.879000	0.98667	0.650000	0.86243	AGT	.		0.458	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		T	37053037	C	T	37053037	3	4	151	1	0	0	0	0	1	0	0	0	5078	565	20	2	907	2	ELMO1	7	37053037	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		37053037	122085626	68	13551											
MLL5	55904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	104717538	104717538	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtgagggtgttcagagggaGgcacaaagaatagctctgag	13	7	16	5	0	2	4	1	2	1	2	2	5	2	5	0	3	1	3	0	3	3	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:104717538G>C	ENST00000311117.3	+	10	1442	c.897G>C	c.(895-897)gaG>gaC	p.E299D	KMT2E_ENST00000476671.1_Missense_Mutation_p.E299D|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000334877.4_Missense_Mutation_p.E299D|KMT2E_ENST00000257745.4_Missense_Mutation_p.E299D	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	299					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TTCAGAGGGAGGCACAAAGAA	0.393																																					p.E299D		.											.	MLL5-93	0			c.G897C						.						125	115	118					7																	104717538		2203	4300	6503	SO:0001583	missense	55904	exon9			GAGGGAGGCACAA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.897G>C	7.37:g.104717538G>C	ENSP00000312379:p.Glu299Asp	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	166	19	NM_018682	0	0	4	6	2	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576129	0.65878	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95756	-2.92;-2.54;-2.92;-3.8;-3.28	6.07	4.28	0.50868	.	0.000000	0.64402	D	0.000001	D	0.94185	0.8134	L	0.44542	1.39	0.80722	D	1	D;P	0.67145	0.996;0.943	P;P	0.54499	0.754;0.576	D	0.91766	0.5424	10	0.14656	T	0.56	.	12.3705	0.55252	0.1346:0.0:0.8654:0.0	.	299;299	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	D	299;299;299;299;299;157;299;233	ENSP00000312379:E299D;ENSP00000335599:E299D;ENSP00000257745:E299D;ENSP00000419883:E157D;ENSP00000417888:E299D	ENSP00000257745:E299D	E	+	3	2	MLL5	104504774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.197000	0.72100	1.587000	0.49959	-0.136000	0.14681	GAG	.		0.393	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			C	104717538	G	C	104717538	3	2	151	1	0	0	0	0	1	0	0	0	9649	991	35	4	927	4	MLL5	7	104717538	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	67664501	104717538	54421125	69	13552											
LAMB4	22798	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	107732109	107732120	+	In_Frame_Del	DEL	CCTCGTAGAGAT	CCTCGTAGAGAT	-																															gagtgttgtggcttcctctgCctcgtagagatagaaattca																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	CCTCGTAGAGAT	CCTCGTAGAGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:107732109_107732120delCCTCGTAGAGAT	ENST00000388781.3	-	14	1735_1746	c.1652_1663delATCTCTACGAGG	c.(1651-1665)tatctctacgaggca>tca	p.551_555YLYEA>S	LAMB4_ENST00000418464.1_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000414450.2_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000388780.3_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000205386.4_In_Frame_Del_p.551_555YLYEA>S	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	551	Laminin EGF-like 5; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.|Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.Y553D(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GCTTCCTCTGCCTCGTAGAGATAGAAATTCAA	0.491																																					p.551_555del		.											.	LAMB4-140	1	Substitution - Missense(1)	prostate(1)	c.1652_1663del						.																																			SO:0001651	inframe_deletion	22798	exon14			.	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"Laminins"	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1652_1663delATCTCTACGAGG	7.37:g.107732109_107732120delCCTCGTAGAGAT	ENSP00000373433:p.Tyr551_Ala555delinsSer	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	119	23	NM_007356	0	0	0	0	0	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	In_Frame_Del	DEL	ENST00000388781.3	37	CCDS34732.1																																																																																			.		0.491	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		-	107732120	CCTCGTAGAGAT	-	107732109	7	5	151	1	0	1	0	1	0	0	0	0	8634	739	26	0	3706	0	LAMB4	7	107732109	In_Frame_Del	DEL	CCTCGTAGAGAT	TCGA-MH-A561-01A-11D-A26P-10	3014571	107732109	51406554	70	13553											
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgccagtgaagtggaTggctttggaaagtctgcaaa	13	9	13	6	0	1	1	0	1	1	0	1	3	1	3	1	3	3	3	1	3	4	1	rs121913245		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000397752.3_Missense_Mutation_p.M1250T|MET_ENST00000539704.1_Missense_Mutation_p.M120T			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.M1268T(4)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET-5874	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	.						93	92	92					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"hepatocyte growth factor receptor"	164860	"met proto-oncogene"			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3803T>C	7.37:g.116423474T>C	ENSP00000317272:p.Met1268Thr	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	83	27	NM_001127500	0	0	82	163	81	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	5.68	5.68	0.88126	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423474	T	C	116423474	3	2	151	1	0	0	0	0	1	0	0	0	9510	1464	51	3	3873	3	MET	7	116423474	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	8691365	116423474	42715189	71	13554											
GPR37	2861	hgsc.bcm.edu	37	chr7	124405027	124405027	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagaagcgcgcccggggctcGcatggcttggtgagggcaca	7	5	18	11	4	0	2	0	1	0	1	1	3	0	2	1	5	1	4	1	5	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:124405027G>A	ENST00000303921.2	-	1	654	c.4C>T	c.(4-6)Cga>Tga	p.R2*		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	2					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CCCGGGGCTCGCATGGCTTGG	0.637																																					p.R2X		.											.	GPR37-523	0			c.C4T						.						7	6	7					7																	124405027		2164	4249	6413	SO:0001587	stop_gained	2861	exon1			GGGCTCGCATGGC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.4C>T	7.37:g.124405027G>A	ENSP00000306449:p.Arg2*	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	6	4	NM_005302	0	0	0	0	0	A4D0Y6|O00348|O14768|Q8TD39	Nonsense_Mutation	SNP	ENST00000303921.2	37	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	40	8.449312	0.98815	.	.	ENSG00000170775	ENST00000303921	.	.	.	5.31	3.45	0.39498	.	0.960325	0.08673	N	0.910555	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-4.8252	6.6615	0.23016	0.0898:0.0:0.7349:0.1753	.	.	.	.	X	2	.	ENSP00000306449:R2X	R	-	1	2	GPR37	124192263	0.983000	0.35010	0.703000	0.30354	0.397000	0.30659	1.951000	0.40333	0.767000	0.33267	0.655000	0.94253	CGA	.		0.637	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		A	124405027	G	A	124405027	4	1	151	1	0	0	0	0	0	1	0	0	6711	1095	38	1	1845	1	GPR37	7	124405027	Nonsense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	7981553	124405027	34733636	72	13555											
NRG1	3084	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	32616873	32616873	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcatattgttgagagagAagcagagacatccttttcca	13	11	10	7	0	0	4	0	2	0	3	2	7	2	4	2	0	2	3	2	0	2	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:32616873A>T	ENST00000405005.3	+	10	980	c.980A>T	c.(979-981)gAa>gTa	p.E327V	NRG1_ENST00000338921.4_Missense_Mutation_p.E335V|NRG1_ENST00000287842.3_Missense_Mutation_p.E324V|NRG1_ENST00000287845.5_Missense_Mutation_p.E298V|NRG1_ENST00000539990.1_Missense_Mutation_p.E170V|NRG1_ENST00000356819.4_Missense_Mutation_p.E332V|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000523079.1_Missense_Mutation_p.E324V|NRG1_ENST00000519301.1_Missense_Mutation_p.E277V|NRG1_ENST00000521670.1_Missense_Mutation_p.E327V			Q02297	NRG1_HUMAN	neuregulin 1	327					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		GTTGAGAGAGAAGCAGAGACA	0.408																																					p.E332V		.											.	NRG1-525	0			c.A995T						.						201	169	180					8																	32616873		2203	4300	6503	SO:0001583	missense	3084	exon11			AGAGAGAAGCAGA	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.980A>T	8.37:g.32616873A>T	ENSP00000384620:p.Glu327Val	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	145	41	NM_013956	0	0	2	2	0	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.300044	0.81136	.	.	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03	6.16	6.16	0.99307	Neuregulin 1-related, C-terminal (1);	0.100274	0.64402	D	0.000002	T	0.70824	0.3268	L	0.41573	1.285	0.53688	D	0.999971	D;D;D;D;D;D;D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;1.0;1.0;0.983;0.999;0.999;1.0;1.0	D;D;D;D;D;D;P;D;D;D;D	0.97110	0.997;0.999;1.0;0.984;0.991;1.0;0.592;0.984;0.985;0.984;0.999	T	0.64694	-0.6347	10	0.14252	T	0.57	-8.3311	16.8061	0.85666	1.0:0.0:0.0:0.0	.	170;173;324;298;332;323;335;324;327;332;327	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	V	294;277;400;324;335;332;327;298;324;327;327;170	ENSP00000430053:E294V;ENSP00000429582:E277V;ENSP00000429067:E400V;ENSP00000430120:E324V;ENSP00000343395:E335V;ENSP00000349275:E332V;ENSP00000287840:E327V;ENSP00000287845:E298V;ENSP00000287842:E324V;ENSP00000384620:E327V;ENSP00000428828:E327V;ENSP00000439276:E170V	ENSP00000287840:E327V	E	+	2	0	NRG1	32736415	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.312000	0.65792	2.367000	0.80283	0.528000	0.53228	GAA	.		0.408	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			T	32616873	A	T	32616873	3	4	151	1	0	0	0	0	1	0	0	0	10673	246	9	5	2614	5	NRG1	8	32616873	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		32616873	113747149	73	13556											
NKX6-3	157848	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	41504065	41504065	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtccgagtcggggtccagcGgcttgttgtactcgtcgtcc	3	11	14	13	6	0	0	0	0	0	0	6	1	3	0	3	3	2	3	3	3	1	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:41504065G>T	ENST00000524115.2	-	2	314	c.311C>A	c.(310-312)cCg>cAg	p.P104Q		NM_152568.2	NP_689781.1	A6NJ46	NKX63_HUMAN	NK6 homeobox 3	234					cell fate determination (GO:0001709)|glandular epithelial cell differentiation (GO:0002067)|negative regulation of epithelial cell differentiation (GO:0030857)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(1)	1	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GGGGTCCAGCGGCTTGTTGTA	0.731																																					p.P104Q		.											.	NKX6-3-90	0			c.C311A						.						43	38	39					8																	41504065		2201	4300	6501	SO:0001583	missense	157848	exon2			TCCAGCGGCTTGT	AK057898	CCDS6118.1	8p11.21	2014-08-12	2007-07-09		ENSG00000165066	ENSG00000165066		"Homeoboxes / ANTP class : NKL subclass"	26328	protein-coding gene	gene with protein product		610772	"NK6 transcription factor related, locus 3 (Drosophila)"			16326147	Standard	XM_005273422		Approved	FLJ25169	uc003xoa.2	A6NJ46	OTTHUMG00000164083	ENST00000524115.2:c.311C>A	8.37:g.41504065G>T	ENSP00000429553:p.Pro104Gln	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	24	15	NM_152568	0	0	0	1	1	Q96LR0	Missense_Mutation	SNP	ENST00000524115.2	37	CCDS6118.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124514	0.94429	.	.	ENSG00000165066	ENST00000524115;ENST00000425142;ENST00000518699	T;T	0.57907	0.37;0.37	4.9	4.02	0.46733	.	0.000000	0.85682	D	0.000000	T	0.70718	0.3256	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.73170	-0.4067	9	0.56958	D	0.05	.	12.1998	0.54319	0.0832:0.0:0.9168:0.0	.	104	A6NJ46-2	.	Q	104;234;234	ENSP00000429553:P104Q;ENSP00000428361:P234Q	ENSP00000414183:P234Q	P	-	2	0	NKX6-3	41623222	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.856000	0.86956	1.066000	0.40716	0.491000	0.48974	CCG	.		0.731	NKX6-3-002	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000377166.2	NM_152568		T	41504065	G	T	41504065	3	4	151	1	0	0	0	0	1	0	0	0	10485	1116	39	4	100	4	NKX6-3	8	41504065	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	8887192	41504065	104859957	74	13557											
NCOA2	10499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	71053580	71053580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctcacagccgaactctgcGgtgcccattctccagatggc	7	9	9	16	2	3	1	1	0	3	1	5	2	3	1	3	2	4	0	3	2	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:71053580G>A	ENST00000452400.2	-	14	3048	c.2867C>T	c.(2866-2868)cCg>cTg	p.P956L	NCOA2_ENST00000267974.4_Missense_Mutation_p.P44L	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	956					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CGAACTCTGCGGTGCCCATTC	0.532			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P956L		.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2-639	0			c.C2867T						.						57	60	59					8																	71053580		2052	4211	6263	SO:0001583	missense	10499	exon14			CTCTGCGGTGCCC	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2867C>T	8.37:g.71053580G>A	ENSP00000399968:p.Pro956Leu	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	152	28	NM_006540	0	0	2	3	1	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.585|1.585	-0.530666|-0.530666	0.04112|0.04112	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000452400;ENST00000267974|ENST00000518363	T;T|.	0.06849|.	4.9;3.25|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.483437|.	0.22937|.	N|.	0.053835|.	T|T	0.28532|0.28532	0.0706|0.0706	N|N	0.04880|0.04880	-0.145|-0.145	0.09310|0.09310	N|N	0.999999|0.999999	P;B|.	0.35192|.	0.489;0.059|.	B;B|.	0.24974|.	0.057;0.01|.	T|T	0.19289|0.19289	-1.0310|-1.0310	10|5	0.02654|.	T|.	1|.	.|.	16.5528|16.5528	0.84476|0.84476	0.0:0.1389:0.8611:0.0|0.0:0.1389:0.8611:0.0	.|.	44;956|.	F8WAJ2;Q15596|.	.;NCOA2_HUMAN|.	L|C	956;44|57	ENSP00000399968:P956L;ENSP00000267974:P44L|.	ENSP00000267974:P44L|.	P|R	-|-	2|1	0|0	NCOA2|NCOA2	71216134|71216134	0.778000|0.778000	0.28640|0.28640	0.149000|0.149000	0.22428|0.22428	0.831000|0.831000	0.47069|0.47069	4.231000|4.231000	0.58639|0.58639	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CCG|CGC	.		0.532	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			A	71053580	G	A	71053580	3	1	151	1	0	0	0	0	1	0	0	0	10255	1116	39	1	1567	1	NCOA2	8	71053580	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	29549515	71053580	75310442	75	13558											
CSMD3	114788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	113316994	113316994	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccaactccaagtaccattaGgaagacattcgatggaggca	14	8	9	10	1	0	1	0	0	0	1	3	4	2	3	3	3	2	2	3	3	5	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:113316994G>A	ENST00000297405.5	-	52	8466	c.8222C>T	c.(8221-8223)cCt>cTt	p.P2741L	CSMD3_ENST00000455883.2_Intron|CSMD3_ENST00000352409.3_Missense_Mutation_p.P2671L|CSMD3_ENST00000343508.3_Missense_Mutation_p.P2701L	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2741	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGTACCATTAGGAAGACATTC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P2741L		.											.	CSMD3-1132	0			c.C8222T						.						133	118	123					8																	113316994		2203	4300	6503	SO:0001583	missense	114788	exon52			CCATTAGGAAGAC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.8222C>T	8.37:g.113316994G>A	ENSP00000297405:p.Pro2741Leu	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	136	53	NM_198123	0	0	0	0	0	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.891954	0.52014	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	4.9	4.9	0.64082	Complement control module (2);Sushi/SCR/CCP (3);	0.178361	0.34200	N	0.004165	T	0.48259	0.1490	N	0.13272	0.32	0.54753	D	0.99998	B;B	0.30211	0.273;0.006	B;B	0.30105	0.111;0.026	T	0.47849	-0.9085	10	0.38643	T	0.18	.	18.4479	0.90691	0.0:0.0:1.0:0.0	.	2741;2701	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	L	2701;2741;2011;2671	ENSP00000345799:P2701L;ENSP00000297405:P2741L;ENSP00000341558:P2011L;ENSP00000343124:P2671L	ENSP00000297405:P2741L	P	-	2	0	CSMD3	113386170	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	9.775000	0.98995	2.385000	0.81259	0.561000	0.74099	CCT	.		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113316994	G	A	113316994	3	1	151	1	0	0	0	0	1	0	0	0	3952	1000	35	2	2981	2	CSMD3	8	113316994	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	42263414	113316994	33047028	76	13559											
PHF20L1	51105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133806739	133806739	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagtcatcgttatgatgAgtggatttactgggatagca	10	13	13	5	1	1	2	1	2	0	0	2	5	1	5	0	3	2	2	0	3	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:133806739A>G	ENST00000395386.2	+	3	466	c.167A>G	c.(166-168)gAg>gGg	p.E56G	PHF20L1_ENST00000395390.2_Missense_Mutation_p.E56G|PHF20L1_ENST00000395379.1_Missense_Mutation_p.E56G|PHF20L1_ENST00000395376.1_Missense_Mutation_p.E56G|PHF20L1_ENST00000337920.4_Missense_Mutation_p.E56G|PHF20L1_ENST00000220847.7_5'UTR	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	56	Tudor 1.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CGTTATGATGAGTGGATTTAC	0.408																																					p.E56G		.											.	PHF20L1-92	0			c.A167G						.						134	122	126					8																	133806739		2203	4300	6503	SO:0001583	missense	51105	exon3			ATGATGAGTGGAT	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.167A>G	8.37:g.133806739A>G	ENSP00000378784:p.Glu56Gly	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	140	48	NM_016018	0	0	0	0	0	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	A	31	5.078557	0.94050	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000522580;ENST00000395390	T;T;T;T;T;T;T;T	0.56275	0.53;0.48;0.51;1.1;0.47;0.49;0.55;1.13	5.91	5.91	0.95273	Tudor-like, plant (1);Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.90759	3.145	0.80722	D	1	D;P;D;D;P	0.89917	1.0;0.735;1.0;1.0;0.714	D;P;D;D;P	0.91635	0.997;0.734;0.999;0.994;0.669	T	0.82833	-0.0262	10	0.87932	D	0	7.5356	15.5298	0.75948	1.0:0.0:0.0:0.0	.	56;56;56;56;56	F8W9L8;A8MW92;A8MW92-4;A8MW92-2;A8MUE8	.;P20L1_HUMAN;.;.;.	G	56;56;56;56;56;56;56;14;56	ENSP00000378781:E56G;ENSP00000378777:E56G;ENSP00000355301:E56G;ENSP00000378784:E56G;ENSP00000324519:E56G;ENSP00000338269:E56G;ENSP00000378775:E56G;ENSP00000378788:E56G	ENSP00000324519:E56G	E	+	2	0	PHF20L1	133875921	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	2.259000	0.74868	0.528000	0.53228	GAG	.		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		G	133806739	A	G	133806739	3	3	151	1	0	0	0	0	1	0	0	0	11858	304	11	3	173	3	PHF20L1	8	133806739	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	20489745	133806739	12557283	77	13560											
ZNF16	7564	bcgsc.ca	37	chr8	146156384	146156384	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggtgtagggtttttcccCagtatgaactttctggtggt	7	15	12	7	0	1	1	0	1	1	0	2	1	2	1	2	4	1	3	2	4	3	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:146156384C>T	ENST00000276816.4	-	4	1975	c.1789G>A	c.(1789-1791)Ggg>Agg	p.G597R	ZNF16_ENST00000394909.2_Missense_Mutation_p.G597R	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	597					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|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(2)|endometrium(1)|kidney(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		GGTTTTTCCCCAGTATGAACT	0.488																																					p.G597R													.	ZNF16-95	0			c.G1789A						.						102	93	96					8																	146156384		2203	4300	6503	SO:0001583	missense	7564	exon3			TTTCCCCAGTATG	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"Zinc fingers, C2H2-type"	12947	protein-coding gene	gene with protein product		601262	"zinc finger protein 16 (KOX 9)"				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.1789G>A	8.37:g.146156384C>T	ENSP00000276816:p.Gly597Arg	Somatic	80	1		WXS	Illumina HiSeq	Phase_1	50	4	NM_006958	0	0	4	4	0	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	37	CCDS6437.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318705	0.60524	.	.	ENSG00000170631	ENST00000276816;ENST00000394909	T;T	0.26223	1.75;1.75	4.0	4.0	0.46444	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46658	0.1404	L	0.55103	1.725	0.31838	N	0.623894	D	0.89917	1.0	D	0.97110	1.0	T	0.55270	-0.8167	9	0.72032	D	0.01	.	15.0179	0.71600	0.0:1.0:0.0:0.0	.	597	P17020	ZNF16_HUMAN	R	597	ENSP00000276816:G597R;ENSP00000378369:G597R	ENSP00000276816:G597R	G	-	1	0	ZNF16	146127188	0.869000	0.29996	1.000000	0.80357	0.924000	0.55760	3.212000	0.51145	2.058000	0.61347	0.462000	0.41574	GGG	.		0.488	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		T	146156384	C	T	146156384	3	4	151	1	0	0	0	0	1	0	0	0	17770	594	21	2	263	2	ZNF16	8	146156384	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	12349645	146156384	207638	78	13561											
AQP3	360	bcgsc.ca	37	chr9	33447471	33447471	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcgcctgtcggagcagccGgtagcggatgtggagcatct	7	7	16	11	4	1	0	0	0	1	0	2	3	1	3	2	4	5	3	2	4	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:33447471G>A	ENST00000297991.4	-	1	138	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	20					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		CGGAGCAGCCGGTAGCGGATG	0.716																																					p.R20W													.	AQP3-90	0			c.C58T						.						18	21	20					9																	33447471		2187	4290	6477	SO:0001583	missense	360	exon1			GCAGCCGGTAGCG		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.58C>T	9.37:g.33447471G>A	ENSP00000297991:p.Arg20Trp	Somatic	176	1		WXS	Illumina HiSeq	Phase_1	120	5	NM_004925	0	0	12	12	0	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Missense_Mutation	SNP	ENST00000297991.4	37	CCDS6542.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.136024	0.77662	.	.	ENSG00000165272	ENST00000297991;ENST00000343952	D	0.85629	-2.01	5.74	4.79	0.61399	Aquaporin-like (2);	0.457287	0.23211	N	0.050673	D	0.87904	0.6295	L	0.42245	1.32	0.32753	N	0.506114	D;D;D	0.76494	0.999;0.99;0.999	D;P;P	0.69479	0.964;0.536;0.865	D	0.88979	0.3406	10	0.59425	D	0.04	-2.3009	11.196	0.48713	0.0:0.0:0.743:0.257	.	20;20;20	C9JAH5;Q92482;B4E034	.;AQP3_HUMAN;.	W	20	ENSP00000297991:R20W	ENSP00000297991:R20W	R	-	1	2	AQP3	33437471	0.999000	0.42202	1.000000	0.80357	0.566000	0.35808	0.585000	0.23879	2.712000	0.92718	0.561000	0.74099	CGG	.		0.716	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925		A	33447471	G	A	33447471	3	1	151	1	0	0	0	0	1	0	0	0	827	1115	39	1	844	1	AQP3	9	33447471	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		33447471	107765960	79	13562											
SLC28A3	64078	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	86900438	86900438	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgaaggaaaagggcatgAagatgtaggagcagattagc	16	7	14	4	0	1	4	1	2	0	2	1	6	1	6	0	3	2	3	0	3	6	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:86900438A>T	ENST00000376238.4	-	14	1518	c.1469T>A	c.(1468-1470)tTc>tAc	p.F490Y	RP11-380F14.2_ENST00000419815.1_RNA|SLC28A3_ENST00000537648.1_Missense_Mutation_p.F421Y	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	490					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	AAAGGGCATGAAGATGTAGGA	0.413																																					p.F490Y	Ovarian(106;425 1539 34835 42413 43572)												.	SLC28A3-94	0			c.T1469A						.						87	84	85					9																	86900438		2203	4300	6503	SO:0001583	missense	64078	exon14			GGCATGAAGATGT	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"Solute carriers"	16484	protein-coding gene	gene with protein product		608269	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1469T>A	9.37:g.86900438A>T	ENSP00000365413:p.Phe490Tyr	Somatic	164	1		WXS	Illumina HiSeq	Phase_I	171	62	NM_001199633	0	0	0	0	0	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	37	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.918255	0.92249	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	T;T	0.09911	2.93;2.93	5.74	5.74	0.90152	Na dependent nucleoside transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.46210	0.1381	H	0.94771	3.58	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.61232	-0.7104	10	0.87932	D	0	-28.3331	16.3305	0.83010	1.0:0.0:0.0:0.0	.	490	Q9HAS3	S28A3_HUMAN	Y	490;421	ENSP00000365413:F490Y;ENSP00000446438:F421Y	ENSP00000365413:F490Y	F	-	2	0	SLC28A3	86090258	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.273000	0.95719	2.317000	0.78254	0.459000	0.35465	TTC	.		0.413	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		T	86900438	A	T	86900438	3	4	151	1	0	0	0	0	1	0	0	0	14565	246	9	5	626	5	SLC28A3	9	86900438	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	53452967	86900438	54312993	80	13563											
PTPN3	5774	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	112219466	112219466	+	Frame_Shift_Del	DEL	C	C	-																															caccaaccttttaactgcttCctgatggctttgcttgcttc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:112219466delC	ENST00000374541.2	-	4	380	c.276delG	c.(274-276)aggfs	p.R92fs	PTPN3_ENST00000262539.3_Frame_Shift_Del_p.E10fs	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	92	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TTAACTGCTTCCTGATGGCTT	0.413																																					p.R92fs		.											.	PTPN3-229	0			c.276delG						.						197	168	177					9																	112219466		2203	4300	6503	SO:0001589	frameshift_variant	5774	exon4			.		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.276delG	9.37:g.112219466delC	ENSP00000363667:p.Arg92fs	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	113	32	NM_001145368	0	0	0	0	0	A0AUW9|E7EN99|E9PGU7	Frame_Shift_Del	DEL	ENST00000374541.2	37	CCDS6776.1																																																																																			.		0.413	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			-	112219466	C	-	112219466	7	5	151	1	0	1	0	1	0	0	0	0	12821	854	30	0	2557	0	PTPN3	9	112219466	Frame_Shift_Del	DEL	C	TCGA-MH-A561-01A-11D-A26P-10	25319028	112219466	28993965	81	13564											
PALM2	114299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	112705604	112705604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggccggtctcagacaccAcagagccctcatccccagaa	11	4	10	16	1	2	3	2	0	1	3	4	4	3	4	5	3	1	0	5	3	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:112705604A>G	ENST00000374531.2	+	7	1113	c.1039A>G	c.(1039-1041)Aca>Gca	p.T347A	AKAP2_ENST00000555236.1_Intron|PALM2-AKAP2_ENST00000302798.7_Intron|PALM2_ENST00000483909.1_Missense_Mutation_p.T345A|AKAP2_ENST00000510514.5_Intron|PALM2_ENST00000314527.4_Missense_Mutation_p.T379A|PALM2_ENST00000448454.2_Missense_Mutation_p.T381A|PALM2-AKAP2_ENST00000374530.3_Intron	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	347					regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						CTCAGACACCACAGAGCCCTC	0.552																																					p.T379A		.											.	PALM2-71	0			c.A1135G						.						113	110	111					9																	112705604		2203	4300	6503	SO:0001583	missense	114299	exon7			GACACCACAGAGC	AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444			15845	protein-coding gene	gene with protein product						11478809	Standard	NM_001037293		Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.1039A>G	9.37:g.112705604A>G	ENSP00000363656:p.Thr347Ala	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	128	19	NM_053016	0	0	0	0	0	A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	37	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711967	0.48517	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654	ENST00000374531;ENST00000448454;ENST00000483909;ENST00000314527;ENST00000413420	T;T;T;T;T	0.22945	2.36;2.36;2.36;2.36;1.93	5.86	5.86	0.93980	.	.	.	.	.	T	0.33498	0.0865	L	0.59436	1.845	0.80722	D	1	P;P	0.48503	0.788;0.911	P;P	0.51516	0.548;0.672	T	0.13710	-1.0499	9	0.05351	T	0.99	.	15.4456	0.75228	1.0:0.0:0.0:0.0	.	347;381	Q8IXS6;D3YTA4	PALM2_HUMAN;.	A	347;381;345;379;379	ENSP00000363656:T347A;ENSP00000400206:T381A;ENSP00000417525:T345A;ENSP00000323805:T379A;ENSP00000397839:T379A	ENSP00000397839:T379A	T	+	1	0	PALM2-AKAP2;PALM2	111745425	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.339000	0.96797	2.244000	0.73946	0.528000	0.53228	ACA	.		0.552	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293		G	112705604	A	G	112705604	3	3	151	1	0	0	0	0	1	0	0	0	11435	159	6	3	1171	3	PALM2	9	112705604	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	486138	112705604	28507827	82	13565											
FAM102A	399665	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	130707096	130707096	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtgaaatcctggctctgcacGatcttctccacgatggcatc	8	11	9	13	2	3	1	0	1	3	0	6	3	4	1	2	2	1	3	2	2	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:130707096G>A	ENST00000373095.1	-	9	1374	c.999C>T	c.(997-999)atC>atT	p.I333I	FAM102A_ENST00000300434.3_5'UTR|FAM102A_ENST00000373084.4_Silent_p.I191I	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	333										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						GGCTCTGCACGATCTTCTCCA	0.672																																					p.I333I		.											.	FAM102A-91	0			c.C999T						.						89	64	72					9																	130707096		2203	4300	6503	SO:0001819	synonymous_variant	399665	exon9			CTGCACGATCTTC		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.999C>T	9.37:g.130707096G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	39	23	NM_001035254	0	0	1	6	5	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	37	CCDS35150.1																																																																																			.		0.672	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			A	130707096	G	A	130707096	2	1	151	1	0	0	0	0	0	0	0	1	5398	1048	37	1		1	FAM102A	9	130707096	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	18001492	130707096	10506335	83	13566											
NUP188	23511	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	131749966	131749966	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggcattggcgtggacaccaTtgacatggtgatggctgctc	7	10	15	9	1	0	2	0	2	0	0	1	3	0	3	1	5	1	3	1	5	0	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:131749966T>C	ENST00000372577.2	+	23	2384	c.2363T>C	c.(2362-2364)aTt>aCt	p.I788T		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	788					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GTGGACACCATTGACATGGTG	0.493																																					p.I788T													.	NUP188-207	0			c.T2363C						.						170	146	154					9																	131749966		2203	4300	6503	SO:0001583	missense	23511	exon23			ACACCATTGACAT	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"KIAA0169"	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2363T>C	9.37:g.131749966T>C	ENSP00000361658:p.Ile788Thr	Somatic	182	2		WXS	Illumina HiSeq	Phase_I	147	48	NM_015354	0	0	1	4	3	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.407163	0.83230	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.32753	1.44	5.65	5.65	0.86999	.	0.045126	0.85682	D	0.000000	T	0.35219	0.0924	L	0.29908	0.895	0.58432	D	0.999999	P;P	0.51537	0.822;0.946	P;P	0.51550	0.493;0.673	T	0.13150	-1.0520	10	0.87932	D	0	-16.8028	15.3584	0.74448	0.0:0.0:0.0:1.0	.	121;788	E9PET9;Q5SRE5	.;NU188_HUMAN	T	677;788	ENSP00000361658:I788T	ENSP00000349125:I677T	I	+	2	0	NUP188	130789787	1.000000	0.71417	0.959000	0.39883	0.993000	0.82548	7.459000	0.80802	2.279000	0.76181	0.533000	0.62120	ATT	.		0.493	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			C	131749966	T	C	131749966	3	2	151	1	0	0	0	0	1	0	0	0	10784	1493	52	3	2453	3	NUP188	9	131749966	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	1042870	131749966	9463465	84	13567											
AKR1C2	1646	broad.mit.edu	37	chr10	5038014	5038014	+	Frame_Shift_Del	DEL	A	A	-																															caatgtcttttgacttgcagAaatccagcagttttctctgg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:5038014delA	ENST00000380753.4	-	6	801	c.614delT	c.(613-615)ttcfs	p.F205fs	AKR1C2_ENST00000421196.3_Frame_Shift_Del_p.F179fs|RP11-499O7.7_ENST00000440414.1_RNA|AKR1C2_ENST00000407674.1_Frame_Shift_Del_p.F205fs|RP11-499O7.7_ENST00000451575.2_RNA	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	205					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	TGACTTGCAGAAATCCAGCAG	0.393																																					p.F205fs													.	AKR1C2-514	0			c.614delT						.						62	57	59					10																	5038014		2203	4296	6499	SO:0001589	frameshift_variant	1646	exon8			TTGCAGAAATCCA	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"Aldo-keto reductases"	385	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"	600450	"aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)", "testicular 17,20-desmolase deficiency"	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.614delT	10.37:g.5038014delA	ENSP00000370129:p.Phe205fs	Somatic	719	0		WXS	Illumina HiSeq	Phase_I	650	51	NM_001354	0	0	0	0	0	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Frame_Shift_Del	DEL	ENST00000380753.4	37	CCDS7062.1																																																																																			.		0.393	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		-	5038014	A	-	5038014	7	5	151	1	0	1	0	1	0	0	0	0	470	246	9	0	373	0	AKR1C2	10	5038014	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10		5038014	130496733	85	13568											
KIN	22944	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	7822115	7822115	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgatgtattcgttgtagaCaatgttgttgtggacccttt	7	17	11	6	1	0	2	0	1	0	1	1	3	0	3	1	1	0	6	1	1	3	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:7822115C>G	ENST00000379562.4	-	4	327	c.280G>C	c.(280-282)Gtc>Ctc	p.V94L	KIN_ENST00000535925.1_Missense_Mutation_p.V94L|KIN_ENST00000543003.1_5'UTR	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						TCGTTGTAGACAATGTTGTTG	0.403																																					p.V94L													.	KIN-230	0			c.G280C						.						274	240	252					10																	7822115		2203	4300	6503	SO:0001583	missense	22944	exon4			TGTAGACAATGTT	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.280G>C	10.37:g.7822115C>G	ENSP00000368881:p.Val94Leu	Somatic	202	1		WXS	Illumina HiSeq	Phase_I	159	60	NM_012311	0	0	7	12	5		Missense_Mutation	SNP	ENST00000379562.4	37	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225063	0.58668	.	.	ENSG00000151657	ENST00000535925;ENST00000379562	.	.	.	5.92	5.0	0.66597	DNA/RNA-binding protein Kin17, conserved domain (1);	0.122083	0.56097	D	0.000033	T	0.73434	0.3586	M	0.90705	3.14	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.004;0.005	T	0.73729	-0.3891	9	0.66056	D	0.02	-21.4135	14.5956	0.68403	0.1459:0.8541:0.0:0.0	.	94;94	B4DX32;O60870	.;KIN17_HUMAN	L	94	.	ENSP00000368881:V94L	V	-	1	0	KIN	7862121	1.000000	0.71417	0.986000	0.45419	0.959000	0.62525	3.866000	0.56040	1.448000	0.47680	0.655000	0.94253	GTC	.		0.403	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311		G	7822115	C	G	7822115	3	3	151	1	0	0	0	0	1	0	0	0	8336	478	17	4	941	4	KIN	10	7822115	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	2784101	7822115	127712632	86	13569											
SORBS1	10580	broad.mit.edu;bcgsc.ca	37	chr10	97170380	97170388	+	Splice_Site	DEL	CCTCTCTTA	CCTCTCTTA	-																															ggctgggagtggggcacaagCctctcttacctcgattgtgt																								rs376551293		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	CCTCTCTTA	CCTCTCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:97170380_97170388delCCTCTCTTA	ENST00000361941.3	-	8	982		c.e8+1		SORBS1_ENST00000474353.2_Splice_Site|SORBS1_ENST00000306402.6_Splice_Site|SORBS1_ENST00000371241.1_Splice_Site|SORBS1_ENST00000277982.5_Splice_Site|SORBS1_ENST00000371246.2_Splice_Site|SORBS1_ENST00000371249.2_Splice_Site|SORBS1_ENST00000607232.1_Splice_Site|SORBS1_ENST00000371247.2_Splice_Site|SORBS1_ENST00000354106.3_Splice_Site|SORBS1_ENST00000371245.3_Splice_Site|SORBS1_ENST00000347291.4_Splice_Site|SORBS1_ENST00000371227.4_Splice_Site|SORBS1_ENST00000353505.5_Splice_Site|SORBS1_ENST00000393949.1_Splice_Site|SORBS1_ENST00000371239.1_Splice_Site	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GGGGCACAAGCCTCTCTTACCTCGATTGT	0.45																																					.													.	SORBS1-155	0			.						.																																			SO:0001630	splice_region_variant	10580	.			CACAAGCCTCTCT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.955+1TAAGAGAGG>-	10.37:g.97170380_97170388delCCTCTCTTA		Somatic	133	0		WXS	Illumina HiSeq	Phase_I	110	29	.	0	0	0	0	0		Splice_Site	DEL	ENST00000361941.3	37	CCDS31255.1																																																																																			.		0.45	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		Intron	-	97170388	CCTCTCTTA	-	97170380	8	5	151	1	0	1	0	1	0	0	1	0	14959	754	26	0		0	SORBS1	10	97170380	Splice_Site	DEL	CCTCTCTTA	TCGA-MH-A561-01A-11D-A26P-10	89348265	97170380	38364367	87	13570											
MTG1	92170	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	135209749	135209750	+	Frame_Shift_Ins	INS	-	-	GC																															gtcctcaacaagatggacttINSggcggatcttacagagcagc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:135209749_135209750insGC	ENST00000317502.6	+	3	310_311	c.260_261insGC	c.(259-264)ttggcgfs	p.A88fs	RP11-108K14.8_ENST00000468317.2_Frame_Shift_Ins_p.A93fs|MTG1_ENST00000477902.2_Frame_Shift_Ins_p.A47fs	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	88	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		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)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AAGATGGACTTGGCGGATCTTA	0.515																																					p.L87fs		.											.	MTG1-91	0			c.260_261insGC						.																																			SO:0001589	frameshift_variant	92170	exon3			.		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"GTP-binding protein 7", "GTP-binding protein 7 (putative)", "mitochondrial GTPase 1 homolog (S. cerevisiae)"	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	Exception_encountered	10.37:g.135209749_135209750insGC	ENSP00000323047:p.Ala88fs	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	108	42	NM_138384	0	0	0	0	0	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Frame_Shift_Ins	INS	ENST00000317502.6	37	CCDS31320.1																																																																																			.		0.515	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384		GC	135209750	-	GC	135209749	7	5	151	1	0	1	1	0	0	0	0	0	9951	1821	63	0	270	0	MTG1	10	135209749	Frame_Shift_Ins	INS	-	TCGA-MH-A561-01A-11D-A26P-10	38039369	135209749	324998	88	13571											
INS	3630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	2181135	2181135	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagatgctggtacagcattGttccacaatgccacgcttct	9	11	9	12	1	1	1	0	0	1	1	2	1	2	1	2	1	4	6	2	1	2	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:2181135G>T	ENST00000397262.1	-	2	512	c.280C>A	c.(280-282)Caa>Aaa	p.Q94K	INS-IGF2_ENST00000481781.1_5'Flank|INS_ENST00000381330.4_Missense_Mutation_p.Q94K|INS-IGF2_ENST00000397270.1_Intron|INS_ENST00000512523.1_Missense_Mutation_p.Q82K|INS_ENST00000250971.3_Missense_Mutation_p.Q94K	NM_001185098.1	NP_001172027.1	P01308	INS_HUMAN	insulin	94					activation of protein kinase B activity (GO:0032148)|acute-phase response (GO:0006953)|alpha-beta T cell activation (GO:0046631)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of fatty acid metabolic process (GO:0045922)|negative regulation of feeding behavior (GO:2000252)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of glycogen catabolic process (GO:0045818)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of protein secretion (GO:0050709)|negative regulation of proteolysis (GO:0045861)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|negative regulation of vasodilation (GO:0045908)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of respiratory burst (GO:0060267)|positive regulation of vasodilation (GO:0045909)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of insulin secretion (GO:0050796)|regulation of protein localization (GO:0032880)|regulation of protein secretion (GO:0050708)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transmembrane transporter activity (GO:0022898)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	endoplasmic reticulum lumen (GO:0005788)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)|identical protein binding (GO:0042802)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protease binding (GO:0002020)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		Lung NSC(207;8.94e-06)|all_epithelial(84;3.17e-05)|all_lung(207;3.67e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.14)		GTACAGCATTGTTCCACAATG	0.672																																					p.Q94K		.											.	INS-522	0			c.C280A						.						63	53	57					11																	2181135		2187	4293	6480	SO:0001583	missense	3630	exon3			AGCATTGTTCCAC	X70508	CCDS7729.1	11p15.5	2014-02-03			ENSG00000254647	ENSG00000254647			6081	protein-coding gene	gene with protein product		176730	"insulin-dependent diabetes mellitus 2"	IDDM2, IDDM1		6243748, 7773291	Standard	NM_000207		Approved			P01308	OTTHUMG00000009558	ENST00000397262.1:c.280C>A	11.37:g.2181135G>T	ENSP00000380432:p.Gln94Lys	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	51	18	NM_001185097	0	0	0	0	0	Q5EEX2	Missense_Mutation	SNP	ENST00000397262.1	37	CCDS7729.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.445461	0.43429	.	.	ENSG00000254647	ENST00000397262;ENST00000250971;ENST00000381330;ENST00000512523	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	3.68	2.73	0.32206	Insulin-like (4);	.	.	.	.	D	0.94466	0.8219	M	0.89534	3.04	0.52501	D	0.999953	D;B	0.60160	0.987;0.437	D;P	0.69307	0.963;0.511	D	0.94552	0.7754	9	0.72032	D	0.01	.	11.9365	0.52876	0.0:0.1778:0.8222:0.0	.	82;94	A6XGL2;P01308	.;INS_HUMAN	K	94;94;94;82	ENSP00000380432:Q94K;ENSP00000250971:Q94K;ENSP00000370731:Q94K;ENSP00000424008:Q82K	ENSP00000250971:Q94K	Q	-	1	0	INS	2137711	1.000000	0.71417	0.918000	0.36340	0.079000	0.17450	4.878000	0.63093	0.860000	0.35481	0.462000	0.41574	CAA	.		0.672	INS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026395.3	NM_000207		T	2181135	G	T	2181135	3	4	151	1	0	0	0	0	1	0	0	0	7783	1386	48	4	56	4	INS	11	2181135	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		2181135	132825381	89	13572											
PDE3B	5140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	14808189	14808189	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggattttacccctgttctgaAatagaggacccagctgagaa	12	10	10	9	0	1	3	0	2	1	2	1	6	1	5	3	2	2	2	3	2	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:14808189A>T	ENST00000282096.4	+	3	1589	c.1236A>T	c.(1234-1236)gaA>gaT	p.E412D	PDE3B_ENST00000455098.2_Intron	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	412					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	CCTGTTCTGAAATAGAGGACC	0.373																																					p.E412D		.											.	PDE3B-90	0			c.A1236T						.						120	130	126					11																	14808189		2200	4294	6494	SO:0001583	missense	5140	exon3			TTCTGAAATAGAG	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.1236A>T	11.37:g.14808189A>T	ENSP00000282096:p.Glu412Asp	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	150	59	NM_000922	0	0	0	0	0	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	37	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	a	14.21	2.468783	0.43839	.	.	ENSG00000152270	ENST00000282096	T	0.34275	1.37	5.72	3.42	0.39159	.	0.151781	0.27749	U	0.018012	T	0.36552	0.0971	N	0.20986	0.625	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.22312	-1.0220	10	0.05959	T	0.93	.	9.8395	0.40991	0.8619:0.0:0.1381:0.0	.	412	Q13370	PDE3B_HUMAN	D	412	ENSP00000282096:E412D	ENSP00000282096:E412D	E	+	3	2	PDE3B	14764765	1.000000	0.71417	0.992000	0.48379	0.978000	0.69477	3.979000	0.56888	0.452000	0.26830	0.456000	0.33151	GAA	.		0.373	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		T	14808189	A	T	14808189	3	4	151	1	0	0	0	0	1	0	0	0	11664	11	1	5	1246	5	PDE3B	11	14808189	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	12627054	14808189	120198327	90	13573											
CHRM1	1128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62677207	62677207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctatcagcattggcgggaggGagtgcggtgcacggagccag	8	6	18	9	3	1	0	1	0	0	0	1	3	1	3	1	5	4	2	1	5	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:62677207G>A	ENST00000306960.3	-	2	1907	c.1366C>T	c.(1366-1368)Ccc>Tcc	p.P456S	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	456					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	TGGCGGGAGGGAGTGCGGTGC	0.667																																					p.P456S		.											.	CHRM1-90	0			c.C1366T						.						72	79	77					11																	62677207		2201	4298	6499	SO:0001583	missense	1128	exon2			GGGAGGGAGTGCG	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1366C>T	11.37:g.62677207G>A	ENSP00000306490:p.Pro456Ser	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	70	15	NM_000738	0	0	0	0	0	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	37	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857391	0.51376	.	.	ENSG00000168539	ENST00000306960	T	0.57595	0.39	4.53	3.58	0.41010	.	0.211607	0.23760	N	0.044839	T	0.37892	0.1020	N	0.24115	0.695	0.35793	D	0.822568	B	0.12630	0.006	B	0.14578	0.011	T	0.40289	-0.9571	10	0.42905	T	0.14	-15.4337	11.7385	0.51780	0.0:0.2317:0.7683:0.0	.	456	P11229	ACM1_HUMAN	S	456	ENSP00000306490:P456S	ENSP00000306490:P456S	P	-	1	0	CHRM1	62433783	1.000000	0.71417	0.993000	0.49108	0.930000	0.56654	5.691000	0.68249	0.995000	0.38917	0.561000	0.74099	CCC	.		0.667	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		A	62677207	G	A	62677207	3	1	151	1	0	0	0	0	1	0	0	0	3382	1174	41	2	20	2	CHRM1	11	62677207	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	47869018	62677207	72329309	91	13574											
CHRM1	1128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62677510	62677510	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttctccttgaccagcgagaAggtcttccgcttggccagct	6	11	10	14	2	2	2	0	1	2	1	4	3	3	2	4	2	2	2	4	2	1	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:62677510A>T	ENST00000306960.3	-	2	1604	c.1063T>A	c.(1063-1065)Ttc>Atc	p.F355I	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	355					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	ACCAGCGAGAAGGTCTTCCGC	0.592																																					p.F355I		.											.	CHRM1-90	0			c.T1063A						.						55	53	54					11																	62677510		2201	4298	6499	SO:0001583	missense	1128	exon2			GCGAGAAGGTCTT	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1063T>A	11.37:g.62677510A>T	ENSP00000306490:p.Phe355Ile	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	59	25	NM_000738	0	0	0	0	0	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	37	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696730	0.30142	.	.	ENSG00000168539	ENST00000306960;ENST00000543973	T;T	0.72051	-0.62;-0.62	4.49	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.232532	0.26293	N	0.025212	T	0.43634	0.1256	N	0.04275	-0.24	0.36087	D	0.843175	B	0.14805	0.011	B	0.17098	0.017	T	0.45920	-0.9228	10	0.17369	T	0.5	-24.428	7.3553	0.26714	0.8052:0.0:0.0:0.1948	.	355	P11229	ACM1_HUMAN	I	355	ENSP00000306490:F355I;ENSP00000441188:F355I	ENSP00000306490:F355I	F	-	1	0	CHRM1	62434086	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.101000	0.31037	1.870000	0.54199	0.459000	0.35465	TTC	.		0.592	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		T	62677510	A	T	62677510	3	4	151	1	0	0	0	0	1	0	0	0	3382	72	3	5	323	5	CHRM1	11	62677510	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	303	62677510	72329006	92	13575											
C11orf2	738	broad.mit.edu	37	chr11	64875862	64875862	+	Frame_Shift_Del	DEL	G	G	-																															tgttagagttcaccgaccatGgaggcagtggcttcgtgggc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:64875862delG	ENST00000279281.3	+	5	1011	c.919delG	c.(919-921)ggafs	p.G308fs	AP003068.9_ENST00000528887.1_RNA|VPS51_ENST00000527646.1_3'UTR	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	308					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CACCGACCATGGAGGCAGTGG	0.706																																					p.G307fs													.	.	0			c.919delG						.						21	25	24					11																	64875862		2197	4295	6492	SO:0001589	frameshift_variant	738	exon5			GACCATGGAGGCA	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"fat-free homolog (zebrafish)"	615738	"chromosome 11 open reading frame 3", "chromosome 11 open reading frame 2"	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.919delG	11.37:g.64875862delG	ENSP00000279281:p.Gly308fs	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	20	7	NM_013265	0	0	0	0	0	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Frame_Shift_Del	DEL	ENST00000279281.3	37	CCDS8093.1																																																																																			.		0.706	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265		-	64875862	G	-	64875862	7	5	151	1	0	1	0	1	0	0	0	0	1637	1349	47	0	937	0	C11orf2	11	64875862	Frame_Shift_Del	DEL	G	TCGA-MH-A561-01A-11D-A26P-10	2198352	64875862	70130654	93	13576											
OVOL1	5017	broad.mit.edu	37	chr11	65562811	65562812	+	Nonstop_Mutation	DNP	GA	GA	TT																															gcagggcagcccccacctgtGagtggctcgagccctggggg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:65562811_65562812GA>TT	ENST00000335987.3	+	4	1155_1156	c.803_804GA>TT	c.(802-804)tGA>tTT	p.*268F	OVOL1_ENST00000532448.1_Nonstop_Mutation_p.*206F|RP11-770G2.5_ENST00000531155.1_RNA	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1	0					cytoskeleton organization (GO:0007010)|epidermal cell differentiation (GO:0009913)|germline cell cycle switching, mitotic to meiotic cell cycle (GO:0051729)|kidney development (GO:0001822)|mesoderm development (GO:0007498)|negative regulation of meiotic cell cycle phase transition (GO:1901994)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6				READ - Rectum adenocarcinoma(159;0.17)		CCCCACCTGTGAGTGGCTCGAG	0.653																																					.													.	OVOL1-68	0			c.A804T						.																																			SO:0001578	stop_lost	5017	exon4			CCTGTGAGTGGCT	BC059408	CCDS8112.1	11q13	2013-10-17	2013-10-17		ENSG00000172818	ENSG00000172818		"Zinc fingers, C2H2-type"	8525	protein-coding gene	gene with protein product		602313	"ovo (Drosophila) homolog-like 1", "ovo-like 1(Drosophila)"			9383297	Standard	NM_004561		Approved	HOVO1	uc001ofp.3	O14753	OTTHUMG00000166600	Exception_encountered	11.37:g.65562811_65562812delinsTT	Exception_encountered	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	41	3	NM_004561	0	0	0	0	0	Q6PCB1	Nonstop_Mutation	DNP	ENST00000335987.3	37	CCDS8112.1																																																																																			.		0.653	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	NM_004561		TT	65562812	GA	TT	65562811	4	4	151	1	0	0	0	0	0	0	0	0	11352	1285	45	4	817	4	OVOL1	11	65562811	Nonstop_Mutation	DNP	GA	TCGA-MH-A561-01A-11D-A26P-10	686949	65562811	69443705	94	13577											
SYTL2	54843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	85409045	85409045	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaacaaaagaatttagatgActtccccttagcagtggtag	14	12	8	7	0	0	3	0	1	0	2	1	3	1	3	2	1	2	2	2	1	7	6	rs554484063		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:85409045A>C	ENST00000528231.1	-	16	2707	c.2430T>G	c.(2428-2430)agT>agG	p.S810R	SYTL2_ENST00000527523.1_Missense_Mutation_p.S778R|SYTL2_ENST00000525702.1_Missense_Mutation_p.S252R|SYTL2_ENST00000354566.3_Missense_Mutation_p.S1148R|SYTL2_ENST00000316356.4_Missense_Mutation_p.S811R|SYTL2_ENST00000359152.5_Missense_Mutation_p.S1656R|SYTL2_ENST00000525423.1_Missense_Mutation_p.S1132R|SYTL2_ENST00000389958.3_Missense_Mutation_p.S241R|SYTL2_ENST00000533892.1_Missense_Mutation_p.S212R|SYTL2_ENST00000529581.1_Missense_Mutation_p.S252R|SYTL2_ENST00000389960.4_Missense_Mutation_p.S786R|SYTL2_ENST00000524452.1_Missense_Mutation_p.S786R	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	810	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		AATTTAGATGACTTCCCCTTA	0.393																																					p.S1148R		.											.	SYTL2-137	0			c.T3444G						.						96	87	90					11																	85409045		2203	4299	6502	SO:0001583	missense	54843	exon11			TAGATGACTTCCC	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"chromosome 11 synaptotagmin", "breast cancer-associated antigen SGA-72M", "protein phosphatase 1, regulatory subunit 151"	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.2430T>G	11.37:g.85409045A>C	ENSP00000431701:p.Ser810Arg	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	50	7	NM_206927	0	0	113	132	19	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.679575	0.47886	.	.	ENSG00000137501	ENST00000389960;ENST00000359152;ENST00000354566;ENST00000316356;ENST00000525702;ENST00000525423;ENST00000529581;ENST00000389958;ENST00000530351;ENST00000528231;ENST00000533892;ENST00000527523;ENST00000524452	T;T;T;T;T;T;T;T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12	5.93	4.98	0.66077	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.357017	0.24240	N	0.040262	T	0.09335	0.0230	N	0.12637	0.245	0.30841	N	0.735693	B;B;B;B;B;D;P;D;B;B	0.54047	0.284;0.409;0.154;0.135;0.288;0.964;0.939;0.964;0.137;0.041	B;B;B;B;B;P;P;P;B;B	0.54346	0.091;0.091;0.148;0.091;0.091;0.749;0.681;0.749;0.091;0.023	T	0.10268	-1.0637	9	.	.	.	-1.3853	11.3673	0.49679	0.191:0.0:0.809:0.0	.	778;786;810;811;628;1108;1132;1148;241;212	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15;Q9HCH5-11;Q9HCH5-7;Q9HCH5-8;Q9HCH5-9;Q9HCH5-4	.;.;SYTL2_HUMAN;.;.;.;.;.;.;.	R	786;1656;1148;811;252;1132;252;241;527;810;212;778;786	ENSP00000374610:S786R;ENSP00000352065:S1656R;ENSP00000346576:S1148R;ENSP00000318803:S811R;ENSP00000432996:S252R;ENSP00000432694:S1132R;ENSP00000435855:S252R;ENSP00000374608:S241R;ENSP00000435009:S527R;ENSP00000431701:S810R;ENSP00000432144:S212R;ENSP00000434010:S778R;ENSP00000435238:S786R	.	S	-	3	2	SYTL2	85086693	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.506000	0.45433	1.497000	0.48584	-0.177000	0.13119	AGT	.		0.393	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		C	85409045	A	C	85409045	3	2	151	1	0	0	0	0	1	0	0	0	15515	272	10	5	386	5	SYTL2	11	85409045	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	19846234	85409045	49597471	95	13578											
ANKRD49	54851	broad.mit.edu	37	chr11	94231479	94231479	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgcagcatgatgcagatatCaatgcccaaacaaaaggcct	15	7	8	11	0	1	2	1	1	0	1	1	2	1	2	2	1	5	3	2	1	5	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:94231479C>T	ENST00000544612.1	+	3	998	c.501C>T	c.(499-501)atC>atT	p.I167I	ANKRD49_ENST00000302755.4_Silent_p.I167I|ANKRD49_ENST00000538535.1_3'UTR|ANKRD49_ENST00000544253.1_3'UTR	NM_017704.2	NP_060174.2	Q8WVL7	ANR49_HUMAN	ankyrin repeat domain 49	167					positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)				autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|urinary_tract(1)	12		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ATGCAGATATCAATGCCCAAA	0.498																																					p.I167I	Melanoma(113;823 1621 4352 9582 22033)												.	ANKRD49-90	0			c.C501T						.						89	78	82					11																	94231479		2201	4298	6499	SO:0001819	synonymous_variant	54851	exon3			AGATATCAATGCC	AF025354	CCDS8300.1	11q21	2013-01-10				ENSG00000168876		"Ankyrin repeat domain containing"	25970	protein-coding gene	gene with protein product						11162141	Standard	NM_017704		Approved	FLJ20189, FGIF, GBIF	uc001pew.3	Q8WVL7		ENST00000544612.1:c.501C>T	11.37:g.94231479C>T		Somatic	129	0		WXS	Illumina HiSeq	Phase_I	99	4	NM_017704	0	0	4	4	0	Q8NDF2|Q96JE5|Q9NXK7	Silent	SNP	ENST00000544612.1	37	CCDS8300.1																																																																																			.		0.498	ANKRD49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396314.2	NM_017704		T	94231479	C	T	94231479	2	4	151	1	0	0	0	0	0	0	0	1	675	816	29	2		2	ANKRD49	11	94231479	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	8822434	94231479	40775037	96	13579											
NCAPD3	23310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	134063948	134063948	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagactggagggcctgcttcCggacagacactgcagggtcc	8	6	15	12	1	0	2	0	0	0	2	2	5	2	4	3	4	2	2	3	4	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:134063948C>T	ENST00000534548.2	-	15	1851	c.1787G>A	c.(1786-1788)cGg>cAg	p.R596Q		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	596					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GGCCTGCTTCCGGACAGACAC	0.443																																					p.R596Q		.											.	NCAPD3-229	0			c.G1787A						.						70	67	68					11																	134063948		2201	4297	6498	SO:0001583	missense	23310	exon15			TGCTTCCGGACAG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1787G>A	11.37:g.134063948C>T	ENSP00000433681:p.Arg596Gln	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	100	14	NM_015261	0	0	1	1	0	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777630	0.90195	.	.	ENSG00000151503	ENST00000534548	T	0.75938	-0.98	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.110622	0.64402	D	0.000010	D	0.87795	0.6267	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.88588	0.3141	10	0.72032	D	0.01	-26.9521	19.8686	0.96842	0.0:1.0:0.0:0.0	.	596	P42695	CNDD3_HUMAN	Q	596	ENSP00000433681:R596Q	ENSP00000431612:R596Q	R	-	2	0	NCAPD3	133569158	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.278000	0.51662	2.768000	0.95171	0.655000	0.94253	CGG	.		0.443	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		T	134063948	C	T	134063948	3	4	151	1	0	0	0	0	1	0	0	0	10232	652	23	1	2793	1	NCAPD3	11	134063948	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	39832469	134063948	942568	97	13580											
YARS2	51067	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	32908454	32908454	+	Frame_Shift_Del	DEL	G	G	-																															acggccgctcgggtctcccaGgcgcgccgtggcgcctccca																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:32908454delG	ENST00000324868.8	-	1	382	c.355delC	c.(355-357)ctgfs	p.L119fs		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	119					gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	GGGTCTCCCAGGCGCGCCGTG	0.682											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L119fs		.											.	YARS2-90	0			c.355delC						.						14	16	16					12																	32908454		2196	4290	6486	SO:0001589	frameshift_variant	51067	exon1			.	AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"Aminoacyl tRNA synthetases / Class I"	24249	protein-coding gene	gene with protein product	"tyrosine tRNA ligase 2, mitochondrial"	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.355delC	12.37:g.32908454delG	ENSP00000320658:p.Leu119fs	Somatic	29	0	836	WXS	Illumina HiSeq	Phase_I	47	18	NM_001040436	0	0	0	0	0	D3DUW8|Q9H817	Frame_Shift_Del	DEL	ENST00000324868.8	37	CCDS31770.1																																																																																			.		0.682	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936		-	32908454	G	-	32908454	7	5	151	1	0	1	0	1	0	0	0	0	17501	991	35	0	1098	0	YARS2	12	32908454	Frame_Shift_Del	DEL	G	TCGA-MH-A561-01A-11D-A26P-10		32908454	100943441	98	13581											
GALNT6	11226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	51758021	51758021	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggactctgcccctctggacGggcttggcgaactcaaaagt	8	9	12	12	2	3	0	1	0	2	0	3	3	3	2	2	4	2	1	2	4	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:51758021G>C	ENST00000543196.2	-	5	1138	c.933C>G	c.(931-933)ccC>ccG	p.P311P	GALNT6_ENST00000356317.3_Silent_p.P311P			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	311					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCCTCTGGACGGGCTTGGCGA	0.577																																					p.P311P		.											.	GALNT6-92	0			c.C933G						.						97	90	92					12																	51758021		2203	4300	6503	SO:0001819	synonymous_variant	11226	exon6			CTGGACGGGCTTG	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.933C>G	12.37:g.51758021G>C		Somatic	291	0		WXS	Illumina HiSeq	Phase_I	270	97	NM_007210	0	0	1	2	1	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	37	CCDS8813.1																																																																																			.		0.577	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		C	51758021	G	C	51758021	2	2	151	1	0	0	0	0	0	0	0	1	6237	1103	39	4		4	GALNT6	12	51758021	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	18849567	51758021	82093874	99	13582											
GCN1L1	10985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120569801	120569801	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacacagttcccctaggcacCcggctgaggagatgcgagtg	9	6	13	13	2	0	2	0	1	0	1	1	4	1	2	3	3	1	3	3	3	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:120569801C>T	ENST00000300648.6	-	54	7355	c.7343G>A	c.(7342-7344)gGg>gAg	p.G2448E		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2448					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCTAGGCACCCGGCTGAGGA	0.567																																					p.G2448E		.											.	GCN1L1-94	0			c.G7343A						.						58	60	60					12																	120569801		2016	4171	6187	SO:0001583	missense	10985	exon54			AGGCACCCGGCTG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7343G>A	12.37:g.120569801C>T	ENSP00000300648:p.Gly2448Glu	Somatic	221	0		WXS	Illumina HiSeq	Phase_I	173	25	NM_006836	0	0	39	46	7	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379586	0.82682	.	.	ENSG00000089154	ENST00000300648	T	0.61040	0.14	4.19	4.19	0.49359	Armadillo-like helical (1);Armadillo-type fold (1);	0.124142	0.53938	D	0.000052	T	0.75184	0.3815	M	0.77103	2.36	0.80722	D	1	D	0.71674	0.998	D	0.70935	0.971	T	0.76462	-0.2950	10	0.39692	T	0.17	-19.3318	17.0673	0.86562	0.0:1.0:0.0:0.0	.	2448	Q92616	GCN1L_HUMAN	E	2448	ENSP00000300648:G2448E	ENSP00000300648:G2448E	G	-	2	0	GCN1L1	119054184	1.000000	0.71417	0.969000	0.41365	0.975000	0.68041	6.918000	0.75788	2.330000	0.79161	0.655000	0.94253	GGG	.		0.567	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120569801	C	T	120569801	3	4	151	1	0	0	0	0	1	0	0	0	6319	623	22	2	692	2	GCN1L1	12	120569801	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	68811780	120569801	13282094	100	13583											
PSPC1	55269	broad.mit.edu;bcgsc.ca	37	chr13	20277500	20277500	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaggaaatctgtcattgtGctatgataccacacaataag	14	12	8	7	0	2	2	1	2	1	0	2	3	2	3	1	1	2	1	1	1	5	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr13:20277500G>A	ENST00000338910.4	-	9	1546	c.1387C>T	c.(1387-1389)Cac>Tac	p.H463Y		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	463	Gly-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CTGTCATTGTGCTATGATACC	0.433																																					p.H463Y													.	PSPC1-135	0			c.C1387T						.						15	16	16					13																	20277500		1803	4037	5840	SO:0001630	splice_region_variant	55269	exon10			CATTGTGCTATGA	AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.1387-1C>T	13.37:g.20277500G>A		Somatic	678	1		WXS	Illumina HiSeq	Phase_I	673	55	NM_001042414	0	0	0	0	0	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795081	0.31777	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.13901	2.55	5.4	5.4	0.78164	.	0.109676	0.64402	D	0.000006	T	0.10937	0.0267	L	0.36672	1.1	0.43652	D	0.996064	P	0.43826	0.818	B	0.32090	0.14	T	0.20538	-1.0272	10	0.19147	T	0.46	-17.5429	19.1702	0.93574	0.0:0.0:1.0:0.0	.	463	Q8WXF1	PSPC1_HUMAN	Y	463;403	ENSP00000343966:H463Y	ENSP00000343966:H463Y	H	-	1	0	PSPC1	19175500	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	7.438000	0.80431	2.529000	0.85273	0.484000	0.47621	CAC	.		0.433	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2		Missense_Mutation	A	20277500	G	A	20277500	5	1	151	1	0	0	0	0	0	0	1	0	12745	1333	46	2	188	2	PSPC1	13	20277500	Splice_Site	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		20277500	94892378	101	13584											
ATP11A	23250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	113526110	113526110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatggtgttcacagttacacTaaaggtaagtggtctcgcgc	10	11	12	8	2	2	0	1	0	1	0	3	1	2	0	0	3	1	3	0	3	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr13:113526110T>C	ENST00000487903.1	+	26	3141	c.3053T>C	c.(3052-3054)cTa>cCa	p.L1018P	ATP11A_ENST00000375630.2_Missense_Mutation_p.L1018P|ATP11A_ENST00000375645.3_Missense_Mutation_p.L1018P|ATP11A_ENST00000283558.8_Missense_Mutation_p.L1018P			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1018					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACAGTTACACTAAAGGTAAGT	0.483																																					p.L1018P		.											.	ATP11A-138	0			c.T3053C						.						159	151	154					13																	113526110		2203	4300	6503	SO:0001583	missense	23250	exon26			TTACACTAAAGGT	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.3053T>C	13.37:g.113526110T>C	ENSP00000420387:p.Leu1018Pro	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	77	33	NM_032189	0	0	0	0	0	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.016751	0.54468	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000419631	T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71	4.15	4.15	0.48705	.	0.410679	0.24585	N	0.037266	T	0.75191	0.3816	H	0.96175	3.78	0.80722	D	1	D;D	0.67145	0.996;0.978	P;P	0.62014	0.897;0.841	D	0.83543	0.0097	10	0.66056	D	0.02	.	13.4786	0.61322	0.0:0.0:0.0:1.0	.	1018;1018	E9PEJ6;P98196	.;AT11A_HUMAN	P	1018;1018;1018;1018;10	ENSP00000420387:L1018P;ENSP00000364781:L1018P;ENSP00000364796:L1018P;ENSP00000283558:L1018P;ENSP00000410824:L10P	ENSP00000283558:L1018P	L	+	2	0	ATP11A	112574111	0.962000	0.33011	0.392000	0.26245	0.244000	0.25665	7.271000	0.78506	1.628000	0.50416	0.379000	0.24179	CTA	.		0.483	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		C	113526110	T	C	113526110	3	2	151	1	0	0	0	0	1	0	0	0	1120	1522	53	3	3155	3	ATP11A	13	113526110	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	93248610	113526110	1643768	102	13585											
OR11H12	440153	broad.mit.edu;bcgsc.ca	37	chr14	19378076	19378076	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgtgccaaactggtcatActgtgctgggtttgtggatt	6	15	12	8	0	2	0	1	0	1	0	2	1	2	1	1	3	4	2	1	3	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:19378076A>G	ENST00000550708.1	+	1	555	c.483A>G	c.(481-483)atA>atG	p.I161M		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I161I(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		AACTGGTCATACTGTGCTGGG	0.473																																					p.I161M													.	OR11H12-24	1	Substitution - coding silent(1)	lung(1)	c.A483G						.						155	168	163					14																	19378076		2201	4294	6495	SO:0001583	missense	440153	exon1			GGTCATACTGTGC		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"GPCR / Class A : Olfactory receptors"	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.483A>G	14.37:g.19378076A>G	ENSP00000449002:p.Ile161Met	Somatic	1608	3		WXS	Illumina HiSeq	Phase_I	1478	104	NM_001013354	0	0	0	0	0		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	a	1.849	-0.465596	0.04476	.	.	ENSG00000257115	ENST00000550708	T	0.38722	1.12	0.585	-1.17	0.09648	GPCR, rhodopsin-like superfamily (1);	0.551366	0.14814	N	0.296879	T	0.28665	0.0710	L	0.37697	1.125	0.22851	N	0.998651	B	0.28998	0.23	B	0.34346	0.18	T	0.23190	-1.0195	9	0.40728	T	0.16	.	3.7785	0.08671	0.6099:0.0:0.0:0.3901	.	161	B2RN74	O11HC_HUMAN	M	161	ENSP00000449002:I161M	ENSP00000449002:I161M	I	+	3	3	CR383656.1	18448076	0.000000	0.05858	0.739000	0.30968	0.212000	0.24457	-1.607000	0.02070	-0.821000	0.04312	0.055000	0.15244	ATA	.		0.473	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354		G	19378076	A	G	19378076	3	3	151	1	0	0	0	0	1	0	0	0	10953	381	14	3	485	3	OR11H12	14	19378076	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		19378076	87971464	103	13586											
CDH24	64403	broad.mit.edu;bcgsc.ca	37	chr14	23517629	23517629	+	Frame_Shift_Del	DEL	C	C	-																															ctctcggacgtcctcctcctCcagtaccatcagtgcttctt																								rs138543733	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:23517629delC	ENST00000267383.5	-	12	2112	c.2020delG	c.(2020-2022)gagfs	p.E676fs	CDH24_ENST00000487137.2_Frame_Shift_Del_p.E638fs|CDH24_ENST00000397359.3_Frame_Shift_Del_p.E676fs|CDH24_ENST00000554034.1_Frame_Shift_Del_p.E638fs|CDH24_ENST00000485922.1_5'UTR			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	676					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TCCTCCTCCTCCAGTACCATC	0.662																																					p.E674fs													.	CDH24-90	0			c.2020delG						.						74	78	76					14																	23517629		2202	4300	6502	SO:0001589	frameshift_variant	64403	exon13			CCTCCTCCAGTAC	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"Cadherins / Major cadherins"	14265	protein-coding gene	gene with protein product			"cadherin-like 24"			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.2020delG	14.37:g.23517629delC	ENSP00000267383:p.Glu676fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	25	9	NM_022478	0	0	0	0	0	D3DS44|Q86UP1|Q9NT84	Frame_Shift_Del	DEL	ENST00000267383.5	37	CCDS9585.1																																																																																			.		0.662	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478		-	23517629	C	-	23517629	7	5	151	1	0	1	0	1	0	0	0	0	3115	864	30	0	443	0	CDH24	14	23517629	Frame_Shift_Del	DEL	C	TCGA-MH-A561-01A-11D-A26P-10	4139553	23517629	83831911	104	13587											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23744820	23744820	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcatcatcatcatcatcAtcatcttcctcctcctcctc	9	14	0	18	0	8	0	7	0	1	0	13	0	12	0	4	0	0	0	4	0	0	1	rs200818825		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:23744820A>T	ENST00000357460.5	-	2	1781	c.1617T>A	c.(1615-1617)gaT>gaA	p.D539E	HOMEZ_ENST00000561013.1_Missense_Mutation_p.D541E|HOMEZ_ENST00000431326.2_Missense_Mutation_p.D541E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	539	Poly-Asp.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		catcatcatcatcatcttcct	0.468																																					p.D539E		.											.	HOMEZ-22	0			c.T1617A						.						38	38	38					14																	23744820		2192	4245	6437	SO:0001583	missense	57594	exon2			ATCATCATCATCT	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"Homeoboxes / ZF class"	20164	protein-coding gene	gene with protein product		608119	"KIAA1443"	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1617T>A	14.37:g.23744820A>T	ENSP00000350049:p.Asp539Glu	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	153	39	NM_020834	0	0	3	3	0	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	-	0.013	-1.624939	0.00820	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.61742	0.08;0.08	5.83	-11.7	0.00046	Armadillo-like helical (1);	.	.	.	.	T	0.24624	0.0597	N	0.08118	0	0.09310	N	0.999997	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.37572	-0.9700	9	0.33141	T	0.24	-1.9885	2.2937	0.04144	0.2718:0.3133:0.3242:0.0907	.	541;539	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	E	539;541	ENSP00000350049:D539E;ENSP00000406579:D541E	ENSP00000350049:D539E	D	-	3	2	HOMEZ	22814660	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-7.177000	0.00042	-5.316000	0.00017	-1.163000	0.01768	GAT	.		0.468	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		T	23744820	A	T	23744820	3	4	151	1	0	0	0	0	1	0	0	0	7302	214	8	5	39	5	HOMEZ	14	23744820	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	227191	23744820	83604720	105	13588											
GPHN	10243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	67291218	67291218	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgatagattggtgtgatgaAaaggaacttaatttgatatt	14	15	10	2	0	0	5	0	4	0	1	0	6	0	6	0	2	1	0	0	2	6	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:67291218A>C	ENST00000315266.5	+	4	1349	c.228A>C	c.(226-228)gaA>gaC	p.E76D	GPHN_ENST00000305960.9_Intron|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000478722.1_Missense_Mutation_p.E76D|GPHN_ENST00000459628.1_Intron|GPHN_ENST00000543237.1_Missense_Mutation_p.E76D	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	76	MPT Mo-transferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GGTGTGATGAAAAGGAACTTA	0.393			T	MLL	AL																																p.E76D		.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN-228	0			c.A228C						.						97	92	94					14																	67291218		2203	4300	6503	SO:0001583	missense	10243	exon4			TGATGAAAAGGAA	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.228A>C	14.37:g.67291218A>C	ENSP00000312771:p.Glu76Asp	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	70	19	NM_001024218	0	0	5	10	5	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.761655	0.31228	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000555456	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.48	4.33	0.51752	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.046743	0.85682	D	0.000000	T	0.56572	0.1994	N	0.10664	0.02	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.46721	-0.9171	10	0.16896	T	0.51	-9.6865	11.3654	0.49668	0.9283:0.0:0.0717:0.0	.	76;76;76	F5H039;Q9NQX3;Q9NQX3-2	.;GEPH_HUMAN;.	D	76;76;76;9	ENSP00000312771:E76D;ENSP00000417901:E76D;ENSP00000438404:E76D;ENSP00000450706:E9D	ENSP00000312771:E76D	E	+	3	2	GPHN	66360971	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.444000	0.35068	0.910000	0.36722	0.254000	0.18369	GAA	.		0.393	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67291218	A	C	67291218	3	2	151	1	0	0	0	0	1	0	0	0	6630	11	1	5	242	5	GPHN	14	67291218	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	43546398	67291218	40058322	106	13589											
C14orf174	161394	broad.mit.edu	37	chr14	77846826	77846826	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaactttgaggacatgaaggTgagttgtgtccaaagtttcc	12	12	11	6	0	0	3	0	3	0	0	2	4	2	4	2	2	1	2	2	2	3	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:77846826T>C	ENST00000216471.4	+	2	2074		c.e2+2		SAMD15_ENST00000533095.2_Splice_Site	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15											breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GACATGAAGGTGAGTTGTGTC	0.463																																					.													.	SAMD15-90	0			c.1788+2T>C						.						113	86	96					14																	77846826		2203	4300	6503	SO:0001630	splice_region_variant	161394	exon2			TGAAGGTGAGTTG	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"Sterile alpha motif (SAM) domain containing"	18631	protein-coding gene	gene with protein product			"family with sequence similarity 15, member A", "chromosome 14 open reading frame 174"	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.1788+2T>C	14.37:g.77846826T>C		Somatic	164	1		WXS	Illumina HiSeq	Phase_I	133	4	NM_001010860	0	0	0	0	0	Q2M3P3	Splice_Site	SNP	ENST00000216471.4	37	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936328	0.73442	.	.	ENSG00000100583	ENST00000533095;ENST00000216471	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7935	0.63157	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SAMD15	76916579	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.841000	0.62824	1.888000	0.54679	0.459000	0.35465	.	.		0.463	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	Intron	C	77846826	T	C	77846826	5	2	151	1	0	0	0	0	0	0	1	0	1763	1710	59	3	1796	3	C14orf174	14	77846826	Splice_Site	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	10555608	77846826	29502714	107	13590											
PPIP5K1	9677	hgsc.bcm.edu	37	chr15	43863609	43863609	+	Splice_Site	DEL	C	C	-																															ttcccaaggccctctcattaCctccatggaaccagcttttc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:43863609delC	ENST00000396923.3	-	24	3089		c.e24+1		PPIP5K1_ENST00000348806.6_Splice_Site|PPIP5K1_ENST00000360301.4_Splice_Site|PPIP5K1_ENST00000420765.1_Splice_Site|PPIP5K1_ENST00000432870.3_Splice_Site|PPIP5K1_ENST00000381879.4_Splice_Site|PPIP5K1_ENST00000360135.4_Splice_Site|PPIP5K1_ENST00000334933.4_Splice_Site|PPIP5K1_ENST00000381885.1_Splice_Site			Q6PFW1	VIP1_HUMAN	diphosphoinositol pentakisphosphate kinase 1						inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			large_intestine(1)	1						CCTCTCATTACCTCCATGGAA	0.557																																					.		.											.	PPIP5K1-90	0			c.2955+1G>-						.																																			SO:0001630	splice_region_variant	9677	exon25			.	AF502586	CCDS32215.1, CCDS45252.1, CCDS53937.1	15q15.3	2010-01-27	2010-01-26	2010-01-26	ENSG00000168781	ENSG00000168781	2.7.4.24		29023	protein-coding gene	gene with protein product		610979	"histidine acid phosphatase domain containing 2A"	HISPPD2A		17412958, 17690096, 18981179	Standard	NM_001190214		Approved	KIAA0377, IPS1, VIP1	uc001zrw.3	Q6PFW1	OTTHUMG00000059758	ENST00000396923.3:c.2967+1G>-	15.37:g.43863609delC		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	91	18	NM_014659	0	0	0	0	0	O15082|Q5HYF8|Q7Z3A7|Q86TE7|Q86UV3|Q86UV4|Q86XW8|Q8IZN0	Splice_Site	DEL	ENST00000396923.3	37	CCDS45252.1																																																																																			.		0.557	PPIP5K1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132907.1	NM_014659	Intron	-	43863609	C	-	43863609	8	5	151	1	0	1	0	1	0	0	1	0	12361	521	18	0	1485	0	PPIP5K1	15	43863609	Splice_Site	DEL	C	TCGA-MH-A561-01A-11D-A26P-10		43863609	58667783	108	13591											
VPS13C	54832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	62211634	62211634	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggatatttgcaacttctgTatatccatgaggtactaagg	12	13	10	6	0	1	1	0	1	1	0	2	2	2	2	1	3	3	3	1	3	6	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:62211634T>C	ENST00000261517.5	-	58	7565	c.7492A>G	c.(7492-7494)Aca>Gca	p.T2498A	VPS13C_ENST00000395896.4_Missense_Mutation_p.T2498A|VPS13C_ENST00000249837.3_Missense_Mutation_p.T2455A|VPS13C_ENST00000395898.3_Missense_Mutation_p.T2455A	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GCAACTTCTGTATATCCATGA	0.378																																					p.T2498A		.											.	VPS13C-92	0			c.A7492G						.						127	126	126					15																	62211634		2203	4299	6502	SO:0001583	missense	54832	exon58			CTTCTGTATATCC	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"vacuolar protein sorting 13C (yeast)"				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.7492A>G	15.37:g.62211634T>C	ENSP00000261517:p.Thr2498Ala	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	103	42	NM_020821	0	0	0	0	0		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.059562	0.55325	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.44881	0.92;0.91;1.09	5.08	5.08	0.68730	.	0.343050	0.31071	N	0.008307	T	0.38585	0.1046	M	0.69823	2.125	0.36345	D	0.85969	B;B;B;P	0.35745	0.257;0.171;0.257;0.518	B;B;B;B	0.30316	0.089;0.089;0.089;0.114	T	0.49753	-0.8906	10	0.30078	T	0.28	.	11.1995	0.48733	0.0:0.0745:0.0:0.9255	.	2455;2498;2455;2498	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	A	2455;2498;2498;2498	ENSP00000249837:T2455A;ENSP00000261517:T2498A;ENSP00000379233:T2498A	ENSP00000249837:T2455A	T	-	1	0	VPS13C	59998926	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	2.093000	0.41710	2.023000	0.59567	0.533000	0.62120	ACA	.		0.378	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62211634	T	C	62211634	3	2	151	1	0	0	0	0	1	0	0	0	17224	1638	57	3	3909	3	VPS13C	15	62211634	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	18348025	62211634	40319758	109	13592											
ADAMTSL3	57188	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	84592737	84592737	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgtgtgatatggtccaccGtcctccagccatgagccagg	7	10	11	13	1	0	2	0	2	0	0	3	2	3	2	6	2	2	0	6	2	1	2	rs148020587		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:84592737G>A	ENST00000286744.5	+	17	2293	c.2069G>A	c.(2068-2070)cGt>cAt	p.R690H	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R690H	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	690						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			ATGGTCCACCGTCCTCCAGCC	0.537																																					p.R690H													.	ADAMTSL3-1153	0			c.G2069A						.						114	81	92					15																	84592737		2203	4300	6503	SO:0001583	missense	57188	exon17			TCCACCGTCCTCC	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2069G>A	15.37:g.84592737G>A	ENSP00000286744:p.Arg690His	Somatic	279	1		WXS	Illumina HiSeq	Phase_I	229	70	NM_207517	0	0	1	3	2	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614408	0.66672	.	.	ENSG00000156218	ENST00000286744	T	0.69040	-0.37	5.25	5.25	0.73442	.	0.071450	0.53938	D	0.000044	D	0.82453	0.5040	M	0.89478	3.035	0.39210	D	0.963298	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.945	D	0.85861	0.1410	10	0.72032	D	0.01	.	9.9604	0.41693	0.0927:0.0:0.9073:0.0	.	690;690	P82987-2;P82987	.;ATL3_HUMAN	H	690	ENSP00000286744:R690H	ENSP00000286744:R690H	R	+	2	0	ADAMTSL3	82383741	0.979000	0.34478	0.948000	0.38648	0.668000	0.39293	3.573000	0.53856	2.451000	0.82905	0.637000	0.83480	CGT	G|1.000;T|0.000		0.537	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		A	84592737	G	A	84592737	3	1	151	1	0	0	0	0	1	0	0	0	276	1145	40	1	2131	1	ADAMTSL3	15	84592737	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	22381103	84592737	17938655	110	13593											
C15orf32	145858	broad.mit.edu	37	chr15	93016234	93016234	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtagctgatgtgtgtacagaTtgcaaattcaattgcggaag	12	12	12	5	1	1	2	1	1	0	1	1	3	1	3	0	1	4	4	0	1	5	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:93016234T>C	ENST00000333334.2	+	2	921	c.426T>C	c.(424-426)gaT>gaC	p.D142D	RP11-763K15.1_ENST00000554440.1_lincRNA|C15orf32_ENST00000556865.1_Silent_p.D142D	NM_153040.2	NP_694585.1	Q32M92	CO032_HUMAN	chromosome 15 open reading frame 32	142										endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	12	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0493)|OV - Ovarian serous cystadenocarcinoma(32;0.125)			TGTGTACAGATTGCAAATTCA	0.473																																					p.D142D													.	C15orf32-91	0			c.T426C						.						132	122	125					15																	93016234		2198	4298	6496	SO:0001819	synonymous_variant	145858	exon2			TACAGATTGCAAA		CCDS10373.1, CCDS73784.1	15q26.1	2014-09-10			ENSG00000183643	ENSG00000183643			26549	protein-coding gene	gene with protein product							Standard	NM_153040		Approved	FLJ32831	uc002brc.1	Q32M92	OTTHUMG00000149844	ENST00000333334.2:c.426T>C	15.37:g.93016234T>C		Somatic	152	0		WXS	Illumina HiSeq	Phase_I	122	3	NM_153040	0	0	0	0	0	C5HTZ8|Q96M45	Silent	SNP	ENST00000333334.2	37	CCDS10373.1																																																																																			.		0.473	C15orf32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313527.2	NM_153040		C	93016234	T	C	93016234	2	2	151	1	0	0	0	0	0	0	0	1	1794	1490	52	3		3	C15orf32	15	93016234	Silent	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	8423497	93016234	9515158	111	13594											
RPL3L	6123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1995508	1995508	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggtgagctcaccatgaaggCcctcttctcttgggctgtct	5	12	11	13	1	4	2	1	2	3	0	5	2	4	2	2	3	1	2	2	3	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:1995508C>A	ENST00000268661.7	-	9	1253	c.1159G>T	c.(1159-1161)Gcc>Tcc	p.A387S	MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000399753.2_5'Flank|MSRB1_ENST00000564908.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	387					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						ACCATGAAGGCCCTCTTCTCT	0.597																																					p.A387S		.											.	RPL3L-90	0			c.G1159T						.						55	46	50					16																	1995508		2199	4300	6499	SO:0001583	missense	6123	exon9			TGAAGGCCCTCTT	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"L ribosomal proteins"	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.1159G>T	16.37:g.1995508C>A	ENSP00000268661:p.Ala387Ser	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_005061	0	0	0	0	0		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.430672	0.25726	.	.	ENSG00000140986	ENST00000268661	T	0.32753	1.44	3.92	3.92	0.45320	.	0.259903	0.37178	N	0.002207	T	0.39384	0.1076	M	0.69248	2.105	0.50632	D	0.999888	P	0.44139	0.827	P	0.45856	0.495	T	0.40553	-0.9557	10	0.46703	T	0.11	-1.9802	15.4739	0.75461	0.0:1.0:0.0:0.0	.	387	Q92901	RL3L_HUMAN	S	387	ENSP00000268661:A387S	ENSP00000268661:A387S	A	-	1	0	RPL3L	1935509	1.000000	0.71417	0.999000	0.59377	0.185000	0.23345	4.700000	0.61803	2.185000	0.69588	0.563000	0.77884	GCC	.		0.597	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		A	1995508	C	A	1995508	3	1	151	1	0	0	0	0	1	0	0	0	13626	739	26	4	72	4	RPL3L	16	1995508	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		1995508	88359245	112	13595											
SCNN1B	6338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	23360139	23360139	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcatcttcatcaggacCtacttgagctgggaggtcag	8	10	14	9	0	4	1	3	1	1	0	4	3	4	3	1	5	2	2	1	5	1	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:23360139C>G	ENST00000343070.2	+	2	395	c.219C>G	c.(217-219)acC>acG	p.T73T	SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000307331.5_Silent_p.T118T|SCNN1B_ENST00000568923.1_Silent_p.T73T|SCNN1B_ENST00000568085.1_Silent_p.T73T	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	73					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	TCATCAGGACCTACTTGAGCT	0.587																																					p.T73T		.											.	SCNN1B-157	0			c.C219G						.						84	69	74					16																	23360139		2197	4300	6497	SO:0001819	synonymous_variant	6338	exon2			CAGGACCTACTTG	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.219C>G	16.37:g.23360139C>G		Somatic	289	0		WXS	Illumina HiSeq	Phase_I	227	102	NM_000336	0	0	0	0	0	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Silent	SNP	ENST00000343070.2	37	CCDS10609.1																																																																																			C|1.000;A|0.000		0.587	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			G	23360139	C	G	23360139	2	3	151	1	0	0	0	0	0	0	0	1	13960	668	24	4		4	SCNN1B	16	23360139	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	21364631	23360139	66994614	113	13596											
RBBP6	5930	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	24581493	24581493	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgtagataaagattttgAgtcttcttcaatgaaaatct	14	14	8	5	1	4	4	1	2	3	2	4	4	4	4	0	1	0	1	0	1	6	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:24581493A>T	ENST00000319715.4	+	17	3914	c.3482A>T	c.(3481-3483)gAg>gTg	p.E1161V	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Missense_Mutation_p.E1127V	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1161					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		AAAGATTTTGAGTCTTCTTCA	0.348																																					p.E1161V													.	RBBP6-230	0			c.A3482T						.						56	63	61					16																	24581493		2197	4299	6496	SO:0001583	missense	5930	exon17			ATTTTGAGTCTTC		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"proliferation potential-related protein"	600938	"retinoblastoma-binding protein 6"			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3482A>T	16.37:g.24581493A>T	ENSP00000317872:p.Glu1161Val	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	109	39	NM_006910	0	0	1	6	5	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.404459	0.62288	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.18960	2.22;2.18	5.86	5.86	0.93980	.	0.091798	0.47093	D	0.000252	T	0.19805	0.0476	N	0.24115	0.695	0.37760	D	0.92627	B;B	0.34214	0.435;0.442	B;B	0.38755	0.281;0.146	T	0.10497	-1.0627	10	0.45353	T	0.12	-7.1997	16.2436	0.82429	1.0:0.0:0.0:0.0	.	1127;1161	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	V	1161;1127	ENSP00000317872:E1161V;ENSP00000316291:E1127V	ENSP00000317872:E1161V	E	+	2	0	RBBP6	24488994	1.000000	0.71417	0.976000	0.42696	0.991000	0.79684	5.840000	0.69402	2.232000	0.73038	0.533000	0.62120	GAG	.		0.348	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24581493	A	T	24581493	3	4	151	1	0	0	0	0	1	0	0	0	13135	304	11	5	3602	5	RBBP6	16	24581493	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	1221354	24581493	65773260	114	13597											
MYLK3	91807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	46781755	46781755	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgtccaccgcagccacCatcctgaagagggcctccag	8	5	10	18	1	0	2	0	1	0	1	3	2	3	2	8	1	1	1	8	1	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:46781755C>A	ENST00000394809.4	-	1	466	c.351G>T	c.(349-351)atG>atT	p.M117I	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	117					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCGCAGCCACCATCCTGAAGA	0.657																																					p.M117I		.											.	MYLK3-374	0			c.G351T						.						45	40	42					16																	46781755		2203	4300	6503	SO:0001583	missense	91807	exon1			AGCCACCATCCTG	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.351G>T	16.37:g.46781755C>A	ENSP00000378288:p.Met117Ile	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	93	48	NM_182493	0	0	0	0	0	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530435	0.45073	.	.	ENSG00000140795	ENST00000394809	T	0.69435	-0.4	4.87	4.87	0.63330	.	0.000000	0.43260	D	0.000583	T	0.65101	0.2659	M	0.67953	2.075	0.80722	D	1	P	0.38922	0.651	B	0.33521	0.165	T	0.69942	-0.5008	10	0.46703	T	0.11	.	18.3666	0.90392	0.0:1.0:0.0:0.0	.	117	Q32MK0	MYLK3_HUMAN	I	117	ENSP00000378288:M117I	ENSP00000378288:M117I	M	-	3	0	MYLK3	45339256	1.000000	0.71417	1.000000	0.80357	0.273000	0.26683	2.195000	0.42677	2.394000	0.81467	0.491000	0.48974	ATG	.		0.657	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		A	46781755	C	A	46781755	3	1	151	1	0	0	0	0	1	0	0	0	10083	594	21	4	2160	4	MYLK3	16	46781755	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	22200262	46781755	43572998	115	13598											
EDC4	23644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67910858	67910858	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtgtctaactccttctTggcctatgccattcggggtg	4	15	11	11	1	2	0	0	0	2	0	4	0	3	0	3	3	3	1	3	3	2	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:67910858T>G	ENST00000358933.5	+	4	673	c.434T>G	c.(433-435)tTg>tGg	p.L145W	AC040162.1_ENST00000408599.1_RNA|EDC4_ENST00000574770.1_3'UTR	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	145					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AACTCCTTCTTGGCCTATGCC	0.507																																					p.L145W		.											.	EDC4-92	0			c.T434G						.						136	130	132					16																	67910858		2198	4300	6498	SO:0001583	missense	23644	exon4			CCTTCTTGGCCTA	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.434T>G	16.37:g.67910858T>G	ENSP00000351811:p.Leu145Trp	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	123	50	NM_014329	0	0	13	24	11	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	37	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.935710	0.92458	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	T	0.42131	0.98	5.83	5.83	0.93111	WD40 repeat-like-containing domain (1);	0.081121	0.51477	D	0.000086	T	0.62901	0.2466	M	0.69823	2.125	0.58432	D	0.999996	D;D	0.71674	0.998;0.997	D;P	0.65140	0.932;0.903	T	0.66740	-0.5847	10	0.87932	D	0	-7.7554	15.8624	0.79035	0.0:0.0:0.0:1.0	.	77;145	B7Z7V8;Q6P2E9	.;EDC4_HUMAN	W	145;77	ENSP00000351811:L145W	ENSP00000351811:L145W	L	+	2	0	EDC4	66468359	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.997000	0.88414	2.235000	0.73313	0.533000	0.62120	TTG	.		0.507	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		G	67910858	T	G	67910858	3	3	151	1	0	0	0	0	1	0	0	0	4919	1821	63	5	448	5	EDC4	16	67910858	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	21129103	67910858	22443895	116	13599											
AARS	16	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	70301662	70301662	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcacctcttcttcattaatGatgtccttcaccatgtctgg	7	16	6	12	0	5	1	2	1	3	0	6	1	6	1	3	1	1	1	3	1	1	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:70301662G>A	ENST00000261772.8	-	9	1265	c.1122C>T	c.(1120-1122)atC>atT	p.I374I	AARS_ENST00000564359.1_5'Flank	NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		CTTCATTAATGATGTCCTTCA	0.517											OREG0023913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I374I													.	AARS-91	0			c.C1122T						.						150	133	138					16																	70301662		2198	4300	6498	SO:0001819	synonymous_variant	16	exon9			ATTAATGATGTCC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.1122C>T	16.37:g.70301662G>A		Somatic	138	1	1121	WXS	Illumina HiSeq	Phase_I	107	8	NM_001605	0	0	67	78	11		Silent	SNP	ENST00000261772.8	37	CCDS32474.1																																																																																			.		0.517	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		A	70301662	G	A	70301662	2	1	151	1	0	0	0	0	0	0	0	1	19	1280	45	2		2	AARS	16	70301662	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	2390804	70301662	20053091	117	13600											
HYDIN	54768	bcgsc.ca	37	chr16	71127828	71127828	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttgattcggaggggcagacgGatttctcggcctagaaaaac	11	9	13	8	3	1	3	0	1	1	2	3	5	1	5	1	5	1	1	1	5	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:71127828G>A	ENST00000393567.2	-	11	1488	c.1338C>T	c.(1336-1338)atC>atT	p.I446I	RP11-23E19.1_ENST00000563968.1_RNA|HYDIN_ENST00000288168.10_Silent_p.I463I|HYDIN_ENST00000448691.1_Silent_p.I446I|HYDIN_ENST00000393550.2_Silent_p.I446I|HYDIN_ENST00000541601.1_Silent_p.I463I|HYDIN_ENST00000448089.2_Silent_p.I446I|HYDIN_ENST00000321489.5_Silent_p.I446I|HYDIN_ENST00000538248.1_Silent_p.I473I	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	446					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGGGCAGACGGATTTCTCGGC	0.408																																					p.I473I													.	HYDIN-92	0			c.C1419T						.						58	58	58					16																	71127828		2198	4300	6498	SO:0001819	synonymous_variant	54768	exon11			CAGACGGATTTCT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	19368	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 31"	610812	"hydrocephalus inducing", "hydrocephalus inducing homolog (mouse)"			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.1338C>T	16.37:g.71127828G>A		Somatic	65	0		WXS	Illumina HiSeq	Phase_1	64	4	NM_001198542	0	0	0	0	0	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			.		0.408	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71127828	G	A	71127828	2	1	151	1	0	0	0	0	0	0	0	1	7488	1164	41	2		2	HYDIN	16	71127828	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	826166	71127828	19226925	118	13601											
USP10	9100	bcgsc.ca	37	chr16	84797744	84797744	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggtcaatgaagaagagcaGgaagaacaaggtgaaggaag	18	4	15	4	1	1	5	1	2	0	3	2	7	1	7	0	4	2	1	0	4	8	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:84797744G>A	ENST00000219473.7	+	10	1820	c.1707G>A	c.(1705-1707)caG>caA	p.Q569Q	USP10_ENST00000570191.1_Silent_p.Q573Q	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	569	USP.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						AAGAAGAGCAGGAAGAACAAG	0.493																																					p.Q573Q													.	USP10-636	0			c.G1719A						.						57	58	58					16																	84797744		1887	4097	5984	SO:0001819	synonymous_variant	9100	exon11			AGAGCAGGAAGAA	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"Ubiquitin-specific peptidases"	12608	protein-coding gene	gene with protein product		609818	"ubiquitin specific protease 10"			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.1707G>A	16.37:g.84797744G>A		Somatic	246	5		WXS	Illumina HiSeq	Phase_1	213	11	NM_001272075	0	0	55	55	0	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			.		0.493	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			A	84797744	G	A	84797744	2	1	151	1	0	0	0	0	0	0	0	1	17074	991	35	2		2	USP10	16	84797744	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	13669916	84797744	5557009	119	13602											
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	18057182	18057182	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttctacggctatcaggacgCcccctggaagatcttcctgc	7	10	9	15	2	3	1	1	0	2	1	4	3	4	3	3	3	2	1	3	3	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:18057182C>G	ENST00000205890.5	+	43	8398	c.8060C>G	c.(8059-8061)gCc>gGc	p.A2687G	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_5'UTR	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2687	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TATCAGGACGCCCCCTGGAAG	0.657																																					p.A2687G		.											.	MYO15A-97	0			c.C8060G						.						45	46	46					17																	18057182		1888	4114	6002	SO:0001583	missense	51168	exon42			AGGACGCCCCCTG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"Myosins / Myosin superfamily : Class XV"	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8060C>G	17.37:g.18057182C>G	ENSP00000205890:p.Ala2687Gly	Somatic	272	0		WXS	Illumina HiSeq	Phase_I	294	70	NM_016239	0	0	0	0	0	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536404	0.65085	.	.	ENSG00000091536	ENST00000205890	D	0.88586	-2.4	5.07	2.79	0.32731	.	.	.	.	.	T	0.82263	0.4999	M	0.64997	1.995	0.80722	D	1	P	0.35433	0.501	B	0.27608	0.081	T	0.80400	-0.1398	9	0.87932	D	0	.	2.5033	0.04638	0.222:0.4596:0.0:0.3183	.	2687	Q9UKN7	MYO15_HUMAN	G	2687	ENSP00000205890:A2687G	ENSP00000205890:A2687G	A	+	2	0	MYO15A	17997907	1.000000	0.71417	0.800000	0.32199	0.904000	0.53231	2.694000	0.47035	1.107000	0.41642	0.563000	0.77884	GCC	.		0.657	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18057182	C	G	18057182	3	3	151	1	0	0	0	0	1	0	0	0	10088	739	26	4	8222	4	MYO15A	17	18057182	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		18057182	63138028	120	13603											
KLHL11	55175	broad.mit.edu	37	chr17	40021223	40021223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcatctccacccgtcccgagCgggactcggaaaactggccc	8	5	11	17	4	1	0	0	0	1	0	4	3	2	2	4	3	2	1	4	3	2	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:40021223C>T	ENST00000319121.3	-	1	461	c.401G>A	c.(400-402)cGc>cAc	p.R134H	ACLY_ENST00000588779.1_5'Flank	NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	134	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				CCGTCCCGAGCGGGACTCGGA	0.692																																					p.R134H													.	KLHL11-90	0			c.G401A						.						27	29	28					17																	40021223		2201	4293	6494	SO:0001583	missense	55175	exon1			CCCGAGCGGGACT		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.401G>A	17.37:g.40021223C>T	ENSP00000314608:p.Arg134His	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	71	4	NM_018143	0	0	1	1	0		Missense_Mutation	SNP	ENST00000319121.3	37	CCDS11411.1	.	.	.	.	.	.	.	.	.	.	c	29.2	4.988187	0.93106	.	.	ENSG00000178502	ENST00000319121	T	0.66638	-0.22	4.69	4.69	0.59074	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.161290	0.42964	D	0.000627	T	0.61223	0.2330	L	0.36672	1.1	0.46437	D	0.999044	D	0.63046	0.992	B	0.43754	0.43	T	0.67562	-0.5639	10	0.56958	D	0.05	0.02	17.8294	0.88676	0.0:1.0:0.0:0.0	.	134	Q9NVR0	KLH11_HUMAN	H	134	ENSP00000314608:R134H	ENSP00000314608:R134H	R	-	2	0	KLHL11	37274749	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.550000	0.67268	2.437000	0.82529	0.645000	0.84053	CGC	.		0.692	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		T	40021223	C	T	40021223	3	4	151	1	0	0	0	0	1	0	0	0	8388	768	27	1	1733	1	KLHL11	17	40021223	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	21964041	40021223	41173987	121	13604											
ITGA2B	3674	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr17	42449792	42449792	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgcttgaagaagccgacCtgggggtacacgggggccaa	9	6	15	11	3	0	2	0	1	0	1	1	3	1	2	4	4	2	2	4	4	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:42449792C>T	ENST00000262407.5	-	30	3092		c.e30-1		ITGA2B_ENST00000353281.4_Splice_Site	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)						axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	AGAAGCCGACCTGGGGGTACA	0.577																																					.		.											.	ITGA2B-228	0			c.3061-1G>A						.						58	44	49					17																	42449792		2203	4300	6503	SO:0001630	splice_region_variant	3674	exon31			GCCGACCTGGGGG		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"CD molecules", "Integrins"	6138	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 93"	607759	"integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.3061-1G>A	17.37:g.42449792C>T		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	97	22	NM_000419	0	0	0	0	0	B2RCY8|O95366|Q14443|Q17R67	Splice_Site	SNP	ENST00000262407.5	37	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306424	0.60305	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8074	0.69968	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITGA2B	39805318	0.993000	0.37304	0.275000	0.24674	0.303000	0.27691	4.088000	0.57678	2.357000	0.79964	0.561000	0.74099	.	.		0.577	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		Intron	T	42449792	C	T	42449792	5	4	151	1	0	0	0	0	0	0	1	0	7897	695	24	2	63	2	ITGA2B	17	42449792	Splice_Site	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	2428569	42449792	38745418	122	13605											
C17orf104	284071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42744196	42744196	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgaagcaccactacagcAaaaaagggcagagatgtttc	15	8	9	9	0	1	2	0	1	1	1	2	3	1	2	1	1	3	4	1	1	5	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:42744196A>T	ENST00000409122.2	+	5	1059	c.917A>T	c.(916-918)cAa>cTa	p.Q306L	C17orf104_ENST00000359945.3_Missense_Mutation_p.Q306L|C17orf104_ENST00000409464.1_Missense_Mutation_p.Q140L	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	306										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						CCACTACAGCAAAAAAGGGCA	0.348																																					p.Q306L		.											.	C17orf104-22	0			c.A917T						.						27	28	28					17																	42744196		2202	4298	6500	SO:0001583	missense	284071	exon5			TACAGCAAAAAAG		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.917A>T	17.37:g.42744196A>T	ENSP00000386452:p.Gln306Leu	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	40	14	NM_001145080	0	0	0	0	0	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	A	1.742	-0.491410	0.04322	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000409464	T;T;T;T	0.35421	1.31;1.31;1.37;1.31	5.45	4.38	0.52667	.	0.063895	0.64402	D	0.000008	T	0.25975	0.0633	N	0.24115	0.695	0.24874	N	0.992265	B;B;B	0.31548	0.328;0.161;0.161	B;B;B	0.35413	0.202;0.202;0.202	T	0.19257	-1.0311	10	0.59425	D	0.04	-14.3041	8.5529	0.33462	0.8008:0.1303:0.0689:0.0	.	306;306;140	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	L	306;306;140;140	ENSP00000353028:Q306L;ENSP00000386452:Q306L;ENSP00000399809:Q140L;ENSP00000386586:Q140L	ENSP00000353028:Q306L	Q	+	2	0	C17orf104	40099722	1.000000	0.71417	0.998000	0.56505	0.014000	0.08584	4.646000	0.61411	1.017000	0.39495	-0.388000	0.06559	CAA	.		0.348	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		T	42744196	A	T	42744196	3	4	151	1	0	0	0	0	1	0	0	0	1855	130	5	5	935	5	C17orf104	17	42744196	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	294404	42744196	38451014	123	13606											
SPAG9	9043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	49067112	49067112	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaagacatgctctgtgtaGacgccagtttgggagatgtc	10	11	13	7	1	1	3	0	0	1	3	2	4	1	3	1	1	1	4	1	1	3	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:49067112G>T	ENST00000262013.7	-	21	2947	c.2739C>A	c.(2737-2739)gtC>gtA	p.V913V	SPAG9_ENST00000505279.1_Silent_p.V903V|SPAG9_ENST00000357122.4_Silent_p.V899V|SPAG9_ENST00000510283.1_Silent_p.V756V	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	913					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GCTCTGTGTAGACGCCAGTTT	0.473																																					p.V913V		.											.	SPAG9-659	0			c.C2739A						.						165	133	144					17																	49067112		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon21			TGTGTAGACGCCA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"sperm surface protein", "JNK/SAPK-associated protein", "JNK interacting protein", "sperm specific protein", "c-Jun NH2-terminal kinase-associated leucine zipper protein", "Max-binding protein", "JNK-associated leucine-zipper protein", "HLC-4 protein", "lung cancer oncogene 4", "proliferation-inducing gene 6", "cancer/testis antigen 89"	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2739C>A	17.37:g.49067112G>T		Somatic	221	0		WXS	Illumina HiSeq	Phase_I	259	56	NM_001130528	0	0	14	21	7	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	9.197	1.027489	0.19512	.	.	ENSG00000008294	ENST00000513906	.	.	.	5.77	0.0229	0.14135	.	.	.	.	.	T	0.41627	0.1167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24548	-1.0157	4	.	.	.	-12.8707	1.4604	0.02394	0.2848:0.2293:0.3304:0.1555	.	.	.	.	Y	157	.	.	S	-	2	0	SPAG9	46422111	0.969000	0.33509	0.999000	0.59377	0.960000	0.62799	0.071000	0.14594	0.094000	0.17404	-1.467000	0.01014	TCT	.		0.473	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		T	49067112	G	T	49067112	2	4	151	1	0	0	0	0	0	0	0	1	15017	929	33	4		4	SPAG9	17	49067112	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	6322916	49067112	32128098	124	13607											
C17orf95	124512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	74729098	74729098	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccaggaattttggctgcCaaatgtggtgcagaagtaat	11	12	11	7	0	0	1	0	0	0	1	1	2	1	2	2	3	2	3	2	3	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:74729098C>A	ENST00000341249.6	+	3	455	c.123C>A	c.(121-123)gcC>gcA	p.A41A	METTL23_ENST00000590964.1_5'UTR|METTL23_ENST00000586752.1_5'UTR|METTL23_ENST00000586200.1_Intron|METTL23_ENST00000589977.1_Silent_p.A41A|METTL23_ENST00000591571.1_5'UTR|METTL23_ENST00000586738.1_Silent_p.A41A|METTL23_ENST00000588822.1_5'UTR|MFSD11_ENST00000586622.1_5'Flank|METTL23_ENST00000588783.1_Silent_p.A41A|RP11-318A15.7_ENST00000587459.1_Silent_p.A13A|METTL23_ENST00000588302.1_5'UTR	NM_001206984.1	NP_001193913.1	Q86XA0	MET23_HUMAN	methyltransferase like 23	41						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	methyltransferase activity (GO:0008168)			large_intestine(2)|lung(1)	3						TTTTGGCTGCCAAATGTGGTG	0.438																																					p.A41A		.											.	.	0			c.C123A						.						26	24	25					17																	74729098		1915	4132	6047	SO:0001819	synonymous_variant	124512	exon3			GGCTGCCAAATGT		CCDS45787.1, CCDS59298.1	17q25.2	2011-03-03	2011-03-03	2011-03-03	ENSG00000181038	ENSG00000181038			26988	protein-coding gene	gene with protein product		615262	"chromosome 17 open reading frame 95"	C17orf95		12477932	Standard	NM_001080510		Approved	LOC124512	uc021udl.1	Q86XA0		ENST00000341249.6:c.123C>A	17.37:g.74729098C>A		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	80	13	NM_001206984	0	0	58	85	27	H9ZYJ0|K7EK32	Silent	SNP	ENST00000341249.6	37	CCDS45787.1																																																																																			.		0.438	METTL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451002.1	NM_001080510		A	74729098	C	A	74729098	2	1	151	1	0	0	0	0	0	0	0	1	1897	581	21	4		4	C17orf95	17	74729098	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	25661986	74729098	6466112	125	13608											
AATK	9625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	79095314	79095314	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcctcctccgagggaagtgGggctccctcctgggatgggg	4	7	18	12	1	0	0	0	0	0	0	4	3	4	2	5	7	0	1	5	7	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:79095314G>T	ENST00000326724.4	-	11	2446	c.2422C>A	c.(2422-2424)Cca>Aca	p.P808T	AATK_ENST00000417379.1_Missense_Mutation_p.P705T	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	808	Pro-rich.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GAGGGAAGTGGGGCTCCCTCC	0.701																																					p.P808T		.											.	AATK-933	0			c.C2422A						.						16	21	19					17																	79095314		2062	4182	6244	SO:0001583	missense	9625	exon11			GAAGTGGGGCTCC	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"lemur tyrosine kinase 1", "protein phosphatase 1, regulatory subunit 77"	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.2422C>A	17.37:g.79095314G>T	ENSP00000324196:p.Pro808Thr	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	60	15	NM_001080395	0	0	0	0	0	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	G	7.050	0.564179	0.13498	.	.	ENSG00000181409	ENST00000326724;ENST00000374792	T;T	0.78246	-1.06;-1.16	4.36	2.21	0.28008	.	0.938651	0.08819	U	0.889000	T	0.66366	0.2782	L	0.43152	1.355	0.19575	N	0.999966	B	0.15141	0.012	B	0.09377	0.004	T	0.50276	-0.8847	10	0.22706	T	0.39	.	5.0003	0.14261	0.1085:0.0:0.552:0.3395	.	808	Q6ZMQ8	LMTK1_HUMAN	T	808;772	ENSP00000324196:P808T;ENSP00000363924:P772T	ENSP00000324196:P808T	P	-	1	0	AATK	76709909	0.000000	0.05858	0.647000	0.29507	0.154000	0.21943	0.726000	0.25984	0.801000	0.34066	0.561000	0.74099	CCA	.		0.701	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79095314	G	T	79095314	3	4	151	1	0	0	0	0	1	0	0	0	26	1232	43	4	1718	4	AATK	17	79095314	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	4366216	79095314	2099896	126	13609											
MALT1	10892	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	56400802	56400802	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttattggatatgtgtaggAaaaggtaagttttctaatct	12	17	9	3	0	3	0	0	0	3	0	3	2	3	2	0	3	0	3	0	3	7	8			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr18:56400802A>G	ENST00000348428.3	+	11	1654	c.1396A>G	c.(1396-1398)Aaa>Gaa	p.K466E	MALT1_ENST00000345724.3_Missense_Mutation_p.K455E|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	466	Caspase-like.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						TATGTGTAGGAAAAGGTAAGT	0.313			T	BIRC3	MALT																																p.K466E		.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1-660	0			c.A1396G						.						59	66	64					18																	56400802		2203	4299	6502	SO:0001583	missense	10892	exon11			TGTAGGAAAAGGT		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1396A>G	18.37:g.56400802A>G	ENSP00000319279:p.Lys466Glu	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	66	5	NM_006785	0	0	0	0	0	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	37	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599615	0.87055	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.41400	1.0;1.0	5.52	5.52	0.82312	Peptidase C14, caspase catalytic (1);	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.66767	-0.5840	10	0.72032	D	0.01	.	15.304	0.73979	1.0:0.0:0.0:0.0	.	455;466	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	E	466;455	ENSP00000319279:K466E;ENSP00000304161:K455E	ENSP00000304161:K455E	K	+	1	0	MALT1	54551782	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.153000	0.77428	2.106000	0.64143	0.528000	0.53228	AAA	.		0.313	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2			G	56400802	A	G	56400802	3	3	151	1	0	0	0	0	1	0	0	0	9227	247	9	3	1438	3	MALT1	18	56400802	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		56400802	21676446	127	13610											
CHAF1A	10036	broad.mit.edu	37	chr19	4433329	4433329	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtgctggtacgtgcacccGcaggtgctacagagcttcca	8	9	12	12	2	0	1	0	0	0	1	1	1	1	1	2	2	6	6	2	2	2	3	rs368347266		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:4433329G>A	ENST00000301280.5	+	13	2567	c.2466G>A	c.(2464-2466)ccG>ccA	p.P822P	CTB-50L17.5_ENST00000590159.1_RNA	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	822	Binds to p60.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGTGCACCCGCAGGTGCTAC	0.617								Chromatin Structure																													p.P822P													.	CHAF1A-92	0			c.G2466A						.	G		1,4405	2.1+/-5.4	0,1,2202	76	74	75		2466	-10.3	0.1	19		75	0,8600		0,0,4300	no	coding-synonymous	CHAF1A	NM_005483.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		822/957	4433329	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10036	exon13			GCACCCGCAGGTG	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2466G>A	19.37:g.4433329G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	67	3	NM_005483	0	0	15	15	0	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	37	CCDS32875.1																																																																																			.		0.617	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		A	4433329	G	A	4433329	2	1	151	1	0	0	0	0	0	0	0	1	3317	1074	38	1		1	CHAF1A	19	4433329	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		4433329	54695654	128	13611											
SPC24	147841	broad.mit.edu	37	chr19	11259779	11259779	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaaaaggatataggaggctgGccttcagacgggtgtcctcc	10	8	14	9	1	1	1	1	0	0	1	3	4	3	3	3	5	0	1	3	5	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:11259779G>T	ENST00000592540.1	-	2	327	c.296C>A	c.(295-297)gCc>gAc	p.A99D		NM_182513.2	NP_872319.1	Q8NBT2	SPC24_HUMAN	SPC24, NDC80 kinetochore complex component	99	Interaction with the N-terminus of SPBC25.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleolus (GO:0005730)|nucleus (GO:0005634)				autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)	5						TAGGAGGCTGGCCTTCAGACG	0.592																																					p.A99D													.	.	0			c.C296A						.						15	18	17					19																	11259779		1690	3413	5103	SO:0001583	missense	147841	exon2			AGGCTGGCCTTCA	AK075287	CCDS45974.1	19p13.2	2013-06-05	2013-06-05	2007-03-02		ENSG00000161888			26913	protein-coding gene	gene with protein product		609394	"spindle pole body component 24 homolog (S. cerevisiae)", "SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	SPBC24			Standard	NM_182513		Approved	FLJ90806	uc002mql.2	Q8NBT2		ENST00000592540.1:c.296C>A	19.37:g.11259779G>T	ENSP00000465075:p.Ala99Asp	Somatic	176	1		WXS	Illumina HiSeq	Phase_I	90	4	NM_182513	0	0	0	0	0	B4DZZ7|C9JGC4	Missense_Mutation	SNP	ENST00000592540.1	37	CCDS45974.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.804761	0.31961	.	.	ENSG00000161888	ENST00000423327	.	.	.	4.2	1.97	0.26223	.	0.086068	0.47852	U	0.000206	T	0.62332	0.2419	M	0.64997	1.995	0.58432	D	0.999999	P	0.48998	0.918	P	0.51135	0.66	T	0.64377	-0.6422	9	0.72032	D	0.01	-0.9392	11.9287	0.52835	0.0:0.3382:0.6618:0.0	.	99	Q8NBT2	SPC24_HUMAN	D	99	.	ENSP00000397131:A99D	A	-	2	0	SPC24	11120779	0.995000	0.38212	0.982000	0.44146	0.032000	0.12392	3.051000	0.49885	0.239000	0.21243	-0.310000	0.09108	GCC	.		0.592	SPC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453059.1	NM_182513		T	11259779	G	T	11259779	3	4	151	1	0	0	0	0	1	0	0	0	15053	1203	42	4	313	4	SPC24	19	11259779	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	6826450	11259779	47869204	129	13612											
SYDE1	85360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15220001	15220001	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacggggagcctacctgcaaAgcctggagcccagtagccgc	9	4	13	15	2	0	0	0	0	0	0	0	2	0	2	5	3	6	2	5	3	3	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:15220001A>T	ENST00000342784.2	+	2	254	c.223A>T	c.(223-225)Agc>Tgc	p.S75C	SYDE1_ENST00000600252.1_5'UTR|SYDE1_ENST00000600440.1_Intron	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	75	Pro-rich.				activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						CTACCTGCAAAGCCTGGAGCC	0.706																																					p.S75C		.											.	SYDE1-92	0			c.A223T						.						13	13	13					19																	15220001		2148	4200	6348	SO:0001583	missense	85360	exon2			CTGCAAAGCCTGG	BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.223A>T	19.37:g.15220001A>T	ENSP00000341489:p.Ser75Cys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	37	13	NM_033025	0	0	8	12	4	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	37	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.951011	0.73787	.	.	ENSG00000105137	ENST00000342784	T	0.13778	2.56	4.32	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.26484	0.0647	L	0.47716	1.5	0.27009	N	0.964736	D	0.76494	0.999	D	0.80764	0.994	T	0.02781	-1.1111	10	0.87932	D	0	.	8.0008	0.30295	0.7926:0.2074:0.0:0.0	.	75	Q6ZW31	SYDE1_HUMAN	C	75	ENSP00000341489:S75C	ENSP00000341489:S75C	S	+	1	0	SYDE1	15081001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.770000	0.62309	1.598000	0.50083	0.533000	0.62120	AGC	.		0.706	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		T	15220001	A	T	15220001	3	4	151	1	0	0	0	0	1	0	0	0	15467	72	3	5	229	5	SYDE1	19	15220001	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	3960222	15220001	43908982	130	13613											
PDCD5	9141	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	33077794	33077794	+	Frame_Shift_Del	DEL	A	A	-																															aaggtttaatagaaatccttAaaaaagtaagccaacaaaca																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:33077794delA	ENST00000590247.2	+	5	483	c.289delA	c.(289-291)aaafs	p.K98fs	PDCD5_ENST00000592786.1_Stop_Codon_Del|PDCD5_ENST00000419343.3_3'UTR|PDCD5_ENST00000586035.1_Frame_Shift_Del_p.K60fs|PDCD5_ENST00000379316.3_Intron	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	98					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					AGAAATCCTTAAAAAAGTAAG	0.323																																					p.K97fs		.											.	PDCD5-228	0			c.289delA						.						81	87	85					19																	33077794		2203	4300	6503	SO:0001589	frameshift_variant	9141	exon5			.	AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"TFAR19 novel apoptosis-related", "TF1 cell apoptosis-related gene 19"	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.289delA	19.37:g.33077794delA	ENSP00000466214:p.Lys98fs	Somatic	144	0		WXS	Illumina HiSeq	Phase_I	124	43	NM_004708	0	0	0	0	0	B4DE64|Q53YC9|Q6IB70	Frame_Shift_Del	DEL	ENST00000590247.2	37	CCDS12423.1																																																																																			.		0.323	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708		-	33077794	A	-	33077794	7	5	151	1	0	1	0	1	0	0	0	0	11648	363	13	0	307	0	PDCD5	19	33077794	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	17857793	33077794	26051189	131	13614											
ZNF792	126375	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	35450211	35450211	+	Frame_Shift_Del	DEL	T	T	-																															ttctgatagggttgtgtacgTtctgctgcacctgtttccgg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:35450211delT	ENST00000404801.1	-	4	934	c.548delA	c.(547-549)aacfs	p.N183fs	ZNF792_ENST00000605484.1_Frame_Shift_Del_p.N116fs	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GTTGTGTACGTTCTGCTGCAC	0.542																																					p.N183fs	GBM(1;7 183 21053 22581 22847)	.											.	.	0			c.548delA						.						256	248	251					19																	35450211		2203	4300	6503	SO:0001589	frameshift_variant	126375	exon4			.	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"Zinc fingers, C2H2-type", "-"	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.548delA	19.37:g.35450211delT	ENSP00000385099:p.Asn183fs	Somatic	348	0		WXS	Illumina HiSeq	Phase_I	273	101	NM_175872	0	0	0	0	0	B4E333|Q495L1|Q495L3|Q8N932	Frame_Shift_Del	DEL	ENST00000404801.1	37	CCDS12440.2																																																																																			.		0.542	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872		-	35450211	T	-	35450211	7	5	151	1	0	1	0	1	0	0	0	0	18196	1725	60	0	1354	0	ZNF792	19	35450211	Frame_Shift_Del	DEL	T	TCGA-MH-A561-01A-11D-A26P-10	2372417	35450211	23678772	132	13615											
ZNF256	10172	hgsc.bcm.edu;bcgsc.ca	37	chr19	58452565	58452565	+	Frame_Shift_Del	DEL	A	A	-																															tctccggtgtgacttctcctAtgtctaatgaggctggagct																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:58452565delA	ENST00000282308.3	-	3	1807	c.1611delT	c.(1609-1611)catfs	p.H537fs	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	537					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|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)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GACTTCTCCTATGTCTAATGA	0.468																																					p.H537fs	NSCLC(55;1313 1552 8040 11996)	.											.	ZNF256-92	0			c.1611delT						.						66	58	61					19																	58452565		2203	4300	6503	SO:0001589	frameshift_variant	10172	exon3			.	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1611delT	19.37:g.58452565delA	ENSP00000282308:p.His537fs	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	98	19	NM_005773	0	0	0	0	0	B2RA92|Q53Y85|Q9BV71	Frame_Shift_Del	DEL	ENST00000282308.3	37	CCDS12966.1																																																																																			.		0.468	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			-	58452565	A	-	58452565	7	5	151	1	0	1	0	1	0	0	0	0	17831	446	16	0	276	0	ZNF256	19	58452565	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	23002354	58452565	676418	133	13616											
PLTP	5360	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	44539886	44539886	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaagcgcagcccctcctgCttcactgaagcagcagagaa	13	5	10	13	1	1	3	1	1	0	2	2	4	2	3	3	0	5	4	3	0	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:44539886C>T	ENST00000477313.1	-	2	699	c.105G>A	c.(103-105)aaG>aaA	p.K35K	PLTP_ENST00000372431.3_Silent_p.K35K|PLTP_ENST00000542937.1_Silent_p.K55K|PLTP_ENST00000354050.4_Silent_p.K35K|PLTP_ENST00000420868.2_Silent_p.K35K|PLTP_ENST00000372420.1_5'Flank			P55058	PLTP_HUMAN	phospholipid transfer protein	35					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GCCCCTCCTGCTTCACTGAAG	0.602																																					p.K35K		.											.	PLTP-91	0			c.G105A						.						70	71	71					20																	44539886		2203	4300	6503	SO:0001819	synonymous_variant	5360	exon3			CTCCTGCTTCACT	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.105G>A	20.37:g.44539886C>T		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	91	32	NM_182676	0	0	0	0	0	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Silent	SNP	ENST00000477313.1	37	CCDS13386.1																																																																																			.		0.602	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44539886	C	T	44539886	2	4	151	1	0	0	0	0	0	0	0	1	12140	796	28	2		2	PLTP	20	44539886	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		44539886	18485634	134	13617											
ZNF831	128611	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	57782069	57782069	+	Frame_Shift_Del	DEL	A	A	-																															ctcccgcacttgagggactgAagccatgcaggacccctggg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:57782069delA	ENST00000371030.2	+	3	3985	c.3985delA	c.(3985-3987)aagfs	p.K1329fs		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1329							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					TGAGGGACTGAAGCCATGCAG	0.577																																					p.K1329fs		.											.	ZNF831-126	0			c.3985delA						.						68	73	71					20																	57782069		1968	4144	6112	SO:0001589	frameshift_variant	128611	exon3			.	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 174"	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3985delA	20.37:g.57782069delA	ENSP00000360069:p.Lys1329fs	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	104	43	NM_178457	0	0	0	0	0	Q5TDR4|Q8TCP0	Frame_Shift_Del	DEL	ENST00000371030.2	37	CCDS42894.1																																																																																			.		0.577	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		-	57782069	A	-	57782069	7	5	151	1	0	1	0	1	0	0	0	0	18217	247	9	0	3995	0	ZNF831	20	57782069	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	13242183	57782069	5243451	135	13618											
C20orf11	54994	broad.mit.edu;bcgsc.ca	37	chr20	61574952	61574952	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagagccgagagtgcctcAcagagatggagcgtaccctg	11	5	15	10	2	1	3	1	0	0	3	1	7	1	4	3	2	4	1	3	2	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:61574952A>G	ENST00000266069.3	+	4	568	c.421A>G	c.(421-423)Aca>Gca	p.T141A		NM_017896.2	NP_060366.1	Q9NWU2	GID8_HUMAN	GID complex subunit 8	141						cell junction (GO:0030054)|nucleus (GO:0005634)											AGAGTGCCTCACAGAGATGGA	0.642																																					p.T141A													.	.	0			c.A421G						.						58	48	51					20																	61574952		2203	4300	6503	SO:0001583	missense	54994	exon4			TGCCTCACAGAGA	AK000609	CCDS13510.1	20q13.33	2013-07-31	2013-07-31	2012-07-20	ENSG00000101193	ENSG00000101193			15857	protein-coding gene	gene with protein product		611625	"chromosome 20 open reading frame 11", "GID complex subunit 8 homolog (S. cerevisiae)"	C20orf11		12559565	Standard	NM_017896		Approved	FLJ20602, bA305P22.1, TWA1	uc002ydy.3	Q9NWU2	OTTHUMG00000032949	ENST00000266069.3:c.421A>G	20.37:g.61574952A>G	ENSP00000266069:p.Thr141Ala	Somatic	268	1		WXS	Illumina HiSeq	Phase_I	218	14	NM_017896	0	0	41	47	6	E1P5I3|Q8N5M5	Missense_Mutation	SNP	ENST00000266069.3	37	CCDS13510.1	.	.	.	.	.	.	.	.	.	.	A	6.461	0.453146	0.12283	.	.	ENSG00000101193	ENST00000266069	.	.	.	5.65	5.65	0.86999	Ran binding protein-like, CRA domain (1);Ran binding protein, CRA domain (1);	0.000000	0.85682	D	0.000000	T	0.40015	0.1100	N	0.10809	0.05	0.58432	D	0.999996	B	0.14012	0.009	B	0.16722	0.016	T	0.23332	-1.0191	9	0.22706	T	0.39	-29.1609	16.161	0.81712	1.0:0.0:0.0:0.0	.	141	Q9NWU2	CT011_HUMAN	A	141	.	ENSP00000266069:T141A	T	+	1	0	C20orf11	61045397	1.000000	0.71417	0.997000	0.53966	0.164000	0.22412	5.766000	0.68843	2.274000	0.75844	0.533000	0.62120	ACA	.		0.642	GID8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080097.2	NM_017896		G	61574952	A	G	61574952	3	3	151	1	0	0	0	0	1	0	0	0	2085	159	6	3	431	3	C20orf11	20	61574952	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	3792883	61574952	1450568	136	13619											
SAMSN1	64092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	15889252	15889252	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgatgtactttttacccacTtttttcttcattgtccatga	7	21	4	9	0	2	2	1	2	1	0	3	2	3	2	2	0	2	1	2	0	2	10			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr21:15889252T>A	ENST00000400566.1	-	3	321	c.240A>T	c.(238-240)aaA>aaT	p.K80N	SAMSN1_ENST00000285670.2_Missense_Mutation_p.K148N|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	80					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		TTTTACCCACTTTTTTCTTCA	0.328																																					p.K148N		.											.	SAMSN1-94	0			c.A444T						.						124	109	114					21																	15889252		1797	4068	5865	SO:0001583	missense	64092	exon4			ACCCACTTTTTTC	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	10528	protein-coding gene	gene with protein product	"nuclear localization signals, SAM and SH3 domain containing 1", "SAM and SH3 domain containing 2", "hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1", "Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.240A>T	21.37:g.15889252T>A	ENSP00000383411:p.Lys80Asn	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	51	21	NM_001256370	0	0	5	5	0	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520541	0.44866	.	.	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.57752	0.38;0.38	5.35	5.35	0.76521	.	0.100854	0.64402	D	0.000003	T	0.66076	0.2753	M	0.83953	2.67	0.43750	D	0.996253	D;D	0.56746	0.977;0.962	P;P	0.55923	0.787;0.688	T	0.71500	-0.4574	10	0.87932	D	0	-16.1663	7.6865	0.28544	0.0:0.1638:0.0:0.8362	.	148;80	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	N	148;80	ENSP00000285670:K148N;ENSP00000383411:K80N	ENSP00000285670:K148N	K	-	3	2	SAMSN1	14811123	1.000000	0.71417	0.880000	0.34516	0.214000	0.24535	2.251000	0.43187	2.033000	0.60031	0.533000	0.62120	AAA	.		0.328	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			A	15889252	T	A	15889252	3	1	151	1	0	0	0	0	1	0	0	0	13862	1606	56	5	905	5	SAMSN1	21	15889252	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10		15889252	32240643	137	13620											
TRPM2	7226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45825794	45825794	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgcccggcggccaggctcatCccggcgacgctgtaccccgg	4	5	14	18	6	1	0	1	0	0	0	2	1	2	0	5	5	2	3	5	5	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr21:45825794C>T	ENST00000397928.1	+	18	3109	c.2664C>T	c.(2662-2664)atC>atT	p.I888I	TRPM2_ENST00000397932.2_Silent_p.I888I|TRPM2_ENST00000300482.5_Silent_p.I888I|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Silent_p.I868I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	888					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CCAGGCTCATCCCGGCGACGC	0.642																																					p.I888I		.											.	TRPM2-92	0			c.C2664T						.						67	71	70					21																	45825794		2203	4297	6500	SO:0001819	synonymous_variant	7226	exon18			GCTCATCCCGGCG	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"Voltage-gated ion channels / Transient receptor potential cation channels", "Nudix motif containing"	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2664C>T	21.37:g.45825794C>T		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	19	10	NM_003307	0	0	0	0	0	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			.		0.642	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		T	45825794	C	T	45825794	2	4	151	1	0	0	0	0	0	0	0	1	16619	845	30	2		2	TRPM2	21	45825794	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	29936542	45825794	2304101	138	13621											
ADORA2A	135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24836558	24836558	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcttctccccaggtacaatGgcttggtgaccggcacgagg	7	9	12	13	2	2	1	0	1	2	0	3	2	2	1	3	5	1	3	3	5	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr22:24836558G>T	ENST00000337539.7	+	3	799	c.340G>T	c.(340-342)Ggc>Tgc	p.G114C	ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A_ENST00000496497.1_3'UTR|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000427813.2_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	114					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CAGGTACAATGGCTTGGTGAC	0.567																																					p.G114C		.											.	ADORA2A-90	0			c.G340T						.						107	101	103					22																	24836558		2203	4300	6503	SO:0001583	missense	135	exon3			TACAATGGCTTGG	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.340G>T	22.37:g.24836558G>T	ENSP00000336630:p.Gly114Cys	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	129	50	NM_000675	0	0	0	0	0	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	37	CCDS13826.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.71|15.71	2.914051|2.914051	0.52546|0.52546	.|.	.|.	ENSG00000128271|ENSG00000258555	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596|ENST00000493440	T;T|.	0.20332|.	2.08;2.08|.	4.97|4.97	3.95|3.95	0.45737|0.45737	GPCR, rhodopsin-like superfamily (1);|.	0.205313|.	0.49305|.	D|.	0.000152|.	T|T	0.56217|0.56217	0.1970|0.1970	L|L	0.45470|0.45470	1.425|1.425	0.43814|0.43814	D|D	0.996375|0.996375	D|.	0.65815|.	0.995|.	P|.	0.62014|.	0.897|.	T|T	0.51872|0.51872	-0.8650|-0.8650	10|5	0.59425|.	D|.	0.04|.	-27.3119|-27.3119	9.0177|9.0177	0.36179|0.36179	0.1684:0.0:0.8316:0.0|0.1684:0.0:0.8316:0.0	.|.	114|.	P29274|.	AA2AR_HUMAN|.	C|I	114|46	ENSP00000414802:G114C;ENSP00000336630:G114C|.	ENSP00000336630:G114C|.	G|M	+|+	1|3	0|0	ADORA2A|KB-1896H10.1	23166558|23166558	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.973000|0.973000	0.67179|0.67179	3.477000|3.477000	0.53151|0.53151	1.213000|1.213000	0.43380|0.43380	0.563000|0.563000	0.77884|0.77884	GGC|ATG	.		0.567	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24836558	G	T	24836558	3	4	151	1	0	0	0	0	1	0	0	0	327	1348	47	4	346	4	ADORA2A	22	24836558	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		24836558	26468008	139	13622											
CBX6	23466	broad.mit.edu;bcgsc.ca	37	chr22	39262330	39262330	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaccgtcaggaggttgcTggtgacatcggtgacgacca	8	9	15	9	3	1	3	1	3	0	0	2	5	1	4	2	4	1	2	2	4	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr22:39262330T>G	ENST00000407418.3	-	5	1246	c.1123A>C	c.(1123-1125)Agc>Cgc	p.S375R	CBX6_ENST00000216083.6_Missense_Mutation_p.S357R			O95503	CBX6_HUMAN	chromobox homolog 6	375					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(58;0.04)					AGGAGGTTGCTGGTGACATCG	0.657																																					p.S375R													.	CBX6-226	0			c.A1123C						.						56	57	57					22																	39262330		2203	4300	6503	SO:0001583	missense	23466	exon5			GGTTGCTGGTGAC		CCDS13980.1	22q13.1	2013-04-23			ENSG00000183741	ENSG00000183741			1556	protein-coding gene	gene with protein product							Standard	NM_014292		Approved		uc003awl.3	O95503	OTTHUMG00000150456	ENST00000407418.3:c.1123A>C	22.37:g.39262330T>G	ENSP00000384490:p.Ser375Arg	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	110	34	NM_014292	0	0	4	7	3	A8KAH0|Q96EM5	Missense_Mutation	SNP	ENST00000407418.3	37	CCDS13980.1	.	.	.	.	.	.	.	.	.	.	T	18.12	3.554120	0.65425	.	.	ENSG00000183741	ENST00000407418;ENST00000216083	.	.	.	4.23	4.23	0.50019	.	0.240026	0.26899	N	0.021925	T	0.62588	0.2440	L	0.50333	1.59	0.40639	D	0.981929	D	0.59357	0.985	P	0.53360	0.724	T	0.68217	-0.5467	9	0.66056	D	0.02	.	13.4862	0.61366	0.0:0.0:0.0:1.0	.	375	O95503	CBX6_HUMAN	R	375;357	.	ENSP00000216083:S357R	S	-	1	0	CBX6	37592276	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.312000	0.59154	1.773000	0.52216	0.334000	0.21626	AGC	.		0.657	CBX6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318190.1	NM_014292		G	39262330	T	G	39262330	3	3	151	1	0	0	0	0	1	0	0	0	2728	1580	55	5	119	5	CBX6	22	39262330	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	14425772	39262330	12042236	140	13623											
FAM48B1	100130302	broad.mit.edu	37	chrX	24382371	24382373	+	IGR	DEL	TAT	TAT	-																															ccattttctgctgctgctgcTattgctgctgctgctgctgc																								rs371342199|rs35206911|rs2695489|rs201827126		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	TAT	TAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:24382371_24382373delTAT								AC004552.1 (15348 upstream) : PDK3 (100964 downstream)																							ctgctgctgctattgctgctgct	0.576																																					p.498_499del													.	.	0			c.1494_1496del						.			51,3098		12,21,6,1318,441						0.1	0		dbSNP_130	9	95,5572		7,39,42,2032,1469	no	coding	FAM48B1	NM_001136234.1		19,60,48,3350,1910	A1A1,A1R,A1,RR,R		1.6764,1.6196,1.6561				146,8670				SO:0001628	intergenic_variant	100130302	exon1			TGCTGCTATTGCT																													X.37:g.24382371_24382373delTAT		Somatic	376	0		WXS	Illumina HiSeq	Phase_I	300	7	NM_001136234	0	0	0	0	0		In_Frame_Del	DEL		37																																																																																				.	0	0.576									-	24382373	TAT	-	24382371	6	5	151	0	1	1	0	1	0	0	0	0	5592	1509	53	0		0	FAM48B1	23	24382371	IGR	DEL	TAT	TCGA-MH-A561-01A-11D-A26P-10		24382371	130888189	141	13624											
SMC1A	8243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	53440302	53440302	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttcgcttgtcatactcctgCgccagctccccagaacgact	7	11	7	16	3	1	1	1	0	0	1	4	2	3	1	4	0	4	2	4	0	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:53440302C>G	ENST00000322213.4	-	4	622	c.495G>C	c.(493-495)gcG>gcC	p.A165A	SMC1A_ENST00000375340.6_Intron	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	165					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.A165A(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CATACTCCTGCGCCAGCTCCC	0.463																																					p.A165A		.											.	SMC1A-232	1	Substitution - coding silent(1)	lung(1)	c.G495C						.						138	124	129					X																	53440302		2203	4300	6503	SO:0001819	synonymous_variant	8243	exon4			CTCCTGCGCCAGC	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"Structural maintenance of chromosomes proteins"	11111	protein-coding gene	gene with protein product		300040	"SMC1 (structural maintenance of chromosomes 1, yeast)-like 1", "SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.495G>C	X.37:g.53440302C>G		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	50	40	NM_006306	0	0	0	5	5	O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	37	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	C	5.699	0.313435	0.10789	.	.	ENSG00000072501	ENST00000428014	.	.	.	4.63	0.543	0.17179	.	.	.	.	.	T	0.41971	0.1182	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	.	1.4228	0.02316	0.1701:0.1318:0.2791:0.419	.	.	.	.	P	170	.	.	R	-	2	0	SMC1A	53457027	0.002000	0.14202	0.996000	0.52242	0.942000	0.58702	-1.093000	0.03362	-0.226000	0.09899	-1.768000	0.00664	CGC	.		0.463	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		G	53440302	C	G	53440302	2	3	151	1	0	0	0	0	0	0	0	1	14813	755	27	4		4	SMC1A	23	53440302	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	29057931	53440302	101830258	142	13625											
LONRF3	79836	broad.mit.edu;bcgsc.ca	37	chrX	118151559	118151559	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agttcttcccttggaaagccGagctcagctccccttcctag	7	11	8	15	1	2	0	1	0	1	0	5	2	5	1	5	1	3	3	5	1	2	5	rs143959775		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:118151559G>A	ENST00000371628.3	+	11	2217	c.2186G>A	c.(2185-2187)cGa>cAa	p.R729Q	LONRF3_ENST00000422289.2_Missense_Mutation_p.R473Q|LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000304778.7_Missense_Mutation_p.R688Q	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	729	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						TTGGAAAGCCGAGCTCAGCTC	0.502																																					p.R729Q													.	LONRF3-289	0			c.G2186A						.	G	GLN/ARG,GLN/ARG	1,3834		0,1,1631,571	144	119	127		2186,2063	4.7	1	X	dbSNP_134	127	0,6728		0,0,2428,1872	no	missense,missense	LONRF3	NM_001031855.1,NM_024778.4	43,43	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	probably-damaging,probably-damaging	729/760,688/719	118151559	1,10562	2203	4300	6503	SO:0001583	missense	79836	exon11			AAAGCCGAGCTCA	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"RING-type (C3HC4) zinc fingers"	21152	protein-coding gene	gene with protein product			"ring finger protein 127"	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.2186G>A	X.37:g.118151559G>A	ENSP00000360690:p.Arg729Gln	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	53	4	NM_001031855	0	0	2	2	0	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661769	0.88154	2.61E-4	0.0	ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628;ENST00000422289	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.56	4.69	0.59074	Peptidase S16, lon N-terminal (1);PUA-like domain (1);	0.000000	0.64402	D	0.000001	T	0.46444	0.1393	N	0.20766	0.605	0.35057	D	0.761236	D;P;D	0.89917	1.0;0.879;1.0	D;B;D	0.77004	0.971;0.358;0.989	T	0.53279	-0.8461	10	0.28530	T	0.3	-65.9818	13.0438	0.58915	0.0806:0.0:0.9194:0.0	.	473;688;729	B3KUN7;Q496Y0-2;Q496Y0	.;.;LONF3_HUMAN	Q	688;688;729;473	ENSP00000360691:R688Q;ENSP00000307732:R688Q;ENSP00000360690:R729Q;ENSP00000408894:R473Q	ENSP00000307732:R688Q	R	+	2	0	LONRF3	118035587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.352000	0.66028	2.360000	0.80028	0.592000	0.82586	CGA	G|1.000;A|0.000		0.502	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		A	118151559	G	A	118151559	3	1	151	1	0	0	0	0	1	0	0	0	8921	1058	37	1	2228	1	LONRF3	23	118151559	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	64711257	118151559	37119001	143	13626											
UPF3B	65109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	118985467	118985467	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccaggactcacctttattgtCaaggaatacataaccatcaa	15	10	5	11	0	3	0	3	0	0	0	3	2	3	2	3	2	2	0	3	2	6	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:118985467C>G	ENST00000276201.2	-	3	430	c.361G>C	c.(361-363)Gac>Cac	p.D121H	UPF3B_ENST00000345865.2_Missense_Mutation_p.D121H	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	121	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCTTTATTGTCAAGGAATACA	0.363																																					p.D121H		.											.	UPF3B-133	0			c.G361C						.						104	86	92					X																	118985467		2203	4300	6503	SO:0001583	missense	65109	exon3			TATTGTCAAGGAA	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.361G>C	X.37:g.118985467C>G	ENSP00000276201:p.Asp121His	Somatic	214	1		WXS	Illumina HiSeq	Phase_I	159	121	NM_023010	0	0	0	0	0	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	37	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031576	0.75504	.	.	ENSG00000125351	ENST00000276201;ENST00000345865;ENST00000439808	T;T	0.74526	-0.85;-0.85	5.1	5.1	0.69264	Regulator of nonsense-mediated decay, UPF3 (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	D	0.90246	0.6950	H	0.95079	3.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93290	0.6667	10	0.87932	D	0	.	16.142	0.81534	0.0:1.0:0.0:0.0	.	121;121	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	H	121	ENSP00000276201:D121H;ENSP00000245418:D121H	ENSP00000276201:D121H	D	-	1	0	UPF3B	118869495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.226000	0.78060	2.111000	0.64477	0.600000	0.82982	GAC	.		0.363	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			G	118985467	C	G	118985467	3	3	151	1	0	0	0	0	1	0	0	0	17039	826	29	4	1126	4	UPF3B	23	118985467	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	833908	118985467	36285093	144	13627											
ZMPSTE24	10269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	40724033	40724033	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctcttttcctggacagtGtatctttgggagaccttcct	5	16	9	11	0	2	1	0	0	2	1	4	3	4	2	3	2	1	2	3	2	1	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:40724033G>C	ENST00000372759.3	+	1	255	c.90G>C	c.(88-90)gtG>gtC	p.V30V	ZMPSTE24_ENST00000479131.1_3'UTR|RP1-39G22.7_ENST00000567508.1_RNA	NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	30					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			CCTGGACAGTGTATCTTTGGG	0.622																																					p.V30V		.											.	ZMPSTE24-226	0			c.G90C						.						121	104	109					1																	40724033		2203	4300	6503	SO:0001819	synonymous_variant	10269	exon1			GACAGTGTATCTT	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog"	606480	"zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)"			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.90G>C	1.37:g.40724033G>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	99	32	NM_005857	0	0	0	0	0	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Silent	SNP	ENST00000372759.3	37	CCDS449.1																																																																																			.		0.622	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1			C	40724033	G	C	40724033	2	2	152	1	0	0	0	0	0	0	0	1	17730	1364	48	4		4	ZMPSTE24	1	40724033	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		40724033	208526588	1	13628											
GSTM4	2948	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr1	110201466	110201466	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccagaatacttggaggaaCttcctacaatgatgcagcac	14	8	9	10	0	0	2	0	1	0	1	1	4	1	4	2	2	6	2	2	2	5	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:110201466C>A	ENST00000369836.4	+	6	700	c.391C>A	c.(391-393)Ctt>Att	p.L131I	GSTM4_ENST00000495742.1_3'UTR|GSTM4_ENST00000369833.1_Missense_Mutation_p.L90I|GSTM4_ENST00000326729.5_Missense_Mutation_p.L131I|GSTM4_ENST00000336075.5_Missense_Mutation_p.L70I	NM_000850.4	NP_000841.1	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4	131	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	CTTGGAGGAACTTCCTACAAT	0.517																																					p.L131I		.											.	GSTM4-44	0			c.C391A						.						164	158	160					1																	110201466		2203	4300	6503	SO:0001583	missense	2948	exon6			GAGGAACTTCCTA	M96234	CCDS806.1, CCDS807.1	1p13.3	2012-06-22	2008-11-26		ENSG00000168765	ENSG00000168765	2.5.1.18	"Glutathione S-transferases / Soluble"	4636	protein-coding gene	gene with protein product		138333	"glutathione S-transferase M4"			8276420	Standard	NM_000850		Approved		uc001dyf.3	Q03013	OTTHUMG00000011642	ENST00000369836.4:c.391C>A	1.37:g.110201466C>A	ENSP00000358851:p.Leu131Ile	Somatic	327	0		WXS	Illumina HiSeq	Phase_I	303	97	NM_147148	0	0	16	18	2	A8K765|Q05465|Q32NC1|Q4JNT8|Q6FH87	Missense_Mutation	SNP	ENST00000369836.4	37	CCDS807.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.750271	0.49257	.	.	ENSG00000168765	ENST00000369836;ENST00000336075;ENST00000326729;ENST00000369833	T;T;T;T	0.04603	3.59;4.46;3.59;3.59	4.0	-0.554	0.11811	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.201178	0.32473	N	0.006046	T	0.01940	0.0061	L	0.41961	1.31	0.38907	D	0.957449	B;B;B	0.17852	0.024;0.007;0.0	B;B;B	0.23716	0.035;0.048;0.009	T	0.40346	-0.9568	10	0.44086	T	0.13	-16.1138	11.7266	0.51712	0.6127:0.3873:0.0:0.0	.	70;131;131	Q4JNT8;Q03013-2;Q03013	.;.;GSTM4_HUMAN	I	131;70;131;90	ENSP00000358851:L131I;ENSP00000336744:L70I;ENSP00000316471:L131I;ENSP00000358848:L90I	ENSP00000316471:L131I	L	+	1	0	GSTM4	110002989	0.010000	0.17322	0.005000	0.12908	0.847000	0.48162	0.193000	0.17116	-0.165000	0.10908	-0.901000	0.02856	CTT	.		0.517	GSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032187.1	NM_000850		A	110201466	C	A	110201466	3	1	152	1	0	0	0	0	1	0	0	0	6861	565	20	4	413	4	GSTM4	1	110201466	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	69477433	110201466	139049155	2	13629											
IGSF3	3321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	117120184	117120184	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgatggactggagggtgggaCctgaaaagaatcatgagaga	14	7	16	4	0	1	5	1	3	0	2	1	9	1	8	1	4	0	0	1	4	3	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:117120184C>G	ENST00000369486.3	-	11	4100	c.3335G>C	c.(3334-3336)aGt>aCt	p.S1112T	IGSF3_ENST00000369483.1_Splice_Site_p.S1132T|IGSF3_ENST00000318837.6_Splice_Site_p.S1132T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1112					lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GAGGGTGGGACCTGAAAAGAA	0.493																																					p.S1132T		.											.	IGSF3-92	0			c.G3395C						.						98	102	101					1																	117120184		2203	4300	6503	SO:0001630	splice_region_variant	3321	exon12			GTGGGACCTGAAA	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3335-1G>C	1.37:g.117120184C>G		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	88	30	NM_001542	0	0	0	0	0	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	7.587	0.670001	0.14776	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.02890	4.12;4.13;4.13	4.88	4.88	0.63580	.	0.310318	0.31199	N	0.008076	T	0.00695	0.0023	N	0.08118	0	0.32760	N	0.505191	B;B	0.24368	0.084;0.102	B;B	0.22386	0.028;0.039	T	0.52845	-0.8521	10	0.31617	T	0.26	.	9.0162	0.36170	0.0:0.9027:0.0:0.0973	.	1112;1132	O75054;A6NJZ6	IGSF3_HUMAN;.	T	1112;1132;1132	ENSP00000358498:S1112T;ENSP00000358495:S1132T;ENSP00000321184:S1132T	ENSP00000321184:S1132T	S	-	2	0	IGSF3	116921707	0.997000	0.39634	1.000000	0.80357	0.699000	0.40488	3.210000	0.51129	2.536000	0.85505	0.655000	0.94253	AGT	.		0.493	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	Missense_Mutation	G	117120184	C	G	117120184	5	3	152	1	0	0	0	0	0	0	1	0	7622	521	18	4	253	4	IGSF3	1	117120184	Splice_Site	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	6918718	117120184	132130437	3	13630											
PBXIP1	57326	broad.mit.edu	37	chr1	154920116	154920116	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctggagacattcacacatAcctgcctgtcccccacagct	9	9	6	17	0	2	1	1	0	1	1	3	2	3	1	4	1	3	1	4	1	1	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:154920116A>C	ENST00000368463.3	-	8	810		c.e8+1		PBXIP1_ENST00000368465.1_Splice_Site|PBXIP1_ENST00000542459.1_Splice_Site|PBXIP1_ENST00000539880.1_Splice_Site|PBXIP1_ENST00000368460.3_Splice_Site|PBXIP1_ENST00000498553.1_Splice_Site	NM_020524.2	NP_065385.2	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein 1						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)	cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(6)|lung(13)|prostate(1)|urinary_tract(1)	24	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			ATTCACACATACCTGCCTGTC	0.622																																					.													.	PBXIP1-153	0			c.738+2T>G						.						70	78	76					1																	154920116		2203	4300	6503	SO:0001630	splice_region_variant	57326	exon9			ACACATACCTGCC	AF221521	CCDS1074.1	1q22	2008-02-05	2007-01-30		ENSG00000163346	ENSG00000163346			21199	protein-coding gene	gene with protein product			"pre-B-cell leukemia transcription factor interacting protein 1"			7505766, 10825160	Standard	NM_020524		Approved	HPIP	uc001ffr.3	Q96AQ6	OTTHUMG00000037369	ENST00000368463.3:c.738+1T>G	1.37:g.154920116A>C		Somatic	106	18		WXS	Illumina HiSeq	Phase_I	130	27	NM_020524	0	0	0	0	0	Q5T174|Q5T176|Q9H8X6|Q9HA02|Q9HD85	Splice_Site	SNP	ENST00000368463.3	37	CCDS1074.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309902	0.40895	.	.	ENSG00000163346	ENST00000368465;ENST00000368463;ENST00000351146;ENST00000539880;ENST00000543593;ENST00000542459;ENST00000368460	.	.	.	4.25	1.91	0.25777	.	.	.	.	.	.	.	.	.	.	.	0.42929	D	0.994319	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.461	0.21956	0.7777:0.0:0.2223:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PBXIP1	153186740	0.722000	0.28017	0.336000	0.25522	0.408000	0.30992	1.419000	0.34793	0.205000	0.20568	0.260000	0.18958	.	.		0.622	PBXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090943.1	NM_020524	Intron	C	154920116	A	C	154920116	5	2	152	1	0	0	0	0	0	0	1	0	11522	405	14	5	1471	5	PBXIP1	1	154920116	Splice_Site	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	37799932	154920116	94330505	4	13631											
INSRR	3645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156824054	156824054	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgcagttctccagctgacGaagctctgccacctctgagc	7	9	10	15	1	3	2	0	2	3	0	4	3	3	2	3	0	5	5	3	0	1	1	rs140386495		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:156824054G>A	ENST00000368195.3	-	2	523	c.127C>T	c.(127-129)Cgt>Tgt	p.R43C	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	43					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TCCAGCTGACGAAGCTCTGCC	0.622																																					p.R43C		.											.	INSRR-1403	0			c.C127T						.	G	,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	37	39	39		,127	3.1	1	1	dbSNP_134	39	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,180	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	,probably-damaging	,43/1298	156824054	3,13003	2203	4300	6503	SO:0001583	missense	3645	exon2			GCTGACGAAGCTC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"Fibronectin type III domain containing"	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.127C>T	1.37:g.156824054G>A	ENSP00000357178:p.Arg43Cys	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	59	14	NM_014215	0	0	0	0	0	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703881	0.48412	2.27E-4	2.33E-4	ENSG00000027644	ENST00000368195	T	0.32272	1.46	5.06	3.13	0.36017	.	0.000000	0.43416	D	0.000563	T	0.19604	0.0471	.	.	.	0.48288	D	0.999626	D	0.67145	0.996	P	0.46885	0.53	T	0.03403	-1.1040	9	0.72032	D	0.01	.	7.1713	0.25721	0.0913:0.0:0.7361:0.1726	.	43	P14616	INSRR_HUMAN	C	43	ENSP00000357178:R43C	ENSP00000357178:R43C	R	-	1	0	INSRR	155090678	0.003000	0.15002	1.000000	0.80357	0.342000	0.28953	1.267000	0.33050	1.098000	0.41479	0.557000	0.71058	CGT	G|1.000;A|0.000		0.622	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156824054	G	A	156824054	3	1	152	1	0	0	0	0	1	0	0	0	7795	1058	37	1	3849	1	INSRR	1	156824054	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	1903938	156824054	92426567	5	13632											
KLHDC9	126823	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	161069269	161069269	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagctgaaccagaagtagctGggcattggagtcatgggaaa	13	8	14	6	0	1	2	1	1	0	1	1	4	1	4	1	3	3	4	1	3	5	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:161069269G>A	ENST00000368011.4	+	2	803	c.661G>A	c.(661-663)Ggg>Agg	p.G221R	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Missense_Mutation_p.G221R|KLHDC9_ENST00000490724.2_3'UTR	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	221										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			AGAAGTAGCTGGGCATTGGAG	0.498																																					p.G221R		.											.	KLHDC9-22	0			c.G661A						.						120	122	121					1																	161069269		2203	4300	6503	SO:0001583	missense	126823	exon2			GTAGCTGGGCATT	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.661G>A	1.37:g.161069269G>A	ENSP00000356990:p.Gly221Arg	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	230	70	NM_001007255	0	0	26	39	13	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Missense_Mutation	SNP	ENST00000368011.4	37	CCDS30919.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.580835	0.46006	.	.	ENSG00000162755	ENST00000368011;ENST00000392192	T;T	0.59364	1.77;0.27	4.47	3.55	0.40652	Galactose oxidase/kelch, beta-propeller (1);	0.000000	0.64402	D	0.000018	T	0.64583	0.2611	M	0.72118	2.19	0.35694	D	0.815117	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.68500	-0.5392	10	0.46703	T	0.11	-6.0987	13.2992	0.60315	0.0878:0.0:0.9122:0.0	.	221;221	Q8NEP7-2;Q8NEP7	.;KLDC9_HUMAN	R	221	ENSP00000356990:G221R;ENSP00000376030:G221R	ENSP00000356990:G221R	G	+	1	0	KLHDC9	159335893	1.000000	0.71417	0.955000	0.39395	0.891000	0.51852	3.599000	0.54045	0.526000	0.28541	-0.797000	0.03246	GGG	.		0.498	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		A	161069269	G	A	161069269	3	1	152	1	0	0	0	0	1	0	0	0	8385	1348	47	2	667	2	KLHDC9	1	161069269	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	4245215	161069269	88181352	6	13633											
IARS2	55699	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	220311360	220311360	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattggcccatccgtgctcaAtgctgccagagatgatatta	11	11	9	10	1	1	2	1	1	0	1	2	3	2	2	3	1	3	2	3	1	4	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:220311360A>G	ENST00000302637.5	+	17	2254	c.2150A>G	c.(2149-2151)aAt>aGt	p.N717S	IARS2_ENST00000366922.1_Missense_Mutation_p.N645S|snoU13_ENST00000459443.1_RNA	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	717					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TCCGTGCTCAATGCTGCCAGA	0.408																																					p.N717S		.											.	IARS2-94	0			c.A2150G						.						141	126	131					1																	220311360		2203	4300	6503	SO:0001583	missense	55699	exon17			TGCTCAATGCTGC	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.2150A>G	1.37:g.220311360A>G	ENSP00000303279:p.Asn717Ser	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	142	11	NM_018060	0	0	7	7	0	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Missense_Mutation	SNP	ENST00000302637.5	37	CCDS1523.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.868965	0.51588	.	.	ENSG00000067704	ENST00000366922;ENST00000302637	T;T	0.41758	0.99;0.99	5.94	-2.49	0.06403	.	0.500458	0.25060	N	0.033452	T	0.22820	0.0551	N	0.26162	0.8	0.29693	N	0.840771	B	0.06786	0.001	B	0.08055	0.003	T	0.05289	-1.0894	10	0.54805	T	0.06	-2.622	5.3859	0.16218	0.4679:0.2548:0.2773:0.0	.	717	Q9NSE4	SYIM_HUMAN	S	645;717	ENSP00000355889:N645S;ENSP00000303279:N717S	ENSP00000303279:N717S	N	+	2	0	IARS2	218377983	0.015000	0.18098	0.161000	0.22692	0.442000	0.32017	0.217000	0.17603	-0.335000	0.08451	-0.385000	0.06624	AAT	.		0.408	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		G	220311360	A	G	220311360	3	3	152	1	0	0	0	0	1	0	0	0	7495	101	4	3	2216	3	IARS2	1	220311360	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	59242091	220311360	28939261	7	13634											
URB2	9816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	229771821	229771821	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgaggcactgaggcaGcctgtgctggcctcgggccc	4	7	16	14	1	0	2	0	2	0	0	1	2	0	2	3	4	3	5	3	4	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:229771821G>A	ENST00000258243.2	+	4	1597	c.1461G>A	c.(1459-1461)caG>caA	p.Q487Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	487						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						CACTGAGGCAGCCTGTGCTGG	0.582																																					p.Q487Q		.											.	URB2-174	0			c.G1461A						.						111	119	116					1																	229771821		2203	4300	6503	SO:0001819	synonymous_variant	9816	exon4			GAGGCAGCCTGTG	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.1461G>A	1.37:g.229771821G>A		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	117	55	NM_014777	0	0	0	0	0	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			.		0.582	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229771821	G	A	229771821	2	1	152	1	0	0	0	0	0	0	0	1	17058	962	34	2		2	URB2	1	229771821	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	9460461	229771821	19478800	8	13635											
HNRNPU	3192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	245018785	245018785	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagttccctctgtttgagtAactaccacggccaggaaaaa	12	10	9	10	1	1	1	0	1	1	0	2	2	2	2	3	2	2	4	3	2	5	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:245018785A>G	ENST00000283179.9	-	12	2456	c.2293T>C	c.(2293-2295)Tac>Cac	p.Y765H	HNRNPU-AS1_ENST00000489705.1_RNA|HNRNPU_ENST00000444376.2_Missense_Mutation_p.Y746H|HNRNPU-AS1_ENST00000475997.1_RNA			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	765	Gly-rich.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			CTGTTTGAGTAACTACCACGG	0.512																																					p.Y765H	NSCLC(33;911 1010 3329 23631 49995)	.											.	HNRNPU-22	0			c.T2293C						.						169	168	168					1																	245018785		2203	4300	6503	SO:0001583	missense	3192	exon12			TTGAGTAACTACC	X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.2293T>C	1.37:g.245018785A>G	ENSP00000283179:p.Tyr765His	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	119	45	NM_031844	0	0	75	110	35	O75507|Q8N174|Q96HY9|Q9BQ09	Missense_Mutation	SNP	ENST00000283179.9	37	CCDS41479.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094744	0.56075	.	.	ENSG00000153187	ENST00000444376;ENST00000283179;ENST00000427948	T;T	0.47177	0.85;0.86	5.51	5.51	0.81932	.	0.337558	0.31936	N	0.006827	T	0.42177	0.1191	N	0.04508	-0.205	0.44289	D	0.997152	D;D;P	0.69078	0.997;0.995;0.919	P;P;P	0.62184	0.899;0.795;0.543	T	0.42732	-0.9434	10	0.15952	T	0.53	-5.3765	15.623	0.76824	1.0:0.0:0.0:0.0	.	746;765;489	Q00839-2;Q00839;Q5RI19	.;HNRPU_HUMAN;.	H	746;765;690	ENSP00000393151:Y746H;ENSP00000283179:Y765H	ENSP00000283179:Y765H	Y	-	1	0	HNRNPU	243085408	1.000000	0.71417	0.798000	0.32154	0.954000	0.61252	6.268000	0.72552	2.088000	0.63022	0.482000	0.46254	TAC	.		0.512	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844		G	245018785	A	G	245018785	3	3	152	1	0	0	0	0	1	0	0	0	7294	362	13	3	196	3	HNRNPU	1	245018785	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	15246964	245018785	4231836	9	13636											
RAD51AP2	729475	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	17692220	17692220	+	Frame_Shift_Del	DEL	T	T	-																															aatgccatgtggaaagtgacTacctaaaaatataagacaat																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:17692220delT	ENST00000399080.2	-	3	3354	c.3331delA	c.(3331-3333)agtfs	p.S1111fs		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	1111	Interaction with RAD51.									endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGAAAGTGACTACCTAAAAAT	0.313																																					p.S1111fs		.											.	RAD51AP2-23	0			c.3331delA						.						82	72	75					2																	17692220		1815	4072	5887	SO:0001589	frameshift_variant	729475	exon3			.	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.3331delA	2.37:g.17692220delT	ENSP00000382030:p.Ser1111fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	105	17	NM_001099218	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000399080.2	37	CCDS42656.1																																																																																			.		0.313	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		-	17692220	T	-	17692220	7	5	152	1	0	1	0	1	0	0	0	0	13019	1522	53	0	152	0	RAD51AP2	2	17692220	Frame_Shift_Del	DEL	T	TCGA-MH-A562-01A-11D-A26P-10		17692220	225507153	10	13637											
OSR1	130497	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	19552164	19552164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagggcttctctttggagtGaatatatctgagggcagaaa	12	11	13	5	0	2	3	0	2	2	1	3	5	2	4	0	3	0	2	0	3	5	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:19552164G>A	ENST00000272223.2	-	3	1017	c.673C>T	c.(673-675)Cac>Tac	p.H225Y	OSR1_ENST00000536433.1_Missense_Mutation_p.H225Y	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	225					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				TCTTTGGAGTGAATATATCTG	0.493																																					p.H225Y		.											.	OSR1-257	0			c.C673T						.						119	109	112					2																	19552164		2203	4300	6503	SO:0001583	missense	130497	exon3			TGGAGTGAATATA	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.673C>T	2.37:g.19552164G>A	ENSP00000272223:p.His225Tyr	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	101	9	NM_145260	0	0	0	0	0	B3KV97|D6W521	Missense_Mutation	SNP	ENST00000272223.2	37	CCDS1694.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550306	0.86127	.	.	ENSG00000143867	ENST00000272223;ENST00000536433	D;D	0.88896	-2.44;-2.44	5.01	5.01	0.66863	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.049292	0.85682	D	0.000000	D	0.95245	0.8458	M	0.93283	3.4	0.58432	D	0.999996	P	0.38148	0.62	P	0.52758	0.708	D	0.95373	0.8466	9	.	.	.	-8.151	18.0945	0.89485	0.0:0.0:1.0:0.0	.	225	Q8TAX0	OSR1_HUMAN	Y	225	ENSP00000272223:H225Y;ENSP00000441801:H225Y	.	H	-	1	0	OSR1	19415645	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.595000	0.98260	2.606000	0.88127	0.561000	0.74099	CAC	.		0.493	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		A	19552164	G	A	19552164	3	1	152	1	0	0	0	0	1	0	0	0	11319	1290	45	2	131	2	OSR1	2	19552164	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	1859944	19552164	223647209	11	13638											
PNO1	56902	broad.mit.edu	37	chr2	68385203	68385203	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagggcggggatgcgggccGcatggacacagaggaggcca	10	2	20	9	3	0	2	0	0	0	2	0	5	0	5	2	7	1	1	2	7	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:68385203G>A	ENST00000263657.2	+	1	228	c.137G>A	c.(136-138)cGc>cAc	p.R46H	WDR92_ENST00000492039.2_5'Flank|RP11-474G23.1_ENST00000406334.3_Missense_Mutation_p.R163W|WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000295121.6_5'Flank|WDR92_ENST00000406245.2_5'Flank	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	46						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						GATGCGGGCCGCATGGACACA	0.677																																					p.R46H	NSCLC(83;642 1410 13044 32832 40058)												.	PNO1-68	0			c.G137A						.						18	26	23					2																	68385203		2202	4297	6499	SO:0001583	missense	56902	exon1			CGGGCCGCATGGA	AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"RNA binding protein"		"KH-type RNA binding protein 1", "KH-type RNA-binding protein 1"	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.137G>A	2.37:g.68385203G>A	ENSP00000263657:p.Arg46His	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	45	4	NM_020143	0	0	0	0	0	A8K6Q0|Q53G13|Q8WVB8	Missense_Mutation	SNP	ENST00000263657.2	37	CCDS1885.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171546	0.38315	.	.	ENSG00000115946	ENST00000263657	T	0.41400	1.0	6.03	-1.94	0.07571	.	0.478698	0.19273	N	0.118341	T	0.15392	0.0371	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08868	-1.0701	10	0.52906	T	0.07	0.9051	0.011	0.00001	0.289:0.1962:0.2222:0.2926	.	46	Q9NRX1	PNO1_HUMAN	H	46	ENSP00000263657:R46H	ENSP00000263657:R46H	R	+	2	0	PNO1	68238707	0.014000	0.17966	0.015000	0.15790	0.004000	0.04260	0.190000	0.17057	-0.050000	0.13356	-1.832000	0.00591	CGC	.		0.677	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143		A	68385203	G	A	68385203	3	1	152	1	0	0	0	0	1	0	0	0	12187	1087	38	1	139	1	PNO1	2	68385203	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	48833039	68385203	174814170	12	13639											
MPHOSPH10	10199	broad.mit.edu;bcgsc.ca	37	chr2	71368372	71368378	+	Frame_Shift_Del	DEL	ATGTAGT	ATGTAGT	-																															tatgtttcaggcttgggatgAtgtagtacgtaaagaaaaac																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	ATGTAGT	ATGTAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:71368372_71368378delATGTAGT	ENST00000244230.2	+	7	1671_1677	c.1319_1325delATGTAGT	c.(1318-1326)gatgtagtafs	p.DVV440fs		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	440					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						GCTTGGGATGATGTAGTACGTAAAGAA	0.324																																					p.440_442del													.	MPHOSPH10-93	0			c.1319_1325del						.																																			SO:0001589	frameshift_variant	10199	exon7			GGGATGATGTAGT	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 106"	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1319_1325delATGTAGT	2.37:g.71368372_71368378delATGTAGT	ENSP00000244230:p.Asp440fs	Somatic	187	0		WXS	Illumina HiSeq	Phase_I	155	16	NM_005791	0	0	0	0	0	A0AVJ8	Frame_Shift_Del	DEL	ENST00000244230.2	37	CCDS1916.1																																																																																			.		0.324	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		-	71368378	ATGTAGT	-	71368372	7	5	152	1	0	1	0	1	0	0	0	0	9750	333	12	0	1345	0	MPHOSPH10	2	71368372	Frame_Shift_Del	DEL	ATGTAGT	TCGA-MH-A562-01A-11D-A26P-10	2983169	71368372	171831001	13	13640											
IP6K2	51447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	48728866	48728866	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttcttctctacagtgtagtAcaagacttcagatttcttta	10	17	5	9	0	4	2	1	0	3	2	5	2	4	2	0	0	2	2	0	0	5	9			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:48728866A>G	ENST00000328631.5	-	4	701	c.478T>C	c.(478-480)Tac>Cac	p.Y160H		NM_001005909.2|NM_016291.3	NP_001005909.1|NP_057375.2	Q9UHH9	IP6K2_HUMAN	inositol hexakisphosphate kinase 2	160					cytokine-mediated signaling pathway (GO:0019221)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell growth (GO:0030308)|phosphate ion transport (GO:0006817)|phosphatidylinositol phosphorylation (GO:0046854)|positive regulation of apoptotic process (GO:0043065)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	15						ACAGTGTAGTACAAGACTTCA	0.363																																					p.Y160H		.											.	IP6K2-265	0			c.T478C						.						154	146	149					3																	48728866		2203	4300	6503	SO:0001583	missense	51447	exon4			TGTAGTACAAGAC	AF177145	CCDS2777.1, CCDS33752.1, CCDS54579.1, CCDS54580.1, CCDS54581.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000068745	ENSG00000068745			17313	protein-coding gene	gene with protein product		606992	"inositol hexaphosphate kinase 2"	IHPK2		10574768	Standard	NM_016291		Approved		uc003cup.3	Q9UHH9	OTTHUMG00000133543	ENST00000328631.5:c.478T>C	3.37:g.48728866A>G	ENSP00000331103:p.Tyr160His	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	146	51	NM_016291	0	0	8	14	6	A8K3B1|B4E3G6|G8JLL6|Q6P0N8|Q9BSZ6|Q9BUW3|Q9H4P7|Q9NT63|Q9UFU6	Missense_Mutation	SNP	ENST00000328631.5	37	CCDS2777.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.109209	0.77096	.	.	ENSG00000068745	ENST00000328631	T	0.18657	2.2	5.6	5.6	0.85130	.	0.169966	0.53938	D	0.000049	T	0.23330	0.0564	L	0.58101	1.795	0.80722	D	1	P	0.49447	0.924	B	0.40782	0.34	T	0.03852	-1.0998	10	0.22706	T	0.39	-18.3925	15.8359	0.78796	1.0:0.0:0.0:0.0	.	160	Q9UHH9	IP6K2_HUMAN	H	160	ENSP00000331103:Y160H	ENSP00000331103:Y160H	Y	-	1	0	IP6K2	48703870	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	7.511000	0.81718	2.141000	0.66446	0.524000	0.50904	TAC	.		0.363	IP6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257521.2	NM_016291		G	48728866	A	G	48728866	3	3	152	1	0	0	0	0	1	0	0	0	7810	391	14	3	814	3	IP6K2	3	48728866	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		48728866	149293564	14	13641											
LAMB2	3913	broad.mit.edu	37	chr3	49158999	49158999	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggccttcaccgtctggtaCtgatcacccagaggaccgcg	8	7	12	14	3	3	2	2	1	1	1	3	3	3	3	4	3	1	1	4	3	1	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:49158999C>T	ENST00000418109.1	-	32	5291	c.5127G>A	c.(5125-5127)caG>caA	p.Q1709Q	USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Silent_p.Q1709Q|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1709	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCGTCTGGTACTGATCACCCA	0.607																																					p.Q1709Q													.	LAMB2-93	0			c.G5127A						.						48	48	48					3																	49158999		2203	4300	6503	SO:0001819	synonymous_variant	3913	exon31			CTGGTACTGATCA		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"Laminins"	6487	protein-coding gene	gene with protein product	"laminin S"	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5127G>A	3.37:g.49158999C>T		Somatic	234	0		WXS	Illumina HiSeq	Phase_I	266	6	NM_002292	0	0	287	291	4	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																			.		0.607	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		T	49158999	C	T	49158999	2	4	152	1	0	0	0	0	0	0	0	1	8632	564	20	2		2	LAMB2	3	49158999	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	430133	49158999	148863431	15	13642											
OR5H2	79310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	98001882	98001882	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgtggaaccttggtctgAttgctcttatctggaatgac	7	16	11	7	0	3	2	0	2	3	0	3	4	3	4	1	3	2	1	1	3	3	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:98001882A>C	ENST00000355273.2	+	1	151	c.151A>C	c.(151-153)Att>Ctt	p.I51L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						CCTTGGTCTGATTGCTCTTAT	0.433																																					p.I51L		.											.	OR5H2-71	0			c.A151C						.						359	331	340					3																	98001882		2203	4300	6503	SO:0001583	missense	79310	exon1			GGTCTGATTGCTC		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"GPCR / Class A : Olfactory receptors"	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.151A>C	3.37:g.98001882A>C	ENSP00000347418:p.Ile51Leu	Somatic	252	0		WXS	Illumina HiSeq	Phase_I	275	97	NM_001005482	0	0	0	0	0	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	A	9.652	1.141906	0.21205	.	.	ENSG00000197938	ENST00000355273	T	0.00614	6.21	3.2	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.180712	0.26582	U	0.023580	T	0.01061	0.0035	L	0.52905	1.665	0.09310	N	1	P	0.45768	0.866	P	0.46585	0.521	T	0.48864	-0.8997	10	0.72032	D	0.01	.	5.7492	0.18138	0.7608:0.0:0.0:0.2391	.	51	Q8NGV7	OR5H2_HUMAN	L	51	ENSP00000347418:I51L	ENSP00000347418:I51L	I	+	1	0	OR5H2	99484572	0.003000	0.15002	0.516000	0.27786	0.041000	0.13682	0.917000	0.28665	1.458000	0.47871	0.443000	0.29094	ATT	.		0.433	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			C	98001882	A	C	98001882	3	2	152	1	0	0	0	0	1	0	0	0	11188	333	12	5	153	5	OR5H2	3	98001882	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	48842883	98001882	100020548	16	13643											
RG9MTD1	54931	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	101284160	101284160	+	Frame_Shift_Del	DEL	T	T	-																															ataaacagaaaaactttctaTttttacgactttgggatagg																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:101284160delT	ENST00000309922.6	+	2	689	c.535delT	c.(535-537)tttfs	p.F179fs		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	179					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										AAACTTTCTATTTTTACGACT	0.408																																					p.F179fs		.											.	.	0			c.535delT						.						84	80	81					3																	101284160		1827	4080	5907	SO:0001589	frameshift_variant	54931	exon2			.	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.535delT	3.37:g.101284160delT	ENSP00000312356:p.Phe179fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	46	18	NM_017819	0	0	0	0	0	Q9NRG5|Q9NX54|Q9Y596	Frame_Shift_Del	DEL	ENST00000309922.6	37	CCDS43122.1																																																																																			.		0.408	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		-	101284160	T	-	101284160	7	5	152	1	0	1	0	1	0	0	0	0	13303	1493	52	0	537	0	RG9MTD1	3	101284160	Frame_Shift_Del	DEL	T	TCGA-MH-A562-01A-11D-A26P-10	3282278	101284160	96738270	17	13644											
TPRA1	131601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	127292425	127292425	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgatgctgccagtgtggcagGgcatggaagcgatgtcatcc	8	9	15	9	1	1	1	1	1	0	0	2	3	2	2	2	3	3	3	2	3	1	0	rs201165800	byFrequency	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:127292425G>C	ENST00000355552.3	-	11	1437	c.1061C>G	c.(1060-1062)cCc>cGc	p.P354R	TPRA1_ENST00000296210.7_3'UTR|TPRA1_ENST00000465915.1_5'Flank|TPRA1_ENST00000450633.2_Missense_Mutation_p.P354R|TPRA1_ENST00000489960.1_Missense_Mutation_p.P354R	NM_001136053.1	NP_001129525.1	Q86W33	TPRA1_HUMAN	transmembrane protein, adipocyte asscociated 1	354					aging (GO:0007568)|G-protein coupled receptor signaling pathway (GO:0007186)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	9						AGTGTGGCAGGGCATGGAAGC	0.657																																					p.P354R		.											.	TPRA1-90	0			c.C1061G						.						47	48	47					3																	127292425		2202	4300	6502	SO:0001583	missense	131601	exon11			TGGCAGGGCATGG	AK056759	CCDS3042.1, CCDS46899.1	3q21.2	2012-08-22	2009-07-08	2009-07-08	ENSG00000163870	ENSG00000163870		"GPCR / Unclassified : 7TM orphan receptors"	30413	protein-coding gene	gene with protein product	"transmembrane protein 227"	608336	"G protein-coupled receptor 175"	GPR175		10342878	Standard	NM_001136053		Approved	TPRA40, FLJ32197, TMEM227	uc003ejn.3	Q86W33	OTTHUMG00000159639	ENST00000355552.3:c.1061C>G	3.37:g.127292425G>C	ENSP00000347748:p.Pro354Arg	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	74	24	NM_001136053	0	0	54	117	63	A8MVB8|D3DNA9|Q8WZ24|Q96AJ6|Q9P2R4	Missense_Mutation	SNP	ENST00000355552.3	37	CCDS3042.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553183	0.86127	.	.	ENSG00000163870	ENST00000450633;ENST00000355552;ENST00000489960	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.66489	0.2794	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70135	-0.4955	9	0.56958	D	0.05	-26.1417	18.2482	0.89993	0.0:0.0:1.0:0.0	.	354	Q86W33	TPRA1_HUMAN	R	354	.	ENSP00000347748:P354R	P	-	2	0	TPRA1	128775115	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.058000	0.93896	2.305000	0.77605	0.491000	0.48974	CCC	G|0.999;A|0.001		0.657	TPRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356624.1	NM_016372		C	127292425	G	C	127292425	3	2	152	1	0	0	0	0	1	0	0	0	16450	1232	43	4	64	4	TPRA1	3	127292425	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	26008265	127292425	70730005	18	13645											
TNK2	10188	broad.mit.edu;bcgsc.ca	37	chr3	195615329	195615329	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgatcttctccaggtccTcattcttgacgtactcaaag	8	13	7	13	2	5	1	2	1	3	0	7	2	6	1	3	1	2	1	3	1	2	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:195615329T>C	ENST00000333602.6	-	2	748	c.131A>G	c.(130-132)gAg>gGg	p.E44G	TNK2_ENST00000381916.2_Missense_Mutation_p.E107G|TNK2_ENST00000428187.1_Missense_Mutation_p.E76G|TNK2_ENST00000316664.3_Missense_Mutation_p.E44G|TNK2_ENST00000392400.1_Missense_Mutation_p.E44G|TNK2_ENST00000468819.1_5'UTR	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	44	SAM-like domain.				cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CTCCAGGTCCTCATTCTTGAC	0.597																																					p.E107G													.	TNK2-957	0			c.A320G						.						137	118	125					3																	195615329		2203	4300	6503	SO:0001583	missense	10188	exon2			AGGTCCTCATTCT	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"activated Cdc42-associated kinase 1"	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.131A>G	3.37:g.195615329T>C	ENSP00000329425:p.Glu44Gly	Somatic	280	0		WXS	Illumina HiSeq	Phase_I	255	8	NM_001010938	0	0	0	0	0	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.84|18.84	3.709073|3.709073	0.68615|0.68615	.|.	.|.	ENSG00000061938|ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664;ENST00000433111;ENST00000427576|ENST00000438207	T;T;T;T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0;2.0;2.0;2.0|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72011|0.72011	0.3408|0.3408	M|M	0.78456|0.78456	2.415|2.415	0.49389|0.49389	D|D	0.999786|0.999786	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.976|.	D;D;D;D|.	0.91635|.	0.997;0.997;0.999;0.909|.	T|T	0.73620|0.73620	-0.3925|-0.3925	10|5	0.72032|.	D|.	0.01|.	.|.	9.6494|9.6494	0.39888|0.39888	0.1553:0.0:0.0:0.8447|0.1553:0.0:0.0:0.8447	.|.	44;44;107;76|.	Q07912-2;Q07912;Q07912-3;C9J1X3|.	.;ACK1_HUMAN;.;.|.	G|G	44;107;76;44;44;44;108|43	ENSP00000329425:E44G;ENSP00000371341:E107G;ENSP00000392546:E76G;ENSP00000376201:E44G;ENSP00000323216:E44G;ENSP00000395154:E44G;ENSP00000390088:E108G|.	ENSP00000323216:E44G|.	E|R	-|-	2|1	0|2	TNK2|TNK2	197099726|197099726	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.480000|0.480000	0.33159|0.33159	5.977000|5.977000	0.70492|0.70492	1.975000|1.975000	0.57531|0.57531	0.383000|0.383000	0.25322|0.25322	GAG|AGG	.		0.597	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		C	195615329	T	C	195615329	3	2	152	1	0	0	0	0	1	0	0	0	16350	1551	54	3	3090	3	TNK2	3	195615329	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	68322904	195615329	2407101	19	13646											
SLC26A1	10861	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	982690	982690	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcacggcatcgtgcacActgaggaacagctgctcctc	8	8	11	14	2	1	1	0	1	1	0	4	2	2	2	1	2	5	5	1	2	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:982690A>G	ENST00000361661.2	-	4	2414	c.2037T>C	c.(2035-2037)agT>agC	p.S679S	SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000509744.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Silent_p.S679S|SLC26A1_ENST00000398520.2_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	679	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CATCGTGCACACTGAGGAACA	0.672																																					p.S679S													.	SLC26A1-91	0			c.T2037C						.						26	23	24					4																	982690		2188	4289	6477	SO:0001819	synonymous_variant	10861	exon3			GTGCACACTGAGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.2037T>C	4.37:g.982690A>G		Somatic	106	1		WXS	Illumina HiSeq	Phase_I	114	29	NM_022042	0	0	0	0	0	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	37	CCDS33934.1																																																																																			.		0.672	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		G	982690	A	G	982690	2	3	152	1	0	0	0	0	0	0	0	1	14546	156	6	3		3	SLC26A1	4	982690	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		982690	190171586	20	13647											
ADD1	118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	2883755	2883755	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accaaatgtctacccagcagCtccgcaaggagggatggctg	11	6	12	12	1	1	0	0	0	1	0	2	2	2	2	3	3	3	4	3	3	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:2883755C>A	ENST00000398129.1	+	2	346	c.326C>A	c.(325-327)gCt>gAt	p.A109D	ADD1_ENST00000398123.2_Missense_Mutation_p.A109D|ADD1_ENST00000446856.1_Missense_Mutation_p.A109D|ADD1_ENST00000398125.1_Missense_Mutation_p.A109D|ADD1_ENST00000513328.2_Missense_Mutation_p.A109D|ADD1_ENST00000355842.3_Missense_Mutation_p.A109D|ADD1_ENST00000503455.2_Missense_Mutation_p.A109D|ADD1_ENST00000264758.7_Missense_Mutation_p.A109D			P35611	ADDA_HUMAN	adducin 1 (alpha)	109					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TACCCAGCAGCTCCGCAAGGA	0.423																																					p.A109D	Esophageal Squamous(71;505 1201 20414 34538 37449)	.											.	ADD1-92	0			c.C326A						.						152	144	147					4																	2883755		2203	4300	6503	SO:0001583	missense	118	exon3			CAGCAGCTCCGCA	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.326C>A	4.37:g.2883755C>A	ENSP00000381197:p.Ala109Asp	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	220	91	NM_014190	0	0	0	0	0	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	37	CCDS43205.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894195	0.52121	.	.	ENSG00000087274	ENST00000264758;ENST00000446856;ENST00000398125;ENST00000398124;ENST00000511797;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129	T;T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	N	0.22421	0.69	0.80722	D	1	B;B;P;B;B;P;B	0.42556	0.003;0.0;0.783;0.005;0.014;0.741;0.19	B;B;B;B;B;B;B	0.40477	0.006;0.002;0.33;0.01;0.022;0.238;0.042	T	0.04386	-1.0955	10	0.45353	T	0.12	-22.0196	18.2285	0.89926	0.0:1.0:0.0:0.0	.	109;109;109;109;109;109;109	E7ENY0;B4DI79;Q86XM2;P35611;P35611-3;P35611-2;A2A3N8	.;.;.;ADDA_HUMAN;.;.;.	D	109	ENSP00000264758:A109D;ENSP00000399828:A109D;ENSP00000381193:A109D;ENSP00000421918:A109D;ENSP00000421907:A109D;ENSP00000423024:A109D;ENSP00000348100:A109D;ENSP00000381191:A109D;ENSP00000381197:A109D	ENSP00000264758:A109D	A	+	2	0	ADD1	2853553	1.000000	0.71417	0.863000	0.33907	0.601000	0.36947	5.634000	0.67833	2.540000	0.85666	0.491000	0.48974	GCT	.		0.423	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		A	2883755	C	A	2883755	3	1	152	1	0	0	0	0	1	0	0	0	304	797	28	4	332	4	ADD1	4	2883755	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	1901065	2883755	188270521	21	13648											
SLC34A2	10568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	25676246	25676246	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaatgcattgaggagttcaCtccaggtcaggacttggggc	9	9	14	9	0	2	1	2	1	0	0	3	3	3	3	1	5	1	3	1	5	1	3	rs375377923		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:25676246C>G	ENST00000382051.3	+	12	1503	c.1453C>G	c.(1453-1455)Ctc>Gtc	p.L485V	SLC34A2_ENST00000504570.1_Missense_Mutation_p.L484V|SLC34A2_ENST00000503434.1_Missense_Mutation_p.L484V	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	485					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				GAGGAGTTCACTCCAGGTCAG	0.602			T	ROS1	NSCLC																																p.L485V		.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2-95	0			c.C1453G						.						69	74	72					4																	25676246		2203	4300	6503	SO:0001583	missense	10568	exon12			AGTTCACTCCAGG	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.1453C>G	4.37:g.25676246C>G	ENSP00000371483:p.Leu485Val	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	206	80	NM_006424	0	0	0	0	0	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	37	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	C	3.915	-0.019199	0.07634	.	.	ENSG00000157765	ENST00000504570;ENST00000382051;ENST00000503434	D;D;D	0.86497	-2.13;-2.13;-2.13	5.31	3.54	0.40534	.	0.068142	0.64402	D	0.000012	D	0.84079	0.5393	L	0.55103	1.725	0.42232	D	0.991895	P;P	0.35944	0.473;0.529	B;P	0.44696	0.336;0.458	T	0.78534	-0.2167	10	0.37606	T	0.19	-25.8301	2.7152	0.05185	0.3196:0.4244:0.1554:0.1006	.	484;485	O95436-2;O95436	.;NPT2B_HUMAN	V	484;485;484	ENSP00000425501:L484V;ENSP00000371483:L485V;ENSP00000423021:L484V	ENSP00000371483:L485V	L	+	1	0	SLC34A2	25285344	0.105000	0.21958	0.623000	0.29173	0.023000	0.10783	0.614000	0.24314	0.698000	0.31739	0.561000	0.74099	CTC	.		0.602	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		G	25676246	C	G	25676246	3	3	152	1	0	0	0	0	1	0	0	0	14600	565	20	4	1495	4	SLC34A2	4	25676246	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	22792491	25676246	165478030	22	13649											
CWH43	80157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	49032879	49032879	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttggagagtgatgcttcTaagccctatatggggaacaa	12	12	11	6	0	1	2	0	1	1	1	1	4	1	3	1	3	3	1	1	3	5	6			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:49032879T>G	ENST00000226432.4	+	11	1593	c.1410T>G	c.(1408-1410)tcT>tcG	p.S470S	CWH43_ENST00000513409.1_Silent_p.S443S	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	470					GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						GTGATGCTTCTAAGCCCTATA	0.403																																					p.S470S		.											.	CWH43-93	0			c.T1410G						.						130	131	130					4																	49032879		2203	4300	6503	SO:0001819	synonymous_variant	80157	exon11			TGCTTCTAAGCCC		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.1410T>G	4.37:g.49032879T>G		Somatic	142	0		WXS	Illumina HiSeq	Phase_I	115	41	NM_025087	0	0	0	0	0	B2RPD7	Silent	SNP	ENST00000226432.4	37	CCDS3486.1																																																																																			.		0.403	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		G	49032879	T	G	49032879	2	3	152	1	0	0	0	0	0	0	0	1	4079	1509	53	5		5	CWH43	4	49032879	Silent	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	23356633	49032879	142121397	23	13650											
PRKG2	5593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	82061797	82061797	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttatacacttcatagcaaaAgcaacattctcattttttac	14	15	2	10	0	2	0	2	0	1	0	3	0	2	0	0	0	5	2	0	0	7	8			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:82061797A>T	ENST00000395578.1	-	12	1550	c.1434T>A	c.(1432-1434)gcT>gcA	p.A478A	PRKG2_ENST00000264399.1_Silent_p.A478A|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_Silent_p.A58A|PRKG2_ENST00000418486.2_Silent_p.A449A			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	478	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TCATAGCAAAAGCAACATTCT	0.353																																					p.A478A		.											.	PRKG2-524	0			c.T1434A						.						130	116	121					4																	82061797		2203	4300	6503	SO:0001819	synonymous_variant	5593	exon11			AGCAAAAGCAACA	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1434T>A	4.37:g.82061797A>T		Somatic	139	0		WXS	Illumina HiSeq	Phase_I	156	37	NM_006259	0	0	0	0	0	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																			.		0.353	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		T	82061797	A	T	82061797	2	4	152	1	0	0	0	0	0	0	0	1	12552	59	3	5		5	PRKG2	4	82061797	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	33028918	82061797	109092479	24	13651											
DSPP	1834	bcgsc.ca	37	chr4	88537018	88537018	+	Silent	SNP	T	T	C																															gacagcagcgacagcagtgaTagcagtgacagcagtgacag																								rs370264407		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:88537018T>C	ENST00000282478.7	+	4	3237	c.3204T>C	c.(3202-3204)gaT>gaC	p.D1068D	DSPP_ENST00000399271.1_Silent_p.D1068D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1068	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagcagtgaca	0.532																																					p.D1068D													.	DSPP-90	0			c.T3204C						.	T		27,3131		0,27,1552	54	66	62		3204	0.6	0.3	4	dbSNP_134	62	95,5593		2,91,2751	no	coding-synonymous	DSPP	NM_014208.3		2,118,4303	CC,CT,TT		1.6702,0.855,1.3792		1068/1302	88537018	122,8724	1579	2844	4423	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3204T>C	4.37:g.88537018T>C		Somatic	274	8		WXS	Illumina HiSeq	Phase_1	361	24	NM_014208	0	0	0	0	0	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.532	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537018	T	C	88537018	2	2	152	1	0	0	0	0	0	0	0	1	4793	1403	49	3		3	DSPP	4	88537018	Silent	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	6475221	88537018	102617258	25	13652	146	2									
DSPP	1834	bcgsc.ca	37	chr4	88537027	88537027	+	Missense_Mutation	SNP	C	C	A																															gacagcagtgatagcagtgaCagcagtgacagcagcgacag																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:88537027C>A	ENST00000282478.7	+	4	3246	c.3213C>A	c.(3211-3213)gaC>gaA	p.D1071E	DSPP_ENST00000399271.1_Missense_Mutation_p.D1071E|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1071	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		atagcagtgacagcagtgaca	0.542																																					p.D1071E													.	DSPP-90	0			c.C3213A						.						56	66	63					4																	88537027		1577	2848	4425	SO:0001583	missense	1834	exon5			CAGTGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3213C>A	4.37:g.88537027C>A	ENSP00000282478:p.Asp1071Glu	Somatic	253	1		WXS	Illumina HiSeq	Phase_1	338	20	NM_014208	0	0	0	0	0	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	c	2.636	-0.285341	0.05605	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88124	-2.34;-2.34	1.15	-2.31	0.06765	.	.	.	.	.	T	0.69196	0.3084	L	0.38175	1.15	0.09310	N	1	P	0.46952	0.887	B	0.36766	0.232	T	0.66364	-0.5942	9	0.02654	T	1	.	2.058	0.03586	0.2533:0.3578:0.0:0.3889	.	1071	Q9NZW4	DSPP_HUMAN	E	1071	ENSP00000382213:D1071E;ENSP00000282478:D1071E	ENSP00000282478:D1071E	D	+	3	2	DSPP	88756051	0.029000	0.19370	0.018000	0.16275	0.040000	0.13550	-0.117000	0.10708	-0.986000	0.03498	0.282000	0.19409	GAC	.		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88537027	C	A	88537027	3	1	152	1	0	0	0	0	1	0	0	0	4793	477	17	4	3227	4	DSPP	4	88537027	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	9	88537027	102617249	26	13653	146	2									
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	187627969	187627969	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaaactggctttcccttgtCtttggccctcacagtgagat	8	13	9	11	0	2	2	1	1	1	2	3	3	3	2	2	2	1	1	2	2	1	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:187627969C>T	ENST00000441802.2	-	2	3222	c.3013G>A	c.(3013-3015)Gac>Aac	p.D1005N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1005	Cadherin 8. {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						TTTCCCTTGTCTTTGGCCCTC	0.458										HNSCC(5;0.00058)																											p.D1005N	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.G3013A						.						108	110	109					4																	187627969		1971	4147	6118	SO:0001583	missense	2195	exon2			CCTTGTCTTTGGC	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.3013G>A	4.37:g.187627969C>T	ENSP00000406229:p.Asp1005Asn	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	262	91	NM_005245	0	0	0	2	2		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374390	0.82573	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.65364	-0.15	4.55	4.55	0.56014	Cadherin (5);Cadherin-like (1);	0.106734	0.64402	D	0.000008	T	0.79191	0.4404	M	0.82132	2.575	0.80722	D	1	D	0.59767	0.986	D	0.63703	0.917	T	0.82963	-0.0196	10	0.87932	D	0	.	17.8551	0.88760	0.0:1.0:0.0:0.0	.	1005	Q14517	FAT1_HUMAN	N	1005	ENSP00000406229:D1005N	ENSP00000260147:D1005N	D	-	1	0	FAT1	187864963	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	7.606000	0.82863	2.508000	0.84585	0.491000	0.48974	GAC	.		0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187627969	C	T	187627969	3	4	152	1	0	0	0	0	1	0	0	0	5708	913	32	2	10857	2	FAT1	4	187627969	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	99090942	187627969	3526307	27	13654											
SKIV2L2	23517	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	54635905	54635905	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccaattaaggctctgAgtaaccaaaaataccgtgaa	16	7	7	11	1	1	2	0	2	1	0	1	2	1	2	4	1	3	2	4	1	7	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:54635905A>G	ENST00000230640.5	+	6	837	c.583A>G	c.(583-585)Agt>Ggt	p.S195G	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.S94G	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	195	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TAAGGCTCTGAGTAACCAAAA	0.363																																					p.S195G	Melanoma(2;92 134 23744 29976 33782)	.											.	SKIV2L2-92	0			c.A583G						.						141	137	139					5																	54635905		2203	4300	6503	SO:0001583	missense	23517	exon6			GCTCTGAGTAACC	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 118"		"KIAA0052"	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.583A>G	5.37:g.54635905A>G	ENSP00000230640:p.Ser195Gly	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	80	24	NM_015360	0	0	0	0	0	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	37	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543682	0.86022	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.15139	2.45;2.45	5.98	5.98	0.97165	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.088703	0.85682	D	0.000000	T	0.55289	0.1911	H	0.94345	3.525	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.68704	-0.5338	10	0.87932	D	0	-18.2935	16.4566	0.84019	1.0:0.0:0.0:0.0	.	94;195	F5H7E2;P42285	.;SK2L2_HUMAN	G	195;94	ENSP00000230640:S195G;ENSP00000442583:S94G	ENSP00000230640:S195G	S	+	1	0	SKIV2L2	54671662	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	7.102000	0.77005	2.293000	0.77203	0.477000	0.44152	AGT	.		0.363	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54635905	A	G	54635905	3	3	152	1	0	0	0	0	1	0	0	0	14392	304	11	3	605	3	SKIV2L2	5	54635905	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		54635905	126279355	28	13655											
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	82815685	82815685	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgtaactgaaacaccattGgtaactgcaagaatgatcct	14	10	7	10	0	0	3	0	2	0	1	1	3	1	3	3	1	4	3	3	1	5	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:82815685G>A	ENST00000265077.3	+	7	2125	c.1560G>A	c.(1558-1560)ttG>ttA	p.L520L	VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Silent_p.L520L|VCAN_ENST00000512590.2_Silent_p.L472L	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	520	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAACACCATTGGTAACTGCAA	0.393																																					p.L520L		.											.	VCAN-238	0			c.G1560A						.						127	127	127					5																	82815685		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon7			ACCATTGGTAACT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.1560G>A	5.37:g.82815685G>A		Somatic	148	0		WXS	Illumina HiSeq	Phase_I	134	43	NM_004385	0	0	0	0	0	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			.		0.393	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82815685	G	A	82815685	2	1	152	1	0	0	0	0	0	0	0	1	17171	1339	47	2		2	VCAN	5	82815685	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	28179780	82815685	98099575	29	13656											
VCAN	1462	broad.mit.edu	37	chr5	82836607	82836608	+	Frame_Shift_Del	DEL	AG	AG	-																															gacattcttggaatgcaaacAgatatagatacagaggtacc																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:82836607_82836608delAG	ENST00000265077.3	+	8	8350_8351	c.7785_7786delAG	c.(7783-7788)acagatfs	p.D2596fs	VCAN_ENST00000343200.5_Frame_Shift_Del_p.D1609fs|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2596	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GAATGCAAACAGATATAGATAC	0.376																																					p.2595_2596del													.	VCAN-238	0			c.7785_7786del						.																																			SO:0001589	frameshift_variant	1462	exon8			GCAAACAGATATA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	2464	protein-coding gene	gene with protein product	"versican proteoglycan"	118661	"chondroitin sulfate proteoglycan 2"	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7785_7786delAG	5.37:g.82836607_82836608delAG	ENSP00000265077:p.Asp2596fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	139	8	NM_004385	0	0	0	0	0	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Frame_Shift_Del	DEL	ENST00000265077.3	37	CCDS4060.1																																																																																			.		0.376	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		-	82836608	AG	-	82836607	7	5	152	1	0	1	0	1	0	0	0	0	17171	175	7	0	7811	0	VCAN	5	82836607	Frame_Shift_Del	DEL	AG	TCGA-MH-A562-01A-11D-A26P-10	20922	82836607	98078653	30	13657											
CHD1	1105	ucsc.edu;bcgsc.ca	37	chr5	98238644	98238644	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacctcacttgatgagtcatCggaatcttcactgctagagg	10	11	10	10	1	4	3	3	2	1	1	5	5	4	4	1	2	1	1	1	2	2	3	rs368581644		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:98238644C>T	ENST00000284049.3	-	4	546	c.397G>A	c.(397-399)Gat>Aat	p.D133N		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	133	Ser-rich.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GATGAGTCATCGGAATCTTCA	0.294																																					p.D133N													.	CHD1-274	0			c.G397A						.	C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	77	74	75		397	4.8	1	5		75	0,8584		0,0,4292	no	missense	CHD1	NM_001270.2	23	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	133/1711	98238644	1,12989	2203	4292	6495	SO:0001583	missense	1105	exon4			AGTCATCGGAATC	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.397G>A	5.37:g.98238644C>T	ENSP00000284049:p.Asp133Asn	Somatic	37	0		WXS	Illumina HiSeq		37	4	NM_001270	0	0	0	0	0	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.809530	0.31961	2.27E-4	0.0	ENSG00000153922	ENST00000284049;ENST00000540681	D	0.89746	-2.56	4.84	4.84	0.62591	.	0.000000	0.34460	U	0.003957	D	0.86674	0.5989	L	0.55481	1.735	0.58432	D	0.999995	B	0.10296	0.003	B	0.04013	0.001	T	0.81967	-0.0690	10	0.25751	T	0.34	.	18.4531	0.90711	0.0:1.0:0.0:0.0	.	133	O14646	CHD1_HUMAN	N	133	ENSP00000284049:D133N	ENSP00000284049:D133N	D	-	1	0	CHD1	98266544	0.998000	0.40836	0.998000	0.56505	0.887000	0.51463	4.282000	0.58971	2.632000	0.89209	0.462000	0.41574	GAT	.		0.294	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		T	98238644	C	T	98238644	3	4	152	1	0	0	0	0	1	0	0	0	3329	884	31	1	4863	1	CHD1	5	98238644	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	15402037	98238644	82676616	31	13658											
BTNL8	79908	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	180338541	180338541	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctctgaccgtccaagagaaCgccgggagcatatcctgttc	9	9	10	13	3	1	2	0	1	1	1	5	4	3	3	4	1	2	2	4	1	3	2	rs377605273		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:180338541C>T	ENST00000340184.4	+	3	806	c.600C>T	c.(598-600)aaC>aaT	p.N200N	BTNL8_ENST00000508408.1_Silent_p.N200N|BTNL8_ENST00000533815.2_Silent_p.N16N|BTNL8_ENST00000511704.1_Silent_p.N84N|BTNL8_ENST00000231229.4_Silent_p.N200N|BTNL8_ENST00000400707.3_Silent_p.N75N|BTNL8_ENST00000505126.1_5'UTR|Y_RNA_ENST00000410920.1_RNA	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	200	Ig-like V-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCAAGAGAACGCCGGGAGCA	0.537																																					p.N200N													.	BTNL8-24	0			c.C600T						.	C	,,,,,	0,4406		0,0,2203	82	80	80		600,252,600,225,48,600	-7.4	0	5		80	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	,,,,,	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	,,,,,	200/501,84/385,200/341,75/376,16/317,200/348	180338541	1,12997	2203	4296	6499	SO:0001819	synonymous_variant	79908	exon3			AGAGAACGCCGGG	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.600C>T	5.37:g.180338541C>T		Somatic	83	1		WXS	Illumina HiSeq	Phase_I	96	30	NM_001159708	0	0	0	0	0	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																			.		0.537	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850		T	180338541	C	T	180338541	2	4	152	1	0	0	0	0	0	0	0	1	1570	535	19	1		1	BTNL8	5	180338541	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	82099897	180338541	576719	32	13659											
PHACTR1	221692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	13283687	13283687	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccacggtggaagagcttcggGaaagaaagatcctcatccgc	12	6	12	11	3	1	3	1	0	0	3	4	5	3	5	3	3	1	1	3	3	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:13283687G>C	ENST00000379335.3	+	3	340	c.235G>C	c.(235-237)Gaa>Caa	p.E79Q	RP1-257A7.4_ENST00000606150.1_RNA|PHACTR1_ENST00000332995.7_Missense_Mutation_p.E515Q|PHACTR1_ENST00000457702.2_Missense_Mutation_p.E370Q|PHACTR1_ENST00000379329.1_Missense_Mutation_p.E79Q|RP1-257A7.4_ENST00000399446.2_RNA			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	515					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			AGAGCTTCGGGAAAGAAAGAT	0.597																																					p.E515Q		.											.	.	0			c.G1543C						.						125	138	134					6																	13283687		2033	4200	6233	SO:0001583	missense	221692	exon13			CTTCGGGAAAGAA	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379335.3:c.235G>C	6.37:g.13283687G>C	ENSP00000368639:p.Glu79Gln	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	124	43	NM_030948	0	0	2	2	0	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379335.3	37		.	.	.	.	.	.	.	.	.	.	G	21.1	4.095811	0.76870	.	.	ENSG00000112137	ENST00000332995;ENST00000457702;ENST00000379335;ENST00000379329	T;T	0.32988	1.43;1.43	5.78	5.78	0.91487	.	0.094270	0.64402	D	0.000001	T	0.32224	0.0822	N	0.21448	0.665	0.80722	D	1	D	0.63046	0.992	D	0.67548	0.952	T	0.03193	-1.1062	10	0.33940	T	0.23	-15.365	19.0064	0.92852	0.0:0.0:1.0:0.0	.	515	Q9C0D0	PHAR1_HUMAN	Q	515;370;79;79	ENSP00000329880:E515Q;ENSP00000397669:E370Q	ENSP00000329880:E515Q	E	+	1	0	PHACTR1	13391666	1.000000	0.71417	0.985000	0.45067	0.919000	0.55068	9.623000	0.98386	2.738000	0.93877	0.655000	0.94253	GAA	.		0.597	PHACTR1-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000039878.1	XM_166420		C	13283687	G	C	13283687	3	2	152	1	0	0	0	0	1	0	0	0	11835	1175	41	4	1585	4	PHACTR1	6	13283687	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		13283687	157831380	33	13660											
ZFP57	346171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	29643249	29643249	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgattagctctggcttaTgcagaaagattctggctgat	9	14	12	6	0	2	4	0	2	2	2	2	4	2	4	0	3	2	4	0	3	3	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:29643249T>C	ENST00000488757.1	-	3	416	c.266A>G	c.(265-267)cAt>cGt	p.H89R	ZFP57_ENST00000376881.3_Missense_Mutation_p.H69R|ZFP57_ENST00000376883.1_Missense_Mutation_p.H69R	NM_001109809.2	NP_001103279.2	Q9NU63	ZFP57_HUMAN	ZFP57 zinc finger protein	61					DNA methylation involved in embryo development (GO:0043045)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system development (GO:0007422)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	nuclear heterochromatin (GO:0005720)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(16)|ovary(4)|skin(4)|urinary_tract(5)	44						CTCTGGCTTATGCAGAAAGAT	0.483																																					p.H89R		.											.	ZFP57-5	0			c.A266G						.						221	207	212					6																	29643249		1947	4153	6100	SO:0001583	missense	346171	exon3			GGCTTATGCAGAA	AL050328	CCDS43436.1, CCDS43436.2	6p22.1	2013-01-08	2012-11-27	2005-07-20	ENSG00000204644	ENSG00000204644		"Zinc fingers, C2H2-type", "-"	18791	protein-coding gene	gene with protein product		612192	"chromosome 6 open reading frame 40", "zinc finger protein 57 homolog (mouse)"	C6orf40			Standard	NM_001109809		Approved	ZNF698, bA145L22, bA145L22.2	uc011dlw.2	Q9NU63	OTTHUMG00000031158	ENST00000488757.1:c.266A>G	6.37:g.29643249T>C	ENSP00000418259:p.His89Arg	Somatic	223	0		WXS	Illumina HiSeq	Phase_I	218	91	NM_001109809	0	0	0	0	0	B0S894|B0V254|B2RXJ7|Q5SSB1	Missense_Mutation	SNP	ENST00000488757.1	37	CCDS43436.2	.	.	.	.	.	.	.	.	.	.	T	4.922	0.171264	0.09391	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	T;T;T	0.00768	5.72;5.72;5.72	4.36	0.288	0.15719	.	0.866899	0.09598	N	0.780620	T	0.00210	0.0006	N	0.14661	0.345	0.09310	N	1	B;B	0.25169	0.119;0.119	B;B	0.23574	0.047;0.047	T	0.25152	-1.0140	10	0.34782	T	0.22	0.7587	4.8209	0.13390	0.173:0.0:0.599:0.2281	.	89;69	Q9NU63-3;Q9NU63-2	.;.	R	89;69;69	ENSP00000418259:H89R;ENSP00000366078:H69R;ENSP00000366080:H69R	ENSP00000366078:H69R	H	-	2	0	ZFP57	29751228	0.003000	0.15002	0.001000	0.08648	0.153000	0.21895	0.428000	0.21395	-0.071000	0.12886	-0.313000	0.08912	CAT	.		0.483	ZFP57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355773.1	XM_294093		C	29643249	T	C	29643249	3	2	152	1	0	0	0	0	1	0	0	0	17683	1464	51	3	1352	3	ZFP57	6	29643249	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	16359562	29643249	141471818	34	13661											
BAT5	7920	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31657863	31657863	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggtctcaccgtgcttcCagcaaagcctggatgattcc	9	10	10	12	1	1	2	1	1	1	1	4	3	3	3	4	2	3	2	4	2	1	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:31657863C>T	ENST00000395952.3	-	11	1111	c.949G>A	c.(949-951)Gga>Aga	p.G317R	ABHD16A_ENST00000440843.2_Missense_Mutation_p.G284R|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000375842.4_Missense_Mutation_p.G98R	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	317						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						ACCGTGCTTCCAGCAAAGCCT	0.547																																					p.G317R		.											.	ABHD16A-91	0			c.G949A						.						68	56	60					6																	31657863		1511	2709	4220	SO:0001583	missense	7920	exon11			TGCTTCCAGCAAA	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.949G>A	6.37:g.31657863C>T	ENSP00000379282:p.Gly317Arg	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	76	25	NM_021160	0	0	0	0	0	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Missense_Mutation	SNP	ENST00000395952.3	37	CCDS4713.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.733977	0.89482	.	.	ENSG00000204427	ENST00000395952;ENST00000375842;ENST00000440843	T;T;T	0.21191	2.02;2.02;2.02	5.4	5.4	0.78164	.	0.108527	0.64402	D	0.000008	T	0.30792	0.0776	L	0.55834	1.745	0.80722	D	1	D;D	0.76494	0.96;0.999	P;D	0.71656	0.772;0.974	T	0.00909	-1.1518	10	0.30078	T	0.28	-9.9061	16.6668	0.85255	0.0:1.0:0.0:0.0	.	284;317	B7Z4R6;O95870	.;ABHGA_HUMAN	R	317;98;284	ENSP00000379282:G317R;ENSP00000365002:G98R;ENSP00000410347:G284R	ENSP00000365002:G98R	G	-	1	0	ABHD16A	31765842	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.008000	0.63991	2.536000	0.85505	0.655000	0.94253	GGA	.		0.547	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			T	31657863	C	T	31657863	3	4	152	1	0	0	0	0	1	0	0	0	1325	603	21	2	767	2	BAT5	6	31657863	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	2014614	31657863	139457204	35	13662											
STXBP5	134957	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	147648298	147648298	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaatggcattgctatggttGactacctccagaaagcagtg	11	10	11	9	0	0	2	0	1	0	1	1	2	1	2	2	2	3	5	2	2	4	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:147648298G>C	ENST00000321680.6	+	18	1966	c.1966G>C	c.(1966-1968)Gac>Cac	p.D656H	STXBP5_ENST00000367480.3_Missense_Mutation_p.D656H|STXBP5_ENST00000367481.3_Missense_Mutation_p.D656H|STXBP5_ENST00000179882.6_Missense_Mutation_p.D327H	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	656					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGCTATGGTTGACTACCTCCA	0.403																																					p.D656H													.	STXBP5-90	0			c.G1966C						.						147	139	142					6																	147648298		2203	4300	6503	SO:0001583	missense	134957	exon18			ATGGTTGACTACC	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"WD repeat domain containing"	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1966G>C	6.37:g.147648298G>C	ENSP00000321826:p.Asp656His	Somatic	83	1		WXS	Illumina HiSeq	Phase_I	86	28	NM_139244	0	0	0	0	0	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.016315	0.93404	.	.	ENSG00000164506	ENST00000367479;ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.74737	0.99;1.31;0.85;-0.87	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.87014	0.6072	M	0.83774	2.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.87084	0.2168	10	0.87932	D	0	.	20.6525	0.99598	0.0:0.0:1.0:0.0	.	656;656;327	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	H	3;656;656;656;327	ENSP00000356451:D656H;ENSP00000321826:D656H;ENSP00000356450:D656H;ENSP00000179882:D327H	ENSP00000179882:D327H	D	+	1	0	STXBP5	147689991	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	9.813000	0.99286	2.890000	0.99128	0.585000	0.79938	GAC	.		0.403	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			C	147648298	G	C	147648298	3	2	152	1	0	0	0	0	1	0	0	0	15388	1290	45	4	2036	4	STXBP5	6	147648298	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	115990435	147648298	23466769	36	13663											
GRB10	2887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	50742288	50742288	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtctgactgcatgctgcaGgccgagtacaggctctccag	7	9	13	12	1	2	1	0	1	2	0	3	2	2	1	2	2	4	5	2	2	1	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr7:50742288G>A	ENST00000401949.1	-	6	676	c.207C>T	c.(205-207)gcC>gcT	p.A69A	GRB10_ENST00000398812.2_Silent_p.A69A|GRB10_ENST00000398810.2_Silent_p.A11A|GRB10_ENST00000439599.1_Silent_p.A63A|GRB10_ENST00000357271.5_Silent_p.A69A|GRB10_ENST00000402497.1_Silent_p.A11A|GRB10_ENST00000402578.1_Silent_p.A11A|GRB10_ENST00000403097.1_Silent_p.A63A|GRB10_ENST00000335866.3_Silent_p.A11A|GRB10_ENST00000406641.1_Silent_p.A11A|GRB10_ENST00000407526.1_Silent_p.A11A			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	69					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					GCATGCTGCAGGCCGAGTACA	0.587									Russell-Silver syndrome																												p.A69A		.											.	GRB10-1272	0			c.C207T						.						57	63	61					7																	50742288		2066	4214	6280	SO:0001819	synonymous_variant	2887	exon3	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	GCTGCAGGCCGAG		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.207C>T	7.37:g.50742288G>A		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	91	8	NM_005311	0	0	2	2	0	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																			.		0.587	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			A	50742288	G	A	50742288	2	1	152	1	0	0	0	0	0	0	0	1	6777	987	35	2		2	GRB10	7	50742288	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		50742288	108396375	37	13664											
WDR91	29062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	134893687	134893687	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaaccaatccttccactcagCctggttctggagttccgtgg	8	11	9	13	1	2	0	1	0	1	0	5	1	5	1	5	3	2	2	5	3	2	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr7:134893687C>A	ENST00000354475.4	-	3	398	c.367G>T	c.(367-369)Gct>Tct	p.A123S	WDR91_ENST00000485942.1_5'Flank|WDR91_ENST00000344400.5_Missense_Mutation_p.A123S|WDR91_ENST00000423565.1_Missense_Mutation_p.A88S	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	123										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						TTCCACTCAGCCTGGTTCTGG	0.537																																					p.A123S		.											.	WDR91-137	0			c.G367T						.						184	155	165					7																	134893687		2203	4300	6503	SO:0001583	missense	29062	exon3			ACTCAGCCTGGTT	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.367G>T	7.37:g.134893687C>A	ENSP00000346466:p.Ala123Ser	Somatic	290	0		WXS	Illumina HiSeq	Phase_I	521	195	NM_014149	0	0	0	3	3	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.488114	0.26686	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	D;D;D	0.91521	-2.86;-2.86;-2.86	5.77	4.89	0.63831	.	0.145674	0.64402	D	0.000009	D	0.82733	0.5101	N	0.25890	0.77	0.58432	D	0.999999	P	0.41524	0.753	B	0.35278	0.199	T	0.81028	-0.1118	10	0.18276	T	0.48	-19.4769	15.1712	0.72875	0.0:0.9322:0.0:0.0678	.	123	A4D1P6	WDR91_HUMAN	S	123;123;88	ENSP00000340877:A123S;ENSP00000346466:A123S;ENSP00000392555:A88S	ENSP00000340877:A123S	A	-	1	0	WDR91	134544227	1.000000	0.71417	0.998000	0.56505	0.041000	0.13682	4.739000	0.62080	1.587000	0.49959	-0.145000	0.13849	GCT	.		0.537	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		A	134893687	C	A	134893687	3	1	152	1	0	0	0	0	1	0	0	0	17371	739	26	4	1928	4	WDR91	7	134893687	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	84151399	134893687	24244976	38	13665											
CSMD1	64478	bcgsc.ca	37	chr8	2832127	2832127	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcgttggcagggaccccTgggtgtccacacgatatagc	8	7	14	12	3	0	0	0	0	0	0	1	2	1	1	3	4	1	2	3	4	2	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr8:2832127T>C	ENST00000520002.1	-	57	9144	c.8589A>G	c.(8587-8589)ccA>ccG	p.P2863P	CSMD1_ENST00000537824.1_Silent_p.P2862P|CSMD1_ENST00000602723.1_Silent_p.P2805P|CSMD1_ENST00000400186.3_Silent_p.P2805P|CSMD1_ENST00000542608.1_Silent_p.P2804P|CSMD1_ENST00000602557.1_Silent_p.P2863P			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2863	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGGGACCCCTGGGTGTCCAC	0.502																																					p.P2862P													.	CSMD1-86	0			c.A8586G						.						32	34	34					8																	2832127		1949	4131	6080	SO:0001819	synonymous_variant	64478	exon56			GACCCCTGGGTGT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.8589A>G	8.37:g.2832127T>C		Somatic	64	0		WXS	Illumina HiSeq	Phase_1	54	4	NM_033225	0	0	0	0	0	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	T	1.147	-0.647742	0.03506	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.81	-9.87	0.00470	.	.	.	.	.	T	0.44180	0.1281	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53514	-0.8428	4	.	.	.	.	7.2183	0.25971	0.374:0.3553:0.0:0.2707	.	.	.	.	G	2280	.	.	R	-	1	2	CSMD1	2819534	0.049000	0.20398	0.145000	0.22337	0.041000	0.13682	-0.674000	0.05233	-1.259000	0.02468	0.533000	0.62120	AGG	.		0.502	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	2832127	T	C	2832127	2	2	152	1	0	0	0	0	0	0	0	1	3950	1567	55	3		3	CSMD1	8	2832127	Silent	SNP	T	TCGA-MH-A562-01A-11D-A26P-10		2832127	143531895	39	13666											
ZFHX4	79776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	77616434	77616434	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtgccagagaaagttgcaggGatggagcctgacagggaaaa	14	5	16	6	0	0	2	0	1	0	1	0	6	0	5	2	3	3	2	2	3	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr8:77616434G>A	ENST00000521891.2	+	2	559	c.111G>A	c.(109-111)ggG>ggA	p.G37G	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Silent_p.G37G|ZFHX4_ENST00000455469.2_Silent_p.G37G|ZFHX4_ENST00000518282.1_Silent_p.G37G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	37					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAGTTGCAGGGATGGAGCCTG	0.502										HNSCC(33;0.089)																											p.G37G		.											.	ZFHX4-98	0			c.G111A						.						64	67	66					8																	77616434		2025	4211	6236	SO:0001819	synonymous_variant	79776	exon2			TGCAGGGATGGAG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.111G>A	8.37:g.77616434G>A		Somatic	238	0		WXS	Illumina HiSeq	Phase_I	274	84	NM_024721	0	0	0	0	0	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																			.		0.502	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77616434	G	A	77616434	2	1	152	1	0	0	0	0	0	0	0	1	17667	1161	41	2		2	ZFHX4	8	77616434	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	74784307	77616434	68747588	40	13667											
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145654714	145654714	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaggggaccctggacggCgcagcctgcggaggggaaga	8	2	19	12	3	0	1	0	0	0	1	0	5	0	5	3	7	2	1	3	7	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr8:145654714C>T	ENST00000409379.3	-	26	3978	c.3949G>A	c.(3949-3951)Gcc>Acc	p.A1317T	VPS28_ENST00000529182.1_5'Flank|VPS28_ENST00000526054.1_5'Flank|VPS28_ENST00000526734.1_5'Flank|VPS28_ENST00000377348.2_5'Flank|VPS28_ENST00000292510.4_5'Flank	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1317					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CCCTGGACGGCGCAGCCTGCG	0.706																																					p.A1317T		.											.	TONSL-92	0			c.G3949A						.						5	5	5					8																	145654714		2056	4038	6094	SO:0001583	missense	4796	exon26			GGACGGCGCAGCC		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"Ankyrin repeat domain containing"	7801	protein-coding gene	gene with protein product		604546	"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3949G>A	8.37:g.145654714C>T	ENSP00000386239:p.Ala1317Thr	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	5	NM_013432	0	0	0	0	0	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	c	8.974	0.973627	0.18736	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.52983	0.64	5.39	0.26	0.15588	.	0.776034	0.12482	N	0.465083	T	0.35624	0.0938	L	0.47016	1.485	0.09310	N	1	B	0.20052	0.041	B	0.06405	0.002	T	0.28522	-1.0041	10	0.54805	T	0.06	-3.5453	5.4749	0.16690	0.5793:0.2411:0.0:0.1796	.	1317	Q96HA7	TONSL_HUMAN	T	1317;1316	ENSP00000386239:A1317T	ENSP00000386239:A1317T	A	-	1	0	TONSL	145625522	0.000000	0.05858	0.421000	0.26609	0.136000	0.21042	-0.691000	0.05133	0.097000	0.17492	0.511000	0.50034	GCC	.		0.706	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		T	145654714	C	T	145654714	3	4	152	1	0	0	0	0	1	0	0	0	10408	768	27	1	191	1	NFKBIL2	8	145654714	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	68038280	145654714	709308	41	13668											
CD274	29126	broad.mit.edu	37	chr9	5457410	5457410	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gactacaagcgaattactgtGaaagtcaatggtaagaatta	17	10	9	5	1	1	2	1	1	0	1	1	4	1	2	0	1	3	1	0	1	9	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr9:5457410G>A	ENST00000381577.3	+	3	470	c.384G>A	c.(382-384)gtG>gtA	p.V128V	CD274_ENST00000498261.1_3'UTR|CD274_ENST00000381573.4_Intron	NM_014143.3	NP_054862.1	Q9NZQ7	PD1L1_HUMAN	CD274 molecule	128					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		GAATTACTGTGAAAGTCAATG	0.398			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.V128V				Dom	yes		9	9p24	29126	CD274 molecule		L	.	CD274-227	0			c.G384A						.						38	41	40					9																	5457410		2203	4300	6503	SO:0001819	synonymous_variant	29126	exon3			TACTGTGAAAGTC	AF177937	CCDS6464.1, CCDS59118.1	9p24.1	2014-01-30	2006-03-28	2005-02-25	ENSG00000120217	ENSG00000120217		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Endogenous ligands"	17635	protein-coding gene	gene with protein product	"B7 homolog 1"	605402	"programmed cell death 1 ligand 1", "CD274 antigen"	PDCD1LG1		11015443, 10581077	Standard	NM_014143		Approved	B7-H, B7H1, PD-L1, PDL1, B7-H1	uc003zje.3	Q9NZQ7	OTTHUMG00000019503	ENST00000381577.3:c.384G>A	9.37:g.5457410G>A		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	101	3	NM_014143	0	0	0	0	0	B2RBA2|B4DU27|Q14CJ2|Q2V8D5|Q66RK1|Q6WEX4|Q9NUZ5	Silent	SNP	ENST00000381577.3	37	CCDS6464.1																																																																																			.		0.398	CD274-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051631.2	NM_014143		A	5457410	G	A	5457410	2	1	152	1	0	0	0	0	0	0	0	1	2997	1277	45	2		2	CD274	9	5457410	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		5457410	135756021	42	13669											
FOXD4L5	653427	broad.mit.edu	37	chr9	70177822	70177822	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgcagccccggctggagTgactgctctaggaactgctg	7	8	13	13	1	1	1	0	1	1	0	1	3	1	3	3	3	5	4	3	3	2	1	rs199878768	byFrequency	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr9:70177822T>C	ENST00000377420.1	-	1	993	c.162A>G	c.(160-162)tcA>tcG	p.S54S		NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5	54					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						CCGGCTGGAGTGACTGCTCTA	0.642													C|||	4144	0.827476	0.5461	0.9337	5008	,	,		2717	0.8869		0.9573	False		,,,				2504	0.9376				p.S54S													.	.	0			c.A162G						.						23	1	10					9																	70177822		359	613	972	SO:0001819	synonymous_variant	653427	exon1			CTGGAGTGACTGC		CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	ENST00000377420.1:c.162A>G	9.37:g.70177822T>C		Somatic	194	1		WXS	Illumina HiSeq	Phase_I	234	6	NM_001126334	0	0	0	0	0		Silent	SNP	ENST00000377420.1	37	CCDS47977.1																																																																																			C|1.000;|0.000		0.642	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037122.1	NM_001126334		C	70177822	T	C	70177822	2	2	152	1	0	0	0	0	0	0	0	1	6021	1683	59	3		3	FOXD4L5	9	70177822	Silent	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	64720412	70177822	71035609	43	13670											
NRP1	8829	ucsc.edu;bcgsc.ca	37	chr10	33543118	33543118	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccagagcttccatacatttGaaatctgaagggaaaaacag	16	8	8	9	0	1	3	0	2	1	1	2	4	2	4	2	1	3	1	2	1	5	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr10:33543118G>A	ENST00000265371.4	-	7	1344	c.819C>T	c.(817-819)ttC>ttT	p.F273F	NRP1_ENST00000374867.2_Silent_p.F273F|NRP1_ENST00000374822.4_Silent_p.F273F|NRP1_ENST00000374816.3_Silent_p.F273F|NRP1_ENST00000374821.5_Silent_p.F273F|NRP1_ENST00000374823.5_Silent_p.F273F|NRP1_ENST00000432372.2_Silent_p.F273F|NRP1_ENST00000395995.1_Silent_p.F273F|NRP1_ENST00000374875.1_Silent_p.F92F			O14786	NRP1_HUMAN	neuropilin 1	273					angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	CCATACATTTGAAATCTGAAG	0.418																																					p.F273F	Melanoma(104;886 1489 44640 45944 51153)												.	NRP1-525	0			c.C819T						.						69	67	68					10																	33543118		2203	4300	6503	SO:0001819	synonymous_variant	8829	exon6			ACATTTGAAATCT	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.819C>T	10.37:g.33543118G>A		Somatic	73	0		WXS	Illumina HiSeq		46	5	NM_001244973	0	0	0	0	0	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	G	9.065	0.995376	0.19043	.	.	ENSG00000099250	ENST00000455749	.	.	.	5.28	2.14	0.27477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-24.4103	8.6907	0.34264	0.3214:0.0:0.6786:0.0	.	.	.	.	X	74	.	.	Q	-	1	0	NRP1	33583124	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	1.436000	0.34980	0.214000	0.20742	0.650000	0.86243	CAA	.		0.418	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			A	33543118	G	A	33543118	2	1	152	1	0	0	0	0	0	0	0	1	10686	1281	45	2		2	NRP1	10	33543118	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		33543118	101991629	44	13671											
OPN4	94233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	88419072	88419072	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggcgcctacgtgcccgaggGgttgctgacatcctgctcct	5	9	13	14	3	0	1	0	1	0	0	2	2	2	1	4	3	4	3	4	3	1	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr10:88419072G>A	ENST00000241891.5	+	5	814	c.647G>A	c.(646-648)gGg>gAg	p.G216E	OPN4_ENST00000372071.2_Missense_Mutation_p.G227E	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	216					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)	p.G227V(2)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GTGCCCGAGGGGTTGCTGACA	0.612																																					p.G227E		.											.	OPN4-69	2	Substitution - Missense(2)	liver(2)	c.G680A						.						167	135	146					10																	88419072		2203	4300	6503	SO:0001583	missense	94233	exon6			CCGAGGGGTTGCT	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.647G>A	10.37:g.88419072G>A	ENSP00000241891:p.Gly216Glu	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	77	29	NM_001030015	0	0	0	0	0	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.985781	0.93044	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.70282	-0.47;-0.47;-0.47	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86694	0.5994	M	0.87269	2.87	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.89121	0.3503	10	0.87932	D	0	.	18.6376	0.91384	0.0:0.0:1.0:0.0	.	227;216;227	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	E	227;216;227	ENSP00000361141:G227E;ENSP00000241891:G216E;ENSP00000393132:G227E	ENSP00000241891:G216E	G	+	2	0	OPN4	88409052	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.705000	0.98719	2.397000	0.81536	0.655000	0.94253	GGG	.		0.612	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		A	88419072	G	A	88419072	3	1	152	1	0	0	0	0	1	0	0	0	10908	1232	43	2	702	2	OPN4	10	88419072	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	54875954	88419072	47115675	45	13672											
KCNA4	3739	hgsc.bcm.edu;broad.mit.edu	37	chr11	30034138	30034138	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagtgagcaagcctctcccGctcccgggcccgggcctggg	4	5	16	16	3	1	1	0	1	1	0	3	2	2	2	5	4	2	2	5	4	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:30034138G>A	ENST00000328224.6	-	2	1321	c.88C>T	c.(88-90)Cgg>Tgg	p.R30W	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	30					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	AGCCTCTCCCGCTCCCGGGCC	0.637																																					p.R30W		.											.	KCNA4-517	0			c.C88T						.						58	60	59					11																	30034138		1910	4113	6023	SO:0001583	missense	3739	exon2			TCTCCCGCTCCCG	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.88C>T	11.37:g.30034138G>A	ENSP00000328511:p.Arg30Trp	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	12	5	NM_002233	0	0	0	0	0		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988463	0.53934	.	.	ENSG00000182255	ENST00000328224	D	0.98012	-4.66	4.97	2.88	0.33553	Potassium channel, voltage dependent, Kv1.4, tandem inactivation (2);	269.221000	0.00166	N	0.000002	D	0.95290	0.8472	N	0.24115	0.695	0.47276	D	0.999375	B	0.29671	0.254	B	0.21360	0.034	T	0.80362	-0.1414	10	0.87932	D	0	.	14.4391	0.67303	0.0:0.0:0.6478:0.3522	.	30	P22459	KCNA4_HUMAN	W	30	ENSP00000328511:R30W	ENSP00000328511:R30W	R	-	1	2	KCNA4	29990714	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	0.619000	0.24388	1.065000	0.40693	0.655000	0.94253	CGG	.		0.637	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		A	30034138	G	A	30034138	3	1	152	1	0	0	0	0	1	0	0	0	8026	1086	38	1	1877	1	KCNA4	11	30034138	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		30034138	104972378	46	13673											
API5	8539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	43350300	43350300	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaagaggcagaaaatggAgagaatgctggtaatgaaga	18	5	14	4	0	0	6	0	1	0	5	0	8	0	7	1	3	1	3	1	3	6	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:43350300A>T	ENST00000531273.1	+	9	1123	c.984A>T	c.(982-984)ggA>ggT	p.G328G	API5_ENST00000378852.3_Silent_p.G328G|API5_ENST00000455725.2_Silent_p.G317G|API5_ENST00000420461.2_Silent_p.G274G|API5_ENST00000534695.1_Intron|RP11-484D2.2_ENST00000526220.1_RNA|API5_ENST00000534600.1_Silent_p.G328G|Y_RNA_ENST00000516843.1_RNA			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	328	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						CAGAAAATGGAGAGAATGCTG	0.373																																					p.G328G	Pancreas(1;98 122 5625 20895 49453)	.											.	API5-136	0			c.A984T						.						82	72	75					11																	43350300		2203	4300	6503	SO:0001819	synonymous_variant	8539	exon9			AAATGGAGAGAAT	U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.984A>T	11.37:g.43350300A>T		Somatic	244	0		WXS	Illumina HiSeq	Phase_I	234	73	NM_006595	0	0	2	2	0	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Silent	SNP	ENST00000531273.1	37	CCDS44572.1																																																																																			.		0.373	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		T	43350300	A	T	43350300	2	4	152	1	0	0	0	0	0	0	0	1	773	291	11	5		5	API5	11	43350300	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	13316162	43350300	91656216	47	13674											
NRXN2	9379	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64428553	64428553	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcactctccaggtccagAatctcgctgtctccagtggc	7	10	9	15	1	4	1	1	0	3	1	8	1	5	1	3	2	1	2	3	2	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:64428553A>T	ENST00000377551.1	-	9	2068	c.1857T>A	c.(1855-1857)atT>atA	p.I619I	NRXN2_ENST00000377559.3_Silent_p.I588I|NRXN2_ENST00000265459.6_Silent_p.I619I|NRXN2_ENST00000409571.1_Silent_p.I612I|AP001092.4_ENST00000433606.1_RNA|NRXN2_ENST00000496291.1_5'UTR			Q9P2S2	NRX2A_HUMAN	neurexin 2	619	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						CCAGGTCCAGAATCTCGCTGT	0.637																																					p.I619I													.	NRXN2-232	0			c.T1857A						.						28	31	30					11																	64428553		2201	4297	6498	SO:0001819	synonymous_variant	9379	exon10			GTCCAGAATCTCG		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"neurexin II"	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1857T>A	11.37:g.64428553A>T		Somatic	146	2		WXS	Illumina HiSeq	Phase_I	174	72	NM_015080	0	0	0	0	0	A7E2C1|Q9Y2D6	Silent	SNP	ENST00000377551.1	37	CCDS8077.1																																																																																			.		0.637	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64428553	A	T	64428553	2	4	152	1	0	0	0	0	0	0	0	1	10692	242	9	5		5	NRXN2	11	64428553	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	21078253	64428553	70577963	48	13675											
MCAM	4162	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	119185945	119185945	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacctccaccagctcaggCgcaggctgctcagcctctcc	6	7	8	20	1	3	0	2	0	1	0	6	0	5	0	6	2	3	4	6	2	0	0	rs558009680		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:119185945C>T	ENST00000264036.4	-	2	110	c.96G>A	c.(94-96)gcG>gcA	p.A32A	MCAM_ENST00000530144.2_5'UTR|MCAM_ENST00000392814.1_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	32	Ig-like V-type 1.				anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CCAGCTCAGGCGCAGGCTGCT	0.682													C|||	1	0.000199681	8e-04	0	5008	,	,		15849	0		0	False		,,,				2504	0				p.A32A		.											.	MCAM-137	0			c.G96A						.						41	37	38					11																	119185945		2199	4294	6493	SO:0001819	synonymous_variant	4162	exon2			CTCAGGCGCAGGC	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.96G>A	11.37:g.119185945C>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	48	5	NM_006500	0	0	0	0	0	O95812|Q59E86|Q6PHR3|Q6ZTR2	Silent	SNP	ENST00000264036.4	37	CCDS31690.1																																																																																			.		0.682	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			T	119185945	C	T	119185945	2	4	152	1	0	0	0	0	0	0	0	1	9393	755	27	1		1	MCAM	11	119185945	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	54757392	119185945	15820571	49	13676											
KIAA0528	9847	broad.mit.edu	37	chr12	22646273	22646273	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgagtttctggttcatcTgaaaaataaattttaaatca	14	16	5	6	1	5	1	2	1	3	0	6	2	5	1	0	1	0	2	0	1	6	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:22646273T>A	ENST00000333957.4	-	11	1403		c.e11-2		C2CD5_ENST00000446597.1_Splice_Site|C2CD5_ENST00000536386.1_Splice_Site|C2CD5_ENST00000396028.2_Splice_Site|C2CD5_ENST00000545552.1_Splice_Site|C2CD5_ENST00000544930.1_Splice_Site|C2CD5_ENST00000542676.1_Splice_Site	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5						cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTGGTTCATCTGAAAAATAAA	0.318																																					.													.	.	0			c.1148-2A>T						.						151	136	141					12																	22646273		2203	4300	6503	SO:0001630	splice_region_variant	9847	exon12			TTCATCTGAAAAA	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"138 kDa C2 domain-containing phosphoprotein"		"KIAA0528"	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.1148-2A>T	12.37:g.22646273T>A		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	39	3	NM_014802	0	0	0	0	0	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Splice_Site	SNP	ENST00000333957.4	37	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.474467	0.84640	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930;ENST00000535555	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5538	0.68086	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0528	22537540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.895000	0.87343	2.176000	0.68965	0.477000	0.44152	.	.		0.318	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	Intron	A	22646273	T	A	22646273	5	1	152	1	0	0	0	0	0	0	1	0	8203	1594	55	5	1916	5	KIAA0528	12	22646273	Splice_Site	SNP	T	TCGA-MH-A562-01A-11D-A26P-10		22646273	111205622	50	13677											
GLI1	2735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57861257	57861257	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgaccgagccaagcacCagaatcggacccattccaat	13	5	8	15	2	0	2	0	1	0	1	2	4	1	3	6	1	2	1	6	1	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:57861257C>A	ENST00000228682.2	+	9	1145	c.1054C>A	c.(1054-1056)Cag>Aag	p.Q352K	GLI1_ENST00000543426.1_Missense_Mutation_p.Q224K|GLI1_ENST00000546141.1_Missense_Mutation_p.Q311K	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	352					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			AGCCAAGCACCAGAATCGGAC	0.547																																					p.Q352K	Pancreas(157;841 1936 10503 41495 50368)	.											.	GLI1-722	0			c.C1054A						.						120	80	94					12																	57861257		2203	4300	6503	SO:0001583	missense	2735	exon9			AAGCACCAGAATC		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1054C>A	12.37:g.57861257C>A	ENSP00000228682:p.Gln352Lys	Somatic	214	0		WXS	Illumina HiSeq	Phase_I	368	92	NM_005269	0	0	0	0	0	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.001063	0.93227	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	4.77	4.77	0.60923	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000133	T	0.34454	0.0898	N	0.14661	0.345	0.80722	D	1	D	0.59357	0.985	D	0.68765	0.96	T	0.34601	-0.9822	10	0.87932	D	0	.	17.1156	0.86688	0.0:1.0:0.0:0.0	.	352	P08151	GLI1_HUMAN	K	224;352;311;311;224	ENSP00000437607:Q224K;ENSP00000228682:Q352K;ENSP00000441006:Q311K;ENSP00000434408:Q311K	ENSP00000228682:Q352K	Q	+	1	0	GLI1	56147524	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.578000	0.82498	2.644000	0.89710	0.655000	0.94253	CAG	.		0.547	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57861257	C	A	57861257	3	1	152	1	0	0	0	0	1	0	0	0	6457	595	21	4	1084	4	GLI1	12	57861257	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	35214984	57861257	75990638	51	13678											
PAWR	5074	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	80083606	80083606	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttcctggcactggggcccGagctcttgcccttctctggg	2	12	12	15	1	2	0	0	0	2	0	4	1	3	0	3	4	2	2	3	4	0	3	rs369162125		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:80083606G>A	ENST00000328827.4	-	2	791	c.419C>T	c.(418-420)tCg>tTg	p.S140L	RP11-530C5.1_ENST00000551995.1_lincRNA|PAWR_ENST00000547571.1_5'UTR	NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	140					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						ACTGGGGCCCGAGCTCTTGCC	0.706																																					p.S140L		.											.	PAWR-90	0			c.C419T						.	G	LEU/SER	0,4392		0,0,2196	11	11	11		419	2.6	1	12		11	1,8579		0,1,4289	no	missense	PAWR	NM_002583.2	145	0,1,6485	AA,AG,GG		0.0117,0.0,0.0077	possibly-damaging	140/341	80083606	1,12971	2196	4290	6486	SO:0001583	missense	5074	exon2			GGGCCCGAGCTCT	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.419C>T	12.37:g.80083606G>A	ENSP00000328088:p.Ser140Leu	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	100	5	NM_002583	0	0	0	0	0	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	37	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494262	0.85069	0.0	1.17E-4	ENSG00000177425	ENST00000328827	T	0.10192	2.9	3.48	2.59	0.31030	.	0.352131	0.26887	N	0.021991	T	0.08133	0.0203	L	0.50333	1.59	0.42430	D	0.992671	P	0.35944	0.529	B	0.28305	0.088	T	0.29274	-1.0017	9	.	.	.	-1.0638	6.7459	0.23460	0.0988:0.1793:0.7219:0.0	.	140	Q96IZ0	PAWR_HUMAN	L	140	ENSP00000328088:S140L	.	S	-	2	0	PAWR	78607737	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	6.058000	0.71126	0.650000	0.30769	0.563000	0.77884	TCG	.		0.706	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		A	80083606	G	A	80083606	3	1	152	1	0	0	0	0	1	0	0	0	11503	1059	37	1	627	1	PAWR	12	80083606	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	22222349	80083606	53768289	52	13679											
P2RX2	22953	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	133197702	133197702	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caagcacgtgcctgcctcgtCaggctacaacttcaggtgct	8	9	10	14	2	2	0	2	0	0	0	3	0	2	0	2	2	6	3	2	2	3	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:133197702C>T	ENST00000389110.3	+	8	927	c.890C>T	c.(889-891)tCa>tTa	p.S297L	P2RX2_ENST00000449132.2_Missense_Mutation_p.S263L|P2RX2_ENST00000343948.4_Missense_Mutation_p.S297L|P2RX2_ENST00000352418.4_Missense_Mutation_p.S225L|P2RX2_ENST00000348800.5_Missense_Mutation_p.S297L|P2RX2_ENST00000351222.4_Missense_Mutation_p.S205L|P2RX2_ENST00000350048.5_Missense_Mutation_p.S273L	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	297					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		CCTGCCTCGTCAGGCTACAAC	0.607																																					p.S297L		.											.	P2RX2-68	0			c.C890T						.						103	84	90					12																	133197702		2203	4300	6503	SO:0001583	missense	22953	exon8			CCTCGTCAGGCTA	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	15459	protein-coding gene	gene with protein product		600844	"deafness, autosomal dominant 41"	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.890C>T	12.37:g.133197702C>T	ENSP00000373762:p.Ser297Leu	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	182	11	NM_170683	0	0	0	0	0	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Missense_Mutation	SNP	ENST00000389110.3	37	CCDS31931.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138279	0.56936	.	.	ENSG00000187848	ENST00000389110;ENST00000449132;ENST00000343948;ENST00000352418;ENST00000350048;ENST00000351222;ENST00000348800	T;T;T;T;T;T;T	0.04406	3.63;3.63;3.63;3.63;3.63;3.63;3.63	4.96	4.96	0.65561	.	0.120057	0.64402	D	0.000017	T	0.13628	0.0330	M	0.76002	2.32	0.28672	N	0.905593	P;P;P;D;P;P;P;P	0.53745	0.751;0.58;0.928;0.962;0.716;0.716;0.849;0.575	P;P;P;B;B;P;P;B	0.49887	0.527;0.476;0.625;0.341;0.407;0.487;0.622;0.392	T	0.01375	-1.1371	10	0.54805	T	0.06	-13.2945	16.1502	0.81611	0.0:1.0:0.0:0.0	.	297;263;205;225;273;297;297;297	Q32MC3;Q9UBL9-7;Q9UBL9-5;Q9UBL9-6;Q9UBL9-3;Q9UBL9-4;Q9UBL9;Q9UBL9-2	.;.;.;.;.;.;P2RX2_HUMAN;.	L	297;263;297;225;273;205;297	ENSP00000373762:S297L;ENSP00000405531:S263L;ENSP00000343339:S297L;ENSP00000341419:S225L;ENSP00000343904:S273L;ENSP00000344502:S205L;ENSP00000345095:S297L	ENSP00000343339:S297L	S	+	2	0	P2RX2	131707775	0.343000	0.24818	0.655000	0.29622	0.406000	0.30931	3.786000	0.55431	2.584000	0.87258	0.561000	0.74099	TCA	.		0.607	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1			T	133197702	C	T	133197702	3	4	152	1	0	0	0	0	1	0	0	0	11366	838	29	2	920	2	P2RX2	12	133197702	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	53114096	133197702	654193	53	13680											
POU4F1	5457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	79175599	79175599	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctgcttctgtctctggttgCaaaaccacacccgcaccacg	8	10	7	16	2	3	0	0	0	3	0	4	0	3	0	3	1	3	4	3	1	2	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr13:79175599C>A	ENST00000377208.5	-	2	1422	c.1211G>T	c.(1210-1212)tGc>tTc	p.C404F	RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000607205.1_RNA|RP11-52L5.6_ENST00000607269.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	404					axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		TCTCTGGTTGCAAAACCACAC	0.597																																					p.C404F	Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	.											.	POU4F1-515	0			c.G1211T						.						91	88	89					13																	79175599		2203	4300	6503	SO:0001583	missense	5457	exon2			TGGTTGCAAAACC	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"Homeoboxes / POU class"	9218	protein-coding gene	gene with protein product		601632	"POU domain class 4, transcription factor 1"	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.1211G>T	13.37:g.79175599C>A	ENSP00000366413:p.Cys404Phe	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	43	12	NM_006237	0	0	0	0	0	Q14986|Q15318|Q5T227	Missense_Mutation	SNP	ENST00000377208.5	37	CCDS31996.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.260312	0.59431	.	.	ENSG00000152192	ENST00000377208	D	0.96232	-3.95	4.35	4.35	0.52113	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);Homeobox, conserved site (1);	0.053289	0.85682	U	0.000000	D	0.98239	0.9417	M	0.87758	2.905	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99560	1.0968	10	0.87932	D	0	.	16.8947	0.86097	0.0:1.0:0.0:0.0	.	404	Q01851	PO4F1_HUMAN	F	404	ENSP00000366413:C404F	ENSP00000366413:C404F	C	-	2	0	POU4F1	78073600	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.629000	0.83207	2.159000	0.67721	0.499000	0.49734	TGC	.		0.597	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3			A	79175599	C	A	79175599	3	1	152	1	0	0	0	0	1	0	0	0	12304	710	25	4	52	4	POU4F1	13	79175599	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		79175599	35994279	54	13681											
CTAGE5	4253	broad.mit.edu	37	chr14	39815176	39815179	+	Frame_Shift_Del	DEL	CTGT	CTGT	-																															tttgttctaattctggtagaCtgtctggaccagcagaactc																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr14:39815176_39815179delCTGT	ENST00000280083.3	+	21	2214_2217	c.1900_1903delCTGT	c.(1900-1905)ctgtctfs	p.LS634fs	CTAGE5_ENST00000557038.1_Frame_Shift_Del_p.LS554fs|CTAGE5_ENST00000341502.5_Frame_Shift_Del_p.LS634fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Del_p.LS605fs|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.LS1169fs|CTAGE5_ENST00000341749.3_Frame_Shift_Del_p.LS622fs|CTAGE5_ENST00000396165.4_Frame_Shift_Del_p.LS605fs|CTAGE5_ENST00000556148.1_Frame_Shift_Del_p.LS559fs|CTAGE5_ENST00000348007.3_Frame_Shift_Del_p.LS591fs|CTAGE5_ENST00000553352.1_Frame_Shift_Del_p.LS605fs|CTAGE5_ENST00000396158.2_Frame_Shift_Del_p.LS639fs			O15320	CTGE5_HUMAN	CTAGE family, member 5	634	Pro-rich.				positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TTCTGGTAGACTGTCTGGACCAGC	0.353																																					p.639_640del													.	CTAGE5-90	0			c.1915_1918del						.																																			SO:0001589	frameshift_variant	4253	exon21			GGTAGACTGTCTG	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"meningioma expressed antigen 6 (coiled-coil proline-rich)"	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1900_1903delCTGT	14.37:g.39815176_39815179delCTGT	ENSP00000280083:p.Leu634fs	Somatic	220	0		WXS	Illumina HiSeq	Phase_I	200	11	NM_001247989	0	0	0	0	0	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Del	DEL	ENST00000280083.3	37	CCDS9674.1																																																																																			.		0.353	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		-	39815179	CTGT	-	39815176	7	5	152	1	0	1	0	1	0	0	0	0	4000	564	20	0	2013	0	CTAGE5	14	39815176	Frame_Shift_Del	DEL	CTGT	TCGA-MH-A562-01A-11D-A26P-10		39815176	67534364	55	13682											
DCAF5	8816	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	69521317	69521317	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggttgtctttgtggctggTtcctgctctcccttcatctg	1	18	11	11	0	4	0	1	0	3	0	6	0	5	0	2	3	1	4	2	3	0	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr14:69521317T>C	ENST00000341516.5	-	9	2233	c.2086A>G	c.(2086-2088)Acc>Gcc	p.T696A	DCAF5_ENST00000556847.1_Missense_Mutation_p.T614A|DCAF5_ENST00000554215.1_Missense_Mutation_p.T614A|DCAF5_ENST00000557386.1_Missense_Mutation_p.T695A|DCAF5_ENST00000553293.1_5'Flank	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	696					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						TTGTGGCTGGTTCCTGCTCTC	0.527																																					p.T696A		.											.	DCAF5-91	0			c.A2086G						.						110	118	115					14																	69521317		2203	4300	6503	SO:0001583	missense	8816	exon9			GGCTGGTTCCTGC	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20224	protein-coding gene	gene with protein product		603812	"WD repeat domain 22"	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.2086A>G	14.37:g.69521317T>C	ENSP00000341351:p.Thr696Ala	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	68	21	NM_003861	0	0	8	14	6	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Missense_Mutation	SNP	ENST00000341516.5	37	CCDS32106.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.875191	0.51695	.	.	ENSG00000139990	ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386	T;T;T;T	0.71461	-0.57;-0.41;-0.41;0.08	4.99	3.83	0.44106	.	0.081881	0.51477	D	0.000095	T	0.56292	0.1975	L	0.29908	0.895	0.80722	D	1	P;P	0.37864	0.61;0.476	B;B	0.35114	0.196;0.096	T	0.53056	-0.8492	10	0.33141	T	0.24	-17.9216	11.9573	0.52988	0.0:0.0:0.1454:0.8546	.	695;696	G3V4J7;Q96JK2	.;DCAF5_HUMAN	A	696;614;614;695	ENSP00000341351:T696A;ENSP00000451551:T614A;ENSP00000452052:T614A;ENSP00000451845:T695A	ENSP00000341351:T696A	T	-	1	0	DCAF5	68591070	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.462000	0.53042	0.902000	0.36520	0.459000	0.35465	ACC	.		0.527	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		C	69521317	T	C	69521317	3	2	152	1	0	0	0	0	1	0	0	0	4279	1725	60	3	746	3	DCAF5	14	69521317	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	29706141	69521317	37828223	56	13683											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493794	77493794	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgctgctgTtgctgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1	rs377151545|rs28718623|rs71125518	byFrequency	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr14:77493794T>C	ENST00000238647.3	-	1	1240	c.342A>G	c.(340-342)caA>caG	p.Q114Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	114	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgttgctgctgct	0.697													T|||	1146	0.228834	0.1649	0.1758	5008	,	,		5976	0.2659		0.2614	False		,,,				2504	0.2812				p.Q114Q		.											.	IRF2BPL-90	0			c.A342G						.	-		160,2330		6,148,1091	2	2	2		342	0.6	0	14	dbSNP_125	2	324,4012		7,310,1851	no	coding-synonymous	IRF2BPL	NM_024496.2		13,458,2942	CC,CT,TT		7.4723,6.4257,7.0905		114/797	77493794	484,6342	1245	2168	3413	SO:0001819	synonymous_variant	64207	exon1			CTGCTGTTGCTGC	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"enhanced at puberty 1"	611720	"chromosome 14 open reading frame 4"	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.342A>G	14.37:g.77493794T>C		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_024496	1	2	8	4805	4794	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			.		0.697	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		C	77493794	T	C	77493794	2	2	152	1	0	0	0	0	0	0	0	1	1777	1722	60	3		3	C14orf4	14	77493794	Silent	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	7972477	77493794	29855746	57	13684											
IGDCC4	57722	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65684246	65684246	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgccttctccgtcttgccCttccacactgctgcatagcc	4	11	8	18	2	2	0	0	0	2	0	4	0	3	0	5	1	4	2	5	1	1	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr15:65684246C>G	ENST00000352385.2	-	12	2405	c.2196G>C	c.(2194-2196)aaG>aaC	p.K732N		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	732	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CCGTCTTGCCCTTCCACACTG	0.612																																					p.K732N		.											.	IGDCC4-93	0			c.G2196C						.						122	120	121					15																	65684246		2201	4299	6500	SO:0001583	missense	57722	exon12			CTTGCCCTTCCAC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	13770	protein-coding gene	gene with protein product	"likely ortholog of mouse neighbor of Punc E11"						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2196G>C	15.37:g.65684246C>G	ENSP00000319623:p.Lys732Asn	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	112	40	NM_020962	0	0	0	0	0	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416366	0.83449	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.59638	0.25	5.15	4.22	0.49857	Fibronectin, type III (2);	0.055747	0.64402	D	0.000002	T	0.62708	0.2450	L	0.59436	1.845	0.48135	D	0.999599	D	0.65815	0.995	P	0.52856	0.711	T	0.64799	-0.6322	10	0.49607	T	0.09	-22.1714	12.3562	0.55176	0.0:0.9194:0.0:0.0806	.	732	Q8TDY8	IGDC4_HUMAN	N	732;461	ENSP00000319623:K732N	ENSP00000319623:K732N	K	-	3	2	IGDCC4	63471299	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	1.066000	0.30604	2.406000	0.81754	0.561000	0.74099	AAG	.		0.612	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		G	65684246	C	G	65684246	3	3	152	1	0	0	0	0	1	0	0	0	7590	680	24	4	1592	4	IGDCC4	15	65684246	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		65684246	36847146	58	13685											
SLC24A1	9187	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65942809	65942809	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaactgaagagaaaagtggAggtgaaactcaaccagaagg	19	4	13	5	0	1	4	1	2	0	2	1	7	1	5	1	3	3	0	1	3	7	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr15:65942809A>G	ENST00000261892.6	+	7	2609	c.2322A>G	c.(2320-2322)ggA>ggG	p.G774G	SLC24A1_ENST00000449142.2_3'UTR|SLC24A1_ENST00000546330.1_Silent_p.G756G|SLC24A1_ENST00000339868.6_Silent_p.G756G|SLC24A1_ENST00000544319.2_Silent_p.G660G|SLC24A1_ENST00000537259.1_Silent_p.G756G|SLC24A1_ENST00000399033.4_Silent_p.G774G	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	774					calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						agaaaagtggaggtgaaactc	0.463																																					p.G774G													.	.	0			c.A2322G						.						79	84	82					15																	65942809		1489	2962	4451	SO:0001819	synonymous_variant	9187	exon7			AAGTGGAGGTGAA	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"Solute carriers"	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.2322A>G	15.37:g.65942809A>G		Somatic	229	2		WXS	Illumina HiSeq	Phase_I	226	72	NM_004727	0	0	3	3	0	O43485|O75184|Q17RM9	Silent	SNP	ENST00000261892.6	37	CCDS45284.1																																																																																			.		0.463	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727		G	65942809	A	G	65942809	2	3	152	1	0	0	0	0	0	0	0	1	14497	291	11	3		3	SLC24A1	15	65942809	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	258563	65942809	36588583	59	13686											
SGK269	79834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	77472613	77472613	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatttggtccagttccactAgtaattagttctactttagg	10	16	7	8	0	1	0	0	0	1	0	3	0	3	0	2	2	1	3	2	2	5	9			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr15:77472613A>T	ENST00000560626.2	-	4	2131	c.1656T>A	c.(1654-1656)acT>acA	p.T552T	PEAK1_ENST00000558305.1_Silent_p.T552T|PEAK1_ENST00000312493.4_Silent_p.T552T			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	552					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CAGTTCCACTAGTAATTAGTT	0.413																																					p.T552T		.											.	.	0			c.T1656A						.						217	198	204					15																	77472613		1881	4115	5996	SO:0001819	synonymous_variant	0	exon5			TCCACTAGTAATT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.1656T>A	15.37:g.77472613A>T		Somatic	140	0		WXS	Illumina HiSeq	Phase_I	110	35	NM_024776	0	0	0	0	0	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	37	CCDS42062.1																																																																																			.		0.413	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			T	77472613	A	T	77472613	2	4	152	1	0	0	0	0	0	0	0	1	14243	407	15	5		5	SGK269	15	77472613	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	11529804	77472613	25058779	60	13687											
CARHSP1	23589	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	8953055	8953055	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggtcctcgtccggcgagtgGgcagtgggcttgggaccacg	5	7	18	11	4	0	0	0	0	0	0	3	2	2	1	3	5	0	2	3	5	0	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:8953055G>A	ENST00000396593.2	-	2	490	c.131C>T	c.(130-132)cCc>cTc	p.P44L	CARHSP1_ENST00000562843.1_Missense_Mutation_p.P44L|CARHSP1_ENST00000567626.1_5'Flank|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000561530.1_Missense_Mutation_p.P44L|CARHSP1_ENST00000567554.1_Missense_Mutation_p.P44L|CARHSP1_ENST00000311052.5_Missense_Mutation_p.P44L	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	44					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						CCGGCGAGTGGGCAGTGGGCT	0.652																																					p.P44L		.											.	CARHSP1-90	0			c.C131T						.						27	23	25					16																	8953055		2195	4300	6495	SO:0001583	missense	23589	exon2			CGAGTGGGCAGTG	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"calcium regulated heat stable protein 1 (24kD)"			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.131C>T	16.37:g.8953055G>A	ENSP00000379838:p.Pro44Leu	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	112	42	NM_001042476	0	0	46	90	44	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Missense_Mutation	SNP	ENST00000396593.2	37	CCDS10537.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.292618	0.80914	.	.	ENSG00000153048	ENST00000396593;ENST00000311052	.	.	.	5.35	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.77811	0.4186	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.64877	0.93	T	0.77389	-0.2606	9	0.19590	T	0.45	-3.558	14.7061	0.69191	0.0:0.1461:0.8539:0.0	.	44	Q9Y2V2	CHSP1_HUMAN	L	44	.	ENSP00000311847:P44L	P	-	2	0	CARHSP1	8860556	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	9.057000	0.93889	1.221000	0.43506	0.563000	0.77884	CCC	.		0.652	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316		A	8953055	G	A	8953055	3	1	152	1	0	0	0	0	1	0	0	0	2659	1232	43	2	324	2	CARHSP1	16	8953055	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		8953055	81401698	61	13688											
IL4R	3566	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	27374134	27374134	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacctgacttgcacagagacGcccctcgtcatcgcaggcaa	11	6	9	15	3	1	2	1	1	0	1	3	3	1	2	3	1	2	3	3	1	2	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:27374134G>A	ENST00000395762.2	+	11	1720	c.1461G>A	c.(1459-1461)acG>acA	p.T487T	IL4R_ENST00000543915.2_Silent_p.T487T|IL4R_ENST00000170630.2_Silent_p.T487T|IL4R_ENST00000380922.3_Silent_p.T472T	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	487	Required for IRS1 activation and IL4- induced cell growth.				defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GCACAGAGACGCCCCTCGTCA	0.642																																					p.T487T		.											.	IL4R-227	0			c.G1461A						.						91	94	93					16																	27374134		2197	4300	6497	SO:0001819	synonymous_variant	3566	exon11			AGAGACGCCCCTC	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"Interleukins and interleukin receptors", "CD molecules"	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1461G>A	16.37:g.27374134G>A		Somatic	86	0		WXS	Illumina HiSeq	Phase_I	117	40	NM_000418	0	0	0	0	0	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			.		0.642	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			A	27374134	G	A	27374134	2	1	152	1	0	0	0	0	0	0	0	1	7719	1074	38	1		1	IL4R	16	27374134	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	18421079	27374134	62980619	62	13689											
SETD1A	9739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30970101	30970101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggccccgagcttccagTggcggaactacaagctcatc	11	6	11	13	2	1	1	1	0	0	1	3	3	2	2	3	3	4	2	3	3	4	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:30970101T>C	ENST00000262519.8	+	2	735	c.49T>C	c.(49-51)Tgg>Cgg	p.W17R		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	17					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						GAGCTTCCAGTGGCGGAACTA	0.557																																					p.W17R		.											.	SETD1A-93	0			c.T49C						.						109	105	107					16																	30970101		2197	4300	6497	SO:0001583	missense	9739	exon2			TTCCAGTGGCGGA	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"Chromatin-modifying enzymes / K-methyltransferases", "RNA binding motif (RRM) containing"	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.49T>C	16.37:g.30970101T>C	ENSP00000262519:p.Trp17Arg	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	152	46	NM_014712	0	0	0	0	0	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	37	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.389372	0.61956	.	.	ENSG00000099381	ENST00000262519;ENST00000452917;ENST00000449974	D	0.94828	-3.53	5.1	5.1	0.69264	.	0.000000	0.64402	U	0.000001	D	0.96494	0.8856	M	0.68593	2.085	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.96642	0.9475	10	0.56958	D	0.05	.	13.8869	0.63714	0.0:0.0:0.0:1.0	.	17	O15047	SET1A_HUMAN	R	17	ENSP00000262519:W17R	ENSP00000262519:W17R	W	+	1	0	SETD1A	30877602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.599000	0.82757	1.920000	0.55613	0.533000	0.62120	TGG	.		0.557	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		C	30970101	T	C	30970101	3	2	152	1	0	0	0	0	1	0	0	0	14162	1696	59	3	51	3	SETD1A	16	30970101	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	3595967	30970101	59384652	63	13690											
SALL1	6299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	51171349	51171349	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgccgccaaatccttctggaAcatttctgggaacttgacgg	9	11	10	11	2	2	1	0	1	2	0	3	3	3	3	3	3	3	0	3	3	3	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:51171349A>C	ENST00000251020.4	-	3	3682	c.3649T>G	c.(3649-3651)Ttc>Gtc	p.F1217V	SALL1_ENST00000566102.1_3'UTR|SALL1_ENST00000440970.1_Missense_Mutation_p.F1120V|SALL1_ENST00000541611.1_Missense_Mutation_p.F40V	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1217					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TCCTTCTGGAACATTTCTGGG	0.562																																					p.F1217V	GBM(103;1352 1446 1855 4775 8890)	.											.	SALL1-98	0			c.T3649G						.						54	51	52					16																	51171349		2198	4300	6498	SO:0001583	missense	6299	exon3			TCTGGAACATTTC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"Zinc fingers, C2H2-type"	10524	protein-coding gene	gene with protein product		602218	"sal (Drosophila)-like 1", "sal-like 1 (Drosophila)"	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3649T>G	16.37:g.51171349A>C	ENSP00000251020:p.Phe1217Val	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	116	29	NM_002968	0	0	5	7	2	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.837676	0.50951	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559;ENST00000541611	T;T;T	0.47869	3.22;3.21;0.83	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	M	0.76170	2.325	0.80722	D	1	D;B	0.76494	0.999;0.372	D;B	0.78314	0.991;0.083	T	0.64188	-0.6466	10	0.20046	T	0.44	.	15.6652	0.77225	1.0:0.0:0.0:0.0	.	1217;40	Q9NSC2;F5H733	SALL1_HUMAN;.	V	1217;1120;1181;40	ENSP00000251020:F1217V;ENSP00000407914:F1120V;ENSP00000442827:F40V	ENSP00000251020:F1217V	F	-	1	0	SALL1	49728850	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.311000	0.96282	2.104000	0.64026	0.523000	0.50628	TTC	.		0.562	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51171349	A	C	51171349	3	2	152	1	0	0	0	0	1	0	0	0	13842	43	2	5	329	5	SALL1	16	51171349	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	20201248	51171349	39183404	64	13691											
RANBP10	57610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67761787	67761787	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccgcagagctgccgccgaGgatgcctgtcatctgcatcc	6	7	11	17	3	2	1	1	0	1	1	3	3	3	2	6	1	4	3	6	1	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:67761787G>T	ENST00000317506.3	-	12	1602	c.1487C>A	c.(1486-1488)cCt>cAt	p.P496H	RANBP10_ENST00000536251.1_Missense_Mutation_p.P267H|RANBP10_ENST00000602677.1_Missense_Mutation_p.P526H|RANBP10_ENST00000448631.2_Missense_Mutation_p.P470H|RANBP10_ENST00000411657.2_Missense_Mutation_p.P409H	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	496					microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		CTGCCGCCGAGGATGCCTGTC	0.622																																					p.P496H		.											.	RANBP10-227	0			c.C1487A						.						34	31	32					16																	67761787		2198	4300	6498	SO:0001583	missense	57610	exon12			CGCCGAGGATGCC	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.1487C>A	16.37:g.67761787G>T	ENSP00000316589:p.Pro496His	Somatic	118	0		WXS	Illumina HiSeq	Phase_I	108	32	NM_020850	0	0	0	0	0	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Missense_Mutation	SNP	ENST00000317506.3	37	CCDS32469.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.057947	0.36277	.	.	ENSG00000141084	ENST00000317506;ENST00000448631;ENST00000536251;ENST00000411657	.	.	.	5.93	5.93	0.95920	.	0.631540	0.17547	N	0.170307	T	0.69006	0.3063	M	0.62723	1.935	0.80722	D	1	P;B;B	0.37573	0.6;0.006;0.012	P;B;B	0.46110	0.504;0.007;0.02	T	0.67413	-0.5677	9	0.48119	T	0.1	-12.1716	15.4231	0.75028	0.0:0.1386:0.8614:0.0	.	409;470;496	B4DID0;B4DQH9;Q6VN20	.;.;RBP10_HUMAN	H	496;470;267;409	.	ENSP00000316589:P496H	P	-	2	0	RANBP10	66319288	0.996000	0.38824	0.997000	0.53966	0.794000	0.44872	4.807000	0.62576	2.814000	0.96858	0.563000	0.77884	CCT	.		0.622	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		T	67761787	G	T	67761787	3	4	152	1	0	0	0	0	1	0	0	0	13058	1000	35	4	387	4	RANBP10	16	67761787	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	16590438	67761787	22592966	65	13692											
CDK10	8558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	89760632	89760632	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	accacgcagaccaccagcatCgacatgtggtgaggagatac	13	5	11	12	2	0	3	0	1	0	2	1	5	0	3	3	2	2	2	3	2	1	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:89760632C>T	ENST00000353379.7	+	9	703	c.660C>T	c.(658-660)atC>atT	p.I220I	CDK10_ENST00000505473.1_Silent_p.I149I|CDK10_ENST00000331006.8_Silent_p.I173I	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		CCACCAGCATCGACATGTGGT	0.632																																					p.I220I		.											.	CDK10-508	0			c.C660T						.						102	78	86					16																	89760632		2198	4300	6498	SO:0001819	synonymous_variant	8558	exon9			CAGCATCGACATG	L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"Cyclin-dependent kinases"	1770	protein-coding gene	gene with protein product		603464	"cyclin-dependent kinase (CDC2-like) 10"			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.660C>T	16.37:g.89760632C>T		Somatic	169	0		WXS	Illumina HiSeq	Phase_I	158	65	NM_052988	0	0	6	32	26	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Silent	SNP	ENST00000353379.7	37	CCDS10984.2																																																																																			.		0.632	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2			T	89760632	C	T	89760632	2	4	152	1	0	0	0	0	0	0	0	1	3131	874	31	1		1	CDK10	16	89760632	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	21998845	89760632	594121	66	13693											
CAMTA2	23125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	4877742	4877742	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgctgcgatctctgccaTccgcttctccatctgctcca	5	12	7	17	2	3	0	0	0	3	0	7	1	5	0	4	0	5	4	4	0	0	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:4877742T>G	ENST00000348066.3	-	12	2077	c.1954A>C	c.(1954-1956)Atg>Ctg	p.M652L	CAMTA2_ENST00000381311.5_Missense_Mutation_p.M654L|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000572543.1_Missense_Mutation_p.M657L|CAMTA2_ENST00000358183.4_Missense_Mutation_p.M652L|CAMTA2_ENST00000361571.5_Missense_Mutation_p.M651L|CAMTA2_ENST00000414043.3_Missense_Mutation_p.M675L	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	652					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						ATCTCTGCCATCCGCTTCTCC	0.597																																					p.M675L		.											.	CAMTA2-91	0			c.A2023C						.						155	119	132					17																	4877742		2203	4300	6503	SO:0001583	missense	23125	exon12			CTGCCATCCGCTT	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1954A>C	17.37:g.4877742T>G	ENSP00000321813:p.Met652Leu	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	193	89	NM_001171167	0	0	0	1	1	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	37	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111402	0.56398	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.27557	2.87;1.91;1.66;1.91;1.69	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.30885	0.0779	N	0.11560	0.145	0.44454	D	0.997389	B;B;P;B;P	0.43024	0.077;0.077;0.471;0.34;0.798	B;B;P;P;P	0.60236	0.045;0.152;0.65;0.448;0.871	T	0.11891	-1.0569	10	0.13108	T	0.6	-18.4138	13.2241	0.59905	0.0:0.0:0.0:1.0	.	628;675;654;652;651	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	L	675;654;651;652;652	ENSP00000412886:M675L;ENSP00000370712:M654L;ENSP00000354828:M651L;ENSP00000350910:M652L;ENSP00000321813:M652L	ENSP00000321813:M652L	M	-	1	0	CAMTA2	4818466	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.777000	0.85628	2.232000	0.73038	0.482000	0.46254	ATG	.		0.597	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		G	4877742	T	G	4877742	3	3	152	1	0	0	0	0	1	0	0	0	2620	1435	50	5	1752	5	CAMTA2	17	4877742	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10		4877742	76317468	67	13694											
SLC5A10	125206	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	18880267	18880267	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccccatgggcctgatcaTcatgccgggcatgatcagcc	7	8	11	15	1	3	2	3	2	0	0	4	2	4	2	5	2	2	2	5	2	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:18880267T>A	ENST00000395645.3	+	9	965	c.947T>A	c.(946-948)aTc>aAc	p.I316N	FAM83G_ENST00000585154.2_Intron|SLC5A10_ENST00000395642.1_Missense_Mutation_p.I233N|SLC5A10_ENST00000417251.2_Missense_Mutation_p.I316N|SLC5A10_ENST00000317977.6_Missense_Mutation_p.I233N|FAM83G_ENST00000388995.6_Intron|SLC5A10_ENST00000395647.2_Missense_Mutation_p.I316N|FAM83G_ENST00000345041.4_Intron|SLC5A10_ENST00000395643.2_Missense_Mutation_p.I289N	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	316					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						GGCCTGATCATCATGCCGGGC	0.637																																					p.I316N													.	SLC5A10-91	0			c.T947A						.						112	91	98					17																	18880267		2203	4300	6503	SO:0001583	missense	125206	exon9			TGATCATCATGCC		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"Solute carriers"	23155	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 10"				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.947T>A	17.37:g.18880267T>A	ENSP00000379007:p.Ile316Asn	Somatic	82	1		WXS	Illumina HiSeq	Phase_I	134	73	NM_001042450	0	0	0	0	0	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	37	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.632337	0.87660	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48;-2.48	5.97	5.97	0.96955	.	0.102615	0.64402	D	0.000004	D	0.93867	0.8038	M	0.82823	2.61	0.80722	D	1	D;D;D;D;D	0.58970	0.977;0.971;0.977;0.971;0.984	P;P;P;P;P	0.62089	0.898;0.771;0.853;0.847;0.894	D	0.94502	0.7710	10	0.87932	D	0	.	13.4408	0.61112	0.0:0.0:0.1303:0.8697	.	316;289;316;316;233	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	N	233;316;233;316;316;289	ENSP00000324346:I233N;ENSP00000379008:I316N;ENSP00000379004:I233N;ENSP00000401875:I316N;ENSP00000379007:I316N;ENSP00000379005:I289N	ENSP00000324346:I233N	I	+	2	0	SLC5A10	18820992	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.173000	0.71937	2.288000	0.76882	0.533000	0.62120	ATC	.		0.637	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351		A	18880267	T	A	18880267	3	1	152	1	0	0	0	0	1	0	0	0	14694	1435	50	5	981	5	SLC5A10	17	18880267	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	14002525	18880267	62314943	68	13695											
LGALS9B	284194	broad.mit.edu	37	chr17	20355185	20355185	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcccggaatggtggtgatGaaaggcatcggctgtcagaa	10	8	14	9	2	1	3	1	2	0	1	3	4	2	4	2	5	0	2	2	5	3	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:20355185G>A	ENST00000423676.3	-	9	747	c.684C>T	c.(682-684)ttC>ttT	p.F228F	LGALS9B_ENST00000324290.5_Silent_p.F227F			Q3B8N2	LEG9B_HUMAN	lectin, galactoside-binding, soluble, 9B	228	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	10						TGGTGGTGATGAAAGGCATCG	0.572																																					p.F227F													.	LGALS9B-23	0			c.C681T						.						23	17	19					17																	20355185		2192	4110	6302	SO:0001819	synonymous_variant	284194	exon9			GGTGATGAAAGGC		CCDS42283.1	17p11.2	2011-08-04			ENSG00000170298	ENSG00000170298		"Lectins, galactoside-binding"	24842	protein-coding gene	gene with protein product						11997339	Standard	NM_001042685		Approved		uc002gwz.1	Q3B8N2	OTTHUMG00000130730	ENST00000423676.3:c.684C>T	17.37:g.20355185G>A		Somatic	199	0		WXS	Illumina HiSeq	Phase_I	243	7	NM_001042685	0	0	0	0	0	A6NLF8|A8K2J8	Silent	SNP	ENST00000423676.3	37																																																																																				.		0.572	LGALS9B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000253230.2	NM_001042685		A	20355185	G	A	20355185	2	1	152	1	0	0	0	0	0	0	0	1	8771	1281	45	2		2	LGALS9B	17	20355185	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	1474918	20355185	60840025	69	13696											
EZH1	2145	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	40880917	40880920	+	Frame_Shift_Del	DEL	AGTA	AGTA	-																															agatttcacttttcttttccAgtaagtgatacatttggagg																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	AGTA	AGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:40880917_40880920delAGTA	ENST00000428826.2	-	3	161_164	c.40_43delTACT	c.(40-45)tactggfs	p.YW14fs	EZH1_ENST00000415827.2_Frame_Shift_Del_p.YW14fs|EZH1_ENST00000435174.1_5'UTR|EZH1_ENST00000585893.1_Frame_Shift_Del_p.YW14fs|EZH1_ENST00000590078.1_Intron|EZH1_ENST00000592743.1_Frame_Shift_Del_p.YW14fs			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	14					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TTTCTTTTCCAGTAAGTGATACAT	0.373																																					p.14_15del		.											.	EZH1-229	0			c.40_43del						.																																			SO:0001589	frameshift_variant	2145	exon3			.		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.40_43delTACT	17.37:g.40880917_40880920delAGTA	ENSP00000404658:p.Tyr14fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	93	26	NM_001991	0	0	0	0	0	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Frame_Shift_Del	DEL	ENST00000428826.2	37	CCDS32659.1																																																																																			.		0.373	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		-	40880920	AGTA	-	40880917	7	5	152	1	0	1	0	1	0	0	0	0	5346	188	7	0	2276	0	EZH1	17	40880917	Frame_Shift_Del	DEL	AGTA	TCGA-MH-A562-01A-11D-A26P-10	20525732	40880917	40314293	70	13697											
ASB16	92591	broad.mit.edu	37	chr17	42255640	42255640	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggcagctgcagcacctggCccgactagctgtgcgcgctc	7	6	13	15	3	0	0	0	0	0	0	1	1	0	0	2	2	5	6	2	2	2	1	rs192236945		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:42255640C>G	ENST00000293414.1	+	5	1328	c.1244C>G	c.(1243-1245)gCc>gGc	p.A415G	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000592897.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	415	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CAGCACCTGGCCCGACTAGCT	0.662																																					p.A415G													.	ASB16-227	0			c.C1244G						.						40	34	36					17																	42255640		2203	4300	6503	SO:0001583	missense	92591	exon5			ACCTGGCCCGACT	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"Ankyrin repeat domain containing"	19768	protein-coding gene	gene with protein product		615056	"ankyrin repeat and SOCS box-containing 16"			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.1244C>G	17.37:g.42255640C>G	ENSP00000293414:p.Ala415Gly	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	25	6	NM_080863	0	0	0	0	0	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	37	CCDS11478.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.798393	0.70567	.	.	ENSG00000161664	ENST00000293414	T	0.46451	0.87	5.36	5.36	0.76844	SOCS protein, C-terminal (3);	0.245753	0.42548	D	0.000691	T	0.61148	0.2324	M	0.69358	2.11	0.34275	D	0.681456	D	0.76494	0.999	D	0.72338	0.977	T	0.70479	-0.4860	10	0.52906	T	0.07	-19.0493	13.7126	0.62678	0.0:0.8453:0.1547:0.0	.	415	Q96NS5	ASB16_HUMAN	G	415	ENSP00000293414:A415G	ENSP00000293414:A415G	A	+	2	0	ASB16	39611166	0.992000	0.36948	1.000000	0.80357	0.682000	0.39822	2.768000	0.47645	2.793000	0.96121	0.561000	0.74099	GCC	C|0.999;T|0.001		0.662	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			G	42255640	C	G	42255640	3	3	152	1	0	0	0	0	1	0	0	0	1021	739	26	4	1262	4	ASB16	17	42255640	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	1374723	42255640	38939570	71	13698											
SCRN2	90507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45916860	45916860	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgtctccagcacccacGcctcagtgcggtcagccagc	7	6	10	18	2	3	0	2	0	1	0	4	0	3	0	4	1	5	2	4	1	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:45916860G>A	ENST00000290216.9	-	4	631	c.506C>T	c.(505-507)gCg>gTg	p.A169V	SCRN2_ENST00000407215.3_Missense_Mutation_p.A169V|SCRN2_ENST00000584123.1_Missense_Mutation_p.A177V	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	169						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						CAGCACCCACGCCTCAGTGCG	0.612																																					p.A169V		.											.	SCRN2-91	0			c.C506T						.						78	72	74					17																	45916860		2203	4300	6503	SO:0001583	missense	90507	exon4			ACCCACGCCTCAG	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.506C>T	17.37:g.45916860G>A	ENSP00000290216:p.Ala169Val	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	220	108	NM_138355	0	0	17	58	41	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	37	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593412	0.86953	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.17370	2.28;2.28	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.42207	-0.9465	10	0.87932	D	0	-27.8264	17.8079	0.88607	0.0:0.0:1.0:0.0	.	169;169;169	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	V	169	ENSP00000290216:A169V;ENSP00000383935:A169V	ENSP00000290216:A169V	A	-	2	0	SCRN2	43271859	1.000000	0.71417	0.935000	0.37517	0.396000	0.30629	9.756000	0.98918	2.504000	0.84457	0.561000	0.74099	GCG	.		0.612	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45916860	G	A	45916860	3	1	152	1	0	0	0	0	1	0	0	0	13971	1087	38	1	809	1	SCRN2	17	45916860	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	3661220	45916860	35278350	72	13699											
NXPH3	11248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	47656051	47656051	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccccgggtgcctcggaagCggggccacatctcacctaag	7	5	14	15	3	1	0	1	0	1	0	3	1	1	1	5	5	2	0	5	5	2	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:47656051C>T	ENST00000328741.5	+	2	510	c.148C>T	c.(148-150)Cgg>Tgg	p.R50W	RP5-1029K10.4_ENST00000503624.1_RNA|NXPH3_ENST00000513748.1_Missense_Mutation_p.R50W	NM_007225.2	NP_009156.2	O95157	NXPH3_HUMAN	neurexophilin 3	50	II.				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(3)|lung(4)|pancreas(1)|skin(2)	12	all_cancers(4;7.45e-14)|Breast(4;1.08e-27)|all_epithelial(4;2.27e-17)					GCCTCGGAAGCGGGGCCACAT	0.677																																					p.R50W		.											.	NXPH3-70	0			c.C148T						.						35	39	37					17																	47656051		2203	4299	6502	SO:0001583	missense	11248	exon2			CGGAAGCGGGGCC	AF043468	CCDS11550.1	17q	2008-07-03				ENSG00000182575			8077	protein-coding gene	gene with protein product		604636				9570794	Standard	NM_007225		Approved	NPH3	uc002ipa.3	O95157		ENST00000328741.5:c.148C>T	17.37:g.47656051C>T	ENSP00000329295:p.Arg50Trp	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	169	101	NM_007225	0	0	0	0	0	Q8NDC3|Q8TBF6|Q9ULR1	Missense_Mutation	SNP	ENST00000328741.5	37	CCDS11550.1	.	.	.	.	.	.	.	.	.	.	c	16.57	3.159520	0.57368	.	.	ENSG00000182575	ENST00000328741;ENST00000513748	.	.	.	4.55	3.56	0.40772	.	0.310331	0.31381	N	0.007749	T	0.34250	0.0891	N	0.08118	0	0.09310	N	1	D;D	0.89917	1.0;0.998	D;P	0.70935	0.971;0.834	T	0.07578	-1.0765	9	0.72032	D	0.01	-23.4594	7.973	0.30138	0.428:0.4299:0.1421:0.0	.	50;50	D6RGW2;O95157	.;NXPH3_HUMAN	W	50	.	ENSP00000329295:R50W	R	+	1	2	NXPH3	45011050	0.037000	0.19845	1.000000	0.80357	0.994000	0.84299	0.755000	0.26405	1.110000	0.41699	0.556000	0.70494	CGG	.		0.677	NXPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365143.1			T	47656051	C	T	47656051	3	4	152	1	0	0	0	0	1	0	0	0	10818	759	27	1	154	1	NXPH3	17	47656051	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	1739191	47656051	33539159	73	13700											
SCN4A	6329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62045582	62045582	+	Silent	SNP	C	C	T																															ggcgggggccagcgcacacaCttctgcctcaggtttcccat																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:62045582C>T	ENST00000435607.1	-	6	913	c.837G>A	c.(835-837)aaG>aaA	p.K279K	SCN4A_ENST00000578147.1_Silent_p.K279K	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	279					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGCGCACACACTTCTGCCTCA	0.547																																					p.K279K		.											.	SCN4A-93	0			c.G837A						.																																			SO:0001819	synonymous_variant	6329	exon6			CACACACTTCTGC	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.837G>A	17.37:g.62045582C>T		Somatic	365	0		WXS	Illumina HiSeq	Phase_I	518	129	NM_000334	0	0	0	0	0	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			.		0.547	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62045582	C	T	62045582	2	4	152	1	0	0	0	0	0	0	0	1	13952	564	20	2		2	SCN4A	17	62045582	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	14389531	62045582	19149628	74	13701	147	2									
SCN4A	6329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	62045585	62045585	+	Silent	SNP	C	C	T																															gggggccagcgcacacacttCtgcctcaggtttcccatgaa																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:62045585C>T	ENST00000435607.1	-	6	910	c.834G>A	c.(832-834)caG>caA	p.Q278Q	SCN4A_ENST00000578147.1_Silent_p.Q278Q	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	278					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCACACACTTCTGCCTCAGGT	0.542																																					p.Q278Q		.											.	SCN4A-93	0			c.G834A						.						136	140	139					17																	62045585		2180	4283	6463	SO:0001819	synonymous_variant	6329	exon6			ACACTTCTGCCTC	U24693		17q23.3	2012-02-26	2007-01-23					"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.834G>A	17.37:g.62045585C>T		Somatic	359	0		WXS	Illumina HiSeq	Phase_I	504	125	NM_000334	0	0	0	0	0	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			.		0.542	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62045585	C	T	62045585	2	4	152	1	0	0	0	0	0	0	0	1	13952	912	32	2		2	SCN4A	17	62045585	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	3	62045585	19149625	75	13702	147	2									
DENND1C	79958	hgsc.bcm.edu	37	chr19	6475944	6475944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggacgcgtggacgcacgagGtcagctggggagcgatggcg	8	4	20	9	6	1	0	1	0	0	0	1	5	1	3	0	6	2	2	0	6	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:6475944G>A	ENST00000381480.2	-	11	795	c.683C>T	c.(682-684)aCc>aTc	p.T228I	DENND1C_ENST00000543576.1_Missense_Mutation_p.T184I|DENND1C_ENST00000591030.1_5'Flank	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	228	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GACGCACGAGGTCAGCTGGGG	0.672																																					p.T228I		.											.	DENND1C-67	0			c.C683T						.						8	10	9					19																	6475944		2158	4249	6407	SO:0001583	missense	79958	exon11			CACGAGGTCAGCT	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"DENN/MADD domain containing"	26225	protein-coding gene	gene with protein product		613634	"family with sequence similarity 31, member C"	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.683C>T	19.37:g.6475944G>A	ENSP00000370889:p.Thr228Ile	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	8	6	NM_024898	0	0	0	0	0	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	32	5.166750	0.94768	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.13089	2.62;2.62	5.31	5.31	0.75309	DENN (3);	0.054596	0.64402	D	0.000001	T	0.47040	0.1424	M	0.90870	3.155	0.50171	D	0.999858	D	0.67145	0.996	D	0.79784	0.993	T	0.58211	-0.7676	10	0.87932	D	0	-9.2935	16.4592	0.84031	0.0:0.0:1.0:0.0	.	228	Q8IV53	DEN1C_HUMAN	I	228;184	ENSP00000370889:T228I;ENSP00000437805:T184I	ENSP00000370889:T228I	T	-	2	0	DENND1C	6426944	1.000000	0.71417	0.950000	0.38849	0.890000	0.51754	8.957000	0.93082	2.498000	0.84270	0.561000	0.74099	ACC	.		0.672	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		A	6475944	G	A	6475944	3	1	152	1	0	0	0	0	1	0	0	0	4439	1261	44	2	1774	2	DENND1C	19	6475944	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		6475944	52653039	76	13703											
CYP4F22	126410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	15651480	15651480	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgaggcctggcttaaggcCaagcaggggaagaccttgga	10	5	16	10	1	0	1	0	0	0	1	0	4	0	3	4	6	1	2	4	6	3	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:15651480C>T	ENST00000269703.3	+	8	1090	c.891C>T	c.(889-891)gcC>gcT	p.A297A	CYP4F22_ENST00000601005.2_Silent_p.A297A	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	297						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						GGCTTAAGGCCAAGCAGGGGA	0.652																																					p.A297A		.											.	CYP4F22-92	0			c.C891T						.						52	47	49					19																	15651480		2203	4300	6503	SO:0001819	synonymous_variant	126410	exon8			TAAGGCCAAGCAG		CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"Cytochrome P450s"	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.891C>T	19.37:g.15651480C>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	102	23	NM_173483	0	0	0	0	0	Q8N8H4	Silent	SNP	ENST00000269703.3	37	CCDS12331.1																																																																																			.		0.652	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		T	15651480	C	T	15651480	2	4	152	1	0	0	0	0	0	0	0	1	4195	581	21	2		2	CYP4F22	19	15651480	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	9175536	15651480	43477503	77	13704											
NCAN	1463	broad.mit.edu	37	chr19	19338433	19338433	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccaccgccacggctccAccctcccctgctgcagagac	7	4	10	20	2	0	1	0	0	0	1	2	3	2	1	7	2	2	3	7	2	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:19338433A>C	ENST00000252575.6	+	8	2103	c.2004A>C	c.(2002-2004)ccA>ccC	p.P668P	NCAN_ENST00000538881.1_Silent_p.P119P	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	668					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	CCACGGCTCCACCCTCCCCTG	0.617																																					p.P668P													.	NCAN-94	0			c.A2004C						.						94	97	96					19																	19338433		2203	4300	6503	SO:0001819	synonymous_variant	1463	exon8			GGCTCCACCCTCC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans", "Endogenous ligands"	2465	protein-coding gene	gene with protein product	"neurocan proteoglycan"	600826	"chondroitin sulfate proteoglycan 3"	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.2004A>C	19.37:g.19338433A>C		Somatic	134	9		WXS	Illumina HiSeq	Phase_I	175	27	NM_004386	0	0	0	0	0	Q9UPK6	Silent	SNP	ENST00000252575.6	37	CCDS12397.1																																																																																			.		0.617	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		C	19338433	A	C	19338433	2	2	152	1	0	0	0	0	0	0	0	1	10230	146	6	5		5	NCAN	19	19338433	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	3686953	19338433	39790550	78	13705											
MLL4	9757	ucsc.edu;bcgsc.ca	37	chr19	36210764	36210764	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctagcagatgtggctcctaCccccccaaagacccctgccc	8	6	7	20	0	0	2	0	0	0	2	1	2	1	2	8	1	3	2	8	1	3	2	rs60207923	byFrequency	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:36210764C>A	ENST00000222270.7	+	3	515	c.515C>A	c.(514-516)aCc>aAc	p.T172N	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000341701.1_Missense_Mutation_p.T172N|KMT2B_ENST00000420124.1_Missense_Mutation_p.T172N	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	172			T -> I (in dbSNP:rs60207923).		chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GTGGCTCCTACCCCCCCAAAG	0.632																																					p.T172N													.	MLL4-697	0			c.C515A						.						44	52	50					19																	36210764		1952	4133	6085	SO:0001583	missense	8085	exon3			CTCCTACCCCCCC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"Chromatin-modifying enzymes / K-methyltransferases"	15840	protein-coding gene	gene with protein product	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.515C>A	19.37:g.36210764C>A	ENSP00000222270:p.Thr172Asn	Somatic	254	1		WXS	Illumina HiSeq		200	74	NM_014727	0	0	0	0	0	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.186587	0.57909	.	.	ENSG00000105663	ENST00000222270;ENST00000420124;ENST00000341701	D;D;T	0.84944	-1.92;-1.92;0.74	5.06	0.327	0.15913	.	1.012260	0.07944	N	0.979811	T	0.68540	0.3012	N	0.08118	0	0.23260	N	0.998024	B	0.02656	0.0	B	0.01281	0.0	T	0.56968	-0.7891	10	0.66056	D	0.02	.	4.2499	0.10689	0.1601:0.5853:0.0:0.2545	.	172	Q9UMN6	MLL4_HUMAN	N	172	ENSP00000222270:T172N;ENSP00000398837:T172N;ENSP00000345761:T172N	ENSP00000222270:T172N	T	+	2	0	AD000671.1	40902604	0.045000	0.20229	0.988000	0.46212	0.996000	0.88848	0.030000	0.13688	0.019000	0.15079	0.561000	0.74099	ACC	C|0.998;T|0.002		0.632	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		A	36210764	C	A	36210764	3	1	152	1	0	0	0	0	1	0	0	0	9648	507	18	4	525	4	MLL4	19	36210764	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	16872331	36210764	22918219	79	13706											
CAPN12	147968	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	39226166	39226166	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagactgcaggtctgcgctGatcacgtcgtcgatctccct	7	10	11	13	4	3	2	1	1	2	1	6	4	3	2	1	1	2	2	1	1	0	0	rs267605468		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:39226166G>T	ENST00000328867.4	-	13	1910	c.1602C>A	c.(1600-1602)atC>atA	p.I534I	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.I385I	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	534	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GGTCTGCGCTGATCACGTCGT	0.642																																					p.I534I		.											.	CAPN12-91	0			c.C1602A						.						38	36	37					19																	39226166		2192	4295	6487	SO:0001819	synonymous_variant	147968	exon13			TGCGCTGATCACG	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"EF-hand domain containing"	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1602C>A	19.37:g.39226166G>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	75	26	NM_144691	0	0	0	6	6		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			.		0.642	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39226166	G	T	39226166	2	4	152	1	0	0	0	0	0	0	0	1	2631	1280	45	4		4	CAPN12	19	39226166	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	3015402	39226166	19902817	80	13707											
PSG5	5673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	43689069	43689069	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcattggaatatactgtttCtcgtccagtgtatgcaggcc	8	14	10	9	1	1	0	0	0	1	0	3	1	2	1	2	2	3	4	2	2	4	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:43689069C>A	ENST00000366175.3	-	2	425	c.295G>T	c.(295-297)Gaa>Taa	p.E99*	PSG5_ENST00000342951.6_Nonsense_Mutation_p.E99*|PSG5_ENST00000407568.1_Nonsense_Mutation_p.E99*|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000404580.1_Nonsense_Mutation_p.E99*|PSG5_ENST00000599812.1_Nonsense_Mutation_p.E99*|PSG5_ENST00000407356.1_Nonsense_Mutation_p.E99*			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	99	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TATACTGTTTCTCGTCCAGTG	0.438																																					p.E99X		.											.	PSG5-93	0			c.G295T						.						331	309	317					19																	43689069		2203	4295	6498	SO:0001587	stop_gained	5673	exon2			CTGTTTCTCGTCC		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9522	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta 1 glycoprotein"	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.295G>T	19.37:g.43689069C>A	ENSP00000382334:p.Glu99*	Somatic	254	0		WXS	Illumina HiSeq	Phase_I	252	79	NM_002781	0	0	0	0	0	Q15239|Q96QJ1|Q9UQ75	Nonsense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	.	.	.	.	.	.	.	.	.	.	N	17.25	3.342999	0.61073	.	.	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000407568;ENST00000342951;ENST00000404580;ENST00000401992	.	.	.	1.58	1.58	0.23477	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.6423	0.22917	0.0:1.0:0.0:0.0	.	.	.	.	X	99	.	ENSP00000344413:E99X	E	-	1	0	PSG5	48380909	0.000000	0.05858	0.161000	0.22692	0.021000	0.10359	-0.245000	0.08890	1.195000	0.43115	0.423000	0.28283	GAA	.		0.438	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781		A	43689069	C	A	43689069	4	1	152	1	0	0	0	0	0	1	0	0	12687	922	32	4	728	4	PSG5	19	43689069	Nonsense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	4462903	43689069	15439914	81	13708											
MYPOP	339344	broad.mit.edu	37	chr19	46394285	46394285	+	Frame_Shift_Del	DEL	G	G	-																															ggcgttggcagtctcctgctGggcccgcaggaagtccaggg																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:46394285delG	ENST00000322217.5	-	3	882	c.796delC	c.(796-798)cagfs	p.Q267fs		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	267	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						GTCTCCTGCTGGGCCCGCAGG	0.706																																					p.Q266fs													.	MYPOP-90	0			c.796delC						.						6	5	6					19																	46394285		2129	4163	6292	SO:0001589	frameshift_variant	339344	exon3			CCTGCTGGGCCCG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"p42 Myb-related transcription factor, partner of profilin"					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.796delC	19.37:g.46394285delG	ENSP00000325402:p.Gln267fs	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	17	7	NM_001012643	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000322217.5	37	CCDS33055.1																																																																																			.		0.706	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643		-	46394285	G	-	46394285	7	5	152	1	0	1	0	1	0	0	0	0	10124	1357	47	0	407	0	MYPOP	19	46394285	Frame_Shift_Del	DEL	G	TCGA-MH-A562-01A-11D-A26P-10	2705216	46394285	12734698	82	13709											
LILRB3	11025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54721052	54721052	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcagttgccttccgtctaagGgtcaagctgtgcagctgggc	6	11	13	11	1	3	0	2	0	1	0	4	0	4	0	2	2	4	4	2	2	2	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:54721052G>T	ENST00000391750.1	-	14	1942	c.1806C>A	c.(1804-1806)acC>acA	p.T602T	LILRA6_ENST00000419410.2_Silent_p.T603T|LILRB3_ENST00000245620.9_Silent_p.T603T|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Silent_p.T602T|LILRB3_ENST00000407860.2_Silent_p.T619T|LILRA6_ENST00000270464.5_Silent_p.T603T|LILRB3_ENST00000424807.1_Silent_p.T602T|LILRB3_ENST00000346401.6_Silent_p.T614T|LILRA6_ENST00000391735.3_3'UTR			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	602					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCCGTCTAAGGGTCAAGCTGT	0.632																																					p.T603T		.											.	LILRB3-93	0			c.C1809A						.						104	105	105					19																	54721052		2202	4300	6502	SO:0001819	synonymous_variant	11025	exon13			TCTAAGGGTCAAG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1806C>A	19.37:g.54721052G>T		Somatic	180	0		WXS	Illumina HiSeq	Phase_I	189	101	NM_001081450	0	0	0	0	0	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			.		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		T	54721052	G	T	54721052	2	4	152	1	0	0	0	0	0	0	0	1	8814	1219	43	4		4	LILRB3	19	54721052	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	8326767	54721052	4407931	83	13710											
BCL2L1	598	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	30253881	30253881	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttcccatagagttccacAaaagtatcctgcagggagag	12	10	10	9	0	0	2	0	0	0	2	3	3	3	2	3	1	1	4	3	1	4	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr20:30253881A>G	ENST00000307677.4	-	3	983	c.573T>C	c.(571-573)ttT>ttC	p.F191F	BCL2L1_ENST00000376062.2_Silent_p.F191F|BCL2L1_ENST00000376055.4_Silent_p.F128F|BCL2L1_ENST00000420653.1_Silent_p.F191F	NM_138578.1	NP_612815.1	Q07817	B2CL1_HUMAN	BCL2-like 1	191					apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process in bone marrow (GO:0071839)|cell proliferation (GO:0008283)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to alkaloid (GO:0071312)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cytokinesis (GO:0000910)|endocytosis (GO:0006897)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fertilization (GO:0009566)|germ cell development (GO:0007281)|growth (GO:0040007)|hepatocyte apoptotic process (GO:0097284)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|release of cytochrome c from mitochondria (GO:0001836)|response to cycloheximide (GO:0046898)|response to cytokine (GO:0034097)|spermatogenesis (GO:0007283)|suppression by virus of host apoptotic process (GO:0019050)	Bcl-2 family protein complex (GO:0097136)|cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synapse (GO:0045202)	BH3 domain binding (GO:0051434)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			AGAGTTCCACAAAAGTATCCT	0.567																																					p.F191F	Colon(51;693 1004 1401 20431 21026)	.											.	BCL2L1-1084	0			c.T573C						.						84	78	80					20																	30253881		2203	4300	6503	SO:0001819	synonymous_variant	598	exon3			TTCCACAAAAGTA	Z23115	CCDS13188.1, CCDS13189.1	20q11.21	2014-03-07			ENSG00000171552	ENSG00000171552		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	992	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 52"	600039				8358789	Standard	NM_001191		Approved	BCLX, BCL2L, Bcl-X, bcl-xL, bcl-xS, PPP1R52	uc002wwl.3	Q07817	OTTHUMG00000032192	ENST00000307677.4:c.573T>C	20.37:g.30253881A>G		Somatic	84	0		WXS	Illumina HiSeq	Phase_I	137	71	NM_138578	0	0	0	0	0	E1P5L6|Q5CZ89|Q5TE65|Q92976	Silent	SNP	ENST00000307677.4	37	CCDS13189.1																																																																																			.		0.567	BCL2L1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078575.1	NM_138578		G	30253881	A	G	30253881	2	3	152	1	0	0	0	0	0	0	0	1	1368	127	5	3		3	BCL2L1	20	30253881	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		30253881	32771639	84	13711											
ADAMTS5	11096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	28305272	28305272	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctgggagcagggttattaCagtgacgataggcaaactgc	11	10	13	7	1	1	1	0	1	1	0	1	3	1	2	0	3	4	3	0	3	4	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr21:28305272C>G	ENST00000284987.5	-	5	1902	c.1781G>C	c.(1780-1782)tGt>tCt	p.C594S	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	594	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						AGGGTTATTACAGTGACGATA	0.567																																					p.C594S	Esophageal Squamous(53;683 1080 10100 14424 45938)	.											.	ADAMTS5-229	0			c.G1781C						.						152	105	121					21																	28305272		2203	4300	6503	SO:0001583	missense	11096	exon5			TTATTACAGTGAC	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1781G>C	21.37:g.28305272C>G	ENSP00000284987:p.Cys594Ser	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	198	57	NM_007038	0	0	0	0	0	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	33	5.248311	0.95305	.	.	ENSG00000154736	ENST00000284987	T	0.69040	-0.37	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.91778	0.7399	H	0.99922	4.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95071	0.8204	10	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	594	Q9UNA0	ATS5_HUMAN	S	594	ENSP00000284987:C594S	ENSP00000284987:C594S	C	-	2	0	ADAMTS5	27227143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.854000	0.98071	0.655000	0.94253	TGT	.		0.567	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			G	28305272	C	G	28305272	3	3	152	1	0	0	0	0	1	0	0	0	269	478	17	4	1027	4	ADAMTS5	21	28305272	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		28305272	19824623	85	13712											
SEZ6L	23544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	26761491	26761491	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaccatccgctgcatcctggGacagccatcccactggaacg	9	6	10	16	2	0	0	0	0	0	0	3	3	3	2	5	2	3	2	5	2	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr22:26761491G>A	ENST00000248933.6	+	13	2848	c.2753G>A	c.(2752-2754)gGa>gAa	p.G918E	SEZ6L_ENST00000529632.2_Missense_Mutation_p.G918E|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G918E|SEZ6L_ENST00000343706.4_Intron|SEZ6L_ENST00000411842.2_Missense_Mutation_p.G115E|SEZ6L_ENST00000402979.1_Missense_Mutation_p.G691E|SEZ6L_ENST00000403121.1_Intron|SEZ6L_ENST00000360929.3_Missense_Mutation_p.G854E|SEZ6L_ENST00000494013.1_3'UTR			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	918	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TGCATCCTGGGACAGCCATCC	0.582																																					p.G918E		.											.	SEZ6L-95	0			c.G2753A						.						82	73	76					22																	26761491		2203	4300	6503	SO:0001583	missense	23544	exon13			TCCTGGGACAGCC	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"seizure related gene 6 (mouse)-like"				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2753G>A	22.37:g.26761491G>A	ENSP00000248933:p.Gly918Glu	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	149	49	NM_021115	0	0	0	0	0	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.605986	0.87157	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000402979;ENST00000411842	T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	5.27	5.27	0.74061	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.53938	D	0.000046	T	0.80884	0.4709	M	0.80332	2.49	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.83060	-0.0148	10	0.87932	D	0	.	18.0747	0.89423	0.0:0.0:1.0:0.0	.	918;918;854;918;918	B7ZLJ8;B7ZLJ6;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;SE6L1_HUMAN	E	918;918;854;918;691;115	ENSP00000384772:G918E;ENSP00000437037:G918E;ENSP00000354185:G854E;ENSP00000248933:G918E;ENSP00000384733:G691E;ENSP00000397274:G115E	ENSP00000248933:G918E	G	+	2	0	SEZ6L	25091491	1.000000	0.71417	0.997000	0.53966	0.731000	0.41821	8.973000	0.93428	2.735000	0.93741	0.655000	0.94253	GGA	.		0.582	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26761491	G	A	26761491	3	1	152	1	0	0	0	0	1	0	0	0	14175	1174	41	2	2803	2	SEZ6L	22	26761491	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		26761491	24543075	86	13713											
PTCHD1	139411	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	23411325	23411325	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggttttacatatatgagtctAtagaatactggaacactagt	14	14	8	5	0	1	2	0	1	1	1	1	3	1	3	0	2	3	1	0	2	9	8			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chrX:23411325A>G	ENST00000379361.4	+	3	2550	c.1690A>G	c.(1690-1692)Ata>Gta	p.I564V		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	564					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						ATATGAGTCTATAGAATACTG	0.413																																					p.I564V													.	PTCHD1-135	0			c.A1690G						.						94	89	91					X																	23411325		2203	4300	6503	SO:0001583	missense	139411	exon3			GAGTCTATAGAAT	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1690A>G	X.37:g.23411325A>G	ENSP00000368666:p.Ile564Val	Somatic	56	1		WXS	Illumina HiSeq	Phase_I	41	10	NM_173495	0	0	0	0	0	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	37	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	A	6.272	0.418245	0.11870	.	.	ENSG00000165186	ENST00000379361	D	0.84800	-1.9	5.69	5.69	0.88448	.	0.106864	0.64402	D	0.000004	T	0.73009	0.3532	N	0.20685	0.6	0.33814	D	0.628248	B	0.17667	0.023	B	0.12837	0.008	T	0.71988	-0.4426	10	0.15066	T	0.55	.	10.9815	0.47497	0.8463:0.1537:0.0:0.0	.	564	Q96NR3	PTHD1_HUMAN	V	564	ENSP00000368666:I564V	ENSP00000368666:I564V	I	+	1	0	PTCHD1	23321246	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.967000	0.76079	1.904000	0.55121	0.486000	0.48141	ATA	.		0.413	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		G	23411325	A	G	23411325	3	3	152	1	0	0	0	0	1	0	0	0	12761	449	16	3	1700	3	PTCHD1	23	23411325	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		23411325	131859235	87	13714											
PLS3	5358	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	114880464	114880465	+	Frame_Shift_Ins	INS	-	-	A																															ctgttgactggagtaaggttINSaataaacctccatacccgaa																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chrX:114880464_114880465insA	ENST00000420625.2	+	12	1469_1470	c.1335_1336insA	c.(1336-1338)aatfs	p.N446fs	PLS3_ENST00000289290.3_Frame_Shift_Ins_p.N410fs|PLS3_ENST00000537301.1_Frame_Shift_Ins_p.N433fs|PLS3_ENST00000355899.3_Frame_Shift_Ins_p.N446fs|PLS3_ENST00000539310.1_Frame_Shift_Ins_p.N401fs|PLS3_ENST00000543070.1_Frame_Shift_Ins_p.N40fs	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	446	Actin-binding 2.|CH 3. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						GGAGTAAGGTTAATAAACCTCC	0.322																																					p.V445fs	Colon(160;1047 1864 8490 12969 29601)	.											.	PLS3-193	0			c.1335_1336insA						.																																			SO:0001589	frameshift_variant	5358	exon12			.	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"EF-hand domain containing"	9091	protein-coding gene	gene with protein product		300131	"plastin 3 (T isoform)"			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.1337dupA	X.37:g.114880466_114880466dupA	ENSP00000398945:p.Asn446fs	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	141	92	NM_005032	0	0	0	0	0	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Frame_Shift_Ins	INS	ENST00000420625.2	37	CCDS14568.1																																																																																			.		0.322	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			A	114880465	-	A	114880464	7	5	152	1	0	1	1	0	0	0	0	0	12134	1741	61	0	1377	0	PLS3	23	114880464	Frame_Shift_Ins	INS	-	TCGA-MH-A562-01A-11D-A26P-10	91469139	114880464	40390096	88	13715											
GNB1	2782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	1720557	1720557	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcgtacccagcaaggaggAggcgcccgctcttggagaag	9	5	15	12	4	1	1	0	0	1	1	2	4	1	3	2	4	2	3	2	4	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:1720557A>C	ENST00000378609.4	-	10	1182	c.851T>G	c.(850-852)cTc>cGc	p.L284R		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	284					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		AGCAAGGAGGAGGCGCCCGCT	0.572											OREG0012998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L284R		.											.	GNB1-227	0			c.T851G						.						100	94	96					1																	1720557		2203	4300	6503	SO:0001583	missense	2782	exon10			AGGAGGAGGCGCC	BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"WD repeat domain containing"	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.851T>G	1.37:g.1720557A>C	ENSP00000367872:p.Leu284Arg	Somatic	143	0	598	WXS	Illumina HiSeq	Phase_I	145	67	NM_002074	0	0	97	140	43	B1AJZ7|P04697|P04901|Q1RMY8	Missense_Mutation	SNP	ENST00000378609.4	37	CCDS34.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.290122|4.290122	0.80914|0.80914	.|.	.|.	ENSG00000078369|ENSG00000078369	ENST00000378609;ENST00000455156;ENST00000378606|ENST00000424622	T|.	0.62105|.	0.05|.	5.52|5.52	5.52|5.52	0.82312|0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76528|0.76528	0.4000|0.4000	M|M	0.80847|0.80847	2.515|2.515	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.81914|.	0.995|.	T|T	0.78219|0.78219	-0.2289|-0.2289	10|5	0.51188|.	T|.	0.08|.	-9.8798|-9.8798	14.8181|14.8181	0.70050|0.70050	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	284|.	P62873|.	GBB1_HUMAN|.	R|A	284;184;284|142	ENSP00000367872:L284R|.	ENSP00000367869:L284R|.	L|S	-|-	2|1	0|0	GNB1|GNB1	1710417|1710417	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.885000|0.885000	0.51271|0.51271	9.126000|9.126000	0.94411|0.94411	2.096000|2.096000	0.63516|0.63516	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.		0.572	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	NM_002074		C	1720557	A	C	1720557	3	2	153	1	0	0	0	0	1	0	0	0	6535	304	11	5	179	5	GNB1	1	1720557	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		1720557	247530064	1	13716											
HES3	390992	hgsc.bcm.edu	37	chr1	6305201	6305201	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgcccaggggagccgagcaAccgtcgggcttccgcagctg	6	5	16	14	4	0	0	0	0	0	0	2	2	1	1	4	3	5	4	4	3	1	1	rs188463518	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:6305201A>C	ENST00000377898.3	+	4	260	c.195A>C	c.(193-195)caA>caC	p.Q65H		NM_001024598.3	NP_001019769.1	Q5TGS1	HES3_HUMAN	hes family bHLH transcription factor 3	65	Orange.				hindbrain morphogenesis (GO:0021575)|in utero embryonic development (GO:0001701)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oculomotor nerve development (GO:0021557)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription, DNA-templated (GO:0006351)|trochlear nerve development (GO:0021558)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			lung(2)|skin(1)	3	Ovarian(185;0.0634)	all_cancers(23;2.48e-32)|all_epithelial(116;1.14e-17)|all_lung(118;2.85e-06)|all_neural(13;3.68e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;3.77e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.2e-37)|GBM - Glioblastoma multiforme(13;3.2e-29)|OV - Ovarian serous cystadenocarcinoma(86;2.52e-19)|Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00308)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.241)		GAGCCGAGCAACCGTCGGGCT	0.721													C|||	221	0.0441294	0.0741	0.0159	5008	,	,		7481	0.0308		0.007	False		,,,				2504	0.0757				p.Q65H		.											.	HES3-514	0			c.A195C						.	C	HIS/GLN	138,3116		2,134,1491	3	3	3		195	2.3	0.4	1		3	36,7122		0,36,3543	no	missense	HES3	NM_001024598.3	24	2,170,5034	CC,CA,AA		0.5029,4.2409,1.6711	benign	65/187	6305201	174,10238	1627	3579	5206	SO:0001583	missense	390992	exon4			CGAGCAACCGTCG		CCDS41238.1	1p36.31	2013-10-17	2013-10-17		ENSG00000173673	ENSG00000173673		"Basic helix-loop-helix proteins"	26226	protein-coding gene	gene with protein product		609971	"hairy and enhancer of split 3 (Drosophila)"				Standard	NM_001024598		Approved	bHLHb43	uc009vly.2	Q5TGS1	OTTHUMG00000001271	ENST00000377898.3:c.195A>C	1.37:g.6305201A>C	ENSP00000367130:p.Gln65His	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	21	9	NM_001024598	0	0	0	0	0	Q5TGS0	Missense_Mutation	SNP	ENST00000377898.3	37	CCDS41238.1	73	0.033424908424908424	40	0.08130081300813008	7	0.019337016574585635	19	0.033216783216783216	7	0.009234828496042216	C	9.558	1.117756	0.20877	0.042409	0.005029	ENSG00000173673	ENST00000377898	T	0.31510	1.49	3.2	2.28	0.28536	.	0.393226	0.19492	N	0.112980	T	0.00580	0.0019	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18178	-1.0345	10	0.66056	D	0.02	-10.1808	4.0729	0.09891	0.2297:0.645:0.0:0.1253	.	65	Q5TGS1	HES3_HUMAN	H	65	ENSP00000367130:Q65H	ENSP00000367130:Q65H	Q	+	3	2	HES3	6227788	0.055000	0.20627	0.403000	0.26384	0.425000	0.31504	0.673000	0.25203	0.398000	0.25338	-0.763000	0.03452	CAA	A|0.967;C|0.033		0.721	HES3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003716.3	NM_001024598		C	6305201	A	C	6305201	3	2	153	1	0	0	0	0	1	0	0	0	7088	40	2	5	205	5	HES3	1	6305201	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	4584644	6305201	242945420	2	13717											
DNAJC16	23341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	15855696	15855696	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggattttgacccatacagAgtcctaggggtcagccgaac	10	10	11	10	1	1	2	1	1	0	1	2	4	2	3	3	3	3	0	3	3	3	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:15855696A>C	ENST00000375847.3	+	2	260	c.96A>C	c.(94-96)agA>agC	p.R32S	CASP9_ENST00000469637.1_5'Flank|DNAJC16_ENST00000375838.1_Missense_Mutation_p.R32S|DNAJC16_ENST00000375849.1_Missense_Mutation_p.R32S	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	32	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		ACCCATACAGAGTCCTAGGGG	0.443																																					p.R32S		.											.	DNAJC16-226	0			c.A96C						.						109	107	108					1																	15855696		2203	4300	6503	SO:0001583	missense	23341	exon2			ATACAGAGTCCTA	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.96A>C	1.37:g.15855696A>C	ENSP00000365007:p.Arg32Ser	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	120	47	NM_015291	0	0	0	0	0	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	37	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678494	0.47886	.	.	ENSG00000116138	ENST00000375847;ENST00000375838;ENST00000375849;ENST00000546230	T;T;T	0.72282	-0.64;-0.64;-0.64	5.41	5.41	0.78517	Heat shock protein DnaJ, N-terminal (5);	0.092613	0.64402	D	0.000001	T	0.41465	0.1160	N	0.02111	-0.68	0.24628	N	0.99364	B;B	0.28208	0.166;0.203	B;B	0.24848	0.056;0.052	T	0.29518	-1.0009	10	0.38643	T	0.18	-23.0336	8.0421	0.30527	0.9101:0.0:0.0899:0.0	.	32;32	Q9Y2G8;Q5TDG9	DJC16_HUMAN;.	S	32	ENSP00000365007:R32S;ENSP00000364998:R32S;ENSP00000365009:R32S	ENSP00000364998:R32S	R	+	3	2	DNAJC16	15728283	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.233000	0.51311	2.060000	0.61445	0.460000	0.39030	AGA	.		0.443	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		C	15855696	A	C	15855696	3	2	153	1	0	0	0	0	1	0	0	0	4646	301	11	5	98	5	DNAJC16	1	15855696	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	9550495	15855696	233394925	3	13718											
UBR4	23352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	19500887	19500887	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgcaagcagggctgtcaGtgcagcataaagctcatcat	12	8	11	10	0	3	0	3	0	0	0	3	0	3	0	0	1	6	7	0	1	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:19500887G>T	ENST00000375254.3	-	22	2935	c.2908C>A	c.(2908-2910)Ctg>Atg	p.L970M	UBR4_ENST00000375217.2_Missense_Mutation_p.L970M|UBR4_ENST00000375267.2_Missense_Mutation_p.L970M|UBR4_ENST00000375226.2_Missense_Mutation_p.L970M	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	970					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AGGGCTGTCAGTGCAGCATAA	0.438																																					p.L970M		.											.	UBR4-612	0			c.C2908A						.						120	102	108					1																	19500887		2203	4300	6503	SO:0001583	missense	23352	exon22			CTGTCAGTGCAGC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"Ubiquitin protein ligase E3 component n-recognins"	30313	protein-coding gene	gene with protein product		609890	"zinc finger, UBR1 type 1"	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.2908C>A	1.37:g.19500887G>T	ENSP00000364403:p.Leu970Met	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	37	11	NM_020765	0	0	3	3	0	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.982527	0.53827	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.36699	1.26;1.26;1.24;1.24	5.76	-1.65	0.08291	.	0.000000	0.64402	D	0.000001	T	0.44371	0.1290	L	0.39898	1.24	0.80722	D	1	D	0.65815	0.995	D	0.70487	0.969	T	0.26467	-1.0102	10	0.87932	D	0	.	11.0624	0.47955	0.5235:0.0:0.4765:0.0	.	970	Q5T4S7	UBR4_HUMAN	M	970;970;970;970;186	ENSP00000364403:L970M;ENSP00000364416:L970M;ENSP00000364365:L970M;ENSP00000364374:L970M	ENSP00000364365:L970M	L	-	1	2	UBR4	19373474	0.850000	0.29656	0.011000	0.14972	0.823000	0.46562	1.167000	0.31847	-0.623000	0.05618	-0.768000	0.03414	CTG	.		0.438	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19500887	G	T	19500887	3	4	153	1	0	0	0	0	1	0	0	0	16937	1020	36	4	12983	4	UBR4	1	19500887	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	3645191	19500887	229749734	4	13719											
USP48	84196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	22073615	22073615	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgagaagccaatgtaggtAttcagctttttcttatgtcc	9	16	8	8	0	3	1	1	1	2	1	4	2	4	1	2	1	2	3	2	1	5	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:22073615A>G	ENST00000308271.9	-	8	1584	c.936T>C	c.(934-936)aaT>aaC	p.N312N	USP48_ENST00000529637.1_Silent_p.N312N|USP48_ENST00000400301.1_Silent_p.N312N|USP48_ENST00000421625.2_Silent_p.N312N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	312	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CAATGTAGGTATTCAGCTTTT	0.313																																					p.N312N		.											.	USP48-659	0			c.T936C						.						94	91	92					1																	22073615		2203	4300	6503	SO:0001819	synonymous_variant	84196	exon8			GTAGGTATTCAGC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"Ubiquitin-specific peptidases"	18533	protein-coding gene	gene with protein product			"ubiquitin specific protease 31", "ubiquitin specific protease 48"	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.936T>C	1.37:g.22073615A>G		Somatic	18	0		WXS	Illumina HiSeq	Phase_I	18	5	NM_001032730	0	0	0	2	2	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			.		0.313	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		G	22073615	A	G	22073615	2	3	153	1	0	0	0	0	0	0	0	1	17112	446	16	3		3	USP48	1	22073615	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	2572728	22073615	227177006	5	13720											
MECR	51102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	29520638	29520638	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagcaggcaggggctgtgaGctggcctcggcggatgagat	7	6	20	8	2	0	2	0	2	0	1	1	5	0	4	1	7	2	4	1	7	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:29520638G>C	ENST00000263702.6	-	10	1043	c.1018C>G	c.(1018-1020)Ctc>Gtc	p.L340V	MECR_ENST00000373791.3_Missense_Mutation_p.L264V			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	340					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		GGGGCTGTGAGCTGGCCTCGG	0.572																																					p.L340V		.											.	MECR-91	0			c.C1018G						.						102	109	107					1																	29520638		2203	4300	6503	SO:0001583	missense	51102	exon10			CTGTGAGCTGGCC		CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"nuclear receptor binding factor 1", "mitochondrial 2-enoyl thioester reductase"	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.1018C>G	1.37:g.29520638G>C	ENSP00000263702:p.Leu340Val	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	96	30	NM_016011	0	0	22	65	43	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	ENST00000263702.6	37	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.554761	0.65425	.	.	ENSG00000116353	ENST00000373791;ENST00000263702	T;T	0.05199	3.48;3.49	5.48	5.48	0.80851	NAD(P)-binding domain (1);	0.133396	0.53938	D	0.000051	T	0.27169	0.0666	M	0.88181	2.935	0.58432	D	0.999999	P	0.45348	0.856	P	0.55749	0.783	T	0.01583	-1.1319	10	0.59425	D	0.04	.	16.849	0.85988	0.0:0.0:1.0:0.0	.	340	Q9BV79	MECR_HUMAN	V	264;340	ENSP00000362896:L264V;ENSP00000263702:L340V	ENSP00000263702:L340V	L	-	1	0	MECR	29393225	1.000000	0.71417	1.000000	0.80357	0.411000	0.31082	6.509000	0.73725	2.584000	0.87258	0.563000	0.77884	CTC	.		0.572	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	NM_016011		C	29520638	G	C	29520638	3	2	153	1	0	0	0	0	1	0	0	0	9449	971	34	4	107	4	MECR	1	29520638	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	7447023	29520638	219729983	6	13721											
SMAP2	64744	ucsc.edu;bcgsc.ca	37	chr1	40839876	40839876	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggataacaagttttgTgcagattgccagtctaaagg	13	10	13	5	0	1	1	0	0	1	1	1	4	1	3	1	3	3	2	1	3	4	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:40839876T>A								COL9A2 (56910 upstream) : SMAP2 (22630 downstream)																							ACAAGTTTTGTGCAGATTGCC	0.642																																					p.C28X													.	SMAP2-68	0			c.T84A						.						79	67	71					1																	40839876		2203	4300	6503	SO:0001628	intergenic_variant	64744	exon1			GTTTTGTGCAGAT																													1.37:g.40839876T>A		Somatic	366	2		WXS	Illumina HiSeq		575	220	NM_022733	0	0	1	1	0		Nonsense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	T	42	9.178274	0.99091	.	.	ENSG00000084070	ENST00000435168;ENST00000372718	.	.	.	5.25	1.62	0.23740	.	0.313290	0.36002	N	0.002852	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0719	3.5082	0.07699	0.1643:0.1819:0.0:0.6538	.	.	.	.	X	28	.	ENSP00000361803:C28X	C	+	3	2	SMAP2	40612463	0.999000	0.42202	0.988000	0.46212	0.991000	0.79684	0.291000	0.18994	0.015000	0.14971	0.460000	0.39030	TGT	.	0	0.642									A	40839876	T	A	40839876	1	1	153	0	1	0	0	0	0	0	0	0	14799	1702	59	5		5	SMAP2	1	40839876	IGR	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	11319238	40839876	208410745	7	13722											
PTPRF	5792	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	44083552	44083552	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcgcacggccactgtggtCatgatgacacggctggagga	9	6	15	11	3	1	2	1	2	0	0	1	4	1	4	1	5	1	2	1	5	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:44083552C>T	ENST00000359947.4	+	25	4681	c.4341C>T	c.(4339-4341)gtC>gtT	p.V1447V	PTPRF_ENST00000372413.3_Silent_p.V1438V|PTPRF_ENST00000372414.3_Silent_p.V1447V|PTPRF_ENST00000422171.2_Silent_p.V806V|PTPRF_ENST00000438120.1_Silent_p.V1438V|PTPRF_ENST00000496447.1_3'UTR	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1447	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCACTGTGGTCATGATGACAC	0.637																																					p.V1447V													.	PTPRF-232	0			c.C4341T						.						48	47	47					1																	44083552		2203	4300	6503	SO:0001819	synonymous_variant	5792	exon25			TGTGGTCATGATG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4341C>T	1.37:g.44083552C>T		Somatic	263	1		WXS	Illumina HiSeq	Phase_I	330	114	NM_002840	0	0	18	32	14	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.16|10.16	1.275097|1.275097	0.23307|0.23307	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.58|5.58	4.67|4.67	0.58626|0.58626	.|.	.|.	.|.	.|.	.|.	T|T	0.70509|0.70509	0.3232|0.3232	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.70256|0.70256	-0.4922|-0.4922	4|4	.|.	.|.	.|.	.|.	14.8271|14.8271	0.70122|0.70122	0.0:0.9307:0.0:0.0693|0.0:0.9307:0.0:0.0693	.|.	.|.	.|.	.|.	Y|L	831;872|1093	.|.	.|.	H|S	+|+	1|2	0|0	PTPRF|PTPRF	43856139|43856139	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	0.916000|0.916000	0.28651|0.28651	1.506000|1.506000	0.48736|0.48736	-0.140000|-0.140000	0.14226|0.14226	CAT|TCA	.		0.637	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44083552	C	T	44083552	2	4	153	1	0	0	0	0	0	0	0	1	12833	813	29	2		2	PTPRF	1	44083552	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	3243676	44083552	205167069	8	13723											
INADL	10207	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	62271194	62271194	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgggtcctgattatgaagtaAtggtatgttaaaatgctcta	12	15	10	4	0	1	2	0	2	1	0	2	2	2	2	1	2	1	4	1	2	7	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:62271194A>G	ENST00000371158.2	+	13	1738	c.1624A>G	c.(1624-1626)Atg>Gtg	p.M542V	INADL_ENST00000316485.6_Missense_Mutation_p.M542V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	542					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TTATGAAGTAATGGTATGTTA	0.358																																					p.M542V		.											.	INADL-94	0			c.A1624G						.						93	99	97					1																	62271194		2203	4300	6503	SO:0001583	missense	10207	exon13			GAAGTAATGGTAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1624A>G	1.37:g.62271194A>G	ENSP00000360200:p.Met542Val	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	73	25	NM_176877	0	0	0	0	0	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	17.77	3.472247	0.63737	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.08546	3.27;3.08	5.69	5.69	0.88448	PDZ/DHR/GLGF (1);	0.057835	0.64402	D	0.000002	T	0.21186	0.0510	M	0.62723	1.935	0.80722	D	1	D;D;P	0.67145	0.996;0.986;0.488	D;D;P	0.77557	0.99;0.965;0.508	T	0.08868	-1.0701	10	0.02654	T	1	.	14.5128	0.67800	1.0:0.0:0.0:0.0	.	542;542;542	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	V	542	ENSP00000360200:M542V;ENSP00000326199:M542V	ENSP00000255202:M542V	M	+	1	0	INADL	62043782	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.401000	0.52601	2.174000	0.68829	0.528000	0.53228	ATG	.		0.358	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62271194	A	G	62271194	3	3	153	1	0	0	0	0	1	0	0	0	7752	101	4	3	1670	3	INADL	1	62271194	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	18187642	62271194	186979427	9	13724											
CCDC18	343099	broad.mit.edu;bcgsc.ca	37	chr1	93705010	93705043	+	Splice_Site	DEL	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	-																															agatcagacaaagacagagcTagaaaagaaaacaaatgctg																								rs550574161		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:93705010_93705043delTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	ENST00000343253.7	+	20	3246_3266	c.2744_2764delTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	c.(2743-2766)ctagaaaagaaaacaaatgctggt>cgt	p.LEKKTNAG915fs	CCDC18_ENST00000401026.3_Splice_Site_p.LEKKTNAG916fs|CCDC18_ENST00000334652.5_Splice_Site_p.LEKKTNAG211fs|CCDC18_ENST00000557479.1_Splice_Site_p.LEKKTNAG1034fs|CCDC18_ENST00000421014.2_3'UTR|CCDC18_ENST00000338949.4_Splice_Site_p.LEKKTNAG671fs			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	915										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAGACAGAGCTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGTTAGATGAGTA	0.363																																					p.916_923del													.	CCDC18-138	0			c.2747_2767del						.																																			SO:0001630	splice_region_variant	343099	exon20			CAGAGCTAGAAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.2764+1TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT>-	1.37:g.93705010_93705043delTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT		Somatic	185	0		WXS	Illumina HiSeq	Phase_I	144	8	NM_206886	0	0	0	0	0	Q6ZU17	In_Frame_Del	DEL	ENST00000343253.7	37																																																																																				.		0.363	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	Frame_Shift_Del	-	93705043	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	-	93705010	8	5	153	1	0	1	0	1	0	0	1	0	2800	1522	53	0	3179	0	CCDC18	1	93705010	Splice_Site	DEL	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	TCGA-P4-A5E6-01A-11D-A28G-10	31433816	93705010	155545611	10	13725											
PRMT6	55170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	107599742	107599742	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctggaggaccgggtgcacgtCctgccgggaccagtggagac	7	5	17	12	3	0	1	0	0	0	1	1	5	1	4	4	5	2	1	4	5	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:107599742C>T	ENST00000370078.1	+	1	442	c.405C>T	c.(403-405)gtC>gtT	p.V135V	PRMT6_ENST00000361318.5_Silent_p.V76V			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	135	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		GGGTGCACGTCCTGCCGGGAC	0.672																																					p.V135V		.											.	PRMT6-90	0			c.C405T						.						72	85	81					1																	107599742		2178	4281	6459	SO:0001819	synonymous_variant	55170	exon1			GCACGTCCTGCCG	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.405C>T	1.37:g.107599742C>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	24	8	NM_018137	0	0	2	2	0	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Silent	SNP	ENST00000370078.1	37	CCDS41360.2	.	.	.	.	.	.	.	.	.	.	C	5.305	0.241690	0.10077	.	.	ENSG00000198890	ENST00000540389	.	.	.	5.75	1.4	0.22301	.	.	.	.	.	T	0.48537	0.1505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53753	-0.8394	5	0.87932	D	0	-18.1897	6.1728	0.20427	0.0:0.3898:0.4219:0.1884	.	.	.	.	S	29	.	ENSP00000440829:P29S	P	+	1	0	PRMT6	107401265	0.574000	0.26684	0.997000	0.53966	0.007000	0.05969	-0.426000	0.07008	0.714000	0.32081	0.544000	0.68410	CCT	.		0.672	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		T	107599742	C	T	107599742	2	4	153	1	0	0	0	0	0	0	0	1	12569	842	30	2		2	PRMT6	1	107599742	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	13894732	107599742	141650879	11	13726											
CRNN	49860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	152384603	152384603	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcaaactcttgctccaagAgtcttttcagctcccctcgg	7	11	8	15	2	3	1	1	0	2	1	6	1	5	1	3	2	3	3	3	2	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:152384603A>G	ENST00000271835.3	-	2	169	c.107T>C	c.(106-108)cTc>cCc	p.L36P	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	36					response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGCTCCAAGAGTCTTTTCAG	0.557																																					p.L36P		.											.	CRNN-93	0			c.T107C						.						152	132	139					1																	152384603		2203	4300	6503	SO:0001583	missense	49860	exon2			TCCAAGAGTCTTT	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"EF-hand domain containing"	1230	protein-coding gene	gene with protein product		611312	"chromosome 1 open reading frame 10"	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.107T>C	1.37:g.152384603A>G	ENSP00000271835:p.Leu36Pro	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	170	74	NM_016190	0	0	0	0	0	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518486	0.64634	.	.	ENSG00000143536	ENST00000271835;ENST00000451038	T	0.36340	1.26	4.78	3.65	0.41850	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.164580	0.29021	N	0.013391	T	0.54175	0.1842	M	0.92507	3.315	0.51233	D	0.999918	D	0.89917	1.0	D	0.80764	0.994	T	0.61652	-0.7019	10	0.87932	D	0	.	7.0943	0.25301	0.8983:0.0:0.1017:0.0	.	36	Q9UBG3	CRNN_HUMAN	P	36	ENSP00000271835:L36P	ENSP00000271835:L36P	L	-	2	0	CRNN	150651227	0.903000	0.30736	0.739000	0.30968	0.985000	0.73830	3.133000	0.50531	0.861000	0.35504	0.482000	0.46254	CTC	.		0.557	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		G	152384603	A	G	152384603	3	3	153	1	0	0	0	0	1	0	0	0	3898	304	11	3	1388	3	CRNN	1	152384603	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	44784861	152384603	96866018	12	13727											
INTS3	65123	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	153735733	153735733	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagagggagtttcgcttccAccctatcaaggagacagttg	11	9	12	9	1	1	2	1	0	0	2	3	5	2	3	2	2	0	3	2	2	3	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:153735733A>T	ENST00000318967.2	+	16	2229	c.1661A>T	c.(1660-1662)cAc>cTc	p.H554L	INTS3_ENST00000456435.1_Missense_Mutation_p.H348L|INTS3_ENST00000435409.2_Missense_Mutation_p.H554L|INTS3_ENST00000512605.1_Missense_Mutation_p.H348L|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	555					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TTTCGCTTCCACCCTATCAAG	0.493																																					p.H554L													.	INTS3-93	0			c.A1661T						.						162	160	161					1																	153735733		2203	4300	6503	SO:0001583	missense	65123	exon16			GCTTCCACCCTAT	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"sensor of single-strand DNA complex subunit A"	611347	"chromosome 1 open reading frame 60"	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.1661A>T	1.37:g.153735733A>T	ENSP00000318641:p.His554Leu	Somatic	171	1		WXS	Illumina HiSeq	Phase_I	179	52	NM_023015	0	0	20	52	32	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.054197	0.36277	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.13	5.13	0.70059	.	0.055820	0.64402	D	0.000001	T	0.28830	0.0715	L	0.40543	1.245	0.54753	D	0.999987	B;B;B	0.27732	0.187;0.039;0.187	B;B;B	0.27500	0.08;0.017;0.038	T	0.13098	-1.0522	9	0.10636	T	0.68	.	12.941	0.58345	1.0:0.0:0.0:0.0	.	348;555;554	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	L	554;348;554;348	.	ENSP00000318641:H554L	H	+	2	0	INTS3	152002357	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.808000	0.62583	2.153000	0.67306	0.459000	0.35465	CAC	.		0.493	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		T	153735733	A	T	153735733	3	4	153	1	0	0	0	0	1	0	0	0	7800	159	6	5	1723	5	INTS3	1	153735733	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	1351130	153735733	95514888	13	13728											
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C																															tgacacctgctcctgctgctGctgctgctgctgctgctgtt																								rs3835302|rs199597671		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		.											.	DENND4B-69	0			c.C2722G						.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	1.37:g.153907287G>C	ENSP00000354597:p.Gln908Glu	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	90	9	NM_014856	0	0	4	4	0	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	153	1	0	0	0	0	1	0	0	0	4445	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	171554	153907287	95343334	14	13729	148	2									
DENND4B	9909	broad.mit.edu	37	chr1	153907294	153907294	+	Silent	SNP	C	C	T																															tgctcctgctgctgctgctgCtgctgctgctgttgctgctg																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:153907294C>T	ENST00000361217.4	-	18	3133	c.2715G>A	c.(2713-2715)caG>caA	p.Q905Q	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	905	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			gctgctgctgctgctgctgct	0.632																																					p.Q905Q													.	DENND4B-69	0			c.G2715A						.						27	35	32					1																	153907294		2181	4275	6456	SO:0001819	synonymous_variant	9909	exon18			CTGCTGCTGCTGC	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2715G>A	1.37:g.153907294C>T		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	101	0	NM_014856	0	1	808	809	0	Q5T4K0	Silent	SNP	ENST00000361217.4	37	CCDS44228.1																																																																																			.		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		T	153907294	C	T	153907294	2	4	153	1	0	0	0	0	0	0	0	1	4445	796	28	2		2	DENND4B	1	153907294	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	7	153907294	95343327	15	13730	148	2									
KIAA0907	22889	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155903553	155903553	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtggtgcccccaggacttccCccactgctggtgacctcccc	4	8	10	19	0	0	1	0	1	0	0	2	2	2	2	7	3	2	1	7	3	0	1	rs147323254		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:155903553C>G	ENST00000368321.3	-	2	149	c.126G>C	c.(124-126)ggG>ggC	p.G42G	KIAA0907_ENST00000368320.3_Silent_p.G42G|KIAA0907_ENST00000368319.3_Silent_p.G42G|KIAA0907_ENST00000482337.1_5'UTR	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	42							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			CAGGACTTCCCCCACTGCTGG	0.617													C|||	1	0.000199681	8e-04	0	5008	,	,		14922	0		0	False		,,,				2504	0				p.G42G		.											.	KIAA0907-90	0			c.G126C						.	C		1,4405		0,1,2202	27	31	30		126	1	1	1	dbSNP_134	30	0,8600		0,0,4300	no	coding-synonymous	KIAA0907	NM_014949.2		0,1,6502	GG,GC,CC		0.0,0.0227,0.0077		42/615	155903553	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22889	exon2			ACTTCCCCCACTG	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.126G>C	1.37:g.155903553C>G		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	52	15	NM_014949	0	0	2	2	0	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Silent	SNP	ENST00000368321.3	37	CCDS30885.1																																																																																			C|1.000;G|0.000		0.617	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		G	155903553	C	G	155903553	2	3	153	1	0	0	0	0	0	0	0	1	8220	610	22	4		4	KIAA0907	1	155903553	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	1996259	155903553	93347068	16	13731											
HDGF	3068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156713547	156713547	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaggcccccggccagagcCgggctcagagggggtgctat	6	4	19	12	2	1	2	1	0	0	2	1	3	1	3	4	6	2	2	4	6	1	1	rs375226201		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:156713547C>T	ENST00000357325.5	-	5	927	c.613G>A	c.(613-615)Ggc>Agc	p.G205S	HDGF_ENST00000368209.5_Missense_Mutation_p.G198S|MRPL24_ENST00000368211.4_5'Flank|HDGF_ENST00000537739.1_Missense_Mutation_p.G205S|HDGF_ENST00000368206.5_Missense_Mutation_p.G221S|HDGF_ENST00000416666.2_Missense_Mutation_p.G173S|HDGF_ENST00000465180.1_5'UTR|MRPL24_ENST00000361531.2_5'Flank	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	205	Glu-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		CGGCCAGAGCCGGGCTCAGAG	0.587																																					p.G221S		.											.	HDGF-226	0			c.G661A						.	C	SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	30	33	32		661,592,613	0.6	0.1	1		32	1,8599		0,1,4299	no	missense,missense,missense	HDGF	NM_001126050.1,NM_001126051.1,NM_004494.2	56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	221/257,198/234,205/241	156713547	1,13005	2203	4300	6503	SO:0001583	missense	3068	exon5			CAGAGCCGGGCTC	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"high-mobility group protein 1-like"	600339	"hepatoma-derived growth factor (high-mobility group protein 1-like)"			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.613G>A	1.37:g.156713547C>T	ENSP00000349878:p.Gly205Ser	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	63	33	NM_001126050	0	0	46	61	15	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Missense_Mutation	SNP	ENST00000357325.5	37	CCDS1156.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352591	0.24512	0.0	1.16E-4	ENSG00000143321	ENST00000357325;ENST00000368209;ENST00000537739;ENST00000416666;ENST00000368206;ENST00000406805	T;T;T;T;T	0.30448	2.05;1.56;2.05;1.6;1.53	4.55	0.546	0.17196	.	1.032050	0.07707	N	0.941443	T	0.06280	0.0162	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.28291	0.206;0.206;0.034;0.014	B;B;B;B	0.14023	0.01;0.01;0.004;0.002	T	0.38628	-0.9652	10	0.15952	T	0.53	-2.1192	6.8306	0.23907	0.0:0.6085:0.0:0.3915	.	180;221;198;205	B7Z958;Q5SZ07;Q5SZ08;P51858	.;.;.;HDGF_HUMAN	S	205;198;205;173;221;228	ENSP00000349878:G205S;ENSP00000357192:G198S;ENSP00000443120:G205S;ENSP00000416752:G173S;ENSP00000357189:G221S	ENSP00000349878:G205S	G	-	1	0	HDGF	154980171	0.000000	0.05858	0.089000	0.20774	0.788000	0.44548	-0.589000	0.05767	-0.053000	0.13289	0.456000	0.33151	GGC	.		0.587	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494		T	156713547	C	T	156713547	3	4	153	1	0	0	0	0	1	0	0	0	7039	652	23	1	117	1	HDGF	1	156713547	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	809994	156713547	92537074	17	13732											
IPO9	55705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201842054	201842054	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggagatctacagcatggAtgagggcatccgcacccgct	11	6	13	11	2	1	3	0	1	1	2	2	5	2	4	2	3	2	4	2	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:201842054A>C	ENST00000361565.4	+	20	2744	c.2675A>C	c.(2674-2676)gAt>gCt	p.D892A		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	892					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						TACAGCATGGATGAGGGCATC	0.532																																					p.D892A		.											.	IPO9-228	0			c.A2675C						.						97	88	91					1																	201842054		2203	4300	6503	SO:0001583	missense	55705	exon20			GCATGGATGAGGG	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"Importins"	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.2675A>C	1.37:g.201842054A>C	ENSP00000354742:p.Asp892Ala	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	181	78	NM_018085	0	0	17	23	6	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.859721	0.51376	.	.	ENSG00000198700	ENST00000361565	.	.	.	5.23	5.23	0.72850	Armadillo-like helical (1);Armadillo-type fold (1);	0.136301	0.64402	D	0.000004	T	0.40498	0.1119	N	0.17723	0.515	0.80722	D	1	B	0.17038	0.02	B	0.16722	0.016	T	0.26677	-1.0096	9	0.12103	T	0.63	-31.3306	13.3919	0.60829	1.0:0.0:0.0:0.0	.	892	Q96P70	IPO9_HUMAN	A	892	.	ENSP00000354742:D892A	D	+	2	0	IPO9	200108677	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	8.726000	0.91474	2.107000	0.64212	0.533000	0.62120	GAT	.		0.532	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		C	201842054	A	C	201842054	3	2	153	1	0	0	0	0	1	0	0	0	7820	333	12	5	2753	5	IPO9	1	201842054	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	45128507	201842054	47408567	18	13733											
YOD1	55432	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	207222409	207222409	+	Frame_Shift_Del	DEL	C	C	-																															gcctgtctccttggcatgttCccttgcttctgcttgtccag																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:207222409delC	ENST00000315927.4	-	2	1049	c.1003delG	c.(1003-1005)gaafs	p.E335fs	PFKFB2_ENST00000411990.2_5'Flank|YOD1_ENST00000367084.1_Frame_Shift_Del_p.E291fs|YOD1_ENST00000391927.1_Frame_Shift_Del_p.E291fs	NM_018566.3	NP_061036.3	Q5VVQ6	OTU1_HUMAN	YOD1 deubiquitinase	335					cellular amino acid metabolic process (GO:0006520)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)		Lys48-specific deubiquitinase activity (GO:1990380)|metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11	Prostate(682;0.19)					TTGGCATGTTCCCTTGCTTCT	0.478																																					p.E335fs		.											.	YOD1-522	0			c.1003delG						.						271	251	257					1																	207222409		2203	4300	6503	SO:0001589	frameshift_variant	55432	exon2			.		CCDS31002.1, CCDS60402.1	1q32.2	2013-06-04	2013-06-04		ENSG00000180667	ENSG00000180667		"OTU domain containing"	25035	protein-coding gene	gene with protein product		612023	"YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)", "YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)"				Standard	NM_001276320		Approved	DKFZp451J1719, OTUD2, DUBA8	uc001hfe.1	Q5VVQ6	OTTHUMG00000036032	ENST00000315927.4:c.1003delG	1.37:g.207222409delC	ENSP00000326813:p.Glu335fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	131	40	NM_018566	0	0	0	0	0	B2RNX3|Q5VVQ5|Q6ZRS6|Q86T63|Q9P1L8	Frame_Shift_Del	DEL	ENST00000315927.4	37	CCDS31002.1																																																																																			.		0.478	YOD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087837.1	NM_018566		-	207222409	C	-	207222409	7	5	153	1	0	1	0	1	0	0	0	0	17521	864	30	0	47	0	YOD1	1	207222409	Frame_Shift_Del	DEL	C	TCGA-P4-A5E6-01A-11D-A28G-10	5380355	207222409	42028212	19	13734											
CENPF	1063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	214813548	214813548	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaactctgttttcttgttggAaaagtgaaaacgaaaaactt	16	13	7	5	1	2	1	0	1	2	0	2	3	2	2	0	1	3	2	0	1	7	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:214813548A>T	ENST00000366955.3	+	12	2035	c.1867A>T	c.(1867-1869)Aaa>Taa	p.K623*		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TTCTTGTTGGAAAAGTGAAAA	0.333																																					p.K623X	Colon(80;575 1284 11000 14801 43496)	.											.	CENPF-567	0			c.A1867T						.						32	37	36					1																	214813548		2198	4298	6496	SO:0001587	stop_gained	1063	exon12			TGTTGGAAAAGTG	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.1867A>T	1.37:g.214813548A>T	ENSP00000355922:p.Lys623*	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	51	21	NM_016343	0	0	0	0	0	Q13171|Q13246|Q5VVM7	Nonsense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	40	8.443638	0.98813	.	.	ENSG00000117724	ENST00000366955	.	.	.	5.6	5.6	0.85130	.	0.000000	0.39407	N	0.001364	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7907	0.78357	1.0:0.0:0.0:0.0	.	.	.	.	X	623	.	ENSP00000355922:K623X	K	+	1	0	CENPF	212880171	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.770000	0.85390	2.126000	0.65437	0.443000	0.29094	AAA	.		0.333	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214813548	A	T	214813548	4	4	153	1	0	0	0	0	0	1	0	0	3237	247	9	5	1909	5	CENPF	1	214813548	Nonsense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	7591139	214813548	34437073	20	13735											
EPRS	2058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	220154162	220154162	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgccaaagaaattcacgaGtacgtaggaaaggctgagga	15	6	12	8	2	1	2	1	1	0	1	1	5	1	4	2	3	2	3	2	3	5	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:220154162G>C	ENST00000366923.3	-	25	3760	c.3491C>G	c.(3490-3492)aCt>aGt	p.T1164S		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1164	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AAATTCACGAGTACGTAGGAA	0.388																																					p.T1164S		.											.	EPRS-92	0			c.C3491G						.						64	60	61					1																	220154162		2203	4300	6503	SO:0001583	missense	2058	exon25			TCACGAGTACGTA	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3491C>G	1.37:g.220154162G>C	ENSP00000355890:p.Thr1164Ser	Somatic	202	0		WXS	Illumina HiSeq	Phase_I	207	80	NM_004446	0	0	3	6	3	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	G	32	5.174061	0.94807	.	.	ENSG00000136628	ENST00000366923	T	0.68025	-0.3	6.06	6.06	0.98353	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.78046	0.4222	L	0.39326	1.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76865	-0.2801	10	0.56958	D	0.05	-28.6459	20.6397	0.99537	0.0:0.0:1.0:0.0	.	1164	P07814	SYEP_HUMAN	S	1164	ENSP00000355890:T1164S	ENSP00000355890:T1164S	T	-	2	0	EPRS	218220785	1.000000	0.71417	0.980000	0.43619	0.980000	0.70556	9.577000	0.98196	2.880000	0.98712	0.650000	0.86243	ACT	.		0.388	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		C	220154162	G	C	220154162	3	2	153	1	0	0	0	0	1	0	0	0	5204	1029	36	4	1079	4	EPRS	1	220154162	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	5340614	220154162	29096459	21	13736											
TLR5	7100	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	223285316	223285316	+	Frame_Shift_Del	DEL	C	C	-																															gtagtccatagaaattcgaaCtgtaaagttcccccagaagg																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:223285316delC	ENST00000540964.1	-	4	1519	c.1058delG	c.(1057-1059)agtfs	p.S354fs	TLR5_ENST00000342210.6_Frame_Shift_Del_p.S354fs			O60602	TLR5_HUMAN	toll-like receptor 5	354					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		GAAATTCGAACTGTAAAGTTC	0.353																																					p.S353fs		.											.	TLR5-525	0			c.1058delG						.						93	93	93					1																	223285316		2203	4300	6503	SO:0001589	frameshift_variant	7100	exon6			.		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"Toll/interleukin-1 receptor-like protein 3"	603031	"systemic lupus erythematosus susceptibility 1"	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1058delG	1.37:g.223285316delC	ENSP00000440643:p.Ser354fs	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	57	25	NM_003268	0	0	0	0	0	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Frame_Shift_Del	DEL	ENST00000540964.1	37	CCDS31033.1																																																																																			.		0.353	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		-	223285316	C	-	223285316	7	5	153	1	0	1	0	1	0	0	0	0	15986	565	20	0	1522	0	TLR5	1	223285316	Frame_Shift_Del	DEL	C	TCGA-P4-A5E6-01A-11D-A28G-10	3131154	223285316	25965305	22	13737											
C1orf65	164127	hgsc.bcm.edu	37	chr1	223567036	223567036	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accccgcggcctcgcaggcgCgggtgctcagattcactgcg	5	6	14	16	6	2	1	2	0	0	1	3	1	2	1	3	3	2	2	3	3	0	1	rs369292167	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:223567036C>T	ENST00000366875.3	+	1	322	c.219C>T	c.(217-219)cgC>cgT	p.R73R		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		73	Arg-rich.									breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CTCGCAGGCGCGGGTGCTCAG	0.736													C|||	6	0.00119808	0.0045	0	5008	,	,		13138	0		0	False		,,,				2504	0				p.R73R		.											.	C1orf65-91	0			c.C219T						.	C		15,3615		0,15,1800	4	6	5		219	0.3	0	1		5	0,7554		0,0,3777	no	coding-synonymous	C1orf65	NM_152610.2		0,15,5577	TT,TC,CC		0.0,0.4132,0.1341		73/624	223567036	15,11169	1815	3777	5592	SO:0001819	synonymous_variant	164127	exon1			CAGGCGCGGGTGC																												ENST00000366875.3:c.219C>T	1.37:g.223567036C>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	50	17	NM_152610	0	0	0	0	0	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	37	CCDS1537.1																																																																																			.		0.736	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223567036	C	T	223567036	2	4	153	1	0	0	0	0	0	0	0	1	2061	755	27	1		1	C1orf65	1	223567036	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	281720	223567036	25683585	23	13738											
ITPKB	3707	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	226924770	226924784	+	In_Frame_Del	DEL	CTTCCTCTTGGCCTC	CTTCCTCTTGGCCTC	-																															tcgcgctgcaagatccgcagCttcctcttggcctcctccgg																								rs140396711|rs144653273|rs531138740|rs563769960	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	CTTCCTCTTGGCCTC	CTTCCTCTTGGCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:226924770_226924784delCTTCCTCTTGGCCTC	ENST00000272117.3	-	1	375_389	c.376_390delGAGGCCAAGAGGAAG	c.(376-390)gaggccaagaggaagdel	p.EAKRK126del	ITPKB_ENST00000429204.1_In_Frame_Del_p.EAKRK126del|ITPKB_ENST00000366784.1_In_Frame_Del_p.EAKRK126del			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	126					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.A127A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				AGATCCGCAGCTTCCTCTTGGCCTCCTCCGGCCCT	0.656																																					p.126_130del	Colon(84;110 1851 5306 33547)	.											.	ITPKB-230	1	Substitution - coding silent(1)	large_intestine(1)	c.376_390del						.																																			SO:0001651	inframe_deletion	3707	exon2			.	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.376_390delGAGGCCAAGAGGAAG	1.37:g.226924770_226924784delCTTCCTCTTGGCCTC	ENSP00000272117:p.Glu126_Lys130del	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	76	17	NM_002221	0	0	0	0	0	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	In_Frame_Del	DEL	ENST00000272117.3	37	CCDS1555.1																																																																																			.		0.656	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		-	226924784	CTTCCTCTTGGCCTC	-	226924770	7	5	153	1	0	1	0	1	0	0	0	0	7939	796	28	0	2478	0	ITPKB	1	226924770	In_Frame_Del	DEL	CTTCCTCTTGGCCTC	TCGA-P4-A5E6-01A-11D-A28G-10	3357734	226924770	22325851	24	13739											
NLRP3	114548	ucsc.edu;bcgsc.ca	37	chr1	247588675	247588675	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcaggaggaggacttcgtgCaaagggccatggactatttc	10	9	14	8	1	0	0	0	0	0	0	2	4	0	4	1	5	2	2	1	5	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:247588675C>T	ENST00000336119.3	+	3	2676	c.1930C>T	c.(1930-1932)Caa>Taa	p.Q644*	NLRP3_ENST00000348069.2_Nonsense_Mutation_p.Q644*|NLRP3_ENST00000366496.2_Nonsense_Mutation_p.Q644*|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366497.2_Nonsense_Mutation_p.Q644*|NLRP3_ENST00000391828.3_Nonsense_Mutation_p.Q644*|NLRP3_ENST00000391827.2_Nonsense_Mutation_p.Q644*	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	644					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			GGACTTCGTGCAAAGGGCCAT	0.473																																					p.Q644X													.	NLRP3-674	0			c.C1930T						.						86	75	79					1																	247588675		2203	4300	6503	SO:0001587	stop_gained	114548	exon3			TTCGTGCAAAGGG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"Nucleotide-binding domain and leucine rich repeat containing"	16400	protein-coding gene	gene with protein product	"Cryopyrin", "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"	606416	"cold autoinflammatory syndrome 1"	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1930C>T	1.37:g.247588675C>T	ENSP00000337383:p.Gln644*	Somatic	170	3		WXS	Illumina HiSeq		209	73	NM_183395	0	0	0	0	0	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Nonsense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	C	43	10.352876	0.99389	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	.	.	.	3.96	3.02	0.34903	.	0.689062	0.12788	N	0.439137	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9426	0.35740	0.221:0.779:0.0:0.0	.	.	.	.	X	644	.	ENSP00000337383:Q644X	Q	+	1	0	NLRP3	245655298	0.000000	0.05858	0.802000	0.32245	0.910000	0.53928	0.449000	0.21744	1.210000	0.43336	0.655000	0.94253	CAA	.		0.473	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247588675	C	T	247588675	4	4	153	1	0	0	0	0	0	1	0	0	10504	711	25	2	1940	2	NLRP3	1	247588675	Nonsense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	20663905	247588675	1661946	25	13740											
OR2M5	127059	broad.mit.edu;bcgsc.ca	37	chr1	248309355	248309355	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaggtgaccagagcactcagGaaagtgttaggaaagggcaa	15	5	15	6	0	1	2	1	1	0	1	1	5	1	4	1	4	1	3	1	4	4	1	rs201158893	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:248309355G>A	ENST00000366476.1	+	1	906	c.906G>A	c.(904-906)agG>agA	p.R302R		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			GAGCACTCAGGAAAGTGTTAG	0.453													g|||	3	0.000599042	0	0	5008	,	,		17536	0		0	False		,,,				2504	0.0031				p.R302R													.	OR2M5-71	0			c.G906A						.						62	58	59					1																	248309355		2203	4300	6503	SO:0001819	synonymous_variant	127059	exon1			ACTCAGGAAAGTG		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.906G>A	1.37:g.248309355G>A		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	175	8	NM_001004690	0	0	0	0	0		Silent	SNP	ENST00000366476.1	37	CCDS31105.1																																																																																			G|0.999;A|0.001		0.453	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		A	248309355	G	A	248309355	2	1	153	1	0	0	0	0	0	0	0	1	11039	1165	41	2		2	OR2M5	1	248309355	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	720680	248309355	941266	26	13741											
MXD1	4084	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	70165384	70165384	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcatcaagagaataaagctgCaggacagtcacaaggcgtgt	15	6	12	8	1	2	1	2	0	0	1	2	3	2	2	0	2	2	3	0	2	5	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:70165384C>G	ENST00000264444.2	+	6	894	c.634C>G	c.(634-636)Cag>Gag	p.Q212E	MXD1_ENST00000540449.1_Missense_Mutation_p.Q202E|MXD1_ENST00000465446.1_3'UTR	NM_001202513.1|NM_001202514.1|NM_002357.3	NP_001189442.1|NP_001189443.1|NP_002348.1	Q05195	MAD1_HUMAN	MAX dimerization protein 1	212					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						AATAAAGCTGCAGGACAGTCA	0.547																																					p.Q212E		.											.	MXD1-226	0			c.C634G						.						103	101	101					2																	70165384		2203	4300	6503	SO:0001583	missense	4084	exon6			AAGCTGCAGGACA		CCDS1896.1, CCDS56123.1	2p13-p12	2010-07-07		2005-02-11	ENSG00000059728	ENSG00000059728		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	6761	protein-coding gene	gene with protein product		600021		MAD		7829091	Standard	NM_002357		Approved	MAD1, bHLHc58	uc002sfy.3	Q05195	OTTHUMG00000129646	ENST00000264444.2:c.634C>G	2.37:g.70165384C>G	ENSP00000264444:p.Gln212Glu	Somatic	328	0		WXS	Illumina HiSeq	Phase_I	335	22	NM_002357	0	0	3	3	0	B2R6V8|B7ZLI6|D6W5G2|Q6FI41	Missense_Mutation	SNP	ENST00000264444.2	37	CCDS1896.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677983	0.68042	.	.	ENSG00000059728	ENST00000435990;ENST00000264444;ENST00000540449	T;T;T	0.45276	0.9;0.91;0.91	5.75	5.75	0.90469	.	0.527941	0.22156	N	0.063844	T	0.35537	0.0935	N	0.22421	0.69	0.47214	D	0.999358	B;B;B	0.23316	0.083;0.083;0.083	B;B;B	0.24006	0.05;0.05;0.05	T	0.13072	-1.0523	10	0.66056	D	0.02	.	18.875	0.92331	0.0:1.0:0.0:0.0	.	202;211;212	B7ZLI6;B7ZLI7;Q05195	.;.;MAD1_HUMAN	E	180;212;202	ENSP00000410672:Q180E;ENSP00000264444:Q212E;ENSP00000443935:Q202E	ENSP00000264444:Q212E	Q	+	1	0	MXD1	70018888	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	5.131000	0.64751	2.866000	0.98385	0.650000	0.86243	CAG	.		0.547	MXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251845.3	NM_002357		G	70165384	C	G	70165384	3	3	153	1	0	0	0	0	1	0	0	0	10024	711	25	4	656	4	MXD1	2	70165384	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		70165384	173033989	27	13742											
RGPD4	285190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	108488583	108488583	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaagatgttggtcaatggAaagaaaggggcattggtgat	15	10	14	2	0	1	3	1	1	0	2	1	4	1	4	0	5	0	2	0	5	5	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:108488583A>G	ENST00000408999.3	+	20	4200	c.4123A>G	c.(4123-4125)Aaa>Gaa	p.K1375E	RGPD4_ENST00000354986.4_Missense_Mutation_p.K1375E	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1375	RanBD1 2. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						TGGTCAATGGAAAGAAAGGGG	0.353																																					p.K1375E		.											.	RGPD4-2	0			c.A4123G						.						3	3	3					2																	108488583		568	1292	1860	SO:0001583	missense	285190	exon20			CAATGGAAAGAAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.4123A>G	2.37:g.108488583A>G	ENSP00000386810:p.Lys1375Glu	Somatic	237	1		WXS	Illumina HiSeq	Phase_I	290	198	NM_182588	0	0	0	0	0	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	12.87	2.068566	0.36470	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.53423	0.62;0.62	2.33	2.33	0.28932	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.70745	0.3259	M	0.91406	3.205	0.37032	D	0.896721	D	0.76494	0.999	D	0.80764	0.994	T	0.77611	-0.2523	9	0.87932	D	0	-35.6834	9.2036	0.37275	1.0:0.0:0.0:0.0	.	1375	Q7Z3J3	RGPD4_HUMAN	E	1375	ENSP00000347081:K1375E;ENSP00000386810:K1375E	ENSP00000347081:K1375E	K	+	1	0	RGPD4	107855015	1.000000	0.71417	1.000000	0.80357	0.405000	0.30901	9.032000	0.93736	1.072000	0.40860	0.136000	0.15936	AAA	.		0.353	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		G	108488583	A	G	108488583	3	3	153	1	0	0	0	0	1	0	0	0	13320	247	9	3	4201	3	RGPD4	2	108488583	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	38323199	108488583	134710790	28	13743											
SP5	389058	hgsc.bcm.edu	37	chr2	171572792	171572792	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcacccccagcgcctccccGgacctgggcaagcactcgcc	6	3	10	22	4	0	0	0	0	0	0	2	1	1	1	7	2	2	3	7	2	1	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:171572792G>A	ENST00000375281.3	+	2	237	c.75G>A	c.(73-75)ccG>ccA	p.P25P	SP5_ENST00000487037.1_3'UTR|AC007405.2_ENST00000409786.1_5'Flank	NM_001003845.2	NP_001003845.1	Q6BEB4	SP5_HUMAN	Sp5 transcription factor	25					bone morphogenesis (GO:0060349)|post-anal tail morphogenesis (GO:0036342)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(2)|lung(1)|prostate(1)	5						GCGCCTCCCCGGACCTGGGCA	0.736																																					p.P25P		.											.	SP5-90	0			c.G75A						.						16	22	20					2																	171572792		2004	3993	5997	SO:0001819	synonymous_variant	389058	exon2			CTCCCCGGACCTG		CCDS33322.1	2q31	2013-01-08			ENSG00000204335	ENSG00000204335		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14529	protein-coding gene	gene with protein product		609391					Standard	NM_001003845		Approved		uc002uge.3	Q6BEB4	OTTHUMG00000154053	ENST00000375281.3:c.75G>A	2.37:g.171572792G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	5	5	NM_001003845	0	0	0	0	0		Silent	SNP	ENST00000375281.3	37	CCDS33322.1																																																																																			.		0.736	SP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333670.1	XM_371581		A	171572792	G	A	171572792	2	1	153	1	0	0	0	0	0	0	0	1	14999	1103	39	1		1	SP5	2	171572792	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	63084209	171572792	71626581	29	13744											
FZD7	8324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	202900342	202900342	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgcttctcggacgatggctaCcgcacggtggcgcagggcac	6	6	15	14	6	1	0	0	0	1	0	2	2	1	1	1	5	1	5	1	5	1	2	rs571062625		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:202900342C>G	ENST00000286201.1	+	1	1033	c.972C>G	c.(970-972)taC>taG	p.Y324*	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	324					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of ectodermal cell fate specification (GO:0042666)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of catenin import into nucleus (GO:0035412)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|stem cell maintenance (GO:0019827)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|endometrium(6)|large_intestine(6)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	31						ACGATGGCTACCGCACGGTGG	0.632											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y324X		.											.	FZD7-659	0			c.C972G						.						65	64	65					2																	202900342		2203	4300	6503	SO:0001587	stop_gained	8324	exon1			TGGCTACCGCACG	AB010881	CCDS2351.1	2q33	2014-01-29	2014-01-29		ENSG00000155760	ENSG00000155760		"GPCR / Class F : Frizzled receptors"	4045	protein-coding gene	gene with protein product		603410	"frizzled (Drosophila) homolog 7", "frizzled homolog 7 (Drosophila)", "frizzled 7, seven transmembrane spanning receptor", "frizzled family receptor 7"			9707618, 9813155	Standard	NM_003507		Approved	FzE3	uc002uyw.1	O75084	OTTHUMG00000132841	ENST00000286201.1:c.972C>G	2.37:g.202900342C>G	ENSP00000286201:p.Tyr324*	Somatic	179	0	2133	WXS	Illumina HiSeq	Phase_I	217	67	NM_003507	0	0	0	0	0	O94816|Q53S59|Q96B74	Nonsense_Mutation	SNP	ENST00000286201.1	37	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	C	36	5.730939	0.96856	.	.	ENSG00000155760	ENST00000286201	.	.	.	5.54	5.54	0.83059	.	0.140083	0.49916	D	0.000138	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4882	0.95039	0.0:1.0:0.0:0.0	.	.	.	.	X	324	.	ENSP00000286201:Y324X	Y	+	3	2	FZD7	202608587	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.927000	0.63440	2.618000	0.88619	0.563000	0.77884	TAC	.		0.632	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		G	202900342	C	G	202900342	4	3	153	1	0	0	0	0	0	1	0	0	6154	518	18	4	974	4	FZD7	2	202900342	Nonsense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	31327550	202900342	40299031	30	13745											
FAM117B	150864	hgsc.bcm.edu	37	chr2	203500481	203500481	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgaagctcgccggagaagAggagccccagcgccccggtt	8	3	15	15	5	0	2	0	0	0	2	1	5	0	3	6	3	3	2	6	3	2	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:203500481A>C	ENST00000392238.2	+	1	571	c.571A>C	c.(571-573)Agg>Cgg	p.R191R	FAM117B_ENST00000303116.6_5'UTR			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	191										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						GCCGGAGAAGAGGAGCCCCAG	0.731																																					p.R191R		.											.	FAM117B-91	0			c.A571C						.						2	2	2					2																	203500481		404	1189	1593	SO:0001819	synonymous_variant	150864	exon1			GAGAAGAGGAGCC	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.571A>C	2.37:g.203500481A>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	5	5	NM_173511	0	0	1	4	3	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Silent	SNP	ENST00000392238.2	37	CCDS33362.2																																																																																			.		0.731	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		C	203500481	A	C	203500481	2	2	153	1	0	0	0	0	0	0	0	1	5426	295	11	5		5	FAM117B	2	203500481	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	600139	203500481	39698892	31	13746											
RPE	6120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	210881324	210881324	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggttatgacagtggaaccgGggtttggagggcagaaattc	10	10	16	5	1	0	2	0	1	0	1	1	4	0	4	1	6	1	3	1	6	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:210881324G>A	ENST00000359429.6	+	4	533	c.436G>A	c.(436-438)Ggg>Agg	p.G146R	RPE_ENST00000435437.2_Missense_Mutation_p.G146R|RPE_ENST00000452025.1_Missense_Mutation_p.G146R|RPE_ENST00000429907.1_Missense_Mutation_p.G78R|RPE_ENST00000354506.6_Missense_Mutation_p.G138R|RPE_ENST00000445268.1_Missense_Mutation_p.G78R|RPE_ENST00000411934.2_Missense_Mutation_p.G78R|RPE_ENST00000438204.2_Missense_Mutation_p.G78R|RPE_ENST00000436630.2_Missense_Mutation_p.G96R|RPE_ENST00000429921.1_Missense_Mutation_p.G96R|RPE_ENST00000454822.1_Missense_Mutation_p.G96R|RPE_ENST00000540255.1_Missense_Mutation_p.G146R	NM_199229.1	NP_954699.1	Q96AT9	RPE_HUMAN	ribulose-5-phosphate-3-epimerase	146	Substrate binding.				carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|ribulose-phosphate 3-epimerase activity (GO:0004750)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	9				Epithelial(149;0.00241)|Lung(261;0.041)|all cancers(144;0.0429)|LUSC - Lung squamous cell carcinoma(261;0.0431)		AGTGGAACCGGGGTTTGGAGG	0.438																																					p.G146R		.											.	RPE-90	0			c.G436A						.						132	129	130					2																	210881324		2203	4300	6503	SO:0001583	missense	6120	exon4			GAACCGGGGTTTG		CCDS2388.1, CCDS42810.1, CCDS63107.1, CCDS63108.1	2q32-q33.3	2012-10-02			ENSG00000197713	ENSG00000197713	5.1.3.1		10293	protein-coding gene	gene with protein product		180480					Standard	NM_199229		Approved		uc002vdn.4	Q96AT9	OTTHUMG00000154690	ENST00000359429.6:c.436G>A	2.37:g.210881324G>A	ENSP00000352401:p.Gly146Arg	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	159	118	NM_199229	0	0	0	19	19	A8K4S0|B4E016|C9JPQ7|O43767|Q53TV9|Q8N215|Q96N34|Q9BSB5	Missense_Mutation	SNP	ENST00000359429.6	37	CCDS2388.1	.	.	.	.	.	.	.	.	.	.	G	34	5.304604	0.95601	.	.	ENSG00000197713	ENST00000359429;ENST00000436630;ENST00000408981;ENST00000454822;ENST00000429921;ENST00000540255;ENST00000438265;ENST00000429907;ENST00000441588;ENST00000445268;ENST00000452025;ENST00000438204;ENST00000411934;ENST00000435437;ENST00000354506	.	.	.	5.45	5.45	0.79879	Aldolase-type TIM barrel (1);Ribulose-phosphate binding barrel (1);	0.000000	0.85682	D	0.000000	D	0.85852	0.5793	M	0.90369	3.11	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.88209	0.2889	9	0.87932	D	0	-3.1604	19.2659	0.93985	0.0:0.0:1.0:0.0	.	146;138;146;146	B4E016;E7EW52;Q96AT9;C9J9T0	.;.;RPE_HUMAN;.	R	146;96;78;96;96;146;96;78;78;78;146;78;78;146;138	.	ENSP00000346501:G138R	G	+	1	0	RPE	210589569	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.777000	0.99008	2.725000	0.93324	0.655000	0.94253	GGG	.		0.438	RPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336574.2	NM_006916		A	210881324	G	A	210881324	3	1	153	1	0	0	0	0	1	0	0	0	13576	1232	43	2	508	2	RPE	2	210881324	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	7380843	210881324	32318049	32	13747											
CUL3	8452	hgsc.bcm.edu;bcgsc.ca	37	chr2	225449678	225449678	+	Frame_Shift_Del	DEL	G	G	-																															caccggaaaggcccggatccGcatcttggtgtccttccggc																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:225449678delG	ENST00000264414.4	-	1	387	c.49delC	c.(49-51)cggfs	p.R17fs	CUL3_ENST00000344951.4_Frame_Shift_Del_p.R17fs	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	17					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GCCCGGATCCGCATCTTGGTG	0.736																																					p.R17fs		.											.	CUL3-229	0			c.49delC						.						37	35	35					2																	225449678		2200	4300	6500	SO:0001589	frameshift_variant	8452	exon1			.	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.49delC	2.37:g.225449678delG	ENSP00000264414:p.Arg17fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	126	89	NM_003590	0	0	0	0	0	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Frame_Shift_Del	DEL	ENST00000264414.4	37	CCDS2462.1																																																																																			.		0.736	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			-	225449678	G	-	225449678	7	5	153	1	0	1	0	1	0	0	0	0	4062	1086	38	0	2321	0	CUL3	2	225449678	Frame_Shift_Del	DEL	G	TCGA-P4-A5E6-01A-11D-A28G-10	14568354	225449678	17749695	33	13748	149	2									
CUL3	8452	bcgsc.ca	37	chr2	225449679	225449679	+	Missense_Mutation	SNP	C	C	T																															accggaaaggcccggatccgCatcttggtgtccttccggct																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:225449679C>T	ENST00000264414.4	-	1	386	c.48G>A	c.(46-48)atG>atA	p.M16I	CUL3_ENST00000344951.4_Missense_Mutation_p.M16I	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	16					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CCCGGATCCGCATCTTGGTGT	0.736																																					p.M16I													.	CUL3-229	0			c.G48A						.						37	35	35					2																	225449679		2200	4300	6500	SO:0001583	missense	8452	exon1			GATCCGCATCTTG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.48G>A	2.37:g.225449679C>T	ENSP00000264414:p.Met16Ile	Somatic	79	2		WXS	Illumina HiSeq	Phase_1	128	90	NM_003590	0	0	0	0	0	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.887994	0.33348	.	.	ENSG00000036257	ENST00000264414;ENST00000344951	T;T	0.66995	-0.24;-0.15	2.95	1.93	0.25924	.	0.000000	0.85682	U	0.000000	T	0.40862	0.1134	N	0.14661	0.345	0.20196	N	0.999924	B;P	0.35077	0.011;0.483	B;B	0.27887	0.043;0.084	T	0.24225	-1.0166	10	0.22109	T	0.4	.	9.904	0.41364	0.0:0.7891:0.2109:0.0	.	16;16	Q13618-3;Q13618	.;CUL3_HUMAN	I	16	ENSP00000264414:M16I;ENSP00000343601:M16I	ENSP00000264414:M16I	M	-	3	0	CUL3	225157923	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.228000	0.42981	1.170000	0.42753	0.313000	0.20887	ATG	.		0.736	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			T	225449679	C	T	225449679	3	4	153	1	0	0	0	0	1	0	0	0	4062	710	25	2	2322	2	CUL3	2	225449679	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	1	225449679	17749694	34	13749	149	2									
BHLHE40	8553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	5024970	5024970	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgggagaaaggatcggcgcaAttaagcaagagtccgaagaa	16	5	14	6	3	0	3	0	0	0	3	2	6	1	4	1	3	1	2	1	3	6	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:5024970A>C	ENST00000256495.3	+	5	1435	c.832A>C	c.(832-834)Att>Ctt	p.I278L		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	278					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						GATCGGCGCAATTAAGCAAGA	0.537																																					p.I278L		.											.	BHLHE40-91	0			c.A832C						.						76	77	77					3																	5024970		2203	4300	6503	SO:0001583	missense	8553	exon5			GGCGCAATTAAGC	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"Basic helix-loop-helix proteins"	1046	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1"	604256	"basic helix-loop-helix domain containing, class B, 2"	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.832A>C	3.37:g.5024970A>C	ENSP00000256495:p.Ile278Leu	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	96	38	NM_003670	0	0	56	94	38	Q96TD3	Missense_Mutation	SNP	ENST00000256495.3	37	CCDS2565.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513068	0.64522	.	.	ENSG00000134107	ENST00000256495	T	0.79845	-1.31	5.62	4.47	0.54385	.	0.309371	0.35970	N	0.002872	D	0.85944	0.5815	M	0.75615	2.305	0.80722	D	1	D	0.56035	0.974	P	0.57911	0.829	D	0.85230	0.1032	10	0.46703	T	0.11	.	11.0922	0.48123	0.9283:0.0:0.0717:0.0	.	278	O14503	BHE40_HUMAN	L	278	ENSP00000256495:I278L	ENSP00000256495:I278L	I	+	1	0	BHLHE40	4999970	1.000000	0.71417	0.912000	0.35992	0.165000	0.22458	7.345000	0.79337	0.983000	0.38602	0.533000	0.62120	ATT	.		0.537	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670		C	5024970	A	C	5024970	3	2	153	1	0	0	0	0	1	0	0	0	1424	101	4	5	850	5	BHLHE40	3	5024970	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		5024970	192997460	35	13750											
XPC	7508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	14188804	14188804	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	actgaccttgggcccgtagcGacgcttcagcctctccctga	6	9	10	16	3	2	2	1	2	1	0	3	3	2	2	4	1	2	2	4	1	1	3	rs373301509		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:14188804G>C	ENST00000285021.7	-	15	2804	c.2590C>G	c.(2590-2592)Cgc>Ggc	p.R864G	AC093495.4_ENST00000428681.3_RNA|RP11-434D12.1_ENST00000608606.1_Intron|RP11-434D12.1_ENST00000601399.1_Intron|AC093495.4_ENST00000420253.1_RNA|XPC_ENST00000449060.2_Missense_Mutation_p.R827G	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	864	Interaction with CETN2.|Interaction with ERCC2 and GTF2H1.				DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGCCCGTAGCGACGCTTCAGC	0.547			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R864G		.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"xeroderma pigmentosum, complementation group C"		E	.	XPC-662	0			c.C2590G						.						53	57	56					3																	14188804		1998	4157	6155	SO:0001583	missense	7508	exon15	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CGTAGCGACGCTT		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"xeroderma pigmentosum group C protein"	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2590C>G	3.37:g.14188804G>C	ENSP00000285021:p.Arg864Gly	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	110	8	NM_004628	0	0	1	1	0	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770436	0.69992	.	.	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.36157	1.27;1.29	5.18	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.59959	0.2232	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.996;0.999	P;D	0.70716	0.903;0.97	T	0.64437	-0.6408	10	0.49607	T	0.09	-14.9319	15.159	0.72767	0.0:0.0:0.8577:0.1423	.	827;864	E9PH69;Q01831	.;XPC_HUMAN	G	864;827	ENSP00000285021:R864G;ENSP00000404002:R827G	ENSP00000285021:R864G	R	-	1	0	XPC	14163805	1.000000	0.71417	0.891000	0.34965	0.837000	0.47467	6.671000	0.74472	1.385000	0.46445	0.591000	0.81541	CGC	.		0.547	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628		C	14188804	G	C	14188804	3	2	153	1	0	0	0	0	1	0	0	0	17474	1058	37	4	240	4	XPC	3	14188804	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	9163834	14188804	183833626	36	13751											
DAG1	1605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49568609	49568609	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcttctcagaagtagagcTtcacaacatgaaattagtgc	14	10	9	8	0	2	3	2	1	1	2	3	4	2	3	0	0	4	3	0	0	5	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:49568609T>C	ENST00000539901.1	+	3	1223	c.665T>C	c.(664-666)cTt>cCt	p.L222P	DAG1_ENST00000545947.1_Missense_Mutation_p.L222P|DAG1_ENST00000538711.1_Missense_Mutation_p.L222P|DAG1_ENST00000515359.2_Missense_Mutation_p.L222P|DAG1_ENST00000308775.2_Missense_Mutation_p.L222P|DAG1_ENST00000541308.1_Missense_Mutation_p.L222P	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	222	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GAAGTAGAGCTTCACAACATG	0.493																																					p.L222P		.											.	DAG1-92	0			c.T665C						.						76	81	80					3																	49568609		2203	4300	6503	SO:0001583	missense	1605	exon4			TAGAGCTTCACAA	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.665T>C	3.37:g.49568609T>C	ENSP00000439334:p.Leu222Pro	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	116	47	NM_001177642	0	0	4	4	0	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	37	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798715	0.31777	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711;ENST00000415315	T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46	5.92	3.55	0.40652	.	0.170769	0.52532	N	0.000062	T	0.76652	0.4017	M	0.65975	2.015	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.70368	-0.4891	10	0.51188	T	0.08	-12.03	9.6231	0.39734	0.0:0.1436:0.0:0.8564	.	222	Q14118	DAG1_HUMAN	P	222;222;222;222;222;222;21	ENSP00000440705:L222P;ENSP00000312435:L222P;ENSP00000442600:L222P;ENSP00000440590:L222P;ENSP00000439334:L222P;ENSP00000438421:L222P	ENSP00000312435:L222P	L	+	2	0	DAG1	49543613	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	4.211000	0.58507	0.496000	0.27904	0.533000	0.62120	CTT	.		0.493	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			C	49568609	T	C	49568609	3	2	153	1	0	0	0	0	1	0	0	0	4231	1609	56	3	671	3	DAG1	3	49568609	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	35379805	49568609	148453821	37	13752											
MAPKAPK3	7867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	50685441	50685441	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaaaaaagcaggcaggCagctcctctgcctcacaggg	13	4	13	11	0	2	1	1	0	1	1	3	2	3	1	2	4	3	4	2	4	3	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:50685441C>G	ENST00000446044.1	+	13	1709	c.1113C>G	c.(1111-1113)ggC>ggG	p.G371G	MAPKAPK3_ENST00000357955.2_Silent_p.G371G	NM_001243926.1	NP_001230855.1	Q16644	MAPK3_HUMAN	mitogen-activated protein kinase-activated protein kinase 3	371					activation of MAPK activity (GO:0000187)|innate immune response (GO:0045087)|macropinocytosis (GO:0044351)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|Ras protein signal transduction (GO:0007265)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223)		AGCAGGCAGGCAGCTCCTCTG	0.562																																					p.G371G		.											.	MAPKAPK3-1423	0			c.C1113G						.						69	69	69					3																	50685441		2203	4300	6503	SO:0001819	synonymous_variant	7867	exon11			GGCAGGCAGCTCC	U43784	CCDS2832.1	3p21.3	2004-03-10			ENSG00000114738	ENSG00000114738			6888	protein-coding gene	gene with protein product		602130				8626550, 8622688	Standard	NM_004635		Approved	3pK, MAPKAP3, 3PK	uc003dba.2	Q16644	OTTHUMG00000156850	ENST00000446044.1:c.1113C>G	3.37:g.50685441C>G		Somatic	246	1		WXS	Illumina HiSeq	Phase_I	260	110	NM_004635	0	0	21	44	23	B5BU67	Silent	SNP	ENST00000446044.1	37	CCDS2832.1	.	.	.	.	.	.	.	.	.	.	C	9.156	1.017372	0.19355	.	.	ENSG00000114738	ENST00000451680	.	.	.	5.73	2.59	0.31030	.	.	.	.	.	T	0.53626	0.1808	.	.	.	0.45733	D	0.998639	.	.	.	.	.	.	T	0.49194	-0.8965	4	.	.	.	-29.6661	6.4693	0.21999	0.2822:0.5832:0.0:0.1346	.	.	.	.	E	86	.	.	Q	+	1	0	MAPKAPK3	50660445	0.089000	0.21612	0.973000	0.42090	0.978000	0.69477	0.290000	0.18975	1.409000	0.46915	0.655000	0.94253	CAG	.		0.562	MAPKAPK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346237.1	NM_004635		G	50685441	C	G	50685441	2	3	153	1	0	0	0	0	0	0	0	1	9315	697	25	4		4	MAPKAPK3	3	50685441	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	1116832	50685441	147336989	38	13753											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65425597	65425597	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgttgctgCtgctgttgctgctgctgctg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs571281009	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:65425597C>T	ENST00000497477.2	-	9	1226	c.1227G>A	c.(1225-1227)caG>caA	p.Q409Q	MAGI1_ENST00000483466.1_Silent_p.Q409Q|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000402939.2_Silent_p.Q409Q|MAGI1_ENST00000330909.8_Silent_p.Q409Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	409	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		gctgttgctgctgctgttgct	0.532											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	49	0.00978435	0.0325	0.0043	5008	,	,		14951	0.003		0	False		,,,				2504	0				p.Q409Q		.											.	MAGI1-661	0			c.G1227A						.						68	64	65					3																	65425597		2202	4296	6498	SO:0001819	synonymous_variant	9223	exon9			TTGCTGCTGCTGT	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1227G>A	3.37:g.65425597C>T		Somatic	38	0	1084	WXS	Illumina HiSeq	Phase_I	41	7	NM_001033057	0	0	0	0	0	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	1.115	-0.657141	0.03480	.	.	ENSG00000151276	ENST00000460329	.	.	.	3.23	1.37	0.22104	.	.	.	.	.	T	0.23014	0.0556	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.22277	-1.0221	4	.	.	.	0.0018	2.6711	0.05067	0.2253:0.507:0.0:0.2677	.	.	.	.	N	290	.	.	S	-	2	0	MAGI1	65400637	0.651000	0.27340	0.048000	0.18961	0.002000	0.02628	-0.987000	0.03743	0.095000	0.17434	-0.850000	0.03035	AGC	.		0.532	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	65425597	C	T	65425597	2	4	153	1	0	0	0	0	0	0	0	1	9215	796	28	2		2	MAGI1	3	65425597	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	14740156	65425597	132596833	39	13754											
MYH15	22989	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	108174686	108174687	+	Frame_Shift_Ins	INS	-	-	T																															cttgctctttggaaaggtccINSttggattcagaatgcagtac																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:108174686_108174687insT	ENST00000273353.3	-	21	2274_2275	c.2218_2219insA	c.(2218-2220)aggfs	p.R740fs	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	740	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TGGAAAGGTCCTTGGATTCAGA	0.361																																					p.R740fs		.											.	MYH15-73	0			c.2219_2220insA						.																																			SO:0001589	frameshift_variant	22989	exon21			.	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"Myosins / Myosin superfamily : Class II"	31073	protein-coding gene	gene with protein product		609929	"myosin, heavy polypeptide 15"			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2219dupA	3.37:g.108174688_108174688dupT	ENSP00000273353:p.Arg740fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	55	15	NM_014981	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000273353.3	37	CCDS43127.1																																																																																			.		0.361	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108174687	-	T	108174686	7	5	153	1	0	1	1	0	0	0	0	0	10059	681	24	0	3709	0	MYH15	3	108174686	Frame_Shift_Ins	INS	-	TCGA-P4-A5E6-01A-11D-A28G-10	42749089	108174686	89847744	40	13755											
ABHD10	55347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	111710242	111710242	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctaaaaaaggaagtagagAtgaaaggtgtgtggagcatg	17	7	15	2	0	0	2	0	1	0	1	0	5	0	4	0	3	2	3	0	3	6	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:111710242A>C	ENST00000273359.3	+	5	622	c.595A>C	c.(595-597)Atg>Ctg	p.M199L	ABHD10_ENST00000494817.1_3'UTR|ABHD10_ENST00000534857.1_Missense_Mutation_p.M42L	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	199					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						GGAAGTAGAGATGAAAGGTGT	0.323																																					p.M199L		.											.	ABHD10-90	0			c.A595C						.						79	75	76					3																	111710242		2203	4300	6503	SO:0001583	missense	55347	exon5			GTAGAGATGAAAG	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.595A>C	3.37:g.111710242A>C	ENSP00000273359:p.Met199Leu	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	151	34	NM_018394	0	0	13	24	11	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	37	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.064132	0.36373	.	.	ENSG00000144827	ENST00000534857;ENST00000273359	T;T	0.66099	1.02;-0.19	5.47	-3.29	0.05017	.	0.598228	0.18438	N	0.141217	T	0.33585	0.0868	N	0.19112	0.55	0.23445	N	0.997665	B	0.02656	0.0	B	0.06405	0.002	T	0.06661	-1.0814	10	0.30078	T	0.28	-12.4265	1.0289	0.01533	0.3041:0.125:0.3257:0.2452	.	199	Q9NUJ1	ABHDA_HUMAN	L	42;199	ENSP00000442932:M42L;ENSP00000273359:M199L	ENSP00000273359:M199L	M	+	1	0	ABHD10	113192932	1.000000	0.71417	0.986000	0.45419	0.987000	0.75469	1.234000	0.32660	-0.436000	0.07254	0.443000	0.29094	ATG	.		0.323	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394		C	111710242	A	C	111710242	3	2	153	1	0	0	0	0	1	0	0	0	74	333	12	5	613	5	ABHD10	3	111710242	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	3535556	111710242	86312188	41	13756											
GP9	2815	broad.mit.edu	37	chr3	128780901	128780901	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggaggaccgcacgcccgagGccctgctgcaggtccgctgt	5	6	15	15	4	0	0	0	0	0	0	1	3	1	2	4	4	2	4	4	4	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:128780901G>T	ENST00000307395.4	+	3	541	c.319G>T	c.(319-321)Gcc>Tcc	p.A107S		NM_000174.3	NP_000165.1	P14770	GPIX_HUMAN	glycoprotein IX (platelet)	107	LRRCT.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|lung(4)	6					Quinine(DB00468)	CACGCCCGAGGCCCTGCTGCA	0.701																																					p.A107S													.	GP9-90	0			c.G319T						.						20	20	20					3																	128780901		2199	4296	6495	SO:0001583	missense	2815	exon3			CCCGAGGCCCTGC		CCDS3055.1	3q21.3	2014-09-17				ENSG00000169704		"CD molecules"	4444	protein-coding gene	gene with protein product		173515				2253772	Standard	XM_005247374		Approved	CD42a, GPIX	uc003elm.2	P14770		ENST00000307395.4:c.319G>T	3.37:g.128780901G>T	ENSP00000303942:p.Ala107Ser	Somatic	37	2		WXS	Illumina HiSeq	Phase_I	162	12	NM_000174	0	0	0	0	0	Q14445|Q8N1D1|Q92525	Missense_Mutation	SNP	ENST00000307395.4	37	CCDS3055.1	.	.	.	.	.	.	.	.	.	.	G	6.262	0.416458	0.11870	.	.	ENSG00000169704	ENST00000307395	D	0.90069	-2.61	4.26	-0.227	0.13102	Cysteine-rich flanking region, C-terminal (1);	1.070780	0.07282	U	0.870998	T	0.72309	0.3444	N	0.05414	-0.055	0.09310	N	1	B	0.19445	0.036	B	0.18263	0.021	T	0.58211	-0.7676	10	0.17369	T	0.5	-0.9252	1.9494	0.03364	0.2082:0.1579:0.4733:0.1606	.	107	P14770	GPIX_HUMAN	S	107	ENSP00000303942:A107S	ENSP00000303942:A107S	A	+	1	0	GP9	130263591	0.000000	0.05858	0.002000	0.10522	0.150000	0.21749	0.045000	0.14013	0.051000	0.15978	0.462000	0.41574	GCC	.		0.701	GP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358428.1			T	128780901	G	T	128780901	3	4	153	1	0	0	0	0	1	0	0	0	6605	1203	42	4	321	4	GP9	3	128780901	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	17070659	128780901	69241529	42	13757											
ARRDC3	57561	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	90669948	90669948	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taccttcaggtctttcaggaAgtgataaactgagccagttc	11	12	9	9	0	3	2	2	2	1	0	4	3	3	3	2	2	3	1	2	2	4	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:90669948A>C	ENST00000265138.3	-	6	1282	c.1016T>G	c.(1015-1017)cTt>cGt	p.L339R	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	339					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		TCTTTCAGGAAGTGATAAACT	0.373																																					p.L339R		.											.	ARRDC3-136	0			c.T1016G						.						187	185	186					5																	90669948		2203	4300	6503	SO:0001583	missense	57561	exon6			TCAGGAAGTGATA	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.1016T>G	5.37:g.90669948A>C	ENSP00000265138:p.Leu339Arg	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	113	33	NM_020801	0	0	0	1	1	A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	37	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263139	0.80358	.	.	ENSG00000113369	ENST00000265138	T	0.08984	3.03	5.77	5.77	0.91146	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	T	0.26085	0.0636	M	0.62723	1.935	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.00473	-1.1718	10	0.34782	T	0.22	-10.2226	16.086	0.81049	1.0:0.0:0.0:0.0	.	339	Q96B67	ARRD3_HUMAN	R	339	ENSP00000265138:L339R	ENSP00000265138:L339R	L	-	2	0	ARRDC3	90705704	1.000000	0.71417	0.981000	0.43875	0.932000	0.56968	9.339000	0.96797	2.207000	0.71202	0.528000	0.53228	CTT	.		0.373	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		C	90669948	A	C	90669948	3	2	153	1	0	0	0	0	1	0	0	0	985	72	3	5	240	5	ARRDC3	5	90669948	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		90669948	90245312	43	13758											
PAM	5066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	102285295	102285295	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttatccaatgcatgtctttgCctatagagttcacactcacc	10	14	5	12	0	3	1	2	0	1	1	4	1	4	1	3	0	2	2	3	0	4	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:102285295C>T	ENST00000438793.3	+	9	1168	c.698C>T	c.(697-699)gCc>gTc	p.A233V	PAM_ENST00000304400.7_Missense_Mutation_p.A233V|PAM_ENST00000348126.2_Missense_Mutation_p.A233V|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000455264.2_Missense_Mutation_p.A233V|PAM_ENST00000274392.9_Missense_Mutation_p.A136V|PAM_ENST00000346918.2_Missense_Mutation_p.A233V	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	233	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CATGTCTTTGCCTATAGAGTT	0.323																																					p.A233V		.											.	PAM-68	0			c.C698T						.						106	108	107					5																	102285295		2203	4297	6500	SO:0001583	missense	5066	exon9			TCTTTGCCTATAG	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.698C>T	5.37:g.102285295C>T	ENSP00000396493:p.Ala233Val	Somatic	264	0		WXS	Illumina HiSeq	Phase_I	259	24	NM_138822	0	0	3	3	0	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	37	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	C	32	5.156388	0.94686	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000274392;ENST00000455264	T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	6.02	6.02	0.97574	Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site (1);PHM/PNGase F domain (1);Copper type II, ascorbate-dependent monooxygenase-like, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91036	0.7180	M	0.90650	3.135	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.91659	0.5341	10	0.87932	D	0	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	136;233;233;233;233;233	F8WE90;P19021;P19021-4;P19021-3;P19021-5;P19021-2	.;AMD_HUMAN;.;.;.;.	V	233;233;233;233;136;233	ENSP00000396493:A233V;ENSP00000282992:A233V;ENSP00000314638:A233V;ENSP00000306100:A233V;ENSP00000274392:A136V;ENSP00000403461:A233V	ENSP00000274392:A136V	A	+	2	0	PAM	102313194	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.290000	0.72712	2.857000	0.98124	0.650000	0.86243	GCC	.		0.323	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		T	102285295	C	T	102285295	3	4	153	1	0	0	0	0	1	0	0	0	11438	739	26	2	732	2	PAM	5	102285295	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	11615347	102285295	78629965	44	13759											
PCDHGB6	56100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	140788348	140788348	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatggtggcaaatacccagaGttatctctggagaaactcct	12	10	10	9	0	1	2	0	0	1	2	3	4	2	2	2	3	2	2	2	3	4	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:140788348G>T	ENST00000520790.1	+	1	579	c.579G>T	c.(577-579)gaG>gaT	p.E193D	PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	193	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATACCCAGAGTTATCTCTGG	0.403																																					p.E193D		.											.	.	0			c.G579T						.						26	26	26					5																	140788348		1835	4088	5923	SO:0001583	missense	56100	exon1			CCCAGAGTTATCT	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"Cadherins / Protocadherins : Clustered"	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.579G>T	5.37:g.140788348G>T	ENSP00000428603:p.Glu193Asp	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	53	22	NM_032100	0	0	0	0	0	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	g	13.81	2.348524	0.41599	.	.	ENSG00000253305	ENST00000520790	T	0.21734	1.99	5.34	1.01	0.19927	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.40909	0.1136	M	0.77616	2.38	0.09310	N	0.999999	D;D	0.71674	0.994;0.998	D;D	0.70016	0.948;0.967	T	0.12760	-1.0535	9	0.66056	D	0.02	.	6.0351	0.19702	0.382:0.0:0.4936:0.1244	.	193;193	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	D	193	ENSP00000428603:E193D	ENSP00000428603:E193D	E	+	3	2	PCDHGB6	140768532	0.000000	0.05858	0.987000	0.45799	0.966000	0.64601	-1.583000	0.02115	0.257000	0.21650	-0.373000	0.07131	GAG	.		0.403	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140788348	G	T	140788348	3	4	153	1	0	0	0	0	1	0	0	0	11593	1020	36	4	581	4	PCDHGB6	5	140788348	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	38503053	140788348	40126912	45	13760											
SPINK1	6690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	147207646	147207646	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tccatcagtcccacagacagGgtcatatatcttggtgcatc	10	11	8	12	0	3	1	2	0	1	1	6	1	5	1	2	2	1	1	2	2	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:147207646G>A	ENST00000296695.5	-	3	341	c.133C>T	c.(133-135)Cct>Tct	p.P45S	SPINK1_ENST00000510027.2_Missense_Mutation_p.P45S	NM_003122.3	NP_003113.2	P00995	ISK1_HUMAN	serine peptidase inhibitor, Kazal type 1	45	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of calcium ion import (GO:0090281)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of serine-type endopeptidase activity (GO:1900004)|regulation of acrosome reaction (GO:0060046)|regulation of store-operated calcium entry (GO:2001256)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACAGACAGGGTCATATATC	0.328									Hereditary Pancreatitis																												p.P45S		.											.	SPINK1-90	0			c.C133T						.						126	119	121					5																	147207646		2203	4300	6503	SO:0001583	missense	6690	exon3	Familial Cancer Database		AGACAGGGTCATA		CCDS4286.1	5q32	2011-08-31	2005-08-17		ENSG00000164266	ENSG00000164266		"Serine peptidase inhibitors, Kazal type"	11244	protein-coding gene	gene with protein product		167790	"serine protease inhibitor, Kazal type 1"				Standard	XM_005268501		Approved	Spink3, PCTT, PSTI, TATI	uc003los.2	P00995	OTTHUMG00000129730	ENST00000296695.5:c.133C>T	5.37:g.147207646G>A	ENSP00000296695:p.Pro45Ser	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	114	24	NM_003122	0	0	0	0	0		Missense_Mutation	SNP	ENST00000296695.5	37	CCDS4286.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.042553	0.55003	.	.	ENSG00000164266	ENST00000296695;ENST00000510027	D;D	0.85339	-1.97;-1.97	4.9	4.9	0.64082	Proteinase inhibitor I1, Kazal (3);	0.000000	0.64402	D	0.000001	D	0.91991	0.7463	.	.	.	0.43708	D	0.996175	D	0.89917	1.0	D	0.97110	1.0	D	0.92165	0.5739	9	0.56958	D	0.05	-21.6312	15.9791	0.80094	0.0:0.0:1.0:0.0	.	45	P00995	ISK1_HUMAN	S	45	ENSP00000296695:P45S;ENSP00000427376:P45S	ENSP00000296695:P45S	P	-	1	0	SPINK1	147187839	1.000000	0.71417	0.938000	0.37757	0.224000	0.24922	4.936000	0.63506	2.725000	0.93324	0.655000	0.94253	CCT	.		0.328	SPINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251940.2	NM_003122		A	147207646	G	A	147207646	3	1	153	1	0	0	0	0	1	0	0	0	15089	1232	43	2	114	2	SPINK1	5	147207646	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	6419298	147207646	33707614	46	13761											
C5orf40	408263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	156770121	156770121	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtaagaccatcgcggctCatggcaacggacacaccaga	12	5	10	14	3	1	2	1	0	0	2	2	3	1	3	3	3	1	3	3	3	2	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:156770121C>A	ENST00000312349.4	-	2	611	c.424G>T	c.(424-426)Gag>Tag	p.E142*	CYFIP2_ENST00000377576.3_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000347377.6_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	142						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						CATCGCGGCTCATGGCAACGG	0.607											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E142X		.											.	FNDC9-68	0			c.G424T						.						64	62	63					5																	156770121		2203	4300	6503	SO:0001587	stop_gained	408263	exon2			GCGGCTCATGGCA	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"Fibronectin type III domain containing"	33547	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 40"	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.424G>T	5.37:g.156770121C>A	ENSP00000310594:p.Glu142*	Somatic	116	0	1781	WXS	Illumina HiSeq	Phase_I	136	43	NM_001001343	0	0	0	0	0	A8K0Y6	Nonsense_Mutation	SNP	ENST00000312349.4	37	CCDS4337.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805183	0.70682	.	.	ENSG00000172568	ENST00000312349;ENST00000520782	.	.	.	5.08	4.15	0.48705	.	0.241065	0.28784	N	0.014157	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-4.2189	9.3255	0.37990	0.16:0.6848:0.1551:0.0	.	.	.	.	X	142	.	ENSP00000310594:E142X	E	-	1	0	FNDC9	156702699	0.304000	0.24472	0.997000	0.53966	0.674000	0.39518	0.688000	0.25422	2.369000	0.80426	0.491000	0.48974	GAG	.		0.607	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343		A	156770121	C	A	156770121	4	1	153	1	0	0	0	0	0	1	0	0	2305	835	29	4	254	4	C5orf40	5	156770121	Nonsense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	9562475	156770121	24145139	47	13762											
GABRB2	2561	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	160886718	160886718	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaatgacttcttatcgtTcaggaaataggtatcaggca	14	11	8	8	1	3	1	2	1	1	0	4	2	3	2	0	3	0	3	0	3	5	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:160886718T>A	ENST00000393959.1	-	4	369	c.370A>T	c.(370-372)Aac>Tac	p.N124Y	GABRB2_ENST00000520240.1_Missense_Mutation_p.N124Y|GABRB2_ENST00000274547.2_Missense_Mutation_p.N124Y|GABRB2_ENST00000517901.1_Missense_Mutation_p.N61Y|GABRB2_ENST00000353437.6_Missense_Mutation_p.N124Y|GABRB2_ENST00000517547.1_Intron			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	124					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		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)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|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)	TTCTTATCGTTCAGGAAATAG	0.478																																					p.N124Y													.	GABRB2-91	0			c.A370T						.						105	94	97					5																	160886718		2203	4300	6503	SO:0001583	missense	2561	exon5			TATCGTTCAGGAA		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.370A>T	5.37:g.160886718T>A	ENSP00000377531:p.Asn124Tyr	Somatic	221	1		WXS	Illumina HiSeq	Phase_I	252	111	NM_021911	0	0	0	0	0	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	37	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.702239	0.88924	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901	D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23	4.97	4.97	0.65823	Neurotransmitter-gated ion-channel ligand-binding (3);	0.096322	0.64402	D	0.000002	D	0.95698	0.8601	H	0.96662	3.86	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97208	0.9869	10	0.87932	D	0	.	14.9655	0.71188	0.0:0.0:0.0:1.0	.	124;61;124;124	B7Z4P0;E7EV50;P47870;P47870-1	.;.;GBRB2_HUMAN;.	Y	124;124;124;124;61	ENSP00000377531:N124Y;ENSP00000274547:N124Y;ENSP00000274546:N124Y;ENSP00000429320:N124Y;ENSP00000430532:N61Y	ENSP00000274547:N124Y	N	-	1	0	GABRB2	160819296	1.000000	0.71417	0.994000	0.49952	0.982000	0.71751	7.867000	0.87062	1.988000	0.58038	0.533000	0.62120	AAC	.		0.478	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			A	160886718	T	A	160886718	3	1	153	1	0	0	0	0	1	0	0	0	6186	1783	62	5	1196	5	GABRB2	5	160886718	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	4116597	160886718	20028542	48	13763											
FAM65B	9750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	24843494	24843494	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcaggttttctgggctcctCtgggtcttcctccttcaggt	2	15	12	12	0	4	0	1	0	3	0	7	0	7	0	3	5	0	3	3	5	0	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:24843494C>G	ENST00000259698.4	-	14	1691	c.1516G>C	c.(1516-1518)Gag>Cag	p.E506Q	FAM65B_ENST00000540914.1_Missense_Mutation_p.E456Q|FAM65B_ENST00000510784.2_Missense_Mutation_p.E490Q|FAM65B_ENST00000473070.1_5'Flank|FAM65B_ENST00000538035.1_Missense_Mutation_p.E485Q|FAM65B_ENST00000378023.4_Missense_Mutation_p.E456Q	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	506					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						CTGGGCTCCTCTGGGTCTTCC	0.577																																					p.E506Q		.											.	FAM65B-91	0			c.G1516C						.						86	82	83					6																	24843494		1916	4115	6031	SO:0001583	missense	9750	exon14			GCTCCTCTGGGTC	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"myogenesis-related and NCAM-associated protein homolog (chicken)"	611410	"chromosome 6 open reading frame 32"	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1516G>C	6.37:g.24843494C>G	ENSP00000259698:p.Glu506Gln	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	99	33	NM_014722	0	0	2	2	0	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	C	9.393	1.076084	0.20227	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.3	2.46	0.29980	.	1.536000	0.03262	N	0.183420	T	0.06917	0.0176	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.16396	0.017;0.004;0.009;0.004	B;B;B;B	0.11329	0.006;0.003;0.004;0.004	T	0.23404	-1.0189	10	0.13853	T	0.58	-0.5328	7.1945	0.25845	0.0:0.6914:0.1422:0.1664	.	490;485;456;506	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	Q	506;485;456;456;490	ENSP00000259698:E506Q;ENSP00000441138:E485Q;ENSP00000367262:E456Q;ENSP00000438425:E456Q;ENSP00000441305:E490Q	ENSP00000259698:E506Q	E	-	1	0	FAM65B	24951473	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	0.333000	0.19768	0.417000	0.25871	0.655000	0.94253	GAG	.		0.577	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			G	24843494	C	G	24843494	3	3	153	1	0	0	0	0	1	0	0	0	5619	922	32	4	1740	4	FAM65B	6	24843494	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		24843494	146271573	49	13764											
HLA-E	3133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	30459405	30459405	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggagctgtggttgctgcTgtgatatggaggaagaagag	9	11	17	4	0	1	3	0	1	1	2	1	6	1	6	0	4	3	4	0	4	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:30459405T>C	ENST00000376630.4	+	5	1043	c.978T>C	c.(976-978)gcT>gcC	p.A326A		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	326					antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|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)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						TGGTTGCTGCTGTGATATGGA	0.557																																					p.A326A		.											.	HLA-E-516	0			c.T978C						.						153	162	159					6																	30459405		1509	2709	4218	SO:0001819	synonymous_variant	3133	exon5			TGCTGCTGTGATA	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.978T>C	6.37:g.30459405T>C		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	100	27	NM_005516	0	0	205	373	168	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Silent	SNP	ENST00000376630.4	37	CCDS34379.1																																																																																			.		0.557	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516		C	30459405	T	C	30459405	2	2	153	1	0	0	0	0	0	0	0	1	7231	1567	55	3		3	HLA-E	6	30459405	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	5615911	30459405	140655662	50	13765											
C6orf10	10665	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32261299	32261299	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacaccagactgactcttcTttacttgggattcctgtctt	8	15	7	11	0	3	3	0	1	3	2	4	4	4	4	2	1	1	0	2	1	1	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:32261299T>G	ENST00000447241.2	-	23	1323	c.1151A>C	c.(1150-1152)aAg>aCg	p.K384T	C6orf10_ENST00000375007.4_Missense_Mutation_p.K382T|C6orf10_ENST00000527965.1_Missense_Mutation_p.K368T|C6orf10_ENST00000442822.2_Missense_Mutation_p.K375T|C6orf10_ENST00000375015.4_Missense_Mutation_p.K383T|C6orf10_ENST00000533191.1_Missense_Mutation_p.K382T	NM_006781.3	NP_006772.3	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	384						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	25						CTGACTCTTCTTTACTTGGGA	0.502																																					.													.	C6orf10-91	0			.						.						192	206	201					6																	32261299		1511	2709	4220	SO:0001583	missense	10665	.			CTCTTCTTTACTT	U60665	CCDS34422.1, CCDS69082.1, CCDS75430.1	6p21.32	2012-11-20			ENSG00000204296	ENSG00000204296			13922	protein-coding gene	gene with protein product	"testis specific basic protein"					10803852	Standard	XM_005248810		Approved	TSBP	uc021yvs.1	Q5SRN2	OTTHUMG00000031107	ENST00000447241.2:c.1151A>C	6.37:g.32261299T>G	ENSP00000415517:p.Lys384Thr	Somatic	103	1		WXS	Illumina HiSeq	Phase_I	122	47	.	0	0	0	0	0	A2BET1|A2BET2|A6NME2|B0S7R2|B0S7R3|E9PMB1|Q5SPI9|Q5SPJ0|Q5SPK9|Q5SPL0|Q5SRN3|Q5TG25|Q5TG26|Q8N4B6	Missense_Mutation	SNP	ENST00000447241.2	37	CCDS34422.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223109	0.39300	.	.	ENSG00000204296	ENST00000442822;ENST00000447241;ENST00000375015;ENST00000533191;ENST00000527965;ENST00000375007;ENST00000375002;ENST00000305725	T;T;T;T;T;T	0.05081	3.5;3.58;3.55;3.56;3.56;3.59	3.83	1.33	0.21861	.	.	.	.	.	T	0.07818	0.0196	M	0.67397	2.05	0.09310	N	1	D;D	0.89917	0.991;1.0	P;D	0.87578	0.858;0.998	T	0.18116	-1.0347	9	0.59425	D	0.04	-1.1846	2.4408	0.04494	0.2053:0.224:0.0:0.5707	.	384;375	Q5SRN2;C9J9T8	CF010_HUMAN;.	T	375;384;383;382;368;382;381;381	ENSP00000411164:K375T;ENSP00000415517:K384T;ENSP00000364155:K383T;ENSP00000431199:K382T;ENSP00000435103:K368T;ENSP00000364146:K382T	ENSP00000303292:K381T	K	-	2	0	C6orf10	32369277	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.908000	0.28545	0.271000	0.22005	0.528000	0.53228	AAG	.		0.502	C6orf10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076178.4	NM_006781		G	32261299	T	G	32261299	3	3	153	1	0	0	0	0	1	0	0	0	2323	1609	56	5	544	5	C6orf10	6	32261299	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	1801894	32261299	138853768	51	13766											
PRICKLE4	29964	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	41751890	41751890	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtcctgcagttctgagcttgGgttccctttgcctggacacc	4	13	11	13	0	1	1	0	1	1	0	3	2	3	2	4	2	3	4	4	2	0	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:41751890G>A	ENST00000394260.1	+	1	34	c.34G>A	c.(34-36)Ggt>Agt	p.G12S	PRICKLE4_ENST00000394263.1_Missense_Mutation_p.G52S|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.G52S|PRICKLE4_ENST00000394259.1_Missense_Mutation_p.G12S|PRICKLE4_ENST00000458694.1_Missense_Mutation_p.G52S			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	12	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCTGAGCTTGGGTTCCCTTTG	0.542																																					p.G52S		.											.	PRICKLE4-22	0			c.G154A						.						140	115	123					6																	41751890		2203	4300	6503	SO:0001583	missense	29964	exon4			AGCTTGGGTTCCC	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"chromosome 6 open reading frame 49"	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.34G>A	6.37:g.41751890G>A	ENSP00000377803:p.Gly12Ser	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	169	58	NM_013397	0	0	7	7	0	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		.	.	.	.	.	.	.	.	.	.	G	15.41	2.826744	0.50739	.	.	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	T;T;T;T;T	0.68624	-0.14;-0.33;-0.14;-0.34;-0.12	4.61	2.79	0.32731	.	0.160117	0.29892	N	0.010940	T	0.41442	0.1159	L	0.57536	1.79	0.09310	N	1	P	0.47910	0.902	P	0.46543	0.52	T	0.28650	-1.0037	10	0.15952	T	0.53	-8.6317	5.2819	0.15680	0.1041:0.0:0.6944:0.2015	.	52	Q2TBC4-3	.	S	52;52;52;12;12	ENSP00000404911:G52S;ENSP00000352128:G52S;ENSP00000377806:G52S;ENSP00000377802:G12S;ENSP00000377803:G12S	ENSP00000335185:G52S	G	+	1	0	PRICKLE4	41859868	0.041000	0.20044	0.003000	0.11579	0.193000	0.23685	1.999000	0.40806	0.540000	0.28808	0.491000	0.48974	GGT	.		0.542	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		A	41751890	G	A	41751890	3	1	153	1	0	0	0	0	1	0	0	0	12518	1232	43	2	160	2	PRICKLE4	6	41751890	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	9490591	41751890	129363177	52	13767											
CASP8AP2	9994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	90578032	90578032	+	RNA	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaagaaatctcacactctGttggggaacatcttccaaac	13	10	8	10	0	3	1	1	0	3	1	5	3	4	3	1	3	2	1	1	3	4	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:90578032G>C	ENST00000551025.1	+	0	6460									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		CTCACACTCTGTTGGGGAACA	0.378																																					p.V1675L	Colon(187;1656 2025 17045 31481 39901)	.											.	CASP8AP2-24	0			c.G5023C						.						49	50	49					6																	90578032		1888	4122	6010			9994	exon8			CACTCTGTTGGGG	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90578032G>C		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	62	29	NM_001137667	0	0	0	1	1		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		C	90578032	G	C	90578032	1	2	153	0	1	0	0	0	0	0	0	0	2684	1377	48	4		4	CASP8AP2	6	90578032	RNA	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	48826142	90578032	80537035	53	13768											
RFX6	222546	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	117203548	117203548	+	Frame_Shift_Del	DEL	C	C	-																															agacaattcgccagaagtttCccctcctaacaacaaggcgg																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:117203548delC	ENST00000332958.2	+	4	539	c.523delC	c.(523-525)cccfs	p.P175fs		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	175					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						CCAGAAGTTTCCCCTCCTAAC	0.413																																					p.P175fs		.											.	RFX6-93	0			c.523delC						.						105	92	96					6																	117203548		2203	4300	6503	SO:0001589	frameshift_variant	222546	exon4			.	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"regulatory factor X domain containing 1"	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.523delC	6.37:g.117203548delC	ENSP00000332208:p.Pro175fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	77	35	NM_173560	0	0	0	0	0	Q5T6B3	Frame_Shift_Del	DEL	ENST00000332958.2	37	CCDS5113.1																																																																																			.		0.413	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		-	117203548	C	-	117203548	7	5	153	1	0	1	0	1	0	0	0	0	13299	855	30	0	537	0	RFX6	6	117203548	Frame_Shift_Del	DEL	C	TCGA-P4-A5E6-01A-11D-A28G-10	26625516	117203548	53911519	54	13769											
NFE2L3	9603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	26224503	26224503	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgatgagataaacttaatGtcattggccacagaagacaa	16	11	8	6	0	1	4	1	2	0	3	1	5	1	4	1	1	1	0	1	1	5	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr7:26224503G>T	ENST00000056233.3	+	4	1444	c.1185G>T	c.(1183-1185)atG>atT	p.M395I		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	395					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						TAAACTTAATGTCATTGGCCA	0.363																																					p.M395I		.											.	NFE2L3-94	0			c.G1185T						.						89	93	92					7																	26224503		2203	4300	6503	SO:0001583	missense	9603	exon4			CTTAATGTCATTG	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1185G>T	7.37:g.26224503G>T	ENSP00000056233:p.Met395Ile	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	80	29	NM_004289	0	0	3	8	5	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.714423	0.30413	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	T	0.32988	1.43	5.12	1.16	0.20824	.	0.373144	0.32328	N	0.006247	T	0.33030	0.0849	M	0.78049	2.395	0.28293	N	0.923461	B	0.14805	0.011	B	0.13407	0.009	T	0.34950	-0.9808	10	0.54805	T	0.06	-0.9264	10.7382	0.46137	0.3412:0.0:0.6588:0.0	.	395	Q9Y4A8	NF2L3_HUMAN	I	395;101	ENSP00000056233:M395I	ENSP00000056233:M395I	M	+	3	0	NFE2L3	26191028	0.998000	0.40836	0.717000	0.30585	0.799000	0.45148	2.503000	0.45407	0.259000	0.21709	-0.229000	0.12294	ATG	.		0.363	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			T	26224503	G	T	26224503	3	4	153	1	0	0	0	0	1	0	0	0	10395	1377	48	4	1199	4	NFE2L3	7	26224503	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10		26224503	132914160	55	13770											
NAMPT	10135	broad.mit.edu	37	chr7	105903928	105903928	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actattaaatgtcttagatcTtcaccccatattttctcaca	12	16	2	11	0	4	1	2	0	3	1	5	1	4	1	2	0	0	0	2	0	5	7			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr7:105903928T>G	ENST00000222553.3	-	7	1186	c.879A>C	c.(877-879)gaA>gaC	p.E293D	NAMPT_ENST00000354289.4_Missense_Mutation_p.E293D	NM_005746.2	NP_005737.1	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	293					cell-cell signaling (GO:0007267)|circadian regulation of gene expression (GO:0032922)|NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|nicotinamide metabolic process (GO:0006769)|positive regulation of cell proliferation (GO:0008284)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|nicotinamide phosphoribosyltransferase activity (GO:0047280)|nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						GTCTTAGATCTTCACCCCATA	0.368																																					p.E293D													.	NAMPT-577	0			c.A879C						.						104	94	98					7																	105903928		2203	4299	6502	SO:0001583	missense	10135	exon7			TAGATCTTCACCC	U02020	CCDS5737.1	7q22.3	2012-10-02	2008-03-27	2008-03-27	ENSG00000105835	ENSG00000105835			30092	protein-coding gene	gene with protein product	"visfatin"	608764	"pre-B-cell colony enhancing factor 1"	PBEF1		8289818	Standard	NM_005746		Approved	PBEF	uc003vdq.3	P43490	OTTHUMG00000140388	ENST00000222553.3:c.879A>C	7.37:g.105903928T>G	ENSP00000222553:p.Glu293Asp	Somatic	199	1		WXS	Illumina HiSeq	Phase_I	169	14	NM_005746	0	0	18	22	4	A4D0Q9|A4D0R0|Q3KQV0|Q8WW95	Missense_Mutation	SNP	ENST00000222553.3	37	CCDS5737.1	.	.	.	.	.	.	.	.	.	.	T	9.068	0.996237	0.19043	.	.	ENSG00000105835	ENST00000222553;ENST00000354289	.	.	.	5.39	4.23	0.50019	Quinolinate phosphoribosyl transferase, C-terminal (1);	0.047647	0.85682	D	0.000000	T	0.32466	0.0830	N	0.21448	0.665	0.40718	D	0.982633	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.0	T	0.08994	-1.0695	9	0.15952	T	0.53	-10.4608	6.1952	0.20546	0.1046:0.0644:0.1083:0.7227	.	206;274;293	B7Z8W6;Q5SYT8;P43490	.;.;NAMPT_HUMAN	D	293	.	ENSP00000222553:E293D	E	-	3	2	NAMPT	105691164	0.999000	0.42202	1.000000	0.80357	0.971000	0.66376	0.564000	0.23563	0.426000	0.26116	-1.139000	0.01908	GAA	.		0.368	NAMPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277146.1	NM_182790		G	105903928	T	G	105903928	3	3	153	1	0	0	0	0	1	0	0	0	10174	1606	56	5	616	5	NAMPT	7	105903928	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	79679425	105903928	53234735	56	13771											
FLNC	2318	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	128494117	128494117	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acacccgcacggagcgcacgGagatcagcaagacgcggggc	11	1	15	14	6	1	2	1	0	0	2	1	4	1	3	1	4	2	3	1	4	1	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr7:128494117G>C	ENST00000325888.8	+	40	6835	c.6574G>C	c.(6574-6576)Gag>Cag	p.E2192Q	FLNC_ENST00000346177.6_Missense_Mutation_p.E2159Q|RP11-309L24.2_ENST00000469965.1_RNA	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2192	Intradomain insert; mediate targeting to Z lines.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGAGCGCACGGAGATCAGCAA	0.652																																					p.E2192Q													.	FLNC-141	0			c.G6574C						.						20	25	23					7																	128494117		2098	4228	6326	SO:0001583	missense	2318	exon40			CGCACGGAGATCA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"actin binding protein 280"	102565	"filamin C, gamma (actin binding protein 280)"	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6574G>C	7.37:g.128494117G>C	ENSP00000327145:p.Glu2192Gln	Somatic	162	3		WXS	Illumina HiSeq	Phase_I	295	107	NM_001458	0	0	0	0	0	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.363533	0.41902	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85773	-2.03;-2.03	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.87537	0.6202	L	0.28192	0.835	0.54753	D	0.999988	D;P	0.67145	0.996;0.627	D;B	0.75484	0.986;0.198	D	0.86369	0.1722	10	0.34782	T	0.22	.	17.1975	0.86897	0.0:0.0:1.0:0.0	.	2159;2192	Q14315-2;Q14315	.;FLNC_HUMAN	Q	2192;2159	ENSP00000327145:E2192Q;ENSP00000344002:E2159Q	ENSP00000327145:E2192Q	E	+	1	0	FLNC	128281353	1.000000	0.71417	1.000000	0.80357	0.517000	0.34286	9.621000	0.98376	2.655000	0.90218	0.655000	0.94253	GAG	.		0.652	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			C	128494117	G	C	128494117	3	2	153	1	0	0	0	0	1	0	0	0	5954	1175	41	4	6732	4	FLNC	7	128494117	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	22590189	128494117	30644546	57	13772											
FAM40B	57464	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	129104562	129104562	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactcctcaaacacttcaaaCtcaaccatatctaccaggtg	14	10	3	14	0	4	0	3	0	1	0	5	0	5	0	3	1	5	0	3	1	6	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr7:129104562C>G	ENST00000249344.2	+	16	1799	c.1759C>G	c.(1759-1761)Ctc>Gtc	p.L587V	STRIP2_ENST00000435494.2_Missense_Mutation_p.L587V	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	587					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											ACACTTCAAACTCAACCATAT	0.478																																					p.L587V													.	.	0			c.C1759G						.						146	139	141					7																	129104562		2203	4300	6503	SO:0001583	missense	57464	exon16			TTCAAACTCAACC	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog B (yeast)"		"family with sequence similarity 40, member B"	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.1759C>G	7.37:g.129104562C>G	ENSP00000249344:p.Leu587Val	Somatic	77	1		WXS	Illumina HiSeq	Phase_I	103	38	NM_020704	0	0	0	3	3	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404795	0.62288	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.49139	0.79;0.79	5.22	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.53270	0.1786	L	0.33792	1.035	0.80722	D	1	D;P	0.69078	0.997;0.815	D;P	0.79108	0.992;0.674	T	0.37384	-0.9708	10	0.20046	T	0.44	-16.1153	12.634	0.56673	0.0:0.9198:0.0:0.0802	.	587;587	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	V	587	ENSP00000249344:L587V;ENSP00000392393:L587V	ENSP00000249344:L587V	L	+	1	0	FAM40B	128891798	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.948000	0.63590	2.620000	0.88729	0.655000	0.94253	CTC	.		0.478	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		G	129104562	C	G	129104562	3	3	153	1	0	0	0	0	1	0	0	0	5580	565	20	4	1821	4	FAM40B	7	129104562	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	610445	129104562	30034101	58	13773											
HR	55806	hgsc.bcm.edu	37	chr8	21978269	21978269	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggaagaggtggaagccaCgccgagggcaaggctggggc	9	3	19	10	2	0	1	0	0	0	1	0	4	0	3	3	7	1	2	3	7	3	0	rs114871775	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr8:21978269C>T	ENST00000381418.4	-	11	4050	c.2570G>A	c.(2569-2571)cGt>cAt	p.R857H	HR_ENST00000312841.8_Missense_Mutation_p.R857H	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	857					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GTGGAAGCCACGCCGAGGGCA	0.741													C|||	61	0.0121805	0.0454	0	5008	,	,		13295	0		0.001	False		,,,				2504	0				p.R857H		.											.	HR-154	0			c.G2570A						.	C	HIS/ARG,HIS/ARG	107,3239		0,107,1566	2	3	2		2570,2570	0.6	0	8	dbSNP_132	2	4,6868		0,4,3432	yes	missense,missense	HR	NM_005144.4,NM_018411.4	29,29	0,111,4998	TT,TC,CC		0.0582,3.1978,1.0863	benign,benign	857/1190,857/1135	21978269	111,10107	1673	3436	5109	SO:0001583	missense	55806	exon11			AAGCCACGCCGAG	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"hairless (mouse) homolog", "hairless homolog (mouse)"	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.2570G>A	8.37:g.21978269C>T	ENSP00000370826:p.Arg857His	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	15	7	NM_018411	0	0	0	0	0	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	22	0.010073260073260074	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	7.312	0.615246	0.14129	0.031978	5.82E-4	ENSG00000168453	ENST00000381418;ENST00000312841;ENST00000517699	T;T;T	0.71461	-0.57;-0.57;0.94	5.06	0.547	0.17202	.	0.836181	0.10478	N	0.670017	T	0.12646	0.0307	N	0.02315	-0.6	0.09310	N	1	B;B	0.17667	0.023;0.007	B;B	0.13407	0.009;0.004	T	0.09862	-1.0655	10	0.23891	T	0.37	-0.1927	6.1814	0.20474	0.0:0.4668:0.0:0.5332	.	857;857	O43593-2;O43593	.;HAIR_HUMAN	H	857;857;80	ENSP00000370826:R857H;ENSP00000326765:R857H;ENSP00000430413:R80H	ENSP00000326765:R857H	R	-	2	0	HR	22034214	0.001000	0.12720	0.000000	0.03702	0.426000	0.31534	0.809000	0.27168	0.243000	0.21327	-0.339000	0.08088	CGT	C|0.990;T|0.010		0.741	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			T	21978269	C	T	21978269	3	4	153	1	0	0	0	0	1	0	0	0	7368	536	19	1	1035	1	HR	8	21978269	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		21978269	124385753	59	13774											
SDC2	6383	ucsc.edu	37	chr8	97605816	97605816	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacgcttctgcgtctggcTcgggtaaggtggctgcttct	4	13	13	11	3	3	0	0	0	3	0	4	0	3	0	0	4	3	5	0	4	2	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr8:97605816T>A	ENST00000302190.4	+	2	1090	c.169T>A	c.(169-171)Tcg>Acg	p.S57T	SDC2_ENST00000518385.1_Intron|SDC2_ENST00000519914.1_Missense_Mutation_p.S28T|SDC2_ENST00000522911.1_Missense_Mutation_p.S28T	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	57					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	TGCGTCTGGCTCGGGTAAGGT	0.483																																					p.S57T													.	SDC2-516	0			c.T169A						.						122	93	103					8																	97605816		2203	4300	6503	SO:0001583	missense	6383	exon2			TCTGGCTCGGGTA	BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"Proteoglycans / Cell Surface : Syndecans", "CD molecules"	10659	protein-coding gene	gene with protein product	"syndecan proteoglycan 2"	142460	"heparan sulfate proteoglycan 1, cell surface-associated"	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.169T>A	8.37:g.97605816T>A	ENSP00000307046:p.Ser57Thr	Somatic	80	0		WXS	Illumina HiSeq		59	1	NM_002998	0	0	0	0	0	B3KQA3|Q6PIS6|Q9H6V1	Missense_Mutation	SNP	ENST00000302190.4	37	CCDS6272.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.939239	0.73557	.	.	ENSG00000169439	ENST00000302190;ENST00000545117;ENST00000546193;ENST00000522911;ENST00000519914;ENST00000521590;ENST00000523877	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.53965	0.1829	M	0.71581	2.175	0.52099	D	0.999948	P	0.47253	0.892	P	0.45753	0.492	T	0.60576	-0.7236	10	0.72032	D	0.01	-11.9994	13.8671	0.63594	0.0:0.0:0.0:1.0	.	57	P34741	SDC2_HUMAN	T	57;57;47;28;28;28;28	ENSP00000307046:S57T;ENSP00000427784:S28T;ENSP00000428256:S28T;ENSP00000429121:S28T	ENSP00000307046:S57T	S	+	1	0	SDC2	97674992	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	4.485000	0.60279	2.320000	0.78422	0.528000	0.53228	TCG	.		0.483	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998		A	97605816	T	A	97605816	3	1	153	1	0	0	0	0	1	0	0	0	13984	1551	54	5	175	5	SDC2	8	97605816	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	75627547	97605816	48758206	60	13775											
COL14A1	7373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	121357692	121357692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggactgtccaagggcctcCtggggagcctgggaggccag	6	5	17	13	1	0	0	0	0	0	0	2	3	2	3	6	6	1	0	6	6	1	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr8:121357692C>T	ENST00000297848.3	+	45	5237	c.4967C>T	c.(4966-4968)cCt>cTt	p.P1656L	COL14A1_ENST00000309791.4_Missense_Mutation_p.P1656L|COL14A1_ENST00000247781.3_Missense_Mutation_p.P1561L	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CAAGGGCCTCCTGGGGAGCCT	0.622																																					p.P1656L		.											.	COL14A1-543	0			c.C4967T						.						59	58	58					8																	121357692		2203	4300	6503	SO:0001583	missense	7373	exon45			GGCCTCCTGGGGA		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"Collagens", "Fibronectin type III domain containing"	2191	protein-coding gene	gene with protein product		120324	"undulin"	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4967C>T	8.37:g.121357692C>T	ENSP00000297848:p.Pro1656Leu	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	97	40	NM_021110	0	0	1	1	0		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621078	0.87460	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.98684	-3.87;-3.87;-3.87;-5.07	5.54	4.67	0.58626	.	0.048120	0.85682	D	0.000000	D	0.99032	0.9669	M	0.86502	2.82	0.80722	D	1	D	0.56746	0.977	D	0.69307	0.963	D	0.99226	1.0880	10	0.49607	T	0.09	.	12.3879	0.55343	0.0:0.9213:0.0:0.0787	.	1656	Q05707	COEA1_HUMAN	L	1656;1656;1561;3	ENSP00000311809:P1656L;ENSP00000297848:P1656L;ENSP00000247781:P1561L;ENSP00000403640:P3L	ENSP00000247781:P1561L	P	+	2	0	COL14A1	121426873	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.600000	0.74132	1.364000	0.46038	0.555000	0.69702	CCT	.		0.622	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121357692	C	T	121357692	3	4	153	1	0	0	0	0	1	0	0	0	3677	681	24	2	5141	2	COL14A1	8	121357692	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	23751876	121357692	25006330	61	13776											
EIF2C2	27161	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	141557696	141557696	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcactgcgtggccatccccAgcaccgtgtctcccacgcgc	5	6	10	20	5	1	0	0	0	1	0	3	0	2	0	5	1	2	2	5	1	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr8:141557696A>G	ENST00000220592.5	-	13	1731	c.1619T>C	c.(1618-1620)cTg>cCg	p.L540P	AGO2_ENST00000519980.1_Missense_Mutation_p.L540P	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	540	Interaction with guide RNA.|Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GGCCATCCCCAGCACCGTGTC	0.637																																					p.L540P		.											.	.	0			c.T1619C						.						182	140	154					8																	141557696		2203	4300	6503	SO:0001583	missense	27161	exon13			ATCCCCAGCACCG	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1619T>C	8.37:g.141557696A>G	ENSP00000220592:p.Leu540Pro	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	110	38	NM_012154	0	0	0	0	0	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	37	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.212273	0.79240	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.35236	1.32;1.32	5.49	5.49	0.81192	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.69958	0.3169	M	0.94021	3.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.79259	-0.1877	10	0.87932	D	0	-13.6154	15.5836	0.76465	1.0:0.0:0.0:0.0	.	540;540	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	P	540	ENSP00000220592:L540P;ENSP00000430176:L540P	ENSP00000220592:L540P	L	-	2	0	EIF2C2	141626878	1.000000	0.71417	0.973000	0.42090	0.690000	0.40134	9.193000	0.94954	2.076000	0.62316	0.533000	0.62120	CTG	.		0.637	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			G	141557696	A	G	141557696	3	3	153	1	0	0	0	0	1	0	0	0	5017	188	7	3	988	3	EIF2C2	8	141557696	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	20200004	141557696	4806326	62	13777											
TRPM6	140803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	77435298	77435298	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agactaaagttgaaagtgttCtgaatcatgcagatgatctc	14	12	9	6	0	3	5	1	3	2	2	4	5	3	5	0	0	1	3	0	0	4	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:77435298C>G	ENST00000360774.1	-	9	1293	c.1056G>C	c.(1054-1056)caG>caC	p.Q352H	TRPM6_ENST00000451710.3_Missense_Mutation_p.Q352H|TRPM6_ENST00000376871.3_Missense_Mutation_p.Q352H|TRPM6_ENST00000376864.4_Missense_Mutation_p.Q352H|TRPM6_ENST00000376872.3_Missense_Mutation_p.Q352H|TRPM6_ENST00000483186.1_5'UTR|TRPM6_ENST00000361255.3_Missense_Mutation_p.Q347H|TRPM6_ENST00000449912.2_Missense_Mutation_p.Q347H	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	352					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TGAAAGTGTTCTGAATCATGC	0.438																																					p.Q352H		.											.	TRPM6-335	0			c.G1056C						.						148	135	140					9																	77435298		2203	4300	6503	SO:0001583	missense	140803	exon9			AGTGTTCTGAATC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"Voltage-gated ion channels / Transient receptor potential cation channels"	17995	protein-coding gene	gene with protein product		607009	"hypomagnesemia, secondary hypocalcemia"	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1056G>C	9.37:g.77435298C>G	ENSP00000354006:p.Gln352His	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	87	8	NM_017662	0	0	0	0	0	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544685	0.65198	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.37	4.36	0.52297	.	0.122952	0.64402	D	0.000020	T	0.79476	0.4452	M	0.78456	2.415	0.43617	D	0.995992	D;D;P;P	0.71674	0.998;0.998;0.951;0.896	D;D;P;P	0.67382	0.951;0.951;0.765;0.694	T	0.81861	-0.0738	10	0.87932	D	0	.	11.9834	0.53133	0.0:0.8466:0.0:0.1534	.	352;352;352;347	Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3	.;.;TRPM6_HUMAN;.	H	352;352;352;352;347;347;352;15;15	ENSP00000354006:Q352H;ENSP00000407341:Q352H;ENSP00000366068:Q352H;ENSP00000366067:Q352H;ENSP00000396672:Q347H;ENSP00000354962:Q347H;ENSP00000366060:Q352H	ENSP00000309693:Q15H	Q	-	3	2	TRPM6	76625118	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.737000	0.26144	2.500000	0.84329	0.655000	0.94253	CAG	.		0.438	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77435298	C	G	77435298	3	3	153	1	0	0	0	0	1	0	0	0	16623	912	32	4	5136	4	TRPM6	9	77435298	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		77435298	63778133	63	13778											
GOLM1	51280	ucsc.edu	37	chr9	88692380	88692380	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctggaagttgtggctggActggattttgtcaagctgct	7	13	14	7	0	1	0	1	0	0	0	1	3	1	3	0	4	3	5	0	4	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:88692380A>G	ENST00000388712.3	-	3	424	c.256T>C	c.(256-258)Tcc>Ccc	p.S86P	GOLM1_ENST00000388711.3_Missense_Mutation_p.S86P|GOLM1_ENST00000257504.6_5'UTR	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	86					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						TTGTGGCTGGACTGGATTTTG	0.562																																					p.S86P													.	GOLM1-22	0			c.T256C						.						116	103	107					9																	88692380		2203	4300	6503	SO:0001583	missense	51280	exon3			GGCTGGACTGGAT	AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"golgi phosphoprotein 2", "chromosome 9 open reading frame 155"	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.256T>C	9.37:g.88692380A>G	ENSP00000373364:p.Ser86Pro	Somatic	131	7		WXS	Illumina HiSeq		130	11	NM_016548	0	0	3	9	6	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.258712	0.80246	.	.	ENSG00000135052	ENST00000388712;ENST00000388711;ENST00000486130	T;T;D	0.90732	0.91;0.91;-2.72	5.08	5.08	0.68730	.	0.273079	0.41294	D	0.000904	D	0.94165	0.8128	M	0.68593	2.085	0.38371	D	0.944862	D	0.76494	0.999	D	0.71656	0.974	D	0.95318	0.8418	10	0.59425	D	0.04	-11.2339	14.9684	0.71213	1.0:0.0:0.0:0.0	.	86	Q8NBJ4	GOLM1_HUMAN	P	86	ENSP00000373364:S86P;ENSP00000373363:S86P;ENSP00000419076:S86P	ENSP00000373363:S86P	S	-	1	0	GOLM1	87882200	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.159000	0.64923	2.263000	0.75096	0.379000	0.24179	TCC	.		0.562	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937		G	88692380	A	G	88692380	3	3	153	1	0	0	0	0	1	0	0	0	6587	275	10	3	981	3	GOLM1	9	88692380	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	11257082	88692380	52521051	64	13779											
TEX10	54881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	103109141	103109141	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcactttctctcaacctaCtggatccatctgccaaggcc	8	12	5	16	0	4	0	2	0	2	0	6	1	5	1	4	2	3	0	4	2	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:103109141C>G	ENST00000374902.4	-	3	904	c.728G>C	c.(727-729)aGt>aCt	p.S243T	TEX10_ENST00000535814.1_Missense_Mutation_p.S246T|TEX10_ENST00000537512.1_Missense_Mutation_p.S178T	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	243						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TCTCAACCTACTGGATCCATC	0.448																																					p.S246T		.											.	TEX10-92	0			c.G737C						.						122	118	119					9																	103109141		2203	4300	6503	SO:0001583	missense	54881	exon3			AACCTACTGGATC	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"testis expressed gene 10", "testis expressed sequence 10"			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.728G>C	9.37:g.103109141C>G	ENSP00000364037:p.Ser243Thr	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	84	28	NM_001161584	0	0	1	1	0	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	37	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	C	9.748	1.166577	0.21621	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730;ENST00000537512	.	.	.	5.26	4.31	0.51392	Armadillo-type fold (1);	0.430875	0.29932	N	0.010833	T	0.29288	0.0729	N	0.12182	0.205	0.38372	D	0.944907	B;B;B;B;B	0.29766	0.002;0.007;0.11;0.256;0.002	B;B;B;B;B	0.21360	0.003;0.004;0.011;0.034;0.003	T	0.20638	-1.0269	9	0.29301	T	0.29	-9.3945	9.3406	0.38079	0.0:0.7187:0.1367:0.1446	.	178;246;111;111;243	B7Z9D5;B4DYV2;E7ERG2;B4DQR0;Q9NXF1	.;.;.;.;TEX10_HUMAN	T	246;243;111;178	.	ENSP00000364037:S243T	S	-	2	0	TEX10	102148962	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.669000	0.37492	2.450000	0.82876	0.655000	0.94253	AGT	.		0.448	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		G	103109141	C	G	103109141	3	3	153	1	0	0	0	0	1	0	0	0	15804	565	20	4	2113	4	TEX10	9	103109141	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	14416761	103109141	38104290	65	13780											
EGFL7	51162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139564703	139564703	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agttactggtgccagtgttgGgaggggcacagcctgtctgc	6	10	16	9	0	1	0	0	0	1	0	1	1	1	1	2	4	4	3	2	4	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:139564703G>C	ENST00000371699.1	+	7	1403	c.492G>C	c.(490-492)tgG>tgC	p.W164C	EGFL7_ENST00000406555.3_Missense_Mutation_p.W164C|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000308874.7_Missense_Mutation_p.W164C|EGFL7_ENST00000371698.3_Missense_Mutation_p.W164C|MIR126_ENST00000362291.1_RNA			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	164	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		GCCAGTGTTGGGAGGGGCACA	0.652																																					p.W164C		.											.	EGFL7-523	0			c.G492C						.						28	30	29					9																	139564703		2198	4297	6495	SO:0001583	missense	51162	exon8			GTGTTGGGAGGGG	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.492G>C	9.37:g.139564703G>C	ENSP00000360764:p.Trp164Cys	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	157	47	NM_016215	0	0	8	8	0	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	37	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.802260	0.50315	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	5.26	2.31	0.28768	EGF-like calcium-binding (2);	1.149640	0.06146	N	0.673294	T	0.37785	0.1016	L	0.32530	0.975	0.45822	D	0.998694	D	0.56968	0.978	P	0.50754	0.649	T	0.04454	-1.0950	10	0.46703	T	0.11	-0.7885	7.8608	0.29509	0.1492:0.1325:0.7182:0.0	.	164	Q9UHF1	EGFL7_HUMAN	C	164	ENSP00000360764:W164C;ENSP00000307843:W164C;ENSP00000385639:W164C;ENSP00000360763:W164C	ENSP00000307843:W164C	W	+	3	0	EGFL7	138684524	0.247000	0.23920	0.257000	0.24404	0.612000	0.37316	0.439000	0.21575	0.188000	0.20168	0.561000	0.74099	TGG	.		0.652	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		C	139564703	G	C	139564703	3	2	153	1	0	0	0	0	1	0	0	0	4975	1241	43	4	510	4	EGFL7	9	139564703	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	36455562	139564703	1648728	66	13781											
TRAF2	7186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139794876	139794876	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatattcctctccccaggcCttcccagataatgctgcccg	7	10	8	16	1	1	1	0	0	1	1	4	2	3	2	6	2	2	1	6	2	2	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:139794876C>G	ENST00000247668.2	+	4	322	c.270C>G	c.(268-270)gcC>gcG	p.A90A	TRAF2_ENST00000536468.1_Silent_p.A90A|TRAF2_ENST00000359662.3_Silent_p.A90A	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	90					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		CTCCCCAGGCCTTCCCAGATA	0.577																																					p.A90A		.											.	TRAF2-660	0			c.C270G						.						43	38	39					9																	139794876		2203	4300	6503	SO:0001819	synonymous_variant	7186	exon4			CCAGGCCTTCCCA	U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"RING-type (C3HC4) zinc fingers"	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.270C>G	9.37:g.139794876C>G		Somatic	51	0		WXS	Illumina HiSeq	Phase_I	50	14	NM_021138	0	0	0	0	0	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	CCDS7013.1																																																																																			.		0.577	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		G	139794876	C	G	139794876	2	3	153	1	0	0	0	0	0	0	0	1	16471	668	24	4		4	TRAF2	9	139794876	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	230173	139794876	1418555	67	13782											
VIM	7431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	17278345	17278345	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccactcaaaaaggacactTctgattaagacggttgaaac	16	8	7	10	1	2	3	1	2	1	1	2	4	2	4	1	2	1	1	1	2	4	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:17278345T>G	ENST00000224237.5	+	8	1471	c.1326T>G	c.(1324-1326)ctT>ctG	p.L442L	VIM_ENST00000544301.1_Silent_p.L442L|RP11-124N14.3_ENST00000456355.1_RNA			P08670	VIME_HUMAN	vimentin	442	Tail.			L -> F (in Ref. 1; AAA61279). {ECO:0000305}.	apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AAAGGACACTTCTGATTAAGA	0.348																																					p.L442L		.											.	VIM-291	0			c.T1326G						.						150	165	160					10																	17278345		2203	4300	6503	SO:0001819	synonymous_variant	7431	exon9			GACACTTCTGATT	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1326T>G	10.37:g.17278345T>G		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	91	39	NM_003380	1	3	2551	5224	2669	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Silent	SNP	ENST00000224237.5	37	CCDS7120.1																																																																																			.		0.348	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		G	17278345	T	G	17278345	2	3	153	1	0	0	0	0	0	0	0	1	17199	1770	62	5		5	VIM	10	17278345	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10		17278345	118256402	68	13783											
ARHGAP21	57584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	24873742	24873742	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttcagattctctctcccCgctctgctcatgcactttcc	6	14	5	16	1	5	1	2	0	3	1	8	1	6	1	3	0	2	4	3	0	1	3	rs370251256		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:24873742C>T	ENST00000396432.2	-	26	5962	c.5476G>A	c.(5476-5478)Ggg>Agg	p.G1826R		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1825	Interaction with CTNNA1.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TCTCTCTCCCCGCTCTGCTCA	0.498																																					p.G1826R		.											.	ARHGAP21-235	0			c.G5476A						.	C	ARG/GLY	0,4406		0,0,2203	62	63	63		5476	3.3	0	10		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARHGAP21	NM_020824.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1826/1959	24873742	1,13005	2203	4300	6503	SO:0001583	missense	57584	exon26			TCTCCCCGCTCTG	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.5476G>A	10.37:g.24873742C>T	ENSP00000379709:p.Gly1826Arg	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	101	53	NM_020824	0	0	4	6	2	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	1.589	-0.529652	0.04112	0.0	1.16E-4	ENSG00000107863	ENST00000396432;ENST00000447364	T	0.11712	2.75	5.13	3.27	0.37495	.	1.152260	0.06177	N	0.678642	T	0.06416	0.0165	N	0.16307	0.4	0.18873	N	0.999984	B	0.09022	0.002	B	0.04013	0.001	T	0.42207	-0.9465	10	0.18710	T	0.47	.	2.6596	0.05023	0.2147:0.4829:0.0:0.3023	.	1825	Q5T5U3	RHG21_HUMAN	R	1826;1275	ENSP00000379709:G1826R	ENSP00000379709:G1826R	G	-	1	0	ARHGAP21	24913748	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.682000	0.25335	1.139000	0.42245	0.655000	0.94253	GGG	.		0.498	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		T	24873742	C	T	24873742	3	4	153	1	0	0	0	0	1	0	0	0	871	652	23	1	404	1	ARHGAP21	10	24873742	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	7595397	24873742	110661005	69	13784											
RBP3	5949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	48388918	48388918	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtctgccccacgacctctgGccgagcatagtgggcctcca	6	7	12	16	2	2	0	0	0	2	0	3	2	3	0	6	3	2	1	6	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:48388918G>C	ENST00000224600.4	-	1	2073	c.1960C>G	c.(1960-1962)Cca>Gca	p.P654A	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	654	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	ACGACCTCTGGCCGAGCATAG	0.672																																					p.P654A		.											.	RBP3-153	0			c.C1960G						.						16	18	17					10																	48388918		2197	4286	6483	SO:0001583	missense	5949	exon1			CCTCTGGCCGAGC	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"retinol-binding protein 3, interstitial"				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.1960C>G	10.37:g.48388918G>C	ENSP00000224600:p.Pro654Ala	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	102	43	NM_002900	0	0	0	0	0	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	37	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	7.421	0.636769	0.14386	.	.	ENSG00000107618	ENST00000224600	T	0.39997	1.05	5.53	5.53	0.82687	.	0.128692	0.53938	D	0.000058	T	0.47322	0.1439	M	0.76170	2.325	0.38359	D	0.944551	P	0.34562	0.457	B	0.31390	0.129	T	0.57894	-0.7732	10	0.87932	D	0	-14.2089	18.4586	0.90729	0.0:0.0:1.0:0.0	.	654	P10745	RET3_HUMAN	A	654	ENSP00000224600:P654A	ENSP00000224600:P654A	P	-	1	0	RBP3	48008924	1.000000	0.71417	0.047000	0.18901	0.002000	0.02628	5.637000	0.67854	2.628000	0.89032	0.561000	0.74099	CCA	.		0.672	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		C	48388918	G	C	48388918	3	2	153	1	0	0	0	0	1	0	0	0	13189	1203	42	4	1799	4	RBP3	10	48388918	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	23515176	48388918	87145829	70	13785											
ERCC6	2074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	50681040	50681040	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacacctaagccgcccaccCgcgtggtcagaagaaacaca	13	4	9	15	3	1	3	1	1	0	2	1	3	1	3	4	1	2	0	4	1	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:50681040C>T	ENST00000355832.5	-	15	2822	c.2744G>A	c.(2743-2745)cGg>cAg	p.R915Q	RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Missense_Mutation_p.R285Q|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	915	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GCCGCCCACCCGCGTGGTCAG	0.498								Direct reversal of damage;Nucleotide excision repair (NER)																													p.T915N		.											.	ERCC6-1153	0			c.C2744A						.						66	61	63					10																	50681040		2203	4300	6503	SO:0001583	missense	2074	exon15			CCCACCCGCGTGG	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"Cockayne syndrome B protein"	609413	"excision repair cross-complementing rodent repair deficiency, complementation group 6"	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2744G>A	10.37:g.50681040C>T	ENSP00000348089:p.Arg915Gln	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	231	92	NM_000124	0	0	0	0	0	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.199652	0.79015	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	T;T	0.74842	-0.88;-0.88	5.88	5.88	0.94601	Helicase, C-terminal (3);	.	.	.	.	D	0.88093	0.6344	M	0.83603	2.65	0.48341	D	0.999631	D;D	0.89917	1.0;0.999	D;D	0.76575	0.987;0.988	D	0.88520	0.3095	9	0.72032	D	0.01	-20.7418	20.2422	0.98381	0.0:1.0:0.0:0.0	.	915;292	Q03468;Q59FF6	ERCC6_HUMAN;.	Q	915;292;285	ENSP00000348089:R915Q;ENSP00000445134:R285Q	ENSP00000348089:R915Q	R	-	2	0	ERCC6	50351046	0.998000	0.40836	0.702000	0.30337	0.338000	0.28826	3.873000	0.56093	2.782000	0.95742	0.655000	0.94253	CGG	.		0.498	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		T	50681040	C	T	50681040	3	4	153	1	0	0	0	0	1	0	0	0	5230	652	23	1	1765	1	ERCC6	10	50681040	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	2292122	50681040	84853707	71	13786											
CSTF2T	23283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	53458361	53458361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccaggagtcacgggtcCgcgaggtataggagctctag	10	6	14	11	3	2	0	1	0	1	0	3	3	3	2	3	4	1	2	3	4	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:53458361C>T	ENST00000331173.4	-	1	994	c.949G>A	c.(949-951)Gga>Aga	p.G317R	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	317	Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G317R(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		GTCACGGGTCCGCGAGGTATA	0.567																																					p.G317R		.											.	CSTF2T-91	1	Substitution - Missense(1)	large_intestine(1)	c.G949A						.						72	68	70					10																	53458361		2203	4300	6503	SO:0001583	missense	23283	exon1			CGGGTCCGCGAGG	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.949G>A	10.37:g.53458361C>T	ENSP00000332444:p.Gly317Arg	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	64	14	NM_015235	0	0	0	4	4	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	37	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169805	0.78452	.	.	ENSG00000177613	ENST00000331173	T	0.22539	1.95	4.7	4.7	0.59300	.	0.449653	0.22819	N	0.055255	T	0.41994	0.1183	L	0.55481	1.735	0.53688	D	0.999972	D	0.89917	1.0	D	0.97110	1.0	T	0.13737	-1.0498	10	0.52906	T	0.07	-7.9329	15.5353	0.75998	0.0:1.0:0.0:0.0	.	317	Q9H0L4	CSTFT_HUMAN	R	317	ENSP00000332444:G317R	ENSP00000332444:G317R	G	-	1	0	CSTF2T	53128367	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.116000	0.71571	2.613000	0.88420	0.655000	0.94253	GGA	.		0.567	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		T	53458361	C	T	53458361	3	4	153	1	0	0	0	0	1	0	0	0	3991	661	23	1	905	1	CSTF2T	10	53458361	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	2777321	53458361	82076386	72	13787											
COL13A1	1305	hgsc.bcm.edu	37	chr10	71562297	71562297	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggagcgcggcgcacggctgCcgagtccagggtcgtgcggg	4	4	20	13	8	0	0	0	0	0	0	2	2	1	1	2	5	3	2	2	5	0	0	rs561022104	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:71562297C>T	ENST00000398978.3	+	1	610	c.118C>T	c.(118-120)Ccg>Tcg	p.P40S	COL13A1_ENST00000520267.1_Missense_Mutation_p.P40S|COL13A1_ENST00000517713.1_Missense_Mutation_p.P40S|COL13A1_ENST00000398966.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398972.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398971.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398968.3_Missense_Mutation_p.P40S|COL13A1_ENST00000520133.1_Missense_Mutation_p.P40S|COL13A1_ENST00000398969.3_Missense_Mutation_p.P40S|COL13A1_ENST00000354547.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398973.3_Missense_Mutation_p.P40S|COL13A1_ENST00000357811.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398964.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398974.3_Missense_Mutation_p.P40S|COL13A1_ENST00000356340.3_Missense_Mutation_p.P40S|COL13A1_ENST00000522165.1_Missense_Mutation_p.P40S	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						CGCACGGCTGCCGAGTCCAGG	0.766													C|||	2	0.000399361	0.0015	0	5008	,	,		8844	0		0	False		,,,				2504	0				p.P40S		.											.	COL13A1-91	0			c.C118T						.						12	14	13					10																	71562297		1839	3975	5814	SO:0001583	missense	1305	exon1			CGGCTGCCGAGTC	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"Collagens"	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.118C>T	10.37:g.71562297C>T	ENSP00000381949:p.Pro40Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	17	4	NM_080802	0	0	0	0	0		Missense_Mutation	SNP	ENST00000398978.3	37	CCDS44419.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024834	0.54683	.	.	ENSG00000197467	ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000398964;ENST00000398969;ENST00000356340;ENST00000398972;ENST00000398973;ENST00000398978;ENST00000354547;ENST00000357811;ENST00000520267;ENST00000517713;ENST00000522165;ENST00000520133	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91686	-2.74;-2.66;-2.7;-2.79;-2.89;-2.7;-2.73;-2.6;-2.72;-2.72;-2.7;-2.71;-2.66;-2.61;-2.66;-2.61	5.24	5.24	0.73138	.	0.000000	0.42294	D	0.000732	D	0.92172	0.7518	N	0.22421	0.69	0.29823	N	0.830659	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.69078	0.993;0.996;0.997;0.993;0.994;0.994;0.994;0.997;0.994;0.994;0.997;0.997;0.997;0.996;0.997;0.997;0.994;0.996	D;D;P;D;P;P;P;D;P;P;P;P;D;D;P;P;P;D	0.78314	0.979;0.991;0.9;0.979;0.796;0.796;0.796;0.986;0.796;0.723;0.9;0.9;0.986;0.991;0.9;0.9;0.796;0.991	D	0.88496	0.3079	10	0.44086	T	0.13	-5.5417	13.2925	0.60278	0.0:0.9204:0.0:0.0796	.	40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40	Q5TAT6;Q5TAT6-5;Q5TAT6-6;E9PEG9;E7ES55;E7ES51;E7ES47;E7ES46;E7ES49;E7EWL8;Q5TAT6-3;Q5TAT6-4;E7EX21;Q5TAT6-7;Q5TAT6-8;Q5TAT6-2;E7ES56;G5E987	CODA1_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	40	ENSP00000381946:P40S;ENSP00000381943:P40S;ENSP00000381940:P40S;ENSP00000381938:P40S;ENSP00000381936:P40S;ENSP00000381941:P40S;ENSP00000348695:P40S;ENSP00000381944:P40S;ENSP00000381945:P40S;ENSP00000381949:P40S;ENSP00000346553:P40S;ENSP00000350463:P40S;ENSP00000428057:P40S;ENSP00000430061:P40S;ENSP00000428342:P40S;ENSP00000430173:P40S	ENSP00000346553:P40S	P	+	1	0	COL13A1	71232303	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.084000	0.50143	2.462000	0.83206	0.456000	0.33151	CCG	.		0.766	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		T	71562297	C	T	71562297	3	4	153	1	0	0	0	0	1	0	0	0	3676	739	26	2	120	2	COL13A1	10	71562297	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	18103936	71562297	63972450	73	13788											
ZMIZ1	57178	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	81037038	81037038	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggaaactccccatgcagccCcctctcagctccatgagctc	8	7	8	18	0	1	1	1	1	1	0	5	2	3	2	5	1	5	3	5	1	1	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:81037038C>G	ENST00000334512.5	+	8	953	c.381C>G	c.(379-381)ccC>ccG	p.P127P	ZMIZ1_ENST00000478357.1_3'UTR	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	127					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CCATGCAGCCCCCTCTCAGCT	0.622																																					p.P127P													.	ZMIZ1-292	0			c.C381G						.						57	55	55					10																	81037038		2203	4300	6503	SO:0001819	synonymous_variant	57178	exon8			GCAGCCCCCTCTC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"Zinc fingers, MIZ-type"	16493	protein-coding gene	gene with protein product		607159	"retinoic acid induced 17"	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.381C>G	10.37:g.81037038C>G		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	53	5	NM_020338	0	0	4	4	0	Q5JSH9|Q7Z7E6	Silent	SNP	ENST00000334512.5	37	CCDS7357.1																																																																																			.		0.622	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		G	81037038	C	G	81037038	2	3	153	1	0	0	0	0	0	0	0	1	17728	610	22	4		4	ZMIZ1	10	81037038	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	9474741	81037038	54497709	74	13789											
RNLS	55328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	90342858	90342858	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagccttgtcccacacagcAaggtacaagggaccggacgt	11	6	11	13	2	1	0	1	0	0	0	2	2	2	2	3	3	3	2	3	3	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:90342858A>C	ENST00000331772.4	-	1	112	c.90T>G	c.(88-90)ctT>ctG	p.L30L	RNLS_ENST00000466945.1_5'UTR|RNLS_ENST00000371947.3_Silent_p.L30L|Y_RNA_ENST00000364678.1_RNA|RNLS_ENST00000437752.1_Silent_p.L30L	NM_001031709.2	NP_001026879.2	Q5VYX0	RNLS_HUMAN	renalase, FAD-dependent amine oxidase	30					cardiac left ventricle morphogenesis (GO:0003214)|dopamine metabolic process (GO:0042417)|epinephrine metabolic process (GO:0042414)|heart contraction (GO:0060047)|norepinephrine metabolic process (GO:0042415)|phosphate ion homeostasis (GO:0055062)|regulation of systemic arterial blood pressure (GO:0003073)|response to epinephrine (GO:0071871)|response to ischemia (GO:0002931)|response to norepinephrine (GO:0071873)|response to salt (GO:1902074)	extracellular space (GO:0005615)	oxidoreductase activity (GO:0016491)			breast(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7						CCCACACAGCAAGGTACAAGG	0.632											OREG0020353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L30L		.											.	RNLS-91	0			c.T90G						.						65	63	64					10																	90342858		2203	4300	6503	SO:0001819	synonymous_variant	55328	exon1			CACAGCAAGGTAC	BC005364	CCDS7388.1, CCDS31239.1	10q23.31	2009-04-22	2009-04-22	2009-04-22	ENSG00000184719	ENSG00000184719			25641	protein-coding gene	gene with protein product		609360	"chromosome 10 open reading frame 59"	C10orf59		15841207, 17565281	Standard	NM_001031709		Approved	FLJ11218, renalase	uc001kfe.3	Q5VYX0	OTTHUMG00000018692	ENST00000331772.4:c.90T>G	10.37:g.90342858A>C		Somatic	121	0	1274	WXS	Illumina HiSeq	Phase_I	164	57	NM_001031709	0	0	0	12	12	Q9BS33|Q9NUP8	Silent	SNP	ENST00000331772.4	37	CCDS31239.1																																																																																			.		0.632	RNLS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049250.1	NM_018363		C	90342858	A	C	90342858	2	2	153	1	0	0	0	0	0	0	0	1	13537	117	5	5		5	RNLS	10	90342858	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	9305820	90342858	45191889	75	13790											
NOC3L	64318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	96121495	96121495	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctttcacagcttgccttagTttcctctgttcttttcggta	4	20	6	11	1	4	0	1	0	3	0	6	0	5	0	2	1	2	4	2	1	2	8			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:96121495T>C	ENST00000371361.3	-	2	244	c.144A>G	c.(142-144)aaA>aaG	p.K48K	NOC3L_ENST00000371350.1_Silent_p.K48K|NOC3L_ENST00000463649.1_5'UTR	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	48					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CTTGCCTTAGTTTCCTCTGTT	0.368																																					p.K48K		.											.	NOC3L-91	0			c.A144G						.						308	272	284					10																	96121495		2203	4300	6503	SO:0001819	synonymous_variant	64318	exon2			CCTTAGTTTCCTC	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.144A>G	10.37:g.96121495T>C		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	79	27	NM_022451	0	0	0	0	0	Q9H5M6|Q9H9D8	Silent	SNP	ENST00000371361.3	37	CCDS7433.1																																																																																			.		0.368	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		C	96121495	T	C	96121495	2	2	153	1	0	0	0	0	0	0	0	1	10540	1722	60	3		3	NOC3L	10	96121495	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	5778637	96121495	39413252	76	13791											
GPAM	57678	ucsc.edu;bcgsc.ca	37	chr10	113920407	113920407	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgaagtaccccattgctgtAgaagttgagttcgaagactg	12	11	11	7	1	0	4	0	2	0	2	1	5	0	4	2	0	2	5	2	0	5	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:113920407A>T	ENST00000348367.4	-	16	1911	c.1714T>A	c.(1714-1716)Tac>Aac	p.Y572N	GPAM_ENST00000423155.1_Missense_Mutation_p.Y572N|GPAM_ENST00000369425.1_Missense_Mutation_p.Y572N			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	572					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		CCATTGCTGTAGAAGTTGAGT	0.418																																					p.Y572N	Ovarian(161;1017 2606 18293 52943)												.	GPAM-92	0			c.T1714A						.						128	113	118					10																	113920407		2203	4300	6503	SO:0001583	missense	57678	exon16			TGCTGTAGAAGTT	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"glycerol-3-phosphate acyltransferase 1, mitochondrial"	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1714T>A	10.37:g.113920407A>T	ENSP00000265276:p.Tyr572Asn	Somatic	237	2		WXS	Illumina HiSeq		251	107	NM_001244949	0	0	0	0	0	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.605939	0.87157	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.76839	-1.05;-1.05;-0.99	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.85669	0.5750	L	0.56769	1.78	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.991	D	0.86451	0.1773	10	0.59425	D	0.04	-19.1551	14.819	0.70055	1.0:0.0:0.0:0.0	.	572;572	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	N	572	ENSP00000265276:Y572N;ENSP00000409242:Y572N;ENSP00000358433:Y572N	ENSP00000265276:Y572N	Y	-	1	0	GPAM	113910397	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.809000	0.91944	2.241000	0.73720	0.533000	0.62120	TAC	.		0.418	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		T	113920407	A	T	113920407	3	4	153	1	0	0	0	0	1	0	0	0	6608	420	15	5	800	5	GPAM	10	113920407	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	17798912	113920407	21614340	77	13792											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119134718	119134718	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccagcacggccgacgccagGatcatgagcagcagccccat	10	3	11	17	3	1	1	1	1	0	0	1	3	1	2	5	2	4	3	5	2	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:119134718G>T	ENST00000334464.5	-	1	260	c.21C>A	c.(19-21)atC>atA	p.I7I		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	7					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		CCGACGCCAGGATCATGAGCA	0.741																																					p.I7I		.											.	PDZD8-90	0			c.C21A						.																																			SO:0001819	synonymous_variant	118987	exon1			CGCCAGGATCATG	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.21C>A	10.37:g.119134718G>T		Somatic	10	0		WXS	Illumina HiSeq	Phase_I	59	38	NM_173791	0	0	0	0	0	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	37	CCDS7600.1																																																																																			.		0.741	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		T	119134718	G	T	119134718	2	4	153	1	0	0	0	0	0	0	0	1	11731	1164	41	4		4	PDZD8	10	119134718	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	5214311	119134718	16400029	78	13793											
MUC2	4583	broad.mit.edu	37	chr11	1093099	1093099	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaccaccactacggtgaccCcaaccccaacacccaccggc	11	2	5	23	2	0	1	0	1	0	0	0	1	0	1	9	2	3	0	9	2	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:1093099C>A	ENST00000441003.2	+	30	4945	c.4918C>A	c.(4918-4920)Cca>Aca	p.P1640T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1607T|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tacggtgaccccaaccccaac	0.632																																					p.P1640T													.	MUC2-90	0			c.C4918A						.						63	117	98					11																	1093099		1809	3438	5247	SO:0001583	missense	4583	exon30			GTGACCCCAACCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4918C>A	11.37:g.1093099C>A	ENSP00000415183:p.Pro1640Thr	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	132	3	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.382	-0.341784	0.05243	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12465	2.68;3.14	1.07	-2.15	0.07102	.	0.513936	0.13039	U	0.418649	T	0.05686	0.0149	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.40496	-0.9560	9	0.15952	T	0.53	.	3.2486	0.06806	0.348:0.4185:0.2335:0.0	.	1640	E7EUV1	.	T	1640;1607	ENSP00000415183:P1640T;ENSP00000351956:P1607T	ENSP00000351956:P1607T	P	+	1	0	MUC2	1083099	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-1.638000	0.02013	-1.307000	0.02321	0.121000	0.15741	CCA	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093099	C	A	1093099	3	1	153	1	0	0	0	0	1	0	0	0	10000	623	22	4	5036	4	MUC2	11	1093099	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		1093099	133913417	79	13794											
MUC2	4583	broad.mit.edu	37	chr11	1093376	1093376	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaccactacggtgacccCaaccccaacacccaccggca	12	2	5	22	2	0	1	0	1	0	0	0	1	0	1	8	2	3	1	8	2	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:1093376C>T	ENST00000441003.2	+	30	5222	c.5195C>T	c.(5194-5196)cCa>cTa	p.P1732L	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1699L|MUC2_ENST00000333592.6_Missense_Mutation_p.P20L	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	acggtgaccccaaccccaaca	0.652																																					p.P1732L													.	MUC2-90	0			c.C5195T						.						159	216	197					11																	1093376		1982	3848	5830	SO:0001583	missense	4583	exon30			TGACCCCAACCCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5195C>T	11.37:g.1093376C>T	ENSP00000415183:p.Pro1732Leu	Somatic	140	2		WXS	Illumina HiSeq	Phase_I	140	5	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	4.814	0.151307	0.09185	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.10668	3.06;3.09;2.85	1.24	-0.195	0.13236	.	498.391000	0.02047	U	0.049780	T	0.07234	0.0183	.	.	.	0.09310	N	1	B	0.20261	0.043	B	0.08055	0.003	T	0.33369	-0.9871	9	0.41790	T	0.15	.	2.831	0.05499	0.3014:0.3985:0.3:0.0	.	1732	E7EUV1	.	L	1732;1699;20	ENSP00000415183:P1732L;ENSP00000351956:P1699L;ENSP00000331373:P20L	ENSP00000331373:P20L	P	+	2	0	MUC2	1083376	0.002000	0.14202	0.001000	0.08648	0.006000	0.05464	0.947000	0.29082	0.612000	0.30071	0.195000	0.17529	CCA	.		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093376	C	T	1093376	3	4	153	1	0	0	0	0	1	0	0	0	10000	594	21	2	5313	2	MUC2	11	1093376	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	277	1093376	133913140	80	13795											
ZFP91	80829	hgsc.bcm.edu	37	chr11	58346868	58346868	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggccccctgaggcggtcgcGgcggcgcctgcagggaccac	4	3	17	17	6	0	1	0	1	0	0	1	2	0	2	4	6	1	1	4	6	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:58346868G>A	ENST00000316059.6	+	1	285	c.114G>A	c.(112-114)gcG>gcA	p.A38A	LPXN_ENST00000528954.1_5'Flank|ZFP91-CNTF_ENST00000389919.4_Silent_p.A38A|LPXN_ENST00000528489.1_5'Flank	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	38	Ala-rich.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				AGGCGGTCGCGGCGGCGCCTG	0.771																																					p.A38A		.											.	ZFP91-91	0			c.G114A						.						2	2	2					11																	58346868		1047	2260	3307	SO:0001819	synonymous_variant	80829	exon1			GGTCGCGGCGGCG	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.114G>A	11.37:g.58346868G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	15	8	NM_001197051	0	0	0	0	0	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Silent	SNP	ENST00000316059.6	37	CCDS31553.1																																																																																			.		0.771	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		A	58346868	G	A	58346868	2	1	153	1	0	0	0	0	0	0	0	1	17687	1103	39	1		1	ZFP91	11	58346868	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	57253492	58346868	76659648	81	13796											
ATG2A	23130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	64681557	64681557	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggggcctgctcaccagtCtcaatggtctgggcaaacat	9	8	13	11	0	3	0	2	0	2	0	4	1	3	1	2	5	2	2	2	5	2	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:64681557C>A	ENST00000377264.3	-	3	595	c.483G>T	c.(481-483)gaG>gaT	p.E161D	ATG2A_ENST00000421419.2_Missense_Mutation_p.E161D	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	161					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GCTCACCAGTCTCAATGGTCT	0.667																																					p.E161D		.											.	ATG2A-69	0			c.G483T						.						27	31	29					11																	64681557		2165	4236	6401	SO:0001583	missense	23130	exon3			ACCAGTCTCAATG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"ATG2 autophagy related 2 homolog A (S. cerevisiae)"			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.483G>T	11.37:g.64681557C>A	ENSP00000366475:p.Glu161Asp	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	154	54	NM_015104	0	0	0	0	0	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	c	16.16	3.045338	0.55110	.	.	ENSG00000110046	ENST00000421419;ENST00000377264;ENST00000227459	T;T	0.56444	0.46;0.46	3.89	1.99	0.26369	.	0.000000	0.64402	D	0.000001	T	0.55449	0.1921	L	0.41236	1.265	0.44366	D	0.997264	D	0.63880	0.993	D	0.70016	0.967	T	0.49542	-0.8929	10	0.33940	T	0.23	.	5.9448	0.19213	0.0:0.666:0.0:0.334	.	161	Q2TAZ0	ATG2A_HUMAN	D	161	ENSP00000410522:E161D;ENSP00000366475:E161D	ENSP00000227459:E161D	E	-	3	2	ATG2A	64438133	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	0.697000	0.25556	0.439000	0.26476	0.457000	0.33378	GAG	.		0.667	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		A	64681557	C	A	64681557	3	1	153	1	0	0	0	0	1	0	0	0	1094	912	32	4	5489	4	ATG2A	11	64681557	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	6334689	64681557	70324959	82	13797											
FOLR2	2350	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	71931920	71931920	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcttccccacccagtgcagtCcctggaagaagaatgcctgc	9	8	9	15	0	1	2	0	0	1	2	3	3	3	3	5	1	3	1	5	1	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:71931920C>A	ENST00000298223.6	+	3	344	c.157C>A	c.(157-159)Ccc>Acc	p.P53T	FOLR2_ENST00000454954.2_Missense_Mutation_p.P12T|FOLR2_ENST00000449475.2_Missense_Mutation_p.P70T	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	53					folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)			breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	CCAGTGCAGTCCCTGGAAGAA	0.587																																					p.P53T													.	FOLR2-290	0			c.C157A						.						46	44	44					11																	71931920		2200	4293	6493	SO:0001583	missense	2350	exon3			TGCAGTCCCTGGA	AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.157C>A	11.37:g.71931920C>A	ENSP00000298223:p.Pro53Thr	Somatic	103	2		WXS	Illumina HiSeq	Phase_I	105	37	NM_001113535	0	0	0	0	0	Q05CA5|Q6GTE8	Missense_Mutation	SNP	ENST00000298223.6	37	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	c	17.57	3.422312	0.62622	.	.	ENSG00000165457	ENST00000449475;ENST00000298223;ENST00000413873;ENST00000454954;ENST00000541003;ENST00000539412;ENST00000536778;ENST00000535625;ENST00000321324;ENST00000538353	T;T;T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	4.25	2.38	0.29361	Folate receptor-like (1);	0.000000	0.85682	D	0.000000	D	0.88976	0.6584	M	0.93678	3.445	0.39744	D	0.971793	D	0.89917	1.0	D	0.97110	1.0	D	0.88102	0.2820	10	0.56958	D	0.05	.	8.6185	0.33847	0.0:0.8112:0.0:0.1888	.	53	P14207	FOLR2_HUMAN	T	70;53;70;12;99;64;68;53;66;53	ENSP00000405638:P70T;ENSP00000298223:P53T;ENSP00000414094:P12T;ENSP00000443307:P99T;ENSP00000441547:P64T;ENSP00000438568:P68T;ENSP00000444794:P53T;ENSP00000321957:P66T;ENSP00000440337:P53T	ENSP00000298223:P53T	P	+	1	0	FOLR2	71609568	0.920000	0.31207	0.934000	0.37439	0.977000	0.68977	3.796000	0.55507	0.435000	0.26365	0.455000	0.32223	CCC	.		0.587	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		A	71931920	C	A	71931920	3	1	153	1	0	0	0	0	1	0	0	0	6001	855	30	4	163	4	FOLR2	11	71931920	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	7250363	71931920	63074596	83	13798											
BARX2	8538	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	129321185	129321185	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcaggggcaggaggagcTctgtgaagcacaggaaccga	11	5	15	10	1	2	1	1	1	2	0	3	5	2	4	1	5	3	3	1	5	2	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:129321185T>A	ENST00000281437.4	+	4	824	c.728T>A	c.(727-729)cTc>cAc	p.L243H	BARX2_ENST00000526127.1_Missense_Mutation_p.L98H|BARX2_ENST00000531946.1_Missense_Mutation_p.L121H	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	243					cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|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)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		CAGGAGGAGCTCTGTGAAGCA	0.582																																					p.L243H		.											.	BARX2-90	0			c.T728A						.						72	66	68					11																	129321185		2201	4297	6498	SO:0001583	missense	8538	exon4			AGGAGCTCTGTGA	AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039		"Homeoboxes / ANTP class : NKL subclass"	956	protein-coding gene	gene with protein product		604823	"BarH-like homeobox 2"			10644443	Standard	NM_003658		Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.728T>A	11.37:g.129321185T>A	ENSP00000281437:p.Leu243His	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	134	53	NM_003658	0	0	1	3	2	O43518|Q6NT51	Missense_Mutation	SNP	ENST00000281437.4	37	CCDS8481.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.632445	0.67015	.	.	ENSG00000043039	ENST00000281437;ENST00000526127;ENST00000531946	D;D;D	0.90385	-2.66;-2.27;-2.27	5.51	-1.59	0.08453	.	0.906017	0.09601	N	0.780189	D	0.83769	0.5326	L	0.29908	0.895	0.09310	N	0.999999	P	0.45348	0.856	B	0.40101	0.319	T	0.72701	-0.4214	10	0.41790	T	0.15	.	12.1971	0.54303	0.0:0.6898:0.0:0.3102	.	243	Q9UMQ3	BARX2_HUMAN	H	243;98;121	ENSP00000281437:L243H;ENSP00000451113:L98H;ENSP00000450418:L121H	ENSP00000281437:L243H	L	+	2	0	BARX2	128826395	0.188000	0.23250	0.043000	0.18650	0.326000	0.28443	0.364000	0.20325	-0.288000	0.09051	0.533000	0.62120	CTC	.		0.582	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	NM_003658		A	129321185	T	A	129321185	3	1	153	1	0	0	0	0	1	0	0	0	1317	1551	54	5	742	5	BARX2	11	129321185	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	57389265	129321185	5685331	84	13799											
GLS2	27165	ucsc.edu	37	chr12	56865334	56865334	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcctcagcctgagtttcAgagagtgtgtaggagtcctg	7	11	14	9	0	2	2	2	1	0	1	3	4	3	3	3	1	2	3	3	1	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:56865334A>G	ENST00000311966.4	-	18	2024	c.1746T>C	c.(1744-1746)tcT>tcC	p.S582S	MIP_ENST00000555551.1_5'Flank|GLS2_ENST00000476991.1_5'Flank	NM_013267.2	NP_037399.2	Q9UI32	GLSL_HUMAN	glutaminase 2 (liver, mitochondrial)	582					cellular amino acid biosynthetic process (GO:0008652)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate secretion (GO:0014047)|glutamine metabolic process (GO:0006541)|neurotransmitter secretion (GO:0007269)|reactive oxygen species metabolic process (GO:0072593)|regulation of apoptotic process (GO:0042981)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13					L-Glutamine(DB00130)	CCTGAGTTTCAGAGAGTGTGT	0.517																																					p.S582S													.	GLS2-91	0			c.T1746C						.						72	63	66					12																	56865334		2203	4300	6503	SO:0001819	synonymous_variant	27165	exon18			AGTTTCAGAGAGT		CCDS8921.1, CCDS73482.1	12q13	2013-01-10			ENSG00000135423	ENSG00000135423		"Ankyrin repeat domain containing"	29570	protein-coding gene	gene with protein product		606365				11130979, 10620514	Standard	NM_013267		Approved	GA, GLS, LGA, hLGA	uc001slj.3	Q9UI32	OTTHUMG00000140379	ENST00000311966.4:c.1746T>C	12.37:g.56865334A>G		Somatic	137	1		WXS	Illumina HiSeq		148	2	NM_013267	0	0	1	2	1	B7Z8Q9|Q8IX91|Q9NYY2|Q9UI31	Silent	SNP	ENST00000311966.4	37	CCDS8921.1																																																																																			.		0.517	GLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277113.1	NM_013267		G	56865334	A	G	56865334	2	3	153	1	0	0	0	0	0	0	0	1	6484	175	7	3		3	GLS2	12	56865334	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		56865334	76986561	85	13800											
SHMT2	6472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57624649	57624649	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagcacagcaacgcagccCagactcagactggggaagca	13	3	11	14	1	2	2	2	0	0	2	2	3	2	3	1	2	5	4	1	2	2	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:57624649C>G	ENST00000328923.3	+	2	549	c.97C>G	c.(97-99)Cag>Gag	p.Q33E	SHMT2_ENST00000449049.3_Missense_Mutation_p.Q12E|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000414700.3_Missense_Mutation_p.Q12E|SHMT2_ENST00000553474.1_Missense_Mutation_p.Q12E|SHMT2_ENST00000393827.4_5'UTR|SHMT2_ENST00000557487.1_Missense_Mutation_p.Q33E|Y_RNA_ENST00000365197.1_RNA	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	33					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CAACGCAGCCCAGACTCAGAC	0.582																																					p.Q33E	Esophageal Squamous(150;1369 2416 49071 49364)	.											.	SHMT2-91	0			c.C97G						.						92	77	82					12																	57624649		2203	4300	6503	SO:0001583	missense	6472	exon2			GCAGCCCAGACTC	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.97C>G	12.37:g.57624649C>G	ENSP00000333667:p.Gln33Glu	Somatic	346	0		WXS	Illumina HiSeq	Phase_I	402	161	NM_005412	0	0	4	7	3	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	37	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	C	8.946	0.966931	0.18659	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.81	3.85	0.44370	.	0.335256	0.29537	N	0.011879	T	0.10551	0.0258	N	0.08118	0	0.80722	D	1	B;B	0.11235	0.004;0.002	B;B	0.12837	0.008;0.005	T	0.31586	-0.9938	10	0.02654	T	1	-12.6294	3.4496	0.07493	0.1727:0.5679:0.1666:0.0929	.	33;33	Q8N1A5;P34897	.;GLYM_HUMAN	E	33;33;33;12;12;12;12;12;12;12;12;12;12	ENSP00000333667:Q33E;ENSP00000452315:Q33E;ENSP00000406881:Q12E;ENSP00000452419:Q12E;ENSP00000413770:Q12E	ENSP00000333667:Q33E	Q	+	1	0	SHMT2	55910916	0.139000	0.22563	1.000000	0.80357	0.972000	0.66771	0.472000	0.22116	2.668000	0.90789	0.655000	0.94253	CAG	.		0.582	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		G	57624649	C	G	57624649	3	3	153	1	0	0	0	0	1	0	0	0	14318	595	21	4	103	4	SHMT2	12	57624649	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	759315	57624649	76227246	86	13801											
CCDC41	51134	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	94763803	94763804	+	Frame_Shift_Ins	INS	-	-	T																															agtttgtttgaatgtttaagINSttcttttacctgttgataat																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:94763803_94763804insT	ENST00000397809.5	-	9	1491_1492	c.942_943insA	c.(940-945)gaacttfs	p.L315fs	CCDC41_ENST00000547575.1_Frame_Shift_Ins_p.L315fs|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000397807.2_Frame_Shift_Ins_p.L282fs|CCDC41_ENST00000339839.5_Frame_Shift_Ins_p.L315fs	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		307					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						GAATGTTTAAGTTCTTTTACCT	0.332																																					p.L315fs		.											.	CCDC41-90	0			c.943_944insA						.																																			SO:0001589	frameshift_variant	51134	exon8			.																												ENST00000397809.5:c.943dupA	12.37:g.94763805_94763805dupT	ENSP00000380911:p.Leu315fs	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	58	21	NM_001042399	0	0	0	0	0	A4FVB1|Q08AP1	Frame_Shift_Ins	INS	ENST00000397809.5	37	CCDS41820.1																																																																																			.		0.332	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			T	94763804	-	T	94763803	7	5	153	1	0	1	1	0	0	0	0	0	2819	1029	36	0	1198	0	CCDC41	12	94763803	Frame_Shift_Ins	INS	-	TCGA-P4-A5E6-01A-11D-A28G-10	37139154	94763803	39088092	87	13802											
C12orf24	29902	hgsc.bcm.edu	37	chr12	110906786	110906786	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcgtagctcttctgcagagCcgcccgctgtggccgggacc	5	7	14	15	4	2	1	0	0	2	1	2	2	2	2	4	2	4	4	4	2	1	2	rs202079205	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:110906786C>T	ENST00000377673.5	+	1	618	c.106C>T	c.(106-108)Ccg>Tcg	p.P36S	GPN3_ENST00000537466.2_5'Flank|GPN3_ENST00000543199.1_5'Flank|GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000228827.3_5'Flank	NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	36																	TTCTGCAGAGCCGCCCGCTGT	0.771													C|||	12	0.00239617	0.0091	0	5008	,	,		13111	0		0	False		,,,				2504	0				p.P36S		.											.	.	0			c.C106T						.	C	SER/PRO	24,3054		0,24,1515	2	2	2		106	3.3	0.1	12		2	0,6186		0,0,3093	yes	missense	C12orf24	NM_013300.2	74	0,24,4608	TT,TC,CC		0.0,0.7797,0.2591	probably-damaging	36/274	110906786	24,9240	1539	3093	4632	SO:0001583	missense	29902	exon1			GCAGAGCCGCCCG	U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 24"	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.106C>T	12.37:g.110906786C>T	ENSP00000366901:p.Pro36Ser	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	22	15	NM_013300	0	0	1	1	0	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	37	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171608	0.78452	0.007797	0.0	ENSG00000204856	ENST00000377673;ENST00000538285	T	0.51071	0.72	4.16	3.27	0.37495	.	0.000000	0.39544	N	0.001336	T	0.32645	0.0836	L	0.56769	1.78	0.27811	N	0.942126	B;B	0.30709	0.291;0.129	B;B	0.26693	0.072;0.031	T	0.41645	-0.9497	10	0.87932	D	0	-0.6948	9.2806	0.37727	0.0:0.8974:0.0:0.1026	.	36;36	F5GZE4;Q8WUB2	.;CL024_HUMAN	S	36	ENSP00000366901:P36S	ENSP00000366901:P36S	P	+	1	0	C12orf24	109391169	0.943000	0.32029	0.132000	0.22025	0.895000	0.52256	2.944000	0.49034	1.096000	0.41439	0.462000	0.41574	CCG	.		0.771	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300		T	110906786	C	T	110906786	3	4	153	1	0	0	0	0	1	0	0	0	1682	739	26	2	108	2	C12orf24	12	110906786	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	16142983	110906786	22945109	88	13803											
TPCN1	53373	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113715129	113715129	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgccagggagcgctatcttAccttcaaggccctgaatcag	9	9	11	12	1	3	1	2	1	1	0	3	2	3	2	3	2	3	1	3	2	4	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:113715129A>C	ENST00000335509.6	+	12	1458	c.1144A>C	c.(1144-1146)Acc>Ccc	p.T382P	TPCN1_ENST00000541517.1_Missense_Mutation_p.T454P|TPCN1_ENST00000550785.1_Missense_Mutation_p.T454P|TPCN1_ENST00000392569.4_Missense_Mutation_p.T314P	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	382					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						GCGCTATCTTACCTTCAAGGC	0.577																																					p.T454P													.	TPCN1-93	0			c.A1360C						.						63	61	62					12																	113715129		2203	4300	6503	SO:0001583	missense	53373	exon13			TATCTTACCTTCA	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"Voltage-gated ion channels / Two-pore channels"	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.1144A>C	12.37:g.113715129A>C	ENSP00000335300:p.Thr382Pro	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	60	19	NM_001143819	0	0	10	23	13	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	37	CCDS31908.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.30|14.30	2.494445|2.494445	0.44352|0.44352	.|.	.|.	ENSG00000186815|ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569|ENST00000546781	D;D;D;D|.	0.97066|.	-4.12;-4.23;-4.23;-4.17|.	5.25|5.25	4.11|4.11	0.48088|0.48088	.|.	0.051926|.	0.85682|.	D|.	0.000000|.	T|T	0.56834|0.56834	0.2012|0.2012	L|L	0.47716|0.47716	1.5|1.5	0.50813|0.50813	D|D	0.999894|0.999894	D;D;D|.	0.76494|.	0.999;0.999;0.994|.	D;D;P|.	0.66196|.	0.942;0.931;0.795|.	T|T	0.52170|0.52170	-0.8611|-0.8611	10|5	0.37606|.	T|.	0.19|.	-8.6888|-8.6888	9.5973|9.5973	0.39582|0.39582	0.9198:0.0:0.0802:0.0|0.9198:0.0:0.0802:0.0	.|.	382;454;382|.	A5PKY2;Q9ULQ1-3;Q9ULQ1|.	.;.;TPC1_HUMAN|.	P|S	382;454;454;314|68	ENSP00000335300:T382P;ENSP00000448083:T454P;ENSP00000438125:T454P;ENSP00000376350:T314P|.	ENSP00000335300:T382P|.	T|Y	+|+	1|2	0|0	TPCN1|TPCN1	112199512|112199512	1.000000|1.000000	0.71417|0.71417	0.133000|0.133000	0.22050|0.22050	0.178000|0.178000	0.23041|0.23041	7.773000|7.773000	0.85462|0.85462	1.010000|1.010000	0.39314|0.39314	-0.363000|-0.363000	0.07495|0.07495	ACC|TAC	.		0.577	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		C	113715129	A	C	113715129	3	2	153	1	0	0	0	0	1	0	0	0	16428	391	14	5	1406	5	TPCN1	12	113715129	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	2808343	113715129	20136766	89	13804											
CLYBL	171425	hgsc.bcm.edu	37	chr13	100258999	100258999	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcggagctgcggcggcggCgctgctgaggctgtgagtgc	3	6	21	11	6	0	2	0	2	0	0	0	3	0	3	0	5	4	4	0	5	0	0	rs200020595		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr13:100258999C>T	ENST00000376360.1	+	1	77	c.50C>T	c.(49-51)gCg>gTg	p.A17V	CLYBL_ENST00000339105.4_Missense_Mutation_p.A17V|CLYBL_ENST00000376354.1_Missense_Mutation_p.A17V|CLYBL_ENST00000376355.3_Missense_Mutation_p.A17V|CLYBL_ENST00000444838.2_Missense_Mutation_p.A17V			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	17						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCGGCGGCGGCGCTGCTGAGG	0.776																																					p.A17V		.											.	CLYBL-90	0			c.C50T						.						6	8	7					13																	100258999		1843	3595	5438	SO:0001583	missense	171425	exon1			CGGCGGCGCTGCT	AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.50C>T	13.37:g.100258999C>T	ENSP00000365538:p.Ala17Val	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	16	12	NM_206808	0	0	0	0	0	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.689931	0.29962	.	.	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105	T;T;T;T;T	0.24350	1.86;1.88;1.86;1.86;1.88	3.41	1.64	0.23874	.	0.599921	0.15592	N	0.254333	T	0.10766	0.0263	N	0.08118	0	0.22552	N	0.998997	B;B;B	0.15719	0.014;0.01;0.003	B;B;B	0.10450	0.002;0.005;0.001	T	0.30357	-0.9981	10	0.23302	T	0.38	.	5.6733	0.17735	0.0:0.7452:0.0:0.2548	.	17;17;17	B4DU60;Q8N0X4-2;Q8N0X4	.;.;CLYBL_HUMAN	V	17	ENSP00000365533:A17V;ENSP00000365538:A17V;ENSP00000404768:A17V;ENSP00000365532:A17V;ENSP00000342991:A17V	ENSP00000342991:A17V	A	+	2	0	CLYBL	99057000	0.995000	0.38212	1.000000	0.80357	0.521000	0.34408	0.074000	0.14662	0.436000	0.26393	0.313000	0.20887	GCG	.		0.776	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1			T	100258999	C	T	100258999	3	4	153	1	0	0	0	0	1	0	0	0	3579	768	27	1	52	1	CLYBL	13	100258999	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		100258999	14910879	90	13805											
MYH7	4625	ucsc.edu;bcgsc.ca	37	chr14	23898982	23898982	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaagaatccctgcctcccAccttcagtgccgtctggctc	6	9	7	19	1	2	1	1	0	1	1	5	1	4	1	6	1	2	1	6	1	2	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:23898982A>G	ENST00000355349.3	-	12	1301		c.e12+1			NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta						adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CCTGCCTCCCACCTTCAGTGC	0.502																																					.													.	MYH7-94	0			c.1138+2T>C						.						74	70	71					14																	23898982		2203	4300	6503	SO:0001630	splice_region_variant	4625	exon13			CCTCCCACCTTCA	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1138+1T>C	14.37:g.23898982A>G		Somatic	40	0		WXS	Illumina HiSeq		41	4	NM_000257	0	0	0	0	0	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Splice_Site	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	a	19.39	3.817501	0.70912	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	.	.	.	3.08	3.08	0.35506	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4148	0.49945	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYH7	22968822	1.000000	0.71417	0.819000	0.32651	0.554000	0.35429	5.627000	0.67784	1.262000	0.44165	0.375000	0.23000	.	.		0.502	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	Intron	G	23898982	A	G	23898982	5	3	153	1	0	0	0	0	0	0	1	0	10064	173	6	3	4783	3	MYH7	14	23898982	Splice_Site	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		23898982	83450558	91	13806											
LGALS3	3958	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	55604955	55604955	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctggagcacctggagcttatCccggagcacctgcacctgga	8	7	12	14	1	0	0	0	0	0	0	1	4	1	4	4	4	4	4	4	4	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:55604955C>T	ENST00000254301.9	+	3	472	c.211C>T	c.(211-213)Ccc>Tcc	p.P71S	LGALS3_ENST00000554715.1_Missense_Mutation_p.P71S|LGALS3_ENST00000553755.1_3'UTR	NM_002306.3	NP_002297.2	P17931	LEG3_HUMAN	lectin, galactoside-binding, soluble, 3	71	8 X 9 AA tandem repeats of Y-P-G-X(3)-P- G-A.				eosinophil chemotaxis (GO:0048245)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|mononuclear cell migration (GO:0071674)|mRNA processing (GO:0006397)|negative regulation of endocytosis (GO:0045806)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of immunological synapse formation (GO:2000521)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell receptor signaling pathway (GO:0050860)|neutrophil chemotaxis (GO:0030593)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of mononuclear cell migration (GO:0071677)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of T cell apoptotic process (GO:0070232)|regulation of T cell proliferation (GO:0042129)|RNA splicing (GO:0008380)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)	carbohydrate binding (GO:0030246)|chemoattractant activity (GO:0042056)|IgE binding (GO:0019863)|laminin binding (GO:0043236)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|prostate(1)	3						TGGAGCTTATCCCGGAGCACC	0.682																																					p.P71S		.											.	LGALS3-514	0			c.C211T						.						21	24	23					14																	55604955		1813	4069	5882	SO:0001583	missense	3958	exon3			GCTTATCCCGGAG	M64303	CCDS41956.1	14q22.3	2014-03-19	2007-02-01		ENSG00000131981	ENSG00000131981		"Lectins, galactoside-binding", "Endogenous ligands"	6563	protein-coding gene	gene with protein product	"galectin 3"	153619		LGALS2		2009535, 8063692	Standard	NR_003225		Approved	MAC-2, GALIG	uc001xbr.3	P17931	OTTHUMG00000171030	ENST00000254301.9:c.211C>T	14.37:g.55604955C>T	ENSP00000254301:p.Pro71Ser	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	78	29	NM_002306	0	0	95	130	35	B2RC38|Q16005|Q6IBA7|Q96J47	Missense_Mutation	SNP	ENST00000254301.9	37	CCDS41956.1	.	.	.	.	.	.	.	.	.	.	C	7.633	0.679349	0.14907	.	.	ENSG00000131981	ENST00000553493;ENST00000254301;ENST00000554715	T;T;T	0.74315	-0.83;3.24;2.45	5.35	4.45	0.53987	.	0.209237	0.50627	N	0.000111	T	0.77751	0.4177	M	0.86178	2.8	0.45662	D	0.998582	B	0.11235	0.004	B	0.16722	0.016	T	0.73830	-0.3859	10	0.62326	D	0.03	.	14.3618	0.66776	0.0:0.921:0.0:0.079	.	71	P17931	LEG3_HUMAN	S	71	ENSP00000451526:P71S;ENSP00000254301:P71S;ENSP00000451381:P71S	ENSP00000254301:P71S	P	+	1	0	LGALS3	54674708	0.991000	0.36638	0.823000	0.32752	0.087000	0.18053	2.632000	0.46511	0.647000	0.30713	-0.797000	0.03246	CCC	.		0.682	LGALS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411309.1	NM_002306		T	55604955	C	T	55604955	3	4	153	1	0	0	0	0	1	0	0	0	8764	855	30	2	217	2	LGALS3	14	55604955	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	31705973	55604955	51744585	92	13807											
ZFYVE26	23503	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	68268851	68268851	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaggccaggtcctcagaGaggctgtctttgcagtcctg	6	10	14	11	0	2	2	1	1	1	1	4	3	4	2	3	3	1	3	3	3	0	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:68268851G>T	ENST00000347230.4	-	10	1722	c.1584C>A	c.(1582-1584)ctC>ctA	p.L528L	ZFYVE26_ENST00000555452.1_Silent_p.L528L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	528					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GGTCCTCAGAGAGGCTGTCTT	0.537																																					p.L528L		.											.	ZFYVE26-162	0			c.C1584A						.						139	126	130					14																	68268851		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon10			CTCAGAGAGGCTG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"Zinc fingers, FYVE domain containing"	20761	protein-coding gene	gene with protein product	"spastizin", "FYVE-CENT"	612012	"spastic paraplegia 15 (complicated, autosomal recessive)"	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.1584C>A	14.37:g.68268851G>T		Somatic	128	0		WXS	Illumina HiSeq	Phase_I	188	71	NM_015346	0	0	0	0	0	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	37	CCDS9788.1																																																																																			.		0.537	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68268851	G	T	68268851	2	4	153	1	0	0	0	0	0	0	0	1	17700	929	33	4		4	ZFYVE26	14	68268851	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	12663896	68268851	39080689	93	13808											
GPR65	8477	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	88478074	88478074	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctgtactgttttgtaaccGaaacaggaagatatgatatg	13	14	9	5	1	1	2	0	1	1	1	1	4	1	3	1	1	3	3	1	1	6	7			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:88478074G>A	ENST00000267549.3	+	2	1441	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	RP11-300J18.2_ENST00000554433.1_RNA	NM_003608.3	NP_003599.2	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	295					actin cytoskeleton reorganization (GO:0031532)|activation of Rho GTPase activity (GO:0032862)|apoptotic process (GO:0006915)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of stress fiber assembly (GO:0051496)|response to acidic pH (GO:0010447)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)	16						TTTTGTAACCGAAACAGGAAG	0.353																																					p.E295K		.											.	GPR65-90	0			c.G883A						.						95	90	91					14																	88478074		2203	4300	6503	SO:0001583	missense	8477	exon2			GTAACCGAAACAG	U95218	CCDS9879.1	14q31-q32.1	2012-08-21			ENSG00000140030	ENSG00000140030		"GPCR / Class A : Orphans"	4517	protein-coding gene	gene with protein product		604620				9655242	Standard	NM_003608		Approved	hTDAG8, TDAG8	uc001xvv.3	Q8IYL9	OTTHUMG00000028648	ENST00000267549.3:c.883G>A	14.37:g.88478074G>A	ENSP00000267549:p.Glu295Lys	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	185	10	NM_003608	0	0	13	13	0	O75819	Missense_Mutation	SNP	ENST00000267549.3	37	CCDS9879.1	.	.	.	.	.	.	.	.	.	.	G	31	5.063367	0.93898	.	.	ENSG00000140030	ENST00000267549	T	0.30714	1.52	5.98	5.98	0.97165	.	0.000000	0.56097	D	0.000037	T	0.33556	0.0867	N	0.08118	0	0.44417	D	0.99733	D	0.71674	0.998	P	0.58820	0.846	T	0.20009	-1.0288	10	0.29301	T	0.29	.	20.4581	0.99154	0.0:0.0:1.0:0.0	.	295	Q8IYL9	PSYR_HUMAN	K	295	ENSP00000267549:E295K	ENSP00000267549:E295K	E	+	1	0	GPR65	87547827	1.000000	0.71417	0.654000	0.29608	0.919000	0.55068	6.201000	0.72124	2.835000	0.97688	0.650000	0.86243	GAA	.		0.353	GPR65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071564.4			A	88478074	G	A	88478074	3	1	153	1	0	0	0	0	1	0	0	0	6726	1059	37	1	885	1	GPR65	14	88478074	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	20209223	88478074	18871466	94	13809											
PPP4R4	57718	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	94733352	94733352	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggttaggaaagacttctgTgctttcactagctggtaagt	10	13	12	6	0	2	1	1	0	1	1	2	2	2	2	0	3	2	4	0	3	4	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:94733352T>A	ENST00000304338.3	+	23	2589	c.2435T>A	c.(2434-2436)gTg>gAg	p.V812E		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	812					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						AAGACTTCTGTGCTTTCACTA	0.299																																					p.V812E													.	PPP4R4-94	0			c.T2435A						.						80	78	79					14																	94733352		2202	4295	6497	SO:0001583	missense	57718	exon23			CTTCTGTGCTTTC	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	23788	protein-coding gene	gene with protein product	"cilia and flagella associated protein 14"		"KIAA1622"	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.2435T>A	14.37:g.94733352T>A	ENSP00000305924:p.Val812Glu	Somatic	52	1		WXS	Illumina HiSeq	Phase_I	63	20	NM_058237	0	0	0	0	0	Q9BUF8|Q9HCF0	Missense_Mutation	SNP	ENST00000304338.3	37	CCDS9921.1	.	.	.	.	.	.	.	.	.	.	T	10.60	1.395792	0.25205	.	.	ENSG00000119698	ENST00000304338	.	.	.	5.83	4.69	0.59074	.	1.582440	0.03220	N	0.177378	T	0.44871	0.1314	N	0.08118	0	0.80722	D	1	B	0.26258	0.145	B	0.29942	0.109	T	0.23583	-1.0184	9	0.59425	D	0.04	0.0344	9.9904	0.41868	0.0:0.076:0.0:0.924	.	812	Q6NUP7	PP4R4_HUMAN	E	812	.	ENSP00000305924:V812E	V	+	2	0	PPP4R4	93803105	0.906000	0.30813	0.249000	0.24280	0.367000	0.29736	3.233000	0.51311	2.225000	0.72522	0.383000	0.25322	GTG	.		0.299	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		A	94733352	T	A	94733352	3	1	153	1	0	0	0	0	1	0	0	0	12434	1696	59	5	2598	5	PPP4R4	14	94733352	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	6255278	94733352	12616188	95	13810											
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105350539	105350539	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcgggagaagacagaggaaCggctgggcagcccctcgccc	10	2	16	13	3	0	3	0	0	0	3	1	5	0	4	3	4	3	2	3	4	2	0	rs373443985		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:105350539C>T	ENST00000414716.3	+	9	1651	c.1423C>T	c.(1423-1425)Cgg>Tgg	p.R475W	CEP170B_ENST00000453495.1_Missense_Mutation_p.R476W|CEP170B_ENST00000418279.1_Missense_Mutation_p.R405W|CEP170B_ENST00000556508.1_Missense_Mutation_p.R405W	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	475						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GACAGAGGAACGGCTGGGCAG	0.736																																					p.R475W		.											.	.	0			c.C1423T						.	C	TRP/ARG,TRP/ARG	2,3338		0,2,1668	4	7	6		1423,1213	4.1	1	14		6	1,7387		0,1,3693	no	missense,missense	KIAA0284	NM_001112726.2,NM_015005.2	101,101	0,3,5361	TT,TC,CC		0.0135,0.0599,0.028	probably-damaging,probably-damaging	475/1555,405/1520	105350539	3,10725	1670	3694	5364	SO:0001583	missense	283638	exon9			GAGGAACGGCTGG	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"Cep170-related"		"KIAA0284"	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.1423C>T	14.37:g.105350539C>T	ENSP00000404151:p.Arg475Trp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_001112726	0	0	2	5	3	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	37	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695399	0.68386	5.99E-4	1.35E-4	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.51574	0.71;0.7;0.71;0.71	4.09	4.09	0.47781	.	0.577739	0.16725	N	0.202119	T	0.61751	0.2372	L	0.49350	1.555	0.52501	D	0.999953	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.989	T	0.62845	-0.6768	10	0.62326	D	0.03	-12.0906	12.3112	0.54929	0.1701:0.8299:0.0:0.0	.	475;475;405	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	W	405;475;476;405	ENSP00000451249:R405W;ENSP00000404151:R475W;ENSP00000407238:R476W;ENSP00000415006:R405W	ENSP00000404151:R475W	R	+	1	2	KIAA0284	104421584	0.739000	0.28196	0.982000	0.44146	0.376000	0.30014	1.841000	0.39240	1.813000	0.52934	0.313000	0.20887	CGG	.		0.736	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		T	105350539	C	T	105350539	3	4	153	1	0	0	0	0	1	0	0	0	8187	527	19	1	1453	1	KIAA0284	14	105350539	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	10617187	105350539	1999001	96	13811											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923447	24923447	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttagtgagcagtgcctcTgcagcatcgttatccaagcc	9	11	9	12	1	1	1	0	1	1	0	3	1	2	1	3	0	5	4	3	0	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:24923447T>A	ENST00000329468.2	+	1	2907	c.2433T>A	c.(2431-2433)tcT>tcA	p.S811S		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	811					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GCAGTGCCTCTGCAGCATCGT	0.522																																					p.S811S		.											.	.	0			c.T2433A						.						138	133	135					15																	24923447		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TGCCTCTGCAGCA	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2433T>A	15.37:g.24923447T>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	69	4	NM_018958	0	0	0	0	0		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.		0.522	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923447	T	A	24923447	2	1	153	1	0	0	0	0	0	0	0	1	1788	1567	55	5		5	C15orf2	15	24923447	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10		24923447	77607945	97	13812											
OTUD7A	161725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	31818596	31818596	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaagtgtgtgcgcggctcGctggaggccagcttcagcag	6	8	16	11	3	1	1	1	1	0	0	2	2	1	2	1	3	3	4	1	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:31818596G>A	ENST00000307050.4	-	6	920	c.828C>T	c.(826-828)agC>agT	p.S276S	OTUD7A_ENST00000382902.1_Silent_p.S283S	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	276	Catalytic. {ECO:0000250}.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding. {ECO:0000250}.				protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		TGCGCGGCTCGCTGGAGGCCA	0.677																																					p.S276S		.											.	OTUD7A-502	0			c.C828T						.						37	34	35					15																	31818596		2202	4300	6502	SO:0001819	synonymous_variant	161725	exon6			CGGCTCGCTGGAG	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"OTU domain containing"	20718	protein-coding gene	gene with protein product		612024	"chromosome 15 open reading frame 16", "OTU domain containing 7", "OTU domain containing 7A"	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.828C>T	15.37:g.31818596G>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	22	5	NM_130901	0	0	0	0	0	Q8IWK5	Silent	SNP	ENST00000307050.4	37	CCDS10026.1																																																																																			.		0.677	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		A	31818596	G	A	31818596	2	1	153	1	0	0	0	0	0	0	0	1	11344	1078	38	1		1	OTUD7A	15	31818596	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	6895149	31818596	70712796	98	13813											
C15orf53	400359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	38988831	38988831	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctacaaggggcccaagAggacctgggcatttccctct	9	7	13	12	0	1	1	0	0	1	1	2	3	2	3	3	5	2	2	3	5	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:38988831A>C	ENST00000318792.1	+	1	33	c.23A>C	c.(22-24)gAg>gCg	p.E8A		NM_207444.2	NP_997327.1	Q8NAA6	CO053_HUMAN	chromosome 15 open reading frame 53	8										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)		GGGGCCCAAGAGGACCTGGGC	0.562																																					p.E8A		.											.	C15orf53-492	0			c.A23C						.						96	91	93					15																	38988831		2200	4297	6497	SO:0001583	missense	400359	exon1			CCCAAGAGGACCT		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.23A>C	15.37:g.38988831A>C	ENSP00000325144:p.Glu8Ala	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	159	46	NM_207444	0	0	0	0	0		Missense_Mutation	SNP	ENST00000318792.1	37	CCDS10048.1	.	.	.	.	.	.	.	.	.	.	A	9.365	1.069014	0.20147	.	.	ENSG00000175779	ENST00000318792	T	0.34667	1.35	3.31	-1.66	0.08265	.	.	.	.	.	T	0.23330	0.0564	N	0.08118	0	0.09310	N	1	D	0.54207	0.965	P	0.52554	0.702	T	0.12477	-1.0546	9	0.87932	D	0	.	3.0108	0.06044	0.4664:0.0:0.3378:0.1958	.	8	Q8NAA6	CO053_HUMAN	A	8	ENSP00000325144:E8A	ENSP00000325144:E8A	E	+	2	0	C15orf53	36776123	0.001000	0.12720	0.000000	0.03702	0.074000	0.17049	0.566000	0.23593	-0.349000	0.08274	-0.415000	0.06103	GAG	.		0.562	C15orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252081.1	NM_207444		C	38988831	A	C	38988831	3	2	153	1	0	0	0	0	1	0	0	0	1805	304	11	5	25	5	C15orf53	15	38988831	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	7170235	38988831	63542561	99	13814											
DUOX1	53905	broad.mit.edu	37	chr15	45427438	45427438	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgctgcccttccagagAagccgctgggaccccgagac	7	6	14	14	2	0	2	0	0	0	2	1	5	1	3	5	2	3	2	5	2	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:45427438A>G	ENST00000321429.4	+	6	851	c.444A>G	c.(442-444)agA>agG	p.R148R	DUOX1_ENST00000389037.3_Silent_p.R148R	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	148	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CCTTCCAGAGAAGCCGCTGGG	0.721																																					p.R148R													.	DUOX1-142	0			c.A444G						.						16	19	18					15																	45427438		2191	4286	6477	SO:0001819	synonymous_variant	53905	exon6			CCAGAGAAGCCGC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"EF-hand domain containing"	3062	protein-coding gene	gene with protein product	"NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase"	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.444A>G	15.37:g.45427438A>G		Somatic	78	3		WXS	Illumina HiSeq	Phase_I	178	9	NM_017434	0	0	0	0	0	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			.		0.721	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		G	45427438	A	G	45427438	2	3	153	1	0	0	0	0	0	0	0	1	4811	243	9	3		3	DUOX1	15	45427438	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	6438607	45427438	57103954	100	13815											
MYO5A	4644	hgsc.bcm.edu;broad.mit.edu	37	chr15	52680095	52680096	+	Missense_Mutation	DNP	AC	AC	CA																															ttcttttcgagaaatccttcAcactggtattccacctgaaa																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:52680095_52680096AC>CA	ENST00000399231.3	-	14	1925_1926	c.1682_1683GT>TG	c.(1681-1683)tGT>tTG	p.C561L	MYO5A_ENST00000553916.1_Missense_Mutation_p.C561L|MYO5A_ENST00000356338.6_Missense_Mutation_p.C561L|MYO5A_ENST00000399233.2_Missense_Mutation_p.C561L|MYO5A_ENST00000358212.6_Missense_Mutation_p.C561L	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	561	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GAAATCCTTCACACTGGTATTC	0.307																																					p.C561L		.											.	MYO5A-93	0			c.G1682T						.																																			SO:0001583	missense	4644	exon14			CCTTCACACTGGT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"Myosins / Myosin superfamily : Class V"	7602	protein-coding gene	gene with protein product	"myosin, heavy polypeptide kinase", "myosin heavy chain 12", "myoxin", "myosin V"	160777	"myosin VA (heavy polypeptide 12, myoxin)"	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.1682_1683delinsCA	15.37:g.52680095_52680096delinsCA	ENSP00000382177:p.Cys561Leu	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	13	5	NM_000259	0	0	0	0	0	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	DNP	ENST00000399231.3	37	CCDS42037.1																																																																																			.		0.307	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		CA	52680096	AC	CA	52680095	3	2	153	1	0	0	0	0	1	0	0	0	10103	157	6	5	3996	5	MYO5A	15	52680095	Missense_Mutation	DNP	AC	TCGA-P4-A5E6-01A-11D-A28G-10	7252657	52680095	49851297	101	13816											
SLCO3A1	28232	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	92647568	92647568	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcctggtggggtggctttCtgctctgcggtgccttactc	2	13	15	11	1	2	0	0	0	2	0	3	1	2	0	2	5	5	2	2	5	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:92647568C>A	ENST00000318445.6	+	4	1019	c.805C>A	c.(805-807)Ctg>Atg	p.L269M	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.L269M|SLCO3A1_ENST00000555549.1_3'UTR	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	269					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	GGGTGGCTTTCTGCTCTGCGG	0.577																																					p.L269M													.	SLCO3A1-91	0			c.C805A						.						226	203	211					15																	92647568		2198	4298	6496	SO:0001583	missense	28232	exon4			GGCTTTCTGCTCT	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"Solute carriers"	10952	protein-coding gene	gene with protein product		612435	"solute carrier family 21 (organic anion transporter), member 11"	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.805C>A	15.37:g.92647568C>A	ENSP00000320634:p.Leu269Met	Somatic	66	1		WXS	Illumina HiSeq	Phase_I	82	26	NM_013272	0	0	1	1	0	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	37	CCDS10371.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.091915	0.76756	.	.	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000556649	T;T	0.56444	0.46;0.46	5.12	5.12	0.69794	Major facilitator superfamily domain, general substrate transporter (1);	0.076624	0.53938	D	0.000045	T	0.69904	0.3163	M	0.71920	2.185	0.80722	D	1	P;D;D	0.76494	0.928;0.963;0.999	P;P;D	0.77004	0.668;0.715;0.989	T	0.72903	-0.4151	10	0.66056	D	0.02	.	12.9394	0.58333	0.0:0.9216:0.0:0.0784	.	211;269;269	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	M	269;269;62	ENSP00000320634:L269M;ENSP00000387846:L269M	ENSP00000320634:L269M	L	+	1	2	SLCO3A1	90448572	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.517000	0.53443	2.353000	0.79882	0.655000	0.94253	CTG	.		0.577	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		A	92647568	C	A	92647568	3	1	153	1	0	0	0	0	1	0	0	0	14760	912	32	4	819	4	SLCO3A1	15	92647568	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	39967473	92647568	9883824	102	13817											
WDR90	197335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	707787	707787	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtatgcccggatgccccCgcgagccccagcgccctggc	5	5	13	18	4	0	0	0	0	0	0	0	2	0	1	6	3	4	1	6	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:707787C>T	ENST00000293879.4	+	21	2499	c.2499C>T	c.(2497-2499)ccC>ccT	p.P833P	WDR90_ENST00000549091.1_Silent_p.P833P|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	833										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CGGATGCCCCCGCGAGCCCCA	0.726																																					p.P833P		.											.	WDR90-92	0			c.C2499T						.						8	11	10					16																	707787		1929	4048	5977	SO:0001819	synonymous_variant	197335	exon21			TGCCCCCGCGAGC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"WD repeat domain containing"	26960	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18"	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2499C>T	16.37:g.707787C>T		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	281	89	NM_145294	0	0	3	3	0	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.		0.726	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	707787	C	T	707787	2	4	153	1	0	0	0	0	0	0	0	1	17370	639	23	1		1	WDR90	16	707787	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		707787	89646966	103	13818											
VASN	114990	hgsc.bcm.edu	37	chr16	4432672	4432672	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtgggggcagcctactgTgtgcggcgggggcgggccat	3	6	22	10	4	0	0	0	0	0	0	0	0	0	0	2	7	3	1	2	7	1	1	rs370088997	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:4432672T>C	ENST00000304735.3	+	2	1949	c.1794T>C	c.(1792-1794)tgT>tgC	p.C598C	CORO7_ENST00000537233.2_Intron|CORO7_ENST00000539968.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000251166.4_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	598					cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CAGCCTACTGTGTGCGGCGGG	0.741													T|||	5	0.000998403	0.0038	0	5008	,	,		13454	0		0	False		,,,				2504	0				p.C598C		.											.	VASN-68	0			c.T1794C						.	T	,,,,	8,3802		0,8,1897	4	7	6		,,,,1794	-1.7	1	16		6	0,7642		0,0,3821	no	intron,intron,intron,intron,coding-synonymous	CORO7,VASN,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4,NM_138440.2	,,,,	0,8,5718	CC,CT,TT		0.0,0.21,0.0699	,,,,	,,,,598/674	4432672	8,11444	1905	3821	5726	SO:0001819	synonymous_variant	114990	exon2			CTACTGTGTGCGG	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"slit-like 2 (Drosophila)"	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1794T>C	16.37:g.4432672T>C		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_138440	0	0	17	30	13	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			.		0.741	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		C	4432672	T	C	4432672	2	2	153	1	0	0	0	0	0	0	0	1	17160	1702	59	3		3	VASN	16	4432672	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	3724885	4432672	85922081	104	13819											
ITGAD	3681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	31414951	31414951	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctgacgttcacggccacggGcatcctgacagtggtgtaag	8	8	13	12	3	1	2	1	2	0	0	2	2	2	2	3	3	0	3	3	3	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:31414951G>A	ENST00000389202.2	+	7	738	c.689G>A	c.(688-690)gGc>gAc	p.G230D	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	230	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ACGGCCACGGGCATCCTGACA	0.607																																					p.G230D		.											.	ITGAD-226	0			c.G689A						.						96	78	84					16																	31414951		2197	4300	6497	SO:0001583	missense	3681	exon7			CCACGGGCATCCT	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"CD molecules", "Integrins"	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.689G>A	16.37:g.31414951G>A	ENSP00000373854:p.Gly230Asp	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	157	59	NM_005353	0	0	1	1	0	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810704	0.70797	.	.	ENSG00000156886	ENST00000316569;ENST00000444228;ENST00000389202	D	0.86030	-2.06	4.7	3.7	0.42460	von Willebrand factor, type A (3);	.	.	.	.	D	0.92492	0.7616	M	0.86864	2.845	0.34300	D	0.684244	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.996	D	0.94979	0.8124	9	0.87932	D	0	.	12.6978	0.57014	0.0:0.1801:0.8199:0.0	.	230;246;230	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	D	94;246;230	ENSP00000373854:G230D	ENSP00000323325:G94D	G	+	2	0	ITGAD	31322452	1.000000	0.71417	0.706000	0.30403	0.134000	0.20937	1.683000	0.37638	2.434000	0.82447	0.508000	0.49915	GGC	.		0.607	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31414951	G	A	31414951	3	1	153	1	0	0	0	0	1	0	0	0	7905	1203	42	2	715	2	ITGAD	16	31414951	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	26982279	31414951	58939802	105	13820											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31475859	31475859	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcaccacgcacccaacgCactccgggccgcagccccgc	7	1	11	22	6	0	0	0	0	0	0	1	0	1	0	6	2	2	4	6	2	1	0	rs115663676	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:31475859C>T	ENST00000563544.1	+	5	2061	c.1515C>T	c.(1513-1515)cgC>cgT	p.R505R	ARMC5_ENST00000408912.3_Silent_p.R600R|ARMC5_ENST00000457010.2_Silent_p.R505R|ARMC5_ENST00000412665.2_Silent_p.R149R|ARMC5_ENST00000268314.4_Silent_p.R505R|ARMC5_ENST00000538189.1_Silent_p.R537R			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	505										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GCACCCAACGCACTCCGGGCC	0.741													C|||	36	0.0071885	0.025	0.0043	5008	,	,		9106	0		0	False		,,,				2504	0				p.R505R		.											.	ARMC5-24	0			c.C1515T						.	C	,	68,3728		0,68,1830	6	8	8		1515,1515	2.7	0.5	16	dbSNP_132	8	1,7875		0,1,3937	no	coding-synonymous,coding-synonymous	ARMC5	NM_001105247.1,NM_024742.2	,	0,69,5767	TT,TC,CC		0.0127,1.7914,0.5912	,	505/936,505/726	31475859	69,11603	1898	3938	5836	SO:0001819	synonymous_variant	79798	exon4			CCAACGCACTCCG	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1515C>T	16.37:g.31475859C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	13	12	NM_024742	1	0	0	5	4	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			C|0.992;T|0.008		0.741	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		T	31475859	C	T	31475859	2	4	153	1	0	0	0	0	0	0	0	1	955	697	25	2		2	ARMC5	16	31475859	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	60908	31475859	58878894	106	13821											
PHKB	5257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	47622955	47622955	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	taaacgtttcttgagagatgGgtatagaacatcattggaag	14	12	11	4	1	2	3	1	1	1	2	2	5	2	4	0	2	2	2	0	2	6	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:47622955G>A	ENST00000323584.5	+	10	1034	c.1010G>A	c.(1009-1011)gGg>gAg	p.G337E	PHKB_ENST00000455779.1_Missense_Mutation_p.G330E|PHKB_ENST00000567402.1_3'UTR|PHKB_ENST00000566044.1_Missense_Mutation_p.G330E|PHKB_ENST00000299167.8_Missense_Mutation_p.G337E	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	337					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TTGAGAGATGGGTATAGAACA	0.353																																					p.G337E		.											.	PHKB-154	0			c.G1010A						.						70	74	73					16																	47622955		2201	4300	6501	SO:0001583	missense	5257	exon10			GAGATGGGTATAG		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.1010G>A	16.37:g.47622955G>A	ENSP00000313504:p.Gly337Glu	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	107	27	NM_000293	0	0	2	4	2	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099043	0.94197	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91792	-2.91;-2.91	5.83	5.83	0.93111	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.97232	0.9095	M	0.92923	3.36	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.79108	0.992;0.918	D	0.97532	1.0080	10	0.87932	D	0	-10.5585	20.127	0.97984	0.0:0.0:1.0:0.0	.	337;330	Q93100;Q93100-4	KPBB_HUMAN;.	E	330;330;337	ENSP00000414345:G330E;ENSP00000313504:G337E	ENSP00000299167:G330E	G	+	2	0	PHKB	46180456	1.000000	0.71417	0.964000	0.40570	0.946000	0.59487	9.717000	0.98755	2.775000	0.95449	0.585000	0.79938	GGG	.		0.353	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47622955	G	A	47622955	3	1	153	1	0	0	0	0	1	0	0	0	11871	1232	43	2	1107	2	PHKB	16	47622955	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	16147096	47622955	42731798	107	13822											
RBL2	5934	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	53514563	53514563	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcctcccacacctactcGcctcacaggtgccaacagtg	8	8	7	18	1	1	0	1	0	0	0	4	0	3	0	5	1	4	1	5	1	2	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:53514563G>A	ENST00000262133.6	+	20	3103	c.2966G>A	c.(2965-2967)cGc>cAc	p.R989H	RBL2_ENST00000544545.1_Intron|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	989	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ACACCTACTCGCCTCACAGGT	0.517																																					p.R989H													.	RBL2-841	0			c.G2966A						.						132	113	119					16																	53514563		2198	4300	6498	SO:0001583	missense	5934	exon20			CTACTCGCCTCAC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2966G>A	16.37:g.53514563G>A	ENSP00000262133:p.Arg989His	Somatic	229	1		WXS	Illumina HiSeq	Phase_I	289	72	NM_005611	0	0	12	18	6	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533269	0.64972	.	.	ENSG00000103479	ENST00000262133;ENST00000379935	D	0.90069	-2.61	5.67	3.48	0.39840	Retinoblastoma-associated protein, B-box (1);Cyclin-like (1);	0.232291	0.42548	N	0.000684	D	0.90841	0.7123	L	0.50333	1.59	0.49798	D	0.999827	D;D	0.76494	0.999;0.998	D;P	0.66351	0.943;0.905	D	0.88546	0.3113	10	0.41790	T	0.15	-4.2222	10.6092	0.45412	0.1771:0.0:0.8229:0.0	.	699;989	E9PG04;Q08999	.;RBL2_HUMAN	H	989;699	ENSP00000262133:R989H	ENSP00000262133:R989H	R	+	2	0	RBL2	52072064	0.993000	0.37304	0.216000	0.23742	0.932000	0.56968	2.600000	0.46240	0.564000	0.29238	0.650000	0.86243	CGC	.		0.517	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		A	53514563	G	A	53514563	3	1	153	1	0	0	0	0	1	0	0	0	13142	1087	38	1	3044	1	RBL2	16	53514563	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	5891608	53514563	36840190	108	13823											
DBNDD1	79007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	90075270	90075270	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctggtccgacatgtcggTgagctcagtgaggtccagga	7	9	14	11	2	1	2	1	2	0	0	5	4	4	3	3	4	1	1	3	4	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:90075270T>A	ENST00000002501.6	-	3	372	c.241A>T	c.(241-243)Acc>Tcc	p.T81S	DBNDD1_ENST00000304733.3_Missense_Mutation_p.T101S|DBNDD1_ENST00000568838.1_Missense_Mutation_p.T201S|DBNDD1_ENST00000392973.3_Missense_Mutation_p.T87S	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	81						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		GACATGTCGGTGAGCTCAGTG	0.642																																					p.T101S		.											.	DBNDD1-90	0			c.A301T						.						32	37	35					16																	90075270		2016	4160	6176	SO:0001583	missense	79007	exon3			TGTCGGTGAGCTC	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.241A>T	16.37:g.90075270T>A	ENSP00000002501:p.Thr81Ser	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	119	28	NM_024043	0	0	14	30	16	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	37	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.480743	0.63849	.	.	ENSG00000003249	ENST00000304733;ENST00000002501;ENST00000392973	T;T	0.34072	1.38;1.38	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.61274	0.2334	M	0.78637	2.42	0.49299	D	0.999773	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.994	T	0.64415	-0.6413	9	.	.	.	-34.7701	15.1222	0.72453	0.0:0.0:0.0:1.0	.	81;101	Q9H9R9;Q9H9R9-2	DBND1_HUMAN;.	S	101;81;201	ENSP00000306407:T101S;ENSP00000002501:T81S	.	T	-	1	0	DBNDD1	88602771	1.000000	0.71417	0.992000	0.48379	0.282000	0.26991	5.761000	0.68801	1.992000	0.58205	0.260000	0.18958	ACC	.		0.642	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043		A	90075270	T	A	90075270	3	1	153	1	0	0	0	0	1	0	0	0	4259	1696	59	5	243	5	DBNDD1	16	90075270	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	36560707	90075270	279483	109	13824											
ZNF594	84622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	5086862	5086862	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttccccctactgtggattctCtggtgcaggacaaggtttga	7	13	11	10	0	1	1	0	1	1	0	3	3	2	3	2	4	2	2	2	4	2	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:5086862C>G	ENST00000399604.4	-	1	830	c.690G>C	c.(688-690)caG>caC	p.Q230H	ZNF594_ENST00000575779.1_Missense_Mutation_p.Q230H			Q96JF6	ZN594_HUMAN	zinc finger protein 594	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q230H(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TGTGGATTCTCTGGTGCAGGA	0.438																																					p.Q230H		.											.	ZNF594-71	1	Substitution - Missense(1)	cervix(1)	c.G690C						.						104	107	106					17																	5086862		2051	4221	6272	SO:0001583	missense	84622	exon2			GATTCTCTGGTGC	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"Zinc fingers, C2H2-type"	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.690G>C	17.37:g.5086862C>G	ENSP00000382513:p.Gln230His	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	68	32	NM_032530	0	0	0	0	0	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	C	3.775	-0.046880	0.07407	.	.	ENSG00000180626	ENST00000399604	T	0.18502	2.21	2.36	1.36	0.22044	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22859	0.0552	L	0.48986	1.54	0.20638	N	0.99988	D	0.57899	0.981	P	0.53035	0.716	T	0.08186	-1.0734	9	0.52906	T	0.07	.	6.6334	0.22869	0.0:0.8341:0.0:0.1659	.	230	Q96JF6	ZN594_HUMAN	H	230	ENSP00000382513:Q230H	ENSP00000382513:Q230H	Q	-	3	2	ZNF594	5027586	0.000000	0.05858	0.612000	0.29024	0.229000	0.25112	-0.361000	0.07612	1.314000	0.45095	0.462000	0.41574	CAG	.		0.438	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		G	5086862	C	G	5086862	3	3	153	1	0	0	0	0	1	0	0	0	18056	912	32	4	1737	4	ZNF594	17	5086862	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		5086862	76108348	110	13825											
KIAA0100	9703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26971163	26971163	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atctttagctccgcctgcagCttccgctgacaccacttggt	6	12	8	15	2	1	1	0	1	1	0	3	1	3	1	4	1	3	4	4	1	1	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:26971163C>A	ENST00000528896.2	-	2	185	c.111G>T	c.(109-111)aaG>aaT	p.K37N	KIAA0100_ENST00000389003.3_5'UTR|KIAA0100_ENST00000544884.1_5'UTR	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	37						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CCGCCTGCAGCTTCCGCTGAC	0.488											OREG0024280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K37N		.											.	KIAA0100-93	0			c.G111T						.						59	69	65					17																	26971163		2203	4300	6503	SO:0001583	missense	9703	exon2			CTGCAGCTTCCGC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"cancer/testis antigen 101", "breast cancer overexpressed gene 1"	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.111G>T	17.37:g.26971163C>A	ENSP00000436773:p.Lys37Asn	Somatic	90	0	790	WXS	Illumina HiSeq	Phase_I	77	25	NM_014680	0	0	0	0	0	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673269	0.29693	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896	T	0.26373	1.74	5.18	4.2	0.49525	FMP27, N-terminal (1);	0.354102	0.32719	N	0.005740	T	0.19127	0.0459	L	0.27053	0.805	0.80722	D	1	B;B	0.15141	0.012;0.0	B;B	0.12156	0.007;0.002	T	0.03619	-1.1019	10	0.62326	D	0.03	.	11.8337	0.52309	0.1379:0.7294:0.1327:0.0	.	37;37	F6XS94;Q14667	.;K0100_HUMAN	N	37	ENSP00000436773:K37N	ENSP00000005905:K37N	K	-	3	2	KIAA0100	23995290	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.047000	0.30367	1.295000	0.44724	-0.310000	0.09108	AAG	.		0.488	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26971163	C	A	26971163	3	1	153	1	0	0	0	0	1	0	0	0	8175	796	28	4	6748	4	KIAA0100	17	26971163	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	21884301	26971163	54224047	111	13826											
NUFIP2	57532	hgsc.bcm.edu;bcgsc.ca	37	chr17	27614566	27614566	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatgaaattcttggttttaAttcctgctttcccaaaggtg	10	16	8	7	0	1	1	0	1	1	0	3	2	3	1	2	2	1	2	2	2	4	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:27614566A>G	ENST00000225388.4	-	2	504	c.446T>C	c.(445-447)aTt>aCt	p.I149T	NUFIP2_ENST00000579665.1_Intron	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	149						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			CTTGGTTTTAATTCCTGCTTT	0.408																																					p.I149T		.											.	NUFIP2-138	0			c.T446C						.						121	120	121					17																	27614566		2203	4300	6503	SO:0001583	missense	57532	exon2			GTTTTAATTCCTG	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.446T>C	17.37:g.27614566A>G	ENSP00000225388:p.Ile149Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_020772	0	0	0	0	0	A1L3A6|Q9P2M5	Missense_Mutation	SNP	ENST00000225388.4	37	CCDS32600.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020017	0.35606	.	.	ENSG00000108256	ENST00000225388	.	.	.	6.17	6.17	0.99709	.	0.134082	0.52532	D	0.000080	T	0.41328	0.1154	N	0.12182	0.205	0.80722	D	1	B	0.24721	0.11	B	0.25291	0.059	T	0.37384	-0.9708	9	0.56958	D	0.05	-12.34	12.6398	0.56702	0.8623:0.1377:0.0:0.0	.	149	Q7Z417	NUFP2_HUMAN	T	149	.	ENSP00000225388:I149T	I	-	2	0	NUFIP2	24638692	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.852000	0.55934	2.371000	0.80710	0.533000	0.62120	ATT	.		0.408	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		G	27614566	A	G	27614566	3	3	153	1	0	0	0	0	1	0	0	0	10775	101	4	3	1653	3	NUFIP2	17	27614566	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	643403	27614566	53580644	112	13827											
KLHL11	55175	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40011371	40011371	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaatctgaaagccagtctcTaatgagatggaaaggtaacg	16	8	10	7	1	2	2	0	2	2	1	3	4	2	3	1	2	2	1	1	2	5	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:40011371T>C	ENST00000319121.3	-	2	808	c.748A>G	c.(748-750)Aga>Gga	p.R250G		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	250	BACK.									NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				AGCCAGTCTCTAATGAGATGG	0.398																																					p.R250G		.											.	KLHL11-90	0			c.A748G						.						57	58	58					17																	40011371		2203	4300	6503	SO:0001583	missense	55175	exon2			AGTCTCTAATGAG		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.748A>G	17.37:g.40011371T>C	ENSP00000314608:p.Arg250Gly	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	61	33	NM_018143	0	0	0	0	0		Missense_Mutation	SNP	ENST00000319121.3	37	CCDS11411.1	.	.	.	.	.	.	.	.	.	.	T	6.149	0.395748	0.11638	.	.	ENSG00000178502	ENST00000319121;ENST00000540254	T	0.69040	-0.37	4.99	4.01	0.46588	BTB/Kelch-associated (2);	0.068566	0.56097	D	0.000034	T	0.48892	0.1525	N	0.20986	0.625	0.50313	D	0.999866	P	0.46142	0.873	B	0.38264	0.269	T	0.41215	-0.9521	10	0.21540	T	0.41	-2.2119	13.3418	0.60549	0.0:0.0:0.5227:0.4773	.	250	Q9NVR0	KLH11_HUMAN	G	250;113	ENSP00000314608:R250G	ENSP00000314608:R250G	R	-	1	2	KLHL11	37264897	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.686000	0.37669	1.055000	0.40461	-0.452000	0.05504	AGA	.		0.398	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		C	40011371	T	C	40011371	3	2	153	1	0	0	0	0	1	0	0	0	8388	1530	53	3	1382	3	KLHL11	17	40011371	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	12396805	40011371	41183839	113	13828											
KAT2A	2648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40269761	40269761	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctcattgaccagctccatggGgatgtcacccatcacacgga	10	8	9	14	1	3	1	3	1	0	0	4	3	4	3	3	3	1	1	3	3	0	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:40269761G>C	ENST00000225916.5	-	9	1416	c.1363C>G	c.(1363-1365)Ccc>Gcc	p.P455A		NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	455					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AGCTCCATGGGGATGTCACCC	0.627																																					p.P455A		.											.	KAT2A-523	0			c.C1363G						.						43	36	39					17																	40269761		2203	4300	6503	SO:0001583	missense	2648	exon9			CCATGGGGATGTC	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"Chromatin-modifying enzymes / K-acetyltransferases"	4201	protein-coding gene	gene with protein product		602301	"GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.1363C>G	17.37:g.40269761G>C	ENSP00000225916:p.Pro455Ala	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	132	53	NM_021078	0	0	9	15	6	Q8N1A2|Q9UCW1	Missense_Mutation	SNP	ENST00000225916.5	37	CCDS11417.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470462	0.84533	.	.	ENSG00000108773	ENST00000225916	T	0.08634	3.07	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	M	0.84683	2.71	0.80722	D	1	D	0.61080	0.989	D	0.63192	0.912	T	0.28744	-1.0034	10	0.72032	D	0.01	-17.8967	17.6406	0.88135	0.0:0.0:1.0:0.0	.	455	Q92830	KAT2A_HUMAN	A	455	ENSP00000225916:P455A	ENSP00000225916:P455A	P	-	1	0	KAT2A	37523287	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.811000	0.99226	2.164000	0.68074	0.561000	0.74099	CCC	.		0.627	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		C	40269761	G	C	40269761	3	2	153	1	0	0	0	0	1	0	0	0	8002	1232	43	4	1190	4	KAT2A	17	40269761	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	258390	40269761	40925449	114	13829											
MYST2	11143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	47869395	47869395	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctaagccagagttctcaaGgtaaaaaaaccttcattttt	14	12	7	8	0	2	1	2	0	1	1	3	1	2	1	2	2	2	3	2	2	6	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:47869395G>A	ENST00000259021.4	+	2	443	c.163G>A	c.(163-165)Gat>Aat	p.D55N	KAT7_ENST00000424009.2_Splice_Site_p.D55N|KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000454930.2_Splice_Site_p.G55R|KAT7_ENST00000510819.1_Splice_Site_p.G55R|KAT7_ENST00000509773.1_Splice_Site_p.D55N|KAT7_ENST00000435742.2_5'UTR	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	55	Ser-rich.				chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GAGTTCTCAAGGTAAAAAAAC	0.493																																					p.G55R		.											.	.	0			c.G163A						.						72	69	70					17																	47869395		2203	4300	6503	SO:0001630	splice_region_variant	11143	exon2			TCTCAAGGTAAAA	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.163+1G>A	17.37:g.47869395G>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	36	11	NM_001199158	0	0	0	0	0	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.224482|5.224482	0.95139|0.95139	.|.	.|.	ENSG00000136504|ENSG00000136504	ENST00000259021;ENST00000509773;ENST00000424009|ENST00000454930;ENST00000510819	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.153798|.	0.56097|.	D|.	0.000026|.	T|T	0.76385|0.76385	0.3980|0.3980	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;B;D|D;D	0.60575|0.89917	0.98;0.281;0.988|1.0;1.0	D;B;D|D;D	0.73708|0.97110	0.956;0.083;0.981|1.0;1.0	T|T	0.77747|0.77747	-0.2472|-0.2472	9|8	0.09843|0.87932	T|D	0.71|0	-15.7574|-15.7574	19.1747|19.1747	0.93599|0.93599	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	55;55;55|55;55	B4DFB4;O95251;G5E9K7|B4DFE0;E7ER15	.;KAT7_HUMAN;.|.;.	N|R	55|55	.|.	ENSP00000259021:D55N|ENSP00000413415:G55R	D|G	+|+	1|1	0|0	KAT7|KAT7	45224394|45224394	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	9.448000|9.448000	0.97600|0.97600	2.623000|2.623000	0.88846|0.88846	0.650000|0.650000	0.86243|0.86243	GAT|GGA	.		0.493	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067	Missense_Mutation	A	47869395	G	A	47869395	5	1	153	1	0	0	0	0	0	0	1	0	10128	1014	35	2	169	2	MYST2	17	47869395	Splice_Site	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	7599634	47869395	33325815	115	13830											
FAM59A	64762	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	29867165	29867165	+	Frame_Shift_Del	DEL	A	A	-																															agagagcgagtgagaggctgAtggctgggcttgccttcctc																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr18:29867165delA	ENST00000269209.6	-	4	1398	c.1395delT	c.(1393-1395)catfs	p.H465fs	RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000399218.4_Frame_Shift_Del_p.H465fs|GAREM_ENST00000578619.1_5'Flank			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	465					cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										TGAGAGGCTGATGGCTGGGCT	0.527																																					p.H465fs		.											.	.	0			c.1395delT						.						104	102	103					18																	29867165		2203	4300	6503	SO:0001589	frameshift_variant	64762	exon4			.	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"Grb2-associated and regulator of Erk/MAPK"		"chromosome 18 open reading frame 11", "family with sequence similarity 59, member A"	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1395delT	18.37:g.29867165delA	ENSP00000269209:p.His465fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	66	27	NM_022751	0	0	0	0	0	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Frame_Shift_Del	DEL	ENST00000269209.6	37	CCDS56057.1																																																																																			.		0.527	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		-	29867165	A	-	29867165	7	5	153	1	0	1	0	1	0	0	0	0	5611	330	12	0	1244	0	FAM59A	18	29867165	Frame_Shift_Del	DEL	A	TCGA-P4-A5E6-01A-11D-A28G-10		29867165	48210083	116	13831											
CELF5	60680	hgsc.bcm.edu	37	chr19	3285978	3285978	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcacgcccatcgcgcacAgcgtcccccagccgccgccc	6	3	8	24	6	1	0	1	0	0	0	3	0	2	0	7	0	2	1	7	0	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:3285978A>T	ENST00000292672.2	+	10	1178	c.1141A>T	c.(1141-1143)Agc>Tgc	p.S381C	CELF5_ENST00000541430.2_Missense_Mutation_p.S356C|CELF5_ENST00000588101.1_3'UTR	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	381					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						CATCGCGCACAGCGTCCCCCA	0.756																																					p.S381C		.											.	CELF5-92	0			c.A1141T						.						12	12	12					19																	3285978		2081	4145	6226	SO:0001583	missense	60680	exon10			GCGCACAGCGTCC	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"RNA binding motif (RRM) containing"	14058	protein-coding gene	gene with protein product		612680	"Bruno (Drosophila) -like 5, RNA binding protein", "bruno-like 5, RNA binding protein (Drosophila)"	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.1141A>T	19.37:g.3285978A>T	ENSP00000292672:p.Ser381Cys	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	67	37	NM_021938	0	0	0	0	0	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Missense_Mutation	SNP	ENST00000292672.2	37	CCDS12106.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.488587	0.84854	.	.	ENSG00000161082	ENST00000292672;ENST00000541430;ENST00000334293	T;T;T	0.51071	0.72;1.66;1.56	4.15	4.15	0.48705	.	0.325407	0.28841	N	0.013971	T	0.53867	0.1823	L	0.36672	1.1	0.37559	D	0.919007	D;D;P	0.76494	0.985;0.999;0.944	P;D;P	0.63192	0.731;0.912;0.662	T	0.61451	-0.7060	10	0.62326	D	0.03	-4.5717	11.4083	0.49911	1.0:0.0:0.0:0.0	.	267;356;381	B4DFI3;Q8N6W0-2;Q8N6W0	.;.;CELF5_HUMAN	C	381;356;267	ENSP00000292672:S381C;ENSP00000443498:S356C;ENSP00000335182:S267C	ENSP00000292672:S381C	S	+	1	0	CELF5	3236978	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.948000	0.49066	1.666000	0.50821	0.402000	0.26972	AGC	.		0.756	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938		T	3285978	A	T	3285978	3	4	153	1	0	0	0	0	1	0	0	0	3225	188	7	5	1179	5	CELF5	19	3285978	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		3285978	55843005	117	13832											
ATP13A1	57130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19758062	19758062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtaggccaggatgagggcaTtgagcgccaggatcttgaac	10	8	15	8	1	1	3	0	3	1	0	1	5	1	5	2	4	2	2	2	4	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:19758062T>C	ENST00000357324.6	-	22	3007	c.2981A>G	c.(2980-2982)aAt>aGt	p.N994S	ATP13A1_ENST00000291503.5_Missense_Mutation_p.N876S	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	994						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GATGAGGGCATTGAGCGCCAG	0.632																																					p.N994S	Esophageal Squamous(142;920 1789 9047 14684 24777)	.											.	ATP13A1-138	0			c.A2981G						.						108	109	109					19																	19758062		2203	4300	6503	SO:0001583	missense	57130	exon22			AGGGCATTGAGCG	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"ATPases / P-type"	24215	protein-coding gene	gene with protein product	"cation transporting ATPase"		"ATPase type 13A"	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.2981A>G	19.37:g.19758062T>C	ENSP00000349877:p.Asn994Ser	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	99	19	NM_020410	0	0	67	87	20	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	37	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.274546	0.80580	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	D;D	0.88354	-2.37;-2.37	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	D	0.91784	0.7401	M	0.75264	2.295	0.80722	D	1	D;D	0.59357	0.974;0.985	P;P	0.61592	0.78;0.891	D	0.89608	0.3839	10	0.11794	T	0.64	-19.537	12.2865	0.54795	0.0:0.0:0.0:1.0	.	994;876	Q9HD20;Q9HD20-2	AT131_HUMAN;.	S	876;994	ENSP00000291503:N876S;ENSP00000349877:N994S	ENSP00000291503:N876S	N	-	2	0	ATP13A1	19619062	1.000000	0.71417	0.855000	0.33649	0.995000	0.86356	7.576000	0.82467	1.789000	0.52484	0.529000	0.55759	AAT	.		0.632	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		C	19758062	T	C	19758062	3	2	153	1	0	0	0	0	1	0	0	0	1124	1493	52	3	653	3	ATP13A1	19	19758062	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	16472084	19758062	39370921	118	13833											
GRAMD1A	57655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35506763	35506763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcccgacctctccggcCgcctcctcatcaactctgtc	4	11	6	20	3	4	0	2	0	2	0	8	1	6	0	6	1	2	1	6	1	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:35506763C>T	ENST00000317991.5	+	11	1297	c.1105C>T	c.(1105-1107)Cgc>Tgc	p.R369C	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.R456C|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.R362C|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.R135C	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	369						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CCTCTCCGGCCGCCTCCTCAT	0.642																																					p.R369C		.											.	GRAMD1A-90	0			c.C1105T						.						39	44	42					19																	35506763		2115	4223	6338	SO:0001583	missense	57655	exon11			TCCGGCCGCCTCC	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"KIAA1533"	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.1105C>T	19.37:g.35506763C>T	ENSP00000441032:p.Arg369Cys	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	106	43	NM_020895	0	0	9	22	13	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.127959	0.77549	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.60548	0.18;1.34;1.3	5.01	5.01	0.66863	.	0.067735	0.64402	D	0.000013	T	0.75398	0.3844	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.96;0.994;0.917;0.975	T	0.78443	-0.2202	10	0.87932	D	0	.	10.8825	0.46946	0.1875:0.8125:0.0:0.0	.	369;369;135;362	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2	.;GRM1A_HUMAN;.;.	C	455;135;369;362	ENSP00000423728:R135C;ENSP00000441032:R369C;ENSP00000439267:R362C	ENSP00000441032:R369C	R	+	1	0	GRAMD1A	40198603	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	3.193000	0.50997	2.615000	0.88500	0.555000	0.69702	CGC	.		0.642	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		T	35506763	C	T	35506763	3	4	153	1	0	0	0	0	1	0	0	0	6768	652	23	1	1147	1	GRAMD1A	19	35506763	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	15748701	35506763	23622220	119	13834											
RSPH6A	81492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	46305454	46305454	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctggcccctcatctgccttCtcttcctcctcccccaggtc	2	13	5	21	0	4	0	1	0	3	0	9	0	7	0	7	2	1	0	7	2	0	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:46305454C>G	ENST00000221538.3	-	4	1864	c.1722G>C	c.(1720-1722)gaG>gaC	p.E574D	RSPH6A_ENST00000597055.1_Missense_Mutation_p.E574D|RSPH6A_ENST00000600188.1_Missense_Mutation_p.E310D	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	574	Glu-rich.					intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						catctgccttctcttcctcct	0.622																																					p.E574D		.											.	RSPH6A-91	0			c.G1722C						.						111	73	86					19																	46305454		2203	4300	6503	SO:0001583	missense	81492	exon4			TGCCTTCTCTTCC	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"radial spokehead-like 1"	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1722G>C	19.37:g.46305454C>G	ENSP00000221538:p.Glu574Asp	Somatic	107	0		WXS	Illumina HiSeq	Phase_I	139	50	NM_030785	0	0	0	0	0	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	11.81	1.748680	0.30955	.	.	ENSG00000104941	ENST00000221538	T	0.19806	2.12	4.27	2.08	0.27032	.	0.108659	0.64402	D	0.000011	T	0.15912	0.0383	L	0.48986	1.54	0.27895	N	0.939171	P	0.41978	0.767	B	0.38985	0.287	T	0.08827	-1.0703	10	0.26408	T	0.33	-9.2878	6.3085	0.21151	0.0:0.764:0.0:0.236	.	574	Q9H0K4	RSH6A_HUMAN	D	574	ENSP00000221538:E574D	ENSP00000221538:E574D	E	-	3	2	RSPH6A	50997294	0.980000	0.34600	1.000000	0.80357	0.407000	0.30961	0.054000	0.14205	0.710000	0.31997	-0.390000	0.06520	GAG	.		0.622	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			G	46305454	C	G	46305454	3	3	153	1	0	0	0	0	1	0	0	0	13739	912	32	4	443	4	RSPH6A	19	46305454	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	10798691	46305454	12823529	120	13835											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48183660	48183660	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggccagaacgtggtgctGtcgggcttccccgcgcctgc	3	7	16	15	5	0	1	0	0	0	1	2	1	1	1	4	3	3	2	4	3	1	1	rs145963832	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:48183660G>A	ENST00000396720.3	+	6	1427	c.1233G>A	c.(1231-1233)ctG>ctA	p.L411L	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	411										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		ACGTGGTGCTGTCGGGCTTCC	0.741													G|||	75	0.014976	0.0469	0.0058	5008	,	,		9935	0		0.007	False		,,,				2504	0.002				p.L411L		.											.	GLTSCR1-48	0			c.G1233A						.	G		101,3065		2,97,1484	5	8	7		1233	-4.3	0.6	19	dbSNP_134	7	28,6636		0,28,3304	no	coding-synonymous	GLTSCR1	NM_015711.3		2,125,4788	AA,AG,GG		0.4202,3.1901,1.3123		411/1561	48183660	129,9701	1583	3332	4915	SO:0001819	synonymous_variant	29998	exon6			GGTGCTGTCGGGC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.1233G>A	19.37:g.48183660G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	9	7	NM_015711	0	0	1	1	0	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			G|0.985;A|0.015		0.741	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		A	48183660	G	A	48183660	2	1	153	1	0	0	0	0	0	0	0	1	6494	1364	48	2		2	GLTSCR1	19	48183660	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	1878206	48183660	10945323	121	13836											
GLTSCR1	29998	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	48183987	48183987	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcctcacaaaccagaacctGgcgggcccactgagcctggg	10	5	11	15	1	1	2	1	1	0	1	2	2	2	2	5	3	3	0	5	3	2	0	rs377326337		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:48183987G>T	ENST00000396720.3	+	6	1754	c.1560G>T	c.(1558-1560)ctG>ctT	p.L520L	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	520										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		ACCAGAACCTGGCGGGCCCAC	0.726																																					p.L520L		.											.	GLTSCR1-48	0			c.G1560T						.						26	32	30					19																	48183987		1884	4062	5946	SO:0001819	synonymous_variant	29998	exon6			GAACCTGGCGGGC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.1560G>T	19.37:g.48183987G>T		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	108	42	NM_015711	0	0	0	0	0	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			.		0.726	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48183987	G	T	48183987	2	4	153	1	0	0	0	0	0	0	0	1	6494	1335	47	4		4	GLTSCR1	19	48183987	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	327	48183987	10944996	122	13837											
SBK2	646643	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	56047489	56047489	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctcgtagagctcgtccAcctcggctcggaccagggtc	5	9	11	16	4	0	1	0	0	0	1	7	2	2	2	4	3	1	3	4	3	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:56047489A>C	ENST00000413299.1	-	2	210	c.173T>G	c.(172-174)gTg>gGg	p.V58G	SBK2_ENST00000344158.3_Missense_Mutation_p.V58G	NM_001101401.2	NP_001094871.2	P0C263	SBK2_HUMAN	SH3 domain binding kinase family, member 2	58							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9						GAGCTCGTCCACCTCGGCTCG	0.657																																					p.V58G													.	SBK2-68	0			c.T173G						.						33	37	36					19																	56047489		2120	4212	6332	SO:0001583	missense	646643	exon2			TCGTCCACCTCGG		CCDS42631.1	19q13.42	2013-09-27	2013-09-27		ENSG00000187550	ENSG00000187550			34416	protein-coding gene	gene with protein product			"SH3-binding domain kinase family, member 2"				Standard	NM_001101401		Approved	SGK069	uc010ygc.2	P0C263	OTTHUMG00000155830	ENST00000413299.1:c.173T>G	19.37:g.56047489A>C	ENSP00000389015:p.Val58Gly	Somatic	97	1		WXS	Illumina HiSeq	Phase_I	124	40	NM_001101401	0	0	0	0	0		Missense_Mutation	SNP	ENST00000413299.1	37	CCDS42631.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.714242	0.68730	.	.	ENSG00000187550	ENST00000413299;ENST00000344158	T;T	0.72615	-0.67;-0.67	4.44	3.42	0.39159	Protein kinase-like domain (1);	0.145674	0.45361	D	0.000372	T	0.55673	0.1935	N	0.24115	0.695	0.58432	D	0.999995	P	0.44659	0.84	B	0.42062	0.374	T	0.56649	-0.7944	10	0.72032	D	0.01	-26.5917	8.3241	0.32147	0.9021:0.0:0.0979:0.0	.	58	P0C263	SBK2_HUMAN	G	58	ENSP00000389015:V58G;ENSP00000345044:V58G	ENSP00000345044:V58G	V	-	2	0	SBK2	60739301	0.757000	0.28394	0.995000	0.50966	0.864000	0.49448	6.326000	0.72905	0.673000	0.31224	0.379000	0.24179	GTG	.		0.657	SBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341919.1	NM_001101401		C	56047489	A	C	56047489	3	2	153	1	0	0	0	0	1	0	0	0	13893	159	6	5	884	5	SBK2	19	56047489	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	7863502	56047489	3081494	123	13838											
VSX1	30813	hgsc.bcm.edu	37	chr20	25062342	25062342	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcgctgcgcttctggcGgccgagcgcaggcggcggac	3	6	18	14	7	1	0	0	0	1	0	2	2	1	1	1	5	2	4	1	5	0	1	rs6050307	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr20:25062342G>T	ENST00000376709.4	-	1	654	c.391C>A	c.(391-393)Cgc>Agc	p.R131S	VSX1_ENST00000398332.1_Missense_Mutation_p.R131S|VSX1_ENST00000444511.2_Missense_Mutation_p.R131S|VSX1_ENST00000429762.3_Missense_Mutation_p.R131S|VSX1_ENST00000376707.3_Missense_Mutation_p.R131S|VSX1_ENST00000424574.1_Missense_Mutation_p.R131S|VSX1_ENST00000451258.1_Missense_Mutation_p.R131S	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	131			R -> S (in dbSNP:rs6050307). {ECO:0000269|PubMed:15051220}.		neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						CGCTTCTGGCGGCCGAGCGCA	0.741													G|||	206	0.0411342	0.1483	0.0144	5008	,	,		11176	0		0	False		,,,				2504	0				p.R131S		.											.	VSX1-90	0			c.C391A						.	G	SER/ARG,SER/ARG	328,3228		8,312,1458	4	4	4		391,391	-3.9	0	20	dbSNP_114	4	13,6761		0,13,3374	yes	missense,missense	VSX1	NM_014588.4,NM_199425.1	110,110	8,325,4832	TT,TG,GG		0.1919,9.2238,3.3011	benign,benign	131/366,131/240	25062342	341,9989	1778	3387	5165	SO:0001583	missense	30813	exon1			TCTGGCGGCCGAG	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"Homeoboxes / PRD class"	12723	protein-coding gene	gene with protein product		605020	"posterior polymorphous corneal dystrophy", "visual system homeobox 1 homolog, CHX10-like (zebrafish)"	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.391C>A	20.37:g.25062342G>T	ENSP00000365899:p.Arg131Ser	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	19	10	NM_014588	0	0	0	0	0	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	90	0.04120879120879121	82	0.16666666666666666	8	0.022099447513812154	0	0.0	0	0.0	G	3.761	-0.049660	0.07407	0.092238	0.001919	ENSG00000100987	ENST00000429762;ENST00000444511;ENST00000424574;ENST00000451258;ENST00000376709;ENST00000376707;ENST00000398332	D;D;D;D;D;D;T	0.91792	-2.73;-2.91;-2.72;-2.77;-2.82;-2.83;-0.0	4.14	-3.91	0.04168	.	1.617690	0.02904	N	0.135773	T	0.00412	0.0013	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B	0.09022	0.001;0.0;0.002;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.56992	-0.7887	9	0.06625	T	0.88	.	0.1523	0.00094	0.3252:0.149:0.2095:0.3163	rs6050307;rs61429181	131;131;131;131	Q9NZR4-7;Q9NZR4-8;Q9NZR4-2;Q9NZR4	.;.;.;VSX1_HUMAN	S	131	ENSP00000401690:R131S;ENSP00000387720:R131S;ENSP00000399496:R131S;ENSP00000389654:R131S;ENSP00000365899:R131S;ENSP00000365897:R131S;ENSP00000381376:R131S	ENSP00000365897:R131S	R	-	1	0	VSX1	25010342	0.000000	0.05858	0.000000	0.03702	0.543000	0.35085	-0.882000	0.04174	-0.591000	0.05859	0.563000	0.77884	CGC	G|0.959;T|0.041		0.741	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3			T	25062342	G	T	25062342	3	4	153	1	0	0	0	0	1	0	0	0	17264	1116	39	4	819	4	VSX1	20	25062342	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10		25062342	37963178	124	13839											
ZBTB46	140685	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	62378613	62378613	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcggcggacatgaagacgcgGctgcacaccttgcacacata	11	5	12	13	4	0	2	0	1	0	1	0	3	0	3	1	3	2	3	1	3	2	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr20:62378613G>T	ENST00000245663.4	-	5	1590	c.1440C>A	c.(1438-1440)agC>agA	p.S480R	ZBTB46_ENST00000302995.2_Missense_Mutation_p.S480R|RP4-583P15.10_ENST00000447343.2_RNA|RP4-583P15.10_ENST00000433905.2_RNA|ZBTB46_ENST00000395104.1_Missense_Mutation_p.S480R	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	480					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					TGAAGACGCGGCTGCACACCT	0.701																																					p.S480R		.											.	ZBTB46-154	0			c.C1440A						.						9	7	8					20																	62378613		2124	4163	6287	SO:0001583	missense	140685	exon5			GACGCGGCTGCAC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1440C>A	20.37:g.62378613G>T	ENSP00000245663:p.Ser480Arg	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	138	52	NM_025224	0	0	0	0	0	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	37	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.585999	0.46110	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.15487	2.42;2.42;2.42	4.29	3.16	0.36331	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.174840	0.48767	D	0.000179	T	0.11793	0.0287	L	0.28504	0.86	0.46336	D	0.998998	P	0.38048	0.616	B	0.35278	0.199	T	0.09509	-1.0671	10	0.39692	T	0.17	.	10.1961	0.43056	0.1118:0.0:0.8882:0.0	.	480	Q86UZ6	ZBT46_HUMAN	R	480	ENSP00000245663:S480R;ENSP00000303102:S480R;ENSP00000378536:S480R	ENSP00000245663:S480R	S	-	3	2	ZBTB46	61849057	1.000000	0.71417	0.991000	0.47740	0.822000	0.46500	2.148000	0.42235	0.504000	0.28082	0.462000	0.41574	AGC	.		0.701	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62378613	G	T	62378613	3	4	153	1	0	0	0	0	1	0	0	0	17579	1194	42	4	333	4	ZBTB46	20	62378613	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	37316271	62378613	646907	125	13840											
MICAL3	57553	hgsc.bcm.edu;broad.mit.edu	37	chr22	18300505	18300505	+	Frame_Shift_Del	DEL	T	T	-																															caggccggcgctccttgcccTgggagggtgctgaggacgcc																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr22:18300505delT	ENST00000441493.2	-	26	5274	c.4922delA	c.(4921-4923)cagfs	p.Q1641fs	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1641					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CTCCTTGCCCTGGGAGGGTGC	0.711																																					p.Q1641fs		.											.	MICAL3-68	0			c.4922delA						.						13	18	16					22																	18300505		1932	4104	6036	SO:0001589	frameshift_variant	57553	exon26			.	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.4922delA	22.37:g.18300505delT	ENSP00000416015:p.Gln1641fs	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	29	12	NM_015241	0	0	0	0	0	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	37	CCDS46659.1																																																																																			.		0.711	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			-	18300505	T	-	18300505	7	5	153	1	0	1	0	1	0	0	0	0	9596	1580	55	0	1114	0	MICAL3	22	18300505	Frame_Shift_Del	DEL	T	TCGA-P4-A5E6-01A-11D-A28G-10		18300505	33004061	126	13841											
RRP7A	27341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	42912080	42912080	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctctcagccaggtccggCttctcctgcaactctacaga	7	9	10	15	1	3	1	1	0	3	1	6	1	4	1	3	3	4	3	3	3	2	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr22:42912080C>A	ENST00000323013.6	-	3	294	c.279G>T	c.(277-279)aaG>aaT	p.K93N		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	93							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						CCAGGTCCGGCTTCTCCTGCA	0.617																																					p.K93N		.											.	RRP7A-91	0			c.G279T						.						57	51	53					22																	42912080		2203	4300	6503	SO:0001583	missense	27341	exon3			GTCCGGCTTCTCC	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.279G>T	22.37:g.42912080C>A	ENSP00000321449:p.Lys93Asn	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	121	50	NM_015703	0	0	26	37	11	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.907011	0.33628	.	.	ENSG00000189306	ENST00000323013	T	0.15952	2.38	3.93	2.9	0.33743	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.106611	0.64402	D	0.000007	T	0.30103	0.0754	M	0.72576	2.205	0.51012	D	0.999906	D	0.56035	0.974	P	0.55577	0.779	T	0.03818	-1.1001	10	0.72032	D	0.01	-34.7209	8.4778	0.33023	0.0:0.7373:0.0:0.2627	.	93	Q9Y3A4	RRP7A_HUMAN	N	93	ENSP00000321449:K93N	ENSP00000321449:K93N	K	-	3	2	RRP7A	41242024	1.000000	0.71417	0.993000	0.49108	0.007000	0.05969	0.731000	0.26058	0.946000	0.37632	-0.346000	0.07831	AAG	.		0.617	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703		A	42912080	C	A	42912080	3	1	153	1	0	0	0	0	1	0	0	0	13721	796	28	4	583	4	RRP7A	22	42912080	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	24611575	42912080	8392486	127	13842											
KIF1B	23095	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10328310	10328310	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgataatgagaccaaccttTccactgagaaggtaggagag	15	7	11	8	1	0	3	0	2	0	3	1	7	1	3	3	2	1	1	3	2	4	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:10328310T>C	ENST00000377086.1	+	7	911	c.709T>C	c.(709-711)Tcc>Ccc	p.S237P	KIF1B_ENST00000263934.6_Missense_Mutation_p.S237P|KIF1B_ENST00000377093.4_Missense_Mutation_p.S237P|KIF1B_ENST00000377083.1_Missense_Mutation_p.S237P|KIF1B_ENST00000377081.1_Missense_Mutation_p.S237P			O60333	KIF1B_HUMAN	kinesin family member 1B	237	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.			NLSTE -> ILATV (in Ref. 3; AAK49332, 4; AAK85155 and 5; AAN17742). {ECO:0000305}.	anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GACCAACCTTTCCACTGAGAA	0.448																																					p.S237P													.	KIF1B-93	0			c.T709C						.						81	71	74					1																	10328310		2203	4300	6503	SO:0001583	missense	23095	exon7			AACCTTTCCACTG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"Kinesins", "Pleckstrin homology (PH) domain containing"	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.709T>C	1.37:g.10328310T>C	ENSP00000366290:p.Ser237Pro	Somatic	144	1		WXS	Illumina HiSeq	Phase_I	110	26	NM_183416	0	0	0	0	0	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	T	20.9	4.073545	0.76415	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4	5.94	4.8	0.61643	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	D	0.86944	0.6055	N	0.20610	0.595	0.58432	D	0.999998	P;P;P;P;B;D;B	0.62365	0.62;0.62;0.853;0.736;0.032;0.991;0.142	P;P;P;P;B;P;B	0.56088	0.53;0.53;0.53;0.53;0.05;0.791;0.103	D	0.86389	0.1734	10	0.44086	T	0.13	.	12.4278	0.55557	0.126:0.0:0.0:0.874	.	237;237;237;237;237;237;237	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2;O60333-3	.;.;.;.;KIF1B_HUMAN;.;.	P	237	ENSP00000263934:S237P;ENSP00000366297:S237P;ENSP00000366290:S237P;ENSP00000366287:S237P;ENSP00000366284:S237P	ENSP00000263934:S237P	S	+	1	0	KIF1B	10250897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.719000	0.47244	1.040000	0.40099	0.528000	0.53228	TCC	.		0.448	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			C	10328310	T	C	10328310	3	2	154	1	0	0	0	0	1	0	0	0	8305	1783	62	3	731	3	KIF1B	1	10328310	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		10328310	238922311	1	13843											
VPS13D	55187	bcgsc.ca	37	chr1	12378145	12378145	+	Frame_Shift_Del	DEL	T	T	-																															atagatctaccaaggattccTcctgctttacagtagttctc																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:12378145delT	ENST00000358136.3	+	31	7295	c.7165delT	c.(7165-7167)tccfs	p.S2389fs	VPS13D_ENST00000356315.4_Frame_Shift_Del_p.S2389fs	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CAAGGATTCCTCCTGCTTTAC	0.358																																					p.S2389fs													.	VPS13D-95	0			c.7165delT						.						174	178	177					1																	12378145		2203	4300	6503	SO:0001589	frameshift_variant	55187	exon31			GATTCCTCCTGCT	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"vacuolar protein sorting 13D (yeast)"				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.7165delT	1.37:g.12378145delT	ENSP00000350854:p.Ser2389fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	30	6	NM_015378	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000358136.3	37	CCDS30588.1																																																																																			.		0.358	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		-	12378145	T	-	12378145	7	5	154	1	0	1	0	1	0	0	0	0	17225	1551	54	0	7283	0	VPS13D	1	12378145	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	2049835	12378145	236872476	2	13844											
HMGCL	3155	hgsc.bcm.edu	37	chr1	24151846	24151846	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggctcggggcacttacAgcccggagggacgccaagcc	7	3	16	15	5	0	0	0	0	0	0	1	2	0	2	3	6	3	2	3	6	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:24151846A>G	ENST00000374490.3	-	1	103	c.60T>C	c.(58-60)gcT>gcC	p.A20A	HMGCL_ENST00000509389.1_5'UTR|HMGCL_ENST00000436439.2_Splice_Site_p.A20A|HMGCL_ENST00000374483.4_Intron	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	20					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		GGGCACTTACAGCCCGGAGGG	0.706																																					p.A20A		.											.	HMGCL-90	0			c.T60C						.						10	11	10					1																	24151846		2085	4077	6162	SO:0001630	splice_region_variant	3155	exon1			ACTTACAGCCCGG	BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.60+1T>C	1.37:g.24151846A>G		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	87	27	NM_000191	0	0	1	1	0	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Silent	SNP	ENST00000374490.3	37	CCDS243.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.232145	0.58777	.	.	ENSG00000117305	ENST00000235958	.	.	.	5.66	2.13	0.27403	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45483	-0.9258	4	.	.	.	-1.3076	6.689	0.23161	0.7318:0.0:0.2682:0.0	.	.	.	.	P	16	.	.	L	-	2	0	HMGCL	24024433	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	0.764000	0.26532	0.516000	0.28340	0.533000	0.62120	CTG	.		0.706	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191	Silent	G	24151846	A	G	24151846	5	3	154	1	0	0	0	0	0	0	1	0	7250	202	7	3	953	3	HMGCL	1	24151846	Splice_Site	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	11773701	24151846	225098775	3	13845											
SYNC	81493	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	33161106	33161106	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggagcaatacaagctcaTggatgagctgatccctctcc	10	8	9	14	1	2	2	1	2	1	0	4	4	3	4	3	2	4	3	3	2	3	1	rs554437078		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:33161106T>G	ENST00000409190.3	-	2	1051	c.593A>C	c.(592-594)cAt>cCt	p.H198P	SYNC_ENST00000373484.3_Missense_Mutation_p.H198P	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	198	Coil 1A.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TACAAGCTCATGGATGAGCTG	0.567																																					p.H198P		.											.	SYNC-91	0			c.A593C						.						89	78	82					1																	33161106		692	1591	2283	SO:0001583	missense	81493	exon2			AGCTCATGGATGA	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"Intermediate filaments type III"	28897	protein-coding gene	gene with protein product		611750	"syncoilin, intermediate filament 1"	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.593A>C	1.37:g.33161106T>G	ENSP00000386439:p.His198Pro	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	88	24	NM_001161708	0	0	5	6	1	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	37	CCDS367.2	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123508	0.56613	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	T;T	0.24350	1.86;1.86	4.57	4.57	0.56435	Filament (1);	.	.	.	.	T	0.27559	0.0677	N	0.14661	0.345	0.31839	N	0.623691	D;D	0.76494	0.998;0.999	P;D	0.75020	0.905;0.985	T	0.17471	-1.0368	9	0.31617	T	0.26	-9.3582	5.8491	0.18683	0.0:0.0877:0.1689:0.7435	.	198;198	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	P	198	ENSP00000362583:H198P;ENSP00000386439:H198P	ENSP00000362583:H198P	H	-	2	0	SYNC	32933693	0.988000	0.35896	0.997000	0.53966	0.958000	0.62258	1.916000	0.39986	1.853000	0.53794	0.459000	0.35465	CAT	.		0.567	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786		G	33161106	T	G	33161106	3	3	154	1	0	0	0	0	1	0	0	0	15475	1464	51	5	933	5	SYNC	1	33161106	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	9009260	33161106	216089515	4	13846											
ZC3H12A	80149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	37949045	37949045	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcaggagcccgtggggcAgggcaggcagcctggccaag	7	3	19	12	1	0	0	0	0	0	0	0	1	0	1	3	7	2	4	3	7	1	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:37949045A>T	ENST00000373087.6	+	6	1749	c.1633A>T	c.(1633-1635)Agg>Tgg	p.R545W		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCCGTGGGGCAGGGCAGGCAG	0.647																																					p.R545W		.											.	ZC3H12A-92	0			c.A1633T						.						48	58	55					1																	37949045		2203	4300	6503	SO:0001583	missense	80149	exon6			TGGGGCAGGGCAG		CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"Zinc fingers, CCCH-type domain containing"	26259	protein-coding gene	gene with protein product	"MCP induced protein 1"	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.1633A>T	1.37:g.37949045A>T	ENSP00000362179:p.Arg545Trp	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	196	53	NM_025079	0	0	11	19	8		Missense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.033050	0.35893	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.45668	0.89	5.15	2.9	0.33743	.	0.653715	0.14763	N	0.299862	T	0.37544	0.1007	N	0.22421	0.69	0.09310	N	0.999998	D;P	0.59767	0.986;0.923	P;B	0.52554	0.702;0.221	T	0.14868	-1.0457	10	0.66056	D	0.02	-9.4135	7.823	0.29298	0.2651:0.0:0.7349:0.0	.	340;545	B3KSD3;Q5D1E8	.;ZC12A_HUMAN	W	545	ENSP00000362179:R545W	ENSP00000362174:R545W	R	+	1	2	ZC3H12A	37721632	0.000000	0.05858	0.097000	0.21041	0.675000	0.39556	0.003000	0.13083	0.284000	0.22305	0.459000	0.35465	AGG	.		0.647	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		T	37949045	A	T	37949045	3	4	154	1	0	0	0	0	1	0	0	0	17593	179	7	5	1651	5	ZC3H12A	1	37949045	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	4787939	37949045	211301576	5	13847											
KTI12	112970	hgsc.bcm.edu	37	chr1	52499078	52499078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttctcgttcgcgcccgccAcctgaggtcccgcgatcggg	3	8	14	16	7	1	1	0	1	1	0	5	2	2	1	4	3	0	2	4	3	0	2	rs563103084|rs377187997	byFrequency	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:52499078A>G	ENST00000371614.1	-	1	410	c.356T>C	c.(355-357)gTg>gCg	p.V119A	RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000371626.4_Intron	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	119							ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CGCGCCCGCCACCTGAGGTCC	0.721																																					p.V119A		.											.	KTI12-91	0			c.T356C						.						28	34	32					1																	52499078		2194	4277	6471	SO:0001583	missense	112970	exon1			CCCGCCACCTGAG		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.356T>C	1.37:g.52499078A>G	ENSP00000360676:p.Val119Ala	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	43	13	NM_138417	0	0	2	8	6		Missense_Mutation	SNP	ENST00000371614.1	37	CCDS562.1	.	.	.	.	.	.	.	.	.	.	A	9.740	1.164503	0.21538	.	.	ENSG00000198841	ENST00000371614	T	0.39997	1.05	4.93	-9.87	0.00470	.	.	.	.	.	T	0.11750	0.0286	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15150	-1.0447	9	0.05959	T	0.93	.	2.3401	0.04257	0.1327:0.1704:0.3566:0.3403	.	119	Q96EK9	KTI12_HUMAN	A	119	ENSP00000360676:V119A	ENSP00000360676:V119A	V	-	2	0	KTI12	52271666	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-2.926000	0.00691	-2.213000	0.00735	-0.256000	0.11100	GTG	.		0.721	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417		G	52499078	A	G	52499078	3	3	154	1	0	0	0	0	1	0	0	0	8605	159	6	3	712	3	KTI12	1	52499078	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	14550033	52499078	196751543	6	13848											
DHCR24	1718	broad.mit.edu	37	chr1	55317995	55317995	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcagcttgtggtacaaggAgccatcaaacatctcccaga	12	8	9	12	1	2	1	1	0	1	1	4	2	2	2	2	2	4	3	2	2	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:55317995A>C	ENST00000371269.3	-	9	1560	c.1462T>G	c.(1462-1464)Tcc>Gcc	p.S488A	DHCR24_ENST00000535035.1_Missense_Mutation_p.S447A|DHCR24_ENST00000537443.1_Missense_Mutation_p.S272A	NM_014762.3	NP_055577.1	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase	488					amyloid precursor protein catabolic process (GO:0042987)|apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cholesterol biosynthetic process (GO:0006695)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|oxidation-reduction process (GO:0055114)|plasminogen activation (GO:0031639)|protein localization (GO:0008104)|Ras protein signal transduction (GO:0007265)|regulation of neuron death (GO:1901214)|response to hormone (GO:0009725)|response to oxidative stress (GO:0006979)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|tissue development (GO:0009888)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	delta24(24-1) sterol reductase activity (GO:0000246)|delta24-sterol reductase activity (GO:0050614)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|peptide antigen binding (GO:0042605)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			large_intestine(2)|liver(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						TGGTACAAGGAGCCATCAAAC	0.597																																					p.S488A	Pancreas(39;516 1021 24601 30715 32780)												.	DHCR24-91	0			c.T1462G						.						141	123	130					1																	55317995		2203	4300	6503	SO:0001583	missense	1718	exon9			ACAAGGAGCCATC	AF261758	CCDS600.1	1p32.3	2008-02-05			ENSG00000116133	ENSG00000116133			2859	protein-coding gene	gene with protein product		606418				11519011	Standard	NM_014762		Approved	KIAA0018, seladin-1	uc001cyc.1	Q15392	OTTHUMG00000009989	ENST00000371269.3:c.1462T>G	1.37:g.55317995A>C	ENSP00000360316:p.Ser488Ala	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_014762	0	0	176	178	2	B7Z817|D3DQ51|Q9HBA8	Missense_Mutation	SNP	ENST00000371269.3	37	CCDS600.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.52|13.52	2.262766|2.262766	0.39995|0.39995	.|.	.|.	ENSG00000116133|ENSG00000116133	ENST00000436604|ENST00000539536;ENST00000371269;ENST00000537443;ENST00000535035	.|T;T;T	.|0.69306	.|-0.39;-0.39;-0.39	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	.|0.277164	.|0.40064	.|N	.|0.001199	T|T	0.47451|0.47451	0.1446|0.1446	N|N	0.16478|0.16478	0.41|0.41	0.36209|0.36209	D|D	0.851231|0.851231	.|B;B;B	.|0.16166	.|0.016;0.007;0.016	.|B;B;B	.|0.14023	.|0.01;0.004;0.007	T|T	0.51236|0.51236	-0.8731|-0.8731	5|10	.|0.14252	.|T	.|0.57	-42.9406|-42.9406	11.5029|11.5029	0.50448|0.50448	0.8501:0.1499:0.0:0.0|0.8501:0.1499:0.0:0.0	.|.	.|447;447;488	.|B7Z817;B7ZAV4;Q15392	.|.;.;DHC24_HUMAN	R|A	125|214;488;272;447	.|ENSP00000360316:S488A;ENSP00000439852:S272A;ENSP00000440191:S447A	.|ENSP00000360316:S488A	L|S	-|-	2|1	0|0	DHCR24|DHCR24	55090583|55090583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.827000|0.827000	0.46813|0.46813	3.617000|3.617000	0.54181|0.54181	2.079000|2.079000	0.62486|0.62486	0.379000|0.379000	0.24179|0.24179	CTC|TCC	.		0.597	DHCR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027680.1	NM_014762		C	55317995	A	C	55317995	3	2	154	1	0	0	0	0	1	0	0	0	4487	304	11	5	92	5	DHCR24	1	55317995	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	2818917	55317995	193932626	7	13849											
NRAS	4893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	115256491	115256491	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaggaagccttcgcctgTcctcatgtattggtctctca	8	12	9	12	1	3	1	2	0	1	1	6	2	4	2	3	2	1	1	3	2	2	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:115256491T>A	ENST00000369535.4	-	3	473	c.220A>T	c.(220-222)Aca>Tca	p.T74S		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	74					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTTCGCCTGTCCTCATGTAT	0.418		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.T74S		.		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	.	NRAS-32773	0			c.A220T						.						186	159	168					1																	115256491		2203	4300	6503	SO:0001583	missense	4893	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CGCCTGTCCTCAT	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.220A>T	1.37:g.115256491T>A	ENSP00000358548:p.Thr74Ser	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	74	28	NM_002524	0	0	7	13	6	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.602254	0.87055	.	.	ENSG00000213281	ENST00000369535	T	0.76186	-1.0	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000022	T	0.46054	0.1373	N	0.04373	-0.215	0.80722	D	1	B	0.31640	0.333	B	0.37833	0.259	T	0.59209	-0.7497	10	0.51188	T	0.08	.	15.0132	0.71565	0.0:0.0:0.0:1.0	.	74	P01111	RASN_HUMAN	S	74	ENSP00000358548:T74S	ENSP00000358548:T74S	T	-	1	0	NRAS	115058014	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.787000	0.85759	2.120000	0.65058	0.533000	0.62120	ACA	.		0.418	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		A	115256491	T	A	115256491	3	1	154	1	0	0	0	0	1	0	0	0	10666	1667	58	5	361	5	NRAS	1	115256491	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	59938496	115256491	133994130	8	13850											
GON4L	54856	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	155723012	155723012	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cacctgaaacaggcatctctCcctttctggtggtcctgaca	8	11	8	14	0	2	2	0	2	2	0	5	2	4	2	3	3	1	1	3	3	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:155723012C>G	ENST00000368331.1	-	29	5873	c.5825G>C	c.(5824-5826)gGa>gCa	p.G1942A	GON4L_ENST00000271883.5_Missense_Mutation_p.G1942A|GON4L_ENST00000437809.1_Missense_Mutation_p.G1942A	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1942					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					AGGCATCTCTCCCTTTCTGGT	0.562																																					p.G1942A													.	GON4L-93	0			c.G5825C						.						87	97	94					1																	155723012		2081	4197	6278	SO:0001583	missense	54856	exon29			ATCTCTCCCTTTC	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5825G>C	1.37:g.155723012C>G	ENSP00000357315:p.Gly1942Ala	Somatic	182	1		WXS	Illumina HiSeq	Phase_I	176	51	NM_001037533	0	0	10	14	4	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	C	16.55	3.155475	0.57259	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.11385	2.78;2.78;2.78	5.19	3.29	0.37713	.	0.446861	0.22376	N	0.060873	T	0.05731	0.0150	L	0.34521	1.04	0.31285	N	0.690131	P;D	0.55385	0.952;0.971	B;P	0.50617	0.444;0.646	T	0.14337	-1.0476	10	0.62326	D	0.03	.	8.7526	0.34626	0.0:0.7683:0.1511:0.0806	.	1942;1942	Q3T8J9;Q3T8J9-3	GON4L_HUMAN;.	A	1942	ENSP00000396117:G1942A;ENSP00000357315:G1942A;ENSP00000271883:G1942A	ENSP00000271883:G1942A	G	-	2	0	GON4L	153989636	0.112000	0.22096	0.988000	0.46212	0.791000	0.44710	0.586000	0.23894	0.739000	0.32628	0.557000	0.71058	GGA	.		0.562	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		G	155723012	C	G	155723012	3	3	154	1	0	0	0	0	1	0	0	0	6592	855	30	4	913	4	GON4L	1	155723012	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	40466521	155723012	93527609	9	13851											
C1orf61	10485	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	156386616	156386616	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caagttaaatgttatgagatCctcagtcaggaacatgccag	14	10	9	8	0	2	1	2	1	0	1	3	3	3	2	2	1	2	2	2	1	5	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:156386616C>A	ENST00000368243.1	-	3	132	c.16G>T	c.(16-18)Gat>Tat	p.D6Y		NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	6						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					GTTATGAGATCCTCAGTCAGG	0.438																																					p.D6Y													.	C1orf61-91	0			c.G16T						.						117	117	117					1																	156386616		2203	4300	6503	SO:0001583	missense	10485	exon3			TGAGATCCTCAGT		CCDS1142.1	1q22	2014-03-17			ENSG00000125462	ENSG00000125462			30780	protein-coding gene	gene with protein product	"contingent replication of cDNA-4", "transcriptional activator of the c fos promoter"					10995546, 23012322	Standard	XM_005244832		Approved	CROC4	uc001fou.1	Q13536	OTTHUMG00000031022	ENST00000368243.1:c.16G>T	1.37:g.156386616C>A	ENSP00000357226:p.Asp6Tyr	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	153	42	NM_006365	0	0	0	0	0	B1ALL5|B1ALL8	Missense_Mutation	SNP	ENST00000368243.1	37	CCDS1142.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.690548	0.29962	.	.	ENSG00000125462	ENST00000368243	.	.	.	2.88	-0.293	0.12835	.	.	.	.	.	T	0.15435	0.0372	N	0.14661	0.345	0.09310	N	1	D	0.58268	0.982	P	0.58780	0.845	T	0.04678	-1.0934	8	0.87932	D	0	.	3.3	0.06979	0.0:0.5063:0.2219:0.2718	.	6	Q13536	CROC4_HUMAN	Y	6	.	ENSP00000357226:D6Y	D	-	1	0	C1orf61	154653240	0.000000	0.05858	0.008000	0.14137	0.014000	0.08584	-0.398000	0.07259	-0.056000	0.13221	0.491000	0.48974	GAT	.		0.438	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075988.1	NM_006365		A	156386616	C	A	156386616	3	1	154	1	0	0	0	0	1	0	0	0	2058	855	30	4	474	4	C1orf61	1	156386616	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	663604	156386616	92864005	10	13852											
DDR2	4921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	162729664	162729664	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacccatgaataccacgtGtggcccggctatgactatgt	10	9	10	12	2	0	3	0	2	0	1	0	3	0	3	3	2	1	1	3	2	4	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:162729664G>A	ENST00000367922.3	+	9	1188	c.750G>A	c.(748-750)gtG>gtA	p.V250V	DDR2_ENST00000367921.3_Silent_p.V250V	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	250					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	AATACCACGTGTGGCCCGGCT	0.532																																					p.V250V	NSCLC(161;314 2006 8283 19651 23192)	.											.	DDR2-1464	0			c.G750A						.						119	105	110					1																	162729664		2203	4300	6503	SO:0001819	synonymous_variant	4921	exon9			CCACGTGTGGCCC	AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"discoidin domain receptor family, member 2"	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.750G>A	1.37:g.162729664G>A		Somatic	198	0		WXS	Illumina HiSeq	Phase_I	172	52	NM_001014796	0	0	0	0	0	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1																																																																																			.		0.532	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		A	162729664	G	A	162729664	2	1	154	1	0	0	0	0	0	0	0	1	4343	1364	48	2		2	DDR2	1	162729664	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	6343048	162729664	86520957	11	13853											
C1orf114	57821	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	169390718	169390718	+	Frame_Shift_Del	DEL	A	A	-																															gcagactgtgtcctgtgattAgatttcccattccctttact																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:169390718delA	ENST00000367806.3	-	3	1103	c.951delT	c.(949-951)tctfs	p.S317fs	CCDC181_ENST00000545005.1_Frame_Shift_Del_p.S317fs|CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000367805.3_Frame_Shift_Del_p.S317fs	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	317						nucleus (GO:0005634)											TCCTGTGATTAGATTTCCCAT	0.463																																					p.S317fs		.											.	C1orf114-68	0			c.951delT						.						159	145	150					1																	169390718		2203	4300	6503	SO:0001589	frameshift_variant	57821	exon3			.	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 114"	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.951delT	1.37:g.169390718delA	ENSP00000356780:p.Ser317fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	77	35	NM_021179	0	0	0	0	0	O60780|Q53FD5|Q5TID9|Q8TC48	Frame_Shift_Del	DEL	ENST00000367806.3	37																																																																																				.		0.463	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		-	169390718	A	-	169390718	7	5	154	1	0	1	0	1	0	0	0	0	1993	407	15	0	591	0	C1orf114	1	169390718	Frame_Shift_Del	DEL	A	TCGA-P4-A5E7-01A-31D-A28G-10	6661054	169390718	79859903	12	13854											
TTC27	55622	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	33002960	33002960	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctttgcagctcggggtgtgGttttctctcggttgtgccta	2	17	13	9	2	2	0	0	0	2	0	5	0	2	0	1	4	3	4	1	4	1	5			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:33002960G>A	ENST00000317907.4	+	14	1923	c.1692G>A	c.(1690-1692)tgG>tgA	p.W564*		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	564										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						TCGGGGTGTGGTTTTCTCTCG	0.403																																					p.W564X													.	TTC27-90	0			c.G1692A						.						225	214	218					2																	33002960		2203	4300	6503	SO:0001587	stop_gained	55622	exon14			GGTGTGGTTTTCT	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1692G>A	2.37:g.33002960G>A	ENSP00000313953:p.Trp564*	Somatic	142	1		WXS	Illumina HiSeq	Phase_I	114	40	NM_017735	0	0	8	9	1	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Nonsense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	40	8.398930	0.98794	.	.	ENSG00000018699	ENST00000317907	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.7926	19.3169	0.94218	0.0:0.0:1.0:0.0	.	.	.	.	X	564	.	ENSP00000313953:W564X	W	+	3	0	TTC27	32856464	1.000000	0.71417	1.000000	0.80357	0.256000	0.26092	9.537000	0.98070	2.553000	0.86117	0.557000	0.71058	TGG	.		0.403	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		A	33002960	G	A	33002960	4	1	154	1	0	0	0	0	0	1	0	0	16728	1270	44	2	1746	2	TTC27	2	33002960	Nonsense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		33002960	210196413	13	13855											
FAM98A	25940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	33813426	33813426	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcaatcccgctgaagaaTtggaacatagttatattggc	12	14	8	7	1	1	2	1	1	0	1	2	3	2	3	1	2	1	2	1	2	7	7	rs561820764		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:33813426T>C	ENST00000238823.8	-	4	638	c.498A>G	c.(496-498)caA>caG	p.Q166Q	FAM98A_ENST00000441530.2_Intron|FAM98A_ENST00000403368.1_Silent_p.Q166Q|FAM98A_ENST00000498340.1_Intron			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	166							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					CGCTGAAGAATTGGAACATAG	0.363																																					p.Q166Q		.											.	FAM98A-91	0			c.A498G						.						173	175	174					2																	33813426		2203	4300	6503	SO:0001819	synonymous_variant	25940	exon4			GAAGAATTGGAAC		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.498A>G	2.37:g.33813426T>C		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	75	32	NM_015475	0	0	9	24	15	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																			.		0.363	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		C	33813426	T	C	33813426	2	2	154	1	0	0	0	0	0	0	0	1	5675	1490	52	3		3	FAM98A	2	33813426	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	810466	33813426	209385947	14	13856											
ANTXR1	84168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	69409663	69409663	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggctccacagaagaaggtgcTaagttggaaaaggcaaagaa	17	5	13	6	0	0	3	0	0	0	3	1	4	1	4	1	4	1	4	1	4	7	2	rs138963459	byFrequency	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:69409663T>G	ENST00000303714.4	+	16	1546	c.1224T>G	c.(1222-1224)gcT>gcG	p.A408A	RNA5SP96_ENST00000516041.1_RNA|RNU6-1216P_ENST00000362590.2_RNA	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1	408					actin cytoskeleton reorganization (GO:0031532)|reproductive process (GO:0022414)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|lamellipodium membrane (GO:0031258)	actin filament binding (GO:0051015)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|transmembrane signaling receptor activity (GO:0004888)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						AAGAAGGTGCTAAGTTGGAAA	0.428									Familial Infantile Hemangioma				T|||	2	0.000399361	0	0	5008	,	,		20375	0.002		0	False		,,,				2504	0				p.A408A		.											.	ANTXR1-94	0			c.T1224G						.						119	112	114					2																	69409663		2203	4300	6503	SO:0001819	synonymous_variant	84168	exon16	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	AGGTGCTAAGTTG	AF421380	CCDS1892.1, CCDS46313.1, CCDS46314.1	2p13.1	2006-04-12			ENSG00000169604	ENSG00000169604			21014	protein-coding gene	gene with protein product	"anthrax toxin receptor", "tumor endothelial marker 8 precursor"	606410				10947988, 11559528	Standard	NM_032208		Approved	TEM8, FLJ21776, FLJ10601, ATR	uc002sfg.3	Q9H6X2	OTTHUMG00000129575	ENST00000303714.4:c.1224T>G	2.37:g.69409663T>G		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	85	24	NM_032208	0	0	14	22	8	A8K7U8|J7K7G4|J7KF88|Q4ZFV6|Q53QD8|Q96P02|Q9NVP3	Silent	SNP	ENST00000303714.4	37	CCDS1892.1																																																																																			T|1.000;G|0.000		0.428	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	NM_032208		G	69409663	T	G	69409663	2	3	154	1	0	0	0	0	0	0	0	1	711	1509	53	5		5	ANTXR1	2	69409663	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	35596237	69409663	173789710	15	13857											
TTC31	64427	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	74718487	74718487	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaacccagttcagggacaGtgtggtgaagaagaggtgag	13	6	17	5	0	1	4	1	2	0	2	1	6	1	6	1	4	1	1	1	4	3	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:74718487G>A	ENST00000233623.5	+	7	676	c.669G>A	c.(667-669)caG>caA	p.Q223Q	TTC31_ENST00000410003.1_Silent_p.Q223Q|TTC31_ENST00000442235.2_Silent_p.Q79Q|TTC31_ENST00000463189.1_3'UTR	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	223										breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						TTCAGGGACAGTGTGGTGAAG	0.537																																					p.Q223Q		.											.	TTC31-90	0			c.G669A						.						127	138	134					2																	74718487		1930	4124	6054	SO:0001819	synonymous_variant	64427	exon7			GGGACAGTGTGGT	AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"Tetratricopeptide (TTC) repeat domain containing"	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.669G>A	2.37:g.74718487G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	84	22	NM_022492	0	0	8	14	6	Q4KN40|Q53FD4|Q9H9F7	Silent	SNP	ENST00000233623.5	37	CCDS42701.1																																																																																			.		0.537	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492		A	74718487	G	A	74718487	2	1	154	1	0	0	0	0	0	0	0	1	16733	1020	36	2		2	TTC31	2	74718487	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	5308824	74718487	168480886	16	13858											
SUCLG1	8802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	84652539	84652539	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccactgttggagctcacCttgtagatcgtggttcccag	6	11	13	11	1	1	1	1	0	0	1	3	2	2	2	3	3	1	4	3	3	1	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:84652539C>T	ENST00000393868.2	-	8	1224	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	SUCLG1_ENST00000491123.1_5'UTR	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	338					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	TGGAGCTCACCTTGTAGATCG	0.532																																					p.K338K	Ovarian(48;203 1101 37206 40305 50790)	.											.	SUCLG1-90	0			c.G1014A						.						77	69	71					2																	84652539		2203	4300	6503	SO:0001630	splice_region_variant	8802	exon8			GCTCACCTTGTAG	Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"succinate-CoA ligase, GDP-forming, alpha subunit"			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.1014+1G>A	2.37:g.84652539C>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	119	36	NM_003849	0	0	2	4	2	Q9BWB0|Q9UNP6	Silent	SNP	ENST00000393868.2	37	CCDS1967.2																																																																																			.		0.532	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252298.2	NM_003849	Silent	T	84652539	C	T	84652539	5	4	154	1	0	0	0	0	0	0	1	0	15396	695	24	2	34	2	SUCLG1	2	84652539	Splice_Site	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	9934052	84652539	158546834	17	13859											
KCNIP3	30818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95976175	95976175	+	Missense_Mutation	SNP	A	A	G																															cacttagcaagaaggagggtAtcaagtggcagaggccgagg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:95976175A>G	ENST00000295225.5	+	2	223	c.88A>G	c.(88-90)Atc>Gtc	p.I30V	KCNIP3_ENST00000377181.2_Intron|KCNIP3_ENST00000360990.3_Missense_Mutation_p.I30V	NM_013434.4	NP_038462.1	Q9Y2W7	CSEN_HUMAN	Kv channel interacting protein 3, calsenilin	30					apoptotic process (GO:0006915)|behavioral response to pain (GO:0048266)|intracellular protein transport (GO:0006886)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	axon terminus (GO:0043679)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|voltage-gated ion channel activity (GO:0005244)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	16				READ - Rectum adenocarcinoma(193;0.13)		GAAGGAGGGTATCAAGTGGCA	0.622																																					p.I30V		.											.	KCNIP3-154	0			c.A88G						.						79	86	84					2																	95976175		2203	4300	6503	SO:0001583	missense	30818	exon2			GAGGGTATCAAGT	AF199599	CCDS2013.1, CCDS33245.1	2q21.1	2013-01-10	2006-02-11	2006-02-11	ENSG00000115041	ENSG00000115041		"EF-hand domain containing"	15523	protein-coding gene	gene with protein product		604662	"calsenilin, presenilin-binding protein, EF hand transcription factor"	CSEN		9771752, 10078534	Standard	NM_013434		Approved	DREAM, KCHIP3, calsenilin	uc002sup.3	Q9Y2W7	OTTHUMG00000130392	ENST00000295225.5:c.88A>G	2.37:g.95976175A>G	ENSP00000295225:p.Ile30Val	Somatic	356	1		WXS	Illumina HiSeq	Phase_I	364	110	NM_013434	0	0	0	0	0	H7BY46|Q3YAC3|Q3YAC4|Q53TJ5|Q96T40|Q9UJ84|Q9UJ85	Missense_Mutation	SNP	ENST00000295225.5	37	CCDS2013.1	.	.	.	.	.	.	.	.	.	.	A	0.862	-0.734899	0.03111	.	.	ENSG00000115041	ENST00000295225;ENST00000360990	T;T	0.69926	-0.27;-0.44	5.02	-2.69	0.06022	.	1.487590	0.04089	N	0.310881	T	0.38983	0.1061	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23547	-1.0185	10	0.20519	T	0.43	.	11.1112	0.48235	0.6262:0.0:0.3738:0.0	.	30;30	Q9Y2W7;Q3YAC4	CSEN_HUMAN;.	V	30	ENSP00000295225:I30V;ENSP00000354261:I30V	ENSP00000295225:I30V	I	+	1	0	KCNIP3	95339902	0.154000	0.22792	0.361000	0.25849	0.847000	0.48162	0.311000	0.19380	-0.418000	0.07450	-0.810000	0.03169	ATC	.		0.622	KCNIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252770.1	NM_013434		G	95976175	A	G	95976175	3	3	154	1	0	0	0	0	1	0	0	0	8062	449	16	3	94	3	KCNIP3	2	95976175	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	11323636	95976175	147223198	18	13860	150	2									
KCNIP3	30818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	95976177	95976177	+	Silent	SNP	C	C	T																															cttagcaagaaggagggtatCaagtggcagaggccgaggct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:95976177C>T	ENST00000295225.5	+	2	225	c.90C>T	c.(88-90)atC>atT	p.I30I	KCNIP3_ENST00000377181.2_Intron|KCNIP3_ENST00000360990.3_Silent_p.I30I	NM_013434.4	NP_038462.1	Q9Y2W7	CSEN_HUMAN	Kv channel interacting protein 3, calsenilin	30					apoptotic process (GO:0006915)|behavioral response to pain (GO:0048266)|intracellular protein transport (GO:0006886)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	axon terminus (GO:0043679)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|voltage-gated ion channel activity (GO:0005244)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	16				READ - Rectum adenocarcinoma(193;0.13)		AGGAGGGTATCAAGTGGCAGA	0.627																																					p.I30I		.											.	KCNIP3-154	0			c.C90T						.						79	86	83					2																	95976177		2203	4300	6503	SO:0001819	synonymous_variant	30818	exon2			GGGTATCAAGTGG	AF199599	CCDS2013.1, CCDS33245.1	2q21.1	2013-01-10	2006-02-11	2006-02-11	ENSG00000115041	ENSG00000115041		"EF-hand domain containing"	15523	protein-coding gene	gene with protein product		604662	"calsenilin, presenilin-binding protein, EF hand transcription factor"	CSEN		9771752, 10078534	Standard	NM_013434		Approved	DREAM, KCHIP3, calsenilin	uc002sup.3	Q9Y2W7	OTTHUMG00000130392	ENST00000295225.5:c.90C>T	2.37:g.95976177C>T		Somatic	352	1		WXS	Illumina HiSeq	Phase_I	361	109	NM_013434	0	0	0	0	0	H7BY46|Q3YAC3|Q3YAC4|Q53TJ5|Q96T40|Q9UJ84|Q9UJ85	Silent	SNP	ENST00000295225.5	37	CCDS2013.1																																																																																			.		0.627	KCNIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252770.1	NM_013434		T	95976177	C	T	95976177	2	4	154	1	0	0	0	0	0	0	0	1	8062	816	29	2		2	KCNIP3	2	95976177	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	2	95976177	147223196	19	13861	150	2									
SLC5A7	60482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	108604763	108604763	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtggccgagatattggttTattggttggtggatttacca	7	16	14	4	1	0	1	0	0	0	1	0	3	0	2	2	6	1	2	2	6	3	8			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:108604763T>A	ENST00000264047.2	+	2	428	c.152T>A	c.(151-153)tTa>tAa	p.L51*	SLC5A7_ENST00000409059.1_Nonsense_Mutation_p.L51*|SLC5A7_ENST00000540517.1_Intron	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	51					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GATATTGGTTTATTGGTTGGT	0.532																																					p.L51X		.											.	SLC5A7-93	0			c.T152A						.						148	131	137					2																	108604763		2203	4300	6503	SO:0001587	stop_gained	60482	exon2			TTGGTTTATTGGT	AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.152T>A	2.37:g.108604763T>A	ENSP00000264047:p.Leu51*	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	142	41	NM_021815	0	0	0	0	0	Q53TF2	Nonsense_Mutation	SNP	ENST00000264047.2	37	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	T	38	6.986976	0.97983	.	.	ENSG00000115665	ENST00000409059;ENST00000264047	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-15.1779	16.3634	0.83296	0.0:0.0:0.0:1.0	.	.	.	.	X	51	.	ENSP00000264047:L51X	L	+	2	0	SLC5A7	107971195	1.000000	0.71417	0.256000	0.24389	0.386000	0.30323	7.655000	0.83696	2.324000	0.78689	0.533000	0.62120	TTA	.		0.532	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			A	108604763	T	A	108604763	4	1	154	1	0	0	0	0	0	1	0	0	14702	1764	61	5	154	5	SLC5A7	2	108604763	Nonsense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	12628586	108604763	134594610	20	13862											
ZRANB3	84083	hgsc.bcm.edu;broad.mit.edu	37	chr2	135988115	135988115	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagtctcacacatttcaCaataaggtaactctgaatta	15	11	7	8	0	3	1	2	1	2	0	4	3	3	2	0	2	1	1	0	2	5	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:135988115C>T	ENST00000264159.6	-	13	2038	c.1922G>A	c.(1921-1923)tGt>tAt	p.C641Y	ZRANB3_ENST00000536680.1_Missense_Mutation_p.C641Y|ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000401392.1_Missense_Mutation_p.C641Y	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	641					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		ACACATTTCACAATAAGGTAA	0.473																																					p.C641Y		.											.	ZRANB3-658	0			c.G1922A						.						111	103	105					2																	135988115		1967	4164	6131	SO:0001583	missense	84083	exon13			ATTTCACAATAAG	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"Zinc fingers, RAN-binding domain containing"	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1922G>A	2.37:g.135988115C>T	ENSP00000264159:p.Cys641Tyr	Somatic	94	0		WXS	Illumina HiSeq	Phase_I	96	5	NM_032143	0	0	6	6	0	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.360568	0.61403	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.99797	-6.79;-6.79;-6.79	5.61	5.61	0.85477	Zinc finger, RanBP2-type (4);	0.047816	0.85682	D	0.000000	D	0.99864	0.9936	H	0.96175	3.78	0.49213	D	0.999763	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96707	0.9522	10	0.87932	D	0	-12.7436	17.4074	0.87477	0.0:1.0:0.0:0.0	.	641;641	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	Y	106;106;641;641;641	ENSP00000383979:C641Y;ENSP00000264159:C641Y;ENSP00000441320:C641Y	ENSP00000264159:C641Y	C	-	2	0	ZRANB3	135704585	1.000000	0.71417	0.995000	0.50966	0.454000	0.32378	5.258000	0.65479	2.638000	0.89438	0.563000	0.77884	TGT	.		0.473	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		T	135988115	C	T	135988115	3	4	154	1	0	0	0	0	1	0	0	0	18256	478	17	2	1353	2	ZRANB3	2	135988115	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	27383352	135988115	107211258	21	13863											
SSB	6741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170667495	170667495	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggagaggtggaaaaagAagcactgaagaaaataatag	22	4	13	2	0	0	5	0	1	0	4	0	7	0	6	0	3	1	1	0	3	9	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:170667495A>C	ENST00000409333.1	+	10	1185	c.938A>C	c.(937-939)gAa>gCa	p.E313A	METTL5_ENST00000409837.1_Intron|SSB_ENST00000260956.4_Missense_Mutation_p.E313A			P05455	LA_HUMAN	Sjogren syndrome antigen B (autoantigen La)	313					histone mRNA metabolic process (GO:0008334)|tRNA modification (GO:0006400)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(3)|large_intestine(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GTGGAAAAAGAAGCACTGAAG	0.348																																					p.E313A		.											.	SSB-94	0			c.A938C						.						66	68	67					2																	170667495		2203	4299	6502	SO:0001583	missense	6741	exon10			AAAAAGAAGCACT		CCDS2237.1	2q31.1	2014-02-14		2005-06-16	ENSG00000138385	ENSG00000138385		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	11316	protein-coding gene	gene with protein product	"La ribonucleoprotein domain family, member 3"	109090					Standard	NM_003142		Approved	LARP3, La, La/SSB	uc002ufk.3	P05455	OTTHUMG00000132212	ENST00000409333.1:c.938A>C	2.37:g.170667495A>C	ENSP00000386636:p.Glu313Ala	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	133	42	NM_003142	0	0	64	121	57	Q15367|Q53XJ4	Missense_Mutation	SNP	ENST00000409333.1	37	CCDS2237.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217202	0.39201	.	.	ENSG00000138385	ENST00000260956;ENST00000409005;ENST00000409333	T;T	0.47528	0.84;0.84	4.86	-0.881	0.10607	Nucleotide-binding, alpha-beta plait (1);RNA-binding motif (1);	0.493908	0.22411	N	0.060419	T	0.49508	0.1561	M	0.85710	2.77	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.12156	0.003;0.007	T	0.50285	-0.8846	10	0.31617	T	0.26	-0.5081	14.1431	0.65331	0.4664:0.5336:0.0:0.0	.	313;313	E9PFH8;P05455	.;LA_HUMAN	A	313	ENSP00000260956:E313A;ENSP00000386636:E313A	ENSP00000260956:E313A	E	+	2	0	SSB	170375741	1.000000	0.71417	0.890000	0.34922	0.989000	0.77384	1.295000	0.33377	-0.310000	0.08766	0.383000	0.25322	GAA	.		0.348	SSB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333316.1	NM_003142		C	170667495	A	C	170667495	3	2	154	1	0	0	0	0	1	0	0	0	15210	246	9	5	972	5	SSB	2	170667495	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	34679380	170667495	72531878	22	13864											
TNS1	7145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	218678511	218678511	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcggatgatgaaggccccCggctcctggtccttgaggag	6	8	15	12	3	0	3	0	3	0	0	3	5	2	5	4	5	0	1	4	5	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:218678511C>G	ENST00000171887.4	-	26	4898	c.4446G>C	c.(4444-4446)ccG>ccC	p.P1482P	TNS1_ENST00000430930.1_Silent_p.P1461P|TNS1_ENST00000419504.1_Silent_p.P1469P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1482	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P1482P(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGAAGGCCCCCGGCTCCTGGT	0.572																																					p.P1482P		.											.	TNS1-156	1	Substitution - coding silent(1)	large_intestine(1)	c.G4446C						.						58	58	58					2																	218678511		2203	4300	6503	SO:0001819	synonymous_variant	7145	exon26			GGCCCCCGGCTCC	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing"	11973	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 155"	600076	"tensin", "matrix-remodelling associated 6"	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4446G>C	2.37:g.218678511C>G		Somatic	124	0		WXS	Illumina HiSeq	Phase_I	110	34	NM_022648	0	0	16	22	6	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			.		0.572	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218678511	C	G	218678511	2	3	154	1	0	0	0	0	0	0	0	1	16375	639	23	4		4	TNS1	2	218678511	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	48011016	218678511	24520862	23	13865											
PTPRN	5798	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	220164041	220164041	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttacctgcttgttgggtcAcatcagccaaagacaggttc	10	12	9	10	0	2	1	2	0	0	1	3	1	2	1	2	2	3	3	2	2	2	5			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:220164041A>T	ENST00000295718.2	-	11	1829	c.1589T>A	c.(1588-1590)gTg>gAg	p.V530E	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000497977.1_5'Flank|PTPRN_ENST00000423636.2_Missense_Mutation_p.V440E|PTPRN_ENST00000409251.3_Missense_Mutation_p.V501E	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	530					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		TTGTTGGGTCACATCAGCCAA	0.557											OREG0015221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V530E													.	PTPRN-229	0			c.T1589A						.						167	161	163					2																	220164041		2203	4300	6503	SO:0001583	missense	5798	exon11			TGGGTCACATCAG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1589T>A	2.37:g.220164041A>T	ENSP00000295718:p.Val530Glu	Somatic	138	1	2264	WXS	Illumina HiSeq	Phase_I	138	57	NM_002846	0	0	0	0	0	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813832	0.90790	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.07800	3.36;3.17;3.16	5.59	5.59	0.84812	.	0.198382	0.31834	N	0.006989	T	0.27098	0.0664	M	0.68952	2.095	0.58432	D	0.999996	D;D	0.76494	0.999;0.992	D;D	0.68483	0.958;0.958	T	0.00756	-1.1579	10	0.87932	D	0	.	15.4479	0.75248	1.0:0.0:0.0:0.0	.	501;530	Q6NSL1;Q16849	.;PTPRN_HUMAN	E	501;530;501;440	ENSP00000386638:V501E;ENSP00000295718:V530E;ENSP00000444244:V440E	ENSP00000295718:V530E	V	-	2	0	PTPRN	219872285	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.728000	0.84847	2.120000	0.65058	0.459000	0.35465	GTG	.		0.557	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			T	220164041	A	T	220164041	3	4	154	1	0	0	0	0	1	0	0	0	12839	159	6	5	1402	5	PTPRN	2	220164041	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	1485530	220164041	23035332	24	13866											
PTPRN	5798	bcgsc.ca	37	chr2	220164916	220164916	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctggcagtggggtgtccAggcatgggggatgtgcgggc	4	7	23	7	1	0	0	0	0	0	0	1	1	1	1	1	8	1	3	1	8	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:220164916A>G	ENST00000295718.2	-	9	1467	c.1227T>C	c.(1225-1227)ccT>ccC	p.P409P	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Silent_p.P319P|PTPRN_ENST00000409251.3_Silent_p.P409P	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	409					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		TGGGGTGTCCAGGCATGGGGG	0.637																																					p.P409P													.	PTPRN-229	0			c.T1227C						.						61	69	66					2																	220164916		2203	4300	6503	SO:0001819	synonymous_variant	5798	exon9			GTGTCCAGGCATG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1227T>C	2.37:g.220164916A>G		Somatic	46	0		WXS	Illumina HiSeq	Phase_1	45	4	NM_002846	0	0	0	0	0	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	37	CCDS2440.1																																																																																			.		0.637	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			G	220164916	A	G	220164916	2	3	154	1	0	0	0	0	0	0	0	1	12839	175	7	3		3	PTPRN	2	220164916	Silent	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	875	220164916	23034457	25	13867											
ANKMY1	51281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	241465102	241465102	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggccaccggggggcttacCtggggctcaggtatggtccg	4	8	18	11	2	1	0	1	0	0	0	2	0	2	0	4	8	1	3	4	8	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:241465102C>T	ENST00000272972.3	-	6	1282	c.1068G>A	c.(1066-1068)caG>caA	p.Q356Q	ANKMY1_ENST00000373318.2_Splice_Site_p.Q215Q|ANKMY1_ENST00000405523.3_Splice_Site_p.Q215Q|ANKMY1_ENST00000406958.1_Splice_Site_p.Q215Q|ANKMY1_ENST00000405002.1_Splice_Site_p.Q126Q|ANKMY1_ENST00000403283.1_Splice_Site_p.Q294Q|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000401804.1_Splice_Site_p.Q445Q|ANKMY1_ENST00000391987.1_Splice_Site_p.Q356Q|ANKMY1_ENST00000536462.1_Splice_Site_p.Q168Q|ANKMY1_ENST00000373320.4_Splice_Site_p.Q126Q|ANKMY1_ENST00000361678.4_Splice_Site_p.Q215Q	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	356							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GGGGGCTTACCTGGGGCTCAG	0.587																																					p.Q356Q		.											.	ANKMY1-90	0			c.G1068A						.						78	68	72					2																	241465102		2202	4300	6502	SO:0001630	splice_region_variant	51281	exon6			GCTTACCTGGGGC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1068+1G>A	2.37:g.241465102C>T		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	121	45	NM_016552	0	0	0	0	0	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Silent	SNP	ENST00000272972.3	37	CCDS2536.1																																																																																			.		0.587	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	Silent	T	241465102	C	T	241465102	5	4	154	1	0	0	0	0	0	0	1	0	634	695	24	2	1805	2	ANKMY1	2	241465102	Splice_Site	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	21300186	241465102	1734271	26	13868											
CAMP	820	bcgsc.ca	37	chr3	48266885	48266885	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagaatcaaggattttttgCggaatcttgtacccaggaca	13	11	10	7	1	2	1	1	0	1	1	2	5	2	4	1	3	2	1	1	3	4	5	rs374668266		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:48266885C>T	ENST00000576243.1	+	4	624	c.484C>T	c.(484-486)Cgg>Tgg	p.R162W	CAMP_ENST00000296435.2_Missense_Mutation_p.R165W			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	162					antibacterial humoral response (GO:0019731)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptidoglycan (GO:0071224)|cellular response to tumor necrosis factor (GO:0071356)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of growth of symbiont on or near host surface (GO:0044140)|phagosome maturation (GO:0090382)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	cell projection (GO:0042995)|cell wall (GO:0005618)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|specific granule (GO:0042581)		p.R162W(1)		endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGATTTTTTGCGGAATCTTGT	0.443																																					p.R165W													.	CAMP-91	1	Substitution - Missense(1)	endometrium(1)	c.C493T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	107	118	114		484	-9	0	3		114	0,8600		0,0,4300	no	missense	CAMP	NM_004345.4	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	162/171	48266885	1,13005	2203	4300	6503	SO:0001583	missense	820	exon4			TTTTTGCGGAATC	BC055089	CCDS2762.1, CCDS2762.2	3p21.3	2014-01-30			ENSG00000164047	ENSG00000164047		"Endogenous ligands"	1472	protein-coding gene	gene with protein product		600474				7624374	Standard	NM_004345		Approved	CAP18, FALL39, FALL-39, LL37	uc003csj.3	P49913	OTTHUMG00000133526	ENST00000576243.1:c.484C>T	3.37:g.48266885C>T	ENSP00000458149:p.Arg162Trp	Somatic	36	0		WXS	Illumina HiSeq	Phase_1	62	5	NM_004345	0	0	0	0	0	Q71SN9	Missense_Mutation	SNP	ENST00000576243.1	37		.	.	.	.	.	.	.	.	.	.	C	11.52	1.662538	0.29515	2.27E-4	0.0	ENSG00000164047	ENST00000296435	.	.	.	4.51	-9.01	0.00744	Cathelicidin, antimicrobial peptide, C-terminal (1);	4.491740	0.00397	N	0.000045	T	0.18173	0.0436	N	0.19112	0.55	0.09310	N	1	D	0.58620	0.983	P	0.44394	0.448	T	0.47799	-0.9089	9	0.66056	D	0.02	-7.4456	4.5323	0.12011	0.416:0.3384:0.1735:0.0721	.	162	P49913	CAMP_HUMAN	W	162	.	ENSP00000296435:R162W	R	+	1	2	CAMP	48241889	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.240000	0.02914	-1.762000	0.01308	-2.178000	0.00318	CGG	.		0.443	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345		T	48266885	C	T	48266885	3	4	154	1	0	0	0	0	1	0	0	0	2616	759	27	1	498	1	CAMP	3	48266885	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10		48266885	149755545	27	13869											
C3orf54	7318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49842183	49842183	+	IGR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcctgagacagggagtgaAgggggtgacggaggtgggca	9	5	21	6	1	0	3	0	3	0	1	0	6	0	5	1	6	1	1	1	6	1	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:49842183A>C	ENST00000333486.3	-	0	3299				MIR5193_ENST00000584510.1_RNA|FAM212A_ENST00000333323.4_Missense_Mutation_p.E209D	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CAGGGAGTGAAGGGGGTGACG	0.652																																					p.E209D		.											.	.	0			c.A627C						.						78	78	78					3																	49842183		2203	4300	6503	SO:0001628	intergenic_variant	389119	exon2			GAGTGAAGGGGGT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267		3.37:g.49842183A>C		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	305	151	NM_203370	0	0	1	1	0	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673205	0.47781	.	.	ENSG00000185614	ENST00000333323	.	.	.	5.64	-0.363	0.12556	.	0.000000	0.52532	D	0.000077	T	0.61627	0.2362	L	0.44542	1.39	0.39146	D	0.962132	D	0.71674	0.998	D	0.63488	0.915	T	0.62358	-0.6871	9	0.56958	D	0.05	.	10.7234	0.46052	0.5054:0.0:0.4946:0.0	.	207	Q96EL1	CC054_HUMAN	D	209	.	ENSP00000329735:E209D	E	+	3	2	C3orf54	49817187	1.000000	0.71417	0.885000	0.34714	0.348000	0.29142	0.471000	0.22100	-0.003000	0.14444	0.459000	0.35465	GAA	.		0.652	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		C	49842183	A	C	49842183	1	2	154	0	1	0	0	0	0	0	0	0	2239	69	3	5		5	C3orf54	3	49842183	IGR	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	1575298	49842183	148180247	28	13870											
ROBO1	6091	broad.mit.edu	37	chr3	79639003	79639003	+	Frame_Shift_Del	DEL	T	T	-																															gctgggccagaaacaggtgaTttggggataagctgaggagt																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:79639003delT	ENST00000464233.1	-	2	172	c.59delA	c.(58-60)aatfs	p.N20fs		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	20					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AAACAGGTGATTTGGGGATAA	0.393																																					p.N20fs													.	ROBO1-67	0			c.59delA						.						165	164	164					3																	79639003		1916	4117	6033	SO:0001589	frameshift_variant	6091	exon2			AGGTGATTTGGGG	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.59delA	3.37:g.79639003delT	ENSP00000420321:p.Asn20fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	167	11	NM_002941	0	0	0	0	0	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Frame_Shift_Del	DEL	ENST00000464233.1	37	CCDS54611.1																																																																																			.		0.393	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		-	79639003	T	-	79639003	7	5	154	1	0	1	0	1	0	0	0	0	13545	1493	52	0	5088	0	ROBO1	3	79639003	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	29796820	79639003	118383427	29	13871											
ARHGAP31	57514	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	119099827	119099827	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggagcttcctccatcccActataggtaagaatggttgg	10	10	10	11	0	0	1	0	0	0	1	3	2	3	2	4	4	1	3	4	4	4	5			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:119099827A>G	ENST00000264245.4	+	4	957	c.425A>G	c.(424-426)cAc>cGc	p.H142R		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	142	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						CCTCCATCCCACTATAGGTAA	0.493																																					p.H142R	Pancreas(7;176 297 5394 51128 51241)												.	ARHGAP31-92	0			c.A425G						.						84	84	84					3																	119099827		1967	4162	6129	SO:0001583	missense	57514	exon4			CATCCCACTATAG		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.425A>G	3.37:g.119099827A>G	ENSP00000264245:p.His142Arg	Somatic	172	1		WXS	Illumina HiSeq	Phase_I	173	79	NM_020754	0	0	0	0	0	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	37	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.119225	0.77323	.	.	ENSG00000031081	ENST00000264245;ENST00000543280;ENST00000482743	T;T	0.24538	2.66;1.85	5.18	5.18	0.71444	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.64402	D	0.000001	T	0.57460	0.2055	M	0.89840	3.065	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.66567	-0.5891	10	0.87932	D	0	.	12.9105	0.58177	1.0:0.0:0.0:0.0	.	142	Q2M1Z3	RHG31_HUMAN	R	142;142;113	ENSP00000264245:H142R;ENSP00000418429:H113R	ENSP00000264245:H142R	H	+	2	0	ARHGAP31	120582517	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	8.109000	0.89561	2.171000	0.68590	0.482000	0.46254	CAC	.		0.493	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			G	119099827	A	G	119099827	3	3	154	1	0	0	0	0	1	0	0	0	880	159	6	3	439	3	ARHGAP31	3	119099827	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	39460824	119099827	78922603	30	13872											
GOLGB1	2804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121415217	121415217	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgttctaggccagcaatttGtagttggctgctttccaatt	8	16	9	8	0	1	0	0	0	1	0	2	0	2	0	2	2	2	6	2	2	4	7			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:121415217G>A	ENST00000340645.5	-	13	4263	c.4138C>T	c.(4138-4140)Caa>Taa	p.Q1380*	GOLGB1_ENST00000393667.3_Nonsense_Mutation_p.Q1385*	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1380					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CCAGCAATTTGTAGTTGGCTG	0.413																																					p.Q1385X		.											.	GOLGB1-161	0			c.C4153T						.						157	162	160					3																	121415217		2203	4299	6502	SO:0001587	stop_gained	2804	exon13			CAATTTGTAGTTG	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"macrogolgin", "golgi integral membrane protein 1"	602500	"golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1", "golgin B1, golgi integral membrane protein"			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.4138C>T	3.37:g.121415217G>A	ENSP00000341848:p.Gln1380*	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	59	12	NM_001256486	0	0	22	23	1	B2ZZ91|D3DN92|E7EP74|Q14398	Nonsense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	G	39	7.740962	0.98465	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	.	.	.	6.17	3.41	0.39046	.	0.324362	0.26746	N	0.022716	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.993	0.19478	0.0:0.6622:0.1652:0.1726	.	.	.	.	X	1380;1385;1344	.	ENSP00000341848:Q1380X	Q	-	1	0	GOLGB1	122897907	0.273000	0.24181	0.748000	0.31131	0.666000	0.39218	0.959000	0.29240	0.464000	0.27142	-0.165000	0.13383	CAA	.		0.413	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121415217	G	A	121415217	4	1	154	1	0	0	0	0	0	1	0	0	6585	1386	48	2	5681	2	GOLGB1	3	121415217	Nonsense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	2315390	121415217	76607213	31	13873											
ARMC8	25852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	137982982	137982982	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctttgtagatgtttgcaCagtttatccagatctgtgca	9	17	8	7	0	2	2	0	0	2	2	3	2	3	2	1	0	2	5	1	0	2	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:137982982C>T	ENST00000469044.1	+	14	1498	c.1227C>T	c.(1225-1227)caC>caT	p.H409H	ARMC8_ENST00000393058.3_Silent_p.H399H|ARMC8_ENST00000491704.1_Silent_p.H367H|ARMC8_ENST00000481646.1_Silent_p.H395H|NME9_ENST00000341790.5_Intron|NME9_ENST00000536478.1_Intron|NME9_ENST00000317876.4_Intron|NME9_ENST00000383180.2_Intron|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000538260.1_Silent_p.H378H|ARMC8_ENST00000461822.1_Silent_p.H342H|ARMC8_ENST00000485396.1_Silent_p.H336H	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	409										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						GATGTTTGCACAGTTTATCCA	0.368																																					p.H395H		.											.	ARMC8-90	0			c.C1185T						.						100	89	92					3																	137982982		1850	4099	5949	SO:0001819	synonymous_variant	25852	exon15			TTTGCACAGTTTA		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"Armadillo repeat containing"	24999	protein-coding gene	gene with protein product	"GID complex subunit 5, VID28 homolog (S. cerevisiae)"					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1227C>T	3.37:g.137982982C>T		Somatic	55	0		WXS	Illumina HiSeq	Phase_I	83	24	NM_015396	0	0	0	0	0	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Silent	SNP	ENST00000469044.1	37																																																																																				.		0.368	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		T	137982982	C	T	137982982	2	4	154	1	0	0	0	0	0	0	0	1	958	477	17	2		2	ARMC8	3	137982982	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	16567765	137982982	60039448	32	13874											
RBP1	5947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	139237296	139237296	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaccctcgatccactgggtCcagccacgcccctccttctc	5	9	6	21	2	2	0	1	0	1	0	7	1	5	0	7	1	1	0	7	1	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:139237296C>A	ENST00000232219.2	-	3	617	c.507G>T	c.(505-507)tgG>tgT	p.W169C	RP11-319G6.1_ENST00000515247.1_RNA	NM_002899.3	NP_002890.2	P09455	RET1_HUMAN	retinol binding protein 1, cellular	107					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	TCCACTGGGTCCAGCCACGCC	0.592																																					p.W169C		.											.	RBP1-514	0			c.G507T						.						120	95	104					3																	139237296		2203	4300	6503	SO:0001583	missense	5947	exon3			CTGGGTCCAGCCA		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"Fatty acid binding protein family"	9919	protein-coding gene	gene with protein product		180260	"retinol-binding protein 1, cellular"			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000232219.2:c.507G>T	3.37:g.139237296C>A	ENSP00000232219:p.Trp169Cys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	86	25	NM_002899	0	0	40	43	3	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000232219.2	37	CCDS3110.2	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491184	0.84962	.	.	ENSG00000114115	ENST00000232219	T	0.23147	1.92	5.93	5.93	0.95920	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.54759	0.1878	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55477	-0.8135	10	0.72032	D	0.01	.	17.8376	0.88704	0.0:1.0:0.0:0.0	.	107	P09455	RET1_HUMAN	C	169	ENSP00000232219:W169C	ENSP00000232219:W169C	W	-	3	0	RBP1	140719986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.088000	0.76901	2.815000	0.96918	0.561000	0.74099	TGG	.		0.592	RBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341495.1	NM_002899		A	139237296	C	A	139237296	3	1	154	1	0	0	0	0	1	0	0	0	13187	856	30	4	94	4	RBP1	3	139237296	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	1254314	139237296	58785134	33	13875											
LEPREL1	55214	ucsc.edu	37	chr3	189711953	189711953	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaatctctgaggcccctcAcatagggtccggcattctgt	8	11	9	13	1	4	1	2	1	2	0	6	1	5	1	3	3	0	1	3	3	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:189711953A>G	ENST00000319332.5	-	3	950	c.753T>C	c.(751-753)tgT>tgC	p.C251C	LEPREL1_ENST00000427335.2_Silent_p.C70C	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	251					collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GAGGCCCCTCACATAGGGTCC	0.378																																					p.C251C													.	LEPREL1-155	0			c.T753C						.						78	79	78					3																	189711953		2203	4300	6503	SO:0001819	synonymous_variant	55214	exon3			CCCCTCACATAGG		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"prolyl 3-hydroxylase 2"	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.753T>C	3.37:g.189711953A>G		Somatic	30	0		WXS	Illumina HiSeq		40	4	NM_018192	0	0	22	22	0	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																			.		0.378	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192		G	189711953	A	G	189711953	2	3	154	1	0	0	0	0	0	0	0	1	8751	157	6	3		3	LEPREL1	3	189711953	Silent	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	50474657	189711953	8310477	34	13876											
EXOC1	55763	hgsc.bcm.edu	37	chr4	56738102	56738102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggagactggccagtcaccTcaacaatgtttttgttcaac	10	11	8	12	1	3	1	3	0	0	1	3	2	3	1	3	2	2	2	3	2	3	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr4:56738102T>C	ENST00000381295.2	+	8	1400	c.1052T>C	c.(1051-1053)cTc>cCc	p.L351P	EXOC1_ENST00000346134.7_Missense_Mutation_p.L351P|EXOC1_ENST00000349598.6_Missense_Mutation_p.L351P	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	351					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					GCCAGTCACCTCAACAATGTT	0.393																																					p.L351P		.											.	EXOC1-950	0			c.T1052C						.						76	76	76					4																	56738102		2203	4300	6503	SO:0001583	missense	55763	exon8			GTCACCTCAACAA	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"SEC3-like 1 (S. cerevisiae)"	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1052T>C	4.37:g.56738102T>C	ENSP00000370695:p.Leu351Pro	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_018261	0	0	22	22	0	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.548026	0.86022	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.80813	0.4695	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.83261	-0.0048	9	0.87932	D	0	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	351;351	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	P	351	.	ENSP00000326514:L351P	L	+	2	0	EXOC1	56432859	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.546000	0.82137	2.323000	0.78572	0.528000	0.53228	CTC	.		0.393	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56738102	T	C	56738102	3	2	154	1	0	0	0	0	1	0	0	0	5314	1551	54	3	1078	3	EXOC1	4	56738102	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		56738102	134416174	35	13877											
REST	5978	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	57797826	57797826	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgccagagggtgaaactttAaatggtaaacatcagactga	16	8	10	7	1	1	4	1	2	0	2	1	4	1	4	1	2	2	1	1	2	5	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr4:57797826A>C	ENST00000309042.7	+	4	3116	c.2802A>C	c.(2800-2802)ttA>ttC	p.L934F		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	934					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					GTGAAACTTTAAATGGTAAAC	0.393																																					p.L934F		.											.	REST-232	0			c.A2802C						.						63	61	62					4																	57797826		2203	4300	6503	SO:0001583	missense	5978	exon4			AACTTTAAATGGT	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2802A>C	4.37:g.57797826A>C	ENSP00000311816:p.Leu934Phe	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	110	43	NM_001193508	0	0	12	14	2	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698194	0.30142	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.09445	2.98	5.44	-0.433	0.12287	.	1.916850	0.03006	N	0.148774	T	0.10337	0.0253	L	0.44542	1.39	0.09310	N	1	B;B	0.22146	0.065;0.002	B;B	0.19946	0.027;0.003	T	0.36890	-0.9729	10	0.62326	D	0.03	3.7839	2.7257	0.05213	0.5094:0.2758:0.0816:0.1332	.	911;934	F8WAN5;Q13127	.;REST_HUMAN	F	934;911	ENSP00000311816:L934F	ENSP00000311816:L934F	L	+	3	2	REST	57492583	0.001000	0.12720	0.000000	0.03702	0.092000	0.18411	0.791000	0.26915	0.082000	0.17018	0.459000	0.35465	TTA	.		0.393	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		C	57797826	A	C	57797826	3	2	154	1	0	0	0	0	1	0	0	0	13266	359	13	5	2812	5	REST	4	57797826	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	1059724	57797826	133356450	36	13878											
RAPGEF2	9693	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	160268070	160268070	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccaccagcacataaaaTcaaccagggactacaggttc	15	5	7	14	0	1	0	1	0	0	0	2	1	1	1	4	2	3	2	4	2	4	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr4:160268070T>C	ENST00000264431.4	+	19	3568	c.3149T>C	c.(3148-3150)aTc>aCc	p.I1050T		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1050					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GCACATAAAATCAACCAGGGA	0.522																																					p.I1050T													.	RAPGEF2-637	0			c.T3149C						.						77	90	86					4																	160268070		2010	4186	6196	SO:0001583	missense	9693	exon19			ATAAAATCAACCA	AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"Rap GEP"	609530	"PDZ domain containing guanine nucleotide exchange factor (GEF) 1"	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3149T>C	4.37:g.160268070T>C	ENSP00000264431:p.Ile1050Thr	Somatic	72	1		WXS	Illumina HiSeq	Phase_I	72	22	NM_014247	0	0	6	9	3	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.351|7.351	0.622902|0.622902	0.14193|0.14193	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000264431|ENST00000510253	T|.	0.36878|.	1.23|.	6.17|6.17	-4.18|-4.18	0.03846|0.03846	.|.	1.187630|.	0.05843|.	N|.	0.619694|.	T|T	0.15132|0.15132	0.0365|0.0365	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.12156|.	0.007|.	T|T	0.30909|0.30909	-0.9962|-0.9962	10|5	0.10636|.	T|.	0.68|.	.|.	7.3539|7.3539	0.26709|0.26709	0.0:0.3427:0.2057:0.4516|0.0:0.3427:0.2057:0.4516	.|.	1050|.	Q9Y4G8|.	RPGF2_HUMAN|.	T|P	1050|82	ENSP00000264431:I1050T|.	ENSP00000264431:I1050T|.	I|S	+|+	2|1	0|0	RAPGEF2|RAPGEF2	160487520|160487520	0.005000|0.005000	0.15991|0.15991	0.000000|0.000000	0.03702|0.03702	0.300000|0.300000	0.27592|0.27592	-0.012000|-0.012000	0.12699|0.12699	-0.941000|-0.941000	0.03700|0.03700	-1.931000|-1.931000	0.00510|0.00510	ATC|TCA	.		0.522	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247		C	160268070	T	C	160268070	3	2	154	1	0	0	0	0	1	0	0	0	13076	1435	50	3	3223	3	RAPGEF2	4	160268070	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	102470244	160268070	30886206	37	13879											
UFSP2	55325	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	186334930	186334930	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaagtatgtggatttctaaTgtaaccatctttgtatggct	10	17	9	5	0	2	0	0	0	2	0	2	1	2	1	1	2	1	5	1	2	5	7			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr4:186334930T>C	ENST00000264689.6	-	7	897	c.781A>G	c.(781-783)Att>Gtt	p.I261V	UFSP2_ENST00000502282.1_5'Flank|Y_RNA_ENST00000384502.1_RNA	NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	261						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	small conjugating protein-specific protease activity (GO:0019783)|thiolester hydrolase activity (GO:0016790)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		GGATTTCTAATGTAACCATCT	0.363																																					p.I261V													.	UFSP2-90	0			c.A781G						.						178	177	177					4																	186334930		2203	4300	6503	SO:0001583	missense	55325	exon7			TTCTAATGTAACC	AK002062	CCDS3842.1	4q35.1	2008-03-25	2008-03-25	2008-03-25	ENSG00000109775	ENSG00000109775			25640	protein-coding gene	gene with protein product		611482	"chromosome 4 open reading frame 20"	C4orf20		17182609	Standard	NM_018359		Approved	FLJ11200	uc003ixo.2	Q9NUQ7	OTTHUMG00000160441	ENST00000264689.6:c.781A>G	4.37:g.186334930T>C	ENSP00000264689:p.Ile261Val	Somatic	149	1		WXS	Illumina HiSeq	Phase_I	145	42	NM_018359	0	0	18	33	15	Q6IA77|Q96FS3	Missense_Mutation	SNP	ENST00000264689.6	37	CCDS3842.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.46|14.46	2.540584|2.540584	0.45280|0.45280	.|.	.|.	ENSG00000109775|ENSG00000109775	ENST00000511485|ENST00000264689	.|T	.|0.30448	.|1.53	6.04|6.04	3.62|3.62	0.41486|0.41486	.|.	.|0.130647	.|0.52532	.|D	.|0.000066	T|T	0.24470|0.24470	0.0593|0.0593	L|L	0.44542|0.44542	1.39|1.39	0.36491|0.36491	D|D	0.86842|0.86842	.|B;B	.|0.15473	.|0.013;0.001	.|B;B	.|0.14023	.|0.006;0.01	T|T	0.14671|0.14671	-1.0464|-1.0464	5|10	.|0.49607	.|T	.|0.09	-25.5742|-25.5742	8.1278|8.1278	0.31010|0.31010	0.0:0.0717:0.3242:0.6041|0.0:0.0717:0.3242:0.6041	.|.	.|261;161	.|Q9NUQ7;B3KRI4	.|UFSP2_HUMAN;.	R|V	174|261	.|ENSP00000264689:I261V	.|ENSP00000264689:I261V	H|I	-|-	2|1	0|0	UFSP2|UFSP2	186571924|186571924	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	4.485000|4.485000	0.60279|0.60279	1.085000|1.085000	0.41206|0.41206	0.459000|0.459000	0.35465|0.35465	CAT|ATT	.		0.363	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359		C	186334930	T	C	186334930	3	2	154	1	0	0	0	0	1	0	0	0	16971	1464	51	3	652	3	UFSP2	4	186334930	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	26066860	186334930	4819346	38	13880											
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	67588157	67588158	+	Frame_Shift_Ins	INS	-	-	G																															ataacaatatgtccttacaaINSgatgctgaatggtactgggg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr5:67588157_67588158insG	ENST00000521381.1	+	8	1603_1604	c.987_988insG	c.(988-990)gatfs	p.D330fs	PIK3R1_ENST00000523872.1_5'Flank|PIK3R1_ENST00000336483.5_Frame_Shift_Ins_p.D60fs|PIK3R1_ENST00000320694.8_Frame_Shift_Ins_p.D30fs|PIK3R1_ENST00000274335.5_Frame_Shift_Ins_p.D330fs|PIK3R1_ENST00000521657.1_Frame_Shift_Ins_p.D330fs|PIK3R1_ENST00000396611.1_Frame_Shift_Ins_p.D330fs	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	330				D -> N (in Ref. 1; M61906). {ECO:0000305}.	B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TGTCCTTACAAGATGCTGAATG	0.396			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.Q329fs		.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1-4332	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.987_988insG						.																																			SO:0001589	frameshift_variant	5295	exon8			.	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.988dupG	5.37:g.67588158_67588158dupG	ENSP00000428056:p.Asp330fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	55	24	NM_181523	0	0	0	0	0	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Ins	INS	ENST00000521381.1	37	CCDS3993.1																																																																																			.		0.396	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67588158	-	G	67588157	7	5	154	1	0	1	1	0	0	0	0	0	11944	69	3	0	1143	0	PIK3R1	5	67588157	Frame_Shift_Ins	INS	-	TCGA-P4-A5E7-01A-31D-A28G-10		67588157	113327103	39	13881											
C5orf30	90355	ucsc.edu;bcgsc.ca	37	chr5	102611692	102611692	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccctggggctgaggccaaCtccccgggaaaggcggaggc	7	5	16	13	2	0	1	0	1	0	0	2	3	2	3	4	7	1	1	4	7	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr5:102611692C>T	ENST00000319933.2	+	3	380	c.72C>T	c.(70-72)aaC>aaT	p.N24N	C5orf30_ENST00000510890.1_Silent_p.N24N|C5orf30_ENST00000515669.1_Silent_p.N24N	NM_033211.2	NP_149988.1	Q96GV9	CE030_HUMAN	chromosome 5 open reading frame 30	24					cilium morphogenesis (GO:0060271)|protein transport (GO:0015031)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9		all_cancers(142;2.22e-05)|all_epithelial(76;9.54e-08)|Prostate(80;0.0174)|Colorectal(57;0.0551)|Ovarian(225;0.11)|Lung NSC(167;0.136)|all_lung(232;0.18)		Epithelial(69;2.84e-14)|COAD - Colon adenocarcinoma(37;0.00762)		CTGAGGCCAACTCCCCGGGAA	0.567																																					p.N24N													.	C5orf30-68	0			c.C72T						.						41	42	42					5																	102611692		2203	4299	6502	SO:0001819	synonymous_variant	90355	exon3			GGCCAACTCCCCG		CCDS4095.1	5q21.1	2012-02-23			ENSG00000181751	ENSG00000181751			25052	protein-coding gene	gene with protein product						22085962	Standard	NM_033211		Approved	FLJ25291	uc003kog.1	Q96GV9	OTTHUMG00000128738	ENST00000319933.2:c.72C>T	5.37:g.102611692C>T		Somatic	245	3		WXS	Illumina HiSeq		250	87	NM_033211	0	0	2	4	2		Silent	SNP	ENST00000319933.2	37	CCDS4095.1																																																																																			.		0.567	C5orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250649.1	NM_033211		T	102611692	C	T	102611692	2	4	154	1	0	0	0	0	0	0	0	1	2296	564	20	2		2	C5orf30	5	102611692	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	35023535	102611692	78303568	40	13882											
NQO2	4835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	3010268	3010268	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctgatttaggtaagaaagTactcattgtctatgcacacc	12	13	7	9	0	2	2	1	1	1	1	3	2	3	2	2	1	2	3	2	1	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:3010268T>C	ENST00000338130.2	+	6	729	c.17T>C	c.(16-18)gTa>gCa	p.V6A	NQO2_ENST00000380454.4_Missense_Mutation_p.V6A|NQO2_ENST00000380455.4_Missense_Mutation_p.V6A|NQO2_ENST00000380430.1_Missense_Mutation_p.V6A|NQO2_ENST00000606474.1_3'UTR|NQO2_ENST00000380441.1_Missense_Mutation_p.V6A			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	6					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	GGTAAGAAAGTACTCATTGTC	0.423																																					p.V6A		.											.	NQO2-91	0			c.T17C						.						97	87	90					6																	3010268		2203	4300	6503	SO:0001583	missense	4835	exon3			AGAAAGTACTCAT	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"NAD(P)H menadione oxidoreductase 2, dioxin-inducible"	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.17T>C	6.37:g.3010268T>C	ENSP00000337773:p.Val6Ala	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	104	30	NM_000904	0	0	0	0	0	B2R492|Q5TD04	Missense_Mutation	SNP	ENST00000338130.2	37	CCDS4481.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.034069	0.35893	.	.	ENSG00000124588	ENST00000426637;ENST00000380472;ENST00000538898;ENST00000397717;ENST00000338130;ENST00000380441;ENST00000380455;ENST00000380454;ENST00000380430	T;T;T;T;T;T;T;T	0.11930	2.81;2.73;2.73;2.81;2.81;2.81;2.81;2.81	5.63	5.63	0.86233	Flavodoxin-like fold (1);	0.123571	0.56097	D	0.000034	T	0.18800	0.0451	L	0.52823	1.66	0.44771	D	0.997777	P;D	0.89917	0.613;1.0	P;D	0.91635	0.851;0.999	T	0.06516	-1.0822	10	0.16896	T	0.51	-27.3633	13.5807	0.61901	0.0:0.0:0.0:1.0	.	6;53	P16083;Q59EN2	NQO2_HUMAN;.	A	6;6;53;6;6;6;6;6;6	ENSP00000406951:V6A;ENSP00000369839:V6A;ENSP00000380829:V6A;ENSP00000337773:V6A;ENSP00000369806:V6A;ENSP00000369822:V6A;ENSP00000369821:V6A;ENSP00000369795:V6A	ENSP00000337773:V6A	V	+	2	0	NQO2	2955267	0.985000	0.35326	1.000000	0.80357	0.371000	0.29859	1.927000	0.40094	2.140000	0.66376	0.460000	0.39030	GTA	.		0.423	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1			C	3010268	T	C	3010268	3	2	154	1	0	0	0	0	1	0	0	0	10638	1638	57	3	23	3	NQO2	6	3010268	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		3010268	168104799	41	13883											
PRPF4B	8899	bcgsc.ca	37	chr6	4032300	4032315	+	Frame_Shift_Del	DEL	AAGTAAAAGCAGATCC	AAGTAAAAGCAGATCC	-																															aaaattactacaaagaaacgAagtaaaagcagatccaaaga																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	AAGTAAAAGCAGATCC	AAGTAAAAGCAGATCC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:4032300_4032315delAAGTAAAAGCAGATCC	ENST00000337659.6	+	2	649_664	c.549_564delAAGTAAAAGCAGATCC	c.(547-564)cgaagtaaaagcagatccfs	p.RSKSRS183fs	PRPF4B_ENST00000538861.1_Frame_Shift_Del_p.RSKSRS169fs	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	183	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				CAAAGAAACGAAGTAAAAGCAGATCCAAAGAACGGA	0.356																																					p.183_188del													.	PRPF4B-1308	0			c.549_564del						.																																			SO:0001589	frameshift_variant	8899	exon2			GAAACGAAGTAAA	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.549_564delAAGTAAAAGCAGATCC	6.37:g.4032300_4032315delAAGTAAAAGCAGATCC	ENSP00000337194:p.Arg183fs	Somatic	120	0		WXS	Illumina HiSeq	Phase_1	77	8	NM_003913	0	0	0	0	0	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Frame_Shift_Del	DEL	ENST00000337659.6	37	CCDS4488.1																																																																																			.		0.356	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			-	4032315	AAGTAAAAGCAGATCC	-	4032300	7	5	154	1	0	1	0	1	0	0	0	0	12602	233	9	0	555	0	PRPF4B	6	4032300	Frame_Shift_Del	DEL	AAGTAAAAGCAGATCC	TCGA-P4-A5E7-01A-31D-A28G-10	1022032	4032300	167082767	42	13884											
GABBR1	2550	hgsc.bcm.edu	37	chr6	29595420	29595420	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgatgtacactgcgcgcCgttctgaggaggggtgcggg	5	7	17	12	5	1	1	0	1	1	0	1	3	1	2	3	4	3	2	3	4	1	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:29595420C>T	ENST00000377034.4	-	6	835	c.500G>A	c.(499-501)cGg>cAg	p.R167Q	GABBR1_ENST00000377012.4_Missense_Mutation_p.R50Q|GABBR1_ENST00000355973.3_Missense_Mutation_p.R50Q|GABBR1_ENST00000376977.3_Missense_Mutation_p.R167Q|GABBR1_ENST00000377016.4_Missense_Mutation_p.R105Q	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	167					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CACTGCGCGCCGTTCTGAGGA	0.716																																					p.R167Q		.											.	GABBR1-521	0			c.G500A						.						5	5	5					6																	29595420		1961	3937	5898	SO:0001583	missense	2550	exon6			GCGCGCCGTTCTG	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"GABA receptors", "GPCR / Class C : GABA(B) receptors"	4070	protein-coding gene	gene with protein product	"GABA-B receptor"	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.500G>A	6.37:g.29595420C>T	ENSP00000366233:p.Arg167Gln	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_001470	0	0	4	6	2	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.313674	0.60414	.	.	ENSG00000204681	ENST00000355973;ENST00000376977;ENST00000377016;ENST00000377012;ENST00000377034	D;T;D;D;T	0.82984	-1.67;-0.98;-1.57;-1.67;-0.45	3.25	3.25	0.37280	.	0.279410	0.27912	U	0.017356	T	0.57257	0.2041	L	0.46157	1.445	0.33376	D	0.574201	B;B;B;B	0.28208	0.071;0.065;0.063;0.203	B;B;B;B	0.21151	0.033;0.01;0.011;0.028	T	0.49263	-0.8958	10	0.22109	T	0.4	-24.9114	6.2007	0.20575	0.0:0.8596:0.0:0.1404	.	167;105;167;50	Q9UBS5-5;Q9UBS5-3;Q9UBS5;Q5SUJ9	.;.;GABR1_HUMAN;.	Q	50;167;105;50;167	ENSP00000348248:R50Q;ENSP00000366176:R167Q;ENSP00000366215:R105Q;ENSP00000366211:R50Q;ENSP00000366233:R167Q	ENSP00000348248:R50Q	R	-	2	0	GABBR1	29703399	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.661000	0.46758	1.645000	0.50612	0.455000	0.32223	CGG	.		0.716	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29595420	C	T	29595420	3	4	154	1	0	0	0	0	1	0	0	0	6174	652	23	1	2457	1	GABBR1	6	29595420	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	25563120	29595420	141519647	43	13885											
NFKBIL1	4795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	31526116	31526116	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	accccagaggagcggggaggGgcagcctctggcgatttggt	7	6	18	10	2	1	1	0	0	1	1	1	4	1	3	3	7	2	1	3	7	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:31526116G>A	ENST00000376148.4	+	4	988	c.874G>A	c.(874-876)Ggc>Agc	p.G292S	NFKBIL1_ENST00000376145.4_Missense_Mutation_p.G277S	NM_005007.3	NP_004998.3	Q9UBC1	IKBL1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1	292					cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of transcription factor (GO:0042994)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)	cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						AGCGGGGAGGGGCAGCCTCTG	0.711																																					p.G292S		.											.	NFKBIL1-90	0			c.G874A						.						7	7	7					6																	31526116		1474	2672	4146	SO:0001583	missense	4795	exon4			GGGAGGGGCAGCC	X77909	CCDS4700.1, CCDS47399.1, CCDS47400.1	6p21.3	2010-02-17			ENSG00000204498	ENSG00000204498			7800	protein-coding gene	gene with protein product		601022		NFKBIL		8081366	Standard	NM_005007		Approved	IKBL	uc003nub.3	Q9UBC1	OTTHUMG00000031038	ENST00000376148.4:c.874G>A	6.37:g.31526116G>A	ENSP00000365318:p.Gly292Ser	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	69	23	NM_005007	0	0	12	27	15	A6NL91|B4DUW1|Q14625|Q5HYU4|Q5RJ72|Q5ST96|Q5STV4|Q5STV5|Q9UBX4	Missense_Mutation	SNP	ENST00000376148.4	37	CCDS4700.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.218538	0.39201	.	.	ENSG00000204498	ENST00000376146;ENST00000376148;ENST00000376145	T;T;T	0.30448	1.53;1.53;1.53	5.95	3.09	0.35607	.	0.261597	0.36555	N	0.002538	T	0.04318	0.0119	N	0.11560	0.145	0.31038	N	0.71666	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.39820	-0.9595	10	0.17369	T	0.5	-13.1009	5.6448	0.17584	0.1708:0.1613:0.6679:0.0	.	269;277;292	Q5STV6;Q5STV4;Q9UBC1	.;.;IKBL1_HUMAN	S	269;292;277	ENSP00000365316:G269S;ENSP00000365318:G292S;ENSP00000365315:G277S	ENSP00000365315:G277S	G	+	1	0	NFKBIL1	31634095	0.998000	0.40836	0.997000	0.53966	0.980000	0.70556	0.920000	0.28705	0.863000	0.35553	0.563000	0.77884	GGC	.		0.711	NFKBIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076036.3	NM_005007		A	31526116	G	A	31526116	3	1	154	1	0	0	0	0	1	0	0	0	10407	1232	43	2	888	2	NFKBIL1	6	31526116	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	1930696	31526116	139588951	44	13886											
ZBTB22	9278	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	33284267	33284267	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcggagtagttcagtgcActtgtccacaatgtgccaca	9	12	9	11	1	2	0	1	0	1	0	4	1	3	1	2	1	2	3	2	1	2	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:33284267A>G	ENST00000431845.2	-	2	578	c.427T>C	c.(427-429)Tgc>Cgc	p.C143R	TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000489157.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.C143R|TAPBP_ENST00000456592.2_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	143					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)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						AGTTCAGTGCACTTGTCCACA	0.587																																					p.C143R													.	ZBTB22-69	0			c.T427C						.						111	108	109					6																	33284267		2203	4300	6503	SO:0001583	missense	9278	exon2			CAGTGCACTTGTC	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	13085	protein-coding gene	gene with protein product		611439	"zinc finger protein 297"	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110	ENST00000431845.2:c.427T>C	6.37:g.33284267A>G	ENSP00000407545:p.Cys143Arg	Somatic	119	1		WXS	Illumina HiSeq	Phase_I	131	57	NM_001145338	0	0	16	29	13	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	.	.	.	.	.	.	.	.	.	.	A	16.56	3.158170	0.57368	.	.	ENSG00000236104	ENST00000418724;ENST00000431845;ENST00000441117	T;T;T	0.33438	1.41;1.41;1.41	4.24	4.24	0.50183	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.36555	N	0.002524	T	0.62270	0.2414	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75563	-0.3274	10	0.72032	D	0.01	.	11.3566	0.49620	1.0:0.0:0.0:0.0	.	143	O15209	ZBT22_HUMAN	R	143	ENSP00000404403:C143R;ENSP00000407545:C143R;ENSP00000413172:C143R	ENSP00000404403:C143R	C	-	1	0	ZBTB22	33392245	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.104000	0.94239	1.784000	0.52394	0.450000	0.29827	TGC	.		0.587	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			G	33284267	A	G	33284267	3	3	154	1	0	0	0	0	1	0	0	0	17562	159	6	3	1481	3	ZBTB22	6	33284267	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	1758151	33284267	137830800	45	13887											
HCRTR2	3062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	55039411	55039411	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cggcaccaaattggaggactCccccccttgtcgcaactggt	8	8	10	15	2	0	0	0	0	0	0	2	2	1	2	4	4	1	2	4	4	2	2	rs76774128		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:55039411C>G	ENST00000370862.3	+	1	362	c.26C>G	c.(25-27)tCc>tGc	p.S9C		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	9					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)	p.P11fs*11(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TTGGAGGACTCCCCCCCTTGT	0.567																																					p.S9C		.											.	HCRTR2-525	1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)	c.C26G						.						101	96	98					6																	55039411		2203	4300	6503	SO:0001583	missense	3062	exon1			AGGACTCCCCCCC	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"GPCR / Class A : Hypocretin (orexin) receptors"	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.26C>G	6.37:g.55039411C>G	ENSP00000359899:p.Ser9Cys	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	130	47	NM_001526	0	0	0	0	0	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	37	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.922205	0.33908	.	.	ENSG00000137252	ENST00000370862	T	0.62232	0.04	4.81	3.94	0.45596	.	0.414369	0.27084	N	0.021005	T	0.30572	0.0769	L	0.36672	1.1	0.32083	N	0.592878	B	0.02656	0.0	B	0.04013	0.001	T	0.14227	-1.0480	10	0.42905	T	0.14	.	8.2548	0.31748	0.0:0.7582:0.1587:0.0831	.	9	O43614	OX2R_HUMAN	C	9	ENSP00000359899:S9C	ENSP00000359899:S9C	S	+	2	0	HCRTR2	55147370	0.019000	0.18553	1.000000	0.80357	0.907000	0.53573	0.521000	0.22893	1.246000	0.43901	-0.257000	0.10917	TCC	.		0.567	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			G	55039411	C	G	55039411	3	3	154	1	0	0	0	0	1	0	0	0	7023	855	30	4	28	4	HCRTR2	6	55039411	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	21755144	55039411	116075656	46	13888											
COL12A1	1303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	75848659	75848659	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcagtaatctttaagtttGttggggctggcacgggtcct	6	15	12	8	1	2	0	1	0	1	0	3	0	3	0	1	4	0	5	1	4	2	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:75848659G>T	ENST00000322507.8	-	28	5285	c.4976C>A	c.(4975-4977)aCa>aAa	p.T1659K	COL12A1_ENST00000345356.6_Missense_Mutation_p.T495K|COL12A1_ENST00000483888.2_Missense_Mutation_p.T1659K|COL12A1_ENST00000416123.2_Missense_Mutation_p.T1659K	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1659	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTTTAAGTTTGTTGGGGCTGG	0.403																																					p.T1659K		.											.	COL12A1-142	0			c.C4976A						.						102	102	102					6																	75848659		1847	4078	5925	SO:0001583	missense	1303	exon28			AAGTTTGTTGGGG	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens", "Fibronectin type III domain containing"	2188	protein-coding gene	gene with protein product	"collagen type XII proteoglycan"	120320	"collagen, type XII, alpha 1-like"	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4976C>A	6.37:g.75848659G>T	ENSP00000325146:p.Thr1659Lys	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	63	16	NM_004370	0	0	2	2	0	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.188|0.188	-1.055736|-1.055736	0.01965|0.01965	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|T;T;T;T	.|0.57752	.|0.38;0.38;0.38;0.38	5.95|5.95	4.98|4.98	0.66077|0.66077	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.429258	.|0.26428	.|N	.|0.024432	T|T	0.11410|0.11410	0.0278|0.0278	N|N	0.20685|0.20685	0.6|0.6	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.08055	.|0.002;0.003	T|T	0.34850|0.34850	-0.9812|-0.9812	5|10	.|0.02654	.|T	.|1	.|.	5.5016|5.5016	0.16831|0.16831	0.1314:0.0:0.661:0.2076|0.1314:0.0:0.661:0.2076	.|.	.|495;1659	.|Q99715-2;Q99715	.|.;COCA1_HUMAN	K|K	400|1659;1659;495;1659;1659	.|ENSP00000325146:T1659K;ENSP00000305147:T495K;ENSP00000412864:T1659K;ENSP00000421216:T1659K	.|ENSP00000325146:T1659K	N|T	-|-	3|2	2|0	COL12A1|COL12A1	75905379|75905379	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.021000|0.021000	0.10359|0.10359	2.434000|2.434000	0.44802|0.44802	2.827000|2.827000	0.97445|0.97445	0.650000|0.650000	0.86243|0.86243	AAC|ACA	.		0.403	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75848659	G	T	75848659	3	4	154	1	0	0	0	0	1	0	0	0	3675	1377	48	4	4371	4	COL12A1	6	75848659	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	20809248	75848659	95266408	47	13889											
RSPH3	83861	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	159398820	159398821	+	Frame_Shift_Del	DEL	TG	TG	-																															cctcgggttctggagactgaTgtgtgtcttccccatgctca																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:159398820_159398821delTG	ENST00000252655.1	-	8	1621_1622	c.1432_1433delCA	c.(1432-1434)catfs	p.H478fs	RSPH3_ENST00000367069.2_Frame_Shift_Del_p.H336fs|RSPH3_ENST00000297262.3_Frame_Shift_Del_p.H382fs|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000449822.1_Frame_Shift_Del_p.H240fs	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	478										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TGGAGACTGATGTGTGTCTTCC	0.48																																					p.478_478del		.											.	RSPH3-92	0			c.1432_1433del						.																																			SO:0001589	frameshift_variant	83861	exon8			.	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1432_1433delCA	6.37:g.159398824_159398825delTG	ENSP00000252655:p.His478fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	77	23	NM_031924	0	0	0	0	0	Q96LQ5|Q96LX2|Q9BX75	Frame_Shift_Del	DEL	ENST00000252655.1	37	CCDS5260.1																																																																																			.		0.48	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		-	159398821	TG	-	159398820	7	5	154	1	0	1	0	1	0	0	0	0	13737	1464	51	0	253	0	RSPH3	6	159398820	Frame_Shift_Del	DEL	TG	TCGA-P4-A5E7-01A-31D-A28G-10	83550161	159398820	11716247	48	13890											
FOXK1	221937	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	4794196	4794196	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggcagcagagtttgcagcaAaggccgcgtcggagcagcag	10	5	16	10	3	0	1	0	0	0	1	1	2	0	2	1	3	5	7	1	3	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:4794196A>C	ENST00000328914.4	+	3	853	c.853A>C	c.(853-855)Aag>Cag	p.K285Q	FOXK1_ENST00000446823.1_Missense_Mutation_p.K122Q	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTTTGCAGCAAAGGCCGCGTC	0.662																																					p.K285Q													.	FOXK1-516	0			c.A853C						.						63	51	55					7																	4794196		2203	4300	6503	SO:0001583	missense	221937	exon3			GCAGCAAAGGCCG	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.853A>C	7.37:g.4794196A>C	ENSP00000328720:p.Lys285Gln	Somatic	42	1		WXS	Illumina HiSeq	Phase_I	109	58	NM_001037165	0	0	2	6	4		Missense_Mutation	SNP	ENST00000328914.4	37	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.336663	0.60963	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.95918	-3.51;-3.85	5.23	5.23	0.72850	.	0.049490	0.85682	D	0.000000	D	0.88680	0.6502	L	0.29908	0.895	0.45342	D	0.998338	P;B;B	0.38922	0.651;0.053;0.045	B;B;B	0.30495	0.116;0.053;0.02	D	0.86192	0.1613	10	0.17832	T	0.49	.	8.9324	0.35680	0.9174:0.0:0.0826:0.0	.	285;168;122	P85037;F5H8G8;P85037-2	FOXK1_HUMAN;.;.	Q	122;49;285;168	ENSP00000394442:K122Q;ENSP00000328720:K285Q	ENSP00000328720:K285Q	K	+	1	0	FOXK1	4760722	1.000000	0.71417	0.901000	0.35422	0.980000	0.70556	7.413000	0.80104	1.977000	0.57605	0.528000	0.53228	AAG	.		0.662	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			C	4794196	A	C	4794196	3	2	154	1	0	0	0	0	1	0	0	0	6033	15	1	5	863	5	FOXK1	7	4794196	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		4794196	154344467	49	13891											
THSD7A	221981	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	11486930	11486931	+	Frame_Shift_Ins	INS	-	-	T																															aaaacttggaccagctggtcINSaattgacagtcatcctggca																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:11486930_11486931insT	ENST00000423059.4	-	12	2977_2978	c.2726_2727insA	c.(2725-2727)ttgfs	p.L909fs	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	909	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		ACCAGCTGGTCAATTGACAGTC	0.53										HNSCC(18;0.044)																											p.L909fs		.											.	THSD7A-71	0			c.2727_2728insA						.																																			SO:0001589	frameshift_variant	221981	exon12			.		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2726_2727insA	7.37:g.11486930_11486931insT	ENSP00000406482:p.Leu909fs	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	167	84	NM_015204	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000423059.4	37	CCDS47543.1																																																																																			.		0.53	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11486931	-	T	11486930	7	5	154	1	0	1	1	0	0	0	0	0	15911	825	29	0	2310	0	THSD7A	7	11486930	Frame_Shift_Ins	INS	-	TCGA-P4-A5E7-01A-31D-A28G-10	6692734	11486930	147651733	50	13892											
AHR	196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	17375399	17375399	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gattatatcattgtaactcaGagaccactaacgtaagcaca	16	10	6	9	1	2	1	2	0	0	1	2	3	2	1	1	0	3	3	1	0	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:17375399G>C	ENST00000242057.4	+	9	1792	c.1149G>C	c.(1147-1149)caG>caC	p.Q383H	AHR_ENST00000492120.1_3'UTR	NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	383	PAC.				apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q383H(2)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TTGTAACTCAGAGACCACTAA	0.348																																					p.Q383H		.											.	AHR-227	2	Substitution - Missense(2)	lung(2)	c.G1149C						.						71	63	66					7																	17375399		2202	4300	6502	SO:0001583	missense	196	exon9			AACTCAGAGACCA	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1149G>C	7.37:g.17375399G>C	ENSP00000242057:p.Gln383His	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	71	40	NM_001621	0	0	0	0	0	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930150	0.52759	.	.	ENSG00000106546	ENST00000242057	T	0.05447	3.44	5.98	-1.41	0.08941	.	0.000000	0.85682	D	0.000000	T	0.06917	0.0176	L	0.43152	1.355	0.44798	D	0.997802	B	0.28128	0.201	B	0.31390	0.129	T	0.22277	-1.0221	10	0.62326	D	0.03	.	12.8346	0.57765	0.6126:0.0:0.3874:0.0	.	383	P35869	AHR_HUMAN	H	383	ENSP00000242057:Q383H	ENSP00000242057:Q383H	Q	+	3	2	AHR	17341924	0.995000	0.38212	0.977000	0.42913	0.859000	0.49053	0.361000	0.20267	-0.292000	0.08999	0.591000	0.81541	CAG	.		0.348	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		C	17375399	G	C	17375399	3	2	154	1	0	0	0	0	1	0	0	0	416	933	33	4	1183	4	AHR	7	17375399	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	5888469	17375399	141763264	51	13893											
AUTS2	26053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	69364300	69364300	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacttaagcctcaggaacGtgtggagaaacgccagacgc	13	5	12	11	3	1	2	1	0	0	2	1	4	1	3	2	2	4	1	2	2	3	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:69364300G>A	ENST00000342771.4	+	2	659	c.338G>A	c.(337-339)cGt>cAt	p.R113H	AUTS2_ENST00000403018.2_Missense_Mutation_p.R113H|AUTS2_ENST00000406775.2_Missense_Mutation_p.R113H	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	113								p.R113L(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CCTCAGGAACGTGTGGAGAAA	0.473																																					p.R113H		.											.	AUTS2-92	1	Substitution - Missense(1)	lung(1)	c.G338A						.						86	79	81					7																	69364300		2203	4300	6503	SO:0001583	missense	26053	exon2			AGGAACGTGTGGA	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.338G>A	7.37:g.69364300G>A	ENSP00000344087:p.Arg113His	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	130	22	NM_001127231	0	0	0	0	0	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345953	0.82022	.	.	ENSG00000158321	ENST00000406775;ENST00000342771;ENST00000403018	T;T	0.39787	1.06;1.08	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000019	T	0.56187	0.1968	L	0.46157	1.445	0.23872	N	0.9966	D;D;D	0.89917	0.997;0.994;1.0	P;P;D	0.69824	0.862;0.754;0.966	T	0.48980	-0.8986	9	.	.	.	-11.4592	14.7871	0.69810	0.0:0.2577:0.7423:0.0	.	113;113;113	Q8WXX7-2;Q8WXX7;Q6PJU5	.;AUTS2_HUMAN;.	H	113	ENSP00000385263:R113H;ENSP00000344087:R113H	.	R	+	2	0	AUTS2	69002236	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.796000	0.62496	2.941000	0.99782	0.655000	0.94253	CGT	.		0.473	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	69364300	G	A	69364300	3	1	154	1	0	0	0	0	1	0	0	0	1226	1145	40	1	344	1	AUTS2	7	69364300	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	51988901	69364300	89774363	52	13894											
BAZ1B	9031	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	72873963	72873963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttttgcttgggagccatgAagccttggagaaatttcttt	8	16	10	7	0	2	2	0	1	2	1	2	4	2	3	2	2	3	1	2	2	2	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:72873963A>G	ENST00000339594.4	-	13	3673	c.3335T>C	c.(3334-3336)tTc>tCc	p.F1112S	BAZ1B_ENST00000404251.1_Missense_Mutation_p.F1112S	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1112					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GGGAGCCATGAAGCCTTGGAG	0.398																																					p.F1112S	Esophageal Squamous(112;1167 1561 21085 43672 48228)	.											.	BAZ1B-159	0			c.T3335C						.						146	140	142					7																	72873963		2203	4300	6503	SO:0001583	missense	9031	exon13			GCCATGAAGCCTT	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"Zinc fingers, PHD-type"	961	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 9", "Williams-Beuren syndrome chromosome region 10", "transcription factor WSTF"	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.3335T>C	7.37:g.72873963A>G	ENSP00000342434:p.Phe1112Ser	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	70	43	NM_032408	0	0	23	96	73	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.902860	0.92035	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.59364	0.27;0.27	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.64305	0.2586	L	0.32530	0.975	0.58432	D	0.999999	D	0.71674	0.998	D	0.71656	0.974	T	0.59963	-0.7355	10	0.22109	T	0.4	-20.6332	14.9627	0.71169	1.0:0.0:0.0:0.0	.	1112	Q9UIG0	BAZ1B_HUMAN	S	1112	ENSP00000342434:F1112S;ENSP00000385442:F1112S	ENSP00000342434:F1112S	F	-	2	0	BAZ1B	72511899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.697000	0.91307	2.125000	0.65367	0.533000	0.62120	TTC	.		0.398	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		G	72873963	A	G	72873963	3	3	154	1	0	0	0	0	1	0	0	0	1331	246	9	3	1144	3	BAZ1B	7	72873963	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	3509663	72873963	86264700	53	13895											
CUX1	1523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	101882763	101882763	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggaggcgctgaaacgagcGtatcagcaaaagccataccc	15	4	11	11	3	1	1	1	1	0	0	1	3	1	2	2	2	5	3	2	2	6	2	rs140169027		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:101882763G>A	ENST00000292535.7	+	23	3824	c.3786G>A	c.(3784-3786)gcG>gcA	p.A1262A	CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Silent_p.A1273A|CUX1_ENST00000556210.1_Silent_p.A1104A|CUX1_ENST00000549414.2_Silent_p.A1240A|CUX1_ENST00000550008.2_Silent_p.A1206A|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000546411.2_Silent_p.A1160A|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000547394.2_Intron|AC005088.1_ENST00000580604.1_RNA	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1262					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TGAAACGAGCGTATCAGCAAA	0.597																																					p.A1273A		.											.	CUX1-160	0			c.G3819A						.	G	,,,,,,	0,4406		0,0,2203	113	109	110		3819,,,,,,3786	-9.8	0	7	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,	1273/1517,,,,,,1262/1506	101882763	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1523	exon23			ACGAGCGTATCAG	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"Homeoboxes / CUT class"	2557	protein-coding gene	gene with protein product	"golgi integral membrane protein 6"	116896	"cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)"	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.3786G>A	7.37:g.101882763G>A		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	158	98	NM_001202543	0	0	2	4	2	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																			G|1.000;A|0.000		0.597	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101882763	G	A	101882763	2	1	154	1	0	0	0	0	0	0	0	1	4070	1132	40	1		1	CUX1	7	101882763	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	29008800	101882763	57255900	54	13896											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	151845991	151845991	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctgcaatcttcaaaccCaccatggacagctcttagcc	10	8	7	16	1	3	0	1	0	2	0	3	1	3	1	4	2	4	2	4	2	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:151845991C>A	ENST00000262189.6	-	52	13239	c.13021G>T	c.(13021-13023)Ggg>Tgg	p.G4341W	KMT2C_ENST00000355193.2_Missense_Mutation_p.G4398W	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4341					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TCTTCAAACCCACCATGGACA	0.493																																					p.G4341W		.											.	MLL3-1398	0			c.G13021T						.						63	59	60					7																	151845991		2203	4300	6503	SO:0001583	missense	58508	exon52			CAAACCCACCATG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13021G>T	7.37:g.151845991C>A	ENSP00000262189:p.Gly4341Trp	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	97	23	NM_170606	0	0	10	18	8	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.63|13.63	2.295838|2.295838	0.40594|0.40594	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.88975|.	-1.77;-1.77;-2.45|.	5.4|5.4	4.52|4.52	0.55395|0.55395	.|.	0.152286|.	0.29892|.	U|.	0.010923|.	T|T	0.64670|0.64670	0.2619|0.2619	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D;D|.	0.69078|.	0.997;0.997;0.997|.	P;D;D|.	0.68483|.	0.907;0.958;0.958|.	T|T	0.63637|0.63637	-0.6592|-0.6592	10|5	0.49607|.	T|.	0.09|.	.|.	10.7105|10.7105	0.45980|0.45980	0.0:0.8351:0.0:0.1649|0.0:0.8351:0.0:0.1649	.|.	4341;3459;4398|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	W|L	4341;4398;958|1901	ENSP00000262189:G4341W;ENSP00000347325:G4398W;ENSP00000410411:G958W|.	ENSP00000262189:G4341W|.	G|W	-|-	1|2	0|0	MLL3|MLL3	151476924|151476924	0.007000|0.007000	0.16637|0.16637	0.015000|0.015000	0.15790|0.15790	0.970000|0.970000	0.65996|0.65996	1.934000|1.934000	0.40163|0.40163	1.273000|1.273000	0.44346|0.44346	0.650000|0.650000	0.86243|0.86243	GGG|TGG	.		0.493	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151845991	C	A	151845991	3	1	154	1	0	0	0	0	1	0	0	0	9647	594	21	4	1746	4	MLL3	7	151845991	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	49963228	151845991	7292672	55	13897											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	151873882	151873883	+	Frame_Shift_Del	DEL	TT	TT	-																															atttgcactggggccagcagTttctcgattggttcttttct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:151873882_151873883delTT	ENST00000262189.6	-	38	8873_8874	c.8655_8656delAA	c.(8653-8658)gaaactfs	p.ET2885fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.ET2885fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2885					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GGGCCAGCAGTTTCTCGATTGG	0.441																																					p.2885_2886del		.											.	MLL3-1398	0			c.8655_8656del						.																																			SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8655_8656delAA	7.37:g.151873882_151873883delTT	ENSP00000262189:p.Glu2885fs	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	164	98	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.441	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151873883	TT	-	151873882	7	5	154	1	0	1	0	1	0	0	0	0	9647	1725	60	0	6167	0	MLL3	7	151873882	Frame_Shift_Del	DEL	TT	TCGA-P4-A5E7-01A-31D-A28G-10	27891	151873882	7264781	56	13898											
VDAC3	7419	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	42259309	42259309	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgtttgtttattgcagaaaGaagagtgggaaattgaaggc	13	13	13	2	0	0	4	0	1	0	3	0	5	0	5	0	2	1	3	0	2	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr8:42259309G>C	ENST00000022615.4	+	7	395	c.327G>C	c.(325-327)aaG>aaC	p.K109N	VDAC3_ENST00000521158.1_Missense_Mutation_p.K110N|VDAC3_ENST00000522572.1_Missense_Mutation_p.K110N|VDAC3_ENST00000392935.3_Missense_Mutation_p.K110N			Q9Y277	VDAC3_HUMAN	voltage-dependent anion channel 3	109					adenine transport (GO:0015853)	extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)	ATTGCAGAAAGAAGAGTGGGA	0.378																																					p.K110N		.											.	VDAC3-91	0			c.G330C						.						100	100	100					8																	42259309		2203	4300	6503	SO:0001583	missense	7419	exon7			CAGAAAGAAGAGT	AF038962	CCDS6131.1, CCDS47850.1	8p11.21	2011-11-15			ENSG00000078668	ENSG00000078668		"Voltage-dependent anion channels"	12674	protein-coding gene	gene with protein product		610029				9653160, 9781040	Standard	NM_001135694		Approved	HD-VDAC3	uc003xpc.3	Q9Y277	OTTHUMG00000164168	ENST00000022615.4:c.327G>C	8.37:g.42259309G>C	ENSP00000022615:p.Lys109Asn	Somatic	64	0		WXS	Illumina HiSeq	Phase_I	72	22	NM_001135694	0	0	0	0	0	Q9UIS0	Missense_Mutation	SNP	ENST00000022615.4	37	CCDS6131.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.761925	0.69763	.	.	ENSG00000078668	ENST00000518563;ENST00000392935;ENST00000520115;ENST00000522069;ENST00000522572;ENST00000521158;ENST00000022615	T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.73962	2.25	0.80722	D	1	D	0.67145	0.996	D	0.70935	0.971	T	0.61936	-0.6960	10	0.40728	T	0.16	-12.3041	17.6115	0.88055	0.0:0.0:1.0:0.0	.	109	Q9Y277	VDAC3_HUMAN	N	77;110;109;109;110;110;109	ENSP00000428977:K77N;ENSP00000442811:K110N;ENSP00000428519:K109N;ENSP00000429006:K109N;ENSP00000428029:K110N;ENSP00000428845:K110N;ENSP00000022615:K109N	ENSP00000022615:K109N	K	+	3	2	VDAC3	42378466	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.582000	0.74049	2.832000	0.97577	0.650000	0.86243	AAG	.		0.378	VDAC3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377574.1			C	42259309	G	C	42259309	3	2	154	1	0	0	0	0	1	0	0	0	17181	933	33	4	348	4	VDAC3	8	42259309	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		42259309	104104713	57	13899											
SLC7A13	157724	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	87235298	87235298	+	Frame_Shift_Del	DEL	T	T	-																															ggtaacgcagtaaatatgcaTttgggaattgttgttctggg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr8:87235298delT	ENST00000297524.3	-	2	823	c.720delA	c.(718-720)aaafs	p.K240fs	SLC7A13_ENST00000520624.1_5'UTR|SLC7A13_ENST00000419776.2_Frame_Shift_Del_p.K231fs	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	240						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						TAAATATGCATTTGGGAATTG	0.363																																					p.K240fs		.											.	SLC7A13-90	0			c.720delA						.						147	152	150					8																	87235298		2203	4300	6503	SO:0001589	frameshift_variant	157724	exon2			.	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"Solute carriers"	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.720delA	8.37:g.87235298delT	ENSP00000297524:p.Lys240fs	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	55	16	NM_138817	0	0	0	0	0	Q05C37|Q08AH9|Q96N84	Frame_Shift_Del	DEL	ENST00000297524.3	37	CCDS34917.1																																																																																			.		0.363	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		-	87235298	T	-	87235298	7	5	154	1	0	1	0	1	0	0	0	0	14727	1490	52	0	704	0	SLC7A13	8	87235298	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	44975989	87235298	59128724	58	13900											
KCNS2	3788	bcgsc.ca	37	chr8	99440470	99440470	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctgcatttctatcacaccgGcaagcttcacgtcatggctg	8	11	9	13	2	4	0	3	0	1	0	4	0	4	0	1	2	2	5	1	2	2	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr8:99440470G>A	ENST00000287042.4	+	2	613	c.263G>A	c.(262-264)gGc>gAc	p.G88D	KCNS2_ENST00000521839.1_Missense_Mutation_p.G88D	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	88					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.G88D(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TATCACACCGGCAAGCTTCAC	0.542																																					p.G88D	Pancreas(138;844 2489 9202 24627)												.	KCNS2-91	1	Substitution - Missense(1)	lung(1)	c.G263A						.						135	109	118					8																	99440470		2203	4300	6503	SO:0001583	missense	3788	exon2			ACACCGGCAAGCT	AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.263G>A	8.37:g.99440470G>A	ENSP00000287042:p.Gly88Asp	Somatic	91	2		WXS	Illumina HiSeq	Phase_1	105	36	NM_020697	0	0	0	0	0	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376631	0.82682	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	T;T	0.55930	0.49;0.49	5.41	5.41	0.78517	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.055844	0.64402	D	0.000001	T	0.80864	0.4705	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85918	0.1444	10	0.87932	D	0	.	19.1973	0.93695	0.0:0.0:1.0:0.0	.	88	Q9ULS6	KCNS2_HUMAN	D	88	ENSP00000287042:G88D;ENSP00000430712:G88D	ENSP00000287042:G88D	G	+	2	0	KCNS2	99509646	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.527000	0.85204	0.563000	0.77884	GGC	.		0.542	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		A	99440470	G	A	99440470	3	1	154	1	0	0	0	0	1	0	0	0	8110	1203	42	2	265	2	KCNS2	8	99440470	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	12205172	99440470	46923552	59	13901											
KIFC2	90990	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	145694989	145694989	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggcgccatcgtcgattcCgcctagactgggtcttccct	4	10	13	14	4	1	1	0	0	1	1	5	2	3	1	4	3	0	0	4	3	1	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr8:145694989C>A	ENST00000301332.2	+	12	1716	c.1339C>A	c.(1339-1341)Cgc>Agc	p.R447S	KIFC2_ENST00000301331.5_Missense_Mutation_p.R195S	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	447	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			TCGTCGATTCCGCCTAGACTG	0.627																																					p.R447S													.	KIFC2-92	0			c.C1339A						.						54	52	52					8																	145694989		2203	4300	6503	SO:0001583	missense	90990	exon12			CGATTCCGCCTAG	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"Kinesins"	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.1339C>A	8.37:g.145694989C>A	ENSP00000301332:p.Arg447Ser	Somatic	42	1		WXS	Illumina HiSeq	Phase_I	49	22	NM_145754	0	0	10	23	13	E9PHB2|Q96NN6	Missense_Mutation	SNP	ENST00000301332.2	37	CCDS6427.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.86|15.86	2.956735|2.956735	0.53293|0.53293	.|.	.|.	ENSG00000167702|ENSG00000167702	ENST00000528415|ENST00000301332;ENST00000301331	.|T;T	.|0.74002	.|-0.8;-0.8	4.89|4.89	2.09|2.09	0.27110|0.27110	.|Kinesin, motor domain (4);	.|0.254051	.|0.20863	.|N	.|0.084308	T|T	0.43964|0.43964	0.1271|0.1271	N|N	0.04090|0.04090	-0.28|-0.28	0.25734|0.25734	N|N	0.985236|0.985236	.|B	.|0.17268	.|0.021	.|B	.|0.18871	.|0.023	T|T	0.22836|0.22836	-1.0205|-1.0205	5|10	.|0.11794	.|T	.|0.64	-4.4523|-4.4523	4.0973|4.0973	0.09996|0.09996	0.0:0.5439:0.1773:0.2788|0.0:0.5439:0.1773:0.2788	.|.	.|447	.|Q96AC6	.|KIFC2_HUMAN	Q|S	267|447;195	.|ENSP00000301332:R447S;ENSP00000301331:R195S	.|ENSP00000301331:R195S	P|R	+|+	2|1	0|0	KIFC2|KIFC2	145665797|145665797	0.995000|0.995000	0.38212|0.38212	0.990000|0.990000	0.47175|0.47175	0.988000|0.988000	0.76386|0.76386	1.369000|1.369000	0.34227|0.34227	0.481000|0.481000	0.27557|0.27557	0.591000|0.591000	0.81541|0.81541	CCG|CGC	.		0.627	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		A	145694989	C	A	145694989	3	1	154	1	0	0	0	0	1	0	0	0	8334	652	23	4	1385	4	KIFC2	8	145694989	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	46254519	145694989	669033	60	13902											
LINGO2	158038	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	27950499	27950499	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggtccaagattttggtttcGatgggaatgccctctgggat	8	13	13	7	1	1	1	0	0	1	1	3	4	2	3	2	4	1	1	2	4	2	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr9:27950499G>A	ENST00000379992.2	-	6	620	c.171C>T	c.(169-171)atC>atT	p.I57I	LINGO2_ENST00000308675.3_Silent_p.I57I	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	57	LRRNT.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		TTTTGGTTTCGATGGGAATGC	0.488																																					p.I57I													.	LINGO2-516	0			c.C171T						.						171	173	172					9																	27950499		2203	4300	6503	SO:0001819	synonymous_variant	158038	exon7			GGTTTCGATGGGA	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"Immunoglobulin superfamily / I-set domain containing"	21207	protein-coding gene	gene with protein product		609793	"leucine rich repeat neuronal 6C"	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.171C>T	9.37:g.27950499G>A		Somatic	210	1		WXS	Illumina HiSeq	Phase_I	184	54	NM_001258282	0	0	0	1	1	A8K4K7|B2RPM5|Q6ZMD0	Silent	SNP	ENST00000379992.2	37	CCDS6524.1																																																																																			.		0.488	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570		A	27950499	G	A	27950499	2	1	154	1	0	0	0	0	0	0	0	1	8838	1048	37	1		1	LINGO2	9	27950499	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		27950499	113262932	61	13903											
CEP78	84131	broad.mit.edu;bcgsc.ca	37	chr9	80856624	80856624	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cattttagttatttgtcaagGtataaagagctctatcactc	12	16	6	7	0	3	1	2	0	1	1	4	1	3	1	0	1	1	3	0	1	7	7			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr9:80856624G>T	ENST00000424347.2	+	4	801	c.512G>T	c.(511-513)gGt>gTt	p.G171V	CEP78_ENST00000376597.4_Missense_Mutation_p.G171V|CEP78_ENST00000376598.2_Missense_Mutation_p.G171V|CEP78_ENST00000415759.2_Missense_Mutation_p.G171V|CEP78_ENST00000277082.5_Missense_Mutation_p.G171V			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	171					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						ATTTGTCAAGGTATAAAGAGC	0.343																																					p.G171V													.	CEP78-69	0			c.G512T						.						107	106	106					9																	80856624		1871	4098	5969	SO:0001583	missense	84131	exon4			GTCAAGGTATAAA	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 81"	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.512G>T	9.37:g.80856624G>T	ENSP00000411284:p.Gly171Val	Somatic	90	2		WXS	Illumina HiSeq	Phase_I	87	37	NM_001098802	0	0	0	0	0	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Missense_Mutation	SNP	ENST00000424347.2	37		.	.	.	.	.	.	.	.	.	.	g	14.78	2.638860	0.47153	.	.	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56	5.47	2.5	0.30297	.	0.389211	0.24111	N	0.041443	T	0.38348	0.1037	N	0.14661	0.345	0.51012	D	0.999906	B;P;P;B	0.52316	0.172;0.919;0.952;0.178	B;B;P;B	0.46543	0.05;0.321;0.52;0.035	T	0.26121	-1.0112	10	0.56958	D	0.05	-16.8963	10.0132	0.41999	0.0729:0.256:0.6711:0.0	.	84;171;171;171	B7Z8H9;E9PHX5;Q5JTW2-2;Q5JTW2	.;.;.;CEP78_HUMAN	V	171	ENSP00000411284:G171V;ENSP00000399286:G171V;ENSP00000365782:G171V;ENSP00000277082:G171V;ENSP00000365783:G171V	ENSP00000277082:G171V	G	+	2	0	CEP78	80046444	1.000000	0.71417	0.987000	0.45799	0.969000	0.65631	4.855000	0.62925	0.627000	0.30340	0.645000	0.84053	GGT	.		0.343	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991		T	80856624	G	T	80856624	3	4	154	1	0	0	0	0	1	0	0	0	3268	1261	44	4	526	4	CEP78	9	80856624	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	52906125	80856624	60356807	62	13904											
KIAA0368	23392	broad.mit.edu	37	chr9	114125936	114125936	+	Frame_Shift_Del	DEL	T	T	-																															tcacagatgagtaggtcttaTtttctaaaaagaaatatcat																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr9:114125936delT	ENST00000338205.5	-	48	5531	c.5312delA	c.(5311-5313)aatfs	p.N1771fs	KIAA0368_ENST00000259335.4_Frame_Shift_Del_p.N1949fs|KIAA0368_ENST00000465499.1_5'Flank|KIAA0368_ENST00000374378.3_Intron			Q5VYK3	ECM29_HUMAN	KIAA0368	1777					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GTAGGTCTTATTTTCTAAAAA	0.358																																					p.N1949fs													.	KIAA0368-68	0			c.5846delA						.						64	62	63					9																	114125936		1812	4070	5882	SO:0001589	frameshift_variant	23392	exon50			GTCTTATTTTCTA	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"ECM29 homolog (S. cerevisiae)"					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.5312delA	9.37:g.114125936delT	ENSP00000339889:p.Asn1771fs	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	11	4	NM_001080398	0	0	0	0	0	O15074|Q8WU82	Frame_Shift_Del	DEL	ENST00000338205.5	37																																																																																				.		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		-	114125936	T	-	114125936	7	5	154	1	0	1	0	1	0	0	0	0	8192	1493	52	0	215	0	KIAA0368	9	114125936	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	33269312	114125936	27087495	63	13905											
CRB2	286204	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	126125164	126125164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacggtgccttcagagcccCccagtgcctgtgcctcagac	6	7	12	16	1	2	2	2	0	0	2	2	3	2	3	6	2	4	0	6	2	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr9:126125164C>T	ENST00000373631.3	+	2	116	c.115C>T	c.(115-117)Ccc>Tcc	p.P39S	CRB2_ENST00000359999.3_Missense_Mutation_p.P39S	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	39					cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						TTCAGAGCCCCCCAGTGCCTG	0.652																																					p.P39S													.	CRB2-91	0			c.C115T						.						53	59	57					9																	126125164		2202	4294	6496	SO:0001583	missense	286204	exon2			GAGCCCCCCAGTG	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"crumbs homolog 2 (Drosophila)"			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.115C>T	9.37:g.126125164C>T	ENSP00000362734:p.Pro39Ser	Somatic	61	1		WXS	Illumina HiSeq	Phase_I	75	27	NM_173689	0	0	0	0	0	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	CCDS6852.2	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297123	0.60086	.	.	ENSG00000148204	ENST00000359999;ENST00000373631	D;D	0.85556	-2.0;-1.87	4.7	2.76	0.32466	.	1.331010	0.05353	N	0.532203	T	0.72293	0.3442	N	0.11064	0.09	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.58434	-0.7637	10	0.25106	T	0.35	.	8.3197	0.32121	0.0:0.7535:0.1563:0.0903	.	39;39	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	S	39	ENSP00000353092:P39S;ENSP00000362734:P39S	ENSP00000353092:P39S	P	+	1	0	CRB2	125164985	0.036000	0.19791	0.005000	0.12908	0.812000	0.45895	2.227000	0.42972	1.208000	0.43306	0.448000	0.29417	CCC	.		0.652	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689		T	126125164	C	T	126125164	3	4	154	1	0	0	0	0	1	0	0	0	3855	623	22	2	121	2	CRB2	9	126125164	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	11999228	126125164	15088267	64	13906											
FIBCD1	84929	hgsc.bcm.edu	37	chr9	133813948	133813948	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgtcgcgcggccggtccTcaagttgggcagcgccgccc	3	7	15	16	6	1	0	1	0	0	0	3	0	2	0	4	3	1	3	4	3	1	2	rs199804534	byFrequency	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr9:133813948T>C	ENST00000372338.4	-	1	289	c.47A>G	c.(46-48)gAg>gGg	p.E16G	RP11-83J21.3_ENST00000421067.1_RNA|FIBCD1_ENST00000253018.4_5'UTR|FIBCD1_ENST00000448616.1_Missense_Mutation_p.E16G|FIBCD1_ENST00000486250.1_5'UTR|FIBCD1_ENST00000372337.2_5'Flank	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	16						integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CGGCCGGTCCTCAAGTTGGGC	0.771													T|||	2	0.000399361	0	0	5008	,	,		7809	0		0.002	False		,,,				2504	0				p.E16G		.											.	FIBCD1-90	0			c.A47G						.	T	GLY/GLU,GLY/GLU	0,3824		0,0,1912	5	5	5		47,47	4	1	9		5	11,7363		0,11,3676	yes	missense,missense	FIBCD1	NM_001145106.1,NM_032843.4	98,98	0,11,5588	CC,CT,TT		0.1492,0.0,0.0982	probably-damaging,probably-damaging	16/462,16/462	133813948	11,11187	1912	3687	5599	SO:0001583	missense	84929	exon2			CGGTCCTCAAGTT	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"Fibrinogen C domain containing"	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.47A>G	9.37:g.133813948T>C	ENSP00000361413:p.Glu16Gly	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	7	NM_001145106	0	0	0	0	0	A3KFK0|Q6UXK6|Q96SJ7	Missense_Mutation	SNP	ENST00000372338.4	37	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094138	0.76870	0.0	0.001492	ENSG00000130720	ENST00000448616;ENST00000454493;ENST00000372338;ENST00000451466	T;T;T	0.55413	0.52;0.52;1.07	4.01	4.01	0.46588	.	0.145716	0.45606	D	0.000357	T	0.50188	0.1601	L	0.32530	0.975	0.41099	D	0.985659	D;D	0.61080	0.989;0.989	P;P	0.52031	0.688;0.688	T	0.54655	-0.8261	10	0.72032	D	0.01	.	10.366	0.44024	0.0:0.0:0.0:1.0	.	16;16	A8K8X4;Q8N539	.;FBCD1_HUMAN	G	16	ENSP00000414501:E16G;ENSP00000361413:E16G;ENSP00000393894:E16G	ENSP00000361413:E16G	E	-	2	0	FIBCD1	132803769	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.841000	0.55850	1.460000	0.47911	0.358000	0.22013	GAG	.		0.771	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843		C	133813948	T	C	133813948	3	2	154	1	0	0	0	0	1	0	0	0	5903	1551	54	3	1366	3	FIBCD1	9	133813948	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	7688784	133813948	7399483	65	13907											
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7214001	7214001	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgcagggtgacggccctccgGggccgggccgagggcacctc	4	3	18	16	5	0	1	0	1	0	0	2	2	1	1	5	6	0	2	5	6	0	0	rs370293109		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:7214001G>A	ENST00000361972.4	-	19	2361	c.2271C>T	c.(2269-2271)ccC>ccT	p.P757P	SFMBT2_ENST00000397167.1_Silent_p.P757P	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	757					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CGGCCCTCCGGGGCCGGGCCG	0.746																																					p.P757P		.											.	SFMBT2-141	0			c.C2271T						.	G	,	0,4346		0,0,2173	12	15	14		2271,2271	0.9	1	10		14	1,8505		0,1,4252	no	coding-synonymous,coding-synonymous	SFMBT2	NM_001018039.1,NM_001029880.2	,	0,1,6425	AA,AG,GG		0.0118,0.0,0.0078	,	757/895,757/895	7214001	1,12851	2173	4253	6426	SO:0001819	synonymous_variant	57713	exon19			CCTCCGGGGCCGG	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"Sterile alpha motif (SAM) domain containing"	20256	protein-coding gene	gene with protein product		615392	"Scm-related gene containing four mbt domains 2"			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2271C>T	10.37:g.7214001G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	8	6	NM_001029880	0	0	0	0	0	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																			.		0.746	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		A	7214001	G	A	7214001	2	1	154	1	0	0	0	0	0	0	0	1	14190	1219	43	2		2	SFMBT2	10	7214001	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		7214001	128320746	66	13908											
PLXDC2	84898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	20335920	20335920	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaagattcatggaatattGtccaatactcatcggcaagc	13	11	9	8	1	2	2	2	1	0	1	4	3	3	3	1	2	2	1	1	2	6	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:20335920G>T	ENST00000377252.4	+	3	1288	c.447G>T	c.(445-447)ttG>ttT	p.L149F	PLXDC2_ENST00000377238.2_3'UTR|PLXDC2_ENST00000377242.3_Intron	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	149					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						ATGGAATATTGTCCAATACTC	0.373																																					p.L149F		.											.	PLXDC2-93	0			c.G447T						.						95	93	93					10																	20335920		2203	4300	6503	SO:0001583	missense	84898	exon3			AATATTGTCCAAT	AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"tumor endothelial marker 7-related precursor"	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.447G>T	10.37:g.20335920G>T	ENSP00000366460:p.Leu149Phe	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	58	5	NM_032812	0	0	16	22	6	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294191	0.60086	.	.	ENSG00000120594	ENST00000377252;ENST00000377238;ENST00000536022	T	0.78364	-1.17	5.61	0.195	0.15151	.	0.000000	0.85682	D	0.000000	D	0.82499	0.5050	M	0.79343	2.45	0.58432	D	0.999999	D	0.89917	1.0	D	0.71414	0.973	T	0.77335	-0.2626	10	0.87932	D	0	.	2.1328	0.03754	0.1312:0.2504:0.2267:0.3917	.	149	Q6UX71	PXDC2_HUMAN	F	149;12;135	ENSP00000366460:L149F	ENSP00000366446:L12F	L	+	3	2	PLXDC2	20375926	0.996000	0.38824	0.683000	0.30040	0.886000	0.51366	0.297000	0.19101	-0.233000	0.09797	-0.133000	0.14855	TTG	.		0.373	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20335920	G	T	20335920	3	4	154	1	0	0	0	0	1	0	0	0	12144	1368	48	4	457	4	PLXDC2	10	20335920	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	13121919	20335920	115198827	67	13909											
TET1	80312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	70332130	70332130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatgcaaggccttccagatTagtcaggaaggaagatgtaa	14	8	11	8	0	1	2	1	0	0	2	2	4	2	4	3	3	1	2	3	3	5	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:70332130T>C	ENST00000373644.4	+	2	244	c.35T>C	c.(34-36)tTa>tCa	p.L12S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	12					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CCTTCCAGATTAGTCAGGAAG	0.433																																					p.L12S		.											.	TET1-663	0			c.T35C						.						38	38	38					10																	70332130		2199	4299	6498	SO:0001583	missense	80312	exon2			CCAGATTAGTCAG	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.35T>C	10.37:g.70332130T>C	ENSP00000362748:p.Leu12Ser	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	85	28	NM_030625	0	0	0	0	0	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.210522	0.39102	.	.	ENSG00000138336	ENST00000373644	T	0.08458	3.09	5.24	0.299	0.15771	.	4.959980	0.00166	N	0.000012	T	0.06735	0.0172	N	0.19112	0.55	0.23501	N	0.997547	B	0.28512	0.214	B	0.21151	0.033	T	0.37502	-0.9703	10	0.28530	T	0.3	.	9.3061	0.37876	0.0:0.403:0.0:0.597	.	12	Q8NFU7	TET1_HUMAN	S	12	ENSP00000362748:L12S	ENSP00000362748:L12S	L	+	2	0	TET1	70002136	0.998000	0.40836	0.679000	0.29978	0.998000	0.95712	0.421000	0.21280	-0.188000	0.10499	0.460000	0.39030	TTA	.		0.433	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70332130	T	C	70332130	3	2	154	1	0	0	0	0	1	0	0	0	15801	1764	61	3	37	3	TET1	10	70332130	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	49996210	70332130	65202617	68	13910											
OIT3	170392	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	74692266	74692266	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaggcggcccgatccgcaTcgactgggaggactagttcg	9	6	14	12	5	0	0	0	0	0	0	3	4	1	2	2	4	1	2	2	4	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:74692266T>G	ENST00000334011.5	+	9	1840	c.1622T>G	c.(1621-1623)aTc>aGc	p.I541S		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	541						nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					CCGATCCGCATCGACTGGGAG	0.637																																					p.I541S	Colon(7;19 345 13446 17537)												.	OIT3-70	0			c.T1622G						.						53	50	51					10																	74692266		2203	4300	6503	SO:0001583	missense	170392	exon9			TCCGCATCGACTG		CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.1622T>G	10.37:g.74692266T>G	ENSP00000333900:p.Ile541Ser	Somatic	58	1		WXS	Illumina HiSeq	Phase_I	69	16	NM_152635	0	0	0	0	0	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	37	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	T	18.29	3.591915	0.66219	.	.	ENSG00000138315	ENST00000334011	D	0.84070	-1.8	6.06	6.06	0.98353	.	0.000000	0.56097	D	0.000026	D	0.90566	0.7043	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.91387	0.5132	10	0.87932	D	0	-21.1478	16.6093	0.84858	0.0:0.0:0.0:1.0	.	541	Q8WWZ8	OIT3_HUMAN	S	541	ENSP00000333900:I541S	ENSP00000333900:I541S	I	+	2	0	OIT3	74362272	1.000000	0.71417	0.984000	0.44739	0.036000	0.12997	6.791000	0.75120	2.324000	0.78689	0.533000	0.62120	ATC	.		0.637	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635		G	74692266	T	G	74692266	3	3	154	1	0	0	0	0	1	0	0	0	10875	1435	50	5	1656	5	OIT3	10	74692266	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	4360136	74692266	60842481	69	13911											
KCNMA1	3778	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	78651371	78651371	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtgtctgcggggtgctgtagCcacctctaagggcgttttcc	4	12	14	11	2	2	0	0	0	2	0	3	0	3	0	3	3	3	3	3	3	2	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:78651371C>G	ENST00000286628.8	-	26	3253	c.3254G>C	c.(3253-3255)gGc>gCc	p.G1085A	KCNMA1_ENST00000286627.5_Missense_Mutation_p.G1027A|KCNMA1_ENST00000404857.1_Missense_Mutation_p.G1068A|RP11-443A13.5_ENST00000609102.1_RNA|RP11-443A13.5_ENST00000458661.2_RNA|KCNMA1_ENST00000372443.1_Missense_Mutation_p.G1054A|KCNMA1_ENST00000404771.3_Missense_Mutation_p.G1085A|KCNMA1_ENST00000372440.1_Missense_Mutation_p.G1027A|RP11-443A13.5_ENST00000595702.1_RNA|KCNMA1_ENST00000406533.3_Missense_Mutation_p.G1089A|RP11-443A13.5_ENST00000429850.2_RNA|KCNMA1_ENST00000354353.5_Missense_Mutation_p.G1088A	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	1085					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GGTGCTGTAGCCACCTCTAAG	0.602																																					p.G1085A													.	KCNMA1-93	0			c.G3254C						.						53	51	52					10																	78651371		2203	4300	6503	SO:0001583	missense	3778	exon26			CTGTAGCCACCTC	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6284	protein-coding gene	gene with protein product	"BK channel alpha subunit"	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.3254G>C	10.37:g.78651371C>G	ENSP00000286628:p.Gly1085Ala	Somatic	65	1		WXS	Illumina HiSeq	Phase_I	45	14	NM_001161352	0	0	1	1	0	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	16.97|16.97|16.97	3.269439|3.269439|3.269439	0.59540|0.59540|0.59540	.|.|.	.|.|.	ENSG00000156113|ENSG00000156113|ENSG00000156113	ENST00000372403|ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857;ENST00000412708|ENST00000372421;ENST00000434208	.|D;D;D;D;D;D;D;D;D|.	.|0.85088|.	.|-1.87;-1.88;-1.9;-1.91;-1.84;-1.87;-1.94;-1.94;-1.88|.	5.52|5.52|5.52	5.52|5.52|5.52	0.82312|0.82312|0.82312	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.69486|0.69486|0.69486	0.3116|0.3116|0.3116	L|L|L	0.46741|0.46741|0.46741	1.465|1.465|1.465	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P;B;B;P;B;B;B;B|.	.|0.47191|.	.|0.891;0.037;0.125;0.823;0.123;0.004;0.227;0.037|.	.|P;B;B;P;B;B;B;B|.	.|0.46144|.	.|0.453;0.037;0.109;0.505;0.081;0.023;0.168;0.051|.	T|T|T	0.64905|0.64905|0.64905	-0.6297|-0.6297|-0.6297	5|10|5	.|0.49607|.	.|T|.	.|0.09|.	-14.3897|-14.3897|-14.3897	19.4341|19.4341|19.4341	0.94783|0.94783|0.94783	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|1056;1057;1068;1085;1027;838;1088;1054|.	.|Q12791-4;B7ZMF5;Q12791-2;Q12791;Q12791-5;C9JFZ9;F8WA96;Q5SVJ7|.	.|.;.;.;KCMA1_HUMAN;.;.;.;.|.	P|A|C	978|1027;964;1020;1059;1022;1054;1027;1059;1089;1088;1068;838|1015;734	.|ENSP00000361517:G1027A;ENSP00000361485:G964A;ENSP00000361514:G1020A;ENSP00000396608:G1059A;ENSP00000361520:G1054A;ENSP00000286627:G1027A;ENSP00000385552:G1089A;ENSP00000346321:G1088A;ENSP00000385806:G1068A|.	.|ENSP00000286627:G1027A|.	A|G|W	-|-|-	1|2|3	0|0|0	KCNMA1|KCNMA1|KCNMA1	78321377|78321377|78321377	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.757000|0.757000|0.757000	0.42996|0.42996|0.42996	7.487000|7.487000|7.487000	0.81328|0.81328|0.81328	2.607000|2.607000|2.607000	0.88179|0.88179|0.88179	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	GCT|GGC|TGG	.		0.602	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247		G	78651371	C	G	78651371	3	3	154	1	0	0	0	0	1	0	0	0	8094	739	26	4	497	4	KCNMA1	10	78651371	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	3959105	78651371	56883376	70	13912											
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	89717690	89717690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgacgggaagacaagttcAtgtactttgagttccctcag	11	10	10	10	2	2	2	2	1	0	1	3	4	3	3	1	1	1	3	1	1	3	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:89717690A>G	ENST00000371953.3	+	7	2072	c.715A>G	c.(715-717)Atg>Gtg	p.M239V	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	239	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R234fs*9(1)|p.K237_Y240>N(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AGACAAGTTCATGTACTTTGA	0.418		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.M239V		.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN-17735	50	Whole gene deletion(37)|Deletion - Frameshift(10)|Complex - deletion inframe(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|breast(4)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.A715G						.						153	130	138					10																	89717690		2203	4300	6503	SO:0001583	missense	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	AAGTTCATGTACT	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.715A>G	10.37:g.89717690A>G	ENSP00000361021:p.Met239Val	Somatic	163	0		WXS	Illumina HiSeq	Phase_I	171	49	NM_000314	1	0	50	87	36	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.980414	0.34942	.	.	ENSG00000171862	ENST00000371953	D	0.84660	-1.88	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.038168	0.85682	D	0.000000	T	0.73567	0.3603	N	0.13352	0.335	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.67983	-0.5529	9	.	.	.	-3.0578	14.9657	0.71193	1.0:0.0:0.0:0.0	.	239	P60484	PTEN_HUMAN	V	239	ENSP00000361021:M239V	.	M	+	1	0	PTEN	89707670	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.918000	0.92759	1.928000	0.55862	0.477000	0.44152	ATG	.		0.418	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717690	A	G	89717690	3	3	154	1	0	0	0	0	1	0	0	0	12767	217	8	3	741	3	PTEN	10	89717690	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	11066319	89717690	45817057	71	13913											
C10orf79	80217	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	105928500	105928500	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacctagggttctatctgttAccttaagagctcgacctttc	8	15	7	11	1	2	1	0	0	2	1	4	2	2	1	3	1	3	3	3	1	5	7			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:105928500A>T	ENST00000278064.2	-	21	2810		c.e21+1		WDR96_ENST00000357060.3_Splice_Site|WDR96_ENST00000428666.1_Splice_Site																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TCTATCTGTTACCTTAAGAGC	0.363																																					.													.	WDR96-95	0			c.2691+2T>A						.						140	130	134					10																	105928500		2203	4300	6503	SO:0001630	splice_region_variant	80217	exon22			TCTGTTACCTTAA																												ENST00000278064.2:c.2484+1T>A	10.37:g.105928500A>T		Somatic	32	0		WXS	Illumina HiSeq	Phase_I	22	4	NM_025145	0	0	0	0	0		Splice_Site	SNP	ENST00000278064.2	37		.	.	.	.	.	.	.	.	.	.	A	19.19	3.779896	0.70222	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000434629;ENST00000278064	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4421	0.75190	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR96	105918490	1.000000	0.71417	0.998000	0.56505	0.747000	0.42532	6.878000	0.75567	2.170000	0.68504	0.533000	0.62120	.	.		0.363	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1		Intron	T	105928500	A	T	105928500	5	4	154	1	0	0	0	0	0	0	1	0	1622	405	14	5	2376	5	C10orf79	10	105928500	Splice_Site	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	16210810	105928500	29606247	72	13914											
PDZD8	118987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	119043959	119043959	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctagtgactatagccttaGgtgagggggcttccagtctc	7	13	12	9	0	2	2	0	2	2	0	4	2	3	2	2	3	1	1	2	3	4	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:119043959G>T	ENST00000334464.5	-	5	2524	c.2285C>A	c.(2284-2286)cCt>cAt	p.P762H	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	762					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TATAGCCTTAGGTGAGGGGGC	0.403																																					p.P762H		.											.	PDZD8-90	0			c.C2285A						.						125	111	116					10																	119043959		2203	4300	6503	SO:0001583	missense	118987	exon5			GCCTTAGGTGAGG	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.2285C>A	10.37:g.119043959G>T	ENSP00000334642:p.Pro762His	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	68	23	NM_173791	0	0	10	21	11	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075899	0.76415	.	.	ENSG00000165650	ENST00000334464	D	0.87256	-2.23	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.90889	0.7137	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90836	0.4720	10	0.59425	D	0.04	-12.5235	20.4116	0.99017	0.0:0.0:1.0:0.0	.	762	Q8NEN9	PDZD8_HUMAN	H	762	ENSP00000334642:P762H	ENSP00000334642:P762H	P	-	2	0	PDZD8	119033949	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	9.869000	0.99810	2.827000	0.97445	0.655000	0.94253	CCT	.		0.403	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		T	119043959	G	T	119043959	3	4	154	1	0	0	0	0	1	0	0	0	11731	1000	35	4	1183	4	PDZD8	10	119043959	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	13115459	119043959	16490788	73	13915											
PWWP2B	170394	hgsc.bcm.edu	37	chr10	134218416	134218416	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctccgggacacgtacaagCtgtgggtgccccagccgccg	6	5	15	15	4	0	0	0	0	0	0	1	1	1	1	5	3	4	3	5	3	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:134218416C>T	ENST00000305233.5	+	2	471	c.412C>T	c.(412-414)Ctg>Ttg	p.L138L	PWWP2B_ENST00000368609.4_Silent_p.L138L	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	138	Pro-rich.									central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		CACGTACAAGCTGTGGGTGCC	0.731																																					p.L138L		.											.	PWWP2B-90	0			c.C412T						.						11	10	10					10																	134218416		1839	3661	5500	SO:0001819	synonymous_variant	170394	exon2			TACAAGCTGTGGG	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"PWWP domain containing 2"	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.412C>T	10.37:g.134218416C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	5	4	NM_001098637	0	0	3	3	0	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			.		0.731	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499		T	134218416	C	T	134218416	2	4	154	1	0	0	0	0	0	0	0	1	12878	796	28	2		2	PWWP2B	10	134218416	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	15174457	134218416	1316331	74	13916											
MUC6	4588	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	1018068	1018068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggactgctccctgtaggtGgggagtgtgtggtgaagggt	6	10	20	5	0	0	1	0	1	0	0	1	3	1	3	1	6	1	2	1	6	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:1018068G>A	ENST00000421673.2	-	31	4783	c.4733C>T	c.(4732-4734)cCa>cTa	p.P1578L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1578	Pro-rich.|Thr-rich.		P -> S (in dbSNP:rs10736904).		cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCTGTAGGTGGGGAGTGTGT	0.582																																					p.P1578L		.											.	MUC6-23	0			c.C4733T						.						259	265	263					11																	1018068		2174	4263	6437	SO:0001583	missense	4588	exon31			GTAGGTGGGGAGT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"Mucins"	7517	protein-coding gene	gene with protein product		158374	"mucin 6, gastric"			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4733C>T	11.37:g.1018068G>A	ENSP00000406861:p.Pro1578Leu	Somatic	394	0		WXS	Illumina HiSeq	Phase_I	411	70	NM_005961	0	0	0	0	0	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	9.977	1.227087	0.22542	.	.	ENSG00000184956	ENST00000421673	T	0.15603	2.41	2.31	1.29	0.21616	.	.	.	.	.	T	0.12689	0.0308	L	0.46157	1.445	0.09310	N	1	B	0.24963	0.115	B	0.19946	0.027	T	0.38520	-0.9657	9	0.10902	T	0.67	.	8.0503	0.30575	0.0:0.0:0.7368:0.2632	.	1578	Q6W4X9	MUC6_HUMAN	L	1578	ENSP00000406861:P1578L	ENSP00000406861:P1578L	P	-	2	0	MUC6	1008068	0.000000	0.05858	0.001000	0.08648	0.150000	0.21749	-0.194000	0.09559	0.226000	0.20979	0.297000	0.19635	CCA	.		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1018068	G	A	1018068	3	1	154	1	0	0	0	0	1	0	0	0	10005	1348	47	2	2598	2	MUC6	11	1018068	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		1018068	133988448	75	13917											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253980	1253980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggcgtacagctcagcgActggagggacggcgtctgca	9	5	16	11	4	2	0	1	0	1	0	2	3	2	2	0	4	4	3	0	4	2	1	rs202127660		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:1253980A>G	ENST00000529681.1	+	17	2103	c.2045A>G	c.(2044-2046)gAc>gGc	p.D682G	MUC5B_ENST00000447027.1_Missense_Mutation_p.D685G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	682					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGCTCAGCGACTGGAGGGAC	0.682																																					p.D682G		.											.	.	0			c.A2045G						.						21	24	23					11																	1253980		2116	4228	6344	SO:0001583	missense	727897	exon17			TCAGCGACTGGAG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2045A>G	11.37:g.1253980A>G	ENSP00000436812:p.Asp682Gly	Somatic	19	0		WXS	Illumina HiSeq	Phase_I	89	8	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	A	7.541	0.660740	0.14645	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76060	-0.99;-0.99	4.6	2.72	0.32119	Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.50103	0.1596	N	0.02960	-0.455	0.24874	N	0.992269	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45920	-0.9228	9	0.87932	D	0	.	8.6635	0.34108	0.2416:0.0:0.7584:0.0	.	682;1341;685	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	682;685;683;718	ENSP00000436812:D682G;ENSP00000415793:D685G	ENSP00000343037:D683G	D	+	2	0	MUC5B	1210556	0.999000	0.42202	0.632000	0.29296	0.070000	0.16714	2.607000	0.46300	0.373000	0.24621	-1.983000	0.00453	GAC	.		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1253980	A	G	1253980	3	3	154	1	0	0	0	0	1	0	0	0	10004	275	10	3	2120	3	MUC5B	11	1253980	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	235912	1253980	133752536	76	13918											
MUC5B	727897	bcgsc.ca	37	chr11	1267042	1267042	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccagcaccccggccaccAgctctacggccacgccctcc	6	3	8	24	3	1	0	0	0	1	0	2	0	2	0	9	2	3	2	9	2	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:1267042A>G	ENST00000529681.1	+	31	8990	c.8932A>G	c.(8932-8934)Agc>Ggc	p.S2978G	MUC5B_ENST00000447027.1_Missense_Mutation_p.S2981G|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2978	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCGGCCACCAGCTCTACGGC	0.607																																					p.S2978G													.	.	0			c.A8932G						.						99	124	115					11																	1267042		2045	4175	6220	SO:0001583	missense	727897	exon31			GCCACCAGCTCTA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.8932A>G	11.37:g.1267042A>G	ENSP00000436812:p.Ser2978Gly	Somatic	589	3		WXS	Illumina HiSeq	Phase_1	843	248	NM_002458	0	0	0	0	0	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	1.432	-0.569998	0.03910	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.46	3.57	-7.15	0.01521	.	.	.	.	.	T	0.13114	0.0318	L	0.53249	1.67	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.10450	0.003;0.005	T	0.33420	-0.9869	9	0.87932	D	0	.	4.0918	0.09973	0.1277:0.4665:0.2229:0.1828	.	3561;2981	A7Y9J9;E9PBJ0	.;.	G	2978;2981;2950;2938	ENSP00000436812:S2978G;ENSP00000415793:S2981G	ENSP00000343037:S2950G	S	+	1	0	MUC5B	1223618	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	1.206000	0.32321	-5.261000	0.00018	-0.449000	0.05564	AGC	.		0.607	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1267042	A	G	1267042	3	3	154	1	0	0	0	0	1	0	0	0	10004	188	7	3	9063	3	MUC5B	11	1267042	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	13062	1267042	133739474	77	13919											
AHNAK	79026	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62297916	62297916	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcaggtccacatcaggcaTggagatcttgggggccttga	9	10	13	9	0	3	2	2	1	1	1	4	3	4	2	2	5	0	1	2	5	0	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:62297916T>C	ENST00000378024.4	-	5	4247	c.3973A>G	c.(3973-3975)Atg>Gtg	p.M1325V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1325					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ACATCAGGCATGGAGATCTTG	0.507																																					p.M1325V													.	AHNAK-109	0			c.A3973G						.						178	183	181					11																	62297916		2202	4299	6501	SO:0001583	missense	79026	exon5			CAGGCATGGAGAT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.3973A>G	11.37:g.62297916T>C	ENSP00000367263:p.Met1325Val	Somatic	186	1		WXS	Illumina HiSeq	Phase_I	185	67	NM_001620	0	0	3	9	6	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	t	12.65	2.001709	0.35320	.	.	ENSG00000124942	ENST00000378024	T	0.01745	4.66	4.63	3.5	0.40072	.	0.000000	0.38111	U	0.001806	T	0.03695	0.0105	M	0.81497	2.545	0.29409	N	0.861345	B	0.24675	0.109	B	0.33042	0.157	T	0.19224	-1.0312	10	0.12766	T	0.61	.	9.8561	0.41086	0.0:0.0827:0.0:0.9173	.	1325	Q09666	AHNK_HUMAN	V	1325	ENSP00000367263:M1325V	ENSP00000367263:M1325V	M	-	1	0	AHNAK	62054492	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.831000	0.39141	0.753000	0.32945	0.515000	0.50301	ATG	.		0.507	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62297916	T	C	62297916	3	2	154	1	0	0	0	0	1	0	0	0	414	1464	51	3	13819	3	AHNAK	11	62297916	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	61030874	62297916	72708600	78	13920											
EEF1G	1937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	62334912	62334912	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacagtttcacttcgcccAagacagcccggaactggggc	10	6	10	15	2	1	1	1	0	0	1	2	2	1	2	2	3	2	1	2	3	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:62334912A>C	ENST00000329251.4	-	6	741	c.611T>G	c.(610-612)tTg>tGg	p.L204W	EEF1G_ENST00000378019.3_Missense_Mutation_p.L254W|MIR3654_ENST00000496634.2_3'UTR	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	204	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CACTTCGCCCAAGACAGCCCG	0.552																																					p.L204W		.											.	.	0			c.T611G						.						44	41	42					11																	62334912		1926	4135	6061	SO:0001583	missense	1937	exon6			TCGCCCAAGACAG	X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.611T>G	11.37:g.62334912A>C	ENSP00000331901:p.Leu204Trp	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	99	32	NM_001404	0	0	1505	2605	1100	B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Missense_Mutation	SNP	ENST00000329251.4	37	CCDS44626.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.662133	0.88251	.	.	ENSG00000254772	ENST00000329251;ENST00000378019	T;T	0.21932	1.98;1.98	4.8	4.8	0.61643	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.54159	0.1841	M	0.92459	3.31	0.53005	D	0.999968	D;P	0.89917	1.0;0.905	D;P	0.80764	0.994;0.703	T	0.65487	-0.6156	10	0.72032	D	0.01	.	12.5918	0.56447	1.0:0.0:0.0:0.0	.	254;204	B4DTG2;P26641	.;EF1G_HUMAN	W	204;254	ENSP00000331901:L204W;ENSP00000367258:L254W	ENSP00000331901:L204W	L	-	2	0	EEF1G	62091488	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.903000	0.92573	1.928000	0.55862	0.459000	0.35465	TTG	.		0.552	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1	NM_001404		C	62334912	A	C	62334912	3	2	154	1	0	0	0	0	1	0	0	0	4939	131	5	5	722	5	EEF1G	11	62334912	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	36996	62334912	72671604	79	13921											
DGAT2	84649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	75509414	75509414	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgcatcttccatggtcgaGgcctcttctcctccgacacc	6	11	7	17	2	3	0	0	0	3	0	7	2	5	0	5	2	1	1	5	2	0	2	rs145750206		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:75509414G>C	ENST00000228027.7	+	7	1212	c.952G>C	c.(952-954)Ggc>Cgc	p.G318R	RP11-535A19.1_ENST00000534354.1_RNA|DGAT2_ENST00000376262.3_Missense_Mutation_p.G275R	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	318					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					CCATGGTCGAGGCCTCTTCTC	0.582																																					p.G318R	Melanoma(35;811 1096 8354 24009 39363)	.											.	DGAT2-226	0			c.G952C						.						84	72	76					11																	75509414		2200	4293	6493	SO:0001583	missense	84649	exon7			GGTCGAGGCCTCT		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"diacylglycerol O-acyltransferase homolog 2 (mouse)"			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.952G>C	11.37:g.75509414G>C	ENSP00000228027:p.Gly318Arg	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	97	33	NM_032564	0	0	1	1	0	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Missense_Mutation	SNP	ENST00000228027.7	37	CCDS31642.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248066	0.80024	.	.	ENSG00000062282	ENST00000228027;ENST00000376262;ENST00000525612	T;T	0.18960	2.18;2.18	5.59	4.68	0.58851	.	0.090338	0.85682	D	0.000000	T	0.44498	0.1296	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;0.993	D;D	0.74674	0.984;0.955	T	0.44862	-0.9300	10	0.87932	D	0	-19.5496	9.867	0.41150	0.1582:0.0:0.8418:0.0	.	275;318	Q96PD7-2;Q96PD7	.;DGAT2_HUMAN	R	318;275;272	ENSP00000228027:G318R;ENSP00000365438:G275R	ENSP00000228027:G318R	G	+	1	0	DGAT2	75187062	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.726000	0.68515	1.501000	0.48654	0.655000	0.94253	GGC	G|0.999;A|0.001		0.582	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		C	75509414	G	C	75509414	3	2	154	1	0	0	0	0	1	0	0	0	4469	1000	35	4	978	4	DGAT2	11	75509414	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	13174502	75509414	59497102	80	13922											
KLRC3	3823	hgsc.bcm.edu;broad.mit.edu	37	chr12	10573086	10573086	+	Frame_Shift_Del	DEL	T	T	-																															tttattgcctttaggtttccTttgctgccactttgggtcct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:10573086delT	ENST00000396439.2	-	1	108	c.64delA	c.(64-66)aggfs	p.R22fs	NKG2-E_ENST00000539033.1_Intron|KLRC3_ENST00000381903.2_Frame_Shift_Del_p.R22fs|KLRC3_ENST00000381904.2_Frame_Shift_Del_p.R22fs	NM_002261.2	NP_002252.2	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C, member 3	22					cellular defense response (GO:0006968)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						TTAGGTTTCCTTTGCTGCCAC	0.438																																					p.R22fs		.											.	KLRC3-517	0			c.64delA						.						98	96	97					12																	10573086		2203	4297	6500	SO:0001589	frameshift_variant	3823	exon1			.	L14542	CCDS31744.1, CCDS41755.1	12p13	2008-08-05			ENSG00000205810	ENSG00000205810		"Killer cell lectin-like receptors"	6376	protein-coding gene	gene with protein product		602892				9598306	Standard	NM_002261		Approved	NKG2-E	uc001qyi.1	Q07444	OTTHUMG00000167149	ENST00000396439.2:c.64delA	12.37:g.10573086delT	ENSP00000379716:p.Arg22fs	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	48	13	NM_007333	0	0	0	0	0	Q8WXA4|Q96RL0|Q9UP04	Frame_Shift_Del	DEL	ENST00000396439.2	37	CCDS41755.1																																																																																			.		0.438	KLRC3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393471.1	NM_002261		-	10573086	T	-	10573086	7	5	154	1	0	1	0	1	0	0	0	0	8438	1608	56	0	782	0	KLRC3	12	10573086	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10		10573086	123278809	81	13923											
KLRC2	3823	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	10588522	10588522	+	Frame_Shift_Del	DEL	T	T	-																															tttattgcctttaggtttccTttgctgccgctttgggtcct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:10588522delT	ENST00000539033.1	-	1	78	c.64delA	c.(64-66)aggfs	p.R22fs	KLRC2_ENST00000536833.2_Intron|KLRC2_ENST00000381902.2_Frame_Shift_Del_p.R22fs|KLRC2_ENST00000381901.1_Frame_Shift_Del_p.R22fs																							TTAGGTTTCCTTTGCTGCCGC	0.438																																					p.R22fs		.											.	KLRC2-514	0			c.64delA						.						250	250	250					12																	10588522		2203	4300	6503	SO:0001589	frameshift_variant	3822	exon1			.																												ENST00000539033.1:c.64delA	12.37:g.10588522delT	ENSP00000437563:p.Arg22fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	154	34	NM_002260	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000539033.1	37																																																																																				.		0.438	NKG2-E-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000400274.1			-	10588522	T	-	10588522	7	5	154	1	0	1	0	1	0	0	0	0	8437	1608	56	0	655	0	KLRC2	12	10588522	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	15436	10588522	123263373	82	13924											
DDX11	1663	ucsc.edu	37	chr12	31244689	31244689	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atcagatgctgctgcatgcgGccactcggcaggccgcgggc	6	6	15	14	4	1	1	1	0	0	1	2	1	1	1	2	4	4	4	2	4	0	0	rs397842879		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:31244689G>A	ENST00000407793.2	+	10	1377	c.1126G>A	c.(1126-1128)Gcc>Acc	p.A376T	DDX11_ENST00000350437.4_Missense_Mutation_p.A376T|DDX11_ENST00000545668.1_Missense_Mutation_p.A376T|DDX11_ENST00000542838.1_Missense_Mutation_p.A376T|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000228264.6_Missense_Mutation_p.A350T	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	376	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GCTGCATGCGGCCACTCGGCA	0.672										Multiple Myeloma(12;0.14)																											p.A376T													.	DDX11-229	0			c.G1126A						.						26	25	26					12																	31244689		2194	4289	6483	SO:0001583	missense	1663	exon10			CATGCGGCCACTC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1126G>A	12.37:g.31244689G>A	ENSP00000384703:p.Ala376Thr	Somatic	128	20		WXS	Illumina HiSeq		344	30	NM_030653	0	0	3	7	4	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	7.984	0.751761	0.15778	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.71461	-0.57;1.0;-0.57;1.0;1.0	3.05	3.05	0.35203	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.324166	0.32703	N	0.005754	T	0.68109	0.2965	L	0.55834	1.745	0.80722	D	1	P;P;D;P;P	0.59767	0.633;0.814;0.986;0.814;0.905	P;B;P;B;B	0.49799	0.507;0.313;0.622;0.294;0.392	T	0.69300	-0.5181	10	0.56958	D	0.05	.	7.318	0.26511	0.0:0.0:0.738:0.262	.	101;350;376;376;376	Q93000;Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;.;DDX11_HUMAN;.;.	T	376;376;101;350;376;376	ENSP00000443426:A376T;ENSP00000384703:A376T;ENSP00000228264:A350T;ENSP00000440402:A376T;ENSP00000309965:A376T	ENSP00000228264:A350T	A	+	1	0	DDX11	31135956	0.935000	0.31712	0.573000	0.28510	0.048000	0.14542	1.665000	0.37449	1.535000	0.49220	0.505000	0.49811	GCC	.		0.672	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		A	31244689	G	A	31244689	3	1	154	1	0	0	0	0	1	0	0	0	4349	1203	42	2	1160	2	DDX11	12	31244689	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	20656167	31244689	102607206	83	13925											
DENND5B	160518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	31551284	31551284	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgcctttccccagccaccgCccacatgggaatctggtagg	8	8	10	15	1	1	0	0	0	1	0	2	1	2	1	6	3	2	1	6	3	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:31551284C>T	ENST00000389082.5	-	17	3345	c.3081G>A	c.(3079-3081)ggG>ggA	p.G1027G	DENND5B_ENST00000306833.6_Silent_p.G1062G|RNU6-618P_ENST00000363518.1_RNA|DENND5B_ENST00000536562.1_Silent_p.G1062G	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1027	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CCAGCCACCGCCCACATGGGA	0.453																																					p.G1027G		.											.	DENND5B-24	0			c.G3081A						.						45	41	42					12																	31551284		1778	3993	5771	SO:0001819	synonymous_variant	160518	exon17			CCACCGCCCACAT	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"DENN/MADD domain containing"	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.3081G>A	12.37:g.31551284C>T		Somatic	44	0		WXS	Illumina HiSeq	Phase_I	24	9	NM_144973	0	0	3	5	2	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	37	CCDS44857.1																																																																																			.		0.453	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		T	31551284	C	T	31551284	2	4	154	1	0	0	0	0	0	0	0	1	4448	726	26	2		2	DENND5B	12	31551284	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	306595	31551284	102300611	84	13926											
PRPH	5630	hgsc.bcm.edu	37	chr12	49689459	49689459	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcgagagctggagctgttggGccgcgagcgtgaccgggtgc	5	6	20	10	5	0	2	0	1	0	1	0	5	0	3	2	3	4	3	2	3	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:49689459G>A	ENST00000257860.4	+	1	1975	c.476G>A	c.(475-477)gGc>gAc	p.G159D	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						GAGCTGTTGGGCCGCGAGCGT	0.766																																					p.G159D		.											.	PRPH-90	0			c.G476A						.						2	3	3					12																	49689459		1611	3196	4807	SO:0001583	missense	5630	exon1			TGTTGGGCCGCGA		CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.476G>A	12.37:g.49689459G>A	ENSP00000257860:p.Gly159Asp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	7	4	NM_006262	0	0	0	0	0	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000257860.4	37	CCDS8783.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422107	0.62622	.	.	ENSG00000135406	ENST00000257860;ENST00000451891	D	0.88741	-2.42	4.51	2.61	0.31194	Filament (1);	0.000000	0.40554	N	0.001080	D	0.89022	0.6597	L	0.58669	1.825	0.46096	D	0.998869	P	0.46987	0.888	P	0.52109	0.69	D	0.84585	0.0663	10	0.18710	T	0.47	.	12.3528	0.55157	0.0:0.3262:0.6738:0.0	.	159	P41219	PERI_HUMAN	D	159;46	ENSP00000257860:G159D	ENSP00000257860:G159D	G	+	2	0	PRPH	47975726	0.835000	0.29415	0.999000	0.59377	0.608000	0.37181	1.757000	0.38400	0.501000	0.28013	0.462000	0.41574	GGC	.		0.766	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		A	49689459	G	A	49689459	3	1	154	1	0	0	0	0	1	0	0	0	12605	1203	42	2	478	2	PRPH	12	49689459	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	18138175	49689459	84162436	85	13927											
KRT2	3849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53045499	53045499	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccaccagggtatcctccaGgcccaaagccaccaggaccc	10	4	9	18	0	0	0	0	0	0	0	2	1	2	1	8	3	2	1	8	3	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:53045499G>C	ENST00000309680.3	-	1	449	c.428C>G	c.(427-429)cCt>cGt	p.P143R		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	143	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		GTATCCTCCAGGCCCAAAGCC	0.597																																					p.P143R		.											.	KRT2-92	0			c.C428G						.						82	83	83					12																	53045499		2203	4300	6503	SO:0001583	missense	3849	exon1			CCTCCAGGCCCAA		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.428C>G	12.37:g.53045499G>C	ENSP00000310861:p.Pro143Arg	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	117	39	NM_000423	0	0	0	0	0	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	37	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.938619	0.52972	.	.	ENSG00000172867	ENST00000309680	D	0.85556	-2.0	5.54	5.54	0.83059	.	.	.	.	.	D	0.92296	0.7556	M	0.83603	2.65	0.38710	D	0.953191	D	0.76494	0.999	D	0.69307	0.963	D	0.93716	0.7028	9	0.87932	D	0	.	15.3671	0.74531	0.0:0.0:1.0:0.0	.	143	P35908	K22E_HUMAN	R	143	ENSP00000310861:P143R	ENSP00000310861:P143R	P	-	2	0	KRT2	51331766	0.164000	0.22935	0.998000	0.56505	0.983000	0.72400	-0.229000	0.09098	2.791000	0.96007	0.655000	0.94253	CCT	.		0.597	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		C	53045499	G	C	53045499	3	2	154	1	0	0	0	0	1	0	0	0	8478	1000	35	4	1527	4	KRT2	12	53045499	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	3356040	53045499	80806396	86	13928											
MDM1	56890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	68696605	68696605	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcagaggatcaactgttttTataccagcagctggagaagt	12	10	12	7	0	1	2	1	0	0	2	1	4	1	3	1	3	4	4	1	3	4	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:68696605T>A	ENST00000303145.7	-	12	1853	c.1767A>T	c.(1765-1767)atA>atT	p.I589I	MDM1_ENST00000540418.1_Silent_p.I309I|MDM1_ENST00000411698.2_Silent_p.I554I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	589					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		CAACTGTTTTTATACCAGCAG	0.358																																					p.I589I		.											.	MDM1-95	0			c.A1767T						.						90	92	91					12																	68696605		2203	4300	6503	SO:0001819	synonymous_variant	56890	exon12			TGTTTTTATACCA	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1767A>T	12.37:g.68696605T>A		Somatic	37	0		WXS	Illumina HiSeq	Phase_I	27	6	NM_017440	0	0	10	10	0	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Silent	SNP	ENST00000303145.7	37	CCDS8983.1																																																																																			.		0.358	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		A	68696605	T	A	68696605	2	1	154	1	0	0	0	0	0	0	0	1	9437	1744	61	5		5	MDM1	12	68696605	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	15651106	68696605	65155290	87	13929											
BTBD11	121551	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	108035881	108035881	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcaggttcaaagcactccTctccagcaagccgacaaatg	12	8	8	13	1	3	0	2	0	1	0	5	1	4	0	3	1	3	4	3	1	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:108035881T>G	ENST00000280758.5	+	14	3383	c.2855T>G	c.(2854-2856)cTc>cGc	p.L952R	BTBD11_ENST00000490090.2_Missense_Mutation_p.L952R|BTBD11_ENST00000357167.4_Missense_Mutation_p.L489R|BTBD11_ENST00000420571.2_Missense_Mutation_p.L833R|BTBD11_ENST00000494235.2_Missense_Mutation_p.L31R	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	952	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AAAGCACTCCTCTCCAGCAAG	0.458																																					p.L952R													.	BTBD11-93	0			c.T2855G						.						149	141	144					12																	108035881		2203	4300	6503	SO:0001583	missense	121551	exon14			CACTCCTCTCCAG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2855T>G	12.37:g.108035881T>G	ENSP00000280758:p.Leu952Arg	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	82	26	NM_001018072	0	0	1	1	0	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.034913	0.75617	.	.	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167;ENST00000494235	T;T;T;T;T	0.70869	-0.52;-0.52;-0.52;-0.52;-0.52	5.31	5.31	0.75309	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.059561	0.64402	D	0.000002	D	0.87931	0.6302	M	0.94021	3.485	0.40862	D	0.983844	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.83275	0.996;0.982;0.992	D	0.91528	0.5240	10	0.87932	D	0	.	15.2236	0.73333	0.0:0.0:0.0:1.0	.	489;952;952	E9PHS4;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	R	952;833;952;489;31	ENSP00000280758:L952R;ENSP00000413889:L833R;ENSP00000447319:L952R;ENSP00000349690:L489R;ENSP00000448322:L31R	ENSP00000280758:L952R	L	+	2	0	BTBD11	106560011	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	6.855000	0.75445	2.138000	0.66242	0.459000	0.35465	CTC	.		0.458	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		G	108035881	T	G	108035881	3	3	154	1	0	0	0	0	1	0	0	0	1542	1551	54	5	3014	5	BTBD11	12	108035881	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	39339276	108035881	25816014	88	13930											
SRRM4	84530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	119583229	119583229	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgacctctttaccaaaacagCcagcccgctcaccacctcgc	10	7	5	19	2	2	1	1	1	1	0	3	1	2	1	6	0	4	1	6	0	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:119583229C>A	ENST00000267260.4	+	9	1203	c.815C>A	c.(814-816)gCc>gAc	p.A272D		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	272	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						ACCAAAACAGCCAGCCCGCTC	0.597																																					p.A272D		.											.	SRRM4-2	0			c.C815A						.						27	29	29					12																	119583229		1987	4156	6143	SO:0001583	missense	84530	exon9			AAACAGCCAGCCC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"neural-specific SR-related protein of 100 kDa"	613103	"KIAA1853"	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.815C>A	12.37:g.119583229C>A	ENSP00000267260:p.Ala272Asp	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	106	28	NM_194286	0	0	0	0	0	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431158	0.43122	.	.	ENSG00000139767	ENST00000267260	T	0.23147	1.92	5.48	3.26	0.37387	.	0.608931	0.17277	N	0.180174	T	0.16854	0.0405	L	0.40543	1.245	0.33704	D	0.614946	B	0.12013	0.005	B	0.09377	0.004	T	0.13469	-1.0508	9	.	.	.	-16.4361	4.1827	0.10383	0.2661:0.5295:0.1154:0.089	.	272	A7MD48	SRRM4_HUMAN	D	272	ENSP00000267260:A272D	.	A	+	2	0	SRRM4	118067612	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	1.389000	0.34453	1.274000	0.44362	0.655000	0.94253	GCC	.		0.597	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119583229	C	A	119583229	3	1	154	1	0	0	0	0	1	0	0	0	15203	739	26	4	849	4	SRRM4	12	119583229	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	11547348	119583229	14268666	89	13931											
ATP12A	479	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	25265339	25265339	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggactccatcatcttcctcaTtggcatcattgtggccaatg	8	13	8	12	0	4	0	3	0	1	0	6	1	6	1	3	3	0	1	3	3	1	3	rs372819883		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr13:25265339T>C	ENST00000381946.3	+	8	1186	c.1019T>C	c.(1018-1020)aTt>aCt	p.I340T	ATP12A_ENST00000218548.6_Missense_Mutation_p.I346T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	340					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		ATCTTCCTCATTGGCATCATT	0.547																																					p.I346T	Pancreas(156;1582 1935 18898 22665 26498)												.	ATP12A-137	0			c.T1037C						.	T	THR/ILE,THR/ILE	1,4405	2.1+/-5.4	0,1,2202	106	79	88		1037,1019	5.2	1	13		88	0,8600		0,0,4300	no	missense,missense	ATP12A	NM_001185085.1,NM_001676.5	89,89	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging,probably-damaging	346/1046,340/1040	25265339	1,13005	2203	4300	6503	SO:0001583	missense	479	exon8			TCCTCATTGGCAT	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"ATPases / P-type"	13816	protein-coding gene	gene with protein product	"ATPase, Na+K+ transporting, alpha-1 polypeptide-like", "potassium-transporting ATPase alpha chain 2", "proton pump", "non-gastric H(+)/K(+) ATPase alpha subunit", "sodium/potassium ATPase, alpha polypeptide-like"	182360	"ATPase, Na+/K+ transporting, alpha polypeptide-like 1"	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1019T>C	13.37:g.25265339T>C	ENSP00000371372:p.Ile340Thr	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	101	37	NM_001185085	0	0	0	0	0	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.104092	0.76983	2.27E-4	0.0	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.92199	-2.99;-2.99	5.16	5.16	0.70880	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.96962	0.9008	H	0.94503	3.545	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.91635	0.995;0.999	D	0.97789	1.0237	10	0.87932	D	0	.	12.9956	0.58644	0.0:0.0:0.0:1.0	.	346;340	P54707-2;P54707	.;AT12A_HUMAN	T	346;340	ENSP00000218548:I346T;ENSP00000371372:I340T	ENSP00000218548:I346T	I	+	2	0	ATP12A	24163339	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	7.649000	0.83500	2.170000	0.68504	0.379000	0.24179	ATT	.		0.547	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		C	25265339	T	C	25265339	3	2	154	1	0	0	0	0	1	0	0	0	1123	1493	52	3	1067	3	ATP12A	13	25265339	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		25265339	89904539	90	13932											
RABGGTA	5875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	24734893	24734893	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgcccaccgcttggcacagCgggttaccctgcaggttgag	7	8	13	13	2	0	1	0	1	0	0	0	1	0	1	3	3	4	5	3	3	1	3	rs369935041		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr14:24734893C>T	ENST00000399409.3	-	16	2115	c.1632G>A	c.(1630-1632)ccG>ccA	p.P544P	TGM1_ENST00000206765.6_5'Flank|RABGGTA_ENST00000560777.1_Silent_p.P153P|RABGGTA_ENST00000216840.6_Silent_p.P544P|TGM1_ENST00000544573.1_5'Flank	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	544					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		CTTGGCACAGCGGGTTACCCT	0.612																																					p.P544P		.											.	.	0			c.G1632A						.	C	,	0,4034		0,0,2017	38	42	41		1632,1632	-4.9	0.9	14		41	1,8365		0,1,4182	no	coding-synonymous,coding-synonymous	RABGGTA	NM_004581.3,NM_182836.1	,	0,1,6199	TT,TC,CC		0.012,0.0,0.0081	,	544/568,544/568	24734893	1,12399	2017	4183	6200	SO:0001819	synonymous_variant	5875	exon16			GCACAGCGGGTTA		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"Prenyltransferase alpha subunit repeat containing"	9795	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 3"	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.1632G>A	14.37:g.24734893C>T		Somatic	119	0		WXS	Illumina HiSeq	Phase_I	116	40	NM_004581	0	0	19	27	8	A8K5N2|D3DS69	Silent	SNP	ENST00000399409.3	37	CCDS45088.1																																																																																			.		0.612	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836		T	24734893	C	T	24734893	2	4	154	1	0	0	0	0	0	0	0	1	12999	755	27	1		1	RABGGTA	14	24734893	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10		24734893	82614647	91	13933											
RALGAPA1	253959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	36143779	36143779	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaacttgagcatgtatttcAggatccatgattgaatttac	14	14	7	6	0	1	3	1	3	0	0	2	4	2	4	1	1	3	2	1	1	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr14:36143779A>C	ENST00000389698.3	-	22	3633	c.3243T>G	c.(3241-3243)ccT>ccG	p.P1081P	RALGAPA1_ENST00000307138.6_Silent_p.P1081P|RALGAPA1_ENST00000382366.3_Silent_p.P1094P|RALGAPA1_ENST00000258840.6_Silent_p.P1128P	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1081					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CATGTATTTCAGGATCCATGA	0.388																																					p.P1081P		.											.	RALGAPA1-138	0			c.T3243G						.						26	27	27					14																	36143779		2201	4288	6489	SO:0001819	synonymous_variant	253959	exon22			TATTTCAGGATCC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.3243T>G	14.37:g.36143779A>C		Somatic	246	0		WXS	Illumina HiSeq	Phase_I	243	72	NM_194301	0	0	2	5	3	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Silent	SNP	ENST00000389698.3	37	CCDS32065.1																																																																																			.		0.388	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36143779	A	C	36143779	2	2	154	1	0	0	0	0	0	0	0	1	13045	175	7	5		5	RALGAPA1	14	36143779	Silent	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	11408886	36143779	71205761	92	13934											
TTLL5	23093	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	76243163	76243163	+	Frame_Shift_Del	DEL	A	A	-																															ggaagatggggtgaatatggAaaactttcaggagttcatca																								rs372279209		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr14:76243163delA	ENST00000298832.9	+	23	2562	c.2357delA	c.(2356-2358)gaafs	p.E786fs	TTLL5_ENST00000555422.1_3'UTR|TTLL5_ENST00000556893.1_Frame_Shift_Del_p.E337fs|TTLL5_ENST00000557636.1_Frame_Shift_Del_p.E800fs|TTLL5_ENST00000554510.1_Frame_Shift_Del_p.E295fs	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	786					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GTGAATATGGAAAACTTTCAG	0.403																																					p.E786fs		.											.	TTLL5-92	0			c.2357delA						.						130	127	128					14																	76243163		2203	4300	6503	SO:0001589	frameshift_variant	23093	exon23			.	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"Tubulin tyrosine ligase-like family"	19963	protein-coding gene	gene with protein product		612268	"KIAA0998"	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.2357delA	14.37:g.76243163delA	ENSP00000298832:p.Glu786fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	97	21	NM_015072	0	0	0	0	0	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Frame_Shift_Del	DEL	ENST00000298832.9	37	CCDS32124.1																																																																																			.		0.403	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		-	76243163	A	-	76243163	7	5	154	1	0	1	0	1	0	0	0	0	16763	246	9	0	2443	0	TTLL5	14	76243163	Frame_Shift_Del	DEL	A	TCGA-P4-A5E7-01A-31D-A28G-10	40099384	76243163	31106377	93	13935											
C15orf2	23742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	24923342	24923342	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctcaacccaaatttggggcCcctgatgggccgcagcagaa	10	6	11	14	1	1	2	1	1	0	1	1	2	1	2	5	3	2	2	5	3	3	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr15:24923342C>T	ENST00000329468.2	+	1	2802	c.2328C>T	c.(2326-2328)gcC>gcT	p.A776A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	776					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A776A(1)									AATTTGGGGCCCCTGATGGGC	0.552																																					p.A776A		.											.	.	1	Substitution - coding silent(1)	lung(1)	c.C2328T						.						109	128	121					15																	24923342		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TGGGGCCCCTGAT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"chromosome 15 open reading frame 2"	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2328C>T	15.37:g.24923342C>T		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_018958	0	0	0	0	0		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.		0.552	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24923342	C	T	24923342	2	4	154	1	0	0	0	0	0	0	0	1	1788	610	22	2		2	C15orf2	15	24923342	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10		24923342	77608050	94	13936											
CILP	8483	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65495764	65495764	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagagacacgctctgcccagCtctccgtgcttttgtctcag	6	11	9	15	2	3	1	1	0	3	1	5	2	3	1	2	0	3	3	2	0	0	2	rs185181701	byFrequency	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr15:65495764C>G	ENST00000261883.4	-	7	1130	c.964G>C	c.(964-966)Gct>Cct	p.A322P		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	322	Ig-like C2-type.				negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						CTCTGCCCAGCTCTCCGTGCT	0.498																																					p.A322P													.	CILP-97	0			c.G964C						.						115	101	106					15																	65495764		2201	4299	6500	SO:0001583	missense	8483	exon7			GCCCAGCTCTCCG	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.964G>C	15.37:g.65495764C>G	ENSP00000261883:p.Ala322Pro	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	94	29	NM_003613	0	0	0	0	0	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511219	0.85389	.	.	ENSG00000138615	ENST00000261883	T	0.14391	2.51	5.24	4.12	0.48240	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.166542	0.52532	D	0.000066	T	0.20455	0.0492	L	0.42581	1.335	0.39174	D	0.962657	P	0.52316	0.952	P	0.51701	0.677	T	0.01537	-1.1330	10	0.59425	D	0.04	-1.8098	13.8023	0.63208	0.0:0.912:0.0:0.088	.	322	O75339	CILP1_HUMAN	P	322	ENSP00000261883:A322P	ENSP00000261883:A322P	A	-	1	0	CILP	63282817	0.977000	0.34250	1.000000	0.80357	0.978000	0.69477	4.030000	0.57260	2.446000	0.82766	0.561000	0.74099	GCT	C|0.999;T|0.001		0.498	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		G	65495764	C	G	65495764	3	3	154	1	0	0	0	0	1	0	0	0	3435	797	28	4	2602	4	CILP	15	65495764	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	40572422	65495764	37035628	95	13937											
ZNF75A	7627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3363138	3363138	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaaggccctctacaatgaTgtaatgcaggaaaactatga	16	8	9	8	0	1	3	0	2	1	1	1	4	1	4	1	2	3	2	1	2	7	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr16:3363138T>A	ENST00000574298.1	+	4	536	c.63T>A	c.(61-63)gaT>gaA	p.D21E	ZNF75A_ENST00000498240.2_Intron	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	21	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|large_intestine(3)|lung(7)|prostate(1)	12						TCTACAATGATGTAATGCAGG	0.408																																					p.D21E		.											.	ZNF75A-153	0			c.T63A						.						131	118	122					16																	3363138		2197	4300	6497	SO:0001583	missense	7627	exon4			CAATGATGTAATG	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"Zinc fingers, C2H2-type", "-"	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.63T>A	16.37:g.3363138T>A	ENSP00000459566:p.Asp21Glu	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	170	84	NM_153028	0	0	1	3	2	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	37	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.452955	0.43531	.	.	ENSG00000162086	ENST00000293995	.	.	.	3.48	1.13	0.20643	Krueppel-associated box (4);	.	.	.	.	T	0.40694	0.1127	L	0.42487	1.325	0.80722	D	1	B	0.16603	0.018	B	0.16722	0.016	T	0.12760	-1.0535	8	0.22706	T	0.39	.	2.7142	0.05183	0.1927:0.2235:0.0:0.5838	.	21	Q96N20	ZN75A_HUMAN	E	21	.	ENSP00000293995:D21E	D	+	3	2	ZNF75A	3303139	0.292000	0.24362	0.996000	0.52242	0.996000	0.88848	-0.885000	0.04161	0.207000	0.20607	0.379000	0.24179	GAT	.		0.408	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028		A	3363138	T	A	3363138	3	1	154	1	0	0	0	0	1	0	0	0	18165	1461	51	5	65	5	ZNF75A	16	3363138	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		3363138	86991615	96	13938											
LOC81691	81691	broad.mit.edu;bcgsc.ca	37	chr16	20851720	20851720	+	Frame_Shift_Del	DEL	G	G	-																															tagcaaaaattgcaatctcaGggctctgaagaggctgttta																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr16:20851720delG	ENST00000261377.6	+	15	1765	c.1556delG	c.(1555-1557)aggfs	p.R519fs	ERI2_ENST00000564349.1_Intron|AC004381.6_ENST00000564274.1_Frame_Shift_Del_p.R519fs|AC004381.6_ENST00000348433.6_Frame_Shift_Del_p.R519fs	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2																					TGCAATCTCAGGGCTCTGAAG	0.408																																					p.R519fs													.	LOC81691-92	0			c.1556delG						.						113	115	115					16																	20851720		2201	4300	6501	SO:0001589	frameshift_variant	0	exon15			ATCTCAGGGCTCT																												ENST00000261377.6:c.1556delG	16.37:g.20851720delG	ENSP00000261377:p.Arg519fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	70	34	NM_030941	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000261377.6	37	CCDS10591.1																																																																																			.		0.408	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			-	20851720	G	-	20851720	7	5	154	1	0	1	0	1	0	0	0	0	8915	1000	35	0	1610	0	LOC81691	16	20851720	Frame_Shift_Del	DEL	G	TCGA-P4-A5E7-01A-31D-A28G-10	17488582	20851720	69503033	97	13939											
IRX3	79191	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	54319068	54319068	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtcgtcagccaggccctcgCcccccgtgtcctcctcctcc	2	8	8	23	4	1	0	1	0	0	0	7	0	5	0	9	1	1	0	9	1	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr16:54319068C>T	ENST00000329734.3	-	2	1437	c.725G>A	c.(724-726)gGc>gAc	p.G242D		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	242	Asp/Glu-rich (acidic).				mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						caggccctcgccccccgtgtc	0.687																																					p.G242D	GBM(143;1830 1866 4487 4646 37383)												.	IRX3-90	0			c.G725A						.						52	31	39					16																	54319068		2197	4299	6496	SO:0001583	missense	79191	exon2			CCCTCGCCCCCCG	U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"Homeoboxes / TALE class"	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.725G>A	16.37:g.54319068C>T	ENSP00000331608:p.Gly242Asp	Somatic	48	1		WXS	Illumina HiSeq	Phase_I	130	37	NM_024336	0	0	27	50	23	Q7Z4A4|Q7Z4A5|Q8IVC6	Missense_Mutation	SNP	ENST00000329734.3	37	CCDS10750.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.330432	0.24167	.	.	ENSG00000177508	ENST00000329734	T	0.52295	0.67	4.3	4.3	0.51218	.	0.274240	0.31257	N	0.007970	T	0.33440	0.0863	L	0.36672	1.1	0.32156	N	0.583631	P	0.38504	0.634	B	0.33690	0.168	T	0.36962	-0.9726	10	0.11182	T	0.66	-12.5443	14.2989	0.66334	0.0:1.0:0.0:0.0	.	242	P78415	IRX3_HUMAN	D	242	ENSP00000331608:G242D	ENSP00000331608:G242D	G	-	2	0	IRX3	52876569	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	3.575000	0.53870	2.221000	0.72209	0.455000	0.32223	GGC	.		0.687	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2			T	54319068	C	T	54319068	3	4	154	1	0	0	0	0	1	0	0	0	7866	739	26	2	792	2	IRX3	16	54319068	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	33467348	54319068	36035685	98	13940											
ACADVL	37	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7127679	7127679	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctgagtctcagcggactTgtccacccggagttgagtcg	6	9	14	12	3	1	2	1	2	1	0	4	4	2	4	3	3	1	1	3	3	0	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:7127679T>C	ENST00000356839.5	+	16	1751	c.1572T>C	c.(1570-1572)ctT>ctC	p.L524L	ACADVL_ENST00000543245.2_Silent_p.L547L|ACADVL_ENST00000350303.5_Silent_p.L502L|MIR324_ENST00000362183.1_RNA	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	524					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						TCAGCGGACTTGTCCACCCGG	0.657																																					p.L547L		.											.	ACADVL-93	0			c.T1641C						.						54	54	54					17																	7127679		2203	4300	6503	SO:0001819	synonymous_variant	37	exon17			CGGACTTGTCCAC	BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"acyl-Coenzyme A dehydrogenase, very long chain"			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.1572T>C	17.37:g.7127679T>C		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	106	49	NM_001270447	1	0	178	507	328	B4DEB6|F5H2A9|O76056|Q8WUL0	Silent	SNP	ENST00000356839.5	37	CCDS11090.1																																																																																			.		0.657	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018		C	7127679	T	C	7127679	2	2	154	1	0	0	0	0	0	0	0	1	116	1799	63	3		3	ACADVL	17	7127679	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		7127679	74067531	99	13941											
POLR2A	5430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7405000	7405000	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaatacaataacttcaaGtctatggtcgtgtccggagc	11	12	9	9	2	3	1	1	1	2	0	5	2	4	2	1	2	3	0	1	2	6	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:7405000G>A	ENST00000322644.6	+	14	2700	c.2301G>A	c.(2299-2301)aaG>aaA	p.K767K		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	767					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ATAACTTCAAGTCTATGGTCG	0.488																																					p.K767K		.											.	POLR2A-91	0			c.G2301A						.						71	67	68					17																	7405000		2203	4300	6503	SO:0001819	synonymous_variant	5430	exon14			CTTCAAGTCTATG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"RNA polymerase subunits"	9187	protein-coding gene	gene with protein product	"DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit", "RNA polymerase II subunit B1"	180660	"polymerase (RNA) II (DNA directed) polypeptide A (220kD)"	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.2301G>A	17.37:g.7405000G>A		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	140	34	NM_000937	0	0	0	0	0	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			.		0.488	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		A	7405000	G	A	7405000	2	1	154	1	0	0	0	0	0	0	0	1	12240	1020	36	2		2	POLR2A	17	7405000	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	277321	7405000	73790210	100	13942											
SLC46A1	113235	ucsc.edu;bcgsc.ca	37	chr17	26731871	26731871	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagatgtcctgggccccaaAgtgcacagtgatcaccacga	12	7	10	12	1	1	2	1	1	0	1	2	3	2	2	4	1	1	1	4	1	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:26731871A>C	ENST00000440501.1	-	2	939	c.844T>G	c.(844-846)Ttt>Gtt	p.F282V	CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|SLC46A1_ENST00000321666.5_Missense_Mutation_p.F282V|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	282					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	TGGGCCCCAAAGTGCACAGTG	0.532																																					p.F282V													.	SLC46A1-22	0			c.T844G						.						110	118	115					17																	26731871		2016	4183	6199	SO:0001583	missense	113235	exon2			CCCCAAAGTGCAC	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"Solute carriers"	30521	protein-coding gene	gene with protein product	"heme carrier protein 1", "proton-coupled folate transporter"	611672	"solute carrier family 46, member 1"			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.844T>G	17.37:g.26731871A>C	ENSP00000395653:p.Phe282Val	Somatic	196	2		WXS	Illumina HiSeq		256	48	NM_001242366	0	0	7	9	2	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	37		.	.	.	.	.	.	.	.	.	.	A	12.80	2.046796	0.36085	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;T	0.81078	-1.45;-1.45	5.35	4.28	0.50868	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.461581	0.26262	N	0.025398	T	0.64972	0.2647	.	.	.	0.42947	D	0.994369	B;B;B	0.23249	0.009;0.082;0.026	B;B;B	0.25140	0.022;0.058;0.035	T	0.53823	-0.8384	9	0.16420	T	0.52	-7.2339	5.5623	0.17150	0.7666:0.0:0.0822:0.1512	.	282;282;282	B4DJ17;Q96NT5-2;Q96NT5	.;.;PCFT_HUMAN	V	282	ENSP00000395653:F282V;ENSP00000318828:F282V	ENSP00000318828:F282V	F	-	1	0	SLC46A1	23755998	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.341000	0.52151	0.893000	0.36288	0.460000	0.39030	TTT	.		0.532	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		C	26731871	A	C	26731871	3	2	154	1	0	0	0	0	1	0	0	0	14676	72	3	5	552	5	SLC46A1	17	26731871	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	19326871	26731871	54463339	101	13943											
MRPL45	84311	broad.mit.edu;bcgsc.ca	37	chr17	36478132	36478132	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctatggaagctggagaatgCataccaagatcgttccccca	12	8	9	12	1	0	2	0	0	0	2	2	4	1	3	4	2	3	3	4	2	5	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:36478132C>T	ENST00000312513.5	+	7	945	c.784C>T	c.(784-786)Cat>Tat	p.H262Y		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	262						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTGGAGAATGCATACCAAGAT	0.507											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H262Y													.	MRPL45-90	0			c.C784T						.						127	105	112					17																	36478132		2203	4300	6503	SO:0001583	missense	84311	exon7			AGAATGCATACCA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"Mitochondrial ribosomal proteins / large subunits"	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.784C>T	17.37:g.36478132C>T	ENSP00000308901:p.His262Tyr	Somatic	92	2	863	WXS	Illumina HiSeq	Phase_I	119	63	NM_032351	0	0	28	82	54	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	37	CCDS11326.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.186161	0.57909	.	.	ENSG00000174100	ENST00000312513	T	0.18338	2.22	5.97	5.97	0.96955	.	0.094381	0.64402	N	0.000001	T	0.47154	0.1430	M	0.88181	2.935	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.51212	-0.8734	10	0.06625	T	0.88	-14.6417	20.0942	0.97832	0.0:1.0:0.0:0.0	.	262	Q9BRJ2	RM45_HUMAN	Y	262	ENSP00000308901:H262Y	ENSP00000308901:H262Y	H	+	1	0	MRPL45	33731659	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.771000	0.85420	2.855000	0.98099	0.536000	0.68110	CAT	.		0.507	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351		T	36478132	C	T	36478132	3	4	154	1	0	0	0	0	1	0	0	0	9834	710	25	2	740	2	MRPL45	17	36478132	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	9746261	36478132	44717078	102	13944											
GPR179	440435	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	36492994	36492994	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acggtgtggcatccatgcagCtggtgcagccctcaggacat	8	8	13	12	1	1	0	1	0	0	0	2	1	2	1	2	4	4	4	2	4	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:36492994C>T	ENST00000342292.4	-	4	1114	c.1094G>A	c.(1093-1095)aGc>aAc	p.S365N		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	365					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				ATCCATGCAGCTGGTGCAGCC	0.632																																					p.S365N		.											.	GPR179-93	0			c.G1094A						.						27	31	29					17																	36492994		2097	4237	6334	SO:0001583	missense	440435	exon4			ATGCAGCTGGTGC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"GPCR / Class C : Orphans"	31371	protein-coding gene	gene with protein product		614515	"GPR158-like 1", "GPR179"	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.1094G>A	17.37:g.36492994C>T	ENSP00000345060:p.Ser365Asn	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	78	14	NM_001004334	0	0	0	0	0		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.554853	0.65425	.	.	ENSG00000188888	ENST00000342292	T	0.52295	0.67	5.19	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.36248	0.0960	L	0.46157	1.445	0.32221	N	0.57526	B	0.34290	0.447	B	0.32149	0.141	T	0.46331	-0.9199	10	0.37606	T	0.19	-10.9887	7.967	0.30104	0.0:0.6539:0.2598:0.0863	.	365	Q6PRD1	GP179_HUMAN	N	365	ENSP00000345060:S365N	ENSP00000345060:S365N	S	-	2	0	GPR179	33746520	0.669000	0.27502	0.999000	0.59377	0.940000	0.58332	0.856000	0.27818	2.709000	0.92574	0.561000	0.74099	AGC	.		0.632	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36492994	C	T	36492994	3	4	154	1	0	0	0	0	1	0	0	0	6694	797	28	2	6041	2	GPR179	17	36492994	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	14862	36492994	44702216	103	13945											
KRTAP4-5	85289	hgsc.bcm.edu;broad.mit.edu	37	chr17	39305911	39305912	+	In_Frame_Ins	INS	-	-	GCAGCAGGTGGTCCT																															ggcttgcagcagctggggcgINSgcagcaggtggtcctgcagc																								rs557154279|rs141058010	byFrequency	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:39305911_39305912insGCAGCAGGTGGTCCT	ENST00000343246.4	-	1	142_143	c.108_109insAGGACCACCTGCTGC	c.(106-111)tgccgc>tgcAGGACCACCTGCTGCcgc	p.36_37CR>CRTTCCR		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	36	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGGGCGGCAGCAGGTGG	0.658														26	0.00519169	0	0.0115	5008	,	,		16446	0		0.0149	False		,,,				2504	0.0031				p.R37delinsRTTCCR		.											.	KRTAP4-5-90	0			c.109_110insAGGACCACCTGCTGC						.			55,4055		3,49,2003						-1.8	0.7			27	192,7870		2,188,3841	no	coding	KRTAP4-5	NM_033188.3		5,237,5844	A1A1,A1R,RR		2.3815,1.3382,2.0292				247,11925				SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.94_108dupAGGACCACCTGCTGC	17.37:g.39305911_39305912insGCAGCAGGTGGTCCT	ENSP00000340546:p.Arg32_Cys36dup	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	106	33	NM_033188	0	0	0	0	0		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.		0.658	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			GCAGCAGGTGGTCCT	39305912	-	GCAGCAGGTGGTCCT	39305911	7	5	154	1	0	1	1	0	0	0	0	0	8575	1116	39	0	440	0	KRTAP4-5	17	39305911	In_Frame_Ins	INS	-	TCGA-P4-A5E7-01A-31D-A28G-10	2812917	39305911	41889299	104	13946											
GPATCH8	23131	hgsc.bcm.edu;bcgsc.ca	37	chr17	42475173	42475176	+	Frame_Shift_Del	DEL	TGAG	TGAG	-																															gcagggtggccagggatgatTgagtgagtgaggtgggacaa																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TGAG	TGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:42475173_42475176delTGAG	ENST00000591680.1	-	8	4299_4302	c.4269_4272delCTCA	c.(4267-4272)cactcafs	p.HS1423fs	GPATCH8_ENST00000434000.1_Frame_Shift_Del_p.HS1345fs	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1423							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		CAGGGATGATTGAGTGAGTGAGGT	0.588																																					p.1423_1424del		.											.	GPATCH8-94	0			c.4269_4272del						.																																			SO:0001589	frameshift_variant	23131	exon8			.	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.4269_4272delCTCA	17.37:g.42475181_42475184delTGAG	ENSP00000467556:p.His1423fs	Somatic	206	0		WXS	Illumina HiSeq	Phase_I	263	112	NM_001002909	0	0	0	0	0	B9EGP9|O60300|Q8TB99	Frame_Shift_Del	DEL	ENST00000591680.1	37	CCDS32666.1																																																																																			.		0.588	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		-	42475176	TGAG	-	42475173	7	5	154	1	0	1	0	1	0	0	0	0	6614	1799	63	0	240	0	GPATCH8	17	42475173	Frame_Shift_Del	DEL	TGAG	TCGA-P4-A5E7-01A-31D-A28G-10	3169262	42475173	38720037	105	13947											
OTOP3	347741	broad.mit.edu	37	chr17	72942796	72942796	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgcctcaatgccaccgcGtgtgaagctttccggagagg	7	9	13	12	3	1	2	1	1	0	1	2	3	2	2	4	2	3	1	4	2	2	1	rs200903740		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:72942796G>A	ENST00000328801.4	+	6	846	c.846G>A	c.(844-846)gcG>gcA	p.A282A		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	282						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					ATGCCACCGCGTGTGAAGCTT	0.567																																					p.A282A													.	OTOP3-69	0			c.G846A						.	G		0,4406		0,0,2203	132	125	127		846	2.1	0.1	17		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OTOP3	NM_178233.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		282/597	72942796	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	347741	exon6			CACCGCGTGTGAA	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.846G>A	17.37:g.72942796G>A		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_178233	0	0	0	0	0		Silent	SNP	ENST00000328801.4	37	CCDS11709.1																																																																																			G|0.999;A|0.001		0.567	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233		A	72942796	G	A	72942796	2	1	154	1	0	0	0	0	0	0	0	1	11333	1132	40	1		1	OTOP3	17	72942796	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	30467623	72942796	8252414	106	13948											
CCDC40	55036	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	78055491	78055491	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	actgctgcagaagctcaccaCccagtgcctgaccaagcagg	11	5	10	15	0	1	2	1	1	0	1	1	2	1	2	4	1	5	4	4	1	2	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:78055491C>A	ENST00000397545.4	+	11	1736	c.1709C>A	c.(1708-1710)aCc>aAc	p.T570N	CCDC40_ENST00000374877.3_Missense_Mutation_p.T570N	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	570					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			AAGCTCACCACCCAGTGCCTG	0.562																																					p.T570N													.	CCDC40-71	0			c.C1709A						.						40	47	45					17																	78055491		2110	4238	6348	SO:0001583	missense	55036	exon11			TCACCACCCAGTG	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.1709C>A	17.37:g.78055491C>A	ENSP00000380679:p.Thr570Asn	Somatic	138	1		WXS	Illumina HiSeq	Phase_I	230	56	NM_017950	0	0	7	12	5	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	.	.	.	.	.	.	.	.	.	.	C	7.817	0.716970	0.15372	.	.	ENSG00000141519	ENST00000374877;ENST00000397545	T;T	0.44482	0.92;0.94	5.35	3.24	0.37175	.	.	.	.	.	T	0.26991	0.0661	N	0.19112	0.55	0.09310	N	1	P;P	0.38767	0.514;0.646	B;B	0.33295	0.106;0.161	T	0.04737	-1.0930	9	0.20046	T	0.44	-8.4893	15.6447	0.77039	0.0:0.7408:0.2592:0.0	.	570;353	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	N	570	ENSP00000364011:T570N;ENSP00000380679:T570N	ENSP00000364011:T570N	T	+	2	0	CCDC40	75670086	0.009000	0.17119	0.131000	0.22000	0.525000	0.34531	1.890000	0.39728	1.203000	0.43233	0.655000	0.94253	ACC	.		0.562	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		A	78055491	C	A	78055491	3	1	154	1	0	0	0	0	1	0	0	0	2818	507	18	4	1751	4	CCDC40	17	78055491	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	5112695	78055491	3139719	107	13949											
MYL12B	103910	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	3273023	3273023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggccttcaacatgattgatCagaacagagatggcttcatc	13	10	9	9	0	3	4	3	2	0	2	4	5	3	4	1	2	2	1	1	2	2	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr18:3273023C>G	ENST00000581193.1	+	2	510	c.127C>G	c.(127-129)Cag>Gag	p.Q43E	MYL12B_ENST00000584539.1_Missense_Mutation_p.Q43E|MYL12B_ENST00000400175.5_Missense_Mutation_p.Q43E|MYL12B_ENST00000237500.5_Missense_Mutation_p.Q43E	NM_001144945.1	NP_001138417.1	O14950	ML12B_HUMAN	myosin, light chain 12B, regulatory	43	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				axon guidance (GO:0007411)|muscle contraction (GO:0006936)|regulation of cell shape (GO:0008360)	apical part of cell (GO:0045177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)|lung(2)	4						CATGATTGATCAGAACAGAGA	0.403																																					p.Q43E													.	MYL12B-90	0			c.C127G						.						202	190	194					18																	3273023		2203	4300	6503	SO:0001583	missense	103910	exon2			ATTGATCAGAACA	AY320408	CCDS11831.1	18p11.31	2013-01-10			ENSG00000118680	ENSG00000118680		"Myosins / Light chain", "EF-hand domain containing"	29827	protein-coding gene	gene with protein product	"myosin regulatory light chain 2"	609211				11942626	Standard	NM_033546		Approved	MRLC2	uc002klt.4	O14950	OTTHUMG00000131510	ENST00000581193.1:c.127C>G	18.37:g.3273023C>G	ENSP00000463559:p.Gln43Glu	Somatic	171	2		WXS	Illumina HiSeq	Phase_I	177	54	NM_033546	0	1	695	1283	587	D3DUH6|Q13182|Q7Z5Z4	Missense_Mutation	SNP	ENST00000581193.1	37	CCDS11831.1	.	.	.	.	.	.	.	.	.	.	C	33	5.221026	0.95139	.	.	ENSG00000118680	ENST00000237500;ENST00000400177;ENST00000400175;ENST00000400174	T;T	0.71103	-0.54;-0.54	5.66	5.66	0.87406	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.81837	0.4907	M	0.82433	2.59	0.80722	D	1	D	0.60160	0.987	P	0.51833	0.681	D	0.84469	0.0598	10	0.87932	D	0	.	20.1076	0.97898	0.0:1.0:0.0:0.0	.	43	O14950	ML12B_HUMAN	E	43	ENSP00000237500:Q43E;ENSP00000383037:Q43E	ENSP00000237500:Q43E	Q	+	1	0	MYL12B	3263023	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.760000	0.85248	2.823000	0.97156	0.650000	0.86243	CAG	.		0.403	MYL12B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258908.1	NM_033546		G	3273023	C	G	3273023	3	3	154	1	0	0	0	0	1	0	0	0	10071	827	29	4	129	4	MYL12B	18	3273023	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10		3273023	74804225	108	13950											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1081736	1081736	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggcgggcgctgcgcaccaAggtgaggcgggggaggaagc	7	2	22	10	5	0	1	0	1	0	0	0	3	0	3	1	7	2	2	1	7	2	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:1081736A>C	ENST00000313093.2	+	18	2609	c.2378A>C	c.(2377-2379)aAg>aCg	p.K793T	HMHA1_ENST00000590214.1_Splice_Site_p.K820T|HMHA1_ENST00000539243.2_Splice_Site_p.K809T|HMHA1_ENST00000543365.1_Splice_Site_p.K676T|HMHA1_ENST00000586866.1_Splice_Site_p.K797T|HMHA1_ENST00000536472.1_Splice_Site_p.K661T|HMHA1_ENST00000590577.1_Splice_Site_p.K428T	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	793	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGCGCACCAAGGTGAGGCGG	0.731																																					p.K809T		.											.	HMHA1-91	0			c.A2426C						.						6	7	7					19																	1081736		2129	4218	6347	SO:0001630	splice_region_variant	23526	exon18			GCACCAAGGTGAG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"Rho GTPase activating proteins"	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.2379+1A>C	19.37:g.1081736A>C		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	31	10	NM_001258328	0	0	0	1	1	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	a	22.3	4.273106	0.80580	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.55	4.55	0.56014	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.43787	0.1263	L	0.49455	1.56	0.58432	D	0.999996	D;D;D;D;D	0.69078	0.997;0.993;0.996;0.993;0.995	D;D;D;P;D	0.74674	0.928;0.945;0.984;0.892;0.967	T	0.40421	-0.9564	10	0.87932	D	0	-45.2741	13.1017	0.59224	1.0:0.0:0.0:0.0	.	661;809;428;676;793	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	T	809;793;793;661;787;676	ENSP00000439601:K809T;ENSP00000316772:K793T;ENSP00000445109:K661T;ENSP00000438979:K676T	ENSP00000316772:K793T	K	+	2	0	HMHA1	1032736	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	8.654000	0.91092	1.684000	0.51022	0.449000	0.29647	AAG	.		0.731	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		Missense_Mutation	C	1081736	A	C	1081736	5	2	154	1	0	0	0	0	0	0	1	0	7261	86	3	5	2448	5	HMHA1	19	1081736	Splice_Site	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		1081736	58047247	109	13951											
EVI5L	115704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	7917990	7917990	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agtacttccagagagtgatcCcccaccagttcgacagctgc	10	8	9	14	1	0	2	0	1	0	1	3	4	2	2	4	0	3	3	4	0	1	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:7917990C>G	ENST00000270530.4	+	9	1202	c.1006C>G	c.(1006-1008)Ccc>Gcc	p.P336A	EVI5L_ENST00000538904.2_Missense_Mutation_p.P336A	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	336					negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						GAGAGTGATCCCCCACCAGTT	0.627											OREG0025211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P336A		.											.	EVI5L-91	0			c.C1006G						.						123	122	123					19																	7917990		2203	4300	6503	SO:0001583	missense	115704	exon8			GTGATCCCCCACC	BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.1006C>G	19.37:g.7917990C>G	ENSP00000270530:p.Pro336Ala	Somatic	79	0	645	WXS	Illumina HiSeq	Phase_I	112	43	NM_001159944	0	0	10	19	9	B9A6I9	Missense_Mutation	SNP	ENST00000270530.4	37	CCDS12188.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.277895	0.80692	.	.	ENSG00000142459	ENST00000270530;ENST00000538904	T;T	0.23147	1.92;1.92	3.8	3.8	0.43715	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.46639	0.1403	M	0.64567	1.98	0.58432	D	0.999999	D;P	0.89917	1.0;0.951	D;P	0.91635	0.999;0.727	T	0.47497	-0.9113	10	0.59425	D	0.04	-42.9871	13.5149	0.61535	0.0:1.0:0.0:0.0	.	336;336	B9A6I9;Q96CN4	.;EVI5L_HUMAN	A	336	ENSP00000270530:P336A;ENSP00000445905:P336A	ENSP00000270530:P336A	P	+	1	0	EVI5L	7823990	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.584000	0.82572	2.124000	0.65301	0.462000	0.41574	CCC	.		0.627	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245		G	7917990	C	G	7917990	3	3	154	1	0	0	0	0	1	0	0	0	5303	623	22	4	1036	4	EVI5L	19	7917990	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	6836254	7917990	51210993	110	13952											
HOOK2	29911	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	12874398	12874398	+	Frame_Shift_Del	DEL	T	T	-																															ctgctcccgctgacttcggcTtttctcaaagtccatctgtc																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:12874398delT	ENST00000397668.3	-	22	2027	c.1954delA	c.(1954-1956)agcfs	p.S652fs	HOOK2_ENST00000264827.5_Frame_Shift_Del_p.S650fs|HOOK2_ENST00000589965.1_5'Flank	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	652	Required for localization to the centrosome and induction of aggresome formation.|Sufficient for interaction with CNTRL.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						TGACTTCGGCTTTTCTCAAAG	0.522																																					p.S652fs		.											.	HOOK2-92	0			c.1954delA						.						185	194	191					19																	12874398		2203	4300	6503	SO:0001589	frameshift_variant	29911	exon22			.	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1954delA	19.37:g.12874398delT	ENSP00000380785:p.Ser652fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	118	40	NM_013312	0	0	0	0	0	O60562	Frame_Shift_Del	DEL	ENST00000397668.3	37	CCDS42508.1																																																																																			.		0.522	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		-	12874398	T	-	12874398	7	5	154	1	0	1	0	1	0	0	0	0	7304	1609	56	0	213	0	HOOK2	19	12874398	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	4956408	12874398	46254585	111	13953											
PGLYRP2	114770	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	15582776	15582776	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgttggctgcgcagcgcGtgaagtccgtgcagggtggt	5	9	18	9	4	0	1	0	1	0	0	1	1	1	1	1	3	3	5	1	3	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:15582776G>A	ENST00000340880.4	-	3	1748	c.1268C>T	c.(1267-1269)aCg>aTg	p.T423M	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.T423M	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	423					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						TGCGCAGCGCGTGAAGTCCGT	0.672																																					p.T423M		.											.	PGLYRP2-93	0			c.C1268T						.						63	53	56					19																	15582776		2203	4300	6503	SO:0001583	missense	114770	exon3			CAGCGCGTGAAGT	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"peptidoglycan recognition protein L precursor", "peptidoglycan recognition protein-like", "N-acetylmuramoyl-L-alanine amidase"	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.1268C>T	19.37:g.15582776G>A	ENSP00000345968:p.Thr423Met	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	88	5	NM_052890	0	0	0	0	0	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	G	6.484	0.457468	0.12342	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.14391	2.51;2.51	4.62	-7.33	0.01431	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	2.474620	0.01368	N	0.012465	T	0.17704	0.0425	L	0.60455	1.87	0.09310	N	1	P;P	0.52316	0.952;0.889	P;P	0.49597	0.616;0.505	T	0.48068	-0.9067	10	0.52906	T	0.07	-14.711	4.6458	0.12572	0.0767:0.2083:0.1616:0.5534	.	423;423	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	M	423	ENSP00000345968:T423M;ENSP00000292609:T423M	ENSP00000292609:T423M	T	-	2	0	PGLYRP2	15443776	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.143000	0.10296	-1.075000	0.03129	-1.001000	0.02504	ACG	.		0.672	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15582776	G	A	15582776	3	1	154	1	0	0	0	0	1	0	0	0	11820	1145	40	1	474	1	PGLYRP2	19	15582776	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	2708378	15582776	43546207	112	13954											
TMEM38A	79041	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	16793291	16793291	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tccgaggggtctggaagccaGagaccaacgagatcctgcac	11	5	13	12	2	1	2	0	0	1	2	3	6	3	3	4	3	3	1	4	3	2	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:16793291G>C	ENST00000187762.2	+	4	617	c.526G>C	c.(526-528)Gag>Cag	p.E176Q		NM_024074.1	NP_076979.1	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	176						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)	15						CTGGAAGCCAGAGACCAACGA	0.582																																					p.E176Q		.											.	TMEM38A-92	0			c.G526C						.						149	123	132					19																	16793291		2203	4300	6503	SO:0001583	missense	79041	exon4			AAGCCAGAGACCA	AK025981	CCDS12349.1	19p13.11	2013-05-23				ENSG00000072954			28462	protein-coding gene	gene with protein product		611235				17611541	Standard	NM_024074		Approved	MGC3169, TRIC-A	uc002nes.3	Q9H6F2		ENST00000187762.2:c.526G>C	19.37:g.16793291G>C	ENSP00000187762:p.Glu176Gln	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	133	42	NM_024074	0	0	4	8	4	A8K9P9	Missense_Mutation	SNP	ENST00000187762.2	37	CCDS12349.1	.	.	.	.	.	.	.	.	.	.	g	24.0	4.482621	0.84747	.	.	ENSG00000072954	ENST00000187762	.	.	.	5.38	4.35	0.52113	.	0.053986	0.64402	D	0.000001	T	0.72835	0.3510	M	0.71206	2.165	0.58432	D	0.999998	D	0.57571	0.98	P	0.58130	0.833	T	0.74325	-0.3702	9	0.46703	T	0.11	-30.6059	13.1225	0.59336	0.077:0.0:0.923:0.0	.	176	Q9H6F2	TM38A_HUMAN	Q	176	.	ENSP00000187762:E176Q	E	+	1	0	TMEM38A	16654291	1.000000	0.71417	0.674000	0.29902	0.978000	0.69477	7.723000	0.84788	1.258000	0.44101	0.655000	0.94253	GAG	.		0.582	TMEM38A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462841.1	NM_024074		C	16793291	G	C	16793291	3	2	154	1	0	0	0	0	1	0	0	0	16191	943	33	4	540	4	TMEM38A	19	16793291	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	1210515	16793291	42335692	113	13955											
C19orf62	29086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17384931	17384931	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctgtctggcctgaccTccgacccccgcgagctctgt	4	9	11	17	3	2	1	0	1	2	0	3	3	3	1	5	1	3	3	5	1	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:17384931T>C	ENST00000359435.4	+	5	674	c.481T>C	c.(481-483)Tcc>Ccc	p.S161P	CTD-2278I10.6_ENST00000596542.1_Missense_Mutation_p.S83P|BABAM1_ENST00000595632.1_Intron|BABAM1_ENST00000601043.1_Missense_Mutation_p.S161P|BABAM1_ENST00000598188.1_Missense_Mutation_p.S161P|BABAM1_ENST00000447614.2_Missense_Mutation_p.S161P|BABAM1_ENST00000448635.2_Intron	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	161	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGGCCTGACCTCCGACCCCCG	0.667																																					p.S161P		.											.	.	0			c.T481C						.						57	66	63					19																	17384931		2060	4203	6263	SO:0001583	missense	29086	exon5			CTGACCTCCGACC	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"Mediator of Rap80 Interactions and Targeting 40 kD", "new component of the BRCA1 A complex"	612766	"chromosome 19 open reading frame 62"	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.481T>C	19.37:g.17384931T>C	ENSP00000352408:p.Ser161Pro	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	51	23	NM_014173	0	0	45	73	28	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Missense_Mutation	SNP	ENST00000359435.4	37	CCDS46012.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812432	0.70912	.	.	ENSG00000105393	ENST00000359435;ENST00000447614;ENST00000300965	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.76666	0.4019	M	0.66939	2.045	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.77885	-0.2421	9	0.52906	T	0.07	-27.2018	14.0114	0.64498	0.0:0.0:0.0:1.0	.	161	Q9NWV8	BABA1_HUMAN	P	161;161;83	.	ENSP00000300965:S83P	S	+	1	0	BABAM1	17245931	1.000000	0.71417	0.979000	0.43373	0.276000	0.26787	5.510000	0.67018	2.192000	0.70111	0.533000	0.62120	TCC	.		0.667	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173		C	17384931	T	C	17384931	3	2	154	1	0	0	0	0	1	0	0	0	1950	1551	54	3	495	3	C19orf62	19	17384931	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	591640	17384931	41744052	114	13956											
UNC13A	23025	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	17767189	17767189	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctccccggaagaggcataGcggctgctacccgtggggct	7	6	15	13	3	0	1	0	0	0	1	1	2	1	2	3	5	4	5	3	5	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:17767189G>T	ENST00000519716.2	-	10	785	c.786C>A	c.(784-786)cgC>cgA	p.R262R	UNC13A_ENST00000552293.1_Silent_p.R262R|UNC13A_ENST00000428389.2_Silent_p.R350R|UNC13A_ENST00000550896.1_Silent_p.R262R|UNC13A_ENST00000252773.7_Silent_p.R262R|UNC13A_ENST00000551649.1_Silent_p.R262R	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	262					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						AAGAGGCATAGCGGCTGCTAC	0.632																																					p.R262R													.	UNC13A-25	0			c.C786A						.						8	8	8					19																	17767189		1983	4138	6121	SO:0001819	synonymous_variant	23025	exon10			GGCATAGCGGCTG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.786C>A	19.37:g.17767189G>T		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	27	7	NM_001080421	0	0	0	0	0	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			.		0.632	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17767189	G	T	17767189	2	4	154	1	0	0	0	0	0	0	0	1	17017	958	34	4		4	UNC13A	19	17767189	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	382258	17767189	41361794	115	13957											
SFRS14	10147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	19106027	19106027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccagcccatcttctgcagCatctggaagcccaggttctt	7	12	8	14	0	4	0	0	0	4	0	5	1	5	1	3	2	4	3	3	2	1	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:19106027C>T	ENST00000601879.1	-	9	3351	c.3054G>A	c.(3052-3054)atG>atA	p.M1018I	SUGP2_ENST00000337018.6_Missense_Mutation_p.M1018I|SUGP2_ENST00000456085.2_Missense_Mutation_p.M787I|AC004447.2_ENST00000594142.1_RNA|SUGP2_ENST00000600377.1_Missense_Mutation_p.M1032I|SUGP2_ENST00000452918.2_Missense_Mutation_p.M1018I			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	1018	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TCTTCTGCAGCATCTGGAAGC	0.627																																					p.M1018I		.											.	SUGP2-91	0			c.G3054A						.						64	53	57					19																	19106027		2203	4300	6503	SO:0001583	missense	10147	exon9			CTGCAGCATCTGG	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.3054G>A	19.37:g.19106027C>T	ENSP00000472286:p.Met1018Ile	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	57	19	NM_014884	0	0	21	39	18	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	37	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.017731	0.93404	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918;ENST00000456085	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.05	5.05	0.67936	D111/G-patch (3);	0.000000	0.85682	D	0.000000	T	0.61236	0.2331	M	0.73962	2.25	0.58432	D	0.999999	D;D;D	0.59357	0.969;0.985;0.969	D;D;D	0.72338	0.968;0.977;0.951	T	0.65627	-0.6122	10	0.72032	D	0.01	-26.6822	16.9459	0.86230	0.0:1.0:0.0:0.0	.	787;1018;1018	E7ETX7;A8K5G0;Q8IX01	.;.;SUGP2_HUMAN	I	1018;966;1018;787	ENSP00000337926:M1018I;ENSP00000332373:M966I;ENSP00000389380:M1018I;ENSP00000409603:M787I	ENSP00000332373:M966I	M	-	3	0	SUGP2	18967027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.709000	0.74665	2.349000	0.79799	0.462000	0.41574	ATG	.		0.627	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		T	19106027	C	T	19106027	3	4	154	1	0	0	0	0	1	0	0	0	14202	710	25	2	202	2	SFRS14	19	19106027	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	1338838	19106027	40022956	116	13958											
ETHE1	23474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	44030496	44030497	+	Missense_Mutation	DNP	TA	TA	AT																															gtggtccgcgtggcagtgggTattcactgggagagagagga																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:44030496_44030497TA>AT	ENST00000292147.2	-	3	297_298	c.231_232TA>AT	c.(229-234)aaTAcc>aaATcc	p.77_78NT>KS	ZNF575_ENST00000458714.2_Intron|ETHE1_ENST00000600651.1_Missense_Mutation_p.77_78NT>KS	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	77					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				TGGCAGTGGGTATTCACTGGGA	0.634																																					p.NT77KS		.											.	ETHE1-90	0			c.T231A						.																																			SO:0001583	missense	23474	exon3			GTGGGTATTCACT		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.231_232delinsAT	19.37:g.44030496_44030497delinsAT	ENSP00000292147:p.N77_T78delinsKS	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	131	43	NM_014297	0	0	0	0	0	Q96HR0|Q9H001	Missense_Mutation	DNP	ENST00000292147.2	37	CCDS12622.1																																																																																			.		0.634	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297		AT	44030497	TA	AT	44030496	3	1	154	1	0	0	0	0	1	0	0	0	5285	1638	57	5	552	5	ETHE1	19	44030496	Missense_Mutation	DNP	TA	TCGA-P4-A5E7-01A-31D-A28G-10	24924469	44030496	15098487	117	13959											
NUP62	23636	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	50411616	50411633	+	In_Frame_Del	DEL	GTCCATGTGCGCATTGAG	GTCCATGTGCGCATTGAG	-																															tggtcgatccactgcagtgaGtccatgtgcgcattgaggat																								rs139913264|rs61751953|rs151075180		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	GTCCATGTGCGCATTGAG	GTCCATGTGCGCATTGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:50411616_50411633delGTCCATGTGCGCATTGAG	ENST00000596217.1	-	2	3319_3336	c.1432_1449delCTCAATGCGCACATGGAC	c.(1432-1449)ctcaatgcgcacatggacdel	p.LNAHMD478del	NUP62_ENST00000597723.1_In_Frame_Del_p.LNAHMD402del|NUP62_ENST00000413454.1_In_Frame_Del_p.LNAHMD478del|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597029.1_In_Frame_Del_p.LNAHMD478del|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000422090.2_In_Frame_Del_p.LNAHMD478del|NUP62_ENST00000352066.3_In_Frame_Del_p.LNAHMD478del|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	478					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)	p.A480A(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		ACTGCAGTGAGTCCATGTGCGCATTGAGGATCTTGCAG	0.628																																					p.478_483del		.											.	NUP62-615	1	Substitution - coding silent(1)	lung(1)	c.1432_1449del						.																																			SO:0001651	inframe_deletion	23636	exon3			.	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.1432_1449delCTCAATGCGCACATGGAC	19.37:g.50411616_50411633delGTCCATGTGCGCATTGAG	ENSP00000471191:p.Leu478_Asp483del	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	62	17	NM_153719	0	0	0	0	0	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	In_Frame_Del	DEL	ENST00000596217.1	37	CCDS12788.1																																																																																			.		0.628	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		-	50411633	GTCCATGTGCGCATTGAG	-	50411616	7	5	154	1	0	1	0	1	0	0	0	0	10794	1020	36	0	123	0	NUP62	19	50411616	In_Frame_Del	DEL	GTCCATGTGCGCATTGAG	TCGA-P4-A5E7-01A-31D-A28G-10	6381120	50411616	8717367	118	13960											
PRKCG	5582	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	54401854	54401854	+	Frame_Shift_Del	DEL	C	C	-																															cggccggccccacttcctcaCccagctccactccaccttcc																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:54401854delC	ENST00000263431.3	+	11	1535	c.1253delC	c.(1252-1254)accfs	p.T418fs	PRKCG_ENST00000540413.1_Frame_Shift_Del_p.T418fs|PRKCG_ENST00000542049.1_Frame_Shift_Del_p.T305fs	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CACTTCCTCACCCAGCTCCAC	0.662																																					p.T418fs		.											.	PRKCG-1367	0			c.1253delC						.						12	13	13					19																	54401854		2200	4285	6485	SO:0001589	frameshift_variant	5582	exon11			.	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1253delC	19.37:g.54401854delC	ENSP00000263431:p.Thr418fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	71	28	NM_002739	0	0	0	0	0	B7Z8Q0	Frame_Shift_Del	DEL	ENST00000263431.3	37	CCDS12867.1																																																																																			.		0.662	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		-	54401854	C	-	54401854	7	5	154	1	0	1	0	1	0	0	0	0	12541	507	18	0	1295	0	PRKCG	19	54401854	Frame_Shift_Del	DEL	C	TCGA-P4-A5E7-01A-31D-A28G-10	3990238	54401854	4727129	119	13961											
JAG1	182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	10653490	10653490	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggccgtgacgcgggactgAtactccttgaggcacacttt	7	9	12	13	4	0	3	0	3	0	0	1	4	1	4	3	3	1	1	3	3	1	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:10653490A>C	ENST00000254958.5	-	2	761	c.246T>G	c.(244-246)taT>taG	p.Y82*	RP11-103J8.1_ENST00000605292.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	82					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CGCGGGACTGATACTCCTTGA	0.662									Alagille Syndrome																												p.Y82X		.											.	JAG1-1273	0			c.T246G						.						51	50	51					20																	10653490		2203	4299	6502	SO:0001587	stop_gained	182	exon2	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGACTGATACTCC	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.246T>G	20.37:g.10653490A>C	ENSP00000254958:p.Tyr82*	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	94	25	NM_000214	0	0	15	20	5	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Nonsense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	A	41	8.923643	0.99004	.	.	ENSG00000101384	ENST00000254958	.	.	.	5.28	1.45	0.22620	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9719	0.41759	0.4136:0.0:0.5864:0.0	.	.	.	.	X	82	.	ENSP00000254958:Y82X	Y	-	3	2	JAG1	10601490	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.053000	0.41326	0.554000	0.29061	0.459000	0.35465	TAT	.		0.662	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		C	10653490	A	C	10653490	4	2	154	1	0	0	0	0	0	1	0	0	7955	340	12	5	3510	5	JAG1	20	10653490	Nonsense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		10653490	52372030	120	13962											
C20orf12	55184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	18414380	18414380	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggagtgttcatgggtacCaagcttctgcattctgcaca	9	12	11	9	0	3	0	1	0	2	0	3	1	3	1	1	2	4	5	1	2	2	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:18414380C>T	ENST00000358866.6	-	8	799	c.777G>A	c.(775-777)ttG>ttA	p.L259L	DZANK1_ENST00000357236.4_Silent_p.L145L|DZANK1_ENST00000262547.5_Silent_p.L259L|RNA5SP476_ENST00000516613.1_RNA|DZANK1_ENST00000329494.5_Silent_p.L261L|DZANK1_ENST00000487128.1_5'UTR			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	259							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						TCATGGGTACCAAGCTTCTGC	0.458																																					p.L259L		.											.	.	0			c.G777A						.						112	109	110					20																	18414380		2000	4182	6182	SO:0001819	synonymous_variant	55184	exon9			GGGTACCAAGCTT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.777G>A	20.37:g.18414380C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	61	14	NM_001099407	0	0	1	1	0	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	37	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	C	0.837	-0.743265	0.03088	.	.	ENSG00000089091	ENST00000358866	.	.	.	4.97	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.6738	10.7045	0.45948	0.0:0.9065:0.0:0.0935	.	.	.	.	X	58	.	.	W	-	2	0	C20orf12	18362380	1.000000	0.71417	0.803000	0.32268	0.023000	0.10783	1.732000	0.38146	2.448000	0.82819	0.655000	0.94253	TGG	.		0.458	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		T	18414380	C	T	18414380	2	4	154	1	0	0	0	0	0	0	0	1	2091	593	21	2		2	C20orf12	20	18414380	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	7760890	18414380	44611140	121	13963											
PLUNC	51297	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	31829269	31829269	+	Frame_Shift_Del	DEL	G	G	-																															gtcctgcctgagttggttcaGggcaacgtaagtaggcaagg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:31829269delG	ENST00000354297.4	+	6	731	c.660delG	c.(658-660)cagfs	p.Q220fs	BPIFA1_ENST00000375422.2_Frame_Shift_Del_p.Q220fs|BPIFA1_ENST00000375413.4_Frame_Shift_Del_p.Q220fs	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	220				Q -> K (in Ref. 1; AAF70860). {ECO:0000305}.	antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										AGTTGGTTCAGGGCAACGTAA	0.512																																					p.Q220fs		.											.	.	0			c.660delG						.						164	158	160					20																	31829269		2203	4300	6503	SO:0001589	frameshift_variant	51297	exon6			.	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"BPI fold containing"	15749	protein-coding gene	gene with protein product		607412	"palate, lung and nasal epithelium carcinoma associated", "palate, lung and nasal epithelium associated"	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.660delG	20.37:g.31829269delG	ENSP00000346251:p.Gln220fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	85	20	NM_016583	0	0	0	0	0	A8K9R3|E1P5M9|Q9NZT0	Frame_Shift_Del	DEL	ENST00000354297.4	37	CCDS13217.1																																																																																			.		0.512	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		-	31829269	G	-	31829269	7	5	154	1	0	1	0	1	0	0	0	0	12141	991	35	0	678	0	PLUNC	20	31829269	Frame_Shift_Del	DEL	G	TCGA-P4-A5E7-01A-31D-A28G-10	13414889	31829269	31196251	122	13964											
TRPC4AP	26133	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	33622951	33622951	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgctctgactcctcattGgccactcgcatcagggcatc	6	12	9	14	1	3	1	2	1	1	0	6	1	4	1	2	2	1	3	2	2	0	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:33622951G>T	ENST00000252015.2	-	8	1115	c.1026C>A	c.(1024-1026)gcC>gcA	p.A342A	TRPC4AP_ENST00000432634.2_Silent_p.A303A|TRPC4AP_ENST00000539834.1_5'UTR|TRPC4AP_ENST00000451813.2_Silent_p.A342A			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	342	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			ACTCCTCATTGGCCACTCGCA	0.537																																					p.A342A													.	TRPC4AP-91	0			c.C1026A						.						141	123	129					20																	33622951		2203	4300	6503	SO:0001819	synonymous_variant	26133	exon8			CTCATTGGCCACT	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.1026C>A	20.37:g.33622951G>T		Somatic	107	2		WXS	Illumina HiSeq	Phase_I	130	57	NM_199368	0	0	24	40	16	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			.		0.537	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		T	33622951	G	T	33622951	2	4	154	1	0	0	0	0	0	0	0	1	16614	1335	47	4		4	TRPC4AP	20	33622951	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	1793682	33622951	29402569	123	13965											
SS18L1	26039	hgsc.bcm.edu	37	chr20	60738629	60738629	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcagggcagccaggggagCagcatgatggggcagcggcc	8	2	21	10	1	0	1	0	1	0	0	0	2	0	2	2	7	4	5	2	7	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:60738629C>A	ENST00000331758.3	+	6	698	c.672C>A	c.(670-672)agC>agA	p.S224R	SS18L1_ENST00000370848.4_Missense_Mutation_p.S227R|SS18L1_ENST00000421564.1_Missense_Mutation_p.S224R	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	224	Gln-rich.|Methionine-rich intra-molecular domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GCCAGGGGAGCAGCATGATGG	0.731			T	SSX1	synovial sarcoma																																p.S224R		.		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	.	SS18L1-660	0			c.C672A						.						23	25	25					20																	60738629		2195	4294	6489	SO:0001583	missense	26039	exon6			GGGGAGCAGCATG	AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.672C>A	20.37:g.60738629C>A	ENSP00000333012:p.Ser224Arg	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	98	43	NM_198935	0	0	1	1	0	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Missense_Mutation	SNP	ENST00000331758.3	37	CCDS13491.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499248	0.64298	.	.	ENSG00000184402	ENST00000421564;ENST00000331758;ENST00000370848	T;T;T	0.32515	1.45;1.45;1.46	4.99	3.03	0.35002	.	0.269496	0.44483	D	0.000453	T	0.28499	0.0705	L	0.47716	1.5	0.25078	N	0.990947	P;P	0.45902	0.651;0.868	B;B	0.42319	0.198;0.383	T	0.11036	-1.0604	10	0.87932	D	0	-10.1574	11.0441	0.47849	0.0:0.8465:0.0:0.1535	.	224;224	B4DSR7;O75177	.;CREST_HUMAN	R	224;224;227	ENSP00000393999:S224R;ENSP00000333012:S224R;ENSP00000359885:S227R	ENSP00000333012:S224R	S	+	3	2	SS18L1	60172024	1.000000	0.71417	0.766000	0.31476	0.987000	0.75469	1.854000	0.39368	0.498000	0.27948	0.467000	0.42956	AGC	.		0.731	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			A	60738629	C	A	60738629	3	1	154	1	0	0	0	0	1	0	0	0	15208	709	25	4	694	4	SS18L1	20	60738629	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	27115678	60738629	2286891	124	13966											
PWP2	5822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	45534138	45534138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggctctgtgcacagtgTgtccttctcccctgatggca	6	11	11	13	0	2	1	0	1	2	0	4	1	3	1	3	2	1	3	3	2	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr21:45534138T>C	ENST00000291576.7	+	4	432	c.305T>C	c.(304-306)gTg>gCg	p.V102A		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	102					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GTGCACAGTGTGTCCTTCTCC	0.652											OREG0026247	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V102A		.											.	PWP2-91	0			c.T305C						.						113	94	100					21																	45534138		2203	4300	6503	SO:0001583	missense	5822	exon4			ACAGTGTGTCCTT		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"WD repeat domain containing"	9711	protein-coding gene	gene with protein product		601475	"PWP2 (periodic tryptophan protein, yeast) homolog"	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.305T>C	21.37:g.45534138T>C	ENSP00000291576:p.Val102Ala	Somatic	89	0	932	WXS	Illumina HiSeq	Phase_I	85	17	NM_005049	0	0	1	1	0	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498423	0.64298	.	.	ENSG00000241945	ENST00000291576	T	0.50001	0.76	4.8	4.8	0.61643	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.213399	0.38720	N	0.001592	T	0.35451	0.0932	L	0.33624	1.015	0.46131	D	0.998884	B	0.31383	0.321	B	0.25506	0.061	T	0.21999	-1.0229	10	0.42905	T	0.14	-8.6121	12.8724	0.57972	0.0:0.0:0.0:1.0	.	102	Q15269	PWP2_HUMAN	A	102	ENSP00000291576:V102A	ENSP00000291576:V102A	V	+	2	0	PWP2	44358566	0.995000	0.38212	0.948000	0.38648	0.736000	0.42039	5.690000	0.68241	1.929000	0.55896	0.402000	0.26972	GTG	.		0.652	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049		C	45534138	T	C	45534138	3	2	154	1	0	0	0	0	1	0	0	0	12876	1696	59	3	319	3	PWP2	21	45534138	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		45534138	2595757	125	13967											
C22orf15	150248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	24106287	24106287	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccacagctggctgctcggtGctggtgaacacctcttgcag	6	10	12	13	1	1	1	0	1	1	0	3	1	2	1	2	3	5	5	2	3	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:24106287G>A	ENST00000402217.3	+	2	292	c.39G>A	c.(37-39)gtG>gtA	p.V13V	C22orf15_ENST00000382821.3_Silent_p.V13V|C22orf15_ENST00000305199.5_Silent_p.V13V	NM_182520.2	NP_872326.2	Q8WYQ4	CV015_HUMAN	chromosome 22 open reading frame 15	13										breast(1)|pancreas(1)	2		Medulloblastoma(6;6.27e-05)|all_neural(6;0.00518)				GCTGCTCGGTGCTGGTGAACA	0.602																																					p.V13V		.											.	C22orf15-90	0			c.G39A						.						86	90	89					22																	24106287		692	1591	2283	SO:0001819	synonymous_variant	150248	exon2			CTCGGTGCTGGTG	AB050773	CCDS13814.2	22q11.23	2012-11-13			ENSG00000169314	ENSG00000169314			15558	protein-coding gene	gene with protein product							Standard	NM_182520		Approved	FLJ36561, N27C7-3	uc011aja.2	Q8WYQ4	OTTHUMG00000150740	ENST00000402217.3:c.39G>A	22.37:g.24106287G>A		Somatic	95	0		WXS	Illumina HiSeq	Phase_I	65	25	NM_182520	0	0	0	0	0	Q6ICJ7	Silent	SNP	ENST00000402217.3	37	CCDS13814.2																																																																																			.		0.602	C22orf15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319887.2	NM_182520		A	24106287	G	A	24106287	2	1	154	1	0	0	0	0	0	0	0	1	2142	1306	46	2		2	C22orf15	22	24106287	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		24106287	27198279	126	13968											
GATSL3	652968	hgsc.bcm.edu	37	chr22	30685454	30685454	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacgggcgacgctcagcacCcgcacccggtgttctaggat	7	6	14	14	5	2	0	1	0	1	0	2	3	2	2	2	4	1	4	2	4	1	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:30685454C>T	ENST00000407689.3	-	1	162	c.33G>A	c.(31-33)cgG>cgA	p.R11R	GATSL3_ENST00000459785.1_5'Flank|GATSL3_ENST00000404953.3_Silent_p.R11R|RP1-130H16.18_ENST00000447976.1_Intron	NM_001037666.2	NP_001032755.1	Q8WTX7	GATL3_HUMAN	GATS protein-like 3	11										breast(1)|endometrium(1)|lung(1)	3						CGCTCAGCACCCGCACCCGGT	0.741																																					p.R11R		.											.	GATSL3-135	0			c.G33A						.						11	18	16					22																	30685454		1870	4079	5949	SO:0001819	synonymous_variant	652968	exon1			CAGCACCCGCACC		CCDS43001.1	22q12	2010-06-23			ENSG00000239282	ENSG00000239282			34423	protein-coding gene	gene with protein product							Standard	NM_001037666		Approved			Q8WTX7	OTTHUMG00000150929	ENST00000407689.3:c.33G>A	22.37:g.30685454C>T		Somatic	8	0		WXS	Illumina HiSeq	Phase_I	56	20	NM_001037666	0	0	2	3	1	O76052|Q96ND9|Q9UIE8	Silent	SNP	ENST00000407689.3	37	CCDS43001.1																																																																																			.		0.741	GATSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320581.2	NM_001037666		T	30685454	C	T	30685454	2	4	154	1	0	0	0	0	0	0	0	1	6285	610	22	2		2	GATSL3	22	30685454	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	6579167	30685454	20619112	127	13969											
CBY1	25776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	39066951	39066951	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggatccccgactatgaacctGgcagggcaaagcctgaagtt	11	7	12	11	1	0	2	0	2	0	0	1	4	1	3	4	3	2	3	4	3	4	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:39066951G>A	ENST00000216029.3	+	3	275	c.141G>A	c.(139-141)ctG>ctA	p.L47L	RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000422408.2_RNA|RP3-508I15.10_ENST00000423346.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA	NM_015373.3	NP_056188.1	Q9Y3M2	CBY1_HUMAN	chibby homolog 1 (Drosophila)	47					cardiac muscle cell differentiation (GO:0055007)|cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein localization (GO:0008104)	ciliary basal body (GO:0036064)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-catenin binding (GO:0008013)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)	4	Melanoma(58;0.04)					CTATGAACCTGGCAGGGCAAA	0.527																																					p.L90L		.											.	CBY1-91	0			c.G270A						.						144	143	143					22																	39066951		2203	4300	6503	SO:0001819	synonymous_variant	25776	exon4			GAACCTGGCAGGG	BK005534	CCDS13974.1, CCDS74861.1	22q12	2014-02-06	2007-01-26	2007-01-26	ENSG00000100211	ENSG00000100211			1307	protein-coding gene	gene with protein product	"chibby CTNNB1-mediated transcription inhibitor"	607757	"chromosome 22 open reading frame 2", "PKD2 interactor, golgi and endoplasmic reticulum associated 1"	C22orf2, PGEA1		10591208, 15194699	Standard	NM_015373		Approved	PIGEA14, PIGEA-14, Chibby, Cby	uc003awb.4	Q9Y3M2	OTTHUMG00000150990	ENST00000216029.3:c.141G>A	22.37:g.39066951G>A		Somatic	64	0		WXS	Illumina HiSeq	Phase_I	67	14	NM_001002880	0	0	41	68	27	B2R4S2|Q66GT6|Q9UIK9	Silent	SNP	ENST00000216029.3	37	CCDS13974.1																																																																																			.		0.527	CBY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320832.1	NM_015373		A	39066951	G	A	39066951	2	1	154	1	0	0	0	0	0	0	0	1	2731	1335	47	2		2	CBY1	22	39066951	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	8381497	39066951	12237615	128	13970											
C22orf9	23313	broad.mit.edu	37	chr22	45599044	45599044	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccaaacgacatcttctgtgCcatgcgggcggccacgctca	8	7	11	15	4	3	0	1	0	2	0	3	1	3	0	3	2	3	1	3	2	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:45599044C>T	ENST00000336156.5	-	7	744	c.679G>A	c.(679-681)Gca>Aca	p.A227T	KIAA0930_ENST00000251993.7_Missense_Mutation_p.A232T|KIAA0930_ENST00000443310.3_Missense_Mutation_p.A209T|KIAA0930_ENST00000391627.2_Missense_Mutation_p.A193T|MIR1249_ENST00000408671.1_RNA|KIAA0930_ENST00000474515.1_5'Flank	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930	227										endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						ATCTTCTGTGCCATGCGGGCG	0.667																																					p.A232T													.	KIAA0930-90	0			c.G694A						.						93	99	97					22																	45599044		2203	4300	6503	SO:0001583	missense	23313	exon7			TCTGTGCCATGCG	AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 9"	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.679G>A	22.37:g.45599044C>T	ENSP00000336720:p.Ala227Thr	Somatic	39	1		WXS	Illumina HiSeq	Phase_I	98	30	NM_015264	0	0	41	73	32	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Missense_Mutation	SNP	ENST00000336156.5	37	CCDS33665.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.924082	0.73213	.	.	ENSG00000100364	ENST00000336156;ENST00000423262;ENST00000251993;ENST00000391627;ENST00000443310	.	.	.	4.88	3.85	0.44370	.	0.279975	0.39985	N	0.001216	T	0.54159	0.1841	L	0.49350	1.555	0.58432	D	0.999999	B;B;P;B	0.36990	0.089;0.294;0.577;0.437	B;B;B;B	0.38264	0.094;0.206;0.269;0.235	T	0.58885	-0.7557	9	0.62326	D	0.03	-31.0172	14.6102	0.68510	0.1469:0.8531:0.0:0.0	.	209;227;232;298	B0AZU2;Q6ICG6;Q6ICG6-2;Q8IUY4	.;K0930_HUMAN;.;.	T	227;112;232;193;209	.	ENSP00000251993:A232T	A	-	1	0	KIAA0930	43977708	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	7.226000	0.78060	1.052000	0.40392	0.555000	0.69702	GCA	.		0.667	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880		T	45599044	C	T	45599044	3	4	154	1	0	0	0	0	1	0	0	0	2157	739	26	2	551	2	C22orf9	22	45599044	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	6532093	45599044	5705522	129	13971											
SLC6A14	11254	broad.mit.edu	37	chrX	115568961	115568961	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattttttcttccccagaaaGtgtcggcttcatcagagaat	10	15	7	9	1	3	2	2	0	1	2	5	3	4	2	2	1	0	1	2	1	3	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chrX:115568961G>C	ENST00000371900.4	+	2	140	c.52G>C	c.(52-54)Gtg>Ctg	p.V18L		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	18					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TCCCCAGAAAGTGTCGGCTTC	0.393																																					p.V18L													.	SLC6A14-133	0			c.G52C						.						172	184	180					X																	115568961		2203	4300	6503	SO:0001583	missense	11254	exon2			CAGAAAGTGTCGG	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"Solute carriers"	11047	protein-coding gene	gene with protein product		300444	"solute carrier family 6 (neurotransmitter transporter), member 14"			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.52G>C	X.37:g.115568961G>C	ENSP00000360967:p.Val18Leu	Somatic	56	2		WXS	Illumina HiSeq	Phase_I	43	10	NM_007231	0	0	0	0	0	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	37	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.117382	0.37339	.	.	ENSG00000087916	ENST00000371900	T	0.72725	-0.68	5.17	5.17	0.71159	.	0.572600	0.16156	N	0.227033	T	0.46600	0.1401	N	0.08118	0	0.28155	N	0.929232	B	0.12013	0.005	B	0.09377	0.004	T	0.16600	-1.0397	10	0.05620	T	0.96	.	12.6956	0.57001	0.0:0.0:1.0:0.0	.	18	Q9UN76	S6A14_HUMAN	L	18	ENSP00000360967:V18L	ENSP00000360967:V18L	V	+	1	0	SLC6A14	115482989	0.995000	0.38212	0.976000	0.42696	0.957000	0.61999	2.073000	0.41519	2.393000	0.81446	0.544000	0.68410	GTG	.		0.393	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			C	115568961	G	C	115568961	3	2	154	1	0	0	0	0	1	0	0	0	14709	1029	36	4	58	4	SLC6A14	23	115568961	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		115568961	39701599	130	13972											
EIF4G3	8672	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	21133827	21133829	+	In_Frame_Del	DEL	CTC	CTC	-																															aagttttagttatcctcagaCtcctcttctgcttcccgcag																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:21133827_21133829delCTC	ENST00000264211.8	-	31	4935_4937	c.4741_4743delGAG	c.(4741-4743)gagdel	p.E1581del	EIF4G3_ENST00000374935.3_In_Frame_Del_p.E1301del|EIF4G3_ENST00000536266.1_In_Frame_Del_p.E1185del|EIF4G3_ENST00000602326.1_In_Frame_Del_p.E1587del|EIF4G3_ENST00000374937.3_In_Frame_Del_p.E1587del|EIF4G3_ENST00000400422.1_In_Frame_Del_p.E1581del|EIF4G3_ENST00000537738.1_In_Frame_Del_p.E1071del	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1581	EIF4A-binding. {ECO:0000250}.|Necessary but not sufficient for MKNK1- binding. {ECO:0000250}.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TATCCTCAGACTCCTCTTCTGCT	0.438																																					p.1617_1617del		.											.	EIF4G3-91	0			c.4849_4851del						.																																			SO:0001651	inframe_deletion	8672	exon35			.	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.4741_4743delGAG	1.37:g.21133830_21133832delCTC	ENSP00000264211:p.Glu1581del	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	99	33	NM_001198801	0	0	0	0	0	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	In_Frame_Del	DEL	ENST00000264211.8	37	CCDS214.1																																																																																			.		0.438	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		-	21133829	CTC	-	21133827	7	5	155	1	0	1	0	1	0	0	0	0	5051	564	20	0	18	0	EIF4G3	1	21133827	In_Frame_Del	DEL	CTC	TCGA-P4-A5E8-01A-11D-A28G-10		21133827	228116794	1	13973											
MSH4	4438	hgsc.bcm.edu	37	chr1	76346925	76346930	+	Splice_Site	DEL	TTTCAG	TTTCAG	-																															acatgtcttaccaaacgtgtTttcaggatagtgtgcaaact																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TTTCAG	TTTCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:76346925_76346930delTTTCAG	ENST00000263187.3	+	14	1885		c.e14-1			NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4						ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						CCAAACGTGTTTTCAGGATAGTGTGC	0.301								Mismatch excision repair (MMR)																													.		.											.	MSH4-660	0			.						.																																			SO:0001630	splice_region_variant	4438	.			.	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1782-1TTTCAG>-	1.37:g.76346925_76346930delTTTCAG		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	59	11	.	0	0	0	0	0	Q5T4U6|Q8NEB3|Q9UNP8	Splice_Site	DEL	ENST00000263187.3	37	CCDS670.1																																																																																			.		0.301	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	Intron	-	76346930	TTTCAG	-	76346925	8	5	155	1	0	1	0	1	0	0	1	0	9897	1856	64	0		0	MSH4	1	76346925	Splice_Site	DEL	TTTCAG	TCGA-P4-A5E8-01A-11D-A28G-10	55213098	76346925	172903696	2	13974	151	2									
MSH4	4438	bcgsc.ca	37	chr1	76346930	76346930	+	Splice_Site	DEL	G	G	-																															tcttaccaaacgtgttttcaGgatagtgtgcaaactgctta																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:76346930delG	ENST00000263187.3	+	14	1885		c.e14-1			NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4						ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						CGTGTTTTCAGGATAGTGTGC	0.303								Mismatch excision repair (MMR)																													.													.	MSH4-660	0			c.1782-1G>-						.						142	130	134					1																	76346930		2203	4299	6502	SO:0001630	splice_region_variant	4438	exon14			TTTTCAGGATAGT	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1782-1G>-	1.37:g.76346930delG		Somatic	82	0		WXS	Illumina HiSeq	Phase_1	58	22	NM_002440	0	0	0	0	0	Q5T4U6|Q8NEB3|Q9UNP8	Splice_Site	DEL	ENST00000263187.3	37	CCDS670.1																																																																																			.		0.303	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	Intron	-	76346930	G	-	76346930	8	5	155	1	0	1	0	1	0	0	1	0	9897	1014	35	0	1835	0	MSH4	1	76346930	Splice_Site	DEL	G	TCGA-P4-A5E8-01A-11D-A28G-10	5	76346930	172903691	3	13975	151	2									
LYSMD1	388695	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151134570	151134570	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggtttgcacgtttaatctGttccatcttaaaaaaaaaag	14	13	7	7	2	2	0	0	0	2	0	3	0	3	0	1	1	1	4	1	1	6	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:151134570G>T	ENST00000368908.5	-	2	847	c.187C>A	c.(187-189)Cag>Aag	p.Q63K	LYSMD1_ENST00000440902.2_Missense_Mutation_p.Q15K	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1	63										endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGTTTAATCTGTTCCATCTTA	0.378																																					p.Q63K		.											.	LYSMD1-90	0			c.C187A						.						50	51	51					1																	151134570		2203	4300	6503	SO:0001583	missense	388695	exon2			TAATCTGTTCCAT	BX647911	CCDS986.1, CCDS44218.1	1q21.2	2008-02-05			ENSG00000163155	ENSG00000163155			32070	protein-coding gene	gene with protein product						12477932	Standard	NM_212551		Approved	SB145, MGC35223, RP11-68I18.5	uc001ewy.3	Q96S90	OTTHUMG00000012260	ENST00000368908.5:c.187C>A	1.37:g.151134570G>T	ENSP00000357904:p.Gln63Lys	Somatic	69	0		WXS	Illumina HiSeq	Phase_I	71	27	NM_212551	0	0	0	0	0	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	37	CCDS986.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637942	0.67130	.	.	ENSG00000163155	ENST00000368908;ENST00000440902	T;T	0.40225	1.12;1.04	5.66	4.73	0.59995	Peptidoglycan-binding Lysin subgroup (1);Peptidoglycan-binding lysin domain (1);	0.000000	0.85682	D	0.000000	T	0.20210	0.0486	L	0.33189	0.99	0.49915	D	0.99983	P;B	0.41450	0.75;0.235	B;B	0.36766	0.232;0.103	T	0.07520	-1.0768	10	0.87932	D	0	-2.7477	14.7732	0.69696	0.0:0.0:0.8542:0.1457	.	15;63	Q96S90-2;Q96S90	.;LYSM1_HUMAN	K	63;15	ENSP00000357904:Q63K;ENSP00000404059:Q15K	ENSP00000357904:Q63K	Q	-	1	0	LYSMD1	149401194	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.056000	0.93881	1.345000	0.45676	0.467000	0.42956	CAG	.		0.378	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551		T	151134570	G	T	151134570	3	4	155	1	0	0	0	0	1	0	0	0	9149	1386	48	4	504	4	LYSMD1	1	151134570	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	74787640	151134570	98116051	4	13976											
SHC1	6464	broad.mit.edu	37	chr1	154938022	154938022	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctgccacactcaccacAccctcagggtccaccagtag	10	6	6	19	0	3	0	2	0	1	0	4	0	4	0	6	1	1	1	6	1	1	1			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:154938022A>C	ENST00000368445.5	-	11	1834	c.1620T>G	c.(1618-1620)ggT>ggG	p.G540G	SHC1_ENST00000368450.1_Silent_p.G430G|SHC1_ENST00000448116.2_Silent_p.G541G|SHC1_ENST00000368453.4_Silent_p.G431G|SHC1_ENST00000368449.4_Silent_p.G311G|SHC1_ENST00000490667.1_Intron|PYGO2_ENST00000483463.1_5'Flank|RP11-307C12.12_ENST00000605085.1_RNA|SHC1_ENST00000606391.1_Silent_p.G341G	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	540	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CACTCACCACACCCTCAGGGT	0.547																																					p.G541G	NSCLC(4;32 234 1864 2492 3259 13747 17376)												.	SHC1-847	0			c.T1623G						.						144	132	136					1																	154938022		2203	4300	6503	SO:0001819	synonymous_variant	6464	exon11			CACCACACCCTCA	U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"SH2 domain containing"	10840	protein-coding gene	gene with protein product		600560	"SHC (Src homology 2 domain-containing) transforming protein 1"	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.1620T>G	1.37:g.154938022A>C		Somatic	152	6		WXS	Illumina HiSeq	Phase_I	145	11	NM_001130040	0	0	1	1	0	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	A	9.344	1.063853	0.20067	.	.	ENSG00000160691	ENST00000444664	.	.	.	4.76	1.06	0.20224	.	.	.	.	.	T	0.29190	0.0726	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14755	-1.0461	4	.	.	.	.	3.707	0.08404	0.4984:0.0:0.2612:0.2404	.	.	.	.	G	204	.	.	C	-	1	0	SHC1	153204646	0.687000	0.27671	1.000000	0.80357	0.994000	0.84299	-0.117000	0.10708	0.324000	0.23333	0.455000	0.32223	TGT	.		0.547	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001		C	154938022	A	C	154938022	2	2	155	1	0	0	0	0	0	0	0	1	14302	146	6	5		5	SHC1	1	154938022	Silent	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	3803452	154938022	94312599	5	13977											
TOR1AIP2	163590	hgsc.bcm.edu;broad.mit.edu	37	chr1	179815212	179815212	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgtgcttagctttagaaAaggcacccctgttcttctat	8	15	7	11	0	3	1	0	0	3	1	3	1	3	1	2	1	2	4	2	1	5	6			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:179815212A>C	ENST00000367612.3	-	6	1794	c.1407T>G	c.(1405-1407)ctT>ctG	p.L469L	TOR1AIP2_ENST00000609928.1_Silent_p.L469L	NM_145034.4	NP_659471.1	Q9H496	IFG15_HUMAN	torsin A interacting protein 2	0										cervix(1)|endometrium(3)|large_intestine(1)|lung(10)|ovary(1)|skin(2)	18						AGCTTTAGAAAAGGCACCCCT	0.423																																					p.L469L		.											.	TOR1AIP2-69	0			c.T1407G						.						90	88	89					1																	179815212		2203	4300	6503	SO:0001819	synonymous_variant	163590	exon7			TTAGAAAAGGCAC		CCDS1334.1	1q25.2	2012-02-09			ENSG00000169905	ENSG00000169905			24055	protein-coding gene	gene with protein product		614513				15767459	Standard	NM_145034		Approved	LULL1, NET9, IFRG15	uc001gnk.3	Q8NFQ8	OTTHUMG00000035265	ENST00000367612.3:c.1407T>G	1.37:g.179815212A>C		Somatic	118	0		WXS	Illumina HiSeq	Phase_I	110	6	NM_001199260	0	0	2	2	0	Q05BU2	Silent	SNP	ENST00000367612.3	37	CCDS1334.1																																																																																			.		0.423	TOR1AIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085304.1	NM_145034		C	179815212	A	C	179815212	2	2	155	1	0	0	0	0	0	0	0	1	16406	1	1	5		5	TOR1AIP2	1	179815212	Silent	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	24877190	179815212	69435409	6	13978											
GPR37L1	9283	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	202097307	202097311	+	Frame_Shift_Del	DEL	CTCAA	CTCAA	-																															acgagcagtgtgagagccagCtcaacagcaccgtggtgggc																								rs76841249	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CTCAA	CTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:202097307_202097311delCTCAA	ENST00000367282.5	+	2	1175_1179	c.1069_1073delCTCAA	c.(1069-1074)ctcaacfs	p.LN357fs		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	357					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						TGAGAGCCAGCTCAACAGCACCGTG	0.639																																					p.357_358del		.											.	GPR37L1-91	0			c.1069_1073del						.																																			SO:0001589	frameshift_variant	9283	exon2			.	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"GPCR / Class A : Orphans"	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1069_1073delCTCAA	1.37:g.202097307_202097311delCTCAA	ENSP00000356251:p.Leu357fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	86	37	NM_004767	0	0	0	0	0	B2R7M9|Q5SXP7|Q86VP7	Frame_Shift_Del	DEL	ENST00000367282.5	37	CCDS1420.1																																																																																			.		0.639	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		-	202097311	CTCAA	-	202097307	7	5	155	1	0	1	0	1	0	0	0	0	6712	797	28	0	1075	0	GPR37L1	1	202097307	Frame_Shift_Del	DEL	CTCAA	TCGA-P4-A5E8-01A-11D-A28G-10	22282095	202097307	47153314	7	13979											
THUMPD2	80745	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	39964198	39964199	+	Splice_Site	DEL	CT	CT	-																															ggttccgccaacatgaagcaCtctgtgacaaaaaaaaaatg																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:39964198_39964199delCT	ENST00000505747.1	-	10	1215_1216	c.1188_1189delAG	c.(1186-1191)agagtg>agtg	p.RV396fs	THUMPD2_ENST00000260619.6_Splice_Site_p.RV366fs	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	396							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				ACATGAAGCACTCTGTGACAAA	0.356																																					p.396_397del		.											.	THUMPD2-91	0			c.1188_1189del						.																																			SO:0001630	splice_region_variant	80745	exon10			.	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.1188-1AG>-	2.37:g.39964200_39964201delCT		Somatic	94	0		WXS	Illumina HiSeq	Phase_I	124	23	NM_025264	0	0	0	0	0	A8K7I7|Q53TT8|Q53TV0	Frame_Shift_Del	DEL	ENST00000505747.1	37	CCDS1805.2																																																																																			.		0.356	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264	Frame_Shift_Del	-	39964199	CT	-	39964198	8	5	155	1	0	1	0	1	0	0	1	0	15915	579	20	0	326	0	THUMPD2	2	39964198	Splice_Site	DEL	CT	TCGA-P4-A5E8-01A-11D-A28G-10		39964198	203235175	8	13980	152	2									
THUMPD2	80745	hgsc.bcm.edu	37	chr2	39964200	39964200	+	Splice_Site	SNP	C	C	G																															ttccgccaacatgaagcactCtgtgacaaaaaaaaaatggt																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:39964200C>G	ENST00000505747.1	-	10	1215		c.e10-1		THUMPD2_ENST00000260619.6_Splice_Site	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2								methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				ATGAAGCACTCTGTGACAAAA	0.353																																					.		.											.	THUMPD2-91	0			c.1188-1G>C						.						66	62	63					2																	39964200		2203	4300	6503	SO:0001630	splice_region_variant	80745	exon11			AGCACTCTGTGAC	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.1188-1G>C	2.37:g.39964200C>G		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	94	8	NM_025264	0	0	0	0	0	A8K7I7|Q53TT8|Q53TV0	Splice_Site	SNP	ENST00000505747.1	37	CCDS1805.2	.	.	.	.	.	.	.	.	.	.	C	15.08	2.726690	0.48833	.	.	ENSG00000138050	ENST00000505747;ENST00000260619	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2156	0.73264	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	THUMPD2	39817704	1.000000	0.71417	1.000000	0.80357	0.548000	0.35241	4.572000	0.60886	2.664000	0.90586	0.655000	0.94253	.	.		0.353	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264	Intron	G	39964200	C	G	39964200	5	3	155	1	0	0	0	0	0	0	1	0	15915	927	32	4	328	4	THUMPD2	2	39964200	Splice_Site	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	2	39964200	203235173	9	13981	152	2									
PPM1B	5495	broad.mit.edu	37	chr2	44429130	44429130	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttaaatctaggcttgaggtAtctgatgacctggaaaatgt	12	13	11	5	0	2	3	0	3	2	0	2	4	2	4	1	3	0	3	1	3	6	4			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:44429130A>G	ENST00000282412.4	+	2	1204	c.792A>G	c.(790-792)gtA>gtG	p.V264V	PPM1B_ENST00000378551.2_Silent_p.V264V|PPM1B_ENST00000409895.4_Silent_p.V264V|PPM1B_ENST00000345249.4_Intron|PPM1B_ENST00000409432.3_Silent_p.V264V|PPM1B_ENST00000378540.4_3'UTR	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	264					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GGCTTGAGGTATCTGATGACC	0.358																																					p.V264V													.	PPM1B-227	0			c.A792G						.						110	107	108					2																	44429130		2203	4300	6503	SO:0001819	synonymous_variant	5495	exon2			TGAGGTATCTGAT	AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9276	protein-coding gene	gene with protein product	"protein phosphatase 2C, beta isoform"	603770	"protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.792A>G	2.37:g.44429130A>G		Somatic	145	0		WXS	Illumina HiSeq	Phase_I	162	5	NM_001033556	0	0	18	18	0	Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Silent	SNP	ENST00000282412.4	37	CCDS1817.1																																																																																			.		0.358	PPM1B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250672.1	NM_002706		G	44429130	A	G	44429130	2	3	155	1	0	0	0	0	0	0	0	1	12365	436	16	3		3	PPM1B	2	44429130	Silent	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	4464930	44429130	198770243	10	13982											
TEKT4	150483	broad.mit.edu	37	chr2	95539829	95539830	+	Frame_Shift_Ins	INS	-	-	G																															accgaggtgcaggctcatccINSgtactccaccaccttccaag																								rs149873671		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:95539829_95539830insG	ENST00000295201.4	+	3	826_827	c.689_690insG	c.(688-693)ccgtacfs	p.Y231fs	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	231					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.P230P(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CAGGCTCATCCGTACTCCACCA	0.663																																					p.P230fs													.	TEKT4-155	1	Substitution - coding silent(1)	lung(1)	c.689_690insG						.																																			SO:0001589	frameshift_variant	150483	exon3			CTCATCCGTACTC	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.690dupG	2.37:g.95539830_95539830dupG	ENSP00000295201:p.Tyr231fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	171	7	NM_144705	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000295201.4	37	CCDS2005.1																																																																																			.		0.663	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		G	95539830	-	G	95539829	7	5	155	1	0	1	1	0	0	0	0	0	15787	652	23	0	699	0	TEKT4	2	95539829	Frame_Shift_Ins	INS	-	TCGA-P4-A5E8-01A-11D-A28G-10	51110699	95539829	147659544	11	13983											
TSGA10	80705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	99634687	99634687	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctaatgatcgatctaggcctCggtcaggagatcgatggtga	10	10	13	8	3	2	3	1	2	1	1	5	6	2	3	1	4	0	0	1	4	2	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:99634687C>T	ENST00000393483.3	-	20	2892	c.2048G>A	c.(2047-2049)cGa>cAa	p.R683Q	TSGA10_ENST00000539964.1_Missense_Mutation_p.R683Q|TSGA10_ENST00000355053.4_Missense_Mutation_p.R683Q|TSGA10_ENST00000410001.1_Missense_Mutation_p.R683Q	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	683	Interaction with HIF1A. {ECO:0000250}.				cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						ATCTAGGCCTCGGTCAGGAGA	0.383																																					p.R683Q		.											.	TSGA10-91	0			c.G2048A						.						115	109	111					2																	99634687		2203	4300	6503	SO:0001583	missense	80705	exon19			AGGCCTCGGTCAG	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"cancer/testis antigen 79"	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.2048G>A	2.37:g.99634687C>T	ENSP00000377123:p.Arg683Gln	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	87	30	NM_182911	0	0	0	0	0	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.604396	0.87157	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482	T;T;T;T;T;T	0.54071	0.66;0.66;0.66;0.66;0.59;0.72	5.04	4.16	0.48862	.	0.368291	0.23162	N	0.051240	T	0.39384	0.1076	L	0.27053	0.805	0.80722	D	1	B	0.18461	0.028	B	0.10450	0.005	T	0.21827	-1.0234	10	0.39692	T	0.17	-2.5563	12.49	0.55895	0.0:0.9177:0.0:0.0823	.	683	Q9BZW7	TSG10_HUMAN	Q	683;683;683;683;613;683	ENSP00000377123:R683Q;ENSP00000386956:R683Q;ENSP00000347161:R683Q;ENSP00000444419:R683Q;ENSP00000386508:R613Q;ENSP00000377122:R683Q	ENSP00000347161:R683Q	R	-	2	0	TSGA10	99001119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.166000	0.64965	1.472000	0.48140	0.655000	0.94253	CGA	.		0.383	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		T	99634687	C	T	99634687	3	4	155	1	0	0	0	0	1	0	0	0	16650	884	31	1	56	1	TSGA10	2	99634687	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	4094858	99634687	143564686	12	13984											
EPC2	26122	broad.mit.edu;bcgsc.ca	37	chr2	149519453	149519453	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgattaagagaagagagaaaAcaaaacgagaattattgcac	21	7	9	4	1	0	5	0	1	0	4	0	8	0	5	0	0	3	1	0	0	8	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:149519453A>T	ENST00000258484.6	+	5	803	c.769A>T	c.(769-771)Aca>Tca	p.T257S		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	257					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		AAGAGAGAAAACAAAACGAGA	0.343																																					p.T257S													.	EPC2-137	0			c.A769T						.						79	73	75					2																	149519453		1825	4078	5903	SO:0001583	missense	26122	exon5			GAGAAAACAAAAC	AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.769A>T	2.37:g.149519453A>T	ENSP00000258484:p.Thr257Ser	Somatic	304	0		WXS	Illumina HiSeq	Phase_I	294	9	NM_015630	0	0	2	2	0	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	37	CCDS46422.1	.	.	.	.	.	.	.	.	.	.	A	8.123	0.781269	0.16120	.	.	ENSG00000135999	ENST00000258484	.	.	.	5.6	5.6	0.85130	.	0.115719	0.56097	D	0.000030	T	0.27313	0.0670	N	0.03084	-0.415	0.80722	D	1	B	0.19073	0.033	B	0.10450	0.005	T	0.25641	-1.0126	9	0.02654	T	1	-4.0144	15.7881	0.78326	1.0:0.0:0.0:0.0	.	257	Q52LR7	EPC2_HUMAN	S	257	.	ENSP00000258484:T257S	T	+	1	0	EPC2	149235923	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.309000	0.59135	2.137000	0.66172	0.482000	0.46254	ACA	.		0.343	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		T	149519453	A	T	149519453	3	4	155	1	0	0	0	0	1	0	0	0	5174	43	2	5	787	5	EPC2	2	149519453	Missense_Mutation	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	49884766	149519453	93679920	13	13985											
HOXD10	3236	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	176981597	176981599	+	In_Frame_Del	DEL	TTT	TTT	-																															agctctcctgctgctaatacTtttttagtagattccttgat																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:176981597_176981599delTTT	ENST00000249501.4	+	1	291_293	c.36_38delTTT	c.(34-39)actttt>act	p.F13del	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	13					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		CTGCTAATACTTTTTTAGTAGAT	0.453																																					p.12_13del		.											.	HOXD10-91	0			c.36_38del						.																																			SO:0001651	inframe_deletion	3236	exon1			.		CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"Homeoboxes / ANTP class : HOXL subclass"	5133	protein-coding gene	gene with protein product		142984	"homeo box D10"	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.36_38delTTT	2.37:g.176981600_176981602delTTT	ENSP00000249501:p.Phe13del	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	80	33	NM_002148	0	0	0	0	0	Q6NT10	In_Frame_Del	DEL	ENST00000249501.4	37	CCDS2266.1																																																																																			.		0.453	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2			-	176981599	TTT	-	176981597	7	5	155	1	0	1	0	1	0	0	0	0	7340	1596	56	0	38	0	HOXD10	2	176981597	In_Frame_Del	DEL	TTT	TCGA-P4-A5E8-01A-11D-A28G-10	27462144	176981597	66217776	14	13986											
GLS	2744	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	191788697	191788701	+	Frame_Shift_Del	DEL	AAAAG	AAAAG	-																															tttgcaataggatattacttAaaagaaaagaaggtttttaa																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AAAAG	AAAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:191788697_191788701delAAAAG	ENST00000320717.3	+	10	1443_1447	c.1185_1189delAAAAG	c.(1183-1191)ttaaaagaafs	p.KE396fs	GLS_ENST00000338435.4_Frame_Shift_Del_p.KE396fs	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	396					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	GATATTACTTAAAAGAAAAGAAGGT	0.259																																					p.395_397del		.											.	GLS-92	0			c.1185_1189del						.																																			SO:0001589	frameshift_variant	2744	exon10			.	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.1185_1189delAAAAG	2.37:g.191788702_191788706delAAAAG	ENSP00000317379:p.Lys396fs	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	120	34	NM_014905	0	0	0	0	0	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Frame_Shift_Del	DEL	ENST00000320717.3	37	CCDS2308.1																																																																																			.		0.259	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			-	191788701	AAAAG	-	191788697	7	5	155	1	0	1	0	1	0	0	0	0	6483	359	13	0	1223	0	GLS	2	191788697	Frame_Shift_Del	DEL	AAAAG	TCGA-P4-A5E8-01A-11D-A28G-10	14807100	191788697	51410676	15	13987											
BBS12	166379	ucsc.edu	37	chr4	123664664	123664664	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaggtcttccttggaggTggtgcagttgaatttttgtg	8	15	14	4	0	1	1	0	1	1	0	2	3	2	2	1	4	1	2	1	4	3	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr4:123664664T>C	ENST00000314218.3	+	2	1810	c.1617T>C	c.(1615-1617)ggT>ggC	p.G539G	BBS12_ENST00000542236.1_Silent_p.G539G	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	539			G -> D (in BBS12). {ECO:0000269|PubMed:21344540}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TCCTTGGAGGTGGTGCAGTTG	0.413									Bardet-Biedl syndrome																												p.G539G													.	BBS12-92	0			c.T1617C						.						159	158	158					4																	123664664		2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TGGAGGTGGTGCA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"Heat Shock Proteins / Chaperonins"	26648	protein-coding gene	gene with protein product		610683	"chromosome 4 open reading frame 24"	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1617T>C	4.37:g.123664664T>C		Somatic	123	0		WXS	Illumina HiSeq		80	2	NM_001178007	0	0	6	7	1	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			.		0.413	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		C	123664664	T	C	123664664	2	2	155	1	0	0	0	0	0	0	0	1	1338	1683	59	3		3	BBS12	4	123664664	Silent	SNP	T	TCGA-P4-A5E8-01A-11D-A28G-10		123664664	67489612	16	13988											
TMEM184C	55751	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	148545023	148545023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcttggtttattgctggaatCtttttgctgttgactattcc	5	20	9	7	0	1	1	0	1	1	0	2	2	2	2	1	2	2	5	1	2	3	9			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr4:148545023C>G	ENST00000296582.3	+	2	736	c.162C>G	c.(160-162)atC>atG	p.I54M	TMEM184C_ENST00000508208.1_Missense_Mutation_p.I54M	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	54						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						TTGCTGGAATCTTTTTGCTGT	0.333																																					p.I54M		.											.	TMEM184C-90	0			c.C162G						.						137	135	135					4																	148545023		2202	4299	6501	SO:0001583	missense	55751	exon2			TGGAATCTTTTTG	AF305823	CCDS3770.1	4q31.22	2008-06-05	2008-06-05	2008-06-05		ENSG00000164168			25587	protein-coding gene	gene with protein product		613937	"transmembrane protein 34"	TMEM34			Standard	NM_018241		Approved	FLJ10846	uc003ila.4	Q9NVA4		ENST00000296582.3:c.162C>G	4.37:g.148545023C>G	ENSP00000296582:p.Ile54Met	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	65	37	NM_018241	0	0	0	7	7	D3DP04|Q86X84|Q969I7|Q9NXM2	Missense_Mutation	SNP	ENST00000296582.3	37	CCDS3770.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.130269	0.37630	.	.	ENSG00000164168	ENST00000296582;ENST00000508208	T;T	0.45668	0.89;0.89	5.28	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.45994	0.1370	L	0.60904	1.88	0.50171	D	0.999858	P	0.42456	0.78	P	0.45138	0.471	T	0.45425	-0.9262	10	0.54805	T	0.06	-23.423	13.982	0.64310	0.54:0.46:0.0:0.0	.	54	Q9NVA4	T184C_HUMAN	M	54	ENSP00000296582:I54M;ENSP00000425940:I54M	ENSP00000296582:I54M	I	+	3	3	TMEM184C	148764473	0.945000	0.32115	1.000000	0.80357	0.993000	0.82548	0.073000	0.14640	0.644000	0.30656	0.455000	0.32223	ATC	.		0.333	TMEM184C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364644.1	NM_018241		G	148545023	C	G	148545023	3	3	155	1	0	0	0	0	1	0	0	0	16138	903	32	4	168	4	TMEM184C	4	148545023	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	24880359	148545023	42609253	17	13989											
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	187629210	187629211	+	Frame_Shift_Del	DEL	AC	AC	-																															catctgcatcaatagcagaaAcagtggttatttgctctccc																								rs572691033	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr4:187629210_187629211delAC	ENST00000441802.2	-	2	1980_1981	c.1771_1772delGT	c.(1771-1773)gttfs	p.V591fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	591	Cadherin 5. {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						AATAGCAGAAACAGTGGTTATT	0.396										HNSCC(5;0.00058)																											p.591_591del	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.1771_1772del						.																																			SO:0001589	frameshift_variant	2195	exon2			.	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.1771_1772delGT	4.37:g.187629210_187629211delAC	ENSP00000406229:p.Val591fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	53	25	NM_005245	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																			.		0.396	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187629211	AC	-	187629210	7	5	155	1	0	1	0	1	0	0	0	0	5708	43	2	0	12098	0	FAT1	4	187629210	Frame_Shift_Del	DEL	AC	TCGA-P4-A5E8-01A-11D-A28G-10	39084187	187629210	3525066	18	13990											
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	36986201	36986204	+	Frame_Shift_Del	DEL	AAAG	AAAG	-																															ggcaatgttactcaggagacAaagaaaatggaaatgaaagg																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:36986201_36986204delAAAG	ENST00000282516.8	+	10	3418_3421	c.2919_2922delAAAG	c.(2917-2922)acaaagfs	p.TK973fs	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Frame_Shift_Del_p.TK973fs	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	973					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CTCAGGAGACAAAGAAAATGGAAA	0.373																																					p.973_974del		.											.	NIPBL-293	0			c.2919_2922del	GRCh37	CD063575	NIPBL	D		.																																			SO:0001589	frameshift_variant	25836	exon10			.	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"sister chromatid cohesion 2 homolog (yeast)"	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2919_2922delAAAG	5.37:g.36986201_36986204delAAAG	ENSP00000282516:p.Thr973fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	80	17	NM_015384	0	0	0	0	0	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	37	CCDS3920.1																																																																																			.		0.373	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	36986204	AAAG	-	36986201	7	5	155	1	0	1	0	1	0	0	0	0	10454	117	5	0	2953	0	NIPBL	5	36986201	Frame_Shift_Del	DEL	AAAG	TCGA-P4-A5E8-01A-11D-A28G-10		36986201	143929059	19	13991											
C5orf35	133383	broad.mit.edu;bcgsc.ca	37	chr5	56210690	56210691	+	Frame_Shift_Del	DEL	AG	AG	-																															tgatgtgcttgttcctagacAgagcagctaatgtctgttat																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:56210690_56210691delAG	ENST00000285947.2	+	5	1095_1096	c.709_710delAG	c.(709-711)agafs	p.R237fs	SETD9_ENST00000475908.1_3'UTR|SETD9_ENST00000541720.1_Frame_Shift_Del_p.R237fs	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	237	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)										GTTCCTAGACAGAGCAGCTAAT	0.356																																					p.237_237del													.	.	0			c.709_710del						.																																			SO:0001589	frameshift_variant	133383	exon5			CTAGACAGAGCAG	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 35"	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.709_710delAG	5.37:g.56210692_56210693delAG	ENSP00000285947:p.Arg237fs	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	97	11	NM_153706	0	0	0	0	0	F5H713	Frame_Shift_Del	DEL	ENST00000285947.2	37	CCDS3972.1																																																																																			.		0.356	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		-	56210691	AG	-	56210690	7	5	155	1	0	1	0	1	0	0	0	0	2300	180	7	0	727	0	C5orf35	5	56210690	Frame_Shift_Del	DEL	AG	TCGA-P4-A5E8-01A-11D-A28G-10	19224489	56210690	124704570	20	13992											
MAST4	375449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	66456396	66456396	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgaggcggagcaagaaatCcaagaagaaagaaagtctcg	17	4	14	6	2	1	5	0	1	1	4	3	6	2	6	1	3	1	1	1	3	6	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:66456396C>A	ENST00000403625.2	+	27	4056	c.3761C>A	c.(3760-3762)tCc>tAc	p.S1254Y	MAST4_ENST00000403666.1_Missense_Mutation_p.S1065Y|MAST4_ENST00000261569.7_Missense_Mutation_p.S1060Y|MAST4_ENST00000404260.3_Missense_Mutation_p.S1257Y|MAST4_ENST00000405643.1_Missense_Mutation_p.S1075Y	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1257						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGCAAGAAATCCAAGAAGAAA	0.393																																					p.S1254Y		.											.	MAST4-647	0			c.C3761A						.						104	106	106					5																	66456396		1862	4094	5956	SO:0001583	missense	375449	exon27			AGAAATCCAAGAA	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.3761C>A	5.37:g.66456396C>A	ENSP00000385727:p.Ser1254Tyr	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	76	25	NM_001164664	0	0	0	4	4	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031570	0.75504	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T	0.68331	-0.28;-0.28;-0.32;-0.32;-0.28	5.81	4.93	0.64822	.	0.234815	0.43260	D	0.000587	T	0.79106	0.4390	M	0.73217	2.22	0.34416	D	0.696926	D;D	0.69078	0.99;0.997	P;D	0.65443	0.862;0.935	D	0.85389	0.1124	10	0.72032	D	0.01	-19.186	14.3064	0.66386	0.0:0.9294:0.0:0.0706	.	1257;1065	O15021;O15021-3	MAST4_HUMAN;.	Y	1257;1254;1065;1075;1075;1060;993	ENSP00000385048:S1257Y;ENSP00000385727:S1254Y;ENSP00000384313:S1065Y;ENSP00000384099:S1075Y;ENSP00000261569:S1060Y	ENSP00000261569:S1060Y	S	+	2	0	MAST4	66492152	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.264000	0.51553	2.736000	0.93811	0.655000	0.94253	TCC	.		0.393	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66456396	C	A	66456396	3	1	155	1	0	0	0	0	1	0	0	0	9352	855	30	4	3997	4	MAST4	5	66456396	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	10245706	66456396	114458864	21	13993											
EPB41L4A	64097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	111506049	111506049	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttcttcggacaatccggatGgatccacaagttcttttctg	8	14	9	10	2	3	0	0	0	3	0	6	3	5	3	2	3	0	2	2	3	2	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:111506049G>A	ENST00000261486.5	-	20	1964	c.1688C>T	c.(1687-1689)cCa>cTa	p.P563L	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	563						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CAATCCGGATGGATCCACAAG	0.378																																					p.P563L		.											.	EPB41L4A-91	0			c.C1688T						.						118	111	113					5																	111506049		1832	4086	5918	SO:0001583	missense	64097	exon20			CCGGATGGATCCA	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.1688C>T	5.37:g.111506049G>A	ENSP00000261486:p.Pro563Leu	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	68	22	NM_022140	0	0	3	6	3	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	37	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543095	0.86022	.	.	ENSG00000129595	ENST00000261486	D	0.84070	-1.8	5.21	5.21	0.72293	.	0.131978	0.51477	D	0.000100	D	0.86703	0.5996	L	0.32530	0.975	0.58432	D	0.999998	D;D	0.89917	0.986;1.0	P;D	0.87578	0.655;0.998	D	0.85851	0.1404	10	0.36615	T	0.2	.	17.5611	0.87908	0.0:0.0:1.0:0.0	.	563;190	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	L	563	ENSP00000261486:P563L	ENSP00000261486:P563L	P	-	2	0	EPB41L4A	111533948	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.409000	0.80053	2.415000	0.81967	0.563000	0.77884	CCA	.		0.378	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			A	111506049	G	A	111506049	3	1	155	1	0	0	0	0	1	0	0	0	5168	1348	47	2	388	2	EPB41L4A	5	111506049	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	45049653	111506049	69409211	22	13994											
APC	324	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	112154880	112154880	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggctcgggccagggccaGtgcagcactccacaacatca	11	4	12	14	1	1	1	1	0	0	1	3	1	2	1	3	3	3	3	3	3	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:112154880G>T	ENST00000457016.1	+	10	1531	c.1151G>T	c.(1150-1152)aGt>aTt	p.S384I	APC_ENST00000508376.2_Missense_Mutation_p.S384I|APC_ENST00000257430.4_Missense_Mutation_p.S384I			P25054	APC_HUMAN	adenomatous polyposis coli	384	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GCCAGGGCCAGTGCAGCACTC	0.507		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.S384I	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC-12026	0			c.G1151T	GRCh37	CD021189	APC	D		.						58	54	55					5																	112154880		2202	4300	6502	SO:0001583	missense	324	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	GGGCCAGTGCAGC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing"	583	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 46"	611731	"adenomatosis polyposis coli"			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1151G>T	5.37:g.112154880G>T	ENSP00000413133:p.Ser384Ile	Somatic	178	1		WXS	Illumina HiSeq	Phase_I	165	66	NM_001127510	0	0	0	0	0	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.943910	0.73672	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.94	5.94	0.96194	Armadillo-like helical (1);Armadillo-type fold (1);	0.183721	0.64402	D	0.000012	T	0.80127	0.4566	M	0.72894	2.215	0.51012	D	0.999907	D;D	0.76494	0.999;0.999	D;D	0.77557	0.971;0.99	T	0.80405	-0.1396	10	0.87932	D	0	-18.3668	20.419	0.99029	0.0:0.0:1.0:0.0	.	386;384	Q4LE70;P25054	.;APC_HUMAN	I	384;366;384;384;384	ENSP00000413133:S384I;ENSP00000423224:S366I;ENSP00000257430:S384I;ENSP00000427089:S384I;ENSP00000423828:S384I	ENSP00000257430:S384I	S	+	2	0	APC	112182779	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.632000	0.83247	2.832000	0.97577	0.650000	0.86243	AGT	.		0.507	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112154880	G	T	112154880	3	4	155	1	0	0	0	0	1	0	0	0	763	1029	36	4	1185	4	APC	5	112154880	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	648831	112154880	68760380	23	13995											
DMXL1	1657	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	118556763	118556765	+	In_Frame_Del	DEL	GAG	GAG	-																															tggtagtacacagactggcaGaggagcatctgtggtatgta																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:118556763_118556765delGAG	ENST00000311085.8	+	36	8281_8283	c.8201_8203delGAG	c.(8200-8205)agagga>aga	p.G2735del	DMXL1_ENST00000505312.1_3'UTR|DMXL1_ENST00000539542.1_In_Frame_Del_p.G2756del	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2735										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CAGACTGGCAGAGGAGCATCTGT	0.35																																					p.2734_2735del		.											.	DMXL1-92	0			c.8201_8203del						.																																			SO:0001651	inframe_deletion	1657	exon36			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"WD repeat domain containing"	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8201_8203delGAG	5.37:g.118556766_118556768delGAG	ENSP00000309690:p.Gly2735del	Somatic	385	0		WXS	Illumina HiSeq	Phase_I	313	96	NM_005509	0	0	0	0	0		In_Frame_Del	DEL	ENST00000311085.8	37	CCDS4125.1																																																																																			.		0.35	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		-	118556765	GAG	-	118556763	7	5	155	1	0	1	0	1	0	0	0	0	4605	942	33	0	8343	0	DMXL1	5	118556763	In_Frame_Del	DEL	GAG	TCGA-P4-A5E8-01A-11D-A28G-10	6401883	118556763	62358497	24	13996											
TRIM39	56658	hgsc.bcm.edu;bcgsc.ca	37	chr6	30303731	30303752	+	Splice_Site	DEL	GTCAGGCTTCGAGATGCTTAAG	GTCAGGCTTCGAGATGCTTAAG	-																															gtggagggcaagtgcttacaGtcaggcttcgagatgcttaa																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	GTCAGGCTTCGAGATGCTTAAG	GTCAGGCTTCGAGATGCTTAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr6:30303731_30303752delGTCAGGCTTCGAGATGCTTAAG	ENST00000396547.1	+	4	919_940	c.759_780delGTCAGGCTTCGAGATGCTTAAG	c.(757-780)cagtcaggcttcgagatgcttaag>ca	p.QSGFEMLK253fs	TRIM39_ENST00000376656.4_Splice_Site_p.QSGFEMLK253fs|TRIM39_ENST00000540416.1_Splice_Site_p.QSGFEMLK253fs|TRIM39-RPP21_ENST00000513556.1_Splice_Site_p.QSGFEMLK165fs|TRIM39_ENST00000376659.5_Splice_Site_p.QSGFEMLK253fs|TRIM39_ENST00000396548.1_Splice_Site_p.QSGFEMLK253fs|TRIM39_ENST00000396551.3_Splice_Site_p.QSGFEMLK253fs			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	253					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.K260Q(1)		ovary(3)	3						AGTGCTTACAGTCAGGCTTCGAGATGCTTAAGGTTCGACCTT	0.577																																					p.253_260del		.											.	TRIM39-161	1	Substitution - Missense(1)	lung(1)	c.759_780del						.																																			SO:0001630	splice_region_variant	56658	exon5			.	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10065	protein-coding gene	gene with protein product		605700	"ring finger protein 23", "tripartite motif-containing 39"	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.780+1GTCAGGCTTCGAGATGCTTAAG>-	6.37:g.30303731_30303752delGTCAGGCTTCGAGATGCTTAAG		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	40	13	NM_172016	0	0	0	0	0	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Frame_Shift_Del	DEL	ENST00000396547.1	37	CCDS34377.1																																																																																			.		0.577	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	Frame_Shift_Del	-	30303752	GTCAGGCTTCGAGATGCTTAAG	-	30303731	8	5	155	1	0	1	0	1	0	0	1	0	16546	1020	36	0	769	0	TRIM39	6	30303731	Splice_Site	DEL	GTCAGGCTTCGAGATGCTTAAG	TCGA-P4-A5E8-01A-11D-A28G-10		30303731	140811336	25	13997											
LAMA4	3910	broad.mit.edu	37	chr6	112463434	112463434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaggcctttaagtcatccaTactggttctcgagtgcactt	9	13	9	10	1	2	0	1	0	1	0	4	2	3	0	2	2	2	2	2	2	3	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr6:112463434T>C	ENST00000230538.7	-	20	2951	c.2554A>G	c.(2554-2556)Atg>Gtg	p.M852V	LAMA4_ENST00000424408.2_Missense_Mutation_p.M845V|LAMA4_ENST00000522006.1_Missense_Mutation_p.M845V|LAMA4_ENST00000389463.4_Missense_Mutation_p.M845V	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	852	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AAGTCATCCATACTGGTTCTC	0.493																																					p.M852V													.	LAMA4-140	0			c.A2554G						.						141	127	132					6																	112463434		2203	4300	6503	SO:0001583	missense	3910	exon20			CATCCATACTGGT		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"Laminins"	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.2554A>G	6.37:g.112463434T>C	ENSP00000230538:p.Met852Val	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	121	4	NM_001105206	0	0	0	0	0	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	T	0.027	-1.359370	0.01245	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	6.07	-3.39	0.04868	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin II (1);	0.783647	0.12814	N	0.436927	T	0.02193	0.0068	N	0.00368	-1.59	0.20196	N	0.999921	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43376	-0.9395	10	0.10111	T	0.7	.	13.534	0.61638	0.1124:0.7719:0.0:0.1157	.	852;845	Q16363;Q16363-2	LAMA4_HUMAN;.	V	852;845;845;845	ENSP00000230538:M852V;ENSP00000429488:M845V;ENSP00000374114:M845V;ENSP00000416470:M845V	ENSP00000230538:M852V	M	-	1	0	LAMA4	112570127	0.010000	0.17322	0.004000	0.12327	0.410000	0.31052	0.135000	0.15952	-1.093000	0.03058	-0.248000	0.11899	ATG	.		0.493	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		C	112463434	T	C	112463434	3	2	155	1	0	0	0	0	1	0	0	0	8629	1406	49	3	2997	3	LAMA4	6	112463434	Missense_Mutation	SNP	T	TCGA-P4-A5E8-01A-11D-A28G-10	82159703	112463434	58651633	26	13998											
NMBR	4829	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	142396953	142396953	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccacagcagagttggctgttGaaatgcctcctgaagctttc	9	11	10	11	0	0	3	0	2	0	1	2	3	1	3	3	1	3	5	3	1	2	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr6:142396953G>A	ENST00000258042.1	-	3	1145	c.1005C>T	c.(1003-1005)ttC>ttT	p.F335F	NMBR_ENST00000480652.1_5'UTR	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	335					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)			breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		GTTGGCTGTTGAAATGCCTCC	0.473																																					p.F335F		.											.	NMBR-946	0			c.C1005T						.						109	104	106					6																	142396953		2203	4300	6503	SO:0001819	synonymous_variant	4829	exon3			GCTGTTGAAATGC		CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"GPCR / Class A : Bombesin receptors"	7843	protein-coding gene	gene with protein product	"bombesin receptor 1"	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.1005C>T	6.37:g.142396953G>A		Somatic	149	0		WXS	Illumina HiSeq	Phase_I	138	8	NM_002511	0	0	0	0	0	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	37	CCDS5196.1																																																																																			.		0.473	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			A	142396953	G	A	142396953	2	1	155	1	0	0	0	0	0	0	0	1	10513	1281	45	2		2	NMBR	6	142396953	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	29933519	142396953	28718114	27	13999											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725800	15725800	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgctgatggtggtgatgGtggtggtggtggtggtggtg	2	14	23	2	0	0	2	0	2	0	0	0	2	0	2	0	9	2	2	0	9	0	0	rs113582077	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:15725800G>A	ENST00000262041.5	-	1	637	c.228C>T	c.(226-228)caC>caT	p.H76H	AC005550.4_ENST00000442176.1_lincRNA|AC005550.5_ENST00000438923.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	76	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)	p.H80delH(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtgatggtggtggtggt	0.612																																					p.H76H	Esophageal Squamous(140;197 1769 16409 18257 29929)	.											.	MEOX2-515	1	Deletion - In frame(1)	stomach(1)	c.C228T						.						11	13	13					7																	15725800		2192	4293	6485	SO:0001819	synonymous_variant	4223	exon1			GTGATGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.228C>T	7.37:g.15725800G>A		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	32	7	NM_005924	0	0	0	0	0	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	37	CCDS34605.1																																																																																			.		0.612	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725800	G	A	15725800	2	1	155	1	0	0	0	0	0	0	0	1	9499	1252	44	2		2	MEOX2	7	15725800	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		15725800	143412863	28	14000											
HOXA7	3204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	27194707	27194707	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaccagatcttaatctggcGctcggtgaggcagagcgcgt	9	8	14	10	4	2	3	0	1	2	2	3	4	2	3	1	3	2	2	1	3	2	1			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:27194707G>A	ENST00000242159.3	-	2	647	c.514C>T	c.(514-516)Cgc>Tgc	p.R172C	HOXA-AS3_ENST00000521231.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000524304.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA7_ENST00000523796.2_5'UTR|HOXA-AS3_ENST00000521197.1_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	172					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						TTAATCTGGCGCTCGGTGAGG	0.632																																					p.R172C		.											.	HOXA7-90	0			c.C514T						.						87	99	95					7																	27194707		2203	4300	6503	SO:0001583	missense	3204	exon2			TCTGGCGCTCGGT		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"Homeoboxes / ANTP class : HOXL subclass"	5108	protein-coding gene	gene with protein product		142950	"homeo box A7"	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.514C>T	7.37:g.27194707G>A	ENSP00000242159:p.Arg172Cys	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	119	32	NM_006896	0	0	8	11	3	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349382	0.61183	.	.	ENSG00000122592	ENST00000242159	D	0.96774	-4.12	4.96	3.98	0.46160	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98365	0.9457	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98696	1.0698	10	0.87932	D	0	.	12.334	0.55056	0.0:0.0:0.6713:0.3287	.	172	P31268	HXA7_HUMAN	C	172	ENSP00000242159:R172C	ENSP00000242159:R172C	R	-	1	0	HOXA7	27161232	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.882000	0.39648	2.324000	0.78689	0.456000	0.33151	CGC	.		0.632	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			A	27194707	G	A	27194707	3	1	155	1	0	0	0	0	1	0	0	0	7318	1087	38	1	182	1	HOXA7	7	27194707	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	11468907	27194707	131943956	29	14001											
SAMD9	54809	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	92731495	92731495	+	Frame_Shift_Del	DEL	T	T	-																															ttcttctaagagacaaaataTatctacatatttcttaaaat																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:92731495delT	ENST00000379958.2	-	3	4185	c.3916delA	c.(3916-3918)atafs	p.I1306fs		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1306						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AGACAAAATATATCTACATAT	0.373																																					p.I1306fs		.											.	SAMD9-140	0			c.3916delA						.						73	81	78					7																	92731495		2197	4295	6492	SO:0001589	frameshift_variant	54809	exon2			.	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"Sterile alpha motif (SAM) domain containing"	1348	protein-coding gene	gene with protein product		610456	"chromosome 7 open reading frame 5"	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.3916delA	7.37:g.92731495delT	ENSP00000369292:p.Ile1306fs	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	32	12	NM_001193307	0	0	0	0	0	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Frame_Shift_Del	DEL	ENST00000379958.2	37	CCDS34680.1																																																																																			.		0.373	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		-	92731495	T	-	92731495	7	5	155	1	0	1	0	1	0	0	0	0	13858	1406	49	0	857	0	SAMD9	7	92731495	Frame_Shift_Del	DEL	T	TCGA-P4-A5E8-01A-11D-A28G-10	65536788	92731495	66407168	30	14002											
PILRA	29992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99972037	99972037	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtccatcgaggggacCaaactctccatcacccaggg	10	6	11	14	1	2	0	1	0	1	0	5	2	3	1	4	4	1	1	4	4	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:99972037C>T	ENST00000198536.2	+	2	647	c.435C>T	c.(433-435)acC>acT	p.T145T	PILRA_ENST00000350573.2_Silent_p.T145T|PILRA_ENST00000474013.1_3'UTR|PILRA_ENST00000453419.1_Silent_p.T145T|PILRA_ENST00000394000.2_Silent_p.T145T	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	145	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCGAGGGGACCAAACTCTCCA	0.592																																					p.T145T		.											.	PILRA-91	0			c.C435T						.						76	73	74					7																	99972037		2203	4300	6503	SO:0001819	synonymous_variant	29992	exon2			GGGGACCAAACTC	AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"Immunoglobulin superfamily / V-set domain containing"	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.435C>T	7.37:g.99972037C>T		Somatic	85	0		WXS	Illumina HiSeq	Phase_I	79	21	NM_013439	0	0	4	5	1	Q8NHI1	Silent	SNP	ENST00000198536.2	37	CCDS5691.1																																																																																			.		0.592	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439		T	99972037	C	T	99972037	2	4	155	1	0	0	0	0	0	0	0	1	11951	581	21	2		2	PILRA	7	99972037	Silent	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	7240542	99972037	59166626	31	14003											
MLL5	55904	broad.mit.edu	37	chr7	104750955	104750955	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgtgtctcatgttcaccGagtcatgttcagtcttcacc	7	14	7	13	1	6	0	5	0	2	0	7	1	6	0	3	0	0	2	3	0	0	3	rs375343033		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:104750955G>T	ENST00000311117.3	+	25	4421	c.3876G>T	c.(3874-3876)ccG>ccT	p.P1292P	SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000334914.7_Silent_p.P347P|KMT2E_ENST00000257745.4_Silent_p.P1292P|KMT2E_ENST00000334877.4_Intron	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1292					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										CATGTTCACCGAGTCATGTTC	0.463																																					p.P1292P													.	MLL5-93	0			c.G3876T						.						267	253	257					7																	104750955		2203	4300	6503	SO:0001819	synonymous_variant	55904	exon24			TTCACCGAGTCAT	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3876G>T	7.37:g.104750955G>T		Somatic	151	0		WXS	Illumina HiSeq	Phase_I	134	5	NM_018682	0	0	5	5	0	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	37	CCDS34723.1																																																																																			.		0.463	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104750955	G	T	104750955	2	4	155	1	0	0	0	0	0	0	0	1	9649	1045	37	4		4	MLL5	7	104750955	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	4778918	104750955	54387708	32	14004											
KIF13B	23303	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	28984749	28984749	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaagtcccagattcctgcaCtgacttcacttcgacttgaa	11	12	6	12	1	1	3	1	2	0	1	4	4	3	3	2	0	1	1	2	0	3	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr8:28984749C>G	ENST00000524189.1	-	25	3150	c.3112G>C	c.(3112-3114)Gtg>Ctg	p.V1038L	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1038					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		GATTCCTGCACTGACTTCACT	0.443																																					p.V1038L		.											.	KIF13B-22	0			c.G3112C						.						149	147	148					8																	28984749		1920	4132	6052	SO:0001583	missense	23303	exon25			CCTGCACTGACTT	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"Kinesins"	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3112G>C	8.37:g.28984749C>G	ENSP00000427900:p.Val1038Leu	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	132	9	NM_015254	0	0	11	13	2	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812352	0.70912	.	.	ENSG00000197892	ENST00000524189	T	0.77620	-1.11	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.77665	0.4164	M	0.66939	2.045	0.80722	D	1	B	0.32620	0.378	B	0.38378	0.272	T	0.78155	-0.2314	10	0.54805	T	0.06	.	12.1601	0.54099	0.0:0.9224:0.0:0.0776	.	1038	F8VPJ2	.	L	1038	ENSP00000427900:V1038L	ENSP00000427900:V1038L	V	-	1	0	KIF13B	29040668	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.510000	0.60455	2.649000	0.89929	0.655000	0.94253	GTG	.		0.443	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			G	28984749	C	G	28984749	3	3	155	1	0	0	0	0	1	0	0	0	8296	565	20	4	2432	4	KIF13B	8	28984749	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		28984749	117379273	33	14005											
DCAF13	25879	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	104432551	104432551	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcccacgagaatatataagaGctttaaatgctaccaaactg	16	10	6	9	1	0	2	0	0	0	2	1	3	1	2	2	0	4	2	2	0	8	6			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr8:104432551G>T	ENST00000297579.5	+	2	863	c.586G>T	c.(586-588)Gct>Tct	p.A196S	DCAF13_ENST00000521716.1_Missense_Mutation_p.A40S|DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000521971.1_Missense_Mutation_p.A40S|DCAF13_ENST00000519682.1_Missense_Mutation_p.A40S	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	44					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ATATATAAGAGCTTTAAATGC	0.388																																					p.A196S		.											.	DCAF13-135	0			c.G586T						.						102	96	98					8																	104432551		2203	4300	6503	SO:0001583	missense	25879	exon2			ATAAGAGCTTTAA	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.586G>T	8.37:g.104432551G>T	ENSP00000297579:p.Ala196Ser	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	135	48	NM_015420	0	0	13	28	15	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	G	33	5.265050	0.95399	.	.	ENSG00000164934	ENST00000297579;ENST00000521716;ENST00000521971;ENST00000388778;ENST00000519682	T;T;T;T	0.01313	5.02;5.02;5.02;5.02	5.2	5.2	0.72013	.	0.050275	0.85682	N	0.000000	T	0.16128	0.0388	H	0.96489	3.83	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.13818	-1.0495	10	0.87932	D	0	-21.6277	18.7279	0.91722	0.0:0.0:1.0:0.0	.	44	B3KME9	.	S	196;40;40;44;40	ENSP00000297579:A196S;ENSP00000430645:A40S;ENSP00000430883:A40S;ENSP00000430411:A40S	ENSP00000297579:A196S	A	+	1	0	DCAF13	104501727	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.260000	0.95568	2.420000	0.82092	0.655000	0.94253	GCT	.		0.388	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		T	104432551	G	T	104432551	3	4	155	1	0	0	0	0	1	0	0	0	4272	971	34	4	592	4	DCAF13	8	104432551	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	75447802	104432551	41931471	34	14006											
KIAA2026	158358	broad.mit.edu	37	chr9	5923077	5923078	+	Frame_Shift_Del	DEL	AC	AC	-																															gtatgctttgattcactgaaAcagtcaatctgcacatcact																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr9:5923077_5923078delAC	ENST00000399933.3	-	8	2917_2918	c.2918_2919delGT	c.(2917-2919)tgtfs	p.C973fs	KIAA2026_ENST00000381461.2_Frame_Shift_Del_p.C943fs	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	973										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		ATTCACTGAAACAGTCAATCTG	0.426																																					p.973_973del													.	KIAA2026-92	0			c.2918_2919del						.																																			SO:0001589	frameshift_variant	158358	exon8			ACTGAAACAGTCA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.2918_2919delGT	9.37:g.5923077_5923078delAC	ENSP00000382815:p.Cys973fs	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	250	10	NM_001017969	0	0	0	0	0	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Frame_Shift_Del	DEL	ENST00000399933.3	37																																																																																				.		0.426	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		-	5923078	AC	-	5923077	7	5	155	1	0	1	0	1	0	0	0	0	8291	41	2	0	3396	0	KIAA2026	9	5923077	Frame_Shift_Del	DEL	AC	TCGA-P4-A5E8-01A-11D-A28G-10		5923077	135290354	35	14007											
C9orf93	203238	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	15745613	15745613	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctatggctgaattacaagaCgtcattggtaaagcaggtat	13	12	10	6	1	2	2	1	1	1	1	2	2	2	2	0	3	2	4	0	3	7	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr9:15745613C>T	ENST00000380701.3	+	18	2983	c.2655C>T	c.(2653-2655)gaC>gaT	p.D885D	CCDC171_ENST00000297641.3_Silent_p.D885D	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	885								p.D152D(1)|p.D885D(1)									AATTACAAGACGTCATTGGTA	0.363																																					p.D885D		.											.	.	2	Substitution - coding silent(2)	lung(2)	c.C2655T						.						222	221	221					9																	15745613		2203	4300	6503	SO:0001819	synonymous_variant	203238	exon18			ACAAGACGTCATT	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"myosin tail domain containing protein"		"chromosome 9 open reading frame 93"	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.2655C>T	9.37:g.15745613C>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	44	16	NM_173550	0	0	0	0	0	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	37	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	C	0.248	-1.008817	0.02112	.	.	ENSG00000164989	ENST00000449575	.	.	.	5.03	-4.4	0.03600	.	.	.	.	.	T	0.40297	0.1111	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37641	-0.9697	4	.	.	.	-0.9084	3.9218	0.09247	0.3234:0.4014:0.0625:0.2128	.	.	.	.	M	125	.	.	T	+	2	0	C9orf93	15735613	0.998000	0.40836	0.941000	0.38009	0.154000	0.21943	0.535000	0.23114	-0.699000	0.05077	-1.604000	0.00809	ACG	.		0.363	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		T	15745613	C	T	15745613	2	4	155	1	0	0	0	0	0	0	0	1	2512	535	19	1		1	C9orf93	9	15745613	Silent	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	9822536	15745613	125467818	36	14008											
ITIH5	80760	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	7621949	7621949	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgatgagggacacgctcCggtctccaatgccactgtgg	9	7	13	12	3	1	2	0	1	1	1	3	4	2	3	3	3	1	1	3	3	1	0	rs368004189		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr10:7621949C>T	ENST00000256861.6	-	9	1265	c.1187G>A	c.(1186-1188)cGg>cAg	p.R396Q	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397145.2_Missense_Mutation_p.R396Q|ITIH5_ENST00000298441.6_Missense_Mutation_p.R182Q|ITIH5_ENST00000397146.2_Missense_Mutation_p.R396Q|ITIH5_ENST00000446830.2_Missense_Mutation_p.R178Q	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	396	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						GGACACGCTCCGGTCTCCAAT	0.632																																					p.R396Q		.											.	ITIH5-92	0			c.G1187A						.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	79	69	72		1187,1187,545	4.4	1	10		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	396/703,396/943,182/729	7621949	1,13005	2203	4300	6503	SO:0001583	missense	80760	exon9			ACGCTCCGGTCTC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"inter-alpha (globulin) inhibitor H5"			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1187G>A	10.37:g.7621949C>T	ENSP00000256861:p.Arg396Gln	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	60	33	NM_001001851	0	0	0	0	0	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	14.84	2.656967	0.47467	0.0	1.16E-4	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	5.33	4.41	0.53225	von Willebrand factor, type A (3);	0.152288	0.64402	D	0.000015	D	0.83792	0.5331	.	.	.	0.31433	N	0.672876	P;D;D	0.69078	0.948;0.997;0.997	P;P;P	0.60886	0.745;0.88;0.809	D	0.84790	0.0778	9	0.72032	D	0.01	-30.2968	10.6617	0.45706	0.0:0.8514:0.0:0.1486	.	396;396;182	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	Q	396;396;182;178;396	ENSP00000256861:R396Q;ENSP00000380333:R396Q;ENSP00000298441:R182Q;ENSP00000387969:R178Q;ENSP00000380332:R396Q	ENSP00000256861:R396Q	R	-	2	0	ITIH5	7661955	1.000000	0.71417	0.994000	0.49952	0.106000	0.19336	2.775000	0.47702	2.491000	0.84063	0.561000	0.74099	CGG	.		0.632	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7621949	C	T	7621949	3	4	155	1	0	0	0	0	1	0	0	0	7928	652	23	1	1788	1	ITIH5	10	7621949	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		7621949	127912798	37	14009											
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	24832228	24832229	+	Frame_Shift_Del	DEL	AG	AG	-																															gatcaagaggttatcacgacAgattttggccaagttgttct																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr10:24832228_24832229delAG	ENST00000376454.3	+	19	4059_4060	c.4029_4030delAG	c.(4027-4032)acagatfs	p.D1344fs	KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000376451.2_Frame_Shift_Del_p.D1027fs|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000376452.3_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1344					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TTATCACGACAGATTTTGGCCA	0.411																																					p.1343_1344del		.											.	KIAA1217-98	0			c.4029_4030del						.																																			SO:0001589	frameshift_variant	56243	exon19			.	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"sickle tail"					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.4029_4030delAG	10.37:g.24832228_24832229delAG	ENSP00000365637:p.Asp1344fs	Somatic	304	0		WXS	Illumina HiSeq	Phase_I	309	132	NM_019590	0	0	0	0	0	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Frame_Shift_Del	DEL	ENST00000376454.3	37	CCDS31165.1																																																																																			.		0.411	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		-	24832229	AG	-	24832228	7	5	155	1	0	1	0	1	0	0	0	0	8237	175	7	0	4103	0	KIAA1217	10	24832228	Frame_Shift_Del	DEL	AG	TCGA-P4-A5E8-01A-11D-A28G-10	17210279	24832228	110702519	38	14010											
CPXM2	119587	broad.mit.edu	37	chr10	125651141	125651141	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcactgccaggagcaccaggGccagcgctggggtagcggtc	7	5	16	13	2	1	0	1	0	0	0	2	1	1	1	3	5	4	3	3	5	1	1	rs201350090		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr10:125651141G>T	ENST00000241305.3	-	1	189	c.35C>A	c.(34-36)gCc>gAc	p.A12D	CPXM2_ENST00000368854.3_Intron	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	12					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		GAGCACCAGGGCCAGCGCTGG	0.766																																					p.A12D													.	CPXM2-92	0			c.C35A						.						5	7	6					10																	125651141		1452	2778	4230	SO:0001583	missense	119587	exon1			ACCAGGGCCAGCG	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase"					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.35C>A	10.37:g.125651141G>T	ENSP00000241305:p.Ala12Asp	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	31	5	NM_198148	0	0	1	1	0	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	g	9.202	1.028774	0.19512	.	.	ENSG00000121898	ENST00000241305;ENST00000418782	D	0.96427	-4.01	3.45	1.48	0.22813	.	2.186560	0.02563	N	0.096968	D	0.90480	0.7018	N	0.08118	0	0.22424	N	0.999119	B	0.32160	0.358	B	0.30716	0.119	D	0.85783	0.1362	10	0.87932	D	0	0.2476	5.6694	0.17713	0.2726:0.0:0.7274:0.0	.	12	Q8N436	CPXM2_HUMAN	D	12	ENSP00000241305:A12D	ENSP00000241305:A12D	A	-	2	0	CPXM2	125641131	0.036000	0.19791	0.475000	0.27278	0.067000	0.16453	0.517000	0.22832	0.646000	0.30693	0.298000	0.19748	GCC	.		0.766	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		T	125651141	G	T	125651141	3	4	155	1	0	0	0	0	1	0	0	0	3844	1203	42	4	2291	4	CPXM2	10	125651141	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	100818913	125651141	9883606	39	14011											
ACY3	91703	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	67413212	67413212	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacttcgtgggaggacttcGcgattaagcaggtgcccatg	9	9	14	9	3	0	1	0	0	0	1	2	4	0	3	1	3	2	1	1	3	1	3	rs368150084		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:67413212G>A	ENST00000255082.3	-	4	553	c.383C>T	c.(382-384)gCg>gTg	p.A128V	ACY3_ENST00000529256.1_Missense_Mutation_p.A7V	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	128	Hydrolytic domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	GGAGGACTTCGCGATTAAGCA	0.642																																					p.A128V	GBM(56;346 1011 27014 29495 46841)	.											.	ACY3-90	0			c.C383T						.	G	VAL/ALA	2,4398	4.2+/-10.8	0,2,2198	170	152	158		383	0.6	0	11		158	0,8588		0,0,4294	no	missense	ACY3	NM_080658.1	64	0,2,6492	AA,AG,GG		0.0,0.0455,0.0154	benign	128/320	67413212	2,12986	2200	4294	6494	SO:0001583	missense	91703	exon4			GACTTCGCGATTA	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.383C>T	11.37:g.67413212G>A	ENSP00000255082:p.Ala128Val	Somatic	195	0		WXS	Illumina HiSeq	Phase_I	203	12	NM_080658	0	0	0	0	0		Missense_Mutation	SNP	ENST00000255082.3	37	CCDS8175.1	.	.	.	.	.	.	.	.	.	.	G	1.017	-0.686076	0.03328	4.55E-4	0.0	ENSG00000132744	ENST00000255082;ENST00000529256	D;D	0.97505	-4.41;-4.41	3.79	0.623	0.17654	.	2.785610	0.01103	N	0.005413	D	0.86049	0.5840	N	0.00347	-1.61	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.82808	-0.0274	10	0.22109	T	0.4	.	4.3548	0.11172	0.2931:0.3178:0.3891:0.0	.	128	Q96HD9	ACY3_HUMAN	V	128;7	ENSP00000255082:A128V;ENSP00000434270:A7V	ENSP00000255082:A128V	A	-	2	0	ACY3	67169788	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.470000	0.06639	-0.081000	0.12662	-0.258000	0.10820	GCG	.		0.642	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658		A	67413212	G	A	67413212	3	1	155	1	0	0	0	0	1	0	0	0	227	1087	38	1	596	1	ACY3	11	67413212	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		67413212	67593304	40	14012											
POU2AF1	5450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	111228192	111228192	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgacattggtgatgagtggcGgagaggcataggtcaacact	11	9	15	6	1	1	4	1	3	0	1	1	5	1	4	0	5	1	1	0	5	2	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:111228192G>A	ENST00000393067.3	-	4	948	c.434C>T	c.(433-435)cCg>cTg	p.P145L		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	145					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		GATGAGTGGCGGAGAGGCATA	0.572			T	BCL6	NHL																																p.P145L		.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1-658	0			c.C434T						.						81	70	73					11																	111228192		2201	4297	6498	SO:0001583	missense	5450	exon4			AGTGGCGGAGAGG		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"POU domain class 2, associating factor 1"			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.434C>T	11.37:g.111228192G>A	ENSP00000376786:p.Pro145Leu	Somatic	370	1		WXS	Illumina HiSeq	Phase_I	338	131	NM_006235	0	0	1	1	0	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	37	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.610386	0.28712	.	.	ENSG00000110777	ENST00000393067	T	0.28255	1.62	4.95	3.9	0.45041	.	0.326590	0.29376	N	0.012335	T	0.18718	0.0449	N	0.22421	0.69	0.44937	D	0.997956	B	0.28820	0.224	B	0.22601	0.04	T	0.05007	-1.0912	10	0.27082	T	0.32	-8.7718	10.5839	0.45271	0.0:0.0:0.2373:0.7627	.	145	Q16633	OBF1_HUMAN	L	145	ENSP00000376786:P145L	ENSP00000376786:P145L	P	-	2	0	POU2AF1	110733402	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	3.360000	0.52299	0.893000	0.36288	0.492000	0.49549	CCG	.		0.572	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		A	111228192	G	A	111228192	3	1	155	1	0	0	0	0	1	0	0	0	12296	1116	39	1	344	1	POU2AF1	11	111228192	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	43814980	111228192	23778324	41	14013											
HTR3A	3359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113846045	113846045	+	5'UTR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctatgcttggaaagctcGctatgctgctgtgggtccag	6	12	12	11	1	0	0	0	0	0	0	3	1	2	1	2	2	4	5	2	2	3	3	rs200513646		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:113846045G>A	ENST00000504030.2	+	0	443				HTR3A_ENST00000299961.5_5'Flank|HTR3A_ENST00000375498.2_Missense_Mutation_p.A6T|HTR3A_ENST00000355556.2_Missense_Mutation_p.A6T|HTR3A_ENST00000506841.2_5'UTR|HTR3A_ENST00000535865.1_5'UTR			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	TGGAAAGCTCGCTATGCTGCT	0.632													G|||	1	0.000199681	8e-04	0	5008	,	,		19934	0		0	False		,,,				2504	0				p.A6T		.											.	HTR3A-90	0			c.G16A						.	G	THR/ALA,THR/ALA	4,4398	8.1+/-20.4	0,4,2197	62	55	58		16,16	-5.2	0	11		58	0,8592		0,0,4296	yes	missense,missense	HTR3A	NM_213621.3,NM_000869.5	58,58	0,4,6493	AA,AG,GG		0.0,0.0909,0.0308	benign,benign	6/517,6/485	113846045	4,12990	2201	4296	6497	SO:0001623	5_prime_UTR_variant	3359	exon1			AAGCTCGCTATGC	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.-3G>A	11.37:g.113846045G>A		Somatic	53	0		WXS	Illumina HiSeq	Phase_I	26	8	NM_000869	0	0	0	1	1	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	G	9.618	1.133138	0.21041	9.09E-4	0.0	ENSG00000166736	ENST00000355556;ENST00000375498	T;T	0.77098	-0.99;-1.07	4.94	-5.23	0.02798	.	.	.	.	.	T	0.54615	0.1869	N	0.08118	0	0.29946	N	0.820675	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.001	T	0.33033	-0.9884	9	0.29301	T	0.29	.	12.1527	0.54059	0.5992:0.0:0.4008:0.0	.	6;6	G5E986;Q7KZM7	.;.	T	6	ENSP00000347754:A6T;ENSP00000364648:A6T	ENSP00000347754:A6T	A	+	1	0	HTR3A	113351255	0.000000	0.05858	0.000000	0.03702	0.240000	0.25518	-1.991000	0.01478	-1.239000	0.02532	-0.119000	0.15052	GCT	.		0.632	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		A	113846045	G	A	113846045	1	1	155	0	1	0	0	0	0	0	0	0	7465	1087	38	1		1	HTR3A	11	113846045	5'UTR	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	2617853	113846045	21160471	42	14014											
IGFBP6	3489	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	53494509	53494509	+	Frame_Shift_Del	DEL	T	T	-																															cctccagttgcagaggagaaTcctaaggagagtaaacccca																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr12:53494509delT	ENST00000301464.3	+	2	621	c.348delT	c.(346-348)aatfs	p.N116fs	SOAT2_ENST00000301466.3_5'Flank|IGFBP6_ENST00000548547.1_Frame_Shift_Del_p.N114fs|IGFBP6_ENST00000549628.1_3'UTR	NM_002178.2	NP_002169.1	P24592	IBP6_HUMAN	insulin-like growth factor binding protein 6	116					cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				large_intestine(1)|lung(3)|ovary(1)|pancreas(1)	6						CAGAGGAGAATCCTAAGGAGA	0.567																																					p.N116fs	Esophageal Squamous(83;1656 1718 30141 34380)	.											.	IGFBP6-523	0			c.348delT						.						95	93	94					12																	53494509		2203	4300	6503	SO:0001589	frameshift_variant	3489	exon2			.		CCDS8846.1	12q13	2008-07-28				ENSG00000167779			5475	protein-coding gene	gene with protein product		146735				1850258, 10087296	Standard	NM_002178		Approved		uc001sbu.1	P24592	OTTHUMG00000169773	ENST00000301464.3:c.348delT	12.37:g.53494509delT	ENSP00000301464:p.Asn116fs	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	71	30	NM_002178	0	0	0	0	0	Q14492	Frame_Shift_Del	DEL	ENST00000301464.3	37	CCDS8846.1																																																																																			.		0.567	IGFBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405813.1			-	53494509	T	-	53494509	7	5	155	1	0	1	0	1	0	0	0	0	7604	1432	50	0	354	0	IGFBP6	12	53494509	Frame_Shift_Del	DEL	T	TCGA-P4-A5E8-01A-11D-A28G-10		53494509	80357386	43	14015											
FLT1	2321	broad.mit.edu	37	chr13	29008265	29008265	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttcacaggtcagaagcccTatttctttgtacgttgcatt	8	15	8	10	1	3	1	2	0	1	1	3	1	3	1	1	1	3	4	1	1	3	7			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr13:29008265T>C	ENST00000282397.4	-	5	857	c.606A>G	c.(604-606)atA>atG	p.I202M	FLT1_ENST00000541932.1_Missense_Mutation_p.I202M|FLT1_ENST00000539099.1_Missense_Mutation_p.I202M	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	202	Ig-like C2-type 2.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCAGAAGCCCTATTTCTTTGT	0.398																																					p.I202M													.	FLT1-1406	0			c.A606G						.						172	140	151					13																	29008265		2203	4300	6503	SO:0001583	missense	2321	exon5			AAGCCCTATTTCT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.606A>G	13.37:g.29008265T>C	ENSP00000282397:p.Ile202Met	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	88	3	NM_002019	0	0	3	3	0	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.120898	0.56613	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	T;T;T	0.12147	2.71;2.71;2.71	5.78	-4.6	0.03390	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.169796	0.49305	D	0.000151	T	0.18800	0.0451	L	0.52573	1.65	0.38449	D	0.946908	P;P;P;D	0.53745	0.773;0.773;0.773;0.962	P;P;P;D	0.65233	0.849;0.849;0.849;0.933	T	0.12243	-1.0555	10	0.54805	T	0.06	.	4.0105	0.09621	0.5245:0.058:0.1903:0.2273	.	202;202;202;202	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	M	202	ENSP00000282397:I202M;ENSP00000437631:I202M;ENSP00000442630:I202M	ENSP00000282397:I202M	I	-	3	3	FLT1	27906265	0.773000	0.28580	0.941000	0.38009	0.916000	0.54674	-0.246000	0.08878	-1.020000	0.03354	-0.341000	0.08007	ATA	.		0.398	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	29008265	T	C	29008265	3	2	155	1	0	0	0	0	1	0	0	0	5960	1512	53	3	3777	3	FLT1	13	29008265	Missense_Mutation	SNP	T	TCGA-P4-A5E8-01A-11D-A28G-10		29008265	86161613	44	14016											
POSTN	10631	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	38166281	38166281	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattctcatataaccagggCaacattcatataacacagtc	15	10	4	12	0	2	0	2	0	1	0	4	0	2	0	2	1	3	1	2	1	5	6			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr13:38166281C>A	ENST00000379747.4	-	3	356	c.239G>T	c.(238-240)tGc>tTc	p.C80F	POSTN_ENST00000541179.1_Missense_Mutation_p.C80F|POSTN_ENST00000379749.4_Missense_Mutation_p.C80F|POSTN_ENST00000541481.1_Missense_Mutation_p.C80F|POSTN_ENST00000379742.4_Missense_Mutation_p.C80F|POSTN_ENST00000379743.4_Missense_Mutation_p.C80F	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	80	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		ATAACCAGGGCAACATTCATA	0.294																																					p.C80F													.	POSTN-516	0			c.G239T						.						65	63	64					13																	38166281		2203	4300	6503	SO:0001583	missense	10631	exon3			CCAGGGCAACATT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.239G>T	13.37:g.38166281C>A	ENSP00000369071:p.Cys80Phe	Somatic	222	2		WXS	Illumina HiSeq	Phase_I	116	59	NM_006475	0	0	3	3	0	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337174	0.81911	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87;-2.87;-2.87	5.38	5.38	0.77491	EMI domain (1);FAS1 domain (1);	0.000000	0.85682	D	0.000000	D	0.95335	0.8486	M	0.74258	2.255	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.994;1.0;1.0;0.999;0.996;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.988;0.998;0.999;0.998;0.995;1.0;0.999	D	0.95462	0.8544	10	0.87932	D	0	.	19.4972	0.95079	0.0:1.0:0.0:0.0	.	80;80;80;80;80;80;80	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	F	80	ENSP00000437959:C80F;ENSP00000369073:C80F;ENSP00000369071:C80F;ENSP00000369067:C80F;ENSP00000369066:C80F;ENSP00000437953:C80F	ENSP00000369066:C80F	C	-	2	0	POSTN	37064281	1.000000	0.71417	0.999000	0.59377	0.925000	0.55904	7.421000	0.80204	2.668000	0.90789	0.563000	0.77884	TGC	.		0.294	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		A	38166281	C	A	38166281	3	1	155	1	0	0	0	0	1	0	0	0	12285	710	25	4	2355	4	POSTN	13	38166281	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	9158016	38166281	77003597	45	14017											
HIF1A	3091	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	62194216	62194223	+	Frame_Shift_Del	DEL	AACCAACC	AACCAACC	-																															acgtatatgataccaacagtAaccaacctcagtgtgggtat																								rs369217648		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AACCAACC	AACCAACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr14:62194216_62194223delAACCAACC	ENST00000337138.4	+	6	881_888	c.616_623delAACCAACC	c.(616-624)aaccaacctfs	p.NQP206fs	HIF1A_ENST00000323441.6_Frame_Shift_Del_p.NQP206fs|HIF1A_ENST00000557538.1_Frame_Shift_Del_p.NQP147fs|HIF1A_ENST00000394997.1_Frame_Shift_Del_p.NQP207fs|HIF1A_ENST00000539097.1_Frame_Shift_Del_p.NQP230fs|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000557206.1_3'UTR	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	206	Interaction with TSGA10. {ECO:0000250}.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TACCAACAGTAACCAACCTCAGTGTGGG	0.385																																					p.230_232del		.											.	HIF1A-1149	0			c.688_695del						.																																			SO:0001589	frameshift_variant	3091	exon6			.	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.616_623delAACCAACC	14.37:g.62194216_62194223delAACCAACC	ENSP00000338018:p.Asn206fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	93	15	NM_001243084	0	0	0	0	0	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Frame_Shift_Del	DEL	ENST00000337138.4	37	CCDS9753.1																																																																																			.		0.385	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		-	62194223	AACCAACC	-	62194216	7	5	155	1	0	1	0	1	0	0	0	0	7124	362	13	0	638	0	HIF1A	14	62194216	Frame_Shift_Del	DEL	AACCAACC	TCGA-P4-A5E8-01A-11D-A28G-10		62194216	45155324	46	14018	153	2									
HIF1A	3091	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	62194225	62194225	+	Frame_Shift_Del	DEL	C	C	-																															ataccaacagtaaccaacctCagtgtgggtataagaaacca																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr14:62194225delC	ENST00000337138.4	+	6	890	c.625delC	c.(625-627)cagfs	p.Q209fs	HIF1A_ENST00000323441.6_Frame_Shift_Del_p.Q209fs|HIF1A_ENST00000557538.1_Frame_Shift_Del_p.Q150fs|HIF1A_ENST00000394997.1_Frame_Shift_Del_p.Q210fs|HIF1A_ENST00000539097.1_Frame_Shift_Del_p.Q233fs|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000557206.1_3'UTR	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	209	Interaction with TSGA10. {ECO:0000250}.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TAACCAACCTCAGTGTGGGTA	0.383																																					p.Q233fs		.											.	HIF1A-1149	0			c.697delC						.						166	142	150					14																	62194225		2203	4300	6503	SO:0001589	frameshift_variant	3091	exon6			.	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.625delC	14.37:g.62194225delC	ENSP00000338018:p.Gln209fs	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	98	15	NM_001243084	0	0	0	0	0	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Frame_Shift_Del	DEL	ENST00000337138.4	37	CCDS9753.1																																																																																			.		0.383	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		-	62194225	C	-	62194225	7	5	155	1	0	1	0	1	0	0	0	0	7124	827	29	0	647	0	HIF1A	14	62194225	Frame_Shift_Del	DEL	C	TCGA-P4-A5E8-01A-11D-A28G-10	9	62194225	45155315	47	14019	153	2									
TP53BP1	7158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43748237	43748237	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttctcctgagtttggggctGctgcaactcctggtcaagtc	5	14	11	11	0	2	1	1	1	1	0	5	1	3	1	2	3	3	4	2	3	2	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr15:43748237G>A	ENST00000263801.3	-	12	2806	c.2554C>T	c.(2554-2556)Cag>Tag	p.Q852*	TP53BP1_ENST00000382044.4_Nonsense_Mutation_p.Q857*|TP53BP1_ENST00000450115.2_Nonsense_Mutation_p.Q857*|TP53BP1_ENST00000382039.3_Nonsense_Mutation_p.Q857*|TP53BP1_ENST00000605155.1_5'UTR	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	852					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GTTTGGGGCTGCTGCAACTCC	0.458								Other conserved DNA damage response genes																													p.Q857X		.											.	TP53BP1-294	0			c.C2569T						.						181	178	179					15																	43748237		2201	4298	6499	SO:0001587	stop_gained	7158	exon12			GGGGCTGCTGCAA	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"tumor protein p53-binding protein, 1"			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2554C>T	15.37:g.43748237G>A	ENSP00000263801:p.Gln852*	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	70	26	NM_001141980	0	0	2	2	0	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Nonsense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	37	6.362726	0.97507	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	.	.	.	5.37	4.44	0.53790	.	0.405695	0.25091	N	0.033212	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-1.0009	12.5477	0.56210	0.0:0.1669:0.833:0.0	.	.	.	.	X	852;857;857;857;857	.	ENSP00000263801:Q852X	Q	-	1	0	TP53BP1	41535529	0.317000	0.24589	0.067000	0.19924	0.006000	0.05464	1.799000	0.38824	1.364000	0.46038	0.650000	0.86243	CAG	.		0.458	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43748237	G	A	43748237	4	1	155	1	0	0	0	0	0	1	0	0	16416	1328	46	2	3432	2	TP53BP1	15	43748237	Nonsense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		43748237	58783155	48	14020											
NOX5	79400	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	69339166	69339166	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctactccctgcagggctCtgagatacttttggagaaac	9	11	10	11	0	2	2	0	1	2	2	3	4	3	2	1	2	4	3	1	2	3	4			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr15:69339166C>A	ENST00000388866.3	+	11	1693	c.1652C>A	c.(1651-1653)tCt>tAt	p.S551Y	NOX5_ENST00000448182.3_Missense_Mutation_p.S505Y|NOX5_ENST00000530406.2_Missense_Mutation_p.S523Y|NOX5_ENST00000455873.3_Missense_Mutation_p.S516Y|NOX5_ENST00000525163.1_3'UTR|NOX5_ENST00000260364.5_Missense_Mutation_p.S533Y	NM_001184779.1|NM_024505.3	NP_001171708.1|NP_078781.3	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	551	C-terminal catalytic region.|FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cytokine secretion (GO:0050663)|cytokinesis (GO:0000910)|endothelial cell proliferation (GO:0001935)|oxidation-reduction process (GO:0055114)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|proton transport (GO:0015992)|regulation of fusion of sperm to egg plasma membrane (GO:0043012)|regulation of proton transport (GO:0010155)|superoxide anion generation (GO:0042554)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|hydrogen ion channel activity (GO:0015252)|NADP binding (GO:0050661)|superoxide-generating NADPH oxidase activity (GO:0016175)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35						CTGCAGGGCTCTGAGATACTT	0.468																																					p.S551Y													.	NOX5-136	0			c.C1652A						.						110	108	109					15																	69339166		2200	4298	6498	SO:0001583	missense	79400	exon11			AGGGCTCTGAGAT	AF317889	CCDS32276.1, CCDS32276.2, CCDS53953.1, CCDS53954.1	15q22.31	2013-01-10			ENSG00000255346	ENSG00000255346		"EF-hand domain containing"	14874	protein-coding gene	gene with protein product		606572				11483596	Standard	NM_001184779		Approved	NOX5A, NOX5B	uc002ars.2	Q96PH1	OTTHUMG00000133320	ENST00000388866.3:c.1652C>A	15.37:g.69339166C>A	ENSP00000373518:p.Ser551Tyr	Somatic	75	1		WXS	Illumina HiSeq	Phase_I	88	28	NM_024505	0	0	0	0	0	B2RBJ4|Q08AN2|Q08AN3|Q8TEQ1|Q8TER4|Q96PH2|Q96PJ8|Q96PJ9|Q9H6E0|Q9HAM8	Missense_Mutation	SNP	ENST00000388866.3	37	CCDS32276.2	.	.	.	.	.	.	.	.	.	.	C	12.47	1.947923	0.34377	.	.	ENSG00000255346	ENST00000455873;ENST00000448182;ENST00000388866;ENST00000530406	D;D;D	0.94138	-2.81;-3.36;-2.81	2.86	2.86	0.33363	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.767112	0.11794	N	0.528874	D	0.93766	0.8007	M	0.63843	1.955	0.35333	D	0.785795	P;D;P	0.53885	0.755;0.963;0.874	B;P;P	0.52267	0.444;0.694;0.568	D	0.94240	0.7484	10	0.62326	D	0.03	-0.7529	11.1896	0.48677	0.0:1.0:0.0:0.0	.	516;551;523	Q96PH1-6;Q96PH1;Q96PH1-3	.;NOX5_HUMAN;.	Y	516;533;551;523	ENSP00000416828:S516Y;ENSP00000373518:S551Y;ENSP00000432440:S523Y	ENSP00000373518:S551Y	S	+	2	0	NOX5	67126220	0.005000	0.15991	0.010000	0.14722	0.009000	0.06853	0.085000	0.14912	1.558000	0.49541	0.407000	0.27541	TCT	.		0.468	NOX5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257124.2	NM_024505		A	69339166	C	A	69339166	3	1	155	1	0	0	0	0	1	0	0	0	10585	913	32	4	1727	4	NOX5	15	69339166	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	25590929	69339166	33192226	49	14021											
VASN	114990	broad.mit.edu	37	chr16	4432543	4432543	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcggggaggcccatacAcccccagccgtccactccaa	8	4	10	19	2	0	0	0	0	0	0	2	1	2	1	7	3	3	0	7	3	2	1			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr16:4432543A>C	ENST00000304735.3	+	2	1820	c.1665A>C	c.(1663-1665)acA>acC	p.T555T	CORO7_ENST00000537233.2_Intron|CORO7_ENST00000539968.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000251166.4_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	555	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						AGGCCCATACACCCCCAGCCG	0.731																																					p.T555T													.	VASN-68	0			c.A1665C						.						11	17	15					16																	4432543		2155	4252	6407	SO:0001819	synonymous_variant	114990	exon2			CCATACACCCCCA	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"slit-like 2 (Drosophila)"	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1665A>C	16.37:g.4432543A>C		Somatic	58	6		WXS	Illumina HiSeq	Phase_I	120	28	NM_138440	0	0	3	3	0	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			.		0.731	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		C	4432543	A	C	4432543	2	2	155	1	0	0	0	0	0	0	0	1	17160	146	6	5		5	VASN	16	4432543	Silent	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10		4432543	85922210	50	14022											
ABCC1	4363	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	16177358	16177358	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtgccctcctcccagacctgGaaatcctgcccagtggggat	7	8	11	15	0	0	1	0	0	0	1	3	3	3	3	6	3	2	0	6	3	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr16:16177358G>A	ENST00000399410.3	+	17	2426	c.2251G>A	c.(2251-2253)Gaa>Aaa	p.E751K	ABCC1_ENST00000345148.5_Missense_Mutation_p.E751K|ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000346370.5_Missense_Mutation_p.E751K|ABCC1_ENST00000351154.5_Intron|ABCC1_ENST00000399408.2_Missense_Mutation_p.E751K	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	751	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CCCAGACCTGGAAATCCTGCC	0.517																																					p.E751K		.											.	ABCC1-94	0			c.G2251A						.						82	84	83					16																	16177358		2014	4202	6216	SO:0001583	missense	4363	exon17			GACCTGGAAATCC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"ATP binding cassette transporters / subfamily C"	51	protein-coding gene	gene with protein product		158343	"multidrug resistance associated protein 1"	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2251G>A	16.37:g.16177358G>A	ENSP00000382342:p.Glu751Lys	Somatic	209	0		WXS	Illumina HiSeq	Phase_I	253	52	NM_004996	0	0	4	9	5	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334110	0.81801	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000345148;ENST00000536381	D;D;D;D	0.93906	-3.31;-3.31;-2.69;-3.31	5.29	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.045819	0.85682	D	0.000000	D	0.94122	0.8115	N	0.25890	0.77	0.80722	D	1	P;D;P;P	0.71674	0.877;0.998;0.583;0.877	P;D;P;B	0.80764	0.538;0.994;0.455;0.438	D	0.94049	0.7316	10	0.41790	T	0.15	-18.2126	17.9191	0.88961	0.0:0.0:1.0:0.0	.	751;751;751;751	P33527-4;P33527-3;P33527;P33527-9	.;.;MRP1_HUMAN;.	K	751;751;751;751;425	ENSP00000382342:E751K;ENSP00000382340:E751K;ENSP00000263019:E751K;ENSP00000263014:E751K	ENSP00000263014:E751K	E	+	1	0	ABCC1	16084859	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.549000	0.73900	2.484000	0.83849	0.563000	0.77884	GAA	.		0.517	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16177358	G	A	16177358	3	1	155	1	0	0	0	0	1	0	0	0	49	1175	41	2	2317	2	ABCC1	16	16177358	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	11744815	16177358	74177395	51	14023											
RLTPR	146206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	67683208	67683208	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccagctcatgcaggacgaCgattgtgtgagttcacggga	9	9	14	9	3	2	1	2	1	0	0	3	5	3	3	1	2	2	3	1	2	0	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr16:67683208C>T	ENST00000334583.6	+	19	2068	c.1740C>T	c.(1738-1740)gaC>gaT	p.D580D	RLTPR_ENST00000545661.1_Silent_p.D544D	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	580	Tropomodulin-like.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TGCAGGACGACGATTGTGTGA	0.612																																					p.D580D		.											.	RLTPR-67	0			c.C1740T						.						64	71	69					16																	67683208		2055	4210	6265	SO:0001819	synonymous_variant	146206	exon19			GGACGACGATTGT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1740C>T	16.37:g.67683208C>T		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	48	20	NM_001013838	0	0	0	0	0	B8X2Z3	Silent	SNP	ENST00000334583.6	37	CCDS45513.1																																																																																			.		0.612	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		T	67683208	C	T	67683208	2	4	155	1	0	0	0	0	0	0	0	1	13426	535	19	1		1	RLTPR	16	67683208	Silent	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	51505850	67683208	22671545	52	14024											
CFDP1	10428	broad.mit.edu	37	chr16	75446511	75446512	+	Frame_Shift_Ins	INS	-	-	T																															cccagagttcgtcctccttcINStttttcctggcatcctctga																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr16:75446511_75446512insT	ENST00000283882.3	-	3	455_456	c.323_324insA	c.(322-324)aagfs	p.K108fs	CFDP1_ENST00000564286.1_5'UTR|RP11-77K12.1_ENST00000561887.1_5'Flank	NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	108	Glu-rich.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						CGTCCTCCTTCTTTTTCCTGGC	0.485																																					p.K108fs													.	CFDP1-91	0			c.324_325insA						.																																			SO:0001589	frameshift_variant	10428	exon3			CTCCTTCTTTTTC	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"Bucentaur", "centromere protein 29"	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.324dupA	16.37:g.75446516_75446516dupT	ENSP00000283882:p.Lys108fs	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	212	7	NM_006324	0	0	0	0	0	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Frame_Shift_Ins	INS	ENST00000283882.3	37	CCDS10916.1																																																																																			.		0.485	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324		T	75446512	-	T	75446511	7	5	155	1	0	1	1	0	0	0	0	0	3288	912	32	0	595	0	CFDP1	16	75446511	Frame_Shift_Ins	INS	-	TCGA-P4-A5E8-01A-11D-A28G-10	7763303	75446511	14908242	53	14025											
MYO18A	399687	broad.mit.edu	37	chr17	27437604	27437604	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagagcaccgtggcactGcctgcgcggcccagaaacag	10	3	13	15	3	0	2	0	0	0	2	0	3	0	2	4	2	4	2	4	2	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:27437604G>T	ENST00000527372.1	-	18	3117	c.2937C>A	c.(2935-2937)ggC>ggA	p.G979G	MYO18A_ENST00000533112.1_Silent_p.G979G|MYO18A_ENST00000531253.1_Silent_p.G979G|MYO18A_ENST00000354329.4_Silent_p.G979G	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	979	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)	p.G979G(2)		NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CCGTGGCACTGCCTGCGCGGC	0.627																																					p.G979G	Esophageal Squamous(182;472 2015 7001 15270 22562)												.	MYO18A-22	2	Substitution - coding silent(2)	endometrium(2)	c.C2937A						.						39	43	42					17																	27437604		1981	4171	6152	SO:0001819	synonymous_variant	399687	exon18			GGCACTGCCTGCG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"Myosins / Myosin superfamily : Class XVIII"	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2937C>A	17.37:g.27437604G>T		Somatic	24	1		WXS	Illumina HiSeq	Phase_I	42	9	NM_078471	0	0	2	2	0	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			.		0.627	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27437604	G	T	27437604	2	4	155	1	0	0	0	0	0	0	0	1	10090	1306	46	4		4	MYO18A	17	27437604	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		27437604	53757606	54	14026											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305775	+	Missense_Mutation	DNP	CT	CT	GC																															gtggtcctgcagcaggtggtCtggcagcagcaggggcggca																								rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:39305774_39305775CT>GC	ENST00000343246.4	-	1	279_280	c.245_246AG>GC	c.(244-246)cAG>cGC	p.Q82R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.Q82H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcaggtggtctggcagcagca	0.653																																					p.Q82R		.											.	KRTAP4-5-90	1	Substitution - Missense(1)	lung(1)	c.A245G						.																																			SO:0001583	missense	85289	exon1			GTGGTCTGGCAGC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"Keratin associated proteins"	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.245_246delinsGC	17.37:g.39305774_39305775delinsGC	ENSP00000340546:p.Gln82Arg	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	86	26	NM_033188	0	0	0	0	0		Missense_Mutation	DNP	ENST00000343246.4	37	CCDS32650.1																																																																																			.		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			GC	39305775	CT	GC	39305774	3	3	155	1	0	0	0	0	1	0	0	0	8575	912	32	4	303	4	KRTAP4-5	17	39305774	Missense_Mutation	DNP	CT	TCGA-P4-A5E8-01A-11D-A28G-10	11868170	39305774	41889436	55	14027											
SP6	80320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	45925061	45925061	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcttcttgcccccatcGggcccacatggagcccccag	5	9	9	18	1	2	0	0	0	2	0	3	1	2	1	5	2	3	1	5	2	0	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:45925061G>A	ENST00000536300.1	-	2	1066	c.735C>T	c.(733-735)ccC>ccT	p.P245P	SP6_ENST00000342234.2_Silent_p.P245P	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	245					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						TGCCCCCATCGGGCCCACATG	0.672																																					p.P245P		.											.	SP6-91	0			c.C735T						.						21	23	22					17																	45925061		2182	4251	6433	SO:0001819	synonymous_variant	80320	exon2			CCCATCGGGCCCA		CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14530	protein-coding gene	gene with protein product	"epiprofin"	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.735C>T	17.37:g.45925061G>A		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	83	31	NM_001258248	0	0	0	0	0	B3KXS4	Silent	SNP	ENST00000536300.1	37	CCDS11520.1																																																																																			.		0.672	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262		A	45925061	G	A	45925061	2	1	155	1	0	0	0	0	0	0	0	1	15000	1103	39	1		1	SP6	17	45925061	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	6619287	45925061	35270149	56	14028											
TANC2	26115	ucsc.edu;bcgsc.ca	37	chr17	61432303	61432303	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggcaaaatggacaatactAcatttggcaaactcagttct	15	11	7	8	0	2	0	1	0	1	0	2	1	2	1	0	3	3	3	0	3	6	4			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:61432303A>G	ENST00000424789.2	+	12	1916	c.1912A>G	c.(1912-1914)Aca>Gca	p.T638A	TANC2_ENST00000389520.4_Missense_Mutation_p.T638A	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	638					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						GGACAATACTACATTTGGCAA	0.428																																					p.T638A													.	TANC2-24	0			c.A1912G						.						181	171	174					17																	61432303		1917	4133	6050	SO:0001583	missense	26115	exon12			AATACTACATTTG	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.1912A>G	17.37:g.61432303A>G	ENSP00000387593:p.Thr638Ala	Somatic	214	4		WXS	Illumina HiSeq		257	104	NM_025185	0	0	0	0	0	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	37	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	A	6.277	0.419168	0.11870	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.67865	-0.29;-0.29	5.93	3.7	0.42460	.	0.000000	0.85682	D	0.000000	T	0.43411	0.1246	N	0.15975	0.35	0.41042	D	0.985233	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.002	T	0.21348	-1.0248	10	0.07175	T	0.84	.	10.4681	0.44620	0.8681:0.0:0.1319:0.0	.	638;548;638	Q9HCD6-2;D3DU10;Q9HCD6	.;.;TANC2_HUMAN	A	638	ENSP00000374171:T638A;ENSP00000387593:T638A	ENSP00000374171:T638A	T	+	1	0	TANC2	58786035	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	5.351000	0.66022	0.488000	0.27723	-0.250000	0.11733	ACA	.		0.428	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			G	61432303	A	G	61432303	3	3	155	1	0	0	0	0	1	0	0	0	15577	391	14	3	1958	3	TANC2	17	61432303	Missense_Mutation	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	15507242	61432303	19762907	57	14029											
DNAI2	64446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72306227	72306227	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcgcctgcggctcccagctGgggacaaccaccctgctgga	7	6	12	16	2	0	0	0	0	0	0	2	2	1	2	4	4	4	3	4	4	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:72306227G>T	ENST00000311014.6	+	11	1486	c.1419G>T	c.(1417-1419)ctG>ctT	p.L473L	AC103809.1_ENST00000516976.1_RNA|RP11-647F2.2_ENST00000585167.1_RNA|DNAI2_ENST00000446837.2_Silent_p.L473L|DNAI2_ENST00000579490.1_Silent_p.L530L|DNAI2_ENST00000307504.5_Silent_p.L330L|DNAI2_ENST00000582036.1_Silent_p.L461L			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	473					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GCTCCCAGCTGGGGACAACCA	0.622									Kartagener syndrome																												p.L473L		.											.	DNAI2-92	0			c.G1419T						.						55	51	52					17																	72306227		2203	4300	6503	SO:0001819	synonymous_variant	64446	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCAGCTGGGGACA	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"Axonemal dyneins", "WD repeat domain containing"	18744	protein-coding gene	gene with protein product	"dynein intermediate chain 2"	605483	"dynein, axonemal, intermediate polypeptide 2"			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.1419G>T	17.37:g.72306227G>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	93	32	NM_023036	0	0	0	0	0	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			.		0.622	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		T	72306227	G	T	72306227	2	4	155	1	0	0	0	0	0	0	0	1	4621	1335	47	4		4	DNAI2	17	72306227	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	10873924	72306227	8888983	58	14030											
RAB40B	10966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	80617514	80617514	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaccagcggttcgcaatgTcatagaccaggatcacaccc	13	6	9	13	2	2	2	2	0	0	2	3	3	2	3	3	2	1	2	3	2	3	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:80617514T>A	ENST00000571995.1	-	4	415	c.284A>T	c.(283-285)gAc>gTc	p.D95V	RAB40B_ENST00000538809.2_Missense_Mutation_p.D95V|RAB40B_ENST00000269347.6_5'UTR|RAB40B_ENST00000571880.1_5'Flank	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	95					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(2)	10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			GTTCGCAATGTCATAGACCAG	0.517																																					p.D95V		.											.	RAB40B-227	0			c.A284T						.						149	114	126					17																	80617514		2203	4300	6503	SO:0001583	missense	10966	exon4			GCAATGTCATAGA	U05227	CCDS11816.1	17q25.3	2014-08-12			ENSG00000141542	ENSG00000141542		"RAB, member RAS oncogene"	18284	protein-coding gene	gene with protein product						11697911	Standard	NM_006822		Approved	SEC4L, RAR	uc002kft.3	Q12829	OTTHUMG00000177806	ENST00000571995.1:c.284A>T	17.37:g.80617514T>A	ENSP00000461785:p.Asp95Val	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	128	51	NM_006822	0	0	12	23	11	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	37	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259217	0.80246	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	4.56	4.56	0.56223	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.88093	0.6344	H	0.98155	4.16	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92358	0.5895	9	0.87932	D	0	.	14.2775	0.66189	0.0:0.0:0.0:1.0	.	95	Q12829	RB40B_HUMAN	V	95;129	.	ENSP00000269347:D95V	D	-	2	0	RAB40B	78210803	1.000000	0.71417	0.997000	0.53966	0.803000	0.45373	7.768000	0.85345	1.992000	0.58205	0.533000	0.62120	GAC	.		0.517	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1			A	80617514	T	A	80617514	3	1	155	1	0	0	0	0	1	0	0	0	12973	1667	58	5	564	5	RAB40B	17	80617514	Missense_Mutation	SNP	T	TCGA-P4-A5E8-01A-11D-A28G-10	8311287	80617514	577696	59	14031											
MBD1	4152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	47802004	47802004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggacacatttccactggCgcctgagaccagggcgggga	8	6	15	12	2	0	1	0	1	0	1	1	4	1	3	3	5	0	1	3	5	0	1			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr18:47802004C>T	ENST00000591416.1	-	8	1189	c.758G>A	c.(757-759)cGc>cAc	p.R253H	MBD1_ENST00000591535.1_Missense_Mutation_p.R253H|MBD1_ENST00000269471.5_Missense_Mutation_p.R253H|MBD1_ENST00000269468.5_Missense_Mutation_p.R253H|MBD1_ENST00000349085.2_Missense_Mutation_p.R253H|MBD1_ENST00000457839.2_Missense_Mutation_p.R253H|MBD1_ENST00000587605.1_Missense_Mutation_p.R253H|MBD1_ENST00000585595.1_Missense_Mutation_p.R253H|MBD1_ENST00000347968.3_Missense_Mutation_p.R253H|MBD1_ENST00000382948.5_Missense_Mutation_p.R253H|MBD1_ENST00000398488.1_Missense_Mutation_p.R253H|MBD1_ENST00000398495.2_Missense_Mutation_p.R253H|MBD1_ENST00000424334.2_Missense_Mutation_p.R279H|MBD1_ENST00000339998.6_Missense_Mutation_p.R253H|MBD1_ENST00000436910.1_Missense_Mutation_p.R253H|MBD1_ENST00000398493.1_Missense_Mutation_p.R253H|MBD1_ENST00000353909.3_Missense_Mutation_p.R204H|MBD1_ENST00000588937.1_Missense_Mutation_p.R253H|MBD1_ENST00000590208.1_Missense_Mutation_p.R253H|MBD1_ENST00000585672.1_Missense_Mutation_p.R204H			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	253					negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R253L(4)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						TTTCCACTGGCGCCTGAGACC	0.602																																					p.R253H		.											.	MBD1-228	4	Substitution - Missense(4)	lung(4)	c.G758A						.						47	47	47					18																	47802004		2203	4300	6503	SO:0001583	missense	4152	exon8			CACTGGCGCCTGA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.758G>A	18.37:g.47802004C>T	ENSP00000467017:p.Arg253His	Somatic	239	0		WXS	Illumina HiSeq	Phase_I	224	74	NM_001204137	0	0	11	20	9	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144536	0.77888	.	.	ENSG00000141644	ENST00000382948;ENST00000353909;ENST00000349085;ENST00000269468;ENST00000347968;ENST00000436910;ENST00000269471;ENST00000424334;ENST00000339998;ENST00000398495;ENST00000457839;ENST00000398493;ENST00000398488	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97232	-4.22;-3.92;-4.04;-4.22;-4.05;-4.18;-4.16;-4.3;-4.17;-4.06;-4.29;-4.05;-4.04	5.29	5.29	0.74685	Zinc finger, CXXC-type (2);	0.000000	0.56097	D	0.000023	D	0.97508	0.9184	L	0.56769	1.78	0.32700	N	0.513027	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.998;0.999;1.0;0.999;0.997;0.999;0.996;1.0;0.998;1.0;0.998	D	0.97757	1.0218	10	0.52906	T	0.07	-14.4062	10.2988	0.43639	0.0:0.9098:0.0:0.0902	.	253;279;253;253;253;253;204;253;253;253;253;253	B4DUR3;B4DI41;Q9UIS9-8;A8K654;Q9UIS9-6;Q9UIS9-2;Q9UIS9-5;Q9UIS9-4;Q9UIS9;Q9UIS9-7;B4DXJ5;Q9UIS9-3	.;.;.;.;.;.;.;.;MBD1_HUMAN;.;.;.	H	253;204;253;253;253;253;253;279;253;253;253;253;253	ENSP00000372407:R253H;ENSP00000269469:R204H;ENSP00000342531:R253H;ENSP00000269468:R253H;ENSP00000285102:R253H;ENSP00000409561:R253H;ENSP00000269471:R253H;ENSP00000408846:R279H;ENSP00000339546:R253H;ENSP00000381508:R253H;ENSP00000405268:R253H;ENSP00000381506:R253H;ENSP00000381502:R253H	ENSP00000269468:R253H	R	-	2	0	MBD1	46056002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.576000	0.46033	2.653000	0.90120	0.655000	0.94253	CGC	.		0.602	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846		T	47802004	C	T	47802004	3	4	155	1	0	0	0	0	1	0	0	0	9367	768	27	1	1289	1	MBD1	18	47802004	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		47802004	30275244	60	14032											
SPTBN4	57731	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	41076606	41076606	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctactgcgcaagcgcgagCtcgacgctaaccgcaagtcg	9	6	11	15	7	0	0	0	0	0	0	3	2	1	0	2	0	5	4	2	0	4	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr19:41076606C>T	ENST00000352632.3	+	33	7377	c.7291C>T	c.(7291-7293)Ctc>Ttc	p.L2431F	SPTBN4_ENST00000598249.1_Missense_Mutation_p.L2431F|SPTBN4_ENST00000392025.1_Missense_Mutation_p.L1174F			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2431	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CAAGCGCGAGCTCGACGCTAA	0.711																																					p.L2431F		.											.	SPTBN4-94	0			c.C7291T						.						13	13	13					19																	41076606		2130	4092	6222	SO:0001583	missense	57731	exon33			CGCGAGCTCGACG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"Pleckstrin homology (PH) domain containing"	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.7291C>T	19.37:g.41076606C>T	ENSP00000263373:p.Leu2431Phe	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	74	27	NM_020971	0	0	0	0	0	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496244	0.44352	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000392025	T;T	0.31769	1.48;1.48	4.64	3.59	0.41128	Pleckstrin homology-type (1);Pleckstrin homology domain, spectrin-type (1);Pleckstrin homology domain (3);	0.111049	0.37623	U	0.002018	T	0.36441	0.0967	L	0.42245	1.32	0.80722	D	1	P;P	0.50943	0.94;0.94	P;P	0.51833	0.681;0.681	T	0.08973	-1.0696	10	0.39692	T	0.17	.	13.6768	0.62458	0.0:0.8434:0.1566:0.0	.	1174;2431	C9JY79;Q9H254	.;SPTN4_HUMAN	F	2431;2431;1174	ENSP00000263373:L2431F;ENSP00000375879:L1174F	ENSP00000263373:L2431F	L	+	1	0	SPTBN4	45768446	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	2.096000	0.41738	1.145000	0.42336	0.491000	0.48974	CTC	.		0.711	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			T	41076606	C	T	41076606	3	4	155	1	0	0	0	0	1	0	0	0	15153	797	28	2	7511	2	SPTBN4	19	41076606	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		41076606	18052377	61	14033											
ZNF577	84765	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	52376124	52376124	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctctcttatgtgagttttCtcatgtttaatgaggactga	8	18	9	6	0	3	3	1	3	3	0	5	4	3	4	0	1	0	2	0	1	2	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr19:52376124C>A	ENST00000301399.5	-	7	1484	c.1119G>T	c.(1117-1119)gaG>gaT	p.E373D	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.E314D|ZNF577_ENST00000451628.2_Missense_Mutation_p.E314D|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	373			E -> K (in dbSNP:rs10407547).		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)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TGTGAGTTTTCTCATGTTTAA	0.448																																					p.E373D		.											.	ZNF577-91	0			c.G1119T						.						89	94	92					19																	52376124		2203	4300	6503	SO:0001583	missense	84765	exon7			AGTTTTCTCATGT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"Zinc fingers, C2H2-type", "-"	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1119G>T	19.37:g.52376124C>A	ENSP00000301399:p.Glu373Asp	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	84	40	NM_032679	0	0	0	0	0	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	7.724	0.697762	0.15106	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	3.06	2.02	0.26589	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25419	0.0618	N	0.08118	0	0.09310	N	0.999994	B;B	0.25007	0.016;0.116	B;B	0.25884	0.007;0.064	T	0.20840	-1.0263	9	0.87932	D	0	.	4.8679	0.13618	0.0:0.6085:0.0:0.3915	.	373;314	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	D	373;314;314;373	ENSP00000301399:E373D;ENSP00000413476:E314D;ENSP00000389652:E314D;ENSP00000404509:E373D	ENSP00000301399:E373D	E	-	3	2	ZNF577	57067936	0.000000	0.05858	0.007000	0.13788	0.327000	0.28475	0.103000	0.15292	0.592000	0.29728	0.655000	0.94253	GAG	.		0.448	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		A	52376124	C	A	52376124	3	1	155	1	0	0	0	0	1	0	0	0	18041	912	32	4	342	4	ZNF577	19	52376124	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	11299518	52376124	6752859	62	14034											
NCOA6	23054	bcgsc.ca	37	chr20	33337464	33337464	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcccatggcctgagaagTggtttcccgaggcactgttt	8	11	11	11	1	0	1	0	1	0	1	2	3	2	1	3	3	0	3	3	3	1	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr20:33337464T>C	ENST00000374796.2	-	10	5104	c.2534A>G	c.(2533-2535)cAc>cGc	p.H845R	NCOA6_ENST00000359003.2_Missense_Mutation_p.H845R			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	845	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|NCOA6IP-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GCCTGAGAAGTGGTTTCCCGA	0.493																																					p.H845R													.	NCOA6-292	0			c.A2534G						.						130	122	125					20																	33337464		2203	4300	6503	SO:0001583	missense	23054	exon9			GAGAAGTGGTTTC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.2534A>G	20.37:g.33337464T>C	ENSP00000363929:p.His845Arg	Somatic	237	6		WXS	Illumina HiSeq	Phase_1	234	94	NM_014071	0	0	4	4	0	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365448	0.82463	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.31247	1.5;1.5	5.86	5.86	0.93980	.	0.000000	0.64402	D	0.000001	T	0.38348	0.1037	L	0.29908	0.895	0.58432	D	0.999999	D	0.69078	0.997	P	0.58520	0.84	T	0.06303	-1.0834	10	0.23302	T	0.38	-7.2245	16.2605	0.82541	0.0:0.0:0.0:1.0	.	845	Q14686	NCOA6_HUMAN	R	845	ENSP00000363929:H845R;ENSP00000351894:H845R	ENSP00000351894:H845R	H	-	2	0	NCOA6	32801125	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.237000	0.73441	0.460000	0.39030	CAC	.		0.493	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33337464	T	C	33337464	3	2	155	1	0	0	0	0	1	0	0	0	10259	1696	59	3	3685	3	NCOA6	20	33337464	Missense_Mutation	SNP	T	TCGA-P4-A5E8-01A-11D-A28G-10		33337464	29688056	63	14035											
EPB41L1	2036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	34778710	34778710	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtacaccatgtcccgcagcCttgatggaggtatggcccaa	9	8	12	12	1	0	1	0	1	0	0	1	2	1	2	4	4	2	3	4	4	3	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr20:34778710C>G	ENST00000338074.2	+	11	1452	c.1291C>G	c.(1291-1293)Ctt>Gtt	p.L431V	EPB41L1_ENST00000202028.5_Missense_Mutation_p.L369V|EPB41L1_ENST00000441639.1_Missense_Mutation_p.L369V|EPB41L1_ENST00000373946.3_Missense_Mutation_p.L400V|EPB41L1_ENST00000373950.2_Missense_Mutation_p.L334V|EPB41L1_ENST00000373941.1_Missense_Mutation_p.L431V	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	431					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					GTCCCGCAGCCTTGATGGAGG	0.602																																					p.L431V		.											.	EPB41L1-93	0			c.C1291G						.						47	42	43					20																	34778710		2203	4300	6503	SO:0001583	missense	2036	exon12			CGCAGCCTTGATG	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1291C>G	20.37:g.34778710C>G	ENSP00000337168:p.Leu431Val	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	38	12	NM_001258329	0	0	0	0	0	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	37	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499624	0.64298	.	.	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000344237;ENST00000338074;ENST00000373941	D;D;D;D;D;D	0.86297	-1.95;-1.92;-1.95;-1.94;-2.1;-2.1	5.48	5.48	0.80851	.	0.292495	0.38005	N	0.001858	D	0.84844	0.5562	N	0.24115	0.695	0.39057	D	0.960441	B;P;P;P;B;P	0.45569	0.249;0.861;0.539;0.794;0.3;0.783	B;P;B;P;B;P	0.47891	0.186;0.471;0.439;0.487;0.13;0.56	D	0.87969	0.2735	10	0.87932	D	0	-4.2264	17.9268	0.88986	0.0:1.0:0.0:0.0	.	431;431;400;334;334;369	B7Z653;Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;E41L1_HUMAN;.;.;.;.	V	369;334;431;334;369;400;5;431;431	ENSP00000202028:L369V;ENSP00000363061:L334V;ENSP00000399214:L369V;ENSP00000363057:L400V;ENSP00000337168:L431V;ENSP00000363052:L431V	ENSP00000202028:L369V	L	+	1	0	EPB41L1	34242124	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.048000	0.30379	2.556000	0.86216	0.561000	0.74099	CTT	.		0.602	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		G	34778710	C	G	34778710	3	3	155	1	0	0	0	0	1	0	0	0	5165	681	24	4	1329	4	EPB41L1	20	34778710	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	1441246	34778710	28246810	64	14036											
FAM83D	81610	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	37570604	37570604	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccctgtttcacctgtaggtGattgcagtggtcatggacgt	6	14	12	9	1	2	1	2	1	0	0	3	2	3	2	2	3	1	3	2	3	1	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr20:37570604G>A	ENST00000217429.4	+	2	617	c.576G>A	c.(574-576)gtG>gtA	p.V192V		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	162					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				ACCTGTAGGTGATTGCAGTGG	0.483																																					p.V192V		.											.	FAM83D-93	0			c.G576A						.						149	152	151					20																	37570604		2058	4205	6263	SO:0001819	synonymous_variant	81610	exon2			GTAGGTGATTGCA	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 129"	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.576G>A	20.37:g.37570604G>A		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	151	53	NM_030919	0	0	0	0	0	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Silent	SNP	ENST00000217429.4	37	CCDS42872.1																																																																																			.		0.483	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			A	37570604	G	A	37570604	2	1	155	1	0	0	0	0	0	0	0	1	5655	1277	45	2		2	FAM83D	20	37570604	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	2791894	37570604	25454916	65	14037											
PLXNB2	23654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50728592	50728593	+	Missense_Mutation	DNP	TT	TT	AC																															cattgctggccacgaaagacTtctccccgctgccgtcctcg																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr22:50728592_50728593TT>AC	ENST00000449103.1	-	3	561_562	c.421_422AA>GT	c.(421-423)AAg>GTg	p.K141V	PLXNB2_ENST00000359337.4_Missense_Mutation_p.K141V			O15031	PLXB2_HUMAN	plexin B2	141	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CACGAAAGACTTCTCCCCGCTG	0.644																																					p.K141V		.											.	PLXNB2-211	0			c.A421G						.																																			SO:0001583	missense	23654	exon3			AAGACTTCTCCCC		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.421_422delinsAC	22.37:g.50728592_50728593delinsAC	ENSP00000409171:p.Lys141Val	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	113	41	NM_012401	0	0	0	0	0	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	DNP	ENST00000449103.1	37	CCDS43035.1																																																																																			.		0.644	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		AC	50728593	TT	AC	50728592	3	1	155	1	0	0	0	0	1	0	0	0	12150	1609	56	5	5234	5	PLXNB2	22	50728592	Missense_Mutation	DNP	TT	TCGA-P4-A5E8-01A-11D-A28G-10		50728592	575974	66	14038											
ARSE	415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	2861169	2861169	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgattctctagggaaccgcCgtgatccgacgtaaaataaa	13	10	9	9	4	1	2	0	2	1	0	3	4	2	3	3	1	1	1	3	1	6	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chrX:2861169C>T	ENST00000381134.3	-	8	1129	c.1063G>A	c.(1063-1065)Ggc>Agc	p.G355S	ARSE_ENST00000540563.1_Missense_Mutation_p.G310S|ARSE_ENST00000545496.1_Missense_Mutation_p.G380S	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	355					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGGGAACCGCCGTGATCCGAC	0.473																																					p.G355S		.											.	ARSE-131	0			c.G1063A						.						89	83	85					X																	2861169		2203	4300	6503	SO:0001583	missense	415	exon8			AACCGCCGTGATC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"Arylsulfatase family"	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1063G>A	X.37:g.2861169C>T	ENSP00000370526:p.Gly355Ser	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	91	62	NM_000047	0	0	0	30	30	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	37	CCDS14122.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.687965	0.68271	.	.	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.99809	-6.86;-6.86;-6.86	3.66	2.8	0.32819	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.109135	0.64402	D	0.000009	D	0.99887	0.9946	H	0.99929	4.97	0.51482	D	0.999923	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96969	0.9707	10	0.87932	D	0	.	9.8836	0.41249	0.0:0.8911:0.0:0.1089	.	310;380;355	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	S	310;380;355	ENSP00000438198:G310S;ENSP00000441417:G380S;ENSP00000370526:G355S	ENSP00000370526:G355S	G	-	1	0	ARSE	2871169	0.999000	0.42202	0.003000	0.11579	0.000000	0.00434	6.039000	0.70972	0.545000	0.28902	-0.191000	0.12829	GGC	.		0.473	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		T	2861169	C	T	2861169	3	4	155	1	0	0	0	0	1	0	0	0	991	652	23	1	722	1	ARSE	23	2861169	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		2861169	152409391	67	14039											
EPHA2	1969	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	16459720	16459721	+	Frame_Shift_Ins	INS	-	-	TG																															atgatgttgtggtggctgaaINSctggcccatgatgccggcct																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:16459720_16459721insTG	ENST00000358432.5	-	11	2161_2162	c.2007_2008insCA	c.(2005-2010)cagttcfs	p.F670fs		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	670	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	TGGTGGCTGAACTGGCCCATGA	0.629																																					p.F670fs		.											.	EPHA2-1419	0			c.2008_2009insCA						.																																			SO:0001589	frameshift_variant	1969	exon11			.	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3386	protein-coding gene	gene with protein product		176946	"EphA2"	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.2007_2008insCA	1.37:g.16459720_16459721insTG	ENSP00000351209:p.Phe670fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	56	13	NM_004431	0	0	0	0	0	B5A968|Q8N3Z2	Frame_Shift_Ins	INS	ENST00000358432.5	37	CCDS169.1																																																																																			.		0.629	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		TG	16459721	-	TG	16459720	7	5	156	1	0	1	1	0	0	0	0	0	5180	43	2	0	950	0	EPHA2	1	16459720	Frame_Shift_Ins	INS	-	TCGA-P4-A5EA-01A-11D-A28G-10		16459720	232790901	1	14040											
MAP3K6	9064	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	27687435	27687435	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caacatctcccccgcgccctCcgcctcctccgcgggcgccg	3	5	9	24	7	1	0	0	0	1	0	5	0	4	0	8	1	1	0	8	1	1	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:27687435C>T	ENST00000493901.1	-	15	2136	c.1897G>A	c.(1897-1899)Gag>Aag	p.E633K	MAP3K6_ENST00000357582.2_Missense_Mutation_p.E633K|MAP3K6_ENST00000374040.3_Missense_Mutation_p.E625K	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	633					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CCCGCGCCCTCCGCCTCCTCC	0.736																																					p.E633K		.											.	MAP3K6-1523	0			c.G1897A						.						10	14	13					1																	27687435		2139	4246	6385	SO:0001583	missense	9064	exon14			CGCCCTCCGCCTC	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6858	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 2"	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.1897G>A	1.37:g.27687435C>T	ENSP00000419591:p.Glu633Lys	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	102	35	NM_004672	0	0	0	0	0	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901459	0.33535	.	.	ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582	T;T;T	0.68025	-0.3;-0.3;-0.3	4.67	3.73	0.42828	.	.	.	.	.	T	0.61999	0.2392	M	0.62723	1.935	0.09310	N	1	B;B	0.25609	0.13;0.079	B;B	0.24701	0.055;0.025	T	0.54860	-0.8230	9	0.48119	T	0.1	.	8.9619	0.35851	0.0:0.8957:0.0:0.1043	.	625;633	O95382-3;O95382	.;M3K6_HUMAN	K	625;633;356;633	ENSP00000363152:E625K;ENSP00000419591:E633K;ENSP00000350195:E633K	ENSP00000350195:E633K	E	-	1	0	MAP3K6	27560022	0.005000	0.15991	0.073000	0.20177	0.013000	0.08279	1.483000	0.35497	2.433000	0.82419	0.655000	0.94253	GAG	.		0.736	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		T	27687435	C	T	27687435	3	4	156	1	0	0	0	0	1	0	0	0	9279	864	30	2	2033	2	MAP3K6	1	27687435	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	11227715	27687435	221563186	2	14041											
ZSWIM5	57643	broad.mit.edu	37	chr1	45671664	45671664	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagcagcgccggcgccggggCcgccccggtactggaagctg	5	3	17	16	6	0	0	0	0	0	0	0	1	0	1	5	5	4	3	5	5	2	1	rs565101218		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:45671664C>A	ENST00000359600.5	-	1	564	c.359G>T	c.(358-360)gGc>gTc	p.G120V	ZSWIM5_ENST00000464588.1_Intron	NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	120						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					ggcgccggggccgccccggTA	0.781																																					p.G120V													.	ZSWIM5-22	0			c.G359T						.						6	7	7					1																	45671664		1628	3773	5401	SO:0001583	missense	57643	exon1			CCGGGGCCGCCCC	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"Zinc fingers, SWIM-type"	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.359G>T	1.37:g.45671664C>A	ENSP00000352614:p.Gly120Val	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	25	4	NM_020883	0	0	0	0	0	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	37	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	C	7.574	0.667370	0.14710	.	.	ENSG00000162415	ENST00000359600	T	0.68765	-0.35	2.14	-0.388	0.12459	.	0.311011	0.20497	U	0.091165	T	0.46092	0.1375	L	0.34521	1.04	0.34312	D	0.685593	B	0.20780	0.048	B	0.15484	0.013	T	0.33214	-0.9877	10	0.30078	T	0.28	-0.8426	4.5086	0.11899	0.0:0.6055:0.2312:0.1633	.	120	Q9P217	ZSWM5_HUMAN	V	120	ENSP00000352614:G120V	ENSP00000352614:G120V	G	-	2	0	ZSWIM5	45444251	0.015000	0.18098	0.365000	0.25901	0.495000	0.33615	0.095000	0.15127	0.219000	0.20840	0.121000	0.15741	GGC	.		0.781	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581		A	45671664	C	A	45671664	3	1	156	1	0	0	0	0	1	0	0	0	18276	739	26	4	3254	4	ZSWIM5	1	45671664	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	17984229	45671664	203578957	3	14042											
NASP	4678	broad.mit.edu;bcgsc.ca	37	chr1	46073053	46073073	+	In_Frame_Del	DEL	CCAAAAAAACAGAAGACAAGT	CCAAAAAAACAGAAGACAAGT	-																															catgggagaaaaagaagaagCcaaaaaaacagaagacaagt																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CCAAAAAAACAGAAGACAAGT	CCAAAAAAACAGAAGACAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:46073053_46073073delCCAAAAAAACAGAAGACAAGT	ENST00000350030.3	+	6	557_577	c.470_490delCCAAAAAAACAGAAGACAAGT	c.(469-492)gccaaaaaaacagaagacaagtct>gct	p.KKTEDKS158del	NASP_ENST00000372052.4_Intron|NASP_ENST00000537798.1_In_Frame_Del_p.KKTEDKS94del|NASP_ENST00000402363.3_In_Frame_Del_p.KKTEDKS160del|NASP_ENST00000351223.3_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	158	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AAAGAAGAAGCCAAAAAAACAGAAGACAAGTCTTTGGCAAA	0.412																																					p.157_164del													.	NASP-91	0			c.470_490del						.																																			SO:0001651	inframe_deletion	4678	exon6			AAGAAGCCAAAAA	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.470_490delCCAAAAAAACAGAAGACAAGT	1.37:g.46073053_46073073delCCAAAAAAACAGAAGACAAGT	ENSP00000255120:p.Lys158_Ser164del	Somatic	229	0		WXS	Illumina HiSeq	Phase_I	178	13	NM_002482	0	0	0	0	0	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	In_Frame_Del	DEL	ENST00000350030.3	37	CCDS524.1																																																																																			.		0.412	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		-	46073073	CCAAAAAAACAGAAGACAAGT	-	46073053	7	5	156	1	0	1	0	1	0	0	0	0	10197	739	26	0	569	0	NASP	1	46073053	In_Frame_Del	DEL	CCAAAAAAACAGAAGACAAGT	TCGA-P4-A5EA-01A-11D-A28G-10	401389	46073053	203177568	4	14043											
PRKACB	5567	ucsc.edu	37	chr1	84663465	84663465	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagaacttggacattatgTggaactccagagtatttggc	11	11	12	7	0	0	2	0	0	0	2	1	4	1	4	1	4	2	2	1	4	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:84663465T>C	ENST00000370689.2	+	7	864	c.600T>C	c.(598-600)tgT>tgC	p.C200C	PRKACB_ENST00000394838.2_Silent_p.C207C|PRKACB_ENST00000370685.3_Silent_p.C247C|PRKACB_ENST00000394839.2_Silent_p.C170C|PRKACB_ENST00000370688.3_Silent_p.C200C|PRKACB_ENST00000370682.3_Silent_p.C204C|PRKACB_ENST00000370680.1_Silent_p.C206C	NM_001242862.1|NM_002731.2	NP_001229791.1|NP_002722.1	P22694	KAPCB_HUMAN	protein kinase, cAMP-dependent, catalytic, beta	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of protein processing (GO:0070613)|response to clozapine (GO:0097338)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|magnesium ion binding (GO:0000287)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|lung(11)|ovary(1)	16				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		GGACATTATGTGGAACTCCAG	0.343																																					p.C247C													.	PRKACB-1083	0			c.T741C						.						102	113	109					1																	84663465		2203	4299	6502	SO:0001819	synonymous_variant	5567	exon7			ATTATGTGGAACT	BC035058	CCDS691.1, CCDS692.1, CCDS693.1, CCDS55610.1, CCDS55611.1, CCDS72812.1, CCDS72813.1, CCDS72814.1, CCDS72815.1, CCDS72816.1	1p36.1	2012-10-02			ENSG00000142875	ENSG00000142875	2.7.11.1		9381	protein-coding gene	gene with protein product		176892					Standard	XM_005271016		Approved	PKACb	uc001djl.3	P22694	OTTHUMG00000009975	ENST00000370689.2:c.600T>C	1.37:g.84663465T>C		Somatic	44	0		WXS	Illumina HiSeq		37	1	NM_182948	0	0	7	7	0	B1APG4|B4DKB0|B4E2Q1|Q14VH1|Q59GC0|Q5BNE9|Q5BNF0|Q5BNF1|Q5BNF2|Q5BNF3|Q5CZ92|Q5T1K3|Q7Z3M1|Q8IYR5|Q8IZQ0|Q96B09	Silent	SNP	ENST00000370689.2	37	CCDS691.1																																																																																			.		0.343	PRKACB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027641.1	NM_182948		C	84663465	T	C	84663465	2	2	156	1	0	0	0	0	0	0	0	1	12527	1702	59	3		3	PRKACB	1	84663465	Silent	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	38590412	84663465	164587156	5	14044											
PHTF1	10745	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	114255942	114255943	+	Frame_Shift_Del	DEL	TT	TT	-																															tgaaaattttgctttctctcTtgtttgccacattctaatct																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:114255942_114255943delTT	ENST00000369604.1	-	8	1224_1225	c.741_742delAA	c.(739-744)acaagafs	p.R248fs	PHTF1_ENST00000369598.1_Frame_Shift_Del_p.R203fs|PHTF1_ENST00000447664.2_Intron|PHTF1_ENST00000369596.2_Frame_Shift_Del_p.R195fs|PHTF1_ENST00000393357.2_Frame_Shift_Del_p.R248fs|PHTF1_ENST00000357783.2_Frame_Shift_Del_p.R248fs|PHTF1_ENST00000369600.1_Frame_Shift_Del_p.R195fs|PHTF1_ENST00000474926.1_5'UTR			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	248					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTTCTCTCTTGTTTGCCACA	0.371																																					p.247_248del		.											.	PHTF1-91	0			c.741_742del						.																																			SO:0001589	frameshift_variant	10745	exon7			.	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.741_742delAA	1.37:g.114255942_114255943delTT	ENSP00000358617:p.Arg248fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	81	20	NM_006608	0	0	0	0	0	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Frame_Shift_Del	DEL	ENST00000369604.1	37	CCDS861.1																																																																																			.		0.371	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		-	114255943	TT	-	114255942	7	5	156	1	0	1	0	1	0	0	0	0	11888	1617	56	0	1594	0	PHTF1	1	114255942	Frame_Shift_Del	DEL	TT	TCGA-P4-A5EA-01A-11D-A28G-10	29592477	114255942	134994679	6	14045											
TUFT1	7286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	151552139	151552139	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcagctccagaattcaaaAgctgtgatccagtcaaagga	14	9	9	9	0	2	2	2	1	0	1	4	3	4	3	2	1	3	3	2	1	4	2	rs201062061		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:151552139A>G	ENST00000368849.3	+	11	1001	c.939A>G	c.(937-939)aaA>aaG	p.K313K	TUFT1_ENST00000368848.2_Silent_p.K288K|TUFT1_ENST00000392712.3_Silent_p.K258K|TUFT1_ENST00000538902.1_Silent_p.K332K|TUFT1_ENST00000353024.3_Silent_p.K254K	NM_020127.2	NP_064512.1	Q9NNX1	TUFT1_HUMAN	tuftelin 1	313					bone mineralization (GO:0030282)|odontogenesis (GO:0042476)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	structural constituent of tooth enamel (GO:0030345)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGAATTCAAAAGCTGTGATCC	0.547																																					p.K313K		.											.	TUFT1-90	0			c.A939G						.						58	53	55					1																	151552139		2203	4300	6503	SO:0001819	synonymous_variant	7286	exon11			TTCAAAAGCTGTG	AF254260	CCDS1000.1, CCDS44223.1	1q21	2008-02-05			ENSG00000143367	ENSG00000143367			12422	protein-coding gene	gene with protein product		600087				7919663	Standard	NM_020127		Approved		uc001eyl.3	Q9NNX1	OTTHUMG00000012536	ENST00000368849.3:c.939A>G	1.37:g.151552139A>G		Somatic	170	0		WXS	Illumina HiSeq	Phase_I	138	17	NM_020127	0	0	0	0	0	B2RD57|D3DV21|D3DV22|Q5T384|Q5T385|Q9BU28|Q9H5L1	Silent	SNP	ENST00000368849.3	37	CCDS1000.1																																																																																			.		0.547	TUFT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035022.1	NM_020127		G	151552139	A	G	151552139	2	3	156	1	0	0	0	0	0	0	0	1	16805	69	3	3		3	TUFT1	1	151552139	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	37296197	151552139	97698482	7	14046											
GATAD2B	57459	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	153792180	153792180	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agacaaaacaatgatgtctgGtgagggagttagccttcctc	12	10	11	8	0	1	3	0	2	1	1	3	4	2	4	2	2	2	1	2	2	4	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:153792180G>C	ENST00000368655.4	-	3	610	c.367C>G	c.(367-369)Cca>Gca	p.P123A		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	123					ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ATGATGTCTGGTGAGGGAGTT	0.408																																					p.P123A		.											.	GATAD2B-90	0			c.C367G						.						111	112	112					1																	153792180		2203	4300	6503	SO:0001583	missense	57459	exon3			TGTCTGGTGAGGG	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"GATA zinc finger domain containing"	30778	protein-coding gene	gene with protein product	"transcription repressor p66 beta component of the MeCP1 complex"	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.367C>G	1.37:g.153792180G>C	ENSP00000357644:p.Pro123Ala	Somatic	241	0		WXS	Illumina HiSeq	Phase_I	193	17	NM_020699	0	0	0	0	0	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Missense_Mutation	SNP	ENST00000368655.4	37	CCDS1054.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821458	0.90873	.	.	ENSG00000143614	ENST00000368655	T	0.41400	1.0	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.53029	0.1771	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.42982	-0.9419	10	0.35671	T	0.21	-15.871	17.5737	0.87942	0.0:0.0:1.0:0.0	.	123	Q8WXI9	P66B_HUMAN	A	123	ENSP00000357644:P123A	ENSP00000357644:P123A	P	-	1	0	GATAD2B	152058804	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.086000	0.94088	2.682000	0.91365	0.557000	0.71058	CCA	.		0.408	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699		C	153792180	G	C	153792180	3	2	156	1	0	0	0	0	1	0	0	0	6281	1261	44	4	1450	4	GATAD2B	1	153792180	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	2240041	153792180	95458441	8	14047											
EFNA1	1942	ucsc.edu	37	chr1	155104060	155104060	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagttccagcgcttcacacCtttcaccctgggcaaggagt	9	9	10	13	1	2	0	2	0	0	0	3	2	3	1	3	2	1	3	3	2	2	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:155104060C>T	ENST00000368407.3	+	2	856	c.338C>T	c.(337-339)cCt>cTt	p.P113L	EFNA1_ENST00000469878.1_3'UTR|EFNA1_ENST00000368406.2_Missense_Mutation_p.P113L	NM_004428.2	NP_004419.2	P20827	EFNA1_HUMAN	ephrin-A1	113	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1)	5	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			CGCTTCACACCTTTCACCCTG	0.547																																					p.P113L													.	EFNA1-90	0			c.C338T						.						54	48	50					1																	155104060		2203	4300	6503	SO:0001583	missense	1942	exon2			TCACACCTTTCAC		CCDS1091.1, CCDS1092.1	1q21-q22	2011-03-09			ENSG00000169242	ENSG00000169242		"Ephrins"	3221	protein-coding gene	gene with protein product		191164		TNFAIP4, EPLG1		2233719, 8660976	Standard	NM_182685		Approved	LERK1, ECKLG	uc001fhh.3	P20827	OTTHUMG00000035312	ENST00000368407.3:c.338C>T	1.37:g.155104060C>T	ENSP00000357392:p.Pro113Leu	Somatic	338	0		WXS	Illumina HiSeq		249	1	NM_182685	0	0	4	4	0	D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578	Missense_Mutation	SNP	ENST00000368407.3	37	CCDS1091.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556530	0.86231	.	.	ENSG00000169242	ENST00000368407;ENST00000368406	T;T	0.73363	-0.74;-0.74	5.22	4.3	0.51218	Ephrin, conserved site (1);Cupredoxin (2);	0.154283	0.64402	D	0.000015	D	0.84969	0.5590	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.88382	0.3002	10	0.87932	D	0	-7.7709	13.8904	0.63736	0.0:0.8459:0.1541:0.0	.	113;113	P20827-2;P20827	.;EFNA1_HUMAN	L	113	ENSP00000357392:P113L;ENSP00000357391:P113L	ENSP00000357391:P113L	P	+	2	0	EFNA1	153370684	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	5.710000	0.68392	1.314000	0.45095	0.655000	0.94253	CCT	.		0.547	EFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085428.1	NM_004428		T	155104060	C	T	155104060	3	4	156	1	0	0	0	0	1	0	0	0	4961	681	24	2	344	2	EFNA1	1	155104060	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	1311880	155104060	94146561	9	14048											
FAM82A1	151393	bcgsc.ca	37	chr2	38156861	38156861	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatagttcagaggaagcagaAagtgaaggagggtaagtttc	16	8	14	3	0	1	3	1	1	0	2	2	5	1	5	0	3	1	4	0	3	6	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:38156861A>G	ENST00000406384.1	+	2	635	c.441A>G	c.(439-441)gaA>gaG	p.E147E	RMDN2_ENST00000354545.2_Silent_p.E147E	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2	147						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)											AGGAAGCAGAAAGTGAAGGAG	0.338																																					p.E147E													.	.	0			c.A441G						.						29	27	28					2																	38156861		692	1591	2283	SO:0001819	synonymous_variant	151393	exon2			AGCAGAAAGTGAA	AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"family with sequence similarity 82, member A1"	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.441A>G	2.37:g.38156861A>G		Somatic	80	1		WXS	Illumina HiSeq	Phase_1	65	4	NM_001170792	0	0	0	0	0	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Silent	SNP	ENST00000406384.1	37	CCDS54351.1																																																																																			.		0.338	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713		G	38156861	A	G	38156861	2	3	156	1	0	0	0	0	0	0	0	1	5649	11	1	3		3	FAM82A1	2	38156861	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10		38156861	205042512	10	14049											
SOCS5	9655	broad.mit.edu	37	chr2	46987222	46987224	+	In_Frame_Del	DEL	ATT	ATT	-																															ggattttttaaaagagtatcAttataaacaaaaagttagag																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:46987222_46987224delATT	ENST00000306503.5	+	2	1725_1727	c.1553_1555delATT	c.(1552-1557)cattat>cat	p.Y519del	SOCS5_ENST00000394861.2_In_Frame_Del_p.Y519del	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	519	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			AAAGAGTATCATTATAAACAAAA	0.433																																					p.518_519del													.	SOCS5-659	0			c.1553_1555del						.																																			SO:0001651	inframe_deletion	9655	exon2			AGTATCATTATAA	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"Suppressors of cytokine signaling", "SH2 domain containing"	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1553_1555delATT	2.37:g.46987222_46987224delATT	ENSP00000305133:p.Tyr519del	Somatic	233	0		WXS	Illumina HiSeq	Phase_I	212	10	NM_144949	0	0	0	0	0	Q53SD4|Q8IYZ4	In_Frame_Del	DEL	ENST00000306503.5	37	CCDS1830.1																																																																																			.		0.433	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2			-	46987224	ATT	-	46987222	7	5	156	1	0	1	0	1	0	0	0	0	14949	217	8	0	1555	0	SOCS5	2	46987222	In_Frame_Del	DEL	ATT	TCGA-P4-A5EA-01A-11D-A28G-10	8830361	46987222	196212151	11	14050											
ASPRV1	151516	broad.mit.edu	37	chr2	70188625	70188626	+	Frame_Shift_Del	DEL	AG	AG	-																															cgccaagaagagaaacccacAgagcagtgtcggcgcaatca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:70188625_70188626delAG	ENST00000320256.4	-	1	771_772	c.195_196delCT	c.(193-198)ctctgtfs	p.C66fs	PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000418564.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						AGAAACCCACAGAGCAGTGTCG	0.653																																					p.65_66del													.	ASPRV1-69	0			c.195_196del						.																																			SO:0001589	frameshift_variant	151516	exon1			ACCCACAGAGCAG	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"Skin ASpartic Protease"	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.195_196delCT	2.37:g.70188627_70188628delAG	ENSP00000315383:p.Cys66fs	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	163	14	NM_152792	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000320256.4	37	CCDS1897.1																																																																																			.		0.653	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792		-	70188626	AG	-	70188625	7	5	156	1	0	1	0	1	0	0	0	0	1059	188	7	0	839	0	ASPRV1	2	70188625	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	23201403	70188625	173010748	12	14051											
ALMS1	7840	broad.mit.edu	37	chr2	73675809	73675809	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctctactccccactcacatAgagagaagcctggtattttt	10	13	6	12	0	2	2	1	0	1	2	4	3	3	2	3	1	2	1	3	1	4	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:73675809A>T	ENST00000264448.6	+	8	2263	c.2152A>T	c.(2152-2154)Aga>Tga	p.R718*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.R676*|ALMS1_ENST00000377715.1_Nonsense_Mutation_p.R718*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	718	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCACTCACATAGAGAGAAGCC	0.478																																					p.R718X													.	ALMS1-142	0			c.A2152T						.						126	123	124					2																	73675809		1876	4104	5980	SO:0001587	stop_gained	7840	exon8			TCACATAGAGAGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.2152A>T	2.37:g.73675809A>T	ENSP00000264448:p.Arg718*	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	91	3	NM_015120	0	0	0	0	0	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	32	5.117870	0.94385	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	.	.	.	4.11	-2.77	0.05877	.	0.983825	0.08315	N	0.964810	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	5.0571	0.14539	0.4523:0.1607:0.387:0.0	.	.	.	.	X	676;718;718	.	ENSP00000264448:R718X	R	+	1	2	ALMS1	73529317	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.167000	0.09940	-0.488000	0.06726	0.533000	0.62120	AGA	.		0.478	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73675809	A	T	73675809	4	4	156	1	0	0	0	0	0	1	0	0	535	412	15	5	2182	5	ALMS1	2	73675809	Nonsense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	3487184	73675809	169523564	13	14052											
TTL	150465	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	113260608	113260609	+	Frame_Shift_Del	DEL	AT	AT	-																															caaaacctgccatttgaccaAtcactgcattcaaaaagagt																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:113260608_113260609delAT	ENST00000233336.6	+	5	916_917	c.725_726delAT	c.(724-726)aatfs	p.N242fs		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	242	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		CATTTGACCAATCACTGCATTC	0.376			T	ETV6	ALL																																p.242_242del		.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	.	TTL-658	0			c.725_726del						.																																			SO:0001589	frameshift_variant	150465	exon5			.		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.725_726delAT	2.37:g.113260608_113260609delAT	ENSP00000233336:p.Asn242fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	123	33	NM_153712	0	0	0	0	0	Q585T3|Q7Z302|Q8N426	Frame_Shift_Del	DEL	ENST00000233336.6	37	CCDS2096.1																																																																																			.		0.376	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		-	113260609	AT	-	113260608	7	5	156	1	0	1	0	1	0	0	0	0	16754	101	4	0	743	0	TTL	2	113260608	Frame_Shift_Del	DEL	AT	TCGA-P4-A5EA-01A-11D-A28G-10	39584799	113260608	129938765	14	14053											
PHOSPHO2	493911	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	170557975	170557975	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaatttgtagataaacagtTacaacagggagtgaattata	18	11	9	3	0	0	3	0	1	0	2	0	4	0	4	0	1	3	2	0	1	9	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:170557975T>A	ENST00000359744.3	+	4	882	c.494T>A	c.(493-495)tTa>tAa	p.L165*	KLHL23_ENST00000602521.1_Intron|KLHL23_ENST00000272797.4_Intron	NM_001008489.3|NM_001199285.1|NM_001199286.1|NM_001199288.1	NP_001008489.1|NP_001186214.1|NP_001186215.1|NP_001186217.1	Q8TCD6	PHOP2_HUMAN	phosphatase, orphan 2	165							metal ion binding (GO:0046872)|pyridoxal phosphatase activity (GO:0033883)			breast(1)|large_intestine(1)|lung(6)|skin(2)	10						GATAAACAGTTACAACAGGGA	0.343																																					p.L165X													.	PHOSPHO2-91	0			c.T494A						.						67	68	67					2																	170557975		2202	4299	6501	SO:0001587	stop_gained	493911	exon4			AACAGTTACAACA	BC022324	CCDS33319.1	2q31.1	2008-02-05			ENSG00000144362	ENSG00000144362			28316	protein-coding gene	gene with protein product						16054448	Standard	NM_001199285		Approved	MGC22679	uc021vsh.1	Q8TCD6	OTTHUMG00000153981	ENST00000359744.3:c.494T>A	2.37:g.170557975T>A	ENSP00000352782:p.Leu165*	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	53	6	NM_001199286	0	0	2	2	0	B2RC30|D3DPC7	Nonsense_Mutation	SNP	ENST00000359744.3	37	CCDS33319.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.368506	0.42003	.	.	ENSG00000144362	ENST00000359744	.	.	.	6.06	0.949	0.19566	.	0.731679	0.12670	U	0.448875	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	9.8927	0.41300	0.0:0.3207:0.0:0.6793	.	.	.	.	X	165	.	ENSP00000352782:L165X	L	+	2	0	PHOSPHO2	170266221	0.716000	0.27956	0.041000	0.18516	0.050000	0.14768	1.014000	0.29950	0.172000	0.19760	-0.250000	0.11733	TTA	.		0.343	PHOSPHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333304.1	NM_001008489		A	170557975	T	A	170557975	4	1	156	1	0	0	0	0	0	1	0	0	11883	1764	61	5	496	5	PHOSPHO2	2	170557975	Nonsense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	57297367	170557975	72641398	15	14054											
FARP2	9855	broad.mit.edu	37	chr2	242433486	242433487	+	Frame_Shift_Ins	INS	-	-	G																															ccccaagcatcgtgcaggatINSggcccccaaccctcctcagg																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:242433486_242433487insG	ENST00000264042.3	+	27	3281_3282	c.3111_3112insG	c.(3112-3114)ggcfs	p.G1038fs	STK25_ENST00000478403.1_5'Flank|STK25_ENST00000316586.4_3'UTR	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	1038					actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		TCGTGCAGGATGGCCCCCAACC	0.634																																					p.D1037fs													.	FARP2-93	0			c.3111_3112insG						.																																			SO:0001589	frameshift_variant	9855	exon27			GCAGGATGGCCCC	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.3113dupG	2.37:g.242433488_242433488dupG	ENSP00000264042:p.Gly1038fs	Somatic	415	0		WXS	Illumina HiSeq	Phase_I	398	8	NM_014808	0	0	0	0	0	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Ins	INS	ENST00000264042.3	37	CCDS33424.1																																																																																			.		0.634	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			G	242433487	-	G	242433486	7	5	156	1	0	1	1	0	0	0	0	0	5696	1461	51	0	3213	0	FARP2	2	242433486	Frame_Shift_Ins	INS	-	TCGA-P4-A5EA-01A-11D-A28G-10	71875511	242433486	765887	16	14055											
IL17RC	84818	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9959173	9959173	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttggctcagcaaagccttagCctggctcctgtcactgctgc	6	11	10	14	0	2	0	2	0	0	0	3	0	3	0	3	2	5	4	3	2	2	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:9959173C>T	ENST00000295981.3	+	1	392	c.174C>T	c.(172-174)agC>agT	p.S58S	IL17RC_ENST00000413608.1_Intron|RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000416074.2_Intron|IL17RC_ENST00000383812.4_Intron|IL17RC_ENST00000455057.1_Intron|IL17RC_ENST00000403601.3_Intron	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	58					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AAAGCCTTAGCCTGGCTCCTG	0.592																																					p.S58S													.	IL17RC-92	0			c.C174T						.						81	85	84					3																	9959173		2203	4300	6503	SO:0001819	synonymous_variant	84818	exon1			CCTTAGCCTGGCT	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"Interleukins and interleukin receptors"	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.174C>T	3.37:g.9959173C>T		Somatic	160	1		WXS	Illumina HiSeq	Phase_I	193	20	NM_153461	0	0	0	3	3	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			.		0.592	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		T	9959173	C	T	9959173	2	4	156	1	0	0	0	0	0	0	0	1	7662	738	26	2		2	IL17RC	3	9959173	Silent	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10		9959173	188063257	17	14056											
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	37365077	37365078	+	Splice_Site	DEL	AG	AG	-																															tgcatctgtttttaattaacAgagaattcttgaattggaaa																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:37365077_37365078delAG	ENST00000361924.2	+	14	2075		c.e14-1		GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Splice_Site	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4						Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TTTAATTAACAGAGAATTCTTG	0.307																																					.		.											.	GOLGA4-93	0			.						.																																			SO:0001630	splice_region_variant	2803	.			.	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"golgin 245"	602509	"golgi autoantigen, golgin subfamily a, 4"			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1702-1AG>-	3.37:g.37365079_37365080delAG		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	128	33	.	0	0	0	0	0	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Splice_Site	DEL	ENST00000361924.2	37	CCDS2666.1																																																																																			.		0.307	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	Intron	-	37365078	AG	-	37365077	8	5	156	1	0	1	0	1	0	0	1	0	6575	202	7	0	1824	0	GOLGA4	3	37365077	Splice_Site	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	27405904	37365077	160657353	18	14057											
ROBO1	6091	ucsc.edu	37	chr3	78685208	78685208	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agttgactcagggagcatcaGatttgtttgtttgttatcca	9	16	10	6	0	2	2	2	1	0	1	3	3	3	3	1	1	1	5	1	1	1	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:78685208G>A	ENST00000464233.1	-	23	3201	c.3088C>T	c.(3088-3090)Ctg>Ttg	p.L1030L	ROBO1_ENST00000467549.1_Intron|ROBO1_ENST00000495273.1_Silent_p.L985L|ROBO1_ENST00000436010.2_Silent_p.L991L	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1030					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGGAGCATCAGATTTGTTTGT	0.378																																					p.L1030L													.	ROBO1-67	0			c.C3088T						.						66	65	66					3																	78685208		1907	4115	6022	SO:0001819	synonymous_variant	6091	exon23			GCATCAGATTTGT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3088C>T	3.37:g.78685208G>A		Somatic	163	0		WXS	Illumina HiSeq		199	1	NM_002941	0	0	0	0	0	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			.		0.378	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78685208	G	A	78685208	2	1	156	1	0	0	0	0	0	0	0	1	13545	933	33	2		2	ROBO1	3	78685208	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	41320131	78685208	119337222	19	14058											
NFKBIZ	64332	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	101572345	101572345	+	Frame_Shift_Del	DEL	C	C	-																															tcccccgcttatgaaccaaaCctctttgatggtccagaatc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:101572345delC	ENST00000326172.5	+	5	1090	c.975delC	c.(973-975)aacfs	p.N325fs	NFKBIZ_ENST00000394054.2_Frame_Shift_Del_p.N225fs|NFKBIZ_ENST00000326151.5_Intron	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	325	Required for transcriptional activity. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						ATGAACCAAACCTCTTTGATG	0.468																																					p.N325fs		.											.	NFKBIZ-92	0			c.975delC						.						128	124	125					3																	101572345		2203	4300	6503	SO:0001589	frameshift_variant	64332	exon5			.	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"Ankyrin repeat domain containing"	29805	protein-coding gene	gene with protein product	"IL-1 inducible nuclear ankyrin-repeat protein"	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.975delC	3.37:g.101572345delC	ENSP00000325663:p.Asn325fs	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	91	17	NM_031419	0	0	0	0	0	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Frame_Shift_Del	DEL	ENST00000326172.5	37	CCDS2946.1																																																																																			.		0.468	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419		-	101572345	C	-	101572345	7	5	156	1	0	1	0	1	0	0	0	0	10409	506	18	0	993	0	NFKBIZ	3	101572345	Frame_Shift_Del	DEL	C	TCGA-P4-A5EA-01A-11D-A28G-10	22887137	101572345	96450085	20	14059											
CD96	10225	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	111297955	111297955	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacttaaagatagagtcaagCttggtacagactacagactc	15	10	8	8	0	1	4	1	0	0	4	2	4	1	4	0	1	4	2	0	1	7	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:111297955C>T	ENST00000283285.5	+	5	804	c.673C>T	c.(673-675)Ctt>Ttt	p.L225F	CD96_ENST00000438817.2_Missense_Mutation_p.L209F|CD96_ENST00000352690.4_Missense_Mutation_p.L209F	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	225	Ig-like V-type 2.				cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						TAGAGTCAAGCTTGGTACAGA	0.423									Opitz Trigonocephaly syndrome																												p.L225F		.											.	CD96-93	0			c.C673T						.						120	108	112					3																	111297955		2203	4300	6503	SO:0001583	missense	10225	exon5	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	GTCAAGCTTGGTA	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16892	protein-coding gene	gene with protein product		606037	"CD96 antigen"			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.673C>T	3.37:g.111297955C>T	ENSP00000283285:p.Leu225Phe	Somatic	178	0		WXS	Illumina HiSeq	Phase_I	178	14	NM_198196	0	0	12	12	0	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	37	CCDS2959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.734|5.734	0.319968|0.319968	0.10845|0.10845	.|.	.|.	ENSG00000153283|ENSG00000153283	ENST00000465428|ENST00000352690;ENST00000283285;ENST00000438817	.|T;T;T	.|0.73258	.|1.54;-0.73;1.54	5.18|5.18	1.28|1.28	0.21552|0.21552	.|Immunoglobulin subtype (1);	.|0.567715	.|0.14720	.|N	.|0.302408	T|T	0.59702|0.59702	0.2213|0.2213	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|P;P;P;P	.|0.44946	.|0.761;0.846;0.761;0.761	.|B;P;B;B	.|0.46585	.|0.322;0.521;0.443;0.322	T|T	0.50800|0.50800	-0.8785|-0.8785	5|10	.|0.51188	.|T	.|0.08	-0.8167|-0.8167	5.5178|5.5178	0.16916|0.16916	0.2453:0.5587:0.1213:0.0747|0.2453:0.5587:0.1213:0.0747	.|.	.|209;209;225;209	.|E9PEJ1;P40200-2;P40200;Q8WUE2	.|.;.;TACT_HUMAN;.	V|F	50|209;225;209	.|ENSP00000342040:L209F;ENSP00000283285:L225F;ENSP00000389801:L209F	.|ENSP00000283285:L225F	A|L	+|+	2|1	0|0	CD96|CD96	112780645|112780645	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	0.121000|0.121000	0.15667|0.15667	-0.203000|-0.203000	0.10251|0.10251	-1.886000|-1.886000	0.00541|0.00541	GCT|CTT	.		0.423	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2			T	111297955	C	T	111297955	3	4	156	1	0	0	0	0	1	0	0	0	3054	797	28	2	691	2	CD96	3	111297955	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	9725610	111297955	86724475	21	14060											
GSK3B	2932	bcgsc.ca	37	chr3	119642255	119642255	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggagcgtctgtttggctcGactatagtgtctggcaactc	7	12	13	9	2	2	0	0	0	2	0	4	2	2	1	0	3	2	3	0	3	3	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:119642255G>T	ENST00000264235.8	-	4	1424	c.442C>A	c.(442-444)Cga>Aga	p.R148R	GSK3B_ENST00000316626.5_Silent_p.R148R	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	TGTTTGGCTCGACTATAGTGT	0.358																																					p.R148R													.	GSK3B-978	0			c.C442A						.						62	59	60					3																	119642255		2203	4300	6503	SO:0001819	synonymous_variant	2932	exon4			TGGCTCGACTATA	BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.442C>A	3.37:g.119642255G>T		Somatic	53	0		WXS	Illumina HiSeq	Phase_1	51	4	NM_002093	0	0	3	3	0	D3DN89|Q9BWH3|Q9UL47	Silent	SNP	ENST00000264235.8	37	CCDS54628.1																																																																																			.		0.358	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2			T	119642255	G	T	119642255	2	4	156	1	0	0	0	0	0	0	0	1	6845	1066	37	4		4	GSK3B	3	119642255	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	8344300	119642255	78380175	22	14061											
ZIC1	7545	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	147128794	147128794	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatccgcgtgcacacgggcGagaagccctttccctgcccc	7	6	10	18	4	0	1	0	0	0	1	2	2	2	1	5	1	3	1	5	1	1	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:147128794G>T	ENST00000282928.4	+	1	1624	c.895G>T	c.(895-897)Gag>Tag	p.E299*		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	299					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						GCACACGGGCGAGAAGCCCTT	0.562																																					p.E299X		.											.	ZIC1-91	0			c.G895T						.						91	94	93					3																	147128794		2203	4300	6503	SO:0001587	stop_gained	7545	exon1			ACGGGCGAGAAGC	D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"Zinc fingers, C2H2-type"	12872	protein-coding gene	gene with protein product		600470	"Zic family member 1 (odd-paired Drosophila homolog)", "Zic family member 1 (odd-paired homolog, Drosophila)"			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.895G>T	3.37:g.147128794G>T	ENSP00000282928:p.Glu299*	Somatic	169	0		WXS	Illumina HiSeq	Phase_I	160	36	NM_003412	0	0	0	0	0	Q2M3N1	Nonsense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	G	43	9.911065	0.99294	.	.	ENSG00000152977	ENST00000282928	.	.	.	3.89	3.89	0.44902	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.2006	0.82071	0.0:0.0:1.0:0.0	.	.	.	.	X	299	.	ENSP00000282928:E299X	E	+	1	0	ZIC1	148611484	1.000000	0.71417	0.997000	0.53966	0.889000	0.51656	7.528000	0.81941	1.862000	0.54008	0.561000	0.74099	GAG	.		0.562	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128794	G	T	147128794	4	4	156	1	0	0	0	0	0	1	0	0	17710	1059	37	4	897	4	ZIC1	3	147128794	Nonsense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	27486539	147128794	50893636	23	14062											
MAEA	10296	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	1332242	1332242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggacggcagctccaagaGccctgactgccctgtgtgca	8	6	14	13	1	0	2	0	1	0	1	1	4	1	4	3	3	4	3	3	3	1	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr4:1332242G>A	ENST00000303400.4	+	8	995	c.932G>A	c.(931-933)aGc>aAc	p.S311N	MAEA_ENST00000452175.2_Missense_Mutation_p.S232N|MAEA_ENST00000510794.1_Missense_Mutation_p.S310N|MAEA_ENST00000264750.6_Missense_Mutation_p.S270N|MAEA_ENST00000512289.1_3'UTR|MAEA_ENST00000514708.1_Missense_Mutation_p.S243N|MAEA_ENST00000505177.2_Missense_Mutation_p.S349N|MAEA_ENST00000505839.1_Missense_Mutation_p.S263N	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	311					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	AGCTCCAAGAGCCCTGACTGC	0.662																																					p.S311N		.											.	MAEA-91	0			c.G932A						.						61	61	61					4																	1332242		2203	4300	6503	SO:0001583	missense	10296	exon8			CCAAGAGCCCTGA	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"GID complex subunit 9, FYV10 homolog (S. cerevisiae)"	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.932G>A	4.37:g.1332242G>A	ENSP00000302830:p.Ser311Asn	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	68	18	NM_001017405	0	0	6	11	5	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	37	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	G	7.811	0.715683	0.15306	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000264750;ENST00000382947;ENST00000539495;ENST00000452175;ENST00000514708;ENST00000510794;ENST00000505839	T;T;T;T;T;T;T	0.10763	2.84;2.84;2.84;2.84;2.84;2.84;2.84	5.41	4.44	0.53790	.	0.178095	0.64402	D	0.000005	T	0.04770	0.0129	N	0.20328	0.56	0.46260	D	0.998958	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.0	T	0.34254	-0.9836	10	0.05959	T	0.93	-33.7543	3.5266	0.07761	0.3654:0.0:0.6346:0.0	.	310;349;97;243;270;311	B4DVN3;E7ESC7;B3KRN7;D6RIB6;Q7L5Y9-3;Q7L5Y9	.;.;.;.;.;MAEA_HUMAN	N	311;349;270;243;290;232;243;310;263	ENSP00000302830:S311N;ENSP00000422215:S349N;ENSP00000264750:S270N;ENSP00000411415:S232N;ENSP00000427512:S243N;ENSP00000426807:S310N;ENSP00000424436:S263N	ENSP00000264750:S270N	S	+	2	0	MAEA	1322242	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.331000	0.79192	2.531000	0.85337	0.655000	0.94253	AGC	.		0.662	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882		A	1332242	G	A	1332242	3	1	156	1	0	0	0	0	1	0	0	0	9178	971	34	2	962	2	MAEA	4	1332242	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		1332242	189822034	24	14063											
HTT	3064	broad.mit.edu	37	chr4	3076604	3076606	+	In_Frame_Del	DEL	CAG	CAG	-																															tcgagtccctcaagtccttcCagcagcagcagcagcagcag																								rs71180116|rs374076986	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr4:3076604_3076606delCAG	ENST00000355072.5	+	1	197_199	c.52_54delCAG	c.(52-54)cagdel	p.Q38del	HTT-AS_ENST00000503893.1_RNA	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	38	Poly-Gln.				anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CAAGTCCTTCcagcagcagcagc	0.704																																					p.18_18del													.	HTT-281	0			c.52_54del						.																																			SO:0001651	inframe_deletion	3064	exon1			TCCTTCCAGCAGC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.52_54delCAG	4.37:g.3076613_3076615delCAG	ENSP00000347184:p.Gln38del	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	9	3	NM_002111	0	0	0	0	0	Q9UQB7	In_Frame_Del	DEL	ENST00000355072.5	37	CCDS43206.1																																																																																			.		0.704	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		-	3076606	CAG	-	3076604	7	5	156	1	0	1	0	1	0	0	0	0	7478	595	21	0	54	0	HTT	4	3076604	In_Frame_Del	DEL	CAG	TCGA-P4-A5EA-01A-11D-A28G-10	1744362	3076604	188077672	25	14064											
SLC30A9	10463	ucsc.edu	37	chr4	42077746	42077746	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcagaagtagattttgaTgggcgagttgttacaagatc	13	11	13	4	1	0	4	0	1	0	3	1	5	0	4	0	2	1	4	0	2	5	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr4:42077746T>C	ENST00000264451.7	+	16	1671	c.1491T>C	c.(1489-1491)gaT>gaC	p.D497D		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	497					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TAGATTTTGATGGGCGAGTTG	0.323																																					p.D497D													.	SLC30A9-91	0			c.T1491C						.						108	107	108					4																	42077746		2203	4300	6503	SO:0001819	synonymous_variant	10463	exon16			TTTTGATGGGCGA	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.1491T>C	4.37:g.42077746T>C		Somatic	280	0		WXS	Illumina HiSeq		236	1	NM_006345	0	0	7	7	0	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Silent	SNP	ENST00000264451.7	37	CCDS3465.1																																																																																			.		0.323	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			C	42077746	T	C	42077746	2	2	156	1	0	0	0	0	0	0	0	1	14594	1461	51	3		3	SLC30A9	4	42077746	Silent	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	39001142	42077746	149076530	26	14065											
TLL1	7092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	166996130	166996130	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtaatggatttgtgctacaTgacaataaacatgattgcaa	15	12	8	6	1	0	2	0	2	0	0	0	3	0	3	0	1	4	3	0	1	6	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr4:166996130T>C	ENST00000061240.2	+	17	2936	c.2289T>C	c.(2287-2289)caT>caC	p.H763H	TLL1_ENST00000507499.1_Silent_p.H786H	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	763	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TTGTGCTACATGACAATAAAC	0.403																																					p.H763H		.											.	TLL1-158	0			c.T2289C						.						296	244	262					4																	166996130		2203	4300	6503	SO:0001819	synonymous_variant	7092	exon17			GCTACATGACAAT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2289T>C	4.37:g.166996130T>C		Somatic	223	0		WXS	Illumina HiSeq	Phase_I	161	18	NM_012464	0	0	0	0	0	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																			.		0.403	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			C	166996130	T	C	166996130	2	2	156	1	0	0	0	0	0	0	0	1	15977	1461	51	3		3	TLL1	4	166996130	Silent	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	124918384	166996130	24158146	27	14066											
MAP3K1	4214	bcgsc.ca	37	chr5	56183244	56183245	+	Frame_Shift_Ins	INS	-	-	TA																															agcactggtcagagactaagINSaattgcagattttggagctg																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:56183244_56183245insTA	ENST00000399503.3	+	18	4154_4155	c.4154_4155insTA	c.(4153-4158)agaattfs	p.RI1385fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1385	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CAGAGACTAAGAATTGCAGATT	0.421																																					p.R1385fs													.	MAP3K1-956	0			c.4154_4155insTA						.																																			SO:0001589	frameshift_variant	4214	exon18			GACTAAGAATTGC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	Exception_encountered	5.37:g.56183244_56183245insTA	ENSP00000382423:p.Arg1385fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_1	116	15	NM_005921	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000399503.3	37	CCDS43318.1																																																																																			.		0.421	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		TA	56183245	-	TA	56183244	7	5	156	1	0	1	1	0	0	0	0	0	9268	942	33	0	4224	0	MAP3K1	5	56183244	Frame_Shift_Ins	INS	-	TCGA-P4-A5EA-01A-11D-A28G-10		56183244	124732016	28	14067											
FCHO2	115548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	72359736	72359736	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcctgcttccagaccaaagCttacttcaggcaaactcagt	11	9	8	13	0	2	1	2	0	0	1	3	1	3	1	3	2	4	3	3	2	3	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:72359736C>A	ENST00000430046.2	+	18	1530	c.1414C>A	c.(1414-1416)Ctt>Att	p.L472I	FCHO2_ENST00000512348.1_Missense_Mutation_p.L439I|FCHO2_ENST00000341845.6_Missense_Mutation_p.L472I	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	472	Ser-rich.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		CAGACCAAAGCTTACTTCAGG	0.403																																					p.L472I		.											.	FCHO2-23	0			c.C1414A						.						65	61	62					5																	72359736		1850	4087	5937	SO:0001583	missense	115548	exon18			CCAAAGCTTACTT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.1414C>A	5.37:g.72359736C>A	ENSP00000393776:p.Leu472Ile	Somatic	193	0		WXS	Illumina HiSeq	Phase_I	139	43	NM_138782	0	0	0	0	0	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	37	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967806	0.74131	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.39056	1.1;1.11;3.55	5.62	5.62	0.85841	.	0.164332	0.40728	N	0.001021	T	0.52933	0.1765	L	0.56769	1.78	0.41260	D	0.986778	D;D	0.67145	0.99;0.996	P;P	0.60415	0.76;0.874	T	0.43956	-0.9359	10	0.18710	T	0.47	-12.133	12.5234	0.56073	0.0:0.8806:0.0:0.1194	.	439;472	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	I	472;472;439	ENSP00000393776:L472I;ENSP00000344034:L472I;ENSP00000427296:L439I	ENSP00000344034:L472I	L	+	1	0	FCHO2	72395492	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.706000	0.47135	2.637000	0.89404	0.650000	0.86243	CTT	.		0.403	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		A	72359736	C	A	72359736	3	1	156	1	0	0	0	0	1	0	0	0	5807	797	28	4	1484	4	FCHO2	5	72359736	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	16176492	72359736	108555524	29	14068											
IQGAP2	10788	broad.mit.edu	37	chr5	75960882	75960882	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatagtaaaaagctgaacaAgaaaaaaggaggagaaatgg	23	4	11	3	0	0	3	0	1	0	2	0	5	0	4	0	3	2	2	0	3	10	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:75960882A>T	ENST00000274364.6	+	22	2858	c.2561A>T	c.(2560-2562)aAg>aTg	p.K854M	IQGAP2_ENST00000379730.3_Missense_Mutation_p.K356M|IQGAP2_ENST00000396234.3_Missense_Mutation_p.K350M|IQGAP2_ENST00000502745.1_Missense_Mutation_p.K350M	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	854					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAGCTGAACAAGAAAAAAGGA	0.328																																					p.K854M													.	IQGAP2-96	0			c.A2561T						.						87	84	85					5																	75960882		2203	4300	6503	SO:0001583	missense	10788	exon22			TGAACAAGAAAAA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.2561A>T	5.37:g.75960882A>T	ENSP00000274364:p.Lys854Met	Somatic	143	0		WXS	Illumina HiSeq	Phase_I	134	4	NM_006633	0	0	0	0	0	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.530557	0.85706	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000514001;ENST00000396234;ENST00000502745	T;T;T;T;T;T	0.05717	4.11;4.02;4.09;3.4;4.02;4.02	5.3	5.3	0.74995	.	0.197976	0.52532	D	0.000072	T	0.25494	0.0620	M	0.78344	2.41	0.58432	D	0.999997	D;D;D;D	0.76494	0.999;0.999;0.998;0.997	D;D;D;P	0.70935	0.967;0.971;0.952;0.88	T	0.01165	-1.1431	10	0.72032	D	0.01	-31.5248	14.9093	0.70743	1.0:0.0:0.0:0.0	.	356;804;350;854	F5H7S7;E7EWC2;Q13576-2;Q13576	.;.;.;IQGA2_HUMAN	M	854;356;804;407;350;350	ENSP00000274364:K854M;ENSP00000442313:K356M;ENSP00000421097:K804M;ENSP00000422661:K407M;ENSP00000379535:K350M;ENSP00000426027:K350M	ENSP00000274364:K854M	K	+	2	0	IQGAP2	75996638	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.105000	0.94246	1.993000	0.58246	0.482000	0.46254	AAG	.		0.328	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75960882	A	T	75960882	3	4	156	1	0	0	0	0	1	0	0	0	7836	72	3	5	2647	5	IQGAP2	5	75960882	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	3601146	75960882	104954378	30	14069											
RASA1	5921	hgsc.bcm.edu;bcgsc.ca	37	chr5	86564698	86564699	+	Frame_Shift_Del	DEL	CC	CC	-																															tgccccctcccccttacctgCcccctttgggggcgggcctc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:86564698_86564699delCC	ENST00000274376.6	+	1	994_995	c.430_431delCC	c.(430-432)cccfs	p.P145fs	RASA1_ENST00000506290.1_5'Flank|RASA1_ENST00000456692.2_5'Flank|RASA1_ENST00000512763.1_5'Flank	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	145					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCCTTACCTGCCCCCTTTGGGG	0.624																																					p.144_144del		.											.	RASA1-661	0			c.430_431del						.																																			SO:0001589	frameshift_variant	5921	exon1			.		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.430_431delCC	5.37:g.86564700_86564701delCC	ENSP00000274376:p.Pro145fs	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	35	12	NM_002890	0	0	0	0	0	B2R6W3|Q9UDI1	Frame_Shift_Del	DEL	ENST00000274376.6	37	CCDS34200.1																																																																																			.		0.624	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		-	86564699	CC	-	86564698	7	5	156	1	0	1	0	1	0	0	0	0	13092	739	26	0	432	0	RASA1	5	86564698	Frame_Shift_Del	DEL	CC	TCGA-P4-A5EA-01A-11D-A28G-10	10603816	86564698	94350562	31	14070											
ANKHD1-EIF4EBP3	8637	broad.mit.edu;bcgsc.ca	37	chr5	139928645	139928646	+	Frame_Shift_Del	DEL	AG	AG	-																															gagctgaaggagcaggagacAgaggaagagatacccggtaa																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:139928645_139928646delAG	ENST00000310331.2	+	2	330_331	c.258_259delAG	c.(256-261)acagagfs	p.E89fs	ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.R2612fs|ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.R2612fs|SRA1_ENST00000520427.1_5'Flank	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3	89					negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAGGAGACAGAGGAAGAGAT	0.564																																					p.2612_2612del													.	ANKHD1-EIF4EBP3-28	0			c.7834_7835del						.																																			SO:0001589	frameshift_variant	404734	exon35			GGAGACAGAGGAA	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498	ENST00000310331.2:c.258_259delAG	5.37:g.139928647_139928648delAG	ENSP00000308472:p.Glu89fs	Somatic	125	0		WXS	Illumina HiSeq	Phase_I	89	12	NM_020690	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000310331.2	37	CCDS4226.1																																																																																			.		0.564	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732		-	139928646	AG	-	139928645	7	5	156	1	0	1	0	1	0	0	0	0	629	180	7	0	7972	0	ANKHD1-EIF4EBP3	5	139928645	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	53363947	139928645	40986615	32	14071											
PCDHB5	26167	broad.mit.edu;bcgsc.ca	37	chr5	140515133	140515134	+	Frame_Shift_Del	DEL	AG	AG	-																															tattccataccagaagaaacAgaaagtggctattctgtggc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:140515133_140515134delAG	ENST00000231134.5	+	1	334_335	c.117_118delAG	c.(115-120)acagaafs	p.E40fs		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	40	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGAAGAAACAGAAAGTGGCTA	0.49																																					p.39_40del													.	PCDHB5-95	0			c.117_118del						.																																			SO:0001589	frameshift_variant	26167	exon1			AGAAACAGAAAGT	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.117_118delAG	5.37:g.140515133_140515134delAG	ENSP00000231134:p.Glu40fs	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	102	11	NM_015669	0	0	0	0	0	Q549F4|Q9UFU9	Frame_Shift_Del	DEL	ENST00000231134.5	37	CCDS4247.1																																																																																			.		0.49	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		-	140515134	AG	-	140515133	7	5	156	1	0	1	0	1	0	0	0	0	11571	175	7	0	119	0	PCDHB5	5	140515133	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	586488	140515133	40400127	33	14072											
NR3C1	2908	ucsc.edu	37	chr5	142680190	142680190	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaggttcaataacctccAacagtgacaccagggtaggg	12	8	10	11	0	2	1	2	1	0	0	3	1	3	1	3	3	2	2	3	3	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:142680190A>G	ENST00000343796.2	-	5	2600	c.1607T>C	c.(1606-1608)tTg>tCg	p.L536S	NR3C1_ENST00000504572.1_Missense_Mutation_p.L537S|NR3C1_ENST00000415690.2_Missense_Mutation_p.L536S|NR3C1_ENST00000504336.1_5'UTR|NR3C1_ENST00000503201.1_Missense_Mutation_p.L536S|NR3C1_ENST00000394466.2_Missense_Mutation_p.L537S|NR3C1_ENST00000394464.2_Missense_Mutation_p.L536S|NR3C1_ENST00000424646.2_Missense_Mutation_p.L510S|NR3C1_ENST00000231509.3_Missense_Mutation_p.L537S|NR3C1_ENST00000416954.2_Missense_Mutation_p.L139S	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	536	Interaction with CLOCK.|Interaction with CRY1.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	AATAACCTCCAACAGTGACAC	0.463																																					p.L537S													.	NR3C1-92	0			c.T1610C						.						233	213	220					5																	142680190		2203	4300	6503	SO:0001583	missense	2908	exon5			ACCTCCAACAGTG	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1607T>C	5.37:g.142680190A>G	ENSP00000343205:p.Leu536Ser	Somatic	217	0		WXS	Illumina HiSeq		183	2	NM_001024094	0	0	7	7	0	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	37	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.697339	0.88830	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;T;D;D;D;D;D;D	0.96619	-4.07;-4.07;1.06;-4.07;-4.07;-4.07;-4.07;-4.07;-4.07	5.69	5.69	0.88448	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.85682	D	0.000000	D	0.98595	0.9530	M	0.93763	3.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.99686	1.1000	10	0.72032	D	0.01	.	15.94	0.79747	1.0:0.0:0.0:0.0	.	536;536;537	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	S	536;536;536;510;537;537;537;139;536	ENSP00000377977:L536S;ENSP00000343205:L536S;ENSP00000387672:L536S;ENSP00000405282:L510S;ENSP00000422518:L537S;ENSP00000377979:L537S;ENSP00000231509:L537S;ENSP00000404218:L139S;ENSP00000427672:L536S	ENSP00000231509:L537S	L	-	2	0	NR3C1	142660383	1.000000	0.71417	0.963000	0.40424	0.919000	0.55068	6.979000	0.76154	2.156000	0.67533	0.533000	0.62120	TTG	.		0.463	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			G	142680190	A	G	142680190	3	3	156	1	0	0	0	0	1	0	0	0	10656	131	5	3	798	3	NR3C1	5	142680190	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	2165057	142680190	38235070	34	14073											
C6orf145	221749	broad.mit.edu	37	chr6	3751742	3751742	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatgttcacgagcgacgtGccctcaaacaccgccgaggc	11	5	10	15	5	2	0	2	0	0	0	2	3	2	0	3	1	4	1	3	1	2	1	rs199672547		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr6:3751742G>T	ENST00000380283.4	-	1	518	c.24C>A	c.(22-24)ggC>ggA	p.G8G	PXDC1_ENST00000477592.2_5'UTR|RP11-420L9.5_ENST00000603791.1_RNA	NM_183373.3	NP_899229.2	Q5TGL8	PXDC1_HUMAN	PX domain containing 1	8	PX.						phosphatidylinositol binding (GO:0035091)										CGAGCGACGTGCCCTCAAACA	0.726																																					p.G8G													.	.	0			c.C24A						.						14	13	13					6																	3751742		2177	4274	6451	SO:0001819	synonymous_variant	221749	exon1			CGACGTGCCCTCA	AJ420534	CCDS4486.1	6p25.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000168994	ENSG00000168994			21361	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 145"	C6orf145			Standard	NM_183373		Approved		uc003mvt.2	Q5TGL8	OTTHUMG00000014146	ENST00000380283.4:c.24C>A	6.37:g.3751742G>T		Somatic	53	1		WXS	Illumina HiSeq	Phase_I	69	5	NM_183373	0	0	5	5	0	A8K0N3|Q6PGP0|Q86XB7	Silent	SNP	ENST00000380283.4	37	CCDS4486.1																																																																																			G|0.996;A|0.004		0.726	PXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039688.1	NM_183373		T	3751742	G	T	3751742	2	4	156	1	0	0	0	0	0	0	0	1	2340	1306	46	4		4	C6orf145	6	3751742	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		3751742	167363325	35	14074											
APOM	55937	broad.mit.edu	37	chr6	31625014	31625014	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctctgcaggaaagatgggctCtgtgtgccccggaaatggat	9	9	14	9	1	2	1	0	0	2	1	2	4	2	4	2	4	2	2	2	4	2	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr6:31625014C>G	ENST00000375916.3	+	3	778	c.282C>G	c.(280-282)ctC>ctG	p.L94L	APOM_ENST00000375920.4_Silent_p.L22L|C6orf47-AS1_ENST00000422049.1_RNA|APOM_ENST00000375918.2_Silent_p.L22L	NM_019101.2	NP_061974.2	O95445	APOM_HUMAN	apolipoprotein M	94					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|response to glucose (GO:0009749)|reverse cholesterol transport (GO:0043691)	discoidal high-density lipoprotein particle (GO:0034365)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|lipid transporter activity (GO:0005319)|phospholipid binding (GO:0005543)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(1)	7						AAGATGGGCTCTGTGTGCCCC	0.507																																					p.L94L	Colon(39;129 858 13764 41453 42617)												.	APOM-90	0			c.C282G						.						117	106	110					6																	31625014		1510	2709	4219	SO:0001819	synonymous_variant	55937	exon3			TGGGCTCTGTGTG	AJ245434	CCDS4710.1, CCDS59004.1	6p21	2014-01-22			ENSG00000204444	ENSG00000204444		"Apolipoproteins", "Lipocalins"	13916	protein-coding gene	gene with protein product		606907				10531326, 11418126	Standard	NM_019101		Approved	ApoM, G3a, NG20	uc003nvl.3	O95445	OTTHUMG00000031250	ENST00000375916.3:c.282C>G	6.37:g.31625014C>G		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	102	4	NM_019101	0	0	0	0	0	B0UX98|Q5SRP4|Q9P046|Q9UMP6	Silent	SNP	ENST00000375916.3	37	CCDS4710.1																																																																																			.		0.507	APOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076527.3	NM_019101		G	31625014	C	G	31625014	2	3	156	1	0	0	0	0	0	0	0	1	812	900	32	4		4	APOM	6	31625014	Silent	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	27873272	31625014	139490053	36	14075											
RARS2	57038	ucsc.edu;bcgsc.ca	37	chr6	88299660	88299660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggcaagcaatagcgcggcGaaagccgcacgccatgtcca	11	4	12	14	5	0	0	0	0	0	0	1	1	1	0	3	2	3	3	3	2	4	1	rs201899366	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr6:88299660G>A	ENST00000369536.5	-	1	61	c.16C>T	c.(16-18)Cgc>Tgc	p.R6C	ORC3_ENST00000392844.3_5'Flank|ORC3_ENST00000546266.1_5'Flank|ORC3_ENST00000417380.2_5'Flank|ORC3_ENST00000257789.4_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	6					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.R6C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		ATAGCGCGGCGAAAGCCGCAC	0.672											OREG0031911	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	G|||	2	0.000399361	0	0.0014	5008	,	,		12638	0.001		0	False		,,,				2504	0				p.R6C													.	RARS2-92	1	Substitution - Missense(1)	breast(1)	c.C16T						.						26	32	30					6																	88299660		2202	4300	6502	SO:0001583	missense	57038	exon1			CGCGGCGAAAGCC	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	21406	protein-coding gene	gene with protein product	"arginine tRNA ligase 2, mitochondrial (putative)"	611524	"arginyl-tRNA synthetase-like"	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.16C>T	6.37:g.88299660G>A	ENSP00000358549:p.Arg6Cys	Somatic	83	11	1258	WXS	Illumina HiSeq		81	34	NM_020320	0	0	3	3	0	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	17.34	3.364729	0.61513	.	.	ENSG00000146282	ENST00000369536	T	0.73897	-0.79	5.11	5.11	0.69529	Arginyl tRNA synthetase, class Ia, N-terminal (2);	0.101495	0.64402	D	0.000003	T	0.70753	0.3260	L	0.55481	1.735	0.80722	D	1	D	0.69078	0.997	P	0.50231	0.635	T	0.75277	-0.3374	10	0.87932	D	0	.	14.2251	0.65853	0.0:0.0:1.0:0.0	.	6	Q5T160	SYRM_HUMAN	C	6	ENSP00000358549:R6C	ENSP00000358549:R6C	R	-	1	0	RARS2	88356379	1.000000	0.71417	0.978000	0.43139	0.031000	0.12232	2.529000	0.45632	2.826000	0.97356	0.655000	0.94253	CGC	G|0.999;A|0.000		0.672	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		A	88299660	G	A	88299660	3	1	156	1	0	0	0	0	1	0	0	0	13091	1058	37	1	1800	1	RARS2	6	88299660	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	56674646	88299660	82815407	37	14076											
MTRF1L	54516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	153315714	153315714	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acgcggccttgcttttctgtCtttggcactctttgtactct	3	18	8	12	2	4	0	0	0	4	0	4	0	4	0	1	2	2	3	1	2	1	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr6:153315714C>G	ENST00000367233.5	-	4	620	c.621G>C	c.(619-621)aaG>aaC	p.K207N	MTRF1L_ENST00000367230.1_Missense_Mutation_p.K171N|MTRF1L_ENST00000367231.5_Missense_Mutation_p.K207N|MTRF1L_ENST00000464135.1_5'UTR	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	207						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		GCTTTTCTGTCTTTGGCACTC	0.502																																					p.K207N		.											.	MTRF1L-90	0			c.G621C						.						164	143	150					6																	153315714		2203	4300	6503	SO:0001583	missense	54516	exon4			TTCTGTCTTTGGC	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.621G>C	6.37:g.153315714C>G	ENSP00000356202:p.Lys207Asn	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	112	14	NM_019041	0	0	1	1	0	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	37	CCDS5243.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560810	0.65538	.	.	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771;ENST00000448966	T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76	4.97	3.11	0.35812	.	0.096199	0.64402	D	0.000001	T	0.18718	0.0449	M	0.78801	2.425	0.40959	D	0.984603	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.76071	0.964;0.973;0.987;0.974	T	0.01102	-1.1451	10	0.56958	D	0.05	-12.0679	8.928	0.35652	0.0:0.7454:0.0:0.2546	.	171;207;171;207	B4DMX1;Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;.;RF1ML_HUMAN	N	207;207;171;58;71	ENSP00000356202:K207N;ENSP00000356200:K207N;ENSP00000356199:K171N;ENSP00000414383:K58N;ENSP00000415113:K71N	ENSP00000356199:K171N	K	-	3	2	MTRF1L	153357407	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	1.344000	0.33941	0.558000	0.29135	0.585000	0.79938	AAG	.		0.502	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		G	153315714	C	G	153315714	3	3	156	1	0	0	0	0	1	0	0	0	9985	912	32	4	537	4	MTRF1L	6	153315714	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	65016054	153315714	17799353	38	14077											
CARD11	84433	broad.mit.edu	37	chr7	2956956	2956956	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaaaaggaagcttgctcGcgagagacgggggctgaccc	11	4	15	11	3	0	2	0	1	0	1	1	5	0	3	2	3	2	3	2	3	3	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr7:2956956G>A	ENST00000396946.4	-	20	3074	c.2671C>T	c.(2671-2673)Cga>Tga	p.R891*		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	891					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		AAGCTTGCTCGCGAGAGACGG	0.557			Mis		DLBCL																																p.R891X				Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11-870	0			c.C2671T						.						39	52	47					7																	2956956		2203	4300	6503	SO:0001587	stop_gained	84433	exon20			TTGCTCGCGAGAG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"card-maguk protein 1", "bcl10-interacting maguk protein 3"	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2671C>T	7.37:g.2956956G>A	ENSP00000380150:p.Arg891*	Somatic	30	1		WXS	Illumina HiSeq	Phase_I	35	5	NM_032415	0	0	8	8	0	A4D1Z7|Q2NKN7|Q548H3	Nonsense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	37	6.455396	0.97581	.	.	ENSG00000198286	ENST00000396946	.	.	.	4.99	-2.13	0.07144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2197	16.1139	0.81289	0.0:0.0:0.3409:0.6591	.	.	.	.	X	891	.	ENSP00000380150:R891X	R	-	1	2	CARD11	2923482	0.094000	0.21725	0.016000	0.15963	0.402000	0.30811	0.308000	0.19314	-0.204000	0.10235	-0.314000	0.08810	CGA	.		0.557	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2956956	G	A	2956956	4	1	156	1	0	0	0	0	0	1	0	0	2651	1095	38	1	817	1	CARD11	7	2956956	Nonsense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		2956956	156181707	39	14078											
BZW2	28969	broad.mit.edu	37	chr7	16721024	16721024	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgaaaccatccgaaactatGctcaggtagagcctgtttga	13	10	9	9	1	1	3	1	2	0	1	2	4	2	3	3	1	4	3	3	1	4	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr7:16721024G>T	ENST00000433922.2	+	4	512	c.334G>T	c.(334-336)Gct>Tct	p.A112S	BZW2_ENST00000452975.2_Missense_Mutation_p.A112S|BZW2_ENST00000258761.3_Missense_Mutation_p.A112S|BZW2_ENST00000432311.1_3'UTR|BZW2_ENST00000405202.1_Missense_Mutation_p.A36S	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	112					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	membrane (GO:0016020)				cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		CCGAAACTATGCTCAGGTAGA	0.438																																					p.A112S													.	BZW2-92	0			c.G334T						.						109	96	100					7																	16721024		2203	4300	6503	SO:0001583	missense	28969	exon4			AACTATGCTCAGG	AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261			18808	protein-coding gene	gene with protein product						11042152	Standard	NM_001159767		Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.334G>T	7.37:g.16721024G>T	ENSP00000397249:p.Ala112Ser	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	54	5	NM_014038	0	0	0	0	0	A4D123|Q3B779|Q96JW5|Q9H3F7	Missense_Mutation	SNP	ENST00000433922.2	37	CCDS5362.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.565035	0.86439	.	.	ENSG00000136261	ENST00000415365;ENST00000258761;ENST00000433922;ENST00000452975;ENST00000405202;ENST00000446596;ENST00000438834;ENST00000430000	T;T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.59528	0.2200	L	0.54908	1.71	0.80722	D	1	D;D;D	0.89917	0.993;1.0;0.993	D;D;D	0.83275	0.968;0.996;0.968	T	0.47114	-0.9142	10	0.10111	T	0.7	-6.5489	20.2527	0.98410	0.0:0.0:1.0:0.0	.	112;112;112	E7ETZ4;Q96JW5;Q9Y6E2	.;.;BZW2_HUMAN	S	112;112;112;112;36;112;112;112	ENSP00000403481:A112S;ENSP00000258761:A112S;ENSP00000397249:A112S;ENSP00000411715:A112S;ENSP00000385577:A36S;ENSP00000412750:A112S;ENSP00000415924:A112S;ENSP00000416531:A112S	ENSP00000258761:A112S	A	+	1	0	BZW2	16687549	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.810000	0.99221	2.788000	0.95919	0.557000	0.71058	GCT	.		0.438	BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2	NM_014038		T	16721024	G	T	16721024	3	4	156	1	0	0	0	0	1	0	0	0	1582	1319	46	4	344	4	BZW2	7	16721024	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	13764068	16721024	142417639	40	14079											
AUTS2	26053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	70231266	70231266	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccagcacaccttcacgccGttcccccacgccatcccacc	8	5	4	24	3	1	0	1	0	0	0	3	0	3	0	8	0	1	2	8	0	0	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr7:70231266G>A	ENST00000342771.4	+	9	1956	c.1635G>A	c.(1633-1635)ccG>ccA	p.P545P	AUTS2_ENST00000406775.2_Silent_p.P545P	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	545	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		cCTTCACGCCGTTCCCCCACG	0.642																																					p.P545P		.											.	AUTS2-92	0			c.G1635A						.						278	255	263					7																	70231266		2203	4300	6503	SO:0001819	synonymous_variant	26053	exon9			CACGCCGTTCCCC	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1635G>A	7.37:g.70231266G>A		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	90	31	NM_001127231	0	0	0	0	0	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.455200	0.26161	.	.	ENSG00000158321	ENST00000443672	.	.	.	5.56	-2.87	0.05700	.	.	.	.	.	T	0.50343	0.1610	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45131	-0.9282	4	.	.	.	-11.6373	6.7468	0.23466	0.1273:0.5083:0.2255:0.1389	.	.	.	.	H	87	.	.	R	+	2	0	AUTS2	69869202	0.862000	0.29867	0.976000	0.42696	0.997000	0.91878	-0.056000	0.11787	-0.475000	0.06852	0.561000	0.74099	CGT	.		0.642	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	70231266	G	A	70231266	2	1	156	1	0	0	0	0	0	0	0	1	1226	1132	40	1		1	AUTS2	7	70231266	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	53510242	70231266	88907397	41	14080											
FASTK	10922	bcgsc.ca	37	chr7	150775936	150775938	+	In_Frame_Del	DEL	GCT	GCT	-																															ccccctccagcacctgccagGctgctgatcagatgctgccg																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	GCT	GCT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr7:150775936_150775938delGCT	ENST00000297532.6	-	3	753_755	c.676_678delAGC	c.(676-678)agcdel	p.S226del	FASTK_ENST00000482571.1_Intron|FASTK_ENST00000489884.1_Intron|FASTK_ENST00000540185.1_Intron|FASTK_ENST00000353841.2_In_Frame_Del_p.S85del|RP11-148K1.12_ENST00000485974.1_RNA	NM_006712.4	NP_006703.1	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase	226					apoptotic signaling pathway (GO:0097190)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|Fas-activated serine/threonine kinase activity (GO:0033867)|protein serine/threonine kinase activity (GO:0004674)			lung(4)|stomach(2)	6			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		CACCTGCCAGGCTGCTGATCAGA	0.616																																					p.226_226del													.	FASTK-359	0			c.676_678del						.																																			SO:0001651	inframe_deletion	10922	exon3			TGCCAGGCTGCTG		CCDS5918.1, CCDS5919.1, CCDS59088.1	7q35	2006-07-06			ENSG00000164896	ENSG00000164896			24676	protein-coding gene	gene with protein product		606965				7544399, 15572676	Standard	NM_006712		Approved	FAST	uc003wix.2	Q14296	OTTHUMG00000158694	ENST00000297532.6:c.676_678delAGC	7.37:g.150775939_150775941delGCT	ENSP00000297532:p.Ser226del	Somatic	70	0		WXS	Illumina HiSeq	Phase_1	59	6	NM_006712	0	0	0	0	0	A8K867|F8VTW9|Q59EM8|Q8IVA0	In_Frame_Del	DEL	ENST00000297532.6	37	CCDS5918.1																																																																																			.		0.616	FASTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351832.2	NM_006712		-	150775938	GCT	-	150775936	7	5	156	1	0	1	0	1	0	0	0	0	5703	1194	42	0	1003	0	FASTK	7	150775936	In_Frame_Del	DEL	GCT	TCGA-P4-A5EA-01A-11D-A28G-10	80544670	150775936	8362727	42	14081											
MLL3	58508	broad.mit.edu	37	chr7	151945198	151945198	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catctgccttgcttatgtctGctgatgatgaaaatgatgac	10	14	9	8	0	2	5	0	5	2	0	2	5	2	5	1	0	3	2	1	0	3	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr7:151945198G>C	ENST00000262189.6	-	14	2539	c.2321C>G	c.(2320-2322)gCa>gGa	p.A774G	KMT2C_ENST00000355193.2_Missense_Mutation_p.A774G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	774					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GCTTATGTCTGCTGATGATGA	0.423																																					p.A774G													.	MLL3-1398	0			c.C2321G						.						184	163	170					7																	151945198		2203	4300	6503	SO:0001583	missense	58508	exon14			ATGTCTGCTGATG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2321C>G	7.37:g.151945198G>C	ENSP00000262189:p.Ala774Gly	Somatic	771	0		WXS	Illumina HiSeq	Phase_I	627	13	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	1.692	-0.503696	0.04261	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83591	-1.74;-1.74	5.25	-0.131	0.13494	.	0.953037	0.08585	N	0.923914	T	0.66287	0.2774	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48375	-0.9041	10	0.22109	T	0.4	.	5.4057	0.16320	0.3328:0.4327:0.2345:0.0	.	774	Q8NEZ4	MLL3_HUMAN	G	774	ENSP00000262189:A774G;ENSP00000347325:A774G	ENSP00000262189:A774G	A	-	2	0	MLL3	151576131	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	0.369000	0.20416	-0.035000	0.13691	-0.145000	0.13849	GCA	.		0.423	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151945198	G	C	151945198	3	2	156	1	0	0	0	0	1	0	0	0	9647	1319	46	4	12598	4	MLL3	7	151945198	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	1169262	151945198	7193465	43	14082											
WDR67	93594	broad.mit.edu;ucsc.edu	37	chr8	124094982	124094982	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacaagcttgcacagctCtggcctttaatcttcgtagg	9	11	9	12	1	2	0	0	0	2	0	3	0	2	0	1	2	4	5	1	2	3	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr8:124094982C>A	ENST00000287380.1	+	3	355	c.265C>A	c.(265-267)Ctg>Atg	p.L89M	TBC1D31_ENST00000521676.1_Intron|TBC1D31_ENST00000309336.3_Missense_Mutation_p.L89M|TBC1D31_ENST00000378080.2_Intron|TBC1D31_ENST00000327098.5_Missense_Mutation_p.L89M|TBC1D31_ENST00000522420.1_Intron	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	89						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										TTGCACAGCTCTGGCCTTTAA	0.343																																					p.L89M													.	WDR67-226	0			c.C265A						.						111	103	106					8																	124094982		2203	4300	6503	SO:0001583	missense	93594	exon3			ACAGCTCTGGCCT	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"WD repeat domain containing"	30888	protein-coding gene	gene with protein product			"WD repeat domain 67"	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.265C>A	8.37:g.124094982C>A	ENSP00000287380:p.Leu89Met	Somatic	28	0		WXS	Illumina HiSeq	Phase_I	32	4	NM_001145088	0	0	0	0	0	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Missense_Mutation	SNP	ENST00000287380.1	37	CCDS6338.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669778	0.67814	.	.	ENSG00000156787	ENST00000287380;ENST00000309336;ENST00000327098;ENST00000522276	T;T;T;T	0.74421	-0.51;1.29;1.29;-0.84	5.7	5.7	0.88788	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.081913	0.51477	D	0.000088	T	0.80793	0.4691	M	0.70595	2.14	0.80722	D	1	D;D;D	0.67145	0.992;0.996;0.986	D;D;P	0.64410	0.919;0.925;0.796	T	0.79650	-0.1715	10	0.35671	T	0.21	-11.8875	5.9847	0.19428	0.1856:0.7013:0.0:0.1131	.	89;89;89	B7ZL19;Q96DN5;Q3KRB0	.;WDR67_HUMAN;.	M	89;89;89;79	ENSP00000287380:L89M;ENSP00000308358:L89M;ENSP00000312701:L89M;ENSP00000428891:L79M	ENSP00000287380:L89M	L	+	1	2	WDR67	124164163	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.479000	0.45197	2.689000	0.91719	0.591000	0.81541	CTG	.		0.343	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647		A	124094982	C	A	124094982	3	1	156	1	0	0	0	0	1	0	0	0	17351	912	32	4	275	4	WDR67	8	124094982	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10		124094982	22269040	44	14083											
OPLAH	26873	broad.mit.edu	37	chr8	145111554	145111554	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccccgaagtcccccgcaCggggcgagcgggctgtggct	4	5	16	16	5	0	0	0	0	0	0	1	2	1	0	4	4	2	3	4	4	1	0	rs200399200		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr8:145111554C>T	ENST00000426825.1	-	13	1892	c.1811G>A	c.(1810-1812)cGt>cAt	p.R604H	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	604					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)			GTCCCCCGCACGGGGCGAGCG	0.667																																					p.R604H													.	OPLAH-68	0			c.G1811A						.	C	HIS/ARG	0,4232		0,0,2116	20	27	24		1811	0.8	0	8		24	1,8449		0,1,4224	no	missense	OPLAH	NM_017570.3	29	0,1,6340	TT,TC,CC		0.0118,0.0,0.0079	possibly-damaging	604/1289	145111554	1,12681	2116	4225	6341	SO:0001583	missense	26873	exon13			CCCGCACGGGGCG	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.1811G>A	8.37:g.145111554C>T	ENSP00000475943:p.Arg604His	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	108	3	NM_017570	0	0	0	0	0	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	C	5.999	0.368217	0.11352	0.0	1.18E-4	ENSG00000178814	ENST00000426825	.	.	.	4.69	0.788	0.18601	.	0.196928	0.44097	D	0.000484	T	0.22589	0.0545	.	.	.	0.40220	D	0.977721	P	0.43701	0.815	B	0.38712	0.28	T	0.19289	-1.0310	7	0.45353	T	0.12	.	4.0517	0.09798	0.1541:0.4819:0.0:0.364	.	604	O14841	OPLA_HUMAN	H	604	.	ENSP00000412071:R604H	R	-	2	0	OPLAH	145183542	0.007000	0.16637	0.012000	0.15200	0.255000	0.26057	0.188000	0.17018	0.093000	0.17368	0.514000	0.50259	CGT	.		0.667	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		T	145111554	C	T	145111554	3	4	156	1	0	0	0	0	1	0	0	0	10902	536	19	1	2117	1	OPLAH	8	145111554	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	21016572	145111554	1252468	45	14084											
ZNF7	7553	broad.mit.edu	37	chr8	146066868	146066869	+	Frame_Shift_Del	DEL	TC	TC	-																															atcctggctttggagacgttTctgattctgaggtctggtta																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr8:146066868_146066869delTC	ENST00000528372.1	+	5	616_617	c.376_377delTC	c.(376-378)tctfs	p.S126fs	ZNF7_ENST00000532393.1_3'UTR|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000544249.1_Frame_Shift_Del_p.S30fs|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000446747.2_Frame_Shift_Del_p.S137fs|ZNF7_ENST00000529819.1_Intron|ZNF7_ENST00000325241.6_Frame_Shift_Del_p.S126fs			P17097	ZNF7_HUMAN	zinc finger protein 7	126					multicellular organismal development (GO:0007275)|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)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TGGAGACGTTTCTGATTCTGAG	0.485																																					p.126_126del													.	ZNF7-94	0			c.376_377del						.																																			SO:0001589	frameshift_variant	7553	exon5			GACGTTTCTGATT	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.376_377delTC	8.37:g.146066868_146066869delTC	ENSP00000432724:p.Ser126fs	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	87	10	NM_003416	0	0	0	0	0	B4DT08|D3DWN6|P17015|Q8N8Y4	Frame_Shift_Del	DEL	ENST00000528372.1	37	CCDS6435.1																																																																																			.		0.485	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		-	146066869	TC	-	146066868	7	5	156	1	0	1	0	1	0	0	0	0	18134	1783	62	0	390	0	ZNF7	8	146066868	Frame_Shift_Del	DEL	TC	TCGA-P4-A5EA-01A-11D-A28G-10	955314	146066868	297154	46	14085											
COL27A1	85301	broad.mit.edu	37	chr9	117052570	117052570	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcctcgagggcatcgctggaCcagatgggcttcctggcagg	6	7	16	12	2	0	1	0	0	0	1	3	3	1	2	3	5	0	4	3	5	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr9:117052570C>A	ENST00000356083.3	+	47	4718	c.4327C>A	c.(4327-4329)Cca>Aca	p.P1443T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1443	Collagen-like 14.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CATCGCTGGACCAGATGGGCT	0.637																																					p.P1443T													.	COL27A1-94	0			c.C4327A						.						30	24	26					9																	117052570		2193	4288	6481	SO:0001583	missense	85301	exon47			GCTGGACCAGATG	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"Collagens"	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4327C>A	9.37:g.117052570C>A	ENSP00000348385:p.Pro1443Thr	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	155	5	NM_032888	0	0	10	10	0	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	C	9.195	1.027065	0.19512	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.93133	-3.17	5.47	2.6	0.31112	.	.	.	.	.	D	0.86932	0.6052	L	0.31157	0.91	0.23425	N	0.99771	B	0.24186	0.099	B	0.22601	0.04	T	0.70070	-0.4973	9	0.15499	T	0.54	.	9.8448	0.41021	0.0:0.7351:0.1199:0.145	.	1443	Q8IZC6	CORA1_HUMAN	T	1443	ENSP00000348385:P1443T	ENSP00000348385:P1443T	P	+	1	0	COL27A1	116092391	0.676000	0.27567	0.993000	0.49108	0.959000	0.62525	0.352000	0.20113	0.020000	0.15106	-1.961000	0.00478	CCA	.		0.637	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117052570	C	A	117052570	3	1	156	1	0	0	0	0	1	0	0	0	3691	507	18	4	4513	4	COL27A1	9	117052570	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10		117052570	24160861	47	14086											
TRIM32	22954	broad.mit.edu;bcgsc.ca	37	chr9	119461631	119461631	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagggcttaggcctcaatcTggagaatcggcagaatgagc	11	7	13	10	1	2	3	1	1	1	2	3	4	2	3	2	4	1	2	2	4	4	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr9:119461631T>A	ENST00000450136.1	+	2	1771	c.1610T>A	c.(1609-1611)cTg>cAg	p.L537Q	ASTN2_ENST00000313400.4_Intron|TRIM32_ENST00000373983.2_Missense_Mutation_p.L537Q|ASTN2_ENST00000373996.3_Intron|ASTN2_ENST00000361209.2_Intron|ASTN2_ENST00000361477.3_Intron	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	537					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						GGCCTCAATCTGGAGAATCGG	0.557																																					p.L537Q	Esophageal Squamous(92;212 1916 19711 26951)												.	TRIM32-650	0			c.T1610A						.						71	66	67					9																	119461631		2203	4300	6503	SO:0001583	missense	22954	exon2			TCAATCTGGAGAA	U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16380	protein-coding gene	gene with protein product		602290	"limb girdle muscular dystrophy 2H (autosomal recessive)", "tripartite motif-containing 32"	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.1610T>A	9.37:g.119461631T>A	ENSP00000408292:p.Leu537Gln	Somatic	168	1		WXS	Illumina HiSeq	Phase_I	150	12	NM_012210	0	0	0	1	1	Q9NQP8	Missense_Mutation	SNP	ENST00000450136.1	37	CCDS6817.1	.	.	.	.	.	.	.	.	.	.	T	15.49	2.849798	0.51270	.	.	ENSG00000119401	ENST00000450136;ENST00000373983	D;D	0.83419	-1.72;-1.72	5.56	5.56	0.83823	Six-bladed beta-propeller, TolB-like (1);	0.184376	0.35936	N	0.002883	T	0.71762	0.3378	N	0.08118	0	0.46823	D	0.999217	D	0.56968	0.978	P	0.45881	0.496	T	0.73341	-0.4013	9	.	.	.	-4.4367	15.6974	0.77512	0.0:0.0:0.0:1.0	.	537	Q13049	TRI32_HUMAN	Q	537	ENSP00000408292:L537Q;ENSP00000363095:L537Q	.	L	+	2	0	TRIM32	118501452	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.665000	0.83852	2.098000	0.63641	0.528000	0.53228	CTG	.		0.557	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210		A	119461631	T	A	119461631	3	1	156	1	0	0	0	0	1	0	0	0	16539	1580	55	5	1612	5	TRIM32	9	119461631	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	2409061	119461631	21751800	48	14087											
LMX1B	4010	broad.mit.edu	37	chr9	129376780	129376780	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggtgcttccctcgcgggCagacggactgcgccaagatg	8	6	15	12	4	0	3	0	0	0	3	2	4	1	4	2	3	2	2	2	3	1	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr9:129376780C>A	ENST00000373474.4	+	1	59	c.52C>A	c.(52-54)Cag>Aag	p.Q18K	LMX1B_ENST00000425646.2_5'UTR|RP11-123K19.1_ENST00000432418.1_RNA|RP11-123K19.1_ENST00000451449.2_RNA|LMX1B_ENST00000526117.1_Missense_Mutation_p.Q18K|LMX1B_ENST00000355497.5_Missense_Mutation_p.Q18K|RP11-123K19.1_ENST00000425370.1_RNA|LMX1B_ENST00000561065.1_5'UTR			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	18					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						CCCTCGCGGGCAGACGGACTG	0.721									Nail-Patella Syndrome																												p.Q18K	Pancreas(110;1796 2278 18357 20466)												.	LMX1B-90	0			c.C52A						.						19	17	18					9																	129376780		2195	4295	6490	SO:0001583	missense	4010	exon1	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	CGCGGGCAGACGG	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"Homeoboxes / LIM class"	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.52C>A	9.37:g.129376780C>A	ENSP00000362573:p.Gln18Lys	Somatic	62	1		WXS	Illumina HiSeq	Phase_I	125	6	NM_001174146	0	0	0	0	0	F8W7W6|O75463|Q5JU95|Q6ISC9	Missense_Mutation	SNP	ENST00000373474.4	37	CCDS55342.1	.	.	.	.	.	.	.	.	.	.	c	12.88	2.070080	0.36566	.	.	ENSG00000136944	ENST00000526117;ENST00000373474;ENST00000355497	D;D;D	0.85258	-1.8;-1.79;-1.96	3.04	3.04	0.35103	.	0.120313	0.35262	U	0.003325	T	0.69771	0.3148	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.64859	-0.6308	8	0.07030	T	0.85	.	12.8315	0.57748	0.0:1.0:0.0:0.0	.	.	.	.	K	18	ENSP00000436930:Q18K;ENSP00000362573:Q18K;ENSP00000347684:Q18K	ENSP00000347684:Q18K	Q	+	1	0	LMX1B	128416601	0.998000	0.40836	1.000000	0.80357	0.948000	0.59901	1.351000	0.34022	1.569000	0.49696	0.388000	0.25769	CAG	.		0.721	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2			A	129376780	C	A	129376780	3	1	156	1	0	0	0	0	1	0	0	0	8885	711	25	4	54	4	LMX1B	9	129376780	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	9915149	129376780	11836651	49	14088											
LAMC3	10319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	133914285	133914285	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccgctccgaggaatgcacGtttgatcgggagctcttccg	6	9	14	12	5	1	1	0	1	1	0	4	4	3	3	3	3	2	4	3	3	1	2	rs201170354	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr9:133914285G>A	ENST00000361069.4	+	5	1144	c.1011G>A	c.(1009-1011)acG>acA	p.T337T	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	337	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		AGGAATGCACGTTTGATCGGG	0.617													g|||	3	0.000599042	0.0015	0.0014	5008	,	,		19786	0		0	False		,,,				2504	0				p.T337T		.											.	LAMC3-93	0			c.G1011A						.						77	80	79					9																	133914285		2203	4300	6503	SO:0001819	synonymous_variant	10319	exon5			ATGCACGTTTGAT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1011G>A	9.37:g.133914285G>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	58	8	NM_006059	0	0	0	0	0	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			G|0.999;A|0.000		0.617	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133914285	G	A	133914285	2	1	156	1	0	0	0	0	0	0	0	1	8637	1132	40	1		1	LAMC3	9	133914285	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	4537505	133914285	7299146	50	14089											
PFKP	5214	hgsc.bcm.edu	37	chr10	3150955	3150955	+	Frame_Shift_Del	DEL	A	A	-																															ctcgggcacgtgcagagaggAgggaccccttcggcattcga																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr10:3150955delA	ENST00000381125.4	+	9	1009	c.933delA	c.(931-933)ggafs	p.G312fs	PFKP_ENST00000381075.2_Frame_Shift_Del_p.G304fs	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	312	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TGCAGAGAGGAGGGACCCCTT	0.562																																					p.G311fs		.											.	PFKP-253	0			c.933delA						.						148	132	138					10																	3150955		2203	4300	6503	SO:0001589	frameshift_variant	5214	exon9			.	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"Phosphofructokinase, platelet type"	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.933delA	10.37:g.3150955delA	ENSP00000370517:p.Gly312fs	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	156	35	NM_002627	0	0	0	0	0	B3KS15|Q5VSR7|Q5VSR8	Frame_Shift_Del	DEL	ENST00000381125.4	37	CCDS7059.1																																																																																			.		0.562	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		-	3150955	A	-	3150955	7	5	156	1	0	1	0	1	0	0	0	0	11792	291	11	0	967	0	PFKP	10	3150955	Frame_Shift_Del	DEL	A	TCGA-P4-A5EA-01A-11D-A28G-10		3150955	132383792	51	14090											
PITRM1	10531	broad.mit.edu;bcgsc.ca	37	chr10	3207428	3207429	+	Splice_Site	DEL	AC	AC	-																															ataaaaaaggaagaaaacttAcaaacgctcccttcatctca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr10:3207428_3207429delAC	ENST00000224949.4	-	6	665		c.e6+1		PITRM1_ENST00000380989.2_Splice_Site|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000451104.2_Splice_Site|PITRM1-AS1_ENST00000598280.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1						positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						AAGAAAACTTACAAACGCTCCC	0.411																																					.													.	PITRM1-91	0			.						.																																			SO:0001630	splice_region_variant	10531	.			AAACTTACAAACG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.630+1GT>-	10.37:g.3207428_3207429delAC		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	94	9	.	0	0	0	0	0	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Splice_Site	DEL	ENST00000224949.4	37	CCDS59208.1																																																																																			.		0.411	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		Intron	-	3207429	AC	-	3207428	8	5	156	1	0	1	0	1	0	0	1	0	11979	405	14	0	2569	0	PITRM1	10	3207428	Splice_Site	DEL	AC	TCGA-P4-A5EA-01A-11D-A28G-10	56473	3207428	132327319	52	14091											
CAMK1D	57118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	12856228	12856228	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcctttttatgatgaaaatGactccaagctctttgagcag	11	14	7	9	0	1	4	0	4	1	0	3	4	3	4	2	0	2	2	2	0	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr10:12856228G>A	ENST00000378847.3	+	7	1013	c.676G>A	c.(676-678)Gac>Aac	p.D226N	CAMK1D_ENST00000378845.1_Missense_Mutation_p.D226N	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		TGATGAAAATGACTCCAAGCT	0.483																																					p.D226N		.											.	CAMK1D-334	0			c.G676A						.						101	90	94					10																	12856228		2203	4300	6503	SO:0001583	missense	57118	exon7			GAAAATGACTCCA	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.676G>A	10.37:g.12856228G>A	ENSP00000368124:p.Asp226Asn	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	99	10	NM_153498	0	0	0	0	0	B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	37	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064215	0.93898	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.65364	-0.15;-0.15	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70011	0.3175	L	0.35723	1.085	0.80722	D	1	D;B	0.54047	0.964;0.267	D;B	0.63703	0.917;0.344	T	0.68907	-0.5285	10	0.42905	T	0.14	-37.1453	16.7965	0.85603	0.0:0.0:1.0:0.0	.	226;226	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	N	226	ENSP00000368124:D226N;ENSP00000368122:D226N	ENSP00000368122:D226N	D	+	1	0	CAMK1D	12896234	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.517000	0.98020	2.556000	0.86216	0.555000	0.69702	GAC	.		0.483	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		A	12856228	G	A	12856228	3	1	156	1	0	0	0	0	1	0	0	0	2603	1290	45	2	702	2	CAMK1D	10	12856228	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	9648800	12856228	122678519	53	14092											
ZNF33B	7582	ucsc.edu	37	chr10	43088083	43088083	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attcataaggtttttctcctAtgtgtgttctctgatgtaca	8	19	7	7	0	3	1	1	1	2	0	5	1	3	1	1	1	1	3	1	1	3	7			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr10:43088083A>G	ENST00000359467.3	-	5	2429	c.2315T>C	c.(2314-2316)aTa>aCa	p.I772T	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	772					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)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						TTTTTCTCCTATGTGTGTTCT	0.413																																					p.I772T	Melanoma(137;1247 1767 16772 25727 43810)												.	ZNF33B-90	0			c.T2315C						.						122	117	119					10																	43088083		2203	4300	6503	SO:0001583	missense	7582	exon5			TCTCCTATGTGTG	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"Zinc fingers, C2H2-type", "-"	13097	protein-coding gene	gene with protein product		194522	"zinc finger protein 33b (KOX 31)", "zinc finger protein 11B"	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.2315T>C	10.37:g.43088083A>G	ENSP00000352444:p.Ile772Thr	Somatic	149	0		WXS	Illumina HiSeq		120	1	NM_006955	0	0	4	4	0	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.955903	0.00470	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.11712	2.75	2.5	-0.594	0.11664	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.829025	0.09911	N	0.739814	T	0.02156	0.0067	N	0.00496	-1.435	0.24656	N	0.993495	B	0.02656	0.0	B	0.01281	0.0	T	0.44711	-0.9310	10	0.02654	T	1	.	6.666	0.23041	0.3882:0.0:0.6118:0.0	.	772	Q06732	ZN33B_HUMAN	T	772;738	ENSP00000352444:I772T	ENSP00000352444:I772T	I	-	2	0	ZNF33B	42408089	0.175000	0.23083	0.845000	0.33349	0.880000	0.50808	0.511000	0.22739	-0.125000	0.11703	-0.537000	0.04273	ATA	.		0.413	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		G	43088083	A	G	43088083	3	3	156	1	0	0	0	0	1	0	0	0	17887	449	16	3	25	3	ZNF33B	10	43088083	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	30231855	43088083	92446664	54	14093											
IKZF5	64376	broad.mit.edu;bcgsc.ca	37	chr10	124754057	124754057	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaggaagacctagtaccttTaattggtaccattttatgct	12	15	7	7	0	0	1	0	0	0	1	0	2	0	2	3	2	3	3	3	2	7	9			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr10:124754057T>C	ENST00000368886.5	-	5	819	c.499A>G	c.(499-501)Aaa>Gaa	p.K167E	PSTK_ENST00000497219.1_Intron	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN	IKAROS family zinc finger 5 (Pegasus)	167					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|lung(3)|prostate(1)	6		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		CTAGTACCTTTAATTGGTACC	0.408																																					p.K167E													.	IKZF5-90	0			c.A499G						.						144	132	136					10																	124754057		1925	4126	6051	SO:0001583	missense	64376	exon5			TACCTTTAATTGG	AF230808	CCDS41574.1	10q26	2011-05-31	2006-08-25	2006-08-25	ENSG00000095574	ENSG00000095574		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	14283	protein-coding gene	gene with protein product		606238	"zinc finger protein, subfamily 1A, 5", "zinc finger protein, subfamily 1A, 5 (Pegasus)"	ZNFN1A5		10978333	Standard	NM_001271840		Approved	Pegasus, FLJ22973	uc021qaj.2	Q9H5V7	OTTHUMG00000019192	ENST00000368886.5:c.499A>G	10.37:g.124754057T>C	ENSP00000357881:p.Lys167Glu	Somatic	163	1		WXS	Illumina HiSeq	Phase_I	122	7	NM_001271840	0	0	0	0	0	B3KVH7|D3DRE7|Q9H2T0	Missense_Mutation	SNP	ENST00000368886.5	37	CCDS41574.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.823756	0.50739	.	.	ENSG00000095574	ENST00000368886	T	0.05319	3.46	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.06234	0.0161	N	0.24115	0.695	0.80722	D	1	B	0.25719	0.132	B	0.17098	0.017	T	0.37430	-0.9706	10	0.45353	T	0.12	-14.6901	16.4237	0.83790	0.0:0.0:0.0:1.0	.	167	Q9H5V7	IKZF5_HUMAN	E	167	ENSP00000357881:K167E	ENSP00000357881:K167E	K	-	1	0	IKZF5	124744047	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.857000	0.69525	2.279000	0.76181	0.533000	0.62120	AAA	.		0.408	IKZF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050820.2	NM_022466		C	124754057	T	C	124754057	3	2	156	1	0	0	0	0	1	0	0	0	7639	1763	61	3	764	3	IKZF5	10	124754057	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	81665974	124754057	10780690	55	14094											
MUC2	4583	bcgsc.ca	37	chr11	1093312	1093312	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccactacggtgaccccaaccCcaacacccaccggcacacag	12	2	6	21	2	0	1	0	1	0	0	0	1	0	1	7	2	3	1	7	2	3	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:1093312C>G	ENST00000441003.2	+	30	5158	c.5131C>G	c.(5131-5133)Cca>Gca	p.P1711A	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1678A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaaccccaacacccac	0.637																																					p.P1711A													.	MUC2-90	0			c.C5131G						.						145	191	175					11																	1093312		1907	3560	5467	SO:0001583	missense	4583	exon30			CCAACCCCAACAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5131C>G	11.37:g.1093312C>G	ENSP00000415183:p.Pro1711Ala	Somatic	124	4		WXS	Illumina HiSeq	Phase_1	97	8	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.304	-0.972196	0.02215	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.08458	3.09;3.11	1.4	-2.79	0.05841	.	0.190326	0.20108	U	0.099085	T	0.02533	0.0077	.	.	.	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.41106	-0.9527	9	0.08179	T	0.78	.	2.4144	0.04432	0.4935:0.3028:0.0:0.2036	.	1711	E7EUV1	.	A	1711;1678	ENSP00000415183:P1711A;ENSP00000351956:P1678A	ENSP00000351956:P1678A	P	+	1	0	MUC2	1083312	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-5.838000	0.00095	-0.673000	0.05259	-1.098000	0.02139	CCA	.		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093312	C	G	1093312	3	3	156	1	0	0	0	0	1	0	0	0	10000	623	22	4	5249	4	MUC2	11	1093312	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10		1093312	133913204	56	14095											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2466535	2466535	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccctgcgtccccggccgcGcccgccgcgcccccagttgc	1	4	11	25	7	0	0	0	0	0	0	1	0	1	0	9	1	2	1	9	1	0	1	rs587781009		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:2466535G>T	ENST00000155840.5	+	1	315	c.207G>T	c.(205-207)gcG>gcT	p.A69A		NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	69					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	ccccggccgcgcccgccgcgc	0.811																																					p.A69A		.											.	KCNQ1-515	0			c.G207T						.						3	4	3					11																	2466535		1287	2827	4114	SO:0001819	synonymous_variant	3784	exon1			GGCCGCGCCCGCC	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6294	protein-coding gene	gene with protein product	"Jervell and Lange-Nielsen syndrome 1"	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.207G>T	11.37:g.2466535G>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_000218	0	0	0	0	0	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			.		0.811	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		T	2466535	G	T	2466535	2	4	156	1	0	0	0	0	0	0	0	1	8103	1074	38	4		4	KCNQ1	11	2466535	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	1373223	2466535	132539981	57	14096											
TRIM68	55128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4621750	4621750	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtactcatcggtgcctgctCggtactcatttcccttcctc	4	14	8	15	2	2	0	2	0	0	0	7	0	4	0	3	3	4	3	3	3	2	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:4621750C>T	ENST00000300747.5	-	7	1503	c.1214G>A	c.(1213-1215)cGa>cAa	p.R405Q		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	405	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		GGTGCCTGCTCGGTACTCATT	0.517																																					p.R405Q		.											.	TRIM68-91	0			c.G1214A						.						100	84	89					11																	4621750		2201	4298	6499	SO:0001583	missense	55128	exon7			CCTGCTCGGTACT	AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21161	protein-coding gene	gene with protein product		613184	"ring finger protein 137", "tripartite motif-containing 68"	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.1214G>A	11.37:g.4621750C>T	ENSP00000300747:p.Arg405Gln	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	164	35	NM_018073	0	0	0	0	0	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	37	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473848	0.63737	.	.	ENSG00000167333	ENST00000300747;ENST00000544055	T	0.68181	-0.31	4.99	0.918	0.19386	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.160187	0.29932	N	0.010838	T	0.44582	0.1300	L	0.33753	1.03	0.28223	N	0.926426	P	0.34837	0.472	B	0.34824	0.19	T	0.23762	-1.0179	10	0.12766	T	0.61	.	3.2819	0.06918	0.1772:0.4704:0.0:0.3524	.	405	Q6AZZ1	TRI68_HUMAN	Q	405;126	ENSP00000300747:R405Q	ENSP00000300747:R405Q	R	-	2	0	TRIM68	4578326	0.000000	0.05858	0.996000	0.52242	0.995000	0.86356	-0.456000	0.06754	0.351000	0.24027	0.561000	0.74099	CGA	.		0.517	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073		T	4621750	C	T	4621750	3	4	156	1	0	0	0	0	1	0	0	0	16574	884	31	1	247	1	TRIM68	11	4621750	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	2155215	4621750	130384766	58	14097											
CD59	966	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	33731752	33731752	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgataaggatgtcccacCattttcaagctgttcgttaa	10	14	7	10	1	2	1	1	1	1	0	4	2	3	2	2	1	1	3	2	1	3	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:33731752C>T	ENST00000395850.3	-	4	382	c.307G>A	c.(307-309)Ggt>Agt	p.G103S	CD59_ENST00000437761.2_Missense_Mutation_p.G103S|CD59_ENST00000528700.1_Missense_Mutation_p.G103S|CD59_ENST00000426650.2_Missense_Mutation_p.G103S|CD59_ENST00000445143.2_Missense_Mutation_p.G103S|CD59_ENST00000527577.1_Missense_Mutation_p.G103S|CD59_ENST00000534312.1_Splice_Site_p.D103N|CD59_ENST00000415002.2_Missense_Mutation_p.G103S|CD59_ENST00000533403.1_3'UTR|CD59_ENST00000351554.3_Missense_Mutation_p.G103S	NM_000611.5|NM_001127225.1|NM_001127226.1|NM_001127227.1|NM_203329.2|NM_203330.2|NM_203331.2	NP_000602.1|NP_001120697.1|NP_001120698.1|NP_001120699.1|NP_976074.1|NP_976075.1|NP_976076.1	P13987	CD59_HUMAN	CD59 molecule, complement regulatory protein	103	UPAR/Ly6.				blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|negative regulation of activation of membrane attack complex (GO:0001971)|negative regulation of apoptotic process (GO:0043066)|positive regulation of T cell proliferation (GO:0042102)|regulation of complement activation (GO:0030449)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|compact myelin (GO:0043218)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	complement binding (GO:0001848)			endometrium(1)|lung(2)	3						GATGTCCCACCATTTTCAAGC	0.473																																					p.G103S													.	CD59-90	0			c.G307A						.						160	124	136					11																	33731752		2202	4298	6500	SO:0001583	missense	966	exon5			TCCCACCATTTTC		CCDS7886.1	11p13	2014-09-17	2006-03-28			ENSG00000085063		"CD molecules", "Complement system"	1689	protein-coding gene	gene with protein product		107271	"CD59 antigen p18-20 (antigen identified by monoclonal antibodies 16.3A5, EJ16, EJ30, EL32 and G344)", "CD59 antigen, complement regulatory protein"	MIC11, MIN1, MSK21, MIN2, MIN3		7691713	Standard	NM_001127223		Approved	16.3A5, EJ16, EJ30, EL32, G344, p18-20	uc001mus.4	P13987		ENST00000395850.3:c.307G>A	11.37:g.33731752C>T	ENSP00000379191:p.Gly103Ser	Somatic	215	2		WXS	Illumina HiSeq	Phase_I	215	25	NM_203331	0	0	144	195	51		Missense_Mutation	SNP	ENST00000395850.3	37	CCDS7886.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.01|11.01	1.513538|1.513538	0.27123|0.27123	.|.	.|.	ENSG00000085063|ENSG00000085063	ENST00000534312|ENST00000527926;ENST00000395850;ENST00000351554;ENST00000415002;ENST00000445143;ENST00000426650;ENST00000437761;ENST00000527577;ENST00000528700	D|D;T;T;T;T;T;T;T;T	0.92249|0.94184	-3.0|-3.37;2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89	1.71|1.71	-1.94|-1.94	0.07571|0.07571	.|Ly-6 antigen / uPA receptor -like (1);	.|1.089460	.|0.06889	.|N	.|0.803918	D|D	0.92609|0.92609	0.7652|0.7652	L|L	0.59436|0.59436	1.845|1.845	0.09310|0.09310	N|N	1|1	.|D	.|0.55385	.|0.971	.|P	.|0.54238	.|0.746	D|D	0.83396|0.83396	0.0020|0.0020	7|10	0.05620|0.38643	T|T	0.96|0.18	-12.9057|-12.9057	4.096|4.096	0.09991|0.09991	0.0:0.3422:0.4816:0.1762|0.0:0.3422:0.4816:0.1762	.|.	.|103	.|P13987	.|CD59_HUMAN	N|S	103|103	ENSP00000432362:D103N|ENSP00000437122:G103S;ENSP00000379191:G103S;ENSP00000340210:G103S;ENSP00000404822:G103S;ENSP00000403511:G103S;ENSP00000402425:G103S;ENSP00000410182:G103S;ENSP00000432942:G103S;ENSP00000434617:G103S	ENSP00000432362:D103N|ENSP00000340210:G103S	D|G	-|-	1|1	0|0	CD59|CD59	33688328|33688328	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	0.162000|0.162000	0.16501|0.16501	-0.554000|-0.554000	0.06150|0.06150	-0.304000|-0.304000	0.09214|0.09214	GAC|GGT	.		0.473	CD59-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000388809.1	NM_203329		T	33731752	C	T	33731752	3	4	156	1	0	0	0	0	1	0	0	0	3032	594	21	2	83	2	CD59	11	33731752	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	29110002	33731752	101274764	59	14098											
AHNAK	79026	broad.mit.edu;bcgsc.ca	37	chr11	62285795	62285796	+	Frame_Shift_Del	DEL	AG	AG	-																															cctgcaggcttggtcccctcAgtgtcacatctggtgcccca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:62285795_62285796delAG	ENST00000378024.4	-	5	16367_16368	c.16093_16094delCT	c.(16093-16095)ctgfs	p.L5365fs	AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5365					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGGTCCCCTCAGTGTCACATCT	0.545																																					p.5365_5365del													.	AHNAK-109	0			c.16093_16094del						.																																			SO:0001589	frameshift_variant	79026	exon5			CCCCTCAGTGTCA	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.16093_16094delCT	11.37:g.62285795_62285796delAG	ENSP00000367263:p.Leu5365fs	Somatic	180	0		WXS	Illumina HiSeq	Phase_I	153	16	NM_001620	0	0	0	0	0	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	37	CCDS31584.1																																																																																			.		0.545	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62285796	AG	-	62285795	7	5	156	1	0	1	0	1	0	0	0	0	414	188	7	0	1698	0	AHNAK	11	62285795	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	28554043	62285795	72720721	60	14099											
MTA2	9219	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	62364175	62364176	+	Frame_Shift_Del	DEL	CT	CT	-																															gcctcctcaaatagcatggcCtctgaggctgaccattcctc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:62364175_62364176delCT	ENST00000278823.2	-	9	1204_1205	c.815_816delAG	c.(814-816)gagfs	p.E272fs	MTA2_ENST00000524902.1_Frame_Shift_Del_p.E99fs|MTA2_ENST00000527204.1_Frame_Shift_Del_p.E99fs	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	272	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin assembly or disassembly (GO:0006333)|DNA methylation (GO:0006306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	histone deacetylase complex (GO:0000118)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|histone deacetylase activity (GO:0004407)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	26						ATAGCATGGCCTCTGAGGCTGA	0.55																																					p.272_272del		.											.	MTA2-92	0			c.815_816del						.																																			SO:0001589	frameshift_variant	9219	exon9			.	AB016591	CCDS8022.1	11q12-q13.1	2013-01-25	2004-12-15	2003-12-17	ENSG00000149480	ENSG00000149480		"GATA zinc finger domain containing"	7411	protein-coding gene	gene with protein product		603947	"metastasis associated gene family, member 2"	MTA1L1		9929979	Standard	NM_004739		Approved	MTA1-L1	uc001ntq.2	O94776	OTTHUMG00000167684	ENST00000278823.2:c.815_816delAG	11.37:g.62364177_62364178delCT	ENSP00000278823:p.Glu272fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	134	24	NM_004739	0	0	0	0	0	Q68DB1|Q9UQB5	Frame_Shift_Del	DEL	ENST00000278823.2	37	CCDS8022.1																																																																																			.		0.55	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1	NM_004739		-	62364176	CT	-	62364175	7	5	156	1	0	1	0	1	0	0	0	0	9934	680	24	0	1230	0	MTA2	11	62364175	Frame_Shift_Del	DEL	CT	TCGA-P4-A5EA-01A-11D-A28G-10	78380	62364175	72642341	61	14100											
ZNHIT2	741	hgsc.bcm.edu	37	chr11	64884755	64884755	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accaccacggccgccatggaGgcagcagccgcccggcctca	8	2	12	19	4	1	0	1	0	0	0	1	1	1	1	7	4	2	2	7	4	0	0	rs200126440		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:64884755G>A	ENST00000310597.4	-	1	415	c.371C>T	c.(370-372)cCt>cTt	p.P124L	AP003068.12_ENST00000527789.1_RNA	NM_014205.2	NP_055020.1	Q9UHR6	ZNHI2_HUMAN	zinc finger, HIT-type containing 2	124							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						CCGCCATGGAGGCAGCAGCCG	0.731													G|||	1	0.000199681	0	0	5008	,	,		11861	0		0.001	False		,,,				2504	0				p.P124L		.											.	ZNHIT2-153	0			c.C371T						.	G	LEU/PRO	0,3516		0,0,1758	6	8	7		371	4.6	1	11		7	3,7301		0,3,3649	no	missense	ZNHIT2	NM_014205.2	98	0,3,5407	AA,AG,GG		0.0411,0.0,0.0277	probably-damaging	124/404	64884755	3,10817	1758	3652	5410	SO:0001583	missense	741	exon1			CATGGAGGCAGCA		CCDS8094.1	11q13	2012-08-08	2010-09-15	2004-07-14	ENSG00000174276	ENSG00000174276		"Zinc fingers, HIT-type"	1177	protein-coding gene	gene with protein product		604575	"chromosome 11 open reading frame 5", "zinc finger, HIT domain containing 2"	C11orf5			Standard	NM_014205		Approved	FON	uc001ocw.3	Q9UHR6	OTTHUMG00000165604	ENST00000310597.4:c.371C>T	11.37:g.64884755G>A	ENSP00000308548:p.Pro124Leu	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	13	8	NM_014205	0	0	1	3	2	Q3SY14|Q8IUV0	Missense_Mutation	SNP	ENST00000310597.4	37	CCDS8094.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129799	0.77549	0.0	4.11E-4	ENSG00000174276	ENST00000310597	T	0.34472	1.36	4.55	4.55	0.56014	.	0.142165	0.47455	U	0.000232	T	0.59959	0.2232	M	0.74881	2.28	0.53005	D	0.999966	D	0.89917	1.0	D	0.83275	0.996	T	0.64757	-0.6332	10	0.72032	D	0.01	-12.5655	14.8345	0.70172	0.0:0.0:1.0:0.0	.	124	Q9UHR6	ZNHI2_HUMAN	L	124	ENSP00000308548:P124L	ENSP00000308548:P124L	P	-	2	0	ZNHIT2	64641331	0.995000	0.38212	0.958000	0.39756	0.786000	0.44442	2.667000	0.46808	2.366000	0.80165	0.561000	0.74099	CCT	.		0.731	ZNHIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385260.1	NM_014205		A	64884755	G	A	64884755	3	1	156	1	0	0	0	0	1	0	0	0	18239	1000	35	2	844	2	ZNHIT2	11	64884755	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	2520580	64884755	70121761	62	14101											
DSCAML1	57453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117352683	117352683	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggggtgctcaccttcaGtgtggagacgacctcgtcgc	5	9	16	11	3	2	1	2	0	0	1	4	3	2	1	2	4	1	1	2	4	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:117352683G>C	ENST00000321322.6	-	12	2735	c.2734C>G	c.(2734-2736)Ctg>Gtg	p.L912V	DSCAML1_ENST00000527706.1_Missense_Mutation_p.L642V	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	852	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CTCACCTTCAGTGTGGAGACG	0.622																																					p.L912V		.											.	DSCAML1-159	0			c.C2734G						.						104	73	84					11																	117352683		2201	4296	6497	SO:0001583	missense	57453	exon12			CCTTCAGTGTGGA		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2734C>G	11.37:g.117352683G>C	ENSP00000315465:p.Leu912Val	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	97	33	NM_020693	0	0	0	0	0	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397882	0.42512	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.73681	-0.77;-0.77	3.89	2.97	0.34412	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.85111	0.5622	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.85651	0.1282	9	0.62326	D	0.03	.	11.2591	0.49071	0.09:0.0:0.91:0.0	.	852	Q8TD84	DSCL1_HUMAN	V	642;912;619	ENSP00000434335:L642V;ENSP00000315465:L912V	ENSP00000315465:L912V	L	-	1	2	DSCAML1	116857893	1.000000	0.71417	0.934000	0.37439	0.083000	0.17756	4.754000	0.62191	0.844000	0.35094	0.485000	0.47835	CTG	.		0.622	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		C	117352683	G	C	117352683	3	2	156	1	0	0	0	0	1	0	0	0	4780	1020	36	4	3695	4	DSCAML1	11	117352683	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	52467928	117352683	17653833	63	14102											
IL10RA	3587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	117869470	117869470	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcatcttcatcagccagcGtccctccccagagacccaag	9	8	6	18	1	4	1	3	0	1	1	6	2	6	1	5	0	2	0	5	0	1	2	rs576666901	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:117869470G>T	ENST00000227752.3	+	7	971	c.851G>T	c.(850-852)cGt>cTt	p.R284L	IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Missense_Mutation_p.R264L|IL10RA_ENST00000545409.1_Missense_Mutation_p.R135L	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	284					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		ATCAGCCAGCGTCCCTCCCCA	0.582																																					p.R284L		.											.	IL10RA-91	0			c.G851T						.						90	73	79					11																	117869470		2200	4296	6496	SO:0001583	missense	3587	exon7			GCCAGCGTCCCTC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"Interleukins and interleukin receptors", "CD molecules"	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.851G>T	11.37:g.117869470G>T	ENSP00000227752:p.Arg284Leu	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	115	18	NM_001558	0	0	16	16	0	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	8.140	0.784909	0.16189	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.23950	1.88;1.88;1.88	5.26	-3.16	0.05217	.	4.015810	0.00166	N	0.000015	T	0.07052	0.0179	N	0.01267	-0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20505	-1.0273	10	0.10377	T	0.69	-0.0195	1.5109	0.02496	0.1162:0.2378:0.2516:0.3945	.	264;284	F5GYV8;Q13651	.;I10R1_HUMAN	L	284;264;135;264	ENSP00000227752:R284L;ENSP00000441397:R264L;ENSP00000443019:R135L	ENSP00000227752:R284L	R	+	2	0	IL10RA	117374680	0.000000	0.05858	0.000000	0.03702	0.289000	0.27227	-1.174000	0.03105	-0.149000	0.11215	-0.457000	0.05445	CGT	.		0.582	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869470	G	T	117869470	3	4	156	1	0	0	0	0	1	0	0	0	7641	1145	40	4	877	4	IL10RA	11	117869470	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	516787	117869470	17137046	64	14103											
OR8D1	283159	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	124180084	124180085	+	Frame_Shift_Del	DEL	GT	GT	-																															aaaagtagaagctcattgagGtgtgtgttggagcaggagag																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:124180084_124180085delGT	ENST00000357821.2	-	1	648_649	c.578_579delAC	c.(577-579)cacfs	p.H193fs		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H193Q(1)		kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GCTCATTGAGGTGTGTGTTGGA	0.46																																					p.193_193del		.											.	OR8D1-71	1	Substitution - Missense(1)	ovary(1)	c.578_579del						.																																			SO:0001589	frameshift_variant	283159	exon1			.	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.578_579delAC	11.37:g.124180090_124180091delGT	ENSP00000350474:p.His193fs	Somatic	198	0		WXS	Illumina HiSeq	Phase_I	214	45	NM_001002917	0	0	0	0	0	B2RNL4|Q6IEW1|Q8NGH0	Frame_Shift_Del	DEL	ENST00000357821.2	37	CCDS31706.1																																																																																			.		0.46	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		-	124180085	GT	-	124180084	7	5	156	1	0	1	0	1	0	0	0	0	11257	1252	44	0	350	0	OR8D1	11	124180084	Frame_Shift_Del	DEL	GT	TCGA-P4-A5EA-01A-11D-A28G-10	6310614	124180084	10826432	65	14104											
LRRK2	120892	broad.mit.edu	37	chr12	40742254	40742254	+	Frame_Shift_Del	DEL	G	G	-																															gccccatggcctatggttgaGaaattaattaaacagtgttt																								rs10878405	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:40742254delG	ENST00000298910.7	+	43	6382	c.6324delG	c.(6322-6324)gagfs	p.E2108fs		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTATGGTTGAGAAATTAATTA	0.308																																					p.E2108fs													.	LRRK2-533	0			c.6324delG						.						87	86	86					12																	40742254		2203	4299	6502	SO:0001589	frameshift_variant	120892	exon43			GGTTGAGAAATTA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6324delG	12.37:g.40742254delG	ENSP00000298910:p.Glu2108fs	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	148	9	NM_198578	0	0	0	0	0	A6NJU2|Q6ZS50|Q8NCX9	Frame_Shift_Del	DEL	ENST00000298910.7	37	CCDS31774.1																																																																																			.		0.308	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		-	40742254	G	-	40742254	7	5	156	1	0	1	0	1	0	0	0	0	9058	933	33	0	6494	0	LRRK2	12	40742254	Frame_Shift_Del	DEL	G	TCGA-P4-A5EA-01A-11D-A28G-10		40742254	93109641	66	14105	154	2									
LRRK2	120892	broad.mit.edu	37	chr12	40742257	40742259	+	In_Frame_Del	DEL	ATT	ATT	-																															ccatggcctatggttgagaaAttaattaaacagtgtttgaa																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:40742257_40742259delATT	ENST00000298910.7	+	43	6385_6387	c.6327_6329delATT	c.(6325-6330)aaatta>aaa	p.L2110del		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TGGTTGAGAAATTAATTAAACAG	0.315																																					p.2109_2110del													.	LRRK2-533	0			c.6327_6329del						.																																			SO:0001651	inframe_deletion	120892	exon43			TGAGAAATTAATT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"Parkinson disease"	18618	protein-coding gene	gene with protein product		609007	"Parkinson disease (autosomal dominant) 8"	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6327_6329delATT	12.37:g.40742257_40742259delATT	ENSP00000298910:p.Leu2110del	Somatic	207	0		WXS	Illumina HiSeq	Phase_I	146	9	NM_198578	0	0	0	0	0	A6NJU2|Q6ZS50|Q8NCX9	In_Frame_Del	DEL	ENST00000298910.7	37	CCDS31774.1																																																																																			.		0.315	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		-	40742259	ATT	-	40742257	7	5	156	1	0	1	0	1	0	0	0	0	9058	98	4	0	6497	0	LRRK2	12	40742257	In_Frame_Del	DEL	ATT	TCGA-P4-A5EA-01A-11D-A28G-10	3	40742257	93109638	67	14106	154	2									
SOAT2	8435	broad.mit.edu;bcgsc.ca	37	chr12	53499371	53499372	+	Frame_Shift_Del	DEL	AG	AG	-																															ggagccatccctggggaaacAgaaagttttcatcatccgca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:53499371_53499372delAG	ENST00000301466.3	+	4	362_363	c.302_303delAG	c.(301-303)cagfs	p.Q101fs		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	101					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	CTGGGGAAACAGAAAGTTTTCA	0.5																																					p.101_101del													.	SOAT2-91	0			c.302_303del						.																																			SO:0001589	frameshift_variant	8435	exon4			GGAAACAGAAAGT	AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.302_303delAG	12.37:g.53499371_53499372delAG	ENSP00000301466:p.Gln101fs	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	88	9	NM_003578	0	0	0	0	0	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Frame_Shift_Del	DEL	ENST00000301466.3	37	CCDS8847.1																																																																																			.		0.5	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1			-	53499372	AG	-	53499371	7	5	156	1	0	1	0	1	0	0	0	0	14943	188	7	0	316	0	SOAT2	12	53499371	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	12757114	53499371	80352524	68	14107											
UTP20	27340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	101720912	101720912	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtaaaactcaggggaaatCtgcttcaggcacccgcatgg	12	7	12	10	1	3	0	2	0	1	0	3	2	3	1	1	4	2	4	1	4	3	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:101720912C>A	ENST00000261637.4	+	26	3269	c.3095C>A	c.(3094-3096)tCt>tAt	p.S1032Y		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1032					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CAGGGGAAATCTGCTTCAGGC	0.453																																					p.S1032Y		.											.	UTP20-155	0			c.C3095A						.						103	103	103					12																	101720912		2203	4300	6503	SO:0001583	missense	27340	exon26			GGAAATCTGCTTC	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"down regulated in metastasis"	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.3095C>A	12.37:g.101720912C>A	ENSP00000261637:p.Ser1032Tyr	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	82	13	NM_014503	0	0	0	0	0	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501228	0.85176	.	.	ENSG00000120800	ENST00000261637	T	0.20881	2.04	5.02	5.02	0.67125	Down-regulated-in-metastasis protein (1);Armadillo-type fold (1);	0.112147	0.64402	D	0.000007	T	0.45637	0.1352	M	0.63843	1.955	0.58432	D	0.999997	D	0.89917	1.0	D	0.77557	0.99	T	0.33624	-0.9861	10	0.49607	T	0.09	-16.674	18.7119	0.91661	0.0:1.0:0.0:0.0	.	1032	O75691	UTP20_HUMAN	Y	1032	ENSP00000261637:S1032Y	ENSP00000261637:S1032Y	S	+	2	0	UTP20	100245043	0.999000	0.42202	0.997000	0.53966	0.758000	0.43043	7.357000	0.79456	2.491000	0.84063	0.305000	0.20034	TCT	.		0.453	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101720912	C	A	101720912	3	1	156	1	0	0	0	0	1	0	0	0	17132	913	32	4	3197	4	UTP20	12	101720912	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	48221541	101720912	32130983	69	14108											
PAH	5053	broad.mit.edu	37	chr12	103271308	103271308	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatctgtccagctcttgaaTggttcttgggaaccagggca	10	11	11	9	0	3	1	0	1	3	0	4	2	4	2	2	3	2	3	2	3	3	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:103271308T>A	ENST00000553106.1	-	4	845	c.373A>T	c.(373-375)Att>Ttt	p.I125F	PAH_ENST00000307000.2_Missense_Mutation_p.I120F|PAH_ENST00000551988.1_5'UTR	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	125					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	AGCTCTTGAATGGTTCTTGGG	0.507																																					p.I125F													.	PAH-72	0			c.A373T						.						150	138	142					12																	103271308		2203	4300	6503	SO:0001583	missense	5053	exon4			CTTGAATGGTTCT	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"phenylalanine 4-monooxygenase"	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.373A>T	12.37:g.103271308T>A	ENSP00000448059:p.Ile125Phe	Somatic	74	1		WXS	Illumina HiSeq	Phase_I	81	4	NM_000277	0	0	0	0	0	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.844247	0.91197	.	.	ENSG00000171759	ENST00000553106;ENST00000307000;ENST00000551337	D;D;D	0.99695	-6.43;-6.43;-5.58	5.86	5.86	0.93980	Aromatic amino acid hydroxylase, C-terminal (3);	0.095070	0.64402	D	0.000001	D	0.99834	0.9925	H	0.96604	3.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	D	0.96686	0.9507	10	0.87932	D	0	-9.0062	16.2436	0.82429	0.0:0.0:0.0:1.0	.	125;125	B4DPN2;P00439	.;PH4H_HUMAN	F	125;120;125	ENSP00000448059:I125F;ENSP00000303500:I120F;ENSP00000447620:I125F	ENSP00000303500:I120F	I	-	1	0	PAH	101795438	1.000000	0.71417	0.997000	0.53966	0.863000	0.49368	5.866000	0.69590	2.232000	0.73038	0.533000	0.62120	ATT	.		0.507	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			A	103271308	T	A	103271308	3	1	156	1	0	0	0	0	1	0	0	0	11420	1464	51	5	1025	5	PAH	12	103271308	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	1550396	103271308	30580587	70	14109											
GCN1L1	10985	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	120572149	120572149	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgatgtttttccggatgacGgcatccactttggcccctgc	6	12	10	13	3	0	1	0	1	0	0	2	3	2	2	4	3	1	2	4	3	0	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:120572149G>C	ENST00000300648.6	-	53	7275	c.7263C>G	c.(7261-7263)gcC>gcG	p.A2421A		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2421					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCCGGATGACGGCATCCACTT	0.592																																					p.A2421A													.	GCN1L1-94	0			c.C7263G						.						116	118	117					12																	120572149		2115	4229	6344	SO:0001819	synonymous_variant	10985	exon53			GATGACGGCATCC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7263C>G	12.37:g.120572149G>C		Somatic	69	1		WXS	Illumina HiSeq	Phase_I	76	9	NM_006836	0	0	1	8	7	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			.		0.592	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			C	120572149	G	C	120572149	2	2	156	1	0	0	0	0	0	0	0	1	6319	1103	39	4		4	GCN1L1	12	120572149	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	17300841	120572149	13279746	71	14110											
TNFRSF19	55504	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	24167593	24167593	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccaggcatggagttgtctaAggtatattggatacatggca	11	11	13	6	0	1	0	0	0	1	0	1	2	1	2	1	5	1	4	1	5	4	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:24167593A>C	ENST00000382258.4	+	3	383	c.179A>C	c.(178-180)aAg>aCg	p.K60T	TNFRSF19_ENST00000248484.4_Splice_Site_p.K60T|TNFRSF19_ENST00000403372.2_Intron|TNFRSF19_ENST00000382263.3_Splice_Site_p.K60T|TNFRSF19_ENST00000464735.1_3'UTR	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	60					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		GAGTTGTCTAAGGTATATTGG	0.408																																					p.K60T													.	TNFRSF19-228	0			c.A179C						.						125	122	123					13																	24167593		2203	4300	6503	SO:0001630	splice_region_variant	55504	exon3			TGTCTAAGGTATA	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"Tumor necrosis factor receptor superfamily"	11915	protein-coding gene	gene with protein product	"toxicity and JNK inducer"	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.180+1A>C	13.37:g.24167593A>C		Somatic	147	1		WXS	Illumina HiSeq	Phase_I	122	17	NM_018647	0	0	0	0	0	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.533748	0.64972	.	.	ENSG00000127863	ENST00000248484;ENST00000382258;ENST00000382263	T;T;T	0.21361	2.01;2.01;2.01	5.3	5.3	0.74995	TNFR/CD27/30/40/95 cysteine-rich region (3);	0.000000	0.85682	D	0.000000	T	0.42630	0.1211	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	T	0.21861	-1.0233	10	0.46703	T	0.11	-31.0155	13.0516	0.58958	1.0:0.0:0.0:0.0	.	60;60;60	Q9NS68;A8KA09;Q9NS68-2	TNR19_HUMAN;.;.	T	60	ENSP00000248484:K60T;ENSP00000371693:K60T;ENSP00000371698:K60T	ENSP00000248484:K60T	K	+	2	0	TNFRSF19	23065593	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	6.400000	0.73252	2.135000	0.66039	0.482000	0.46254	AAG	.		0.408	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	Missense_Mutation	C	24167593	A	C	24167593	5	2	156	1	0	0	0	0	0	0	1	0	16324	86	3	5	185	5	TNFRSF19	13	24167593	Splice_Site	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10		24167593	91002285	72	14111											
HMGB1	3146	broad.mit.edu	37	chr13	31036768	31036768	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacatctctcccagtttcttCgcaacatcaccaatggacag	11	10	5	15	1	3	0	1	0	2	0	6	1	4	1	2	1	1	2	2	1	2	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:31036768C>T	ENST00000405805.1	-	4	1318	c.378G>A	c.(376-378)gcG>gcA	p.A126A	HMGB1_ENST00000399489.1_Silent_p.A126A|HMGB1_ENST00000339872.4_Silent_p.A126A|HMGB1_ENST00000326004.4_Silent_p.A126A|HMGB1_ENST00000341423.5_Silent_p.A126A|HMGB1_ENST00000399494.1_Silent_p.A126A|HMGB1_ENST00000468384.1_5'Flank			P09429	HMGB1_HUMAN	high mobility group box 1	126					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)	p.A126A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CCAGTTTCTTCGCAACATCAC	0.413																																					p.A126A													.	HMGB1-227	1	Substitution - coding silent(1)	large_intestine(1)	c.G378A						.						96	88	91					13																	31036768		2202	4280	6482	SO:0001819	synonymous_variant	3146	exon4			TTTCTTCGCAACA	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.378G>A	13.37:g.31036768C>T		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	89	4	NM_002128	0	0	406	418	12	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Silent	SNP	ENST00000405805.1	37	CCDS9335.1																																																																																			.		0.413	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		T	31036768	C	T	31036768	2	4	156	1	0	0	0	0	0	0	0	1	7246	871	31	1		1	HMGB1	13	31036768	Silent	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	6869175	31036768	84133110	73	14112											
C13orf18	80183	broad.mit.edu;bcgsc.ca	37	chr13	46946278	46946278	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggagaagcgctgccaacGgagtctgtggtatcctcaga	9	8	15	9	2	2	2	1	0	1	2	3	4	3	3	2	4	3	2	2	4	3	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:46946278G>A	ENST00000429979.1	-	3	937	c.333C>T	c.(331-333)tcC>tcT	p.S111S	KIAA0226L_ENST00000534925.1_5'UTR|RNU2-6P_ENST00000411404.1_RNA|KIAA0226L_ENST00000378781.3_Silent_p.S111S|KIAA0226L_ENST00000378797.2_Silent_p.S111S|KIAA0226L_ENST00000378784.4_Silent_p.S44S|KIAA0226L_ENST00000378787.3_Silent_p.S111S|KIAA0226L_ENST00000480935.1_5'UTR|KIAA0226L_ENST00000409879.2_Intron|KIAA0226L_ENST00000389908.3_Silent_p.S111S|KIAA0226L_ENST00000322896.6_Intron	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	111	Ser-rich.									NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						CGCTGCCAACGGAGTCTGTGG	0.572																																					p.S111S													.	.	0			c.C333T						.						92	88	89					13																	46946278		2203	4300	6503	SO:0001819	synonymous_variant	80183	exon3			GCCAACGGAGTCT	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 18"	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.333C>T	13.37:g.46946278G>A		Somatic	123	0		WXS	Illumina HiSeq	Phase_I	122	6	NM_025113	0	0	0	0	0	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Silent	SNP	ENST00000429979.1	37	CCDS31970.2																																																																																			.		0.572	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113		A	46946278	G	A	46946278	2	1	156	1	0	0	0	0	0	0	0	1	1724	1103	39	1		1	C13orf18	13	46946278	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	15909510	46946278	68223600	74	14113											
TPP2	7174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	103328750	103328750	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaaccaacaaaagaaaactgGaaaaattgtattcaagtaag	23	7	6	5	0	1	1	1	0	0	1	1	2	1	2	1	1	3	2	1	1	11	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:103328750G>T	ENST00000376065.4	+	28	3681	c.3645G>T	c.(3643-3645)tgG>tgT	p.W1215C	TPP2_ENST00000376052.3_Missense_Mutation_p.W1228C|TPP2_ENST00000466153.1_3'UTR	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1215					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AAGAAAACTGGAAAAATTGTA	0.303																																					p.W1215C		.											.	TPP2-92	0			c.G3645T						.						56	60	58					13																	103328750		2201	4290	6491	SO:0001583	missense	7174	exon28			AAACTGGAAAAAT	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.3645G>T	13.37:g.103328750G>T	ENSP00000365233:p.Trp1215Cys	Somatic	137	0		WXS	Illumina HiSeq	Phase_I	117	11	NM_003291	0	0	40	40	0	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	37	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.891078	0.33348	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.8	5.8	0.92144	.	0.162876	0.56097	D	0.000022	T	0.39733	0.1089	N	0.22421	0.69	0.80722	D	1	P	0.41748	0.761	B	0.37780	0.258	T	0.28073	-1.0055	9	0.38643	T	0.18	.	15.1747	0.72901	0.0692:0.0:0.9308:0.0	.	1215	P29144	TPP2_HUMAN	C	1215;1228	.	ENSP00000365220:W1228C	W	+	3	0	TPP2	102126751	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.923000	0.70045	2.746000	0.94184	0.563000	0.77884	TGG	.		0.303	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			T	103328750	G	T	103328750	3	4	156	1	0	0	0	0	1	0	0	0	16445	1183	41	4	3755	4	TPP2	13	103328750	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	56382472	103328750	11841128	75	14114											
IRS2	8660	hgsc.bcm.edu	37	chr13	110435073	110435073	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcccgacacctgctccatgaGgctcagcctcttcacgcccg	6	8	8	19	3	3	1	2	1	1	0	5	2	5	1	5	1	2	2	5	1	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:110435073G>A	ENST00000375856.3	-	1	3842	c.3328C>T	c.(3328-3330)Ctc>Ttc	p.L1110F		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1110					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGCTCCATGAGGCTCAGCCTC	0.731																																					p.L1110F	Melanoma(100;613 2409 40847)	.											.	IRS2-1334	0			c.C3328T						.						5	6	6					13																	110435073		2027	4070	6097	SO:0001583	missense	8660	exon1			CCATGAGGCTCAG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.3328C>T	13.37:g.110435073G>A	ENSP00000365016:p.Leu1110Phe	Somatic	8	0		WXS	Illumina HiSeq	Phase_I	54	21	NM_003749	0	0	0	0	0	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	37	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.514438	0.27123	.	.	ENSG00000185950	ENST00000375856	T	0.46063	0.88	3.92	2.96	0.34315	.	0.608901	0.14485	U	0.316713	T	0.58323	0.2114	M	0.64404	1.975	0.36281	D	0.855788	D	0.76494	0.999	D	0.75484	0.986	T	0.62324	-0.6878	10	0.35671	T	0.21	-24.5425	12.0667	0.53592	0.1011:0.0:0.8989:0.0	.	1110	Q9Y4H2	IRS2_HUMAN	F	1110	ENSP00000365016:L1110F	ENSP00000365016:L1110F	L	-	1	0	IRS2	109233074	1.000000	0.71417	0.997000	0.53966	0.010000	0.07245	3.062000	0.49971	2.039000	0.60335	0.644000	0.83932	CTC	.		0.731	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		A	110435073	G	A	110435073	3	1	156	1	0	0	0	0	1	0	0	0	7862	1000	35	2	696	2	IRS2	13	110435073	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	7106323	110435073	4734805	76	14115											
C14orf145	145508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	81251281	81251284	+	Frame_Shift_Del	DEL	CTTA	CTTA	-																															tcagcctcactcttttctttCttaaagtgcttcataagctc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CTTA	CTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr14:81251281_81251284delCTTA	ENST00000555265.1	-	15	2541_2544	c.2166_2169delTAAG	c.(2164-2169)tttaagfs	p.FK722fs	CEP128_ENST00000281129.3_Frame_Shift_Del_p.FK722fs			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	722						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TCTTTTCTTTCTTAAAGTGCTTCA	0.412																																					p.722_723del		.											.	CEP128-91	0			c.2166_2169del						.																																			SO:0001589	frameshift_variant	145508	exon14			.	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 61", "chromosome 14 open reading frame 145"	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2166_2169delTAAG	14.37:g.81251281_81251284delCTTA	ENSP00000451162:p.Phe722fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	75	25	NM_152446	0	0	0	0	0	B9EK52|Q86X97|Q96ML4	Frame_Shift_Del	DEL	ENST00000555265.1	37	CCDS32130.1																																																																																			.		0.412	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		-	81251284	CTTA	-	81251281	7	5	156	1	0	1	0	1	0	0	0	0	1753	912	32	0	1159	0	C14orf145	14	81251281	Frame_Shift_Del	DEL	CTTA	TCGA-P4-A5EA-01A-11D-A28G-10		81251281	26098259	77	14116											
KIAA1409	57578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	94052953	94052953	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcttcacagcagtaaagaatGataccgaaagaaaattttgc	17	10	7	7	1	2	3	1	1	1	2	2	4	2	3	1	0	3	2	1	0	7	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr14:94052953G>C	ENST00000393151.2	+	21	2815	c.2815G>C	c.(2815-2817)Gat>Cat	p.D939H	UNC79_ENST00000553484.1_Missense_Mutation_p.D939H|UNC79_ENST00000555664.1_Missense_Mutation_p.D939H|UNC79_ENST00000256339.4_Missense_Mutation_p.D762H			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	939					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGTAAAGAATGATACCGAAAG	0.333																																					p.D762H		.											.	.	0			c.G2284C						.						51	51	51					14																	94052953		2202	4299	6501	SO:0001583	missense	57578	exon21			AAGAATGATACCG	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"KIAA1409"	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.2815G>C	14.37:g.94052953G>C	ENSP00000376858:p.Asp939His	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	30	7	NM_020818	0	0	0	0	0	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	G	19.14	3.769262	0.69992	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18810	2.2;2.2;2.19;2.2	5.94	5.94	0.96194	.	0.110277	0.64402	D	0.000009	T	0.33235	0.0856	L	0.34521	1.04	0.42647	D	0.99343	D	0.57571	0.98	P	0.55965	0.788	T	0.00860	-1.1537	10	0.51188	T	0.08	-21.7402	20.3736	0.98901	0.0:0.0:1.0:0.0	.	939	C9JQL1	.	H	762;939;939;939;939	ENSP00000256339:D762H;ENSP00000450868:D939H;ENSP00000451360:D939H;ENSP00000376858:D939H	ENSP00000256339:D762H	D	+	1	0	KIAA1409	93122706	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.130000	0.77235	2.820000	0.97059	0.650000	0.86243	GAT	.		0.333	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		C	94052953	G	C	94052953	3	2	156	1	0	0	0	0	1	0	0	0	8251	1290	45	4	2354	4	KIAA1409	14	94052953	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	12801672	94052953	13296587	78	14117											
GLCE	26035	hgsc.bcm.edu;bcgsc.ca	37	chr15	69553563	69553564	+	Frame_Shift_Del	DEL	AG	AG	-																															tatatgaaacagcagaagacAgagacaaaaacaagcctaat																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr15:69553563_69553564delAG	ENST00000261858.2	+	4	952_953	c.724_725delAG	c.(724-726)agafs	p.R242fs	GLCE_ENST00000559500.1_3'UTR|GLCE_ENST00000559420.2_Frame_Shift_Del_p.R178fs	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	242					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)	p.R242K(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						AGCAGAAGACAGAGACAAAAAC	0.401																																					p.242_242del		.											.	GLCE-92	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.724_725del						.																																			SO:0001589	frameshift_variant	26035	exon4			.	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"heparan sulfate epimerase"	612134	"D-glucuronyl C5-epimerase", "UDP-glucuronic acid epimerase"			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.724_725delAG	15.37:g.69553565_69553566delAG	ENSP00000261858:p.Arg242fs	Somatic	157	0		WXS	Illumina HiSeq	Phase_I	105	22	NM_015554	0	0	0	0	0	Q6GUQ2	Frame_Shift_Del	DEL	ENST00000261858.2	37	CCDS32277.1																																																																																			.		0.401	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		-	69553564	AG	-	69553563	7	5	156	1	0	1	0	1	0	0	0	0	6452	180	7	0	730	0	GLCE	15	69553563	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10		69553563	32977829	79	14118											
C15orf39	56905	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	75500838	75500838	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgcaggggctgctggccAagctgctgtctcagctgcag	5	9	16	11	0	1	0	1	0	1	0	2	0	1	0	1	3	6	7	1	3	1	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr15:75500838A>G	ENST00000360639.2	+	2	2769	c.2449A>G	c.(2449-2451)Aag>Gag	p.K817E	RP11-69H7.3_ENST00000563568.1_RNA|C15orf39_ENST00000567617.1_Missense_Mutation_p.K817E|C15orf39_ENST00000394987.4_Missense_Mutation_p.K817E			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	817						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						GCTGCTGGCCAAGCTGCTGTC	0.667																																					p.K817E		.											.	C15orf39-90	0			c.A2449G						.						22	18	19					15																	75500838		2188	4288	6476	SO:0001583	missense	56905	exon2			CTGGCCAAGCTGC	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 38~Name Same As HGNC:28782"				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.2449A>G	15.37:g.75500838A>G	ENSP00000353854:p.Lys817Glu	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	42	7	NM_015492	0	0	3	3	0	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	A	7.085	0.571051	0.13623	.	.	ENSG00000167173	ENST00000360639;ENST00000394987;ENST00000446981	T;T	0.16324	2.35;2.35	5.07	1.05	0.20165	.	0.591269	0.18433	N	0.141368	T	0.12178	0.0296	L	0.45581	1.43	0.09310	N	0.999999	B;P	0.37370	0.234;0.592	B;B	0.34652	0.14;0.187	T	0.14062	-1.0486	10	0.46703	T	0.11	-8.4875	4.778	0.13189	0.5116:0.3589:0.1295:0.0	.	379;817	Q2VPA3;Q6ZRI6	.;CO039_HUMAN	E	817;817;215	ENSP00000353854:K817E;ENSP00000378438:K817E	ENSP00000353854:K817E	K	+	1	0	C15orf39	73287891	0.993000	0.37304	0.863000	0.33907	0.025000	0.11179	2.862000	0.48388	0.735000	0.32537	0.459000	0.35465	AAG	.		0.667	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		G	75500838	A	G	75500838	3	3	156	1	0	0	0	0	1	0	0	0	1797	131	5	3	2451	3	C15orf39	15	75500838	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	5947275	75500838	27030554	80	14119											
UBE2I	7329	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	1370453	1370453	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacagatcctattaggaatAcaggaacttctaaatgaacc	16	9	7	9	0	1	2	0	1	1	1	2	4	2	4	2	2	3	1	2	2	8	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:1370453A>G	ENST00000355803.4	+	6	899	c.348A>G	c.(346-348)atA>atG	p.I116M	UBE2I_ENST00000397515.2_Missense_Mutation_p.I116M|LA16c-358B7.3_ENST00000567829.1_RNA|UBE2I_ENST00000397514.3_Missense_Mutation_p.I116M|UBE2I_ENST00000402301.1_Missense_Mutation_p.I116M|UBE2I_ENST00000403747.2_Missense_Mutation_p.I116M|LA16c-358B7.3_ENST00000568106.1_RNA|UBE2I_ENST00000566587.1_Missense_Mutation_p.I116M|UBE2I_ENST00000325437.5_Missense_Mutation_p.I116M|UBE2I_ENST00000406620.1_Missense_Mutation_p.I116M	NM_194260.2	NP_919236.1	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	116					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	5		Hepatocellular(780;0.00369)				TATTAGGAATACAGGAACTTC	0.512																																					p.I116M		.											.	UBE2I-290	0			c.A348G						.						96	95	95					16																	1370453		2199	4300	6499	SO:0001583	missense	7329	exon6			AGGAATACAGGAA	D45050	CCDS10433.1	16p13.3	2011-05-19	2011-05-19		ENSG00000103275	ENSG00000103275	6.3.2.19	"Ubiquitin-conjugating enzymes E2"	12485	protein-coding gene	gene with protein product		601661	"ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)", "ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)"			8565643	Standard	NM_003345		Approved	UBC9	uc002cld.2	P63279	OTTHUMG00000047845	ENST00000355803.4:c.348A>G	16.37:g.1370453A>G	ENSP00000348056:p.Ile116Met	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	36	5	NM_003345	0	0	92	111	19	D3DU69|P50550|Q15698|Q59GX1|Q86VB3	Missense_Mutation	SNP	ENST00000355803.4	37	CCDS10433.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254235	0.59212	.	.	ENSG00000103275	ENST00000325437;ENST00000355803;ENST00000397514;ENST00000397515;ENST00000406620;ENST00000403747;ENST00000402301	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.13	2.85	0.33270	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	H	0.96805	3.885	0.80722	D	1	P;B	0.49961	0.93;0.326	P;B	0.47827	0.558;0.342	T	0.67856	-0.5562	10	0.87932	D	0	.	6.5449	0.22400	0.686:0.1604:0.0:0.1536	.	116;116	B0QYN7;P63279	.;UBC9_HUMAN	M	116	ENSP00000324897:I116M;ENSP00000348056:I116M;ENSP00000380649:I116M;ENSP00000380650:I116M;ENSP00000384568:I116M;ENSP00000385009:I116M;ENSP00000384361:I116M	ENSP00000324897:I116M	I	+	3	3	UBE2I	1310454	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.052000	0.30429	0.406000	0.25560	0.459000	0.35465	ATA	.		0.512	UBE2I-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250317.2	NM_003345		G	1370453	A	G	1370453	3	3	156	1	0	0	0	0	1	0	0	0	16892	381	14	3	366	3	UBE2I	16	1370453	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10		1370453	88984300	81	14120											
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3817823	3817823	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcacttcaggtttcttttCatccacttccattggttctg	5	20	5	11	0	5	0	3	0	2	0	7	0	7	0	2	2	0	2	2	2	0	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:3817823C>A	ENST00000262367.5	-	16	3957	c.3148G>T	c.(3148-3150)Gaa>Taa	p.E1050*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.E1012*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1050					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GGTTTCTTTTCATCCACTTCC	0.433			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.E1050X		.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP-1807	0			c.G3148T						.						250	223	232					16																	3817823		2197	4300	6497	SO:0001587	stop_gained	1387	exon16			TCTTTTCATCCAC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3148G>T	16.37:g.3817823C>A	ENSP00000262367:p.Glu1050*	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	110	30	NM_004380	0	0	1	2	1	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	C	49	15.549454	0.99837	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.61	5.61	0.85477	.	0.069937	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-12.7639	20.0086	0.97443	0.0:1.0:0.0:0.0	.	.	.	.	X	1050;1080;1012	.	ENSP00000262367:E1050X	E	-	1	0	CREBBP	3757824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.451000	0.66632	2.808000	0.96608	0.655000	0.94253	GAA	.		0.433	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3817823	C	A	3817823	4	1	156	1	0	0	0	0	0	1	0	0	3867	835	29	4	4244	4	CREBBP	16	3817823	Nonsense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	2447370	3817823	86536930	82	14121											
SRCAP	10847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	30744761	30744761	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggatctactagagttgaAcagagacaggtaacccaggt	14	8	12	7	0	1	3	0	1	1	2	1	6	1	4	1	3	3	2	1	3	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:30744761A>G	ENST00000262518.4	+	28	6673	c.6288A>G	c.(6286-6288)gaA>gaG	p.E2096E	SRCAP_ENST00000395059.2_Silent_p.E2034E|SRCAP_ENST00000344771.4_Silent_p.E1938E	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2096	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CTAGAGTTGAACAGAGACAGG	0.527																																					p.E2096E		.											.	SRCAP-94	0			c.A6288G						.						82	72	75					16																	30744761		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon28			AGTTGAACAGAGA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"Swi2/Snf2-related ATPase homolog (S. cerevisiae)", "domino homolog 1 (Drosophila)"	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.6288A>G	16.37:g.30744761A>G		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	100	25	NM_006662	0	0	0	0	0	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																			.		0.527	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30744761	A	G	30744761	2	3	156	1	0	0	0	0	0	0	0	1	15167	40	2	3		3	SRCAP	16	30744761	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	26926938	30744761	59609992	83	14122											
CDH8	1006	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	61823266	61823266	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttactaatttcagtagcaatGattgttatgttgtgccatac	11	17	7	6	0	1	1	1	1	0	0	1	1	1	1	1	0	4	4	1	0	6	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:61823266G>C	ENST00000577390.1	-	8	2352	c.1398C>G	c.(1396-1398)atC>atG	p.I466M	CDH8_ENST00000299345.6_Missense_Mutation_p.I466M|CDH8_ENST00000584337.1_Missense_Mutation_p.I466M|CDH8_ENST00000577730.1_Missense_Mutation_p.I466M	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	466	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CAGTAGCAATGATTGTTATGT	0.403																																					p.I466M		.											.	CDH8-161	0			c.C1398G						.						234	196	209					16																	61823266		2203	4300	6503	SO:0001583	missense	1006	exon8			AGCAATGATTGTT	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"Cadherins / Major cadherins"	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1398C>G	16.37:g.61823266G>C	ENSP00000462701:p.Ile466Met	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	157	11	NM_001796	0	0	0	0	0	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012887	0.35511	.	.	ENSG00000150394	ENST00000299345	T	0.68025	-0.3	5.44	5.44	0.79542	Cadherin (4);Cadherin-like (1);	0.056358	0.64402	D	0.000001	T	0.70404	0.3220	M	0.77486	2.375	0.36180	D	0.849374	B;B	0.26845	0.001;0.161	B;B	0.39152	0.01;0.292	T	0.76454	-0.2953	10	0.87932	D	0	.	7.413	0.27027	0.2018:0.0:0.7982:0.0	.	282;466	Q3LID3;P55286	.;CADH8_HUMAN	M	466	ENSP00000299345:I466M	ENSP00000299345:I466M	I	-	3	3	CDH8	60380767	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.084000	0.41625	2.716000	0.92895	0.491000	0.48974	ATC	.		0.403	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61823266	G	C	61823266	3	2	156	1	0	0	0	0	1	0	0	0	3122	1280	45	4	1021	4	CDH8	16	61823266	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	31078505	61823266	28531487	84	14123											
PKD1L2	114780	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	81197248	81197248	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaggtatgagttgaccaCtagggctggtcacacggagg	10	8	14	9	1	2	2	2	2	0	0	2	3	2	3	1	5	0	3	1	5	2	3	rs200120814		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:81197248C>T	ENST00000525539.1	-	0	3433				PKD1L2_ENST00000533478.1_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GAGTTGACCACTAGGGCTGGT	0.532																																					.													.	PKD1L2-92	0			.						.	C	ASN/SER	0,3888		0,0,1944	52	49	50		3434	2.1	0.5	16		50	2,8290		0,2,4144	yes	missense	PKD1L2	NM_052892.3	46	0,2,6088	TT,TC,CC		0.0241,0.0,0.0164	benign	1145/2460	81197248	2,12178	1944	4146	6090			114780	.			TGACCACTAGGGC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81197248C>T		Somatic	98	0		WXS	Illumina HiSeq	Phase_I	105	26	.	0	0	0	0	0	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37																																																																																				.		0.532	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			T	81197248	C	T	81197248	1	4	156	0	1	0	0	0	0	0	0	0	11991	565	20	2		2	PKD1L2	16	81197248	RNA	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	19373982	81197248	9157505	85	14124											
SPIRE2	84501	broad.mit.edu;bcgsc.ca	37	chr16	89924825	89924826	+	Frame_Shift_Del	DEL	AG	AG	-																															tgcatcaacctgtcagtcacAgatgctgggggcagcgccca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:89924825_89924826delAG	ENST00000378247.3	+	8	1225_1226	c.1182_1183delAG	c.(1180-1185)acagatfs	p.D395fs	SPIRE2_ENST00000393062.2_Frame_Shift_Del_p.D395fs	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	395					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TGTCAGTCACAGATGCTGGGGG	0.629																																					p.394_395del													.	SPIRE2-90	0			c.1182_1183del						.																																			SO:0001589	frameshift_variant	84501	exon8			AGTCACAGATGCT	AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"spire homolog 2 (Drosophila)", "spire family actin nucleation factor 2"			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.1182_1183delAG	16.37:g.89924825_89924826delAG	ENSP00000367494:p.Asp395fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	102	12	NM_032451	0	0	0	0	0	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Frame_Shift_Del	DEL	ENST00000378247.3	37	CCDS32516.1																																																																																			.		0.629	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		-	89924826	AG	-	89924825	7	5	156	1	0	1	0	1	0	0	0	0	15104	175	7	0	1212	0	SPIRE2	16	89924825	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	8727577	89924825	429928	86	14125											
RPH3AL	9501	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	131631	131631	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggggaggcctcgatcccacaTttggtgcagactttctacaa	9	10	11	11	1	1	1	0	0	1	1	3	3	2	2	2	4	2	1	2	4	2	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:131631T>A	ENST00000331302.7	-	6	673	c.366A>T	c.(364-366)aaA>aaT	p.K122N	RPH3AL_ENST00000576001.1_5'UTR|RPH3AL_ENST00000323434.8_Intron|RPH3AL_ENST00000536489.2_Intron	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	122	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CGATCCCACATTTGGTGCAGA	0.587																																					p.K122N		.											.	RPH3AL-91	0			c.A366T						.						81	81	81					17																	131631		2203	4300	6503	SO:0001583	missense	9501	exon6			CCCACATTTGGTG		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"Synaptotagmins"	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.366A>T	17.37:g.131631T>A	ENSP00000328977:p.Lys122Asn	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	231	46	NM_006987	0	0	0	0	0	D3DTG7|Q9BSB3	Missense_Mutation	SNP	ENST00000331302.7	37	CCDS10994.1	.	.	.	.	.	.	.	.	.	.	T	15.21	2.767130	0.49574	.	.	ENSG00000181031	ENST00000323434	.	.	.	5.02	-8.63	0.00878	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	D	0.000008	T	0.71426	0.3338	M	0.70903	2.155	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.82818	-0.0269	9	0.87932	D	0	-14.7906	16.2241	0.82283	0.0:0.5791:0.0:0.4208	.	122	Q9UNE2	RPH3L_HUMAN	N	122	.	ENSP00000319210:K122N	K	-	3	2	RPH3AL	131631	0.328000	0.24687	0.618000	0.29105	0.943000	0.58893	-0.811000	0.04500	-2.189000	0.00758	-1.660000	0.00751	AAA	.		0.587	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987		A	131631	T	A	131631	3	1	156	1	0	0	0	0	1	0	0	0	13584	1490	52	5	601	5	RPH3AL	17	131631	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10		131631	81063579	87	14126											
TRPV3	162514	broad.mit.edu	37	chr17	3438998	3438998	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcgatggcgatgttcagcGccgtctgccctgcggagcgg	4	8	16	13	6	2	0	1	0	1	0	3	3	2	1	2	3	4	2	2	3	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:3438998G>T	ENST00000576742.1	-	7	974	c.653C>A	c.(652-654)gCg>gAg	p.A218E	TRPV3_ENST00000301365.4_Missense_Mutation_p.A218E|TRPV3_ENST00000572519.1_Missense_Mutation_p.A218E	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	218					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GATGTTCAGCGCCGTCTGCCC	0.736																																					p.A218E													.	TRPV3-94	0			c.C653A						.						8	9	9					17																	3438998		2163	4231	6394	SO:0001583	missense	162514	exon7			TTCAGCGCCGTCT	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.653C>A	17.37:g.3438998G>T	ENSP00000461518:p.Ala218Glu	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	80	7	NM_001258205	0	0	0	0	0	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	G	36	5.688246	0.96784	.	.	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	T	0.71341	-0.56	5.03	5.03	0.67393	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	D	0.89491	0.6730	H	0.96111	3.77	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;0.999;0.997;0.999;1.0;1.0;0.997	D;D;D;D;D;D;P	0.91635	0.979;0.993;0.933;0.993;0.999;0.999;0.89	D	0.92506	0.6012	10	0.87932	D	0	-11.7793	18.2979	0.90153	0.0:0.0:1.0:0.0	.	202;202;218;202;218;218;218	E7EV24;B7ZKP9;Q2M3L1;B7ZKP6;Q8NET8-3;Q8NET8;Q8NET8-2	.;.;.;.;.;TRPV3_HUMAN;.	E	218;218;202	ENSP00000301365:A218E	ENSP00000301365:A218E	A	-	2	0	TRPV3	3385748	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.422000	0.97458	2.741000	0.93983	0.555000	0.69702	GCG	.		0.736	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		T	3438998	G	T	3438998	3	4	156	1	0	0	0	0	1	0	0	0	16630	1087	38	4	1767	4	TRPV3	17	3438998	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	3307367	3438998	77756212	88	14127											
RPL26	6154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	8283223	8283223	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacctggactactttgccaAtttgctgacctttatagtgt	10	15	7	9	0	0	1	0	1	0	0	0	2	0	2	3	1	4	1	3	1	5	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:8283223A>C	ENST00000584164.1	-	3	591	c.200T>G	c.(199-201)aTt>aGt	p.I67S	RPL26_ENST00000583011.1_Missense_Mutation_p.I67S|RP11-849F2.5_ENST00000579904.1_RNA|RPL26_ENST00000578812.1_Missense_Mutation_p.I67S|RPL26_ENST00000585176.1_5'UTR|RPL26_ENST00000293842.5_Missense_Mutation_p.I67S|RP11-849F2.5_ENST00000585181.1_RNA|RPL26_ENST00000582556.1_Missense_Mutation_p.I67S|RP11-849F2.7_ENST00000582471.1_Missense_Mutation_p.I67S			P61254	RL26_HUMAN	ribosomal protein L26	67					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			skin(1)|urinary_tract(1)	2						TACTTTGCCAATTTGCTGACC	0.373																																					p.I67S		.											.	RPL26-227	0			c.T200G						.						51	51	51					17																	8283223		2203	4300	6503	SO:0001583	missense	6154	exon3			TTGCCAATTTGCT		CCDS11142.1	17p13	2011-04-06			ENSG00000161970	ENSG00000161970		"L ribosomal proteins"	10327	protein-coding gene	gene with protein product		603704				8479925	Standard	XM_005256749		Approved	L26	uc002glh.1	P61254	OTTHUMG00000108191	ENST00000584164.1:c.200T>G	17.37:g.8283223A>C	ENSP00000463784:p.Ile67Ser	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	117	14	NM_000987	1	0	3518	3788	269	B2R4F0|D3DTR8|Q02877|Q6IPY2	Missense_Mutation	SNP	ENST00000584164.1	37	CCDS11142.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.367500	0.42003	.	.	ENSG00000161970	ENST00000293842	.	.	.	4.7	4.7	0.59300	KOW (2);Translation protein SH3-like (1);Ribosomal protein L24/L26, conserved site (1);Ribosomal protein L24, SH3-like (1);	0.000000	0.85682	D	0.000000	T	0.44582	0.1300	N	0.22421	0.69	0.58432	D	0.999995	B	0.13145	0.007	B	0.25506	0.061	T	0.36016	-0.9765	9	0.37606	T	0.19	-1.2756	12.4268	0.55551	1.0:0.0:0.0:0.0	.	67	P61254	RL26_HUMAN	S	67	.	ENSP00000293842:I67S	I	-	2	0	RPL26	8223948	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.239000	0.95389	1.871000	0.54225	0.523000	0.50628	ATT	.		0.373	RPL26-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442322.1	NM_000987		C	8283223	A	C	8283223	3	2	156	1	0	0	0	0	1	0	0	0	13605	101	4	5	245	5	RPL26	17	8283223	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	4844225	8283223	72911987	89	14128											
CCDC45	90799	bcgsc.ca	37	chr17	62528114	62528114	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagtctaagaggtggccTcccaaagccaaataaagcag	15	5	11	10	0	1	2	0	0	1	2	2	2	2	2	3	2	2	2	3	2	5	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:62528114T>C	ENST00000556440.2	+	14	2156	c.1646T>C	c.(1645-1647)cTc>cCc	p.L549P	CEP95_ENST00000553412.1_Missense_Mutation_p.L385P|AC009994.2_ENST00000579926.1_RNA	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	549						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						AGAGGTGGCCTCCCAAAGCCA	0.428																																					p.L549P													.	CEP95-23	0			c.T1646C						.						79	75	76					17																	62528114		1871	4096	5967	SO:0001583	missense	90799	exon14			GTGGCCTCCCAAA	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.1646T>C	17.37:g.62528114T>C	ENSP00000450461:p.Leu549Pro	Somatic	77	0		WXS	Illumina HiSeq	Phase_1	63	4	NM_138363	0	0	16	16	0	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	37	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.363258	0.41902	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.34472	1.36;1.36	5.97	4.89	0.63831	.	0.942091	0.09055	N	0.855130	T	0.43809	0.1264	L	0.54323	1.7	0.28087	N	0.93197	D	0.56035	0.974	P	0.51135	0.66	T	0.20638	-1.0269	10	0.35671	T	0.21	0.0229	8.2179	0.31524	0.0:0.0693:0.1338:0.7969	.	549	Q96GE4	CEP95_HUMAN	P	484;549;385	ENSP00000450461:L549P;ENSP00000450906:L385P	ENSP00000438458:L484P	L	+	2	0	CEP95	59958576	0.101000	0.21875	0.994000	0.49952	0.384000	0.30261	0.957000	0.29215	1.048000	0.40298	0.533000	0.62120	CTC	.		0.428	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		C	62528114	T	C	62528114	3	2	156	1	0	0	0	0	1	0	0	0	2822	1551	54	3	1700	3	CCDC45	17	62528114	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	54244891	62528114	18667096	90	14129											
C17orf80	55028	broad.mit.edu	37	chr17	71232036	71232037	+	Frame_Shift_Del	DEL	CA	CA	-																															tccaagaagaaaccaaggctCagttttacgcatcagagaaa																								rs373362252|rs555089459		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:71232036_71232037delCA	ENST00000535032.2	+	2	528_529	c.415_416delCA	c.(415-417)cagfs	p.Q139fs	FAM104A_ENST00000583178.1_Intron|C17orf80_ENST00000426147.2_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000582793.1_Intron|C17orf80_ENST00000359042.2_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000577615.1_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000268942.8_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000255557.4_Frame_Shift_Del_p.Q139fs			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	139						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			AACCAAGGCTCAGTTTTACGCA	0.381																																					p.139_139del													.	C17orf80-91	0			c.415_416del						.																																			SO:0001589	frameshift_variant	55028	exon3			AAGGCTCAGTTTT	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"sperm-expressed protein 1", "migration-inducing protein 3"					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.415_416delCA	17.37:g.71232036_71232037delCA	ENSP00000440551:p.Gln139fs	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	197	12	NM_001100621	0	0	0	0	0	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Frame_Shift_Del	DEL	ENST00000535032.2	37	CCDS11694.1																																																																																			.		0.381	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941		-	71232037	CA	-	71232036	7	5	156	1	0	1	0	1	0	0	0	0	1890	827	29	0	417	0	C17orf80	17	71232036	Frame_Shift_Del	DEL	CA	TCGA-P4-A5EA-01A-11D-A28G-10	8703922	71232036	9963174	91	14130											
GGA3	23163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	73239164	73239164	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttggacttctcctcatcatCaaaaacagggtttttgggac	10	13	8	10	0	4	0	3	0	1	0	5	2	4	2	1	3	1	1	1	3	2	4	rs35542883		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:73239164C>G	ENST00000245541.6	-	6	724	c.508G>C	c.(508-510)Gat>Cat	p.D170H	GGA3_ENST00000351904.7_Missense_Mutation_p.D137H|GGA3_ENST00000538886.1_Missense_Mutation_p.D48H|GGA3_ENST00000537686.1_Intron|GGA3_ENST00000582717.1_Missense_Mutation_p.D98H|GGA3_ENST00000582486.1_Missense_Mutation_p.D98H|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000578348.1_Missense_Mutation_p.D48H	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	170	Binds to ARF1 (in long isoform).				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			TCCTCATCATCAAAAACAGGG	0.547																																					p.D170H		.											.	GGA3-154	0			c.G508C						.						161	149	153					17																	73239164		2203	4300	6503	SO:0001583	missense	23163	exon6			CATCATCAAAAAC	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.508G>C	17.37:g.73239164C>G	ENSP00000245541:p.Asp170His	Somatic	240	0		WXS	Illumina HiSeq	Phase_I	284	77	NM_138619	0	0	0	0	0	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879725	0.51801	.	.	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	T;T	0.52983	2.01;0.64	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.67449	0.2894	M	0.67397	2.05	0.80722	D	1	D;P;D	0.89917	1.0;0.522;1.0	D;P;D	0.72982	0.972;0.729;0.979	T	0.69465	-0.5138	10	0.54805	T	0.06	-21.0362	18.153	0.89682	0.0:1.0:0.0:0.0	.	48;137;170	B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;GGA3_HUMAN	H	170;137;98;48	ENSP00000245541:D170H;ENSP00000326575:D137H	ENSP00000245541:D170H	D	-	1	0	GGA3	70750759	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.646000	0.83445	2.505000	0.84491	0.563000	0.77884	GAT	.		0.547	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619		G	73239164	C	G	73239164	3	3	156	1	0	0	0	0	1	0	0	0	6374	826	29	4	1799	4	GGA3	17	73239164	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	2007128	73239164	7956046	92	14131											
UTS2R	2837	broad.mit.edu	37	chr17	80333066	80333066	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaccaccaggccccgctggCgccgcggacggcgcgcatcg	5	3	15	18	8	0	0	0	0	0	0	1	1	0	1	5	4	1	3	5	4	1	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:80333066C>A	ENST00000313135.2	+	1	914	c.866C>A	c.(865-867)gCg>gAg	p.A289E		NM_018949.1	NP_061822.1	Q9UKP6	UR2R_HUMAN	urotensin 2 receptor	289					blood circulation (GO:0008015)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell growth (GO:0030307)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of vasoconstriction (GO:0045907)|regulation of vasodilation (GO:0042312)|response to drug (GO:0042493)|signal transduction (GO:0007165)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|urotensin II receptor activity (GO:0001604)			breast(1)|endometrium(4)|kidney(1)|lung(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			GCCCCGCTGGCGCCGCGGACG	0.672																																					p.A289E													.	UTS2R-153	0			c.C866A						.																																			SO:0001583	missense	2837	exon1			CGCTGGCGCCGCG	AF140631	CCDS11810.1	17q25.3	2013-04-30	2004-07-13	2004-07-13		ENSG00000181408			4468	protein-coding gene	gene with protein product		600896	"G protein-coupled receptor 14"	GPR14		8666380, 10499587	Standard	NM_018949		Approved		uc010wvl.2	Q9UKP6		ENST00000313135.2:c.866C>A	17.37:g.80333066C>A	ENSP00000323516:p.Ala289Glu	Somatic	50	2		WXS	Illumina HiSeq	Phase_I	102	13	NM_018949	0	0	0	0	0	B2RMV8	Missense_Mutation	SNP	ENST00000313135.2	37	CCDS11810.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.313287	0.40996	.	.	ENSG00000181408	ENST00000313135	T	0.72051	-0.62	4.95	1.39	0.22231	GPCR, rhodopsin-like superfamily (1);	0.338048	0.28257	U	0.016009	T	0.61375	0.2342	N	0.17723	0.515	0.09310	N	1	P	0.42973	0.796	P	0.50791	0.65	T	0.55711	-0.8098	10	0.07644	T	0.81	.	14.9821	0.71319	0.0:0.5448:0.4552:0.0	.	289	Q9UKP6	UR2R_HUMAN	E	289	ENSP00000323516:A289E	ENSP00000323516:A289E	A	+	2	0	UTS2R	77926355	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	0.380000	0.20602	0.518000	0.28383	0.637000	0.83480	GCG	.		0.672	UTS2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443506.1	NM_018949		A	80333066	C	A	80333066	3	1	156	1	0	0	0	0	1	0	0	0	17139	768	27	4	868	4	UTS2R	17	80333066	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	7093902	80333066	862144	93	14132											
RNMT	8731	ucsc.edu	37	chr18	13746266	13746266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtctacaaaaaaacatttcTggaattctacgaagaaaaga	20	9	6	6	1	3	2	0	0	3	2	3	4	3	3	0	1	3	0	0	1	9	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr18:13746266T>C	ENST00000383314.2	+	9	1427	c.1187T>C	c.(1186-1188)cTg>cCg	p.L396P	RNMT_ENST00000262173.3_Missense_Mutation_p.L396P|RNMT_ENST00000543302.2_Missense_Mutation_p.L396P|RNMT_ENST00000535051.1_Missense_Mutation_p.L154P|RNMT_ENST00000592764.1_Missense_Mutation_p.L396P|RNMT_ENST00000589866.1_Missense_Mutation_p.L396P			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	396	mRNA cap 0 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00895}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						AAAACATTTCTGGAATTCTAC	0.308																																					p.L396P	GBM(29;474 594 19092 36647 41529)												.	RNMT-90	0			c.T1187C						.						65	70	69					18																	13746266		2203	4300	6503	SO:0001583	missense	8731	exon9			CATTTCTGGAATT	AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.1187T>C	18.37:g.13746266T>C	ENSP00000372804:p.Leu396Pro	Somatic	321	0		WXS	Illumina HiSeq		274	1	NM_003799	0	0	0	0	0	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Missense_Mutation	SNP	ENST00000383314.2	37	CCDS11867.1	.	.	.	.	.	.	.	.	.	.	T	8.940	0.965691	0.18583	.	.	ENSG00000101654	ENST00000383314;ENST00000535051;ENST00000543302;ENST00000262173	.	.	.	5.55	3.11	0.35812	.	0.418121	0.25935	N	0.027358	T	0.39682	0.1087	N	0.16307	0.4	0.48830	D	0.999714	B;B	0.26876	0.134;0.162	B;B	0.31495	0.108;0.131	T	0.09422	-1.0675	9	0.27082	T	0.32	-28.1696	9.4478	0.38708	0.1136:0.0:0.4992:0.3872	.	396;396	O43148-2;O43148	.;MCES_HUMAN	P	396;154;396;396	.	ENSP00000262173:L396P	L	+	2	0	RNMT	13736266	0.510000	0.26171	1.000000	0.80357	0.841000	0.47740	0.549000	0.23329	0.376000	0.24707	-0.680000	0.03767	CTG	.		0.308	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799		C	13746266	T	C	13746266	3	2	156	1	0	0	0	0	1	0	0	0	13538	1580	55	3	1213	3	RNMT	18	13746266	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10		13746266	64330982	94	14133											
CTAGE1	64693	broad.mit.edu	37	chr18	19995948	19995948	+	5'Flank	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaaggcatattaaaacttctGagttctgctggtccagagag	12	11	11	7	0	2	2	0	1	2	1	3	4	3	2	1	2	2	3	1	2	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr18:19995948G>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Silent_p.L609L			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					TAAAACTTCTGAGTTCTGCTG	0.388																																					p.L609L													.	CTAGE1-1	0			c.C1827G						.						89	97	94					18																	19995948		2190	4291	6481	SO:0001631	upstream_gene_variant	64693	exon1			ACTTCTGAGTTCT	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma-associated antigen 1", "cutaneous T-cell lymphoma-associated antigen 2", "cancer/testis antigen family 21, member 1", "cancer/testis antigen family 21, member 2"	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19995948G>C	Exception_encountered	Somatic	156	1		WXS	Illumina HiSeq	Phase_I	120	11	NM_172241	0	0	13	13	0	B0YIZ3	Silent	SNP	ENST00000525417.1	37																																																																																				.		0.388	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241		C	19995948	G	C	19995948	1	2	156	0	1	0	0	0	0	0	0	0	3998	1277	45	4		4	CTAGE1	18	19995948	5'Flank	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	6249682	19995948	58081300	95	14134											
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1003374	1003374	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcctggccccgatggcggcGccagtggggggtgaagcacc	5	4	18	14	4	0	1	0	1	0	0	0	2	0	1	5	6	1	1	5	6	1	0	rs34585248	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:1003374G>A	ENST00000234389.3	+	2	691	c.672G>A	c.(670-672)gcG>gcA	p.A224A	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	224					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CGATGGCGGCGCCAGTGGGGG	0.746													g|||	158	0.0315495	0.0015	0.0173	5008	,	,		11320	0.0754		0.0338	False		,,,				2504	0.0348				p.A224A		.											.	GRIN3B-90	0			c.G672A						.	G		37,3905		0,37,1934	4	6	5		672	-8.1	0	19	dbSNP_126	5	211,7611		3,205,3703	no	coding-synonymous	GRIN3B	NM_138690.1		3,242,5637	AA,AG,GG		2.6975,0.9386,2.1081		224/1044	1003374	248,11516	1971	3911	5882	SO:0001819	synonymous_variant	116444	exon2			GGCGGCGCCAGTG		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.672G>A	19.37:g.1003374G>A		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	60	36	NM_138690	0	0	0	0	0	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			G|0.966;A|0.034		0.746	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			A	1003374	G	A	1003374	2	1	156	1	0	0	0	0	0	0	0	1	6805	1074	38	1		1	GRIN3B	19	1003374	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		1003374	58125609	96	14135											
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9058716	9058716	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caggggtcagagatgacattGactctatctcaatccttgta	11	12	9	9	0	3	3	2	2	2	1	5	4	4	3	1	2	0	1	1	2	3	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:9058716G>C	ENST00000397910.4	-	3	28933	c.28730C>G	c.(28729-28731)tCa>tGa	p.S9577*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9579	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGATGACATTGACTCTATCTC	0.488																																					p.S9577X		.											.	MUC16-566	0			c.C28730G						.						90	84	86					19																	9058716		2003	4163	6166	SO:0001587	stop_gained	94025	exon3			GACATTGACTCTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28730C>G	19.37:g.9058716G>C	ENSP00000381008:p.Ser9577*	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	155	31	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	60	44.522612	0.99986	.	.	ENSG00000181143	ENST00000397910	.	.	.	2.5	1.41	0.22369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.6673	0.23047	0.0:0.0:0.7208:0.2792	.	.	.	.	X	9577	.	ENSP00000381008:S9577X	S	-	2	0	MUC16	8919716	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.009000	0.12765	0.597000	0.29811	0.305000	0.20034	TCA	.		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9058716	G	C	9058716	4	2	156	1	0	0	0	0	0	1	0	0	9998	1294	45	4	15121	4	MUC16	19	9058716	Nonsense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	8055342	9058716	50070267	97	14136											
KIAA0892	23383	hgsc.bcm.edu	37	chr19	19431690	19431704	+	In_Frame_Del	DEL	GCGGCCCAGGCGGCG	GCGGCCCAGGCGGCG	-																															tggcggctcaggcggcggcaGcggcccaggcggcggcggcc																								rs553682593|rs375425486|rs550594758	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	GCGGCCCAGGCGGCG	GCGGCCCAGGCGGCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:19431690_19431704delGCGGCCCAGGCGGCG	ENST00000392313.6	+	1	201_215	c.22_36delGCGGCCCAGGCGGCG	c.(22-36)gcggcccaggcggcgdel	p.AAQAA13del	SUGP1_ENST00000334782.5_5'Flank|SUGP1_ENST00000247001.5_5'Flank|SUGP1_ENST00000585763.1_5'Flank|MAU2_ENST00000262815.8_In_Frame_Del_p.AAQAA13del	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	13	Ala-rich.|Sufficient for interaction with NIPBL.				maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						ggcggcggcagcggcccaggcggcggcggcccagg	0.735																																					p.8_12del		.											.	MAU2-91	0			c.22_36del						.			89,1901		39,11,945						-8.2	0.6			3	148,4936		53,42,2447	no	coding	MAU2	NM_015329.3		92,53,3392	A1A1,A1R,RR		2.9111,4.4724,3.3503				237,6837				SO:0001651	inframe_deletion	23383	exon1			.	AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"sister chromatid cohesion 4"	614560	"KIAA0892", "MAU2 chromatid cohesion factor homolog (C. elegans)"	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.22_36delGCGGCCCAGGCGGCG	19.37:g.19431690_19431704delGCGGCCCAGGCGGCG	ENSP00000376127:p.Ala13_Ala17del	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	40	28	NM_015329	0	0	0	0	0	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	In_Frame_Del	DEL	ENST00000392313.6	37	CCDS32969.2																																																																																			.		0.735	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6	NM_015329		-	19431704	GCGGCCCAGGCGGCG	-	19431690	7	5	156	1	0	1	0	1	0	0	0	0	8217	971	34	0	24	0	KIAA0892	19	19431690	In_Frame_Del	DEL	GCGGCCCAGGCGGCG	TCGA-P4-A5EA-01A-11D-A28G-10	10372974	19431690	39697293	98	14137											
ZNF257	113835	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	22271296	22271296	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcacaccttactcaacataaGgtaattcatactagagagaa	17	10	5	9	0	3	2	3	0	0	2	3	3	3	2	1	1	3	1	1	1	7	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:22271296G>A	ENST00000594947.1	+	4	888	c.744G>A	c.(742-744)aaG>aaA	p.K248K		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				CTCAACATAAGGTAATTCATA	0.388																																					p.K248K													.	ZNF257-90	0			c.G744A						.						37	40	39					19																	22271296		2124	4259	6383	SO:0001819	synonymous_variant	113835	exon4			ACATAAGGTAATT	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.744G>A	19.37:g.22271296G>A		Somatic	81	1		WXS	Illumina HiSeq	Phase_I	71	7	NM_033468	0	0	0	0	0	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	37	CCDS46030.1																																																																																			.		0.388	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			A	22271296	G	A	22271296	2	1	156	1	0	0	0	0	0	0	0	1	17832	991	35	2		2	ZNF257	19	22271296	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	2839606	22271296	36857687	99	14138											
PRKCG	5582	broad.mit.edu	37	chr19	54401866	54401866	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cttcctcacccagctccactCcaccttccagaccccggtaa	8	8	4	21	1	1	1	1	0	0	1	5	1	5	1	8	1	1	2	8	1	1	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:54401866C>G	ENST00000263431.3	+	11	1547	c.1265C>G	c.(1264-1266)tCc>tGc	p.S422C	PRKCG_ENST00000542049.1_Missense_Mutation_p.S309C|PRKCG_ENST00000540413.1_Missense_Mutation_p.S422C	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	422	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CAGCTCCACTCCACCTTCCAG	0.657																																					p.S422C													.	PRKCG-1367	0			c.C1265G						.						10	11	10					19																	54401866		2188	4281	6469	SO:0001583	missense	5582	exon11			TCCACTCCACCTT	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"PKC-gamma"	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1265C>G	19.37:g.54401866C>G	ENSP00000263431:p.Ser422Cys	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	89	9	NM_002739	0	0	4	4	0	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861903	0.51482	.	.	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.25749	1.78;1.78;1.78	5.02	2.85	0.33270	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.20088	0.0483	N	0.21448	0.665	0.48040	D	0.999578	B;P;P	0.45531	0.0;0.86;0.732	B;P;P	0.46479	0.003;0.501;0.518	T	0.01863	-1.1258	9	0.34782	T	0.22	.	8.9808	0.35964	0.0:0.7671:0.1491:0.0838	.	309;422;422	B7Z8Q0;F5H5C4;P05129	.;.;KPCG_HUMAN	C	422;422;309	ENSP00000443493:S422C;ENSP00000263431:S422C;ENSP00000438090:S309C	ENSP00000263431:S422C	S	+	2	0	PRKCG	59093678	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	2.711000	0.47177	0.629000	0.30376	-0.291000	0.09656	TCC	.		0.657	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		G	54401866	C	G	54401866	3	3	156	1	0	0	0	0	1	0	0	0	12541	855	30	4	1307	4	PRKCG	19	54401866	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	32130570	54401866	4727117	100	14139											
MBOAT7	79143	broad.mit.edu	37	chr19	54684811	54684811	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccccggggaagggctgcTccagccagtccaggtaggtg	6	6	16	13	1	0	0	0	0	0	0	2	1	2	1	5	5	3	3	5	5	2	1	rs200188828		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:54684811T>C	ENST00000245615.1	-	6	1013	c.533A>G	c.(532-534)gAg>gGg	p.E178G	MBOAT7_ENST00000391754.1_Missense_Mutation_p.E178G|MBOAT7_ENST00000474910.1_5'Flank|MBOAT7_ENST00000338624.6_Missense_Mutation_p.E105G|MBOAT7_ENST00000431666.2_Missense_Mutation_p.E105G	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	178					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GAAGGGCTGCTCCAGCCAGTC	0.721											OREG0003644	type=REGULATORY REGION|Gene=AK123290|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.E178G	NSCLC(97;826 2151 10470 22540)												.	MBOAT7-68	0			c.A533G						.						2	4	3					19																	54684811		1737	3558	5295	SO:0001583	missense	79143	exon6			GGCTGCTCCAGCC	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"lysophosphatidylinositol acyltransferase"	606048	"leukocyte receptor cluster (LRC) member 4"	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.533A>G	19.37:g.54684811T>C	ENSP00000245615:p.Glu178Gly	Somatic	12	0	1002	WXS	Illumina HiSeq	Phase_I	38	9	NM_001146082	0	0	5	5	0	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Missense_Mutation	SNP	ENST00000245615.1	37	CCDS12883.1	.	.	.	.	.	.	.	.	.	.	t	15.07	2.724382	0.48728	.	.	ENSG00000125505	ENST00000431666;ENST00000338624;ENST00000245615;ENST00000391754;ENST00000414665	T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89	4.06	4.06	0.47325	.	0.184664	0.23762	U	0.044815	T	0.65123	0.2661	L	0.46157	1.445	0.31189	N	0.701203	B;B;P	0.39576	0.351;0.302;0.679	B;B;B	0.35039	0.129;0.057;0.194	T	0.70410	-0.4879	10	0.42905	T	0.14	-18.9591	12.37	0.55250	0.0:0.0:0.0:1.0	.	160;105;178	B4DDH8;Q96N66-2;Q96N66	.;.;MBOA7_HUMAN	G	105;105;178;178;178	ENSP00000410503:E105G;ENSP00000344377:E105G;ENSP00000245615:E178G;ENSP00000375634:E178G;ENSP00000388250:E178G	ENSP00000245615:E178G	E	-	2	0	MBOAT7	59376623	0.351000	0.24887	1.000000	0.80357	0.817000	0.46193	0.664000	0.25068	1.646000	0.50622	0.446000	0.29264	GAG	.		0.721	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		C	54684811	T	C	54684811	3	2	156	1	0	0	0	0	1	0	0	0	9383	1551	54	3	901	3	MBOAT7	19	54684811	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	282945	54684811	4444172	101	14140											
SAPS1	22870	broad.mit.edu	37	chr19	55743012	55743012	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtggcttcctgaggtgcTgaggggggtgtggggtcctg	2	12	20	7	0	1	2	0	2	1	0	3	2	3	2	2	7	1	2	2	7	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:55743012T>G	ENST00000412770.2	-	20	2897	c.2331A>C	c.(2329-2331)tcA>tcC	p.S777S	AC010327.1_ENST00000581390.1_RNA|PPP6R1_ENST00000587283.1_Silent_p.S777S|TMEM86B_ENST00000327042.4_5'Flank	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	777	Pro-rich.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						CCTGAGGTGCTGAGGGGGGTG	0.667																																					p.S777S													.	PPP6R1-67	0			c.A2331C						.						24	29	27					19																	55743012		1983	4161	6144	SO:0001819	synonymous_variant	22870	exon20			AGGTGCTGAGGGG	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	29195	protein-coding gene	gene with protein product		610875	"KIAA1115", "SAPS domain family, member 1"	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.2331A>C	19.37:g.55743012T>G		Somatic	60	0		WXS	Illumina HiSeq	Phase_I	68	5	NM_014931	0	0	51	59	8	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Silent	SNP	ENST00000412770.2	37	CCDS46186.1																																																																																			.		0.667	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		G	55743012	T	G	55743012	2	3	156	1	0	0	0	0	0	0	0	1	13868	1567	55	5		5	SAPS1	19	55743012	Silent	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	1058201	55743012	3385971	102	14141											
ZNF814	730051	ucsc.edu	37	chr19	58384712	58384712	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acataaggtctttctccagtAtggccatgctggtgtagaat	10	13	10	8	0	2	1	0	0	2	1	3	1	2	1	2	3	1	3	2	3	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:58384712A>G	ENST00000435989.2	-	3	2280	c.2046T>C	c.(2044-2046)caT>caC	p.H682H	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	682					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTTCTCCAGTATGGCCATGCT	0.408																																					p.H682H													.	.	0			c.T2046C						.						68	57	60					19																	58384712		692	1591	2283	SO:0001819	synonymous_variant	730051	exon3			TCCAGTATGGCCA		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.2046T>C	19.37:g.58384712A>G		Somatic	160	0		WXS	Illumina HiSeq		142	1	NM_001144989	0	0	2	2	0	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.408	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		G	58384712	A	G	58384712	2	3	156	1	0	0	0	0	0	0	0	1	18208	446	16	3		3	ZNF814	19	58384712	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	2641700	58384712	744271	103	14142											
TASP1	55617	broad.mit.edu	37	chr20	13561621	13561621	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggcaaccgagactgggttCttgattcctataaaaaaaaa	15	11	8	7	1	1	2	0	1	1	1	2	3	2	2	2	2	1	2	2	2	7	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr20:13561621C>T	ENST00000337743.4	-	6	531	c.411G>A	c.(409-411)aaG>aaA	p.K137K	TASP1_ENST00000480436.1_5'UTR|TASP1_ENST00000539805.1_Intron	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	137					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						AGACTGGGTTCTTGATTCCta	0.408																																					p.K137K													.	TASP1-90	0			c.G411A						.						78	77	77					20																	13561621		2203	4300	6503	SO:0001819	synonymous_variant	55617	exon6			TGGGTTCTTGATT	AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"chromosome 20 open reading frame 13"	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.411G>A	20.37:g.13561621C>T		Somatic	41	2		WXS	Illumina HiSeq	Phase_I	26	6	NM_017714	0	0	0	0	0	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Silent	SNP	ENST00000337743.4	37	CCDS13116.1																																																																																			.		0.408	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714		T	13561621	C	T	13561621	2	4	156	1	0	0	0	0	0	0	0	1	15621	912	32	2		2	TASP1	20	13561621	Silent	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10		13561621	49463899	104	14143											
C22orf39	128977	broad.mit.edu	37	chr22	19435297	19435299	+	In_Frame_Del	DEL	AGA	AGA	-																															gcacctcgtgatcgactgacAgaagaactaatgagcaccga																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:19435297_19435299delAGA	ENST00000399562.4	-	1	456_458	c.24_26delTCT	c.(22-27)cttctg>ctg	p.8_9LL>L	HIRA_ENST00000541063.1_5'Flank|C22orf39_ENST00000399568.1_5'Flank|AC000068.5_ENST00000431090.1_RNA|HIRA_ENST00000546308.1_5'Flank|C22orf39_ENST00000542103.1_In_Frame_Del_p.8_9LL>L|C22orf39_ENST00000333059.5_5'Flank	NM_173793.4	NP_776154.3	Q6P5X5	CV039_HUMAN	chromosome 22 open reading frame 39	8												Colorectal(54;0.0993)					ATCGACTGACAGAAGAACTAATG	0.591																																					p.8_9del													.	C22orf39-22	0			c.24_26del						.																																			SO:0001651	inframe_deletion	128977	exon1			ACTGACAGAAGAA		CCDS33599.1, CCDS33599.2, CCDS54498.1	22q11.21	2008-10-31			ENSG00000242259	ENSG00000242259			27012	protein-coding gene	gene with protein product							Standard	NM_173793		Approved	MGC74441	uc002zpk.2	Q6P5X5	OTTHUMG00000150137	ENST00000399562.4:c.24_26delTCT	22.37:g.19435300_19435302delAGA	ENSP00000382474:p.Leu9del	Somatic	259	0		WXS	Illumina HiSeq	Phase_I	305	14	NM_173793	0	0	0	0	0	A8MTW6|D3DX18|F5H3A8|J3KNP9	In_Frame_Del	DEL	ENST00000399562.4	37	CCDS33599.2																																																																																			.		0.591	C22orf39-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316494.3	NM_173793		-	19435299	AGA	-	19435297	7	5	156	1	0	1	0	1	0	0	0	0	2153	188	7	0	469	0	C22orf39	22	19435297	In_Frame_Del	DEL	AGA	TCGA-P4-A5EA-01A-11D-A28G-10		19435297	31869269	105	14144											
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	30057329	30057329	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctcgtacagtgacaaggagGtaggacatgtgtgtactgca	11	10	13	7	1	1	1	0	1	1	0	2	3	1	3	0	3	3	4	0	3	4	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:30057329G>A	ENST00000338641.4	+	8	1251		c.e8+1		NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000413209.2_Intron|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000347330.5_Splice_Site|NF2_ENST00000361166.4_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						TGACAAGGAGGTAGGACATGT	0.532			"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.810+1G>A						.						117	108	111					22																	30057329		2203	4300	6503	SO:0001630	splice_region_variant	4771	exon8	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	AAGGAGGTAGGAC	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.810+1G>A	22.37:g.30057329G>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	42	14	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	33	5.287845	0.95517	.	.	ENSG00000186575	ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0795	0.97766	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28387329	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.864000	0.99589	2.747000	0.94245	0.650000	0.86243	.	.		0.532	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	A	30057329	G	A	30057329	5	1	156	1	0	0	0	0	0	0	1	0	10383	1275	44	2	841	2	NF2	22	30057329	Splice_Site	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	10622032	30057329	21247237	106	14145											
TOM1	10043	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	35723290	35723291	+	Missense_Mutation	DNP	GA	GA	TC																															aagctgcgcagtgagctggaGatggtgagtgggaacgtgag																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:35723290_35723291GA>TC	ENST00000449058.2	+	7	800_801	c.675_676GA>TC	c.(673-678)gaGAtg>gaTCtg	p.225_226EM>DL	TOM1_ENST00000436462.2_Missense_Mutation_p.187_188EM>DL|TOM1_ENST00000447733.1_Missense_Mutation_p.192_193EM>DL|TOM1_ENST00000425375.1_Missense_Mutation_p.180_181EM>DL|TOM1_ENST00000382034.5_Missense_Mutation_p.158_159EM>DL|TOM1_ENST00000411850.1_Missense_Mutation_p.225_226EM>DL	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	225	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						GTGAGCTGGAGATGGTGAGTGG	0.604																																					p.EM234DL													.	TOM1-91	0			c.A676C						.																																			SO:0001583	missense	10043	exon7			CTGGAGATGGTGA	AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"target of myb1 (chicken) homolog"			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	Exception_encountered	22.37:g.35723290_35723291delinsTC	ENSP00000394466:p.E225_M226delinsDL	Somatic	101	1		WXS	Illumina HiSeq	Phase_I	72	10	NM_001135732	0	0	0	0	0	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Missense_Mutation	DNP	ENST00000449058.2	37	CCDS13913.1																																																																																			.		0.604	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488		TC	35723291	GA	TC	35723290	3	4	156	1	0	0	0	0	1	0	0	0	16383	933	33	4	701	4	TOM1	22	35723290	Missense_Mutation	DNP	GA	TCGA-P4-A5EA-01A-11D-A28G-10	5665961	35723290	15581276	107	14146											
C22orf33	339669	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	37396006	37396008	+	In_Frame_Del	DEL	TCA	TCA	-																															ttttctggccctcgaagactTcatcaatagccttttgagcc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:37396006_37396008delTCA	ENST00000405091.2	-	5	758_760	c.507_509delTGA	c.(505-510)gatgaa>gaa	p.D169del	TEX33_ENST00000381821.1_In_Frame_Del_p.D169del|TEX33_ENST00000402860.3_In_Frame_Del_p.D84del			O43247	TEX33_HUMAN	testis expressed 33	169																	CTCGAAGACTTCATCAATAGCCT	0.542																																					p.169_170del		.											.	.	0			c.507_509del						.																																			SO:0001651	inframe_deletion	339669	exon4			.	BC042635	CCDS13937.1, CCDS54524.1	22q12.3	2013-10-11	2012-02-16	2012-02-16	ENSG00000185264	ENSG00000185264			28568	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 33"	C22orf33		22332119	Standard	NM_178552		Approved	MGC35206, EAN57	uc003aqf.3	O43247	OTTHUMG00000150531	ENST00000405091.2:c.507_509delTGA	22.37:g.37396009_37396011delTCA	ENSP00000386118:p.Asp169del	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	88	25	NM_001163857	0	0	0	0	0	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	In_Frame_Del	DEL	ENST00000405091.2	37	CCDS54524.1																																																																																			.		0.542	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552		-	37396008	TCA	-	37396006	7	5	156	1	0	1	0	1	0	0	0	0	2151	1783	62	0	345	0	C22orf33	22	37396006	In_Frame_Del	DEL	TCA	TCGA-P4-A5EA-01A-11D-A28G-10	1672716	37396006	13908560	108	14147											
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15841231	15841236	+	In_Frame_Del	DEL	AGCCGG	AGCCGG	-																															accgcagccggggccggggcAgccggagccggagccggagc																								rs199648317		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AGCCGG	AGCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:15841231_15841236delAGCCGG	ENST00000307771.7	+	11	1339_1344	c.1315_1320delAGCCGG	c.(1315-1320)agccggdel	p.SR447del		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	447	Arg/Ser-rich (RS domain).				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					GGGCCGGGGCagccggagccggagcc	0.636			"F, S, Mis"		"MDS, CLL"																																p.439_440del	NSCLC(197;1631 3042 5741 31152)	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2-133	0			c.1315_1320del						.			17,138,2720		4,1,5,3,32,53,20,1147,368						3	0.1			9	24,75,5168		3,0,9,9,11,35,18,1934,1256	no	codingComplex	ZRSR2	NM_005089.3		7,1,14,12,43,88,38,3081,1624	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		1.8796,5.3913,3.1196				41,213,7888				SO:0001651	inframe_deletion	8233	exon11			.	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1315_1320delAGCCGG	X.37:g.15841237_15841242delAGCCGG	ENSP00000303015:p.Ser447_Arg448del	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_005089	0	0	0	0	0	Q14D69	In_Frame_Del	DEL	ENST00000307771.7	37	CCDS14172.1																																																																																			.		0.636	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		-	15841236	AGCCGG	-	15841231	7	5	156	1	0	1	0	1	0	0	0	0	18257	188	7	0	1357	0	ZRSR2	23	15841231	In_Frame_Del	DEL	AGCCGG	TCGA-P4-A5EA-01A-11D-A28G-10		15841231	139429329	109	14148											
BCOR	54880	broad.mit.edu	37	chrX	39913206	39913207	+	Frame_Shift_Del	DEL	AC	AC	-																															ctctgaaaattcaaattcaaAcacatcgctataggcatcgt																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:39913206_39913207delAC	ENST00000378444.4	-	14	5136_5137	c.4908_4909delGT	c.(4906-4911)gtgtttfs	p.F1637fs	BCOR_ENST00000378463.1_Frame_Shift_Del_p.F480fs|BCOR_ENST00000397354.3_Frame_Shift_Del_p.F1603fs|BCOR_ENST00000342274.4_Frame_Shift_Del_p.F1603fs|BCOR_ENST00000378455.4_Frame_Shift_Del_p.F1585fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1637	Necessary and sufficient for interaction with PCGF1.				heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TCAAATTCAAACACATCGCTAT	0.465			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.1636_1637del				Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR-229	0			c.4908_4909del						.																																			SO:0001589	frameshift_variant	54880	exon14			ATTCAAACACATC	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"Ankyrin repeat domain containing"	20893	protein-coding gene	gene with protein product		300485	"BCL6 co-repressor"			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4908_4909delGT	X.37:g.39913208_39913209delAC	ENSP00000367705:p.Phe1637fs	Somatic	261	0		WXS	Illumina HiSeq	Phase_I	235	19	NM_001123385	0	0	0	0	0	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Del	DEL	ENST00000378444.4	37	CCDS48093.1																																																																																			.		0.465	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		-	39913207	AC	-	39913206	7	5	156	1	0	1	0	1	0	0	0	0	1387	43	2	0	366	0	BCOR	23	39913206	Frame_Shift_Del	DEL	AC	TCGA-P4-A5EA-01A-11D-A28G-10	24071975	39913206	115357354	110	14149											
USP9X	8239	broad.mit.edu	37	chrX	41022128	41022128	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagaacggcttaacttcctTaggtttgttttatacagtta	11	16	7	7	1	0	1	0	0	0	1	1	1	1	1	1	2	3	4	1	2	7	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:41022128T>C	ENST00000324545.8	+	15	2616	c.1983T>C	c.(1981-1983)ctT>ctC	p.L661L	USP9X_ENST00000378308.2_Silent_p.L661L	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	661					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTAACTTCCTTAGGTTTGTTT	0.368																																					p.L661L	Ovarian(172;1807 2695 35459 49286)												.	USP9X-563	0			c.T1983C						.						129	121	124					X																	41022128		2189	4297	6486	SO:0001819	synonymous_variant	8239	exon15			CTTCCTTAGGTTT	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"Ubiquitin-specific peptidases"	12632	protein-coding gene	gene with protein product		300072	"ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)", "ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)", "ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.1983T>C	X.37:g.41022128T>C		Somatic	250	0		WXS	Illumina HiSeq	Phase_I	217	6	NM_001039591	0	0	0	0	0	O75550|Q8WWT3|Q8WX12	Silent	SNP	ENST00000324545.8	37	CCDS43930.1																																																																																			.		0.368	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		C	41022128	T	C	41022128	2	2	156	1	0	0	0	0	0	0	0	1	17123	1741	61	3		3	USP9X	23	41022128	Silent	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	1108922	41022128	114248432	111	14150											
TFE3	7030	broad.mit.edu	37	chrX	48888986	48888986	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccaggtctttggagcgctGctgctccttctgcagcttgc	3	13	11	14	1	2	0	0	0	2	0	4	1	4	1	2	2	6	5	2	2	0	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:48888986G>A	ENST00000315869.7	-	9	1469	c.1210C>T	c.(1210-1212)Cag>Tag	p.Q404*	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	404					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						TTGGAGCGCTGCTGCTCCTTC	0.602			T	"SFPQ, ASPSCR1, PRCC, NONO, CLTC"	"papillary renal, alveolar soft part sarcoma, renal"																																p.Q404X				Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	TFE3-658	0			c.C1210T						.						33	30	31					X																	48888986		2202	4297	6499	SO:0001587	stop_gained	7030	exon9			AGCGCTGCTGCTC	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"Basic helix-loop-helix proteins"	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.1210C>T	X.37:g.48888986G>A	ENSP00000314129:p.Gln404*	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	76	4	NM_006521	0	0	26	26	0	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Nonsense_Mutation	SNP	ENST00000315869.7	37	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	g	39	7.717535	0.98450	.	.	ENSG00000068323	ENST00000315869	.	.	.	5.64	3.88	0.44766	.	0.056288	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.6987	10.5431	0.45045	0.1621:0.0:0.8379:0.0	.	.	.	.	X	404	.	ENSP00000314129:Q404X	Q	-	1	0	TFE3	48775930	1.000000	0.71417	0.249000	0.24280	0.956000	0.61745	7.905000	0.87416	0.549000	0.28973	0.462000	0.41574	CAG	.		0.602	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		A	48888986	G	A	48888986	4	1	156	1	0	0	0	0	0	1	0	0	15832	1328	46	2	525	2	TFE3	23	48888986	Nonsense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	7866858	48888986	106381574	112	14151											
DGKK	139189	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	50144042	50144042	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttaactactcaccatcgccTttggggtcgcttagagcagt	8	13	9	11	2	1	1	1	0	0	1	3	1	1	1	2	2	3	2	2	2	3	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:50144042T>C	ENST00000376025.2	-	0	1463							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					CACCATCGCCTTTGGGGTCGC	0.473																																					.													.	DGKK-227	0			.						.						71	60	64					X																	50144042		1948	4121	6069			139189	.			ATCGCCTTTGGGG	AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50144042T>C		Somatic	363	0		WXS	Illumina HiSeq	Phase_I	363	93	.	0	0	0	0	0	B2RP91	Silent	SNP	ENST00000376025.2	37																																																																																				.		0.473	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1	NM_001013742		C	50144042	T	C	50144042	1	2	156	0	1	0	0	0	0	0	0	0	4483	1606	56	3		3	DGKK	23	50144042	RNA	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	1255056	50144042	105126518	113	14152											
ZXDB	158586	hgsc.bcm.edu	37	chrX	57618715	57618715	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgttggcgccgaggacCgatcaacctagcggcggcgg	7	5	16	13	6	1	0	1	0	0	0	1	3	1	1	4	5	3	1	4	5	2	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:57618715C>T	ENST00000374888.1	+	1	447	c.234C>T	c.(232-234)acC>acT	p.T78T		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	78					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						CGCCGAGGACCGATCAACCTA	0.756													C|||	1	0.000264901	0	0	3775	,	,		6694	0		0.001	False		,,,				2504	0				p.T78T		.											.	ZXDB-130	0			c.C234T						.						3	5	4					X																	57618715		1444	3093	4537	SO:0001819	synonymous_variant	158586	exon1			GAGGACCGATCAA	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.234C>T	X.37:g.57618715C>T		Somatic	4	0		WXS	Illumina HiSeq	Phase_I	12	8	NM_007157	0	0	0	0	0	A8K151|Q9UBB3	Silent	SNP	ENST00000374888.1	37	CCDS35313.1																																																																																			.		0.756	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		T	57618715	C	T	57618715	2	4	156	1	0	0	0	0	0	0	0	1	18283	639	23	1		1	ZXDB	23	57618715	Silent	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	7474673	57618715	97651845	114	14153											
GLUD2	2747	ucsc.edu	37	chrX	120182480	120182480	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatttggtaatgtgggcctAcactctatgagatatttaca	11	14	10	6	0	1	1	0	1	1	1	1	3	1	2	1	3	2	1	1	3	5	7			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:120182480A>G	ENST00000328078.1	+	1	1019	c.942A>G	c.(940-942)ctA>ctG	p.L314L		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	314					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						ATGTGGGCCTACACTCTATGA	0.383																																					p.L314L													.	GLUD2-131	0			c.A942G						.						230	212	218					X																	120182480		2203	4300	6503	SO:0001819	synonymous_variant	2747	exon1			GGGCCTACACTCT	U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"glutamate dehydrogenase pseudogene 1"	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.942A>G	X.37:g.120182480A>G		Somatic	461	4		WXS	Illumina HiSeq		317	4	NM_012084	0	0	0	6	6	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																			.		0.383	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		G	120182480	A	G	120182480	2	3	156	1	0	0	0	0	0	0	0	1	6497	378	14	3		3	GLUD2	23	120182480	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	62563765	120182480	35088080	115	14154											
THOC2	57187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	122757675	122757675	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagatctggcctcttctcttTttcttcttggcagattttgt	4	21	7	9	0	5	2	0	0	5	2	6	2	5	2	1	2	0	1	1	2	1	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:122757675T>C	ENST00000245838.8	-	28	3497	c.3466A>G	c.(3466-3468)Aaa>Gaa	p.K1156E	THOC2_ENST00000491737.1_Missense_Mutation_p.K1041E|THOC2_ENST00000355725.4_Missense_Mutation_p.K1156E	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1156					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CTCTTCTCTTTTTCTTCTTGG	0.348																																					p.K1156E		.											.	THOC2-133	0			c.A3466G						.						150	119	128					X																	122757675		1809	4080	5889	SO:0001583	missense	57187	exon28			TCTCTTTTTCTTC	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3466A>G	X.37:g.122757675T>C	ENSP00000245838:p.Lys1156Glu	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	42	7	NM_001081550	0	0	10	10	0	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.88|19.88	3.909495|3.909495	0.72868|0.72868	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000438358	.|.	.|.	.|.	5.9|5.9	5.9|5.9	0.94986|0.94986	THO complex, subunitTHOC2, C-terminal (1);|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.72661|0.72661	0.3488|0.3488	M|M	0.67625|0.67625	2.065|2.065	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.72293|0.72293	-0.4336|-0.4336	9|6	0.13470|.	T|.	0.59|.	-17.2559|-17.2559	15.2657|15.2657	0.73660|0.73660	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1156|.	Q8NI27|.	THOC2_HUMAN|.	E|R	1156;1156;1041|228	.|.	ENSP00000245838:K1156E|.	K|K	-|-	1|2	0|0	THOC2|THOC2	122585356|122585356	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	1.988000|1.988000	0.58038|0.58038	0.481000|0.481000	0.45027|0.45027	AAA|AAA	.		0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122757675	T	C	122757675	3	2	156	1	0	0	0	0	1	0	0	0	15897	1850	64	3	1359	3	THOC2	23	122757675	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	2575195	122757675	32512885	116	14155											
CASZ1	54897	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	10700024	10700024	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagcatcttccgggaggacgCcgtcttccgccgcttgccga	5	8	12	16	6	2	0	0	0	2	0	4	3	4	2	5	2	2	2	5	2	0	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:10700024C>A	ENST00000377022.3	-	21	4572	c.4255G>T	c.(4255-4257)Gcg>Tcg	p.A1419S	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1419					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CGGGAGGACGCCGTCTTCCGC	0.617																																					p.A1419S													.	CASZ1-113	0			c.G4255T						.						39	45	43					1																	10700024		2097	4204	6301	SO:0001583	missense	54897	exon21			AGGACGCCGTCTT	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"Zinc fingers, C2H2-type"	26002	protein-coding gene	gene with protein product	"zinc finger protein 693", "survival related gene"	609895	"castor homolog 1, zinc finger (Drosophila)"			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.4255G>T	1.37:g.10700024C>A	ENSP00000366221:p.Ala1419Ser	Somatic	80	1		WXS	Illumina HiSeq	Phase_I	95	22	NM_001079843	0	0	0	0	0	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513284	0.85389	.	.	ENSG00000130940	ENST00000377022	.	.	.	5.23	5.23	0.72850	.	0.000000	0.45606	U	0.000359	T	0.30039	0.0752	N	0.08118	0	0.80722	D	1	P	0.52316	0.952	B	0.43251	0.413	T	0.12734	-1.0536	9	0.08599	T	0.76	-17.5652	18.7817	0.91934	0.0:1.0:0.0:0.0	.	1419	Q86V15	CASZ1_HUMAN	S	1419	.	ENSP00000366221:A1419S	A	-	1	0	CASZ1	10622611	0.995000	0.38212	0.937000	0.37676	0.969000	0.65631	3.242000	0.51384	2.435000	0.82474	0.460000	0.39030	GCG	.		0.617	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10700024	C	A	10700024	3	1	157	1	0	0	0	0	1	0	0	0	2691	739	26	4	1028	4	CASZ1	1	10700024	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		10700024	238550597	1	14156											
FBXO6	26270	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	11728776	11728776	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgagctgcccgagaacatcCtgctggagctgttcacgcac	9	7	11	14	3	1	1	1	0	0	1	2	4	2	2	2	1	5	5	2	1	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:11728776C>G	ENST00000376753.4	+	2	196	c.61C>G	c.(61-63)Ctg>Gtg	p.L21V		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	21	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CGAGAACATCCTGCTGGAGCT	0.632																																					p.L21V	NSCLC(54;506 1562 46490 51389)												.	FBXO6-226	0			c.C61G						.						54	57	56					1																	11728776		2203	4300	6503	SO:0001583	missense	26270	exon2			AACATCCTGCTGG	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"F-boxes /  "other""	13585	protein-coding gene	gene with protein product		605647	"F-box only protein 6"			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.61C>G	1.37:g.11728776C>G	ENSP00000365944:p.Leu21Val	Somatic	105	1		WXS	Illumina HiSeq	Phase_I	114	36	NM_018438	0	0	47	47	0	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	.	.	.	.	.	.	.	.	.	.	C	12.25	1.881321	0.33255	.	.	ENSG00000116663	ENST00000376753	T	0.68331	-0.32	5.15	3.27	0.37495	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.244528	0.34435	N	0.003979	T	0.76212	0.3956	M	0.65677	2.01	0.37077	D	0.898797	D	0.76494	0.999	D	0.85130	0.997	T	0.76296	-0.3011	10	0.37606	T	0.19	-6.9754	8.6849	0.34232	0.0:0.821:0.0:0.179	.	21	Q9NRD1	FBX6_HUMAN	V	21	ENSP00000365944:L21V	ENSP00000365944:L21V	L	+	1	2	FBXO6	11651363	0.953000	0.32496	1.000000	0.80357	0.718000	0.41266	1.306000	0.33505	0.679000	0.31345	0.650000	0.86243	CTG	.		0.632	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438		G	11728776	C	G	11728776	3	3	157	1	0	0	0	0	1	0	0	0	5778	680	24	4	63	4	FBXO6	1	11728776	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1028752	11728776	237521845	2	14157											
AADACL4	343066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	12711237	12711237	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaaaggaccctgaacttgtGgtgaccgacctgcgttttgg	10	10	12	9	2	0	2	0	2	0	0	0	4	0	3	3	3	2	1	3	3	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:12711237G>T	ENST00000376221.1	+	2	264	c.264G>T	c.(262-264)gtG>gtT	p.V88V		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	88						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		CTGAACTTGTGGTGACCGACC	0.498																																					p.V88V		.											.	AADACL4-68	0			c.G264T						.						98	96	97					1																	12711237		2203	4300	6503	SO:0001819	synonymous_variant	343066	exon2			ACTTGTGGTGACC		CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.264G>T	1.37:g.12711237G>T		Somatic	121	0		WXS	Illumina HiSeq	Phase_I	120	66	NM_001013630	0	0	0	0	0		Silent	SNP	ENST00000376221.1	37	CCDS30590.1																																																																																			.		0.498	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630		T	12711237	G	T	12711237	2	4	157	1	0	0	0	0	0	0	0	1	13	1335	47	4		4	AADACL4	1	12711237	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	982461	12711237	236539384	3	14158											
RHD	6007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	25628090	25628090	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgaaaggaagaatgccgtGttcaacacctactatgctgt	13	10	9	9	2	1	1	1	0	0	1	2	3	1	2	2	1	4	2	2	1	6	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:25628090G>A	ENST00000328664.4	+	5	869	c.714G>A	c.(712-714)gtG>gtA	p.V238V	RHD_ENST00000454452.2_Silent_p.V238V|RHD_ENST00000568195.1_Silent_p.V238V|RHD_ENST00000342055.5_Silent_p.V238V|RHD_ENST00000423810.2_Silent_p.V238V|RHD_ENST00000423253.1_3'UTR|RHD_ENST00000357542.4_Silent_p.V238V|RHD_ENST00000417538.2_Silent_p.V238V	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	238			V -> M (in RhDVa(TO) and RhDVa(TT); dbSNP:rs1053360). {ECO:0000269|Ref.9}.			integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGAATGCCGTGTTCAACACCT	0.562																																					p.V238V		.											.	RHD-153	0			c.G714A						.						199	154	171					1																	25628090		2122	3769	5891	SO:0001819	synonymous_variant	6007	exon5			TGCCGTGTTCAAC	AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"CD molecules", "Blood group antigens"	10009	protein-coding gene	gene with protein product		111680	"Rhesus blood group, D antigen", "Rh blood group, D antigen"	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.714G>A	1.37:g.25628090G>A		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	134	123	NM_001127691	0	0	0	0	0	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Silent	SNP	ENST00000328664.4	37	CCDS262.1																																																																																			.		0.562	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124		A	25628090	G	A	25628090	2	1	157	1	0	0	0	0	0	0	0	1	13359	1364	48	2		2	RHD	1	25628090	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	12916853	25628090	223622531	4	14159											
CSMD2	114784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	34015918	34015918	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctccagacatctgggagtGaggcggggagcccggatggc	7	6	18	10	2	2	2	0	1	2	1	3	5	2	5	2	6	1	0	2	6	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:34015918G>T	ENST00000373381.4	-	56	8952	c.8776C>A	c.(8776-8778)Cac>Aac	p.H2926N		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2901	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ATCTGGGAGTGAGGCGGGGAG	0.572																																					p.H2782N		.											.	CSMD2-103	0			c.C8344A						.						58	57	57					1																	34015918		2203	4300	6503	SO:0001583	missense	114784	exon55			GGGAGTGAGGCGG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8776C>A	1.37:g.34015918G>T	ENSP00000362479:p.His2926Asn	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	186	106	NM_052896	0	0	0	0	0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	0.673	-0.801317	0.02841	.	.	ENSG00000121904	ENST00000373381	T	0.64618	-0.11	5.71	5.71	0.89125	Complement control module (2);Sushi/SCR/CCP (3);	0.060404	0.64402	D	0.000002	T	0.27241	0.0668	N	0.00661	-1.28	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.01	T	0.43294	-0.9400	10	0.02654	T	1	.	13.8354	0.63406	0.0:0.0:0.8474:0.1526	.	2782;2926	Q7Z408;E7EUA6	CSMD2_HUMAN;.	N	2926	ENSP00000362479:H2926N	ENSP00000241312:H2782N	H	-	1	0	CSMD2	33788505	1.000000	0.71417	0.982000	0.44146	0.320000	0.28249	3.614000	0.54160	2.720000	0.93068	0.650000	0.86243	CAC	.		0.572	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34015918	G	T	34015918	3	4	157	1	0	0	0	0	1	0	0	0	3951	1290	45	4	2179	4	CSMD2	1	34015918	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8387828	34015918	215234703	5	14160											
EIF2C3	192669	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36479547	36479547	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcaacaccgagccatggagTatgggacatgcgagggaaac	14	4	14	9	2	0	0	0	0	0	0	0	5	0	3	2	3	5	2	2	3	3	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:36479547T>A	ENST00000373191.4	+	11	1653	c.1304T>A	c.(1303-1305)gTa>gAa	p.V435E	AGO3_ENST00000246314.6_Missense_Mutation_p.V201E|RP4-665N4.8_ENST00000466576.2_RNA|RP4-665N4.8_ENST00000479395.2_RNA	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	435					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										AGCCATGGAGTATGGGACATG	0.398																																					p.V435E													.	.	0			c.T1304A						.						127	117	120					1																	36479547		2203	4300	6503	SO:0001583	missense	192669	exon11			ATGGAGTATGGGA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"Argonaute/PIWI family"	18421	protein-coding gene	gene with protein product	"argonaute 3"	607355	"eukaryotic translation initiation factor 2C, 3"	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.1304T>A	1.37:g.36479547T>A	ENSP00000362287:p.Val435Glu	Somatic	369	2		WXS	Illumina HiSeq	Phase_I	366	38	NM_024852	0	0	2	2	0	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	37	CCDS399.1	.	.	.	.	.	.	.	.	.	.	T	18.81	3.703233	0.68501	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.05447	3.44;3.44	5.65	5.65	0.86999	.	0.055978	0.64402	D	0.000001	T	0.16769	0.0403	M	0.90922	3.16	0.80722	D	1	B	0.23891	0.093	B	0.34452	0.183	T	0.28964	-1.0027	10	0.06891	T	0.86	-12.758	15.9324	0.79675	0.0:0.0:0.0:1.0	.	435	Q9H9G7	AGO3_HUMAN	E	435;201	ENSP00000362287:V435E;ENSP00000246314:V201E	ENSP00000246314:V201E	V	+	2	0	EIF2C3	36252134	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	8.031000	0.88826	2.169000	0.68431	0.529000	0.55759	GTA	.		0.398	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		A	36479547	T	A	36479547	3	1	157	1	0	0	0	0	1	0	0	0	5018	1638	57	5	1346	5	EIF2C3	1	36479547	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	2463629	36479547	212771074	6	14161											
MACF1	23499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	39853737	39853737	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atctgaggaactttactcagGgtctggtagaagatgcccca	11	10	11	9	0	3	3	1	1	2	2	3	4	3	4	2	3	3	1	2	3	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:39853737G>C	ENST00000372915.3	+	57	15325	c.15238G>C	c.(15238-15240)Ggt>Cgt	p.G5080R	MACF1_ENST00000567887.1_Missense_Mutation_p.G5112R|MACF1_ENST00000545844.1_Missense_Mutation_p.G3013R|MACF1_ENST00000539005.1_Missense_Mutation_p.G2992R|MACF1_ENST00000317713.7_Missense_Mutation_p.G3013R|MACF1_ENST00000361689.2_Missense_Mutation_p.G3013R|MACF1_ENST00000289893.4_Missense_Mutation_p.G3515R|MACF1_ENST00000564288.1_Missense_Mutation_p.G5075R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5080					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTTTACTCAGGGTCTGGTAGA	0.502																																					p.G3013R		.											.	MACF1-165	0			c.G9037C						.						51	52	52					1																	39853737		2203	4300	6503	SO:0001583	missense	23499	exon54			ACTCAGGGTCTGG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"EF-hand domain containing"	13664	protein-coding gene	gene with protein product	"actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7"	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.15238G>C	1.37:g.39853737G>C	ENSP00000362006:p.Gly5080Arg	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	138	42	NM_012090	0	0	4	5	1	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.13|17.13	3.311133|3.311133	0.60414|0.60414	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.32272	.|1.46;1.46;1.46;1.46;1.46;1.46	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000005|0.000005	T|T	0.55273|0.55273	0.1910|0.1910	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.99;0.991	.|D;D;D	.|0.97110	.|1.0;0.952;0.962	T|T	0.43475|0.43475	-0.9389|-0.9389	6|10	.|0.44086	.|T	.|0.13	.|.	20.5568|20.5568	0.99304|0.99304	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|5080;3013;2957	.|Q9UPN3;F8W8Q1;Q9UPN3-3	.|MACF1_HUMAN;.;.	A|R	2125|3013;5080;3013;3013;2992;3515	.|ENSP00000439537:G3013R;ENSP00000362006:G5080R;ENSP00000354573:G3013R;ENSP00000313438:G3013R;ENSP00000444364:G2992R;ENSP00000289893:G3515R	.|ENSP00000289893:G3515R	G|G	+|+	2|1	0|0	MACF1|MACF1	39626324|39626324	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.947000|0.947000	0.59692|0.59692	9.869000|9.869000	0.99810|0.99810	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	GGG|GGT	.		0.502	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39853737	G	C	39853737	3	2	157	1	0	0	0	0	1	0	0	0	9169	1232	43	4	15398	4	MACF1	1	39853737	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	3374190	39853737	209396884	7	14162											
MAST2	23139	hgsc.bcm.edu;bcgsc.ca	37	chr1	46496701	46496702	+	Frame_Shift_Del	DEL	TC	TC	-																															tacggaagcggctgtcggtgTctgagtcatcccacacagag																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:46496701_46496702delTC	ENST00000361297.2	+	23	3014_3015	c.2731_2732delTC	c.(2731-2733)tctfs	p.S911fs	MAST2_ENST00000372009.2_Frame_Shift_Del_p.S841fs	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					GCTGTCGGTGTCTGAGTCATCC	0.629																																					p.911_911del		.											.	MAST2-581	0			c.2731_2732del						.																																			SO:0001589	frameshift_variant	23139	exon23			.	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.2731_2732delTC	1.37:g.46496701_46496702delTC	ENSP00000354671:p.Ser911fs	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	99	34	NM_015112	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000361297.2	37	CCDS41326.1																																																																																			.		0.629	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		-	46496702	TC	-	46496701	7	5	157	1	0	1	0	1	0	0	0	0	9350	1667	58	0	2821	0	MAST2	1	46496701	Frame_Shift_Del	DEL	TC	TCGA-P4-A5EB-01A-11D-A28G-10	6642964	46496701	202753920	8	14163											
PCSK9	255738	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	55529096	55529096	+	Frame_Shift_Del	DEL	G	G	-																															ctggctgcagtgccctccctGggacctcccacgtcctgggg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:55529096delG	ENST00000302118.5	+	12	2208	c.1918delG	c.(1918-1920)gggfs	p.G640fs	PCSK9_ENST00000543384.1_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	640	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TGCCCTCCCTGGGACCTCCCA	0.662																																					p.G640fs	Pancreas(137;1454 1827 5886 22361 42375)	.											.	PCSK9-93	0			c.1918delG						.						34	34	34					1																	55529096		2203	4300	6503	SO:0001589	frameshift_variant	255738	exon12			.	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"hypercholesterolemia, autosomal dominant 3"	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1918delG	1.37:g.55529096delG	ENSP00000303208:p.Gly640fs	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	232	129	NM_174936	0	0	0	0	0	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Frame_Shift_Del	DEL	ENST00000302118.5	37	CCDS603.1																																																																																			.		0.662	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		-	55529096	G	-	55529096	7	5	157	1	0	1	0	1	0	0	0	0	11632	1348	47	0	1964	0	PCSK9	1	55529096	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	9032395	55529096	193721525	9	14164											
ITGB3BP	23421	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	63974218	63974218	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattttcttctaacagaccaTccaacttcagtgatctttta	11	16	3	11	0	4	2	1	1	3	1	5	2	5	2	2	0	2	0	2	0	3	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:63974218T>G	ENST00000271002.10	-	2	110	c.29A>C	c.(28-30)gAt>gCt	p.D10A	ITGB3BP_ENST00000283568.8_Missense_Mutation_p.D10A|ITGB3BP_ENST00000371092.3_Missense_Mutation_p.D49A	NM_014288.4	NP_055103.3	Q13352	CENPR_HUMAN	integrin beta 3 binding protein (beta3-endonexin)	10					apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.D10G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9						TAACAGACCATCCAACTTCAG	0.259																																					p.D49A													.	ITGB3BP-90	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A146C						.						28	28	28					1																	63974218		2149	4215	6364	SO:0001583	missense	23421	exon3			AGACCATCCAACT	U37139	CCDS30736.1, CCDS55603.1	1p31.3	2013-11-05			ENSG00000142856	ENSG00000142856			6157	protein-coding gene	gene with protein product	"centromere protein R"	605494				7593198, 10490654	Standard	NM_014288		Approved	NRIF3, HSU37139, TAP20, CENPR	uc001dbb.2	Q13352	OTTHUMG00000013364	ENST00000271002.10:c.29A>C	1.37:g.63974218T>G	ENSP00000271002:p.Asp10Ala	Somatic	292	2		WXS	Illumina HiSeq	Phase_I	201	53	NM_001206739	0	0	7	10	3	B2R7D8|Q13353|Q5RJ42|Q5RJ44|Q5RJ45|Q7KYX2|Q96CD5|Q9UKB6	Missense_Mutation	SNP	ENST00000271002.10	37	CCDS30736.1	.	.	.	.	.	.	.	.	.	.	T	3.341	-0.134587	0.06711	.	.	ENSG00000142856	ENST00000271002;ENST00000371092;ENST00000283568	T;T;T	0.67698	-0.27;0.25;-0.28	4.91	3.79	0.43588	.	0.260117	0.25997	N	0.026964	T	0.46073	0.1374	N	0.19112	0.55	0.38496	D	0.948093	P;P;P	0.51537	0.944;0.946;0.78	P;P;B	0.50825	0.651;0.592;0.265	T	0.53947	-0.8366	10	0.66056	D	0.02	-2.1447	10.3835	0.44125	0.0:0.0772:0.0:0.9228	.	10;49;10	Q13352-2;Q13352-5;Q13352	.;.;CENPR_HUMAN	A	10;49;10	ENSP00000271002:D10A;ENSP00000360133:D49A;ENSP00000283568:D10A	ENSP00000271002:D10A	D	-	2	0	ITGB3BP	63746806	1.000000	0.71417	0.469000	0.27204	0.029000	0.11900	5.252000	0.65445	0.732000	0.32470	-0.256000	0.11100	GAT	.		0.259	ITGB3BP-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000037242.2	NM_014288		G	63974218	T	G	63974218	3	3	157	1	0	0	0	0	1	0	0	0	7917	1435	50	5	532	5	ITGB3BP	1	63974218	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	8445122	63974218	185276403	10	14165											
GNG12	55970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	68171150	68171150	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccactataagatgatgcaaGtttttttatccttgaaaggg	12	15	8	6	0	0	3	0	2	0	1	2	3	2	3	2	1	1	2	2	1	5	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:68171150G>C	ENST00000370982.3	-	4	402	c.203C>G	c.(202-204)aCt>aGt	p.T68S		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	68					cellular response to glucagon stimulus (GO:0071377)|cerebral cortex development (GO:0021987)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			lung(3)	3						GATGATGCAAGTTTTTTTATC	0.433																																					p.T68S		.											.	GNG12-227	0			c.C203G						.						173	163	167					1																	68171150		2203	4300	6503	SO:0001583	missense	55970	exon4			ATGCAAGTTTTTT	AF119663	CCDS30749.1	1p31.2	2008-02-05			ENSG00000172380	ENSG00000172380			19663	protein-coding gene	gene with protein product		615405				10819326	Standard	NM_018841		Approved		uc001dea.2	Q9UBI6	OTTHUMG00000009545	ENST00000370982.3:c.203C>G	1.37:g.68171150G>C	ENSP00000360021:p.Thr68Ser	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	89	43	NM_018841	0	0	14	40	26	Q69YP5|Q9BRV5	Missense_Mutation	SNP	ENST00000370982.3	37	CCDS30749.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.282741	0.59867	.	.	ENSG00000172380	ENST00000370982	T	0.20200	2.09	5.79	5.79	0.91817	G-protein gamma domain (3);	0.054877	0.85682	D	0.000000	T	0.05502	0.0145	.	.	.	0.41685	D	0.98931	B	0.27625	0.183	B	0.31495	0.131	T	0.08146	-1.0736	9	0.02654	T	1	-5.209	18.8047	0.92032	0.0:0.0:1.0:0.0	.	68	Q9UBI6	GBG12_HUMAN	S	68	ENSP00000360021:T68S	ENSP00000360021:T68S	T	-	2	0	GNG12	67943738	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	7.072000	0.76777	2.749000	0.94314	0.491000	0.48974	ACT	.		0.433	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2			C	68171150	G	C	68171150	3	2	157	1	0	0	0	0	1	0	0	0	6545	1029	36	4	19	4	GNG12	1	68171150	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4196932	68171150	181079471	11	14166											
GNAI3	2773	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	110125084	110125084	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatgatctggatagaataTcccagtctaactacattcca	15	12	5	9	0	2	2	0	1	2	1	4	3	4	3	2	1	2	0	2	1	7	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:110125084T>G	ENST00000369851.4	+	5	597	c.487T>G	c.(487-489)Tcc>Gcc	p.S163A		NM_006496.3	NP_006487.1	P08754	GNAI3_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 3	163					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|negative regulation of adenylate cyclase activity (GO:0007194)|platelet activation (GO:0030168)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle fusion (GO:0006906)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|plasma membrane (GO:0005886)|zymogen granule (GO:0042588)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	12		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237)		GGATAGAATATCCCAGTCTAA	0.368																																					p.S163A													.	GNAI3-228	0			c.T487G						.						113	107	109					1																	110125084		2203	4300	6503	SO:0001583	missense	2773	exon5			AGAATATCCCAGT	M27543	CCDS802.1	1p13	2012-10-02			ENSG00000065135	ENSG00000065135			4387	protein-coding gene	gene with protein product		139370				3109953	Standard	NM_006496		Approved	87U6	uc001dxz.3	P08754	OTTHUMG00000011648	ENST00000369851.4:c.487T>G	1.37:g.110125084T>G	ENSP00000358867:p.Ser163Ala	Somatic	210	1		WXS	Illumina HiSeq	Phase_I	213	46	NM_006496	0	0	48	55	7	P17539|Q5TZX1	Missense_Mutation	SNP	ENST00000369851.4	37	CCDS802.1	.	.	.	.	.	.	.	.	.	.	T	7.473	0.646985	0.14516	.	.	ENSG00000065135	ENST00000369851	D	0.87412	-2.25	5.92	4.78	0.61160	G protein alpha subunit, helical insertion (2);	0.050812	0.85682	D	0.000000	T	0.47358	0.1441	N	0.03115	-0.41	0.47905	D	0.999546	B	0.02656	0.0	B	0.09377	0.004	T	0.53851	-0.8380	10	0.02654	T	1	.	7.964	0.30087	0.0:0.0706:0.1352:0.7942	.	163	P08754	GNAI3_HUMAN	A	163	ENSP00000358867:S163A	ENSP00000358867:S163A	S	+	1	0	GNAI3	109926607	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.446000	0.52928	2.255000	0.74692	0.533000	0.62120	TCC	.		0.368	GNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032222.1	NM_006496		G	110125084	T	G	110125084	3	3	157	1	0	0	0	0	1	0	0	0	6526	1435	50	5	505	5	GNAI3	1	110125084	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	41953934	110125084	139125537	12	14167											
KCNA2	3737	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	111147091	111147091	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cttcagagaatatatctaagGgcacattcacaggtcgcctc	12	10	8	11	1	3	1	2	0	1	1	5	2	3	1	1	2	0	1	1	2	4	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:111147091G>C	ENST00000485317.1	-	3	987	c.314C>G	c.(313-315)cCc>cGc	p.P105R	KCNA2_ENST00000440270.1_Missense_Mutation_p.P105R|KCNA2_ENST00000525120.1_Intron|KCNA2_ENST00000369770.3_Missense_Mutation_p.P105R|KCNA2_ENST00000316361.4_Missense_Mutation_p.P105R			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	105					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	TATATCTAAGGGCACATTCAC	0.473																																					p.P105R	Pancreas(18;568 735 10587 23710 36357)												.	KCNA2-91	0			c.C314G						.						43	46	45					1																	111147091		2203	4300	6503	SO:0001583	missense	3737	exon3			TCTAAGGGCACAT	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.314C>G	1.37:g.111147091G>C	ENSP00000433109:p.Pro105Arg	Somatic	84	1		WXS	Illumina HiSeq	Phase_I	73	47	NM_001204269	0	0	0	0	0	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035653	0.54896	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	6.02	5.11	0.69529	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.112102	0.64402	D	0.000009	D	0.90195	0.6935	H	0.96048	3.76	0.80722	D	1	D;D	0.76494	0.999;0.995	D;D	0.76071	0.987;0.913	D	0.93211	0.6600	10	0.66056	D	0.02	.	15.1629	0.72798	0.0674:0.0:0.9326:0.0	.	105;105	Q86XG6;P16389	.;KCNA2_HUMAN	R	105	ENSP00000358785:P105R;ENSP00000433109:P105R;ENSP00000415257:P105R;ENSP00000314520:P105R	ENSP00000314520:P105R	P	-	2	0	KCNA2	110948614	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.807000	0.99171	1.551000	0.49450	0.655000	0.94253	CCC	.		0.473	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		C	111147091	G	C	111147091	3	2	157	1	0	0	0	0	1	0	0	0	8024	1232	43	4	1189	4	KCNA2	1	111147091	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1022007	111147091	138103530	13	14168											
KCNN3	3782	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154841897	154841897	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggggcttcatgaccccacCgctatacttgcaggagctca	9	8	11	13	1	2	1	2	1	0	0	2	3	2	2	3	3	3	4	3	3	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:154841897C>T	ENST00000271915.4	-	1	859	c.544G>A	c.(544-546)Ggt>Agt	p.G182S	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	187					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ATGACCCCACCGCTATACTTG	0.672																																					p.G182S													.	KCNN3-91	0			c.G544A						.						41	45	43					1																	154841897		2203	4300	6503	SO:0001583	missense	3782	exon1			CCCCACCGCTATA	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.544G>A	1.37:g.154841897C>T	ENSP00000271915:p.Gly182Ser	Somatic	64	1		WXS	Illumina HiSeq	Phase_I	100	34	NM_001204087	0	0	0	0	0	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553945	0.86231	.	.	ENSG00000143603	ENST00000271915	D	0.99578	-6.21	4.75	4.75	0.60458	.	0.315768	0.23144	N	0.051433	D	0.98896	0.9626	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.99894	1.1143	10	0.87932	D	0	-8.6442	15.2952	0.73898	0.0:1.0:0.0:0.0	.	188;187	Q6JXY2;Q9UGI6	.;KCNN3_HUMAN	S	182	ENSP00000271915:G182S	ENSP00000271915:G182S	G	-	1	0	KCNN3	153108521	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	7.464000	0.80887	2.461000	0.83175	0.563000	0.77884	GGT	.		0.672	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154841897	C	T	154841897	3	4	157	1	0	0	0	0	1	0	0	0	8101	652	23	1	1705	1	KCNN3	1	154841897	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	43694806	154841897	94408724	14	14169											
ZBTB7B	51043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	154987232	154987232	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagcagcgccagctgggccaCctatgtgacctcaccatccg	8	6	11	16	2	1	1	1	1	0	0	2	2	2	1	6	1	3	2	6	1	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:154987232C>G	ENST00000368426.3	+	3	233	c.96C>G	c.(94-96)caC>caG	p.H32Q	ZBTB7B_ENST00000417934.2_Missense_Mutation_p.H66Q|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.H32Q|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000292176.2_Missense_Mutation_p.H32Q	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	32					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGCTGGGCCACCTATGTGACC	0.587																																					p.H66Q		.											.	ZBTB7B-90	0			c.C198G						.						68	69	69					1																	154987232		2203	4300	6503	SO:0001583	missense	51043	exon4			GGGCCACCTATGT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18668	protein-coding gene	gene with protein product	"zinc finger and BTB domain containing 15"	607646	"zinc finger protein 67 homolog (mouse)"	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.96C>G	1.37:g.154987232C>G	ENSP00000357411:p.His32Gln	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	80	26	NM_001252406	0	0	5	14	9	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	37	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.439712	0.25900	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	3.59	-1.19	0.09585	BTB/POZ (1);BTB/POZ fold (2);	0.413847	0.21695	N	0.070510	T	0.12561	0.0305	N	0.02539	-0.55	0.27857	N	0.940546	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.08055	0.003;0.002;0.003	T	0.21075	-1.0256	10	0.66056	D	0.02	.	5.0228	0.14370	0.0:0.4765:0.1713:0.3521	.	32;32;66	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	Q	32;32;66;32	ENSP00000438647:H32Q;ENSP00000357411:H32Q;ENSP00000406286:H66Q;ENSP00000292176:H32Q	ENSP00000292176:H32Q	H	+	3	2	ZBTB7B	153253856	0.762000	0.28451	0.963000	0.40424	0.981000	0.71138	-0.185000	0.09684	-0.072000	0.12864	-0.379000	0.06801	CAC	.		0.587	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		G	154987232	C	G	154987232	3	3	157	1	0	0	0	0	1	0	0	0	17586	506	18	4	98	4	ZBTB7B	1	154987232	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	145335	154987232	94263389	15	14170											
KLHDC8A	55220	bcgsc.ca	37	chr1	205306599	205306599	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acacctcccacggcgaggagGcagttcttgacgactatgct	9	8	11	13	3	1	1	0	1	1	0	2	4	2	2	2	3	1	3	2	3	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:205306599G>T	ENST00000367156.3	-	9	1797	c.981C>A	c.(979-981)tgC>tgA	p.C327*	KLHDC8A_ENST00000537168.1_Nonsense_Mutation_p.C214*|KLHDC8A_ENST00000460687.1_Nonsense_Mutation_p.C193*|KLHDC8A_ENST00000539253.1_Nonsense_Mutation_p.C327*|KLHDC8A_ENST00000367155.3_Nonsense_Mutation_p.C327*	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	327										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CGGCGAGGAGGCAGTTCTTGA	0.602																																					p.C327X													.	KLHDC8A-91	0			c.C981A						.						215	199	204					1																	205306599		2203	4300	6503	SO:0001587	stop_gained	55220	exon6			GAGGAGGCAGTTC		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.981C>A	1.37:g.205306599G>T	ENSP00000356124:p.Cys327*	Somatic	106	3		WXS	Illumina HiSeq	Phase_1	102	59	NM_018203	0	0	0	0	0	B3KU70|Q9NVG5	Nonsense_Mutation	SNP	ENST00000367156.3	37	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	G	36	5.757579	0.96898	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253;ENST00000537168	.	.	.	5.43	3.46	0.39613	.	0.049173	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-27.1551	5.738	0.18077	0.1704:0.0:0.6798:0.1498	.	.	.	.	X	327;327;327;214	.	ENSP00000356123:C327X	C	-	3	2	KLHDC8A	203573222	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.937000	0.40193	1.185000	0.42971	0.591000	0.81541	TGC	.		0.602	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		T	205306599	G	T	205306599	4	4	157	1	0	0	0	0	0	1	0	0	8383	1195	42	4	75	4	KLHDC8A	1	205306599	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	50319367	205306599	43944022	16	14171											
RCOR3	55758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	211462545	211462545	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactgaacaacctgtccaaaCtagcaagattggacttggaa	15	9	8	9	0	0	2	0	1	0	1	1	4	1	4	2	2	5	1	2	2	7	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:211462545C>A	ENST00000367005.4	+	7	713	c.572C>A	c.(571-573)aCt>aAt	p.T191N	RCOR3_ENST00000452621.2_Missense_Mutation_p.T249N|RCOR3_ENST00000367006.4_Missense_Mutation_p.T249N|RCOR3_ENST00000419091.2_Missense_Mutation_p.T249N	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CCTGTCCAAACTAGCAAGATT	0.378																																					p.T249N		.											.	RCOR3-91	0			c.C746A						.						127	113	118					1																	211462545		2203	4300	6503	SO:0001583	missense	55758	exon8			TCCAAACTAGCAA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.572C>A	1.37:g.211462545C>A	ENSP00000355972:p.Thr191Asn	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	244	26	NM_001136223	0	0	18	19	1	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	37	CCDS31016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.33|13.33	2.205841|2.205841	0.39003|0.39003	.|.	.|.	ENSG00000117625|ENSG00000117625	ENST00000534460|ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005;ENST00000529763	.|T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61	5.62|5.62	4.7|4.7	0.59300|0.59300	.|.	.|0.488580	.|0.25119	.|N	.|0.032996	T|T	0.17874|0.17874	0.0429|0.0429	N|N	0.11201|0.11201	0.11|0.11	0.38814|0.38814	D|D	0.955493|0.955493	.|B;B;B;B	.|0.17268	.|0.002;0.0;0.021;0.018	.|B;B;B;B	.|0.15052	.|0.003;0.001;0.006;0.012	T|T	0.06250|0.06250	-1.0837|-1.0837	5|10	.|0.14252	.|T	.|0.57	-7.2822|-7.2822	16.1088|16.1088	0.81244|0.81244	0.0:0.8548:0.1452:0.0|0.0:0.8548:0.1452:0.0	.|.	.|249;191;249;249	.|Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.|.;RCOR3_HUMAN;.;.	K|N	35|249;249;249;191;9	.|ENSP00000355973:T249N;ENSP00000398558:T249N;ENSP00000413929:T249N;ENSP00000355972:T191N	.|ENSP00000355972:T191N	N|T	+|+	3|2	2|0	RCOR3|RCOR3	209529168|209529168	0.981000|0.981000	0.34729|0.34729	0.995000|0.995000	0.50966|0.50966	0.997000|0.997000	0.91878|0.91878	2.148000|2.148000	0.42235|0.42235	1.335000|1.335000	0.45486|0.45486	0.655000|0.655000	0.94253|0.94253	AAC|ACT	.		0.378	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		A	211462545	C	A	211462545	3	1	157	1	0	0	0	0	1	0	0	0	13216	565	20	4	776	4	RCOR3	1	211462545	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	6155946	211462545	37788076	17	14172											
AKT3	10000	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	243800913	243800913	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aactttaataaatcagttacCtttgcaataatgacttcttt	14	17	3	7	0	2	1	1	1	1	0	2	1	2	1	1	0	3	2	1	0	7	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:243800913C>T	ENST00000366539.1	-	6	761	c.561G>A	c.(559-561)aaG>aaA	p.K187K	AKT3_ENST00000366540.1_Splice_Site_p.K187K|AKT3_ENST00000336199.5_Splice_Site_p.K187K|AKT3_ENST00000263826.5_Splice_Site_p.K187K			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	187	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			AATCAGTTACCTTTGCAATAA	0.328																																					p.K187K		.											.	AKT3-1423	0			c.G561A						.						81	81	81					1																	243800913		2202	4295	6497	SO:0001630	splice_region_variant	10000	exon6			AGTTACCTTTGCA	AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"Pleckstrin homology (PH) domain containing"	393	protein-coding gene	gene with protein product	"protein kinase B, gamma"	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.561+1G>A	1.37:g.243800913C>T		Somatic	75	0		WXS	Illumina HiSeq	Phase_I	42	6	NM_001206729	0	0	0	0	0	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Silent	SNP	ENST00000366539.1	37	CCDS31077.1																																																																																			.		0.328	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690	Silent	T	243800913	C	T	243800913	5	4	157	1	0	0	0	0	0	0	1	0	481	695	24	2	962	2	AKT3	1	243800913	Splice_Site	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	32338368	243800913	5449708	18	14173											
OR2C3	81472	broad.mit.edu	37	chr1	247694872	247694872	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatttgcgccagcttgccTgcagagccacagcagttctc	9	10	9	13	1	1	1	0	0	1	1	2	1	1	1	3	0	6	4	3	0	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:247694872T>A	ENST00000366487.3	-	2	1303	c.942A>T	c.(940-942)gcA>gcT	p.A314A	GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000531662.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	314						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			CCAGCTTGCCTGCAGAGCCAC	0.517																																					p.A314A													.	OR2C3-70	0			c.A942T						.						58	54	56					1																	247694872		2203	4300	6503	SO:0001819	synonymous_variant	81472	exon2			CTTGCCTGCAGAG	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.942A>T	1.37:g.247694872T>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	150	5	NM_198074	0	0	0	0	0	Q5JQS4|Q6IEZ1|Q8NGW7	Silent	SNP	ENST00000366487.3	37	CCDS1634.2																																																																																			.		0.517	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		A	247694872	T	A	247694872	2	1	157	1	0	0	0	0	0	0	0	1	11019	1567	55	5		5	OR2C3	1	247694872	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	3893959	247694872	1555749	19	14174											
KCNS3	3790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	18113163	18113163	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagatcctacggcttatgagGattttccgaattctaaagct	11	13	8	9	2	1	2	0	1	1	1	3	4	3	3	2	2	2	2	2	2	5	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:18113163G>C	ENST00000403915.1	+	3	1339	c.888G>C	c.(886-888)agG>agC	p.R296S	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.R296S	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	296					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGCTTATGAGGATTTTCCGAA	0.502																																					p.R296S		.											.	KCNS3-94	0			c.G888C						.						109	107	108					2																	18113163		2203	4300	6503	SO:0001583	missense	3790	exon3			TATGAGGATTTTC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.888G>C	2.37:g.18113163G>C	ENSP00000385968:p.Arg296Ser	Somatic	161	0		WXS	Illumina HiSeq	Phase_I	220	83	NM_002252	0	0	6	18	12	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808968	0.50421	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.99594	-6.25;-6.25	5.86	1.98	0.26296	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99638	0.9867	H	0.96301	3.8	0.52099	D	0.999942	D	0.76494	0.999	D	0.85130	0.997	D	0.99194	1.0871	10	0.87932	D	0	.	6.5286	0.22314	0.2607:0.1183:0.621:0.0	.	296	Q9BQ31	KCNS3_HUMAN	S	296	ENSP00000385968:R296S;ENSP00000305824:R296S	ENSP00000305824:R296S	R	+	3	2	KCNS3	17976644	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.263000	0.33004	0.374000	0.24650	0.655000	0.94253	AGG	.		0.502	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		C	18113163	G	C	18113163	3	2	157	1	0	0	0	0	1	0	0	0	8111	1165	41	4	890	4	KCNS3	2	18113163	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		18113163	225086210	20	14175											
KHK	3795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	27315218	27315218	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggtgtttgtcccagagatgGcagcgcggaggcaacgcgtc	8	7	16	10	4	0	1	0	0	0	1	2	3	1	2	1	4	2	3	1	4	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:27315218G>T	ENST00000260599.6	+	2	624	c.111G>T	c.(109-111)tgG>tgT	p.W37C	KHK_ENST00000260598.5_Missense_Mutation_p.W37C|KHK_ENST00000490823.1_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	37					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCAGAGATGGCAGCGCGGAG	0.607																																					p.W37C		.											.	KHK-115	0			c.G111T						.						91	80	84					2																	27315218		2203	4300	6503	SO:0001583	missense	3795	exon2			GAGATGGCAGCGC		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.111G>T	2.37:g.27315218G>T	ENSP00000260599:p.Trp37Cys	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	65	31	NM_006488	0	0	89	197	108	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	37	CCDS1734.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.750913	0.49257	.	.	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.75938	-0.98;-0.98;-0.98	5.5	5.5	0.81552	Carbohydrate/purine kinase (1);	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.90082	3.085	0.80722	D	1	D;P;D	0.76494	0.999;0.495;0.999	D;B;D	0.75020	0.985;0.122;0.985	D	0.89208	0.3562	10	0.46703	T	0.11	-18.2402	16.8828	0.86067	0.0:0.0:1.0:0.0	.	37;37;37	Q6IBK2;P50053-2;P50053	.;.;KHK_HUMAN	C	37	ENSP00000260599:W37C;ENSP00000260598:W37C;ENSP00000404741:W37C	ENSP00000260598:W37C	W	+	3	0	KHK	27168722	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	8.964000	0.93389	2.595000	0.87683	0.462000	0.41574	TGG	.		0.607	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1			T	27315218	G	T	27315218	3	4	157	1	0	0	0	0	1	0	0	0	8170	1212	42	4	117	4	KHK	2	27315218	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	9202055	27315218	215884155	21	14176											
ERLEC1	27248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	54028861	54028861	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgaacaggttcagagcatCtcctgtgaatgacatatttt	12	13	8	8	0	2	4	1	3	1	1	3	4	2	4	1	1	2	2	1	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:54028861C>A	ENST00000185150.4	+	8	892	c.761C>A	c.(760-762)tCt>tAt	p.S254Y	ERLEC1_ENST00000378239.5_Missense_Mutation_p.S254Y|ASB3_ENST00000406625.2_Intron|ERLEC1_ENST00000405123.3_Missense_Mutation_p.S254Y|ASB3_ENST00000498475.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	254					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)			endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						TTCAGAGCATCTCCTGTGAAT	0.418																																					p.S254Y		.											.	ERLEC1-92	0			c.C761A						.						102	92	96					2																	54028861		2203	4300	6503	SO:0001583	missense	27248	exon8			GAGCATCTCCTGT	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"erlectin 1"	611229	"chromosome 2 open reading frame 30"	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.761C>A	2.37:g.54028861C>A	ENSP00000185150:p.Ser254Tyr	Somatic	122	0		WXS	Illumina HiSeq	Phase_I	128	61	NM_015701	0	0	0	0	0	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Missense_Mutation	SNP	ENST00000185150.4	37	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.909863	0.92107	.	.	ENSG00000068912	ENST00000405123;ENST00000185150;ENST00000378239	T;T	0.47528	0.84;0.84	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.71350	0.3329	.	.	.	0.80722	D	1	D;P;D	0.71674	0.997;0.756;0.998	D;B;D	0.69479	0.964;0.283;0.931	T	0.72567	-0.4254	9	0.72032	D	0.01	-13.4706	20.4024	0.99000	0.0:1.0:0.0:0.0	.	254;254;254	Q96DZ1-2;B5MC72;Q96DZ1	.;.;ERLEC_HUMAN	Y	254	ENSP00000385629:S254Y;ENSP00000185150:S254Y	ENSP00000185150:S254Y	S	+	2	0	ERLEC1	53882365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.827000	0.97445	0.650000	0.86243	TCT	.		0.418	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701		A	54028861	C	A	54028861	3	1	157	1	0	0	0	0	1	0	0	0	5244	913	32	4	791	4	ERLEC1	2	54028861	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	26713643	54028861	189170512	22	14177											
NAGK	55577	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	71304704	71304704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggtcttgttccagggcaAgattggactccccatcctgt	7	11	10	13	0	1	1	0	0	1	1	4	2	4	2	5	3	0	2	5	3	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:71304704A>G	ENST00000244204.6	+	9	844	c.782A>G	c.(781-783)aAg>aGg	p.K261R	NAGK_ENST00000443872.2_Missense_Mutation_p.K113R|NAGK_ENST00000455662.2_Missense_Mutation_p.K307R|NAGK_ENST00000443938.2_Missense_Mutation_p.K257R|NAGK_ENST00000418807.3_Missense_Mutation_p.K210R			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	261					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	TTCCAGGGCAAGATTGGACTC	0.602																																					p.K307R		.											.	NAGK-115	0			c.A920G						.						66	53	57					2																	71304704		2203	4300	6503	SO:0001583	missense	55577	exon9			AGGGCAAGATTGG	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.782A>G	2.37:g.71304704A>G	ENSP00000244204:p.Lys261Arg	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	99	38	NM_017567	0	0	150	244	94	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.73|11.73	1.724892|1.724892	0.30593|0.30593	.|.	.|.	ENSG00000124357|ENSG00000124357	ENST00000244204;ENST00000455662;ENST00000418807|ENST00000443938	T;T;T|.	0.44083|.	1.52;1.49;0.93|.	5.63|5.63	1.85|1.85	0.25348|0.25348	ATPase, BadF/BadG/BcrA/BcrD type (1);|.	0.811995|.	0.11191|.	N|.	0.589950|.	T|T	0.17619|0.17619	0.0423|0.0423	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.18398|0.18398	-1.0338|-1.0338	10|5	0.18276|.	T|.	0.48|.	-17.2471|-17.2471	2.0065|2.0065	0.03478|0.03478	0.4877:0.2795:0.0916:0.1411|0.4877:0.2795:0.0916:0.1411	.|.	261|.	Q9UJ70|.	NAGK_HUMAN|.	R|G	261;307;210|279	ENSP00000244204:K261R;ENSP00000389087:K307R;ENSP00000396070:K210R|.	ENSP00000244204:K261R|.	K|R	+|+	2|1	0|2	NAGK|NAGK	71158212|71158212	0.037000|0.037000	0.19845|0.19845	0.003000|0.003000	0.11579|0.11579	0.043000|0.043000	0.13939|0.13939	1.412000|1.412000	0.34714|0.34714	0.937000|0.937000	0.37394|0.37394	-0.336000|-0.336000	0.08194|0.08194	AAG|AGA	.		0.602	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1			G	71304704	A	G	71304704	3	3	157	1	0	0	0	0	1	0	0	0	10167	72	3	3	954	3	NAGK	2	71304704	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	17275843	71304704	171894669	23	14178											
RANBP2	5903	bcgsc.ca	37	chr2	109382102	109382103	+	Missense_Mutation	DNP	AC	AC	GT																															aaactacttctgcagtttcaAcacctgcctcttcagagaca																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AC	AC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:109382102_109382103AC>GT	ENST00000283195.6	+	20	5233_5234	c.5107_5108AC>GT	c.(5107-5109)ACa>GTa	p.T1703V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1703					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGCAGTTTCAACACCTGCCTCT	0.436																																					p.T1703V													.	RANBP2-675	0			c.C5108T						.																																			SO:0001583	missense	5903	exon20			TTTCAACACCTGC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"Tetratricopeptide (TTC) repeat domain containing"	9848	protein-coding gene	gene with protein product		601181	"acute necrotizing encephalopathy 1 (autosomal dominant)"	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	Exception_encountered	2.37:g.109382102_109382103delinsGT	ENSP00000283195:p.Thr1703Val	Somatic	732	6		WXS	Illumina HiSeq	Phase_1	944	350	NM_006267	0	0	0	0	0	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	DNP	ENST00000283195.6	37	CCDS2079.1																																																																																			.		0.436	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		GT	109382103	AC	GT	109382102	3	3	157	1	0	0	0	0	1	0	0	0	13060	43	2	3	5185	3	RANBP2	2	109382102	Missense_Mutation	DNP	AC	TCGA-P4-A5EB-01A-11D-A28G-10	38077398	109382102	133817271	24	14179											
UGGT1	56886	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	128941262	128941262	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattcagtgcactatatgttGtggatctgaagaagtttagg	11	15	11	4	0	2	2	1	1	1	1	2	3	2	3	0	2	1	3	0	2	6	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:128941262G>T	ENST00000259253.6	+	38	4305	c.4258G>T	c.(4258-4260)Gtg>Ttg	p.V1420L	UGGT1_ENST00000375990.3_Missense_Mutation_p.V1396L	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1420	Glucosyltransferase. {ECO:0000250}.				'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ACTATATGTTGTGGATCTGAA	0.438																																					p.V1420L		.											.	UGGT1-91	0			c.G4258T						.						107	102	104					2																	128941262		2203	4300	6503	SO:0001583	missense	56886	exon38			TATGTTGTGGATC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"UDP-glucose ceramide glucosyltransferase-like 1"	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.4258G>T	2.37:g.128941262G>T	ENSP00000259253:p.Val1420Leu	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	141	59	NM_020120	0	0	24	39	15	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733269	0.89482	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.37411	1.2;1.2	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.71978	0.3404	H	0.96175	3.78	0.80722	D	1	D	0.71674	0.998	D	0.69307	0.963	T	0.82600	-0.0377	9	.	.	.	.	18.0955	0.89488	0.0:0.0:1.0:0.0	.	1420	Q9NYU2	UGGG1_HUMAN	L	1396;1420	ENSP00000365158:V1396L;ENSP00000259253:V1420L	.	V	+	1	0	UGGT1	128657732	1.000000	0.71417	0.994000	0.49952	0.844000	0.47949	9.090000	0.94144	2.577000	0.86979	0.563000	0.77884	GTG	.		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		T	128941262	G	T	128941262	3	4	157	1	0	0	0	0	1	0	0	0	16974	1377	48	4	4408	4	UGGT1	2	128941262	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	19559160	128941262	114258111	25	14180											
YSK4	80122	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	135744072	135744072	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcatggactgctcaggtgtCtgagccaagttcatgggatg	8	12	13	8	0	4	1	3	1	1	0	4	3	4	3	1	3	2	2	1	3	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:135744072C>G	ENST00000375845.3	-	7	2400	c.2370G>C	c.(2368-2370)caG>caC	p.Q790H	MAP3K19_ENST00000392915.1_Missense_Mutation_p.Q807H|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000358371.4_Missense_Mutation_p.Q677H|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392917.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	790							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										GCTCAGGTGTCTGAGCCAAGT	0.398																																					p.Q790H		.											.	.	0			c.G2370C						.						65	65	65					2																	135744072		2203	4300	6503	SO:0001583	missense	80122	exon7			AGGTGTCTGAGCC	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	26249	protein-coding gene	gene with protein product			"Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)", "YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.2370G>C	2.37:g.135744072C>G	ENSP00000365005:p.Gln790His	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	112	40	NM_025052	0	0	0	0	0	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	0.926	-0.714163	0.03206	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.72615	-0.53;-0.53;1.83;-0.67	4.61	0.257	0.15574	.	0.519636	0.16240	N	0.223204	T	0.48607	0.1509	N	0.17082	0.46	0.09310	N	0.999998	B;B;B	0.23854	0.023;0.092;0.014	B;B;B	0.22880	0.028;0.042;0.013	T	0.31971	-0.9924	10	0.35671	T	0.21	.	6.5935	0.22659	0.0:0.5532:0.2308:0.2159	.	677;807;790	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	H	790;677;807;180	ENSP00000365005:Q790H;ENSP00000351140:Q677H;ENSP00000376647:Q807H;ENSP00000392827:Q180H	ENSP00000351140:Q677H	Q	-	3	2	YSK4	135460542	0.000000	0.05858	0.005000	0.12908	0.148000	0.21650	-0.294000	0.08309	0.133000	0.18654	0.407000	0.27541	CAG	.		0.398	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		G	135744072	C	G	135744072	3	3	157	1	0	0	0	0	1	0	0	0	17528	912	32	4	1632	4	YSK4	2	135744072	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	6802810	135744072	107455301	26	14181											
GCA	25801	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	163208899	163208899	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgtttgacacagtctggaAttaatggaacttactctcgt	11	14	9	7	1	2	1	0	1	2	0	3	4	2	3	0	2	2	1	0	2	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:163208899A>C	ENST00000437150.2	+	3	405	c.244A>C	c.(244-246)Att>Ctt	p.I82L	GCA_ENST00000233612.4_Missense_Mutation_p.I63L|GCA_ENST00000429691.2_Missense_Mutation_p.I63L|GCA_ENST00000473240.1_3'UTR	NM_012198.3	NP_036330.1	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	82	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				membrane fusion (GO:0061025)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	9						ACAGTCTGGAATTAATGGAAC	0.308																																					p.I82L		.											.	GCA-90	0			c.A244C						.						175	175	175					2																	163208899		2203	4300	6503	SO:0001583	missense	25801	exon3			TCTGGAATTAATG	M81637	CCDS2218.1	2q24.2	2013-01-10	2001-11-28		ENSG00000115271	ENSG00000115271		"EF-hand domain containing"	15990	protein-coding gene	gene with protein product		607030	"grancalcin, EF-hand calcium-binding protein"			1737748, 1530588, 12804766	Standard	NM_012198		Approved	GCL	uc002ucg.3	P28676	OTTHUMG00000132057	ENST00000437150.2:c.244A>C	2.37:g.163208899A>C	ENSP00000394842:p.Ile82Leu	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	119	58	NM_012198	0	0	19	31	12	B2R5X3|Q53TB5|Q59EP3	Missense_Mutation	SNP	ENST00000437150.2	37	CCDS2218.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.845886	0.51164	.	.	ENSG00000115271	ENST00000446271;ENST00000429691;ENST00000437150;ENST00000453113;ENST00000233612	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.19	5.19	0.71726	EF-hand-like domain (1);	0.726139	0.12958	N	0.425264	T	0.77471	0.4135	M	0.72118	2.19	0.52501	D	0.999952	B	0.33940	0.433	B	0.43536	0.423	T	0.69892	-0.5022	10	0.09843	T	0.71	.	14.0628	0.64810	1.0:0.0:0.0:0.0	.	82	P28676	GRAN_HUMAN	L	108;63;82;63;63	ENSP00000393218:I108L;ENSP00000412899:I63L;ENSP00000394842:I82L;ENSP00000403805:I63L;ENSP00000233612:I63L	ENSP00000233612:I63L	I	+	1	0	GCA	162917145	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	6.473000	0.73572	1.951000	0.56629	0.528000	0.53228	ATT	.		0.308	GCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255080.3	NM_012198		C	163208899	A	C	163208899	3	2	157	1	0	0	0	0	1	0	0	0	6303	101	4	5	254	5	GCA	2	163208899	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	27464827	163208899	79990474	27	14182											
XIRP2	129446	broad.mit.edu;bcgsc.ca	37	chr2	168102112	168102112	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagatttctgaagaatcaCataatattatgcccagtatt	15	14	5	7	0	3	3	2	1	1	2	3	3	3	3	1	0	1	1	1	0	6	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:168102112C>G	ENST00000409195.1	+	9	4299	c.4210C>G	c.(4210-4212)Cat>Gat	p.H1404D	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.H1182D|XIRP2_ENST00000295237.9_Missense_Mutation_p.H1404D|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1229					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGAAGAATCACATAATATTAT	0.338																																					p.H1404D													.	XIRP2-104	0			c.C4210G						.						63	58	60					2																	168102112		1838	4095	5933	SO:0001583	missense	129446	exon9			GAATCACATAATA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"myomaxin"	609778	"cardiomyopathy associated 3"	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4210C>G	2.37:g.168102112C>G	ENSP00000386840:p.His1404Asp	Somatic	177	1		WXS	Illumina HiSeq	Phase_I	198	82	NM_152381	0	0	0	0	0	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	1.094	-0.663261	0.03428	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02395	4.31;4.31;4.31	5.67	3.71	0.42584	.	0.488681	0.22341	N	0.061335	T	0.02156	0.0067	L	0.34521	1.04	0.09310	N	1	P;P;B	0.37864	0.475;0.61;0.137	B;B;B	0.32864	0.073;0.154;0.037	T	0.48103	-0.9064	10	0.22109	T	0.4	-0.0519	6.3874	0.21568	0.3388:0.5672:0.0:0.094	.	1229;1229;1182	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	D	1404;1404;1182	ENSP00000386840:H1404D;ENSP00000295237:H1404D;ENSP00000387255:H1182D	ENSP00000295237:H1404D	H	+	1	0	XIRP2	167810358	0.000000	0.05858	0.004000	0.12327	0.096000	0.18686	1.193000	0.32162	1.407000	0.46875	-0.253000	0.11424	CAT	.		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168102112	C	G	168102112	3	3	157	1	0	0	0	0	1	0	0	0	17463	478	17	4	4240	4	XIRP2	2	168102112	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	4893213	168102112	75097261	28	14183											
SPC25	57405	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	169746011	169746011	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tatgcttttatcgaaaagtgCcagttcgtcctctaccatta	10	15	6	10	2	1	0	0	0	1	0	4	1	2	0	3	0	3	2	3	0	6	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:169746011C>G	ENST00000282074.2	-	2	160	c.19G>C	c.(19-21)Gca>Cca	p.A7P	SPC25_ENST00000472216.2_5'UTR	NM_020675.3	NP_065726.1	Q9HBM1	SPC25_HUMAN	SPC25, NDC80 kinetochore complex component	7	Interaction with the N-terminus of SPBC24.|Interaction with the NDC80-NUF2 subcomplex.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	condensed chromosome kinetochore (GO:0000777)|cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	9						TCGAAAAGTGCCAGTTCGTCC	0.368																																					p.A7P		.											.	SPC25-226	0			c.G19C						.						59	55	57					2																	169746011		2203	4300	6503	SO:0001583	missense	57405	exon2			AAAGTGCCAGTTC	AF225416	CCDS2229.1	2q31.1	2013-06-05	2013-06-05	2007-03-02	ENSG00000152253	ENSG00000152253			24031	protein-coding gene	gene with protein product		609395	"spindle pole body component 25 homolog (S. cerevisiae)", "SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	SPBC25		12477932	Standard	NM_020675		Approved	MGC22228, AD024	uc002uel.3	Q9HBM1	OTTHUMG00000132181	ENST00000282074.2:c.19G>C	2.37:g.169746011C>G	ENSP00000282074:p.Ala7Pro	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	44	18	NM_020675	0	0	0	0	0	A8K4X8|D3DPC0	Missense_Mutation	SNP	ENST00000282074.2	37	CCDS2229.1	.	.	.	.	.	.	.	.	.	.	C	8.902	0.956561	0.18507	.	.	ENSG00000152253	ENST00000282074;ENST00000451987	.	.	.	6.16	3.38	0.38709	.	0.449522	0.26963	N	0.021614	T	0.18257	0.0438	L	0.27053	0.805	0.26399	N	0.976457	P	0.43169	0.8	B	0.37943	0.261	T	0.08330	-1.0727	9	0.46703	T	0.11	0.0356	6.4946	0.22136	0.0:0.693:0.1487:0.1583	.	7	Q9HBM1	SPC25_HUMAN	P	7	.	ENSP00000282074:A7P	A	-	1	0	SPC25	169454257	0.107000	0.21998	0.161000	0.22692	0.012000	0.07955	0.142000	0.16096	0.469000	0.27268	-0.142000	0.14014	GCA	.		0.368	SPC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255233.2	NM_020675		G	169746011	C	G	169746011	3	3	157	1	0	0	0	0	1	0	0	0	15054	739	26	4	679	4	SPC25	2	169746011	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1643899	169746011	73453362	29	14184											
METTL5	29081	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	170677784	170677784	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcaaatccaacacacaacCtataaatacaaaacacatac	21	7	1	12	0	1	0	1	0	0	0	2	0	2	0	2	0	5	0	2	0	10	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:170677784C>A	ENST00000260953.5	-	3	541		c.e3-1		METTL5_ENST00000308099.3_Splice_Site|METTL5_ENST00000410097.1_Splice_Site|METTL5_ENST00000409340.1_Intron|METTL5_ENST00000409965.1_Splice_Site|METTL5_ENST00000409837.1_Splice_Site|METTL5_ENST00000392640.2_Splice_Site	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5								methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						AACACACAACCTATAAATACA	0.299																																					.		.											.	METTL5-90	0			c.225-1G>T						.						75	75	75					2																	170677784		2203	4298	6501	SO:0001630	splice_region_variant	29081	exon4			CACAACCTATAAA	AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.225-1G>T	2.37:g.170677784C>A		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	114	39	NM_014168	0	0	0	0	0	D3DPC9|Q9NVX1	Splice_Site	SNP	ENST00000260953.5	37	CCDS33320.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065087	0.76187	.	.	ENSG00000138382	ENST00000409837;ENST00000540464;ENST00000260953;ENST00000409965;ENST00000392640;ENST00000308099;ENST00000410097	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7542	0.91826	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	METTL5	170386030	1.000000	0.71417	0.932000	0.37286	0.983000	0.72400	7.590000	0.82653	2.490000	0.84030	0.655000	0.94253	.	.		0.299	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168	Intron	A	170677784	C	A	170677784	5	1	157	1	0	0	0	0	0	0	1	0	9528	695	24	4	425	4	METTL5	2	170677784	Splice_Site	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	931773	170677784	72521589	30	14185											
RAPH1	65059	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	204304774	204304775	+	Frame_Shift_Del	DEL	AC	AC	-																															cagaacaggggcttttgctgAcacacacccttgttggagaa																								rs201752703		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:204304774_204304775delAC	ENST00000319170.5	-	14	3437_3438	c.3138_3139delGT	c.(3136-3141)gtgtcafs	p.S1047fs	RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000374493.3_Frame_Shift_Del_p.S1099fs	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1047					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GCTTTTGCTGACACACACCCTT	0.545																																					p.1046_1047del		.											.	RAPH1-1151	0			c.3138_3139del						.																																			SO:0001589	frameshift_variant	65059	exon14			.	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3138_3139delGT	2.37:g.204304780_204304781delAC	ENSP00000316543:p.Ser1047fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	79	37	NM_213589	0	0	0	0	0	Q96Q37|Q9C0I2	Frame_Shift_Del	DEL	ENST00000319170.5	37	CCDS2359.1																																																																																			.		0.545	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		-	204304775	AC	-	204304774	7	5	157	1	0	1	0	1	0	0	0	0	13082	275	10	0	617	0	RAPH1	2	204304774	Frame_Shift_Del	DEL	AC	TCGA-P4-A5EB-01A-11D-A28G-10	33626990	204304774	38894599	31	14186											
NHEJ1	79840	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	220022946	220022946	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacactagtgtccacctgttCatgccacacctgttgaagat	10	11	7	13	0	1	2	1	1	0	1	2	2	2	2	4	0	1	2	4	0	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:220022946C>T	ENST00000356853.5	-	2	272	c.139G>A	c.(139-141)Gaa>Aaa	p.E47K	NHEJ1_ENST00000409720.1_Missense_Mutation_p.E47K	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	47	Globular head.				B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		TCCACCTGTTCATGCCACACC	0.527								Non-homologous end-joining																													p.E47K		.											.	NHEJ1-227	0			c.G139A						.						158	135	143					2																	220022946		2203	4300	6503	SO:0001583	missense	79840	exon2			CCTGTTCATGCCA	AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736			25737	protein-coding gene	gene with protein product		611290				16439204, 16439205	Standard	NM_024782		Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.139G>A	2.37:g.220022946C>T	ENSP00000349313:p.Glu47Lys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	112	47	NM_024782	0	0	12	28	16	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	Missense_Mutation	SNP	ENST00000356853.5	37	CCDS2432.1	.	.	.	.	.	.	.	.	.	.	C	34	5.320702	0.95682	.	.	ENSG00000187736	ENST00000409720;ENST00000356853;ENST00000457600	T;T;T	0.71698	-0.59;-0.59;-0.59	5.7	5.7	0.88788	DNA double-strand break repair and VJ recombination XRCC4, N-terminal (1);	0.000000	0.85682	U	0.000000	D	0.85414	0.5691	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86392	0.1736	10	0.87932	D	0	0.2919	19.8022	0.96513	0.0:1.0:0.0:0.0	.	47	Q9H9Q4	NHEJ1_HUMAN	K	47	ENSP00000387290:E47K;ENSP00000349313:E47K;ENSP00000407201:E47K	ENSP00000349313:E47K	E	-	1	0	NHEJ1	219731190	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	4.959000	0.63666	2.683000	0.91414	0.655000	0.94253	GAA	.		0.527	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256817.2	NM_024782		T	220022946	C	T	220022946	3	4	157	1	0	0	0	0	1	0	0	0	10428	835	29	2	788	2	NHEJ1	2	220022946	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	15718172	220022946	23176427	32	14187											
SPEG	10290	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	220354060	220354064	+	Frame_Shift_Del	DEL	TCTTC	TCTTC	-																															attttctctctctcttagatTcttcagctgtgccatctgct																								rs78622154	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TCTTC	TCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:220354060_220354064delTCTTC	ENST00000312358.7	+	36	8452_8456	c.8320_8324delTCTTC	c.(8320-8325)tcttcafs	p.SS2774fs	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2774	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TCTCTTAGATTCTTCAGCTGTGCCA	0.62																																					p.2774_2775del		.											.	SPEG-383	0			c.8320_8324del						.																																			SO:0001589	frameshift_variant	10290	exon36			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8320_8324delTCTTC	2.37:g.220354060_220354064delTCTTC	ENSP00000311684:p.Ser2774fs	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	61	25	NM_005876	0	0	0	0	0	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	37	CCDS42824.1																																																																																			.		0.62	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		-	220354064	TCTTC	-	220354060	7	5	157	1	0	1	0	1	0	0	0	0	15068	1783	62	0	8474	0	SPEG	2	220354060	Frame_Shift_Del	DEL	TCTTC	TCGA-P4-A5EB-01A-11D-A28G-10	331114	220354060	22845313	33	14188											
SETD5	55209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	9475587	9475587	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagcgtgtattccactcatAattatgggaccactcagagg	12	10	10	9	1	2	2	2	0	0	2	3	3	3	3	2	2	1	1	2	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:9475587A>G	ENST00000406341.1	+	3	320	c.130A>G	c.(130-132)Aat>Gat	p.N44D	SETD5_ENST00000402466.1_5'UTR|SETD5_ENST00000407969.1_Missense_Mutation_p.N44D|SETD5_ENST00000402198.1_Missense_Mutation_p.N44D|SETD5_ENST00000302463.6_5'UTR			Q9C0A6	SETD5_HUMAN	SET domain containing 5	44										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		TTCCACTCATAATTATGGGAC	0.468																																					p.N44D		.											.	SETD5-70	0			c.A130G						.						204	200	201					3																	9475587		2010	4171	6181	SO:0001583	missense	55209	exon4			ACTCATAATTATG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.130A>G	3.37:g.9475587A>G	ENSP00000383939:p.Asn44Asp	Somatic	168	0		WXS	Illumina HiSeq	Phase_I	155	41	NM_001080517	0	0	1	3	2	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.537828	0.27475	.	.	ENSG00000168137	ENST00000450326;ENST00000402198;ENST00000406341;ENST00000407969	T;D;D;D	0.90261	1.45;-2.64;-2.64;-2.59	6.07	6.07	0.98685	.	.	.	.	.	D	0.82986	0.5156	L	0.47716	1.5	0.80722	D	1	P	0.38922	0.651	B	0.30401	0.115	T	0.79579	-0.1745	9	0.11485	T	0.65	-13.9018	9.0586	0.36421	0.8937:0.0:0.1063:0.0	.	44	Q9C0A6	SETD5_HUMAN	D	44	ENSP00000413786:N44D;ENSP00000385852:N44D;ENSP00000383939:N44D;ENSP00000384114:N44D	ENSP00000385852:N44D	N	+	1	0	SETD5	9450587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.856000	0.75450	2.330000	0.79161	0.477000	0.44152	AAT	.		0.468	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9475587	A	G	9475587	3	3	157	1	0	0	0	0	1	0	0	0	14166	362	13	3	136	3	SETD5	3	9475587	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		9475587	188546843	34	14189											
TWF2	11344	broad.mit.edu;bcgsc.ca	37	chr3	52265541	52265541	+	Frame_Shift_Del	DEL	C	C	-																															gcccgcgtggccgcgtacagCatcttcagccgcacctgaag																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:52265541delC	ENST00000305533.5	-	4	540	c.297delG	c.(295-297)atgfs	p.M99fs	TWF2_ENST00000499914.2_Frame_Shift_Del_p.M99fs|TLR9_ENST00000597542.1_5'UTR|TLR9_ENST00000494383.1_5'Flank	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	99	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCGCGTACAGCATCTTCAGCC	0.597											OREG0015610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M99fs													.	TWF2-757	0			c.297delG						.						101	94	96					3																	52265541		2203	4300	6503	SO:0001589	frameshift_variant	11344	exon4			GTACAGCATCTTC	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"protein tyrosine kinase 9-like (A6-related protein)", "PTK9L protein tyrosine kinase 9-like (A6-related protein)", "twinfilin, actin-binding protein, homolog 2 (Drosophila)"	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.297delG	3.37:g.52265541delC	ENSP00000303908:p.Met99fs	Somatic	52	0	983	WXS	Illumina HiSeq	Phase_I	29	7	NM_007284	0	0	0	0	0	Q9Y3F5	Frame_Shift_Del	DEL	ENST00000305533.5	37	CCDS2849.1																																																																																			.		0.597	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2			-	52265541	C	-	52265541	7	5	157	1	0	1	0	1	0	0	0	0	16815	710	25	0	776	0	TWF2	3	52265541	Frame_Shift_Del	DEL	C	TCGA-P4-A5EB-01A-11D-A28G-10	42789954	52265541	145756889	35	14190	155	2									
TWF2	11344	broad.mit.edu;bcgsc.ca	37	chr3	52265543	52265555	+	Splice_Site	DEL	TCTTCAGCCGCAC	TCTTCAGCCGCAC	-																															ccgcgtggccgcgtacagcaTcttcagccgcacctgaaggg																								rs199817219		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TCTTCAGCCGCAC	TCTTCAGCCGCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:52265543_52265555delTCTTCAGCCGCAC	ENST00000305533.5	-	4	526_538	c.283_295delGTGCGGCTGAAGA	c.(283-297)gtgcggctgaagatg>tg	p.VRLKM95fs	TWF2_ENST00000499914.2_Splice_Site_p.VRLKM95fs|TLR9_ENST00000597542.1_5'UTR|TLR9_ENST00000494383.1_5'Flank	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	95	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)	p.R96G(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GCGTACAGCATCTTCAGCCGCACCTGAAGGGCA	0.606											OREG0015610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.95_99del													.	TWF2-757	1	Substitution - Missense(1)	lung(1)	c.283_295del						.																																			SO:0001630	splice_region_variant	11344	exon4			ACAGCATCTTCAG	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"protein tyrosine kinase 9-like (A6-related protein)", "PTK9L protein tyrosine kinase 9-like (A6-related protein)", "twinfilin, actin-binding protein, homolog 2 (Drosophila)"	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.283-1GTGCGGCTGAAGA>-	3.37:g.52265543_52265555delTCTTCAGCCGCAC		Somatic	50	0	983	WXS	Illumina HiSeq	Phase_I	29	7	NM_007284	0	0	0	0	0	Q9Y3F5	Frame_Shift_Del	DEL	ENST00000305533.5	37	CCDS2849.1																																																																																			.		0.606	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2		Frame_Shift_Del	-	52265555	TCTTCAGCCGCAC	-	52265543	8	5	157	1	0	1	0	1	0	0	1	0	16815	1435	50	0	778	0	TWF2	3	52265543	Splice_Site	DEL	TCTTCAGCCGCAC	TCGA-P4-A5EB-01A-11D-A28G-10	2	52265543	145756887	36	14191	155	2									
DNAH1	25981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	52428521	52428521	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgggggctccatctcgaTcatgactgagaatccggcac	8	9	12	12	2	3	2	1	2	2	1	6	4	5	2	2	3	0	2	2	3	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:52428521T>C	ENST00000420323.2	+	67	10928	c.10667T>C	c.(10666-10668)aTc>aCc	p.I3556T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3621					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCATCTCGATCATGACTGAG	0.622																																					p.I3556T		.											.	DNAH1-67	0			c.T10667C						.						72	79	77					3																	52428521		2065	4195	6260	SO:0001583	missense	25981	exon67			TCTCGATCATGAC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"Axonemal dyneins"	2940	protein-coding gene	gene with protein product		603332	"dynein, axonemal, heavy polypeptide 1"			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.10667T>C	3.37:g.52428521T>C	ENSP00000401514:p.Ile3556Thr	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	115	58	NM_015512	0	0	0	4	4	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	1.598	-0.527373	0.04141	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	D	0.87103	-2.21	5.27	-5.01	0.02991	.	1.697270	0.03317	N	0.191372	T	0.70996	0.3288	N	0.12569	0.235	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.56721	-0.7932	10	0.33141	T	0.24	.	2.3064	0.04175	0.1418:0.4088:0.1794:0.27	.	3556;3621	C9JXH6;Q9P2D7-2	.;.	T	3556;309	ENSP00000401514:I3556T	ENSP00000273600:I309T	I	+	2	0	DNAH1	52403561	0.000000	0.05858	0.000000	0.03702	0.215000	0.24574	-0.451000	0.06795	-0.554000	0.06150	-0.274000	0.10170	ATC	.		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52428521	T	C	52428521	3	2	157	1	0	0	0	0	1	0	0	0	4608	1435	50	3	10929	3	DNAH1	3	52428521	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	162978	52428521	145593909	37	14192											
ABHD6	57406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	58242370	58242370	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcacgctggccatcccAatcctggcatttgtggcttc	5	10	12	14	2	0	0	0	0	0	0	3	0	2	0	3	5	0	4	3	5	1	2	rs11544005		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:58242370A>T	ENST00000478253.1	+	3	558	c.57A>T	c.(55-57)ccA>ccT	p.P19P	ABHD6_ENST00000295962.4_Silent_p.P19P			Q9BV23	ABHD6_HUMAN	abhydrolase domain containing 6	19					long term synaptic depression (GO:0060292)|negative regulation of cell migration (GO:0030336)|regulation of endocannabinoid signaling pathway (GO:2000124)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acylglycerol lipase activity (GO:0047372)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	16				BRCA - Breast invasive adenocarcinoma(55;0.000225)|KIRC - Kidney renal clear cell carcinoma(284;0.0471)|Kidney(284;0.0589)|OV - Ovarian serous cystadenocarcinoma(275;0.209)		TGGCCATCCCAATCCTGGCAT	0.463																																					p.P19P		.											.	ABHD6-92	0			c.A57T						.						174	165	168					3																	58242370		2203	4300	6503	SO:0001819	synonymous_variant	57406	exon2			CATCCCAATCCTG	AF225418	CCDS2887.1	3p21.2	2006-03-10			ENSG00000163686	ENSG00000163686		"Abhydrolase domain containing"	21398	protein-coding gene	gene with protein product							Standard	NM_020676		Approved		uc003djs.4	Q9BV23	OTTHUMG00000159150	ENST00000478253.1:c.57A>T	3.37:g.58242370A>T		Somatic	106	0		WXS	Illumina HiSeq	Phase_I	103	23	NM_020676	0	0	22	31	9	B2R7Y9|Q6ZMF7	Silent	SNP	ENST00000478253.1	37	CCDS2887.1																																																																																			.		0.463	ABHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353511.1	NM_020676		T	58242370	A	T	58242370	2	4	157	1	0	0	0	0	0	0	0	1	86	117	5	5		5	ABHD6	3	58242370	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	5813849	58242370	139780060	38	14193											
ZNF654	55279	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	88189810	88189810	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagatcctgctttgaaaatTgatacaaacagaatcaggac	16	10	7	8	0	2	4	2	2	0	2	3	5	3	5	1	1	3	1	1	1	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:88189810T>G	ENST00000309495.5	+	1	1557	c.1350T>G	c.(1348-1350)atT>atG	p.I450M	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	450					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(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		CTTTGAAAATTGATACAAACA	0.383																																					p.I450M													.	ZNF654-69	0			c.T1350G						.						85	83	83					3																	88189810		1881	4102	5983	SO:0001583	missense	55279	exon1			GAAAATTGATACA	AF543494	CCDS46874.1	3p11.1	2005-01-10			ENSG00000175105	ENSG00000175105			25612	protein-coding gene	gene with protein product							Standard	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	Q8IZM8	OTTHUMG00000159097	ENST00000309495.5:c.1350T>G	3.37:g.88189810T>G	ENSP00000312141:p.Ile450Met	Somatic	223	1		WXS	Illumina HiSeq	Phase_I	236	86	NM_018293	0	0	1	1	0	Q9H791|Q9NV14	Missense_Mutation	SNP	ENST00000309495.5	37	CCDS46874.1	.	.	.	.	.	.	.	.	.	.	t	0.623	-0.820178	0.02755	.	.	ENSG00000175105	ENST00000309495	T	0.10005	2.92	5.23	-2.35	0.06684	.	.	.	.	.	T	0.04907	0.0132	N	0.14661	0.345	0.09310	N	0.99999	B	0.02656	0.0	B	0.04013	0.001	T	0.39941	-0.9589	9	0.44086	T	0.13	.	2.3057	0.04173	0.233:0.0753:0.3389:0.3529	.	450	Q8IZM8	ZN654_HUMAN	M	450	ENSP00000312141:I450M	ENSP00000312141:I450M	I	+	3	3	ZNF654	88272500	0.029000	0.19370	0.803000	0.32268	0.354000	0.29330	0.080000	0.14802	-0.023000	0.13963	-0.420000	0.06012	ATT	.		0.383	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2	NM_018293		G	88189810	T	G	88189810	3	3	157	1	0	0	0	0	1	0	0	0	18099	1800	63	5	1352	5	ZNF654	3	88189810	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	29947440	88189810	109832620	39	14194											
CBLB	868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	105572285	105572285	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgactgttcttcatacattCtctccttgccttctttaaag	7	18	5	11	0	4	1	1	1	3	0	6	1	5	1	2	0	2	1	2	0	3	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:105572285C>A	ENST00000264122.4	-	3	713	c.392G>T	c.(391-393)aGa>aTa	p.R131I	CBLB_ENST00000405772.1_Missense_Mutation_p.R131I|CBLB_ENST00000394027.3_Missense_Mutation_p.R153I|CBLB_ENST00000403724.1_Missense_Mutation_p.R131I|CBLB_ENST00000545639.1_Missense_Mutation_p.R153I	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	131	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						TTCATACATTCTCTCCTTGCC	0.343			Mis S		AML																																p.R131I	GBM(93;588 1337 9788 29341 43499)	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB-849	0			c.G392T						.						240	242	241					3																	105572285		2203	4300	6503	SO:0001583	missense	868	exon3			TACATTCTCTCCT	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"RING-type (C3HC4) zinc fingers"	1542	protein-coding gene	gene with protein product		604491	"Cas-Br-M (murine) ectropic retroviral transforming sequence b", "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.392G>T	3.37:g.105572285C>A	ENSP00000264122:p.Arg131Ile	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	135	33	NM_170662	0	0	4	7	3	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	37	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280158	0.95489	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772;ENST00000545639;ENST00000438603;ENST00000447441;ENST00000443752	T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.69	5.69	0.88448	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.85682	D	0.000000	D	0.85991	0.5826	L	0.50333	1.59	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.74348	0.983;0.972;0.937	D	0.86563	0.1842	10	0.87932	D	0	-13.8454	19.8034	0.96518	0.0:1.0:0.0:0.0	.	153;131;131	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	I	131;153;131;131;153;153;131;131	ENSP00000264122:R131I;ENSP00000377595:R153I;ENSP00000384816:R131I;ENSP00000384938:R131I;ENSP00000446116:R153I;ENSP00000409750:R153I;ENSP00000400949:R131I;ENSP00000393906:R131I	ENSP00000264122:R131I	R	-	2	0	CBLB	107054975	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.603000	0.82811	2.669000	0.90835	0.655000	0.94253	AGA	.		0.343	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		A	105572285	C	A	105572285	3	1	157	1	0	0	0	0	1	0	0	0	2707	913	32	4	2624	4	CBLB	3	105572285	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	17382475	105572285	92450145	40	14195											
EAF2	55840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	121554190	121554190	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgagcgggttctcaagttaGgggagagtttcgagaagcag	10	8	17	6	3	1	2	1	0	1	2	3	5	1	2	0	3	2	4	0	3	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:121554190G>A	ENST00000273668.2	+	1	129	c.58G>A	c.(58-60)Ggg>Agg	p.G20R	EAF2_ENST00000451944.2_Missense_Mutation_p.G20R|IQCB1_ENST00000310864.6_5'Flank|IQCB1_ENST00000349820.6_5'Flank|EAF2_ENST00000465664.1_3'UTR	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	20	Necessary for interaction with ELL.				apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	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)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TCTCAAGTTAGGGGAGAGTTT	0.592																																					p.G20R	Esophageal Squamous(194;1942 2097 24663 29345 31866)	.											.	EAF2-90	0			c.G58A						.						60	57	58					3																	121554190		2203	4300	6503	SO:0001583	missense	55840	exon1			AAGTTAGGGGAGA	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.58G>A	3.37:g.121554190G>A	ENSP00000273668:p.Gly20Arg	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	97	9	NM_018456	0	0	12	14	2	Q9NZ82	Missense_Mutation	SNP	ENST00000273668.2	37	CCDS3006.1	.	.	.	.	.	.	.	.	.	.	G	36	5.612769	0.96637	.	.	ENSG00000145088	ENST00000273668;ENST00000451944	.	.	.	5.95	5.95	0.96441	Transcription elognation factor  Eaf, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84238	0.5428	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.85853	0.1405	9	0.87932	D	0	-12.3041	17.8686	0.88804	0.0:0.0:1.0:0.0	.	20	Q96CJ1	EAF2_HUMAN	R	20	.	ENSP00000273668:G20R	G	+	1	0	EAF2	123036880	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.606000	0.82863	2.817000	0.96982	0.563000	0.77884	GGG	.		0.592	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456		A	121554190	G	A	121554190	3	1	157	1	0	0	0	0	1	0	0	0	4887	1000	35	2	60	2	EAF2	3	121554190	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	15981905	121554190	76468240	41	14196											
PARP14	54625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	122436993	122436993	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agactttgtccagaaaggatCagcccagtctgtgaaaaaag	15	8	10	8	0	2	3	1	1	1	2	3	4	3	4	2	1	1	0	2	1	4	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:122436993C>G	ENST00000474629.2	+	13	4342	c.4076C>G	c.(4075-4077)tCa>tGa	p.S1359*		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1359	Macro 3. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CAGAAAGGATCAGCCCAGTCT	0.388																																					p.S1359X		.											.	PARP14-525	0			c.C4076G						.						88	82	84					3																	122436993		1860	4108	5968	SO:0001587	stop_gained	54625	exon13			AAGGATCAGCCCA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"Poly (ADP-ribose) polymerases"	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4076C>G	3.37:g.122436993C>G	ENSP00000418194:p.Ser1359*	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	185	102	NM_017554	0	0	4	4	0	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Nonsense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	C	40	8.082615	0.98646	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000398157	.	.	.	5.28	-1.14	0.09741	.	1.436610	0.04490	N	0.379296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	5.3252	0.15903	0.1259:0.4927:0.0:0.3814	.	.	.	.	X	1359;1278;355	.	ENSP00000381224:S355X	S	+	2	0	PARP14	123919683	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	0.777000	0.26718	-0.442000	0.07190	0.650000	0.86243	TCA	.		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122436993	C	G	122436993	4	3	157	1	0	0	0	0	0	1	0	0	11484	838	29	4	4126	4	PARP14	3	122436993	Nonsense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	882803	122436993	75585437	42	14197											
RBP2	5948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	139195286	139195286	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccatctcccaggttccatTctggtcccttgtcatggtgg	4	14	9	14	0	3	0	1	0	2	0	7	0	6	0	4	4	0	1	4	4	0	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:139195286T>A	ENST00000232217.2	-	1	72	c.16A>T	c.(16-18)Aat>Tat	p.N6Y	RP11-319G6.1_ENST00000515247.1_RNA	NM_004164.2	NP_004155.2	P50120	RET2_HUMAN	retinol binding protein 2, cellular	6					epidermis development (GO:0008544)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12					Vitamin A(DB00162)	CAGGTTCCATTCTGGTCCCTT	0.537																																					p.N6Y		.											.	RBP2-91	0			c.A16T						.						154	132	139					3																	139195286		2203	4300	6503	SO:0001583	missense	5948	exon1			TTCCATTCTGGTC	U13831	CCDS3109.1	3q23	2013-03-01	2001-11-28		ENSG00000114113	ENSG00000114113		"Fatty acid binding protein family"	9920	protein-coding gene	gene with protein product		180280	"retinol-binding protein 2, cellular"			7657783, 10072590	Standard	NM_004164		Approved	CRBP2, RBPC2, CRBPII, CRABP-II	uc003eth.3	P50120	OTTHUMG00000159956	ENST00000232217.2:c.16A>T	3.37:g.139195286T>A	ENSP00000232217:p.Asn6Tyr	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	74	11	NM_004164	0	0	0	0	0	A8K7G3|Q6ISQ9|Q6ISS7	Missense_Mutation	SNP	ENST00000232217.2	37	CCDS3109.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.138577	0.77775	.	.	ENSG00000114113	ENST00000232217;ENST00000511956;ENST00000506825	T;T	0.08102	3.13;3.13	5.44	5.44	0.79542	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.550372	0.21049	N	0.081028	T	0.17023	0.0409	L	0.29908	0.895	0.54753	D	0.999987	D	0.76494	0.999	D	0.68039	0.955	T	0.01666	-1.1300	10	0.44086	T	0.13	.	13.5403	0.61671	0.0:0.0:0.0:1.0	.	6	P50120	RET2_HUMAN	Y	6	ENSP00000232217:N6Y;ENSP00000424333:N6Y	ENSP00000232217:N6Y	N	-	1	0	RBP2	140677976	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	3.604000	0.54081	2.194000	0.70268	0.460000	0.39030	AAT	.		0.537	RBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358490.1	NM_004164		A	139195286	T	A	139195286	3	1	157	1	0	0	0	0	1	0	0	0	13188	1783	62	5	404	5	RBP2	3	139195286	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	16758293	139195286	58827144	43	14198											
ZBTB38	253461	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	141162052	141162058	+	Frame_Shift_Del	DEL	TTCGGAT	TTCGGAT	-																															acattctccataccacaggaTtcggattcagccacagaaaa																								rs549239683		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TTCGGAT	TTCGGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:141162052_141162058delTTCGGAT	ENST00000514251.1	+	4	1101_1107	c.822_828delTTCGGAT	c.(820-828)gattcggatfs	p.DSD274fs	ZBTB38_ENST00000321464.5_Frame_Shift_Del_p.DSD275fs|ZBTB38_ENST00000441582.2_Frame_Shift_Del_p.DSD274fs					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TACCACAGGATTCGGATTCAGCCACAG	0.459																																					p.274_276del		.											.	ZBTB38-25	0			c.822_828del						.																																			SO:0001589	frameshift_variant	253461	exon8			.	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.822_828delTTCGGAT	3.37:g.141162052_141162058delTTCGGAT	ENSP00000426387:p.Asp274fs	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	65	14	NM_001080412	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000514251.1	37	CCDS43157.1																																																																																			.		0.459	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			-	141162058	TTCGGAT	-	141162052	7	5	157	1	0	1	0	1	0	0	0	0	17571	1490	52	0	824	0	ZBTB38	3	141162052	Frame_Shift_Del	DEL	TTCGGAT	TCGA-P4-A5EB-01A-11D-A28G-10	1966766	141162052	56860378	44	14199											
SR140	23350	bcgsc.ca	37	chr3	142762057	142762057	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaagaagaaatgactgagtCtaagttctctaagtactctg	15	11	8	7	0	3	4	0	2	3	2	4	4	3	4	0	0	1	2	0	0	6	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:142762057C>T	ENST00000473835.2	+	24	2573	c.2483C>T	c.(2482-2484)tCt>tTt	p.S828F	U2SURP_ENST00000493598.2_Missense_Mutation_p.S827F|U2SURP_ENST00000397933.2_Missense_Mutation_p.S419F	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	828	Glu-rich.				RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ATGACTGAGTCTAAGTTCTCT	0.353																																					p.S828F													.	U2SURP-71	0			c.C2483T						.						69	61	64					3																	142762057		1861	4102	5963	SO:0001583	missense	23350	exon24			CTGAGTCTAAGTT	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"RNA binding motif (RRM) containing"	30855	protein-coding gene	gene with protein product	"functional spliceosome-associated protein a", "Ser/Arg-rich domain protein, 140 kDa", "U2 associated SR140 protein"					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.2483C>T	3.37:g.142762057C>T	ENSP00000418563:p.Ser828Phe	Somatic	591	4		WXS	Illumina HiSeq	Phase_1	550	319	NM_001080415	0	0	6	20	14	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Missense_Mutation	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595735	0.46318	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000397933;ENST00000493598;ENST00000480029	T;T;T;D	0.97505	0.89;0.89;0.89;-4.41	5.65	5.65	0.86999	.	0.107341	0.64402	D	0.000004	D	0.93331	0.7874	N	0.14661	0.345	0.52501	D	0.999956	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.001	D	0.88459	0.3054	10	0.37606	T	0.19	-8.4043	19.7129	0.96103	0.0:1.0:0.0:0.0	.	827;419;828	O15042-2;O15042-3;O15042	.;.;SR140_HUMAN	F	828;828;419;827;395	ENSP00000418563:S828F;ENSP00000381027:S419F;ENSP00000422011:S827F;ENSP00000417441:S395F	ENSP00000322376:S828F	S	+	2	0	U2SURP	144244747	0.991000	0.36638	1.000000	0.80357	0.981000	0.71138	3.465000	0.53064	2.658000	0.90341	0.650000	0.86243	TCT	.		0.353	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		T	142762057	C	T	142762057	3	4	157	1	0	0	0	0	1	0	0	0	15163	913	32	2	2577	2	SR140	3	142762057	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1600005	142762057	55260373	45	14200											
HPS3	84343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	148857880	148857881	+	Frame_Shift_Ins	INS	-	-	GT																															taaaaggactgaaaactctcINSgtgtgtgtatccgaatgatt																								rs541164156		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:148857880_148857881insGT	ENST00000296051.2	+	2	447_448	c.307_308insGT	c.(307-309)cgtfs	p.R103fs	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	103					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.R103S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGAAAACTCTCGTGTGTGTATC	0.426									Hermansky-Pudlak syndrome																												p.R103fs		.											.	HPS3-158	1	Substitution - Missense(1)	lung(1)	c.307_308insGT						.																																			SO:0001589	frameshift_variant	84343	exon2	Familial Cancer Database	HPS, HPS1-8	.	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.314_315dupGT	3.37:g.148857887_148857888dupGT	ENSP00000296051:p.Arg103fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	131	30	NM_032383	0	0	0	0	0	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Frame_Shift_Ins	INS	ENST00000296051.2	37	CCDS3140.1																																																																																			.		0.426	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		GT	148857881	-	GT	148857880	7	5	157	1	0	1	1	0	0	0	0	0	7361	884	31	0	313	0	HPS3	3	148857880	Frame_Shift_Ins	INS	-	TCGA-P4-A5EB-01A-11D-A28G-10	6095823	148857880	49164550	46	14201											
PLD1	5337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	171395429	171395429	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctttccatgccagaatctGgtttccccatgcagctctcc	6	13	6	16	0	2	1	0	0	2	1	6	1	5	1	6	1	3	3	6	1	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:171395429G>A	ENST00000351298.4	-	17	2049	c.1923C>T	c.(1921-1923)acC>acT	p.T641T	PLD1_ENST00000356327.5_Silent_p.T603T|PLD1_ENST00000340989.4_Silent_p.T641T|PLD1_ENST00000342215.6_Missense_Mutation_p.P532L	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	641	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GCCAGAATCTGGTTTCCCCAT	0.498																																					p.T641T	NSCLC(149;2174 3517 34058)	.											.	PLD1-660	0			c.C1923T						.						169	150	157					3																	171395429		2203	4300	6503	SO:0001819	synonymous_variant	5337	exon17			GAATCTGGTTTCC	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"Pleckstrin homology (PH) domain containing"	9067	protein-coding gene	gene with protein product	"choline phosphatase 1"	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1923C>T	3.37:g.171395429G>A		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	118	31	NM_002662	0	0	10	12	2		Silent	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196234	0.38806	.	.	ENSG00000075651	ENST00000342215	T	0.34072	1.38	6.16	0.406	0.16366	.	.	.	.	.	T	0.25827	0.0629	.	.	.	0.30550	N	0.765587	.	.	.	.	.	.	T	0.31110	-0.9955	6	0.27785	T	0.31	-24.3912	4.8638	0.13598	0.1371:0.3306:0.4295:0.1029	.	.	.	.	L	532	ENSP00000339936:P532L	ENSP00000339936:P532L	P	-	2	0	PLD1	172878123	0.948000	0.32251	0.748000	0.31131	0.981000	0.71138	0.123000	0.15708	0.117000	0.18138	0.650000	0.86243	CCA	.		0.498	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171395429	G	A	171395429	2	1	157	1	0	0	0	0	0	0	0	1	12071	1335	47	2		2	PLD1	3	171395429	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	22537549	171395429	26627001	47	14202											
RFC4	5984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	186508173	186508173	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaggcagcaaatactccaTcaattttctcagctggtatt	12	12	7	10	0	2	0	2	0	1	0	4	1	3	0	1	2	3	4	1	2	4	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:186508173T>A	ENST00000392481.2	-	9	1105	c.824A>T	c.(823-825)gAt>gTt	p.D275V	RFC4_ENST00000296273.2_Missense_Mutation_p.D275V|SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA|RFC4_ENST00000433496.1_Intron	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	275					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.D275G(1)		breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		AAATACTCCATCAATTTTCTC	0.428																																					p.D275V		.											.	RFC4-291	1	Substitution - Missense(1)	kidney(1)	c.A824T						.						112	112	112					3																	186508173		2203	4300	6503	SO:0001583	missense	5984	exon9			ACTCCATCAATTT		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"ATPases / AAA-type"	9972	protein-coding gene	gene with protein product	"A1 37 kDa subunit", "activator 1 37 kDa subunit", "RFC 37 kDa subunit"	102577	"replication factor C (activator 1) 4 (37kD)"			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.824A>T	3.37:g.186508173T>A	ENSP00000376272:p.Asp275Val	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	144	36	NM_181573	0	0	9	13	4	B4DM41|D3DNV2|Q6FHX7	Missense_Mutation	SNP	ENST00000392481.2	37	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.670832	0.29693	.	.	ENSG00000163918	ENST00000392481;ENST00000296273;ENST00000417876	T;T;T	0.44083	0.93;0.93;0.93	5.32	2.79	0.32731	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.428568	0.30538	N	0.009405	T	0.44808	0.1311	M	0.84326	2.69	0.80722	D	1	B	0.18013	0.025	B	0.27887	0.084	T	0.46373	-0.9196	10	0.54805	T	0.06	.	6.9715	0.24652	0.0:0.0842:0.1493:0.7664	.	275	P35249	RFC4_HUMAN	V	275;275;50	ENSP00000376272:D275V;ENSP00000296273:D275V;ENSP00000401429:D50V	ENSP00000296273:D275V	D	-	2	0	RFC4	187990867	0.999000	0.42202	0.697000	0.30258	0.437000	0.31866	2.471000	0.45127	0.970000	0.38263	0.459000	0.35465	GAT	.		0.428	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		A	186508173	T	A	186508173	3	1	157	1	0	0	0	0	1	0	0	0	13279	1435	50	5	279	5	RFC4	3	186508173	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	15112744	186508173	11514257	48	14203											
IDUA	3425	broad.mit.edu	37	chr4	996204	996204	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgcttccaggtcaacaacAcccgcccgccgcacgtgcag	8	4	10	19	6	1	0	1	0	0	0	2	0	2	0	4	1	3	3	4	1	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:996204A>C	ENST00000247933.4	+	8	1208	c.1120A>C	c.(1120-1122)Acc>Ccc	p.T374P	IDUA_ENST00000514224.1_Missense_Mutation_p.T242P|IDUA_ENST00000453894.1_Missense_Mutation_p.T396P	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	374					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGTCAACAACACCCGCCCGCC	0.711																																					p.T374P													.	IDUA-91	0			c.A1120C						.						26	28	27					4																	996204		2185	4282	6467	SO:0001583	missense	3425	exon8			AACAACACCCGCC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.1120A>C	4.37:g.996204A>C	ENSP00000247933:p.Thr374Pro	Somatic	74	19		WXS	Illumina HiSeq	Phase_I	180	85	NM_000203	0	0	3	4	1	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117066	0.77323	.	.	ENSG00000127415	ENST00000247933;ENST00000453894;ENST00000514224	D;D;D	0.94280	-3.39;-3.39;-3.39	5.31	5.31	0.75309	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.156849	0.56097	D	0.000026	D	0.96611	0.8894	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.96508	0.9376	10	0.46703	T	0.11	-7.29	13.2474	0.60029	1.0:0.0:0.0:0.0	.	396;374	B3KWK6;P35475	.;IDUA_HUMAN	P	374;396;242	ENSP00000247933:T374P;ENSP00000396458:T396P;ENSP00000425081:T242P	ENSP00000247933:T374P	T	+	1	0	IDUA	986204	1.000000	0.71417	0.995000	0.50966	0.426000	0.31534	5.967000	0.70403	2.024000	0.59613	0.454000	0.30748	ACC	.		0.711	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203		C	996204	A	C	996204	3	2	157	1	0	0	0	0	1	0	0	0	7525	159	6	5	1150	5	IDUA	4	996204	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		996204	190158072	49	14204											
HTT	3064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	3162057	3162057	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagtttggagggtttctcCgctcagccttggatgttctt	7	15	11	8	1	3	0	1	0	2	0	4	2	3	2	2	3	1	4	2	3	2	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:3162057C>T	ENST00000355072.5	+	29	3947	c.3802C>T	c.(3802-3804)Cgc>Tgc	p.R1268C		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1268					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGGGTTTCTCCGCTCAGCCTT	0.512																																					p.R1268C		.											.	HTT-281	0			c.C3802T						.																																			SO:0001583	missense	3064	exon29			TTTCTCCGCTCAG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"Endogenous ligands"	4851	protein-coding gene	gene with protein product		613004	"huntingtin (Huntington disease)"	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.3802C>T	4.37:g.3162057C>T	ENSP00000347184:p.Arg1268Cys	Somatic	173	0		WXS	Illumina HiSeq	Phase_I	181	67	NM_002111	0	0	0	3	3	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674542	0.29693	.	.	ENSG00000197386	ENST00000355072	T	0.65916	-0.18	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	L	0.52364	1.645	0.80722	D	1	B	0.18166	0.026	B	0.11329	0.006	T	0.57946	-0.7723	10	0.44086	T	0.13	.	16.6252	0.84968	0.0:1.0:0.0:0.0	.	1268	P42858	HD_HUMAN	C	1268	ENSP00000347184:R1268C	ENSP00000347184:R1268C	R	+	1	0	HTT	3131855	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	4.125000	0.57931	2.069000	0.61940	0.563000	0.77884	CGC	.		0.512	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3162057	C	T	3162057	3	4	157	1	0	0	0	0	1	0	0	0	7478	652	23	1	3916	1	HTT	4	3162057	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	2165853	3162057	187992219	50	14205											
CCDC149	91050	broad.mit.edu	37	chr4	24838061	24838061	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catcatgattttgctaccttGtatttggcaatgtttgattt	8	20	7	6	0	1	2	1	2	0	0	1	2	1	2	1	1	2	4	1	1	3	8	rs189623642		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:24838061G>T	ENST00000389609.4	-	8	875	c.732C>A	c.(730-732)taC>taA	p.Y244*	CCDC149_ENST00000502801.1_Intron|CCDC149_ENST00000428116.2_Intron|CCDC149_ENST00000504487.1_Nonsense_Mutation_p.Y244*	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	189										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				TTGCTACCTTGTATTTGGCAA	0.348																																					p.Y244X													.	CCDC149-68	0			c.C732A						.						285	261	269					4																	24838061		2203	4300	6503	SO:0001587	stop_gained	91050	exon8			TACCTTGTATTTG		CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.732C>A	4.37:g.24838061G>T	ENSP00000374260:p.Tyr244*	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	136	3	NM_173463	0	0	0	0	0	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Nonsense_Mutation	SNP	ENST00000389609.4	37	CCDS33967.2	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213945	0.79352	.	.	ENSG00000181982	ENST00000504487;ENST00000389609;ENST00000382116;ENST00000503881	.	.	.	4.56	2.64	0.31445	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.9336	9.4249	0.38574	0.2483:0.0:0.7517:0.0	.	.	.	.	X	244;244;168;189	.	ENSP00000371550:Y168X	Y	-	3	2	CCDC149	24447159	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.292000	0.51772	1.119000	0.41883	0.650000	0.86243	TAC	G|0.999;A|0.000		0.348	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463		T	24838061	G	T	24838061	4	4	157	1	0	0	0	0	0	1	0	0	2789	1372	48	4	885	4	CCDC149	4	24838061	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	21676004	24838061	166316215	51	14206											
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25235821	25235821	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcccgaccggttggcgtcCgcggacggcgggagcccgga	5	3	19	14	8	0	0	0	0	0	0	1	5	1	3	4	6	2	1	4	6	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:25235821C>A	ENST00000264864.6	+	1	225	c.36C>A	c.(34-36)tcC>tcA	p.S12S	PI4K2B_ENST00000512921.1_Intron	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	12					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				GGTTGGCGTCCGCGGACGGCG	0.731																																					p.S12S		.											.	PI4K2B-229	0			c.C36A						.						3	3	3					4																	25235821		1446	3354	4800	SO:0001819	synonymous_variant	55300	exon1			GGCGTCCGCGGAC	AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.36C>A	4.37:g.25235821C>A		Somatic	7	0		WXS	Illumina HiSeq	Phase_I	44	13	NM_018323	0	0	3	4	1	Q9NUW2	Silent	SNP	ENST00000264864.6	37	CCDS3433.1																																																																																			.		0.731	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		A	25235821	C	A	25235821	2	1	157	1	0	0	0	0	0	0	0	1	11898	639	23	4		4	PI4K2B	4	25235821	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	397760	25235821	165918455	52	14207											
ARAP2	116984	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	36152575	36152575	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggcagataacttcattGatattaatggtgccattagg	12	12	10	7	0	1	2	1	1	0	1	1	2	1	2	2	3	2	1	2	3	4	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:36152575G>T	ENST00000303965.4	-	16	3333	c.2844C>A	c.(2842-2844)atC>atA	p.I948I		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	948	PH 3. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TAACTTCATTGATATTAATGG	0.343																																					p.I948I													.	ARAP2-93	0			c.C2844A						.						169	174	172					4																	36152575		2203	4298	6501	SO:0001819	synonymous_variant	116984	exon16			TTCATTGATATTA	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16924	protein-coding gene	gene with protein product		606645	"centaurin, delta 1"	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.2844C>A	4.37:g.36152575G>T		Somatic	121	1		WXS	Illumina HiSeq	Phase_I	115	36	NM_015230	0	0	1	1	0	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	37	CCDS3441.1																																																																																			.		0.343	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		T	36152575	G	T	36152575	2	4	157	1	0	0	0	0	0	0	0	1	839	1280	45	4		4	ARAP2	4	36152575	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	10916754	36152575	155001701	53	14208											
RFC1	5981	bcgsc.ca	37	chr4	39306550	39306551	+	Splice_Site	INS	-	-	AAAAAA																															gtagctgtatcccaactcctINSaatcaaaatattggaaacca																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:39306550_39306551insAAAAAA	ENST00000381897.1	-	15	2132		c.e15-2		RFC1_ENST00000349703.2_Splice_Site	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa						DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						TCCCAACTCCTAATCAAAATAT	0.426																																					.	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)												.	RFC1-230	0			c.1996-2->TTTTTT						.																																			SO:0001630	splice_region_variant	5981	exon16			AACTCCTAATCAA	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"ATPases / AAA-type"	9969	protein-coding gene	gene with protein product		102579	"replication factor C (activator 1) 1 (145kD)"			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1999-2->TTTTTT	4.37:g.39306550_39306551insAAAAAA		Somatic	53	0		WXS	Illumina HiSeq	Phase_1	33	6	NM_002913	0	0	0	0	0	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Splice_Site	INS	ENST00000381897.1	37	CCDS56329.1																																																																																			.		0.426	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	Intron	AAAAAA	39306551	-	AAAAAA	39306550	8	5	157	1	0	1	1	0	0	0	1	0	13276	1536	53	0	1493	0	RFC1	4	39306550	Splice_Site	INS	-	TCGA-P4-A5EB-01A-11D-A28G-10	3153975	39306550	151847726	54	14209											
RCHY1	25898	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr4	76416940	76416940	+	Frame_Shift_Del	DEL	A	A	-																															agatgttactttacctatgtAaaagatgtccacatggcaag																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:76416940delA	ENST00000324439.5	-	6	901	c.503delT	c.(502-504)ttafs	p.L168fs	RCHY1_ENST00000513257.1_Frame_Shift_Del_p.L168fs|RCHY1_ENST00000451788.1_Frame_Shift_Del_p.L168fs|RCHY1_ENST00000380840.2_Frame_Shift_Del_p.L128fs|RCHY1_ENST00000512706.1_Frame_Shift_Del_p.L146fs|RCHY1_ENST00000514021.1_5'Flank	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	168					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TTACCTATGTAAAAGATGTCC	0.308																																					p.L168fs		.											.	RCHY1-228	0			c.503delT						.						59	59	59					4																	76416940		2203	4297	6500	SO:0001589	frameshift_variant	25898	exon6			.	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.503delT	4.37:g.76416940delA	ENSP00000321239:p.Leu168fs	Somatic	282	0		WXS	Illumina HiSeq	Phase_I	221	125	NM_001008925	0	0	0	0	0	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Frame_Shift_Del	DEL	ENST00000324439.5	37	CCDS3567.1																																																																																			.		0.308	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		-	76416940	A	-	76416940	7	5	157	1	0	1	0	1	0	0	0	0	13209	372	13	0	298	0	RCHY1	4	76416940	Frame_Shift_Del	DEL	A	TCGA-P4-A5EB-01A-11D-A28G-10	37110390	76416940	114737336	55	14210											
DSPP	1834	bcgsc.ca	37	chr4	88536999	88536999	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatagcagtgacagcagtgAcagcagcgacagcagtgata	15	5	12	9	1	0	3	0	3	0	0	0	4	0	3	0	0	5	4	0	0	3	2	rs202222170		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:88536999A>G	ENST00000282478.7	+	4	3218	c.3185A>G	c.(3184-3186)gAc>gGc	p.D1062G	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1062G			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1062	Asp/Ser-rich.			D -> G (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgacagcagcgac	0.532																																					p.D1062G													.	DSPP-90	0			c.A3185G						.						48	61	56					4																	88536999		1554	2803	4357	SO:0001583	missense	1834	exon5			GCAGTGACAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3185A>G	4.37:g.88536999A>G	ENSP00000282478:p.Asp1062Gly	Somatic	309	0		WXS	Illumina HiSeq	Phase_1	317	14	NM_014208	0	0	0	0	0	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	6.732	0.503863	0.12822	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88975	-2.45;-2.45	1.51	1.51	0.23008	.	.	.	.	.	D	0.87716	0.6247	L	0.29908	0.895	0.21762	N	0.99955	D	0.76494	0.999	D	0.74023	0.982	T	0.76072	-0.3093	9	0.24483	T	0.36	.	5.1866	0.15187	1.0:0.0:0.0:0.0	.	1062	Q9NZW4	DSPP_HUMAN	G	1062	ENSP00000382213:D1062G;ENSP00000282478:D1062G	ENSP00000282478:D1062G	D	+	2	0	DSPP	88756023	0.386000	0.25180	0.936000	0.37596	0.006000	0.05464	2.307000	0.43682	0.963000	0.38082	0.242000	0.17961	GAC	.		0.532	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		G	88536999	A	G	88536999	3	3	157	1	0	0	0	0	1	0	0	0	4793	275	10	3	3199	3	DSPP	4	88536999	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	12120059	88536999	102617277	56	14211											
MMRN1	22915	broad.mit.edu;bcgsc.ca	37	chr4	90857474	90857474	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccttattatatttcagttaaAaaaggcagtgtagttacaaa	16	14	6	5	0	1	0	1	0	0	0	1	0	1	0	1	1	1	4	1	1	9	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:90857474A>C	ENST00000394980.1	+	7	2962	c.2643A>C	c.(2641-2643)aaA>aaC	p.K881N	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000508372.1_Missense_Mutation_p.K623N|MMRN1_ENST00000264790.2_Missense_Mutation_p.K881N			Q13201	MMRN1_HUMAN	multimerin 1	881					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		TTTCAGTTAAAAAAGGCAGTG	0.353																																					p.K881N													.	MMRN1-94	0			c.A2643C						.						41	45	44					4																	90857474		2192	4293	6485	SO:0001583	missense	22915	exon6			AGTTAAAAAAGGC	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"EMI domain containing"	7178	protein-coding gene	gene with protein product	"glycoprotein Ia*"	601456	"multimerin"	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2643A>C	4.37:g.90857474A>C	ENSP00000378431:p.Lys881Asn	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	148	5	NM_007351	0	0	0	0	0	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.358105	0.24598	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.71103	-0.24;-0.24;-0.54	5.3	2.83	0.33086	.	0.063651	0.64402	D	0.000005	T	0.63745	0.2537	M	0.66939	2.045	0.80722	D	1	B	0.19583	0.037	B	0.17433	0.018	T	0.58381	-0.7646	10	0.46703	T	0.11	.	6.1628	0.20373	0.7239:0.1367:0.1393:0.0	.	881	Q13201	MMRN1_HUMAN	N	881;881;623	ENSP00000378431:K881N;ENSP00000264790:K881N;ENSP00000426461:K623N	ENSP00000264790:K881N	K	+	3	2	MMRN1	91076497	1.000000	0.71417	0.910000	0.35882	0.768000	0.43524	0.904000	0.28491	0.514000	0.28300	-0.291000	0.09656	AAA	.		0.353	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		C	90857474	A	C	90857474	3	2	157	1	0	0	0	0	1	0	0	0	9695	11	1	5	2665	5	MMRN1	4	90857474	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	2320475	90857474	100296802	57	14212											
SYNPO2	171024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	119952707	119952707	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctcctcctgtggcctataAtcctatccactcgccgtctt	6	13	5	17	2	1	0	0	0	1	0	6	0	5	0	7	1	0	0	7	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:119952707A>T	ENST00000429713.2	+	4	2959	c.2777A>T	c.(2776-2778)aAt>aTt	p.N926I	SYNPO2_ENST00000307142.4_Missense_Mutation_p.N926I|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.N926I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	926						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GTGGCCTATAATCCTATCCAC	0.572																																					p.N926I		.											.	SYNPO2-92	0			c.A2777T						.						87	83	84					4																	119952707		2203	4300	6503	SO:0001583	missense	171024	exon4			CCTATAATCCTAT	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2777A>T	4.37:g.119952707A>T	ENSP00000395143:p.Asn926Ile	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	78	11	NM_001128934	0	0	0	0	0	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.067512|4.067512	0.76301|0.76301	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.14893|.	2.47;2.58;2.47|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.77239|.	0.4101|.	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;0.999;0.997|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.997;0.972|.	T|.	0.78874|.	-0.2032|.	9|.	.|.	.|.	.|.	-24.3416|-24.3416	15.8861|15.8861	0.79251|0.79251	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	926;926;926;926|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	926|877	ENSP00000306015:N926I;ENSP00000395143:N926I;ENSP00000390965:N926I|.	.|.	N|X	+|+	2|3	0|2	SYNPO2|SYNPO2	120172155|120172155	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.914000|0.914000	0.54420|0.54420	9.339000|9.339000	0.96797|0.96797	2.156000|2.156000	0.67533|0.67533	0.533000|0.533000	0.62120|0.62120	AAT|TAA	.		0.572	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			T	119952707	A	T	119952707	3	4	157	1	0	0	0	0	1	0	0	0	15489	101	4	5	2791	5	SYNPO2	4	119952707	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	29095233	119952707	71201569	58	14213											
IQGAP2	10788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	75888702	75888702	+	Missense_Mutation	SNP	G	G	A																															aagaaagagatgcttatgaaGaactgctgacacaagcagaa																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75888702G>A	ENST00000274364.6	+	9	1156	c.859G>A	c.(859-861)Gaa>Aaa	p.E287K	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	287					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TGCTTATGAAGAACTGCTGAC	0.323																																					p.E287K		.											.	IQGAP2-96	0			c.G859A						.						138	145	142					5																	75888702		2203	4300	6503	SO:0001583	missense	10788	exon9			TATGAAGAACTGC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.859G>A	5.37:g.75888702G>A	ENSP00000274364:p.Glu287Lys	Somatic	316	0		WXS	Illumina HiSeq	Phase_I	466	78	NM_006633	0	0	13	13	0	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141279	0.94560	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.39787	4.12;1.06;4.13	5.83	5.83	0.93111	.	0.100666	0.64402	D	0.000002	T	0.54287	0.1849	M	0.80616	2.505	0.80722	D	1	P	0.42483	0.781	P	0.44732	0.459	T	0.50988	-0.8762	10	0.21540	T	0.41	-17.3562	20.1863	0.98216	0.0:0.0:1.0:0.0	.	287	Q13576	IQGA2_HUMAN	K	287;260;237	ENSP00000274364:E287K;ENSP00000423672:E260K;ENSP00000421097:E237K	ENSP00000274364:E287K	E	+	1	0	IQGAP2	75924458	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	9.798000	0.99111	2.781000	0.95711	0.650000	0.86243	GAA	.		0.323	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75888702	G	A	75888702	3	1	157	1	0	0	0	0	1	0	0	0	7836	943	33	2	893	2	IQGAP2	5	75888702	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		75888702	105026558	59	14214	156	2									
IQGAP2	10788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	75888710	75888710	+	Silent	SNP	G	G	A																															gatgcttatgaagaactgctGacacaagcagaaatccaagg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75888710G>A	ENST00000274364.6	+	9	1164	c.867G>A	c.(865-867)ctG>ctA	p.L289L	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	289					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAGAACTGCTGACACAAGCAG	0.333																																					p.L289L		.											.	IQGAP2-96	0			c.G867A						.						145	152	149					5																	75888710		2203	4300	6503	SO:0001819	synonymous_variant	10788	exon9			ACTGCTGACACAA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.867G>A	5.37:g.75888710G>A		Somatic	344	0		WXS	Illumina HiSeq	Phase_I	484	78	NM_006633	0	0	20	20	0	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	CCDS34188.1																																																																																			.		0.333	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75888710	G	A	75888710	2	1	157	1	0	0	0	0	0	0	0	1	7836	1277	45	2		2	IQGAP2	5	75888710	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8	75888710	105026550	60	14215	156	2									
IQGAP2	10788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	75973147	75973147	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaaccagtcatttatatttCaattgaagaaatcatcagca	17	12	4	8	0	4	2	4	1	0	1	4	2	4	2	1	0	2	1	1	0	6	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75973147C>T	ENST00000274364.6	+	28	3929	c.3632C>T	c.(3631-3633)tCa>tTa	p.S1211L	IQGAP2_ENST00000502745.1_Missense_Mutation_p.S707L|IQGAP2_ENST00000379730.3_Missense_Mutation_p.S713L|IQGAP2_ENST00000396234.3_Missense_Mutation_p.S707L	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1211					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ATTTATATTTCAATTGAAGAA	0.393																																					p.S1211L		.											.	IQGAP2-96	0			c.C3632T						.						65	66	65					5																	75973147		2203	4300	6503	SO:0001583	missense	10788	exon28			ATATTTCAATTGA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3632C>T	5.37:g.75973147C>T	ENSP00000274364:p.Ser1211Leu	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	95	11	NM_006633	0	0	33	33	0	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	C	32	5.108409	0.94292	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	4.98	4.98	0.66077	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.329934	0.33144	N	0.005221	T	0.73094	0.3543	M	0.84326	2.69	0.80722	D	1	D;D;P	0.65815	0.995;0.995;0.792	P;P;B	0.60609	0.877;0.877;0.322	T	0.77910	-0.2411	10	0.72032	D	0.01	-12.9253	18.4229	0.90597	0.0:1.0:0.0:0.0	.	713;707;1211	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	L	1211;713;1161;707;707	ENSP00000274364:S1211L;ENSP00000442313:S713L;ENSP00000421097:S1161L;ENSP00000379535:S707L;ENSP00000426027:S707L	ENSP00000274364:S1211L	S	+	2	0	IQGAP2	76008903	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	7.557000	0.82243	2.597000	0.87782	0.591000	0.81541	TCA	.		0.393	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75973147	C	T	75973147	3	4	157	1	0	0	0	0	1	0	0	0	7836	838	29	2	3742	2	IQGAP2	5	75973147	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	84437	75973147	104942113	61	14216											
REEP5	7905	broad.mit.edu;bcgsc.ca	37	chr5	112257770	112257770	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgacccccggccacccacCaagagcgatgaagctcctgt	9	4	11	17	3	0	2	0	1	0	1	1	4	1	2	6	2	2	1	6	2	2	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:112257770C>A	ENST00000379638.4	-	1	466	c.118G>T	c.(118-120)Ggt>Tgt	p.G40C	REEP5_ENST00000545426.1_Splice_Site_p.G40C|REEP5_ENST00000513339.1_Splice_Site_p.G40C|REEP5_ENST00000474542.2_5'Flank|REEP5_ENST00000504247.1_Splice_Site_p.G40C	NM_005669.4	NP_005660.4	Q00765	REEP5_HUMAN	receptor accessory protein 5	40						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)		GGCCACCCACCAAGAGCGATG	0.657																																					p.G40C													.	REEP5-280	0			c.G118T						.						49	52	51					5																	112257770		2202	4300	6502	SO:0001630	splice_region_variant	7905	exon1			ACCCACCAAGAGC	BC000232	CCDS4109.2	5q22-q23	2008-02-05	2006-02-07	2006-02-07	ENSG00000129625	ENSG00000129625		"Receptor accessory proteins"	30077	protein-coding gene	gene with protein product	"deleted in polyposis 1", "polyposis locus protein 1", "polyposis coli region hypothetical protein DP1"	125265	"chromosome 5 open reading frame 18"	C5orf18		16271481, 15550249	Standard	NM_005669		Approved	DP1, TB2, D5S346	uc003kqe.1	Q00765	OTTHUMG00000128807	ENST00000379638.4:c.118+1G>T	5.37:g.112257770C>A		Somatic	66	1		WXS	Illumina HiSeq	Phase_I	217	81	NM_005669	0	0	0	48	48	B7Z681|D3DT04|Q04198|Q5QGT0|Q9BWH9	Missense_Mutation	SNP	ENST00000379638.4	37	CCDS4109.2	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436733	0.62955	.	.	ENSG00000129625	ENST00000379638;ENST00000513339;ENST00000545426;ENST00000504247	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	4.17	4.17	0.49024	.	0.119316	0.53938	D	0.000045	T	0.73682	0.3618	M	0.89715	3.055	0.80722	D	1	D;D	0.89917	1.0;0.988	D;P	0.76575	0.988;0.843	T	0.80812	-0.1215	9	.	.	.	-39.0882	16.0678	0.80897	0.0:1.0:0.0:0.0	.	40;40	B7Z510;Q00765	.;REEP5_HUMAN	C	40	ENSP00000368959:G40C;ENSP00000425901:G40C;ENSP00000442940:G40C;ENSP00000421881:G40C	.	G	-	1	0	REEP5	112285669	1.000000	0.71417	0.997000	0.53966	0.043000	0.13939	6.323000	0.72891	1.861000	0.53984	0.563000	0.77884	GGT	.		0.657	REEP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250739.2	NM_005669	Missense_Mutation	A	112257770	C	A	112257770	5	1	157	1	0	0	0	0	0	0	1	0	13240	608	21	4	471	4	REEP5	5	112257770	Splice_Site	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	36284623	112257770	68657490	62	14217											
FNIP1	96459	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	131007961	131007961	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttttccacaaccattcCtgtggatctcattgctttgc	6	19	5	11	0	1	0	1	0	1	0	4	1	3	1	3	1	3	1	3	1	1	7	rs367969091		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:131007961C>T	ENST00000510461.1	-	14	2271	c.2176G>A	c.(2176-2178)Gga>Aga	p.G726R	CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307954.8_Missense_Mutation_p.G681R|FNIP1_ENST00000307968.7_Missense_Mutation_p.G698R	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	726					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		ACAACCATTCCTGTGGATCTC	0.448																																					p.G726R		.											.	FNIP1-92	0			c.G2176A						.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	218	207	211		2092,2176	4.9	1	5		211	0,8600		0,0,4300	no	missense,missense	FNIP1	NM_001008738.2,NM_133372.2	125,125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	698/1139,726/1167	131007961	1,13005	2203	4300	6503	SO:0001583	missense	96459	exon14			CCATTCCTGTGGA	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2176G>A	5.37:g.131007961C>T	ENSP00000421985:p.Gly726Arg	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	109	63	NM_133372	0	0	3	5	2	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212357	0.58452	2.27E-4	0.0	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.42131	0.98;0.98;0.98	5.76	4.89	0.63831	.	.	.	.	.	T	0.45538	0.1347	L	0.43152	1.355	0.80722	D	1	P;P;P	0.46512	0.879;0.879;0.773	P;P;B	0.50708	0.648;0.494;0.414	T	0.31420	-0.9944	9	0.49607	T	0.09	-8.8964	12.306	0.54902	0.0:0.8667:0.0:0.1333	.	726;698;726	A8K8V8;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	R	698;681;478;726	ENSP00000309266:G698R;ENSP00000310453:G681R;ENSP00000421985:G726R	ENSP00000310453:G681R	G	-	1	0	FNIP1	131035860	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.191000	0.58372	2.726000	0.93360	0.655000	0.94253	GGA	.		0.448	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		T	131007961	C	T	131007961	3	4	157	1	0	0	0	0	1	0	0	0	5994	690	24	2	1344	2	FNIP1	5	131007961	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	18750191	131007961	49907299	63	14218											
NSD1	64324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176721020	176721020	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcctctggaacctggggaGatccgtgagtatgtgcctcc	8	10	12	11	1	1	2	0	1	1	1	4	4	4	3	5	3	2	1	5	3	3	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:176721020G>T	ENST00000439151.2	+	23	6696	c.6651G>T	c.(6649-6651)gaG>gaT	p.E2217D	NSD1_ENST00000347982.4_Missense_Mutation_p.E1948D|NSD1_ENST00000354179.4_Missense_Mutation_p.E1948D|NSD1_ENST00000361032.4_Missense_Mutation_p.E2114D	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2217	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AACCTGGGGAGATCCGTGAGT	0.562			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.E2217D		.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1-188	0			c.G6651T						.						81	80	81					5																	176721020		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TGGGGAGATCCGT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6651G>T	5.37:g.176721020G>T	ENSP00000395929:p.Glu2217Asp	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	120	46	NM_022455	0	0	11	24	13	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840800	0.71488	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000002	D	0.84419	0.5468	L	0.27053	0.805	0.53688	D	0.999975	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.933	D	0.84097	0.0393	10	0.51188	T	0.08	.	11.9775	0.53100	0.1325:0.0:0.8675:0.0	.	1948;2217	Q96L73-2;Q96L73	.;NSD1_HUMAN	D	1948;2217;1948;2114	ENSP00000346111:E1948D;ENSP00000395929:E2217D;ENSP00000343209:E1948D;ENSP00000354310:E2114D	ENSP00000343209:E1948D	E	+	3	2	NSD1	176653626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.583000	0.53928	2.941000	0.99782	0.655000	0.94253	GAG	.		0.562	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176721020	G	T	176721020	3	4	157	1	0	0	0	0	1	0	0	0	10695	933	33	4	6737	4	NSD1	5	176721020	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	45713059	176721020	4194240	64	14219											
CLK4	57396	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	178050363	178050363	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccacgatagctttcatgtcCccagctttctctgctatccc	6	14	5	16	1	2	0	1	0	1	0	6	1	5	0	4	0	3	3	4	0	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:178050363C>A	ENST00000316308.4	-	2	223	c.55G>T	c.(55-57)Gga>Tga	p.G19*	CLK4_ENST00000520957.1_Nonsense_Mutation_p.G19*	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	19					protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		CTTTCATGTCCCCAGCTTTCT	0.438																																					p.G19X		.											.	CLK4-359	0			c.G55T						.						207	181	190					5																	178050363		2203	4300	6503	SO:0001587	stop_gained	57396	exon2			CATGTCCCCAGCT	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.55G>T	5.37:g.178050363C>A	ENSP00000316948:p.Gly19*	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	135	60	NM_020666	0	0	0	7	7		Nonsense_Mutation	SNP	ENST00000316308.4	37	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	C	38	7.083910	0.98051	.	.	ENSG00000113240	ENST00000316308;ENST00000536763;ENST00000520957	.	.	.	5.83	4.97	0.65823	.	0.325167	0.32548	N	0.005960	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	10.8916	0.46998	0.0:0.9136:0.0:0.0864	.	.	.	.	X	19	.	ENSP00000316948:G19X	G	-	1	0	CLK4	177982969	0.989000	0.36119	0.999000	0.59377	0.962000	0.63368	2.363000	0.44178	1.477000	0.48234	0.491000	0.48974	GGA	.		0.438	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			A	178050363	C	A	178050363	4	1	157	1	0	0	0	0	0	1	0	0	3545	632	22	4	1438	4	CLK4	5	178050363	Nonsense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1329343	178050363	2864897	65	14220											
PRPF4B	8899	broad.mit.edu;bcgsc.ca	37	chr6	4060772	4060772	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaaggacttgttggaccaGattctgatgttggacccagc	10	11	11	9	0	1	2	0	1	1	1	1	5	1	5	2	3	1	2	2	3	2	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:4060772G>T	ENST00000337659.6	+	15	3046	c.2946G>T	c.(2944-2946)caG>caT	p.Q982H	PRPF4B_ENST00000494674.1_3'UTR|PRPF4B_ENST00000538861.1_Missense_Mutation_p.Q968H	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	982	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				TGTTGGACCAGATTCTGATGT	0.448																																					p.Q982H													.	PRPF4B-1308	0			c.G2946T						.						74	65	68					6																	4060772		2203	4300	6503	SO:0001583	missense	8899	exon15			GGACCAGATTCTG	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"PRP4 pre-mRNA processing factor 4 homolog B (yeast)"			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.2946G>T	6.37:g.4060772G>T	ENSP00000337194:p.Gln982His	Somatic	237	0		WXS	Illumina HiSeq	Phase_I	255	7	NM_003913	0	0	26	26	0	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845731	0.32606	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.66280	-0.2;-0.2	5.3	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000008	T	0.59459	0.2195	L	0.35341	1.055	0.80722	D	1	D	0.61697	0.99	P	0.56343	0.796	T	0.61436	-0.7063	10	0.48119	T	0.1	.	18.9491	0.92635	0.0:0.0:1.0:0.0	.	982	Q13523	PRP4B_HUMAN	H	982;968	ENSP00000337194:Q982H;ENSP00000439331:Q968H	ENSP00000337194:Q982H	Q	+	3	2	PRPF4B	4005771	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.912000	0.69948	2.451000	0.82905	0.655000	0.94253	CAG	.		0.448	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			T	4060772	G	T	4060772	3	4	157	1	0	0	0	0	1	0	0	0	12602	933	33	4	3004	4	PRPF4B	6	4060772	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		4060772	167054295	66	14221											
ZSCAN23	222696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	28402345	28402345	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcataaggtctctctccaGtgtgaattctctgatgctta	9	16	7	9	0	4	2	1	2	3	0	7	2	4	2	1	1	1	1	1	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:28402345G>A	ENST00000289788.4	-	4	1212	c.1067C>T	c.(1066-1068)aCt>aTt	p.T356I	ZSCAN23_ENST00000486481.1_5'Flank	NM_001012455.1	NP_001012458.1	Q3MJ62	ZSC23_HUMAN	zinc finger and SCAN domain containing 23	356					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)|stomach(2)	4						TCTCTCTCCAGTGTGAATTCT	0.448																																					p.T356I		.											.	ZSCAN23-68	0			c.C1067T						.						158	136	142					6																	28402345		692	1591	2283	SO:0001583	missense	222696	exon4			TCTCCAGTGTGAA	AK092117	CCDS47393.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000187987	ENSG00000187987		"-", "Zinc fingers, C2H2-type"	21193	protein-coding gene	gene with protein product			"zinc finger protein 453", "zinc finger protein 390"	ZNF453, ZNF390			Standard	NM_001012455		Approved	dJ29K1.3.1	uc003nli.4	Q3MJ62	OTTHUMG00000016346	ENST00000289788.4:c.1067C>T	6.37:g.28402345G>A	ENSP00000289788:p.Thr356Ile	Somatic	99	0		WXS	Illumina HiSeq	Phase_I	110	61	NM_001012455	0	0	1	1	0	Q96KV9	Missense_Mutation	SNP	ENST00000289788.4	37	CCDS47393.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245900	0.80024	.	.	ENSG00000187987	ENST00000289788	T	0.25749	1.78	3.93	3.93	0.45458	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39909	N	0.001229	T	0.36386	0.0965	M	0.80183	2.485	0.34741	D	0.730734	D	0.55385	0.971	P	0.56788	0.806	T	0.46541	-0.9184	10	0.87932	D	0	.	13.4765	0.61312	0.0:0.0:1.0:0.0	.	356	Q3MJ62	ZSC23_HUMAN	I	356	ENSP00000289788:T356I	ENSP00000289788:T356I	T	-	2	0	ZSCAN23	28510324	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.856000	0.69518	2.007000	0.58848	0.650000	0.86243	ACT	.		0.448	ZSCAN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043751.2	XM_167147		A	28402345	G	A	28402345	3	1	157	1	0	0	0	0	1	0	0	0	18267	1029	36	2	106	2	ZSCAN23	6	28402345	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	24341573	28402345	142712722	67	14222											
TNXB	7148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	32016288	32016288	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actgcctggggctgcccctgCgcgtccctgtactgtaccag	4	9	12	16	2	0	0	0	0	0	0	1	0	1	0	5	2	5	3	5	2	2	2	rs373655652		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:32016288C>T	ENST00000375244.3	-	29	10098	c.9897G>A	c.(9895-9897)gcG>gcA	p.A3299A	TNXB_ENST00000375247.2_Silent_p.A3297A|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3344	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCTGCCCCTGCGCGTCCCTGT	0.687																																					p.A3297A		.											.	TNXB-90	0			c.G9891A						.	C		0,3902		0,0,1951	17	21	19		9891	-7.3	0	6		19	3,8267		0,3,4132	no	coding-synonymous	TNXB	NM_019105.6		0,3,6083	TT,TC,CC		0.0363,0.0,0.0246		3297/4243	32016288	3,12169	1951	4135	6086	SO:0001819	synonymous_variant	7148	exon29			CCCCTGCGCGTCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9897G>A	6.37:g.32016288C>T		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	173	105	NM_019105	0	0	0	0	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				.		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32016288	C	T	32016288	2	4	157	1	0	0	0	0	0	0	0	1	16378	755	27	1		1	TNXB	6	32016288	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	3613943	32016288	139098779	68	14223											
TNXB	7148	broad.mit.edu;bcgsc.ca	37	chr6	32063589	32063589	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ggcgctggctggaggctcttCctgcccgcagtcctcaccgc	3	8	13	17	3	2	0	1	0	1	0	4	1	4	1	4	4	1	4	4	4	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:32063589C>G	ENST00000479795.1	-	3	2181	c.2041G>C	c.(2041-2043)Gaa>Caa	p.E681Q	TNXB_ENST00000375247.2_Missense_Mutation_p.E681Q|TNXB_ENST00000375244.3_Missense_Mutation_p.E681Q			P22105	TENX_HUMAN	tenascin XB	681					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGAGGCTCTTCCTGCCCGCAG	0.701																																					p.E681Q													.	TNXB-90	0			c.G2041C						.						16	20	18					6																	32063589		2114	4231	6345	SO:0001583	missense	7148	exon3			GCTCTTCCTGCCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.2041G>C	6.37:g.32063589C>G	ENSP00000418248:p.Glu681Gln	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	291	13	NM_019105	0	0	0	0	0	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000479795.1	37		.	.	.	.	.	.	.	.	.	.	C	20.2	3.955354	0.73902	.	.	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;T	0.08546	3.08;3.08;3.08	4.78	4.78	0.61160	.	0.000000	0.45126	D	0.000397	T	0.08088	0.0202	L	0.37750	1.13	0.26200	N	0.979459	D	0.65815	0.995	P	0.61477	0.889	T	0.19549	-1.0302	10	0.30078	T	0.28	.	13.3295	0.60479	0.0:1.0:0.0:0.0	.	681	P22105-3	.	Q	681	ENSP00000364393:E681Q;ENSP00000364396:E681Q;ENSP00000418248:E681Q	ENSP00000364393:E681Q	E	-	1	0	TNXB	32171567	0.970000	0.33590	0.850000	0.33497	0.919000	0.55068	0.746000	0.26275	2.198000	0.70561	0.563000	0.77884	GAA	.		0.701	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105		G	32063589	C	G	32063589	3	3	157	1	0	0	0	0	1	0	0	0	16378	864	30	4	12840	4	TNXB	6	32063589	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	47301	32063589	139051478	69	14224											
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	38818063	38818080	+	In_Frame_Del	DEL	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	-																															agaatattgacaagtcttggAtaaaaataatgcagcgagct																								rs200056261|rs201568629|rs547165959		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:38818063_38818080delATAAAAATAATGCAGCGA	ENST00000359357.3	+	36	4839_4856	c.4585_4602delATAAAAATAATGCAGCGA	c.(4585-4602)ataaaaataatgcagcgadel	p.IKIMQR1529del	DNAH8_ENST00000449981.2_In_Frame_Del_p.IKIMQR1746del|DNAH8_ENST00000441566.1_In_Frame_Del_p.IKIMQR1529del			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1529					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I1529I(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CAAGTCTTGGATAAAAATAATGCAGCGAGCTCATGAGA	0.362																																					p.1746_1751del		.											.	DNAH8-615	2	Substitution - coding silent(2)	lung(2)	c.5236_5253del						.																																			SO:0001651	inframe_deletion	1769	exon38			.	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"Axonemal dyneins"	2952	protein-coding gene	gene with protein product		603337	"dynein, axonemal, heavy polypeptide 8"			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.4585_4602delATAAAAATAATGCAGCGA	6.37:g.38818063_38818080delATAAAAATAATGCAGCGA	ENSP00000352312:p.Ile1529_Arg1534del	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	65	25	NM_001206927	0	0	0	0	0	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	In_Frame_Del	DEL	ENST00000359357.3	37																																																																																				.		0.362	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		-	38818080	ATAAAAATAATGCAGCGA	-	38818063	7	5	157	1	0	1	0	1	0	0	0	0	4618	333	12	0	4719	0	DNAH8	6	38818063	In_Frame_Del	DEL	ATAAAAATAATGCAGCGA	TCGA-P4-A5EB-01A-11D-A28G-10	6754474	38818063	132297004	70	14225											
CUL9	23113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43155541	43155541	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagtagtcgatttgagggcAgcactctcaatgacctgctc	9	11	10	11	1	2	2	2	2	1	0	5	3	2	2	1	1	2	4	1	1	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:43155541A>G	ENST00000252050.4	+	7	1756	c.1672A>G	c.(1672-1674)Agc>Ggc	p.S558G	CUL9_ENST00000354495.3_Missense_Mutation_p.S448G|CUL9_ENST00000372647.2_Missense_Mutation_p.S558G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	558					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ATTTGAGGGCAGCACTCTCAA	0.517																																					p.S558G		.											.	CUL9-529	0			c.A1672G						.						122	121	121					6																	43155541		2203	4300	6503	SO:0001583	missense	23113	exon7			GAGGGCAGCACTC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1672A>G	6.37:g.43155541A>G	ENSP00000252050:p.Ser558Gly	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	84	19	NM_015089	0	0	7	9	2	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.245727	0.39697	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.77489	-1.1;-0.91;-1.0	5.5	4.35	0.52113	.	0.665930	0.17251	N	0.181151	T	0.50343	0.1610	L	0.43152	1.355	0.27626	N	0.948198	B;B;B	0.16603	0.018;0.018;0.003	B;B;B	0.16722	0.016;0.016;0.002	T	0.40794	-0.9544	10	0.48119	T	0.1	-13.3974	4.4793	0.11759	0.702:0.0:0.1464:0.1516	.	558;558;558	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	G	558;448;558	ENSP00000252050:S558G;ENSP00000346490:S448G;ENSP00000361730:S558G	ENSP00000252050:S558G	S	+	1	0	CUL9	43263519	0.994000	0.37717	1.000000	0.80357	0.943000	0.58893	1.801000	0.38843	2.090000	0.63153	0.383000	0.25322	AGC	.		0.517	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		G	43155541	A	G	43155541	3	3	157	1	0	0	0	0	1	0	0	0	4067	188	7	3	1694	3	CUL9	6	43155541	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	4337478	43155541	127959526	71	14226											
PKHD1	5314	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr6	51586795	51586795	+	Intron	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctcctctattctgaaaTcttcaaagcctgctcagtgg	8	13	7	13	0	5	1	2	1	3	0	7	1	7	1	3	1	2	2	3	1	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:51586795T>G	ENST00000371117.3	-	60	10432				PKHD1_ENST00000340994.4_Missense_Mutation_p.I3394L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)						cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TATTCTGAAATCTTCAAAGCC	0.448																																					p.I3394L		.											.	PKHD1-603	0			c.A10180C						.						71	70	70					6																	51586795		2203	4300	6503	SO:0001627	intron_variant	5314	exon61			CTGAAATCTTCAA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10156+22387A>C	6.37:g.51586795T>G		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	76	32	NM_170724	0	0	0	0	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692382	0.30052	.	.	ENSG00000170927	ENST00000340994	D	0.86627	-2.15	3.72	-0.352	0.12598	.	.	.	.	.	T	0.61949	0.2388	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.54275	-0.8318	8	0.54805	T	0.06	.	4.5853	0.12279	0.0:0.1103:0.3908:0.4988	.	3394	P08F94-2	.	L	3394	ENSP00000341097:I3394L	ENSP00000341097:I3394L	I	-	1	0	PKHD1	51694754	0.000000	0.05858	0.000000	0.03702	0.220000	0.24768	0.004000	0.13106	-0.046000	0.13446	0.379000	0.24179	ATT	.		0.448	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51586795	T	G	51586795	1	3	157	0	1	0	0	0	0	0	0	0	11997	1435	50	5		5	PKHD1	6	51586795	Intron	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	8431254	51586795	119528272	72	14227											
COL21A1	81578	hgsc.bcm.edu;bcgsc.ca	37	chr6	55933890	55933890	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatgtatcctggttctcctGgggaacccgttgctcctggt	4	13	11	13	1	1	0	0	0	1	0	4	1	3	1	5	4	2	4	5	4	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:55933890G>T	ENST00000244728.5	-	22	2442	c.2045C>A	c.(2044-2046)cCa>cAa	p.P682Q	COL21A1_ENST00000370808.2_Missense_Mutation_p.P82Q|COL21A1_ENST00000370819.1_Missense_Mutation_p.P679Q|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000535941.1_Missense_Mutation_p.P682Q	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	682	Collagen-like 4.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGGTTCTCCTGGGGAACCCGT	0.423																																					p.P682Q		.											.	COL21A1-24	0			c.C2045A						.						62	62	62					6																	55933890		1831	4076	5907	SO:0001583	missense	81578	exon22			TCTCCTGGGGAAC	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"Collagens"	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2045C>A	6.37:g.55933890G>T	ENSP00000244728:p.Pro682Gln	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	95	5	NM_030820	0	0	0	0	0	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143568	0.37825	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.97752	-4.52;-4.52;-4.52;-4.52	4.38	3.48	0.39840	.	0.000000	0.49305	U	0.000144	D	0.95968	0.8687	L	0.28192	0.835	0.47407	D	0.999413	P;P;D	0.89917	0.886;0.77;1.0	B;P;D	0.97110	0.381;0.515;1.0	D	0.94500	0.7709	10	0.27785	T	0.31	.	12.3453	0.55118	0.0:0.0:0.8294:0.1705	.	82;682;682	Q96P44-2;B7ZLK3;Q96P44	.;.;COLA1_HUMAN	Q	682;679;682;679;82	ENSP00000244728:P682Q;ENSP00000359855:P679Q;ENSP00000444384:P682Q;ENSP00000359844:P82Q	ENSP00000244728:P682Q	P	-	2	0	COL21A1	56041849	1.000000	0.71417	0.163000	0.22734	0.829000	0.46940	4.396000	0.59684	0.905000	0.36596	0.557000	0.71058	CCA	.		0.423	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	55933890	G	T	55933890	3	4	157	1	0	0	0	0	1	0	0	0	3686	1348	47	4	864	4	COL21A1	6	55933890	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4347095	55933890	115181177	73	14228											
UBE2CBP	90025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	83767555	83767555	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattactcacttgtgcctaaTtttgcttgcgtctgcagtcg	6	17	8	10	2	2	0	1	0	1	0	3	0	2	0	1	0	5	2	1	0	3	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:83767555T>G	ENST00000369747.3	-	2	386	c.264A>C	c.(262-264)aaA>aaC	p.K88N		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	88					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TTGTGCCTAATTTTGCTTGCG	0.443											OREG0017549	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K88N		.											.	.	0			c.A264C						.						67	68	68					6																	83767555		2203	4300	6503	SO:0001583	missense	90025	exon2			GCCTAATTTTGCT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.264A>C	6.37:g.83767555T>G	ENSP00000358762:p.Lys88Asn	Somatic	83	0	1224	WXS	Illumina HiSeq	Phase_I	78	39	NM_198920	0	0	0	0	0	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	37	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490288	0.26686	.	.	ENSG00000118420	ENST00000369747	T	0.30714	1.52	5.27	-10.5	0.00291	.	0.631105	0.16070	N	0.231043	T	0.02767	0.0083	N	0.08118	0	0.09310	N	0.999998	B;B	0.20164	0.042;0.002	B;B	0.18871	0.023;0.002	T	0.20009	-1.0288	10	0.33141	T	0.24	-18.3097	5.2116	0.15320	0.1807:0.4793:0.1961:0.1438	.	88;88	D6RD24;Q7Z6J8	.;UB2CB_HUMAN	N	88	ENSP00000358762:K88N	ENSP00000358762:K88N	K	-	3	2	UBE2CBP	83824274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.412000	0.02476	-2.085000	0.00864	-0.911000	0.02809	AAA	.		0.443	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		G	83767555	T	G	83767555	3	3	157	1	0	0	0	0	1	0	0	0	16880	1490	52	5	941	5	UBE2CBP	6	83767555	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	27833665	83767555	87347512	74	14229											
COQ3	51805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	99823846	99823846	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacagcagcactgtaaaaaTgtttctagatcaatcacatg	15	11	7	8	0	3	2	2	1	1	1	3	2	3	2	0	0	2	4	0	0	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:99823846T>A	ENST00000254759.3	-	5	723	c.699A>T	c.(697-699)acA>acT	p.T233T	COQ3_ENST00000369240.1_Intron|COQ3_ENST00000369242.1_Intron|COQ3_ENST00000479163.1_5'Flank	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	233					glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		ACTGTAAAAATGTTTCTAGAT	0.368																																					p.T233T		.											.	COQ3-91	0			c.A699T						.						154	149	151					6																	99823846		2203	4300	6503	SO:0001819	synonymous_variant	51805	exon5			TAAAAATGTTTCT	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"polyprenyldihydroxybenzoate methyltransferase"	605196	"coenzyme Q3 homolog, methyltransferase (yeast)", "coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.699A>T	6.37:g.99823846T>A		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	79	26	NM_017421	0	0	5	7	2	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Silent	SNP	ENST00000254759.3	37	CCDS5042.1																																																																																			.		0.368	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421		A	99823846	T	A	99823846	2	1	157	1	0	0	0	0	0	0	0	1	3752	1451	51	5		5	COQ3	6	99823846	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	16056291	99823846	71291221	75	14230											
HECA	51696	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	139487930	139487930	+	Frame_Shift_Del	DEL	G	G	-																															cagtgggtgccgcagcctacGgtgcccgttcccccggtggc																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:139487930delG	ENST00000367658.2	+	2	1066	c.781delG	c.(781-783)ggtfs	p.G261fs	RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	261					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		CGCAGCCTACGGTGCCCGTTC	0.682																																					p.G261fs		.											.	HECA-90	0			c.781delG						.						15	18	17					6																	139487930		2203	4297	6500	SO:0001589	frameshift_variant	51696	exon2			.	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.781delG	6.37:g.139487930delG	ENSP00000356630:p.Gly261fs	Somatic	75	0		WXS	Illumina HiSeq	Phase_I	66	21	NM_016217	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000367658.2	37	CCDS5194.1																																																																																			.		0.682	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		-	139487930	G	-	139487930	7	5	157	1	0	1	0	1	0	0	0	0	7059	1116	39	0	787	0	HECA	6	139487930	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	39664084	139487930	31627137	76	14231											
LATS1	9113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	149997827	149997827	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	catcgacagcttgagggatcCccccattcattactgaaatc	11	10	7	13	1	1	2	1	2	0	0	4	4	2	3	3	1	2	1	3	1	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:149997827C>G	ENST00000543571.1	-	6	3187	c.2640G>C	c.(2638-2640)ggG>ggC	p.G880G	LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Silent_p.G880G	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TTGAGGGATCCCCCCATTCAT	0.473																																					p.G880G		.											.	LATS1-992	0			c.G2640C						.						73	63	66					6																	149997827		2203	4300	6503	SO:0001819	synonymous_variant	9113	exon6			GGGATCCCCCCAT	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2640G>C	6.37:g.149997827C>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	71	20	NM_004690	0	0	0	0	0		Silent	SNP	ENST00000543571.1	37	CCDS34551.1																																																																																			.		0.473	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		G	149997827	C	G	149997827	2	3	157	1	0	0	0	0	0	0	0	1	8667	610	22	4		4	LATS1	6	149997827	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	10509897	149997827	21117240	77	14232											
RBAK	57786	hgsc.bcm.edu;bcgsc.ca	37	chr7	5104550	5104550	+	Frame_Shift_Del	DEL	G	G	-																															agagaaatcccatgaatgtaGtgaatgtggaaagttctctc																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:5104550delG	ENST00000353796.3	+	6	1787	c.1463delG	c.(1462-1464)agtfs	p.S488fs	RBAK_ENST00000396912.1_Frame_Shift_Del_p.S488fs|RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	488	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		CATGAATGTAGTGAATGTGGA	0.373																																					p.S488fs		.											.	RBAK-653	0			c.1463delG						.						64	64	64					7																	5104550		2203	4299	6502	SO:0001589	frameshift_variant	57786	exon6			.	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1463delG	7.37:g.5104550delG	ENSP00000275423:p.Ser488fs	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	105	58	NM_001204456	0	0	0	0	0	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Frame_Shift_Del	DEL	ENST00000353796.3	37	CCDS5337.1																																																																																			.		0.373	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		-	5104550	G	-	5104550	7	5	157	1	0	1	0	1	0	0	0	0	13132	1029	36	0	1477	0	RBAK	7	5104550	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10		5104550	154034113	78	14233											
RNF216	54476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	5781127	5781127	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agatgatgactttctgctctGatctggggttgacaatgtca	9	14	11	7	0	4	5	1	4	3	1	4	5	4	5	0	2	1	2	0	2	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:5781127G>C	ENST00000425013.2	-	4	574	c.350C>G	c.(349-351)tCa>tGa	p.S117*	RNF216_ENST00000389902.3_Nonsense_Mutation_p.S174*	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	117					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TTTCTGCTCTGATCTGGGGTT	0.463																																					p.S174X		.											.	RNF216-274	0			c.C521G						.						267	250	256					7																	5781127		2203	4300	6503	SO:0001587	stop_gained	54476	exon4			TGCTCTGATCTGG	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"RING-type (C3HC4) zinc fingers"	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.350C>G	7.37:g.5781127G>C	ENSP00000404602:p.Ser117*	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	147	74	NM_207111	0	0	11	12	1	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Nonsense_Mutation	SNP	ENST00000425013.2	37	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.567910	0.65651	.	.	ENSG00000011275	ENST00000425013;ENST00000389902	.	.	.	5.97	3.93	0.45458	.	0.519284	0.17997	N	0.155007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-4.5609	7.8068	0.29206	0.2458:0.0:0.7542:0.0	.	.	.	.	X	117;174	.	ENSP00000374550:S117X	S	-	2	0	RNF216	5747653	0.000000	0.05858	0.995000	0.50966	0.994000	0.84299	0.252000	0.18278	1.509000	0.48786	0.561000	0.74099	TCA	.		0.463	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		C	5781127	G	C	5781127	4	2	157	1	0	0	0	0	0	1	0	0	13512	1294	45	4	2306	4	RNF216	7	5781127	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	676577	5781127	153357536	79	14234											
VSTM2A	222008	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	54612346	54612346	+	Frame_Shift_Del	DEL	G	G	-																															gagtttccgcggaacgtgacGgcgaccgaggggcagaatgt																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:54612346delG	ENST00000407838.3	+	2	517	c.111delG	c.(109-111)acgfs	p.T37fs	VSTM2A_ENST00000302287.3_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000402026.2_Frame_Shift_Del_p.T36fs|VSTM2A_ENST00000402613.3_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000404951.1_Frame_Shift_Del_p.T37fs	NM_182546.2	NP_872352.2	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2A	37	Ig-like V-type.					extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(12)|prostate(1)	16			STAD - Stomach adenocarcinoma(5;0.0525)			GGAACGTGACGGCGACCGAGG	0.577																																					p.T37fs		.											.	.	0			c.111delG						.						61	60	60					7																	54612346		2203	4300	6503	SO:0001589	frameshift_variant	222008	exon2			.	BC028404	CCDS5512.2, CCDS75604.1	7p11.2	2013-01-11	2007-08-10	2007-08-10	ENSG00000170419	ENSG00000170419		"Immunoglobulin superfamily / V-set domain containing"	28499	protein-coding gene	gene with protein product			"V-set and transmembrane domain containing 2"	VSTM2		12477932	Standard	XM_006715663		Approved	MGC33530	uc010kzf.3	Q8TAG5	OTTHUMG00000129271	ENST00000407838.3:c.111delG	7.37:g.54612346delG	ENSP00000384967:p.Thr37fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	167	50	NM_182546	0	0	0	0	0	A4D2E9|B5MC94	Frame_Shift_Del	DEL	ENST00000407838.3	37	CCDS5512.2																																																																																			.		0.577	VSTM2A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318694.1	NM_182546		-	54612346	G	-	54612346	7	5	157	1	0	1	0	1	0	0	0	0	17262	1103	39	0	117	0	VSTM2A	7	54612346	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	48831219	54612346	104526317	80	14235											
STAG3L4	64940	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	66774599	66774599	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttgccctccaactgagtcTgcacgaagatatcaatcagc	12	9	8	12	1	3	2	2	1	1	1	4	3	4	2	2	0	4	2	2	0	4	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:66774599T>G	ENST00000416602.2	+	0	616					NR_040586.1		Q8TBR4	ST3L4_HUMAN	stromal antigen 3-like 4 (pseudogene)											endometrium(2)|lung(5)	7		Lung NSC(55;0.0839)|all_lung(88;0.181)				CAACTGAGTCTGCACGAAGAT	0.483																																					.													.	STAG3L4-68	0			.						.						131	138	136					7																	66774599		2203	4300	6503			64940	.			TGAGTCTGCACGA			7q11.21	2013-06-26	2013-06-26		ENSG00000106610	ENSG00000106610			33887	pseudogene	pseudogene			"stromal antigen 3-like 4"				Standard	NR_040585		Approved	FLJ13195, STAG3L4P	uc010laj.3	Q8TBR4	OTTHUMG00000156920		7.37:g.66774599T>G		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	92	34	.	0	0	0	13	13	Q9H8W0	RNA	SNP	ENST00000416602.2	37		.	.	.	.	.	.	.	.	.	.	t	7.912	0.736640	0.15574	.	.	ENSG00000106610	ENST00000416602;ENST00000437742	.	.	.	0.524	0.524	0.17066	STAG (1);	0.297117	0.24136	N	0.041215	T	0.45696	0.1355	.	.	.	.	.	.	P	0.47034	0.889	P	0.50270	0.636	T	0.53927	-0.8369	7	0.49607	T	0.09	.	5.3623	0.16095	0.0:2.0E-4:0.0:0.9998	.	114	Q8TBR4	STG34_HUMAN	R	114	.	ENSP00000408597:L114R	L	+	2	0	STAG3L4	66412034	0.998000	0.40836	0.719000	0.30619	0.035000	0.12851	5.174000	0.65015	0.472000	0.27344	0.113000	0.15668	CTG	.		0.483	STAG3L4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000346611.1	NM_022906		G	66774599	T	G	66774599	1	3	157	0	1	0	0	0	0	0	0	0	15279	1580	55	5		5	STAG3L4	7	66774599	RNA	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	12162253	66774599	92364064	81	14236											
SEMA3A	10371	broad.mit.edu	37	chr7	83739849	83739849	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagcccccgttccacaggcGtacaagtgagtctgattata	12	9	9	11	2	1	2	0	2	1	0	2	2	2	2	3	1	2	2	3	1	5	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:83739849G>A	ENST00000265362.4	-	4	704	c.390C>T	c.(388-390)taC>taT	p.Y130Y	SEMA3A_ENST00000436949.1_Silent_p.Y130Y	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	130	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)	p.Y130Y(1)		breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						TTCCACAGGCGTACAAGTGAG	0.383																																					p.Y130Y													.	SEMA3A-156	1	Substitution - coding silent(1)	breast(1)	c.C390T						.						126	116	120					7																	83739849		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon4			ACAGGCGTACAAG	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10723	protein-coding gene	gene with protein product	"sema III"	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.390C>T	7.37:g.83739849G>A		Somatic	176	0		WXS	Illumina HiSeq	Phase_I	154	5	NM_006080	0	0	0	0	0		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			.		0.383	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83739849	G	A	83739849	2	1	157	1	0	0	0	0	0	0	0	1	14056	1140	40	1		1	SEMA3A	7	83739849	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	16965250	83739849	75398814	82	14237											
AKAP9	10142	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	91632281	91632281	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcatgtgatactcaagtaaGctctttattagatggagttg	11	15	10	5	0	3	2	2	1	1	1	3	3	3	3	0	1	2	3	0	1	5	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:91632281G>A	ENST00000359028.2	+	9	3311	c.3086G>A	c.(3085-3087)aGc>aAc	p.S1029N	AKAP9_ENST00000356239.3_Missense_Mutation_p.S1017N|AKAP9_ENST00000358100.2_Missense_Mutation_p.S1029N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1029					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACTCAAGTAAGCTCTTTATTA	0.358			T	BRAF	papillary thyroid																																p.S1017N				Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9-755	0			c.G3050A						.						86	86	86					7																	91632281		2202	4299	6501	SO:0001583	missense	10142	exon8			AAGTAAGCTCTTT	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	379	protein-coding gene	gene with protein product	"A-kinase anchoring protein 450", "AKAP9-BRAF fusion protein", "AKAP120-like protein", "centrosome- and golgi-localized protein kinase N-associated protein", "protein kinase A anchoring protein 9", "A-kinase anchor protein, 350kDa", "protein phosphatase 1, regulatory subunit 45", "yotiao"	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.3086G>A	7.37:g.91632281G>A	ENSP00000351922:p.Ser1029Asn	Somatic	160	1		WXS	Illumina HiSeq	Phase_I	140	81	NM_005751	0	0	0	0	0	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	G	8.175	0.792556	0.16258	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.03441	3.94;3.93;3.93	5.72	2.61	0.31194	.	0.622892	0.14300	N	0.328352	T	0.04407	0.0121	L	0.54323	1.7	0.09310	N	1	B;B;B;B	0.13145	0.001;0.007;0.001;0.001	B;B;B;B	0.08055	0.001;0.003;0.002;0.003	T	0.45234	-0.9275	10	0.15499	T	0.54	.	9.0655	0.36460	0.423:0.0:0.577:0.0	.	1029;1017;1017;1029	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	N	1017;1029;1029;1029;1029	ENSP00000348573:S1017N;ENSP00000351922:S1029N;ENSP00000350813:S1029N	ENSP00000348573:S1017N	S	+	2	0	AKAP9	91470217	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.613000	0.24299	0.274000	0.22072	0.650000	0.86243	AGC	.		0.358	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91632281	G	A	91632281	3	1	157	1	0	0	0	0	1	0	0	0	459	971	34	2	3080	2	AKAP9	7	91632281	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	7892432	91632281	67506382	83	14238											
ZNF655	79027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	99158261	99158261	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggagacccagtctgagtgtCtgtccccagagcctcagttt	7	11	11	12	0	3	3	1	1	2	2	4	4	4	3	4	1	1	1	4	1	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:99158261C>T	ENST00000394163.2	+	2	262	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	GS1-259H13.10_ENST00000486324.1_3'UTR|ZNF655_ENST00000449244.1_Silent_p.L27L|GS1-259H13.10_ENST00000455905.1_Silent_p.L27L|ZNF655_ENST00000454654.1_Silent_p.L27L|ZNF655_ENST00000357864.2_Silent_p.L27L|ZNF655_ENST00000252713.4_Silent_p.L27L|ZNF655_ENST00000425063.1_Silent_p.L27L|ZNF655_ENST00000493277.1_Silent_p.L27L|ZNF655_ENST00000320583.5_Silent_p.L27L|ZNF655_ENST00000440391.1_Silent_p.L27L|ZNF655_ENST00000424881.1_Silent_p.L27L	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	27					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					GTCTGAGTGTCTGTCCCCAGA	0.567																																					p.L27L		.											.	ZNF655-91	0			c.C79T						.						118	113	114					7																	99158261		2203	4300	6503	SO:0001819	synonymous_variant	79027	exon2			GAGTGTCTGTCCC	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"Zinc fingers, C2H2-type", "-"	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.79C>T	7.37:g.99158261C>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	79	21	NM_024061	0	0	7	13	6	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Silent	SNP	ENST00000394163.2	37	CCDS5669.1																																																																																			.		0.567	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494		T	99158261	C	T	99158261	2	4	157	1	0	0	0	0	0	0	0	1	18100	912	32	2		2	ZNF655	7	99158261	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	7525980	99158261	59980402	84	14239											
DLD	1738	broad.mit.edu	37	chr7	107545820	107545820	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaaggttgttcatgtcaaTggatatggaaagataactgg	14	12	12	3	0	2	1	2	0	0	1	2	3	2	3	0	4	1	3	0	4	6	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:107545820T>C	ENST00000205402.5	+	7	734	c.453T>C	c.(451-453)aaT>aaC	p.N151N	DLD_ENST00000440410.1_Silent_p.N128N|DLD_ENST00000537148.1_Silent_p.N52N|DLD_ENST00000494441.1_3'UTR|DLD_ENST00000437604.2_Intron	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	151					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	TTCATGTCAATGGATATGGAA	0.313																																					p.N151N													.	DLD-226	0			c.T453C						.						79	76	77					7																	107545820		2203	4300	6503	SO:0001819	synonymous_variant	1738	exon7			TGTCAATGGATAT	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.453T>C	7.37:g.107545820T>C		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	42	3	NM_000108	0	0	115	115	0	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Silent	SNP	ENST00000205402.5	37	CCDS5749.1																																																																																			.		0.313	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		C	107545820	T	C	107545820	2	2	157	1	0	0	0	0	0	0	0	1	4562	1461	51	3		3	DLD	7	107545820	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	8387559	107545820	51592843	85	14240											
C7orf45	136263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	129856036	129856036	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacggagtatggcagtgaagAgtctaactcagaagcctcct	12	9	11	9	1	2	3	1	1	1	2	3	4	3	4	2	2	3	2	2	2	5	3	rs144099660		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:129856036A>T	ENST00000297819.3	+	3	512	c.461A>T	c.(460-462)gAg>gTg	p.E154V		NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	154						integral component of membrane (GO:0016021)											GGCAGTGAAGAGTCTAACTCA	0.478																																					p.E154V		.											.	.	0			c.A461T						.						98	99	99					7																	129856036		2203	4300	6503	SO:0001583	missense	0	exon3			GTGAAGAGTCTAA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 45"	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.461A>T	7.37:g.129856036A>T	ENSP00000297819:p.Glu154Val	Somatic	171	0		WXS	Illumina HiSeq	Phase_I	185	48	NM_145268	0	0	0	0	0		Missense_Mutation	SNP	ENST00000297819.3	37	CCDS5816.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921732	0.52653	.	.	ENSG00000165120	ENST00000297819	T	0.55052	0.54	5.56	3.09	0.35607	.	0.365080	0.26103	N	0.026340	T	0.48589	0.1508	M	0.63428	1.95	0.32923	D	0.516117	B	0.20671	0.047	B	0.24541	0.054	T	0.56044	-0.8044	10	0.87932	D	0	-6.405	8.8929	0.35446	0.702:0.0:0.0:0.2979	.	154	Q8WWF3	CG045_HUMAN	V	154	ENSP00000297819:E154V	ENSP00000297819:E154V	E	+	2	0	C7orf45	129643272	0.962000	0.33011	0.961000	0.40146	0.396000	0.30629	2.242000	0.43106	0.352000	0.24053	0.402000	0.26972	GAG	A|1.000;C|0.000		0.478	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268		T	129856036	A	T	129856036	3	4	157	1	0	0	0	0	1	0	0	0	2401	304	11	5	471	5	C7orf45	7	129856036	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	22310216	129856036	29282627	86	14241											
HIPK2	28996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr7	139258060	139258060	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgttgtgcgggaaggagtaCggagcctgggccatggtggg	6	8	20	7	2	0	0	0	0	0	0	0	3	0	3	2	6	3	2	2	6	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:139258060C>A	ENST00000406875.3	-	15	3304	c.3210G>T	c.(3208-3210)ccG>ccT	p.P1070P	HIPK2_ENST00000428878.2_Silent_p.P1043P	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	1070	Autoinhibitory domain (AID).				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GGAAGGAGTACGGAGCCTGGG	0.682																																					p.P1070P		.											.	HIPK2-785	0			c.G3210T						.						84	104	97					7																	139258060		2181	4276	6457	SO:0001819	synonymous_variant	28996	exon15			GGAGTACGGAGCC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.3210G>T	7.37:g.139258060C>A		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	37	12	NM_022740	0	0	7	8	1	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				.		0.682	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		A	139258060	C	A	139258060	2	1	157	1	0	0	0	0	0	0	0	1	7138	523	19	4		4	HIPK2	7	139258060	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	9402024	139258060	19880603	87	14242											
CRISPLD1	83690	ucsc.edu;bcgsc.ca	37	chr8	75932278	75932278	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaacaactgtggaacagcTctgtccatttcataagcctg	12	11	8	10	0	2	1	1	1	1	0	3	2	3	2	2	1	5	1	2	1	4	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:75932278T>A	ENST00000262207.4	+	12	1676	c.1208T>A	c.(1207-1209)cTc>cAc	p.L403H	CRISPLD1_ENST00000523524.1_Missense_Mutation_p.L215H|CRISPLD1_ENST00000517786.1_Missense_Mutation_p.L217H	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	403	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			GTGGAACAGCTCTGTCCATTT	0.413																																					p.L403H													.	CRISPLD1-91	0			c.T1208A						.						135	123	127					8																	75932278		2203	4300	6503	SO:0001583	missense	83690	exon12			AACAGCTCTGTCC	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"LCCL domain containing cysteine-rich secretory protein 1"	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.1208T>A	8.37:g.75932278T>A	ENSP00000262207:p.Leu403His	Somatic	137	2		WXS	Illumina HiSeq		115	55	NM_031461	0	0	0	1	1	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	37	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.610809	0.87258	.	.	ENSG00000121005	ENST00000262207;ENST00000523524;ENST00000517786	D;D;D	0.90004	-2.6;-2.6;-2.6	5.44	5.44	0.79542	LCCL (5);	0.074942	0.49305	D	0.000149	D	0.93367	0.7885	L	0.61387	1.9	0.52501	D	0.999953	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.934	D	0.94015	0.7287	10	0.87932	D	0	.	15.6638	0.77209	0.0:0.0:0.0:1.0	.	217;403	B7Z929;Q9H336	.;CRLD1_HUMAN	H	403;215;217	ENSP00000262207:L403H;ENSP00000430105:L215H;ENSP00000429746:L217H	ENSP00000262207:L403H	L	+	2	0	CRISPLD1	76094833	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.493000	0.81493	2.285000	0.76669	0.528000	0.53228	CTC	.		0.413	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		A	75932278	T	A	75932278	3	1	157	1	0	0	0	0	1	0	0	0	3888	1551	54	5	1250	5	CRISPLD1	8	75932278	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10		75932278	70431744	88	14243											
LRRCC1	85444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	86057651	86057651	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaattgaaaaagaaatgcgtGaacttttggaagaaacatgc	19	9	9	4	1	0	4	0	2	0	2	0	5	0	5	0	1	4	0	0	1	7	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:86057651G>T	ENST00000360375.3	+	19	3153	c.3004G>T	c.(3004-3006)Gaa>Taa	p.E1002*	LRRCC1_ENST00000414626.2_Nonsense_Mutation_p.E982*	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1002					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AGAAATGCGTGAACTTTTGGA	0.269																																					p.E1002X		.											.	LRRCC1-90	0			c.G3004T						.						49	45	46					8																	86057651		1795	4056	5851	SO:0001587	stop_gained	85444	exon19			ATGCGTGAACTTT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3004G>T	8.37:g.86057651G>T	ENSP00000353538:p.Glu1002*	Somatic	335	0		WXS	Illumina HiSeq	Phase_I	275	71	NM_033402	0	0	7	12	5	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Nonsense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	G	38	6.807978	0.97853	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	.	.	.	4.97	4.06	0.47325	.	0.467007	0.15962	N	0.236193	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-1.6865	14.481	0.67582	0.0:0.2766:0.7234:0.0	.	.	.	.	X	1002;982	.	ENSP00000353538:E1002X	E	+	1	0	LRRCC1	86244903	1.000000	0.71417	0.956000	0.39512	0.626000	0.37791	3.387000	0.52501	2.567000	0.86603	0.491000	0.48974	GAA	.		0.269	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		T	86057651	G	T	86057651	4	4	157	1	0	0	0	0	0	1	0	0	9051	1291	45	4	3078	4	LRRCC1	8	86057651	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	10125373	86057651	60306371	89	14244											
CSMD3	114788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	113678545	113678545	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagagtgtccaggttcagctTcaatcacccactcacaattc	11	11	6	13	0	4	1	4	0	0	1	6	1	5	1	2	1	1	2	2	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:113678545T>G	ENST00000297405.5	-	17	3021	c.2777A>C	c.(2776-2778)gAa>gCa	p.E926A	CSMD3_ENST00000455883.2_Missense_Mutation_p.E822A|CSMD3_ENST00000352409.3_Missense_Mutation_p.E926A|CSMD3_ENST00000343508.3_Missense_Mutation_p.E886A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	926	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGGTTCAGCTTCAATCACCCA	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E926A		.											.	CSMD3-1132	0			c.A2777C						.						66	64	65					8																	113678545		2203	4300	6503	SO:0001583	missense	114788	exon17			TCAGCTTCAATCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2777A>C	8.37:g.113678545T>G	ENSP00000297405:p.Glu926Ala	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	141	90	NM_198123	0	0	0	0	0	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.621461	0.87460	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.97	5.97	0.96955	CUB (5);	0.000000	0.64402	D	0.000001	T	0.38214	0.1032	L	0.58428	1.81	0.46028	D	0.998827	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.03374	-1.1043	10	0.25751	T	0.34	.	16.4523	0.83996	0.0:0.0:0.0:1.0	.	822;926;886	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	886;926;266;822;926	ENSP00000345799:E886A;ENSP00000297405:E926A;ENSP00000341558:E266A;ENSP00000412263:E822A;ENSP00000343124:E926A	ENSP00000297405:E926A	E	-	2	0	CSMD3	113747721	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.286000	0.76751	0.455000	0.32223	GAA	.		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113678545	T	G	113678545	3	3	157	1	0	0	0	0	1	0	0	0	3952	1783	62	5	8566	5	CSMD3	8	113678545	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	27620894	113678545	32685477	90	14245											
PLAA	9373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	26925951	26925951	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatctgtcctctgctgttgtCacaaagtctaaaattaatga	12	14	7	8	0	4	1	1	1	3	0	5	2	5	1	1	0	1	2	1	0	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:26925951C>A	ENST00000397292.3	-	6	1158	c.741G>T	c.(739-741)gtG>gtT	p.V247V	PLAA_ENST00000520884.1_Silent_p.V247V	NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	247					inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		CTGCTGTTGTCACAAAGTCTA	0.373																																					p.V247V	Melanoma(175;2670 2735 14091 35526)	.											.	PLAA-514	0			c.G741T						.						90	80	83					9																	26925951		2203	4300	6503	SO:0001819	synonymous_variant	9373	exon6			TGTTGTCACAAAG	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.741G>T	9.37:g.26925951C>A		Somatic	92	0		WXS	Illumina HiSeq	Phase_I	81	48	NM_001031689	0	0	0	0	0	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Silent	SNP	ENST00000397292.3	37	CCDS35000.1	.	.	.	.	.	.	.	.	.	.	C	6.836	0.523440	0.13066	.	.	ENSG00000137055	ENST00000523212	.	.	.	4.07	3.16	0.36331	.	.	.	.	.	T	0.47710	0.1460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35871	-0.9771	4	.	.	.	-2.2178	4.411	0.11432	0.1594:0.5773:0.0:0.2632	.	.	.	.	Y	224	.	.	D	-	1	0	PLAA	26915951	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.336000	0.19823	0.817000	0.34445	0.585000	0.79938	GAC	.		0.373	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		A	26925951	C	A	26925951	2	1	157	1	0	0	0	0	0	0	0	1	12037	813	29	4		4	PLAA	9	26925951	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		26925951	114287480	91	14246											
RUSC2	9853	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	35547875	35547875	+	Frame_Shift_Del	DEL	G	G	-																															acctattccagaagccagaaGtccagccagaggaacaagaa																								rs375840925		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35547875delG	ENST00000455600.1	+	2	1926	c.1357delG	c.(1357-1359)gtcfs	p.V453fs		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	453						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			GAAGCCAGAAGTCCAGCCAGA	0.572																																					p.V453fs		.											.	RUSC2-91	0			c.1357delG						.						107	127	120					9																	35547875		2203	4300	6503	SO:0001589	frameshift_variant	9853	exon2			.	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.1357delG	9.37:g.35547875delG	ENSP00000393922:p.Val453fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	86	53	NM_014806	0	0	0	0	0	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Frame_Shift_Del	DEL	ENST00000455600.1	37	CCDS35008.1																																																																																			.		0.572	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		-	35547875	G	-	35547875	7	5	157	1	0	1	0	1	0	0	0	0	13783	1029	36	0	1359	0	RUSC2	9	35547875	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	8621924	35547875	105665556	92	14247											
TLN1	7094	broad.mit.edu	37	chr9	35699091	35699097	+	Frame_Shift_Del	DEL	CAGCTCC	CAGCTCC	-																															tgcagcctcaatggcggctgCagctcccaggagctcattct																								rs370191540		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	CAGCTCC	CAGCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35699091_35699097delCAGCTCC	ENST00000314888.9	-	52	7284_7290	c.6931_6937delGGAGCTG	c.(6931-6939)ggagctgcafs	p.GAA2311fs	TLN1_ENST00000540444.1_Frame_Shift_Del_p.GAA2199fs	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2311	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ATGGCGGCTGCAGCTCCCAGGAGCTCA	0.585																																					p.2311_2313del													.	TLN1-609	0			c.6931_6937del						.																																			SO:0001589	frameshift_variant	7094	exon52			CGGCTGCAGCTCC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6931_6937delGGAGCTG	9.37:g.35699091_35699097delCAGCTCC	ENSP00000316029:p.Gly2311fs	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	53	9	NM_006289	0	0	0	0	0	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Frame_Shift_Del	DEL	ENST00000314888.9	37	CCDS35009.1																																																																																			.		0.585	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		-	35699097	CAGCTCC	-	35699091	7	5	157	1	0	1	0	1	0	0	0	0	15979	710	25	0	712	0	TLN1	9	35699091	Frame_Shift_Del	DEL	CAGCTCC	TCGA-P4-A5EB-01A-11D-A28G-10	151216	35699091	105514340	93	14248											
TLN1	7094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	35711276	35711276	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagctgcagccagctgactcTtgaggttaggggcagcaggg	8	7	16	10	0	1	2	0	2	1	0	1	2	1	2	1	4	5	6	1	4	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35711276T>A	ENST00000314888.9	-	30	4348	c.3995A>T	c.(3994-3996)aAg>aTg	p.K1332M	TLN1_ENST00000540444.1_Missense_Mutation_p.K1332M	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1332	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGCTGACTCTTGAGGTTAGG	0.562																																					p.K1332M		.											.	TLN1-609	0			c.A3995T						.						51	49	50					9																	35711276		2203	4300	6503	SO:0001583	missense	7094	exon30			TGACTCTTGAGGT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3995A>T	9.37:g.35711276T>A	ENSP00000316029:p.Lys1332Met	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	57	21	NM_006289	0	0	40	40	0	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775730	0.90195	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.18810	2.19;2.19	5.82	5.82	0.92795	Vinculin-binding site-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44138	0.1279	M	0.83953	2.67	0.80722	D	1	P	0.52316	0.952	P	0.53954	0.738	T	0.48234	-0.9053	10	0.62326	D	0.03	-24.4418	16.1778	0.81874	0.0:0.0:0.0:1.0	.	1332	Q9Y490	TLN1_HUMAN	M	1332	ENSP00000316029:K1332M;ENSP00000442981:K1332M	ENSP00000316029:K1332M	K	-	2	0	TLN1	35701276	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.040000	0.89188	2.225000	0.72522	0.459000	0.35465	AAG	.		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35711276	T	A	35711276	3	1	157	1	0	0	0	0	1	0	0	0	15979	1609	56	5	3742	5	TLN1	9	35711276	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	12185	35711276	105502155	94	14249											
TJP2	9414	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	71869284	71869285	+	Frame_Shift_Ins	INS	-	-	T																															cccgataccgggacacagaaINSttatagatgtctgagcacgg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:71869284_71869285insT	ENST00000377245.4	+	23	3775_3776	c.3567_3568insT	c.(3568-3570)ttafs	p.L1190fs	TJP2_ENST00000453658.2_Frame_Shift_Ins_p.L1020fs|TJP2_ENST00000535702.1_Frame_Shift_Ins_p.L1157fs|TJP2_ENST00000539225.1_Frame_Shift_Ins_p.L1221fs|TJP2_ENST00000348208.4_Frame_Shift_Ins_p.L1043fs	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	1190	Interaction with SCRIB.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GGGACACAGAATTATAGATGTC	0.579																																					p.E1220fs		.											.	TJP2-115	0			c.3660_3661insT						.																																			SO:0001589	frameshift_variant	9414	exon23			.	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"Friedreich ataxia region gene X104 (tight junction protein ZO-2)", "zona occludens 2"	607709	"deafness, autosomal dominant 51"	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.3569dupT	9.37:g.71869286_71869286dupT	ENSP00000366453:p.Leu1190fs	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	78	21	NM_001170416	0	0	0	0	0	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Frame_Shift_Ins	INS	ENST00000377245.4	37	CCDS6627.1																																																																																			.		0.579	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		T	71869285	-	T	71869284	7	5	157	1	0	1	1	0	0	0	0	0	15962	98	4	0	3916	0	TJP2	9	71869284	Frame_Shift_Ins	INS	-	TCGA-P4-A5EB-01A-11D-A28G-10	36158008	71869284	69344147	95	14250											
WNK2	65268	broad.mit.edu	37	chr9	96030146	96030146	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgccgaccgtggctccgAcccagggaccagcccgccac	8	2	12	19	5	0	1	0	0	0	1	1	4	1	2	7	2	1	1	7	2	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:96030146A>C	ENST00000297954.4	+	16	3815	c.3815A>C	c.(3814-3816)gAc>gCc	p.D1272A	WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Missense_Mutation_p.D884A|WNK2_ENST00000427277.2_Missense_Mutation_p.D884A|WNK2_ENST00000395477.2_Missense_Mutation_p.D1272A	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1272					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CGTGGCTCCGACCCAGGGACC	0.647																																					p.D1272A													.	WNK2-765	0			c.A3815C						.						37	34	35					9																	96030146		2203	4300	6503	SO:0001583	missense	65268	exon16			GCTCCGACCCAGG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"serologically defined colon cancer antigen 43"	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3815A>C	9.37:g.96030146A>C	ENSP00000297954:p.Asp1272Ala	Somatic	119	26		WXS	Illumina HiSeq	Phase_I	162	30	NM_006648	0	0	0	0	0	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.77|17.77	3.471405|3.471405	0.63737|0.63737	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000432730;ENST00000448251	T;T;T;T|.	0.33216|.	1.42;1.42;1.42;1.42|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.119947|.	0.53938|.	D|.	0.000041|.	T|T	0.63022|0.63022	0.2476|0.2476	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.999|.	D;D;D;D|.	0.87578|.	0.998;0.965;0.984;0.994|.	T|T	0.60301|0.60301	-0.7290|-0.7290	10|5	0.59425|.	D|.	0.04|.	.|.	15.846|15.846	0.78890|0.78890	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1272;875;1272;1272|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	A|P	1272;1272;884;884|1268;69	ENSP00000297954:D1272A;ENSP00000378860:D1272A;ENSP00000297876:D884A;ENSP00000411181:D884A|.	ENSP00000297954:D1272A|.	D|T	+|+	2|1	0|0	WNK2|WNK2	95069967|95069967	1.000000|1.000000	0.71417|0.71417	0.956000|0.956000	0.39512|0.39512	0.086000|0.086000	0.17979|0.17979	7.075000|7.075000	0.76798|0.76798	2.190000|2.190000	0.69967|0.69967	0.528000|0.528000	0.53228|0.53228	GAC|ACC	.		0.647	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		C	96030146	A	C	96030146	3	2	157	1	0	0	0	0	1	0	0	0	17411	275	10	5	3877	5	WNK2	9	96030146	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	24160862	96030146	45183285	96	14251											
RNF20	56254	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	104302538	104302538	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatcgcaagctggcagaaatGttggatcagcggcaggccat	12	7	13	9	2	1	1	1	0	0	1	2	2	1	2	1	4	2	5	1	4	3	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:104302538G>C	ENST00000389120.3	+	3	273	c.183G>C	c.(181-183)atG>atC	p.M61I	RNF20_ENST00000481046.1_3'UTR	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	61					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGGCAGAAATGTTGGATCAGC	0.438																																					p.M61I		.											.	RNF20-231	0			c.G183C						.						98	88	92					9																	104302538		2203	4300	6503	SO:0001583	missense	56254	exon3			AGAAATGTTGGAT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.183G>C	9.37:g.104302538G>C	ENSP00000373772:p.Met61Ile	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	76	48	NM_019592	0	0	2	13	11	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	37	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120440	0.37436	.	.	ENSG00000155827	ENST00000389120;ENST00000478347;ENST00000488264;ENST00000374819;ENST00000479306;ENST00000466817	T	0.29655	1.56	4.17	3.28	0.37604	.	0.193183	0.56097	D	0.000035	T	0.21387	0.0515	N	0.22421	0.69	0.36185	D	0.849654	B	0.02656	0.0	B	0.01281	0.0	T	0.16453	-1.0402	10	0.87932	D	0	-19.2966	11.9251	0.52814	0.0866:0.0:0.9134:0.0	.	61	Q5VTR2	BRE1A_HUMAN	I	61;49;47;61;61;61	ENSP00000373772:M61I	ENSP00000363952:M61I	M	+	3	0	RNF20	103342359	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	4.058000	0.57463	1.125000	0.41998	-0.379000	0.06801	ATG	.		0.438	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		C	104302538	G	C	104302538	3	2	157	1	0	0	0	0	1	0	0	0	13505	1377	48	4	189	4	RNF20	9	104302538	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8272392	104302538	36910893	97	14252											
ABCA1	19	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	107573100	107573100	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctgacaaatgtgtactgttCgttgtacatccagggctgaa	10	12	10	9	1	0	2	0	2	0	0	2	2	1	2	2	1	2	5	2	1	4	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:107573100C>G	ENST00000374736.3	-	29	4550	c.4156G>C	c.(4156-4158)Gaa>Caa	p.E1386Q		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1386					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GTGTACTGTTCGTTGTACATC	0.507																																					p.E1386Q		.											.	ABCA1-1016	0			c.G4156C						.						198	175	183					9																	107573100		2203	4300	6503	SO:0001583	missense	19	exon29			ACTGTTCGTTGTA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"ATP binding cassette transporters / subfamily A"	29	protein-coding gene	gene with protein product	"Tangier disease"	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4156G>C	9.37:g.107573100C>G	ENSP00000363868:p.Glu1386Gln	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	146	24	NM_005502	0	0	6	9	3	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077801	0.36662	.	.	ENSG00000165029	ENST00000374736	D	0.92299	-3.01	5.55	5.55	0.83447	.	0.095616	0.64402	D	0.000001	D	0.88840	0.6546	L	0.37466	1.105	0.80722	D	1	B	0.21309	0.054	B	0.26416	0.069	D	0.83736	0.0201	10	0.15499	T	0.54	.	19.8667	0.96806	0.0:1.0:0.0:0.0	.	1386	O95477	ABCA1_HUMAN	Q	1386	ENSP00000363868:E1386Q	ENSP00000363868:E1386Q	E	-	1	0	ABCA1	106612921	1.000000	0.71417	0.988000	0.46212	0.947000	0.59692	6.015000	0.70791	2.773000	0.95371	0.655000	0.94253	GAA	.		0.507	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		G	107573100	C	G	107573100	3	3	157	1	0	0	0	0	1	0	0	0	28	893	31	4	2717	4	ABCA1	9	107573100	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	3270562	107573100	33640331	98	14253											
RPL7A	6130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	136216489	136216489	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcggcagagagccatcCtctataagcggctgaaagtg	11	7	13	10	2	1	2	0	1	1	1	2	3	2	2	2	2	4	3	2	2	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:136216489C>A	ENST00000323345.6	+	3	238	c.208C>A	c.(208-210)Ctc>Atc	p.L70I	MED22_ENST00000471524.1_5'Flank|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000343730.5_5'Flank|RPL7A_ENST00000315731.4_Intron|RPL7A_ENST00000463740.1_3'UTR|SNORD36B_ENST00000363961.1_RNA|SNORD36A_ENST00000362874.1_RNA|MED22_ENST00000371999.1_5'Flank|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000476080.1_5'Flank|SURF1_ENST00000495952.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	70					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		GAGAGCCATCCTCTATAAGCG	0.552																																					p.L70I		.											.	RPL7A-90	0			c.C208A						.						43	48	46					9																	136216489		2203	4294	6497	SO:0001583	missense	6130	exon3			GCCATCCTCTATA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.208C>A	9.37:g.136216489C>A	ENSP00000361076:p.Leu70Ile	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	88	31	NM_000972	0	1	1247	1825	577	P11518|Q5T8U4	Missense_Mutation	SNP	ENST00000323345.6	37	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.158547	0.57368	.	.	ENSG00000148303	ENST00000323345;ENST00000426651	T;T	0.70164	-0.46;-0.13	4.03	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.75539	0.3863	M	0.89287	3.02	0.80722	D	1	B	0.22604	0.072	B	0.34346	0.18	T	0.78841	-0.2045	10	0.66056	D	0.02	.	15.1827	0.72972	0.0:1.0:0.0:0.0	.	70	P62424	RL7A_HUMAN	I	70;97	ENSP00000361076:L70I;ENSP00000416638:L97I	ENSP00000361076:L70I	L	+	1	0	RPL7A	135206310	1.000000	0.71417	0.648000	0.29521	0.115000	0.19883	5.276000	0.65580	1.816000	0.52996	0.313000	0.20887	CTC	.		0.552	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		A	136216489	C	A	136216489	3	1	157	1	0	0	0	0	1	0	0	0	13632	681	24	4	218	4	RPL7A	9	136216489	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	28643389	136216489	4996942	99	14254											
LHX3	8022	hgsc.bcm.edu	37	chr9	139089398	139089398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagggaggctctgcggggCggcgggggatggggggacac	5	3	24	9	3	1	0	0	0	1	0	1	3	1	3	1	10	1	1	1	10	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:139089398C>T	ENST00000371748.5	-	6	1063	c.967G>A	c.(967-969)Gcc>Acc	p.A323T	LHX3_ENST00000371746.3_Missense_Mutation_p.A328T	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	323					inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		CTCTGCGGGGCGGCGGGGGAT	0.736																																					p.A328T		.											.	LHX3-91	0			c.G982A						.						2	2	2					9																	139089398		1495	3217	4712	SO:0001583	missense	8022	exon6			GCGGGGCGGCGGG	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"Homeoboxes / LIM class"	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.967G>A	9.37:g.139089398C>T	ENSP00000360813:p.Ala323Thr	Somatic	7	0		WXS	Illumina HiSeq	Phase_I	12	6	NM_014564	0	0	0	0	0	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	37	CCDS6994.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.336|6.336	0.430180|0.430180	0.12045|0.12045	.|.	.|.	ENSG00000107187|ENSG00000107187	ENST00000371748;ENST00000371746|ENST00000325195	D;D|.	0.88818|.	-2.27;-2.43|.	4.04|4.04	1.96|1.96	0.26148|0.26148	.|.	0.152719|.	0.45361|.	N|.	0.000361|.	T|T	0.28433|0.28433	0.0703|0.0703	L|L	0.36672|0.36672	1.1|1.1	0.22961|0.22961	N|N	0.998502|0.998502	B;P|.	0.34462|.	0.308;0.454|.	B;B|.	0.29942|.	0.109;0.075|.	T|T	0.20371|0.20371	-1.0277|-1.0277	10|6	0.17369|0.33940	T|T	0.5|0.23	.|.	4.7565|4.7565	0.13086|0.13086	0.3922:0.4882:0.0:0.1196|0.3922:0.4882:0.0:0.1196	.|.	323;328|.	Q9UBR4;F1T0D9|.	LHX3_HUMAN;.|.	T|H	323;328|324	ENSP00000360813:A323T;ENSP00000360811:A328T|.	ENSP00000360811:A328T|ENSP00000319224:R324H	A|R	-|-	1|2	0|0	LHX3|LHX3	138229219|138229219	0.831000|0.831000	0.29352|0.29352	0.042000|0.042000	0.18584|0.18584	0.173000|0.173000	0.22820|0.22820	1.670000|1.670000	0.37502|0.37502	0.891000|0.891000	0.36235|0.36235	0.491000|0.491000	0.48974|0.48974	GCC|CGC	.		0.736	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3			T	139089398	C	T	139089398	3	4	157	1	0	0	0	0	1	0	0	0	8794	768	27	1	230	1	LHX3	9	139089398	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	2872909	139089398	2124033	100	14255											
OPTN	10133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	13160994	13160994	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtgcctaagggaagggaatCagaaggtggagagacttgaa	14	7	16	4	0	1	3	1	1	0	2	1	7	1	6	1	4	1	0	1	4	5	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:13160994C>T	ENST00000378748.3	+	8	1095	c.733C>T	c.(733-735)Cag>Tag	p.Q245*	OPTN_ENST00000378757.2_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378764.2_Nonsense_Mutation_p.Q239*|OPTN_ENST00000263036.5_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378747.3_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378752.3_Nonsense_Mutation_p.Q239*	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	245					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GGAAGGGAATCAGAAGGTGGA	0.428																																					p.Q245X		.											.	OPTN-70	0			c.C733T						.						93	91	91					10																	13160994		2203	4300	6503	SO:0001587	stop_gained	10133	exon7			GGGAATCAGAAGG	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"glaucoma 1, open angle, E (adult-onset)"	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.733C>T	10.37:g.13160994C>T	ENSP00000368022:p.Gln245*	Somatic	199	0		WXS	Illumina HiSeq	Phase_I	175	100	NM_001008212	0	0	41	42	1	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Nonsense_Mutation	SNP	ENST00000378748.3	37	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	C	39	7.381482	0.98248	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	.	.	.	6.16	6.16	0.99307	.	0.099240	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-22.7994	19.6313	0.95704	0.0:1.0:0.0:0.0	.	.	.	.	X	245;239;245;239;245;245	.	ENSP00000263036:Q245X	Q	+	1	0	OPTN	13201000	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.672000	0.46850	2.937000	0.99478	0.650000	0.86243	CAG	.		0.428	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		T	13160994	C	T	13160994	4	4	157	1	0	0	0	0	0	1	0	0	10915	827	29	2	751	2	OPTN	10	13160994	Nonsense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		13160994	122373753	101	14256											
KIAA1462	57608	broad.mit.edu;bcgsc.ca	37	chr10	30336674	30336674	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccttggggttatcctcgCgtgatgctggggggtctctt	2	13	15	11	2	1	1	0	1	1	0	4	1	2	1	3	5	1	2	3	5	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:30336674C>T	ENST00000375377.1	-	2	169	c.68G>A	c.(67-69)cGc>cAc	p.R23H		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	23					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						GTTATCCTCGCGTGATGCTGG	0.607																																					p.R23H													.	KIAA1462-72	0			c.G68A						.						73	79	77					10																	30336674		2036	4192	6228	SO:0001583	missense	57608	exon2			TCCTCGCGTGATG	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"junctional protein associated with coronary artery disease"	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.68G>A	10.37:g.30336674C>T	ENSP00000364526:p.Arg23His	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	128	6	NM_020848	0	0	0	0	0	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	C	7.772	0.707679	0.15239	.	.	ENSG00000165757	ENST00000375377	T	0.11604	2.76	5.3	-1.25	0.09405	.	0.823638	0.10809	N	0.631817	T	0.03434	0.0099	N	0.03115	-0.41	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.46992	-0.9151	10	0.11794	T	0.64	-5.5506	5.0393	0.14451	0.0:0.4095:0.1523:0.4382	.	23	Q9P266	K1462_HUMAN	H	23	ENSP00000364526:R23H	ENSP00000364526:R23H	R	-	2	0	KIAA1462	30376680	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.154000	0.10130	-0.048000	0.13401	-0.373000	0.07131	CGC	.		0.607	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30336674	C	T	30336674	3	4	157	1	0	0	0	0	1	0	0	0	8255	768	27	1	4023	1	KIAA1462	10	30336674	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	17175680	30336674	105198073	102	14257											
TYSND1	219743	hgsc.bcm.edu	37	chr10	71905802	71905819	+	In_Frame_Del	DEL	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	-																															cagcgcaaaccagcccagcgCtctcagttgatccgcctcct																								rs370610523|rs572542997|rs562289648|rs553877350	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:71905802_71905819delCTCTCAGTTGATCCGCCT	ENST00000287078.6	-	1	523_540	c.524_541delAGGCGGATCAACTGAGAG	c.(523-543)gaggcggatcaactgagagcg>gcg	p.EADQLR175del	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_In_Frame_Del_p.EADQLR175del	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	175					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CAGCCCAGCGCTCTCAGTTGATCCGCCTCCTCGTCCTC	0.711														5	0.000998403	8e-04	0	5008	,	,		14648	0.002		0	False		,,,				2504	0.002				p.175_181del		.											.	TYSND1-135	0			c.524_541del						.		,	1,4251		0,1,2125					,	3.9	1			26	18,8216		0,18,4099	no	coding,coding	TYSND1	NM_173555.2,NM_001040273.1	,	0,19,6224	A1A1,A1R,RR		0.2186,0.0235,0.1522	,	,		19,12467				SO:0001651	inframe_deletion	219743	exon1			.	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.524_541delAGGCGGATCAACTGAGAG	10.37:g.71905802_71905819delCTCTCAGTTGATCCGCCT	ENSP00000287078:p.Glu175_Arg180del	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	112	32	NM_173555	0	0	0	0	0	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	In_Frame_Del	DEL	ENST00000287078.6	37	CCDS31213.1																																																																																			.		0.711	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		-	71905819	CTCTCAGTTGATCCGCCT	-	71905802	7	5	157	1	0	1	0	1	0	0	0	0	16850	797	28	0	1175	0	TYSND1	10	71905802	In_Frame_Del	DEL	CTCTCAGTTGATCCGCCT	TCGA-P4-A5EB-01A-11D-A28G-10	41569128	71905802	63628945	103	14258											
ZNF518A	9849	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	97917491	97917491	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acaaaatgtatgttcaccagGctcacagtcaggtgctgcaa	13	9	9	10	0	3	0	3	0	0	0	3	0	3	0	1	2	2	5	1	2	4	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:97917491G>T	ENST00000534948.1	+	0	2269							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						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(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		TGTTCACCAGGCTCACAGTCA	0.398																																					.													.	ZNF518A-23	0			.						.						115	114	114					10																	97917491		1879	4103	5982			9849	.			CACCAGGCTCACA	AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"Zinc fingers, C2H2-type"	29009	protein-coding gene	gene with protein product			"zinc finger protein 518"	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97917491G>T		Somatic	218	0		WXS	Illumina HiSeq	Phase_I	216	120	.	0	0	2	2	0	A0PJI5|O15044|Q32MP4	Missense_Mutation	SNP	ENST00000534948.1	37																																																																																				.		0.398	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		T	97917491	G	T	97917491	1	4	157	0	1	0	0	0	0	0	0	0	17994	1203	42	4		4	ZNF518A	10	97917491	RNA	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	26011689	97917491	37617256	104	14259											
KNDC1	85442	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr10	135013012	135013012	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgccactttctgtggcGccatttccgagaagttctgt	5	15	9	12	2	2	1	0	0	2	1	3	2	3	1	4	1	1	1	4	1	1	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:135013012G>A	ENST00000304613.3	+	15	2830	c.2809G>A	c.(2809-2811)Gcc>Acc	p.A937T	KNDC1_ENST00000368572.2_Missense_Mutation_p.A939T|KNDC1_ENST00000368571.2_Missense_Mutation_p.A872T			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	937					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.A937T(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TTTCTGTGGCGCCATTTCCGA	0.532																																					p.A937T		.											.	KNDC1-229	1	Substitution - Missense(1)	large_intestine(1)	c.G2809A						.						177	150	159					10																	135013012		2203	4300	6503	SO:0001583	missense	85442	exon15			TGTGGCGCCATTT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2809G>A	10.37:g.135013012G>A	ENSP00000304437:p.Ala937Thr	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	192	14	NM_152643	0	0	0	0	0	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244556	0.59103	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.12984	2.63;2.63;2.63	3.99	3.99	0.46301	.	0.479232	0.18727	N	0.132851	T	0.34571	0.0902	M	0.66939	2.045	0.41003	D	0.984944	D;D;D	0.89917	0.993;1.0;0.997	D;D;P	0.72338	0.919;0.977;0.74	T	0.18116	-1.0347	10	0.72032	D	0.01	-25.397	13.9012	0.63804	0.0:0.0:1.0:0.0	.	937;872;937	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	T	937;939;872	ENSP00000304437:A937T;ENSP00000357561:A939T;ENSP00000357560:A872T	ENSP00000304437:A937T	A	+	1	0	KNDC1	134863002	0.937000	0.31787	0.821000	0.32701	0.124000	0.20399	2.706000	0.47135	1.957000	0.56846	0.313000	0.20887	GCC	.		0.532	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135013012	G	A	135013012	3	1	157	1	0	0	0	0	1	0	0	0	8447	1087	38	1	2867	1	KNDC1	10	135013012	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	37095521	135013012	521735	105	14260											
OR51D1	390038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	4661643	4661643	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtactgacaccagggtcaAtgtggtttatggactcttca	9	13	10	9	0	3	1	2	1	1	0	3	2	3	2	1	3	1	2	1	3	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:4661643A>T	ENST00000357605.2	+	1	699	c.623A>T	c.(622-624)aAt>aTt	p.N208I		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	208						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)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACCAGGGTCAATGTGGTTTAT	0.468																																					p.N208I		.											.	OR51D1-68	0			c.A623T						.						290	242	259					11																	4661643		2201	4298	6499	SO:0001583	missense	390038	exon1			GGGTCAATGTGGT	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.623A>T	11.37:g.4661643A>T	ENSP00000350222:p.Asn208Ile	Somatic	141	0		WXS	Illumina HiSeq	Phase_I	172	74	NM_001004751	0	0	0	0	0	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	37	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.781247	0.31502	.	.	ENSG00000197428	ENST00000357605	T	0.00231	8.49	4.29	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000197	T	0.00580	0.0019	M	0.88906	2.99	0.43330	D	0.995366	P	0.44877	0.845	D	0.63793	0.918	T	0.66272	-0.5965	10	0.87932	D	0	.	9.16	0.37016	0.9102:0.0:0.0898:0.0	.	208	Q8NGF3	O51D1_HUMAN	I	208	ENSP00000350222:N208I	ENSP00000350222:N208I	N	+	2	0	OR51D1	4618219	0.644000	0.27277	0.752000	0.31206	0.008000	0.06430	1.567000	0.36407	0.752000	0.32923	0.460000	0.39030	AAT	.		0.468	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		T	4661643	A	T	4661643	3	4	157	1	0	0	0	0	1	0	0	0	11119	101	4	5	625	5	OR51D1	11	4661643	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		4661643	130344873	106	14261											
EIF4G2	1982	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	10820842	10820842	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaacgtgatcatgaagaaaTttctgcattactggcttgaa	13	13	8	7	1	3	4	2	3	1	1	3	4	3	4	0	1	3	2	0	1	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:10820842T>G	ENST00000526148.1	-	20	2964	c.2454A>C	c.(2452-2454)aaA>aaC	p.K818N	EIF4G2_ENST00000396525.2_Missense_Mutation_p.K780N|SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000339995.5_Missense_Mutation_p.K818N|EIF4G2_ENST00000525681.1_Missense_Mutation_p.K818N|RP11-685M7.5_ENST00000532365.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CATGAAGAAATTTCTGCATTA	0.443																																					p.K818N		.											.	EIF4G2-91	0			c.A2454C						.						154	144	148					11																	10820842		2201	4294	6495	SO:0001583	missense	1982	exon20			AAGAAATTTCTGC	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.2454A>C	11.37:g.10820842T>G	ENSP00000433664:p.Lys818Asn	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	120	61	NM_001172705	0	0	339	624	285		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.896251	0.72639	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000528839;ENST00000379653	T;T;T;T	0.22743	1.94;1.94;1.94;1.96	6.07	0.912	0.19349	eIF4-gamma/eIF5/eIF2-epsilon (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	M	0.76727	2.345	0.53005	D	0.999965	P;D	0.63880	0.949;0.993	P;P	0.52109	0.493;0.69	T	0.47086	-0.9144	9	0.59425	D	0.04	-9.3023	8.4006	0.32583	0.0:0.5799:0.0:0.4201	.	818;891	P78344;B4DZF2	IF4G2_HUMAN;.	N	818;818;818;780;891;166;200	ENSP00000433664:K818N;ENSP00000433371:K818N;ENSP00000340281:K818N;ENSP00000379778:K780N	ENSP00000340281:K818N	K	-	3	2	EIF4G2	10777418	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.781000	0.26774	0.149000	0.19098	0.533000	0.62120	AAA	.		0.443	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		G	10820842	T	G	10820842	3	3	157	1	0	0	0	0	1	0	0	0	5050	1490	52	5	281	5	EIF4G2	11	10820842	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	6159199	10820842	124185674	107	14262											
SPON1	10418	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	14063070	14063070	+	RNA	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccactggttttccgtagatCatagacgaagaagaaactca	14	9	8	10	2	2	4	2	0	0	4	3	5	3	4	2	1	1	2	2	1	5	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:14063070C>T	ENST00000310358.7	+	0	886							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		TTCCGTAGATCATAGACGAAG	0.418																																					.													.	SPON1-1	0			.						.						174	172	173					11																	14063070		1901	4123	6024			10418	.			GTAGATCATAGAC	AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"spondin 1, (f-spondin) extracellular matrix protein"			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		11.37:g.14063070C>T		Somatic	48	0		WXS	Illumina HiSeq	Phase_I	72	22	.	0	0	0	0	0	A8K6W5|O94862|Q8NCD7|Q8WUR5	Silent	SNP	ENST00000310358.7	37																																																																																				.		0.418	SPON1-201	KNOWN	basic	processed_transcript	processed_transcript		NM_145584		T	14063070	C	T	14063070	1	4	157	0	1	0	0	0	0	0	0	0	15114	816	29	2		2	SPON1	11	14063070	RNA	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	3242228	14063070	120943446	108	14263											
CKAP5	9793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	46799004	46799004	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tttaccttgctgtctccaagGactgtgatgatagggatgcc	8	13	11	9	0	1	2	0	2	1	0	2	4	1	4	3	2	3	1	3	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:46799004G>C	ENST00000529230.1	-	23	2893	c.2847C>G	c.(2845-2847)gtC>gtG	p.V949V	CKAP5_ENST00000354558.3_Silent_p.V949V|CKAP5_ENST00000415402.1_Silent_p.V949V|CKAP5_ENST00000312055.5_Silent_p.V949V			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	949					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TGTCTCCAAGGACTGTGATGA	0.413																																					p.V949V	Ovarian(4;85 273 2202 4844 13323)	.											.	CKAP5-92	0			c.C2847G						.						137	125	129					11																	46799004		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon23			TCCAAGGACTGTG		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.2847C>G	11.37:g.46799004G>C		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	104	43	NM_001008938	0	0	7	11	4	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	37	CCDS31477.1																																																																																			.		0.413	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46799004	G	C	46799004	2	2	157	1	0	0	0	0	0	0	0	1	3451	1161	41	4		4	CKAP5	11	46799004	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	32735934	46799004	88207512	109	14264											
NUP160	23279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	47837537	47837537	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacttctttcttcagttcActccaggaaagatccaaatt	12	14	5	10	0	4	1	2	0	2	1	6	2	6	2	2	1	1	2	2	1	3	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:47837537A>G	ENST00000378460.2	-	12	1522	c.1476T>C	c.(1474-1476)agT>agC	p.S492S	NUP160_ENST00000531016.1_5'UTR|NUP160_ENST00000530326.1_Silent_p.S378S|NUP160_ENST00000528501.1_Silent_p.S56S|NUP160_ENST00000528071.1_Silent_p.S378S	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	492					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						TCTTCAGTTCACTCCAGGAAA	0.363																																					p.S492S		.											.	NUP160-209	0			c.T1476C						.						92	89	90					11																	47837537		2201	4298	6499	SO:0001819	synonymous_variant	23279	exon12			CAGTTCACTCCAG	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.1476T>C	11.37:g.47837537A>G		Somatic	264	0		WXS	Illumina HiSeq	Phase_I	361	175	NM_015231	0	0	6	14	8	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	37	CCDS31484.1																																																																																			.		0.363	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231		G	47837537	A	G	47837537	2	3	157	1	0	0	0	0	0	0	0	1	10783	156	6	3		3	NUP160	11	47837537	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	1038533	47837537	87168979	110	14265											
PTPRJ	5795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	48142728	48142728	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catggtgtaacatcacaggcTtacgtccagcgacttcatat	11	11	8	11	2	2	0	2	0	0	0	3	1	3	0	1	2	3	2	1	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:48142728T>G	ENST00000418331.2	+	4	878	c.526T>G	c.(526-528)Tta>Gta	p.L176V	PTPRJ_ENST00000440289.2_Missense_Mutation_p.L176V	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	176	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CATCACAGGCTTACGTCCAGC	0.423																																					p.L176V		.											.	PTPRJ-541	0			c.T526G						.						163	147	153					11																	48142728		2201	4298	6499	SO:0001583	missense	5795	exon4			ACAGGCTTACGTC	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"CD molecules", "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.526T>G	11.37:g.48142728T>G	ENSP00000400010:p.Leu176Val	Somatic	282	1		WXS	Illumina HiSeq	Phase_I	323	131	NM_001098503	0	0	7	11	4	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149018	0.57151	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000534219	D;D;D	0.84800	-1.9;-1.9;-1.9	5.41	1.8	0.24995	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89894	0.6847	M	0.75615	2.305	0.09310	N	1	D;D	0.71674	0.992;0.998	P;D	0.72338	0.908;0.977	T	0.78858	-0.2038	9	0.72032	D	0.01	.	6.633	0.22867	0.0:0.2796:0.0:0.7204	.	176;176	Q12913;Q6P4H4	PTPRJ_HUMAN;.	V	176;176;176;97	ENSP00000400010:L176V;ENSP00000409733:L176V;ENSP00000432686:L97V	ENSP00000278456:L176V	L	+	1	2	PTPRJ	48099304	0.000000	0.05858	0.014000	0.15608	0.075000	0.17131	-0.197000	0.09518	0.346000	0.23899	0.482000	0.46254	TTA	.		0.423	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			G	48142728	T	G	48142728	3	3	157	1	0	0	0	0	1	0	0	0	12836	1606	56	5	540	5	PTPRJ	11	48142728	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	305191	48142728	86863788	111	14266											
ANKK1	255239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	113265705	113265705	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccacccggatgcagtacAtcgagaggtcggctctgcgg	8	7	14	12	4	1	1	0	0	1	1	4	3	2	2	2	4	3	3	2	4	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:113265705A>C	ENST00000303941.3	+	3	629	c.535A>C	c.(535-537)Atc>Ctc	p.I179L		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	179	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GATGCAGTACATCGAGAGGTC	0.552																																					p.I179L		.											.	ANKK1-628	0			c.A535C						.						52	51	51					11																	113265705		2003	4170	6173	SO:0001583	missense	255239	exon3			CAGTACATCGAGA	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"Ankyrin repeat domain containing"	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.535A>C	11.37:g.113265705A>C	ENSP00000306678:p.Ile179Leu	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	192	87	NM_178510	0	0	0	0	0		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	A	7.078	0.569692	0.13560	.	.	ENSG00000170209	ENST00000303941	D	0.82167	-1.58	4.25	3.11	0.35812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	U	0.000079	T	0.76786	0.4036	L	0.27053	0.805	0.42141	D	0.991513	P	0.43231	0.801	P	0.48089	0.566	T	0.72301	-0.4334	10	0.34782	T	0.22	-24.2177	9.4598	0.38778	0.8415:0.0:0.0:0.1585	.	179	Q8NFD2	ANKK1_HUMAN	L	179	ENSP00000306678:I179L	ENSP00000306678:I179L	I	+	1	0	ANKK1	112770915	0.995000	0.38212	0.250000	0.24296	0.020000	0.10135	3.696000	0.54757	0.654000	0.30846	-1.026000	0.02426	ATC	.		0.552	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		C	113265705	A	C	113265705	3	2	157	1	0	0	0	0	1	0	0	0	631	217	8	5	545	5	ANKK1	11	113265705	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	65122977	113265705	21740811	112	14267											
B4GALNT3	283358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	660177	660177	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggatgggcttcctctgcagCgctaccagggactccggttt	5	11	13	12	2	1	0	0	0	1	0	3	2	3	2	3	4	3	4	3	4	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:660177C>T	ENST00000266383.5	+	11	1100	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	363					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TCCTCTGCAGCGCTACCAGGG	0.607																																					p.R363C		.											.	B4GALNT3-92	0			c.C1087T						.						172	151	158					12																	660177		2203	4300	6503	SO:0001583	missense	283358	exon11			CTGCAGCGCTACC	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"Beta 4-glycosyltransferases"	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1087C>T	12.37:g.660177C>T	ENSP00000266383:p.Arg363Cys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	163	37	NM_173593	0	0	0	0	0	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	C	31	5.064455	0.93898	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.72725	-0.68;-0.68	5.22	5.22	0.72569	.	0.107194	0.64402	D	0.000004	D	0.84428	0.5470	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.926	D	0.86089	0.1549	10	0.87932	D	0	-22.1916	18.9627	0.92682	0.0:1.0:0.0:0.0	.	265;363	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	C	363;265	ENSP00000266383:R363C;ENSP00000322953:R265C	ENSP00000266383:R363C	R	+	1	0	B4GALNT3	530438	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.267000	0.65530	2.715000	0.92844	0.655000	0.94253	CGC	.		0.607	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		T	660177	C	T	660177	3	4	157	1	0	0	0	0	1	0	0	0	1269	768	27	1	1129	1	B4GALNT3	12	660177	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		660177	133191718	113	14268											
LRTM2	654429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	1940301	1940301	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaagctgggctttcgccAacctctccagcctgcagcgg	6	8	11	16	2	1	0	0	0	1	0	3	0	1	0	5	2	6	3	5	2	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:1940301A>T	ENST00000543818.1	+	4	1110	c.268A>T	c.(268-270)Aac>Tac	p.N90Y	LRTM2_ENST00000543730.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000588077.1_Intron|LRTM2_ENST00000299194.1_Missense_Mutation_p.N90Y|LRTM2_ENST00000535041.1_Missense_Mutation_p.N90Y|CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000382722.5_Intron	NM_001039029.2|NM_001163925.1|NM_001163926.1	NP_001034118.1|NP_001157397.1|NP_001157398.1	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	90						integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	20	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)			GGCTTTCGCCAACCTCTCCAG	0.617																																					p.N90Y		.											.	LRTM2-135	0			c.A268T						.						57	65	62					12																	1940301		2203	4300	6503	SO:0001583	missense	654429	exon4			TTCGCCAACCTCT	AK095610	CCDS31726.1	12p13.33	2008-02-05				ENSG00000166159			32443	protein-coding gene	gene with protein product							Standard	NM_001039029		Approved		uc010sdx.1	Q8N967		ENST00000543818.1:c.268A>T	12.37:g.1940301A>T	ENSP00000446278:p.Asn90Tyr	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	59	30	NM_001039029	0	0	0	0	0	A7E2U6	Missense_Mutation	SNP	ENST00000543818.1	37	CCDS31726.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379726	0.61845	.	.	ENSG00000166159	ENST00000543818;ENST00000299194;ENST00000535041;ENST00000546167;ENST00000543694	T;T;T;D;D	0.85013	0.52;0.52;0.52;-1.93;-1.93	5.04	3.87	0.44632	.	0.000000	0.85682	D	0.000000	D	0.88224	0.6379	L	0.54323	1.7	0.58432	D	0.999996	D	0.59357	0.985	P	0.61328	0.887	D	0.87459	0.2406	10	0.62326	D	0.03	.	10.9074	0.47088	0.925:0.0:0.075:0.0	.	90	Q8N967	LRTM2_HUMAN	Y	90	ENSP00000446278:N90Y;ENSP00000299194:N90Y;ENSP00000444737:N90Y;ENSP00000438678:N90Y;ENSP00000444104:N90Y	ENSP00000299194:N90Y	N	+	1	0	LRTM2	1810562	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.182000	0.58310	0.748000	0.32831	0.459000	0.35465	AAC	.		0.617	LRTM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398055.1			T	1940301	A	T	1940301	3	4	157	1	0	0	0	0	1	0	0	0	9070	130	5	5	274	5	LRTM2	12	1940301	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	1280124	1940301	131911594	114	14269											
MANSC1	54682	broad.mit.edu	37	chr12	12483849	12483849	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtaagagagaatcttcctgGggtaactcttggcttggcaa	10	12	12	7	0	2	2	0	0	2	2	3	3	3	2	1	4	1	4	1	4	4	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:12483849G>T	ENST00000535902.1	-	4	971	c.408C>A	c.(406-408)ccC>ccA	p.P136P	MANSC1_ENST00000545735.1_Silent_p.P55P|MANSC1_ENST00000396349.3_Silent_p.P102P			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	136						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		AATCTTCCTGGGGTAACTCTT	0.423																																					p.P136P													.	MANSC1-90	0			c.C408A						.						101	97	99					12																	12483849		2203	4300	6503	SO:0001819	synonymous_variant	54682	exon4			TTCCTGGGGTAAC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.408C>A	12.37:g.12483849G>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_I	143	4	NM_018050	0	0	28	28	0	Q8NEC1|Q9NW60	Silent	SNP	ENST00000535902.1	37	CCDS8648.1																																																																																			.		0.423	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050		T	12483849	G	T	12483849	2	4	157	1	0	0	0	0	0	0	0	1	9249	1219	43	4		4	MANSC1	12	12483849	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	10543548	12483849	121368046	115	14270											
WBP11	51729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	14943406	14943406	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctggaggtggaccaggAggaaggcctgtaggtggccc	8	7	17	9	0	0	0	0	0	0	0	0	4	0	4	4	8	1	1	4	8	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:14943406A>G	ENST00000261167.2	-	10	1526	c.1293T>C	c.(1291-1293)ccT>ccC	p.P431P		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	431	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						GTGGACCAGGAGGAAGGCCTG	0.473																																					p.P431P		.											.	WBP11-92	0			c.T1293C						.						99	103	102					12																	14943406		2203	4300	6503	SO:0001819	synonymous_variant	51729	exon10			ACCAGGAGGAAGG	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1293T>C	12.37:g.14943406A>G		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	134	24	NM_016312	0	0	41	54	13	Q96AY8	Silent	SNP	ENST00000261167.2	37	CCDS8666.1																																																																																			.		0.473	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		G	14943406	A	G	14943406	2	3	157	1	0	0	0	0	0	0	0	1	17291	291	11	3		3	WBP11	12	14943406	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	2459557	14943406	118908489	116	14271											
KCNH3	23416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	49944077	49944077	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgctctggctccatggAggtgctcaagggtggcaccg	5	10	15	11	1	3	0	1	0	2	0	4	1	4	1	2	5	2	4	2	5	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:49944077A>C	ENST00000257981.6	+	10	2143	c.1883A>C	c.(1882-1884)gAg>gCg	p.E628A		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	628					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GGCTCCATGGAGGTGCTCAAG	0.647																																					p.E628A		.											.	KCNH3-90	0			c.A1883C						.						73	66	68					12																	49944077		2203	4300	6503	SO:0001583	missense	23416	exon10			CCATGGAGGTGCT	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.1883A>C	12.37:g.49944077A>C	ENSP00000257981:p.Glu628Ala	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	93	48	NM_012284	0	0	1	1	0	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	A	31	5.069017	0.93950	.	.	ENSG00000135519	ENST00000257981	D	0.93307	-3.2	5.48	5.48	0.80851	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.48767	D	0.000161	D	0.96620	0.8897	M	0.84219	2.685	0.58432	D	0.999997	D	0.76494	0.999	D	0.87578	0.998	D	0.97133	0.9819	10	0.87932	D	0	.	13.8224	0.63331	1.0:0.0:0.0:0.0	.	628	Q9ULD8	KCNH3_HUMAN	A	628	ENSP00000257981:E628A	ENSP00000257981:E628A	E	+	2	0	KCNH3	48230344	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.224000	0.72417	0.533000	0.62120	GAG	.		0.647	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		C	49944077	A	C	49944077	3	2	157	1	0	0	0	0	1	0	0	0	8054	304	11	5	1921	5	KCNH3	12	49944077	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	35000671	49944077	83907818	117	14272											
CSAD	51380	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	53554015	53554015	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcggccacactgcaccaccTtgtctcccgtgtccagagcc	6	7	10	18	2	1	1	0	0	1	1	3	1	2	1	6	2	2	1	6	2	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:53554015T>C	ENST00000444623.1	-	14	1322	c.1055A>G	c.(1054-1056)aAg>aGg	p.K352R	CSAD_ENST00000453446.2_Missense_Mutation_p.K352R|CSAD_ENST00000379846.1_Missense_Mutation_p.K205R|CSAD_ENST00000267085.4_Missense_Mutation_p.K379R|CSAD_ENST00000379843.3_Missense_Mutation_p.K205R|RP11-1136G11.8_ENST00000550908.1_lincRNA	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	352					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	CTGCACCACCTTGTCTCCCGT	0.612																																					p.K379R	Ovarian(109;252 1546 16882 28524 44645)	.											.	CSAD-91	0			c.A1136G						.						117	104	108					12																	53554015		2203	4300	6503	SO:0001583	missense	51380	exon14			ACCACCTTGTCTC	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1055A>G	12.37:g.53554015T>C	ENSP00000415485:p.Lys352Arg	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	120	60	NM_015989	0	0	4	6	2	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	37	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	T	33	5.207752	0.95033	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	4.67	4.67	0.58626	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.047421	0.85682	D	0.000000	T	0.59376	0.2189	L	0.61387	1.9	0.80722	D	1	D;D;P	0.69078	0.997;0.994;0.871	D;D;B	0.68765	0.96;0.96;0.247	T	0.62062	-0.6933	10	0.56958	D	0.05	-26.8125	13.5402	0.61671	0.0:0.0:0.0:1.0	.	379;352;205	Q9Y600-3;Q9Y600;Q9Y600-2	.;CSAD_HUMAN;.	R	441;205;379;205;352;313;352	ENSP00000369172:K205R;ENSP00000267085:K379R;ENSP00000369175:K205R;ENSP00000415485:K352R;ENSP00000410648:K352R	ENSP00000267085:K379R	K	-	2	0	CSAD	51840282	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.430000	0.80321	2.100000	0.63781	0.533000	0.62120	AAG	.		0.612	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		C	53554015	T	C	53554015	3	2	157	1	0	0	0	0	1	0	0	0	3931	1609	56	3	442	3	CSAD	12	53554015	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	3609938	53554015	80297880	118	14273											
GPR84	53831	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	54756649	54756649	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aagaaggggatgtagctcagGgcaaagcagaggaacacagc	16	3	15	7	0	1	2	1	0	0	2	1	4	1	4	0	4	4	4	0	4	5	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:54756649G>A	ENST00000551809.1	-	1	1622	c.987C>T	c.(985-987)gcC>gcT	p.A329A	GPR84_ENST00000267015.3_Silent_p.A329A|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	329						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						TGTAGCTCAGGGCAAAGCAGA	0.537																																					p.A329A		.											.	GPR84-523	0			c.C987T						.						139	138	138					12																	54756649		2203	4300	6503	SO:0001819	synonymous_variant	53831	exon2			GCTCAGGGCAAAG	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.987C>T	12.37:g.54756649G>A		Somatic	153	0		WXS	Illumina HiSeq	Phase_I	202	15	NM_020370	0	0	2	2	0	B6V9G7	Silent	SNP	ENST00000551809.1	37	CCDS8878.1																																																																																			.		0.537	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			A	54756649	G	A	54756649	2	1	157	1	0	0	0	0	0	0	0	1	6734	1219	43	2		2	GPR84	12	54756649	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1202634	54756649	79095246	119	14274											
SMARCC2	6601	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56578005	56578005	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacacaacatgggaggcattGttcttatcctcagtgactgt	10	13	9	9	0	2	1	1	1	1	0	3	2	3	2	1	2	2	2	1	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:56578005G>T	ENST00000267064.4	-	6	602	c.516C>A	c.(514-516)aaC>aaA	p.N172K	SMARCC2_ENST00000550164.1_Missense_Mutation_p.N172K|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Missense_Mutation_p.N172K|SMARCC2_ENST00000394023.3_Missense_Mutation_p.N172K|SMARCC2_ENST00000550859.1_5'UTR	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	172					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			GGGAGGCATTGTTCTTATCCT	0.498																																					p.N172K		.											.	SMARCC2-229	0			c.C516A						.						116	94	101					12																	56578005		2203	4300	6503	SO:0001583	missense	6601	exon6			GGCATTGTTCTTA	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.516C>A	12.37:g.56578005G>T	ENSP00000267064:p.Asn172Lys	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	135	55	NM_139067	0	0	14	30	16	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028067	0.35797	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.38	4.49	0.54785	BRCT (1);	0.717108	0.14170	N	0.336810	T	0.28067	0.0692	N	0.04508	-0.205	0.22610	N	0.998937	B;B;B;B;B	0.18310	0.016;0.027;0.016;0.016;0.027	B;B;B;B;B	0.17098	0.007;0.017;0.007;0.007;0.017	T	0.14504	-1.0470	10	0.25751	T	0.34	-3.7705	7.6019	0.28081	0.2492:0.0:0.7508:0.0	.	61;172;177;172;172	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	K	172	ENSP00000377591:N172K;ENSP00000449396:N172K;ENSP00000302919:N172K;ENSP00000267064:N172K	ENSP00000267064:N172K	N	-	3	2	SMARCC2	54864272	0.956000	0.32656	0.998000	0.56505	0.994000	0.84299	1.519000	0.35888	1.412000	0.46977	0.561000	0.74099	AAC	.		0.498	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			T	56578005	G	T	56578005	3	4	157	1	0	0	0	0	1	0	0	0	14808	1368	48	4	3317	4	SMARCC2	12	56578005	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1821356	56578005	77273890	120	14275											
R3HDM2	22864	ucsc.edu;bcgsc.ca	37	chr12	57674168	57674168	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatgtgattattcaagggTggctgttgctgaggcgtggg	7	13	16	5	1	2	2	2	2	0	0	2	2	2	2	0	4	1	3	0	4	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:57674168T>C	ENST00000347140.3	-	14	1665	c.1275A>G	c.(1273-1275)ccA>ccG	p.P425P	R3HDM2_ENST00000413953.2_Silent_p.P152P|R3HDM2_ENST00000403821.2_Silent_p.P425P|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.P439P|R3HDM2_ENST00000441731.2_Silent_p.P86P|R3HDM2_ENST00000358907.2_Silent_p.P425P			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	425	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TATTCAAGGGTGGCTGTTGCT	0.542																																					p.P425P													.	R3HDM2-92	0			c.A1275G						.						197	177	184					12																	57674168		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon12			CAAGGGTGGCTGT	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1275A>G	12.37:g.57674168T>C		Somatic	93	2		WXS	Illumina HiSeq		144	24	NM_014925	0	0	25	30	5	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472998	0.43942	.	.	ENSG00000179912	ENST00000466401	.	.	.	4.8	0.768	0.18487	.	.	.	.	.	T	0.42359	0.1199	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21999	-1.0229	4	.	.	.	-6.0267	1.5745	0.02621	0.1636:0.1072:0.1705:0.5587	.	.	.	.	R	23	.	.	H	-	2	0	R3HDM2	55960435	0.998000	0.40836	0.998000	0.56505	0.998000	0.95712	0.140000	0.16056	-0.023000	0.13963	0.459000	0.35465	CAC	.		0.542	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		C	57674168	T	C	57674168	2	2	157	1	0	0	0	0	0	0	0	1	12920	1683	59	3		3	R3HDM2	12	57674168	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	1096163	57674168	76177727	121	14276											
METTL1	25895	broad.mit.edu;bcgsc.ca	37	chr12	58165807	58165807	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagtgagcacgttgccggtaGtagcgcttctggggcggtgg	5	9	19	8	4	1	1	0	1	1	0	1	2	1	1	1	5	3	5	1	5	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:58165807G>A	ENST00000300209.8	+	0	0				METTL1_ENST00000324871.7_Silent_p.Y20Y|METTL21B_ENST00000551420.1_5'Flank|AC025165.1_ENST00000582738.1_RNA|METTL1_ENST00000257848.7_Silent_p.Y20Y|RP11-571M6.15_ENST00000471530.1_5'Flank|METTL1_ENST00000548681.1_5'UTR|METTL21B_ENST00000548256.1_Intron|METTL21B_ENST00000333012.5_5'Flank	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						GTTGCCGGTAGTAGCGCTTCT	0.642																																					p.Y20Y													.	METTL1-492	0			c.C60T						.						71	69	70					12																	58165807		2203	4300	6503	SO:0001631	upstream_gene_variant	4234	exon1			CCGGTAGTAGCGC	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		12.37:g.58165807G>A	Exception_encountered	Somatic	71	2		WXS	Illumina HiSeq	Phase_I	128	50	NM_023033	0	0	16	22	6	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																			.		0.642	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		A	58165807	G	A	58165807	1	1	157	0	1	0	0	0	0	0	0	0	9518	1024	36	2		2	METTL1	12	58165807	5'Flank	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	491639	58165807	75686088	122	14277											
APAF1	317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	99093184	99093184	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttattactttaattcaaAgctttgggatgcgacatcag	11	17	7	6	1	2	0	2	0	0	0	2	2	2	1	0	1	3	1	0	1	4	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:99093184A>C	ENST00000551964.1	+	17	3040		c.e17-1		APAF1_ENST00000333991.1_Intron|APAF1_ENST00000339433.3_Splice_Site|APAF1_ENST00000357310.1_Splice_Site|APAF1_ENST00000547045.1_Splice_Site|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000550527.1_Splice_Site|APAF1_ENST00000549007.1_Splice_Site|APAF1_ENST00000359972.2_Splice_Site	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	TTTAATTCAAAGCTTTGGGAT	0.323																																					.		.											.	APAF1-229	0			c.2272-2A>C						.						52	51	51					12																	99093184		2203	4300	6503	SO:0001630	splice_region_variant	317	exon17			ATTCAAAGCTTTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.2305-1A>C	12.37:g.99093184A>C		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	58	22	NM_001160	0	0	0	0	0	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Splice_Site	SNP	ENST00000551964.1	37	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598135	0.46318	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5583	0.61773	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	APAF1	97617315	1.000000	0.71417	0.949000	0.38748	0.676000	0.39594	7.031000	0.76491	2.186000	0.69663	0.533000	0.62120	.	.		0.323	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	Intron	C	99093184	A	C	99093184	5	2	157	1	0	0	0	0	0	0	1	0	755	86	3	5	2365	5	APAF1	12	99093184	Splice_Site	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	40927377	99093184	34758711	123	14278											
DAO	1610	broad.mit.edu	37	chr12	109290784	109290784	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgccctgaatcaacaggtGgacgccccttggatgaagca	10	7	11	13	1	1	2	1	2	0	0	1	4	1	4	4	3	3	1	4	3	3	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:109290784G>T	ENST00000228476.3	+	8	819	c.615G>T	c.(613-615)gtG>gtT	p.V205V	DAO_ENST00000551281.1_Silent_p.V139V	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	205					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	ATCAACAGGTGGACGCCCCTT	0.542																																					p.V205V													.	DAO-92	0			c.G615T						.						134	104	115					12																	109290784		2203	4300	6503	SO:0001819	synonymous_variant	1610	exon8			ACAGGTGGACGCC	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.615G>T	12.37:g.109290784G>T		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	105	4	NM_001917	0	0	0	0	0	B2R7I5|Q16758|Q8N6R2	Silent	SNP	ENST00000228476.3	37	CCDS9122.1																																																																																			.		0.542	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			T	109290784	G	T	109290784	2	4	157	1	0	0	0	0	0	0	0	1	4237	1335	47	4		4	DAO	12	109290784	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	10197600	109290784	24561111	124	14279											
LHX5	64211	hgsc.bcm.edu	37	chr12	113901232	113901232	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagcggcggttccagcgcTcccagcggcgtcgagccggg	4	4	18	15	8	0	0	0	0	0	0	3	2	2	0	3	4	4	2	3	4	0	1	rs202131487	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:113901232T>C	ENST00000261731.3	-	5	1545	c.972A>G	c.(970-972)ggA>ggG	p.G324G		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	324					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						GTTCCAGCGCTCCCAGCGGCG	0.736													G|||	18	0.00359425	8e-04	0.0029	5008	,	,		9203	0.001		0.0099	False		,,,				2504	0.0041				p.G324G		.											.	LHX5-90	0			c.A972G						.	G		3,4059		0,3,2028	7	10	9		972	-1	1	12		9	56,7872		0,56,3908	no	coding-synonymous	LHX5	NM_022363.2		0,59,5936	CC,CT,TT		0.7064,0.0739,0.4921		324/403	113901232	59,11931	2031	3964	5995	SO:0001819	synonymous_variant	64211	exon5			CAGCGCTCCCAGC	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"Homeoboxes / LIM class"	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.972A>G	12.37:g.113901232T>C		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	34	14	NM_022363	0	0	0	0	0	Q32MA4	Silent	SNP	ENST00000261731.3	37	CCDS9171.1																																																																																			.		0.736	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		C	113901232	T	C	113901232	2	2	157	1	0	0	0	0	0	0	0	1	8796	1538	54	3		3	LHX5	12	113901232	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	4610448	113901232	19950663	125	14280											
MLEC	9761	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	121132908	121132908	+	Frame_Shift_Del	DEL	A	A	-																															cttttcctaggggtactatgAcaatcccaaggtctgtgcac																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:121132908delA	ENST00000228506.3	+	4	1030	c.602delA	c.(601-603)gacfs	p.D201fs	RP11-173P15.3_ENST00000541383.1_RNA|MLEC_ENST00000412616.2_Intron	NM_014730.2	NP_055545.1	Q14165	MLEC_HUMAN	malectin	201					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|enzyme binding (GO:0019899)	p.D201G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	16						GGGTACTATGACAATCCCAAG	0.498																																					p.D201fs		.											.	MLEC-91	1	Substitution - Missense(1)	lung(1)	c.602delA						.						381	352	362					12																	121132908		2203	4300	6503	SO:0001589	frameshift_variant	9761	exon4			.	BC000371	CCDS9206.1	12q24.31	2013-03-06	2008-11-05	2008-11-05	ENSG00000110917	ENSG00000110917			28973	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	613802	"KIAA0152"	KIAA0152		18524852	Standard	NM_014730		Approved		uc001tyy.1	Q14165	OTTHUMG00000169187	ENST00000228506.3:c.602delA	12.37:g.121132908delA	ENSP00000228506:p.Asp201fs	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	162	72	NM_014730	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000228506.3	37	CCDS9206.1																																																																																			.		0.498	MLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402781.2	NM_014730		-	121132908	A	-	121132908	7	5	157	1	0	1	0	1	0	0	0	0	9638	275	10	0	616	0	MLEC	12	121132908	Frame_Shift_Del	DEL	A	TCGA-P4-A5EB-01A-11D-A28G-10	7231676	121132908	12718987	126	14281											
CHFR	55743	broad.mit.edu	37	chr12	133430112	133430112	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtggggaggctgcgccGcctgccttctgtactcagga	5	8	16	12	2	2	0	1	0	1	0	2	2	2	2	3	5	3	3	3	5	1	2	rs374229656		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:133430112G>T	ENST00000432561.2	-	11	1386	c.1313C>A	c.(1312-1314)gCg>gAg	p.A438E	CHFR_ENST00000315585.7_Missense_Mutation_p.A397E|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000537522.1_Missense_Mutation_p.A60E|CHFR_ENST00000443047.2_Missense_Mutation_p.A346E|CHFR_ENST00000450056.2_Missense_Mutation_p.A426E|CHFR_ENST00000266880.7_Missense_Mutation_p.A438E			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	438					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		AGGCTGCGCCGCCTGCCTTCT	0.682																																					p.A438E													.	CHFR-227	0			c.C1313A						.						16	16	16					12																	133430112		2126	4164	6290	SO:0001583	missense	55743	exon11			TGCGCCGCCTGCC	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"RING-type (C3HC4) zinc fingers"	20455	protein-coding gene	gene with protein product		605209	"checkpoint with forkhead and ring finger domains"			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1313C>A	12.37:g.133430112G>T	ENSP00000392395:p.Ala438Glu	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	161	4	NM_001161344	0	0	15	15	0	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Missense_Mutation	SNP	ENST00000432561.2	37	CCDS53849.1	.	.	.	.	.	.	.	.	.	.	G	3.829	-0.036126	0.07497	.	.	ENSG00000072609	ENST00000315585;ENST00000443047;ENST00000450056;ENST00000266880;ENST00000537522;ENST00000541228;ENST00000432561	T;T;T;T;T;T	0.31247	2.47;2.21;2.49;2.19;1.5;2.5	4.39	-5.95	0.02241	.	1.192850	0.05624	N	0.580503	T	0.19967	0.0480	L	0.36672	1.1	0.09310	N	1	B;B;B;B;P	0.35124	0.403;0.009;0.005;0.009;0.485	B;B;B;B;B	0.37692	0.256;0.019;0.009;0.007;0.244	T	0.16571	-1.0398	10	0.27082	T	0.32	-12.7448	3.1221	0.06395	0.367:0.1758:0.3682:0.089	.	346;438;438;426;397	Q96EP1-5;Q96EP1-4;Q96EP1;Q96EP1-2;Q96EP1-3	.;.;CHFR_HUMAN;.;.	E	397;346;426;438;60;238;438	ENSP00000320557:A397E;ENSP00000416431:A346E;ENSP00000398735:A426E;ENSP00000266880:A438E;ENSP00000442327:A60E;ENSP00000392395:A438E	ENSP00000266880:A438E	A	-	2	0	CHFR	131940185	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.254000	0.18314	-1.584000	0.01636	-2.048000	0.00412	GCG	.		0.682	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2			T	133430112	G	T	133430112	3	4	157	1	0	0	0	0	1	0	0	0	3343	1087	38	4	713	4	CHFR	12	133430112	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	12297204	133430112	421783	127	14282											
DCLK1	9201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	36383187	36383187	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggaaaccacacagcaggatAtaagtgattacacctgctgc	14	7	10	10	0	0	1	0	1	0	0	0	3	0	3	2	2	5	2	2	2	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr13:36383187A>G	ENST00000360631.3	-	13	1945	c.1734T>C	c.(1732-1734)taT>taC	p.Y578Y	DCLK1_ENST00000255448.4_Silent_p.Y578Y|DCLK1_ENST00000379893.1_Silent_p.Y271Y			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	578	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		ACAGCAGGATATAAGTGATTA	0.473																																					p.Y578Y		.											.	DCLK1-826	0			c.T1734C						.						101	88	92					13																	36383187		2203	4300	6503	SO:0001819	synonymous_variant	9201	exon13			CAGGATATAAGTG	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"doublecortin and CaM kinase-like 1"	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1734T>C	13.37:g.36383187A>G		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	150	51	NM_004734	0	0	2	5	3	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				.		0.473	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		G	36383187	A	G	36383187	2	3	157	1	0	0	0	0	0	0	0	1	4297	456	16	3		3	DCLK1	13	36383187	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		36383187	78786691	128	14283											
UGGT2	55757	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	96684163	96684163	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtttgcttataaattgctAattcttgcacagtttccaaa	11	17	5	8	0	1	0	0	0	1	0	2	0	2	0	1	0	3	5	1	0	5	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr13:96684163A>G	ENST00000376747.3	-	2	291	c.221T>C	c.(220-222)tTa>tCa	p.L74S	UGGT2_ENST00000376712.4_Missense_Mutation_p.L74S|UGGT2_ENST00000376714.3_Missense_Mutation_p.L74S|UGGT2_ENST00000397618.3_Missense_Mutation_p.L74S	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	74					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						ATAAATTGCTAATTCTTGCAC	0.259																																					p.L74S		.											.	UGGT2-92	0			c.T221C						.						59	62	61					13																	96684163		2198	4277	6475	SO:0001583	missense	55757	exon2			ATTGCTAATTCTT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"UDP-glucose:glycoprotein glucosyltransferase 2"	605898	"UDP-glucose ceramide glucosyltransferase-like 2"	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.221T>C	13.37:g.96684163A>G	ENSP00000365938:p.Leu74Ser	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	102	38	NM_020121	0	0	4	9	5	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.578856	0.65878	.	.	ENSG00000102595	ENST00000376747;ENST00000376722;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.32272	3.07;1.46	5.93	5.93	0.95920	.	0.075675	0.56097	D	0.000039	T	0.61565	0.2357	M	0.84683	2.71	0.53688	D	0.999975	D;D;P	0.89917	1.0;1.0;0.937	D;D;P	0.91635	0.999;0.999;0.512	T	0.67772	-0.5584	10	0.87932	D	0	-7.6383	16.3943	0.83563	1.0:0.0:0.0:0.0	.	74;74;74	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	S	74	ENSP00000365938:L74S;ENSP00000380743:L74S	ENSP00000365902:L74S	L	-	2	0	UGGT2	95482164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.701000	0.84566	2.281000	0.76405	0.533000	0.62120	TTA	.		0.259	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		G	96684163	A	G	96684163	3	3	157	1	0	0	0	0	1	0	0	0	16975	372	13	3	4481	3	UGGT2	13	96684163	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	60300976	96684163	18485715	129	14284											
RPGRIP1	57096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21769308	21769308	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccactgcgtcggccctgcCagcccccgccgcgcccagcc	3	5	10	23	5	0	0	0	0	0	0	2	0	1	0	8	1	4	0	8	1	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:21769308C>T	ENST00000400017.2	+	3	402	c.402C>T	c.(400-402)gcC>gcT	p.A134A	RPGRIP1_ENST00000556336.1_Silent_p.A134A|RPGRIP1_ENST00000557771.1_Silent_p.A134A|RPGRIP1_ENST00000206660.6_Silent_p.A134A	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	134					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TCGGCCCTGCCAGCCCCCGCC	0.682																																					p.A134A		.											.	RPGRIP1-140	0			c.C402T						.						10	14	13					14																	21769308		1990	4127	6117	SO:0001819	synonymous_variant	57096	exon3			CCCTGCCAGCCCC	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.402C>T	14.37:g.21769308C>T		Somatic	114	0		WXS	Illumina HiSeq	Phase_I	229	57	NM_020366	0	0	0	0	0	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																			.		0.682	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21769308	C	T	21769308	2	4	157	1	0	0	0	0	0	0	0	1	13581	581	21	2		2	RPGRIP1	14	21769308	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		21769308	85580232	130	14285											
OXA1L	9056	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	23240479	23240479	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcttctctttacacaggcTggaaaaatgctgaaatgacg	12	12	9	8	1	1	2	0	2	1	0	2	3	1	3	0	2	3	3	0	2	4	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:23240479T>A	ENST00000397532.3	-	0	2447				OXA1L_ENST00000604262.1_Missense_Mutation_p.W369R|OXA1L_ENST00000358043.5_Missense_Mutation_p.W353R|OXA1L_ENST00000412791.1_Intron|OXA1L_ENST00000285848.5_Missense_Mutation_p.W429R|SLC7A7_ENST00000554061.1_5'Flank			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7						amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		TTACACAGGCTGGAAAAATGC	0.473																																					p.W429R													.	OXA1L-204	0			c.T1285A						.						61	64	63					14																	23240479		2203	4300	6503	SO:0001628	intergenic_variant	5018	exon9			ACAGGCTGGAAAA	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"Solute carriers"	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692		14.37:g.23240479T>A		Somatic	91	1		WXS	Illumina HiSeq	Phase_I	82	45	NM_005015	0	0	0	0	0	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Missense_Mutation	SNP	ENST00000397532.3	37	CCDS9574.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.565970	0.86439	.	.	ENSG00000155463	ENST00000285848;ENST00000358043	T;T	0.34667	1.35;1.4	5.71	5.71	0.89125	.	0.112616	0.64402	D	0.000004	T	0.58750	0.2144	M	0.83012	2.62	0.80722	D	1	P;D	0.65815	0.942;0.995	P;P	0.59012	0.818;0.85	T	0.65619	-0.6124	10	0.87932	D	0	-9.9776	13.4947	0.61419	0.0:0.0:0.0:1.0	.	369;429	Q15070;Q2M1J6	OXA1L_HUMAN;.	R	429;353	ENSP00000285848:W429R;ENSP00000350740:W353R	ENSP00000285848:W429R	W	+	1	0	OXA1L	22310319	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.969000	0.70422	2.162000	0.67917	0.496000	0.49642	TGG	.		0.473	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3			A	23240479	T	A	23240479	1	1	157	0	1	0	0	0	0	0	0	0	11354	1580	55	5		5	OXA1L	14	23240479	IGR	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	1471171	23240479	84109061	131	14286											
EFS	10278	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	23828918	23828918	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gggagcctctggccccagcaGaggcacatcgtagatcccct	8	6	12	15	1	1	2	0	0	1	2	3	3	2	3	5	3	2	3	5	3	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:23828918G>A	ENST00000216733.3	-	4	1376	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	EFS_ENST00000429593.2_Intron|RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000351354.3_Silent_p.L164L	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	257	Pro-rich.				cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GGCCCCAGCAGAGGCACATCG	0.642																																					p.L257L		.											.	EFS-153	0			c.C769T						.						37	45	42					14																	23828918		2203	4300	6503	SO:0001819	synonymous_variant	10278	exon4			CCAGCAGAGGCAC	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"Cas scaffolding proteins"	16898	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 3"	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.769C>T	14.37:g.23828918G>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_005864	0	0	0	0	0	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	37	CCDS9595.1																																																																																			.		0.642	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			A	23828918	G	A	23828918	2	1	157	1	0	0	0	0	0	0	0	1	4970	933	33	2		2	EFS	14	23828918	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	588439	23828918	83520622	132	14287											
PPIL5	122769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	50081041	50081041	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggataccgcaaaaatttgtGtttgtggaagattctgtctg	10	15	11	5	1	2	1	0	0	2	1	2	3	2	3	1	2	1	2	1	2	4	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:50081041G>T	ENST00000298288.6	+	4	1396	c.1072G>T	c.(1072-1074)Gtt>Ttt	p.V358F	LRR1_ENST00000318317.4_Missense_Mutation_p.C117F	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	358					protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AAAAATTTGTGTTTGTGGAAG	0.368																																					p.V358F		.											.	LRR1-227	0			c.G1072T						.						117	111	113					14																	50081041		2203	4300	6503	SO:0001583	missense	122769	exon4			ATTTGTGTTTGTG	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"LRR-repeat protein 1"	609193	"peptidylprolyl isomerase (cyclophilin)-like 5"	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.1072G>T	14.37:g.50081041G>T	ENSP00000298288:p.Val358Phe	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	53	11	NM_152329	0	0	6	8	2	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	37	CCDS9686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.98|12.98	2.100514|2.100514	0.37048|0.37048	.|.	.|.	ENSG00000165501|ENSG00000165501	ENST00000318317|ENST00000298288	.|T	.|0.42513	.|0.97	5.55|5.55	3.74|3.74	0.42951|0.42951	.|.	.|0.342603	.|0.30820	.|N	.|0.008808	T|T	0.29850|0.29850	0.0746|0.0746	L|L	0.48642|0.48642	1.525|1.525	0.23050|0.23050	N|N	0.998374|0.998374	P|P	0.48503|0.37864	0.911|0.61	B|B	0.42282|0.30646	0.382|0.118	T|T	0.12785|0.12785	-1.0534|-1.0534	7|10	.|0.33940	.|T	.|0.23	-1.8537|-1.8537	8.4558|8.4558	0.32899|0.32899	0.149:0.1617:0.6893:0.0|0.149:0.1617:0.6893:0.0	.|.	117|358	Q96L50-2|Q96L50	.|LLR1_HUMAN	F|F	117|358	.|ENSP00000298288:V358F	.|ENSP00000298288:V358F	C|V	+|+	2|1	0|0	LRR1|LRR1	49150791|49150791	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.566000|0.566000	0.35808|0.35808	4.799000|4.799000	0.62517|0.62517	0.839000|0.839000	0.34971|0.34971	-0.142000|-0.142000	0.14014|0.14014	TGT|GTT	.		0.368	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467		T	50081041	G	T	50081041	3	4	157	1	0	0	0	0	1	0	0	0	12359	1377	48	4	1086	4	PPIL5	14	50081041	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	26252123	50081041	57268499	133	14288											
PPP2R5E	5529	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	63881922	63881922	+	Frame_Shift_Del	DEL	A	A	-																															gttggaattcttggctttccAaaaatcgtatgaaaaattca																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:63881922delA	ENST00000337537.3	-	5	1087	c.485delT	c.(484-486)ttgfs	p.L162fs	PPP2R5E_ENST00000555899.1_Frame_Shift_Del_p.L162fs|PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Frame_Shift_Del_p.L86fs	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	162					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TTGGCTTTCCAAAAATCGTAT	0.313																																					p.L162fs		.											.	PPP2R5E-658	0			c.485delT						.						87	91	90					14																	63881922		2202	4298	6500	SO:0001589	frameshift_variant	5529	exon5			.	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.485delT	14.37:g.63881922delA	ENSP00000337641:p.Leu162fs	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	95	51	NM_006246	0	0	0	0	0	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Frame_Shift_Del	DEL	ENST00000337537.3	37	CCDS9758.1																																																																																			.		0.313	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246		-	63881922	A	-	63881922	7	5	157	1	0	1	0	1	0	0	0	0	12425	131	5	0	958	0	PPP2R5E	14	63881922	Frame_Shift_Del	DEL	A	TCGA-P4-A5EB-01A-11D-A28G-10	13800881	63881922	43467618	134	14289											
FAM164C	79696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	75537677	75537677	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctttacaaagaaacgagttgGagtggaccgggcgttcccat	11	9	12	9	3	0	1	0	0	0	1	1	4	1	3	2	3	2	2	2	3	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:75537677G>T	ENST00000524913.1	+	2	890	c.401G>T	c.(400-402)gGa>gTa	p.G134V	ZC2HC1C_ENST00000526748.1_Intron|ZC2HC1C_ENST00000439583.2_Missense_Mutation_p.G134V|ZC2HC1C_ENST00000238686.8_Missense_Mutation_p.G134V|ACYP1_ENST00000555463.1_5'Flank	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	134							metal ion binding (GO:0046872)										AAACGAGTTGGAGTGGACCGG	0.522																																					p.G134V		.											.	.	0			c.G401T						.						98	96	97					14																	75537677		1869	4100	5969	SO:0001583	missense	79696	exon2			GAGTTGGAGTGGA	AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"Zinc fingers, C2HC-type containing"	20354	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 140", "family with sequence similarity 164, member C"	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.401G>T	14.37:g.75537677G>T	ENSP00000435550:p.Gly134Val	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	95	31	NM_024643	0	0	1	4	3	E9PJQ0|Q9BTA8|Q9H5S9	Missense_Mutation	SNP	ENST00000524913.1	37	CCDS41972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.709290|2.709290	0.48517|0.48517	.|.	.|.	ENSG00000119703|ENSG00000119703	ENST00000532198|ENST00000524913;ENST00000238686;ENST00000554763;ENST00000439583;ENST00000526130	.|T	.|0.76578	.|-1.03	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.080328	.|0.49916	.|D	.|0.000121	.|D	.|0.87111	.|0.6096	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.997	.|D	.|0.87264	.|0.2281	.|9	.|.	.|.	.|.	-17.5211|-17.5211	17.4741|17.4741	0.87655|0.87655	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|134;134	.|Q53FD0;E9PJQ0	.|F164C_HUMAN;.	X|V	1|134	.|ENSP00000435550:G134V	.|.	E|G	+|+	1|2	0|0	FAM164C|FAM164C	74607430|74607430	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.325000|0.325000	0.28411|0.28411	6.888000|6.888000	0.75622|0.75622	2.356000|2.356000	0.79943|0.79943	0.557000|0.557000	0.71058|0.71058	GAG|GGA	.		0.522	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430		T	75537677	G	T	75537677	3	4	157	1	0	0	0	0	1	0	0	0	5495	1174	41	4	403	4	FAM164C	14	75537677	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	11655755	75537677	31811863	135	14290											
KIAA1737	85457	broad.mit.edu	37	chr14	77580242	77580242	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccagtctgaccttcgctTcccccgccagtcctgtctgc	3	11	7	20	2	2	1	0	1	2	0	6	1	5	1	6	0	1	1	6	0	0	2	rs74069038		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:77580242T>C	ENST00000361786.2	+	4	1098	c.781T>C	c.(781-783)Tcc>Ccc	p.S261P	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		261					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		GACCTTCGCTTCCCCCGCCAG	0.562																																					p.S261P													.	KIAA1737-90	0			c.T781C						.						88	74	79					14																	77580242		2203	4300	6503	SO:0001583	missense	85457	exon4			TTCGCTTCCCCCG																												ENST00000361786.2:c.781T>C	14.37:g.77580242T>C	ENSP00000355319:p.Ser261Pro	Somatic	50	4		WXS	Illumina HiSeq	Phase_I	68	18	NM_033426	0	0	3	3	0	B2RCI1|Q8N389|Q8NDZ1	Missense_Mutation	SNP	ENST00000361786.2	37	CCDS9855.1	.	.	.	.	.	.	.	.	.	.	T	15.35	2.807816	0.50421	.	.	ENSG00000198894	ENST00000361786	T	0.32988	1.43	5.58	2.99	0.34606	.	0.707769	0.14711	N	0.302928	T	0.30103	0.0754	L	0.51422	1.61	0.19300	N	0.999979	P;P	0.34757	0.467;0.467	B;B	0.37888	0.26;0.133	T	0.13710	-1.0499	10	0.42905	T	0.14	-7.2446	10.5458	0.45060	0.0:0.0:0.3101:0.6899	.	261;163	Q9C0C6;B3KU75	K1737_HUMAN;.	P	261	ENSP00000355319:S261P	ENSP00000355319:S261P	S	+	1	0	KIAA1737	76649995	0.055000	0.20627	0.472000	0.27241	0.974000	0.67602	1.196000	0.32198	1.019000	0.39547	0.454000	0.30748	TCC	T|0.500;C|0.500		0.562	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1			C	77580242	T	C	77580242	3	2	157	1	0	0	0	0	1	0	0	0	8276	1783	62	3	791	3	KIAA1737	14	77580242	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	2042565	77580242	29769298	136	14291											
DYNC1H1	1778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	102478240	102478240	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctatcagatcacccagaTcaatcatggcctgatgatgg	11	10	9	11	0	5	4	4	2	1	2	5	4	5	4	2	2	0	1	2	2	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:102478240T>C	ENST00000360184.4	+	33	6811	c.6647T>C	c.(6646-6648)aTc>aCc	p.I2216T		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2216	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATCACCCAGATCAATCATGGC	0.602																																					p.I2216T		.											.	DYNC1H1-98	0			c.T6647C						.						86	74	78					14																	102478240		2203	4300	6503	SO:0001583	missense	1778	exon33			CCCAGATCAATCA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"Cytoplasmic dyneins"	2961	protein-coding gene	gene with protein product		600112	"dynein, cytoplasmic, heavy polypeptide 1"	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.6647T>C	14.37:g.102478240T>C	ENSP00000348965:p.Ile2216Thr	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	87	27	NM_001376	0	0	12	19	7	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705776	0.68615	.	.	ENSG00000197102	ENST00000360184	T	0.27402	1.67	5.8	5.8	0.92144	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.33265	0.0857	L	0.44542	1.39	0.80722	D	1	P	0.45348	0.856	P	0.44394	0.448	T	0.03423	-1.1038	10	0.40728	T	0.16	.	16.1547	0.81649	0.0:0.0:0.0:1.0	.	2216	Q14204	DYHC1_HUMAN	T	2216	ENSP00000348965:I2216T	ENSP00000348965:I2216T	I	+	2	0	DYNC1H1	101547993	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.991000	0.88244	2.221000	0.72209	0.528000	0.53228	ATC	.		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102478240	T	C	102478240	3	2	157	1	0	0	0	0	1	0	0	0	4852	1435	50	3	6777	3	DYNC1H1	14	102478240	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	24897998	102478240	4871300	137	14292											
PACS2	23241	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	105833603	105833603	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgagcctctgcagcagcatCaaggaggcccccgtcaaggc	9	5	12	15	1	3	1	2	1	1	0	3	2	3	2	3	3	4	3	3	3	2	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:105833603C>T	ENST00000325438.8	+	5	981	c.477C>T	c.(475-477)atC>atT	p.I159I	PACS2_ENST00000430725.2_Silent_p.I92I|PACS2_ENST00000547217.1_Silent_p.I129I|PACS2_ENST00000458164.2_Silent_p.I159I|PACS2_ENST00000447393.1_Silent_p.I159I			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	159					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		GCAGCAGCATCAAGGAGGCCC	0.647																																					p.I159I													.	PACS2-69	0			c.C477T						.						51	56	54					14																	105833603		2203	4300	6503	SO:0001819	synonymous_variant	23241	exon5			CAGCATCAAGGAG	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"phosphofurin acidic cluster sorting protein 1-like"	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.477C>T	14.37:g.105833603C>T		Somatic	148	1		WXS	Illumina HiSeq	Phase_I	210	60	NM_001100913	0	0	17	32	15	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			.		0.647	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355		T	105833603	C	T	105833603	2	4	157	1	0	0	0	0	0	0	0	1	11399	816	29	2		2	PACS2	14	105833603	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	3355363	105833603	1515937	138	14293											
HERC2	8924	broad.mit.edu;ucsc.edu	37	chr15	28437274	28437274	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttcagctgttttccagaacGgccacaaaataccgcagact	12	9	7	13	2	1	2	1	0	0	2	2	2	2	2	3	1	3	3	3	1	4	4	rs543946257		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:28437274G>C	ENST00000261609.7	-	53	8392	c.8284C>G	c.(8284-8286)Cgt>Ggt	p.R2762G		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R2762G(3)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TTTCCAGAACGGCCACAAAAT	0.493											OREG0022997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	8e-04	0	5008	,	,		17962	0		0	False		,,,				2504	0				p.R2762G													.	HERC2-234	3	Substitution - Missense(3)	ovary(1)|NS(1)|central_nervous_system(1)	c.C8284G						.						97	96	96					15																	28437274		2203	4300	6503	SO:0001583	missense	8924	exon53			CAGAACGGCCACA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"hect domain and RLD 2"			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8284C>G	15.37:g.28437274G>C	ENSP00000261609:p.Arg2762Gly	Somatic	34	0	801	WXS	Illumina HiSeq	Phase_I	67	5	NM_004667	0	0	5	8	3		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874685	0.72180	.	.	ENSG00000128731	ENST00000261609	T	0.62788	0.0	5.67	5.67	0.87782	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.054132	0.85682	D	0.000000	T	0.77157	0.4089	L	0.53249	1.67	0.80722	D	1	D;D	0.69078	0.997;0.987	D;D	0.76071	0.987;0.953	T	0.77861	-0.2430	10	0.72032	D	0.01	.	19.7646	0.96335	0.0:0.0:1.0:0.0	.	229;2762	A8KAQ8;O95714	.;HERC2_HUMAN	G	2762	ENSP00000261609:R2762G	ENSP00000261609:R2762G	R	-	1	0	HERC2	26110869	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.808000	0.99193	2.675000	0.91044	0.471000	0.43371	CGT	.		0.493	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28437274	G	C	28437274	3	2	157	1	0	0	0	0	1	0	0	0	7079	1116	39	4	6384	4	HERC2	15	28437274	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		28437274	74094118	139	14294											
TRIM69	140691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	45048565	45048565	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattctatttgatattcccaGgaggagcttgccatccaaca	12	12	7	10	0	1	1	0	1	1	0	3	3	3	3	3	2	3	1	3	2	4	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:45048565G>C	ENST00000559390.1	+	4	1411		c.e4-1		TRIM69_ENST00000558173.1_Splice_Site|TRIM69_ENST00000558329.1_Splice_Site|TRIM69_ENST00000329464.4_Splice_Site|TRIM69_ENST00000560442.1_Splice_Site|TRIM69_ENST00000561043.1_Splice_Site|TRIM69_ENST00000338264.4_Splice_Site			Q86WT6	TRI69_HUMAN	tripartite motif containing 69						apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GATATTCCCAGGAGGAGCTTG	0.488																																					.	Pancreas(84;519 1450 1802 20427 34706)	.											.	TRIM69-90	0			c.7-1G>C						.						41	39	40					15																	45048565		1927	3624	5551	SO:0001630	splice_region_variant	140691	exon2			TTCCCAGGAGGAG	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	17857	protein-coding gene	gene with protein product			"ring finger protein 36", "tripartite motif-containing 69"	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.484-1G>C	15.37:g.45048565G>C		Somatic	93	0		WXS	Illumina HiSeq	Phase_I	130	61	NM_080745	0	0	0	0	0	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Splice_Site	SNP	ENST00000559390.1	37	CCDS32220.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350808	0.24512	.	.	ENSG00000185880	ENST00000329464;ENST00000338264	.	.	.	5.34	4.43	0.53597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9849	0.53142	0.0847:0.0:0.9153:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIM69	42835857	1.000000	0.71417	0.995000	0.50966	0.200000	0.23975	4.849000	0.62882	1.391000	0.46566	0.655000	0.94253	.	.		0.488	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		Intron	C	45048565	G	C	45048565	5	2	157	1	0	0	0	0	0	0	1	0	16575	1014	35	4	493	4	TRIM69	15	45048565	Splice_Site	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	16611291	45048565	57482827	140	14295											
FBN1	2200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	48748937	48748937	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccattttcacagacccctggGatctcccggcactcatcaat	9	10	6	16	1	4	1	3	0	1	1	5	2	4	2	4	2	0	1	4	2	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:48748937G>T	ENST00000316623.5	-	44	5774	c.5319C>A	c.(5317-5319)atC>atA	p.I1773I		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1773	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGACCCCTGGGATCTCCCGGC	0.468																																					p.I1773I		.											.	FBN1-92	0			c.C5319A						.						112	99	103					15																	48748937		2198	4296	6494	SO:0001819	synonymous_variant	2200	exon44			CCCTGGGATCTCC	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"Marfan syndrome"	134797	"fibrillin 1 (Marfan syndrome)"	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5319C>A	15.37:g.48748937G>T		Somatic	70	0		WXS	Illumina HiSeq	Phase_I	112	44	NM_000138	0	0	0	0	0	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																			.		0.468	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48748937	G	T	48748937	2	4	157	1	0	0	0	0	0	0	0	1	5721	1164	41	4		4	FBN1	15	48748937	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	3700372	48748937	53782455	141	14296											
CILP	8483	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	65494241	65494241	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgggcaaccttggacttCacagccccagcatcactctg	9	8	9	15	0	3	0	2	0	1	0	3	1	3	1	3	2	4	3	3	2	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:65494241C>A	ENST00000261883.4	-	8	1321	c.1155G>T	c.(1153-1155)gtG>gtT	p.V385V		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	385	Ig-like C2-type.				negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						CCTTGGACTTCACAGCCCCAG	0.587																																					p.V385V													.	CILP-97	0			c.G1155T						.						74	66	68					15																	65494241		2202	4299	6501	SO:0001819	synonymous_variant	8483	exon8			GGACTTCACAGCC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.1155G>T	15.37:g.65494241C>A		Somatic	68	1		WXS	Illumina HiSeq	Phase_I	109	42	NM_003613	0	0	0	0	0	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	37	CCDS10203.1																																																																																			.		0.587	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65494241	C	A	65494241	2	1	157	1	0	0	0	0	0	0	0	1	3435	813	29	4		4	CILP	15	65494241	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	16745304	65494241	37037151	142	14297											
SV2B	9899	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr15	91811781	91811781	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgtgtacggcgccacaaTcaacttcacgatggaaaatc	13	8	9	11	3	2	0	2	0	0	0	3	2	2	1	1	2	2	2	1	2	5	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:91811781T>A	ENST00000394232.1	+	9	1789	c.1319T>A	c.(1318-1320)aTc>aAc	p.I440N	SV2B_ENST00000545111.2_Missense_Mutation_p.I289N|SV2B_ENST00000330276.4_Missense_Mutation_p.I440N	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	440					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GGCGCCACAATCAACTTCACG	0.428																																					p.I440N		.											.	SV2B-97	0			c.T1319A						.						139	136	137					15																	91811781		2198	4298	6496	SO:0001583	missense	9899	exon10			CCACAATCAACTT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1319T>A	15.37:g.91811781T>A	ENSP00000377779:p.Ile440Asn	Somatic	176	0		WXS	Illumina HiSeq	Phase_I	271	21	NM_014848	0	0	0	0	0	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561903	0.86335	.	.	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.61980	0.06;0.06;0.06	5.49	5.49	0.81192	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.043947	0.85682	D	0.000000	T	0.55273	0.1910	L	0.34521	1.04	0.43761	D	0.99627	P	0.41159	0.74	B	0.43386	0.418	T	0.52260	-0.8599	10	0.24483	T	0.36	-35.1417	14.7146	0.69257	0.0:0.0:0.0:1.0	.	440	Q7L1I2	SV2B_HUMAN	N	289;440;440	ENSP00000443243:I289N;ENSP00000377779:I440N;ENSP00000332818:I440N	ENSP00000332818:I440N	I	+	2	0	SV2B	89612785	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.750000	0.85110	2.212000	0.71576	0.533000	0.62120	ATC	.		0.428	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		A	91811781	T	A	91811781	3	1	157	1	0	0	0	0	1	0	0	0	15450	1435	50	5	1349	5	SV2B	15	91811781	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	26317540	91811781	10719611	143	14298											
PGPEP1L	145814	hgsc.bcm.edu	37	chr15	99544418	99544418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaactgtaacactcaccaCgagagtccgcggcttcattc	12	8	8	13	3	2	2	2	0	0	2	4	3	3	2	2	1	2	2	2	1	3	3	rs149174294	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:99544418C>T	ENST00000378919.6	-	2	224	c.19G>A	c.(19-21)Gtg>Atg	p.V7M	PGPEP1L_ENST00000535714.1_Intron|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	7							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						acactcaccacgagagtccgc	0.458													C|||	773	0.154353	0.0469	0.17	5008	,	,		20819	0.3502		0.0457	False		,,,				2504	0.1984				p.V7M		.											.	.	0			c.G19A						.						1	1	1					15																	99544418		193	151	344	SO:0001583	missense	145814	exon2			TCACCACGAGAGT		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.19G>A	15.37:g.99544418C>T	ENSP00000368199:p.Val7Met	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	4	4	NM_001102612	0	0	1	1	0	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	325	0.1488095238095238	28	0.056910569105691054	49	0.13535911602209943	211	0.3688811188811189	37	0.048812664907651716	C	1.763	-0.486281	0.04352	.	.	ENSG00000183571	ENST00000378919	T	0.31510	1.49	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.45190	-0.9278	6	0.49607	T	0.09	-8.6959	.	.	.	.	7	A6NFU8	PGPIL_HUMAN	M	7	ENSP00000368199:V7M	ENSP00000368199:V7M	V	-	1	0	PGPEP1L	97361941	0.007000	0.16637	0.018000	0.16275	0.019000	0.09904	0.145000	0.16157	0.119000	0.18210	0.121000	0.15741	GTG	C|0.851;T|0.149		0.458	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2		T	99544418	C	T	99544418	3	4	157	1	0	0	0	0	1	0	0	0	11830	536	19	1	587	1	PGPEP1L	15	99544418	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	7732637	99544418	2986974	144	14299											
WFIKKN1	117166	broad.mit.edu	37	chr16	683832	683832	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggcctcaagttcttgggCaccaagtacctggaggtgac	9	9	13	10	0	2	1	1	1	1	0	2	2	2	2	3	4	1	3	3	4	3	3	rs541743223		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:683832C>A	ENST00000319070.2	+	2	1744	c.1422C>A	c.(1420-1422)ggC>ggA	p.G474G		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	474	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				AGTTCTTGGGCACCAAGTACC	0.677																																					p.G474G													.	WFIKKN1-90	0			c.C1422A						.						76	42	53					16																	683832		2178	4291	6469	SO:0001819	synonymous_variant	117166	exon2			CTTGGGCACCAAG	AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"Immunoglobulin superfamily / I-set domain containing", "WAP four-disulfide core domain containing"	30912	protein-coding gene	gene with protein product	"WAP four-disulfide core domain 20A"	608021	"chromosome 16 open reading frame 12"	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.1422C>A	16.37:g.683832C>A		Somatic	68	1		WXS	Illumina HiSeq	Phase_I	235	8	NM_053284	0	0	0	0	0	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			.		0.677	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284		A	683832	C	A	683832	2	1	157	1	0	0	0	0	0	0	0	1	17391	697	25	4		4	WFIKKN1	16	683832	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		683832	89670921	145	14300											
RPL3L	6123	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	1995884	1995884	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtaccagcaatacaacccttCagcatgacgaagtcgttgtt	12	10	8	11	2	1	1	1	1	0	0	2	2	1	1	2	0	5	5	2	0	5	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:1995884C>T	ENST00000268661.7	-	8	1093	c.999G>A	c.(997-999)ctG>ctA	p.L333L	MSRB1_ENST00000399753.2_5'Flank|MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000564908.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	333					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						TACAACCCTTCAGCATGACGA	0.602																																					p.L333L		.											.	RPL3L-90	0			c.G999A						.						164	138	147					16																	1995884		2199	4300	6499	SO:0001819	synonymous_variant	6123	exon8			ACCCTTCAGCATG	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"L ribosomal proteins"	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.999G>A	16.37:g.1995884C>T		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	74	5	NM_005061	0	0	0	0	0		Silent	SNP	ENST00000268661.7	37	CCDS10450.1																																																																																			.		0.602	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		T	1995884	C	T	1995884	2	4	157	1	0	0	0	0	0	0	0	1	13626	813	29	2		2	RPL3L	16	1995884	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1312052	1995884	88358869	146	14301											
PKMYT1	9088	hgsc.bcm.edu	37	chr16	3025761	3025761	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtccttggggccccggaatGgtgacatggaacgctttacc	7	9	14	11	2	0	1	0	1	0	0	1	3	1	3	4	6	2	1	4	6	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3025761G>A	ENST00000262300.8	-	4	939	c.431C>T	c.(430-432)cCa>cTa	p.P144L	PKMYT1_ENST00000431515.2_Missense_Mutation_p.P144L|PKMYT1_ENST00000573944.1_Missense_Mutation_p.P135L|PKMYT1_ENST00000440027.2_Missense_Mutation_p.P144L|PKMYT1_ENST00000574730.1_Missense_Mutation_p.P75L|PKMYT1_ENST00000574385.1_Missense_Mutation_p.P135L	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GCCCCGGAATGGTGACATGGA	0.667																																					p.P144L		.											.	PKMYT1-765	0			c.C431T						.						25	27	26					16																	3025761		2153	4235	6388	SO:0001583	missense	9088	exon4			CGGAATGGTGACA	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase", "protein phosphatase 1, regulatory subunit 126"	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.431C>T	16.37:g.3025761G>A	ENSP00000262300:p.Pro144Leu	Somatic	5	0		WXS	Illumina HiSeq	Phase_I	86	33	NM_182687	0	0	1	1	0	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	37	CCDS10486.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.938404	0.52972	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059815	0.64402	D	0.000002	T	0.47266	0.1436	N	0.11818	0.18	0.80722	D	1	P;P;P;P	0.43701	0.56;0.704;0.56;0.815	B;B;B;B	0.39068	0.217;0.217;0.217;0.289	T	0.56498	-0.7969	10	0.66056	D	0.02	-14.3456	17.2983	0.87175	0.0:0.0:1.0:0.0	.	135;75;144;144	A6NHV6;B4DXD4;Q99640;F8W164	.;.;PMYT1_HUMAN;.	L	144;144;144;144;135	ENSP00000392855:P144L;ENSP00000262300:P144L;ENSP00000397739:P144L;ENSP00000371675:P135L	ENSP00000262300:P144L	P	-	2	0	PKMYT1	2965762	1.000000	0.71417	0.237000	0.24090	0.956000	0.61745	4.915000	0.63355	2.676000	0.91093	0.655000	0.94253	CCA	.		0.667	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203		A	3025761	G	A	3025761	3	1	157	1	0	0	0	0	1	0	0	0	12004	1348	47	2	1130	2	PKMYT1	16	3025761	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1029877	3025761	87328992	147	14302											
NLRC3	197358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	3614323	3614323	+	RNA	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctgggactgccaccgccagGctgggctccccgacgtgcgg	4	5	16	16	4	0	0	0	0	0	0	1	2	1	1	5	4	2	3	5	4	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3614323G>C	ENST00000301749.7	-	0	1020				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCACCGCCAGGCTGGGCTCCC	0.662																																					p.S205R		.											.	NLRC3-96	0			c.C615G						.						31	37	35					16																	3614323		2003	4170	6173			197358	exon5			CGCCAGGCTGGGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3614323G>C		Somatic	57	0		WXS	Illumina HiSeq	Phase_I	95	32	NM_178844	0	0	0	0	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	G	1.295	-0.606481	0.03717	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	4.84	0.17	0.15021	.	0.625501	0.16533	N	0.210300	T	0.55625	0.1932	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.15870	0.014	T	0.32107	-0.9919	9	0.17832	T	0.49	.	4.5952	0.12325	0.0829:0.2788:0.4949:0.1434	.	252	C9JLH9	.	R	205;205;205;252;187	ENSP00000301749:S205R;ENSP00000352039:S205R;ENSP00000414415:S252R;ENSP00000323897:S187R	ENSP00000301749:S205R	S	-	3	2	NLRC3	3554324	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	0.471000	0.22100	0.074000	0.16767	0.655000	0.94253	AGC	.		0.662	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		C	3614323	G	C	3614323	1	2	157	0	1	0	0	0	0	0	0	0	10494	1194	42	4		4	NLRC3	16	3614323	RNA	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	588562	3614323	86740430	148	14303											
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu	37	chr16	3779018	3779018	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcatgctgggcatgacgggCccgctcacctggttgggtcg	4	8	17	12	3	1	1	1	1	0	0	2	1	1	1	2	5	1	5	2	5	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3779018C>T	ENST00000262367.5	-	31	6839	c.6030G>A	c.(6028-6030)ggG>ggA	p.G2010G	CREBBP_ENST00000382070.3_Silent_p.G1972G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2010					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GCATGACGGGCCCGCTCACCT	0.692			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.G2010G		.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP-1807	0			c.G6030A						.						12	14	13					16																	3779018		2185	4287	6472	SO:0001819	synonymous_variant	1387	exon31			GACGGGCCCGCTC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"Chromatin-modifying enzymes / K-acetyltransferases"	2348	protein-coding gene	gene with protein product		600140	"Rubinstein-Taybi syndrome"	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.6030G>A	16.37:g.3779018C>T		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	58	18	NM_004380	0	0	10	16	6	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																			.		0.692	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3779018	C	T	3779018	2	4	157	1	0	0	0	0	0	0	0	1	3867	726	26	2		2	CREBBP	16	3779018	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	164695	3779018	86575735	149	14304											
C16orf68	79091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	8736394	8736394	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacagattgaaaaatgccTgcacagccatactgtcggtg	12	8	9	12	1	0	2	0	1	0	1	1	2	0	2	3	1	4	1	3	1	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:8736394T>C	ENST00000381920.3	+	9	1240	c.982T>C	c.(982-984)Tgc>Cgc	p.C328R	METTL22_ENST00000568967.1_3'UTR|METTL22_ENST00000561758.1_Missense_Mutation_p.C272R	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	328						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						GAAAAATGCCTGCACAGCCAT	0.532																																					p.C328R		.											.	METTL22-90	0			c.T982C						.						124	139	134					16																	8736394		2055	4190	6245	SO:0001583	missense	79091	exon9			AATGCCTGCACAG	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"chromosome 16 open reading frame 68"	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.982T>C	16.37:g.8736394T>C	ENSP00000371345:p.Cys328Arg	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	157	65	NM_024109	0	0	20	32	12	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307330	0.23821	.	.	ENSG00000067365	ENST00000381920	T	0.40756	1.02	5.18	5.18	0.71444	.	0.177884	0.49305	D	0.000145	T	0.43590	0.1254	L	0.41710	1.295	0.80722	D	1	D;P	0.53462	0.96;0.752	P;P	0.54312	0.748;0.469	T	0.19976	-1.0289	10	0.14252	T	0.57	-39.2838	11.4298	0.50034	0.0:0.0:0.0:1.0	.	103;328	Q9BUU2-3;Q9BUU2	.;MET22_HUMAN	R	328	ENSP00000371345:C328R	ENSP00000371345:C328R	C	+	1	0	METTL22	8643895	1.000000	0.71417	1.000000	0.80357	0.286000	0.27126	2.384000	0.44362	1.956000	0.56807	0.533000	0.62120	TGC	.		0.532	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109		C	8736394	T	C	8736394	3	2	157	1	0	0	0	0	1	0	0	0	1831	1580	55	3	1012	3	C16orf68	16	8736394	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	4957376	8736394	81618359	150	14305											
ERN2	10595	broad.mit.edu;ucsc.edu	37	chr16	23713536	23713536	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctctgcagttccactcccCagggtgggatggaccctcag	6	9	12	14	0	2	0	1	0	1	0	5	2	4	2	4	3	1	2	4	3	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:23713536C>T	ENST00000457008.2	-	11	1178	c.1140G>A	c.(1138-1140)ctG>ctA	p.L380L	ERN2_ENST00000256797.4_Silent_p.L428L					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		TTCCACTCCCCAGGGTGGGAT	0.607																																					p.L428L													.	ERN2-322	0			c.G1284A						.						90	95	94					16																	23713536		2197	4300	6497	SO:0001819	synonymous_variant	10595	exon11			ACTCCCCAGGGTG	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"ER to nucleus signalling 2"			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1140G>A	16.37:g.23713536C>T		Somatic	45	1		WXS	Illumina HiSeq	Phase_I	80	15	NM_033266	0	0	0	0	0		Silent	SNP	ENST00000457008.2	37																																																																																				.		0.607	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			T	23713536	C	T	23713536	2	4	157	1	0	0	0	0	0	0	0	1	5251	581	21	2		2	ERN2	16	23713536	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	14977142	23713536	66641217	151	14306											
CETP	1071	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	57012127	57012127	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaaattcctctttccacGcccagaccagcaacattctg	10	10	7	14	1	2	2	0	1	2	1	4	2	4	2	4	1	2	1	4	1	2	3	rs144949752		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:57012127G>A	ENST00000566128.1	+	11	1178	c.911G>A	c.(910-912)cGc>cAc	p.R304H	CETP_ENST00000200676.3_Missense_Mutation_p.R369H|CETP_ENST00000379780.2_Missense_Mutation_p.R309H					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CTCTTTCCACGCCCAGACCAG	0.542																																					p.R369H													.	CETP-91	0			c.G1106A						.	G	HIS/ARG	1,4395	2.1+/-5.4	0,1,2197	165	149	155		1106	-6.8	0	16	dbSNP_134	155	0,8600		0,0,4300	no	missense	CETP	NM_000078.2	29	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	benign	369/494	57012127	1,12995	2198	4300	6498	SO:0001583	missense	1071	exon11			TTCCACGCCCAGA	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"BPI fold containing"	1869	protein-coding gene	gene with protein product	"BPI fold containing family F"	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.911G>A	16.37:g.57012127G>A	ENSP00000456276:p.Arg304His	Somatic	144	1		WXS	Illumina HiSeq	Phase_I	198	21	NM_000078	0	0	9	9	0		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	G	7.501	0.652743	0.14580	2.27E-4	0.0	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.09445	2.98;2.98	4.23	-6.83	0.01693	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.648930	0.03515	N	0.220082	T	0.05410	0.0143	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.36456	-0.9747	10	0.35671	T	0.21	-6.9101	9.1715	0.37083	0.5114:0.0989:0.3897:0.0	.	309;369	P11597-2;P11597	.;CETP_HUMAN	H	369;309	ENSP00000200676:R369H;ENSP00000369106:R309H	ENSP00000200676:R369H	R	+	2	0	CETP	55569628	0.000000	0.05858	0.000000	0.03702	0.161000	0.22273	-1.331000	0.02672	-1.478000	0.01869	-0.252000	0.11476	CGC	G|1.000;A|0.000		0.542	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078		A	57012127	G	A	57012127	3	1	157	1	0	0	0	0	1	0	0	0	3283	1087	38	1	1148	1	CETP	16	57012127	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	33298591	57012127	33342626	152	14307											
DHRS7C	201140	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	9683157	9683157	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacctttcgtcaatgtgaTggggccaaagtaattggcat	11	11	12	7	1	1	2	1	1	0	1	2	3	1	2	2	3	0	2	2	3	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:9683157T>A	ENST00000330255.5	-	3	478	c.466A>T	c.(466-468)Atc>Ttc	p.I156F	DHRS7C_ENST00000571134.1_Missense_Mutation_p.I155F	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	156					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						GTCAATGTGATGGGGCCAAAG	0.478																																					p.I156F		.											.	.	0			c.A466T						.						49	47	47					17																	9683157		1906	4125	6031	SO:0001583	missense	201140	exon3			ATGTGATGGGGCC		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	32423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 32C, member 2"					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.466A>T	17.37:g.9683157T>A	ENSP00000327975:p.Ile156Phe	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	108	8	NM_001220493	0	0	0	0	0	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	37	CCDS56020.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223879	0.39300	.	.	ENSG00000184544	ENST00000330255	D	0.86865	-2.18	5.75	5.75	0.90469	NAD(P)-binding domain (1);	0.045861	0.85682	D	0.000000	D	0.90000	0.6878	L	0.37630	1.12	0.47511	D	0.999443	D;D	0.71674	0.998;0.998	D;D	0.71184	0.972;0.94	D	0.91167	0.4965	10	0.87932	D	0	.	15.0365	0.71751	0.0:0.0:0.0:1.0	.	156;152	A6NNS2;B9EJH3	DRS7C_HUMAN;.	F	156	ENSP00000327975:I156F	ENSP00000327975:I156F	I	-	1	0	DHRS7C	9623882	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.823000	0.69272	2.193000	0.70182	0.533000	0.62120	ATC	.		0.478	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912		A	9683157	T	A	9683157	3	1	157	1	0	0	0	0	1	0	0	0	4508	1464	51	5	488	5	DHRS7C	17	9683157	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10		9683157	71512053	153	14308											
COX10	1352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	13980322	13980322	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaagagatgaagctgcaaGtgtatgatttgccaggaatt	14	10	13	4	0	0	3	0	2	0	1	0	6	0	5	1	2	3	3	1	2	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:13980322G>C	ENST00000261643.3	+	3	525	c.448G>C	c.(448-450)Gtg>Ctg	p.V150L	COX10_ENST00000429152.2_Missense_Mutation_p.V150L|COX10_ENST00000536205.1_5'UTR|COX10_ENST00000537334.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	150					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GAAGCTGCAAGTGTATGATTT	0.368																																					p.V150L		.											.	COX10-226	0			c.G448C						.						83	88	87					17																	13980322		2203	4300	6503	SO:0001583	missense	1352	exon3			CTGCAAGTGTATG	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.448G>C	17.37:g.13980322G>C	ENSP00000261643:p.Val150Leu	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	161	69	NM_001303	0	0	9	22	13	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.143|0.143	-1.100268|-1.100268	0.01843|0.01843	.|.	.|.	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	T|T	0.37235|0.61980	1.21|0.06	5.35|5.35	-6.73|-6.73	0.01749|0.01749	.|.	.|1.554890	.|0.03407	.|N	.|0.204147	T|T	0.36880|0.36880	0.0983|0.0983	N|N	0.25890|0.25890	0.77|0.77	0.34746|0.34746	D|D	0.731242|0.731242	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.49978|0.49978	-0.8881|-0.8881	6|10	.|0.02654	.|T	.|1	0.0067|0.0067	3.698|3.698	0.08372|0.08372	0.2638:0.4606:0.1338:0.1418|0.2638:0.4606:0.1338:0.1418	.|.	.|150	.|Q12887	.|COX10_HUMAN	T|L	110|150	ENSP00000397750:S110T|ENSP00000261643:V150L	.|ENSP00000261643:V150L	S|V	+|+	2|1	0|0	COX10|COX10	13921047|13921047	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.223000|0.223000	0.24884|0.24884	-0.888000|-0.888000	0.04148|0.04148	-0.666000|-0.666000	0.05310|0.05310	0.655000|0.655000	0.94253|0.94253	AGT|GTG	.		0.368	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		C	13980322	G	C	13980322	3	2	157	1	0	0	0	0	1	0	0	0	3768	1029	36	4	458	4	COX10	17	13980322	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4297165	13980322	67214888	154	14309											
FAM18B2	201158	ucsc.edu	37	chr17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaactcacagagaagaCagacgatgattgcactgact	15	7	10	9	1	1	6	1	3	0	3	1	8	1	6	0	0	3	2	0	0	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000519970.1_Intron|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y	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	265	268					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	254	27		WXS	Illumina HiSeq		388	34	NM_145301	0	0	10	40	30	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		T	15457087	C	T	15457087	3	4	157	1	0	0	0	0	1	0	0	0	5536	478	17	2	848	2	FAM18B2	17	15457087	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1476765	15457087	65738123	155	14310											
SLFN12L	100506736	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	33807110	33807110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctattgttctctccaagaGtgactcttcccacatttaga	9	16	5	11	0	3	3	0	1	3	2	6	3	5	3	2	0	0	1	2	0	3	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:33807110G>A	ENST00000260908.7	-	2	236	c.119C>T	c.(118-120)aCt>aTt	p.T40I	SLFN12L_ENST00000449046.1_Missense_Mutation_p.T71I|SLFN12L_ENST00000361112.4_Missense_Mutation_p.T69I|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	40						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						CTCTCCAAGAGTGACTCTTCC	0.403																																					p.T40I		.											.	SLFN12L-23	0			c.C119T						.						57	44	48					17																	33807110		692	1591	2283	SO:0001583	missense	100506736	exon2			CCAAGAGTGACTC	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.119C>T	17.37:g.33807110G>A	ENSP00000437635:p.Thr40Ile	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	103	8	NM_001195790	0	0	0	0	0	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	37	CCDS56026.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968021	0.53507	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.06528	3.32;3.64;3.29	2.72	2.72	0.32119	.	.	.	.	.	T	0.16599	0.0399	L	0.57536	1.79	0.09310	N	1	D	0.65815	0.995	D	0.63703	0.917	T	0.03993	-1.0986	9	0.48119	T	0.1	.	8.9486	0.35773	0.0:0.0:1.0:0.0	.	69	Q6IEE8-2	.	I	40;69;71	ENSP00000437635:T40I;ENSP00000354412:T69I;ENSP00000389348:T71I	ENSP00000437635:T40I	T	-	2	0	SLFN12L	30831223	0.000000	0.05858	0.017000	0.16124	0.662000	0.39071	-0.169000	0.09911	1.504000	0.48704	0.205000	0.17691	ACT	.		0.403	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		A	33807110	G	A	33807110	3	1	157	1	0	0	0	0	1	0	0	0	14767	1029	36	2	1659	2	SLFN12L	17	33807110	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	18350023	33807110	47388100	156	14311											
KRT38	8687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39596920	39596920	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattccaatgttgccaggaAtgtggcaggtccctggcaag	10	9	13	9	0	0	1	0	0	0	1	2	2	2	2	3	4	1	3	3	4	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:39596920A>C	ENST00000246646.3	-	1	253	c.254T>G	c.(253-255)aTt>aGt	p.I85S		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	85	Head.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GTTGCCAGGAATGTGGCAGGT	0.607																																					p.I85S		.											.	KRT38-92	0			c.T254G						.						73	68	70					17																	39596920		2203	4300	6503	SO:0001583	missense	8687	exon1			CCAGGAATGTGGC	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"-", "Intermediate filaments type I, keratins (acidic)"	6456	protein-coding gene	gene with protein product		604542	"keratin, hair, acidic, 8"	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.254T>G	17.37:g.39596920A>C	ENSP00000246646:p.Ile85Ser	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	212	88	NM_006771	0	0	0	0	0	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337461	0.41398	.	.	ENSG00000171360	ENST00000246646	D	0.82167	-1.58	4.89	3.82	0.43975	.	0.130125	0.34460	N	0.003941	D	0.84511	0.5488	L	0.50333	1.59	0.09310	N	1	D	0.89917	1.0	D	0.69307	0.963	T	0.72830	-0.4174	10	0.28530	T	0.3	.	5.4631	0.16627	0.6239:0.2845:0.0915:0.0	.	85	O76015	KRT38_HUMAN	S	85	ENSP00000246646:I85S	ENSP00000246646:I85S	I	-	2	0	KRT38	36850446	0.089000	0.21612	0.031000	0.17742	0.359000	0.29487	1.205000	0.32308	0.906000	0.36621	0.528000	0.53228	ATT	.		0.607	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		C	39596920	A	C	39596920	3	2	157	1	0	0	0	0	1	0	0	0	8496	101	4	5	1144	5	KRT38	17	39596920	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	5789810	39596920	41598290	157	14312											
JUP	3728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39925817	39925817	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggttggtggcctgcccCtccacctgggtggccagcag	4	8	15	14	0	0	0	0	0	0	0	1	0	1	0	6	5	3	3	6	5	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:39925817C>G	ENST00000393931.3	-	3	439	c.321G>C	c.(319-321)gaG>gaC	p.E107D	JUP_ENST00000310706.5_Missense_Mutation_p.E107D|JUP_ENST00000540235.1_Missense_Mutation_p.E107D|JUP_ENST00000393930.1_Missense_Mutation_p.E107D	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	107					adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		TGGCCTGCCCCTCCACCTGGG	0.647																																					p.E107D	Colon(16;42 520 6044 17852 28530)	.											.	JUP-479	0			c.G321C						.						31	29	29					17																	39925817		2201	4297	6498	SO:0001583	missense	3728	exon3			CTGCCCCTCCACC	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"Armadillo repeat containing"	6207	protein-coding gene	gene with protein product		173325	"catenin (cadherin-associated protein), gamma 80kDa"	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.321G>C	17.37:g.39925817C>G	ENSP00000377508:p.Glu107Asp	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	123	27	NM_021991	0	0	133	169	36	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	37	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	c	8.550	0.875277	0.17395	.	.	ENSG00000173801	ENST00000540235;ENST00000393930;ENST00000310706;ENST00000393931;ENST00000449889;ENST00000437187;ENST00000420370;ENST00000424457	T;T;T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	5.52	-7.03	0.01584	.	0.239681	0.42053	D	0.000764	T	0.27454	0.0674	N	0.08118	0	0.22591	N	0.998951	D;B	0.54207	0.965;0.001	B;B	0.43950	0.437;0.003	T	0.51663	-0.8677	10	0.22109	T	0.4	-21.4947	1.588	0.02648	0.2613:0.236:0.089:0.4138	.	107;107	B4DE59;P14923	.;PLAK_HUMAN	D	107	ENSP00000441751:E107D;ENSP00000377507:E107D;ENSP00000311113:E107D;ENSP00000377508:E107D;ENSP00000389886:E107D;ENSP00000394146:E107D;ENSP00000411449:E107D;ENSP00000401034:E107D	ENSP00000311113:E107D	E	-	3	2	JUP	37179343	0.000000	0.05858	0.979000	0.43373	0.992000	0.81027	-4.131000	0.00289	-0.505000	0.06568	0.556000	0.70494	GAG	.		0.647	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1			G	39925817	C	G	39925817	3	3	157	1	0	0	0	0	1	0	0	0	7993	680	24	4	1964	4	JUP	17	39925817	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	328897	39925817	41269393	158	14313											
STAT5A	6776	broad.mit.edu	37	chr17	40452261	40452262	+	Frame_Shift_Ins	INS	-	-	G																															agcagctggccgggaacggcINSgggccccccgagggcagcct																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:40452261_40452262insG	ENST00000345506.4	+	8	1437_1438	c.795_796insG	c.(796-798)gggfs	p.G266fs	STAT5A_ENST00000588868.1_Frame_Shift_Ins_p.G266fs|STAT5A_ENST00000590949.1_Frame_Shift_Ins_p.G266fs|STAT5A_ENST00000546010.2_Frame_Shift_Ins_p.G236fs|STAT5A_ENST00000452307.2_Frame_Shift_Ins_p.G266fs	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	266					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		CCGGGAACGGCGGGCCCCCCGA	0.688																																					p.G265fs													.	STAT5A-846	0			c.795_796insG						.			24,266		11,2,132						-4.4	0.9			1	96,1048		28,40,504	no	frameshift	STAT5A	NM_003152.3		39,42,636	A1A1,A1R,RR		8.3916,8.2759,8.3682				120,1314				SO:0001589	frameshift_variant	6776	exon8			GAACGGCGGGCCC	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.798dupG	17.37:g.40452264_40452264dupG	ENSP00000341208:p.Gly266fs	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	236	9	NM_003152	0	0	0	0	0	Q1KLZ6	Frame_Shift_Ins	INS	ENST00000345506.4	37	CCDS11424.1																																																																																			.		0.688	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		G	40452262	-	G	40452261	7	5	157	1	0	1	1	0	0	0	0	0	15300	755	27	0	817	0	STAT5A	17	40452261	Frame_Shift_Ins	INS	-	TCGA-P4-A5EB-01A-11D-A28G-10	526444	40452261	40742949	159	14314											
ERN1	2081	broad.mit.edu	37	chr17	62152600	62152600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaattctgggatggtaaaaGgaagtttctttaaaaaaaaa	18	11	8	4	0	2	0	0	0	2	0	2	2	2	2	1	3	0	2	1	3	9	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:62152600G>A	ENST00000433197.3	-	5	385	c.290C>T	c.(289-291)cCt>cTt	p.P97L	ERN1_ENST00000577567.1_5'UTR	NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GATGGTAAAAGGAAGTTTCTT	0.358																																					p.P97L													.	ERN1-784	0			c.C290T						.						15	14	14					17																	62152600		1561	3443	5004	SO:0001583	missense	2081	exon5			GTAAAAGGAAGTT	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"inositol-requiring enzyme 1"	604033	"ER to nucleus signalling 1"			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.290C>T	17.37:g.62152600G>A	ENSP00000401445:p.Pro97Leu	Somatic	63	4		WXS	Illumina HiSeq	Phase_I	69	10	NM_001433	0	0	0	0	0		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.859641	0.91433	.	.	ENSG00000178607	ENST00000433197	T	0.29397	1.57	5.87	5.87	0.94306	Quinonprotein alcohol dehydrogenase-like (2);	0.000000	0.85682	D	0.000000	T	0.64382	0.2593	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68108	-0.5496	10	0.66056	D	0.02	-24.3325	20.1991	0.98252	0.0:0.0:1.0:0.0	.	97	O75460	ERN1_HUMAN	L	97	ENSP00000401445:P97L	ENSP00000401445:P97L	P	-	2	0	ERN1	59506332	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	9.476000	0.97823	2.775000	0.95449	0.650000	0.86243	CCT	.		0.358	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		A	62152600	G	A	62152600	3	1	157	1	0	0	0	0	1	0	0	0	5250	1000	35	2	2715	2	ERN1	17	62152600	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	21700339	62152600	19042610	160	14315											
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	65105385	65105385	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgctccggaattacagcttCtgcaggaggagactgtggcc	8	9	13	11	1	1	1	0	0	1	1	2	4	2	3	2	4	4	3	2	4	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:65105385C>T	ENST00000358691.5	-	29	4502	c.4336G>A	c.(4336-4338)Gaa>Aaa	p.E1446K	HELZ_ENST00000580168.1_Missense_Mutation_p.E1447K	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1446						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					ATTACAGCTTCTGCAGGAGGA	0.547																																					p.E1446K		.											.	HELZ-92	0			c.G4336A						.						65	73	70					17																	65105385		2028	4202	6230	SO:0001583	missense	9931	exon29			CAGCTTCTGCAGG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"Zinc fingers, CCCH-type domain containing"	16878	protein-coding gene	gene with protein product	"down-regulated in human cancers"	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.4336G>A	17.37:g.65105385C>T	ENSP00000351524:p.Glu1446Lys	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	111	43	NM_014877	0	0	7	11	4	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.701438	0.48307	.	.	ENSG00000198265	ENST00000358691	D	0.83419	-1.72	5.9	4.92	0.64577	.	0.199043	0.53938	D	0.000060	T	0.74801	0.3764	N	0.19112	0.55	0.43777	D	0.996308	B;B	0.20261	0.043;0.043	B;B	0.19391	0.025;0.025	T	0.70945	-0.4734	10	0.62326	D	0.03	-11.4842	16.9692	0.86294	0.0:0.8723:0.1277:0.0	.	1447;1446	B7ZLW2;P42694	.;HELZ_HUMAN	K	1446	ENSP00000351524:E1446K	ENSP00000351524:E1446K	E	-	1	0	HELZ	62535847	0.991000	0.36638	0.996000	0.52242	0.966000	0.64601	2.728000	0.47319	1.460000	0.47911	0.549000	0.68633	GAA	.		0.547	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65105385	C	T	65105385	3	4	157	1	0	0	0	0	1	0	0	0	7070	922	32	2	1512	2	HELZ	17	65105385	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	2952785	65105385	16089825	161	14316											
EXOC7	23265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr17	74081440	74081440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gctcaatgtgctcccggtagGagcgctcagcagtcttctgt	6	11	12	12	2	4	0	2	0	2	0	5	1	5	1	1	2	3	5	1	2	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:74081440G>A	ENST00000335146.7	-	16	1873	c.1820C>T	c.(1819-1821)tCc>tTc	p.S607F	EXOC7_ENST00000607838.1_Missense_Mutation_p.S579F|EXOC7_ENST00000411744.2_Missense_Mutation_p.S548F|EXOC7_ENST00000589210.1_Missense_Mutation_p.S556F|EXOC7_ENST00000591724.1_5'Flank|EXOC7_ENST00000467929.2_Missense_Mutation_p.S528F|EXOC7_ENST00000405575.4_Missense_Mutation_p.S579F|EXOC7_ENST00000332065.5_Missense_Mutation_p.S525F			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	607					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTCCCGGTAGGAGCGCTCAGC	0.637																																					p.S607F		.											.	EXOC7-90	0			c.C1820T						.						57	47	50					17																	74081440		2202	4300	6502	SO:0001583	missense	23265	exon16			CGGTAGGAGCGCT	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1820C>T	17.37:g.74081440G>A	ENSP00000334100:p.Ser607Phe	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	45	4	NM_001145297	0	0	77	93	16	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	g	11.91	1.778418	0.31502	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.43	4.43	0.53597	Cullin repeat-like-containing domain (1);	0.133958	0.50627	D	0.000114	T	0.54615	0.1869	L	0.40543	1.245	0.80722	D	1	P;B;P;B;P;P;P	0.51653	0.947;0.006;0.844;0.059;0.918;0.809;0.578	B;B;P;B;B;B;B	0.46389	0.283;0.028;0.515;0.028;0.384;0.317;0.129	T	0.54200	-0.8329	9	0.30078	T	0.28	-19.663	17.099	0.86644	0.0:0.0:1.0:0.0	.	548;579;528;493;607;525;556	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	F	525;445;579;607;556;493;548	.	ENSP00000333806:S525F	S	-	2	0	EXOC7	71593035	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	6.700000	0.74619	2.035000	0.60131	0.479000	0.44913	TCC	.		0.637	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74081440	G	A	74081440	3	1	157	1	0	0	0	0	1	0	0	0	5323	1174	41	2	407	2	EXOC7	17	74081440	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8976055	74081440	7113770	162	14317											
RNF138	51444	broad.mit.edu	37	chr18	29709106	29709106	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagctagatgaagaaaccCaataccaaactgctgttgaa	16	9	7	9	0	1	4	1	2	0	2	1	4	1	4	2	0	5	3	2	0	7	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr18:29709106C>A	ENST00000261593.3	+	8	1152	c.694C>A	c.(694-696)Caa>Aaa	p.Q232K	RNF138_ENST00000257190.5_Missense_Mutation_p.Q138K	NM_001191324.1|NM_016271.4	NP_001178253.2|NP_057355.2	Q8WVD3	RN138_HUMAN	ring finger protein 138, E3 ubiquitin protein ligase	232					protein ubiquitination (GO:0016567)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	ligase activity (GO:0016874)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						TGAAGAAACCCAATACCAAAC	0.358																																					p.Q232K													.	RNF138-226	0			c.C694A						.						151	148	149					18																	29709106		2203	4300	6503	SO:0001583	missense	51444	exon7			GAAACCCAATACC	AF162680	CCDS11903.1, CCDS11904.1	18q12.1	2013-01-28	2012-02-23		ENSG00000134758	ENSG00000134758		"RING-type (C3HC4) zinc fingers"	17765	protein-coding gene	gene with protein product	"nemo-like kinase associated ring finger protein"		"ring finger protein 138"			22155992, 16714285	Standard	NM_016271		Approved	STRIN, NARF	uc021uip.2	Q8WVD3	OTTHUMG00000132265	ENST00000261593.3:c.694C>A	18.37:g.29709106C>A	ENSP00000261593:p.Gln232Lys	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	40	3	NM_001191324	0	0	5	5	0	B2RE17|Q9H8K2|Q9UF87|Q9UKI6	Missense_Mutation	SNP	ENST00000261593.3	37	CCDS11903.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.119150	0.56505	.	.	ENSG00000134758	ENST00000261593;ENST00000257190	D	0.87491	-2.26	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	D	0.89928	0.6857	M	0.64997	1.995	0.80722	D	1	D;D	0.61697	0.99;0.976	P;P	0.53146	0.719;0.629	D	0.87443	0.2396	10	0.25751	T	0.34	-4.4744	19.4797	0.95005	0.0:1.0:0.0:0.0	.	138;232	Q8WVD3-2;Q8WVD3	.;RN138_HUMAN	K	232;138	ENSP00000261593:Q232K	ENSP00000257190:Q138K	Q	+	1	0	RNF138	27963104	0.997000	0.39634	0.993000	0.49108	0.845000	0.48019	4.841000	0.62824	2.684000	0.91462	0.650000	0.86243	CAA	.		0.358	RNF138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255352.2	NM_016271		A	29709106	C	A	29709106	3	1	157	1	0	0	0	0	1	0	0	0	13473	595	21	4	720	4	RNF138	18	29709106	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		29709106	48368142	163	14318											
SETBP1	26040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	42533244	42533244	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaacgtacagggaaaaggaCatccaagccttcaagatgaa	17	5	11	8	1	1	2	1	1	0	1	2	5	2	5	2	3	3	1	2	3	7	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr18:42533244C>T	ENST00000282030.5	+	4	4235	c.3939C>T	c.(3937-3939)gaC>gaT	p.D1313D		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1313						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GGGAAAAGGACATCCAAGCCT	0.443									Schinzel-Giedion syndrome																												p.D1313D		.											.	SETBP1-155	0			c.C3939T						.						130	120	123					18																	42533244		2203	4300	6503	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AAAGGACATCCAA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3939C>T	18.37:g.42533244C>T		Somatic	158	0		WXS	Illumina HiSeq	Phase_I	144	38	NM_015559	0	0	0	0	0	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																			.		0.443	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		T	42533244	C	T	42533244	2	4	157	1	0	0	0	0	0	0	0	1	14161	477	17	2		2	SETBP1	18	42533244	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	12824138	42533244	35544004	164	14319											
PTPRS	5802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	5286082	5286082	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctgctgcacagcctccaaCgagcaggaccacaaggaggc	11	5	11	14	1	1	0	0	0	1	0	2	3	2	2	3	3	5	3	3	3	2	1	rs200430287	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:5286082C>A	ENST00000587303.1	-	1	169	c.70G>T	c.(70-72)Gtt>Ttt	p.V24F	PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.V24F|PTPRS_ENST00000372412.4_Missense_Mutation_p.V24F|PTPRS_ENST00000588012.1_Missense_Mutation_p.V24F|PTPRS_ENST00000353284.2_Missense_Mutation_p.V24F|PTPRS_ENST00000592099.1_Missense_Mutation_p.V24F|PTPRS_ENST00000348075.2_Missense_Mutation_p.V24F|PTPRS_ENST00000590509.1_Missense_Mutation_p.V24F|PTPRS_ENST00000357368.4_Missense_Mutation_p.V24F			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	24					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	CAGCCTCCAACGAGCAGGACC	0.617																																					p.V24F		.											.	PTPRS-357	0			c.G70T						.						52	46	48					19																	5286082		2203	4299	6502	SO:0001583	missense	5802	exon2			CTCCAACGAGCAG	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.70G>T	19.37:g.5286082C>A	ENSP00000467537:p.Val24Phe	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	160	81	NM_130854	0	0	1	5	4	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	6.878	0.531372	0.13127	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.56776	0.62;0.61;0.57;0.44;0.53	4.14	1.83	0.25207	.	1.741500	0.04678	U	0.411808	T	0.32971	0.0847	N	0.08118	0	0.09310	N	0.999997	B;B;B;B;P;B;B	0.34462	0.275;0.207;0.275;0.275;0.454;0.089;0.18	B;B;B;B;B;B;B	0.34138	0.091;0.176;0.091;0.091;0.045;0.017;0.025	T	0.35251	-0.9796	10	0.59425	D	0.04	.	5.1867	0.15187	0.0:0.6502:0.2297:0.1202	.	24;24;24;24;24;24;50	F8W800;Q8NHS7;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;.;PTPRS_HUMAN;.	F	50;24;24;24;24;24;24;24;24;24	ENSP00000361489:V24F;ENSP00000349932:V24F;ENSP00000262963:V24F;ENSP00000269907:V24F;ENSP00000327313:V24F	ENSP00000262963:V24F	V	-	1	0	PTPRS	5237082	0.861000	0.29849	0.878000	0.34440	0.011000	0.07611	1.123000	0.31308	0.973000	0.38340	-0.362000	0.07510	GTT	C|0.999;T|0.001		0.617	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5286082	C	A	5286082	3	1	157	1	0	0	0	0	1	0	0	0	12843	536	19	4	5924	4	PTPRS	19	5286082	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		5286082	53842901	165	14320											
KEAP1	9817	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	10610178	10610178	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcattgctggggtccagctGctgcaccaggaagtcactgc	7	8	14	12	0	1	0	1	0	0	0	2	1	2	1	2	4	5	5	2	4	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:10610178G>A	ENST00000171111.5	-	2	1079	c.532C>T	c.(532-534)Cag>Tag	p.Q178*	KEAP1_ENST00000588024.1_5'UTR|KEAP1_ENST00000393623.2_Nonsense_Mutation_p.Q178*	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	178					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GGGTCCAGCTGCTGCACCAGG	0.572																																					p.Q178X		.											.	KEAP1-637	0			c.C532T						.						137	109	118					19																	10610178		2203	4300	6503	SO:0001587	stop_gained	9817	exon2			CCAGCTGCTGCAC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.532C>T	19.37:g.10610178G>A	ENSP00000171111:p.Gln178*	Somatic	141	1		WXS	Illumina HiSeq	Phase_I	104	91	NM_012289	0	0	3	12	9	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Nonsense_Mutation	SNP	ENST00000171111.5	37	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	38	6.966030	0.97967	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	.	.	.	4.81	4.81	0.61882	.	0.116198	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.3825	0.74669	0.0:0.0:1.0:0.0	.	.	.	.	X	178	.	ENSP00000171111:Q178X	Q	-	1	0	KEAP1	10471178	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.704000	0.84595	2.232000	0.73038	0.561000	0.74099	CAG	.		0.572	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10610178	G	A	10610178	4	1	157	1	0	0	0	0	0	1	0	0	8162	1328	46	2	1362	2	KEAP1	19	10610178	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	5324096	10610178	48518805	166	14321											
BRD4	23476	bcgsc.ca	37	chr19	15353721	15353721	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaccacttaccggttgagtaGgggtccgacttgtggtgccg	6	10	15	10	3	0	1	0	1	0	0	1	3	1	1	4	4	2	2	4	4	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:15353721G>T	ENST00000263377.2	-	14	3380	c.3159C>A	c.(3157-3159)ccC>ccA	p.P1053P		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1053	C-terminal (CTD) region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			CGGTTGAGTAGGGGTCCGACT	0.622			T	C15orf55	lethal midline carcinoma of young people																																p.P1053P				Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4-767	0			c.C3159A						.						42	31	35					19																	15353721		2194	4299	6493	SO:0001819	synonymous_variant	23476	exon14			TGAGTAGGGGTCC	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"chromosome-associated protein"	608749	"bromodomain-containing 4"			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.3159C>A	19.37:g.15353721G>T		Somatic	104	2		WXS	Illumina HiSeq	Phase_1	96	82	NM_058243	0	0	0	0	0	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																			.		0.622	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		T	15353721	G	T	15353721	2	4	157	1	0	0	0	0	0	0	0	1	1507	987	35	4		4	BRD4	19	15353721	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4743543	15353721	43775262	167	14322											
TSHZ3	57616	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	31769094	31769094	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagtgccgttctgggccttGttgattgcggatgtcactgt	4	14	15	8	2	2	1	1	1	1	0	2	3	2	3	2	3	2	2	2	3	0	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:31769094G>T	ENST00000240587.4	-	2	1932	c.1605C>A	c.(1603-1605)aaC>aaA	p.N535K		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	535					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TCTGGGCCTTGTTGATTGCGG	0.522																																					p.N535K													.	TSHZ3-232	0			c.C1605A						.						138	137	138					19																	31769094		2203	4300	6503	SO:0001583	missense	57616	exon2			GGCCTTGTTGATT	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	30700	protein-coding gene	gene with protein product	"teashirt 3"	614119	"zinc finger protein 537", "teashirt family zinc finger 3"	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1605C>A	19.37:g.31769094G>T	ENSP00000240587:p.Asn535Lys	Somatic	121	1		WXS	Illumina HiSeq	Phase_I	125	25	NM_020856	0	0	0	0	0	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	G	15.18	2.755931	0.49362	.	.	ENSG00000121297	ENST00000240587	T	0.47177	0.85	5.4	2.05	0.26809	.	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	M	0.64404	1.975	0.58432	D	0.999998	D	0.63880	0.993	D	0.72982	0.979	T	0.57533	-0.7795	10	0.52906	T	0.07	-48.9465	9.5255	0.39162	0.3438:0.0:0.6562:0.0	.	535	Q63HK5	TSH3_HUMAN	K	535	ENSP00000240587:N535K	ENSP00000240587:N535K	N	-	3	2	TSHZ3	36460934	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.160000	0.42348	0.245000	0.21373	0.655000	0.94253	AAC	.		0.522	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31769094	G	T	31769094	3	4	157	1	0	0	0	0	1	0	0	0	16658	1368	48	4	1644	4	TSHZ3	19	31769094	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	16415373	31769094	27359889	168	14323											
SLC7A9	11136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	33350841	33350841	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacgccgtcaccagggggAtcccgatgataatggccaaa	12	5	12	12	3	1	1	1	1	0	0	2	3	2	2	4	3	1	1	4	3	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33350841A>G	ENST00000023064.4	-	8	970	c.779T>C	c.(778-780)aTc>aCc	p.I260T	RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Missense_Mutation_p.I260T|SLC7A9_ENST00000590341.1_Missense_Mutation_p.I260T	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	260					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	CACCAGGGGGATCCCGATGAT	0.607																																					p.I260T	GBM(181;1335 2108 9644 44178 46689)	.											.	SLC7A9-91	0			c.T779C						.						100	82	88					19																	33350841		2203	4300	6503	SO:0001583	missense	11136	exon8			AGGGGGATCCCGA	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"Solute carriers"	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.779T>C	19.37:g.33350841A>G	ENSP00000023064:p.Ile260Thr	Somatic	185	0		WXS	Illumina HiSeq	Phase_I	210	108	NM_001243036	0	0	42	117	75	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	37	CCDS12425.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.776707	0.70107	.	.	ENSG00000021488	ENST00000023064	D	0.90620	-2.7	5.64	5.64	0.86602	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.96469	0.9347	10	0.87932	D	0	.	15.8639	0.79047	1.0:0.0:0.0:0.0	.	260;260	Q53FY4;P82251	.;BAT1_HUMAN	T	260	ENSP00000023064:I260T	ENSP00000023064:I260T	I	-	2	0	SLC7A9	38042681	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.192000	0.94947	2.161000	0.67846	0.379000	0.24179	ATC	.		0.607	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			G	33350841	A	G	33350841	3	3	157	1	0	0	0	0	1	0	0	0	14737	333	12	3	708	3	SLC7A9	19	33350841	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	1581747	33350841	25778142	169	14324											
CEBPA	1050	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	33793108	33793108	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaactcgtcgttgaaggcGgccgggtcgatgtaggcgct	7	8	17	9	6	0	1	0	1	0	0	3	3	0	2	1	5	1	3	1	5	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33793108G>T	ENST00000498907.2	-	1	362	c.213C>A	c.(211-213)gcC>gcA	p.A71A	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.9_ENST00000593041.1_lincRNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	71					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A72fs*89(1)|p.Y7_G130del(1)|p.A72fs*90(1)|p.A72fs*37(1)|p.S61fs*88(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CGTTGAAGGCGGCCGGGTCGA	0.751			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.A71A		.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA-7558	5	Insertion - Frameshift(3)|Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.C213A						.						4	5	4					19																	33793108		1229	2522	3751	SO:0001819	synonymous_variant	1050	exon1	Familial Cancer Database	Familial AML	GAAGGCGGCCGGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.213C>A	19.37:g.33793108G>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	83	30	NM_004364	0	0	0	0	0	A7LNP2|P78319|Q05CA4	Silent	SNP	ENST00000498907.2	37	CCDS54243.1																																																																																			.		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33793108	G	T	33793108	2	4	157	1	0	0	0	0	0	0	0	1	3205	1103	39	4		4	CEBPA	19	33793108	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	442267	33793108	25335875	170	14325			1	41		2	2	13	G		7.36486e-05
CEBPA	1050	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	33793120	33793120	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaaggcggccgggtcgatGtaggcgctgatgtcgatgga	7	9	18	7	5	0	2	0	2	0	0	2	5	0	3	1	5	0	2	1	5	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33793120G>T	ENST00000498907.2	-	1	350	c.201C>A	c.(199-201)taC>taA	p.Y67*	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.9_ENST00000593041.1_lincRNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	67					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.I68fs*41(4)|p.Y67fs*92(2)|p.S61fs*88(1)|p.Y67fs*95(1)|p.I68fs*39(1)|p.Y7_G130del(1)|p.Y67fs*42(1)|p.Y67fs*37(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CCGGGTCGATGTAGGCGCTGA	0.751			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.Y67X		.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.	CEBPA-7558	12	Insertion - Frameshift(6)|Deletion - Frameshift(5)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(12)	c.C201A						.						4	5	5					19																	33793120		1255	2546	3801	SO:0001587	stop_gained	1050	exon1	Familial Cancer Database	Familial AML	GTCGATGTAGGCG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.201C>A	19.37:g.33793120G>T	ENSP00000427514:p.Tyr67*	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	84	29	NM_004364	0	0	0	0	0	A7LNP2|P78319|Q05CA4	Nonsense_Mutation	SNP	ENST00000498907.2	37	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	g	33	5.204863	0.95033	.	.	ENSG00000245848	ENST00000498907	.	.	.	3.93	2.89	0.33648	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1768	0.25749	0.2127:0.0:0.7873:0.0	.	.	.	.	X	67	.	ENSP00000427514:Y67X	Y	-	3	2	CEBPA	38484960	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	5.273000	0.65564	0.631000	0.30412	0.282000	0.19409	TAC	.		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33793120	G	T	33793120	4	4	157	1	0	0	0	0	0	1	0	0	3205	1372	48	4	879	4	CEBPA	19	33793120	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	12	33793120	25335863	171	14326			1	41		2	2	13	G		7.36486e-05
WTIP	126374	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	34991065	34991065	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcagctgagcggggaggaggGacgccgttgctatcccctgg	6	6	18	11	3	0	1	0	1	0	0	1	4	1	4	3	5	3	4	3	5	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:34991065G>A	ENST00000590071.2	+	8	1521	c.1184G>A	c.(1183-1185)gGa>gAa	p.G395E	WTIP_ENST00000270288.6_Missense_Mutation_p.G619E	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	395	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			GGGGAGGAGGGACGCCGTTGC	0.667																																					p.G395E		.											.	WTIP-68	0			c.G1184A						.						32	40	38					19																	34991065		2142	4235	6377	SO:0001583	missense	126374	exon8			AGGAGGGACGCCG	AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279			20964	protein-coding gene	gene with protein product	"WT1-interacting protein"	614790				14736876	Standard	NM_001080436		Approved		uc002nvm.3	A6NIX2		ENST00000590071.2:c.1184G>A	19.37:g.34991065G>A	ENSP00000466953:p.Gly395Glu	Somatic	21	0		WXS	Illumina HiSeq	Phase_I	41	20	NM_001080436	0	0	2	6	4		Missense_Mutation	SNP	ENST00000590071.2	37	CCDS59375.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.337153	0.60963	.	.	ENSG00000142279	ENST00000270288	T	0.63580	-0.05	4.35	4.35	0.52113	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	T	0.72835	0.3510	M	0.76838	2.35	0.80722	D	1	P	0.37370	0.592	P	0.47528	0.549	T	0.77760	-0.2467	10	0.66056	D	0.02	.	15.9833	0.80130	0.0:0.0:1.0:0.0	.	619	A6NIX2	WTIP_HUMAN	E	619	ENSP00000270288:G619E	ENSP00000270288:G619E	G	+	2	0	WTIP	39682905	1.000000	0.71417	0.991000	0.47740	0.294000	0.27393	9.098000	0.94202	2.101000	0.63845	0.305000	0.20034	GGA	.		0.667	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459381.3	XM_059037		A	34991065	G	A	34991065	3	1	157	1	0	0	0	0	1	0	0	0	17443	1174	41	2	1214	2	WTIP	19	34991065	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1197945	34991065	24137918	172	14327											
LSR	51599	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	35758028	35758028	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccatgagtgaagtcacCtccctccacgaggacgactg	10	6	11	14	2	1	2	1	2	0	0	3	5	3	3	4	1	1	1	4	1	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:35758028C>A	ENST00000361790.3	+	9	1464	c.1305C>A	c.(1303-1305)acC>acA	p.T435T	AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000360798.3_Silent_p.T367T|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000427250.1_Silent_p.T279T|LSR_ENST00000347609.4_Silent_p.T377T|LSR_ENST00000354900.3_Silent_p.T416T|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000602122.1_Silent_p.T415T	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	435					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTGAAGTCACCTCCCTCCACG	0.677																																					p.T435T		.											.	LSR-90	0			c.C1305A						.						31	40	37					19																	35758028		2134	4246	6380	SO:0001819	synonymous_variant	51599	exon9			AGTCACCTCCCTC	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1305C>A	19.37:g.35758028C>A		Somatic	110	0		WXS	Illumina HiSeq	Phase_I	161	93	NM_205834	0	0	19	104	85	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	37	CCDS12450.1																																																																																			.		0.677	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		A	35758028	C	A	35758028	2	1	157	1	0	0	0	0	0	0	0	1	9089	668	24	4		4	LSR	19	35758028	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	766963	35758028	23370955	173	14328											
ARHGAP33	115703	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr19	36279064	36279064	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgaagccgttcagatccCggtcccccagtcccccgcct	5	6	8	22	4	1	1	1	0	0	1	4	2	4	1	9	1	1	1	9	1	1	1	rs182833371		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:36279064C>T	ENST00000007510.4	+	21	3741	c.3597C>T	c.(3595-3597)ccC>ccT	p.P1199P	ARHGAP33_ENST00000314737.5_Silent_p.P1038P|AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000378944.5_Silent_p.P1035P			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1199					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						GTTCAGATCCCGGTCCCCCAG	0.687													C|||	0	0	0	0	5008	,	,		10087	0		0	False		,,,				2504	0				p.P1038P		.											.	ARHGAP33-229	0			c.C3114T						.						23	30	27					19																	36279064		2187	4285	6472	SO:0001819	synonymous_variant	115703	exon21			AGATCCCGGTCCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3597C>T	19.37:g.36279064C>T		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	50	17	NM_052948	0	0	3	4	1	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				C|0.999;T|0.000		0.687	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		T	36279064	C	T	36279064	2	4	157	1	0	0	0	0	0	0	0	1	882	639	23	1		1	ARHGAP33	19	36279064	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	521036	36279064	22849919	174	14329											
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	40357745	40357745	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgctgcagtctgaggtcaGcagggaggagtttacctgtg	7	10	15	9	1	2	1	1	1	1	0	3	3	2	3	1	3	3	4	1	3	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:40357745G>T	ENST00000221347.6	-	34	15575	c.15568C>A	c.(15568-15570)Ctg>Atg	p.L5190M		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5190	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TCTGAGGTCAGCAGGGAGGAG	0.577																																					p.L5190M		.											.	FCGBP-98	0			c.C15568A						.						52	48	49					19																	40357745		2203	4300	6503	SO:0001583	missense	8857	exon34			AGGTCAGCAGGGA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"IgG Fc binding protein", "Human Fc gamma BP"					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.15568C>A	19.37:g.40357745G>T	ENSP00000221347:p.Leu5190Met	Somatic	166	0		WXS	Illumina HiSeq	Phase_I	199	23	NM_003890	0	0	15	15	0	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321017	0.41096	.	.	ENSG00000090920	ENST00000221347	T	0.05649	3.41	4.69	1.09	0.20402	.	0.754197	0.11458	N	0.562013	T	0.07728	0.0194	L	0.28694	0.88	0.22796	N	0.99872	P	0.46395	0.877	P	0.51016	0.656	T	0.39702	-0.9601	10	0.23302	T	0.38	.	7.3143	0.26491	0.0:0.3807:0.4452:0.1741	.	5190	Q9Y6R7	FCGBP_HUMAN	M	5190	ENSP00000221347:L5190M	ENSP00000221347:L5190M	L	-	1	2	FCGBP	45049585	0.892000	0.30473	0.997000	0.53966	0.846000	0.48090	0.111000	0.15458	0.563000	0.29222	0.655000	0.94253	CTG	.		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40357745	G	T	40357745	3	4	157	1	0	0	0	0	1	0	0	0	5797	962	34	4	661	4	FCGBP	19	40357745	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4078681	40357745	18771238	175	14330											
NUP62	23636	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	50412996	50412996	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcaggtgtggttgttgcCgtctttgcagtgccaaacgt	6	13	14	8	2	1	0	0	0	1	0	1	0	1	0	2	2	5	5	2	2	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:50412996C>T	ENST00000596217.1	-	2	1956	c.69G>A	c.(67-69)acG>acA	p.T23T	IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Silent_p.T23T|NUP62_ENST00000413454.1_Silent_p.T23T|CTC-326K19.6_ENST00000451973.1_3'UTR|NUP62_ENST00000597723.1_Silent_p.T23T|NUP62_ENST00000597029.1_Silent_p.T23T|NUP62_ENST00000352066.3_Silent_p.T23T|NUP62_ENST00000600583.1_5'UTR|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	23	15 X 9 AA approximate repeats.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TGGTTGTTGCCGTCTTTGCAG	0.567																																					p.T23T		.											.	NUP62-615	0			c.G69A						.						48	55	53					19																	50412996		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			TGTTGCCGTCTTT	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"nuclear pore glycoprotein p62"	605815	"nucleoporin 62kD"			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.69G>A	19.37:g.50412996C>T		Somatic	82	0		WXS	Illumina HiSeq	Phase_I	88	50	NM_153719	0	0	11	32	21	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			.		0.567	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		T	50412996	C	T	50412996	2	4	157	1	0	0	0	0	0	0	0	1	10794	639	23	1		1	NUP62	19	50412996	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	10055251	50412996	8715987	176	14331											
MBOAT7	79143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	54687463	54687463	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccatcagggagggcacgTcgggcagcagccccagggtg	7	5	16	13	2	2	0	1	0	1	0	4	1	2	1	3	4	2	3	3	4	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:54687463T>A	ENST00000245615.1	-	5	914	c.434A>T	c.(433-435)gAc>gTc	p.D145V	MBOAT7_ENST00000474910.1_5'UTR|MBOAT7_ENST00000338624.6_Missense_Mutation_p.D72V|MBOAT7_ENST00000431666.2_Missense_Mutation_p.D72V|MBOAT7_ENST00000391754.1_Missense_Mutation_p.D145V	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	145					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGAGGGCACGTCGGGCAGCAG	0.617																																					p.D145V	NSCLC(97;826 2151 10470 22540)	.											.	MBOAT7-68	0			c.A434T						.						105	84	91					19																	54687463		2203	4300	6503	SO:0001583	missense	79143	exon5			GGCACGTCGGGCA	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"lysophosphatidylinositol acyltransferase"	606048	"leukocyte receptor cluster (LRC) member 4"	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.434A>T	19.37:g.54687463T>A	ENSP00000245615:p.Asp145Val	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	97	52	NM_001146082	0	0	10	40	30	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Missense_Mutation	SNP	ENST00000245615.1	37	CCDS12883.1	.	.	.	.	.	.	.	.	.	.	T	8.074	0.770996	0.15983	.	.	ENSG00000125505	ENST00000431666;ENST00000338624;ENST00000245615;ENST00000449249;ENST00000391754;ENST00000414665;ENST00000453320	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	4.2	1.95	0.26073	.	0.659654	0.15733	N	0.247337	T	0.46718	0.1407	N	0.20685	0.6	0.09310	N	1	B;B;B	0.30973	0.033;0.302;0.033	B;B;B	0.21917	0.023;0.037;0.023	T	0.28650	-1.0037	10	0.40728	T	0.16	-2.1121	4.0508	0.09795	0.0:0.1914:0.1877:0.6209	.	127;72;145	B4DDH8;Q96N66-2;Q96N66	.;.;MBOA7_HUMAN	V	72;72;145;97;145;145;145	ENSP00000410503:D72V;ENSP00000344377:D72V;ENSP00000245615:D145V;ENSP00000375634:D145V;ENSP00000388250:D145V	ENSP00000245615:D145V	D	-	2	0	MBOAT7	59379275	0.001000	0.12720	0.058000	0.19502	0.792000	0.44763	1.025000	0.30090	1.714000	0.51371	0.363000	0.22086	GAC	.		0.617	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		A	54687463	T	A	54687463	3	1	157	1	0	0	0	0	1	0	0	0	9383	1667	58	5	1004	5	MBOAT7	19	54687463	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	4274467	54687463	4441520	177	14332											
PTPRH	5794	broad.mit.edu	37	chr19	55716805	55716805	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccacggtgatgttagtgtGtgctgtgcttcgagtccctg	5	14	13	9	2	0	1	0	1	0	0	3	2	2	1	2	1	2	3	2	1	1	2	rs200319382		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:55716805G>A	ENST00000376350.3	-	4	530	c.508C>T	c.(508-510)Cac>Tac	p.H170Y	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	170	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		ATGTTAGTGTGTGCTGTGCTT	0.567													t|||	1	0.000199681	0	0	5008	,	,		19765	0.001		0	False		,,,				2504	0				p.H170Y													.	PTPRH-138	0			c.C508T						.						162	144	150					19																	55716805		2203	4299	6502	SO:0001583	missense	5794	exon4			TAGTGTGTGCTGT		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.508C>T	19.37:g.55716805G>A	ENSP00000365528:p.His170Tyr	Somatic	196	1		WXS	Illumina HiSeq	Phase_I	254	7	NM_002842	0	0	0	0	0	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	t	14.77	2.635065	0.47049	.	.	ENSG00000080031	ENST00000376350	T	0.57436	0.4	3.93	-1.55	0.08558	Fibronectin, type III (4);Immunoglobulin-like fold (1);	3.173960	0.01664	N	0.025272	T	0.37046	0.0989	N	0.14661	0.345	0.09310	N	1	B	0.31519	0.327	B	0.35607	0.206	T	0.21759	-1.0236	10	0.51188	T	0.08	.	4.2695	0.10780	0.0:0.3384:0.3199:0.3416	.	170	Q9HD43	PTPRH_HUMAN	Y	170	ENSP00000365528:H170Y	ENSP00000365528:H170Y	H	-	1	0	PTPRH	60408617	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.994000	0.00656	-0.644000	0.05465	-2.191000	0.00312	CAC	.		0.567	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			A	55716805	G	A	55716805	3	1	157	1	0	0	0	0	1	0	0	0	12835	1377	48	2	2907	2	PTPRH	19	55716805	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1029342	55716805	3412178	178	14333											
ZNF814	730051	bcgsc.ca	37	chr19	58385280	58385281	+	Frame_Shift_Del	DEL	TG	TG	-																															atttcccacattctccacacTgataaggtctttctccactg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TG	TG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:58385280_58385281delTG	ENST00000435989.2	-	3	1711_1712	c.1477_1478delCA	c.(1477-1479)cagfs	p.Q493fs	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	493					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTCTCCACACTGATAAGGTCTT	0.47																																					p.493_493del													.	.	0			c.1477_1478del						.																																			SO:0001589	frameshift_variant	730051	exon3			CCACACTGATAAG		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"Zinc fingers, C2H2-type", "-"	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1477_1478delCA	19.37:g.58385280_58385281delTG	ENSP00000410545:p.Gln493fs	Somatic	130	0		WXS	Illumina HiSeq	Phase_1	125	12	NM_001144989	0	0	0	0	0	A6NF35	Frame_Shift_Del	DEL	ENST00000435989.2	37	CCDS46212.1																																																																																			.		0.47	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		-	58385281	TG	-	58385280	7	5	157	1	0	1	0	1	0	0	0	0	18208	1580	55	0	1093	0	ZNF814	19	58385280	Frame_Shift_Del	DEL	TG	TCGA-P4-A5EB-01A-11D-A28G-10	2668475	58385280	743703	179	14334											
KCNK15	140730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	43378853	43378853	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgggcatcccgctgacgctgGtcactttccagagcctgggc	5	9	13	14	2	1	2	1	1	0	1	3	2	3	2	3	3	1	3	3	3	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr20:43378853G>A	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Missense_Mutation_p.V123I	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				GCTGACGCTGGTCACTTTCCA	0.682																																					p.V123I		.											.	KCNK15-90	0			c.G367A						.						35	31	33					20																	43378853		2203	4300	6503	SO:0001628	intergenic_variant	60598	exon2			ACGCTGGTCACTT		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		20.37:g.43378853G>A		Somatic	61	0		WXS	Illumina HiSeq	Phase_I	136	40	NM_022358	0	0	0	1	1	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418600	0.83559	.	.	ENSG00000124249	ENST00000372861	T	0.28454	1.61	4.08	4.08	0.47627	Ion transport 2 (1);	0.000000	0.64402	U	0.000004	T	0.43100	0.1232	L	0.31578	0.945	0.54753	D	0.999989	D	0.69078	0.997	D	0.72075	0.976	T	0.38351	-0.9665	10	0.45353	T	0.12	.	16.4786	0.84151	0.0:0.0:1.0:0.0	.	123	Q9H427	KCNKF_HUMAN	I	123	ENSP00000361952:V123I	ENSP00000361952:V123I	V	+	1	0	KCNK15	42812267	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	6.347000	0.73004	2.095000	0.63458	0.655000	0.94253	GTC	.		0.682	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		A	43378853	G	A	43378853	1	1	157	0	1	0	0	0	0	0	0	0	8083	1261	44	2		2	KCNK15	20	43378853	IGR	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		43378853	19646667	180	14335											
EYA2	2139	bcgsc.ca	37	chr20	45801422	45801422	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaacctgtgcctgggctctGgcgtgcacggcggcgtggac	4	7	16	14	4	1	0	0	0	1	0	1	1	1	1	3	5	3	2	3	5	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr20:45801422G>C	ENST00000327619.5	+	12	1479	c.1105G>C	c.(1105-1107)Ggc>Cgc	p.G369R	EYA2_ENST00000357410.3_Missense_Mutation_p.G369R|EYA2_ENST00000317304.6_Missense_Mutation_p.G339R	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	369					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				CCTGGGCTCTGGCGTGCACGG	0.597																																					p.G369R	Pancreas(120;56 1725 18501 25218 43520)												.	EYA2-523	0			c.G1105C						.						116	94	101					20																	45801422		2203	4300	6503	SO:0001583	missense	2139	exon12			GGCTCTGGCGTGC		CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"Protein tyrosine phosphatases / Asp-based PTPs"	3520	protein-coding gene	gene with protein product		601654	"eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)"			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.1105G>C	20.37:g.45801422G>C	ENSP00000333640:p.Gly369Arg	Somatic	90	2		WXS	Illumina HiSeq	Phase_1	152	39	NM_172110	0	0	3	7	4	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Missense_Mutation	SNP	ENST00000327619.5	37	CCDS13403.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.006264	0.74932	.	.	ENSG00000064655	ENST00000327619;ENST00000357410;ENST00000484200;ENST00000317304	D;D;D	0.82081	-1.57;-1.57;-1.57	5.59	3.66	0.41972	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.052802	0.85682	N	0.000000	D	0.91150	0.7213	M	0.86864	2.845	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.91363	0.5113	10	0.87932	D	0	-14.6465	11.6637	0.51363	0.1423:0.0:0.8577:0.0	.	369;339;369;369	O00167-3;E7ETN2;A8KAG7;O00167	.;.;.;EYA2_HUMAN	R	369;369;339;339	ENSP00000333640:G369R;ENSP00000349986:G369R;ENSP00000321590:G339R	ENSP00000321590:G339R	G	+	1	0	EYA2	45234829	1.000000	0.71417	0.016000	0.15963	0.779000	0.44077	9.719000	0.98760	0.733000	0.32492	0.655000	0.94253	GGC	.		0.597	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244		C	45801422	G	C	45801422	3	2	157	1	0	0	0	0	1	0	0	0	5342	1348	47	4	1147	4	EYA2	20	45801422	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	2422569	45801422	17224098	181	14336											
LIPI	149998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	15554119	15554119	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatccacaaactttgcatcCgtgtaatctaatctgctata	13	13	4	11	1	2	0	0	0	2	0	4	0	4	0	2	0	3	3	2	0	5	5	rs368826576		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:15554119C>T	ENST00000536861.1	-	4	602	c.603G>A	c.(601-603)acG>acA	p.T201T	LIPI_ENST00000344577.2_Silent_p.T222T			Q6XZB0	LIPI_HUMAN	lipase, member I	201					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		ACTTTGCATCCGTGTAATCTA	0.388																																					p.T222T		.											.	LIPI-70	0			c.G666A						.	A		0,4406		0,0,2203	104	98	100		666	-5.4	0.9	21		100	1,8599		0,1,4299	no	coding-synonymous	LIPI	NM_198996.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		222/482	15554119	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	149998	exon4			TGCATCCGTGTAA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.603G>A	21.37:g.15554119C>T		Somatic	52	0		WXS	Illumina HiSeq	Phase_I	66	18	NM_198996	0	0	0	0	0	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	37		.	.	.	.	.	.	.	.	.	.	A	8.536	0.872084	0.17322	0.0	1.16E-4	ENSG00000188992	ENST00000400211	.	.	.	5.46	-5.41	0.02648	.	.	.	.	.	T	0.35508	0.0934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36648	-0.9739	4	.	.	.	.	1.1112	0.01704	0.2909:0.094:0.2357:0.3795	.	.	.	.	R	81	.	.	G	-	1	0	LIPI	14475990	0.021000	0.18746	0.905000	0.35620	0.056000	0.15407	-0.820000	0.04457	-1.108000	0.03000	-4.655000	0.00004	GGA	.		0.388	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		T	15554119	C	T	15554119	2	4	157	1	0	0	0	0	0	0	0	1	8848	639	23	1		1	LIPI	21	15554119	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		15554119	32575776	182	14337											
NCAM2	4685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	22906941	22906941	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaagatgggagcccagtaaAtgagccaaatgaaaccacac	17	4	10	10	1	0	3	0	2	0	1	0	5	0	4	3	1	3	1	3	1	5	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:22906941A>T	ENST00000400546.1	+	17	2615	c.2366A>T	c.(2365-2367)aAt>aTt	p.N789I	NCAM2_ENST00000284894.7_Missense_Mutation_p.N647I	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	789					axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGCCCAGTAAATGAGCCAAAT	0.393																																					p.N789I		.											.	NCAM2-94	0			c.A2366T						.						113	108	109					21																	22906941		1920	4124	6044	SO:0001583	missense	4685	exon17			CAGTAAATGAGCC		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.2366A>T	21.37:g.22906941A>T	ENSP00000383392:p.Asn789Ile	Somatic	132	0		WXS	Illumina HiSeq	Phase_I	122	35	NM_004540	0	0	0	0	0	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935591	0.73442	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.44083	0.93;0.93	5.49	5.49	0.81192	.	0.210687	0.48286	D	0.000186	T	0.49729	0.1574	L	0.41236	1.265	0.80722	D	1	D;D	0.61697	0.99;0.985	P;P	0.56398	0.797;0.724	T	0.49978	-0.8881	10	0.54805	T	0.06	-29.9197	14.4086	0.67101	1.0:0.0:0.0:0.0	.	647;789	B7Z5K2;O15394	.;NCAM2_HUMAN	I	789;647	ENSP00000383392:N789I;ENSP00000284894:N647I	ENSP00000284894:N647I	N	+	2	0	NCAM2	21828812	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.778000	0.75043	2.088000	0.63022	0.377000	0.23210	AAT	.		0.393	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22906941	A	T	22906941	3	4	157	1	0	0	0	0	1	0	0	0	10229	101	4	5	2432	5	NCAM2	21	22906941	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	7352822	22906941	25222954	183	14338											
PLAC4	25825	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	42551431	42551431	+	Intron	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agggtgaggagtgacggtgtCtggggtgagtgagggtgtcc	6	9	22	4	1	1	4	0	4	1	0	2	5	2	5	1	6	0	0	1	6	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:42551431C>T	ENST00000330333.6	+	1	775				BACE2_ENST00000328735.6_Intron|PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000430327.2_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000536486.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				GTGACGGTGTCTGGGGTGAGT	0.607																																					p.R42K		.											.	.	0			c.G125A						.						125	109	114					21																	42551431		2196	4274	6470	SO:0001627	intron_variant	191585	exon1			CGGTGTCTGGGGT	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10929C>T	21.37:g.42551431C>T		Somatic	137	0		WXS	Illumina HiSeq	Phase_I	179	49	NM_182832	0	0	0	0	0	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			T	42551431	C	T	42551431	1	4	157	0	1	0	0	0	0	0	0	0	12040	913	32	2		2	PLAC4	21	42551431	Intron	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	19644490	42551431	5578464	184	14339											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaagtctccaacgaaggagGaagcaaagtcccctgagaag	15	4	11	11	1	1	1	0	1	1	1	3	5	2	3	4	2	2	1	4	2	6	0	rs370929798		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		.											.	NEFH-90	0			c.G1933A						.						82	88	86					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	180	9	NM_021076	0	0	0	0	0	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885562	G	A	29885562	3	1	157	1	0	0	0	0	1	0	0	0	10340	1175	41	2	1947	2	NEFH	22	29885562	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		29885562	21419004	185	14340											
SHANK3	85358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	51160316	51160316	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accccctgcccctgagtctgCagccgactctggggtggagg	5	7	14	15	1	2	1	0	1	2	0	2	3	2	2	5	4	3	1	5	4	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr22:51160316C>T	ENST00000414786.2	+	21	4240	c.4013C>T	c.(4012-4014)gCa>gTa	p.A1338V	SHANK3_ENST00000262795.3_Missense_Mutation_p.A1368V|SHANK3_ENST00000445220.2_Missense_Mutation_p.A1354V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1352	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCTGAGTCTGCAGCCGACTCT	0.701																																					p.A1338V		.											.	SHANK3-69	0			c.C4013T						.						9	11	10					22																	51160316		1919	4032	5951	SO:0001583	missense	85358	exon21			AGTCTGCAGCCGA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	14294	protein-coding gene	gene with protein product	"proline rich synapse associated protein 2", "shank postsynaptic density protein"	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4013C>T	22.37:g.51160316C>T	ENSP00000464552:p.Ala1338Val	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	87	53	NM_033517	0	0	1	5	4	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		.	.	.	.	.	.	.	.	.	.	C	8.474	0.858312	0.17178	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.13089	2.62;2.62	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.13543	0.0328	N	0.24115	0.695	0.27140	N	0.961671	D;P;D	0.56521	0.97;0.941;0.976	P;B;B	0.51895	0.683;0.43;0.441	T	0.12837	-1.0532	10	0.02654	T	1	.	16.0382	0.80645	0.0:1.0:0.0:0.0	.	1352;1353;1368	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	V	1368;1354	ENSP00000442518:A1368V;ENSP00000446078:A1354V	ENSP00000442518:A1368V	A	+	2	0	SHANK3	49507182	1.000000	0.71417	0.900000	0.35374	0.856000	0.48823	5.501000	0.66950	2.381000	0.81170	0.462000	0.41574	GCA	.		0.701	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51160316	C	T	51160316	3	4	157	1	0	0	0	0	1	0	0	0	14298	710	25	2	4189	2	SHANK3	22	51160316	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	21274754	51160316	144250	186	14341											
OFD1	8481	hgsc.bcm.edu;bcgsc.ca	37	chrX	13762547	13762547	+	Frame_Shift_Del	DEL	T	T	-																															tttttaggttttcttatgcaTtttttaaaagaattggcaga																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:13762547delT	ENST00000340096.6	+	6	753	c.426delT	c.(424-426)catfs	p.H142fs	OFD1_ENST00000398395.3_Frame_Shift_Del_p.H142fs|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380567.1_Frame_Shift_Del_p.H2fs|OFD1_ENST00000380550.3_Frame_Shift_Del_p.H142fs	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	142					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TTCTTATGCATTTTTTAAAAG	0.308																																					p.H142fs		.											.	OFD1-108	0			c.426delT						.						66	59	61					X																	13762547		2203	4299	6502	SO:0001589	frameshift_variant	8481	exon6			.	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.426delT	X.37:g.13762547delT	ENSP00000344314:p.His142fs	Somatic	225	0		WXS	Illumina HiSeq	Phase_I	290	96	NM_003611	0	0	0	0	0	B9ZVU5|O75666|Q4VAK4	Frame_Shift_Del	DEL	ENST00000340096.6	37	CCDS14157.1																																																																																			.		0.308	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		-	13762547	T	-	13762547	7	5	157	1	0	1	0	1	0	0	0	0	10864	1490	52	0	448	0	OFD1	23	13762547	Frame_Shift_Del	DEL	T	TCGA-P4-A5EB-01A-11D-A28G-10		13762547	141508013	187	14342											
DMD	1756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	32305751	32305751	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggcgttgcactttgcaatGctgctgtcttcttgctatga	6	15	10	10	1	2	1	0	1	2	0	2	1	2	1	0	1	5	6	0	1	2	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:32305751G>T	ENST00000357033.4	-	43	6391	c.6185C>A	c.(6184-6186)gCa>gAa	p.A2062E	DMD_ENST00000378677.2_Missense_Mutation_p.A2058E	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2062					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ACTTTGCAATGCTGCTGTCTT	0.368																																					p.A2062E		.											.	DMD-265	0			c.C6185A						.						131	105	114					X																	32305751		2202	4300	6502	SO:0001583	missense	1756	exon43			TGCAATGCTGCTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"muscular dystrophy, Duchenne and Becker types"	300377	"dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272", "mental retardation, X-linked 85"	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6185C>A	X.37:g.32305751G>T	ENSP00000354923:p.Ala2062Glu	Somatic	31	0		WXS	Illumina HiSeq	Phase_I	29	28	NM_004006	0	0	0	0	0	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	8.237	0.805865	0.16467	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.35048	1.33;1.33	4.36	2.59	0.31030	.	0.000000	0.36778	U	0.002408	T	0.28830	0.0715	L	0.53249	1.67	0.80722	D	1	B;P;B;B;B	0.38677	0.275;0.642;0.322;0.259;0.44	B;B;B;B;B	0.34418	0.088;0.182;0.144;0.138;0.096	T	0.05835	-1.0861	10	0.72032	D	0.01	.	7.2118	0.25937	0.3674:0.0:0.6326:0.0	.	2054;2062;2058;721;718	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	E	2054;721;718;2058;2062;2062;1939	ENSP00000367948:A2058E;ENSP00000354923:A2062E	ENSP00000354923:A2062E	A	-	2	0	DMD	32215672	0.996000	0.38824	0.224000	0.23877	0.172000	0.22775	2.060000	0.41394	0.416000	0.25844	-0.191000	0.12829	GCA	.		0.368	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32305751	G	T	32305751	3	4	157	1	0	0	0	0	1	0	0	0	4591	1319	46	4	5168	4	DMD	23	32305751	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	18543204	32305751	122964809	188	14343											
BMP15	9210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	50658768	50658768	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttctgcaggtacctggcatAtacagatcctgggctttcct	7	13	9	12	0	1	1	0	0	1	1	3	1	3	1	3	3	3	4	3	3	3	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:50658768A>T	ENST00000252677.3	+	2	340	c.340A>T	c.(340-342)Ata>Tta	p.I114L		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	114					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					TACCTGGCATATACAGATCCT	0.438																																					p.I114L		.											.	BMP15-132	0			c.A340T						.						95	90	91					X																	50658768		2203	4299	6502	SO:0001583	missense	9210	exon2			TGGCATATACAGA	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"Bone morphogenetic proteins"	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.340A>T	X.37:g.50658768A>T	ENSP00000252677:p.Ile114Leu	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	113	108	NM_005448	0	0	0	0	0	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	37	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	a	2.291	-0.362548	0.05103	.	.	ENSG00000130385	ENST00000252677	T	0.77489	-1.1	5.42	-3.73	0.04398	.	1.153060	0.05985	N	0.645013	T	0.69006	0.3063	M	0.65975	2.015	0.09310	N	1	B	0.19583	0.037	B	0.16289	0.015	T	0.49214	-0.8963	10	0.10377	T	0.69	.	6.9598	0.24591	0.3592:0.0:0.4995:0.1413	.	114	O95972	BMP15_HUMAN	L	114	ENSP00000252677:I114L	ENSP00000252677:I114L	I	+	1	0	BMP15	50675508	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.129000	0.10515	-0.754000	0.04715	-0.670000	0.03821	ATA	.		0.438	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		T	50658768	A	T	50658768	3	4	157	1	0	0	0	0	1	0	0	0	1459	449	16	5	346	5	BMP15	23	50658768	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	18353017	50658768	104611792	189	14344											
UBQLN2	29978	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	56592091	56592092	+	Frame_Shift_Del	DEL	AA	AA	-																															ctcaacgcaatggggttcttAaaccgtgaagcaaacttgca																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:56592091_56592092delAA	ENST00000338222.5	+	1	2066_2067	c.1785_1786delAA	c.(1783-1788)ttaaacfs	p.N596fs		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	596	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						TGGGGTTCTTAAACCGTGAAGC	0.515																																					p.595_596del	Esophageal Squamous(104;218 1492 6022 10838 28884)	.											.	UBQLN2-131	0			c.1785_1786del						.																																			SO:0001589	frameshift_variant	29978	exon1			.	AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"Ubiquilin family"	12509	protein-coding gene	gene with protein product	"NEDD4 binding protein 4"	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.1785_1786delAA	X.37:g.56592091_56592092delAA	ENSP00000345195:p.Asn596fs	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	167	146	NM_013444	0	0	0	0	0	O94798|Q5D027|Q9H3W6|Q9HAZ4	Frame_Shift_Del	DEL	ENST00000338222.5	37	CCDS14374.1																																																																																			.		0.515	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		-	56592092	AA	-	56592091	7	5	157	1	0	1	0	1	0	0	0	0	16930	359	13	0	1787	0	UBQLN2	23	56592091	Frame_Shift_Del	DEL	AA	TCGA-P4-A5EB-01A-11D-A28G-10	5933323	56592091	98678469	190	14345											
UPRT	139596	hgsc.bcm.edu;bcgsc.ca	37	chrX	74494317	74494318	+	Frame_Shift_Del	DEL	AG	AG	-																															ggcggctccagcctcaactcAgagggcaacagtggtagtgg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:74494317_74494318delAG	ENST00000373383.4	+	1	395_396	c.228_229delAG	c.(226-231)tcagagfs	p.E77fs	UPRT_ENST00000531704.1_3'UTR|UPRT_ENST00000373379.1_Frame_Shift_Del_p.E77fs|UPRT_ENST00000530743.1_5'Flank	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	77					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						GCCTCAACTCAGAGGGCAACAG	0.639																																					p.76_77del		.											.	UPRT-130	0			c.228_229del						.																																			SO:0001589	frameshift_variant	139596	exon1			.	BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.228_229delAG	X.37:g.74494319_74494320delAG	ENSP00000362481:p.Glu77fs	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	146	23	NM_145052	0	0	0	0	0	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Frame_Shift_Del	DEL	ENST00000373383.4	37	CCDS14429.1																																																																																			.		0.639	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052		-	74494318	AG	-	74494317	7	5	157	1	0	1	0	1	0	0	0	0	17047	175	7	0	230	0	UPRT	23	74494317	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EB-01A-11D-A28G-10	17902226	74494317	80776243	191	14346											
ATRX	546	bcgsc.ca	37	chrX	76777834	76777834	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgacagggggtaaattggtCccagttggtatgttgaaacg	10	11	14	6	1	0	2	0	2	0	0	1	2	1	2	1	4	1	4	1	4	4	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:76777834C>A	ENST00000373344.5	-	32	7096	c.6882G>T	c.(6880-6882)ggG>ggT	p.G2294G	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Silent_p.G2256G	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2294					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						GTAAATTGGTCCCAGTTGGTA	0.388			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.G2294G				Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	ATRX-248	0			c.G6882T						.						90	85	87					X																	76777834		2203	4296	6499	SO:0001819	synonymous_variant	546	exon32			ATTGGTCCCAGTT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"RAD54 homolog (S. cerevisiae)"	300032	"alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)", "Juberg-Marsidi syndrome"	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6882G>T	X.37:g.76777834C>A		Somatic	101	3		WXS	Illumina HiSeq	Phase_1	118	106	NM_000489	0	0	0	25	25	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Silent	SNP	ENST00000373344.5	37	CCDS14434.1																																																																																			.		0.388	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		A	76777834	C	A	76777834	2	1	157	1	0	0	0	0	0	0	0	1	1209	842	30	4		4	ATRX	23	76777834	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	2283517	76777834	78492726	192	14347											
TNFRSF25	8718	broad.mit.edu	37	chr1	6522060	6522060	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgatgtcccttaccaagagCtctgctgggcaactggtccc	7	10	10	14	0	1	2	0	1	1	1	3	2	3	2	3	2	4	3	3	2	3	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr1:6522060C>A	ENST00000356876.3	-	9	1006	c.919G>T	c.(919-921)Gct>Tct	p.A307S	TNFRSF25_ENST00000348333.3_Missense_Mutation_p.A262S|TNFRSF25_ENST00000377782.3_Missense_Mutation_p.A316S|TNFRSF25_ENST00000351748.3_Missense_Mutation_p.A124S|TNFRSF25_ENST00000461703.2_5'Flank|TNFRSF25_ENST00000351959.5_Missense_Mutation_p.A270S	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	307					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		TTACCAAGAGCTCTGCTGGGC	0.607																																					p.A316S													.	TNFRSF25-714	0			c.G946T						.						70	68	69					1																	6522060		2203	4300	6503	SO:0001583	missense	8718	exon9			CAAGAGCTCTGCT	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"Tumor necrosis factor receptor superfamily"	11910	protein-coding gene	gene with protein product		603366	"tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.919G>T	1.37:g.6522060C>A	ENSP00000349341:p.Ala307Ser	Somatic	66	1		WXS	Illumina HiSeq	Phase_I	77	6	NM_148965	0	0	0	0	0	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Missense_Mutation	SNP	ENST00000356876.3	37	CCDS71.1	.	.	.	.	.	.	.	.	.	.	C	9.902	1.207079	0.22205	.	.	ENSG00000215788	ENST00000356876;ENST00000377782;ENST00000351959;ENST00000351748;ENST00000348333	D;D;D;T;D	0.92699	-2.92;-3.09;-2.98;2.53;-2.01	4.71	2.8	0.32819	.	529.136000	0.00541	U	0.000220	D	0.89901	0.6849	M	0.65975	2.015	0.23685	N	0.997118	B;B;B;B;B;P	0.43938	0.138;0.112;0.228;0.04;0.138;0.822	B;B;B;B;B;B	0.38264	0.044;0.032;0.121;0.02;0.044;0.269	T	0.74337	-0.3698	10	0.13470	T	0.59	-0.2417	6.9581	0.24582	0.0:0.7774:0.0:0.2226	.	316;262;270;307;308;124	Q93038-11;Q93038-9;Q93038-10;Q93038;Q93038-2;Q93038-8	.;.;.;TNR25_HUMAN;.;.	S	307;316;270;124;262	ENSP00000349341:A307S;ENSP00000367013:A316S;ENSP00000337713:A270S;ENSP00000326762:A124S;ENSP00000314451:A262S	ENSP00000314451:A262S	A	-	1	0	TNFRSF25	6444647	0.001000	0.12720	0.902000	0.35471	0.897000	0.52465	-0.227000	0.09126	0.476000	0.27440	0.655000	0.94253	GCT	.		0.607	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965		A	6522060	C	A	6522060	3	1	158	1	0	0	0	0	1	0	0	0	16328	797	28	4	342	4	TNFRSF25	1	6522060	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		6522060	242728561	1	14348											
DCLRE1B	64858	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	114454514	114454514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccccactgggattttcagtgCacttaaggtctacagatgag	10	11	10	10	0	2	2	1	1	1	1	2	3	2	3	2	2	2	1	2	2	2	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr1:114454514C>T	ENST00000369563.3	+	4	1746	c.1300C>T	c.(1300-1302)Cac>Tac	p.H434Y	DCLRE1B_ENST00000466480.1_Intron	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	434					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTTTCAGTGCACTTAAGGTC	0.473								Other identified genes with known or suspected DNA repair function																													p.H434Y		.											.	DCLRE1B-227	0			c.C1300T						.						168	186	180					1																	114454514		2203	4300	6503	SO:0001583	missense	64858	exon4			TCAGTGCACTTAA	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"APOLLO", "PSO2 homolog (S. cerevisiae)"	609683	"DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.1300C>T	1.37:g.114454514C>T	ENSP00000358576:p.His434Tyr	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	134	18	NM_022836	0	0	4	4	0	Q9H9E5	Missense_Mutation	SNP	ENST00000369563.3	37	CCDS866.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.075166	0.55646	.	.	ENSG00000118655	ENST00000369563	T	0.75260	-0.92	5.75	2.18	0.27775	.	1.219440	0.05575	N	0.571775	T	0.42086	0.1187	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.42241	-0.9463	10	0.66056	D	0.02	-11.1736	5.1932	0.15220	0.2671:0.6065:0.0:0.1264	.	434	Q9H816	DCR1B_HUMAN	Y	434	ENSP00000358576:H434Y	ENSP00000358576:H434Y	H	+	1	0	DCLRE1B	114256037	0.002000	0.14202	0.004000	0.12327	0.624000	0.37722	0.606000	0.24194	1.186000	0.42985	0.655000	0.94253	CAC	.		0.473	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836		T	114454514	C	T	114454514	3	4	158	1	0	0	0	0	1	0	0	0	4301	710	25	2	1314	2	DCLRE1B	1	114454514	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	107932454	114454514	134796107	2	14349											
ACP6	51205	broad.mit.edu	37	chr1	147142085	147142085	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcagctcggccagggccAcccgccgctggtgcaggcag	5	4	15	17	3	0	0	0	0	0	0	1	0	0	0	5	4	3	5	5	4	0	0	rs201678741		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr1:147142085A>C	ENST00000369238.6	-	1	533	c.86T>G	c.(85-87)gTg>gGg	p.V29G	ACP6_ENST00000392988.2_Missense_Mutation_p.V29G	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	29					dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					GGCCAGGGCCACCCGCCGCTG	0.657																																					p.V29G													.	ACP6-94	0			c.T86G						.						12	10	11					1																	147142085		2053	4027	6080	SO:0001583	missense	51205	exon1			AGGGCCACCCGCC	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.86T>G	1.37:g.147142085A>C	ENSP00000358241:p.Val29Gly	Somatic	33	7		WXS	Illumina HiSeq	Phase_I	151	41	NM_016361	0	0	1	1	0	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Missense_Mutation	SNP	ENST00000369238.6	37	CCDS928.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.149393	0.37923	.	.	ENSG00000162836	ENST00000369238;ENST00000392988	T;T	0.48522	2.65;0.81	5.28	-5.16	0.02857	.	0.609019	0.16327	N	0.219309	T	0.09555	0.0235	L	0.34521	1.04	0.43385	D	0.99549	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.22730	-1.0208	10	0.19147	T	0.46	.	1.0577	0.01593	0.2021:0.3491:0.2212:0.2275	.	29;29	Q9NPH0-2;Q9NPH0	.;PPA6_HUMAN	G	29	ENSP00000358241:V29G;ENSP00000376714:V29G	ENSP00000358241:V29G	V	-	2	0	ACP6	145608709	0.001000	0.12720	0.927000	0.36925	0.947000	0.59692	-0.635000	0.05471	-0.919000	0.03803	-0.460000	0.05396	GTG	.		0.657	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361		C	147142085	A	C	147142085	3	2	158	1	0	0	0	0	1	0	0	0	165	159	6	5	1240	5	ACP6	1	147142085	Missense_Mutation	SNP	A	TCGA-P4-A5ED-01A-11D-A28G-10	32687571	147142085	102108536	3	14350											
MTA3	57504	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	42886918	42886918	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagtgctgttgggacattCgccagagccctggattgcag	7	11	13	10	1	1	1	1	0	0	1	2	3	1	3	2	2	3	3	2	2	0	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr2:42886918C>A	ENST00000405094.1	+	8	618	c.618C>A	c.(616-618)ttC>ttA	p.F206L	MTA3_ENST00000407270.3_Missense_Mutation_p.F206L|MTA3_ENST00000405592.1_Missense_Mutation_p.F150L|MTA3_ENST00000406652.1_Missense_Mutation_p.F150L|MTA3_ENST00000406911.1_Missense_Mutation_p.F206L			Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	206	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.					intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						TTGGGACATTCGCCAGAGCCC	0.413																																					p.F206L		.											.	MTA3-24	0			c.C618A						.						78	70	72					2																	42886918		1938	4145	6083	SO:0001583	missense	57504	exon8			GACATTCGCCAGA	AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935		"GATA zinc finger domain containing"	23784	protein-coding gene	gene with protein product		609050	"metastasis associated gene family, member 3"			12705869, 14613024	Standard	NM_001282755		Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000405094.1:c.618C>A	2.37:g.42886918C>A	ENSP00000385823:p.Phe206Leu	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	84	5	NM_020744	0	0	5	5	0	Q9NSP2|Q9ULF4	Missense_Mutation	SNP	ENST00000405094.1	37		.	.	.	.	.	.	.	.	.	.	C	16.73	3.205367	0.58234	.	.	ENSG00000057935	ENST00000405592;ENST00000406652;ENST00000407270;ENST00000282366;ENST00000406911;ENST00000405094	T;T;T;T;T	0.54866	0.55;0.55;0.61;0.59;0.57	4.96	-7.42	0.01388	.	0.000000	0.85682	D	0.000000	T	0.72645	0.3486	M	0.88105	2.93	0.50171	D	0.999857	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.988;0.994;0.999	T	0.80522	-0.1345	10	0.54805	T	0.06	-18.0256	20.3549	0.98835	0.0:0.0897:0.0:0.9103	.	206;206;150	E7EQY4;Q9BTC8-2;D6W5A2	.;.;.	L	150;150;206;206;206;206	ENSP00000383973:F150L;ENSP00000384249:F150L;ENSP00000385045:F206L;ENSP00000385241:F206L;ENSP00000385823:F206L	ENSP00000282366:F206L	F	+	3	2	MTA3	42740422	0.997000	0.39634	0.147000	0.22382	0.489000	0.33432	0.317000	0.19487	-1.514000	0.01786	-0.252000	0.11476	TTC	.		0.413	MTA3-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318159.1	NM_020744		A	42886918	C	A	42886918	3	1	158	1	0	0	0	0	1	0	0	0	9935	883	31	4	648	4	MTA3	2	42886918	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		42886918	200312455	4	14351											
WDSUB1	151525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	160139417	160139417	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacagcagcagtggacagcaTaggtatgaaacttcaatgga	16	7	11	7	0	1	1	1	1	0	0	1	3	1	3	0	3	5	4	0	3	5	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr2:160139417T>C	ENST00000409990.3	-	2	420	c.164A>G	c.(163-165)tAt>tGt	p.Y55C	WDSUB1_ENST00000392796.3_Missense_Mutation_p.Y55C|WDSUB1_ENST00000359774.4_Missense_Mutation_p.Y55C|WDSUB1_ENST00000358147.4_Missense_Mutation_p.Y55C|WDSUB1_ENST00000409124.1_Missense_Mutation_p.Y55C	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	55							ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						GTGGACAGCATAGGTATGAAA	0.443																																					p.Y55C		.											.	WDSUB1-90	0			c.A164G						.						138	135	136					2																	160139417		2203	4300	6503	SO:0001583	missense	151525	exon2			ACAGCATAGGTAT	AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"WD repeat domain containing", "Sterile alpha motif (SAM) domain containing", "U-box domain containing"	26697	protein-coding gene	gene with protein product			"WD repeat and SAM domain containing 1", "WD repeat, SAM and U-box domain containing 1"	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.164A>G	2.37:g.160139417T>C	ENSP00000387078:p.Tyr55Cys	Somatic	243	0		WXS	Illumina HiSeq	Phase_I	261	27	NM_152528	0	0	0	1	1	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360032	0.82353	.	.	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990;ENST00000409124	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74359	0.3706	M	0.69185	2.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.76353	-0.2990	10	0.56958	D	0.05	.	15.6902	0.77446	0.0:0.0:0.0:1.0	.	55;55;55	Q8N9V3-2;B8ZZF2;Q8N9V3	.;.;WSDU1_HUMAN	C	55	ENSP00000352820:Y55C;ENSP00000350866:Y55C;ENSP00000376545:Y55C;ENSP00000387078:Y55C;ENSP00000386891:Y55C	ENSP00000350866:Y55C	Y	-	2	0	WDSUB1	159847663	1.000000	0.71417	0.989000	0.46669	0.987000	0.75469	7.910000	0.87451	2.115000	0.64714	0.528000	0.53228	TAT	.		0.443	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528		C	160139417	T	C	160139417	3	2	158	1	0	0	0	0	1	0	0	0	17374	1406	49	3	1306	3	WDSUB1	2	160139417	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	117252499	160139417	83059956	5	14352											
SF3B1	23451	ucsc.edu	37	chr2	198270048	198270048	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggttttaaaaatggaagaTttccagatggctggtcatta	13	13	10	5	0	1	2	1	0	0	2	2	3	2	3	1	4	0	2	1	4	5	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr2:198270048T>C	ENST00000335508.6	-	10	1479	c.1388A>G	c.(1387-1389)aAt>aGt	p.N463S	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	463	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AAATGGAAGATTTCCAGATGG	0.343			Mis		myelodysplastic syndrome																																p.N463S				Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1-140	0			c.A1388G						.						53	56	55					2																	198270048		2203	4300	6503	SO:0001583	missense	23451	exon10			GGAAGATTTCCAG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"splicing factor 3b, subunit 1, 155kD"			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1388A>G	2.37:g.198270048T>C	ENSP00000335321:p.Asn463Ser	Somatic	136	0		WXS	Illumina HiSeq		185	1	NM_012433	0	0	0	5	5	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.663572	0.47572	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.26666	0.0652	N	0.01109	-1.01	0.80722	D	1	B	0.09022	0.002	B	0.14023	0.01	T	0.13953	-1.0490	9	0.41790	T	0.15	.	15.7937	0.78388	0.0:0.0:0.0:1.0	.	463	O75533	SF3B1_HUMAN	S	463	.	ENSP00000335321:N463S	N	-	2	0	SF3B1	197978293	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.883000	0.87264	2.188000	0.69820	0.533000	0.62120	AAT	.		0.343	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198270048	T	C	198270048	3	2	158	1	0	0	0	0	1	0	0	0	14181	1493	52	3	2590	3	SF3B1	2	198270048	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	38130631	198270048	44929325	6	14353											
ING5	84289	broad.mit.edu	37	chr2	242664404	242664404	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgcgcctttcttgtcacagGttctgtccacggtgtgtcca	4	14	10	13	2	3	0	1	0	2	0	5	0	5	0	3	2	1	1	3	2	0	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr2:242664404G>T	ENST00000313552.6	+	8	707	c.681G>T	c.(679-681)tgG>tgT	p.W227C	AC114730.11_ENST00000435195.1_RNA	NM_032329.4	NP_115705.2	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5	227					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|skin(1)	3		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		CTTGTCACAGGTTCTGTCCAC	0.622																																					p.W227C													.	.	0			c.G681T						.						104	100	102					2																	242664404		2203	4296	6499	SO:0001630	splice_region_variant	84289	exon8			TCACAGGTTCTGT	AF189286	CCDS33425.1	2q37.3	2013-01-28			ENSG00000168395	ENSG00000168395		"Zinc fingers, PHD-type"	19421	protein-coding gene	gene with protein product		608525				12750254	Standard	NM_032329		Approved	FLJ23842, p28ING5	uc002wcd.3	Q8WYH8	OTTHUMG00000151501	ENST00000313552.6:c.681-1G>T	2.37:g.242664404G>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	114	5	NM_032329	0	0	0	0	0	A8K1P3|Q53NU6|Q57Z54|Q9BS30	Missense_Mutation	SNP	ENST00000313552.6	37	CCDS33425.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039152	0.75617	.	.	ENSG00000168395	ENST00000313552	D	0.92348	-3.02	4.8	4.8	0.61643	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	U	0.000000	D	0.98112	0.9377	H	0.99820	4.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99327	1.0908	9	.	.	.	.	15.0483	0.71844	0.0:0.0:1.0:0.0	.	227	Q8WYH8	ING5_HUMAN	C	227	ENSP00000322142:W227C	.	W	+	3	0	ING5	242313077	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	6.130000	0.71663	2.217000	0.71921	0.551000	0.68910	TGG	.		0.622	ING5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322901.3	NM_032329	Missense_Mutation	T	242664404	G	T	242664404	5	4	158	1	0	0	0	0	0	0	1	0	7760	1275	44	4	711	4	ING5	2	242664404	Splice_Site	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	44394356	242664404	534969	7	14354											
C3orf39	84892	broad.mit.edu	37	chr3	43121560	43121560	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtatggtttgaatgagggacGggatgtccaccttggtgtcc	7	12	15	7	1	0	2	0	2	0	0	2	4	2	4	3	4	0	2	3	4	2	3	rs368757710		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr3:43121560G>A	ENST00000344697.2	-	2	1709	c.1364C>T	c.(1363-1365)cCg>cTg	p.P455L	POMGNT2_ENST00000441964.1_Missense_Mutation_p.P455L	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	455					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										AATGAGGGACGGGATGTCCAC	0.612																																					p.P455L													.	.	0			c.C1364T						.	G	LEU/PRO	0,4406		0,0,2203	40	40	40		1364	4.6	0.3	3		40	1,8599	1.2+/-3.3	0,1,4299	no	missense	C3orf39	NM_032806.4	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	455/581	43121560	1,13005	2203	4300	6503	SO:0001583	missense	84892	exon2			AGGGACGGGATGT	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"chromosome 3 open reading frame 39", "glycosyltransferase-like domain containing 2"	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1364C>T	3.37:g.43121560G>A	ENSP00000344125:p.Pro455Leu	Somatic	140	0		WXS	Illumina HiSeq	Phase_I	145	3	NM_032806	0	0	0	0	0	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514589	0.44763	0.0	1.16E-4	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.78003	-1.14;-1.14	5.53	4.56	0.56223	.	0.180058	0.49916	D	0.000134	T	0.77505	0.4140	M	0.78456	2.415	0.58432	D	0.999992	B	0.22003	0.063	B	0.19148	0.024	T	0.75091	-0.3440	10	0.52906	T	0.07	-28.5664	13.1243	0.59344	0.083:0.0:0.917:0.0	.	455	Q8NAT1	AGO61_HUMAN	L	455	ENSP00000408992:P455L;ENSP00000344125:P455L	ENSP00000344125:P455L	P	-	2	0	C3orf39	43096564	1.000000	0.71417	0.317000	0.25265	0.982000	0.71751	5.425000	0.66470	1.184000	0.42957	0.650000	0.86243	CCG	.		0.612	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806		A	43121560	G	A	43121560	3	1	158	1	0	0	0	0	1	0	0	0	2235	1116	39	1	382	1	C3orf39	3	43121560	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		43121560	154900870	8	14355											
ETV5	2119	broad.mit.edu	37	chr3	185797720	185797720	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaggctctggaagcgaaTggggggcgggggcggggccc	5	4	22	10	3	1	0	0	0	1	0	2	2	2	1	2	9	1	1	2	9	2	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr3:185797720T>G	ENST00000306376.5	-	7	782	c.536A>C	c.(535-537)cAt>cCt	p.H179P	ETV5_ENST00000434744.1_Missense_Mutation_p.H179P|ETV5_ENST00000537818.1_Missense_Mutation_p.H221P|ETV5-AS1_ENST00000453370.1_RNA	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	179					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)			TGGAAGCGAATGGGGGGCGGG	0.617			T	"TMPRSS2, SCL45A3"	Prostate																																p.H179P				Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5-706	0			c.A536C						.						54	61	59					3																	185797720		2203	4300	6503	SO:0001583	missense	2119	exon7			AGCGAATGGGGGG	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.536A>C	3.37:g.185797720T>G	ENSP00000306894:p.His179Pro	Somatic	63	6		WXS	Illumina HiSeq	Phase_I	51	8	NM_004454	0	0	0	0	0	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	37	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.509461	0.27036	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	T;T;T	0.10860	2.86;2.86;2.83	5.32	5.32	0.75619	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.445754	0.24894	N	0.034741	T	0.12135	0.0295	N	0.25647	0.755	0.44123	D	0.996905	B;D	0.54207	0.0;0.965	B;P	0.49451	0.001;0.611	T	0.15206	-1.0445	10	0.28530	T	0.3	.	12.7886	0.57520	0.0:0.0:0.0:1.0	.	179;221	P41161;B7Z7D7	ETV5_HUMAN;.	P	179;179;221	ENSP00000306894:H179P;ENSP00000413755:H179P;ENSP00000441737:H221P	ENSP00000306894:H179P	H	-	2	0	ETV5	187280414	0.997000	0.39634	0.611000	0.29010	0.524000	0.34500	3.006000	0.49529	2.009000	0.58944	0.460000	0.39030	CAT	.		0.617	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		G	185797720	T	G	185797720	3	3	158	1	0	0	0	0	1	0	0	0	5295	1464	51	5	1024	5	ETV5	3	185797720	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	142676160	185797720	12224710	9	14356											
DOK7	285489	broad.mit.edu	37	chr4	3494664	3494664	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtgggtgcctcaaggccAccccccaagccgctgcgtcc	6	6	12	17	2	1	0	1	0	0	0	2	0	2	0	7	3	3	1	7	3	2	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr4:3494664A>C	ENST00000340083.5	+	7	1016	c.951A>C	c.(949-951)ccA>ccC	p.P317P	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Silent_p.P317P	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	317	Ser-rich.				neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCTCAAGGCCACCCCCCAAGC	0.692																																					p.P317P													.	DOK7-91	0			c.A951C						.						7	8	7					4																	3494664		2122	4167	6289	SO:0001819	synonymous_variant	285489	exon7			AAGGCCACCCCCC	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"chromosome 4 open reading frame 25"	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.951A>C	4.37:g.3494664A>C		Somatic	30	2		WXS	Illumina HiSeq	Phase_I	134	39	NM_173660	0	0	0	0	0	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																			.		0.692	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660		C	3494664	A	C	3494664	2	2	158	1	0	0	0	0	0	0	0	1	4713	146	6	5		5	DOK7	4	3494664	Silent	SNP	A	TCGA-P4-A5ED-01A-11D-A28G-10		3494664	187659612	10	14357											
BST1	683	hgsc.bcm.edu	37	chr4	15704874	15704874	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggcgcgcgcgcggtggcgcgGggagggcaccagcgcacact	5	2	20	14	8	0	0	0	0	0	0	0	1	0	1	1	6	1	2	1	6	0	0	rs2302468	byFrequency	TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr4:15704874G>C	ENST00000265016.4	+	1	302	c.107G>C	c.(106-108)gGg>gCg	p.G36A	BST1_ENST00000382346.3_Missense_Mutation_p.G36A	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	36				G -> A (in Ref. 1; BAA04885). {ECO:0000305}.	humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						cggtggcgcggggAGGGCACC	0.736													G|||	381	0.0760783	0.0212	0.0389	5008	,	,		9714	0.2103		0.008	False		,,,				2504	0.1084				p.G36A		.											.	BST1-90	0			c.G107C						.	G	ALA/GLY	23,3787		0,23,1882	3	4	4		107	3.4	1	4	dbSNP_100	4	19,7693		0,19,3837	no	missense	BST1	NM_004334.2	60	0,42,5719	CC,CG,GG		0.2464,0.6037,0.3645	possibly-damaging	36/319	15704874	42,11480	1905	3856	5761	SO:0001583	missense	683	exon1			GGCGCGGGGAGGG	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"CD molecules"	1118	protein-coding gene	gene with protein product	"NAD(+) nucleosidase", "ADP-ribosyl cyclase 2"	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.107G>C	4.37:g.15704874G>C	ENSP00000265016:p.Gly36Ala	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	18	7	NM_004334	0	0	0	0	0	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	141	0.06456043956043957	13	0.026422764227642278	10	0.027624309392265192	112	0.1958041958041958	6	0.0079155672823219	G	14.40	2.524166	0.44866	0.006037	0.002464	ENSG00000109743	ENST00000265016;ENST00000382346	T;T	0.17370	2.28;2.28	3.39	3.39	0.38822	.	0.510528	0.20699	N	0.087320	T	0.00039	0.0001	M	0.63843	1.955	0.36618	P	0.12441999999999998	D	0.76494	0.999	D	0.80764	0.994	T	0.04005	-1.0985	9	0.62326	D	0.03	-9.3919	10.4016	0.44233	0.0:0.0:1.0:0.0	rs2302468	36	Q10588	BST1_HUMAN	A	36	ENSP00000265016:G36A;ENSP00000371783:G36A	ENSP00000265016:G36A	G	+	2	0	BST1	15313972	0.859000	0.29813	0.955000	0.39395	0.020000	0.10135	2.992000	0.49417	1.879000	0.54435	0.462000	0.41574	GGG	G|0.084;C|0.916		0.736	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334		C	15704874	G	C	15704874	3	2	158	1	0	0	0	0	1	0	0	0	1536	1232	43	4	109	4	BST1	4	15704874	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	12210210	15704874	175449402	11	14358											
WDFY3	23001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	85675021	85675021	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagatccctcttcttctgaTtgccaaggctgttatgggga	8	13	10	10	0	3	2	0	1	3	1	4	3	4	3	2	3	1	2	2	3	3	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr4:85675021T>C	ENST00000295888.4	-	35	5975	c.5568A>G	c.(5566-5568)caA>caG	p.Q1856Q	WDFY3_ENST00000322366.6_Silent_p.Q1856Q	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1856					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CTTCTTCTGATTGCCAAGGCT	0.403																																					p.Q1856Q		.											.	WDFY3-93	0			c.A5568G						.						89	80	83					4																	85675021		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon35			TTCTGATTGCCAA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"Zinc fingers, FYVE domain containing", "WD repeat domain containing"	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.5568A>G	4.37:g.85675021T>C		Somatic	127	0		WXS	Illumina HiSeq	Phase_I	145	39	NM_014991	0	0	0	0	0	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1																																																																																			.		0.403	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85675021	T	C	85675021	2	2	158	1	0	0	0	0	0	0	0	1	17303	1490	52	3		3	WDFY3	4	85675021	Silent	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	69970147	85675021	105479255	12	14359											
MTRR	4552	broad.mit.edu	37	chr5	7878351	7878351	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcctcacttacccgttcggtAcccccactctcacaagcctc	7	10	4	20	2	2	0	2	0	1	0	6	0	3	0	5	1	3	2	5	1	3	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr5:7878351A>C	ENST00000264668.2	+	5	807	c.777A>C	c.(775-777)gtA>gtC	p.V259V	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Silent_p.V232V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	259	Hinge.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	CCCGTTCGGTACCCCCACTCT	0.443																																					p.V259V													.	MTRR-91	0			c.A777C						.						130	134	133					5																	7878351		2203	4300	6503	SO:0001819	synonymous_variant	4552	exon5			TTCGGTACCCCCA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.777A>C	5.37:g.7878351A>C		Somatic	99	16		WXS	Illumina HiSeq	Phase_I	96	12	NM_024010	0	0	2	2	0	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			.		0.443	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			C	7878351	A	C	7878351	2	2	158	1	0	0	0	0	0	0	0	1	9986	378	14	5		5	MTRR	5	7878351	Silent	SNP	A	TCGA-P4-A5ED-01A-11D-A28G-10		7878351	173036909	13	14360											
SNX2	6643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	122154607	122154607	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagagctttgtctcagctTgcagaggttgaggagaagat	10	12	13	6	0	2	5	1	1	2	4	3	6	2	5	0	2	3	4	0	2	2	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr5:122154607T>G	ENST00000379516.2	+	11	1209	c.1101T>G	c.(1099-1101)ctT>ctG	p.L367L	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Silent_p.L250L	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	367					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		TGTCTCAGCTTGCAGAGGTTG	0.393																																					p.L367L		.											.	SNX2-226	0			c.T1101G						.						124	117	119					5																	122154607		2203	4300	6503	SO:0001819	synonymous_variant	6643	exon11			TCAGCTTGCAGAG	AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1101T>G	5.37:g.122154607T>G		Somatic	100	0		WXS	Illumina HiSeq	Phase_I	123	7	NM_003100	0	0	14	19	5	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Silent	SNP	ENST00000379516.2	37	CCDS34217.1																																																																																			.		0.393	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		G	122154607	T	G	122154607	2	3	158	1	0	0	0	0	0	0	0	1	14923	1799	63	5		5	SNX2	5	122154607	Silent	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	114276256	122154607	58760653	14	14361											
ARHGAP26	23092	broad.mit.edu	37	chr5	142281554	142281554	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atcaccatggttacgaactgGccaaggatttcggggacttc	10	10	11	10	2	1	0	1	0	0	0	3	3	1	2	2	5	2	1	2	5	3	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr5:142281554G>A	ENST00000274498.4	+	7	1030	c.652G>A	c.(652-654)Gcc>Acc	p.A218T	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.A218T	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	218					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTACGAACTGGCCAAGGATTT	0.443																																					p.A218T													.	ARHGAP26-660	0			c.G652A						.						161	138	146					5																	142281554		2203	4300	6503	SO:0001583	missense	23092	exon7			GAACTGGCCAAGG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.652G>A	5.37:g.142281554G>A	ENSP00000274498:p.Ala218Thr	Somatic	224	0		WXS	Illumina HiSeq	Phase_I	233	4	NM_015071	0	0	0	0	0	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	37	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135201	0.94517	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.04275	3.66;3.66	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.19287	0.0463	M	0.66506	2.035	0.80722	D	1	D;P	0.63880	0.993;0.729	D;P	0.67103	0.949;0.544	T	0.01334	-1.1382	10	0.21540	T	0.41	.	19.6157	0.95633	0.0:0.0:1.0:0.0	.	218;218	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	T	218	ENSP00000274498:A218T;ENSP00000367243:A218T	ENSP00000274498:A218T	A	+	1	0	ARHGAP26	142261738	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.739000	0.93911	0.563000	0.77884	GCC	.		0.443	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		A	142281554	G	A	142281554	3	1	158	1	0	0	0	0	1	0	0	0	875	1203	42	2	678	2	ARHGAP26	5	142281554	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	20126947	142281554	38633706	15	14362											
NKX2-5	1482	broad.mit.edu	37	chr5	172659730	172659730	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaaggcccggcggggtaagCggcagtgcagctgtagccag	8	4	19	10	3	0	0	0	0	0	0	0	1	0	1	2	6	4	5	2	6	3	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr5:172659730C>A	ENST00000329198.4	-	2	1090	c.817G>T	c.(817-819)Gct>Tct	p.A273S		NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	273	Ala/Pro-rich.				adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCGGGGTAAGCGGCAGTGCAG	0.672																																					p.A273S	Esophageal Squamous(72;810 1219 2387 13420 44943)												.	NKX2-5-90	0			c.G817T						.						11	13	12					5																	172659730		2196	4286	6482	SO:0001583	missense	1482	exon2			GGTAAGCGGCAGT	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.817G>T	5.37:g.172659730C>A	ENSP00000327758:p.Ala273Ser	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	224	13	NM_004387	0	0	0	0	0	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	.	.	.	.	.	.	.	.	.	.	C	6.919	0.539183	0.13250	.	.	ENSG00000183072	ENST00000329198	D	0.89810	-2.57	4.07	4.07	0.47477	.	.	.	.	.	T	0.70535	0.3235	N	0.02960	-0.455	0.80722	D	1	B	0.25743	0.133	B	0.19391	0.025	T	0.68062	-0.5508	9	0.06625	T	0.88	.	11.6143	0.51080	0.0:1.0:0.0:0.0	.	273	P52952	NKX25_HUMAN	S	273	ENSP00000327758:A273S	ENSP00000327758:A273S	A	-	1	0	NKX2-5	172592336	0.895000	0.30542	0.787000	0.31911	0.085000	0.17905	1.416000	0.34759	2.083000	0.62718	0.542000	0.68232	GCT	.		0.672	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			A	172659730	C	A	172659730	3	1	158	1	0	0	0	0	1	0	0	0	10479	768	27	4	161	4	NKX2-5	5	172659730	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	30378176	172659730	8255530	16	14363											
SERPINB6	5269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	2955761	2955761	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gagcaagtatgacttactgaGaggaaatcacaagacttttc	15	10	9	7	0	1	3	1	2	0	2	2	6	1	4	0	1	2	2	0	1	5	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr6:2955761G>C	ENST00000380520.1	-	2	2303	c.309C>G	c.(307-309)ctC>ctG	p.L103L	SERPINB6_ENST00000380529.1_Silent_p.L103L|SERPINB6_ENST00000380524.1_Silent_p.L103L|SERPINB6_ENST00000380539.1_Silent_p.L103L|SERPINB6_ENST00000335686.5_Silent_p.L103L|SERPINB6_ENST00000380546.3_Silent_p.L103L			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	103					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	GACTTACTGAGAGGAAATCAC	0.493																																					p.L122L		.											.	SERPINB6-226	0			c.C366G						.						78	78	78					6																	2955761		2203	4300	6503	SO:0001819	synonymous_variant	5269	exon3			TACTGAGAGGAAA	Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"Serine (or cysteine) peptidase inhibitors"	8950	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase"	173321	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6", "deafness, autosomal recessive 91"	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.309C>G	6.37:g.2955761G>C		Somatic	88	0		WXS	Illumina HiSeq	Phase_I	94	9	NM_001271823	0	0	0	0	0	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Silent	SNP	ENST00000380520.1	37	CCDS4479.1																																																																																			.		0.493	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1			C	2955761	G	C	2955761	2	2	158	1	0	0	0	0	0	0	0	1	14137	929	33	4		4	SERPINB6	6	2955761	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		2955761	168159306	17	14364											
SRRT	51593	broad.mit.edu	37	chr7	100482130	100482130	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcctaggggacggggagcGcaaaaccaacgacaaggatg	14	2	16	9	3	0	0	0	0	0	0	0	4	0	3	2	6	3	1	2	6	5	1	rs140745082		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr7:100482130G>A	ENST00000347433.4	+	7	1057	c.899G>A	c.(898-900)cGc>cAc	p.R300H	SRRT_ENST00000457580.2_Missense_Mutation_p.R300H|SRRT_ENST00000388793.4_Missense_Mutation_p.R300H|SRRT_ENST00000432932.1_Missense_Mutation_p.R300H			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	300	Glu-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GACGGGGAGCGCAAAACCAAC	0.637																																					p.R300H													.	SRRT-92	0			c.G899A						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4404		0,0,2202	49	51	51		899,899,899,899	3.9	1	7	dbSNP_134	51	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,missense,missense	SRRT	NM_001128852.1,NM_001128853.1,NM_001128854.1,NM_015908.5	29,29,29,29	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	300/876,300/873,300/872,300/877	100482130	3,12999	2202	4299	6501	SO:0001583	missense	51593	exon7			GGGAGCGCAAAAC		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.899G>A	7.37:g.100482130G>A	ENSP00000314491:p.Arg300His	Somatic	191	0		WXS	Illumina HiSeq	Phase_I	199	6	NM_001128853	0	0	30	30	0	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021553	0.35701	0.0	3.49E-4	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000432932;ENST00000347433	T;T	0.17691	2.26;2.26	3.91	3.91	0.45181	.	0.231821	0.36555	N	0.002525	T	0.17831	0.0428	N	0.14661	0.345	0.38836	D	0.955963	D;D;D;D	0.69078	0.997;0.997;0.997;0.995	P;P;P;P	0.56343	0.796;0.796;0.796;0.63	T	0.04885	-1.0920	10	0.42905	T	0.14	.	11.5862	0.50920	0.0:0.0:1.0:0.0	.	300;300;300;300	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	H	300	ENSP00000416553:R300H;ENSP00000314491:R300H	ENSP00000314491:R300H	R	+	2	0	SRRT	100320066	0.917000	0.31117	0.999000	0.59377	0.004000	0.04260	4.689000	0.61723	2.203000	0.70933	0.491000	0.48974	CGC	G|1.000;A|0.000		0.637	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100482130	G	A	100482130	3	1	158	1	0	0	0	0	1	0	0	0	15204	1087	38	1	921	1	SRRT	7	100482130	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		100482130	58656533	18	14365											
SGK223	157285	broad.mit.edu	37	chr8	8239069	8239069	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tccaggcggcagttctcaggCctgggaggcaggcgcggtgg	5	6	19	11	3	1	0	1	0	1	0	3	1	2	1	2	8	0	3	2	8	0	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr8:8239069C>A	ENST00000520004.1	-	2	453	c.189G>T	c.(187-189)agG>agT	p.R63S	SGK223_ENST00000330777.4_Missense_Mutation_p.R63S			Q86YV5	SG223_HUMAN		63							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGTTCTCAGGCCTGGGAGGCA	0.657																																					p.R63S	GBM(34;731 755 10259 33573 33867)												.	.	0			c.G189T						.						48	49	49					8																	8239069		2004	4157	6161	SO:0001583	missense	0	exon1			CTCAGGCCTGGGA																												ENST00000520004.1:c.189G>T	8.37:g.8239069C>A	ENSP00000428054:p.Arg63Ser	Somatic	55	1		WXS	Illumina HiSeq	Phase_I	117	9	NM_001080826	0	0	0	0	0	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236881	0.39498	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59083	0.29;0.29	4.49	2.69	0.31865	.	0.226672	0.30658	N	0.009160	T	0.41696	0.1170	L	0.38531	1.155	0.27832	N	0.941416	B	0.31968	0.349	B	0.24701	0.055	T	0.44802	-0.9304	10	0.72032	D	0.01	.	8.2345	0.31618	0.0:0.7459:0.0:0.2541	.	63	Q86YV5	SG223_HUMAN	S	63	ENSP00000330930:R63S;ENSP00000428054:R63S	ENSP00000330930:R63S	R	-	3	2	AC068353.1	8276479	1.000000	0.71417	0.887000	0.34795	0.775000	0.43874	0.980000	0.29513	1.272000	0.44329	-0.230000	0.12252	AGG	.		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8239069	C	A	8239069	3	1	158	1	0	0	0	0	1	0	0	0	14242	738	26	4	4039	4	SGK223	8	8239069	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		8239069	138124953	19	14366											
TERF1	7013	broad.mit.edu;bcgsc.ca	37	chr8	73926211	73926211	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtttttgacaagaattgcagCaggaaaaacccttggtaaat	15	11	9	6	0	0	2	0	1	0	1	0	3	0	3	1	2	3	4	1	2	6	5			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr8:73926211C>G	ENST00000276603.5	+	2	424	c.401C>G	c.(400-402)gCa>gGa	p.A134G	TERF1_ENST00000276602.6_Missense_Mutation_p.A134G	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	134	TRFH dimerization.				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			AGAATTGCAGCAGGAAAAACC	0.318																																					p.A134G													.	TERF1-228	0			c.C401G						.						57	61	60					8																	73926211		2200	4298	6498	SO:0001583	missense	7013	exon2			TTGCAGCAGGAAA	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.401C>G	8.37:g.73926211C>G	ENSP00000276603:p.Ala134Gly	Somatic	283	0		WXS	Illumina HiSeq	Phase_I	251	7	NM_017489	0	0	0	0	0	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	37	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904898	0.33628	.	.	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000517390;ENST00000538958	.	.	.	5.24	3.15	0.36227	Telomere repeat-binding factor, dimerisation domain (4);	0.401124	0.26840	N	0.022235	T	0.30572	0.0769	L	0.44542	1.39	0.23198	N	0.998131	P;P	0.49090	0.701;0.919	B;P	0.45753	0.205;0.492	T	0.12682	-1.0538	9	0.51188	T	0.08	.	5.681	0.17776	0.2799:0.6202:0.0:0.0999	.	134;134	P54274-2;P54274	.;TERF1_HUMAN	G	134;134;30;30	.	ENSP00000276602:A134G	A	+	2	0	TERF1	74088765	1.000000	0.71417	0.942000	0.38095	0.753000	0.42808	2.151000	0.42263	1.353000	0.45828	0.313000	0.20887	GCA	.		0.318	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		G	73926211	C	G	73926211	3	3	158	1	0	0	0	0	1	0	0	0	15793	710	25	4	407	4	TERF1	8	73926211	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	65687142	73926211	72437811	20	14367											
NBN	4683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	90967743	90967743	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattctgaatttttgttccaTtttggagactttgatttctt	7	22	6	6	0	2	3	0	2	2	1	3	4	3	3	1	1	0	1	1	1	1	9			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr8:90967743T>C	ENST00000265433.3	-	10	1319	c.1165A>G	c.(1165-1167)Atg>Gtg	p.M389V	NBN_ENST00000409330.1_Missense_Mutation_p.M307V	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	389	Interaction with MTOR, MAPKAP1 and RICTOR.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTTTGTTCCATTTTGGAGACT	0.338								Homologous recombination																													p.M389V		.											.	NBN-1395	0			c.A1165G						.						104	98	100					8																	90967743		2203	4300	6503	SO:0001583	missense	4683	exon10			GTTCCATTTTGGA	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"Nijmegen breakage syndrome 1 (nibrin)"	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1165A>G	8.37:g.90967743T>C	ENSP00000265433:p.Met389Val	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	42	14	NM_002485	0	0	0	3	3	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.453422	0.01071	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387	T;T	0.56941	2.1;0.43	5.45	-1.76	0.08006	.	0.952676	0.09006	N	0.862316	T	0.20659	0.0497	N	0.05383	-0.06	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24119	-1.0169	10	0.02654	T	1	3.3137	1.3277	0.02128	0.1323:0.1639:0.2892:0.4145	.	389;389	A6H8Y5;O60934	.;NBN_HUMAN	V	389;307;389	ENSP00000265433:M389V;ENSP00000386924:M307V	ENSP00000265433:M389V	M	-	1	0	NBN	91036919	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.078000	0.14761	-0.233000	0.09797	-0.321000	0.08615	ATG	.		0.338	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90967743	T	C	90967743	3	2	158	1	0	0	0	0	1	0	0	0	10216	1493	52	3	1127	3	NBN	8	90967743	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	17041532	90967743	55396279	21	14368											
FREM1	158326	broad.mit.edu	37	chr9	14770686	14770686	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcctcagtgtcagggtctGatgccttcaacacgcgggaa	8	9	12	12	3	4	1	3	1	1	0	5	2	5	2	2	2	2	0	2	2	2	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr9:14770686G>T	ENST00000380880.3	-	26	5759	c.4976C>A	c.(4975-4977)tCa>tAa	p.S1659*	FREM1_ENST00000380894.1_Nonsense_Mutation_p.S195*|FREM1_ENST00000422223.2_Nonsense_Mutation_p.S1659*|FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000380881.4_Nonsense_Mutation_p.S1660*			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1659					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GTCAGGGTCTGATGCCTTCAA	0.478																																					p.S1659X													.	FREM1-138	0			c.C4976A						.						145	137	139					9																	14770686		1971	4155	6126	SO:0001587	stop_gained	158326	exon27			GGGTCTGATGCCT	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"chromosome 9 open reading frame 154"	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.4976C>A	9.37:g.14770686G>T	ENSP00000370262:p.Ser1659*	Somatic	169	1		WXS	Illumina HiSeq	Phase_I	175	4	NM_144966	0	0	0	0	0	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Nonsense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189900	0.57909	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380894;ENST00000380880;ENST00000380892	.	.	.	5.8	4.9	0.64082	.	0.372091	0.28712	N	0.014390	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-3.8618	11.5807	0.50889	0.136:0.0:0.864:0.0	.	.	.	.	X	1660;1659;195;1659;72	.	ENSP00000370262:S1659X	S	-	2	0	FREM1	14760686	0.648000	0.27313	0.054000	0.19295	0.348000	0.29142	2.486000	0.45259	2.743000	0.94032	0.650000	0.86243	TCA	.		0.478	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14770686	G	T	14770686	4	4	158	1	0	0	0	0	0	1	0	0	6063	1294	45	4	1611	4	FREM1	9	14770686	Nonsense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		14770686	126442745	22	14369											
TAF1L	138474	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	32633310	32633310	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcaagtgcctgcagtaattgGccaggatggagagagcccaa	12	7	13	9	0	1	1	1	0	0	1	1	4	1	3	3	3	3	2	3	3	3	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr9:32633310G>A	ENST00000242310.4	-	1	2357	c.2268C>T	c.(2266-2268)ggC>ggT	p.G756G	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	756					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GCAGTAATTGGCCAGGATGGA	0.443																																					p.G756G		.											.	TAF1L-870	0			c.C2268T						.						184	180	182					9																	32633310		2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			TAATTGGCCAGGA	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2268C>T	9.37:g.32633310G>A		Somatic	254	0		WXS	Illumina HiSeq	Phase_I	254	20	NM_153809	0	0	0	0	0	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			.		0.443	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32633310	G	A	32633310	2	1	158	1	0	0	0	0	0	0	0	1	15555	1190	42	2		2	TAF1L	9	32633310	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	17862624	32633310	108580121	23	14370											
DCAF10	79269	hgsc.bcm.edu	37	chr9	37800965	37800965	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcagcagccaccgggccGccctcgccactacatcccgg	7	3	11	20	4	0	0	0	0	0	0	2	0	1	0	6	3	3	2	6	3	1	1	rs373032176		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr9:37800965G>T	ENST00000377724.3	+	1	467	c.102G>T	c.(100-102)ccG>ccT	p.P34P	RP11-613M10.9_ENST00000540557.1_Intron|DCAF10_ENST00000242323.7_Silent_p.P34P	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	34	Pro-rich.				protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						CCACCGGGCCGCCCTCGCCAC	0.761													G|||	1	0.000199681	0	0	5008	,	,		10350	0		0.001	False		,,,				2504	0				p.P34P		.											.	DCAF10-115	0			c.G102T						.	G		2,2882		0,2,1440	3	4	3		102	-2.9	0.1	9		3	5,6809		0,5,3402	no	coding-synonymous	DCAF10	NM_024345.3		0,7,4842	TT,TG,GG		0.0734,0.0693,0.0722		34/560	37800965	7,9691	1442	3407	4849	SO:0001819	synonymous_variant	79269	exon1			CGGGCCGCCCTCG	BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	23686	protein-coding gene	gene with protein product			"WD repeat domain 32"	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.102G>T	9.37:g.37800965G>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	12	8	NM_024345	0	0	0	0	0	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Silent	SNP	ENST00000377724.3	37	CCDS6613.2																																																																																			.		0.761	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345		T	37800965	G	T	37800965	2	4	158	1	0	0	0	0	0	0	0	1	4267	1074	38	4		4	DCAF10	9	37800965	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	5167655	37800965	103412466	24	14371											
STX17	55014	broad.mit.edu	37	chr9	102730843	102730843	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgcacttggtggtggggTgttgggcttcacaggtggaa	6	11	18	6	0	1	0	1	0	0	0	1	1	1	1	0	7	2	4	0	7	1	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr9:102730843T>G	ENST00000259400.6	+	8	933	c.797T>G	c.(796-798)gTg>gGg	p.V266G	STX17_ENST00000525847.1_3'UTR|STX17_ENST00000525640.1_Missense_Mutation_p.V266G|STX17_ENST00000534052.1_Missense_Mutation_p.V266G	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	266	Necessary and sufficient for localization to autophagosome.				autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				GGTGGTGGGGTGTTGGGCTTC	0.517																																					p.V266G													.	STX17-153	0			c.T797G						.						60	67	65					9																	102730843		2203	4300	6503	SO:0001583	missense	55014	exon8			GTGGGGTGTTGGG	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.797T>G	9.37:g.102730843T>G	ENSP00000259400:p.Val266Gly	Somatic	130	14		WXS	Illumina HiSeq	Phase_I	159	21	NM_017919	0	0	2	2	0	Q4VXC2	Missense_Mutation	SNP	ENST00000259400.6	37	CCDS6745.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222238	0.39300	.	.	ENSG00000136874	ENST00000259400;ENST00000525640;ENST00000534052	.	.	.	5.28	5.28	0.74379	.	0.347306	0.27130	N	0.020792	T	0.48943	0.1528	L	0.34521	1.04	0.58432	D	0.999998	B	0.34214	0.442	B	0.34991	0.193	T	0.54761	-0.8245	9	0.87932	D	0	-7.5824	13.8021	0.63206	0.0:0.0:0.0:1.0	.	266	P56962	STX17_HUMAN	G	266	.	ENSP00000259400:V266G	V	+	2	0	STX17	101770664	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.856000	0.55964	1.999000	0.58509	0.533000	0.62120	GTG	.		0.517	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919		G	102730843	T	G	102730843	3	3	158	1	0	0	0	0	1	0	0	0	15372	1696	59	5	823	5	STX17	9	102730843	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	64929878	102730843	38482588	25	14372											
TM7SF2	7108	hgsc.bcm.edu	37	chr11	64880061	64880061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccgttcgggccccgcgCgcctgctgggtccacccgcg	1	5	15	20	8	0	0	0	0	0	0	2	0	1	0	6	3	1	2	6	3	0	1	rs371186990	byFrequency	TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr11:64880061C>T	ENST00000279263.7	+	2	289	c.127C>T	c.(127-129)Cgc>Tgc	p.R43C	TM7SF2_ENST00000345348.5_Missense_Mutation_p.R43C|TM7SF2_ENST00000540748.1_5'UTR|AP003068.9_ENST00000528887.1_RNA	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	43					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGGCCCCGCGCGCCTGCTGGG	0.761													C|||	2	0.000399361	0	0	5008	,	,		9764	0		0.001	False		,,,				2504	0.001				p.R43C		.											.	TM7SF2-91	0			c.C127T						.	C	CYS/ARG	0,2736		0,0,1368	2	2	2		127	3.8	1	11		2	1,6125		0,1,3062	no	missense	TM7SF2	NM_003273.2	180	0,1,4430	TT,TC,CC		0.0163,0.0,0.0113	probably-damaging	43/419	64880061	1,8861	1368	3063	4431	SO:0001583	missense	7108	exon2			CCCGCGCGCCTGC	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"delta(14)-sterol reductase"	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.127C>T	11.37:g.64880061C>T	ENSP00000279263:p.Arg43Cys	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	13	8	NM_003273	0	0	0	0	0	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	37	CCDS41669.1	.	.	.	.	.	.	.	.	.	.	c	18.67	3.674356	0.67928	0.0	1.63E-4	ENSG00000149809	ENST00000526809;ENST00000279263;ENST00000524986;ENST00000534371;ENST00000525385;ENST00000345348;ENST00000531321;ENST00000529414;ENST00000530750	D;D;D;D;D;D;D;D;T	0.99014	-4.71;-4.76;-4.18;-5.17;-4.38;-4.9;-5.33;-4.27;-1.08	4.77	3.78	0.43462	.	1.425240	0.04660	N	0.408682	D	0.98416	0.9473	N	0.22421	0.69	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66847	0.911;0.947	D	0.95356	0.8451	10	0.56958	D	0.05	-14.5223	9.5491	0.39299	0.3109:0.6891:0.0:0.0	.	43;43	O76062-2;O76062	.;ERG24_HUMAN	C	43;43;14;43;14;43;14;43;43	ENSP00000432171:R43C;ENSP00000279263:R43C;ENSP00000435972:R14C;ENSP00000432187:R43C;ENSP00000433325:R14C;ENSP00000329520:R43C;ENSP00000431300:R14C;ENSP00000433275:R43C;ENSP00000432413:R43C	ENSP00000279263:R43C	R	+	1	0	TM7SF2	64636637	1.000000	0.71417	1.000000	0.80357	0.384000	0.30261	1.094000	0.30951	2.484000	0.83849	0.556000	0.70494	CGC	.		0.761	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		T	64880061	C	T	64880061	3	4	158	1	0	0	0	0	1	0	0	0	16006	768	27	1	133	1	TM7SF2	11	64880061	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		64880061	70126455	26	14373											
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751497	76751497	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgcgcggccgcccgccAcaccccgctcttccccatcg	3	5	9	24	7	1	0	0	0	1	0	3	0	2	0	8	1	1	1	8	1	0	1	rs559157215	byFrequency	TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr11:76751497A>G	ENST00000533140.1	+	2	1040	c.902A>G	c.(901-903)cAc>cGc	p.H301R	B3GNT6_ENST00000421061.1_Intron|B3GNT6_ENST00000354301.5_Missense_Mutation_p.H301R			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						gccgcccgccACACCCCGCTC	0.756													A|||	21	0.00419329	8e-04	0.0288	5008	,	,		10513	0		0	False		,,,				2504	0				p.H301R		.											.	.	0			c.A902G						.																																			SO:0001583	missense	192134	exon2			CCCGCCACACCCC	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.902A>G	11.37:g.76751497A>G	ENSP00000435352:p.His301Arg	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_138706	0	0	0	0	0	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	37	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	A	1.535	-0.543236	0.04053	.	.	ENSG00000198488	ENST00000533140;ENST00000354301	T;T	0.44083	0.93;0.93	2.89	0.53	0.17102	.	0.656353	0.15442	N	0.262162	T	0.21921	0.0528	N	0.21097	0.63	0.09310	N	0.999997	B	0.02656	0.0	B	0.09377	0.004	T	0.24368	-1.0162	10	0.11794	T	0.64	.	6.0489	0.19775	0.753:0.0:0.247:0.0	.	301	Q6ZMB0	B3GN6_HUMAN	R	301	ENSP00000435352:H301R;ENSP00000346256:H301R	ENSP00000346256:H301R	H	+	2	0	B3GNT6	76429145	0.000000	0.05858	0.007000	0.13788	0.109000	0.19521	-0.871000	0.04223	0.080000	0.16959	0.374000	0.22700	CAC	.		0.756	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706		G	76751497	A	G	76751497	3	3	158	1	0	0	0	0	1	0	0	0	1262	159	6	3	904	3	B3GNT6	11	76751497	Missense_Mutation	SNP	A	TCGA-P4-A5ED-01A-11D-A28G-10	11871436	76751497	58255019	27	14374											
GRAMD1B	57476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	123476178	123476178	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacagggagcagtgaggccCccgtctcggtatgggcagtc	7	6	15	13	2	1	1	0	1	1	0	3	2	1	2	3	4	1	3	3	4	1	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr11:123476178C>T	ENST00000529750.1	+	9	1213	c.886C>T	c.(886-888)Ccc>Tcc	p.P296S	GRAMD1B_ENST00000450171.2_5'Flank|GRAMD1B_ENST00000322282.7_Missense_Mutation_p.P296S|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.P303S	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	296						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CAGTGAGGCCCCCGTCTCGGT	0.557																																					p.P296S		.											.	GRAMD1B-69	0			c.C886T						.						142	149	147					11																	123476178		2083	4200	6283	SO:0001583	missense	57476	exon9			GAGGCCCCCGTCT	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.886C>T	11.37:g.123476178C>T	ENSP00000436500:p.Pro296Ser	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	147	45	NM_020716	0	0	0	0	0	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	37	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.911935	0.72983	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000534764	T;T;T;T;T	0.30714	1.92;1.93;1.93;1.92;1.52	5.03	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.31009	0.0783	L	0.34521	1.04	0.58432	D	0.999998	P;P;D;B	0.57899	0.913;0.734;0.981;0.027	B;B;P;B	0.52109	0.424;0.356;0.69;0.065	T	0.02431	-1.1160	10	0.13470	T	0.59	.	13.3208	0.60432	0.0:0.9228:0.0:0.0772	.	256;303;296;303	B7Z4N9;F5H572;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	S	303;303;296;296;256;292	ENSP00000402457:P303S;ENSP00000325628:P296S;ENSP00000436500:P296S;ENSP00000432987:P256S;ENSP00000434214:P292S	ENSP00000325628:P296S	P	+	1	0	GRAMD1B	122981388	0.994000	0.37717	0.842000	0.33263	0.898000	0.52572	3.919000	0.56439	1.112000	0.41740	0.305000	0.20034	CCC	.		0.557	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		T	123476178	C	T	123476178	3	4	158	1	0	0	0	0	1	0	0	0	6769	623	22	2	920	2	GRAMD1B	11	123476178	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	46724681	123476178	11530338	28	14375											
CLEC2D	29121	broad.mit.edu;bcgsc.ca	37	chr12	9840539	9840539	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagagccatcagtatgtcttCaagctgcatgcccagaaagc	13	8	9	11	0	3	2	2	0	1	2	3	2	3	2	2	0	5	3	2	0	4	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr12:9840539C>G	ENST00000290855.6	+	3	236	c.214C>G	c.(214-216)Caa>Gaa	p.Q72E	CLEC2D_ENST00000543300.1_Missense_Mutation_p.Q72E|CLEC2D_ENST00000261340.7_Missense_Mutation_p.Q72E|CLEC2D_ENST00000261339.6_Missense_Mutation_p.Q35E|CLEC2D_ENST00000545918.1_Missense_Mutation_p.Q35E	NM_013269.5	NP_037401.1	Q9UHP7	CLC2D_HUMAN	C-type lectin domain family 2, member D	72					cell surface receptor signaling pathway (GO:0007166)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|stomach(1)	9						AGTATGTCTTCAAGCTGCATG	0.323																																					p.Q72E													.	CLEC2D-90	0			c.C214G						.						85	84	84					12																	9840539		2203	4300	6503	SO:0001583	missense	29121	exon3			TGTCTTCAAGCTG	AF133299	CCDS8602.1, CCDS31741.1, CCDS55800.1, CCDS55801.1, CCDS55802.1	12p13.31	2011-05-24	2005-09-29		ENSG00000069493	ENSG00000069493		"C-type lectin domain containing"	14351	protein-coding gene	gene with protein product	"C-type lectin related f", "lectin-like transcript 1"	605659	"C-type lectin superfamily 2, member D"				Standard	NM_013269		Approved	LLT1, CLAX, OCIL	uc001qwf.3	Q9UHP7	OTTHUMG00000168369	ENST00000290855.6:c.214C>G	12.37:g.9840539C>G	ENSP00000290855:p.Gln72Glu	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	48	4	NM_001004419	0	0	18	18	0	D6CI39|D6CI40|D6CI41|Q6YID5|Q8WUP7|Q9HD37|Q9HD38	Missense_Mutation	SNP	ENST00000290855.6	37	CCDS8602.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.928952	0.00493	.	.	ENSG00000069493	ENST00000479410;ENST00000261340;ENST00000290855;ENST00000545918;ENST00000543300;ENST00000261339;ENST00000466035;ENST00000430909;ENST00000544322;ENST00000460309	T;T;T;T;T;T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31;4.61;4.47;4.49;2.31;4.39	3.49	-3.81	0.04294	C-type lectin-like (1);	5.044330	0.01431	N	0.014751	T	0.03959	0.0111	N	0.00707	-1.245	0.09310	N	1	B;B;B	0.13145	0.004;0.007;0.004	B;B;B	0.13407	0.004;0.009;0.003	T	0.22591	-1.0212	9	.	.	.	-1.5275	1.3511	0.02173	0.3326:0.3404:0.1947:0.1323	.	72;72;72	Q9UHP7-5;Q9UHP7;Q9UHP7-3	.;CLC2D_HUMAN;.	E	30;72;72;35;72;35;29;51;46;15	ENSP00000442252:Q30E;ENSP00000261340:Q72E;ENSP00000290855:Q72E;ENSP00000444818:Q35E;ENSP00000443065:Q72E;ENSP00000261339:Q35E;ENSP00000446028:Q29E;ENSP00000413045:Q51E;ENSP00000437861:Q46E;ENSP00000443177:Q15E	.	Q	+	1	0	CLEC2D	9731806	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.558000	0.05978	-0.753000	0.04721	-0.450000	0.05554	CAA	.		0.323	CLEC2D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000335424.2	NM_013269		G	9840539	C	G	9840539	3	3	158	1	0	0	0	0	1	0	0	0	3514	827	29	4	224	4	CLEC2D	12	9840539	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		9840539	124011356	29	14376											
B4GALNT1	2583	broad.mit.edu	37	chr12	58021430	58021430	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgcggctgaggcgggggTcgaaaccgacctcgcgcacc	7	3	15	16	7	0	1	0	1	0	0	2	3	0	1	4	4	1	2	4	4	1	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr12:58021430T>G	ENST00000341156.4	-	10	1939	c.1355A>C	c.(1354-1356)gAc>gCc	p.D452A	B4GALNT1_ENST00000418555.2_Missense_Mutation_p.D397A	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	452					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GAGGCGGGGGTCGAAACCGAC	0.697																																					p.S452S													.	B4GALNT1-514	0			c.C1355C						.						17	20	19					12																	58021430		2182	4277	6459	SO:0001583	missense	2583	exon10			CGGGGGTCGAAAC	M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	4117	protein-coding gene	gene with protein product	"GD2 synthase, GM2 synthase"	601873	"UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)", "UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1", "spastic paraplegia 26"	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.1355A>C	12.37:g.58021430T>G	ENSP00000341562:p.Asp452Ala	Somatic	70	13		WXS	Illumina HiSeq	Phase_I	163	44	NM_001478	0	0	1	1	0	B4DE26|Q8N636	Silent	SNP	ENST00000341156.4	37	CCDS8950.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	25.8|25.8	4.671033|4.671033	0.88348|0.88348	.|.	.|.	ENSG00000135454|ENSG00000135454	ENST00000341156;ENST00000418555|ENST00000547741	T;T|.	0.27104|.	1.69;1.69|.	4.5|4.5	4.5|4.5	0.54988|0.54988	.|.	0.117831|.	0.64402|.	D|.	0.000009|.	T|T	0.75824|0.75824	0.3902|0.3902	M|M	0.83223|0.83223	2.63|2.63	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.997;1.0|.	P;D|.	0.71870|.	0.888;0.975|.	T|T	0.78555|0.78555	-0.2159|-0.2159	10|5	0.87932|.	D|.	0|.	-12.617|-12.617	12.9089|12.9089	0.58169|0.58169	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	397;452|.	B4DE26;Q00973|.	.;B4GN1_HUMAN|.	A|P	452;397|135	ENSP00000341562:D452A;ENSP00000401601:D397A|.	ENSP00000341562:D452A|.	D|T	-|-	2|1	0|0	B4GALNT1|B4GALNT1	56307697|56307697	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.819000|0.819000	0.46315|0.46315	7.338000|7.338000	0.79269|0.79269	1.902000|1.902000	0.55061|0.55061	0.379000|0.379000	0.24179|0.24179	GAC|ACC	.		0.697	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478		G	58021430	T	G	58021430	3	3	158	1	0	0	0	0	1	0	0	0	1267	1667	58	5	254	5	B4GALNT1	12	58021430	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	48180891	58021430	75830465	30	14377											
CUX2	23316	broad.mit.edu	37	chr12	111757856	111757856	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccccgctgagcatcgccaaCggcacgacccccgccagcac	8	2	10	21	5	0	1	0	1	0	0	1	2	0	1	6	1	3	4	6	1	1	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr12:111757856C>T	ENST00000261726.6	+	17	2197	c.2043C>T	c.(2041-2043)aaC>aaT	p.N681N		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	681					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						GCATCGCCAACGGCACGACCC	0.711																																					p.N681N													.	CUX2-140	0			c.C2043T						.						3	4	4					12																	111757856		1882	3888	5770	SO:0001819	synonymous_variant	23316	exon17			CGCCAACGGCACG	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.2043C>T	12.37:g.111757856C>T		Somatic	16	0		WXS	Illumina HiSeq	Phase_I	77	5	NM_015267	0	0	0	0	0	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																			.		0.711	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		T	111757856	C	T	111757856	2	4	158	1	0	0	0	0	0	0	0	1	4071	535	19	1		1	CUX2	12	111757856	Silent	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	53736426	111757856	22094039	31	14378											
BRAP	8315	hgsc.bcm.edu;broad.mit.edu	37	chr12	112096635	112096635	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgttttacttgcaaccagtcGatgaacatagttatctacag	12	14	7	8	1	1	1	0	1	1	0	2	2	1	1	1	0	5	3	1	0	6	6			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr12:112096635G>A	ENST00000327551.6	-	9	1176	c.1036C>T	c.(1036-1038)Cga>Tga	p.R346*	BRAP_ENST00000539060.1_Nonsense_Mutation_p.R197*|BRAP_ENST00000419234.4_Nonsense_Mutation_p.R376*			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	0					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						GCAACCAGTCGATGAACATAG	0.353																																					p.R376X	Pancreas(146;846 1904 7830 25130 26065)	.											.	BRAP-710	0			c.C1126T						.						129	119	122					12																	112096635		2203	4300	6503	SO:0001587	stop_gained	8315	exon9			CCAGTCGATGAAC	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"RING-type (C3HC4) zinc fingers"	1099	protein-coding gene	gene with protein product	"impedes mitogenic signal propagation", "galectin-2-binding protein"	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.1036C>T	12.37:g.112096635G>A	ENSP00000330813:p.Arg346*	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	80	5	NM_006768	0	0	4	4	0	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Nonsense_Mutation	SNP	ENST00000327551.6	37		.	.	.	.	.	.	.	.	.	.	G	36	5.951877	0.97139	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1227	19.4174	0.94706	0.0:0.0:1.0:0.0	.	.	.	.	X	376;197;346;158	.	ENSP00000330813:R346X	R	-	1	2	BRAP	110581018	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.147000	0.94646	2.606000	0.88127	0.650000	0.86243	CGA	.		0.353	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			A	112096635	G	A	112096635	4	1	158	1	0	0	0	0	0	1	0	0	1500	1066	37	1	668	1	BRAP	12	112096635	Nonsense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	338779	112096635	21755260	32	14379											
MED13L	23389	ucsc.edu	37	chr12	116428913	116428913	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggttatccacatactgccgCccctgctccaacgcattaaa	10	9	7	15	2	0	0	0	0	0	0	2	0	2	0	5	1	4	3	5	1	5	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr12:116428913C>T	ENST00000281928.3	-	17	4052	c.3846G>A	c.(3844-3846)ggG>ggA	p.G1282G		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1282						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CATACTGCCGCCCCTGCTCCA	0.512																																					p.G1282G													.	MED13L-232	0			c.G3846A						.						115	110	112					12																	116428913		2203	4300	6503	SO:0001819	synonymous_variant	23389	exon17			CTGCCGCCCCTGC	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"thyroid hormone receptor associated protein 2"	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3846G>A	12.37:g.116428913C>T		Somatic	125	0		WXS	Illumina HiSeq		121	1	NM_015335	0	0	4	4	0	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			.		0.512	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116428913	C	T	116428913	2	4	158	1	0	0	0	0	0	0	0	1	9456	726	26	2		2	MED13L	12	116428913	Silent	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	4332278	116428913	17422982	33	14380											
SEL1L	6400	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	81969202	81969202	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttggtatggttcatgcttgCtgccttttggagataccgat	6	17	11	7	1	1	1	1	0	0	1	1	3	1	1	2	3	4	4	2	3	2	7			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr14:81969202C>T	ENST00000336735.4	-	6	756	c.640G>A	c.(640-642)Gca>Aca	p.A214T	SEL1L_ENST00000555824.1_Missense_Mutation_p.A214T	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	214	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		TTCATGCTTGCTGCCTTTTGG	0.363																																					p.A214T		.											.	SEL1L-227	0			c.G640A						.						146	139	142					14																	81969202		2203	4300	6503	SO:0001583	missense	6400	exon6			TGCTTGCTGCCTT		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"sel-1 suppressor of lin-12-like 1 (C. elegans)"	602329	"sel-1 (suppressor of lin-12, C.elegans)-like"			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.640G>A	14.37:g.81969202C>T	ENSP00000337053:p.Ala214Thr	Somatic	61	0		WXS	Illumina HiSeq	Phase_I	79	22	NM_001244984	0	0	0	0	0	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	37	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191863	0.78902	.	.	ENSG00000071537	ENST00000336735;ENST00000555824	T;T	0.58940	0.35;0.3	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);	0.104952	0.64402	D	0.000004	T	0.71937	0.3399	M	0.66939	2.045	0.80722	D	1	D;D	0.67145	0.985;0.996	D;D	0.64042	0.92;0.921	T	0.74450	-0.3661	10	0.87932	D	0	.	14.4932	0.67665	0.1468:0.8532:0.0:0.0	.	214;214	Q9UBV2;Q9UBV2-2	SE1L1_HUMAN;.	T	214	ENSP00000337053:A214T;ENSP00000450709:A214T	ENSP00000337053:A214T	A	-	1	0	SEL1L	81038955	1.000000	0.71417	0.999000	0.59377	0.746000	0.42486	4.282000	0.58971	2.719000	0.93026	0.655000	0.94253	GCA	.		0.363	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		T	81969202	C	T	81969202	3	4	158	1	0	0	0	0	1	0	0	0	14042	797	28	2	1808	2	SEL1L	14	81969202	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		81969202	25380338	34	14381											
IGDCC3	9543	broad.mit.edu	37	chr15	65628245	65628245	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggaagcgggccacaccAccctcctcacccacggtggc	8	4	10	19	2	1	0	1	0	0	0	2	1	2	1	5	4	1	0	5	4	1	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr15:65628245A>G	ENST00000327987.4	-	3	710	c.459T>C	c.(457-459)ggT>ggC	p.G153G	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	153	Ig-like C2-type 2.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGGCCACACCACCCTCCTCAC	0.582																																					p.G153G													.	IGDCC3-93	0			c.T459C						.						117	102	107					15																	65628245		2201	4299	6500	SO:0001819	synonymous_variant	9543	exon3			CACACCACCCTCC	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.459T>C	15.37:g.65628245A>G		Somatic	185	1		WXS	Illumina HiSeq	Phase_I	171	4	NM_004884	0	0	0	0	0	O95215	Silent	SNP	ENST00000327987.4	37	CCDS10205.1																																																																																			.		0.582	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		G	65628245	A	G	65628245	2	3	158	1	0	0	0	0	0	0	0	1	7589	146	6	3		3	IGDCC3	15	65628245	Silent	SNP	A	TCGA-P4-A5ED-01A-11D-A28G-10		65628245	36903147	35	14382											
ACAN	176	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	89398215	89398215	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	attcccctcagaggagccatCcccctcagaggaaccattcc	10	7	7	17	0	2	2	2	0	0	2	5	4	5	4	7	2	2	0	7	2	1	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr15:89398215C>T	ENST00000561243.1	+	11	2399	c.2399C>T	c.(2398-2400)tCc>tTc	p.S800F	ACAN_ENST00000439576.2_Missense_Mutation_p.S800F|ACAN_ENST00000352105.7_Missense_Mutation_p.S800F|ACAN_ENST00000559004.1_Missense_Mutation_p.S800F			P16112	PGCA_HUMAN	aggrecan	799	12 X 6 AA approximate tandem repeats of E-[GVE]-P-[SFY]-[APT]-[TSP].|KS.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GAGGAGCCATCCCCCTCAGAG	0.597																																					p.S800F													.	ACAN-25	0			c.C2399T						.						31	35	34					15																	89398215		1944	4139	6083	SO:0001583	missense	176	exon12			AGCCATCCCCCTC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans"	319	protein-coding gene	gene with protein product	"aggrecan proteoglycan"	155760	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2399C>T	15.37:g.89398215C>T	ENSP00000453342:p.Ser800Phe	Somatic	131	1		WXS	Illumina HiSeq	Phase_I	190	68	NM_001135	0	0	0	0	0	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	C	4.981	0.182251	0.09495	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02258	4.6;4.37	3.46	0.239	0.15484	.	.	.	.	.	T	0.01124	0.0037	N	0.04880	-0.145	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.49380	-0.8946	9	0.18710	T	0.47	.	4.3783	0.11281	0.0:0.3872:0.1663:0.4465	.	800;800	E7ENV9;E7EX88	.;.	F	800	ENSP00000387356:S800F;ENSP00000341615:S800F	ENSP00000268134:S800F	S	+	2	0	ACAN	87199219	0.000000	0.05858	0.000000	0.03702	0.195000	0.23768	-0.135000	0.10420	-0.205000	0.10219	0.411000	0.27672	TCC	.		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89398215	C	T	89398215	3	4	158	1	0	0	0	0	1	0	0	0	117	855	30	2	2441	2	ACAN	15	89398215	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	23769970	89398215	13133177	36	14383											
HS3ST4	9951	broad.mit.edu;bcgsc.ca	37	chr16	26147018	26147018	+	Frame_Shift_Del	DEL	A	A	-																															caaatgaggctcccaagcgcAttcactccatggccaaggac																										TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr16:26147018delA	ENST00000331351.5	+	2	1212	c.820delA	c.(820-822)attfs	p.I274fs	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	274					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		TCCCAAGCGCATTCACTCCAT	0.498																																					p.I274fs													.	HS3ST4-67	0			c.820delA						.						122	111	115					16																	26147018		1568	3582	5150	SO:0001589	frameshift_variant	9951	exon2			AAGCGCATTCACT	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.820delA	16.37:g.26147018delA	ENSP00000330606:p.Ile274fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	112	12	NM_006040	0	0	0	0	0	Q5QI42|Q8NDC2	Frame_Shift_Del	DEL	ENST00000331351.5	37	CCDS53995.1																																																																																			.		0.498	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		-	26147018	A	-	26147018	7	5	158	1	0	1	0	1	0	0	0	0	7388	217	8	0	826	0	HS3ST4	16	26147018	Frame_Shift_Del	DEL	A	TCGA-P4-A5ED-01A-11D-A28G-10		26147018	64207735	37	14384	157	2									
HS3ST4	9951	broad.mit.edu;bcgsc.ca	37	chr16	26147021	26147023	+	In_Frame_Del	DEL	CAC	CAC	-																															atgaggctcccaagcgcattCactccatggccaaggacatc																										TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr16:26147021_26147023delCAC	ENST00000331351.5	+	2	1215_1217	c.823_825delCAC	c.(823-825)cacdel	p.H275del	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	275					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		CAAGCGCATTCACTCCATGGCCA	0.498																																					p.275_275del													.	HS3ST4-67	0			c.823_825del						.																																			SO:0001651	inframe_deletion	9951	exon2			CGCATTCACTCCA	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"Sulfotransferases, membrane-bound"	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.823_825delCAC	16.37:g.26147021_26147023delCAC	ENSP00000330606:p.His275del	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	115	12	NM_006040	0	0	0	0	0	Q5QI42|Q8NDC2	In_Frame_Del	DEL	ENST00000331351.5	37	CCDS53995.1																																																																																			.		0.498	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		-	26147023	CAC	-	26147021	7	5	158	1	0	1	0	1	0	0	0	0	7388	826	29	0	829	0	HS3ST4	16	26147021	In_Frame_Del	DEL	CAC	TCGA-P4-A5ED-01A-11D-A28G-10	3	26147021	64207732	38	14385	157	2									
MYBBP1A	10514	broad.mit.edu	37	chr17	4445773	4445773	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctcacctgatgacggggccGcaccgggcccgtgatatgct	6	8	13	14	4	1	3	1	3	1	0	2	3	1	3	4	3	1	2	4	3	1	1	rs369018364		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr17:4445773G>A	ENST00000254718.4	-	22	3379	c.3073C>T	c.(3073-3075)Cgg>Tgg	p.R1025W	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.R1025W			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1025					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TGACGGGGCCGCACCGGGCCC	0.617																																					p.R1025W													.	MYBBP1A-92	0			c.C3073T						.	G	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	70	79	76		3073,3073	3.2	0.5	17		76	0,8600		0,0,4300	no	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1025/1333,1025/1329	4445773	1,13005	2203	4300	6503	SO:0001583	missense	10514	exon22			GGGGCCGCACCGG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"p53-activated protein-2"	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.3073C>T	17.37:g.4445773G>A	ENSP00000254718:p.Arg1025Trp	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	89	4	NM_014520	0	0	6	6	0	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165834	0.38217	2.27E-4	0.0	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.68331	-0.32;-0.32	5.3	3.25	0.37280	Armadillo-type fold (1);	0.054052	0.64402	D	0.000001	T	0.77579	0.4151	M	0.67953	2.075	0.38604	D	0.950742	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77832	-0.2441	10	0.49607	T	0.09	-39.9853	10.7458	0.46179	0.0:0.0:0.6537:0.3463	.	1025;1025	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	W	1025	ENSP00000370968:R1025W;ENSP00000254718:R1025W	ENSP00000254718:R1025W	R	-	1	2	MYBBP1A	4392522	0.575000	0.26692	0.542000	0.28115	0.003000	0.03518	1.047000	0.30367	0.578000	0.29487	0.561000	0.74099	CGG	.		0.617	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		A	4445773	G	A	4445773	3	1	158	1	0	0	0	0	1	0	0	0	10033	1086	38	1	973	1	MYBBP1A	17	4445773	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		4445773	76749437	39	14386											
SUPT6H	6830	ucsc.edu	37	chr17	27002024	27002024	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcaaaaaaatgtcagatgacGaggacgatgacgaggaggaa	18	5	13	5	3	2	3	2	2	0	1	2	9	2	6	0	3	0	0	0	3	4	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr17:27002024G>C	ENST00000314616.6	+	5	665	c.382G>C	c.(382-384)Gag>Cag	p.E128Q	SUPT6H_ENST00000347486.4_Missense_Mutation_p.E128Q|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	128	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					GTCAGATGACGAGGACGATGA	0.498																																					p.E128Q													.	SUPT6H-93	0			c.G382C						.						84	78	80					17																	27002024		2203	4300	6503	SO:0001583	missense	6830	exon5			GATGACGAGGACG	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"SH2 domain containing"	11470	protein-coding gene	gene with protein product		601333	"suppressor of Ty (S.cerevisiae) 6 homolog"			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.382G>C	17.37:g.27002024G>C	ENSP00000319104:p.Glu128Gln	Somatic	241	1		WXS	Illumina HiSeq		303	1	NM_003170	0	0	0	9	9	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160827	0.57368	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.41	5.41	0.78517	.	0.098602	0.64402	D	0.000002	T	0.57446	0.2054	M	0.63843	1.955	0.53688	D	0.999971	P	0.49090	0.919	B	0.39503	0.301	T	0.63260	-0.6677	9	0.48119	T	0.1	-16.8028	19.558	0.95361	0.0:0.0:1.0:0.0	.	128	Q7KZ85	SPT6H_HUMAN	Q	128	.	ENSP00000319104:E128Q	E	+	1	0	SUPT6H	24026151	1.000000	0.71417	0.994000	0.49952	0.573000	0.36030	8.702000	0.91338	2.697000	0.92050	0.655000	0.94253	GAG	.		0.498	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		C	27002024	G	C	27002024	3	2	158	1	0	0	0	0	1	0	0	0	15432	1059	37	4	396	4	SUPT6H	17	27002024	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	22556251	27002024	54193186	40	14387											
KIF19	124602	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	72340927	72340927	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgctgatgaaggggaacCggcagaggacccaggagccc	11	3	16	11	1	0	3	0	2	0	1	0	6	0	6	3	5	4	3	3	5	2	0	rs146234533		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr17:72340927C>A	ENST00000389916.4	+	7	748	c.610C>A	c.(610-612)Cgg>Agg	p.R204R		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	204	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GAAGGGGAACCGGCAGAGGAC	0.672																																					p.R204R													.	KIF19-90	0			c.C610A						.						34	38	37					17																	72340927		2199	4294	6493	SO:0001819	synonymous_variant	124602	exon7			GGGAACCGGCAGA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"Kinesins"	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.610C>A	17.37:g.72340927C>A		Somatic	151	2		WXS	Illumina HiSeq	Phase_I	204	53	NM_153209	0	0	0	0	0	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|1.000;T|0.000		0.672	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		A	72340927	C	A	72340927	2	1	158	1	0	0	0	0	0	0	0	1	8303	643	23	4		4	KIF19	17	72340927	Silent	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	45338903	72340927	8854283	41	14388											
BTBD2	55643	broad.mit.edu	37	chr19	1986958	1986958	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctggcccaagacggtgttGctatcggtgtgaataatctg	8	13	12	8	2	2	2	0	1	2	1	3	2	2	2	1	3	1	2	1	3	4	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr19:1986958G>A	ENST00000255608.4	-	8	1303	c.1287C>T	c.(1285-1287)agC>agT	p.S429S	AC005306.3_ENST00000587498.1_RNA|AC005306.3_ENST00000588480.1_RNA	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	429						cytoplasmic mRNA processing body (GO:0000932)				endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGACGGTGTTGCTATCGGTGT	0.662																																					p.S429S													.	BTBD2-92	0			c.C1287T						.						73	83	80					19																	1986958		2203	4300	6503	SO:0001819	synonymous_variant	55643	exon8			GGTGTTGCTATCG	AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"BTB/POZ domain containing"	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.1287C>T	19.37:g.1986958G>A		Somatic	103	0		WXS	Illumina HiSeq	Phase_I	98	3	NM_017797	0	0	111	121	10	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Silent	SNP	ENST00000255608.4	37	CCDS12078.1																																																																																			.		0.662	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2			A	1986958	G	A	1986958	2	1	158	1	0	0	0	0	0	0	0	1	1546	1310	46	2		2	BTBD2	19	1986958	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		1986958	57142025	42	14389											
LSM14A	26065	broad.mit.edu	37	chr19	34710315	34710315	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccaggtgctccttcagcTccaaggagagggcgtggggg	6	7	17	11	1	1	1	1	0	0	1	4	2	4	1	3	5	2	3	3	5	1	1	rs201741862		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr19:34710315T>G	ENST00000433627.5	+	7	876	c.801T>G	c.(799-801)gcT>gcG	p.A267A	LSM14A_ENST00000544216.3_Silent_p.A267A|LSM14A_ENST00000540746.2_Silent_p.A226A	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	267					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.A267A(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					CTCCTTCAGCTCCAAGGAGAG	0.438																																					p.A267A													.	LSM14A-91	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.T801G						.						64	74	71					19																	34710315		2203	4300	6503	SO:0001819	synonymous_variant	26065	exon7			TTCAGCTCCAAGG	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.801T>G	19.37:g.34710315T>G		Somatic	71	2		WXS	Illumina HiSeq	Phase_I	98	3	NM_001114093	0	0	9	9	0	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Silent	SNP	ENST00000433627.5	37	CCDS46040.1																																																																																			T|0.999;G|0.001		0.438	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		G	34710315	T	G	34710315	2	3	158	1	0	0	0	0	0	0	0	1	9079	1538	54	5		5	LSM14A	19	34710315	Silent	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	32723357	34710315	24418668	43	14390											
RYR1	6261	broad.mit.edu	37	chr19	38995663	38995663	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgatcatcccggagaagcTggactccttcattaacaagt	11	11	9	10	1	2	2	2	1	0	1	4	4	4	3	2	2	2	1	2	2	3	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr19:38995663T>C	ENST00000359596.3	+	52	8252	c.8252T>C	c.(8251-8253)cTg>cCg	p.L2751P	RYR1_ENST00000355481.4_Missense_Mutation_p.L2751P|RYR1_ENST00000360985.3_Missense_Mutation_p.L2751P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2751	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCGGAGAAGCTGGACTCCTTC	0.562																																					p.L2751P													.	RYR1-100	0			c.T8252C						.						87	83	85					19																	38995663		2203	4300	6503	SO:0001583	missense	6261	exon52			AGAAGCTGGACTC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"Ion channels / Ryanodine receptors"	10483	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 137"	180901	"central core disease of muscle"	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.8252T>C	19.37:g.38995663T>C	ENSP00000352608:p.Leu2751Pro	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	165	5	NM_001042723	0	0	0	0	0	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.236978	0.58886	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.93247	-3.19;-3.19;-3.19	4.38	4.38	0.52667	Ryanodine receptor Ryr (1);	0.000000	0.52532	U	0.000075	D	0.96956	0.9006	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97601	1.0123	10	0.87932	D	0	.	12.8832	0.58028	0.0:0.0:0.0:1.0	.	2751;2751	P21817-2;P21817	.;RYR1_HUMAN	P	2751	ENSP00000352608:L2751P;ENSP00000347667:L2751P;ENSP00000354254:L2751P	ENSP00000347667:L2751P	L	+	2	0	RYR1	43687503	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	7.890000	0.87313	1.744000	0.51775	0.402000	0.26972	CTG	.		0.562	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	38995663	T	C	38995663	3	2	158	1	0	0	0	0	1	0	0	0	13800	1580	55	3	8458	3	RYR1	19	38995663	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	4285348	38995663	20133320	44	14391											
ZNF628	89887	hgsc.bcm.edu	37	chr19	55993264	55993264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcccccgccccgggtaccgCctccgcggccccgccccccc	1	2	10	28	7	0	0	0	0	0	0	1	0	1	0	12	2	1	1	12	2	1	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr19:55993264C>T	ENST00000598519.1	+	3	1257	c.704C>T	c.(703-705)gCc>gTc	p.A235V	ZNF628_ENST00000391718.2_Missense_Mutation_p.A231V			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	235	Pro-rich.				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)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		ccgggtaccgcctccgcggcc	0.766																																					p.A235V		.											.	ZNF628-22	0			c.C704T						.						3	4	3					19																	55993264		1658	3351	5009	SO:0001583	missense	89887	exon3			GTACCGCCTCCGC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"Zinc fingers, C2H2-type"	28054	protein-coding gene	gene with protein product	"Zinc finger expressed in Embryonal cells and Certain adult organs"	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.704C>T	19.37:g.55993264C>T	ENSP00000469591:p.Ala235Val	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	7	5	NM_033113	0	0	0	0	0	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	37	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	7.048	0.563911	0.13498	.	.	ENSG00000197483	ENST00000391718	T	0.08807	3.05	3.0	1.93	0.25924	.	.	.	.	.	T	0.06325	0.0163	N	0.19112	0.55	0.09310	N	1	B	0.19445	0.036	B	0.24701	0.055	T	0.35919	-0.9769	9	0.54805	T	0.06	-3.6893	8.11	0.30909	0.0:0.7504:0.2496:0.0	.	231	Q5EBL2	ZN628_HUMAN	V	231	ENSP00000375598:A231V	ENSP00000375598:A231V	A	+	2	0	ZNF628	60685076	0.734000	0.28142	0.009000	0.14445	0.152000	0.21847	0.878000	0.28126	0.836000	0.34901	0.459000	0.35465	GCC	.		0.766	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		T	55993264	C	T	55993264	3	4	158	1	0	0	0	0	1	0	0	0	18084	739	26	2	694	2	ZNF628	19	55993264	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	16997601	55993264	3135719	45	14392											
SLCO4A1	28231	broad.mit.edu	37	chr20	61288357	61288357	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgcttatgggcacggggtCgctggtgttcgcgctgcccc	2	10	16	13	4	0	0	0	0	0	0	2	0	0	0	2	4	2	6	2	4	1	2	rs559448067		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr20:61288357C>T	ENST00000370507.1	+	1	647	c.551C>T	c.(550-552)tCg>tTg	p.S184L	SLCO4A1_ENST00000217159.1_Missense_Mutation_p.S184L			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	184					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GGCACGGGGTCGCTGGTGTTC	0.692													C|||	1	0.000199681	0	0	5008	,	,		16738	0		0.001	False		,,,				2504	0				p.S184L	Pancreas(168;741 2006 10379 40139 45334)												.	SLCO4A1-91	0			c.C551T						.						44	40	41					20																	61288357		2202	4298	6500	SO:0001583	missense	28231	exon2			CGGGGTCGCTGGT	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"Solute carriers"	10953	protein-coding gene	gene with protein product		612436	"solute carrier family 21 (organic anion transporter), member 12"	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.551C>T	20.37:g.61288357C>T	ENSP00000359538:p.Ser184Leu	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	121	4	NM_016354	0	0	2	2	0	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.748817	0.69533	.	.	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507;ENST00000342674	T;T	0.44881	0.91;0.91	4.58	4.58	0.56647	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.67373	0.2886	M	0.89840	3.065	0.80722	D	1	D	0.56968	0.978	P	0.58077	0.832	T	0.77062	-0.2727	10	0.66056	D	0.02	.	17.3394	0.87291	0.0:1.0:0.0:0.0	.	184	Q96BD0	SO4A1_HUMAN	L	184	ENSP00000217159:S184L;ENSP00000359538:S184L	ENSP00000217159:S184L	S	+	2	0	SLCO4A1	60758802	1.000000	0.71417	0.689000	0.30133	0.027000	0.11550	5.827000	0.69300	2.085000	0.62840	0.462000	0.41574	TCG	.		0.692	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354		T	61288357	C	T	61288357	3	4	158	1	0	0	0	0	1	0	0	0	14761	893	31	1	553	1	SLCO4A1	20	61288357	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		61288357	1737163	46	14393											
TOP3B	8940	broad.mit.edu	37	chr22	22318552	22318552	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgtcggcccagtaggggTggttggcctgctgccgcaga	4	8	17	12	3	0	1	0	0	0	1	1	1	0	1	4	5	2	4	4	5	1	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr22:22318552T>G	ENST00000398793.2	-	10	1513	c.1079A>C	c.(1078-1080)cAc>cCc	p.H360P	TOP3B_ENST00000413067.2_Missense_Mutation_p.H89P|TOP3B_ENST00000357179.5_Missense_Mutation_p.H360P	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	360					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CCAGTAGGGGTGGTTGGCCTG	0.622																																					p.H360P													.	TOP3B-538	0			c.A1079C						.						107	91	96					22																	22318552		2203	4300	6503	SO:0001583	missense	8940	exon10			TAGGGGTGGTTGG	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1079A>C	22.37:g.22318552T>G	ENSP00000381773:p.His360Pro	Somatic	124	8		WXS	Illumina HiSeq	Phase_I	133	12	NM_003935	0	0	0	0	0	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	37	CCDS13797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.23|17.23	3.336332|3.336332	0.60963|0.60963	.|.	.|.	ENSG00000100038|ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000413067|ENST00000457270	T;T;T|.	0.21932|.	1.98;1.98;1.98|.	5.05|5.05	5.05|5.05	0.67936|0.67936	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central region, subdomain 3 (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);|.	0.134123|.	0.64402|.	D|.	0.000003|.	T|T	0.79387|0.79387	0.4437|0.4437	M|M	0.86864|0.86864	2.845|2.845	0.41223|0.41223	D|D	0.986527|0.986527	P;P|.	0.38565|.	0.637;0.584|.	B;B|.	0.40101|.	0.319;0.213|.	T|T	0.83056|0.83056	-0.0150|-0.0150	10|5	0.52906|.	T|.	0.07|.	.|.	14.9623|14.9623	0.71166|0.71166	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	360;360|.	O95985;O95985-2|.	TOP3B_HUMAN;.|.	P|P	360;360;89|155	ENSP00000349705:H360P;ENSP00000381773:H360P;ENSP00000393118:H89P|.	ENSP00000349705:H360P|.	H|T	-|-	2|1	0|0	TOP3B|TOP3B	20648552|20648552	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.922000|0.922000	0.55478|0.55478	2.975000|2.975000	0.49281|0.49281	2.122000|2.122000	0.65172|0.65172	0.459000|0.459000	0.35465|0.35465	CAC|ACC	.		0.622	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		G	22318552	T	G	22318552	3	3	158	1	0	0	0	0	1	0	0	0	16401	1696	59	5	1545	5	TOP3B	22	22318552	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10		22318552	28986014	47	14394											
RNF128	79589	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	106034465	106034465	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaacacgtgcagtcaacaaGtaagcatcatactaaaggtt	16	8	9	8	1	2	0	2	0	0	0	2	1	2	1	0	2	5	4	0	2	7	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chrX:106034465G>A	ENST00000255499.2	+	6	1403		c.e6+1		RNF128_ENST00000324342.3_Splice_Site	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase						negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						CAGTCAACAAGTAAGCATCAT	0.453																																					.		.											.	RNF128-227	0			c.1075+1G>A						.						172	148	156					X																	106034465		2203	4300	6503	SO:0001630	splice_region_variant	79589	exon6			CAACAAGTAAGCA	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"RING-type (C3HC4) zinc fingers"	21153	protein-coding gene	gene with protein product		300439	"ring finger protein 128"				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.1153+1G>A	X.37:g.106034465G>A		Somatic	141	0		WXS	Illumina HiSeq	Phase_I	136	33	NM_024539	0	0	0	0	0	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Splice_Site	SNP	ENST00000255499.2	37	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781964	0.70222	.	.	ENSG00000133135	ENST00000324342;ENST00000255499	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.497	0.67694	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RNF128	105921121	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	6.181000	0.71988	2.165000	0.68154	0.506000	0.49869	.	.		0.453	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539	Intron	A	106034465	G	A	106034465	5	1	158	1	0	0	0	0	0	0	1	0	13468	1043	36	2	1586	2	RNF128	23	106034465	Splice_Site	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		106034465	49236095	48	14395											
SKI	6497	hgsc.bcm.edu	37	chr1	2238153	2238153	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caggaacagctgtggccgcgGgcccgccccgaggctgcggg	5	3	18	15	5	0	0	0	0	0	0	0	2	0	1	4	5	3	2	4	5	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:2238153G>A	ENST00000378536.4	+	7	2208	c.2136G>A	c.(2134-2136)cgG>cgA	p.R712R		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	712					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		TGTGGCCGCGGGCCCGCCCCG	0.761																																					p.R712R	Ovarian(177;144 1678 13697 20086 27838 40755)	.											.	SKI-838	0			c.G2136A						.						5	6	6					1																	2238153		1501	2825	4326	SO:0001819	synonymous_variant	6497	exon7			GCCGCGGGCCCGC	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.2136G>A	1.37:g.2238153G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	26	21	NM_003036	0	0	1	2	1	Q5SYT7	Silent	SNP	ENST00000378536.4	37	CCDS39.1																																																																																			.		0.761	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		A	2238153	G	A	2238153	2	1	159	1	0	0	0	0	0	0	0	1	14389	1219	43	2		2	SKI	1	2238153	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		2238153	247012468	1	14396											
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	27101241	27101241	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatgacatgacctataattAtgccaacaggcagagcacgg	15	8	9	9	1	0	3	0	2	0	1	0	3	0	3	2	2	3	2	2	2	5	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:27101241A>G	ENST00000324856.7	+	18	4894	c.4523A>G	c.(4522-4524)tAt>tGt	p.Y1508C	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Missense_Mutation_p.Y1125C|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1508					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		ACCTATAATTATGCCAACAGG	0.572			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Y1508C		.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A-584	0			c.A4523G						.						68	72	71					1																	27101241		2203	4300	6503	SO:0001583	missense	8289	exon18			ATAATTATGCCAA	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4523A>G	1.37:g.27101241A>G	ENSP00000320485:p.Tyr1508Cys	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	70	20	NM_006015	0	0	4	14	10	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650090	0.67472	.	.	ENSG00000117713	ENST00000324856;ENST00000374152	T;T	0.05996	3.53;3.36	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.991;0.99;0.996	T	0.00175	-1.1954	10	0.44086	T	0.13	-5.0146	15.8453	0.78883	1.0:0.0:0.0:0.0	.	1125;1508;1161	O14497-3;O14497;Q4LE49	.;ARI1A_HUMAN;.	C	1508;1125	ENSP00000320485:Y1508C;ENSP00000363267:Y1125C	ENSP00000320485:Y1508C	Y	+	2	0	ARID1A	26973828	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.707000	0.74654	2.330000	0.79161	0.528000	0.53228	TAT	.		0.572	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27101241	A	G	27101241	3	3	159	1	0	0	0	0	1	0	0	0	913	449	16	3	4593	3	ARID1A	1	27101241	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	24863088	27101241	222149380	2	14397											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35331687	35331687	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcgggccggaccggtcaCagcctggtctgggcctcggg	3	6	19	13	4	2	0	1	0	1	0	3	1	2	1	4	7	1	0	4	7	0	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:35331687C>T	ENST00000373347.1	-	12	3205	c.2937G>A	c.(2935-2937)ctG>ctA	p.L979L	DLGAP3_ENST00000235180.4_Silent_p.L979L			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	979					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				ggaccggtcacagcctggtct	0.731																																					p.L979L		.											.	DLGAP3-71	0			c.G2937A						.						11	13	12					1																	35331687		2181	4267	6448	SO:0001819	synonymous_variant	58512	exon10			CGGTCACAGCCTG	AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.2937G>A	1.37:g.35331687C>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	45	13	NM_001080418	0	0	0	0	0	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	37	CCDS30670.1																																																																																			.		0.731	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		T	35331687	C	T	35331687	2	4	159	1	0	0	0	0	0	0	0	1	4572	465	17	2		2	DLGAP3	1	35331687	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	8230446	35331687	213918934	3	14398											
INADL	10207	broad.mit.edu	37	chr1	62271195	62271195	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcctgattatgaagtaaTggtatgttaaaatgctctaa	13	14	10	4	0	1	2	0	2	1	0	2	2	2	2	1	2	1	4	1	2	7	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:62271195T>A	ENST00000371158.2	+	13	1739	c.1625T>A	c.(1624-1626)aTg>aAg	p.M542K	INADL_ENST00000316485.6_Splice_Site_p.M542K	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	542					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TATGAAGTAATGGTATGTTAA	0.363																																					p.M542K													.	INADL-94	0			c.T1625A						.						93	99	97					1																	62271195		2203	4300	6503	SO:0001630	splice_region_variant	10207	exon13			AAGTAATGGTATG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1626+1T>A	1.37:g.62271195T>A		Somatic	68	0		WXS	Illumina HiSeq	Phase_I	49	4	NM_176877	0	0	0	0	0	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	T	19.31	3.802160	0.70682	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.13657	2.69;2.57	5.69	5.69	0.88448	PDZ/DHR/GLGF (1);	0.057835	0.64402	D	0.000002	T	0.36744	0.0978	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.998	D;D;D	0.85130	0.997;0.99;0.968	T	0.06516	-1.0822	10	0.30854	T	0.27	.	14.5128	0.67800	0.0:0.0:0.0:1.0	.	542;542;542	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	K	542	ENSP00000360200:M542K;ENSP00000326199:M542K	ENSP00000255202:M542K	M	+	2	0	INADL	62043783	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.172000	0.65003	2.174000	0.68829	0.528000	0.53228	ATG	.		0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	Missense_Mutation	A	62271195	T	A	62271195	5	1	159	1	0	0	0	0	0	0	1	0	7752	1478	51	5	1671	5	INADL	1	62271195	Splice_Site	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	26939508	62271195	186979426	4	14399											
ANKRD35	148741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	145567075	145567075	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcatctccacctacaggaatCatctactgaatgctgctcgg	10	11	7	13	1	4	1	2	1	2	0	6	2	4	2	2	2	4	2	2	2	4	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:145567075C>T	ENST00000355594.4	+	12	3010	c.2923C>T	c.(2923-2925)Cat>Tat	p.H975Y		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	975										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTACAGGAATCATCTACTGAA	0.473																																					p.H975Y	Melanoma(9;127 754 22988 51047)	.											.	ANKRD35-95	0			c.C2923T						.						168	155	160					1																	145567075		2203	4300	6503	SO:0001583	missense	148741	exon12			AGGAATCATCTAC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"Ankyrin repeat domain containing"	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.2923C>T	1.37:g.145567075C>T	ENSP00000347802:p.His975Tyr	Somatic	165	0		WXS	Illumina HiSeq	Phase_I	142	38	NM_144698	0	0	2	2	0	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780583	0.49891	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.58652	0.32	5.12	5.12	0.69794	.	0.000000	0.47852	D	0.000209	T	0.69878	0.3160	M	0.74881	2.28	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.73266	-0.4037	10	0.87932	D	0	-3.866	13.9259	0.63961	0.0:1.0:0.0:0.0	.	975	Q8N283	ANR35_HUMAN	Y	884;975	ENSP00000347802:H975Y	ENSP00000347802:H975Y	H	+	1	0	ANKRD35	144278432	0.991000	0.36638	0.888000	0.34837	0.244000	0.25665	2.767000	0.47637	2.679000	0.91253	0.655000	0.94253	CAT	.		0.473	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		T	145567075	C	T	145567075	3	4	159	1	0	0	0	0	1	0	0	0	664	826	29	2	2969	2	ANKRD35	1	145567075	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	83295880	145567075	103683546	5	14400											
PKP1	5317	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	201285751	201285751	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcagtacctgagctcccagGatgagaaataccaggccatt	12	8	10	11	0	0	2	0	2	0	1	1	4	1	3	4	2	4	3	4	2	3	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:201285751G>A	ENST00000352845.3	+	4	772	c.772G>A	c.(772-774)Gat>Aat	p.D258N	PKP1_ENST00000367324.3_Missense_Mutation_p.D258N|PKP1_ENST00000263946.3_Missense_Mutation_p.D258N|PKP1_ENST00000475988.1_3'UTR			Q13835	PKP1_HUMAN	plakophilin 1	258					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GAGCTCCCAGGATGAGAAATA	0.537																																					p.D258N													.	PKP1-92	0			c.G772A						.						83	62	69					1																	201285751		2203	4300	6503	SO:0001583	missense	5317	exon4			TCCCAGGATGAGA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"Armadillo repeat containing"	9023	protein-coding gene	gene with protein product	"ectodermal dysplasia/skin fragility syndrome"	601975	"plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.772G>A	1.37:g.201285751G>A	ENSP00000295597:p.Asp258Asn	Somatic	250	1		WXS	Illumina HiSeq	Phase_I	207	54	NM_001005337	0	0	0	0	0	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.844590	0.51164	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.55588	0.51;0.51;0.51	4.91	3.96	0.45880	Armadillo-like helical (1);Armadillo-type fold (1);	0.200242	0.51477	D	0.000089	T	0.45397	0.1340	L	0.49778	1.585	0.53688	D	0.99997	P;P	0.49253	0.741;0.921	B;B	0.40940	0.344;0.33	T	0.34428	-0.9829	10	0.19147	T	0.46	-15.2438	14.2686	0.66138	0.0:0.0:0.8497:0.1502	.	258;258	Q13835-2;Q13835	.;PKP1_HUMAN	N	258	ENSP00000356293:D258N;ENSP00000263946:D258N;ENSP00000295597:D258N	ENSP00000263946:D258N	D	+	1	0	PKP1	199552374	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.782000	0.85680	1.008000	0.39264	0.591000	0.81541	GAT	.		0.537	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201285751	G	A	201285751	3	1	159	1	0	0	0	0	1	0	0	0	12010	1174	41	2	786	2	PKP1	1	201285751	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	55718676	201285751	47964870	6	14401											
LEFTY1	10637	broad.mit.edu;bcgsc.ca	37	chr1	226075306	226075306	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggcctcggtcacgtcgaagGccttccagccgctctcgtgg	4	8	13	16	6	2	0	1	0	1	0	6	1	3	0	4	4	1	1	4	4	1	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:226075306G>T	ENST00000272134.5	-	3	609	c.530C>A	c.(529-531)gCc>gAc	p.A177D	RP4-559A3.7_ENST00000432920.2_Silent_p.G285G|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	177					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CACGTCGAAGGCCTTCCAGCC	0.701																																					p.A177D													.	LEFTY1-90	0			c.C530A						.						12	15	14					1																	226075306		2139	4187	6326	SO:0001583	missense	10637	exon3			TCGAAGGCCTTCC	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"left-right determination, factor B"	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.530C>A	1.37:g.226075306G>T	ENSP00000272134:p.Ala177Asp	Somatic	60	1		WXS	Illumina HiSeq	Phase_I	82	21	NM_020997	0	0	5	7	2	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	.	.	.	.	.	.	.	.	.	.	G	9.819	1.185166	0.21870	.	.	ENSG00000243709	ENST00000272134	T	0.65732	-0.17	3.9	-0.769	0.11009	Transforming growth factor-beta, N-terminal (1);	0.381216	0.31392	N	0.007739	T	0.48295	0.1492	L	0.50919	1.6	0.26170	N	0.979875	B	0.09022	0.002	B	0.14578	0.011	T	0.34800	-0.9814	10	0.52906	T	0.07	.	4.8949	0.13746	0.1491:0.3794:0.3732:0.0983	.	177	O75610	LFTY1_HUMAN	D	177	ENSP00000272134:A177D	ENSP00000272134:A177D	A	-	2	0	LEFTY1	224141929	1.000000	0.71417	0.730000	0.30809	0.571000	0.35966	0.567000	0.23608	-0.793000	0.04475	-1.786000	0.00637	GCC	.		0.701	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997		T	226075306	G	T	226075306	3	4	159	1	0	0	0	0	1	0	0	0	8736	1203	42	4	578	4	LEFTY1	1	226075306	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	24789555	226075306	23175315	7	14402											
TAF5L	27097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	229730727	229730727	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagtatctgatggacatgtCttcagaacaagagagcaacc	14	8	9	10	0	3	3	1	1	2	2	3	5	3	4	2	1	3	2	2	1	4	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:229730727C>T	ENST00000366676.1	-	4	1086	c.1087G>A	c.(1087-1089)Gac>Aac	p.D363N	TAF5L_ENST00000258281.2_Missense_Mutation_p.D363N			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	363					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				ATGGACATGTCTTCAGAACAA	0.527																																					p.D363N		.											.	TAF5L-91	0			c.G1087A						.						121	102	108					1																	229730727		2203	4300	6503	SO:0001583	missense	27097	exon5			ACATGTCTTCAGA	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"WD repeat domain containing"	17304	protein-coding gene	gene with protein product	"PCAF associated factor 65 beta"		"TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.1087G>A	1.37:g.229730727C>T	ENSP00000355636:p.Asp363Asn	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	85	5	NM_014409	0	0	7	11	4	Q5TDI5|Q5TDI6|Q8IW31	Missense_Mutation	SNP	ENST00000366676.1	37	CCDS1581.1	.	.	.	.	.	.	.	.	.	.	C	33	5.238803	0.95240	.	.	ENSG00000135801	ENST00000366676;ENST00000258281	D;D	0.88975	-2.45;-2.45	5.88	5.88	0.94601	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.96027	0.8706	M	0.91920	3.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96166	0.9119	10	0.87932	D	0	-34.0939	20.2422	0.98381	0.0:1.0:0.0:0.0	.	363	O75529	TAF5L_HUMAN	N	363	ENSP00000355636:D363N;ENSP00000258281:D363N	ENSP00000258281:D363N	D	-	1	0	TAF5L	227797350	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.811000	0.86092	2.782000	0.95742	0.655000	0.94253	GAC	.		0.527	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409		T	229730727	C	T	229730727	3	4	159	1	0	0	0	0	1	0	0	0	15561	913	32	2	686	2	TAF5L	1	229730727	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	3655421	229730727	19519894	8	14403											
SH3BP5L	80851	hgsc.bcm.edu	37	chr1	249106348	249106348	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctccagccccgcaccctcGgccccctcaatcccgctgtc	4	7	6	24	3	1	0	1	0	0	0	6	0	4	0	8	1	1	2	8	1	1	0	rs202116012	byFrequency	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:249106348G>C	ENST00000366472.5	-	7	2162	c.933C>G	c.(931-933)gcC>gcG	p.A311A	SH3BP5L_ENST00000411742.2_Silent_p.A279A|SH3BP5L_ENST00000475978.1_5'UTR	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	311										endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CCGCACCCTCGGCCCCCTCAA	0.746													G|||	23	0.00459265	8e-04	0.0144	5008	,	,		12601	0		0.0119	False		,,,				2504	0				p.A311A		.											.	SH3BP5L-90	0			c.C933G						.	G		17,4377		0,17,2180	13	16	15		933	-8.6	0.4	1		15	135,8433		2,131,4151	no	coding-synonymous	SH3BP5L	NM_030645.1		2,148,6331	CC,CG,GG		1.5756,0.3869,1.1727		311/394	249106348	152,12810	2197	4284	6481	SO:0001819	synonymous_variant	80851	exon7			ACCCTCGGCCCCC	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.933C>G	1.37:g.249106348G>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	22	17	NM_030645	0	0	0	10	10	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Silent	SNP	ENST00000366472.5	37	CCDS31126.1																																																																																			G|0.991;C|0.008		0.746	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645		C	249106348	G	C	249106348	2	2	159	1	0	0	0	0	0	0	0	1	14280	1103	39	4		4	SH3BP5L	1	249106348	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	19375621	249106348	144273	9	14404											
HEATR5B	54497	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	37286106	37286107	+	Frame_Shift_Ins	INS	-	-	A																															ttcagttagtagctcaggacINSaatgtgcaacgaagctcctc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:37286106_37286107insA	ENST00000233099.5	-	13	1968_1969	c.1873_1874insT	c.(1873-1875)tgtfs	p.C625fs	HEATR5B_ENST00000354531.2_Frame_Shift_Ins_p.C625fs	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	625						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TAGCTCAGGACAATGTGCAACG	0.347																																					p.C625fs		.											.	HEATR5B-142	0			c.1874_1875insT						.																																			SO:0001589	frameshift_variant	54497	exon13			.	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.1874dupT	2.37:g.37286108_37286108dupA	ENSP00000233099:p.Cys625fs	Somatic	309	0		WXS	Illumina HiSeq	Phase_I	284	57	NM_019024	0	0	0	0	0	B5MDU8|Q7Z3B2|Q9NVL7	Frame_Shift_Ins	INS	ENST00000233099.5	37	CCDS33181.1																																																																																			.		0.347	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37286107	-	A	37286106	7	5	159	1	0	1	1	0	0	0	0	0	7053	478	17	0	4437	0	HEATR5B	2	37286106	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10		37286106	205913267	10	14405											
GKN1	56287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	69207170	69207170	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgtcgtgggattccaacAtacatggctgaggagatgca	11	10	13	7	1	0	2	0	1	0	1	2	4	1	3	1	3	3	2	1	3	2	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:69207170A>G	ENST00000377938.2	+	5	546	c.483A>G	c.(481-483)acA>acG	p.T161T		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	161	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						GGATTCCAACATACATGGCTG	0.507																																					p.T161T		.											.	GKN1-153	0			c.A483G						.						156	111	126					2																	69207170		2203	4300	6503	SO:0001819	synonymous_variant	56287	exon5			TCCAACATACATG	AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"BRICHOS domain containing"	23217	protein-coding gene	gene with protein product	"BRICHOS domain containing 1"	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.483A>G	2.37:g.69207170A>G		Somatic	248	0		WXS	Illumina HiSeq	Phase_I	207	41	NM_019617	0	0	0	0	0	Q8IUA9	Silent	SNP	ENST00000377938.2	37	CCDS1891.2																																																																																			.		0.507	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617		G	69207170	A	G	69207170	2	3	159	1	0	0	0	0	0	0	0	1	6444	204	8	3		3	GKN1	2	69207170	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	31921064	69207170	173992203	11	14406											
SMYD5	10322	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	73447218	73447218	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcactagagaaggcagaggAgaatgcccagaggctgaccg	13	3	16	9	1	0	5	0	1	0	4	0	7	0	5	2	4	1	3	2	4	3	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:73447218A>G	ENST00000389501.4	+	3	290	c.245A>G	c.(244-246)gAg>gGg	p.E82G	SMYD5_ENST00000474652.1_3'UTR	NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5	82	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13						AAGGCAGAGGAGAATGCCCAG	0.562																																					p.E82G													.	SMYD5-226	0			c.A245G						.						68	69	69					2																	73447218		2036	4187	6223	SO:0001583	missense	10322	exon3			CAGAGGAGAATGC	U50383	CCDS33221.2	2p12	2007-02-09	2003-05-14	2003-05-16	ENSG00000135632	ENSG00000135632		"Zinc fingers, MYND-type"	16258	protein-coding gene	gene with protein product			"retinoic acid induced 15"	RAI15		8754834	Standard	NM_006062		Approved	RRG1, NN8-4AG, ZMYND23	uc002siw.2	Q6GMV2	OTTHUMG00000150482	ENST00000389501.4:c.245A>G	2.37:g.73447218A>G	ENSP00000374152:p.Glu82Gly	Somatic	143	1		WXS	Illumina HiSeq	Phase_I	147	33	NM_006062	0	0	7	23	16	D6W5H3|Q13558	Missense_Mutation	SNP	ENST00000389501.4	37	CCDS33221.2	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835850	0.71373	.	.	ENSG00000135632	ENST00000389501;ENST00000443900	T	0.50277	0.75	5.38	5.38	0.77491	SET domain (2);	0.227351	0.44483	D	0.000455	T	0.48205	0.1487	M	0.66939	2.045	0.80722	D	1	B	0.14438	0.01	B	0.19391	0.025	T	0.42531	-0.9446	10	0.34782	T	0.22	-17.1101	14.5273	0.67897	1.0:0.0:0.0:0.0	.	82	Q6GMV2	SMYD5_HUMAN	G	82;55	ENSP00000374152:E82G	ENSP00000374152:E82G	E	+	2	0	SMYD5	73300726	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.660000	0.74417	2.169000	0.68431	0.533000	0.62120	GAG	.		0.562	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	NM_006062		G	73447218	A	G	73447218	3	3	159	1	0	0	0	0	1	0	0	0	14857	304	11	3	255	3	SMYD5	2	73447218	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	4240048	73447218	169752155	12	14407											
IMMT	10989	broad.mit.edu;bcgsc.ca	37	chr2	86371928	86371928	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttctgcagatgaggtcttCatgctgtactttaatgcctc	7	16	9	9	0	3	2	1	1	2	1	4	2	3	2	1	1	4	4	1	1	2	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:86371928C>A	ENST00000410111.3	-	15	2127	c.1740G>T	c.(1738-1740)atG>atT	p.M580I	IMMT_ENST00000254636.5_Missense_Mutation_p.M481I|IMMT_ENST00000442664.2_Missense_Mutation_p.M579I|IMMT_ENST00000409051.2_Missense_Mutation_p.M533I|IMMT_ENST00000449247.2_Missense_Mutation_p.M569I	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	580					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						ATGAGGTCTTCATGCTGTACT	0.473																																					p.M580I													.	IMMT-91	0			c.G1740T						.						74	71	72					2																	86371928		1917	4125	6042	SO:0001583	missense	10989	exon15			GGTCTTCATGCTG	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"mitofilin", "mitochondrial inner membrane organizing system 2"	600378	"inner membrane protein, mitochondrial (mitofilin)"			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1740G>T	2.37:g.86371928C>A	ENSP00000387262:p.Met580Ile	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	73	22	NM_006839	0	0	73	116	43	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	37	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.62|13.62	2.291316|2.291316	0.40494|0.40494	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000419070|ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000409715	.|T;T;T;T;T	.|0.26518	.|1.73;1.73;1.73;1.73;1.73	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|0.093246	.|0.64402	.|D	.|0.000001	.|T	.|0.23171	.|0.0560	L|L	0.27053|0.27053	0.805|0.805	0.52099|0.52099	D|D	0.999945|0.999945	.|B;B;B;B;B	.|0.15141	.|0.008;0.009;0.012;0.012;0.008	.|B;B;B;B;B	.|0.23419	.|0.022;0.029;0.027;0.027;0.046	.|T	.|0.03000	.|-1.1084	.|10	.|0.35671	.|T	.|0.21	-19.915|-19.915	19.1497|19.1497	0.93482|0.93482	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|533;568;569;548;580	.|B9A067;B4DKR1;Q16891-2;Q16891-3;Q16891	.|.;.;.;.;IMMT_HUMAN	X|I	435|481;569;580;579;533;569;548;481	.|ENSP00000254636:M481I;ENSP00000396899:M569I;ENSP00000387262:M580I;ENSP00000407788:M579I;ENSP00000387227:M533I	.|ENSP00000254636:M481I	E|M	-|-	1|3	0|0	IMMT|IMMT	86225439|86225439	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	3.829000|3.829000	0.55760|0.55760	2.761000|2.761000	0.94854|0.94854	0.650000|0.650000	0.86243|0.86243	GAA|ATG	.		0.473	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		A	86371928	C	A	86371928	3	1	159	1	0	0	0	0	1	0	0	0	7739	826	29	4	540	4	IMMT	2	86371928	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	12924710	86371928	156827445	13	14408											
LYG2	254773	broad.mit.edu	37	chr2	99861727	99861727	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagtttctagctaaatacctGcatcaagccaaatttaagtc	15	12	5	9	0	2	0	1	0	1	0	3	0	2	0	2	0	4	3	2	0	8	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:99861727G>T	ENST00000409238.1	-	3	399	c.379C>A	c.(379-381)Cag>Aag	p.Q127K	LYG2_ENST00000423800.1_Missense_Mutation_p.Q127K|LYG2_ENST00000409679.1_Missense_Mutation_p.Q127K|LYG2_ENST00000333017.2_Missense_Mutation_p.Q127K			Q86SG7	LYG2_HUMAN	lysozyme G-like 2	127					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|stomach(1)	12						CTAAATACCTGCATCAAGCCA	0.517																																					p.Q127K													.	LYG2-91	0			c.C379A						.						94	88	90					2																	99861727		2203	4300	6503	SO:0001583	missense	254773	exon4			ATACCTGCATCAA	AF323919	CCDS2042.1	2q11.2	2008-02-05			ENSG00000185674	ENSG00000185674			29615	protein-coding gene	gene with protein product						8889548, 12574869	Standard	NM_175735		Approved	LYGH	uc002szw.1	Q86SG7	OTTHUMG00000130643	ENST00000409238.1:c.379C>A	2.37:g.99861727G>T	ENSP00000386939:p.Gln127Lys	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_175735	0	0	0	0	0	Q496G2|Q53RW0	Missense_Mutation	SNP	ENST00000409238.1	37	CCDS2042.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700644	0.88924	.	.	ENSG00000185674	ENST00000409238;ENST00000333017;ENST00000409679;ENST00000423306	.	.	.	5.78	5.78	0.91487	Lytic transglycosylase-like, catalytic (1);Lysozyme-like domain (1);	0.000000	0.64402	D	0.000014	T	0.81143	0.4761	M	0.86178	2.8	0.53005	D	0.999963	D;D;D	0.76494	0.999;0.999;0.997	D;D;D	0.85130	0.997;0.997;0.996	T	0.82694	-0.0330	8	.	.	.	-10.5867	15.5051	0.75731	0.0:0.0:1.0:0.0	.	127;127;127	Q496G2;C9J4J0;Q86SG7	.;.;LYG2_HUMAN	K	127	.	.	Q	-	1	0	LYG2	99228159	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.108000	0.77055	2.745000	0.94114	0.555000	0.69702	CAG	.		0.517	LYG2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330307.1	NM_175735		T	99861727	G	T	99861727	3	4	159	1	0	0	0	0	1	0	0	0	9130	1328	46	4	271	4	LYG2	2	99861727	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	13489799	99861727	143337646	14	14409											
POLR1B	84172	broad.mit.edu;bcgsc.ca	37	chr2	113330280	113330285	+	In_Frame_Del	DEL	CCAATG	CCAATG	-																															ggataactatccaattgggaCcaatgccatcgttgctgtga																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	CCAATG	CCAATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:113330280_113330285delCCAATG	ENST00000263331.5	+	13	2796_2801	c.2216_2221delCCAATG	c.(2215-2223)accaatgcc>acc	p.NA740del	POLR1B_ENST00000409894.3_In_Frame_Del_p.NA557del|POLR1B_ENST00000417433.2_In_Frame_Del_p.NA684del|POLR1B_ENST00000537335.1_In_Frame_Del_p.NA529del|POLR1B_ENST00000541869.1_In_Frame_Del_p.NA778del	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	740					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						CCAATTGGGACCAATGCCATCGTTGC	0.393																																					p.739_741del	Ovarian(16;256 576 9537 23969 41147)												.	POLR1B-91	0			c.2216_2221del						.																																			SO:0001651	inframe_deletion	84172	exon13			TTGGGACCAATGC	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"RNA polymerase subunits"	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.2216_2221delCCAATG	2.37:g.113330280_113330285delCCAATG	ENSP00000263331:p.Asn740_Ala741del	Somatic	170	0		WXS	Illumina HiSeq	Phase_I	121	9	NM_019014	0	0	0	0	0	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	In_Frame_Del	DEL	ENST00000263331.5	37	CCDS2097.1																																																																																			.		0.393	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		-	113330285	CCAATG	-	113330280	7	5	159	1	0	1	0	1	0	0	0	0	12236	507	18	0	2266	0	POLR1B	2	113330280	In_Frame_Del	DEL	CCAATG	TCGA-PJ-A5Z8-01A-11D-A28G-10	13468553	113330280	129869093	15	14410											
DCAF17	80067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	172333421	172333421	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttctcagcatcagatctcTgaagattttgtcattttggc	9	16	8	8	0	4	3	3	1	2	2	6	3	4	3	0	1	1	2	0	1	1	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:172333421T>A	ENST00000375255.3	+	11	1470	c.1143T>A	c.(1141-1143)tcT>tcA	p.S381S	DCAF17_ENST00000468592.1_3'UTR|DCAF17_ENST00000539783.1_Intron	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17	381					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						ATCAGATCTCTGAAGATTTTG	0.323																																					p.S381S		.											.	DCAF17-90	0			c.T1143A						.						70	72	71					2																	172333421		2203	4300	6503	SO:0001819	synonymous_variant	80067	exon11			GATCTCTGAAGAT	AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"DDB1 and CUL4 associated factors"	25784	protein-coding gene	gene with protein product	"Woodhouse-Sakati syndrome"	612515	"chromosome 2 open reading frame 37"	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.1143T>A	2.37:g.172333421T>A		Somatic	150	0		WXS	Illumina HiSeq	Phase_I	144	29	NM_025000	0	0	7	9	2	B2RTW5|Q53TN3|Q9H908	Silent	SNP	ENST00000375255.3	37	CCDS2243.2	.	.	.	.	.	.	.	.	.	.	T	10.52	1.373792	0.24857	.	.	ENSG00000115827	ENST00000339506;ENST00000431110	.	.	.	5.55	4.37	0.52481	.	.	.	.	.	T	0.46405	0.1391	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43015	-0.9417	4	.	.	.	-6.982	2.2645	0.04075	0.1969:0.0804:0.1334:0.5893	.	.	.	.	Q	132;83	.	.	L	+	2	0	DCAF17	172041667	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.499000	0.35671	0.913000	0.36797	0.472000	0.43445	CTG	.		0.323	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000		A	172333421	T	A	172333421	2	1	159	1	0	0	0	0	0	0	0	1	4275	1567	55	5		5	DCAF17	2	172333421	Silent	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	59003141	172333421	70865952	16	14411											
SLC40A1	30061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	190437577	190437577	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcattgagaacttacgagaaCccatccatggtacatggtca	13	10	8	10	1	2	2	2	1	0	2	3	4	3	2	2	2	4	1	2	2	4	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:190437577C>A	ENST00000261024.2	-	4	808	c.382G>T	c.(382-384)Gtt>Ttt	p.V128F	SLC40A1_ENST00000418714.1_5'Flank	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	128					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			CTTACGAGAACCCATCCATGG	0.393																																					p.V128F		.											.	SLC40A1-91	0			c.G382T						.						83	78	80					2																	190437577		2203	4300	6503	SO:0001583	missense	30061	exon4			CGAGAACCCATCC	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"Solute carriers"	10909	protein-coding gene	gene with protein product	"ferroportin 1"	604653	"solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.382G>T	2.37:g.190437577C>A	ENSP00000261024:p.Val128Phe	Somatic	196	0		WXS	Illumina HiSeq	Phase_I	215	42	NM_014585	0	0	0	0	0	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	37	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911373	0.33721	.	.	ENSG00000138449	ENST00000261024;ENST00000427241	D;D	0.94280	-3.39;-3.39	6.03	1.03	0.20045	Major facilitator superfamily domain, general substrate transporter (1);	0.604283	0.17891	N	0.158506	D	0.83848	0.5343	N	0.17474	0.49	0.42059	D	0.991157	B;B	0.09022	0.002;0.002	B;B	0.14578	0.011;0.011	T	0.70040	-0.4981	10	0.20519	T	0.43	-3.6976	7.1323	0.25508	0.0:0.3425:0.3929:0.2646	.	128;128	A8K7Y1;Q9NP59	.;S40A1_HUMAN	F	128	ENSP00000261024:V128F;ENSP00000390005:V128F	ENSP00000261024:V128F	V	-	1	0	SLC40A1	190145822	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	0.700000	0.25601	0.124000	0.18369	0.655000	0.94253	GTT	.		0.393	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			A	190437577	C	A	190437577	3	1	159	1	0	0	0	0	1	0	0	0	14660	507	18	4	1353	4	SLC40A1	2	190437577	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	18104156	190437577	52761796	17	14412											
GLS	2744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	191795284	191795284	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacagtgttaagggaattcActtttgtcacgtaagcatat	13	13	8	7	1	2	0	2	0	0	0	2	1	2	1	0	1	2	3	0	1	5	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:191795284A>G	ENST00000320717.3	+	13	1805	c.1547A>G	c.(1546-1548)cAc>cGc	p.H516R	GLS_ENST00000409428.1_Missense_Mutation_p.H21R|GLS_ENST00000409215.1_Missense_Mutation_p.H21R|GLS_ENST00000409626.1_Missense_Mutation_p.H87R|GLS_ENST00000338435.4_Missense_Mutation_p.H516R	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	516					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	AAGGGAATTCACTTTTGTCAC	0.383																																					p.H516R		.											.	GLS-92	0			c.A1547G						.						128	119	122					2																	191795284		2203	4300	6503	SO:0001583	missense	2744	exon13			GAATTCACTTTTG	AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	3.5.1.2	"Ankyrin repeat domain containing"	4331	protein-coding gene	gene with protein product		138280				10048485	Standard	NM_014905		Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.1547A>G	2.37:g.191795284A>G	ENSP00000317379:p.His516Arg	Somatic	120	0		WXS	Illumina HiSeq	Phase_I	119	31	NM_014905	0	0	0	0	0	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	37	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	A	13.95	2.388942	0.42308	.	.	ENSG00000115419	ENST00000320717;ENST00000338435;ENST00000409626;ENST00000457316;ENST00000409428;ENST00000409215;ENST00000412247	T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.84	5.84	0.93424	Beta-lactamase/transpeptidase-like (1);	0.049755	0.85682	D	0.000000	T	0.26195	0.0639	N	0.10664	0.02	0.54753	D	0.999986	B;B;B;B;B	0.12013	0.003;0.003;0.001;0.003;0.005	B;B;B;B;B	0.12156	0.004;0.006;0.003;0.006;0.007	T	0.06972	-1.0797	10	0.27082	T	0.32	-4.505	16.2233	0.82274	1.0:0.0:0.0:0.0	.	87;516;170;516;516	B7Z2P1;A8K132;Q68D38;O94925;O94925-3	.;.;.;GLSK_HUMAN;.	R	516;516;87;87;21;21;37	ENSP00000317379:H516R;ENSP00000340689:H516R;ENSP00000386417:H87R;ENSP00000395596:H87R;ENSP00000387177:H21R;ENSP00000387135:H21R;ENSP00000403329:H37R	ENSP00000317379:H516R	H	+	2	0	GLS	191503529	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.339000	0.96797	2.243000	0.73865	0.482000	0.46254	CAC	.		0.383	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			G	191795284	A	G	191795284	3	3	159	1	0	0	0	0	1	0	0	0	6483	159	6	3	1597	3	GLS	2	191795284	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	1357707	191795284	51404089	18	14413											
PGAP1	80055	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	197791195	197791195	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagagggcagaaccttaccTgatactccgggtactcaaac	12	7	11	11	1	1	3	1	1	0	2	2	4	2	3	3	3	5	2	3	3	5	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:197791195T>A	ENST00000354764.4	-	1	260	c.146A>T	c.(145-147)cAg>cTg	p.Q49L	PGAP1_ENST00000409188.1_Intron|PGAP1_ENST00000409475.1_Splice_Site_p.Q49L|PGAP1_ENST00000485830.1_Intron	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	49					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						GAACCTTACCTGATACTCCGG	0.562																																					p.Q49L		.											.	PGAP1-93	0			c.A146T						.						184	203	197					2																	197791195		2203	4300	6503	SO:0001630	splice_region_variant	80055	exon1			CTTACCTGATACT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"GPI inositol-deacylase"	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.147+1A>T	2.37:g.197791195T>A		Somatic	197	0		WXS	Illumina HiSeq	Phase_I	220	40	NM_024989	0	0	0	0	0	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.422748	0.43020	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475;ENST00000374738	D	0.83673	-1.75	4.16	4.16	0.48862	.	0.069665	0.64402	D	0.000011	T	0.70745	0.3259	N	0.15975	0.35	0.80722	D	1	B;P	0.48764	0.001;0.915	B;P	0.49361	0.001;0.608	T	0.66284	-0.5962	10	0.11485	T	0.65	-4.6463	6.88	0.24168	0.2059:0.0:0.0:0.7941	.	49;49	Q75T13-3;Q75T13	.;PGAP1_HUMAN	L	49	ENSP00000363870:Q49L	ENSP00000346809:Q49L	Q	-	2	0	PGAP1	197499440	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	2.730000	0.47335	1.752000	0.51891	0.260000	0.18958	CAG	.		0.562	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	Missense_Mutation	A	197791195	T	A	197791195	5	1	159	1	0	0	0	0	0	0	1	0	11803	1594	55	5	2730	5	PGAP1	2	197791195	Splice_Site	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	5995911	197791195	45408178	19	14414											
SGOL2	151246	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	201438489	201438489	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcatttagatctttgtcTgagatacattcacctaacat	13	14	6	8	0	3	2	1	1	2	2	3	3	3	2	1	1	2	1	1	1	4	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:201438489T>G	ENST00000357799.4	+	7	3518	c.3420T>G	c.(3418-3420)tcT>tcG	p.S1140S		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	1140					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GATCTTTGTCTGAGATACATT	0.343																																					p.S1140S		.											.	SGOL2-94	0			c.T3420G						.						109	101	103					2																	201438489		1844	4087	5931	SO:0001819	synonymous_variant	151246	exon7			TTTGTCTGAGATA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.3420T>G	2.37:g.201438489T>G		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	74	13	NM_001160046	0	0	1	3	2	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																			.		0.343	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		G	201438489	T	G	201438489	2	3	159	1	0	0	0	0	0	0	0	1	14249	1567	55	5		5	SGOL2	2	201438489	Silent	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	3647294	201438489	41760884	20	14415											
COPG	22820	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	128993744	128993745	+	Nonsense_Mutation	DNP	GC	GC	TA																															tcatgaaactgaacttcgaaGcagcctgggatgaggtaggg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr3:128993744_128993745GC>TA	ENST00000314797.6	+	22	2424_2425	c.2320_2321GC>TA	c.(2320-2322)GCa>TAa	p.A774*		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	774	Interaction with ZNF289/ARFGAP2.				COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										GAACTTCGAAGCAGCCTGGGAT	0.46																																					p.A774*		.											.	.	0			c.C2321A						.																																			SO:0001587	stop_gained	22820	exon22			TCGAAGCAGCCTG	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"coat protein gamma-cop"	615525	"coatomer protein complex, subunit gamma"	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	Exception_encountered	3.37:g.128993744_128993745delinsTA	ENSP00000325002:p.Ala774*	Somatic	283	0		WXS	Illumina HiSeq	Phase_I	313	64	NM_016128	0	0	0	0	0	A8K6M8|B3KMF6|Q54AC4	Nonsense_Mutation	DNP	ENST00000314797.6	37	CCDS33851.1																																																																																			.		0.46	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		TA	128993745	GC	TA	128993744	4	4	159	1	0	0	0	0	0	1	0	0	3737	971	34	4	2406	4	COPG	3	128993744	Nonsense_Mutation	DNP	GC	TCGA-PJ-A5Z8-01A-11D-A28G-10		128993744	69028686	21	14416											
VPS8	23355	broad.mit.edu;bcgsc.ca	37	chr3	184612489	184612503	+	Splice_Site	DEL	AGGGATCTTTTATTT	AGGGATCTTTTATTT	-																															tctccccccctttctgttacAgggatcttttatttagtcag																								rs200319292		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	AGGGATCTTTTATTT	AGGGATCTTTTATTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr3:184612489_184612503delAGGGATCTTTTATTT	ENST00000437079.3	+	23	1952_1965	c.1781_1794delAGGGATCTTTTATTT	c.(1780-1794)aagggatcttttatt>a	p.KGSFI594del	VPS8_ENST00000436792.2_Splice_Site_p.KGSFI592del|VPS8_ENST00000446204.2_Intron|VPS8_ENST00000287546.4_Splice_Site_p.KGSFI594del	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	594							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TTTCTGTTACAGGGATCTTTTATTTAGTCAGATGT	0.344																																					p.594_598del													.	VPS8-91	0			c.1782_1794del						.																																			SO:0001630	splice_region_variant	23355	exon22			TGTTACAGGGATC	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"KIAA0804"	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.1782-1AGGGATCTTTTATTT>-	3.37:g.184612489_184612503delAGGGATCTTTTATTT		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	38	9	NM_001009921	0	0	0	0	0	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Frame_Shift_Del	DEL	ENST00000437079.3	37	CCDS46971.1																																																																																			.		0.344	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	In_Frame_Del	-	184612503	AGGGATCTTTTATTT	-	184612489	8	5	159	1	0	1	0	1	0	0	1	0	17251	202	7	0	1862	0	VPS8	3	184612489	Splice_Site	DEL	AGGGATCTTTTATTT	TCGA-PJ-A5Z8-01A-11D-A28G-10	55618745	184612489	13409941	22	14417											
CPN2	1370	broad.mit.edu	37	chr3	194062032	194062032	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgcacagccagatcccagCtgccccctgccttgctttcg	5	9	8	19	1	0	1	0	0	0	1	2	1	1	1	6	0	6	3	6	0	0	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr3:194062032C>A	ENST00000323830.3	-	2	1489	c.1400G>T	c.(1399-1401)aGc>aTc	p.S467I	CPN2_ENST00000429275.1_Missense_Mutation_p.S467I	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	467					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		CAGATCCCAGCTGCCCCCTGC	0.667																																					p.S467I													.	CPN2-73	0			c.G1400T						.						59	61	60					3																	194062032		2203	4300	6503	SO:0001583	missense	1370	exon2			TCCCAGCTGCCCC	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"carboxypeptidase N, polypeptide 2, 83kD"	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.1400G>T	3.37:g.194062032C>A	ENSP00000319464:p.Ser467Ile	Somatic	69	1		WXS	Illumina HiSeq	Phase_I	93	6	NM_001080513	0	0	0	0	0	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.864966	0.32977	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.54675	0.56;0.56	5.56	-1.39	0.08997	.	0.701597	0.11887	N	0.519997	T	0.31949	0.0813	N	0.24115	0.695	0.19775	N	0.999959	B	0.18013	0.025	B	0.15052	0.012	T	0.15925	-1.0420	10	0.36615	T	0.2	.	5.7982	0.18399	0.2148:0.3055:0.4123:0.0674	.	467	P22792	CPN2_HUMAN	I	467	ENSP00000319464:S467I;ENSP00000402232:S467I	ENSP00000319464:S467I	S	-	2	0	CPN2	195543727	0.000000	0.05858	0.024000	0.17045	0.890000	0.51754	-2.048000	0.01406	-0.146000	0.11274	0.655000	0.94253	AGC	.		0.667	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		A	194062032	C	A	194062032	3	1	159	1	0	0	0	0	1	0	0	0	3816	797	28	4	241	4	CPN2	3	194062032	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	9449543	194062032	3960398	23	14418											
HPSE	10855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	84240579	84240579	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagggccattccaaccgtaaCttctcctccacatcaggagg	10	9	8	14	1	2	0	1	0	1	0	5	1	4	1	5	3	2	1	5	3	3	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:84240579C>G	ENST00000405413.2	-	4	553	c.417G>C	c.(415-417)aaG>aaC	p.K139N	HPSE_ENST00000513463.1_Missense_Mutation_p.K139N|HPSE_ENST00000311412.5_Missense_Mutation_p.K139N|HPSE_ENST00000512196.1_Missense_Mutation_p.K139N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	139					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	CCAACCGTAACTTCTCCTCCA	0.438																																					p.K139N		.											.	HPSE-227	0			c.G417C						.						148	137	141					4																	84240579		2203	4300	6503	SO:0001583	missense	10855	exon3			CCGTAACTTCTCC	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.417G>C	4.37:g.84240579C>G	ENSP00000384262:p.Lys139Asn	Somatic	104	0		WXS	Illumina HiSeq	Phase_I	113	17	NM_001199830	0	0	10	10	0	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	C	2.151	-0.394512	0.04899	.	.	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.44482	0.94;0.94;0.92;2.02	5.14	0.358	0.16084	Glycoside hydrolase, superfamily (1);	0.691254	0.14121	N	0.340021	T	0.28863	0.0716	L	0.36672	1.1	0.09310	N	1	B;P;P	0.36465	0.0;0.551;0.554	B;B;B	0.40782	0.001;0.34;0.146	T	0.14531	-1.0469	10	0.27082	T	0.32	-4.5686	2.1168	0.03715	0.1217:0.3938:0.1188:0.3657	.	139;139;139	E9PCA9;E9PGR1;Q9Y251	.;.;HPSE_HUMAN	N	139	ENSP00000308107:K139N;ENSP00000384262:K139N;ENSP00000423265:K139N;ENSP00000421365:K139N	ENSP00000308107:K139N	K	-	3	2	HPSE	84459603	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-0.862000	0.04263	-0.150000	0.11195	-0.293000	0.09583	AAG	.		0.438	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		G	84240579	C	G	84240579	3	3	159	1	0	0	0	0	1	0	0	0	7365	564	20	4	1254	4	HPSE	4	84240579	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		84240579	106913697	24	14419											
GRID2	2895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	94436380	94436380	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcaaggtctctccaggacCtttccaagcaaacagaaatc	15	8	6	12	0	2	1	1	0	1	1	6	2	4	2	3	2	2	1	3	2	5	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:94436380C>T	ENST00000282020.4	+	13	2269	c.2011C>T	c.(2011-2013)Ctt>Ttt	p.L671F	GRID2_ENST00000510992.1_Missense_Mutation_p.L576F	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	671					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.L671I(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		TCTCCAGGACCTTTCCAAGCA	0.418																																					p.L671F		.											.	GRID2-159	1	Substitution - Missense(1)	lung(1)	c.C2011T						.						45	44	44					4																	94436380		2203	4300	6503	SO:0001583	missense	2895	exon13			CAGGACCTTTCCA	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.2011C>T	4.37:g.94436380C>T	ENSP00000282020:p.Leu671Phe	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	81	16	NM_001510	0	0	0	0	0	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.826524	0.71143	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.52754	0.65;0.65	4.96	4.96	0.65561	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.062472	0.64402	D	0.000006	T	0.74038	0.3664	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.992;0.997	T	0.79757	-0.1669	10	0.87932	D	0	.	18.5496	0.91058	0.0:1.0:0.0:0.0	.	576;671	E9PH24;O43424	.;GRID2_HUMAN	F	671;576	ENSP00000282020:L671F;ENSP00000421257:L576F	ENSP00000282020:L671F	L	+	1	0	GRID2	94655403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.534000	0.45676	2.448000	0.82819	0.585000	0.79938	CTT	.		0.418	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	94436380	C	T	94436380	3	4	159	1	0	0	0	0	1	0	0	0	6793	681	24	2	2061	2	GRID2	4	94436380	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	10195801	94436380	96717896	25	14420											
ADH6	130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	100129912	100129912	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttcttgaatgggtttcttTaagtcctgagggttgaggca	8	15	12	6	0	2	3	0	3	2	0	3	3	3	3	1	3	0	3	1	3	2	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:100129912T>A	ENST00000237653.7	-	6	1125	c.741A>T	c.(739-741)ttA>ttT	p.L247F	ADH6_ENST00000394897.1_Missense_Mutation_p.L247F|ADH6_ENST00000504257.1_5'UTR|ADH6_ENST00000407820.2_Missense_Mutation_p.L38F|RP11-696N14.1_ENST00000506160.1_RNA|ADH6_ENST00000394899.2_Missense_Mutation_p.L247F|RP11-696N14.1_ENST00000500358.2_RNA|RP11-696N14.1_ENST00000506454.1_RNA	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	247					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	TGGGTTTCTTTAAGTCCTGAG	0.443																																					p.L247F		.											.	ADH6-228	0			c.A741T						.						286	298	294					4																	100129912		2203	4300	6503	SO:0001583	missense	130	exon6			TTTCTTTAAGTCC	AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"Alcohol dehydrogenases"	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.741A>T	4.37:g.100129912T>A	ENSP00000237653:p.Leu247Phe	Somatic	123	0		WXS	Illumina HiSeq	Phase_I	148	39	NM_000672	0	0	0	1	1	B3KS45|Q58F53	Missense_Mutation	SNP	ENST00000237653.7	37	CCDS3647.1	.	.	.	.	.	.	.	.	.	.	T	2.163	-0.391751	0.04932	.	.	ENSG00000172955	ENST00000394897;ENST00000394899;ENST00000407820;ENST00000237653;ENST00000508558	T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69	4.56	-4.66	0.03329	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.483471	0.25219	N	0.032258	T	0.01523	0.0049	N	0.11651	0.15	0.22001	N	0.999427	B;B;B;B	0.14012	0.0;0.0;0.0;0.009	B;B;B;B	0.09377	0.004;0.002;0.002;0.004	T	0.42015	-0.9476	10	0.09338	T	0.73	-7.7887	1.7843	0.03038	0.3579:0.2092:0.3238:0.1091	.	124;247;247;247	B4DPD8;E9PBI1;P28332;P28332-2	.;.;ADH6_HUMAN;.	F	247;247;38;247;183	ENSP00000378358:L247F;ENSP00000378359:L247F;ENSP00000384997:L38F;ENSP00000237653:L247F;ENSP00000426187:L183F	ENSP00000237653:L247F	L	-	3	2	ADH6	100348935	0.000000	0.05858	0.004000	0.12327	0.597000	0.36814	0.028000	0.13644	-1.027000	0.03325	-0.294000	0.09567	TTA	.		0.443	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672		A	100129912	T	A	100129912	3	1	159	1	0	0	0	0	1	0	0	0	312	1751	61	5	406	5	ADH6	4	100129912	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	5693532	100129912	91024364	26	14421											
LARP7	51574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	113568519	113568519	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtccactgaaccccaaaagCagtgctcaaagaaaaagaaa	20	4	7	10	0	1	3	1	1	0	2	2	3	2	3	3	0	3	2	3	0	7	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:113568519C>A	ENST00000344442.5	+	7	1089	c.811C>A	c.(811-813)Cag>Aag	p.Q271K	LARP7_ENST00000509061.1_Missense_Mutation_p.Q278K|MIR302C_ENST00000362232.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000510655.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302A_ENST00000385192.1_RNA|MIR302B_ENST00000362188.1_RNA|MIR302D_ENST00000362275.1_RNA|LARP7_ENST00000324052.6_Missense_Mutation_p.Q271K|MIR302B_ENST00000509938.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	271	Lys-rich.				RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		ACCCCAAAAGCAGTGCTCAAA	0.448																																					p.Q278K		.											.	LARP7-93	0			c.C832A						.						104	102	102					4																	113568519		1871	4114	5985	SO:0001583	missense	51574	exon9			CAAAAGCAGTGCT	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.811C>A	4.37:g.113568519C>A	ENSP00000344950:p.Gln271Lys	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	147	16	NM_001267039	1	0	32	64	31	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	37	CCDS3701.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.204|0.204	-1.041899|-1.041899	0.01997|0.01997	.|.	.|.	ENSG00000174720|ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000505034;ENST00000324052|ENST00000511529	T;T;T;T|.	0.17528|.	2.27;2.27;2.27;2.27|.	5.86|5.86	5.01|5.01	0.66863|0.66863	.|.	0.366809|.	0.30126|.	N|.	0.010347|.	T|T	0.56485|0.56485	0.1988|0.1988	L|L	0.56769|0.56769	1.78|1.78	0.32446|0.32446	N|N	0.546025|0.546025	B;B|.	0.18013|.	0.025;0.025|.	B;B|.	0.18561|.	0.022;0.022|.	T|T	0.65162|0.65162	-0.6235|-0.6235	10|5	0.06236|.	T|.	0.91|.	-6.7457|-6.7457	10.0804|10.0804	0.42386|0.42386	0.0:0.7892:0.1388:0.072|0.0:0.7892:0.1388:0.072	.|.	271;271|.	D6RFF0;Q4G0J3|.	.;LARP7_HUMAN|.	K|R	271;278;271;271|51	ENSP00000344950:Q271K;ENSP00000422626:Q278K;ENSP00000421541:Q271K;ENSP00000314311:Q271K|.	ENSP00000314311:Q271K|.	Q|S	+|+	1|3	0|2	LARP7|LARP7	113787968|113787968	0.865000|0.865000	0.29922|0.29922	0.907000|0.907000	0.35723|0.35723	0.117000|0.117000	0.20001|0.20001	1.026000|1.026000	0.30103|0.30103	1.453000|1.453000	0.47775|0.47775	0.563000|0.563000	0.77884|0.77884	CAG|AGC	.		0.448	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		A	113568519	C	A	113568519	3	1	159	1	0	0	0	0	1	0	0	0	8654	711	25	4	833	4	LARP7	4	113568519	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	13438607	113568519	77585757	27	14422											
CDH12	1010	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr5	21751876	21751876	+	Frame_Shift_Del	DEL	T	T	-																															ttatcagggttataactctcTtcttcgccaaacatgtctgc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr5:21751876delT	ENST00000382254.1	-	15	3441	c.2355delA	c.(2353-2355)gaafs	p.E786fs	CDH12_ENST00000504376.2_Frame_Shift_Del_p.E786fs|CDH12_ENST00000522262.1_Frame_Shift_Del_p.E746fs|CDH12_ENST00000521384.1_5'UTR|RP11-804N13.1_ENST00000522350.1_RNA	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	786					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TATAACTCTCTTCTTCGCCAA	0.428										HNSCC(59;0.17)																											p.E785fs		.											.	CDH12-92	0			c.2355delA						.						81	83	82					5																	21751876		2203	4300	6503	SO:0001589	frameshift_variant	1010	exon15			.	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2355delA	5.37:g.21751876delT	ENSP00000371689:p.Glu786fs	Somatic	111	0		WXS	Illumina HiSeq	Phase_I	121	33	NM_004061	0	0	0	0	0	B2RBT1|B7Z2U6|Q86UD2	Frame_Shift_Del	DEL	ENST00000382254.1	37	CCDS3890.1																																																																																			.		0.428	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		-	21751876	T	-	21751876	7	5	159	1	0	1	0	1	0	0	0	0	3104	1606	56	0	33	0	CDH12	5	21751876	Frame_Shift_Del	DEL	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		21751876	159163384	28	14423											
IQGAP2	10788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	75902074	75902074	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagataacttaagctggaatGaaattcagaattgtattgat	17	13	8	3	0	1	4	1	2	0	2	1	5	1	5	0	1	2	2	0	1	7	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr5:75902074G>A	ENST00000274364.6	+	12	1600	c.1303G>A	c.(1303-1305)Gaa>Aaa	p.E435K	IQGAP2_ENST00000396234.3_5'Flank|IQGAP2_ENST00000379730.3_5'UTR|CTD-2236F14.1_ENST00000511327.1_RNA|IQGAP2_ENST00000502745.1_5'Flank	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	435					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAGCTGGAATGAAATTCAGAA	0.343																																					p.E435K		.											.	IQGAP2-96	0			c.G1303A						.						100	99	100					5																	75902074		2203	4300	6503	SO:0001583	missense	10788	exon12			TGGAATGAAATTC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1303G>A	5.37:g.75902074G>A	ENSP00000274364:p.Glu435Lys	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	122	27	NM_006633	0	0	4	6	2	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.060330	0.76074	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.06849	3.25;3.25;3.25	5.63	4.76	0.60689	.	0.158913	0.56097	N	0.000036	T	0.11879	0.0289	M	0.68952	2.095	0.80722	D	1	P	0.39404	0.672	B	0.35607	0.206	T	0.02526	-1.1146	10	0.49607	T	0.09	-26.3168	14.1512	0.65387	0.0728:0.0:0.9272:0.0	.	435	Q13576	IQGA2_HUMAN	K	435;408;385	ENSP00000274364:E435K;ENSP00000423672:E408K;ENSP00000421097:E385K	ENSP00000274364:E435K	E	+	1	0	IQGAP2	75937830	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.250000	0.89835	1.370000	0.46153	0.650000	0.86243	GAA	.		0.343	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75902074	G	A	75902074	3	1	159	1	0	0	0	0	1	0	0	0	7836	1291	45	2	1349	2	IQGAP2	5	75902074	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	54150198	75902074	105013186	29	14424											
DDX41	51428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	176940458	176940458	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcttcttcggcatggtggCactgaagagcagggtctgtc	8	11	13	9	1	3	2	0	1	3	1	5	2	3	2	0	4	1	3	0	4	2	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr5:176940458C>G	ENST00000507955.1	-	11	1649	c.1126G>C	c.(1126-1128)Gcc>Ccc	p.A376P	DDX41_ENST00000506965.1_5'Flank	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	376	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			GGCATGGTGGCACTGAAGAGC	0.612																																					p.A376P		.											.	DDX41-226	0			c.G1126C						.						129	139	136					5																	176940458		2203	4300	6503	SO:0001583	missense	51428	exon11			TGGTGGCACTGAA	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"DEAD-boxes"	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.1126G>C	5.37:g.176940458C>G	ENSP00000422753:p.Ala376Pro	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	135	27	NM_016222	0	0	28	51	23	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	37	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	C	34	5.359401	0.95854	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.59772	0.24;0.24	5.25	5.25	0.73442	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.055575	0.64402	D	0.000001	D	0.84705	0.5531	H	0.96777	3.88	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.988;0.992	D	0.89650	0.3869	10	0.87932	D	0	-29.9388	19.0273	0.92937	0.0:1.0:0.0:0.0	.	250;376	B3KRK2;Q9UJV9	.;DDX41_HUMAN	P	394;376	ENSP00000330349:A394P;ENSP00000422753:A376P	ENSP00000330349:A394P	A	-	1	0	DDX41	176873064	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.595000	0.82710	2.721000	0.93114	0.655000	0.94253	GCC	.		0.612	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		G	176940458	C	G	176940458	3	3	159	1	0	0	0	0	1	0	0	0	4367	710	25	4	770	4	DDX41	5	176940458	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	101038384	176940458	3974802	30	14425											
KDM1B	221656	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	18218101	18218101	+	Frame_Shift_Del	DEL	C	C	-																															gaagacattcaaggaaccgtCtttttcgctggtgaggtatg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr6:18218101delC	ENST00000297792.5	+	17	1851	c.1674delC	c.(1672-1674)gtcfs	p.V558fs	KDM1B_ENST00000388870.2_Frame_Shift_Del_p.V791fs|KDM1B_ENST00000546309.2_Frame_Shift_Del_p.V81fs|KDM1B_ENST00000397244.1_Frame_Shift_Del_p.V559fs			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	790					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						AAGGAACCGTCTTTTTCGCTG	0.418																																					p.V558fs		.											.	KDM1B-91	0			c.1674delC						.						216	181	193					6																	18218101		2203	4300	6503	SO:0001589	frameshift_variant	221656	exon17			.	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"Chromatin-modifying enzymes / K-demethylases"	21577	protein-coding gene	gene with protein product		613081	"amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1"	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1674delC	6.37:g.18218101delC	ENSP00000297792:p.Val558fs	Somatic	95	0		WXS	Illumina HiSeq	Phase_I	97	22	NM_153042	0	0	0	0	0	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Frame_Shift_Del	DEL	ENST00000297792.5	37	CCDS34343.1																																																																																			.		0.418	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042		-	18218101	C	-	18218101	7	5	159	1	0	1	0	1	0	0	0	0	8144	900	32	0	1732	0	KDM1B	6	18218101	Frame_Shift_Del	DEL	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		18218101	152896966	31	14426											
FHL5	9457	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	97053903	97053904	+	Frame_Shift_Del	DEL	TG	TG	-																															gtggcaattattgtgtgccaTgttttgagaaggagtttgct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr6:97053903_97053904delTG	ENST00000326771.2	+	5	840_841	c.460_461delTG	c.(460-462)tgtfs	p.C154fs	FHL5_ENST00000541107.1_Frame_Shift_Del_p.C154fs	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	154	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TTGTGTGCCATGTTTTGAGAAG	0.396																																					p.154_154del		.											.	FHL5-92	0			c.460_461del						.																																			SO:0001589	frameshift_variant	9457	exon5			.	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.460_461delTG	6.37:g.97053903_97053904delTG	ENSP00000326022:p.Cys154fs	Somatic	146	0		WXS	Illumina HiSeq	Phase_I	139	35	NM_020482	0	0	0	0	0	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Frame_Shift_Del	DEL	ENST00000326771.2	37	CCDS5035.1																																																																																			.		0.396	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		-	97053904	TG	-	97053903	7	5	159	1	0	1	0	1	0	0	0	0	5900	1464	51	0	470	0	FHL5	6	97053903	Frame_Shift_Del	DEL	TG	TCGA-PJ-A5Z8-01A-11D-A28G-10	78835802	97053903	74061164	32	14427											
SKAP2	8935	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	26894415	26894415	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacttacatagactttacAtcttttatcttcttaataag	12	18	4	7	0	3	2	0	1	3	1	3	2	3	2	0	0	2	0	0	0	6	9			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:26894415A>G	ENST00000345317.2	-	2	475	c.162T>C	c.(160-162)gaT>gaC	p.D54D	SKAP2_ENST00000539623.1_5'UTR	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	54	Homodimerization. {ECO:0000250}.				B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						TAGACTTTACATCTTTTATCT	0.284																																					p.D54D													.	SKAP2-91	0			c.T162C						.						83	84	84					7																	26894415		2196	4278	6474	SO:0001819	synonymous_variant	8935	exon2			CTTTACATCTTTT		CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020		"Pleckstrin homology (PH) domain containing"	15687	protein-coding gene	gene with protein product		605215	"src family associated phosphoprotein 2"	SCAP2		9837776, 9755858	Standard	NM_003930		Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.162T>C	7.37:g.26894415A>G		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	19	4	NM_003930	0	0	0	0	0	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	Silent	SNP	ENST00000345317.2	37	CCDS5400.1																																																																																			.		0.284	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214128.1			G	26894415	A	G	26894415	2	3	159	1	0	0	0	0	0	0	0	1	14388	214	8	3		3	SKAP2	7	26894415	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		26894415	132244248	33	14428											
HECW1	23072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	43484075	43484075	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcatggtctctgtgggacCtgaaggggctggggagctcc	5	8	19	9	0	1	1	0	1	1	0	3	3	2	3	2	7	1	3	2	7	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:43484075C>A	ENST00000395891.2	+	11	1909	c.1304C>A	c.(1303-1305)cCt>cAt	p.P435H	HECW1_ENST00000453890.1_Missense_Mutation_p.P435H	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	435					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TCTGTGGGACCTGAAGGGGCT	0.627																																					p.P435H		.											.	HECW1-669	0			c.C1304A						.						22	25	24					7																	43484075		2079	4213	6292	SO:0001583	missense	23072	exon11			TGGGACCTGAAGG	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.1304C>A	7.37:g.43484075C>A	ENSP00000379228:p.Pro435His	Somatic	131	0		WXS	Illumina HiSeq	Phase_I	118	23	NM_015052	0	0	0	1	1	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102929	0.37145	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.33654	1.45;1.4	4.77	3.89	0.44902	.	15.800300	0.00906	N	0.002403	T	0.34221	0.0890	L	0.40543	1.245	0.09310	N	1	P;P	0.51791	0.612;0.948	B;B	0.39185	0.219;0.293	T	0.38564	-0.9655	10	0.52906	T	0.07	.	10.3123	0.43716	0.0:0.844:0.0:0.156	.	435;435	B4DH42;Q76N89	.;HECW1_HUMAN	H	435	ENSP00000379228:P435H;ENSP00000407774:P435H	ENSP00000265522:P435H	P	+	2	0	HECW1	43450600	0.000000	0.05858	0.008000	0.14137	0.181000	0.23173	0.250000	0.18235	1.311000	0.45024	0.591000	0.81541	CCT	.		0.627	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43484075	C	A	43484075	3	1	159	1	0	0	0	0	1	0	0	0	7063	681	24	4	1338	4	HECW1	7	43484075	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	16589660	43484075	115654588	34	14429											
ABCA13	154664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	48563956	48563956	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacattcttgtgttatacAaccttagtaaacattatcga	14	14	6	7	1	1	1	0	0	1	1	2	3	1	1	1	0	3	2	1	0	7	7			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:48563956A>C	ENST00000435803.1	+	54	14188	c.14164A>C	c.(14164-14166)Aac>Cac	p.N4722H	ABCA13_ENST00000544596.1_Missense_Mutation_p.N452H	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4722	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGTGTTATACAACCTTAGTAA	0.363																																					p.N4722H		.											.	ABCA13-521	0			c.A14164C						.						129	128	128					7																	48563956		1842	4094	5936	SO:0001583	missense	154664	exon54			TTATACAACCTTA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"ATP binding cassette transporters / subfamily A"	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.14164A>C	7.37:g.48563956A>C	ENSP00000411096:p.Asn4722His	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	138	30	NM_152701	0	0	0	0	0	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	7.655	0.683805	0.14907	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	T;T;T	0.47869	0.83;0.83;0.83	5.59	3.08	0.35506	ABC transporter-like (1);	0.227351	0.30850	N	0.008743	T	0.30448	0.0765	L	0.31526	0.94	0.22127	N	0.999341	B;B;B	0.28760	0.007;0.013;0.221	B;B;B	0.23716	0.017;0.009;0.048	T	0.16070	-1.0415	10	0.45353	T	0.12	.	6.4339	0.21813	0.7623:0.1574:0.0803:0.0	.	452;2424;4722	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	H	4722;495;452	ENSP00000411096:N4722H;ENSP00000391042:N495H;ENSP00000442634:N452H	ENSP00000391042:N495H	N	+	1	0	ABCA13	48534502	0.928000	0.31464	0.072000	0.20136	0.450000	0.32258	2.185000	0.42584	1.050000	0.40346	0.533000	0.62120	AAC	.		0.363	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48563956	A	C	48563956	3	2	159	1	0	0	0	0	1	0	0	0	31	130	5	5	14207	5	ABCA13	7	48563956	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	5079881	48563956	110574707	35	14430											
LAMB1	3912	broad.mit.edu;bcgsc.ca	37	chr7	107592551	107592555	+	Frame_Shift_Del	DEL	TCACA	TCACA	-																															aggtattgggcgcacagcggTcacagttctgcccgatcaca																								rs376884310		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TCACA	TCACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:107592551_107592555delTCACA	ENST00000222399.6	-	23	3423_3427	c.3193_3197delTGTGA	c.(3193-3198)tgtgacfs	p.CD1065fs	LAMB1_ENST00000393561.1_Frame_Shift_Del_p.CD1089fs	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1065	Laminin EGF-like 11. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						CGCACAGCGGTCACAGTTCTGCCCG	0.571																																					p.1065_1066del													.	LAMB1-97	0			c.3193_3197del						.																																			SO:0001589	frameshift_variant	3912	exon23			CAGCGGTCACAGT	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3193_3197delTGTGA	7.37:g.107592551_107592555delTCACA	ENSP00000222399:p.Cys1065fs	Somatic	244	0		WXS	Illumina HiSeq	Phase_I	219	19	NM_002291	0	0	0	0	0	Q14D91	Frame_Shift_Del	DEL	ENST00000222399.6	37	CCDS5750.1																																																																																			.		0.571	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107592555	TCACA	-	107592551	7	5	159	1	0	1	0	1	0	0	0	0	8631	1667	58	0	2211	0	LAMB1	7	107592551	Frame_Shift_Del	DEL	TCACA	TCGA-PJ-A5Z8-01A-11D-A28G-10	59028595	107592551	51546112	36	14431	158	2									
LAMB1	3912	broad.mit.edu;bcgsc.ca	37	chr7	107592557	107592562	+	In_Frame_Del	DEL	TTCTGC	TTCTGC	-																															tgggcgcacagcggtcacagTtctgcccgatcacattagga																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TTCTGC	TTCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:107592557_107592562delTTCTGC	ENST00000222399.6	-	23	3416_3421	c.3186_3191delGCAGAA	c.(3184-3192)gggcagaac>ggc	p.QN1063del	LAMB1_ENST00000393561.1_In_Frame_Del_p.QN1087del	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1063	Laminin EGF-like 11. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GCGGTCACAGTTCTGCCCGATCACAT	0.558																																					p.1062_1064del													.	LAMB1-97	0			c.3186_3191del						.																																			SO:0001651	inframe_deletion	3912	exon23			TCACAGTTCTGCC	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"Laminins"	6486	protein-coding gene	gene with protein product		150240	"cutis laxa with marfanoid phenotype"	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3186_3191delGCAGAA	7.37:g.107592557_107592562delTTCTGC	ENSP00000222399:p.Gln1063_Asn1064del	Somatic	219	0		WXS	Illumina HiSeq	Phase_I	201	19	NM_002291	0	0	0	0	0	Q14D91	In_Frame_Del	DEL	ENST00000222399.6	37	CCDS5750.1																																																																																			.		0.558	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107592562	TTCTGC	-	107592557	7	5	159	1	0	1	0	1	0	0	0	0	8631	1725	60	0	2217	0	LAMB1	7	107592557	In_Frame_Del	DEL	TTCTGC	TCGA-PJ-A5Z8-01A-11D-A28G-10	6	107592557	51546106	37	14432	158	2									
SSPO	23145	hgsc.bcm.edu;broad.mit.edu	37	chr7	149518182	149518182	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtccctgcagccactcatgCgggcccagagggcagcagag	9	4	14	14	1	1	2	1	0	0	2	2	2	2	2	3	2	4	3	3	2	0	0	rs199773714	byFrequency	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:149518182C>T	ENST00000378016.2	+	0	12525							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCCACTCATGCGGGCCCAGAG	0.692													C|||	2	0.000399361	0	0	5008	,	,		17614	0.002		0	False		,,,				2504	0				p.C4175C		.											.	.	0			c.C12525T						.																																					23145	exon87			CTCATGCGGGCCC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149518182C>T		Somatic	13	0		WXS	Illumina HiSeq	Phase_I	37	6	NM_198455	0	0	0	0	0	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				.		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149518182	C	T	149518182	1	4	159	0	1	0	0	0	0	0	0	0	15221	776	27	1		1	SSPO	7	149518182	RNA	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	41925625	149518182	9620481	38	14433											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	151919708	151919708	+	Frame_Shift_Del	DEL	T	T	-																															tgctacaatcaaaaccaatgTctgctacattttccacttct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:151919708delT	ENST00000262189.6	-	21	3601	c.3383delA	c.(3382-3384)gacfs	p.D1128fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.D1128fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1128					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AAAACCAATGTCTGCTACATT	0.358																																					p.D1128fs		.											.	MLL3-1398	0			c.3383delA						.						62	50	54					7																	151919708		2203	4296	6499	SO:0001589	frameshift_variant	58508	exon21			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3383delA	7.37:g.151919708delT	ENSP00000262189:p.Asp1128fs	Somatic	343	0		WXS	Illumina HiSeq	Phase_I	336	59	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.358	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151919708	T	-	151919708	7	5	159	1	0	1	0	1	0	0	0	0	9647	1667	58	0	11508	0	MLL3	7	151919708	Frame_Shift_Del	DEL	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	2401526	151919708	7218955	39	14434											
OSGIN2	734	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	90936735	90936736	+	Frame_Shift_Ins	INS	-	-	T																															cttttccttttttaggagccINStaaaaggggatcgagttatg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr8:90936735_90936736insT	ENST00000297438.2	+	6	848_849	c.493_494insT	c.(493-495)ctafs	p.L165fs	OSGIN2_ENST00000451899.2_Frame_Shift_Ins_p.L209fs	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	165					meiotic nuclear division (GO:0007126)					breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTTTAGGAGCCTAAAAGGGGAT	0.322																																					p.L209fs		.											.	OSGIN2-68	0			c.625_626insT						.																																			SO:0001589	frameshift_variant	734	exon6			.	AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.494dupT	8.37:g.90936736_90936736dupT	ENSP00000297438:p.Leu165fs	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	83	16	NM_001126111	0	0	0	0	0		Frame_Shift_Ins	INS	ENST00000297438.2	37	CCDS6248.1																																																																																			.		0.322	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		T	90936736	-	T	90936735	7	5	159	1	0	1	1	0	0	0	0	0	11316	680	24	0	647	0	OSGIN2	8	90936735	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10		90936735	55427287	40	14435											
EFR3A	23167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	132996502	132996502	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataactattgaactggctaaTgaagaagtagttattgatct	15	14	8	4	0	1	4	0	3	1	1	1	4	1	4	0	1	2	3	0	1	8	7			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr8:132996502T>G	ENST00000254624.5	+	15	1917	c.1692T>G	c.(1690-1692)aaT>aaG	p.N564K	EFR3A_ENST00000334503.4_Missense_Mutation_p.N564K|EFR3A_ENST00000519656.1_Missense_Mutation_p.N528K	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	564						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			AACTGGCTAATGAAGAAGTAG	0.348																																					p.N564K		.											.	EFR3A-139	0			c.T1692G						.						132	132	132					8																	132996502		2203	4300	6503	SO:0001583	missense	23167	exon15			GGCTAATGAAGAA	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1692T>G	8.37:g.132996502T>G	ENSP00000254624:p.Asn564Lys	Somatic	86	0		WXS	Illumina HiSeq	Phase_I	82	15	NM_015137	0	0	15	24	9	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	37	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	T	19.05	3.752706	0.69533	.	.	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.30182	1.54;1.54;1.54	6.02	3.6	0.41247	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.42698	0.1214	M	0.70275	2.135	0.80722	D	1	P	0.45902	0.868	P	0.51415	0.669	T	0.23084	-1.0198	10	0.51188	T	0.08	-34.8449	10.0781	0.42373	0.0:0.1369:0.0:0.8631	.	564	Q14156	EFR3A_HUMAN	K	564;564;564;528	ENSP00000254624:N564K;ENSP00000334769:N564K;ENSP00000428086:N528K	ENSP00000254624:N564K	N	+	3	2	EFR3A	133065684	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.821000	0.27338	0.491000	0.27793	0.528000	0.53228	AAT	.		0.348	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		G	132996502	T	G	132996502	3	3	159	1	0	0	0	0	1	0	0	0	4969	1461	51	5	1750	5	EFR3A	8	132996502	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	42059767	132996502	13367520	41	14436											
OC90	729330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	133041425	133041426	+	Splice_Site	DNP	AC	AC	TT																															gcagtgatgggacaagcagcAcctaagaccaaggaaaaccc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr8:133041425_133041426AC>TT	ENST00000443356.2	-	14	1166_1167	c.1080_1081GT>AA	c.(1078-1083)agGTgc>agAAgc	p.C361S	OC90_ENST00000254627.3_Splice_Site_p.C345S|OC90_ENST00000603859.1_Splice_Site_p.C345S|OC90_ENST00000262283.5_Splice_Site_p.C557S			Q02509	OC90_HUMAN	otoconin 90	361	Phospholipase A2-like 2.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			GACAAGCAGCACCTAAGACCAA	0.554																																					p.C557S		.											.	OC90-206	0			c.G1032A						.																																			SO:0001630	splice_region_variant	729330	exon13			GCAGCACCTAAGA	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1080_1081delinsTT	8.37:g.133041425_133041426delinsTT		Somatic	105	0		WXS	Illumina HiSeq	Phase_I	94	14	NM_001080399	0	0	0	0	0	B4DNG8	Missense_Mutation	DNP	ENST00000443356.2	37																																																																																				.		0.554	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	Missense_Mutation	TT	133041426	AC	TT	133041425	5	4	159	1	0	0	0	0	0	0	1	0	10840	173	6	5	408	5	OC90	8	133041425	Splice_Site	DNP	AC	TCGA-PJ-A5Z8-01A-11D-A28G-10	44923	133041425	13322597	42	14437											
ABCA2	20	hgsc.bcm.edu;bcgsc.ca	37	chr9	139907277	139907277	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctggggcgggtgcccgccCacactgctggggcaggagaa	7	5	17	12	2	1	1	0	0	1	1	1	2	1	1	2	6	2	2	2	6	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr9:139907277C>G	ENST00000371605.3	-	30	5112	c.4965G>C	c.(4963-4965)gtG>gtC	p.V1655V	ABCA2_ENST00000265662.5_Silent_p.V1656V|ABCA2_ENST00000341511.6_Silent_p.V1656V			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1655					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GGTGCCCGCCCACACTGCTGG	0.677																																					p.V1686V		.											.	ABCA2-90	0			c.G5058C						.						10	14	13					9																	139907277		1886	3995	5881	SO:0001819	synonymous_variant	20	exon31			CCCGCCCACACTG	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"ATP binding cassette transporters / subfamily A"	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.4965G>C	9.37:g.139907277C>G		Somatic	59	0		WXS	Illumina HiSeq	Phase_I	157	23	NM_212533	0	0	8	8	0	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37		.	.	.	.	.	.	.	.	.	.	C	9.881	1.201473	0.22121	.	.	ENSG00000107331	ENST00000477420	.	.	.	4.15	3.22	0.36961	.	.	.	.	.	T	0.48150	0.1484	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43798	-0.9369	4	.	.	.	.	4.4915	0.11815	0.1537:0.609:0.1497:0.0876	.	.	.	.	R	68	.	.	G	-	1	0	ABCA2	139027098	0.859000	0.29813	1.000000	0.80357	0.989000	0.77384	-0.084000	0.11268	2.142000	0.66516	0.491000	0.48974	GGG	.		0.677	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		G	139907277	C	G	139907277	2	3	159	1	0	0	0	0	0	0	0	1	32	581	21	4		4	ABCA2	9	139907277	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		139907277	1306154	43	14438											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61833342	61833342	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaatgttttataagagtCatcagatatgagttgagcag	13	14	9	5	0	3	4	3	2	0	2	3	4	3	4	0	0	1	3	0	0	4	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:61833342C>A	ENST00000280772.2	-	37	7488	c.7297G>T	c.(7297-7299)Gac>Tac	p.D2433Y	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2433					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTATAAGAGTCATCAGATATG	0.418																																					p.D2433Y		.											.	ANK3-107	0			c.G7297T						.						79	80	80					10																	61833342		2203	4300	6503	SO:0001583	missense	288	exon37			AAGAGTCATCAGA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.7297G>T	10.37:g.61833342C>A	ENSP00000280772:p.Asp2433Tyr	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	111	18	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377882	0.61735	.	.	ENSG00000151150	ENST00000280772	T	0.70986	-0.53	5.8	5.8	0.92144	.	0.000000	0.44688	D	0.000436	T	0.81894	0.4919	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.82252	-0.0549	10	0.72032	D	0.01	.	20.0591	0.97667	0.0:1.0:0.0:0.0	.	2433	Q12955	ANK3_HUMAN	Y	2433	ENSP00000280772:D2433Y	ENSP00000280772:D2433Y	D	-	1	0	ANK3	61503348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.810000	0.86072	2.747000	0.94245	0.462000	0.41574	GAC	.		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61833342	C	A	61833342	3	1	159	1	0	0	0	0	1	0	0	0	622	826	29	4	6177	4	ANK3	10	61833342	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		61833342	73701405	44	14439											
ZMYND17	118490	broad.mit.edu;bcgsc.ca	37	chr10	75185982	75185982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccgggtctggccttggccgtCctacactggcccataaggtg	5	9	13	14	2	1	0	0	0	1	0	2	0	2	0	5	5	1	0	5	5	2	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:75185982C>T	ENST00000372912.1	-	4	658	c.656G>A	c.(655-657)gGa>gAa	p.G219E	MSS51_ENST00000299432.2_Missense_Mutation_p.G219E|AL353731.1_ENST00000584907.1_RNA			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	219					social behavior (GO:0035176)		metal ion binding (GO:0046872)										CCTTGGCCGTCCTACACTGGC	0.552																																					p.G219E													.	.	0			c.G656A						.						77	73	74					10																	75185982		2203	4300	6503	SO:0001583	missense	118490	exon5			GGCCGTCCTACAC	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.656G>A	10.37:g.75185982C>T	ENSP00000362003:p.Gly219Glu	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	26	5	NM_001024593	0	0	1	1	0	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	37	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.639367	0.87760	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.47177	0.85;0.85	5.21	5.21	0.72293	.	0.293286	0.37136	N	0.002233	T	0.47116	0.1428	L	0.58101	1.795	0.49051	D	0.999742	P	0.46706	0.883	B	0.41571	0.36	T	0.45760	-0.9239	9	.	.	.	-0.2459	16.3115	0.82873	0.0:1.0:0.0:0.0	.	219	Q4VC12	ZMY17_HUMAN	E	219	ENSP00000299432:G219E;ENSP00000362003:G219E	.	G	-	2	0	ZMYND17	74855988	0.981000	0.34729	0.304000	0.25085	0.948000	0.59901	2.946000	0.49050	2.708000	0.92522	0.585000	0.79938	GGA	.		0.552	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		T	75185982	C	T	75185982	3	4	159	1	0	0	0	0	1	0	0	0	17741	855	30	2	738	2	ZMYND17	10	75185982	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	13352640	75185982	60348765	45	14440											
ENTPD7	57089	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101421214	101421214	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taatttcaggatcagtttttCctacctctgcccagcctcct	7	15	5	14	0	3	0	2	0	1	0	5	1	5	1	5	1	3	1	5	1	2	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:101421214C>A	ENST00000370489.4	+	3	198	c.20C>A	c.(19-21)tCc>tAc	p.S7Y		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	7						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		ATCAGTTTTTCCTACCTCTGC	0.428																																					p.S7Y		.											.	ENTPD7-91	0			c.C20A						.						133	125	128					10																	101421214		2203	4300	6503	SO:0001583	missense	57089	exon3			GTTTTTCCTACCT	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.20C>A	10.37:g.101421214C>A	ENSP00000359520:p.Ser7Tyr	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	61	16	NM_020354	0	0	0	0	0	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.094777	0.76870	.	.	ENSG00000198018	ENST00000370489	T	0.17691	2.26	5.67	5.67	0.87782	.	0.127291	0.53938	D	0.000047	T	0.21631	0.0521	L	0.32530	0.975	0.48040	D	0.999575	P	0.49696	0.927	P	0.47251	0.542	T	0.00348	-1.1799	10	0.54805	T	0.06	-18.4355	18.5275	0.90978	0.0:1.0:0.0:0.0	.	7	Q9NQZ7	ENTP7_HUMAN	Y	7	ENSP00000359520:S7Y	ENSP00000359520:S7Y	S	+	2	0	ENTPD7	101411204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.312000	0.59154	2.664000	0.90586	0.555000	0.69702	TCC	.		0.428	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		A	101421214	C	A	101421214	3	1	159	1	0	0	0	0	1	0	0	0	5157	855	30	4	26	4	ENTPD7	10	101421214	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	26235232	101421214	34113533	46	14441											
DNMBP	23268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	101715503	101715503	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaagtccatgattgaaaaGtggcgtaaaattttatctgg	14	14	9	4	1	1	2	0	2	1	0	2	2	2	2	1	2	0	1	1	2	7	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:101715503G>T	ENST00000324109.4	-	4	1819	c.1728C>A	c.(1726-1728)caC>caA	p.H576Q	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Missense_Mutation_p.H576Q	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	576					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TGATTGAAAAGTGGCGTAAAA	0.507																																					p.H576Q		.											.	DNMBP-233	0			c.C1728A						.						53	57	56					10																	101715503		2203	4300	6503	SO:0001583	missense	23268	exon4			TGAAAAGTGGCGT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1728C>A	10.37:g.101715503G>T	ENSP00000315659:p.His576Gln	Somatic	67	0		WXS	Illumina HiSeq	Phase_I	55	8	NM_015221	0	0	2	5	3	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.953459	0.53293	.	.	ENSG00000107554	ENST00000342239;ENST00000324109	T;T	0.16897	2.35;2.31	6.04	1.56	0.23342	.	0.248667	0.28647	N	0.014613	T	0.14960	0.0361	M	0.71581	2.175	0.80722	D	1	P	0.43477	0.808	B	0.39419	0.299	T	0.16364	-1.0405	10	0.13108	T	0.6	-7.645	6.0919	0.19999	0.3777:0.1336:0.4887:0.0	.	576	Q6XZF7	DNMBP_HUMAN	Q	576	ENSP00000344914:H576Q;ENSP00000315659:H576Q	ENSP00000315659:H576Q	H	-	3	2	DNMBP	101705493	0.999000	0.42202	1.000000	0.80357	0.974000	0.67602	0.487000	0.22356	0.365000	0.24400	0.561000	0.74099	CAC	.		0.507	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		T	101715503	G	T	101715503	3	4	159	1	0	0	0	0	1	0	0	0	4685	1020	36	4	3061	4	DNMBP	10	101715503	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	294289	101715503	33819244	47	14442											
CYP17A1	1586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104590667	104590667	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggatctcacctatacaggagCgaggtcctgctccgaagggc	9	7	13	12	2	1	0	1	0	1	0	4	4	3	2	3	4	3	1	3	4	3	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:104590667C>T	ENST00000369887.3	-	8	1490	c.1319G>A	c.(1318-1320)cGc>cAc	p.R440H	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'Flank	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	440			R -> H (in AH5). {ECO:0000269|PubMed:8027220}.		adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	TATACAGGAGCGAGGTCCTGC	0.597																																					p.R440H		.											.	CYP17A1-90	0			c.G1319A	GRCh37	CM940326	CYP17A1	M		.						34	28	30					10																	104590667		2203	4299	6502	SO:0001583	missense	1586	exon8			CAGGAGCGAGGTC	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.1319G>A	10.37:g.104590667C>T	ENSP00000358903:p.Arg440His	Somatic	177	0		WXS	Illumina HiSeq	Phase_I	151	31	NM_000102	0	0	1	1	0	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	37	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	35	5.529855	0.96446	.	.	ENSG00000148795	ENST00000369887	D	0.92805	-3.11	5.62	5.62	0.85841	Cytochrome P450, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97195	0.9083	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97779	1.0231	10	0.87932	D	0	.	19.259	0.93959	0.0:1.0:0.0:0.0	.	440	P05093	CP17A_HUMAN	H	440	ENSP00000358903:R440H	ENSP00000358903:R440H	R	-	2	0	CYP17A1	104580657	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	7.281000	0.78621	2.650000	0.89964	0.555000	0.69702	CGC	.		0.597	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		T	104590667	C	T	104590667	3	4	159	1	0	0	0	0	1	0	0	0	4153	768	27	1	211	1	CYP17A1	10	104590667	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	2875164	104590667	30944080	48	14443											
CYP17A1	1586	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	104592776	104592776	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgtgcagcaggaaggccaGggtccatttaaccacagagg	12	7	13	9	0	0	1	0	0	0	1	1	2	1	2	3	4	3	2	3	4	2	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:104592776G>T	ENST00000369887.3	-	5	1114	c.943C>A	c.(943-945)Ctg>Atg	p.L315M	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'Flank	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	315					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	AGGAAGGCCAGGGTCCATTTA	0.547																																					p.L315M													.	CYP17A1-90	0			c.C943A						.						130	106	114					10																	104592776		2203	4300	6503	SO:0001583	missense	1586	exon5			AGGCCAGGGTCCA	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.943C>A	10.37:g.104592776G>T	ENSP00000358903:p.Leu315Met	Somatic	248	1		WXS	Illumina HiSeq	Phase_I	265	60	NM_000102	0	0	0	2	2	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	37	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	G	9.265	1.044304	0.19748	.	.	ENSG00000148795	ENST00000369887	D	0.82711	-1.64	5.74	-0.0757	0.13725	.	0.546667	0.20030	N	0.100723	T	0.73644	0.3613	N	0.26162	0.8	0.19775	N	0.999952	B	0.30605	0.287	B	0.39935	0.314	T	0.66101	-0.6007	10	0.62326	D	0.03	.	7.1648	0.25685	0.0:0.5142:0.2368:0.249	.	315	P05093	CP17A_HUMAN	M	315	ENSP00000358903:L315M	ENSP00000358903:L315M	L	-	1	2	CYP17A1	104582766	0.001000	0.12720	0.133000	0.22050	0.195000	0.23768	-0.097000	0.11042	0.072000	0.16694	-0.228000	0.12330	CTG	.		0.547	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		T	104592776	G	T	104592776	3	4	159	1	0	0	0	0	1	0	0	0	4153	991	35	4	599	4	CYP17A1	10	104592776	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	2109	104592776	30941971	49	14444											
GRK5	2869	broad.mit.edu;ucsc.edu	37	chr10	121212789	121212789	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agagactcttcaagcggcagGtgagacacccatgcctggcc	10	6	12	13	1	2	2	1	1	1	2	2	4	2	2	3	3	2	1	3	3	1	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:121212789G>A	ENST00000392870.2	+	15	2003		c.e15+1		GRK5_ENST00000369108.3_Splice_Site	NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		CAAGCGGCAGGTGAGACACCC	0.587																																					.													.	GRK5-547	0			c.1674+1G>A						.						64	66	65					10																	121212789		2203	4300	6503	SO:0001630	splice_region_variant	2869	exon15			CGGCAGGTGAGAC	L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873			4544	protein-coding gene	gene with protein product		600870		GPRK5		7685906	Standard	NM_005308		Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.1674+1G>A	10.37:g.121212789G>A		Somatic	60	1		WXS	Illumina HiSeq	Phase_I	52	8	NM_005308	0	0	0	0	0	D3DRD0|Q5T059	Splice_Site	SNP	ENST00000392870.2	37	CCDS7612.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.835668	0.71373	.	.	ENSG00000198873	ENST00000392870;ENST00000457057;ENST00000369108	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5825	0.87972	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GRK5	121202779	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	9.793000	0.99091	2.162000	0.67917	0.655000	0.94253	.	.		0.587	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050652.2	NM_005308	Intron	A	121212789	G	A	121212789	5	1	159	1	0	0	0	0	0	0	1	0	6813	1275	44	2	1733	2	GRK5	10	121212789	Splice_Site	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	16620013	121212789	14321958	50	14445											
NLRP6	171389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	284253	284253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccactgcaaactccctgAcgcggtctgccgagaccttt	7	9	9	16	3	1	2	0	1	1	1	3	3	3	2	4	1	3	1	4	1	1	1	rs150530901		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:284253A>G	ENST00000312165.5	+	6	2225	c.2225A>G	c.(2224-2226)gAc>gGc	p.D742G	NLRP6_ENST00000534750.1_Missense_Mutation_p.D741G	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	742					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		AAACTCCCTGACGCGGTCTGC	0.627																																					p.D742G		.											.	NLRP6-583	0			c.A2225G						.	A	GLY/ASP	1,4405	2.1+/-5.4	0,1,2202	43	42	42		2225	1.4	0	11	dbSNP_134	42	0,8600		0,0,4300	no	missense	NLRP6	NM_138329.1	94	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	742/893	284253	1,13005	2203	4300	6503	SO:0001583	missense	171389	exon6			TCCCTGACGCGGT	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"Nucleotide-binding domain and leucine rich repeat containing"	22944	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"	609650	"NACHT, leucine rich repeat and PYD containing 6"	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2225A>G	11.37:g.284253A>G	ENSP00000309767:p.Asp742Gly	Somatic	60	0		WXS	Illumina HiSeq	Phase_I	87	25	NM_138329	0	0	0	0	0	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	37	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	A	3.343	-0.134159	0.06711	2.27E-4	0.0	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.57273	0.41;0.41	2.61	1.44	0.22558	.	0.174398	0.23650	U	0.045934	T	0.59018	0.2163	L	0.58354	1.805	0.09310	N	1	D;D	0.63880	0.972;0.993	P;D	0.72338	0.689;0.977	T	0.48222	-0.9054	10	0.19590	T	0.45	.	5.8126	0.18475	0.7241:0.2759:0.0:0.0	.	741;742	E9PJZ8;P59044	.;NALP6_HUMAN	G	741;742	ENSP00000433617:D741G;ENSP00000309767:D742G	ENSP00000309767:D742G	D	+	2	0	NLRP6	274253	0.000000	0.05858	0.013000	0.15412	0.149000	0.21700	0.094000	0.15107	0.419000	0.25927	0.374000	0.22700	GAC	A|1.000;G|0.000		0.627	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		G	284253	A	G	284253	3	3	159	1	0	0	0	0	1	0	0	0	10507	275	10	3	2247	3	NLRP6	11	284253	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		284253	134722263	51	14446											
CTSD	1509	hgsc.bcm.edu	37	chr11	1785082	1785082	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgagcggcagaaggctggagGgctgcatggcggcggcggcc	6	3	21	11	5	0	1	0	0	0	1	0	3	0	2	1	8	2	4	1	8	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:1785082G>A	ENST00000236671.2	-	1	140	c.8C>T	c.(7-9)cCc>cTc	p.P3L	AC068580.5_ENST00000446489.1_RNA|AC068580.6_ENST00000449248.1_RNA|AC068580.1_ENST00000580120.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	3					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	AAGGCTGGAGGGCTGCATGGC	0.736																																					p.P3L		.											.	CTSD-90	0			c.C8T						.																																			SO:0001583	missense	1509	exon1			CTGGAGGGCTGCA	M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"Cathepsins"	2529	protein-coding gene	gene with protein product	"ceroid-lipofuscinosis, neuronal 10"	116840	"cathepsin D (lysosomal aspartyl protease)"	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.8C>T	11.37:g.1785082G>A	ENSP00000236671:p.Pro3Leu	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	23	13	NM_001909	0	0	334	701	367	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	37	CCDS7725.1	.	.	.	.	.	.	.	.	.	.	g	8.700	0.909609	0.17833	.	.	ENSG00000117984	ENST00000236671	T	0.52295	0.67	3.51	1.34	0.21922	.	3.791350	0.01307	N	0.010510	T	0.26231	0.0640	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.19289	-1.0310	10	0.12103	T	0.63	.	4.9541	0.14031	0.122:0.0:0.6694:0.2087	.	3	P07339	CATD_HUMAN	L	3	ENSP00000236671:P3L	ENSP00000236671:P3L	P	-	2	0	CTSD	1741658	0.001000	0.12720	0.258000	0.24420	0.029000	0.11900	0.135000	0.15952	0.769000	0.33313	0.549000	0.68633	CCC	.		0.736	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909		A	1785082	G	A	1785082	3	1	159	1	0	0	0	0	1	0	0	0	4038	1232	43	2	1266	2	CTSD	11	1785082	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	1500829	1785082	133221434	52	14447											
NUP98	4928	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr11	3789956	3789956	+	Frame_Shift_Del	DEL	G	G	-																															caaagagaccacctggatttGttccaaatccagttgtacct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:3789956delG	ENST00000324932.7	-	8	1223	c.803delC	c.(802-804)acafs	p.T268fs	NUP98_ENST00000397007.4_Frame_Shift_Del_p.T268fs|NUP98_ENST00000397004.4_Frame_Shift_Del_p.T268fs|NUP98_ENST00000355260.3_Frame_Shift_Del_p.T268fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.T268fs	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	268	FG repeats 2.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ACCTGGATTTGTTCCAAATCC	0.378			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.T268fs		.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98-703	0			c.803delC						.						121	116	118					11																	3789956		2201	4298	6499	SO:0001589	frameshift_variant	4928	exon8			.	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.803delC	11.37:g.3789956delG	ENSP00000316032:p.Thr268fs	Somatic	49	0		WXS	Illumina HiSeq	Phase_I	52	12	NM_016320	0	0	0	0	0	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Frame_Shift_Del	DEL	ENST00000324932.7	37	CCDS7746.1																																																																																			.		0.378	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		-	3789956	G	-	3789956	7	5	159	1	0	1	0	1	0	0	0	0	10799	1377	48	0	4775	0	NUP98	11	3789956	Frame_Shift_Del	DEL	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	2004874	3789956	131216560	53	14448											
MRGPRX4	117196	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	18195097	18195097	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catctcatccgcaaaatcctCgtttctgtgatgacctttcc	8	14	5	14	2	2	2	1	2	2	0	7	2	5	2	4	0	0	2	4	0	2	2	rs267602809		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:18195097C>T	ENST00000314254.3	+	1	714	c.294C>T	c.(292-294)ctC>ctT	p.L98L	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GCAAAATCCTCGTTTCTGTGA	0.527																																					p.L98L													.	MRGPRX4-91	0			c.C294T						.						129	103	112					11																	18195097		2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			AATCCTCGTTTCT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.294C>T	11.37:g.18195097C>T		Somatic	235	1		WXS	Illumina HiSeq	Phase_I	187	33	NM_054032	0	0	0	0	0	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			.		0.527	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		T	18195097	C	T	18195097	2	4	159	1	0	0	0	0	0	0	0	1	9794	871	31	1		1	MRGPRX4	11	18195097	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	14405141	18195097	116811419	54	14449											
LGALS12	85329	broad.mit.edu;bcgsc.ca	37	chr11	63283171	63283171	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccttcctcttttaccccCagagattctttgaggtaggt	6	14	7	14	0	2	2	0	1	2	1	3	3	3	2	5	2	1	1	5	2	2	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:63283171C>A	ENST00000394618.3	+	8	1141	c.850C>A	c.(850-852)Cag>Aag	p.Q284K	LGALS12_ENST00000415491.2_Missense_Mutation_p.Q223K|LGALS12_ENST00000255684.5_Missense_Mutation_p.Q275K|LGALS12_ENST00000425950.2_Missense_Mutation_p.Q214K|LGALS12_ENST00000340246.5_Missense_Mutation_p.Q285K	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	284	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						CTTTTACCCCCAGAGATTCTT	0.552																																					p.Q285K													.	LGALS12-92	0			c.C853A						.						48	49	49					11																	63283171		2201	4298	6499	SO:0001583	missense	85329	exon8			TACCCCCAGAGAT	AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.850C>A	11.37:g.63283171C>A	ENSP00000378116:p.Gln284Lys	Somatic	50	1		WXS	Illumina HiSeq	Phase_I	31	5	NM_001142535	0	0	0	0	0	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000394618.3	37	CCDS8045.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432768	0.43224	.	.	ENSG00000133317	ENST00000255684;ENST00000394618;ENST00000340246;ENST00000415491;ENST00000425950	T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34	5.78	5.78	0.91487	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (3);Concanavalin A-like lectin/glucanase, subgroup (1);	0.106561	0.42172	D	0.000760	T	0.21145	0.0509	L	0.57536	1.79	0.31596	N	0.653297	B;B;B;B	0.18166	0.026;0.021;0.01;0.026	B;B;B;B	0.18561	0.022;0.011;0.004;0.015	T	0.05289	-1.0894	10	0.46703	T	0.11	-21.8306	15.5052	0.75731	0.0:1.0:0.0:0.0	.	244;285;275;284	Q9NZ03;G5E970;Q96DT0-3;Q96DT0	.;.;.;LEG12_HUMAN	K	275;284;285;223;214	ENSP00000255684:Q275K;ENSP00000378116:Q284K;ENSP00000339374:Q285K;ENSP00000394659:Q223K;ENSP00000399093:Q214K	ENSP00000255684:Q275K	Q	+	1	0	LGALS12	63039747	0.797000	0.28877	0.998000	0.56505	0.952000	0.60782	1.250000	0.32850	2.739000	0.93911	0.561000	0.74099	CAG	.		0.552	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101		A	63283171	C	A	63283171	3	1	159	1	0	0	0	0	1	0	0	0	8760	595	21	4	883	4	LGALS12	11	63283171	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	45088074	63283171	71723345	55	14450											
LRP5	4041	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	68181318	68181318	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggccacctggacttcGtgatggacatcctggtgttc	6	11	12	12	1	0	1	0	1	0	0	4	3	2	3	4	4	0	1	4	4	0	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:68181318G>T	ENST00000294304.7	+	12	2771	c.2665G>T	c.(2665-2667)Gtg>Ttg	p.V889L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	889	Beta-propeller 3.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCTGGACTTCGTGATGGACAT	0.592																																					p.V889L													.	LRP5-661	0			c.G2665T						.						87	76	79					11																	68181318		2200	4294	6494	SO:0001583	missense	4041	exon12			GACTTCGTGATGG	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.2665G>T	11.37:g.68181318G>T	ENSP00000294304:p.Val889Leu	Somatic	59	1		WXS	Illumina HiSeq	Phase_I	67	23	NM_002335	0	0	4	9	5	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.708228	0.89018	.	.	ENSG00000162337	ENST00000294304	D	0.91407	-2.84	5.02	5.02	0.67125	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.43579	U	0.000546	D	0.88815	0.6539	N	0.25957	0.775	0.58432	D	0.999999	P;P	0.39759	0.687;0.687	P;P	0.48368	0.575;0.575	D	0.86093	0.1551	10	0.21540	T	0.41	.	18.5313	0.90993	0.0:0.0:1.0:0.0	.	889;889	Q9UES7;O75197	.;LRP5_HUMAN	L	889	ENSP00000294304:V889L	ENSP00000294304:V889L	V	+	1	0	LRP5	67937894	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.610000	0.54125	2.601000	0.87937	0.561000	0.74099	GTG	.		0.592	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68181318	G	T	68181318	3	4	159	1	0	0	0	0	1	0	0	0	8985	1145	40	4	2711	4	LRP5	11	68181318	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	4898147	68181318	66825198	56	14451											
VWF	7450	ucsc.edu;bcgsc.ca	37	chr12	6090996	6090996	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtacagccacagtcattggTggcagttgaggccaagtacc	10	8	13	10	0	1	1	1	1	0	0	1	1	1	1	3	4	3	4	3	4	3	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:6090996T>G	ENST00000261405.5	-	42	7497	c.7243A>C	c.(7243-7245)Acc>Ccc	p.T2415P		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2415					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CAGTCATTGGTGGCAGTTGAG	0.488																																					p.T2415P													.	VWF-163	0			c.A7243C						.						138	111	120					12																	6090996		2203	4300	6503	SO:0001583	missense	7450	exon42			CATTGGTGGCAGT		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"Endogenous ligands"	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.7243A>C	12.37:g.6090996T>G	ENSP00000261405:p.Thr2415Pro	Somatic	160	3		WXS	Illumina HiSeq		211	39	NM_000552	0	0	0	0	0	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.955414	0.73902	.	.	ENSG00000110799	ENST00000261405	T	0.37411	1.2	5.51	5.51	0.81932	.	0.000000	0.42053	D	0.000776	T	0.62122	0.2402	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.71870	0.975	T	0.65504	-0.6152	10	0.45353	T	0.12	.	14.81	0.69989	0.0:0.0:0.0:1.0	.	2415	P04275	VWF_HUMAN	P	2415	ENSP00000261405:T2415P	ENSP00000261405:T2415P	T	-	1	0	VWF	5961257	1.000000	0.71417	0.972000	0.41901	0.834000	0.47266	5.313000	0.65798	2.088000	0.63022	0.454000	0.30748	ACC	.		0.488	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		G	6090996	T	G	6090996	3	3	159	1	0	0	0	0	1	0	0	0	17279	1696	59	5	1242	5	VWF	12	6090996	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		6090996	127760899	57	14452											
DNAJC14	85406	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	56217194	56217194	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctccaacttacatctcataCtcctttcgcttttcagcatt	8	17	2	14	1	3	0	2	0	2	0	7	0	4	0	2	0	4	2	2	0	3	6	rs541345798		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:56217194C>G	ENST00000357606.3	-	4	1795	c.1506G>C	c.(1504-1506)gaG>gaC	p.E502D	RP11-762I7.5_ENST00000552719.1_5'Flank|RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.V132L|DNAJC14_ENST00000317269.3_Missense_Mutation_p.E502D|DNAJC14_ENST00000317287.5_Missense_Mutation_p.E502D			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	502	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						ACATCTCATACTCCTTTCGCT	0.463																																					p.E502D		.											.	DNAJC14-229	0			c.G1506C						.						95	84	87					12																	56217194		2203	4300	6503	SO:0001583	missense	85406	exon3			CTCATACTCCTTT	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.1506G>C	12.37:g.56217194C>G	ENSP00000350223:p.Glu502Asp	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	86	15	NM_032364	0	0	1	6	5	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Missense_Mutation	SNP	ENST00000357606.3	37	CCDS8894.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.64|17.64	3.439259|3.439259	0.63067|0.63067	.|.	.|.	ENSG00000135392|ENSG00000257390	ENST00000357606;ENST00000317269;ENST00000537962;ENST00000317287|ENST00000546837	T;T;T|.	0.32023|.	1.47;1.47;1.47|.	5.85|5.85	4.7|4.7	0.59300|0.59300	Heat shock protein DnaJ, N-terminal (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.45657|0.45657	0.1353|0.1353	L|L	0.35542|0.35542	1.07|1.07	0.49483|0.49483	D|D	0.999795|0.999795	B;B|.	0.29766|.	0.256;0.256|.	P;P|.	0.50231|.	0.635;0.635|.	T|T	0.33240|0.33240	-0.9876|-0.9876	10|5	0.42905|.	T|.	0.14|.	-16.2803|-16.2803	7.9219|7.9219	0.29850|0.29850	0.0:0.1589:0.0:0.8411|0.0:0.1589:0.0:0.8411	.|.	502;502|.	Q6Y2X3;A8K5A7|.	DJC14_HUMAN;.|.	D|L	502;502;212;502|132	ENSP00000350223:E502D;ENSP00000316240:E502D;ENSP00000317500:E502D|.	ENSP00000316240:E502D|.	E|V	-|-	3|1	2|0	DNAJC14|RP11-762I7.5	54503461|54503461	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	2.807000|2.807000	0.47955|0.47955	1.141000|1.141000	0.42275|0.42275	-0.294000|-0.294000	0.09567|0.09567	GAG|GTA	.		0.463	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		G	56217194	C	G	56217194	3	3	159	1	0	0	0	0	1	0	0	0	4644	564	20	4	622	4	DNAJC14	12	56217194	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	50126198	56217194	77634701	58	14453											
RDH16	8608	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	57346721	57346721	+	Frame_Shift_Del	DEL	A	A	-																															tactggtcacagcagtcttgAaatagccaggttcaatcata																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:57346721delA	ENST00000398138.3	-	3	1482	c.626delT	c.(625-627)ttcfs	p.F209fs	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	209					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						AGCAGTCTTGAAATAGCCAGG	0.507																																					p.F209fs	GBM(179;741 2921 43105 45298)	.											.	RDH16-90	0			c.626delT						.						128	124	125					12																	57346721		1873	4112	5985	SO:0001589	frameshift_variant	8608	exon3			.		CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29674	protein-coding gene	gene with protein product	"microsomal NAD+ dependent retinol dehydrogenase 4", "short chain dehydrogenase/reductase family 9C, member 8"		"retinol dehydrogenase 16 (all-trans and 13-cis)"			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.626delT	12.37:g.57346721delA	ENSP00000381206:p.Phe209fs	Somatic	55	0		WXS	Illumina HiSeq	Phase_I	90	31	NM_003708	0	0	0	0	0	Q9UNV2	Frame_Shift_Del	DEL	ENST00000398138.3	37	CCDS41797.1																																																																																			.		0.507	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708		-	57346721	A	-	57346721	7	5	159	1	0	1	0	1	0	0	0	0	13226	246	9	0	335	0	RDH16	12	57346721	Frame_Shift_Del	DEL	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	1129527	57346721	76505174	59	14454											
MON2	23041	hgsc.bcm.edu;broad.mit.edu	37	chr12	62954348	62954349	+	Frame_Shift_Ins	INS	-	-	T																															caaaaacaatgaagtatctcINStggctgctctgaaaagcttc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:62954348_62954349insT	ENST00000393632.2	+	26	3878_3879	c.3487_3488insT	c.(3487-3489)ctgfs	p.L1163fs	MON2_ENST00000552738.1_Frame_Shift_Ins_p.L1140fs|MON2_ENST00000393630.3_Frame_Shift_Ins_p.L1164fs|MON2_ENST00000546600.1_Frame_Shift_Ins_p.L1163fs|MON2_ENST00000393629.2_Frame_Shift_Ins_p.L1163fs|MON2_ENST00000280379.6_Frame_Shift_Ins_p.L1164fs	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1163					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TGAAGTATCTCTGGCTGCTCTG	0.411																																					p.L1163fs		.											.	MON2-514	0			c.3487_3488insT						.																																			SO:0001589	frameshift_variant	23041	exon26			.		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"MON2 homolog (yeast)"			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.3488dupT	12.37:g.62954349_62954349dupT	ENSP00000377252:p.Leu1163fs	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	43	11	NM_015026	0	0	0	0	0	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Frame_Shift_Ins	INS	ENST00000393632.2	37	CCDS31849.1																																																																																			.		0.411	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62954349	-	T	62954348	7	5	159	1	0	1	1	0	0	0	0	0	9725	912	32	0	3589	0	MON2	12	62954348	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	5607627	62954348	70897547	60	14455											
DDX54	79039	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	113610195	113610195	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtttgcccttggcggggaaGctgtagttgatgacattgtc	7	13	14	7	1	0	2	0	2	0	0	1	3	0	3	1	3	2	4	1	3	2	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:113610195G>A	ENST00000306014.5	-	11	1269	c.1242C>T	c.(1240-1242)agC>agT	p.S414S	DDX54_ENST00000314045.7_Silent_p.S414S	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	414	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TGGCGGGGAAGCTGTAGTTGA	0.637																																					p.S414S		.											.	DDX54-227	0			c.C1242T						.						82	67	72					12																	113610195		2203	4300	6503	SO:0001819	synonymous_variant	79039	exon11			GGGGAAGCTGTAG	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1242C>T	12.37:g.113610195G>A		Somatic	175	0		WXS	Illumina HiSeq	Phase_I	215	72	NM_024072	0	0	35	75	40	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	37	CCDS31907.1																																																																																			.		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		A	113610195	G	A	113610195	2	1	159	1	0	0	0	0	0	0	0	1	4378	962	34	2		2	DDX54	12	113610195	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	50655847	113610195	20241700	61	14456											
RIMBP2	23504	broad.mit.edu	37	chr12	130926698	130926698	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccttgcccaccagcagcGtgcactgcagctcatccgag	7	7	10	17	3	1	0	1	0	0	0	3	1	3	0	4	0	6	4	4	0	0	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:130926698G>A	ENST00000261655.4	-	8	1311	c.1148C>T	c.(1147-1149)aCg>aTg	p.T383M	RIMBP2_ENST00000535703.1_Missense_Mutation_p.T291M|RIMBP2_ENST00000536002.1_Missense_Mutation_p.T291M	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	383	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.T383M(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CACCAGCAGCGTGCACTGCAG	0.637																																					p.T383M													.	RIMBP2-142	1	Substitution - Missense(1)	kidney(1)	c.C1148T						.						114	102	106					12																	130926698		2203	4300	6503	SO:0001583	missense	23504	exon8			AGCAGCGTGCACT	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 133"	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.1148C>T	12.37:g.130926698G>A	ENSP00000261655:p.Thr383Met	Somatic	129	1		WXS	Illumina HiSeq	Phase_I	181	5	NM_015347	0	0	0	0	0	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	g	17.47	3.398389	0.62177	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.55052	0.54;0.54;0.54	4.23	4.23	0.50019	Fibronectin, type III (2);	0.000000	0.85682	D	0.000000	T	0.74680	0.3748	M	0.83953	2.67	0.58432	D	0.999996	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.83275	0.826;0.972;0.996	T	0.80491	-0.1359	10	0.72032	D	0.01	-24.31	16.6129	0.84899	0.0:0.0:1.0:0.0	.	291;291;383	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	M	383;291;291;291	ENSP00000261655:T383M;ENSP00000440347:T291M;ENSP00000439159:T291M	ENSP00000261655:T383M	T	-	2	0	RIMBP2	129492651	1.000000	0.71417	1.000000	0.80357	0.631000	0.37964	4.555000	0.60767	1.867000	0.54127	0.537000	0.68136	ACG	.		0.637	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130926698	G	A	130926698	3	1	159	1	0	0	0	0	1	0	0	0	13395	1145	40	1	2058	1	RIMBP2	12	130926698	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	17316503	130926698	2925197	62	14457											
C14orf106	55320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	45693181	45693181	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgaattaaaccaggtaagCattctaagggatgcctattt	13	12	8	8	0	1	1	0	1	1	0	1	2	1	2	3	2	3	2	3	2	6	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr14:45693181C>T	ENST00000310806.4	-	11	3067	c.2609G>A	c.(2608-2610)tGc>tAc	p.C870Y		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	870					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						ACCAGGTAAGCATTCTAAGGG	0.388																																					p.C870Y		.											.	MIS18BP1-90	0			c.G2609A						.						95	90	91					14																	45693181		2203	4300	6503	SO:0001583	missense	55320	exon11			GGTAAGCATTCTA	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"kinetochore null 2 homolog (C. elegans)"		"chromosome 14 open reading frame 106"	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.2609G>A	14.37:g.45693181C>T	ENSP00000309790:p.Cys870Tyr	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	50	14	NM_018353	0	0	4	9	5	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.229082	0.00280	.	.	ENSG00000129534	ENST00000310806	T	0.17691	2.26	5.72	2.87	0.33458	Homeodomain-like (1);	0.719999	0.14355	N	0.324833	T	0.12220	0.0297	L	0.57536	1.79	0.09310	N	1	P	0.51351	0.944	B	0.40165	0.321	T	0.10590	-1.0623	10	0.02654	T	1	0.5125	5.2769	0.15655	0.162:0.665:0.0:0.173	.	870	Q6P0N0	M18BP_HUMAN	Y	870	ENSP00000309790:C870Y	ENSP00000309790:C870Y	C	-	2	0	MIS18BP1	44762931	0.000000	0.05858	0.007000	0.13788	0.137000	0.21094	0.035000	0.13797	0.413000	0.25759	0.655000	0.94253	TGC	.		0.388	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			T	45693181	C	T	45693181	3	4	159	1	0	0	0	0	1	0	0	0	1742	710	25	2	817	2	C14orf106	14	45693181	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		45693181	61656359	63	14458											
ZBTB1	22890	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	64989255	64989256	+	Frame_Shift_Ins	INS	-	-	T																															actgaaagactttaacattaINSttaaagttactgataaagac																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr14:64989255_64989256insT	ENST00000554015.1	+	4	1464_1465	c.1033_1034insT	c.(1033-1035)attfs	p.I345fs	RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Frame_Shift_Ins_p.I345fs|ZBTB1_ENST00000358738.3_Frame_Shift_Ins_p.I345fs			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	345					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		CTTTAACATTATTAAAGTTACT	0.347																																					p.I345fs		.											.	ZBTB1-91	0			c.1033_1034insT						.																																			SO:0001589	frameshift_variant	22890	exon2			.	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1035dupT	14.37:g.64989257_64989257dupT	ENSP00000451000:p.Ile345fs	Somatic	216	0		WXS	Illumina HiSeq	Phase_I	151	36	NM_014950	0	0	0	0	0	A8K6S8|Q86SW8	Frame_Shift_Ins	INS	ENST00000554015.1	37	CCDS45126.1																																																																																			.		0.347	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			T	64989256	-	T	64989255	7	5	159	1	0	1	1	0	0	0	0	0	17554	449	16	0	1035	0	ZBTB1	14	64989255	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	19296074	64989255	42360285	64	14459											
MTA1	9112	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr14	105936238	105936239	+	Frame_Shift_Ins	INS	-	-	G																															caccaaagtgcgcctgatccINSgggggggctccctgccccca																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr14:105936238_105936239insG	ENST00000331320.7	+	20	2120_2121	c.1906_1907insG	c.(1906-1908)cggfs	p.R636fs	MTA1_ENST00000435036.2_Frame_Shift_Ins_p.R176fs|MTA1_ENST00000406191.1_Frame_Shift_Ins_p.R624fs|RP11-521B24.5_ENST00000552675.1_RNA|MTA1_ENST00000405646.1_Frame_Shift_Ins_p.R619fs	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	636					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		GCGCCTGATCCGGGGGGGCTCC	0.663																																					p.R636fs		.											.	MTA1-135	0			c.1906_1907insG						.																																			SO:0001589	frameshift_variant	9112	exon20			.	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"GATA zinc finger domain containing"	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1913dupG	14.37:g.105936245_105936245dupG	ENSP00000333633:p.Arg636fs	Somatic	153	0		WXS	Illumina HiSeq	Phase_I	139	28	NM_004689	0	0	0	0	0	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Frame_Shift_Ins	INS	ENST00000331320.7	37	CCDS32169.1																																																																																			.		0.663	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			G	105936239	-	G	105936238	7	5	159	1	0	1	1	0	0	0	0	0	9933	643	23	0	1984	0	MTA1	14	105936238	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	40946983	105936238	1413302	65	14460											
STOML1	9399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	74281093	74281093	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccgggtcccagatgcgAaactggacatcggctcccac	10	5	11	15	3	0	1	0	0	0	1	3	3	2	2	3	3	3	2	3	3	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr15:74281093A>G	ENST00000316900.5	-	4	565	c.441T>C	c.(439-441)ttT>ttC	p.F147F	STOML1_ENST00000359750.4_Silent_p.F147F|STOML1_ENST00000561656.1_Silent_p.F60F|STOML1_ENST00000541638.1_Silent_p.F105F|STOML1_ENST00000316911.6_Silent_p.F97F|STOML1_ENST00000564777.1_Silent_p.F97F	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	147						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CCCAGATGCGAAACTGGACAT	0.612																																					p.F147F		.											.	STOML1-91	0			c.T441C						.						108	100	103					15																	74281093		2198	4297	6495	SO:0001819	synonymous_variant	9399	exon4			GATGCGAAACTGG	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.441T>C	15.37:g.74281093A>G		Somatic	89	0		WXS	Illumina HiSeq	Phase_I	71	15	NM_001256672	0	0	3	15	12	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Silent	SNP	ENST00000316900.5	37	CCDS10254.1																																																																																			.		0.612	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		G	74281093	A	G	74281093	2	3	159	1	0	0	0	0	0	0	0	1	15345	243	9	3		3	STOML1	15	74281093	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		74281093	28250299	66	14461											
LMAN1L	79748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75111060	75111060	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atgaacaaactgcccacaggGatggagctagccaagggctg	13	5	13	10	0	0	1	0	1	0	0	0	3	0	3	2	3	5	2	2	3	4	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr15:75111060G>T	ENST00000309664.5	+	5	638	c.499G>T	c.(499-501)Gat>Tat	p.D167Y	RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Splice_Site_p.D167Y	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	167	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGCCCACAGGGATGGAGCTAG	0.577																																					p.D167Y		.											.	LMAN1L-90	0			c.G499T						.						38	32	34					15																	75111060		2197	4295	6492	SO:0001630	splice_region_variant	79748	exon5			CACAGGGATGGAG	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.498-1G>T	15.37:g.75111060G>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_I	68	24	NM_021819	0	0	0	0	0	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	9.914	1.210396	0.22289	.	.	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.69685	-0.42;-0.42	4.89	0.74	0.18330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.786555	0.11191	N	0.589939	T	0.75752	0.3892	M	0.87456	2.885	0.53005	D	0.999961	B;D;B;B	0.59767	0.009;0.986;0.009;0.271	B;P;B;B	0.54100	0.018;0.742;0.018;0.121	T	0.71790	-0.4486	10	0.87932	D	0	.	5.9881	0.19446	0.1621:0.0:0.5719:0.266	.	59;167;95;167	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	Y	167;59;167	ENSP00000310431:D167Y;ENSP00000369031:D167Y	ENSP00000310431:D167Y	D	+	1	0	LMAN1L	72898113	1.000000	0.71417	0.051000	0.19133	0.011000	0.07611	1.479000	0.35453	-0.273000	0.09246	-2.281000	0.00270	GAT	.		0.577	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		Missense_Mutation	T	75111060	G	T	75111060	5	4	159	1	0	0	0	0	0	0	1	0	8860	1188	41	4	517	4	LMAN1L	15	75111060	Splice_Site	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	829967	75111060	27420332	67	14462											
ST8SIA2	8128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	93007416	93007417	+	Missense_Mutation	DNP	TC	TC	AT																															cacacgtttctgcaaacaaaTctacctctacggcttctggc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr15:93007416_93007417TC>AT	ENST00000268164.3	+	6	1166_1167	c.929_930TC>AT	c.(928-930)aTC>aAT	p.I310N	ST8SIA2_ENST00000539113.1_Missense_Mutation_p.I289N	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	310					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			TGCAAACAAATCTACCTCTACG	0.49																																					p.I310N		.											.	ST8SIA2-90	0			c.C930T						.																																			SO:0001583	missense	8128	exon6			ACAAATCTACCTC	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	Exception_encountered	15.37:g.93007416_93007417delinsAT	ENSP00000268164:p.Ile310Asn	Somatic	119	0		WXS	Illumina HiSeq	Phase_I	76	19	NM_006011	0	0	0	0	0	Q4VAZ0|Q92470|Q92746	Missense_Mutation	DNP	ENST00000268164.3	37	CCDS10372.1																																																																																			.		0.49	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		AT	93007417	TC	AT	93007416	3	1	159	1	0	0	0	0	1	0	0	0	15264	1435	50	5	951	5	ST8SIA2	15	93007416	Missense_Mutation	DNP	TC	TCGA-PJ-A5Z8-01A-11D-A28G-10	17896356	93007416	9523976	68	14463											
ARMC5	79798	broad.mit.edu	37	chr16	31471290	31471290	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggggcgtgccggaccgaaGtgcgcagactcggaggcata	10	4	17	10	5	0	1	0	0	0	1	1	4	0	3	2	5	2	2	2	5	3	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:31471290G>T	ENST00000563544.1	+	2	991	c.445G>T	c.(445-447)Gtg>Ttg	p.V149L	ARMC5_ENST00000412665.2_5'UTR|ARMC5_ENST00000457010.2_Missense_Mutation_p.V149L|ARMC5_ENST00000268314.4_Missense_Mutation_p.V149L|ARMC5_ENST00000538189.1_Missense_Mutation_p.V181L|ARMC5_ENST00000408912.3_Missense_Mutation_p.V244L|RP11-452L6.5_ENST00000564629.1_RNA			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	149										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CCGGACCGAAGTGCGCAGACT	0.607																																					p.V149L													.	ARMC5-24	0			c.G445T						.						53	56	55					16																	31471290		2027	4186	6213	SO:0001583	missense	79798	exon1			ACCGAAGTGCGCA	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.445G>T	16.37:g.31471290G>T	ENSP00000456877:p.Val149Leu	Somatic	29	0		WXS	Illumina HiSeq	Phase_I	27	3	NM_024742	0	0	2	4	2	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846415	0.71603	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	4.67	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.70859	0.3272	L	0.55481	1.735	0.80722	D	1	D;D;D;D;D	0.61697	0.986;0.986;0.986;0.986;0.99	P;P;P;P;D	0.73380	0.876;0.876;0.876;0.876;0.98	T	0.73132	-0.4079	9	0.62326	D	0.03	13.2405	15.0988	0.72256	0.0:0.0:1.0:0.0	.	181;181;244;149;149	B4DH27;F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;.;ARMC5_HUMAN;.	L	244;181;149;149	ENSP00000386125:V244L;ENSP00000443995:V181L;ENSP00000268314:V149L;ENSP00000399561:V149L	ENSP00000268314:V149L	V	+	1	0	ARMC5	31378791	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	5.373000	0.66162	2.435000	0.82474	0.561000	0.74099	GTG	.		0.607	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		T	31471290	G	T	31471290	3	4	159	1	0	0	0	0	1	0	0	0	955	1029	36	4	447	4	ARMC5	16	31471290	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		31471290	58883463	69	14464											
NKD1	85407	broad.mit.edu;bcgsc.ca	37	chr16	50583404	50583404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggatcgggagacagcgctgcCcgggcggtgtctcgggaccc	5	5	18	13	5	1	1	0	0	1	1	3	4	1	3	2	5	2	1	2	5	0	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:50583404C>T	ENST00000268459.3	+	3	354	c.130C>T	c.(130-132)Ccg>Tcg	p.P44S	NKD1_ENST00000564336.1_3'UTR|RP11-401P9.1_ENST00000569940.2_RNA	NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	44					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		ACAGCGCTGCCCGGGCGGTGT	0.692																																					p.P44S													.	NKD1-226	0			c.C130T						.						25	27	26					16																	50583404		2196	4299	6495	SO:0001583	missense	85407	exon3			CGCTGCCCGGGCG	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"EF-hand domain containing"	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.130C>T	16.37:g.50583404C>T	ENSP00000268459:p.Pro44Ser	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	179	43	NM_033119	0	0	0	0	0	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	37	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563863	0.45694	.	.	ENSG00000140807	ENST00000268459	T	0.62232	0.04	4.39	2.38	0.29361	.	0.283128	0.35096	N	0.003445	T	0.45438	0.1342	L	0.51422	1.61	0.31422	N	0.674165	B	0.20052	0.041	B	0.20955	0.032	T	0.35051	-0.9804	10	0.07990	T	0.79	-5.5362	3.7264	0.08476	0.0:0.544:0.1991:0.2569	.	44	Q969G9	NKD1_HUMAN	S	44	ENSP00000268459:P44S	ENSP00000268459:P44S	P	+	1	0	NKD1	49140905	0.753000	0.28349	0.778000	0.31720	0.730000	0.41778	0.870000	0.28010	0.465000	0.27167	0.313000	0.20887	CCG	.		0.692	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			T	50583404	C	T	50583404	3	4	159	1	0	0	0	0	1	0	0	0	10467	623	22	2	140	2	NKD1	16	50583404	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	19112114	50583404	39771349	70	14465											
MMP15	4324	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	58079023	58079023	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacttcatgggctgccaggaGcacgtggagccaggcccccg	7	5	15	14	2	1	0	1	0	0	0	1	3	1	2	4	4	3	2	4	4	0	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:58079023G>C	ENST00000219271.3	+	10	2468	c.1683G>C	c.(1681-1683)gaG>gaC	p.E561D		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	561					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	GCTGCCAGGAGCACGTGGAGC	0.682																																					p.E561D		.											.	MMP15-713	0			c.G1683C						.						15	15	15					16																	58079023		2197	4298	6495	SO:0001583	missense	4324	exon10			CCAGGAGCACGTG	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"matrix metalloproteinase 15 (membrane-inserted)"			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.1683G>C	16.37:g.58079023G>C	ENSP00000219271:p.Glu561Asp	Somatic	50	0		WXS	Illumina HiSeq	Phase_I	90	28	NM_002428	0	0	7	8	1	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316412	0.23908	.	.	ENSG00000102996	ENST00000219271	T	0.15952	2.38	4.5	1.48	0.22813	Hemopexin/matrixin (1);	0.444889	0.25380	N	0.031083	T	0.07324	0.0185	N	0.08118	0	0.36663	D	0.878058	P	0.49185	0.92	P	0.45232	0.474	T	0.41662	-0.9496	10	0.15952	T	0.53	.	3.3205	0.07048	0.2891:0.0:0.5282:0.1827	.	561	P51511	MMP15_HUMAN	D	561	ENSP00000219271:E561D	ENSP00000219271:E561D	E	+	3	2	MMP15	56636524	1.000000	0.71417	0.967000	0.41034	0.905000	0.53344	1.330000	0.33781	0.167000	0.19631	-0.277000	0.10078	GAG	.		0.682	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		C	58079023	G	C	58079023	3	2	159	1	0	0	0	0	1	0	0	0	9679	962	34	4	1721	4	MMP15	16	58079023	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	7495619	58079023	32275730	71	14466											
CLEC18B	497190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	74447559	74447559	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacagcccagctggcttgAggtggcccacacgagctaca	9	5	11	16	1	0	1	0	1	0	0	0	2	0	1	3	3	4	3	3	3	1	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:74447559A>T	ENST00000339953.5	-	4	593	c.472T>A	c.(472-474)Tca>Aca	p.S158T		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	158	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						AGCTGGCTTGAGGTGGCCCAC	0.607																																					p.S158T		.											.	CLEC18B-90	0			c.T472A						.						99	99	99					16																	74447559		2198	4298	6496	SO:0001583	missense	497190	exon4			GGCTTGAGGTGGC	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"C-type lectin domain containing"	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.472T>A	16.37:g.74447559A>T	ENSP00000341051:p.Ser158Thr	Somatic	270	0		WXS	Illumina HiSeq	Phase_I	245	21	NM_001011880	0	0	16	17	1	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	37	CCDS32484.1	.	.	.	.	.	.	.	.	.	.	a	14.17	2.454450	0.43634	.	.	ENSG00000140839	ENST00000429489;ENST00000339953;ENST00000268492;ENST00000425714	T	0.08807	3.05	3.1	3.1	0.35709	CAP domain (3);	0.000000	0.64402	D	0.000001	T	0.12390	0.0301	N	0.21545	0.675	0.42457	D	0.992777	D;P;D	0.63880	0.993;0.95;0.983	D;P;D	0.77557	0.99;0.871;0.928	T	0.22871	-1.0204	10	0.23891	T	0.37	.	7.6588	0.28392	1.0:0.0:0.0:0.0	.	78;158;158	Q6UXF7-2;C9JSV1;Q6UXF7	.;.;CL18B_HUMAN	T	158;158;158;78	ENSP00000341051:S158T	ENSP00000268492:S158T	S	-	1	0	CLEC18B	73005060	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.560000	0.73950	1.286000	0.44565	0.438000	0.28831	TCA	.		0.607	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880		T	74447559	A	T	74447559	3	4	159	1	0	0	0	0	1	0	0	0	3509	304	11	5	935	5	CLEC18B	16	74447559	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	16368536	74447559	15907194	72	14467											
CTRB1	1504	broad.mit.edu	37	chr16	75257061	75257061	+	Frame_Shift_Del	DEL	G	G	-																															cctccgacgtggtcgtggctGgggagtttgaccagggctct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:75257061delG	ENST00000361017.4	+	4	267	c.259delG	c.(259-261)gggfs	p.G87fs	RP11-331F4.4_ENST00000489723.1_RNA	NM_001906.4	NP_001897.4	P17538	CTRB1_HUMAN	chymotrypsinogen B1	87	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.166)	Aprotinin(DB06692)	GGTCGTGGCTGGGGAGTTTGA	0.672																																					p.G87fs													.	CTRB1-68	0			c.259delG						.						2	2	2					16																	75257061		1322	2744	4066	SO:0001589	frameshift_variant	1504	exon4			GTGGCTGGGGAGT		CCDS32490.1	16q23.1	2008-02-05			ENSG00000168925	ENSG00000168925	3.4.21.1		2521	protein-coding gene	gene with protein product		118890		CTRB		2917002, 8186414	Standard	NM_001906		Approved		uc002fds.3	P17538	OTTHUMG00000159272	ENST00000361017.4:c.259delG	16.37:g.75257061delG	ENSP00000354294:p.Gly87fs	Somatic	566	1		WXS	Illumina HiSeq	Phase_I	819	83	NM_001906	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000361017.4	37	CCDS32490.1																																																																																			.		0.672	CTRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354300.2	NM_001906		-	75257061	G	-	75257061	7	5	159	1	0	1	0	1	0	0	0	0	4031	1348	47	0	273	0	CTRB1	16	75257061	Frame_Shift_Del	DEL	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	809502	75257061	15097692	73	14468											
ZZEF1	23140	broad.mit.edu	37	chr17	3910206	3910207	+	Frame_Shift_Ins	INS	-	-	G																															acactccacattccagaggcINSgggtggccttgtttgggtag																								rs528609855		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:3910206_3910207insG	ENST00000381638.2	-	55	8987_8988	c.8863_8864insC	c.(8863-8865)cgcfs	p.R2955fs		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2955							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ATTCCAGAGGCGGGTGGCCTTG	0.53																																					p.R2955fs													.	ZZEF1-93	0			c.8864_8865insC						.																																			SO:0001589	frameshift_variant	23140	exon55			CAGAGGCGGGTGG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"Zinc fingers, ZZ-type", "EF-hand domain containing"	29027	protein-coding gene	gene with protein product			"zinc finger, ZZ-type with EF hand domain 1"			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8864dupC	17.37:g.3910209_3910209dupG	ENSP00000371051:p.Arg2955fs	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	101	9	NM_015113	0	0	0	0	0	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Frame_Shift_Ins	INS	ENST00000381638.2	37	CCDS11043.1																																																																																			.		0.53	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		G	3910207	-	G	3910206	7	5	159	1	0	1	1	0	0	0	0	0	18287	768	27	0	25	0	ZZEF1	17	3910206	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10		3910206	77285004	74	14469											
DULLARD	23399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7147902	7147902	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattgggagcaggttgagAagggctgtgtcgctggggtc	7	9	19	6	1	0	1	0	1	0	1	2	3	0	2	0	5	2	5	0	5	1	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:7147902A>G	ENST00000573600.1	-	8	1063	c.642T>C	c.(640-642)ctT>ctC	p.L214L	CTDNEP1_ENST00000574322.1_Silent_p.L214L|CTD-2545G14.7_ENST00000570760.2_Missense_Mutation_p.F18S|GABARAP_ENST00000571253.1_5'Flank|GABARAP_ENST00000302386.5_5'Flank|CTDNEP1_ENST00000572043.1_Silent_p.L81L|GABARAP_ENST00000577035.1_5'Flank|GABARAP_ENST00000571129.1_5'Flank|GABARAP_ENST00000573928.1_5'Flank|CTDNEP1_ENST00000318988.6_Silent_p.L214L			O95476	CNEP1_HUMAN	CTD nuclear envelope phosphatase 1	214	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				gamete generation (GO:0007276)|mesoderm development (GO:0007498)|nuclear envelope organization (GO:0006998)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein dephosphorylation (GO:0006470)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(9)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	15						GCAGGTTGAGAAGGGCTGTGT	0.522																																					p.L214L		.											.	CTDNEP1-91	0			c.T642C						.						70	67	68					17																	7147902		2203	4300	6503	SO:0001819	synonymous_variant	23399	exon7			GTTGAGAAGGGCT	AJ011916	CCDS11093.1	17p13	2012-11-27	2010-10-27	2010-10-27	ENSG00000175826	ENSG00000175826		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	19085	protein-coding gene	gene with protein product	"C-terminal domain nuclear envelope phosphatase 1"	610684	"dullard homolog (Xenopus laevis)"	DULLARD		12083771, 17141153	Standard	NM_015343		Approved	HSA011916, NET56	uc002gfd.2	O95476	OTTHUMG00000102180	ENST00000573600.1:c.642T>C	17.37:g.7147902A>G		Somatic	63	0		WXS	Illumina HiSeq	Phase_I	58	18	NM_001143775	0	0	204	320	116	D3DTN7|Q96GQ9	Silent	SNP	ENST00000573600.1	37	CCDS11093.1																																																																																			.		0.522	CTDNEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440215.1	NM_015343		G	7147902	A	G	7147902	2	3	159	1	0	0	0	0	0	0	0	1	4810	233	9	3		3	DULLARD	17	7147902	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	3237696	7147902	74047308	75	14470											
CHD3	1107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7794342	7794342	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttctctgaggaggattacCacacgctcaccaactacaaa	13	9	7	12	1	2	1	1	1	1	0	3	3	2	3	2	2	3	2	2	2	4	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:7794342C>G	ENST00000330494.7	+	4	619	c.469C>G	c.(469-471)Cac>Gac	p.H157D	CHD3_ENST00000380358.4_Missense_Mutation_p.H216D|CHD3_ENST00000358181.4_Missense_Mutation_p.H157D	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	157					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GGAGGATTACCACACGCTCAC	0.527																																					p.H216D		.											.	CHD3-228	0			c.C646G						.						166	142	150					17																	7794342		2203	4300	6503	SO:0001583	missense	1107	exon4			GATTACCACACGC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"Zinc fingers, PHD-type"	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.469C>G	17.37:g.7794342C>G	ENSP00000332628:p.His157Asp	Somatic	184	0		WXS	Illumina HiSeq	Phase_I	196	47	NM_001005271	0	0	15	21	6	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.56|15.56	2.869301|2.869301	0.51588|0.51588	.|.	.|.	ENSG00000170004|ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494|ENST00000452447	D;D;D|.	0.89746|.	-2.56;-2.49;-2.49|.	4.54|4.54	4.54|4.54	0.55810|0.55810	High mobility group, HMG1/HMG2 (1);CHD, N-terminal (1);|.	0.000000|.	0.48286|.	D|.	0.000185|.	T|T	0.46833|0.46833	0.1413|0.1413	N|N	0.11427|0.11427	0.14|0.14	0.46061|0.46061	D|D	0.998847|0.998847	P;P;P|.	0.42584|.	0.531;0.586;0.784|.	B;B;P|.	0.45753|.	0.275;0.396;0.492|.	T|T	0.43048|0.43048	-0.9415|-0.9415	10|5	0.33940|.	T|.	0.23|.	-20.7739|-20.7739	17.4864|17.4864	0.87689|0.87689	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	157;157;216|.	Q12873-2;Q12873;E9PG89|.	.;CHD3_HUMAN;.|.	D|R	216;157;157|31	ENSP00000369716:H216D;ENSP00000350907:H157D;ENSP00000332628:H157D|.	ENSP00000332628:H157D|.	H|P	+|+	1|2	0|0	CHD3|CHD3	7735067|7735067	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.592000|3.592000	0.53993|0.53993	2.349000|2.349000	0.79799|0.79799	0.557000|0.557000	0.71058|0.71058	CAC|CCA	.		0.527	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		G	7794342	C	G	7794342	3	3	159	1	0	0	0	0	1	0	0	0	3332	594	21	4	764	4	CHD3	17	7794342	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	646440	7794342	73400868	76	14471											
MYH3	4621	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	10558280	10558281	+	Frame_Shift_Del	DEL	GG	GG	-																															accacgaagcaatacgtcttGgcatcaaagggctggttctg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:10558280_10558281delGG	ENST00000583535.1	-	3	188_189	c.101_102delCC	c.(100-102)gccfs	p.A34fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.A34fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	34					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AATACGTCTTGGCATCAAAGGG	0.485																																					p.34_34del		.											.	MYH3-95	0			c.101_102del						.																																			SO:0001589	frameshift_variant	4621	exon3			.		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.101_102delCC	17.37:g.10558280_10558281delGG	ENSP00000464317:p.Ala34fs	Somatic	150	0		WXS	Illumina HiSeq	Phase_I	164	38	NM_002470	0	0	0	0	0	Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	37	CCDS11157.1																																																																																			.		0.485	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		-	10558281	GG	-	10558280	7	5	159	1	0	1	0	1	0	0	0	0	10061	1335	47	0	5876	0	MYH3	17	10558280	Frame_Shift_Del	DEL	GG	TCGA-PJ-A5Z8-01A-11D-A28G-10	2763938	10558280	70636930	77	14472											
COX10	1352	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	13980321	13980321	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggaaagagatgaagctgcaAgtgtatgatttgccaggaat	14	10	13	4	0	0	3	0	2	0	1	0	6	0	5	1	2	3	3	1	2	5	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:13980321A>G	ENST00000261643.3	+	3	524	c.447A>G	c.(445-447)caA>caG	p.Q149Q	COX10_ENST00000429152.2_Silent_p.Q149Q|COX10_ENST00000536205.1_5'UTR|COX10_ENST00000537334.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	149					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TGAAGCTGCAAGTGTATGATT	0.368																																					p.Q149Q													.	COX10-226	0			c.A447G						.						82	88	86					17																	13980321		2203	4300	6503	SO:0001819	synonymous_variant	1352	exon3			GCTGCAAGTGTAT	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.447A>G	17.37:g.13980321A>G		Somatic	121	1		WXS	Illumina HiSeq	Phase_I	123	20	NM_001303	0	0	8	17	9	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1	.	.	.	.	.	.	.	.	.	.	A	0.588	-0.834196	0.02713	.	.	ENSG00000006695	ENST00000429152	T	0.37752	1.18	5.35	-10.7	0.00240	.	.	.	.	.	T	0.15089	0.0364	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.09574	-1.0668	5	.	.	.	0.3183	3.0923	0.06297	0.1393:0.3394:0.3056:0.2157	.	.	.	.	G	110	ENSP00000397750:S110G	.	S	+	1	0	COX10	13921046	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-2.964000	0.00671	-2.362000	0.00609	-1.831000	0.00592	AGT	.		0.368	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		G	13980321	A	G	13980321	2	3	159	1	0	0	0	0	0	0	0	1	3768	69	3	3		3	COX10	17	13980321	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	3422041	13980321	67214889	78	14473											
MAPK7	5598	broad.mit.edu	37	chr17	19285118	19285118	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcgcacccctggaggCtcctgagcctcggaagccgg	6	4	13	18	3	0	1	0	1	0	0	2	3	1	3	7	4	3	2	7	4	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:19285118C>A	ENST00000308406.5	+	5	1888	c.1502C>A	c.(1501-1503)gCt>gAt	p.A501D	MAPK7_ENST00000395604.3_Missense_Mutation_p.A501D|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395602.4_Missense_Mutation_p.A501D|MAPK7_ENST00000299612.7_Missense_Mutation_p.A362D	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	501	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)	p.A501D(1)		autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CCCCTGGAGGCTCCTGAGCCT	0.672																																					p.A501D													.	MAPK7-1402	1	Substitution - Missense(1)	endometrium(1)	c.C1502A						.						10	17	15					17																	19285118		2162	4232	6394	SO:0001583	missense	5598	exon5			TGGAGGCTCCTGA	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1502C>A	17.37:g.19285118C>A	ENSP00000311005:p.Ala501Asp	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	77	10	NM_002749	0	0	25	28	3	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	37	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248312	0.59103	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.74209	-0.57;-0.82;-0.57;-0.57	4.36	3.39	0.38822	.	0.278335	0.34291	N	0.004097	T	0.62792	0.2457	N	0.22421	0.69	0.33339	D	0.569546	P	0.50943	0.94	P	0.47299	0.543	T	0.71846	-0.4469	10	0.87932	D	0	-7.5638	6.6062	0.22726	0.0:0.7883:0.0:0.2117	.	501	Q13164	MK07_HUMAN	D	501;362;501;501	ENSP00000311005:A501D;ENSP00000299612:A362D;ENSP00000378968:A501D;ENSP00000378966:A501D	ENSP00000299612:A362D	A	+	2	0	MAPK7	19225711	0.988000	0.35896	0.980000	0.43619	0.970000	0.65996	1.704000	0.37857	1.055000	0.40461	0.561000	0.74099	GCT	.		0.672	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		A	19285118	C	A	19285118	3	1	159	1	0	0	0	0	1	0	0	0	9307	797	28	4	1516	4	MAPK7	17	19285118	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	5304797	19285118	61910092	79	14474											
SLC47A1	55244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	19449787	19449787	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcagtgggattcggcttaTcttctgcctgtgacaccctc	5	14	9	13	1	3	1	1	1	3	0	6	2	3	2	2	2	1	1	2	2	1	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:19449787T>C	ENST00000270570.4	+	3	363	c.277T>C	c.(277-279)Tct>Cct	p.S93P	SLC47A1_ENST00000575023.1_Missense_Mutation_p.S93P|SLC47A1_ENST00000436810.2_Intron|SLC47A1_ENST00000457293.1_Missense_Mutation_p.S93P|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000571335.1_5'UTR|SLC47A1_ENST00000395585.1_Missense_Mutation_p.S93P|SLC47A1_ENST00000542886.1_Missense_Mutation_p.S93P	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	93					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	ATTCGGCTTATCTTCTGCCTG	0.453																																					p.S93P		.											.	SLC47A1-90	0			c.T277C						.						201	160	174					17																	19449787		2203	4300	6503	SO:0001583	missense	55244	exon3			GGCTTATCTTCTG		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"Solute carriers"	25588	protein-coding gene	gene with protein product	"multidrug and toxin extrusion 1"	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.277T>C	17.37:g.19449787T>C	ENSP00000270570:p.Ser93Pro	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	172	36	NM_018242	0	0	13	17	4	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.790304	0.50102	.	.	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.32	4.17	0.49024	.	0.175212	0.49305	D	0.000151	T	0.65554	0.2702	M	0.91300	3.195	0.39743	D	0.971774	D;D;D	0.71674	0.998;0.984;0.957	D;D;P	0.76575	0.988;0.944;0.906	T	0.75167	-0.3413	10	0.72032	D	0.01	-17.7724	12.3905	0.55356	0.0:0.0:0.1831:0.8169	.	93;93;93	B4DYV3;Q96FL8;Q96FL8-3	.;S47A1_HUMAN;.	P	93	ENSP00000270570:S93P;ENSP00000415586:S93P;ENSP00000440435:S93P;ENSP00000378951:S93P	ENSP00000270570:S93P	S	+	1	0	SLC47A1	19390379	0.016000	0.18221	1.000000	0.80357	0.472000	0.32918	0.078000	0.14761	2.027000	0.59764	0.454000	0.30748	TCT	.		0.453	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		C	19449787	T	C	19449787	3	2	159	1	0	0	0	0	1	0	0	0	14679	1435	50	3	287	3	SLC47A1	17	19449787	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	164669	19449787	61745423	80	14475											
ACACA	31	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	35602012	35602012	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcacctgctgaaccttgctgGggttgtccagttgcattttg	5	15	11	10	0	1	1	1	1	0	0	2	1	2	1	3	2	4	5	3	2	1	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:35602012G>T	ENST00000394406.2	-	20	2658	c.2468C>A	c.(2467-2469)cCc>cAc	p.P823H	ACACA_ENST00000353139.5_Missense_Mutation_p.P860H|ACACA_ENST00000335166.5_Missense_Mutation_p.P745H|ACACA_ENST00000360679.3_Missense_Mutation_p.P765H	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	823					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AACCTTGCTGGGGTTGTCCAG	0.498																																					p.P860H	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)												.	ACACA-154	0			c.C2579A						.						247	237	241					17																	35602012		2203	4300	6503	SO:0001583	missense	31	exon20			TTGCTGGGGTTGT	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"acetyl-CoA carboxylase 1"	200350	"acetyl-Coenzyme A carboxylase alpha"	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.2468C>A	17.37:g.35602012G>T	ENSP00000377928:p.Pro823His	Somatic	125	2		WXS	Illumina HiSeq	Phase_I	148	32	NM_198834	0	0	1	2	1	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.120820	0.77436	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	4.84	3.88	0.44766	Acetyl-CoA carboxylase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.75034	0.3795	M	0.80847	2.515	0.80722	D	1	D;D;D	0.89917	1.0;0.988;1.0	D;D;D	0.77557	0.99;0.934;0.986	T	0.78685	-0.2108	10	0.87932	D	0	-4.7173	12.2513	0.54599	0.0813:0.0:0.9187:0.0	.	860;823;765	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	H	860;765;823;847;745	ENSP00000344789:P860H;ENSP00000353898:P765H;ENSP00000377928:P823H;ENSP00000335323:P745H	ENSP00000335323:P745H	P	-	2	0	ACACA	32676125	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.631000	0.98424	1.271000	0.44313	0.655000	0.94253	CCC	.		0.498	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35602012	G	T	35602012	3	4	159	1	0	0	0	0	1	0	0	0	106	1232	43	4	4720	4	ACACA	17	35602012	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	16152225	35602012	45593198	81	14476											
ACSF2	80221	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	48539795	48539795	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccccaggctcccagatctgaCcacagtcatctcggtggatg	8	8	10	15	1	3	2	1	1	2	1	5	3	4	3	4	3	0	1	4	3	0	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:48539795C>G	ENST00000300441.4	+	6	745	c.641C>G	c.(640-642)aCc>aGc	p.T214S	ACSF2_ENST00000541920.1_Missense_Mutation_p.T54S|ACSF2_ENST00000427954.2_Missense_Mutation_p.T239S|ACSF2_ENST00000502667.1_Missense_Mutation_p.T201S|ACSF2_ENST00000504392.1_Missense_Mutation_p.T171S	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	214					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CCAGATCTGACCACAGTCATC	0.617																																					p.T214S													.	ACSF2-68	0			c.C641G						.						67	65	66					17																	48539795		2203	4300	6503	SO:0001583	missense	80221	exon6			ATCTGACCACAGT	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.641C>G	17.37:g.48539795C>G	ENSP00000300441:p.Thr214Ser	Somatic	67	1		WXS	Illumina HiSeq	Phase_I	90	13	NM_025149	0	0	14	31	17	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	37	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.457499	0.43634	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.57	5.57	0.84162	AMP-dependent synthetase/ligase (1);	0.433445	0.24249	N	0.040200	T	0.29945	0.0749	N	0.17872	0.535	0.29725	N	0.83833	B;B;B;B	0.32968	0.146;0.392;0.146;0.146	B;B;B;B	0.30401	0.101;0.115;0.101;0.101	T	0.31752	-0.9932	10	0.52906	T	0.07	-26.9977	14.3982	0.67025	0.1477:0.8523:0.0:0.0	.	201;239;171;214	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	S	214;54;171;239;201	ENSP00000300441:T214S;ENSP00000437987:T54S;ENSP00000425964:T171S;ENSP00000401831:T239S;ENSP00000421884:T201S	ENSP00000300441:T214S	T	+	2	0	ACSF2	45894794	0.958000	0.32768	1.000000	0.80357	0.695000	0.40330	1.695000	0.37763	2.618000	0.88619	0.563000	0.77884	ACC	.		0.617	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		G	48539795	C	G	48539795	3	3	159	1	0	0	0	0	1	0	0	0	175	507	18	4	663	4	ACSF2	17	48539795	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	12937783	48539795	32655415	82	14477											
MRC2	9902	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	60753774	60753774	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttcgtcagcagcctcatCtacaactgggagggcgagta	9	8	12	12	2	3	0	2	0	1	0	4	2	3	1	2	2	4	2	2	2	3	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:60753774C>A	ENST00000303375.5	+	11	2118	c.1716C>A	c.(1714-1716)atC>atA	p.I572I		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	572	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GCAGCCTCATCTACAACTGGG	0.607																																					p.I572I													.	MRC2-117	0			c.C1716A						.						94	77	83					17																	60753774		2203	4300	6503	SO:0001819	synonymous_variant	9902	exon11			CCTCATCTACAAC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"CD molecules", "C-type lectin domain containing"	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.1716C>A	17.37:g.60753774C>A		Somatic	82	1		WXS	Illumina HiSeq	Phase_I	85	18	NM_006039	0	0	30	35	5	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																			.		0.607	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60753774	C	A	60753774	2	1	159	1	0	0	0	0	0	0	0	1	9783	903	32	4		4	MRC2	17	60753774	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	12213979	60753774	20441436	83	14478											
LRRC37A3	374819	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr17	62855782	62855782	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtccggataacatgagcAatgagccttctcacattgtt	12	11	9	9	1	1	2	1	2	1	0	3	3	2	3	2	2	3	2	2	2	3	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:62855782A>T	ENST00000584306.1	-	11	5012	c.4482T>A	c.(4480-4482)atT>atA	p.I1494I	LRRC37A3_ENST00000334962.5_Silent_p.I471I|LRRC37A3_ENST00000319651.5_Silent_p.I1494I|LRRC37A3_ENST00000400877.3_Silent_p.I532I|LRRC37A3_ENST00000339474.5_Silent_p.I612I	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1494						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TAACATGAGCAATGAGCCTTC	0.522																																					p.I1494I		.											.	LRRC37A3-90	0			c.T4482A						.						186	189	188					17																	62855782		2203	4300	6503	SO:0001819	synonymous_variant	374819	exon11			ATGAGCAATGAGC	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.4482T>A	17.37:g.62855782A>T		Somatic	440	0		WXS	Illumina HiSeq	Phase_I	433	90	NM_199340	0	0	30	37	7	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	37	CCDS32708.1																																																																																			.		0.522	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		T	62855782	A	T	62855782	2	4	159	1	0	0	0	0	0	0	0	1	9018	126	5	5		5	LRRC37A3	17	62855782	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	2102008	62855782	18339428	84	14479											
MC5R	4161	broad.mit.edu;bcgsc.ca	37	chr18	13826448	13826448	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccggggccagctctgcGcggcagaggaccagcatgca	7	4	15	15	3	1	1	0	0	1	1	1	2	1	2	3	4	5	4	3	4	0	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr18:13826448G>A	ENST00000324750.3	+	1	906	c.684G>A	c.(682-684)gcG>gcA	p.A228A	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	228				ALPGASSARQRTSM -> LCPGPALRGRGPAW (in Ref. 1). {ECO:0000305}.	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						CCAGCTCTGCGCGGCAGAGGA	0.617																																					p.A228A													.	MC5R-526	0			c.G684A						.						210	180	190					18																	13826448		2203	4300	6503	SO:0001819	synonymous_variant	4161	exon1			CTCTGCGCGGCAG	AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"GPCR / Class A : Melanocortin receptors"	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.684G>A	18.37:g.13826448G>A		Somatic	45	1		WXS	Illumina HiSeq	Phase_I	125	28	NM_005913	0	0	0	0	0	B0YJ34|Q502V1	Silent	SNP	ENST00000324750.3	37	CCDS11868.1																																																																																			.		0.617	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913		A	13826448	G	A	13826448	2	1	159	1	0	0	0	0	0	0	0	1	9392	1074	38	1		1	MC5R	18	13826448	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		13826448	64250800	85	14480											
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	21508155	21508158	+	Frame_Shift_Del	DEL	GATT	GATT	-																															gaaaaccagtggtgtcgttaGattgaatgatactgtgggag																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GATT	GATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr18:21508155_21508158delGATT	ENST00000313654.9	+	63	8487_8490	c.8246_8249delGATT	c.(8245-8250)agattgfs	p.RL2749fs	LAMA3_ENST00000269217.6_Frame_Shift_Del_p.RL1140fs|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Frame_Shift_Del_p.RL1084fs|LAMA3_ENST00000399516.3_Frame_Shift_Del_p.RL2693fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2749	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGTGTCGTTAGATTGAATGATACT	0.436																																					p.2749_2750del		.											.	LAMA3-100	0			c.8246_8249del						.																																			SO:0001589	frameshift_variant	3909	exon63			.	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"Laminins"	6483	protein-coding gene	gene with protein product		600805	"laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.8246_8249delGATT	18.37:g.21508155_21508158delGATT	ENSP00000324532:p.Arg2749fs	Somatic	215	0		WXS	Illumina HiSeq	Phase_I	208	41	NM_198129	0	0	0	0	0	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	37	CCDS42419.1																																																																																			.		0.436	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21508158	GATT	-	21508155	7	5	159	1	0	1	0	1	0	0	0	0	8628	942	33	0	8671	0	LAMA3	18	21508155	Frame_Shift_Del	DEL	GATT	TCGA-PJ-A5Z8-01A-11D-A28G-10	7681707	21508155	56569093	86	14481											
HNRNPM	4670	ucsc.edu	37	chr19	8527467	8527467	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgaaggaaagtcaagggTaagtgtctgagagaatttct	13	10	13	5	1	3	3	1	2	2	1	3	5	3	4	0	2	0	2	0	2	5	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:8527467T>G	ENST00000325495.4	+	3	377		c.e3+2		HNRNPM_ENST00000348943.3_Splice_Site	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						AAGTCAAGGGTAAGTGTCTGA	0.428																																					.													.	HNRNPM-68	0			c.336+2T>G						.						241	220	227					19																	8527467		2203	4300	6503	SO:0001630	splice_region_variant	4670	exon3			CAAGGGTAAGTGT	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"RNA binding motif (RRM) containing"	5046	protein-coding gene	gene with protein product	"CEA receptor"	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.336+2T>G	19.37:g.8527467T>G		Somatic	164	1		WXS	Illumina HiSeq		152	2	NM_031203	0	0	1	1	0	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Splice_Site	SNP	ENST00000325495.4	37	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580056	0.65992	.	.	ENSG00000099783	ENST00000325495;ENST00000348943	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0018	0.71479	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNRNPM	8433467	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.225000	0.72522	0.459000	0.35465	.	.		0.428	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		Intron	G	8527467	T	G	8527467	5	3	159	1	0	0	0	0	0	0	1	0	7292	1652	57	5	348	5	HNRNPM	19	8527467	Splice_Site	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		8527467	50601516	87	14482											
MAP1S	55201	hgsc.bcm.edu	37	chr19	17837417	17837417	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccgccggcgccgagcgcacGctggcctctgtgtgcgccct	2	7	14	18	7	1	0	0	0	1	0	2	1	2	0	5	2	2	2	5	2	0	0	rs138676223	byFrequency	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:17837417G>A	ENST00000324096.4	+	5	1375	c.1224G>A	c.(1222-1224)acG>acA	p.T408T	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron|MAP1S_ENST00000544059.2_Silent_p.T382T	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	408	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCGAGCGCACGCTGGCCTCTG	0.736													G|||	45	0.00898562	0.0015	0.0144	5008	,	,		12480	0		0.0268	False		,,,				2504	0.0061				p.T408T		.											.	MAP1S-90	0			c.G1224A						.	G		21,4095		0,21,2037	5	5	5		1224	-2.1	0	19	dbSNP_134	5	121,7915		1,119,3898	no	coding-synonymous	MAP1S	NM_018174.4		1,140,5935	AA,AG,GG		1.5057,0.5102,1.1685		408/1060	17837417	142,12010	2058	4018	6076	SO:0001819	synonymous_variant	55201	exon5			GCGCACGCTGGCC	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"chromosome 19 open reading frame 5", "VCY2 interacting protein 1", "BPY2 interacting protein 1"	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1224G>A	19.37:g.17837417G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	10	NM_018174	0	0	1	2	1	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	37	CCDS32954.1																																																																																			G|0.987;A|0.013		0.736	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		A	17837417	G	A	17837417	2	1	159	1	0	0	0	0	0	0	0	1	9259	1074	38	1		1	MAP1S	19	17837417	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	9309950	17837417	41291566	88	14483											
IL12RB1	3594	broad.mit.edu	37	chr19	18194264	18194265	+	Frame_Shift_Ins	INS	-	-	G																															agtctgcatccggatatggcINSgggtcctgaaaacagcactc																								rs113524129|rs146978336	byFrequency	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:18194264_18194265insG	ENST00000600835.2	-	3	399_400	c.101_102insC	c.(100-102)ccgfs	p.P34fs	IL12RB1_ENST00000322153.7_Frame_Shift_Ins_p.P34fs|IL12RB1_ENST00000593993.2_Frame_Shift_Ins_p.P34fs			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	34					cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						CCGGATATGGCGGGTCCTGAAA	0.564																																					p.P34fs													.	IL12RB1-91	0			c.102_103insC						.																																			SO:0001589	frameshift_variant	3594	exon2			ATATGGCGGGTCC	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.102dupC	19.37:g.18194267_18194267dupG	ENSP00000470788:p.Pro34fs	Somatic	160	0		WXS	Illumina HiSeq	Phase_I	186	9	NM_153701	0	0	0	0	0	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Frame_Shift_Ins	INS	ENST00000600835.2	37	CCDS54232.1																																																																																			.		0.564	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			G	18194265	-	G	18194264	7	5	159	1	0	1	1	0	0	0	0	0	7647	755	27	0	2079	0	IL12RB1	19	18194264	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	356847	18194264	40934719	89	14484											
GPATCH1	55094	broad.mit.edu	37	chr19	33603471	33603471	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agacacgtttgagtggcaccCtgacaagcttctatgtaaga	12	10	10	9	1	1	4	0	2	1	2	1	4	1	4	1	1	1	4	1	1	3	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:33603471C>A	ENST00000170564.2	+	13	2158	c.1844C>A	c.(1843-1845)cCt>cAt	p.P615H		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	615					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					GAGTGGCACCCTGACAAGCTT	0.413																																					p.P615H	Pancreas(67;88 1713 4567 18227)												.	GPATCH1-91	0			c.C1844A						.						159	142	148					19																	33603471		2203	4300	6503	SO:0001583	missense	55094	exon13			GGCACCCTGACAA	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"G patch domain containing"	24658	protein-coding gene	gene with protein product	"evolutionarily conserved G patch domain containing"			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.1844C>A	19.37:g.33603471C>A	ENSP00000170564:p.Pro615His	Somatic	93	0		WXS	Illumina HiSeq	Phase_I	106	4	NM_018025	0	0	3	3	0	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.748457	0.89753	.	.	ENSG00000076650	ENST00000170564	T	0.37058	1.22	5.62	5.62	0.85841	.	0.047492	0.85682	D	0.000000	T	0.67363	0.2885	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72830	-0.4174	10	0.87932	D	0	-15.72	18.6704	0.91508	0.0:1.0:0.0:0.0	.	615	Q9BRR8	GPTC1_HUMAN	H	615	ENSP00000170564:P615H	ENSP00000170564:P615H	P	+	2	0	GPATCH1	38295311	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.937000	0.75898	2.640000	0.89533	0.655000	0.94253	CCT	.		0.413	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		A	33603471	C	A	33603471	3	1	159	1	0	0	0	0	1	0	0	0	6610	681	24	4	1894	4	GPATCH1	19	33603471	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	15409207	33603471	25525512	90	14485											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40578806	40578806	+	IGR	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacactaaagagagataaccAaatgcaatgcagattctgca	18	8	7	8	0	1	3	0	0	1	3	1	4	1	3	1	0	5	3	1	0	6	4	rs528950544		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:40578806A>T	ENST00000595687.2	-	0	3472				ZNF780A_ENST00000450241.2_3'UTR|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000414720.2_Missense_Mutation_p.F145L	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A						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(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					agagataaccaaatgcaatgc	0.353																																					p.F145L		.											.	ZNF780A-22	0			c.T435A						.						112	98	103					19																	40578806		692	1591	2283	SO:0001628	intergenic_variant	284323	exon8			ATAACCAAATGCA	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"Zinc fingers, C2H2-type", "-"	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119		19.37:g.40578806A>T		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	59	4	NM_001142579	0	0	2	2	0	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	A	11.53	1.666731	0.29604	.	.	ENSG00000197782	ENST00000414720	T	0.00620	6.17	0.516	0.516	0.17019	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.21256	N	0.999747	P	0.46395	0.877	P	0.51866	0.682	T	0.55341	-0.8156	7	0.25751	T	0.34	.	.	.	.	.	145	O75290-2	.	L	145	ENSP00000416294:F145L	ENSP00000416294:F145L	F	-	3	2	ZNF780A	45270646	0.004000	0.15560	0.096000	0.21009	0.182000	0.23217	0.148000	0.16224	0.452000	0.26830	0.254000	0.18369	TTT	.		0.353	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		T	40578806	A	T	40578806	1	4	159	0	1	0	0	0	0	0	0	0	18184	127	5	5		5	ZNF780A	19	40578806	IGR	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	6975335	40578806	18550177	91	14486											
ZNF320	162967	ucsc.edu	37	chr19	53384827	53384827	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttgtatggtttctctccAgtatgaattatcctatgtat	9	19	6	7	0	1	1	0	1	1	0	4	1	3	1	2	1	0	4	2	1	6	7			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:53384827A>G	ENST00000595635.1	-	8	1053	c.552T>C	c.(550-552)acT>acC	p.T184T	ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Silent_p.T184T	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	184					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)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		GTTTCTCTCCAGTATGAATTA	0.358																																					p.T184T													.	ZNF320-91	0			c.T552C						.						67	64	65					19																	53384827		2203	4300	6503	SO:0001819	synonymous_variant	162967	exon4			CTCTCCAGTATGA	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.552T>C	19.37:g.53384827A>G		Somatic	76	0		WXS	Illumina HiSeq		80	1	NM_207333	0	0	14	14	0	Q8NDR6	Silent	SNP	ENST00000595635.1	37	CCDS33095.1																																																																																			.		0.358	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		G	53384827	A	G	53384827	2	3	159	1	0	0	0	0	0	0	0	1	17871	175	7	3		3	ZNF320	19	53384827	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	12806021	53384827	5744156	92	14487											
EPS8L1	54869	ucsc.edu;bcgsc.ca	37	chr19	55591878	55591878	+	Intron	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacatgaacagaacatggcCaagaaggatctgggggagca	15	4	15	7	0	1	3	0	1	1	2	1	6	1	6	1	5	3	1	1	5	4	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:55591878C>G	ENST00000201647.6	+	6	485				EPS8L1_ENST00000588359.1_Missense_Mutation_p.P6R|EPS8L1_ENST00000592824.1_Intron|EPS8L1_ENST00000245618.5_Missense_Mutation_p.P6R|EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000540810.1_Intron	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1						positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		AGAACATGGCCAAGAAGGATC	0.597																																					p.P6R	Ovarian(149;255 1863 3636 27051 29647)												.	EPS8L1-115	0			c.C17G						.						77	64	69					19																	55591878		2203	4299	6502	SO:0001627	intron_variant	54869	exon1			CATGGCCAAGAAG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.429+232C>G	19.37:g.55591878C>G		Somatic	179	1		WXS	Illumina HiSeq		158	28	NM_017729	0	0	0	0	0	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	C	4.831	0.154443	0.09236	.	.	ENSG00000131037	ENST00000245618;ENST00000539118	T	0.05649	3.41	2.3	-2.0	0.07433	.	.	.	.	.	T	0.04363	0.0120	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.40553	-0.9557	8	0.62326	D	0.03	.	3.2435	0.06789	0.4533:0.2805:0.2662:0.0	.	6	Q8TE68-2	.	R	6	ENSP00000245618:P6R	ENSP00000245618:P6R	P	+	2	0	EPS8L1	60283690	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.491000	0.00974	-0.646000	0.05452	-0.302000	0.09304	CCA	.		0.597	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		G	55591878	C	G	55591878	1	3	159	0	1	0	0	0	0	0	0	0	5208	594	21	4		4	EPS8L1	19	55591878	Intron	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	2207051	55591878	3537105	93	14488											
UBOX5	22888	bcgsc.ca	37	chr20	3102507	3102507	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggatccaggaactcctcagGcacatcctgaatgatctcgg	10	8	11	12	1	2	2	1	2	1	0	6	4	5	4	3	4	1	1	3	4	2	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr20:3102507G>A	ENST00000217173.2	-	3	1249	c.778C>T	c.(778-780)Cct>Tct	p.P260S	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.P260S	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						AACTCCTCAGGCACATCCTGA	0.587																																					p.P260S													.	UBOX5-227	0			c.C778T						.						47	45	46					20																	3102507		2203	4300	6503	SO:0001583	missense	22888	exon3			CCTCAGGCACATC	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"RING-type (C3HC4) zinc fingers", "U-box domain containing"	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.778C>T	20.37:g.3102507G>A	ENSP00000217173:p.Pro260Ser	Somatic	56	0		WXS	Illumina HiSeq	Phase_1	62	5	NM_014948	0	0	10	10	0		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566214	0.86439	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.65732	-0.17;-0.12	5.42	5.42	0.78866	Zinc finger, RING/FYVE/PHD-type (1);U box domain (1);	0.061903	0.64402	U	0.000003	D	0.86096	0.5851	H	0.95504	3.68	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.90141	0.4213	10	0.87932	D	0	-11.3099	19.2336	0.93849	0.0:0.0:1.0:0.0	.	260;260;260	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	S	260	ENSP00000217173:P260S;ENSP00000311726:P260S	ENSP00000217173:P260S	P	-	1	0	UBOX5	3050507	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.246000	0.89828	2.534000	0.85438	0.563000	0.77884	CCT	.		0.587	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3102507	G	A	3102507	3	1	159	1	0	0	0	0	1	0	0	0	16927	1203	42	2	859	2	UBOX5	20	3102507	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		3102507	59923013	94	14489											
TRPC4AP	26133	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	33603843	33603844	+	Frame_Shift_Ins	INS	-	-	AA																															cagttctggttgtgaccatgINSgaggacaagggcagatgctg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr20:33603843_33603844insAA	ENST00000252015.2	-	10	1406_1407	c.1317_1318insTT	c.(1315-1320)ctccatfs	p.H440fs	TRPC4AP_ENST00000432634.2_Frame_Shift_Ins_p.H401fs|TRPC4AP_ENST00000451813.2_Frame_Shift_Ins_p.H432fs|TRPC4AP_ENST00000539834.1_Frame_Shift_Ins_p.H42fs			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	440					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TTGTGACCATGGAGGACAAGGG	0.5																																					p.H440fs		.											.	TRPC4AP-91	0			c.1318_1319insTT						.																																			SO:0001589	frameshift_variant	26133	exon10			.	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 158"	608430	"chromosome 20 open reading frame 188"	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.1317_1318insTT	20.37:g.33603843_33603844insAA	ENSP00000252015:p.His440fs	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	143	32	NM_015638	0	0	0	0	0	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Frame_Shift_Ins	INS	ENST00000252015.2	37	CCDS13246.1																																																																																			.		0.5	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		AA	33603844	-	AA	33603843	7	5	159	1	0	1	1	0	0	0	0	0	16614	1348	47	0	1115	0	TRPC4AP	20	33603843	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	30501336	33603843	29421677	95	14490											
DLGAP4	22839	hgsc.bcm.edu	37	chr20	35064566	35064566	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgctgtccccacgcgagacgGatgccgcggccgagggccct	5	5	15	16	6	0	1	0	0	0	1	1	4	1	2	5	3	2	1	5	3	0	0	rs199988815		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr20:35064566G>A	ENST00000373907.2	+	3	1253	c.1054G>A	c.(1054-1056)Gat>Aat	p.D352N	DLGAP4_ENST00000373913.3_Missense_Mutation_p.D352N|DLGAP4_ENST00000401952.2_Missense_Mutation_p.D352N|DLGAP4_ENST00000339266.5_Missense_Mutation_p.D352N			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	352					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				ACGCGAGACGGATGCCGCGGC	0.721																																					p.D352N		.											.	DLGAP4-94	0			c.G1054A						.	G	ASN/ASP	0,4334		0,0,2167	9	11	10		1054	4.2	0.2	20		10	2,8418		0,2,4208	no	missense	DLGAP4	NM_014902.4	23	0,2,6375	AA,AG,GG		0.0238,0.0,0.0157	benign	352/990	35064566	2,12752	2167	4210	6377	SO:0001583	missense	22839	exon3			GAGACGGATGCCG	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.1054G>A	20.37:g.35064566G>A	ENSP00000363014:p.Asp352Asn	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	34	21	NM_014902	0	0	0	0	0	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	37		.	.	.	.	.	.	.	.	.	.	G	15.46	2.840492	0.51057	0.0	2.38E-4	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.22	4.22	0.49857	.	1.057480	0.07332	N	0.879344	T	0.12178	0.0296	N	0.22421	0.69	0.09310	N	1	B	0.19200	0.034	B	0.18871	0.023	T	0.22591	-1.0212	10	0.27082	T	0.32	.	13.7551	0.62933	0.0:0.0:1.0:0.0	.	352	Q9Y2H0-1	.	N	352	ENSP00000363023:D352N;ENSP00000384954:D352N;ENSP00000363014:D352N;ENSP00000341633:D352N	ENSP00000341633:D352N	D	+	1	0	DLGAP4	34497980	0.998000	0.40836	0.243000	0.24186	0.629000	0.37895	3.978000	0.56881	1.913000	0.55393	0.555000	0.69702	GAT	.		0.721	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902		A	35064566	G	A	35064566	3	1	159	1	0	0	0	0	1	0	0	0	4573	1174	41	2	1060	2	DLGAP4	20	35064566	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	1460723	35064566	27960954	96	14491											
PRDM15	63977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	43241557	43241557	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcacctccatgatgtgcttCaggtactccttcccccggcc	5	11	8	17	1	1	1	1	1	0	0	4	1	4	1	6	2	3	3	6	2	1	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr21:43241557C>T	ENST00000269844.3	-	23	3134	c.3024G>A	c.(3022-3024)ctG>ctA	p.L1008L	PRDM15_ENST00000422911.1_Silent_p.L699L|PRDM15_ENST00000447207.2_Silent_p.L642L|PRDM15_ENST00000398548.1_Silent_p.L679L|PRDM15_ENST00000538201.1_Silent_p.L662L	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1008					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TGATGTGCTTCAGGTACTCCT	0.612																																					p.L1008L		.											.	PRDM15-90	0			c.G3024A						.						171	113	132					21																	43241557		2203	4300	6503	SO:0001819	synonymous_variant	63977	exon23			GTGCTTCAGGTAC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3024G>A	21.37:g.43241557C>T		Somatic	115	0		WXS	Illumina HiSeq	Phase_I	105	24	NM_022115	0	0	3	3	0	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			.		0.612	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		T	43241557	C	T	43241557	2	4	159	1	0	0	0	0	0	0	0	1	12485	813	29	2		2	PRDM15	21	43241557	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		43241557	4888338	97	14492											
PLXNB2	23654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr22	50716444	50716444	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaactgctgcagtgtgcccTgtgggggggagggtctcagc	6	8	17	10	0	1	0	1	0	1	0	2	1	1	1	1	4	5	2	1	4	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr22:50716444T>C	ENST00000449103.1	-	32	5028		c.e32-2		PLXNB2_ENST00000359337.4_Splice_Site			O15031	PLXB2_HUMAN	plexin B2						brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CAGTGTGCCCTGTGGGGGGGA	0.682																																					.		.											.	PLXNB2-211	0			c.4888-2A>G						.						32	37	35					22																	50716444		2093	4223	6316	SO:0001630	splice_region_variant	23654	exon33			GTGCCCTGTGGGG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"Plexins"	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.4888-2A>G	22.37:g.50716444T>C		Somatic	97	0		WXS	Illumina HiSeq	Phase_I	124	17	NM_012401	0	0	0	4	4	A6QRH0|Q7KZU3|Q9BSU7	Splice_Site	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.831563	0.50845	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000399991;ENST00000399964;ENST00000411680	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4923	0.61402	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLXNB2	49058571	1.000000	0.71417	0.983000	0.44433	0.517000	0.34286	7.524000	0.81866	1.827000	0.53221	0.402000	0.26972	.	.		0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	Intron	C	50716444	T	C	50716444	5	2	159	1	0	0	0	0	0	0	1	0	12150	1594	55	3	654	3	PLXNB2	22	50716444	Splice_Site	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		50716444	588122	98	14493											
COL4A6	1288	bcgsc.ca	37	chrX	107430496	107430496	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttttcacctgggaagcccTgtccaccatcaccctagaca	9	9	6	17	0	2	1	2	0	0	1	3	2	3	2	6	1	1	0	6	1	2	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chrX:107430496T>A	ENST00000372216.4	-	23	1884	c.1784A>T	c.(1783-1785)cAg>cTg	p.Q595L	COL4A6_ENST00000538570.1_Missense_Mutation_p.Q594L|COL4A6_ENST00000394872.2_Missense_Mutation_p.Q595L|COL4A6_ENST00000334504.7_Missense_Mutation_p.Q594L|COL4A6_ENST00000545689.1_Missense_Mutation_p.Q594L	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	595	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						TGGGAAGCCCTGTCCACCATC	0.488									Alport syndrome with Diffuse Leiomyomatosis																												p.Q595L	Melanoma(87;1895 1945 2589 7165)												.	COL4A6-199	0			c.A1784T						.						83	75	78					X																	107430496		2203	4300	6503	SO:0001583	missense	1288	exon23	Familial Cancer Database		AAGCCCTGTCCAC	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.1784A>T	X.37:g.107430496T>A	ENSP00000361290:p.Gln595Leu	Somatic	95	0		WXS	Illumina HiSeq	Phase_1	78	5	NM_001847	0	0	0	0	0	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	37	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	T	11.98	1.801554	0.31869	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.94138	-3.36;-3.36;-3.24;-3.36;-3.24	5.2	-0.678	0.11353	.	0.455403	0.16593	N	0.207690	D	0.90920	0.7146	L	0.33339	1.005	0.09310	N	1	P;P;D;P	0.53885	0.955;0.955;0.963;0.955	P;P;P;P	0.57425	0.725;0.725;0.82;0.636	T	0.83084	-0.0136	10	0.46703	T	0.11	.	6.0005	0.19517	0.5972:0.0:0.1297:0.2731	.	594;594;595;594	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	L	595;594;595;594;594;594	ENSP00000361290:Q595L;ENSP00000334733:Q594L;ENSP00000378340:Q595L;ENSP00000443707:Q594L;ENSP00000445236:Q594L	ENSP00000334733:Q594L	Q	-	2	0	COL4A6	107317152	0.009000	0.17119	0.015000	0.15790	0.791000	0.44710	0.903000	0.28475	-0.009000	0.14296	0.430000	0.28490	CAG	.		0.488	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			A	107430496	T	A	107430496	3	1	159	1	0	0	0	0	1	0	0	0	3701	1580	55	5	3383	5	COL4A6	23	107430496	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		107430496	47840064	99	14494											
AVPR2	554	broad.mit.edu	37	chrX	153171162	153171163	+	Frame_Shift_Ins	INS	-	-	G																															cctagctcggcggggccggcINSggggccactgggcacccata																								rs61733408	byFrequency	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chrX:153171162_153171163insG	ENST00000358927.2	+	3	411_412	c.202_203insG	c.(202-204)cggfs	p.R68fs	AVPR2_ENST00000370049.1_Frame_Shift_Ins_p.R68fs|AVPR2_ENST00000337474.5_Frame_Shift_Ins_p.R68fs			P30518	V2R_HUMAN	arginine vasopressin receptor 2	68					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)	p.R68W(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	GCGGGGCCGGCGGGGCCACTGG	0.688																																					p.R68fs													.	AVPR2-625	1	Substitution - Missense(1)	endometrium(1)	c.202_203insG						.																																			SO:0001589	frameshift_variant	554	exon2			GGCCGGCGGGGCC	Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"GPCR / Class A : Vasopressin and oxytocin receptors"	897	protein-coding gene	gene with protein product	"nephrogenic diabetes insipidus"	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.206dupG	X.37:g.153171166_153171166dupG	ENSP00000351805:p.Arg68fs	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	120	9	NM_001146151	0	0	0	0	0	C5HF20|O43192|Q3MJD3|Q9UCV9	Frame_Shift_Ins	INS	ENST00000358927.2	37	CCDS14735.1																																																																																			.		0.688	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2			G	153171163	-	G	153171162	7	5	159	1	0	1	1	0	0	0	0	0	1234	759	27	0	208	0	AVPR2	23	153171162	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	45740666	153171162	2099398	100	14495											
IL22RA1	58985	broad.mit.edu	37	chr1	24465122	24465122	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtgccctccggcccgctGtcccacgtcaggatgttttc	3	10	13	15	3	1	0	1	0	0	0	4	1	3	1	4	4	1	2	4	4	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:24465122G>T	ENST00000270800.1	-	2	164	c.126C>A	c.(124-126)gaC>gaA	p.D42E		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	42	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		CCGGCCCGCTGTCCCACGTCA	0.592																																					p.D42E													.	IL22RA1-91	0			c.C126A						.						95	90	91					1																	24465122		2203	4300	6503	SO:0001583	missense	58985	exon2			CCCGCTGTCCCAC	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"Interleukins and interleukin receptors"	13700	protein-coding gene	gene with protein product		605457	"interleukin 22 receptor"	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.126C>A	1.37:g.24465122G>T	ENSP00000270800:p.Asp42Glu	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	86	4	NM_021258	0	0	3	3	0	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	37	CCDS247.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720222	0.30503	.	.	ENSG00000142677	ENST00000270800	T	0.72051	-0.62	5.11	-4.84	0.03151	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.653399	0.15693	N	0.249302	T	0.40743	0.1129	N	0.21545	0.675	0.18873	N	0.999988	B	0.02656	0.0	B	0.06405	0.002	T	0.44097	-0.9350	10	0.02654	T	1	-26.1547	4.4884	0.11801	0.0834:0.4551:0.2255:0.2361	.	42	Q8N6P7	I22R1_HUMAN	E	42	ENSP00000270800:D42E	ENSP00000270800:D42E	D	-	3	2	IL22RA1	24337709	0.000000	0.05858	0.105000	0.21289	0.781000	0.44180	-0.962000	0.03841	-0.414000	0.07495	-0.234000	0.12200	GAC	.		0.592	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			T	24465122	G	T	24465122	3	4	160	1	0	0	0	0	1	0	0	0	7694	1368	48	4	1622	4	IL22RA1	1	24465122	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		24465122	224785499	1	14496											
TEKT2	27285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	36552574	36552574	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatgacttcagtcggttcaaCaaggaccgagcggaggctga	11	7	14	9	3	2	2	2	2	0	0	3	6	2	4	1	4	2	2	1	4	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:36552574C>T	ENST00000207457.3	+	6	802	c.675C>T	c.(673-675)aaC>aaT	p.N225N	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	225					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GTCGGTTCAACAAGGACCGAG	0.592																																					p.N225N		.											.	TEKT2-90	0			c.C675T						.						58	54	55					1																	36552574		2203	4300	6503	SO:0001819	synonymous_variant	27285	exon6			GTTCAACAAGGAC	AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.675C>T	1.37:g.36552574C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	47	17	NM_014466	0	0	5	8	3	A6NIS6|O60638	Silent	SNP	ENST00000207457.3	37	CCDS401.1																																																																																			.		0.592	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		T	36552574	C	T	36552574	2	4	160	1	0	0	0	0	0	0	0	1	15785	477	17	2		2	TEKT2	1	36552574	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	12087452	36552574	212698047	2	14497											
SLC35D1	23169	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	67519574	67519574	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagccggcggccagcagcttCagaaacacggtcagcgtttc	10	6	12	13	4	2	1	2	0	0	1	3	1	2	1	2	3	5	3	2	3	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:67519574C>A	ENST00000235345.5	-	1	208	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SLC35D1_ENST00000506472.2_5'Flank	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	41					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						CCAGCAGCTTCAGAAACACGG	0.612																																					p.L41L		.											.	SLC35D1-90	0			c.G123T						.						47	50	49					1																	67519574		2203	4300	6503	SO:0001819	synonymous_variant	23169	exon1			CAGCTTCAGAAAC	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.123G>T	1.37:g.67519574C>A		Somatic	194	0		WXS	Illumina HiSeq	Phase_I	115	35	NM_015139	0	0	0	0	0	A8K185|B7Z3X2|Q52LU5|Q92548	Silent	SNP	ENST00000235345.5	37	CCDS636.1																																																																																			.		0.612	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		A	67519574	C	A	67519574	2	1	160	1	0	0	0	0	0	0	0	1	14613	813	29	4		4	SLC35D1	1	67519574	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	30967000	67519574	181731047	3	14498											
C1orf173	127254	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	75037280	75037280	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaggaggaggctttatttgCtattgttttctcctcggctg	7	16	11	7	1	1	0	0	0	1	0	3	2	1	2	1	4	1	4	1	4	3	7			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:75037280C>A	ENST00000326665.5	-	14	4332	c.4114G>T	c.(4114-4116)Gca>Tca	p.A1372S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1372	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GCTTTATTTGCTATTGTTTTC	0.522																																					p.A1372S		.											.	C1orf173-94	0			c.G4114T						.						130	133	132					1																	75037280		2203	4300	6503	SO:0001583	missense	127254	exon14			TATTTGCTATTGT																												ENST00000326665.5:c.4114G>T	1.37:g.75037280C>A	ENSP00000322609:p.Ala1372Ser	Somatic	149	0		WXS	Illumina HiSeq	Phase_I	97	37	NM_001002912	0	0	0	0	0	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	8.132	0.783370	0.16189	.	.	ENSG00000178965	ENST00000326665	T	0.14516	2.5	5.0	3.1	0.35709	.	.	.	.	.	T	0.02688	0.0081	N	0.24115	0.695	0.09310	N	1	B	0.15473	0.013	B	0.16289	0.015	T	0.45789	-0.9237	9	0.18710	T	0.47	-4.6121	10.2042	0.43103	0.0:0.7597:0.0:0.2403	.	1372	Q5RHP9	CA173_HUMAN	S	1372	ENSP00000322609:A1372S	ENSP00000322609:A1372S	A	-	1	0	C1orf173	74809868	0.148000	0.22702	0.009000	0.14445	0.260000	0.26232	0.903000	0.28475	0.528000	0.28580	-1.134000	0.01955	GCA	.		0.522	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75037280	C	A	75037280	3	1	160	1	0	0	0	0	1	0	0	0	2020	797	28	4	482	4	C1orf173	1	75037280	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	7517706	75037280	174213341	4	14499											
USP33	23032	broad.mit.edu;bcgsc.ca	37	chr1	78194350	78194350	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccatgacttgctctttcaaTtcttcatgaagcaaatccat	11	15	4	11	0	4	2	2	2	2	0	6	2	6	2	2	0	2	2	2	0	3	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:78194350T>C	ENST00000370793.1	-	11	1204	c.858A>G	c.(856-858)gaA>gaG	p.E286E	USP33_ENST00000370792.3_Silent_p.E286E|USP33_ENST00000357428.1_Silent_p.E286E|USP33_ENST00000370794.3_Silent_p.E255E	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	286	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						GCTCTTTCAATTCTTCATGAA	0.368																																					p.E286E	Melanoma(152;72 1870 11110 26780 42647)												.	USP33-659	0			c.A858G						.						125	110	115					1																	78194350		2203	4300	6503	SO:0001819	synonymous_variant	23032	exon11			TTTCAATTCTTCA	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"Ubiquitin-specific peptidases"	20059	protein-coding gene	gene with protein product		615146	"ubiquitin specific protease 33"			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.858A>G	1.37:g.78194350T>C		Somatic	44	1		WXS	Illumina HiSeq	Phase_I	37	16	NM_201626	0	0	0	0	0	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1																																																																																			.		0.368	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		C	78194350	T	C	78194350	2	2	160	1	0	0	0	0	0	0	0	1	17097	1490	52	3		3	USP33	1	78194350	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	3157070	78194350	171056271	5	14500											
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	94546179	94546179	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccacacaggaggtcagacagGatgcccatcagctttgtaaa	13	7	10	11	0	2	1	2	0	0	1	2	3	2	3	2	3	2	2	2	3	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:94546179G>A	ENST00000370225.3	-	8	1040	c.954C>T	c.(952-954)atC>atT	p.I318I	ABCA4_ENST00000535735.1_Silent_p.I318I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	318					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGTCAGACAGGATGCCCATCA	0.542																																					p.I318I		.											.	ABCA4-162	0			c.C954T						.						99	91	94					1																	94546179		2203	4300	6503	SO:0001819	synonymous_variant	24	exon8			AGACAGGATGCCC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"ATP binding cassette transporters / subfamily A"	34	protein-coding gene	gene with protein product	"Stargardt disease"	601691	"ATP-binding cassette transporter, retinal-specific"	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.954C>T	1.37:g.94546179G>A		Somatic	138	0		WXS	Illumina HiSeq	Phase_I	97	30	NM_000350	0	0	0	0	0	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			.		0.542	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94546179	G	A	94546179	2	1	160	1	0	0	0	0	0	0	0	1	34	1164	41	2		2	ABCA4	1	94546179	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	16351829	94546179	154704442	6	14501											
SLC30A7	148867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	101387350	101387350	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaattttggtctgatgatAgcagatcctatctgttcaat	12	15	7	7	0	3	3	1	2	2	1	4	3	4	3	1	1	1	2	1	1	5	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:101387350A>G	ENST00000370112.4	+	8	982	c.795A>G	c.(793-795)atA>atG	p.I265M	SLC30A7_ENST00000357650.4_Missense_Mutation_p.I265M	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	265					cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)			endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		GTCTGATGATAGCAGATCCTA	0.328																																					p.I265M	NSCLC(91;473 1491 3102 16827 21633)	.											.	SLC30A7-90	0			c.A795G						.						166	157	160					1																	101387350		2202	4299	6501	SO:0001583	missense	148867	exon8			GATGATAGCAGAT	AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"Solute carriers"	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.795A>G	1.37:g.101387350A>G	ENSP00000359130:p.Ile265Met	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	31	11	NM_133496	0	0	2	2	0	B2R949|D3DT61|Q8TCH2	Missense_Mutation	SNP	ENST00000370112.4	37	CCDS776.1	.	.	.	.	.	.	.	.	.	.	A	18.12	3.552196	0.65311	.	.	ENSG00000162695	ENST00000370112;ENST00000357650	T;T	0.64803	-0.12;-0.12	5.62	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	M	0.83692	2.655	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.72232	-0.4353	10	0.48119	T	0.1	-9.0402	7.9394	0.29950	0.721:0.1427:0.0:0.1363	.	265	Q8NEW0	ZNT7_HUMAN	M	265	ENSP00000359130:I265M;ENSP00000350278:I265M	ENSP00000350278:I265M	I	+	3	3	SLC30A7	101159938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.388000	0.34442	0.920000	0.36970	0.533000	0.62120	ATA	.		0.328	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496		G	101387350	A	G	101387350	3	3	160	1	0	0	0	0	1	0	0	0	14592	410	15	3	825	3	SLC30A7	1	101387350	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	6841171	101387350	147863271	7	14502											
FCGR2C	2214	broad.mit.edu	37	chr1	161559585	161559585	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccagaccagcctcagcgacCctgtgcatctgactgtgctt	7	9	10	15	1	2	2	1	1	1	1	2	3	2	2	4	0	4	2	4	0	0	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:161559585C>T	ENST00000540048.1	-	2	94				FCGR2C_ENST00000473530.2_RNA|FCGR2B_ENST00000367960.5_Intron|FCGR2C_ENST00000466542.2_RNA|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000403078.3_Intron|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2B_ENST00000367962.4_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCTCAGCGACCCTGTGCATCT	0.587																																					.													.	.	0			.						.						27	28	28					1																	161559585		2149	4150	6299	SO:0001627	intron_variant	9103	.			AGCGACCCTGTGC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3619	protein-coding gene	gene with protein product		146740	"Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+40572G>A	1.37:g.161559585C>T		Somatic	504	1		WXS	Illumina HiSeq	Phase_I	369	56	.	0	0	23	23	0	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	RNA	SNP	ENST00000540048.1	37																																																																																				.		0.587	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569		T	161559585	C	T	161559585	1	4	160	0	1	0	0	0	0	0	0	0	5802	623	22	2		2	FCGR2C	1	161559585	Intron	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	60172235	161559585	87691036	8	14503											
MIA3	375056	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr1	222803477	222803477	+	Frame_Shift_Del	DEL	A	A	-																															gagcctgccctataatatggAaaaagtcctagataaggtct																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:222803477delA	ENST00000344922.5	+	4	2940	c.2915delA	c.(2914-2916)gaafs	p.E972fs	MIA3_ENST00000344441.6_Frame_Shift_Del_p.E972fs|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	972					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.V974fs*4(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TATAATATGGAAAAAGTCCTA	0.428																																					p.E972fs		.											.	MIA3-98	1	Insertion - Frameshift(1)	large_intestine(1)	c.2915delA						.						74	72	73					1																	222803477		1967	4169	6136	SO:0001589	frameshift_variant	375056	exon4			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.2915delA	1.37:g.222803477delA	ENSP00000340900:p.Glu972fs	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	73	32	NM_198551	0	0	0	0	0	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Frame_Shift_Del	DEL	ENST00000344922.5	37	CCDS41470.1																																																																																			.		0.428	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		-	222803477	A	-	222803477	7	5	160	1	0	1	0	1	0	0	0	0	9590	246	9	0	2929	0	MIA3	1	222803477	Frame_Shift_Del	DEL	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	61243892	222803477	26447144	9	14504											
IRF2BP2	359948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	234743060	234743060	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtctggagcaagggaagcaGaacttgtgcgaagggacgga	12	6	17	6	2	1	1	0	0	1	1	1	6	1	5	0	4	4	2	0	4	4	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:234743060G>A	ENST00000366609.3	-	2	1617	c.1587C>T	c.(1585-1587)ttC>ttT	p.F529F	IRF2BP2_ENST00000366610.3_Silent_p.F513F|IRF2BP2_ENST00000491430.1_5'UTR|RP4-781K5.2_ENST00000436039.1_RNA	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	529	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			AAGGGAAGCAGAACTTGTGCG	0.587																																					p.F529F		.											.	IRF2BP2-90	0			c.C1587T						.						81	87	85					1																	234743060		2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			GAAGCAGAACTTG	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1587C>T	1.37:g.234743060G>A		Somatic	99	0		WXS	Illumina HiSeq	Phase_I	99	38	NM_182972	0	0	36	73	37	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			.		0.587	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		A	234743060	G	A	234743060	2	1	160	1	0	0	0	0	0	0	0	1	7851	933	33	2		2	IRF2BP2	1	234743060	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	11939583	234743060	14507561	10	14505											
LRP1B	53353	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	141771172	141771172	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcccaaataggggtggtCtttcatgcctcagcaatgtc	10	10	11	10	0	3	0	2	0	1	0	4	1	3	0	2	3	3	1	2	3	4	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:141771172C>A	ENST00000389484.3	-	14	3304	c.2333G>T	c.(2332-2334)aGa>aTa	p.R778I		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	778					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TAGGGGTGGTCTTTCATGCCT	0.343										TSP Lung(27;0.18)																											p.R778I	Colon(99;50 2074 2507 20106)												.	LRP1B-311	0			c.G2333T						.						143	136	138					2																	141771172		2203	4300	6503	SO:0001583	missense	53353	exon14			GGTGGTCTTTCAT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"Low density lipoprotein receptors"	6693	protein-coding gene	gene with protein product	"LRP-deleted in tumors"	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2333G>T	2.37:g.141771172C>A	ENSP00000374135:p.Arg778Ile	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	187	40	NM_018557	0	0	0	0	0	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167516	0.78339	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90732	-2.72	5.64	5.64	0.86602	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	U	0.000000	D	0.93103	0.7804	L	0.41961	1.31	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.90084	0.4172	10	0.18710	T	0.47	.	19.7014	0.96054	0.0:1.0:0.0:0.0	.	778	Q9NZR2	LRP1B_HUMAN	I	778;716	ENSP00000374135:R778I	ENSP00000374135:R778I	R	-	2	0	LRP1B	141487642	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.938000	0.70170	2.660000	0.90430	0.563000	0.77884	AGA	.		0.343	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141771172	C	A	141771172	3	1	160	1	0	0	0	0	1	0	0	0	8980	913	32	4	11778	4	LRP1B	2	141771172	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		141771172	101428201	11	14506											
GRB14	2888	hgsc.bcm.edu	37	chr2	165477654	165477654	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcacagccgcgggtccCgtccggaaggggcaggagcg	7	3	18	13	5	0	0	0	0	0	0	2	2	2	2	3	5	4	3	3	5	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:165477654C>G	ENST00000263915.3	-	1	704	c.166G>C	c.(166-168)Ggg>Cgg	p.G56R		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	56					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CCGCGGGTCCCGTCCGGAAGG	0.771																																					p.G56R		.											.	GRB14-420	0			c.G166C						.						2	3	3					2																	165477654		1387	3094	4481	SO:0001583	missense	2888	exon1			GGGTCCCGTCCGG		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.166G>C	2.37:g.165477654C>G	ENSP00000263915:p.Gly56Arg	Somatic	2	0		WXS	Illumina HiSeq	Phase_I	53	30	NM_004490	0	0	0	0	0	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638721	0.47153	.	.	ENSG00000115290	ENST00000263915	T	0.23552	1.9	3.52	3.52	0.40303	.	0.650759	0.12693	N	0.447067	T	0.14570	0.0352	N	0.08118	0	0.80722	D	1	B	0.28055	0.199	B	0.28139	0.086	T	0.10660	-1.0620	10	0.66056	D	0.02	-0.5305	10.4807	0.44691	0.0:1.0:0.0:0.0	.	56	Q14449	GRB14_HUMAN	R	56	ENSP00000263915:G56R	ENSP00000263915:G56R	G	-	1	0	GRB14	165185900	0.128000	0.22383	0.967000	0.41034	0.993000	0.82548	1.792000	0.38754	1.822000	0.53115	0.585000	0.79938	GGG	.		0.771	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			G	165477654	C	G	165477654	3	3	160	1	0	0	0	0	1	0	0	0	6778	652	23	4	1512	4	GRB14	2	165477654	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	23706482	165477654	77721719	12	14507											
RNF25	64320	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	219536685	219536685	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcagctgcagacgcagaCgccgccatatcttcaccggc	8	6	10	17	4	2	2	1	0	1	2	2	2	2	2	4	1	3	4	4	1	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:219536685C>G	ENST00000295704.2	-	1	449	c.9G>C	c.(7-9)gcG>gcC	p.A3A	STK36_ENST00000440309.1_5'Flank|STK36_ENST00000295709.3_5'Flank|STK36_ENST00000392106.2_5'Flank|STK36_ENST00000392105.3_5'Flank	NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25	3					positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGACGCAGACGCCGCCATAT	0.612																																					p.A3A													.	RNF25-227	0			c.G9C						.						33	35	34					2																	219536685		2203	4300	6503	SO:0001819	synonymous_variant	64320	exon1			CGCAGACGCCGCC		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"RING-type (C3HC4) zinc fingers"	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077	ENST00000295704.2:c.9G>C	2.37:g.219536685C>G		Somatic	192	2		WXS	Illumina HiSeq	Phase_I	247	155	NM_022453	0	0	6	12	6	A8K0D6|Q53HQ5|Q9H874	Silent	SNP	ENST00000295704.2	37	CCDS2420.1																																																																																			.		0.612	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453		G	219536685	C	G	219536685	2	3	160	1	0	0	0	0	0	0	0	1	13517	523	19	4		4	RNF25	2	219536685	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	54059031	219536685	23662688	13	14508											
ATG9A	79065	hgsc.bcm.edu	37	chr2	220085516	220085516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgagccctcttcgggcaCgggctcagggtgccttgatg	4	9	14	14	3	2	1	1	1	1	0	4	2	3	1	3	3	2	2	3	3	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:220085516C>T	ENST00000409618.1	-	15	2906	c.2467G>A	c.(2467-2469)Gtg>Atg	p.V823M	ABCB6_ENST00000439002.2_5'Flank|ATG9A_ENST00000409422.1_Missense_Mutation_p.V762M|ATG9A_ENST00000361242.4_Missense_Mutation_p.V823M|ABCB6_ENST00000265316.3_5'Flank|ATG9A_ENST00000396761.2_Missense_Mutation_p.V823M			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	823					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTTCGGGCACGGGCTCAGGG	0.607																																					p.V823M		.											.	ATG9A-91	0			c.G2467A						.						46	47	47					2																	220085516		1899	4124	6023	SO:0001583	missense	79065	exon15			CGGGCACGGGCTC	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)"	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.2467G>A	2.37:g.220085516C>T	ENSP00000386710:p.Val823Met	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	73	4	NM_001077198	1	0	53	54	0	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	37	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071397	0.55646	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.06	5.06	0.68205	.	0.064569	0.64402	D	0.000010	T	0.65984	0.2744	L	0.34521	1.04	0.46874	D	0.999238	D	0.58268	0.982	P	0.44732	0.459	T	0.70722	-0.4794	10	0.56958	D	0.05	-11.0302	18.6114	0.91286	0.0:1.0:0.0:0.0	.	823	Q7Z3C6	ATG9A_HUMAN	M	823;823;823;762	ENSP00000379983:V823M;ENSP00000386710:V823M;ENSP00000355173:V823M;ENSP00000386535:V762M	ENSP00000355173:V823M	V	-	1	0	ATG9A	219793760	0.997000	0.39634	0.956000	0.39512	0.708000	0.40852	3.656000	0.54467	2.627000	0.88993	0.655000	0.94253	GTG	.		0.607	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		T	220085516	C	T	220085516	3	4	160	1	0	0	0	0	1	0	0	0	1103	536	19	1	60	1	ATG9A	2	220085516	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	548831	220085516	23113857	14	14509											
DES	1674	hgsc.bcm.edu	37	chr2	220283244	220283245	+	Missense_Mutation	DNP	GG	GG	AT																															taccgccgcaccttcggcggGgccccgggcttcccactcgg																								rs1058253		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:220283244_220283245GG>AT	ENST00000373960.3	+	1	146_147	c.60_61GG>AT	c.(58-63)ggGGcc>ggATcc	p.A21S		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	21	Head.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCTTCGGCGGGGCCCCGGGCTT	0.733																																					p.A21S		.											.	DES-514	0			c.G61T						.																																			SO:0001583	missense	1674	exon1			GGCGGGGCCCCGG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"Intermediate filaments type III"	2770	protein-coding gene	gene with protein product	"intermediate filament protein"	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	Exception_encountered	2.37:g.220283244_220283245delinsAT	ENSP00000363071:p.Ala21Ser	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	31	24	NM_001927	0	0	0	0	0	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	DNP	ENST00000373960.3	37	CCDS33383.1																																																																																			.		0.733	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		AT	220283245	GG	AT	220283244	3	1	160	1	0	0	0	0	1	0	0	0	4460	1219	43	2	62	2	DES	2	220283244	Missense_Mutation	DNP	GG	TCGA-PJ-A5Z9-01A-11D-A28G-10	197728	220283244	22916129	15	14510											
TOP2B	7155	hgsc.bcm.edu	37	chr3	25705758	25705758	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgccgccgcccacgccggCtcccgcgccgcagccacccg	3	3	12	23	8	0	0	0	0	0	0	1	0	1	0	8	1	2	3	8	1	0	1	rs145455403	byFrequency	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:25705758C>T	ENST00000264331.4	-	1	30	c.31G>A	c.(31-33)Gcc>Acc	p.A11T	TOP2B_ENST00000435706.2_Missense_Mutation_p.A11T|MIR4442_ENST00000583412.1_RNA	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	11					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	CCCACGCCGGCTCCCGCGCCG	0.771													C|||	45	0.00898562	8e-04	0.0231	5008	,	,		6677	0		0.0199	False		,,,				2504	0.0082				p.A11T		.											.	TOP2B-273	0			c.G31A						.	C	THR/ALA	8,3016		0,8,1504	4	8	7		31	-1.1	0.3	3	dbSNP_134	7	129,6473		1,127,3173	no	missense	TOP2B	NM_001068.2	58	1,135,4677	TT,TC,CC		1.954,0.2646,1.4232	possibly-damaging	11/1622	25705758	137,9489	1512	3301	4813	SO:0001583	missense	7155	exon1			CGCCGGCTCCCGC	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"topoisomerase (DNA) II beta (180kD)"			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.31G>A	3.37:g.25705758C>T	ENSP00000264331:p.Ala11Thr	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	8	NM_001068	0	0	1	2	1	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		36	0.016483516483516484	6	0.012195121951219513	11	0.03038674033149171	6	0.01048951048951049	13	0.017150395778364115	c	16.12	3.034111	0.54896	0.002646	0.01954	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.44083	0.93;0.93	2.62	-1.06	0.10002	.	0.994270	0.08145	U	0.990988	T	0.09949	0.0244	N	0.08118	0	0.30757	N	0.744492	P	0.46395	0.877	P	0.51866	0.682	T	0.13899	-1.0492	10	0.29301	T	0.29	.	1.1455	0.01774	0.2237:0.407:0.22:0.1492	.	11	Q02880-2	.	T	11	ENSP00000396704:A11T;ENSP00000264331:A11T	ENSP00000264331:A11T	A	-	1	0	TOP2B	25680762	0.194000	0.23325	0.294000	0.24946	0.849000	0.48306	0.298000	0.19120	-0.467000	0.06932	0.457000	0.33378	GCC	C|0.983;T|0.016		0.771	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				T	25705758	C	T	25705758	3	4	160	1	0	0	0	0	1	0	0	0	16399	797	28	2	4978	2	TOP2B	3	25705758	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		25705758	172316672	16	14511											
SETD2	29072	hgsc.bcm.edu	37	chr3	47164505	47164505	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttagaatatgatgaccctcGtcggaatcccagttcattag	11	12	8	10	2	1	3	1	2	0	1	4	4	2	4	2	1	0	1	2	1	5	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:47164505G>T	ENST00000409792.3	-	3	1663	c.1621C>A	c.(1621-1623)Cga>Aga	p.R541R		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	541					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GATGACCCTCGTCGGAATCCC	0.358			"N, F, S, Mis"		clear cell renal carcinoma																																p.R541R		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2-1273	0			c.C1621A						.						100	100	100					3																	47164505		2200	4292	6492	SO:0001819	synonymous_variant	29072	exon3			ACCCTCGTCGGAA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1621C>A	3.37:g.47164505G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_I	77	4	NM_014159	0	0	0	0	0	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.358	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47164505	G	T	47164505	2	4	160	1	0	0	0	0	0	0	0	1	14163	1153	40	4		4	SETD2	3	47164505	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	21458747	47164505	150857925	17	14512											
GMPPB	29925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49759370	49759370	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggcacactccccgcccctctCcccacccagcccagcccaca	7	3	5	26	1	1	0	0	0	1	0	3	0	2	0	9	1	2	1	9	1	0	0	rs71324991		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:49759370C>T	ENST00000480687.1	-	9	1068				GMPPB_ENST00000308375.6_Missense_Mutation_p.E327K|AMIGO3_ENST00000320431.7_5'Flank|AMIGO3_ENST00000535833.1_Intron|GMPPB_ENST00000308388.6_Intron			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCGCCCCTCTCCCCACCCAGC	0.632																																					p.E327K		.											.	GMPPB-90	0			c.G979A						.						52	52	52					3																	49759370		2203	4300	6503	SO:0001627	intron_variant	29925	exon8			CCCTCTCCCCACC	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.951+27G>A	3.37:g.49759370C>T		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	113	67	NM_013334	0	0	0	0	0	A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	37	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	C	4.938	0.174300	0.09391	.	.	ENSG00000173540	ENST00000308375	T	0.72942	-0.7	4.7	1.73	0.24493	.	1.157320	0.06701	N	0.771475	T	0.53722	0.1814	.	.	.	0.32702	N	0.512756	B	0.02656	0.0	B	0.01281	0.0	T	0.51988	-0.8635	9	0.24483	T	0.36	-2.0563	5.6606	0.17667	0.0:0.442:0.3934:0.1645	.	327	Q9Y5P6-2	.	K	327	ENSP00000309092:E327K	ENSP00000309092:E327K	E	-	1	0	GMPPB	49734374	0.000000	0.05858	0.023000	0.16930	0.167000	0.22549	-0.551000	0.06027	0.524000	0.28502	0.655000	0.94253	GAG	C|0.500;T|0.500		0.632	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		T	49759370	C	T	49759370	1	4	160	0	1	0	0	0	0	0	0	0	6515	864	30	2		2	GMPPB	3	49759370	Intron	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	2594865	49759370	148263060	18	14513											
UBA7	7318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	49847782	49847782	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctctgtggtgggatccAgtgggtaggtgagcgggatc	5	11	19	6	1	1	1	0	1	1	0	3	3	2	3	1	5	2	2	1	5	1	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:49847782A>T	ENST00000333486.3	-	13	1705	c.1547T>A	c.(1546-1548)cTg>cAg	p.L516Q	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	516	2 approximate repeats.				cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GGTGGGATCCAGTGGGTAGGT	0.587																																					p.L516Q		.											.	UBA7-228	0			c.T1547A						.						102	104	103					3																	49847782		2203	4300	6503	SO:0001583	missense	7318	exon13			GGATCCAGTGGGT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.1547T>A	3.37:g.49847782A>T	ENSP00000333266:p.Leu516Gln	Somatic	270	0		WXS	Illumina HiSeq	Phase_I	254	148	NM_003335	0	0	0	1	1	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249400	0.80024	.	.	ENSG00000182179	ENST00000333486	T	0.67345	-0.26	5.67	5.67	0.87782	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.331674	0.29631	N	0.011601	D	0.86180	0.5871	M	0.93854	3.465	0.52501	D	0.999951	D	0.76494	0.999	D	0.74674	0.984	D	0.89830	0.3995	10	0.87932	D	0	-8.7204	15.9043	0.79412	1.0:0.0:0.0:0.0	.	516	P41226	UBA7_HUMAN	Q	516	ENSP00000333266:L516Q	ENSP00000333266:L516Q	L	-	2	0	UBA7	49822786	1.000000	0.71417	0.352000	0.25734	0.711000	0.40976	8.947000	0.93000	2.169000	0.68431	0.459000	0.35465	CTG	.		0.587	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		T	49847782	A	T	49847782	3	4	160	1	0	0	0	0	1	0	0	0	16866	188	7	5	1539	5	UBA7	3	49847782	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	88412	49847782	148174648	19	14514											
ACTR8	93973	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	53913972	53913972	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtttttgacttacatttagTccctcccttaggagccaact	8	15	6	12	1	0	1	0	1	0	0	2	2	2	2	3	1	3	1	3	1	4	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:53913972T>C	ENST00000335754.3	-	2	388	c.288A>G	c.(286-288)ggA>ggG	p.G96G	AC012467.1_ENST00000410956.1_RNA|ACTR8_ENST00000231909.7_5'Flank|ACTR8_ENST00000482349.1_5'UTR	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	96					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		TTACATTTAGTCCCTCCCTTA	0.478																																					p.G96G													.	ACTR8-91	0			c.A288G						.						164	157	159					3																	53913972		2203	4300	6503	SO:0001819	synonymous_variant	93973	exon2			ATTTAGTCCCTCC		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"INO80 complex subunits"	14672	protein-coding gene	gene with protein product	"INO80 complex subunit N"		"ARP8 (actin-related protein 8, yeast) homolog"			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.288A>G	3.37:g.53913972T>C		Somatic	147	2		WXS	Illumina HiSeq	Phase_I	121	72	NM_022899	0	0	0	0	0	B3KSW7|Q8N566|Q9H663	Silent	SNP	ENST00000335754.3	37	CCDS2875.1																																																																																			.		0.478	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899		C	53913972	T	C	53913972	2	2	160	1	0	0	0	0	0	0	0	1	217	1654	58	3		3	ACTR8	3	53913972	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	4066190	53913972	144108458	20	14515											
ERC2	26059	broad.mit.edu	37	chr3	56114913	56114913	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcatgtcacgaatttcacCggccagtgtccccttctctt	6	15	6	14	2	4	0	3	0	1	0	6	1	5	0	4	1	0	0	4	1	1	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:56114913C>T	ENST00000288221.6	-	7	1828	c.1573G>A	c.(1573-1575)Ggt>Agt	p.G525S		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	525						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CGAATTTCACCGGCCAGTGTC	0.408																																					p.G525S													.	ERC2-24	0			c.G1573A						.						146	130	135					3																	56114913		1865	4101	5966	SO:0001583	missense	26059	exon7			TTTCACCGGCCAG	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.1573G>A	3.37:g.56114913C>T	ENSP00000288221:p.Gly525Ser	Somatic	81	0		WXS	Illumina HiSeq	Phase_I	66	4	NM_015576	0	0	0	0	0	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.147764	0.78001	.	.	ENSG00000187672	ENST00000288221	T	0.77358	-1.09	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.85017	0.5601	L	0.43646	1.37	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82969	-0.0193	10	0.39692	T	0.17	-17.3627	20.0714	0.97726	0.0:1.0:0.0:0.0	.	525	O15083	ERC2_HUMAN	S	525	ENSP00000288221:G525S	ENSP00000288221:G525S	G	-	1	0	ERC2	56089953	1.000000	0.71417	0.991000	0.47740	0.877000	0.50540	7.818000	0.86416	2.750000	0.94351	0.585000	0.79938	GGT	.		0.408	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		T	56114913	C	T	56114913	3	4	160	1	0	0	0	0	1	0	0	0	5224	652	23	1	1334	1	ERC2	3	56114913	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	2200941	56114913	141907517	21	14516											
IGF2BP2	10644	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr3	185542743	185542743	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcccgatgtaaagcttgttCatcatccgtctcttccccga	7	14	6	14	3	3	0	2	0	1	0	7	2	6	0	4	0	1	3	4	0	2	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:185542743C>G	ENST00000382199.2	-	1	101	c.6G>C	c.(4-6)atG>atC	p.M2I	IGF2BP2_ENST00000346192.3_Missense_Mutation_p.M2I|IGF2BP2_ENST00000457616.2_Missense_Mutation_p.M2I	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	2					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			AAAGCTTGTTCATCATCCGTC	0.706																																					p.M2I		.											.	IGF2BP2-226	0			c.G6C						.						22	24	24					3																	185542743		2202	4300	6502	SO:0001583	missense	10644	exon1			CTTGTTCATCATC	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"RNA binding motif (RRM) containing"	28867	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 2"	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.6G>C	3.37:g.185542743C>G	ENSP00000371634:p.Met2Ile	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	169	34	NM_001007225	0	0	2	2	0	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Missense_Mutation	SNP	ENST00000382199.2	37	CCDS3273.2	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612112	0.87258	.	.	ENSG00000073792	ENST00000382199;ENST00000457616;ENST00000346192	T;T;T	0.20332	2.11;2.31;2.08	2.43	2.43	0.29744	.	0.000000	0.64402	U	0.000001	T	0.47358	0.1441	M	0.85197	2.74	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.77557	0.978;0.99;0.965	T	0.56914	-0.7900	10	0.87932	D	0	-7.2297	11.9545	0.52974	0.0:1.0:0.0:0.0	.	2;2;2	F8W930;Q9Y6M1-1;Q9Y6M1	.;.;IF2B2_HUMAN	I	2	ENSP00000371634:M2I;ENSP00000410242:M2I;ENSP00000320204:M2I	ENSP00000320204:M2I	M	-	3	0	IGF2BP2	187025437	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.717000	0.74707	1.354000	0.45846	0.393000	0.25936	ATG	.		0.706	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		G	185542743	C	G	185542743	3	3	160	1	0	0	0	0	1	0	0	0	7595	826	29	4	1857	4	IGF2BP2	3	185542743	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	129427830	185542743	12479687	22	14517											
NKX3-2	579	hgsc.bcm.edu	37	chr4	13545664	13545664	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctcacagaccggctggccGaggctcaaggatccccccgc	8	4	12	17	3	2	1	2	0	0	1	3	3	3	2	5	4	1	3	5	4	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:13545664G>A	ENST00000382438.5	-	1	1010	c.375C>T	c.(373-375)ctC>ctT	p.L125L	AC006445.8_ENST00000501050.1_lincRNA	NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	125					determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						CCGGCTGGCCGAGGCTCAAGG	0.721																																					p.L125L		.											.	NKX3-2-68	0			c.C375T						.						3	4	4					4																	13545664		1713	3631	5344	SO:0001819	synonymous_variant	579	exon1			CTGGCCGAGGCTC	AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"Homeoboxes / ANTP class : NKL subclass"	951	protein-coding gene	gene with protein product		602183	"bagpipe homeobox homolog 1 (Drosophila)"	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.375C>T	4.37:g.13545664G>A		Somatic	3	0		WXS	Illumina HiSeq	Phase_I	29	18	NM_001189	0	0	0	0	0	Q2M2I7	Silent	SNP	ENST00000382438.5	37	CCDS3410.1																																																																																			.		0.721	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3			A	13545664	G	A	13545664	2	1	160	1	0	0	0	0	0	0	0	1	10482	1045	37	1		1	NKX3-2	4	13545664	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		13545664	177608612	23	14518											
NIPAL1	152519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	48037862	48037862	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggcactggacacctttaaTacctctcttgtgacacccat	11	11	6	13	0	1	1	0	1	1	0	2	2	1	2	3	2	1	1	3	2	3	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:48037862T>C	ENST00000295461.5	+	6	972	c.906T>C	c.(904-906)aaT>aaC	p.N302N		NM_207330.1	NP_997213.1	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	302						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|large_intestine(1)|lung(3)|skin(2)	8						ACACCTTTAATACCTCTCTTG	0.423																																					p.N302N		.											.	NIPAL1-68	0			c.T906C						.						138	122	127					4																	48037862		2203	4300	6503	SO:0001819	synonymous_variant	152519	exon6			CTTTAATACCTCT	BC067881	CCDS3479.1	4p12	2009-03-24		2009-03-24	ENSG00000163293	ENSG00000163293			27194	protein-coding gene	gene with protein product				NPAL1			Standard	NM_207330		Approved	DKFZp686A06115	uc003gxw.3	Q6NVV3	OTTHUMG00000128622	ENST00000295461.5:c.906T>C	4.37:g.48037862T>C		Somatic	201	0		WXS	Illumina HiSeq	Phase_I	145	58	NM_207330	0	0	0	0	0	B3KTB0|Q68DA9	Silent	SNP	ENST00000295461.5	37	CCDS3479.1																																																																																			.		0.423	NIPAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250491.4	NM_207330		C	48037862	T	C	48037862	2	2	160	1	0	0	0	0	0	0	0	1	10450	1403	49	3		3	NIPAL1	4	48037862	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	34492198	48037862	143116414	24	14519											
DSPP	1834	bcgsc.ca	37	chr4	88537018	88537018	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacagcagcgacagcagtgaTagcagtgacagcagtgacag	14	4	14	9	1	0	3	0	3	0	0	0	5	0	3	0	0	5	4	0	0	1	1	rs370264407		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:88537018T>C	ENST00000282478.7	+	4	3237	c.3204T>C	c.(3202-3204)gaT>gaC	p.D1068D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1068D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1068	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagcagtgaca	0.532																																					p.D1068D													.	DSPP-90	0			c.T3204C						.	T		27,3131		0,27,1552	54	66	62		3204	0.6	0.3	4	dbSNP_134	62	95,5593		2,91,2751	no	coding-synonymous	DSPP	NM_014208.3		2,118,4303	CC,CT,TT		1.6702,0.855,1.3792		1068/1302	88537018	122,8724	1579	2844	4423	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3204T>C	4.37:g.88537018T>C		Somatic	515	13		WXS	Illumina HiSeq	Phase_1	328	16	NM_014208	0	0	0	0	0	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.532	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537018	T	C	88537018	2	2	160	1	0	0	0	0	0	0	0	1	4793	1403	49	3		3	DSPP	4	88537018	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	40499156	88537018	102617258	25	14520											
IRX2	153572	broad.mit.edu;bcgsc.ca	37	chr5	2748624	2748624	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctggccctgcagcgccgCgttcaagttcccgtagtttg	5	10	11	15	4	1	0	1	0	0	0	2	0	2	0	4	1	2	5	4	1	2	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:2748624C>T	ENST00000382611.6	-	3	1446	c.1198G>A	c.(1198-1200)Gcg>Acg	p.A400T	IRX2_ENST00000302057.5_Missense_Mutation_p.A400T|IRX2_ENST00000502957.1_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	400					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		TGCAGCGCCGCGTTCAAGTTC	0.706																																					p.A400T													.	IRX2-226	0			c.G1198A						.						37	38	38					5																	2748624		2189	4286	6475	SO:0001583	missense	153572	exon3			GCGCCGCGTTCAA	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"Homeoboxes / TALE class"	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.1198G>A	5.37:g.2748624C>T	ENSP00000372056:p.Ala400Thr	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	68	9	NM_001134222	0	0	0	0	0	Q68A19|Q7Z2I7	Missense_Mutation	SNP	ENST00000382611.6	37	CCDS3868.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780307	0.49891	.	.	ENSG00000170561	ENST00000382611;ENST00000302057	T;T	0.65178	-0.14;-0.14	4.43	4.43	0.53597	.	0.067153	0.64402	D	0.000011	T	0.53077	0.1774	L	0.39898	1.24	0.37331	D	0.909994	D	0.57899	0.981	B	0.40134	0.32	T	0.61950	-0.6957	10	0.33940	T	0.23	-19.73	17.4343	0.87547	0.0:1.0:0.0:0.0	.	400	Q9BZI1	IRX2_HUMAN	T	400	ENSP00000372056:A400T;ENSP00000307006:A400T	ENSP00000307006:A400T	A	-	1	0	IRX2	2801624	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.982000	0.70532	2.184000	0.69523	0.561000	0.74099	GCG	.		0.706	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2			T	2748624	C	T	2748624	3	4	160	1	0	0	0	0	1	0	0	0	7865	768	27	1	225	1	IRX2	5	2748624	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		2748624	178166636	26	14521											
PRDM9	56979	bcgsc.ca	37	chr5	23527640	23527640	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtgggcggggctttagcAataagtcacacctcctcaga	10	9	12	10	1	2	1	2	0	0	1	3	1	3	1	2	3	1	2	2	3	3	3	rs202203985	byFrequency	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:23527640A>T	ENST00000296682.3	+	11	2625	c.2443A>T	c.(2443-2445)Aat>Tat	p.N815Y		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	815					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGCTTTAGCAATAAGTCACA	0.567										HNSCC(3;0.000094)			a|||	116	0.0231629	0.0643	0.0043	5008	,	,		22804	0.0099		0.005	False		,,,				2504	0.0133				p.N815Y													.	PRDM9-139	0			c.A2443T						.																																			SO:0001583	missense	56979	exon11			TTTAGCAATAAGT	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"-", "Zinc fingers, C2H2-type"	13994	protein-coding gene	gene with protein product	"PR-domain containing protein 9"	609760	"minisatellite binding protein 3, 115kDa", "minisatellite binding protein 3 (115kD)"	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2443A>T	5.37:g.23527640A>T	ENSP00000296682:p.Asn815Tyr	Somatic	233	1		WXS	Illumina HiSeq	Phase_1	182	62	NM_020227	0	0	0	0	0	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	a	0.525	-0.860379	0.02610	.	.	ENSG00000164256	ENST00000296682	T	0.19532	2.14	3.02	-6.05	0.02172	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13713	0.0332	N	0.25245	0.725	0.09310	N	1	B	0.26400	0.148	B	0.35770	0.21	T	0.32613	-0.9900	9	0.37606	T	0.19	16.5357	7.1248	0.25465	0.093:0.115:0.5628:0.2292	.	815	Q9NQV7	PRDM9_HUMAN	Y	815	ENSP00000296682:N815Y	ENSP00000296682:N815Y	N	+	1	0	PRDM9	23563397	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-11.912000	0.00002	-4.540000	0.00043	-3.331000	0.00043	AAT	.		0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23527640	A	T	23527640	3	4	160	1	0	0	0	0	1	0	0	0	12492	130	5	5	2481	5	PRDM9	5	23527640	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	20779016	23527640	157387620	27	14522											
FYB	2533	bcgsc.ca	37	chr5	39202408	39202408	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacccttttgatgaagacaCattcttcatggggctttcgt	8	14	10	9	1	2	3	1	2	1	1	3	4	2	4	1	3	0	1	1	3	1	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:39202408C>G	ENST00000351578.6	-	2	845	c.655G>C	c.(655-657)Gtg>Ctg	p.V219L	FYB_ENST00000515010.1_Missense_Mutation_p.V219L|FYB_ENST00000505428.1_Missense_Mutation_p.V219L|FYB_ENST00000540520.1_Missense_Mutation_p.V229L|FYB_ENST00000512982.1_Missense_Mutation_p.V219L	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	219					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			GATGAAGACACATTCTTCATG	0.532																																					p.V229L													.	FYB-24	0			c.G685C						.						66	66	66					5																	39202408		1841	4077	5918	SO:0001583	missense	2533	exon2			AAGACACATTCTT	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"FYN-binding protein (FYB-120/130)"			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.655G>C	5.37:g.39202408C>G	ENSP00000316460:p.Val219Leu	Somatic	83	0		WXS	Illumina HiSeq	Phase_1	66	4	NM_001243093	0	0	0	0	0	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	C	6.014	0.370969	0.11409	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.24908	1.83;1.83;1.84;1.84;1.87	6.07	-3.59	0.04583	.	2.202910	0.01678	N	0.025958	T	0.16769	0.0403	L	0.34521	1.04	0.09310	N	1	B;B	0.24483	0.104;0.001	B;B	0.18871	0.023;0.001	T	0.10405	-1.0631	10	0.28530	T	0.3	3.1834	3.5355	0.07793	0.089:0.4575:0.1745:0.2791	.	229;219	B4DLN2;O15117	.;FYB_HUMAN	L	219;219;219;219;229;219	ENSP00000316460:V219L;ENSP00000426346:V219L;ENSP00000425845:V219L;ENSP00000427114:V219L;ENSP00000442840:V229L	ENSP00000316460:V219L	V	-	1	0	FYB	39238165	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.158000	0.16422	-0.608000	0.05731	-1.261000	0.01458	GTG	.		0.532	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		G	39202408	C	G	39202408	3	3	160	1	0	0	0	0	1	0	0	0	6143	478	17	4	1906	4	FYB	5	39202408	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	15674768	39202408	141712852	28	14523											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56170960	56170960	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgtcagtggggccctgctGttggcaaatggggagagcac	8	8	17	8	0	1	1	1	0	0	1	1	3	1	1	1	5	2	4	1	5	1	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:56170960G>T	ENST00000399503.3	+	10	1788	c.1788G>T	c.(1786-1788)ctG>ctT	p.L596L		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	596					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GGGCCCTGCTGTTGGCAAATG	0.552																																					p.L596L		.											.	MAP3K1-956	0			c.G1788T						.						88	87	87					5																	56170960		1908	4114	6022	SO:0001819	synonymous_variant	4214	exon10			CCTGCTGTTGGCA	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6848	protein-coding gene	gene with protein product		600982	"mitogen-activated protein kinase kinase kinase 1"	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1788G>T	5.37:g.56170960G>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	72	4	NM_005921	0	0	2	2	0		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			.		0.552	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		T	56170960	G	T	56170960	2	4	160	1	0	0	0	0	0	0	0	1	9268	1364	48	4		4	MAP3K1	5	56170960	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	16968552	56170960	124744300	29	14524											
TRIM23	373	broad.mit.edu;bcgsc.ca	37	chr5	64892965	64892965	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accatccaatcctaacgtaaCgacccgaatttccatttttg	12	12	4	13	3	0	0	0	0	0	0	3	2	3	0	5	0	2	1	5	0	4	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:64892965C>T	ENST00000231524.9	-	8	1593	c.1222G>A	c.(1222-1224)Gtt>Att	p.V408I	TRIM23_ENST00000274327.7_Missense_Mutation_p.V408I|TRIM23_ENST00000381018.3_Missense_Mutation_p.V408I	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	408	ARF-like.				GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V408I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		CCTAACGTAACGACCCGAATT	0.323																																					p.V408I													.	TRIM23-230	1	Substitution - Missense(1)	kidney(1)	c.G1222A						.						119	113	115					5																	64892965		2203	4300	6503	SO:0001583	missense	373	exon8			ACGTAACGACCCG	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	660	protein-coding gene	gene with protein product		601747	"ADP-ribosylation factor domain protein 1, 64kDa", "tripartite motif-containing 23"	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.1222G>A	5.37:g.64892965C>T	ENSP00000231524:p.Val408Ile	Somatic	110	0		WXS	Illumina HiSeq	Phase_I	84	5	NM_033228	0	0	3	3	0	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.483114	0.84747	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.63744	-0.06;-0.06;-0.06	5.97	5.97	0.96955	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.66257	0.2771	L	0.28608	0.87	0.80722	D	1	D;D;D	0.61697	0.975;0.99;0.989	P;P;P	0.54100	0.742;0.525;0.674	T	0.67469	-0.5663	10	0.62326	D	0.03	.	20.4324	0.99085	0.0:1.0:0.0:0.0	.	408;408;408	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	I	408	ENSP00000231524:V408I;ENSP00000370406:V408I;ENSP00000274327:V408I	ENSP00000231524:V408I	V	-	1	0	TRIM23	64928721	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	5.920000	0.70017	2.833000	0.97629	0.585000	0.79938	GTT	.		0.323	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		T	64892965	C	T	64892965	3	4	160	1	0	0	0	0	1	0	0	0	16530	536	19	1	585	1	TRIM23	5	64892965	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	8722005	64892965	116022295	30	14525											
MSH3	4437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	79970928	79970928	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagggacaaaaaaaagggcaAcatttttattggcattgtgg	15	11	11	4	0	0	0	0	0	0	0	0	1	0	1	0	4	1	2	0	4	7	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:79970928A>T	ENST00000265081.6	+	7	1234	c.1154A>T	c.(1153-1155)aAc>aTc	p.N385I		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	385					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AAAAAGGGCAACATTTTTATT	0.333								Mismatch excision repair (MMR)																													p.N385I	Melanoma(88;1010 1399 13793 26548 36275)	.											.	MSH3-661	0			c.A1154T						.						148	152	151					5																	79970928		2203	4300	6503	SO:0001583	missense	4437	exon7			AGGGCAACATTTT	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"Divergent upstream protein", "Mismatch repair protein 1"	600887	"mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)"				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1154A>T	5.37:g.79970928A>T	ENSP00000265081:p.Asn385Ile	Somatic	148	0		WXS	Illumina HiSeq	Phase_I	98	41	NM_002439	0	0	0	0	0	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	A	8.987	0.976749	0.18812	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88664	-2.41	5.6	-5.6	0.02497	DNA mismatch repair protein MutS, connector (2);	0.642828	0.16451	N	0.213870	T	0.79405	0.4440	L	0.53249	1.67	0.09310	N	1	B	0.33318	0.408	B	0.34138	0.176	T	0.67783	-0.5581	9	.	.	.	-1.1852	2.0942	0.03664	0.3478:0.3369:0.2064:0.1089	.	385	P20585	MSH3_HUMAN	I	385;376	ENSP00000265081:N385I	.	N	+	2	0	MSH3	80006684	0.010000	0.17322	0.000000	0.03702	0.294000	0.27393	0.093000	0.15086	-0.822000	0.04306	-0.367000	0.07326	AAC	.		0.333	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		T	79970928	A	T	79970928	3	4	160	1	0	0	0	0	1	0	0	0	9896	43	2	5	1180	5	MSH3	5	79970928	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	15077963	79970928	100944332	31	14526											
KDM3B	51780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	137717257	137717257	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatccatgtgatgctgatggAtaattcagcgcctcaaagcg	12	10	10	9	2	2	2	2	2	0	0	3	3	3	3	2	1	3	1	2	1	3	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:137717257A>C	ENST00000314358.5	+	6	958	c.758A>C	c.(757-759)gAt>gCt	p.D253A		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	253					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						ATGCTGATGGATAATTCAGCG	0.433																																					p.D253A		.											.	KDM3B-542	0			c.A758C						.						134	117	123					5																	137717257		2203	4300	6503	SO:0001583	missense	51780	exon6			TGATGGATAATTC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"Chromatin-modifying enzymes / K-demethylases"	1337	protein-coding gene	gene with protein product		609373	"chromosome 5 open reading frame 7", "jumonji domain containing 1B"	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.758A>C	5.37:g.137717257A>C	ENSP00000326563:p.Asp253Ala	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	72	25	NM_016604	0	0	0	0	0	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253034	0.80135	.	.	ENSG00000120733	ENST00000314358;ENST00000545151	T	0.68025	-0.3	4.79	4.79	0.61399	.	0.104922	0.64402	D	0.000006	T	0.70876	0.3274	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.75357	-0.3346	10	0.72032	D	0.01	-8.6271	14.278	0.66194	1.0:0.0:0.0:0.0	.	253	Q7LBC6	KDM3B_HUMAN	A	253;43	ENSP00000326563:D253A	ENSP00000326563:D253A	D	+	2	0	KDM3B	137745156	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	6.004000	0.70709	1.905000	0.55150	0.460000	0.39030	GAT	.		0.433	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137717257	A	C	137717257	3	2	160	1	0	0	0	0	1	0	0	0	8148	333	12	5	780	5	KDM3B	5	137717257	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	57746329	137717257	43198003	32	14527											
ZNF354B	117608	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr5	178310106	178310106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaacgctataaatgcagtaCatgtgaaaaagccttcattc	16	10	7	8	1	1	1	1	1	0	0	2	2	1	1	1	0	4	3	1	0	7	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:178310106C>T	ENST00000322434.3	+	5	879	c.653C>T	c.(652-654)aCa>aTa	p.T218I	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	218					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(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAATGCAGTACATGTGAAAAA	0.299																																					p.T218I													.	ZNF354B-92	0			c.C653T						.						72	80	77					5																	178310106		2201	4295	6496	SO:0001583	missense	117608	exon5			GCAGTACATGTGA	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"Zinc fingers, C2H2-type", "-"	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.653C>T	5.37:g.178310106C>T	ENSP00000327143:p.Thr218Ile	Somatic	99	1		WXS	Illumina HiSeq	Phase_I	80	33	NM_058230	0	0	2	3	1	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	37	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	C	4.307	0.056302	0.08291	.	.	ENSG00000178338	ENST00000322434	T	0.26810	1.71	3.53	-2.54	0.06307	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09905	0.0243	N	0.04959	-0.14	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25950	-1.0117	9	0.52906	T	0.07	-33.0293	3.159	0.06514	0.3538:0.1876:0.0:0.4585	.	218	Q96LW1	Z354B_HUMAN	I	218	ENSP00000327143:T218I	ENSP00000327143:T218I	T	+	2	0	ZNF354B	178242712	0.000000	0.05858	0.447000	0.26932	0.752000	0.42762	-0.127000	0.10547	-0.216000	0.10048	-0.291000	0.09656	ACA	.		0.299	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		T	178310106	C	T	178310106	3	4	160	1	0	0	0	0	1	0	0	0	17897	478	17	2	667	2	ZNF354B	5	178310106	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	40592849	178310106	2605154	33	14528											
ZNF184	7738	ucsc.edu;bcgsc.ca	37	chr6	27420593	27420593	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acattcattacatttgtaggGtttttctccagtatgtgttc	8	19	7	7	0	2	0	1	0	1	0	4	0	2	0	1	1	1	4	1	1	3	8			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:27420593G>T	ENST00000211936.6	-	6	1029	c.745C>A	c.(745-747)Ccc>Acc	p.P249T	ZNF184_ENST00000377419.1_Missense_Mutation_p.P249T	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						CATTTGTAGGGTTTTTCTCCA	0.348																																					p.P249T													.	ZNF184-91	0			c.C745A						.						121	127	125					6																	27420593		2203	4300	6503	SO:0001583	missense	7738	exon6			TGTAGGGTTTTTC	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.745C>A	6.37:g.27420593G>T	ENSP00000211936:p.Pro249Thr	Somatic	32	0		WXS	Illumina HiSeq		33	4	NM_007149	0	0	2	2	0	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	37	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	G	14.86	2.660854	0.47572	.	.	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087	T;T	0.28895	1.59;1.59	5.12	5.12	0.69794	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000247	T	0.50257	0.1605	M	0.86573	2.825	0.40341	D	0.979033	D	0.64830	0.994	D	0.65323	0.934	T	0.51060	-0.8753	10	0.33940	T	0.23	.	16.0902	0.81086	0.0:0.0:1.0:0.0	.	249	Q99676	ZN184_HUMAN	T	249	ENSP00000211936:P249T;ENSP00000366636:P249T	ENSP00000211936:P249T	P	-	1	0	ZNF184	27528572	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	6.225000	0.72271	2.660000	0.90430	0.555000	0.69702	CCC	.		0.348	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		T	27420593	G	T	27420593	3	4	160	1	0	0	0	0	1	0	0	0	17783	1261	44	4	1514	4	ZNF184	6	27420593	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		27420593	143694474	34	14529											
C4A	720	broad.mit.edu;bcgsc.ca	37	chr6	31962347	31962347	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggctggcccagcaggtgctgGtgcctgcgggctctgcccgg	2	7	18	14	2	1	0	0	0	1	0	1	0	1	0	3	6	5	4	3	6	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:31962347G>A	ENST00000428956.2	+	21	2749	c.2665G>A	c.(2665-2667)Gtg>Atg	p.V889M	C4A_ENST00000498271.1_Missense_Mutation_p.V889M	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	889					complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	GCAGGTGCTGGTGCCTGCGGG	0.687																																					p.V889M													.	C4A-44	0			c.G2665A						.						9	12	11					6																	31962347		1943	3861	5804	SO:0001583	missense	720	exon21			GTGCTGGTGCCTG	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"Blood group antigens", "Complement system"	1323	protein-coding gene	gene with protein product		120810	"complement component 4A"				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.2665G>A	6.37:g.31962347G>A	ENSP00000396688:p.Val889Met	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	181	45	NM_007293	0	0	80	110	30	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Missense_Mutation	SNP	ENST00000428956.2	37	CCDS47404.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.561139	0.45590	.	.	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.46063	0.88;0.88	3.22	2.22	0.28083	.	0.583336	0.16838	N	0.197448	T	0.47154	0.1430	M	0.74258	2.255	0.58432	D	0.999994	D;D	0.71674	0.998;0.998	D;D	0.65684	0.916;0.937	T	0.49021	-0.8982	10	0.51188	T	0.08	.	7.0474	0.25052	0.0:0.0:0.7297:0.2703	.	889;889	A6H8M8;P0C0L4	.;CO4A_HUMAN	M	889	ENSP00000396688:V889M;ENSP00000420212:V889M	ENSP00000396688:V889M	V	+	1	0	C4A	32070326	0.999000	0.42202	0.872000	0.34217	0.722000	0.41435	2.548000	0.45794	1.846000	0.53633	0.121000	0.15741	GTG	.		0.687	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293		A	31962347	G	A	31962347	3	1	160	1	0	0	0	0	1	0	0	0	2253	1261	44	2	2747	2	C4A	6	31962347	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	4541754	31962347	139152720	35	14530											
SYNGAP1	8831	broad.mit.edu;bcgsc.ca	37	chr6	33393615	33393615	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccggaggagcgagtccaGtcgcaacaaactgctgagac	12	4	14	11	3	0	1	0	1	0	1	2	6	1	4	2	3	4	2	2	3	2	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:33393615G>C	ENST00000418600.2	+	3	331	c.230G>C	c.(229-231)aGt>aCt	p.S77T	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.S77T	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	77					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						AGCGAGTCCAGTCGCAACAAA	0.682																																					p.S77T													.	SYNGAP1-48	0			c.G230C						.						54	46	48					6																	33393615		2203	4300	6503	SO:0001583	missense	8831	exon3			AGTCCAGTCGCAA	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"synaptic Ras GTPase activating protein 1 homolog (rat)"			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.230G>C	6.37:g.33393615G>C	ENSP00000403636:p.Ser77Thr	Somatic	143	1		WXS	Illumina HiSeq	Phase_I	160	48	NM_006772	0	0	0	0	0	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	g	2.923	-0.222722	0.06061	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372	T;T	0.16324	2.35;2.44	2.75	2.75	0.32379	Pleckstrin homology domain (1);	0.269330	0.27787	U	0.017849	T	0.01695	0.0054	N	0.12182	0.205	0.25547	N	0.987124	B;B;B	0.26445	0.092;0.149;0.0	B;B;B	0.17098	0.007;0.017;0.0	T	0.45527	-0.9255	10	0.02654	T	1	.	5.7389	0.18081	0.1499:0.0:0.8501:0.0	.	77;77;77	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	T	77	ENSP00000293748:S77T;ENSP00000403636:S77T	ENSP00000293748:S77T	S	+	2	0	SYNGAP1	33501593	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.565000	0.45939	1.874000	0.54306	0.281000	0.19383	AGT	.		0.682	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		C	33393615	G	C	33393615	3	2	160	1	0	0	0	0	1	0	0	0	15479	1029	36	4	240	4	SYNGAP1	6	33393615	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	1431268	33393615	137721452	36	14531											
CASP8AP2	9994	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	90573643	90573643	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaaatgataattcagatTattgtggtatttctgaaggt	15	15	9	2	0	2	4	1	2	1	2	2	4	2	4	0	2	0	1	0	2	6	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:90573643T>C	ENST00000551025.1	+	0	3652									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TAATTCAGATTATTGTGGTAT	0.403																																					p.Y739H	Colon(187;1656 2025 17045 31481 39901)	.											.	CASP8AP2-24	0			c.T2215C						.						69	67	67					6																	90573643		1866	4106	5972			9994	exon7			TCAGATTATTGTG	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90573643T>C		Somatic	113	0		WXS	Illumina HiSeq	Phase_I	68	5	NM_001137667	0	0	0	0	0		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.		0.403	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		C	90573643	T	C	90573643	1	2	160	0	1	0	0	0	0	0	0	0	2684	1754	61	3		3	CASP8AP2	6	90573643	RNA	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	57180028	90573643	80541424	37	14532											
LAMA2	3908	bcgsc.ca	37	chr6	129573388	129573388	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacagtgcttgcgaatttgAagagagtcctcctacaaatc	12	11	9	9	1	0	3	0	2	0	1	3	5	2	3	2	0	3	1	2	0	4	3	rs202247790		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:129573388A>G	ENST00000421865.2	+	14	2093	c.2044A>G	c.(2044-2046)Aag>Gag	p.K682E		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	682	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TGCGAATTTGAAGAGAGTCCT	0.393																																					p.K682E													.	LAMA2-162	0			c.A2044G						.						96	91	93					6																	129573388		2203	4300	6503	SO:0001583	missense	3908	exon14			AATTTGAAGAGAG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"Laminins"	6482	protein-coding gene	gene with protein product	"merosin", "congenital muscular dystrophy"	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.2044A>G	6.37:g.129573388A>G	ENSP00000400365:p.Lys682Glu	Somatic	80	0		WXS	Illumina HiSeq	Phase_1	56	4	NM_000426	0	0	0	0	0	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	A	5.993	0.367107	0.11352	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.32988	1.43	5.53	-3.2	0.05156	Laminin B type IV (2);Laminin B, subgroup (1);	0.195277	0.44483	N	0.000442	T	0.03053	0.0090	N	0.16266	0.395	0.09310	N	0.999995	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.40098	-0.9581	10	0.02654	T	1	.	7.0643	0.25143	0.5637:0.1131:0.3232:0.0	.	682;682	A6NF00;P24043	.;LAMA2_HUMAN	E	682	ENSP00000400365:K682E	ENSP00000346769:K682E	K	+	1	0	LAMA2	129615081	0.996000	0.38824	0.003000	0.11579	0.784000	0.44337	1.676000	0.37565	-0.713000	0.04981	-0.334000	0.08254	AAG	.		0.393	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			G	129573388	A	G	129573388	3	3	160	1	0	0	0	0	1	0	0	0	8627	247	9	3	2098	3	LAMA2	6	129573388	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	38999745	129573388	41541679	38	14533											
REPS1	85021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	139262487	139262487	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttacctgctgaatcttccaAatcaatcagtttgggcatta	11	14	6	10	0	3	1	2	1	1	0	4	1	4	1	2	1	2	3	2	1	5	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:139262487A>T	ENST00000450536.2	-	8	1694	c.1120T>A	c.(1120-1122)Ttg>Atg	p.L374M	REPS1_ENST00000258062.5_Missense_Mutation_p.L374M|REPS1_ENST00000415951.2_Missense_Mutation_p.L374M|REPS1_ENST00000367663.4_Missense_Mutation_p.L374M|REPS1_ENST00000409812.2_Missense_Mutation_p.L374M			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	374	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		GAATCTTCCAAATCAATCAGT	0.388																																					p.L374M		.											.	REPS1-522	0			c.T1120A						.						167	170	169					6																	139262487		2203	4300	6503	SO:0001583	missense	85021	exon8			CTTCCAAATCAAT		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"EF-hand domain containing"	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1120T>A	6.37:g.139262487A>T	ENSP00000392065:p.Leu374Met	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	64	12	NM_001128617	0	0	4	5	1	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	37		.	.	.	.	.	.	.	.	.	.	A	18.47	3.630297	0.67015	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.35789	1.31;1.35;1.33;1.34;1.29;1.36	5.91	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.23014	0.0556	N	0.08118	0	0.80722	D	1	D;D;D;P;P	0.89917	1.0;1.0;1.0;0.82;0.872	D;D;D;P;B	0.80764	0.992;0.981;0.994;0.451;0.393	T	0.23904	-1.0175	10	0.45353	T	0.12	-6.2792	8.9289	0.35657	0.8584:0.0:0.1416:0.0	.	374;322;374;374;374	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	M	374;374;360;374;374;374;322	ENSP00000392065:L374M;ENSP00000356635:L374M;ENSP00000434251:L360M;ENSP00000386699:L374M;ENSP00000258062:L374M;ENSP00000397941:L374M	ENSP00000258062:L374M	L	-	1	2	REPS1	139304180	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.783000	0.47766	1.074000	0.40909	0.533000	0.62120	TTG	.		0.388	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			T	139262487	A	T	139262487	3	4	160	1	0	0	0	0	1	0	0	0	13260	11	1	5	1322	5	REPS1	6	139262487	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	9689099	139262487	31852580	39	14534											
PDE1C	5137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	31862809	31862809	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcggggcacttccctctgaaCcagaggtcttgacacctgat	8	10	10	13	1	2	4	0	3	2	1	4	4	3	4	3	3	1	1	3	3	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr7:31862809C>A	ENST00000396191.1	-	14	1915	c.1460G>T	c.(1459-1461)gGt>gTt	p.G487V	PDE1C_ENST00000321453.7_Missense_Mutation_p.G487V|PDE1C_ENST00000479980.1_5'Flank|PDE1C_ENST00000396182.2_Missense_Mutation_p.G487V|PDE1C_ENST00000396193.1_Missense_Mutation_p.G547V|PDE1C_ENST00000396184.3_Missense_Mutation_p.G487V	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	487	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TCCCTCTGAACCAGAGGTCTT	0.443																																					p.G547V		.											.	PDE1C-94	0			c.G1640T						.						107	96	100					7																	31862809		2203	4300	6503	SO:0001583	missense	5137	exon15			TCTGAACCAGAGG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"Phosphodiesterases"	8776	protein-coding gene	gene with protein product		602987	"phosphodiesterase 1C, calmodulin-dependent (70kD)"			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1460G>T	7.37:g.31862809C>A	ENSP00000379494:p.Gly487Val	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	117	38	NM_001191058	0	0	0	0	0	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.415990	0.62511	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.63;-0.63	5.91	5.91	0.95273	.	0.634852	0.16753	N	0.200964	T	0.76730	0.4028	L	0.29908	0.895	0.80722	D	1	B;B;D	0.65815	0.081;0.23;0.995	B;B;P	0.60949	0.056;0.082;0.881	T	0.76537	-0.2923	10	0.54805	T	0.06	.	19.9003	0.96983	0.0:1.0:0.0:0.0	.	487;547;487	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	V	547;487;487;487;487	ENSP00000379496:G547V;ENSP00000379494:G487V;ENSP00000318105:G487V;ENSP00000379487:G487V;ENSP00000379485:G487V	ENSP00000318105:G487V	G	-	2	0	PDE1C	31829334	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.060000	0.76692	2.808000	0.96608	0.655000	0.94253	GGT	.		0.443	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			A	31862809	C	A	31862809	3	1	160	1	0	0	0	0	1	0	0	0	11661	507	18	4	460	4	PDE1C	7	31862809	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		31862809	127275854	40	14535											
CSMD1	64478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	2824167	2824167	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgagccctgaggtcttgtAgccttcccagcaggcataga	9	9	11	12	0	1	3	0	2	1	1	2	3	2	3	3	2	3	3	3	2	2	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:2824167A>G	ENST00000520002.1	-	59	9583	c.9028T>C	c.(9028-9030)Tac>Cac	p.Y3010H	CSMD1_ENST00000602557.1_Missense_Mutation_p.Y3010H|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000537824.1_Missense_Mutation_p.Y3009H|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3010	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GAGGTCTTGTAGCCTTCCCAG	0.547																																					p.Y3009H		.											.	CSMD1-86	0			c.T9025C						.						72	76	75					8																	2824167		2071	4221	6292	SO:0001583	missense	64478	exon58			TCTTGTAGCCTTC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14026	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 24"	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9028T>C	8.37:g.2824167A>G	ENSP00000430733:p.Tyr3010His	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	122	50	NM_033225	0	0	0	0	0	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.86|18.86	3.714217|3.714217	0.68730|0.68730	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|T;T	.|0.40756	.|1.02;1.02	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.079141	.|0.53938	.|D	.|0.000060	T|T	0.69495|0.69495	0.3117|0.3117	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.83275	.|0.996;0.992	T|T	0.76113|0.76113	-0.3078|-0.3078	5|10	.|0.87932	.|D	.|0	.|.	15.5456|15.5456	0.76097|0.76097	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|3010;3010	.|E5RIG2;Q96PZ7	.|.;CSMD1_HUMAN	P|H	2426|3010;2871;3009	.|ENSP00000430733:Y3010H;ENSP00000441462:Y3009H	.|ENSP00000320445:Y2871H	L|Y	-|-	2|1	0|0	CSMD1|CSMD1	2811574|2811574	1.000000|1.000000	0.71417|0.71417	0.807000|0.807000	0.32361|0.32361	0.329000|0.329000	0.28539|0.28539	9.116000|9.116000	0.94341|0.94341	2.068000|2.068000	0.61886|0.61886	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.		0.547	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2824167	A	G	2824167	3	3	160	1	0	0	0	0	1	0	0	0	3950	420	15	3	1721	3	CSMD1	8	2824167	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10		2824167	143539855	41	14536											
NEFL	4747	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr8	24813800	24813800	+	RNA	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgaggtcgttgctgatggcgGctacctggctcaggtcgagg	5	10	17	9	3	1	2	1	2	0	0	3	3	1	2	1	6	2	4	1	6	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:24813800G>A	ENST00000221169.5	-	0	824				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		GCTGATGGCGGCTACCTGGCT	0.637																																					p.A77V		.											.	NEFL-24	0			c.C230T						.						30	33	32					8																	24813800		2172	4272	6444			4747	exon1			ATGGCGGCTACCT		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24813800G>A		Somatic	174	0		WXS	Illumina HiSeq	Phase_I	173	13	NM_006158	0	0	62	66	4	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	37																																																																																				.		0.637	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24813800	G	A	24813800	1	1	160	0	1	0	0	0	0	0	0	0	10341	1203	42	2		2	NEFL	8	24813800	RNA	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	21989633	24813800	121550222	42	14537											
MATN2	4147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	99039960	99039960	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acccaaggagaaggggccagGcccctttccacaagggtgcc	10	4	13	14	0	0	1	0	0	0	1	1	2	1	1	6	5	1	0	6	5	3	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:99039960G>T	ENST00000520016.1	+	13	2383	c.2259G>T	c.(2257-2259)agG>agT	p.R753S	MATN2_ENST00000524308.1_Missense_Mutation_p.R712S|MATN2_ENST00000522025.2_Missense_Mutation_p.R469S|MATN2_ENST00000521689.1_Missense_Mutation_p.R753S|RPL30_ENST00000518164.1_Intron|MATN2_ENST00000254898.5_Missense_Mutation_p.R753S			O00339	MATN2_HUMAN	matrilin 2	753	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AAGGGGCCAGGCCCCTTTCCA	0.562																																					p.R753S		.											.	MATN2-24	0			c.G2259T						.						41	42	42					8																	99039960		1887	4109	5996	SO:0001583	missense	4147	exon14			GGCCAGGCCCCTT	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.2259G>T	8.37:g.99039960G>T	ENSP00000430487:p.Arg753Ser	Somatic	124	0		WXS	Illumina HiSeq	Phase_I	137	52	NM_002380	0	0	6	13	7	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.65|18.65|18.65	3.670245|3.670245|3.670245	0.67814|0.67814|0.67814	.|.|.	.|.|.	ENSG00000132561|ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000519582|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|.|D;D;D;D;D	.|.|0.87571	.|.|-2.27;-2.27;-2.27;-2.27;-2.27	5.24|5.24|5.24	4.34|4.34|4.34	0.51931|0.51931|0.51931	.|.|von Willebrand factor, type A (3);	.|.|0.000000	.|.|0.64402	.|.|D	.|.|0.000002	D|D|D	0.94548|0.94548|0.94548	0.8244|0.8244|0.8244	H|H|H	0.95187|0.95187|0.95187	3.635|3.635|3.635	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0	.|.|D;D;D	.|.|0.91635	.|.|0.999;0.999;0.999	D|D|D	0.94271|0.94271|0.94271	0.7511|0.7511|0.7511	5|5|10	.|.|0.87932	.|.|D	.|.|0	-23.5915|-23.5915|-23.5915	8.2515|8.2515|8.2515	0.31724|0.31724|0.31724	0.2672:0.0:0.7328:0.0|0.2672:0.0:0.7328:0.0|0.2672:0.0:0.7328:0.0	.|.|.	.|.|753;753;753	.|.|E9PF03;O00339-2;O00339	.|.|.;.;MATN2_HUMAN	S|V|S	536|9|753;753;712;712;469;753	.|.|ENSP00000429977:R753S;ENSP00000254898:R753S;ENSP00000430221:R712S;ENSP00000429010:R469S;ENSP00000430487:R753S	.|.|ENSP00000254898:R753S	A|G|R	+|+|+	1|2|3	0|0|2	MATN2|MATN2|MATN2	99109136|99109136|99109136	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.934000|0.934000|0.934000	0.57294|0.57294|0.57294	3.500000|3.500000|3.500000	0.53318|0.53318|0.53318	1.272000|1.272000|1.272000	0.44329|0.44329|0.44329	0.555000|0.555000|0.555000	0.69702|0.69702|0.69702	GCC|GGC|AGG	.		0.562	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99039960	G	T	99039960	3	4	160	1	0	0	0	0	1	0	0	0	9359	1194	42	4	2309	4	MATN2	8	99039960	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	74226160	99039960	47324062	43	14538											
GPR20	2843	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	142367789	142367789	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggcccgggtgcggcagcAgaagacgtacagcgccagcc	8	4	15	14	4	0	2	0	0	0	2	0	2	0	2	3	3	5	3	3	3	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:142367789A>T	ENST00000377741.3	-	2	325	c.235T>A	c.(235-237)Tgc>Agc	p.C79S	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	79					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			GTGCGGCAGCAGAAGACGTAC	0.647																																					p.C79S													.	GPR20-91	0			c.T235A						.						86	86	86					8																	142367789		2203	4300	6503	SO:0001583	missense	2843	exon2			GGCAGCAGAAGAC	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"GPCR / Class A : Orphans"	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.235T>A	8.37:g.142367789A>T	ENSP00000366970:p.Cys79Ser	Somatic	103	1		WXS	Illumina HiSeq	Phase_I	158	49	NM_005293	0	0	0	0	0	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.493963	0.64186	.	.	ENSG00000204882	ENST00000377741	T	0.36520	1.25	4.62	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	0.180691	0.48767	D	0.000162	T	0.38268	0.1034	M	0.61703	1.905	0.45995	D	0.998809	P	0.42010	0.768	P	0.46026	0.501	T	0.12451	-1.0547	10	0.66056	D	0.02	-18.3354	6.7304	0.23381	0.6853:0.1674:0.0:0.1472	.	79	Q99678	GPR20_HUMAN	S	79	ENSP00000366970:C79S	ENSP00000366970:C79S	C	-	1	0	GPR20	142436971	1.000000	0.71417	0.999000	0.59377	0.714000	0.41099	1.841000	0.39240	0.131000	0.18576	0.459000	0.35465	TGC	.		0.647	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293		T	142367789	A	T	142367789	3	4	160	1	0	0	0	0	1	0	0	0	6700	188	7	5	845	5	GPR20	8	142367789	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	43327829	142367789	3996233	44	14539											
PLEC	5339	hgsc.bcm.edu	37	chr8	145024821	145024825	+	Frame_Shift_Del	DEL	CACCT	CACCT	-																															atcacgccctcgcggaagagCacctcatagatggcccgcag																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CACCT	CACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:145024821_145024825delCACCT	ENST00000322810.4	-	1	219_223	c.50_54delAGGTG	c.(49-54)gaggtgfs	p.EV17fs	PLEC_ENST00000354958.2_Intron|PLEC_ENST00000356346.3_Intron|PLEC_ENST00000436759.2_Intron|PLEC_ENST00000527096.1_Intron	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	17	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CGCGGAAGAGCACCTCATAGATGGC	0.683																																					p.17_18del		.											.	PLEC-141	0			c.50_54del						.																																			SO:0001589	frameshift_variant	5339	exon1			.	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"plectin 1, intermediate filament binding protein, 500kD", "epidermolysis bullosa simplex 1 (Ogna)", "plectin 1, intermediate filament binding protein 500kDa"	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.50_54delAGGTG	8.37:g.145024821_145024825delCACCT	ENSP00000323856:p.Glu17fs	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	46	17	NM_201380	0	0	0	0	0	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Frame_Shift_Del	DEL	ENST00000322810.4	37	CCDS43772.1																																																																																			.		0.683	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		-	145024825	CACCT	-	145024821	7	5	160	1	0	1	0	1	0	0	0	0	12078	697	25	0	14508	0	PLEC	8	145024821	Frame_Shift_Del	DEL	CACCT	TCGA-PJ-A5Z9-01A-11D-A28G-10	2657032	145024821	1339201	45	14540											
KIAA1797	54914	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	20988333	20988333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atacccttttcatttcaggcGttttgaagagaatggagtgg	10	14	11	6	1	2	2	2	1	0	1	2	4	2	3	1	3	1	1	1	3	3	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:20988333G>A	ENST00000380249.1	+	43	5273	c.4909G>A	c.(4909-4911)Gtt>Att	p.V1637I	FOCAD_ENST00000605086.1_Missense_Mutation_p.V1073I|FOCAD_ENST00000338382.6_Missense_Mutation_p.V1637I	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1637						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CATTTCAGGCGTTTTGAAGAG	0.378																																					p.V1637I		.											.	.	0			c.G4909A						.						144	133	137					9																	20988333		2203	4300	6503	SO:0001583	missense	54914	exon43			TCAGGCGTTTTGA	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"KIAA1797"	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4909G>A	9.37:g.20988333G>A	ENSP00000369599:p.Val1637Ile	Somatic	103	0		WXS	Illumina HiSeq	Phase_I	91	8	NM_017794	0	0	0	0	0	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415680	0.62511	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.52597	0.1744	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	T	0.36383	-0.9750	10	0.45353	T	0.12	-28.3855	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1637	Q5VW36	K1797_HUMAN	I	1637	ENSP00000369599:V1637I;ENSP00000344307:V1637I	ENSP00000344307:V1637I	V	+	1	0	KIAA1797	20978333	1.000000	0.71417	0.317000	0.25265	0.044000	0.14063	5.911000	0.69939	2.941000	0.99782	0.655000	0.94253	GTT	.		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20988333	G	A	20988333	3	1	160	1	0	0	0	0	1	0	0	0	8279	1145	40	1	5067	1	KIAA1797	9	20988333	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		20988333	120225098	46	14541											
TOPORS	10210	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	32541932	32541932	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaactatctctacacttaggCtccgggtcttcctttttctc	7	16	5	13	1	3	0	0	0	3	0	7	0	5	0	2	2	2	1	2	2	4	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:32541932C>T	ENST00000360538.2	-	3	2707	c.2591G>A	c.(2590-2592)aGc>aAc	p.S864N	TOPORS_ENST00000379858.1_Missense_Mutation_p.S799N	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	864	Interaction with TOP1.|Interaction with UBE2I.|Lys-rich.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TACACTTAGGCTCCGGGTCTT	0.358																																					p.S864N		.											.	TOPORS-230	0			c.G2591A						.						203	207	205					9																	32541932		2203	4300	6503	SO:0001583	missense	10210	exon3			CTTAGGCTCCGGG	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"RING-type (C3HC4) zinc fingers"	21653	protein-coding gene	gene with protein product		609507	"retinitis pigmentosa 31 (autosomal dominant)", "topoisomerase I binding, arginine/serine-rich"	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2591G>A	9.37:g.32541932C>T	ENSP00000353735:p.Ser864Asn	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	38	11	NM_005802	0	0	7	8	1	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202662	0.58234	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.34072	1.38;1.44	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000011	T	0.52468	0.1736	L	0.32530	0.975	0.39310	D	0.965069	D	0.89917	1.0	D	0.83275	0.996	T	0.53982	-0.8361	10	0.87932	D	0	-9.414	19.0572	0.93070	0.0:1.0:0.0:0.0	.	864	Q9NS56	TOPRS_HUMAN	N	864;799	ENSP00000353735:S864N;ENSP00000369187:S799N	ENSP00000353735:S864N	S	-	2	0	TOPORS	32531932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.479000	0.60236	2.803000	0.96430	0.650000	0.86243	AGC	.		0.358	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32541932	C	T	32541932	3	4	160	1	0	0	0	0	1	0	0	0	16403	797	28	2	550	2	TOPORS	9	32541932	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	11553599	32541932	108671499	47	14542											
BAT2L1	84726	broad.mit.edu	37	chr9	134351684	134351685	+	Frame_Shift_Ins	INS	-	-	G																															cagcgagcggcgggagcggcINSgggaaggccctgggtccgag																								rs376130854		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:134351684_134351685insG	ENST00000357304.4	+	15	4223_4224	c.4168_4169insG	c.(4168-4170)cggfs	p.R1390fs	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1390							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCGGGAGCGGCGGGAAGGCCCT	0.649											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R1390fs													.	PRRC2B-24	0			c.4168_4169insG						.			25,3565		0,25,1770						5.9	1			12	73,7729		0,73,3828	no	frameshift	PRRC2B	NM_013318.3		0,98,5598	A1A1,A1R,RR		0.9357,0.6964,0.8603				98,11294				SO:0001589	frameshift_variant	84726	exon15			GAGCGGCGGGAAG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1"	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4171dupG	9.37:g.134351687_134351687dupG	ENSP00000349856:p.Arg1390fs	Somatic	45	0	1610	WXS	Illumina HiSeq	Phase_I	88	13	NM_013318	0	0	0	0	0	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Frame_Shift_Ins	INS	ENST00000357304.4	37	CCDS48044.1																																																																																			.		0.649	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	134351685	-	G	134351684	7	5	160	1	0	1	1	0	0	0	0	0	1321	759	27	0	4226	0	BAT2L1	9	134351684	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z9-01A-11D-A28G-10	101809752	134351684	6861747	48	14543											
FCN2	2220	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	137777085	137777085	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccccgggttcccttcccagGcccgcgtacctgcaaggacc	5	7	10	19	3	0	0	0	0	0	0	3	1	3	1	7	3	2	3	7	3	2	3	rs529779645	byFrequency	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:137777085G>T	ENST00000291744.6	+	5	312	c.302G>T	c.(301-303)gGc>gTc	p.G101V	FCN2_ENST00000350339.2_Splice_Site_p.G63V	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	101	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CCCTTCCCAGGCCCGCGTACC	0.667																																					p.G101V		.											.	FCN2-153	0			c.G302T						.						53	52	52					9																	137777085		2203	4300	6503	SO:0001630	splice_region_variant	2220	exon5			TCCCAGGCCCGCG	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"Fibrinogen C domain containing"	3624	protein-coding gene	gene with protein product	"hucolin", "collagen/fibrinogen domain-containing protein 2", "ficolin B", "serum lectin p35", "L-ficolin"	601624	"ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.302-1G>T	9.37:g.137777085G>T		Somatic	54	0		WXS	Illumina HiSeq	Phase_I	45	16	NM_004108	0	0	0	0	0	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	6.759	0.508916	0.12883	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.19394	2.15;2.15	3.59	2.66	0.31614	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (3);	.	.	.	.	T	0.40815	0.1132	M	0.89353	3.025	0.30440	N	0.776243	P;P	0.49696	0.927;0.763	P;P	0.51701	0.462;0.677	T	0.48258	-0.9051	8	.	.	.	.	9.7179	0.40284	0.0:0.4147:0.5853:0.0	.	63;101	Q15485-2;Q15485	.;FCN2_HUMAN	V	63;101	ENSP00000291741:G63V;ENSP00000291744:G101V	.	G	+	2	0	FCN2	136916906	0.229000	0.23729	0.063000	0.19743	0.018000	0.09664	0.409000	0.21082	0.444000	0.26612	0.462000	0.41574	GGC	.		0.667	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	Missense_Mutation	T	137777085	G	T	137777085	5	4	160	1	0	0	0	0	0	0	1	0	5811	1217	42	4	320	4	FCN2	9	137777085	Splice_Site	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	3425401	137777085	3436346	49	14544											
KCNT1	402381	hgsc.bcm.edu	37	chr9	138594140	138594140	+	5'Flank	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcgcggaccccggggggCgtctgccgggaggcgcgcgg	2	2	24	13	8	1	0	0	0	1	0	1	2	1	2	3	9	1	0	3	9	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:138594140C>G	ENST00000298466.5	-	0	0				KCNT1_ENST00000487664.1_Silent_p.G12G|SOHLH1_ENST00000425225.1_5'Flank|KCNT1_ENST00000298480.5_Silent_p.G12G|KCNT1_ENST00000371757.2_Silent_p.G12G	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		ccccggggggcgtctgccggg	0.731																																					p.G12G		.											.	KCNT1-137	0			c.C36G						.						12	16	15					9																	138594140		2168	4247	6415	SO:0001631	upstream_gene_variant	57582	exon1			GGGGGGCGTCTGC	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"Basic helix-loop-helix proteins"	27845	protein-coding gene	gene with protein product	"spermatogenesis associated 27"	610224	"chromosome 9 open reading frame 157"	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915		9.37:g.138594140C>G	Exception_encountered	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	23	14	NM_001272003	0	0	0	0	0	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	37	CCDS35174.1																																																																																			.		0.731	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		G	138594140	C	G	138594140	1	3	160	0	1	0	0	0	0	0	0	0	8112	755	27	4		4	KCNT1	9	138594140	5'Flank	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	817055	138594140	2619291	50	14545											
DHTKD1	55526	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	12160902	12160902	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacagcaagagatgagcaaaTacaaacatgttaaaggtaag	20	7	9	5	0	0	2	0	1	0	1	0	3	0	2	0	1	5	4	0	1	8	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:12160902T>C	ENST00000263035.4	+	15	2619	c.2557T>C	c.(2557-2559)Tac>Cac	p.Y853H	U6_ENST00000606801.1_RNA	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	853					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			GATGAGCAAATACAAACATGT	0.433																																					p.Y853H													.	DHTKD1-515	0			c.T2557C						.						124	119	121					10																	12160902		2203	4300	6503	SO:0001583	missense	55526	exon15			AGCAAATACAAAC	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2557T>C	10.37:g.12160902T>C	ENSP00000263035:p.Tyr853His	Somatic	65	1		WXS	Illumina HiSeq	Phase_I	43	16	NM_018706	0	0	6	10	4	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049542	0.75846	.	.	ENSG00000181192	ENST00000263035	T	0.09538	2.97	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.35451	0.0932	M	0.92169	3.28	0.80722	D	1	D	0.57571	0.98	P	0.54856	0.762	T	0.51466	-0.8702	10	0.87932	D	0	-7.7955	14.7709	0.69679	0.0:0.0:0.0:1.0	.	853	Q96HY7	DHTK1_HUMAN	H	853	ENSP00000263035:Y853H	ENSP00000263035:Y853H	Y	+	1	0	DHTKD1	12200908	1.000000	0.71417	0.699000	0.30290	0.831000	0.47069	7.619000	0.83057	1.955000	0.56771	0.379000	0.24179	TAC	.		0.433	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		C	12160902	T	C	12160902	3	2	160	1	0	0	0	0	1	0	0	0	4511	1406	49	3	2615	3	DHTKD1	10	12160902	Missense_Mutation	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10		12160902	123373845	51	14546											
PTPLA	9200	broad.mit.edu	37	chr10	17636308	17636308	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattcctgttttcttcacaTgcggcaaggcagcgtatatt	9	14	8	10	2	2	0	1	0	1	0	3	0	3	0	1	2	2	4	1	2	3	7			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:17636308T>A	ENST00000361271.3	-	6	717	c.680A>T	c.(679-681)cAt>cTt	p.H227L		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	227			H -> Y (in dbSNP:rs1053926). {ECO:0000269|PubMed:10644438, ECO:0000269|PubMed:11054553}.		fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						TTTCTTCACATGCGGCAAGGC	0.323																																					p.H227L													.	PTPLA-226	0			c.A680T						.						69	70	70					10																	17636308		2203	4294	6497	SO:0001583	missense	9200	exon6			TTCACATGCGGCA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.680A>T	10.37:g.17636308T>A	ENSP00000355308:p.His227Leu	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	106	3	NM_014241	0	0	8	8	0	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.540937	0.45280	.	.	ENSG00000165996	ENST00000361271	T	0.28255	1.62	5.72	5.72	0.89469	.	0.165083	0.56097	D	0.000036	T	0.26702	0.0653	L	0.31752	0.955	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.02877	-1.1099	10	0.62326	D	0.03	-17.2091	16.2962	0.82776	0.0:0.0:0.0:1.0	.	227	B0YJ81	HACD1_HUMAN	L	227	ENSP00000355308:H227L	ENSP00000355308:H227L	H	-	2	0	PTPLA	17676314	0.998000	0.40836	0.703000	0.30354	0.544000	0.35116	2.640000	0.46579	2.304000	0.77564	0.528000	0.53228	CAT	.		0.323	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		A	17636308	T	A	17636308	3	1	160	1	0	0	0	0	1	0	0	0	12804	1464	51	5	194	5	PTPLA	10	17636308	Missense_Mutation	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	5475406	17636308	117898439	52	14547											
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	61829169	61829169	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcctgatgagactttcaCtgggttatctttctctgtgg	5	19	9	8	0	3	2	1	2	2	1	5	3	4	2	1	2	0	1	1	2	1	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:61829169C>T	ENST00000280772.2	-	37	11661	c.11470G>A	c.(11470-11472)Gtg>Atg	p.V3824M	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3824					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GAGACTTTCACTGGGTTATCT	0.378																																					p.V3824M		.											.	ANK3-107	0			c.G11470A						.						241	236	238					10																	61829169		2203	4300	6503	SO:0001583	missense	288	exon37			CTTTCACTGGGTT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"Ankyrin repeat domain containing"	494	protein-coding gene	gene with protein product	"ankyrin-3, node of Ranvier", "ankyrin-G"	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11470G>A	10.37:g.61829169C>T	ENSP00000280772:p.Val3824Met	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	57	23	NM_020987	0	0	0	0	0	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048577	0.36181	.	.	ENSG00000151150	ENST00000280772	T	0.43688	0.94	4.99	3.09	0.35607	.	0.226364	0.22221	N	0.062959	T	0.22666	0.0547	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04537	-1.0944	10	0.45353	T	0.12	.	5.5172	0.16914	0.0:0.6224:0.1464:0.2312	.	3824	Q12955	ANK3_HUMAN	M	3824	ENSP00000280772:V3824M	ENSP00000280772:V3824M	V	-	1	0	ANK3	61499175	0.975000	0.34042	1.000000	0.80357	0.979000	0.70002	0.968000	0.29357	0.581000	0.29539	0.650000	0.86243	GTG	.		0.378	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61829169	C	T	61829169	3	4	160	1	0	0	0	0	1	0	0	0	622	565	20	2	2004	2	ANK3	10	61829169	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	44192861	61829169	73705578	53	14548											
MMRN2	79812	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	88703695	88703695	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctcctggaagtcagccctGgccacggcactgtcctggac	7	7	12	15	1	1	0	1	0	0	0	3	2	3	2	4	4	2	2	4	4	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:88703695G>A	ENST00000372027.5	-	6	1167	c.846C>T	c.(844-846)gcC>gcT	p.A282A	MMRN2_ENST00000488950.1_5'UTR	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	282					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						AGTCAGCCCTGGCCACGGCAC	0.602																																					p.A282A		.											.	MMRN2-153	0			c.C846T						.						62	58	59					10																	88703695		2203	4300	6503	SO:0001819	synonymous_variant	79812	exon6			AGCCCTGGCCACG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"EMI domain containing"	19888	protein-coding gene	gene with protein product		608925	"elastin microfibril interfacer 3"	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.846C>T	10.37:g.88703695G>A		Somatic	109	0		WXS	Illumina HiSeq	Phase_I	89	41	NM_024756	0	0	0	0	0	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	37	CCDS7379.1																																																																																			.		0.602	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756		A	88703695	G	A	88703695	2	1	160	1	0	0	0	0	0	0	0	1	9696	1335	47	2		2	MMRN2	10	88703695	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	26874526	88703695	46831052	54	14549											
RRP12	23223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	99160073	99160073	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccctacctccttgtgggCagccgagttggactcccaga	6	8	11	16	2	0	1	0	0	0	1	2	3	2	2	6	2	2	2	6	2	1	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:99160073C>T	ENST00000370992.4	-	2	469	c.358G>A	c.(358-360)Gcc>Acc	p.A120T	RRP12_ENST00000414986.1_Missense_Mutation_p.A120T|RP11-452K12.7_ENST00000422848.1_RNA|RRP12_ENST00000315563.6_Missense_Mutation_p.A120T	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	120						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TCCTTGTGGGCAGCCGAGTTG	0.582																																					p.A120T		.											.	RRP12-92	0			c.G358A						.						119	119	119					10																	99160073		2203	4300	6503	SO:0001583	missense	23223	exon2			TGTGGGCAGCCGA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"KIAA0690"	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.358G>A	10.37:g.99160073C>T	ENSP00000360031:p.Ala120Thr	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	75	22	NM_001145114	0	0	0	0	0	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.406058	0.42715	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986	T;T;T	0.64260	-0.09;1.52;1.51	5.7	4.8	0.61643	Armadillo-type fold (1);	0.208574	0.49916	D	0.000127	T	0.51295	0.1666	L	0.40543	1.245	0.80722	D	1	P;P;B	0.45715	0.787;0.865;0.001	B;B;B	0.39503	0.158;0.301;0.005	T	0.48246	-0.9052	10	0.13108	T	0.6	-11.1652	15.9236	0.79592	0.1366:0.8634:0.0:0.0	.	120;120;120	E9PCK7;Q5JTH9-2;Q5JTH9	.;.;RRP12_HUMAN	T	120	ENSP00000360031:A120T;ENSP00000324315:A120T;ENSP00000414863:A120T	ENSP00000324315:A120T	A	-	1	0	RRP12	99150063	0.992000	0.36948	0.983000	0.44433	0.965000	0.64279	3.045000	0.49838	1.429000	0.47314	-0.361000	0.07541	GCC	.		0.582	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99160073	C	T	99160073	3	4	160	1	0	0	0	0	1	0	0	0	13718	710	25	2	3667	2	RRP12	10	99160073	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	10456378	99160073	36374674	55	14550											
STK32C	282974	hgsc.bcm.edu	37	chr10	134036392	134036392	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acgaagcccggctccaccctCttctcgctcaggtggtccca	6	8	9	18	3	3	0	1	0	2	0	6	1	5	0	4	3	1	2	4	3	1	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:134036392C>T	ENST00000368622.1	-	9	1122	c.741G>A	c.(739-741)aaG>aaA	p.K247K	STK32C_ENST00000368625.4_Silent_p.K377K					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		GCTCCACCCTCTTCTCGCTCA	0.711																																					p.K364K		.											.	STK32C-1083	0			c.G1092A						.						20	22	21					10																	134036392		2183	4281	6464	SO:0001819	synonymous_variant	282974	exon9			CACCCTCTTCTCG	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.741G>A	10.37:g.134036392C>T		Somatic	2	0		WXS	Illumina HiSeq	Phase_I	51	19	NM_173575	0	0	3	3	0		Silent	SNP	ENST00000368622.1	37																																																																																				.		0.711	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575		T	134036392	C	T	134036392	2	4	160	1	0	0	0	0	0	0	0	1	15331	912	32	2		2	STK32C	10	134036392	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	34876319	134036392	1498355	56	14551											
SLC22A18	5002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	2937874	2937874	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttcagtgcccggccatcctgGctgccctggccaccctcctg	3	9	10	19	1	1	0	1	0	0	0	3	0	3	0	7	3	2	1	7	3	0	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr11:2937874G>T	ENST00000380574.1	+	6	990	c.559G>T	c.(559-561)Gct>Tct	p.A187S	SLC22A18_ENST00000312221.5_Missense_Mutation_p.A187S|SLC22A18_ENST00000449793.2_Missense_Mutation_p.A89S|SLC22A18_ENST00000347936.2_Missense_Mutation_p.A187S			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	187					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		GGCCATCCTGGCTGCCCTGGC	0.687																																					p.A187S		.											.	SLC22A18-92	0			c.G559T						.						41	44	43					11																	2937874		2202	4299	6501	SO:0001583	missense	5002	exon6			ATCCTGGCTGCCC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"Solute carriers"	10964	protein-coding gene	gene with protein product		602631	"solute carrier family 22 (organic cation transporter), member 1-like"	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.559G>T	11.37:g.2937874G>T	ENSP00000369948:p.Ala187Ser	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	124	50	NM_002555	0	0	36	67	31	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.451570	0.43531	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574	T;T;T;T	0.81163	0.34;0.34;-1.46;0.34	3.77	2.8	0.32819	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.460037	0.20295	N	0.095157	D	0.84316	0.5445	M	0.62723	1.935	0.09310	N	1	D;D	0.59357	0.97;0.985	P;P	0.61070	0.681;0.883	T	0.74343	-0.3696	10	0.59425	D	0.04	-12.6812	8.7536	0.34633	0.0:0.0:0.7726:0.2273	.	89;187	E9PRM7;Q96BI1	.;S22AI_HUMAN	S	187;187;89;187	ENSP00000307859:A187S;ENSP00000311139:A187S;ENSP00000392072:A89S;ENSP00000369948:A187S	ENSP00000311139:A187S	A	+	1	0	SLC22A18	2894450	0.031000	0.19500	0.002000	0.10522	0.012000	0.07955	1.338000	0.33873	0.814000	0.34374	0.491000	0.48974	GCT	.		0.687	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233		T	2937874	G	T	2937874	3	4	160	1	0	0	0	0	1	0	0	0	14481	1203	42	4	577	4	SLC22A18	11	2937874	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		2937874	132068642	57	14552											
PAMR1	25891	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	35454107	35454107	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatatcagaaggggcagtggGttcccagctggcacagaaca	12	6	14	9	0	1	2	1	0	0	2	2	3	2	2	1	4	2	4	1	4	3	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr11:35454107G>A	ENST00000378880.2	-	11	2405	c.1960C>T	c.(1960-1962)Ccc>Tcc	p.P654S	PAMR1_ENST00000378878.3_Missense_Mutation_p.P543S|PAMR1_ENST00000532848.1_Missense_Mutation_p.P614S|PAMR1_ENST00000278360.3_Missense_Mutation_p.P671S	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	654	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						GGGGCAGTGGGTTCCCAGCTG	0.592																																					p.P671S													.	PAMR1-70	0			c.C2011T						.						83	71	75					11																	35454107		2202	4298	6500	SO:0001583	missense	25891	exon12			CAGTGGGTTCCCA		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"regeneration-associated muscle protease"					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1960C>T	11.37:g.35454107G>A	ENSP00000368158:p.Pro654Ser	Somatic	137	1		WXS	Illumina HiSeq	Phase_I	91	46	NM_015430	0	0	0	0	0	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.779438	0.49891	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	D;D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07;-3.07	5.34	3.31	0.37934	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.101061	0.64402	D	0.000002	D	0.89458	0.6721	L	0.46157	1.445	0.45930	D	0.998768	P;P;P	0.45126	0.851;0.811;0.465	B;B;B	0.43838	0.253;0.433;0.124	D	0.89858	0.4014	10	0.87932	D	0	.	12.0084	0.53272	0.0:0.1315:0.732:0.1366	.	543;654;671	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	S	671;654;543;614;631	ENSP00000278360:P671S;ENSP00000368158:P654S;ENSP00000368156:P543S;ENSP00000433868:P614S;ENSP00000432591:P631S	ENSP00000278360:P671S	P	-	1	0	PAMR1	35410683	1.000000	0.71417	0.982000	0.44146	0.289000	0.27227	3.841000	0.55850	1.361000	0.45981	0.561000	0.74099	CCC	.		0.592	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		A	35454107	G	A	35454107	3	1	160	1	0	0	0	0	1	0	0	0	11439	1261	44	2	206	2	PAMR1	11	35454107	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	32516233	35454107	99552409	58	14553											
CLSTN3	9746	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	7295575	7295575	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agtgcctctatgcatgtcggGaggggctggactatagggat	8	10	16	7	1	1	0	0	0	1	0	2	3	1	3	1	5	2	2	1	5	3	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr12:7295575G>C	ENST00000266546.6	+	11	2101	c.1651G>C	c.(1651-1653)Gag>Cag	p.E551Q	CLSTN3_ENST00000537408.1_Missense_Mutation_p.E563Q	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	551					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						TGCATGTCGGGAGGGGCTGGA	0.602																																					p.E551Q													.	CLSTN3-153	0			c.G1651C						.						78	64	69					12																	7295575		2203	4300	6503	SO:0001583	missense	9746	exon11			TGTCGGGAGGGGC	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1651G>C	12.37:g.7295575G>C	ENSP00000266546:p.Glu551Gln	Somatic	210	2		WXS	Illumina HiSeq	Phase_I	174	101	NM_014718	0	0	16	35	19	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941192	0.92526	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.37058	1.22;1.22	5.08	5.08	0.68730	.	0.105878	0.64402	D	0.000007	T	0.63522	0.2518	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.97110	0.979;1.0	T	0.68804	-0.5312	10	0.87932	D	0	-30.0082	18.4777	0.90799	0.0:0.0:1.0:0.0	.	563;551	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	Q	551;563	ENSP00000266546:E551Q;ENSP00000440679:E563Q	ENSP00000266546:E551Q	E	+	1	0	CLSTN3	7186842	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.455000	0.97625	2.353000	0.79882	0.442000	0.29010	GAG	.		0.602	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		C	7295575	G	C	7295575	3	2	160	1	0	0	0	0	1	0	0	0	3569	1175	41	4	1693	4	CLSTN3	12	7295575	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		7295575	126556320	59	14554											
MARS	4141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	57894254	57894254	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtggctatgaggaggctcgGggtgaccagtgtgacaagtg	8	9	18	6	1	0	3	0	3	0	0	1	4	0	4	1	5	0	2	1	5	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr12:57894254G>C	ENST00000262027.5	+	10	1376	c.1242G>C	c.(1240-1242)cgG>cgC	p.R414R	MARS_ENST00000315473.5_Silent_p.R180R|MARS_ENST00000447721.2_3'UTR	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	414					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	AGGAGGCTCGGGGTGACCAGT	0.562																																					p.R414R		.											.	MARS-654	0			c.G1242C						.						147	115	126					12																	57894254		2203	4300	6503	SO:0001819	synonymous_variant	4141	exon10			GGCTCGGGGTGAC	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1242G>C	12.37:g.57894254G>C		Somatic	213	0		WXS	Illumina HiSeq	Phase_I	187	44	NM_004990	0	0	28	40	12	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	37	CCDS8942.1																																																																																			.		0.562	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		C	57894254	G	C	57894254	2	2	160	1	0	0	0	0	0	0	0	1	9341	1219	43	4		4	MARS	12	57894254	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	50598679	57894254	75957641	60	14555											
NBEA	26960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	35770159	35770159	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaattagaaacaagtacaGgccctgatgccatgagtgaa	16	7	10	8	0	0	5	0	3	0	2	0	5	0	5	2	1	3	1	2	1	6	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr13:35770159G>T	ENST00000400445.3	+	31	5620	c.5086G>T	c.(5086-5088)Ggc>Tgc	p.G1696C	NBEA_ENST00000540320.1_Missense_Mutation_p.G1696C|NBEA_ENST00000379939.2_Missense_Mutation_p.G1693C|NBEA_ENST00000310336.4_Missense_Mutation_p.G1696C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1696					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AACAAGTACAGGCCCTGATGC	0.433																																					p.G1696C		.											.	NBEA-144	0			c.G5086T						.						79	78	78					13																	35770159		1906	4130	6036	SO:0001583	missense	26960	exon31			AGTACAGGCCCTG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"A-kinase anchor proteins", "WD repeat domain containing"	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5086G>T	13.37:g.35770159G>T	ENSP00000383295:p.Gly1696Cys	Somatic	100	0		WXS	Illumina HiSeq	Phase_I	111	57	NM_015678	0	0	0	0	0	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376162	0.82682	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.76688	0.4022	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.80764	0.846;0.994	T	0.77742	-0.2474	10	0.72032	D	0.01	.	13.6145	0.62099	0.0706:0.0:0.9294:0.0	.	1696;1693	Q8NFP9;Q5T321	NBEA_HUMAN;.	C	1696;1696;1693;1696;323	ENSP00000440951:G1696C;ENSP00000383295:G1696C;ENSP00000369271:G1693C;ENSP00000308534:G1696C	ENSP00000308534:G1696C	G	+	1	0	NBEA	34668159	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.455000	0.80726	2.843000	0.97960	0.585000	0.79938	GGC	.		0.433	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35770159	G	T	35770159	3	4	160	1	0	0	0	0	1	0	0	0	10212	1000	35	4	5208	4	NBEA	13	35770159	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		35770159	79399719	61	14556											
FSIP1	161835	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40056080	40056080	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttgtattttccatctcCtctttactttgccaagcttc	5	22	3	11	0	2	0	0	0	2	0	5	0	3	0	3	0	3	2	3	0	3	10			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:40056080C>T	ENST00000350221.3	-	5	710	c.501G>A	c.(499-501)gaG>gaA	p.E167E		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	167										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TTTCCATCTCCTCTTTACTTT	0.299																																					p.E167E		.											.	FSIP1-517	0			c.G501A						.						51	57	55					15																	40056080		2201	4293	6494	SO:0001819	synonymous_variant	161835	exon5			CATCTCCTCTTTA	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.501G>A	15.37:g.40056080C>T		Somatic	155	0		WXS	Illumina HiSeq	Phase_I	121	49	NM_152597	0	0	0	0	0	Q6X2C8|Q86Y89	Silent	SNP	ENST00000350221.3	37	CCDS10050.1																																																																																			.		0.299	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		T	40056080	C	T	40056080	2	4	160	1	0	0	0	0	0	0	0	1	6093	680	24	2		2	FSIP1	15	40056080	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		40056080	62475312	62	14557											
NDUFAF1	51103	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	41689069	41689069	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccaaagcaacttctttctgGtgatctccttgcaaatcccc	9	13	5	14	0	3	1	0	1	3	0	6	1	5	1	4	1	3	2	4	1	3	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:41689069G>A	ENST00000260361.4	-	2	570	c.189C>T	c.(187-189)caC>caT	p.H63H		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	63					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		CTTCTTTCTGGTGATCTCCTT	0.423																																					p.H63H		.											.	NDUFAF1-91	0			c.C189T						.						118	121	120					15																	41689069		2203	4300	6503	SO:0001819	synonymous_variant	51103	exon2			TTTCTGGTGATCT	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.189C>T	15.37:g.41689069G>A		Somatic	77	0		WXS	Illumina HiSeq	Phase_I	60	24	NM_016013	0	0	12	18	6	Q9BVZ5	Silent	SNP	ENST00000260361.4	37	CCDS10075.1																																																																																			.		0.423	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		A	41689069	G	A	41689069	2	1	160	1	0	0	0	0	0	0	0	1	10300	1252	44	2		2	NDUFAF1	15	41689069	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	1632989	41689069	60842323	63	14558											
SPG11	80208	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	44855441	44855441	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggtaaacatcttcacaatAtgtgagtaatttcttcaggt	13	14	7	7	0	4	1	2	1	2	0	4	1	4	1	0	2	1	2	0	2	5	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:44855441A>T	ENST00000261866.7	-	40	7226	c.7210T>A	c.(7210-7212)Tat>Aat	p.Y2404N	SPG11_ENST00000535302.2_Missense_Mutation_p.Y2291N|SPG11_ENST00000427534.2_3'UTR	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	2404					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TCTTCACAATATGTGAGTAAT	0.348																																					p.Y2404N													.	SPG11-95	0			c.T7210A						.						132	122	126					15																	44855441		2198	4298	6496	SO:0001583	missense	80208	exon40			CACAATATGTGAG		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.7210T>A	15.37:g.44855441A>T	ENSP00000261866:p.Tyr2404Asn	Somatic	151	1		WXS	Illumina HiSeq	Phase_I	104	43	NM_025137	0	0	14	38	24	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	A	15.36	2.809037	0.50421	.	.	ENSG00000104133	ENST00000261866;ENST00000535302	T;T	0.77098	-1.07;-0.75	5.95	5.95	0.96441	.	0.182785	0.48767	D	0.000161	D	0.86280	0.5895	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.989;0.989	D	0.85452	0.1161	10	0.35671	T	0.21	.	12.2098	0.54373	0.9321:0.0:0.0679:0.0	.	2291;2404;2404	F5H3N6;C4B7M4;Q96JI7	.;.;SPTCS_HUMAN	N	2404;2291	ENSP00000261866:Y2404N;ENSP00000445278:Y2291N	ENSP00000261866:Y2404N	Y	-	1	0	SPG11	42642733	0.998000	0.40836	0.961000	0.40146	0.958000	0.62258	3.705000	0.54823	2.276000	0.75962	0.528000	0.53228	TAT	.		0.348	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			T	44855441	A	T	44855441	3	4	160	1	0	0	0	0	1	0	0	0	15073	449	16	5	125	5	SPG11	15	44855441	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	3166372	44855441	57675951	64	14559											
C15orf42	90381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	90167321	90167321	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagccttcatgggcacGcctcagaatcaaacacacca	13	5	8	15	1	3	1	3	0	0	1	3	1	3	1	3	1	3	3	3	1	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:90167321G>A	ENST00000268138.7	+	20	3885	c.3780G>A	c.(3778-3780)acG>acA	p.T1260T	KIF7_ENST00000558928.1_Intron|TICRR_ENST00000560985.1_Silent_p.T1259T			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1260	Pro-rich.				cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TCATGGGCACGCCTCAGAATC	0.542																																					p.T1260T		.											.	.	0			c.G3780A						.						66	70	69					15																	90167321		2200	4299	6499	SO:0001819	synonymous_variant	90381	exon20			GGGCACGCCTCAG	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)"	613298	"chromosome 15 open reading frame 42"	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.3780G>A	15.37:g.90167321G>A		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	39	17	NM_152259	0	0	0	0	0	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			.		0.542	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90167321	G	A	90167321	2	1	160	1	0	0	0	0	0	0	0	1	1800	1074	38	1		1	C15orf42	15	90167321	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	45311880	90167321	12364071	65	14560											
ANKS3	124401	hgsc.bcm.edu	37	chr16	4748510	4748510	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggaggtcctcgcgggcgcGgtcctgctccagcaggcagc	4	6	16	15	4	0	0	0	0	0	0	4	1	3	1	3	5	3	3	3	5	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:4748510G>T	ENST00000304283.4	-	14	1936	c.1642C>A	c.(1642-1644)Cgc>Agc	p.R548S	ANKS3_ENST00000446014.2_Missense_Mutation_p.R419S|ANKS3_ENST00000585773.1_Missense_Mutation_p.R475S	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	548										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						TCGCGGGCGCGGTCCTGCTCC	0.736																																					p.R548S		.											.	ANKS3-90	0			c.C1642A						.						6	7	6					16																	4748510		2086	4135	6221	SO:0001583	missense	124401	exon14			GGGCGCGGTCCTG	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.1642C>A	16.37:g.4748510G>T	ENSP00000304586:p.Arg548Ser	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	25	17	NM_133450	0	0	14	44	30	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	37	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318757	0.41096	.	.	ENSG00000168096	ENST00000304283;ENST00000446014	T;T	0.31510	1.49;3.24	5.46	-6.97	0.01616	.	1.035280	0.07528	N	0.911661	T	0.04815	0.0130	N	0.00289	-1.7	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.30001	-0.9993	10	0.08837	T	0.75	0.351	3.7451	0.08545	0.0874:0.2626:0.181:0.469	.	548	Q6ZW76	ANKS3_HUMAN	S	548;419	ENSP00000304586:R548S;ENSP00000406796:R419S	ENSP00000304586:R548S	R	-	1	0	ANKS3	4688511	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	-0.450000	0.06803	-1.265000	0.02449	-0.371000	0.07208	CGC	.		0.736	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450		T	4748510	G	T	4748510	3	4	160	1	0	0	0	0	1	0	0	0	690	1116	39	4	344	4	ANKS3	16	4748510	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		4748510	85606243	66	14561											
GRIN2A	2903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	10273887	10273887	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gatcatagatgcgcccccatGaatgcccaagatggggacga	12	6	12	11	2	1	3	1	1	0	2	1	6	1	4	3	2	2	0	3	2	3	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:10273887G>C	ENST00000396573.2	-	3	691	c.382C>G	c.(382-384)Cat>Gat	p.H128D	GRIN2A_ENST00000396575.2_Missense_Mutation_p.H128D|GRIN2A_ENST00000562109.1_Missense_Mutation_p.H128D|GRIN2A_ENST00000404927.2_Missense_Mutation_p.H128D|GRIN2A_ENST00000330684.3_Missense_Mutation_p.H128D	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	128					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCGCCCCCATGAATGCCCAAG	0.597																																					p.H128D		.											.	GRIN2A-349	0			c.C382G						.						56	52	53					16																	10273887		2197	4300	6497	SO:0001583	missense	2903	exon3			CCCCATGAATGCC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors"	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.382C>G	16.37:g.10273887G>C	ENSP00000379818:p.His128Asp	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	158	42	NM_000833	0	0	0	0	0	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862300	0.71949	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	4.54	4.54	0.55810	Extracellular ligand-binding receptor (1);	0.062818	0.64402	D	0.000007	D	0.91068	0.7189	M	0.75447	2.3	0.80722	D	1	D;P;P	0.67145	0.996;0.879;0.803	D;P;P	0.64776	0.929;0.677;0.479	D	0.91402	0.5144	9	.	.	.	.	16.2901	0.82747	0.0:0.0:1.0:0.0	.	128;128;128	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	D	128	ENSP00000379818:H128D;ENSP00000385872:H128D;ENSP00000332549:H128D;ENSP00000379820:H128D	.	H	-	1	0	GRIN2A	10181388	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.938000	0.87678	2.088000	0.63022	0.561000	0.74099	CAT	.		0.597	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			C	10273887	G	C	10273887	3	2	160	1	0	0	0	0	1	0	0	0	6800	1290	45	4	4060	4	GRIN2A	16	10273887	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	5525377	10273887	80080866	67	14562											
DBNDD1	79007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	90072805	90072805	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gactgtggcctgccgctcggGgtcgcctaggggctgcttct	2	10	16	13	3	1	0	0	0	1	0	3	1	1	0	3	5	2	3	3	5	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:90072805G>T	ENST00000002501.6	-	4	546	c.415C>A	c.(415-417)Ccc>Acc	p.P139T	DBNDD1_ENST00000568838.1_Missense_Mutation_p.P259T|DBNDD1_ENST00000392973.3_Missense_Mutation_p.P145T|DBNDD1_ENST00000304733.3_Missense_Mutation_p.P159T	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	139						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		TGCCGCTCGGGGTCGCCTAGG	0.677																																					p.P159T		.											.	DBNDD1-90	0			c.C475A						.						35	45	42					16																	90072805		2023	4188	6211	SO:0001583	missense	79007	exon4			GCTCGGGGTCGCC	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.415C>A	16.37:g.90072805G>T	ENSP00000002501:p.Pro139Thr	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	62	16	NM_024043	0	0	11	15	4	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	37	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990417	0.35131	.	.	ENSG00000003249	ENST00000304733;ENST00000002501;ENST00000392973	T;T	0.30448	1.53;1.53	5.64	0.925	0.19424	.	0.270724	0.37577	N	0.002024	T	0.18002	0.0432	L	0.46157	1.445	0.25250	N	0.989681	B;B	0.20052	0.023;0.041	B;B	0.15052	0.012;0.011	T	0.13098	-1.0522	10	0.16420	T	0.52	-4.1737	1.4458	0.02364	0.2704:0.1553:0.4171:0.1571	.	139;159	Q9H9R9;Q9H9R9-2	DBND1_HUMAN;.	T	159;139;259	ENSP00000306407:P159T;ENSP00000002501:P139T	ENSP00000002501:P139T	P	-	1	0	DBNDD1	88600306	1.000000	0.71417	0.003000	0.11579	0.131000	0.20780	1.604000	0.36804	0.321000	0.23259	0.491000	0.48974	CCC	.		0.677	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043		T	90072805	G	T	90072805	3	4	160	1	0	0	0	0	1	0	0	0	4259	1232	43	4	65	4	DBNDD1	16	90072805	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	79798918	90072805	281948	68	14563											
DNAH2	146754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	7727530	7727530	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgctgcagctggcagagcAcatgggcatggcccagcgct	7	6	14	14	1	0	1	0	0	0	1	0	1	0	1	2	3	5	7	2	3	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:7727530A>T	ENST00000572933.1	+	76	13030	c.11570A>T	c.(11569-11571)cAc>cTc	p.H3857L	DNAH2_ENST00000389173.2_Missense_Mutation_p.H3857L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3857	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGGCAGAGCACATGGGCATG	0.662																																					p.H3857L		.											.	DNAH2-102	0			c.A11570T						.						63	56	59					17																	7727530		2203	4300	6503	SO:0001583	missense	146754	exon75			CAGAGCACATGGG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"Axonemal dyneins"	2948	protein-coding gene	gene with protein product		603333	"dynein, axonemal, heavy polypeptide 2", "dynein heavy chain domain 3"	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.11570A>T	17.37:g.7727530A>T	ENSP00000458355:p.His3857Leu	Somatic	27	0		WXS	Illumina HiSeq	Phase_I	100	56	NM_020877	0	0	0	2	2	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.321206	0.41096	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.08193	3.12	4.9	4.9	0.64082	Dynein heavy chain (1);	0.564059	0.19257	N	0.118766	T	0.05731	0.0150	N	0.11201	0.11	0.80722	D	1	B;B	0.14012	0.007;0.009	B;B	0.12156	0.004;0.007	T	0.38802	-0.9644	10	0.40728	T	0.16	.	13.4924	0.61405	1.0:0.0:0.0:0.0	.	3818;3857	Q9P225-2;Q9P225	.;DYH2_HUMAN	L	3818;3857	ENSP00000373825:H3857L	ENSP00000353818:H3818L	H	+	2	0	DNAH2	7668255	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.869000	0.63028	1.848000	0.53677	0.334000	0.21626	CAC	.		0.662	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7727530	A	T	7727530	3	4	160	1	0	0	0	0	1	0	0	0	4613	159	6	5	11868	5	DNAH2	17	7727530	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10		7727530	73467680	69	14564											
MAPK7	5598	broad.mit.edu	37	chr17	19285118	19285118	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcgcacccctggaggCtcctgagcctcggaagccgg	6	4	13	18	3	0	1	0	1	0	0	2	3	1	3	7	4	3	2	7	4	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:19285118C>A	ENST00000308406.5	+	5	1888	c.1502C>A	c.(1501-1503)gCt>gAt	p.A501D	MAPK7_ENST00000299612.7_Missense_Mutation_p.A362D|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000395602.4_Missense_Mutation_p.A501D|MAPK7_ENST00000395604.3_Missense_Mutation_p.A501D|MAPK7_ENST00000571657.1_Intron	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	501	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)	p.A501D(1)		autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CCCCTGGAGGCTCCTGAGCCT	0.672																																					p.A501D													.	MAPK7-1402	1	Substitution - Missense(1)	endometrium(1)	c.C1502A						.						10	17	15					17																	19285118		2162	4232	6394	SO:0001583	missense	5598	exon5			TGGAGGCTCCTGA	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"Mitogen-activated protein kinase cascade / Kinases"	6880	protein-coding gene	gene with protein product	"BMK1 kinase", "extracellular-signal-regulated kinase 5"	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1502C>A	17.37:g.19285118C>A	ENSP00000311005:p.Ala501Asp	Somatic	17	0		WXS	Illumina HiSeq	Phase_I	91	12	NM_002749	0	0	7	8	1	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	37	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248312	0.59103	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.74209	-0.57;-0.82;-0.57;-0.57	4.36	3.39	0.38822	.	0.278335	0.34291	N	0.004097	T	0.62792	0.2457	N	0.22421	0.69	0.33339	D	0.569546	P	0.50943	0.94	P	0.47299	0.543	T	0.71846	-0.4469	10	0.87932	D	0	-7.5638	6.6062	0.22726	0.0:0.7883:0.0:0.2117	.	501	Q13164	MK07_HUMAN	D	501;362;501;501	ENSP00000311005:A501D;ENSP00000299612:A362D;ENSP00000378968:A501D;ENSP00000378966:A501D	ENSP00000299612:A362D	A	+	2	0	MAPK7	19225711	0.988000	0.35896	0.980000	0.43619	0.970000	0.65996	1.704000	0.37857	1.055000	0.40461	0.561000	0.74099	GCT	.		0.672	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		A	19285118	C	A	19285118	3	1	160	1	0	0	0	0	1	0	0	0	9307	797	28	4	1516	4	MAPK7	17	19285118	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	11557588	19285118	61910092	70	14565											
SPAG5	10615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	26912886	26912886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcctgtcaccttaccgcaTccttgcctctgagagccatt	7	12	7	15	1	2	1	1	1	1	1	3	2	3	1	6	0	4	1	6	0	1	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:26912886T>C	ENST00000321765.5	-	7	2068	c.1736A>G	c.(1735-1737)gAt>gGt	p.D579G		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	579	Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTTACCGCATCCTTGCCTCT	0.498																																					p.D579G		.											.	SPAG5-90	0			c.A1736G						.						225	197	206					17																	26912886		2203	4300	6503	SO:0001583	missense	10615	exon7			ACCGCATCCTTGC	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.1736A>G	17.37:g.26912886T>C	ENSP00000323300:p.Asp579Gly	Somatic	74	0		WXS	Illumina HiSeq	Phase_I	79	48	NM_006461	0	0	0	0	0	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.907625	0.52333	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	5.82	3.52	0.40303	.	0.549745	0.17799	N	0.161643	T	0.25827	0.0629	L	0.29908	0.895	0.22096	N	0.999364	P	0.48294	0.908	B	0.39660	0.306	T	0.05099	-1.0906	9	0.56958	D	0.05	-1.7343	10.252	0.43375	0.0:0.0:0.3183:0.6817	.	579	Q96R06	SPAG5_HUMAN	G	579;76	.	ENSP00000323300:D579G	D	-	2	0	SPAG5	23937013	0.989000	0.36119	0.994000	0.49952	0.917000	0.54804	1.208000	0.32345	0.414000	0.25790	0.533000	0.62120	GAT	.		0.498	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26912886	T	C	26912886	3	2	160	1	0	0	0	0	1	0	0	0	15013	1435	50	3	1917	3	SPAG5	17	26912886	Missense_Mutation	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	7627768	26912886	54282324	71	14566											
KRT13	3860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	39658844	39658844	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accgtgttctccagccccgcTttctggtggagcgacagaca	7	9	11	14	3	2	1	0	0	2	1	3	3	2	2	4	2	2	2	4	2	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:39658844T>C	ENST00000246635.3	-	6	1072	c.1026A>G	c.(1024-1026)aaA>aaG	p.K342K	AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000587544.1_Silent_p.K342K|KRT13_ENST00000336861.3_Silent_p.K342K	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	342	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				CCAGCCCCGCTTTCTGGTGGA	0.627																																					p.K342K		.											.	KRT13-95	0			c.A1026G						.						70	66	67					17																	39658844		2203	4300	6503	SO:0001819	synonymous_variant	3860	exon6			CCCCGCTTTCTGG		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"-", "Intermediate filaments type I, keratins (acidic)"	6415	protein-coding gene	gene with protein product	"keratin, type I cytoskeletal 13", "cytokeratin 13"	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.1026A>G	17.37:g.39658844T>C		Somatic	67	0		WXS	Illumina HiSeq	Phase_I	63	19	NM_002274	0	0	0	0	0	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	37	CCDS11396.1																																																																																			.		0.627	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		C	39658844	T	C	39658844	2	2	160	1	0	0	0	0	0	0	0	1	8471	1606	56	3		3	KRT13	17	39658844	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	12745958	39658844	41536366	72	14567											
SLC14A1	6563	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr18	43316457	43316458	+	Frame_Shift_Ins	INS	-	-	A																															cattgaattccatgctcagcINSaaatgggacctccccgtctt																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr18:43316457_43316458insA	ENST00000321925.4	+	6	739_740	c.507_508insA	c.(508-510)aaafs	p.K170fs	SLC14A1_ENST00000402943.2_Frame_Shift_Ins_p.K65fs|RP11-116O18.3_ENST00000589510.1_RNA|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000589700.1_Frame_Shift_Ins_p.K170fs|SLC14A1_ENST00000415427.3_Frame_Shift_Ins_p.K226fs|SLC14A1_ENST00000436407.3_Frame_Shift_Ins_p.K226fs|SLC14A1_ENST00000502059.2_Frame_Shift_Ins_p.K62fs|SLC14A1_ENST00000586142.1_Frame_Shift_Ins_p.K170fs|SLC14A1_ENST00000535474.1_Frame_Shift_Ins_p.K38fs|SLC14A1_ENST00000591943.1_Intron	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	170					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						CCATGCTCAGCAAATGGGACCT	0.455																																					p.S225fs		.											.	SLC14A1-515	0			c.675_676insA						.																																			SO:0001589	frameshift_variant	6563	exon7			.	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.510dupA	18.37:g.43316460_43316460dupA	ENSP00000318546:p.Lys170fs	Somatic	156	0		WXS	Illumina HiSeq	Phase_I	128	51	NM_001128588	0	0	0	0	0	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Frame_Shift_Ins	INS	ENST00000321925.4	37	CCDS11925.1																																																																																			.		0.455	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		A	43316458	-	A	43316457	7	5	160	1	0	1	1	0	0	0	0	0	14428	709	25	0	693	0	SLC14A1	18	43316457	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z9-01A-11D-A28G-10		43316457	34760791	73	14568											
ZNF516	9658	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr18	74091620	74091620	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caccgagggcaggcggggggCccgtgcgtccgctccgggaa	5	3	19	14	6	0	0	0	0	0	0	2	2	2	1	4	6	1	2	4	6	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr18:74091620C>G	ENST00000443185.2	-	4	2767	c.2450G>C	c.(2449-2451)gGc>gCc	p.G817A	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	817					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AGGCGGGGGGCCCGTGCGTCC	0.622																																					p.G817A													.	ZNF516-69	0			c.G2450C						.						38	46	43					18																	74091620		1946	4125	6071	SO:0001583	missense	9658	exon4			GGGGGGCCCGTGC	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"Zinc fingers, C2H2-type"	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2450G>C	18.37:g.74091620C>G	ENSP00000394757:p.Gly817Ala	Somatic	111	1		WXS	Illumina HiSeq	Phase_I	99	37	NM_014643	0	0	0	0	0		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	C	17.81	3.481490	0.63849	.	.	ENSG00000101493	ENST00000443185	T	0.63580	-0.05	4.31	4.31	0.51392	.	0.000000	0.51477	D	0.000095	T	0.79015	0.4375	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82412	-0.0470	9	0.87932	D	0	-15.9958	15.5252	0.75898	0.0:1.0:0.0:0.0	.	817	Q92618	ZN516_HUMAN	A	817	ENSP00000394757:G817A	ENSP00000394757:G817A	G	-	2	0	ZNF516	72220608	1.000000	0.71417	0.844000	0.33320	0.431000	0.31685	6.499000	0.73683	2.387000	0.81309	0.561000	0.74099	GGC	.		0.622	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		G	74091620	C	G	74091620	3	3	160	1	0	0	0	0	1	0	0	0	17992	739	26	4	1058	4	ZNF516	18	74091620	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	30775163	74091620	3985628	74	14569											
ELAVL1	1994	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	8038748	8038748	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttgatcacctctgagctcggGcgagcatacgacaccttggg	8	9	12	12	3	2	2	1	2	1	0	3	4	2	2	2	2	3	2	2	2	1	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr19:8038748G>A	ENST00000407627.2	-	4	420	c.291C>T	c.(289-291)cgC>cgT	p.R97R	ELAVL1_ENST00000593807.1_Silent_p.R97R|ELAVL1_ENST00000351593.5_Silent_p.R124R|ELAVL1_ENST00000596459.1_Silent_p.R97R	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	97	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CTGAGCTCGGGCGAGCATACG	0.542																																					p.R97R													.	ELAVL1-90	0			c.C291T						.						138	105	116					19																	8038748		2203	4300	6503	SO:0001819	synonymous_variant	1994	exon4			GCTCGGGCGAGCA	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"RNA binding motif (RRM) containing"	3312	protein-coding gene	gene with protein product	"embryonic lethal, abnormal vision, drosophila, homolog-like 1", "Hu antigen R"	603466	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.291C>T	19.37:g.8038748G>A		Somatic	257	1		WXS	Illumina HiSeq	Phase_I	190	34	NM_001419	0	0	8	12	4	B4DVB8|Q53XN6|Q9BTT1	Silent	SNP	ENST00000407627.2	37	CCDS12193.1																																																																																			.		0.542	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419		A	8038748	G	A	8038748	2	1	160	1	0	0	0	0	0	0	0	1	5062	1190	42	2		2	ELAVL1	19	8038748	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		8038748	51090235	75	14570											
MUC16	94025	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9077779	9077779	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaggagaatttctcacagTggacctgatctctgggctga	10	10	11	10	0	2	3	1	2	2	1	4	5	2	4	2	3	0	1	2	3	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr19:9077779T>G	ENST00000397910.4	-	3	9870	c.9667A>C	c.(9667-9669)Act>Cct	p.T3223P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3224	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTTCTCACAGTGGACCTGATC	0.512																																					p.T3223P													.	MUC16-566	0			c.A9667C						.						144	141	142					19																	9077779		1972	4160	6132	SO:0001583	missense	94025	exon3			TCACAGTGGACCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9667A>C	19.37:g.9077779T>G	ENSP00000381008:p.Thr3223Pro	Somatic	186	1		WXS	Illumina HiSeq	Phase_I	115	34	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	4.351	0.064560	0.08388	.	.	ENSG00000181143	ENST00000397910	T	0.02579	4.24	2.1	2.1	0.27182	.	.	.	.	.	T	0.04407	0.0121	N	0.08118	0	.	.	.	D	0.71674	0.998	D	0.80764	0.994	T	0.40646	-0.9552	8	0.87932	D	0	.	6.1843	0.20488	0.0:0.0:0.0:1.0	.	3223	B5ME49	.	P	3223	ENSP00000381008:T3223P	ENSP00000381008:T3223P	T	-	1	0	MUC16	8938779	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-1.277000	0.02812	1.204000	0.43247	0.260000	0.18958	ACT	.		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9077779	T	G	9077779	3	3	160	1	0	0	0	0	1	0	0	0	9998	1696	59	5	34184	5	MUC16	19	9077779	Missense_Mutation	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	1039031	9077779	50051204	76	14571											
ILVBL	10994	broad.mit.edu	37	chr19	15227275	15227275	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agctcctccacccagtctggGgcccaggtctggccctgaag	6	7	12	16	0	2	1	0	1	2	0	4	1	4	1	5	4	1	1	5	4	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr19:15227275G>T	ENST00000263383.3	-	11	1384	c.1245C>A	c.(1243-1245)gcC>gcA	p.A415A	ILVBL_ENST00000531635.1_5'Flank|ILVBL_ENST00000534378.1_Silent_p.A308A	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	415						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CCCAGTCTGGGGCCCAGGTCT	0.647																																					p.A415A													.	ILVBL-92	0			c.C1245A						.						53	55	54					19																	15227275		2203	4300	6503	SO:0001819	synonymous_variant	10994	exon11			GTCTGGGGCCCAG	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1245C>A	19.37:g.15227275G>T		Somatic	81	0		WXS	Illumina HiSeq	Phase_I	84	3	NM_006844	0	1	78	79	0	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	37	CCDS12325.1																																																																																			.		0.647	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		T	15227275	G	T	15227275	2	4	160	1	0	0	0	0	0	0	0	1	7736	1219	43	4		4	ILVBL	19	15227275	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	6149496	15227275	43901708	77	14572											
TMEM149	79713	hgsc.bcm.edu	37	chr19	36230984	36230986	+	In_Frame_Del	DEL	CGG	CGG	-																															cagtgccccttggcagggacCggcctctggggataaggggt																								rs200340760		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr19:36230984_36230986delCGG	ENST00000592537.1	-	4	446_448	c.346_348delCCG	c.(346-348)ccgdel	p.P116del	IGFLR1_ENST00000588992.1_Intron|IGFLR1_ENST00000587101.1_5'UTR|IGFLR1_ENST00000344990.3_Intron|IGFLR1_ENST00000592889.1_Intron|IGFLR1_ENST00000246532.1_In_Frame_Del_p.P116del|AD000671.6_ENST00000589807.1_3'UTR|KMT2B_ENST00000607650.1_RNA			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						TGGCAGGGACCGGCCTCTGGGGA	0.621																																					p.116_116del		.											.	IGFLR1-90	0			c.346_348del						.																																			SO:0001651	inframe_deletion	79713	exon4			.	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 4", "transmembrane protein 149"	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.346_348delCCG	19.37:g.36230984_36230986delCGG	ENSP00000466181:p.Pro116del	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	34	11	NM_024660	0	0	0	0	0	Q8N5X0	In_Frame_Del	DEL	ENST00000592537.1	37	CCDS12472.1																																																																																			.		0.621	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660		-	36230986	CGG	-	36230984	7	5	160	1	0	1	0	1	0	0	0	0	16094	639	23	0	727	0	TMEM149	19	36230984	In_Frame_Del	DEL	CGG	TCGA-PJ-A5Z9-01A-11D-A28G-10	21003709	36230984	22897999	78	14573											
TMC2	117532	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	2592879	2592879	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agaacatcactcactggactCtgtttaactattacaactct	13	13	4	11	0	4	1	2	0	2	1	4	2	4	2	0	1	4	1	0	1	5	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:2592879C>G	ENST00000358864.1	+	13	1651	c.1636C>G	c.(1636-1638)Ctg>Gtg	p.L546V	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	546					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TCACTGGACTCTGTTTAACTA	0.512																																					p.L546V		.											.	TMC2-93	0			c.C1636G						.						155	134	141					20																	2592879		2203	4300	6503	SO:0001583	missense	117532	exon13			TGGACTCTGTTTA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"transmembrane, cochlear expressed, 2"	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1636C>G	20.37:g.2592879C>G	ENSP00000351732:p.Leu546Val	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	78	10	NM_080751	0	0	0	0	0	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603805	0.46423	.	.	ENSG00000149488	ENST00000358864	T	0.66099	-0.19	5.85	5.85	0.93711	.	0.076272	0.53938	D	0.000052	T	0.69540	0.3122	M	0.73962	2.25	0.49051	D	0.999745	B;P;P;P	0.41524	0.382;0.563;0.753;0.638	B;B;P;B	0.46299	0.091;0.139;0.511;0.313	T	0.64609	-0.6367	10	0.22706	T	0.39	-10.7732	18.0364	0.89305	0.0:1.0:0.0:0.0	.	377;378;546;546	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	V	546	ENSP00000351732:L546V	ENSP00000351732:L546V	L	+	1	2	TMC2	2540879	0.933000	0.31639	1.000000	0.80357	0.997000	0.91878	1.970000	0.40520	2.941000	0.99782	0.655000	0.94253	CTG	.		0.512	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			G	2592879	C	G	2592879	3	3	160	1	0	0	0	0	1	0	0	0	16017	912	32	4	1686	4	TMC2	20	2592879	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		2592879	60432641	79	14574											
PANK2	80025	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	3869791	3869791	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacgcgtccattgggcggCgccgccatcactctcttctg	4	9	10	18	5	3	0	1	0	2	0	5	0	4	0	4	2	0	0	4	2	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:3869791C>T	ENST00000316562.4	+	1	50	c.44C>T	c.(43-45)gCg>gTg	p.A15V	RP11-119B16.2_ENST00000451507.1_RNA|PANK2_ENST00000610179.1_5'Flank|PANK2_ENST00000497424.1_Intron	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	15					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CATTGGGCGGCGCCGCCATCA	0.701																																					p.A15V		.											.	PANK2-115	0			c.C44T						.						19	14	16					20																	3869791		2183	4282	6465	SO:0001583	missense	80025	exon1			GGGCGGCGCCGCC	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"Hallervorden-Spatz syndrome"	606157	"neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.44C>T	20.37:g.3869791C>T	ENSP00000313377:p.Ala15Val	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	113	34	NM_153638	0	0	0	0	0	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Missense_Mutation	SNP	ENST00000316562.4	37	CCDS13071.2	.	.	.	.	.	.	.	.	.	.	C	6.152	0.396211	0.11638	.	.	ENSG00000125779	ENST00000316562	D	0.97455	-4.39	4.57	-1.13	0.09775	.	0.546626	0.15407	N	0.263980	D	0.88691	0.6505	N	0.08118	0	0.21933	N	0.99946	B	0.06786	0.001	B	0.04013	0.001	T	0.80320	-0.1432	10	0.30854	T	0.27	-4.0E-4	4.3121	0.10976	0.0:0.4:0.1682:0.4318	.	15	Q9BZ23	PANK2_HUMAN	V	15	ENSP00000313377:A15V	ENSP00000313377:A15V	A	+	2	0	PANK2	3817791	0.959000	0.32827	0.677000	0.29947	0.004000	0.04260	-0.096000	0.11059	-0.135000	0.11495	-0.175000	0.13238	GCG	.		0.701	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		T	3869791	C	T	3869791	3	4	160	1	0	0	0	0	1	0	0	0	11443	768	27	1	46	1	PANK2	20	3869791	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	1276912	3869791	59155729	80	14575											
VAPB	9217	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr20	57009683	57009684	+	Frame_Shift_Ins	INS	-	-	C																															tacagcctttcgattatgatINScccaatgagaaaagtaaaca																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:57009683_57009684insC	ENST00000475243.1	+	3	575_576	c.237_238insC	c.(238-240)cccfs	p.P80fs	VAPB_ENST00000265619.2_Intron|VAPB_ENST00000395802.3_Intron	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	80	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			TCGATTATGATCCCAATGAGAA	0.361																																					p.D79fs		.											.	VAPB-226	0			c.237_238insC						.																																			SO:0001589	frameshift_variant	9217	exon3			.	AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.240dupC	20.37:g.57009686_57009686dupC	ENSP00000417175:p.Pro80fs	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	79	21	NM_004738	0	0	0	0	0	A2A2F2|O95293|Q9P0H0	Frame_Shift_Ins	INS	ENST00000475243.1	37	CCDS33498.1																																																																																			.		0.361	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2			C	57009684	-	C	57009683	7	5	160	1	0	1	1	0	0	0	0	0	17155	1432	50	0	247	0	VAPB	20	57009683	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z9-01A-11D-A28G-10	53139892	57009683	6015837	81	14576											
KRTAP19-5	337972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr21	31874285	31874285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccgtatccgtagcctcCgtagccaccgccatagccca	9	6	9	17	4	0	1	0	0	0	1	2	1	2	1	8	0	4	3	8	0	4	4	rs370535457		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr21:31874285C>T	ENST00000334151.2	-	1	150	c.124G>A	c.(124-126)Gga>Aga	p.G42R		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	42						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						CCGTAGCCTCCGTAGCCACCG	0.572													C|||	1	0.000199681	8e-04	0	5008	,	,		17165	0		0	False		,,,				2504	0				p.G42R		.											.	KRTAP19-5-68	0			c.G124A						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	128	122	124		124	-0.3	0	21		124	0,8600		0,0,4300	no	missense	KRTAP19-5	NM_181611.1	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	42/73	31874285	1,13005	2203	4300	6503	SO:0001583	missense	337972	exon1			AGCCTCCGTAGCC	AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"Keratin associated proteins"	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.124G>A	21.37:g.31874285C>T	ENSP00000334985:p.Gly42Arg	Somatic	172	0		WXS	Illumina HiSeq	Phase_I	48	34	NM_181611	0	0	0	0	0	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	37	CCDS13597.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920297	0.33908	2.27E-4	0.0	ENSG00000186977	ENST00000334151	T	0.11495	2.77	5.06	-0.26	0.12967	.	0.758211	0.10161	U	0.708309	T	0.07279	0.0184	.	.	.	0.09310	N	0.999999	P	0.48089	0.905	B	0.37480	0.251	T	0.30001	-0.9993	9	0.87932	D	0	-0.8878	4.9837	0.14180	0.0:0.5363:0.1489:0.3148	.	42	Q3LI72	KR195_HUMAN	R	42	ENSP00000334985:G42R	ENSP00000334985:G42R	G	-	1	0	KRTAP19-5	30796156	0.001000	0.12720	0.021000	0.16686	0.458000	0.32498	0.145000	0.16157	0.018000	0.15052	0.591000	0.81541	GGA	.		0.572	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			T	31874285	C	T	31874285	3	4	160	1	0	0	0	0	1	0	0	0	8553	661	23	1	97	1	KRTAP19-5	21	31874285	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		31874285	16255610	82	14577											
MYH9	4627	broad.mit.edu	37	chr22	36702092	36702092	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgagatgcgggtccagcttGccggcctggagaagaaaaca	12	5	14	10	3	0	3	0	0	0	3	1	5	1	3	3	3	4	1	3	3	3	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr22:36702092G>T	ENST00000216181.5	-	17	2273	c.2043C>A	c.(2041-2043)ggC>ggA	p.G681G		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	681	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.G681G(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GGTCCAGCTTGCCGGCCTGGA	0.597			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.G681G				Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9-292	1	Substitution - coding silent(1)	kidney(1)	c.C2043A						.						61	58	59					22																	36702092		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon17	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CAGCTTGCCGGCC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"Myosins / Myosin superfamily : Class II"	7579	protein-coding gene	gene with protein product	"nonmuscle myosin heavy chain II-A"	160775	"myosin, heavy polypeptide 9, non-muscle"	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.2043C>A	22.37:g.36702092G>T		Somatic	72	1		WXS	Illumina HiSeq	Phase_I	76	7	NM_002473	0	0	0	0	0	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			.		0.597	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36702092	G	T	36702092	2	4	160	1	0	0	0	0	0	0	0	1	10067	1306	46	4		4	MYH9	22	36702092	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		36702092	14602474	83	14578											
SREBF2	6721	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr22	42289217	42289217	+	Frame_Shift_Del	DEL	T	T	-																															gccaccccctgggccagaagTttttcatggagcggagctgg																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr22:42289217delT	ENST00000361204.4	+	12	2471	c.2305delT	c.(2305-2307)tttfs	p.F770fs	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	770					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						GGGCCAGAAGTTTTTCATGGA	0.582																																					p.F769fs		.											.	SREBF2-154	0			c.2305delT						.						55	58	57					22																	42289217		2203	4300	6503	SO:0001589	frameshift_variant	6721	exon12			.	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"Basic helix-loop-helix proteins"	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2305delT	22.37:g.42289217delT	ENSP00000354476:p.Phe770fs	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	70	24	NM_004599	0	0	0	0	0	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Frame_Shift_Del	DEL	ENST00000361204.4	37	CCDS14023.1																																																																																			.		0.582	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		-	42289217	T	-	42289217	7	5	160	1	0	1	0	1	0	0	0	0	15174	1725	60	0	2351	0	SREBF2	22	42289217	Frame_Shift_Del	DEL	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	5587125	42289217	9015349	84	14579											
TBL1X	6907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	9683003	9683003	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcgaggtgtgctggaacgCccgaggagacaaagtgggtg	9	7	17	8	3	0	1	0	0	0	1	1	5	0	2	1	4	2	1	1	4	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:9683003C>T	ENST00000217964.7	+	17	2307	c.1667C>T	c.(1666-1668)gCc>gTc	p.A556V	TBL1X_ENST00000536365.1_Missense_Mutation_p.A505V|TBL1X_ENST00000407597.2_Missense_Mutation_p.A556V|TBL1X_ENST00000424279.1_Missense_Mutation_p.A505V|TBL1X_ENST00000380961.1_Missense_Mutation_p.A505V	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	556					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				TGCTGGAACGCCCGAGGAGAC	0.592																																					p.A556V		.											.	TBL1X-131	0			c.C1667T						.						86	62	70					X																	9683003		2203	4300	6503	SO:0001583	missense	6907	exon17			GGAACGCCCGAGG	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1667C>T	X.37:g.9683003C>T	ENSP00000217964:p.Ala556Val	Somatic	272	0		WXS	Illumina HiSeq	Phase_I	178	81	NM_001139466	0	0	1	13	12	A8K044|A8K4J7|Q86UY2	Missense_Mutation	SNP	ENST00000217964.7	37	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297142	0.60086	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000217964	T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47	3.8	3.8	0.43715	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.116908	0.56097	D	0.000024	T	0.77994	0.4214	L	0.58101	1.795	0.44852	D	0.997864	B;B	0.29955	0.263;0.263	B;B	0.29598	0.104;0.104	T	0.80054	-0.1543	10	0.72032	D	0.01	.	15.6252	0.76851	0.0:1.0:0.0:0.0	.	519;556	Q59F53;O60907	.;TBL1X_HUMAN	V	556;505;505;505;556	ENSP00000385988:A556V;ENSP00000394097:A505V;ENSP00000445317:A505V;ENSP00000370348:A505V;ENSP00000217964:A556V	ENSP00000217964:A556V	A	+	2	0	TBL1X	9643003	1.000000	0.71417	0.958000	0.39756	0.937000	0.57800	4.399000	0.59703	1.667000	0.50832	0.429000	0.28392	GCC	.		0.592	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		T	9683003	C	T	9683003	3	4	160	1	0	0	0	0	1	0	0	0	15671	739	26	2	1721	2	TBL1X	23	9683003	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		9683003	145587557	85	14580											
SSX5	6758	broad.mit.edu;bcgsc.ca	37	chrX	48053577	48053578	+	Missense_Mutation	DNP	GG	GG	TT																															ctactcaccctgattcccacGgttagggtcattatcaaaat																								rs146748651	byFrequency	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:48053577_48053578GG>TT	ENST00000376923.1	-	3	266_267	c.267_268CC>AA	c.(265-270)aaCCgt>aaAAgt	p.89_90NR>KS	SSX5_ENST00000347757.1_Missense_Mutation_p.89_90NR>KS|SSX5_ENST00000311798.1_Missense_Mutation_p.130_131NR>KS			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5	89					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						TGATTCCCACGGTTAGGGTCAT	0.5																																					p.NR130KS													.	SSX5-90	0			c.C390A						.																																			SO:0001583	missense	6758	exon5			CCCACGGTTAGGG	BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.267_268delinsTT	X.37:g.48053577_48053578delinsTT	ENSP00000366122:p.N89_R90delinsKS	Somatic	1114	1		WXS	Illumina HiSeq	Phase_I	867	26	NM_021015	0	0	0	0	0	Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	DNP	ENST00000376923.1	37	CCDS14289.1																																																																																			.		0.5	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015		TT	48053578	GG	TT	48053577	3	4	160	1	0	0	0	0	1	0	0	0	15240	1116	39	4	314	4	SSX5	23	48053577	Missense_Mutation	DNP	GG	TCGA-PJ-A5Z9-01A-11D-A28G-10	38370574	48053577	107216983	86	14581											
PHKA1	5255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	71802352	71802352	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccagcatggtgaggacaaGgatggcttcaaccagcagct	11	7	13	10	0	1	1	1	1	0	0	1	3	1	3	2	4	5	4	2	4	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:71802352G>A	ENST00000373542.4	-	31	3553	c.3394C>T	c.(3394-3396)Ctt>Ttt	p.L1132F	PHKA1_ENST00000373545.3_Missense_Mutation_p.L1090F|PHKA1_ENST00000339490.3_Missense_Mutation_p.L1119F|PHKA1_ENST00000373539.3_Missense_Mutation_p.L1149F|PHKA1_ENST00000541944.1_Missense_Mutation_p.L1060F	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1132					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GTGAGGACAAGGATGGCTTCA	0.448																																					p.L1132F		.											.	PHKA1-134	0			c.C3394T						.						114	86	96					X																	71802352		2203	4300	6503	SO:0001583	missense	5255	exon31			GGACAAGGATGGC		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3394C>T	X.37:g.71802352G>A	ENSP00000362643:p.Leu1132Phe	Somatic	417	1		WXS	Illumina HiSeq	Phase_I	293	86	NM_002637	0	0	0	0	0	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819920	0.50633	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91464	-2.84;-2.85;-2.83;-2.82;-2.83	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000001	D	0.93216	0.7839	M	0.63428	1.95	0.48901	D	0.999723	D;P;P;D	0.76494	0.999;0.913;0.794;0.975	D;P;P;P	0.87578	0.998;0.459;0.66;0.835	D	0.92493	0.6002	10	0.46703	T	0.11	-11.3305	8.8082	0.34952	0.1046:0.0:0.8954:0.0	.	1060;1090;1119;1132	B7ZL07;A6NIT2;P46020-2;P46020	.;.;.;KPB1_HUMAN	F	1090;1132;1060;1119;1149	ENSP00000362646:L1090F;ENSP00000362643:L1132F;ENSP00000441251:L1060F;ENSP00000342469:L1119F;ENSP00000362640:L1149F	ENSP00000342469:L1119F	L	-	1	0	PHKA1	71719077	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.085000	0.30840	2.132000	0.65825	0.594000	0.82650	CTT	.		0.448	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71802352	G	A	71802352	3	1	160	1	0	0	0	0	1	0	0	0	11869	1000	35	2	285	2	PHKA1	23	71802352	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	23748775	71802352	83468208	87	14582											
PCDH11X	27328	broad.mit.edu;bcgsc.ca	37	chrX	91873700	91873700	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacaggttattgccctccatCgtagtcaggcccaatcatca	10	10	7	14	1	3	0	3	0	0	0	5	0	4	0	3	2	1	2	3	2	3	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:91873700C>T	ENST00000373094.1	+	7	4650	c.3805C>T	c.(3805-3807)Cgt>Tgt	p.R1269C	PCDH11X_ENST00000373088.1_Missense_Mutation_p.R1232C|PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000406881.1_Missense_Mutation_p.R1261C|PCDH11X_ENST00000373097.1_Missense_Mutation_p.R1259C|PCDH11X_ENST00000361655.2_Missense_Mutation_p.R1251C|PCDH11X_ENST00000298274.8_Missense_Mutation_p.R1232C	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1269					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						TGCCCTCCATCGTAGTCAGGC	0.552																																					p.R1269C	NSCLC(38;925 1092 2571 38200 45895)												.	PCDH11X-193	0			c.C3805T						.						227	202	211					X																	91873700		2203	4300	6503	SO:0001583	missense	27328	exon7			CTCCATCGTAGTC	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"Cadherins / Protocadherins : Non-clustered"	8656	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 119"	300246	"protocadherin 11"	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3805C>T	X.37:g.91873700C>T	ENSP00000362186:p.Arg1269Cys	Somatic	1032	1		WXS	Illumina HiSeq	Phase_I	749	25	NM_032968	0	0	0	0	0	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	4.743	0.138075	0.09083	.	.	ENSG00000102290	ENST00000373094;ENST00000373097;ENST00000373088;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T	0.56444	0.49;0.5;0.47;0.48;0.5;0.46	3.85	1.88	0.25563	.	.	.	.	.	T	0.34716	0.0907	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.003;0.003;0.003;0.002	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.21895	-1.0232	9	0.46703	T	0.11	.	7.3756	0.26827	0.0:0.7432:0.0:0.2568	.	1232;1251;1261;1259;1269	Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7	.;.;.;.;PC11X_HUMAN	C	1269;1259;1232;1251;1261;1269;1232	ENSP00000362186:R1269C;ENSP00000362189:R1259C;ENSP00000362180:R1232C;ENSP00000355105:R1251C;ENSP00000384758:R1261C;ENSP00000298274:R1232C	ENSP00000298274:R1232C	R	+	1	0	PCDH11X	91760356	0.000000	0.05858	0.019000	0.16419	0.198000	0.23893	0.113000	0.15499	0.171000	0.19730	0.466000	0.42574	CGT	.		0.552	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91873700	C	T	91873700	3	4	160	1	0	0	0	0	1	0	0	0	11534	884	31	1	3953	1	PCDH11X	23	91873700	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	20071348	91873700	63396860	88	14583											
GPR50	9248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	150348665	150348665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtcctccctctcctcatcGtgggtttctgctacgtgagg	3	14	10	14	3	3	1	1	1	2	0	8	1	5	1	3	2	2	2	3	2	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:150348665G>A	ENST00000218316.3	+	2	679	c.610G>A	c.(610-612)Gtg>Atg	p.V204M	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	204					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TCTCCTCATCGTGGGTTTCTG	0.532																																					p.V204M		.											.	GPR50-176	0			c.G610A						.						230	203	212					X																	150348665		2123	4223	6346	SO:0001583	missense	9248	exon2			CTCATCGTGGGTT	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"GPCR / Class A : Orphans"	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.610G>A	X.37:g.150348665G>A	ENSP00000218316:p.Val204Met	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	43	12	NM_004224	0	0	0	0	0	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456799	0.63401	.	.	ENSG00000102195	ENST00000535473;ENST00000218316	T	0.35048	1.33	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.50684	0.1630	L	0.53729	1.69	0.47547	D	0.999454	D;P	0.69078	0.997;0.819	D;P	0.64321	0.924;0.668	T	0.47018	-0.9149	10	0.36615	T	0.2	-12.9108	13.7644	0.62986	0.0:0.0:1.0:0.0	.	157;204	F5H1S3;Q13585	.;MTR1L_HUMAN	M	157;204	ENSP00000218316:V204M	ENSP00000218316:V204M	V	+	1	0	GPR50	150099323	1.000000	0.71417	0.981000	0.43875	0.745000	0.42441	9.754000	0.98908	1.903000	0.55091	0.529000	0.55759	GTG	.		0.532	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		A	150348665	G	A	150348665	3	1	160	1	0	0	0	0	1	0	0	0	6717	1145	40	1	616	1	GPR50	23	150348665	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	58474965	150348665	4921895	89	14584											
RENBP	5973	hgsc.bcm.edu	37	chrX	153200791	153200791	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgggggagggggcgggggcgGggcggctcagcagggcgccc	3	1	26	11	5	1	0	1	0	0	0	1	1	1	1	1	10	1	2	1	10	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:153200791G>T	ENST00000393700.3	-	11	1312	c.1232C>A	c.(1231-1233)cCc>cAc	p.P411H	NAA10_ENST00000370009.1_5'Flank|NAA10_ENST00000464845.1_5'Flank|NAA10_ENST00000370015.4_5'Flank|RENBP_ENST00000369997.3_Missense_Mutation_p.P397H|NAA10_ENST00000393712.3_5'Flank|RENBP_ENST00000412763.1_3'UTR|NAA10_ENST00000393710.3_5'Flank	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	411					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	ggcgggggcggggCGGCTCAG	0.751																																					p.P411H		.											.	RENBP-132	0			c.C1232A						.						2	3	2					X																	153200791		1563	2987	4550	SO:0001583	missense	5973	exon11			GGGGCGGGGCGGC		CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"N-acylglucosamine 2-epimerase", "GlcNAc 2-epimerase", "N-acetyl-D-glucosamine 2-epimerase"	312420	"renin-binding protein"			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.1232C>A	X.37:g.153200791G>T	ENSP00000377303:p.Pro411His	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	8	4	NM_002910	0	0	8	8	0	B4DNZ3|Q96BI6	Missense_Mutation	SNP	ENST00000393700.3	37	CCDS14738.2	.	.	.	.	.	.	.	.	.	.	g	13.98	2.398865	0.42512	.	.	ENSG00000102032	ENST00000393700;ENST00000369997;ENST00000451114	T;T	0.32988	1.43;1.43	3.76	-6.35	0.01975	Six-hairpin glycosidase-like (1);	2.963070	0.01364	U	0.012354	T	0.24890	0.0604	L	0.44542	1.39	0.09310	N	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.19353	-1.0308	10	0.45353	T	0.12	1.1156	7.9104	0.29787	0.1647:0.1371:0.6982:0.0	.	411	P51606	RENBP_HUMAN	H	411;397;124	ENSP00000377303:P411H;ENSP00000359014:P397H	ENSP00000359014:P397H	P	-	2	0	RENBP	152853985	0.000000	0.05858	0.000000	0.03702	0.698000	0.40448	-1.269000	0.02834	-1.762000	0.01308	0.445000	0.29226	CCC	.		0.751	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910		T	153200791	G	T	153200791	3	4	160	1	0	0	0	0	1	0	0	0	13257	1232	43	4	55	4	RENBP	23	153200791	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	2852126	153200791	2069769	90	14585											
RERE	473	hgsc.bcm.edu	37	chr1	8419867	8419868	+	Missense_Mutation	DNP	CG	CG	TT																															cccgctctcgctcccgctccCgctccttctccttctccttc																								rs538667090|rs147985313|rs557606465	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:8419867_8419868CG>TT	ENST00000337907.3	-	20	4208_4209	c.3574_3575CG>AA	c.(3574-3576)CGg>AAg	p.R1192K	RERE_ENST00000377464.1_Missense_Mutation_p.R924K|RERE_ENST00000476556.1_Missense_Mutation_p.R638K|RERE_ENST00000400907.2_Intron|RERE_ENST00000400908.2_Missense_Mutation_p.R1192K	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1192	Arg/Glu-rich (mixed charge).				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E1191_R1192insKE(1)		central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		ctcccgctcccgctccttctcc	0.683																																					p.R1192K		.											.	RERE-515	1	Insertion - In frame(1)	ovary(1)	c.C3574A						.																																			SO:0001583	missense	473	exon20			GCTCCCGCTCCTT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"GATA zinc finger domain containing"	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.3574_3575delinsTT	1.37:g.8419867_8419868delinsTT	ENSP00000338629:p.Arg1192Lys	Somatic	15	0		WXS	Illumina HiSeq	Phase_I	45	4	NM_012102	0	0	0	0	0	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	DNP	ENST00000337907.3	37	CCDS95.1																																																																																			.		0.683	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			TT	8419868	CG	TT	8419867	3	4	161	1	0	0	0	0	1	0	0	0	13263	652	23	1	1145	1	RERE	1	8419867	Missense_Mutation	DNP	CG	TCGA-Q2-A5QZ-01A-11D-A28G-10		8419867	240830754	1	14586											
NBPF1	55672	broad.mit.edu	37	chr1	16891326	16891326	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatggtgggttttgatctTcttccccttcttttcttccc	2	19	8	12	0	4	1	0	1	4	0	6	1	6	1	3	3	0	2	3	3	0	8			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:16891326T>C	ENST00000430580.2	-	28	4039	c.3152A>G	c.(3151-3153)gAa>gGa	p.E1051G		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	1031	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GTTTTGAtcttcttccccttc	0.433																																					.													.	.	0			.						.						56	26	40					1																	16891326		617	655	1272	SO:0001583	missense	55672	.			TGATCTTCTTCCC	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"neuroblastoma breakpoint family"	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3152A>G	1.37:g.16891326T>C	ENSP00000474456:p.Glu1051Gly	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	14	4	.	0	0	2	2	0	Q8N4E8|Q9C0H0	Missense_Mutation	SNP	ENST00000430580.2	37																																																																																				.		0.433	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940		C	16891326	T	C	16891326	3	2	161	1	0	0	0	0	1	0	0	0	10217	1783	62	3	275	3	NBPF1	1	16891326	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	8471459	16891326	232359295	2	14587											
CLCA1	1179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	86934706	86934706	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgattcttcaccttctagaaGgggccctgagtaattcactc	9	13	8	11	0	4	3	2	2	2	1	5	3	4	3	2	2	0	1	2	2	3	6	rs377703691		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:86934706G>A	ENST00000234701.3	+	2	403	c.52G>A	c.(52-54)Ggg>Agg	p.G18R	CLCA1_ENST00000394711.1_Missense_Mutation_p.G18R			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	18					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CCTTCTAGAAGGGGCCCTGAG	0.443																																					p.G18R		.											.	CLCA1-91	0			c.G52A						.	G	ARG/GLY	0,4406		0,0,2203	139	134	136		52	6	0.8	1		136	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLCA1	NM_001285.3	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	18/915	86934706	1,13005	2203	4300	6503	SO:0001583	missense	1179	exon1			CTAGAAGGGGCCC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.52G>A	1.37:g.86934706G>A	ENSP00000234701:p.Gly18Arg	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	87	41	NM_001285	0	0	0	0	0	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	37	CCDS709.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577478	0.65878	0.0	1.16E-4	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.11821	2.74;2.74	5.96	5.96	0.96718	Chloride channel calcium-activated (1);	0.298342	0.31415	N	0.007685	T	0.28995	0.0720	M	0.77486	2.375	0.36444	D	0.865661	D	0.89917	1.0	D	0.81914	0.995	T	0.02307	-1.1179	10	0.25106	T	0.35	-15.6633	17.336	0.87281	0.0:0.0:1.0:0.0	.	18	A8K7I4	CLCA1_HUMAN	R	18	ENSP00000234701:G18R;ENSP00000378200:G18R	ENSP00000234701:G18R	G	+	1	0	CLCA1	86707294	0.978000	0.34361	0.836000	0.33094	0.545000	0.35147	2.435000	0.44811	2.831000	0.97527	0.650000	0.86243	GGG	.		0.443	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		A	86934706	G	A	86934706	3	1	161	1	0	0	0	0	1	0	0	0	3463	1000	35	2	54	2	CLCA1	1	86934706	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	70043380	86934706	162315915	3	14588											
LCE1C	353133	hgsc.bcm.edu	37	chr1	152777877	152777877	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cactttgggggacactttggGgtggggcacttgggagggca	6	9	19	7	0	0	0	0	0	0	0	0	2	0	2	0	8	0	2	0	8	0	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:152777877G>A	ENST00000607093.1	-	1	77	c.78C>T	c.(76-78)acC>acT	p.T26T	LCE1C_ENST00000368768.1_Silent_p.T26T			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	26	Pro-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gacactttggggTGgggcact	0.647																																					p.T26T		.											.	LCE1C-90	0			c.C78T						.						45	46	46					1																	152777877		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			CTTTGGGGTGGGG		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"Late cornified envelopes"	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.78C>T	1.37:g.152777877G>A		Somatic	50	0		WXS	Illumina HiSeq	Phase_I	198	18	NM_178351	0	0	0	0	0		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			G|1.000;A|0.000		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351		A	152777877	G	A	152777877	2	1	161	1	0	0	0	0	0	0	0	1	8682	1219	43	2		2	LCE1C	1	152777877	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	65843171	152777877	96472744	4	14589											
IVL	3713	broad.mit.edu	37	chr1	152883269	152883269	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggagcagcaggaggggcaActggagcagctggaggagca	11	3	19	8	0	0	0	0	0	0	0	0	5	0	5	0	7	6	6	0	7	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:152883269A>G	ENST00000368764.3	+	2	1060	c.996A>G	c.(994-996)caA>caG	p.Q332Q	IVL_ENST00000392667.2_Silent_p.Q186Q			P07476	INVO_HUMAN	involucrin	332	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.Q332Q(3)		breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			aggaggggcaactggagcagc	0.662																																					p.Q332Q													.	IVL-93	3	Substitution - coding silent(3)	endometrium(3)	c.A996G						.						17	17	17					1																	152883269		2117	4166	6283	SO:0001819	synonymous_variant	3713	exon2			GGGGCAACTGGAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.996A>G	1.37:g.152883269A>G		Somatic	58	2		WXS	Illumina HiSeq	Phase_I	205	12	NM_005547	0	0	0	0	0	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			.		0.662	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		G	152883269	A	G	152883269	2	3	161	1	0	0	0	0	0	0	0	1	7950	40	2	3		3	IVL	1	152883269	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	105392	152883269	96367352	5	14590											
DUSP23	54935	hgsc.bcm.edu	37	chr1	159751066	159751066	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccccggcctcaccctgcAccgcctgcgcatccccgact	4	6	8	23	4	1	0	1	0	0	0	2	1	2	0	8	1	3	2	8	1	0	0	rs141314838		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:159751066A>T	ENST00000368107.1	+	1	274	c.176A>T	c.(175-177)cAc>cTc	p.H59L	DUSP23_ENST00000368109.1_Missense_Mutation_p.H59L|DUSP23_ENST00000368108.3_Missense_Mutation_p.H59L			Q9BVJ7	DUS23_HUMAN	dual specificity phosphatase 23	59						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			lung(1)	1	all_hematologic(112;0.0537)					CTCACCCTGCACCGCCTGCGC	0.716																																					p.H59L		.											.	DUSP23-226	0			c.A176T						.						4	4	4					1																	159751066		1795	3557	5352	SO:0001583	missense	54935	exon2			CCCTGCACCGCCT		CCDS1187.1	1q23.1	2011-06-09			ENSG00000158716	ENSG00000158716		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	21480	protein-coding gene	gene with protein product						15147733	Standard	XM_005245289		Approved	FLJ20442, DUSP25	uc001ftz.1	Q9BVJ7	OTTHUMG00000022795	ENST00000368107.1:c.176A>T	1.37:g.159751066A>T	ENSP00000357087:p.His59Leu	Somatic	3	0		WXS	Illumina HiSeq	Phase_I	183	78	NM_017823	6	1	287	658	364	Q9NX48	Missense_Mutation	SNP	ENST00000368107.1	37	CCDS1187.1	.	.	.	.	.	.	.	.	.	.	A	9.461	1.093071	0.20471	.	.	ENSG00000158716	ENST00000368109;ENST00000368108;ENST00000368107	D;D;D	0.82711	-1.64;-1.64;-1.64	4.89	3.76	0.43208	Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56062	0.1960	L	0.48935	1.535	0.58432	D	0.999997	B	0.24186	0.099	B	0.17433	0.018	T	0.53521	-0.8427	10	0.07644	T	0.81	-38.779	8.8034	0.34923	0.9101:0.0:0.0899:0.0	.	59	Q9BVJ7	DUS23_HUMAN	L	59	ENSP00000357089:H59L;ENSP00000357088:H59L;ENSP00000357087:H59L	ENSP00000357087:H59L	H	+	2	0	DUSP23	158017690	1.000000	0.71417	0.997000	0.53966	0.010000	0.07245	8.405000	0.90213	0.877000	0.35895	-0.441000	0.05720	CAC	.		0.716	DUSP23-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085552.1	NM_017823		T	159751066	A	T	159751066	3	4	161	1	0	0	0	0	1	0	0	0	4833	159	6	5	178	5	DUSP23	1	159751066	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	6867797	159751066	89499555	6	14591											
FAM5B	57795	broad.mit.edu;bcgsc.ca	37	chr1	177242681	177242690	+	Frame_Shift_Del	DEL	GTCAGTTCTG	GTCAGTTCTG	-																															actatgacaatctggactcaGtcagttctgtcttggtacag																								rs138487282		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	GTCAGTTCTG	GTCAGTTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:177242681_177242690delGTCAGTTCTG	ENST00000361539.4	+	5	1039_1048	c.727_736delGTCAGTTCTG	c.(727-738)gtcagttctgtcfs	p.VSSV243fs	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	243	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											TCTGGACTCAGTCAGTTCTGTCTTGGTACA	0.443																																					p.243_246del													.	FAM5B-28	0			c.727_736del						.																																			SO:0001589	frameshift_variant	57795	exon5			GACTCAGTCAGTT		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.727_736delGTCAGTTCTG	1.37:g.177242681_177242690delGTCAGTTCTG	ENSP00000354481:p.Val243fs	Somatic	127	0		WXS	Illumina HiSeq	Phase_I	186	18	NM_021165	0	0	0	0	0	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Frame_Shift_Del	DEL	ENST00000361539.4	37	CCDS1320.1																																																																																			.		0.443	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		-	177242690	GTCAGTTCTG	-	177242681	7	5	161	1	0	1	0	1	0	0	0	0	5612	1029	36	0	741	0	FAM5B	1	177242681	Frame_Shift_Del	DEL	GTCAGTTCTG	TCGA-Q2-A5QZ-01A-11D-A28G-10	17491615	177242681	72007940	7	14592											
NFASC	23114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr1	204985554	204985554	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcgagggtcagttcaatGaagacggctccttcatcggc	8	9	14	10	3	3	2	3	1	0	1	5	3	4	2	1	4	0	2	1	4	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:204985554G>T	ENST00000401399.1	+	29	3809	c.3610G>T	c.(3610-3612)Gaa>Taa	p.E1204*	NFASC_ENST00000338515.6_Nonsense_Mutation_p.E1221*|NFASC_ENST00000367172.4_Nonsense_Mutation_p.E1311*|NFASC_ENST00000367170.4_Nonsense_Mutation_p.E1232*|NFASC_ENST00000367169.4_Nonsense_Mutation_p.E1035*|NFASC_ENST00000360049.4_Nonsense_Mutation_p.E1133*|NFASC_ENST00000539706.1_Nonsense_Mutation_p.E1138*|NFASC_ENST00000338586.6_Nonsense_Mutation_p.E1188*|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000513543.1_Nonsense_Mutation_p.E1133*|NFASC_ENST00000404076.1_Nonsense_Mutation_p.E1121*|NFASC_ENST00000339876.6_Nonsense_Mutation_p.E1204*|NFASC_ENST00000367171.4_Nonsense_Mutation_p.E1296*|NFASC_ENST00000404907.1_Nonsense_Mutation_p.E1138*			O94856	NFASC_HUMAN	neurofascin	1311	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCAGTTCAATGAAGACGGCTC	0.562																																					p.E1204X		.											.	NFASC-139	0			c.G3610T						.						197	175	182					1																	204985554		2203	4300	6503	SO:0001587	stop_gained	23114	exon30			TTCAATGAAGACG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3610G>T	1.37:g.204985554G>T	ENSP00000385637:p.Glu1204*	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	310	34	NM_001005388	0	0	0	0	0	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Nonsense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	45|45	11.626230|11.626230	0.99583|0.99583	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393;ENST00000447819|ENST00000367173;ENST00000425360	.|.	.|.	.|.	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	0.000000|.	0.51477|.	D|.	0.000096|.	.|T	.|0.74718	.|0.3753	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73553	.|-0.3946	.|4	0.87932|.	D|.	0|.	.|.	18.6493|18.6493	0.91425|0.91425	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	1311;1296;1232;1221;1204;1188;1153;1138;1133;1035;1121;1204;1138;1133;1129;182|1004;261	.|.	ENSP00000295776:E1153X|.	E|M	+|+	1|3	0|0	NFASC|NFASC	203252177|203252177	1.000000|1.000000	0.71417|0.71417	0.966000|0.966000	0.40874|0.40874	0.941000|0.941000	0.58515|0.58515	9.835000|9.835000	0.99442|0.99442	2.484000|2.484000	0.83849|0.83849	0.563000|0.563000	0.77884|0.77884	GAA|ATG	.		0.562	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		T	204985554	G	T	204985554	4	4	161	1	0	0	0	0	0	1	0	0	10385	1291	45	4	4133	4	NFASC	1	204985554	Nonsense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	27742873	204985554	44265067	8	14593											
NRXN1	9378	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	50850682	50850682	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttcatcactgctgctttGaatggggttttgagacaagt	9	16	10	6	0	2	2	2	2	0	1	2	3	2	2	0	2	2	3	0	2	3	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:50850682G>T	ENST00000406316.2	-	6	2380	c.904C>A	c.(904-906)Caa>Aaa	p.Q302K	NRXN1_ENST00000406859.3_Missense_Mutation_p.Q302K|NRXN1_ENST00000404971.1_Missense_Mutation_p.Q335K|NRXN1_ENST00000402717.3_Missense_Mutation_p.Q302K|NRXN1_ENST00000405472.3_Missense_Mutation_p.Q302K|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Missense_Mutation_p.Q302K	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	302	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTGCTGCTTTGAATGGGGTTT	0.393																																					p.Q335K		.											.	NRXN1-92	0			c.C1003A						.						138	129	132					2																	50850682		1869	4095	5964	SO:0001583	missense	9378	exon7			TGCTTTGAATGGG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.904C>A	2.37:g.50850682G>T	ENSP00000384311:p.Gln302Lys	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	79	34	NM_001135659	0	0	0	0	0	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.378078	0.61735	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.19;-1.24;-1.19;-1.24	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.81545	0.4845	L	0.38175	1.15	0.49389	D	0.999783	D;P	0.56035	0.974;0.946	P;D	0.68353	0.793;0.957	T	0.73933	-0.3826	10	0.09084	T	0.74	.	19.2231	0.93806	0.0:0.0:1.0:0.0	.	335;302	Q9ULB1-3;F8WB18	.;.	K	335;302;302;302;336;302;302	ENSP00000385142:Q335K;ENSP00000384311:Q302K;ENSP00000434015:Q302K;ENSP00000385017:Q302K;ENSP00000385434:Q302K;ENSP00000385681:Q302K	ENSP00000385017:Q302K	Q	-	1	0	NRXN1	50704186	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.776000	0.95493	0.650000	0.86243	CAA	.		0.393	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50850682	G	T	50850682	3	4	161	1	0	0	0	0	1	0	0	0	10691	1299	45	4	3975	4	NRXN1	2	50850682	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		50850682	192348691	9	14594											
SPOPL	339745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	139322375	139322375	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgtccttgcagatttgcAcagtgcagaacagttgaaag	11	11	10	9	0	0	3	0	1	0	2	1	3	1	3	2	0	4	4	2	0	2	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:139322375A>G	ENST00000280098.4	+	9	1314	c.935A>G	c.(934-936)cAc>cGc	p.H312R		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	312					negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(2)|cervix(2)|endometrium(2)|large_intestine(2)|lung(11)|skin(2)	21				BRCA - Breast invasive adenocarcinoma(221;0.0296)		GCAGATTTGCACAGTGCAGAA	0.413																																					p.H312R		.											.	SPOPL-92	0			c.A935G						.						170	161	164					2																	139322375		2203	4300	6503	SO:0001583	missense	339745	exon9			ATTTGCACAGTGC		CCDS33298.1	2q22.1	2013-01-09			ENSG00000144228	ENSG00000144228		"BTB/POZ domain containing"	27934	protein-coding gene	gene with protein product	"HIB homolog 2", "roadkill homolog 2"						Standard	NM_001001664		Approved	BTBD33	uc002tvh.3	Q6IQ16	OTTHUMG00000153635	ENST00000280098.4:c.935A>G	2.37:g.139322375A>G	ENSP00000280098:p.His312Arg	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	176	29	NM_001001664	0	0	0	0	0		Missense_Mutation	SNP	ENST00000280098.4	37	CCDS33298.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.545679	0.86022	.	.	ENSG00000144228	ENST00000280098	T	0.76316	-1.01	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.88749	0.6521	M	0.89353	3.025	0.80722	D	1	D	0.71674	0.998	P	0.62813	0.907	D	0.90622	0.4560	9	.	.	.	-9.3536	15.6521	0.77104	1.0:0.0:0.0:0.0	.	312	Q6IQ16	SPOPL_HUMAN	R	312	ENSP00000280098:H312R	.	H	+	2	0	SPOPL	139038845	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.287000	0.95975	2.161000	0.67846	0.533000	0.62120	CAC	.		0.413	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1			G	139322375	A	G	139322375	3	3	161	1	0	0	0	0	1	0	0	0	15117	159	6	3	965	3	SPOPL	2	139322375	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	88471693	139322375	103876998	10	14595											
SCN9A	6335	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr2	167055820	167055820	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atagaacatctcaaagtcatCctcactcagaggttcagtac	14	10	6	11	0	5	2	5	0	1	2	7	2	6	2	1	1	2	2	1	1	4	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:167055820C>T	ENST00000409435.1	-	26	5328	c.5329G>A	c.(5329-5331)Gat>Aat	p.D1777N	SCN9A_ENST00000409672.1_Missense_Mutation_p.D1766N|SCN9A_ENST00000375387.4_Missense_Mutation_p.D1778N|SCN9A_ENST00000303354.6_Missense_Mutation_p.D1778N|AC010127.3_ENST00000447809.2_RNA			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1777					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCAAAGTCATCCTCACTCAGA	0.428																																					p.D1766N		.											.	SCN9A-181	0			c.G5296A						.						121	125	123					2																	167055820		2203	4300	6503	SO:0001583	missense	6335	exon27			AGTCATCCTCACT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10597	protein-coding gene	gene with protein product		603415	"sodium channel, voltage-gated, type IX, alpha polypeptide"			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.5329G>A	2.37:g.167055820C>T	ENSP00000386330:p.Asp1777Asn	Somatic	142	0		WXS	Illumina HiSeq	Phase_I	189	10	NM_002977	0	0	0	0	0	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837192	0.91117	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	T;T;T;T	0.10005	2.92;2.92;2.92;2.92	5.86	5.86	0.93980	.	0.000000	0.64402	D	0.000006	T	0.48169	0.1485	H	0.94847	3.59	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.61028	-0.7145	10	0.87932	D	0	.	20.1802	0.98196	0.0:1.0:0.0:0.0	.	1766	E7EUN6	.	N	1766;1778;1778;1777	ENSP00000386306:D1766N;ENSP00000364536:D1778N;ENSP00000304748:D1778N;ENSP00000386330:D1777N	ENSP00000304748:D1778N	D	-	1	0	SCN9A	166764066	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.689000	0.84165	2.777000	0.95525	0.655000	0.94253	GAT	.		0.428	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167055820	C	T	167055820	3	4	161	1	0	0	0	0	1	0	0	0	13957	855	30	2	641	2	SCN9A	2	167055820	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	27733445	167055820	76143553	11	14596											
TTN	7273	broad.mit.edu	37	chr2	179499952	179499952	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccaggaatgtctgcctctgaGatttctgcatcaaagcttgc	9	12	9	11	0	4	1	1	1	3	1	4	3	4	2	2	1	4	2	2	1	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:179499952G>C	ENST00000591111.1	-	178	37265	c.37041C>G	c.(37039-37041)atC>atG	p.I12347M	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I13988M|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I5048M|TTN_ENST00000342992.6_Missense_Mutation_p.I11420M|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I5115M|TTN_ENST00000460472.2_Missense_Mutation_p.I4923M|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12347					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCCTCTGAGATTTCTGCAT	0.388																																					p.I13988M													.	TTN-636	0			c.C41964G						.						183	168	172					2																	179499952		1877	4107	5984	SO:0001583	missense	7273	exon228			CTCTGAGATTTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12403	protein-coding gene	gene with protein product		188840	"cardiomyopathy, dilated 1G (autosomal dominant)"	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.37041C>G	2.37:g.179499952G>C	ENSP00000465570:p.Ile12347Met	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	147	5	NM_001267550	0	0	0	0	0	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	8.922	0.961252	0.18583	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.85	3.71	0.42584	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56455	0.1986	M	0.83603	2.65	0.39403	D	0.966611	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.61118	-0.7127	9	0.87932	D	0	.	5.0	0.14259	0.2192:0.0:0.5207:0.2601	.	4923;5048;5115;12347	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	11420;4923;5115;5048;4923	ENSP00000343764:I11420M;ENSP00000434586:I4923M;ENSP00000340554:I5115M;ENSP00000352154:I5048M	ENSP00000340554:I5115M	I	-	3	3	TTN	179208197	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	0.435000	0.21510	1.453000	0.47775	0.655000	0.94253	ATC	.		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179499952	G	C	179499952	3	2	161	1	0	0	0	0	1	0	0	0	16768	932	33	4	66269	4	TTN	2	179499952	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	12444132	179499952	63699421	12	14597											
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	233671361	233671361	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtccagctccccctccTcatatggtaagtacctttca	8	11	6	16	0	2	0	2	0	0	0	5	0	5	0	6	2	2	3	6	2	3	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:233671361T>A	ENST00000409547.1	+	17	2111	c.1800T>A	c.(1798-1800)ccT>ccA	p.P600P	GIGYF2_ENST00000409451.3_Silent_p.P621P|GIGYF2_ENST00000409196.3_Silent_p.P594P|GIGYF2_ENST00000373563.4_Silent_p.P600P|GIGYF2_ENST00000373566.3_Silent_p.P622P|GIGYF2_ENST00000409480.1_Silent_p.P622P|GIGYF2_ENST00000452341.2_Silent_p.P431P	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	600					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CTCCCCCTCCTCATATGGTAA	0.433																																					p.P621P		.											.	GIGYF2-28	0			c.T1863A						.						111	108	109					2																	233671361		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon17			CCCTCCTCATATG	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"Trinucleotide (CAG) repeat containing"	11960	protein-coding gene	gene with protein product	"GYF domain containing 2"	612003	"PERQ amino acid rich, with GYF domain 2", "PERQ amino acid rich, with GYF domain 3", "trinucleotide repeat containing 15", "Parkinson disease (autosomal recessive, early onset) 11"	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1800T>A	2.37:g.233671361T>A		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	54	35	NM_001103147	0	0	0	0	0	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	37	CCDS33401.1																																																																																			.		0.433	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233671361	T	A	233671361	2	1	161	1	0	0	0	0	0	0	0	1	6398	1538	54	5		5	GIGYF2	2	233671361	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	54171409	233671361	9528012	13	14598											
IQCA1	79781	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr2	237272540	237272540	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggtgcagatggcatggacCagcattttcttccctacccc	7	11	9	14	1	1	1	0	0	1	1	3	2	2	2	4	3	3	3	4	3	1	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:237272540C>T	ENST00000409907.3	-	15	2026	c.1752G>A	c.(1750-1752)ctG>ctA	p.L584L	IQCA1_ENST00000431676.2_Silent_p.L543L|IQCA1_ENST00000309507.5_Silent_p.L581L	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	584							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TGGCATGGACCAGCATTTTCT	0.512																																					p.L592L													.	IQCA1-23	0			c.G1776A						.						167	165	166					2																	237272540		1994	4155	6149	SO:0001819	synonymous_variant	79781	exon15			ATGGACCAGCATT	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"ATPases / AAA-type"	26195	protein-coding gene	gene with protein product	"dynein regulatory complex subunit 11"		"IQ motif containing with AAA domain"	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1752G>A	2.37:g.237272540C>T		Somatic	94	1		WXS	Illumina HiSeq	Phase_I	187	100	NM_001270585	0	0	0	0	0	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Silent	SNP	ENST00000409907.3	37	CCDS46549.1																																																																																			.		0.512	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		T	237272540	C	T	237272540	2	4	161	1	0	0	0	0	0	0	0	1	7823	581	21	2		2	IQCA1	2	237272540	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	3601179	237272540	5926833	14	14599											
PTPRG	5793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	62189090	62189090	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcccacgcgcctcccgacgGccgcctcagccagcaagcag	7	2	12	20	5	1	0	1	0	0	0	2	1	2	0	6	2	3	2	6	2	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:62189090G>C	ENST00000474889.1	+	12	1998	c.1621G>C	c.(1621-1623)Gcc>Ccc	p.A541P	PTPRG_ENST00000295874.10_Missense_Mutation_p.A541P	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	541					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CCTCCCGACGGCCGCCTCAGC	0.687																																					p.A541P		.											.	PTPRG-419	0			c.G1621C						.						17	15	16					3																	62189090		2203	4297	6500	SO:0001583	missense	5793	exon12			CCGACGGCCGCCT	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.1621G>C	3.37:g.62189090G>C	ENSP00000418112:p.Ala541Pro	Somatic	32	0		WXS	Illumina HiSeq	Phase_I	99	67	NM_002841	0	0	0	0	0	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	G	9.459	1.092688	0.20471	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.55760	0.57;0.5	4.39	3.51	0.40186	.	0.179080	0.48286	D	0.000192	T	0.58836	0.2150	L	0.57536	1.79	0.09310	N	1	D;P	0.61080	0.989;0.93	P;P	0.58266	0.836;0.462	T	0.50750	-0.8791	10	0.59425	D	0.04	.	6.385	0.21556	0.0862:0.0:0.5861:0.3277	.	541;541	P23470-2;P23470	.;PTPRG_HUMAN	P	541	ENSP00000418112:A541P;ENSP00000295874:A541P	ENSP00000295874:A541P	A	+	1	0	PTPRG	62164130	0.995000	0.38212	0.010000	0.14722	0.036000	0.12997	4.014000	0.57145	0.959000	0.37980	0.591000	0.81541	GCC	.		0.687	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		C	62189090	G	C	62189090	3	2	161	1	0	0	0	0	1	0	0	0	12834	1203	42	4	1667	4	PTPRG	3	62189090	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		62189090	135833340	15	14600											
KIAA2018	205717	hgsc.bcm.edu;ucsc.edu	37	chr3	113376122	113376122	+	Silent	SNP	C	C	T																															tgttgctgttgctgctgctgCtgctgctgctgctgctgctg																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:113376122C>T	ENST00000478658.1	-	5	4424	c.4407G>A	c.(4405-4407)caG>caA	p.Q1469Q	KIAA2018_ENST00000316407.4_Silent_p.Q1469Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1469	Gln-rich.					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						gctgctgctgctgctgctgct	0.498																																					p.Q1469Q		.											.	KIAA2018-93	0			c.G4407A						.						55	66	62					3																	113376122		2188	4278	6466	SO:0001819	synonymous_variant	205717	exon7			CTGCTGCTGCTGC	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.4407G>A	3.37:g.113376122C>T		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	98	17	NM_001009899	0	0	32	32	0	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.498	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376122	C	T	113376122	2	4	161	1	0	0	0	0	0	0	0	1	8289	796	28	2		2	KIAA2018	3	113376122	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	51187032	113376122	84646308	16	14601	159	2									
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376128	113376128	+	Silent	SNP	C	C	T																															tgttgctgctgctgctgctgCtgctgctgctgctgctgctt																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:113376128C>T	ENST00000478658.1	-	5	4418	c.4401G>A	c.(4399-4401)caG>caA	p.Q1467Q	KIAA2018_ENST00000316407.4_Silent_p.Q1467Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1467	Gln-rich.					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						gctgctgctgctgctgctgct	0.493																																					p.Q1467Q		.											.	KIAA2018-93	0			c.G4401A						.						52	61	58					3																	113376128		2177	4283	6460	SO:0001819	synonymous_variant	205717	exon7			CTGCTGCTGCTGC	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.4401G>A	3.37:g.113376128C>T		Somatic	21	0		WXS	Illumina HiSeq	Phase_I	93	22	NM_001009899	0	0	911	924	13	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376128	C	T	113376128	2	4	161	1	0	0	0	0	0	0	0	1	8289	796	28	2		2	KIAA2018	3	113376128	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6	113376128	84646302	17	14602	159	2									
ROPN1B	152015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	125690910	125690910	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaatcaatggctcagacaGataagccaacatgcatcccg	15	6	7	13	1	2	2	2	0	0	2	3	2	3	2	3	1	3	2	3	1	4	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:125690910G>T	ENST00000514116.1	+	3	328	c.13G>T	c.(13-15)Gat>Tat	p.D5Y	ROPN1B_ENST00000511862.1_3'UTR|ROPN1B_ENST00000504401.1_Missense_Mutation_p.D5Y|ROPN1B_ENST00000251776.4_Missense_Mutation_p.D5Y			Q9BZX4	ROP1B_HUMAN	rhophilin associated tail protein 1B	5					acrosome reaction (GO:0007340)|cytokinesis (GO:0000910)|fusion of sperm to egg plasma membrane (GO:0007342)|Rho protein signal transduction (GO:0007266)|single organismal cell-cell adhesion (GO:0016337)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(114;0.151)		GGCTCAGACAGATAAGCCAAC	0.517																																					p.D5Y		.											.	ROPN1B-90	0			c.G13T						.						54	56	56					3																	125690910		2203	4300	6503	SO:0001583	missense	152015	exon2			CAGACAGATAAGC	AF231410	CCDS33841.1	3q21.2	2011-01-20	2011-01-20		ENSG00000114547	ENSG00000114547			31927	protein-coding gene	gene with protein product			"ropporin, rhophilin associated protein 1B"				Standard	XM_005247137		Approved		uc003eih.3	Q9BZX4	OTTHUMG00000162651	ENST00000514116.1:c.13G>T	3.37:g.125690910G>T	ENSP00000426271:p.Asp5Tyr	Somatic	30	0		WXS	Illumina HiSeq	Phase_I	86	26	NM_001012337	0	0	0	0	0	D3DNA6|Q96BM7	Missense_Mutation	SNP	ENST00000514116.1	37	CCDS33841.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.986274	0.35036	.	.	ENSG00000114547	ENST00000514116;ENST00000251776;ENST00000504401;ENST00000513830;ENST00000508088;ENST00000509879	T;T;T;T	0.50548	1.7;1.7;1.3;0.74	3.37	2.48	0.30137	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (1);	0.169791	0.40222	N	0.001160	T	0.59224	0.2178	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.995;0.998	T	0.57900	-0.7731	10	0.87932	D	0	-2.9193	7.0352	0.24989	0.1362:0.0:0.8638:0.0	.	5;5	B7Z7H1;Q9BZX4	.;ROP1B_HUMAN	Y	5	ENSP00000426271:D5Y;ENSP00000251776:D5Y;ENSP00000425548:D5Y;ENSP00000423058:D5Y	ENSP00000251776:D5Y	D	+	1	0	ROPN1B	127173600	0.992000	0.36948	0.966000	0.40874	0.278000	0.26855	2.272000	0.43373	0.510000	0.28216	0.305000	0.20034	GAT	.		0.517	ROPN1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369931.1	NM_001012337		T	125690910	G	T	125690910	3	4	161	1	0	0	0	0	1	0	0	0	13556	942	33	4	15	4	ROPN1B	3	125690910	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	12314782	125690910	72331520	18	14603											
PPP2R3A	5523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	135825108	135825108	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgggaccggtttgccgcTgaggagtatgagacgcttgt	7	10	16	8	3	0	2	0	2	0	1	0	6	0	4	2	3	1	4	2	3	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:135825108T>C	ENST00000264977.3	+	13	3890	c.3273T>C	c.(3271-3273)gcT>gcC	p.A1091A	PPP2R3A_ENST00000490467.1_Silent_p.A355A|PPP2R3A_ENST00000334546.2_Silent_p.A470A|PPP2R3A_ENST00000469270.1_3'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	1091					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGTTTGCCGCTGAGGAGTATG	0.453																																					p.A1091A		.											.	PPP2R3A-662	0			c.T3273C						.						74	76	75					3																	135825108		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon13			TGCCGCTGAGGAG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing"	9307	protein-coding gene	gene with protein product		604944	"protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.3273T>C	3.37:g.135825108T>C		Somatic	69	0		WXS	Illumina HiSeq	Phase_I	126	41	NM_002718	0	0	8	9	1	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																			.		0.453	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135825108	T	C	135825108	2	2	161	1	0	0	0	0	0	0	0	1	12417	1567	55	3		3	PPP2R3A	3	135825108	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	10134198	135825108	62197322	19	14604											
FAM194A	131831	broad.mit.edu	37	chr3	150421590	150421590	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcctcctcctccacctcTtcctcctcctcctcctcctc	1	14	0	26	0	1	0	0	0	1	0	13	0	12	0	12	0	0	0	12	0	0	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:150421590T>C	ENST00000295910.6	-	1	148	c.96A>G	c.(94-96)gaA>gaG	p.E32E	RP11-103G8.2_ENST00000471093.1_RNA|FAM194A_ENST00000491361.1_5'UTR|RP11-103G8.2_ENST00000475393.1_RNA	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						cctccacctcttcctcctcct	0.632																																					p.E32E													.	FAM194A-93	0			c.A96G						.						71	65	67					3																	150421590		2203	4300	6503	SO:0001819	synonymous_variant	131831	exon1			CACCTCTTCCTCC																												ENST00000295910.6:c.96A>G	3.37:g.150421590T>C		Somatic	25	2		WXS	Illumina HiSeq	Phase_I	128	12	NM_152394	0	0	0	1	1		Silent	SNP	ENST00000295910.6	37	CCDS3151.2																																																																																			.		0.632	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			C	150421590	T	C	150421590	2	2	161	1	0	0	0	0	0	0	0	1	5542	1606	56	3		3	FAM194A	3	150421590	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	14596482	150421590	47600840	20	14605											
YEATS2	55689	broad.mit.edu	37	chr3	183525842	183525842	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggatcaccctgcagcccgtgGcactccacaggaacgtgtat	9	7	11	14	2	1	0	1	0	0	0	2	2	2	2	3	3	3	3	3	3	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:183525842G>T	ENST00000305135.5	+	29	4231	c.4036G>T	c.(4036-4038)Gca>Tca	p.A1346S	YEATS2-AS1_ENST00000425008.3_RNA|YEATS2-AS1_ENST00000609195.1_RNA|YEATS2-AS1_ENST00000609871.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1346					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GCAGCCCGTGGCACTCCACAG	0.572																																					p.A1346S													.	YEATS2-138	0			c.G4036T						.						44	46	45					3																	183525842		2006	4162	6168	SO:0001583	missense	55689	exon29			CCCGTGGCACTCC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.4036G>T	3.37:g.183525842G>T	ENSP00000306983:p.Ala1346Ser	Somatic	42	0		WXS	Illumina HiSeq	Phase_I	140	6	NM_018023	0	0	7	7	0	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732056	0.69189	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.22134	1.97	5.53	4.63	0.57726	.	0.290196	0.31347	N	0.007819	T	0.12817	0.0311	N	0.08118	0	0.32028	N	0.599863	B	0.20368	0.044	B	0.15870	0.014	T	0.04991	-1.0913	10	0.59425	D	0.04	-14.0042	15.0579	0.71930	0.0:0.1431:0.8569:0.0	.	1346	Q9ULM3	YETS2_HUMAN	S	1346	ENSP00000306983:A1346S	ENSP00000306983:A1346S	A	+	1	0	YEATS2	185008536	1.000000	0.71417	0.918000	0.36340	0.889000	0.51656	5.256000	0.65468	1.291000	0.44653	0.561000	0.74099	GCA	.		0.572	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		T	183525842	G	T	183525842	3	4	161	1	0	0	0	0	1	0	0	0	17505	1203	42	4	4146	4	YEATS2	3	183525842	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	33104252	183525842	14496588	21	14606											
DGKG	1608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr3	185960324	185960324	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttcaggatgtttctctcTcatcacatggaatctgtgtg	7	18	8	8	0	5	0	3	0	3	0	7	2	5	2	0	2	0	1	0	2	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:185960324T>A	ENST00000265022.3	-	20	2334	c.1795A>T	c.(1795-1797)Aga>Tga	p.R599*	DGKG_ENST00000382164.4_Nonsense_Mutation_p.R560*|DGKG_ENST00000544847.1_Nonsense_Mutation_p.R540*|DGKG_ENST00000344484.4_Nonsense_Mutation_p.R574*	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	599					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TGTTTCTCTCTCATCACATGG	0.547											OREG0015965	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R599X		.											.	DGKG-714	0			c.A1795T						.						100	87	92					3																	185960324		2203	4300	6503	SO:0001587	stop_gained	1608	exon20			TCTCTCTCATCAC	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1795A>T	3.37:g.185960324T>A	ENSP00000265022:p.Arg599*	Somatic	27	0	2003	WXS	Illumina HiSeq	Phase_I	111	31	NM_001346	0	0	0	0	0	B2RAH4|Q2M1H4|Q5FWG1	Nonsense_Mutation	SNP	ENST00000265022.3	37	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	T	46	12.295792	0.99654	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	.	.	.	5.38	-0.167	0.13347	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3395	0.66617	0.0:0.0:0.4781:0.5218	.	.	.	.	X	599;574;560;540;563	.	ENSP00000265022:R599X	R	-	1	2	DGKG	187443018	0.993000	0.37304	1.000000	0.80357	0.992000	0.81027	0.192000	0.17096	0.099000	0.17552	0.533000	0.62120	AGA	.		0.547	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			A	185960324	T	A	185960324	4	1	161	1	0	0	0	0	0	1	0	0	4480	1559	54	5	604	5	DGKG	3	185960324	Nonsense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	2434482	185960324	12062106	22	14607											
MUC20	200958	broad.mit.edu	37	chr3	195447900	195447900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgggctgtctctggggtctgGctctgccccttttcttcttc	0	17	11	13	0	5	0	0	0	5	0	7	0	5	0	2	4	1	2	2	4	0	4	rs397844010	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:195447900G>A	ENST00000447234.2	+	1	148	c.22G>A	c.(22-24)Gct>Act	p.A8T	MUC20_ENST00000436408.1_Missense_Mutation_p.A8T|MUC20_ENST00000485430.1_3'UTR|MUC20_ENST00000320736.6_Missense_Mutation_p.A8T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	8					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTGGGGTCTGGCTCTGCCCCT	0.622																																					p.A8T													.	.	0			c.G22A						.																																			SO:0001583	missense	200958	exon1			GGTCTGGCTCTGC	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"Mucins"	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.22G>A	3.37:g.195447900G>A	ENSP00000414350:p.Ala8Thr	Somatic	39	0		WXS	Illumina HiSeq	Phase_I	92	5	NM_152673	0	0	0	0	0	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	G	13.78	2.339003	0.41398	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408	T;T;T	0.23552	1.9;2.15;2.03	2.77	0.921	0.19403	.	.	.	.	.	T	0.17195	0.0413	L	0.29908	0.895	0.09310	N	0.999999	P	0.40332	0.713	B	0.40410	0.328	T	0.14090	-1.0485	9	0.52906	T	0.07	-6.0E-4	4.005	0.09597	0.1435:0.2477:0.6088:0.0	.	8	E9PH32	.	T	8	ENSP00000414350:A8T;ENSP00000325431:A8T;ENSP00000396774:A8T	ENSP00000325431:A8T	A	+	1	0	MUC20	196933571	0.005000	0.15991	0.270000	0.24601	0.793000	0.44817	0.154000	0.16343	0.221000	0.20879	0.462000	0.41574	GCT	.		0.622	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		A	195447900	G	A	195447900	3	1	161	1	0	0	0	0	1	0	0	0	10001	1203	42	2	24	2	MUC20	3	195447900	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	9487576	195447900	2574530	23	14608											
PPP2R2C	5522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr4	6335365	6335365	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtagtcccgggtgagcatgTagcggccgctgtggctgaac	6	8	17	10	3	0	2	0	2	0	0	1	2	1	2	2	4	3	5	2	4	3	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:6335365T>C	ENST00000382599.4	-	7	1100	c.884A>G	c.(883-885)tAc>tGc	p.Y295C	PPP2R2C_ENST00000507294.1_Missense_Mutation_p.Y288C|PPP2R2C_ENST00000335585.5_Missense_Mutation_p.Y295C|PPP2R2C_ENST00000515571.1_Missense_Mutation_p.Y278C|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.Y288C			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	295					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						GGTGAGCATGTAGCGGCCGCT	0.572											OREG0016071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y295C		.											.	PPP2R2C-1084	0			c.A884G						.						110	105	107					4																	6335365		2203	4300	6503	SO:0001583	missense	5522	exon7			AGCATGTAGCGGC	AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9306	protein-coding gene	gene with protein product	"PP2A subunit B isoform gamma"	605997	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform"			10574460, 10945473	Standard	NM_020416		Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.884A>G	4.37:g.6335365T>C	ENSP00000372042:p.Tyr295Cys	Somatic	59	0	633	WXS	Illumina HiSeq	Phase_I	128	77	NM_181876	0	0	0	3	3	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	37		.	.	.	.	.	.	.	.	.	.	T	16.16	3.044169	0.55110	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	4.11	1.24	0.21308	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.286388	0.35320	N	0.003299	T	0.59636	0.2208	H	0.94222	3.51	0.80722	D	1	D;D;D;D	0.67145	0.994;0.987;0.996;0.977	D;D;D;P	0.67900	0.933;0.926;0.954;0.87	T	0.66228	-0.5976	10	0.87932	D	0	.	9.1465	0.36937	0.3036:0.0:0.0:0.6964	.	288;295;278;295	B7Z3Y1;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;2ABG_HUMAN;.;.	C	295;288;278;295;288	ENSP00000335083:Y295C;ENSP00000423649:Y288C;ENSP00000422374:Y278C;ENSP00000372042:Y295C;ENSP00000425247:Y288C	ENSP00000335083:Y295C	Y	-	2	0	PPP2R2C	6386266	1.000000	0.71417	0.995000	0.50966	0.715000	0.41141	5.431000	0.66507	0.586000	0.29626	0.402000	0.26972	TAC	.		0.572	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		C	6335365	T	C	6335365	3	2	161	1	0	0	0	0	1	0	0	0	12415	1638	57	3	471	3	PPP2R2C	4	6335365	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		6335365	184818911	24	14609											
ATP10D	57205	broad.mit.edu	37	chr4	47593174	47593174	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctcaagaagtggagagggGctggaaagatgaatcaagtg	14	7	15	5	0	2	4	2	1	1	3	3	6	2	5	0	4	0	1	0	4	5	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:47593174G>T	ENST00000273859.3	+	23	4326	c.4057G>T	c.(4057-4059)Gct>Tct	p.A1353S		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1353					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						GTGGAGAGGGGCTGGAAAGAT	0.468																																					p.A1353S													.	ATP10D-93	0			c.G4057T						.						107	108	108					4																	47593174		2203	4300	6503	SO:0001583	missense	57205	exon23			AGAGGGGCTGGAA	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"ATPases / P-type"	13549	protein-coding gene	gene with protein product			"ATPase, Class V, type 10D"			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.4057G>T	4.37:g.47593174G>T	ENSP00000273859:p.Ala1353Ser	Somatic	77	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_020453	0	0	0	0	0	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.305821	0.40795	.	.	ENSG00000145246	ENST00000273859	T	0.38401	1.14	4.62	-2.03	0.07365	.	0.657993	0.13943	N	0.352047	T	0.20981	0.0505	L	0.51422	1.61	0.19775	N	0.999953	B	0.13145	0.007	B	0.08055	0.003	T	0.34576	-0.9823	10	0.09590	T	0.72	-0.9921	1.5641	0.02601	0.337:0.1313:0.3977:0.1341	.	1353	Q9P241	AT10D_HUMAN	S	1353	ENSP00000273859:A1353S	ENSP00000273859:A1353S	A	+	1	0	ATP10D	47287931	0.000000	0.05858	0.000000	0.03702	0.410000	0.31052	-0.016000	0.12613	-0.789000	0.04498	0.460000	0.39030	GCT	.		0.468	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		T	47593174	G	T	47593174	3	4	161	1	0	0	0	0	1	0	0	0	1119	1203	42	4	4143	4	ATP10D	4	47593174	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	41257809	47593174	143561102	25	14610											
DSPP	1834	bcgsc.ca	37	chr4	88536238	88536238	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatagcagcaacagcagtgaTagcagtgatagcagtgacag	15	6	13	7	0	0	3	0	3	0	0	0	4	0	3	0	0	6	5	0	0	4	3	rs555978267	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:88536238T>C	ENST00000282478.7	+	4	2457	c.2424T>C	c.(2422-2424)gaT>gaC	p.D808D	DSPP_ENST00000399271.1_Silent_p.D808D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	808	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagcagtgata	0.488																																					p.D808D													.	DSPP-90	0			c.T2424C						.						98	115	109					4																	88536238		1660	2960	4620	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2424T>C	4.37:g.88536238T>C		Somatic	193	2		WXS	Illumina HiSeq	Phase_1	500	32	NM_014208	0	0	0	0	0	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88536238	T	C	88536238	2	2	161	1	0	0	0	0	0	0	0	1	4793	1403	49	3		3	DSPP	4	88536238	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	40943064	88536238	102618038	26	14611											
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcgatagcagtgacagcagCaacagcagtgacagcagtga	15	4	13	9	1	0	3	0	3	0	0	0	4	0	3	0	0	7	5	0	0	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		.											.	DSPP-90	0			c.C2622T						.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	4.37:g.88536436C>T		Somatic	131	0		WXS	Illumina HiSeq	Phase_I	371	30	NM_014208	0	0	0	0	0	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	161	1	0	0	0	0	0	0	0	1	4793	709	25	2		2	DSPP	4	88536436	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	198	88536436	102617840	27	14612											
PLEKHG4B	153478	broad.mit.edu	37	chr5	169688	169688	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcactgccccttggccgtggGccgcagtttcctgagacacg	5	8	13	15	3	0	1	0	1	0	1	1	2	1	1	5	2	1	3	5	2	0	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:169688G>T	ENST00000283426.6	+	12	2692	c.2642G>T	c.(2641-2643)gGc>gTc	p.G881V		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	881	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		TTGGCCGTGGGCCGCAGTTTC	0.647																																					p.G881V													.	PLEKHG4B-228	0			c.G2642T						.						54	56	55					5																	169688		2203	4300	6503	SO:0001583	missense	153478	exon12			CCGTGGGCCGCAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"Pleckstrin homology (PH) domain containing"	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2642G>T	5.37:g.169688G>T	ENSP00000283426:p.Gly881Val	Somatic	24	1		WXS	Illumina HiSeq	Phase_I	64	4	NM_052909	0	0	0	0	0		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.847182	0.51164	.	.	ENSG00000153404	ENST00000283426	T	0.38401	1.14	3.55	3.55	0.40652	Dbl homology (DH) domain (5);	.	.	.	.	T	0.70245	0.3202	H	0.97465	4.01	0.58432	D	0.999997	D	0.67145	0.996	D	0.67231	0.95	T	0.81243	-0.1021	9	0.87932	D	0	.	12.6189	0.56592	0.0:0.0:1.0:0.0	.	881	Q96PX9	PKH4B_HUMAN	V	881	ENSP00000283426:G881V	ENSP00000283426:G881V	G	+	2	0	PLEKHG4B	222688	1.000000	0.71417	0.059000	0.19551	0.536000	0.34869	6.237000	0.72345	1.514000	0.48869	0.467000	0.42956	GGC	.		0.647	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	169688	G	T	169688	3	4	161	1	0	0	0	0	1	0	0	0	12098	1203	42	4	2688	4	PLEKHG4B	5	169688	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		169688	180745572	28	14613											
SLC9A3	6550	broad.mit.edu	37	chr5	475168	475168	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggggaccaccgtctccccGggagacagccagggcggcag	8	2	17	14	3	1	1	0	0	1	1	2	4	1	2	5	5	1	1	5	5	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:475168G>A	ENST00000264938.3	-	16	2340	c.2331C>T	c.(2329-2331)ccC>ccT	p.P777P	SLC9A3_ENST00000514375.1_Silent_p.P768P|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.5_ENST00000510714.1_5'Flank|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.5_ENST00000510604.1_5'Flank|CTD-2228K2.5_ENST00000342584.3_5'Flank	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	777					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CCGTCTCCCCGGGAGACAGCC	0.677																																					p.P777P													.	SLC9A3-90	0			c.C2331T						.						25	32	30					5																	475168		2202	4298	6500	SO:0001819	synonymous_variant	6550	exon16			CTCCCCGGGAGAC		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"Solute carriers"	11073	protein-coding gene	gene with protein product		182307	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3"	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2331C>T	5.37:g.475168G>A		Somatic	20	0		WXS	Illumina HiSeq	Phase_I	169	4	NM_004174	0	0	0	0	0	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			.		0.677	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		A	475168	G	A	475168	2	1	161	1	0	0	0	0	0	0	0	1	14745	1103	39	1		1	SLC9A3	5	475168	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	305480	475168	180440092	29	14614											
FAM105A	54491	broad.mit.edu;bcgsc.ca	37	chr5	14601482	14601482	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacctcagtgtggaggcagaGgttgatttactcagttattg	10	13	12	6	0	2	2	2	1	0	1	2	3	2	3	1	3	2	3	1	3	3	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:14601482G>A	ENST00000274217.3	+	4	399	c.279G>A	c.(277-279)gaG>gaA	p.E93E		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	93										large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TGGAGGCAGAGGTTGATTTAC	0.423																																					p.E93E													.	FAM105A-91	0			c.G279A						.						90	85	87					5																	14601482		2203	4300	6503	SO:0001819	synonymous_variant	54491	exon4			GGCAGAGGTTGAT		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.279G>A	5.37:g.14601482G>A		Somatic	96	2		WXS	Illumina HiSeq	Phase_I	212	47	NM_019018	0	0	0	0	0	Q53H50|Q9H037	Silent	SNP	ENST00000274217.3	37	CCDS3884.1																																																																																			.		0.423	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		A	14601482	G	A	14601482	2	1	161	1	0	0	0	0	0	0	0	1	5403	991	35	2		2	FAM105A	5	14601482	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	14126314	14601482	166313778	30	14615											
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132161622	132161622	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcgtcgggcggggcggggcCcgggccgccccaaaccacac	6	1	17	17	6	0	0	0	0	0	0	1	0	0	0	5	6	2	0	5	6	1	0	rs201865788	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:132161622C>G	ENST00000378679.3	-	4	1015	c.211G>C	c.(211-213)Ggc>Cgc	p.G71R	SHROOM1_ENST00000319854.3_Missense_Mutation_p.G71R|SHROOM1_ENST00000378676.1_Missense_Mutation_p.G71R|SHROOM1_ENST00000488072.1_5'Flank	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	71					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ggggcggggcccgggccgccc	0.761													C|||	30	0.00599042	0.0197	0.0058	5008	,	,		9659	0		0	False		,,,				2504	0				p.G71R		.											.	SHROOM1-91	0			c.G211C						.	C	ARG/GLY,ARG/GLY	47,3713		0,47,1833	3	5	4		211,211	-0.3	0	5		4	6,7770		0,6,3882	yes	missense,missense	SHROOM1	NM_001172700.1,NM_133456.2	125,125	0,53,5715	GG,GC,CC		0.0772,1.25,0.4594	probably-damaging,probably-damaging	71/853,71/848	132161622	53,11483	1880	3888	5768	SO:0001583	missense	134549	exon1			CGGGGCCCGGGCC	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.211G>C	5.37:g.132161622C>G	ENSP00000367950:p.Gly71Arg	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	33	17	NM_133456	0	0	0	0	0	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	C	9.057	0.993651	0.19043	0.0125	7.72E-4	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676;ENST00000440118	T;T;T;T	0.46063	1.88;1.88;1.88;0.88	3.95	-0.277	0.12898	.	1.015780	0.07909	N	0.973959	T	0.18841	0.0452	N	0.19112	0.55	0.09310	N	1	P;P	0.47677	0.899;0.838	B;B	0.42522	0.39;0.218	T	0.12451	-1.0547	10	0.54805	T	0.06	-0.006	2.8428	0.05534	0.2105:0.4294:0.0:0.3601	.	71;71	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	R	71	ENSP00000367950:G71R;ENSP00000324245:G71R;ENSP00000367947:G71R;ENSP00000388049:G71R	ENSP00000324245:G71R	G	-	1	0	SHROOM1	132189521	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.865000	0.04250	0.025000	0.15241	0.407000	0.27541	GGC	.		0.761	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		G	132161622	C	G	132161622	3	3	161	1	0	0	0	0	1	0	0	0	14325	623	22	4	2375	4	SHROOM1	5	132161622	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	117560140	132161622	48753638	31	14616											
NR3C1	2908	broad.mit.edu	37	chr5	142678363	142678363	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtcatttggtcatccaggtGtaagttcctgaaacctgaat	10	13	10	8	0	2	2	2	2	0	0	4	2	4	2	3	3	1	2	3	3	3	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:142678363G>T	ENST00000343796.2	-	6	2755	c.1762C>A	c.(1762-1764)Cac>Aac	p.H588N	NR3C1_ENST00000231509.3_Missense_Mutation_p.H589N|NR3C1_ENST00000503201.1_Missense_Mutation_p.H588N|NR3C1_ENST00000415690.2_Missense_Mutation_p.H588N|NR3C1_ENST00000504572.1_Missense_Mutation_p.H589N|NR3C1_ENST00000504336.1_5'Flank|NR3C1_ENST00000416954.2_Missense_Mutation_p.H191N|NR3C1_ENST00000394466.2_Missense_Mutation_p.H589N|NR3C1_ENST00000394464.2_Missense_Mutation_p.H588N|NR3C1_ENST00000424646.2_Missense_Mutation_p.H562N	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	588	Interaction with CLOCK.|Interaction with CRY1.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TCATCCAGGTGTAAGTTCCTG	0.423																																					p.H589N													.	NR3C1-92	0			c.C1765A						.						103	95	98					5																	142678363		2203	4300	6503	SO:0001583	missense	2908	exon6			CCAGGTGTAAGTT	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1762C>A	5.37:g.142678363G>T	ENSP00000343205:p.His588Asn	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	90	4	NM_001024094	0	0	0	0	0	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	37	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350242	0.82132	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;D;D;D;D;D;D;D	0.96427	-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01;-4.01	5.88	5.88	0.94601	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.045994	0.85682	D	0.000000	D	0.97458	0.9168	M	0.76938	2.355	0.80722	D	1	P;P;P	0.39782	0.632;0.559;0.688	P;B;P	0.49683	0.619;0.257;0.563	D	0.97432	1.0016	10	0.66056	D	0.02	.	20.2314	0.98350	0.0:0.0:1.0:0.0	.	588;588;589	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	N	588;588;588;562;589;589;589;191;588	ENSP00000377977:H588N;ENSP00000343205:H588N;ENSP00000387672:H588N;ENSP00000405282:H562N;ENSP00000422518:H589N;ENSP00000377979:H589N;ENSP00000231509:H589N;ENSP00000404218:H191N;ENSP00000427672:H588N	ENSP00000231509:H589N	H	-	1	0	NR3C1	142658556	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.967000	0.87967	2.789000	0.95967	0.591000	0.81541	CAC	.		0.423	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			T	142678363	G	T	142678363	3	4	161	1	0	0	0	0	1	0	0	0	10656	1377	48	4	639	4	NR3C1	5	142678363	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	10516741	142678363	38236897	32	14617											
TLX3	30012	hgsc.bcm.edu	37	chr5	170736390	170736390	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggaggcgcccgccagcgcGcagaccccgcacccgcacga	8	1	13	19	7	0	1	0	0	0	1	0	3	0	2	5	2	1	3	5	2	0	0	rs537348276		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:170736390G>A	ENST00000296921.5	+	1	103	c.21G>A	c.(19-21)gcG>gcA	p.A7A		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	7					central nervous system development (GO:0007417)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of transcription, DNA-templated (GO:0006355)|respiratory gaseous exchange (GO:0007585)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCGCCAGCGCGCAGACCCCGC	0.771			T	BCL11B	T-ALL																																p.A7A	Esophageal Squamous(33;43 807 3116 3348 30094)	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3-658	0			c.G21A						.						11	13	12					5																	170736390		2176	4263	6439	SO:0001819	synonymous_variant	30012	exon1			CAGCGCGCAGACC	AJ223798	CCDS34288.1	5q35.1	2011-06-20	2005-12-22	2002-05-31	ENSG00000164438	ENSG00000164438		"Homeoboxes / ANTP class : NKL subclass"	13532	protein-coding gene	gene with protein product		604640	"homeo box 11-like 2", "T-cell leukemia, homeobox 3"	HOX11L2		11435718, 11435716	Standard	NM_021025		Approved	RNX	uc003mbf.3	O43711	OTTHUMG00000163207	ENST00000296921.5:c.21G>A	5.37:g.170736390G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	45	21	NM_021025	0	0	0	0	0	Q96AD3	Silent	SNP	ENST00000296921.5	37	CCDS34288.1																																																																																			.		0.771	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			A	170736390	G	A	170736390	2	1	161	1	0	0	0	0	0	0	0	1	15994	1074	38	1		1	TLX3	5	170736390	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	28058027	170736390	10178870	33	14618											
DBN1	1627	broad.mit.edu	37	chr5	176885609	176885609	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctggcccccggggaggcGcctgtgcctgagggggctcc	2	6	18	15	2	0	1	0	1	0	0	1	2	1	2	6	6	2	1	6	6	0	0	rs369597152		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:176885609G>A	ENST00000309007.5	-	12	1445	c.1226C>T	c.(1225-1227)gCg>gTg	p.A409V	DBN1_ENST00000393565.1_Missense_Mutation_p.A455V|DBN1_ENST00000292385.5_Missense_Mutation_p.A411V|DBN1_ENST00000393563.4_Missense_Mutation_p.A141V|DBN1_ENST00000512501.1_Missense_Mutation_p.A141V	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	409					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCGGGGAGGCGCCTGTGCCTG	0.687																																					p.A411V													.	DBN1-587	0			c.C1232T						.	G	VAL/ALA,VAL/ALA	0,4390		0,0,2195	18	22	21		1232,1226	-2	0	5		21	1,8593		0,1,4296	no	missense,missense	DBN1	NM_080881.2,NM_004395.3	64,64	0,1,6491	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	411/652,409/650	176885609	1,12983	2195	4297	6492	SO:0001583	missense	1627	exon13			GGAGGCGCCTGTG		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1226C>T	5.37:g.176885609G>A	ENSP00000308532:p.Ala409Val	Somatic	23	0		WXS	Illumina HiSeq	Phase_I	129	4	NM_080881	0	0	8	8	0	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	G	2.283	-0.364221	0.05103	0.0	1.16E-4	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563	T;T;T;T;T	0.32753	1.49;1.48;1.49;1.44;1.49	4.77	-2.02	0.07388	.	1.821730	0.02661	N	0.107568	T	0.14830	0.0358	N	0.08118	0	0.09310	N	1	B;B;B;B	0.09022	0.0;0.002;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.20538	-1.0272	10	0.49607	T	0.09	-6.766	2.1505	0.03798	0.4484:0.0767:0.133:0.3419	.	359;455;409;411	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	V	409;411;455;141;141	ENSP00000308532:A409V;ENSP00000292385:A411V;ENSP00000377195:A455V;ENSP00000423208:A141V;ENSP00000377193:A141V	ENSP00000292385:A411V	A	-	2	0	DBN1	176818215	0.000000	0.05858	0.015000	0.15790	0.035000	0.12851	-0.219000	0.09228	-0.099000	0.12263	-1.744000	0.00683	GCG	.		0.687	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		A	176885609	G	A	176885609	3	1	161	1	0	0	0	0	1	0	0	0	4258	1087	38	1	735	1	DBN1	5	176885609	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	6149219	176885609	4029651	34	14619											
OR10C1	442194	hgsc.bcm.edu;broad.mit.edu	37	chr6	29408232	29408232	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacagctagctgggtcggCgtgggcctgtggggtgctgg	3	10	19	9	2	1	0	0	0	1	0	2	0	1	0	1	6	4	3	1	6	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:29408232C>T	ENST00000444197.2	+	1	1150	c.440C>T	c.(439-441)gCg>gTg	p.A147V	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GCTGGGTCGGCGTGGGCCTGT	0.622																																					p.A147V		.											.	OR10C1-22	0			c.C440T						.						80	91	87					6																	29408232		1509	2709	4218	SO:0001583	missense	442194	exon1			GGTCGGCGTGGGC		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"GPCR / Class A : Olfactory receptors"	8165	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily C, member 2", "olfactory receptor, family 10, subfamily C, member 1"	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.440C>T	6.37:g.29408232C>T	ENSP00000419119:p.Ala147Val	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	61	4	NM_013941	0	0	0	0	0	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434952	0.43224	.	.	ENSG00000206474	ENST00000444197	T	0.34859	1.34	3.53	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38897	N	0.001526	T	0.29028	0.0721	N	0.16708	0.43	0.09310	N	1	D	0.67145	0.996	D	0.67725	0.953	T	0.18650	-1.0330	10	0.87932	D	0	.	14.9009	0.70678	0.0:1.0:0.0:0.0	.	147	Q96KK4	O10C1_HUMAN	V	147	ENSP00000419119:A147V	ENSP00000419119:A147V	A	+	2	0	OR10C1	29516211	0.000000	0.05858	0.027000	0.17364	0.033000	0.12548	-1.281000	0.02802	1.805000	0.52779	0.508000	0.49915	GCG	.		0.622	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			T	29408232	C	T	29408232	3	4	161	1	0	0	0	0	1	0	0	0	10924	768	27	1	442	1	OR10C1	6	29408232	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		29408232	141706835	35	14620											
TUBB	203068	broad.mit.edu	37	chr6	30692075	30692075	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atggagttcaccgaggctgaGagcaacatgaacgacctcgt	12	7	12	10	3	1	2	1	2	0	1	2	6	1	3	2	2	3	3	2	2	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:30692075G>C	ENST00000327892.8	+	4	1542	c.1236G>C	c.(1234-1236)gaG>gaC	p.E412D	XXbac-BPG252P9.9_ENST00000607476.1_RNA|TUBB_ENST00000435534.1_Missense_Mutation_p.E211D|TUBB_ENST00000396384.1_Missense_Mutation_p.E340D|TUBB_ENST00000330914.3_Missense_Mutation_p.E340D|TUBB_ENST00000396389.1_Missense_Mutation_p.E394D	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	412					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	CCGAGGCTGAGAGCAACATGA	0.587																																					p.E412D													.	TUBB-91	0			c.G1236C						.						78	71	74					6																	30692075		2202	4300	6502	SO:0001583	missense	203068	exon4			GGCTGAGAGCAAC	AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"Tubulins"	20778	protein-coding gene	gene with protein product	"class I beta-tubulin", "beta1-tubulin"	191130	"tubulin, beta polypeptide", "tubulin, beta"			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.1236G>C	6.37:g.30692075G>C	ENSP00000339001:p.Glu412Asp	Somatic	56	0		WXS	Illumina HiSeq	Phase_I	132	9	NM_178014	0	0	1395	1395	0	P05218|Q8WUC1|Q9CY33	Missense_Mutation	SNP	ENST00000327892.8	37	CCDS4687.1	.	.	.	.	.	.	.	.	.	.	G	17.20	3.329595	0.60743	.	.	ENSG00000196230	ENST00000327892;ENST00000422827;ENST00000435534;ENST00000330914;ENST00000396389;ENST00000396384	T;T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84;-0.84	4.62	3.75	0.43078	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80476	0.4630	M	0.80332	2.49	0.25294	N	0.989331	D;B	0.62365	0.991;0.418	D;B	0.83275	0.996;0.346	T	0.74112	-0.3770	10	0.87932	D	0	.	11.9247	0.52812	0.0:0.0:0.8249:0.1751	.	412;412	P07437;F8VW92	TBB5_HUMAN;.	D	412;321;211;340;394;340	ENSP00000339001:E412D;ENSP00000391672:E211D;ENSP00000365578:E340D;ENSP00000379672:E394D;ENSP00000379668:E340D	ENSP00000339001:E412D	E	+	3	2	TUBB	30800054	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.175000	0.71949	1.166000	0.42689	-0.230000	0.12252	GAG	.		0.587	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014		C	30692075	G	C	30692075	3	2	161	1	0	0	0	0	1	0	0	0	16785	933	33	4	1250	4	TUBB	6	30692075	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	1283843	30692075	140422992	36	14621											
ABCC10	89845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	43412898	43412898	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgcccaaagctgcccccaAtggctcctcagacatccgtt	9	8	7	17	1	1	1	1	0	0	1	3	1	3	1	5	1	3	3	5	1	2	1	rs200602946	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:43412898A>G	ENST00000372530.4	+	14	3091	c.2876A>G	c.(2875-2877)aAt>aGt	p.N959S	ABCC10_ENST00000244533.3_Missense_Mutation_p.N931S	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	959	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GCTGCCCCCAATGGCTCCTCA	0.592													A|||	2	0.000399361	8e-04	0	5008	,	,		17616	0		0	False		,,,				2504	0.001				p.N959S		.											.	ABCC10-96	0			c.A2876G						.	A	SER/ASN,SER/ASN	3,4403	6.2+/-15.9	0,3,2200	120	98	105		2876,2792	5.1	1	6		105	0,8600		0,0,4300	no	missense,missense	ABCC10	NM_001198934.1,NM_033450.2	46,46	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	benign,benign	959/1493,931/1465	43412898	3,13003	2203	4300	6503	SO:0001583	missense	89845	exon14			CCCCCAATGGCTC	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"ATP binding cassette transporters / subfamily C"	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2876A>G	6.37:g.43412898A>G	ENSP00000361608:p.Asn959Ser	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	674	260	NM_001198934	0	0	3	7	4	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	19.68	3.873050	0.72180	6.81E-4	0.0	ENSG00000124574	ENST00000372530;ENST00000244533	D;D	0.89875	-2.58;-2.58	5.08	5.08	0.68730	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.055422	0.64402	D	0.000002	T	0.80454	0.4626	N	0.21373	0.66	0.53005	D	0.999967	B;P	0.52170	0.39;0.951	B;P	0.54544	0.257;0.755	T	0.80099	-0.1524	10	0.07813	T	0.8	-0.0074	14.8585	0.70359	1.0:0.0:0.0:0.0	.	931;959	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	S	959;931	ENSP00000361608:N959S;ENSP00000244533:N931S	ENSP00000244533:N931S	N	+	2	0	ABCC10	43520876	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.580000	0.60942	1.911000	0.55334	0.379000	0.24179	AAT	A|0.999;G|0.000		0.592	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		G	43412898	A	G	43412898	3	3	161	1	0	0	0	0	1	0	0	0	50	101	4	3	2838	3	ABCC10	6	43412898	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	12720823	43412898	127702169	37	14622											
CD2AP	23607	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	47471115	47471115	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaaaaagctacaggaggAagggtggctggaaggagaac	15	5	17	4	0	0	2	0	1	0	1	0	6	0	5	0	6	3	2	0	6	6	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:47471115A>T	ENST00000359314.5	+	2	560	c.104A>T	c.(103-105)gAa>gTa	p.E35V		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	35	Interaction with ANLN and localization to the midbody.|SH3 1; truncated. {ECO:0000255|PROSITE- ProRule:PRU00192}.				mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			CTACAGGAGGAAGGGTGGCTG	0.378																																					p.E35V		.											.	CD2AP-92	0			c.A104T						.						139	134	135					6																	47471115		2203	4300	6503	SO:0001583	missense	23607	exon2			AGGAGGAAGGGTG	AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.104A>T	6.37:g.47471115A>T	ENSP00000352264:p.Glu35Val	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	384	30	NM_012120	0	0	0	0	0	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024553	0.75390	.	.	ENSG00000198087	ENST00000359314	T	0.54071	0.59	4.68	4.68	0.58851	Src homology-3 domain (4);	0.560263	0.21123	N	0.079786	T	0.63698	0.2533	M	0.75264	2.295	0.48452	D	0.999652	D	0.89917	1.0	D	0.83275	0.996	T	0.64935	-0.6290	10	0.38643	T	0.18	-17.8438	14.1476	0.65360	1.0:0.0:0.0:0.0	.	35	Q9Y5K6	CD2AP_HUMAN	V	35	ENSP00000352264:E35V	ENSP00000352264:E35V	E	+	2	0	CD2AP	47579074	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.530000	0.73816	1.735000	0.51646	0.533000	0.62120	GAA	.		0.378	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			T	47471115	A	T	47471115	3	4	161	1	0	0	0	0	1	0	0	0	3000	246	9	5	110	5	CD2AP	6	47471115	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	4058217	47471115	123643952	38	14623											
C6orf138	442213	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	48036108	48036108	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggcttttggactggTccagggggaaaaggctgctg	8	9	17	7	0	0	1	0	0	0	1	1	3	1	3	1	6	2	4	1	6	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:48036108T>C	ENST00000339488.4	-	1	317	c.284A>G	c.(283-285)gAc>gGc	p.D95G	PTCHD4_ENST00000543600.1_Missense_Mutation_p.D78G	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	95						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										TTTGGACTGGTCCAGGGGGAA	0.627																																					p.D95G		.											.	.	0			c.A284G						.						72	79	77					6																	48036108		1946	4139	6085	SO:0001583	missense	442213	exon1			GACTGGTCCAGGG		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 138"	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.284A>G	6.37:g.48036108T>C	ENSP00000341914:p.Asp95Gly	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	377	19	NM_001013732	0	0	2	2	0	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	37	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	T	18.19	3.569479	0.65765	.	.	ENSG00000244694	ENST00000339488;ENST00000543600	D;T	0.92397	-3.03;0.62	4.88	4.88	0.63580	.	0.103230	0.64402	D	0.000006	D	0.91088	0.7195	L	0.51422	1.61	0.80722	D	1	P;D	0.67145	0.826;0.996	B;P	0.57620	0.438;0.824	D	0.90227	0.4276	10	0.34782	T	0.22	.	14.4665	0.67488	0.0:0.0:0.0:1.0	.	95;78	Q6ZW05;B0QZ29	CF138_HUMAN;.	G	95;78	ENSP00000341914:D95G;ENSP00000439864:D78G	ENSP00000341914:D95G	D	-	2	0	C6orf138	48144067	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.602000	0.82796	1.813000	0.52934	0.460000	0.39030	GAC	.		0.627	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		C	48036108	T	C	48036108	3	2	161	1	0	0	0	0	1	0	0	0	2338	1667	58	3	2268	3	C6orf138	6	48036108	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	564993	48036108	123078959	39	14624											
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	51890186	51890186	+	Frame_Shift_Del	DEL	C	C	-																															cttatgaaaagagtgcaattCccctgacactcgctggttag																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:51890186delC	ENST00000371117.3	-	32	4697	c.4422delG	c.(4420-4422)gggfs	p.G1474fs	PKHD1_ENST00000340994.4_Frame_Shift_Del_p.G1474fs	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1474	IPT/TIG 9.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAGTGCAATTCCCCTGACACT	0.542																																					p.G1474fs		.											.	PKHD1-603	0			c.4422delG						.						57	52	54					6																	51890186		2203	4300	6503	SO:0001589	frameshift_variant	5314	exon32			.	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"tigmin", "polyductin", "fibrocystin"	606702	"TIG multiple domains 1"	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.4422delG	6.37:g.51890186delC	ENSP00000360158:p.Gly1474fs	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	239	53	NM_170724	0	0	0	0	0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	37	CCDS4935.1																																																																																			.		0.542	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		-	51890186	C	-	51890186	7	5	161	1	0	1	0	1	0	0	0	0	11997	842	30	0	7985	0	PKHD1	6	51890186	Frame_Shift_Del	DEL	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	3854078	51890186	119224881	40	14625											
LRRC1	55227	broad.mit.edu	37	chr6	53764574	53764575	+	Frame_Shift_Del	DEL	TT	TT	-																															aatctgaagaacctgctgtgTttagatgtctctgaaaacag																								rs550591899		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:53764574_53764575delTT	ENST00000370888.1	+	8	949_950	c.672_673delTT	c.(670-675)tgtttafs	p.L225fs		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	225						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		ACCTGCTGTGTTTAGATGTCTC	0.391																																					p.224_225del													.	LRRC1-91	0			c.672_673del						.																																			SO:0001589	frameshift_variant	55227	exon8			GCTGTGTTTAGAT	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.672_673delTT	6.37:g.53764574_53764575delTT	ENSP00000359925:p.Leu225fs	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	412	32	NM_018214	0	0	0	0	0	Q5TGN3|Q9HAC0|Q9NVF1	Frame_Shift_Del	DEL	ENST00000370888.1	37	CCDS4953.2																																																																																			.		0.391	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		-	53764575	TT	-	53764574	7	5	161	1	0	1	0	1	0	0	0	0	8991	1731	60	0	702	0	LRRC1	6	53764574	Frame_Shift_Del	DEL	TT	TCGA-Q2-A5QZ-01A-11D-A28G-10	1874388	53764574	117350493	41	14626											
ZNF451	26036	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr6	56989656	56989656	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agagaagaatagagcattcaGagtatgtgctattttaattg	15	13	10	3	0	1	4	1	0	0	4	1	5	1	4	0	0	2	3	0	0	6	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:56989656G>A	ENST00000370706.4	+	4	555	c.311G>A	c.(310-312)aGa>aAa	p.R104K	RP11-203B9.4_ENST00000586432.1_RNA|ZNF451_ENST00000357489.3_Splice_Site_p.R104K|RP11-203B9.4_ENST00000587815.1_RNA|ZNF451_ENST00000491832.2_Splice_Site_p.R104K|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	104					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGAGCATTCAGAGTATGTGCT	0.289																																					p.R104K		.											.	ZNF451-93	0			c.G311A						.						35	33	34					6																	56989656		2203	4298	6501	SO:0001630	splice_region_variant	26036	exon4			CATTCAGAGTATG	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.312+1G>A	6.37:g.56989656G>A		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	253	16	NM_001031623	0	0	0	0	0	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	37	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.456326	0.26161	.	.	ENSG00000112200	ENST00000510483;ENST00000370706;ENST00000357489;ENST00000491832	T;T;T;T	0.05996	3.36;3.36;3.36;3.36	5.37	5.37	0.77165	.	0.061002	0.64402	D	0.000003	T	0.01156	0.0038	N	0.17082	0.46	0.80722	D	1	B;B;B;B	0.20887	0.049;0.037;0.027;0.037	B;B;B;B	0.15484	0.013;0.008;0.008;0.008	T	0.43360	-0.9396	10	0.06625	T	0.88	-16.7164	7.7021	0.28630	0.2013:0.0:0.7987:0.0	.	104;104;104;104	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	K	76;104;104;104	ENSP00000427558:R76K;ENSP00000359740:R104K;ENSP00000350083:R104K;ENSP00000421645:R104K	ENSP00000350083:R104K	R	+	2	0	ZNF451	57097615	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.870000	0.63035	2.665000	0.90641	0.655000	0.94253	AGA	.		0.289	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	Missense_Mutation	A	56989656	G	A	56989656	5	1	161	1	0	0	0	0	0	0	1	0	17954	956	33	2	325	2	ZNF451	6	56989656	Splice_Site	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	3225082	56989656	114125411	42	14627											
PHF3	23469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	64394128	64394128	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggaagactgtatctactGctaaagcaggagtgaaacaa	15	8	11	7	0	1	2	0	1	1	1	1	4	1	4	0	2	4	3	0	2	7	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:64394128G>A	ENST00000262043.3	+	4	845	c.505G>A	c.(505-507)Gct>Act	p.A169T	PHF3_ENST00000393387.1_Missense_Mutation_p.A169T|PHF3_ENST00000509330.1_Missense_Mutation_p.A169T			Q92576	PHF3_HUMAN	PHD finger protein 3	169					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TGTATCTACTGCTAAAGCAGG	0.418																																					p.A169T	GBM(135;136 1820 29512 34071 46235)	.											.	PHF3-229	0			c.G505A						.						176	182	180					6																	64394128		2203	4300	6503	SO:0001583	missense	23469	exon3			TCTACTGCTAAAG	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"Zinc fingers, PHD-type"	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.505G>A	6.37:g.64394128G>A	ENSP00000262043:p.Ala169Thr	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	233	92	NM_015153	0	0	0	0	0	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	G	7.135	0.580718	0.13686	.	.	ENSG00000118482	ENST00000481385;ENST00000262043;ENST00000494284;ENST00000509330;ENST00000393387;ENST00000514822	T;T;T;T;T	0.41758	2.0;2.31;1.99;0.99;2.31	5.92	2.2	0.27929	.	1.243890	0.06006	N	0.648726	T	0.05686	0.0149	N	0.03608	-0.345	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29941	-0.9995	10	0.21540	T	0.41	-2.6584	2.9393	0.05825	0.1274:0.5534:0.1251:0.1941	.	169;169	Q92576;D6R9X2	PHF3_HUMAN;.	T	81;169;122;169;169;99	ENSP00000425227:A81T;ENSP00000262043:A169T;ENSP00000424078:A122T;ENSP00000422841:A169T;ENSP00000377048:A169T	ENSP00000262043:A169T	A	+	1	0	PHF3	64452087	0.066000	0.20996	0.643000	0.29450	0.707000	0.40811	0.935000	0.28924	0.120000	0.18254	-0.139000	0.14373	GCT	.		0.418	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			A	64394128	G	A	64394128	3	1	161	1	0	0	0	0	1	0	0	0	11862	1319	46	2	515	2	PHF3	6	64394128	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	7404472	64394128	106720939	43	14628											
IBTK	25998	hgsc.bcm.edu;broad.mit.edu	37	chr6	82883139	82883139	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttgccttctggtcctggggTaccatgggtagagcatctgc	5	12	14	10	0	2	1	0	0	2	1	3	1	3	1	3	4	4	4	3	4	2	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:82883139T>C	ENST00000306270.7	-	27	4291	c.3742A>G	c.(3742-3744)Acc>Gcc	p.T1248A	IBTK_ENST00000503631.1_Missense_Mutation_p.T1047A|IBTK_ENST00000510291.1_Missense_Mutation_p.T1233A	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1248					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GGTCCTGGGGTACCATGGGTA	0.373																																					p.T1248A		.											.	IBTK-92	0			c.A3742G						.						126	126	126					6																	82883139		2203	4300	6503	SO:0001583	missense	25998	exon27			CTGGGGTACCATG	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3742A>G	6.37:g.82883139T>C	ENSP00000305721:p.Thr1248Ala	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	52	3	NM_015525	0	0	3	3	0	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.994795	0.00435	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.26518	2.06;1.73;2.06	5.41	0.249	0.15531	.	0.949376	0.08860	N	0.883161	T	0.06826	0.0174	L	0.46157	1.445	0.09310	N	1	B;B;B;B	0.13145	0.007;0.0;0.004;0.0	B;B;B;B	0.15484	0.007;0.0;0.013;0.0	T	0.42207	-0.9465	10	0.22109	T	0.4	1.4624	5.9681	0.19336	0.1213:0.1927:0.0:0.686	.	1047;1233;199;1248	E9PDR5;E7EPI0;B3KX60;Q9P2D0	.;.;.;IBTK_HUMAN	A	1248;1047;1233	ENSP00000305721:T1248A;ENSP00000422762:T1047A;ENSP00000426405:T1233A	ENSP00000305721:T1248A	T	-	1	0	IBTK	82939858	0.180000	0.23148	0.001000	0.08648	0.009000	0.06853	1.043000	0.30316	-0.339000	0.08401	-1.937000	0.00501	ACC	.		0.373	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		C	82883139	T	C	82883139	3	2	161	1	0	0	0	0	1	0	0	0	7497	1638	57	3	331	3	IBTK	6	82883139	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	18489011	82883139	88231928	44	14629											
MAP3K5	4217	hgsc.bcm.edu	37	chr6	137113272	137113272	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggcacagagaaagtgatGccctcgtccgcctccgtgct	7	8	13	13	3	0	2	0	1	0	1	3	3	2	2	4	2	2	2	4	2	1	0	rs142989545	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:137113272G>A	ENST00000359015.4	-	1	384	c.24C>T	c.(22-24)ggC>ggT	p.G8G		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	8					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		AGAAAGTGATGCCCTCGTCCG	0.751													G|||	47	0.00938498	0.0325	0.0058	5008	,	,		8970	0		0	False		,,,				2504	0				p.G8G		.											.	MAP3K5-982	0			c.C24T						.	G		74,3452		1,72,1690	4	5	5		24	3.8	1	6	dbSNP_134	5	2,6840		0,2,3419	no	coding-synonymous	MAP3K5	NM_005923.3		1,74,5109	AA,AG,GG		0.0292,2.0987,0.733		8/1375	137113272	76,10292	1763	3421	5184	SO:0001819	synonymous_variant	4217	exon1			AGTGATGCCCTCG	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6857	protein-coding gene	gene with protein product	"apoptosis signal regulating kinase 1"	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.24C>T	6.37:g.137113272G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	40	16	NM_005923	0	0	0	0	0	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			G|0.988;A|0.012		0.751	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1			A	137113272	G	A	137113272	2	1	161	1	0	0	0	0	0	0	0	1	9278	1306	46	2		2	MAP3K5	6	137113272	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	54230133	137113272	34001795	45	14630											
GPR126	57211	broad.mit.edu	37	chr6	142741042	142741042	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttctgaacattgccatgttCattgtggtaatggtgcagat	9	16	10	6	0	2	2	1	1	1	1	2	2	2	2	1	2	3	3	1	2	2	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:142741042C>T	ENST00000230173.6	+	22	3596	c.3120C>T	c.(3118-3120)ttC>ttT	p.F1040F	GPR126_ENST00000296932.8_Silent_p.F1012F|GPR126_ENST00000367608.2_Silent_p.F1012F|GPR126_ENST00000367609.3_Silent_p.F1040F	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1040					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)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TTGCCATGTTCATTGTGGTAA	0.428																																					p.F1040F													.	GPR126-91	0			c.C3120T						.						259	237	244					6																	142741042		1927	4143	6070	SO:0001819	synonymous_variant	57211	exon22			CATGTTCATTGTG	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3120C>T	6.37:g.142741042C>T		Somatic	112	0		WXS	Illumina HiSeq	Phase_I	190	3	NM_198569	0	0	0	0	0	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Silent	SNP	ENST00000230173.6	37	CCDS47490.1																																																																																			.		0.428	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142741042	C	T	142741042	2	4	161	1	0	0	0	0	0	0	0	1	6660	825	29	2		2	GPR126	6	142741042	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	5627770	142741042	28374025	46	14631											
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161413041	161413041	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgccatggaggagccgccGccaccgccgccgccgccacc	5	1	13	22	7	0	0	0	0	0	0	0	2	0	2	11	2	1	0	11	2	0	0	rs78823261	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:161413041G>A	ENST00000392142.4	+	1	226	c.78G>A	c.(76-78)ccG>ccA	p.P26P	MAP3K4_ENST00000366920.2_Silent_p.P26P|MAP3K4_ENST00000348824.7_Silent_p.P26P|RP3-428L16.2_ENST00000608721.1_RNA|MAP3K4_ENST00000366919.2_Silent_p.P26P	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	26	Poly-Pro.				activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGGAgccgccgccaccgccgc	0.741													G|||	94	0.01877	0.0303	0.0202	5008	,	,		9039	0.004		0.0129	False		,,,				2504	0.0235				p.P26P		.											.	MAP3K4-548	0			c.G78A						.						2	4	3					6																	161413041		1452	3068	4520	SO:0001819	synonymous_variant	4216	exon1			GCCGCCGCCACCG	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.78G>A	6.37:g.161413041G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	21	10	NM_006724	0	0	0	0	0	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																			.		0.741	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161413041	G	A	161413041	2	1	161	1	0	0	0	0	0	0	0	1	9277	1074	38	1		1	MAP3K4	6	161413041	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	18671999	161413041	9702026	47	14632											
UNC93A	54346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr6	167709627	167709627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacacacatgcagagaaggCgggaaagcgtggcaaagaca	18	2	13	8	2	0	2	0	0	0	2	0	4	0	3	0	3	3	2	0	3	4	0	rs538293568		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:167709627C>T	ENST00000230256.3	+	3	552	c.377C>T	c.(376-378)gCg>gTg	p.A126V	UNC93A_ENST00000366830.2_3'UTR|UNC93A_ENST00000366829.2_Missense_Mutation_p.A126V	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCAGAGAAGGCGGGAAAGCGT	0.547													C|||	1	0.000199681	0	0	5008	,	,		22340	0.001		0	False		,,,				2504	0				p.A126V		.											.	UNC93A-90	0			c.C377T						.						224	203	210					6																	167709627		2203	4300	6503	SO:0001583	missense	54346	exon3			AGAAGGCGGGAAA	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"unc93 (C.elegans) homolog A"			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.377C>T	6.37:g.167709627C>T	ENSP00000230256:p.Ala126Val	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	270	109	NM_018974	0	0	0	2	2	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	.	.	.	.	.	.	.	.	.	.	C	5.524	0.281564	0.10458	.	.	ENSG00000112494	ENST00000503433;ENST00000230256;ENST00000366829	T;T;T	0.30981	1.51;3.54;3.52	5.53	-3.43	0.04810	Major facilitator superfamily domain, general substrate transporter (1);	1.006790	0.07968	N	0.983528	T	0.04634	0.0126	N	0.17723	0.515	0.09310	N	1	B;B	0.16166	0.016;0.006	B;B	0.13407	0.009;0.009	T	0.37244	-0.9714	10	0.25106	T	0.35	-1.2474	4.3328	0.11071	0.3325:0.2722:0.0:0.3953	.	126;126	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	V	126	ENSP00000421484:A126V;ENSP00000230256:A126V;ENSP00000355794:A126V	ENSP00000230256:A126V	A	+	2	0	UNC93A	167629617	0.020000	0.18652	0.000000	0.03702	0.018000	0.09664	1.103000	0.31062	-1.274000	0.02421	-0.890000	0.02929	GCG	.		0.547	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974		T	167709627	C	T	167709627	3	4	161	1	0	0	0	0	1	0	0	0	17029	768	27	1	387	1	UNC93A	6	167709627	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6296586	167709627	3405440	48	14633											
PDCD2	5134	hgsc.bcm.edu	37	chr6	170893454	170893454	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcagcggtggaaggcgtcCgggcggccaggcagcggcgc	6	3	20	12	6	0	0	0	0	0	0	1	1	1	1	2	7	3	2	2	7	1	0	rs200023629	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:170893454C>T	ENST00000541970.1	-	1	294	c.216G>A	c.(214-216)ccG>ccA	p.P72P	PDCD2_ENST00000542896.1_Silent_p.P72P|PDCD2_ENST00000392090.2_Silent_p.P39P|PDCD2_ENST00000453163.2_Silent_p.P72P|PDCD2_ENST00000443345.2_Silent_p.P39P|PDCD2_ENST00000537445.1_Silent_p.P39P	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	72					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		GGAAGGCGTCCGGGCGGCCAG	0.751													.|||	27	0.00539137	0.0204	0	5008	,	,		10592	0		0	False		,,,				2504	0				p.P72P	Colon(60;1476 1726 39478)	.											.	PDCD2-227	0			c.G216A						.	C	,,,,,	21,3659		0,21,1819	13	15	14		216,117,117,117,216,216	-6.7	0	6		14	0,7658		0,0,3829	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDCD2	NM_001199461.1,NM_001199462.1,NM_001199463.1,NM_001199464.1,NM_002598.3,NM_144781.2	,,,,,	0,21,5648	TT,TC,CC		0.0,0.5707,0.1852	,,,,,	72/222,39/312,39/196,39/189,72/345,72/229	170893454	21,11317	1840	3829	5669	SO:0001819	synonymous_variant	5134	exon1			GGCGTCCGGGCGG	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"Zinc fingers, MYND-type"	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.216G>A	6.37:g.170893454C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	50	21	NM_002598	0	0	0	0	0	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Silent	SNP	ENST00000541970.1	37	CCDS5316.1																																																																																			C|0.997;T|0.003		0.751	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598		T	170893454	C	T	170893454	2	4	161	1	0	0	0	0	0	0	0	1	11645	639	23	1		1	PDCD2	6	170893454	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	3183827	170893454	221613	49	14634											
AGR3	155465	broad.mit.edu	37	chr7	16901068	16901068	+	Frame_Shift_Del	DEL	C	C	-																															taaattcttatcagtggtttCatgctagcaggagaagaaaa																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:16901068delC	ENST00000310398.2	-	6	377	c.307delG	c.(307-309)gaafs	p.E103fs	AGR3_ENST00000402239.3_Frame_Shift_Del_p.E103fs	NM_176813.3	NP_789783.1	Q8TD06	AGR3_HUMAN	anterior gradient 3	103						extracellular region (GO:0005576)	dystroglycan binding (GO:0002162)			central_nervous_system(1)|kidney(8)|lung(2)|skin(1)|stomach(1)	13	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		TCAGTGGTTTCATGCTAGCAG	0.323																																					p.E103fs													.	AGR3-90	0			c.307delG						.						110	109	109					7																	16901068		2203	4295	6498	SO:0001589	frameshift_variant	155465	exon6			TGGTTTCATGCTA	AY069977	CCDS5365.1	7p21.1	2013-07-31	2013-07-31		ENSG00000173467	ENSG00000173467		"Protein disulfide isomerases"	24167	protein-coding gene	gene with protein product	"breast cancer membrane protein 11", "protein disulfide isomerase family A, member 18"	609482	"anterior gradient 3 homolog (Xenopus laevis)"			12592373, 12477722	Standard	NM_176813		Approved	HAG3, hAG-3, BCMP11, PDIA18	uc003sts.3	Q8TD06	OTTHUMG00000128411	ENST00000310398.2:c.307delG	7.37:g.16901068delC	ENSP00000308606:p.Glu103fs	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	207	9	NM_176813	0	0	0	0	0	A4D120	Frame_Shift_Del	DEL	ENST00000310398.2	37	CCDS5365.1																																																																																			.		0.323	AGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250191.2	NM_176813		-	16901068	C	-	16901068	7	5	161	1	0	1	0	1	0	0	0	0	396	835	29	0	205	0	AGR3	7	16901068	Frame_Shift_Del	DEL	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		16901068	142237595	50	14635											
TRA2A	29896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	23547073	23547073	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	catgtagatgcctggtgttgGtgtgtgcgctctcttggtta	4	16	14	7	1	1	1	0	0	1	1	2	1	1	1	1	3	2	4	1	3	2	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:23547073G>A	ENST00000297071.4	-	5	823	c.607C>T	c.(607-609)Cca>Tca	p.P203S	TRA2A_ENST00000474586.1_5'UTR|TRA2A_ENST00000392502.4_Missense_Mutation_p.P102S|TRA2A_ENST00000538367.1_Missense_Mutation_p.P102S	NM_013293.3	NP_037425.1	Q13595	TRA2A_HUMAN	transformer 2 alpha homolog (Drosophila)	203	Linker.				mRNA splicing, via spliceosome (GO:0000398)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10						CCTGGTGTTGGTGTGTGCGCT	0.413																																					p.P203S	Pancreas(121;2137 2973 46590)	.											.	TRA2A-91	0			c.C607T						.						249	237	241					7																	23547073		2203	4300	6503	SO:0001583	missense	29896	exon5			GTGTTGGTGTGTG	U53209	CCDS5383.1, CCDS64609.1, CCDS75569.1	7p15.3	2014-02-12			ENSG00000164548	ENSG00000164548		"RNA binding motif (RRM) containing"	16645	protein-coding gene	gene with protein product		602718				8799144, 9546399	Standard	XM_005249725		Approved	htra-2-alpha, tra2a, AWMS1	uc003swi.3	Q13595	OTTHUMG00000128459	ENST00000297071.4:c.607C>T	7.37:g.23547073G>A	ENSP00000297071:p.Pro203Ser	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	102	37	NM_013293	0	0	6	6	0	B4DUA9	Missense_Mutation	SNP	ENST00000297071.4	37	CCDS5383.1	.	.	.	.	.	.	.	.	.	.	G	34	5.300909	0.95601	.	.	ENSG00000164548	ENST00000297071;ENST00000392502;ENST00000538367	T;T;T	0.74106	-0.81;-0.81;-0.81	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.87293	0.6141	M	0.88906	2.99	0.80722	D	1	D	0.55800	0.973	P	0.58577	0.841	D	0.88826	0.3302	10	0.59425	D	0.04	-12.1484	19.5178	0.95171	0.0:0.0:1.0:0.0	.	203	Q13595	TRA2A_HUMAN	S	203;102;102	ENSP00000297071:P203S;ENSP00000376290:P102S;ENSP00000441116:P102S	ENSP00000297071:P203S	P	-	1	0	TRA2A	23513598	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.831000	0.99420	2.615000	0.88500	0.650000	0.86243	CCA	.		0.413	TRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250257.1	NM_013293		A	23547073	G	A	23547073	3	1	161	1	0	0	0	0	1	0	0	0	16466	1261	44	2	257	2	TRA2A	7	23547073	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	6646005	23547073	135591590	51	14636											
VWC2	375567	hgsc.bcm.edu	37	chr7	49815181	49815181	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggagaagcgtgagcaCgcctctcgggacggcccggg	7	3	18	13	5	1	2	0	1	1	1	2	4	1	3	3	5	2	1	3	5	1	0	rs201551578	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:49815181C>T	ENST00000340652.4	+	2	706	c.150C>T	c.(148-150)caC>caT	p.H50H		NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	50					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)				cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						AGCGTGAGCACGCCTCTCGGG	0.726													C|||	32	0.00638978	0.0227	0.0029	5008	,	,		8632	0		0	False		,,,				2504	0				p.H50H		.											.	VWC2-514	0			c.C150T						.	C		89,4175		1,87,2044	9	8	8		150	4.8	1	7		8	3,8303		0,3,4150	no	coding-synonymous	VWC2	NM_198570.3		1,90,6194	TT,TC,CC		0.0361,2.0872,0.7319		50/326	49815181	92,12478	2132	4153	6285	SO:0001819	synonymous_variant	375567	exon2			TGAGCACGCCTCT	AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"brorin", "brain-specific chordin-like"	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.150C>T	7.37:g.49815181C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	41	25	NM_198570	0	0	0	0	0	Q6UXE2	Silent	SNP	ENST00000340652.4	37	CCDS5508.1																																																																																			C|0.997;T|0.003		0.726	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570		T	49815181	C	T	49815181	2	4	161	1	0	0	0	0	0	0	0	1	17276	535	19	1		1	VWC2	7	49815181	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	26268108	49815181	109323482	52	14637											
KIAA1324L	222223	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	86577110	86577110	+	Frame_Shift_Del	DEL	A	A	-																															catgaatgttgcgatgttagAaaatcctgccggcaattcat																								rs536741266		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:86577110delA	ENST00000450689.2	-	3	624	c.439delT	c.(439-441)tctfs	p.S147fs	KIAA1324L_ENST00000444627.1_Frame_Shift_Del_p.S147fs|KIAA1324L_ENST00000416314.1_Intron	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	147						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					GCGATGTTAGAAAATCCTGCC	0.473																																					p.S147fs		.											.	KIAA1324L-97	0			c.439delT						.						124	101	108					7																	86577110		692	1591	2283	SO:0001589	frameshift_variant	222223	exon3			.	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.439delT	7.37:g.86577110delA	ENSP00000413445:p.Ser147fs	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	178	64	NM_001142749	0	0	0	0	0	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Frame_Shift_Del	DEL	ENST00000450689.2	37	CCDS47632.1																																																																																			.		0.473	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		-	86577110	A	-	86577110	7	5	161	1	0	1	0	1	0	0	0	0	8245	246	9	0	2730	0	KIAA1324L	7	86577110	Frame_Shift_Del	DEL	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	36761929	86577110	72561553	53	14638											
ARPC1B	10095	hgsc.bcm.edu	37	chr7	98990335	98990335	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttcacctatgacgccgcCgcggggatgctgagcttcgg	5	9	14	13	5	1	2	1	2	0	0	2	3	1	3	3	3	2	3	3	3	1	3	rs530272604	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:98990335C>T	ENST00000451682.1	+	10	1134	c.825C>T	c.(823-825)gcC>gcT	p.A275A	PDAP1_ENST00000496335.1_5'UTR|ARPC1B_ENST00000252725.5_Silent_p.A275A			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	275					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			ATGACGCCGCCGCGGGGATGC	0.697													C|||	4	0.000798722	0.003	0	5008	,	,		13061	0		0	False		,,,				2504	0				p.A275A		.											.	ARPC1B-90	0			c.C825T						.						4	5	4					7																	98990335		1777	3378	5155	SO:0001819	synonymous_variant	10095	exon8			CGCCGCCGCGGGG	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.825C>T	7.37:g.98990335C>T		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	147	84	NM_005720	0	0	259	650	391	Q9BU00	Silent	SNP	ENST00000451682.1	37	CCDS5661.1																																																																																			.		0.697	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		T	98990335	C	T	98990335	2	4	161	1	0	0	0	0	0	0	0	1	971	639	23	1		1	ARPC1B	7	98990335	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	12413225	98990335	60148328	54	14639											
OPN1SW	611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	128415147	128415147	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcggaagttgccgaagggCttacagatgacaatgtagcg	13	7	14	7	3	0	2	0	1	0	1	0	4	0	3	1	2	4	3	1	2	6	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:128415147C>T	ENST00000249389.2	-	2	413	c.414G>A	c.(412-414)aaG>aaA	p.K138K		NM_001708.2	NP_001699.1	P03999	OPSB_HUMAN	opsin 1 (cone pigments), short-wave-sensitive	138					phototransduction (GO:0007602)|phototransduction, visible light (GO:0007603)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)|receptor activity (GO:0004872)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|stomach(1)	19						TGCCGAAGGGCTTACAGATGA	0.547																																					p.K138K		.											.	OPN1SW-68	0			c.G414A						.						96	75	82					7																	128415147		2203	4300	6503	SO:0001819	synonymous_variant	611	exon2			GAAGGGCTTACAG	U53874	CCDS5806.1	7q31.3-q32	2013-01-08	2008-04-16		ENSG00000128617	ENSG00000128617		"GPCR / Class A : Opsin receptors"	1012	protein-coding gene	gene with protein product	"color blindness, tritan", "blue-sensitive opsin"	613522	"blue cone photoreceptor pigment"	BCP		2937147, 8270261	Standard	NM_001708		Approved	BOP, CBT	uc003vnt.4	P03999	OTTHUMG00000158311	ENST00000249389.2:c.414G>A	7.37:g.128415147C>T		Somatic	62	0		WXS	Illumina HiSeq	Phase_I	197	54	NM_001708	0	0	0	0	0	Q13877	Silent	SNP	ENST00000249389.2	37	CCDS5806.1																																																																																			.		0.547	OPN1SW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350655.1	NM_001708		T	128415147	C	T	128415147	2	4	161	1	0	0	0	0	0	0	0	1	10906	796	28	2		2	OPN1SW	7	128415147	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	29424812	128415147	30723516	55	14640											
CLEC2L	154790	hgsc.bcm.edu	37	chr7	139208786	139208786	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcgcccgcagaggctgaggCccgcggccccgaggggctgc	4	4	17	16	5	0	2	0	1	0	1	1	3	0	2	4	5	1	3	4	5	0	1	rs111447865	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:139208786C>A	ENST00000422142.2	+	1	185	c.113C>A	c.(112-114)gCc>gAc	p.A38D		NM_001080511.2	NP_001073980.2	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	38						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|kidney(2)|lung(1)	5	Melanoma(164;0.233)					GAGGCTGAGGCCCGCGGCCCC	0.831													C|||	64	0.0127796	0.0454	0.0043	5008	,	,		4163	0		0.001	False		,,,				2504	0				p.A38D		.											.	.	0			c.C113A						.						1	3	2					7																	139208786		285	1021	1306	SO:0001583	missense	154790	exon1			CTGAGGCCCGCGG	AK057548	CCDS47724.1	7q34	2011-05-18			ENSG00000236279	ENSG00000236279		"C-type lectin domain containing"	21969	protein-coding gene	gene with protein product							Standard	NM_001080511		Approved	FLJ32986	uc010lnd.3	P0C7M8	OTTHUMG00000164900	ENST00000422142.2:c.113C>A	7.37:g.139208786C>A	ENSP00000390661:p.Ala38Asp	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	23	10	NM_001080511	0	0	0	0	0		Missense_Mutation	SNP	ENST00000422142.2	37	CCDS47724.1	.	.	.	.	.	.	.	.	.	.	c	11.60	1.686495	0.29962	.	.	ENSG00000236279	ENST00000422142	T	0.03889	3.77	2.96	-1.4	0.08968	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.28054	N	0.933269	B	0.22414	0.069	B	0.14023	0.01	T	0.46541	-0.9184	9	0.18710	T	0.47	.	11.9064	0.52715	0.0:0.7171:0.2829:0.0	.	38	P0C7M8	CLC2L_HUMAN	D	38	ENSP00000390661:A38D	ENSP00000390661:A38D	A	+	2	0	CLEC2L	138859326	1.000000	0.71417	0.768000	0.31515	0.245000	0.25701	0.831000	0.27476	-0.490000	0.06707	0.283000	0.19423	GCC	A|1.000;|0.000		0.831	CLEC2L-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380878.1	NM_001080511		A	139208786	C	A	139208786	3	1	161	1	0	0	0	0	1	0	0	0	3515	739	26	4	115	4	CLEC2L	7	139208786	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	10793639	139208786	19929877	56	14641											
AGAP3	116988	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr7	150839014	150839014	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agtcgtttgaatttgtggtgGtgtccctcactgggcagacg	6	13	14	8	2	1	2	1	1	0	1	3	2	2	2	1	3	0	2	1	3	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:150839014G>A	ENST00000463381.1	+	12	1337	c.841G>A	c.(841-843)Gtg>Atg	p.V281M	AGAP3_ENST00000397238.2_Missense_Mutation_p.V612M	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	576	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						ATTTGTGGTGGTGTCCCTCAC	0.612																																					p.V612M		.											.	AGAP3-92	0			c.G1834A						.						94	112	106					7																	150839014		2150	4240	6390	SO:0001583	missense	116988	exon14			GTGGTGGTGTCCC	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.841G>A	7.37:g.150839014G>A	ENSP00000418016:p.Val281Met	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	327	124	NM_031946	0	0	12	16	4	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000463381.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.553104|4.553104	0.86127|0.86127	.|.	.|.	ENSG00000133612|ENSG00000133612	ENST00000463381;ENST00000397232;ENST00000397238;ENST00000335355|ENST00000461065	T;T|.	0.19394|.	2.15;2.15|.	4.24|4.24	4.24|4.24	0.50183|0.50183	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.64402|.	D|.	0.000008|.	T|.	0.74558|.	0.3732|.	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	D;D;D;P|.	0.89917|.	1.0;0.999;0.999;0.95|.	D;D;D;P|.	0.97110|.	1.0;0.981;0.964;0.755|.	T|.	0.75977|.	-0.3127|.	10|.	0.72032|.	D|.	0.01|.	.|.	16.1835|16.1835	0.81929|0.81929	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	576;111;612;281|.	Q96P47;E7ETI2;Q96P47-4;B3KNZ8|.	AGAP3_HUMAN;.;.;.|.	M|X	281;111;612;576|104	ENSP00000418016:V281M;ENSP00000380413:V612M|.	ENSP00000334157:V576M|.	V|W	+|+	1|3	0|0	AGAP3|AGAP3	150469947|150469947	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.458000|7.458000	0.80787|0.80787	2.346000|2.346000	0.79739|0.79739	0.655000|0.655000	0.94253|0.94253	GTG|TGG	.		0.612	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946		A	150839014	G	A	150839014	3	1	161	1	0	0	0	0	1	0	0	0	369	1261	44	2	1955	2	AGAP3	7	150839014	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	11630228	150839014	8299649	57	14642											
RHEB	6009	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	151188050	151188050	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttttctatggttggatcgtAggagtccacaaattggcctt	8	15	11	7	1	1	0	0	0	1	0	3	2	2	2	2	4	0	3	2	4	3	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:151188050A>T	ENST00000262187.5	-	2	515	c.103T>A	c.(103-105)Tac>Aac	p.Y35N	RHEB_ENST00000496004.1_5'UTR|RHEB_ENST00000472642.1_5'UTR	NM_005614.3	NP_005605.1	Q15382	RHEB_HUMAN	Ras homolog enriched in brain	35					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|positive regulation of TOR signaling (GO:0032008)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)	p.Y35N(1)		breast(3)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)	14			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		GTTGGATCGTAGGAGTCCACA	0.358																																					p.Y35N	Pancreas(98;671 892 8111 15140 36556 39178 39939 44184)	.											.	RHEB-910	1	Substitution - Missense(1)	kidney(1)	c.T103A						.						103	100	101					7																	151188050		2203	4300	6503	SO:0001583	missense	6009	exon2			GATCGTAGGAGTC	D78132	CCDS5927.1	7q36	2014-05-09	2003-07-14	2003-07-14	ENSG00000106615	ENSG00000106615			10011	protein-coding gene	gene with protein product		601293	"Ras homolog enriched in brain 2"	RHEB2		8661031	Standard	NM_005614		Approved		uc003wkh.1	Q15382	OTTHUMG00000157330	ENST00000262187.5:c.103T>A	7.37:g.151188050A>T	ENSP00000262187:p.Tyr35Asn	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	87	5	NM_005614	0	0	6	6	0	B3KWN6|D3DX13|Q53Y56|Q99444	Missense_Mutation	SNP	ENST00000262187.5	37	CCDS5927.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708820	0.89018	.	.	ENSG00000106615	ENST00000262187	T	0.81247	-1.47	5.42	5.42	0.78866	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.91841	0.7418	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93659	0.6980	10	0.87932	D	0	.	13.3975	0.60863	1.0:0.0:0.0:0.0	.	35	Q15382	RHEB_HUMAN	N	35	ENSP00000262187:Y35N	ENSP00000262187:Y35N	Y	-	1	0	RHEB	150818983	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.143000	0.89621	2.051000	0.60960	0.533000	0.62120	TAC	.		0.358	RHEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348468.2	NM_005614		T	151188050	A	T	151188050	3	4	161	1	0	0	0	0	1	0	0	0	13360	420	15	5	479	5	RHEB	7	151188050	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	349036	151188050	7950613	58	14643											
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr7	152012386	152012386	+	Frame_Shift_Del	DEL	T	T	-																															gtctccttgtcctaaggaacTtttttccccacagtaacaaa																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:152012386delT	ENST00000262189.6	-	4	645	c.427delA	c.(427-429)agtfs	p.S144fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.S144fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	144					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CCTAAGGAACTTTTTTCCCCA	0.378																																					p.S143fs		.											.	MLL3-1398	0			c.427delA						.						136	126	129					7																	152012386		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon4			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.427delA	7.37:g.152012386delT	ENSP00000262189:p.Ser144fs	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	144	52	NM_170606	0	0	0	0	0	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	37	CCDS5931.1																																																																																			.		0.378	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	152012386	T	-	152012386	7	5	161	1	0	1	0	1	0	0	0	0	9647	1609	56	0	14532	0	MLL3	7	152012386	Frame_Shift_Del	DEL	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	824336	152012386	7126277	59	14644											
SGK223	157285	broad.mit.edu	37	chr8	8239069	8239069	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tccaggcggcagttctcaggCctgggaggcaggcgcggtgg	5	6	19	11	3	1	0	1	0	1	0	3	1	2	1	2	8	0	3	2	8	0	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr8:8239069C>A	ENST00000520004.1	-	2	453	c.189G>T	c.(187-189)agG>agT	p.R63S	SGK223_ENST00000330777.4_Missense_Mutation_p.R63S			Q86YV5	SG223_HUMAN		63							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGTTCTCAGGCCTGGGAGGCA	0.657																																					p.R63S	GBM(34;731 755 10259 33573 33867)												.	.	0			c.G189T						.						48	49	49					8																	8239069		2004	4157	6161	SO:0001583	missense	0	exon1			CTCAGGCCTGGGA																												ENST00000520004.1:c.189G>T	8.37:g.8239069C>A	ENSP00000428054:p.Arg63Ser	Somatic	14	0		WXS	Illumina HiSeq	Phase_I	129	9	NM_001080826	0	0	0	0	0	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236881	0.39498	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59083	0.29;0.29	4.49	2.69	0.31865	.	0.226672	0.30658	N	0.009160	T	0.41696	0.1170	L	0.38531	1.155	0.27832	N	0.941416	B	0.31968	0.349	B	0.24701	0.055	T	0.44802	-0.9304	10	0.72032	D	0.01	.	8.2345	0.31618	0.0:0.7459:0.0:0.2541	.	63	Q86YV5	SG223_HUMAN	S	63	ENSP00000330930:R63S;ENSP00000428054:R63S	ENSP00000330930:R63S	R	-	3	2	AC068353.1	8276479	1.000000	0.71417	0.887000	0.34795	0.775000	0.43874	0.980000	0.29513	1.272000	0.44329	-0.230000	0.12252	AGG	.		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8239069	C	A	8239069	3	1	161	1	0	0	0	0	1	0	0	0	14242	738	26	4	4039	4	SGK223	8	8239069	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		8239069	138124953	60	14645											
ADAM18	8749	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr8	39550201	39550201	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaatgcaaagggaaaggggTaagtcacttttgtatctgaa	16	10	11	4	0	2	1	1	1	1	0	2	2	2	2	0	3	1	3	0	3	7	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr8:39550201T>A	ENST00000265707.5	+	17	1947		c.e17+2		ADAM18_ENST00000541111.1_Splice_Site|ADAM18_ENST00000379866.1_Splice_Site|ADAM18_ENST00000523755.1_Splice_Site	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			GGGAAAGGGGTAAGTCACTTT	0.348																																					.													.	ADAM18-228	0			c.1902+2T>A						.						93	96	95					8																	39550201		2203	4299	6502	SO:0001630	splice_region_variant	8749	exon17			AAGGGGTAAGTCA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"ADAM metallopeptidase domain containing"	196	protein-coding gene	gene with protein product			"a disintegrin and metalloproteinase domain 18"			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1902+2T>A	8.37:g.39550201T>A		Somatic	119	1		WXS	Illumina HiSeq	Phase_I	189	67	NM_014237	0	0	0	0	0	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Splice_Site	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.798603	0.50208	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	.	.	.	3.95	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5062	0.39048	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM18	39669358	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	3.170000	0.50816	2.023000	0.59567	0.455000	0.32223	.	.		0.348	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	Intron	A	39550201	T	A	39550201	5	1	161	1	0	0	0	0	0	0	1	0	239	1652	57	5	1970	5	ADAM18	8	39550201	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	31311132	39550201	106813821	61	14646											
LRRCC1	85444	ucsc.edu	37	chr8	86057688	86057688	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcaagaacaaaaaaacaaTggaagcaaaaattaagcaac	25	4	6	6	0	0	1	0	0	0	1	0	2	0	2	0	1	6	3	0	1	11	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr8:86057688T>C	ENST00000360375.3	+	19	3190	c.3041T>C	c.(3040-3042)aTg>aCg	p.M1014T	LRRCC1_ENST00000414626.2_Missense_Mutation_p.M994T	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1014					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AAAAAAACAATGGAAGCAAAA	0.299																																					p.M1014T													.	LRRCC1-90	0			c.T3041C						.						53	51	51					8																	86057688		1810	4061	5871	SO:0001583	missense	85444	exon19			AAACAATGGAAGC	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3041T>C	8.37:g.86057688T>C	ENSP00000353538:p.Met1014Thr	Somatic	258	0		WXS	Illumina HiSeq		363	2	NM_033402	0	0	16	16	0	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.618150	0.46736	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.35048	1.33;1.33	5.12	5.12	0.69794	.	0.000000	0.43260	D	0.000600	T	0.50360	0.1611	M	0.65498	2.005	0.80722	D	1	D;D;P	0.62365	0.991;0.989;0.841	P;P;B	0.58266	0.805;0.836;0.313	T	0.45234	-0.9275	10	0.13470	T	0.59	-9.9528	15.0645	0.71983	0.0:0.0:0.0:1.0	.	994;921;1014	Q9C099-2;E9PE41;Q9C099	.;.;LRCC1_HUMAN	T	1014;994	ENSP00000353538:M1014T;ENSP00000394695:M994T	ENSP00000353538:M1014T	M	+	2	0	LRRCC1	86244940	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	6.443000	0.73447	2.138000	0.66242	0.402000	0.26972	ATG	.		0.299	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		C	86057688	T	C	86057688	3	2	161	1	0	0	0	0	1	0	0	0	9051	1464	51	3	3115	3	LRRCC1	8	86057688	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	46507487	86057688	60306334	62	14647											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140744445	140744445	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtccgtccaccagcacaTctgtaagggacacgagactg	10	7	11	13	2	1	1	0	0	1	1	3	3	3	2	3	1	1	3	3	1	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr8:140744445T>G	ENST00000438773.2	-	22	3189	c.3056A>C	c.(3055-3057)gAt>gCt	p.D1019A	TRAPPC9_ENST00000389327.3_Splice_Site_p.D1010A|TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389328.4_Splice_Site_p.D1117A	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1019					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CACCAGCACATCTGTAAGGGA	0.677																																					p.D1117A		.											.	TRAPPC9-228	0			c.A3350C						.						13	15	14					8																	140744445		2197	4283	6480	SO:0001630	splice_region_variant	83696	exon22			AGCACATCTGTAA	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"Trafficking protein particle complex"	30832	protein-coding gene	gene with protein product	"TRAPP 120 kDa subunit", "tularik gene 1"	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.3056-1A>C	8.37:g.140744445T>G		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	27	12	NM_031466	0	0	0	0	0	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	37	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420212	0.62622	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.64360	0.2591	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.995;0.996	T	0.64241	-0.6454	9	0.39692	T	0.17	.	13.8481	0.63479	0.0:0.0:0.0:1.0	.	1019;1117	Q96Q05;Q96Q05-2	TPPC9_HUMAN;.	A	1117;1010;1019	.	ENSP00000373978:D1010A	D	-	2	0	TRAPPC9	140813627	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	7.220000	0.78008	1.911000	0.55334	0.533000	0.62120	GAT	.		0.677	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	Missense_Mutation	G	140744445	T	G	140744445	5	3	161	1	0	0	0	0	0	0	1	0	16498	1449	50	5	398	5	TRAPPC9	8	140744445	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	54686757	140744445	5619577	63	14648											
C9orf66	157983	hgsc.bcm.edu	37	chr9	214741	214741	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgctgggcccacgccctcctCgcccgccgctgcctgcgcgc	1	5	12	23	7	0	0	0	0	0	0	2	0	1	0	6	1	2	2	6	1	0	0	rs200440314	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:214741C>T	ENST00000382387.2	-	1	1152	c.656G>A	c.(655-657)cGa>cAa	p.R219Q	DOCK8_ENST00000432829.2_5'Flank|DOCK8_ENST00000453981.1_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	219	Arg-rich.									central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		ACGCCCTCCTCGCCCGCCGCT	0.766													C|||	3	0.000599042	0.0023	0	5008	,	,		10580	0		0	False		,,,				2504	0				p.R219Q		.											.	C9orf66-514	0			c.G656A						.						2	3	3					9																	214741		1384	2827	4211	SO:0001583	missense	157983	exon1			CCTCCTCGCCCGC	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.656G>A	9.37:g.214741C>T	ENSP00000371824:p.Arg219Gln	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	10	NM_152569	0	0	0	0	0	Q96NB0	Missense_Mutation	SNP	ENST00000382387.2	37	CCDS6439.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	10.68	1.417416	0.25552	.	.	ENSG00000183784	ENST00000382387	T	0.23147	1.92	3.25	1.33	0.21861	.	.	.	.	.	T	0.06872	0.0175	N	0.08118	0	0.09310	N	1	P	0.42649	0.786	B	0.33620	0.167	T	0.15065	-1.0450	9	0.87932	D	0	.	4.4837	0.11780	0.0:0.637:0.2315:0.1315	.	219	Q5T8R8	CI066_HUMAN	Q	219	ENSP00000371824:R219Q	ENSP00000371824:R219Q	R	-	2	0	C9orf66	204741	0.003000	0.15002	0.054000	0.19295	0.561000	0.35649	0.910000	0.28571	0.367000	0.24454	0.484000	0.47621	CGA	C|0.997;T|0.003		0.766	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569		T	214741	C	T	214741	3	4	161	1	0	0	0	0	1	0	0	0	2496	884	31	1	235	1	C9orf66	9	214741	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		214741	140998690	64	14649											
PTPRD	5789	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	8504321	8504321	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccaggccttgaggggagcGtgcagccagacggaaatagt	11	5	15	10	2	0	2	0	1	0	1	0	4	0	4	3	4	3	1	3	4	2	2	rs200847027	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:8504321G>A	ENST00000381196.4	-	20	2305	c.1762C>T	c.(1762-1764)Cgc>Tgc	p.R588C	PTPRD_ENST00000397611.3_Missense_Mutation_p.R585C|PTPRD_ENST00000358503.5_Missense_Mutation_p.R575C|PTPRD_ENST00000540109.1_Missense_Mutation_p.R588C|PTPRD_ENST00000355233.5_Missense_Mutation_p.R588C|PTPRD_ENST00000356435.5_Missense_Mutation_p.R588C|PTPRD_ENST00000486161.1_Missense_Mutation_p.R588C|PTPRD_ENST00000360074.4_Missense_Mutation_p.R575C|PTPRD_ENST00000397617.3_Missense_Mutation_p.R578C|PTPRD_ENST00000397606.3_Missense_Mutation_p.R578C|PTPRD_ENST00000537002.1_Missense_Mutation_p.R585C	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	588	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TGAGGGGAGCGTGCAGCCAGA	0.458										TSP Lung(15;0.13)			G|||	2	0.000399361	0	0	5008	,	,		19317	0.001		0.001	False		,,,				2504	0				p.R588C		.											.	PTPRD-912	0			c.C1762T						.						253	220	231					9																	8504321		2203	4300	6503	SO:0001583	missense	5789	exon12			GGGAGCGTGCAGC	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1762C>T	9.37:g.8504321G>A	ENSP00000370593:p.Arg588Cys	Somatic	76	0		WXS	Illumina HiSeq	Phase_I	139	8	NM_130392	0	0	0	0	0	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	20.8	4.057013	0.76074	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33;0.33	5.53	5.53	0.82687	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.74550	0.3731	M	0.62154	1.92	0.80722	D	1	D;D;D;D;B;D;D;D;D	0.89917	0.997;0.999;1.0;0.999;0.052;0.998;1.0;1.0;1.0	P;D;D;P;B;P;D;D;D	0.79784	0.849;0.959;0.993;0.892;0.055;0.886;0.96;0.969;0.976	T	0.72653	-0.4228	9	.	.	.	.	19.4728	0.94969	0.0:0.0:1.0:0.0	.	578;582;588;588;585;585;575;588;588	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	C	588;588;575;575;588;578;585;585;588;588;588;578	ENSP00000370593:R588C;ENSP00000348812:R588C;ENSP00000353187:R575C;ENSP00000351293:R575C;ENSP00000347373:R588C;ENSP00000380741:R578C;ENSP00000380735:R585C;ENSP00000440515:R585C;ENSP00000438164:R588C;ENSP00000417093:R588C;ENSP00000380731:R578C	.	R	-	1	0	PTPRD	8494321	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	6.250000	0.72435	2.602000	0.87976	0.467000	0.42956	CGC	G|0.999;A|0.000		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			A	8504321	G	A	8504321	3	1	161	1	0	0	0	0	1	0	0	0	12831	1145	40	1	4140	1	PTPRD	9	8504321	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	8289580	8504321	132709110	65	14650											
FRMPD1	22844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	37745145	37745145	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	actaaataatgtctctcaagGagacacactagagctccagt	15	9	7	10	0	2	2	1	0	1	2	4	3	3	2	1	1	1	1	1	1	5	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:37745145G>A	ENST00000539465.1	+	16	3709	c.3116G>A	c.(3115-3117)gGa>gAa	p.G1039E	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.G1039E			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1039						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GTCTCTCAAGGAGACACACTA	0.488																																					p.G1039E		.											.	FRMPD1-159	0			c.G3116A						.						75	81	79					9																	37745145		2202	4299	6501	SO:0001583	missense	22844	exon16			CTCAAGGAGACAC	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3116G>A	9.37:g.37745145G>A	ENSP00000444411:p.Gly1039Glu	Somatic	33	0		WXS	Illumina HiSeq	Phase_I	47	18	NM_014907	0	0	0	0	0	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702580	0.68501	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07908	3.15;3.15	5.17	3.32	0.38043	.	3.748350	0.00496	N	0.000156	T	0.08358	0.0208	N	0.24115	0.695	0.80722	D	1	B	0.12630	0.006	B	0.15052	0.012	T	0.17592	-1.0364	10	0.46703	T	0.11	-5.6669	7.1991	0.25871	0.0943:0.1842:0.7215:0.0	.	1039	Q5SYB0	FRPD1_HUMAN	E	1039	ENSP00000366995:G1039E;ENSP00000444411:G1039E	ENSP00000366995:G1039E	G	+	2	0	FRMPD1	37735145	0.009000	0.17119	0.861000	0.33841	0.973000	0.67179	0.191000	0.17076	0.557000	0.29117	0.462000	0.41574	GGA	.		0.488	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37745145	G	A	37745145	3	1	161	1	0	0	0	0	1	0	0	0	6076	1174	41	2	3174	2	FRMPD1	9	37745145	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	29240824	37745145	103468286	66	14651											
PRKACG	5568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	71628295	71628295	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgggctggtcggcgtagaaGggtgggaagcccacggccat	8	6	18	9	3	0	1	0	0	0	1	1	2	0	2	2	6	1	2	2	6	3	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:71628295G>A	ENST00000377276.2	-	1	744	c.714C>T	c.(712-714)ccC>ccT	p.P238P		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	238	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CGGCGTAGAAGGGTGGGAAGC	0.597																																					p.P238P	Esophageal Squamous(110;2236 2623 32146)	.											.	PRKACG-1061	0			c.C714T						.						70	68	69					9																	71628295		2203	4300	6503	SO:0001819	synonymous_variant	5568	exon1			GTAGAAGGGTGGG	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.714C>T	9.37:g.71628295G>A		Somatic	35	0		WXS	Illumina HiSeq	Phase_I	96	34	NM_002732	0	0	0	0	0	O60850|Q5VZ02|Q86YI1	Silent	SNP	ENST00000377276.2	37	CCDS6625.1																																																																																			.		0.597	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			A	71628295	G	A	71628295	2	1	161	1	0	0	0	0	0	0	0	1	12528	987	35	2		2	PRKACG	9	71628295	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	33883150	71628295	69585136	67	14652											
FAM75C1	441452	hgsc.bcm.edu;ucsc.edu	37	chr9	90534184	90534184	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcccagcgtcatcttgtctcCcagcgtcatcttgtctccca	5	13	6	17	2	6	0	2	0	4	0	9	0	7	0	3	0	2	0	3	0	0	2	rs374457389|rs368404840	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:90534184C>T	ENST00000602681.1	+	0	930							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ATCTTGTCTCCCAGCGTCATC	0.612													.|||	47	0.00938498	0.0348	0.0014	5008	,	,		14138	0		0	False		,,,				2504	0				p.S68S		.											.	.	0			c.C204T						.	C		44,1340		0,44,648	140	113	121		204	0.1	0	9		121	0,3182		0,0,1591	no	coding-synonymous	FAM75C1	NM_001145124.1		0,44,2239	TT,TC,CC		0.0,3.1792,0.9636		68/1189	90534184	44,4522	692	1591	2283			441452	exon2			TGTCTCCCAGCGT	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"family with sequence similarity 75, member C1"	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		9.37:g.90534184C>T		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	499	149	NM_001145124	0	0	0	0	0		Silent	SNP	ENST00000602681.1	37																																																																																				.		0.612	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124		T	90534184	C	T	90534184	1	4	161	0	1	0	0	0	0	0	0	0	5642	610	22	2		2	FAM75C1	9	90534184	RNA	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	18905889	90534184	50679247	68	14653											
NIPSNAP3A	25934	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	107521616	107521616	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatcgttttcaccactgaaAtagttttctactgaaataca	14	14	4	9	1	2	2	1	2	1	0	3	2	2	2	1	0	2	2	1	0	5	7	rs546236502	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:107521616A>C	ENST00000374767.4	+	6	846	c.741A>C	c.(739-741)aaA>aaC	p.K247N		NM_015469.1	NP_056284.1	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A (C. elegans)	247						cytoplasm (GO:0005737)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	8						CACCACTGAAATAGTTTTCTA	0.358																																					p.K247N		.											.	NIPSNAP3A-90	0			c.A741C						.						105	97	100					9																	107521616		2203	4300	6503	SO:0001583	missense	25934	exon6			ACTGAAATAGTTT	BC005935	CCDS6760.1	9q31.3	2003-11-27			ENSG00000136783	ENSG00000136783			23619	protein-coding gene	gene with protein product		608871				12477932	Standard	NM_015469		Approved	DKFZp564D177, FLJ13953, HSPC299, MGC14553		Q9UFN0	OTTHUMG00000020413	ENST00000374767.4:c.741A>C	9.37:g.107521616A>C	ENSP00000363899:p.Lys247Asn	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	85	24	NM_015469	0	0	3	3	0	A6NM55|Q5VX32|Q9BRV7|Q9H843|Q9P083	Missense_Mutation	SNP	ENST00000374767.4	37	CCDS6760.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.325054	0.60634	.	.	ENSG00000136783	ENST00000374767	T	0.73047	-0.71	3.97	2.82	0.32997	Dimeric alpha-beta barrel (1);	0.047557	0.85682	D	0.000000	T	0.80166	0.4573	M	0.81239	2.535	0.37125	D	0.901004	D	0.76494	0.999	D	0.71656	0.974	T	0.80739	-0.1248	10	0.87932	D	0	.	4.8972	0.13757	0.6882:0.0:0.3118:0.0	.	247	Q9UFN0	NPS3A_HUMAN	N	247	ENSP00000363899:K247N	ENSP00000363899:K247N	K	+	3	2	NIPSNAP3A	106561437	0.997000	0.39634	1.000000	0.80357	0.978000	0.69477	0.441000	0.21611	0.697000	0.31718	0.482000	0.46254	AAA	.		0.358	NIPSNAP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053484.1	NM_015469		C	107521616	A	C	107521616	3	2	161	1	0	0	0	0	1	0	0	0	10456	98	4	5	763	5	NIPSNAP3A	9	107521616	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	16987432	107521616	33691815	69	14654											
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	113233740	113233740	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctataagtatttctgatgCaagctgaaaggaatacatgg	14	11	11	5	0	1	2	0	2	1	0	1	3	1	3	0	3	3	4	0	3	7	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:113233740C>A	ENST00000401783.2	-	16	3238	c.2902G>T	c.(2902-2904)Gca>Tca	p.A968S	SVEP1_ENST00000302728.8_Missense_Mutation_p.A968S|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.A945S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	968					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ATTTCTGATGCAAGCTGAAAG	0.428																																					p.A968S		.											.	SVEP1-75	0			c.G2902T						.						122	112	115					9																	113233740		1855	4107	5962	SO:0001583	missense	79987	exon16			CTGATGCAAGCTG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"chromosome 9 open reading frame 13"	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.2902G>T	9.37:g.113233740C>A	ENSP00000384917:p.Ala968Ser	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	152	16	NM_153366	0	0	0	0	0	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	7.630	0.678635	0.14841	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.78246	-1.01;-1.02;-1.16	5.49	5.49	0.81192	.	0.158375	0.56097	D	0.000024	T	0.56834	0.2012	N	0.08118	0	0.27524	N	0.951309	B;B	0.17268	0.021;0.012	B;B	0.15052	0.012;0.012	T	0.37033	-0.9723	10	0.10902	T	0.67	.	12.9639	0.58473	0.283:0.717:0.0:0.0	.	968;968	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	S	968;945;968	ENSP00000384917:A968S;ENSP00000363593:A945S;ENSP00000304118:A968S	ENSP00000304118:A968S	A	-	1	0	SVEP1	112273561	1.000000	0.71417	0.854000	0.33618	0.607000	0.37147	2.741000	0.47426	2.583000	0.87209	0.650000	0.86243	GCA	.		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113233740	C	A	113233740	3	1	161	1	0	0	0	0	1	0	0	0	15452	710	25	4	7945	4	SVEP1	9	113233740	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	5712124	113233740	27979691	70	14655											
CIZ1	25792	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr9	130947865	130947865	+	Frame_Shift_Del	DEL	T	T	-																															gaggaggaggtccgggcctgTttctgggggttccgtcctga																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:130947865delT	ENST00000393608.1	-	5	751	c.549delA	c.(547-549)aaafs	p.K183fs	CIZ1_ENST00000325721.8_Frame_Shift_Del_p.K159fs|CIZ1_ENST00000357558.5_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000372954.1_Frame_Shift_Del_p.K159fs|CIZ1_ENST00000372948.3_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000372938.5_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000277465.4_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000541172.1_Frame_Shift_Del_p.K82fs	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	183					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TCCGGGCCTGTTTCTGGGGGT	0.637																																					p.K213fs		.											.	CIZ1-92	0			c.639delA						.						67	68	68					9																	130947865		2203	4300	6503	SO:0001589	frameshift_variant	25792	exon5			.	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.549delA	9.37:g.130947865delT	ENSP00000377232:p.Lys183fs	Somatic	45	0		WXS	Illumina HiSeq	Phase_I	118	36	NM_001257975	0	0	0	0	0	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Frame_Shift_Del	DEL	ENST00000393608.1	37	CCDS6894.1																																																																																			.		0.637	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		-	130947865	T	-	130947865	7	5	161	1	0	1	0	1	0	0	0	0	3447	1722	60	0	2199	0	CIZ1	9	130947865	Frame_Shift_Del	DEL	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	17714125	130947865	10265566	71	14656											
MED27	9442	hgsc.bcm.edu;broad.mit.edu	37	chr9	134735980	134735980	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcggaaatccctccatgtcGggggaaggccgtcctgcaga	8	8	13	12	3	0	1	0	0	0	1	5	3	3	3	4	4	1	1	4	4	2	1	rs557626461	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:134735980G>A	ENST00000292035.5	-	8	944	c.881C>T	c.(880-882)cCg>cTg	p.P294L	MED27_ENST00000357028.2_Missense_Mutation_p.P258L	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	294					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.P294L(4)|p.P294fs*>18(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		CCTCCATGTCGGGGGAAGGCC	0.597													G|||	40	0.00798722	0.003	0.0072	5008	,	,		18345	0		0.0169	False		,,,				2504	0.0143				p.P294L	Colon(41;784 923 6932 42329 52483)	.											.	MED27-69	5	Substitution - Missense(4)|Deletion - Frameshift(1)	endometrium(2)|kidney(2)|large_intestine(1)	c.C881T						.						30	29	29					9																	134735980		2203	4300	6503	SO:0001583	missense	9442	exon8			CATGTCGGGGGAA	AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.881C>T	9.37:g.134735980G>A	ENSP00000292035:p.Pro294Leu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	145	9	NM_004269	0	0	33	33	0	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Missense_Mutation	SNP	ENST00000292035.5	37	CCDS6945.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095595	0.94197	.	.	ENSG00000160563	ENST00000292035;ENST00000357028;ENST00000372184	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.84014	0.5379	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.86894	0.2050	9	0.87932	D	0	-0.1478	16.105	0.81213	0.0:0.0:1.0:0.0	.	258;294	Q6P2C8-2;Q6P2C8	.;MED27_HUMAN	L	294;220;258	.	ENSP00000292035:P294L	P	-	2	0	MED27	133725801	1.000000	0.71417	0.949000	0.38748	0.987000	0.75469	7.762000	0.85270	2.472000	0.83506	0.655000	0.94253	CCG	.		0.597	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269		A	134735980	G	A	134735980	3	1	161	1	0	0	0	0	1	0	0	0	9470	1116	39	1	58	1	MED27	9	134735980	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	3788115	134735980	6477451	72	14657											
SDCCAG3	10807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr9	139302279	139302279	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacagtgccgtggatttaccTttgcataaattctgctggcc	8	13	9	11	1	1	0	0	0	1	0	1	1	1	1	3	2	4	2	3	2	3	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:139302279T>G	ENST00000357365.3	-	4	530	c.401A>C	c.(400-402)aAg>aCg	p.K134T	PMPCA_ENST00000371717.3_5'Flank|PMPCA_ENST00000371720.1_5'Flank|PMPCA_ENST00000399219.3_5'Flank|SDCCAG3_ENST00000461693.1_5'Flank|SDCCAG3_ENST00000371725.3_Splice_Site_p.K61T|SDCCAG3_ENST00000298537.7_Splice_Site_p.K111T	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	134						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		TGGATTTACCTTTGCATAAAT	0.522																																					p.K134T		.											.	SDCCAG3-90	0			c.A401C						.						117	127	124					9																	139302279		1996	4158	6154	SO:0001630	splice_region_variant	10807	exon4			TTTACCTTTGCAT	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.402+1A>C	9.37:g.139302279T>G		Somatic	28	0		WXS	Illumina HiSeq	Phase_I	43	11	NM_001039707	0	0	0	0	0	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	37	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.632253	0.46944	.	.	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725;ENST00000371723	T;T;T;T	0.39406	2.24;2.31;2.29;1.08	5.34	5.34	0.76211	.	0.221148	0.38837	N	0.001555	T	0.58366	0.2117	M	0.63843	1.955	0.42845	D	0.994066	D;D;D	0.76494	0.99;0.997;0.999	P;D;D	0.68353	0.864;0.928;0.957	T	0.59627	-0.7419	10	0.45353	T	0.12	-23.4229	11.7031	0.51581	0.0:0.0:0.0:1.0	.	61;111;134	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	T	134;111;61;84	ENSP00000349929:K134T;ENSP00000298537:K111T;ENSP00000360790:K61T;ENSP00000360788:K84T	ENSP00000298537:K111T	K	-	2	0	SDCCAG3	138422100	1.000000	0.71417	0.628000	0.29241	0.117000	0.20001	4.054000	0.57434	2.012000	0.59069	0.528000	0.53228	AAG	.		0.522	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	Missense_Mutation	G	139302279	T	G	139302279	5	3	161	1	0	0	0	0	0	0	1	0	13990	1623	56	5	934	5	SDCCAG3	9	139302279	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	4566299	139302279	1911152	73	14658											
CUL2	8453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	35360197	35360197	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcttttattgtcgtcaaaaGtttgttccatgtttcatcaa	9	18	7	7	1	3	0	3	0	0	0	5	0	4	0	1	1	0	4	1	1	4	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:35360197G>C	ENST00000374748.1	-	3	362	c.49C>G	c.(49-51)Ctt>Gtt	p.L17V	CUL2_ENST00000374749.3_Missense_Mutation_p.L17V|CUL2_ENST00000602371.1_5'UTR|CUL2_ENST00000478044.1_5'UTR|CUL2_ENST00000374751.3_Missense_Mutation_p.L17V|CUL2_ENST00000374742.1_Missense_Mutation_p.L17V|CUL2_ENST00000374746.1_Missense_Mutation_p.L17V|CUL2_ENST00000537177.1_Missense_Mutation_p.L36V			Q13617	CUL2_HUMAN	cullin 2	17					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						GTCGTCAAAAGTTTGTTCCAT	0.358																																					p.L36V		.											.	CUL2-229	0			c.C106G						.						148	122	131					10																	35360197		2203	4300	6503	SO:0001583	missense	8453	exon2			TCAAAAGTTTGTT	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.49C>G	10.37:g.35360197G>C	ENSP00000363880:p.Leu17Val	Somatic	116	0		WXS	Illumina HiSeq	Phase_I	173	41	NM_001198778	0	0	0	0	0	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	37	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.585575	0.66105	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374742;ENST00000537177;ENST00000421317	T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.92	4.06	0.47325	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.058793	0.64402	N	0.000001	T	0.65491	0.2696	L	0.58101	1.795	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	D;P;D	0.66497	0.944;0.875;0.923	T	0.67150	-0.5743	10	0.87932	D	0	-7.8946	11.7589	0.51890	0.0663:0.1241:0.8097:0.0	.	17;36;17	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	V	17;17;17;17;17;36;17	ENSP00000363883:L17V;ENSP00000363880:L17V;ENSP00000363878:L17V;ENSP00000363881:L17V;ENSP00000363874:L17V;ENSP00000444856:L36V;ENSP00000414095:L17V	ENSP00000363874:L17V	L	-	1	0	CUL2	35400203	1.000000	0.71417	0.282000	0.24776	0.833000	0.47200	6.391000	0.73208	0.824000	0.34613	0.655000	0.94253	CTT	.		0.358	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		C	35360197	G	C	35360197	3	2	161	1	0	0	0	0	1	0	0	0	4061	1029	36	4	2268	4	CUL2	10	35360197	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		35360197	100174550	74	14659											
TET1	80312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	70404893	70404893	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acactgcaaaccataaaaacGctatgagctctgttgctact	14	10	6	11	1	1	1	0	1	1	0	1	1	1	1	1	0	6	5	1	0	6	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:70404893G>T	ENST00000373644.4	+	4	2616	c.2407G>T	c.(2407-2409)Gct>Tct	p.A803S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	803					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.A803T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CCATAAAAACGCTATGAGCTC	0.353																																					p.A803S		.											.	TET1-663	1	Substitution - Missense(1)	endometrium(1)	c.G2407T						.						100	100	100					10																	70404893		2203	4300	6503	SO:0001583	missense	80312	exon4			AAAAACGCTATGA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"leukemia-associated protein with a CXXC domain", "ten-eleven translocation-1"	607790	"CXXC zinc finger 6", "tet oncogene 1"	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.2407G>T	10.37:g.70404893G>T	ENSP00000362748:p.Ala803Ser	Somatic	102	0		WXS	Illumina HiSeq	Phase_I	84	10	NM_030625	0	0	0	0	0	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.609899	0.46527	.	.	ENSG00000138336	ENST00000373644	T	0.08458	3.09	5.92	4.93	0.64822	.	0.759080	0.12137	N	0.496237	T	0.05318	0.0141	L	0.27053	0.805	0.27338	N	0.956599	P	0.44429	0.835	B	0.38056	0.264	T	0.21449	-1.0245	10	0.24483	T	0.36	.	4.6605	0.12639	0.2192:0.0:0.7808:0.0	.	803	Q8NFU7	TET1_HUMAN	S	803	ENSP00000362748:A803S	ENSP00000362748:A803S	A	+	1	0	TET1	70074899	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	1.045000	0.30341	2.822000	0.97130	0.650000	0.86243	GCT	.		0.353	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70404893	G	T	70404893	3	4	161	1	0	0	0	0	1	0	0	0	15801	1087	38	4	2417	4	TET1	10	70404893	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	35044696	70404893	65129854	75	14660											
C10orf129	142827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr10	96967018	96967018	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccaagaaaattcgctatCaattacgcatgtctaaggcc	13	10	7	11	2	2	1	1	0	1	1	3	1	2	1	2	1	2	2	2	1	7	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:96967018C>A	ENST00000394005.3	+	3	466	c.457C>A	c.(457-459)Caa>Aaa	p.Q153K	C10orf129_ENST00000430183.1_5'UTR|C10orf129_ENST00000341686.3_Missense_Mutation_p.Q153K			Q6P461	ACSM6_HUMAN		153					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		AATTCGCTATCAATTACGCAT	0.468																																					p.Q153K		.											.	C10orf129-90	0			c.C457A						.						82	76	78					10																	96967018		2203	4300	6503	SO:0001583	missense	142827	exon4			CGCTATCAATTAC																												ENST00000394005.3:c.457C>A	10.37:g.96967018C>A	ENSP00000377573:p.Gln153Lys	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	94	20	NM_207321	0	0	0	0	0	A4FU95|A4IF38|Q5VZX2|Q6ZTX1	Missense_Mutation	SNP	ENST00000394005.3	37	CCDS7440.2	.	.	.	.	.	.	.	.	.	.	C	6.282	0.420077	0.11928	.	.	ENSG00000173124	ENST00000539707;ENST00000341686;ENST00000394005	T;T	0.41065	1.01;1.01	1.2	0.259	0.15583	AMP-dependent synthetase/ligase (1);	.	.	.	.	T	0.23249	0.0562	N	0.14661	0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.09377	0.004	T	0.21586	-1.0241	9	0.87932	D	0	.	5.4913	0.16777	0.0:0.7911:0.0:0.2089	.	153	Q6P461	ACSM6_HUMAN	K	179;153;153	ENSP00000340296:Q153K;ENSP00000377573:Q153K	ENSP00000340296:Q153K	Q	+	1	0	C10orf129	96957008	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	-1.319000	0.02702	0.134000	0.18681	0.579000	0.79373	CAA	.		0.468	C10orf129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049506.2			A	96967018	C	A	96967018	3	1	161	1	0	0	0	0	1	0	0	0	1597	827	29	4	467	4	C10orf129	10	96967018	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	26562125	96967018	38567729	76	14661											
PDZD7	79955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr10	102783355	102783355	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatcttgtcccccacgcacAggccagcccgctctgcacca	7	7	8	19	2	2	1	0	1	2	0	3	1	3	1	5	1	2	3	5	1	0	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:102783355A>G	ENST00000370215.3	-	4	605	c.380T>C	c.(379-381)cTg>cCg	p.L127P	PDZD7_ENST00000470414.1_Missense_Mutation_p.L127P	NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	127	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CCCCACGCACAGGCCAGCCCG	0.657																																					p.L127P		.											.	PDZD7-136	0			c.T380C						.						62	54	57					10																	102783355		2203	4300	6503	SO:0001583	missense	79955	exon4			ACGCACAGGCCAG	AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.380T>C	10.37:g.102783355A>G	ENSP00000359234:p.Leu127Pro	Somatic	13	0		WXS	Illumina HiSeq	Phase_I	31	13	NM_001195263	0	0	0	0	0	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403886	0.83230	.	.	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.50548	0.74	5.05	5.05	0.67936	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.79581	0.4470	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.961	D	0.87162	0.2215	10	0.87932	D	0	.	14.7786	0.69749	1.0:0.0:0.0:0.0	.	127;127	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	P	127	ENSP00000359234:L127P	ENSP00000359234:L127P	L	-	2	0	PDZD7	102773345	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.224000	0.95209	1.893000	0.54813	0.459000	0.35465	CTG	.		0.657	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		G	102783355	A	G	102783355	3	3	161	1	0	0	0	0	1	0	0	0	11730	188	7	3	1201	3	PDZD7	10	102783355	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	5816337	102783355	32751392	77	14662											
MUC2	4583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	1078339	1078339	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgatgtggtgtgtgaggatcCcgaggaggaggtggcccccg	6	7	19	9	3	0	1	0	1	0	0	1	6	1	4	3	6	0	0	3	6	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:1078339C>T	ENST00000441003.2	+	5	653	c.626C>T	c.(625-627)cCc>cTc	p.P209L	MUC2_ENST00000359061.5_Missense_Mutation_p.P209L	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	209	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TGTGAGGATCCCGAGGAGGAG	0.642																																					p.P209L		.											.	MUC2-90	0			c.C626T						.						76	90	86					11																	1078339		2086	4194	6280	SO:0001583	missense	4583	exon5			AGGATCCCGAGGA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"Mucins"	7512	protein-coding gene	gene with protein product		158370	"mucin 2, intestinal/tracheal"			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.626C>T	11.37:g.1078339C>T	ENSP00000415183:p.Pro209Leu	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	224	60	NM_002457	0	0	0	0	0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	12.34	1.909914	0.33721	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14766	2.54;2.48	4.08	4.08	0.47627	.	0.567974	0.14666	U	0.305646	T	0.21881	0.0527	L	0.53729	1.69	0.45554	D	0.998508	P	0.37525	0.598	B	0.43386	0.418	T	0.04454	-1.0950	10	0.48119	T	0.1	.	16.2743	0.82636	0.0:1.0:0.0:0.0	.	209	E7EUV1	.	L	209	ENSP00000415183:P209L;ENSP00000351956:P209L	ENSP00000351956:P209L	P	+	2	0	MUC2	1068339	0.995000	0.38212	0.394000	0.26270	0.046000	0.14306	2.838000	0.48199	1.818000	0.53035	0.561000	0.74099	CCC	.		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1078339	C	T	1078339	3	4	161	1	0	0	0	0	1	0	0	0	10000	623	22	2	644	2	MUC2	11	1078339	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		1078339	133928177	78	14663											
PDE3B	5140	hgsc.bcm.edu	37	chr11	14666027	14666027	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcttcctcacctgcttcCtcacccggaccaagcgggga	6	10	8	17	2	4	0	2	0	2	0	6	2	6	2	5	3	2	1	5	3	1	3	rs373522381	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:14666027C>G	ENST00000282096.4	+	1	759	c.406C>G	c.(406-408)Ctc>Gtc	p.L136V	PDE3B_ENST00000455098.2_Missense_Mutation_p.L136V|PDE3B_ENST00000534317.1_3'UTR|PSMA1_ENST00000418988.2_5'Flank	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	136					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	CACCTGCTTCCTCACCCGGAC	0.692													C|||	2	0.000399361	0.0015	0	5008	,	,		14055	0		0	False		,,,				2504	0				p.L136V		.											.	PDE3B-90	0			c.C406G						.						29	32	31					11																	14666027		2199	4294	6493	SO:0001583	missense	5140	exon1			TGCTTCCTCACCC	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.406C>G	11.37:g.14666027C>G	ENSP00000282096:p.Leu136Val	Somatic	10	0		WXS	Illumina HiSeq	Phase_I	146	52	NM_000922	0	0	0	0	0	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	37	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.170982	0.57584	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.74842	-0.72;-0.88	3.78	0.801	0.18679	.	8.111930	0.00166	N	0.000000	T	0.73953	0.3653	L	0.40543	1.245	0.31630	N	0.649153	P;P;P	0.52842	0.884;0.884;0.956	B;B;P	0.50659	0.358;0.358;0.647	T	0.62058	-0.6934	10	0.45353	T	0.12	.	6.7026	0.23232	0.0:0.5775:0.0:0.4225	.	136;136;136	B7ZM37;Q13370;A7E2E5	.;PDE3B_HUMAN;.	V	136	ENSP00000282096:L136V;ENSP00000388644:L136V	ENSP00000282096:L136V	L	+	1	0	PDE3B	14622603	1.000000	0.71417	0.998000	0.56505	0.834000	0.47266	1.686000	0.37669	0.130000	0.18549	0.313000	0.20887	CTC	.		0.692	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		G	14666027	C	G	14666027	3	3	161	1	0	0	0	0	1	0	0	0	11664	681	24	4	408	4	PDE3B	11	14666027	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	13587688	14666027	120340489	79	14664											
OR4X1	390113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	48285602	48285602	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatttctttctcagctacTtatcctttgtggagatctgc	6	19	7	9	0	3	1	1	0	3	1	5	2	4	1	1	1	3	2	1	1	3	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:48285602T>G	ENST00000320048.1	+	1	190	c.190T>G	c.(190-192)Tta>Gta	p.L64V		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						TCTCAGCTACTTATCCTTTGT	0.493																																					p.L64V		.											.	OR4X1-71	0			c.T190G						.						148	135	139					11																	48285602		2201	4298	6499	SO:0001583	missense	390113	exon1			AGCTACTTATCCT	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"GPCR / Class A : Olfactory receptors"	14854	protein-coding gene	gene with protein product			"olfactory receptor, family 4, subfamily X, member 1"				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.190T>G	11.37:g.48285602T>G	ENSP00000321506:p.Leu64Val	Somatic	66	0		WXS	Illumina HiSeq	Phase_I	156	18	NM_001004726	0	0	0	0	0	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	37	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.313474	0.23908	.	.	ENSG00000176567	ENST00000320048	T	0.00507	6.92	4.29	-3.51	0.04696	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01976	0.0062	H	0.97540	4.025	0.20403	N	0.999903	D	0.57571	0.98	P	0.56960	0.81	T	0.01084	-1.1457	9	0.87932	D	0	.	8.1735	0.31268	0.0:0.4875:0.1294:0.3831	.	64	Q8NH49	OR4X1_HUMAN	V	64	ENSP00000321506:L64V	ENSP00000321506:L64V	L	+	1	2	OR4X1	48242178	0.000000	0.05858	0.901000	0.35422	0.022000	0.10575	-2.554000	0.00926	-1.009000	0.03400	-2.821000	0.00108	TTA	.		0.493	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		G	48285602	T	G	48285602	3	3	161	1	0	0	0	0	1	0	0	0	11110	1606	56	5	192	5	OR4X1	11	48285602	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	33619575	48285602	86720914	80	14665											
SLC43A3	29015	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	57182149	57182149	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccatgagcaggccattccaGggggcacacagcactccgaa	11	5	11	14	1	0	1	0	1	0	0	3	2	3	1	4	3	2	3	4	3	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:57182149G>A	ENST00000395123.2	-	11	1303	c.999C>T	c.(997-999)ccC>ccT	p.P333P	SLC43A3_ENST00000529554.1_Silent_p.P333P|SLC43A3_ENST00000352187.1_Silent_p.P333P|SLC43A3_ENST00000528098.1_5'Flank|SLC43A3_ENST00000395124.1_Silent_p.P333P|SLC43A3_ENST00000533524.1_Silent_p.P346P	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	333					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						GGCCATTCCAGGGGGCACACA	0.537																																					p.P333P													.	SLC43A3-90	0			c.C999T						.						209	206	207					11																	57182149		2201	4296	6497	SO:0001819	synonymous_variant	29015	exon11			ATTCCAGGGGGCA	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.999C>T	11.37:g.57182149G>A		Somatic	60	1		WXS	Illumina HiSeq	Phase_I	182	63	NM_017611	0	0	0	0	0	B4DNR8|E7EQD2|Q9NSS4	Silent	SNP	ENST00000395123.2	37	CCDS7956.1																																																																																			.		0.537	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		A	57182149	G	A	57182149	2	1	161	1	0	0	0	0	0	0	0	1	14666	987	35	2		2	SLC43A3	11	57182149	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	8896547	57182149	77824367	81	14666											
MLL	4297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr11	118373932	118373932	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtaaagaaactttcaaagAaaagcattccagtaaatctt	18	11	5	7	0	2	2	1	0	1	2	3	2	3	2	1	0	2	3	1	0	8	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:118373932A>C	ENST00000389506.5	+	27	7316	c.7316A>C	c.(7315-7317)gAa>gCa	p.E2439A	KMT2A_ENST00000354520.4_Missense_Mutation_p.E2401A|KMT2A_ENST00000534358.1_Missense_Mutation_p.E2442A			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2439					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										ACTTTCAAAGAAAAGCATTCC	0.403																																					p.E2442A		.											.	MLL-1255	0			c.A7325C						.						62	65	64					11																	118373932		2199	4296	6495	SO:0001583	missense	4297	exon27			TCAAAGAAAAGCA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.7316A>C	11.37:g.118373932A>C	ENSP00000374157:p.Glu2439Ala	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	87	34	NM_001197104	0	0	0	0	0	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.794138	0.31777	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.83591	-1.74;-1.74;-1.71	5.85	5.85	0.93711	.	0.109676	0.64402	D	0.000008	T	0.70064	0.3181	N	0.19112	0.55	0.49915	D	0.999833	P;P	0.49090	0.919;0.919	B;B	0.33339	0.162;0.162	T	0.76889	-0.2792	10	0.72032	D	0.01	.	16.2303	0.82332	1.0:0.0:0.0:0.0	.	2442;2439	E9PQG7;Q03164	.;MLL1_HUMAN	A	2442;2439;2401;1349	ENSP00000436786:E2442A;ENSP00000374157:E2439A;ENSP00000346516:E2401A	ENSP00000346516:E2401A	E	+	2	0	MLL	117879142	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.414000	0.73318	2.233000	0.73108	0.533000	0.62120	GAA	.		0.403	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		C	118373932	A	C	118373932	3	2	161	1	0	0	0	0	1	0	0	0	9645	246	9	5	7422	5	MLL	11	118373932	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	61191783	118373932	16632584	82	14667											
HINFP	25988	broad.mit.edu;bcgsc.ca	37	chr11	119001447	119001447	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ttctacagaggaagaattctCctgcttgtggcaggaatgtg	10	12	12	7	0	2	2	0	0	2	2	3	4	2	4	1	3	2	2	1	3	4	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:119001447C>G	ENST00000350777.2	+	3	257	c.194C>G	c.(193-195)tCc>tGc	p.S65C	HINFP_ENST00000527410.1_Missense_Mutation_p.S65C|HINFP_ENST00000527354.1_3'UTR	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	65					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GAAGAATTCTCCTGCTTGTGG	0.498																																					p.S65C													.	HINFP-320	0			c.C194G						.						94	92	93					11																	119001447		2200	4295	6495	SO:0001583	missense	25988	exon4			AATTCTCCTGCTT	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"Zinc fingers, C2H2-type"	17850	protein-coding gene	gene with protein product	"histone nuclear factor P"	607099	"MBD2-interacting zinc finger 1", "MBD2-interacting zinc finger"	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.194C>G	11.37:g.119001447C>G	ENSP00000318085:p.Ser65Cys	Somatic	70	2		WXS	Illumina HiSeq	Phase_I	137	54	NM_015517	0	0	0	0	0	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	37	CCDS8414.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.259891	0.39995	.	.	ENSG00000172273	ENST00000350777;ENST00000529988;ENST00000527410;ENST00000532312	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	5.84	5.84	0.93424	Zinc finger, C2H2-like (1);	0.196552	0.53938	D	0.000047	T	0.28566	0.0707	N	0.22421	0.69	0.39422	D	0.966933	B;B	0.18610	0.029;0.013	B;B	0.17433	0.018;0.007	T	0.06006	-1.0851	10	0.54805	T	0.06	-29.6023	15.5998	0.76616	0.0:0.8631:0.1369:0.0	.	65;65	B4DTN3;Q9BQA5	.;HINFP_HUMAN	C	65	ENSP00000318085:S65C;ENSP00000431468:S65C;ENSP00000436815:S65C;ENSP00000434574:S65C	ENSP00000318085:S65C	S	+	2	0	HINFP	118506657	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.044000	0.41241	2.779000	0.95612	0.655000	0.94253	TCC	.		0.498	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517		G	119001447	C	G	119001447	3	3	161	1	0	0	0	0	1	0	0	0	7131	855	30	4	200	4	HINFP	11	119001447	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	627515	119001447	16005069	83	14668											
SCNN1A	6337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	6457064	6457064	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcccccccagaggacaggtgGaggaactggcccctgcagag	9	3	15	14	0	0	2	0	0	0	2	0	5	0	5	5	5	2	1	5	5	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:6457064G>A	ENST00000228916.2	-	13	2083	c.1985C>T	c.(1984-1986)tCc>tTc	p.S662F	SCNN1A_ENST00000543768.1_Missense_Mutation_p.S685F|SCNN1A_ENST00000540037.1_Missense_Mutation_p.S362F|SCNN1A_ENST00000396966.2_3'UTR|SCNN1A_ENST00000360168.3_Missense_Mutation_p.S721F|SCNN1A_ENST00000358945.3_Missense_Mutation_p.S684F	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	662					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGGACAGGTGGAGGAACTGGC	0.672																																					p.S721F		.											.	SCNN1A-90	0			c.C2162T						.						7	8	7					12																	6457064		2098	4115	6213	SO:0001583	missense	6337	exon12			CAGGTGGAGGAAC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1985C>T	12.37:g.6457064G>A	ENSP00000228916:p.Ser662Phe	Somatic	34	0		WXS	Illumina HiSeq	Phase_I	95	31	NM_001159576	0	0	0	0	0	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383587	0.42207	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000540037;ENST00000228916;ENST00000543768	T;T;T;T;T	0.73258	-0.73;-0.69;-0.44;-0.63;-0.67	3.95	1.82	0.25136	.	1.972990	0.02819	N	0.125281	T	0.70090	0.3184	M	0.63428	1.95	0.09310	N	1	B;B;B	0.32693	0.38;0.38;0.226	B;B;B	0.29267	0.085;0.085;0.1	T	0.60627	-0.7226	10	0.72032	D	0.01	-0.3348	11.2996	0.49298	0.0:0.3534:0.6466:0.0	.	685;662;721	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	F	721;684;362;662;685	ENSP00000353292:S721F;ENSP00000351825:S684F;ENSP00000440876:S362F;ENSP00000228916:S662F;ENSP00000438739:S685F	ENSP00000228916:S662F	S	-	2	0	SCNN1A	6327325	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.471000	0.22100	0.933000	0.37291	0.555000	0.69702	TCC	.		0.672	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6457064	G	A	6457064	3	1	161	1	0	0	0	0	1	0	0	0	13959	1174	41	2	28	2	SCNN1A	12	6457064	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		6457064	127394831	84	14669											
KLRK1	22914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	10539523	10539523	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttctctacatttgctttTgactactggacatctttgct	7	20	5	9	0	2	1	0	1	2	0	3	2	2	2	0	1	4	2	0	1	2	8			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:10539523T>C	ENST00000240618.6	-	3	267	c.127A>G	c.(127-129)Aaa>Gaa	p.K43E	RP11-277P12.20_ENST00000500682.1_RNA|KLRC4-KLRK1_ENST00000539300.1_3'UTR|KLRK1_ENST00000540818.1_Missense_Mutation_p.K43E	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	43					cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						CATTTGCTTTTGACTACTGGA	0.323																																					p.K43E		.											.	.	0			c.A127G						.						207	186	193					12																	10539523		2203	4298	6501	SO:0001583	missense	0	exon8			TGCTTTTGACTAC	AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"Killer cell lectin-like receptors", "CD molecules"	18788	protein-coding gene	gene with protein product		611817	"DNA segment on chromosome 12 (unique) 2489 expressed sequence"	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.127A>G	12.37:g.10539523T>C	ENSP00000240618:p.Lys43Glu	Somatic	47	0		WXS	Illumina HiSeq	Phase_I	85	32	NM_001199805	0	0	0	0	0	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	37	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.445773	0.25987	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01474	4.85;4.85	4.24	1.81	0.25067	.	0.304503	0.23859	N	0.043877	T	0.01661	0.0053	L	0.36672	1.1	0.09310	N	1	B;B;B	0.26775	0.056;0.159;0.081	B;B;B	0.29524	0.029;0.103;0.028	T	0.46527	-0.9185	10	0.34782	T	0.22	.	4.666	0.12666	0.1788:0.0:0.2431:0.5781	.	43;24;43	Q8WZ67;Q1HEA1;P26718	.;.;NKG2D_HUMAN	E	43	ENSP00000240618:K43E;ENSP00000446003:K43E	ENSP00000240618:K43E	K	-	1	0	KLRK1	10430790	0.005000	0.15991	0.001000	0.08648	0.025000	0.11179	0.895000	0.28363	0.250000	0.21479	0.455000	0.32223	AAA	.		0.323	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		C	10539523	T	C	10539523	3	2	161	1	0	0	0	0	1	0	0	0	8444	1821	63	3	547	3	KLRK1	12	10539523	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	4082459	10539523	123312372	85	14670											
PTPRO	5800	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	15673198	15673198	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaccatggtgacgtggggaGatccagaattgagctgctgt	9	11	14	7	1	0	4	0	2	0	2	1	5	1	4	2	3	3	2	2	3	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:15673198G>A	ENST00000281171.4	+	10	2173	c.1843G>A	c.(1843-1845)Gat>Aat	p.D615N	PTPRO_ENST00000348962.2_Missense_Mutation_p.D615N	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	615	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				GACGTGGGGAGATCCAGAATT	0.478																																					p.D615N		.											.	PTPRO-271	0			c.G1843A						.						138	124	129					12																	15673198		2203	4300	6503	SO:0001583	missense	5800	exon10			TGGGGAGATCCAG	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9678	protein-coding gene	gene with protein product	"osteoclastic transmembrane protein-tyrosine phosphatase"	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.1843G>A	12.37:g.15673198G>A	ENSP00000281171:p.Asp615Asn	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	262	78	NM_002848	0	0	0	0	0	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	37	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956744	0.92726	.	.	ENSG00000151490	ENST00000281171;ENST00000348962	T;T	0.53640	3.8;0.61	5.2	5.2	0.72013	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.249218	0.27922	N	0.017316	T	0.41558	0.1164	N	0.19112	0.55	0.80722	D	1	P;P	0.41188	0.741;0.624	B;B	0.43658	0.426;0.245	T	0.44952	-0.9294	10	0.72032	D	0.01	.	17.0929	0.86627	0.0:0.0:1.0:0.0	.	615;615	Q16827-2;Q16827	.;PTPRO_HUMAN	N	615	ENSP00000281171:D615N;ENSP00000343434:D615N	ENSP00000281171:D615N	D	+	1	0	PTPRO	15564465	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.851000	0.92205	2.689000	0.91719	0.655000	0.94253	GAT	.		0.478	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			A	15673198	G	A	15673198	3	1	161	1	0	0	0	0	1	0	0	0	12841	942	33	2	1881	2	PTPRO	12	15673198	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	5133675	15673198	118178697	86	14671											
DDN	23109	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	49391677	49391677	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggggatggctgtcgctacCactgttcaggtcagcagcag	7	10	14	10	1	2	0	2	0	0	0	3	1	2	1	1	4	3	5	1	4	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:49391677C>T	ENST00000421952.2	-	2	1003	c.982G>A	c.(982-984)Ggt>Agt	p.G328S	RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	328						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						CTGTCGCTACCACTGTTCAGG	0.677																																					p.G328S		.											.	DDN-90	0			c.G982A						.						46	53	51					12																	49391677		2203	4299	6502	SO:0001583	missense	23109	exon2			CGCTACCACTGTT	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.982G>A	12.37:g.49391677C>T	ENSP00000390590:p.Gly328Ser	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	53	11	NM_015086	0	0	0	0	0		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	C	18.60	3.658359	0.67586	.	.	ENSG00000181418	ENST00000421952	T	0.44881	0.91	3.88	2.05	0.26809	.	0.148751	0.31601	N	0.007378	T	0.21387	0.0515	N	0.24115	0.695	0.09310	N	1	P	0.40909	0.732	B	0.31191	0.125	T	0.10776	-1.0615	10	0.42905	T	0.14	-3.234	7.9639	0.30087	0.0:0.798:0.0:0.202	.	328	O94850	DEND_HUMAN	S	328	ENSP00000390590:G328S	ENSP00000390590:G328S	G	-	1	0	DDN	47677944	0.000000	0.05858	0.001000	0.08648	0.743000	0.42351	0.617000	0.24359	0.617000	0.30160	0.561000	0.74099	GGT	.		0.677	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			T	49391677	C	T	49391677	3	4	161	1	0	0	0	0	1	0	0	0	4339	594	21	2	1157	2	DDN	12	49391677	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	33718479	49391677	84460218	87	14672											
METAP2	10988	broad.mit.edu	37	chr12	95867964	95867964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcgggcaacatggcgggTgtggaggaggtagcggcctc	6	7	18	10	3	1	0	0	0	1	0	3	2	1	2	1	7	2	2	1	7	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:95867964T>G	ENST00000323666.5	+	1	238	c.9T>G	c.(7-9)ggT>ggG	p.G3G	METAP2_ENST00000261220.9_Silent_p.G3G|METAP2_ENST00000546753.1_Silent_p.G3G|METAP2_ENST00000551840.1_Silent_p.G3G|METAP2_ENST00000550777.1_Silent_p.G3G	NM_006838.3	NP_006829.1			methionyl aminopeptidase 2											endometrium(3)|large_intestine(2)|lung(7)|prostate(1)	13						ACATGGCGGGTGTGGAGGAGG	0.652																																					p.G3G													.	METAP2-90	0			c.T9G						.						34	42	39					12																	95867964		2203	4297	6500	SO:0001819	synonymous_variant	10988	exon1			GGCGGGTGTGGAG	U13261	CCDS9052.1	12q22	2014-09-04			ENSG00000111142		3.4.11.18		16672	protein-coding gene	gene with protein product	"Peptidase M"	601870				7644482, 8858118	Standard	NM_006838		Approved	MNPEP, p67, MAP2	uc001tec.3	P50579	OTTHUMG00000170280	ENST00000323666.5:c.9T>G	12.37:g.95867964T>G		Somatic	41	4		WXS	Illumina HiSeq	Phase_I	166	27	NM_006838	0	0	1	1	0		Silent	SNP	ENST00000323666.5	37	CCDS9052.1																																																																																			.		0.652	METAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408296.1	NM_006838		G	95867964	T	G	95867964	2	3	161	1	0	0	0	0	0	0	0	1	9512	1683	59	5		5	METAP2	12	95867964	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	46476287	95867964	37983931	88	14673											
TCP11L2	255394	broad.mit.edu	37	chr12	106729801	106729811	+	Splice_Site	DEL	ATATGTTAGAC	ATATGTTAGAC	-																															tatttttatattttaaataaAtatgttagacacttatgaca																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	ATATGTTAGAC	ATATGTTAGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:106729801_106729811delATATGTTAGAC	ENST00000299045.3	+	8	1134_1136	c.960_962delATATGTTAGAC	c.(958-963)gaatat>gat	p.EY320fs		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	320										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						ttttaaataaatatGTTAGACACTTATGACA	0.327																																					p.321_321del													.	TCP11L2-93	0			c.961_962del						.																																			SO:0001630	splice_region_variant	255394	exon8			AAATAAATATGTT	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.961-1ATATGTTAGAC>-	12.37:g.106729801_106729811delATATGTTAGAC		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	18	7	NM_152772	0	0	0	0	0	B2RA65|G3V1Y9	Frame_Shift_Del	DEL	ENST00000299045.3	37	CCDS9104.1																																																																																			.		0.327	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772	Frame_Shift_Del	-	106729811	ATATGTTAGAC	-	106729801	8	5	161	1	0	1	0	1	0	0	1	0	15747	116	4	0		0	TCP11L2	12	106729801	Splice_Site	DEL	ATATGTTAGAC	TCGA-Q2-A5QZ-01A-11D-A28G-10	10861837	106729801	27122094	89	14674											
C12orf24	29902	hgsc.bcm.edu	37	chr12	110906786	110906786	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcgtagctcttctgcagagCcgcccgctgtggccgggacc	5	7	14	15	4	2	1	0	0	2	1	2	2	2	2	4	2	4	4	4	2	1	2	rs202079205	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:110906786C>T	ENST00000377673.5	+	1	618	c.106C>T	c.(106-108)Ccg>Tcg	p.P36S	GPN3_ENST00000228827.3_5'Flank|GPN3_ENST00000537466.2_5'Flank|GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000543199.1_5'Flank	NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	36																	TTCTGCAGAGCCGCCCGCTGT	0.771													C|||	12	0.00239617	0.0091	0	5008	,	,		13111	0		0	False		,,,				2504	0				p.P36S		.											.	.	0			c.C106T						.	C	SER/PRO	24,3054		0,24,1515	2	2	2		106	3.3	0.1	12		2	0,6186		0,0,3093	yes	missense	C12orf24	NM_013300.2	74	0,24,4608	TT,TC,CC		0.0,0.7797,0.2591	probably-damaging	36/274	110906786	24,9240	1539	3093	4632	SO:0001583	missense	29902	exon1			GCAGAGCCGCCCG	U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 24"	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.106C>T	12.37:g.110906786C>T	ENSP00000366901:p.Pro36Ser	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	25	12	NM_013300	0	0	0	1	1	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	37	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171608	0.78452	0.007797	0.0	ENSG00000204856	ENST00000377673;ENST00000538285	T	0.51071	0.72	4.16	3.27	0.37495	.	0.000000	0.39544	N	0.001336	T	0.32645	0.0836	L	0.56769	1.78	0.27811	N	0.942126	B;B	0.30709	0.291;0.129	B;B	0.26693	0.072;0.031	T	0.41645	-0.9497	10	0.87932	D	0	-0.6948	9.2806	0.37727	0.0:0.8974:0.0:0.1026	.	36;36	F5GZE4;Q8WUB2	.;CL024_HUMAN	S	36	ENSP00000366901:P36S	ENSP00000366901:P36S	P	+	1	0	C12orf24	109391169	0.943000	0.32029	0.132000	0.22025	0.895000	0.52256	2.944000	0.49034	1.096000	0.41439	0.462000	0.41574	CCG	.		0.771	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300		T	110906786	C	T	110906786	3	4	161	1	0	0	0	0	1	0	0	0	1682	739	26	2	108	2	C12orf24	12	110906786	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	4176985	110906786	22945109	90	14675											
RAD9B	160760	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr12	110969392	110969392	+	3'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgcagtgtgctgcaggaaAgaatttaatggaagtgatgc	12	12	13	4	0	0	2	0	1	0	1	0	4	0	4	0	2	4	3	0	2	4	3	rs139110749	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:110969392A>G	ENST00000354300.3	-	0	6653				RAD9B_ENST00000409300.1_3'UTR|RAD9B_ENST00000409425.1_3'UTR|RAD9B_ENST00000409246.1_3'UTR|RAD9B_ENST00000392672.4_Silent_p.K416K|RAD9B_ENST00000409778.3_Missense_Mutation_p.K311R	NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)							mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						GCTGCAGGAAAGAATTTAATG	0.353																																					p.K416K		.											.	RAD9B-228	0			c.A1248G						.						94	83	87					12																	110969392		1566	3582	5148	SO:0001624	3_prime_UTR_variant	144715	exon12			CAGGAAAGAATTT	AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"T cell activation protein phosphatase 2C"	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.*5450T>C	12.37:g.110969392A>G		Somatic	12	0		WXS	Illumina HiSeq	Phase_I	27	9	NM_152442	0	0	4	4	0	B3KWC5|Q68DZ7|Q6UY82	Silent	SNP	ENST00000354300.3	37	CCDS9149.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.352501	0.41700	.	.	ENSG00000151164	ENST00000409778	T	0.19250	2.16	4.49	2.08	0.27032	.	155.184000	0.02530	U	0.093532	T	0.15609	0.0376	.	.	.	0.09310	N	1	B	0.26635	0.155	B	0.23574	0.047	T	0.21211	-1.0252	9	0.40728	T	0.16	14.2473	4.9792	0.14157	0.6246:0.1916:0.0:0.1837	.	311	B4DYM6	.	R	311	ENSP00000386697:K311R	ENSP00000386697:K311R	K	+	2	0	RAD9B	109453775	0.009000	0.17119	0.001000	0.08648	0.372000	0.29890	1.856000	0.39389	0.343000	0.23821	0.397000	0.26171	AAG	.		0.353	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283		G	110969392	A	G	110969392	1	3	161	0	1	0	0	0	0	0	0	0	13028	69	3	3		3	RAD9B	12	110969392	3'UTR	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	62606	110969392	22882503	91	14676											
CUX2	23316	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr12	111785758	111785759	+	Frame_Shift_Ins	INS	-	-	A																															ctgtccctcacttcatccccINSaacaggagagtgaggccggg																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:111785758_111785759insA	ENST00000261726.6	+	22	4244_4245	c.4090_4091insA	c.(4090-4092)caafs	p.Q1364fs		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1364	Pro-rich.				cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						ACTTCATCCCCAACAGGAGAGT	0.604																																					p.Q1364fs		.											.	CUX2-140	0			c.4090_4091insA						.																																			SO:0001589	frameshift_variant	23316	exon22			.	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"Homeoboxes / CUT class"	19347	protein-coding gene	gene with protein product		610648	"cut-like 2 (Drosophila)"	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.4092dupA	12.37:g.111785760_111785760dupA	ENSP00000261726:p.Gln1364fs	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	69	24	NM_015267	0	0	0	0	0	A7E2Y4	Frame_Shift_Ins	INS	ENST00000261726.6	37	CCDS41837.1																																																																																			.		0.604	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111785759	-	A	111785758	7	5	161	1	0	1	1	0	0	0	0	0	4071	595	21	0	4176	0	CUX2	12	111785758	Frame_Shift_Ins	INS	-	TCGA-Q2-A5QZ-01A-11D-A28G-10	816366	111785758	22066137	92	14677											
RBM19	9904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	114385205	114385205	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagggaacatgaaggtgatGaatgcaaaacccttgggttt	13	10	12	6	0	1	3	1	3	0	0	1	4	1	4	1	3	3	2	1	3	5	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:114385205G>A	ENST00000545145.2	-	11	1419	c.1341C>T	c.(1339-1341)ttC>ttT	p.F447F	RBM19_ENST00000392561.3_Silent_p.F447F|RBM19_ENST00000261741.5_Silent_p.F447F	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	447	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TGAAGGTGATGAATGCAAAAC	0.602																																					p.F447F		.											.	RBM19-95	0			c.C1341T						.						144	122	130					12																	114385205		2203	4300	6503	SO:0001819	synonymous_variant	9904	exon11			GGTGATGAATGCA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"RNA binding motif (RRM) containing"	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1341C>T	12.37:g.114385205G>A		Somatic	73	0		WXS	Illumina HiSeq	Phase_I	278	64	NM_001146699	0	0	0	3	3	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			.		0.602	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		A	114385205	G	A	114385205	2	1	161	1	0	0	0	0	0	0	0	1	13153	1281	45	2		2	RBM19	12	114385205	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	2599447	114385205	19466690	93	14678											
BRI3BP	140707	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr12	125509640	125509640	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctggcctactggttcttgtcCctgaccctgggcttcacttt	3	15	9	14	0	2	1	1	1	1	0	3	1	3	1	3	3	1	2	3	3	1	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:125509640C>A	ENST00000341446.8	+	3	511	c.420C>A	c.(418-420)tcC>tcA	p.S140S		NM_080626.5	NP_542193.3			BRI3 binding protein											large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		GGTTCTTGTCCCTGACCCTGG	0.632																																					p.S140S		.											.	BRI3BP-91	0			c.C420A						.						100	83	89					12																	125509640		2203	4300	6503	SO:0001819	synonymous_variant	140707	exon3			CTTGTCCCTGACC	AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.420C>A	12.37:g.125509640C>A		Somatic	25	0		WXS	Illumina HiSeq	Phase_I	85	32	NM_080626	0	0	8	15	7		Silent	SNP	ENST00000341446.8	37	CCDS9262.1																																																																																			.		0.632	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626		A	125509640	C	A	125509640	2	1	161	1	0	0	0	0	0	0	0	1	1516	610	22	4		4	BRI3BP	12	125509640	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	11124435	125509640	8342255	94	14679											
N6AMT2	221143	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	21306119	21306119	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctttcgggtaagtccaaTggattattgtaatcatagaa	13	15	8	5	1	2	1	1	0	1	1	4	2	3	2	1	2	0	2	1	2	6	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr13:21306119T>C	ENST00000382758.1	-	4	416	c.369A>G	c.(367-369)ccA>ccG	p.P123P	N6AMT2_ENST00000382754.4_Silent_p.P123P			Q8WVE0	N6MT2_HUMAN	N-6 adenine-specific DNA methyltransferase 2 (putative)	123						extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(3)|lung(3)	7		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)		GTAAGTCCAATGGATTATTGT	0.378																																					p.P123P		.											.	N6AMT2-68	0			c.A369G						.						121	116	118					13																	21306119		2203	4300	6503	SO:0001819	synonymous_variant	221143	exon4			GTCCAATGGATTA	AK055408	CCDS9293.1	13q12.11	2006-12-14			ENSG00000150456	ENSG00000150456			27351	protein-coding gene	gene with protein product						12477932	Standard	NM_174928		Approved		uc001uno.1	Q8WVE0	OTTHUMG00000016519	ENST00000382758.1:c.369A>G	13.37:g.21306119T>C		Somatic	83	0		WXS	Illumina HiSeq	Phase_I	82	37	NM_174928	0	0	0	4	4	B5G4V1	Silent	SNP	ENST00000382758.1	37	CCDS9293.1																																																																																			.		0.378	N6AMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044083.1	NM_174928		C	21306119	T	C	21306119	2	2	161	1	0	0	0	0	0	0	0	1	10140	1451	51	3		3	N6AMT2	13	21306119	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		21306119	93863759	95	14680											
FARP1	10160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr13	99092299	99092299	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatcatcgtggccgccaggTaactcgggagcccgcccctt	6	7	11	17	4	1	0	1	0	0	0	3	1	1	1	6	3	2	1	6	3	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr13:99092299T>A	ENST00000319562.6	+	22	2781		c.e22+2		FARP1_ENST00000595437.1_Splice_Site|FARP1_ENST00000376586.2_Splice_Site	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)						dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GGCCGCCAGGTAACTCGGGAG	0.627																																					.		.											.	FARP1-290	0			c.2516+2T>A						.						103	116	112					13																	99092299		2203	4300	6503	SO:0001630	splice_region_variant	10160	exon22			GCCAGGTAACTCG	AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"Rho guanine nucleotide exchange factors", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Pleckstrin homology (PH) domain containing"	3591	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 75"	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.2516+2T>A	13.37:g.99092299T>A		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	70	13	NM_005766	0	0	0	1	1	Q5JVI9|Q6IQ29	Splice_Site	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843475	0.91197	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0308	0.64615	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FARP1	97890300	1.000000	0.71417	0.999000	0.59377	0.910000	0.53928	5.986000	0.70563	1.917000	0.55516	0.533000	0.62120	.	.		0.627	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	Intron	A	99092299	T	A	99092299	5	1	161	1	0	0	0	0	0	0	1	0	5695	1652	57	5	2823	5	FARP1	13	99092299	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	77786180	99092299	16077579	96	14681											
FLJ10357	55701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr14	21543565	21543565	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctgtgcaggaaggaaaagggGacaacattccagaagaggcc	15	4	14	8	0	0	2	0	0	0	2	1	5	1	5	2	5	2	1	2	5	5	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr14:21543565G>C	ENST00000298694.4	+	4	1652	c.1525G>C	c.(1525-1527)Gac>Cac	p.D509H	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.D509H			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	509						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						AGGAAAAGGGGACAACATTCC	0.557																																					p.D509H		.											.	ARHGEF40-228	0			c.G1525C						.						131	127	128					14																	21543565		2203	4300	6503	SO:0001583	missense	55701	exon4			AAAGGGGACAACA		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"Rho guanine nucleotide exchange factors"	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1525G>C	14.37:g.21543565G>C	ENSP00000298694:p.Asp509His	Somatic	108	0		WXS	Illumina HiSeq	Phase_I	227	62	NM_018071	0	0	0	0	0	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	37	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	G	0.307	-0.970175	0.02232	.	.	ENSG00000165801	ENST00000298694;ENST00000555038;ENST00000298693	T;T	0.02472	4.34;4.28	5.12	2.29	0.28610	.	0.113584	0.39210	N	0.001427	T	0.02230	0.0069	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.44329	-0.9335	10	0.40728	T	0.16	.	7.8371	0.29376	0.0851:0.308:0.6069:0.0	.	509;509	Q8TER5;G3V3N2	ARH40_HUMAN;.	H	509	ENSP00000298694:D509H;ENSP00000298693:D509H	ENSP00000298693:D509H	D	+	1	0	ARHGEF40	20613405	0.142000	0.22610	0.001000	0.08648	0.002000	0.02628	1.389000	0.34453	0.272000	0.22027	-0.225000	0.12378	GAC	.		0.557	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			C	21543565	G	C	21543565	3	2	161	1	0	0	0	0	1	0	0	0	5945	1174	41	4	1539	4	FLJ10357	14	21543565	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		21543565	85805975	97	14682											
KIAA1737	85457	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	chr14	77580238	77580238	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaagctcccagtctgaccttCgcttcccccgccagtcctgt	6	10	7	18	2	1	1	0	1	1	0	5	1	4	1	6	0	1	2	6	0	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr14:77580238C>T	ENST00000361786.2	+	4	1094	c.777C>T	c.(775-777)ttC>ttT	p.F259F	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		259					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		GTCTGACCTTCGCTTCCCCCG	0.572																																					p.F259F		.											.	KIAA1737-90	0			c.C777T						.						84	68	74					14																	77580238		2203	4300	6503	SO:0001819	synonymous_variant	85457	exon4			GACCTTCGCTTCC																												ENST00000361786.2:c.777C>T	14.37:g.77580238C>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_I	48	24	NM_033426	0	0	0	0	0	B2RCI1|Q8N389|Q8NDZ1	Silent	SNP	ENST00000361786.2	37	CCDS9855.1																																																																																			.		0.572	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1			T	77580238	C	T	77580238	2	4	161	1	0	0	0	0	0	0	0	1	8276	883	31	1		1	KIAA1737	14	77580238	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	56036673	77580238	29769302	98	14683											
ITPK1	3705	hgsc.bcm.edu	37	chr14	93408017	93408017	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcttggcggtgccgccCgcgtcggcctcagccttcca	3	7	14	17	5	1	0	1	0	0	0	3	0	2	0	5	4	3	2	5	4	0	2	rs563090061	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr14:93408017C>T	ENST00000267615.6	-	11	1307	c.1134G>A	c.(1132-1134)gcG>gcA	p.A378A	ITPK1_ENST00000354313.3_Intron|ITPK1_ENST00000555495.1_Silent_p.A259A|ITPK1_ENST00000556603.2_Silent_p.A378A			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	378					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		CGGTGCCGCCCGCGTCGGCCT	0.736													C|||	4	0.000798722	8e-04	0.0014	5008	,	,		13386	0.001		0	False		,,,				2504	0.001				p.A378A		.											.	ITPK1-115	0			c.G1134A						.						3	3	3					14																	93408017		1665	3314	4979	SO:0001819	synonymous_variant	3705	exon11			GCCGCCCGCGTCG	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.1134G>A	14.37:g.93408017C>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	14	12	NM_001142593	0	0	0	1	1	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	37	CCDS9907.1																																																																																			.		0.736	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93408017	C	T	93408017	2	4	161	1	0	0	0	0	0	0	0	1	7937	639	23	1		1	ITPK1	14	93408017	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	15827779	93408017	13941523	99	14684											
CASC5	57082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	40915310	40915310	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagtgtttgtagataatcatGttgaactagaaatgacagag	15	13	10	3	0	1	5	1	2	0	3	1	5	1	5	0	0	1	3	0	0	6	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:40915310G>T	ENST00000346991.5	+	11	3316	c.2926G>T	c.(2926-2928)Gtt>Ttt	p.V976F	CASC5_ENST00000399668.2_Missense_Mutation_p.V950F|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	976	2 X 104 AA approximate repeats.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AGATAATCATGTTGAACTAGA	0.378																																					p.V976F		.											.	CASC5-660	0			c.G2926T						.						92	86	88					15																	40915310		1860	4104	5964	SO:0001583	missense	57082	exon11			AATCATGTTGAAC	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	24054	protein-coding gene	gene with protein product	"cancer/testis antigen 29", "kinetochore null 1 homolog (C. elegans)", "blinkin, bub-linking kinetochore protein", "protein phosphatase 1, regulatory subunit 55"	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.2926G>T	15.37:g.40915310G>T	ENSP00000335463:p.Val976Phe	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	88	21	NM_170589	0	0	0	0	0	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.757693	0.31137	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.16897	2.31;2.31	4.64	0.322	0.15888	.	0.547984	0.17535	N	0.170730	T	0.07503	0.0189	N	0.08118	0	0.09310	N	1	B;B;P	0.39352	0.101;0.009;0.669	B;B;B	0.34652	0.053;0.001;0.187	T	0.24621	-1.0155	10	0.62326	D	0.03	.	9.0014	0.36083	0.436:0.0:0.564:0.0	.	950;976;950	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	F	976;950;950	ENSP00000335463:V976F;ENSP00000382576:V950F	ENSP00000260369:V950F	V	+	1	0	CASC5	38702602	0.000000	0.05858	0.020000	0.16555	0.900000	0.52787	-0.061000	0.11693	0.051000	0.15978	0.557000	0.71058	GTT	.		0.378	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40915310	G	T	40915310	3	4	161	1	0	0	0	0	1	0	0	0	2669	1377	48	4	2964	4	CASC5	15	40915310	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		40915310	61616082	100	14685											
TGM7	116179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	43585144	43585145	+	Missense_Mutation	DNP	GC	GC	TT																															ggtccccagcagctctgacgGcttgggtcctgtgtaggaga																								rs267604217		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:43585144_43585145GC>TT	ENST00000452443.2	-	3	205_206	c.201_202GC>AA	c.(199-204)aaGCcg>aaAAcg	p.P68T		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	68					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	AGCTCTGACGGCTTGGGTCCTG	0.559																																					p.P68T		.											.	TGM7-92	0			c.G201A						.																																			SO:0001583	missense	116179	exon3			TGACGGCTTGGGT	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"Transglutaminases"	30790	protein-coding gene	gene with protein product	"transglutaminase Z"	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.201_202delinsTT	15.37:g.43585144_43585145delinsTT	ENSP00000389466:p.Pro68Thr	Somatic	44	0		WXS	Illumina HiSeq	Phase_I	62	14	NM_052955	0	0	0	0	0		Missense_Mutation	DNP	ENST00000452443.2	37	CCDS32213.1																																																																																			.		0.559	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		TT	43585145	GC	TT	43585144	3	4	161	1	0	0	0	0	1	0	0	0	15867	1203	42	4	1974	4	TGM7	15	43585144	Missense_Mutation	DNP	GC	TCGA-Q2-A5QZ-01A-11D-A28G-10	2669834	43585144	58946248	101	14686											
HDC	3067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	50535435	50535435	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcaaaatatttagccatttCagtaccctggaattgcaagt	13	14	6	8	0	2	0	2	0	0	0	2	1	2	1	2	1	3	2	2	1	7	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:50535435C>T	ENST00000267845.3	-	11	1549	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	HDC_ENST00000543581.1_Missense_Mutation_p.E350K|RN7SL494P_ENST00000461517.2_RNA	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TTAGCCATTTCAGTACCCTGG	0.403																																					p.E383K	GBM(95;1627 1936 6910 9570)	.											.	HDC-156	0			c.G1147A						.						65	65	65					15																	50535435		2196	4295	6491	SO:0001583	missense	3067	exon11			CCATTTCAGTACC		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1147G>A	15.37:g.50535435C>T	ENSP00000267845:p.Glu383Lys	Somatic	106	0		WXS	Illumina HiSeq	Phase_I	155	62	NM_002112	0	0	0	0	0		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043666	0.55003	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.39592	1.07;1.07	5.82	4.9	0.64082	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.280579	0.41605	N	0.000857	T	0.37972	0.1023	L	0.28694	0.88	0.58432	D	0.999998	P;P	0.35894	0.526;0.526	B;B	0.43508	0.422;0.307	T	0.10200	-1.0640	10	0.18276	T	0.48	-10.5182	14.7799	0.69756	0.0:0.9307:0.0:0.0693	.	350;383	B7ZM01;P19113	.;DCHS_HUMAN	K	383;350	ENSP00000267845:E383K;ENSP00000440252:E350K	ENSP00000267845:E383K	E	-	1	0	HDC	48322727	0.999000	0.42202	0.897000	0.35233	0.970000	0.65996	3.899000	0.56288	1.462000	0.47948	0.467000	0.42956	GAA	.		0.403	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			T	50535435	C	T	50535435	3	4	161	1	0	0	0	0	1	0	0	0	7036	835	29	2	849	2	HDC	15	50535435	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6950291	50535435	51995957	102	14687											
MYO5C	55930	hgsc.bcm.edu	37	chr15	52500781	52500781	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtactgcttcaggcaattGagaaaatgacaagtgttgga	13	11	11	6	0	1	2	1	2	0	1	1	4	1	3	0	2	2	4	0	2	5	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:52500781G>T	ENST00000261839.7	-	36	4517	c.4356C>A	c.(4354-4356)ctC>ctA	p.L1452L	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1452	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TCAGGCAATTGAGAAAATGAC	0.438											OREG0023129	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1452L		.											.	MYO5C-145	0			c.C4356A						.						105	107	106					15																	52500781		1889	4099	5988	SO:0001819	synonymous_variant	55930	exon36			GCAATTGAGAAAA	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"Myosins / Myosin superfamily : Class V"	7604	protein-coding gene	gene with protein product	"myosin 5C"	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.4356C>A	15.37:g.52500781G>T		Somatic	58	0	985	WXS	Illumina HiSeq	Phase_I	108	9	NM_018728	0	0	0	0	0	Q6P1W8	Silent	SNP	ENST00000261839.7	37	CCDS42036.1																																																																																			.		0.438	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		T	52500781	G	T	52500781	2	4	161	1	0	0	0	0	0	0	0	1	10105	1277	45	4		4	MYO5C	15	52500781	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	1965346	52500781	50030611	103	14688											
CSPG4	1464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr15	75982866	75982866	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tcgggggtcagaggccggagGaggctgcggccattgagggt	6	6	21	8	3	1	2	1	1	0	1	2	4	1	4	2	8	1	1	2	8	0	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:75982866G>C	ENST00000308508.5	-	3	632	c.540C>G	c.(538-540)ctC>ctG	p.L180L		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	180	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GAGGCCGGAGGAGGCTGCGGC	0.647																																					p.L180L		.											.	CSPG4-229	0			c.C540G						.						35	40	38					15																	75982866		2147	4173	6320	SO:0001819	synonymous_variant	1464	exon3			CCGGAGGAGGCTG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"Proteoglycans / Cell surface : Other"	2466	protein-coding gene	gene with protein product	"melanoma-associated chondroitin sulfate proteoglycan"	601172	"chondroitin sulfate proteoglycan 4 (melanoma-associated)"			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.540C>G	15.37:g.75982866G>C		Somatic	43	0		WXS	Illumina HiSeq	Phase_I	62	20	NM_001897	0	0	0	0	0	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			.		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75982866	G	C	75982866	2	2	161	1	0	0	0	0	0	0	0	1	3966	1161	41	4		4	CSPG4	15	75982866	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	23482085	75982866	26548526	104	14689											
HMOX2	3163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	4557977	4557977	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccatgcatacacccgCtacatgggggatctctcggg	7	8	13	13	2	1	0	0	0	1	0	3	1	1	1	2	4	3	2	2	4	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:4557977C>T	ENST00000570646.1	+	4	1073	c.468C>T	c.(466-468)cgC>cgT	p.R156R	HMOX2_ENST00000414777.1_Silent_p.R156R|HMOX2_ENST00000219700.6_Silent_p.R156R|HMOX2_ENST00000406590.2_Silent_p.R156R|HMOX2_ENST00000458134.3_Silent_p.R156R|HMOX2_ENST00000575120.1_Silent_p.R127R|HMOX2_ENST00000398595.3_Silent_p.R156R	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	156					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						CATACACCCGCTACATGGGGG	0.617																																					p.R156R		.											.	HMOX2-90	0			c.C468T						.						39	43	41					16																	4557977		2197	4300	6497	SO:0001819	synonymous_variant	3163	exon4			CACCCGCTACATG		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.468C>T	16.37:g.4557977C>T		Somatic	80	0		WXS	Illumina HiSeq	Phase_I	216	85	NM_001127205	0	0	43	107	64	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	37	CCDS10517.1																																																																																			.		0.617	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			T	4557977	C	T	4557977	2	4	161	1	0	0	0	0	0	0	0	1	7265	784	28	2		2	HMOX2	16	4557977	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		4557977	85796776	105	14690											
LAT	27040	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chr16	28996234	28996234	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgtccccgtcttgggggggGccagcagacccttggtgagt	4	9	16	12	1	1	2	0	1	1	1	2	2	2	2	4	5	1	1	4	5	0	2	rs572112079	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:28996234G>A	ENST00000360872.5	+	0	0				LAT_ENST00000454369.2_5'Flank|LAT_ENST00000395461.3_Missense_Mutation_p.A18T|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000354453.4_5'Flank|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000395456.2_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA			O43561	LAT_HUMAN	linker for activation of T cells						blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				CTTGGGGGGGGCCAGCAGACC	0.731																																					p.A18T		.											.	LAT-44	0			c.G52A						.						7	8	8					16																	28996234		690	1584	2274	SO:0001631	upstream_gene_variant	27040	exon1			GGGGGGGCCAGCA	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"linker for activation of T cells, transmembrane adaptor"	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761		16.37:g.28996234G>A	Exception_encountered	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	91	29	NM_001014989	0	0	0	0	0	B7WPI0|C7C5T6|G5E9K3|O43919	Missense_Mutation	SNP	ENST00000360872.5	37	CCDS10647.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.247385	0.22880	.	.	ENSG00000213658	ENST00000395461	.	.	.	2.5	-1.56	0.08532	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.19300	N	0.999973	B	0.02656	0.0	B	0.01281	0.0	T	0.21655	-1.0239	8	0.87932	D	0	-0.7971	3.9972	0.09564	0.1852:0.4888:0.326:0.0	.	18	B7WPI0	.	T	18	.	ENSP00000378845:A18T	A	+	1	0	LAT	28903735	0.000000	0.05858	0.002000	0.10522	0.036000	0.12997	-0.751000	0.04803	-0.063000	0.13065	-0.264000	0.10439	GCC	.		0.731	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			A	28996234	G	A	28996234	1	1	161	0	1	0	0	0	0	0	0	0	8665	1203	42	2		2	LAT	16	28996234	5'Flank	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	24438257	28996234	61358519	106	14691											
PRRT2	112476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr16	29825753	29825753	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggtggggggagtcctcAtcatcatcgcctcctgcgtc	4	10	13	14	3	3	0	3	0	0	0	7	1	5	1	3	4	1	1	3	4	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:29825753A>C	ENST00000358758.7	+	3	1262	c.979A>C	c.(979-981)Atc>Ctc	p.I327L	AC009133.20_ENST00000569039.1_RNA|PAGR1_ENST00000609618.1_5'Flank|AC009133.14_ENST00000569981.1_RNA|PRRT2_ENST00000567659.1_Missense_Mutation_p.I327L|PAGR1_ENST00000320330.6_5'Flank|PRRT2_ENST00000300797.6_3'UTR	NM_001256442.1|NM_001256443.1|NM_145239.2	NP_001243371.1|NP_001243372.1|NP_660282.2	Q7Z6L0	PRRT2_HUMAN	proline-rich transmembrane protein 2	327					neuromuscular process controlling posture (GO:0050884)|response to biotic stimulus (GO:0009607)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	8						GGGAGTCCTCATCATCATCGC	0.642																																					p.I327L		.											.	PRRT2-68	0			c.A979C						.						73	81	78					16																	29825753		2197	4300	6497	SO:0001583	missense	112476	exon3			GTCCTCATCATCA	BC011405	CCDS10654.1, CCDS58445.1, CCDS58446.1	16p11.2	2014-02-03			ENSG00000167371	ENSG00000167371		"Proline-rich transmembrane proteins"	30500	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 1"	614386	"infantile convulsions and paroxysmal choreoathetosis"	ICCA		22101681, 22243967	Standard	NM_145239		Approved	FLJ25513, DKFZp547J199, IFITMD1, FICCA	uc002dud.3	Q7Z6L0	OTTHUMG00000177142	ENST00000358758.7:c.979A>C	16.37:g.29825753A>C	ENSP00000351608:p.Ile327Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	59	18	NM_001256442	0	0	0	1	1	A8K8M8|Q8N2N8|Q8NAQ7|Q8ND36|Q96FA8	Missense_Mutation	SNP	ENST00000358758.7	37	CCDS10654.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.815687	0.70912	.	.	ENSG00000167371	ENST00000358758	D	0.85339	-1.97	3.71	3.71	0.42584	.	0.745808	0.12408	N	0.471504	D	0.86410	0.5926	N	0.25380	0.74	0.80722	D	1	D;D	0.63046	0.992;0.99	D;D	0.76071	0.987;0.978	T	0.82796	-0.0280	10	0.40728	T	0.16	-8.8013	10.7234	0.46052	1.0:0.0:0.0:0.0	.	327;327	Q7Z6L0;Q7Z6L0-2	PRRT2_HUMAN;.	L	327	ENSP00000351608:I327L	ENSP00000351608:I327L	I	+	1	0	PRRT2	29733254	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.922000	0.48860	1.481000	0.48307	0.372000	0.22366	ATC	.		0.642	PRRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255161.3	NM_145239		C	29825753	A	C	29825753	3	2	161	1	0	0	0	0	1	0	0	0	12639	217	8	5	985	5	PRRT2	16	29825753	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	829519	29825753	60529000	107	14692											
ESRP2	80004	broad.mit.edu	37	chr16	68267896	68267896	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggttttccttcaggagcataCcttcctggaggcctcggggt	5	12	13	11	1	1	0	1	0	0	0	4	2	3	2	4	6	2	2	4	6	1	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:68267896C>G	ENST00000565858.1	-	3	528		c.e3+1		ESRP2_ENST00000473183.2_Splice_Site|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2						mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						CAGGAGCATACCTTCCTGGAG	0.617																																					.													.	ESRP2-91	0			c.441+1G>C						.						47	46	46					16																	68267896		2198	4300	6498	SO:0001630	splice_region_variant	80004	exon4			AGCATACCTTCCT	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"RNA binding motif (RRM) containing"	26152	protein-coding gene	gene with protein product		612960	"RNA binding motif protein 35B"	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.441+1G>C	16.37:g.68267896C>G		Somatic	44	2		WXS	Illumina HiSeq	Phase_I	98	28	NM_024939	0	0	0	0	0	Q8N6H8|Q8WZ15|Q9H6I4	Splice_Site	SNP	ENST00000565858.1	37		.	.	.	.	.	.	.	.	.	.	C	20.9	4.072387	0.76415	.	.	ENSG00000103067	ENST00000473183	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5613	0.87908	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ESRP2	66825397	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.127000	0.77210	2.663000	0.90544	0.655000	0.94253	.	.		0.617	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	Intron	G	68267896	C	G	68267896	5	3	161	1	0	0	0	0	0	0	1	0	5272	521	18	4	1763	4	ESRP2	16	68267896	Splice_Site	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	38442143	68267896	22086857	108	14693											
DHX38	9785	broad.mit.edu	37	chr16	72141342	72141342	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctcaagtccctcGgggtgcaggacctgctgcag	5	9	14	13	1	1	0	1	0	0	0	3	1	2	1	2	3	6	6	2	3	1	0	rs374391366		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:72141342G>A	ENST00000268482.3	+	20	3213	c.2704G>A	c.(2704-2706)Ggg>Agg	p.G902R	DHX38_ENST00000536867.1_Missense_Mutation_p.G214R	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	902	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CAAGTCCCTCGGGGTGCAGGA	0.597																																					p.G902R	Melanoma(97;711 1442 7855 13832 28836)												.	DHX38-227	0			c.G2704A						.	G	ARG/GLY	2,4394	4.2+/-10.8	0,2,2196	42	37	38		2704	5.3	1	16		38	0,8600		0,0,4300	no	missense	DHX38	NM_014003.3	125	0,2,6496	AA,AG,GG		0.0,0.0455,0.0154	possibly-damaging	902/1228	72141342	2,12994	2198	4300	6498	SO:0001583	missense	9785	exon20			TCCCTCGGGGTGC	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"DEAH-boxes"	17211	protein-coding gene	gene with protein product		605584	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.2704G>A	16.37:g.72141342G>A	ENSP00000268482:p.Gly902Arg	Somatic	25	0		WXS	Illumina HiSeq	Phase_I	118	5	NM_014003	0	0	5	5	0	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.651253	0.88056	4.55E-4	0.0	ENSG00000140829	ENST00000268482;ENST00000536867	T;T	0.04156	3.69;3.69	5.28	5.28	0.74379	Helicase, C-terminal (1);	0.125696	0.52532	D	0.000067	T	0.14743	0.0356	M	0.85462	2.755	0.80722	D	1	D;P	0.53885	0.963;0.936	B;P	0.45449	0.429;0.481	T	0.01604	-1.1314	10	0.72032	D	0.01	.	18.7055	0.91637	0.0:0.0:1.0:0.0	.	214;902	B4DVG8;Q92620	.;PRP16_HUMAN	R	902;214	ENSP00000268482:G902R;ENSP00000437898:G214R	ENSP00000268482:G902R	G	+	1	0	DHX38	70698843	1.000000	0.71417	0.966000	0.40874	0.973000	0.67179	9.190000	0.94934	2.745000	0.94114	0.655000	0.94253	GGG	.		0.597	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72141342	G	A	72141342	3	1	161	1	0	0	0	0	1	0	0	0	4522	1116	39	1	2778	1	DHX38	16	72141342	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	3873446	72141342	18213411	109	14694											
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu	37	chr16	72923790	72923790	+	Frame_Shift_Del	DEL	G	G	-																															aggttgagcttggccttggtGgagtagttgcacagaacgca																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:72923790delG	ENST00000268489.5	-	4	3960	c.3288delC	c.(3286-3288)tccfs	p.S1096fs	ZFHX3_ENST00000397992.5_Frame_Shift_Del_p.S182fs	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1096					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TGGCCTTGGTGGAGTAGTTGC	0.557																																					p.S1096fs		.											.	ZFHX3-72	0			c.3288delC						.						107	75	86					16																	72923790		2198	4300	6498	SO:0001589	frameshift_variant	463	exon4			.	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	777	protein-coding gene	gene with protein product		104155	"AT-binding transcription factor 1"	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.3288delC	16.37:g.72923790delG	ENSP00000268489:p.Ser1096fs	Somatic	16	0		WXS	Illumina HiSeq	Phase_I	42	14	NM_006885	0	0	0	0	0	D3DWS8|O15101|Q13719	Frame_Shift_Del	DEL	ENST00000268489.5	37	CCDS10908.1																																																																																			.		0.557	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		-	72923790	G	-	72923790	7	5	161	1	0	1	0	1	0	0	0	0	17666	1335	47	0	7851	0	ZFHX3	16	72923790	Frame_Shift_Del	DEL	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	782448	72923790	17430963	110	14695											
TNK1	8711	hgsc.bcm.edu	37	chr17	7287558	7287558	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcatgggcgggccccgcccTatcccctacgcctggtgaga	5	7	13	16	3	1	1	1	1	0	1	2	2	2	1	6	3	1	0	6	3	2	2	rs17853470	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:7287558T>C	ENST00000576812.1	+	6	1221	c.852T>C	c.(850-852)ccT>ccC	p.P284P	TNK1_ENST00000570896.1_Silent_p.P284P|TNK1_ENST00000311668.2_Silent_p.P284P	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				GGCCCCGCCCTATCCCCTACG	0.746													.|||	51	0.0101837	8e-04	0.0317	5008	,	,		12772	0		0.0239	False		,,,				2504	0.0041				p.P284P		.											.	TNK1-547	0			c.T852C						.	C		2,2808		0,2,1403	2	2	2		852	2	1	17	dbSNP_123	2	22,6184		0,22,3081	no	coding-synonymous	TNK1	NM_003985.3		0,24,4484	CC,CT,TT		0.3545,0.0712,0.2662		284/662	7287558	24,8992	1405	3103	4508	SO:0001819	synonymous_variant	8711	exon6			CCGCCCTATCCCC	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.852T>C	17.37:g.7287558T>C		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	9	4	NM_003985	0	0	0	0	0		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			T|0.979;C|0.021		0.746	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985		C	7287558	T	C	7287558	2	2	161	1	0	0	0	0	0	0	0	1	16349	1509	53	3		3	TNK1	17	7287558	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		7287558	73907652	111	14696											
LYZL6	57151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	34263772	34263772	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcctcaccagttgttcatccCccgtgctccggacacaatcc	7	10	6	18	2	2	0	2	0	0	0	6	1	6	1	6	1	1	3	6	1	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:34263772C>G	ENST00000585556.1	-	4	698	c.364G>C	c.(364-366)Ggg>Cgg	p.G122R	LYZL6_ENST00000394523.3_Missense_Mutation_p.G122R|LYZL6_ENST00000293274.4_Missense_Mutation_p.G122R|LYZL6_ENST00000492340.2_5'UTR			O75951	LYZL6_HUMAN	lysozyme-like 6	122					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTGTTCATCCCCCGTGCTCCG	0.572																																					p.G122R		.											.	LYZL6-90	0			c.G364C						.						114	103	107					17																	34263772		2203	4300	6503	SO:0001583	missense	57151	exon3			TCATCCCCCGTGC	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.364G>C	17.37:g.34263772C>G	ENSP00000468094:p.Gly122Arg	Somatic	20	0		WXS	Illumina HiSeq	Phase_I	115	61	NM_020426	0	0	0	0	0	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	37	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.733915	0.30684	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.75589	-0.95;-0.95	4.89	3.9	0.45041	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000001	D	0.88273	0.6392	M	0.93462	3.42	0.09310	N	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.81048	-0.1109	10	0.87932	D	0	-6.5656	10.8134	0.46559	0.1893:0.8107:0.0:0.0	.	122	O75951	LYZL6_HUMAN	R	122	ENSP00000293274:G122R;ENSP00000378031:G122R	ENSP00000293274:G122R	G	-	1	0	LYZL6	31287885	0.102000	0.21896	0.008000	0.14137	0.071000	0.16799	1.597000	0.36729	1.168000	0.42723	0.561000	0.74099	GGG	.		0.572	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426		G	34263772	C	G	34263772	3	3	161	1	0	0	0	0	1	0	0	0	9159	623	22	4	90	4	LYZL6	17	34263772	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	26976214	34263772	46931438	112	14697											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274238	39274238	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacacagcagctggggcgAcagcagctggagatgcagca	12	3	15	11	1	0	1	0	0	0	1	0	4	0	1	0	3	6	6	0	3	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:39274238A>G	ENST00000391413.2	-	1	368	c.330T>C	c.(328-330)tgT>tgC	p.C110C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	110	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agctggggcgacagcagctgg	0.652																																					p.C110C		.											.	.	0			c.T330C						.						5	9	8					17																	39274238		657	1550	2207	SO:0001819	synonymous_variant	653240	exon1			GGGGCGACAGCAG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"Keratin associated proteins"	18911	protein-coding gene	gene with protein product			"keratin associated protein 4-14"	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.330T>C	17.37:g.39274238A>G		Somatic	27	0		WXS	Illumina HiSeq	Phase_I	116	14	NM_033059	0	0	0	0	0	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			G	39274238	A	G	39274238	2	3	161	1	0	0	0	0	0	0	0	1	8570	273	10	3		3	KRTAP4-11	17	39274238	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	5010466	39274238	41920972	113	14698											
KRTAP4-3	85290	bcgsc.ca	37	chr17	39324104	39324104	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggaaggcctgcagcaactAgaaatgcagcagctggggcg	12	4	15	10	1	0	1	0	0	0	1	0	2	0	2	1	4	6	5	1	4	4	1	rs368619075		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:39324104A>G	ENST00000391356.2	-	1	320	c.321T>C	c.(319-321)tcT>tcC	p.S107S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	107	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].		Missing (in allele KAP3-v2). {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.S107S(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			TGCAGCAACTAGAAATGCAGC	0.597																																					p.S107S													.	KRTAP4-3-22	1	Substitution - coding silent(1)	large_intestine(1)	c.T321C						.						18	23	21					17																	39324104		2109	4252	6361	SO:0001819	synonymous_variant	85290	exon1			GCAACTAGAAATG	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"Keratin associated proteins"	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.321T>C	17.37:g.39324104A>G		Somatic	34	0		WXS	Illumina HiSeq	Phase_1	317	20	NM_033187	0	0	0	0	0		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.		0.597	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			G	39324104	A	G	39324104	2	3	161	1	0	0	0	0	0	0	0	1	8573	407	15	3		3	KRTAP4-3	17	39324104	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	49866	39324104	41871106	114	14699											
TTC25	83538	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	40113444	40113444	+	RNA	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcatcagagaactgaggaaAaccaactacgtggagaatct	17	7	9	8	1	3	3	2	1	1	2	3	6	3	4	1	2	4	0	1	2	6	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:40113444A>T	ENST00000591658.1	+	0	1359							Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm (GO:0005737)				endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				AACTGAGGAAAACCAACTACG	0.468																																					.													.	TTC25-23	0			.						.						49	49	49					17																	40113444		1884	4113	5997			83538	.			GAGGAAAACCAAC	AK055498	CCDS74063.1	17q21.2	2014-08-12			ENSG00000204815	ENSG00000204815		"Tetratricopeptide (TTC) repeat domain containing"	25280	protein-coding gene	gene with protein product							Standard	XM_006722129		Approved	DKFZP434H0115	uc002hyj.4	Q96NG3	OTTHUMG00000175837		17.37:g.40113444A>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	145	59	.	0	0	0	1	1	Q6NX40|Q6PJ04|Q9H0K5	Missense_Mutation	SNP	ENST00000591658.1	37																																																																																				.		0.468	TTC25-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000449237.1	NM_031421		T	40113444	A	T	40113444	1	4	161	0	1	0	0	0	0	0	0	0	16726	11	1	5		5	TTC25	17	40113444	RNA	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	789340	40113444	41081766	115	14700											
TUBG1	7283	broad.mit.edu;bcgsc.ca	37	chr17	40765685	40765685	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtggtgctggacaacacagcCctgaaccggattgccacaga	11	6	12	12	1	0	2	0	1	0	1	0	4	0	4	3	3	5	1	3	3	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:40765685C>T	ENST00000251413.3	+	7	689	c.627C>T	c.(625-627)gcC>gcT	p.A209A		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	209					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic spindle organization (GO:0000212)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	apical part of cell (GO:0045177)|cell leading edge (GO:0031252)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)|polar microtubule (GO:0005827)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A209A(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Vinblastine(DB00570)	ACAACACAGCCCTGAACCGGA	0.562																																					p.A209A	Colon(20;114 698 11420 22864)												.	TUBG1-91	1	Substitution - coding silent(1)	large_intestine(1)	c.C627T						.						176	166	169					17																	40765685		2203	4300	6503	SO:0001819	synonymous_variant	7283	exon7			CACAGCCCTGAAC	BC000619	CCDS11433.1	17q21.31	2010-03-15	2000-01-20		ENSG00000131462	ENSG00000131462		"Tubulins"	12417	protein-coding gene	gene with protein product		191135	"tubulin, gamma polypeptide"	TUBG		1904010	Standard	NM_001070		Approved	TUBGCP1	uc002ian.3	P23258		ENST00000251413.3:c.627C>T	17.37:g.40765685C>T		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	200	8	NM_001070	0	0	33	33	0	Q53X79|Q9BW59	Silent	SNP	ENST00000251413.3	37	CCDS11433.1																																																																																			.		0.562	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070		T	40765685	C	T	40765685	2	4	161	1	0	0	0	0	0	0	0	1	16797	610	22	2		2	TUBG1	17	40765685	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	652241	40765685	40429525	116	14701											
SOST	50964	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	41835944	41835944	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgttctccgcccggttcaTggtcttgttgttctccagct	2	16	9	14	3	4	0	1	0	3	0	7	0	5	0	4	2	1	5	4	2	0	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:41835944T>C	ENST00000301691.2	-	1	212	c.166A>G	c.(166-168)Atg>Gtg	p.M56V		NM_025237.2	NP_079513.1	Q9BQB4	SOST_HUMAN	sclerostin	56					cellular response to parathyroid hormone stimulus (GO:0071374)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|response to mechanical stimulus (GO:0009612)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(3)|prostate(1)	6		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)		GCCCGGTTCATGGTCTTGTTG	0.597																																					p.M56V		.											.	SOST-90	0			c.A166G						.						57	54	55					17																	41835944		2203	4300	6503	SO:0001583	missense	50964	exon1			GGTTCATGGTCTT	AF326736	CCDS11468.1	17q12-q21	2014-06-28	2010-04-28			ENSG00000167941			13771	protein-coding gene	gene with protein product		605740	"sclerosteosis"			11179006, 11181578	Standard	NM_025237		Approved	VBCH	uc002iec.1	Q9BQB4		ENST00000301691.2:c.166A>G	17.37:g.41835944T>C	ENSP00000301691:p.Met56Val	Somatic	22	0		WXS	Illumina HiSeq	Phase_I	87	26	NM_025237	0	0	0	0	0	Q495N9	Missense_Mutation	SNP	ENST00000301691.2	37	CCDS11468.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.155167	0.57259	.	.	ENSG00000167941	ENST00000301691	T	0.76578	-1.03	4.26	3.15	0.36227	.	0.404445	0.25642	N	0.029277	T	0.67702	0.2921	L	0.55481	1.735	0.35701	D	0.815622	B	0.33171	0.4	B	0.24394	0.053	T	0.69756	-0.5059	10	0.48119	T	0.1	-0.6649	8.7222	0.34447	0.1693:0.0:0.0:0.8307	.	56	Q9BQB4	SOST_HUMAN	V	56	ENSP00000301691:M56V	ENSP00000301691:M56V	M	-	1	0	SOST	39191470	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.993000	0.49425	0.648000	0.30732	0.454000	0.30748	ATG	.		0.597	SOST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453502.1	NM_025237		C	41835944	T	C	41835944	3	2	161	1	0	0	0	0	1	0	0	0	14970	1464	51	3	483	3	SOST	17	41835944	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	1070259	41835944	39359266	117	14702											
HDAC5	10014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr17	42171119	42171119	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagcccaccagagccccccGtagctccacagggctggggc	8	3	13	17	1	0	2	0	0	0	2	1	2	1	2	6	3	3	3	6	3	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:42171119G>A	ENST00000393622.2	-	4	509	c.178C>T	c.(178-180)Cgg>Tgg	p.R60W	HDAC5_ENST00000225983.6_Missense_Mutation_p.R61W|HDAC5_ENST00000586802.1_Missense_Mutation_p.R60W|HDAC5_ENST00000336057.5_Missense_Mutation_p.R60W	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	60					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		AGAGCCCCCCGTAGCTCCACA	0.667																																					p.R61W		.											.	HDAC5-227	0			c.C181T						.						13	15	15					17																	42171119		2197	4295	6492	SO:0001583	missense	10014	exon4			CCCCCCGTAGCTC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.178C>T	17.37:g.42171119G>A	ENSP00000377244:p.Arg60Trp	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	156	73	NM_001015053	0	0	0	0	0	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	37	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.604577	0.66445	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.50001	0.78;0.78;0.76	4.14	4.14	0.48551	.	0.240511	0.26859	N	0.022121	T	0.56891	0.2016	L	0.32530	0.975	0.42561	D	0.993142	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.69654	0.965;0.924;0.965;0.924	T	0.63189	-0.6693	10	0.87932	D	0	-23.2017	15.156	0.72743	0.0:0.0:1.0:0.0	.	60;60;61;60	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	W	61;60;60	ENSP00000225983:R61W;ENSP00000377244:R60W;ENSP00000337290:R60W	ENSP00000225983:R61W	R	-	1	2	HDAC5	39526645	0.996000	0.38824	0.992000	0.48379	0.875000	0.50365	3.362000	0.52314	1.858000	0.53909	0.462000	0.41574	CGG	.		0.667	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		A	42171119	G	A	42171119	3	1	161	1	0	0	0	0	1	0	0	0	7031	1144	40	1	3286	1	HDAC5	17	42171119	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	335175	42171119	39024091	118	14703											
PHB	5245	hgsc.bcm.edu;bcgsc.ca	37	chr17	47489082	47489082	+	Frame_Shift_Del	DEL	G	G	-																															cacattacgtggtcgagaacGgcagtcaaagataattggtt																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:47489082delG	ENST00000300408.3	-	3	280	c.208delC	c.(208-210)cgtfs	p.R70fs	PHB_ENST00000511832.1_Frame_Shift_Del_p.R70fs|PHB_ENST00000508009.1_Intron|RP11-81K2.1_ENST00000576461.1_Intron	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	70					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			GGTCGAGAACGGCAGTCAAAG	0.488																																					p.R70fs		.											.	PHB-90	0			c.208delC						.						96	69	78					17																	47489082		2203	4300	6503	SO:0001589	frameshift_variant	5245	exon3			.		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.208delC	17.37:g.47489082delG	ENSP00000300408:p.Arg70fs	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	245	74	NM_002634	0	0	0	0	0	B4DY47|Q4VBQ0	Frame_Shift_Del	DEL	ENST00000300408.3	37	CCDS11548.1																																																																																			.		0.488	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634		-	47489082	G	-	47489082	7	5	161	1	0	1	0	1	0	0	0	0	11840	1116	39	0	630	0	PHB	17	47489082	Frame_Shift_Del	DEL	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	5317963	47489082	33706128	119	14704											
NPB	256933	hgsc.bcm.edu	37	chr17	79860378	79860378	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgcctccccggagctgcaActgcaccccaggctgcggag	6	4	14	17	3	0	0	0	0	0	0	1	2	1	2	5	4	5	4	5	4	1	0	rs182909729	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:79860378A>G	ENST00000333383.7	+	1	394	c.225A>G	c.(223-225)caA>caG	p.Q75Q	NPB_ENST00000573081.1_Silent_p.Q75Q|PCYT2_ENST00000538936.2_3'UTR	NM_148896.3	NP_683694.1	Q8NG41	NPB_HUMAN	neuropeptide B	75					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)						all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CGGAGCTGCAACTGCACCCCA	0.776													A|||	48	0.00958466	0.0363	0	5008	,	,		8657	0		0	False		,,,				2504	0				p.Q75Q		.											.	.	0			c.A225G						.	A		56,2216		0,56,1080	1	2	2		225	-0.5	0	17		2	0,5066		0,0,2533	no	coding-synonymous	NPB	NM_148896.3		0,56,3613	GG,GA,AA		0.0,2.4648,0.7632		75/126	79860378	56,7282	1136	2533	3669	SO:0001819	synonymous_variant	256933	exon1			GCTGCAACTGCAC		CCDS11790.1	17q25.3	2013-02-26			ENSG00000183979	ENSG00000183979		"Endogenous ligands"	30099	protein-coding gene	gene with protein product	"prepro-NPB"	607996				12118011, 12401809	Standard	NM_148896		Approved	PPL7, PPNPB	uc002kcd.3	Q8NG41	OTTHUMG00000177983	ENST00000333383.7:c.225A>G	17.37:g.79860378A>G		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	14	6	NM_148896	0	0	1	3	2	A0AUX9|A6NJD6|B9EJC3	Silent	SNP	ENST00000333383.7	37	CCDS11790.1																																																																																			A|0.994;G|0.006		0.776	NPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440109.2	NM_148896		G	79860378	A	G	79860378	2	3	161	1	0	0	0	0	0	0	0	1	10593	40	2	3		3	NPB	17	79860378	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	32371296	79860378	1334832	120	14705											
UTS2R	2837	broad.mit.edu	37	chr17	80333066	80333066	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaccaccaggccccgctggCgccgcggacggcgcgcatcg	5	3	15	18	8	0	0	0	0	0	0	1	1	0	1	5	4	1	3	5	4	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:80333066C>A	ENST00000313135.2	+	1	914	c.866C>A	c.(865-867)gCg>gAg	p.A289E		NM_018949.1	NP_061822.1	Q9UKP6	UR2R_HUMAN	urotensin 2 receptor	289					blood circulation (GO:0008015)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell growth (GO:0030307)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of vasoconstriction (GO:0045907)|regulation of vasodilation (GO:0042312)|response to drug (GO:0042493)|signal transduction (GO:0007165)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|urotensin II receptor activity (GO:0001604)			breast(1)|endometrium(4)|kidney(1)|lung(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			GCCCCGCTGGCGCCGCGGACG	0.672																																					p.A289E													.	UTS2R-153	0			c.C866A						.																																			SO:0001583	missense	2837	exon1			CGCTGGCGCCGCG	AF140631	CCDS11810.1	17q25.3	2013-04-30	2004-07-13	2004-07-13		ENSG00000181408			4468	protein-coding gene	gene with protein product		600896	"G protein-coupled receptor 14"	GPR14		8666380, 10499587	Standard	NM_018949		Approved		uc010wvl.2	Q9UKP6		ENST00000313135.2:c.866C>A	17.37:g.80333066C>A	ENSP00000323516:p.Ala289Glu	Somatic	16	1		WXS	Illumina HiSeq	Phase_I	217	16	NM_018949	0	0	0	0	0	B2RMV8	Missense_Mutation	SNP	ENST00000313135.2	37	CCDS11810.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.313287	0.40996	.	.	ENSG00000181408	ENST00000313135	T	0.72051	-0.62	4.95	1.39	0.22231	GPCR, rhodopsin-like superfamily (1);	0.338048	0.28257	U	0.016009	T	0.61375	0.2342	N	0.17723	0.515	0.09310	N	1	P	0.42973	0.796	P	0.50791	0.65	T	0.55711	-0.8098	10	0.07644	T	0.81	.	14.9821	0.71319	0.0:0.5448:0.4552:0.0	.	289	Q9UKP6	UR2R_HUMAN	E	289	ENSP00000323516:A289E	ENSP00000323516:A289E	A	+	2	0	UTS2R	77926355	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	0.380000	0.20602	0.518000	0.28383	0.637000	0.83480	GCG	.		0.672	UTS2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443506.1	NM_018949		A	80333066	C	A	80333066	3	1	161	1	0	0	0	0	1	0	0	0	17139	768	27	4	868	4	UTS2R	17	80333066	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	472688	80333066	862144	121	14706											
KCTD1	284252	hgsc.bcm.edu	37	chr18	24128223	24128225	+	Intron	DEL	TCC	TCC	-																															ccagccccatctcctcctctTcctcctcctcctcgtcctcc																								rs143299522	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr18:24128223_24128225delTCC	ENST00000408011.3	-	1	545				KCTD1_ENST00000580059.1_5'Flank|KCTD1_ENST00000579973.1_Intron|KCTD1_ENST00000317932.7_Intron|KCTD1_ENST00000417602.1_In_Frame_Del_p.92_93EE>E	NM_001136205.2	NP_001129677.1	Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1						negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			ctcctcctcttcctcctcctcct	0.655														134	0.0267572	0.0673	0.0086	5008	,	,		6875	0		0.008	False		,,,				2504	0.0317				p.92_93del		.											.	KCTD1-91	0			c.276_278del						.		,,	187,3139		43,101,1519					,,	-0.1	1		dbSNP_134	4	78,6614		13,52,3281	no	intron,coding,intron	KCTD1	NM_198991.2,NM_001142730.1,NM_001136205.1	,,	56,153,4800	A1A1,A1R,RR		1.1656,5.6224,2.6452	,,	,,		265,9753				SO:0001627	intron_variant	284252	exon1			.	AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"potassium channel tetramerisation domain containing 1"	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000408011.3:c.14+629GGA>-	18.37:g.24128232_24128234delTCC		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	11	10	NM_001142730	0	0	0	0	0	A8K1F5	In_Frame_Del	DEL	ENST00000408011.3	37	CCDS11888.1																																																																																			TCC|0.976;-|0.024		0.655	KCTD1-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446265.1	XM_209091		-	24128225	TCC	-	24128223	6	5	161	0	1	1	0	1	0	0	0	0	8117	1783	62	0		0	KCTD1	18	24128223	Intron	DEL	TCC	TCGA-Q2-A5QZ-01A-11D-A28G-10		24128223	53949025	122	14707											
WDR18	57418	hgsc.bcm.edu	37	chr19	991962	991962	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccgcgccccccaggcccagtCaccaatgccgccatcctgct	6	5	8	22	3	1	0	1	0	0	0	2	0	2	0	9	1	2	1	9	1	1	0	rs200830437	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:991962C>T	ENST00000251289.5	+	8	962	c.939C>T	c.(937-939)gtC>gtT	p.V313V	WDR18_ENST00000587001.2_Silent_p.V313V	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	313					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCCCAGTCACCAATGCCG	0.716													c|||	2	0.000399361	0.0015	0	5008	,	,		7424	0		0	False		,,,				2504	0				p.V313V		.											.	WDR18-91	0			c.C939T						.	C		6,4168		0,6,2081	7	9	8		939	0.7	1	19		8	0,8224		0,0,4112	no	coding-synonymous	WDR18	NM_024100.3		0,6,6193	TT,TC,CC		0.0,0.1437,0.0484		313/433	991962	6,12392	2087	4112	6199	SO:0001819	synonymous_variant	57418	exon8			CCCAGTCACCAAT		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.939C>T	19.37:g.991962C>T		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	42	9	NM_024100	0	0	0	0	0	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			C|0.999;T|0.001		0.716	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			T	991962	C	T	991962	2	4	161	1	0	0	0	0	0	0	0	1	17311	813	29	2		2	WDR18	19	991962	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		991962	58137021	123	14708											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2210451	2210451	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcgagagcaagagcaacgCggccacgcccactaagggcc	11	1	14	15	5	0	2	0	0	0	2	0	3	0	2	3	2	3	2	3	2	3	1	rs138206172	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:2210451C>G	ENST00000398665.3	+	13	1094	c.1058C>G	c.(1057-1059)gCg>gGg	p.A353G	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	353					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGCAACGCGGCCACGCCC	0.726													C|||	3	0.000599042	0	0.0014	5008	,	,		14189	0		0.002	False		,,,				2504	0				p.A353G		.											.	DOT1L-132	0			c.C1058G						.						7	10	9					19																	2210451		1904	4036	5940	SO:0001583	missense	84444	exon13			GCAACGCGGCCAC	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"Chromatin-modifying enzymes / K-methyltransferases"	24948	protein-coding gene	gene with protein product	"histone methyltransferase DOT1L"	607375	"DOT1-like, histone H3 methyltransferase (S. cerevisiae)"			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.1058C>G	19.37:g.2210451C>G	ENSP00000381657:p.Ala353Gly	Somatic	3	1		WXS	Illumina HiSeq	Phase_I	52	11	NM_032482	0	0	0	0	0	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	C|C	14.57|14.57	2.574930|2.574930	0.45902|0.45902	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000398665;ENST00000221482|ENST00000440640	T|.	0.23147|.	1.92|.	4.64|4.64	4.64|4.64	0.57946|0.57946	.|.	0.153320|.	0.56097|.	D|.	0.000025|.	T|T	0.43523|0.43523	0.1251|0.1251	N|N	0.22421|0.22421	0.69|0.69	0.31975|0.31975	N|N	0.606602|0.606602	P|.	0.36683|.	0.565|.	B|.	0.40864|.	0.342|.	T|T	0.49153|0.49153	-0.8969|-0.8969	10|5	0.87932|.	D|.	0|.	-12.8566|-12.8566	16.8583|16.8583	0.86011|0.86011	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	353|.	Q8TEK3-2|.	.|.	G|G	353|140	ENSP00000381657:A353G|.	ENSP00000221482:A353G|.	A|R	+|+	2|1	0|2	DOT1L|DOT1L	2161451|2161451	0.996000|0.996000	0.38824|0.38824	0.523000|0.523000	0.27875|0.27875	0.003000|0.003000	0.03518|0.03518	3.247000|3.247000	0.51422|0.51422	2.280000|2.280000	0.76307|0.76307	0.561000|0.561000	0.74099|0.74099	GCG|CGG	C|0.999;G|0.001		0.726	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		G	2210451	C	G	2210451	3	3	161	1	0	0	0	0	1	0	0	0	4720	768	27	4	1108	4	DOT1L	19	2210451	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	1218489	2210451	56918532	124	14709											
OR7E24	26648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr19	9362181	9362181	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgcactaccgaatcatcatGaacccacgcctctgtggctt	9	10	7	15	2	3	1	2	1	1	0	3	2	3	1	3	1	3	2	3	1	3	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:9362181G>C	ENST00000456448.1	+	1	576	c.462G>C	c.(460-462)atG>atC	p.M154I		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						GAATCATCATGAACCCACGCC	0.443																																					p.M154I		.											.	OR7E24-47	0			c.G462C						.						130	144	139					19																	9362181		2193	4296	6489	SO:0001583	missense	26648	exon1			CATCATGAACCCA	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.462G>C	19.37:g.9362181G>C	ENSP00000387523:p.Met154Ile	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	124	36	NM_001079935	0	0	0	0	0	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	37	CCDS45955.1	.	.	.	.	.	.	.	.	.	.	g	10.46	1.356506	0.24598	.	.	ENSG00000237521	ENST00000456448	T	0.00551	6.65	2.39	2.39	0.29439	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00906	0.0030	M	0.80847	2.515	0.28275	N	0.924234	B	0.19706	0.038	B	0.16289	0.015	T	0.12293	-1.0553	9	0.66056	D	0.02	.	11.6917	0.51519	0.0:0.0:1.0:0.0	.	154	Q6IFN5	O7E24_HUMAN	I	154	ENSP00000387523:M154I	ENSP00000387523:M154I	M	+	3	0	OR7E24	9223181	0.999000	0.42202	0.492000	0.27490	0.028000	0.11728	2.571000	0.45990	1.353000	0.45828	0.436000	0.28706	ATG	.		0.443	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			C	9362181	G	C	9362181	3	2	161	1	0	0	0	0	1	0	0	0	11247	1290	45	4	464	4	OR7E24	19	9362181	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	7151730	9362181	49766802	125	14710											
MAN2B1	4125	broad.mit.edu;bcgsc.ca	37	chr19	12760979	12760979	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgctgtcctgggtacaggcGaaccacctgggaacaccaag	10	5	12	14	2	0	0	0	0	0	0	1	2	1	1	5	3	3	2	5	3	4	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:12760979G>A	ENST00000456935.2	-	17	2144	c.2104C>T	c.(2104-2106)Cgc>Tgc	p.R702C	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.R701C	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	702					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGGTACAGGCGAACCACCTGG	0.627																																					p.R702C													.	MAN2B1-94	0			c.C2104T						.						132	111	118					19																	12760979		2203	4300	6503	SO:0001583	missense	4125	exon17			ACAGGCGAACCAC		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2104C>T	19.37:g.12760979G>A	ENSP00000395473:p.Arg702Cys	Somatic	43	0		WXS	Illumina HiSeq	Phase_I	166	8	NM_000528	0	0	75	78	3	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667589	0.88348	.	.	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.86097	-2.07;-2.07	4.91	4.91	0.64330	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.45126	D	0.000392	D	0.94565	0.8249	H	0.95328	3.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95872	0.8892	10	0.87932	D	0	-28.1246	15.638	0.76970	0.0:0.0:1.0:0.0	.	701;702	G5E928;O00754	.;MA2B1_HUMAN	C	702;641;701	ENSP00000395473:R702C;ENSP00000221363:R701C	ENSP00000221363:R701C	R	-	1	0	MAN2B1	12621979	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	7.042000	0.76565	2.564000	0.86499	0.555000	0.69702	CGC	.		0.627	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			A	12760979	G	A	12760979	3	1	161	1	0	0	0	0	1	0	0	0	9241	1058	37	1	963	1	MAN2B1	19	12760979	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	3398798	12760979	46368004	126	14711											
ZNF571	51276	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	chr19	38056037	38056037	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgttcactaagttgtttGccacaaataaaggcctttcc	11	14	7	9	0	1	1	1	1	0	0	2	1	2	1	3	1	1	3	3	1	4	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:38056037G>A	ENST00000328550.2	-	4	1392	c.1293C>T	c.(1291-1293)ggC>ggT	p.G431G	ZNF571-AS1_ENST00000589750.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571_ENST00000451802.2_Silent_p.G431G|ZNF571_ENST00000593133.1_Silent_p.G431G|ZNF571-AS1_ENST00000591430.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000589802.1_RNA|ZNF571_ENST00000358744.3_Silent_p.G431G			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	431					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)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAAGTTGTTTGCCACAAATAA	0.363																																					p.G431G		.											.	ZNF571-90	0			c.C1293T						.						48	52	51					19																	38056037		2203	4299	6502	SO:0001819	synonymous_variant	51276	exon4			TTGTTTGCCACAA	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"Zinc fingers, C2H2-type", "-"	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.1293C>T	19.37:g.38056037G>A		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	34	20	NM_016536	0	0	0	0	0	Q2HIY0|Q3ZCU3|Q9NZX7	Silent	SNP	ENST00000328550.2	37	CCDS12505.1																																																																																			.		0.363	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536		A	38056037	G	A	38056037	2	1	161	1	0	0	0	0	0	0	0	1	18035	1306	46	2		2	ZNF571	19	38056037	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	25295058	38056037	21072946	127	14712											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39226803	39226803	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtgaagtcagcctcgtcGccggcgtgggcggtgctcgg	5	7	18	11	6	1	2	1	1	0	1	4	2	1	2	2	4	2	1	2	4	1	0	rs201698633	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:39226803G>A	ENST00000328867.4	-	12	1838	c.1530C>T	c.(1528-1530)ggC>ggT	p.G510G	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.G361G	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	510	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			CAGCCTCGTCGCCGGCGTGGG	0.731													G|||	57	0.0113818	0.0431	0	5008	,	,		4562	0		0	False		,,,				2504	0				p.G510G		.											.	CAPN12-91	0			c.C1530T						.	G		90,3020		0,90,1465	5	7	6		1530	0	0	19		6	3,5705		0,3,2851	no	coding-synonymous	CAPN12	NM_144691.3		0,93,4316	AA,AG,GG		0.0526,2.8939,1.0547		510/720	39226803	93,8725	1555	2854	4409	SO:0001819	synonymous_variant	147968	exon12			CTCGTCGCCGGCG	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"EF-hand domain containing"	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1530C>T	19.37:g.39226803G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	37	5	NM_144691	0	0	0	0	0		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.992;A|0.008		0.731	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			A	39226803	G	A	39226803	2	1	161	1	0	0	0	0	0	0	0	1	2631	1074	38	1		1	CAPN12	19	39226803	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	1170766	39226803	19902180	128	14713											
B9D2	80776	hgsc.bcm.edu;broad.mit.edu	37	chr19	41869392	41869392	+	Frame_Shift_Del	DEL	T	T	-																															tccgagaaaccgctggccccTatgatctgcccgatcacgtg																								rs2241714	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:41869392delT	ENST00000243578.3	-	2	252	c.33delA	c.(31-33)atafs	p.I11fs	CTC-435M10.3_ENST00000604424.1_Intron|TMEM91_ENST00000413014.2_5'Flank|TMEM91_ENST00000539627.1_Intron|TMEM91_ENST00000604123.1_Intron|B9D2_ENST00000601597.1_5'UTR	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2	11	B9. {ECO:0000255|PROSITE- ProRule:PRU00713}.		I -> M (in dbSNP:rs2241714). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						CGCTGGCCCCTATGATCTGCC	0.537																																					p.I11fs		.											.	B9D2-69	0			c.33delA						.						69	58	62					19																	41869392		2203	4300	6503	SO:0001589	frameshift_variant	80776	exon2			.	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9		ENST00000243578.3:c.33delA	19.37:g.41869392delT	ENSP00000243578:p.Ile11fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	124	67	NM_030578	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000243578.3	37	CCDS12579.1																																																																																			.		0.537	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578		-	41869392	T	-	41869392	7	5	161	1	0	1	0	1	0	0	0	0	1279	1512	53	0	506	0	B9D2	19	41869392	Frame_Shift_Del	DEL	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	2642589	41869392	17259591	129	14714											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48183862	48183862	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcctactgcctggcgccccgGcggtccagctcccgcagcag	4	6	12	19	4	0	0	0	0	0	0	3	0	3	0	6	3	4	3	6	3	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:48183862G>C	ENST00000396720.3	+	6	1629	c.1435G>C	c.(1435-1437)Gcg>Ccg	p.A479P	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	479										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		TGGCGCCCCGGCGGTCCAGCT	0.692																																					p.A479P		.											.	GLTSCR1-48	0			c.G1435C						.						16	21	19					19																	48183862		2061	4175	6236	SO:0001583	missense	29998	exon6			GCCCCGGCGGTCC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.1435G>C	19.37:g.48183862G>C	ENSP00000379946:p.Ala479Pro	Somatic	1	0		WXS	Illumina HiSeq	Phase_I	44	12	NM_015711	0	0	0	0	0	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	37	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	G	2.717	-0.267452	0.05754	.	.	ENSG00000063169	ENST00000396720	T	0.38722	1.12	4.7	-0.598	0.11649	.	.	.	.	.	T	0.40862	0.1134	L	0.38531	1.155	0.27198	N	0.960237	D	0.53885	0.963	P	0.56042	0.79	T	0.32295	-0.9912	9	0.31617	T	0.26	.	6.572	0.22543	0.2611:0.0:0.6073:0.1316	.	479	Q9NZM4	GSCR1_HUMAN	P	479	ENSP00000379946:A479P	ENSP00000379946:A479P	A	+	1	0	GLTSCR1	52875674	0.160000	0.22878	0.002000	0.10522	0.054000	0.15201	0.417000	0.21214	0.077000	0.16863	0.491000	0.48974	GCG	.		0.692	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		C	48183862	G	C	48183862	3	2	161	1	0	0	0	0	1	0	0	0	6494	1203	42	4	1449	4	GLTSCR1	19	48183862	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	6314470	48183862	10945121	130	14715											
PRR12	57479	hgsc.bcm.edu	37	chr19	50100554	50100554	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccccggcccccctgcttatGatccctatgggccctactgt	4	10	8	19	1	0	1	0	1	0	0	1	1	1	1	7	2	2	1	7	2	3	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:50100554G>A	ENST00000418929.2	+	4	2974	c.2962G>A	c.(2962-2964)Gat>Aat	p.D988N		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							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)		CCCTGCTTATGATCCCTATGG	0.736																																					p.D988N		.											.	PRR12-70	0			c.G2962A						.						3	4	4					19																	50100554		1585	3699	5284	SO:0001583	missense	57479	exon4			GCTTATGATCCCT	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.2962G>A	19.37:g.50100554G>A	ENSP00000394510:p.Asp988Asn	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	36	26	NM_020719	0	0	0	0	0	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.231566	0.39399	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	T	0.24350	1.86	4.79	4.79	0.61399	.	0.000000	0.45126	D	0.000382	T	0.37571	0.1008	L	0.38175	1.15	0.45690	D	0.998604	D	0.89917	1.0	D	0.87578	0.998	T	0.03473	-1.1033	10	0.13108	T	0.6	-21.245	14.8476	0.70272	0.0:0.0:1.0:0.0	.	988	Q9ULL5-3	.	N	988;168;168	ENSP00000394510:D988N	ENSP00000246798:D168N	D	+	1	0	PRR12	54792366	0.986000	0.35501	0.979000	0.43373	0.599000	0.36880	2.157000	0.42320	2.476000	0.83614	0.491000	0.48974	GAT	.		0.736	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		A	50100554	G	A	50100554	3	1	161	1	0	0	0	0	1	0	0	0	12613	1290	45	2	2976	2	PRR12	19	50100554	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	1916692	50100554	9028429	131	14716											
IGLON5	402665	hgsc.bcm.edu	37	chr19	51831097	51831097	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaactatacgtgtcgcgcCgccaaccgactgggagcgtc	8	6	13	14	6	0	0	0	0	0	0	2	2	0	1	3	2	4	1	3	2	4	2	rs200107403	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:51831097C>A	ENST00000270642.8	+	7	879	c.879C>A	c.(877-879)gcC>gcA	p.A293A		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	293	Ig-like C2-type 3.					extracellular region (GO:0005576)				large_intestine(5)|lung(6)|prostate(1)	12						CGTGTCGCGCCGCCAACCGAC	0.716													C|||	76	0.0151757	0.0166	0.0072	5008	,	,		8555	0.0208		0.005	False		,,,				2504	0.0235				p.A293A		.											.	.	0			c.C879A						.	C		51,3629		0,51,1789	9	10	10		879	-10.1	0.9	19		10	25,7827		1,23,3902	no	coding-synonymous	IGLON5	NM_001101372.1		1,74,5691	AA,AC,CC		0.3184,1.3859,0.659		293/337	51831097	76,11456	1840	3926	5766	SO:0001819	synonymous_variant	402665	exon7			TCGCGCCGCCAAC		CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.879C>A	19.37:g.51831097C>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	60	21	NM_001101372	0	0	0	0	0		Silent	SNP	ENST00000270642.8	37	CCDS46158.1																																																																																			C|0.991;A|0.009		0.716	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372		A	51831097	C	A	51831097	2	1	161	1	0	0	0	0	0	0	0	1	7616	639	23	4		4	IGLON5	19	51831097	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	1730543	51831097	7297886	132	14717											
LRRN4	164312	hgsc.bcm.edu	37	chr20	6033147	6033147	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggtcagcacctgcagcTgctccaggtggccgagctcg	6	6	15	14	2	1	0	1	0	0	0	3	1	2	0	3	3	5	6	3	3	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr20:6033147T>C	ENST00000378858.4	-	2	523	c.299A>G	c.(298-300)cAg>cGg	p.Q100R		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	100					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						CACCTGCAGCTGCTCCAGGTG	0.731																																					p.Q100R		.											.	LRRN4-93	0			c.A299G						.						6	8	7					20																	6033147		2113	4185	6298	SO:0001583	missense	164312	exon2			TGCAGCTGCTCCA	AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"Fibronectin type III domain containing"	16208	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 75"	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.299A>G	20.37:g.6033147T>C	ENSP00000368135:p.Gln100Arg	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	31	13	NM_152611	0	0	0	0	0	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	37	CCDS13097.1	.	.	.	.	.	.	.	.	.	.	T	1.702	-0.501239	0.04261	.	.	ENSG00000125872	ENST00000378858	T	0.04406	3.63	5.37	0.364	0.16124	.	0.918843	0.09178	N	0.837822	T	0.02970	0.0088	N	0.16233	0.39	0.18873	N	0.999982	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.48399	-0.9039	10	0.25751	T	0.34	-6.0721	4.5538	0.12126	0.2133:0.256:0.0:0.5307	.	100;100	Q6ZMD1;Q8WUT4	.;LRRN4_HUMAN	R	100	ENSP00000368135:Q100R	ENSP00000368135:Q100R	Q	-	2	0	LRRN4	5981147	0.002000	0.14202	0.402000	0.26371	0.002000	0.02628	-0.227000	0.09126	-0.136000	0.11475	-0.516000	0.04426	CAG	.		0.731	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		C	6033147	T	C	6033147	3	2	161	1	0	0	0	0	1	0	0	0	9062	1580	55	3	1939	3	LRRN4	20	6033147	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		6033147	56992373	133	14718											
ARFGAP1	55738	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chr20	61918934	61918934	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcccctcggagggccacagTtatcagaacagcggtctgga	10	6	13	12	2	2	1	1	0	1	1	3	3	2	3	3	4	3	1	3	4	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr20:61918934T>G	ENST00000370283.4	+	13	1070	c.930T>G	c.(928-930)agT>agG	p.S310R	ARFGAP1_ENST00000370275.4_Missense_Mutation_p.V390G|ARFGAP1_ENST00000518794.2_3'UTR|MIR4326_ENST00000582203.1_RNA|ARFGAP1_ENST00000353546.3_Missense_Mutation_p.S318R|ARFGAP1_ENST00000547204.1_Missense_Mutation_p.S244R|ARFGAP1_ENST00000519604.1_Missense_Mutation_p.S265R|ARFGAP1_ENST00000519273.2_Missense_Mutation_p.S197R	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	310					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					AGGGCCACAGTTATCAGAACA	0.542																																					p.S318R		.											.	ARFGAP1-91	0			c.T954G						.						44	45	44					20																	61918934		2201	4299	6500	SO:0001583	missense	55738	exon14			CCACAGTTATCAG	AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"ADP-ribosylation factor GTPase activating proteins"	15852	protein-coding gene	gene with protein product		608377	"ADP-ribosylation factor 1 GTPase activating protein"	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.930T>G	20.37:g.61918934T>G	ENSP00000359306:p.Ser310Arg	Somatic	35	0		WXS	Illumina HiSeq	Phase_I	76	26	NM_175609	0	0	0	10	10	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Missense_Mutation	SNP	ENST00000370283.4	37	CCDS13515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.23|13.23	2.173905|2.173905	0.38413|0.38413	.|.	.|.	ENSG00000101199|ENSG00000101199	ENST00000370283;ENST00000547204;ENST00000549047;ENST00000523460;ENST00000519604;ENST00000519273;ENST00000353546|ENST00000370275	T;T;T;T;T;T|T	0.50001|0.38560	1.39;0.77;0.85;0.78;0.76;1.41|1.13	4.81|4.81	-0.361|-0.361	0.12564|0.12564	.|.	0.782541|.	0.12772|.	N|.	0.440467|.	T|T	0.36663|0.36663	0.0975|0.0975	L|L	0.60455|0.60455	1.87|1.87	0.49798|0.49798	D|D	0.999824|0.999824	D;D;P;P|B	0.60160|0.26318	0.958;0.987;0.859;0.913|0.146	P;P;P;P|B	0.57960|0.24974	0.663;0.83;0.556;0.742|0.057	T|T	0.33548|0.33548	-0.9864|-0.9864	10|9	0.32370|0.87932	T|D	0.25|0	-9.8078|-9.8078	9.7438|9.7438	0.40435|0.40435	0.0:0.6144:0.0:0.3856|0.0:0.6144:0.0:0.3856	.|.	197;265;310;318|390	B7Z8H8;E7EV62;Q8N6T3;Q8N6T3-2|B7ZBI2	.;.;ARFG1_HUMAN;.|.	R|G	310;244;236;66;265;197;318|390	ENSP00000359306:S310R;ENSP00000449800:S244R;ENSP00000447037:S236R;ENSP00000430500:S265R;ENSP00000443716:S197R;ENSP00000314615:S318R|ENSP00000359298:V390G	ENSP00000314615:S318R|ENSP00000359298:V390G	S|V	+|+	3|2	2|0	ARFGAP1|ARFGAP1	61389379|61389379	1.000000|1.000000	0.71417|0.71417	0.316000|0.316000	0.25252|0.25252	0.180000|0.180000	0.23129|0.23129	1.634000|1.634000	0.37123|0.37123	0.106000|0.106000	0.17784|0.17784	0.379000|0.379000	0.24179|0.24179	AGT|GTT	.		0.542	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209		G	61918934	T	G	61918934	3	3	161	1	0	0	0	0	1	0	0	0	849	1722	60	5	1010	5	ARFGAP1	20	61918934	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	55885787	61918934	1106586	134	14719											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62197379	62197379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgccgctccacgcactcacgGatgaagctctcccagagctt	8	8	9	16	3	2	2	1	1	1	1	4	3	3	3	3	1	3	4	3	1	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr20:62197379G>A	ENST00000467148.1	-	8	2865	c.2796C>T	c.(2794-2796)atC>atT	p.I932I	HELZ2_ENST00000427522.2_Silent_p.I363I	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	932	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CGCACTCACGGATGAAGCTCT	0.701																																					p.I932I		.											.	.	0			c.C2796T						.						16	16	16					20																	62197379		2174	4285	6459	SO:0001819	synonymous_variant	85441	exon9			CTCACGGATGAAG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"peroxisomal proliferator activated receptor A interacting complex 285", "PPARG-DBD-interacting protein 1"	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.2796C>T	20.37:g.62197379G>A		Somatic	5	0		WXS	Illumina HiSeq	Phase_I	78	32	NM_001037335	0	0	0	0	0	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			.		0.701	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62197379	G	A	62197379	2	1	161	1	0	0	0	0	0	0	0	1	12514	1164	41	2		2	PRIC285	20	62197379	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	278445	62197379	828141	135	14720											
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28338045	28338045	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgggttgctgtgcgccggAgcatgctcgtgggcctccgg	2	9	17	13	5	0	0	0	0	0	0	3	1	1	1	3	4	4	4	3	4	0	1	rs369445782	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:28338045A>T	ENST00000284987.5	-	1	787	c.666T>A	c.(664-666)gcT>gcA	p.A222A		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	222					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						TGTGCGCCGGAGCATGCTCGT	0.716													A|||	4	0.000798722	0.0023	0	5008	,	,		14660	0		0.001	False		,,,				2504	0				p.A222A	Esophageal Squamous(53;683 1080 10100 14424 45938)	.											.	ADAMTS5-229	0			c.T666A						.	A		15,4337		0,15,2161	9	12	11		666	-4.4	0	21		11	2,8476		0,2,4237	no	coding-synonymous	ADAMTS5	NM_007038.3		0,17,6398	TT,TA,AA		0.0236,0.3447,0.1325		222/931	28338045	17,12813	2176	4239	6415	SO:0001819	synonymous_variant	11096	exon1			CGCCGGAGCATGC	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"ADAM metallopeptidases with thrombospondin type 1 motif"	221	protein-coding gene	gene with protein product	"aggrecanase-2"	605007	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.666T>A	21.37:g.28338045A>T		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	73	33	NM_007038	0	0	0	0	0	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																			.		0.716	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			T	28338045	A	T	28338045	2	4	161	1	0	0	0	0	0	0	0	1	269	291	11	5		5	ADAMTS5	21	28338045	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10		28338045	19791850	136	14721											
OLIG1	116448	broad.mit.edu	37	chr21	34442709	34442717	+	In_Frame_Del	DEL	TCCTCCACT	TCCTCCACT	-																															cctcctccacctcctccaccTcctccacttcctcctcctcc																								rs367752518		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TCCTCCACT	TCCTCCACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:34442709_34442717delTCCTCCACT	ENST00000382348.1	+	1	260_268	c.157_165delTCCTCCACT	c.(157-165)tcctccactdel	p.SST53del	OLIG1_ENST00000333063.5_In_Frame_Del_p.SST37del|AP000282.2_ENST00000454622.1_RNA|AP000282.2_ENST00000420356.1_RNA	NM_138983.2	NP_620450.2	Q8TAK6	OLIG1_HUMAN	oligodendrocyte transcription factor 1	53	Ser-rich.				neuron fate commitment (GO:0048663)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)	1						ctcctccacctcctccacttcctcctcct	0.746																																					p.53_55del													.	OLIG1-446	0			c.157_165del						.			209,2581		57,95,1243						1	0.2			4	188,5876		52,84,2896	no	coding	OLIG1	NM_138983.2		109,179,4139	A1A1,A1R,RR		3.1003,7.491,4.4838				397,8457				SO:0001651	inframe_deletion	116448	exon1			TCCACCTCCTCCA	AP000109	CCDS42920.1, CCDS42920.2	21q22.11	2013-05-21			ENSG00000184221	ENSG00000184221		"Basic helix-loop-helix proteins"	16983	protein-coding gene	gene with protein product	"oligodendrocyte-specific bHLH transcription factor 1", "oligodendrocyte lineage transcription factor 1", "basic domain, helix-loop-helix protein, class B, 6"	606385				11526205	Standard	NM_138983		Approved	BHLHB6, bHLHe21	uc002yqz.3	Q8TAK6	OTTHUMG00000065064	ENST00000382348.1:c.157_165delTCCTCCACT	21.37:g.34442709_34442717delTCCTCCACT	ENSP00000371785:p.Ser53_Thr55del	Somatic	4	0		WXS	Illumina HiSeq	Phase_I	16	7	NM_138983	0	0	0	0	0	Q7RTS0	In_Frame_Del	DEL	ENST00000382348.1	37	CCDS42920.2																																																																																			.		0.746	OLIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139730.1	NM_138983		-	34442717	TCCTCCACT	-	34442709	7	5	161	1	0	1	0	1	0	0	0	0	10886	1551	54	0	159	0	OLIG1	21	34442709	In_Frame_Del	DEL	TCCTCCACT	TCGA-Q2-A5QZ-01A-11D-A28G-10	6104664	34442709	13687186	137	14722											
TTC3	7267	hgsc.bcm.edu;bcgsc.ca	37	chr21	38519809	38519809	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagaaatttgttgaagaatGcaagttccctccagtgccag	13	10	10	8	0	0	3	0	1	0	2	2	4	2	3	3	0	2	3	3	0	4	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:38519809G>A	ENST00000399017.2	+	22	4669	c.1922G>A	c.(1921-1923)tGc>tAc	p.C641Y	TTC3_ENST00000355666.1_Missense_Mutation_p.C641Y|TTC3_ENST00000354749.2_Missense_Mutation_p.C641Y|TTC3_ENST00000540756.1_Missense_Mutation_p.C331Y|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	641					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTTGAAGAATGCAAGTTCCCT	0.323																																					p.C641Y	Ovarian(38;194 1649 35661)	.											.	TTC3-590	0			c.G1922A						.						111	108	109					21																	38519809		2203	4300	6503	SO:0001583	missense	7267	exon22			AAGAATGCAAGTT	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"RING-type (C3HC4) zinc fingers", "Tetratricopeptide (TTC) repeat domain containing"	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1922G>A	21.37:g.38519809G>A	ENSP00000381981:p.Cys641Tyr	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	56	4	NM_001001894	0	0	0	0	0	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.0|20.0	3.930568|3.930568	0.73327|0.73327	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000414818|ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	.|T;T;T;T;T;T;T	.|0.53640	.|2.42;0.66;2.43;2.72;0.61;2.72;2.72	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	.|0.294582	.|0.30020	.|N	.|0.010617	T|T	0.57227|0.57227	0.2039|0.2039	N|N	0.20986|0.20986	0.625|0.625	0.58432|0.58432	D|D	0.999993|0.999993	.|D;D	.|0.76494	.|0.998;0.999	.|D;D	.|0.83275	.|0.994;0.996	T|T	0.63589|0.63589	-0.6603|-0.6603	5|10	.|0.87932	.|D	.|0	-11.1008|-11.1008	17.997|17.997	0.89187|0.89187	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|331;641	.|B4DSZ9;P53804	.|.;TTC3_HUMAN	T|Y	39|641;641;623;641;331;641;641	.|ENSP00000403943:C641Y;ENSP00000408456:C641Y;ENSP00000391891:C623Y;ENSP00000347889:C641Y;ENSP00000442875:C331Y;ENSP00000381981:C641Y;ENSP00000346791:C641Y	.|ENSP00000346791:C641Y	A|C	+|+	1|2	0|0	TTC3|TTC3	37441679|37441679	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.912000|7.912000	0.87465|0.87465	2.409000|2.409000	0.81822|0.81822	0.650000|0.650000	0.86243|0.86243	GCA|TGC	.		0.323	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			A	38519809	G	A	38519809	3	1	161	1	0	0	0	0	1	0	0	0	16730	1319	46	2	2004	2	TTC3	21	38519809	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	4077100	38519809	9610086	138	14723											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43221434	43221434	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctgctgctgctgctccGcctgcacctggggctgggcc	1	10	14	16	1	1	0	0	0	1	0	2	0	2	0	4	3	6	7	4	3	0	0	rs147616045		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:43221434G>A	ENST00000269844.3	-	31	4600	c.4490C>T	c.(4489-4491)gCg>gTg	p.A1497V	PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Missense_Mutation_p.A1168V|PRDM15_ENST00000422911.1_Missense_Mutation_p.A1188V|PRDM15_ENST00000538201.1_Missense_Mutation_p.A1151V|PRDM15_ENST00000447207.2_Missense_Mutation_p.A1131V	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						CTGCTGCTCCGCCTGCACCTG	0.637													g|||	1	0.000199681	8e-04	0	5008	,	,		15122	0		0	False		,,,				2504	0				p.A1497V		.											.	PRDM15-90	0			c.C4490T						.		VAL/ALA,VAL/ALA	5,4369		0,5,2182	33	38	36		3503,4490	3.7	0	21	dbSNP_134	36	2,8498		0,2,4248	yes	missense,missense	PRDM15	NM_001040424.1,NM_022115.3	64,64	0,7,6430	AA,AG,GG		0.0235,0.1143,0.0544	possibly-damaging,possibly-damaging	1168/1179,1497/1508	43221434	7,12867	2187	4250	6437	SO:0001583	missense	63977	exon31			TGCTCCGCCTGCA	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"Zinc fingers, C2H2-type"	13999	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 83"	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4490C>T	21.37:g.43221434G>A	ENSP00000269844:p.Ala1497Val	Somatic	0	0		WXS	Illumina HiSeq	Phase_I	24	10	NM_022115	0	0	0	0	0	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	g	13.53	2.264687	0.40095	0.001143	2.35E-4	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.08546	3.16;3.17;3.17;3.16;3.08	4.56	3.65	0.41850	.	.	.	.	.	T	0.04952	0.0133	N	0.14661	0.345	0.09310	N	1	P;B;B	0.35226	0.491;0.043;0.043	B;B;B	0.22753	0.041;0.012;0.007	T	0.33420	-0.9869	9	0.72032	D	0.01	-4.2914	10.8161	0.46575	0.0:0.0:0.6437:0.3563	.	1497;1188;1168	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	V	1188;1168;1151;1131;1497	ENSP00000408592:A1188V;ENSP00000381556:A1168V;ENSP00000444044:A1151V;ENSP00000390245:A1131V;ENSP00000269844:A1497V	ENSP00000269844:A1497V	A	-	2	0	PRDM15	42094503	0.050000	0.20438	0.003000	0.11579	0.735000	0.41995	2.502000	0.45398	0.847000	0.35167	0.558000	0.71614	GCG	G|1.000;A|0.000		0.637	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43221434	G	A	43221434	3	1	161	1	0	0	0	0	1	0	0	0	12485	1087	38	1	37	1	PRDM15	21	43221434	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	4701625	43221434	4908461	139	14724											
KRTAP10-7	386675	broad.mit.edu	37	chr21	46020576	46020576	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgagctacggcagccgcGtctgccttcctggttcctgt	4	11	11	15	3	1	1	0	1	1	0	3	1	3	1	5	2	4	3	5	2	1	3	rs587669788		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:46020576G>A	ENST00000380102.2	+	1	80	c.55G>A	c.(55-57)Gtc>Atc	p.V19I	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	19						keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						CGGCAGCCGCGTCTGCCTTCC	0.642																																					p.V19I													.	.	0			c.G55A						.						36	46	42					21																	46020576		2057	4186	6243	SO:0001583	missense	386675	exon1			AGCCGCGTCTGCC	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"Keratin associated proteins"	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.55G>A	21.37:g.46020576G>A	ENSP00000369445:p.Val19Ile	Somatic	38	0		WXS	Illumina HiSeq	Phase_I	200	9	NM_198689	0	0	0	1	1	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	37		.	.	.	.	.	.	.	.	.	.	g	3.948	-0.012856	0.07727	.	.	ENSG00000205441	ENST00000380102	T	0.00648	5.99	4.54	2.71	0.32032	.	.	.	.	.	T	0.00666	0.0022	L	0.43701	1.375	0.09310	N	1	B	0.28470	0.213	B	0.22753	0.041	T	0.44892	-0.9298	9	0.12766	T	0.61	.	7.0396	0.25013	0.2171:0.0:0.7829:0.0	.	19	P60409-2	.	I	19	ENSP00000369445:V19I	ENSP00000369445:V19I	V	+	1	0	KRTAP10-7	44845004	0.003000	0.15002	0.076000	0.20297	0.112000	0.19704	-0.474000	0.06607	0.369000	0.24510	0.467000	0.42956	GTC	.		0.642	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		A	46020576	G	A	46020576	3	1	161	1	0	0	0	0	1	0	0	0	8535	1145	40	1	57	1	KRTAP10-7	21	46020576	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	2799142	46020576	2109319	140	14725											
GSC2	2928	hgsc.bcm.edu	37	chr22	19137290	19137290	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcctgcagctgctcttcgctGaagatggtgcggtggcgcct	4	10	15	12	3	1	2	0	1	1	1	2	2	1	2	2	3	4	4	2	3	1	1	rs201641909	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr22:19137290G>A	ENST00000086933.2	-	2	398	c.399C>T	c.(397-399)ttC>ttT	p.F133F		NM_005315.1	NP_005306.1	O15499	GSC2_HUMAN	goosecoid homeobox 2	133					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(2)	4	Colorectal(54;0.0993)					GCTCTTCGCTGAAGATGGTGC	0.716													g|||	8	0.00159744	0.0053	0.0014	5008	,	,		8606	0		0	False		,,,				2504	0				p.F133F		.											.	GSC2-68	0			c.C399T						.			4,4216		0,4,2106	8	10	10		399	3.5	1	22		10	0,8348		0,0,4174	no	coding-synonymous	GSC2	NM_005315.1		0,4,6280	AA,AG,GG		0.0,0.0948,0.0318		133/206	19137290	4,12564	2110	4174	6284	SO:0001819	synonymous_variant	2928	exon2			TTCGCTGAAGATG		CCDS13757.1	22q11.21	2011-06-20	2007-08-28	2007-08-28	ENSG00000063515	ENSG00000063515		"Homeoboxes / PRD class"	4613	protein-coding gene	gene with protein product		601845	"goosecoid-like"	GSCL		9150167	Standard	NM_005315		Approved		uc011ags.2	O15499	OTTHUMG00000150122	ENST00000086933.2:c.399C>T	22.37:g.19137290G>A		Somatic	1	0		WXS	Illumina HiSeq	Phase_I	17	5	NM_005315	0	0	0	0	0		Silent	SNP	ENST00000086933.2	37	CCDS13757.1																																																																																			G|0.999;A|0.001		0.716	GSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316440.2	NM_005315		A	19137290	G	A	19137290	2	1	161	1	0	0	0	0	0	0	0	1	6836	1281	45	2		2	GSC2	22	19137290	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		19137290	32167276	141	14726											
PRPS2	5634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	12840843	12840843	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtcattgacatttccatgatCttggccgaagcaatccgaag	11	11	9	10	2	2	2	1	2	1	0	4	4	4	2	3	1	1	1	3	1	3	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:12840843C>G	ENST00000380668.5	+	7	1013	c.885C>G	c.(883-885)atC>atG	p.I295M	PRPS2_ENST00000398491.2_Missense_Mutation_p.I298M	NM_001039091.2|NM_002765.4	NP_001034180.1|NP_002756.1	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	295					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|AMP biosynthetic process (GO:0006167)|nucleobase-containing compound metabolic process (GO:0006139)|organ regeneration (GO:0031100)	extracellular vesicular exosome (GO:0070062)|ribose phosphate diphosphokinase complex (GO:0002189)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|carbohydrate binding (GO:0030246)|GDP binding (GO:0019003)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	16						TTTCCATGATCTTGGCCGAAG	0.453																																					p.I298M		.											.	PRPS2-130	0			c.C894G						.						174	117	136					X																	12840843		2203	4300	6503	SO:0001583	missense	5634	exon7			CATGATCTTGGCC	Y00971	CCDS14150.1, CCDS43918.1	Xp22.2	2012-10-02			ENSG00000101911	ENSG00000101911	2.7.6.1		9465	protein-coding gene	gene with protein product	"PRS II", "ribose-phosphate diphosphokinase 2"	311860				1962753	Standard	NM_002765		Approved		uc004cva.3	P11908	OTTHUMG00000021139	ENST00000380668.5:c.885C>G	X.37:g.12840843C>G	ENSP00000370043:p.Ile295Met	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	232	69	NM_001039091	0	0	0	0	0	Q0VDH9|Q0VDI0|Q15245|Q2TAK7	Missense_Mutation	SNP	ENST00000380668.5	37	CCDS14150.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.559940	0.27827	.	.	ENSG00000101911	ENST00000380668;ENST00000398491;ENST00000461630;ENST00000460220	T;T;T	0.73363	-0.74;-0.74;-0.74	5.12	-0.0434	0.13859	.	0.000000	0.85682	D	0.000000	T	0.58018	0.2093	N	0.25485	0.75	0.80722	D	1	B;B	0.20164	0.042;0.012	B;B	0.37451	0.25;0.238	T	0.21586	-1.0241	10	0.12103	T	0.63	-23.1539	4.2961	0.10902	0.2341:0.3845:0.0:0.3814	.	295;298	P11908;P11908-2	PRPS2_HUMAN;.	M	295;298;150;127	ENSP00000370043:I295M;ENSP00000381504:I298M;ENSP00000418911:I150M	ENSP00000370043:I295M	I	+	3	3	PRPS2	12750764	0.945000	0.32115	0.987000	0.45799	0.993000	0.82548	0.139000	0.16036	0.131000	0.18576	0.513000	0.50165	ATC	.		0.453	PRPS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055772.2	NM_002765		G	12840843	C	G	12840843	3	3	161	1	0	0	0	0	1	0	0	0	12609	903	32	4	920	4	PRPS2	23	12840843	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		12840843	142429717	142	14727											
PHKA2	5256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	18919658	18919658	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcctctcagttttggtgactCcggtatggcccacctcgtgg	4	13	11	13	2	1	1	1	1	1	0	5	1	3	1	4	4	0	2	4	4	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:18919658C>A	ENST00000379942.4	-	27	3637	c.2972G>T	c.(2971-2973)gGa>gTa	p.G991V		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	991					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					TTTGGTGACTCCGGTATGGCC	0.547																																					p.G991V		.											.	PHKA2-131	0			c.G2972T						.						180	139	153					X																	18919658		2203	4300	6503	SO:0001583	missense	5256	exon27			GTGACTCCGGTAT		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.2972G>T	X.37:g.18919658C>A	ENSP00000369274:p.Gly991Val	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	186	65	NM_000292	0	0	0	1	1	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573963	0.86542	.	.	ENSG00000044446	ENST00000379942	D	0.90955	-2.76	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.94798	0.8320	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.93740	0.7049	10	0.41790	T	0.15	-16.0545	19.5104	0.95139	0.0:1.0:0.0:0.0	.	991	P46019	KPB2_HUMAN	V	991	ENSP00000369274:G991V	ENSP00000369274:G991V	G	-	2	0	PHKA2	18829579	1.000000	0.71417	0.996000	0.52242	0.959000	0.62525	7.400000	0.79949	2.562000	0.86427	0.600000	0.82982	GGA	.		0.547	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		A	18919658	C	A	18919658	3	1	161	1	0	0	0	0	1	0	0	0	11870	855	30	4	763	4	PHKA2	23	18919658	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6078815	18919658	136350902	143	14728											
BRWD3	254065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	80001213	80001213	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tacagccggttaattgcctgGcagaggtgatattcactgaa	11	11	11	8	1	1	3	1	2	0	1	1	3	1	3	2	3	3	2	2	3	4	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:80001213G>A	ENST00000373275.4	-	7	662	c.446C>T	c.(445-447)gCc>gTc	p.A149V		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	149					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TAATTGCCTGGCAGAGGTGAT	0.343																																					p.A149V		.											.	BRWD3-134	0			c.C446T						.						36	33	34					X																	80001213		2203	4298	6501	SO:0001583	missense	254065	exon7			TGCCTGGCAGAGG		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"WD repeat domain containing"	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.446C>T	X.37:g.80001213G>A	ENSP00000362372:p.Ala149Val	Somatic	204	0		WXS	Illumina HiSeq	Phase_I	303	98	NM_153252	0	0	0	0	0	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873392	0.91664	.	.	ENSG00000165288	ENST00000373275	T	0.29397	1.57	4.96	4.08	0.47627	.	0.065291	0.64402	D	0.000010	T	0.46580	0.1400	M	0.64997	1.995	0.49798	D	0.999826	D	0.67145	0.996	P	0.57911	0.829	T	0.42832	-0.9428	9	.	.	.	-1.3369	14.4752	0.67541	0.0:0.144:0.856:0.0	.	149	Q6RI45	BRWD3_HUMAN	V	149	ENSP00000362372:A149V	.	A	-	2	0	BRWD3	79887869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.170000	0.64990	1.065000	0.40693	0.544000	0.68410	GCC	.		0.343	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		A	80001213	G	A	80001213	3	1	161	1	0	0	0	0	1	0	0	0	1529	1203	42	2	5102	2	BRWD3	23	80001213	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	61081555	80001213	75269347	144	14729											
SH3BGRL	6451	broad.mit.edu;ucsc.edu;bcgsc.ca	37	chrX	80532507	80532507	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaagaaacaacaagatgtgCttggtttcctagaagccaac	16	8	9	8	0	0	4	0	0	0	4	1	4	1	4	2	1	5	2	2	1	7	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:80532507C>A	ENST00000373212.5	+	2	328	c.70C>A	c.(70-72)Ctt>Att	p.L24I	SH3BGRL_ENST00000481106.1_3'UTR	NM_003022.2	NP_003013.1	O75368	SH3L1_HUMAN	SH3 domain binding glutamate-rich protein like	24					positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(2)|ovary(1)	4		all_lung(315;5.94e-05)				ACAAGATGTGCTTGGTTTCCT	0.358																																					p.L24I													.	SH3BGRL-131	0			c.C70A						.						50	47	48					X																	80532507		2203	4299	6502	SO:0001583	missense	6451	exon2			GATGTGCTTGGTT	AF042081	CCDS14449.1	Xq13.3	2014-02-19	2014-02-19		ENSG00000131171	ENSG00000131171			10823	protein-coding gene	gene with protein product		300190	"SH3 domain binding glutamic acid-rich protein like"			9642120	Standard	NM_003022		Approved	MGC117402	uc004eef.3	O75368	OTTHUMG00000021910	ENST00000373212.5:c.70C>A	X.37:g.80532507C>A	ENSP00000362308:p.Leu24Ile	Somatic	164	2		WXS	Illumina HiSeq	Phase_I	244	79	NM_003022	0	0	0	2	2	Q3SYL1|Q5JT50|Q6FIE8|Q9H0N8	Missense_Mutation	SNP	ENST00000373212.5	37	CCDS14449.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153276	0.57259	.	.	ENSG00000131171	ENST00000373212	T	0.76709	-1.04	5.7	4.66	0.58398	Thioredoxin-like fold (2);	0.052265	0.85682	D	0.000000	D	0.82728	0.5100	L	0.57536	1.79	0.46981	D	0.999275	B;P	0.43973	0.225;0.823	P;P	0.57244	0.456;0.816	T	0.82159	-0.0595	10	0.44086	T	0.13	-7.3431	12.2228	0.54443	0.0:0.8504:0.0:0.1496	.	23;24	D3DTE6;O75368	.;SH3L1_HUMAN	I	24	ENSP00000362308:L24I	ENSP00000362308:L24I	L	+	1	0	SH3BGRL	80419163	0.986000	0.35501	0.998000	0.56505	0.840000	0.47671	1.248000	0.32827	2.380000	0.81148	0.600000	0.82982	CTT	.		0.358	SH3BGRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057350.1	NM_003022		A	80532507	C	A	80532507	3	1	161	1	0	0	0	0	1	0	0	0	14273	797	28	4	76	4	SH3BGRL	23	80532507	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	531294	80532507	74738053	145	14730											
GPR112	139378	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	135475736	135475737	+	Frame_Shift_Ins	INS	-	-	AAAAT																															cttttgggattttgagaataINSatagtaagtatttttgttag																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:135475736_135475737insAAAAT	ENST00000394143.1	+	18	8368_8369	c.8077_8078insAAAAT	c.(8077-8079)aatfs	p.-2692fs	GPR112_ENST00000287534.4_Frame_Shift_Ins_p.-2445fs|GPR112_ENST00000394141.1_Frame_Shift_Ins_p.-2487fs|GPR112_ENST00000370652.1_Frame_Shift_Ins_p.-2692fs|GPR112_ENST00000412101.1_Frame_Shift_Ins_p.-2487fs	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112						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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTTGAGAATAATAGTAAGTAT	0.371																																					p.N2693fs		.											.	GPR112-183	0			c.8077_8078insAAAAT						.																																			SO:0001589	frameshift_variant	139378	exon18			.	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	Exception_encountered	X.37:g.135475736_135475737insAAAAT	ENSP00000377699:p.Asn2692fs	Somatic	52	0		WXS	Illumina HiSeq	Phase_I	58	16	NM_153834	0	0	0	0	0	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Frame_Shift_Ins	INS	ENST00000394143.1	37	CCDS35409.1																																																																																			.		0.371	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			AAAAT	135475737	-	AAAAT	135475736	7	5	161	1	0	1	1	0	0	0	0	0	6649	362	13	0	8135	0	GPR112	23	135475736	Frame_Shift_Ins	INS	-	TCGA-Q2-A5QZ-01A-11D-A28G-10	54943229	135475736	19794824	146	14731											
GABRQ	55879	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	chrX	151808889	151808890	+	Frame_Shift_Del	DEL	TG	TG	-																															aaagattttggacagggtgcTgtcaagatacgatgtccgcc																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:151808889_151808890delTG	ENST00000370306.2	+	2	220_221	c.200_201delTG	c.(199-201)ctgfs	p.L67fs		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	67					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|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)	GACAGGGTGCTGTCAAGATACG	0.47																																					p.67_67del		.											.	GABRQ-133	0			c.200_201del						.																																			SO:0001589	frameshift_variant	55879	exon2			.	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	14454	protein-coding gene	gene with protein product	"GABA(A) receptor, theta"	300349	"gamma-aminobutyric acid (GABA) receptor, theta"			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.200_201delTG	X.37:g.151808889_151808890delTG	ENSP00000359329:p.Leu67fs	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	159	56	NM_018558	0	0	0	0	0	A6NFN1|Q32MB4|Q9NZK8	Frame_Shift_Del	DEL	ENST00000370306.2	37	CCDS14707.1																																																																																			.		0.47	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		-	151808890	TG	-	151808889	7	5	161	1	0	1	0	1	0	0	0	0	6194	1580	55	0	206	0	GABRQ	23	151808889	Frame_Shift_Del	DEL	TG	TCGA-Q2-A5QZ-01A-11D-A28G-10	16333153	151808889	3461671	147	14732											
PNCK	139728	broad.mit.edu	37	chrX	152938523	152938523	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctccgtgtgtttcttcagCagcagcatgtctgcaggggc	5	12	12	12	1	3	0	1	0	2	0	5	0	5	0	2	2	4	5	2	2	0	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:152938523C>A	ENST00000370150.1	-	2	187	c.9G>T	c.(7-9)ctG>ctT	p.L3L	PNCK_ENST00000340888.3_Silent_p.L3L|PNCK_ENST00000475172.1_5'UTR|PNCK_ENST00000370142.1_Silent_p.L3L|PNCK_ENST00000393831.2_Silent_p.L3L|PNCK_ENST00000370145.4_Silent_p.L20L|PNCK_ENST00000447676.2_Silent_p.L86L			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	3						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTTTCTTCAGCAGCAGCATGT	0.667																																					p.L86L													.	PNCK-207	0			c.G258T						.						56	39	45					X																	152938523		2203	4297	6500	SO:0001819	synonymous_variant	139728	exon2			CTTCAGCAGCAGC	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.9G>T	X.37:g.152938523C>A		Somatic	46	0		WXS	Illumina HiSeq	Phase_I	227	5	NM_001039582	0	0	0	0	0	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Silent	SNP	ENST00000370150.1	37																																																																																				.		0.667	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		A	152938523	C	A	152938523	2	1	161	1	0	0	0	0	0	0	0	1	12171	697	25	4		4	PNCK	23	152938523	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	1129634	152938523	2332037	148	14733											
